Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011958.1 Corchorus olitorius cultivar O-4 contig11991, 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: 49373
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:4232 original size:28 final size:27
Alignment explanation
Indices: 4145--4246 Score: 114
Period size: 27 Copynumber: 3.7 Consensus size: 27
4135 GGGTCAACTA
* * *
4145 AGGGGTATTTTAGTCATTTGCATGTTT
1 AGGGGCATTTTAGTCATTTGCATATTC
* * *
4172 AGGGGTATTTTAGTCATTTGCACATCC
1 AGGGGCATTTTAGTCATTTGCATATTC
*
4199 AGGGGCATTTTGGTCATTTTGCATATTC
1 AGGGGCATTTTAGTCA-TTTGCATATTC
* *
4227 AAGGGCATTTTGGTCATTTG
1 AGGGGCATTTTAGTCATTTG
4247 TACTTCAGGG
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
27 41 0.63
28 24 0.37
ACGTcount: A:0.20, C:0.13, G:0.25, T:0.42
Consensus pattern (27 bp):
AGGGGCATTTTAGTCATTTGCATATTC
Found at i:4411 original size:21 final size:21
Alignment explanation
Indices: 4372--4415 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4362 TGTTGTGTTC
**
4372 TTTTGCATATTTGTATCACAT
1 TTTTGCATATTAATATCACAT
*
4393 TTTTGCATATTAATCTCACAT
1 TTTTGCATATTAATATCACAT
4414 TT
1 TT
4416 GCATCTACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.16, G:0.07, T:0.52
Consensus pattern (21 bp):
TTTTGCATATTAATATCACAT
Found at i:9399 original size:15 final size:14
Alignment explanation
Indices: 9379--9411 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
9369 AAATGGTTGC
9379 TTTGTTTTGTTTCGG
1 TTTGTTTTGTTTC-G
9394 TTTGTTTTGTTTCG
1 TTTGTTTTGTTTCG
9408 TTTG
1 TTTG
9412 CTCTGACGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.00, C:0.06, G:0.24, T:0.70
Consensus pattern (14 bp):
TTTGTTTTGTTTCG
Found at i:20864 original size:17 final size:17
Alignment explanation
Indices: 20842--20876 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
20832 AAAGGCAATC
20842 TTTTGTGTGTTTTGTTT
1 TTTTGTGTGTTTTGTTT
*
20859 TTTTGTTTGTTTTGTTT
1 TTTTGTGTGTTTTGTTT
20876 T
1 T
20877 GTTTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (17 bp):
TTTTGTGTGTTTTGTTT
Found at i:20888 original size:17 final size:18
Alignment explanation
Indices: 20843--20880 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
20833 AAGGCAATCT
*
20843 TTTGTGTGTTTTGTTTT-
1 TTTGTTTGTTTTGTTTTG
20860 TTTGTTTGTTTTGTTTTG
1 TTTGTTTGTTTTGTTTTG
20878 TTT
1 TTT
20881 TTTTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 16 0.84
18 3 0.16
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (18 bp):
TTTGTTTGTTTTGTTTTG
Found at i:21197 original size:24 final size:24
Alignment explanation
Indices: 21170--21217 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
21160 TTGGAAATTG
21170 CATCCTATTTAAAAGAAAAAGAGA
1 CATCCTATTTAAAAGAAAAAGAGA
21194 CATCCTATTTAAAAGAAAAAGAGA
1 CATCCTATTTAAAAGAAAAAGAGA
21218 TATAATTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.21
Consensus pattern (24 bp):
CATCCTATTTAAAAGAAAAAGAGA
Found at i:21228 original size:21 final size:23
Alignment explanation
Indices: 21178--21240 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
21168 TGCATCCTAT
* *
21178 TTAAAAGAAAAAGAGACATCCTAT
1 TTAAAAGAAAAAGAGA-ATCATAA
21202 TTAAAAGAAAAAGAG-AT-ATAA
1 TTAAAAGAAAAAGAGAATCATAA
21223 TTAAAAGAAAGAAG-GAAT
1 TTAAAAGAAA-AAGAGAAT
21241 GGCTAACACT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 13 0.37
22 7 0.20
24 15 0.43
ACGTcount: A:0.60, C:0.05, G:0.16, T:0.19
Consensus pattern (23 bp):
TTAAAAGAAAAAGAGAATCATAA
Found at i:21734 original size:40 final size:40
Alignment explanation
Indices: 21650--21886 Score: 282
Period size: 40 Copynumber: 6.0 Consensus size: 40
21640 TGGTAAAAAG
* * * * *
21650 ATGATCCTAAATAGGATTCTAAAATTGA-CTGATAAAGAA
1 ATGATCCTGAATAGGATTCTGAAATTAATTTGATAAAGCA
* *
21689 ATGATCCTGAATAGGATTCTGAAATTCACTTGATAAAGCA
1 ATGATCCTGAATAGGATTCTGAAATTAATTTGATAAAGCA
* * *
21729 ATGATCCTGAGTAGGATTCTGAAATTTATTTGGTAAAGCA
1 ATGATCCTGAATAGGATTCTGAAATTAATTTGATAAAGCA
* * *
21769 ATGATACT-AAGAAGGATTTTGAAATTAATTTGATAAAGCA
1 ATGATCCTGAA-TAGGATTCTGAAATTAATTTGATAAAGCA
** *
21809 ATGATCCTGAGCAGGATTCTGGAATTAATTTGATAAAGCA
1 ATGATCCTGAATAGGATTCTGAAATTAATTTGATAAAGCA
*
21849 ATGATCCT-AAGTAGGATTTTGAAATTAATTTGATAAAG
1 ATGATCCTGAA-TAGGATTCTGAAATTAATTTGATAAAG
21887 AGAAATGATT
Statistics
Matches: 170, Mismatches: 24, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
39 27 0.16
40 142 0.84
41 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (40 bp):
ATGATCCTGAATAGGATTCTGAAATTAATTTGATAAAGCA
Found at i:22196 original size:145 final size:144
Alignment explanation
Indices: 21995--22404 Score: 587
Period size: 145 Copynumber: 2.9 Consensus size: 144
21985 GGAATGCCCA
* * * * *
21995 GAGGATTTATCAGAATTAATACCCAGAGGTTTCTGAAATTGTACCCGAAGGTCTTACAAATGCAC
1 GAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGT-GCCGGAGGTCTTACAAATGCAA
* * * **
22060 ACTCGACCATGAGCAAGGTTTTGATTTTGAAATTTAAACGCAGTTTTGATTAAAAAATTGATGAA
65 ACTCAACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACGCAACTTTGATTAAAAAATTGATGAA
*
22125 ATGAAATGATACCCG
130 ATGAAATGATACCAG
*
22140 GAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTGCCTGGAGGACTTACAAATGCAA
1 GAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTGCC-GGAGGTCTTACAAATGCAA
* *
22205 ACTCAACCTTGAGCAAGGTTTTGATTTTGAAACTTAAATGCAACTTTGATTAAAAACTTGATGAA
65 ACTCAACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACGCAACTTTGATTAAAAAATTGATGAA
* *
22270 ATTATATGATACCAG
130 ATGAAATGATACCAG
22285 GAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTGTCCGGAGGTCTTACAAATGCAA
1 GAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTG-CCGGAGGTCTTACAAATGCAA
* *
22350 ACTCAATCTTGAGCAAGG-TTT-A--TTGAAACTTAAACACAACTTTG-TTGAAAAAATT
65 ACTCAACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACGCAACTTTGATT-AAAAAATT
22405 ACCAAAATGG
Statistics
Matches: 241, Mismatches: 21, Indels: 10
0.89 0.08 0.04
Matches are distributed among these distances:
140 2 0.01
141 27 0.11
143 1 0.00
144 5 0.02
145 204 0.85
146 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (144 bp):
GAGGATTTATCAGAATTAATACCCGGAGGTTTCTGAAATGGTGCCGGAGGTCTTACAAATGCAAA
CTCAACCTTGAGCAAGGTTTTGATTTTGAAACTTAAACGCAACTTTGATTAAAAAATTGATGAAA
TGAAATGATACCAG
Found at i:43686 original size:15 final size:16
Alignment explanation
Indices: 43666--43699 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
43656 TGAAAAATAA
43666 CAATTAAA-AAGAAAG
1 CAATTAAACAAGAAAG
*
43681 CAATTAAACTAGAAAG
1 CAATTAAACAAGAAAG
43697 CAA
1 CAA
43700 AGCAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.15
Consensus pattern (16 bp):
CAATTAAACAAGAAAG
Found at i:47690 original size:53 final size:53
Alignment explanation
Indices: 47610--47719 Score: 220
Period size: 53 Copynumber: 2.1 Consensus size: 53
47600 AGAGATTTCC
47610 TGAAAAAAGGAAATCCAAGCTCTTACCCCGTGGAGATGATCCATTCCAAGTGT
1 TGAAAAAAGGAAATCCAAGCTCTTACCCCGTGGAGATGATCCATTCCAAGTGT
47663 TGAAAAAAGGAAATCCAAGCTCTTACCCCGTGGAGATGATCCATTCCAAGTGT
1 TGAAAAAAGGAAATCCAAGCTCTTACCCCGTGGAGATGATCCATTCCAAGTGT
47716 TGAA
1 TGAA
47720 GAGGATCAAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.23
Consensus pattern (53 bp):
TGAAAAAAGGAAATCCAAGCTCTTACCCCGTGGAGATGATCCATTCCAAGTGT
Done.