Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013430.1 Corchorus olitorius cultivar O-4 contig13463, 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: 20140
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1203 original size:19 final size:19
Alignment explanation
Indices: 1179--1215 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1169 AGCTTAGGAC
1179 ATAATGCAATAAAGTTTAA
1 ATAATGCAATAAAGTTTAA
*
1198 ATAATGCAATGAAGTTTA
1 ATAATGCAATAAAGTTTA
1216 GGCAAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.05, G:0.14, T:0.32
Consensus pattern (19 bp):
ATAATGCAATAAAGTTTAA
Found at i:2549 original size:24 final size:25
Alignment explanation
Indices: 2503--2550 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
2493 ATTGGAGTAT
*
2503 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
2528 TTATTT-TCTTGTTTATTTATTTT
1 TTATTTATCTTGTTGATTAATTTT
2551 TATTGTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:6194 original size:42 final size:42
Alignment explanation
Indices: 6147--6271 Score: 126
Period size: 42 Copynumber: 2.9 Consensus size: 42
6137 TCAGCATCAT
*
6147 CACCATTTCCAGGCA-TTTCAACTTCTTCAACTGGATTTCCAA
1 CACCATATCCAGG-ATTTTCAACTTCTTCAACTGGATTTCCAA
* * * * *
6189 CACCATCATCTATTGAATTTTCAACTCCATCAACTGGATTTTCAA
1 CACCAT-ATCCA--GGATTTTCAACTTCTTCAACTGGATTTCCAA
* * *
6234 AACCATCTCCTGGATTTTCAACTTCTTCAACTGGATTT
1 CACCATATCCAGGATTTTCAACTTCTTCAACTGGATTT
6272 TCTTTCTCAT
Statistics
Matches: 66, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
42 30 0.45
43 3 0.05
44 3 0.05
45 30 0.45
ACGTcount: A:0.27, C:0.28, G:0.09, T:0.36
Consensus pattern (42 bp):
CACCATATCCAGGATTTTCAACTTCTTCAACTGGATTTCCAA
Found at i:6229 original size:21 final size:21
Alignment explanation
Indices: 6162--6273 Score: 89
Period size: 21 Copynumber: 5.2 Consensus size: 21
6152 TTTCCAGGCA
* *
6162 TTTCAACTTCTTCAACTGGAT
1 TTTCAACTCCATCAACTGGAT
* * * *
6183 TTCCAACACCATCATCTATTGAAT
1 TTTCAACTCCATCA---ACTGGAT
6207 TTTCAACTCCATCAACTGGAT
1 TTTCAACTCCATCAACTGGAT
** **
6228 TTTCAAAACCATCTCCTGGAT
1 TTTCAACTCCATCAACTGGAT
* *
6249 TTTCAACTTCTTCAACTGGAT
1 TTTCAACTCCATCAACTGGAT
6270 TTTC
1 TTTC
6274 TTTCTCATAT
Statistics
Matches: 68, Mismatches: 20, Indels: 6
0.72 0.21 0.06
Matches are distributed among these distances:
21 51 0.75
24 17 0.25
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (21 bp):
TTTCAACTCCATCAACTGGAT
Found at i:6272 original size:42 final size:44
Alignment explanation
Indices: 6162--6273 Score: 147
Period size: 45 Copynumber: 2.6 Consensus size: 44
6152 TTTCCAGGCA
* * *
6162 TTTCAACTTCTTCAACTGGATTTCCAACACCATCATCTATTGAAT
1 TTTCAACTTCTTCAACTGGATTTTCAAAACCATCATC-ACTGAAT
* * *
6207 TTTCAACTCCATCAACTGGATTTTCAAAACCATC-TC-CTGGAT
1 TTTCAACTTCTTCAACTGGATTTTCAAAACCATCATCACTGAAT
6249 TTTCAACTTCTTCAACTGGATTTTC
1 TTTCAACTTCTTCAACTGGATTTTC
6274 TTTCTCATAT
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
42 27 0.46
44 2 0.03
45 30 0.51
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (44 bp):
TTTCAACTTCTTCAACTGGATTTTCAAAACCATCATCACTGAAT
Found at i:7494 original size:16 final size:16
Alignment explanation
Indices: 7461--7492 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
7451 TCTTTTCTGG
7461 TTAAATTAAATTAATT
1 TTAAATTAAATTAATT
7477 TTAAA-TAAATT-ATT
1 TTAAATTAAATTAATT
7491 TT
1 TT
7493 TTTTCAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 6 0.38
16 5 0.31
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAATTAAATTAATT
Found at i:7636 original size:30 final size:30
Alignment explanation
Indices: 7581--7641 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
7571 AAATTGATGG
* * *
7581 TTTGTCCCAAATTGACGCGAATTGAAAACGT
1 TTTGACCCAAATAGACGCAAATTG-AAACGT
7612 TTTGACCCAAATAGAC-CAAATTGAAACGT
1 TTTGACCCAAATAGACGCAAATTGAAACGT
7641 T
1 T
7642 GTACCCCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 7 0.26
30 6 0.22
31 14 0.52
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (30 bp):
TTTGACCCAAATAGACGCAAATTGAAACGT
Found at i:7649 original size:29 final size:31
Alignment explanation
Indices: 7586--7652 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 31
7576 GATGGTTTGT
* * *
7586 CCCAAATTGACGCGAATTGAAAACGTTTTGA
1 CCCAAATAGACGCAAATTGAAAACGTTGTGA
7617 CCCAAATAGAC-CAAATTG-AAACGTTGT-A
1 CCCAAATAGACGCAAATTGAAAACGTTGTGA
7645 CCCCAAAT
1 -CCCAAAT
7653 TAGGTCGAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 1 0.03
29 15 0.47
30 6 0.19
31 10 0.31
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (31 bp):
CCCAAATAGACGCAAATTGAAAACGTTGTGA
Found at i:8374 original size:12 final size:11
Alignment explanation
Indices: 8341--8382 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
8331 TTAAAAATTG
8341 GAAAATAAAAAA
1 GAAAA-AAAAAA
8353 CG-AAAAAAAAA
1 -GAAAAAAAAAA
8364 GAAAAAGAAAAA
1 GAAAAA-AAAAA
8376 GAAAAAA
1 GAAAAAA
8383 TGGCTTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 1 0.04
11 11 0.41
12 14 0.52
13 1 0.04
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.02
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:9582 original size:53 final size:53
Alignment explanation
Indices: 9520--9629 Score: 202
Period size: 53 Copynumber: 2.1 Consensus size: 53
9510 TCTTTAAATC
*
9520 CAATAGTTCATTGCATTTTGTATTATTTGGTATGTGTGCTTATTTAATAGGTT
1 CAATAGTTCATTGCATTTTGTATTAATTGGTATGTGTGCTTATTTAATAGGTT
*
9573 CAATAGTTCATTGCATTTTGTATTAATTGGTATGTGTGTTTATTTAATAGGTT
1 CAATAGTTCATTGCATTTTGTATTAATTGGTATGTGTGCTTATTTAATAGGTT
9626 CAAT
1 CAAT
9630 TGAATAAGTA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.25, C:0.07, G:0.18, T:0.50
Consensus pattern (53 bp):
CAATAGTTCATTGCATTTTGTATTAATTGGTATGTGTGCTTATTTAATAGGTT
Found at i:14854 original size:16 final size:16
Alignment explanation
Indices: 14833--14867 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
14823 ATACTTTGTT
*
14833 AAAAAAGGAA-AAAAG
1 AAAAAAAGAACAAAAG
14848 AAAAAAAGAACAAAAG
1 AAAAAAAGAACAAAAG
14864 AAAA
1 AAAA
14868 GGAGTAGACG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAACAAAAG
Found at i:15520 original size:16 final size:15
Alignment explanation
Indices: 15501--15543 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
15491 GGTTATTGTT
15501 TTTGTTGTTTCTTCCC
1 TTTGTT-TTTCTTCCC
* *
15517 TTTGTTTGTTCTTGCT
1 TTTGTTT-TTCTTCCC
15533 TTTGTTTTTCT
1 TTTGTTTTTCT
15544 ATTTCTCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.00, C:0.16, G:0.14, T:0.70
Consensus pattern (15 bp):
TTTGTTTTTCTTCCC
Found at i:17947 original size:24 final size:24
Alignment explanation
Indices: 17920--17979 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
17910 ATGGATACTA
*
17920 TTATATTCATCTTATATAGATTTC
1 TTATATTCATCTTATATAGATTAC
17944 TTATATTCATCTTATATAGATTAC
1 TTATATTCATCTTATATAGATTAC
*
17968 TTATATTAATCT
1 TTATATTCATCT
17980 AAAATTATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.32, C:0.12, G:0.03, T:0.53
Consensus pattern (24 bp):
TTATATTCATCTTATATAGATTAC
Found at i:20110 original size:2 final size:2
Alignment explanation
Indices: 20103--20140 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
20093 TATAATTGGA
20103 AT AT AT AT AT 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 AT AT AT AT AT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.