Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001373.1 Corchorus capsularis cultivar CVL-1 contig01373, 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, 610
Length: 1018
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Found at i:255 original size:22 final size:22
Alignment explanation
Indices: 230--386 Score: 100
Period size: 22 Copynumber: 6.9 Consensus size: 22
220 TTGTCTCTAT
*
230 ATGGTTATCAAAATTTCATAAA
1 ATGGTTATCAAAATTTCATAGA
* *
252 ATGGTTATTACAATTTCATGAGA
1 ATGGTTATCAAAATTTCAT-AGA
*
275 A-GGTTATCAAAATTCCATAGTGTA
1 ATGGTTATCAAAATTTCATA--G-A
* * *
299 CTGGTTACCAAAATTTCATAGT
1 ATGGTTATCAAAATTTCATAGA
* * *
321 GTGGTTACCAAAATTTCATAGG
1 ATGGTTATCAAAATTTCATAGA
* * * *
343 ATCAGGTTATTAAAATCTCTTAGG
1 AT--GGTTATCAAAATTTCATAGA
* **
367 TTGGTTATTGAAATTTCATA
1 ATGGTTATCAAAATTTCATA
387 AGGTGGTTAA
Statistics
Matches: 107, Mismatches: 21, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
21 1 0.01
22 67 0.63
23 5 0.05
24 18 0.17
25 16 0.15
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGGTTATCAAAATTTCATAGA
Found at i:555 original size:22 final size:22
Alignment explanation
Indices: 508--660 Score: 61
Period size: 22 Copynumber: 6.7 Consensus size: 22
498 TCATGGGGAG
*
508 GTTATCAAAATTTTATAGTG--T
1 GTTATCAAAATTTCATA-TGAAT
529 GGTTATCAAAATTTCATATGAAT
1 -GTTATCAAAATTTCATATGAAT
* *
552 GTTAT-AAAAGTCTCAATTTTAT-AAG
1 GTTATCAAAA-TTTC-A---TATGAAT
* *
577 GAGTACCAAAATTTCATA-GAGAT
1 G-TTATCAAAATTTCATATGA-AT
*
600 CAGATTATCAAAATTT-ATA-GAAA
1 --G-TTATCAAAATTTCATATGAAT
*
623 GATTATCAAAATTTCATAGTG-TT
1 G-TTATCAAAATTTCATA-TGAAT
646 GTTATCAAAATTTCA
1 GTTATCAAAATTTCA
661 AAGCGAGGTT
Statistics
Matches: 103, Mismatches: 12, Indels: 32
0.70 0.08 0.22
Matches are distributed among these distances:
21 20 0.19
22 44 0.43
23 5 0.05
24 6 0.06
25 16 0.16
26 8 0.08
27 4 0.04
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (22 bp):
GTTATCAAAATTTCATATGAAT
Found at i:626 original size:21 final size:24
Alignment explanation
Indices: 583--641 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 24
573 TAAGGAGTAC
583 CAAAATTTCATAGAGATCAGATTAT
1 CAAAATTTCATAGAGA-CAGATTAT
608 CAAAATTT-ATAGA-A-AGATTAT
1 CAAAATTTCATAGAGACAGATTAT
629 CAAAATTTCATAG
1 CAAAATTTCATAG
642 TGTTGTTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
21 15 0.45
22 4 0.12
23 1 0.03
24 5 0.15
25 8 0.24
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.32
Consensus pattern (24 bp):
CAAAATTTCATAGAGACAGATTAT
Found at i:671 original size:22 final size:22
Alignment explanation
Indices: 604--772 Score: 114
Period size: 22 Copynumber: 7.7 Consensus size: 22
594 AGAGATCAGA
* * *
604 TTATCAAAATTT-ATAGAAAGA
1 TTATCAAAATTTCAAAGAGAGG
* * **
625 TTATCAAAATTTCATAGTGTTG
1 TTATCAAAATTTCAAAGAGAGG
*
647 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCAAAGAGAGG
* *
669 TTATCAAAATTACATAATGTGA--
1 TTATCAAAATTTCA-AA-GAGAGG
* * *
691 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCAAAGAGAGG
* * *
713 TCAACAAAATTTTATAA-AGAGG
1 TTATCAAAATTTCA-AAGAGAGG
735 TTATCAAAATTTCATAA-AGAGG
1 TTATCAAAATTTCA-AAGAGAGG
*
757 TTATCAAATTTTCAAA
1 TTATCAAAATTTCAAA
773 AATGTGATTA
Statistics
Matches: 116, Mismatches: 26, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
20 2 0.02
21 15 0.13
22 93 0.80
23 3 0.03
24 3 0.03
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (22 bp):
TTATCAAAATTTCAAAGAGAGG
Found at i:694 original size:66 final size:66
Alignment explanation
Indices: 604--770 Score: 169
Period size: 66 Copynumber: 2.5 Consensus size: 66
594 AGAGATCAGA
* * ** * * *
604 TTATCAAAATT-TATAGAA-AGATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCG
1 TTATCAAAATTACATA-AAGAGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-AG
666 AGG
64 AGG
* * * *
669 TTATCAAAATTACATAATGTGATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAG
1 TTATCAAAATTACATAAAGAGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAG
734 G
66 G
* * *
735 TTATCAAAATTTCATAAAGAGGTTATCAAATTTTCA
1 TTATCAAAATTACATAAAGAGATTATCAAAATTTCA
771 AAAATGTGAT
Statistics
Matches: 82, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
65 12 0.15
66 68 0.83
67 2 0.02
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (66 bp):
TTATCAAAATTACATAAAGAGATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAG
G
Found at i:695 original size:44 final size:44
Alignment explanation
Indices: 602--793 Score: 167
Period size: 44 Copynumber: 4.4 Consensus size: 44
592 ATAGAGATCA
* * * *
602 GATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATG-T
* *
646 G-TTATCAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * * * * * *
689 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGA
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * *
733 GGTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAAATGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTC-ATAATGT
778 GATTA-CAAAAATTTCA
1 GATTATC-AAAATTTCA
794 TAGTGGTATT
Statistics
Matches: 115, Mismatches: 28, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
43 14 0.12
44 83 0.72
45 18 0.16
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
Done.