Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010911.1 Corchorus capsularis cultivar CVL-1 contig10932, 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: 26574
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:510 original size:19 final size:18
Alignment explanation
Indices: 471--514 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
461 ATTTTCCTAA
*
471 TTTCCTTTTTCCTTTTCC
1 TTTCTTTTTTCCTTTTCC
489 TTTTCTTTTTTCC-TTTCTC
1 -TTTCTTTTTTCCTTTTC-C
508 TTTCTTT
1 TTTCTTT
515 GGATTGGGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTCTTTTTTCCTTTTCC
Found at i:625 original size:12 final size:12
Alignment explanation
Indices: 604--635 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
594 ATGCGCAGGC
*
604 CCGCGTGCTGGG
1 CCGCGCGCTGGG
616 CCGCGCGCTGGG
1 CCGCGCGCTGGG
628 CCGCGCGC
1 CCGCGCGC
636 AGGCCGGCCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.44, G:0.47, T:0.09
Consensus pattern (12 bp):
CCGCGCGCTGGG
Found at i:1671 original size:18 final size:18
Alignment explanation
Indices: 1648--1685 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1638 GAACCTAATG
1648 TAATTAAAACTCTATATA
1 TAATTAAAACTCTATATA
1666 TAATTAAAACTCTATATA
1 TAATTAAAACTCTATATA
1684 TA
1 TA
1686 CTGCTGCTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (18 bp):
TAATTAAAACTCTATATA
Found at i:2852 original size:7 final size:7
Alignment explanation
Indices: 2840--2866 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2830 AGGATGTGTC
2840 TTGTCAA
1 TTGTCAA
2847 TTGTCAA
1 TTGTCAA
2854 TTGTCAA
1 TTGTCAA
2861 TTGTCA
1 TTGTCA
2867 TTATTATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (7 bp):
TTGTCAA
Found at i:2886 original size:18 final size:18
Alignment explanation
Indices: 2863--2898 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2853 ATTGTCAATT
2863 GTCATTATTATATGTTTA
1 GTCATTATTATATGTTTA
2881 GTCATTATTATATGTTTA
1 GTCATTATTATATGTTTA
2899 TATTTATACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.11, T:0.56
Consensus pattern (18 bp):
GTCATTATTATATGTTTA
Found at i:6149 original size:33 final size:35
Alignment explanation
Indices: 6100--6171 Score: 96
Period size: 33 Copynumber: 2.1 Consensus size: 35
6090 ATCATTCGCC
* *
6100 AAAAGAAATTTGCTTATGATCCT-CTTTGAAAAAGA
1 AAAAGAAATTTGCTTATGAACCTCCTTGGAAAAA-A
6135 AAAAG-AA-TTGCTTATGAACCTCCTTGGAAAAAA
1 AAAAGAAATTTGCTTATGAACCTCCTTGGAAAAAA
6168 AAAA
1 AAAA
6172 TTATACCGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 18 0.53
34 11 0.32
35 5 0.15
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.26
Consensus pattern (35 bp):
AAAAGAAATTTGCTTATGAACCTCCTTGGAAAAAA
Found at i:9175 original size:105 final size:104
Alignment explanation
Indices: 9032--9225 Score: 280
Period size: 105 Copynumber: 1.9 Consensus size: 104
9022 CTGTCAGAAA
* * *
9032 AGTATTAGTCGATGAAAACTTCAATTTTAATTCCAGTATTAATCAACTAAAACTCCAAGTTTTCT
1 AGTATTAGTCGATGAAAACTCCAATTTTAATTCCAGTATTAATCAACTAAAACTCCAAGTCTTCA
* *
9097 CTTTCAAAAATGTGGCAGTGTTGACAGCGAACCCGAAGGC
66 CTTT-AAAAAAGTGGCAATGTTGACAGCGAACCCGAAGGC
* * ** * *
9137 AGTATTAGTTGATGAAAACTCCAGTTTTAATTTTAGTATTAATCGACTAAAGCTCCAAGTCTTCA
1 AGTATTAGTCGATGAAAACTCCAATTTTAATTCCAGTATTAATCAACTAAAACTCCAAGTCTTCA
9202 CTTTAAAAAAGTGGCAATGTTGAC
66 CTTTAAAAAAGTGGCAATGTTGAC
9226 GACCACACAA
Statistics
Matches: 78, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
104 18 0.23
105 60 0.77
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (104 bp):
AGTATTAGTCGATGAAAACTCCAATTTTAATTCCAGTATTAATCAACTAAAACTCCAAGTCTTCA
CTTTAAAAAAGTGGCAATGTTGACAGCGAACCCGAAGGC
Found at i:13131 original size:20 final size:20
Alignment explanation
Indices: 13091--13132 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
13081 CCTCACAAGA
* *
13091 TTCTAGCCGTTGGAGCTCTT
1 TTCTAGCCGTTAGAGCACTT
*
13111 TTCTAGCCGTTATAGCACTT
1 TTCTAGCCGTTAGAGCACTT
13131 TT
1 TT
13133 TCCACCTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
TTCTAGCCGTTAGAGCACTT
Found at i:16869 original size:24 final size:24
Alignment explanation
Indices: 16819--16869 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
16809 GATGGCTATG
* * ***
16819 AAATGAAATGGAATGAAAAATCCA
1 AAATCAAATGAAATGAAAAAAAAA
16843 AAATCAAATGAAATGAAAAAAAAA
1 AAATCAAATGAAATGAAAAAAAAA
16867 AAA
1 AAA
16870 AAAGAAAAGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.69, C:0.06, G:0.12, T:0.14
Consensus pattern (24 bp):
AAATCAAATGAAATGAAAAAAAAA
Found at i:21404 original size:2 final size:2
Alignment explanation
Indices: 21399--21441 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
21389 AAATAGAAAA
21399 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
21441 A
1 A
21442 AGACACGTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:22232 original size:18 final size:19
Alignment explanation
Indices: 22198--22233 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
22188 CCTTTTAAGT
22198 GCTGATGTGGAAATTTTTA
1 GCTGATGTGGAAATTTTTA
22217 GCTGATGTGG-AATTTTT
1 GCTGATGTGGAAATTTTT
22234 CTGTGGGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.22, C:0.06, G:0.28, T:0.44
Consensus pattern (19 bp):
GCTGATGTGGAAATTTTTA
Found at i:23728 original size:21 final size:21
Alignment explanation
Indices: 23702--24131 Score: 204
Period size: 21 Copynumber: 20.5 Consensus size: 21
23692 TTTACTGAAC
23702 TACTGATTACTCTTTACTCTT
1 TACTGATTACTCTTTACTCTT
23723 TACTGATTACTCTTTACCATTTTTCTT
1 TACTGATTACTCTTTA-C-----TCTT
23750 TACTGATTACTCTTT--TCTT
1 TACTGATTACTCTTTACTCTT
**
23769 TACTCTTTACTCTTTAC-CATTT
1 TACTGATTACTCTTTACTC--TT
* * **
23791 TACT-TTTATTAATTACTCTT
1 TACTGATTACTCTTTACTCTT
** *
23811 TACTTTTTACTATTT--TACTT
1 TACTGATTACTCTTTACT-CTT
* * *
23831 TGCTGATTACTCTTCACTCCT
1 TACTGATTACTCTTTACTCTT
23852 TACT-A-T--T-TTT-CT-TT
1 TACTGATTACTCTTTACTCTT
*
23866 -ACTAATTACTCTTTACTCTT
1 TACTGATTACTCTTTACTCTT
*
23886 TACTGATTACTCTTTTACTTTT
1 TACTGATTACTC-TTTACTCTT
* * * * *
23908 TGCTGATTGCCTTTTTGCTTTT
1 TACTGATT-ACTCTTTACTCTT
23930 TACTGATTAC-CTTTTACT-TCT
1 TACTGATTACTC-TTTACTCT-T
*
23951 TACTGATTAGCTTTTTACTCTT
1 TACTGATTA-CTCTTTACTCTT
23973 TACTGATTAC-CTTTTACT-TCT
1 TACTGATTACTC-TTTACTCT-T
*
23994 TACTGATTACTATTTTACTC-T
1 TACTGATTACT-CTTTACTCTT
* * *
24015 TACTAATTACTATTTACTTTT
1 TACTGATTACTCTTTACTCTT
* * *
24036 TGCCGATTACTATTTTACTC-T
1 TACTGATTACT-CTTTACTCTT
* *
24057 TACTAATTAC-CTTTTACTTTT
1 TACTGATTACTC-TTTACTCTT
* *
24078 TACTGACTACTATTTTACTC-T
1 TACTGATTACT-CTTTACTCTT
* *
24099 TACTAATTAC-CTTCTTACTTTT
1 TACTGATTACTC-T-TTACTCTT
24121 TACTGATTACT
1 TACTGATTACT
24132 ATTTTCTTCT
Statistics
Matches: 313, Mismatches: 51, Indels: 88
0.69 0.11 0.19
Matches are distributed among these distances:
13 3 0.01
14 2 0.01
15 3 0.01
16 2 0.01
17 2 0.01
18 3 0.01
19 21 0.07
20 38 0.12
21 133 0.42
22 84 0.27
23 3 0.01
27 19 0.06
ACGTcount: A:0.20, C:0.21, G:0.04, T:0.55
Consensus pattern (21 bp):
TACTGATTACTCTTTACTCTT
Found at i:23775 original size:7 final size:7
Alignment explanation
Indices: 23708--23900 Score: 98
Period size: 7 Copynumber: 28.3 Consensus size: 7
23698 GAACTACTGA
23708 TTACTCT
1 TTACTCT
23715 TTACTCT
1 TTACTCT
**
23722 TTACTGA
1 TTACTCT
23729 TTACTCT
1 TTACTCT
23736 TTAC-CAT
1 TTACTC-T
*
23743 TT-TTCT
1 TTACTCT
**
23749 TTACTGA
1 TTACTCT
23756 TTACTCT
1 TTACTCT
23763 TT--TCT
1 TTACTCT
23768 TTACTCT
1 TTACTCT
23775 TTACTCT
1 TTACTCT
23782 TTAC-CATT
1 TTACTC--T
23790 TTACT-T
1 TTACTCT
* **
23796 TTATTAA
1 TTACTCT
23803 TTACTCT
1 TTACTCT
*
23810 TTACTTT
1 TTACTCT
*
23817 TTACTAT
1 TTACTCT
23824 TT--TACT
1 TTACT-CT
* **
23830 TTGCTGA
1 TTACTCT
23837 TTACTCT
1 TTACTCT
* *
23844 TCACTCC
1 TTACTCT
*
23851 TTACTAT
1 TTACTCT
*
23858 TT-TTCT
1 TTACTCT
**
23864 TTACTAA
1 TTACTCT
23871 TTACTCT
1 TTACTCT
23878 TTACTCT
1 TTACTCT
**
23885 TTACTGA
1 TTACTCT
23892 TTACTCT
1 TTACTCT
23899 TT
1 TT
23901 TACTTTTTGC
Statistics
Matches: 134, Mismatches: 39, Indels: 26
0.67 0.20 0.13
Matches are distributed among these distances:
5 6 0.04
6 17 0.13
7 105 0.78
8 6 0.04
ACGTcount: A:0.19, C:0.22, G:0.03, T:0.56
Consensus pattern (7 bp):
TTACTCT
Found at i:23855 original size:34 final size:34
Alignment explanation
Indices: 23768--23889 Score: 163
Period size: 34 Copynumber: 3.6 Consensus size: 34
23758 ACTCTTTTCT
* *
23768 TTACTCTTTACTCTTTACCATTTTACTTTTATTAA
1 TTACTCTTTACTCTTTACTATTTTAC-TTTACTAA
* * *
23803 TTACTCTTTACTTTTTACTATTTTACTTTGCTGA
1 TTACTCTTTACTCTTTACTATTTTACTTTACTAA
* * *
23837 TTACTCTTCACTCCTTACTATTTTTCTTTACTAA
1 TTACTCTTTACTCTTTACTATTTTACTTTACTAA
23871 TTACTCTTTACTCTTTACT
1 TTACTCTTTACTCTTTACT
23890 GATTACTCTT
Statistics
Matches: 74, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
34 50 0.68
35 24 0.32
ACGTcount: A:0.20, C:0.22, G:0.02, T:0.57
Consensus pattern (34 bp):
TTACTCTTTACTCTTTACTATTTTACTTTACTAA
Found at i:23908 original size:7 final size:7
Alignment explanation
Indices: 23871--24081 Score: 57
Period size: 7 Copynumber: 29.7 Consensus size: 7
23861 TCTTTACTAA
*
23871 TTACTCT
1 TTACTTT
*
23878 TTACTCT
1 TTACTTT
**
23885 TTACTGA
1 TTACTTT
23892 TTACTCTT
1 TTACT-TT
23900 TTACTTT
1 TTACTTT
* *
23907 TTGCTGAT
1 TTACT-TT
**
23915 TGCCTTT
1 TTACTTT
*
23922 TTGCTTT
1 TTACTTT
**
23929 TTACTGA
1 TTACTTT
*
23936 TTACCTT
1 TTACTTT
*
23943 TTACTTC
1 TTACTTT
**
23950 TTACTGA
1 TTACTTT
23957 TTAGCTTT
1 TTA-CTTT
*
23965 TTACTCT
1 TTACTTT
**
23972 TTACTGA
1 TTACTTT
*
23979 TTACCTT
1 TTACTTT
*
23986 TTACTTC
1 TTACTTT
**
23993 TTACTGA
1 TTACTTT
24000 TTACTATT
1 TTACT-TT
*
24008 TTAC-TC
1 TTACTTT
**
24014 TTACTAA
1 TTACTTT
*
24021 TTACTAT
1 TTACTTT
24028 TTACTTT
1 TTACTTT
* ***
24035 TTGCCGA
1 TTACTTT
24042 TTACTATT
1 TTACT-TT
*
24050 TTAC-TC
1 TTACTTT
**
24056 TTACTAA
1 TTACTTT
*
24063 TTACCTT
1 TTACTTT
24070 TTACTTT
1 TTACTTT
24077 TTACT
1 TTACT
24082 GACTACTATT
Statistics
Matches: 142, Mismatches: 55, Indels: 14
0.67 0.26 0.07
Matches are distributed among these distances:
6 10 0.07
7 110 0.77
8 22 0.15
ACGTcount: A:0.19, C:0.20, G:0.06, T:0.55
Consensus pattern (7 bp):
TTACTTT
Found at i:24017 original size:14 final size:14
Alignment explanation
Indices: 24000--24136 Score: 74
Period size: 14 Copynumber: 9.7 Consensus size: 14
23990 TTCTTACTGA
24000 TTACTATTTTACTC
1 TTACTATTTTACTC
* *
24014 TTACTA-ATTACTAT
1 TTACTATTTTACT-C
*
24028 TTACT-TTTTGC-C
1 TTACTATTTTACTC
24040 GATTACTATTTTACTC
1 --TTACTATTTTACTC
* *
24056 TTACTA-ATTACCTT
1 TTACTATTTTA-CTC
24070 TTACT-TTTTACTGAC
1 TTACTATTTTACT--C
24085 -TACTATTTTACTC
1 TTACTATTTTACTC
*
24098 TTACTA-ATTACCTTC
1 TTACTATTTTA-C-TC
*
24113 TTACT-TTTTACTGA
1 TTACTATTTTACT-C
24127 TTACTATTTT
1 TTACTATTTT
24137 CTTCTCCTTT
Statistics
Matches: 93, Mismatches: 13, Indels: 33
0.67 0.09 0.24
Matches are distributed among these distances:
13 15 0.16
14 51 0.55
15 26 0.28
16 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.03, T:0.54
Consensus pattern (14 bp):
TTACTATTTTACTC
Found at i:24017 original size:28 final size:27
Alignment explanation
Indices: 23986--24102 Score: 78
Period size: 28 Copynumber: 4.2 Consensus size: 27
23976 TGATTACCTT
*
23986 TTACTTCTTACTGATTACTATTTTACTC
1 TTACTTTTTACT-ATTACTATTTTACTC
** *
24014 TTACTAATTACTATTTACT-TTTTGC-C
1 TTACTTTTTACTA-TTACTATTTTACTC
* * *
24040 GATTACTATTTTACTCTTACTA-ATTACCTT
1 --TTACT-TTTTACTATTACTATTTTA-CTC
*
24070 TTACTTTTTACTGACTACTATTTTACTC
1 TTACTTTTTACT-ATTACTATTTTACTC
24098 TTACT
1 TTACT
24103 AATTACCTTC
Statistics
Matches: 67, Mismatches: 13, Indels: 18
0.68 0.13 0.18
Matches are distributed among these distances:
26 1 0.01
27 13 0.19
28 44 0.66
29 9 0.13
ACGTcount: A:0.23, C:0.21, G:0.03, T:0.53
Consensus pattern (27 bp):
TTACTTTTTACTATTACTATTTTACTC
Found at i:24132 original size:43 final size:42
Alignment explanation
Indices: 23863--24136 Score: 322
Period size: 43 Copynumber: 6.4 Consensus size: 42
23853 ACTATTTTTC
* * *
23863 TTTACTAATTACT-CTTTACTCTTTACTGATTACTCTTTTACTT
1 TTTACTGATTACTATTTTACTC-TTACTAATTAC-CTTTTACTT
* * * * *
23906 TTTGCTGATTGCCT-TTTTGCTTTTTACTGATTACCTTTTACTT
1 TTTACTGATT-ACTATTTTAC-TCTTACTAATTACCTTTTACTT
* *
23949 CTTACTGATTAGCT-TTTTACTCTTTACTGATTACCTTTTACTT
1 TTTACTGATTA-CTATTTTACTC-TTACTAATTACCTTTTACTT
*
23992 CTTACTGATTACTATTTTACTCTTACTAATTA-CTATTTACTT
1 TTTACTGATTACTATTTTACTCTTACTAATTACCT-TTTACTT
* *
24034 TTTGCCGATTACTATTTTACTCTTACTAATTACCTTTTACTT
1 TTTACTGATTACTATTTTACTCTTACTAATTACCTTTTACTT
*
24076 TTTACTGACTACTATTTTACTCTTACTAATTACCTTCTTACTT
1 TTTACTGATTACTATTTTACTCTTACTAATTACCTT-TTACTT
24119 TTTACTGATTACTATTTT
1 TTTACTGATTACTATTTT
24137 CTTCTCCTTT
Statistics
Matches: 204, Mismatches: 19, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
41 2 0.01
42 88 0.43
43 96 0.47
44 17 0.08
45 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.05, T:0.54
Consensus pattern (42 bp):
TTTACTGATTACTATTTTACTCTTACTAATTACCTTTTACTT
Found at i:24169 original size:26 final size:28
Alignment explanation
Indices: 24117--24171 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
24107 ACCTTCTTAC
* * *
24117 TTTTTACTGATTACTATTTTCTTCTCCT
1 TTTTTACTGATTACCATTTGCTACTCCT
24145 TTTTTACTGATTACCA-TTGC-ACTCCT
1 TTTTTACTGATTACCATTTGCTACTCCT
24171 T
1 T
24172 GAATTGAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 6 0.25
27 3 0.12
28 15 0.62
ACGTcount: A:0.16, C:0.24, G:0.05, T:0.55
Consensus pattern (28 bp):
TTTTTACTGATTACCATTTGCTACTCCT
Found at i:24898 original size:25 final size:25
Alignment explanation
Indices: 24855--24919 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
24845 CAAAATTCAC
* *
24855 AAAGCCTAAATGCAGAAAACCAATA
1 AAAGCCCAAATGCAGAAAACAAATA
** * *
24880 AAAGCCCAAATGCTTAAAATAAATT
1 AAAGCCCAAATGCAGAAAACAAATA
24905 AAAGTCCCAAATGCA
1 AAAG-CCCAAATGCA
24920 TCAGTTAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 23 0.72
26 9 0.28
ACGTcount: A:0.52, C:0.20, G:0.11, T:0.17
Consensus pattern (25 bp):
AAAGCCCAAATGCAGAAAACAAATA
Done.