Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005224.1 Kokia drynarioides strain JFW-HI SEQ_119106, 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: 2737
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Found at i:871 original size:437 final size:433
Alignment explanation
Indices: 1--2737 Score: 2243
Period size: 437 Copynumber: 6.3 Consensus size: 433
* * * *
1 TTTAATTCAAGGACCAAAAAGTTGTTTCCAAAATGACAAACTATTTAGACCGAATGATGCTATTT
1 TTTAATTCAAAGACC-AAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* * ** * * *
66 CCCGAGCACAGAATGTTCGAAATATTGATCGAAGGAATGGATCGTCT-T-GAATACTTTAAGGAA
65 -TCGAGAATGGAATGTTCGAAA-ATTGCTCGAAAGAATGGATCTTCTATAGAATACTTTAAGGAA
* * * ** *
129 CCAAAGTTATAAAAGAACTCGTAAAAAGCTTGACCAGTTCAAAAGTTCATCTAAGAACCAA-AGG
128 CCGAAGTTATAAAAGAACTCGT-AAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGA-G
* * * ** * *
193 AGAAACAATTCTCACATAATTAAGTTTTTAGTTTGAAGACCAAAACTTGGTTTTCAAAATGACAA
191 AGAAACAAATCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTT-GTTTACAAAATGACAA
* * * * * **
258 ACTATTTAGACCAAAAGATGCAATTT-CTCGAGCATGTAATGTTTGGAA-AA-TTGCTCGTAAAA
255 ACTATTTAGACCAAATGATGCGATTTAC-CGAACATGGAATG-TTCGAACAATTTGCTCG-AAGG
* * * * *
320 AACGGAT-GTTC-TTGAATACTTTAAGGAACCGAAGTTATAAAATAACTCGTAAAAGTTTTACAA
317 AATGGATCG--CATAGAATACTTTAAGGAACCTAAGTTATAAAAGAACTCGTAAAAGTTTGACAA
* * * * * * *
383 -TTCGGTAGTTCATCCAAAAATCAAGAGAGAGACAATTTTCACATAAATAAGTT
380 GTTCAGAAGTTCATCCAAGAACCAAGAAAGAAACAATTCTCACATAAATAAGTT
* * * * ** *
436 CTTAATTCAAAGACCAAAAGTTATTTACAAAATGACAAACTATTTAAACCAAAAGATTTGCTTTT
1 TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTT
* * * *
501 CGGAGAATGGAATGTTCGAAAATTGCTCG-ATGAAGTGGATCATTTATATATAATACACTTCAAG
66 C-GAGAATGGAATGTTCGAAAATTGCTCGAAAGAA-TGGATC--TTCTATAGAAT--ACTTTAAG
* * * * * *
565 GAACCGAAGTTTTAAAAGAACTTGTAAAAGTTTGACAAGTCCGGAGGTTCGTCGAAGAACCAAGA
125 GAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGA
* * * *
630 GAGAAACAAATCCCACGTCAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATAACAA
190 GAGAAACAAATCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* ** * * *
695 ACTATTTAGATCAAATGATGCGATTTACCGAACATTCAATGCTCGAACAATTTG-TAGAGGGAAT
255 ACTATTTAGACCAAATGATGCGATTTACCGAACATGGAATGTTCGAACAATTTGCTCGAAGGAAT
* * * *
759 GGATCGCATAGAATGCTTTAAGGAACCTAAGTTGTAAAAGGACTCGTAGAAGTTTGACAAGTTCA
320 GGATCGCATAGAATACTTTAAGGAACCTAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCA
* * *
824 GAAGTTCATCCAGGATCTAAGAAAGAAACAATTCTCACATAAATAAGTT
385 GAAGTTCATCCAAGAACCAAGAAAGAAACAATTCTCACATAAATAAGTT
* * *
873 TTTAATTCAGAA-ACCAAAAGTTGTTTAC-AAATGACAAAATATTTAGGCCGAATGATGCGATTT
1 TTTAATTCA-AAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* * * * ** * **
936 CTCGAGTATGGAAAGTTTAGAATATTATTTGAAAGAATGGATCGCCT-TA-AATACTTTAAGGAA
65 -TCGAGAATGGAATG-TTCGAAAATTGCTCGAAAGAATGGATCTTCTATAGAATACTTTAAGGAA
* * * *
999 CC-AATGTCATAAAAGAACTCGTAAAAGTTTGAAAAGTTCAGAAGTTCAT--------C--TA-A
128 CCGAA-GTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGA
* * *
1052 G-AAC---TCTCGCGTAAATAAGTTTTAAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
192 GAAACAAATCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
* * * * * *
1113 TATTTAGACCAAGTGATGCGATTT-CTCGAGCATGGAATGTTC-AAAAAATTGCTCGAAGAAACG
257 TATTTAGACCAAATGATGCGATTTAC-CGAACATGGAATGTTCGAACAATTTGCTCGAAGGAATG
* * * * * * ** *
1176 GATCATC-TTGAATACTTTATGGAA-CTGAAGTTATAACAGAAATAGTAAAAGTTTTCCTAGTTC
321 GATC-GCATAGAATACTTTAAGGAACCT-AAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTC
* * * *
1239 -GAAAGTTCGTCCAAGAACCAAGAGATAAACAATT-TACACATAAATAAGTA
384 AG-AAGTTCATCCAAGAACCAAGAAAGAAACAATTCT-CACATAAATAAGTT
* * * * * *
1289 TTTAATTCAATGACCAATAGTTTTTTTA-AGAAATGGCAAACTATTTTGACCGAATGATGCGATT
1 TTTAATTCAAAGACCAAAAG-TTGTTTACA-AAATGACAAACTATTTAGACCAAATGATGCGATT
** * * * * * * *
1353 TTCCGAGCCTTGAATGTTCAGAATATTGCTCGAAGGATTGGATCATCT-T-GAATAGTTTAAGAA
64 TT-CGAGAATGGAATGTTC-GAAAATTGCTCGAAAGAATGGATCTTCTATAGAATACTTTAAGGA
* * * * * ** * ** *
1416 ACCGAAGTTAGTATAGGAGAAATAGTAAAAGCTTGACAAGTTCAGAAGTTTGTCTAAGAATGAAA
127 ACCGAAGTTA-TA-A-AAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAG
* * * * *
1481 AGATAAATAATTCTCACATAAATATA-TTTTTAATTCAAGGACCAAAAAGTTGTTTCCAAAATGA
189 AGAGAAACAAATCTCACATAAATA-AGTTTTTAATTCAAAGACC-AAAAGTTGTTTACAAAATGA
* * * * ** * *
1545 CAAACTATTTAGACCGAATGATGCTATTTCCCGAGCACAGAATGTTCG--GAATATTGATCGAAG
252 CAAACTATTTAGACCAAATGATGCGATTTACCGAACATGGAATGTTCGAACAAT-TTGCTCGAAG
* * * * *
1608 GAATGGATCGTC-TTGAATACTTTAAGGGACCAAAGTTATAAAAGAACTCGTAAAAAGCTTGACT
316 GAATGGATCG-CATAGAATACTTTAAGGAACCTAAGTTATAAAAGAACTCGT-AAAAGTTTGACA
* * * *
1672 AGTTCAGAAGTTCGTCTAAGAACCAA-AGGAGAAACAATTCTCACGTAAATAAGTT
379 AGTTCAGAAGTTCATCCAAGAACCAAGA-AAGAAACAATTCTCACATAAATAAGTT
* ** * * * * *
1727 TTTAGTTTGAAGACCAAAACTTGGTTTTCAAAATGAGAAACTATTTAGACCAAAAGATGCAATTT
1 TTTAATTCAAAGACCAAAAGTT-GTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* * * * *
1792 CTCGAGCATGGAATGTTTGGAAAATTGCTCGTAAAAAACGGATGTTCT-T-GAATACTTTAAGG-
65 -TCGAGAATGGAATG-TTCGAAAATTGCTCG-AAAGAATGGATCTTCTATAGAATACTTTAAGGA
* * * *
1854 ATCGAAGTTATAAAATAACTCGTAAAAGTTTTACAAGTTCGGTAGTTCATCCAAGAACCAAGAGA
127 ACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGA
* * * *
1919 GAGACAATTTTCACATAAATAAGTTTCTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
192 GAAACAAATCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
* * * * * * * *
1984 TATTTAAACCAAAAGTTTCGATTTTCGGAGA-ATGGAATGTTC-AA-AAATTGCTCG-ATGAAGT
257 TATTTAGACCAAATGATGCGATTTACCGA-ACATGGAATGTTCGAACAATTTGCTCGAAGGAA-T
** * * * * *
2045 GGATCATTTATATATAATACACTTCAAGGAACCGAAGTTTTAAAAGAACTTGTAAAAGTTTGACA
320 GGATC----GCATAGAAT--ACTTTAAGGAACCTAAGTTATAAAAGAACTCGTAAAAGTTTGACA
* * * * * * * *
2110 AGTCCGGAGGTTCGTCCAAGAACCAAGAAAGAAACAAATCCCACGTCAATAAGTT
379 AGTTCAGAAGTTCATCCAAGAACCAAGAAAGAAACAATTCTCACATAAATAAGTT
* *
2165 TTTAATTCAAAGACCAAAAGTTGTTCACAAAATGACAAACTATTTAGATCAAATGATGCGATTTT
1 TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTT
* * * * * * * *
2230 CTGA-ACGTTGAATGTTCGAAAAATTTG-TAGAAGGAAAGGATC-GC-ATAGAATGCTTTGAGGA
66 C-GAGA-ATGGAATGTTCG-AAAA-TTGCTCGAAAGAATGGATCTTCTATAGAATACTTTAAGGA
** * * * *
2291 ACCTTAGTTGTAAAAGGACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACTAAGAAA
127 ACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGA
* * *
2356 GAAACAAATCCCACTTCAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
192 GAAACAAATCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAAC
* ** * *
2421 TATTTAGATCAAATGATGCGATTTACCGAACATTCAATGTTCGAACAATTTG-TAGAGGGAATGG
257 TATTTAGACCAAATGATGCGATTTACCGAACATGGAATGTTCGAACAATTTGCTCGAAGGAATGG
* * *
2485 ATCGCATAGAATGCTTTAAGGAACCTAAG-TAGTAAAAGGACTCGTAGAAGTTTGACAAGTTCAG
322 ATCGCATAGAATACTTTAAGGAACCTAAGTTA-TAAAAGAACTCGTAAAAGTTTGACAAGTTCAG
* * *
2549 AAGTTCATCCAGGATCTAAGAAAGAAACAATTCTCACATAAATAAGTT
386 AAGTTCATCCAAGAACCAAGAAAGAAACAATTCTCACATAAATAAGTT
* * * *
2597 TTTAATTCAGAA-ACCAAAAGTTGTTTAC-AAATGACAAAATATTTAGGCCGAATGATACGATTT
1 TTTAATTCA-AAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* * * ** * **
2660 CTCGAGCATGGAATGTTTAGAATATTTATTGAAAGAATGGATCGCCT-TA-AATACTTTAAGGAA
65 -TCGAGAATGGAATG-TTCGAAAATTGCTCGAAAGAATGGATCTTCTATAGAATACTTTAAGGAA
*
2723 CC-AATGTCATAAAAG
128 CCGAA-GTTATAAAAG
Statistics
Matches: 1822, Mismatches: 379, Indels: 206
0.76 0.16 0.09
Matches are distributed among these distances:
415 13 0.01
416 193 0.11
417 10 0.01
418 79 0.04
419 7 0.00
420 3 0.00
421 31 0.02
423 1 0.00
430 5 0.00
431 125 0.07
432 121 0.07
433 33 0.02
434 121 0.07
435 89 0.05
436 147 0.08
437 450 0.25
438 299 0.16
439 95 0.05
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (433 bp):
TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTT
CGAGAATGGAATGTTCGAAAATTGCTCGAAAGAATGGATCTTCTATAGAATACTTTAAGGAACCG
AAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAGAGAGAAA
CAAATCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATT
TAGACCAAATGATGCGATTTACCGAACATGGAATGTTCGAACAATTTGCTCGAAGGAATGGATCG
CATAGAATACTTTAAGGAACCTAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTT
CATCCAAGAACCAAGAAAGAAACAATTCTCACATAAATAAGTT
Found at i:878 original size:216 final size:213
Alignment explanation
Indices: 1--2737 Score: 2127
Period size: 216 Copynumber: 12.7 Consensus size: 213
* * * *
1 TTTAATTCAAGGACCAAAAAGTTGTTTCCAAAATGACAAACTATTTAGACCGAATGATGCTATTT
1 TTTAATTCAAAGACC-AAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
** * * *
66 CCCGAGCACAGAATGTTCG-AAATATTGATCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAC
65 -CCGAGCATGGAATGTTCGAAAAT-TTGCTAG-AGGAATGGATCG-CTAGAATACTTTAAGGAAC
* * * * * *
130 CAAAGTTATAAAAGAACTCGTAAAAAGCTTGACCAGTTCAAAAGTTCATCTAAGAACCAA-AGGA
126 CGAAGTTATAAAAGAACTCGT-AAAAGTTTGACAAGTTCAGAAGTTCATCCAAGAACCAAGA-AA
*
194 GAAACAATTCTCACATAATTAAGTT
189 GAAACAATTCTCACATAAATAAGTT
* ** * * * *
219 TTTAGTTTGAAGACCAAAACTTGGTTTTCAAAATGACAAACTATTTAGACCAAAAGATGCAATTT
1 TTTAATTCAAAGACCAAAAGTT-GTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* * * ** * *
284 CTCGAGCATGTAATGTTTGGAAAA-TTGCTCGTAAAAAACGGAT-GTTCTTGAATACTTTAAGGA
65 C-CGAGCATGGAATG-TTCGAAAATTTGCTAG--AGGAATGGATCG--CTAGAATACTTTAAGGA
* * * * * * *
347 ACCGAAGTTATAAAATAACTCGTAAAAGTTTTACAA-TTCGGTAGTTCATCCAAAAATCAAGAGA
124 ACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCATCCAAGAACCAAGAAA
* *
411 GAGACAATTTTCACATAAATAAGTT
189 GAAACAATTCTCACATAAATAAGTT
* * * * *
436 CTTAATTCAAAGACCAAAAGTTATTTACAAAATGACAAACTATTTAAACCAAAAGATTTGC-TTT
1 TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGA--TGCGATT
* * * * ** * *
500 TCGGAGAATGGAATGTTCGAAAA-TTGCTCGATGAAGTGGATCATTTATATATAATACACTTCAA
64 TCCGAGCATGGAATGTTCGAAAATTTGCTAGAGGAA-TGGATC-----GCTAGAAT--ACTTTAA
* * * * * * *
564 GGAACCGAAGTTTTAAAAGAACTTGTAAAAGTTTGACAAGTCCGGAGGTTCGTCGAAGAACCAAG
121 GGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCATCCAAGAACCAAG
* * * * *
629 AGAGAAACAAATCCCACGTCAATAAGTT
186 AAAGAAACAATTCTCACATAAATAAGTT
* *
657 TTTAATTCAAAGACCAAAAGTTGTTTACAAAATAACAAACTATTTAGATCAAATGATGCGATTTA
1 TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT-
* ** * *
722 CCGAACATTCAATGCTCGAACAATTTG-TAGAGGGAATGGATCGCATAGAATGCTTTAAGGAACC
65 CCGAGCATGGAATGTTCGAA-AATTTGCTAGA-GGAATGGATCGC-TAGAATACTTTAAGGAACC
* * * * * * *
786 TAAGTTGTAAAAGGACTCGTAGAAGTTTGACAAGTTCAGAAGTTCATCCAGGATCTAAGAAAGAA
127 GAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCATCCAAGAACCAAGAAAGAA
851 ACAATTCTCACATAAATAAGTT
192 ACAATTCTCACATAAATAAGTT
* * *
873 TTTAATTCAGAA-ACCAAAAGTTGTTTAC-AAATGACAAAATATTTAGGCCGAATGATGCGATTT
1 TTTAATTCA-AAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* * * *
936 CTCGAGTATGGAAAGTTTAGAATATTATTTG--A-AAGAATGGATCGCCTTA-AATACTTTAAGG
65 C-CGAGCATGGAATG-TTCGAA-A--ATTTGCTAGAGGAATGGATCG-C-TAGAATACTTTAAGG
* * *
997 AACC-AATGTCATAAAAGAACTCGTAAAAGTTTGAAAAGTTCAGAAGTTCAT--------C---T
123 AACCGAA-GTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCATCCAAGAACCAAGA
* *
1050 AAG-AAC---TCTCGCGTAAATAAGTT
187 AAGAAACAATTCTCACATAAATAAGTT
* *
1073 TTAAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAGTGATGCGATTTC
1 TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTC
* * * * * * * * *
1138 TCGAGCATGGAATGTTCAAAAAATTGCTCGAAGAAACGGATCATCTTGAATACTTTATGGAACTG
66 -CGAGCATGGAATGTTCGAAAATTTGCTAG-AGGAATGGATC-GCTAGAATACTTTAAGGAACCG
* * * ** * * * *
1203 AAGTTATAACAGAAATAGTAAAAGTTTTCCTAGTTC-GAAAGTTCGTCCAAGAACCAAGAGATAA
128 AAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAG-AAGTTCATCCAAGAACCAAGAAAGAA
*
1267 ACAATT-TACACATAAATAAGTA
192 ACAATTCT-CACATAAATAAGTT
* * * * * *
1289 TTTAATTCAATGACCAATAGTTTTTTTA-AGAAATGGCAAACTATTTTGACCGAATGATGCGATT
1 TTTAATTCAAAGACCAAAAG-TTGTTTACA-AAATGACAAACTATTTAGACCAAATGATGCGA-T
* * * * * * * * *
1353 TTCCGAGCCTTGAATGTTC-AGAATATTGCTCGAAGGATTGGATCATCTTGAATAGTTTAAGAAA
63 TTCCGAGCATGGAATGTTCGAAAAT-TTGCTAG-AGGAATGGATC-GCTAGAATACTTTAAGGAA
* * * * ** * **
1417 CCGAAGTTAGTATAGGAGAAATAGTAAAAGCTTGACAAGTTCAGAAGTTTGTCTAAGAATGAA-A
125 CCGAAGTTA-TA-A-AAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCATCCAAGAACCAAGA
* *
1481 AGATAAATAATTCTCACATAAATATA-TT
187 A-AGAAACAATTCTCACATAAATA-AGTT
* * * *
1509 TTTAATTCAAGGACCAAAAAGTTGTTTCCAAAATGACAAACTATTTAGACCGAATGATGCTATTT
1 TTTAATTCAAAGACC-AAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
** * * * * *
1574 CCCGAGCACAGAATGTTCG-GAATATTGATCGAAGGAATGGATCGTCTTGAATACTTTAAGGGAC
65 -CCGAGCATGGAATGTTCGAAAAT-TTGCTAG-AGGAATGGATCG-CTAGAATACTTTAAGGAAC
* * * * * *
1638 CAAAGTTATAAAAGAACTCGTAAAAAGCTTGACTAGTTCAGAAGTTCGTCTAAGAACCAA-AGGA
126 CGAAGTTATAAAAGAACTCGT-AAAAGTTTGACAAGTTCAGAAGTTCATCCAAGAACCAAGA-AA
*
1702 GAAACAATTCTCACGTAAATAAGTT
189 GAAACAATTCTCACATAAATAAGTT
* ** * * * * *
1727 TTTAGTTTGAAGACCAAAACTTGGTTTTCAAAATGAGAAACTATTTAGACCAAAAGATGCAATTT
1 TTTAATTCAAAGACCAAAAGTT-GTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* * ** * *
1792 CTCGAGCATGGAATGTTTGGAAAA-TTGCTCGTAAAAAACGGAT-GTTCTTGAATACTTTAAGG-
65 C-CGAGCATGGAATG-TTCGAAAATTTGCTAG--AGGAATGGATCG--CTAGAATACTTTAAGGA
* * * * * *
1854 ATCGAAGTTATAAAATAACTCGTAAAAGTTTTACAAGTTCGGTAGTTCATCCAAGAACCAAGAGA
124 ACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCATCCAAGAACCAAGAAA
* *
1919 GAGACAATTTTCACATAAATAAGTT
189 GAAACAATTCTCACATAAATAAGTT
* * * * *
1944 TCTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAAACCAAAAGTTTCGATTTT
1 TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA-TTT
* * * * * ** * *
2009 CGGAGAATGGAATGTTC-AAAAATTGCTCGATGAAGTGGATCATTTATATATAATACACTTCAAG
65 CCGAGCATGGAATGTTCGAAAATTTGCTAGAGGAA-TGGATC-----GCTAGAAT--ACTTTAAG
* * * * * *
2073 GAACCGAAGTTTTAAAAGAACTTGTAAAAGTTTGACAAGTCCGGAGGTTCGTCCAAGAACCAAGA
122 GAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCATCCAAGAACCAAGA
* * * *
2138 AAGAAACAAATCCCACGTCAATAAGTT
187 AAGAAACAATTCTCACATAAATAAGTT
* *
2165 TTTAATTCAAAGACCAAAAGTTGTTCACAAAATGACAAACTATTTAGATCAAATGATGCGATTTT
1 TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGA-TTT
* * * * * * *
2230 CTGAACGTTGAATGTTCGAAAAATTTG-TAGAAGGAAAGGATCGCATAGAATGCTTTGAGGAACC
65 CCGAGCATGGAATGTTCG-AAAATTTGCTAG-AGGAATGGATCGC-TAGAATACTTTAAGGAACC
** * * * *
2294 TTAGTTGTAAAAGGACTCGTAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACTAAGAAAGAA
127 GAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCATCCAAGAACCAAGAAAGAA
* * * *
2359 ACAAATCCCACTTCAATAAGTT
192 ACAATTCTCACATAAATAAGTT
*
2381 TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGATCAAATGATGCGATTTA
1 TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT-
* ** *
2446 CCGAACATTCAATGTTCGAACAATTTG-TAGAGGGAATGGATCGCATAGAATGCTTTAAGGAACC
65 CCGAGCATGGAATGTTCGAA-AATTTGCTAGA-GGAATGGATCGC-TAGAATACTTTAAGGAACC
* * * * * *
2510 TAAG-TAGTAAAAGGACTCGTAGAAGTTTGACAAGTTCAGAAGTTCATCCAGGATCTAAGAAAGA
127 GAAGTTA-TAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCATCCAAGAACCAAGAAAGA
2574 AACAATTCTCACATAAATAAGTT
191 AACAATTCTCACATAAATAAGTT
* * * *
2597 TTTAATTCAGAA-ACCAAAAGTTGTTTAC-AAATGACAAAATATTTAGGCCGAATGATACGATTT
1 TTTAATTCA-AAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* * * * *
2660 CTCGAGCATGGAATGTTTAGAATATTT-ATTGAAAGAATGGATCGCCTTA-AATACTTTAAGGAA
65 C-CGAGCATGGAATG-TTCGAAAATTTGCTAG-AGGAATGGATCG-C-TAGAATACTTTAAGGAA
*
2723 CC-AATGTCATAAAAG
125 CCGAA-GTTATAAAAG
Statistics
Matches: 2051, Mismatches: 356, Indels: 227
0.78 0.14 0.09
Matches are distributed among these distances:
197 4 0.00
199 3 0.00
200 45 0.02
201 100 0.05
202 2 0.00
203 3 0.00
204 3 0.00
209 1 0.00
212 1 0.00
213 9 0.00
214 18 0.01
215 211 0.10
216 543 0.26
217 255 0.12
218 253 0.12
219 88 0.04
220 221 0.11
221 256 0.12
222 18 0.01
223 17 0.01
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (213 bp):
TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTC
CGAGCATGGAATGTTCGAAAATTTGCTAGAGGAATGGATCGCTAGAATACTTTAAGGAACCGAAG
TTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCATCCAAGAACCAAGAAAGAAACAA
TTCTCACATAAATAAGTT
Found at i:1909 original size:655 final size:642
Alignment explanation
Indices: 1--2676 Score: 2319
Period size: 655 Copynumber: 4.1 Consensus size: 642
* * * *
1 TTTAATTCAAGGACCAAAAAGTTGTTTCCAAAATGACAAACTATTTAGACCGAATGATGCTATTT
1 TTTAATTCAAAGACC-AAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* ** * * *
66 CCCGAGCACAGAATGTTCGAAATATTGATCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACC
65 TCCGAGCATTGAATGTTCGAAA-ATTGCTCGAAGGAATGGATCATCTTGAATAGTTTAAGGAACC
* * * *
131 AAAGTTATAAAAGAACTCGTAAAAAGCTTGACCAGTTCAAAAGTTCATCTAAGAACCAA-AGGAG
129 GAAGTT-TAAAAGAACTCGT-AAAAGCTTGACAAGTTCAGAAGTTCATCTAAGAACCAAGA-AAG
* * * * *
195 AAACAATTCTCACATAATTAAGTTTTTAGTTTGAA-GACCAAAACTTGGTTTTCAAAATGACAAA
191 AAACAATTCTCACATAAATAAGTTTTTA-ATTCAAGGACCAAAAGTT-GTTTCCAAAATGACAAA
* * * * * * *
259 CTATTTAGACCAAAAGATGCAATTTCTCGAGCA-TGTAATGTTTGGAAAATTGCTCGTAAAAAAC
254 CTATTTAGACCAAATGATGCGATTTCCCGAGCATTG-AATGTTCGGAAAATTGATCG-AAAGAAT
* * *
323 GGAT-GTTCTTGAATACTTTAAGGAACCGAAGTTATAAAATAACTCGTAAAAGTTTTACAA-TTC
317 GGATCG-TCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTC
* * * * * * *
386 GGTAGTTCATCCAAAAATCAAGAGAGAGACAATTTTCACATAAATAAGTTCTTAATTCAAAGACC
381 AGAAGTTCATCCAAGAA-CAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACC
* * ** * *
451 AAAAGTTATTTACAAAATGACAAACTATTTAAACCAAAAGATTTGCTTT-TCGGAGAATGGAATG
445 AAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAAAGATGCGATTTCTC-GAGCATGGAATG
* * ** * * * *
515 -TTCGAAAATTGCTCGATGAAGTGGATCATTTATATATAATACACTTCAAGGAACCGAAGTTTTA
509 TTTAGAAAATTGCTCGAAGAAACGGATC--TTCT-T-GAAT--ACTTTAAGGAA-CGAAGTTATA
* * * * * **
579 AAAGAACTTGTAAAAGTTTGACAAGTCCGGAGGTTCGTCGAAGAACCAAGAGAGAAACAAATCCC
567 AAAGAACTAGTAAAAGTTTTACAAGTTCGGA-GTTCGTCCAAGAACCAAGAGAGAAACAATTTAC
* *
644 ACGTCAATAAGTT
631 ACATAAATAAG-T
* * *
657 TTTAATTCAAAGACCAAAAGTTGTTTACAAAATAACAAACTATTTAGATCAAATGATGCGATTTA
1 TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTT
* * * * * * *
722 CCGAACATTCAATGCTCGAACAATTTG-TAGAGGGAATGGATC-GCATAGAAT-GCTTTAAGGAA
66 CCGAGCATTGAATGTTCGAA-AA-TTGCTCGAAGGAATGGATCATC-TTGAATAG-TTTAAGGAA
* * * * * * * *
784 CCTAAGTTGTAAAAGGACTCGTAGAAGTTTGACAAGTTCAGAAGTTCATCCAGGATCTAAGAAAG
127 CCGAAGTT-TAAAAGAACTCGTAAAAGCTTGACAAGTTCAGAAGTTCATCTAAGAACCAAGAAAG
* * *
849 AAACAATTCTCACATAAATAAGTTTTTAATTC-AGAAACCAAAAGTTGTTTAC-AAATGACAAAA
191 AAACAATTCTCACATAAATAAGTTTTTAATTCAAG-GACCAAAAGTTGTTTCCAAAATGACAAAC
* * * * * * ** * *
912 TATTTAGGCCGAATGATGCGATTTCTCGAGTATGGAAAGTTTAGAATATT-ATTTGAAAGAATGG
255 TATTTAGACCAAATGATGCGATTTCCCGAGCATTGAATGTTCGGAAAATTGA-TCGAAAGAATGG
* * * * *
976 ATCGCCTTAAATACTTTAAGGAACCAATGTCATAAAAGAACTCGTAAAAGTTTGAAAAGTTCAGA
319 ATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGA
* * *
1041 AGTTCAT-------C--TA-AG-AAC---TCTCGCGTAAATAAGTTTTAAATTCAAAGACCAAAA
384 AGTTCATCCAAGAACAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAA
** * *
1092 GTTGTTTACAAAATGACAAACTATTTAGACCAAGTGATGCGATTTCTCGAGCATGGAATGTTCAA
449 GTTGTTTACAAAATGACAAACTATTTAGACCAAAAGATGCGATTTCTCGAGCATGGAATGTTTAG
* * * *
1157 AAAATTGCTCGAAGAAACGGATCATCTTGAATACTTTATGGAACTGAAGTTATAACAGAAATAGT
514 AAAATTGCTCGAAGAAACGGATCTTCTTGAATACTTTAAGGAAC-GAAGTTATAAAAGAACTAGT
* * * *
1222 AAAAGTTTTCCTAGTTCGAAAGTTCGTCCAAGAACCAAGAGATAAACAATTTACACATAAATAAG
578 AAAAGTTTTACAAGTTCG-GAGTTCGTCCAAGAACCAAGAGAGAAACAATTTACACATAAATAAG
1287 T
642 T
* * * * * *
1288 ATTTAATTCAATGACCAATAGTTTTTTTA-AGAAATGGCAAACTATTTTGACCGAATGATGCGAT
1 -TTTAATTCAAAGACCAAAAG-TTGTTTACA-AAATGACAAACTATTTAGACCAAATGATGCGAT
* * * *
1352 TTTCCGAGCCTTGAATGTTCAGAATATTGCTCGAAGGATTGGATCATCTTGAATAGTTTAAGAAA
63 TTTCCGAGCATTGAATGTTC-GAAAATTGCTCGAAGGAATGGATCATCTTGAATAGTTTAAGGAA
* * * ** **
1417 CCGAAGTTAGTATAGGAGAAATAGTAAAAGCTTGACAAGTTCAGAAGTTTGTCTAAGAATGAA-A
127 CCGAAGTT--TA-A-AAGAACTCGTAAAAGCTTGACAAGTTCAGAAGTTCATCTAAGAACCAAGA
* *
1481 AGATAAATAATTCTCACATAAATATA-TTTTTAATTCAAGGACCAAAAAGTTGTTTCCAAAATGA
188 A-AGAAACAATTCTCACATAAATA-AGTTTTTAATTCAAGGACC-AAAAGTTGTTTCCAAAATGA
* * ** * *
1545 CAAACTATTTAGACCGAATGATGCTATTTCCCGAGCACAGAATGTTCGGAATATTGATCGAAGGA
250 CAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATTGAATGTTCGGAAAATTGATCGAAAGA
* * *
1610 ATGGATCGTCTTGAATACTTTAAGGGACCAAAGTTATAAAAGAACTCGTAAAAAGCTTGACTAGT
315 ATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGT-AAAAGTTTGACAAGT
* * * **
1675 TCAGAAGTTCGTCTAAGAACCAA-AGGAGAAACAATTCTCACGTAAATAAGTTTTTAGTTTGAAG
379 TCAGAAGTTCATCCAAGAA-CAAGA-GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAG
* * * *
1739 ACCAAAACTTGGTTTTCAAAATGAGAAACTATTTAGACCAAAAGATGCAATTTCTCGAGCATGGA
442 ACCAAAAGTT-GTTTACAAAATGACAAACTATTTAGACCAAAAGATGCGATTTCTCGAGCATGGA
* * * *
1804 ATGTTTGGAAAATTGCTCGTAAAAAACGGATGTTCTTGAATACTTTAAGGATCGAAGTTATAAAA
506 ATGTTTAGAAAATTGCTCG-AAGAAACGGATCTTCTTGAATACTTTAAGGAACGAAGTTATAAAA
* * * * *
1869 TAACTCGTAAAAGTTTTACAAGTTCGGTAGTTCATCCAAGAACCAAGAGAGAGACAATTTTCACA
570 GAACTAGTAAAAGTTTTACAAGTTCGG-AGTTCGTCCAAGAACCAAGAGAGAAACAATTTACACA
1934 TAAATAAGT
634 TAAATAAGT
* * * *
1943 TTCTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAAACCAAAAGTTTCGATTT
1 TT-TAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
* * * * * * *
2008 TCGGAGAATGGAATGTTCAAAAATTGCTCG-ATGAAGTGGATCAT-TTATATATAATACACTTCA
65 TCCGAGCATTGAATGTTCGAAAATTGCTCGAAGGAA-TGGATCATCTT-GA-ATAGT----TT-A
* * * * * * *
2071 AGGAACCGAAGTTTTAAAAGAACTTGTAAAAGTTTGACAAGTCCGGAGGTTCGTCCAAGAACCAA
122 AGGAACCGAAG-TTTAAAAGAACTCGTAAAAGCTTGACAAGTTCAGAAGTTCATCTAAGAACCAA
* * * * *
2136 GAAAGAAACAAATCCCACGTCAATAAGTTTTTAATTCAAAGACCAAAAGTTG-TTCACAAAATGA
186 GAAAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAGGACCAAAAGTTGTTTC-CAAAATGA
* * * * * * * *
2200 CAAACTATTTAGATCAAATGATGCGATTTTCTGAACGTTGAATGTTCGAAAAATTTG-TAGAAGG
250 CAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATTGAATGTTCGGAAAA-TTGATCGAAAG
* * * * ** * *
2264 AAAGGATCG-CATAGAATGCTTTGAGGAACCTTAGTTGTAAAAGGACTCGTAAAAGTTTGACAAG
314 AATGGATCGTC-TTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAG
* * * * * *
2328 TTCGGAAGTTCATCCAAGAACTAAGAAAGAAACAAATCCCACTTCAATAAGTTTTTAATTCAAAG
378 TTCAGAAGTTCATCCAAGAAC-AAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAG
* * * **
2393 ACCAAAAGTTGTTTACAAAATGACAAACTATTTAGATCAAATGATGCGATTTAC-CGAACATTCA
442 ACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAAAGATGCGATTT-CTCGAGCATGGA
* * * * * * * * *
2457 ATG-TTCGAACAATTTG-TAGAGGGAATGGATC-GCATAGAATGCTTTAAGGAACCTAAG-TAGT
506 ATGTTTAGAA-AA-TTGCTCGAAGAAACGGATCTTC-TTGAATACTTTAAGGAA-CGAAGTTA-T
* * * * * * * * * *
2518 AAAAGGACTCGTAGAAGTTTGACAAGTTCAGAAGTTCATCCAGGATCTAAGAAAGAAACAATTCT
566 AAAAGAACTAGTAAAAGTTTTACAAGTTC-GGAGTTCGTCCAAGAACCAAGAGAGAAACAATT-T
2583 -CACATAAATAAGTT
629 ACACATAAATAAG-T
* * * *
2597 TTTAATTCAGAA-ACCAAAAGTTGTTTAC-AAATGACAAAATATTTAGGCCGAATGATACGA-TT
1 TTTAATTCA-AAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTT
*
2659 TCTCGAGCATGGAATGTT
65 TC-CGAGCATTGAATGTT
2677 TAGAATATTT
Statistics
Matches: 1637, Mismatches: 303, Indels: 164
0.78 0.14 0.08
Matches are distributed among these distances:
631 2 0.00
632 98 0.06
633 83 0.05
634 11 0.01
635 4 0.00
636 70 0.04
637 95 0.06
638 124 0.08
639 24 0.01
640 2 0.00
641 2 0.00
642 1 0.00
644 1 0.00
647 1 0.00
648 1 0.00
650 2 0.00
651 63 0.04
652 135 0.08
653 170 0.10
654 242 0.15
655 368 0.22
656 118 0.07
657 3 0.00
658 4 0.00
659 11 0.01
660 2 0.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (642 bp):
TTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAGACCAAATGATGCGATTTT
CCGAGCATTGAATGTTCGAAAATTGCTCGAAGGAATGGATCATCTTGAATAGTTTAAGGAACCGA
AGTTTAAAAGAACTCGTAAAAGCTTGACAAGTTCAGAAGTTCATCTAAGAACCAAGAAAGAAACA
ATTCTCACATAAATAAGTTTTTAATTCAAGGACCAAAAGTTGTTTCCAAAATGACAAACTATTTA
GACCAAATGATGCGATTTCCCGAGCATTGAATGTTCGGAAAATTGATCGAAAGAATGGATCGTCT
TGAATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCAT
CCAAGAACAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTT
ACAAAATGACAAACTATTTAGACCAAAAGATGCGATTTCTCGAGCATGGAATGTTTAGAAAATTG
CTCGAAGAAACGGATCTTCTTGAATACTTTAAGGAACGAAGTTATAAAAGAACTAGTAAAAGTTT
TACAAGTTCGGAGTTCGTCCAAGAACCAAGAGAGAAACAATTTACACATAAATAAGT
Done.