Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011187.1 Kokia drynarioides strain JFW-HI SEQ_126163, 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: 28552
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Warning! 366 characters in sequence are not A, C, G, or T
Found at i:1604 original size:46 final size:46
Alignment explanation
Indices: 1551--1648 Score: 169
Period size: 46 Copynumber: 2.1 Consensus size: 46
1541 ACAACTAATC
*
1551 ACAAAGCGAAGATAAAAATAAAAACTCTTAGCAAAAATGGATATAA
1 ACAAAGCGAAGATAAAAATAAAAACACTTAGCAAAAATGGATATAA
*
1597 ACAAAGCGAAGATAAAAATAAAAACACTTTGCAAAAATGGATATAA
1 ACAAAGCGAAGATAAAAATAAAAACACTTAGCAAAAATGGATATAA
*
1643 AAAAAG
1 ACAAAG
1649 TATCCTTGCA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.60, C:0.10, G:0.13, T:0.16
Consensus pattern (46 bp):
ACAAAGCGAAGATAAAAATAAAAACACTTAGCAAAAATGGATATAA
Found at i:2251 original size:670 final size:669
Alignment explanation
Indices: 928--2267 Score: 2330
Period size: 670 Copynumber: 2.0 Consensus size: 669
918 ACAACTAATG
*
928 ACAAAGCAAAGATAAAAATAAAAACTCTTAGCAAAAATGGATATAAAAAAAAGTATCATTGCATA
1 ACAAAGCAAAGATAAAAATAAAAACACTTAGCAAAAATGGATATAAAAAAAAGTATCATTGCATA
* *
993 TCAATATCGCCCAATTTACATTCCTACCTACAACTAATTTTATTATTATTAAAATATATATTTTA
66 TCAATATCGCCCAATTTACATTCCTACCTACAACAAAGTTTATTATTATTAAAATATATATTTTA
* * *
1058 TTTATGAAGACATGTTCTAAGTTATTTTTGTTTTATATTATGTTTTGCATAGATAATCTATTCAC
131 TATATGAAGACATGTTCTAAGTTATTTTTGTTTTATATTATGTTTTGCATAAATAATATATTCAC
*
1123 AGAATAATTTGTGATCATATATATTGTATTTCAAAAAAAAAAAGTCAGAAATCTGATTGCTGGCC
196 AGAATAATTTGTGATCATATATATCGTATTTCAAAAAAAAAAAGTCAGAAATCTGATTGCTGGCC
* *
1188 CTCTTCCCTATAGCGAAAAAAGCTTGATATTATGTATATATATACATAACCTTACCAGGGATGTC
261 CTCTTCCCGATAGCGAAAAAAGCTTGATATTATGTATATATATACATAACCTTAACAGGGATGTC
*
1253 AATGAGGCGGGTTTCGTAGAGTCCCGTTTCACTTTGCACCTAATTTGGTGGAGATAAATACAGGT
326 AATGAGGCGGGTTTCGTAGAGTCCCGTTTCACTTCGCACCTAATTTGGTGGAGATAAATACAGGT
1318 TTCGTGGATGATGGAGATAAAAATTAGACCTACCATGAGTGGTGGGGCAGACGTGAATATGACTT
391 TTCGTGGATGATGGAGATAAAAATTAGACCTACCATGAGTGGTGGGGCAGACGTGAATATGACTT
* * * *
1383 TGTACACGCTTCATCCCTGCTTACCCCGTGTAATATAATCCATCGCGGGGTGGATATAGCAAGGA
456 TGTACACGCTTCATCCCCGCTTACCCCATATAATATAATCCATCGCGGGGTGGATAAAGCAAGGA
*
1448 TTAGATGGATCTGAGGACCCACGTGAGTGATGGAACGAAGATAGTTTTAATCTTACGGGTCGCAG
521 TTAGATGGATCTGAGGACCCACGTGAGTGATGAAACGAAGATAGTTTTAATCTTACGGGTCGCAG
* *
1513 GACGAGAATAATTTTGAATTTTGTACCCACAACTAATCACAAAGCGAAGATAAAAATAAAAACTC
586 GACAAGAATAATTTTGAATTTTGTACCCACAACTAATCACAAAGCAAAGATAAAAATAAAAACTC
1578 TTAGCAAAAATGGATATAA
651 TTAGCAAAAATGGATATAA
* * *
1597 ACAAAGCGAAGATAAAAATAAAAACACTTTGCAAAAATGGATAT-AAAAAAAGTATCCTTGCATA
1 ACAAAGCAAAGATAAAAATAAAAACACTTAGCAAAAATGGATATAAAAAAAAGTATCATTGCATA
* * *
1661 TCCAT-TC-CATCCAATTTACATTCCTACCTGCAACAAAGTTTATTATTATTAAAATATATTTTT
66 TCAATATCGC--CCAATTTACATTCCTACCTACAACAAAGTTTATTATTATTAAAATATATATTT
* *
1724 TATATATGAAGACATGTT-T-ATTTTTGTTTTGTTTTATATTATGTTTTGCATAAATAATATATT
129 TATATATGAAGACATGTTCTAAGTTAT-TTTTGTTTTATATTATGTTTTGCATAAATAATATATT
1787 CACAGAATAATTTGTGATCATATATATCGTATTTCAAAAAAAAAAAAAAGTCAGAAATCTGATTG
193 CACAGAATAATTTGTGATCATATATATCGTATTTC---AAAAAAAAAAAGTCAGAAATCTGATTG
*
1852 CTGGCCCTCTTCCCGATAGCGAAAAAAGCTTGATATTATGTATATATATTCATAACCTTAACAGG
255 CTGGCCCTCTTCCCGATAGCGAAAAAAGCTTGATATTATGTATATATATACATAACCTTAACAGG
1917 GATGTCAATGAGGCGGGTTTCGTAGAGTCCCGTTTCACTTCGCACCTAATTTGGTGGAGATAAAT
320 GATGTCAATGAGGCGGGTTTCGTAGAGTCCCGTTTCACTTCGCACCTAATTTGGTGGAGATAAAT
* * *
1982 TCAGGTTTCGTGGATGGTGGAGATAAAAATTAGACCTACCATGAGTGGTGGGGCAGACGTGAGTA
385 ACAGGTTTCGTGGATGATGGAGATAAAAATTAGACCTACCATGAGTGGTGGGGCAGACGTGAATA
2047 TGACTTTGTACACGCTTCATCCCCGCTTACCCCATATAATATAATCCATCGCGGGGTGGATAAAG
450 TGACTTTGTACACGCTTCATCCCCGCTTACCCCATATAATATAATCCATCGCGGGGTGGATAAAG
2112 CAAGGATTAGATGGATCTGAGGACCCACGTGAGTGATGAAACGAAGATAGTTTTAATCTTACGGG
515 CAAGGATTAGATGGATCTGAGGACCCACGTGAGTGATGAAACGAAGATAGTTTTAATCTTACGGG
2177 TCGCAGGACAAGAATAATTTTGAATTTTGTACCCACAACTAATCACAAAGCAAAGATAAAAATAA
580 TCGCAGGACAAGAATAATTTTGAATTTTGTACCCACAACTAATCACAAAGCAAAGATAAAAATAA
2242 AAACTCTTAGCAAAAATGGATATAA
645 AAACTCTTAGCAAAAATGGATATAA
2267 A
1 A
2268 AAAAAGTATC
Statistics
Matches: 636, Mismatches: 29, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
666 5 0.01
667 72 0.11
668 89 0.14
669 41 0.06
670 429 0.67
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (669 bp):
ACAAAGCAAAGATAAAAATAAAAACACTTAGCAAAAATGGATATAAAAAAAAGTATCATTGCATA
TCAATATCGCCCAATTTACATTCCTACCTACAACAAAGTTTATTATTATTAAAATATATATTTTA
TATATGAAGACATGTTCTAAGTTATTTTTGTTTTATATTATGTTTTGCATAAATAATATATTCAC
AGAATAATTTGTGATCATATATATCGTATTTCAAAAAAAAAAAGTCAGAAATCTGATTGCTGGCC
CTCTTCCCGATAGCGAAAAAAGCTTGATATTATGTATATATATACATAACCTTAACAGGGATGTC
AATGAGGCGGGTTTCGTAGAGTCCCGTTTCACTTCGCACCTAATTTGGTGGAGATAAATACAGGT
TTCGTGGATGATGGAGATAAAAATTAGACCTACCATGAGTGGTGGGGCAGACGTGAATATGACTT
TGTACACGCTTCATCCCCGCTTACCCCATATAATATAATCCATCGCGGGGTGGATAAAGCAAGGA
TTAGATGGATCTGAGGACCCACGTGAGTGATGAAACGAAGATAGTTTTAATCTTACGGGTCGCAG
GACAAGAATAATTTTGAATTTTGTACCCACAACTAATCACAAAGCAAAGATAAAAATAAAAACTC
TTAGCAAAAATGGATATAA
Found at i:3009 original size:16 final size:17
Alignment explanation
Indices: 2988--3020 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2978 ATCAAGACAT
*
2988 GTTTATGTTAT-TTTTG
1 GTTTATATTATGTTTTG
3004 GTTTATATTATGTTTTG
1 GTTTATATTATGTTTTG
3021 CATATATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.15, C:0.00, G:0.18, T:0.67
Consensus pattern (17 bp):
GTTTATATTATGTTTTG
Found at i:3022 original size:622 final size:622
Alignment explanation
Indices: 1--3129 Score: 5001
Period size: 623 Copynumber: 5.0 Consensus size: 622
1 GGATGTCAATGAGGCGGGTTTCGTAGAGTCCCGTTTCACTTTGCACCTAATTTGGTGGAGATAAA
1 GGATGTCAATGAGGCGGGTTTCGTAGAGTCCCGTTTCACTTTGCACCTAATTTGGTGGAGATAAA
* * * *
66 TACAGGTTTCGTGGATGATAGAGATTAAAATTAGATCTACCATGAGTGGTGGGGCAGACGTGAAT
66 TACAGGTTTCGTGGATGATGGAGATAAAAATTAGACCTACCATGAGTGGTGGGGCAGACGTGAGT
*
131 ATTACTTTGTACACGCTTCATCCCTGCTTACCCCGTATAATATAATCCATCGCGGGGTGGATATA
131 ATGACTTTGTACACGCTTCATCCCTGCTTACCCCGTATAATATAATCCATCGCGGGGTGGATATA
196 GCAAGGATTAGATGGATCTGAGGACCCACGTGAGTGATGGAACGAAGATAGTTTTAATCTTACGG
196 GCAAGGATTAGATGGATCTGAGGACCCACGTGAGTGATGGAACGAAGATAGTTTTAATCTTACGG
** *
261 GGAGCAGGACGAGAATAATTTTGAATTTTGTACCCACAACTAATCACAAAGCAAAGATAAAAATT
261 GTCGCAGGACGAGAATAATTTTGAATTTTGTACCCACAACTAATCACAAAGCAAAGATAAAAATA
*
326 AAAACTCTTAGCAAAAATGGATAT-AAAAAAAGTATCATTGCATATCAATTCCGCCCAATTTACA
326 AAAACTCTTAGCAAAAATGGATATAAAAAAAAGTATCCTTGCATATCAATTCCGCCCAATTTACA
* *
390 TTCCTACTTGCAACTAAGTTTATTATTATTAAAATATATATTTTATATATGAAGACATGTTTTAA
391 TTCCTACCTGCAACTAAGTTTATTATTATTAAAATATATATTTTATATATGAAGACATG-TTTAT
455 GTTATTTTTGTTTTATATTATGTTTTGCATAGATAATCTATTCACAGAATAATTTGTGATCATAT
455 GTTATTTTTGTTTTATATTATGTTTTGCATAGATAATCTATTCACAGAATAATTTGTGATCATAT
* *
520 ATATTGTATTTCAAAAAAAAAAAGTCAGAAATCTGATTGCTGGCCATCTTCCCGATAGCGAATAA
520 ATATTGTATTTCAAAAAAAAAAAGTCAGAAATCTGATTGCTGGCCCTCTTCCCGATAGCGAAAAA
585 AGCTTGATATTATGTATATATATACATAACCTTACCAG
585 AGCTTGATATTATGTATATATATACATAACCTTACCAG
* *
623 GGATGTCAATGAGACGGGTTTCGTAGTGTCCCGTTTCACTTTGCACCTAATTTGGTGGAGATAAA
1 GGATGTCAATGAGGCGGGTTTCGTAGAGTCCCGTTTCACTTTGCACCTAATTTGGTGGAGATAAA
688 TACAGGTTTCGTGGATGATGGAGATAAAAATTAGACCTACCATGAGTGGTGGGGCAGACGTGAGT
66 TACAGGTTTCGTGGATGATGGAGATAAAAATTAGACCTACCATGAGTGGTGGGGCAGACGTGAGT
*
753 ATGACTTTGTACACGCTTCATCCCTACTTACCCCGTATAATATAATCCATCGCGGGGTGGATATA
131 ATGACTTTGTACACGCTTCATCCCTGCTTACCCCGTATAATATAATCCATCGCGGGGTGGATATA
* * * * *
818 ACAAGGATTAGATGGATCTGAGGTCACACGTGAGTAATGGAACGTAGATAGTTTTAATCTTACGG
196 GCAAGGATTAGATGGATCTGAGGACCCACGTGAGTGATGGAACGAAGATAGTTTTAATCTTACGG
* * *
883 TTCGCAGGACGAGAATAATTTTGAATTTTGTTCCCACAACTAATGACAAAGCAAAGATAAAAATA
261 GTCGCAGGACGAGAATAATTTTGAATTTTGTACCCACAACTAATCACAAAGCAAAGATAAAAATA
*
948 AAAACTCTTAGCAAAAATGGATATAAAAAAAAGTATCATTGCATATCAATAT-CGCCCAATTTAC
326 AAAACTCTTAGCAAAAATGGATATAAAAAAAAGTATCCTTGCATATCAAT-TCCGCCCAATTTAC
* * *
1012 ATTCCTACCTACAACTAATTTTATTATTATTAAAATATATATTTTATTTATGAAGACATGTTCTA
390 ATTCCTACCTGCAACTAAGTTTATTATTATTAAAATATATATTTTATATATGAAGACATGTT-TA
*
1077 AGTTATTTTTGTTTTATATTATGTTTTGCATAGATAATCTATTCACAGAATAATTTGTGATCATA
454 TGTTATTTTTGTTTTATATTATGTTTTGCATAGATAATCTATTCACAGAATAATTTGTGATCATA
*
1142 TATATTGTATTTCAAAAAAAAAAAGTCAGAAATCTGATTGCTGGCCCTCTTCCCTATAGCGAAAA
519 TATATTGTATTTCAAAAAAAAAAAGTCAGAAATCTGATTGCTGGCCCTCTTCCCGATAGCGAAAA
1207 AAGCTTGATATTATGTATATATATACATAACCTTACCAG
584 AAGCTTGATATTATGTATATATATACATAACCTTACCAG
1246 GGATGTCAATGAGGCGGGTTTCGTAGAGTCCCGTTTCACTTTGCACCTAATTTGGTGGAGATAAA
1 GGATGTCAATGAGGCGGGTTTCGTAGAGTCCCGTTTCACTTTGCACCTAATTTGGTGGAGATAAA
*
1311 TACAGGTTTCGTGGATGATGGAGATAAAAATTAGACCTACCATGAGTGGTGGGGCAGACGTGAAT
66 TACAGGTTTCGTGGATGATGGAGATAAAAATTAGACCTACCATGAGTGGTGGGGCAGACGTGAGT
*
1376 ATGACTTTGTACACGCTTCATCCCTGCTTACCCCGTGTAATATAATCCATCGCGGGGTGGATATA
131 ATGACTTTGTACACGCTTCATCCCTGCTTACCCCGTATAATATAATCCATCGCGGGGTGGATATA
1441 GCAAGGATTAGATGGATCTGAGGACCCACGTGAGTGATGGAACGAAGATAGTTTTAATCTTACGG
196 GCAAGGATTAGATGGATCTGAGGACCCACGTGAGTGATGGAACGAAGATAGTTTTAATCTTACGG
*
1506 GTCGCAGGACGAGAATAATTTTGAATTTTGTACCCACAACTAATCACAAAGCGAAGATAAAAATA
261 GTCGCAGGACGAGAATAATTTTGAATTTTGTACCCACAACTAATCACAAAGCAAAGATAAAAATA
1571 AAAACTCTTAGCAAAAATGGATATAAACAAAGCGAAGATAAAAATAAAAACACTTTGCAAAAATG
326 AAAACTCTTAGCAAAAATGGATATAAA-AAA---AAG-T----AT-----C-C-TTGC-------
* *
1636 GATATAAAAAAAGTATCCTTGCATATCCATTCCATCCAATTTACATTCCTACCTGCAACAAAGTT
368 -ATAT----CAA-T-TCC--G-----------C--CCAATTTACATTCCTACCTGCAACTAAGTT
* *
1701 TATTATTATTAAAATATATTTTTTATATATGAAGACATGTTTAT-TTTTGTTTTGTTTTATATTA
411 TATTATTATTAAAATATATATTTTATATATGAAGACATGTTTATGTTAT-TTTTGTTTTATATTA
* * *
1765 TGTTTTGCATAAATAATATATTCACAGAATAATTTGTGATCATATATATCGTATTTCAAAAAAAA
475 TGTTTTGCATAGATAATCTATTCACAGAATAATTTGTGATCATATATATTGTATTTC---AAAAA
1830 AAAAAAGTCAGAAATCTGATTGCTGGCCCTCTTCCCGATAGCGAAAAAAGCTTGATATTATGTAT
537 AAAAAAGTCAGAAATCTGATTGCTGGCCCTCTTCCCGATAGCGAAAAAAGCTTGATATTATGTAT
* *
1895 ATATATTCATAACCTTAACAG
602 ATATATACATAACCTTACCAG
*
1916 GGATGTCAATGAGGCGGGTTTCGTAGAGTCCCGTTTCACTTCGCACCTAATTTGGTGGAGATAAA
1 GGATGTCAATGAGGCGGGTTTCGTAGAGTCCCGTTTCACTTTGCACCTAATTTGGTGGAGATAAA
* *
1981 TTCAGGTTTCGTGGATGGTGGAGATAAAAATTAGACCTACCATGAGTGGTGGGGCAGACGTGAGT
66 TACAGGTTTCGTGGATGATGGAGATAAAAATTAGACCTACCATGAGTGGTGGGGCAGACGTGAGT
* * *
2046 ATGACTTTGTACACGCTTCATCCCCGCTTACCCCATATAATATAATCCATCGCGGGGTGGATAAA
131 ATGACTTTGTACACGCTTCATCCCTGCTTACCCCGTATAATATAATCCATCGCGGGGTGGATATA
*
2111 GCAAGGATTAGATGGATCTGAGGACCCACGTGAGTGATGAAACGAAGATAGTTTTAATCTTACGG
196 GCAAGGATTAGATGGATCTGAGGACCCACGTGAGTGATGGAACGAAGATAGTTTTAATCTTACGG
*
2176 GTCGCAGGACAAGAATAATTTTGAATTTTGTACCCACAACTAATCACAAAGCAAAGATAAAAATA
261 GTCGCAGGACGAGAATAATTTTGAATTTTGTACCCACAACTAATCACAAAGCAAAGATAAAAATA
*
2241 AAAACTCTTAGCAAAAATGGATATAAAAAAAAGTATCCTTGCATATCCATTCCGCCCAATTTACA
326 AAAACTCTTAGCAAAAATGGATATAAAAAAAAGTATCCTTGCATATCAATTCCGCCCAATTTACA
*
2306 TTCCTACCTGCAACTAAGTTTATTATAATTAAAAAATATATATTTTATATATGAAGACATGTTTA
391 TTCCTACCTGCAACTAAGTTTATTATTATT--AAAATATATATTTTATATATGAAGACATGTTTA
* * *
2371 TGTTATTTTTGTTTTATATTATGTTTTGCATAGATAATTTATTCACAGAATAATTTGTGATAAAA
454 TGTTATTTTTGTTTTATATTATGTTTTGCATAGATAATCTATTCACAGAATAATTTGTGATCATA
* * *
2436 TATCTTGTATTTC-AAAAAAAAAAGTCATAAATCTGATTGCTGGCCCTCTTCCCTATAGCGAAAA
519 TATATTGTATTTCAAAAAAAAAAAGTCAGAAATCTGATTGCTGGCCCTCTTCCCGATAGCGAAAA
2500 AAGCTTGATATTATGTATATATATACATAACCTTACCAG
584 AAGCTTGATATTATGTATATATATACATAACCTTACCAG
* *
2539 GGGTGTCAATGAGGCGGGTTTCGTAGAGTCCCGTTTCACTTCGCACCTAA-TTGAGTGGAGATAA
1 GGATGTCAATGAGGCGGGTTTCGTAGAGTCCCGTTTCACTTTGCACCTAATTTG-GTGGAGATAA
2603 ATACAGGTTTCGTGGATGATGGAGATAAAAATTAGACCTACCATGAGTGGTGGGGCAGACGTGAG
65 ATACAGGTTTCGTGGATGATGGAGATAAAAATTAGACCTACCATGAGTGGTGGGGCAGACGTGAG
*
2668 TATGACTTTGTACACGCTTCATCCCCGCTTACCCCGTATAATATAATCCATCGCGGGGTGGATAT
130 TATGACTTTGTACACGCTTCATCCCTGCTTACCCCGTATAATATAATCCATCGCGGGGTGGATAT
* *
2733 AGCAAGGATTAGATGGATCCGAGGACCCACGTGAGTGATGGAACGAAGATATTTTTAATCTTACG
195 AGCAAGGATTAGATGGATCTGAGGACCCACGTGAGTGATGGAACGAAGATAGTTTTAATCTTACG
*
2798 GGTCGCAGGACGAGAATAATTTTGAATTTTGTACCCACAACTAATCACAAAGCGAAGATAAAAAT
260 GGTCGCAGGACGAGAATAATTTTGAATTTTGTACCCACAACTAATCACAAAGCAAAGATAAAAAT
* * ** *
2863 AAAAACTCTTAGCAAAAATGGATATAAAAAAAACATATCCTTGCATATCCATTTTGTCCAATTTA
325 AAAAACTCTTAGCAAAAATGGATATAAAAAAAA-GTATCCTTGCATATCAATTCCGCCCAATTTA
* *
2928 CATTCCTACCTGCAACAAAGTTTATTATTATTAAAATATATATTTTATATATCAAGACATGTTTA
389 CATTCCTACCTGCAACTAAGTTTATTATTATTAAAATATATATTTTATATATGAAGACATGTTTA
* * * *
2993 TGTTATTTTTGGTTTATATTATGTTTTGCATATATAATCTATTCATAAAATAATTTGTGATCATA
454 TGTTATTTTTGTTTTATATTATGTTTTGCATAGATAATCTATTCACAGAATAATTTGTGATCATA
* * *
3058 TATATTATATTTC-AAAAAAAAATGTCAGAAATCTGATTGCTGGCACTCTTCCCGATAGCGAAAA
519 TATATTGTATTTCAAAAAAAAAAAGTCAGAAATCTGATTGCTGGCCCTCTTCCCGATAGCGAAAA
*
3122 TAGCTTGA
584 AAGCTTGA
3130 CTTTTGGGCT
Statistics
Matches: 2337, Mismatches: 113, Indels: 114
0.91 0.04 0.04
Matches are distributed among these distances:
622 490 0.21
623 1028 0.44
624 61 0.03
625 38 0.02
627 103 0.04
628 4 0.00
632 2 0.00
637 1 0.00
638 1 0.00
639 4 0.00
640 3 0.00
641 1 0.00
642 1 0.00
646 4 0.00
647 4 0.00
651 2 0.00
652 3 0.00
653 1 0.00
654 4 0.00
655 2 0.00
656 1 0.00
661 2 0.00
665 1 0.00
666 7 0.00
667 71 0.03
668 66 0.03
669 3 0.00
670 429 0.18
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (622 bp):
GGATGTCAATGAGGCGGGTTTCGTAGAGTCCCGTTTCACTTTGCACCTAATTTGGTGGAGATAAA
TACAGGTTTCGTGGATGATGGAGATAAAAATTAGACCTACCATGAGTGGTGGGGCAGACGTGAGT
ATGACTTTGTACACGCTTCATCCCTGCTTACCCCGTATAATATAATCCATCGCGGGGTGGATATA
GCAAGGATTAGATGGATCTGAGGACCCACGTGAGTGATGGAACGAAGATAGTTTTAATCTTACGG
GTCGCAGGACGAGAATAATTTTGAATTTTGTACCCACAACTAATCACAAAGCAAAGATAAAAATA
AAAACTCTTAGCAAAAATGGATATAAAAAAAAGTATCCTTGCATATCAATTCCGCCCAATTTACA
TTCCTACCTGCAACTAAGTTTATTATTATTAAAATATATATTTTATATATGAAGACATGTTTATG
TTATTTTTGTTTTATATTATGTTTTGCATAGATAATCTATTCACAGAATAATTTGTGATCATATA
TATTGTATTTCAAAAAAAAAAAGTCAGAAATCTGATTGCTGGCCCTCTTCCCGATAGCGAAAAAA
GCTTGATATTATGTATATATATACATAACCTTACCAG
Found at i:3714 original size:17 final size:16
Alignment explanation
Indices: 3680--3725 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
3670 AATTTAAGTT
3680 ATAAATAT-TTTAAAAA
1 ATAAATATATTT-AAAA
3696 ATTAAATATATTTAAAA
1 A-TAAATATATTTAAAA
*
3713 ATATATATATTTA
1 ATAAATATATTTA
3726 TTTATTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 12 0.44
17 12 0.44
18 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAAATATATTTAAAA
Found at i:6182 original size:20 final size:23
Alignment explanation
Indices: 6157--6199 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
6147 AAAATTAATT
6157 TTTG-AAAAA-TTAATA-TTTAA
1 TTTGAAAAAATTTAATACTTTAA
6177 TTTGAAAAAATTTAATACTTTAA
1 TTTGAAAAAATTTAATACTTTAA
6200 AATTATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 5 0.25
22 6 0.30
23 5 0.25
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (23 bp):
TTTGAAAAAATTTAATACTTTAA
Found at i:18583 original size:25 final size:25
Alignment explanation
Indices: 18555--18605 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
18545 ATTAACGTAA
*
18555 AGCTAAACTTAGAATTTAATAATTT
1 AGCTAAACTTACAATTTAATAATTT
**
18580 AGCTCGACTTACAATTTAATAATTT
1 AGCTAAACTTACAATTTAATAATTT
18605 A
1 A
18606 AATTTAGTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (25 bp):
AGCTAAACTTACAATTTAATAATTT
Found at i:19894 original size:61 final size:62
Alignment explanation
Indices: 19757--19908 Score: 148
Period size: 61 Copynumber: 2.5 Consensus size: 62
19747 GTGTAGTGGT
* * * * *
19757 CACACGGGCGTGTG-TCTAGGCCATGTAACTCATTATTTGTGTATTAAGGCCACACAGGCAGA
1 CACACGAGCGTGTGTTC-AAGCCGTGTAACTCACTATTTGTGTATGAAGGCCACACAGGCAGA
* * * * * *
19819 CACATGAGCATGTGTTC-AGCCGTGTAACTCACTGTTTGTGTATGAAGGCCGCAC-GAGCTGC
1 CACACGAGCGTGTGTTCAAGCCGTGTAACTCACTATTTGTGTATGAAGGCCACACAG-GCAGA
* *
19880 CACACGAGCGTGTGTGCAAGTCGTGTAAC
1 CACACGAGCGTGTGTTCAAGCCGTGTAAC
19909 ATTGTTTTGA
Statistics
Matches: 72, Mismatches: 15, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
60 1 0.01
61 48 0.67
62 21 0.29
63 2 0.03
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (62 bp):
CACACGAGCGTGTGTTCAAGCCGTGTAACTCACTATTTGTGTATGAAGGCCACACAGGCAGA
Found at i:21424 original size:22 final size:23
Alignment explanation
Indices: 21387--21446 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
21377 AACAAGCATC
21387 AAAATTATGTATAAATGA-CATTAA
1 AAAATTAT-TA-AAATGATCATTAA
21411 AAAATTATTAAAAT-ATCATTAA
1 AAAATTATTAAAATGATCATTAA
*
21433 ATAATTA--AAAATGA
1 AAAATTATTAAAATGA
21447 ACCATGAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
20 5 0.15
21 2 0.06
22 16 0.48
23 2 0.06
24 8 0.24
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.33
Consensus pattern (23 bp):
AAAATTATTAAAATGATCATTAA
Found at i:21679 original size:7 final size:7
Alignment explanation
Indices: 21642--21682 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
21632 CTTAACTTTG
21642 AATTTAAT
1 AATTT-AT
21650 AATTTAT
1 AATTTAT
*
21657 ATTTTAT
1 AATTTAT
21664 AA-TTA-
1 AATTTAT
21669 AATTTAT
1 AATTTAT
21676 AATTTAT
1 AATTTAT
21683 GGTAACTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
5 2 0.07
6 6 0.21
7 16 0.55
8 5 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTAT
Found at i:25816 original size:29 final size:30
Alignment explanation
Indices: 25784--26023 Score: 162
Period size: 30 Copynumber: 8.2 Consensus size: 30
25774 AAAAGAGTAA
*
25784 TTTTGAGAG-TTCGAGGTCAAAAATGGAGTT
1 TTTTGAGAGTTTCGAGGTCAAAAATGGA-AT
* * *
25814 TTTTGACA-TTTGGGGGT-AAAAATGGAAT
1 TTTTGAGAGTTTCGAGGTCAAAAATGGAAT
* * *
25842 TTTTGGGAGTTTTGGGGTCAAAAATGGAAT
1 TTTTGAGAGTTTCGAGGTCAAAAATGGAAT
* ** *
25872 ATTTG-GAAATTCGAGGGT-AAAAATGGAAA
1 TTTTGAGAGTTTCGA-GGTCAAAAATGGAAT
*
25901 TTTT-AGGAGTTTCGAGGTCAAAAATAGAAT
1 TTTTGA-GAGTTTCGAGGTCAAAAATGGAAT
* * * *
25931 TTTTGAAAGTTTTGGGGTCAAAAAT-AATAT
1 TTTTGAGAGTTTCGAGGTCAAAAATGGA-AT
* *
25961 TTTTG-GAAG-TTCGGGGGT--AAAATAGAAT
1 TTTTGAG-AGTTTC-GAGGTCAAAAATGGAAT
*
25989 TTTTG-GAATTTTCGAGGTCAAAAATGGAAT
1 TTTTGAG-AGTTTCGAGGTCAAAAATGGAAT
26019 TTTTG
1 TTTTG
26024 GAAGTTTTTG
Statistics
Matches: 167, Mismatches: 28, Indels: 30
0.74 0.12 0.13
Matches are distributed among these distances:
28 26 0.16
29 45 0.27
30 95 0.57
31 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (30 bp):
TTTTGAGAGTTTCGAGGTCAAAAATGGAAT
Found at i:25858 original size:30 final size:30
Alignment explanation
Indices: 25822--26090 Score: 200
Period size: 30 Copynumber: 9.1 Consensus size: 30
25812 TTTTTTGACA
*
25822 TTTGGGGGTAAAAATGGAATTTTTGGGAGT
1 TTTGGGGGTAAAAATGGAATTTTTGGAAGT
* *
25852 TTT-GGGGTCAAAAATGGAATATTTGGAA-A
1 TTTGGGGGT-AAAAATGGAATTTTTGGAAGT
* * *
25881 TTCGAGGGTAAAAATGGAAATTTTAGG-AG-
1 TTTGGGGGTAAAAATGG-AATTTTTGGAAGT
* * * *
25910 TTTCGAGGTCAAAAATAGAATTTTTGAAAGT
1 TTTGGGGGT-AAAAATGGAATTTTTGGAAGT
*
25941 TTT-GGGGTCAAAAAT-AATATTTTTGGAAG-
1 TTTGGGGGT-AAAAATGGA-ATTTTTGGAAGT
* *
25970 TTCGGGGGT-AAAATAGAATTTTTGGAA-T
1 TTTGGGGGTAAAAATGGAATTTTTGGAAGT
* *
25998 TTTCGAGGTCAAAAATGGAATTTTTGGAAGT
1 TTTGGGGGT-AAAAATGGAATTTTTGGAAGT
* *
26029 TTTTGGGTTAAAAAT-GAGATTTTTGGAAG-
1 TTTGGGGGTAAAAATGGA-ATTTTTGGAAGT
* * * *
26058 TTCGAGGGTAAAAACGAAATTTTTGGACAGT
1 TTTGGGGGTAAAAATGGAATTTTTGGA-AGT
26089 TT
1 TT
26091 AAGGACCTCC
Statistics
Matches: 189, Mismatches: 32, Indels: 35
0.74 0.12 0.14
Matches are distributed among these distances:
28 21 0.11
29 53 0.28
30 103 0.54
31 12 0.06
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (30 bp):
TTTGGGGGTAAAAATGGAATTTTTGGAAGT
Found at i:25885 original size:88 final size:86
Alignment explanation
Indices: 25791--26084 Score: 315
Period size: 88 Copynumber: 3.3 Consensus size: 86
25781 TAATTTTGAG
* * * * *
25791 AGTTCGAGGTCAAAAATGGAGTTTTTTGACATTTGGGGGT-AAAAATGGAATTTTTGGGAGTTTT
1 AGTTCGAGGT-AAAAATGGAATTTTTGGA-ATTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTT
25855 GGGGTCAAAAATGGAATATTTGGA
64 GGGGTCAAAAAT-GAATATTTGGA
* * * * *
25879 AATTCGAGGGTAAAAATGGAAATTTTAGGAGTTTCGAGGTCAAAAATAGAATTTTTGAAAGTTTT
1 AGTTCGA-GGTAAAAATGG-AATTTTTGGAATTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTT
25944 GGGGTCAAAAAT-AATATTTTTGGA
64 GGGGTCAAAAATGAATA--TTTGGA
* *
25968 AGTTCGGGGGT-AAAATAGAATTTTTGGAATTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTT
1 AGTTC-GAGGTAAAAATGGAATTTTTGGAA-TTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTT
* * *
26032 TGGGTTAAAAATGAGATTTTTGGA
64 GGGGTCAAAAATGA-ATATTTGGA
* *
26056 AGTTCGAGGGTAAAAACGAAATTTTTGGA
1 AGTTCGA-GGTAAAAATGGAATTTTTGGA
26085 CAGTTTAAGG
Statistics
Matches: 171, Mismatches: 24, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
87 14 0.08
88 83 0.49
89 71 0.42
90 3 0.02
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (86 bp):
AGTTCGAGGTAAAAATGGAATTTTTGGAATTTCGAGGTCAAAAATGGAATTTTTGGAAGTTTTGG
GGTCAAAAATGAATATTTGGA
Found at i:25890 original size:59 final size:59
Alignment explanation
Indices: 25798--26090 Score: 251
Period size: 59 Copynumber: 4.9 Consensus size: 59
25788 GAGAGTTCGA
* * * * * * *
25798 GGTCAAAAATGGAGTTTTTTGACATTTGGGGGTAAAAATGGAATTTTTGGGAGTTTTGG
1 GGTCAAAAATAGAATTTTTGGAAATTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGG
* * * * *
25857 GGTCAAAAATGGAATATTTGGAAATTCGAGGGTAAAAATGGAAATTTTAGG-AGTTTCGA
1 GGTCAAAAATAGAATTTTTGGAAATTCGAGGGTAAAAATGG-AATTTTTGGAAGTTTTGG
* * **
25916 GGTCAAAAATAGAATTTTT-GAAAGTTTTG-GGGTCAAAAAT-AATATTTTTGGAAGTTCGGG
1 GGTCAAAAATAGAATTTTTGGAAA--TTCGAGGGT-AAAAATGGA-ATTTTTGGAAGTTTTGG
* *
25976 GGT--AAAATAGAATTTTTGGAATTTTCGA-GGTCAAAAATGGAATTTTTGGAAGTTTTTG
1 GGTCAAAAATAGAATTTTTGGAA-ATTCGAGGGT-AAAAATGGAATTTTTGGAAGTTTTGG
* * * *
26034 GGTTAAAAAT-GAGATTTTTGGAAGTTCGAGGGTAAAAACGAAATTTTTGGACAGTTT
1 GGTCAAAAATAGA-ATTTTTGGAAATTCGAGGGTAAAAATGGAATTTTTGGA-AGTTT
26091 AAGGACCTCC
Statistics
Matches: 193, Mismatches: 26, Indels: 29
0.78 0.10 0.12
Matches are distributed among these distances:
58 49 0.25
59 96 0.50
60 48 0.25
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (59 bp):
GGTCAAAAATAGAATTTTTGGAAATTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGG
Found at i:26784 original size:23 final size:23
Alignment explanation
Indices: 26740--26784 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
26730 TCTGCCGGTA
* * *
26740 CACGCGCCACCATTCTCGCCTTC
1 CACGCGCCACCATGCACACCTTC
*
26763 CACGCGCCTCCATGCACACCTT
1 CACGCGCCACCATGCACACCTT
26785 TTTCAGGTAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.16, C:0.51, G:0.13, T:0.20
Consensus pattern (23 bp):
CACGCGCCACCATGCACACCTTC
Found at i:27210 original size:13 final size:13
Alignment explanation
Indices: 27172--27225 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
27162 TTTCATTTTA
*
27172 TTATTAATA-TTT
1 TTATTAATACTAT
27184 TTATT-A-AC-AT
1 TTATTAATACTAT
*
27194 TTATTAATGCTAT
1 TTATTAATACTAT
*
27207 TTATTACTACTAT
1 TTATTAATACTAT
27220 TTATTA
1 TTATTA
27226 TTAATAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
10 7 0.21
11 2 0.06
12 6 0.18
13 19 0.56
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.57
Consensus pattern (13 bp):
TTATTAATACTAT
Found at i:28047 original size:17 final size:17
Alignment explanation
Indices: 28022--28111 Score: 74
Period size: 17 Copynumber: 5.1 Consensus size: 17
28012 GACTTTTTAA
* **
28022 TTAAGTTTTAAATCCAT
1 TTAAATTTTAAATAAAT
*
28039 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
*
28056 TTAAA-TTTAAAGCAAAT
1 TTAAATTTTAAA-TAAAT
*
28073 TTAAATTTAAAAGATAAAT
1 TTAAATTT-TAA-ATAAAT
*
28092 TTAAATTTAAAAATAAAT
1 TTAAATTT-TAAATAAAT
28110 TT
1 TT
28112 GAATAAATTT
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
16 5 0.08
17 27 0.44
18 10 0.16
19 18 0.30
20 1 0.02
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:28051 original size:6 final size:6
Alignment explanation
Indices: 28037--28124 Score: 67
Period size: 6 Copynumber: 15.2 Consensus size: 6
28027 TTTTAAATCC
* **
28037 ATTTAA ATTTTA A-TTAA ATTTAA ATTTAA A-GCAA ATTTAA ATTTAAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA
** ** *
28084 AGATAA ATTTAA ATTTAA AAATAA ATTTGA A--TAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
28125 CCCAATAAAA
Statistics
Matches: 61, Mismatches: 16, Indels: 10
0.70 0.18 0.11
Matches are distributed among these distances:
4 3 0.05
5 7 0.11
6 47 0.77
7 4 0.07
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (6 bp):
ATTTAA
Done.