Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005836.1 Corchorus capsularis cultivar CVL-1 contig05854, 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: 19538
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:659 original size:23 final size:23
Alignment explanation
Indices: 631--679 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
621 ACATCTCACA
631 CACTAGTATTAACTAACATCTTG
1 CACTAGTATTAACTAACATCTTG
654 CACTAGTATTAACTAACATCTTG
1 CACTAGTATTAACTAACATCTTG
677 CAC
1 CAC
680 AAAATGTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.33
Consensus pattern (23 bp):
CACTAGTATTAACTAACATCTTG
Found at i:3669 original size:1 final size:1
Alignment explanation
Indices: 3663--3709 Score: 67
Period size: 1 Copynumber: 47.0 Consensus size: 1
3653 ATACTGAATT
* * *
3663 AAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAAACAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3710 CAAACAAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3682 original size:14 final size:14
Alignment explanation
Indices: 3663--3758 Score: 97
Period size: 14 Copynumber: 6.7 Consensus size: 14
3653 ATACTGAATT
3663 AAAAAAAAA-AAAA
1 AAAAAAAAACAAAA
3676 AAAAAAAAACAAAA
1 AAAAAAAAACAAAA
3690 AAAAAAAAACAAAA
1 AAAAAAAAACAAAA
*
3704 ACAAAACAAACAAACA
1 A-AAAAAAAACAAA-A
*
3720 AACAAACAAAC-AAA
1 AA-AAAAAAACAAAA
* *
3734 CAAACAAAACAAAA
1 AAAAAAAAACAAAA
*
3748 CAAAACAAAAC
1 -AAAAAAAAAC
3759 TGGGTTAGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
13 15 0.21
14 24 0.33
15 23 0.32
16 10 0.14
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAACAAAA
Found at i:3710 original size:5 final size:5
Alignment explanation
Indices: 3663--3758 Score: 86
Period size: 5 Copynumber: 21.0 Consensus size: 5
3653 ATACTGAATT
* * *
3663 AAAA- AAAA- AAAAA AAAAA AAAAC AAAA- AAAAA AAAAC AAAAAC AAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC -AAAAC AAAAC
3711 -AAAC -AAAC -AAAC -AAAC -AAAC -AAAC -AAAC AAAAC AAAAC AAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC AAAAC
3754 AAAAC
1 AAAAC
3759 TGGGTTAGGC
Statistics
Matches: 86, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
4 40 0.47
5 41 0.48
6 5 0.06
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:3714 original size:4 final size:4
Alignment explanation
Indices: 3682--3756 Score: 77
Period size: 4 Copynumber: 18.8 Consensus size: 4
3672 AAAAAAAAAA
*
3682 AAAC AAA- AAA- AAAA AAAC -AA- AAAC AAAAC AAAC AAAC AAAC AAAC
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC -AAAC AAAC AAAC AAAC AAAC
3727 AAAC AAAC AAAC AAAAC AAAAC AAAAC AAA
1 AAAC AAAC AAAC -AAAC -AAAC -AAAC AAA
3757 ACTGGGTTAG
Statistics
Matches: 65, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
3 10 0.15
4 37 0.57
5 18 0.28
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:9022 original size:29 final size:29
Alignment explanation
Indices: 8989--9048 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
8979 GTAACTATTC
*
8989 CCTCCGTCCCATATTATCTGTCCACTTTT
1 CCTCCGTCCCATATTATCTATCCACTTTT
*
9018 CCTCCGTCCCATATTATCTATCTACTTTT
1 CCTCCGTCCCATATTATCTATCCACTTTT
9047 CC
1 CC
9049 CCTAATAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.15, C:0.38, G:0.05, T:0.42
Consensus pattern (29 bp):
CCTCCGTCCCATATTATCTATCCACTTTT
Found at i:14106 original size:2 final size:2
Alignment explanation
Indices: 14101--14180 Score: 54
Period size: 2 Copynumber: 39.5 Consensus size: 2
14091 TAAAAAATTA
* * * * *
14101 AT AT AT AT AT AT AT AT GT AC ACT AT AT AC AT AT AT CT AT AT CT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* * * *
14144 AT AT CT AT AT CT AT AT CT AT TT AT -T AT ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
14181 AAAGTACGAG
Statistics
Matches: 57, Mismatches: 18, Indels: 6
0.70 0.22 0.07
Matches are distributed among these distances:
1 1 0.02
2 53 0.93
3 3 0.05
ACGTcount: A:0.40, C:0.11, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:14146 original size:12 final size:12
Alignment explanation
Indices: 14131--14163 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
14121 ACTATATACA
14131 TATATCTATATC
1 TATATCTATATC
14143 TATATCTATATC
1 TATATCTATATC
14155 TATATCTAT
1 TATATCTAT
14164 TTATTATACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (12 bp):
TATATCTATATC
Found at i:15299 original size:3 final size:3
Alignment explanation
Indices: 15293--15367 Score: 134
Period size: 3 Copynumber: 25.3 Consensus size: 3
15283 GTAGTTCTTC
*
15293 CAT CAT CAT CAT CAT CAT CAT CAC CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
15341 CAT CAT CAT CAT CAT CAT CAT CA- CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
15368 TTCCGTGAGC
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 67 0.97
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:16318 original size:53 final size:52
Alignment explanation
Indices: 16251--16353 Score: 152
Period size: 53 Copynumber: 2.0 Consensus size: 52
16241 AAAAAGGTGT
** * *
16251 AACCAAACGGGGTGATCTGAGATCACCTCGCAAAATCACCAACAGGTGATCCC
1 AACCAAACAAGGTGATCTGAGATCACCACCCAAAATCACC-ACAGGTGATCCC
*
16304 AACCAAACAAGGTGATCTGAGATCACCACCCAAGATCACCACAGGTGATC
1 AACCAAACAAGGTGATCTGAGATCACCACCCAAAATCACCACAGGTGATC
16354 AAACCAACCA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 10 0.22
53 35 0.78
ACGTcount: A:0.36, C:0.30, G:0.19, T:0.15
Consensus pattern (52 bp):
AACCAAACAAGGTGATCTGAGATCACCACCCAAAATCACCACAGGTGATCCC
Found at i:17891 original size:22 final size:21
Alignment explanation
Indices: 17835--17960 Score: 83
Period size: 22 Copynumber: 5.8 Consensus size: 21
17825 GTCTCTTTAT
*
17835 AGTTATCAAAATTTCATAAGA
1 AGTTATCAAAATTTCATAGGA
* * *
17856 TGGTTATTATAATTTCATGAGGA
1 -AGTTATCAAAATTTCAT-AGGA
* * *
17879 AGTTATGAAAATTCCAT-GGTTT
1 AGTTATCAAAATTTCATAGG--A
* *
17901 GGTTACCAAAATTTCATACGGA
1 AGTTATCAAAATTTCATA-GGA
*
17923 AGTTATCAAAATTTCATAAAGA
1 AGTTATCAAAATTTCAT-AGGA
* *
17945 GGTTATCAAATTTTCA
1 AGTTATCAAAATTTCA
17961 AAATGTGATT
Statistics
Matches: 79, Mismatches: 19, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
20 2 0.03
22 71 0.90
23 4 0.05
24 2 0.03
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (21 bp):
AGTTATCAAAATTTCATAGGA
Found at i:17949 original size:44 final size:43
Alignment explanation
Indices: 17835--17960 Score: 121
Period size: 44 Copynumber: 2.9 Consensus size: 43
17825 GTCTCTTTAT
* *
17835 AGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGGA
1 AGTTATCAAAATTTCATAAGA-GGTTATCAAAATTTCATGAGGA
* * * * *
17879 AGTTATGAAAATTCCAT-GGTTTGGTTACCAAAATTTCAT-ACGGA
1 AGTTATCAAAATTTCATAAG--AGGTTATCAAAATTTCATGA-GGA
*
17923 AGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCA
1 AGTTATCAAAATTTCAT-AAGAGGTTATCAAAATTTCA
17961 AAATGTGATT
Statistics
Matches: 64, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
43 2 0.03
44 61 0.95
46 1 0.02
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (43 bp):
AGTTATCAAAATTTCATAAGAGGTTATCAAAATTTCATGAGGA
Found at i:18120 original size:21 final size:21
Alignment explanation
Indices: 18066--18544 Score: 118
Period size: 22 Copynumber: 22.5 Consensus size: 21
18056 TTATGGAGTA
** *
18066 ATCAAAATTTCA-GGGAGGAT
1 ATCAAAATTTCATATGAGGTT
18086 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATATG-AGGTT
*
18108 ATCAAAA-TTCATAGTTTA-GTT
1 ATCAAAATTTCATA--TGAGGTT
* *
18129 TTCAAAATTTCATAAGAGAGTT
1 ATCAAAATTTCATATGAG-GTT
* *
18151 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATATG-AGGT-T
18173 ATCAAAATTTCATA--A----
1 ATCAAAATTTCATATGAGGTT
18188 A-CAAAATTTCATAATGAGGTT
1 ATCAAAATTTCAT-ATGAGGTT
** * *
18209 ATCAAAAAATCATAGGGATGTT
1 ATCAAAATTTCATA-TGAGGTT
* *
18231 ATC-AAAGTT--TGT-A-GTT
1 ATCAAAATTTCATATGAGGTT
* * *
18247 ATCAAGATTTTATAAGGAGGTT
1 ATCAAAATTTCAT-ATGAGGTT
* * *
18269 ATCGAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATA-TGAGG-TT
*
18292 ATCAAAATTTTATA-GAAAGGTT
1 ATCAAAATTTCATATG--AGGTT
* *
18314 ATCAAAATTTTATAGCGAGGTT
1 ATCAAAATTTCATA-TGAGGTT
* * * *
18336 ATCACAGTTTCATAGTGTGATT
1 ATCAAAATTTCATA-TGAGGTT
* * * *
18358 ATCAAAATTTAAGAGTGTGATT
1 ATCAAAATTTCATA-TGAGGTT
18380 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATAT-GAGGTT
* * * * *
18402 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCAT-ATGAGGTT
** *
18424 ATCAGTATATCATATGGAGGTT
1 ATCAAAATTTCATAT-GAGGTT
* * * *
18446 ATCAACATCTCATAATGTTGATT
1 ATCAAAATTTCAT-ATG-AGGTT
18469 ATCAAAATTTCATAGTGAGGTCT
1 ATCAAAATTTCATA-TGAGGT-T
* *
18492 -TCAAAA-TTCTTTAGAGAGGTT
1 ATCAAAATTTC-ATA-TGAGGTT
* *
18513 AACAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATATG-AGGTT
**
18535 AAAAAAATTT
1 ATCAAAATTT
18545 TATAAAAAAG
Statistics
Matches: 348, Mismatches: 66, Indels: 88
0.69 0.13 0.18
Matches are distributed among these distances:
14 11 0.03
15 2 0.01
16 6 0.02
17 6 0.02
19 2 0.01
20 14 0.04
21 38 0.11
22 224 0.64
23 44 0.13
24 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (21 bp):
ATCAAAATTTCATATGAGGTT
Found at i:18178 original size:44 final size:42
Alignment explanation
Indices: 18085--18187 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 42
18075 TCAGGGAGGA
*
18085 TATCAAAATTTCATATGAAGGTTATCAAAATTCATAGTTTAG
1 TATCAAAATTTCATAAGAAGGTTATCAAAATTCATAGTTTAG
*
18127 TTTTCAAAATTTCATAAG-AGAGTTATCAAAATTTCATAGTATGTAG
1 -TATCAAAATTTCATAAGAAG-GTTATCAAAA-TTCATAGT-T-TAG
18173 -ATCAAAATTTCATAA
1 TATCAAAATTTCATAA
18188 ACAAAATTTC
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
42 2 0.04
43 25 0.47
44 22 0.42
45 1 0.02
46 3 0.06
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.38
Consensus pattern (42 bp):
TATCAAAATTTCATAAGAAGGTTATCAAAATTCATAGTTTAG
Found at i:18194 original size:14 final size:14
Alignment explanation
Indices: 18175--18201 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18165 GTATGTAGAT
18175 CAAAATTTCATAAA
1 CAAAATTTCATAAA
18189 CAAAATTTCATAA
1 CAAAATTTCATAA
18202 TGAGGTTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (14 bp):
CAAAATTTCATAAA
Found at i:18278 original size:22 final size:22
Alignment explanation
Indices: 18244--18367 Score: 124
Period size: 22 Copynumber: 5.6 Consensus size: 22
18234 AAAGTTTGTA
*
18244 GTTATCAAGATTTTATA-AGGAG
1 GTTATCAAAATTTTATAGA-GAG
* *
18266 GTTATCGAAATTTTATAGGGAG
1 GTTATCAAAATTTTATAGAGAG
*
18288 GTTTATCAAAATTTTATAGAAAG
1 G-TTATCAAAATTTTATAGAGAG
*
18311 GTTATCAAAATTTTATAGCGAG
1 GTTATCAAAATTTTATAGAGAG
* * * * *
18333 GTTATCACAGTTTCATAGTGTG
1 GTTATCAAAATTTTATAGAGAG
*
18355 ATTATCAAAATTT
1 GTTATCAAAATTT
18368 AAGAGTGTGA
Statistics
Matches: 84, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
22 65 0.77
23 19 0.23
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (22 bp):
GTTATCAAAATTTTATAGAGAG
Found at i:18313 original size:45 final size:44
Alignment explanation
Indices: 18244--18339 Score: 131
Period size: 45 Copynumber: 2.2 Consensus size: 44
18234 AAAGTTTGTA
* * * *
18244 GTTATCAAGATTTTATAAGGAGGTTATCGAAATTTTATAGGGAG
1 GTTATCAAAATTTTATAAGAAGGTTATCAAAATTTTATAGCGAG
18288 GTTTATCAAAATTTTAT-AGAAAGGTTATCAAAATTTTATAGCGAG
1 G-TTATCAAAATTTTATAAG-AAGGTTATCAAAATTTTATAGCGAG
18333 GTTATCA
1 GTTATCA
18340 CAGTTTCATA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
44 9 0.20
45 37 0.80
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (44 bp):
GTTATCAAAATTTTATAAGAAGGTTATCAAAATTTTATAGCGAG
Found at i:18544 original size:22 final size:22
Alignment explanation
Indices: 18508--18549 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
18498 TTCTTTAGAG
*
18508 AGGTTAACAAAATTTCATAAGA
1 AGGTTAAAAAAATTTCATAAGA
*
18530 AGGTTAAAAAAATTTTATAA
1 AGGTTAAAAAAATTTCATAA
18550 AAAAGTTCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.31
Consensus pattern (22 bp):
AGGTTAAAAAAATTTCATAAGA
Found at i:18767 original size:27 final size:28
Alignment explanation
Indices: 18737--18791 Score: 87
Period size: 27 Copynumber: 2.0 Consensus size: 28
18727 AATGACCTAG
18737 CAACATAG-TATTACAT-AAATTTGGATT
1 CAACAT-GCTATTACATAAAATTTGGATT
18764 CAACATGCTATTACATAAAATTTGGATT
1 CAACATGCTATTACATAAAATTTGGATT
18792 TGATTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 1 0.04
27 14 0.54
28 11 0.42
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (28 bp):
CAACATGCTATTACATAAAATTTGGATT
Found at i:18986 original size:30 final size:31
Alignment explanation
Indices: 18927--19007 Score: 110
Period size: 30 Copynumber: 2.6 Consensus size: 31
18917 GCTAAATACC
* * *
18927 CAAAAAAATCTCTTATATTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTTGCTTTTGGGA
*
18958 CAAAATAATCCCTTATGTTTT-TTTTTGGGA
1 CAAAATAATCCCTTATGTTTTGCTTTTGGGA
*
18988 CAAATTAATCCCTTATGTTT
1 CAAAATAATCCCTTATGTTT
19008 CAAAAATGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 27 0.60
31 18 0.40
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.44
Consensus pattern (31 bp):
CAAAATAATCCCTTATGTTTTGCTTTTGGGA
Found at i:19202 original size:30 final size:30
Alignment explanation
Indices: 19120--19211 Score: 150
Period size: 31 Copynumber: 3.1 Consensus size: 30
19110 AAGGGACTAA
*
19120 TTTGTCCCCAAA-AAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAACATAAGGGATTTT
*
19149 TTTGTCCCAAAAGAAAAATATAAGGGATTTT
1 TTTGTCCCAAAAG-AAAACATAAGGGATTTT
19180 TTTGTCCCAAAAGAAAACATAAGGGATTTT
1 TTTGTCCCAAAAGAAAACATAAGGGATTTT
19210 TT
1 TT
19212 AGTATTTATT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
29 11 0.19
30 18 0.31
31 29 0.50
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (30 bp):
TTTGTCCCAAAAGAAAACATAAGGGATTTT
Done.