Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013368.1 Corchorus capsularis cultivar CVL-1 contig13389, 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: 52397
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:640 original size:2 final size:2
Alignment explanation
Indices: 633--662 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
623 ACATACATAC
633 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
663 CTTTTGTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1905 original size:26 final size:27
Alignment explanation
Indices: 1872--1941 Score: 72
Period size: 32 Copynumber: 2.4 Consensus size: 27
1862 TAATACGATT
1872 AAAATGAACTTAT-A-ATAATTCAAAAA
1 AAAATGAACTTATGACATAATT-AAAAA
1898 AAAATGAACATAATATGGGACATAATTAAAAA
1 AAAATGAAC-T--TAT--GACATAATTAAAAA
1930 AAAATGAACTTA
1 AAAATGAACTTA
1942 ATGGGACAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
26 9 0.24
27 1 0.03
29 5 0.14
31 1 0.03
32 15 0.41
33 6 0.16
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.24
Consensus pattern (27 bp):
AAAATGAACTTATGACATAATTAAAAA
Found at i:3910 original size:20 final size:20
Alignment explanation
Indices: 3885--3924 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3875 TGGATTATAC
3885 CTCAAATAGAAATTACCTCA
1 CTCAAATAGAAATTACCTCA
3905 CTCAAATAGAAATTACCTCA
1 CTCAAATAGAAATTACCTCA
3925 TTGAAAGGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.25
Consensus pattern (20 bp):
CTCAAATAGAAATTACCTCA
Found at i:9524 original size:2 final size:2
Alignment explanation
Indices: 9517--9542 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9507 ATAATATGTT
9517 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
9543 CTTATATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:22546 original size:7 final size:7
Alignment explanation
Indices: 22536--22568 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
22526 CATTTGCCCT
22536 TGCCAAA
1 TGCCAAA
22543 TGCCAAA
1 TGCCAAA
22550 TGCCAAA
1 TGCCAAA
*
22557 TGCCAAT
1 TGCCAAA
22564 TGCCA
1 TGCCA
22569 TGCCATCCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.36, C:0.30, G:0.15, T:0.18
Consensus pattern (7 bp):
TGCCAAA
Found at i:32520 original size:27 final size:27
Alignment explanation
Indices: 32482--32537 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
32472 TACATCCTGC
32482 AACCTGTCAACCAAAGATCAATCAAAG
1 AACCTGTCAACCAAAGATCAATCAAAG
32509 AACCTGTCAACCAAAGATCAATCAAAG
1 AACCTGTCAACCAAAGATCAATCAAAG
32536 AA
1 AA
32538 GCTGCCTGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.50, C:0.25, G:0.11, T:0.14
Consensus pattern (27 bp):
AACCTGTCAACCAAAGATCAATCAAAG
Found at i:43344 original size:25 final size:25
Alignment explanation
Indices: 43316--43364 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
43306 TTTAAGCAGA
* *
43316 TCTCGGGTTGGATCGAGTAGTAAGG
1 TCTCCGGTTGGATCAAGTAGTAAGG
*
43341 TCTCCGTTTGGATCAAGTAGTAAG
1 TCTCCGGTTGGATCAAGTAGTAAG
43365 CGGCTTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.22, C:0.14, G:0.33, T:0.31
Consensus pattern (25 bp):
TCTCCGGTTGGATCAAGTAGTAAGG
Found at i:45804 original size:18 final size:18
Alignment explanation
Indices: 45781--45816 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
45771 AAATCCATCA
45781 GCAATTGAATTTCTTATC
1 GCAATTGAATTTCTTATC
45799 GCAATTGAATTTCTTATC
1 GCAATTGAATTTCTTATC
45817 AATTATTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (18 bp):
GCAATTGAATTTCTTATC
Found at i:50052 original size:14 final size:14
Alignment explanation
Indices: 50033--50064 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
50023 TTTGGGCATT
50033 ATATGTCATATAAA
1 ATATGTCATATAAA
*
50047 ATATGTCATATATA
1 ATATGTCATATAAA
50061 ATAT
1 ATAT
50065 ATAAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (14 bp):
ATATGTCATATAAA
Found at i:50073 original size:8 final size:8
Alignment explanation
Indices: 50054--50092 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
50044 AAAATATGTC
50054 ATATAT-A
1 ATATATAA
50061 ATATATAA
1 ATATATAA
50069 ATATATAA
1 ATATATAA
* *
50077 ATAAATAT
1 ATATATAA
50085 ATATATAA
1 ATATATAA
50093 GGCAAGCGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATATAA
Found at i:50450 original size:31 final size:31
Alignment explanation
Indices: 50415--50473 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
50405 ATGTTTTCTG
50415 ATTGTACCCTTATT-TTTAAAATATATTTTCA
1 ATTGTA-CCTTATTCTTTAAAATATATTTTCA
*
50446 ATTGTACCTTTTTCTTTAAAATATATTT
1 ATTGTACCTTATTCTTTAAAATATATTT
50474 CTAAATTACT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 6 0.23
31 20 0.77
ACGTcount: A:0.31, C:0.12, G:0.03, T:0.54
Consensus pattern (31 bp):
ATTGTACCTTATTCTTTAAAATATATTTTCA
Found at i:50813 original size:19 final size:20
Alignment explanation
Indices: 50786--50823 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
50776 TACTATTATT
50786 TTTTGAATTT-AATATTTTAC
1 TTTTGAATTTCAAT-TTTTAC
50806 TTTT-AATTTCAATTTTTA
1 TTTTGAATTTCAATTTTTA
50824 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTGAATTTCAATTTTTAC
Found at i:51017 original size:22 final size:22
Alignment explanation
Indices: 50989--51121 Score: 101
Period size: 22 Copynumber: 5.9 Consensus size: 22
50979 TCTCTCTATG
50989 TGGTTATCAAAATTTCATGAG-A
1 TGGTTATCAAAATTTCAT-AGTA
* *
51011 TGGTTATTATAATTTCAT-G-A
1 TGGTTATCAAAATTTCATAGTA
* *
51031 TGAGGTTATCAAAATTCCATAGTG
1 T--GGTTATCAAAATTTCATAGTA
* *
51055 TGGTTACCAAAATTTTCATAGTG
1 TGGTTATCAAAA-TTTCATAGTA
* *
51078 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAGTA
**
51100 TCAGGTTATTGAAATTTCATAG
1 T--GGTTATCAAAATTTCATAG
51122 GGTGGTTAAT
Statistics
Matches: 91, Mismatches: 13, Indels: 12
0.78 0.11 0.10
Matches are distributed among these distances:
20 3 0.03
22 49 0.54
23 22 0.24
24 17 0.19
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGTA
Found at i:51078 original size:23 final size:22
Alignment explanation
Indices: 50987--51097 Score: 109
Period size: 22 Copynumber: 5.0 Consensus size: 22
50977 CTTCTCTCTA
*
50987 TGTGGTTATCAAAATTTCATGAG
1 TGTGGTTACCAAAATTTCAT-AG
* ** *
51010 -ATGGTTATTATAATTTCAT-G
1 TGTGGTTACCAAAATTTCATAG
* * *
51030 ATGAGGTTATCAAAATTCCATAG
1 -TGTGGTTACCAAAATTTCATAG
51053 TGTGGTTACCAAAATTTTCATAG
1 TGTGGTTACCAAAA-TTTCATAG
51076 TGTGGTTACCAAAATTTCATAG
1 TGTGGTTACCAAAATTTCATAG
51098 GATCAGGTTA
Statistics
Matches: 73, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
20 1 0.01
22 50 0.68
23 22 0.30
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (22 bp):
TGTGGTTACCAAAATTTCATAG
Found at i:51211 original size:56 final size:56
Alignment explanation
Indices: 51151--51279 Score: 129
Period size: 56 Copynumber: 2.3 Consensus size: 56
51141 TTTATAGAAA
51151 GGTTATCAAAGAGATT-ATCAAA-ATGTCATAACGAGGTTAT-AAGAATTTCATAGTGT
1 GGTTATCAAA-A-ATTCATCAAATATGTCATAACGAGGTTATCAA-AATTTCATAGTGT
* * * * *** *
51207 GGTTAACAAAATTTCATTAAATATTTCATGGGGAGGTTATCAAAATTTTATAGTGT
1 GGTTATCAAAAATTCATCAAATATGTCATAACGAGGTTATCAAAATTTCATAGTGT
*
51263 GGTTATCAAAATTTCAT
1 GGTTATCAAAAATTCAT
51280 ATGAAGGTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
54 2 0.03
55 6 0.10
56 51 0.84
57 2 0.03
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (56 bp):
GGTTATCAAAAATTCATCAAATATGTCATAACGAGGTTATCAAAATTTCATAGTGT
Found at i:51288 original size:22 final size:22
Alignment explanation
Indices: 51229--51294 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
51219 TTCATTAAAT
* *
51229 ATTTCATGGGGAGGTTATCAAA
1 ATTTCATAGTGAGGTTATCAAA
* *
51251 ATTTTATAGTGTGGTTATCAAA
1 ATTTCATAGTGAGGTTATCAAA
51273 ATTTCATA-TGAAGGTTAT-AAA
1 ATTTCATAGTG-AGGTTATCAAA
51294 A
1 A
51295 GTCTAAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
21 6 0.16
22 31 0.84
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (22 bp):
ATTTCATAGTGAGGTTATCAAA
Found at i:51342 original size:20 final size:22
Alignment explanation
Indices: 51319--51419 Score: 64
Period size: 21 Copynumber: 4.5 Consensus size: 22
51309 AGAAGTACCA
*
51319 AAATTTGATAGA-AGATTATC-
1 AAATTTCATAGAGAGATTATCG
* *
51339 AAATCTCATAGAGTGATTATCG
1 AAATTTCATAGAGAGATTATCG
* *
51361 AAATTTTATAGAGATCGCGGATTATCA
1 AAATTTCATAGAGA-----GATTATCG
* * *
51388 AAATTT-ATAGAAATATTATCA
1 AAATTTCATAGAGAGATTATCG
51409 AAATTTCATAG
1 AAATTTCATAG
51420 CGTTGTTATC
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
20 10 0.16
21 20 0.31
22 15 0.23
26 6 0.09
27 13 0.20
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.35
Consensus pattern (22 bp):
AAATTTCATAGAGAGATTATCG
Found at i:51356 original size:21 final size:22
Alignment explanation
Indices: 51332--51373 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
51322 TTTGATAGAA
51332 GATTATC-AAATCTCATAGAGT
1 GATTATCGAAATCTCATAGAGT
* *
51353 GATTATCGAAATTTTATAGAG
1 GATTATCGAAATCTCATAGAG
51374 ATCGCGGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
GATTATCGAAATCTCATAGAGT
Found at i:51526 original size:21 final size:22
Alignment explanation
Indices: 51382--51529 Score: 86
Period size: 22 Copynumber: 6.6 Consensus size: 22
51372 AGATCGCGGA
**
51382 TTATCAAAATTT-ATAGAA-ATA
1 TTATCAAAATTTCATA-AAGAGG
** **
51403 TTATCAAAATTTCATAGCGTTG
1 TTATCAAAATTTCATAAAGAGG
* * * * *
51425 TTATCAAAATTACGTAATGTGAT
1 TTATCAAAATTTCATAAAGAG-G
* *
51448 TTATCAGAATTTCATATAGAGGGG
1 TTATCAAAATTTCATA-A-AGAGG
* *
51472 TCAACAAAATCTT-ATAAAGAGG
1 TTATCAAAAT-TTCATAAAGAGG
51494 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAAAGAGG
*
51516 TTATCAAATTTTCA
1 TTATCAAAATTTCA
51530 AAATGTGATT
Statistics
Matches: 97, Mismatches: 23, Indels: 13
0.73 0.17 0.10
Matches are distributed among these distances:
21 14 0.14
22 54 0.56
23 14 0.14
24 11 0.11
25 4 0.04
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTCATAAAGAGG
Found at i:51676 original size:22 final size:22
Alignment explanation
Indices: 51648--52120 Score: 160
Period size: 22 Copynumber: 21.7 Consensus size: 22
51638 TCAGGGAGGA
51648 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
51670 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
51692 TTTCAAAATTTCACAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
51714 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
51735 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
51758 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
51780 TATCAAAAAAATCATAGGGAGGT
1 TATC-AAAATTTCATATGAAGGT
*
51803 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
51819 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* *
51841 TATCAAAATATT-ATAGGGAGGTT
1 TATCAAAAT-TTCATATGAAGG-T
* * * *
51864 TATCGAAATTTTATAGGAAGATT
1 TATCAAAATTTCATATGAAG-GT
*
51887 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
51909 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
51931 TATCAAAATTTC--A-G-AGTGT
1 TATCAAAATTTCATATGAAG-GT
* * *
51950 GATCTAACAA-TTCATATGGAGCT
1 TATC-AA-AATTTCATATGAAGGT
* * * * *
51973 TTTTAAATTTTCATAACG-TGGT
1 TATCAAAATTTCAT-ATGAAGGT
* *
51995 TATCAATATATCATAT-AGAGGT
1 TATCAAAATTTCATATGA-AGGT
* * **
52017 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
**
52040 TATCAAAATTTCATGGGGAA-GT
1 TATCAAAATTTCAT-ATGAAGGT
*
52062 TATCAAAATTTCATATTAAGGT
1 TATCAAAATTTCATATGAAGGT
* * * *
52084 CT-TCAAAATTCCTTAAGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* *
52106 TAACCAAATTTCATA
1 TATCAAAATTTCATA
52121 AGGTTAAAAA
Statistics
Matches: 329, Mismatches: 85, Indels: 74
0.67 0.17 0.15
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 4 0.01
19 4 0.01
20 8 0.02
21 12 0.04
22 207 0.63
23 80 0.24
24 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:51785 original size:44 final size:44
Alignment explanation
Indices: 51643--52120 Score: 236
Period size: 44 Copynumber: 11.0 Consensus size: 44
51633 AAAATTCAGG
* * * *
51643 GAGGATATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTT
1 GAGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAG-T
* * *
51688 TA-GTTTTCAAAATTTCACAAGAGG-G-TTATCAAAATTTCATAGT
1 GAGGTTATCAAAATTTCA-TAG-GGAGATTATCAAAATTTCATAGT
* * * *
51731 -ATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAAT
1 GAGGT-TATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGT
** *
51775 GAGGTTATCAAAAAAATCATAGGGAGGTTATCAAAA-TT--T-GT
1 GAGGTTATC-AAAATTTCATAGGGAGATTATCAAAATTTCATAGT
* * * *
51816 -A-GTTATCAAGATTTCATA-AGAAAGTTATCAAAATATT-ATAGG
1 GAGGTTATCAAAATTTCATAGGGAGA-TTATCAAAAT-TTCATAGT
* * * *
51858 GAGGTTTATCGAAATTTTATAGGAAGATTTATCAAAATTTCATAGC
1 GAGG-TTATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGT
* * * *
51904 GAGGTTATCACAATTTCATAGTGTGATTATCAAAATTTCAGAGT
1 GAGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGT
* * * * * * **
51948 ---GTGATCTAACAA-TTCATATGGAGCTTTTTAAATTTTCATAAC
1 GAGGTTATC-AA-AATTTCATAGGGAGATTATCAAAATTTCATAGT
* * * ** * * *
51990 GTGGTTATCAATATATCATATAGAGGTTATCAACATCTCATAGT
1 GAGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGT
* * *
52034 GTTGGTTATCAAAATTTCATGGGGA-AGTTATCAAAATTTCATATT
1 G-AGGTTATCAAAATTTCATAGGGAGA-TTATCAAAATTTCATAGT
* * * * * * *
52079 AAGGTCT-TCAAAATTCCTTAAGGAGGTTAACCAAATTTCATA
1 GAGGT-TATCAAAATTTCATAGGGAGATTATCAAAATTTCATA
52121 AGGTTAAAAA
Statistics
Matches: 322, Mismatches: 83, Indels: 57
0.70 0.18 0.12
Matches are distributed among these distances:
37 2 0.01
38 17 0.05
39 6 0.02
40 3 0.01
41 7 0.02
42 26 0.08
43 10 0.03
44 132 0.41
45 98 0.30
46 21 0.07
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (44 bp):
GAGGTTATCAAAATTTCATAGGGAGATTATCAAAATTTCATAGT
Found at i:51810 original size:45 final size:44
Alignment explanation
Indices: 51711--51813 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 44
51701 TTCACAAGAG
* * **
51711 GGTTATCAAAATTTCATAGTATGTAGATCAAAATTTCATAGGGA
1 GGTTATCAAAATTTCATAATAGGTAGATCAAAAAATCATAGGGA
* * *
51755 GATTAACAAAATTTCATAATGAGGT-TATCAAAAAAATCATAGGGA
1 GGTTATCAAAATTTCATAAT-AGGTAGATC-AAAAAATCATAGGGA
51800 GGTTATCAAAATTT
1 GGTTATCAAAATTT
51814 GTAGTTATCA
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
44 20 0.42
45 28 0.58
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.32
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAATAGGTAGATCAAAAAATCATAGGGA
Found at i:52183 original size:22 final size:22
Alignment explanation
Indices: 52152--52205 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
52142 ATTTTTCTCG
* * * *
52152 AAATTCCATAGTATCGTTATTA
1 AAATTTCATAGGAACGTTATCA
*
52174 AAATTTCATAGGAAGGTTATCA
1 AAATTTCATAGGAACGTTATCA
52196 AAATTTCATA
1 AAATTTCATA
52206 ATGGGATCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (22 bp):
AAATTTCATAGGAACGTTATCA
Found at i:52331 original size:2 final size:2
Alignment explanation
Indices: 52324--52395 Score: 90
Period size: 2 Copynumber: 34.5 Consensus size: 2
52314 TACATGATAA
* * *
52324 AT AT AT AT ACT AT AGT AT AG AT AG AT AG AT AGT AT AT AT AT AT
1 AT AT AT AT A-T AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT
52367 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
52396 GT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 55 0.90
3 6 0.10
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.43
Consensus pattern (2 bp):
AT
Done.