Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008525.1 Corchorus capsularis cultivar CVL-1 contig08546, 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: 23531
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Found at i:402 original size:16 final size:16
Alignment explanation
Indices: 383--546 Score: 156
Period size: 16 Copynumber: 10.5 Consensus size: 16
373 CTGACCCATT
383 TGACCCGAGACCCGAA
1 TGACCCGAGACCCGAA
** *
399 TGACCCGA-AGTCTAA
1 TGACCCGAGACCCGAA
414 --ACCCGA-ACCCGAA
1 TGACCCGAGACCCGAA
* *
427 TAACCCGAGACCCGAT
1 TGACCCGAGACCCGAA
* **
443 TAACCCGAGAATCGAA
1 TGACCCGAGACCCGAA
*
459 TGACCCGAAACCCGAA
1 TGACCCGAGACCCGAA
*
475 TAACCCGAGACCCGAA
1 TGACCCGAGACCCGAA
* *
491 TAACCCGAGACCCGAT
1 TGACCCGAGACCCGAA
* *
507 TGACCCGAAACCCGAT
1 TGACCCGAGACCCGAA
* *
523 TGACCCGAAACCCAAA
1 TGACCCGAGACCCGAA
539 TGACCCGA
1 TGACCCGA
547 AAAAACTGAC
Statistics
Matches: 124, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
13 10 0.08
15 10 0.08
16 104 0.84
ACGTcount: A:0.35, C:0.36, G:0.19, T:0.10
Consensus pattern (16 bp):
TGACCCGAGACCCGAA
Found at i:485 original size:48 final size:48
Alignment explanation
Indices: 385--546 Score: 188
Period size: 48 Copynumber: 3.5 Consensus size: 48
375 GACCCATTTG
* * *
385 ACCCGAGACCCGAATGACCCGA-AGTCTAA--ACCCG-AACCCGAATA
1 ACCCGAGACCCGAATAACCCGAGAATCGAATGACCCGAAACCCGAATA
*
429 ACCCGAGACCCGATTAACCCGAGAATCGAATGACCCGAAACCCGAATA
1 ACCCGAGACCCGAATAACCCGAGAATCGAATGACCCGAAACCCGAATA
** * * *
477 ACCCGAGACCCGAATAACCCGAGACCCGATTGACCCGAAACCCGATTG
1 ACCCGAGACCCGAATAACCCGAGAATCGAATGACCCGAAACCCGAATA
* * *
525 ACCCGAAACCCAAATGACCCGA
1 ACCCGAGACCCGAATAACCCGA
547 AAAAACTGAC
Statistics
Matches: 101, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
44 20 0.20
45 5 0.05
47 5 0.05
48 71 0.70
ACGTcount: A:0.36, C:0.36, G:0.19, T:0.09
Consensus pattern (48 bp):
ACCCGAGACCCGAATAACCCGAGAATCGAATGACCCGAAACCCGAATA
Found at i:3067 original size:3 final size:3
Alignment explanation
Indices: 3061--3102 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
3051 TTGCTCTCAC
3061 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3103 TCTAGTTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3264 original size:21 final size:21
Alignment explanation
Indices: 3238--3280 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3228 TTTAGGTAAG
3238 TTTCTTAAATATCAAAAATAT
1 TTTCTTAAATATCAAAAATAT
3259 TTTCTTAAATATCAAAAATAT
1 TTTCTTAAATATCAAAAATAT
3280 T
1 T
3281 CTATTTCACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTCTTAAATATCAAAAATAT
Found at i:4346 original size:13 final size:13
Alignment explanation
Indices: 4328--4356 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4318 CTCAAGTTGC
4328 CAATAATCAAAAT
1 CAATAATCAAAAT
4341 CAATAATCAAAAT
1 CAATAATCAAAAT
4354 CAA
1 CAA
4357 ATAAATTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.62, C:0.17, G:0.00, T:0.21
Consensus pattern (13 bp):
CAATAATCAAAAT
Found at i:8090 original size:17 final size:17
Alignment explanation
Indices: 8068--8100 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
8058 TTAATTCAAA
8068 CATATTAGGTCACGTGT
1 CATATTAGGTCACGTGT
8085 CATATTAGGTCACGTG
1 CATATTAGGTCACGTG
8101 CTACGTGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (17 bp):
CATATTAGGTCACGTGT
Found at i:10128 original size:13 final size:13
Alignment explanation
Indices: 10110--10137 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
10100 GTTAAAAATA
10110 ATATATAGTATAT
1 ATATATAGTATAT
10123 ATATATAGTATAT
1 ATATATAGTATAT
10136 AT
1 AT
10138 TATTATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (13 bp):
ATATATAGTATAT
Found at i:21010 original size:13 final size:13
Alignment explanation
Indices: 20992--21016 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20982 ATACAGATGT
20992 TAAAATCTAAAGA
1 TAAAATCTAAAGA
21005 TAAAATCTAAAG
1 TAAAATCTAAAG
21017 GGAAGGGTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (13 bp):
TAAAATCTAAAGA
Found at i:21315 original size:143 final size:144
Alignment explanation
Indices: 21105--21393 Score: 427
Period size: 143 Copynumber: 2.0 Consensus size: 144
21095 TCACCACTCA
* * *
21105 GGCCTAGTTTGGCATTGCGTTTGAAGATAAAAAAAAACTGCTTTTGACCCAAAACGAAATACCAA
1 GGCCTAGTTTGGCATTGCATTTGAAGAT-AAAAAAAACTCCTTTTGAACCAAAACGAAATACCAA
* *
21170 ATAAATCCTGATTTGTGTCAAAAGCTAAATTTGAACGCAAAAGCCATGCCAACCCGAAAAGCTAA
65 ATAAATCATGATTTGTGTCAAAAGCTAAATTTGAACGCAAAAGCCAAGCCAACCCGAAAAGCTAA
21235 TCCTTAGGTGCTTTT
130 TCCTTAGGTGCTTTT
* * * *
21250 GGCCTGGTTTGGCATTGCATTTGGAGAT-AAAAAAGCTCCTTTTGAACCAAAACGCAATACCAAA
1 GGCCTAGTTTGGCATTGCATTTGAAGATAAAAAAAACTCCTTTTGAACCAAAACGAAATACCAAA
* * * * *
21314 TAAATCATGGTTTGTGTCAAAAGTTGATTTTGAACGCAAAAGCCAAGCCAACCCGAGAAGCTAAT
66 TAAATCATGATTTGTGTCAAAAGCTAAATTTGAACGCAAAAGCCAAGCCAACCCGAAAAGCTAAT
*
21379 CCTTGGGTGCTTTT
131 CCTTAGGTGCTTTT
21393 G
1 G
21394 CGTTTCAAAA
Statistics
Matches: 129, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
143 104 0.81
145 25 0.19
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (144 bp):
GGCCTAGTTTGGCATTGCATTTGAAGATAAAAAAAACTCCTTTTGAACCAAAACGAAATACCAAA
TAAATCATGATTTGTGTCAAAAGCTAAATTTGAACGCAAAAGCCAAGCCAACCCGAAAAGCTAAT
CCTTAGGTGCTTTT
Found at i:22372 original size:31 final size:32
Alignment explanation
Indices: 22337--22403 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
22327 AACTTTATGT
*
22337 TTTCCGATTGTACCCTTATTTTT-AAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAAACATA
*
22368 TTTCCAATTGTACCCTTTTTTTTAAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAAACATA
22400 TTTC
1 TTTC
22404 TTAATTGCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
31 21 0.64
32 12 0.36
ACGTcount: A:0.28, C:0.19, G:0.04, T:0.48
Consensus pattern (32 bp):
TTTCCAATTGTACCCTTATTTTTAAAAACATA
Found at i:22750 original size:44 final size:44
Alignment explanation
Indices: 22680--22885 Score: 150
Period size: 44 Copynumber: 4.6 Consensus size: 44
22670 TGTCTCTATG
* ** *
22680 TGGTTATCAAAATTTCATAAG-ATGGTTATTATAATTCCATGAGGA
1 TGGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTCCAT-AGGA
* * *
22725 -GGTTATCAAAATTTCGTAGTGTGGTTACCAAAATTTCATAGTA
1 TGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTCCATAGGA
* * *
22768 TGGTTACCAAAATTTCATAGTGTAGTTACCAAAATTTCATA-GA
1 TGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTCCATAGGA
* * ** * * *
22811 GTGGCTAACAAAATTTCATAG-GATCAGGTTATTAAAATTTCTTAGGT
1 -TGGTTATCAAAATTTCATAGTG-T--GGTTACCAAAATTCCATAGGA
** *
22858 TGGTTATTGAAATTTCATAGGGTGGTTA
1 TGGTTATCAAAATTTCATAGTGTGGTTA
22886 ATTATCACAA
Statistics
Matches: 131, Mismatches: 22, Indels: 17
0.77 0.13 0.10
Matches are distributed among these distances:
43 7 0.05
44 91 0.69
46 31 0.24
47 2 0.02
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.37
Consensus pattern (44 bp):
TGGTTATCAAAATTTCATAGTGTGGTTACCAAAATTCCATAGGA
Found at i:22801 original size:66 final size:65
Alignment explanation
Indices: 22678--22831 Score: 168
Period size: 66 Copynumber: 2.3 Consensus size: 65
22668 CTTGTCTCTA
* ** * * *
22678 TGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTCCATGAGGAGGTTATCAAAATTTCGTA
1 TGTGGTTAACAAAATTTCAT-AGATGGTTACCAAAATTCCATGAGGAGGTTACCAAAATTTCATA
22743 G
65 G
* *
22744 TGTGGTTACCAAAATTTCATAGTATGGTTACCAAAATTTCAT-AGTGTA-GTTACCAAAATTTCA
1 TGTGGTTAACAAAATTTCATAG-ATGGTTACCAAAATTCCATGAG-G-AGGTTACCAAAATTTCA
22807 TAG
63 TAG
* *
22810 AGTGGCTAACAAAATTTCATAG
1 TGTGGTTAACAAAATTTCATAG
22832 GATCAGGTTA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
65 4 0.05
66 70 0.93
67 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.36
Consensus pattern (65 bp):
TGTGGTTAACAAAATTTCATAGATGGTTACCAAAATTCCATGAGGAGGTTACCAAAATTTCATAG
Found at i:22856 original size:24 final size:22
Alignment explanation
Indices: 22681--22878 Score: 120
Period size: 22 Copynumber: 8.9 Consensus size: 22
22671 GTCTCTATGT
* *
22681 GGTTATCAAAATTTCATAAG-A
1 GGTTATTAAAATTTCATAGGTA
* *
22702 TGGTTATTATAATTCCATGAGG-A
1 -GGTTATTAAAATTTCAT-AGGTA
* *
22725 GGTTATCAAAATTTCGTAGTGT-
1 GGTTATTAAAATTTCATAG-GTA
**
22747 GGTTACCAAAATTTCATA-GTA
1 GGTTATTAAAATTTCATAGGTA
**
22768 TGGTTACCAAAATTTCATAGTGTA
1 -GGTTATTAAAATTTCATAG-GTA
**
22792 -GTTACCAAAATTTCATAGAGT-
1 GGTTATTAAAATTTCATAG-GTA
* **
22813 GGCTAACAAAATTTCATAGGATCA
1 GGTTATTAAAATTTCATAGG-T-A
* *
22837 GGTTATTAAAATTTCTTAGGTT
1 GGTTATTAAAATTTCATAGGTA
*
22859 GGTTATTGAAATTTCATAGG
1 GGTTATTAAAATTTCATAGG
22879 GTGGTTAATT
Statistics
Matches: 145, Mismatches: 20, Indels: 22
0.78 0.11 0.12
Matches are distributed among these distances:
20 2 0.01
21 3 0.02
22 117 0.81
23 4 0.03
24 19 0.13
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (22 bp):
GGTTATTAAAATTTCATAGGTA
Found at i:23057 original size:22 final size:22
Alignment explanation
Indices: 22939--23306 Score: 92
Period size: 22 Copynumber: 16.5 Consensus size: 22
22929 TGCCATAGCG
22939 AGGTTATACAAAAATTTCATAGTG-
1 AGGTTAT-C-AAAATTTCATA-TGA
* *
22963 TGGTTAACAAAATTTCAT-TAGA
1 AGGTTATCAAAATTTCATAT-GA
* * ** *
22985 AGGTTA-CTAATACTTCATCGGG
1 AGGTTATC-AAAATTTCATATGA
*
23007 AGGTTATCAAAATTTGATAGTG-
1 AGGTTATCAAAATTTCATA-TGA
*
23029 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATATGA
*
23051 AGGTTAT-AAAAGTCTCAATTTCAT-A
1 AGGTTATCAAAA-TTTC-A--T-ATGA
* *
23076 ATGAG-TACCAAAATTTGATA-GA
1 A-G-GTTATCAAAATTTCATATGA
*
23098 AGGTTATC-AAATCTCATA-G-
1 AGGTTATCAAAATTTCATATGA
* * *
23117 AGTGATTATCGAAATTTCGTAAAGA
1 AG-G-TTATCAAAATTTCAT-ATGA
23142 TAGGATTATCAAAATTT-ATATGA
1 -AGG-TTATCAAAATTTCATATGA
**
23165 ATATTATCAAAATTTCATAGTG-
1 AGGTTATCAAAATTTCATA-TGA
** * *
23187 TTGTTATCAAAATTTCAAAACG-
1 AGGTTATCAAAATTTC-ATATGA
* *
23209 AGGTTATCAAAA-ATAATAATG-
1 AGGTTATCAAAATTTCAT-ATGA
* * *
23230 TGATTTTCAAAATTTCATA-GA
1 AGGTTATCAAAATTTCATATGA
* * * *
23251 GGGGTCAACAAAATTT--TATAA
1 -AGGTTATCAAAATTTCATATGA
23272 AGATGTTATCAAAATTTCATAT-A
1 AG--GTTATCAAAATTTCATATGA
23295 GAGGTTATCAAA
1 -AGGTTATCAAA
23307 TTTTTAAAAT
Statistics
Matches: 254, Mismatches: 53, Indels: 76
0.66 0.14 0.20
Matches are distributed among these distances:
19 2 0.01
20 17 0.07
21 43 0.17
22 135 0.53
23 14 0.06
24 12 0.05
25 17 0.07
26 9 0.04
27 5 0.02
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATGA
Found at i:23309 original size:21 final size:22
Alignment explanation
Indices: 23067--23306 Score: 111
Period size: 22 Copynumber: 11.0 Consensus size: 22
23057 TAAAAGTCTC
* *
23067 AATTTCATAATGA-G-TACCAA
1 AATTTCATAAAGAGGTTATCAA
* *
23087 AATTTGATAGA-AGGTTATC-A
1 AATTTCATAAAGAGGTTATCAA
* * * * *
23107 AATCTCATAGAGTGATTATCGA
1 AATTTCATAAAGAGGTTATCAA
*
23129 AATTTCGTAAAGATAGGATTATCAA
1 AATTTCATAAAG--AGG-TTATCAA
*
23154 AATTT-ATATGAATA--TTATCAA
1 AATTTCATA--AAGAGGTTATCAA
** **
23175 AATTTCATAGTGTTGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
23197 AATTTCA-AAACGAGGTTATCAA
1 AATTTCATAAA-GAGGTTATCAA
* * * * * *
23219 AA-ATAATAATGTGATTTTCAA
1 AATTTCATAAAGAGGTTATCAA
* * * *
23240 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAAAGAGGTTATCAA
* *
23262 AATTTTATAAAGATGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
*
23284 AATTTCATATAGAGGTTATCAA
1 AATTTCATAAAGAGGTTATCAA
23306 A
1 A
23307 TTTTTAAAAT
Statistics
Matches: 157, Mismatches: 48, Indels: 28
0.67 0.21 0.12
Matches are distributed among these distances:
19 1 0.01
20 19 0.12
21 34 0.22
22 86 0.55
24 4 0.03
25 11 0.07
26 2 0.01
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.35
Consensus pattern (22 bp):
AATTTCATAAAGAGGTTATCAA
Found at i:23312 original size:44 final size:43
Alignment explanation
Indices: 23190--23337 Score: 124
Period size: 44 Copynumber: 3.4 Consensus size: 43
23180 CATAGTGTTG
** * *
23190 TTATCAAAATTTCA-AAACGAGGTTATCAAAAATAATAATGTGA
1 TTATCAAAATTTCATAAA-GAGGTTATCAAATTTTATAAAGTGA
* * * * *
23233 TTTTCAAAATTTCATAGAGGGGTCAACAAAATTTTATAAAGATG-
1 TTATCAAAATTTCATAAAGAGGTTATC-AAATTTTATAAAG-TGA
*
23277 TTATCAAAATTTCATATAGAGGTTATCAAATTTT-TAAAATGTGA
1 TTATCAAAATTTCATAAAGAGGTTATCAAATTTTAT-AAA-GTGA
23321 TTA-CAAAAATTTCATAA
1 TTATC-AAAATTTCATAA
23338 TGGTATTTCT
Statistics
Matches: 83, Mismatches: 15, Indels: 13
0.75 0.14 0.12
Matches are distributed among these distances:
42 1 0.01
43 32 0.39
44 48 0.58
45 2 0.02
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (43 bp):
TTATCAAAATTTCATAAAGAGGTTATCAAATTTTATAAAGTGA
Found at i:23453 original size:19 final size:19
Alignment explanation
Indices: 23418--23484 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
23408 TGAAGTAGTA
*
23418 ATCAAAATTTCAAGGAGGAT
1 ATCAAAA-TTCAGGGAGGAT
*
23438 ACCAAAATTCAGGGAGGAT
1 ATCAAAATTCAGGGAGGAT
* *
23457 ATCGAAATTCAGTGAGGAT
1 ATCAAAATTCAGGGAGGAT
23476 ATCAAAATT
1 ATCAAAATT
23485 TCATATGAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 35 0.85
20 6 0.15
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (19 bp):
ATCAAAATTCAGGGAGGAT
Found at i:23501 original size:22 final size:22
Alignment explanation
Indices: 23475--23531 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
23465 TCAGTGAGGA
*
23475 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATAAGAAGGT
* *
23497 TATCAAATTTTCATAAGAGGGT
1 TATCAAAATTTCATAAGAAGGT
23519 TATCAAAATTTCA
1 TATCAAAATTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (22 bp):
TATCAAAATTTCATAAGAAGGT
Done.