Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007514.1 Corchorus capsularis cultivar CVL-1 contig07535, 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: 38830
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:3175 original size:30 final size:30
Alignment explanation
Indices: 3130--3195 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
3120 AAAGGATCGA
* *
3130 ATGGCTGGTTCTGGCCGGATGGCCCGTGCG
1 ATGGCCGGTTCTGGCCGGATGGCCCATGCG
*
3160 ATGGCCGGTTGTGGCCGGATGGCCCATGCG
1 ATGGCCGGTTCTGGCCGGATGGCCCATGCG
3190 ATGGCC
1 ATGGCC
3196 CGTGCGATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.09, C:0.27, G:0.42, T:0.21
Consensus pattern (30 bp):
ATGGCCGGTTCTGGCCGGATGGCCCATGCG
Found at i:5138 original size:475 final size:475
Alignment explanation
Indices: 4244--5183 Score: 1781
Period size: 475 Copynumber: 2.0 Consensus size: 475
4234 TTTCTACAAC
*
4244 AGGTGATAGGAGGGTGAGGAGAGGAGGATGAGGCGTCCCTCATGGTGATAAGAGACTTCCCTCCT
1 AGGTGATAGGAGGGTGAGGAGAGGAGGATGAGGCGTCCCTCATGGTGATAAGAGACTTCCCTCCC
4309 ATGGTACCAGGTATGATGAGGTACTAGGTGGCATAAGGTGCTAGATAACATCTGCTGTATCAGGT
66 ATGGTACCAGGTATGATGAGGTACTAGGTGGCATAAGGTGCTAGATAACATCTGCTGTATCAGGT
* *
4374 GTAGTCTTTGTTGCCTCCTTTGAGCTGATATCACTTGATTGGCTGATAGGTGACCCTGCGTCATG
131 GTAGTCTCTATTGCCTCCTTTGAGCTGATATCACTTGATTGGCTGATAGGTGACCCTGCGTCATG
*
4439 GAACTAAGTACCTTGGCCATGAAACAACTCATAATTAGCCATATTTAGCTCTTCAAATCGTAGAA
196 GAACTAAGTACCTTGGCAATGAAACAACTCATAATTAGCCATATTTAGCTCTTCAAATCGTAGAA
4504 ACATCCTTTAATTAAGAACCATGAATAAACCGGGGTGATAAAGCCACTTTGTCCTTAACTGAAGA
261 ACATCCTTTAATTAAGAACCATGAATAAACCGGGGTGATAAAGCCACTTTGTCCTTAACTGAAGA
*
4569 AGTTGTAAAAGTTGCAAACGAACTTGGATCGAGCTCAAACTTCACCAGTATGGTTCATGTATCAG
326 AGTTGTAAAAGTTGCAAACGAAATTGGATCGAGCTCAAACTTCACCAGTATGGTTCATGTATCAG
*
4634 CCACAGAACATGGTAAAAATCTTGGCTTGATCCGAGCCTTTCTTCATAGTAAACCGAACTTCTCA
391 CCACAGAACATGGTAAAAATCTAGGCTTGATCCGAGCCTTTCTTCATAGTAAACCGAACTTCTCA
*
4699 CCTGAAACTGGTGAAGTTTG
456 CCTCAAACTGGTGAAGTTTG
*
4719 AGGTGATAGGATGGTGAGGAGAGGAGGATGAGGCGTCCCTCATGGTGATAAGAGACTTCCCTCCC
1 AGGTGATAGGAGGGTGAGGAGAGGAGGATGAGGCGTCCCTCATGGTGATAAGAGACTTCCCTCCC
*
4784 ATGGTACCAGGTATGATGAGGTACTAGGTGGCATGAGGTGCTAGATAACATCTGCTGTATCAGGT
66 ATGGTACCAGGTATGATGAGGTACTAGGTGGCATAAGGTGCTAGATAACATCTGCTGTATCAGGT
4849 GTAGTCTCTATTGCCTCCTTTGAGCTGATATCACTTGATTGGCTGATAGGTGACCCTGCGTCATG
131 GTAGTCTCTATTGCCTCCTTTGAGCTGATATCACTTGATTGGCTGATAGGTGACCCTGCGTCATG
*
4914 GAACTAAGTACCTTGGCAATGAAACCACTCATAATTAGCCATATTTAGCTCTTCAAATCGTAGAA
196 GAACTAAGTACCTTGGCAATGAAACAACTCATAATTAGCCATATTTAGCTCTTCAAATCGTAGAA
4979 ACATCCTTTAATTAAGAACCATGAATAAACCGGGGTGATAAAGCCACTTTGTCCTTAACTGAAGA
261 ACATCCTTTAATTAAGAACCATGAATAAACCGGGGTGATAAAGCCACTTTGTCCTTAACTGAAGA
5044 AGTTGTAAAAGTTGCAAACGAAATTGGATCGAGCTCAAACTTCACCAGTATGGTTCATGTATCAG
326 AGTTGTAAAAGTTGCAAACGAAATTGGATCGAGCTCAAACTTCACCAGTATGGTTCATGTATCAG
*
5109 CCACAGACCATGGTAAAAATCTAGGCTTGATCCGAGCCTTTCTTCATAGTAAACCGAACTTCTCA
391 CCACAGAACATGGTAAAAATCTAGGCTTGATCCGAGCCTTTCTTCATAGTAAACCGAACTTCTCA
5174 CCTCAAACTG
456 CCTCAAACTG
5184 TCCTTAAATG
Statistics
Matches: 454, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
475 454 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (475 bp):
AGGTGATAGGAGGGTGAGGAGAGGAGGATGAGGCGTCCCTCATGGTGATAAGAGACTTCCCTCCC
ATGGTACCAGGTATGATGAGGTACTAGGTGGCATAAGGTGCTAGATAACATCTGCTGTATCAGGT
GTAGTCTCTATTGCCTCCTTTGAGCTGATATCACTTGATTGGCTGATAGGTGACCCTGCGTCATG
GAACTAAGTACCTTGGCAATGAAACAACTCATAATTAGCCATATTTAGCTCTTCAAATCGTAGAA
ACATCCTTTAATTAAGAACCATGAATAAACCGGGGTGATAAAGCCACTTTGTCCTTAACTGAAGA
AGTTGTAAAAGTTGCAAACGAAATTGGATCGAGCTCAAACTTCACCAGTATGGTTCATGTATCAG
CCACAGAACATGGTAAAAATCTAGGCTTGATCCGAGCCTTTCTTCATAGTAAACCGAACTTCTCA
CCTCAAACTGGTGAAGTTTG
Found at i:11735 original size:21 final size:20
Alignment explanation
Indices: 11696--11740 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
11686 CCAGATTAAT
* *
11696 TAAAAAGAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
11716 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
11737 TAAA
1 TAAA
11741 TCTAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Found at i:13914 original size:21 final size:19
Alignment explanation
Indices: 13882--13920 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
13872 CAATCAAGCA
13882 AATCAAGATTCAAAGCATC
1 AATCAAGATTCAAAGCATC
*
13901 AATCATAGCATTCATAGCAT
1 AATCA-AG-ATTCAAAGCAT
13921 ATGAGTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.26
Consensus pattern (19 bp):
AATCAAGATTCAAAGCATC
Found at i:16951 original size:21 final size:20
Alignment explanation
Indices: 16912--16956 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
16902 CCAGATTAAT
* *
16912 TAAAAAGAAAGCAATTAAAC
1 TAAAAACAAAGCAAGTAAAC
*
16932 TAAAAACAAAGCAAAGTAAAT
1 TAAAAACAAAGC-AAGTAAAC
16953 TAAA
1 TAAA
16957 TCTAAATCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.67, C:0.09, G:0.09, T:0.16
Consensus pattern (20 bp):
TAAAAACAAAGCAAGTAAAC
Found at i:22683 original size:11 final size:11
Alignment explanation
Indices: 22665--22697 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
22655 AATGGTCTTC
22665 AAATCTTCAAA
1 AAATCTTCAAA
*
22676 ATATCTTCAAA
1 AAATCTTCAAA
22687 AAATCTTCAAA
1 AAATCTTCAAA
22698 TATGAACTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.52, C:0.18, G:0.00, T:0.30
Consensus pattern (11 bp):
AAATCTTCAAA
Found at i:38441 original size:31 final size:29
Alignment explanation
Indices: 38403--38504 Score: 100
Period size: 31 Copynumber: 3.4 Consensus size: 29
38393 GGCTAATTGT
38403 TCAAATAAGGGTCTAACATTTGATAAAATGC
1 TCAAATAAGGGTCTAAC-TTTG-TAAAATGC
* **
38434 TCAAATAAGGGTCTGATCTTT-TAATTTGGC
1 TCAAATAAGGGTCT-AACTTTGTAAAAT-GC
*
38464 -CAAATAAGGGTCTAACGTTTGCCAAAATGC
1 TCAAATAAGGGTCTAAC-TTTG-TAAAATGC
38494 TCAAATAAGGG
1 TCAAATAAGGG
38505 CCCGATCTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
28 2 0.03
29 20 0.34
30 4 0.07
31 30 0.52
32 2 0.03
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (29 bp):
TCAAATAAGGGTCTAACTTTGTAAAATGC
Found at i:38497 original size:60 final size:60
Alignment explanation
Indices: 38404--38566 Score: 254
Period size: 60 Copynumber: 2.7 Consensus size: 60
38394 GCTAATTGTT
* ** * * *
38404 CAAATAAGGGTCTAACATTTGATAAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGC
38464 CAAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGC
1 CAAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGC
* *
38524 CAAATAAGGGCCTAATGTTTGCCAAAATGCTCAAATAAGGGCC
1 CAAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGCC
38567 TATCTCACGT
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 95 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (60 bp):
CAAATAAGGGTCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCGATCTTTGAATTTGGC
Found at i:38544 original size:29 final size:29
Alignment explanation
Indices: 38435--38544 Score: 89
Period size: 29 Copynumber: 3.7 Consensus size: 29
38425 ATAAAATGCT
* * *
38435 CAAATAAGGGTCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAATCTTTGAATTTGGC
* **
38464 CAAATAAGGGTCTAA-CGTTTGCCAAAAT-GC
1 CAAATAAGGGCCTAATC-TTTG--AATTTGGC
**
38494 TCAAATAAGGGCCCGATCTTTGAATTTGGC
1 -CAAATAAGGGCCTAATCTTTGAATTTGGC
*
38524 CAAATAAGGGCCTAATGTTTG
1 CAAATAAGGGCCTAATCTTTG
38545 CCAAAATGCT
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
28 1 0.02
29 38 0.60
30 4 0.06
31 19 0.30
32 1 0.02
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (29 bp):
CAAATAAGGGCCTAATCTTTGAATTTGGC
Found at i:38562 original size:31 final size:31
Alignment explanation
Indices: 38464--38568 Score: 117
Period size: 31 Copynumber: 3.5 Consensus size: 31
38454 TTAATTTGGC
* *
38464 CAAATAAGGGTCTAACGTTTGCCAAAATGCT
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCT
** * **
38495 CAAATAAGGGCCCGATCTTTG--AATTTGGC-
1 CAAATAAGGGCCTAATGTTTGCCAAAAT-GCT
38524 CAAATAAGGGCCTAATGTTTGCCAAAATGCT
1 CAAATAAGGGCCTAATGTTTGCCAAAATGCT
38555 CAAATAAGGGCCTA
1 CAAATAAGGGCCTA
38569 TCTCACGTGT
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
29 21 0.36
30 4 0.07
31 33 0.57
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (31 bp):
CAAATAAGGGCCTAATGTTTGCCAAAATGCT
Found at i:38636 original size:31 final size:30
Alignment explanation
Indices: 38598--38727 Score: 140
Period size: 31 Copynumber: 4.3 Consensus size: 30
38588 TGACACCAGG
38598 CCCTTATTTGAGCATTTTCGATAACGTTAGA
1 CCCTTATTTGAGCATTTTC-ATAACGTTAGA
* *
38629 CCCTTATTTGAGCATTTTTTATAACGTTAGG
1 CCCTTATTTGAGCA-TTTTCATAACGTTAGA
* * *
38660 CCCTTATTTG-GCCATATT-A-AAAGATCAGA
1 CCCTTATTTGAG-CATTTTCATAACG-TTAGA
*
38689 CCCTTATTTGAGCATTTTCAATAACGTTAGG
1 CCCTTATTTGAGCATTTTC-ATAACGTTAGA
38720 CCCTTATT
1 CCCTTATT
38728 AGGCCAAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 14
0.77 0.09 0.13
Matches are distributed among these distances:
28 3 0.04
29 19 0.23
30 5 0.06
31 48 0.59
32 7 0.09
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTCATAACGTTAGA
Found at i:38698 original size:29 final size:29
Alignment explanation
Indices: 38657--38758 Score: 100
Period size: 29 Copynumber: 3.4 Consensus size: 29
38647 TTATAACGTT
38657 AGGCCCTTATTTGGCCATATTAAAAGATC
1 AGGCCCTTATTTGGCCATATTAAAAGATC
* * *
38686 AGACCCTTATTTGAG-CATTTTCAATAACG-TT
1 AGGCCCTTATTTG-GCCATATT-AA-AA-GATC
* *
38717 AGGCCCTTATTAGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGGCCATATTAAAAGATC
*
38746 CGGCCCTTATTTG
1 AGGCCCTTATTTG
38759 AGAATTTTGG
Statistics
Matches: 57, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
28 1 0.02
29 31 0.54
30 6 0.11
31 18 0.32
32 1 0.02
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (29 bp):
AGGCCCTTATTTGGCCATATTAAAAGATC
Found at i:38698 original size:60 final size:60
Alignment explanation
Indices: 38626--38789 Score: 233
Period size: 60 Copynumber: 2.7 Consensus size: 60
38616 CGATAACGTT
** *
38626 AGACCCTTATTTGAGCATTTTTTATAACGTTAGGCCCTTATTTGGCCATATTAAAAGATC
1 AGACCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
*
38686 AGACCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTAGGCCAAATTAAAAGATC
1 AGACCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
* * *
38746 CGGCCCTTATTTGAGAATTTTGGC-A-AACGTTAGGCCCTTATTTG
1 AGACCCTTATTTGAGCATTTT--CAATAACGTTAGGCCCTTATTTG
38790 AGCAATTAGC
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
60 92 0.98
61 1 0.01
62 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (60 bp):
AGACCCTTATTTGAGCATTTTCAATAACGTTAGGCCCTTATTTGGCCAAATTAAAAGATC
Done.