Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024673.1 Corchorus olitorius cultivar O-4 contig24706, 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: 7591
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:2217 original size:42 final size:42
Alignment explanation
Indices: 2152--2244 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 42
2142 ATCCATTGAT
*
2152 ATATG-TCATACATCCTACATGCATCGTCCATGT-CTTTGTAC
1 ATATGTTCATACATCCTACATGCATCATCCAT-TCCTTTGTAC
* *
2193 ATATGTTCATACATCC-ATCGTGCATCATCCATTCCTTTGTAT
1 ATATGTTCATACATCCTA-CATGCATCATCCATTCCTTTGTAC
2235 ATATGTTCAT
1 ATATGTTCAT
2245 GCATAGGTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
41 7 0.15
42 39 0.85
ACGTcount: A:0.25, C:0.25, G:0.11, T:0.40
Consensus pattern (42 bp):
ATATGTTCATACATCCTACATGCATCATCCATTCCTTTGTAC
Found at i:2443 original size:139 final size:139
Alignment explanation
Indices: 2193--2473 Score: 481
Period size: 139 Copynumber: 2.0 Consensus size: 139
2183 GTCTTTGTAC
* * *
2193 ATATGTTCATACATCCATCGTGCATCATCCATTCCTTTGTATATATGTTCATGCATAGGTTATGC
1 ATATGTTCATACATCCATCGTGCATCATCCATTCCTTCGTATATATGTTCATGCACAGGTCATGC
* * *
2258 ATTCTCCTTTCATTACCACATGCATCTATTTTTGCATTATCCTTATCTTTTGTAAATAGATGCAT
66 ATTATCCATTCATTACCACATGCATCTATTTTTGCATTATCCTTATCTTTTGTAAATAGATACAT
*
2323 TTTGTGCAT
131 TTCGTGCAT
2332 ATATGTTCATACATCCATCGTGCATCATCCATTCCTTCGTATATATGTTCATGCACAGGTCATGC
1 ATATGTTCATACATCCATCGTGCATCATCCATTCCTTCGTATATATGTTCATGCACAGGTCATGC
* *
2397 ATTATCCATTCATTACTATATGCATCTATTTTTGCATTATCCTTATCTTTTGTAAATAGATACAT
66 ATTATCCATTCATTACCACATGCATCTATTTTTGCATTATCCTTATCTTTTGTAAATAGATACAT
2462 TTCGTGCAT
131 TTCGTGCAT
2471 ATA
1 ATA
2474 GGCAATACAT
Statistics
Matches: 133, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
139 133 1.00
ACGTcount: A:0.25, C:0.21, G:0.11, T:0.43
Consensus pattern (139 bp):
ATATGTTCATACATCCATCGTGCATCATCCATTCCTTCGTATATATGTTCATGCACAGGTCATGC
ATTATCCATTCATTACCACATGCATCTATTTTTGCATTATCCTTATCTTTTGTAAATAGATACAT
TTCGTGCAT
Found at i:3486 original size:15 final size:13
Alignment explanation
Indices: 3463--3505 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
3453 GATTTCCCAA
3463 AAAAT-GAAAATG
1 AAAATGGAAAATG
3475 AAAATGAAGAAAATG
1 AAAATG--GAAAATG
3490 AAAAATGGAAAATG
1 -AAAATGGAAAATG
3504 AA
1 AA
3506 GGCACTTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 5 0.19
13 2 0.07
14 7 0.26
15 7 0.26
16 6 0.22
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.14
Consensus pattern (13 bp):
AAAATGGAAAATG
Found at i:3939 original size:22 final size:23
Alignment explanation
Indices: 3890--3932 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3880 AAAAAAAAAG
3890 AAAAAAATCAAATCAAAGTCAAT
1 AAAAAAATCAAATCAAAGTCAAT
3913 AAAAAAATC-AATCAAA-TCAA
1 AAAAAAATCAAATCAAAGTCAA
3933 ATCAAAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 7 0.35
23 9 0.45
ACGTcount: A:0.67, C:0.14, G:0.02, T:0.16
Consensus pattern (23 bp):
AAAAAAATCAAATCAAAGTCAAT
Found at i:4608 original size:50 final size:51
Alignment explanation
Indices: 4532--4670 Score: 192
Period size: 50 Copynumber: 2.8 Consensus size: 51
4522 CAAGATTTCT
* *
4532 TTCCATTTATGAGTTCAAGATCAAAATTCGCTTTTCAAAAG-AAAATTGCG
1 TTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAAGTAAAATTGCA
* * * *
4582 TTCCATTTGTAAGTTCAAGATTAAAATTCGCTTTTC-AAGGTAAGATTGCA
1 TTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAAGTAAAATTGCA
* *
4632 TTCCAGTTGTGAGTCCAAGATCAAAATTCGCTTTTCAAA
1 TTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAA
4671 GGGCATTTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
49 3 0.04
50 72 0.94
51 2 0.03
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (51 bp):
TTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAAAAGTAAAATTGCA
Found at i:5330 original size:50 final size:50
Alignment explanation
Indices: 5271--5588 Score: 573
Period size: 50 Copynumber: 6.3 Consensus size: 50
5261 CGAAGCTTTT
* *
5271 GGCTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCGATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
5321 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
5371 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
*
5421 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATAATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
*
5471 GGCTTTTCCATAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
*
5521 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATGG
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACAT-A
*
5572 GGCTTTTCCATAAGCCA
1 GGCTTTTCCACAAGCCA
5589 CGGTTCGTTC
Statistics
Matches: 259, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
50 243 0.94
51 16 0.06
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.29
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCGATTATCAACATA
Found at i:5666 original size:35 final size:34
Alignment explanation
Indices: 5620--5857 Score: 318
Period size: 35 Copynumber: 6.8 Consensus size: 34
5610 TTACCATCTT
5620 CTCAGATGACTCGGTGTAGCATCTTCAAAGTTATA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAGTTA-A
*
5655 CTCAGATGACTCGGTGTAGCATCTTCAAAATTGAA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAGTT-AA
*
5690 CTCAGATGACTCGGTGTAGCATCTCCAAAGTTGAA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAGTT-AA
*
5725 TTCAGATGACTCGGTGTAGCATCTTCGAAA-TTAA
1 CTCAGATGACTCGGTGTAGCATCTTC-AAAGTTAA
* *
5759 ATCCAGATGACTCGGTGTAACATCTTCAAA-TATGAA
1 CT-CAGATGACTCGGTGTAGCATCTTCAAAGT-T-AA
* *
5795 TTCAGATGACTCGGTGTAGCATCTTCAAAGATGAA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAG-TTAA
*
5830 TTCAGATGACTCGGTGTAGCATCTTCAA
1 CTCAGATGACTCGGTGTAGCATCTTCAA
5858 TATGAACTCG
Statistics
Matches: 186, Mismatches: 10, Indels: 14
0.89 0.05 0.07
Matches are distributed among these distances:
34 7 0.04
35 171 0.92
36 7 0.04
37 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (34 bp):
CTCAGATGACTCGGTGTAGCATCTTCAAAGTTAA
Found at i:5733 original size:70 final size:70
Alignment explanation
Indices: 5620--5857 Score: 358
Period size: 70 Copynumber: 3.4 Consensus size: 70
5610 TTACCATCTT
*
5620 CTCAGATGACTCGGTGTAGCATCTTCAAAGTT-ATACTCAGATGACTCGGTGTAGCATCTTCAAA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAGTTGA-ATTCAGATGACTCGGTGTAGCATCTTCAAA
5684 ATTGAA
65 ATTGAA
* *
5690 CTCAGATGACTCGGTGTAGCATCTCCAAAGTTGAATTCAGATGACTCGGTGTAGCATCTTCGAAA
1 CTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAATTCAGATGACTCGGTGTAGCATCTTCAAAA
5755 TT-AA
66 TTGAA
* *
5759 ATCCAGATGACTCGGTGTAACATCTTCAAA-TATGAATTCAGATGACTCGGTGTAGCATCTTCAA
1 CT-CAGATGACTCGGTGTAGCATCTTCAAAGT-TGAATTCAGATGACTCGGTGTAGCATCTTCAA
5823 AGA-TGAA
64 A-ATTGAA
*
5830 TTCAGATGACTCGGTGTAGCATCTTCAA
1 CTCAGATGACTCGGTGTAGCATCTTCAA
5858 TATGAACTCG
Statistics
Matches: 154, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
69 4 0.03
70 145 0.94
71 5 0.03
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (70 bp):
CTCAGATGACTCGGTGTAGCATCTTCAAAGTTGAATTCAGATGACTCGGTGTAGCATCTTCAAAA
TTGAA
Found at i:5803 original size:105 final size:105
Alignment explanation
Indices: 5621--5857 Score: 381
Period size: 105 Copynumber: 2.3 Consensus size: 105
5611 TACCATCTTC
* *
5621 TCAGATGACTCGGTGTAGCATCTTCAAAGTTATACTCAGATGACTCGGTGTAGCATCTTCAAAAT
1 TCAGATGACTCGGTGTAGCATCTTCAAAGTTAAACTCAGATGACTCGGTGTAACATCTTCAAAAT
*
5686 TGAACTCAGATGACTCGGTGTAGCATCTCCAAAGTTGAAT
66 TGAACTCAGATGACTCGGTGTAGCATCTCCAAAGATGAAT
5726 TCAGATGACTCGGTGTAGCATCTTCGAAA-TTAAA-TCCAGATGACTCGGTGTAACATCTTC-AA
1 TCAGATGACTCGGTGTAGCATCTTC-AAAGTTAAACT-CAGATGACTCGGTGTAACATCTTCAAA
* *
5788 ATATGAATTCAGATGACTCGGTGTAGCATCTTCAAAGATGAAT
64 AT-TGAACTCAGATGACTCGGTGTAGCATCTCCAAAGATGAAT
5831 TCAGATGACTCGGTGTAGCATCTTCAA
1 TCAGATGACTCGGTGTAGCATCTTCAA
5858 TATGAACTCG
Statistics
Matches: 124, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
104 7 0.06
105 114 0.92
106 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (105 bp):
TCAGATGACTCGGTGTAGCATCTTCAAAGTTAAACTCAGATGACTCGGTGTAACATCTTCAAAAT
TGAACTCAGATGACTCGGTGTAGCATCTCCAAAGATGAAT
Found at i:6150 original size:27 final size:26
Alignment explanation
Indices: 6113--6209 Score: 108
Period size: 27 Copynumber: 3.7 Consensus size: 26
6103 GTCACTTAAG
*
6113 GGGGCATTTTGGTCATTCGCATGTTCA
1 GGGGCACTTTGGTCATTCGCATGTT-A
*
6140 GGGGCACTTTGGTCATTTTTGCA--TTA
1 GGGGCACTTTGGTCA--TTCGCATGTTA
*
6166 GGGGCATTTTGGTCATTCGCATGTTAA
1 GGGGCACTTTGGTCATTCGCATGTT-A
*
6193 GGGGCACGTTGGTCATT
1 GGGGCACTTTGGTCATT
6210 TTAAGCTCAT
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
24 5 0.08
26 17 0.29
27 32 0.54
29 5 0.08
ACGTcount: A:0.15, C:0.16, G:0.31, T:0.37
Consensus pattern (26 bp):
GGGGCACTTTGGTCATTCGCATGTTA
Done.