Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017236.1 Corchorus olitorius cultivar O-4 contig17269, 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: 28307
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:6102 original size:21 final size:21
Alignment explanation
Indices: 6062--6120 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
6052 AGGGAGATCA
* * *
6062 ACAAAATCTCACAAGAAGGTT
1 ACAAAATATCATAGGAAGGTT
6083 ATCAAAA-ATCATAGGAAGGTT
1 A-CAAAATATCATAGGAAGGTT
*
6104 ACAAAATTTCATAGGAA
1 ACAAAATATCATAGGAA
6121 TATTTATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.16
21 22 0.69
22 5 0.16
ACGTcount: A:0.49, C:0.14, G:0.15, T:0.22
Consensus pattern (21 bp):
ACAAAATATCATAGGAAGGTT
Found at i:6158 original size:22 final size:23
Alignment explanation
Indices: 6124--6228 Score: 87
Period size: 22 Copynumber: 4.7 Consensus size: 23
6114 ATAGGAATAT
* *
6124 TTATTAAAATTTCATAAT-TAGG
1 TTATCAAAATTTCATAATGGAGG
* *
6146 TTATCAAAGTTTCAT-ATGGAGT
1 TTATCAAAATTTCATAATGGAGG
*
6168 TTATCAAAATTTCAT-A-GCGTGG
1 TTATCAAAATTTCATAATG-GAGG
* *
6190 TTATCAAAATTCCAT-A-GCATGG
1 TTATCAAAATTTCATAATGGA-GG
6212 TTATCAAAATTTCATAA
1 TTATCAAAATTTCATAA
6229 AAATATTTAA
Statistics
Matches: 68, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
21 3 0.04
22 64 0.94
23 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.12, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTCATAATGGAGG
Found at i:7914 original size:30 final size:30
Alignment explanation
Indices: 7858--7917 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
7848 CAATTCTTGC
* **
7858 TCTTGAAATTATTCTTCAATGGTCTTCAAA
1 TCTTCAAATTATTCTTCAATAATCTTCAAA
7888 TCTTCAAATTA-TCTTCAATAAATCTTCAAA
1 TCTTCAAATTATTCTTCAAT-AATCTTCAAA
7918 CACGAACTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.42
Consensus pattern (30 bp):
TCTTCAAATTATTCTTCAATAATCTTCAAA
Found at i:8879 original size:31 final size:31
Alignment explanation
Indices: 8837--8898 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
8827 GAGTTTTGTA
* *
8837 AAACTTCTGAATCGCCTATTATATCCTTATT
1 AAACTTCTGAATCACCTATAATATCCTTATT
*
8868 AAACTTTTGAATCACCTATAATATCCTTATT
1 AAACTTCTGAATCACCTATAATATCCTTATT
8899 TTTCGAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (31 bp):
AAACTTCTGAATCACCTATAATATCCTTATT
Found at i:10713 original size:42 final size:43
Alignment explanation
Indices: 10653--10756 Score: 167
Period size: 42 Copynumber: 2.4 Consensus size: 43
10643 TTTAATGTTT
10653 TATATA-TATTATTATATTATTATTGACCAACCCAATTTCTAC-
1 TATATATTATTATT-TATTATTATTGACCAACCCAATTTCTACA
*
10695 TATATATTATTATTTATTATTATTGGCCAACCCAATTTCTACTA
1 TATATATTATTATTTATTATTATTGACCAACCCAATTTCTAC-A
10739 TATATATTATTATTTATT
1 TATATATTATTATTTATT
10757 TATGATTTAA
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
42 33 0.57
43 7 0.12
44 18 0.31
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.50
Consensus pattern (43 bp):
TATATATTATTATTTATTATTATTGACCAACCCAATTTCTACA
Found at i:11755 original size:22 final size:22
Alignment explanation
Indices: 11723--11792 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
11713 TAATAGGTAA
*
11723 TTATCAAAATTTCATATGGAGT
1 TTATCAAAATTTTATATGGAGT
* *
11745 TTATCACAATTTTATA-GGTA-A
1 TTATCAAAATTTTATATGG-AGT
*
11766 TTATCAAAATTTTATTTGGAGT
1 TTATCAAAATTTTATATGGAGT
11788 TTATC
1 TTATC
11793 TGCCCTTCGA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 17 0.44
22 22 0.56
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.46
Consensus pattern (22 bp):
TTATCAAAATTTTATATGGAGT
Found at i:11771 original size:21 final size:21
Alignment explanation
Indices: 11715--11780 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
11705 GTGATCTATA
*
11715 ATAGGTAATTATCAAAATTTC
1 ATAGGTAATTATCAAAATTTT
* *
11736 ATATGG-AGTTTATCACAATTTT
1 ATA-GGTA-ATTATCAAAATTTT
11758 ATAGGTAATTATCAAAATTTT
1 ATAGGTAATTATCAAAATTTT
11779 AT
1 AT
11781 TTGGAGTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
21 20 0.54
22 17 0.46
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (21 bp):
ATAGGTAATTATCAAAATTTT
Found at i:18444 original size:22 final size:22
Alignment explanation
Indices: 18418--18459 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
18408 TTTCAACAAA
*
18418 CCTATGGTTAGATATTAGTTTG
1 CCTATGGTTAGATAATAGTTTG
18440 CCTATGGTTAGATAATAGTT
1 CCTATGGTTAGATAATAGTT
18460 AGTTAGCAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.10, G:0.21, T:0.43
Consensus pattern (22 bp):
CCTATGGTTAGATAATAGTTTG
Found at i:21889 original size:22 final size:22
Alignment explanation
Indices: 21846--21889 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
21836 TTTCAACTAA
* *
21846 CCTATGGTTTGATATTAGTTAG
1 CCTATGGTTAGATACTAGTTAG
*
21868 CCTATGGTTAGATACTATTTAG
1 CCTATGGTTAGATACTAGTTAG
21890 TTAGCAGTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.43
Consensus pattern (22 bp):
CCTATGGTTAGATACTAGTTAG
Found at i:22176 original size:12 final size:11
Alignment explanation
Indices: 22158--22198 Score: 57
Period size: 12 Copynumber: 3.7 Consensus size: 11
22148 GCTTCTTCCC
22158 CTCTCTCCTTT
1 CTCTCTCCTTT
*
22169 CTTCTCTCCTTA
1 C-TCTCTCCTTT
22181 CTCTCT-CTTT
1 CTCTCTCCTTT
22191 CTCTCTCC
1 CTCTCTCC
22199 GTTGCTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 9 0.35
11 7 0.27
12 10 0.38
ACGTcount: A:0.02, C:0.46, G:0.00, T:0.51
Consensus pattern (11 bp):
CTCTCTCCTTT
Found at i:24711 original size:12 final size:11
Alignment explanation
Indices: 24673--24704 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
24663 TAATAAATTT
24673 AAGTACTAAAAA
1 AAGT-CTAAAAA
24685 AAGTCTAAAAA
1 AAGTCTAAAAA
24696 AAGTCTAAA
1 AAGTCTAAA
24705 TTTAAGTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.19
Consensus pattern (11 bp):
AAGTCTAAAAA
Found at i:27297 original size:21 final size:21
Alignment explanation
Indices: 27273--27355 Score: 64
Period size: 22 Copynumber: 3.8 Consensus size: 21
27263 TATCTTAGAT
27273 ATAAT-ATATATTATTAAATAA
1 ATAATAATATATT-TTAAATAA
27294 ATAATAAATATATTTTAAAT-A
1 ATAAT-AATATATTTTAAATAA
* **
27315 ATAAATAATGA-GTTCAAAATAA
1 AT-AATAAT-ATATTTTAAATAA
27337 ATAAATAATATATATTTAA
1 AT-AATAATATAT-TTTAA
27356 TTACTAAACA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
21 18 0.37
22 21 0.43
23 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (21 bp):
ATAATAATATATTTTAAATAA
Found at i:27638 original size:9 final size:9
Alignment explanation
Indices: 27626--27654 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
27616 AGTCAAGAGG
27626 CCCAAGTGC
1 CCCAAGTGC
27635 CCCAAGTGC
1 CCCAAGTGC
27644 CCCAAGTGC
1 CCCAAGTGC
27653 CC
1 CC
27655 TCATCATAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.48, G:0.21, T:0.10
Consensus pattern (9 bp):
CCCAAGTGC
Done.