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# Program: needle
# Rundate: Mon 14 Jul 2008 11:45:42
# Commandline: needle
#    [-asequence] asis:TGTGGTTAGGTTTGGTTTTATTGGGGGCTTGGTTTGGGCCCACCCCAAATAGGGAGTGGGGGTATGACCTCAGATAGACGAGCTTATTTTAGGGCGGCGACTATAATTATTTCGTTTCCTACAAGGATTAAAGTTTTTTCTTTTACTGTGGGAGGGGGTTTGGTATTAAGAAACGCTAGTCCGGATGTGGCTCTCCATGATACTTATTGTGTAGTAGCTCATTTTCATTATGTTCTTCGAATGGGAGCAGTCATTGGTATTTTTTTGGTTTTTTTTTGAAATTTTTAGGTTATTTAGACCATTTTTTTTTGTTTCGCTAATTAGAATTTTATTAGCCTTTGGTTTTTTTTTATTTTTTGGGGTTAAGACAAGGTGTCGTTGAATTAGTTTAGCAAAATACTGCTTAAGGTAGGCTATAGGATCTACCTTTTATCTTTCTAATCTTTTGTTTTAGTATAATTGGTCTTCGATTCAACAATTTTTAGTCTTCAGTCTTTTTTTTTATTTTGAAAAGGTTTTAACACTCTTGGTTTTGGAGGCTTTGGCTTTCTTCTTACTCTTAGGAGGATGGGCGCTAGAAAGAGTTTTAAGAGGGTGTGAAAGGGGGTTAATAGC
#    [-bsequence] asis:TTATTAATCTTATGGTTTTGCCGTAAAATTTCTTTCTTTATTTTTTATTGTTAGGATTTTGTTGATTTTATTTTTCTCAAGAATTTTTAGGTCAATTAGACCGGCTTATTTTTTTGTCAGTGTTTAAAGTTTTATTAATTTTTGGGGGGGGGGGGAGACGGGGTGTTATCTGAATTAGTTTTTGGGAGTCTCTAGACATCTCATGGGTTGGCCGGGGGCCTGCCGTCTATAGTTCTTATTCCTTTTAAGGGAGTAAGAATTTCGATTCAGCAACTTTAGTTCACAGTCTTTTTTTTTATTAAGAAAGGTTT
#    -filter
# Align_format: srspair
# Report_file: stdout
########################################

#=======================================
#
# Aligned_sequences: 2
# 1: asis
# 2: asis
# Matrix: EDNAFULL
# Gap_penalty: 10.0
# Extend_penalty: 0.5
#
# Length: 667
# Identity:     210/667 (31.5%)
# Similarity:   210/667 (31.5%)
# Gaps:         408/667 (61.2%)
# Score: 561.0
# 
#
#=======================================

asis               1 TGTGGTTAGGTTTGGTTTTATTGGGGGCTTGGTTTGGGCCCACCCCAAAT     50
                                                                       
asis               0 --------------------------------------------------      0

asis              51 AGGGAGTGGGGGTATGACCTCAGATAGACGAGCTTATTTTAGGGCGGCGA    100
                                                                       
asis               0 --------------------------------------------------      0

asis             101 CTATAATTATTTCGTTTCCTACAAGGATTAAAGTTTTTTCTTTTACTGTG    150
                                                                       
asis               0 --------------------------------------------------      0

asis             151 GGAGGGGGTTTGGTATTAAGAAACGCTAGTCCGGATGTGGCTCTCCATGA    200
                                 .||||||                               
asis               1 ------------TTATTAA-------------------------------      7

asis             201 TACTTATTGT------GTAGTAGCTCATTTTCATTATGTTCTTCGAATGG    244
                      .|||||.||      |||..|..||  ||||.||||.||.|    ||.|
asis               8 -TCTTATGGTTTTGCCGTAAAATTTC--TTTCTTTATTTTTT----ATTG     50

asis             245 GAGCAGTCATTGGTATTTTTTTGGTTTTTTTTT------GAAATTTTTAG    288
                              ||.|.|||||.|||.||||.||||      | |||||||||
asis              51 ---------TTAGGATTTTGTTGATTTTATTTTTCTCAAG-AATTTTTAG     90

asis             289 GTTATTTAGACC-----ATTTTTTTTT--GTTTCGCTAATTAGAATTTTA    331
                     ||.|.|||||||     ||||||||.|  ||.|      |||.|.|||||
asis              91 GTCAATTAGACCGGCTTATTTTTTTGTCAGTGT------TTAAAGTTTTA    134

asis             332 TTAGCCTTTGGTTTTTTTTTATTTTT----TGGGGTTAAGACAAGGTGTC    377
                     |||                 ||||||    .||||...||||..|||||.
asis             135 TTA-----------------ATTTTTGGGGGGGGGGGGAGACGGGGTGTT    167

asis             378 GT-TGAATTAGTTTAGCAAAATACTGCTTAAGGTAGGCTATA--------    418
                     .| |||||||||||             ||  ||.||.||.||        
asis             168 ATCTGAATTAGTTT-------------TT--GGGAGTCTCTAGACATCTC    202

asis             419 -------------GGATCTACCTTTTATCTTTCTAAT--CTTTT----GT    449
                                  ||..||.||.|.|||..||||.||  |||||    | 
asis             203 ATGGGTTGGCCGGGGGCCTGCCGTCTATAGTTCTTATTCCTTTTAAGGG-    251

asis             450 TTTAGT-ATAATTGGTCTTCGATTCAACAATTTTTAGTCTTCAGTCTTTT    498
                        ||| |.|||     |||||||||.||| .||||||...|||||||||
asis             252 ---AGTAAGAAT-----TTCGATTCAGCAA-CTTTAGTTCACAGTCTTTT    292

asis             499 TTTTTATTTTGAAAAGGTTTTAACACTCTTGGTTTTGGAGGCTTTGGCTT    548
                     ||||||||..| ||||||||                              
asis             293 TTTTTATTAAG-AAAGGTTT------------------------------    311

asis             549 TCTTCTTACTCTTAGGAGGATGGGCGCTAGAAAGAGTTTTAAGAGGGTGT    598
                                                                       
asis             311 --------------------------------------------------    311

asis             599 GAAAGGGGGTTAATAGC    615
                                      
asis             311 -----------------    311


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