Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020842.1 Corchorus olitorius cultivar O-4 contig20875, 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: 4143
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:415 original size:65 final size:66
Alignment explanation
Indices: 301--450 Score: 196
Period size: 65 Copynumber: 2.3 Consensus size: 66
291 AGCAAAATTT
* * **
301 CAATTACCAAAATTTCAAATCTTGTTATTAAAATTTCATAAGCAGGGTTATCAAAATCTAATAG-
1 CAATTAACAAAATTTCAAACCTTGTTAACAAAATTTCATAAGCAGGGTTATCAAAATCTAATAGC
365 G
66 G
* * * *
366 CCATTAACAAAATCTCAAACCTTCGTTAACAAAATTTCATAAGGA-GGTTATCAAAATTTAATAG
1 CAATTAACAAAATTTCAAACCTT-GTTAACAAAATTTCATAAGCAGGGTTATCAAAATCTAATAG
430 CG
65 CG
*
432 CAATTATCAAAATTTCAAA
1 CAATTAACAAAATTTCAAA
451 GATTTTCTTA
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
65 37 0.51
66 35 0.49
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.31
Consensus pattern (66 bp):
CAATTAACAAAATTTCAAACCTTGTTAACAAAATTTCATAAGCAGGGTTATCAAAATCTAATAGC
G
Found at i:492 original size:22 final size:22
Alignment explanation
Indices: 467--658 Score: 147
Period size: 22 Copynumber: 8.7 Consensus size: 22
457 CTTAGGGAGA
*
467 TTACCAGAATTTAATAGAGAGG
1 TTACCAGAATTTCATAGAGAGG
489 TTACCAGAATTTCATA-ATGAGG
1 TTACCAGAATTTCATAGA-GAGG
* * *
511 TCACCACAATTTCATAGAGAGA
1 TTACCAGAATTTCATAGAGAGG
* * *
533 TTACCAAAATTTCAT-GGGATGA
1 TTACCAGAATTTCATAGAGA-GG
* * *
555 ATACCAGAATTTCGTAGTGAGG
1 TTACCAGAATTTCATAGAGAGG
* * *
577 TTACCGGAATTACATAGGGAGG
1 TTACCAGAATTTCATAGAGAGG
* * * *
599 TTACCAAAATTTTATAGTGTGG
1 TTACCAGAATTTCATAGAGAGG
* * *
621 TTACTAAAATTTCATA-AGGAAG
1 TTACCAGAATTTCATAGA-GAGG
*
643 TTACCAAAATTTCATA
1 TTACCAGAATTTCATA
659 ATGTGATTAT
Statistics
Matches: 136, Mismatches: 29, Indels: 10
0.78 0.17 0.06
Matches are distributed among these distances:
21 4 0.03
22 128 0.94
23 4 0.03
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (22 bp):
TTACCAGAATTTCATAGAGAGG
Found at i:632 original size:66 final size:66
Alignment explanation
Indices: 459--637 Score: 180
Period size: 66 Copynumber: 2.7 Consensus size: 66
449 AAGATTTTCT
* * *
459 TAGGGAGATTACCAGAATTTAATAGAGAGGTTACCAGAATTTCATAATGAGGTCACCACAATTTC
1 TAGGGAGATTACCAAAATTTAATAGAGTGGTTACCAGAATTTCATAATGAGGTCACCACAATTAC
524 A
66 A
* * * ** * * * **
525 TAGAGAGATTACCAAAATTTCAT-GGGATGAATACCAGAATTTCGTAGTGAGGTTACCGGAATTA
1 TAGGGAGATTACCAAAATTTAATAGAG-TGGTTACCAGAATTTCATAATGAGGTCACCACAATTA
589 CA
65 CA
* * * * *
591 TAGGGAGGTTACCAAAATTTTATAGTGTGGTTACTAAAATTTCATAA
1 TAGGGAGATTACCAAAATTTAATAGAGTGGTTACCAGAATTTCATAA
638 GGAAGTTACC
Statistics
Matches: 88, Mismatches: 23, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
65 2 0.02
66 84 0.95
67 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (66 bp):
TAGGGAGATTACCAAAATTTAATAGAGTGGTTACCAGAATTTCATAATGAGGTCACCACAATTAC
A
Found at i:659 original size:22 final size:22
Alignment explanation
Indices: 488--699 Score: 89
Period size: 22 Copynumber: 9.6 Consensus size: 22
478 TAATAGAGAG
* * *
488 GTTACCAGAATTTCATAATGAG
1 GTTACCAAAATTTCATAAGGAA
* *
510 GTCACCACAATTTCAT-A-GAGA
1 GTTACCAAAATTTCATAAGGA-A
* *
531 GATTACCAAAATTTCAT-GGGAT
1 G-TTACCAAAATTTCATAAGGAA
* * * *
553 GAATACCAGAATTTCGT-AGTGAG
1 G-TTACCAAAATTTCATAAG-GAA
** * * *
576 GTTACCGGAATTACATAGGGAG
1 GTTACCAAAATTTCATAAGGAA
* **
598 GTTACCAAAATTTTAT-AGTGTG
1 GTTACCAAAATTTCATAAG-GAA
*
620 GTTACTAAAATTTCATAAGGAA
1 GTTACCAAAATTTCATAAGGAA
642 GTTACCAAAATTTCATAATGTG-A
1 GTTACCAAAATTTCATAA-G-GAA
* *
665 -TTATCAAAATTTCCTAA-GAA
1 GTTACCAAAATTTCATAAGGAA
*
685 GGTTATCAAAATTTC
1 -GTTACCAAAATTTC
700 GTACGGAGGT
Statistics
Matches: 148, Mismatches: 30, Indels: 24
0.73 0.15 0.12
Matches are distributed among these distances:
19 1 0.01
20 3 0.02
21 3 0.02
22 130 0.88
23 10 0.07
24 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (22 bp):
GTTACCAAAATTTCATAAGGAA
Found at i:674 original size:44 final size:44
Alignment explanation
Indices: 584--699 Score: 128
Period size: 44 Copynumber: 2.6 Consensus size: 44
574 AGGTTACCGG
* * * * * *
584 AATTACATAGGGAGGTTACCAAAATTTTATAGTGTGGTTACTAA
1 AATTTCATAAGGAAGTTACCAAAATTTCATAATGTGATTACTAA
628 AATTTCATAAGGAAGTTACCAAAATTTCATAATGTGATTA-TCAA
1 AATTTCATAAGGAAGTTACCAAAATTTCATAATGTGATTACT-AA
* *
672 AATTTCCTAA-GAAGGTTATCAAAATTTC
1 AATTTCATAAGGAA-GTTACCAAAATTTC
700 GTACGGAGGT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
43 4 0.06
44 58 0.94
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (44 bp):
AATTTCATAAGGAAGTTACCAAAATTTCATAATGTGATTACTAA
Found at i:709 original size:22 final size:22
Alignment explanation
Indices: 626--719 Score: 75
Period size: 22 Copynumber: 4.2 Consensus size: 22
616 TGTGGTTACT
* *
626 AAAATTTCATAAGGAA-GTTACC
1 AAAATTTCCTAA-GAAGGTTATC
* * *
648 AAAATTTCATAATG-TGATTATC
1 AAAATTTCCTAA-GAAGGTTATC
670 AAAATTTCCTAAGAAGGTTATC
1 AAAATTTCCTAAGAAGGTTATC
* * *
692 AAAATTTCGTACGGAGGTTATC
1 AAAATTTCCTAAGAAGGTTATC
714 GAAAAT
1 -AAAAT
720 CGTGATGCGT
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
21 1 0.02
22 53 0.90
23 5 0.08
ACGTcount: A:0.41, C:0.12, G:0.15, T:0.32
Consensus pattern (22 bp):
AAAATTTCCTAAGAAGGTTATC
Found at i:1359 original size:332 final size:329
Alignment explanation
Indices: 798--1407 Score: 800
Period size: 332 Copynumber: 1.8 Consensus size: 329
788 AAACGAAAAA
* *
798 TTTTTCCTCAATGTTTGGCCACAATACTCATAAAAAATATATGATTCAACGCCAAAAATATTTAT
1 TTTTTCCTCAATGTTTGACCACAATACTCATAAAAAATATA-GATTCAACGCCAAAAAGATTTAT
* *
863 GAGTTTTTCACGCTTCAAATATGGTTTTTCCAATTTTTTCCAAATTAATTACTGATAAAATCGAA
65 GAGCTTTTCACGCTTCAAATATGGTTTTTCCAATTTTTTCCAAATTAATTACTAATAAAATCGAA
* * * * *
928 ACAAGATTAAGATGCTCGTAAAAACATATCCTTCAATCCAATGTGGCTGGGATTTTATTAGATGA
130 ACAAGATTAAGAAGCTCGTAAAAACATATCCTTAAATCCAATGTGACTGAGATTTGATTAGATGA
* *
993 ATATAAATATTTCAAGGAGTCTCGGCGCCAAAAATCTTGCAAAACTGAGCCGGGGCCACGGAACG
195 ATATAAATATTTCAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGCCGGGGCCACGGAACG
*
1058 CCTTTTCAGCCAGAAACCATGGTGTAGTACACGATTTCAGCTGAAATTTGCAAAAAATGATCCAA
260 CCTTTTCAGCAAGAAACCATGGTGTAGTACACGATTTCAGCTGAAATTTGCAAAAAATGATCCAA
1123 ATTTT
325 ATTTT
* *
1128 TTTTTTCTCAAAT-TTTGACCACAATACTCCTGAAAAAATATA-ATTCAACGCCAAAAAGATTTC
1 TTTTTCCTC-AATGTTTGACCACAATACTCAT-AAAAAATATAGATTCAACGCCAAAAAGATTT-
* * ** *
1191 A-GGGCTTTTCATGCTTCAAATATGGTTTTTCCTCTTTTTTATTCC-AATTAATTTTCTAATAAA
63 ATGAGCTTTTCACGCTTCAAATATGGTTTTT-C-CAATTTT-TTCCAAATTAA-TTACTAATAAA
* * **
1254 ATTGAATCAAGATTCAA-AAGCTCGTAAAAACATATCCTTAAATCTGATGTGACTGAGATTTGAT
124 ATCGAAACAAGATT-AAGAAGCTCGTAAAAACATATCCTTAAATCCAATGTGACTGAGATTTGAT
* ** * * * *
1318 TAGATTAATATTGATACTTT-AAGGAGTTTTGATGTCAAAAATCATGCAAAACTGAGCCGGGGCC
188 TAGATGAATATAAATA-TTTCAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGCCGGGGCC
* *
1382 TCGGAACGCGTTTTCAGCAAGAAACC
252 ACGGAACGCCTTTTCAGCAAGAAACC
1408 GGGCTAAATG
Statistics
Matches: 239, Mismatches: 32, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
329 45 0.19
330 26 0.11
331 24 0.10
332 139 0.58
333 5 0.02
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (329 bp):
TTTTTCCTCAATGTTTGACCACAATACTCATAAAAAATATAGATTCAACGCCAAAAAGATTTATG
AGCTTTTCACGCTTCAAATATGGTTTTTCCAATTTTTTCCAAATTAATTACTAATAAAATCGAAA
CAAGATTAAGAAGCTCGTAAAAACATATCCTTAAATCCAATGTGACTGAGATTTGATTAGATGAA
TATAAATATTTCAAGGAGTCTCGACGCCAAAAATCATGCAAAACTGAGCCGGGGCCACGGAACGC
CTTTTCAGCAAGAAACCATGGTGTAGTACACGATTTCAGCTGAAATTTGCAAAAAATGATCCAAA
TTTT
Found at i:1740 original size:3 final size:3
Alignment explanation
Indices: 1732--1765 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
1722 ACCCTGATTT
1732 TTC TTC TTC TTC TTC TTC TAT- TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC T-TC TTC TTC TTC TTC T
1766 CGTGCTTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.03
3 27 0.93
4 1 0.03
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Done.