Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006118.1 Corchorus capsularis cultivar CVL-1 contig06136, 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: 28617
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:9985 original size:12 final size:13
Alignment explanation
Indices: 9968--10009 Score: 52
Period size: 12 Copynumber: 3.4 Consensus size: 13
9958 TTTATGCACC
9968 CAAAACATTTAT-
1 CAAAACATTTATA
9980 CAAAACATTT-TA
1 CAAAACATTTATA
*
9992 CAAAGCATTTATA
1 CAAAACATTTATA
*
10005 TAAAA
1 CAAAA
10010 ACAGTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
11 1 0.04
12 19 0.76
13 5 0.20
ACGTcount: A:0.52, C:0.14, G:0.02, T:0.31
Consensus pattern (13 bp):
CAAAACATTTATA
Found at i:17088 original size:16 final size:18
Alignment explanation
Indices: 17056--17092 Score: 60
Period size: 16 Copynumber: 2.2 Consensus size: 18
17046 CCTGATATCA
17056 TGAATTCTCTGAAATTTG
1 TGAATTCTCTGAAATTTG
17074 TGAATTCT-T-AAATTTG
1 TGAATTCTCTGAAATTTG
17090 TGA
1 TGA
17093 CTATGTATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
17 1 0.05
18 8 0.42
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (18 bp):
TGAATTCTCTGAAATTTG
Found at i:17167 original size:18 final size:18
Alignment explanation
Indices: 17140--17175 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17130 AAAAATGTTT
*
17140 ATTCTTAATTCTAATTGG
1 ATTCTGAATTCTAATTGG
*
17158 ATTCTGAATTCTGATTGG
1 ATTCTGAATTCTAATTGG
17176 TTTTTGTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.11, G:0.17, T:0.47
Consensus pattern (18 bp):
ATTCTGAATTCTAATTGG
Found at i:20373 original size:437 final size:436
Alignment explanation
Indices: 19489--20373 Score: 1006
Period size: 437 Copynumber: 2.0 Consensus size: 436
19479 GAAAATAGCT
* * *
19489 GTTAATAGAGATCTTGAAACATAAAAATTCCCTTTTGAACCCTCCATGAAACTCGTAGATCAAAT
1 GTTAATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCCTCAACGAAACTCGTAGATCAAAT
* * * * * *
19554 TAACTTTCGGGTTCTTCATGAAAATCATAGACCATACAGTGACCTTTTAATCGACACTTGAATAA
66 TAACTTTCGGGTTATTCATGAAAATCATAAACCATACAATAACCTTTTAACCGACACTTCAATAA
* * * * * * * *
19619 CTTTAATTGGACATGTGGATCGAAAGTTATATGGTATTAAATAGACCAACAATCGAAACAACCAA
131 CTTCAATCGGACATGTGGATCAAAAATTATACGATATTAAATAGACCAACAATCAAAACAACAAA
* * * ** *
19684 ATTCAGGAAGCATTTTTTTGAATTGAAACATAAAAAATTACTTTTGAGTCATTCCTGAAAGTTGT
196 ATTCAGGAACCATTTTTTAGAATTCAAACATAAAAAATTACTTTTGAGTCATTAATGAAAATTGT
*
19749 AAATAATGAAATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAAAACAAAGAAT
261 AAATAATGAAATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAACAAAACAAAGAAT
* * * *
19814 AAAAAAATAAAGCTTAAACGTCAGATTAAGATAGAATTTGTAAAGGACTAAATAGTATAAAGTAG
326 AAAAAAATAAAGCTCAAACGTCAAATTAACATAGAATTTGTAAAGGACTAAATAGCATAAAGTAG
* * * * *
19879 AAAAGTATGAGAGTCATTTCATAAATAATCCAAATAAAAAAATGTTT
391 AAAAGTATGAGAGTCACTACATAAAAAATCCAAAT-AAAAAATATTA
*
19926 GTTAATGGAGATCTTGAAACATAAAAATTCCCTTTT-AACCCTTAACGAAACTCGTAGATCAAAT
1 GTTAATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCCTCAACGAAACTCGTAGATCAAA-
* * * *
19990 TTAGCTTTCGGGTTATTCATGAAAGTCATAAATCATGCAATAACCTTTTAACCGACACTTCAATA
65 TTAACTTTCGGGTTATTCATGAAAATCATAAACCATACAATAACCTTTTAACCGACACTTCAATA
** *
20055 ACTTCAATCGGACATGTGGA-CAAAAAATTATACGATATTAAATTA-ACCGGCAATCAAAACCAC
130 ACTTCAATCGGACATGTGGATC-AAAAATTATACGATATTAAA-TAGACCAACAATCAAAACAAC
* * **
20118 AAAATTTC-TGAACCATTTTTTAGAA-TCAACACAT-TAAAATTGGTTTTTGAGTTC-TTAATGA
193 AAAA-TTCAGGAACCATTTTTTAGAATTCAA-ACATAAAAAATT-ACTTTTGAG-TCATTAATGA
* * * *
20179 AAATTGTAGATCATGAAATTACCTTTTAATAGACACTTGAATCACCTTAATCGGACAAACAGAAA
254 AAATTGTAAATAATGAAATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAACA-AAA
* * * * *
20244 -AAA-AATACAAAAATAAAAGC-CAACGCGTTAAATCGTCCAACCTATAA-TTGTAAAGGACTAA
318 CAAAGAATAAAAAAAT-AAAGCTCAA-ACGTCAAAT--T--AACATAGAATTTGTAAAGGACTAA
* * *
20305 ATAGCATAAAGTATAAAAGTATGAG-GATCACTAGATAAAAAATCC-AAT-AAAAGTATTA
377 ATAGCATAAAGTAGAAAAGTATGAGAG-TCACTACATAAAAAATCCAAATAAAAAATATTA
*
20363 GTTTATGGAGA
1 GTTAATGGAGA
20374 CTGGGCCCCA
Statistics
Matches: 375, Mismatches: 58, Indels: 30
0.81 0.13 0.06
Matches are distributed among these distances:
436 46 0.12
437 257 0.69
438 10 0.03
439 5 0.01
440 51 0.14
441 6 0.02
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (436 bp):
GTTAATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCCTCAACGAAACTCGTAGATCAAAT
TAACTTTCGGGTTATTCATGAAAATCATAAACCATACAATAACCTTTTAACCGACACTTCAATAA
CTTCAATCGGACATGTGGATCAAAAATTATACGATATTAAATAGACCAACAATCAAAACAACAAA
ATTCAGGAACCATTTTTTAGAATTCAAACATAAAAAATTACTTTTGAGTCATTAATGAAAATTGT
AAATAATGAAATTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAACAAAACAAAGAAT
AAAAAAATAAAGCTCAAACGTCAAATTAACATAGAATTTGTAAAGGACTAAATAGCATAAAGTAG
AAAAGTATGAGAGTCACTACATAAAAAATCCAAATAAAAAATATTA
Done.