Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011835.1 Corchorus olitorius cultivar O-4 contig11868, 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: 32893
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1635 original size:30 final size:30
Alignment explanation
Indices: 1334--1627 Score: 399
Period size: 30 Copynumber: 9.7 Consensus size: 30
1324 GAAAGGTAAA
* *
1334 ATCATGACAACTTCTGGTGTCAATTGAATAAA
1 ATCATGACAACTTCTGGTGTCAATTG--CAAG
* * *** *
1366 ATTATGACATCTTCAAATATCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
1396 ATCATGACAACTTATGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
1426 ATCATGACAACTTCTGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
1456 ATCATGACAACTTCTGGTGTCAATTGCAAC
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* *
1486 ATTATGACAACTTCTGGTGTCAATTGCAAA
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
1516 ATCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
1546 AGCATGACAACTTCTGGTGTCAATTGCAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
* * * *
1576 ATTATGACAACTTTTGGTGTCATTTGTAAG
1 ATCATGACAACTTCTGGTGTCAATTGCAAG
*
1606 ACCATGACAACTTCTGGTGTCA
1 ATCATGACAACTTCTGGTGTCA
1628 TTTGTAAGTA
Statistics
Matches: 232, Mismatches: 30, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
30 212 0.91
32 20 0.09
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (30 bp):
ATCATGACAACTTCTGGTGTCAATTGCAAG
Found at i:2770 original size:22 final size:24
Alignment explanation
Indices: 2735--2793 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 24
2725 ATAAATGTTG
* *
2735 CTGATAA-TCTTCT-CTTTTATCT
1 CTGATAATTCTTCTCCATTTATCA
2757 CTGATAATTC-TCTCCATTTATCA
1 CTGATAATTCTTCTCCATTTATCA
2780 CTTGATAATATCTT
1 C-TGATAAT-TCTT
2794 GCCAGATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 10 0.33
23 10 0.33
24 7 0.23
25 2 0.07
26 1 0.03
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (24 bp):
CTGATAATTCTTCTCCATTTATCA
Found at i:3068 original size:9 final size:9
Alignment explanation
Indices: 3046--3092 Score: 58
Period size: 9 Copynumber: 5.1 Consensus size: 9
3036 CCGTAAGTTA
*
3046 TTTTTCTCT
1 TTTTTCTTT
*
3055 CTTTTCTTTT
1 TTTTTC-TTT
3065 TTTTTCTTT
1 TTTTTCTTT
3074 TTTTTCTTT
1 TTTTTCTTT
*
3083 TTTTTGTTT
1 TTTTTCTTT
3092 T
1 T
3093 GTTGCTCGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
9 26 0.79
10 7 0.21
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.85
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:3069 original size:10 final size:10
Alignment explanation
Indices: 3056--3087 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
3046 TTTTTCTCTC
3056 TTTTCTTTTT
1 TTTTCTTTTT
3066 TTTTC-TTTT
1 TTTTCTTTTT
3075 TTTTCTTTTT
1 TTTTCTTTTT
3085 TTT
1 TTT
3088 GTTTTGTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:3070 original size:19 final size:19
Alignment explanation
Indices: 3046--3087 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
3036 CCGTAAGTTA
3046 TTTTTCTCTCTTTTCTTTT
1 TTTTTCTCTCTTTTCTTTT
* *
3065 TTTTTCTTTTTTTTCTTTT
1 TTTTTCTCTCTTTTCTTTT
3084 TTTT
1 TTTT
3088 GTTTTGTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (19 bp):
TTTTTCTCTCTTTTCTTTT
Found at i:5785 original size:131 final size:131
Alignment explanation
Indices: 5532--5789 Score: 387
Period size: 132 Copynumber: 2.0 Consensus size: 131
5522 TTTTTTAAAC
* *
5532 CTTTTATAGTTTTACTCAACTAAAATGTCTATTTTTATTTAATTAAATCTAATATCCTTATAACT
1 CTTTTATACTTTTACTCAACTAAAATGTCTATTTTTATTTAATTAAATATAATATCCTTATAACT
* * *
5597 ATTTACTTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATGTATTAGAATTTTTAAATAT
66 ATTTACTTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATATTAGAATTTTTAAATAT
5662 A
131 A
* * *
5663 CTTTTATACTTTTAGTCAACTAAAAAT-TCTATTTTTTATTTAATTAAATATAATATTCTTATAC
1 CTTTTATACTTTTACTCAACT-AAAATGTCTA-TTTTTATTTAATTAAATATAATATCCTTATAA
*
5727 CTATTTTA-TTTTTTCCATTTTACTAATTTAATT-AAAAAACTTAGATATATTAGAATTTTTAAA
64 CTA-TTTACTTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATATTAGAATTTTTAAA
5790 AATGTTTCTT
Statistics
Matches: 115, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
131 51 0.44
132 60 0.52
133 4 0.03
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.50
Consensus pattern (131 bp):
CTTTTATACTTTTACTCAACTAAAATGTCTATTTTTATTTAATTAAATATAATATCCTTATAACT
ATTTACTTTTTACCATTTTACTAATTTAATTAAAAAAACTTAGATATATTAGAATTTTTAAATAT
A
Found at i:18702 original size:31 final size:31
Alignment explanation
Indices: 18651--18720 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
18641 CCTTTTTATT
*
18651 TTTTTTTTCAAAACACAAAACACAAAACAAAA
1 TTTTTTTTCAAAACAAAAAACAC-AAACAAAA
* * * *
18683 TTTTTTTT-AAAATAAAAAACGCAAAGAAAT
1 TTTTTTTTCAAAACAAAAAACACAAACAAAA
18713 TTTTTTTT
1 TTTTTTTT
18721 TCAGAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 14 0.42
31 11 0.33
32 8 0.24
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (31 bp):
TTTTTTTTCAAAACAAAAAACACAAACAAAA
Found at i:18721 original size:31 final size:32
Alignment explanation
Indices: 18648--18723 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
18638 AAACCTTTTT
*
18648 ATTTTTTTTTTCAAAACACAAAACACAAAACA
1 ATTTTTTTTTTCAAAACAAAAAACACAAAACA
** * *
18680 AAATTTTTTTT-AAAATAAAAAACGCAAAGA-A
1 ATTTTTTTTTTCAAAACAAAAAACACAAA-ACA
18711 ATTTTTTTTTTCA
1 ATTTTTTTTTTCA
18724 GAAAAAACGC
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
31 24 0.69
32 11 0.31
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (32 bp):
ATTTTTTTTTTCAAAACAAAAAACACAAAACA
Found at i:20968 original size:6 final size:6
Alignment explanation
Indices: 20957--20991 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
20947 TGCAGGAAAA
20957 GTTTTT GTTTTT G-TTTT -TTTTT GTTTTT GTTTTT G
1 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT G
20992 CCAGCATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 8 0.30
6 19 0.70
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (6 bp):
GTTTTT
Found at i:20979 original size:16 final size:16
Alignment explanation
Indices: 20958--20990 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
20948 GCAGGAAAAG
20958 TTTTTGTTTTTGTTTT
1 TTTTTGTTTTTGTTTT
20974 TTTTTGTTTTTGTTTT
1 TTTTTGTTTTTGTTTT
20990 T
1 T
20991 GCCAGCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (16 bp):
TTTTTGTTTTTGTTTT
Found at i:24688 original size:17 final size:16
Alignment explanation
Indices: 24664--24699 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
24654 GAAGTATAAA
24664 AGAAAAGAGAATATAG
1 AGAAAAGAGAATATAG
*
24680 AGAACAAGAGAATATGG
1 AGAA-AAGAGAATATAG
24697 AGA
1 AGA
24700 CGGGGAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.58, C:0.03, G:0.28, T:0.11
Consensus pattern (16 bp):
AGAAAAGAGAATATAG
Found at i:28462 original size:23 final size:23
Alignment explanation
Indices: 28432--28479 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
28422 CAGATAAAAC
*
28432 AATACTAGCTCTTCCGGAGCTTT
1 AATACTAGCTCTTCCGGAGCCTT
*
28455 AATACTAGCTCTTCTGGAGCCTT
1 AATACTAGCTCTTCCGGAGCCTT
28478 AA
1 AA
28480 ATCAATTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (23 bp):
AATACTAGCTCTTCCGGAGCCTT
Found at i:28689 original size:2 final size:2
Alignment explanation
Indices: 28682--28709 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28672 TTAATGCGAA
28682 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
28710 CCAATATCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30051 original size:31 final size:31
Alignment explanation
Indices: 30016--30075 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
30006 TATCTAACCT
*
30016 TAGACTTGTATGATTCAACTATCAATCTCCG
1 TAGACTTGTATGATTAAACTATCAATCTCCG
* *
30047 TAGACTTGTATGATTAAACTTTCATTCTC
1 TAGACTTGTATGATTAAACTATCAATCTC
30076 GATCTTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (31 bp):
TAGACTTGTATGATTAAACTATCAATCTCCG
Found at i:30123 original size:36 final size:36
Alignment explanation
Indices: 30076--30145 Score: 122
Period size: 36 Copynumber: 1.9 Consensus size: 36
30066 TTTCATTCTC
*
30076 GATCTTTTTGAACTTTTTAATCGTCACTTAAACTCG
1 GATCTTTTTGAACTTCTTAATCGTCACTTAAACTCG
*
30112 GATCTTTTTGAACTTCTTGATCGTCACTTAAACT
1 GATCTTTTTGAACTTCTTAATCGTCACTTAAACT
30146 TGCAAGATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.44
Consensus pattern (36 bp):
GATCTTTTTGAACTTCTTAATCGTCACTTAAACTCG
Done.