Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010709.1 Kokia drynarioides strain JFW-HI SEQ_125659, 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: 19034
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:635 original size:21 final size:18
Alignment explanation
Indices: 609--659 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 18
599 CAAAAAAATA
609 GAAAAAGAAAAAGAGCATGAG
1 GAAAAAGAAAAAGAG-A-G-G
*
630 GGAAAAGAAAAAGAGAGG
1 GAAAAAGAAAAAGAGAGG
648 GAAAAAGAAAAA
1 GAAAAAGAAAAA
660 ATAAAAGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 12 0.43
19 1 0.04
20 1 0.04
21 14 0.50
ACGTcount: A:0.67, C:0.02, G:0.29, T:0.02
Consensus pattern (18 bp):
GAAAAAGAAAAAGAGAGG
Found at i:1557 original size:46 final size:46
Alignment explanation
Indices: 1505--1594 Score: 171
Period size: 46 Copynumber: 2.0 Consensus size: 46
1495 ATTGTTTGCA
*
1505 AATTTTAAGAAATGTTCTTTCTGCACTGATAAATTGGTATTCTTCG
1 AATTTTAAGAAATGTCCTTTCTGCACTGATAAATTGGTATTCTTCG
1551 AATTTTAAGAAATGTCCTTTCTGCACTGATAAATTGGTATTCTT
1 AATTTTAAGAAATGTCCTTTCTGCACTGATAAATTGGTATTCTT
1595 AGGTTTCGTC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.43
Consensus pattern (46 bp):
AATTTTAAGAAATGTCCTTTCTGCACTGATAAATTGGTATTCTTCG
Found at i:4037 original size:48 final size:48
Alignment explanation
Indices: 3805--4022 Score: 328
Period size: 48 Copynumber: 4.5 Consensus size: 48
3795 ATTAAGTGTT
* * * *
3805 TTTTTTTTGTTAAATGCATCTTTGTTTAATAATCTGCATCATTAAGTG
1 TTTTGTTTGTTAAATGCATCTTTGTTTAATAATATGCATTATTAACTG
* * *
3853 CTTTGTTTGTTAAATGAATCTTTGTTTAATAATCTGCATTATTAACTG
1 TTTTGTTTGTTAAATGCATCTTTGTTTAATAATATGCATTATTAACTG
* *
3901 TTTTGTTTGTTAAATGCATCTTTTTTTAGTAATATGCATTATTAACTG
1 TTTTGTTTGTTAAATGCATCTTTGTTTAATAATATGCATTATTAACTG
*
3949 TTTTGTTTGTTAAATGCATCTTTGTTTAGTAATATGCATTATTAACTG
1 TTTTGTTTGTTAAATGCATCTTTGTTTAATAATATGCATTATTAACTG
**
3997 TTTCATTTGTTAAATGCATCTTTGTT
1 TTTTGTTTGTTAAATGCATCTTTGTT
4023 AAATGCCTTG
Statistics
Matches: 157, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 157 1.00
ACGTcount: A:0.25, C:0.10, G:0.13, T:0.53
Consensus pattern (48 bp):
TTTTGTTTGTTAAATGCATCTTTGTTTAATAATATGCATTATTAACTG
Found at i:4560 original size:80 final size:79
Alignment explanation
Indices: 4461--4625 Score: 287
Period size: 80 Copynumber: 2.1 Consensus size: 79
4451 TTCATTAAGG
* * *
4461 AGAAA-TGCCATGCCTTTTTAGCTACATCAGATCCTAATGAAGAGACATGACTCATTGGCTTTCC
1 AGAAATTGCCATGCCTTTTTAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCC
4525 TACAAGAGTTAAAA
66 TACAAGAGTTAAAA
4539 ACGAAATTGCCATGCCTTTTTAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCC
1 A-GAAATTGCCATGCCTTTTTAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCC
4604 CTACAAGAGTTAAAA
65 CTACAAGAGTTAAAA
4619 AGAAATT
1 AGAAATT
4626 AGTGTTTGTA
Statistics
Matches: 82, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
78 1 0.01
79 10 0.12
80 71 0.87
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (79 bp):
AGAAATTGCCATGCCTTTTTAACTACATCAGATCCTAATGAAGAGACATGACTCATTAGCTTCCC
TACAAGAGTTAAAA
Found at i:5461 original size:216 final size:214
Alignment explanation
Indices: 5076--6575 Score: 1632
Period size: 216 Copynumber: 6.9 Consensus size: 214
5066 GAGCTCATAT
* * *
5076 CAATTCTCACGTAAATAAGTTTTTAACTCAAAGAACAAAAGTTGTTTACAAAATGGA-AAACCAT
1 CAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAAT-GACAAACTAT
* *
5140 TTAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAAATGAATGGATTG
65 TTAGACCAAATGATGCGATTT-CCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCG
* * * * * **
5205 TCATGAATACTTTAAGGAACCAAAGTTATAAAATAACTCGTAAAACTTTGTCAAGATCAGAAAAT
129 TCATGAATACTTTAAGGAACTAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTT
* * *
5270 CGTGCAAGATGCAAGAGAGAAA
194 CATCCAAGA-CCAAGAGAGAAA
* * * * *
5292 AAATTCTCACGTAAATAAGTTTTTAATTCAAAGAGCAAAGGTTGTTTACCAAATGATAAACTATT
1 CAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATT
* * * * *
5357 TAGACAAAACGATGTGATTTCCGGTGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCGC
66 TAGACCAAATGATGCGATTTCC-GAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCGT
* * *
5422 CATGAATACTTTAAGGAACTGAAGTTATTAAAGAACTCGTAAAAGTTCT-CCAAGTTCAGAAGTT
130 CATGAATACTTTAAGGAACTAAAGTTATAAAAGAACTCGTAAAAGTT-TGACAAGTTCAGAAGTT
** *
5486 CATCCAAGAACCAATTGCGAAA
194 CATCCAAG-ACCAAGAGAGAAA
* *
5508 CAATTCTCACGTAAATAAGTTTTTAACTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTGTT
1 CAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATT
* * * * * * * * *
5573 TAAACCAAATGATGTGATTTCTCGACCATGGAATGTTCGAAAAGTTACTCGATGGAACGGATCGA
66 TAGACCAAATGATGCGATTTC-CGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCGT
* ** * * *
5638 CATGAATAATTTAACAAACTAAAGTTATAAAAGAACTCATAAAAGTTTGCCAAGTTCGGAAGTTC
130 CATGAATACTTTAAGGAACTAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTC
* * * * *
5703 GTTCGAGAACCAAAAGTGAAA
195 ATCCAAG-ACCAAGAGAGAAA
* * * * * *
5724 CAATTCTCATG-AAAGAAGTTTTTAATTCATAA-ACCAAAAGTTTTTTTCGAAATGAAAAACTAT
1 CAATTCTCACGTAAATAAGTTTTTAATTCA-AAGACCAAAAGTTGTTTACAAAATGACAAACTAT
* * * *
5787 TTAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTGGAAAATTGCTCGAAGGAATGGATTG
65 TTAGACCAAATGATGCGATTTC-CGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCG
* * * * * * *
5852 TCATGAAAACTTTAAGGAACCAAAGTTATAGAAGAACTCGTAAAAGATTGTCAGGTTCGGAAGTT
129 TCATGAATACTTTAAGGAACTAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTT
* * *
5917 CGTCCATGATCCAAGAGAGAAT
194 CATCCAAGA-CCAAGAGAGAAA
* * * **
5939 CAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACTAAATGGCAAAAAATT
1 CAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATT
* * * *
6004 TAGACAAAATGATGCGATTTTTCGAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATTGT
66 TAGACCAAATGATGCGA-TTTCCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCGT
* * * *
6069 CATGAATACTTTAAGGAATTAAAGTTATAAAAGAGCTCGTAAAAGTTTGACAAGTTTAGAATTTC
130 CATGAATACTTTAAGGAACTAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTC
* *
6134 ATCCAAGAACAAAGAGAGAAT
195 ATCCAAG-ACCAAGAGAGAAA
* *
6155 CAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACCATATGACAAACTATT
1 CAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATT
* * * * *
6220 TAAACCAGATGATGCGAATTTTCGAGCAAGGAATGTTC-AGAAAATTGAT-AGAAGGAATGGATC
66 TAGACCAAATGATGCG-ATTTCCGAGCATGGAATGTTCGA-AAAATTGCTCA-AAGGAATGGATC
* * * * ** ** *
6283 GTCTTTAATACTTTAAGGAACTGAAGTTATAAAATAACTAATAAAAGTTTGACAAGTTTGGAATT
128 GTCATGAATACTTTAAGGAACTAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGT
*
6348 TCATCCAAGAACTAAGAGAGAAA
193 TCATCCAAG-ACCAAGAGAGAAA
* * *
6371 CAATTCTCACGTAAAAAAAAGTTTTTAATTCGAAGCCCAAAAGTTGTTTACAAAATGACAAACTA
1 CAATTCTCACGT--AAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTA
* * **
6436 TTTAGACCAAATGATGCGATTTCATGAGCATGG-ATAGTTCGAAAAATAT-ATTGAAGGAATGGA
64 TTTAGACCAAATGATGCGATTTC-CGAGCATGGAAT-GTTCGAAAAAT-TGCTCAAAGGAATGGA
* * * * * ** * *
6499 TCTTCTTGAATATTTTATGGAA-TCAAATTTATAAAAGAACTCACAAAAGTTTGACAAGTTTAAA
126 TCGTCATGAATACTTTAAGGAACT-AAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGA
*
6563 AGTTCGTCCAAGA
190 AGTTCATCCAAGA
6576 TCCATGTAAC
Statistics
Matches: 1091, Mismatches: 170, Indels: 45
0.84 0.13 0.03
Matches are distributed among these distances:
214 1 0.00
215 182 0.17
216 739 0.68
217 16 0.01
218 151 0.14
219 2 0.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (214 bp):
CAATTCTCACGTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATT
TAGACCAAATGATGCGATTTCCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATCGTC
ATGAATACTTTAAGGAACTAAAGTTATAAAAGAACTCGTAAAAGTTTGACAAGTTCAGAAGTTCA
TCCAAGACCAAGAGAGAAA
Found at i:6329 original size:647 final size:646
Alignment explanation
Indices: 5076--6540 Score: 1832
Period size: 647 Copynumber: 2.3 Consensus size: 646
5066 GAGCTCATAT
* * * * * *
5076 CAATTCTCACGTAAATAAGTTTTTAACTCAAAGAACAAAAGTTGTTTACAAAATGGAAAACCATT
1 CAATTCTCATG-AAAAAAGTTTTTAATTCAAA-ACCAAAAGTTGTTTACAAAATGAAAAACTATT
* *
5141 TAGACCAAATGATGCGATTTCCCGAGCATGGAATGTTCGAAAAATTGCTCAAATGAATGGATTGT
64 TAGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATTGT
* * *
5206 CATGAATACTTTAAGGAACCAAAGTTATAAAATAACTCGTAAAACTTTGTCAAGATCAGAAAATC
129 CATGAAAACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAACATTGTCAAGATCAGAAAATC
* * * * *
5271 GTGCAAGATGCAAGAGAGAAAAAATTCTCACGTAAATAAGTTTTTAATTCAAAGAGCAAAGGTTG
194 GTCCAAGATCCAAGAGAGAAAAAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTG
* ** * *
5336 TTTACCAAATGATAAACTATTTAGACAAAACGATGTGATTTCCGGTGCATGGAATGTTCGAAAAA
259 TTTACCAAATGACAAAAAATTTAGACAAAACGATGCGATTTCCGGAGCATGGAATGTTCGAAAAA
* *
5401 TTGCTCAAAGGAATGGATCGCCATGAATACTTTAAGGAACTGAAGTTATTAAAGAACTCGTAAAA
324 TTGCTCAAAGGAATGGATCGCCATGAATACTTTAAGGAACTAAAGTTATAAAAGAACTCGTAAAA
* * ** *
5466 GTTCTCCAAGTTCAGAAGTTCATCCAAGAACCAATTGCGAAACAATTCTCACGTAAATAAGTTTT
389 GTTCTACAAGTTCAGAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTT
* *
5531 TAACTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTGTTTAAACCAAATGATGTGATTTCTC
454 TAACTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAAACCAAATGATGCGATTTCTC
* * *
5596 GACCATGGAATGTTCGAAAAGTTACTCGATGGAACGGATCGACATGAATAATTTAACAAACTAAA
519 GACCAAGGAATGTTCGAAAAGTTACTAGAAGGAACGGATCGACATGAATAATTTAACAAACTAAA
* * * * * *
5661 GTTATAAAAGAACTCATAAAAGTTTGCCAAGTTCGGAAGTTCGTTCGAGAACCAAAAGTGAAA
584 GTTATAAAAGAACTAATAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAAAGAGAAA
* * * *
5724 CAATTCTCATGAAAGAAGTTTTTAATTCATAAACCAAAAGTTTTTTTCGAAATGAAAAACTATTT
1 CAATTCTCATGAAAAAAGTTTTTAATTCA-AAACCAAAAGTTGTTTACAAAATGAAAAACTATTT
* * *
5789 AGACCAAATGATGCGATTTCTCGAGCATGGAATGTTTGGAAAATTGCTCGAAGGAATGGATTGTC
65 AGACCAAATGATGCGATTTCTCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATTGTC
* * * * * **
5854 ATGAAAACTTTAAGGAACCAAAGTTATAGAAGAACTCGTAAAAGATTGTCAGGTTCGGAAGTTCG
130 ATGAAAACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAACATTGTCAAGATCAGAAAATCG
* **
5919 TCCATGATCCAAGAGAGAATCAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGT
195 TCCAAGATCCAAGAGAGAAAAAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGT
* * * *
5984 TTACTAAATGGCAAAAAATTTAGACAAAATGATGCGATTTTTC-GAGCATGGAATGTTCGAAAAA
260 TTACCAAATGACAAAAAATTTAGACAAAACGATGCGA-TTTCCGGAGCATGGAATGTTCGAAAAA
* * * * *
6048 TTGCTCGAAGGAATGGATTGTCATGAATACTTTAAGGAATTAAAGTTATAAAAGAGCTCGTAAAA
324 TTGCTCAAAGGAATGGATCGCCATGAATACTTTAAGGAACTAAAGTTATAAAAGAACTCGTAAAA
* * *
6113 GTT-TGACAAGTTTAGAATTTCATCCAAGAACAAAGAGAGAATCAATTCTCACGTAAATAAGTTT
389 GTTCT-ACAAGTTCAGAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTT
* * * *
6177 TTAATTCAAAGACCAAAAGTTGTTTACCATATGACAAACTATTTAAACCAGATGATGCGAATTT-
453 TTAACTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAAACCAAATGATGCG-ATTTC
* * * * * * **
6241 TCGAGCAAGGAATGTTCAGAAAA-TTGA-TAGAAGGAATGGATCGTCTTTAATACTTTAAGGAAC
517 TCGACCAAGGAATGTTC-GAAAAGTT-ACTAGAAGGAACGGATCGACATGAATAATTTAACAAAC
* * * * * *
6304 TGAAGTTATAAAATAACTAATAAAAGTTTGACAAGTTTGGAATTTCATCCAAGAACTAAGAGAGA
580 TAAAGTTATAAAAGAACTAATAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAAAGAGA
6369 AA
645 AA
* ** *
6371 CAATTCTCACGTAAAAAAAAGTTTTTAATTCGAAGCCCAAAAGTTGTTTACAAAATGACAAACTA
1 CAATTCTCA--T-GAAAAAAGTTTTTAATTC-AAAACCAAAAGTTGTTTACAAAATGAAAAACTA
* **
6436 TTTAGACCAAATGATGCGATTTCAT-GAGCATGG-ATAGTTCGAAAAATAT-ATTGAAGGAATGG
62 TTTAGACCAAATGATGCGATTTC-TCGAGCATGGAAT-GTTCGAAAAAT-TGCTCAAAGGAATGG
* * * * * *
6498 ATCT-TCTTGAATATTTTATGGAATCAAATTTATAAAAGAACTC
124 AT-TGTCATGAAAACTTTAAGGAACCAAAGTTATAAAAGAACTC
6541 ACAAAAGTTT
Statistics
Matches: 699, Mismatches: 104, Indels: 26
0.84 0.13 0.03
Matches are distributed among these distances:
646 1 0.00
647 538 0.77
648 26 0.04
649 3 0.00
650 127 0.18
651 4 0.01
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (646 bp):
CAATTCTCATGAAAAAAGTTTTTAATTCAAAACCAAAAGTTGTTTACAAAATGAAAAACTATTTA
GACCAAATGATGCGATTTCTCGAGCATGGAATGTTCGAAAAATTGCTCAAAGGAATGGATTGTCA
TGAAAACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAACATTGTCAAGATCAGAAAATCGT
CCAAGATCCAAGAGAGAAAAAATTCTCACATAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTT
TACCAAATGACAAAAAATTTAGACAAAACGATGCGATTTCCGGAGCATGGAATGTTCGAAAAATT
GCTCAAAGGAATGGATCGCCATGAATACTTTAAGGAACTAAAGTTATAAAAGAACTCGTAAAAGT
TCTACAAGTTCAGAAGTTCATCCAAGAACAAAGAGAGAAACAATTCTCACGTAAATAAGTTTTTA
ACTCAAAGACCAAAAGTTGTTTACAAAATGACAAACTATTTAAACCAAATGATGCGATTTCTCGA
CCAAGGAATGTTCGAAAAGTTACTAGAAGGAACGGATCGACATGAATAATTTAACAAACTAAAGT
TATAAAAGAACTAATAAAAGTTTGACAAGTTCGGAAGTTCATCCAAGAACCAAAAGAGAAA
Found at i:6702 original size:2 final size:2
Alignment explanation
Indices: 6684--6728 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
6674 GTCAATTATT
* *
6684 TA TA TA AA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6726 TA T
1 TA T
6729 TATTTTAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:9291 original size:21 final size:21
Alignment explanation
Indices: 9267--9318 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
9257 TGAAGCAGTA
*
9267 CTACCGATACAAGTGAGACTT
1 CTACCGATACAAGTCAGACTT
* * *
9288 CTACCGAAACATGTCATACTT
1 CTACCGATACAAGTCAGACTT
9309 CTACCGATAC
1 CTACCGATAC
9319 TAAAAACTCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.25
Consensus pattern (21 bp):
CTACCGATACAAGTCAGACTT
Found at i:11548 original size:43 final size:43
Alignment explanation
Indices: 11485--11571 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
11475 CGTCTCGTAT
* *
11485 CATAACCTCATGCTCGTCCCGAGACATGAGTCTTCCATTTATG
1 CATAACCTCATGCTCATCCCGAGACATGAGTATTCCATTTATG
*
11528 CATAATCTCATGCTCATCCCGAGACATGAGTATTCCATTTATG
1 CATAACCTCATGCTCATCCCGAGACATGAGTATTCCATTTATG
11571 C
1 C
11572 CAAGTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (43 bp):
CATAACCTCATGCTCATCCCGAGACATGAGTATTCCATTTATG
Found at i:12510 original size:16 final size:16
Alignment explanation
Indices: 12486--12517 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12476 TCCTTACAAA
*
12486 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
12502 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
12518 AAAAATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:17261 original size:21 final size:21
Alignment explanation
Indices: 17237--17287 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
17227 GAAGCAGTAT
*
17237 TACCGATACAAGTGAGACTTC
1 TACCGATACAAGTCAGACTTC
* * *
17258 TACCGCTACATGTCATACTTC
1 TACCGATACAAGTCAGACTTC
*
17279 TATCGATAC
1 TACCGATAC
17288 TAAAAACTCT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.29
Consensus pattern (21 bp):
TACCGATACAAGTCAGACTTC
Found at i:18077 original size:43 final size:43
Alignment explanation
Indices: 17953--18162 Score: 255
Period size: 43 Copynumber: 5.0 Consensus size: 43
17943 TATACTCTAC
** * * *
17953 CGAGTCATAAGTCTTCC-TTTAAACATAATATCATTCTCATTT
1 CGAGTCACGAGTCTTCCATTTATACATAATCTCATGCTCATTT
* *
17995 CGAGTCACGAGCCTTCC--TTAAACATAATCTCATGCTCATTT
1 CGAGTCACGAGTCTTCCATTTATACATAATCTCATGCTCATTT
* *
18036 CGAGTCACGAGTCTTCCATTTATACATAAGCTCTTGCTCATTT
1 CGAGTCACGAGTCTTCCATTTATACATAATCTCATGCTCATTT
* ** **
18079 CGAGTCACGAGTCTTCTATTTATACATAATCTCATGCTTGTCC
1 CGAGTCACGAGTCTTCCATTTATACATAATCTCATGCTCATTT
* *
18122 CGAGACATGAGTCTTCCATTTATACATAATCTCATGCTCAT
1 CGAGTCACGAGTCTTCCATTTATACATAATCTCATGCTCAT
18163 CCTAAGACAT
Statistics
Matches: 145, Mismatches: 21, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
41 38 0.26
42 14 0.10
43 93 0.64
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (43 bp):
CGAGTCACGAGTCTTCCATTTATACATAATCTCATGCTCATTT
Found at i:18171 original size:43 final size:43
Alignment explanation
Indices: 17962--18187 Score: 235
Period size: 43 Copynumber: 5.3 Consensus size: 43
17952 CCGAGTCATA
* * * * *
17962 AGTCTTCC-TTTAAACATAATATCATTCTCATTTCGAGTCACG
1 AGTCTTCCATTTATACATAATCTCATGCTCATCTCGAGACACG
* * * *
18004 AGCCTTCC--TTAAACATAATCTCATGCTCATTTCGAGTCACG
1 AGTCTTCCATTTATACATAATCTCATGCTCATCTCGAGACACG
* * * *
18045 AGTCTTCCATTTATACATAAGCTCTTGCTCATTTCGAGTCACG
1 AGTCTTCCATTTATACATAATCTCATGCTCATCTCGAGACACG
* ** * *
18088 AGTCTTCTATTTATACATAATCTCATGCTTGTCCCGAGACATG
1 AGTCTTCCATTTATACATAATCTCATGCTCATCTCGAGACACG
* *
18131 AGTCTTCCATTTATACATAATCTCATGCTCATC-CTAAGACATG
1 AGTCTTCCATTTATACATAATCTCATGCTCATCTC-GAGACACG
18174 AGTCTTCCATTTAT
1 AGTCTTCCATTTAT
18188 GTCAAGTGAT
Statistics
Matches: 161, Mismatches: 20, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
41 38 0.24
42 8 0.05
43 115 0.71
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.37
Consensus pattern (43 bp):
AGTCTTCCATTTATACATAATCTCATGCTCATCTCGAGACACG
Done.