Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015869.1 Corchorus capsularis cultivar CVL-1 contig15890, 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: 29697
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1113 original size:21 final size:22
Alignment explanation
Indices: 1087--1131 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
1077 TAAAAGGGGA
1087 TTGCTAAATACCGTCCCA-TTT
1 TTGCTAAATACCGTCCCACTTT
** *
1108 TTGCTATTTACCGTCTCACTTT
1 TTGCTAAATACCGTCCCACTTT
1130 TT
1 TT
1132 ACACTTTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.18, C:0.27, G:0.09, T:0.47
Consensus pattern (22 bp):
TTGCTAAATACCGTCCCACTTT
Found at i:1312 original size:32 final size:32
Alignment explanation
Indices: 1268--1373 Score: 133
Period size: 32 Copynumber: 3.3 Consensus size: 32
1258 AAAATAGCCG
1268 AGCCGCCCCACCGAGGTGGCCTGCCGTGGCGA
1 AGCCGCCCCACCGAGGTGGCCTGCCGTGGCGA
* *
1300 AGTCGCCCCACCGGGGTGGCCTGCCGTGGCGA
1 AGCCGCCCCACCGAGGTGGCCTGCCGTGGCGA
* * * *
1332 AGCCGCCCCA-AGAGGGCGGCCTGCCCATGGTGA
1 AGCCGCCCCACCGA-GGTGGCCTG-CCGTGGCGA
1365 AGCCGCCCC
1 AGCCGCCCC
1374 GGTCATCAGT
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
31 1 0.02
32 47 0.73
33 16 0.25
ACGTcount: A:0.13, C:0.41, G:0.37, T:0.09
Consensus pattern (32 bp):
AGCCGCCCCACCGAGGTGGCCTGCCGTGGCGA
Found at i:2191 original size:2 final size:2
Alignment explanation
Indices: 2186--2211 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2176 AAAATTAACT
2186 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
2212 AAATCCAACT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2941 original size:38 final size:37
Alignment explanation
Indices: 2877--2972 Score: 122
Period size: 38 Copynumber: 2.6 Consensus size: 37
2867 AATTTGACTT
*
2877 TTTGTTTCCAACGTTCTATTTAATTTTGCCTTTTGTC
1 TTTGTTTCCAACGTTCTATTTAATTTTACCTTTTGTC
* *
2914 TTTGTTTCCAATCGTTGTATTTAATTTTACTTTTTGTC
1 TTTGTTTCCAA-CGTTCTATTTAATTTTACCTTTTGTC
* *
2952 TTCGTCTT-CAACGTCCTATTT
1 TTTGT-TTCCAACGTTCTATTT
2973 TGGCTTAGAT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
37 19 0.37
38 30 0.59
39 2 0.04
ACGTcount: A:0.15, C:0.19, G:0.10, T:0.56
Consensus pattern (37 bp):
TTTGTTTCCAACGTTCTATTTAATTTTACCTTTTGTC
Found at i:3058 original size:22 final size:21
Alignment explanation
Indices: 3030--3151 Score: 86
Period size: 22 Copynumber: 5.6 Consensus size: 21
3020 TGATCCAATT
*
3030 TCAAAATTTCAAAGCGCGGTTA
1 TCAAAATTTCAAAGAG-GGTTA
* * *
3052 TCAAAATTACATAATG-TGATTA
1 TCAAAATTTCA-AA-GAGGGTTA
*
3074 TCAAAATTTCATAGAGGGTTA
1 TCAAAATTTCAAAGAGGGTTA
* * *
3095 ACAAAATTTTATAGAGAGGTTA
1 TCAAAATTTCAAAGAG-GGTTA
3117 TCAAAATTTCATAA-AGAGGTTA
1 TCAAAATTTCA-AAGAG-GGTTA
* *
3139 TCATATTTTCAAA
1 TCAAAATTTCAAA
3152 ATATGATTAC
Statistics
Matches: 81, Mismatches: 14, Indels: 11
0.76 0.13 0.10
Matches are distributed among these distances:
20 1 0.01
21 21 0.26
22 55 0.68
23 3 0.04
24 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.34
Consensus pattern (21 bp):
TCAAAATTTCAAAGAGGGTTA
Found at i:3411 original size:44 final size:44
Alignment explanation
Indices: 3274--3831 Score: 229
Period size: 44 Copynumber: 12.8 Consensus size: 44
3264 TCAGGGAGGA
* * * *
3274 TATCAAAATTTCAAATGAAGGTTATCAAAATTTCATAGTTTAGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGATGAGT
* *
3318 TTTCAAAATTTCATAAGAAGGTTATCAAAATTTCATAGTATGTAG-
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAG-ATG-AGT
* * *
3363 -ATCAAAATTTCATAGGGAGATTAACAAAATTTCATA-ATGAGCT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGATGAG-T
* *
3406 TATCAAAAAATT-ATAGGGAGGTTATCAAAA-TT--T-G-T-AGT
1 TATC-AAAATTTCATAGGAAGGTTATCAAAATTTCATAGATGAGT
* * * *
3444 TATCAAGATTTCAT--G-AGGTTATCAAAATTTTACAG-GGAGTTT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGATGAG--T
* * *
3486 TATCAAAATTTTATTGGAAGGTTTATCAAAATTTCATAG-CGAGGT
1 TATCAAAATTTCATAGGAAGG-TTATCAAAATTTCATAGATGA-GT
* * * * * * *
3531 TATCACAATTTTATAGTATGATTATCAAAATTTCAGAG-TGTGAT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGATGAG-T
* * * * ** * *
3575 TACTGACAA-TTCATATGG-AGGTTTTTAACTTTTCATA-ACGTGTT
1 TA-TCAAAATTTCATA-GGAAGGTTATCAAAATTTCATAGATGAG-T
* * * *
3619 TATCAATATATCATATGG-AGGTTATCAACATCTT-ATAG-TGTTGAT
1 TATCAAAATTTCATA-GGAAGGTTATCAAAAT-TTCATAGATG-AG-T
* * * *
3664 TATCAAAATTTCATTTGGAA-GTTATTAAAACTTGATAG-TGAGGT
1 TATCAAAATTTCA-TAGGAAGGTTATCAAAATTTCATAGATGA-GT
* * *
3708 CT-TCAAAATTCCTTAGGGAGGTTAAT-AAAATTTCATAAGATG-GT
1 -TATCAAAATTTCATAGGAAGGTT-ATCAAAATTTCAT-AGATGAGT
** ** * * *
3752 TAAAAAAATTT-ATAAAAAGGTTCTCGAAATTTCATAGTAT-CGT
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAG-ATGAGT
** *
3795 TATTGAAATTTCAGAGGAAGGTTATCAAAATTTCATA
1 TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATA
3832 AAGACGTCAT
Statistics
Matches: 391, Mismatches: 81, Indels: 84
0.70 0.15 0.15
Matches are distributed among these distances:
35 12 0.03
36 3 0.01
37 5 0.01
38 7 0.02
39 3 0.01
40 3 0.01
41 3 0.01
42 19 0.05
43 39 0.10
44 202 0.52
45 71 0.18
46 23 0.06
47 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (44 bp):
TATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGATGAGT
Found at i:3492 original size:23 final size:23
Alignment explanation
Indices: 3462--3519 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
3452 TTTCATGAGG
* *
3462 TTATCAAAATTTTACAGGGAGTT
1 TTATCAAAATTTTACAGGAAGGT
**
3485 TTATCAAAATTTTATTGGAAGGT
1 TTATCAAAATTTTACAGGAAGGT
3508 TTATCAAAATTT
1 TTATCAAAATTT
3520 CATAGCGAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (23 bp):
TTATCAAAATTTTACAGGAAGGT
Found at i:3530 original size:23 final size:21
Alignment explanation
Indices: 3259--3831 Score: 195
Period size: 22 Copynumber: 26.5 Consensus size: 21
3249 GGAGTAATCC
* *
3259 AAATTTCA-GGGAGGATATCA
1 AAATTTCATAGGAGGTTATCA
* *
3279 AAATTTCAAATGAAGGTTATCA
1 AAATTTCATA-GGAGGTTATCA
* *
3301 AAATTTCATAGTTTA-GTTTTCA
1 AAATTTCATAG--GAGGTTATCA
*
3323 AAATTTCATAAGAAGGTTATCA
1 AAATTTCAT-AGGAGGTTATCA
* * *
3345 AAATTTCATAGTATGTAGATCA
1 AAATTTCATAGGAGGT-TATCA
* *
3367 AAATTTCATAGGGAGATTAACA
1 AAATTTCATA-GGAGGTTATCA
* *
3389 AAATTTCATAATGAGCTTATCAA
1 AAATTTCAT-AGGAGGTTATC-A
*
3412 AAAATT-ATAGGGAGGTTATCA
1 AAATTTCATA-GGAGGTTATCA
*
3433 AAA-TT--T-GTA-GTTATCA
1 AAATTTCATAGGAGGTTATCA
*
3449 AGATTTCAT--GAGGTTATCA
1 AAATTTCATAGGAGGTTATCA
* * *
3468 AAATTTTACAGGGAGTTTTATCA
1 AAATTTCATA-GGAG-GTTATCA
* *
3491 AAATTTTATTGGAAGGTTTATCA
1 AAATTTCATAGG-AGG-TTATCA
3514 AAATTTCATAGCGAGGTTATCA
1 AAATTTCATAG-GAGGTTATCA
* * * *
3536 CAATTTTATAGTATGATTATCA
1 AAATTTCATAGGA-GGTTATCA
* * * *
3558 AAATTTCAGAGTGTGATTACTGA
1 AAATTTCATAG-GAGGTTA-TCA
* * *
3581 CAA-TTCATATGGAGGTTTTTA
1 AAATTTCATA-GGAGGTTATCA
** * * *
3602 ACTTTTCATAACGTGTTTATCA
1 AAATTTCAT-AGGAGGTTATCA
* *
3624 ATATATCATATGGAGGTTATCA
1 AAATTTCATA-GGAGGTTATCA
* * *
3646 ACATCTT-ATAGTGTTGATTATCA
1 AAAT-TTCATAG-G-AGGTTATCA
* * *
3669 AAATTTCATTTGGAAGTTATTA
1 AAATTTCA-TAGGAGGTTATCA
* *
3691 AAACTTGATAGTGAGGTCT-TCA
1 AAATTTCATAG-GAGGT-TATCA
* *
3713 AAATTCCTTAGGGAGGTTAAT-A
1 AAATTTCATA-GGAGGTT-ATCA
* **
3735 AAATTTCATAAGATGGTTAAAA
1 AAATTTCATAGGA-GGTTATCA
** * *
3757 AAATTT-ATAAAAAGGTTCTCG
1 AAATTTCAT-AGGAGGTTATCA
* * **
3778 AAATTTCATAGTATCGTTATTG
1 AAATTTCATAGGA-GGTTATCA
*
3800 AAATTTCAGAGGAAGGTTATCA
1 AAATTTCATAGG-AGGTTATCA
3822 AAATTTCATA
1 AAATTTCATA
3832 AAGACGTCAT
Statistics
Matches: 405, Mismatches: 103, Indels: 88
0.68 0.17 0.15
Matches are distributed among these distances:
16 9 0.02
17 4 0.01
18 1 0.00
19 15 0.04
20 10 0.02
21 37 0.09
22 256 0.63
23 70 0.17
24 3 0.01
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (21 bp):
AAATTTCATAGGAGGTTATCA
Found at i:3702 original size:45 final size:45
Alignment explanation
Indices: 3618--3703 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
3608 CATAACGTGT
* * *
3618 TTATCAATATATCATATGGAGGTTATCAACATCTTATAGTGTTGA
1 TTATCAAAATATCATATGGAAGTTATCAACAACTTATAGTGTTGA
* * *
3663 TTATCAAAATTTCATTTGGAAGTTATTAA-AACTTGATAGTG
1 TTATCAAAATATCATATGGAAGTTATCAACAACTT-ATAGTG
3704 AGGTCTTCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 4 0.12
45 30 0.88
ACGTcount: A:0.35, C:0.09, G:0.15, T:0.41
Consensus pattern (45 bp):
TTATCAAAATATCATATGGAAGTTATCAACAACTTATAGTGTTGA
Found at i:3918 original size:40 final size:40
Alignment explanation
Indices: 3816--3923 Score: 153
Period size: 40 Copynumber: 2.7 Consensus size: 40
3806 CAGAGGAAGG
* * * * *
3816 TTATCAAAATTTCATAAAGACGTCATAAAAAATAGTGTAA
1 TTATCATAATTTCATAAAAAGGTTATCAAAAATAGTGTAA
*
3856 TTATCATAATTTCATAAGAAGGTTATCAAAAATAGTGTAA
1 TTATCATAATTTCATAAAAAGGTTATCAAAAATAGTGTAA
*
3896 TTATCATAATTTAATAAAAAGGTTATCA
1 TTATCATAATTTCATAAAAAGGTTATCA
3924 TAATTTCGTA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.34
Consensus pattern (40 bp):
TTATCATAATTTCATAAAAAGGTTATCAAAAATAGTGTAA
Found at i:5966 original size:27 final size:26
Alignment explanation
Indices: 5905--5979 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 26
5895 TTAGGGTCAC
* *
5905 CTAGGGGCATTTTGGTCATTTTTCGCA
1 CTAGGGGCATTTTGGTCA-TTTGCACA
*
5932 CTAAGGGCATTTTGGTCATTTGCACA
1 CTAGGGGCATTTTGGTCATTTGCACA
* *
5958 TTTAGGGGCATTTTGGTAATTT
1 -CTAGGGGCATTTTGGTCATTT
5980 TTAGTACACT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.15
27 35 0.85
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.41
Consensus pattern (26 bp):
CTAGGGGCATTTTGGTCATTTGCACA
Found at i:7212 original size:16 final size:17
Alignment explanation
Indices: 7180--7212 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
7170 CTTCAACGAG
*
7180 CTCCTTGTGCCAGCTCA
1 CTCCTTGTGCCACCTCA
7197 CTCCTT-TGCCACCTCA
1 CTCCTTGTGCCACCTCA
7213 GCTAGTCCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.12, C:0.45, G:0.12, T:0.30
Consensus pattern (17 bp):
CTCCTTGTGCCACCTCA
Found at i:11064 original size:20 final size:21
Alignment explanation
Indices: 11017--11066 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
11007 ATATTTGGTT
* *
11017 ATTCTTTATTTGTTTCTTTTTT
1 ATTCTTT-TTTGTTTCCTTTTC
*
11039 AATCTTTTTT-TTTCCTTTTC
1 ATTCTTTTTTGTTTCCTTTTC
11059 ATTCTTTT
1 ATTCTTTT
11067 GTTTATAGCC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 15 0.62
21 3 0.12
22 6 0.25
ACGTcount: A:0.10, C:0.14, G:0.02, T:0.74
Consensus pattern (21 bp):
ATTCTTTTTTGTTTCCTTTTC
Found at i:13718 original size:19 final size:19
Alignment explanation
Indices: 13694--13730 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13684 TTTGGATCCA
*
13694 AAACGGTGGTGAAACGGTC
1 AAACGGTGGCGAAACGGTC
13713 AAACGGTGGCGAAACGGT
1 AAACGGTGGCGAAACGGT
13731 GTACTAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.38, T:0.14
Consensus pattern (19 bp):
AAACGGTGGCGAAACGGTC
Found at i:16371 original size:18 final size:18
Alignment explanation
Indices: 16348--16384 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
16338 CAGTGTTCTC
16348 TTTTTTCTAATGAGACTTT
1 TTTTTTC-AATGAGACTTT
*
16367 TTTTTTCACTGAGACTTT
1 TTTTTTCAATGAGACTTT
16385 GGTGCTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.19, C:0.14, G:0.11, T:0.57
Consensus pattern (18 bp):
TTTTTTCAATGAGACTTT
Found at i:19161 original size:28 final size:28
Alignment explanation
Indices: 19117--19173 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
19107 TAAATTAGGG
*
19117 TTTTTTTTAGGTTAATTTTACATGTAGT
1 TTTTTTTTAGGTAAATTTTACATGTAGT
19145 TTTTTTTTA-GTGAAATTTTACATGTAGT
1 TTTTTTTTAGGT-AAATTTTACATGTAGT
19173 T
1 T
19174 GAGTTGAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.23, C:0.04, G:0.14, T:0.60
Consensus pattern (28 bp):
TTTTTTTTAGGTAAATTTTACATGTAGT
Found at i:20603 original size:46 final size:46
Alignment explanation
Indices: 20536--20629 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
20526 ATCCTATAAT
20536 TAATCATTCATTTTCCAATCCCTCTAGCTATCCTAGAATATCTAAG
1 TAATCATTCATTTTCCAATCCCTCTAGCTATCCTAGAATATCTAAG
* * *
20582 TAATCATTCGTTTTCCAATCCCTCTAGCTATCCTGGAATATTTAAG
1 TAATCATTCATTTTCCAATCCCTCTAGCTATCCTAGAATATCTAAG
20628 TA
1 TA
20630 CATTTTGATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (46 bp):
TAATCATTCATTTTCCAATCCCTCTAGCTATCCTAGAATATCTAAG
Found at i:25276 original size:21 final size:21
Alignment explanation
Indices: 25226--25287 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
25216 TGCTTGGAGC
25226 AAGAATATTCCAATCGATTCT
1 AAGAATATTCCAATCGATTCT
* * *
25247 ATTG-CTATTACAATCGATTCT
1 A-AGAATATTCCAATCGATTCT
*
25268 AAGAATATTCCAATCAATTC
1 AAGAATATTCCAATCGATTC
25288 CAAGTTTTGC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.35
Consensus pattern (21 bp):
AAGAATATTCCAATCGATTCT
Found at i:26483 original size:21 final size:20
Alignment explanation
Indices: 26457--26496 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
26447 TACAAACCCT
26457 ATTGGAGACAAGTGGTACAAA
1 ATTGGA-ACAAGTGGTACAAA
*
26478 ATTGGATCAAGTGGTACAA
1 ATTGGAACAAGTGGTACAA
26497 GGGTTTTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.40, C:0.10, G:0.28, T:0.23
Consensus pattern (20 bp):
ATTGGAACAAGTGGTACAAA
Done.