Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006680.1 Corchorus capsularis cultivar CVL-1 contig06701, 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: 10888
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Found at i:2694 original size:22 final size:23
Alignment explanation
Indices: 2666--2831 Score: 85
Period size: 22 Copynumber: 7.9 Consensus size: 23
2656 GAAGAAAGAT
*
2666 GCAATCAGTAAAAG-GTATAATG
1 GCAATCAGTAAAAGAGTAAAATG
2688 GCAATCAGT-AAAGAGTAAAATG
1 GCAATCAGTAAAAGAGTAAAATG
* *
2710 GTAATCAGT-AAAGAGT--AATA
1 GCAATCAGTAAAAGAGTAAAATG
* * *
2730 GAAATCAGTAAGA-AGT--AATA
1 GCAATCAGTAAAAGAGTAAAATG
* *
2750 GTAAACAGTAAAA-AGTAAAA-G
1 GCAATCAGTAAAAGAGTAAAATG
*
2771 GTAATCAGTAAAA-AGTGAAAA-G
1 GCAATCAGTAAAAGAGT-AAAATG
* * *
2793 G-TATC--TGAAAGGGTAAAATG
1 GCAATCAGTAAAAGAGTAAAATG
* *
2813 ACAATTAGT-AAAGAGTAAA
1 GCAATCAGTAAAAGAGTAAA
2832 GAGTAATCAG
Statistics
Matches: 117, Mismatches: 17, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
19 8 0.07
20 34 0.29
21 26 0.22
22 48 0.41
23 1 0.01
ACGTcount: A:0.52, C:0.06, G:0.22, T:0.20
Consensus pattern (23 bp):
GCAATCAGTAAAAGAGTAAAATG
Found at i:2737 original size:20 final size:20
Alignment explanation
Indices: 2690--2782 Score: 82
Period size: 20 Copynumber: 4.5 Consensus size: 20
2680 GTATAATGGC
* *
2690 AATCAGTAAAGAGTAAAATGGT
1 AATCAGTAAAGAGT--AATAGA
2712 AATCAGTAAAGAGTAATAGA
1 AATCAGTAAAGAGTAATAGA
2732 AATCAGT-AAGAAGTAATAGTA
1 AATCAGTAAAG-AGTAATAG-A
* * *
2753 AA-CAGTAAAAAGTAAAAGGT
1 AATCAGTAAAGAGTAATA-GA
2773 AATCAGTAAA
1 AATCAGTAAA
2783 AAGTGAAAAG
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
19 3 0.05
20 31 0.51
21 13 0.21
22 14 0.23
ACGTcount: A:0.55, C:0.05, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCAGTAAAGAGTAATAGA
Found at i:2907 original size:8 final size:8
Alignment explanation
Indices: 2894--2928 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
2884 AATAGTAAGA
2894 GTAAAAAG
1 GTAAAAAG
*
2902 GTAAAATG
1 GTAAAAAG
2910 GTAAAAA-
1 GTAAAAAG
2917 GTAAAAAG
1 GTAAAAAG
2925 GTAA
1 GTAA
2929 TCAGTAAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (8 bp):
GTAAAAAG
Found at i:2920 original size:7 final size:7
Alignment explanation
Indices: 2893--2994 Score: 53
Period size: 8 Copynumber: 13.7 Consensus size: 7
2883 TAATAGTAAG
2893 AGTAAAA
1 AGTAAAA
2900 AGGTAAAA
1 A-GTAAAA
*
2908 TGGTAAAA
1 -AGTAAAA
2916 AGTAAAA
1 AGTAAAA
**
2923 AGGTAATC
1 A-GTAAAA
2931 AGTAAAA
1 AGTAAAA
*
2938 GGTAAAA
1 AGTAAAA
**
2945 TAGTAATT
1 -AGTAAAA
2953 AG-AAAA
1 AGTAAAA
2959 GAGTAAAA
1 -AGTAAAA
* **
2967 TGGTAATC
1 -AGTAAAA
2975 AGTAAAA
1 AGTAAAA
2982 AGTAAAA
1 AGTAAAA
2989 GAGTAA
1 -AGTAA
2995 TCAATCAAGA
Statistics
Matches: 69, Mismatches: 19, Indels: 13
0.68 0.19 0.13
Matches are distributed among these distances:
6 2 0.03
7 33 0.48
8 34 0.49
ACGTcount: A:0.58, C:0.02, G:0.21, T:0.20
Consensus pattern (7 bp):
AGTAAAA
Found at i:2920 original size:15 final size:15
Alignment explanation
Indices: 2894--2994 Score: 66
Period size: 15 Copynumber: 6.7 Consensus size: 15
2884 AATAGTAAGA
2894 GTAAAAAGGTAAAATG
1 GTAAAAA-GTAAAATG
*
2910 GTAAAAAGTAAAAAG
1 GTAAAAAGTAAAATG
**
2925 GTAATCAGTAAAA-G
1 GTAAAAAGTAAAATG
* *
2939 GTAAAATAGT-AATTA
1 GTAAAA-AGTAAAATG
2954 G-AAAAGAGTAAAATG
1 GTAAAA-AGTAAAATG
** *
2969 GTAATCAGTAAAA-A
1 GTAAAAAGTAAAATG
2983 GTAAAAGAGTAA
1 GTAAAA-AGTAA
2995 TCAATCAAGA
Statistics
Matches: 65, Mismatches: 15, Indels: 11
0.71 0.16 0.12
Matches are distributed among these distances:
14 18 0.28
15 38 0.58
16 9 0.14
ACGTcount: A:0.57, C:0.02, G:0.21, T:0.20
Consensus pattern (15 bp):
GTAAAAAGTAAAATG
Found at i:2935 original size:22 final size:22
Alignment explanation
Indices: 2877--2997 Score: 101
Period size: 22 Copynumber: 5.5 Consensus size: 22
2867 AATGATAAAG
*
2877 AAAGAGTAAT-AGT-AAGAGTAA
1 AAAG-GTAATCAGTAAAAAGTAA
*
2898 AAAGGTAAAAT-GGTAAAAAGTAA
1 AAAGGT--AATCAGTAAAAAGTAA
*
2921 AAAGGTAATCAGTAAAAGGTAA
1 AAAGGTAATCAGTAAAAAGTAA
*
2943 AATA-GTAATTAG-AAAAGAGTAA
1 AA-AGGTAATCAGTAAAA-AGTAA
*
2965 AATGGTAATCAGTAAAAAGT-A
1 AAAGGTAATCAGTAAAAAGTAA
2986 AAAGAGTAATCA
1 AAAG-GTAATCA
2998 ATCAAGAAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
20 2 0.02
21 15 0.18
22 47 0.57
23 18 0.22
ACGTcount: A:0.57, C:0.02, G:0.21, T:0.20
Consensus pattern (22 bp):
AAAGGTAATCAGTAAAAAGTAA
Found at i:2964 original size:44 final size:43
Alignment explanation
Indices: 2912--2995 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 43
2902 GTAAAATGGT
* *
2912 AAAAAGTAAAAAGGTAATCAGTAAAAGGTAAAATAGTAATTAG
1 AAAAAGTAAAAAGGTAATCAGTAAAAAGTAAAAGAGTAATTAG
*
2955 AAAAGAGTAAAATGGTAATCAGTAAAAAGTAAAAGAGTAAT
1 AAAA-AGTAAAAAGGTAATCAGTAAAAAGTAAAAGAGTAAT
2996 CAATCAAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
43 4 0.11
44 33 0.89
ACGTcount: A:0.58, C:0.02, G:0.19, T:0.20
Consensus pattern (43 bp):
AAAAAGTAAAAAGGTAATCAGTAAAAAGTAAAAGAGTAATTAG
Found at i:3214 original size:16 final size:16
Alignment explanation
Indices: 3195--3228 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3185 GTAAGAAGGT
*
3195 AATCAGTAAAGAGTAA
1 AATCAGCAAAGAGTAA
3211 AATCAGCAAAGAGTAA
1 AATCAGCAAAGAGTAA
3227 AA
1 AA
3229 AAGTAATCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.59, C:0.09, G:0.18, T:0.15
Consensus pattern (16 bp):
AATCAGCAAAGAGTAA
Found at i:3418 original size:29 final size:28
Alignment explanation
Indices: 3357--3420 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 28
3347 GTGGTAACAA
*
3357 ATAAAAGAAAGTAAGAAAAGAGTAATTG
1 ATAAAAGAAAGTAAGAAAAGAGTAAATG
* *
3385 GTAAAA-AGAGTAAGAAAAGAGTAAAAATG
1 ATAAAAGAAAGTAAGAAAAGAGT--AAATG
3414 ATAAAAG
1 ATAAAAG
3421 TAGCAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 15 0.52
28 5 0.17
29 9 0.31
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.16
Consensus pattern (28 bp):
ATAAAAGAAAGTAAGAAAAGAGTAAATG
Found at i:4995 original size:8 final size:9
Alignment explanation
Indices: 4975--5007 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
4965 AGTTATATCG
*
4975 AAAAATATA
1 AAAAAAATA
4984 AAAAAAATA
1 AAAAAAATA
4993 AAAAAAATA
1 AAAAAAATA
5002 AAAAAA
1 AAAAAA
5008 GTTTCGACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAAATA
Found at i:6546 original size:33 final size:33
Alignment explanation
Indices: 6468--6572 Score: 113
Period size: 33 Copynumber: 3.2 Consensus size: 33
6458 TTGTAAAGAG
* * *
6468 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
* * * * *
6501 CGATTT-GAGTGTTGTTTGCAATGACACTAAATA
1 TGTTTTAG-GTGTTGTTTGCGATGAAACTAAATC
*
6534 TGTTTTAGGTGTTGTTTGTGATGAAACTAAATC
1 TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
6567 TGTTTT
1 TGTTTT
6573 GGATGCTAAT
Statistics
Matches: 57, Mismatches: 13, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
32 1 0.02
33 55 0.96
34 1 0.02
ACGTcount: A:0.25, C:0.10, G:0.22, T:0.44
Consensus pattern (33 bp):
TGTTTTAGGTGTTGTTTGCGATGAAACTAAATC
Found at i:6638 original size:33 final size:33
Alignment explanation
Indices: 6601--6706 Score: 185
Period size: 33 Copynumber: 3.2 Consensus size: 33
6591 AAACATATCA
6601 GTTTTGGTTGATCATAGCATTGCAAATAATTCT
1 GTTTTGGTTGATCATAGCATTGCAAATAATTCT
6634 GTTTTGGTTGATCATAGCATTGCAAATAATTCT
1 GTTTTGGTTGATCATAGCATTGCAAATAATTCT
* * *
6667 ATTTTGGTTGATCATAACATTGAAAATAATTCT
1 GTTTTGGTTGATCATAGCATTGCAAATAATTCT
6700 GTTTTGG
1 GTTTTGG
6707 GTGAAAAGAA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.28, C:0.10, G:0.18, T:0.43
Consensus pattern (33 bp):
GTTTTGGTTGATCATAGCATTGCAAATAATTCT
Found at i:8563 original size:12 final size:13
Alignment explanation
Indices: 8522--8566 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
8512 AATTATTGAT
8522 TGCTTTATTAATC
1 TGCTTTATTAATC
*
8535 TGCTTTATTAATT
1 TGCTTTATTAATC
8548 TGCTTTA-TAATC
1 TGCTTTATTAATC
8560 TGCTTTA
1 TGCTTTA
8567 GATTTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.22, C:0.13, G:0.09, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:8595 original size:5 final size:6
Alignment explanation
Indices: 8563--8594 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
8553 TATAATCTGC
8563 TTTAGA TTTAGA TTTAGA TTTAGA TTT-GA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
8595 GCTTGCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:8951 original size:30 final size:30
Alignment explanation
Indices: 8915--8973 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
8905 CAAGGGGGAG
*
8915 GGAATGATGCGCCCAAGG-CTTATCATGGAA
1 GGAATGATACG-CCAAGGACTTATCATGGAA
8945 GGAATGATACGCCAAGGACTTATCATGGA
1 GGAATGATACGCCAAGGACTTATCATGGA
8974 CTTGAAGACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.20
Consensus pattern (30 bp):
GGAATGATACGCCAAGGACTTATCATGGAA
Found at i:9956 original size:21 final size:21
Alignment explanation
Indices: 9930--9971 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
9920 GCACAAGTGA
*
9930 CCGGCCATGCGACTTGGAGAT
1 CCGGCCACGCGACTTGGAGAT
9951 CCGGCCACGCGACTTGGAGAT
1 CCGGCCACGCGACTTGGAGAT
9972 GCCCGCGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.31, G:0.33, T:0.17
Consensus pattern (21 bp):
CCGGCCACGCGACTTGGAGAT
Found at i:9996 original size:33 final size:33
Alignment explanation
Indices: 9951--10046 Score: 113
Period size: 33 Copynumber: 2.9 Consensus size: 33
9941 ACTTGGAGAT
* *
9951 CCGGCCACGCGACTTGGAGATGCCC-GCGCAACA
1 CCGGCCACGCGACATCGAGATGCCCGGC-CAACA
* *
9984 CCGGCCATGCGACATCGAGATGCCCGGCCATCA
1 CCGGCCACGCGACATCGAGATGCCCGGCCAACA
* **
10017 CCGGCCACGCGACATGGCCATGCCCGGCCA
1 CCGGCCACGCGACATCGAGATGCCCGGCCA
10047 CATGACTCGG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
33 52 0.96
34 2 0.04
ACGTcount: A:0.20, C:0.42, G:0.29, T:0.09
Consensus pattern (33 bp):
CCGGCCACGCGACATCGAGATGCCCGGCCAACA
Done.