Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007804.1 Corchorus capsularis cultivar CVL-1 contig07825, 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: 47188
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:35 original size:22 final size:21
Alignment explanation
Indices: 10--104 Score: 59
Period size: 22 Copynumber: 4.3 Consensus size: 21
1 TCATAACGA
10 GGTTATAAGAATTTCATAGTGT
1 GGTTATAA-AATTTCATAGTGT
*
32 GGTTAACAAAAATTTCATTAG-GAT
1 GGTT-A-TAAAATTTCA-TAGTG-T
* * * *
56 -GTTACTAATATTTCATGGGGA
1 GGTTA-TAAAATTTCATAGTGT
*
77 GGTTATCAAAATTTTATAGTGT
1 GGTTAT-AAAATTTCATAGTGT
99 GGTTAT
1 GGTTAT
105 GAAGCTTATA
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
21 3 0.05
22 35 0.62
23 12 0.21
24 6 0.11
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.40
Consensus pattern (21 bp):
GGTTATAAAATTTCATAGTGT
Found at i:292 original size:42 final size:44
Alignment explanation
Indices: 201--299 Score: 107
Period size: 42 Copynumber: 2.3 Consensus size: 44
191 ATAGAGATCA
* * *
201 GATTATCAAAATTTATAGGAAGATTATCAAAATTTCACAGTGTT
1 GATTATCAAAATTTATACGAAGATTATCAAAATTACACAATGTT
* *
245 G-TTATCAAAATTTGA-ACG-AGGTTATCAAAATTACATAATG-T
1 GATTATCAAAATTT-ATACGAAGATTATCAAAATTACACAATGTT
*
286 GATTATCAGAATTT
1 GATTATCAAAATTT
300 CATAGAGGGG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
41 2 0.04
42 29 0.62
43 14 0.30
44 2 0.04
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.36
Consensus pattern (44 bp):
GATTATCAAAATTTATACGAAGATTATCAAAATTACACAATGTT
Found at i:355 original size:22 final size:22
Alignment explanation
Indices: 123--391 Score: 126
Period size: 22 Copynumber: 12.4 Consensus size: 22
113 TAAAAGTCTC
*
123 AATTTCATAAAGA-G-TACCAA
1 AATTTCATAAAGAGGTTATCAA
* *
143 AATTTGATAGA-AGGTTATC-A
1 AATTTCATAAAGAGGTTATCAA
* * * * * *
163 AATCTCATAGAGTGATTACCGA
1 AATTTCATAAAGAGGTTATCAA
* *
185 AATTTCATAGAGATCAGATTATCAA
1 AATTTCATA-A-A-GAGGTTATCAA
210 AATTT-ATAGGAAGA--TTATCAA
1 AATTTCATA--AAGAGGTTATCAA
* ** **
231 AATTTCACAGTGTTGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
* *
253 AATTT--GAACGAGGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
* * * * *
273 AATTACATAATGTGATTATCAG
1 AATTTCATAAAGAGGTTATCAA
* * * *
295 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAAAGAGGTTATCAA
*
317 AATTTTATAAAGAGGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
339 AATTTCATAAAGAGGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
* * * *
361 ATTTTCA-AAATGTGATTATAAA
1 AATTTCATAAA-GAGGTTATCAA
383 AATTTCATA
1 AATTTCATA
392 GTGGTATTTC
Statistics
Matches: 185, Mismatches: 49, Indels: 27
0.71 0.19 0.10
Matches are distributed among these distances:
19 1 0.01
20 35 0.19
21 23 0.12
22 105 0.57
23 2 0.01
24 5 0.03
25 14 0.08
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.33
Consensus pattern (22 bp):
AATTTCATAAAGAGGTTATCAA
Found at i:492 original size:20 final size:20
Alignment explanation
Indices: 467--505 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
457 CTTTTATTAT
*
467 GGAGGATATCAAATTTTCAG
1 GGAGGATATCAAAATTTCAG
487 GGAGGATATCAAAATTTCA
1 GGAGGATATCAAAATTTCA
506 TAGTTTAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.28
Consensus pattern (20 bp):
GGAGGATATCAAAATTTCAG
Found at i:647 original size:23 final size:23
Alignment explanation
Indices: 441--698 Score: 105
Period size: 22 Copynumber: 11.6 Consensus size: 23
431 GTTATCAAAT
* * *
441 TAGGAAGGTTATTAAACTTTT-A
1 TAGGGAGGTTATCAAAATTTTCA
* *
463 TTATGGAGGATATC-AAATTTTC-
1 -TAGGGAGGTTATCAAAATTTTCA
*
485 -AGGGAGGATATCAAAA-TTTCA
1 TAGGGAGGTTATCAAAATTTTCA
** *
506 TAGTTTA-GTTTTCAAAATTTT-A
1 TAG-GGAGGTTATCAAAATTTTCA
* *
528 TA-AGAGGGTTATCAAAA-TTTCG
1 TAGGGA-GGTTATCAAAATTTTCA
* * * *
550 TA-GTATGTAGATCAAAA-TATCA
1 TAGGGAGGT-TATCAAAATTTTCA
* *
572 TAGGGAGATTAACAAAA-TTTCA
1 TAGGGAGGTTATCAAAATTTTCA
** **
594 TAACGAGGTTATCAAAA-AATCA
1 TAGGGAGGTTATCAAAATTTTCA
* *
616 TAGGAAGGTTATCAAAATTTTAA
1 TAGGGAGGTTATCAAAATTTTCA
*
639 TAGGGAGGTTTATCAAACTTTT-A
1 TAGGGAGG-TTATCAAAATTTTCA
* *
662 TAGGAAGATTTATCAAAA-TTTCA
1 TAGGGAG-GTTATCAAAATTTTCA
**
685 TAGCAAGGTTATCA
1 TAGGGAGGTTATCA
699 CACTTTCATG
Statistics
Matches: 175, Mismatches: 45, Indels: 31
0.70 0.18 0.12
Matches are distributed among these distances:
20 16 0.09
21 8 0.05
22 92 0.53
23 47 0.27
24 12 0.07
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (23 bp):
TAGGGAGGTTATCAAAATTTTCA
Found at i:660 original size:24 final size:23
Alignment explanation
Indices: 615--698 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
605 TCAAAAAATC
615 ATAGGAAGG-TTATCAAAATTTT
1 ATAGGAAGGTTTATCAAAATTTT
* *
637 AATAGGGAGGTTTATCAAACTTTT
1 -ATAGGAAGGTTTATCAAAATTTT
* *
661 ATAGGAAGATTTATCAAAATTTC
1 ATAGGAAGGTTTATCAAAATTTT
*
684 ATAGCAAGG-TTATCA
1 ATAGGAAGGTTTATCA
699 CACTTTCATG
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
22 6 0.12
23 34 0.65
24 12 0.23
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (23 bp):
ATAGGAAGGTTTATCAAAATTTT
Found at i:705 original size:22 final size:23
Alignment explanation
Indices: 648--707 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
638 ATAGGGAGGT
* * *
648 TTATCAAACTTTTATAGGAAGAT
1 TTATCAAACTTTCATAGCAAGAG
*
671 TTATCAAAATTTCATAGCAAG-G
1 TTATCAAACTTTCATAGCAAGAG
*
693 TTATCACACTTTCAT
1 TTATCAAACTTTCAT
708 GATGTGATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (23 bp):
TTATCAAACTTTCATAGCAAGAG
Found at i:795 original size:22 final size:21
Alignment explanation
Indices: 765--841 Score: 55
Period size: 22 Copynumber: 3.5 Consensus size: 21
755 TAGGTTTTTA
765 AATATTCATAACGTGGTTATC
1 AATATTCATAACGTGGTTATC
** *
786 AATATATCATATGGAGGTTATC
1 AATAT-TCATAACGTGGTTATC
* **
808 AACATCTCATAGTGTTGGTTATC
1 AATAT-TCATAACG-TGGTTATC
*
831 AAAATTTCATA
1 AATA-TTCATA
842 TTAAGATCTT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
21 5 0.11
22 23 0.52
23 15 0.34
24 1 0.02
ACGTcount: A:0.35, C:0.13, G:0.14, T:0.38
Consensus pattern (21 bp):
AATATTCATAACGTGGTTATC
Found at i:831 original size:23 final size:22
Alignment explanation
Indices: 777--842 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
767 TATTCATAAC
*
777 GTGGTTATCAATATATCATATG
1 GTGGTTATCAAAATATCATATG
* * *
799 GAGGTTATCAACATCTCATAGTG
1 GTGGTTATCAAAATATCATA-TG
* *
822 TTGGTTATCAAAATTTCATAT
1 GTGGTTATCAAAATATCATAT
843 TAAGATCTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
22 18 0.50
23 18 0.50
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (22 bp):
GTGGTTATCAAAATATCATATG
Found at i:1038 original size:13 final size:13
Alignment explanation
Indices: 1020--1044 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1010 GATTATTACA
1020 ATTTCATTTAAAT
1 ATTTCATTTAAAT
1033 ATTTCATTTAAA
1 ATTTCATTTAAA
1045 CGTGTTGGGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTCATTTAAAT
Found at i:1153 original size:6 final size:6
Alignment explanation
Indices: 1142--1181 Score: 53
Period size: 6 Copynumber: 6.2 Consensus size: 6
1132 TTGTAGATAC
1142 ATCATA ATCATA ATCATA ATCATATA ATCATAA ATCATA A
1 ATCATA ATCATA ATCATA ATC--ATA ATCAT-A ATCATA A
1182 GAAGTAGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 19 0.61
7 6 0.19
8 6 0.19
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.33
Consensus pattern (6 bp):
ATCATA
Found at i:4085 original size:87 final size:87
Alignment explanation
Indices: 3939--4112 Score: 348
Period size: 87 Copynumber: 2.0 Consensus size: 87
3929 AGAGACGGAC
3939 CAACACTTGTTAGGTTGAGTAGAATGAGCTTAATGTCAATAAATAAGGTTACAGGTTTGAGTATT
1 CAACACTTGTTAGGTTGAGTAGAATGAGCTTAATGTCAATAAATAAGGTTACAGGTTTGAGTATT
4004 GTGAATGATGAAAACAGCTGCT
66 GTGAATGATGAAAACAGCTGCT
4026 CAACACTTGTTAGGTTGAGTAGAATGAGCTTAATGTCAATAAATAAGGTTACAGGTTTGAGTATT
1 CAACACTTGTTAGGTTGAGTAGAATGAGCTTAATGTCAATAAATAAGGTTACAGGTTTGAGTATT
4091 GTGAATGATGAAAACAGCTGCT
66 GTGAATGATGAAAACAGCTGCT
4113 GACAGGGGCT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 87 1.00
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.31
Consensus pattern (87 bp):
CAACACTTGTTAGGTTGAGTAGAATGAGCTTAATGTCAATAAATAAGGTTACAGGTTTGAGTATT
GTGAATGATGAAAACAGCTGCT
Found at i:5463 original size:8 final size:8
Alignment explanation
Indices: 5450--5497 Score: 55
Period size: 8 Copynumber: 6.1 Consensus size: 8
5440 TCACCCCACT
5450 TTTTACAC
1 TTTTACAC
5458 TTTTAC-C
1 TTTTACAC
*
5465 CTTTAC-C
1 TTTTACAC
*
5472 TTTTACCAT
1 TTTTA-CAC
5481 TTTTACAC
1 TTTTACAC
5489 TTTTACAC
1 TTTTACAC
5497 T
1 T
5498 GAGCCTCCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
7 11 0.32
8 18 0.53
9 5 0.15
ACGTcount: A:0.21, C:0.27, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTTACAC
Found at i:5476 original size:14 final size:15
Alignment explanation
Indices: 5451--5494 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
5441 CACCCCACTT
5451 TTTACACTTTTACCC
1 TTTACACTTTTACCC
*
5466 TTTAC-CTTTTACCATT
1 TTTACACTTTTACC--C
5482 TTTACACTTTTAC
1 TTTACACTTTTAC
5495 ACTGAGCCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 8 0.32
15 5 0.20
16 5 0.20
17 7 0.28
ACGTcount: A:0.20, C:0.27, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTACACTTTTACCC
Found at i:5642 original size:62 final size:65
Alignment explanation
Indices: 5537--5711 Score: 207
Period size: 64 Copynumber: 2.7 Consensus size: 65
5527 GGCGGAGCCT
* * * * * * *
5537 CCTCACTGGGGCGGCTTCTCCATGGGCAGGCCACCC-CACTGGGGCGGTTTCGCCACGGCAAACT
1 CCTCA-TGGGGCGGCTTCGCCA-AGGCAGGCCGCCCTCACTGGGGCGGCTTCACCACAGCAAACC
5601 G-
64 GC
5602 CCT-ATGGGGCGGCTTCGCCAAGGCAGGCCGCCCTCA-TGGGGCGGCTTCACCACAGCAAACCGC
1 CCTCATGGGGCGGCTTCGCCAAGGCAGGCCGCCCTCACTGGGGCGGCTTCACCACAGCAAACCGC
* * *
5665 CCTCATGGGGCGGCTTTGCCACGGCAGGCCGCCCT-AGTGGGGCGGCT
1 CCTCATGGGGCGGCTTCGCCAAGGCAGGCCGCCCTCACTGGGGCGGCT
5712 AGACCAAATT
Statistics
Matches: 97, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
62 33 0.34
63 21 0.22
64 40 0.41
65 3 0.03
ACGTcount: A:0.14, C:0.37, G:0.34, T:0.15
Consensus pattern (65 bp):
CCTCATGGGGCGGCTTCGCCAAGGCAGGCCGCCCTCACTGGGGCGGCTTCACCACAGCAAACCGC
Found at i:5643 original size:32 final size:33
Alignment explanation
Indices: 5537--5711 Score: 150
Period size: 32 Copynumber: 5.5 Consensus size: 33
5527 GGCGGAGCCT
* * *
5537 CCTCACTGGGGCGGCTTCTCCATGGGCAGGCCAC
1 CCTCACTGGGGCGGCTTCGCCA-AGGCAGGCCGC
* * ** *
5571 CC-CACTGGGGCGGTTTCGCCACGGCAAACTG-
1 CCTCACTGGGGCGGCTTCGCCAAGGCAGGCCGC
5602 CCT-A-TGGGGCGGCTTCGCCAAGGCAGGCCGC
1 CCTCACTGGGGCGGCTTCGCCAAGGCAGGCCGC
* **
5633 CCTCA-TGGGGCGGCTTCACCACA-GCAAACCGC
1 CCTCACTGGGGCGGCTTCGCCA-AGGCAGGCCGC
* *
5665 CCTCA-TGGGGCGGCTTTGCCACGGCAGGCCGC
1 CCTCACTGGGGCGGCTTCGCCAAGGCAGGCCGC
*
5697 CCT-AGTGGGGCGGCT
1 CCTCACTGGGGCGGCT
5712 AGACCAAATT
Statistics
Matches: 115, Mismatches: 20, Indels: 14
0.77 0.13 0.09
Matches are distributed among these distances:
30 21 0.18
31 7 0.06
32 67 0.58
33 18 0.16
34 2 0.02
ACGTcount: A:0.14, C:0.37, G:0.34, T:0.15
Consensus pattern (33 bp):
CCTCACTGGGGCGGCTTCGCCAAGGCAGGCCGC
Found at i:5898 original size:32 final size:33
Alignment explanation
Indices: 5767--5900 Score: 132
Period size: 32 Copynumber: 4.2 Consensus size: 33
5757 AAAATAGCCG
* *
5767 AGCCGCCCCACTGGCGCGGCCTG-CCGTGGCGA
1 AGCCGCCCCACTGGGGCGGCCTGCCCATGGCGA
*
5799 AGCCGCCCCACTTGGGCGGCCTGCCC-TGGCGA
1 AGCCGCCCCACTGGGGCGGCCTGCCCATGGCGA
* *** * *
5831 AGCCG-CCCAGTGGGGCGGCCTATTCATAGTGA
1 AGCCGCCCCACTGGGGCGGCCTGCCCATGGCGA
* * *
5863 AGCCGCCCTAGTGGGGCGGCCTGCCCATGG-TA
1 AGCCGCCCCACTGGGGCGGCCTGCCCATGGCGA
5895 AGCCGC
1 AGCCGC
5901 TCTCTTGGGG
Statistics
Matches: 84, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
31 15 0.18
32 48 0.57
33 21 0.25
ACGTcount: A:0.13, C:0.38, G:0.36, T:0.13
Consensus pattern (33 bp):
AGCCGCCCCACTGGGGCGGCCTGCCCATGGCGA
Found at i:6612 original size:2 final size:2
Alignment explanation
Indices: 6607--6662 Score: 55
Period size: 2 Copynumber: 28.5 Consensus size: 2
6597 TTATTTTGTG
* *
6607 TA TA TA TA -A CTA AA TA T- TA TA TA TA TGA -A TA TG TA TA TA TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
6648 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
6663 TTATGTATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
1 3 0.07
2 40 0.89
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:6771 original size:10 final size:9
Alignment explanation
Indices: 6744--6770 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
6734 TGCCTTTGTC
6744 CTTTTTTTT
1 CTTTTTTTT
6753 CTTTTTTTT
1 CTTTTTTTT
6762 CTTTTTTTT
1 CTTTTTTTT
6771 TAACTCTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:9424 original size:16 final size:16
Alignment explanation
Indices: 9403--9523 Score: 217
Period size: 16 Copynumber: 7.6 Consensus size: 16
9393 GGCAATTGGG
9403 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
*
9419 CGGGTTCGGGTAATTT
1 CGGGTTCGGGTATTTT
9435 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
9451 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
*
9467 CGGGTTCGGGTTTTTT
1 CGGGTTCGGGTATTTT
9483 CGGGTTCGGGTA-TTT
1 CGGGTTCGGGTATTTT
9498 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
9514 CGGGTTCGGG
1 CGGGTTCGGG
9524 CTAGGGTCGG
Statistics
Matches: 100, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
15 15 0.15
16 85 0.85
ACGTcount: A:0.06, C:0.13, G:0.40, T:0.41
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:9444 original size:32 final size:32
Alignment explanation
Indices: 9403--9541 Score: 217
Period size: 32 Copynumber: 4.3 Consensus size: 32
9393 GGCAATTGGG
9403 CGGGTTCGGGTATTTTCGGGTTCGGGTAATTT
1 CGGGTTCGGGTATTTTCGGGTTCGGGTAATTT
*
9435 CGGGTTCGGGTATTTTCGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTTCGGGTTCGGGTAATTT
*
9467 CGGGTTCGGGTTTTTTCGGGTTCGGGT-ATTT
1 CGGGTTCGGGTATTTTCGGGTTCGGGTAATTT
***
9498 CGGGTTCGGGTATTTTCGGGTTCGGGCTAGGGT
1 CGGGTTCGGGTATTTTCGGGTTCGGG-TAATTT
9531 CGGGTTCGGGT
1 CGGGTTCGGGT
9542 TCACTTTCGA
Statistics
Matches: 98, Mismatches: 7, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
31 28 0.29
32 58 0.59
33 12 0.12
ACGTcount: A:0.06, C:0.14, G:0.41, T:0.40
Consensus pattern (32 bp):
CGGGTTCGGGTATTTTCGGGTTCGGGTAATTT
Found at i:9474 original size:48 final size:47
Alignment explanation
Indices: 9403--9541 Score: 215
Period size: 48 Copynumber: 2.9 Consensus size: 47
9393 GGCAATTGGG
9403 CGGGTTCGGGTATTTTCGGGTTCGGGTAATTTCGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTTCGGGTTCGGGTAATTTCGGGTTCGGGTA-TTT
**
9451 CGGGTTCGGGTATTTTCGGGTTCGGGTTTTTTCGGGTTCGGGTATTT
1 CGGGTTCGGGTATTTTCGGGTTCGGGTAATTTCGGGTTCGGGTATTT
***
9498 CGGGTTCGGGTATTTTCGGGTTCGGGCTAGGGTCGGGTTCGGGT
1 CGGGTTCGGGTATTTTCGGGTTCGGG-TAATTTCGGGTTCGGGT
9542 TCACTTTCGA
Statistics
Matches: 84, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
47 29 0.35
48 55 0.65
ACGTcount: A:0.06, C:0.14, G:0.41, T:0.40
Consensus pattern (47 bp):
CGGGTTCGGGTATTTTCGGGTTCGGGTAATTTCGGGTTCGGGTATTT
Found at i:10296 original size:6 final size:6
Alignment explanation
Indices: 10285--10342 Score: 68
Period size: 6 Copynumber: 10.2 Consensus size: 6
10275 TATTTTGATA
**
10285 TCGGGT TCGGG- TCGGGT TCGGGT TCGGGT TCGGG- -CGGGT TCGAAT
1 TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT TCGGGT
*
10330 TCGGAT TCGGGT T
1 TCGGGT TCGGGT T
10343 GTCTCGAGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
4 4 0.09
5 5 0.11
6 36 0.80
ACGTcount: A:0.05, C:0.17, G:0.47, T:0.31
Consensus pattern (6 bp):
TCGGGT
Found at i:10299 original size:11 final size:11
Alignment explanation
Indices: 10285--10326 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
10275 TATTTTGATA
10285 TCGGGTTCGGG
1 TCGGGTTCGGG
10296 TCGGGTTCGGG
1 TCGGGTTCGGG
10307 TTCGGGTTCGGG
1 -TCGGGTTCGGG
10319 -CGGGTTCG
1 TCGGGTTCG
10327 AATTCGGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.27
11 11 0.37
12 11 0.37
ACGTcount: A:0.00, C:0.19, G:0.52, T:0.29
Consensus pattern (11 bp):
TCGGGTTCGGG
Found at i:10307 original size:17 final size:17
Alignment explanation
Indices: 10285--10326 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
10275 TATTTTGATA
10285 TCGGGTTCGGG-TCGGG
1 TCGGGTTCGGGTTCGGG
10301 TTCGGGTTCGGGTTCGGG
1 -TCGGGTTCGGGTTCGGG
10319 -CGGGTTCG
1 TCGGGTTCG
10327 AATTCGGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.33
17 11 0.46
18 5 0.21
ACGTcount: A:0.00, C:0.19, G:0.52, T:0.29
Consensus pattern (17 bp):
TCGGGTTCGGGTTCGGG
Found at i:10325 original size:22 final size:23
Alignment explanation
Indices: 10285--10341 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
10275 TATTTTGATA
**
10285 TCGGGTTCGGGTCGGGTTCGGGT
1 TCGGGTTCGGGTCGGGTTCGAAT
10308 TCGGGTTCGGG-CGGGTTCGAAT
1 TCGGGTTCGGGTCGGGTTCGAAT
*
10330 TCGGATTCGGGT
1 TCGGGTTCGGGT
10342 TGTCTCGAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.05, C:0.18, G:0.47, T:0.30
Consensus pattern (23 bp):
TCGGGTTCGGGTCGGGTTCGAAT
Found at i:10369 original size:16 final size:16
Alignment explanation
Indices: 10350--10390 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
10340 GTTGTCTCGA
10350 GTTCGGGTATTTTCGG
1 GTTCGGGTATTTTCGG
10366 GTTCGGGTATTTTCGG
1 GTTCGGGTATTTTCGG
10382 GTTCGGGTA
1 GTTCGGGTA
10391 CGGGCGGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.07, C:0.12, G:0.39, T:0.41
Consensus pattern (16 bp):
GTTCGGGTATTTTCGG
Found at i:10371 original size:32 final size:32
Alignment explanation
Indices: 10329--10390 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
10319 CGGGTTCGAA
10329 TTCGGATTCGGGT-TGTCTCGAGTTCGGGTATT
1 TTCGGATTCGGGTAT-TCTCGAGTTCGGGTATT
* * *
10361 TTCGGGTTCGGGTATTTTCGGGTTCGGGTA
1 TTCGGATTCGGGTATTCTCGAGTTCGGGTA
10391 CGGGCGGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 25 0.96
33 1 0.04
ACGTcount: A:0.08, C:0.15, G:0.37, T:0.40
Consensus pattern (32 bp):
TTCGGATTCGGGTATTCTCGAGTTCGGGTATT
Found at i:10463 original size:17 final size:17
Alignment explanation
Indices: 10437--10470 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
10427 CGGGTAATTT
10437 CGGGTTCGGG-TTCGGG
1 CGGGTTCGGGTTTCGGG
10453 CGGGTTTCGGGTTTCGGG
1 CGGG-TTCGGGTTTCGGG
10471 TTCATTTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 6 0.38
18 6 0.38
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (17 bp):
CGGGTTCGGGTTTCGGG
Found at i:13693 original size:12 final size:12
Alignment explanation
Indices: 13676--13700 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13666 GGCGGGATTC
13676 TCACATTGTTGT
1 TCACATTGTTGT
13688 TCACATTGTTGT
1 TCACATTGTTGT
13700 T
1 T
13701 TAACGGAGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (12 bp):
TCACATTGTTGT
Found at i:15664 original size:27 final size:27
Alignment explanation
Indices: 15620--15673 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
15610 CTAAAACTTT
*
15620 TGGGAGTCTCCGTGTATTTGACAATGG
1 TGGGAGTCTCCGTATATTTGACAATGG
*
15647 TGGGAGTCTCCTTATATTTGACAATGG
1 TGGGAGTCTCCGTATATTTGACAATGG
15674 CAATTTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.20, C:0.15, G:0.30, T:0.35
Consensus pattern (27 bp):
TGGGAGTCTCCGTATATTTGACAATGG
Found at i:19915 original size:60 final size:60
Alignment explanation
Indices: 19842--19959 Score: 236
Period size: 60 Copynumber: 2.0 Consensus size: 60
19832 GTTTTAAGCA
19842 TGATCAACCTTTTATTCATTCAGATCTGTGGTAAAATCGTTGTAATCATTTTCTTTTGAG
1 TGATCAACCTTTTATTCATTCAGATCTGTGGTAAAATCGTTGTAATCATTTTCTTTTGAG
19902 TGATCAACCTTTTATTCATTCAGATCTGTGGTAAAATCGTTGTAATCATTTTCTTTTG
1 TGATCAACCTTTTATTCATTCAGATCTGTGGTAAAATCGTTGTAATCATTTTCTTTTG
19960 GGTGCCAAGG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.46
Consensus pattern (60 bp):
TGATCAACCTTTTATTCATTCAGATCTGTGGTAAAATCGTTGTAATCATTTTCTTTTGAG
Found at i:22951 original size:108 final size:104
Alignment explanation
Indices: 22635--22955 Score: 315
Period size: 108 Copynumber: 3.0 Consensus size: 104
22625 GATCCTACTA
* *
22635 TATAATTAATAGTATAAAATTT-AAACTTACCCTATAAAATAATCTCTAGTG-ATTAGTTGCTAA
1 TATAATTAATA-TTTAAAATTTAAAACTTACCCTATAAAATAAT-TTTAGTGAATTAG-TGCTAA
* * ** *
22698 ACCTTGTGATAATTTGTTTGAGATTTTAAATCTAAAACCCTAC
63 A-CTTGTGATAAATTGTTTGAAATTTTATTTCTTAAACCCTAC
* * * *
22741 TATATTTAATATTTAAAATATTAAAACTTACCCTATAAAATAATTTCTAATGAATTTGTGGTTAA
1 TATAATTAATATTTAAAAT-TTAAAACTTACCCTATAAAATAATTT-TAGTGAATTAGT-GCTAA
* ** * *
22806 ACTTTATGATGCATTCTTTTGATATTTTATTTC-TAAACCCATAC
63 AC-TTGTGATAAATT-GTTTGAAATTTTATTTCTTAAACCC-TAC
* * * *
22850 TATAATTAATATTTCAAATTTAAAACTTACCCTATTAAATAACTTTTCGTGAATTAGAGACTAAA
1 TATAATTAATATTTAAAATTTAAAACTTACCCTATAAAATAA-TTTTAGTGAATTAGTG-CTAAA
*
22915 CTTCGTGATAAATTGTTTGAAATTTCATTTCTTAAACCCTA
64 CTT-GTGATAAATTGTTTGAAATTTTATTTCTTAAACCCTA
22956 GAATAAAGAT
Statistics
Matches: 174, Mismatches: 29, Indels: 23
0.77 0.13 0.10
Matches are distributed among these distances:
105 7 0.04
106 13 0.07
107 46 0.26
108 72 0.41
109 36 0.21
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.41
Consensus pattern (104 bp):
TATAATTAATATTTAAAATTTAAAACTTACCCTATAAAATAATTTTAGTGAATTAGTGCTAAACT
TGTGATAAATTGTTTGAAATTTTATTTCTTAAACCCTAC
Found at i:28424 original size:46 final size:46
Alignment explanation
Indices: 28357--28449 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
28347 TATCCCCCAC
28357 TACATTATGGAACCAATGGTAGCCTGCCACCCGAGATGGCTCAAGG
1 TACATTATGGAACCAATGGTAGCCTGCCACCCGAGATGGCTCAAGG
28403 TACATTATGGAACCAATGGTAGCCTGCCACCCGAGATGGCTCAAGG
1 TACATTATGGAACCAATGGTAGCCTGCCACCCGAGATGGCTCAAGG
28449 T
1 T
28450 GGCAACTTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (46 bp):
TACATTATGGAACCAATGGTAGCCTGCCACCCGAGATGGCTCAAGG
Found at i:28746 original size:16 final size:15
Alignment explanation
Indices: 28725--28760 Score: 63
Period size: 16 Copynumber: 2.3 Consensus size: 15
28715 AATGTATATC
28725 TTAAAATATAAAATT
1 TTAAAATATAAAATT
28740 ATTAAAATATAAAATT
1 -TTAAAATATAAAATT
28756 TTAAA
1 TTAAA
28761 TATTTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TTAAAATATAAAATT
Found at i:29473 original size:16 final size:16
Alignment explanation
Indices: 29452--29488 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
29442 GGTTAAAGGG
29452 TTTTTACTCTATTTTC
1 TTTTTACTCTATTTTC
* *
29468 TTTTTATTTTATTTTC
1 TTTTTACTCTATTTTC
29484 TTTTT
1 TTTTT
29489 CCGCCAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTACTCTATTTTC
Found at i:37237 original size:22 final size:22
Alignment explanation
Indices: 37196--37237 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
37186 CGCCGGGAGC
* *
37196 AATAGTCCGGCACCACACGAGG
1 AATAGTCCCGCAACACACGAGG
*
37218 AATAGTCCCGCAACATACGA
1 AATAGTCCCGCAACACACGA
37238 TTATCTAGCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.31, G:0.21, T:0.12
Consensus pattern (22 bp):
AATAGTCCCGCAACACACGAGG
Found at i:37390 original size:15 final size:15
Alignment explanation
Indices: 37364--37416 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 15
37354 ACCAATATAC
37364 TAAATATACAAACAAA
1 TAAAT-TACAAACAAA
37380 TAAATTAC-AA-AAA
1 TAAATTACAAACAAA
* *
37393 -AAACT-CACACAAA
1 TAAATTACAAACAAA
37406 TAAATTACAAA
1 TAAATTACAAA
37417 GAAAACTCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 9
0.69 0.10 0.21
Matches are distributed among these distances:
11 1 0.03
12 5 0.17
13 6 0.21
14 6 0.21
15 6 0.21
16 5 0.17
ACGTcount: A:0.66, C:0.15, G:0.00, T:0.19
Consensus pattern (15 bp):
TAAATTACAAACAAA
Found at i:37411 original size:26 final size:26
Alignment explanation
Indices: 37375--37427 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
37365 AAATATACAA
37375 ACAAATAAATTACAAAAAAAACTCAC
1 ACAAATAAATTACAAAAAAAACTCAC
*
37401 ACAAATAAATTACAAAGAAAACTCAC
1 ACAAATAAATTACAAAAAAAACTCAC
37427 A
1 A
37428 TTTCGTGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.64, C:0.19, G:0.02, T:0.15
Consensus pattern (26 bp):
ACAAATAAATTACAAAAAAAACTCAC
Found at i:38102 original size:22 final size:21
Alignment explanation
Indices: 38077--38124 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
38067 CCATACCGAC
*
38077 AACCGACCCGCTAACCCGAATA
1 AACCGACCC-CTAAACCGAATA
* *
38099 AACCGACTCTTAAACCGAATA
1 AACCGACCCCTAAACCGAATA
38120 AACCG
1 AACCG
38125 CGAAACCGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.40, C:0.35, G:0.12, T:0.12
Consensus pattern (21 bp):
AACCGACCCCTAAACCGAATA
Found at i:41826 original size:6 final size:6
Alignment explanation
Indices: 41812--41841 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
41802 GACATTTCAT
*
41812 GGGATG GGGAGG GGGAGG GGGAGG GGGAGG
1 GGGAGG GGGAGG GGGAGG GGGAGG GGGAGG
41842 TAATGATGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.80, T:0.03
Consensus pattern (6 bp):
GGGAGG
Found at i:43889 original size:36 final size:36
Alignment explanation
Indices: 43842--43914 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
43832 ATGCTCCTGT
*
43842 AACCATCACGATATCAATTATGCAGATATCAAGTTA
1 AACCACCACGATATCAATTATGCAGATATCAAGTTA
43878 AACCACCACGATATCAATTATGCAGATATCAAGTTA
1 AACCACCACGATATCAATTATGCAGATATCAAGTTA
43914 A
1 A
43915 CATAGTTTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.21, G:0.11, T:0.26
Consensus pattern (36 bp):
AACCACCACGATATCAATTATGCAGATATCAAGTTA
Found at i:44309 original size:20 final size:20
Alignment explanation
Indices: 44281--44318 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44271 AATCCCTTTC
*
44281 TCTCAAACCTTGAAATAATT
1 TCTCAAACCTAGAAATAATT
*
44301 TCTCCAACCTAGAAATAA
1 TCTCAAACCTAGAAATAA
44319 CCCAAATTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.24, G:0.05, T:0.29
Consensus pattern (20 bp):
TCTCAAACCTAGAAATAATT
Found at i:44973 original size:5 final size:5
Alignment explanation
Indices: 44963--44987 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
44953 TTCTCTATCT
44963 TTTCC TTTCC TTTCC TTTCC TTTCC
1 TTTCC TTTCC TTTCC TTTCC TTTCC
44988 CTCCCCCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTCC
Found at i:45367 original size:29 final size:30
Alignment explanation
Indices: 45325--45394 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 30
45315 CGTTTAGATG
45325 TTTTGCCCCCTGAACTTCAATCTT-GGACA
1 TTTTGCCCCCTGAACTTCAATCTTGGGACA
* * * *
45354 TTTTACCCCCTGAACTTTAATTTTGGGACG
1 TTTTGCCCCCTGAACTTCAATCTTGGGACA
45384 TTTTGCCCCCT
1 TTTTGCCCCCT
45395 CAACCTAACG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.17, C:0.30, G:0.14, T:0.39
Consensus pattern (30 bp):
TTTTGCCCCCTGAACTTCAATCTTGGGACA
Found at i:45471 original size:29 final size:30
Alignment explanation
Indices: 45413--45492 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 30
45403 CGGCTCCGTT
*
45413 AAGTTGAGGGGGCAAAACGTCCCAAAATTG
1 AAGTTCAGGGGGCAAAACGTCCCAAAATTG
* * *
45443 AAGTTCAGGGGACAAAATGT-CCAAGATTG
1 AAGTTCAGGGGGCAAAACGTCCCAAAATTG
*
45472 AAGTTCGGGGGGCAAAACGTC
1 AAGTTCAGGGGGCAAAACGTC
45493 TAAACGCTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 25 0.60
30 17 0.40
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.17
Consensus pattern (30 bp):
AAGTTCAGGGGGCAAAACGTCCCAAAATTG
Done.