Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011885.1 Corchorus capsularis cultivar CVL-1 contig11906, 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: 9552
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:1120 original size:20 final size:23
Alignment explanation
Indices: 1081--1126 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 23
1071 CAATTGGAGT
*
1081 TTTTTTTAATAACTTGAATTTTA
1 TTTTTTTAATAACTTGAATTTAA
1104 TTTTTTT-ATAA-TT-AATTTAA
1 TTTTTTTAATAACTTGAATTTAA
1124 TTT
1 TTT
1127 ATTGATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 9 0.41
21 2 0.09
22 4 0.18
23 7 0.32
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTTTTAATAACTTGAATTTAA
Found at i:4095 original size:30 final size:29
Alignment explanation
Indices: 4033--4102 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
4023 ACCGAACCGT
****
4033 CAAATAAGCCCCTGAACTATTATTTCGGC
1 CAAATAAGCCCCTGAACTATTAAAAAGGC
*
4062 CAAATAAGCCCCTGAACTCTTAAAAAAGGC
1 CAAATAAGCCCCTGAACTATT-AAAAAGGC
4092 CAAATAAGCCC
1 CAAATAAGCCC
4103 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAGGC
Found at i:5040 original size:2 final size:2
Alignment explanation
Indices: 5033--5065 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
5023 CGTTCGGCAA
5033 AT AT AT AT AT AT AT AT AT A- AT AT ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
5066 CTAAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:6067 original size:108 final size:109
Alignment explanation
Indices: 5871--6068 Score: 301
Period size: 108 Copynumber: 1.8 Consensus size: 109
5861 TCGAATTAGC
* * *
5871 TAACCACCTACTGACTTATATGATAAGAACCGAGAGAAAAAAAAAACGCTATAACTAAATTAATT
1 TAACCACCTACTCACATATATGATAAGAACC-AGAGAAAAAAAAAACGCTAAAACTAAATTAATT
* *
5936 TGCTAGCCACATATCAAGAATGCTCGATGCGCCAGCGCGAGCCGA
65 TGATAGCCACAAATCAAGAATGCTCGATGCGCCAGCGCGAGCCGA
* *
5981 TAACCACCTACTCACATATATGATAAGAACC-GAGAAAAAAAAAACTCTAAAACTTAAA-TCATT
1 TAACCACCTACTCACATATATGATAAGAACCAGAGAAAAAAAAAACGCTAAAAC-TAAATTAATT
6044 TGATAGCCACAAATCAAGAATGCTC
65 TGATAGCCACAAATCAAGAATGCTC
6069 AACGCGTCAA
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
108 47 0.59
109 4 0.05
110 29 0.36
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.21
Consensus pattern (109 bp):
TAACCACCTACTCACATATATGATAAGAACCAGAGAAAAAAAAAACGCTAAAACTAAATTAATTT
GATAGCCACAAATCAAGAATGCTCGATGCGCCAGCGCGAGCCGA
Found at i:6407 original size:168 final size:165
Alignment explanation
Indices: 6131--6614 Score: 637
Period size: 168 Copynumber: 2.9 Consensus size: 165
6121 AACATATGGA
* ** * * * ** *
6131 AATTACTAAAAGATCCCCACCCCGGATTAATGAGGAGCGAGAGAACTAATTTTTTTCATCTTTTC
1 AATTAATAAAAGATCCCCACCAAGGATTGATTAAGAGTTAGAGAACTAATTTTTTTCGTCTTTTC
* * * *
6196 AC-ACTTGACCGATTACTTAAATGCCCTAACTTTTGATTCTTGAGGTGATTAAATAACTAGACTT
66 -CTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTA-ACTT
*
6260 TTTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGG
129 TTTGGTCATTTCTCAATTGACTTGAATAGAGTAGTGG
* * * * ** *
6297 AATTACTAAAAGATCCCTACCAAGGCTTGCTTTTGGAGTTAGAGAACTTATTTCTTTTCGTCTTT
1 AATTAATAAAAGATCCCCACCAAGGATTG-ATTAAGAGTTAGAGAACTAATTT-TTTTCGTCTTT
*
6362 TCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAAGTAATCT
64 TCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAA-CT
* *
6427 TTTTGGTAATTTCTCAATGGACTTGAATAGAGTAGTGG
128 TTTTGGTCATTTCTCAATTGACTTGAATAGAGTAGTGG
* * *
6465 AATTAATAAAAGATCCCCATCAAGGATTGATTAAGAGTTAGAGAACTAATCTTTTTCGTCTTTAC
1 AATTAATAAAAGATCCCCACCAAGGATTGATTAAGAGTTAGAGAACTAATTTTTTTCGTCTTTTC
*
6530 CTACTTGGCATATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAACTTT
66 CTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACT-AACTTT
* *
6595 TTTGTCATTTTTCAATTGAC
130 TTGGTCATTTCTCAATTGAC
6615 AAATGACTCA
Statistics
Matches: 277, Mismatches: 36, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
166 112 0.40
167 39 0.14
168 126 0.45
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (165 bp):
AATTAATAAAAGATCCCCACCAAGGATTGATTAAGAGTTAGAGAACTAATTTTTTTCGTCTTTTC
CTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAACTTTT
TGGTCATTTCTCAATTGACTTGAATAGAGTAGTGG
Found at i:7721 original size:11 final size:11
Alignment explanation
Indices: 7707--7744 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
7697 ATTCATAACA
7707 AATTTATAATT
1 AATTTATAATT
7718 AATTTATAATT
1 AATTTATAATT
7729 -ATTTGATAATT
1 AATTT-ATAATT
*
7740 TATTT
1 AATTT
7745 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:9544 original size:166 final size:166
Alignment explanation
Indices: 9167--9552 Score: 510
Period size: 166 Copynumber: 2.3 Consensus size: 166
9157 TGAATAAACA
* * * * *
9167 TGTGGAATTACTAAAAGATCCCCACTC-CGGATTAATGAGGAGCGAGAGAACTAATTTTTTTCGT
1 TGTGGAATTACTAAAAGATCCCCA-TCAAGGATTGATGATGAGCTAGAGAACTAATATTTTTCGT
9231 CTTTTCCCACTTGACAGATTACTTAAATATCCTAACTTTTGATTCTTGAGGGGATTAAATAACTA
65 CTTTTCCCACTTGACAGATTACTTAAATATCCTAACTTTTGATTCTTGAGGGGATTAAATAACTA
* * *
9296 GACTTTTTGGTCATTTCTTAATTGACTTTAATAGAGT
130 GACTTTTTGGTCATTTCTCAATGGACTTGAATAGAGT
* * ** * * **
9333 AGTAG-ATTACTAAAAGATCCTTACCAA-GACTTGCTTTTGGAGCTAGAGAACTAATATTTTTCG
1 TGTGGAATTACTAAAAGATCCCCATCAAGGA-TTGATGAT-GAGCTAGAGAACTAATATTTTTCG
* * * *
9396 TCTTTTCCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTGAGGGGATTAAATAAGT
64 TCTTTTCCCACTTGACAGATTACTTAAATATCCTAACTTTTGATTCTTGAGGGGATTAAATAACT
*
9461 A-ATCTTTTTTGTCATTTCTCAATGGACTTGAATAGAGT
129 AGA-CTTTTTGGTCATTTCTCAATGGACTTGAATAGAGT
*
9499 TGTGGAATTACTAAAAGATCCCCGTCAAGGATTGATGATGAGCTAGAGAACTAA
1 TGTGGAATTACTAAAAGATCCCCATCAAGGATTGATGATGAGCTAGAGAACTAA
Statistics
Matches: 184, Mismatches: 30, Indels: 12
0.81 0.13 0.05
Matches are distributed among these distances:
164 3 0.02
165 20 0.11
166 136 0.74
167 23 0.12
168 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (166 bp):
TGTGGAATTACTAAAAGATCCCCATCAAGGATTGATGATGAGCTAGAGAACTAATATTTTTCGTC
TTTTCCCACTTGACAGATTACTTAAATATCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAG
ACTTTTTGGTCATTTCTCAATGGACTTGAATAGAGT
Done.