Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009158.1 Corchorus capsularis cultivar CVL-1 contig09179, 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: 35534
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.31
Found at i:7815 original size:21 final size:20
Alignment explanation
Indices: 7767--7816 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
7757 CCAGCTGGGG
* *
7767 GCCCATGTGGTATGCTTGGC
1 GCCCATGTGGTATGCCTCGC
*
7787 GCCTCATGTGGTTTGCCTCGC
1 GCC-CATGTGGTATGCCTCGC
7808 GACCCATGT
1 G-CCCATGT
7817 CCTCCAGTGC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 20 0.80
22 2 0.08
ACGTcount: A:0.10, C:0.30, G:0.30, T:0.30
Consensus pattern (20 bp):
GCCCATGTGGTATGCCTCGC
Found at i:15912 original size:437 final size:430
Alignment explanation
Indices: 14933--15931 Score: 1156
Period size: 437 Copynumber: 2.3 Consensus size: 430
14923 TTTCAAAAGT
* **
14933 ATTTTTTGGAATTGAAACATTAAAAATTAGCTTTTGAG-TCTTTCAT-AAAAGTTAG-AGATCAT
1 ATTTTTTAGAATCAAAACA-TAAAAATTAGCTTTTGAGTTC-TTCATGAAAA-TT-GTAGATCAT
* * * * * * *
14995 AAAATTACCTTTTTATAAACACCTGAATTACCTTAATTGGATAAATAGAACAAAGAAAATAAAAA
62 GAAATTACCTTTTAATAGACACATGAATCACCTTAATCGGACAAATAGAACAAAGAAAATAAAAA
* *
15060 AGAAATGAAGCGTTAAATCGAATAAGATAGAATTTGAAAATGACTAAGTAGCAAAATAAAAAAGC
127 A-AAAT--A-CGTTAAATAGAATAAGATAGAATTTGAAAAGGACTAAGTAGCAAAATAAAAAAGC
* * * *
15125 ATTAGGGTCATTTGATAACTAATTCAAAAAGAAAATATTTCTTAATGGATATCTTGAAACATAAA
188 ATGAGGGTCATTTGATAAATAATCCAAAAAGAAAATATTTCTTAATGGAGATCTTGAAACATAAA
* * * *
15190 AATTCCCTTTTAAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCGGGTTCTTCATGAAACG
253 AATTCCCTTTTAAACCCTTCATGAAACTCGCAAATCAAATTAACTTTCGGGTCCTTCATGAAACA
* * * * *
15255 TAGATCATACAGTACCTTTTAACCAACACTTGAATAATTTTAATCGGAAATGTGGATCGAAAAAT
318 TAAATCATACAATACCTTTTAACCAACACTTCAATAACTTCAATCGGAAATGTGGATCGAAAAAT
* * * * *
15320 TATATGATATTAAATAGATCAACAATCGAAACGATCAAATTTAGGAAGC
383 TATAAGAAATTAAATAGACCAACAATCAAAACCATCAAATTTAGG-AGC
* * * * * *
15369 ATTTTTTTGAATTAAAACATAAAAATTTGCTTTTAAGTCCTTCATGAAAGTTGTAGATCATGAAA
1 ATTTTTTAGAATCAAAACATAAAAATTAGCTTTTGAGTTCTTCATGAAAATTGTAGATCATGAAA
*
15434 TTACCTTTTAATAGACACATGAATCAACTTAATCGGACAAATAGAACAAAGAATAATAAAAAAAA
66 TTACCTTTTAATAGACACATGAATCACCTTAATCGGACAAATAGAACAAAGAA-AATAAAAAAAA
* * * *
15499 AT-C-TTAAACATTAGATTAAGATAGAATTTGTAAAGGACTAAGTAGTATAAAGTAGAAAAA-TA
130 ATACGTT-AA-A-TAGAATAAGATAGAATTTGAAAAGGACTAAGTAGCA-AAA-TA-AAAAAGCA
* * *
15561 TGAGGGTCATTTGATAAATAATCCAAATAAGAAAATGTTTGTTAATGGAGATCTTGAAGCATAAA
189 TGAGGGTCATTTGATAAATAATCCAAA-AAGAAAATATTTCTTAATGGAGATCTTGAAACATAAA
* * * *
15626 AATTCCCTTTTGAACCCTTCATGAAACTCGCAAATCAAGTTTAGCTTTCTGGTCCTTCATGAAAA
253 AATTCCCTTTTAAACCCTTCATGAAACTCGCAAATCAA-ATTAACTTTCGGGTCCTTCATG-AAA
* ** *
15691 TCATAAATCATGCAATAACCTTTTAACTGACACTTCAATAACTTCAATCGGACATGTGGA-CGAA
316 -CATAAATCATACAAT-ACCTTTTAACCAACACTTCAATAACTTCAATCGGAAATGTGGATCGAA
* * *
15755 AAATTATAAGAAATTAAATTGACCGACAATCAAAACCA-CAAAATTTCGG-GC
379 AAATTATAAGAAATTAAATAGACCAACAATCAAAACCATC-AAATTTAGGAGC
* * * *
15806 ATTTTTTAGAATCAAAATATTAAAATTGGCTTTTGAGTTCTGCATGAAAATTGTAGATCATGAAA
1 ATTTTTTAGAATCAAAACATAAAAATTAGCTTTTGAGTTCTTCATGAAAATTGTAGATCATGAAA
* * * *
15871 TTACCTTTTAATAGACACTTGAATCACCTTACTCAGACAAATAGAA-AAA-AAAATACAAAAA
66 TTACCTTTTAATAGACACATGAATCACCTTAATCGGACAAATAGAACAAAGAAAATAAAAAAA
15932 TAAAAGGCAA
Statistics
Matches: 481, Mismatches: 66, Indels: 34
0.83 0.11 0.06
Matches are distributed among these distances:
430 2 0.00
431 3 0.01
432 1 0.00
433 31 0.06
434 13 0.03
435 112 0.23
436 106 0.22
437 118 0.25
438 4 0.01
439 54 0.11
440 37 0.08
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (430 bp):
ATTTTTTAGAATCAAAACATAAAAATTAGCTTTTGAGTTCTTCATGAAAATTGTAGATCATGAAA
TTACCTTTTAATAGACACATGAATCACCTTAATCGGACAAATAGAACAAAGAAAATAAAAAAAAA
TACGTTAAATAGAATAAGATAGAATTTGAAAAGGACTAAGTAGCAAAATAAAAAAGCATGAGGGT
CATTTGATAAATAATCCAAAAAGAAAATATTTCTTAATGGAGATCTTGAAACATAAAAATTCCCT
TTTAAACCCTTCATGAAACTCGCAAATCAAATTAACTTTCGGGTCCTTCATGAAACATAAATCAT
ACAATACCTTTTAACCAACACTTCAATAACTTCAATCGGAAATGTGGATCGAAAAATTATAAGAA
ATTAAATAGACCAACAATCAAAACCATCAAATTTAGGAGC
Found at i:22713 original size:75 final size:75
Alignment explanation
Indices: 22623--22769 Score: 285
Period size: 75 Copynumber: 2.0 Consensus size: 75
22613 ACGTGAGTCC
*
22623 CAGTGTGGGTTCCCAACTTAACTCGGATTCATTAGCCATGGAGCCATTTTTAATGCTGGAAACAA
1 CAGTGTGGGTTCCCAACTTAACTCAGATTCATTAGCCATGGAGCCATTTTTAATGCTGGAAACAA
22688 GCCAAATTTA
66 GCCAAATTTA
22698 CAGTGTGGGTTCCCAACTTAACTCAGATTCATTAGCCATGGAGCCATTTTTAATGCTGGAAACAA
1 CAGTGTGGGTTCCCAACTTAACTCAGATTCATTAGCCATGGAGCCATTTTTAATGCTGGAAACAA
22763 GCCAAAT
66 GCCAAAT
22770 AAATTTGCCG
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.29
Consensus pattern (75 bp):
CAGTGTGGGTTCCCAACTTAACTCAGATTCATTAGCCATGGAGCCATTTTTAATGCTGGAAACAA
GCCAAATTTA
Found at i:23643 original size:83 final size:83
Alignment explanation
Indices: 23504--23672 Score: 338
Period size: 83 Copynumber: 2.0 Consensus size: 83
23494 ATCTGCCAAA
23504 TTAAGAAAACAAGAGGGTGAGAGATATTTGCAGCTACTCTTAGAATATTACACAGAAATCTGCAG
1 TTAAGAAAACAAGAGGGTGAGAGATATTTGCAGCTACTCTTAGAATATTACACAGAAATCTGCAG
23569 GGTTTTTTTAACTTGCAT
66 GGTTTTTTTAACTTGCAT
23587 TTAAGAAAACAAGAGGGTGAGAGATATTTGCAGCTACTCTTAGAATATTACACAGAAATCTGCAG
1 TTAAGAAAACAAGAGGGTGAGAGATATTTGCAGCTACTCTTAGAATATTACACAGAAATCTGCAG
23652 GGTTTTTTTAACTTGCAT
66 GGTTTTTTTAACTTGCAT
23670 TTA
1 TTA
23673 GATAAAGGTC
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 86 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (83 bp):
TTAAGAAAACAAGAGGGTGAGAGATATTTGCAGCTACTCTTAGAATATTACACAGAAATCTGCAG
GGTTTTTTTAACTTGCAT
Found at i:27887 original size:9 final size:9
Alignment explanation
Indices: 27865--27908 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
27855 TCTTCTGCGT
27865 TTTTCTTTC
1 TTTTCTTTC
*
27874 TTTTTCTTTG
1 -TTTTCTTTC
27884 TTTTC-TTC
1 TTTTCTTTC
27892 TTTTCTTTC
1 TTTTCTTTC
*
27901 CTTTCTTT
1 TTTTCTTT
27909 TCTGTTTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
8 7 0.23
9 15 0.50
10 8 0.27
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.77
Consensus pattern (9 bp):
TTTTCTTTC
Done.