Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019802.1 Corchorus olitorius cultivar O-4 contig19835, 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: 8040
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:688 original size:11 final size:11
Alignment explanation
Indices: 675--709 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
665 TATTTTTATT
675 TTTTC-TTTTC
1 TTTTCTTTTTC
685 TTTTCTTTTTC
1 TTTTCTTTTTC
696 TTTTCTTCTTTC
1 TTTTCTT-TTTC
708 TT
1 TT
710 CCCCACATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 5 0.22
11 12 0.52
12 6 0.26
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:5146 original size:22 final size:22
Alignment explanation
Indices: 5118--5306 Score: 100
Period size: 22 Copynumber: 8.5 Consensus size: 22
5108 TGTCTCTGTG
5118 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
5140 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
5163 -GGTTATCAAATTTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
5184 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
* * *
5207 -AGCTATCAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* * *
5228 TGGTTACCAAAATTTCTTAGGA
1 TGGTTATCAAAATTTCATAAGA
* * *
5250 TCAGGTTATTAAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAAGA
* ** *
5274 AGGTTATTGAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
5296 TGGTTATCAAA
1 TGGTTATCAAA
5307 GAGATTATCA
Statistics
Matches: 123, Mismatches: 33, Indels: 22
0.69 0.19 0.12
Matches are distributed among these distances:
20 2 0.02
21 1 0.01
22 96 0.78
23 4 0.03
24 20 0.16
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:5188 original size:44 final size:44
Alignment explanation
Indices: 5119--5700 Score: 164
Period size: 44 Copynumber: 12.9 Consensus size: 44
5109 GTCTCTGTGT
* ** *
5119 GGTTATCAAAATTTCATAAG-ATGGTTATTATAATTTCATGA-GGA
1 GGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCAT-ATGGA
*
5163 GGTTATCAAATTTTCATAGTGTGGTTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATGGA
* * *
5207 AGCTATCAAAATTTCATAGTGTGGTTACCAAAATTTCTTA-GGATCA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATGG---A
* * * ***
5253 GGTTATTAAAATTTCTTAG-GAAGGTTATTGAAATTTCATAGTGTGGTTATCAAA
1 GGTTATCAAAATTTCATAGTG-TGGTTACCAAAATTTCATA---TGG-------A
* * * *
5307 GAGATTATCAAAATGTCATAGCGAGGTTA-TAAGAATTTCATAT---
1 G-G-TTATCAAAATTTCATAGTGTGGTTACCAA-AATTTCATATGGA
* * * *
5350 GGTTAACAAAATTTCATAAG-GAGGTTACTAATATTTCAT-TGGGA
1 GGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCATAT-GGA
* ** *
5394 GGTTATCAAAATTTCATA-TGAAGGTTATAAAAGTCTCAATTTCATAAGGA
1 GGTTATCAAAATTTCATAGTG-TGGTTA-CCAA-----AATTTCATATGGA
* * ** * *
5444 -G-TACCAAAATTTGATAG-AAGGTTATC-AAATCTCATA--GA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATGGA
* * ** *
5482 GTGATTATCGAAATTTCACAAAGATCGGATTATCAAAATTT-ATA-GGAA
1 G-G-TTATCAAAATTTCATAGTG-T-GG-TTACCAAAATTTCATATGG-A
* * * * *
5530 GATTATCAAAATTTCATAGAGTTGTTATCAAAATTTCA-AAGCGA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATG-GA
* * * *
5574 GGTTATCAAAATTACATAATGTGATTA-CAAAATTTCATA-GAGG
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATG-GA
* * * * * * **
5617 GGTCAACAAAATTTTATAGAGAGGTTATCAAAATTTCATAAAGA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATGGA
* * * *
5661 GGTTATCAAATTTTCAAAATGTGATTACCAAAATTTCATA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATA
5701 GTGGTATTTC
Statistics
Matches: 407, Mismatches: 80, Indels: 102
0.69 0.14 0.17
Matches are distributed among these distances:
38 2 0.00
40 10 0.02
41 27 0.07
42 17 0.04
43 52 0.13
44 161 0.40
45 8 0.02
46 54 0.13
47 12 0.03
48 15 0.04
49 1 0.00
50 12 0.03
53 1 0.00
54 2 0.00
55 3 0.01
56 29 0.07
57 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.35
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATATGGA
Found at i:5233 original size:66 final size:65
Alignment explanation
Indices: 5115--5703 Score: 197
Period size: 66 Copynumber: 9.0 Consensus size: 65
5105 TCTTGTCTCT
* * * * *
5115 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAG-GAGGTTATCAAATTTTCA
1 GTGTGGTTATCAAAATTTCATAGGA-AGTTATTAAAATTTCAT-AGTGTGGTTATCAAAATTTCA
5179 TA
64 TA
* * * * *
5181 GTGTGGTTACCAAAATTTCATATGGAAGCTATCAAAATTTCATAGTGTGGTTACCAAAATTTCTT
1 GTGTGGTTATCAAAATTTCATA-GGAAGTTATTAAAATTTCATAGTGTGGTTATCAAAATTTCAT
5246 A
65 A
* * *
5247 G-GATCAGGTTATTAAAATTTCTTAGGAAGGTTATTGAAATTTCATAGTGTGGTTATC---A---
1 GTG-T--GGTTATCAAAATTTCATAGGAA-GTTATTAAAATTTCATAGTGTGGTTATCAAAATTT
5305 -A-A
62 CATA
* * * * *
5307 --GAGATTATCAAAATGTCATAGCGAGGTTA-TAAGAATTTCATA---TGGTTAACAAAATTTCA
1 GTGTGGTTATCAAAATTTCATAG-GAAGTTATTAA-AATTTCATAGTGTGGTTATCAAAATTTCA
5366 TAA
64 T-A
* * * * * * *
5369 G-GAGGTTA-CTAATATTTCATTGGGAGGTTATCAAAATTTCATA-TGAAGGTTATAAAAGTCTC
1 GTGTGGTTATC-AAAATTTCA-TAGGAAGTTATTAAAATTTCATAGTG-TGGTTAT-CAA-----
5431 AATTTCATAA
57 AATTTCAT-A
* * * * * * * * *
5441 G-G-AG-TACCAAAATTTGATA-GAAGGTTA-TCAAATCTCATAGAGTGATTATCGAAATTTCAC
1 GTGTGGTTATCAAAATTTCATAGGAA-GTTATTAAAATTTCATAGTGTGGTTATCAAAATTTCAT
5501 A
65 A
** * * *
5502 AAGATCGGATTATCAAAATTT-ATAGGAAGATTATCAAAATTTCATAGAGTTGTTATCAAAATTT
1 GTG-T-GG-TTATCAAAATTTCATAGGAAG-TTATTAAAATTTCATAGTGTGGTTATCAAAATTT
*
5566 CAAA
62 CATA
* * * * * * * * * *
5570 GCGAGGTTATCAAAATTACATA--ATGTGATTACAAAATTTCATAGAGGGGTCAACAAAATTTTA
1 GTGTGGTTATCAAAATTTCATAGGAAGTTATT--AAAATTTCATAGTGTGGTTATCAAAATTTCA
5633 TA
64 TA
* * * * * * * * * *
5635 GAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTACCAAAATTTCAT
1 GTGTGGTTATCAAAATTTCAT-AGGAAGTTATTAAAATTTCATAGTGTGGTTATCAAAATTTCAT
5700 A
65 A
5701 GTG
1 GTG
5704 GTATTTCTGG
Statistics
Matches: 389, Mismatches: 86, Indels: 96
0.68 0.15 0.17
Matches are distributed among these distances:
53 7 0.02
55 2 0.01
56 29 0.07
57 2 0.01
59 1 0.00
60 2 0.01
61 1 0.00
62 10 0.03
63 32 0.08
64 6 0.02
65 62 0.16
66 93 0.24
67 25 0.06
68 88 0.23
69 6 0.02
70 9 0.02
71 2 0.01
72 12 0.03
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (65 bp):
GTGTGGTTATCAAAATTTCATAGGAAGTTATTAAAATTTCATAGTGTGGTTATCAAAATTTCATA
Found at i:5385 original size:22 final size:22
Alignment explanation
Indices: 5311--6331 Score: 221
Period size: 22 Copynumber: 46.4 Consensus size: 22
5301 ATCAAAGAGA
*
5311 TTATCAAAATGTCAT-AGCGAGG
1 TTATCAAAATTTCATAAG-GAGG
*
5333 TTAT-AAGAATTTCAT-A--TGG
1 TTATCAA-AATTTCATAAGGAGG
*
5352 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCATAAGGAGG
* **
5374 TTA-CTAATATTTCATTGGGAGG
1 TTATC-AAAATTTCATAAGGAGG
* *
5396 TTATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATAAGGAGG
*
5418 TTATAAAAGTCTCAATTTCATAAGGA-G
1 TTAT-CAA-----AATTTCATAAGGAGG
* * *
5445 -TACCAAAATTTGAT-AGAAGG
1 TTATCAAAATTTCATAAGGAGG
*
5465 TTATC-AAATCTCAT-A-GAGTG
1 TTATCAAAATTTCATAAGGAG-G
* * *
5485 ATTATCGAAATTTCACAAAGATCGG
1 -TTATCAAAATTTCATAAGGA--GG
*
5510 ATTATCAAAATTT-AT-AGGAAGA
1 -TTATCAAAATTTCATAAGG-AGG
5532 TTATCAAAATTTCAT-A-GAGTTG
1 TTATCAAAATTTCATAAGGAG--G
5554 TTATCAAAATTTCA-AAGCGAGG
1 TTATCAAAATTTCATAAG-GAGG
* * * *
5576 TTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAAGGAGG
5598 TTA-CAAAATTTCATAGAGG-GG
1 TTATCAAAATTTCATA-AGGAGG
* * *
5619 TCAACAAAATTTTAT-AGAGAGG
1 TTATCAAAATTTCATAAG-GAGG
*
5641 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAAGGAGG
* * * * *
5663 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAAGGAGG
* *
5685 TTACCAAAATTTCAT-A-GTGG
1 TTATCAAAATTTCATAAGGAGG
* **
5705 TATTTCTGGAGAGGTTTTCA-AA--A--
1 T-TATC---A-A-AATTTCATAAGGAGG
* *
5728 TT-TCATAGTATGATTACCAAATTAGGAAGG
1 TTATCA-A--A--ATT-TC--ATAAGG-AGG
* * * *
5758 TTATTAAACTTTTATTATGGA-G
1 TTATCAAAATTTCA-TAAGGAGG
* *
5780 -TACACAAAATTTC--AGGGAGG
1 TTA-TCAAAATTTCATAAGGAGG
* * *
5800 ATATCAAAATTTCATATGAAGG
1 TTATCAAAATTTCATAAGGAGG
*
5822 TTATCAAAATTTCAT-AGTTTA-G
1 TTATCAAAATTTCATAAG--GAGG
*
5844 TTTTCAAAATTTCATAA-GAGGG
1 TTATCAAAATTTCATAAGGA-GG
* *
5866 TTATCAAAATTTCAT-AGTATG
1 TTATCAAAATTTCATAAGGAGG
* *
5887 TAGATCAAAATTTCATAGGGAGAGG
1 T-TATCAAAATTTCATA-AG-GAGG
*
5912 TTATCAAAA-TT--T--GTA-G
1 TTATCAAAATTTCATAAGGAGG
*
5928 TTATCAAGATTTCATAAGGAGG
1 TTATCAAAATTTCATAAGGAGG
* **
5950 TTATCAAAATTTTATGGGGAGG
1 TTATCAAAATTTCATAAGGAGG
*
5972 TTTATCAAAATTTTAT-AGGAAGG
1 -TTATCAAAATTTCATAAGG-AGG
*
5995 TTTATCAAAATTTCATAACGAGG
1 -TTATCAAAATTTCATAAGGAGG
* * *
6018 TTATTACAATTTCAT-A-G-TG
1 TTATCAAAATTTCATAAGGAGG
* *
6037 TGATCAAAATTTTA-AAGG-GTG
1 TTATCAAAATTTCATAAGGAG-G
*
6058 ATTA-CTAACAA-TTCATATGGAGG
1 -TTATC-AA-AATTTCATAAGGAGG
* * * * *
6081 TTTTTAAATTTTCATAATGTGG
1 TTATCAAAATTTCATAAGGAGG
* * * * *
6103 TTATCAATATATCATATGTAAG
1 TTATCAAAATTTCATAAGGAGG
* * ** *
6125 TTATCAACATCTCATAGATTA-C
1 TTATCAAAATTTCATA-AGGAGG
* *
6147 TTATCAAAATTTCAT-TGCGAAG
1 TTATCAAAATTTCATAAG-GAGG
* *
6169 TTATCAAAATTTTAT-AGTGAGA
1 TTATCAAAATTTCATAAG-GAGG
* * * *
6191 TCT-TTAAAATTACTTAGGGAGG
1 T-TATCAAAATTTCATAAGGAGG
* *
6213 TTAACAAAATTTCATAAGAAGG
1 TTATCAAAATTTCATAAGGAGG
** **
6235 TTAAAAAAAATTT-ATAAAAAGG
1 TT-ATCAAAATTTCATAAGGAGG
* * * * *
6257 TTCTCGAAATTCCAT-AGTATCG
1 TTATCAAAATTTCATAAGGA-GG
*
6279 TTATTAAAATTTCAT-AGGAAGG
1 TTATCAAAATTTCATAAGG-AGG
6301 TTATCAAAATTTCATAAGGAGG
1 TTATCAAAATTTCATAAGGAGG
*
6323 TAATCAAAA
1 TTATCAAAA
6332 ATAGTGTAAT
Statistics
Matches: 726, Mismatches: 172, Indels: 202
0.66 0.16 0.18
Matches are distributed among these distances:
16 9 0.01
17 3 0.00
18 3 0.00
19 35 0.05
20 41 0.06
21 70 0.10
22 417 0.57
23 75 0.10
24 23 0.03
25 20 0.03
26 11 0.02
27 1 0.00
28 13 0.02
30 3 0.00
31 2 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAAGGAGG
Found at i:5611 original size:65 final size:66
Alignment explanation
Indices: 5530--5676 Score: 179
Period size: 65 Copynumber: 2.2 Consensus size: 66
5520 TTTATAGGAA
** * * *
5530 GATTATCAAAATTTCATAGAGTTGTTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATG
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAATG
5595 T
66 T
* * * *
5596 GATTA-CAAAATTTCATAGAGGGGTCAACAAAATTTTATAGAGAGGTTATCAAAATTTCATAAAG
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAATG
*
5660 A
66 T
* *
5661 GGTTATCAAATTTTCA
1 GATTATCAAAATTTCA
5677 AAATGTGATT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
65 54 0.79
66 14 0.21
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCAAAGAGAGGTTATCAAAATTACATAATG
T
Found at i:5630 original size:87 final size:88
Alignment explanation
Indices: 5536--5701 Score: 246
Period size: 87 Copynumber: 1.9 Consensus size: 88
5526 GGAAGATTAT
** * *
5536 CAAAATTTCATAGAGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAATGTGATT
1 CAAAATTTCATAGAGAGGTTATCAAAATTTCATAA-AGAGGTTATCAAAATTACAAAATGTGATT
5600 A-CAAAATTTCATAGAGGGGTCAA
65 ACCAAAATTTCATAGAGGGGTCAA
* * *
5623 CAAAATTTTATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGATTA
1 CAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
5688 CCAAAATTTCATAG
66 CCAAAATTTCATAG
5702 TGGTATTTCT
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
87 55 0.79
88 15 0.21
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (88 bp):
CAAAATTTCATAGAGAGGTTATCAAAATTTCATAAAGAGGTTATCAAAATTACAAAATGTGATTA
CCAAAATTTCATAGAGGGGTCAA
Found at i:5945 original size:84 final size:86
Alignment explanation
Indices: 5802--6007 Score: 224
Period size: 84 Copynumber: 2.4 Consensus size: 86
5792 CAGGGAGGAT
* *
5802 ATCAAAATTTCATATGAAGGTTATCAAAATTTCATAGTTTAGTTTTCAAAATTTCATAA-GAGGG
1 ATCAAAATTTCATAGGAAGGTTATCAAAATTT-ATAG-TTAGTTATCAAAATTTCATAAGGA-GG
5866 TTATCAAAATTTCATAGTATGTAG
63 TTATCAAAATTTCATAGTATGTAG
*
5890 ATCAAAATTTCATAGGGAGAGGTTATCAAAA-TT-T-G-TAGTTATCAAGATTTCATAAGGAGGT
1 ATCAAAATTTCATA-GGA-AGGTTATCAAAATTTATAGTTAGTTATCAAAATTTCATAAGGAGGT
* * * * **
5951 TATCAAAATTTTATGGGGAGGTTT
64 TATCAAAATTTCAT-AGTATGTAG
*
5975 ATCAAAATTTTATAGGAAGGTTTATCAAAATTT
1 ATCAAAATTTCATAGGAAGG-TTATCAAAATTT
6008 CATAACGAGG
Statistics
Matches: 102, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
83 3 0.03
84 46 0.45
85 21 0.21
86 1 0.01
87 1 0.01
88 14 0.14
89 4 0.04
90 12 0.12
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (86 bp):
ATCAAAATTTCATAGGAAGGTTATCAAAATTTATAGTTAGTTATCAAAATTTCATAAGGAGGTTA
TCAAAATTTCATAGTATGTAG
Found at i:5980 original size:23 final size:23
Alignment explanation
Indices: 5928--6007 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 23
5918 AAATTTGTAG
* * *
5928 TTATCAAGATTTCATAAGGAGG-
1 TTATCAAAATTTTATAGGGAGGT
*
5950 TTATCAAAATTTTATGGGGAGGT
1 TTATCAAAATTTTATAGGGAGGT
*
5973 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGGAGGT
5996 TTATCAAAATTT
1 TTATCAAAATTT
6008 CATAACGAGG
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 18 0.35
23 33 0.65
ACGTcount: A:0.36, C:0.06, G:0.19, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGGAGGT
Done.