Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003036.1 Kokia drynarioides strain JFW-HI SEQ_115558, 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: 2542
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.27
Found at i:536 original size:216 final size:216
Alignment explanation
Indices: 4--2542 Score: 2890
Period size: 216 Copynumber: 11.8 Consensus size: 216
1 ACT
* *
4 TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTTCTCGAGCATGTAATGTTCGAAA
1 TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCCGAGCATGTAATGTTCGAAA
* * * * * * *
69 AATTGCTCGAAGGATTTGATCGTCTTGCATACTTTAAGGAACCAAAGCTATAAAAGAACTAGTAA
66 AATTACTCGAAGGATTGGATCGTCTTGAACACTTTAAGGAACCGAAGTTAAAAAAGAACTAGTAA
* * * * * *
134 AAGTTCGACATGTTCGAAAGTTCGTCCAAGTACCAAGAGAGAAACAATTCTCGC-TTAATAAGTT
131 AAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
* *
198 TTTAATTCAAATATCAAAACA
196 TTTAATTCAAAGACCAAAACA
* * * * ** * * *
219 TGTTCATAAAGA-GAAAAACTATTTAGACCAAATGATGCGATTTCCCTCGAACGGAATGTTCGAA
1 TGTTTACAAA-ATGACAAACTTTTTAGACCAAATGATGCGATTTCCCGAGCATGTAATGTTCGAA
* * * * * *
283 AAATTACTTGAAGGAATGGATCGTCCTGAACACTTTAAGGAACTGGATTTAAAAAAGAACTAGTA
65 AAATTACTCGAAGGATTGGATCGTCTTGAACACTTTAAGGAACCGAAGTTAAAAAAGAACTAGTA
* *
348 AAAGTTTGACAAGTTTGGAAGTTCGTCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
130 AAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
*
413 TTTTAATTCAAAGGCCAAAACA
195 TTTTAATTCAAAGACCAAAACA
* * *
435 TGTTTACAAAATGACAAACTTTTTAGACGAAATGATGCGACTTCTCGAGCATGTAATGTTCGAAA
1 TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCCGAGCATGTAATGTTCGAAA
* * * * * * *
500 AATTGCTCGAAGGATTGGATCATCTTGAATACTTTAAGGAATCGAAGCTATAAAAGAACTCGTAA
66 AATTACTCGAAGGATTGGATCGTCTTGAACACTTTAAGGAACCGAAGTTAAAAAAGAACTAGTAA
* * * *
565 AAGTTCGACAAGTTCGAAAGTACGTCCAAGAACCAAGAGAGAAACAATTCTCAC-TTAATAAGTT
131 AAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
* * *
629 TTTAATTAAAATATCAAAACA
196 TTTAATTCAAAGACCAAAACA
* * * * ** * *
650 TGTTTACAAAAAGAAAAACTGTTTAGACCAAATTATGCGATTTCCCTCGCATGGAATGTTCAAAA
1 TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCCGAGCATGTAATGTTCGAAA
* * * * *
715 AATTACTCGAAGGAATGGATCGTGTTGAACATTTTAAGGAACCGGATTTAAAAAAGAACTAGTAA
66 AATTACTCGAAGGATTGGATCGTCTTGAACACTTTAAGGAACCGAAGTTAAAAAAGAACTAGTAA
* * * *
780 AAGTTTGGCACGTTCGGAAGTTCGTCCAACAACCAAGAGAAAAACAATTCTCACGTAAATAAGTT
131 AAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
*
845 TTTAATTCAAAGGCCAAAACA
196 TTTAATTCAAAGACCAAAACA
* ** * * * * * * *
866 TGTTTTCCCAATGACAAACCTTATAGACCAAATGATGTGATTTCCCGGGCATATAACGTTCGGAA
1 TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCCGAGCATGTAATGTTCGAAA
* * * * * * * *
931 AATTGCTCGAAGGATTGGATCGTCATGCATACTTTAAGGAATCGAAGCTATAAAAGAACTCGTAA
66 AATTACTCGAAGGATTGGATCGTCTTGAACACTTTAAGGAACCGAAGTTAAAAAAGAACTAGTAA
* * * * * *
996 AAGTTCGACATGTTCGAAAGTTTGTCCAAGAACCAAGAGAGAAACAATTCTCGC-TTAATAAGTT
131 AAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
* *
1060 TTTAATTCAAATATCAAAACA
196 TTTAATTCAAAGACCAAAACA
* * * ** *
1081 TGTTTACAAAAAGA-AAACCTATTTAGACCAAATTATGCGATTTCCCTCGCATGGAATGTTC-AG
1 TGTTTACAAAATGACAAA-CTTTTTAGACCAAATGATGCGATTTCCCGAGCATGTAATGTTCGA-
* * * * * *
1144 AAAATTACTCGAAGGAATGGATCGTCCTGAACACTTTAAGGAACTGGATTTAAAAAAGAACAAGT
64 AAAATTACTCGAAGGATTGGATCGTCTTGAACACTTTAAGGAACCGAAGTTAAAAAAGAACTAGT
* * * * * *
1209 AAAAGTTTGACAAGTTCGAAAGTTCGTCCAACAACTAAGAGTGAAATAATTCTCATGTAAATAAG
129 AAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
* *
1274 TTTTTAATTCAAAGGCCAAAACT
194 TTTTTAATTCAAAGACCAAAACA
* * * * * * *
1297 TGTTTACTAAATGACAAACTTTTGAGACCAAATGATGTGACTTCCCTAGCTTGTAATGTTTGAAA
1 TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCCGAGCATGTAATGTTCGAAA
* * * *
1362 AATTACTCGAAGGAATGGATCATCTTGAACACTTTAGGGAACC--AGATTCAAAAAATAACTAGT
66 AATTACTCGAAGGATTGGATCGTCTTGAACACTTTAAGGAACCGAAG-TT-AAAAAAGAACTAGT
* * *
1425 AAAAGTTTGACAAGTTCGGAAGTTCGTCCAATAACCAAGAGAAAAACAATTCTCATGTAAATAAG
129 AAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
* *
1490 TTTTTAATTCAAAGGCCAAAACT
194 TTTTTAATTCAAAGACCAAAACA
* *
1513 TGTTTACAAAATGACAAACCTTTTAGACCAAATGATGTGATTTCCCGAGCATGTAATGTTCGAAA
1 TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCCGAGCATGTAATGTTCGAAA
** * * * * *
1578 AATTGTTCAAAGGATTGGATCGTCTTGCATACTTTAAGGAACCGAAGTTATAAAAGAACTCGTAA
66 AATTACTCGAAGGATTGGATCGTCTTGAACACTTTAAGGAACCGAAGTTAAAAAAGAACTAGTAA
* * * * *
1643 AAGTTCT-ACAAGTTTGGAATTTTGTCCAAGAA-CTA-AGAGACACAATTCTCACGTAAATAAGT
131 AAGTT-TGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
* *
1705 TTTTAATTCAAAGATCAAAACC
195 TTTTAATTCAAAGACCAAAACA
* * * * *
1727 TGTTTACGAAATGAAAAACTATTTAGACAAAATGATGCGATTTTCCTCGA--ATGGAATGTTCGA
1 TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGA-TTTCC-CGAGCATGTAATGTTCGA
* * * * * *
1790 AAAATTACTCGAAGGAATGGATCGTCCTGAACACTTTAAGGAACTGGATTTAAAAAAGAACAAGT
64 AAAATTACTCGAAGGATTGGATCGTCTTGAACACTTTAAGGAACCGAAGTTAAAAAAGAACTAGT
* *
1855 -AAAGTGTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAG--ACAATTCTCACGTAAATAAG
129 AAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAG
* *
1917 TTTTTAATTCAAAGGCCAAAACT
194 TTTTTAATTCAAAGACCAAAACA
* * * * *
1940 TGTTTACAAAACGACAAACCTTTTGGACCAAATGATTG-GACTTCCCGAGCATGTAATGTTCGGA
1 TGTTTACAAAATGACAAACTTTTTAGACCAAATGA-TGCGATTTCCCGAGCATGTAATGTTCGAA
* * * * * * *
2004 AAATTGCTCGAAGGATTGGATCGTCTTGCATACTTGAAGGAACCGAAGCTATAAAAGAACTCGTA
65 AAATTACTCGAAGGATTGGATCGTCTTGAACACTTTAAGGAACCGAAGTTAAAAAAGAACTAGTA
* * * *
2069 AAAGTTCGACAAGTTCAGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
130 AAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGT
* *
2134 TTTTAATTCAAAGATCC-AATCT
195 TTTTAATTCAAAGA-CCAAAACA
** * * ** * *
2156 TGTTTACAAAATGACAAACTACTTAGACAAAATGATGCGATTACCCTCGCATGGAATATTCGAAA
1 TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCCGAGCATGTAATGTTCGAAA
* * * *
2221 AATTACTCGAAGGAATT-GATCGTCCTGAACACTTTAAGGAA-CTAGATTTAAAAAAGAACTCGT
66 AATTACTCGAAGG-ATTGGATCGTCTTGAACACTTTAAGGAACCGA-AGTTAAAAAAGAACTAGT
* * * *
2284 TAAAGTTTGACAAGTTCGGAAGTTTGTCCAACAACTAAGAGAGAAACAATTCTCAC-TGAAATAA
129 AAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGT-AAATAA
2348 GTTTTTAATTCAAAGACCAAAACA
193 GTTTTTAATTCAAAGACCAAAACA
* * * *
2372 TGTTTACAAAATAAAAAAACTTTTTAGACCAAATGATGCGACTTCCCGACCATGTAATGTTCGAA
1 TGTTTACAAAAT-GACAAACTTTTTAGACCAAATGATGCGATTTCCCGAGCATGTAATGTTCGAA
* * * * * *
2437 AAATTGCTCGAAGGATTGGATTGTCTTGAATACTTTAAGGAACCGAAGCTATAAAAGAACTCGTA
65 AAATTACTCGAAGGATTGGATCGTCTTGAACACTTTAAGGAACCGAAGTTAAAAAAGAACTAGTA
* * * *
2502 AAAGTTCT-AGAAGTTCGAAATTTTGTCCAAGAACCAAGAGA
130 AAAGTT-TGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGA
Statistics
Matches: 1933, Mismatches: 356, Indels: 68
0.82 0.15 0.03
Matches are distributed among these distances:
211 3 0.00
212 5 0.00
213 159 0.08
214 187 0.10
215 521 0.27
216 918 0.47
217 135 0.07
218 5 0.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.27
Consensus pattern (216 bp):
TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGATTTCCCGAGCATGTAATGTTCGAAA
AATTACTCGAAGGATTGGATCGTCTTGAACACTTTAAGGAACCGAAGTTAAAAAAGAACTAGTAA
AAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACGTAAATAAGTT
TTTAATTCAAAGACCAAAACA
Found at i:807 original size:431 final size:429
Alignment explanation
Indices: 4--2542 Score: 2954
Period size: 431 Copynumber: 5.9 Consensus size: 429
1 ACT
*
4 TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTTCTCGAGCATGTAATGTTCGAAA
1 TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTTCCCGAGCATGTAATGTTCGAAA
* * * * * *
69 AATTGCTCGAAGGATTTGATCGTCTTGCATACTTTAAGGAACCAAAGCTATAAAAGAACTAGTAA
66 AATTACTCGAAGGATTGGATCGTCTTGAACACTTTAAGGAA-CGAAGCTAAAAAAGAACTAGTAA
* * *
134 AAGTTCGACATGTTCGAAAGTTCGTCCAAGTACCAAGAGAGAAACAATTCTCGCTTAATAAGTTT
130 AAGTTCGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACTTAATAAGTTT
* * * * *
199 TTAATTCAAATATCAAAACATGTTCATAAAGAGAAAAACTATTTAGACCAAATGATGCGATTTCC
195 TTAATTCAAAGACCAAAACATGTTTACAAAAAGAAAAACT-TTTAGACCAAATGATGCGATTTCC
* * * * * *
264 CTCGAACGGAATGTTCGAAAAATTACTTGAAGGAATGGATCGTCCTGAACACTTTAAGGAACTGG
259 CTCGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGA
* *
329 ATTTAAAAAAGAACTAGTAAAAGTTTGACAAGTTTGGAAGTTCGTCCAACAACCAAGAGAGAAAC
324 AGTTAAAAAAGAACTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAACAACCAAGAGAGAAAC
394 AATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACA
389 AATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACA
* *
435 TGTTTACAAAATGACAAACTTTTTAGACGAAATGATGCGACTTCTCGAGCATGTAATGTTCGAAA
1 TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTTCCCGAGCATGTAATGTTCGAAA
* * * * *
500 AATTGCTCGAAGGATTGGATCATCTTGAATACTTTAAGGAATCGAAGCTATAAAAGAACTCGTAA
66 AATTACTCGAAGGATTGGATCGTCTTGAACACTTTAAGGAA-CGAAGCTAAAAAAGAACTAGTAA
*
565 AAGTTCGACAAGTTCGAAAGTACGTCCAAGAACCAAGAGAGAAACAATTCTCACTTAATAAGTTT
130 AAGTTCGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACTTAATAAGTTT
* * * *
630 TTAATTAAAATATCAAAACATGTTTACAAAAAGAAAAACTGTTTAGACCAAATTATGCGATTTCC
195 TTAATTCAAAGACCAAAACATGTTTACAAAAAGAAAAACT-TTTAGACCAAATGATGCGATTTCC
* * * *
695 CTCGCATGGAATGTTCAAAAAATTACTCGAAGGAATGGATCGTGTTGAACATTTTAAGGAACCGG
259 CTCGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGA
* * * *
760 ATTTAAAAAAGAACTAGTAAAAGTTTGGCACGTTCGGAAGTTCGTCCAACAACCAAGAGAAAAAC
324 AGTTAAAAAAGAACTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAACAACCAAGAGAGAAAC
825 AATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACA
389 AATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACA
* ** * * * * * * * *
866 TGTTTTCCCAATGACAAACCTTATAGACCAAATGATGTGATTTCCCGGGCATATAACGTTCGGAA
1 TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTTCCCGAGCATGTAATGTTCGAAA
* * * * * *
931 AATTGCTCGAAGGATTGGATCGTCATGCATACTTTAAGGAATCGAAGCTATAAAAGAACTCGTAA
66 AATTACTCGAAGGATTGGATCGTCTTGAACACTTTAAGGAA-CGAAGCTAAAAAAGAACTAGTAA
* * *
996 AAGTTCGACATGTTCGAAAGTTTGTCCAAGAACCAAGAGAGAAACAATTCTCGCTTAATAAGTTT
130 AAGTTCGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACTTAATAAGTTT
* * * *
1061 TTAATTCAAATATCAAAACATGTTTACAAAAAGAAAACCTATTTAGACCAAATTATGCGATTTCC
195 TTAATTCAAAGACCAAAACATGTTTACAAAAAGAAAAACT-TTTAGACCAAATGATGCGATTTCC
* *
1126 CTCGCATGGAATGTTC-AGAAAATTACTCGAAGGAATGGATCGTCCTGAACACTTTAAGGAACTG
259 CTCGCATGGAATGTTCGA-AAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCG
* * * * * *
1190 GATTTAAAAAAGAACAAGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAACAACTAAGAGTGAAA
323 AAGTTAAAAAAGAACTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAACAACCAAGAGAGAAA
* * *
1255 TAATTCTCATGTAAATAAGTTTTTAATTCAAAGGCCAAAACT
388 CAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACA
* * * * * *
1297 TGTTTACTAAATGACAAACTTTTGAGACCAAATGATGTGACTTCCCTAGCTTGTAATGTTTGAAA
1 TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTTCCCGAGCATGTAATGTTCGAAA
* * * * * *
1362 AATTACTCGAAGGAATGGATCATCTTGAACACTTTAGGGAAC-CAGATTCAAAAAATAACTAGTA
66 AATTACTCGAAGGATTGGATCGTCTTGAACACTTTAAGGAACGAAG-CT-AAAAAAGAACTAGTA
* * * *
1426 AAAGTTTGACAAGTTCGGAAGTTCGTCCAATAACCAAGAGAAAAACAATTCTCA-TGTAAATAAG
129 AAAGTTCGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACT-T-AATAAG
* * * * *
1490 TTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACCTTTTAGACCAAATGATGTGATT
192 TTTTTAATTCAAAGACCAAAACATGTTTACAAAAAGA-AAAACTTTTAGACCAAATGATGCGATT
** * ** * * * *
1555 TCCCGAGCATGTAATGTTCGAAAAATTGTTCAAAGGATTGGATCGTCTTGCATACTTTAAGGAAC
256 TCCCTCGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAAC
* * * * * * *
1620 CGAAGTTATAAAAGAACTCGTAAAAGTTCT-ACAAGTTTGGAATTTTGTCCAAGAA-CTA-AGAG
321 CGAAGTTAAAAAAGAACTAGTAAAAGTT-TGACAAGTTCGGAAGTTCGTCCAACAACCAAGAGAG
* ** *
1682 ACACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACC
385 AAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACA
* * * * * *
1727 TGTTTACGAAATGAAAAACTATTTAGACAAAATGATGCGATTTTCCTCGA--ATGGAATGTTCGA
1 TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGA-CTTCC-CGAGCATGTAATGTTCGA
* * * ** *
1790 AAAATTACTCGAAGGAATGGATCGTCCTGAACACTTTAAGGAACTGGATTTAAAAAAGAACAAGT
64 AAAATTACTCGAAGGATTGGATCGTCTTGAACACTTTAAGGAAC-GAAGCTAAAAAAGAACTAGT
* * *
1855 -AAAGTGT-GACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAG--ACAATTCTCACGTAAATAA
128 AAAAGT-TCGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCAC-TTAATAA
* * * * *
1916 GTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAACGACAAACCTTTTGGACCAAATGATTG-GA
191 GTTTTTAATTCAAAGACCAAAACATGTTTACAAAAAGA-AAAACTTTTAGACCAAATGA-TGCGA
* ** * * * * * * *
1980 CTTCCCGAGCATGTAATGTTCGGAAAATTGCTCGAAGGATTGGATCGTCTTGCATACTTGAAGGA
254 TTTCCCTCGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGA
* * * * * *
2045 ACCGAAGCTATAAAAGAACTCGTAAAAGTTCGACAAGTTCAGAAGTTCATCCAACAACCAAGAGA
319 ACCGAAGTTAAAAAAGAACTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAACAACCAAGAGA
* * *
2110 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCC-AATCT
384 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAG-GCCAAAACA
** * ** * *
2156 TGTTTACAAAATGACAAACTACTTAGACAAAATGATGCGA-TTACCCTCGCATGGAATATTCGAA
1 TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTT-CCCGAGCATGTAATGTTCGAA
* * ** *
2220 AAATTACTCGAAGGAATT-GATCGTCCTGAACACTTTAAGGAACTAGATTTAAAAAAGAACTCGT
65 AAATTACTCGAAGG-ATTGGATCGTCTTGAACACTTTAAGGAACGA-AGCTAAAAAAGAACTAGT
* * * * * * *
2284 TAAAGTTTGACAAGTTCGGAAGTTTGTCCAACAACTAAGAGAGAAACAATTCTCACTGAAATAAG
128 AAAAGTTCGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACT-TAATAAG
* *
2349 TTTTTAATTCAAAGACCAAAACATGTTTACAAAATAAAAAAACTTTTTAGACCAAATGATGCGAC
192 TTTTTAATTCAAAGACCAAAACATGTTTACAAAA-AGAAAAAC-TTTTAGACCAAATGATGCGAT
* * * * * *
2414 TTCCCGAC-CATGTAATGTTCGAAAAATTGCTCGAAGGATTGGATTGTCTTGAATACTTTAAGGA
255 TTCCC-TCGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGA
* * * * * * * *
2478 ACCGAAGCTATAAAAGAACTCGTAAAAGTTCT-AGAAGTTCGAAATTTTGTCCAAGAACCAAGAG
319 ACCGAAGTTAAAAAAGAACTAGTAAAAGTT-TGACAAGTTCGGAAGTTCGTCCAACAACCAAGAG
2542 A
383 A
Statistics
Matches: 1859, Mismatches: 214, Indels: 68
0.87 0.10 0.03
Matches are distributed among these distances:
427 185 0.10
428 6 0.00
429 188 0.10
430 183 0.10
431 947 0.51
432 211 0.11
433 139 0.07
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.27
Consensus pattern (429 bp):
TGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTTCCCGAGCATGTAATGTTCGAAA
AATTACTCGAAGGATTGGATCGTCTTGAACACTTTAAGGAACGAAGCTAAAAAAGAACTAGTAAA
AGTTCGACAAGTTCGAAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACTTAATAAGTTTT
TAATTCAAAGACCAAAACATGTTTACAAAAAGAAAAACTTTTAGACCAAATGATGCGATTTCCCT
CGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCGAAG
TTAAAAAAGAACTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAACAACCAAGAGAGAAACAA
TTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACA
Found at i:1239 original size:646 final size:645
Alignment explanation
Indices: 1--2542 Score: 2957
Period size: 646 Copynumber: 3.9 Consensus size: 645
* *
1 ACTTGTTTACAAAATGACAAACTTTTTAGACCAAATGATGCGACTTCTCGAGCATGTAATGTTCG
1 ACTTGTTTACAAAATGAAAAAC-TTTTAGACCAAATGATGCGACTTCCCGAGCATGTAATGTTCG
* * * * * *
66 AAAAATTGCTCGAAGGATTTGATCGTCTTGCATACTTTAAGGAACCAAAGCTATAAAAGAACTAG
65 AAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCAAAGCTAAAAAAGAACTAG
* * ** * * *
131 TAAAAGTTCGACATGTTCGAAAGTTCGTCCAAGTACCAAGAGAGAAACAATTCTCGC-TTAATAA
130 TAAAAGTTCGACAAGTTCGGAAGTTCGTCCAACAACCAAGAGAAAAACAATTCTCACGTAAATAA
*** * * * *
195 GTTTTTAATTCAAATATCAAAACATGTTCATAAAGA-GA-AAAACTATTTAGACCAAATGATGCG
195 GTTTTTAATTCAAAGGCCAAAACATGTTTACAAA-ATGACAAACCT-TATAGACCAAATGATGCG
* * * * *
258 ATTTCCCTCGAACGGAATGTTCGAAAAATTACTTGAAGGAATGGATCGTCCTGAACACTTTAAGG
258 ATTTCCCGCGCATGGAATGTTCGAAAAATTACTCGAAGGATTGGATCGTCCTGAACACTTTAAGG
* * * * * *
323 AACTGGATTTAAAAAAGAACTAGTAAAAGTTTGACAAGTTTGGAAGTTCGTCCAACAACCAAGAG
323 AAC-GAAGTTAAAAAAGAACTCGTAAAAGTTCGACAAGTTCGGAAGTTTGTCCAACAACCAAGAG
* * *
388 AGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAAACATGTTTACAAAATGACAAA
387 AGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACATGTTTACAAAAAGAAAAA
* * * ** * * *
453 CTTTTTAGACGAAATGATGCGACTTCTCGAGCATGTAATGTTCGAAAAATTGCTCGAAGGATTGG
452 CTATTTAGACCAAATGATGCGACTTCCCTCGCATGGAATGTTCGAAAAATTACTCGAAGGAATGG
* * * * ** *
518 ATCATCTTGAATACTTTAAGGAA-TCGAAGCTATAAAAGAACTCGTAAAAGTTCGACAAGTTCGA
517 ATCGTCCTGAACACTTTAAGGAACT-GAAGCTAAAAAAGAACAAGTAAAAGTTTGACAAGTTCGA
* * ***
582 AAGTACGTCCAAGAACCAAGAGAGAAACAATTCTCACTTAATAAGTTTTTAATTAAAATATCAAA
581 AAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACTTAATAAGTTTTTAATTCAAAGGCCAAA
* * * * ** * *
647 ACATGTTTACAAAAAGAAAAACTGTTTAGACCAAATTATGCGATTTCCCTCGCATGGAATGTTCA
1 ACTTGTTTACAAAATGAAAAACT-TTTAGACCAAATGATGCGACTTCCCGAGCATGTAATGTTCG
* * ** **
712 AAAAATTACTCGAAGGAATGGATCGTGTTGAACATTTTAAGGAACCGGATTTAAAAAAGAACTAG
65 AAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCAAAGCTAAAAAAGAACTAG
* * *
777 TAAAAGTTTGGCACGTTCGGAAGTTCGTCCAACAACCAAGAGAAAAACAATTCTCACGTAAATAA
130 TAAAAGTTCGACAAGTTCGGAAGTTCGTCCAACAACCAAGAGAAAAACAATTCTCACGTAAATAA
* ** *
842 GTTTTTAATTCAAAGGCCAAAACATGTTTTCCCAATGACAAACCTTATAGACCAAATGATGTGAT
195 GTTTTTAATTCAAAGGCCAAAACATGTTTACAAAATGACAAACCTTATAGACCAAATGATGCGAT
* ** * * * * * *
907 TTCCCGGGCATATAACGTTCGGAAAATTGCTCGAAGGATTGGATCGTCATGCATACTTTAAGGAA
260 TTCCCGCGCATGGAATGTTCGAAAAATTACTCGAAGGATTGGATCGTCCTGAACACTTTAAGGAA
* * * * *
972 TCGAAGCTATAAAAGAACTCGTAAAAGTTCGACATGTTCGAAAGTTTGTCCAAGAACCAAGAGAG
325 -CGAAGTTAAAAAAGAACTCGTAAAAGTTCGACAAGTTCGGAAGTTTGTCCAACAACCAAGAGAG
* * * * *
1037 AAACAATTCTCGC-TTAATAAGTTTTTAATTCAAATATCAAAACATGTTTACAAAAAGAAAACCT
389 AAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACATGTTTACAAAAAGAAAAACT
* *
1101 ATTTAGACCAAATTATGCGATTTCCCTCGCATGGAATGTTC-AGAAAATTACTCGAAGGAATGGA
454 ATTTAGACCAAATGATGCGACTTCCCTCGCATGGAATGTTCGA-AAAATTACTCGAAGGAATGGA
* **
1165 TCGTCCTGAACACTTTAAGGAACTGGATTTAAAAAAGAACAAGTAAAAGTTTGACAAGTTCGAAA
518 TCGTCCTGAACACTTTAAGGAACTGAAGCTAAAAAAGAACAAGTAAAAGTTTGACAAGTTCGAAA
* * * *
1230 GTTCGTCCAACAACTAAGAGTGAAATAATTCTCA-TGTAAATAAGTTTTTAATTCAAAGGCCAAA
583 GTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACT-T-AATAAGTTTTTAATTCAAAGGCCAAA
* * * * * *
1294 ACTTGTTTACTAAATGACAAACTTTTGAGACCAAATGATGTGACTTCCCTAGCTTGTAATGTTTG
1 ACTTGTTTACAAAATGAAAAACTTTT-AGACCAAATGATGCGACTTCCCGAGCATGTAATGTTCG
* * * * *
1359 AAAAATTACTCGAAGGAATGGATCATCTTGAACACTTTAGGGAACCAGA-TTCAAAAAATAACTA
65 AAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCAAAGCT-AAAAAAGAACTA
* * *
1423 GTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAATAACCAAGAGAAAAACAATTCTCATGTAAATA
129 GTAAAAGTTCGACAAGTTCGGAAGTTCGTCCAACAACCAAGAGAAAAACAATTCTCACGTAAATA
* * *
1488 AGTTTTTAATTCAAAGGCCAAAACTTGTTTACAAAATGACAAACCTTTTAGACCAAATGATGTGA
194 AGTTTTTAATTCAAAGGCCAAAACATGTTTACAAAATGACAAACCTTATAGACCAAATGATGCGA
* * ** * * * *
1553 TTTCCCGAGCATGTAATGTTCGAAAAATTGTTCAAAGGATTGGATCGTCTTGCATACTTTAAGGA
259 TTTCCCGCGCATGGAATGTTCGAAAAATTACTCGAAGGATTGGATCGTCCTGAACACTTTAAGGA
* * * * * *
1618 ACCGAAGTTATAAAAGAACTCGTAAAAGTTCTACAAGTTTGGAATTTTGTCCAAGAA-CTA-AGA
324 A-CGAAGTTAAAAAAGAACTCGTAAAAGTTCGACAAGTTCGGAAGTTTGTCCAACAACCAAGAGA
* * * * *
1681 GACACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACCTGTTTACGAAATGAAAAAC
388 GAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACATGTTTACAAAAAGAAAAAC
* * * *
1746 TATTTAGACAAAATGATGCGATTTTCCTCGAATGGAATGTTCGAAAAATTACTCGAAGGAATGGA
453 TATTTAGACCAAATGATGCGACTTCCCTCGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGA
* ** * *
1811 TCGTCCTGAACACTTTAAGGAACTGGATTTAAAAAAGAACAAGT-AAAGTGTGACAAGTTCGGAA
518 TCGTCCTGAACACTTTAAGGAACTGAAGCTAAAAAAGAACAAGTAAAAGTTTGACAAGTTCGAAA
* *
1875 GTTCATCCAAGAACCAAGAGAG--ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGGCCAAA
583 GTTCGTCCAAGAACCAAGAGAGAAACAATTCTCAC-TTAATAAGTTTTTAATTCAAAGGCCAAA
* * *
1937 ACTTGTTTACAAAACGACAAACCTTTTGGACCAAATGATTG-GACTTCCCGAGCATGTAATGTTC
1 ACTTGTTTACAAAATGA-AAAACTTTTAGACCAAATGA-TGCGACTTCCCGAGCATGTAATGTTC
* * * * * * * * *
2001 GGAAAATTGCTCGAAGGATTGGATCGTCTTGCATACTTGAAGGAACCGAAGCTATAAAAGAACTC
64 GAAAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCAAAGCTAAAAAAGAACTA
* * *
2066 GTAAAAGTTCGACAAGTTCAGAAGTTCATCCAACAACCAAGAGAGAAACAATTCTCACGTAAATA
129 GTAAAAGTTCGACAAGTTCGGAAGTTCGTCCAACAACCAAGAGAAAAACAATTCTCACGTAAATA
* * * *
2131 AGTTTTTAATTCAAAGATCC-AATCTTGTTTACAAAATGACAAA-C-TACTTAGACAAAATGATG
194 AGTTTTTAATTCAAAG-GCCAAAACATGTTTACAAAATGACAAACCTTA--TAGACCAAATGATG
* * *
2193 CGATTACCCTCGCATGGAATATTCGAAAAATTACTCGAAGGAATT-GATCGTCCTGAACACTTTA
256 CGATTTCCCGCGCATGGAATGTTCGAAAAATTACTCGAAGG-ATTGGATCGTCCTGAACACTTTA
* * * * *
2257 AGGAACTAGATTTAAAAAAGAACTCGTTAAAGTTTGACAAGTTCGGAAGTTTGTCCAACAACTAA
320 AGGAACGA-AGTTAAAAAAGAACTCGTAAAAGTTCGACAAGTTCGGAAGTTTGTCCAACAACCAA
*
2322 GAGAGAAACAATTCTCAC-TGAAATAAGTTTTTAATTCAAAGACCAAAACATGTTTACAAAATAA
384 GAGAGAAACAATTCTCACGT-AAATAAGTTTTTAATTCAAAGACCAAAACATGTTTACAAAA-AG
* * * *
2386 AAAAACTTTTTAGACCAAATGATGCGACTTCCCGAC-CATGTAATGTTCGAAAAATTGCTCGAAG
447 AAAAACTATTTAGACCAAATGATGCGACTTCCC-TCGCATGGAATGTTCGAAAAATTACTCGAAG
* * * * * * ** *
2450 GATTGGATTGTCTTGAATACTTTAAGGAACCGAAGCTATAAAAGAACTCGTAAAAGTTCT-AGAA
511 GAATGGATCGTCCTGAACACTTTAAGGAACTGAAGCTAAAAAAGAACAAGTAAAAGTT-TGACAA
* *
2514 GTTCGAAATTTTGTCCAAGAACCAAGAGA
575 GTTCGAAAGTTCGTCCAAGAACCAAGAGA
Statistics
Matches: 1614, Mismatches: 252, Indels: 59
0.84 0.13 0.03
Matches are distributed among these distances:
641 1 0.00
642 3 0.00
643 336 0.21
644 17 0.01
645 109 0.07
646 583 0.36
647 558 0.35
648 7 0.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.27
Consensus pattern (645 bp):
ACTTGTTTACAAAATGAAAAACTTTTAGACCAAATGATGCGACTTCCCGAGCATGTAATGTTCGA
AAAATTACTCGAAGGAATGGATCGTCTTGAACACTTTAAGGAACCAAAGCTAAAAAAGAACTAGT
AAAAGTTCGACAAGTTCGGAAGTTCGTCCAACAACCAAGAGAAAAACAATTCTCACGTAAATAAG
TTTTTAATTCAAAGGCCAAAACATGTTTACAAAATGACAAACCTTATAGACCAAATGATGCGATT
TCCCGCGCATGGAATGTTCGAAAAATTACTCGAAGGATTGGATCGTCCTGAACACTTTAAGGAAC
GAAGTTAAAAAAGAACTCGTAAAAGTTCGACAAGTTCGGAAGTTTGTCCAACAACCAAGAGAGAA
ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACATGTTTACAAAAAGAAAAACTAT
TTAGACCAAATGATGCGACTTCCCTCGCATGGAATGTTCGAAAAATTACTCGAAGGAATGGATCG
TCCTGAACACTTTAAGGAACTGAAGCTAAAAAAGAACAAGTAAAAGTTTGACAAGTTCGAAAGTT
CGTCCAAGAACCAAGAGAGAAACAATTCTCACTTAATAAGTTTTTAATTCAAAGGCCAAA
Done.