Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015915.1 Corchorus olitorius cultivar O-4 contig15948, 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: 20618
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Found at i:1499 original size:18 final size:17
Alignment explanation
Indices: 1476--1510 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1466 AGATAATTTC
1476 TTTTCTTCAAGTGTTTAG
1 TTTTCTTCAAGT-TTTAG
*
1494 TTTTCTTCTAGTTTTAG
1 TTTTCTTCAAGTTTTAG
1511 GCAAGGGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.14, C:0.11, G:0.14, T:0.60
Consensus pattern (17 bp):
TTTTCTTCAAGTTTTAG
Found at i:5538 original size:21 final size:21
Alignment explanation
Indices: 5514--5558 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5504 GGCCACAGCT
5514 CGGCCACCCGAGCCAACTGCC
1 CGGCCACCCGAGCCAACTGCC
* * **
5535 CGGCCATCCGCGCCGCCTGCC
1 CGGCCACCCGAGCCAACTGCC
5556 CGG
1 CGG
5559 TTGAGCCTGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.11, C:0.53, G:0.29, T:0.07
Consensus pattern (21 bp):
CGGCCACCCGAGCCAACTGCC
Found at i:5823 original size:21 final size:21
Alignment explanation
Indices: 5799--5848 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
5789 CGCCCATTCA
**
5799 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCCAAGC
*
5820 CCGTGCCACCACCGGCCATGC
1 CCGTGCCACCACCGGCCAAGC
5841 CCGTGCCA
1 CCGTGCCA
5849 TCGCCATTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.16, C:0.48, G:0.24, T:0.12
Consensus pattern (21 bp):
CCGTGCCACCACCGGCCAAGC
Found at i:10354 original size:32 final size:32
Alignment explanation
Indices: 10313--10376 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
10303 GATCTTTTCC
*
10313 TGTATTTTGGTCTCTGTTATTGTAAAAAGAAA
1 TGTATTTTGGTCTCCGTTATTGTAAAAAGAAA
*
10345 TGTATTTTGGTCTCCGTTATTGTAAATAGAAA
1 TGTATTTTGGTCTCCGTTATTGTAAAAAGAAA
10377 AATGGAAACC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.44
Consensus pattern (32 bp):
TGTATTTTGGTCTCCGTTATTGTAAAAAGAAA
Found at i:15349 original size:18 final size:18
Alignment explanation
Indices: 15326--15368 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
15316 CTTGTGATGC
*
15326 AGATGAGGACGATGAGGA
1 AGATGAGGACAATGAGGA
**
15344 AGATGATTACAATGAGGA
1 AGATGAGGACAATGAGGA
*
15362 TGATGAG
1 AGATGAG
15369 CAGATTTATG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.37, T:0.19
Consensus pattern (18 bp):
AGATGAGGACAATGAGGA
Found at i:19405 original size:119 final size:120
Alignment explanation
Indices: 19194--19679 Score: 519
Period size: 119 Copynumber: 4.1 Consensus size: 120
19184 ATAATGGGTC
* * * *
19194 GTCACCAAATATGAGGAAAATGCTT-AGTTATATGTGACGAAAATGCGAATGTCATATGTATAGG
1 GTCACAAAATATGAGGAAAAT-CTTCA-TTATATGTGACGAAAATGTGAACGTCACATGTATAGG
* * *
19258 TGACGCAAATGTT-GTCATAAAATATTAAATTATAACGTCACTAA-AATTTTTTATT
64 TGACGTAAATGTTCGTCATAAAATATTAAATTATAACGTCACTAACAATTGTTGATT
* *
19313 GTCACAAAATATGAGGAAAATGCGTT-GTTATATGTGACGAAAATGTGAACGTCACATGTATCGG
1 GTCACAAAATATGAGGAAAAT-C-TTCATTATATGTGACGAAAATGTGAACGTCACATGTATAGG
* * *
19377 TGACGTAAAT-TTCGTCATAAAATATTAAAATAAAATGTCACTAACAATTGTTGATT
64 TGACGTAAATGTTCGTCATAAAATATTAAATTATAACGTCACTAACAATTGTTGATT
* * *
19433 GTCACAAAAAAT-AGGAAAATATTCCATTATTTGTGACGAAAAT-TGGAACGTCACATGTATAGG
1 GTCACAAAATATGAGGAAAATCTT-CATTATATGTGACGAAAATGT-GAACGTCACATGTATAGG
* * * *
19496 TGAC--ACAATGTACGTCATAAAATACTACAA-TATAACGTCACTCATAATTGTTGATT
64 TGACGTA-AATGTTCGTCATAAAATATTA-AATTATAACGTCACTAACAATTGTTGATT
* * * ** *
19552 GTCACAAAATATGAGGAAATTTTTCATTAT-TCGTGACGAAAGTCAGAACGTCACAGGTATAGGT
1 GTCACAAAATATGAGGAAAATCTTCATTATAT-GTGACGAAAATGTGAACGTCACATGTATAGGT
* * * ** * *
19616 GACGTAAGT-TTCATTATGCAATATGAGATTATAACGTCACTAACAATTGTTGATT
65 GACGTAAATGTTCGTCATAAAATATTAAATTATAACGTCACTAACAATTGTTGATT
19671 GTCACAAAA
1 GTCACAAAA
19680 AATAGGTAAA
Statistics
Matches: 312, Mismatches: 40, Indels: 30
0.82 0.10 0.08
Matches are distributed among these distances:
117 3 0.01
118 8 0.03
119 265 0.85
120 35 0.11
121 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (120 bp):
GTCACAAAATATGAGGAAAATCTTCATTATATGTGACGAAAATGTGAACGTCACATGTATAGGTG
ACGTAAATGTTCGTCATAAAATATTAAATTATAACGTCACTAACAATTGTTGATT
Found at i:19532 original size:238 final size:238
Alignment explanation
Indices: 19221--19690 Score: 592
Period size: 238 Copynumber: 2.0 Consensus size: 238
19211 AAATGCTTAG
* * * * *
19221 TTATATGTGACGAAAATGCGAATGTCATATGTATAGGTGACGCAAATGTTGTCATAAAATATTAA
1 TTATATGTGACGAAAATGCGAACGTCACATGTATAGGTGACACAAATGTCGTCATAAAATACTAA
* * *
19286 ATTATAACGTCACT-AAAATTTTTTATTGTCACAAAATATGAGGAAAATGCGTT-GTTATAT-GT
66 ATTATAACGTCACTCAAAATTGTTGATTGTCACAAAATATGAGG-AAAT-CGTTCATTAT-TCGT
** * * * * *
19348 GACGAAAATGTGAACGTCACATGTATCGGTGACGTAAATTTCGTCATAAAATATTAAAATAAAAT
128 GACGAAAATCAGAACGTCACAGGTATAGGTGACGTAAATTTCATCATAAAATATGAAAATAAAAC
19413 GTCACTAACAATTGTTGATTGTCACAAAAAATAGGAAAATATTCCA
193 GTCACTAACAATTGTTGATTGTCACAAAAAATAGGAAAATATTCCA
*
19459 TTATTTGTGACGAAAATTG-GAACGTCACATGTATAGGTGACAC-AATGTACGTCATAAAATACT
1 TTATATGTGACGAAAA-TGCGAACGTCACATGTATAGGTGACACAAATGT-CGTCATAAAATACT
* **
19522 ACAA-TATAACGTCACTCATAATTGTTGATTGTCACAAAATATGAGGAAATTTTTCATTATTCGT
64 A-AATTATAACGTCACTCAAAATTGTTGATTGTCACAAAATATGAGGAAATCGTTCATTATTCGT
* * * ** * * *
19586 GACGAAAGTCAGAACGTCACAGGTATAGGTGACGTAAGTTTCATTATGCAATATGAGATTATAAC
128 GACGAAAATCAGAACGTCACAGGTATAGGTGACGTAAATTTCATCATAAAATATGAAAATAAAAC
*
19651 GTCACTAACAATTGTTGATTGTCACAAAAAATAGGTAAAT
193 GTCACTAACAATTGTTGATTGTCACAAAAAATAGGAAAAT
19691 GTTCAGTTAT
Statistics
Matches: 198, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
237 8 0.04
238 160 0.81
239 30 0.15
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (238 bp):
TTATATGTGACGAAAATGCGAACGTCACATGTATAGGTGACACAAATGTCGTCATAAAATACTAA
ATTATAACGTCACTCAAAATTGTTGATTGTCACAAAATATGAGGAAATCGTTCATTATTCGTGAC
GAAAATCAGAACGTCACAGGTATAGGTGACGTAAATTTCATCATAAAATATGAAAATAAAACGTC
ACTAACAATTGTTGATTGTCACAAAAAATAGGAAAATATTCCA
Found at i:19768 original size:238 final size:237
Alignment explanation
Indices: 19253--19768 Score: 526
Period size: 238 Copynumber: 2.2 Consensus size: 237
19243 TGTCATATGT
* * * * *
19253 ATAGGTGACGCAAATG-TTGTCATAAAATATTAAATTATAACGTCACTAAAATTTTTTATTGTCA
1 ATAGGTGACAC-AATGTTTGTCATAAAA-ATAAAAATATAACGTCACTAAAATTGTTGATTGTCA
* ** * *
19317 CAAAATATGAGGAAAATGCGTTGTTATATGTGACGAAAATGTGAACGTCACATGTATCGGTGACG
64 CAAAATATGAGGAAAATGCGTTATTATATGTGACGAAAATCAGAACGTCACAGGTATAGGTGACG
* * *
19382 TAAATTTCGTCATAAAATATTAAAATAAAATGTCACTAACAATTGTTGATTGTCACAAAAAATAG
129 TAAATTTCATCATAAAATATGAAAATAAAACGTCACTAACAATTGTTGATTGTCACAAAAAATAG
** ***
19447 GAAAATATTCCATTATTTGTGACGAAAATTGGAACGTCACATGT
194 GAAAATATTCCATTATTCATGACGAAAATTGGAACGTCACACAA
** * *
19491 ATAGGTGACACAATGTACGTCAT-AAAATACTACAATATAACGTCACTCATAATTGTTGATTGTC
1 ATAGGTGACACAATGTTTGTCATAAAAATA--AAAATATAACGTCACT-AAAATTGTTGATTGTC
** *
19555 ACAAAATATGAGG-AAAT-TTTTCATTAT-TCGTGACGAAAGTCAGAACGTCACAGGTATAGGTG
63 ACAAAATATGAGGAAAATGCGTT-ATTATAT-GTGACGAAAATCAGAACGTCACAGGTATAGGTG
* * ** * * *
19617 ACGTAAGTTTCATTATGCAATATGAGATTATAACGTCACTAACAATTGTTGATTGTCACAAAAAA
126 ACGTAAATTTCATCATAAAATATGAAAATAAAACGTCACTAACAATTGTTGATTGTCACAAAAAA
* * **
19682 TAGGTAAATGTT-CAGTTATTCATGAC-ATGA-TGAGTAACGTCACACAA
191 TAGGAAAATATTCCA-TTATTCATGACGAAAATTG-G-AACGTCACACAA
** *
19729 ATAGGTGACATTATTTTTGTCATGAAAAATAAAAATATAA
1 ATAGGTGACACAATGTTTGTCAT-AAAAATAAAAATATAA
19769 TATCACAAAA
Statistics
Matches: 225, Mismatches: 42, Indels: 22
0.78 0.15 0.08
Matches are distributed among these distances:
236 4 0.02
237 15 0.07
238 174 0.77
239 26 0.12
240 6 0.03
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (237 bp):
ATAGGTGACACAATGTTTGTCATAAAAATAAAAATATAACGTCACTAAAATTGTTGATTGTCACA
AAATATGAGGAAAATGCGTTATTATATGTGACGAAAATCAGAACGTCACAGGTATAGGTGACGTA
AATTTCATCATAAAATATGAAAATAAAACGTCACTAACAATTGTTGATTGTCACAAAAAATAGGA
AAATATTCCATTATTCATGACGAAAATTGGAACGTCACACAA
Done.