Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014296.1 Corchorus capsularis cultivar CVL-1 contig14317, 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: 3280
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Found at i:421 original size:27 final size:27
Alignment explanation
Indices: 389--462 Score: 121
Period size: 27 Copynumber: 2.7 Consensus size: 27
379 AAGTGGACTC
389 AAAATGACCAAAATGCCCCTGAATGTA
1 AAAATGACCAAAATGCCCCTGAATGTA
* * *
416 AGAATGACAAAAATGCCCATGAATGTA
1 AAAATGACCAAAATGCCCCTGAATGTA
443 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
463 AGGTGACCCT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.46, C:0.22, G:0.15, T:0.18
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATGTA
Found at i:750 original size:25 final size:26
Alignment explanation
Indices: 722--774 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
712 GACTAGAGAC
*
722 CTCAAGCAGGA-TTTGAAAT-AAAACT
1 CTCAAACAGGATTTTG-AATCAAAACT
*
747 CTCAAACATGATTTTGAATCAAAACT
1 CTCAAACAGGATTTTGAATCAAAACT
773 CT
1 CT
775 TGAACAGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (26 bp):
CTCAAACAGGATTTTGAATCAAAACT
Found at i:1181 original size:32 final size:32
Alignment explanation
Indices: 1140--1244 Score: 138
Period size: 32 Copynumber: 3.1 Consensus size: 32
1130 GATAAAAATG
1140 AACTTATAAAGCAATGATCCTAGATCAGGATT
1 AACTTATAAAGCAATGATCCTAGATCAGGATT
1172 AACTTATAAAGCAATGATCCTAGATCAGGATT
1 AACTTATAAAGCAATGATCCTAGATCAGGATT
*
1204 AAACATAAATTGATAAAGCAATGATCCTAAATCAGGATT
1 -AAC-----TT-ATAAAGCAATGATCCTAGATCAGGATT
1243 AA
1 AA
1245 AATAAACCCA
Statistics
Matches: 65, Mismatches: 1, Indels: 8
0.88 0.01 0.11
Matches are distributed among these distances:
32 32 0.49
33 3 0.05
38 4 0.06
39 26 0.40
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (32 bp):
AACTTATAAAGCAATGATCCTAGATCAGGATT
Found at i:1229 original size:109 final size:109
Alignment explanation
Indices: 1038--1263 Score: 283
Period size: 109 Copynumber: 2.1 Consensus size: 109
1028 GGATTGAAAA
* * * **
1038 AAAGCCATGATCCTAAATCAGGGAGAAACTAATTAATCAATGATCCTAAATCAGGATTAAAATGC
1 AAAGCAATGATCCTAAATCAGGGAGAAACTAATAAAGCAATGATCCTAAATCAGGATTAAAATAA
* * **
1103 ATTAATAAATCAATGATCCTAAACCAGGATAAAAATGAACTTAT
66 ATTAATAAAGCAATGATCCTAAACCAGGATAAAAATAAACCCAT
* ** * *
1147 AAAGCAATGATCCTAGATCA-GGATTAACTTATAAAGCAATGATCCTAGATCAGGATTAAACATA
1 AAAGCAATGATCCTAAATCAGGGAGAAACTAATAAAGCAATGATCCTAAATCAGGATTAAA-ATA
* * *
1211 AATTGATAAAGCAATGATCCTAAATCAGGATTAAAATAAACCCAT
65 AATTAATAAAGCAATGATCCTAAACCAGGATAAAAATAAACCCAT
1256 AAAGCAAT
1 AAAGCAAT
1264 AATCATGATT
Statistics
Matches: 99, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
108 34 0.34
109 65 0.66
ACGTcount: A:0.47, C:0.15, G:0.13, T:0.24
Consensus pattern (109 bp):
AAAGCAATGATCCTAAATCAGGGAGAAACTAATAAAGCAATGATCCTAAATCAGGATTAAAATAA
ATTAATAAAGCAATGATCCTAAACCAGGATAAAAATAAACCCAT
Found at i:1259 original size:38 final size:38
Alignment explanation
Indices: 1075--1263 Score: 205
Period size: 38 Copynumber: 5.1 Consensus size: 38
1065 ACTAATTAAT
** *
1075 CAATGATCCTAAATCAGGATTAAAATGCA-TTAATAAAT
1 CAATGATCCTAAATCAGGATTAAAATAAACTT-ATAAAG
* * *
1113 CAATGATCCTAAACCAGGATAAAAATGAACTTATAAAG
1 CAATGATCCTAAATCAGGATTAAAATAAACTTATAAAG
*
1151 CAATGATCCTAGATCAGGA-T----T-AACTTATAAAG
1 CAATGATCCTAAATCAGGATTAAAATAAACTTATAAAG
*
1183 CAATGATCCTAGATCAGGATTAAACATAAA-TTGATAAAG
1 CAATGATCCTAAATCAGGATTAAA-ATAAACTT-ATAAAG
**
1222 CAATGATCCTAAATCAGGATTAAAATAAACCCATAAAG
1 CAATGATCCTAAATCAGGATTAAAATAAACTTATAAAG
1260 CAAT
1 CAAT
1264 AATCATGATT
Statistics
Matches: 131, Mismatches: 10, Indels: 20
0.81 0.06 0.12
Matches are distributed among these distances:
32 30 0.23
33 2 0.02
38 66 0.50
39 33 0.25
ACGTcount: A:0.47, C:0.15, G:0.13, T:0.25
Consensus pattern (38 bp):
CAATGATCCTAAATCAGGATTAAAATAAACTTATAAAG
Found at i:1789 original size:69 final size:69
Alignment explanation
Indices: 1533--1875 Score: 517
Period size: 70 Copynumber: 4.9 Consensus size: 69
1523 ACCATAGATC
* * * *
1533 AACTGGAAACAACTTATGAAA-AGCCGCCCTGAGTCGACTGAATCGATCATTCTGACATAAACTT
1 AACTTGAAACAACTGAAGAAAGA-CCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTT
1597 GGATA
65 GGATA
* * * *
1602 AACGTTGAAACTACTGAAGAAAGACCACACTGGGTCGACTGAATCGATCATTCTGACACAAACTT
1 AAC-TTGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTT
1667 GGATA
65 GGATA
1672 AACTTGGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTT
1 AACTT-GAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTT
1737 GGATA
65 GGATA
* * *
1742 AACTTGAAACAACGGAAGAAAGACCGCCCTTGGTTGACTGAATCGATCATTCTGACATAAACTTC
1 AACTTGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTT-
*
1807 GAATA
65 GGATA
*
1812 AACTTGAAAACAATTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
1 AACTTG-AAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
1876 AAAGAAAGAC
Statistics
Matches: 249, Mismatches: 20, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
69 61 0.24
70 134 0.54
71 54 0.22
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (69 bp):
AACTTGAAACAACTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTG
GATA
Found at i:2058 original size:69 final size:70
Alignment explanation
Indices: 1944--2135 Score: 260
Period size: 70 Copynumber: 2.7 Consensus size: 70
1934 TCCGTCATAA
* *
1944 ACTGAAGAAAGAACCACCCTGGGTCAACTGAATCGATCATTCTGACATAAACTTGAATAAACTTG
1 ACTGAAGAAAG-ACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGAATAAACTGG
2009 AAAAC-
65 AAAACT
* * * * * *
2014 ATTGAAGAAAGACCGCCCTGGGTCGACTGAATCGATCATTCTGACAAAAACTTGGATCAACTGGG
1 ACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGAATAAACTGGA
*
2079 AAGCT
66 AAACT
* * *
2084 ACTGAAGAAAGACCACCTTGGGTCGGCTGAATCGATCATTCTGACGTAAACT
1 ACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACT
2136 GGAGAAAAAC
Statistics
Matches: 106, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
69 50 0.47
70 56 0.53
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (70 bp):
ACTGAAGAAAGACCACCCTGGGTCGACTGAATCGATCATTCTGACATAAACTTGAATAAACTGGA
AAACT
Done.