Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008996.1 Corchorus capsularis cultivar CVL-1 contig09017, 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: 9498
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Found at i:110 original size:21 final size:21
Alignment explanation
Indices: 61--114 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
51 AATTCGGTGC
* *
61 AATTAAGAAAATTGGTAATTA
1 AATTAAGTAATTTGGTAATTA
*
82 AGTTAAGTAATTTGGTAATTA
1 AATTAAGTAATTTGGTAATTA
103 AATTAAGTAATT
1 AATTAAGTAATT
115 AACTCAATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.39
Consensus pattern (21 bp):
AATTAAGTAATTTGGTAATTA
Found at i:200 original size:35 final size:35
Alignment explanation
Indices: 161--228 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
151 AAGTAACTTG
*
161 GTAATTAACTTAACTCAGTGTAATTAAGTAAATCA
1 GTAATTAACTTAACTCAGTGTAACTAAGTAAATCA
** * **
196 GTAATTGGCTTAATTTGGTGTAACTAAGTAAAT
1 GTAATTAACTTAACTCAGTGTAACTAAGTAAAT
229 AAATGGCTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (35 bp):
GTAATTAACTTAACTCAGTGTAACTAAGTAAATCA
Found at i:5379 original size:16 final size:16
Alignment explanation
Indices: 5358--5389 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5348 TGTGTTTTGA
5358 GAAGAAGAACAAGGAG
1 GAAGAAGAACAAGGAG
5374 GAAGAAGAACAAGGAG
1 GAAGAAGAACAAGGAG
5390 AAGGAGAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.06, G:0.38, T:0.00
Consensus pattern (16 bp):
GAAGAAGAACAAGGAG
Found at i:5443 original size:15 final size:15
Alignment explanation
Indices: 5422--5463 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
5412 AACGAACTAC
*
5422 ATTTTTCCTTCACTT
1 ATTTTTCATTCACTT
* *
5437 GTTTTTCATTGACTT
1 ATTTTTCATTCACTT
5452 ATTTTTCATTCA
1 ATTTTTCATTCA
5464 GAAATATGTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.17, C:0.19, G:0.05, T:0.60
Consensus pattern (15 bp):
ATTTTTCATTCACTT
Found at i:5678 original size:28 final size:28
Alignment explanation
Indices: 5647--5735 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
5637 GTTGTAATCA
5647 TGCTTCAATCATGATCCTGCGGTAGACC
1 TGCTTCAATCATGATCCTGCGGTAGACC
* * * * * *
5675 TGCTTGATTGATTTGGATCCCGCTGTA-ATCA
1 TGCTTCAATCA--T-GATCCTGCGGTAGA-CC
5706 TGCTTCAATCATGATCCTGCGGTAGACC
1 TGCTTCAATCATGATCCTGCGGTAGACC
5734 TG
1 TG
5736 TTTGATTGAT
Statistics
Matches: 44, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
28 21 0.48
29 2 0.05
30 2 0.05
31 19 0.43
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.33
Consensus pattern (28 bp):
TGCTTCAATCATGATCCTGCGGTAGACC
Found at i:5694 original size:31 final size:30
Alignment explanation
Indices: 5658--5746 Score: 76
Period size: 31 Copynumber: 3.0 Consensus size: 30
5648 GCTTCAATCA
5658 TGATCCTGCGGTAGACCTGCTTGATTGATT
1 TGATCCTGCGGTAGACCTGCTTGATTGATT
* * * * * *
5688 TGGATCCCGCTGTA-ATCATGCTTCAATCA--
1 T-GATCCTGCGGTAGA-CCTGCTTGATTGATT
*
5717 TGATCCTGCGGTAGACCTGTTTGATTGATT
1 TGATCCTGCGGTAGACCTGCTTGATTGATT
5747 CCATCACGCC
Statistics
Matches: 41, Mismatches: 13, Indels: 10
0.64 0.20 0.16
Matches are distributed among these distances:
28 18 0.44
29 2 0.05
30 2 0.05
31 19 0.46
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (30 bp):
TGATCCTGCGGTAGACCTGCTTGATTGATT
Found at i:5720 original size:59 final size:58
Alignment explanation
Indices: 5629--5746 Score: 209
Period size: 59 Copynumber: 2.0 Consensus size: 58
5619 TACTTCAATC
*
5629 TTGGATCCGTTGTAATCATGCTTCAATCATGATCCTGCGGTAGACCTGCTTGATTGAT
1 TTGGATCCGCTGTAATCATGCTTCAATCATGATCCTGCGGTAGACCTGCTTGATTGAT
*
5687 TTGGATCCCGCTGTAATCATGCTTCAATCATGATCCTGCGGTAGACCTGTTTGATTGAT
1 TTGGAT-CCGCTGTAATCATGCTTCAATCATGATCCTGCGGTAGACCTGCTTGATTGAT
5746 T
1 T
5747 CCATCACGCC
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
58 6 0.11
59 51 0.89
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.36
Consensus pattern (58 bp):
TTGGATCCGCTGTAATCATGCTTCAATCATGATCCTGCGGTAGACCTGCTTGATTGAT
Found at i:5900 original size:79 final size:79
Alignment explanation
Indices: 5742--6065 Score: 454
Period size: 79 Copynumber: 4.1 Consensus size: 79
5732 CCTGTTTGAT
* * * * * * * *
5742 TGATTCCATCACGCCTTCCTCAAGTTGGAGCCTGAAG--TCGCAATGCCCAACTTCAACACTAAT
1 TGATTTCATCACTCCCTCCTCAAGTTGGCGCGTGAAGACTCGAAACGCCCAACTTGAACACTAAT
* **
5805 CATTCAAATTGATC
66 GATTCAAACCGATC
* * * *
5819 TGATTTCATCACTCCCTCCTCAAGTTGGCGCGTGAAGATTCGGAACGTCCAACTTGAACACTAAA
1 TGATTTCATCACTCCCTCCTCAAGTTGGCGCGTGAAGACTCGAAACGCCCAACTTGAACACTAAT
*
5884 GATTCAAACCAATC
66 GATTCAAACCGATC
* * *
5898 TGATTTCATCACTCCTTCCTCAAGTTAGCGCGTGAAGACTCGAAACGCCCAACTTGAACACTGAT
1 TGATTTCATCACTCCCTCCTCAAGTTGGCGCGTGAAGACTCGAAACGCCCAACTTGAACACTAAT
5963 GATTCAAACCGATC
66 GATTCAAACCGATC
*
5977 TGATTTCATCACTCCCTCCTCAAGTTGTCGCGTGAAGACTCGAAACGCCCAACTTGAACACTAAT
1 TGATTTCATCACTCCCTCCTCAAGTTGGCGCGTGAAGACTCGAAACGCCCAACTTGAACACTAAT
6042 GATTCAAACCGATC
66 GATTCAAACCGATC
6056 TGATTTCATC
1 TGATTTCATC
6066 GCAATTTACC
Statistics
Matches: 219, Mismatches: 26, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
77 32 0.15
79 187 0.85
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (79 bp):
TGATTTCATCACTCCCTCCTCAAGTTGGCGCGTGAAGACTCGAAACGCCCAACTTGAACACTAAT
GATTCAAACCGATC
Found at i:6144 original size:55 final size:55
Alignment explanation
Indices: 6060--6168 Score: 191
Period size: 55 Copynumber: 2.0 Consensus size: 55
6050 CCGATCTGAT
*
6060 TTCATCGCAATTTACCAGCGGTAATGTAATGACCTCTTCTCACTCATTATCCGCA
1 TTCATCACAATTTACCAGCGGTAATGTAATGACCTCTTCTCACTCATTATCCGCA
* *
6115 TTCATCACAATTTACCTGCGGTAATGTAATGATCTCTTCTCACTCATTATCCGC
1 TTCATCACAATTTACCAGCGGTAATGTAATGACCTCTTCTCACTCATTATCCGC
6169 GGCAACCAAC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (55 bp):
TTCATCACAATTTACCAGCGGTAATGTAATGACCTCTTCTCACTCATTATCCGCA
Found at i:6627 original size:42 final size:42
Alignment explanation
Indices: 6581--6762 Score: 213
Period size: 42 Copynumber: 4.3 Consensus size: 42
6571 CGCCCCGCCA
* *
6581 GAACTAACCTCCTCTTTTCGAAGGCTCTACGCCACCCTGCAG
1 GAACTAACCTCCCCTTTTCGAAGGTTCTACGCCACCCTGCAG
* * * *
6623 GAACTAACCTCCCCTTTTCGAAGGTTTTACCCCCACCTTGCAT
1 GAACTAACCTCCCCTTTTCGAAGGTTCTA-CGCCACCCTGCAG
* * *
6666 GAATTAACCTCCCCTTTTCGAAGGTTCAACGCCACACC-GCAT
1 GAACTAACCTCCCCTTTTCGAAGGTTCTACGCCAC-CCTGCAG
* * **
6708 GAACTAACCTCCCCTTTTCGAAGGTTTTACGTCACCCTGTTG
1 GAACTAACCTCCCCTTTTCGAAGGTTCTACGCCACCCTGCAG
*
6750 AAACTAACCTCCC
1 GAACTAACCTCCC
6763 TTACCGAAGA
Statistics
Matches: 118, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
41 2 0.02
42 79 0.67
43 37 0.31
ACGTcount: A:0.23, C:0.36, G:0.14, T:0.27
Consensus pattern (42 bp):
GAACTAACCTCCCCTTTTCGAAGGTTCTACGCCACCCTGCAG
Found at i:6968 original size:28 final size:28
Alignment explanation
Indices: 6935--7028 Score: 73
Period size: 28 Copynumber: 3.2 Consensus size: 28
6925 CCGTTGTAAT
6935 CATGCTTCAATCATGATCCTGCGGTAGA
1 CATGCTTCAATCATGATCCTGCGGTAGA
* * * * * **
6963 CTTGCTTGATTGATTTGGATCCCGTTGTA-A
1 CATGCTTCAATCA--T-GATCCTGCGGTAGA
6993 TCATGCTTCAATCATGATCCTGCGGTAGA
1 -CATGCTTCAATCATGATCCTGCGGTAGA
*
7022 CCTGCTT
1 CATGCTT
7029 GATTGATTCC
Statistics
Matches: 46, Mismatches: 15, Indels: 10
0.65 0.21 0.14
Matches are distributed among these distances:
28 24 0.52
29 2 0.04
30 2 0.04
31 18 0.39
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.35
Consensus pattern (28 bp):
CATGCTTCAATCATGATCCTGCGGTAGA
Found at i:7010 original size:59 final size:59
Alignment explanation
Indices: 6918--7036 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
6908 TGCTTCAATC
*
6918 TTGGATCCCGTTGTAATCATGCTTCAATCATGATCCTGCGGTAGACTTGCTTGATTGAT
1 TTGGATCCCGTTGTAATCATGCTTCAATCATGATCCTGCGGTAGACCTGCTTGATTGAT
6977 TTGGATCCCGTTGTAATCATGCTTCAATCATGATCCTGCGGTAGACCTGCTTGATTGAT
1 TTGGATCCCGTTGTAATCATGCTTCAATCATGATCCTGCGGTAGACCTGCTTGATTGAT
7036 T
1 T
7037 CCATCAGTAG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (59 bp):
TTGGATCCCGTTGTAATCATGCTTCAATCATGATCCTGCGGTAGACCTGCTTGATTGAT
Found at i:9012 original size:18 final size:18
Alignment explanation
Indices: 8984--9028 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
8974 AAAACAAAGC
8984 AAATCAAATCT-AAATCT
1 AAATCAAATCTAAAATCT
9001 AAATCTAAATCTAAAATCT
1 AAATC-AAATCTAAAATCT
*
9020 AAAGCAAAT
1 AAATCAAAT
9029 TAATAAAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 5 0.20
18 10 0.40
19 10 0.40
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.27
Consensus pattern (18 bp):
AAATCAAATCTAAAATCT
Found at i:9019 original size:7 final size:6
Alignment explanation
Indices: 8984--9022 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
8974 AAAACAAAGC
8984 AAATC- AAATCT AAATCT AAATCT AAATCT AAAATCT AAA
1 AAATCT AAATCT AAATCT AAATCT AAATCT -AAATCT AAA
9023 GCAAATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.16
6 21 0.66
7 6 0.19
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.28
Consensus pattern (6 bp):
AAATCT
Done.