Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010966.1 Corchorus capsularis cultivar CVL-1 contig10987, 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: 48110
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Found at i:5672 original size:25 final size:25
Alignment explanation
Indices: 5638--5687 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5628 GATTGGTTTG
5638 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
5663 TAGAGACCGAGCGAGAGTGCTCAAA
1 TAGAGACCGAGCGAGAGTGCTCAAA
5688 GATTGGTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.20, G:0.32, T:0.12
Consensus pattern (25 bp):
TAGAGACCGAGCGAGAGTGCTCAAA
Found at i:9673 original size:21 final size:23
Alignment explanation
Indices: 9620--9673 Score: 58
Period size: 26 Copynumber: 2.3 Consensus size: 23
9610 TTCATTTCAC
9620 TATTCTTTGTTCATCAGATCAAATT
1 TATT-TTTGTTCATCAGATCAAA-T
9645 TCAGTTTTTGTTCATCA-ATCAAA-
1 T-A-TTTTTGTTCATCAGATCAAAT
9668 TATTTT
1 TATTTT
9674 GATCTGTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
21 4 0.15
22 1 0.04
23 1 0.04
25 7 0.26
26 12 0.44
27 2 0.07
ACGTcount: A:0.28, C:0.15, G:0.07, T:0.50
Consensus pattern (23 bp):
TATTTTTGTTCATCAGATCAAAT
Found at i:14101 original size:20 final size:21
Alignment explanation
Indices: 14076--14116 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
14066 GGGTAAGAGG
14076 AAATT-AAGTTAAAGCCCAAC
1 AAATTAAAGTTAAAGCCCAAC
*
14096 AAATTAGAAGTTAAGGCCCAA
1 AAATTA-AAGTTAAAGCCCAA
14117 ATAAAATGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
22 13 0.72
ACGTcount: A:0.49, C:0.17, G:0.15, T:0.20
Consensus pattern (21 bp):
AAATTAAAGTTAAAGCCCAAC
Found at i:19023 original size:22 final size:22
Alignment explanation
Indices: 18998--19040 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
18988 TGAACACAAA
18998 CAACAATCAAGCTCCCTGCTTC
1 CAACAATCAAGCTCCCTGCTTC
*
19020 CAACAATCAAGCTCCGTGCTT
1 CAACAATCAAGCTCCCTGCTT
19041 TCAATCTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.37, G:0.12, T:0.23
Consensus pattern (22 bp):
CAACAATCAAGCTCCCTGCTTC
Found at i:19294 original size:275 final size:277
Alignment explanation
Indices: 18802--19357 Score: 1053
Period size: 275 Copynumber: 2.0 Consensus size: 277
18792 TGGAGATTTC
18802 CTTGATTAATGAGATTCAGATCAAGATTTAAATGCTGAAGATAAAGCAGAATCAACAGGGGATCA
1 CTTGATTAATGAGATTCAGATCAAGATTTAAATGCTGAAGATAAAGCAGAATCAACAGGGGATCA
* *
18867 TTTCTGGCTGTCGGATTGCATCTAACCCTAGCAGGCCACCCCCTATATAAACGAAGCAGCCTCCA
66 TTTATGGCCGTCGGATTGCATCTAACCCTAGCAGGCCACCCCCTATATAAACGAAGCAGCCTCCA
* * *
18932 ATGTTGAAAGCCTCCCTTCCAACTGCCAATTTCAATCTCAGACTCAAACTTCAACTTGAACACAA
131 ACGTTGAAAGCCTCCCTTCCAACAGCCAATTTCAATCTCAAACTCAAACTTCAACTTGAACACAA
18997 ACAACAATCAAGCTCCCTGCTTCCAACAATCAAGCTCCGTGCTTTCAATCTCTCAAG-CCCTTGT
196 ACAACAATCAAGCTCCCTGCTTCCAACAATCAAGCTCCGTGCTTTCAATCTCTCAAGCCCCTTGT
19061 TGAGCATGGCACAATTG
261 TGAGCATGGCACAATTG
19078 CTTGATTAATGAGATTCAGATCAAGATTTAAATGCTGAAGATAAAGCAGAATCAACA-GGGATCA
1 CTTGATTAATGAGATTCAGATCAAGATTTAAATGCTGAAGATAAAGCAGAATCAACAGGGGATCA
19142 TTTATGGCCGTCGGATTGCATCTAACCCTAGCAGGCCACCCCCTATATAAACGAAGCAGCCTCCA
66 TTTATGGCCGTCGGATTGCATCTAACCCTAGCAGGCCACCCCCTATATAAACGAAGCAGCCTCCA
19207 ACGTTGAAAGCCTCCCTTCCAACAGCCAATTTCAATCTCAAACTCAAACTTCAACTTGAACACAA
131 ACGTTGAAAGCCTCCCTTCCAACAGCCAATTTCAATCTCAAACTCAAACTTCAACTTGAACACAA
19272 ACAACAATCAAGCTCCCTGCTTCCAACAATCAAGCTCCGTGCTTTCAATCTCTCAAGCCCCTTGT
196 ACAACAATCAAGCTCCCTGCTTCCAACAATCAAGCTCCGTGCTTTCAATCTCTCAAGCCCCTTGT
19337 TGAGCATGGCACAATTG
261 TGAGCATGGCACAATTG
19354 CTTG
1 CTTG
19358 GCGCCCGACC
Statistics
Matches: 274, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
275 189 0.69
276 85 0.31
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.25
Consensus pattern (277 bp):
CTTGATTAATGAGATTCAGATCAAGATTTAAATGCTGAAGATAAAGCAGAATCAACAGGGGATCA
TTTATGGCCGTCGGATTGCATCTAACCCTAGCAGGCCACCCCCTATATAAACGAAGCAGCCTCCA
ACGTTGAAAGCCTCCCTTCCAACAGCCAATTTCAATCTCAAACTCAAACTTCAACTTGAACACAA
ACAACAATCAAGCTCCCTGCTTCCAACAATCAAGCTCCGTGCTTTCAATCTCTCAAGCCCCTTGT
TGAGCATGGCACAATTG
Found at i:19298 original size:22 final size:22
Alignment explanation
Indices: 19273--19315 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
19263 TGAACACAAA
19273 CAACAATCAAGCTCCCTGCTTC
1 CAACAATCAAGCTCCCTGCTTC
*
19295 CAACAATCAAGCTCCGTGCTT
1 CAACAATCAAGCTCCCTGCTT
19316 TCAATCTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.37, G:0.12, T:0.23
Consensus pattern (22 bp):
CAACAATCAAGCTCCCTGCTTC
Found at i:19393 original size:23 final size:23
Alignment explanation
Indices: 19362--19463 Score: 116
Period size: 23 Copynumber: 4.4 Consensus size: 23
19352 TGCTTGGCGC
*
19362 CCGACCACTTCCAAGCCTAGCGT
1 CCGACCACTTCCAAGCCTAGCGA
* *
19385 CCCACCACTTCCATGCCTAGCGA
1 CCGACCACTTCCAAGCCTAGCGA
** * *
19408 GTGATCACTTCCATGCCTAGCGA
1 CCGACCACTTCCAAGCCTAGCGA
*
19431 CCGACCACTTCCAAGCCTGGC-A
1 CCGACCACTTCCAAGCCTAGCGA
19453 CCCGACCACTT
1 -CCGACCACTT
19464 GCGACTAAAG
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
22 1 0.02
23 65 0.98
ACGTcount: A:0.22, C:0.43, G:0.17, T:0.19
Consensus pattern (23 bp):
CCGACCACTTCCAAGCCTAGCGA
Found at i:30118 original size:27 final size:27
Alignment explanation
Indices: 30072--30175 Score: 118
Period size: 27 Copynumber: 3.8 Consensus size: 27
30062 AAGTGAACTT
* * **
30072 AAAATGACCCAAGATACCCCTAAATGCA
1 AAAATGA-CCAAAATGCCCCTGGATGCA
* **
30100 AAAATGACCTAAATGCCCCTGGATGTG
1 AAAATGACCAAAATGCCCCTGGATGCA
* *
30127 AAAATGACCAAAATGCTCCTGGGTGCA
1 AAAATGACCAAAATGCCCCTGGATGCA
30154 AAAATGACCAAAATGCCCCTGG
1 AAAATGACCAAAATGCCCCTGG
30176 GCGACCCTAA
Statistics
Matches: 63, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
27 56 0.89
28 7 0.11
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.17
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGGATGCA
Found at i:47830 original size:21 final size:21
Alignment explanation
Indices: 47787--47830 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
47777 GTTATGGGGG
* *
47787 TTGCTAAATACCGCCCTAGTT
1 TTGCTAAATACCACCCCAGTT
*
47808 TTGCTAAATACCACCCCATTT
1 TTGCTAAATACCACCCCAGTT
47829 TT
1 TT
47831 TACACTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.09, T:0.36
Consensus pattern (21 bp):
TTGCTAAATACCACCCCAGTT
Found at i:47977 original size:32 final size:33
Alignment explanation
Indices: 47879--48004 Score: 139
Period size: 33 Copynumber: 3.8 Consensus size: 33
47869 TTACACTAGG
* *
47879 CTCCCCACTAGGACGGCTCAGCCACGGCGGAAC
1 CTCCCCACTAGGGCGGCTCAGCCACGGCGGAGC
* * * *
47912 CTTCCCACTAGGGAGGCTCAACCACGGCAGAGC
1 CTCCCCACTAGGGCGGCTCAGCCACGGCGGAGC
* *
47945 CTCCCCACTGGGGCGGCTC-GCCACGACGGAGC
1 CTCCCCACTAGGGCGGCTCAGCCACGGCGGAGC
* *
47977 CTCCCCAGTGGGGCGGCTTCA-CCACGGC
1 CTCCCCACTAGGGCGGC-TCAGCCACGGC
48005 AAGCCGCCCT
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
32 26 0.34
33 51 0.66
ACGTcount: A:0.17, C:0.41, G:0.30, T:0.11
Consensus pattern (33 bp):
CTCCCCACTAGGGCGGCTCAGCCACGGCGGAGC
Found at i:48005 original size:65 final size:65
Alignment explanation
Indices: 47879--48026 Score: 167
Period size: 65 Copynumber: 2.3 Consensus size: 65
47869 TTACACTAGG
* * *
47879 CTCCCCACTAGGACGGCTCAGCCACGGCGGAACCTTCCCACTAGGGAGGCTCAACCACGGCAGAG
1 CTCCCCACTGGGACGGCTCAGCCACGACGGAACCTCCCCACTAGGGAGGCTCAACCACGGCA-AG
47944 C
65 C
* * * * *
47945 CTCCCCACTGGGGCGGCTC-GCCACGACGGAGCCTCCCCAGTGGGGCGGCTTC-ACCACGGCAAG
1 CTCCCCACTGGGACGGCTCAGCCACGACGGAACCTCCCCACTAGGGAGGC-TCAACCACGGCAAG
48008 C
65 C
*
48009 CGCCCTCA-TGGGACGGCT
1 CTCCC-CACTGGGACGGCT
48027 TTGCCACGGC
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
64 16 0.23
65 35 0.50
66 19 0.27
ACGTcount: A:0.18, C:0.41, G:0.30, T:0.11
Consensus pattern (65 bp):
CTCCCCACTGGGACGGCTCAGCCACGACGGAACCTCCCCACTAGGGAGGCTCAACCACGGCAAGC
Found at i:48026 original size:32 final size:32
Alignment explanation
Indices: 47984--48090 Score: 126
Period size: 32 Copynumber: 3.3 Consensus size: 32
47974 AGCCTCCCCA
* ** *
47984 GTGGGGCGGCTTCACCACGGCAAGCCGCCCTC
1 GTGGGACGGCTTTGCCACGGCAGGCCGCCCTC
* *
48016 ATGGGACGGCTTTGCCACGGCAGGCCGCCCTG
1 GTGGGACGGCTTTGCCACGGCAGGCCGCCCTC
* *
48048 GTGGGGCGGCTTTGCCACGGCGGGCCGCCC-C
1 GTGGGACGGCTTTGCCACGGCAGGCCGCCCTC
48079 GGTGGGACGGCT
1 -GTGGGACGGCT
48091 AGACCAATTT
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 63 1.00
ACGTcount: A:0.09, C:0.36, G:0.41, T:0.14
Consensus pattern (32 bp):
GTGGGACGGCTTTGCCACGGCAGGCCGCCCTC
Done.