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# LAST version 1541
#
# a=26 b=1 A=29 B=1 e=138 d=77 x=137 y=46 z=137 D=1e+07 E=23646.3
# R=01 u=0 s=1 S=1 M=0 T=0 m=100 l=1 n=100 k=1 w=1000 t=4.62434 j=3 Q=0
# Reference sequences=2716 normal letters=3491686
# lambda=0.21926 K=0.327014
#
# A C G T M S K W R Y B D H V
# A 5 -10 -5 -11 3 -7 -8 2 3 -11 -8 1 1 1
# C -10 6 -10 -3 2 3 -5 -5 -10 3 1 -6 1 1
# G -3 -10 6 -10 -5 3 2 -5 3 -10 1 1 -6 1
# T -11 -5 -10 5 -8 -7 3 2 -11 3 1 1 1 -8
# M 2 2 -7 -6 2 0 -6 0 0 -1 -2 -1 1 1
# S -5 3 3 -5 0 3 0 -5 0 0 1 -1 -1 1
# K -6 -7 2 2 -6 0 2 0 -1 0 1 1 -1 -2
# W 2 -7 -7 2 0 -7 0 2 0 0 -1 1 1 -1
# R 3 -10 3 -11 1 0 -1 0 3 -10 -2 1 -1 1
# Y -11 3 -10 3 -1 0 1 0 -10 3 1 -1 1 -2
# B -7 1 1 1 -2 1 1 -1 -2 1 1 -1 0 -1
# D 1 -8 1 0 -1 -2 1 1 1 -1 -1 1 0 0
# H 0 1 -8 1 1 -2 -1 1 -1 1 0 0 1 -1
# V 1 1 1 -7 1 1 -2 -1 1 -2 -1 0 -1 1
# N 0 0 0 0 0 0 0 0 0 0 0 0 0 0
#
# Coordinates are 0-based. For - strand matches, coordinates
# in the reverse complement of the 2nd sequence are used.
#
# name start alnSize strand seqSize alignment
#
# m=1 s=138
#
a score=9472 mismap=1e-10
s L1P1_5end#LINE/L1 0 2110 + 2259 GGGGGNGGAGCCAAGATGGCCGAATAGGAACAGCTCCGGTCTACAGCTCCCAGCGTGAGCGACGCAGAAGACGGGTGATTTCTGCATTTCCANCTGAGGTACCGGGTTCATCTCACTGGGGAGTGCCGGACAGTGGgcgcaggacagtgggtgcagcgcaCCGTGCGCGAGCCGAAGCAGGGCGAGGCATCGCCTCACCCGGGAAGCGCAAGGGGTCAGGGAGTTCCCTTTCCTAGTCAAAGAAAGGGGTGACAGACGGCACCTGGAAAATCGGGTCACTCCCACCCTAATACTGCGCTTTTCCGACGGGCTTAANAAACGGCGCACCAGGAGATTATATCCCGCACCTGGCTCGGAGGGTCCTACGCCCACGGAGCCTCGCTCATTGCTAGCACAGCAGTCTGAGATCAAACTGCAAGGCGGCAGCGAGGCTGGGGGAGGGGCGCCCGCCATTGCCCAGGCTTGANTAGGTAAACAAAGCGGCCGGGAAGCTCGAACTGGGTGGAGCCCACCACAGCTCAAGGAGGCCTGCCTGCCTCTGTAGGCTCCACCTCTGGGGGCAGGGCACAGACAAACAAAAAGACAGCAGTAACCTCTGCAGACTTAAATGTCCCTGTCTGACAGCTTTGAAGAGAGCAGTGGTTCTCCCAGCACGCAGCTGGAGATCTGAGAACGGGCAGACTGCCTCCTCAAGTGGGTCCCTGACC-------CCCGAGCAGCCTAACTGGGAGGCACCCCCCAGTAGGGGCAGACTGACACCTCACACGGCCGGGTACTCCTCTGAGACAAAACTTCCAGAGGAACGATCAGGCAGCAGCATTCGCGGTTCACCAANATCCGCTGTTCTGCAGCCACCGCTGCTGATACCCAGGCAAACAGGGTCTGGAGTGGACCTCCAGCAAACTCCAACAGACCTGCAGCTGAGGGTCCTGNCTGTTAGAAGGAAAACTAACAAACAGAAAGGACATCCACACCAAAAACCCATCTGTACGTCACCATCATCAAAGACCAAAGGTAGATAAAACCACAAAGATGGGGAAAAAACAGAGCAGAAAAACTGGAAACTCTAAAAANCAGAGCGCCTCTCCTCCTCCAAAGGAACGCAGCTCCTCACCAGCAACGGAACAAAGCTGGACGGAGAATGACTTTGACGAGTTGAGAGAAGAAGGCTTCAGACGATCAAACTACTCCGAGCTANAGGAGGAAGTTCGAACCAATGGCAAAGAAGTTAaaaactttgaaaaaaaaTTAGACGAATGGATAACTAGAATAACCAATGCAGAGAAGTCCTTAAAGGACCTGATGGAGCTGAAAGCCAAGGCNCGAGAACTACGTGANGAATGCAGAAGCCTCAGNAGCCGATGCGATCAACTGGAAGAAAGGGTATCAGTGATGGAAGATGAAATGAatgaaatgaaGCGAGAAGGGAAGTTTAGAGAAAAAagaataaaaagaaaCGAACAAAGCCTCCAAGAAATATGGGACTATGTGAAAAGACCAAATCTACGTCTGATTGGTGTACCTGAAAGTGACGGGGAGAATGGAACCAAGTTGGAAAACACTCTGCAGGATATTATCCAGGAGAACTTCCCCAATCTAGCAAGGCAGGCCAACATTCAGATTCAGGAAATACAGAGAACGCCACAAAGATACTCCTCGAGAAGAGCAACTCCAAGACACATAATTGTCAGATTCACCAAAGTTGAAATGAAGGAAAAAATGTTAAGGGCAGCCAGAGAGAAAGGTCGGGTTACCCACAAAGGGAAGCCCATCAGACTAACAGCNGATCTCTCGGCAGAAACTCTACAAGCCAGAAGAGAGTGGGGGCCAATATTCAACATTCTTAAAGAAAAGAATTTTCAACCCAGAATTTCATATCCAGCCAAACTAAGCTTCATAAGTGAAGGAGAAATAAAATACTTTACAGACAAGCAAATGCTGAGAGATTTTGTCACCACCAGGCCTGCCCTAAAAGAGCTCCTGAAGGAAGCACTAAACATGGAAAGGAACAACCGGTACCAGCCACTGCAAAAACATGCCAAATTGTAAAGACCATCGAGGCTAGGAAGAAACTGCATCAACTAACGAGCAAAATAACCAGCTAACATCATAA
s chr15 17013608 2114 + 101991189 GAGGTGGCAGTCAAGATGGCCAAATAGGAGCACCTCTGTTCTACAGCTCCCAGTGTGAGTGACACAGAAGATGGGCAATTTCTTCATTTCCATCTGAGATACCTGGTTCATCTCACTAGGAATTGCCAGACAGTGGGCGCAGGatagtgggtgcaGTGCACCATGAGTGGGCAGAAGCAGAGTGAGTCATTTCCTCACTTGGGAAGTGCAAGTGGTCAGGGAGTTCCCTTACCTAATCAAATAAAGGGGCAACAGATGGCACCTGGGAAATCCAGTCACTCCCACCATAATACTGCTCTTTTTCAATGGGCTTAAAAAATGGCACACCAGGAGATTATATCCCACACCTTGCTTGGAGGGTCCTACGTCCATGGTGTCTCACTGATTGCTAGCACAGCAGTCTGTGATCAAACTACAAGGTGGCAGTGAGGCTGGGGGTGGGGCAACC-CCATTGCCCAGGCTTGCTTAGGTAAACAAAGCTGCTGGAAAGCTCGAAGTAGGTGTAGCCCACCACAGCTCTACGAGGCCTGCCTTCCTCTGTAGGCTCCATCTCTGGGGGCAGGGCACAGACAAACAAAAAGGCAGCAGTAACCTCTGCAGACTTAAATGTCCCTGTCTGACAGCTTTGAAGAGAGAAGTGGTTCTACCGGCACACAGCTGGAGATCTGAGAATGGGCAGACTGCCTCCTCAAGTGGGTACCTGACCTCTGAACCCCGAGCAGCCTAACTGGGAGACACCCCTCAGTAGGGGCagactgacaccTCACACGGCCGTATAGTCCTCTGAGACAAAATTTCCAGAGCAAAGATCAGACAGCAGCATTCGTGGTTTACGAAAATCTGCTGTTCTGCAGTCACCGCTGCTGATACCCAGGCAAACAGGATCTGGAGTGTACCTCTAGCAAACTCCAACAGACCTGCAGCTGAGGGTCCTGTCTGTTAGAAGGAAAACTAAGAAACAGAAAGGACATCCACACCAAAAACCCATCTGTATATCACCATCATCAAAGACCAAAAGTAGATAAAACCACAAAGATGGGGAAAAAACAGAGCAGAAAAACTAGAAACTCTAAAAAGCAGAGTGCCTTTCCTCCTCCAAAGGAATGCAGTTCCTCACCAGCAATGGAACAAAGCTGGACGGAGAATGACTTTGACGAGTTGAGAGAAGAAGGCTTCAGACGATCAAATTACTCCGAGCTGCAGGAGGAAATTCAAACCAAAGGCAAAGAAGTTAAAAACTTtgaaaaaat-tTAGACGAATGTATAACTAGAATAACCAACACAGAGAAGTGCTTAAAGGAGCTGATGGAGCTGAAAGCCAAGGCTCCAGAACTACTTGAAGAATGCAGAAGCCTCAGGAGCCGAGGTGATCAACTGGAAGAAAGGATATCAGTGATGGAAGATGAAATGAATGAAATAAAGTGAGAAGGGAAGTTTAGAGAAAAAAgaataaaaagaaATGAACAAAGACTCCAAGAAATATGAGACTATGTGAAAAGACCATATCTATGTCTGATTGGTGTACCTGAAAGTGATGCGGAGAATGGAACCAAGTTGGAAAACACTCTGCAGGATATTATCCAGGAGAACTTCCCCAATCTAG-AAGGCAGACCAACATTCATATTCAGAAAATACAGAGAATGCCACAAAGATACTCCTCGAGAAGAGCAACTTCAAGACACATAATTGTCAGATTCACCAAAGTTGAAATGAAGGAAAAAATATTAAGGGCAGCCAGAGAGAAAGGTCGGGTTACCCTCAAAGGGAAGCCCATCAGACGAACAGCCGATCTCTTGGCAGAAAGTCTACAAGCCAGAAGAGAGTGTGGGCCAATATTCAACATTTTTAAAGAAAAGAATTTTCAACCCAGAATTTCATATTCAGCCAAACTAAGCTTCATAAGTGAAGGAGAAATAAAATACTTTACAGACGATCAAATGCTGAGAGATTTTGTCACCACCAGGCCTGCTCTAAAAGAGCTCCTGAAGGAAGCACTAAACATGGAAAGGAACAATCAGTACCAGCCACTGCAAAATCATGCCAAATTGTAAAGTCCACTGTGGCTAGTAAGAAACTGCATCAAGTAACGAGAAAAATAACCAGCTAACATCATAA
a score=15792 mismap=1e-10
s L1P1_orf2#LINE/L1 2 3288 + 3294 GACAGGATCAAATTCACACATAACAATATTaactttaaatgtaaatgGACTAAATGCTCCAATTAAAAGACACAGACTGGCAAATTGGATAAAGAGTCAAGACCCATCAGTGTGCTGTATTCAGGAAACCCATCTCACGTGCAGAGACACACATAGGCTCAAAATAAAGGGATGGAGGAAGATCTACCAAGCAAATGGAAAACAaaaaaAGGCAGGGGTTGCAATCCTAGTCTCTGATAAAACAGACTTTAAACCAACAAAGATCAAAAGAGACAAAGAAGGCCATTACATAATGGTAAAGGGATCAATTCAACAAGAAGAGCTAACTATCCTAAATATATATGCACCCAATACAGGAGCACCCAGATTCATAAAGCAAGTCCTGAGTGACCTACAAAGAGACTTAGACTCCCACACANTAATAATGGGAGACTTTAACACCCCACTGTCAACATTAGACAGATCAACGAGACAGAAAGTTAACAAGGATACCCAGGAATTGAACTCAGCTCTGCACCAAGCGGACCTAATAGACATCTACAGAACTCTCCACCCCAAATCAACAGAATATACATTCTTTTCAGCACCACaccacaCCTATTCCAAAATTGACCACATAGTTGGAAGTAAAGCNCTCCTCAGCAAATGTAAAAGAACAGAAATTATAACAAACTGTCTCTCAGACCACAGTGCAATCAAACTAGAACTCAGGATTAAGAAACTCACTCAAAACCGCTCAACTACATGGAAACTGAACAACCTGCTCCTGAATGACTACTGGGTACATAACGAAATGAAGGCAGAAATAAAGATGTTCTTTGAAACCAACGAGAACAAAGACACAACATACCAGAATCTCTGGGACGCATTCAAAGCAGTGTGTAGAGGGAAATTTATAGCACTAAATGCCCACAAGAGAAAGCAGGAAAGATCCAAAATTGACACCCTAACATCACAATTAAAAGAACTAGAAAAGCAAGAGCAAACACATTCAAAAGCTAGCAGAAGGCAAGAAATAACTAAGATCAGAGCAGAACTGAAGGAAATAGAGACACAaaaaaCCCTTCAAAAAATCAATGAATCCAGGAGCTGGTTTTTTGAAAGGATCAACAAAATTGATAGACCGCTAGCAAGACTAATAAAGAAGAAAAGAGAGAAGAATCAAATAGACGCAATAAAAAATGATAAAGGGGATATCACCACCGATCCCACAGAAATACAAACTACCATCAGAGAATACTACAAACACCTCTACGCAAATAAACTAGAAAATCTAGAAGAAATGGATAAATTCCTCGACACATACACCCTCCCAAGACTAAACCAGGAAGAAGTTGAATCTCTGAATAGACCAATAACAGGCTCTGAAATTGNGGCAATAATCAATAGCTTACCAACCAAAAAGAGTCCAGGACCAGATGGATTCACAGCCGAATTCTACCAGAGGTACAAGGAGGAGCTGGTACCATTCCTTCTGAAACTATTCCAATCAATAGAAAAAGAGGGAATCCTCCCTAACTCATTTTATGAGGCCAGCATCATCCTGATACCAAAGCCNGGCAGAGACACAACCAAAAAAGAGAATTTTAGACCAATATCCTTGATGAACATTGATGCAAAAATCCTCAATAAAATACTGGCAAACCGAATCCAGCAGCACATCAAAAAGCTTATCCACCATGATCAAGTGGGCTTCATCCCTGGGATGCAAGGCTGGTTCAACATACGCAAATCAATAAACGTAATCCAGCATATAAACAGAACCAAAGACAAAAACCACATGATTATCTCAATAGATGCAGAAAAGGCCTTTGACAAAATTCAACAACCCTTCATGCTAAAAACTCTCAATAAATTAGGTATTGATGGGACGTATCTCAAAATAATAAGAGCTATCTATGACAAACCCACAGCCAATATCATACTGAATGGGCAAAAACTGGAAGCATTCCCTTTGAAAACTGGCACAAGACAGGGATGCCCTCTCTCACCACTCCTATTCAACATAGTGTTGGAAGTTCTGGCCAGGGCAATCAGGCAGGAGAAGGAAATAAAGGGTATTCAATTAGGAAAAGAGGAAGTCAAATTGTCCCTGTTTGCAGACGACATGATTGTATATCTAGAAAACCCCATCGTCTCAGCCCAAAATCTCCTTAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTGCAAAAATCACAAGCATTCTTATACACCAATAACAGACAAACAGAGAGCCAAATCATGAGTGAACTCCCATTCACAATTGCTTCAAAGAGAATAAAATACCTAGGAATCCAACTTACAAGGGATGTGAAGGACCTCTTCAAGGAGAACTACAAACCACTGCTCAANGAAATAAAAGAGGATACAAACAAATGGAAGAACATTCCATGCTCATGGGTAGGAAGAATCAATATCGTGAAAATGGCCATACTGCCCAAGGTAATTTATAGATTCAATGCCATCCCCATCAAGCTACCAATGACTTTCTTCACAGAATTGGAAAAAACTACTTTAAAGTTCATATGGAACCAAAAAAGAGCCCGCATCGCCAAGTCAATCCTAAGCCAAAAGAACAAAGCTGGAGGCATCACGCTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATGGtactggtaccaaaacagAGATATAGATCAATGGAACAGAACAGAGCCCTCAGAAATAACGCCGCATATCTACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAGACTTAAACGTTAGACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCANTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTCTAAAACACCAAAAGCAATGGCAACAAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAGAATGGGAGAAAATTTTCGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAaaaaacaaacaaCCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCATC
s chr15 17015723 3265 + 101991189 GACAGGATCAAATTCACACATAACAATATTAACTCTAAATGTAAATGGACTAAATGCTTCAATTAAA-GACACAGACTGGCAATTTGGATAAAGAGTCAAGACCCATCAGTGTGCTGTATTCAGGAAACCCATCTCACATGCAGAGACAAACATAGGCTCAAAATGAAAGGATGGTGGAAGATCTACAAAGCAAATGGAaaacaaaaaaagg----ggTTGCAATCCTAGTCTCTGATAAAACAGACTTTAAACCAACAAAGATCAAACGAGACAAAGAAGGCCATTACATAATGGTAAAGGGATCAATTCAGCAAGAAAAGCTAACTATCCTAAATGTATATGCACCCA---------------GATTCTTAAAGCAAGTCCTGAGTGATGTACAAAGAGACTTACACTCCCACACAATAATAATTGGAGACTTTAACACCCCACTGTCAATATTAGACAGATCAACGAGACAAAAAGTTAGCAAGGATCCCCAGGAATTGAACTCAGCTCTGCACCAAGCGGGCCTAATAGACATCTACAGAACTCTCCACCCCAAATCGACAGAATATACATTTTTTTCAGCACCACAccacaCCTATTCCGAAATTGACCACATCGTTGGAAATAAAGCTATCCTCAGCAAATGTAAAAGAACAGAAATTATAACAAACTGTCTCTCAGACCACAGTGCAATCAAACTAGAACTCAGGATTAAGAAACTCACTCAAAACCGCTCAACTACATGGAAACTGAACAACCTGCTCCTGAATGACTACTGGGTACATAACAAAATGAAGGCAGAAATAAAGATGTTCTTTGAAACCAACAAGAACAAAGACACAACATACCAGAATCTCTGGGACACATTCAAAGCAGTGTGTAGAAGGAAATTTATAGCACTAAATGCCCACAAGAGAAAGCAGGAAAGATCCAAAATTGATACCCTAACATCACAATTAAAAGAACTAGAAAAGCAAGAGCAAACGCATTAAAAAGCTAGCAGAAGGCAAGAAATAACTAAAATCAGAGCAGAACTGAAGGAAATAGAGACACaaaaaaaCCTTCAAAAAATTAATGAATCCAGGAGATTGTTTTTTGAAAAGATCAACAAAATTGATAGACCGCTAGCAAGACTAATAAAGAAGAAAAGAGAGAAGAATCAAATAGATGCAATAAAAA-TGATAAAGTGAGTATCACCATCGATCCCACAGAAATACGAACTACTATCAGAGAATACTACATAAACCTCTACACAAACAAACTACAAAATCTAGAAGAAATGGATAAATTCCTTGACACATACACCCTCCCAAGACTAAACCAGGAAGAAGTTGAATCTCTGAATAGACCAATAACAGGCTCTGAAATTGTGGTAATAATCAATAGCTTACCAACCAAAAAGAGTCCAGGACCAGATGGATTCACAGCCGAATTCTACCAGAGGTACAAGGAGGAACTGGTACCATTCCTTCTGAAATTATTCCAATGAATAGAAAAAGAGGGAATCCTCCCTAATTCATTTTATGAGGCCAGCATCATCCTGATACCAAAGCCGGGCAGAGACACAACCAAAAaaCAAAATTTTAGACCAATATCCTTGATGAACATTGATGCAAAAATCCTCAATAAAATACTGGCAAACCGATTCCAGAAGCACATTAAAAAGCTTATCCACCATGATCAAGTGGGCTTCATCCCTAGGATGCAAGGCTGGTTCAATATATGCAAATCAATAAATGTAATCCAGCATATAAACAGAACCAGAGACAAAAACCACATGATTATCTCAATAGATGCAGAAAAGGCCTTTGATAAAATTCAACAACCCTTCATGCTAAAAATACTCAATAAATTAGGTATTGTTGGGACATATCTCAAAATAATAAGAGCTATCTATGACAAACACACAGCCAATATCATACTGAATGGGCAAAAACTGGAAGCATTCCCTTTGAAAACTGGCACAAGATAGGGATGCCCTCTCTCACCACTCCTATTCAACATAGTGTTGGAAGTTCTGGCCAGGGCCATTAGGCAGGAGAAGGAAATAAAGGGTATGCAATTAGGAAAAGAGGAAGTCAAATTGTCCTTGTTTGCAGATGACATGATTGTATATCTAGAAAACCCCATTGTCTCAGCCCAAAATCTCCTGAAGCTGATAAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTACAAAAATCACAAGCATTCTTATACACCAATAACAGACAAACAGAGAGCCAAATCATAAGTGAACTCCCATTCACAATTGCTTCAAAGAGAATAAAATATGTAGGAATCCAACTTACAAGGGACGTGAAGGACCTCTTCAAGGAGAACTACAAACCACTGTTCAATGAAATAAAAGAGGATACAAACAAATGGAAGAACATTCCATGCTCATGAATAGGAAGAATCAATATCGTGAAAATGACCATACTGCCCAAGGTAATTTATAGATTCAATGTCATCCCCAACAAGCTACCAATGACTTTCTTCACAGAATTGGAAAAGACTACTTTAAAGTTCATATGGAACCAAAAAAGATCCTGCATCACCATGTCAATCCTAAGCCGCAAGAACAAAGCTGGAGGCATCAGTCTACCTGACTTCGAACTATACTACAGGGATACAGTAACCAAGACATCATGGTACTGGTACCAAAACAGAAATATAGATCAATGGAACAGAACAGAGCCCTCAGAAATAATGCTGCATATCTACAACTATCTGTTCTTTGATAAACCTGAACAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATTAATTCAAGATGGATTAAAAAGTTaaacgttagacctaaaaccatAAAAATCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCATGGGCAAGGACTTCATGTTTAAAACAACAAAAGCAATGGCAACAAATGCCATAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCAGCAGAGTGAACAGGCAATGTACAAAATGGGAGATAGTTTTCACAACCTACTTATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAaaaaacaaacaaaGCCATCAAAAAGTGGGTGAAGGACATCAACAGACACTTCCC-AAAGAAGACATTTATGCAGCC-AAAAACACATGAAAAAATGCTCATC
a score=3398 mismap=6.76e-06
s L1PA3_3end#LINE/L1 149 750 + 902 ACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATTGCGGCACTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACTATGCAGCCATA-AAAAATGATGAGTTCATGTCCTTTGTAGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATCGCAAGAACAAAAAA-CCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGAACACATGGACACAGGAAGGGGAACATCACACTCTGGGGACTGTTGTGGGgtggggggaggggggagggATAGCATTGGGAGATATACCTAATGCTAGATGACGAGTTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCACATTGTGCACATGTACCCTAAAACTTAAAGTATAataataataaaa
s chr15 17018992 749 + 101991189 ACTGGCCATCAGAGAAATGCAAATGAAAACCACAATGAGATACCACCTCACACCAGTTAGGATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGTTGGAGAGGATGTGGAGAAATAGAAACATTTTTACACTTTTGATGGGGCTGTAAACTAATTCAGCCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGAAGTAGAGCTAGAAATACAATTTGACCCAGCCATCCCATTACTGGGCACGTACCCAA-GGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATTGCAGCACTATTCACAATTGCA--GACTTGGAAACAACCCAAATGTCCAGCAATAACAGAGTGGATTAAGAAAACGTGGCACATATGTACAATGGAATACTATGGAGCCATACAAAAATGATGAGTTCATGTCCTTTGTAGGGACATGGATGAAACTGGAAATCATCATTCTCAGTAAACTATTGCAAGGACAAAAAAACCAAACACTGCATGTTCTCACTCATAGGTGGGAATTGAGCGATGAGAACACATGGACACAGGAAGGGGAACATCACACTCTGGGGACTGATGTGAGGTGgggggaggagggaggGATAGCATTAGGAGATATACCTAATGCTAAATGACGAGTTAATGGGTGCAGCACACCAACATGGCACATGTACACATATGTAACTAACCTGTACAATGTGCACATGTACCCTAAAACTTAAAGTATAataataataaaa
a score=2158 mismap=3.89e-09
s L1PA3_3end#LINE/L1 0 436 - 902 TTTttttattattattatACTTTAAGTTTTAGGGTACATGTGCACAATGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCccctccccccaccccacaACAGTCCCCAGAGTGTGATGTTCCCCTTCCTGTGTCCATGTGTTCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTTCTTGCGATAGTTTACTGAGAATGATGATTTCCAATTTCATCCATGTCCCTACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTA
s chr15 17035566 436 + 101991189 ttttcttattattattattcttTAAGTTTTAGGGTAAATGTGCACAATGTGCAGGTTAGTTACATATGTATACATGTGACATGCTGGTGTGCTGCACCCACTAACCCGTCATCTAGCATTAGATATATCTCCCAATGCTCTCCGTCCCccctccccccaccccacaACAGTCCCCAGAGTGTGATGTTCCCTTTCCTGTGTCCATGTGTTCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGAGGTGTTTGGTTTTTTGTTCTTGCAATATTTTACTGAGAATGTTGATTTCCAATTTCATCCATGTCCCTACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGCGCCACATTTTTTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTA
a score=4053 mismap=8.38e-09
s L1PA3_3end#LINE/L1 39 857 + 902 AAGAAaaaaacaaacaaCCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAGATACCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTGTTGGTGGGACTGTAAACTAGTTCAACCATTGTGGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGAACTAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATATACCCAAAGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATTGCGGCACTATTCACAATAGCAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTAGGGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGAACACATGGACACAGGAAGGGGAACATCACACTCTGGGGACTGTTGTGGGgtggggggaggggggagggATAGCATTGGGAGATATACCTAATGCTAGATGACGAGTTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCACATTGTGCACATGTACCCTAAAACTTAAAGTATAataataata
s chr15 17042713 856 + 101991189 aaaaaacaaacaaataaCCCCTTCAAAAAGTGGGTGAAGGACATGAACATACACTTCTCAAAAGAATATGTTTATGCAGCCAAAAAACACATGAAAAAATGCTCACCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACAATGAAATACCATCACACACCAATTAGAATGGCAGTCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACAAAGTGGGTGGCACTGTAAACTAGTACAACCATTGTAGAAGTCAGTGTGGCGATTCCTCAGGGATCTAGAACCAGAAATACCATTTGACCCAGCCATCCCATTACTGGGTATGTACCCAAAGGACTATAAATCATGCTGCTATAAAGACACATGCACACGTATGTTTATTGCAGCACTAGTCACAATAGCAAAGAGTTGGAACCAACCCAAATGTCCAACAATGATAGACTTGATTAAGAAAATATGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATGTCCTTTGTAGTGACATGGATGAAATTGGAAATCATCATTCTCAGTAAACTATTGCAAGAATAAAAGACCAAACACCGCATATTCTCACTCATAAGTGGGAATTGAACAATGAGAACACATGGACACAGGAAGGGGAATGTCATACTCTGGGGACTGTTGTGGGGTGTGGTGA-GGCGCAGGGATAGCATTATGAGATATACCTAATGCTAAATGACGAGTTAATGGGTGCAGCACACCAGCGTGGTACATGTATACATGTGTAACTAACCTGCACATTGTGCACATGTACCCTAAAACTTAAAGTATAataataata
a score=4305 mismap=5.26e-08
s L1PA2_3end#LINE/L1 9 853 - 902 ttttattatACTTTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACTAACTCGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCcccctccccccaccccaccaCAGTCCCCAGAGTGTGATATTCCCCTTCCTGTGTCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTTCTTGCGATAGTTTACTGAGAATGATGATTTCCAATTTCATCCATGTCCCTACAAAGGACATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCGCAATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATTGCCATTCTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTttgtttttttcT
s chr15 17049334 852 + 101991189 TTTTATTATACTTTAAGTTTTAGGGTACATGTGCACATTGTGCAGATTAGTTACATATGTATACATGTGACATGCTGGTGCGCTGCAGCCACTAACTCGTCATCTAGTATTAGGTATATTTCCTAATGCTATCCCTCCCTCCTGCCCCCACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTGTCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAAAATATGCGGTGTTTGGTTTTT-GTTCTTGTGATAGTTTGCTGAGAATGATGGTTTCCAGTTTCATCCATGTCTCTACAAAGGACATGAACTCTTCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTACCACATTTTCTTAATCCAGTCTATGGTTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAATGCCACAATAAACATATGTGTGCATGTGTCTTTATAGCAGCATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCCAGTTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTAGTTTCCTGACTTTTTAATGATTGCCATTCTAACTGGTGTGAGATGATATCACATTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTTTTTTGGCTGCATAAATGTCTTCTTTTGAGAAGTGTCTGTTCATGTCCTTCACCCACTTTTTGATGGGGTTGTTtgttttttTCT
a score=2956 mismap=1e-10
s L1P1_orf2#LINE/L1 111 575 - 3294 GTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGATGAGTAGGTTGCGAAAATTTTCTCCCATTCTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTTTGGCTTTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTANTGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAGTCTTTAATCCATCTTGAATTAATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAAATAGGGAATCCTTTCCCCATTGCTTGTTTTTCTCAGGTTTGTCAAAGATCAGATAGTTGTAGATATGCGGCGTTATTTCTGAGGGCTCTGTTCTGTTCCATTGATCTATATCTCTGTTTTGGTACCAGTACCATGctgttttggttactgtaGCCTTGTAGTATAGTTTGAAGTCAGGTAGCGTGA
s chr15 17050187 575 + 101991189 GTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGATGAGTAGGTTGCAAAAATTTTCTCCCATTTTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCTATTTGTCAATTTTGTCTTTTGTTGCCATTGCTTTTGGTGTTTTGGACATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTAATGCTTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAATCTTTAATCCATCTTGAATTGATTTTTGTATAAGGTGTAAGGAAGGGATCCAGTTTCAGCTTTCTACATATGGCTAGCCAGTTTTCCCAGCACCATTTATTAAATAGGGAATCCTTTCCCCATTTCTTGTTTTTCTCAGGTTTGTCAAAGGTCAGATAGTTGTAGATATGCGGTGTTATTTCTGAGGGCTCTGTTCTGTTCCATTGATCTATATCTCTGTTTTGGTACCAGTACCATGctgttttggttactgtaGCCTTGTAGTACAGTTTGAAGTCAGGTAGTGTGA
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