Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015580.1 Corchorus olitorius cultivar O-4 contig15613, 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: 48516
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1257 original size:15 final size:15
Alignment explanation
Indices: 1237--1265 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1227 GTACTTTTTA
1237 ATATAGTATAGATAG
1 ATATAGTATAGATAG
1252 ATATAGTATAGATA
1 ATATAGTATAGATA
1266 AACTTTCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.17, T:0.34
Consensus pattern (15 bp):
ATATAGTATAGATAG
Found at i:1339 original size:14 final size:14
Alignment explanation
Indices: 1320--1372 Score: 81
Period size: 14 Copynumber: 3.8 Consensus size: 14
1310 TTTTAATACA
*
1320 TATTTTCAAATTTT
1 TATTTTTAAATTTT
1334 TATTTTTAAATTTT
1 TATTTTTAAATTTT
1348 TATTTTTAAATTTT
1 TATTTTTAAATTTT
1362 T-TTTTATAAAT
1 TATTTT-TAAAT
1373 AATGGTAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
13 4 0.11
14 33 0.89
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTTTAAATTTT
Found at i:7621 original size:3 final size:3
Alignment explanation
Indices: 7613--7652 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
7603 GAGATGAATA
* * *
7613 GTG GTG GTG GTT GTG GTG GTG GTG GTG GAG GGG GTG GTG G
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG G
7653 CGGAGGGATG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.03, C:0.00, G:0.68, T:0.30
Consensus pattern (3 bp):
GTG
Found at i:7657 original size:15 final size:15
Alignment explanation
Indices: 7630--7659 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7620 TGGTTGTGGT
*
7630 GGTGGTGGTGGAGGG
1 GGTGGTGGCGGAGGG
7645 GGTGGTGGCGGAGGG
1 GGTGGTGGCGGAGGG
7660 ATGGCGGCAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.03, G:0.73, T:0.17
Consensus pattern (15 bp):
GGTGGTGGCGGAGGG
Found at i:12588 original size:25 final size:25
Alignment explanation
Indices: 12554--12631 Score: 156
Period size: 25 Copynumber: 3.1 Consensus size: 25
12544 TGGGTTTTAT
12554 TATTTACATCTTAAAATTATATATA
1 TATTTACATCTTAAAATTATATATA
12579 TATTTACATCTTAAAATTATATATA
1 TATTTACATCTTAAAATTATATATA
12604 TATTTACATCTTAAAATTATATATA
1 TATTTACATCTTAAAATTATATATA
12629 TAT
1 TAT
12632 AAAAAAAACC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (25 bp):
TATTTACATCTTAAAATTATATATA
Found at i:23681 original size:40 final size:41
Alignment explanation
Indices: 23637--23722 Score: 120
Period size: 43 Copynumber: 2.1 Consensus size: 41
23627 GTATTACCTA
* *
23637 AATTCTA-CTCCATCTCTAGGTAATTCATCAAACTAAAACT
1 AATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACT
*
23677 AATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAGCT
1 AATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAACT
23720 AAT
1 AAT
23723 ATTAATTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
40 7 0.17
43 33 0.82
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (41 bp):
AATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAACT
Found at i:26048 original size:50 final size:47
Alignment explanation
Indices: 25967--26064 Score: 142
Period size: 50 Copynumber: 2.0 Consensus size: 47
25957 TATATATCTC
* *
25967 TTTTTTTTGTAATTTCTAAAAAAAATAATTTAATTTTGAATTTTGAA
1 TTTTTTTTGTAATTTCTAAAAAAAATAATTTAATTTTAAAATTTGAA
*
26014 TTTTTTTTGTAATTTCTAAAAAAAAAATTAATTTATTTTTAAAATTTGAA
1 TTTTTTTTGTAATTTCT--AAAAAAAA-TAATTTAATTTTAAAATTTGAA
26064 T
1 T
26065 AAATAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
47 17 0.38
49 8 0.18
50 20 0.44
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (47 bp):
TTTTTTTTGTAATTTCTAAAAAAAATAATTTAATTTTAAAATTTGAA
Found at i:26388 original size:21 final size:21
Alignment explanation
Indices: 26362--26528 Score: 198
Period size: 21 Copynumber: 8.1 Consensus size: 21
26352 TATATGAAAC
26362 TTTGGGGTTTGACTATCAAAA
1 TTTGGGGTTTGACTATCAAAA
* * *
26383 TTTGGGGATTGACCATCAAAT
1 TTTGGGGTTTGACTATCAAAA
* *
26404 TTTGGGGTTTGACAATCAAAC
1 TTTGGGGTTTGACTATCAAAA
*
26425 TTTGGGGGTTGACTATCAAAA
1 TTTGGGGTTTGACTATCAAAA
* * *
26446 TTTGGGGGTTGACCATCAAAC
1 TTTGGGGTTTGACTATCAAAA
26467 TTTGGGGTTTGACTATCAAAA
1 TTTGGGGTTTGACTATCAAAA
* * *
26488 TTTGAGATTTGACCATC--AA
1 TTTGGGGTTTGACTATCAAAA
26507 --TGGGGTTTGACTATCAAAA
1 TTTGGGGTTTGACTATCAAAA
26526 TTT
1 TTT
26529 TGGTGATTGA
Statistics
Matches: 122, Mismatches: 20, Indels: 8
0.81 0.13 0.05
Matches are distributed among these distances:
17 12 0.10
19 4 0.03
21 106 0.87
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (21 bp):
TTTGGGGTTTGACTATCAAAA
Found at i:26458 original size:63 final size:63
Alignment explanation
Indices: 26358--26491 Score: 223
Period size: 63 Copynumber: 2.1 Consensus size: 63
26348 TATATATATG
* *
26358 AAACTTTGGGGTTTGACTATCAAAATTTGGGGATTGACCATCAAATTTTGGGGTTTGACAATC
1 AAACTTTGGGGGTTGACTATCAAAATTTGGGGATTGACCATCAAACTTTGGGGTTTGACAATC
* *
26421 AAACTTTGGGGGTTGACTATCAAAATTTGGGGGTTGACCATCAAACTTTGGGGTTTGACTATC
1 AAACTTTGGGGGTTGACTATCAAAATTTGGGGATTGACCATCAAACTTTGGGGTTTGACAATC
*
26484 AAAATTTG
1 AAACTTTG
26492 AGATTTGACC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (63 bp):
AAACTTTGGGGGTTGACTATCAAAATTTGGGGATTGACCATCAAACTTTGGGGTTTGACAATC
Found at i:26839 original size:22 final size:21
Alignment explanation
Indices: 26765--26841 Score: 136
Period size: 21 Copynumber: 3.6 Consensus size: 21
26755 TCACCCAATT
26765 TTTGATGGTCAAACCCCAAAA
1 TTTGATGGTCAAACCCCAAAA
26786 TTTGATGGTCAAACCCCAAAA
1 TTTGATGGTCAAACCCCAAAA
26807 TTTGATGGTCAAACCCCAAAA
1 TTTGATGGTCAAACCCCAAAA
*
26828 GTTTGATAGTCAAA
1 -TTTGATGGTCAAA
26842 GCATGTTAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
21 42 0.78
22 12 0.22
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.26
Consensus pattern (21 bp):
TTTGATGGTCAAACCCCAAAA
Found at i:26927 original size:21 final size:21
Alignment explanation
Indices: 26902--26944 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
26892 TGTGTTTTTA
* * *
26902 CCCAAATTTTGATGGTTAAAC
1 CCCAAAGTTTGATAGTCAAAC
26923 CCCAAAGTTTGATAGTCAAAC
1 CCCAAAGTTTGATAGTCAAAC
26944 C
1 C
26945 ATGTTAAACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (21 bp):
CCCAAAGTTTGATAGTCAAAC
Found at i:26982 original size:101 final size:101
Alignment explanation
Indices: 26800--27045 Score: 361
Period size: 101 Copynumber: 2.4 Consensus size: 101
26790 ATGGTCAAAC
* * *
26800 CCCAAAATTTGATGGTCAAACCCCAAAAGTTTGATAGTCAAAGCATGTTAAATCTTATCAATTGA
1 CCCAAATTTTGATGGTCAAACCCC-AAAGTTTGATAGTCAAACCATGTTAAACCTTATCAATTGA
* * *
26865 AGCAGCCACTATATTTTTGCCCAAAACTGTGTTTTTA
65 AACAGCCACCACATTTTTGCCCAAAACTGTGTTTTTA
*
26902 CCCAAATTTTGATGGTTAAACCCCAAAGTTTGATAGTCAAACCATGTTAAACCTTATCAATTGAA
1 CCCAAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAACCATGTTAAACCTTATCAATTGAA
*
26967 ACA-CACACCACATTTTTGCCCAAAACTGTGTTTTTG
66 ACAGC-CACCACATTTTTGCCCAAAACTGTGTTTTTA
* *
27003 CCCAAATTTTGATGGTCACACCTCAAAGTTTG-TCAGTCAAACC
1 CCCAAATTTTGATGGTCAAACCCCAAAGTTTGAT-AGTCAAACC
27046 CCAAATTTCG
Statistics
Matches: 131, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
100 2 0.02
101 107 0.82
102 22 0.17
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.31
Consensus pattern (101 bp):
CCCAAATTTTGATGGTCAAACCCCAAAGTTTGATAGTCAAACCATGTTAAACCTTATCAATTGAA
ACAGCCACCACATTTTTGCCCAAAACTGTGTTTTTA
Found at i:27098 original size:21 final size:21
Alignment explanation
Indices: 27005--27098 Score: 59
Period size: 21 Copynumber: 4.5 Consensus size: 21
26995 TGTTTTTGCC
* * *
27005 CAAATTTTGATGGTCACACCT
1 CAAAATTTGATGGTCAAATCT
* * *
27026 CAAAGTTTG-TCAGTCAAA-CC
1 CAAAATTTGAT-GGTCAAATCT
* * *
27046 CCAAATTTCGAAGGTCAAATCG
1 CAAAATTT-GATGGTCAAATCT
*
27068 C-AACTTTGATGGTCAAATCT
1 CAAAATTTGATGGTCAAATCT
27088 CAAAATTTGAT
1 CAAAATTTGAT
27099 AGCCAAACCA
Statistics
Matches: 55, Mismatches: 13, Indels: 10
0.71 0.17 0.13
Matches are distributed among these distances:
20 20 0.36
21 33 0.60
22 2 0.04
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (21 bp):
CAAAATTTGATGGTCAAATCT
Found at i:27108 original size:163 final size:163
Alignment explanation
Indices: 26909--27213 Score: 504
Period size: 163 Copynumber: 1.9 Consensus size: 163
26899 TTACCCAAAT
* * *
26909 TTTGATGGTTAAACCCCAAAGTTTGATAGTCAAACCATGTTAAACCTTATCAATTGAAACACACA
1 TTTGATGGTCAAACCCCAAAATTTGATAGCCAAACCATGTTAAACCTTATCAATTGAAACACACA
* * *
26974 CCACATTTTTGCCCAAAACTGTGTTTTTGCCCAAATTTTGATGGTCACACCTCAAAGTTTG-TCA
66 CCACATTTTTGCCCAAAACTGTGTTTTTGCCCAAAATTTGATGGTCAAACCCCAAAGTTTGAT-A
27038 GTCAAACCCCAAATTTCGAAGGTCAAATCGCAAC
130 GTCAAACCCCAAATTTCGAAGGTCAAATCGCAAC
* * * *
27072 TTTGATGGTCAAATCTCAAAATTTGATAGCCAAACCATGTTAAACCTTATCAATTGAAGCACCCA
1 TTTGATGGTCAAACCCCAAAATTTGATAGCCAAACCATGTTAAACCTTATCAATTGAAACACACA
27137 CCACATTTTTGCCCAAAACTGTGTTTTTGCCCAAAATTTGATGGTCAAACCCCAAAGTTTGATAG
66 CCACATTTTTGCCCAAAACTGTGTTTTTGCCCAAAATTTGATGGTCAAACCCCAAAGTTTGATAG
27202 TCAAACCCCAAA
131 TCAAACCCCAAA
27214 ATTTGATAGT
Statistics
Matches: 131, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
163 130 0.99
164 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (163 bp):
TTTGATGGTCAAACCCCAAAATTTGATAGCCAAACCATGTTAAACCTTATCAATTGAAACACACA
CCACATTTTTGCCCAAAACTGTGTTTTTGCCCAAAATTTGATGGTCAAACCCCAAAGTTTGATAG
TCAAACCCCAAATTTCGAAGGTCAAATCGCAAC
Found at i:27192 original size:21 final size:21
Alignment explanation
Indices: 27166--27229 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
27156 TGTGTTTTTG
*
27166 CCCAAAATTTGATGGTCAAAC
1 CCCAAAATTTGATAGTCAAAC
*
27187 CCCAAAGTTTGATAGTCAAAC
1 CCCAAAATTTGATAGTCAAAC
27208 CCCAAAATTTGATAGTCAAAC
1 CCCAAAATTTGATAGTCAAAC
27229 C
1 C
27230 ATGTTAAACC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.39, C:0.25, G:0.12, T:0.23
Consensus pattern (21 bp):
CCCAAAATTTGATAGTCAAAC
Found at i:27596 original size:18 final size:19
Alignment explanation
Indices: 27561--27596 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
27551 TGCTTTTCTT
*
27561 TAATTTCTTTTATTCTTTA
1 TAATTCCTTTTATTCTTTA
27580 TAATTCCTTTT-TTCTTT
1 TAATTCCTTTTATTCTTT
27597 CTTCCCCAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (19 bp):
TAATTCCTTTTATTCTTTA
Found at i:31639 original size:3 final size:3
Alignment explanation
Indices: 31631--31656 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
31621 CTCACAGTTT
31631 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
31657 TTGTTGTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:41482 original size:19 final size:19
Alignment explanation
Indices: 41458--41495 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
41448 TTAAGATTGG
41458 TTTGAGAAAGTCATTATAT
1 TTTGAGAAAGTCATTATAT
41477 TTTGAGAAAGTCATTATAT
1 TTTGAGAAAGTCATTATAT
41496 AATTATTGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (19 bp):
TTTGAGAAAGTCATTATAT
Found at i:48353 original size:2 final size:2
Alignment explanation
Indices: 48346--48370 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
48336 TCATCCATCC
48346 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 A
48371 AAATTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.