Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019423.1 Corchorus olitorius cultivar O-4 contig19456, 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: 68985
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2215 original size:55 final size:55
Alignment explanation
Indices: 2131--2239 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 55
2121 GGCAAAAAAA
2131 TTATTAGTATAAATAAATATTGATTGATACTCATGACATAGAAGATTTCAACAAT
1 TTATTAGTATAAATAAATATTGATTGATACTCATGACATAGAAGATTTCAACAAT
* *
2186 TTATTAGTATAAATTAATGTTGATTGATACTCATGACATAGAAGATTTCAACAA
1 TTATTAGTATAAATAAATATTGATTGATACTCATGACATAGAAGATTTCAACAA
2240 CTTGGTAAGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (55 bp):
TTATTAGTATAAATAAATATTGATTGATACTCATGACATAGAAGATTTCAACAAT
Found at i:3181 original size:22 final size:20
Alignment explanation
Indices: 3156--3197 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
3146 AAAAATTAAA
*
3156 TGAAAAATATAAAAAAGAAAAC
1 TGAAAAA-A-AAAAAAAAAAAC
3178 TGAAAAAAAAAAAAAAAAAC
1 TGAAAAAAAAAAAAAAAAAC
3198 AAAAGCGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 1 0.05
22 7 0.37
ACGTcount: A:0.79, C:0.05, G:0.07, T:0.10
Consensus pattern (20 bp):
TGAAAAAAAAAAAAAAAAAC
Found at i:3340 original size:20 final size:19
Alignment explanation
Indices: 3296--3341 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
3286 CATCCAAAGA
3296 TTCTCTCTTTAACTCTCTC
1 TTCTCTCTTTAACTCTCTC
* *
3315 TCTCTCTCTTTATCTTTCCTC
1 T-TCTCTCTTTAACTCT-CTC
3336 TTCTCT
1 TTCTCT
3342 TCTCTTCCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 18 0.78
21 4 0.17
ACGTcount: A:0.07, C:0.37, G:0.00, T:0.57
Consensus pattern (19 bp):
TTCTCTCTTTAACTCTCTC
Found at i:7114 original size:12 final size:12
Alignment explanation
Indices: 7097--7173 Score: 52
Period size: 12 Copynumber: 6.3 Consensus size: 12
7087 ACATGAATAA
7097 ACATACATGCAT
1 ACATACATGCAT
7109 ACATACA--CAT
1 ACATACATGCAT
* * *
7119 GCGCATACATACAC
1 --ACATACATGCAT
7133 ACATACATGCAT
1 ACATACATGCAT
* *
7145 ACAT-TATGCACAC
1 ACATACATG--CAT
7158 ACATACATGCAT
1 ACATACATGCAT
7170 ACAT
1 ACAT
7174 TATGCATCCA
Statistics
Matches: 49, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
10 3 0.06
11 3 0.06
12 32 0.65
13 6 0.12
14 5 0.10
ACGTcount: A:0.42, C:0.29, G:0.08, T:0.22
Consensus pattern (12 bp):
ACATACATGCAT
Found at i:7160 original size:25 final size:25
Alignment explanation
Indices: 7129--7179 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
7119 GCGCATACAT
7129 ACACACATACATGCATACATTATGC
1 ACACACATACATGCATACATTATGC
7154 ACACACATACATGCATACATTATGC
1 ACACACATACATGCATACATTATGC
7179 A
1 A
7180 TCCATTTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.27, G:0.08, T:0.24
Consensus pattern (25 bp):
ACACACATACATGCATACATTATGC
Found at i:15029 original size:12 final size:12
Alignment explanation
Indices: 15014--15039 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15004 ATTTAATTTA
15014 TTATTATCATAG
1 TTATTATCATAG
15026 TTATTATCATAG
1 TTATTATCATAG
15038 TT
1 TT
15040 TCATTGTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (12 bp):
TTATTATCATAG
Found at i:15428 original size:138 final size:138
Alignment explanation
Indices: 15215--15474 Score: 493
Period size: 138 Copynumber: 1.9 Consensus size: 138
15205 TTAGTTCTAG
*
15215 TCTATCCAGACCATGAGGTCTTGGGTTCAACTCTCACATTTATGGTATAGTTTCTAGTTTGGGTT
1 TCTATCCAGACCATGAGGTCTTGGGTTCAACTCTCACATTTACGGTATAGTTTCTAGTTTGGGTT
* *
15280 GAATTTTCATTTAGATGTCTGGGCATAGAGATTTATTTGAATTGTAATGAGATTTCACTGGTTTG
66 GAATTCTCATTTAGATGTCTGGACATAGAGATTTATTTGAATTGTAATGAGATTTCACTGGTTTG
15345 CTAGCTAA
131 CTAGCTAA
15353 TCTATCCAGACCATGAGGTCTTGGGTTCAACTCTCACATTTACGGTATAGTTTCTAGTTTGGGTT
1 TCTATCCAGACCATGAGGTCTTGGGTTCAACTCTCACATTTACGGTATAGTTTCTAGTTTGGGTT
15418 GAATTCTCATTTAGATGTCTGGACATAGAGATTTATTTGAATTGTAATGAGATTTCA
66 GAATTCTCATTTAGATGTCTGGACATAGAGATTTATTTGAATTGTAATGAGATTTCA
15475 TTGTAATGAG
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
138 119 1.00
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.40
Consensus pattern (138 bp):
TCTATCCAGACCATGAGGTCTTGGGTTCAACTCTCACATTTACGGTATAGTTTCTAGTTTGGGTT
GAATTCTCATTTAGATGTCTGGACATAGAGATTTATTTGAATTGTAATGAGATTTCACTGGTTTG
CTAGCTAA
Found at i:15479 original size:16 final size:16
Alignment explanation
Indices: 15458--15506 Score: 98
Period size: 16 Copynumber: 3.1 Consensus size: 16
15448 ATTTATTTGA
15458 ATTGTAATGAGATTTC
1 ATTGTAATGAGATTTC
15474 ATTGTAATGAGATTTC
1 ATTGTAATGAGATTTC
15490 ATTGTAATGAGATTTC
1 ATTGTAATGAGATTTC
15506 A
1 A
15507 CTGGTTTGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.43
Consensus pattern (16 bp):
ATTGTAATGAGATTTC
Found at i:16131 original size:12 final size:14
Alignment explanation
Indices: 16101--16130 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
16091 TTTTATTAGA
16101 TTTTCATTTTTGTT
1 TTTTCATTTTTGTT
16115 TTTTCATTTTT-TT
1 TTTTCATTTTTGTT
16128 TTT
1 TTT
16131 CTTTAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.07, C:0.07, G:0.03, T:0.83
Consensus pattern (14 bp):
TTTTCATTTTTGTT
Found at i:16441 original size:15 final size:16
Alignment explanation
Indices: 16415--16444 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16405 ATGGTGAAGG
16415 AACAAGCAGCAACAAT
1 AACAAGCAGCAACAAT
16431 AACAA-CAGCAACAA
1 AACAAGCAGCAACAA
16445 CACTGTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.60, C:0.27, G:0.10, T:0.03
Consensus pattern (16 bp):
AACAAGCAGCAACAAT
Found at i:18417 original size:18 final size:17
Alignment explanation
Indices: 18390--18423 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
18380 TCTCTTGTAA
*
18390 AGCTTGTAGTTATGTTTT
1 AGCTTATAGTTA-GTTTT
18408 AGCTTATAGTTAGTTT
1 AGCTTATAGTTAGTTT
18424 ACTTATGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.21, C:0.06, G:0.21, T:0.53
Consensus pattern (17 bp):
AGCTTATAGTTAGTTTT
Found at i:46033 original size:18 final size:18
Alignment explanation
Indices: 46006--46040 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
45996 AGGTGAGGCC
*
46006 TTGGGCCTTTAATTGGTT
1 TTGGGCCTTTAAGTGGTT
*
46024 TTGGGGCTTTAAGTGGT
1 TTGGGCCTTTAAGTGGT
46041 AGGTAGGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.11, C:0.09, G:0.34, T:0.46
Consensus pattern (18 bp):
TTGGGCCTTTAAGTGGTT
Found at i:66758 original size:26 final size:26
Alignment explanation
Indices: 66729--66780 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
66719 TTAATTTATC
*
66729 CTTAGTTCTGTTTTAAGGATTTTAAT
1 CTTAGTTATGTTTTAAGGATTTTAAT
66755 CTTAGTTATGTTTTAAGGATTTTAAT
1 CTTAGTTATGTTTTAAGGATTTTAAT
66781 GTTTGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.25, C:0.06, G:0.15, T:0.54
Consensus pattern (26 bp):
CTTAGTTATGTTTTAAGGATTTTAAT
Found at i:67929 original size:39 final size:39
Alignment explanation
Indices: 67877--67963 Score: 111
Period size: 39 Copynumber: 2.2 Consensus size: 39
67867 AATTGACCCG
* * ** *
67877 AAATATATTTCCTCAATTTCTAGTGAAAATACTCATAAT
1 AAATATATATCCTCAAATTCTAGCAAAAATACTCATAAA
* *
67916 ATATATATATCCTCAAATTCTAGCAAAAATGCTCATAAA
1 AAATATATATCCTCAAATTCTAGCAAAAATACTCATAAA
67955 AAATATATA
1 AAATATATA
67964 ATTCAACGCC
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (39 bp):
AAATATATATCCTCAAATTCTAGCAAAAATACTCATAAA
Found at i:68800 original size:343 final size:333
Alignment explanation
Indices: 67957--68839 Score: 1018
Period size: 343 Copynumber: 2.6 Consensus size: 333
67947 CTCATAAAAA
*
67957 ATATATAATTCAACGCCAAAAAAATT-GA-AAGCCTTTTTCACGCTTCTAATATCGTTTTTCCTA
1 ATATATAATT-AACGCCAAAAAGATTGGAGAA--C-TTTTCACGCTTCTAATATCGTTTTT-CTA
* * * * ** *
68020 TCTTATTTCAAAATTAATTTTCAGATTAAATCGAAACAAGATTTAGAAACTCATAAAAACAAATC
61 T-TT-TTTCTAAATTAATTTT-A-ATTAAATAGAAACAATATTCAGATGCTCGTAAAAACAAATC
* *
68085 CTTAAATACAATGTGGCTGAGATTT-AGTTAGATGAATATATATA-TT-AAGGTGTCTTGCAGCC
122 CTTAAATACAATGTGGCTGAGATTTGA-TTAGATGAATATAGATATTTCAAGGAGTCTTGCAGCC
* * * * **
68147 AAAAATCATGCAAAACTGACCTAGGGCTCTAGAACGCGTTTTTAGCAAAAAAAAAAATTATGATG
186 AAAAATCATGCAAAACTGACCCAGGGCCCCAGAACGCGTTTTTAGAAAAAAAAAAAAACATGATG
*
68212 GTACACGATTTCGGCTAAAATTTTGCACAAATTGACCCGAAATATTTTTCTCAACTTTTAGCCAC
251 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCTCAACTTTTAGCCAC
68277 AATACTCATCAAAGATAT
316 AATACTCATCAAAGATAT
* **
68295 ATA-AT--TTAACGCCAAAAAGATTGAAG-GGTTTCTCACGCTTCTAATATCGTTTTTCTTATTT
1 ATATATAATTAACGCCAAAAAGATTGGAGAACTTT-TCACGCTTCTAATATCGTTTTTC-TA-TT
* * * *
68356 TTTTCTCAAATTATTTTTTAATTAAATTGAAAC-ATGATTCAAATGCTCGTAAAAATAAATCCTT
63 TTTTCT-AAATTA-ATTTTAATTAAATAGAAACAAT-ATTCAGATGCTCGTAAAAACAAATCCTT
* * * * *
68420 AAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTGTTGCCA-CCGAA
125 AAATACAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTG-CAGCCAAA
*
68484 AATCATGCAAAACTGACCCGGGGCCCCAGAACGCGTTTTTAGTAAAAAAAAAAAAAACATGATGG
189 AATCATGCAAAACTGACCCAGGGCCCCAGAACGCGTTTTTAG--AAAAAAAAAAAAACATGATGG
* *
68549 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTTATCCAC
252 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTT-CTCAACTTTTAGCCAC
* *
68614 AATACTCATAGAATATATATATAT
316 AATACTCAT----CA-A-AGATAT
* * *
68638 ATATATAATTAAACGCCAAAAAGATTGGAGAACTCTTCACGCTTTTAATATCGTTTTTC-ATATT
1 ATATATAATT-AACGCCAAAAAGATTGGAGAACTTTTCACGCTTCTAATATCGTTTTTCTATTTT
* *
68702 TTCTGAATTAATTTCTAATTAAATAGAAACAATATTCAGATGCTCGTAAAAACAAATCCTTATAT
65 TTCTAAATTAATTT-TAATTAAATAGAAACAATATTCAGATGCTCGTAAAAACAAATCCTTAAAT
* * * ** *
68767 TCAATGTGACTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGGGAC-AAAATCA
129 ACAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGCAGCCAAAAATCA
68831 TGCAAAACT
194 TGCAAAACT
68840 AAGTCGAGGT
Statistics
Matches: 462, Mismatches: 54, Indels: 54
0.81 0.09 0.09
Matches are distributed among these distances:
331 1 0.00
332 78 0.17
333 35 0.08
334 70 0.15
335 5 0.01
336 65 0.14
337 25 0.05
338 3 0.01
341 1 0.00
342 20 0.04
343 103 0.22
344 11 0.02
345 1 0.00
346 2 0.00
347 40 0.09
348 2 0.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (333 bp):
ATATATAATTAACGCCAAAAAGATTGGAGAACTTTTCACGCTTCTAATATCGTTTTTCTATTTTT
TCTAAATTAATTTTAATTAAATAGAAACAATATTCAGATGCTCGTAAAAACAAATCCTTAAATAC
AATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGCAGCCAAAAATCATG
CAAAACTGACCCAGGGCCCCAGAACGCGTTTTTAGAAAAAAAAAAAAACATGATGGTACACGATT
TCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCTCAACTTTTAGCCACAATACTCATC
AAAGATAT
Done.