Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010283.1 Corchorus capsularis cultivar CVL-1 contig10304, 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: 41274
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3137 original size:30 final size:30
Alignment explanation
Indices: 3097--3170 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
3087 CGTTAGATTG
*
3097 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
1 AGGGGGCAAAACGTCCCAAAATTAAAGTTC
* * *
3127 AGGGGACAAAATGT-CCAAAATTAAAGTTG
1 AGGGGGCAAAACGTCCCAAAATTAAAGTTC
*
3156 AGGGGGTAAAACGTC
1 AGGGGGCAAAACGTC
3171 TAAACAATAC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
29 24 0.67
30 12 0.33
ACGTcount: A:0.39, C:0.15, G:0.28, T:0.18
Consensus pattern (30 bp):
AGGGGGCAAAACGTCCCAAAATTAAAGTTC
Found at i:19737 original size:14 final size:14
Alignment explanation
Indices: 19718--19744 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19708 ACCGCCACCG
19718 CCTCTCTCTCTCCC
1 CCTCTCTCTCTCCC
19732 CCTCTCTCTCTCC
1 CCTCTCTCTCTCC
19745 TCCATCTTCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (14 bp):
CCTCTCTCTCTCCC
Found at i:23999 original size:21 final size:21
Alignment explanation
Indices: 23975--24019 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
23965 ATACCTCTAC
23975 AAGGCAAA-AGAAAAAAACAAA
1 AAGGCAAAGAGAAAAAAA-AAA
*
23996 AAGGGAAATGAGAAAAAAAAAA
1 AAGGCAAA-GAGAAAAAAAAAA
24018 AA
1 AA
24020 CAAATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 7 0.33
22 5 0.24
23 9 0.43
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (21 bp):
AAGGCAAAGAGAAAAAAAAAA
Found at i:29993 original size:8 final size:8
Alignment explanation
Indices: 29980--30039 Score: 56
Period size: 8 Copynumber: 7.8 Consensus size: 8
29970 AAAAAAAAAA
29980 TATATAAT
1 TATATAAT
29988 TATATAAT
1 TATATAAT
29996 TATAT-AT
1 TATATAAT
30003 T-TAT-AT
1 TATATAAT
30009 TATATTATAT
1 TATA-TA-AT
30019 TATAT-AT
1 TATATAAT
*
30026 TGTATAAT
1 TATATAAT
*
30034 AATATA
1 TATATA
30040 TATAGTTTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
6 6 0.14
7 11 0.25
8 20 0.45
9 1 0.02
10 6 0.14
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (8 bp):
TATATAAT
Found at i:33761 original size:28 final size:29
Alignment explanation
Indices: 33729--33783 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
33719 TTTTTTGTAA
*
33729 TTTTGGTATAA-GATTTTGTTGTTATTTT
1 TTTTGGTAAAACGATTTTGTTGTTATTTT
*
33757 TTTTGGTAAAACTATTTTGTTGTTATT
1 TTTTGGTAAAACGATTTTGTTGTTATT
33784 GACTGCTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.20, C:0.02, G:0.16, T:0.62
Consensus pattern (29 bp):
TTTTGGTAAAACGATTTTGTTGTTATTTT
Found at i:34292 original size:54 final size:54
Alignment explanation
Indices: 34200--34327 Score: 195
Period size: 54 Copynumber: 2.4 Consensus size: 54
34190 ATGAATGGAA
* *
34200 CTCAATGTCCTTATCTAAGGTTTTGGGCTTGAGCAAGTGCTGAGAGAGGTTCTT
1 CTCAATGTCCTTAACTAAGGTTTTGGGCTTGAACAAGTGCTGAGAGAGGTTCTT
* * *
34254 CTGAATGTCCTTAACTAAGGTTTTGGGTTTGAATAAGTGCTGAGAGAGGTTCTT
1 CTCAATGTCCTTAACTAAGGTTTTGGGCTTGAACAAGTGCTGAGAGAGGTTCTT
*
34308 CTCAA-GTCTTTAACTAAGGT
1 CTCAATGTCCTTAACTAAGGT
34328 ATCGAAGTTG
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
53 14 0.21
54 53 0.79
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (54 bp):
CTCAATGTCCTTAACTAAGGTTTTGGGCTTGAACAAGTGCTGAGAGAGGTTCTT
Found at i:34348 original size:53 final size:54
Alignment explanation
Indices: 34200--34348 Score: 144
Period size: 54 Copynumber: 2.8 Consensus size: 54
34190 ATGAATGGAA
* * * * *
34200 CTCAATGTCCTTATCTAAGGTTTTGGGCTTG-AGCAAGTGCTGAGAGAGGTTCTT
1 CTCAATGTCCTTAACTAAGGTATCGAGTTTGAAG-AAGTGCTGAGAGAGGTTCTT
* * * * *
34254 CTGAATGTCCTTAACTAAGGTTTTGGGTTTGAATAAGTGCTGAGAGAGGTTCTT
1 CTCAATGTCCTTAACTAAGGTATCGAGTTTGAAGAAGTGCTGAGAGAGGTTCTT
*
34308 CTCAA-GTCTTTAACTAAGGTATCGAAG-TTGAACGAA-TGCTG
1 CTCAATGTCCTTAACTAAGGTATCG-AGTTTGAA-GAAGTGCTG
34349 CCTCTCAAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
53 26 0.32
54 55 0.67
55 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (54 bp):
CTCAATGTCCTTAACTAAGGTATCGAGTTTGAAGAAGTGCTGAGAGAGGTTCTT
Found at i:38459 original size:2 final size:2
Alignment explanation
Indices: 38452--38476 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38442 GGTAAGCTTC
38452 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
38477 CACTTTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39186 original size:2 final size:2
Alignment explanation
Indices: 39179--39205 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39169 ACTTTTATTA
39179 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
39206 AGTTCTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.