Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010811.1 Corchorus capsularis cultivar CVL-1 contig10832, 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: 58953
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Found at i:3696 original size:13 final size:13
Alignment explanation
Indices: 3678--3712 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
3668 AATCTTTATC
*
3678 TAAAGCAGATTAA
1 TAAAGCAAATTAA
3691 TAAAGCAAATTAA
1 TAAAGCAAATTAA
3704 TAAAGCAAA
1 TAAAGCAAA
3713 CAATAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.20
Consensus pattern (13 bp):
TAAAGCAAATTAA
Found at i:8534 original size:18 final size:18
Alignment explanation
Indices: 8511--8545 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
8501 CCAATATCAC
8511 GTGAATTGCAAAACAATA
1 GTGAATTGCAAAACAATA
8529 GTGAATTGCAAAACAAT
1 GTGAATTGCAAAACAAT
8546 TATCCAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.23
Consensus pattern (18 bp):
GTGAATTGCAAAACAATA
Found at i:10045 original size:107 final size:104
Alignment explanation
Indices: 9873--10134 Score: 382
Period size: 107 Copynumber: 2.5 Consensus size: 104
9863 AGTTTAGCCT
**
9873 TAATTTCACTAAGTTTAGTCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTGAAAATT
1 TAATTTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
9938 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAA
65 AATAA--TATTGTTATAGGGTTTTAGAAATAAAATACAAAAA
*
9980 TAATTTCACTAAGTTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* * *
10045 AATAATATTGTTATAGGGTTTTAGAAATAAAATATATAAT
65 AATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAA
* ** * *
10085 TAA-TTCACTAAGTTTAGCCCACATTAAAATTAAAATTTAATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
10135 TAGAAAAATT
Statistics
Matches: 143, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
103 28 0.20
104 14 0.10
105 35 0.24
107 66 0.46
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.42
Consensus pattern (104 bp):
TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
ATAATATTGTTATAGGGTTTTAGAAATAAAATACAAAAA
Found at i:15711 original size:2 final size:2
Alignment explanation
Indices: 15704--15733 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
15694 TTGTTGTGGA
15704 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15734 GTCCGGTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23094 original size:6 final size:6
Alignment explanation
Indices: 23085--23118 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
23075 TCGATTCCAA
*
23085 TCAAAA TCAAAT TCAAAT TCAAAT TCAAAT TCAA
1 TCAAAT TCAAAT TCAAAT TCAAAT TCAAAT TCAA
23119 GACAAGGGCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (6 bp):
TCAAAT
Found at i:26711 original size:15 final size:16
Alignment explanation
Indices: 26683--26712 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26673 TCGACTCTAC
26683 AAGAAAAACTTCAAGA
1 AAGAAAAACTTCAAGA
26699 AAGAAAAAC-TCAAG
1 AAGAAAAACTTCAAG
26713 GGTGAAGTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.63, C:0.13, G:0.13, T:0.10
Consensus pattern (16 bp):
AAGAAAAACTTCAAGA
Found at i:36148 original size:438 final size:437
Alignment explanation
Indices: 35370--36220 Score: 1193
Period size: 438 Copynumber: 1.9 Consensus size: 437
35360 CATCCAGCCT
* * * * * *
35370 ATAATTGTAAAGGATTCAATAGCATGAAACATAAAAGTATGAGGGTCATTAGATAAATATTCCAG
1 ATAATTGTAAAGGATTAAATAGCATAAAACATAAAAGTATAAGGATCATTAGATAAATAATCCAA
* **
35435 CAAAAAAAATATTAGTTTATGAAGACAAAACATAAAAATTCCCTCTTGAATTCTCCACGAAACTC
66 CAAAAAAAATATTAGTTTATGAAGACAAAACATAAAAATTCCCTCTCGAACCCTCCACGAAACTC
* * * * *
35500 ATTAATCAAATTCAACTTTCATGCCCTTAATGAAAGTCGTAGATCACGCAATAACCTTTTAACCT
131 ATTAATCAAATTCAACTTTCAGGCCCTTAACGAAAGTCATAGATCACACAATAACCTTTTAACCG
* * * *
35565 ACACTTGAACAACTTCAATCGGACAAGTGCACCGAAAATTATACGATATTAAATAGACCGGCAAT
196 ACACTTGAACAACCTCAATCGGACAAGTGCACCAAAAATTATACAATATTAAATAGACCGACAAT
* * * **
35630 CGAAATCACAAAATTTAAGAAACATTTTTTAGAATCAAAACATTAAATTGGCTTCTGAGTTTTTC
261 CGAAACCACAAAATTTAAGAAACATTTTTTAGAATCAAAACATAAAATTGGCTTCTCAGTCCTTC
* *
35695 ATGAAAGTTGTAGATCATGAGATTACCTATTAATAGACACTTGAATCACCTTGATCAGACAAATA
326 ATGAAAGTTGTAGATCATGAAATTACATATTAATAGACACTTGAATCACCTTGATCAGACAAATA
* *
35760 GAACAGAAAATACAAAAATAAAAGCCGATGCGATAAATCGTCCAACTC
391 AAACAAAAAATA-AAAAATAAAAGCCGATGCGATAAATCGTCCAACTC
*
35808 ATAATTGTAAAGGATTAAATAGCATAAAACATAAAAGTATAAGGATCATTTGATAAATAATCCAA
1 ATAATTGTAAAGGATTAAATAGCATAAAACATAAAAGTATAAGGATCATTAGATAAATAATCCAA
* * * *
35873 CAAAAAATATATTTGTTTATGGAGATC-AAACATAAAAATTCGCTCTCGAACCCTCCACGAAACT
66 CAAAAAAAATATTAGTTTATGAAGA-CAAAACATAAAAATTCCCTCTCGAACCCTCCACGAAACT
* * * *
35937 CATTAATCAAATTCAGCTTTCAGGTCCTTGACGAAAGTCATATATCACACAATAACCTTTTAACC
130 CATTAATCAAATTCAACTTTCAGGCCCTTAACGAAAGTCATAGATCACACAATAACCTTTTAACC
* * * * *
36002 GACATTTGAACAACCTCAATCGGACAAGTGGATCAAAAATTATATAATATTAGATAGACCGACAA
195 GACACTTGAACAACCTCAATCGGACAAGTGCACCAAAAATTATACAATATTAAATAGACCGACAA
* * * ** *
36067 TTGAGACCACAAAATTTAAGAAGCATTTTTTAGAATTGAAACATGAAAATTGG-TTTTCAGTCCT
260 TCGAAACCACAAAATTTAAGAAACATTTTTTAGAATCAAAACAT-AAAATTGGCTTCTCAGTCCT
* * * *
36131 TCATGAAAGTTGTAGATCATGAAATTATATTTTAATAGACACTTGAATCACCTTGATCGGACAAG
324 TCATGAAAGTTGTAGATCATGAAATTACATATTAATAGACACTTGAATCACCTTGATCAGACAAA
*
36196 TAAAATAAAAAATAAAAAATAAAAG
389 TAAAACAAAAAATAAAAAATAAAAG
36221 AATTAAAGTC
Statistics
Matches: 359, Mismatches: 52, Indels: 5
0.86 0.12 0.01
Matches are distributed among these distances:
437 11 0.03
438 340 0.95
439 8 0.02
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (437 bp):
ATAATTGTAAAGGATTAAATAGCATAAAACATAAAAGTATAAGGATCATTAGATAAATAATCCAA
CAAAAAAAATATTAGTTTATGAAGACAAAACATAAAAATTCCCTCTCGAACCCTCCACGAAACTC
ATTAATCAAATTCAACTTTCAGGCCCTTAACGAAAGTCATAGATCACACAATAACCTTTTAACCG
ACACTTGAACAACCTCAATCGGACAAGTGCACCAAAAATTATACAATATTAAATAGACCGACAAT
CGAAACCACAAAATTTAAGAAACATTTTTTAGAATCAAAACATAAAATTGGCTTCTCAGTCCTTC
ATGAAAGTTGTAGATCATGAAATTACATATTAATAGACACTTGAATCACCTTGATCAGACAAATA
AAACAAAAAATAAAAAATAAAAGCCGATGCGATAAATCGTCCAACTC
Found at i:36522 original size:2 final size:2
Alignment explanation
Indices: 36517--36543 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
36507 TGTTATAAAT
36517 TA 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 T
36544 CCCTCTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.