Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006870.1 Corchorus capsularis cultivar CVL-1 contig06891, 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: 18666
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:6 original size:1 final size:1
Alignment explanation
Indices: 1--37 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
*
1 TTTTTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
38 ATCAAACCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.03, T:0.97
Consensus pattern (1 bp):
T
Found at i:2847 original size:44 final size:44
Alignment explanation
Indices: 2799--2885 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
2789 CATAGAAAGA
* * *
2799 TTATCAAAATTTAATAGTGTGGTTA-CAAAAATTTCATATAGAGT
1 TTATCAAAACTTAATAGTGTAGTTATC-AAAATTTAATATAGAGT
*
2843 TTATCAAAACTTCATAGTGTAGTTATCAAAATTTAATATAGAG
1 TTATCAAAACTTAATAGTGTAGTTATCAAAATTTAATATAGAG
2886 GTTACCGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
44 37 0.97
45 1 0.03
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (44 bp):
TTATCAAAACTTAATAGTGTAGTTATCAAAATTTAATATAGAGT
Found at i:2851 original size:22 final size:21
Alignment explanation
Indices: 2826--2902 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 21
2816 TGTGGTTACA
2826 AAAATTTCATATAGAGTTTATC
1 AAAATTTCATATAGAG-TTATC
*
2848 AAAACTTCATAGT-GTAGTTATC
1 AAAATTTCATA-TAG-AGTTATC
* *
2870 AAAATTTAATATAGAGGTTACC
1 AAAATTTCATATAGA-GTTATC
*
2892 GAAATTTCATA
1 AAAATTTCATA
2903 AAACGGTTAC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
21 2 0.04
22 40 0.89
23 3 0.07
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (21 bp):
AAAATTTCATATAGAGTTATC
Found at i:2866 original size:23 final size:22
Alignment explanation
Indices: 2799--2876 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 22
2789 CATAGAAAGA
* *
2799 TTATCAAAATTTAATAGTGTGG
1 TTATCAAAATTTCATAGTGTAG
2821 TTA-CAAAAATTTCATA-TAG-AG
1 TTATC-AAAATTTCATAGT-GTAG
*
2842 TTTATCAAAACTTCATAGTGTAG
1 -TTATCAAAATTTCATAGTGTAG
2865 TTATCAAAATTT
1 TTATCAAAATTT
2877 AATATAGAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
21 3 0.07
22 39 0.85
23 4 0.09
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTAG
Found at i:2901 original size:44 final size:44
Alignment explanation
Indices: 2803--2902 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 44
2793 GAAAGATTAT
* * * * *
2803 CAAAATTTAATAGTGTGGTTACAAAAATTTCATATAGAGTTTAT
1 CAAAATTTCATAGTGTAGTTACAAAAATTTAATATAGAGGTTAC
*
2847 CAAAACTTCATAGTGTAGTTATC-AAAATTTAATATAGAGGTTAC
1 CAAAATTTCATAGTGTAGTTA-CAAAAATTTAATATAGAGGTTAC
*
2891 CGAAATTTCATA
1 CAAAATTTCATA
2903 AAACGGTTAC
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 46 0.98
45 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (44 bp):
CAAAATTTCATAGTGTAGTTACAAAAATTTAATATAGAGGTTAC
Found at i:2933 original size:22 final size:22
Alignment explanation
Indices: 2908--2972 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
2898 TCATAAAACG
* * *
2908 GTTACCAAAATTTCTTAGGGAT
1 GTTAACAAAATTTCATAGGGAA
* *
2930 GTTAAAAAAATTTCATAGGAAA
1 GTTAACAAAATTTCATAGGGAA
2952 GTTAACAAAATTTCATAGGGA
1 GTTAACAAAATTTCATAGGGA
2973 GGGAAGTTAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.43, C:0.09, G:0.17, T:0.31
Consensus pattern (22 bp):
GTTAACAAAATTTCATAGGGAA
Found at i:2979 original size:26 final size:25
Alignment explanation
Indices: 2924--2987 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 25
2914 AAAATTTCTT
* *
2924 AGGGATGTTAAAAAAATTTCATAGG
1 AGGGAAGTTAACAAAATTTCATAGG
2949 A---AAGTTAACAAAATTTCATAGGG
1 AGGGAAGTTAACAAAATTTCATA-GG
*
2972 AGGGAAGTTACCAAAA
1 AGGGAAGTTAACAAAA
2988 GTTGTGCATA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
22 17 0.53
23 3 0.09
25 1 0.03
26 11 0.34
ACGTcount: A:0.47, C:0.08, G:0.22, T:0.23
Consensus pattern (25 bp):
AGGGAAGTTAACAAAATTTCATAGG
Found at i:3037 original size:21 final size:21
Alignment explanation
Indices: 3000--3041 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2990 TGTGCATATC
3000 AAAATTTCGTAGGGAGGTTATA
1 AAAATTTC-TAGGGAGGTTATA
3022 AAAATTT-TAGGAGAGGTTAT
1 AAAATTTCTAGG-GAGGTTAT
3042 CAAAGATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 8 0.42
22 7 0.37
ACGTcount: A:0.38, C:0.02, G:0.26, T:0.33
Consensus pattern (21 bp):
AAAATTTCTAGGGAGGTTATA
Found at i:3181 original size:22 final size:22
Alignment explanation
Indices: 3155--3299 Score: 121
Period size: 22 Copynumber: 6.6 Consensus size: 22
3145 TTTAGGCAGA
* * *
3155 TTATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATAATGTGG
* * *
3177 TTATCAATATTTCATAGTGTGA
1 TTATCAAAATTTCATAATGTGG
* * *
3199 TTACCAAAATTTCACAGTGTGG
1 TTATCAAAATTTCATAATGTGG
* * *
3221 TTATCAAATTTTCAT-AGGGGG
1 TTATCAAAATTTCATAATGTGG
* *
3242 ATTATCGAAATTTCATAATGCGG
1 -TTATCAAAATTTCATAATGTGG
* *
3265 TTATCAAATTTTCAAAATGTGG
1 TTATCAAAATTTCATAATGTGG
*
3287 TTATCAATATTTC
1 TTATCAAAATTTC
3300 TACATTGGAG
Statistics
Matches: 96, Mismatches: 25, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
21 3 0.03
22 89 0.93
23 4 0.04
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCATAATGTGG
Found at i:3276 original size:44 final size:44
Alignment explanation
Indices: 3153--3278 Score: 155
Period size: 44 Copynumber: 2.9 Consensus size: 44
3143 TATTTAGGCA
* * *
3153 GATTATCAAAATTTCACACTGAGGTTATC-AATATTTCATAGTGT
1 GATTATCAAAATTTCACAATGAGGTTATCAAAT-TTTCATAGGGG
* * *
3197 GATTACCAAAATTTCACAGTGTGGTTATCAAATTTTCATAGGGG
1 GATTATCAAAATTTCACAATGAGGTTATCAAATTTTCATAGGGG
* * *
3241 GATTATCGAAATTTCATAATGCGGTTATCAAATTTTCA
1 GATTATCAAAATTTCACAATGAGGTTATCAAATTTTCA
3279 AAATGTGGTT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
44 68 0.96
45 3 0.04
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (44 bp):
GATTATCAAAATTTCACAATGAGGTTATCAAATTTTCATAGGGG
Found at i:10066 original size:1 final size:1
Alignment explanation
Indices: 10029--10059 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
10019 AAATGATCAG
10029 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
10060 CCTTTTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:12428 original size:6 final size:6
Alignment explanation
Indices: 12419--12532 Score: 89
Period size: 6 Copynumber: 19.2 Consensus size: 6
12409 TAAATATACG
12419 ATAAAT ATAAAT A-ATAA- ATAAA- ATAAAT ATAAAT A-ATAA- ATAAAT
1 ATAAAT ATAAAT ATA-AAT ATAAAT ATAAAT ATAAAT ATA-AAT ATAAAT
* ***
12464 ATAAGAA ATATGCG ATAAAT ATAAAT A-ATAA- ATAAAT ATAAAT ATAAAT
1 ATAA-AT ATA-AAT ATAAAT ATAAAT ATA-AAT ATAAAT ATAAAT ATAAAT
12513 ATAAAT ATAAAT AATAAAT A
1 ATAAAT ATAAAT -ATAAAT A
12533 AATAAACAAA
Statistics
Matches: 89, Mismatches: 7, Indels: 24
0.74 0.06 0.20
Matches are distributed among these distances:
5 17 0.19
6 59 0.66
7 13 0.15
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.29
Consensus pattern (6 bp):
ATAAAT
Found at i:12429 original size:17 final size:15
Alignment explanation
Indices: 12425--12536 Score: 71
Period size: 17 Copynumber: 6.5 Consensus size: 15
12415 TACGATAAAT
*
12425 ATAAATAATAAATAAA
1 ATAAAT-ATAAATATA
12441 ATAAATATAAATAATAA
1 ATAAATATAAAT-AT-A
*
12458 ATAAATATAAGAAATATGCG
1 ATAAATAT---AAATAT--A
12478 ATAAATATAAATAATAA
1 ATAAATATAAAT-AT-A
12495 ATAAATATAAATATAAA
1 ATAAATATAAATAT--A
12512 TATAAATATAAATAATAA
1 -ATAAATATAAAT-AT-A
12530 ATAAATA
1 ATAAATA
12537 AACAAAAGGC
Statistics
Matches: 81, Mismatches: 5, Indels: 19
0.77 0.05 0.18
Matches are distributed among these distances:
15 6 0.07
16 9 0.11
17 34 0.42
18 16 0.20
19 4 0.05
20 12 0.15
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.29
Consensus pattern (15 bp):
ATAAATATAAATATA
Found at i:12438 original size:4 final size:4
Alignment explanation
Indices: 12425--12538 Score: 59
Period size: 4 Copynumber: 29.2 Consensus size: 4
12415 TACGATAAAT
*
12425 ATAA AT-A ATAA ATAAA ATAA AT-- ATAA AT-A ATAA ATAA ATATA AGAA
1 ATAA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA ATAA ATAA ATA-A ATAA
* *
12471 ATATGCG ATAA AT-- ATAA AT-A ATAA ATAA ATATA A-AT ATAA ATATA
1 ATA---A ATAA ATAA ATAA ATAA ATAA ATAA ATA-A ATAA ATAA ATA-A
*
12516 A-AT ATAA AT-A ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
12539 CAAAAGGCCA
Statistics
Matches: 85, Mismatches: 8, Indels: 34
0.67 0.06 0.27
Matches are distributed among these distances:
2 4 0.05
3 14 0.16
4 53 0.62
5 11 0.13
7 3 0.04
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (4 bp):
ATAA
Found at i:12517 original size:59 final size:59
Alignment explanation
Indices: 12410--12532 Score: 196
Period size: 59 Copynumber: 2.1 Consensus size: 59
12400 ATTTAAAAGT
12410 AAATATACGATAAATATAAATAATAAATAAAATAAATATAAATAATAAATA-AATATAAG
1 AAATATACGATAAATATAAATAATAAATAAAATAAATATAAATAATAAATATAA-ATAAG
* *
12469 AAATATGCGATAAATATAAATAATAAATAAATATAAATATAAAT-ATAAATATAAATAAT
1 AAATATACGATAAATATAAATAATAAATAAA-ATAAATATAAATAATAAATATAAATAAG
12528 AAATA
1 AAATA
12533 AATAAACAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
59 46 0.77
60 14 0.23
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (59 bp):
AAATATACGATAAATATAAATAATAAATAAAATAAATATAAATAATAAATATAAATAAG
Found at i:14033 original size:85 final size:84
Alignment explanation
Indices: 13869--14035 Score: 237
Period size: 85 Copynumber: 2.0 Consensus size: 84
13859 CATAAACATG
* * * **
13869 GAAAATCCCATAAACAATTCAACCAAAATATCATAAAACAACAATTTTTTTTTTGAAACCCATAA
1 GAAAAACCCACAAACAATTCAACCAAAAAATCATAAAACAACAATTTTTTTTCAGAAACCCATAA
*
13934 CCCAGAATCAATTATTATC
66 CCCAAAATCAATTATTATC
13953 GAAAAACCCACAAACAATTCAACCCAAAAAATTCATAAAACAACAA-TTTTTTTCAGAAACCCAT
1 GAAAAACCCACAAACAATTCAA-CCAAAAAA-TCATAAAACAACAATTTTTTTTCAGAAACCCAT
* *
14017 ATCCCAAAATCGATTATTA
64 AACCCAAAATCAATTATTA
14036 CCCATAACCC
Statistics
Matches: 73, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
84 20 0.27
85 39 0.53
86 14 0.19
ACGTcount: A:0.48, C:0.23, G:0.04, T:0.26
Consensus pattern (84 bp):
GAAAAACCCACAAACAATTCAACCAAAAAATCATAAAACAACAATTTTTTTTCAGAAACCCATAA
CCCAAAATCAATTATTATC
Done.