Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006455.1 Corchorus capsularis cultivar CVL-1 contig06476, 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: 50311
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:1544 original size:16 final size:15
Alignment explanation
Indices: 1505--1611 Score: 97
Period size: 16 Copynumber: 6.7 Consensus size: 15
1495 GGGTTATTTA
1505 GGTTTCGGGTCATACG
1 GGTTTCGGGTCAT-CG
* *
1521 AGTCTCGGGTCACTCG
1 GGTTTCGGGTCA-TCG
1537 GGTTTCGGGTCATCTG
1 GGTTTCGGGTCATC-G
*
1553 GGTTACGGGTCACTCG
1 GGTTTCGGGTCA-TCG
*
1569 GGTCTCGGGTCATCTG
1 GGTTTCGGGTCATC-G
*
1585 GGTTGCGGGTCACTCG
1 GGTTTCGGGTCA-TCG
* *
1601 TGTCTCGGGTC
1 GGTTTCGGGTC
1612 GGGCGGGTTC
Statistics
Matches: 74, Mismatches: 12, Indels: 10
0.77 0.12 0.10
Matches are distributed among these distances:
15 4 0.05
16 65 0.88
17 5 0.07
ACGTcount: A:0.08, C:0.24, G:0.37, T:0.30
Consensus pattern (15 bp):
GGTTTCGGGTCATCG
Found at i:1546 original size:48 final size:48
Alignment explanation
Indices: 1493--1596 Score: 122
Period size: 48 Copynumber: 2.2 Consensus size: 48
1483 GGTTAACGTC
* * *
1493 TCGGGTTATTTAGGTTTCGGGTCA-TACGAGTCTCGGGTCA-CTCGGGTT
1 TCGGGTCATCTAGGTTACGGGTCACT-CGAGTCTCGGGTCATCT-GGGTT
* *
1541 TCGGGTCATCTGGGTTACGGGTCACTCGGGTCTCGGGTCATCTGGGTT
1 TCGGGTCATCTAGGTTACGGGTCACTCGAGTCTCGGGTCATCTGGGTT
*
1589 GCGGGTCA
1 TCGGGTCA
1597 CTCGTGTCTC
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
48 45 0.94
49 3 0.06
ACGTcount: A:0.11, C:0.21, G:0.37, T:0.32
Consensus pattern (48 bp):
TCGGGTCATCTAGGTTACGGGTCACTCGAGTCTCGGGTCATCTGGGTT
Found at i:1620 original size:32 final size:31
Alignment explanation
Indices: 1525--1611 Score: 138
Period size: 32 Copynumber: 2.7 Consensus size: 31
1515 CATACGAGTC
*
1525 TCGGGTCACTCGGGTTTCGGGTCATCTGGGT
1 TCGGGTCACTCGGGTCTCGGGTCATCTGGGT
1556 TACGGGTCACTCGGGTCTCGGGTCATCTGGGT
1 T-CGGGTCACTCGGGTCTCGGGTCATCTGGGT
*
1588 TGCGGGTCACTCGTGTCTCGGGTC
1 T-CGGGTCACTCGGGTCTCGGGTC
1612 GGGCGGGTTC
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 1 0.02
32 51 0.98
ACGTcount: A:0.07, C:0.25, G:0.38, T:0.30
Consensus pattern (31 bp):
TCGGGTCACTCGGGTCTCGGGTCATCTGGGT
Found at i:2087 original size:215 final size:217
Alignment explanation
Indices: 1713--2525 Score: 1028
Period size: 215 Copynumber: 3.8 Consensus size: 217
1703 GTTTATATCA
* *
1713 TATTAGATGACACTAAATTTATATAGAC-GGGTTTATTCAATTAATTAGGTTGAAAAATATGGAT
1 TATTAGATGACACTAAATTCATATAGACTGGGTTTATTCAATTAATTAGGATG-AAAATATGGAT
* * * *
1777 TGAAACACGTTTAAAGCCAATTTTGGGTATACAAAAAAATGTCAATCTCTAAAGAATTTGGAGAT
65 TAAAACACGTTTAAAGCCAATTTTGGGTATATAAAAAAATAT-AATCTCTAAAAAATTTGGAGAT
* * *
1842 AGTGCATATAATTATTTGGGGATGATGAGAAATGATATGGGTATAAAGTATATCAGTTTGGAGAT
129 GGTGCATATAATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGGAT
* *
1907 ATTGGGTTTTGCATTTGGTTTAAT
194 ATTGGATTTTGCATTTTGTTTAAT
* *
1931 TATTAGATGGCACTAAATTCGTATAGACTGGGTTTATTCAATTAATTAGGATGAAAATAT-GATT
1 TATTAGATGACACTAAATTCATATAGACTGGGTTTATTCAATTAATTAGGATGAAAATATGGATT
**
1995 AAAACTTGTTTAAAGCCAATTTTGGGTATATAAAAAAATAT-ATCTCTAAAAAATTTGGAGATGG
66 AAAACACGTTTAAAGCCAATTTTGGGTATATAAAAAAATATAATCTCTAAAAAATTTGGAGATGG
* * * * * *
2059 TGCATATGATTATTTAGAGATGATGAGAACTTATTTGGGTATAAAGTATATCAGTTTGGGGATAC
131 TGCATATAATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATAT
* * *
2124 TGAATTTTGTATTTTGTTTAAA
196 TGGATTTTGCATTTTGTTTAAT
** *
2146 TATTAGATGGTACTAAATTCATATAGA-TGGGGTTTATTCAATTAATTAAGATGAAAAGTATGGA
1 TATTAGATGACACTAAATTCATATAGACT-GGGTTTATTCAATTAATTAGGATGAAAA-TATGGA
* ** * *
2210 TTAAAACACGTTTAAAGTCAATTTTGGGTATAT--AAAAATGCAATCTCTAAAGAATTTGGGGAT
64 TTAAAACACGTTTAAAGCCAATTTTGGGTATATAAAAAAATATAATCTCTAAAAAATTTGGAGAT
2273 GGTGCATATAATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGGAT
129 GGTGCATATAATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGGAT
2338 ATTGGATTTTGCATTTTGTTTAAT
194 ATTGGATTTTGCATTTTGTTTAAT
*
2362 AATTAGATGACACTAAATTCATATAGACT--G---------------AGGATGAAAATAT-GATT
1 TATTAGATGACACTAAATTCATATAGACTGGGTTTATTCAATTAATTAGGATGAAAATATGGATT
* * * * *
2409 AAAACACATTTAAAGCCAATTTTGGATATATAAAAAATTGTTAATCTCTAAAAACTTT-GATGAT
66 AAAACACGTTTAAAGCCAATTTTGGGTATATAAAAAAAT-ATAATCTCTAAAAAATTTGGA-GAT
* * *
2473 GGTGCTTATGATTATTTGGGGATGATGAGAAATTATTTGGGTATAAAGTATAT
129 GGTGCATATAATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATAT
2526 AACTTCAGGC
Statistics
Matches: 526, Mismatches: 59, Indels: 38
0.84 0.09 0.06
Matches are distributed among these distances:
197 32 0.06
198 3 0.01
199 15 0.03
200 67 0.13
214 2 0.00
215 153 0.29
216 126 0.24
217 73 0.14
218 32 0.06
219 23 0.04
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (217 bp):
TATTAGATGACACTAAATTCATATAGACTGGGTTTATTCAATTAATTAGGATGAAAATATGGATT
AAAACACGTTTAAAGCCAATTTTGGGTATATAAAAAAATATAATCTCTAAAAAATTTGGAGATGG
TGCATATAATTATTTGGGGATGATGAGAAATGATTTGGGTATAAAGTATATCAGTTTGGGGATAT
TGGATTTTGCATTTTGTTTAAT
Found at i:2312 original size:21 final size:23
Alignment explanation
Indices: 2263--2313 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
2253 TCTCTAAAGA
* * *
2263 ATTTGGGGATGGTGCATATAATT
1 ATTTGGGGATGATGCAGATAATG
2286 ATTTGGGGATGATG-AGA-AATG
1 ATTTGGGGATGATGCAGATAATG
2307 ATTTGGG
1 ATTTGGG
2314 TATAAAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.40
22 2 0.08
23 13 0.52
ACGTcount: A:0.27, C:0.02, G:0.35, T:0.35
Consensus pattern (23 bp):
ATTTGGGGATGATGCAGATAATG
Found at i:10922 original size:78 final size:78
Alignment explanation
Indices: 10793--10949 Score: 235
Period size: 78 Copynumber: 2.0 Consensus size: 78
10783 TTATCATAGA
* * * *
10793 CAGGATTTCTACGAACAGGTTCATGTCTTTTAATAGGGCCACCACGAGCCATCTCCACCCTTGGC
1 CAGGATTTCTACAAACAGATACATGTCTTTTAATAGGACCACCACGAGCCATCTCCACCCTTGGC
10858 TTTCAATTGTCGG
66 TTTCAATTGTCGG
*
10871 CAGGATTTCTGCAAACAGATACATGT-TTTTCAATAGGACCACCACGAGCCATCTCCACCCTTGG
1 CAGGATTTCTACAAACAGATACATGTCTTTT-AATAGGACCACCACGAGCCATCTCCACCCTTGG
* *
10935 TTTTCTATTGTCGG
65 CTTTCAATTGTCGG
10949 C
1 C
10950 TTGTCTCCTG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
77 4 0.06
78 67 0.94
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (78 bp):
CAGGATTTCTACAAACAGATACATGTCTTTTAATAGGACCACCACGAGCCATCTCCACCCTTGGC
TTTCAATTGTCGG
Found at i:11549 original size:16 final size:16
Alignment explanation
Indices: 11530--11568 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
11520 AAAAAGTTCA
11530 AACCCGAAAAAACCAG
1 AACCCGAAAAAACCAG
*
11546 AACCCG-AAAAACCCG
1 AACCCGAAAAAACCAG
11561 AACCCGAA
1 AACCCGAA
11569 TAAGAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.51, C:0.36, G:0.13, T:0.00
Consensus pattern (16 bp):
AACCCGAAAAAACCAG
Found at i:11768 original size:32 final size:32
Alignment explanation
Indices: 11724--11807 Score: 141
Period size: 32 Copynumber: 2.6 Consensus size: 32
11714 AGGTCGAACC
*
11724 CGAACCCAAATTAACCTGACACAAATTCAACT
1 CGAACCCGAATTAACCTGACACAAATTCAACT
* *
11756 CGAACCCGAATTAACCCGACTCAAATTCAACT
1 CGAACCCGAATTAACCTGACACAAATTCAACT
11788 CGAACCCGAATTAACCTGAC
1 CGAACCCGAATTAACCTGAC
11808 CTAAAATGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.39, C:0.33, G:0.10, T:0.18
Consensus pattern (32 bp):
CGAACCCGAATTAACCTGACACAAATTCAACT
Found at i:16377 original size:10 final size:10
Alignment explanation
Indices: 16340--16382 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
16330 ACTTCACGTT
16340 TTATATATTG
1 TTATATATTG
16350 TTATTATATTG
1 TTA-TATATTG
16361 -T-TATATTG
1 TTATATATTG
16369 TTATATATTG
1 TTATATATTG
16379 TTAT
1 TTAT
16383 GTTATGTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.23
9 1 0.03
10 15 0.50
11 7 0.23
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (10 bp):
TTATATATTG
Found at i:17276 original size:32 final size:32
Alignment explanation
Indices: 17240--17312 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 32
17230 CCGCTCCAGG
17240 AGGGCGGCTCT-GCCAC-GTGAAGCCGCCCTCCT
1 AGGGCGGCT-TAGCCACGGT-AAGCCGCCCTCCT
*
17272 AGGGCGGCTTGAGCCATGGTAAGCCGCCCTCCT
1 AGGGCGGCTT-AGCCACGGTAAGCCGCCCTCCT
*
17305 GGGGCGGC
1 AGGGCGGC
17313 ACGGGTCATC
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
31 1 0.03
32 9 0.25
33 24 0.67
34 2 0.06
ACGTcount: A:0.12, C:0.36, G:0.37, T:0.15
Consensus pattern (32 bp):
AGGGCGGCTTAGCCACGGTAAGCCGCCCTCCT
Found at i:17683 original size:3 final size:3
Alignment explanation
Indices: 17675--17727 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
17665 GGTAAAATGG
17675 TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
17722 TAT TAT
1 TAT TAT
17728 CATCTATATA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 47 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:17859 original size:27 final size:27
Alignment explanation
Indices: 17807--17922 Score: 74
Period size: 24 Copynumber: 4.7 Consensus size: 27
17797 ATTTCTAAAT
**
17807 TGCCATTATTAAAATATACTTTAATTA
1 TGCCATTATTAAAATATACTAAAATTA
17834 TGCCATTAATTAAAATATA-TAAAATTA
1 TGCCATT-ATTAAAATATACTAAAATTA
* * **
17861 --CCA--A-TATAGTAT--TTTAATTA
1 TGCCATTATTAAAATATACTAAAATTA
**
17881 TGTGATTATTAAAATATA-TAAAA-T-
1 TGCCATTATTAAAATATACTAAAATTA
17905 TGCCATTATTAAAATATA
1 TGCCATTATTAAAATATA
17923 AAGTCCTAAC
Statistics
Matches: 68, Mismatches: 14, Indels: 17
0.69 0.14 0.17
Matches are distributed among these distances:
20 6 0.09
21 6 0.09
22 2 0.03
24 17 0.25
25 10 0.15
26 3 0.04
27 13 0.19
28 11 0.16
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (27 bp):
TGCCATTATTAAAATATACTAAAATTA
Found at i:18925 original size:45 final size:42
Alignment explanation
Indices: 18835--18933 Score: 110
Period size: 45 Copynumber: 2.3 Consensus size: 42
18825 TATAAGGAGA
* * *
18835 TTATAAAAATTTCATTGTGCTTAGCAAAATTTCATATGAAGG
1 TTATAAAAAATTCATTGTGCTTACCAAAAGTTCATATGAAGG
*
18877 TTATAAAAAATTCATGGTGTGGTTACCAAAAAGTTCATAT-AGAGG
1 TTATAAAAAATTCAT--TGTGCTTACC-AAAAGTTCATATGA-AGG
*
18922 TTATAAGAAATT
1 TTATAAAAAATT
18934 TCATAAGGAG
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
42 14 0.29
44 9 0.19
45 25 0.52
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.35
Consensus pattern (42 bp):
TTATAAAAAATTCATTGTGCTTACCAAAAGTTCATATGAAGG
Found at i:18956 original size:22 final size:23
Alignment explanation
Indices: 18910--18956 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
18900 TACCAAAAAG
18910 TTCATATAGAGGTTATAAGAAAT
1 TTCATATAGAGGTTATAAGAAAT
*
18933 TTCATA-AGGAGGTTAT-CGAAAT
1 TTCATATA-GAGGTTATAAGAAAT
18955 TT
1 TT
18957 TACAGTTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.36
Consensus pattern (23 bp):
TTCATATAGAGGTTATAAGAAAT
Found at i:19026 original size:22 final size:22
Alignment explanation
Indices: 18835--19251 Score: 118
Period size: 22 Copynumber: 19.0 Consensus size: 22
18825 TATAAGGAGA
* *
18835 TTATAAAAATTTCAT--TGTGC
1 TTATCAAAATTTCATAGTGTGG
* *
18855 TTAGCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-TGG
* * *
18877 TTATAAAAAATTCATGGTGTGG
1 TTATCAAAATTTCATAGTGTGG
* * *
18899 TTACCAAAAAGTTCATA-TAGAGG
1 TTATC-AAAATTTCATAGT-GTGG
* *
18922 TTATAAGAAATTTCATAAG-GAGG
1 TTATCA-AAATTTCAT-AGTGTGG
* * * *
18945 TTATCGAAATTTTACAGTTTGG
1 TTATCAAAATTTCATAGTGTGG
* * **
18967 TTACCAAATTTTCATAG-GAAATTAT
1 TTATCAAAATTTCATAGTG----TGG
* *
18992 TTAT-AAAAATTCACAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
*
19013 TTATCAAAATTTCATACG-GAGG
1 TTATCAAAATTTCATA-GTGTGG
*
19035 TTA-CAAAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGTGG
*
19056 TTATCAAAATTTCATA--GAGG
1 TTATCAAAATTTCATAGTGTGG
*
19076 TCATCAAAATTTCATTAG-G-GG
1 TTATCAAAATTTCA-TAGTGTGG
* *
19097 -TATCAAAAATTCATAATGTGGAAGG
1 TTATCAAAATTTCAT-A-GT-G-TGG
* * *
19122 TTATTAAATTTTTATTA-TG-GAG
1 TTATCAAAATTTCA-TAGTGTG-G
* *
19144 TAATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-TGG
** * *
19166 TTATTGAAATTTCATAGTTTAGT
1 TTATCAAAATTTCATAGTGT-GG
* * * *
19189 TTTTCAAGATTTGATAGCG-GAG
1 TTATCAAAATTTCATAGTGTG-G
* *
19211 TTATCAGAATTTCATAATGTGG
1 TTATCAAAATTTCATAGTGTGG
*
19233 -T-TCAAAATTTTATAGTGTG
1 TTATCAAAATTTCATAGTGTG
19252 TATTGTGTAA
Statistics
Matches: 284, Mismatches: 78, Indels: 70
0.66 0.18 0.16
Matches are distributed among these distances:
19 1 0.00
20 56 0.20
21 38 0.13
22 108 0.38
23 52 0.18
24 11 0.04
25 7 0.02
26 10 0.04
27 1 0.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGG
Found at i:19041 original size:21 final size:21
Alignment explanation
Indices: 18814--19182 Score: 129
Period size: 22 Copynumber: 16.8 Consensus size: 21
18804 TCTGCATGGG
* *
18814 TATCAAAATTTTATAAGGAGAT
1 TATCAAAATTTCAT-AGGAGGT
* * * *
18836 TATAAAAATTTCAT-TGTGCT
1 TATCAAAATTTCATAGGAGGT
* *
18856 TAGCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATA-GGAGGT
* * * *
18878 TATAAAAAATTCATGGTGTGGT
1 TATCAAAATTTCATAG-GAGGT
* * *
18900 TACCAAAAAGTTCATATAGAGGT
1 TATC-AAAATTTCATA-GGAGGT
*
18923 TATAAGAAATTTCATAAGGAGGT
1 TATCA-AAATTTCAT-AGGAGGT
* * * **
18946 TATCGAAATTTTACAGTTTGGT
1 TATCAAAATTTCATAG-GAGGT
* * **
18968 TACCAAATTTTCATAGGAAAT
1 TATCAAAATTTCATAGGAGGT
* * * *
18989 TATTTATAAAAATTCACAGTGTGGT
1 TA--T-CAAAATTTCATAG-GAGGT
19014 TATCAAAATTTCATACGGAGGT
1 TATCAAAATTTCATA-GGAGGT
* *
19036 TA-CAAAATTTCATAGTGTGAT
1 TATCAAAATTTCATAG-GAGGT
19057 TATCAAAATTTCATA-GAGGT
1 TATCAAAATTTCATAGGAGGT
*
19077 CATCAAAATTTCATTAGG-GG-
1 TATCAAAATTTCA-TAGGAGGT
*
19097 TATCAAAAATTCATAATGTGGAAGGT
1 TATCAAAATTTCAT-A---GG-AGGT
* * *
19123 TATTAAATTTTTATTATGGA-GT
1 TATCAAAATTTCA-TA-GGAGGT
* *
19145 AATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATA-GGAGGT
**
19167 TATTGAAATTTCATAG
1 TATCAAAATTTCATAG
19183 TTTAGTTTTT
Statistics
Matches: 248, Mismatches: 73, Indels: 53
0.66 0.20 0.14
Matches are distributed among these distances:
19 1 0.00
20 43 0.17
21 33 0.13
22 105 0.42
23 36 0.15
24 13 0.05
25 6 0.02
26 10 0.04
27 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (21 bp):
TATCAAAATTTCATAGGAGGT
Found at i:19061 original size:43 final size:42
Alignment explanation
Indices: 18996--19090 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 42
18986 AATTATTTAT
* * * *
18996 AAAAATTCACAGTGTGGTTATCAAAATTTCATACGGAGGTTA-C
1 AAAATTTCATAGTGTGATTATCAAAATTTCATA--GAGGTCATC
19039 AAAATTTCATAGTGTGATTATCAAAATTTCATAGAGGTCATC
1 AAAATTTCATAGTGTGATTATCAAAATTTCATAGAGGTCATC
19081 AAAATTTCAT
1 AAAATTTCAT
19091 TAGGGGTATC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
41 6 0.13
42 11 0.23
43 30 0.64
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34
Consensus pattern (42 bp):
AAAATTTCATAGTGTGATTATCAAAATTTCATAGAGGTCATC
Found at i:19083 original size:20 final size:20
Alignment explanation
Indices: 19011--19111 Score: 107
Period size: 20 Copynumber: 4.9 Consensus size: 20
19001 TTCACAGTGT
19011 GGTTATCAAAATTTCATACGGA
1 GGTTATCAAAATTTCATA--GA
*
19033 GGTTA-CAAAATTTCATAGT
1 GGTTATCAAAATTTCATAGA
19052 GTGATTATCAAAATTTCATAGA
1 G-G-TTATCAAAATTTCATAGA
*
19074 GGTCATCAAAATTTCATTAG-
1 GGTTATCAAAATTTCA-TAGA
* *
19094 GGGTATCAAAAATTCATA
1 GGTTATCAAAATTTCATA
19112 ATGTGGAAGG
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.06
20 27 0.39
21 19 0.28
22 19 0.28
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.34
Consensus pattern (20 bp):
GGTTATCAAAATTTCATAGA
Found at i:19442 original size:22 final size:22
Alignment explanation
Indices: 19363--19448 Score: 82
Period size: 23 Copynumber: 3.8 Consensus size: 22
19353 AAATTTGTGA
* * *
19363 TTATCAAAATTTTATGGTAAGAT
1 TTATCAAAATTTCATAGTAAG-G
* * *
19386 TTATCAAAATTTTATAGGAATG
1 TTATCAAAATTTCATAGTAAGG
*
19408 TCTATCAACATTTCATAGTAAGG
1 T-TATCAAAATTTCATAGTAAGG
*
19431 TTATCACAATTTCATAGT
1 TTATCAAAATTTCATAGT
19449 GTGATCATCA
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
22 16 0.31
23 36 0.69
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTAAGG
Found at i:19640 original size:22 final size:22
Alignment explanation
Indices: 19590--19642 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
19580 ATGACTATGG
19590 TATCAAAAATTTATAAGGAGAT
1 TATCAAAAATTTATAAGGAGAT
* * *
19612 TAACAAAATTTTAT-AGAGAGGT
1 TATCAAAAATTTATAAG-GAGAT
19634 TATCAAAAA
1 TATCAAAAA
19643 AATCATAAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.51, C:0.06, G:0.13, T:0.30
Consensus pattern (22 bp):
TATCAAAAATTTATAAGGAGAT
Found at i:19676 original size:21 final size:23
Alignment explanation
Indices: 19645--19688 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
19635 ATCAAAAAAA
*
19645 TCATAAGAAGG-TTATTTAAATT
1 TCATAAGAAGGTTTATTAAAATT
19667 TCAT-AGAAGGTTTATTAAAATT
1 TCATAAGAAGGTTTATTAAAATT
19689 ATCAGTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (23 bp):
TCATAAGAAGGTTTATTAAAATT
Found at i:19720 original size:22 final size:22
Alignment explanation
Indices: 19709--19768 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
19699 CATTGGGAGT
*
19709 TTATCACAATTTCATAGGGTAA
1 TTATCAAAATTTCATAGGGTAA
* *
19731 TTATCAAAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGGGTAA
19753 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
19769 AAATATTTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCATAGGGTAA
Found at i:20257 original size:17 final size:16
Alignment explanation
Indices: 20203--20253 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 16
20193 ATCACCCCCT
*
20203 AGATCACTAGTGATCTA
1 AGATCACCAGTGATC-A
20220 AGATCACCAGTGATGCA
1 AGATCACCAGTGAT-CA
*
20237 AGATCACCGGTGATCA
1 AGATCACCAGTGATCA
20253 A
1 A
20254 AGATTACATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 3 0.10
17 27 0.87
18 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Found at i:24937 original size:2 final size:2
Alignment explanation
Indices: 24930--24960 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
24920 AATTTTCCAT
24930 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 T
24961 GGTATTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31572 original size:7 final size:7
Alignment explanation
Indices: 31560--31585 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
31550 CTTACATAAA
31560 GGCAATT
1 GGCAATT
31567 GGCAATT
1 GGCAATT
31574 GGCAATT
1 GGCAATT
31581 GGCAA
1 GGCAA
31586 GCACAAGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (7 bp):
GGCAATT
Found at i:35658 original size:60 final size:60
Alignment explanation
Indices: 35565--35684 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
35555 CAAAAAAATG
*
35565 CTTCCTAAATTTGGTCGTTTCGATTGTTGGTCTATTTAATACCATATAATTTTCGATCCA
1 CTTCCTAAATTTGGTCGTTTCGATTGTTGGTCTATTTAACACCATATAATTTTCGATCCA
35625 CTTCCTAAATTTGGTCGTTTCGATTGTTGGTCTATTTAACACCATATAATTTTCGATCCA
1 CTTCCTAAATTTGGTCGTTTCGATTGTTGGTCTATTTAACACCATATAATTTTCGATCCA
35685 TATATATGTC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.44
Consensus pattern (60 bp):
CTTCCTAAATTTGGTCGTTTCGATTGTTGGTCTATTTAACACCATATAATTTTCGATCCA
Found at i:36268 original size:7 final size:7
Alignment explanation
Indices: 36256--36281 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
36246 CTTACATAAA
36256 GGCAATT
1 GGCAATT
36263 GGCAATT
1 GGCAATT
36270 GGCAATT
1 GGCAATT
36277 GGCAA
1 GGCAA
36282 GCACAAGGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (7 bp):
GGCAATT
Found at i:39441 original size:24 final size:24
Alignment explanation
Indices: 39404--39460 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 24
39394 TATATATATA
39404 TATATAGTATATATAATCATAACAAAC
1 TATATA-TATATAT-AT-ATAACAAAC
**
39431 TATATATATATATATATATTAAAC
1 TATATATATATATATATAACAAAC
39455 TATATA
1 TATATA
39461 AAAGAGAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 13 0.46
25 2 0.07
26 7 0.25
27 6 0.21
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (24 bp):
TATATATATATATATATAACAAAC
Found at i:39460 original size:2 final size:2
Alignment explanation
Indices: 39328--39449 Score: 92
Period size: 2 Copynumber: 60.0 Consensus size: 2
39318 GTTTCGAAAA
* *
39328 AT AT AT AT AT AT AT AT AGT AT AT AT A- AT CAT A- AC AA ACT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT -AT AT AT AT A-T AT
* *
39369 AT AT AT AT AT AT AT AT AT A- AC AA ACT AT AT AT AT AT AT AT AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T
* *
39412 AT AT AT A- AT CAT A- AC AA ACT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT -AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
39450 TAAACTATAT
Statistics
Matches: 102, Mismatches: 6, Indels: 24
0.77 0.05 0.18
Matches are distributed among these distances:
1 5 0.05
2 86 0.84
3 11 0.11
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.40
Consensus pattern (2 bp):
AT
Found at i:40436 original size:14 final size:14
Alignment explanation
Indices: 40419--40453 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
40409 ATAAAGCTTA
40419 TACAGTCTTTTCGT
1 TACAGTCTTTTCGT
*
40433 TACAGTCTTTTTGT
1 TACAGTCTTTTCGT
*
40447 TATAGTC
1 TACAGTC
40454 GCAATTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.51
Consensus pattern (14 bp):
TACAGTCTTTTCGT
Found at i:44982 original size:33 final size:33
Alignment explanation
Indices: 44945--45007 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
44935 AGATAAAGGA
* * *
44945 TCATGTGGCCGGTTGTGGCTGGGCATGGCCGAG
1 TCATGTGGCCGGGTATGGCCGGGCATGGCCGAG
44978 TCATGTGGCCGGGTATGGCCGGGCATGGCC
1 TCATGTGGCCGGGTATGGCCGGGCATGGCC
45008 ATGTCGCGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.10, C:0.24, G:0.44, T:0.22
Consensus pattern (33 bp):
TCATGTGGCCGGGTATGGCCGGGCATGGCCGAG
Found at i:45019 original size:33 final size:33
Alignment explanation
Indices: 44949--45022 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
44939 AAAGGATCAT
* * * *
44949 GTGGCCGGTTGTGGCTGGGCATGGCCGAGTCAT
1 GTGGCCGGGTATGGCCGGGCATGGCCGAGTCAC
*
44982 GTGGCCGGGTATGGCCGGGCATGGCC-ATGTCGC
1 GTGGCCGGGTATGGCCGGGCATGGCCGA-GTCAC
45015 GTGGCCGG
1 GTGGCCGG
45023 TCACTTGTGC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 1 0.03
33 34 0.97
ACGTcount: A:0.08, C:0.24, G:0.47, T:0.20
Consensus pattern (33 bp):
GTGGCCGGGTATGGCCGGGCATGGCCGAGTCAC
Found at i:49976 original size:19 final size:18
Alignment explanation
Indices: 49943--49978 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
49933 TTGAAATAAT
49943 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
49961 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
49979 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Done.