Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012952.1 Corchorus capsularis cultivar CVL-1 contig12973, 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: 6643
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.30
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2098 original size:53 final size:54
Alignment explanation
Indices: 2026--2186 Score: 220
Period size: 53 Copynumber: 3.0 Consensus size: 54
2016 AGAGATTGAA
2026 TTTTTAGAGTAATTAGTAAATAAAATTGTAACCTTTGAATAAAAGATTGAATTT
1 TTTTTAGAGTAATTAGTAAATAAAATTGTAACCTTTGAATAAAAGATTGAATTT
* * * * ** *
2080 TTTTTA-AGTAATTGGTAAATAAAAATGTCATCTTTGGGTAAAAGGTTGAA--T
1 TTTTTAGAGTAATTAGTAAATAAAATTGTAACCTTTGAATAAAAGATTGAATTT
* *
2131 TTTTTAGAGTGATTAGTAAATAAAATTTTAACCTTTGAATAAAAGATTGAATTT
1 TTTTTAGAGTAATTAGTAAATAAAATTGTAACCTTTGAATAAAAGATTGAATTT
2185 TT
1 TT
2187 AAGTTTAGTA
Statistics
Matches: 88, Mismatches: 16, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
51 7 0.08
52 35 0.40
53 37 0.42
54 9 0.10
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.42
Consensus pattern (54 bp):
TTTTTAGAGTAATTAGTAAATAAAATTGTAACCTTTGAATAAAAGATTGAATTT
Found at i:2150 original size:105 final size:104
Alignment explanation
Indices: 1996--2186 Score: 319
Period size: 105 Copynumber: 1.8 Consensus size: 104
1986 AACTTAAGTA
*
1996 AAAAATGTCATCTTTAAGTAAGAGATTGAATTTTTAGAGTAATTAGTAAATAAAATTGTAACCTT
1 AAAAATGTCATCTTTAAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAATTGTAACCTT
2061 TGAATAAAAGATTGAATTTTTTTTAAGTAATTGGTAAAT
66 TGAATAAAAGATTGAATTTTTTTTAAGTAATTGGTAAAT
** * * *
2100 AAAAATGTCATCTTTGGGTAAAAGGTTGAATTTTTTAGAGTGATTAGTAAATAAAATTTTAACCT
1 AAAAATGTCATCTTTAAGTAAAAGATTGAA-TTTTTAGAGTAATTAGTAAATAAAATTGTAACCT
2165 TTGAATAAAAGATTGAATTTTT
65 TTGAATAAAAGATTGAATTTTT
2187 AAGTTTAGTA
Statistics
Matches: 80, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
104 26 0.32
105 54 0.68
ACGTcount: A:0.41, C:0.04, G:0.15, T:0.40
Consensus pattern (104 bp):
AAAAATGTCATCTTTAAGTAAAAGATTGAATTTTTAGAGTAATTAGTAAATAAAATTGTAACCTT
TGAATAAAAGATTGAATTTTTTTTAAGTAATTGGTAAAT
Found at i:2167 original size:52 final size:52
Alignment explanation
Indices: 2018--2186 Score: 225
Period size: 52 Copynumber: 3.2 Consensus size: 52
2008 TTTAAGTAAG
2018 AGATTGAA-TTTTTAGAGTAATTAGTAAATAAAATTGTAACCTTTGAATAAA
1 AGATTGAATTTTTTAGAGTAATTAGTAAATAAAATTGTAACCTTTGAATAAA
* * * * **
2069 AGATTGAATTTTTTTTA-AGTAATTGGTAAATAAAAATGTCATCTTTGGGTAAA
1 AGATTGAA--TTTTTTAGAGTAATTAGTAAATAAAATTGTAACCTTTGAATAAA
* * *
2122 AGGTTGAATTTTTTAGAGTGATTAGTAAATAAAATTTTAACCTTTGAATAAA
1 AGATTGAATTTTTTAGAGTAATTAGTAAATAAAATTGTAACCTTTGAATAAA
2174 AGATTGAATTTTT
1 AGATTGAATTTTT
2187 AAGTTTAGTA
Statistics
Matches: 98, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
51 15 0.15
52 40 0.41
53 37 0.38
54 6 0.06
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.41
Consensus pattern (52 bp):
AGATTGAATTTTTTAGAGTAATTAGTAAATAAAATTGTAACCTTTGAATAAA
Found at i:2764 original size:35 final size:35
Alignment explanation
Indices: 2693--2814 Score: 165
Period size: 35 Copynumber: 3.4 Consensus size: 35
2683 TTTGCTTGAG
* *
2693 GAGTAATTAGTAAAGAGTAA-AATGATAAAAAGTAAA
1 GAGTAATCAGTAAA-AG-AAGAATGGTAAAAAGTAAA
2729 GAGTAATCAGTAAAAGAAGAATGGTAAAAAGTAAA
1 GAGTAATCAGTAAAAGAAGAATGGTAAAAAGTAAA
* *
2764 GAGTAATCAGTAAAGGAAGAATGGTAAAGAGTAAAA
1 GAGTAATCAGTAAAAGAAGAATGGTAAAAAGT-AAA
*
2800 GGGTAATCAGTAAAA
1 GAGTAATCAGTAAAA
2815 AGTAAAAAGA
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
34 2 0.03
35 47 0.60
36 29 0.37
ACGTcount: A:0.55, C:0.02, G:0.24, T:0.19
Consensus pattern (35 bp):
GAGTAATCAGTAAAAGAAGAATGGTAAAAAGTAAA
Found at i:2768 original size:28 final size:29
Alignment explanation
Indices: 2701--2769 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 29
2691 AGGAGTAATT
*
2701 AGTAAAGAGTAAAATGATAAAAAGTAAAG
1 AGTAAAGAGTAAAATGATAAAAAGTAAAA
** **
2730 AGTAATCAGTAAAA-GA-AGAATGGTAAAA
1 AGTAAAGAGTAAAATGATA-AAAAGTAAAA
2758 AGTAAAGAGTAA
1 AGTAAAGAGTAA
2770 TCAGTAAAGG
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
27 1 0.03
28 19 0.59
29 12 0.38
ACGTcount: A:0.59, C:0.01, G:0.22, T:0.17
Consensus pattern (29 bp):
AGTAAAGAGTAAAATGATAAAAAGTAAAA
Found at i:2769 original size:14 final size:14
Alignment explanation
Indices: 2701--2820 Score: 50
Period size: 15 Copynumber: 8.4 Consensus size: 14
2691 AGGAGTAATT
2701 AGTAAAGAGTAAAA
1 AGTAAAGAGTAAAA
* * *
2715 TGATAAAAAGTAAAG
1 AG-TAAAGAGTAAAA
**
2730 AGTAATCAGTAAAAGA
1 AGTAAAGAGT-AAA-A
*
2746 AG-AATG-GTAAAA
1 AGTAAAGAGTAAAA
**
2758 AGTAAAGAGTAATC
1 AGTAAAGAGTAAAA
2772 AGTAAAG-G-AAGAA
1 AGTAAAGAGTAA-AA
*
2785 TGGTAAAGAGTAAAA
1 -AGTAAAGAGTAAAA
* **
2800 GGGTAATCAGTAAAA
1 -AGTAAAGAGTAAAA
2815 AGTAAA
1 AGTAAA
2821 AAGATAATCA
Statistics
Matches: 78, Mismatches: 19, Indels: 18
0.68 0.17 0.16
Matches are distributed among these distances:
12 5 0.06
13 7 0.09
14 30 0.38
15 32 0.41
16 4 0.05
ACGTcount: A:0.57, C:0.03, G:0.23, T:0.17
Consensus pattern (14 bp):
AGTAAAGAGTAAAA
Found at i:2812 original size:22 final size:22
Alignment explanation
Indices: 2787--3010 Score: 145
Period size: 22 Copynumber: 10.0 Consensus size: 22
2777 AGGAAGAATG
*
2787 GTAAAGAGTAAAAGGGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* * *
2809 GTAAAAAGTAAAAAGATAATCA
1 GTAAAGAGTAAAATGGTAATCA
*
2831 GTAAAGAATGAAATAGTAGAAGGTAATCA
1 GTAAAGAGT-AAA-A-T----GGTAATCA
* * *
2860 ATAAAAAGT--AATGATAATCA
1 GTAAAGAGTAAAATGGTAATCA
*
2880 GTAAA-AGGTAAAATAGTAATCA
1 GTAAAGA-GTAAAATGGTAATCA
*
2902 GT-AAGAGCAAAATGGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* * *
2923 AT-GAGAGCAAAATGGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* * *
2944 GTAAAGTGTAAAATAGTAATCG
1 GTAAAGAGTAAAATGGTAATCA
* *
2966 GTAAAAAGTAAGAA-GGTAATCG
1 GTAAAGAGTAA-AATGGTAATCA
* *
2988 GTAAAGAGTAAAATAGTGATCA
1 GTAAAGAGTAAAATGGTAATCA
3010 G
1 G
3011 CAAAAGGTAA
Statistics
Matches: 157, Mismatches: 31, Indels: 28
0.73 0.14 0.13
Matches are distributed among these distances:
19 1 0.01
20 13 0.08
21 37 0.24
22 84 0.54
23 5 0.03
24 2 0.01
25 1 0.01
26 1 0.01
29 13 0.08
ACGTcount: A:0.52, C:0.05, G:0.22, T:0.21
Consensus pattern (22 bp):
GTAAAGAGTAAAATGGTAATCA
Found at i:2894 original size:49 final size:50
Alignment explanation
Indices: 2801--2897 Score: 126
Period size: 49 Copynumber: 1.9 Consensus size: 50
2791 AGAGTAAAAG
* *
2801 GGTAATCAGTAAAAAGTAAAAAGATAATCAGTAAAGAATGAAATAGTAGAA
1 GGTAATCAATAAAAAGT-AAAAGATAATCAGTAAAGAATAAAATAGTAGAA
* *
2852 GGTAATCAATAAAAAGT-AATGATAATCAGTAAA-AGGTAAAATAGTA
1 GGTAATCAATAAAAAGTAAAAGATAATCAGTAAAGA-ATAAAATAGTA
2898 ATCAGTAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
48 1 0.02
49 24 0.59
51 16 0.39
ACGTcount: A:0.56, C:0.04, G:0.19, T:0.22
Consensus pattern (50 bp):
GGTAATCAATAAAAAGTAAAAGATAATCAGTAAAGAATAAAATAGTAGAA
Found at i:2919 original size:21 final size:21
Alignment explanation
Indices: 2869--2947 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
2859 AATAAAAAGT
* * *
2869 AATGATAATCAGTAAAAGGTAA
1 AATGGTAATCAGTAAGA-GCAA
*
2891 AATAGTAATCAGTAAGAGCAA
1 AATGGTAATCAGTAAGAGCAA
* *
2912 AATGGTAATCAATGAGAGCAA
1 AATGGTAATCAGTAAGAGCAA
2933 AATGGTAATCAGTAA
1 AATGGTAATCAGTAA
2948 AGTGTAAAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
21 34 0.71
22 14 0.29
ACGTcount: A:0.51, C:0.08, G:0.20, T:0.22
Consensus pattern (21 bp):
AATGGTAATCAGTAAGAGCAA
Found at i:3117 original size:35 final size:36
Alignment explanation
Indices: 2972--3118 Score: 165
Period size: 35 Copynumber: 4.1 Consensus size: 36
2962 ATCGGTAAAA
* *
2972 AGTAAGAAGGTAATCGGTAAAGAGTAAAATAGTGATC
1 AGTAA-AAGGTAATCAGTAAAGAGTAAAATAGTAATC
* *
3009 AGCAAAAGGTAATCAGT-AAGAGTAAAATTGTAATC
1 AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
* ** *
3044 AATCGAAGGTAATCAGTAAAGAG-AAAATACTAATC
1 AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
* * *
3079 AGTAAAAGATAATCAGT-AAGAGTAAAACAGTAACC
1 AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
3114 AGTAA
1 AGTAA
3119 GAGCAAAGTG
Statistics
Matches: 91, Mismatches: 17, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
34 5 0.05
35 66 0.73
36 16 0.18
37 4 0.04
ACGTcount: A:0.50, C:0.09, G:0.20, T:0.20
Consensus pattern (36 bp):
AGTAAAAGGTAATCAGTAAAGAGTAAAATAGTAATC
Found at i:3118 original size:21 final size:21
Alignment explanation
Indices: 3079--3169 Score: 94
Period size: 21 Copynumber: 4.3 Consensus size: 21
3069 AATACTAATC
*
3079 AGTAAAAGA-TAATCAGTAAG
1 AGTAAAATAGTAATCAGTAAG
* *
3099 AGTAAAACAGTAACCAGTAAG
1 AGTAAAATAGTAATCAGTAAG
* * * *
3120 AGCAAAGTGGTAATTAGTAAG
1 AGTAAAATAGTAATCAGTAAG
*
3141 CGTAAAATAGTAATCAGTAAAG
1 AGTAAAATAGTAATCAGT-AAG
3163 AGTAAAA
1 AGTAAAA
3170 GGTGATCAGT
Statistics
Matches: 55, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 8 0.15
21 38 0.69
22 9 0.16
ACGTcount: A:0.52, C:0.08, G:0.21, T:0.20
Consensus pattern (21 bp):
AGTAAAATAGTAATCAGTAAG
Found at i:3181 original size:42 final size:41
Alignment explanation
Indices: 3079--3181 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 41
3069 AATACTAATC
*
3079 AGTAAAAGATAATCAGTAAGAGTAAAACAGTAACCAGTAAG
1 AGTAAAAGGTAATCAGTAAGAGTAAAACAGTAACCAGTAAG
* * * * * *
3120 AGCAAAGTGGTAATTAGTAAGCGTAAAATAGTAATCAGTAAAG
1 AGTAAA-AGGTAATCAGTAAGAGTAAAACAGTAACCAGT-AAG
*
3163 AGTAAAAGGTGATCAGTAA
1 AGTAAAAGGTAATCAGTAA
3182 TTCAAAAGAG
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
41 5 0.10
42 36 0.73
43 8 0.16
ACGTcount: A:0.50, C:0.08, G:0.22, T:0.20
Consensus pattern (41 bp):
AGTAAAAGGTAATCAGTAAGAGTAAAACAGTAACCAGTAAG
Found at i:3259 original size:13 final size:13
Alignment explanation
Indices: 3243--3289 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
3233 GGTAATAAAT
3243 AAAAGAGAGTAAG
1 AAAAGAGAGTAAG
* *
3256 AAAAGAGTAATTAG
1 AAAAGAG-AGTAAG
3270 TAAAA-AGAGTAAG
1 -AAAAGAGAGTAAG
3283 AAAAGAG
1 AAAAGAG
3290 TAAAAATGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.13
Consensus pattern (13 bp):
AAAAGAGAGTAAG
Found at i:3259 original size:29 final size:28
Alignment explanation
Indices: 3234--3296 Score: 94
Period size: 27 Copynumber: 2.3 Consensus size: 28
3224 GTAAAAAGTG
3234 GTAATAAATAAAAGAGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
* *
3262 GTAATTAGTAAAA-AGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
3289 GTAA-AAAT
1 GTAATAAAT
3297 GATAAAAGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 2 0.06
27 18 0.58
28 11 0.35
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (28 bp):
GTAATAAATAAAAGAGAGTAAGAAAAGA
Found at i:6216 original size:19 final size:18
Alignment explanation
Indices: 6192--6228 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
6182 TTGAAGATTT
6192 CTTGAAGACAATTTGAAGA
1 CTTGAAGACAA-TTGAAGA
*
6211 CTTGAAGACCATTGAAGA
1 CTTGAAGACAATTGAAGA
6229 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.24
Consensus pattern (18 bp):
CTTGAAGACAATTGAAGA
Done.