Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015144.1 Corchorus capsularis cultivar CVL-1 contig15165, 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: 100876
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:7698 original size:96 final size:96
Alignment explanation
Indices: 7535--7815 Score: 555
Period size: 96 Copynumber: 2.9 Consensus size: 96
7525 AAAATAGTTA
7535 AGATCAGCAACTAC-GAAAAAACGACTCCACTACCAAATAACATTGGCGATGAGCAAGAGAGACA
1 AGATCAGCAACTACGGAAAAAACGACTCCACTACCAAATAACATTGGCGATGAGCAAGAGAGACA
7599 GAGCAGAATCAAAATGTAACCACTACCTAAT
66 GAGCAGAATCAAAATGTAACCACTACCTAAT
7630 AGATCAGCAACTACGGAAAAAACGACTCCACTACCAAATAACATTGGCGATGAGCAAGAGAGACA
1 AGATCAGCAACTACGGAAAAAACGACTCCACTACCAAATAACATTGGCGATGAGCAAGAGAGACA
7695 GAGCAGAATCAAAATGTAACCACTACCTAAT
66 GAGCAGAATCAAAATGTAACCACTACCTAAT
7726 AGATCAGCAACTACGGAAAAAACGACTCCACTACCAAATAACATTGGCGATGAGCAAGAGAGACA
1 AGATCAGCAACTACGGAAAAAACGACTCCACTACCAAATAACATTGGCGATGAGCAAGAGAGACA
7791 GAGCAGAATCAAAATGTAACCACTA
66 GAGCAGAATCAAAATGTAACCACTA
7816 ATGCAATCGG
Statistics
Matches: 185, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
95 14 0.08
96 171 0.92
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.14
Consensus pattern (96 bp):
AGATCAGCAACTACGGAAAAAACGACTCCACTACCAAATAACATTGGCGATGAGCAAGAGAGACA
GAGCAGAATCAAAATGTAACCACTACCTAAT
Found at i:8100 original size:19 final size:19
Alignment explanation
Indices: 8076--8116 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
8066 TAACAACCTT
*
8076 TATTTTGATTCTTCTAAAC
1 TATTTTGATTCCTCTAAAC
8095 TATTTTGATTCCTCTAAAC
1 TATTTTGATTCCTCTAAAC
8114 TAT
1 TAT
8117 GGGGTTCCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (19 bp):
TATTTTGATTCCTCTAAAC
Found at i:9975 original size:17 final size:17
Alignment explanation
Indices: 9932--9976 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
9922 TATATAAACA
*
9932 TATAGTATATAGTATAT
1 TATAATATATAGTATAT
* *
9949 AATAACATATAGTATAT
1 TATAATATATAGTATAT
*
9966 TATATTATATA
1 TATAATATATA
9977 TAATAATAGG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.44
Consensus pattern (17 bp):
TATAATATATAGTATAT
Found at i:11791 original size:27 final size:27
Alignment explanation
Indices: 11761--11818 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
11751 ATACTCCATC
*
11761 TGTTCCTTTTTAATTGTCCATTTTCCT
1 TGTTCCTTTTTAATTGTCCATTTCCCT
11788 TGTTCCTTTTTAATTGTCCATTTCCCT
1 TGTTCCTTTTTAATTGTCCATTTCCCT
11815 TGTT
1 TGTT
11819 TTCCAGAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.10, C:0.22, G:0.09, T:0.59
Consensus pattern (27 bp):
TGTTCCTTTTTAATTGTCCATTTCCCT
Found at i:11804 original size:14 final size:14
Alignment explanation
Indices: 11761--11804 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
11751 ATACTCCATC
11761 TGTTCCTTTTTAAT
1 TGTTCCTTTTTAAT
* **
11775 TG-TCCATTTTCCT
1 TGTTCCTTTTTAAT
11788 TGTTCCTTTTTAAT
1 TGTTCCTTTTTAAT
11802 TGT
1 TGT
11805 CCATTTCCCT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.11, C:0.18, G:0.09, T:0.61
Consensus pattern (14 bp):
TGTTCCTTTTTAAT
Found at i:13143 original size:9 final size:9
Alignment explanation
Indices: 13131--13165 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
13121 AGGTCCCCAA
*
13131 CCAGGCCCT
1 CCAGGTCCT
13140 CCAGGTCCT
1 CCAGGTCCT
*
13149 CCGGGTCCT
1 CCAGGTCCT
13158 CCAGGTCC
1 CCAGGTCC
13166 AGGTGGTCTC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.09, C:0.49, G:0.26, T:0.17
Consensus pattern (9 bp):
CCAGGTCCT
Found at i:17312 original size:39 final size:39
Alignment explanation
Indices: 17258--17335 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
17248 GAAAGGGAGT
* * *
17258 GTCAATCCAAACGCGAGAAATCTTACCTTCAGCTGCTTC
1 GTCAATCCAAACGCGAAAAATATTACCTCCAGCTGCTTC
17297 GTCAATCCAAACGCGAAAAATATTACCTCCAGCTGCTTC
1 GTCAATCCAAACGCGAAAAATATTACCTCCAGCTGCTTC
17336 CATCTCACCG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.31, C:0.31, G:0.14, T:0.24
Consensus pattern (39 bp):
GTCAATCCAAACGCGAAAAATATTACCTCCAGCTGCTTC
Found at i:18580 original size:2 final size:2
Alignment explanation
Indices: 18575--18599 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18565 TTGTTATATA
18575 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
18600 TTTCACTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:23236 original size:15 final size:15
Alignment explanation
Indices: 23216--23259 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
23206 TAATAATAAG
23216 CATTCAATCGTTAAC
1 CATTCAATCGTTAAC
23231 CATTCAATCGTTAAC
1 CATTCAATCGTTAAC
*
23246 CATTCAATCCTTAA
1 CATTCAATCGTTAA
23260 GGCGCACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.34, C:0.27, G:0.05, T:0.34
Consensus pattern (15 bp):
CATTCAATCGTTAAC
Found at i:27942 original size:15 final size:16
Alignment explanation
Indices: 27917--27949 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
27907 GCTTCAGCTG
*
27917 CTCCTTCCTCCGCCTT
1 CTCCTTCCTCCACCTT
27933 CTCC-TCCTCCACCTT
1 CTCCTTCCTCCACCTT
27948 CT
1 CT
27950 GCTGGTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.03, C:0.58, G:0.03, T:0.36
Consensus pattern (16 bp):
CTCCTTCCTCCACCTT
Found at i:28409 original size:5 final size:5
Alignment explanation
Indices: 28399--28423 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28389 ATTCAACTAG
28399 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
28424 TCTCCTTGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:35685 original size:29 final size:29
Alignment explanation
Indices: 35621--35693 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
35611 GTATAAGGGG
* *
35621 GCAAAACGTCTCAAAATTGAAGTTCAGGAA
1 GCAAAACGTC-CAAAATTGAAATTCAAGAA
* * * *
35651 GTAAAATGTCCAAAATTGAAATTTAAGAT
1 GCAAAACGTCCAAAATTGAAATTCAAGAA
35680 GCAAAACGTCCAAA
1 GCAAAACGTCCAAA
35694 TGTTAGAAGT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 27 0.77
30 8 0.23
ACGTcount: A:0.47, C:0.15, G:0.16, T:0.22
Consensus pattern (29 bp):
GCAAAACGTCCAAAATTGAAATTCAAGAA
Found at i:36310 original size:31 final size:31
Alignment explanation
Indices: 36275--36369 Score: 109
Period size: 31 Copynumber: 3.1 Consensus size: 31
36265 ACGTGGCATG
*
36275 TTTTTGGTACATGTGGCGTGCCACATGTAAC
1 TTTTTGGTACATGTGGCGTGCCACATGTCAC
* * * **
36306 TTTTTGGTACACGTGGTGTGGCATGTGTCAC
1 TTTTTGGTACATGTGGCGTGCCACATGTCAC
* * *
36337 TTTTTGGTACATGTAGCATACCACATGTCAC
1 TTTTTGGTACATGTGGCGTGCCACATGTCAC
36368 TT
1 TT
36370 GTTGTAAAAA
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (31 bp):
TTTTTGGTACATGTGGCGTGCCACATGTCAC
Found at i:43124 original size:2 final size:2
Alignment explanation
Indices: 43119--43149 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
43109 TATATGTGTG
43119 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43150 TTGAGTGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52728 original size:29 final size:29
Alignment explanation
Indices: 52695--52798 Score: 120
Period size: 29 Copynumber: 3.6 Consensus size: 29
52685 TAGTGTGTCA
* * *
52695 AGGACGTTTTGCCCCTTAAATTTCAAATC
1 AGGACATTTTACCCCTTAAACTTCAAATC
52724 AGGACATTTTACCCCTTAAACTTCAAATC
1 AGGACATTTTACCCCTTAAACTTCAAATC
* * *
52753 AGAACATTTTACTCC-TGAACTTCCAAATTC
1 AGGACATTTTACCCCTTAAACTT-CAAA-TC
*
52783 AAGACATTTTACCCCT
1 AGGACATTTTACCCCT
52799 GACAGAAGAG
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
28 6 0.10
29 43 0.68
30 14 0.22
ACGTcount: A:0.32, C:0.27, G:0.09, T:0.33
Consensus pattern (29 bp):
AGGACATTTTACCCCTTAAACTTCAAATC
Found at i:59827 original size:23 final size:23
Alignment explanation
Indices: 59787--59830 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
59777 TAAAATAATT
*
59787 ATAAAAATATTGAATTCAATTAA
1 ATAAAAATAGTGAATTCAATTAA
**
59810 ATAAAAATAGTGTTTTCAATT
1 ATAAAAATAGTGAATTCAATT
59831 GCAAAAGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.39
Consensus pattern (23 bp):
ATAAAAATAGTGAATTCAATTAA
Found at i:72560 original size:57 final size:57
Alignment explanation
Indices: 72375--72564 Score: 253
Period size: 54 Copynumber: 3.3 Consensus size: 57
72365 AAAAAATCAA
*
72375 GAGACGAAAATAGAAACCAAAGGGGAAAATGTGGCTGTGGTGACCAAACCATTGGCTGAG
1 GAGACGAAAATAGAAACCAAAGGGGAAAATGT---TGTGGAGACCAAACCATTGGCTGAG
* * *
72435 GAGACGAAAATAGAAACAAAAGTGGAAAA---TGTGGAGACGAAACCATTGGCTGAG
1 GAGACGAAAATAGAAACCAAAGGGGAAAATGTTGTGGAGACCAAACCATTGGCTGAG
* *
72489 GAGACGAAAATAGAAACCAGAGGGGAAAATGTTGTGGAGACTAAACCATTGGCTGAG
1 GAGACGAAAATAGAAACCAAAGGGGAAAATGTTGTGGAGACCAAACCATTGGCTGAG
*
72546 GAAAC-AAAAGTAGAAACCA
1 GAGACGAAAA-TAGAAACCA
72565 TGCAAGAAAC
Statistics
Matches: 117, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
54 49 0.42
56 4 0.03
57 37 0.32
60 27 0.23
ACGTcount: A:0.44, C:0.13, G:0.29, T:0.14
Consensus pattern (57 bp):
GAGACGAAAATAGAAACCAAAGGGGAAAATGTTGTGGAGACCAAACCATTGGCTGAG
Found at i:72678 original size:42 final size:42
Alignment explanation
Indices: 72583--72687 Score: 151
Period size: 42 Copynumber: 2.5 Consensus size: 42
72573 ACAAAACTTC
*
72583 CTGAAGAGAAAAAGGAAGAAATTGTAGAGGAACAAAAACTGG
1 CTGAAGAGAAACAGGAAGAAATTGTAGAGGAACAAAAACTGG
* *
72625 -TCGAAGAGAAACAGGAAGAAATTGTAGTGGAAGAAAAACTGG
1 CT-GAAGAGAAACAGGAAGAAATTGTAGAGGAACAAAAACTGG
72667 CTGAAGAGAAACCA-GAAGAAA
1 CTGAAGAGAAA-CAGGAAGAAA
72688 CTGCAATAGG
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
41 1 0.02
42 53 0.93
43 3 0.05
ACGTcount: A:0.51, C:0.09, G:0.29, T:0.11
Consensus pattern (42 bp):
CTGAAGAGAAACAGGAAGAAATTGTAGAGGAACAAAAACTGG
Found at i:78597 original size:18 final size:18
Alignment explanation
Indices: 78574--78610 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
78564 ATTTATGGTT
* *
78574 CAAGCTATCTAATCTCTC
1 CAAGCTATCAAATCCCTC
78592 CAAGCTATCAAATCCCTC
1 CAAGCTATCAAATCCCTC
78610 C
1 C
78611 CCAAGGGCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.38, G:0.05, T:0.27
Consensus pattern (18 bp):
CAAGCTATCAAATCCCTC
Found at i:89921 original size:2 final size:2
Alignment explanation
Indices: 89914--89938 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
89904 TATATGTGTC
89914 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
89939 TATTTCTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:95724 original size:7 final size:7
Alignment explanation
Indices: 95712--95747 Score: 63
Period size: 7 Copynumber: 5.1 Consensus size: 7
95702 AAGAGAAGGT
95712 AAAGAAA
1 AAAGAAA
95719 AAAGAAA
1 AAAGAAA
95726 AAAGAAA
1 AAAGAAA
*
95733 AAGGAAA
1 AAAGAAA
95740 AAAGAAA
1 AAAGAAA
95747 A
1 A
95748 GAAAATGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAGAAA
Found at i:95735 original size:13 final size:13
Alignment explanation
Indices: 95712--95752 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
95702 AAGAGAAGGT
95712 AAAGAAAAAAGAAA
1 AAAG-AAAAAGAAA
95726 AAAGAAAAAGGAAA
1 AAAGAAAAA-GAAA
95740 AAAG-AAAAGAAA
1 AAAGAAAAAGAAA
95752 A
1 A
95753 TGAATAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.19
13 9 0.35
14 12 0.46
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Done.