Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006381.1 Corchorus capsularis cultivar CVL-1 contig06402, 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: 51641
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:1140 original size:27 final size:27
Alignment explanation
Indices: 1110--1184 Score: 125
Period size: 27 Copynumber: 2.8 Consensus size: 27
1100 AAAATAGTAT
1110 AAAAA-AGTATTAAATTATTTTACCAA
1 AAAAATAGTATTAAATTATTTTACCAA
* *
1136 AAAAATAGTATTGAATTATTTTAGCAA
1 AAAAATAGTATTAAATTATTTTACCAA
1163 AAAAATAGTATTAAATTATTTT
1 AAAAATAGTATTAAATTATTTT
1185 GAATTTTGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
26 5 0.11
27 40 0.89
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.39
Consensus pattern (27 bp):
AAAAATAGTATTAAATTATTTTACCAA
Found at i:7341 original size:11 final size:10
Alignment explanation
Indices: 7324--7357 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
7314 TTGACAGCAC
7324 AACAAAAACA
1 AACAAAAACA
7334 AGACAAAAACGA
1 A-ACAAAAAC-A
7346 AACAAAAACA
1 AACAAAAACA
7356 AA
1 AA
7358 AAATAAGAAA
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:0.76, C:0.18, G:0.06, T:0.00
Consensus pattern (10 bp):
AACAAAAACA
Found at i:10136 original size:20 final size:20
Alignment explanation
Indices: 10111--10153 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
10101 AGCATCATCC
10111 ATAGTTAAATTTTCATTTCT
1 ATAGTTAAATTTTCATTTCT
10131 ATAGTTAAATTTTCATTTCT
1 ATAGTTAAATTTTCATTTCT
10151 ATA
1 ATA
10154 CAGGTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.09, G:0.05, T:0.53
Consensus pattern (20 bp):
ATAGTTAAATTTTCATTTCT
Found at i:12573 original size:3 final size:3
Alignment explanation
Indices: 12567--12595 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12557 ACTATTATTA
12567 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
12596 TTTCTTTAAA
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:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:14072 original size:12 final size:12
Alignment explanation
Indices: 14055--14082 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
14045 CTTCAAACCA
14055 ATTAATTAAGAT
1 ATTAATTAAGAT
14067 ATTAATTAAGAT
1 ATTAATTAAGAT
14079 ATTA
1 ATTA
14083 CACTTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (12 bp):
ATTAATTAAGAT
Found at i:19170 original size:21 final size:21
Alignment explanation
Indices: 19154--19233 Score: 88
Period size: 21 Copynumber: 3.8 Consensus size: 21
19144 ACTCCACCTT
19154 CAAGAGGAGTCAGTCCAACTC
1 CAAGAGGAGTCAGTCCAACTC
* * *
19175 CAAGGGGTGTCAGTCCAACCC
1 CAAGAGGAGTCAGTCCAACTC
* * *
19196 CAAGGGGCGTCAGTCCAACCC
1 CAAGAGGAGTCAGTCCAACTC
* *
19217 CAAGGGGTGTCAGTCCA
1 CAAGAGGAGTCAGTCCA
19234 TCTCGGCAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.26, C:0.31, G:0.29, T:0.14
Consensus pattern (21 bp):
CAAGAGGAGTCAGTCCAACTC
Found at i:27466 original size:3 final size:3
Alignment explanation
Indices: 27458--27496 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
27448 ATTCTAGACT
27458 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
27497 AATGTTTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:36594 original size:2 final size:2
Alignment explanation
Indices: 36587--36619 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
36577 GAAGGAAAGA
36587 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36620 ACAATCATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38745 original size:21 final size:21
Alignment explanation
Indices: 38719--38768 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
38709 TCGCTGATTA
38719 TAATCTCATCTGTACAGTATC
1 TAATCTCATCTGTACAGTATC
* * *
38740 TAATCTGATCTGTACAGTGTT
1 TAATCTCATCTGTACAGTATC
38761 TAATCTCA
1 TAATCTCA
38769 CAATCTCAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (21 bp):
TAATCTCATCTGTACAGTATC
Found at i:39403 original size:16 final size:16
Alignment explanation
Indices: 39382--39414 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39372 AAAACGCCCT
39382 TTTTCTCATGAACTCA
1 TTTTCTCATGAACTCA
39398 TTTTCTCATGAACTCA
1 TTTTCTCATGAACTCA
39414 T
1 T
39415 AATGAATAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (16 bp):
TTTTCTCATGAACTCA
Found at i:40105 original size:36 final size:36
Alignment explanation
Indices: 40065--40140 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
40055 CAACAAGCTA
40065 TATAATTCTTTTTCATTCAAATTTAATAAGTAACAC
1 TATAATTCTTTTTCATTCAAATTTAATAAGTAACAC
* * *
40101 TATAATTCTTTTTCATTCGAATTTAATGAGTAGCAC
1 TATAATTCTTTTTCATTCAAATTTAATAAGTAACAC
40137 TATA
1 TATA
40141 GTTAGAAGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.45
Consensus pattern (36 bp):
TATAATTCTTTTTCATTCAAATTTAATAAGTAACAC
Found at i:45496 original size:26 final size:26
Alignment explanation
Indices: 45467--45516 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
45457 TTCCATATGC
45467 CATGTGGGGACTTGGTTGCCATGAGT
1 CATGTGGGGACTTGGTTGCCATGAGT
45493 CATGTGGGGACTTGGTTGCCATGA
1 CATGTGGGGACTTGGTTGCCATGA
45517 TACAGCACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.16, C:0.16, G:0.38, T:0.30
Consensus pattern (26 bp):
CATGTGGGGACTTGGTTGCCATGAGT
Found at i:47179 original size:14 final size:14
Alignment explanation
Indices: 47162--47188 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
47152 TGTTATTAGT
47162 ATTAATTAATTAAA
1 ATTAATTAATTAAA
47176 ATTAATTAATTAA
1 ATTAATTAATTAA
47189 TGATAAGTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTAATTAATTAAA
Found at i:47412 original size:48 final size:48
Alignment explanation
Indices: 47341--47434 Score: 179
Period size: 48 Copynumber: 2.0 Consensus size: 48
47331 TTTGATAAGT
47341 AATGAAAATTATTTTGTAATGAAAGCTTAATTAGTTACGTTGCAAAGG
1 AATGAAAATTATTTTGTAATGAAAGCTTAATTAGTTACGTTGCAAAGG
*
47389 AATGAACATTATTTTGTAATGAAAGCTTAATTAGTTACGTTGCAAA
1 AATGAAAATTATTTTGTAATGAAAGCTTAATTAGTTACGTTGCAAA
47435 ATTAAACGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.36
Consensus pattern (48 bp):
AATGAAAATTATTTTGTAATGAAAGCTTAATTAGTTACGTTGCAAAGG
Found at i:47931 original size:23 final size:24
Alignment explanation
Indices: 47905--47954 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
47895 ACCTTATAAA
*
47905 TTTTTTAATAAA-CTTAAAACCTT
1 TTTTTTAACAAACCTTAAAACCTT
*
47928 TTTTTTAGCAAACCTTAAAACCTT
1 TTTTTTAACAAACCTTAAAACCTT
47952 TTT
1 TTT
47955 AGTAAGCAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 10 0.42
24 14 0.58
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.48
Consensus pattern (24 bp):
TTTTTTAACAAACCTTAAAACCTT
Found at i:47962 original size:25 final size:24
Alignment explanation
Indices: 47917--47963 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
47907 TTTTAATAAA
* *
47917 CTTAAAACCTTTTTTTTAGCAAAC
1 CTTAAAACCTTTTTGTAAGCAAAC
47941 CTTAAAACCTTTTTAGTAAGCAA
1 CTTAAAACCTTTTT-GTAAGCAA
47964 GTTTTATAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.38
Consensus pattern (24 bp):
CTTAAAACCTTTTTGTAAGCAAAC
Found at i:48602 original size:89 final size:89
Alignment explanation
Indices: 48450--48615 Score: 269
Period size: 89 Copynumber: 1.9 Consensus size: 89
48440 AACCTTGTAA
* *
48450 ATTTTCTTGGTATGCTTATAAATTTTTCATTAAACTTAAAAGCTTATTAAATAGTTCTGTTAAAT
1 ATTTTCTTGGTAAGCTTATAAATTTTTCATTAAACTTAAAAGCTTATTAAATAGTTCTCTTAAAT
48515 TTATTCAATCACACGTTGTTTAAG
66 TTATTCAATCACACGTTGTTTAAG
* * * * *
48539 ATTTTTTTGGTAAGCTTATAAATTTTTCATTAAACTTAAAAGTTTTTTTAATAGTTTTCTTAAAT
1 ATTTTCTTGGTAAGCTTATAAATTTTTCATTAAACTTAAAAGCTTATTAAATAGTTCTCTTAAAT
48604 TTATTCAATCAC
66 TTATTCAATCAC
48616 CTCGTTAAAG
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
89 70 1.00
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (89 bp):
ATTTTCTTGGTAAGCTTATAAATTTTTCATTAAACTTAAAAGCTTATTAAATAGTTCTCTTAAAT
TTATTCAATCACACGTTGTTTAAG
Found at i:48748 original size:20 final size:21
Alignment explanation
Indices: 48725--48768 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 21
48715 TCTTGTAAGA
48725 TTTATAGTTAA-CTTATGAA-T
1 TTTATAG-TAACCTTATGAAGT
48745 TTTATAGTAACCTTATGAAGT
1 TTTATAGTAACCTTATGAAGT
48766 TTT
1 TTT
48769 TTAATATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.14
20 15 0.68
21 4 0.18
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (21 bp):
TTTATAGTAACCTTATGAAGT
Found at i:51619 original size:201 final size:199
Alignment explanation
Indices: 51253--51641 Score: 600
Period size: 201 Copynumber: 1.9 Consensus size: 199
51243 ATGAATATTT
* * *
51253 ATAAGCGGATTAAGAAGTTGACACATACCTCATTTCATAATTAATTAAATATTTAATTTTAATAC
1 ATAAGCGGATTAAGAAGTTAACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATAC
* *
51318 ATATTCCCTAAGCGGACACATGTCAACCCTTAAACCCCGCACGTTCAGTCTACTAAACTCCACTG
66 ATATTCCCTAAGCGGACACATGTCAACCCTTAAACCCCGAACGTGCAGTCTACTAAACTCCACTG
* * *
51383 ACGGTGTATTGTATAATTTTTCTTATAGTATTATTATACAATACACTGTCAGTGTAAATTTTGGA
131 ACGGTATATTGTACAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGA
51448 CTCC
196 CTCC
* **
51452 ATAAGCGGATTAAGAAGTTAACACATACCCCATTTTTTATAATTAATTAAATATTTAATATTGGT
1 ATAAGCGGATTAAGAAGTTAACACATACCCCA--TTTCATAATTAATTAAATATTTAATATTAAT
* * *
51517 ACATATTCCCTAAGGGGACACATGTCAACCCTTCAACCCCGAACGTGCAGT-TGCTAAACTCCAC
64 ACATATTCCCTAAGCGGACACATGTCAACCCTTAAACCCCGAACGTGCAGTCTACTAAACTCCAC
* *
51581 TGACGGTATATTGTACAATTTTTCTTTATGGGATTATTATACAATACATTGTCAGTGTAAA
129 TGACGGTATATTGTACAATTTTTC-TTATAGGATTATTATACAATACACTGTCAGTGTAAA
Statistics
Matches: 171, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
199 30 0.18
200 34 0.20
201 107 0.63
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.34
Consensus pattern (199 bp):
ATAAGCGGATTAAGAAGTTAACACATACCCCATTTCATAATTAATTAAATATTTAATATTAATAC
ATATTCCCTAAGCGGACACATGTCAACCCTTAAACCCCGAACGTGCAGTCTACTAAACTCCACTG
ACGGTATATTGTACAATTTTTCTTATAGGATTATTATACAATACACTGTCAGTGTAAATTTTGGA
CTCC
Done.