Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023880.1 Corchorus olitorius cultivar O-4 contig23913, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5251
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Found at i:1252 original size:331 final size:331
Alignment explanation
Indices: 541--1752 Score: 1539
Period size: 332 Copynumber: 3.6 Consensus size: 331
531 TATTTTTACA
* * **
541 AGTATTGTGGCAAGAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTACAAAATTCGAGCCGAAA
1 AGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAA
* * * *
606 TCGTGTACCAACCAGCACGG-TTTTGGCTAAAAACGCGTTTCGGGGCCATGGCTCAGTTGTGCAT
66 TCGTGTA-CAACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGGCCCTGGCTCAGTTTTGCAT
* * * * **
670 GATTTTTGGCAGAAAGTCTCCTCGAAATATCTATATTTATCTAACCAAATCTCAGCCGCATTGGA
130 GATTTTTGGCAGAAAGACTTCTCGAAAAATCTATATTCATCTAACCAAATCTCAGCCAAATT-GA
* * *
735 TTTACGGACTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAA
194 TTTACAGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAG-AA
* *
800 AAAAATTGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCATTGAATTATATG
258 AAAAATAGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATG
865 ATTTTTCTG
323 ATTTTTCTG
* * *
874 AGTATTGTGGCAAAAAATTGGAGAACAACTGTTCGGGTCAG-TTTTTGCAAAATTTTAGCCGAAA
1 AGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAA
*
938 TCGTGTAC-ACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGACCCTGGCTCAGTTTTGCATG
66 TCGTGTACAACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGGCCCTGGCTCAGTTTTGCATG
* * *
1002 ATTTTTGGCAGAATGACTTCTCGAAAAATCTATATTCATCTAATCAAATCTCTCAACCATAATT-
131 ATTTTTGGCAGAAAGACTTCTCGAAAAATCTATATTCATCTAACCAAA--TCTCAGCCA-AATTG
* ** * * *
1066 TTTTACAGATTTATTTTT-TTAGTATCCGAATCTTGTTTCCATTTAATTAGAAATAAATTCAGAA
193 ATTTACAGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAA
* * *
1130 AAAAATGGAAAAACGATATTAGAAGCGTTAAAAACCCTAAAATAGTATTGGCGTTGAATTATATG
258 AAAAATAGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATG
1195 ATTTTTCTG
323 ATTTTTCTG
* * * *
1204 AGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGCTCTGTTTTTTGCAAAATGTTAGCCAAAA
1 AGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAA
* * * ** * * *
1269 TCGTGT--AACCATAACAGTTTTTTTGGCTAAAAATGTGTTTCAAGGCCCTGACTCAATTTTGAA
66 TCGTGTACAACCATCAC-G-GTTTTTGGCTAAAAATGCGTTTCGGGGCCCTGGCTCAGTTTTGCA
** * * *
1332 TGGCTTTTGACAGAAAGACTTCTC-AAAATATCTATATTCATCTAACCAAATCTCACCCACATTG
129 TGATTTTTGGCAGAAAGACTTCTCGAAAA-ATCTATATTCATCTAACCAAATCTCAGCCAAATT-
* * *
1396 GATTTAC-GAATTTGTTTTTACGAGCATCTGTATCTTGTTAT-GATTTAATAAGAAATAAATTCA
192 GATTTACAG-ATTTATTTTTACGAGCATCTGAATCTTGTT-TCGATTTAATTAGAAATAAATTCA
* ** *
1459 GAAAAAAATAGAAAAACGAAATTTTAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTAT
255 GAAAAAAATAGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTAT
1524 ATGATTTTTCTG
320 ATGATTTTTCTG
*
1536 AGTATTGAGGCGAAAAAATTGGTGG-AAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGA
1 AGTATTGTGGC-AAAAAATTGG-GGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGA
* * **
1600 AATCGTGTACTGACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGGTCCTTTCTCAGTTTTGC
64 AATCGTGTAC-AACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGGCCCTGGCTCAGTTTTGC
* * * * * *
1665 ATGATTTTTGGCAGAATGATTTCTCGAAATATCTATATTTATCTAATCAAATCCCTCAGTCACAA
128 ATGATTTTTGGCAGAAAGACTTCTCGAAAAATCTATATTCATCTAACCAAAT--CTCAGCCA-AA
1730 -TGCATTTACAGATTTATTTTTAC
190 TTG-ATTTACAGATTTATTTTTAC
1753 AAGTATTGTG
Statistics
Matches: 753, Mismatches: 101, Indels: 47
0.84 0.11 0.05
Matches are distributed among these distances:
329 3 0.00
330 133 0.18
331 169 0.22
332 232 0.31
333 98 0.13
334 80 0.11
335 5 0.01
336 31 0.04
337 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (331 bp):
AGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAA
TCGTGTACAACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGGCCCTGGCTCAGTTTTGCATG
ATTTTTGGCAGAAAGACTTCTCGAAAAATCTATATTCATCTAACCAAATCTCAGCCAAATTGATT
TACAGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAA
AATAGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATT
TTTCTG
Found at i:2025 original size:550 final size:548
Alignment explanation
Indices: 1204--2307 Score: 1604
Period size: 550 Copynumber: 2.0 Consensus size: 548
1194 GATTTTTCTG
* *
1204 AGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGCTCTGTTTTTTGCAAAATGTTAGCCAAAA
1 AGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGCTCAGTTTTTTACAAAATGTTAGCCAAAA
* * * * *
1269 TCGTGTAACCATAACAGTTTTTTTGGCTAAAAATGTGTTTCAAGGCCCTGACTCAATTTTGAATG
66 TCGTGTAACCATAACAG-TGTTTTGGCTAAAAACGCGTTTCAAGGCCATGACTCAATTGTGAATG
* *
1334 GCTTTTGACAGAAAGACTTCTCAAAATATCTATATTCATCTAACCAAATCTCACCCACATTGGAT
130 ACTTTTGACAGAAAGACTCCTCAAAATATCTATATTCATCTAACCAAATCTCACCCACATTGGAT
*
1399 TTACGAATTTGTTTTTACGAGCATCTGTATCTTGTTATGATTTAATAAGAAATAAATTCAGAAAA
195 TTACGAATTTGTTTTTACGAGCATCTGAATCTTGTTATGATTTAATAAGAAATAAATTCAGAAAA
** *
1464 AAATAGAAAAACGAAATTTTAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAATTATATGAT
260 AAATAGAAAAACGAAATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGAT
* *
1529 TTTTCTGAGTATTGAGGCGAAAAAATT-GGTGGAAAACTTTTCGGGTCAGTTTTTTGCAAAATTT
325 TTTTCTGAGTATTGAGGC-AAAAAATTAGG-GAAAAACATTTCGGGTCAGTTTTTTGCAAAATTT
* * * **
1593 TAGCCGAAATCGTGTACTGACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGGTCCTTTCTCA
388 TAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAATGCGTTTCGGGGCCCTGACTCA
* * * *
1658 GTTTTGCATGATTTTTGGCAGAATGATTTCTCGAAATATCTATATTTATCTAATCAAATCCCTCA
453 GTTTTGCATGATTTTTGGCAGAAAGAGTTCTCGAAATATCTATAATCATCTAATCAAATCCCTCA
* *
1723 GTCACAATGCATTTACAGATTTATTTTTACA
518 GCCACAATGCATTTACAGATTAATTTTTACA
* * * *
1754 AGTATTGTGGCAAGAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTACAAAATTTTAGCCGAAA
1 AGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGCTCAGTTTTTTACAAAATGTTAGCCAAAA
* * ** * * *
1819 TCGTGT-ACTAACTATCACG-GTTTTGGCTAAAAACGCGTTTCGGGGCCATGGCTCAGTTGTGCA
66 TCGTGTAAC-CA-TAACA-GTGTTTTGGCTAAAAACGCGTTTCAAGGCCATGACTCAATTGTGAA
* ** * ** * *
1882 TGATTTTTTTCAGAAAGTCTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCGCATTGG
128 TGACTTTTGACAGAAAGACTCCTCAAAATATCTATATTCATCTAACCAAATCTCACCCACATTGG
* * * *
1947 ATTTACGGATTTGTTTTTACTAGCATCTGAATCTTGTT-TCGATTTAATTAGAAATATATTCAGA
193 ATTTACGAATTTGTTTTTACGAGCATCTGAATCTTGTTAT-GATTTAATAAGAAATAAATTCAGA
* *
2011 AAAAAATTGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATAT
257 AAAAAATAGAAAAACGAAATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATAT
*
2076 GATTTTTCTGAGTATTGTGGCAAAAAATTAGGGAAAAACATTTCGGGTCAGTTTTTTGCAAAATT
322 GATTTTTCTGAGTATTGAGGCAAAAAATTAGGGAAAAACATTTCGGGTCAGTTTTTTGCAAAATT
*
2141 TTAGCCGAAATCGTGTATTAACCATCACGATTTTTGGCTAAAAATGCGTTTCGGGGCCCTGACTC
387 TTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAATGCGTTTCGGGGCCCTGACTC
* * *
2206 AGTTTTGCATGATTTTTGGCAGAAAGAGTTCTTGAAATATCTATAATCATCTGATCAAATCTCTC
452 AGTTTTGCATGATTTTTGGCAGAAAGAGTTCTCGAAATATCTATAATCATCTAATCAAATCCCTC
*
2271 AGCCACAATGCATTTACGGATTAATTTTTACA
517 AGCCACAATGCATTTACAGATTAATTTTTACA
2303 AGTAT
1 AGTAT
2308 CTGAGTCTTG
Statistics
Matches: 492, Mismatches: 57, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
549 193 0.39
550 294 0.60
551 4 0.01
552 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (548 bp):
AGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGCTCAGTTTTTTACAAAATGTTAGCCAAAA
TCGTGTAACCATAACAGTGTTTTGGCTAAAAACGCGTTTCAAGGCCATGACTCAATTGTGAATGA
CTTTTGACAGAAAGACTCCTCAAAATATCTATATTCATCTAACCAAATCTCACCCACATTGGATT
TACGAATTTGTTTTTACGAGCATCTGAATCTTGTTATGATTTAATAAGAAATAAATTCAGAAAAA
AATAGAAAAACGAAATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATT
TTTCTGAGTATTGAGGCAAAAAATTAGGGAAAAACATTTCGGGTCAGTTTTTTGCAAAATTTTAG
CCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAATGCGTTTCGGGGCCCTGACTCAGTT
TTGCATGATTTTTGGCAGAAAGAGTTCTCGAAATATCTATAATCATCTAATCAAATCCCTCAGCC
ACAATGCATTTACAGATTAATTTTTACA
Found at i:2025 original size:882 final size:880
Alignment explanation
Indices: 874--2606 Score: 2469
Period size: 882 Copynumber: 2.0 Consensus size: 880
864 GATTTTTCTG
* *
874 AGTATTGTGGCAAAAAATTGGAGAACAACTGTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAAT
1 AGTATTGTGGCAAAAAATTGGAGAAAAACTGTTCGGGTCAGTTTTTACAAAATTTTAGCCGAAAT
* * *
939 CGTGTACACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGACCCTGGCTCAGTTTTGCATGAT
66 CGTGTACACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGACCATGGCTCAGTTGTGCATGAT
* * * * *
1004 TTTTGGCAGAATGACTTCTCGAAAAATCTATATTCATCTAATCAAATCTCTCAACCATAATTTTT
131 TTTTGGCAGAAAGACTCCTCGAAAAATCTATATTCATCTAACCAAA-CTCTCAACCAGAATTATT
* *
1069 TACAGATTTATTTTTTTAGTATCCGAATCTTGTTTCCATTTAATTAGAAATAAATTCAGAAAAAA
195 TACAGATTTATTTTTCTAGCATCCGAATCTTGTTTCCATTTAATTAGAAATAAATTCAGAAAAAA
*
1134 ATGGAAAAACGATATTAGAAGCGTTAAAAACCCTAAAATAGTATTGGCGTTGAATTATATGATTT
260 ATGGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTATTGGCGTTGAATTATATGATTT
* * *
1199 TTCTGAGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGCTCTGTTTTTTGCAAAATGTTAGC
325 TTCTGAGTATTGTGGCAAAAAATTAGGGAAAAACATTTCGGCTCAGTTTTTTGCAAAATGTTAGC
* *
1264 CAAAATCGTG-TAACCATAACAGTTTTTTTGGCTAAAAATGTGTTTCAAGGCCCTGACTCAATTT
390 CAAAATCGTGTTAACCATAAC-G-ATTTTTGGCTAAAAATGCGTTTCAAGGCCCTGACTCAATTT
* *
1328 TGAATGGCTTTTGACAGAAAGACTTCTCAAAATATCTATATTCATCTAACCAAA-TCTCACCCAC
453 TGAATGACTTTTGACAGAAAGACTTCTCAAAATATCTATAATCATCTAACCAAACTCTCACCCAC
* * ** *
1392 ATTGGATTTACGAATTTGTTTTTACGAGCATCTGTA-TCTTGTTAT-GATTTAATAAGAAATAAA
518 AATGCATTTACGAATTAATTTTTACAAGCATCTG-AGTCTTGTT-TCGATTTAATAAGAAATAAA
** *
1455 TTCAGAAAAAAATAGAAAAACGAAATTTTAAGCGTGAAAAACCCTAAAATATTTTTGGCGTTGAA
581 TTCAGAAAAAAATAGAAAAACGAAATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAA
*
1520 TTATATGATTTTTCTGAGTATTGAGGCGAAAAAATTGGTGG-AAAACTTTTCGGGTCAGTTTTTT
646 TTATATGATTTTTCTGAGTATTGAGGC-AAAAAATTGG-GGAAAAACTTTTCGGATCAGTTTTTT
*
1584 GCAAAATTTTAGCCGAAATCGTGTAC-TGACCATCACGG-TTTTTGGCTAAAAATGCGTTTCGGG
709 GCAAAATTTTAGCCGAAATCGTGTACGTGACCATCACGGTTTTTTGGCTAAAAACGCGTTTCGGG
* ** * * * * *
1647 GTCCTTTCTCAGTTTTGCATGATTTTTGGCAGAATGATTTCTCGAAATATCTATATTTATCTAAT
774 GCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTCGAAATATCTATATTCATCTAAC
1712 CAAATCCCTCAGTCACAATGCATTTACAGATTTATTTTTACA
839 CAAATCCCTCAGTCACAATGCATTTACAGATTTATTTTTACA
* * *
1754 AGTATTGTGGCAAGAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTACAAAATTTTAGCCGAAA
1 AGTATTGTGGCAAAAAATTGGAGAAAAACTGTTCGGGTCAG-TTTTTACAAAATTTTAGCCGAAA
* *
1819 TCGTGTACTAACTATCACGG-TTTTGGCTAAAAACGCGTTTCGGGGCCATGGCTCAGTTGTGCAT
65 TCGTGTAC--ACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGACCATGGCTCAGTTGTGCAT
** * * * * *
1883 GATTTTTTTCAGAAAGTCTCCTTGAAATATCTATATTCATCTAACCAAA-TCTCAGCC-GCATTG
128 GATTTTTGGCAGAAAGACTCCTCGAAAAATCTATATTCATCTAACCAAACTCTCAACCAGAATT-
* * * * *
1946 GATTTACGGATTTGTTTTTACTAGCATCTGAATCTTGTTTCGATTTAATTAGAAATATATTCAGA
192 -ATTTACAGATTTATTTTT-CTAGCATCCGAATCTTGTTTCCATTTAATTAGAAATAAATTCAGA
* *
2011 AAAAAATTGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATAT
255 AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTATTGGCGTTGAATTATAT
* *
2076 GATTTTTCTGAGTATTGTGGCAAAAAATTAGGGAAAAACATTTCGGGTCAGTTTTTTGCAAAATT
320 GATTTTTCTGAGTATTGTGGCAAAAAATTAGGGAAAAACATTTCGGCTCAGTTTTTTGCAAAATG
* * **
2141 TTAGCCGAAATCGTGTATTAACCATCACGATTTTTGGCTAAAAATGCGTTTCGGGGCCCTGACTC
385 TTAGCCAAAATCGTG--TTAACCATAACGATTTTTGGCTAAAAATGCGTTTCAAGGCCCTGACTC
* * * * * ** * *
2206 AGTTTTGCATGATTTTTGGCAGAAAGAGTTCTTGAAATATCTATAATCATCTGATCAAATCTCTC
448 AATTTTGAATGACTTTTGACAGAAAGACTTCTCAAAATATCTATAATCATCTAACCAAA-CTCTC
* * * *
2271 AGCCACAATGCATTTACGGATTAATTTTTACAAGTATCTGAGTCTTGTTTCGATTTAATTAGAAA
512 ACCCACAATGCATTTACGAATTAATTTTTACAAGCATCTGAGTCTTGTTTCGATTTAATAAGAAA
* *
2336 TAAATTCAGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGT
577 TAAATTCAGAAAAAAATAGAAAAACGAAATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGT
*
2401 TGAATTATATGATTTTTCTGAGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGATCAGTTTT
642 TGAATTATATGATTTTTCTGAGTATTGAGGCAAAAAATTGGGGAAAAACTTTTCGGATCAGTTTT
* * * *
2466 TTGCAAAATTTTGGCCGAAATCGTGTACGTTACCATTACGGTTTTTTTTTGGCTAAAAACGTGTT
707 TTGCAAAATTTTAGCCGAAATCGTGTACGTGACCATCACGG---TTTTTTGGCTAAAAACGCGTT
*
2531 TCGGGGCCCTGACTCAGTTTTGTATGATTTTTGGCAGAAAGACTCCTCGAAATATCTATATTCAT
769 TCGGGGCCCTGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTCGAAATATCTATATTCAT
2596 CTAACCAAATC
834 CTAACCAAATC
2607 TTAACCGCAT
Statistics
Matches: 750, Mismatches: 84, Indels: 29
0.87 0.10 0.03
Matches are distributed among these distances:
879 3 0.00
880 44 0.06
881 45 0.06
882 257 0.34
883 91 0.12
884 60 0.08
885 165 0.22
889 85 0.11
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (880 bp):
AGTATTGTGGCAAAAAATTGGAGAAAAACTGTTCGGGTCAGTTTTTACAAAATTTTAGCCGAAAT
CGTGTACACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGACCATGGCTCAGTTGTGCATGAT
TTTTGGCAGAAAGACTCCTCGAAAAATCTATATTCATCTAACCAAACTCTCAACCAGAATTATTT
ACAGATTTATTTTTCTAGCATCCGAATCTTGTTTCCATTTAATTAGAAATAAATTCAGAAAAAAA
TGGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTATTGGCGTTGAATTATATGATTTT
TCTGAGTATTGTGGCAAAAAATTAGGGAAAAACATTTCGGCTCAGTTTTTTGCAAAATGTTAGCC
AAAATCGTGTTAACCATAACGATTTTTGGCTAAAAATGCGTTTCAAGGCCCTGACTCAATTTTGA
ATGACTTTTGACAGAAAGACTTCTCAAAATATCTATAATCATCTAACCAAACTCTCACCCACAAT
GCATTTACGAATTAATTTTTACAAGCATCTGAGTCTTGTTTCGATTTAATAAGAAATAAATTCAG
AAAAAAATAGAAAAACGAAATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATA
TGATTTTTCTGAGTATTGAGGCAAAAAATTGGGGAAAAACTTTTCGGATCAGTTTTTTGCAAAAT
TTTAGCCGAAATCGTGTACGTGACCATCACGGTTTTTTGGCTAAAAACGCGTTTCGGGGCCCTGA
CTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTCGAAATATCTATATTCATCTAACCAAATCC
CTCAGTCACAATGCATTTACAGATTTATTTTTACA
Found at i:2777 original size:340 final size:335
Alignment explanation
Indices: 1754--3973 Score: 2762
Period size: 335 Copynumber: 6.5 Consensus size: 335
1744 TATTTTTACA
* *
1754 AGTATTGTGGCAAGAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTACAAAATTTTAGCCGAAA
1 AGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAA
* * * * * *
1819 TCGTGTACTAACTATCACGG-TTTTGGCTAAAAACGCGTTTCGGGGCCATGGCTCAGTTGTGCAT
66 TCGTGTACTTACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGGCCCTGACTCAGTTTTGCAT
** * * * * *
1883 GATTTTTTTCAGAAAGTCTCCTTGAAATATCTATATTCATCTAACCAAA--TCTCAGCCGCATTG
131 GATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAACCAAATCTCTCAGCCACAATG
* * * * *
1946 GATTTACGGATTTGTTTTTACTAGCATCTGAATCTTGTTTCGATTTAATTAGAAATATATTCAGA
196 GATTTACGGATTTATTTTTACAAGTATCTGAATCTTGTTACGATTTAATTAGAAATAAATTCAGA
*
2011 AAAAAATTGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATAT
261 AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATAT
2076 GATTTTTCTG
326 GATTTTTCTG
* *
2086 AGTATTGTGGCAAAAAATTAGGGAAAAACATTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAA
1 AGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAA
*
2151 TCGTGTA-TTAACCATCACGATTTTTGGCTAAAAATGCGTTTCGGGGCCCTGACTCAGTTTTGCA
66 TCGTGTACTT-ACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGGCCCTGACTCAGTTTTGCA
* * * * *
2215 TGATTTTTGGCAGAAAGAGTTCTTGAAATATCTATAATCATCTGATCAAATCTCTCAGCCACAAT
130 TGATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAACCAAATCTCTCAGCCACAAT
* * * *
2280 GCATTTACGGATTAATTTTTACAAGTATCTGAGTCTTGTTTCGATTTAATTAGAAATAAATTCAG
195 GGATTTACGGATTTATTTTTACAAGTATCTGAATCTTGTTACGATTTAATTAGAAATAAATTCAG
2345 AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATA
260 AAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATA
2410 TGATTTTTCTG
325 TGATTTTTCTG
* *
2421 AGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGATCAGTTTTTTGCAAAATTTTGGCCGAAA
1 AGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAA
* * *
2486 TCGTGTACGTTACCATTACGGTTTTTTTTTGGCTAAAAACGTGTTTCGGGGCCCTGACTCAGTTT
66 TCGTGTAC-TTACCATCACGG----TTTTTGGCTAAAAATGCGTTTCGGGGCCCTGACTCAGTTT
* * * *
2551 TGTATGATTTTTGGCAGAAAGACTCCTCGAAATATCTATATTCATCTAACCAAATCT-T-AACCG
126 TGCATGATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAACCAAATCTCTCAGCCA
* * * * * *
2614 CATTGGATTTACGGATTTGTTTTTACGAGAATCTGAATCTTGTTAAGATTTAATTAGATATAAAT
191 CAATGGATTTACGGATTTATTTTTACAAGTATCTGAATCTTGTTACGATTTAATTAGAAATAAAT
* * *
2679 TTAGGAAAAAAATGGGAAAACGATATTAGAAGCGGGAAAAACCCTAAAATAGTTTTGGCGTTGGA
256 TCA-GAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTT-GA
*
2744 ATTATTTGATTTTTCTG
319 ATTATATGATTTTTCTG
* * *
2761 AGTATTGTGCCAAAAAATTGGGGGAAAACATTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAA
1 AGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAA
* *
2826 TCGTGTACTTTTCGGGTCAGTATTGTGCCAAAGTTTTTTGCAAAAACCATCACGGTTTTTGGCTA
66 TCGTGTAC-TTAC----C---A---T--C-ACG------G---------------TTTTTGGCTA
* * *
2891 AAAATGCGTTTCGGGGCCAT-AGCTCAGTTTTGTAGGATTTTTGGCA-AAATGACTTCTCGAAAT
96 AAAATGCGTTTCGGGGCCCTGA-CTCAGTTTTGCATGATTTTTGGCAGAAA-GACTTCTCGAAAT
* * *
2954 ATCTATATTCATCTAATCAAATCTCTCAGCCACAATGAATTTACGGATTTATTTTTACATGTATC
159 ATCTATATTCATCTAACCAAATCTCTCAGCCACAATGGATTTACGGATTTATTTTTACAAGTATC
* *
3019 TGAATCTTGTTACGATTTAATTAGAAATAAGTTCAGAAAAAAATGGAAAAACGATATTATAAGCG
224 TGAATCTTGTTACGATTTAATTAGAAATAAATTCAGAAAAAAATGGAAAAACGATATTAGAAGCG
* * **
3084 TGAAAACCCCCAAAATAGTTTTTCCGTTGAATTATATGATTTATT-TG
289 TGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATATGATTT-TTCTG
** ** *
3131 AGTATAATGGCAAAAAAATAAGGGAAAAACTTTTCGGGTAAGTTTTTAT-CAAAATTTTAGCCGA
1 AGTATTGTGGC-AAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTT-TGCAAAATTTTAGCCGA
* * * * *
3195 AATCGTGTACGTT---ATCACGGTTTTTGACCAAAAATGCATTTCGGGGACCTGGCTCAGTTTTG
64 AATCGTGTAC-TTACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGGCCCTGACTCAGTTTTG
*
3257 CATGATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAACCAAA--TCTCACCCACA
128 CATGATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAACCAAATCTCTCAGCCACA
* * * * * * *
3320 TTGGATTTACGTATTTGTTTTTACGAGTATTTGAATCTTGTTATGATTTAATTAGAAATCAATTC
193 ATGGATTTACGGATTTATTTTTACAAGTATCTGAATCTTGTTACGATTTAATTAGAAATAAATTC
* * * **
3385 AGAAAAAAATGGAAAAACGATATCAGAAGCGTG-AAAACTCCTGAAATATTTTTTCCGTTGAATT
258 AGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAAC-CCTAAAATAGTTTTGGCGTTGAATT
3449 ATATGATTTTTCTG
322 ATATGATTTTTCTG
* *
3463 AGTATTGAGGCAAAAAATTGGGGAAAAACTTTTTGGGTCAGTTTTTTGCAAAATTTTAGCCGAAA
1 AGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAA
* * * * * *
3528 TCGTGTGCTAACCATCACGGTTTTTGACTAAAAATGTGTTTCGGGGCGCTGGCTCAGTTTTGCAT
66 TCGTGTACTTACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGGCCCTGACTCAGTTTTGCAT
* *
3593 GATTTTTGGCAGAATGACTTCTCGAAATATCTATATTCATCTAATCAAATCTCTCAGCCACAATG
131 GATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAACCAAATCTCTCAGCCACAATG
* *
3658 CATTTACGGATTTATTTTTACAAGTATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCAGA
196 GATTTACGGATTTATTTTTACAAGTATCTGAATCTTGTTACGATTTAATTAGAAATAAATTCAG-
* * *
3723 AAAAAAAAATTAGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTATTGGCGTTCAATT
260 --AAAAAAA-TGGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATT
3788 ATATGATTTTTCTG
322 ATATGATTTTTCTG
** *
3802 AGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAACTTTTTGCAAAATTTTAGTCGAAA
1 AGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAA
* * * ** * *
3867 TCATGTACTAACCATCATGGTGTTTTGGCTAAAAATATGTTTCAGGACCCTGACTCAGTTTTGCA
66 TCGTGTACTTACCATCACGGT-TTTTGGCTAAAAATGCGTTTCGGGGCCCTGACTCAGTTTTGCA
* *
3932 TGTTTTTTGGCATAAAGACTTCTCGAAATATCTATATTCATC
130 TGATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATC
3974 ACGGTTTTTT
Statistics
Matches: 1637, Mismatches: 186, Indels: 122
0.84 0.10 0.06
Matches are distributed among these distances:
330 2 0.00
331 62 0.04
332 213 0.13
333 175 0.11
334 80 0.05
335 283 0.17
336 8 0.00
337 2 0.00
338 67 0.04
339 190 0.12
340 258 0.16
344 1 0.00
347 1 0.00
349 1 0.00
350 1 0.00
353 2 0.00
355 2 0.00
356 1 0.00
358 1 0.00
359 1 0.00
361 1 0.00
369 4 0.00
370 108 0.07
371 111 0.07
372 62 0.04
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.35
Consensus pattern (335 bp):
AGTATTGTGGCAAAAAATTGGGGAAAAACTTTTCGGGTCAGTTTTTTGCAAAATTTTAGCCGAAA
TCGTGTACTTACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGGCCCTGACTCAGTTTTGCAT
GATTTTTGGCAGAAAGACTTCTCGAAATATCTATATTCATCTAACCAAATCTCTCAGCCACAATG
GATTTACGGATTTATTTTTACAAGTATCTGAATCTTGTTACGATTTAATTAGAAATAAATTCAGA
AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTAAAATAGTTTTGGCGTTGAATTATAT
GATTTTTCTG
Found at i:4856 original size:331 final size:328
Alignment explanation
Indices: 3979--5250 Score: 1467
Period size: 331 Copynumber: 3.9 Consensus size: 328
3969 TCATCACGGT
** * **
3979 TTTTTG-CTAAAAACGCGTTACGGGGTCCCAGCTC-CTTTTGACATGATTTTTGGAACCAAGCCT
1 TTTTTGTCTAAAAACGC-TTACGGACT-CCAGCTCAGTTTT-ACATGATTTTTGGCGCCAAGCCT
* *
4042 CATTAAAATATCTATATTTATCTAACCAAATCTGAATCACATTGGATTTAAGAATTTTTTTTTTT
63 CATTAAAATATCTATATTTATCTAACCAAATCTCAACCACATTGGATTTAAGAA---TTTTTTTT
* * * * *
4107 ACCAGCATCAGAAACCTGTTTCGATTTAATTAAAAATTAATTTGGAAAAATATATGAAAATCGAT
125 ACTAGCATCAGAAATCTGTTTCGATTTAATTAGAAATTAATTCGGAAAAATATAGGAAAATCGAT
* * * *
4172 ATTAGAAGCGTGAAAAGTCTTTCAATCTTTTTGGAGTTGAATTATATTTTTATTATGAGTATTTT
190 ATTAGAAGCGTGAAAAGCCTTTCAATATTTTTGGAGTTGAATTATATATTTATTATGATTATTTT
* * * * **
4237 GTACAAAAATTGAAGAAAAGTCTTTCAGGTCAATTTTTGCAATATTTTAGCCGAGATCGCATACT
255 ATACAAAAATTGAAGAAAAATCTTTCAGGTAAATTTTTGCAATATTTTAG-CGAAATCGTGTACT
*
4302 AACCATCACGGT
319 AACCATCAC--A
* ** **
4314 TTTTTGGCTAAAAACGCGTTACGGGGTCCCAGCTCCTTTTTACATGATTTTTGGCGCCAAGCCTC
1 TTTTTGTCTAAAAACGC-TTACGGACT-CCAGCTCAGTTTTACATGATTTTTGGCGCCAAGCCTC
*
4379 ATTAAAATATCTATATTTATCTAACCAAATCTCAATCC-CATTGGAGTTAAGAATTTTTTTTACT
64 ATTAAAATATCTATATTTATCTAACCAAATCTCAA-CCACATTGGATTTAAGAATTTTTTTTACT
* *
4443 AGCATCAGAAATCTGTTTCGATTTAAGTAGAAATTAATTCGGAAAAATATAGGAAATTCGATATT
128 AGCATCAGAAATCTGTTTCGATTTAATTAGAAATTAATTCGGAAAAATATAGGAAAATCGATATT
* * * *
4508 AGAAGCGTGAAAAGCCTTTCAATATTTTTGGATTTAAATTACATATTTATTACGATTATTTTATA
193 AGAAGCGTGAAAAGCCTTTCAATATTTTTGGAGTTGAATTATATATTTATTATGATTATTTTATA
* * * * * * *
4573 CAAAAAGTGAAGAAAAATCGTTT-GGGTAAATTTTTTCAAAATTTTAGACAAAATCATGTACTAC
258 CAAAAATTGAAGAAAAATC-TTTCAGGTAAATTTTTGCAATATTTTAG-CGAAATCGTGTACTAA
4637 CCATCACAA
321 CCATCAC-A
* * * *
4646 TTTTTGTCTAAAAACGCATTACGGAACTCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTG
1 TTTTTGTCTAAAAACGC-TTACGG-ACTCCAGCTCAGTTTTACATGATTTTTGGCGCCAAGCCTC
* * * * * ** ** *
4711 AAT-GAATAATCCATATTCATCTAATCAAATCTCGGCCACATTGGATTTAAG-ATACTTTTTACG
64 ATTAAAAT-ATCTATATTTATCTAACCAAATCTCAACCACATTGGATTTAAGAATTTTTTTTACT
* * * * * *
4774 AGCTTCTGAACTTTGTTTCAATTTAATTAGAAATTAATTCGGAAATATATAGGAAAATCGATATT
128 AGCATCAGAAATCTGTTTCGATTTAATTAGAAATTAATTCGGAAAAATATAGGAAAATCGATATT
* * *
4839 AGAAGCGTGAAAAGCCTTTTAAAATTTTTGGAGTTGAATTATATATTTATTATGATTATTTTGTA
193 AGAAGCGTGAAAAGCCTTTCAATATTTTTGGAGTTGAATTATATATTTATTATGATTATTTTATA
* * * *
4904 CAAAAATTGAAGAAAAACCTTTCAGGTCAATTTTTGCAATATTTTAGCTGATATCGTGTATTAAC
258 CAAAAATTGAAGAAAAATCTTTCAGGTAAATTTTTGCAATATTTTAGC-GAAATCGTGTACTAAC
4969 CATCACA
322 CATCACA
* *
4976 -----GT-T------G----C-GTCT-CAGCTCAGTTTTACATGATTTTTGGCGCCTAGCCTCAT
1 TTTTTGTCTAAAAACGCTTACGGACTCCAGCTCAGTTTTACATGATTTTTGGCGCCAAGCCTCAT
* * *
5023 TAAAATATTTATCTTTATCTAACCAAATCTCAATCACATTGGATTTAAGAATTTTTTTTACTAGC
66 TAAAATATCTATATTTATCTAACCAAATCTCAACCACATTGGATTTAAGAATTTTTTTTACTAGC
* *
5088 ATCAGAAATCTGTTTCGATTTAATTAGAAATTAATTCCGAAAAATAAAGGAAAATCGATATTAGA
131 ATCAGAAATCTGTTTCGATTTAATTAGAAATTAATTCGGAAAAATATAGGAAAATCGATATTAGA
* * *
5153 AGCGTGAAAAGCCTTTCAATCTTTTTGGCGTTGAATCATATATTTATTATGATTATTTTATACAA
196 AGCGTGAAAAGCCTTTCAATATTTTTGGAGTTGAATTATATATTTATTATGATTATTTTATACAA
* *
5218 AAATTGAAGAAAAAATTTTTCGGGTAAATTTTT
261 AAATTGAAG-AAAAATCTTTCAGGTAAATTTTT
5251 T
Statistics
Matches: 804, Mismatches: 121, Indels: 47
0.83 0.12 0.05
Matches are distributed among these distances:
310 68 0.08
311 142 0.18
312 20 0.02
313 1 0.00
318 1 0.00
324 1 0.00
325 2 0.00
330 5 0.01
331 183 0.23
332 89 0.11
333 180 0.22
334 3 0.00
335 6 0.01
336 98 0.12
337 5 0.01
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (328 bp):
TTTTTGTCTAAAAACGCTTACGGACTCCAGCTCAGTTTTACATGATTTTTGGCGCCAAGCCTCAT
TAAAATATCTATATTTATCTAACCAAATCTCAACCACATTGGATTTAAGAATTTTTTTTACTAGC
ATCAGAAATCTGTTTCGATTTAATTAGAAATTAATTCGGAAAAATATAGGAAAATCGATATTAGA
AGCGTGAAAAGCCTTTCAATATTTTTGGAGTTGAATTATATATTTATTATGATTATTTTATACAA
AAATTGAAGAAAAATCTTTCAGGTAAATTTTTGCAATATTTTAGCGAAATCGTGTACTAACCATC
ACA
Done.