Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012579.1 Corchorus capsularis cultivar CVL-1 contig12600, 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: 18960
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3463 original size:21 final size:20
Alignment explanation
Indices: 3437--3476 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
3427 TATCTCACTA
3437 AAAATAA-AATATTAATAAAAT
1 AAAATAATAA-ATT-ATAAAAT
3458 AAAATAATAAATTATAAAA
1 AAAATAATAAATTATAAAA
3477 CCCGCAGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 10 0.56
22 2 0.11
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATAATAAATTATAAAAT
Found at i:4830 original size:15 final size:15
Alignment explanation
Indices: 4807--4836 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
4797 ATTTATCATA
4807 AATTATTCATATAAT
1 AATTATTCATATAAT
*
4822 AATTGTTCATATAAT
1 AATTATTCATATAAT
4837 GAAGTTTAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (15 bp):
AATTATTCATATAAT
Found at i:5072 original size:10 final size:10
Alignment explanation
Indices: 5057--5090 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
5047 GTGGGCTCAC
5057 GTGACTAACG
1 GTGACTAACG
5067 GTGACTAACG
1 GTGACTAACG
*
5077 GTGCCGTAACG
1 GTGAC-TAACG
5088 GTG
1 GTG
5091 CTGACGTGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 14 0.64
11 8 0.36
ACGTcount: A:0.24, C:0.21, G:0.35, T:0.21
Consensus pattern (10 bp):
GTGACTAACG
Found at i:5638 original size:12 final size:13
Alignment explanation
Indices: 5607--5635 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5597 GCGGCAGTAT
5607 AAAAA-CAGAAAC
1 AAAAACCAGAAAC
5619 AAAAACCAGAAAC
1 AAAAACCAGAAAC
5632 AAAA
1 AAAA
5636 CCAACATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.76, C:0.17, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAACCAGAAAC
Found at i:7121 original size:52 final size:53
Alignment explanation
Indices: 7067--7232 Score: 190
Period size: 52 Copynumber: 3.0 Consensus size: 53
7057 GCTTAAGTAC
7067 TTTGATGTAGATGCCTCTGTGTTTAGGGATGAATATCCTTGTGTTTGAGGACT
1 TTTGATGTAGATGCCTCTGTGTTTAGGGATGAATATCCTTGTGTTTGAGGACT
* * * * *
7120 TTTAAAG-AGGTGCCTCTGTGTTTAGGGAAGAATACCCTTGTGTTTGAGGACT
1 TTTGATGTAGATGCCTCTGTGTTTAGGGATGAATATCCTTGTGTTTGAGGACT
* * * *
7172 TTTGATATAGAATTGCCTCTGTGTCTAGGGACTTATAAATGCCCTTGTGTTTGAGGACT
1 TTTGATGTAG-A-TGCCTCTGTGTTTAGGGA-TGA-ATAT--CCTTGTGTTTGAGGACT
7231 TT
1 TT
7233 AATTATTTGG
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
52 46 0.50
53 7 0.08
55 17 0.18
56 1 0.01
57 2 0.02
59 19 0.21
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.39
Consensus pattern (53 bp):
TTTGATGTAGATGCCTCTGTGTTTAGGGATGAATATCCTTGTGTTTGAGGACT
Found at i:8617 original size:29 final size:30
Alignment explanation
Indices: 8575--8631 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
8565 ACAGAGGCCC
* *
8575 AAATTGAGATTTCAATGGGCAAAATGTCCA
1 AAATTGAGAATTCAAGGGGCAAAATGTCCA
8605 AAATTGA-AATTCAAGGGGCAAAATGTC
1 AAATTGAGAATTCAAGGGGCAAAATGTC
8632 TAAACGCTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (30 bp):
AAATTGAGAATTCAAGGGGCAAAATGTCCA
Found at i:10223 original size:398 final size:401
Alignment explanation
Indices: 9479--10254 Score: 1106
Period size: 398 Copynumber: 1.9 Consensus size: 401
9469 CTTGGACCCT
* *
9479 GACAAGGCCCGAGTTCCTCTCCTAACAAGTGGTATCAGAGCCAGGTTGAACTCGATCAGTGTGGC
1 GACAAGGCCCGAGTTCCTCTCCCAACAAGTGGTATCAGAGCCAGGTTGAACTCGATCAATGTGGC
* * *
9544 CCATGAGCACGGTAAACCTAGTTGGCAGCAGGCCAGGGGCGTGCAATTGTGGAGTGTTCGTAGCT
66 CCATGAGCACAGTAAACCTAGTTGGCACCAGGCCAGGGGCGTGCAATTGTGGAGTGTTCATAGCT
*
9609 TGCACCACTCCATGGGTTAAGTCTTGCATGACCGGTAATTGGCTTAAAACTTGACGGGTTGGGCC
131 TGCACCACTCCAGGGGTTAAGTCTTGCATGACCGGTAATTGGCTTAAAACTTGACGGGTTGGGCC
* * *
9674 GCACGGGGGAGAGGTGAGGACTCACATGTAAATCGGGTGAGATTGTTAGGGATTCACATGTGAGG
196 GCACGGGGGAAAGATGAGGACTCACATGTAAATCGGGTGAGATTGTTAAGGATTCACATGTGAGG
* * *
9739 GAAACATCACACATCATAAAATGATGGGTTGTTTGAGTGGCATATATACATGAAGGACCCAAGAA
261 GAAACATCACACATCATAAAATGATGGGATGTTGGAGTAGCATATATACATGAAGGACCCAAGAA
* *
9804 ACCATCAGTCTAGGCTTTTGGGTTCGAATTGGTGTCCGGCATGTATATGGGCTACTTGGTGGGCC
326 ACCATCAGTCTAGACTTTTGGGTTCGAATTGGTGTCCGACATGTATATGGGCTACTTGGTGGGCC
9869 TTGCTGAAGCA
391 TTGCTGAAGCA
* *
9880 GACAGGGCCCGAGTTTCTCTCCCAACAAGTGGTATCAGAGCTC-GGTT-AGACTCGATCAATGTG
1 GACAAGGCCCGAGTTCCTCTCCCAACAAGTGGTATCAGAGC-CAGGTTGA-ACTCGATCAATGTG
* * * * * *
9943 GCCCATTAGCACAGTGAGCCT-GGTGTG-ACCA-TCCA-GGGCGTGCATTTGTGGAGTGTTCATA
64 GCCCATGAGCACAGTAAACCTAGTTG-GCACCAGGCCAGGGGCGTGCAATTGTGGAGTGTTCATA
* * * *
10004 GCTTGTACCACTCCAGGGGTTAAGTCTTGGAT-AGTCGGTAATTGGCTTAAGACTTGACGGGTTG
128 GCTTGCACCACTCCAGGGGTTAAGTCTTGCATGA-CCGGTAATTGGCTTAAAACTTGACGGGTTG
*
10068 GGCCGCACGGGGGAAAGATGAGGACTCACATGTGAATCAGGG-GAGATTGTTAAAGGATTCACAT
192 GGCCGCACGGGGGAAAGATGAGGACTCACATGTAAATC-GGGTGAGATTGTT-AAGGATTCACAT
* * **
10132 GTGAGGG-AACATCCCACATCATGAAGA-GATGGGATGTTGGAGTAGTTTATATACATGAAAGG-
255 GTGAGGGAAACATCACACATCAT-AAAATGATGGGATGTTGGAGTAGCATATATACATG-AAGGA
* *
10194 CCCAAGAAACCATTAGTCTAGACTTTTGGGTTCGGATTGGTGTCCGACATGTATATGGGCT
318 CCCAAGAAACCATCAGTCTAGACTTTTGGGTTCGAATTGGTGTCCGACATGTATATGGGCT
10255 GCTTCCCTCA
Statistics
Matches: 334, Mismatches: 33, Indels: 19
0.87 0.09 0.05
Matches are distributed among these distances:
397 1 0.00
398 221 0.66
399 31 0.09
400 7 0.02
401 73 0.22
402 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (401 bp):
GACAAGGCCCGAGTTCCTCTCCCAACAAGTGGTATCAGAGCCAGGTTGAACTCGATCAATGTGGC
CCATGAGCACAGTAAACCTAGTTGGCACCAGGCCAGGGGCGTGCAATTGTGGAGTGTTCATAGCT
TGCACCACTCCAGGGGTTAAGTCTTGCATGACCGGTAATTGGCTTAAAACTTGACGGGTTGGGCC
GCACGGGGGAAAGATGAGGACTCACATGTAAATCGGGTGAGATTGTTAAGGATTCACATGTGAGG
GAAACATCACACATCATAAAATGATGGGATGTTGGAGTAGCATATATACATGAAGGACCCAAGAA
ACCATCAGTCTAGACTTTTGGGTTCGAATTGGTGTCCGACATGTATATGGGCTACTTGGTGGGCC
TTGCTGAAGCA
Found at i:10644 original size:122 final size:122
Alignment explanation
Indices: 10427--10680 Score: 490
Period size: 122 Copynumber: 2.1 Consensus size: 122
10417 CGATTAACAG
10427 GTTCATGAAAGATTCAACCATTCAAGGAGATCTAAAATTAGATACTTTTAAGATTAGACATTATG
1 GTTCATGAAAGATTCAACCATTCAAGGAGATCTAAAATTAGATACTTTTAAGATTAGACATTATG
10492 TTAGTTTGATTTTTGTGGATAGTGTATGCTTTGAAATTAGATTTATATGTTAATTAC
66 TTAGTTTGATTTTTGTGGATAGTGTATGCTTTGAAATTAGATTTATATGTTAATTAC
* *
10549 GTTCATGAAAGATTCAACCATTCAAGGATATCTAAAATTAGATACTTTTAAGATTAGATATTATG
1 GTTCATGAAAGATTCAACCATTCAAGGAGATCTAAAATTAGATACTTTTAAGATTAGACATTATG
10614 TTAGTTTGATTTTTGTGGATAGTGTATGCTTTGAAATTAGATTTATATGTTAATTAC
66 TTAGTTTGATTTTTGTGGATAGTGTATGCTTTGAAATTAGATTTATATGTTAATTAC
10671 GTTCATGAAA
1 GTTCATGAAA
10681 TATTATTACT
Statistics
Matches: 130, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 130 1.00
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (122 bp):
GTTCATGAAAGATTCAACCATTCAAGGAGATCTAAAATTAGATACTTTTAAGATTAGACATTATG
TTAGTTTGATTTTTGTGGATAGTGTATGCTTTGAAATTAGATTTATATGTTAATTAC
Found at i:12215 original size:25 final size:27
Alignment explanation
Indices: 12171--12221 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
12161 TTAAAAATTA
12171 AGAAAATTCAAAAAAAGGAA-AAAATC
1 AGAAAATTCAAAAAAAGGAATAAAATC
* *
12197 AGAAAA-TCAAAAGATGGAATAAAAT
1 AGAAAATTCAAAAAAAGGAATAAAAT
12222 TTGTTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.67, C:0.06, G:0.14, T:0.14
Consensus pattern (27 bp):
AGAAAATTCAAAAAAAGGAATAAAATC
Found at i:14636 original size:12 final size:12
Alignment explanation
Indices: 14619--14644 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
14609 GAACTCTGAG
14619 TAGTTACCATTT
1 TAGTTACCATTT
14631 TAGTTACCATTT
1 TAGTTACCATTT
14643 TA
1 TA
14645 TTAGATACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (12 bp):
TAGTTACCATTT
Done.