Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009535.1 Corchorus olitorius cultivar O-4 contig09567, 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: 4022
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Found at i:2025 original size:28 final size:27
Alignment explanation
Indices: 1993--2074 Score: 103
Period size: 28 Copynumber: 3.0 Consensus size: 27
1983 AATGTGAACT
*
1993 TAAAATGACCATAATGCCCCTGAACATG-
1 TAAAATGACCAAAATGCCCCTG-A-ATGC
2021 TAAAATGACCAAAATGCCCCTGAATGC
1 TAAAATGACCAAAATGCCCCTGAATGC
* *
2048 AAAAATGACCAAAATGGCCCCTAAATG
1 TAAAATGACCAAAAT-GCCCCTGAATG
2075 ACCTAAGTGC
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
26 3 0.06
27 15 0.31
28 31 0.63
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.18
Consensus pattern (27 bp):
TAAAATGACCAAAATGCCCCTGAATGC
Found at i:2537 original size:30 final size:30
Alignment explanation
Indices: 2497--3365 Score: 947
Period size: 30 Copynumber: 29.4 Consensus size: 30
2487 ATCCTAACTC
* *
2497 GGATTGAAATAAAGCAATGATCCTCGACCA
1 GGATTAAAATAAAGCAATGATCCTCAACCA
2527 GGATTAAAATAAAGCAAAT-ATCCTCAACCA
1 GGATTAAAATAAAGC-AATGATCCTCAACCA
* *
2557 GGATTAAAATGAAGCAAATGATCCTCAAACA
1 GGATTAAAATAAAGC-AATGATCCTCAACCA
* * * *
2588 AGATAAAAATAAAACAATGATCCTCAAACA
1 GGATTAAAATAAAGCAATGATCCTCAACCA
*
2618 GGATTAAAATAGAGCAATGATCCTCAACCA
1 GGATTAAAATAAAGCAATGATCCTCAACCA
*
2648 GGATTAAAATAAAGCAAAT-ATCCTCAACAA
1 GGATTAAAATAAAGC-AATGATCCTCAACCA
*
2678 GGATTAAAATGAAGCAAATGATCCTCAA--A
1 GGATTAAAATAAAGC-AATGATCCTCAACCA
* **
2707 -CA--AAGTTAAA--AATGATCCTCAACCA
1 GGATTAAAATAAAGCAATGATCCTCAACCA
* *
2732 GGATTAAAATAAAGCAAAGATCCTCAAACA
1 GGATTAAAATAAAGCAATGATCCTCAACCA
* *
2762 GGATTAAAAATATAGCAATGATCCTCAAACA
1 GGATT-AAAATAAAGCAATGATCCTCAACCA
* *
2793 GGATTAAAATATAA-CAATGATTCTCAAACA
1 GGATTAAAATA-AAGCAATGATCCTCAACCA
*
2823 GGATTAAAATAAAGCAATGATCCTTAACCA
1 GGATTAAAATAAAGCAATGATCCTCAACCA
*
2853 GGATTAAAATAAAGCAATGATCCTCAAACA
1 GGATTAAAATAAAGCAATGATCCTCAACCA
* *
2883 GGATTAAAATAGAGCAATGATCCTCAAACA
1 GGATTAAAATAAAGCAATGATCCTCAACCA
*
2913 AGATTAAAATAAA-C-A--ATCCTCAACCA
1 GGATTAAAATAAAGCAATGATCCTCAACCA
* * **
2939 GGATTAAAATAGAGTAACAATCCTCAACCA
1 GGATTAAAATAAAGCAATGATCCTCAACCA
* *
2969 GGATTAAAATGATGCAAAT-ATCCTCAACCA
1 GGATTAAAATAAAGC-AATGATCCTCAACCA
2999 GGATTAAAAT-AA-C---GATCCTCAACCA
1 GGATTAAAATAAAGCAATGATCCTCAACCA
* * *
3024 GGATTAAAATAAAGTAACGATCTTCAACCA
1 GGATTAAAATAAAGCAATGATCCTCAACCA
* * *
3054 GGATTAAAACAAAGCAAAGATCCTCAAACA
1 GGATTAAAATAAAGCAATGATCCTCAACCA
*
3084 GGATTAAAATAAAGCAACGATCCTCAACCA
1 GGATTAAAATAAAGCAATGATCCTCAACCA
* * *
3114 GGAGTAAAATAAAGCAAAGATCCTCAAACA
1 GGATTAAAATAAAGCAATGATCCTCAACCA
* *
3144 GGATTAAAACAAAGCAACGATCCTCAACCA
1 GGATTAAAATAAAGCAATGATCCTCAACCA
* * * *
3174 GGATTAAAACAAAACAACGATCCTCAAACA
1 GGATTAAAATAAAGCAATGATCCTCAACCA
* * *
3204 GGATTAAGATAGAGCAACGATCCTCAACCA
1 GGATTAAAATAAAGCAATGATCCTCAACCA
* *
3234 GGATTAAAATAAAGCAACGATCCTCAAACA
1 GGATTAAAATAAAGCAATGATCCTCAACCA
* * *
3264 GGATTAAGATAAAGCAAAGATCCTCAAACA
1 GGATTAAAATAAAGCAATGATCCTCAACCA
* * * * * *
3294 TGATTAAATTGATGCAAAT-ATCTTC-AGCA
1 GGATTAAAATAAAGC-AATGATCCTCAACCA
3323 GGATTAAAATAAAGCAATGATCCTCTAA-CA
1 GGATTAAAATAAAGCAATGATCCTC-AACCA
3353 GGATTAAAATAAA
1 GGATTAAAATAAA
3366 ATTGATAAAG
Statistics
Matches: 721, Mismatches: 89, Indels: 58
0.83 0.10 0.07
Matches are distributed among these distances:
23 12 0.02
25 22 0.03
26 29 0.04
28 13 0.02
29 24 0.03
30 552 0.77
31 69 0.10
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.20
Consensus pattern (30 bp):
GGATTAAAATAAAGCAATGATCCTCAACCA
Found at i:3703 original size:68 final size:68
Alignment explanation
Indices: 3613--3782 Score: 277
Period size: 68 Copynumber: 2.5 Consensus size: 68
3603 GTAAGGCTTG
* * *
3613 ACTCATATGGAAACGAATTTGGCTTGTGGAAAAGCCTATATGGCTTGGATGGAACCAAGGCTTAA
1 ACTCATATGG-GACGAGTTTGGCTTGTGGAAAAGCCCATATGGCTTGGATGGAACCAAGGCTTAA
3678 ACTA
65 ACTA
*
3682 ACTCGTATGGGACGAGTTTGGCTTGTGGAAAAGCCCATATGGCTTGGATGGAACCAAGGCTTAAA
1 ACTCATATGGGACGAGTTTGGCTTGTGGAAAAGCCCATATGGCTTGGATGGAACCAAGGCTTAAA
*
3747 CTG
66 CTA
*
3750 ACTCATATGGGACGAGTTTGGCTTATGGAAAAG
1 ACTCATATGGGACGAGTTTGGCTTGTGGAAAAG
3783 GCCAAAGCAT
Statistics
Matches: 94, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
68 85 0.90
69 9 0.10
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (68 bp):
ACTCATATGGGACGAGTTTGGCTTGTGGAAAAGCCCATATGGCTTGGATGGAACCAAGGCTTAAA
CTA
Found at i:4007 original size:35 final size:36
Alignment explanation
Indices: 3942--4022 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 36
3932 ATTTGCGGTA
* * *
3942 AACTGAAATAAACTGCAGAAAAGATCGCCCTGGATC
1 AACTGAAATAAACTGAAGAAAAGACCGCCCTGAATC
*
3978 AACTGAAATAAATTGAAG-AAAGACCGCCCTGAATC
1 AACTGAAATAAACTGAAGAAAAGACCGCCCTGAATC
4013 AACTGAAATA
1 AACTGAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 25 0.61
36 16 0.39
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.17
Consensus pattern (36 bp):
AACTGAAATAAACTGAAGAAAAGACCGCCCTGAATC
Done.