Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008381.1 Corchorus capsularis cultivar CVL-1 contig08402, 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: 25866
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Found at i:160 original size:2 final size:2
Alignment explanation
Indices: 153--182 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
143 TATAATATGG
153 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
183 GATTTCCATT
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:2171 original size:30 final size:30
Alignment explanation
Indices: 2135--2212 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
2125 CATCAGAAAA
2135 GGGCTTATTTGGCCTTTTTAA-AGAGTTCAG
1 GGGCTTATTTGGCC-TTTTAATAGAGTTCAG
**
2165 GGGCTTATTTGG-C-TGCAATTAGAGTTCAG
1 GGGCTTATTTGGCCTTTTAA-TAGAGTTCAG
2194 GGGCTTATTTGGCCGTTTT
1 GGGCTTATTTGGCC-TTTT
2213 GTGTAAATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 3 0.08
29 22 0.56
30 13 0.33
32 1 0.03
ACGTcount: A:0.17, C:0.14, G:0.29, T:0.40
Consensus pattern (30 bp):
GGGCTTATTTGGCCTTTTAATAGAGTTCAG
Found at i:10613 original size:102 final size:101
Alignment explanation
Indices: 10414--10718 Score: 371
Period size: 102 Copynumber: 3.0 Consensus size: 101
10404 CGGATTTTTC
* * * * *
10414 TGTAGTAATTTCCGTTGGAACAAATTT-TTTTGCCGTAAAATATTTGGGCTAGCGGGAATTCGAA
1 TGTAGTAATTTCCGTTGCAA-AAATTTATTTTGGCGCAAAATATTTAGG--AGCGGGAATTCAAA
** *
10478 TTTTAATTTGTCACGAAGGTTAAAATCGTTGCAAAATTT
63 TTTTAATTTGTCACGAAAATTAAATTCGTTGCAAAATTT
*
10517 TGTAGTAATTTCCGTTGCAAAAATTTATTTTGGCGCAAAATATTTAAGGAGCGGGAATTCAAAAT
1 TGTAGTAATTTCCGTTGCAAAAATTTATTTTGGCGCAAAATATTT-AGGAGCGGGAATTCAAATT
* * *
10582 TTAATTTGTTATGAAAACTAAATTCGTTGCAAAATTT
65 TTAATTTGTCACGAAAATTAAATTCGTTGCAAAATTT
* * * *
10619 TGTAATAATTT-CGTTGCAAAAACTAATTTTGGCGCAAAATTTTTGAGCGAGCGGGAATTCAAAT
1 TGTAGTAATTTCCGTTGCAAAAATTTATTTTGGCGCAAAATATTT-AG-GAGCGGGAATTCAAAT
* * *
10683 TTTAATTTGCCACGAAAATTAATTTCGTGGCAAAAT
64 TTTAATTTGTCACGAAAATTAAATTCGTTGCAAAAT
10719 CTGTAGCAAA
Statistics
Matches: 175, Mismatches: 24, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
101 32 0.18
102 106 0.61
103 35 0.20
104 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.36
Consensus pattern (101 bp):
TGTAGTAATTTCCGTTGCAAAAATTTATTTTGGCGCAAAATATTTAGGAGCGGGAATTCAAATTT
TAATTTGTCACGAAAATTAAATTCGTTGCAAAATTT
Found at i:13729 original size:31 final size:31
Alignment explanation
Indices: 13693--13864 Score: 186
Period size: 31 Copynumber: 5.5 Consensus size: 31
13683 ACGGTGTTCG
* * *
13693 ACGTGGCATGCCACGTGGATCAAAAAGTAAC
1 ACGTGGCACGCCACGTGGACCAAAAAGTGAC
* *
13724 ACGTGGCACACCACGTGGATCAAAAAGTGAC
1 ACGTGGCACGCCACGTGGACCAAAAAGTGAC
* *
13755 ACGTGGCATGCCGCGTGTG-CCAAAAAGTGAC
1 ACGTGGCACGCCACGTG-GACCAAAAAGTGAC
* * *
13786 ACGTGGCACGTCACATGTG-CCAAAAAGTGAT
1 ACGTGGCACGCCACGTG-GACCAAAAAGTGAC
* *
13817 ACGTGGCACGCTACGTGTACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGGACCAAAAAGTGAC
* *
13848 ATGTGGCATGCCACGTG
1 ACGTGGCACGCCACGTG
13865 CACTAAAGGA
Statistics
Matches: 119, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.28, T:0.17
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGGACCAAAAAGTGAC
Found at i:15582 original size:2 final size:2
Alignment explanation
Indices: 15577--15611 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
15567 AAAAAACTAG
15577 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15612 GTTCTCCGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16464 original size:31 final size:31
Alignment explanation
Indices: 16429--16501 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
16419 TGAGTATATT
* *
16429 GACTAAATTAATCCAATATTGTAAGTTCATG
1 GACTAAATTAATCCAATATTATAAGTACATG
* * * *
16460 GACTAAATTGACCCAATCTTATGAGTACATG
1 GACTAAATTAATCCAATATTATAAGTACATG
16491 GACT-AATTAAT
1 GACTAAATTAAT
16502 TGATCGCTCT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
30 5 0.15
31 29 0.85
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (31 bp):
GACTAAATTAATCCAATATTATAAGTACATG
Found at i:21365 original size:2 final size:2
Alignment explanation
Indices: 21352--21396 Score: 63
Period size: 2 Copynumber: 22.0 Consensus size: 2
21342 AATATCTATC
* *
21352 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TC TA TA GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
21395 TA
1 TA
21397 AAAGTATGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:21469 original size:31 final size:31
Alignment explanation
Indices: 21431--21489 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
21421 ATGTTTTCCG
*
21431 ATTGTACCCTTATTCTTAAAACATATTTGCA
1 ATTGTACCCTTATTCTAAAAACATATTTGCA
*
21462 ATTGTACCCTTTTTCTAAAAACATATTT
1 ATTGTACCCTTATTCTAAAAACATATTT
21490 CTAAATTGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.44
Consensus pattern (31 bp):
ATTGTACCCTTATTCTAAAAACATATTTGCA
Found at i:21653 original size:22 final size:22
Alignment explanation
Indices: 21604--21689 Score: 127
Period size: 22 Copynumber: 3.8 Consensus size: 22
21594 CCATGAGGAG
* *
21604 GTTATCAAAATTTCATAGTGTGTG
1 GTTACCAAAATTTCATA--GTGTA
21628 GTTACCAAAATTTCATAGTGTA
1 GTTACCAAAATTTCATAGTGTA
*
21650 GTTACCAAAATTTCATAGAGTA
1 GTTACCAAAATTTCATAGTGTA
21672 GTTACCAAAATTTCATAG
1 GTTACCAAAATTTCATAG
21690 GATCAAGTTA
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
22 43 0.73
24 16 0.27
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (22 bp):
GTTACCAAAATTTCATAGTGTA
Found at i:21728 original size:22 final size:22
Alignment explanation
Indices: 21580--21743 Score: 105
Period size: 22 Copynumber: 7.3 Consensus size: 22
21570 TATTTTACTT
* *
21580 TGGTTATTATAATTCCAT-GAGG
1 TGGTTATTAAAATTTCATAG-GG
* *
21602 AGGTTATCAAAATTTCATAGTGTG
1 TGGTTATTAAAATTTCATAG-G-G
** *
21626 TGGTTACCAAAATTTCATAGTG
1 TGGTTATTAAAATTTCATAGGG
* ** *
21648 TAGTTACCAAAATTTCATAGAG
1 TGGTTATTAAAATTTCATAGGG
* ** *
21670 TAGTTACCAAAATTTCATAGGA
1 TGGTTATTAAAATTTCATAGGG
* * *
21692 TCAAGTTATTAAAATTTCTTAGGT
1 T--GGTTATTAAAATTTCATAGGG
*
21716 TGGTTATTGAAATTTCATAGGG
1 TGGTTATTAAAATTTCATAGGG
21738 TGGTTA
1 TGGTTA
21744 ATTATCACAA
Statistics
Matches: 118, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
22 79 0.67
23 2 0.02
24 37 0.31
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (22 bp):
TGGTTATTAAAATTTCATAGGG
Found at i:21912 original size:22 final size:23
Alignment explanation
Indices: 21863--21923 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
21853 CTTCATCGGG
* * *
21863 AGGTTATCAAAATTTTATAGTGT
1 AGGTTATCAAAATCTCATAGTGA
21886 A-GTTATCAAAATCTCATA-TGA
1 AGGTTATCAAAATCTCATAGTGA
21907 AGGTTAT-AAAAGTCTCA
1 AGGTTATCAAAA-TCTCA
21924 ATTTCATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 7 0.21
22 25 0.76
23 1 0.03
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (23 bp):
AGGTTATCAAAATCTCATAGTGA
Found at i:22001 original size:68 final size:68
Alignment explanation
Indices: 21929--22059 Score: 160
Period size: 68 Copynumber: 1.9 Consensus size: 68
21919 TCTCAATTTC
*
21929 ATATGGAGTACCAAAATTTGATA-GAAGGTTATC-AAATCTCATAGAG-TGATTAACGAAATTTC
1 ATAT-GAGTACCAAAATTT-ATATGAAGATTATCAAAATCTCATAGAGTTG-TTAACGAAATTTC
21991 ATAAAG
63 ATAAAG
* * * * *
21997 ATATGATTATCAAAATTTATATGAAGATTATCAAAATTTCATAGCGTTGTTATCGAAATTTCA
1 ATATGAGTACCAAAATTTATATGAAGATTATCAAAATCTCATAGAGTTGTTAACGAAATTTCA
22060 AAGCGAGGTT
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
66 3 0.06
67 21 0.39
68 28 0.52
69 2 0.04
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (68 bp):
ATATGAGTACCAAAATTTATATGAAGATTATCAAAATCTCATAGAGTTGTTAACGAAATTTCATA
AAG
Found at i:22012 original size:25 final size:24
Alignment explanation
Indices: 21975--22193 Score: 89
Period size: 22 Copynumber: 9.8 Consensus size: 24
21965 TCTCATAGAG
* *
21975 TGATTAACGAAATTTCATAAAGATA
1 TGATTATCAAAATTTCATAAAGA-A
*
22000 TGATTATCAAAATTT-AT-ATGAA
1 TGATTATCAAAATTTCATAAAGAA
** *
22022 -GATTATCAAAATTTCATAGCG-T
1 TGATTATCAAAATTTCATAAAGAA
* *
22044 TG-TTATCGAAATTTC--AAAGCGA
1 TGATTATCAAAATTTCATAAAG-AA
* * *
22066 -GGTTATCAAAATTACATAATG--
1 TGATTATCAAAATTTCATAAAGAA
*
22087 TGATTATCAAAATTTCAT--AGAG
1 TGATTATCAAAATTTCATAAAGAA
* * * * *
22109 GGGTCAACAAAATTTTATAAAG-A
1 TGATTATCAAAATTTCATAAAGAA
22132 TG-TTATCAAAATTTCATAAAG-A
1 TGATTATCAAAATTTCATAAAGAA
* * **
22154 -GGTTATCAAATTTTCA-AAA-TC
1 TGATTATCAAAATTTCATAAAGAA
22175 TGATTA-CAAAAATTTCATA
1 TGATTATC-AAAATTTCATA
22194 GTGGTATTTT
Statistics
Matches: 146, Mismatches: 30, Indels: 38
0.68 0.14 0.18
Matches are distributed among these distances:
20 3 0.02
21 20 0.14
22 96 0.66
23 7 0.05
24 7 0.05
25 13 0.09
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (24 bp):
TGATTATCAAAATTTCATAAAGAA
Found at i:22020 original size:18 final size:19
Alignment explanation
Indices: 21997--22035 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
21987 TTTCATAAAG
21997 ATAT-GATTATCAAAATTT
1 ATATAGATTATCAAAATTT
22015 ATATGAAGATTATCAAAATTT
1 ATAT--AGATTATCAAAATTT
22036 CATAGCGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
ATATAGATTATCAAAATTT
Found at i:22078 original size:44 final size:43
Alignment explanation
Indices: 21940--22169 Score: 146
Period size: 44 Copynumber: 5.2 Consensus size: 43
21930 TATGGAGTAC
* * * * * *
21940 CAAAATTTGATAGAAG-GTTATC-AAATCTCATAGAGTGATTAA
1 CAAAATTTCATA-AAGTGTTATCAAAATTTCAAAGAGAGGTTAT
* * *
21982 CGAAATTTCATAAAGATATGATTATCAAAATTT-ATATGA-AGATTAT
1 CAAAATTTCATAAAG---TG-TTATCAAAATTTCA-AAGAGAGGTTAT
** * *
22028 CAAAATTTCATAGCGTTGTTATCGAAATTTCAAAGCGAGGTTAT
1 CAAAATTTCATAAAG-TGTTATCAAAATTTCAAAGAGAGGTTAT
* * * * * *
22072 CAAAATTACATAATGTGATTATCAAAATTTCATAGAGGGGTCAA
1 CAAAATTTCATAAAGTG-TTATCAAAATTTCAAAGAGAGGTTAT
*
22116 CAAAATTTTATAAAGATGTTATCAAAATTTCATAA-AGAGGTTAT
1 CAAAATTTCATAAAG-TGTTATCAAAATTTCA-AAGAGAGGTTAT
*
22160 CAAATTTTCA
1 CAAAATTTCA
22170 AAATCTGATT
Statistics
Matches: 143, Mismatches: 33, Indels: 22
0.72 0.17 0.11
Matches are distributed among these distances:
41 3 0.02
42 10 0.07
43 15 0.10
44 81 0.57
45 4 0.03
46 23 0.16
47 7 0.05
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (43 bp):
CAAAATTTCATAAAGTGTTATCAAAATTTCAAAGAGAGGTTAT
Found at i:22122 original size:66 final size:66
Alignment explanation
Indices: 22021--22169 Score: 156
Period size: 66 Copynumber: 2.3 Consensus size: 66
22011 ATTTATATGA
* ** * * * *
22021 AGATTATCAAAATTTCATAGCGTTGTTATCGAAATTTCA-AAGCGAGGTTATCAAAATTACATAA
1 AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-AGAGGTTATCAAAATTACATAA
*
22085 TG
65 AG
* * * *
22087 TGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTTATAAAGATGTTATCAAAATTTCATAAA
1 AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAAA
22152 G
66 G
* *
22153 AGGTTATCAAATTTTCA
1 AGATTATCAAAATTTCA
22170 AAATCTGATT
Statistics
Matches: 67, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
66 65 0.97
67 2 0.03
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (66 bp):
AGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAAA
G
Found at i:22122 original size:88 final size:88
Alignment explanation
Indices: 22028--22194 Score: 212
Period size: 88 Copynumber: 1.9 Consensus size: 88
22018 TGAAGATTAT
** * * * * *
22028 CAAAATTTCATAGCGTTGTTATCGAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATT
1 CAAAATTTCATAAAGATGTTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAAATCTGATT
22092 ATC-AAAATTTCATAGAGGGGTCAA
65 A-CAAAAATTTCATAGAGGGGTCAA
* * *
22116 CAAAATTTTATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATCTGATTA
1 CAAAATTTCATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATCTGATTA
22181 CAAAAATTTCATAG
66 CAAAAATTTCATAG
22195 TGGTATTTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 1 0.01
88 64 0.96
89 2 0.03
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (88 bp):
CAAAATTTCATAAAGATGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATCTGATTA
CAAAAATTTCATAGAGGGGTCAA
Found at i:22150 original size:22 final size:22
Alignment explanation
Indices: 21984--22169 Score: 130
Period size: 22 Copynumber: 8.4 Consensus size: 22
21974 GTGATTAACG
21984 AAATTTCATAAAGATATGATTATCA
1 AAATTTCATAAAG--ATG-TTATCA
22009 AAATTT-ATATGAAGA--TTATCA
1 AAATTTCATA--AAGATGTTATCA
** * *
22030 AAATTTCATAGCGTTGTTATCG
1 AAATTTCATAAAGATGTTATCA
* *
22052 AAATTTCA-AAGCGAGGTTATCA
1 AAATTTCATAA-AGATGTTATCA
* *
22074 AAATTACATAATG-TGATTATCA
1 AAATTTCATAAAGATG-TTATCA
* ** * *
22096 AAATTTCATAGAGGGGTCAACA
1 AAATTTCATAAAGATGTTATCA
*
22118 AAATTTTATAAAGATGTTATCA
1 AAATTTCATAAAGATGTTATCA
*
22140 AAATTTCATAAAGAGGTTATCA
1 AAATTTCATAAAGATGTTATCA
*
22162 AATTTTCA
1 AAATTTCA
22170 AAATCTGATT
Statistics
Matches: 126, Mismatches: 26, Indels: 21
0.73 0.15 0.12
Matches are distributed among these distances:
20 1 0.01
21 14 0.11
22 95 0.75
23 3 0.02
24 4 0.03
25 6 0.05
26 3 0.02
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (22 bp):
AAATTTCATAAAGATGTTATCA
Found at i:22302 original size:20 final size:20
Alignment explanation
Indices: 22277--22344 Score: 77
Period size: 19 Copynumber: 3.5 Consensus size: 20
22267 ATGGAGTAAT
*
22277 CAAAATTTTAGGGAGGATAC
1 CAAAATTTCAGGGAGGATAC
*
22297 CAAAA-TTCAGGGAGGATAT
1 CAAAATTTCAGGGAGGATAC
* *
22316 CAAAA-TTCAGTGAGGATAT
1 CAAAATTTCAGGGAGGATAC
*
22335 CAATATTTCA
1 CAAAATTTCA
22345 TATGAAGGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 34 0.79
20 9 0.21
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (20 bp):
CAAAATTTCAGGGAGGATAC
Found at i:22334 original size:19 final size:19
Alignment explanation
Indices: 22275--22337 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
22265 TGATGGAGTA
*
22275 ATCAAAATTTTAGGGAGGAT
1 ATCAAAA-TTCAGGGAGGAT
*
22295 ACCAAAATTCAGGGAGGAT
1 ATCAAAATTCAGGGAGGAT
*
22314 ATCAAAATTCAGTGAGGAT
1 ATCAAAATTCAGGGAGGAT
22333 ATCAA
1 ATCAA
22338 TATTTCATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 33 0.85
20 6 0.15
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (19 bp):
ATCAAAATTCAGGGAGGAT
Found at i:22357 original size:22 final size:22
Alignment explanation
Indices: 22332--22868 Score: 154
Period size: 22 Copynumber: 24.7 Consensus size: 22
22322 TCAGTGAGGA
*
22332 TATCAATATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
22354 TATCAAATTTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
22376 TTTCAAAATTTCATAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* * *
22398 TATCAAAATTTCATAGGGAGAT
1 TATCAAAATTTCATATGAAGGT
*
22420 TAACAAAATTTCATAATGAA-GT
1 TATCAAAATTTCAT-ATGAAGGT
** * * *
22442 TATCAAAAAATCATAAGGAGCT
1 TATCAAAATTTCATATGAAGGT
*
22464 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
22480 TATCAAGATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* * *
22502 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
* * *
22525 TATTAAAATTTTATA-GAAAGATT
1 TATCAAAATTTCATATG-AAG-GT
*
22548 TATCAAAATTTCATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
22570 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
22592 TATCAAAATTTTAAAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
22614 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
** * *
22636 T-TTTAAATTT-TTATAAAGTGGT
1 TATCAAAATTTCATATGAA--GGT
* * *
22658 TATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * **
22680 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
22703 TATCAAAATTTCAT-TGGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
22725 TATCAAAATTTCATATTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
22747 CT-TCAAAATTCCTTAGGGAGGT
1 -TATCAAAATTTCATATGAAGGT
* * *
22769 TAACAAAATTTCATAAGAAAGT
1 TATCAAAATTTCATATGAAGGT
* *
22791 T-TAAAAAATTT-ATA-AAAGGAT
1 TAT-CAAAATTTCATATGAAGG-T
* ** * **
22812 TCTTGAAA-TCCATA-GTACCGT
1 TATCAAAATTTCATATG-AAGGT
*
22833 TATCAAAATTTCATA-GGAGGT
1 TATCAAAATTTCATATGAAGGT
22854 TATCAAAATTTCATA
1 TATCAAAATTTCATA
22869 ATGGGATCAT
Statistics
Matches: 376, Mismatches: 100, Indels: 79
0.68 0.18 0.14
Matches are distributed among these distances:
16 8 0.02
17 2 0.01
18 2 0.01
20 12 0.03
21 49 0.13
22 232 0.62
23 65 0.17
24 6 0.02
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:22389 original size:44 final size:44
Alignment explanation
Indices: 22332--22783 Score: 193
Period size: 44 Copynumber: 10.3 Consensus size: 44
22322 TCAGTGAGGA
* * **
22332 TATCAATATTTCATATGAAGGTTATCAAATTTTCATAGTTTAG-T
1 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAG-GGAGAT
* * *
22376 TTTCAAAATTTCATAAGAGGGTTATCAAAATTTCATAGGGAGAT
1 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGGGAGAT
* ** * *
22420 TAACAAAATTTCATAATGAA-GTTATCAAAAAATCATAAGGAGCT
1 TATCAAAATTTCAT-ATGAAGGTTATCAAAATTTCATAGGGAGAT
* * * *
22464 TATCAAAA--T--T-TGTA-GTTATCAAGATTTCATA-AGAAAGT
1 TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGGGAGA-T
* * * * * **
22502 TATCAAAATTTTATAGGGAGGTTTATTAAAATTTTATAGAAAGATT
1 TATCAAAATTTCATATGAAGG-TTATCAAAATTTCATAGGGAGA-T
* * * *
22548 TATCAAAATTTCATA-GCGAGGTTATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATATG-AAGGTTATCAAAATTTCATAGGGAGAT
* * * * * *
22592 TATCAAAATTTTAAAGTG-TGATTA-CTAACAA-TTCATATGGAGGT
1 TATCAAAATTTCATA-TGAAGGTTATC-AA-AATTTCATAGGGAGAT
** * * * * * *
22636 T-TTTAAATTT-TTATAAAGTGGTTATCAATATATCATATGGAGGT
1 TATCAAAATTTCATATGAA--GGTTATCAAAATTTCATAGGGAGAT
* * ** *
22680 TATCAACATCTCATAGTGTTGGTTATCAAAATTTCATTGGGA-AGT
1 TATCAAAATTTCATA-TGAAGGTTATCAAAATTTCATAGGGAGA-T
* * *
22725 TATCAAAATTTCATATTG-AGGTCT-TCAAAATTCCTTAGGGAGGT
1 TATCAAAATTTCATA-TGAAGGT-TATCAAAATTTCATAGGGAGAT
*
22769 TAACAAAATTTCATA
1 TATCAAAATTTCATA
22784 AGAAAGTTTA
Statistics
Matches: 303, Mismatches: 78, Indels: 54
0.70 0.18 0.12
Matches are distributed among these distances:
37 2 0.01
38 26 0.09
40 2 0.01
41 1 0.00
42 3 0.01
43 13 0.04
44 154 0.51
45 76 0.25
46 25 0.08
47 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (44 bp):
TATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGGGAGAT
Found at i:22532 original size:23 final size:23
Alignment explanation
Indices: 22501--22604 Score: 95
Period size: 23 Copynumber: 4.6 Consensus size: 23
22491 CATAAGAAAG
*
22501 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGAGAGGT
* * *
22524 TTATTAAAATTTTATAGAAAGAT
1 TTATCAAAATTTTATAGAGAGGT
* *
22547 TTATCAAAATTTCATAGCGAGG-
1 TTATCAAAATTTTATAGAGAGGT
* * * * *
22569 TTATCACAATTTCATAGTG-TGA
1 TTATCAAAATTTTATAGAGAGGT
22591 TTATCAAAATTTTA
1 TTATCAAAATTTTA
22605 AAGTGTGATT
Statistics
Matches: 66, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
21 1 0.02
22 29 0.44
23 36 0.55
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.40
Consensus pattern (23 bp):
TTATCAAAATTTTATAGAGAGGT
Found at i:22727 original size:45 final size:45
Alignment explanation
Indices: 22654--22739 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
22644 TTTTATAAAG
* * *
22654 TGGTTATCAATATATCATATGGAGGTTATCAACATCTCATAGTGT
1 TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
* *
22699 TGGTTATCAAAATTTCAT-TGGGAAGTTATCAAAATTTCATA
1 TGGTTATCAAAATATCATAT-GGAAGTTATCAAAATCTCATA
22740 TTGAGGTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 1 0.03
45 34 0.97
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (45 bp):
TGGTTATCAAAATATCATATGGAAGTTATCAAAATCTCATAGTGT
Done.