Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024419.1 Corchorus olitorius cultivar O-4 contig24452, 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: 9721
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:445 original size:21 final size:21
Alignment explanation
Indices: 419--460 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
409 ATTCATAAAC
419 CAACGAATAATTATTACAAAT
1 CAACGAATAATTATTACAAAT
440 CAACGAATAATTATTACAAAT
1 CAACGAATAATTATTACAAAT
461 TTAACAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (21 bp):
CAACGAATAATTATTACAAAT
Found at i:2405 original size:60 final size:60
Alignment explanation
Indices: 2279--2411 Score: 137
Period size: 60 Copynumber: 2.2 Consensus size: 60
2269 ACGTTAGGAT
* * * *
2279 CTTATTTAACCAAATTCAAAACATGGACCCTGAATTAAGCATTTTCGCATGCGTTAAGGC
1 CTTATTTAACAAAATTCAAAACATGGACCCTAAATTAAGCATTTTCGCATACATTAAGGC
* * * *
2339 CTTATTTAACAAAATT-AAAAGTAT-GAGCCCTAAATTGAGCATTTTTGCATACATTAGGGAC
1 CTTATTTAACAAAATTCAAAA-CATGGA-CCCTAAATTAAGCATTTTCGCATACATTAAGG-C
2400 C-TATTTGAACAA
1 CTTATTT-AACAA
2412 TTGACCAAGA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
59 6 0.10
60 48 0.79
61 7 0.11
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (60 bp):
CTTATTTAACAAAATTCAAAACATGGACCCTAAATTAAGCATTTTCGCATACATTAAGGC
Found at i:2615 original size:22 final size:22
Alignment explanation
Indices: 2590--2776 Score: 118
Period size: 22 Copynumber: 8.4 Consensus size: 22
2580 ACAAAAAGTA
2590 CATAGGAAGGTTATCAAAATTT
1 CATAGGAAGGTTATCAAAATTT
* *
2612 CATA-GAGTGGTTACCAAAATTT
1 CATAGGA-AGGTTATCAAAATTT
*
2634 CATATGGAA-GTTATCAAAACTT
1 CATA-GGAAGGTTATCAAAATTT
*
2656 CATAGTGCA-GTTATCAAAATTT
1 CATAG-GAAGGTTATCAAAATTT
*
2678 CATA--AAGAGATTACCAAAATTT
1 CATAGGAAG-G-TTATCAAAATTT
* ** *
2700 TATAAAAAATGTTATCAAAATTT
1 CAT-AGGAAGGTTATCAAAATTT
* * *
2723 -ATTAGGGAGGTTATGAAACTTT
1 CA-TAGGAAGGTTATCAAAATTT
* *
2745 TAT-GGAGAGGTTATCAAAATTA
1 CATAGGA-AGGTTATCAAAATTT
2767 CATAGAGAAG
1 CATAG-GAAG
2777 ATATCACAGT
Statistics
Matches: 127, Mismatches: 23, Indels: 29
0.71 0.13 0.16
Matches are distributed among these distances:
19 1 0.01
21 6 0.05
22 96 0.76
23 17 0.13
24 5 0.04
25 2 0.02
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.32
Consensus pattern (22 bp):
CATAGGAAGGTTATCAAAATTT
Found at i:2857 original size:22 final size:22
Alignment explanation
Indices: 2832--2951 Score: 116
Period size: 22 Copynumber: 5.5 Consensus size: 22
2822 TGCGGTTACC
*
2832 AATTTTATAGTGTGATTATCAA
1 AATTTCATAGTGTGATTATCAA
* * *
2854 AATTTTATAGAGAGATTATCAA
1 AATTTCATAGTGTGATTATCAA
* * * *
2876 AATTTCACACTGAGGTTATCAA
1 AATTTCATAGTGTGATTATCAA
* *
2898 AATTTCATAATGTGCTTATCAA
1 AATTTCATAGTGTGATTATCAA
* *
2920 AATTTCACAGTGTGGTTATC-A
1 AATTTCATAGTGTGATTATCAA
2941 AATTTCCATAG
1 AATTT-CATAG
2952 GGAGGTTATT
Statistics
Matches: 82, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
21 6 0.07
22 76 0.93
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (22 bp):
AATTTCATAGTGTGATTATCAA
Found at i:2967 original size:44 final size:44
Alignment explanation
Indices: 2840--2970 Score: 140
Period size: 44 Copynumber: 3.0 Consensus size: 44
2830 CCAATTTTAT
* *
2840 AGTGTGATTATCAAAATTTTATAGAGAGATTATCAAAATTTCAC
1 AGTGTGGTTATCAAAATTTCATAGAGAGATTATCAAAATTTCAC
* * * *
2884 ACTGAGGTTATCAAAATTTCATA-ATGTGCTTATCAAAATTTCAC
1 AGTGTGGTTATCAAAATTTCATAGA-GAGATTATCAAAATTTCAC
* * **
2928 AGTGTGGTTATC-AAATTTCCATAGGGAGGTTATTGAAATTTCA
1 AGTGTGGTTATCAAAATTT-CATAGAGAGATTATCAAAATTTCA
2971 TACATATATA
Statistics
Matches: 71, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
43 7 0.10
44 64 0.90
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (44 bp):
AGTGTGGTTATCAAAATTTCATAGAGAGATTATCAAAATTTCAC
Found at i:3853 original size:28 final size:28
Alignment explanation
Indices: 3811--3865 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
3801 CGTCGTGTTA
3811 GTTTATACTCAATCGCAGAGTTCTTATG
1 GTTTATACTCAATCGCAGAGTTCTTATG
* * *
3839 GTTTTTACTCCATCGCGGAGTTCTTAT
1 GTTTATACTCAATCGCAGAGTTCTTAT
3866 ACTCCATTCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (28 bp):
GTTTATACTCAATCGCAGAGTTCTTATG
Found at i:3879 original size:20 final size:21
Alignment explanation
Indices: 3844--3883 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3834 TTATGGTTTT
3844 TACTCCATCGCGGAGTTCTTA
1 TACTCCATCGCGGAGTTCTTA
*
3865 TACTCCAT-TCGGAGTTCTT
1 TACTCCATCGCGGAGTTCTT
3884 GTAGTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (21 bp):
TACTCCATCGCGGAGTTCTTA
Done.