Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014555.1 Corchorus capsularis cultivar CVL-1 contig14576, 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: 38001
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:612 original size:22 final size:23
Alignment explanation
Indices: 577--622 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
567 ATTTCCCGTG
*
577 TTTTGTGTATATTTTCCGTGGAC
1 TTTTATGTATATTTTCCGTGGAC
*
600 TTTTATGT-TATTTTCCGTTGAC
1 TTTTATGTATATTTTCCGTGGAC
622 T
1 T
623 ACCCTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.13, C:0.13, G:0.17, T:0.57
Consensus pattern (23 bp):
TTTTATGTATATTTTCCGTGGAC
Found at i:799 original size:30 final size:29
Alignment explanation
Indices: 722--799 Score: 120
Period size: 29 Copynumber: 2.7 Consensus size: 29
712 ATTTTCCCCC
*
722 TTTGGACGTTTTGTCCCCTGAATTTTAAT
1 TTTGGACGTTTTGTCCCCTGAATTTCAAT
*
751 TTTGGACATTTTGTCCCCTGAATTTCAAT
1 TTTGGACGTTTTGTCCCCTGAATTTCAAT
*
780 TTTGGGACGTTTTGCCCCCT
1 TTT-GGACGTTTTGTCCCCT
800 TAGACTATTG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 30 0.68
30 14 0.32
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (29 bp):
TTTGGACGTTTTGTCCCCTGAATTTCAAT
Found at i:980 original size:29 final size:29
Alignment explanation
Indices: 925--985 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
915 GATAAAACGT
* * *
925 TCCAAAATTGAAGTTCAAGTGGTAAAATG
1 TCCAAAATTAAAGTTCAAGTGGCAAAAAG
*
954 TCCAAAATTAAAGTT-TAGTGGACAAAAAG
1 TCCAAAATTAAAGTTCAAGTGG-CAAAAAG
983 TCC
1 TCC
986 CAAACGCTAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (29 bp):
TCCAAAATTAAAGTTCAAGTGGCAAAAAG
Found at i:3251 original size:26 final size:26
Alignment explanation
Indices: 3222--3280 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
3212 CAACCTCATC
3222 CAGGAAACCAGAGAAAACAACTAATA
1 CAGGAAACCAGAGAAAACAACTAATA
*
3248 CAGGAAACCAGAGAAAACATCTAATA
1 CAGGAAACCAGAGAAAACAACTAATA
3274 CAGGAAA
1 CAGGAAA
3281 AAACTTCTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.56, C:0.19, G:0.17, T:0.08
Consensus pattern (26 bp):
CAGGAAACCAGAGAAAACAACTAATA
Found at i:15241 original size:27 final size:27
Alignment explanation
Indices: 15203--15255 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
15193 CGTTAAATTT
*
15203 TGAACTCCACAAGTGGGTTGTGGAGTG
1 TGAACTCCACAAGTGGATTGTGGAGTG
15230 TGAACTCCACAAGTGGATTGTGGAGT
1 TGAACTCCACAAGTGGATTGTGGAGT
15256 TGACACATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.25, C:0.15, G:0.34, T:0.26
Consensus pattern (27 bp):
TGAACTCCACAAGTGGATTGTGGAGTG
Found at i:15307 original size:22 final size:22
Alignment explanation
Indices: 15279--15324 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
15269 TTTTTTGAAT
15279 TAATTAAGTTTTAAATGTTACA
1 TAATTAAGTTTTAAATGTTACA
15301 TAATTAAGTTTTAAATGTTACA
1 TAATTAAGTTTTAAATGTTACA
15323 TA
1 TA
15325 GACGATCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (22 bp):
TAATTAAGTTTTAAATGTTACA
Found at i:27944 original size:9 final size:9
Alignment explanation
Indices: 27930--27959 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
27920 CCACTAGTTT
27930 TTTTTTTTC
1 TTTTTTTTC
27939 TTTTTTTTC
1 TTTTTTTTC
27948 TTTTTTTT-
1 TTTTTTTTC
27956 TTTT
1 TTTT
27960 GTATTTTAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:32623 original size:28 final size:27
Alignment explanation
Indices: 32555--32625 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 27
32545 ACGTGTACCA
* *
32555 AAAAATGCCACGTTGGCATGCCACATGT
1 AAAAATGCCAC-ATGGCACGCCACATGT
* * *
32583 ACAAAAGGACACATGGCACGCCACGTGT
1 A-AAAATGCCACATGGCACGCCACATGT
32611 CAAAAATGCCACATG
1 -AAAAATGCCACATG
32626 TCATTTTTGT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
28 25 0.74
29 9 0.26
ACGTcount: A:0.37, C:0.27, G:0.21, T:0.15
Consensus pattern (27 bp):
AAAAATGCCACATGGCACGCCACATGT
Found at i:33943 original size:54 final size:54
Alignment explanation
Indices: 33884--34009 Score: 216
Period size: 54 Copynumber: 2.3 Consensus size: 54
33874 TTCTTGCTTC
* *
33884 ACTGGCTCCACTGATTCTGTTTTAATAGGCTCTACTGATTCTTGTTGCACTGCA
1 ACTGGCTCCACTGATTCTGTTATAATAGGCTCTACTGATTCTTGTTGAACTGCA
* *
33938 ACTGGCTCCACTGGTTCTGTTATAATAGGCTCTGCTGATTCTTGTTGAACTGCA
1 ACTGGCTCCACTGATTCTGTTATAATAGGCTCTACTGATTCTTGTTGAACTGCA
33992 ACTGGCTCCACTGATTCT
1 ACTGGCTCCACTGATTCT
34010 TTCACTGGCT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 67 1.00
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (54 bp):
ACTGGCTCCACTGATTCTGTTATAATAGGCTCTACTGATTCTTGTTGAACTGCA
Found at i:33979 original size:24 final size:24
Alignment explanation
Indices: 33887--33979 Score: 71
Period size: 24 Copynumber: 3.6 Consensus size: 24
33877 TTGCTTCACT
* *
33887 GGCTCCACTGATTCTGTTTTAATA
1 GGCTCTACTGATTCTGTTATAATA
33911 GGCTCTACTGATTCTTGTTGCACTGCAACT-
1 GGCTCTACTGATTC-TGTT--A-T--AA-TA
* *
33941 GGCTCCACTGGTTCTGTTATAATA
1 GGCTCTACTGATTCTGTTATAATA
*
33965 GGCTCTGCTGATTCT
1 GGCTCTACTGATTCT
33980 TGTTGAACTG
Statistics
Matches: 54, Mismatches: 7, Indels: 16
0.70 0.09 0.21
Matches are distributed among these distances:
23 1 0.02
24 27 0.50
25 4 0.07
26 1 0.02
27 1 0.02
28 1 0.02
29 4 0.07
30 14 0.26
31 1 0.02
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (24 bp):
GGCTCTACTGATTCTGTTATAATA
Found at i:34006 original size:30 final size:29
Alignment explanation
Indices: 33911--34010 Score: 95
Period size: 30 Copynumber: 3.6 Consensus size: 29
33901 TGTTTTAATA
*
33911 GGCTCTACTGATTCTTGTTGCACTGCAACT
1 GGCTCCACTGATTCTTGTTG-ACTGCAACT
*
33941 GGCTCCACTGGTTC-TGTT-A-T--AA-T
1 GGCTCCACTGATTCTTGTTGACTGCAACT
**
33964 AGGCTCTGCTGATTCTTGTTGAACTGCAACT
1 -GGCTCCACTGATTCTTGTTG-ACTGCAACT
33995 GGCTCCACTGATTCTT
1 GGCTCCACTGATTCTT
34011 TCACTGGCTC
Statistics
Matches: 55, Mismatches: 7, Indels: 16
0.71 0.09 0.21
Matches are distributed among these distances:
23 1 0.02
24 13 0.24
25 4 0.07
26 1 0.02
27 2 0.04
28 1 0.02
29 4 0.07
30 28 0.51
31 1 0.02
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (29 bp):
GGCTCCACTGATTCTTGTTGACTGCAACT
Found at i:34026 original size:75 final size:75
Alignment explanation
Indices: 33938--34095 Score: 262
Period size: 75 Copynumber: 2.1 Consensus size: 75
33928 TTGCACTGCA
33938 ACTGGCTCCACTGGTTCTGTTATAATAGGCTCTGCTGATTCTTGTTGAACTGCAACTGGCTCCAC
1 ACTGGCTCCACTGGTTCTGTTATAATAGGCTCTGCTGATTCTTGTTGAACTGCAACTGGCTCCAC
34003 TGATTCTTTC
66 TGATTCTTTC
* * * * * *
34013 ACTGGCTCGACTGGTTCTGTTTTAATAGGCTCTGCTGATTCTTGTTGCATTTCCACTGGCTCCAC
1 ACTGGCTCCACTGGTTCTGTTATAATAGGCTCTGCTGATTCTTGTTGAACTGCAACTGGCTCCAC
34078 TGATTCTTTC
66 TGATTCTTTC
34088 ACTGGCTC
1 ACTGGCTC
34096 TGATGGTATG
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.15, C:0.26, G:0.20, T:0.39
Consensus pattern (75 bp):
ACTGGCTCCACTGGTTCTGTTATAATAGGCTCTGCTGATTCTTGTTGAACTGCAACTGGCTCCAC
TGATTCTTTC
Done.