Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011354.1 Corchorus capsularis cultivar CVL-1 contig11375, 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: 33679
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8705 original size:29 final size:29
Alignment explanation
Indices: 8673--8743 Score: 117
Period size: 29 Copynumber: 2.4 Consensus size: 29
8663 CACCTTTTAC
*
8673 AAATTTTAATTTTTCT-AGCTCTTAAAATA
1 AAATTTTAATTTTTCTAATC-CTTAAAATA
8702 AAATTTTAATTTTTCTAATCCTTAAAATA
1 AAATTTTAATTTTTCTAATCCTTAAAATA
8731 AAATTTTAATTTT
1 AAATTTTAATTTT
8744 AATTTGAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 38 0.95
30 2 0.05
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.51
Consensus pattern (29 bp):
AAATTTTAATTTTTCTAATCCTTAAAATA
Found at i:10425 original size:39 final size:39
Alignment explanation
Indices: 10371--10450 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
10361 GCTTGCCAGG
10371 TTGCTATTGTTTCCTTTCGAGTGTTCTTGAATTTAGAAT
1 TTGCTATTGTTTCCTTTCGAGTGTTCTTGAATTTAGAAT
10410 TTGCTATTGTTTCCTTTCGAGTGTTCTTGAATTTAGAAT
1 TTGCTATTGTTTCCTTTCGAGTGTTCTTGAATTTAGAAT
10449 TT
1 TT
10451 TTTCAGTAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.53
Consensus pattern (39 bp):
TTGCTATTGTTTCCTTTCGAGTGTTCTTGAATTTAGAAT
Found at i:16031 original size:22 final size:22
Alignment explanation
Indices: 16006--16050 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
15996 TCACATGTGG
*
16006 AATTAACATATTAATGTA-TCTA
1 AATTAAAATATTAAT-TATTCTA
16028 AATTAAAATATTAATTATTCTA
1 AATTAAAATATTAATTATTCTA
16050 A
1 A
16051 TTGGGATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (22 bp):
AATTAAAATATTAATTATTCTA
Found at i:19017 original size:19 final size:18
Alignment explanation
Indices: 18993--19030 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
18983 ATTTCTTTAA
*
18993 TTTTCGGTATTTTGAGATT
1 TTTTCGGTATCTTG-GATT
19012 TTTTCGGTATCTTGGATT
1 TTTTCGGTATCTTGGATT
19030 T
1 T
19031 GAAAGCTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.13, C:0.08, G:0.21, T:0.58
Consensus pattern (18 bp):
TTTTCGGTATCTTGGATT
Found at i:19356 original size:149 final size:149
Alignment explanation
Indices: 19081--19379 Score: 589
Period size: 149 Copynumber: 2.0 Consensus size: 149
19071 ACCAAGTTTT
19081 TGTGACTTTCATGACTGGTATGATCCAAAAATTCCTGGAAGAGCAAGAGAGATTATATTGGAGCT
1 TGTGACTTTCATGACTGGTATGATCCAAAAATTCCTGGAAGAGCAAGAGAGATTATATTGGAGCT
19146 GAAGAATAGAGAATGGTTCTTGTTTAATCAAGCAAGGATGTTGAAGCAAGAACTGTCAGAAATGA
66 GAAGAATAGAGAATGGTTCTTGTTTAATCAAGCAAGGATGTTGAAGCAAGAACTGTCAGAAATGA
19211 AGGAAAATGCGGTTCACAA
131 AGGAAAATGCGGTTCACAA
19230 TGTGACTTTCATGACTGGTATGATCCAAAAATTCCTGGAAGAGCAAGAGAGATTATATTGGAGCT
1 TGTGACTTTCATGACTGGTATGATCCAAAAATTCCTGGAAGAGCAAGAGAGATTATATTGGAGCT
*
19295 GAAGAATAGAGAATGGTTCTTGTTTAATCAAGCAAGGATGTTGAAGCAAGAACTGTTAGAAATGA
66 GAAGAATAGAGAATGGTTCTTGTTTAATCAAGCAAGGATGTTGAAGCAAGAACTGTCAGAAATGA
19360 AGGAAAATGCGGTTCACAA
131 AGGAAAATGCGGTTCACAA
19379 T
1 T
19380 TTGGAGGCTG
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 149 1.00
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (149 bp):
TGTGACTTTCATGACTGGTATGATCCAAAAATTCCTGGAAGAGCAAGAGAGATTATATTGGAGCT
GAAGAATAGAGAATGGTTCTTGTTTAATCAAGCAAGGATGTTGAAGCAAGAACTGTCAGAAATGA
AGGAAAATGCGGTTCACAA
Found at i:19729 original size:26 final size:26
Alignment explanation
Indices: 19700--19764 Score: 112
Period size: 26 Copynumber: 2.5 Consensus size: 26
19690 ACAATTTAAA
*
19700 AGGCTTAAAATTCGTTGCCAAATAAT
1 AGGCTTGAAATTCGTTGCCAAATAAT
*
19726 AGGCTTGAAATTCGTTGCCATATAAT
1 AGGCTTGAAATTCGTTGCCAAATAAT
19752 AGGCTTGAAATTC
1 AGGCTTGAAATTC
19765 TGCAAATATC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 37 1.00
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (26 bp):
AGGCTTGAAATTCGTTGCCAAATAAT
Found at i:23589 original size:40 final size:40
Alignment explanation
Indices: 23545--23625 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
23535 ATAACATAAC
*
23545 AATTCAAACCCAGAAATATAGTCATATTTCAATCCCAGAA
1 AATTCAAACCAAGAAATATAGTCATATTTCAATCCCAGAA
23585 AATTCAAACCAAGAAATATAGTCATATTTCAATCCCAGAA
1 AATTCAAACCAAGAAATATAGTCATATTTCAATCCCAGAA
23625 A
1 A
23626 TATATAACAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.25
Consensus pattern (40 bp):
AATTCAAACCAAGAAATATAGTCATATTTCAATCCCAGAA
Found at i:23682 original size:15 final size:15
Alignment explanation
Indices: 23662--23691 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
23652 AAACAGAGCT
23662 TTTTAAACCCAGAAA
1 TTTTAAACCCAGAAA
23677 TTTTAAACCCAGAAA
1 TTTTAAACCCAGAAA
23692 ACCCAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (15 bp):
TTTTAAACCCAGAAA
Found at i:24016 original size:11 final size:10
Alignment explanation
Indices: 23999--24035 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
23989 ATCGAGTTCG
23999 AAGAGAGAGA
1 AAGAGAGAGA
24009 ACAGAGAGA-A
1 A-AGAGAGAGA
24019 AAGAGAGAGA
1 AAGAGAGAGA
24029 AA-AGAGA
1 AAGAGAGA
24036 AATTCTCGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 12 0.48
10 6 0.24
11 7 0.28
ACGTcount: A:0.62, C:0.03, G:0.35, T:0.00
Consensus pattern (10 bp):
AAGAGAGAGA
Found at i:24085 original size:23 final size:24
Alignment explanation
Indices: 24035--24087 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
24025 GAGAAAAGAG
* *
24035 AAATTCTCGGGTTGAAAGGGGTTT
1 AAATTTTCGGGCTGAAAGGGGTTT
24059 -AATTTTCGGGCTGAAA-GGGTTT
1 AAATTTTCGGGCTGAAAGGGGTTT
24081 AAATTTT
1 AAATTTT
24088 TTTAACCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.26, C:0.08, G:0.28, T:0.38
Consensus pattern (24 bp):
AAATTTTCGGGCTGAAAGGGGTTT
Found at i:24357 original size:31 final size:30
Alignment explanation
Indices: 24281--24367 Score: 104
Period size: 29 Copynumber: 2.9 Consensus size: 30
24271 CCAAATTGGA
*
24281 CCATTTATAAAAGGTTTGGTACTAAATCGG
1 CCATTTATAAAAGGTTTGGTACTAAATCGC
* **
24311 ACA-AAATAAAAGGTTTGGTACTAAATCGC
1 CCATTTATAAAAGGTTTGGTACTAAATCGC
* *
24340 CCATTTCATGAAAGGTTTGGTACCAAAT
1 CCATTT-ATAAAAGGTTTGGTACTAAAT
24368 TGAGATTTCA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 25 0.54
30 2 0.04
31 19 0.41
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (30 bp):
CCATTTATAAAAGGTTTGGTACTAAATCGC
Found at i:29429 original size:29 final size:31
Alignment explanation
Indices: 29396--29459 Score: 105
Period size: 29 Copynumber: 2.1 Consensus size: 31
29386 TGCCAATTTA
*
29396 GAAATATGTTTTAAAAA-AA-GGTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
29425 GAAATATGTTTTAAAAATAAGGGTACAATCG
1 GAAATATGTTTTAAAAATAAGGGTACAATCG
29456 GAAA
1 GAAA
29460 ACATAAAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 17 0.53
30 2 0.06
31 13 0.41
ACGTcount: A:0.48, C:0.05, G:0.19, T:0.28
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATCG
Found at i:29677 original size:32 final size:33
Alignment explanation
Indices: 29614--29677 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
29604 AAACCCAATC
*
29614 CGAACCCGAATCAACCTGAACTCAAATTTAACT
1 CGAACCCGAATCAACCTGAACCCAAATTTAACT
*
29647 CGAACCCGAATCAAGCTG-ACCCAAATTTAAC
1 CGAACCCGAATCAACCTGAACCCAAATTTAAC
29678 CCAACCTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.39, C:0.31, G:0.11, T:0.19
Consensus pattern (33 bp):
CGAACCCGAATCAACCTGAACCCAAATTTAACT
Found at i:32885 original size:21 final size:21
Alignment explanation
Indices: 32861--32900 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
32851 TTATAACTTC
*
32861 ACTTATGGAATCAATATATCA
1 ACTTATGAAATCAATATATCA
*
32882 ACTTATGAAATTAATATAT
1 ACTTATGAAATCAATATAT
32901 TAATTTATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (21 bp):
ACTTATGAAATCAATATATCA
Found at i:32908 original size:21 final size:21
Alignment explanation
Indices: 32863--32927 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
32853 ATAACTTCAC
* * * *
32863 TTATGGAATCAATATATCAAC
1 TTATGAAATTAATATATTAAT
32884 TTATGAAATTAATATATTAAT
1 TTATGAAATTAATATATTAAT
* * *
32905 TTATCTAGATTAATATGTTAAT
1 TTAT-GAAATTAATATATTAAT
32927 T
1 T
32928 ATTCCAATTG
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
21 21 0.58
22 15 0.42
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.45
Consensus pattern (21 bp):
TTATGAAATTAATATATTAAT
Done.