Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015517.1 Corchorus capsularis cultivar CVL-1 contig15538, 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: 36731
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:177 original size:22 final size:21
Alignment explanation
Indices: 148--251 Score: 93
Period size: 22 Copynumber: 4.8 Consensus size: 21
138 TGAATATTTT
148 TATGAAATTTTGATAACAATCC
1 TATGAAATTTTGATAACAA-CC
* *
170 TATTAAATTTTGATAACAACGT
1 TATGAAATTTTGATAACAAC-C
* **
192 TTTGAAATTTTGATAATTACC
1 TATGAAATTTTGATAACAACC
* *
213 TATGAAATTGTGATAA-ATTCC
1 TATGAAATTTTGATAACA-ACC
*
234 ATATGAAACTTTGATAAC
1 -TATGAAATTTTGATAAC
252 CTAAATATGA
Statistics
Matches: 65, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
21 17 0.26
22 48 0.74
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (21 bp):
TATGAAATTTTGATAACAACC
Found at i:4325 original size:318 final size:318
Alignment explanation
Indices: 3748--4373 Score: 1243
Period size: 318 Copynumber: 2.0 Consensus size: 318
3738 TCCTTAACCA
3748 AGCTTCCTTAATCGGCTTCTTGACTTGCTTTCTCCTATGGAGGGAGAGGGACCGATCCATGGCGA
1 AGCTTCCTTAATCGGCTTCTTGACTTGCTTTCTCCTATGGAGGGAGAGGGACCGATCCATGGCGA
*
3813 TACATTATCACTTTTCTATATGCGTCAAAATGATGTGTTCATTCATAAGTTTTTGACTACTCTTT
66 TACATGATCACTTTTCTATATGCGTCAAAATGATGTGTTCATTCATAAGTTTTTGACTACTCTTT
3878 TCATTTTTCAAGAACTAGCTAGTCATACATTTTATTATTATGGTAGTTTAAAGCTATAGCATAAA
131 TCATTTTTCAAGAACTAGCTAGTCATACATTTTATTATTATGGTAGTTTAAAGCTATAGCATAAA
3943 TATCATATCATATTTCTTTGCCTGGTTTGATTGTGGCTTAGAGTCATGATCTTGGGGAGGTTCTT
196 TATCATATCATATTTCTTTGCCTGGTTTGATTGTGGCTTAGAGTCATGATCTTGGGGAGGTTCTT
4008 ATAGTGGTGGCTATTTGAAATATGGGATTCAGGGTGGCCTTGAAAGTTAGCTTAGCCT
261 ATAGTGGTGGCTATTTGAAATATGGGATTCAGGGTGGCCTTGAAAGTTAGCTTAGCCT
4066 AGCTTCCTTAATCGGCTTCTTGACTTGCTTTCTCCTATGGAGGGAGAGGGACCGATCCATGGCGA
1 AGCTTCCTTAATCGGCTTCTTGACTTGCTTTCTCCTATGGAGGGAGAGGGACCGATCCATGGCGA
4131 TACATGATCACTTTTCTATATGCGTCAAAATGATGTGTTCATTCATAAGTTTTTGACTACTCTTT
66 TACATGATCACTTTTCTATATGCGTCAAAATGATGTGTTCATTCATAAGTTTTTGACTACTCTTT
4196 TCATTTTTCAAGAACTAGCTAGTCATACATTTTATTATTATGGTAGTTTAAAGCTATAGCATAAA
131 TCATTTTTCAAGAACTAGCTAGTCATACATTTTATTATTATGGTAGTTTAAAGCTATAGCATAAA
4261 TATCATATCATATTTCTTTGCCTGGTTTGATTGTGGCTTAGAGTCATGATCTTGGGGAGGTTCTT
196 TATCATATCATATTTCTTTGCCTGGTTTGATTGTGGCTTAGAGTCATGATCTTGGGGAGGTTCTT
4326 ATAGTGGTGGCTATTTGAAATATGGGATTCAGGGTGGCCTTGAAAGTT
261 ATAGTGGTGGCTATTTGAAATATGGGATTCAGGGTGGCCTTGAAAGTT
4374 TTGAATGATC
Statistics
Matches: 307, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
318 307 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (318 bp):
AGCTTCCTTAATCGGCTTCTTGACTTGCTTTCTCCTATGGAGGGAGAGGGACCGATCCATGGCGA
TACATGATCACTTTTCTATATGCGTCAAAATGATGTGTTCATTCATAAGTTTTTGACTACTCTTT
TCATTTTTCAAGAACTAGCTAGTCATACATTTTATTATTATGGTAGTTTAAAGCTATAGCATAAA
TATCATATCATATTTCTTTGCCTGGTTTGATTGTGGCTTAGAGTCATGATCTTGGGGAGGTTCTT
ATAGTGGTGGCTATTTGAAATATGGGATTCAGGGTGGCCTTGAAAGTTAGCTTAGCCT
Found at i:7071 original size:18 final size:18
Alignment explanation
Indices: 7020--7090 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 18
7010 GCAAATGCTA
* *
7020 CACTGTCGCAGGATGTTC
1 CACTGCCGCAGAATGTTC
* * *
7038 TACTGCCGTAGGATGTTC
1 CACTGCCGCAGAATGTTC
*
7056 CACTGCTGCAGAATGTTC
1 CACTGCCGCAGAATGTTC
* *
7074 CATTGCCACAGAATGTT
1 CACTGCCGCAGAATGTT
7091 TCGCTGCCAC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.21, C:0.25, G:0.24, T:0.30
Consensus pattern (18 bp):
CACTGCCGCAGAATGTTC
Found at i:8674 original size:7 final size:6
Alignment explanation
Indices: 8640--8678 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
8630 AAAGCAAAGC
8640 AAATC- AAATCT AAATCT AAATCT AAATCTT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATC-T AAATCT AAA
8679 GCAAAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.16
6 21 0.66
7 6 0.19
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATCT
Found at i:8685 original size:19 final size:18
Alignment explanation
Indices: 8645--8685 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
8635 AAAGCAAATC
* *
8645 AAATCTAAATCTAAATCT
1 AAATCTAAATCTAAAGCA
8663 AAATCTTAAATCTAAAGCA
1 AAATC-TAAATCTAAAGCA
8682 AAAT
1 AAAT
8686 AATAAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.54, C:0.15, G:0.02, T:0.29
Consensus pattern (18 bp):
AAATCTAAATCTAAAGCA
Found at i:8691 original size:13 final size:13
Alignment explanation
Indices: 8675--8709 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
8665 ATCTTAAATC
8675 TAAAGCAAAATAA
1 TAAAGCAAAATAA
* *
8688 TAAAACAAATTAA
1 TAAAGCAAAATAA
8701 TAAAGCAAA
1 TAAAGCAAA
8710 CAATAATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.17
Consensus pattern (13 bp):
TAAAGCAAAATAA
Found at i:15540 original size:7 final size:6
Alignment explanation
Indices: 15506--15544 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
15496 AAAGCAAAGC
15506 AAATC- AAATCT AAATCT AAATCT AAATCTT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATC-T AAATCT AAA
15545 GCAAAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.16
6 21 0.66
7 6 0.19
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (6 bp):
AAATCT
Found at i:15551 original size:19 final size:18
Alignment explanation
Indices: 15511--15551 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
15501 AAAGCAAATC
* *
15511 AAATCTAAATCTAAATCT
1 AAATCTAAATCTAAAGCA
15529 AAATCTTAAATCTAAAGCA
1 AAATC-TAAATCTAAAGCA
15548 AAAT
1 AAAT
15552 AATAAAGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.54, C:0.15, G:0.02, T:0.29
Consensus pattern (18 bp):
AAATCTAAATCTAAAGCA
Found at i:15557 original size:13 final size:13
Alignment explanation
Indices: 15541--15575 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
15531 ATCTTAAATC
15541 TAAAGCAAAATAA
1 TAAAGCAAAATAA
*
15554 TAAAGCAAATTAA
1 TAAAGCAAAATAA
15567 TAAAGCAAA
1 TAAAGCAAA
15576 CAATAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.66, C:0.09, G:0.09, T:0.17
Consensus pattern (13 bp):
TAAAGCAAAATAA
Found at i:15563 original size:12 final size:12
Alignment explanation
Indices: 15541--15581 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
15531 ATCTTAAATC
15541 TAAAGCAAAATAA
1 TAAAGC-AAATAA
15554 TAAAGCAAATTAA
1 TAAAGCAAA-TAA
*
15567 TAAAGCAAACAA
1 TAAAGCAAATAA
15579 TAA
1 TAA
15582 TTATAAAGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 8 0.31
13 18 0.69
ACGTcount: A:0.66, C:0.10, G:0.07, T:0.17
Consensus pattern (12 bp):
TAAAGCAAATAA
Found at i:23265 original size:3 final size:3
Alignment explanation
Indices: 23257--23285 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
23247 GATGAAAATC
23257 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
23286 TGAATATGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:24515 original size:18 final size:18
Alignment explanation
Indices: 24492--24528 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
24482 TTATACTCGC
24492 CTTCCTGCCACTAAACTA
1 CTTCCTGCCACTAAACTA
24510 CTTCCTGCCACTAAACTA
1 CTTCCTGCCACTAAACTA
24528 C
1 C
24529 CTGGCAGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.41, G:0.05, T:0.27
Consensus pattern (18 bp):
CTTCCTGCCACTAAACTA
Found at i:29280 original size:32 final size:32
Alignment explanation
Indices: 29239--29304 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
29229 TATGAGCAAA
29239 ATTCATAATTGAAGAGTTACATTCGTTTATTG
1 ATTCATAATTGAAGAGTTACATTCGTTTATTG
29271 ATTCATAATTGAAGAGTTACATTCGTTTATTG
1 ATTCATAATTGAAGAGTTACATTCGTTTATTG
29303 AT
1 AT
29305 AAATGAACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.44
Consensus pattern (32 bp):
ATTCATAATTGAAGAGTTACATTCGTTTATTG
Found at i:31889 original size:52 final size:52
Alignment explanation
Indices: 31833--31938 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 52
31823 ACCCAAATTA
*
31833 TTAACACAAAAAAATAAGTCTATACTCTACATTAATTCCAAAACTAAAATGG
1 TTAACACAAAAAAATAAATCTATACTCTACATTAATTCCAAAACTAAAATGG
*
31885 TTAACATAAAAAAATAAATCTATACTCTACATTAATTCCAAAACTAAAATGG
1 TTAACACAAAAAAATAAATCTATACTCTACATTAATTCCAAAACTAAAATGG
31937 TT
1 TT
31939 TTTTTTTTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.50, C:0.16, G:0.05, T:0.29
Consensus pattern (52 bp):
TTAACACAAAAAAATAAATCTATACTCTACATTAATTCCAAAACTAAAATGG
Found at i:33135 original size:41 final size:40
Alignment explanation
Indices: 33072--33151 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
33062 TATGGAACCT
* *
33072 AAACCCTAACAAACAATATAAACCCTATGTGAGATAAAAG
1 AAACCCTAAAAAACAATATAAACCCTAGGTGAGATAAAAG
33112 AAACCCTCAAAAAAC-ATATTAAACCCTAGGTGAGATAAAA
1 AAACCCT-AAAAAACAATA-TAAACCCTAGGTGAGATAAAA
33152 ATAAAAAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 10 0.28
41 26 0.72
ACGTcount: A:0.53, C:0.20, G:0.10, T:0.17
Consensus pattern (40 bp):
AAACCCTAAAAAACAATATAAACCCTAGGTGAGATAAAAG
Found at i:33396 original size:2 final size:2
Alignment explanation
Indices: 33389--33422 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
33379 ATTGATTGTT
33389 TA TA TA TA 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 TA TA TA TA
33423 GGTATAGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34111 original size:215 final size:215
Alignment explanation
Indices: 33718--34151 Score: 710
Period size: 215 Copynumber: 2.0 Consensus size: 215
33708 GCATCACCTT
* * *
33718 AATCCTCCTCTTCATTGCTCAAATAGCAGCCATATCAGGGTTGCACGATCACTTTTGGCTAGCCA
1 AATCATCCTCCTCATTCCTCAAATAGCAGCCATATCAGGGTTGCACGATCACTTTTGGCTAGCCA
* * *
33783 TGATGTGGTCGTATGGTTATTGCTCAGACCCTAATACTTCATGTGTCGACCAACCTCCTTACCAC
66 TGATGTGGTCGTATGGTTATTGCTCAGACCCTAACACTCCATGTGTCGACCAACCTCCTGACCAC
* * *
33848 TTGATCATACATTGGCCTTTGGCCAGTAAATGCTACCGACTCGTTGCTATCTAGCTCTGGTTGCG
131 TTAATCATACAATGGCCTTTGGCCAGCAAATGCTACCGACTCGTTGCTATCTAGCTCTGGTTGCG
33913 CTACAAATGGACGCGATTTA
196 CTACAAATGGACGCGATTTA
*
33933 AATCATCCTCCTCATTCCTCACATAGCAGCCATATCAGGGTTGCACGATCACTTTTGGCTAGCCA
1 AATCATCCTCCTCATTCCTCAAATAGCAGCCATATCAGGGTTGCACGATCACTTTTGGCTAGCCA
33998 TGATGTGG-CTGTATGGTTATTGCTCAGACCCTAACACTCCATGTGTCGACCAACCT-CTAGACC
66 TGATGTGGTC-GTATGGTTATTGCTCAGACCCTAACACTCCATGTGTCGACCAACCTCCT-GACC
* * * *
34061 ACTTAATCATACAATGGCTTTTGGCCAGCAGATGCTACCGGCTTGTTGCTATCTAGCTCTGGTTG
129 ACTTAATCATACAATGGCCTTTGGCCAGCAAATGCTACCGACTCGTTGCTATCTAGCTCTGGTTG
34126 CGCTACAAATGGACGCGATTTA
194 CGCTACAAATGGACGCGATTTA
34148 AATC
1 AATC
34152 CAGATTTTCT
Statistics
Matches: 203, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
214 3 0.01
215 200 0.99
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (215 bp):
AATCATCCTCCTCATTCCTCAAATAGCAGCCATATCAGGGTTGCACGATCACTTTTGGCTAGCCA
TGATGTGGTCGTATGGTTATTGCTCAGACCCTAACACTCCATGTGTCGACCAACCTCCTGACCAC
TTAATCATACAATGGCCTTTGGCCAGCAAATGCTACCGACTCGTTGCTATCTAGCTCTGGTTGCG
CTACAAATGGACGCGATTTA
Found at i:35749 original size:13 final size:13
Alignment explanation
Indices: 35731--35755 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35721 ATATTTTATA
35731 GTAGTAATTAATT
1 GTAGTAATTAATT
35744 GTAGTAATTAAT
1 GTAGTAATTAAT
35756 AGAAACATAA
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:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (13 bp):
GTAGTAATTAATT
Found at i:36703 original size:2 final size:2
Alignment explanation
Indices: 36696--36731 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
36686 CAAACCTGCA
36696 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.