Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019117.1 Corchorus olitorius cultivar O-4 contig19150, 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: 14983
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Found at i:3663 original size:23 final size:23
Alignment explanation
Indices: 3637--3685 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
3627 AGAAATTTAG
* * *
3637 CTTTATAGAGTTGATTGTTTAAA
1 CTTTATAGAGATGACTATTTAAA
3660 CTTTATAGAGATGACTATTTAAA
1 CTTTATAGAGATGACTATTTAAA
3683 CTT
1 CTT
3686 AAAAATTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (23 bp):
CTTTATAGAGATGACTATTTAAA
Found at i:5190 original size:40 final size:41
Alignment explanation
Indices: 5129--5221 Score: 145
Period size: 42 Copynumber: 2.3 Consensus size: 41
5119 TCCTCCATTG
5129 TTGAAGGATATTTAAGAATATA-TTTTTAAAAGATTTATTT
1 TTGAAGGATATTTAAGAATATATTTTTTAAAAGATTTATTT
*
5169 TTGAAGGATATTTAA-ATATATATTTTTTTAAAGGATTTATTT
1 TTGAAGGATATTTAAGA-ATATA-TTTTTTAAAAGATTTATTT
5211 TTGAAGGATAT
1 TTGAAGGATAT
5222 ATTATGATGA
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
39 1 0.02
40 20 0.41
42 28 0.57
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (41 bp):
TTGAAGGATATTTAAGAATATATTTTTTAAAAGATTTATTT
Found at i:5217 original size:15 final size:15
Alignment explanation
Indices: 5146--5224 Score: 51
Period size: 15 Copynumber: 5.5 Consensus size: 15
5136 ATATTTAAGA
*
5146 ATATATTTTTAAAAG
1 ATATATTTTTAAAGG
* *
5161 ATTTATTTTTGAAGG
1 ATATATTTTTAAAGG
*
5176 --ATA--TTTAAA-T
1 ATATATTTTTAAAGG
5186 ATATATTTTTTTAAAGG
1 ATATA--TTTTTAAAGG
* *
5203 ATTTATTTTTGAAGG
1 ATATATTTTTAAAGG
5218 ATATATT
1 ATATATT
5225 ATGATGATAT
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
11 5 0.11
12 3 0.06
13 2 0.04
15 27 0.57
16 6 0.13
17 4 0.09
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (15 bp):
ATATATTTTTAAAGG
Found at i:6634 original size:108 final size:107
Alignment explanation
Indices: 6288--6666 Score: 530
Period size: 107 Copynumber: 3.5 Consensus size: 107
6278 CATACTAAAA
* ** *
6288 TAATTTTGATTTTTAAGAGTAAATTAT-GAAATTAAATAATTTTTTATTATAGGGTTTTAGAAAT
1 TAATTTT-A-TTTTAAGAGTAAATT-TCAAAATT-AATAACCTATTATTATAGGGTTTTAGAAAT
* * * *
6352 TAAATATAAAATTAATTTCACTAAGTTTAGTCCCAAATTAAAATTA
62 TAAATATAAAACTAATTTTACTAAGTTTAGTCCTAAATTAAAATTT
* * * *
6398 AAATTTTATTTTAAGGGTAAATTCCAAAATTAATAACCTATTGTTATAGGGTTTTAGAAATTAAA
1 TAATTTTATTTTAAGAGTAAATTTCAAAATTAATAACCTATTATTATAGGGTTTTAGAAATTAAA
6463 TATAAAACTAATTTTACTAAGTTTAGTCCTAAATTAAAATTT
66 TATAAAACTAATTTTACTAAGTTTAGTCCTAAATTAAAATTT
*
6505 TAATTTTATTTTAAGGGTAAATTTCAAAATTAATAACCTATTATTATAGGGTTTTAGAAA-TAAA
1 TAATTTTATTTTAAGAGTAAATTTCAAAATTAATAACCTATTATTATAGGGTTTTAGAAATTAAA
*
6569 TTATAAAACTAAATTTTACTAAGTTTAGGCCTAAATTAAAATTT
66 -TATAAAACT-AATTTTACTAAGTTTAGTCCTAAATTAAAATTT
* *
6613 TAATTTTATTTTAAGAGTAAA-TTCTAAAATTAATAACTTATTATTATATGGTTT
1 TAATTTTATTTTAAGAGTAAATTTC-AAAATTAATAACCTATTATTATAGGGTTT
6667 CAGATATACT
Statistics
Matches: 246, Mismatches: 19, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
106 4 0.02
107 137 0.56
108 98 0.40
109 1 0.00
110 6 0.02
ACGTcount: A:0.42, C:0.06, G:0.09, T:0.43
Consensus pattern (107 bp):
TAATTTTATTTTAAGAGTAAATTTCAAAATTAATAACCTATTATTATAGGGTTTTAGAAATTAAA
TATAAAACTAATTTTACTAAGTTTAGTCCTAAATTAAAATTT
Found at i:10563 original size:40 final size:40
Alignment explanation
Indices: 10508--10587 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
10498 AGGGACATAT
* *
10508 ATCATGGTAAAATATTAGTGATT-ATAGTTGTAACAAATTA
1 ATCATAGTAAAATATTAGTGATTGAGA-TTGTAACAAATTA
*
10548 ATCATAGTAAAATATTAGTGATTGCGATTGTAACAAATTA
1 ATCATAGTAAAATATTAGTGATTGAGATTGTAACAAATTA
10588 TGTATTTTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 35 0.97
41 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.36
Consensus pattern (40 bp):
ATCATAGTAAAATATTAGTGATTGAGATTGTAACAAATTA
Found at i:10851 original size:2 final size:2
Alignment explanation
Indices: 10844--10878 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
10834 ATTCTAGTGA
10844 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10879 CTCCCTCAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11671 original size:124 final size:125
Alignment explanation
Indices: 11560--11805 Score: 372
Period size: 124 Copynumber: 2.0 Consensus size: 125
11550 GATCGATTTT
11560 ACAATTCAGAATTG-GTGACATAGACTCATATATATTGACTTGAGCTGTCAATTATTAATGCAAT
1 ACAATTCAGAATTGTGTGACATAGACTC--ATATATTGACTTGAGCTGTCAATTATTAATGCAAT
* *
11624 TTTTCTCCAAGTGAAGCCAAGAAACCTAAAAATTGTCCCTCATTGAAA-TGAGTAATGTGGA
64 TTTTCTCCAAGTGAAGCCAAGAAACCTAAAAATCGTCCCACATTGAAATTGAGTAATGTGGA
* * * * * *
11685 ACCATTCGGAATTGTGTGACATAGAGTCATATATTGTCTTGAGCTTTCAATTATTAATGCATTTT
1 ACAATTCAGAATTGTGTGACATAGACTCATATATTGACTTGAGCTGTCAATTATTAATGCAATTT
*
11750 TTCTCCAAGTGAAGCCAAGAAACCTAAAAATCGTCCCACATCGAAATT-AGTAATGT
66 TTCTCCAAGTGAAGCCAAGAAACCTAAAAATCGTCCCACATTGAAATTGAGTAATGT
11806 ATTTATTTCA
Statistics
Matches: 110, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
124 85 0.77
125 13 0.12
126 12 0.11
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (125 bp):
ACAATTCAGAATTGTGTGACATAGACTCATATATTGACTTGAGCTGTCAATTATTAATGCAATTT
TTCTCCAAGTGAAGCCAAGAAACCTAAAAATCGTCCCACATTGAAATTGAGTAATGTGGA
Found at i:12264 original size:22 final size:22
Alignment explanation
Indices: 12239--12281 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12229 CTAAAATCAA
12239 TCAATGACCCCTTCAAAAATAG
1 TCAATGACCCCTTCAAAAATAG
**
12261 TCAATGGTCCCTTCAAAAATA
1 TCAATGACCCCTTCAAAAATA
12282 ATATATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.26, G:0.09, T:0.26
Consensus pattern (22 bp):
TCAATGACCCCTTCAAAAATAG
Found at i:14386 original size:22 final size:23
Alignment explanation
Indices: 14358--14426 Score: 81
Period size: 22 Copynumber: 3.1 Consensus size: 23
14348 AAAATTCATT
14358 GTGTGGTTACT-AAAAGTTTAGA
1 GTGTGGTTACTCAAAAGTTTAGA
* *
14380 GTGTGGTT-CTCAAAATTTTATA
1 GTGTGGTTACTCAAAAGTTTAGA
* *
14402 GTGTGGTTA-TCAAAATTTTATA
1 GTGTGGTTACTCAAAAGTTTAGA
14424 GTG
1 GTG
14427 AGTATAGTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.05
22 41 0.95
ACGTcount: A:0.29, C:0.06, G:0.23, T:0.42
Consensus pattern (23 bp):
GTGTGGTTACTCAAAAGTTTAGA
Found at i:14490 original size:22 final size:22
Alignment explanation
Indices: 14438--14658 Score: 137
Period size: 22 Copynumber: 9.8 Consensus size: 22
14428 GTATAGTGTA
* * *
14438 GTTATCACAATTTCAT-GGGAT
1 GTTATCAAAATTTCATAAGGAG
14459 GTTATCAAAATTTCATAAGGAG
1 GTTATCAAAATTTCATAAGGAG
* *
14481 GTTATTAAAATAAAATTTCCTAAGGAG
1 GTTA-T----CAAAATTTCATAAGGAG
* * *
14508 GTTATACTGAAA-GTCAT-GGGAAG
1 GTTAT-C-AAAATTTCATAAGG-AG
* *
14531 GTTATCAAAATTTCACAGGGAG
1 GTTATCAAAATTTCATAAGGAG
****
14553 GTTA-CTAAAATTTCATACTCTG
1 GTTATC-AAAATTTCATAAGGAG
*
14575 GTTATCAAAATTTCATAAGGCG
1 GTTATCAAAATTTCATAAGGAG
* * * *
14597 ATTATCGAAATTTTATATGGAG
1 GTTATCAAAATTTCATAAGGAG
14619 GTTATCAAAATTTCAT-AGGAAG
1 GTTATCAAAATTTCATAAGG-AG
*
14641 ATTATCAAAATTTCATAA
1 GTTATCAAAATTTCATAA
14659 TGCGCTTATA
Statistics
Matches: 154, Mismatches: 32, Indels: 26
0.73 0.15 0.12
Matches are distributed among these distances:
21 21 0.14
22 93 0.60
23 17 0.11
24 3 0.02
26 1 0.01
27 19 0.12
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (22 bp):
GTTATCAAAATTTCATAAGGAG
Found at i:14608 original size:44 final size:44
Alignment explanation
Indices: 14529--14680 Score: 141
Period size: 44 Copynumber: 3.5 Consensus size: 44
14519 AGTCATGGGA
* * *
14529 AGGTTATCAAAATTTCACAGGGAGGTTA-CTAAAATTTCATACT-C
1 AGGTTATCAAAATTTCATAGGAAGATTATC-AAAATTTCATA-TGC
* * * * *
14573 TGGTTATCAAAATTTCATAAGG-CGATTATCGAAATTTTATATGG
1 AGGTTATCAAAATTTCAT-AGGAAGATTATCAAAATTTCATATGC
14617 AGGTTATCAAAATTTCATAGGAAGATTATCAAAATTTCATAATGC
1 AGGTTATCAAAATTTCATAGGAAGATTATCAAAATTTCAT-ATGC
* * *
14662 -GCTTATAAAAATTACATAG
1 AGGTTATCAAAATTTCATAG
14681 TGCGATAGAG
Statistics
Matches: 88, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
43 4 0.05
44 77 0.88
45 7 0.08
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (44 bp):
AGGTTATCAAAATTTCATAGGAAGATTATCAAAATTTCATATGC
Found at i:14667 original size:22 final size:22
Alignment explanation
Indices: 14559--14686 Score: 93
Period size: 22 Copynumber: 5.8 Consensus size: 22
14549 GGAGGTTACT
* *
14559 AAAATTTCATACT-CTGGTTATC
1 AAAATTTCATAATGC-GATTATC
*
14581 AAAATTTCATAAGGCGATTATC
1 AAAATTTCATAATGCGATTATC
* *
14603 GAAATTTTAT-ATG-GAGGTTATC
1 AAAATTTCATAATGCGA--TTATC
* *
14625 AAAATTTCAT-AGGAAGATTATC
1 AAAATTTCATAATG-CGATTATC
* *
14647 AAAATTTCATAATGCGCTTATA
1 AAAATTTCATAATGCGATTATC
* *
14669 AAAATTACATAGTGCGAT
1 AAAATTTCATAATGCGAT
14687 AGAGTGAGCT
Statistics
Matches: 84, Mismatches: 16, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
20 2 0.02
21 2 0.02
22 75 0.89
23 3 0.04
24 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (22 bp):
AAAATTTCATAATGCGATTATC
Found at i:14827 original size:22 final size:21
Alignment explanation
Indices: 14689--14835 Score: 84
Period size: 22 Copynumber: 6.9 Consensus size: 21
14679 AGTGCGATAG
*
14689 AGTGAGCTTATCAAAATTTCA
1 AGTGAGGTTATCAAAATTTCA
** *
14710 AGTGTCGTTACCAAAATTTCA
1 AGTGAGGTTATCAAAATTTCA
* * *
14731 TAGTGTA-ATAATCACAATTTC-
1 -AGTG-AGGTTATCAAAATTTCA
*
14752 A-TAGAGGTTAACAAAATTTCA
1 AGT-GAGGTTATCAAAATTTCA
* * * *
14773 TGGGAGGTTATCGAAATTTTA
1 AGTGAGGTTATCAAAATTTCA
* *
14794 GAGGGAGATTATCAAAATTTCA
1 -AGTGAGGTTATCAAAATTTCA
* *
14816 TTGTGTGGTTATCAAAATTT
1 -AGTGAGGTTATCAAAATTT
14836 TATAATATGG
Statistics
Matches: 92, Mismatches: 27, Indels: 13
0.70 0.20 0.10
Matches are distributed among these distances:
19 2 0.02
20 12 0.13
21 32 0.35
22 46 0.50
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (21 bp):
AGTGAGGTTATCAAAATTTCA
Found at i:14846 original size:22 final size:22
Alignment explanation
Indices: 14802--14846 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
14792 TAGAGGGAGA
** *
14802 TTATCAAAATTTCATTGTGTGG
1 TTATCAAAATTTCATAATATGG
*
14824 TTATCAAAATTTTATAATATGG
1 TTATCAAAATTTCATAATATGG
14846 T
1 T
14847 AGTATTTCAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (22 bp):
TTATCAAAATTTCATAATATGG
Found at i:14934 original size:21 final size:22
Alignment explanation
Indices: 14893--14934 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
14883 TATGGTAATT
*
14893 AAAATTTCATAATGAGTTTATC
1 AAAATTTCATAATGAGATTATC
*
14915 AAAATTT-ATAGTGAGATTAT
1 AAAATTTCATAATGAGATTAT
14935 TAACAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (22 bp):
AAAATTTCATAATGAGATTATC
Done.