Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011536.1 Corchorus capsularis cultivar CVL-1 contig11557, 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: 53051
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:967 original size:7 final size:6
Alignment explanation
Indices: 938--971 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
928 AAAGCAAAGA
938 AAATCT AAATCT AAATCT AAATCTT AAATCT AAA
1 AAATCT AAATCT AAATCT AAATC-T AAATCT AAA
972 GCAAATTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATCT
Found at i:1926 original size:10 final size:10
Alignment explanation
Indices: 1911--1935 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1901 GAGGACTCTA
1911 GAATTTTCTG
1 GAATTTTCTG
1921 GAATTTTCTG
1 GAATTTTCTG
1931 GAATT
1 GAATT
1936 GAGCAGGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:2531 original size:20 final size:22
Alignment explanation
Indices: 2507--2556 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
2497 CAAAATAGGG
2507 TAAAAACACATAAAAATAGC-A
1 TAAAAACACATAAAAATAGCTA
** *
2528 -AAAAGTATATAAAAATAGCTA
1 TAAAAACACATAAAAATAGCTA
2549 TAAAAACA
1 TAAAAACA
2557 TGTATAATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
20 16 0.73
21 1 0.05
22 5 0.23
ACGTcount: A:0.66, C:0.10, G:0.06, T:0.18
Consensus pattern (22 bp):
TAAAAACACATAAAAATAGCTA
Found at i:3489 original size:11 final size:10
Alignment explanation
Indices: 3471--3504 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
3461 AATTGTCTTC
3471 AAATCTTCAA
1 AAATCTTCAA
3481 AATATCTTCAA
1 AA-ATCTTCAA
3492 GAAATCTTCAA
1 -AAATCTTCAA
3503 AA
1 AA
3505 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:14013 original size:40 final size:40
Alignment explanation
Indices: 13929--14016 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
13919 TGGACTCTGC
* *** *
13929 ATATGTATATATATATATATACACTTTTTTTTGAGATAAT
1 ATATATATATATATATATATACACCACTTTTTGAGATAAG
*
13969 ATATATATATATATATATATACACACACTTTTT-AGATTAG
1 ATATATATATATATATATATACAC-CACTTTTTGAGATAAG
14009 ATATATAT
1 ATATATAT
14017 TGATAAAATG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 36 0.88
41 5 0.12
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.47
Consensus pattern (40 bp):
ATATATATATATATATATATACACCACTTTTTGAGATAAG
Found at i:16168 original size:24 final size:25
Alignment explanation
Indices: 16122--16173 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
16112 GATAGAGTAT
16122 TTATTTATCTTGTTACTTAATTTTA
1 TTATTTATCTTGTTACTTAATTTTA
* *
16147 TTATTT-TCTTGTTTATTTATTTTTA
1 TTATTTATCTTG-TTACTTAATTTTA
16172 TT
1 TT
16174 GTTCACTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTACTTAATTTTA
Found at i:16865 original size:30 final size:29
Alignment explanation
Indices: 16827--16891 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 29
16817 TTGAGATAAG
16827 ATGGGGAGCTCACAAACATTAAGAATCAA
1 ATGGGGAGCTCACAAACATTAAGAATCAA
* *
16856 ATAGGGGAGCTCACAAACCTTAGGAATCAA
1 AT-GGGGAGCTCACAAACATTAAGAATCAA
16886 ATGGGG
1 ATGGGG
16892 CAACTTGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 6 0.18
30 27 0.82
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (29 bp):
ATGGGGAGCTCACAAACATTAAGAATCAA
Found at i:20468 original size:42 final size:43
Alignment explanation
Indices: 20403--20485 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 43
20393 CGTGTTTGGC
*
20403 TTATCGTGTCTCGTATCTGAATCGTGTC-AGACACGATTAAGA
1 TTATCGTGTCTCGTATCTGAATCGTATCTAGACACGATTAAGA
* * *
20445 TTATCGTGTTTCGTGT-TGTAATCGTATCTTGACACGATTAA
1 TTATCGTGTCTCGTATCTG-AATCGTATCTAGACACGATTAA
20486 CACGTTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 2 0.06
42 22 0.63
43 11 0.31
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (43 bp):
TTATCGTGTCTCGTATCTGAATCGTATCTAGACACGATTAAGA
Found at i:21372 original size:24 final size:25
Alignment explanation
Indices: 21326--21377 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
21316 ATTGGAGTAT
21326 TTATTTATCTTGTTACTTAATTTTA
1 TTATTTATCTTGTTACTTAATTTTA
* *
21351 TTATTT-TCTTGTTTATTTATTTTTA
1 TTATTTATCTTG-TTACTTAATTTTA
21376 TT
1 TT
21378 GTTCATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTACTTAATTTTA
Found at i:23512 original size:24 final size:23
Alignment explanation
Indices: 23442--23512 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
23432 AAATTGTAAT
* * *
23442 AACCTCGCTATGAAATTTTGACA
1 AACCTCCCTATAAAATTTTGATA
* *
23465 AATCTTCCTATAAAATTTTGATA
1 AACCTCCCTATAAAATTTTGATA
23488 AACCTCCCTATAAAATTTTTGATA
1 AACCTCCCTATAAAA-TTTTGATA
23512 A
1 A
23513 CTTTCTTATG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 31 0.77
24 9 0.22
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.37
Consensus pattern (23 bp):
AACCTCCCTATAAAATTTTGATA
Found at i:23532 original size:46 final size:46
Alignment explanation
Indices: 23442--23534 Score: 107
Period size: 46 Copynumber: 2.0 Consensus size: 46
23432 AAATTGTAAT
* * *
23442 AACCTCGCTATGAAATTTTGACAAATCTTCCTATAAAATTTTGATA
1 AACCTCCCTATAAAATTTTGACAAATCTTCCTATAAAATCTTGATA
* * * *
23488 AACCTCCCTATAAAATTTTTGATAACT-TTCTTATGAAATCTTGATA
1 AACCTCCCTATAAAA-TTTTGACAAATCTTCCTATAAAATCTTGATA
23534 A
1 A
23535 CTACAAATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
46 30 0.77
47 9 0.23
ACGTcount: A:0.37, C:0.17, G:0.08, T:0.39
Consensus pattern (46 bp):
AACCTCCCTATAAAATTTTGACAAATCTTCCTATAAAATCTTGATA
Found at i:23589 original size:22 final size:22
Alignment explanation
Indices: 23143--23708 Score: 240
Period size: 22 Copynumber: 25.9 Consensus size: 22
23133 ATGATCCCAT
*
23143 TATGAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCAC
* * *
23165 AATGAAATTTTAATAACGAT-AC
1 TATGAAATTTTGATAAC-CTCAC
* * * ***
23187 TATGGAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTCAC
* ** *
23209 TAT-AATTTTTTTTAACCTTC-T
1 TATGAAATTTTGATAACC-TCAC
*
23230 TATGAAATTTTG-TAACCTCCC
1 TATGAAATTTTGATAACCTCAC
* ** *
23251 TAAGGGATTTTGA-AGACCTCAA
1 TATGAAATTTTGATA-ACCTCAC
* *
23273 TATGAAATTTTGATAACTTCCC
1 TATGAAATTTTGATAACCTCAC
* *
23295 AATGAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCAC
* *
23318 TATGAGATGTTGATAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* **
23339 -AT-ACAATATATTGATAACCACGT
1 TATGA-AAT-T-TTGATAACCTCAC
* * *
23362 TATGAAAATTTAAAAACCTC-C
1 TATGAAATTTTGATAACCTCAC
* * *
23383 ATATG-AATTGTTAATAATCACAC
1 -TATGAAATT-TTGATAACCTCAC
* * *
23406 TCTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCTCAC
* * *
23428 TATGAAATTGTAATAACCTCGC
1 TATGAAATTTTGATAACCTCAC
* *
23450 TATGAAATTTTGACAAATCTTC-C
1 TATGAAATTTTGA-TAA-CCTCAC
* *
23473 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCAC
* * *
23496 TATAAAATTTTTGATAACTTTC-T
1 TATGAAA-TTTTGATAAC-CTCAC
*
23519 TATGAAATCTTGATAA-CT-AC
1 TATGAAATTTTGATAACCTCAC
* *
23539 ----AAATTTTCATAACCTCCC
1 TATGAAATTTTGATAACCTCAC
** *
23557 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCAC
** * *
23579 TATGAAATTTTTTTAATCTCCC
1 TATGAAATTTTGATAACCTCAC
* *
23601 TATGAAATTTTGATCTACAT-AC
1 TATGAAATTTTGAT-AACCTCAC
* *
23623 TATGAAACTTTGATAACCCTC-T
1 TATGAAATTTTGATAA-CCTCAC
* *
23645 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-CAC
23667 TATGAAATTTTGATAACCTTCA-
1 TATGAAATTTTGATAACC-TCAC
*
23689 TATGAAATTTTGATATCCTC
1 TATGAAATTTTGATAACCTC
23709 CCTTAATTCT
Statistics
Matches: 398, Mismatches: 107, Indels: 79
0.68 0.18 0.14
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
18 1 0.00
19 1 0.00
20 9 0.02
21 37 0.09
22 255 0.64
23 65 0.16
24 17 0.04
25 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCAC
Found at i:23747 original size:19 final size:20
Alignment explanation
Indices: 23691--23741 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
23681 AACCTTCATA
23691 TGAAATTTTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
* *
23711 T-TAATTCTGATATCCTCCC
1 TGAAATTTTGATATCCTCCC
23730 TGAAATTTTGAT
1 TGAAATTTTGAT
23742 TACTCCATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.43
Consensus pattern (20 bp):
TGAAATTTTGATATCCTCCC
Found at i:23918 original size:22 final size:22
Alignment explanation
Indices: 23847--23986 Score: 93
Period size: 22 Copynumber: 6.4 Consensus size: 22
23837 AATCACATTT
* * *
23847 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* *
23869 TGAAATTTTGATAACCTCTTTA
1 TGAAATTTTGATAACCCCTCTA
* * *
23891 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCCCTCTA
* * * **
23913 TGAAATTCTGATAATCACAATA
1 TGAAATTTTGATAACCCCTCTA
* * *
23935 TGTAATTTTGATAACCTCGC-A
1 TGAAATTTTGATAACCCCTCTA
** *
23956 TTGAAATTTTGATAACAACACTA
1 -TGAAATTTTGATAACCCCTCTA
23979 TGAAATTT
1 TGAAATTT
23987 CGAAAATCGA
Statistics
Matches: 92, Mismatches: 24, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
21 1 0.01
22 90 0.98
23 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (22 bp):
TGAAATTTTGATAACCCCTCTA
Found at i:24086 original size:22 final size:22
Alignment explanation
Indices: 24057--24196 Score: 128
Period size: 22 Copynumber: 6.4 Consensus size: 22
24047 AAATTGAGAC
24057 TTTT-ATAACCTTCA-TATGAAA
1 TTTTGATAACC-TCACTATGAAA
* *
24078 TTTTGATAACCACACTATAAAA
1 TTTTGATAACCTCACTATGAAA
* *
24100 TTTTGATAACCTCCCCATGAAA
1 TTTTGATAACCTCACTATGAAA
*
24122 TATT-AGTAACCTC-CTAATGAAA
1 TTTTGA-TAACCTCACT-ATGAAA
* * *
24144 TTTTGTTAACCACACTATAAAA
1 TTTTGATAACCTCACTATGAAA
*
24166 TTCTT-ATAACCTCACTATGACA
1 TT-TTGATAACCTCACTATGAAA
24188 TTTTGATAA
1 TTTTGATAA
24197 TCTCTTTGAT
Statistics
Matches: 95, Mismatches: 16, Indels: 15
0.75 0.13 0.12
Matches are distributed among these distances:
21 10 0.11
22 81 0.85
23 4 0.04
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.36
Consensus pattern (22 bp):
TTTTGATAACCTCACTATGAAA
Found at i:24297 original size:24 final size:23
Alignment explanation
Indices: 24239--24391 Score: 86
Period size: 22 Copynumber: 6.9 Consensus size: 23
24229 AATTAACCAC
*
24239 CCTATGAAATTTCAATAACCAAA
1 CCTATGAAATTTTAATAACCAAA
* * * *
24262 CCTAAGAGATTTTAATAACCTGAT
1 CCTATGAAATTTTAATAACC-AAA
** *
24286 CCTATGAAATTTTGGTAACCACA
1 CCTATGAAATTTTAATAACCAAA
** *
24309 -CTATGAAATTTTTGTAACCACA
1 CCTATGAAATTTTAATAACCAAA
* *
24331 -CTATGGAATTTTGATAACC---
1 CCTATGAAATTTTAATAACCAAA
* * *
24350 TC-ATGAAATTATAATAACC-AT
1 CCTATGAAATTTTAATAACCAAA
* *
24371 CTTATGAAATTTTGATAACCA
1 CCTATGAAATTTTAATAACCA
24392 CATAGAGACA
Statistics
Matches: 101, Mismatches: 23, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
19 14 0.14
20 1 0.01
22 52 0.51
23 17 0.17
24 17 0.17
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (23 bp):
CCTATGAAATTTTAATAACCAAA
Found at i:24315 original size:22 final size:22
Alignment explanation
Indices: 24287--24349 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
24277 TAACCTGATC
24287 CTATGAAATTTTGGTAACCACA
1 CTATGAAATTTTGGTAACCACA
*
24309 CTATGAAATTTTTGTAACCACA
1 CTATGAAATTTTGGTAACCACA
* *
24331 CTATGGAATTTTGATAACC
1 CTATGAAATTTTGGTAACC
24350 TCATGAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (22 bp):
CTATGAAATTTTGGTAACCACA
Found at i:25511 original size:19 final size:19
Alignment explanation
Indices: 25487--25523 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
25477 ATATTATTTT
25487 AATAGTAAAATAACTAAAA
1 AATAGTAAAATAACTAAAA
*
25506 AATAGTAAAATAATTAAA
1 AATAGTAAAATAACTAAA
25524 TTATTATTTA
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:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (19 bp):
AATAGTAAAATAACTAAAA
Found at i:27598 original size:21 final size:23
Alignment explanation
Indices: 27556--27598 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
27546 AAAAAACTAA
* *
27556 GCTCCGCGCTTATTTTCTCTCTG
1 GCTCCGCGCCTATTTTCACTCTG
27579 GCTCCGCGCCT-TTTT-ACTCT
1 GCTCCGCGCCTATTTTCACTCT
27599 TATTCATCAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 4 0.22
23 10 0.56
ACGTcount: A:0.05, C:0.37, G:0.16, T:0.42
Consensus pattern (23 bp):
GCTCCGCGCCTATTTTCACTCTG
Found at i:40239 original size:10 final size:10
Alignment explanation
Indices: 40224--40249 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
40214 TTCATCACGA
40224 GTTCTTACTC
1 GTTCTTACTC
40234 GTTCTTACTC
1 GTTCTTACTC
40244 GTTCTT
1 GTTCTT
40250 CAAAATTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.27, G:0.12, T:0.54
Consensus pattern (10 bp):
GTTCTTACTC
Found at i:40711 original size:15 final size:15
Alignment explanation
Indices: 40691--40741 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
40681 TACATATTAT
40691 ATAATTAATAATGGA
1 ATAATTAATAATGGA
* *
40706 ATAATTTATAAT-TA
1 ATAATTAATAATGGA
**
40720 A-AAAAAATAATGGA
1 ATAATTAATAATGGA
40734 ATAATTAA
1 ATAATTAA
40742 AATATTATTT
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
13 7 0.27
14 4 0.15
15 15 0.58
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (15 bp):
ATAATTAATAATGGA
Done.