Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016564.1 Corchorus olitorius cultivar O-4 contig16597, 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: 18132
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:3751 original size:28 final size:28
Alignment explanation
Indices: 3681--3755 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
3671 TCCGGCATTT
*
3681 AAGGGCAAAACTGTAA-TTTAGTCAACC
1 AAGGGCAAAACAGTAATTTTAGTCAACC
* * *** *
3708 AGGGGTAAAGTGGTAATTTTAGTCGACC
1 AAGGGCAAAACAGTAATTTTAGTCAACC
3736 AAGGGCAAAACAGTAATTTT
1 AAGGGCAAAACAGTAATTTT
3756 GACATCTTAA
Statistics
Matches: 36, Mismatches: 11, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
27 11 0.31
28 25 0.69
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.25
Consensus pattern (28 bp):
AAGGGCAAAACAGTAATTTTAGTCAACC
Found at i:4194 original size:15 final size:15
Alignment explanation
Indices: 4174--4202 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4164 TCTCTTTGAG
4174 TACGATGACATTCTT
1 TACGATGACATTCTT
4189 TACGATGACATTCT
1 TACGATGACATTCT
4203 ACTCAGTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (15 bp):
TACGATGACATTCTT
Found at i:4757 original size:23 final size:23
Alignment explanation
Indices: 4731--4788 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
4721 GCGCAGGCCT
*
4731 GCTACCAGGCCATTGGCCTGGTA
1 GCTACCAGGCCATTGACCTGGTA
* *
4754 GCTACCAGCCCAATGACCTGGTA
1 GCTACCAGGCCATTGACCTGGTA
4777 GCTACCA-GCCAT
1 GCTACCAGGCCAT
4789 AAGCTGAGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 3 0.10
23 27 0.90
ACGTcount: A:0.22, C:0.34, G:0.24, T:0.19
Consensus pattern (23 bp):
GCTACCAGGCCATTGACCTGGTA
Found at i:5525 original size:22 final size:22
Alignment explanation
Indices: 5499--5542 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
5489 CCACCACACC
5499 ATTTAAATTTAA-GTAAAATTTA
1 ATTT-AATTTAATGTAAAATTTA
*
5521 ATTTAATTTAATTTAAAATTTA
1 ATTTAATTTAATGTAAAATTTA
5543 GGCTTCACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTTAATTTAATGTAAAATTTA
Found at i:5752 original size:24 final size:25
Alignment explanation
Indices: 5702--5752 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
5692 TACACATATA
*
5702 ATAATAAAATGAGCGCTAAGCTAGT
1 ATAAAAAAATGAGCGCTAAGCTAGT
* *
5727 ATAAAAAAATGAGTGCTATGCT-GT
1 ATAAAAAAATGAGCGCTAAGCTAGT
5751 AT
1 AT
5753 GCCTGTATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.27
Consensus pattern (25 bp):
ATAAAAAAATGAGCGCTAAGCTAGT
Found at i:6550 original size:23 final size:24
Alignment explanation
Indices: 6524--6568 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
6514 ATCTTATTGT
6524 TATC-AAAAAATATATATTTATGG
1 TATCAAAAAAATATATATTTATGG
6547 TATCAAAAAAATATATATTTAT
1 TATCAAAAAAATATATATTTAT
6569 TTTACATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (24 bp):
TATCAAAAAAATATATATTTATGG
Found at i:9704 original size:21 final size:21
Alignment explanation
Indices: 9659--9705 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
9649 TGTACGCATG
*
9659 GTCAAACCCCAATAGATGATG
1 GTCAAACCCCAATAGATGATA
*
9680 GTCAAACCCCAA-AGTTCGATA
1 GTCAAACCCCAATAGAT-GATA
9701 GTCAA
1 GTCAA
9706 GCCACAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (21 bp):
GTCAAACCCCAATAGATGATA
Found at i:10054 original size:21 final size:21
Alignment explanation
Indices: 10030--10070 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
10020 AACCTCGAAT
*
10030 TTTGATAAG-CAAACCCCAAAG
1 TTTGAT-AGTCAAACCACAAAG
10051 TTTGATAGTCAAACCACAAA
1 TTTGATAGTCAAACCACAAA
10071 AAACATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.44, C:0.22, G:0.12, T:0.22
Consensus pattern (21 bp):
TTTGATAGTCAAACCACAAAG
Found at i:10164 original size:52 final size:52
Alignment explanation
Indices: 10039--10204 Score: 224
Period size: 52 Copynumber: 3.1 Consensus size: 52
10029 TTTTGATAAG
* *
10039 CAAACCCCAAAGTTTGATAGTCAAACCACAAAAAACATTTTATTCTATATGTGTGGT
1 CAAACCCCAAA-TTTGATAGTCAAACCACAAAAAA-A---TATTGTATATGTATGGT
* *
10096 CAAACCCCAAAGTTGATAGTCAAACCACAAAAAAATATTGTATATGTACGGT
1 CAAACCCCAAATTTGATAGTCAAACCACAAAAAAATATTGTATATGTATGGT
* *
10148 CAAACCCCAAATTTGATAGTCAAACCACAAAAATATCATTGTACATGTATGGT
1 CAAACCCCAAATTTGATAGTCAAACCACAAAAAAAT-ATTGTATATGTATGGT
10201 CAAA
1 CAAA
10205 GCTCACAGGA
Statistics
Matches: 100, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
52 48 0.48
53 18 0.18
55 1 0.01
56 22 0.22
57 11 0.11
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (52 bp):
CAAACCCCAAATTTGATAGTCAAACCACAAAAAAATATTGTATATGTATGGT
Found at i:10245 original size:183 final size:188
Alignment explanation
Indices: 9906--10255 Score: 435
Period size: 183 Copynumber: 1.9 Consensus size: 188
9896 AGGATGATGA
* *
9906 TCAAACCCCAAAATTCAATAGTCAAACCACAAAAACATCATTATACATGCATAGTCAAACCCCAA
1 TCAAACCCCAAAATTCAATAGTCAAACCACAAAAAAATCATTATACATGCACAGTCAAACCCCAA
* * * ***
9971 AGTTCGATAGTCAAACCACAAAAAACATTTCATTTTATATGCATGATCAAACCTCGAATTTTGAT
66 AGTTCGATAGTCAAACCAC-AAAAACATATCATTGTACATGCATGATCAAACCTCGAAGGATGAT
10036 AAGCAAACCCCAAAGTTTGATAGTCAAACCACAAAAAACATTTTATTCTATATGTGTGG
130 AAGCAAACCCCAAAGTTTGATAGTCAAACCACAAAAAACATTTTATTCTATATGTGTGG
* * * * * *
10095 TCAAACCCCAAAGTT-GATAGTCAAACCACAAAAAAAT-ATTGTATATGTACGGTCAAACCCCAA
1 TCAAACCCCAAAATTCAATAGTCAAACCACAAAAAAATCATTATACATGCACAGTCAAACCCCAA
* * * *
10158 A-TTTGATAGTCAAACCAC-AAAA-ATATCATTGTACATGTATGGTCAAAGCTC-ACAGGATGAT
66 AGTTCGATAGTCAAACCACAAAAACATATCATTGTACATGCATGATCAAACCTCGA-AGGATGAT
* * *
10219 -GGTTAAATCCCAAAGTTTGATAGTCAAACCACAAAAA
130 AAG-CAAACCCCAAAGTTTGATAGTCAAACCACAAAAA
10256 TCATCATTGT
Statistics
Matches: 138, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
182 2 0.01
183 60 0.43
184 4 0.03
186 16 0.12
187 22 0.16
188 20 0.14
189 14 0.10
ACGTcount: A:0.43, C:0.21, G:0.11, T:0.25
Consensus pattern (188 bp):
TCAAACCCCAAAATTCAATAGTCAAACCACAAAAAAATCATTATACATGCACAGTCAAACCCCAA
AGTTCGATAGTCAAACCACAAAAACATATCATTGTACATGCATGATCAAACCTCGAAGGATGATA
AGCAAACCCCAAAGTTTGATAGTCAAACCACAAAAAACATTTTATTCTATATGTGTGG
Found at i:10392 original size:74 final size:73
Alignment explanation
Indices: 10145--10514 Score: 431
Period size: 74 Copynumber: 4.9 Consensus size: 73
10135 GTATATGTAC
* * *
10145 GGTCAAACCCCAAA-TTTGATAGTCAAACCACAAAAATATCATTGTACATGTATGGTCAAAGCTC
1 GGTCAAACCCCAAAGTTTGATAGTCAAACCAC-AAAA-ATCATTGTACATGCATGGTCAAACCCC
*
10209 ACAGGATGAT
64 AAAGGATGAT
* * * * *
10219 GGTTAAATCCCAAAGTTTGATAGTCAAACCACAAAAATCATCATTGTACATGTATGATCAAACCT
1 GGTCAAACCCCAAAGTTTGATAGTCAAACCAC-AAAA--ATCATTGTACATGCATGGTCAAACCC
10284 CAAAGGATGAT
63 CAAAGGATGAT
* * * *
10295 GGTCAAACCCTGAAA-TTTGATAGTCAAACCACAAAAAGCATTAATTCATTGCATGGTCAAA-CC
1 GGTCAAACCC-CAAAGTTTGATAGTCAAACCACAAAAATCATT-GTACA-TGCATGGTCAAACCC
10358 CAAAGGATGAT
63 CAAAGGATGAT
**
10369 GGTCAAACCCCAAAGTTCAATAGTCAAACCACAAAACATCATTGTACATGCATGGTCAAACCCCA
1 GGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAA-ATCATTGTACATGCATGGTCAAACCCCA
10434 AAGGATGAT
65 AAGGATGAT
* * *
10443 GGTCAAACCCCAAAGTTCGATAGTCAAACTACAAAAAACACTTCATTGTACATGTATGGTCAAAC
1 GGTCAAACCCCAAAGTTTGATAGTCAAAC--CACAAAA-A--TCATTGTACATGCATGGTCAAAC
10508 CCCAAAG
61 CCCAAAG
10515 TTTGATAGTT
Statistics
Matches: 260, Mismatches: 24, Indels: 20
0.86 0.08 0.07
Matches are distributed among these distances:
73 20 0.08
74 100 0.38
75 41 0.16
76 67 0.26
77 3 0.01
78 29 0.11
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (73 bp):
GGTCAAACCCCAAAGTTTGATAGTCAAACCACAAAAATCATTGTACATGCATGGTCAAACCCCAA
AGGATGAT
Found at i:10468 original size:21 final size:21
Alignment explanation
Indices: 10423--10471 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
10413 TACATGCATG
*
10423 GTCAAACCCCAAAGGATGATG
1 GTCAAACCCCAAAGGATGATA
*
10444 GTCAAACCCCAAA-GTTCGATA
1 GTCAAACCCCAAAGGAT-GATA
10465 GTCAAAC
1 GTCAAAC
10472 TACAAAAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.39, C:0.27, G:0.18, T:0.16
Consensus pattern (21 bp):
GTCAAACCCCAAAGGATGATA
Found at i:10534 original size:57 final size:56
Alignment explanation
Indices: 10441--10642 Score: 252
Period size: 54 Copynumber: 3.7 Consensus size: 56
10431 CCAAAGGATG
* * *
10441 ATGGTCAAACCCCAAAGTTCGATAGTCAAACTACAAAAAACACTTCATTGTACATGT
1 ATGGTCAAACCCCAAAGTTTGATAGTTAAACCACAAAAAACACTT-ATTGTACATGT
*
10498 ATGGTCAAACCCCAAAGTTTGATAGTTAAACCACAAAAAACA-TTATTGTACATGC
1 ATGGTCAAACCCCAAAGTTTGATAGTTAAACCACAAAAAACACTTATTGTACATGT
* * * * *
10553 ATGATCAAA-CCCAAAGTTT-AGTAGTGAAACCACAAAAAAAACTTA-T-TATATAT
1 ATGGTCAAACCCCAAAGTTTGA-TAGTTAAACCACAAAAAACACTTATTGTACATGT
* *
10606 ATGGTCAAACCCCAAATTTTGATAGTTAAACCCCAAA
1 ATGGTCAAACCCCAAAGTTTGATAGTTAAACCACAAA
10643 GTTTGATAGT
Statistics
Matches: 127, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
53 13 0.10
54 51 0.40
55 22 0.17
56 2 0.02
57 39 0.31
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.25
Consensus pattern (56 bp):
ATGGTCAAACCCCAAAGTTTGATAGTTAAACCACAAAAAACACTTATTGTACATGT
Found at i:10638 original size:21 final size:21
Alignment explanation
Indices: 10612--10652 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
10602 ATATATGGTC
*
10612 AAACCCCAAATTTTGATAGTT
1 AAACCCCAAAGTTTGATAGTT
10633 AAACCCCAAAGTTTGATAGT
1 AAACCCCAAAGTTTGATAGT
10653 CAAATCACGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (21 bp):
AAACCCCAAAGTTTGATAGTT
Found at i:11651 original size:18 final size:19
Alignment explanation
Indices: 11626--11670 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
11616 CTTTATAATT
11626 TAATTTT-AGATATCAATG
1 TAATTTTAAGATATCAATG
*
11644 TCATTTTAAAGATATCAATG
1 TAATTTT-AAGATATCAATG
11664 TAATTTT
1 TAATTTT
11671 TATAATGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 6 0.26
20 17 0.74
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (19 bp):
TAATTTTAAGATATCAATG
Found at i:11658 original size:20 final size:20
Alignment explanation
Indices: 11633--11670 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11623 ATTTAATTTT
*
11633 AGATATCAATGTCATTTTAA
1 AGATATCAATGTAATTTTAA
11653 AGATATCAATGTAATTTT
1 AGATATCAATGTAATTTT
11671 TATAATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (20 bp):
AGATATCAATGTAATTTTAA
Found at i:11684 original size:69 final size:68
Alignment explanation
Indices: 11572--11702 Score: 244
Period size: 69 Copynumber: 1.9 Consensus size: 68
11562 TTCAATATAC
*
11572 ATGTCATTTTAAAGATATCAATGTAATTTTTATAATGATATTTTCTTTATAATTTAATTTTAGAT
1 ATGTCATTTTAAAGATATCAATGTAATTTTTATAATGAAATTTT-TTTATAATTTAATTTTAGAT
11637 ATCA
65 ATCA
11641 ATGTCATTTTAAAGATATCAATGTAATTTTTATAATGAAATTTTTTTATAATTTAATTTTAG
1 ATGTCATTTTAAAGATATCAATGTAATTTTTATAATGAAATTTTTTTATAATTTAATTTTAG
11703 TTTTTTTTTT
Statistics
Matches: 61, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
68 18 0.30
69 43 0.70
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.51
Consensus pattern (68 bp):
ATGTCATTTTAAAGATATCAATGTAATTTTTATAATGAAATTTTTTTATAATTTAATTTTAGATA
TCA
Done.