Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007847.1 Corchorus capsularis cultivar CVL-1 contig07868, 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: 66059
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:562 original size:28 final size:28
Alignment explanation
Indices: 530--591 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
520 AACACCGCAT
*
530 CCTTTTTTCATTTTGTTATTCATCG-CC
1 CCTTTTTCCATTTTGTTATTCATCGTCC
557 CTCTTTTTCCATTTTGTTATTCATCGTCC
1 C-CTTTTTCCATTTTGTTATTCATCGTCC
586 CCTTTT
1 CCTTTT
592 GTTCCAAGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 1 0.03
28 28 0.88
29 3 0.09
ACGTcount: A:0.10, C:0.27, G:0.06, T:0.56
Consensus pattern (28 bp):
CCTTTTTCCATTTTGTTATTCATCGTCC
Found at i:893 original size:22 final size:20
Alignment explanation
Indices: 846--887 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
836 AAATGAAGGA
846 AAATGAGTTTGAAGATTTGTT
1 AAATGAGTTTGAAGA-TTGTT
867 AAATGAAGTTTGAAG-TTGTT
1 AAATG-AGTTTGAAGATTGTT
887 A
1 A
888 GAAATGGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (20 bp):
AAATGAGTTTGAAGATTGTT
Found at i:898 original size:22 final size:21
Alignment explanation
Indices: 846--899 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
836 AAATGAAGGA
846 AAAT-GAGTTTGAAGATTTGTT
1 AAATGGAGTTTGAAGA-TTGTT
*
867 AAATGAAGTTTGAAG-TTGTT
1 AAATGGAGTTTGAAGATTGTT
887 AGAAATGGAGTTT
1 --AAATGGAGTTT
900 AGGGTTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 5 0.18
21 4 0.14
22 19 0.68
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (21 bp):
AAATGGAGTTTGAAGATTGTT
Found at i:995 original size:20 final size:21
Alignment explanation
Indices: 969--1013 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
959 ACAAAAGTGT
*
969 AAAAAGGGGACGATATTTAGC
1 AAAAGGGGGACGATATTTAGC
*
990 AAAAGGGGGGGCGATATTTAGC
1 AAAA-GGGGGACGATATTTAGC
1012 AA
1 AA
1014 TTCAGTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.40, C:0.09, G:0.33, T:0.18
Consensus pattern (21 bp):
AAAAGGGGGACGATATTTAGC
Found at i:8855 original size:5 final size:5
Alignment explanation
Indices: 8845--8875 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
8835 AATGGCAGCC
8845 CCTAG CCTAG CCTAG CCTAG CCTAG CCTAG C
1 CCTAG CCTAG CCTAG CCTAG CCTAG CCTAG C
8876 GCCTAGCCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.19, C:0.42, G:0.19, T:0.19
Consensus pattern (5 bp):
CCTAG
Found at i:12913 original size:157 final size:154
Alignment explanation
Indices: 12546--12916 Score: 405
Period size: 157 Copynumber: 2.4 Consensus size: 154
12536 TCATCTCAAA
* * * **
12546 TAGACTTAGCATGAAAAACTTATGCTAGTTTTTCAATTAAGGATAGTTTGAGGAGTCAAACCACT
1 TAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGATAGTTTGAGGTGAGAAACCACT
* * * * *
12611 TCTCTATGCTAGATAGTTCAGTTTTACTTAGAATTTTTTCCATAGCTTTATGGTGATAATCTAAG
66 TCACCATGCAAGAGAGCTCAGTTTTACTTAGAATTTTTTCCATAGCTTTATGGTGATAATCTAAG
*
12676 TGTACTGGTGGAAAATCAGCTTCGT
131 TGTACT-GTGGAAAATCAGCTTCAT
* * * * ***
12701 TGGACTTAGTATGGAAAACTTATGCTAGTTTTTCATTTAAGGACAACCT-AGGGTGAGAAACCTA
1 TAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGATAGTTTGA-GGTGAGAAACC-A
* *
12765 GTTCACCAT-CAAGGAGAGCTCAGTTTTACTTAGAATTTTTTTCCATAG-TCTTAT-GTGGATAT
64 CTTCACCATGCAA-GAGAGCTCAGTTTTACTTAGAA-TTTTTTCCATAGCT-TTATGGT-GATAA
*
12827 TCTAAGT-TCCT-TGGCAAAATTTCAGC-TCAT
125 TCTAAGTGTACTGTGG-AAAA--TCAGCTTCAT
12857 TCAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGATAGTTTGAGGTGAGAA
1 T-AGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGATAGTTTGAGGTGAGAA
12917 GCTCGGTTTA
Statistics
Matches: 178, Mismatches: 27, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
154 4 0.02
155 55 0.31
156 37 0.21
157 81 0.46
158 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.36
Consensus pattern (154 bp):
TAGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGATAGTTTGAGGTGAGAAACCACT
TCACCATGCAAGAGAGCTCAGTTTTACTTAGAATTTTTTCCATAGCTTTATGGTGATAATCTAAG
TGTACTGTGGAAAATCAGCTTCAT
Found at i:13465 original size:21 final size:21
Alignment explanation
Indices: 13435--13489 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 21
13425 AGAGTTCGCT
13435 TTCCTCAGCAAGTAAAACGCC
1 TTCCTCAGCAAGTAAAACGCC
* *
13456 TTCTTCAGCAAGT-AAATGCC
1 TTCCTCAGCAAGTAAAACGCC
13476 TTCCTCAGCAAGTA
1 TTCCTCAGCAAGTA
13490 GAAGCCCGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (21 bp):
TTCCTCAGCAAGTAAAACGCC
Found at i:14701 original size:2 final size:2
Alignment explanation
Indices: 14694--14719 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14684 TTAGTTCACC
14694 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
14720 TTTTGTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18626 original size:9 final size:9
Alignment explanation
Indices: 18601--18639 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
18591 AGGAAAGGGA
*
18601 AAGAAACAG
1 AAGAAAAAG
18610 AGAGAAAAAG
1 A-AGAAAAAG
18620 AAGAAAAAG
1 AAGAAAAAG
*
18629 AAGGAAAAG
1 AAGAAAAAG
18638 AA
1 AA
18640 ACAGAAAGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.72, C:0.03, G:0.26, T:0.00
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:19793 original size:54 final size:53
Alignment explanation
Indices: 19730--19884 Score: 201
Period size: 54 Copynumber: 3.0 Consensus size: 53
19720 AAGCTGTTAC
* *
19730 ATGAAGACTTGATTGGAGTGACGTGGTCTAGGGCCGTTATTGTTAGTTAAAACA
1 ATGAAGACTTGATTGG-GTGACGTGGCCTAGGGACGTTATTGTTAGTTAAAACA
* *
19784 ATGAAGACTTGATTGGGGTGACGTGGCCTATGGACGTTATTGTTAGTTAAAACG
1 ATGAAGACTTGATT-GGGTGACGTGGCCTAGGGACGTTATTGTTAGTTAAAACA
** *
19838 ATGAAGA-TTGA---GGTGACAAGGCCTAGGGTCGTTATTGTTAGTTAAAA
1 ATGAAGACTTGATTGGGTGACGTGGCCTAGGGACGTTATTGTTAGTTAAAA
19885 TGGTTTTTAG
Statistics
Matches: 92, Mismatches: 8, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
49 32 0.35
53 4 0.04
54 54 0.59
55 2 0.02
ACGTcount: A:0.28, C:0.10, G:0.30, T:0.31
Consensus pattern (53 bp):
ATGAAGACTTGATTGGGTGACGTGGCCTAGGGACGTTATTGTTAGTTAAAACA
Found at i:29169 original size:25 final size:25
Alignment explanation
Indices: 29121--29170 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
29111 ATTAAACCTT
29121 ATAATTTCTAAAATCTTAGCATTTA
1 ATAATTTCTAAAATCTTAGCATTTA
*
29146 ATAATATTCTAAAATC-TAGGATTTA
1 ATAAT-TTCTAAAATCTTAGCATTTA
29171 CCTTCATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (25 bp):
ATAATTTCTAAAATCTTAGCATTTA
Found at i:38931 original size:28 final size:28
Alignment explanation
Indices: 38891--38947 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
38881 AGTTTTCCCT
38891 TGATTTGGGAAACTCAATTCCGAATTAA
1 TGATTTGGGAAACTCAATTCCGAATTAA
38919 TGATTTGGGAAACTCAATTCCGAATTAA
1 TGATTTGGGAAACTCAATTCCGAATTAA
38947 T
1 T
38948 TGAAATTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (28 bp):
TGATTTGGGAAACTCAATTCCGAATTAA
Found at i:42705 original size:12 final size:12
Alignment explanation
Indices: 42688--42715 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
42678 ACATGTTTAT
42688 ACGACACGAAAC
1 ACGACACGAAAC
42700 ACGACACGAAAC
1 ACGACACGAAAC
42712 ACGA
1 ACGA
42716 AATGTCAGGT
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:0.32, G:0.18, T:0.00
Consensus pattern (12 bp):
ACGACACGAAAC
Found at i:46525 original size:32 final size:32
Alignment explanation
Indices: 46484--46547 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
46474 ATTTCCATAA
*
46484 GAGTCCTATGTAAATAATCAATTGATCTCTCG
1 GAGTCCTATGGAAATAATCAATTGATCTCTCG
*
46516 GAGTCCTATGGAAATGATCAATTGATCTCTCG
1 GAGTCCTATGGAAATAATCAATTGATCTCTCG
46548 ATTTACATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (32 bp):
GAGTCCTATGGAAATAATCAATTGATCTCTCG
Found at i:47711 original size:105 final size:104
Alignment explanation
Indices: 47498--47733 Score: 346
Period size: 105 Copynumber: 2.3 Consensus size: 104
47488 TTGAAACATG
* * * *
47498 AAACTTAAGTATTCATCGATTAATACTGGCTCCGGGTTCGCTGTCAACACCGCCACTTTTCCAAA
1 AAACTGAAGTTTTCATCGACTAATACTGCCTCCGGGTTCGCTGTCAACACCGCCACTTTTCCAAA
*
47563 GTGAAGACTTGGAGCTTTAGTCGATTAATACTGAAATTA
66 GAGAAGACTTGGAGCTTTAGTCGATTAATACTGAAATTA
* * * **
47602 AAACTGGAGTTTTCATCAACTAATACTGCCTCCGGGTTCGCTGTCAACACTGCCACATTTTTGAA
1 AAACTGAAGTTTTCATCGACTAATACTGCCTCCGGGTTCGCTGTCAACACCGCCAC-TTTTCCAA
* *
47667 AGAGAAGACTTGGAGTTTTAGTCGATTAATACTGGAATTA
65 AGAGAAGACTTGGAGCTTTAGTCGATTAATACTGAAATTA
*
47707 AAACTGAAGTTTTCATGGACTAATACT
1 AAACTGAAGTTTTCATCGACTAATACT
47734 TTTCTGACAA
Statistics
Matches: 116, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
104 49 0.42
105 67 0.58
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (104 bp):
AAACTGAAGTTTTCATCGACTAATACTGCCTCCGGGTTCGCTGTCAACACCGCCACTTTTCCAAA
GAGAAGACTTGGAGCTTTAGTCGATTAATACTGAAATTA
Found at i:50489 original size:12 final size:13
Alignment explanation
Indices: 50472--50497 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50462 TGACCATTAG
50472 TTTTTTGGCAATT
1 TTTTTTGGCAATT
50485 TTTTTTGGCAATT
1 TTTTTTGGCAATT
50498 CAATTTTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.15, T:0.62
Consensus pattern (13 bp):
TTTTTTGGCAATT
Found at i:53783 original size:20 final size:20
Alignment explanation
Indices: 53749--53813 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
53739 ATTCAAACTG
53749 CTTCAATAAGTCTTAATAACC
1 CTTC-ATAAGTCTTAATAACC
* *
53770 CTTCATAAGACTTAATAAGC
1 CTTCATAAGTCTTAATAACC
* *
53790 CTTTATAAGTGTTAATAACC
1 CTTCATAAGTCTTAATAACC
53810 CTTC
1 CTTC
53814 CAAAATTTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
20 33 0.89
21 4 0.11
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (20 bp):
CTTCATAAGTCTTAATAACC
Found at i:57716 original size:19 final size:18
Alignment explanation
Indices: 57692--57751 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 18
57682 ATGCCACGTC
*
57692 ATATTTTTTTATTAAAAAA
1 ATATTTTTTTA-AAAAAAA
57711 ATATTTTTTTAAAAAAAA
1 ATATTTTTTTAAAAAAAA
*
57729 ATTATAATTTTTTAAAAAGAA
1 A-TAT--TTTTTTAAAAAAAA
57750 AT
1 AT
57752 TTGGTGAGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
18 7 0.19
19 14 0.39
20 1 0.03
21 14 0.39
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATATTTTTTTAAAAAAAA
Found at i:57729 original size:21 final size:21
Alignment explanation
Indices: 57705--57746 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
57695 TTTTTTTATT
*
57705 AAAAAAATATTTTTTTAAAAA
1 AAAAAAATAATTTTTTAAAAA
**
57726 AAAATTATAATTTTTTAAAAA
1 AAAAAAATAATTTTTTAAAAA
57747 GAAATTTGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAAAAATAATTTTTTAAAAA
Found at i:58498 original size:18 final size:20
Alignment explanation
Indices: 58476--58522 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 20
58466 TTTTTTTTAG
58476 AAAAAATATGTATTTTT-TT
1 AAAAAATATGTATTTTTATT
* *
58495 -AAAAGTAT-TTTTTTTATT
1 AAAAAATATGTATTTTTATT
58513 AAAAAATATG
1 AAAAAATATG
58523 ACGTGCAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 5
0.73 0.10 0.17
Matches are distributed among these distances:
17 6 0.27
18 9 0.41
19 7 0.32
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (20 bp):
AAAAAATATGTATTTTTATT
Found at i:59767 original size:45 final size:45
Alignment explanation
Indices: 59701--59790 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
59691 AACAAATTTA
*
59701 TCACTGTAATTCTAATTTTAGCTGGTTCAATGTTTGGTTTTGGTT
1 TCACTGTAATTCTAATCTTAGCTGGTTCAATGTTTGGTTTTGGTT
**
59746 TCACTGTAATTCTAATCTTAGCTGGTTTGATGTTTGGTTTTGGTT
1 TCACTGTAATTCTAATCTTAGCTGGTTCAATGTTTGGTTTTGGTT
59791 GATTAATCAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.17, C:0.11, G:0.21, T:0.51
Consensus pattern (45 bp):
TCACTGTAATTCTAATCTTAGCTGGTTCAATGTTTGGTTTTGGTT
Found at i:60243 original size:31 final size:31
Alignment explanation
Indices: 60205--60263 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
60195 TTTGGCGCAT
* * *
60205 TTGAAAGGTTTGGTCCTTATCTGGGCAAAAC
1 TTGAAAGGTTGGGCCCTGATCTGGGCAAAAC
*
60236 TTGAAAGGTTGGGCCCTGATTTGGGCAA
1 TTGAAAGGTTGGGCCCTGATCTGGGCAA
60264 TTAGCCTATC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.31
Consensus pattern (31 bp):
TTGAAAGGTTGGGCCCTGATCTGGGCAAAAC
Found at i:64104 original size:5 final size:5
Alignment explanation
Indices: 64098--64139 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
64088 AAAAAAAAAG
* *
64098 AAGAG AAGAG AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AA
64140 AGGTGGTGCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:65037 original size:35 final size:34
Alignment explanation
Indices: 64991--65060 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 34
64981 CAAGACATGA
*
64991 AATTAAAAGGGGAAAAACCTCTGGTAATCAAAATT
1 AATTAAAAGGGGAAAAA-CTCTGGTAACCAAAATT
* * *
65026 AATTAACAGGGGAAAAAGTCTGTTAACCAAAATT
1 AATTAAAAGGGGAAAAACTCTGGTAACCAAAATT
65060 A
1 A
65061 CAAGTTCACT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 15 0.48
35 16 0.52
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.23
Consensus pattern (34 bp):
AATTAAAAGGGGAAAAACTCTGGTAACCAAAATT
Done.