Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013608.1 Corchorus olitorius cultivar O-4 contig13641, 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: 38611
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:589 original size:87 final size:88
Alignment explanation
Indices: 471--637 Score: 309
Period size: 87 Copynumber: 1.9 Consensus size: 88
461 TTTCCATGAG
471 ATCAAATGCTATTAATGTTTAATTTAAAAAATTACGGGAGCATAAATGAATAAAAACTAATTAAA
1 ATCAAATGCTATTAATGTTTAATTTAAAAAATTACGGGAGCATAAATGAATAAAAACTAATTAAA
536 TTAATTTAT-GAAAATGAATCAA
66 TTAATTTATGGAAAATGAATCAA
*
558 ATCAAATGCTATTAATTTTTAATTTAAAAAATTACGGGAGCATAAATGAATAAAAACTAATTAAA
1 ATCAAATGCTATTAATGTTTAATTTAAAAAATTACGGGAGCATAAATGAATAAAAACTAATTAAA
*
623 TTGATTTATGGAAAA
66 TTAATTTATGGAAAA
638 CAATTAAGCA
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
87 72 0.94
88 5 0.06
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.33
Consensus pattern (88 bp):
ATCAAATGCTATTAATGTTTAATTTAAAAAATTACGGGAGCATAAATGAATAAAAACTAATTAAA
TTAATTTATGGAAAATGAATCAA
Found at i:2079 original size:7 final size:7
Alignment explanation
Indices: 2062--2112 Score: 63
Period size: 7 Copynumber: 7.4 Consensus size: 7
2052 TTGTTATCAT
2062 TATAT-A
1 TATATGA
2068 TATATGA
1 TATATGA
2075 TATATGA
1 TATATGA
2082 TATATGA
1 TATATGA
2089 TATAT-A
1 TATATGA
2095 TATGAT-A
1 TAT-ATGA
2102 TGATATGA
1 T-ATATGA
2110 TAT
1 TAT
2113 TACCTCCATT
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
6 9 0.22
7 28 0.68
8 4 0.10
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (7 bp):
TATATGA
Found at i:2086 original size:16 final size:16
Alignment explanation
Indices: 2065--2112 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 16
2055 TTATCATTAT
2065 ATATATATGATATATG
1 ATATATATGATATATG
*
2081 ATATATGATATATATATG
1 ATATAT-AT-GATATATG
2099 ATATGATATGATAT
1 ATAT-ATATGATAT
2113 TACCTCCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 6 0.22
17 6 0.22
18 13 0.48
19 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (16 bp):
ATATATATGATATATG
Found at i:14471 original size:40 final size:42
Alignment explanation
Indices: 14423--14515 Score: 120
Period size: 40 Copynumber: 2.3 Consensus size: 42
14413 TCCTCCATTG
14423 TTGAAGGATATTTAAAAAAATA-TTTTTAAAAGA-TTTATTT
1 TTGAAGGATATTTAAAAAAATATTTTTTAAAAGATTTTATTT
* ** *
14463 CTT-AAGGATATTTAAGAATGTATTTTTTAAAGGATTTTATTT
1 -TTGAAGGATATTTAAAAAAATATTTTTTAAAAGATTTTATTT
14505 TTGAAGGATAT
1 TTGAAGGATAT
14516 ATTATGATGA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
40 16 0.36
41 14 0.31
42 15 0.33
ACGTcount: A:0.39, C:0.01, G:0.14, T:0.46
Consensus pattern (42 bp):
TTGAAGGATATTTAAAAAAATATTTTTTAAAAGATTTTATTT
Found at i:15781 original size:2 final size:2
Alignment explanation
Indices: 15768--15801 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
15758 TTTTACAAAA
*
15768 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15802 TTGTTAGCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:18549 original size:12 final size:12
Alignment explanation
Indices: 18532--18557 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18522 AATTTGGTAC
18532 TATACTTTTGCA
1 TATACTTTTGCA
18544 TATACTTTTGCA
1 TATACTTTTGCA
18556 TA
1 TA
18558 CTGACTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.15, G:0.08, T:0.50
Consensus pattern (12 bp):
TATACTTTTGCA
Found at i:19660 original size:8 final size:8
Alignment explanation
Indices: 19649--19682 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
19639 ATTATATTAT
*
19649 ATAATAAT
1 ATAATAAC
19657 ATAATAAC
1 ATAATAAC
*
19665 GTAATAAC
1 ATAATAAC
19673 ATAATAAC
1 ATAATAAC
19681 AT
1 AT
19683 CATTTTCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (8 bp):
ATAATAAC
Found at i:22655 original size:24 final size:24
Alignment explanation
Indices: 22623--22669 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
22613 ATTTTATTGA
* *
22623 TTTGGTTTATTATCTTGGTTTTAC
1 TTTGATTTATGATCTTGGTTTTAC
*
22647 TTTGATTTATGATTTTGGTTTTA
1 TTTGATTTATGATCTTGGTTTTA
22670 ATGATTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.04, G:0.17, T:0.64
Consensus pattern (24 bp):
TTTGATTTATGATCTTGGTTTTAC
Found at i:27359 original size:28 final size:28
Alignment explanation
Indices: 27328--27382 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
27318 AAATTTTTTC
*
27328 TTTTAAATTAAAAAAAATGCAGAAACAT
1 TTTTAAATTAAAAAAAACGCAGAAACAT
*** *
27356 TTTTTTTTTAGAAAAAACGCAGAAACA
1 TTTTAAATTAAAAAAAACGCAGAAACA
27383 AGAAAAATAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (28 bp):
TTTTAAATTAAAAAAAACGCAGAAACAT
Found at i:27633 original size:20 final size:21
Alignment explanation
Indices: 27608--27654 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
27598 TAAAAATATT
* *
27608 AATTAAAAAGAAAGC-AATTA
1 AATTAAAAACAAAGCAAAGTA
27628 AATTAAAAACAAAGCAAAGTA
1 AATTAAAAACAAAGCAAAGTA
27649 AATTAA
1 AATTAA
27655 TAGATCTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.66, C:0.06, G:0.09, T:0.19
Consensus pattern (21 bp):
AATTAAAAACAAAGCAAAGTA
Found at i:29002 original size:19 final size:18
Alignment explanation
Indices: 28969--29004 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
28959 TTGAGATAAT
28969 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
28987 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
29005 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:30494 original size:29 final size:29
Alignment explanation
Indices: 30457--30559 Score: 147
Period size: 29 Copynumber: 3.6 Consensus size: 29
30447 TTGGTATATC
30457 AAGTGCGGGTTGTGCACTTGTGTTTGTTT
1 AAGTGCGGGTTGTGCACTTGTGTTTGTTT
*
30486 AAGTACGGGTTGTGCACTTGTGTTTGTTT
1 AAGTGCGGGTTGTGCACTTGTGTTTGTTT
* *
30515 AAGTGCGGGTTGTGCACTTGGGATTG-TT
1 AAGTGCGGGTTGTGCACTTGTGTTTGTTT
* *
30543 GAGTGTGGGTT-TGCACT
1 AAGTGCGGGTTGTGCACT
30560 CGGTGTTGAC
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 6 0.09
28 11 0.16
29 51 0.75
ACGTcount: A:0.13, C:0.11, G:0.36, T:0.41
Consensus pattern (29 bp):
AAGTGCGGGTTGTGCACTTGTGTTTGTTT
Found at i:31391 original size:6 final size:6
Alignment explanation
Indices: 31380--31416 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
31370 GCTGAGAATC
31380 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA A
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA A
31417 GGCAATGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAGA
Done.