Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012974.1 Kokia drynarioides strain JFW-HI SEQ_127992, 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: 8627
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Warning! 50 characters in sequence are not A, C, G, or T
Found at i:403 original size:216 final size:215
Alignment explanation
Indices: 3--500 Score: 542
Period size: 216 Copynumber: 2.3 Consensus size: 215
1 AC
* ** * ** *
3 AAATAAGTTTTTAATTCTAAGACCGAAACGTGTTTAGGAAATGACATGCTATTTAGACCAAATGA
1 AAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATGACA-ACTATTTAGACCAAATGA
* * * * *
68 TGCAGTTTCCCGAGCATGGAATGTTCGGAAAAATGCTCAAAGGAATGGGTCATCTTGAATACTTT
65 TGCGGTTTCCCGAGAATGGAATGTTCGGAAAAATGCTCAAAGGAATGGATCATCTCGAATAATTT
* * * * * * * * *
133 AAGGAAGTTAAGCTATAAAAGATCTCCTTAAAGTTGGACAAGTTCGGGAGTTCGTCCATGGACCA
130 AAGGAACTGAAGCTATAAAAGAACTACTAAAAGTTGGACAAGCTCGGAAGTTCGTCCA-AGAACA
* *
198 AGAGT-AG-TACAATTCTCTCGT
194 A-AGTGAGAAACAATTCTCACGT
*
219 AAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATGACAAACTATTTCGACCAAATGA
1 AAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATGAC-AACTATTTAGACCAAATGA
* * * *
284 TGCGGTTTCCTGAGAATGGATTGTTC-GAAAAATTGCTCGAAA-TAATGGATCGTCTCGAATAAT
65 TGCGGTTTCCCGAGAATGGAATGTTCGGAAAAA-TGCTC-AAAGGAATGGATCATCTCGAATAAT
* * * * * * * *
347 TTGAGGATCTGAAGTTATCAAGGAACTAGTAAAAGTTTGACAAGCTCGTAAGTTCGTCCAAGAAC
128 TTAAGGAACTGAAGCTATAAAAGAACTACTAAAAGTTGGACAAGCTCGGAAGTTCGTCCAAGAAC
412 AAAGTGAGAAACAATTCTCACGT
193 AAAGTGAGAAACAATTCTCACGT
* *
435 AAATAAGTTTTGAATTCAAAGA-TCAAAACTTGTTTACAAAATGAC-A-TATTTAGATCAAATGA
1 AAATAAGTTTTTAATTCAAAGACT-AAAACTTGTTTACAAAATGACAACTATTTAGACCAAATGA
497 TGCG
65 TGCG
501 NNNNNNNNNN
Statistics
Matches: 237, Mismatches: 39, Indels: 15
0.81 0.13 0.05
Matches are distributed among these distances:
213 18 0.08
214 4 0.02
215 14 0.06
216 197 0.83
217 4 0.02
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (215 bp):
AAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATGACAACTATTTAGACCAAATGAT
GCGGTTTCCCGAGAATGGAATGTTCGGAAAAATGCTCAAAGGAATGGATCATCTCGAATAATTTA
AGGAACTGAAGCTATAAAAGAACTACTAAAAGTTGGACAAGCTCGGAAGTTCGTCCAAGAACAAA
GTGAGAAACAATTCTCACGT
Found at i:1215 original size:216 final size:217
Alignment explanation
Indices: 569--8627 Score: 7670
Period size: 216 Copynumber: 37.5 Consensus size: 217
559 CAAGAGTAGT
* *
569 ACAATTCTCTCGTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATGACAAACTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
** * * ** *
634 TCCGACCAAATGATGCGATTTCCCGAGAATGGATTG-TTCGAAAAATTGCTCGAAATAATGGATC
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGATT
* * * * * * * *
698 ATCTCGAATACTTT-AGGATCTGAAGTTATCAAGGAACTAGTAAAAGTTTGACAAGCTCGTAAGT
131 GTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGT
762 TCGTCCAAGAACAAAGAGAGAA
196 TCGTCCAAGAACAAAGAGAGAA
* *
784 ACAATTCTCACGTAAATAAGTTTTGAATTCAAAGATCAAAACTTGTTTACAAAATGAC--A-TAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * *
846 TTAGAACAAATGATGCGATTTCCCGAGCATGGAATG-TTCGAAAAATTGCTCTAAGGAATGAATT
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGATT
* * * * ** * * * * ** * *
910 TTGTTGAATGCTTTAGGGAACCAAAGTAAAAAAATAACTCGGAAAAGTTTGACCGGTTTGGAAGT
131 GTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGT
* *
975 TTGTCCAAGAAGAAAGAGAGAA
196 TCGTCCAAGAACAAAGAGAGAA
* * *
997 ACAATTCTCACGTAAATAAGTTTTTAATTCAATGAACAAAACTTGTTTACAAAATGACAATCTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * ** * * * * * *
1062 TTTGACCAAATGATACGATTTCTTGAGCAAGGAATGTTTGGAAAACTT-TTCGACGTAATGGATT
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGATT
* * * * * * * *
1126 GCCTTGAATGCTGTAAGGAACAGAAGGTATAAAAGAAGTCGTAAAAGTTTGACACGTTCAAAAGT
131 GTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGT
* **
1191 TCTTCCAAGAAGTAAGAGAGAA
196 TCGTCCAAGAACAAAGAGAGAA
** * ** *
1213 ACAATTCTCACACAAATAAGTTTTTAATTCCAAGACCAAAACTTGTTTAGGAAATGACATACTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * * * *
1278 TTAGACCAAATGATGC-AGTTTCTCGAGCAAGGAATG-TTCAGAAAAA-TGGTCAAAGGAATGGG
66 TTAGACCAAATGATGCGA-TTTCCCGAGCATGGAATGTTTC-GAAAAATTGCTCGAAGGAATGGA
* * * * * * * * **
1340 TCGTCTTGAATACTTTAAGGAAGTTAAGCTATAAAAGATCTCCTCAAAGTTGGACAAGTTCGGGA
129 TTGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAA
* * * * *
1405 GTTCGTCCATGGACCAAGAGTGAT
194 GTTCGTCCAAGAACAAAGAGAGAA
* *
1429 ACAATTCTCTCGTAAATAAGTTTTTAATTCAAAGACTAAAACTTGTTTACAAAATGACAAACTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * *
1494 TTAGACCAAATGATGTGATTTCCTGAGCATGGAATG-TTC-AGAAAATTGCTCTAAGGAATGGAT
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGA-AAAATTGCTCGAAGGAATGGAT
* * * * * * *
1557 CT-TGTTGAATACTTTAGGGAACCGAAGTTA-AAAATAACTCGTAAAAGCTTGACAACTTCAAAA
130 -TGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAA
1620 GTTCGTCCAAGAACAAAGAGAGAA
194 GTTCGTCCAAGAACAAAGAGAGAA
* * *
1644 ACAATTCTCACGTAAATAATTTTTTAATTCAAAGAGCAAAACTTGTTTGCAAAATGACAAA-TCA
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACT-A
* * *
1708 TTTAGACCAAATGATACGATTT-CCGAGCATGGAATG-TTCGAAAAATTGCTCGAAAGAACGGAT
65 TTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGAT
** * * * * * * * * *
1771 CATCTCGAATACTCTGAGG-ATTCAAAGTTATCAAAGAACTAGTAAAAGTTTGACAAGCTCGTAA
130 TGTCTTGAATACTTTAAGGAACT-GAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAA
*
1835 GTTCGTCCAAGAATAAAGAGAGAA
194 GTTCGTCCAAGAACAAAGAGAGAA
* *
1859 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGATCAGAACTTGTTTAC-AAATGAC--A-TAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * * * *
1920 TTAGATCAAATGATGCAATTTCCCGAGCATGGAATG-TTCAAAAAATTGCTCTAAGGAATAGATT
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGATT
* * * * * ** * * * * * *
1984 TTGTTGAATGCCTTAGGGAACCAAAGTTAAAAAATAATTCGTAAAAGTTTGACCAGTTTGGAAGT
131 GTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGT
* *
2049 TTGTCCAAGAAGAAAGAGAGAA
196 TCGTCCAAGAACAAAGAGAGAA
* * *
2071 ACAATTCTCACGTAAATAAGTTTTTAATTCAACGACCAAAACTTGTTCACAAAATGACAATCTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* ** * * * *
2136 TTTGACCAAATGATGCGATTTCTTGAGCAGGGAATGTTT-GGAAAACTGCTCGAAGGAATGGATC
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGATT
* * * * * *
2200 GCCTTGAATGCTTTAAGGAACAGAAGTTATAAAATAAGTCGTAAAAGTTTGACACGTTCGAAAGT
131 GTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGT
* *
2265 TCTTCCAAGAAGAAAGAGAGAA
196 TCGTCCAAGAACAAAGAGAGAA
* ** * * * ** * *
2287 ACTATTCTCACACAAACAAGGTTTTAATTCCAAGACCAAAACTTGTTTAGGAAATAACATACTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * * * * *
2352 TTAGACCAAATGATACAATTTCCCGAGCAAGGAATG-TTCAGAAAAA-TGGTCAAAGGAATGGGT
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTC-GAAAAATTGCTCGAAGGAATGGAT
* * * * * * * * **
2415 CGTCTTGAATACTTTAAGGAAGTTAAGCTATAAAAGATCTCCTCAAAGTTGGACAAGTTCGGGAG
130 TGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAG
* * * * *
2480 TTCGTCCATGGACCAAGAGTGAT
195 TTCGTCCAAGAACAAAGAGAGAA
* ** * *
2503 ACAATTCTCTCGTAAATAAGTTTTTAAAGCAAAGTCTAAAACTTGTTTACAAAATGACAAACTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * *
2568 TTAAACCAAATGATGCGATTTCCCGAGCATGGAATG-TTC-AGAAATTTGCTCTAAGGAATGGAT
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGA-AAAATTGCTCGAAGGAATGGAT
* * * * *
2631 CT-TGTTGAATACTTTAAGGAACCGATGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTCGAAA
130 -TGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAA
* *
2695 GTTTGTACAAAGAA-AAAGAGAGAA
194 GTTCGT-CCAAGAACAAAGAGAGAA
*
2719 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTATACAAAATGACAAACTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * * * * *
2784 TTAGACCAAATGAAGCGATTTCACAATG-ATGGAAT-ATTCAAAAAATTGCTCAAAGGAATGGAT
66 TTAGACCAAATGATGCGATTTCCCGA-GCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGAT
* * ** * * *
2847 CT-TGTTGAATATTTTTGGGAATTGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGCTT-GAA
130 -TGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAG-TTCGAA
* *
2910 AGTTCGTACAA-AGACCAAGAGAGAA
193 AGTTCGTCCAAGA-ACAAAGAGAGAA
* * * * * *
2935 ACAATTATCATGCAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACACACTAA
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * * * * * * * *
3000 TTAGGCCAAATGATGCAATTTGCCGAGCATCGAATG-TTCGGAAAATTGCTGGATGCAATGGATC
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGATT
* * * *
3064 GTCTTGAATACTTTAAGGATCCGAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGTTCAAAAGT
131 GTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGT
*
3129 TCCTCCAAGAACAAAGAGAG-A
196 TCGTCCAAGAACAAAGAGAGAA
* * * ***** * * * *
3150 A-AGTTCCTCCAAG-AACAAAGAGAGAAACAATTCTCACGTA--AATAAGTTTTTAATTCAAAGA
1 ACAATT-CT-CACGTAA-ATA-AG-TTTTTAATTC-AAAG-ACCAA-AA-CTTGT--TT-----A
* * *
3211 CCAAAACTTGTATACAAAATGACAAACTATTTAGACCAAATGATGCGATTTCCC-ATGGATGGAA
50 -CAAAA--TG---AC--AA--AC-TA-T-TTA-GACCAAATGATGCGATTTCCCGA-GCATGGAA
* * * * * * *
3275 TG-TTCGAAAAATTGCTC-AGAGGAGTGTATTTTGTTGATTACTTTATGGAATTGAAGTTGA-AA
100 TGTTTCGAAAAATTGCTCGA-AGGAATGGATTGTCTTGAATACTTTAAGGAACTGAAGTT-ATAA
* * *
3337 AATAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTACAA-AGAGAAAGAGAGAA
163 AAGAACTCGTAAAAGTTTGACAAGTTCGAAAGTTCGTCCAAGA-ACAAAGAGAGAA
* * *
3392 ACAATTCTCACGTAAATAAGTTTTTAATTCAAACACCAAAACTTATTTGCAAAATGACAAACTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* ** * * * * * *
3457 TTCGAAAAAATGATGCGATTTTCCGAGAATGGAAT-ATTCAAAAAATTGCTCGAAGCAATCGA--
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGATT
* * * * *
3519 --CATGAATACTTTAAGGATCCGAAGTTATAAAAGAACTAGTAAAAGTTTGACAGGTTCGAAAGT
131 GTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGT
*
3582 TCATCCAAGAACAAAGAGAGAA
196 TCGTCCAAGAACAAAGAGAGAA
* * *
3604 ACAATTCTTACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTATACAAAATGAAAAACTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
** * * * * * * *
3669 TTAGACCAAATGAAACGATTTCACAATG-ATGAAAT-ATTC-AGATAATTGCACAAAGGAATGGA
66 TTAGACCAAATGATGCGATTTCCCGA-GCATGGAATGTTTCGA-AAAATTGCTCGAAGGAATGGA
* * * * * * *
3731 TCT-TGTTGAATATTTTAGGGAATTGAAGTTAAAAAATAACTCGTAAAAGTTTGACATGTTCGAA
129 T-TGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAA
*
3795 AGTTCGT-AAAGAGACAAAGAGAGAA
193 AGTTCGTCCAAGA-ACAAAGAGAGAA
* * * * * *
3820 ACAATTATCAAGTAAATAAGTTTTTAATTCAAAGATCAAAACTTGTTTGCAAAATGAGAAACTAA
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * * * * * *
3885 TTAGGCCAAATGATGCAATTTACCGAGCATGGAAT-ATTCGAAAAATTACTCGAAGCAAT-CA--
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGATT
* * * *
3946 -TCTTGAATACTTTAAGGATCCGAAGTTATAAAAGAACTAGTAAAAGTTTGACAGGTTCGAAAGT
131 GTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGT
*
4010 TTGTCCAAGAACAAAGAGAGAA
196 TCGTCCAAGAACAAAGAGAGAA
*
4032 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTATACAAAATGACAAACTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * * * * *
4097 TTAGACCAAATGGA-GCGATTTCACAAGGATGGAATATTT-GGAAAATTGCTCAAAGGAATGGAT
66 TTAGACCAAAT-GATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGAT
* * * * * * *
4160 CT-TGTTGAATATTTTAGGGAATTGAAGTTAAAAAATAATTCGTAAAAGTTTGACAAGTTCGAAA
130 -TGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAA
*
4224 GTTCGTACAATG-ACAAAGAGAGAA
194 GTTCGTCCAA-GAACAAAGAGAGAA
* * * *
4248 ACAATTATCATGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTAA
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * * * * * * * * *
4313 TTAGGCCAATTGATGCAATTTGCCGAGCATGGAAT-ATTCGGAAAATTGCTGGATGCAATGGATC
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGATT
* * * *
4377 GTCTTAAATACTTTAAGGATA-TGTAGTTATAAAAGAACTAGTAAAAGTTTGACAAGTTTGAAAG
131 GTCTTGAATACTTTAAGGA-ACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAG
*
4441 TTCCTCCAAGAACAAAGAGAGAA
195 TTCGTCCAAGAACAAAGAGAGAA
* *
4464 ACAATTCTCACGTAAATAATTTTTTAATTCAAAGACCAAAACTTGTATACAAAATGACAAACTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * * *
4529 TTAGGCCAAATGATGCGAATTCCCGAGCATGGAATG-TTCGAAAAATTACT-GAAAAGAATGGAT
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCG-AAGGAATGGAT
* * * * * * * * **
4592 CGTCTTGAATACGTTAAGGATCCGAAGTTATCAAAGAACTAGTAAAAGTTTGAGAAGCTCGGTAG
130 TGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAG
4657 TTCGTCCAAGAACAAAGAGAGAA
195 TTCGTCCAAGAACAAAGAGAGAA
* * *
4680 ACAATTCTCACGTAAATAAAATTTTTAATTCAAAGATCAAAACTTATTTACAAAATGAC--A-TA
1 ACAATTCTCACGTAAAT-AAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTA
* * * * *
4742 TTTTGATCAAATGATGCGATTTCCTGAGCATGGAATG-TTCAAAAAATTGCTCTAAGGAATGGAT
65 TTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGAT
* * * * * * * * * * * *
4806 TTTGTCGAATGCTTTAGGGAAAC-AAAGTTA-AAAAAAACACGTAAATGTTTGACCAGTTTGGAA
130 TGTCTTGAATACTTTAAGG-AACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAA
* *
4869 GTTCATCCAAAAACAAAGAGAGAA
194 GTTCGTCCAAGAACAAAGAGAGAA
* * * *
4893 ACAATTCTCACGTAAATAAGTTTTTAATTCAACGACCAAAACTTGTTTACAAAACGATAATCTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* ** * * * * * * *
4958 TCAGACCAAATGATGCGATTTCTTGAGCAAGGAATGTCT-GGAAAACTACTCCAAGGAATGGATC
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGATT
* * * * *
5022 GCCTTGAATGCTTTAAGGAAC-GAAAGTTATAAAAGAAGTCGTAAAAGTTTGACACGTTCGAAAT
131 GTCTTGAATACTTTAAGGAACTG-AAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAG
* *
5086 TTCGCCCAAGAAGAAAGAGAGAA
195 TTCGTCCAAGAACAAAGAGAGAA
* * *
5109 ACAATTCTCACGTAAATAAGTTTTTAATTCCAAGACCAAAACTTGTTTATAAAATGACAAACTCT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* ** ** * * ** * *
5174 TTAGTCCAAAAAATGAAATTTCTCAAGCATGGAATG-TTC-AGAAAAGCGCTCAAAGGAATGGGT
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGA-AAAATTGCTCGAAGGAATGGAT
* * * * * * * * * **
5237 CGTCCTGAATATTTTAAGGAAGTTAAGTTATAAAAGATCTCCTCAAAGATTGACAAGTTCGGGAG
130 TGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAG
* * * * **
5302 TTCGTCCATGAACTAACAGTGGT
195 TTCGTCCAAGAACAAAGAGAGAA
* ** * *
5325 ACAATTCTCTCAAAAATAAGTTTTTAATTCAAAGACCAAAACATGTTTACAAAATGATAAACTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
** * *
5390 TTAGAGTAAATGATGTGATTTCCCGAGCATGGAATG-TTCGAAAAATTGCTCTAAGGAATGGATC
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGAT-
* ** ** * *
5454 T-TGTTGAATACTTTCGGGAACCCAAGTTGA-AAAATAACTCGTAAAATTTTGACAAGTTCGAAA
130 TGTCTTGAATACTTTAAGGAACTGAAGTT-ATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAA
* *
5517 GTTCATACAA-AGACAAAGAGAGAA
194 GTTCGTCCAAGA-ACAAAGAGAGAA
*
5541 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * * * *
5606 TTATACCAATTGATGCGATCTCCCGAGCATGGAATG-TTCGAAAAATTGCTCTAACGAATGGATC
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGAT-
* * * * * * * * * * *
5670 T-TGTTGAATGCTTTAGGGAAAC-AAAGTTA-AAAAAAACGCGTAAATGTTCGACCAGTTTGGAA
130 TGTCTTGAATACTTTAAGG-AACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAA
* * *
5732 GTTCATCAAAAAACAAAGAGAGAA
194 GTTCGTCCAAGAACAAAGAGAGAA
* * * *
5756 ACAATTCTCACGTAAATATGTTTTTAATTCAACGACCAAAACTTGTTTACAAAACGACAATCTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * * * * *
5821 TCAGACC-AA--AT--GA--T---GAGC-----CTG----G-AAAACTACTCCAAGGAATGGATC
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGATT
* * * * * *
5866 GCCTTGACTGCTTTAAGGAAC-GAAAGTTATAAAAGAAGTCGTAAAAGTTTGACACGTTCGAAAT
131 GTCTTGAATACTTTAAGGAACTG-AAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAG
* * *
5930 TTTGCCCAAGAAAAAAGAGAGAA
195 TTCGTCCAAGAACAAAGAGAGAA
* * * *
5953 ACAATTCTCACGTAAATAAGTTTTTAATTCCACGACCAAAACTTGTTTACGAAATGACAAACTCT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * * * * *
6018 TTAGACCAAATAATGCAATTTCTCAAGCATGGAATG-TTCAGAAAAA-TGCTCAAAGGAATGGGT
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTC-GAAAAATTGCTCGAAGGAATGGAT
* * * * * * * * * **
6081 CGTCTAGAATATTTTAAGGAAGTTAAGTTATAAAAGATCTCCTCAAAGATTGACAAGTTCGGGAG
130 TGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAG
* * * * *
6146 TTCGTCCATGAACCAACAGTGAT
195 TTCGTCCAAGAACAAAGAGAGAA
* ** * * *
6169 ACAATTCTCTCAAAAATAAGTTTTTAATTCAAAGACAAAAACATGTTTACAAAATGATAAACTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* *
6234 TTAGAGCAAATGATGCGATTTCCCGAGCATGGAATG-TTCGAAAAATTGCTCTAAGGAATGGATC
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGAT-
* ** * * * * * * *
6298 T-TGTTGAATACTTTCGGGAACCGAAGTTAAAAAATAACTCGTAAAATTTTGCCAAGTTCAAAAT
130 TGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAG
*
6362 TTCGTACATAG-ACAAAGAGAGAA
195 TTCGTCCA-AGAACAAAGAGAGAA
* *
6385 ACAATTCTCAAGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * * *
6450 TTAGACCAATTGATGCGATCTT-CCGAGCATGGAATG-TTCGAAAAATTGCTCTAACGAAAGGAT
66 TTAGACCAAATGATGCGAT-TTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGAT
* * * * * *
6513 CT-TGTTGAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGTAAAATTTTGACAAGTTCGAAA
130 -TGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAA
*
6577 GTTCGTACAA-AGACAAAGAGAGAA
194 GTTCGTCCAAGA-ACAAAGAGAGAA
* * * *
6601 ACAATTCTCATGTAATTAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATGACAAACTAA
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * ** * * * * *
6666 TTAGGCCAAATGATGCGATTTACTAAGCATGAAAT-ATTCGGAAAATTGCTCGAAGCAATGGATC
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGATT
* * * ** * * *
6730 GTCATGAATACTTTAAAGATCCAAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGTTTGGAAGT
131 GTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGT
* *
6795 TCATCTAAGAACAAAGAGAGAA
196 TCGTCCAAGAACAAAGAGAGAA
* * * *
6817 ACAATTCCCACGTAAATAAGTTTTTAATTCAAAGACGAAAACTTGTATACAAAATGAAAAACTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * * * * *
6882 TTAGACCAAAATGACGCTATTTCCCAAGGATGGAATG-TTCGAAAATTTGCTCAAAGGAATGGAT
66 TTAGACC-AAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGAT
* * * * * * * *
6946 CT-TGTTGATTACTTTAGGGAACTGAAGTAAAAAAATAACTCGTAAAAGTTTGACAAGTTTGGAA
130 -TGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAA
7010 GTTCGTCCAAGAACAAAGAGAGAA
194 GTTCGTCCAAGAACAAAGAGAGAA
* *
7034 ACAATTCTCACGTAAATAAGTTTTTAATTCAACGACCAAAACTTGTTTGCAAAATGGA-AAACTA
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAAT-GACAAACTA
* * * * *
7098 TTTATACCAAATGATGCGAATTGCCGAGCATGG-A-GTATTCGAAATATTGCT-GAAAGGAACGG
65 TTTAGACCAAATGATGCGATTTCCCGAGCATGGAATGT-TTCGAAAAATTGCTCG-AAGGAATGG
* * * * * *
7160 ATCGTCTTGAATACTTTCAGGATCCGAAGTTATAAAAGAACTTGTAAAAGTTTGAGAAGTTCGAA
128 ATTGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAA
* * * *
7225 AGTTCTTCTAAGAACAAAGACATAA
193 AGTTCGTCCAAGAACAAAGAGAGAA
* * **
7250 ACAATTCTCACGTAAATAAGTGTTGAATTCAAAGAAAAAAACTTGTTTACAAAATGACAAACTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * * * * *
7315 TTAGACCAAATGATGAGATTTCCCAAGTACGGAATG-TTCGCAAAATTGCTCTAA--AA---A--
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGATT
* * * *
7372 ----T---TACTTTAGGGAACTGAAGTTAAAAAATAACTCGTAAAAGTTTGACAAGTTCGAAACT
131 GTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGT
* *
7430 TTGTCCAAGAACAAAGAAAGAA
196 TCGTCCAAGAACAAAGAGAGAA
* ** * * * *
7452 ACAATTCTCACTTAAATAAGTTTTTAATTCAAAGTGCAAAACTTCTTTGCAAAATGACATATTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * * * *
7517 TTGGACCAAATGATGCGTTTTCCCGAGCATGGAATG-TTCAAAAAATTGCTCTAAGGAATGCATC
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGAT-
* * * * *
7581 T-TGTTGATTACTTTAGGGAACTGAAG--A-AAAATAACTCGTAAAAGTTTGACAAATTCGAAAG
130 TGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAG
* *
7642 TTCATACAA-AGACAAAGAGAGAA
195 TTCGTCCAAGA-ACAAAGAGAGAA
* * *
7665 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTAGTTTGCAAAATGACAAACTAA
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * * * * * * *
7730 TTAGGCCAAATGATTCAATTTGCCGAGCATGGAAT-ATTC-AGAAAATTGCTCGATGCAAAGGAT
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGA-AAAATTGCTCGAAGGAATGGAT
* * * *
7793 TGTCTTGAATACTTTAAGGATCCGAAATTATAAAAGAACTAGTAAAAGTTTGACAAGTTCGAAAG
130 TGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAG
*
7858 TTCCTCCAAGAACAAAGAGAGAA
195 TTCGTCCAAGAACAAAGAGAGAA
* *
7881 ACAATTCTTACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTATACAAAATGACAAACTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * * * * *
7946 TTAGACCAAATGATGCGATTTCTCAAGGATGGAATG-TTCGAAAAATTGCTCAAAGGAGTGTATT
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGATT
* * * * * * * *
8010 TTGTTGATTACTTTATGGAACTGAAGTTAAAAAATATCTCGTAAAAGTTTAACAAGTTCGAAAGT
131 GTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGT
* *
8075 TAGTCCAAGAACGAAGAGAGAA
196 TCGTCCAAGAACAAAGAGAGAA
* *** * * * * *
8097 ACAATTCTTACGTAAATAAGTTTTTAATTCAAAGTGTAAAACTTCTTTGCAAAACGAAAAATTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* *
8162 TTAGACCAAATGATGCGATTTCCCGAGCATTGG-ATG-TTCGGAAAATTGCTCTAAGGAATGGAT
66 TTAGACCAAATGATGCGATTTCCCGAGCA-TGGAATGTTTCGAAAAATTGCTCGAAGGAATGGAT
* * * * * * * *
8225 CT-TGTTAAATACTTTAGGGAACCGAAGTTAAAAAATAACTCGTAACAGTTTGACAAGTTCGGAA
130 -TGTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAA
* *
8289 GTTCGTACAA-AGGCAAAGAGAGAA
194 GTTCGTCCAAGA-ACAAAGAGAGAA
* *
8313 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCTAAACTTGTTTGCAAAATGACAAACTAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* * * * *
8378 TTAGACCAATTGATGCGATCTCTCGAGCATGGAATG-TTCAAAAAATTGCTCTAAGGAATGGATC
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGAT-
* * *** * * *
8442 T-TGTTGAATACTTT-AGAAAAAAAAGTTAAAAAAATAACTCGTAAAATTTTGACAAGTTCGAAA
130 TGTCTTGAATACTTTAAGGAACTGAAGTT-ATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAA
*
8505 GTTCGTACAA-AGACAAAGAGAGAA
194 GTTCGTCCAAGA-ACAAAGAGAGAA
* *
8529 ACAATTCTCACGTAGATAAGTTTTTAATTCAAAGATCAAAACTTGTTTACAAAATGAC--A-TAT
1 ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
* *
8591 TTTGATCAAATGATGCGATTTCCCGAGCATGGAATGT
66 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGT
Statistics
Matches: 6410, Mismatches: 1230, Indels: 409
0.80 0.15 0.05
Matches are distributed among these distances:
195 3 0.00
196 37 0.01
197 107 0.02
198 2 0.00
200 4 0.00
202 167 0.03
204 3 0.00
205 5 0.00
207 4 0.00
208 1 0.00
210 2 0.00
211 23 0.00
212 597 0.09
213 401 0.06
214 150 0.02
215 517 0.08
216 3916 0.61
217 272 0.04
218 11 0.00
219 5 0.00
220 6 0.00
222 4 0.00
224 2 0.00
227 2 0.00
228 5 0.00
229 5 0.00
230 2 0.00
233 2 0.00
235 3 0.00
237 6 0.00
238 4 0.00
239 7 0.00
240 7 0.00
241 118 0.02
242 7 0.00
243 3 0.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (217 bp):
ACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTACAAAATGACAAACTAT
TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTTCGAAAAATTGCTCGAAGGAATGGATT
GTCTTGAATACTTTAAGGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCGAAAGT
TCGTCCAAGAACAAAGAGAGAA
Found at i:3152 original size:25 final size:25
Alignment explanation
Indices: 3124--3176 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
3114 GACAAGTTCA
3124 AAAGTTCCTCCAAGAACAAAGAGAG
1 AAAGTTCCTCCAAGAACAAAGAGAG
3149 AAAGTTCCTCCAAGAACAAAGAGAG
1 AAAGTTCCTCCAAGAACAAAGAGAG
3174 AAA
1 AAA
3177 CAATTCTCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.51, C:0.19, G:0.19, T:0.11
Consensus pattern (25 bp):
AAAGTTCCTCCAAGAACAAAGAGAG
Found at i:3351 original size:241 final size:241
Alignment explanation
Indices: 2926--3371 Score: 594
Period size: 241 Copynumber: 1.9 Consensus size: 241
2916 TACAAAGACC
* * *
2926 AAGAGAGAAACAATTATCATGCAAATAAGTTTTTAATTCAAAGACCAAAACTTGTTTGCAAAATG
1 AAGAGAGAAACAATTATCACGCAAATAAGTTTTTAATTCAAAGACCAAAACTTGTATACAAAATG
* * * * *
2991 ACACACTAATTAGGCCAAATGATGCAATTTGCCGAGCATCGAATGTTCGGAAAATTGCTGGATGC
66 ACAAACTAATTAGACCAAATGATGCAATTTGCCCAGCATCGAATGTTCGAAAAATTGCTAGATGC
3056 AATGGATCGTCTTGAATACTTTAAGGATCCGAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGT
131 AATGGATCGTCTTGAATACTTTAAGGATCCGAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGT
3121 TCAAAAGTTCCTCCAAGAACAAAGAGAGAAAGTTCCTCCAAGAACA
196 TCAAAAGTTCCTCCAAGAACAAAGAGAGAAAGTTCCTCCAAGAACA
* *
3167 AAGAGAGAAACAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAACTTGTATACAAAATG
1 AAGAGAGAAACAATTATCACGCAAATAAGTTTTTAATTCAAAGACCAAAACTTGTATACAAAATG
* * * *
3232 ACAAACTATTTAGACCAAATGATGCGATTT-CCCATGGATGGAATGTTCGAAAAATTGCTCAGA-
66 ACAAACTAATTAGACCAAATGATGCAATTTGCCCA-GCATCGAATGTTCGAAAAATTGCT-AGAT
* * * ** * * * * * *
3295 GGAGTGTATTTTGTTGATTACTTTATGGAAT-TGAAGTTGA-AAAATAACTCGTAAAAGTTTGAC
129 GCAATGGATCGTCTTGAATACTTTAAGG-ATCCGAAGTT-ATAAAAGAACTAGTAAAAGTTTGAC
*
3358 AAGTTCGAAAGTTC
192 AAGTTCAAAAGTTC
3372 GTACAAAGAG
Statistics
Matches: 175, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
240 3 0.02
241 167 0.95
242 5 0.03
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (241 bp):
AAGAGAGAAACAATTATCACGCAAATAAGTTTTTAATTCAAAGACCAAAACTTGTATACAAAATG
ACAAACTAATTAGACCAAATGATGCAATTTGCCCAGCATCGAATGTTCGAAAAATTGCTAGATGC
AATGGATCGTCTTGAATACTTTAAGGATCCGAAGTTATAAAAGAACTAGTAAAAGTTTGACAAGT
TCAAAAGTTCCTCCAAGAACAAAGAGAGAAAGTTCCTCCAAGAACA
Done.