Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013014.1 Corchorus capsularis cultivar CVL-1 contig13035, 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: 24473
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Found at i:833 original size:6 final size:6
Alignment explanation
Indices: 817--853 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
807 CTAAGCAAAG
817 TAAAT- TAAATC TAAATC TAAATC TAAATC TAAATC TA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC TA
854 TAGCAATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATC
Found at i:2626 original size:30 final size:30
Alignment explanation
Indices: 2591--2653 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
2581 CAAAAAGTGA
*
2591 AAAAAGCAATCAGTAATTAAGTTCAATAAG
1 AAAAAGCAATCAGTAATCAAGTTCAATAAG
* *
2621 AAAAAGTAATCAGTGATCAAGTTCAATAAG
1 AAAAAGCAATCAGTAATCAAGTTCAATAAG
2651 AAA
1 AAA
2654 GATATAAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.54, C:0.10, G:0.14, T:0.22
Consensus pattern (30 bp):
AAAAAGCAATCAGTAATCAAGTTCAATAAG
Found at i:2734 original size:22 final size:21
Alignment explanation
Indices: 2706--2767 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
2696 TCTGTTAAGG
* *
2706 GTAAAATGTTAATTAGTAAAGA
1 GTAAAATGGTAATCAGTAAA-A
2728 GTAAAATGGTAATCAGTAAAA
1 GTAAAATGGTAATCAGTAAAA
*
2749 GTAAAAGGGTAATCAGTAA
1 GTAAAATGGTAATCAGTAA
2768 TCAGGTTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
21 19 0.51
22 18 0.49
ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26
Consensus pattern (21 bp):
GTAAAATGGTAATCAGTAAAA
Found at i:2753 original size:21 final size:22
Alignment explanation
Indices: 2679--2767 Score: 94
Period size: 22 Copynumber: 4.2 Consensus size: 22
2669 ATGTAAAAAG
* *
2679 GTAAAAAGTAAAA-GGT-ATCT
1 GTAAAGAGTAAAATGGTAATCA
* * * *
2699 GTTAAGGGTAAAATGTTAATTA
1 GTAAAGAGTAAAATGGTAATCA
2721 GTAAAGAGTAAAATGGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
*
2743 GTAAA-AGTAAAAGGGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
2764 GTAA
1 GTAA
2768 TCAGGTTCAA
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 10 0.18
21 21 0.38
22 25 0.45
ACGTcount: A:0.48, C:0.03, G:0.22, T:0.26
Consensus pattern (22 bp):
GTAAAGAGTAAAATGGTAATCA
Found at i:2859 original size:22 final size:21
Alignment explanation
Indices: 2813--2934 Score: 103
Period size: 22 Copynumber: 6.0 Consensus size: 21
2803 AACAGCAAAA
*
2813 AGTAAAA-GGT-ATCTGTTAAG
1 AGTAAAATGGTAATCAG-TAAG
* *
2833 GGTAAAATGGTAATTAGTAAAG
1 AGTAAAATGGTAATCAGT-AAG
2855 AGTAAAATGGTAATCAGTAAG
1 AGTAAAATGGTAATCAGTAAG
* *
2876 AGTAAAATAGTAATCAAT-A-
1 AGTAAAATGGTAATCAGTAAG
**
2895 A--AAAATAATAATCAGTAAAG
1 AGTAAAATGGTAATCAGT-AAG
*
2915 AGTAAAATGGTAGTCAGTAA
1 AGTAAAATGGTAATCAGTAA
2935 TTAAATTCAA
Statistics
Matches: 82, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
17 13 0.16
19 2 0.02
20 8 0.10
21 25 0.30
22 34 0.41
ACGTcount: A:0.50, C:0.04, G:0.20, T:0.25
Consensus pattern (21 bp):
AGTAAAATGGTAATCAGTAAG
Found at i:2901 original size:17 final size:17
Alignment explanation
Indices: 2879--2913 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2869 CAGTAAGAGT
*
2879 AAAATAGTAATCAATAA
1 AAAATAATAATCAATAA
*
2896 AAAATAATAATCAGTAA
1 AAAATAATAATCAATAA
2913 A
1 A
2914 GAGTAAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (17 bp):
AAAATAATAATCAATAA
Found at i:3007 original size:9 final size:9
Alignment explanation
Indices: 2981--3048 Score: 50
Period size: 10 Copynumber: 7.2 Consensus size: 9
2971 GAAAAAGAAG
2981 AAGAGTAAA
1 AAGAGTAAA
*
2990 AAGTGGTAAA
1 AAG-AGTAAA
3000 AAGAGTAAGAA
1 AAGAGT-A-AA
3011 AAGAGT--A
1 AAGAGTAAA
**
3018 ATCAGTAAA
1 AAGAGTAAA
3027 AAGAGTAAGA
1 AAGAGTAA-A
3037 AATGAGTAAA
1 AA-GAGTAAA
3047 AA
1 AA
3049 AAACGGTGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
7 5 0.11
9 12 0.26
10 15 0.33
11 14 0.30
ACGTcount: A:0.60, C:0.01, G:0.24, T:0.15
Consensus pattern (9 bp):
AAGAGTAAA
Found at i:3120 original size:27 final size:25
Alignment explanation
Indices: 3090--3318 Score: 125
Period size: 27 Copynumber: 8.7 Consensus size: 25
3080 AATTAGAAAT
3090 AAAGAGTAAGAAATGGTGATCAGTAAA
1 AAAGAGTAA-AAATGGT-ATCAGTAAA
3117 AAAGAGTAAAAAGTGGTATTCAGTAAA
1 AAAGAGTAAAAA-TGGTA-TCAGTAAA
* *
3144 AAGGGGT-AAAA----AT-AGTAAA
1 AAAGAGTAAAAATGGTATCAGTAAA
* *
3163 AAGGAGTAAAAATGGTATTAAGTAAA
1 AAAGAGTAAAAATGGTA-TCAGTAAA
*
3189 ACAGGAGAGTAAAAAAATGGTAATTAAGT-AA
1 A-A--AGAGT--AAAAATGGT-A-TCAGTAAA
3220 AAAGAGTAAAAAGTGGTATTCAGTAAA
1 AAAGAGTAAAAA-TGGTA-TCAGTAAA
** *
3247 GGCAGTAAG-AAAAAGGGTCATCAGTAAA
1 -AAAG--AGTAAAAATGGT-ATCAGTAAA
*
3275 AAAGAGTAAAATATGGTAATCAGT-AC
1 AAAGAGTAAAA-ATGGT-ATCAGTAAA
3301 AAAGAGTAAAAAATGGTA
1 AAAGAGT-AAAAATGGTA
3319 ACTAGTAATC
Statistics
Matches: 165, Mismatches: 13, Indels: 50
0.72 0.06 0.22
Matches are distributed among these distances:
19 12 0.07
20 5 0.03
21 1 0.01
24 1 0.01
25 4 0.02
26 43 0.26
27 49 0.30
28 18 0.11
29 10 0.06
30 3 0.02
31 12 0.07
32 7 0.04
ACGTcount: A:0.53, C:0.04, G:0.24, T:0.20
Consensus pattern (25 bp):
AAAGAGTAAAAATGGTATCAGTAAA
Found at i:3162 original size:19 final size:19
Alignment explanation
Indices: 3138--3175 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3128 AGTGGTATTC
*
3138 AGTAAAAAGGGGTAAAAAT
1 AGTAAAAAGGAGTAAAAAT
3157 AGTAAAAAGGAGTAAAAAT
1 AGTAAAAAGGAGTAAAAAT
3176 GGTATTAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.24, T:0.16
Consensus pattern (19 bp):
AGTAAAAAGGAGTAAAAAT
Found at i:3180 original size:45 final size:49
Alignment explanation
Indices: 3111--3203 Score: 140
Period size: 46 Copynumber: 2.0 Consensus size: 49
3101 AATGGTGATC
*
3111 AGTAAAAAAGAGTAAAAAGTGGTATTCAGTAAAA-AGG-G-GTAAAAAT
1 AGTAAAAAAGAGTAAAAAGTGGTATTAAGTAAAACAGGAGAGTAAAAAT
*
3157 AGTAAAAAGGAGTAAAAA-TGGTATTAAGTAAAACAGGAGAGTAAAAA
1 AGTAAAAAAGAGTAAAAAGTGGTATTAAGTAAAACAGGAGAGTAAAAA
3204 AATGGTAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
45 14 0.33
46 20 0.48
47 1 0.02
48 7 0.17
ACGTcount: A:0.56, C:0.02, G:0.24, T:0.18
Consensus pattern (49 bp):
AGTAAAAAAGAGTAAAAAGTGGTATTAAGTAAAACAGGAGAGTAAAAAT
Found at i:3281 original size:55 final size:56
Alignment explanation
Indices: 3157--3299 Score: 150
Period size: 55 Copynumber: 2.5 Consensus size: 56
3147 GGGTAAAAAT
* * * *
3157 AGTAAAAAGGAGTAAAAATGGTATTAAGTAAAACAGGAGAGTAAAAAAATGGTAATTA
1 AGTAAAAAAGAGTAAAAATGGTATTCAGT--AACAGGACAGTAAAAAAAGGGTAATTA
* *
3215 AGT-AAAAAGAGTAAAAAGTGGTATTCAGTAA-AGG-CAGTAAGAAAAAGGGTCA-TC
1 AGTAAAAAAGAGTAAAAA-TGGTATTCAGTAACAGGACAGTAA-AAAAAGGGTAATTA
*
3269 AGTAAAAAAGAGTAAAATATGGTAATCAGTA
1 AGTAAAAAAGAGTAAAA-ATGGTATTCAGTA
3300 CAAAGAGTAA
Statistics
Matches: 74, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
54 9 0.12
55 36 0.49
56 3 0.04
57 13 0.18
58 13 0.18
ACGTcount: A:0.52, C:0.04, G:0.23, T:0.20
Consensus pattern (56 bp):
AGTAAAAAAGAGTAAAAATGGTATTCAGTAACAGGACAGTAAAAAAAGGGTAATTA
Found at i:3304 original size:26 final size:26
Alignment explanation
Indices: 3157--3319 Score: 123
Period size: 26 Copynumber: 5.9 Consensus size: 26
3147 GGGTAAAAAT
* *
3157 AGTAAAAAGGAGT-AAAAATGGTATTA
1 AGTAAAAA-GAGTAAAAAATGGTAATC
*
3183 AGTAAAACAGGAGAGTAAAAAAATGGTAATTA
1 AGT-AAA-A--AGAGT-AAAAAATGGTAA-TC
* *
3215 AGTAAAAAGAGTAAAAAGTGGTATTC
1 AGTAAAAAGAGTAAAAAATGGTAATC
* * *
3241 AGT-AAAGGCAGTAAGAAAAAGGGTCATC
1 AGTAAAAAG-AGT-A-AAAAATGGTAATC
*
3269 AGTAAAAAAGAGTAAAATATGGTAATC
1 AGT-AAAAAGAGTAAAAAATGGTAATC
*
3296 AGTACAAAGAGTAAAAAATGGTAA
1 AGTAAAAAGAGTAAAAAATGGTAA
3320 CTAGTAATCA
Statistics
Matches: 110, Mismatches: 15, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
25 4 0.04
26 29 0.26
27 27 0.25
28 19 0.17
29 7 0.06
30 6 0.05
31 13 0.12
32 5 0.05
ACGTcount: A:0.53, C:0.04, G:0.23, T:0.20
Consensus pattern (26 bp):
AGTAAAAAGAGTAAAAAATGGTAATC
Found at i:11984 original size:22 final size:22
Alignment explanation
Indices: 11956--12189 Score: 119
Period size: 22 Copynumber: 10.7 Consensus size: 22
11946 TTCTGCTCAT
11956 TTTTTACTGATTACTCTTTTAC
1 TTTTTACTGATTACTCTTTTAC
* *
11978 TTTTTACTGATTGC-CTTTTGC
1 TTTTTACTGATTACTCTTTTAC
*
11999 TTTTTACTGATTTC-CTTTTTA-
1 TTTTTACTGATTACTC-TTTTAC
* * *
12020 TTTCTTGCTGATTAGCTTTTTTTGC
1 TTT-TTACTGATTA-C-TCTTTTAC
* *
12045 TCTTTACTGATCA-TCTTTTTAC
1 TTTTTACTGATTACTC-TTTTAC
* *
12067 -TCTTACTGATT-TTCCTTTTAC
1 TTTTTACTGATTACT-CTTTTAC
* * *
12088 TTCTTACTTATTACTTTTTTTAC
1 TTTTTACTGATTAC-TCTTTTAC
** * *
12111 -TCATACTAATTACTATTTTAC
1 TTTTTACTGATTACTCTTTTAC
** * *
12132 TTTTTACTGCCTATTATTTTAC
1 TTTTTACTGATTACTCTTTTAC
*
12154 TCTTGT--TGATTAC-CTTCTTAC
1 T-TTTTACTGATTACTCTT-TTAC
12175 TTTTTACTGATTACT
1 TTTTTACTGATTACT
12190 AATTACCATT
Statistics
Matches: 160, Mismatches: 34, Indels: 35
0.70 0.15 0.15
Matches are distributed among these distances:
20 5 0.03
21 55 0.34
22 75 0.47
23 10 0.06
24 13 0.08
25 2 0.01
ACGTcount: A:0.17, C:0.19, G:0.06, T:0.58
Consensus pattern (22 bp):
TTTTTACTGATTACTCTTTTAC
Found at i:12533 original size:29 final size:29
Alignment explanation
Indices: 12501--12588 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 29
12491 TACTGATTAC
12501 TACTACTTTGACTCTGATTAATCTCTTTT
1 TACTACTTTGACTCTGATTAATCTCTTTT
* * * *
12530 TACTTA-ATT-AC-C-GATTTA-CTGATTTC
1 TAC-TACTTTGACTCTGATTAATCT-CTTTT
*
12556 TATTACTTTGACTCTGATTAATCTCTTTT
1 TACTACTTTGACTCTGATTAATCTCTTTT
12585 TACT
1 TACT
12589 TAATTACTGC
Statistics
Matches: 42, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
25 4 0.10
26 12 0.29
27 3 0.07
28 3 0.07
29 16 0.38
30 4 0.10
ACGTcount: A:0.23, C:0.19, G:0.07, T:0.51
Consensus pattern (29 bp):
TACTACTTTGACTCTGATTAATCTCTTTT
Found at i:12549 original size:48 final size:48
Alignment explanation
Indices: 12490--12649 Score: 196
Period size: 48 Copynumber: 3.2 Consensus size: 48
12480 AATTACTGAT
12490 TTACTGA-TTACTACTACTTTGACTCTGATTAATCTCTTTTTACTTAA
1 TTACTGATTTACTACTACTTTGACTCTGATTAATCTCTTTTTACTTAA
*
12537 TTACCGATTTACTGATTTCTATTACTTTGACTCTGATTAATCTCTTTTTACTTAA
1 TTACTGATTTACT-A---C---TACTTTGACTCTGATTAATCTCTTTTTACTTAA
* * * * *
12592 TTACTGCTTTACTATTACCTTAACTCTGATTAATCTCTTCTTACTTAA
1 TTACTGATTTACTACTACTTTGACTCTGATTAATCTCTTTTTACTTAA
12640 TTACTGATTT
1 TTACTGATTT
12650 GCCCTTGATG
Statistics
Matches: 97, Mismatches: 8, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
47 6 0.06
48 44 0.45
49 1 0.01
52 1 0.01
54 1 0.01
55 44 0.45
ACGTcount: A:0.24, C:0.19, G:0.06, T:0.50
Consensus pattern (48 bp):
TTACTGATTTACTACTACTTTGACTCTGATTAATCTCTTTTTACTTAA
Found at i:12563 original size:55 final size:55
Alignment explanation
Indices: 12421--12649 Score: 292
Period size: 55 Copynumber: 4.3 Consensus size: 55
12411 CATTTTAACT
* * *
12421 CTTAATTATCGATTTACTAATTACTATTACCTTGACTCTGATTAATCTTTTTTTTA
1 CTTAATTACCGATTTACTGATTACTATTACCTTGACTCTGATTAATC-TCTTTTTA
* * *
12477 CTTAATTACTGATTTACTGATTACTACTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACCGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
* *
12532 CTTAATTACCGATTTACTGATTTCTATTACTTTGACTCTGATTAATCTCTTTTTA
1 CTTAATTACCGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
* * *
12587 CTTAATTA-C----TGCT--TTACTATTACCTTAACTCTGATTAATCTCTTCTTA
1 CTTAATTACCGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
*
12635 CTTAATTACTGATTT
1 CTTAATTACCGATTT
12650 GCCCTTGATG
Statistics
Matches: 153, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
48 39 0.25
50 3 0.02
53 1 0.01
54 1 0.01
55 67 0.44
56 42 0.27
ACGTcount: A:0.25, C:0.18, G:0.06, T:0.50
Consensus pattern (55 bp):
CTTAATTACCGATTTACTGATTACTATTACCTTGACTCTGATTAATCTCTTTTTA
Found at i:14874 original size:3 final size:3
Alignment explanation
Indices: 14866--14890 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
14856 TGTAAATTCC
14866 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
14891 TATTTTGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:15041 original size:24 final size:24
Alignment explanation
Indices: 15013--15059 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
15003 TACTAATGCT
*
15013 AAATTACTAATTAAAAATATTCTA
1 AAATTACTAATTAAAAACATTCTA
15037 AAATTACTAATTAAAAACATTCT
1 AAATTACTAATTAAAAACATTCT
15060 TGTGTTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (24 bp):
AAATTACTAATTAAAAACATTCTA
Found at i:19814 original size:30 final size:31
Alignment explanation
Indices: 19780--19840 Score: 115
Period size: 30 Copynumber: 2.0 Consensus size: 31
19770 ATTCCTCTAT
19780 TCCCTTTTATTTATCTTTATGTT-GGCCCAA
1 TCCCTTTTATTTATCTTTATGTTAGGCCCAA
19810 TCCCTTTTATTTATCTTTATGTTAGGCCCAA
1 TCCCTTTTATTTATCTTTATGTTAGGCCCAA
19841 GATTGTTTCC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.18, C:0.23, G:0.10, T:0.49
Consensus pattern (31 bp):
TCCCTTTTATTTATCTTTATGTTAGGCCCAA
Done.