Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014880.1 Corchorus olitorius cultivar O-4 contig14913, 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: 5744
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Found at i:27 original size:11 final size:11
Alignment explanation
Indices: 5--50 Score: 74
Period size: 11 Copynumber: 4.1 Consensus size: 11
1 TTTT
5 TTTCAGAAAAAA
1 TTTCA-AAAAAA
*
17 GTTCAAAAAAA
1 TTTCAAAAAAA
28 TTTCAAAAAAA
1 TTTCAAAAAAA
39 TTTCAAAAAAA
1 TTTCAAAAAAA
50 T
1 T
51 AGTTTTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 28 0.88
12 4 0.12
ACGTcount: A:0.61, C:0.09, G:0.04, T:0.26
Consensus pattern (11 bp):
TTTCAAAAAAA
Found at i:574 original size:22 final size:22
Alignment explanation
Indices: 452--684 Score: 134
Period size: 22 Copynumber: 10.6 Consensus size: 22
442 AGCCCTCTCC
* * *
452 CTATGAAATTTCGTTAAAC-TT
1 CTATGAAATTTTGATAACCTTT
***
473 CTTATGAAATTTTGATAACCACA
1 C-TATGAAATTTTGATAACCTTT
* *
496 CTAT-AAATTCTCGATAAAC-TT
1 CTATGAAATT-TTGATAACCTTT
* *
517 CGTATGAAATTTTGTTAACCTTC
1 C-TATGAAATTTTGATAACCTTT
540 CTATGAAATTTTGATAACCTTT
1 CTATGAAATTTTGATAACCTTT
* *
562 CTATGAAAATTTGGTAACCTTT
1 CTATGAAATTTTGATAACCTTT
* * **
584 GTATGAAATTTTGATCA-CTACA
1 CTATGAAATTTTGATAACCT-TT
* *
606 CTATGAAGTTTTGATAACC-TC
1 CTATGAAATTTTGATAACCTTT
* * * **
627 CATACGAAATTTTGGTAAACACT
1 C-TATGAAATTTTGATAACCTTT
* * * *
650 CTATGAGATTTTGATAATCATC
1 CTATGAAATTTTGATAACCTTT
*
672 CTATGCAATTTTG
1 CTATGAAATTTTG
685 GTTTGATTGT
Statistics
Matches: 160, Mismatches: 42, Indels: 19
0.72 0.19 0.09
Matches are distributed among these distances:
21 10 0.06
22 140 0.88
23 10 0.06
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCTTT
Found at i:581 original size:44 final size:44
Alignment explanation
Indices: 430--682 Score: 167
Period size: 44 Copynumber: 5.7 Consensus size: 44
420 ACGTCTCGAG
* *
430 GAAATTTTGATAAGCCCTCTCCCTATGAAATTTCGTTAAACTTCTTAT
1 GAAATTTTGATAA--CCT-T-CCTATGAAATTTCGATAAACTTCGTAT
*
478 GAAATTTTGATAACC-ACACTAT-AAATTCTCGATAAACTTCGTAT
1 GAAATTTTGATAACCTTC-CTATGAAATT-TCGATAAACTTCGTAT
* * *
522 GAAATTTTGTTAACCTTCCTATGAAATTTTGATAACCTTTC-TAT
1 GAAATTTTGATAACCTTCCTATGAAATTTCGATAAAC-TTCGTAT
* * ** * * * *
566 GAAAATTTGGTAACCTTTGTATGAAATTTTGAT-CACTACACTAT
1 GAAATTTTGATAACCTTCCTATGAAATTTCGATAAACTTC-GTAT
* * * * *
610 GAAGTTTTGATAACC-TCCATACGAAATTTTGGTAAACACTC-TAT
1 GAAATTTTGATAACCTTCC-TATGAAATTTCGATAAAC-TTCGTAT
* * * *
654 GAGATTTTGATAATCATCCTATGCAATTT
1 GAAATTTTGATAACCTTCCTATGAAATTT
683 TGGTTTGATT
Statistics
Matches: 165, Mismatches: 29, Indels: 26
0.75 0.13 0.12
Matches are distributed among these distances:
42 2 0.01
43 8 0.05
44 125 0.76
45 14 0.08
46 3 0.02
48 13 0.08
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (44 bp):
GAAATTTTGATAACCTTCCTATGAAATTTCGATAAACTTCGTAT
Found at i:588 original size:66 final size:65
Alignment explanation
Indices: 453--626 Score: 181
Period size: 66 Copynumber: 2.6 Consensus size: 65
443 GCCCTCTCCC
* * *
453 TATGAAATTTCGTTAAACTTCTTATGAAATTTTGATAACCACACTATAAATTCTCGATAAACTTC
1 TATGAAATTTTGTT-AACTTCCTATGAAATTTTGATAACCTCACTATAAATTCTCGATAAACTTC
518 G
65 G
** * *
519 TATGAAATTTTGTTAACCTTCCTATGAAATTTTGATAACCTTTCTATGAAAATT-T-GGTAACCT
1 TATGAAATTTTGTTAA-CTTCCTATGAAATTTTGATAACCTCACTAT--AAATTCTCGATAAACT
*
582 TTG
63 TCG
* * * *
585 TATGAAATTTTGATCACTACACTATGAAGTTTTGATAACCTC
1 TATGAAATTTTGTTAACTTC-CTATGAAATTTTGATAACCTC
627 CATACGAAAT
Statistics
Matches: 91, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
65 5 0.05
66 80 0.88
67 1 0.01
68 5 0.05
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (65 bp):
TATGAAATTTTGTTAACTTCCTATGAAATTTTGATAACCTCACTATAAATTCTCGATAAACTTCG
Found at i:641 original size:66 final size:66
Alignment explanation
Indices: 518--684 Score: 160
Period size: 66 Copynumber: 2.5 Consensus size: 66
508 GATAAACTTC
* * * *
518 GTATGAAATTTTGTTAACCTTCCTATGAAATTTTGATAACCTTTCTATGAAAATTTGGTAACCTT
1 GTATGAAATTTTGATAACCTACCTATGAAATTTTGATAACCTTCCTACGAAAATTTGGTAACCTT
583 T
66 T
* * * *
584 GTATGAAATTTTGATCA-CTACACTATGAAGTTTTGATAACC-TCCATACGAAATTTTGGTAAAC
1 GTATGAAATTTTGATAACCTAC-CTATGAAATTTTGATAACCTTCC-TACGAAAATTTGGTAACC
**
647 ACT
64 TTT
* * * *
650 CTATGAGATTTTGATAATC-ATCCTATGCAATTTTG
1 GTATGAAATTTTGATAACCTA-CCTATGAAATTTTG
685 GTTTGATTGT
Statistics
Matches: 82, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
65 5 0.06
66 75 0.91
67 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (66 bp):
GTATGAAATTTTGATAACCTACCTATGAAATTTTGATAACCTTCCTACGAAAATTTGGTAACCTT
T
Found at i:4408 original size:22 final size:21
Alignment explanation
Indices: 4366--4473 Score: 101
Period size: 22 Copynumber: 5.0 Consensus size: 21
4356 TCAAGAATCT
*
4366 CCCTAT-AATATTTTGAGAACC
1 CCCTATGAA-ATTTTGATAACC
*
4387 CCTCTATGAAATTTTGTTAACC
1 CC-CTATGAAATTTTGATAACC
*
4409 TCCCAATGAAATTTTGATAACC
1 -CCCTATGAAATTTTGATAACC
** *
4431 ATCTAATGAAATTTTGATAAAC
1 CCCT-ATGAAATTTTGATAACC
* *
4453 ACATATGAAATTTTGATAACC
1 CCCTATGAAATTTTGATAACC
4474 AATTTTGATA
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
21 19 0.26
22 49 0.68
23 4 0.06
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.35
Consensus pattern (21 bp):
CCCTATGAAATTTTGATAACC
Found at i:4479 original size:13 final size:13
Alignment explanation
Indices: 4461--4486 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4451 ACACATATGA
4461 AATTTTGATAACC
1 AATTTTGATAACC
4474 AATTTTGATAACC
1 AATTTTGATAACC
4487 TTCATGTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
AATTTTGATAACC
Done.