Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011711.1 Corchorus capsularis cultivar CVL-1 contig11732, 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: 13214
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Found at i:1448 original size:3 final size:3
Alignment explanation
Indices: 1440--1471 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1430 CTTTTGCCTT
1440 TTG TTG TTG TTG TTG TTG TTG TTG -TG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1472 CTATAACGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.00, C:0.00, G:0.34, T:0.66
Consensus pattern (3 bp):
TTG
Found at i:1669 original size:25 final size:25
Alignment explanation
Indices: 1617--1669 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1607 CATATTTATT
** *
1617 TTTTAAAGTAAAATATTATTTAAAC
1 TTTTAAAGTAAAATAAAATGTAAAC
* *
1642 TTTTAATGTAAAATAAAATGTAATC
1 TTTTAAAGTAAAATAAAATGTAAAC
1667 TTT
1 TTT
1670 AAAATTTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (25 bp):
TTTTAAAGTAAAATAAAATGTAAAC
Found at i:4014 original size:84 final size:83
Alignment explanation
Indices: 3910--4197 Score: 368
Period size: 84 Copynumber: 3.4 Consensus size: 83
3900 CCATATAGAA
* * *
3910 ATTGCCCTTGT-TTCATAATTGTGTTTAGGGACTTT-AGTATGGATGCCTCTGTGTTATAAATGT
1 ATTGCCCCTGTGTT-ATAATTGTGCTTGGGGACTTTGA-TATGGATGCCTCTGTGTTATAAATGT
*
3973 GTTTGAGGACTTTTAGAGATG
64 GCTTGAGGAC-TTTAGAGATG
* * *
3994 ATTGCCCATGTGTTATAATTGTGTTTGGGGACTTTGATATAGATGCCTCTGTGTTATAAATGTGC
1 ATTGCCCCTGTGTTATAATTGTGCTTGGGGACTTTGATATGGATGCCTCTGTGTTATAAATGTGC
* *
4059 ATGAGGACTTT-GAAATAG
66 TTGAGGACTTTAGAGAT-G
* *
4077 AGGTGCCCCTGTGTTATAATTGTGCTTGGGGACTTTGATATGGGTGCCTCTGTGTTATAAATGTG
1 A-TTGCCCCTGTGTTATAATTGTGCTTGGGGACTTTGATATGGATGCCTCTGTGTTATAAATGTG
4142 CTTGAGGACTTTAGCAAGA-G
65 CTTGAGGACTTTAG--AGATG
*
4162 AATTGCCCCTGTGTTATAAATGTGCTTGGGGACTTT
1 -ATTGCCCCTGTGTTATAATTGTGCTTGGGGACTTT
4198 AGGGAGAGAG
Statistics
Matches: 181, Mismatches: 15, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
82 4 0.02
83 5 0.03
84 132 0.73
85 37 0.20
86 1 0.01
87 2 0.01
ACGTcount: A:0.22, C:0.12, G:0.27, T:0.39
Consensus pattern (83 bp):
ATTGCCCCTGTGTTATAATTGTGCTTGGGGACTTTGATATGGATGCCTCTGTGTTATAAATGTGC
TTGAGGACTTTAGAGATG
Found at i:4067 original size:41 final size:42
Alignment explanation
Indices: 3953--4197 Score: 248
Period size: 41 Copynumber: 5.8 Consensus size: 42
3943 TTAGTATGGA
* * *
3953 TGCCTCTGTGTTATAAATGTGTTTGAGGACTTTTAGAGAT-GAT
1 TGCCTCTGTGTTATAAATGTGCTTGAGGAC-TTT-GATATAGAG
* * *
3996 TGCC-CATGTGTTATAATTGTGTTTGGGGACTTTGATATAGA-
1 TGCCTC-TGTGTTATAAATGTGCTTGAGGACTTTGATATAGAG
* *
4037 TGCCTCTGTGTTATAAATGTGCATGAGGACTTTGAAATAGAGG
1 TGCCTCTGTGTTATAAATGTGCTTGAGGACTTTGATATAGA-G
* * * *
4080 TGCCCCTGTGTTATAATTGTGCTTGGGGACTTTGATAT-GGG
1 TGCCTCTGTGTTATAAATGTGCTTGAGGACTTTGATATAGAG
* *
4121 TGCCTCTGTGTTATAAATGTGCTTGAGGACTTTAGCA-AGAGAAT
1 TGCCTCTGTGTTATAAATGTGCTTGAGGACTTT-G-ATATAG-AG
* *
4165 TGCCCCTGTGTTATAAATGTGCTTGGGGACTTT
1 TGCCTCTGTGTTATAAATGTGCTTGAGGACTTT
4198 AGGGAGAGAG
Statistics
Matches: 171, Mismatches: 22, Indels: 17
0.81 0.10 0.08
Matches are distributed among these distances:
41 69 0.40
42 10 0.06
43 61 0.36
44 31 0.18
ACGTcount: A:0.22, C:0.13, G:0.27, T:0.38
Consensus pattern (42 bp):
TGCCTCTGTGTTATAAATGTGCTTGAGGACTTTGATATAGAG
Found at i:5720 original size:55 final size:55
Alignment explanation
Indices: 5616--5720 Score: 176
Period size: 55 Copynumber: 1.9 Consensus size: 55
5606 TTGTCCATTG
**
5616 ATACTTTTTCTTGTTGTTATAAGTATCTCAATCTGCTTGTGGATGAATACATATC
1 ATACTTTTTCTTGTTGTTATAAGTATCTCAATCTGCTTGTGGACCAATACATATC
5671 ATACTTTTTCTTGTTGTTATAAGTATCTCAATCTGCTT-TGTGACCAATAC
1 ATACTTTTTCTTGTTGTTATAAGTATCTCAATCTGCTTGTG-GACCAATAC
5721 TGATGGTTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
54 2 0.04
55 45 0.96
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (55 bp):
ATACTTTTTCTTGTTGTTATAAGTATCTCAATCTGCTTGTGGACCAATACATATC
Found at i:11708 original size:35 final size:35
Alignment explanation
Indices: 11669--11861 Score: 269
Period size: 35 Copynumber: 5.5 Consensus size: 35
11659 GAATTTCTTG
* * *
11669 AAATGAGATCACCTCTGATTGTTGGAAACTACTGA
1 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
* * * * *
11704 AAATGTGATCATCTCTGATCGTTGCAAAATATTGA
1 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
*
11739 AAATGCGGTCAACTCTGATCGTTGGAAACTACTGA
1 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
*
11774 AAATGCGATCAACTCTGATTGTTGGAAACTACTGA
1 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
*
11809 AAATGCGATCAACTCTGATCGTTGGAAAATACTGA
1 AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
* *
11844 AAATGAGATCAAATCTGA
1 AAATGCGATCAACTCTGA
11862 CCTCTGAAAA
Statistics
Matches: 140, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 140 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (35 bp):
AAATGCGATCAACTCTGATCGTTGGAAACTACTGA
Found at i:11720 original size:70 final size:70
Alignment explanation
Indices: 11640--12390 Score: 333
Period size: 70 Copynumber: 10.7 Consensus size: 70
11630 AACTCCTCTG
* * * * * *
11640 GATCAACTCTGATCATCGGGAATTTCTTG-AAATGAGATCACCTCTGATTGTTGGAAACTACTGA
1 GATCAACTCTGATCGT-GGAAAATTCTTGAAAATGCGATCAACTCTGATCGTTGGAAACTACTGA
*
11704 AAATGT
65 AAATGA
* * * *
11710 GATCATCTCTGATCGTTGCAAAA-TATTGAAAATGCGGTCAACTCTGATCGTTGGAAACTACTGA
1 GATCAACTCTGATCG-TGGAAAATTCTTGAAAATGCGATCAACTCTGATCGTTGGAAACTACTGA
*
11774 AAATGC
65 AAATGA
* * * *
11780 GATCAACTCTGATTGTTGGAAACTAC-TGAAAATGCGATCAACTCTGATCGTTGGAAAATACTGA
1 GATCAACTCTGATCG-TGGAAAATTCTTGAAAATGCGATCAACTCTGATCGTTGGAAACTACTGA
11844 AAATGA
65 AAATGA
* * * * *
11850 GATCAAATCTGACCTC-T-GAAAACTTCTTGAAATGAATGAGATCAAATCTGA-CCTCTGAAAAC
1 GATCAACTCTGA--TCGTGGAAAA-TTCTTG-AA--AATGCGATCAACTCTGATCGT-TGGAAAC
* *
11912 TTCTTG-GAATGA
59 TAC-TGAAAATGA
* * * * * * *
11924 GATCAACTCTGACCTC-TGGAAACTTCCTG-GAATGAGATCAACTCTGA-CCTCTGAAAACTTCT
1 GATCAACTCTGA--TCGTGGAAAATTCTTGAAAATGCGATCAACTCTGATCGT-TGGAAACTAC-
*
11986 TG-CAATGA
62 TGAAAATGA
* * * * *
11994 GATCAACTCTGACCTC-TGGAAACTTCTTG-GAATGAGATCAACTCTGA-CTTCTGGAAACTTCT
1 GATCAACTCTGA--TCGTGGAAAATTCTTGAAAATGCGATCAACTCTGATCGT-TGGAAACTAC-
*
12056 TG-GAATGA
62 TGAAAATGA
* * * * *
12064 GATCAACTCTGACCTC-TGGAAACTTCTTG-CAATGAGATCAACTCTGA-CCTCTGGAAACTTCT
1 GATCAACTCTGA--TCGTGGAAAATTCTTGAAAATGCGATCAACTCTGATCGT-TGGAAACTAC-
*
12126 TG-AAATTA
62 TGAAAATGA
* ** * *
12134 GATCAACTCTGACCTC-TGGAAACTTCTTG-AAATTAGATCAACTCTGA-CCTCTGGAAACTTCT
1 GATCAACTCTGA--TCGTGGAAAATTCTTGAAAATGCGATCAACTCTGATCGT-TGGAAACTAC-
*
12196 TG-CAATGA
62 TGAAAATGA
* ** * * *
12204 GATCAACTCTGACCTC-TGGAAACTTCTTG-AAATTAGATTAACTCTGA-CCTCTGGAAACTTCT
1 GATCAACTCTGA--TCGTGGAAAATTCTTGAAAATGCGATCAACTCTGATCGT-TGGAAACTAC-
12266 TG-AAATGA
62 TGAAAATGA
* * * * * * * *
12274 GATCAACTTTGACCTC-TGGAAACTTCTTG-GAATGAGATCAACTCTGACCTTTGAAAACTTCTT
1 GATCAACTCTGA--TCGTGGAAAATTCTTGAAAATGCGATCAACTCTGATCGTTGGAAACTAC-T
**
12337 G-GCATGA
63 GAAAATGA
* * * *
12344 GATCAACTCTGACCTC-TGGAAACTTCTTG-GAATGAGATCAACACTGA
1 GATCAACTCTGA--TCGTGGAAAATTCTTGAAAATGCGATCAACTCTGA
12391 CCTGATGACT
Statistics
Matches: 606, Mismatches: 61, Indels: 28
0.87 0.09 0.04
Matches are distributed among these distances:
69 8 0.01
70 534 0.88
71 5 0.01
72 3 0.00
73 2 0.00
74 48 0.08
75 6 0.01
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (70 bp):
GATCAACTCTGATCGTGGAAAATTCTTGAAAATGCGATCAACTCTGATCGTTGGAAACTACTGAA
AATGA
Found at i:11873 original size:105 final size:104
Alignment explanation
Indices: 11640--12393 Score: 752
Period size: 105 Copynumber: 7.1 Consensus size: 104
11630 AACTCCTCTG
* * * * * * *
11640 GATCAACTCTGATCATC-GGGAATTTCTTGAAATGAGATCACCTCTGA-TTGTTGGAAACTAC-T
1 GATCAACTCTGA-CCTCTGGAAACTTCTTGAAATGAGATCAACTCTGACCT-CTGGAAACTTCTT
* * * * * *
11702 GAAAATGTGATCATCTCTGATCGT-TGCAAAATATTGAAAATGC
64 G-AAATGAGATCAACTCTGA-CCTCTGGAAAATACTG-AAATGA
* * * * * * *
11745 GGTCAACTCTGATCGT-TGGAAACTAC-TGAAAATGCGATCAACTCTGA-TTGTTGGAAACTAC-
1 GATCAACTCTGA-CCTCTGGAAACTTCTTG-AAATGAGATCAACTCTGACCT-CTGGAAACTTCT
* *
11806 TGAAAATGCGATCAACTCTGATCGT-TGGAAAATACTGAAAATGA
63 TG-AAATGAGATCAACTCTGA-CCTCTGGAAAATACTG-AAATGA
* * * *
11850 GATCAAATCTGACCTCTGAAAACTTCTTGAAATGAATGAGATCAAATCTGACCTCTGAAAACTTC
1 GATCAACTCTGACCTCTGGAAACTTCTTG--A--AATGAGATCAACTCTGACCTCTGGAAACTTC
* * * *
11915 TTGGAATGAGATCAACTCTGACCTCTGGAAACTTCCTGGAATGA
62 TTGAAATGAGATCAACTCTGACCTCTGGAAA-ATACTGAAATGA
* * *
11959 GATCAACTCTGACCTCTGAAAACTTCTTGCAATGAGATCAACTCTGACCTCTGGAAACTTCTTGG
1 GATCAACTCTGACCTCTGGAAACTTCTTGAAATGAGATCAACTCTGACCTCTGGAAACTTCTTGA
* * * *
12024 AATGAGATCAACTCTGACTTCTGGAAACTTCTTGGAATGA
66 AATGAGATCAACTCTGACCTCTGGAAAATAC-TGAAATGA
*
12064 GATCAACTCTGACCTCTGGAAACTTCTTGCAATGAGATCAACTCTGACCTCTGGAAACTTCTTGA
1 GATCAACTCTGACCTCTGGAAACTTCTTGAAATGAGATCAACTCTGACCTCTGGAAACTTCTTGA
* * * *
12129 AATTAGATCAACTCTGACCTCTGGAAACTTCTTGAAATTA
66 AATGAGATCAACTCTGACCTCTGGAAAATAC-TGAAATGA
*
12169 GATCAACTCTGACCTCTGGAAACTTCTTGCAATGAGATCAACTCTGACCTCTGGAAACTTCTTGA
1 GATCAACTCTGACCTCTGGAAACTTCTTGAAATGAGATCAACTCTGACCTCTGGAAACTTCTTGA
* * * *
12234 AATTAGATTAACTCTGACCTCTGGAAACTTCTTGAAATGA
66 AATGAGATCAACTCTGACCTCTGGAAAATAC-TGAAATGA
* * * * *
12274 GATCAACTTTGACCTCTGGAAACTTCTTGGAATGAGATCAACTCTGACCTTTGAAAACTTCTTGG
1 GATCAACTCTGACCTCTGGAAACTTCTTGAAATGAGATCAACTCTGACCTCTGGAAACTTCTTGA
* * * *
12339 CATGAGATCAACTCTGACCTCTGGAAACTTCTTGGAATGA
66 AATGAGATCAACTCTGACCTCTGGAAAATAC-TGAAATGA
*
12379 GATCAACACTGACCT
1 GATCAACTCTGACCT
12394 GATGACTACA
Statistics
Matches: 582, Mismatches: 55, Indels: 24
0.88 0.08 0.04
Matches are distributed among these distances:
104 6 0.01
105 485 0.83
106 2 0.00
107 2 0.00
108 2 0.00
109 78 0.13
110 7 0.01
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (104 bp):
GATCAACTCTGACCTCTGGAAACTTCTTGAAATGAGATCAACTCTGACCTCTGGAAACTTCTTGA
AATGAGATCAACTCTGACCTCTGGAAAATACTGAAATGA
Found at i:11883 original size:35 final size:35
Alignment explanation
Indices: 11845--12393 Score: 855
Period size: 35 Copynumber: 15.6 Consensus size: 35
11835 AAATACTGAA
* *
11845 AATGAGATCAAATCTGACCTCTGAAAACTTCTTGAAATG
1 AATGAGATCAACTCTGACCTCTGGAAACTTCTTG----G
* *
11884 AATGAGATCAAATCTGACCTCTGAAAACTTCTTGG
1 AATGAGATCAACTCTGACCTCTGGAAACTTCTTGG
*
11919 AATGAGATCAACTCTGACCTCTGGAAACTTCCTGG
1 AATGAGATCAACTCTGACCTCTGGAAACTTCTTGG
* *
11954 AATGAGATCAACTCTGACCTCTGAAAACTTCTTGC
1 AATGAGATCAACTCTGACCTCTGGAAACTTCTTGG
11989 AATGAGATCAACTCTGACCTCTGGAAACTTCTTGG
1 AATGAGATCAACTCTGACCTCTGGAAACTTCTTGG
*
12024 AATGAGATCAACTCTGACTTCTGGAAACTTCTTGG
1 AATGAGATCAACTCTGACCTCTGGAAACTTCTTGG
*
12059 AATGAGATCAACTCTGACCTCTGGAAACTTCTTGC
1 AATGAGATCAACTCTGACCTCTGGAAACTTCTTGG
*
12094 AATGAGATCAACTCTGACCTCTGGAAACTTCTTGA
1 AATGAGATCAACTCTGACCTCTGGAAACTTCTTGG
* *
12129 AATTAGATCAACTCTGACCTCTGGAAACTTCTTGA
1 AATGAGATCAACTCTGACCTCTGGAAACTTCTTGG
* *
12164 AATTAGATCAACTCTGACCTCTGGAAACTTCTTGC
1 AATGAGATCAACTCTGACCTCTGGAAACTTCTTGG
*
12199 AATGAGATCAACTCTGACCTCTGGAAACTTCTTGA
1 AATGAGATCAACTCTGACCTCTGGAAACTTCTTGG
* * *
12234 AATTAGATTAACTCTGACCTCTGGAAACTTCTTGA
1 AATGAGATCAACTCTGACCTCTGGAAACTTCTTGG
*
12269 AATGAGATCAACTTTGACCTCTGGAAACTTCTTGG
1 AATGAGATCAACTCTGACCTCTGGAAACTTCTTGG
* *
12304 AATGAGATCAACTCTGACCTTTGAAAACTTCTTGG
1 AATGAGATCAACTCTGACCTCTGGAAACTTCTTGG
*
12339 CATGAGATCAACTCTGACCTCTGGAAACTTCTTGG
1 AATGAGATCAACTCTGACCTCTGGAAACTTCTTGG
*
12374 AATGAGATCAACACTGACCT
1 AATGAGATCAACTCTGACCT
12394 GATGACTACA
Statistics
Matches: 480, Mismatches: 30, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
35 446 0.93
39 34 0.07
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (35 bp):
AATGAGATCAACTCTGACCTCTGGAAACTTCTTGG
Done.