Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012304.1 Kokia drynarioides strain JFW-HI SEQ_127305, 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: 3021
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Found at i:378 original size:216 final size:215
Alignment explanation
Indices: 3--3002 Score: 3114
Period size: 216 Copynumber: 13.9 Consensus size: 215
1 AT
* * * *
3 TGATGCGCTTTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATTTTGTTGAATGC
1 TGATGCG-ATTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATCTTCTTGAATAC
* * * * * * * *
68 TTTAAGGAACCAAAGTTAAAAAATAACTTGTAGAAGTTTGACCAG-TCTGGATGTTCGTCCAAAA
65 TTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTC-GGAAGTTCGTCCAAGA
* * * * *
132 ACAAAGAGGGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAATACCAAAACCTGTTTGCAAA
129 ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAA
197 ATGACAAACTACTTT-GACCAAA
194 ATGACAAACTA-TTTAGACCAAA
* * * * *
219 TGATGCGATCTGCCGAGCATGAAATGTTCGAAAAATTGCT-TGAAAGAATAGATCATCTTGAATA
1 TGATGCGAT-TCCCGAGCATGGAATGTTCGAAAAATTGCTCT-AAGGAATGGATCTTCTTGAATA
* * * * * * * *
283 CTTTGAGGATCCGAAGTTATCAAAGAACTAGTAAAAGTTTGAGAAGCTCAGAAGTTCGTCCAAGT
64 CTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGA
* * * * **
348 ACAGAGGGAGAAACAATTCTCACATAAATAAGTTCTTAATTCAAAGTTCAAAACTTGTTTACAAA
129 ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAA
* * * * *
413 AT-A-ACA-TATTTTGATCGAT
194 ATGACAAACTATTTAGACCAAA
* * * *
432 TGATGCGCTTTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATTTTATTGAATGC
1 TGATGCG-ATTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATCTTCTTGAATAC
* * * * * ** * * * *
497 TTTAGGGAACCAAAGTTAAAAAATAACTTGTAGTAGTTTGACCAGTTTGGATGTTCGTCCAAAAA
65 TTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAA
* * *
562 CAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATACAACGACCAAAACTCGTTTACAAAA
130 CAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAA
*
627 CGA-AAA-TATATTCAGACCAAA
195 TGACAAACTAT-TT-AGACCAAA
** * * * * * * ** *
648 TGATGCGATTTCTTGAGCAAGGAATGTTTGGAAAATTACTCGAAGGAATGAATCGCCTTGAATGC
1 TGATGCGA-TTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATCTTCTTGAATAC
* * * * * *
713 TTTAAGGAACGGAAGTTATAAAAGAAGTCGTAAAAGTTTGACACGTTCGAAAGTTCCTCCAATAA
65 TTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAA
* * *
778 GAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCCAAGACCAAAACTTGTTTACGAAA
130 CAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAA
*
843 TGACAAACTCTTTAGACC-AA
195 TGACAAACTATTTAGACCAAA
* * *** * * * * *
863 TGTTGCAATTTCTTAAGCATTGAATGTTTAGAAAAA-TGCTCAAAGGAATGGGTCGTCTTGAATA
1 TGATGCGA-TTCCCGAGCATGGAATG-TTCGAAAAATTGCTCTAAGGAATGGATCTTCTTGAATA
*** * * * * * *
927 CTTTAAGGAAGTTAAGTTATAAAAGATCTCCTCAAAGTTTGCCAAGTTCGGGAGTTCGTCCATGA
64 CTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGA
* * * * * * * *
992 ACCAAGAGTGATACAATTCTCTCATAAATAAGTTTTTAATTCAAAAAACAAAACTTGTTCACAAA
129 ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAA
*
1057 ATGGCAAACTATTTAGACCAAA
194 ATGACAAACTATTTAGACCAAA
* * *
1079 TGATGCTATTTCCCGAGCATGGAATGTTC-AGAAAATTTCTCTAAGGAATGGATCTTGTTGAATA
1 TGATGCGA-TTCCCGAGCATGGAATGTTCGA-AAAATTGCTCTAAGGAATGGATCTTCTTGAATA
* * * * * *
1143 CTTCAGGGAACCGAAGTTAGAAAATAACTCGTAAAAGTCTGACAAGTTCGAAAGTTCGTCCAAGA
64 CTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGA
* * ** *
1208 ACAAAGAGAGAAACAATTCTCAAGTAAAAAAGTTTTTAATTCAAAGTGCAAAACTTGTTTGCAAA
129 ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAA
*
1273 ATGACAAATTATTTAGACCAAA
194 ATGACAAACTATTTAGACCAAA
* * *
1295 TGATGCGATTTCCTGAGCATGGAATGTTCGAAAATTTGCTCTAAGGAATGGATCTTGTTGAATAC
1 TGATGCGA-TTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATCTTCTTGAATAC
* * * * * *
1360 TTTACGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATACAAAGA
65 TTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGT-CCAAGA
* *
1425 A-AAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTTGCAA
129 ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTG-TTTACAA
1489 AATGACAAACTATTTAGACCAAA
193 AATGACAAACTATTTAGACCAAA
* * * ** * *
1512 TGATGCGA-TCGGCCGAGCATGAAATGTTCAAAAAATTGCTCGAAAAAATGGATCGTCTTTAATA
1 TGATGCGATTC--CCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATCTTCTTGAATA
* * * ** * * *
1576 CTTTGA-GATCCAAAGTTATCGAAGAACTAGTAAAAGTTTGACAAGCTCGGAAGTTTGTCCAAGA
64 CTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGA
* *
1640 ACAAAGGGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAA
129 ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAA
* ***
1705 ATGAC--A-TATTTTGATTGAA
194 ATGACAAACTATTTAGACCAAA
* * * *
1724 TGATGCGATTTCCCGAGCATGGAATGTTTGAAAAATTGCTCTAAGGAATGGATTTTATTGAATGC
1 TGATGCGA-TTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATCTTCTTGAATAC
* * * * * * * * * * *
1789 TTTAGGGAACCAAAGTTAAAAAATAATTTGTAGAAGTTTGACTAGTTTGGAAGTTCATCCAAAAA
65 TTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAA
* * * *
1854 CAAAGAGAGAAACAATTCTCACGTAAATAACTTTCTAATACAACGACCAAAACTTGTTTACAAAA
130 CAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAA
* * * *
1919 CGACAATCTATTCAGACTAAA
195 TGACAAACTATTTAGACCAAA
** * * * * * * ** *
1940 TGATGCGATTTCTTGAGCAAGGAATGTTTGGAAAACTACTCGAAGGAATGGATCGCCTTGAATGC
1 TGATGCGA-TTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATCTTCTTGAATAC
* * * * * *
2005 TTTAAGGAA-CGAAAGTTATAAAAGAAGTTGTAGAATTTTGACACGTTCGAAAGTTCGTCCAAGA
65 TTTAAGGAACCG-AAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGA
** * *
2069 AGTAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCCAAGACCAAAACTTGTTTACGAA
129 ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAA
*
2134 ATGACAAACTCTTTAGACC-AA
194 ATGACAAACTATTTAGACCAAA
* * *** * * * * *
2155 TGTTGCAATTTCTTAAGCATTGAATGTTTAGAAAAA-TGCTCAAAGGAATGGGTCGTCTTGAATA
1 TGATGCGA-TTCCCGAGCATGGAATG-TTCGAAAAATTGCTCTAAGGAATGGATCTTCTTGAATA
*** * * * * * * *
2219 CTTTAAGGAAGTTAAGTTATAAAAGATCTCCTCAAAGTTTGCCAGGTTCGGGAGTTCGTCCATGA
64 CTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGA
* * * * * * *
2284 ACCAAGAGTGATACAATTCTCTCATAAATAAGTTTTTAATTCAAAAAACAAAACTTGTTTACAAA
129 ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAA
*
2349 ATGGCAAACTATTTAGACCAAA
194 ATGACAAACTATTTAGACCAAA
* * * *
2371 TGATGCTATTTCCCGAGCGTGGAATGTTC-AGAAAATTTCTCTAAGGAATGGATCTTGTTGAATA
1 TGATGCGA-TTCCCGAGCATGGAATGTTCGA-AAAATTGCTCTAAGGAATGGATCTTCTTGAATA
* * * * * *
2435 CTTCAGGGAACCGAAGTTAGAAAATAACTCGTAAAAGTCTGACAAGTTCGAAAGTTCGTCCAAGA
64 CTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGA
* ** *
2500 ACAAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATTCAAAGTGCAAAACTTGTTTGCAAA
129 ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAA
*
2565 ATGACAAATTATTTAGACCAAA
194 ATGACAAACTATTTAGACCAAA
*
2587 TGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATCTTGTTGAATAC
1 TGATGCGA-TTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATCTTCTTGAATAC
* * * * * * * *
2652 TTTACGGAATCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAATTTCGAAAGTTCATACAAAGA
65 TTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGT-CCAAGA
* *
2717 A-AAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTTGCAA
129 ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTG-TTTACAA
2781 AATGACAAACTATTTAGACCAAA
193 AATGACAAACTATTTAGACCAAA
* * * ** * *
2804 TGATGCGA-TCGGCCGAGCATGAAATGTTCAAAAAATTGCTCGAAAAAATGGATCGTCTTTAATA
1 TGATGCGATTC--CCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATCTTCTTGAATA
* * * ** * * *
2868 CTTTGA-GATCCAAAGTTATCGAAGAACTAGTAAAAGTTTGACAAGCTCGGAAGTTTGTCCAAGA
64 CTTTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGA
* *
2932 ACAAAGGGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAA
129 ACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAA
2997 ATGACA
194 ATGACA
3003 TATTTTGATT
Statistics
Matches: 2300, Mismatches: 444, Indels: 81
0.81 0.16 0.03
Matches are distributed among these distances:
212 65 0.03
213 269 0.12
214 14 0.01
215 394 0.17
216 1367 0.59
217 189 0.08
218 2 0.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (215 bp):
TGATGCGATTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATCTTCTTGAATACT
TTAAGGAACCGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAAC
AAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAAT
GACAAACTATTTAGACCAAA
Found at i:1105 original size:431 final size:428
Alignment explanation
Indices: 3--3008 Score: 3337
Period size: 431 Copynumber: 7.0 Consensus size: 428
1 AT
* * * *
3 TGATGCGCTTTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATTTTGTTGAATGC
1 TGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATCTTATTGAATAC
* * * *
68 TTTAAGGAACCAAAGTTAAAAAATAACTTGTAGAAGTTTGACCAG-TCTGGATGTTCGTCCAAAA
66 TTTAAGGAACCAAAGTTAAAAAATAACTCGTA-AAGTTTGACAAGTTC-GGAAGTTCGTCCAAGA
* ** * * *
132 ACAAAGAGGGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAATACCAAAACCTGTTTGCAAA
129 ACAAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAA
* * * *
197 ATGACAAACTACTTT-GACCAAATGATGCGATCTGCCGAGCATGAAATGTTC-GAAAAATTGCTT
194 ATGACAAACTA-TTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAG-AAAATTGCTC
* * * * * *
260 GAAAGAATAGATCATCTTGAATACTTTGAGGATCCGAAGTTATCAAAGAACTAGTAAAAGTTTGA
257 GAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTAGTAAAAGTTTGA
* * * * * * *
325 GAAGCTC-AGAAGTTCGTCCAAGTACAGAGGGAGAAACAATTCTCACATAAATAAGTTCTTAATT
322 CAAGTTCGA-AAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATT
* * * * *
389 CAAAGTTCAAAACTTGTTTACAAAATAACATATTTT-GATCGAT
386 CAAAGATCAAAACTTGTTTACAAAATGACAAATTTTAGA-CCAA
* * *
432 TGATGCGCTTTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATTTTATTGAATGC
1 TGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATCTTATTGAATAC
* * * * * * *
497 TTTAGGGAACCAAAGTTAAAAAATAACTTGTAGTAGTTTGACCAGTTTGGATGTTCGTCCAAAAA
66 TTTAAGGAACCAAAGTTAAAAAATAACTCGTA-AAGTTTGACAAGTTCGGAAGTTCGTCCAAGAA
* * * *
562 CAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATACAACGACCAAAACTCGTTTACAAAA
130 CAAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAA
* ** * ** *
627 CGA-AAA-TATATTCAGACCAAATGATGCGATTTCTTGAGCAAGGAATGTTTGGAAAATTACTCG
195 TGACAAACTAT-TT-AGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCG
* * * * * *
690 AAGGAATGAATCGCCTTGAATGCTTTAAGGAACGGAAGTTATAAAAGAAGTCGTAAAAGTTTGAC
258 AAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTAGTAAAAGTTTGAC
* * * * *
755 ACGTTCGAAAGTTCCTCCAATAAGAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCC
323 AAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCA
* *
820 AAGACCAAAACTTGTTTACGAAATGACAAACTCTTTAGACCAA
388 AAGATCAAAACTTGTTTACAAAATGACAAA-T-TTTAGACCAA
* * *** * * * * * *
863 TGTTGCAATTTCTTAAGCATTGAATGTTTAGAAAAA-TGCTCAAAGGAATGGGTCGTCTTGAATA
1 TGATGCGATTTCCCGAGCATGGAATG-TTCGAAAAATTGCTCTAAGGAATGGATCTTATTGAATA
*** * * * * * * *
927 CTTTAAGGAAGTTAAGTTATAAAAGATCTCCTCAAAGTTTGCCAAGTTCGGGAGTTCGTCCATGA
65 CTTTAAGGAACCAAAGTTAAAAAATAACTCGT-AAAGTTTGACAAGTTCGGAAGTTCGTCCAAGA
* * * * * * *
992 ACCAAGAGTGATACAATTCTCTCATAAATAAGTTTTTAATTCAAAAAACAAAACTTGTTCACAAA
129 ACAAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAA
* * * *
1057 ATGGCAAACTATTTAGACCAAATGATGCTATTTCCCGAGCATGGAATGTTCAGAAAATTTCTCTA
194 ATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCGA
* * * * * * * *
1122 AGGAATGGATCTTGTTGAATACTTCAGGGAACCGAAGTTAGAAAATAACTCGTAAAAGTCTGACA
259 AGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTAGTAAAAGTTTGACA
* *
1187 AGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCAAGTAAAAAAGTTTTTAATTCAA
324 AGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAA
*
1252 AG-TGCAAAACTTGTTTGCAAAATGACAAATTATTTAGACCAAA
389 AGAT-CAAAACTTGTTTACAAAATGACAAA-T-TTTAGACC-AA
* * *
1295 TGATGCGATTTCCTGAGCATGGAATGTTCGAAAATTTGCTCTAAGGAATGGATCTTGTTGAATAC
1 TGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATCTTATTGAATAC
* * * * *
1360 TTTACGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATACAAAGA
66 TTTAAGGAACCAAAGTTAAAAAATAACTCGT-AAAGTTTGACAAGTTCGGAAGTTCGT-CCAAGA
*
1425 A-AAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTTGCAA
129 ACAAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAACTTG-TTTACAA
*** * *
1489 AATGACAAACTATTTAGACCAAATGATGCGATCGGCCGAGCATGAAATGTTCAAAAAATTGCTCG
193 AATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCG
** * * * * **
1554 AAAAAATGGATCGTCTTTAATACTTTGA-GATCCAAAGTTATCGAAGAACTAGTAAAAGTTTGAC
258 AAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTAGTAAAAGTTTGAC
* * * *
1618 AAGCTCGGAAGTTTGTCCAAGAACAAAGGGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCA
323 AAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCA
* **
1683 AAGATCAAAACTTGTTTACAAAATGACATATTTT-GATTGAA
388 AAGATCAAAACTTGTTTACAAAATGACAAATTTTAGA-CCAA
* * *
1724 TGATGCGATTTCCCGAGCATGGAATGTTTGAAAAATTGCTCTAAGGAATGGATTTTATTGAATGC
1 TGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATCTTATTGAATAC
* * * * * * *
1789 TTTAGGGAACCAAAGTTAAAAAATAATTTGTAGAAGTTTGACTAGTTTGGAAGTTCATCCAAAAA
66 TTTAAGGAACCAAAGTTAAAAAATAACTCGTA-AAGTTTGACAAGTTCGGAAGTTCGTCCAAGAA
* * * * *
1854 CAAAGAGAGAAACAATTCTCACGTAAATAACTTTCTAATACAACGACCAAAACTTGTTTACAAAA
130 CAAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAA
* * * * ** * ** * *
1919 CGACAATCTATTCAGACTAAATGATGCGATTTCTTGAGCAAGGAATGTTTGGAAAACTACTCGAA
195 TGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCGAA
* * * * * *
1984 GGAATGGATCGCCTTGAATGCTTTAAGGAA-CGAAAGTTATAAAAGAAGTTGTAGAATTTTGACA
260 GGAATGGATCGTCTTGAATACTTTAAGGAACCG-AAGTTATAAAAGAACTAGTAAAAGTTTGACA
* ** *
2048 CGTTCGAAAGTTCGTCCAAGAAGTAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCCA
324 AGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAA
* *
2113 AGACCAAAACTTGTTTACGAAATGACAAACTCTTTAGACCAA
389 AGATCAAAACTTGTTTACAAAATGACAAA-T-TTTAGACCAA
* * *** * * * * * *
2155 TGTTGCAATTTCTTAAGCATTGAATGTTTAGAAAAA-TGCTCAAAGGAATGGGTCGTCTTGAATA
1 TGATGCGATTTCCCGAGCATGGAATG-TTCGAAAAATTGCTCTAAGGAATGGATCTTATTGAATA
*** * * * * * * * *
2219 CTTTAAGGAAGTTAAGTTATAAAAGATCTCCTCAAAGTTTGCCAGGTTCGGGAGTTCGTCCATGA
65 CTTTAAGGAACCAAAGTTAAAAAATAACTCGT-AAAGTTTGACAAGTTCGGAAGTTCGTCCAAGA
* * * * * *
2284 ACCAAGAGTGATACAATTCTCTCATAAATAAGTTTTTAATTCAAAAAACAAAACTTGTTTACAAA
129 ACAAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAA
* * * * *
2349 ATGGCAAACTATTTAGACCAAATGATGCTATTTCCCGAGCGTGGAATGTTCAGAAAATTTCTCTA
194 ATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCGA
* * * * * * * *
2414 AGGAATGGATCTTGTTGAATACTTCAGGGAACCGAAGTTAGAAAATAACTCGTAAAAGTCTGACA
259 AGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTAGTAAAAGTTTGACA
*
2479 AGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAAAAAGTTTTTAATTCAA
324 AGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAA
*
2544 AG-TGCAAAACTTGTTTGCAAAATGACAAATTATTTAGACCAAA
389 AGAT-CAAAACTTGTTTACAAAATGACAAA-T-TTTAGACC-AA
*
2587 TGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATCTTGTTGAATAC
1 TGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATCTTATTGAATAC
* * * * * * *
2652 TTTACGGAATCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAATTTCGAAAGTTCATACAAAGA
66 TTTAAGGAACCAAAGTTAAAAAATAACTCGT-AAAGTTTGACAAGTTCGGAAGTTCGT-CCAAGA
*
2717 A-AAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTTGCAA
129 ACAAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAACTTG-TTTACAA
*** * *
2781 AATGACAAACTATTTAGACCAAATGATGCGATCGGCCGAGCATGAAATGTTCAAAAAATTGCTCG
193 AATGACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCG
** * * * * **
2846 AAAAAATGGATCGTCTTTAATACTTTGA-GATCCAAAGTTATCGAAGAACTAGTAAAAGTTTGAC
258 AAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTAGTAAAAGTTTGAC
* * * *
2910 AAGCTCGGAAGTTTGTCCAAGAACAAAGGGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCA
323 AAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCA
*
2975 AAGATCAAAACTTGTTTACAAAATGACATATTTT
388 AAGATCAAAACTTGTTTACAAAATGACAAATTTT
3009 GATTGAATGA
Statistics
Matches: 2131, Mismatches: 410, Indels: 71
0.82 0.16 0.03
Matches are distributed among these distances:
426 1 0.00
427 4 0.00
428 87 0.04
429 622 0.29
430 11 0.01
431 692 0.32
432 537 0.25
433 177 0.08
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (428 bp):
TGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATCTTATTGAATAC
TTTAAGGAACCAAAGTTAAAAAATAACTCGTAAAGTTTGACAAGTTCGGAAGTTCGTCCAAGAAC
AAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAAT
GACAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCAGAAAATTGCTCGAAG
GAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAAAGAACTAGTAAAAGTTTGACAAG
TTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAG
ATCAAAACTTGTTTACAAAATGACAAATTTTAGACCAA
Found at i:1293 original size:647 final size:646
Alignment explanation
Indices: 3--3000 Score: 3433
Period size: 647 Copynumber: 4.6 Consensus size: 646
1 AT
* * * * * * * ****
3 TGATGCGCTTTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATTTTGTTGAATGC
1 TGATGCGATTTCCTGAGCAAGGAATGTTTGGAAAATTACTCGAAGGAATGGATCGCCTTGAATGC
* * * * * *
68 TTTAAGGAACCAAAGTTAAAAAATAACTTGTAGAAGTTTGAC-CAG-TCTGGATGTTCGTCCAAA
66 TTTAAGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAC-GTTC-GAAAGTTCATCCAAA
* * * *
131 AACAAAGAGGGAAACAATTCTCATGTAAATAAGTTTTTAATTCAAATACCAAAACCTGTTTGCAA
129 AA-AAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAA
* * *
196 AATGACAAACTACTTT-GACCAAATGATGCGATCTGCCGAGCATGAAATG-TTCGAAAAATTGCT
193 AATGACAAACT-CTTTAGACC-AATGATGCAATCTGCCAAGCATGAAATGTTTAGAAAAATTGC-
* * * * * * * *
259 TGAAAGAATAGATCATCTTGAATACTTTGAGGATCCGAAGTTATCAAAGAACTAGTAAAAGTTTG
255 TCAAAGAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGAACTACTAAAAGTTTG
* * * * *
324 AGAAGCTCAGAAGTTCGTCCAAGTA-CAGAGGGAGAAACAATTCTCACATAAATAAGTTCTTAAT
320 ACAAGCTCGGAAGTTCGTCCAAGAACCA-AGAGAGAAACAATTCTCACATAAATAAGTTTTTAAT
*** * * * * *
388 TCAAAGTTCAAAACTTGTTTACAAAAT--AACATATTTTGATCGATTGATGCGCTTTCCCGAGCA
384 TCAAAAAACAAAACTTGTTTACAAAATGAAAC-TATTTAGACCAAATGATGCGATTTCCCGAGCA
* * *
451 TGGAATGTTC-GAAAAATTGCTCTAAGGAATGGATTTTATTGAATGCTTTAGGGAACCAAAGTTA
448 TGGAATGTTCAGAAAAATTGCTCTAAGGAATGGATCTTATTGAATACTTCAGGGAACCAAAGTTA
* ** * * * * *
515 AAAAATAACTTGTAGTAGTTTGACCAGTTTGGATGTTCGTCCAAAAACAAAGAGAGAAACAATTC
513 AAAAATAACTCGTAAAAGTCTGACAAGTTCGAAAGTTCGTCCAAAAACAAAGAGAGAAACAATTC
* * *
580 TCACGTAAATAAGTTTTTAATACAACGACCAAAACTCGTTTACAAAACGA-AAATATATTCAGAC
578 TCACGTAAAAAAGTTTTTAATACAAAGACCAAAACTTGTTTACAAAACGACAAATATATTCAGAC
644 CAAA
643 CAAA
* *
648 TGATGCGATTTCTTGAGCAAGGAATGTTTGGAAAATTACTCGAAGGAATGAATCGCCTTGAATGC
1 TGATGCGATTTCCTGAGCAAGGAATGTTTGGAAAATTACTCGAAGGAATGGATCGCCTTGAATGC
* * * * *
713 TTTAAGGAACGGAAGTTATAAAAGAAGTCGTAAAAGTTTGACACGTTCGAAAGTTCCTCCAATAA
66 TTTAAGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACACGTTCGAAAGTTCATCCAA-AA
* * * *
778 GAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCCAAGACCAAAACTTGTTTACGAAA
130 AAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAA
* * *
843 TGACAAACTCTTTAGACCAATGTTGCAAT-TTCTTAAGCATTG-AATGTTTAGAAAAA-TGCTCA
195 TGACAAACTCTTTAGACCAATGATGCAATCTGC-CAAGCA-TGAAATGTTTAGAAAAATTGCTCA
* ** * * * *
905 AAGGAATGGGTCGTCTTGAATACTTTAAGGAAGTTAAGTTATAAAAGATCTCCTCAAAGTTTGCC
258 AA-GAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGAACTACTAAAAGTTTGAC
* * * * * *
970 AAGTTCGGGAGTTCGTCCATGAACCAAGAGTGATACAATTCTCTCATAAATAAGTTTTTAATTCA
322 AAGCTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCA
* *
1035 AAAAACAAAACTTGTTCACAAAATGGCAAACTATTTAGACCAAATGATGCTATTTCCCGAGCATG
387 AAAAACAAAACTTGTTTACAAAAT-G-AAACTATTTAGACCAAATGATGCGATTTCCCGAGCATG
* * * *
1100 GAATGTTCAG-AAAATTTCTCTAAGGAATGGATCTTGTTGAATACTTCAGGGAACCGAAGTTAGA
450 GAATGTTCAGAAAAATTGCTCTAAGGAATGGATCTTATTGAATACTTCAGGGAACCAAAGTTAAA
*
1164 AAATAACTCGTAAAAGTCTGACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCTC
515 AAATAACTCGTAAAAGTCTGACAAGTTCGAAAGTTCGTCCAAAAACAAAGAGAGAAACAATTCTC
* * ** * * *
1229 AAGTAAAAAAGTTTTTAATTCAAAGTGCAAAACTTGTTTGCAAAATGACAAAT-TATTTAGACCA
580 ACGTAAAAAAGTTTTTAATACAAAGACCAAAACTTGTTTACAAAACGACAAATATATTCAGACCA
1293 AA
645 AA
* * * * *** *
1295 TGATGCGATTTCCTGAGCATGGAATG-TTCGAAAATTTGCTCTAAGGAATGGATCTTGTTGAATA
1 TGATGCGATTTCCTGAGCAAGGAATGTTTGGAAAA-TTACTCGAAGGAATGGATCGCCTTGAATG
* * *
1359 CTTTACGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCATACAAAG
65 CTTTAAGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACACGTTCGAAAGTTCATCCAAA-
*
1424 AAAAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTTGCAA
129 AAAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTG-TTTGCAA
* * * * *
1489 AATGACAAACTATTTAGACCAAATGATGCGATCGGCCGAGCATGAAATGTTCA-AAAAATTGCTC
193 AATGACAAACTCTTTAGACC-AATGATGCAATCTGCCAAGCATGAAATGTTTAGAAAAATTGCTC
* * * * * ** *
1553 GAAAAAATGGATCGTCTTTAATACTTTGA-GATCCAAAGTTATCGAAGAACTAGTAAAAGTTTGA
257 -AAAGAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGAACTACTAAAAGTTTGA
* * * *
1617 CAAGCTCGGAAGTTTGTCCAAGAACAAAGGGAGAAACAATTCTCACGTAAATAAGTTTTTAATTC
321 CAAGCTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTC
* * * * ***
1682 AAAGATCAAAACTTGTTTACAAAATGACA-TATTTTGATTGAATGATGCGATTTCCCGAGCATGG
386 AAAAAACAAAACTTGTTTACAAAATGAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGG
* * * *
1746 AATGTT-TGAAAAATTGCTCTAAGGAATGGATTTTATTGAATGCTTTAGGGAACCAAAGTTAAAA
451 AATGTTCAGAAAAATTGCTCTAAGGAATGGATCTTATTGAATACTTCAGGGAACCAAAGTTAAAA
* * * * * * * *
1810 AATAATTTGTAGAAGTTTGACTAGTTTGGAAGTTCATCCAAAAACAAAGAGAGAAACAATTCTCA
516 AATAACTCGTAAAAGTCTGACAAGTTCGAAAGTTCGTCCAAAAACAAAGAGAGAAACAATTCTCA
* * * * * *
1875 CGTAAATAACTTTCTAATACAACGACCAAAACTTGTTTACAAAACGAC-AATCTATTCAGACTAA
581 CGTAAAAAAGTTTTTAATACAAAGACCAAAACTTGTTTACAAAACGACAAATATATTCAGACCAA
1939 A
646 A
* *
1940 TGATGCGATTTCTTGAGCAAGGAATGTTTGGAAAACTACTCGAAGGAATGGATCGCCTTGAATGC
1 TGATGCGATTTCCTGAGCAAGGAATGTTTGGAAAATTACTCGAAGGAATGGATCGCCTTGAATGC
* * * * * * *
2005 TTTAAGGAA-CGAAAGTTATAAAAGAAGTTGTAGAATTTTGACACGTTCGAAAGTTCGTCCAAGA
66 TTTAAGGAACCG-AAGTTAAAAAATAACTCGTAAAAGTTTGACACGTTCGAAAGTTCATCCAA-A
** * * *
2069 AGTAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCCAAGACCAAAACTTGTTTACGAA
129 AAAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAA
* * *
2134 ATGACAAACTCTTTAGACCAATGTTGCAAT-TTCTTAAGCATTG-AATGTTTAGAAAAA-TGCTC
194 ATGACAAACTCTTTAGACCAATGATGCAATCTGC-CAAGCA-TGAAATGTTTAGAAAAATTGCTC
* ** * * * *
2196 AAAGGAATGGGTCGTCTTGAATACTTTAAGGAAGTTAAGTTATAAAAGATCTCCTCAAAGTTTGC
257 AAA-GAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGAACTACTAAAAGTTTGA
* * * * * * *
2261 CAGGTTCGGGAGTTCGTCCATGAACCAAGAGTGATACAATTCTCTCATAAATAAGTTTTTAATTC
321 CAAGCTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTC
* *
2326 AAAAAACAAAACTTGTTTACAAAATGGCAAACTATTTAGACCAAATGATGCTATTTCCCGAGCGT
386 AAAAAACAAAACTTGTTTACAAAAT-G-AAACTATTTAGACCAAATGATGCGATTTCCCGAGCAT
* * * *
2391 GGAATGTTCAG-AAAATTTCTCTAAGGAATGGATCTTGTTGAATACTTCAGGGAACCGAAGTTAG
449 GGAATGTTCAGAAAAATTGCTCTAAGGAATGGATCTTATTGAATACTTCAGGGAACCAAAGTTAA
*
2455 AAAATAACTCGTAAAAGTCTGACAAGTTCGAAAGTTCGTCCAAGAACAAAGAGAGAAACAATTCT
514 AAAATAACTCGTAAAAGTCTGACAAGTTCGAAAGTTCGTCCAAAAACAAAGAGAGAAACAATTCT
* ** * * *
2520 CACGTAAAAAAGTTTTTAATTCAAAGTGCAAAACTTGTTTGCAAAATGACAAAT-TATTTAGACC
579 CACGTAAAAAAGTTTTTAATACAAAGACCAAAACTTGTTTACAAAACGACAAATATATTCAGACC
2584 AAA
644 AAA
* * * * * * *** *
2587 TGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCTAAGGAATGGATCTTGTTGAATAC
1 TGATGCGATTTCCTGAGCAAGGAATGTTTGGAAAATTACTCGAAGGAATGGATCGCCTTGAATGC
* * ** *
2652 TTTACGGAATCGAAGTTAAAAAATAACTCGTAAAAGTTTGACAATTTCGAAAGTTCATACAAAGA
66 TTTAAGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACACGTTCGAAAGTTCATCCAAA-A
*
2717 AAAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTTGCAAA
130 AAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTG-TTTGCAAA
* * * * *
2782 ATGACAAACTATTTAGACCAAATGATGCGATCGGCCGAGCATGAAATGTTCA-AAAAATTGCTCG
194 ATGACAAACTCTTTAGACC-AATGATGCAATCTGCCAAGCATGAAATGTTTAGAAAAATTGCTC-
* * * * * ** *
2846 AAAAAATGGATCGTCTTTAATACTTTGA-GATCCAAAGTTATCGAAGAACTAGTAAAAGTTTGAC
257 AAAGAATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGAACTACTAAAAGTTTGAC
* * * *
2910 AAGCTCGGAAGTTTGTCCAAGAACAAAGGGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCA
322 AAGCTCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCA
* *
2975 AAGATCAAAACTTGTTTACAAAATGA
387 AAAAACAAAACTTGTTTACAAAATGA
3001 CATATTTTGA
Statistics
Matches: 1952, Mismatches: 355, Indels: 91
0.81 0.15 0.04
Matches are distributed among these distances:
642 4 0.00
643 52 0.03
644 281 0.14
645 520 0.27
646 27 0.01
647 690 0.35
648 278 0.14
649 92 0.05
650 8 0.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (646 bp):
TGATGCGATTTCCTGAGCAAGGAATGTTTGGAAAATTACTCGAAGGAATGGATCGCCTTGAATGC
TTTAAGGAACCGAAGTTAAAAAATAACTCGTAAAAGTTTGACACGTTCGAAAGTTCATCCAAAAA
AAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAAT
GACAAACTCTTTAGACCAATGATGCAATCTGCCAAGCATGAAATGTTTAGAAAAATTGCTCAAAG
AATGGATCGTCTTGAATACTTTAAGGAACCTAAGTTATAAAAGAACTACTAAAAGTTTGACAAGC
TCGGAAGTTCGTCCAAGAACCAAGAGAGAAACAATTCTCACATAAATAAGTTTTTAATTCAAAAA
ACAAAACTTGTTTACAAAATGAAACTATTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGT
TCAGAAAAATTGCTCTAAGGAATGGATCTTATTGAATACTTCAGGGAACCAAAGTTAAAAAATAA
CTCGTAAAAGTCTGACAAGTTCGAAAGTTCGTCCAAAAACAAAGAGAGAAACAATTCTCACGTAA
AAAAGTTTTTAATACAAAGACCAAAACTTGTTTACAAAACGACAAATATATTCAGACCAAA
Done.