Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020861.1 Corchorus olitorius cultivar O-4 contig20894, 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: 3418
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Found at i:1344 original size:665 final size:661
Alignment explanation
Indices: 1--2387 Score: 3485
Period size: 665 Copynumber: 3.6 Consensus size: 661
* * * *
1 GATGATAAATATAGATATTGCAATGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCGAGGCA
1 GATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTAAGCCG-GGCA
* *
66 CCGAAACGCGTCTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGACAAAAATTTTGCAAA
65 CCGAAACGCGTCTTTAGCCAAAAACCGTGATGGTTACTACACGATTTCGACAAAAATATTGCAAA
* * * *
131 AATTGACCCGAAAGATTTTTCCTCATTTTTTAACCGCAATACTCGTAAAATATATATAATTCAAT
130 AATTGACCCGAAAGATTTTTCCTCAATTTTTAACCACAATACTCGTAAAAAATATATAATTCAAC
* * * *
196 GCCAAAAATATTGAATGGCTTTTCACGCTTCAAATATCATTTTTTCAATTTTTCCCAAATTAATT
195 GCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATCTTTCCCAAATTAATT
261 TCTATTT-AATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGA
260 TCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGA
* * * *
325 TATTT-GGTTAGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGGAAAACTGAG
325 GATTTGGGAT-GATGAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAG
* * * * *
389 CCGGGGCACCGGAACCCGTCTTTAGCCAAAAACCGTGAAGGTTACTACACGATTTCGGCAAAACT
389 CCGGGGCCCCGGAACGCGT-TTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAAT
* * *
454 TTTGC-AAAATCTGACCCGAAAGTATTTTTCCTCAATTTTTAACAGGAAGACTCGTAAAAAAATA
453 TTTGCAAAAAT-TGACCCGAAAG-ATTTTTCCTCAATTTTTAACCGCAATACTCGT-AAAAAATA
* *
518 TATCATTCAAAGCCAAAAAGATTGAACGGCTTTTCACGCTTCTAATATCATTTTTTCAATTTTTC
515 TATAATTCAAAGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTTTTC
* * * *
583 CCGAATTAATTTCTATTTAAATCAAAACAAAATTCAGATGCTCGTAAAATCAAATCCTTAAATCC
580 CCGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCC
*
648 AATGTGGCTGAGATTTGG
645 ATTGTGGCTGAGATTT-G
* * * * *
666 GAAGATGAATATAGATATTTCAATGAGTCTGGGCGCCAAAAATCATGCACATCTAAGCCAGGGC-
1 GATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTAAGCC-GGGCA
* * * * *
730 CTTGAAACGCATCTTTAGCAAAAAACCGTGATGGTTACTACACGATTTCGGCAAAAATTTTGCAA
65 C-CGAAACGCGTCTTTAGCCAAAAACCGTGATGGTTACTACACGATTTCGACAAAAATATTGCAA
*
795 AAACTGACCCGAAAGATTTTTCCTCAATTTTTAACCACAATACTCGTAAAAAATATATAATTCAA
129 AAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCACAATACTCGTAAAAAATATATAATTCAA
*
860 CGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAAATCTTTCCCGAATTAA
194 CGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTC-AATCTTTCCCAAATTAA
* * *
925 TTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAATCAAATCCTTAAATCCAATGTGGCT
258 TTTCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCT
* * * *
990 GAGATTTGGGATGATGAATATAGAGATTTCAATGAGTCTTGGAG-CAATAATAATGCAAAACTGA
323 GAGATTTGGGATGATGAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGA
* * *
1054 GTCGGGGCCCCGGAACGCGTTTGTAGCCAAAAACGGTGATGGTTAGTACACGATTTCGACCAAAA
388 GCCGGGGCCCCGGAACGCGTTT-TAGCCAAAAACCGTGATGGTTAGTACACGATTTCG-GCAAAA
* * *
1119 ATTTTGCAAAAATTGACTCGAAAGATTTTTCCTCAATTTTTAACCTCAATACTCGTTAAAAATAT
451 ATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATAT
* *
1184 ATTATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTC
516 ATAATTCAAAGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATT-TTTC
1249 CCGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCC
580 CCGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCC
1314 ATTGTGGCTGAGATTTG
645 ATTGTGGCTGAGATTTG
1331 GATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCAT-CTAAAACTAAGCCGGGGC
1 GATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGC-AAAACTAAGCC-GGGC
* * * *
1395 ACCGGAACCCGTCTTTAGCCAAAAACCGTGATGGTTACTACACGATTTCGACAAAAAAATCGCAA
64 ACCGAAACGCGTCTTTAGCCAAAAACCGTGATGGTTACTACACGATTTCGACAAAAATATTGCAA
*
1460 AAATTGACCCGAAAGATTTTTCCTAAATTTTTAACCACAATACTCGTAAAAAATATATAATTCAA
129 AAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCACAATACTCGTAAAAAATATATAATTCAA
* * * * * * *
1525 CGGCAAAGAGATTGAAGGGCTTTTAATGCTTCTATTATCATTTTTCCAATTCTTTCCCGAATTAA
194 CGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAA-TCTTTCCCAAATTAA
* *
1590 TTTCTAATTAAATCGAAACAAGATTCAGATAATCGTAAAAA-AAATCCTTAAATCCATTGTGGCT
258 TTTCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCT
** * * *
1654 GAGATTTGATATGATGAATATAGATATTTCAATGAATCTTGGCGCCAAAAATCATGCAAAAATTA
323 GAGATTTGGGATGATGAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGA
* *
1719 GTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCAAAAA
388 GCCGGGGCCCCGGAACGCG-TTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAA
* * *
1784 TATTGCAAAAATTTACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATAAA
452 TTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATA
* * * **
1849 TAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATGATTTTTTCAATTTTTCTA
517 TAATTCAAAGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTTTTCCC
* *
1914 AAATTAATTTCTATTTAAATCGAAACAAGATTTAGATGATCGTAAAAACAAATCCTTAAATCCAT
582 GAATTAATTTCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCAT
*
1979 TGTGACTGAGATTTG
647 TGTGGCTGAGATTTG
* * * * *
1994 AGATAATTAATAGAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGTCGGGCC
1 -GATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTAAGCCGGGCA
* * * * *
2059 CCGGAACGCGTTTTTAGCCAAAAACCGAGATGGTTAGTAACACGATTTCGGCAAAAATATTGCAA
65 CCGAAACGCGTCTTTAGCCAAAAACCGTGATGGTTACT-ACACGATTTCGACAAAAATATTGCAA
* *
2124 AAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAGTACTCGTAAAAAATATATAATTCAA
129 AAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCACAATACTCGTAAAAAATATATAATTCAA
* * * **
2189 TGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTTCAATTTTTCTAAAATTAA-
194 CGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATCTTTCCCAAATTAAT
* * * *
2253 TTATGTTTAAATCGAAACAAGATTTAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGACTG
259 TTCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTG
* * * * *
2318 AAATTTGGGATAATTAATAGAGATATTTCAATGAGTCTTGGCGCTAAAAATCATGCAAAACTGAG
324 AGATTTGGGATGATGAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAG
2383 CCGGG
389 CCGGG
2388 TACACGATTT
Statistics
Matches: 1550, Mismatches: 154, Indels: 38
0.89 0.09 0.02
Matches are distributed among these distances:
662 35 0.02
663 212 0.14
664 364 0.23
665 620 0.40
666 203 0.13
667 108 0.07
668 8 0.01
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (661 bp):
GATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTAAGCCGGGCAC
CGAAACGCGTCTTTAGCCAAAAACCGTGATGGTTACTACACGATTTCGACAAAAATATTGCAAAA
ATTGACCCGAAAGATTTTTCCTCAATTTTTAACCACAATACTCGTAAAAAATATATAATTCAACG
CCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATCTTTCCCAAATTAATTT
CTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAG
ATTTGGGATGATGAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCC
GGGGCCCCGGAACGCGTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAATTTT
GCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATATAAT
TCAAAGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTTTTCCCGAAT
TAATTTCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTG
GCTGAGATTTG
Found at i:1577 original size:332 final size:331
Alignment explanation
Indices: 1--2387 Score: 3462
Period size: 332 Copynumber: 7.2 Consensus size: 331
* * * *
1 GATGATAAATATAGATATTGCAATGAGTCTTTGCGCCAAAAATCATGCAAAACTGAGCCGAGGCA
1 GATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCA
* *
66 CCGAAACGCGTCTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGACAAAAATTTTGCAAA
66 CCGGAACGCGTCTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCAAA
* * * *
131 AATTGACCCGAAAGATTTTTCCTCATTTTTTAACCGCAATACTCGTAAAATATATATAATTCAAT
131 AATTGACCCGAAAGATTTTTCCTCAATTTTTAACCACAATACTCGTAAAAAATATATAATTCAAC
* * * *
196 GCCAAAAATATTGAATGGCTTTTCACGCTTCAAATATCATTTTTTCAATTTTTCCCAAATTAATT
196 GCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTTTTCCCGAATTAATT
261 TCTATTT-AATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGA
261 TCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGA
*
325 TATTTG
326 GATTTG
* *
331 GTTAGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGGAAAACTGAGCCGGGGC
1 GAT-GATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGC
* * * *
396 ACCGGAACCCGTCTTTAGCCAAAAACCGTGAAGGTTACTACACGATTTCGGCAAAACTTTTGC-A
65 ACCGGAACGCGTCTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCAA
* * *
460 AAATCTGACCCGAAAGTATTTTTCCTCAATTTTTAA-CAGGAAGACTCGTAAAAAAATATATCAT
130 AAAT-TGACCCGAAAG-ATTTTTCCTCAATTTTTAACCA-CAATACTCGT-AAAAAATATATAAT
* *
524 TCAAAGCCAAAAAGATTGAACGGCTTTTCACGCTTCTAATATCATTTTTTCAATTTTTCCCGAAT
191 TCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTTTTCCCGAAT
* * * * *
589 TAATTTCTATTTAAATCAAAACAAAATTCAGATGCTCGTAAAATCAAATCCTTAAATCCAATGTG
256 TAATTTCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTG
654 GCTGAGATTTGG
321 GCTGAGATTT-G
* * * * * * *
666 GAAGATGAATATAGATATTTCAATGAGTCTGGGCGCCAAAAATCATGCACATCTAAGCCAGGGC-
1 GATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCA
* * * * *
730 CTTGAAACGCATCTTTAGCAAAAAACCGTGATGGTTACTACACGATTTCGGCAAAAATTTTGCAA
66 C-CGGAACGCGTCTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCAA
*
795 AAACTGACCCGAAAGATTTTTCCTCAATTTTTAACCACAATACTCGTAAAAAATATATAATTCAA
130 AAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCACAATACTCGTAAAAAATATATAATTCAA
*
860 CGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAAATCTTTCCCGAATTAA
195 CGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTC-AATTTTTCCCGAATTAA
* * *
925 TTTCTATTTAAATCGAAACAAGATTCAGATGCTCGTAAAATCAAATCCTTAAATCCAATGTGGCT
259 TTTCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCT
990 GAGATTTGG
324 GAGATTT-G
* * * * * * *
999 GATGATGAATATAGAGATTTCAATGAGTCTTGGAG-CAATAATAATGCAAAACTGAGTCGGGGCC
1 GATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCA
* *
1063 CCGGAACGCGT-TTGTAGCCAAAAACGGTGATGGTTAGTACACGATTTCGACCAAAAATTTTGCA
66 CCGGAACGCGTCTT-TAGCCAAAAACCGTGATGGTTAGTACACGATTTCG-GCAAAAATTTTGCA
* * * *
1127 AAAATTGACTCGAAAGATTTTTCCTCAATTTTTAACCTCAATACTCGTTAAAAATATATTATTCA
129 AAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCACAATACTCGTAAAAAATATATAATTCA
*
1192 ATGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCCCGAATTA
194 ACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATT-TTTCCCGAATTA
1257 ATTTCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGC
258 ATTTCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGC
1322 TGAGATTTG
323 TGAGATTTG
*
1331 GATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCAT-CTAAAACTAAGCCGGGGC
1 GATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGC-AAAACTGAGCCGGGGC
* * * ** *
1395 ACCGGAACCCGTCTTTAGCCAAAAACCGTGATGGTTACTACACGATTTCGACAAAAAAATCGCAA
65 ACCGGAACGCGTCTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCAA
*
1460 AAATTGACCCGAAAGATTTTTCCTAAATTTTTAACCACAATACTCGTAAAAAATATATAATTCAA
130 AAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCACAATACTCGTAAAAAATATATAATTCAA
* * * * * *
1525 CGGCAAAGAGATTGAAGGGCTTTTAATGCTTCTATTATCATTTTTCCAATTCTTTCCCGAATTAA
195 CGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATT-TTTCCCGAATTAA
* *
1590 TTTCTAATTAAATCGAAACAAGATTCAGATAATCGTAAAAA-AAATCCTTAAATCCATTGTGGCT
259 TTTCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCT
1654 GAGATTTG
324 GAGATTTG
* * * * * *
1662 ATATGATGAATATAGATATTTCAATGAATCTTGGCGCCAAAAATCATGCAAAAATTAGTCGGGGC
1 -GATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGC
* * * *
1727 CCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGGCAAAAATATTGCAA
65 ACCGGAACGCGTCTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCAA
* * *
1792 AAATTTACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATAAATAATTCAA
130 AAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCACAATACTCGTAAAAAATATATAATTCAA
* * ***
1857 CGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATGATTTTTTCAATTTTTCTAAAATTAAT
195 CGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTTTTCCCGAATTAAT
* *
1922 TTCTATTTAAATCGAAACAAGATTTAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGACTG
260 TTCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTG
1987 AGATTTG
325 AGATTTG
* * *
1994 AGATAATTAATAGAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGTC-GGGC
1 -GATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGC
* * * *
2058 CCCGGAACGCGTTTTTAGCCAAAAACCGAGATGGTTAGTAACACGATTTCGGCAAAAATATTGCA
65 ACCGGAACGCGTCTTTAGCCAAAAACCGTGATGGTTAGT-ACACGATTTCGGCAAAAATTTTGCA
* *
2123 AAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAGTACTCGTAAAAAATATATAATTCA
129 AAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCACAATACTCGTAAAAAATATATAATTCA
* * ***
2188 ATGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTTCAATTTTTCTAAAATTAA
194 ACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTTTTCCCGAATTAA
* * * *
2253 -TTATGTTTAAATCGAAACAAGATTTAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGACT
259 TTTCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCT
*
2317 GAAATTTGG
324 GAGATTT-G
* * *
2326 GATAATTAATAGAGATATTTCAATGAGTCTTGGCGCTAAAAATCATGCAAAACTGAGCCGGG
1 GATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGG
2388 TACACGATTT
Statistics
Matches: 1870, Mismatches: 163, Indels: 46
0.90 0.08 0.02
Matches are distributed among these distances:
330 7 0.00
331 372 0.20
332 806 0.43
333 500 0.27
334 179 0.10
335 6 0.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (331 bp):
GATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCA
CCGGAACGCGTCTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCAAA
AATTGACCCGAAAGATTTTTCCTCAATTTTTAACCACAATACTCGTAAAAAATATATAATTCAAC
GCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTTTTCCCGAATTAATT
TCTATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGA
GATTTG
Found at i:2885 original size:286 final size:282
Alignment explanation
Indices: 2132--2985 Score: 1184
Period size: 281 Copynumber: 3.0 Consensus size: 282
2122 AAAAATTGAC
2132 CCGAAAGATTTTTCCTCAATTTTTAACCGCAGTACTCGTAAAAAATATATAATTCAATGCCAAAA
1 CCGAAAGATTTTTCCTCAATTTTTAACCGCAGTACTCGTAAAAAATATATAATTCAATGCCAAAA
* ** * *
2197 AGATTGAAGGGTTTTTCACGCTTCTAATATCATTTTTTCAATTTTTCTAAAATTAA-TTATGTTT
66 AGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTTTTCCCAAATTAATTTCTATTT
* *
2261 AAATCGAAACAAGATTTAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGACTGAAATTTGG
131 AAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAAATTTGG
* * * *
2326 GATAATTAATAGAGATATTTCAATGAGTCTTGGCGCTAAAAATCATGCAAAACTGAGCC-GGGTA
196 GATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCA
*
2390 -C--A-CGA-TTTCGGCAAAAATTGA
261 CCGAACCGACTTT-AGCAAAAA---A
** * *
2411 CCAGAAATTTTTTTCCTCAATTTTTAACCGCAGTACTCGTAAAATATATATAATTCAATACCAAA
1 CC-GAAAGATTTTTCCTCAATTTTTAACCGCAGTACTCGTAAAAAATATATAATTCAATGCCAAA
* ** * *
2476 AATATTGAAGGGCTTTTCACTTTTCAAATATCATTTTTTCGATTTTTCCCAAATTAATTTCTATT
65 AAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTTTTCCCAAATTAATTTCTATT
* * * *
2541 TAAATCGAAACAAGATTCAGATAATCGTAAAAACAAATCCTTAAATACATTTTGGCTGAGATTTG
130 TAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAAATTTG
2606 GGATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGC
195 GGATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGC
*
2671 ACCGGAACGCGACTTTAGCCAAAAA
260 ACC-GAAC-CGACTTTAGCAAAAAA
* *
2696 CCGAAAGATTTTTCCTCAATTTTTAACCGCAGTACTACGTAAAAAATATATTATTCAACGCCAAA
1 CCGAAAGATTTTTCCTCAATTTTTAACCGCAGTACT-CGTAAAAAATATATAATTCAATGCCAAA
* *
2761 AAGATTGAAGGGCTTTTCACGCTTCTGATATCATTTTTTTCAATTTTTCCCGAATTAATTTCTAT
65 AAGATTGAAGGGCTTTTCACGCTTCTAATATCA-TTTTTTCAATTTTTCCCAAATTAATTTCTAT
* * *
2826 TTAAATCAAAACAAGATTCAGATGATCGTAAAAACAAATCCCTAAATCCATTGTGGCTGATATTT
129 TTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAAATTT
* * * *
2891 -GGTTAGATTAATATAGATATTTAAAATGAGTCTTGGCGCCAAAAATCATGGAAAACTGAACCGG
194 GGGAT-GATTAATATAGATATTT-CAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGG
* *
2955 GGCACCCGAACCCGTCTTGAGCAAAAAA
257 GGCA-CCGAA-CCGACTTTAGCAAAAAA
2983 CCG
1 CCG
2986 TGATGGTTAG
Statistics
Matches: 507, Mismatches: 52, Indels: 24
0.87 0.09 0.04
Matches are distributed among these distances:
279 2 0.00
280 107 0.21
281 121 0.24
282 4 0.01
283 1 0.00
284 32 0.06
285 58 0.11
286 106 0.21
287 61 0.12
288 12 0.02
289 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.32
Consensus pattern (282 bp):
CCGAAAGATTTTTCCTCAATTTTTAACCGCAGTACTCGTAAAAAATATATAATTCAATGCCAAAA
AGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTTTTCCCAAATTAATTTCTATTT
AAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAAATTTGG
GATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCA
CCGAACCGACTTTAGCAAAAAA
Found at i:3380 original size:333 final size:334
Alignment explanation
Indices: 2696--3418 Score: 1098
Period size: 333 Copynumber: 2.2 Consensus size: 334
2686 TAGCCAAAAA
*
2696 CCGAAAGATTTTTCCTCAATTTTTAACCGCAGTACTACGTAAAAAATATATTATTCAACGCCAAA
1 CCGAAAGATTTTTCCTCAATTTTTAACCGCAGTACT-CGTAAAAAATATATAATTCAACGCCAAA
* *
2761 AAGATTGAAGGGCTTTTCACGCTTCTGATATCATTTTTTTCAATTTTTCCCGAATTAATTTCTAT
65 AAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTTCAATTTTTCCCGAATTAATTTCTAA
*
2826 TTAAATCAAAACAAGATTCAGATGATCGTAAAAACAAATCCCTAAATCCATTGTGGCTGATATTT
130 TTAAATCAAAACAAGATTCAGATGATCGTAAAAACAAATCCCTAAATCCATTGTGGCTGAGATTT
* *
2891 GGTTAGATTAATATAGATATTTAAAATGAGTCTTGGCGCCAAAAATCATGGAAAACTGAACCGGG
195 GGATAGATTAATATAGATATTTAAAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAACCGGG
* *
2956 GCACCCGAACCCGTCTTGAGCAAAAAACCGTGATGGTTAGTCCACGATTTCGAGAAAAATTTTGC
260 GCACCCGAACCCGTCTTGAGCAAAAAACCATGATGGTTAGTACACGATTTCGAGAAAAATTTTGC
3021 AAAAACTGAC
325 AAAAACTGAC
* * *
3031 CCGAAAGATTTTTCCTCAATTTTTAACCACAATACTCCTAAAAAATATATAATTCAACGCCAAAA
1 CCGAAAGATTTTTCCTCAATTTTTAACCGCAGTACTCGTAAAAAATATATAATTCAACGCCAAAA
3096 AGATTGAAGGGCTTTTCACGCTTCTAATATCA-TTTTTTCAATTCTTTCCCGAATTAATTTCTAA
66 AGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTTCAATT-TTTCCCGAATTAATTTCTAA
* * * * **
3160 TTAAATCGAACCAAGATTCAGATGATTGTAAGAA-AAATCTTTAAATCCATTGTGGCTGAGATTT
130 TTAAATCAAAACAAGATTCAGATGATCGTAAAAACAAATCCCTAAATCCATTGTGGCTGAGATTT
* * * **
3224 GGGAT-GATTAATATAGATATTT-CAATGAGTGTTGGCGCCAAAAATCATGCAAAACTTAGTCGG
195 -GGATAGATTAATATAGATATTTAAAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAACCGG
* * *
3287 GGC-CCCGGAACGCGTTTTTAGCAAAAAAACCATGATGGTTAGTACACGATTTCG-GCAAAAATT
259 GGCACCC-GAACCCGTCTTGAGC-AAAAAACCATGATGGTTAGTACACGATTTCGAG-AAAAATT
* *
3350 TTGTAAAAATTGAC
321 TTGCAAAAACTGAC
*
3364 CCGAAAGATATTTCCTCAATTTTTAACCGCAGTACTCGTAAAAAATATATAATTC
1 CCGAAAGATTTTTCCTCAATTTTTAACCGCAGTACTCGTAAAAAATATATAATTC
Statistics
Matches: 352, Mismatches: 31, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
331 3 0.01
332 51 0.14
333 154 0.44
334 110 0.31
335 34 0.10
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (334 bp):
CCGAAAGATTTTTCCTCAATTTTTAACCGCAGTACTCGTAAAAAATATATAATTCAACGCCAAAA
AGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTTCAATTTTTCCCGAATTAATTTCTAAT
TAAATCAAAACAAGATTCAGATGATCGTAAAAACAAATCCCTAAATCCATTGTGGCTGAGATTTG
GATAGATTAATATAGATATTTAAAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAACCGGGG
CACCCGAACCCGTCTTGAGCAAAAAACCATGATGGTTAGTACACGATTTCGAGAAAAATTTTGCA
AAAACTGAC
Done.