Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012742.1 Corchorus capsularis cultivar CVL-1 contig12763, 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: 11880
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.30
Found at i:7737 original size:19 final size:18
Alignment explanation
Indices: 7704--7739 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7694 TTGAAATAAT
7704 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
7722 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
7740 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:8644 original size:29 final size:30
Alignment explanation
Indices: 8586--8700 Score: 115
Period size: 32 Copynumber: 3.7 Consensus size: 30
8576 AATTAAAAAA
* * * *
8586 AAAGAAGTAATCAGTAGAAAGAAATAAAAG
1 AAAGAAGTAATCAGTAGAATGGAGTGAAAG
* *
8616 -AGGAAGTGATCAGTAGAATGGAGTGAAAG
1 AAAGAAGTAATCAGTAGAATGGAGTGAAAG
*
8645 TAAAAGAAGTAATCAGTAAAATGGAGTGAAAG
1 --AAAGAAGTAATCAGTAGAATGGAGTGAAAG
*
8677 TAAAAGAAGTAATCAGTAAAATGG
1 --AAAGAAGTAATCAGTAGAATGG
8701 TAATTAAGAG
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
29 23 0.32
32 50 0.68
ACGTcount: A:0.53, C:0.03, G:0.26, T:0.17
Consensus pattern (30 bp):
AAAGAAGTAATCAGTAGAATGGAGTGAAAG
Found at i:8660 original size:32 final size:32
Alignment explanation
Indices: 8618--8700 Score: 148
Period size: 32 Copynumber: 2.6 Consensus size: 32
8608 AATAAAAGAG
* *
8618 GAAGTGATCAGTAGAATGGAGTGAAAGTAAAA
1 GAAGTAATCAGTAAAATGGAGTGAAAGTAAAA
8650 GAAGTAATCAGTAAAATGGAGTGAAAGTAAAA
1 GAAGTAATCAGTAAAATGGAGTGAAAGTAAAA
8682 GAAGTAATCAGTAAAATGG
1 GAAGTAATCAGTAAAATGG
8701 TAATTAAGAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.49, C:0.04, G:0.28, T:0.19
Consensus pattern (32 bp):
GAAGTAATCAGTAAAATGGAGTGAAAGTAAAA
Found at i:8662 original size:16 final size:16
Alignment explanation
Indices: 8643--8697 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
8633 ATGGAGTGAA
8643 AGTAAAAGAAGTAATC
1 AGTAAAAGAAGTAATC
*
8659 AGTAAAATGGAGTGAA--
1 AGTAAAA-GAAGT-AATC
8675 AGTAAAAGAAGTAATC
1 AGTAAAAGAAGTAATC
8691 AGTAAAA
1 AGTAAAA
8698 TGGTAATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
14 2 0.06
15 4 0.12
16 21 0.64
17 4 0.12
18 2 0.06
ACGTcount: A:0.56, C:0.04, G:0.22, T:0.18
Consensus pattern (16 bp):
AGTAAAAGAAGTAATC
Found at i:8760 original size:16 final size:17
Alignment explanation
Indices: 8734--8767 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
8724 AGTAATCAGT
*
8734 AAATCGGTAAAGAGTAA
1 AAATCGGTAAAAAGTAA
8751 AAAT-GGTAAAAAGTAA
1 AAATCGGTAAAAAGTAA
8767 A
1 A
8768 GAGTAATCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.59, C:0.03, G:0.21, T:0.18
Consensus pattern (17 bp):
AAATCGGTAAAAAGTAA
Found at i:8760 original size:40 final size:39
Alignment explanation
Indices: 8676--8797 Score: 130
Period size: 40 Copynumber: 3.2 Consensus size: 39
8666 TGGAGTGAAA
8676 GTAAAAGAAGTAATCAGTAAAAT-GGTAATTAAGAGTAAAA--
1 GTAAAAGAAGTAATCAGT-AAATCGGT-A--AAGAGTAAAATG
8716 GTAAAAGAAGTAATCAGTAAATCGGTAAAGAGTAAAAATG
1 GTAAAAGAAGTAATCAGTAAATCGGTAAAGAGT-AAAATG
** *
8756 GT-AAA-AAGTAAAGAGT-AATCAGTAAAGAGTAAAATG
1 GTAAAAGAAGTAATCAGTAAATCGGTAAAGAGTAAAATG
8792 GTAAAA
1 GTAAAA
8798 TGGTAATTAA
Statistics
Matches: 74, Mismatches: 3, Indels: 13
0.82 0.03 0.14
Matches are distributed among these distances:
36 8 0.11
37 22 0.30
38 13 0.18
39 8 0.11
40 23 0.31
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.20
Consensus pattern (39 bp):
GTAAAAGAAGTAATCAGTAAATCGGTAAAGAGTAAAATG
Found at i:8885 original size:26 final size:26
Alignment explanation
Indices: 8835--8888 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
8825 ACAAATGGCG
8835 ATTAAATTCAAAGAGTGAAAATAGTA
1 ATTAAATTCAAAGAGTGAAAATAGTA
8861 ATTAAATTCAAGAGAGT-AAAATAGTA
1 ATTAAATTCAA-AGAGTGAAAATAGTA
8887 AT
1 AT
8889 CAGTAAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 22 0.81
27 5 0.19
ACGTcount: A:0.54, C:0.04, G:0.15, T:0.28
Consensus pattern (26 bp):
ATTAAATTCAAAGAGTGAAAATAGTA
Found at i:8900 original size:7 final size:7
Alignment explanation
Indices: 8890--8945 Score: 67
Period size: 7 Copynumber: 7.9 Consensus size: 7
8880 AATAGTAATC
8890 AGTAAAG
1 AGTAAAG
8897 AGTAAAG
1 AGTAAAG
*
8904 AGTAAAAA
1 AGT-AAAG
8912 AGTAAAG
1 AGTAAAG
8919 AGTAAAG
1 AGTAAAG
**
8926 AGTAATC
1 AGTAAAG
*
8933 AGTAAAA
1 AGTAAAG
8940 AGTAAA
1 AGTAAA
8946 AATGGCAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
7 36 0.86
8 6 0.14
ACGTcount: A:0.61, C:0.02, G:0.21, T:0.16
Consensus pattern (7 bp):
AGTAAAG
Found at i:8900 original size:22 final size:21
Alignment explanation
Indices: 8873--9128 Score: 120
Period size: 22 Copynumber: 12.0 Consensus size: 21
8863 TAAATTCAAG
*
8873 AGAGTAAAATAGTAATCAGTAA
1 AGAGT-AAAGAGTAATCAGTAA
**
8895 AGAGTAAAGAGTAAAAAAGTAA
1 AGAGTAAAGAGT-AATCAGTAA
8917 AGAGTAAAGAGTAATCAGTAA
1 AGAGTAAAGAGTAATCAGTAA
* * **
8938 AAAGTAAA-AAT-GGCA--AA
1 AGAGTAAAGAGTAATCAGTAA
*
8955 GAGTAGTAAATAGTAATCAGGTAA
1 -AG-AGTAAAGAGTAATCA-GTAA
*** **
8979 A-AGTAGTCAGTAAAGAGTAA
1 AGAGTAAAGAGTAATCAGTAA
** *
8999 TCAGTAAAGGGAG-AAT-GGTAA
1 AGAGTAAA--GAGTAATCAGTAA
* *
9020 GGAGTAAAGGGTAATCAGTAA
1 AGAGTAAAGAGTAATCAGTAA
*
9041 TAGCA--AAATG-GTAATTAGTAA
1 -AG-AGTAAA-GAGTAATCAGTAA
*
9062 AGAGTAAAATAGTAATCAGTAA
1 AGAGT-AAAGAGTAATCAGTAA
*
9084 AAAGT-AAGAAGGTAATCAGTAA
1 AGAGTAAAG-A-GTAATCAGTAA
9106 AGAGTAAAGTAGTAATCAGTAA
1 AGAGTAAAG-AGTAATCAGTAA
9128 A
1 A
9129 AGGTAATCAG
Statistics
Matches: 175, Mismatches: 36, Indels: 46
0.68 0.14 0.18
Matches are distributed among these distances:
17 2 0.01
18 1 0.01
19 11 0.06
20 15 0.09
21 64 0.37
22 72 0.41
23 8 0.05
24 2 0.01
ACGTcount: A:0.52, C:0.04, G:0.23, T:0.20
Consensus pattern (21 bp):
AGAGTAAAGAGTAATCAGTAA
Found at i:8906 original size:29 final size:28
Alignment explanation
Indices: 8873--8945 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 28
8863 TAAATTCAAG
*
8873 AGAGTAAAATAGTAATCAGTAAAGAGTAA
1 AGAGTAAAA-AGTAAACAGTAAAGAGTAA
*
8902 AGAGTAAAAAAGTAAAGAGTAAAGAGTAA
1 AGAGT-AAAAAGTAAACAGTAAAGAGTAA
**
8931 TCAGTAAAAAGTAAA
1 AGAGTAAAAAGTAAA
8946 AATGGCAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
28 10 0.26
29 25 0.64
30 4 0.10
ACGTcount: A:0.59, C:0.03, G:0.21, T:0.18
Consensus pattern (28 bp):
AGAGTAAAAAGTAAACAGTAAAGAGTAA
Found at i:8946 original size:7 final size:7
Alignment explanation
Indices: 8875--8947 Score: 56
Period size: 7 Copynumber: 10.1 Consensus size: 7
8865 AATTCAAGAG
8875 AGTAAAA
1 AGTAAAA
**
8882 TAGTAATC
1 -AGTAAAA
*
8890 AGTAAAG
1 AGTAAAA
*
8897 AGTAAAG
1 AGTAAAA
8904 AGTAAAAA
1 AGT-AAAA
*
8912 AGTAAAG
1 AGTAAAA
*
8919 AGTAAAG
1 AGTAAAA
**
8926 AGTAATC
1 AGTAAAA
8933 AGTAAAA
1 AGTAAAA
8940 AGTAAAA
1 AGTAAAA
8947 A
1 A
8948 TGGCAAAGAG
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
7 43 0.80
8 11 0.20
ACGTcount: A:0.60, C:0.03, G:0.19, T:0.18
Consensus pattern (7 bp):
AGTAAAA
Found at i:8988 original size:14 final size:14
Alignment explanation
Indices: 8959--9007 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
8949 GGCAAAGAGT
*
8959 AGTAAATAGTAATC
1 AGTAAAGAGTAATC
*
8973 AGGTAAA-AGTAGTC
1 A-GTAAAGAGTAATC
8987 AGTAAAGAGTAATC
1 AGTAAAGAGTAATC
9001 AGTAAAG
1 AGTAAAG
9008 GGAGAATGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 5 0.16
14 21 0.68
15 5 0.16
ACGTcount: A:0.49, C:0.06, G:0.22, T:0.22
Consensus pattern (14 bp):
AGTAAAGAGTAATC
Found at i:8997 original size:28 final size:25
Alignment explanation
Indices: 8952--9006 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 25
8942 TAAAAATGGC
*
8952 AAAGAGTAGTAAATAGTAATCAGGTA
1 AAAGAGTAGTAAAGAGTAATCA-GTA
8978 AAAGTAGTCAGTAAAGAGTAATCAGTA
1 AAAG-AGT-AGTAAAGAGTAATCAGTA
9005 AA
1 AA
9007 GGGAGAATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 4 0.15
27 8 0.31
28 14 0.54
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.22
Consensus pattern (25 bp):
AAAGAGTAGTAAAGAGTAATCAGTA
Found at i:9026 original size:35 final size:35
Alignment explanation
Indices: 8987--9068 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
8977 AAAAGTAGTC
* *
8987 AGTAAAGAGTAATCAGTAA-AGGGAGAATGGTAAGG
1 AGTAAAGAGTAATCAGTAATA-GCAAAATGGTAAGG
* **
9022 AGTAAAGGGTAATCAGTAATAGCAAAATGGTAATT
1 AGTAAAGAGTAATCAGTAATAGCAAAATGGTAAGG
9057 AGTAAAGAGTAA
1 AGTAAAGAGTAA
9069 AATAGTAATC
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
35 39 0.98
36 1 0.03
ACGTcount: A:0.48, C:0.04, G:0.28, T:0.21
Consensus pattern (35 bp):
AGTAAAGAGTAATCAGTAATAGCAAAATGGTAAGG
Found at i:9155 original size:21 final size:21
Alignment explanation
Indices: 9141--9213 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
9131 GTAATCAGTA
9141 AGAGTAAAACAGTAATCAGTA
1 AGAGTAAAACAGTAATCAGTA
* * * *
9162 ATAGCAAAGTC-GTAATTAGTA
1 AGAGTAAA-ACAGTAATCAGTA
*
9183 AGAGTAAAATAGTAATCAGTAA
1 AGAGTAAAACAGTAATCAGT-A
9205 AGAGTAAAA
1 AGAGTAAAA
9214 GGTGATCAGT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
21 29 0.73
22 11 0.28
ACGTcount: A:0.52, C:0.07, G:0.19, T:0.22
Consensus pattern (21 bp):
AGAGTAAAACAGTAATCAGTA
Found at i:9225 original size:42 final size:41
Alignment explanation
Indices: 9123--9225 Score: 127
Period size: 42 Copynumber: 2.5 Consensus size: 41
9113 AGTAGTAATC
*
9123 AGTAAAAGGTAATCAGTAAGAGTAAAACAGTAATCAGTAAT
1 AGTAAAAGGTAATCAGTAAGAGTAAAACAGTAATCAGTAAG
* * *
9164 AG-CAAAGTCGTAATTAGTAAGAGTAAAATAGTAATCAGTAAAG
1 AGTAAAAG--GTAATCAGTAAGAGTAAAACAGTAATCAGT-AAG
*
9207 AGTAAAAGGTGATCAGTAA
1 AGTAAAAGGTAATCAGTAA
9226 TTCAAAGAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
40 4 0.08
41 2 0.04
42 37 0.73
43 4 0.08
44 4 0.08
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.22
Consensus pattern (41 bp):
AGTAAAAGGTAATCAGTAAGAGTAAAACAGTAATCAGTAAG
Found at i:10102 original size:12 final size:12
Alignment explanation
Indices: 10085--10113 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
10075 TGCATTGCAT
10085 GAGCTTACACCG
1 GAGCTTACACCG
10097 GAGCTTACACCG
1 GAGCTTACACCG
10109 GAGCT
1 GAGCT
10114 CTAACCCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.31, G:0.28, T:0.17
Consensus pattern (12 bp):
GAGCTTACACCG
Done.