Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002730.1 Kokia drynarioides strain JFW-HI SEQ_115033, 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: 2430
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Found at i:444 original size:216 final size:215
Alignment explanation
Indices: 3--2068 Score: 2226
Period size: 216 Copynumber: 9.6 Consensus size: 215
1 GT
* ** *
3 AATAAGTTTTTAACTCAAAGACTGAAACTTGTTTGCAAAAAGACAAACTATTTAGACCAAATGAT
1 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
* * ** * *
68 GTGATTTGCCGAGTATGAAATGTTCGGAATATTGC-TCAGAGGAATGGATC-TGTTGAATACTTT
66 GTGATTT-CCGAGCATGGAATGTTCAAAAAATTGCTTGA-AGGAATGGATCGTGTTGAATACTTT
* * * * *
131 AAGGAACCCAATTTATAAAAGATTCAGTAAAAGTTTGACAAGTTCGGATGTTCGTCCAACAAGAA
129 AAGGAACCGAATTTATAAAAGATTTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAA
*
196 AGAGAGAAATAATTCTCACGTA
194 AGAGAGAAACAATTCTCACGTA
* *
218 AATAAGTTTTTATTTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTTTTTAGACCAAATGAT
1 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
* * * *
283 GTAATTTACCGAGCATGGAATGTTCAAAAAATTACTTGAAGAAATGGATCGTGTTGGAGT-CTTT
66 GTGATTT-CCGAGCATGGAATGTTCAAAAAATTGCTTGAAGGAATGGATCGTGTT-GAATACTTT
** * * * *
347 AAGGATTCAAATTTATAAAAGATTTAGAAAAAGTTTGATAAGATCGGAAGTTCGTCCAAGAACAA
129 AAGGAACCGAATTTATAAAAGATTTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAA
* * * *
412 AGTGGGAAACTATTCTCACGTC
194 AGAGAGAAACAATTCTCACGTA
* * **
434 AATAAGTTTTTAATTCAAAGACCAAAACATGTTCGCAACGTGACAAACTATTTAGACCAAATGAT
1 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
* * * * * * * * *
499 GCGATTTCTCGAGCGTTGAATGTTCAGAAAATTGCTCGAAAGAATAGATCGTCTGGAATACTTTA
66 GTGATTTC-CGAGCATGGAATGTTCAAAAAATTGCTTGAAGGAATGGATCGTGTTGAATACTTTA
* * * * * *
564 CGGATCCGAAGTTATAAAAGAACTT-GTAATAGTTTGACAAGTTCGGAAGTTCTTCCAAGAACAA
130 AGGAACCGAATTTATAAAAG-ATTTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAA
628 AGAGAGAAACAATTCTCACGTA
194 AGAGAGAAACAATTCTCACGTA
* * * ** *
650 AATAAGGTTTTAATTCAAAGACAAAAACTTGTTTACAAAATGACAAGTTATTTAGACCAAATTAT
1 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
* * * *
715 GTGATTTCTCGAGCATGGAATGTTCGAAAAATTGCTCT-AAGGAATGGATCTTGTTTAATAGTTT
66 GTGATTTC-CGAGCATGGAATGTTCAAAAAATTGCT-TGAAGGAATGGATCGTGTTGAATACTTT
* * * * * ** * * * * * *
779 AGGGAAACGAAGTTAAAAAATAACTCGAAAAAGTTTGGCAAGTTCGAAAGTTCATCCAAAAACAA
129 AAGGAACCGAATTTATAAAAGATTTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAA
*
844 AGAGAGAAACAATTTTCACGTA
194 AGAGAGAAACAATTCTCACGTA
* *
866 AATAAGTTTTTAATTTAAAGACCAAAACTTGTTAGCAAAATGACAAACTATTTAGACCAAATGAT
1 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
* * * ** * * * *
931 GCGATTTCCTGGGAATGGAATGTTTGAAAAATTGCTCGAAGGAATGGATCGTCTTCAACACTTTA
66 GTGATTTCC-GAGCATGGAATGTTCAAAAAATTGCTTGAAGGAATGGATCGTGTTGAATACTTTA
* * * * *** * * * * * **
996 AGGATCTGAAGTTATAAAATAACAAGTAAAAGTTTGACAAGCTT-AGACGTTCATCTATGATGAA
130 AGGAACCGAATTTATAAAAGATTTAGTAAAAGTTTGACAAG-TTCGGAAGTTCGTCCAAGAACAA
* * *
1060 AGACAGATACCATTCTCACGTA
194 AGAGAGAAACAATTCTCACGTA
* * * * * *
1082 AATAAGTTCTGAATTCAAAGAACAAAACTGTTTTTTCGAAATGACAAACTATTTAGACCAAATGA
1 AATAAGTTTTTAATTCAAAGACCAAAACT-TGTTTGCAAAATGACAAACTATTTAGACCAAATGA
* * * * * * *
1147 TGCGATTTCCCAAGGATGGAATGTTCAGAAAATTGCTCT-AA-AAATTGGATCTTGTTTAATAC-
65 TGTGATTT-CCGAGCATGGAATGTTCAAAAAATTGCT-TGAAGGAA-TGGATCGTGTTGAATACT
* * * * * *
1209 TTAAGGGAACCGAAGTTAAAAAATAACTT-GTAAAAGTTTGACAAGTTCGAAAGTTCGTCCATGA
127 TTAA-GGAACCGAATTTATAAAA-GATTTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGA
*
1273 ACAAAGAGAGAAACAATTCTCAAGT-
190 ACAAAGAGAGAAACAATTCTCACGTA
* * *
1298 AATAAGTTTTTAACTCAAAGACTAAAACTTGTTTGCAAAAGGACAAACTATTTAGACCAAATGAT
1 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
* * * * *
1363 GTGATTTGTCGAGTATGGAATGTTCAAAATATTGC-TCAGAGGAATGGATC-TGTTAAATACTTT
66 GTGATTT-CCGAGCATGGAATGTTCAAAAAATTGCTTGA-AGGAATGGATCGTGTTGAATACTTT
* * * * * * * *
1426 AATGAACCAAATTTATAAAAGATTCAGTGAAAGTTTGACAAGTTCGGATGTTCGTCCAACAATAG
129 AAGGAACCGAATTTATAAAAGATTTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAA
* *
1491 AGAGAGAAATAATTCTCACATA
194 AGAGAGAAACAATTCTCACGTA
*
1513 TATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
1 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
* *
1578 GTAATTTGCCGAGCATGG-A----CGAAAAATTGCTTGAAGGAATGGATCGTGTTGAATACTTTA
66 GTGATTT-CCGAGCATGGAATGTTCAAAAAATTGCTTGAAGGAATGGATCGTGTTGAATACTTTA
* * * * * * *
1638 AGG-ATCGAATGTATAAAAGATTTAATAAAAGTTTGACATGTTGGGAAGTTTGTCCAAGAATAAA
130 AGGAACCGAATTTATAAAAGATTTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAA
*
1702 GAGAGAAACAATTCTCACCTA
195 GAGAGAAACAATTCTCACGTA
* *
1723 AATAAGTTTTTAATTCAAAGACAAAAACTTGTTTGCAAAATGACAAACTATTTAGACTAAATGAT
1 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
* * *
1788 GTGATTTGCCAAGCATGGAATGTTCGAAAAATTGCTTGAAGGAATGGATCGTGTTGAAGACTTTA
66 GTGATTT-CCGAGCATGGAATGTTCAAAAAATTGCTTGAAGGAATGGATCGTGTTGAATACTTTA
** * * * *
1853 AGGATTCAAATTTATAAAAGATTTAGAAAAAGTTTGATAAGATCGGAAGTTCGTCCAAGAACAAA
130 AGGAACCGAATTTATAAAAGATTTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAA
* * ** *
1918 GAGGGAAACTATGGTCACGTC
195 GAGAGAAACAATTCTCACGTA
*
1939 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAACTGACAAACTATTTAGACCAAATGAT
1 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
* * * * * * *
2004 GCGATTTCTCGAGCATGGAATGTTCAGAAAATTGCTCGAAAGAATAGATCGTCTGGAATACTTTA
66 GTGATTTC-CGAGCATGGAATGTTCAAAAAATTGCTTGAAGGAATGGATCGTGTTGAATACTTTA
2069 GACCAAATGA
Statistics
Matches: 1542, Mismatches: 276, Indels: 65
0.82 0.15 0.03
Matches are distributed among these distances:
210 166 0.11
211 18 0.01
213 3 0.00
214 75 0.05
215 294 0.19
216 840 0.54
217 143 0.09
218 3 0.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (215 bp):
AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
GTGATTTCCGAGCATGGAATGTTCAAAAAATTGCTTGAAGGAATGGATCGTGTTGAATACTTTAA
GGAACCGAATTTATAAAAGATTTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAG
AGAGAAACAATTCTCACGTA
Found at i:811 original size:432 final size:428
Alignment explanation
Indices: 3--2430 Score: 2367
Period size: 432 Copynumber: 5.6 Consensus size: 428
1 GT
* ** *
3 AATAAGTTTTTAACTCAAAGACTGAAACTTGTTTGCAAAAAGACAAACTATTTAGACCAAATGAT
1 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
* * * * *
68 GTGATTTGCCGAGTATGAAATGTTCGGAATATTGCTC-AGAGGAATGGATCTGT-TGAATACTTT
66 GCGATTT-CCGAGCATGGAATGTTCAGAAAATTGCTCGA-AGGAATGGATC-GTCTGAATACTTT
* * * * * *
131 AAGGAACCCAATTTATAAAAGA-TTCAGTAAAAGTTTGACAAGTTCGGATGTTCGTCCAACAAGA
128 AAGGATCCGAAGTTATAAAAGACTT-AGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACA
* *
195 AAGAGAGAAATAATTCTCACGTAAATAAGTTTTTATTTCAAAGACCAAAACTTGTTTGCAAAATG
192 AAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATG
* * *
260 ACAAACTTTTTAGACCAAATGATGTAATTTACCGAGCATGGAATGTTCAAAAAATTACT-TGAAG
257 ACAAACTATTTAGACCAAATGATGTGATTT-CCGAGCATGGAATGTTC-AAAAATTGCTCT-AAG
* * * ** * * * * * *
324 AAATGGATCGTGTTGGAGT-CTTTAAGGATTCAAATTTATAAAA-GATTTAGAAAAAGTTTGATA
319 GAATGGATCGTGTT-GAATACTTTAGGGAAACGAAGTTAAAAAATAACTT-GAAAAAGTTTGACA
* * * * *
387 AGATCGGAAGTTCGTCCAAGAACAAAGTGGGAAACTATTCTCACGTC
382 AGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTA
* * **
434 AATAAGTTTTTAATTCAAAGACCAAAACATGTTCGCAACGTGACAAACTATTTAGACCAAATGAT
1 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
* * * *
499 GCGATTTCTCGAGCGTTGAATGTTCAGAAAATTGCTCGAAAGAATAGATCGTCTGGAATACTTTA
66 GCGATTTC-CGAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCT-GAATACTTTA
* * *
564 CGGATCCGAAGTTATAAAAGAACTT-GTAATAGTTTGACAAGTTCGGAAGTTCTTCCAAGAACAA
129 AGGATCCGAAGTTATAAAAG-ACTTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAA
* * *
628 AGAGAGAAACAATTCTCACGTAAATAAGGTTTTAATTCAAAGACAAAAACTTGTTTACAAAATGA
193 AGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGA
** *
693 CAAGTTATTTAGACCAAATTATGTGATTTCTCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGA
258 CAAACTATTTAGACCAAATGATGTGATTTC-CGAGCATGGAATGTTC-AAAAATTGCTCTAAGGA
* * * * *
758 ATGGATCTTGTTTAATAGTTTAGGGAAACGAAGTTAAAAAATAACTCGAAAAAGTTTGGCAAGTT
321 ATGGATCGTGTTGAATACTTTAGGGAAACGAAGTTAAAAAATAACTTGAAAAAGTTTGACAAGTT
* * * *
823 CGAAAGTTCATCCAAAAACAAAGAGAGAAACAATTTTCACGTA
386 CGGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTA
* *
866 AATAAGTTTTTAATTTAAAGACCAAAACTTGTTAGCAAAATGACAAACTATTTAGACCAAATGAT
1 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
* * * * *
931 GCGATTTCCTGGGAATGGAATGTT-TGAAAAATTGCTCGAAGGAATGGATCGTCTTCAACACTTT
66 GCGATTTCC-GAGCATGGAATGTTCAG-AAAATTGCTCGAAGGAATGGATCGTC-TGAATACTTT
* * * * * * * * **
995 AAGGATCTGAAGTTATAAAATAAC-AAGTAAAAGTTTGACAAGCTT-AGACGTTCATCTATGATG
128 AAGGATCCGAAGTTATAAAA-GACTTAGTAAAAGTTTGACAAG-TTCGGAAGTTCGTCCAAGAAC
* * * * * * * * *
1058 AAAGACAGATACCATTCTCACGTAAATAAGTTCTGAATTCAAAGAACAAAACTGTTTTTTCGAAA
191 AAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACT-TGTTTGCAAAA
* * *
1123 TGACAAACTATTTAGACCAAATGATGCGATTTCCCAAGGATGGAATGTTCAGAAAATTGCTCTAA
255 TGACAAACTATTTAGACCAAATGATGTGATTT-CCGAGCATGGAATGTTCA-AAAATTGCTCTAA
* * * * * *
1188 -AAATTGGATCTTGTTTAATACTTAAGGGAACCGAAGTTAAAAAATAACTTGTAAAAGTTTGACA
318 GGAA-TGGATCGTGTTGAATACTTTAGGGAAACGAAGTTAAAAAATAACTTGAAAAAGTTTGACA
* * *
1252 AGTTCGAAAGTTCGTCCATGAACAAAGAGAGAAACAATTCTCAAGT-
382 AGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTA
* * *
1298 AATAAGTTTTTAACTCAAAGACTAAAACTTGTTTGCAAAAGGACAAACTATTTAGACCAAATGAT
1 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
* * * *
1363 GTGATTTGTCGAGTATGGAATGTTCA-AAATATTGCTC-AGAGGAATGGATCTGT-TAAATACTT
66 GCGATTT-CCGAGCATGGAATGTTCAGAAA-ATTGCTCGA-AGGAATGGATC-GTCTGAATACTT
* * * * * * * *
1425 TAATGAACCAAATTTATAAAAGA-TTCAGTGAAAGTTTGACAAGTTCGGATGTTCGTCCAACAAT
127 TAAGGATCCGAAGTTATAAAAGACTT-AGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAAC
* * * *
1489 AGAGAGAGAAATAATTCTCACATATATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAAT
191 AAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAAT
* *
1554 GACAAACTATTTAGACCAAATGATGTAATTTGCCGAGCATGG-ACG---AAAAATTGCT-TGAAG
256 GACAAACTATTTAGACCAAATGATGTGATTT-CCGAGCATGGAATGTTCAAAAATTGCTCT-AAG
* * * *
1614 GAATGGATCGTGTTGAATACTTTAAGG-ATCGAATGTATAAAAGAT---TTAATAAAAGTTTGAC
319 GAATGGATCGTGTTGAATACTTTAGGGAAACGAA-GT-TAAAAAATAACTTGA-AAAAGTTTGAC
* * * * *
1675 ATGTTGGGAAGTTTGTCCAAGAATAAAGAGAGAAACAATTCTCACCTA
381 AAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTA
* *
1723 AATAAGTTTTTAATTCAAAGACAAAAACTTGTTTGCAAAATGACAAACTATTTAGACTAAATGAT
1 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
* * * * *
1788 GTGATTTGCCAAGCATGGAATGTTC-GAAAAATTGCTTGAAGGAATGGATCGTGTTGAAGACTTT
66 GCGATTT-CCGAGCATGGAATGTTCAG-AAAATTGCTCGAAGGAATGGATCGT-CTGAATACTTT
* * * * * * *
1852 AAGGATTCAAATTTATAAAAGATTTAGAAAAAGTTTGATAAGATCGGAAGTTCGTCCAAGAACAA
128 AAGGATCCGAAGTTATAAAAGACTTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAA
* * ** * *
1917 AGAGGGAAACTATGGTCACGTCAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAACTGA
193 AGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGA
* * *
1982 CAAACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCAGAAAATTGCTCGAAAGA
258 CAAACTATTTAGACCAAATGATGTGATTTC-CGAGCATGGAATGTTCA-AAAATTGCTCTAAGGA
* * * ** * ** ** * *
2047 ATAGATCGTCTGGAATACTTTAGACCAAATGATGAGATTTTCCGAGCATGGAATGTTTGGAAAA-
321 ATGGATCGTGTTGAATACTTTAG-GGAAACGA--AG---TT-AAAAAAT--AA--CTTGAAAAAG
* * * * * *
2111 TTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGATCCGAGAACAAAGATAGAAACAATTCT
375 TT--T-G-A-CAA--G-T--TC--GGA-A-GTT--CG-TCCAAGAACAAAGAGAGAAACAATTCT
*
2176 CACATA
423 CACGTA
* *
2182 AATAAGTTTTTAATTCAAAGACCAAAACATGTTTGCAAAATGACAAACTATTTAGACCAAACGAT
1 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
* * * ** *
2247 ACGATTTCCCTAGCATGGAATGTTCAAAAAATTGCTCGTAA-GAATAAATCGTCTAGAATAATTT
66 GCGATTT-CCGAGCATGGAATGTTCAGAAAATTGCTCG-AAGGAATGGATCGTCT-GAATACTTT
* * *
2311 AAGGATCGGAAGTTATAAAAGAACTT-TTAATAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACA
128 AAGGATCCGAAGTTATAAAAG-ACTTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACA
*
2375 AAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTT
192 AAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTT
Statistics
Matches: 1642, Mismatches: 272, Indels: 138
0.80 0.13 0.07
Matches are distributed among these distances:
423 2 0.00
424 58 0.04
425 134 0.08
426 165 0.10
427 4 0.00
429 2 0.00
430 53 0.03
431 228 0.14
432 551 0.34
433 171 0.10
434 4 0.00
435 1 0.00
436 1 0.00
437 4 0.00
442 2 0.00
443 4 0.00
444 3 0.00
445 1 0.00
446 1 0.00
447 1 0.00
449 1 0.00
450 1 0.00
452 1 0.00
454 2 0.00
455 1 0.00
456 2 0.00
458 2 0.00
459 237 0.14
460 5 0.00
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (428 bp):
AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
GCGATTTCCGAGCATGGAATGTTCAGAAAATTGCTCGAAGGAATGGATCGTCTGAATACTTTAAG
GATCCGAAGTTATAAAAGACTTAGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGA
GAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAA
ACTATTTAGACCAAATGATGTGATTTCCGAGCATGGAATGTTCAAAAATTGCTCTAAGGAATGGA
TCGTGTTGAATACTTTAGGGAAACGAAGTTAAAAAATAACTTGAAAAAGTTTGACAAGTTCGGAA
GTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTA
Found at i:1399 original size:648 final size:640
Alignment explanation
Indices: 3--2426 Score: 2401
Period size: 648 Copynumber: 3.7 Consensus size: 640
1 GT
* *
3 AATAAGTTTTTAACTCAAAGACTGAAACTTGTTTGCAAAAAGACAAACTATTTAGACCAAATGAT
1 AATAAGTTTTTAACTCAAAGACTAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
* * * * *
68 GTGATTTGC-CGAGTATGAAATGTTCGGAATATTGCTCAGAGGAATGGATCTGTTGAATACTTTA
66 GTGATTT-CTCGAGCATGGAATGTTC-AAAAATTGCTCAGAGGAATGGATCTGTTAAATACTTTA
* *
132 AGGAACCCAATTTATAAAAGATTCAGTAAAAGTTTGACAAGTTCGGATGTTCGTCCAACAAGAAA
129 AGGAACCAAATTTATAAAAGATTCAGTAAAAGTTTGACAAGTTCGGATGTTCGTCCAACAACAAA
197 GAGAGAAATAATTCTCACGTAAATAAGTTTTT-ATTTCAAAGACCAAAACTTGTTTGCAAAATGA
194 GAGAGAAATAATTCTCACGTAAATAAGTTTTTAATTT-AAAGACCAAAACTTGTTTGCAAAATGA
* * * *
261 CAAACTTTTTAGACCAAATGATGTAATTTACCGAGCATGGAATGTTCAAAAAATTACTTGAAGAA
258 CAAACTATTTAGACCAAATGATGTAATTTACCGAGCATGGAATGTTCGAAAAATTGCTTGAAGGA
* ** * * * *
326 ATGGATCGTGTTGGAGTCTTTAAGGAT-TCAAATTTATAAAAGATTTAGAAAAAGTTTGATAAGA
323 ATGGATCGTGTTGAACACTTTAAGGATCT-GAA-TTATAAAAGATTAAGTAAAAGTTTGACAAG-
* * * * * *
390 TCGGAAGTTCGTCCAAGAACAAAGTGGGAAACTATTCTCACGTCAATAAGTTTTTAATTCAAAGA
385 TTGGAAGTTCGTCCAAG-ATAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGA
* * * * *
455 CCAAAACATG---TTCGCAACGTGACAAACTATTTAGACCAAATGATGCGATTTCTCGAGCG-TT
449 ACAAAAC-TGTTTTTCG-AA-ATGACAAACTATTTAGACCAAATGATGCGATTTCCCAAG-GATG
* * * * *
516 GAATGTTCAGAAAATTGCTCGAAAGAATAGATCGTCTGGAATACTTTACGGATCCGAAGTTATAA
510 GAATGTTCAGAAAATTGCTCTAAA-AATGGATCGTGTTGAATAC-TTAAGGATCCGAAGTTATAA
* *
581 AAGAACTTGTAATAGTTTGACAAGTTCGGAAGTTCTTCCAAGAACAAAGAGAGAAACAATTCTCA
573 AA-AACTTGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCA
646 CGTA
637 CGTA
* * * * ** *
650 AATAAGGTTTTAATTCAAAGACAAAAACTTGTTTACAAAATGACAAGTTATTTAGACCAAATTAT
1 AATAAGTTTTTAACTCAAAGACTAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
* *
715 GTGATTTCTCGAGCATGGAATGTTCGAAAAATTGCTCTA-AGGAATGGATCTTGTTTAATAGTTT
66 GTGATTTCTCGAGCATGGAATGTTC-AAAAATTGCTC-AGAGGAATGGATC-TGTTAAATACTTT
* * * * * * * * * * * * *
779 AGGGAAACGAAGTTAAAAAATAACTC-GAAAAAGTTTGGCAAGTTCGAAAGTTCATCCAAAAACA
128 AAGGAACCAAATTTATAAAA-GATTCAGTAAAAGTTTGACAAGTTCGGATGTTCGTCCAACAACA
* * *
843 AAGAGAGAAACAATTTTCACGTAAATAAGTTTTTAATTTAAAGACCAAAACTTGTTAGCAAAATG
192 AAGAGAGAAATAATTCTCACGTAAATAAGTTTTTAATTTAAAGACCAAAACTTGTTTGCAAAATG
** * * * *
908 ACAAACTATTTAGACCAAATGATGCGATTT-CCTGGGAATGGAATGTTTGAAAAATTGCTCGAAG
257 ACAAACTATTTAGACCAAATGATGTAATTTACC-GAGCATGGAATGTTCGAAAAATTGCTTGAAG
* * * **
972 GAATGGATCGTCTTCAACACTTTAAGGATCTGAAGTTATAAAATAACAAGTAAAAGTTTGACAAG
321 GAATGGATCGTGTTGAACACTTTAAGGATCTGAA-TTATAAAAGATTAAGTAAAAGTTTGACAAG
* * * * * * * * * *
1037 CTTAGACGTTCATCTATGATGAAAGACAGATACCATTCTCACGTAAATAAGTTCTGAATTCAAAG
385 -TTGGAAGTTCGTCCAAGAT-AAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAG
1102 AACAAAACTGTTTTTTCGAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCAAGGATGGA
448 AACAAAACTG-TTTTTCGAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCAAGGATGGA
* * * *
1167 ATGTTCAGAAAATTGCTCTAAAAATTGGATCTTGTTTAATACTTAAGGGAACCGAAGTTAAAAAA
512 ATGTTCAGAAAATTGCTCTAAAAA-TGGATCGTGTTGAATACTTAA-GGATCCGAAGTTATAAAA
* * *
1232 TAACTTGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCATGAACAAAGAGAGAAACAATTCTCAAG
575 -AACTTGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACG
1297 T-
639 TA
*
1298 AATAAGTTTTTAACTCAAAGACTAAAACTTGTTTGCAAAAGGACAAACTATTTAGACCAAATGAT
1 AATAAGTTTTTAACTCAAAGACTAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
* *
1363 GTGATTTGTCGAGTATGGAATGTTCAAAATATTGCTCAGAGGAATGGATCTGTTAAATACTTTAA
66 GTGATTTCTCGAGCATGGAATGTTCAAAA-ATTGCTCAGAGGAATGGATCTGTTAAATACTTTAA
* * * *
1428 TGAACCAAATTTATAAAAGATTCAGTGAAAGTTTGACAAGTTCGGATGTTCGTCCAACAATAGAG
130 GGAACCAAATTTATAAAAGATTCAGTAAAAGTTTGACAAGTTCGGATGTTCGTCCAACAACAAAG
* * *
1493 AGAGAAATAATTCTCACATATATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACA
195 AGAGAAATAATTCTCACGTAAATAAGTTTTTAATTTAAAGACCAAAACTTGTTTGCAAAATGACA
*
1558 AACTATTTAGACCAAATGATGTAATTTGCCGAGCATGG-A----CGAAAAATTGCTTGAAGGAAT
260 AACTATTTAGACCAAATGATGTAATTTACCGAGCATGGAATGTTCGAAAAATTGCTTGAAGGAAT
* *
1618 GGATCGTGTTGAATACTTTAAGGATC-GAATGTATAAAAGATTTAA-TAAAAGTTTGACATGTTG
325 GGATCGTGTTGAACACTTTAAGGATCTGAAT-TATAAAAGA-TTAAGTAAAAGTTTGACAAGTT-
* *
1681 GGAAGTTTGTCCAAGAATAAAGAGAGAAACAATTCTCACCTAAATAAGTTTTTAATTCAAAG-AC
387 GGAAGTTCGTCCAAG-ATAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAAC
* * * * * *
1745 AAAAACT-TGTTTGCAAAATGACAAACTATTTAGACTAAATGATGTGATTTGCCAAGCATGGAAT
451 -AAAACTGT-TTTTCGAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCAAGGATGGAAT
* * * * *
1809 GTTC-GAAAAATTGCT-TGAAGGAATGGATCGTGTTGAAGACTTTAAGGATTCAAATTTATAAAA
514 GTTCAG-AAAATTGCTCT-AA-AAATGGATCGTGTTGAATAC-TTAAGGATCCGAAGTTATAAAA
* * * * * * * **
1872 GATTTAGAAAAAGTTTGATAAGATCGGAAGTTCGTCCAAGAACAAAGAGGGAAACTATGGTCACG
575 AACTT-GTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACG
*
1937 TC
639 TA
* * *
1939 AATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAACTGACAAACTATTTAGACCAAATGAT
1 AATAAGTTTTTAACTCAAAGACTAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
* * * *
2004 GCGATTTCTCGAGCATGGAATGTTCAGAAAATTGCTC-GAAAGAATAGATC-GTCTGGAATACTT
66 GTGATTTCTCGAGCATGGAATGTTCA-AAAATTGCTCAG-AGGAATGGATCTGT-T-AAATACTT
* * * ** * * * *
2067 T-A-G-ACCAAA-TGATGAGATTTTCCGAGCATGGAATGTTTGGAAAATTGCTCGAAGGAATGGA
127 TAAGGAACCAAATTTATAAAAGATT-C-AG--T-AAAAGTTT-GACAA--GTTC---GG-AT-G-
* * * *
2128 TCGTCTTGAATACTTTAAGGATCCGAGAACAAAGATAGAAACAATTCTCACATAAATAAGTTTTT
178 T--TC--G--T-C---CA--A--C---AACAAAGAGAGAAATAATTCTCACGTAAATAAGTTTTT
* * * *** * *
2193 AATTCAAAGACCAAAACATGTTTGCAAAATGACAAACTATTTAGACCAAACGATACGATTTCCCT
226 AATTTAAAGACCAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGATGTAATTTACCG
* * ** * * * * *
2258 AGCATGGAATGTTCAAAAAATTGCTCGTAA-GAATAAATCGTCTAGAATAATTTAAGGATCGGAA
291 AGCATGGAATGTTCGAAAAATTGCTTG-AAGGAATGGATCGTGTTGAACACTTTAAGGATCTGAA
* * *
2322 GTTATAAAAGAACTT--TTAATAGTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAAA
355 -TTATAAAAG-A-TTAAGTAAAAGTTTGACAAGTT-GGAAGTTCGTCCAAG-ATAAAGAGAGAAA
2385 CAATTCTCACGTAAATAAGTTTTTAATTCAAAG-ACTAAAACT
415 CAATTCTCACGTAAATAAGTTTTTAATTCAAAGAAC-AAAACT
2427 TGTT
Statistics
Matches: 1477, Mismatches: 224, Indels: 124
0.81 0.12 0.07
Matches are distributed among these distances:
638 7 0.00
639 13 0.01
640 152 0.10
641 186 0.13
642 58 0.04
643 7 0.00
644 4 0.00
646 8 0.01
647 255 0.17
648 376 0.25
649 158 0.11
650 4 0.00
651 5 0.00
652 1 0.00
654 2 0.00
656 1 0.00
658 1 0.00
659 1 0.00
662 1 0.00
664 1 0.00
666 1 0.00
669 98 0.07
670 1 0.00
674 37 0.03
675 95 0.06
676 4 0.00
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (640 bp):
AATAAGTTTTTAACTCAAAGACTAAAACTTGTTTGCAAAATGACAAACTATTTAGACCAAATGAT
GTGATTTCTCGAGCATGGAATGTTCAAAAATTGCTCAGAGGAATGGATCTGTTAAATACTTTAAG
GAACCAAATTTATAAAAGATTCAGTAAAAGTTTGACAAGTTCGGATGTTCGTCCAACAACAAAGA
GAGAAATAATTCTCACGTAAATAAGTTTTTAATTTAAAGACCAAAACTTGTTTGCAAAATGACAA
ACTATTTAGACCAAATGATGTAATTTACCGAGCATGGAATGTTCGAAAAATTGCTTGAAGGAATG
GATCGTGTTGAACACTTTAAGGATCTGAATTATAAAAGATTAAGTAAAAGTTTGACAAGTTGGAA
GTTCGTCCAAGATAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGAACAAAAC
TGTTTTTCGAAATGACAAACTATTTAGACCAAATGATGCGATTTCCCAAGGATGGAATGTTCAGA
AAATTGCTCTAAAAATGGATCGTGTTGAATACTTAAGGATCCGAAGTTATAAAAAACTTGTAAAA
GTTTGACAAGTTCGGAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTA
Found at i:2115 original size:76 final size:76
Alignment explanation
Indices: 1989--2144 Score: 242
Period size: 76 Copynumber: 2.1 Consensus size: 76
1979 TGACAAACTA
*
1989 TTTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCAGAAAATTGCTCGAAAGAATAGATC
1 TTTAGACCAAATGATGAGATTTCTCGAGCATGGAATGTTCAGAAAATTGCTCGAAAGAATAGATC
2054 GTCTGGAATAC
66 GTCTGGAATAC
** * *
2065 TTTAGACCAAATGATGAGATTT-TCCGAGCATGGAATGTTTGGAAAATTGCTCGAAGGAATGGAT
1 TTTAGACCAAATGATGAGATTTCT-CGAGCATGGAATGTTCAGAAAATTGCTCGAAAGAATAGAT
*
2129 CGTCTTGAATAC
65 CGTCTGGAATAC
2141 TTTA
1 TTTA
2145 AGGATCCGAG
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
75 1 0.01
76 72 0.99
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (76 bp):
TTTAGACCAAATGATGAGATTTCTCGAGCATGGAATGTTCAGAAAATTGCTCGAAAGAATAGATC
GTCTGGAATAC
Done.