Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024610.1 Corchorus olitorius cultivar O-4 contig24643, 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: 17666
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Found at i:225 original size:21 final size:21
Alignment explanation
Indices: 146--225 Score: 79
Period size: 21 Copynumber: 3.8 Consensus size: 21
136 GTGTTTCTTG
*
146 GACAGGTGGTGGAGGAGAGTA
1 GACAGGTGGTGGAGGTGAGTA
* * * *
167 GACGGGTGGTGGTGGGGAATA
1 GACAGGTGGTGGAGGTGAGTA
* *
188 GACAGGGGGAGGAGGTGAGTA
1 GACAGGTGGTGGAGGTGAGTA
* *
209 GACTGGTGGTGGTGGTG
1 GACAGGTGGTGGAGGTG
226 GTGGTGATTG
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.21, C:0.05, G:0.56, T:0.17
Consensus pattern (21 bp):
GACAGGTGGTGGAGGTGAGTA
Found at i:2135 original size:2 final size:2
Alignment explanation
Indices: 2130--2169 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2120 AAAAAACAAT
2130 TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2170 TAAGCAGGGC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5573 original size:15 final size:14
Alignment explanation
Indices: 5552--5580 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5542 CCCACAACTT
5552 TAAAAAAACTTAAG
1 TAAAAAAACTTAAG
5566 TAAAAAAACTTAAG
1 TAAAAAAACTTAAG
5580 T
1 T
5581 GAGACACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.24
Consensus pattern (14 bp):
TAAAAAAACTTAAG
Found at i:9857 original size:41 final size:40
Alignment explanation
Indices: 9794--9873 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
9784 TATGAAACCC
*
9794 AAACCCTAACAAACAATATAAACCCTAAGTGAGATAAAAG
1 AAACCCTAAAAAACAATATAAACCCTAAGTGAGATAAAAG
*
9834 AAACCCTAAAAAAACACAT-TAAACCCTAGGTGAGATAAAA
1 AAACCCT-AAAAAACA-ATATAAACCCTAAGTGAGATAAAA
9874 AGATAAAACA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 7 0.19
41 27 0.75
42 2 0.06
ACGTcount: A:0.55, C:0.20, G:0.10, T:0.15
Consensus pattern (40 bp):
AAACCCTAAAAAACAATATAAACCCTAAGTGAGATAAAAG
Found at i:10338 original size:20 final size:21
Alignment explanation
Indices: 10315--10354 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10305 AAAGACATGA
10315 CATGAAACT-CAAACCCTAAC
1 CATGAAACTACAAACCCTAAC
*
10335 CATGAAATTACAAACCCTAA
1 CATGAAACTACAAACCCTAA
10355 GTGAGATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.47, C:0.30, G:0.05, T:0.17
Consensus pattern (21 bp):
CATGAAACTACAAACCCTAAC
Found at i:10416 original size:25 final size:25
Alignment explanation
Indices: 10369--10416 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
10359 GATGAAGACT
*
10369 AAACCCTAACCATGTCATGAAAGCC
1 AAACCCTAACCATGTCATCAAAGCC
10394 AAACCCTAA-CATGTCATCCAAAG
1 AAACCCTAACCATGTCAT-CAAAG
10417 TGAAGGGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.42, C:0.31, G:0.10, T:0.17
Consensus pattern (25 bp):
AAACCCTAACCATGTCATCAAAGCC
Found at i:11528 original size:180 final size:177
Alignment explanation
Indices: 11161--11544 Score: 475
Period size: 180 Copynumber: 2.1 Consensus size: 177
11151 CCATAAGTAC
* *
11161 AAATTATGTAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACTAATTCTTTGGAAGCA
1 AAATTATATAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACAAATTCTTTGGAAGCA
*
11226 TTTTTTATACCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATGAAAGTTGTAGATCATGGAAC
66 TTTTTTATACCTTGAACATTAAATTTAGTTTTCGAATCCTTCATGAAAGTTGTAGATCATGGAAC
* * * *
11291 AACCTTTCAAGAGACACTTGAATAATCTCAATCAGACATCTGGAGAA
131 AACCTTTCAAGAGACACTTAAATAACCTCAATCAGACAACCGGAGAA
* * *
11338 AAAGTTATATAATATTAAGTGGACCGTCTATTTCCCGTTAAGCGAAATAACAAATT-TTTCGGAA
1 AAA-TTATATAATATTAAGTAGACCGTCTATTT-CCGTTAACCGAAACAACAAATTCTTT-GGAA
* * *
11402 GCTTTTTTTGATA-CTTGAAACATTAAATTTAGTTTTCGAATCCTTTATGAAAGTTGTAGATTAT
63 GCATTTTTT-ATACCTTG-AACATTAAATTTAGTTTTCGAATCCTTCATGAAAGTTGTAGATCAT
* * * * * * ** *
11466 GGAACAATCTTTTAATAGAGACTTAAATCACCTTAATTGGATAACCGGAGAA
126 GGAACAACCTTTCAAGAGACACTTAAATAACCTCAATCAGACAACCGGAGAA
* * *
11518 GAAATTATATAATGTTAAATAAACCGT
1 -AAATTATATAATATTAAGTAGACCGT
11545 TTAATGAAAC
Statistics
Matches: 175, Mismatches: 26, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
177 3 0.02
178 30 0.17
179 35 0.20
180 104 0.59
181 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (177 bp):
AAATTATATAATATTAAGTAGACCGTCTATTTCCGTTAACCGAAACAACAAATTCTTTGGAAGCA
TTTTTTATACCTTGAACATTAAATTTAGTTTTCGAATCCTTCATGAAAGTTGTAGATCATGGAAC
AACCTTTCAAGAGACACTTAAATAACCTCAATCAGACAACCGGAGAA
Found at i:12312 original size:241 final size:243
Alignment explanation
Indices: 11880--12367 Score: 804
Period size: 241 Copynumber: 2.0 Consensus size: 243
11870 TTGTGAACAT
*
11880 AATTTTATATATAGTATATGGTATGAAATTAATTTTTTTAAAGAACTTAGAATTTTTGTTTTCAA
1 AATTTTATATATAGTATATGGTATGAAATTAATATTTTTAAAGAACTTAGAATTTTTGTTTTCAA
11945 AACATGTTATTCACAATTCTGATTACATGAATATATTACGCCAAAAGACTCTTTAAGAGTTTTTG
66 AACATGTTATTCACAATTCTGATTACATGAATATATTACGCCAAAAGACTCTTTAAGAGTTTTTG
* * * *
12010 CAATAAAAAACTAAATGACCGCGTAAGGGCATATCAGTCAATTTGCTGAAATTGGTAAAGAGGTG
131 CAATAAAAAACTAAATAACCGCGCAAGGGCATACCAGTCAATTTGCTGAAATTGATAAAGAGGTG
*
12075 TATAAACATGAAATTGGTGCGCGGAGCAGTAGATTAAAGATCAGAGCG
196 TATAAACATGAAATTGGTGCGCGGAGCAGCAGATTAAAGATCAGAGCG
* *
12123 AATTTTATATATAGTATATGTTGTGAAATTAA-ATTTTTAAAGAACTTAGAATTTTT-TTTTCAA
1 AATTTTATATATAGTATATGGTATGAAATTAATATTTTTAAAGAACTTAGAATTTTTGTTTTCAA
* *
12186 AACATGTTATTCACAATTCTGATTACATGAATATATTGCGCCAAAA-ATCTCTTTGAGAGTTTTT
66 AACATGTTATTCACAATTCTGATTACATGAATATATTACGCCAAAAGA-CTCTTTAAGAGTTTTT
* * **
12250 GCAAT-AAAAACTATATAACCGCGCAAGGGCGTACCAGTCAATTTTTTAGAAATTGATAAAGAGG
130 GCAATAAAAAACTAAATAACCGCGCAAGGGCATACCAGTCAATTTGCT-GAAATTGATAAAGAGG
12314 TGTATAAACATGAAATTGGTGCGCGGAGCAGCAGATTAAAGATCAGAGCG
194 TGTATAAACATGAAATTGGTGCGCGGAGCAGCAGATTAAAGATCAGAGCG
12364 AATT
1 AATT
12368 GTGGGGACTG
Statistics
Matches: 229, Mismatches: 14, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
240 36 0.16
241 140 0.61
242 23 0.10
243 30 0.13
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (243 bp):
AATTTTATATATAGTATATGGTATGAAATTAATATTTTTAAAGAACTTAGAATTTTTGTTTTCAA
AACATGTTATTCACAATTCTGATTACATGAATATATTACGCCAAAAGACTCTTTAAGAGTTTTTG
CAATAAAAAACTAAATAACCGCGCAAGGGCATACCAGTCAATTTGCTGAAATTGATAAAGAGGTG
TATAAACATGAAATTGGTGCGCGGAGCAGCAGATTAAAGATCAGAGCG
Found at i:16724 original size:1 final size:1
Alignment explanation
Indices: 16676--16705 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
16666 GCGAGTTAGG
16676 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
16706 CAGTGAGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.