Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002967.1 Kokia drynarioides strain JFW-HI SEQ_115441, 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: 4081
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Found at i:381 original size:216 final size:214
Alignment explanation
Indices: 3--2626 Score: 2267
Period size: 216 Copynumber: 12.2 Consensus size: 214
1 GG
* * ** *
3 GATTTCCCGAGCATGAAATGTTCGAAACGA-TGCTCGAGGGAATGGATCGTCTTGAATACTTGAA
1 GATTTCCCGAGCATGGAATGTTCGAAA-AATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAA
* * * * * * * * *
67 GGATCCAAAGATACAAAA-ATACTCGTAAAAGTTTGACAAG-TTCGGAAGTTTGTCAAAGAACCA
65 GGAACCGAAGTTATAAAAGA-ACTCG-CAAAGTTTTACAAGATT-GGAAGTTCGTCTATGAA-CA
* * * * *
130 AA-AGAAAAATAATTCTCACGTAAATAAGGTTTTAATTCAAAGGCCAAAACTTGTTTAGAAAATG
126 AATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATG
* *
194 ACAAAATTTTTAGACCAAATGATGC
191 A-AAAATATTTAGACCGAATGATGC
* * * * *
219 GATTTCCCGGGCATGGAATGTACGAAAAATTGCTCGAAAGAATGGATCATCTTGAATACTCTAAA
1 GATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAAG
* * *
284 GAACCGAAATTATAAAAGAACTCGCAAAGTTTCTACAAGATTGGAAGTTCGTATATGAACTAATA
66 GAACCGAAGTTATAAAAGAACTCGCAAAGTTT-TACAAGATTGGAAGTTCGTCTATGAACAAATA
* * * * * * *
349 GAGGAACAATTCTCATGTAGATAAGTTTTTAATTGAAAAACCATAACTTGTTTACAAAATGAGTA
130 GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGA-AA
* *
414 ACTATTTAGACTGAATGATGC
194 AATATTTAGACCGAATGATGC
* * * *
435 GATTTCCCGAGCGTGGATTGTTCGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAG
1 GATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAAG
* * ** *** * * **
500 GAATCGAAGTTATAAAAGAACTTGGCAAAG-TTTACAA-A-ACGAAAAAC-TATTTAGGCCAAAA
66 GAACCGAAGTTATAAAAGAAC-TCGCAAAGTTTTACAAGATTGGAAGTTCGTCTAT-GAAC-AAA
* * *
561 TGAGAGAAACAATTCTCACGTAAAAAAGTTTTAAATTCAAAGACCAAAACTTTTTTACAAAATGA
128 T-AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGA
*
626 AAAACTATTTAGACTGAATGATGC
192 AAAA-TATTTAGACCGAATGATGC
* * * **
650 GATTTCCCGAGCATGGAATGTTCGAAAAACTACT-AAAATGAATGGGCCGTCTTGAATACTTTAA
1 GATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAA-GAATGGATCGTCTTGAATACTTTAA
* * * * * * *** * ** * **
714 GGAACCAAAGTTAAAAGAAGGACTTGTAAAATTTTGTTAGGTTCTAAAGTTCGTCCAACAACAAA
65 GGAACCGAAGTTATAA-AAGAACTCGCAAAGTTTTACAAGATT-GGAAGTTCGTCTATGAACAAA
* ** * * * * *
779 GAGAGAATTAATTCTTATGTAAATAAGTTTTTAATACAAACACCAAAACTTGATTACAAAATGAA
128 TAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAA
*
844 AAACTATATAGACCGAATGATGC
193 AAA-TATTTAGACCGAATGATGC
* * * * * * *
867 AATTTCTCAAGCATGAAATGTTCGAAAAGA-TGCTCGAAGGAATGGATCGTCTTGAACACTTGAA
1 GATTTCCCGAGCATGGAATGTTCGAAAA-ATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAA
* * * * * * *
931 GGAACCAAAGATATAAAAGAACTCGTAAGAGTTTGACAAG-TTCGAAAGTTTGTCTAGGAACCAA
65 GGAACCGAAGTTATAAAAGAACTCGCAA-AGTTTTACAAGATT-GGAAGTTCGTCTATGAA-CAA
* * * *
995 A-AGAGAAACAATTCTCAAGTAAATAAGGTTTTAATTCAAAGGCCAAAACTTGTTTAGAAAATG-
127 ATAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGA
* * * *
1058 ACATTTTTTAGACCAAATGATGC
192 AAAATATTTAGACCGAATGATGC
* * * *
1081 GATTTCTCGGGCATGGAATGTTCGAAAAATTGCTCGAAAGAATGGATCATCTTGAATACTCTAAG
1 GATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAAG
* * * * * *
1146 GAATCGAAGTTATAAAATAACTCACAAAGTTTCTACAAGATTGGAAATTCGTCCAT-AGACTAAT
66 GAACCGAAGTTATAAAAGAACTCGCAAAGTTT-TACAAGATTGGAAGTTCGTCTATGA-ACAAAT
* * * *
1210 AGAGGAACAATTCTCACGTAAATAAGTTTTTAATTGAAAAACCAAAACTTGTTTACAAAATGAGT
129 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGA-A
* * *
1275 AACTATTTAGACCAAATGATAC
193 AAATATTTAGACCGAATGATGC
** * * *
1297 GATTTCTTGAGCGTGAAATGTTAGAAAAATTGCTC-AAAGGAATGGATCGTCTTGAATACTTTAA
1 GATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAA-GAATGGATCGTCTTGAATACTTTAA
* * * *** * * *
1361 GGAATCGAAGTTATAAAAGAACTTGGCGAAGTTTATA-AA-A-T-GAAAAAC-TATTTAGACCAA
65 GGAACCGAAGTTATAAAAGAAC-TCGCAAAGTTT-TACAAGATTGGAAGTTCGTCTAT-GAAC-A
* *
1421 AATGAGATAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTTTTTACAAAAT
126 AAT-AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAAT
* *
1486 GAAAAACTATTGATACCGAATGATGC
190 GAAAAA-TATTTAGACCGAATGATGC
* * ** * *
1512 GATTTCCCGAGCATGGAATGTTCGAAAAAATACTAAAAAGAATGCACCGTCTTGAATACTTTAAG
1 GATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAAG
* * * * * * * * *
1577 GAACCGAAGTTAAAAAAAGGACTTGTAAAATTTTGACAAG-TTCGAAAGTTCGTCCAAGAAAAAA
66 GAACCGAAGTT-ATAAAAGAACTCGCAAAGTTTT-ACAAGATT-GGAAGTTCGTCTATGAACAAA
* ** * * * *
1641 GAGAGAATTAATTCTTACGTAAATAAGTTTTTAATACAAACACCAAAACTTGATTACAAAATGAA
128 TAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAA
*
1706 AAATGATTTAGACCCAATGATGC
193 AAAT-ATTTAGACCGAATGATGC
** * ** * * ** *
1729 GATTTCCCGAGCATAAAATGTTTGAAAAGCTGCTTGAAGGAATTTATCGTCTTGAATACTTGAAG
1 GATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAAG
* * ** * * * * *
1794 GAACCAAAGATATAAAAGAACTCATAAAAGATTGACAAG-TTCGAAAGTTTGTCTAAGAACCAAA
66 GAACCGAAGTTATAAAAGAACTC-GCAAAGTTTTACAAGATT-GGAAGTTCGTCTATGAA-CAAA
* * *
1858 -AGAGAAACAATTCTCACGTAAATAAGGTTTTAATTCAAAGGCCAAAACTTGTTTAGAAAATGAG
128 TAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGA-
* * *
1922 AAAATTTTTAGACCAAATGATCC
192 AAAATATTTAGACCGAATGATGC
* * * * * *
1945 GATTTCTCGGGCATGGAATGTTCAAAAAATTGCTTGAAAGAATGGATCATCTTGAATACTCTAAG
1 GATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAAG
* * * * *
2010 GAACCGAAGTTATAAAAGAAATCGTAAAATTTCTACAAGATTGGAAGTTCATCCATGAA-ATAAT
66 GAACCGAAGTTATAAAAGAACTCGCAAAGTTT-TACAAGATTGGAAGTTCGTCTATGAACA-AAT
* * * *
2074 AGAGGAACAA-T-TCATGTAAATAAGTTTTTAATTGAAAGACCAAAACTTGTTTACAAAATGAGT
129 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGA-A
*
2137 AACTATTTAGACCGAATGATGC
193 AAATATTTAGACCGAATGATGC
* * *
2159 GATTTCCCGAGCGTGGAATGTTCGGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAG
1 GATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAAG
* * * * *** * * *
2224 GAATCAAAGTTATAAAAGAACATGGCAAAG-TTTACAA-AAT-GAAAAACTATTTAGTCAA-AAA
66 GAACCGAAGTTATAAAAGAAC-TCGCAAAGTTTTACAAGATTGGAAGTTC-GTCTA-TGAACAAA
* *
2285 TGAGAGAAACAATTCTCACGTAAATAAGTTTTTAGTTCAAAGACCAAAACTTTTTTA-AGAAATG
128 T-AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACA-AAATG
2349 AAAAACTATTTAGACCGAATGATGC
191 AAAAA-TATTTAGACCGAATGATGC
* * * * * * *
2374 GATTTCTCGAGCCTGGAATGTTCGAAAAACTACT-AAAAGGAATGGACCTTCTTGAATACTTTAA
1 GATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAA-GAATGGATCGTCTTGAATACTTTAA
* * * * * * * * * *
2438 GGAACCGAAGTTAAAAAAGAACTTGTAAAATTTTGACAAGTTTGAAAGTTCATCCAAGAACAAAG
65 GGAACCGAAGTTATAAAAGAACTCGCAAAGTTTT-ACAAGATTGGAAGTTCGTCTATGAACAAAT
* * * * *
2503 AGAGAAATAATTCTTACGTAAATAAGTTTTAAATTTAAAGTCCAAAACTT-TTCTACAAAAT-AA
129 AGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTT-TACAAAATGAA
* * * *
2566 AAACTACTTAGACCAAATAATGT
193 AAA-TATTTAGACCGAATGATGC
* * *
2589 GATTTCTCC-AGCGTGGAAGGTTCGAAAAATTACTCGAA
1 GATTTC-CCGAGCATGGAATGTTCGAAAAATTGCTCGAA
2627 GGCCAAAACT
Statistics
Matches: 1934, Mismatches: 404, Indels: 140
0.78 0.16 0.06
Matches are distributed among these distances:
211 4 0.00
212 14 0.01
213 40 0.02
214 329 0.17
215 510 0.26
216 688 0.36
217 326 0.17
218 12 0.01
219 9 0.00
220 2 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (214 bp):
GATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCGAAAGAATGGATCGTCTTGAATACTTTAAG
GAACCGAAGTTATAAAAGAACTCGCAAAGTTTTACAAGATTGGAAGTTCGTCTATGAACAAATAG
AGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGAAAAA
TATTTAGACCGAATGATGC
Found at i:1677 original size:862 final size:861
Alignment explanation
Indices: 3--4081 Score: 4787
Period size: 862 Copynumber: 4.6 Consensus size: 861
1 GG
* * * *
3 GATTTCCCGAGCATGAAATGTTCGAAACGATGCTCGAGGGAATGGATCGTCTTGAATACTTGAAG
1 GATTTCTCGAGCATGAAATGTTCGAAAAGATGCTCGAAGGAATGTATCGTCTTGAATACTTGAAG
* * * *
68 GATCCAAAGATACAAAA-ATACTCGTAAAAGTTTGACAAGTTCGGAAGTTTGTCAAAGAACCAAA
66 GAACCAAAGATATAAAAGA-ACTCGTAAAAGTTTGACAAGTTCGAAAGTTTGTCTAAGAACCAAA
* *
132 AGAAAAATAATTCTCACGTAAATAAGGTTTTAATTCAAAGGCCAAAACTTGTTTAGAAAATGACA
130 AGAGAAACAATTCTCACGTAAATAAGGTTTTAATTCAAAGGCCAAAACTTGTTTAGAAAATGAC-
*
197 AAATTTTTAGACCAAATGATGCGATTTCCCGGGCATGGAATGTACGAAAAATTGCTCGAAAGAAT
194 -AATTTTTAGACCAAATGATGCGATTTCCCGGGCATGGAATGTTCGAAAAATTGCTCGAAAGAAT
* * *
262 GGATCATCTTGAATACTCTAAAGAACCGAAATTATAAAAGAACTCGCAAAGTTTCTACAAGATTG
258 GGATCATCTTGAATACTCTAAGGAACCGAAGTTATAAAAGAACTCGTAAAGTTTCTACAAGATTG
** * * *
327 GAAGTTCGTATATGAACTAATAGAGGAACAATTCTCATGTAGATAAGTTTTTAATTGAAAAACCA
323 GAAGTTCGTCCATGAACTAATAGAGGAACAATTCTCACGTAAATAAGTTTTTAATTGAAAGACCA
* * * *
392 TAACTTGTTTACAAAATGAGTAACTATTTAGACTGAATGATGCGATTTCCCGAGCGTGGATTGTT
388 AAACTTGTTTACAAAATGAGTAACTATTTAGACCGAATGATGCGATTTCCTGAGCGTGGAATGTT
*
457 CGAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACT
453 CGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACT
* * *
522 TGGCAAAGTTTACAAAACGAAAAACTATTTAGGCCAAAATGAGAGAAACAATTCTCACGTAAAAA
518 TGGCAAAGTTTACAAAATGAAAAACTATTTAGACCAAAATGAGAGAAACAATTCTCACGTAAATA
* *
587 AGTTTTAAATTCAAAGACCAAAACTTTTTTACAAAATGAAAAACTATTTAGACTGAATGATGCGA
583 AGTTTTTAATTCAAAGACCAAAACTTTTTTACAAAATGAAAAACTATTTAGACCGAATGATGCGA
* * *
652 TTTCCCGAGCATGGAATGTTCGAAAAACTACTAAAATGAATGGGCCGTCTTGAATACTTTAAGGA
648 TTTCCCGAGCATGGAATGTTCGAAAAAATACTAAAAGGAATGGACCGTCTTGAATACTTTAAGGA
* * ** * * * *
717 ACCAAAGTTAAAAGAAGGACTTGTAAAATTTTGTTAGGTTCTAAAGTTCGTCCAACAACAAAGAG
713 ACCGAAGTTAAAA-AAGAACTTGTAAAATTTTGACAAGTTCGAAAGTTCGTCCAAGAAAAAAGAG
* *
782 AGAATTAATTCTTATGTAAATAAGTTTTTAATACAAACACCAAAACTTGATTACAAAATGAAAAA
777 AGAAATAATTCTTACGTAAATAAGTTTTTAATACAAACACCAAAACTTGATTACAAAATGAAAAA
*
847 CTATATAGACCGAATGATGC
842 CTATTTAGACCGAATGATGC
* * * *
867 AATTTCTCAAGCATGAAATGTTCGAAAAGATGCTCGAAGGAATGGATCGTCTTGAACACTTGAAG
1 GATTTCTCGAGCATGAAATGTTCGAAAAGATGCTCGAAGGAATGTATCGTCTTGAATACTTGAAG
* *
932 GAACCAAAGATATAAAAGAACTCGTAAGAGTTTGACAAGTTCGAAAGTTTGTCTAGGAACCAAAA
66 GAACCAAAGATATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTTGTCTAAGAACCAAAA
* *
997 GAGAAACAATTCTCAAGTAAATAAGGTTTTAATTCAAAGGCCAAAACTTGTTTAGAAAATGACAT
131 GAGAAACAATTCTCACGTAAATAAGGTTTTAATTCAAAGGCCAAAACTTGTTTAGAAAATGACAA
*
1062 TTTTTAGACCAAATGATGCGATTTCTCGGGCATGGAATGTTCGAAAAATTGCTCGAAAGAATGGA
196 TTTTTAGACCAAATGATGCGATTTCCCGGGCATGGAATGTTCGAAAAATTGCTCGAAAGAATGGA
* * **
1127 TCATCTTGAATACTCTAAGGAATCGAAGTTATAAAATAACTCACAAAGTTTCTACAAGATTGGAA
261 TCATCTTGAATACTCTAAGGAACCGAAGTTATAAAAGAACTCGTAAAGTTTCTACAAGATTGGAA
* *
1192 ATTCGTCCAT-AGACTAATAGAGGAACAATTCTCACGTAAATAAGTTTTTAATTGAAAAACCAAA
326 GTTCGTCCATGA-ACTAATAGAGGAACAATTCTCACGTAAATAAGTTTTTAATTGAAAGACCAAA
* * * * *
1256 ACTTGTTTACAAAATGAGTAACTATTTAGACCAAATGATACGATTTCTTGAGCGTGAAATGTTAG
390 ACTTGTTTACAAAATGAGTAACTATTTAGACCGAATGATGCGATTTCCTGAGCGTGGAATGTTCG
*
1321 AAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTTG
455 AAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTTG
* * *
1386 GCGAAGTTTATAAAATGAAAAACTATTTAGACCAAAATGAGATAAACAATTCTCACGTAAATAAG
520 GCAAAGTTTACAAAATGAAAAACTATTTAGACCAAAATGAGAGAAACAATTCTCACGTAAATAAG
* *
1451 TTTTTAATTCAAAGACCAAAACTTTTTTACAAAATGAAAAACTATTGATACCGAATGATGCGATT
585 TTTTTAATTCAAAGACCAAAACTTTTTTACAAAATGAAAAACTATTTAGACCGAATGATGCGATT
* *
1516 TCCCGAGCATGGAATGTTCGAAAAAATACTAAAAAGAATGCACCGTCTTGAATACTTTAAGGAAC
650 TCCCGAGCATGGAATGTTCGAAAAAATACTAAAAGGAATGGACCGTCTTGAATACTTTAAGGAAC
*
1581 CGAAGTTAAAAAAAGGACTTGTAAAATTTTGACAAGTTCGAAAGTTCGTCCAAGAAAAAAGAGAG
715 CGAAGTT-AAAAAAGAACTTGTAAAATTTTGACAAGTTCGAAAGTTCGTCCAAGAAAAAAGAGAG
*
1646 AATTAATTCTTACGTAAATAAGTTTTTAATACAAACACCAAAACTTGATTACAAAATGAAAAA-T
779 AAATAATTCTTACGTAAATAAGTTTTTAATACAAACACCAAAACTTGATTACAAAATGAAAAACT
*
1710 GATTTAGACCCAATGATGC
844 -ATTTAGACCGAATGATGC
* * * * * *
1729 GATTTCCCGAGCATAAAATGTTTGAAAAGCTGCTTGAAGGAATTTATCGTCTTGAATACTTGAAG
1 GATTTCTCGAGCATGAAATGTTCGAAAAGATGCTCGAAGGAATGTATCGTCTTGAATACTTGAAG
* *
1794 GAACCAAAGATATAAAAGAACTCATAAAAGATTGACAAGTTCGAAAGTTTGTCTAAGAACCAAAA
66 GAACCAAAGATATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTTGTCTAAGAACCAAAA
*
1859 GAGAAACAATTCTCACGTAAATAAGGTTTTAATTCAAAGGCCAAAACTTGTTTAGAAAATGAGAA
131 GAGAAACAATTCTCACGTAAATAAGGTTTTAATTCAAAGGCCAAAACTTGTTTAGAAAAT--GAC
* * * *
1924 AATTTTTAGACCAAATGATCCGATTTCTCGGGCATGGAATGTTCAAAAAATTGCTTGAAAGAATG
194 AATTTTTAGACCAAATGATGCGATTTCCCGGGCATGGAATGTTCGAAAAATTGCTCGAAAGAATG
* *
1989 GATCATCTTGAATACTCTAAGGAACCGAAGTTATAAAAGAAATCGTAAAATTTCTACAAGATTGG
259 GATCATCTTGAATACTCTAAGGAACCGAAGTTATAAAAGAACTCGTAAAGTTTCTACAAGATTGG
* * *
2054 AAGTTCATCCATGAAATAATAGAGGAACAA-T-TCATGTAAATAAGTTTTTAATTGAAAGACCAA
324 AAGTTCGTCCATGAACTAATAGAGGAACAATTCTCACGTAAATAAGTTTTTAATTGAAAGACCAA
*
2117 AACTTGTTTACAAAATGAGTAACTATTTAGACCGAATGATGCGATTTCCCGAGCGTGGAATGTTC
389 AACTTGTTTACAAAATGAGTAACTATTTAGACCGAATGATGCGATTTCCTGAGCGTGGAATGTTC
* * *
2182 GGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATCAAAGTTATAAAAGAACAT
454 GAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTT
* *
2247 GGCAAAGTTTACAAAATGAAAAACTATTTAGTCAAAAATGAGAGAAACAATTCTCACGTAAATAA
519 GGCAAAGTTTACAAAATGAAAAACTATTTAGACCAAAATGAGAGAAACAATTCTCACGTAAATAA
*
2312 GTTTTTAGTTCAAAGACCAAAACTTTTTTA-AGAAATGAAAAACTATTTAGACCGAATGATGCGA
584 GTTTTTAATTCAAAGACCAAAACTTTTTTACA-AAATGAAAAACTATTTAGACCGAATGATGCGA
* * * *
2376 TTTCTCGAGCCTGGAATGTTCGAAAAACTACTAAAAGGAATGGACCTTCTTGAATACTTTAAGGA
648 TTTCCCGAGCATGGAATGTTCGAAAAAATACTAAAAGGAATGGACCGTCTTGAATACTTTAAGGA
* * *
2441 ACCGAAGTTAAAAAAGAACTTGTAAAATTTTGACAAGTTTGAAAGTTCATCCAAGAACAAAGAGA
713 ACCGAAGTTAAAAAAGAACTTGTAAAATTTTGACAAGTTCGAAAGTTCGTCCAAGAAAAAAGAGA
* ** ** *
2506 GAAATAATTCTTACGTAAATAAGTTTTAAATTTAAAGTCCAAAACTT-TTCTACAAAAT-AAAAA
778 GAAATAATTCTTACGTAAATAAGTTTTTAATACAAACACCAAAACTTGAT-TACAAAATGAAAAA
* * * *
2569 CTACTTAGACCAAATAATGT
842 CTATTTAGACCGAATGATGC
* * * * * * ****
2589 GATTTCTCCAGCGTGGAAGGTTCGAAAA-ATTACTCGAAGGCCAAAACTTGTTTACAAAATGACA
1 GATTTCTCGAGCATGAAATGTTCGAAAAGA-TGCTCGAAGG----AA--TGTAT-CGTCTTG---
** * * ***** * * * * * *
2653 AATA-TTTTA-G-TCCAAATGATGTAACTTCCCTCGCATGGAATGTTCGAAAAATTGCTCAAAGG
55 AATACTTGAAGGAACCAAA-GATATAAAAGAACTCG--T-AAAAGTTTG-ACAA--GTTCGAA--
* * * * * *
2715 ATTGGATCATCTTGAATACGTTAAGGAA-CAGAAGTTATAAAAGAACTCGTAAAAGTTCGAAAAG
111 A---G----T-TTG--T-C--TAA-GAACCAAAAG--A-GAAACAATTC-T--CA---CGTAAA-
* * ** * *
2779 TTTGAAAGTTCATCCAAGAACCAAGAGAGACACAATTTTTTCTCATGTAAATAAGTTTTTAATTC
152 --T-AAGGTT--T--TA-ATTCAA-AG-G-C-CAA----A----A-CT---T--G----T--TT-
* * ** * *
2844 AAAGACCAAAACTTTTTTACAAAATGAAAAACTATTTAGACCAATTGATAAGATTTCCCGAGAAT
184 --AG---AAAA-----TGAC--AAT-------T-TTTAGACCAAATGATGCGATTTCCCGGGCAT
* * * * * **
2909 GGATTGTTCGAAAAACTT-CTAGAAGGAATTGGATCATCTTGAATACTTTAATGAATTGAAGTTA
229 GGAATGTTCGAAAAA-TTGCTCGAAAGAA-TGGATCATCTTGAATACTCTAAGGAACCGAAGTTA
* * ** * * * *
2973 TAAAAGAACTCGTAACAGTTTGT-CAA-TTTCAAAAGTTCATCCATGAACCAAGAGAGAAACAAT
292 TAAAAGAACTCGTAA-AGTTTCTACAAGATT-GGAAGTTCGTCCATGAACTAATAGAGGAACAAT
* ** * *
3036 TCTCACGTAAATAAGTTTTTAATTCAAAGATAAAAAATTGTTTACAAAATGA-AAAGCTATTTAG
355 TCTCACGTAAATAAGTTTTTAATTGAAAGACCAAAACTTGTTTACAAAATGAGTAA-CTATTTAG
* * * * * * * *
3100 ACCAAATGATGTGATTTCCCT-CGCATGGAATGTTTGAAAAATTAG-TTGAAGCAATGGATTGTC
419 ACCGAATGATGCGATTT-CCTGAGCGTGGAATGTTCGAAAAATT-GCTCGAAGGAATGGATCGTC
* * * * * * *** * ***
3163 TTGAACACTTTAAGGAACCGGATTTA-AAAAGAAC-TCGTAAATGTTTGACATGTTTG-GATGTT
482 TTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTTGGCAAA-GTTT-ACA-AAATGAAAAACT
** * *
3225 CATCCA-A-CAACCAAT-AGAGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAGGACCAAAA
544 -ATTTAGACCAA--AATGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAA
* * * *
3287 CTTGTTTACTAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGAATGGAATGTTC-A
606 CTTTTTTACAAAATGAAAAACTATTTAGACCGAATGATGCGATTTCCCGAGCATGGAATGTTCGA
3351 AAAAACTACTAAAAGGAATGGACCGTCTTGAATACTTTAAGGAACCGAAGTTAAAAAAGAACTTG
671 AAAAA-TACTAAAAGGAATGGACCGTCTTGAATACTTTAAGGAACCGAAGTTAAAAAAGAACTTG
* *
3416 TAAAATTTTGACAAGTTCGAAAGTTCGACCAAGACAAAAGAGAGAAATAATTCTTACGTAAATAA
735 TAAAATTTTGACAAGTTCGAAAGTTCGTCCAAGAAAAAAGAGAGAAATAATTCTTACGTAAATAA
*
3481 GTTTTTAATACAAACACCAAAACTTGATTACAAAATGAAAAACTATTTGGACCGAATGATGC
800 GTTTTTAATACAAACACCAAAACTTGATTACAAAATGAAAAACTATTTAGACCGAATGATGC
* * *
3543 GATTCCT-GAGCATGAAATGTTCGCAAAAGCTGCTCAAAGGAATGTATCGTCTTGAATACTTGAA
1 GATTTCTCGAGCATGAAATGTTCG-AAAAGATGCTCGAAGGAATGTATCGTCTTGAATACTTGAA
* * * *
3607 GGAACCTAATATATAAAAGAACTCGTAAAAGTTTGACTAGTTCGAAAGTTTGTCTAAGTACCAAA
65 GGAACCAAAGATATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTTGTCTAAGAACCAAA
*
3672 AGAGAAACAATTCTCACGTAAATAAGGTTTTAATTCAAAGGCCAAAACTTGTTTCGAAAATGACA
130 AGAGAAACAATTCTCACGTAAATAAGGTTTTAATTCAAAGGCCAAAACTTGTTTAGAAAATGAC-
*
3737 AAATTTTTAGACCAAATGATGCAATTTCCCGGGCATGGAATGTTCGAAAAATTGCTCGAAAGAAT
194 -AATTTTTAGACCAAATGATGCGATTTCCCGGGCATGGAATGTTCGAAAAATTGCTCGAAAGAAT
* * *
3802 GGATCATCTTGAATACAT-TAATGAACTGAAGTTATAAAAGAACTCGTAAATTTTCTACAAGATT
258 GGATCATCTTGAATAC-TCTAAGGAACCGAAGTTATAAAAGAACTCGTAAAGTTTCTACAAGATT
*
3866 GGAAGTTCGTCCATGAACTAATAGTGGAACAATTCTCACGTAAATAAGTTTTTAATTGAAAGACC
322 GGAAGTTCGTCCATGAACTAATAGAGGAACAATTCTCACGTAAATAAGTTTTTAATTGAAAGACC
* *
3931 AAAAGTTGTTTACAAAATGAGTAACTATTTAGACCGAATGATGAGATTTCCTGAGCGTGGAATGT
387 AAAACTTGTTTACAAAATGAGTAACTATTTAGACCGAATGATGCGATTTCCTGAGCGTGGAATGT
3996 TC-AAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAAC
452 TCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAAC
4060 TTGGCAAAGTTTACAAAATGAA
517 TTGGCAAAGTTTACAAAATGAA
Statistics
Matches: 2719, Mismatches: 354, Indels: 286
0.81 0.11 0.09
Matches are distributed among these distances:
860 49 0.02
861 108 0.04
862 1179 0.43
863 177 0.07
864 382 0.14
865 3 0.00
866 3 0.00
867 8 0.00
868 10 0.00
869 3 0.00
870 5 0.00
871 5 0.00
872 11 0.00
874 5 0.00
876 1 0.00
877 4 0.00
879 1 0.00
880 1 0.00
883 3 0.00
884 3 0.00
885 1 0.00
886 1 0.00
887 1 0.00
889 9 0.00
890 3 0.00
891 2 0.00
892 7 0.00
893 1 0.00
894 1 0.00
895 2 0.00
898 5 0.00
901 1 0.00
902 5 0.00
903 3 0.00
904 2 0.00
905 1 0.00
906 3 0.00
907 8 0.00
908 3 0.00
909 1 0.00
910 2 0.00
911 3 0.00
912 5 0.00
913 1 0.00
916 5 0.00
919 2 0.00
920 1 0.00
921 1 0.00
922 7 0.00
923 2 0.00
924 2 0.00
925 9 0.00
927 1 0.00
928 1 0.00
929 1 0.00
930 3 0.00
931 3 0.00
934 2 0.00
935 1 0.00
937 4 0.00
938 1 0.00
940 6 0.00
942 6 0.00
943 6 0.00
944 5 0.00
945 3 0.00
946 10 0.00
947 7 0.00
948 4 0.00
949 1 0.00
950 50 0.02
951 81 0.03
952 27 0.01
953 385 0.14
954 50 0.02
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (861 bp):
GATTTCTCGAGCATGAAATGTTCGAAAAGATGCTCGAAGGAATGTATCGTCTTGAATACTTGAAG
GAACCAAAGATATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTTGTCTAAGAACCAAAA
GAGAAACAATTCTCACGTAAATAAGGTTTTAATTCAAAGGCCAAAACTTGTTTAGAAAATGACAA
TTTTTAGACCAAATGATGCGATTTCCCGGGCATGGAATGTTCGAAAAATTGCTCGAAAGAATGGA
TCATCTTGAATACTCTAAGGAACCGAAGTTATAAAAGAACTCGTAAAGTTTCTACAAGATTGGAA
GTTCGTCCATGAACTAATAGAGGAACAATTCTCACGTAAATAAGTTTTTAATTGAAAGACCAAAA
CTTGTTTACAAAATGAGTAACTATTTAGACCGAATGATGCGATTTCCTGAGCGTGGAATGTTCGA
AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGAACTTGG
CAAAGTTTACAAAATGAAAAACTATTTAGACCAAAATGAGAGAAACAATTCTCACGTAAATAAGT
TTTTAATTCAAAGACCAAAACTTTTTTACAAAATGAAAAACTATTTAGACCGAATGATGCGATTT
CCCGAGCATGGAATGTTCGAAAAAATACTAAAAGGAATGGACCGTCTTGAATACTTTAAGGAACC
GAAGTTAAAAAAGAACTTGTAAAATTTTGACAAGTTCGAAAGTTCGTCCAAGAAAAAAGAGAGAA
ATAATTCTTACGTAAATAAGTTTTTAATACAAACACCAAAACTTGATTACAAAATGAAAAACTAT
TTAGACCGAATGATGC
Found at i:3526 original size:216 final size:217
Alignment explanation
Indices: 2629--4060 Score: 1529
Period size: 216 Copynumber: 6.6 Consensus size: 217
2619 TACTCGAAGG
* * ** * **
2629 CCAAAACTTGTTTACAAAATGACAAA-TATTTTAGTCCAAATGATGTAACTTCCCTCGCATGGAA
1 CCAAAACTTGTTTACAAAATGAAAAACTA-TTTAGACCAAATGATGCGATTTCCCGAGCATGGAA
* * * *
2693 TGTTCGAAAAATTGCTCAAAGGATTGGATCATCTTGAATACGTTAAGGAACAGAAGTTATAAAAG
65 TGTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAG
* * * * *
2758 AACTCGTAAAAGTTCGAAAAGTTTGAAAGTTCATCCAAGAAC-CAAGAGAGACACAATTTTTTCT
130 AACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAGAACAAAAGAGAGAAACAA----TTCT
*
2822 CATGTAAATAAGTTTTTAATTCAAAGA
191 CACGTAAATAAGTTTTTAATTCAAAGA
* * ** * *
2849 CCAAAACTTTTTTACAAAATGAAAAACTATTTAGACCAATTGATAAGATTTCCCGAGAATGGATT
1 CCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAAT
* * **
2914 GTTCGAAAAACTT-CT-AGAAGGAATTGGATCATCTTGAATACTTTAATGAATTGAAGTTATAAA
66 GTTCGAAAAA-TTGCTCA-AAGGAA-TGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAA
* * * * * *
2977 AGAACTCGTAACAGTTTGTCAATTTCAAAAGTTCATCCATGAAC-CAAGAGAGAAACAATTCTCA
128 AGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAGAACAAAAGAGAGAAACAATTCTCA
3041 CGTAAATAAGTTTTTAATTCAAAGA
193 CGTAAATAAGTTTTTAATTCAAAGA
** * * * **
3066 TAAAAAATTGTTTACAAAATGAAAAGCTATTTAGACCAAATGATGTGATTTCCCTCGCATGGAAT
1 CCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAAT
* ** * * * * *
3131 GTTTGAAAAATTAG-TTGAAGCAATGGATTGTCTTGAACACTTTAAGGAACCGGATTTA-AAAAG
66 GTTCGAAAAATT-GCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAG
* * * * * * * * *
3194 AACTCGTAAATGTTTGACATGTTTGGATGTTCATCCAACAAC-CAATAGAGAAACAATTCTCATG
130 AACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAGAACAAAAGAGAGAAACAATTCTCACG
*
3258 TAAATAAGTTTTTAATTCAAGGA
195 TAAATAAGTTTTTAATTCAAAGA
* *
3281 CCAAAACTTGTTTACTAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGAATGGAAT
1 CCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAAT
* * * * * *
3346 GTTCAAAAAACTACTAAAAGGAATGGACCGTCTTGAATACTTTAAGGAACCGAAGTTAAAAAAGA
66 GTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGA
* * * *
3411 ACTTGTAAAATTTTGACAAGTTCGAAAGTTCGA-CCAAG-ACAAAAGAGAGAAATAATTCTTACG
131 ACTCGTAAAAGTTTGACAAGTTCGAAAGTTC-ATCCAAGAACAAAAGAGAGAAACAATTCTCACG
* *
3474 TAAATAAGTTTTTAATACAAACA
195 TAAATAAGTTTTTAATTCAAAGA
* * * * *
3497 CCAAAACTTGATTACAAAATGAAAAACTATTTGGACCGAATGATGCGA-TTCCTGAGCATGAAAT
1 CCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAAT
** * * *
3561 GTTCGCAAAAGCTGCTCAAAGGAATGTATCGTCTTGAATACTTGAAGGAACCTAA-TATATAAAA
66 GTTCG-AAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGT-TATAAAA
* ** * * *
3625 GAACTCGTAAAAGTTTGACTAGTTCGAAAGTTTGTCTAAGTACCAAA-AGAGAAACAATTCTCAC
129 GAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAGAACAAAAGAGAGAAACAATTCTCAC
* *
3689 GTAAATAAGGTTTTAATTCAAAGG
194 GTAAATAAGTTTTTAATTCAAAGA
* * *
3713 CCAAAACTTGTTT-CGAAAATGACAAAA-TTTTTAGACCAAATGATGCAATTTCCCGGGCATGGA
1 CCAAAACTTGTTTAC-AAAATGA-AAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGA
* * * *
3776 ATGTTCGAAAAATTGCTCGAAA-GAATGGATCATCTTGAATACATTAATGAACTGAAGTTATAAA
64 ATGTTCGAAAAATTGCTC-AAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAA
* * * * * * *
3840 AGAACTCGT-AAATTTTCTACAAGATT-GGAAGTTCGTCCATGAACTAATAGTG-G-AACAATTC
128 AGAACTCGTAAAAGTTT-GACAAG-TTCGAAAGTTCATCCAAGAAC-AAAAGAGAGAAACAATTC
*
3901 TCACGTAAATAAGTTTTTAATTGAAAGA
190 TCACGTAAATAAGTTTTTAATTCAAAGA
* ** * * * *
3929 CCAAAAGTTGTTTACAAAATGAGTAACTATTTAGACCGAATGATGAGATTTCCTGAGCGTGGAAT
1 CCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAAT
* *
3994 GTTC-AAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAATCGAAGTTATAAAAGA
66 GTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGA
4058 ACT
131 ACT
4061 TGGCAAAGTT
Statistics
Matches: 1008, Mismatches: 177, Indels: 59
0.81 0.14 0.05
Matches are distributed among these distances:
214 2 0.00
215 262 0.26
216 451 0.45
217 136 0.13
218 1 0.00
219 1 0.00
220 67 0.07
221 88 0.09
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (217 bp):
CCAAAACTTGTTTACAAAATGAAAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAAT
GTTCGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGA
ACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATCCAAGAACAAAAGAGAGAAACAATTCTCACGT
AAATAAGTTTTTAATTCAAAGA
Done.