Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005275.1 Corchorus capsularis cultivar CVL-1 contig05293, 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: 11576
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Found at i:3115 original size:19 final size:19
Alignment explanation
Indices: 3091--3155 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
3081 TTCTGATGTG
3091 ATTTCTGGATTGGATTGTC
1 ATTTCTGGATTGGATTGTC
* *
3110 ATTTCT-AATTTGTGGTT-TC
1 ATTTCTGGA-TTG-GATTGTC
*
3129 TGATTTCTGGATTGGATTGTG
1 --ATTTCTGGATTGGATTGTC
3150 ATTTCT
1 ATTTCT
3156 TATTTCTGGA
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
18 1 0.03
19 17 0.49
20 6 0.17
21 10 0.29
22 1 0.03
ACGTcount: A:0.15, C:0.09, G:0.23, T:0.52
Consensus pattern (19 bp):
ATTTCTGGATTGGATTGTC
Found at i:3148 original size:26 final size:27
Alignment explanation
Indices: 3119--3186 Score: 95
Period size: 26 Copynumber: 2.6 Consensus size: 27
3109 CATTTCTAAT
*
3119 TTGTGGTTTCTGATTTCTGGATTG-GA
1 TTGTGATTTCTGATTTCTGGATTGTGA
*
3145 TTGTGATTTCTTATTTCTGGATTGTGA
1 TTGTGATTTCTGATTTCTGGATTGTGA
*
3172 -TCTGATTTCTGATTT
1 TTGTGATTTCTGATTT
3187 TTGACAATTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
26 35 0.95
27 2 0.05
ACGTcount: A:0.13, C:0.09, G:0.24, T:0.54
Consensus pattern (27 bp):
TTGTGATTTCTGATTTCTGGATTGTGA
Found at i:3181 original size:19 final size:20
Alignment explanation
Indices: 3141--3182 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
3131 ATTTCTGGAT
*
3141 TGGATTGTGATTTCTTATTTC
1 TGGATTGTGA-TTCTGATTTC
3162 TGGATTGTGA-TCTGATTTC
1 TGGATTGTGATTCTGATTTC
3181 TG
1 TG
3183 ATTTTTGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
21 10 0.50
ACGTcount: A:0.14, C:0.10, G:0.24, T:0.52
Consensus pattern (20 bp):
TGGATTGTGATTCTGATTTC
Found at i:3220 original size:7 final size:7
Alignment explanation
Indices: 3208--3243 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
3198 GCTGGATTGG
3208 TTTCTGA
1 TTTCTGA
3215 TTTCTGA
1 TTTCTGA
3222 TTTCTGA
1 TTTCTGA
3229 TTTCTGA
1 TTTCTGA
3236 TTTCTGA
1 TTTCTGA
3243 T
1 T
3244 GTGATTTCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.58
Consensus pattern (7 bp):
TTTCTGA
Found at i:3250 original size:19 final size:20
Alignment explanation
Indices: 3208--3276 Score: 81
Period size: 19 Copynumber: 3.5 Consensus size: 20
3198 GCTGGATTGG
*
3208 TTTCTGATTTCTGATTTCTGA
1 TTTCTGATTTCTGA-TTGTGA
3229 TTTCTGATTTCTGA-TGTGA
1 TTTCTGATTTCTGATTGTGA
*
3248 TTTCTGGA-TT-GGATTGTGA
1 TTTCT-GATTTCTGATTGTGA
3267 TTTCTGATTT
1 TTTCTGATTT
3277 GCTTATGCTG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
18 4 0.09
19 23 0.53
20 2 0.05
21 14 0.33
ACGTcount: A:0.14, C:0.10, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCTGATTTCTGATTGTGA
Found at i:5537 original size:35 final size:35
Alignment explanation
Indices: 5491--5721 Score: 299
Period size: 35 Copynumber: 6.6 Consensus size: 35
5481 TTCTTACTAA
5491 ACTTAATTACCCTGAATTAAGTTACTTATTGAACT-
1 ACTTAATTACCCTGAATTAAGTTACTTATT-AACTC
5526 ACTTAATTACCCTGAATTAAGTTACTTATTAACTC
1 ACTTAATTACCCTGAATTAAGTTACTTATTAACTC
5561 ACTTAATTACCCTGAATTAAGTTACTTATTGAACT-
1 ACTTAATTACCCTGAATTAAGTTACTTATT-AACTC
5596 ACTTAATTACCCTGAATTAAGTTACTTATTAACTC
1 ACTTAATTACCCTGAATTAAGTTACTTATTAACTC
* *
5631 ACTTAATTACCGTGAATTAAGGTTGA-TTACTAACTC
1 ACTTAATTACCCTGAATTAA-GTT-ACTTATTAACTC
* * * *** *
5667 ACTTAATTGCCCTCAATTCAGTTGA-TTACCGACTT
1 ACTTAATTACCCTGAATTAAGTT-ACTTATTAACTC
*
5702 GCTTAATTACCCTGAATTAA
1 ACTTAATTACCCTGAATTAA
5722 ATTGCTCATT
Statistics
Matches: 178, Mismatches: 13, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
34 8 0.04
35 137 0.77
36 32 0.18
37 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (35 bp):
ACTTAATTACCCTGAATTAAGTTACTTATTAACTC
Found at i:9308 original size:22 final size:22
Alignment explanation
Indices: 9280--9323 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
9270 CTATAAACTA
*
9280 TACTAAATACCAAAATTGAATT
1 TACTAAATACCAAAAGTGAATT
* *
9302 TACTAAATGCCAAGAGTGAATT
1 TACTAAATACCAAAAGTGAATT
9324 AGAAAATGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (22 bp):
TACTAAATACCAAAAGTGAATT
Found at i:9648 original size:36 final size:36
Alignment explanation
Indices: 9608--9814 Score: 136
Period size: 36 Copynumber: 5.8 Consensus size: 36
9598 TAAAATAAGT
* *
9608 AACTGAAGAAAGACCACCCTGGATCATTCCGAACTG
1 AACTGAAGAAAGACCACCCTCGATCATTCCGAACTA
* * *
9644 AACTGAAGAATGACCACCCTCGATAATTCCG-ACGCA
1 AACTGAAGAAAGACCACCCTCGATCATTCCGAAC-TA
* * * * * ** *
9680 TACCGAAGAAAGACCACCCTGGGTCA-ACTAAAATA
1 AACTGAAGAAAGACCACCCTCGATCATTCCGAACTA
* *
9715 AACTGAA-AAACGACCATCCTCGATCATTAC-AACATA
1 AACTGAAGAAA-GACCACCCTCGATCATTCCGAAC-TA
* * * ** *
9751 AACTGAAGAAAGACCATCCTCGGTCA-ACTAAAATA
1 AACTGAAGAAAGACCACCCTCGATCATTCCGAACTA
* * *
9786 AGCTGAAGAACGACTACCCTCGATCATTC
1 AACTGAAGAAAGACCACCCTCGATCATTC
9815 TGACAAAAAG
Statistics
Matches: 127, Mismatches: 36, Indels: 16
0.71 0.20 0.09
Matches are distributed among these distances:
34 3 0.02
35 46 0.36
36 75 0.59
37 3 0.02
ACGTcount: A:0.40, C:0.28, G:0.15, T:0.17
Consensus pattern (36 bp):
AACTGAAGAAAGACCACCCTCGATCATTCCGAACTA
Found at i:9737 original size:71 final size:71
Alignment explanation
Indices: 9608--9919 Score: 277
Period size: 71 Copynumber: 4.4 Consensus size: 71
9598 TAAAATAAGT
* * ** * * * * *
9608 AACTGAAGAAAGACCACCCTGGATCATTCCGAACTGAACTGAAGAATGACCACCCTCGATAATTC
1 AACTGAAGAAAGACCACCCTGGGTCA-ACTAAAATAAACTGAAAAACGACCACCCTCGATCATTC
*
9673 CGACGCA
65 CGACACA
* * * *
9680 TACCGAAGAAAGACCACCCTGGGTCAACTAAAATAAACTGAAAAACGACCATCCTCGATCATTAC
1 AACTGAAGAAAGACCACCCTGGGTCAACTAAAATAAACTGAAAAACGACCACCCTCGATCATTCC
* *
9745 AACATA
66 GACACA
* * * * * *
9751 AACTGAAGAAAGACCATCCTCGGTCAACTAAAATAAGCTGAAGAACGACTACCCTCGATCATTCT
1 AACTGAAGAAAGACCACCCTGGGTCAACTAAAATAAACTGAAAAACGACCACCCTCGATCATTCC
*
9816 GACAAA
66 GACACA
* * * * * * *
9822 AAGTAAAGGAAA-ACCGCCCTGGGCCAACTGAAATGAACTGAAAAACGACCACCTTCGATCATTT
1 AACTGAA-GAAAGACCACCCTGGGTCAACTAAAATAAACTGAAAAACGACCACCCTCGATCA-TT
* * *
9886 CGGGC-TA
64 CCGACACA
9893 AACTGAAGAAAAGACCACCCTGGGTCA
1 AACTGAAG-AAAGACCACCCTGGGTCA
9920 TTGAAGCATT
Statistics
Matches: 189, Mismatches: 47, Indels: 8
0.77 0.19 0.03
Matches are distributed among these distances:
70 1 0.01
71 144 0.76
72 44 0.23
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (71 bp):
AACTGAAGAAAGACCACCCTGGGTCAACTAAAATAAACTGAAAAACGACCACCCTCGATCATTCC
GACACA
Found at i:9807 original size:35 final size:35
Alignment explanation
Indices: 9684--9807 Score: 135
Period size: 35 Copynumber: 3.5 Consensus size: 35
9674 GACGCATACC
*
9684 GAAGAAAGACCACCCTGGGTCAACTAAAATAAACT
1 GAAGAAAGACCACCCTCGGTCAACTAAAATAAACT
* * *
9719 GAA-AAACGACCATCCTCGATCATTAC-AACATAAACT
1 GAAGAAA-GACCACCCTCGGTCA--ACTAAAATAAACT
* *
9755 GAAGAAAGACCATCCTCGGTCAACTAAAATAAGCT
1 GAAGAAAGACCACCCTCGGTCAACTAAAATAAACT
* *
9790 GAAGAACGACTACCCTCG
1 GAAGAAAGACCACCCTCG
9808 ATCATTCTGA
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
34 5 0.07
35 38 0.51
36 26 0.35
37 5 0.07
ACGTcount: A:0.43, C:0.26, G:0.15, T:0.16
Consensus pattern (35 bp):
GAAGAAAGACCACCCTCGGTCAACTAAAATAAACT
Found at i:9996 original size:34 final size:34
Alignment explanation
Indices: 9942--10036 Score: 100
Period size: 35 Copynumber: 2.8 Consensus size: 34
9932 ATAATTGGAG
* * * *
9942 AATTGAAGAAAGACCACCCTGGATCATTGAAGTA
1 AATTGAAGAATGATCGCCCTGGATCATTGAAATA
* *
9976 AATTGAAGAATGATCGCCCTGGACCAATTGAAATT
1 AATTGAAGAATGATCGCCCTGGATC-ATTGAAATA
* * *
10011 AACTGAGGAATGATCGCCCTGTATCA
1 AATTGAAGAATGATCGCCCTGGATCA
10037 ATTAGCTTAA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
34 22 0.44
35 28 0.56
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (34 bp):
AATTGAAGAATGATCGCCCTGGATCATTGAAATA
Done.