Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017602.1 Corchorus olitorius cultivar O-4 contig17635, 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: 15173
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Found at i:4637 original size:12 final size:12
Alignment explanation
Indices: 4620--4644 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4610 CACATTGTAT
4620 GGCAACACTGTC
1 GGCAACACTGTC
4632 GGCAACACTGTC
1 GGCAACACTGTC
4644 G
1 G
4645 TGCTTTTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.28, T:0.16
Consensus pattern (12 bp):
GGCAACACTGTC
Found at i:5702 original size:35 final size:35
Alignment explanation
Indices: 5663--5770 Score: 207
Period size: 35 Copynumber: 3.1 Consensus size: 35
5653 TTGATTACTA
5663 TTTAGCTTGGTTTTTTCGTTATTTCAATATTGGTT
1 TTTAGCTTGGTTTTTTCGTTATTTCAATATTGGTT
*
5698 TTTAGCTTGGTTTTTTCGTTATTTTAATATTGGTT
1 TTTAGCTTGGTTTTTTCGTTATTTCAATATTGGTT
5733 TTTAGCTTGGTTTTTTCGTTATTTCAATATTGGTT
1 TTTAGCTTGGTTTTTTCGTTATTTCAATATTGGTT
5768 TTT
1 TTT
5771 TTCGTTATTC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 71 1.00
ACGTcount: A:0.14, C:0.07, G:0.17, T:0.62
Consensus pattern (35 bp):
TTTAGCTTGGTTTTTTCGTTATTTCAATATTGGTT
Found at i:6443 original size:14 final size:14
Alignment explanation
Indices: 6424--6450 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6414 ATGTCTATTT
6424 AAAAAAAGTAAATC
1 AAAAAAAGTAAATC
6438 AAAAAAAGTAAAT
1 AAAAAAAGTAAAT
6451 GGAGTTTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.04, G:0.07, T:0.15
Consensus pattern (14 bp):
AAAAAAAGTAAATC
Found at i:7886 original size:86 final size:86
Alignment explanation
Indices: 7739--7896 Score: 280
Period size: 86 Copynumber: 1.8 Consensus size: 86
7729 ATTTGGCAAA
* *
7739 CCCATAAGTCACCAATAATATGTTGACAACTGATTGGGGACTACTGCATATCAAGTACAAGAACA
1 CCCATAAGTCACCAATAATATGTTGAAAACTGATTGGGGAATACTGCATATCAAGTACAAGAACA
7804 TGTTCGCACAATGGAACGCAT
66 TGTTCGCACAATGGAACGCAT
* *
7825 CCCATAAGTCACCAATAATATGTTGAAAACTGATTGGGGAATATTGCATATCAAGTGCAAGAACA
1 CCCATAAGTCACCAATAATATGTTGAAAACTGATTGGGGAATACTGCATATCAAGTACAAGAACA
7890 TGTTCGC
66 TGTTCGC
7897 GCAGTGAAAC
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
86 68 1.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (86 bp):
CCCATAAGTCACCAATAATATGTTGAAAACTGATTGGGGAATACTGCATATCAAGTACAAGAACA
TGTTCGCACAATGGAACGCAT
Found at i:8253 original size:46 final size:43
Alignment explanation
Indices: 8186--8307 Score: 172
Period size: 46 Copynumber: 2.7 Consensus size: 43
8176 GCTGTTATTA
*
8186 TTATACTCTTAAATACATAGGAAAAGATAAAAACATAATAAGCTTG
1 TTATACTCTTAAATACATAGGAAAAGATAAAAACAT-AT--GCATG
* *
8232 TTATACTCCTAAACACATAGGAAAAGATAAAAACATATGCATG
1 TTATACTCTTAAATACATAGGAAAAGATAAAAACATATGCATG
*
8275 TTATAACTCTTAAATACATAGAAAAAGATAAAA
1 TTAT-ACTCTTAAATACATAGGAAAAGATAAAA
8308 TTGAGGTAGT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
43 8 0.12
44 25 0.36
45 2 0.03
46 34 0.49
ACGTcount: A:0.52, C:0.12, G:0.10, T:0.26
Consensus pattern (43 bp):
TTATACTCTTAAATACATAGGAAAAGATAAAAACATATGCATG
Found at i:13897 original size:21 final size:23
Alignment explanation
Indices: 13873--13916 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
13863 TTTCATAAGG
13873 AGGTTATC-GAAATTCA-AGGGA
1 AGGTTATCGGAAATTCACAGGGA
*
13894 AGGTTATCGGAATTTCACAGGGA
1 AGGTTATCGGAAATTCACAGGGA
13917 GATTACTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 7 0.35
23 5 0.25
ACGTcount: A:0.34, C:0.11, G:0.30, T:0.25
Consensus pattern (23 bp):
AGGTTATCGGAAATTCACAGGGA
Found at i:13964 original size:22 final size:21
Alignment explanation
Indices: 13675--14045 Score: 209
Period size: 22 Copynumber: 17.0 Consensus size: 21
13665 TTTTAATTTT
*
13675 GGAGGTTATCAAAA-TTCATT
1 GGAGGTTATCAAAATTTCATA
* *
13695 GTGTGGTTA-CTAAAATTTTATA
1 G-GAGGTTATC-AAAATTTCATA
* * *
13717 GTGTA-GTTCTCAAAATTTTATT
1 G-G-AGGTTATCAAAATTTCATA
* *
13739 GTGTGGTTATCAAAATTTTATA
1 G-GAGGTTATCAAAATTTCATA
* * *
13761 GTGAGGTTACCAAACTTTAATA
1 G-GAGGTTATCAAAATTTCATA
* * *
13783 GGTAGGATATTAAAATTTTATA
1 GG-AGGTTATCAAAATTTCATA
* * *
13805 GTGTA-GTTATCACAAGTTCATG
1 G-G-AGGTTATCAAAATTTCATA
* *
13827 GGATGTTATCAAATTTTCATAA
1 GGAGGTTATCAAAATTTCAT-A
*
13849 GGATGTTATCAAAATTTCATAA
1 GGAGGTTATCAAAATTTCAT-A
*
13871 GGAGGTTATCGAAA-TTCA-A
1 GGAGGTTATCAAAATTTCATA
** *
13890 GGGAAGGTTATCGGAATTTCACA
1 -GG-AGGTTATCAAAATTTCATA
*
13913 GGGAGATTA-CTAAAATTTCATA
1 -GGAGGTTATC-AAAATTTCATA
***
13935 CTCTGGTTATCAAAATTTCATA
1 -GGAGGTTATCAAAATTTCATA
*
13957 GGAAGGTTAACAAAATTTCATA
1 GG-AGGTTATCAAAATTTCATA
* *
13979 GG-GCGATTATCGAAATTTTATA
1 GGAG-G-TTATCAAAATTTCATA
14001 TGGAGGTTATCAAAATTTCATA
1 -GGAGGTTATCAAAATTTCATA
*
14023 GGAAGATTATCAAAATTTCATA
1 GG-AGGTTATCAAAATTTCATA
14045 G
1 G
14046 TGTGCTTATA
Statistics
Matches: 278, Mismatches: 51, Indels: 42
0.75 0.14 0.11
Matches are distributed among these distances:
19 1 0.00
20 6 0.02
21 44 0.16
22 214 0.77
23 12 0.04
24 1 0.00
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.36
Consensus pattern (21 bp):
GGAGGTTATCAAAATTTCATA
Found at i:13989 original size:44 final size:43
Alignment explanation
Indices: 13794--14186 Score: 163
Period size: 44 Copynumber: 8.8 Consensus size: 43
13784 GTAGGATATT
* * * * * * *
13794 AAAATTTTATAGTGTAG-TTATCACAAGTTCATGGGATGTTATC
1 AAAATTTCATAG-GAAGATTATCAAAATTTCATAGGAGGTTAAC
* * *
13837 AAATTTTCATAAGGATG-TTATCAAAATTTCATAAGGAGGTTATC
1 AAAATTTCAT-AGGAAGATTATCAAAATTTCAT-AGGAGGTTAAC
* * ** * *
13881 GAAA-TTCA-AGGGAAGGTTATCGGAATTTCACAGGGAGATT-AC
1 AAAATTTCATA-GGAAGATTATCAAAATTTCATA-GGAGGTTAAC
**** *
13923 TAAAATTTCATACTCTGGTTATCAAAATTTCATAGGAAGGTTAAC
1 -AAAATTTCATAGGAAGATTATCAAAATTTCATAGG-AGGTTAAC
** * * *
13968 AAAATTTCATAGGGCGATTATCGAAATTTTATATGGAGGTTATC
1 AAAATTTCATAGGAAGATTATCAAAATTTCATA-GGAGGTTAAC
* *
14012 AAAATTTCATAGGAAGATTATCAAAATTTCATAGTGTGCTTATA-
1 AAAATTTCATAGGAAGATTATCAAAATTTCATAG-GAGGTTA-AC
* ** *
14056 AAAATTGCATAGTGAGATAGAGTAAGCTTATCAAAATTTCA-AGTGTCGTTACC
1 AAAATTTCATA--G-G--A-AG--A--TTATCAAAATTTCATAG-GAGGTTAAC
* * * * *
14109 AAAATTTCATAGTGTA-ATAATCACAATTTCATGGGGAGGTTATC
1 AAAATTTCATAG-GAAGATTATCAAAATTTCAT-AGGAGGTTAAC
* * *
14153 GAAATTTCAGAGGGAGATTATCAAAATTTCATAG
1 AAAATTTCATAGGAAGATTATCAAAATTTCATAG
14187 TGTGATTATC
Statistics
Matches: 264, Mismatches: 59, Indels: 54
0.70 0.16 0.14
Matches are distributed among these distances:
41 1 0.00
42 6 0.02
43 66 0.25
44 143 0.54
45 7 0.03
46 1 0.00
47 1 0.00
48 1 0.00
49 1 0.00
50 2 0.01
51 2 0.01
52 1 0.00
53 18 0.07
54 14 0.05
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.34
Consensus pattern (43 bp):
AAAATTTCATAGGAAGATTATCAAAATTTCATAGGAGGTTAAC
Found at i:14061 original size:66 final size:66
Alignment explanation
Indices: 13674--14207 Score: 285
Period size: 66 Copynumber: 8.0 Consensus size: 66
13664 CTTTTAATTT
* * * *
13674 TGGAGGTTATCAAAA-TTCATTGTG-TGGTTA-CTAAAATTTTATAGTGT-AGTTCTCAAAATTT
1 TGGAGGTTATCAAAATTTCATAG-GAAGGTTATC-AAAATTTCATAGTGTGA-TTATCAAAATTT
13735 TAT-
63 TATA
* * * * * *
13738 TGTGTGGTTATCAAAATTTTATAGTG-AGGTTACCAAACTTTAATAG-GTAGGA-TATTAAAATT
1 TG-GAGGTTATCAAAATTTCATAG-GAAGGTTATCAAAATTTCATAGTGT--GATTATCAAAATT
13800 TTATA
62 TTATA
* * * * * *
13805 GTGTA-GTTATCACAAGTTCAT-GGGATGTTATCAAATTTTCATAAG-GATG-TTATCAAAATTT
1 -TGGAGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCAT-AGTG-TGATTATCAAAATTT
*
13866 CATA
63 TATA
* * ** * * * *
13870 AGGAGGTTATCGAAA-TTCA-AGGGAAGGTTATCGGAATTTCACAGGGAGATTA-CTAAAATTTC
1 TGGAGGTTATCAAAATTTCATA-GGAAGGTTATCAAAATTTCATAGTGTGATTATC-AAAATTTT
13932 ATA
64 ATA
** * * * *
13935 CT-CTGGTTATCAAAATTTCATAGGAAGGTTAACAAAATTTCATAGGGCGATTATCGAAATTTTA
1 -TGGAGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGATTATCAAAATTTTA
13999 TA
65 TA
* * *
14001 TGGAGGTTATCAAAATTTCATAGGAAGATTATCAAAATTTCATAGTGTGCTTATAAAAATTGCAT
1 TGGAGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGATTATCAAAATT---T
*
14066 AGTGAGA
63 --T-ATA
* ** * * * *
14073 TAGAGTAAGCTTATCAAAATTTCA-AGTG-TCGTTACCAAAATTTCATAGTGTAATAATCACAAT
1 T-G-G--AGGTTATCAAAATTTCATAG-GAAGGTTATCAAAATTTCATAGTGTGATTATCAAAAT
* *
14136 TTCATG
61 TTTATA
* * * * *
14142 GGGAGGTTATCGAAATTTCAGAGGGAGATTATCAAAATTTCATAGTGTGATTATCAAAATTTTAT
1 TGGAGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGATTATCAAAATTTTAT
14207 A
66 A
14208 ATATGGTATT
Statistics
Matches: 358, Mismatches: 76, Indels: 70
0.71 0.15 0.14
Matches are distributed among these distances:
64 13 0.04
65 108 0.30
66 173 0.48
67 5 0.01
68 4 0.01
69 2 0.01
71 1 0.00
72 4 0.01
73 1 0.00
74 1 0.00
75 29 0.08
76 17 0.05
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (66 bp):
TGGAGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGTGTGATTATCAAAATTTTAT
A
Found at i:14158 original size:22 final size:23
Alignment explanation
Indices: 14128--14203 Score: 86
Period size: 22 Copynumber: 3.4 Consensus size: 23
14118 TAGTGTAATA
* *
14128 ATCACAATTTCATG-GGGAGGTT
1 ATCAAAATTTCATGAGGGAGATT
*
14150 ATCGAAATTTCA-GAGGGAGATT
1 ATCAAAATTTCATGAGGGAGATT
* *
14172 ATCAAAATTTCAT-AGTGTGATT
1 ATCAAAATTTCATGAGGGAGATT
14194 ATCAAAATTT
1 ATCAAAATTT
14204 TATAATATGG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
21 1 0.02
22 45 0.98
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34
Consensus pattern (23 bp):
ATCAAAATTTCATGAGGGAGATT
Found at i:14196 original size:44 final size:43
Alignment explanation
Indices: 14083--14203 Score: 111
Period size: 44 Copynumber: 2.8 Consensus size: 43
14073 TAGAGTAAGC
* * *
14083 TTATCAAAATTTCA-AGTGTCGTTACCAAAATTTCATAGTGTAA
1 TTATCAAAATTTCATAGTGT-GTTATCAAAATTTCAGAGTGGAA
* * * * * *
14126 TAATCACAATTTCATGGGGAGGTTATCGAAATTTCAGAG-GGAGA
1 TTATCAAAATTTCATAGTG-TGTTATCAAAATTTCAGAGTGGA-A
14170 TTATCAAAATTTCATAGTGTGATTATCAAAATTT
1 TTATCAAAATTTCATAGTGTG-TTATCAAAATTT
14204 TATAATATGG
Statistics
Matches: 59, Mismatches: 15, Indels: 7
0.73 0.19 0.09
Matches are distributed among these distances:
43 15 0.25
44 44 0.75
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (43 bp):
TTATCAAAATTTCATAGTGTGTTATCAAAATTTCAGAGTGGAA
Found at i:14335 original size:22 final size:22
Alignment explanation
Indices: 14253--14336 Score: 78
Period size: 22 Copynumber: 3.8 Consensus size: 22
14243 AATTTTGTGG
**
14253 TAACTAAAATTTCATAATGAGAT
1 TAAC-AAAATTTCATAGGGAGAT
* * * *
14276 TAACAAAATTTGATAGAGTGGT
1 TAACAAAATTTCATAGGGAGAT
** *
14298 TCTCAAAATTTTATAGGGAGAT
1 TAACAAAATTTCATAGGGAGAT
14320 TAACAAAATTTCATAGG
1 TAACAAAATTTCATAGG
14337 CAAGTTATTG
Statistics
Matches: 47, Mismatches: 14, Indels: 1
0.76 0.23 0.02
Matches are distributed among these distances:
22 43 0.91
23 4 0.09
ACGTcount: A:0.43, C:0.08, G:0.15, T:0.33
Consensus pattern (22 bp):
TAACAAAATTTCATAGGGAGAT
Done.