Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008841.1 Corchorus capsularis cultivar CVL-1 contig08862, 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: 23047
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:3206 original size:22 final size:20
Alignment explanation
Indices: 3176--3284 Score: 64
Period size: 22 Copynumber: 5.2 Consensus size: 20
3166 ATTACACTAT
*
3176 TTTTTATAATGTCCTTATGAAA
1 TTTTGATAAT-TCC-TATGAAA
3198 TTTTGATAACATTCCTATGAAA
1 TTTTGAT-A-ATTCCTATGAAA
*
3220 TTATGATAATTACACTAT----
1 TTTTGATAATT-C-CTATGAAA
* *
3238 TTTTTATGATGTCCTTATGAAA
1 TTTTGATAAT-TCC-TATGAAA
3260 TTTTGATAACCTTCCTATGAAA
1 TTTTGATAA--TTCCTATGAAA
3282 TTT
1 TTT
3285 CAATAACGAT
Statistics
Matches: 68, Mismatches: 7, Indels: 24
0.69 0.07 0.24
Matches are distributed among these distances:
17 1 0.01
18 11 0.16
19 1 0.01
20 3 0.04
21 2 0.03
22 40 0.59
23 7 0.10
24 3 0.04
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.47
Consensus pattern (20 bp):
TTTTGATAATTCCTATGAAA
Found at i:3229 original size:62 final size:62
Alignment explanation
Indices: 3132--3283 Score: 259
Period size: 62 Copynumber: 2.5 Consensus size: 62
3122 ATATTCATAC
* * *
3132 GAAATTATGACAACCTTCCTATTAAATTATGATAATTACACTATTTTTTATAATGTCCTTAT
1 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTTATAATGTCCTTAT
* *
3194 GAAATTTTGATAACATTCCTATGAAATTATGATAATTACACTATTTTTTATGATGTCCTTAT
1 GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTTATAATGTCCTTAT
3256 GAAATTTTGATAACCTTCCTATGAAATT
1 GAAATTTTGATAACCTTCCTATGAAATT
3284 TCAATAACGA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
62 84 1.00
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (62 bp):
GAAATTTTGATAACCTTCCTATGAAATTATGATAATTACACTATTTTTTATAATGTCCTTAT
Found at i:3356 original size:22 final size:22
Alignment explanation
Indices: 3251--3400 Score: 85
Period size: 22 Copynumber: 6.8 Consensus size: 22
3241 TTATGATGTC
3251 CTTATGAAATTTTGATAACCTT
1 CTTATGAAATTTTGATAACCTT
* ** * *
3273 CCTATGAAATTTCAATAACGATA
1 CTTATGAAATTTTGATAAC-CTT
* * *
3296 C-TATGGAATTTCGAGAACCTT
1 CTTATGAAATTTTGATAACCTT
*
3317 TTTAT-AAATTTT-ATTTAACCTT
1 CTTATGAAATTTTGA--TAACCTT
* *
3339 CTTATGAAATTTTGTTAACCTC
1 CTTATGAAATTTTGATAACCTT
* * * *
3361 CCTAAGTAATTTTGA-AGATC-T
1 CTTATGAAATTTTGATA-ACCTT
3382 CATTATGAAATTTTGATAA
1 C-TTATGAAATTTTGATAA
3401 TCAACACTAT
Statistics
Matches: 93, Mismatches: 26, Indels: 18
0.68 0.19 0.13
Matches are distributed among these distances:
20 1 0.01
21 8 0.09
22 74 0.80
23 10 0.11
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
CTTATGAAATTTTGATAACCTT
Found at i:3512 original size:22 final size:22
Alignment explanation
Indices: 3474--3533 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
3464 AAAACCAACA
*
3474 TATG-AATTGTCAGTAATCACAC
1 TATGAAATTGTGA-TAATCACAC
* *
3496 TCTGAAATTTTGATAATCACAC
1 TATGAAATTGTGATAATCACAC
3518 TATGAAATTGTGATAA
1 TATGAAATTGTGATAA
3534 CCTCGCTATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 26 0.81
23 6 0.19
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.35
Consensus pattern (22 bp):
TATGAAATTGTGATAATCACAC
Found at i:3565 original size:23 final size:22
Alignment explanation
Indices: 3498--3624 Score: 123
Period size: 23 Copynumber: 5.6 Consensus size: 22
3488 AATCACACTC
* *
3498 TGAAATTTTGATAATCAC-ACTA
1 TGAAATTTTGATAAAC-CTCCTA
*
3520 TGAAATTGTGAT-AACCTCGCTA
1 TGAAATTTTGATAAACCTC-CTA
*
3542 TGACATTTTGATAAACCATCCTA
1 TGAAATTTTGATAAACC-TCCTA
* *
3565 TAAAATTTTGATAAATCTCCCTA
1 TGAAATTTTGATAAACCT-CCTA
*
3588 TAAAATTTTGATAAACCTCCTTA
1 TGAAATTTTGATAAACCTCC-TA
*
3611 TGAAATCTTGATAA
1 TGAAATTTTGATAA
3625 TTACAAATTT
Statistics
Matches: 88, Mismatches: 11, Indels: 11
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.01
21 2 0.02
22 27 0.31
23 56 0.64
24 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (22 bp):
TGAAATTTTGATAAACCTCCTA
Found at i:3699 original size:22 final size:22
Alignment explanation
Indices: 3498--3703 Score: 102
Period size: 22 Copynumber: 9.5 Consensus size: 22
3488 AATCACACTC
* * *
3498 TGAAATTTTGATAATCACACTA
1 TGAAATTTTGATAACCTCATTA
* **
3520 TGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAACCTCATTA
* *
3542 TGACATTTTGATAAACCATC-CTA
1 TGAAATTTTGAT-AACC-TCATTA
* * **
3565 TAAAATTTTGATAAATCTCCCTA
1 TGAAATTTTGAT-AACCTCATTA
* *
3588 TAAAATTTTGATAAACCTCCTTA
1 TGAAATTTTGAT-AACCTCATTA
*
3611 TGAAATCTTGAT-A----ATTA
1 TGAAATTTTGATAACCTCATTA
* **
3628 -CAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCTCATTA
** * *
3649 TGATTTTTTGATAATCACATTA
1 TGAAATTTTGATAACCTCATTA
* * *
3671 TGTAATTTTGATAACCTCGTTT
1 TGAAATTTTGATAACCTCATTA
3693 TGAAATTTTGA
1 TGAAATTTTGA
3704 AATTGGACCA
Statistics
Matches: 142, Mismatches: 33, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
16 9 0.06
17 4 0.03
21 3 0.02
22 69 0.49
23 55 0.39
24 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.40
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCATTA
Found at i:4009 original size:30 final size:32
Alignment explanation
Indices: 3975--4043 Score: 90
Period size: 30 Copynumber: 2.2 Consensus size: 32
3965 GGCAATTTAG
*
3975 AAATATGA-TTTAAAAA-AAAGGTACAAT-TGA
1 AAATAT-ATTTTAAAAATAAAGGTACAATCGGA
*
4005 AAATATATTTTAAAAATAAGGGTACAATCGGA
1 AAATATATTTTAAAAATAAAGGTACAATCGGA
4037 AAATATA
1 AAATATA
4044 AAGTTTCCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 1 0.03
30 14 0.41
31 10 0.29
32 9 0.26
ACGTcount: A:0.55, C:0.04, G:0.13, T:0.28
Consensus pattern (32 bp):
AAATATATTTTAAAAATAAAGGTACAATCGGA
Found at i:4746 original size:123 final size:120
Alignment explanation
Indices: 4526--4773 Score: 340
Period size: 123 Copynumber: 2.0 Consensus size: 120
4516 AATTTGATAT
* *
4526 TGAT-TGTTTGGATTCTGTAATGTATGAATGCCACGTGATAATATTTGTTTGATTTTGAGAATTT
1 TGATATGTTTGGATTCTGTAACGTATGAATGCCACGTGATAATATTTGTTTGATTTTGAGAATCT
* ** * *
4590 GAGTCAAAATTTATATTTGGAAGTTTAGGTGACTAG-TAACGCTCAAATGTCACA
66 GAGTCAAAATTTATATTTGGAAGCTTAAATGACTAGATAAAGCTCAAAAGTCACA
*
4644 TGATATGTTTGGATTCTGTAACGTATGAATGTCACGTGATAATGTTAATTTGTTT-AGTTTTGAG
1 TGATATGTTTGGATTCTGTAACGTATGAATGCCACGTGATAA---T-ATTTGTTTGA-TTTTGAG
*
4708 AATCTGAGTCAAAATTTATATTTGGAAGCTTAAATGACTAGTATAAAGCTTAAAAGTCACA
61 AATCTGAGTCAAAATTTATATTTGGAAGCTTAAATGACTAG-ATAAAGCTCAAAAGTCACA
4769 TGATA
1 TGATA
4774 ATGACTGGTT
Statistics
Matches: 113, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
118 4 0.04
119 35 0.31
122 2 0.02
123 52 0.46
125 20 0.18
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (120 bp):
TGATATGTTTGGATTCTGTAACGTATGAATGCCACGTGATAATATTTGTTTGATTTTGAGAATCT
GAGTCAAAATTTATATTTGGAAGCTTAAATGACTAGATAAAGCTCAAAAGTCACA
Found at i:5689 original size:15 final size:15
Alignment explanation
Indices: 5669--5698 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5659 GTTGGAATTG
5669 GCAGCCATTTGGGTA
1 GCAGCCATTTGGGTA
5684 GCAGCCATTTGGGTA
1 GCAGCCATTTGGGTA
5699 AAAAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.27
Consensus pattern (15 bp):
GCAGCCATTTGGGTA
Found at i:6816 original size:27 final size:27
Alignment explanation
Indices: 6778--6833 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
6768 AAATTCAAAA
* *
6778 TCCTAATTGCACGAATTAGTCGTTGCT
1 TCCTAATAGCACAAATTAGTCGTTGCT
6805 TCCTAATAGCACAAATTAGTCGTTGCT
1 TCCTAATAGCACAAATTAGTCGTTGCT
6832 TC
1 TC
6834 AGGGCTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (27 bp):
TCCTAATAGCACAAATTAGTCGTTGCT
Found at i:9262 original size:21 final size:21
Alignment explanation
Indices: 9236--9280 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
9226 ATGATTTTTA
*
9236 TTTTTTAATTTGGCCCCCTTT
1 TTTTTTAATTTGGCCCCATTT
*
9257 TTTTTTAATTTGTCCCCATTT
1 TTTTTTAATTTGGCCCCATTT
9278 TTT
1 TTT
9281 AATCTGGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.11, C:0.20, G:0.07, T:0.62
Consensus pattern (21 bp):
TTTTTTAATTTGGCCCCATTT
Found at i:11099 original size:35 final size:35
Alignment explanation
Indices: 11057--11137 Score: 99
Period size: 39 Copynumber: 2.2 Consensus size: 35
11047 ATTTCTCATA
*
11057 TTTCTTTTTCTTTTAAGATTTAACAAACTAATTTC
1 TTTCTTTTTCTTTTAAGATTTAACAAACTAATCTC
*
11092 TTTCTTTTTATTTGTTTTAAGATTTAACAAACTAATCTC
1 TTTC---TT-TTTCTTTTAAGATTTAACAAACTAATCTC
*
11131 TTCCTTT
1 TTTCTTT
11138 CTCTCTTGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
35 5 0.13
36 2 0.05
38 2 0.05
39 30 0.77
ACGTcount: A:0.26, C:0.15, G:0.04, T:0.56
Consensus pattern (35 bp):
TTTCTTTTTCTTTTAAGATTTAACAAACTAATCTC
Found at i:12759 original size:156 final size:156
Alignment explanation
Indices: 12419--12801 Score: 424
Period size: 156 Copynumber: 2.5 Consensus size: 156
12409 TGTAGACCAT
* *
12419 CTTGGCTAAGTTTCATCTCAA-ACGGACATA-AGATGAAAAACTTATGCATGTTTTTCATTTAAG
1 CTTGGCAAAGTTTCATCTCAATA-GGACTTAGA-ATGAAAAACTTATGCATGTTTTTCATTTAAG
* * ** * *
12482 GATAGTTTAGGGAAAGAAACCAACTTCACTATGATAAGAAGTTTGGTTTTACTTAGAATTTTTTC
64 GACAGTTTAGGGAAAGAAACCAACTTCACCACCATAAGAAGCTCGGTTTTACTTAGAATTTTTTC
* *
12547 CATAGTTTTATGGGAATAATATAAGCCTA
129 CATAGTCTTATGGAAATAATATAAGCC-A
* * * *
12576 CTGGTGG-AAA--ATCAGCTTC-ATTGGACTTAGAATGAAAAACTTATGCACGTTTTTCATTTAA
1 CT--TGGCAAAGTTTCATC-TCAATAGGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAA
* * *
12637 GGACAGTTTAGGGAAAGAAACCAAGTTTACCACCA-AGGAGAGCTCGGTTTTACTT-GAAATTTT
63 GGACAGTTTAGGGAAAGAAACCAACTTCACCACCATAAGA-AGCTCGGTTTTACTTAG-AATTTT
* *
12700 TTCCATAGTCTTGTGGAAATAATCTAAGTCC-
126 TTCCATAGTCTTATGGAAATAATATAAG-CCA
* **
12731 CTTGGCAAAGTTTCATCTCAATAAGACTTAGAATGAAAAACTTATGTTTGTTTTTCATTTAAGGA
1 CTTGGCAAAGTTTCATCTCAATAGGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAGGA
12796 CAGTTT
66 CAGTTT
12802 GGGGTGTGAA
Statistics
Matches: 188, Mismatches: 26, Indels: 25
0.79 0.11 0.10
Matches are distributed among these distances:
153 3 0.02
154 3 0.02
155 8 0.04
156 162 0.86
157 7 0.04
158 2 0.01
159 3 0.02
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (156 bp):
CTTGGCAAAGTTTCATCTCAATAGGACTTAGAATGAAAAACTTATGCATGTTTTTCATTTAAGGA
CAGTTTAGGGAAAGAAACCAACTTCACCACCATAAGAAGCTCGGTTTTACTTAGAATTTTTTCCA
TAGTCTTATGGAAATAATATAAGCCA
Found at i:13496 original size:22 final size:23
Alignment explanation
Indices: 13453--13497 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
13443 CGCAAAAAAC
*
13453 CAAGCTCCGTGCTTATTTTCTCT
1 CAAGCTCCGTGCCTATTTTCTCT
13476 CAAGCTCCGTGCCT-TTTTCTCT
1 CAAGCTCCGTGCCTATTTTCTCT
13498 TGTTCATCAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.11, C:0.33, G:0.13, T:0.42
Consensus pattern (23 bp):
CAAGCTCCGTGCCTATTTTCTCT
Found at i:16363 original size:120 final size:120
Alignment explanation
Indices: 16150--16380 Score: 345
Period size: 120 Copynumber: 1.9 Consensus size: 120
16140 ATATTAATTA
* * * *
16150 TTTGGATTCTATAACGTACGAATGTCACGTGATGATGTTTGTCCGGTTTTGAGAATCTGAGTCAA
1 TTTGGATTCTATAACGTACGAATGTCACGTGATAATGTTTGTCCGCTTTTAAGAATATGAGTCAA
* * *
16215 AATTTATATTTAGAAGCTTAGGTGACTAGTAACGCTCAAATGTCACATGATAATG
66 AATTTATATTTAGAAACTTAGATGACTAGTAACGCTCAAACGTCACATGATAATG
* * *
16270 TTTGGATTCTGTAACGTATGAATGTCACGTGATAATGTTTGTCTGCTTTTAAGAATATGAGTCAA
1 TTTGGATTCTATAACGTACGAATGTCACGTGATAATGTTTGTCCGCTTTTAAGAATATGAGTCAA
* * *
16335 ATTTTATATTTGGAAACTTAGATGACTAGTAACGCTCGAACGTCAC
66 AATTTATATTTAGAAACTTAGATGACTAGTAACGCTCAAACGTCAC
16381 GTAATGATAC
Statistics
Matches: 98, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
120 98 1.00
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (120 bp):
TTTGGATTCTATAACGTACGAATGTCACGTGATAATGTTTGTCCGCTTTTAAGAATATGAGTCAA
AATTTATATTTAGAAACTTAGATGACTAGTAACGCTCAAACGTCACATGATAATG
Found at i:19423 original size:20 final size:20
Alignment explanation
Indices: 19398--19441 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
19388 TCAAAAGTGG
* *
19398 GAAAAGTGCTATAACGGCTA
1 GAAAAGAGCTACAACGGCTA
*
19418 GAAAAGAGCTCCAACGGCTA
1 GAAAAGAGCTACAACGGCTA
19438 GAAA
1 GAAA
19442 CTTGTGAGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.18, G:0.25, T:0.14
Consensus pattern (20 bp):
GAAAAGAGCTACAACGGCTA
Done.