Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008286.1 Corchorus capsularis cultivar CVL-1 contig08307, 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: 56798
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:3327 original size:17 final size:17
Alignment explanation
Indices: 3307--3340 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3297 AAGCATGTAA
3307 GTCTATTGATTTTTTTT
1 GTCTATTGATTTTTTTT
3324 GTCTATTGATTTTTTTT
1 GTCTATTGATTTTTTTT
3341 TTCATTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.06, G:0.12, T:0.71
Consensus pattern (17 bp):
GTCTATTGATTTTTTTT
Found at i:12815 original size:12 final size:12
Alignment explanation
Indices: 12799--12853 Score: 92
Period size: 12 Copynumber: 4.5 Consensus size: 12
12789 TTAATACAGG
*
12799 TATCGACGGATG
1 TATCGACGGATA
12811 TATCGACGGATA
1 TATCGACGGATA
12823 TATCGAACGGATA
1 TATCG-ACGGATA
12836 TATCGACGGATA
1 TATCGACGGATA
12848 TATCGA
1 TATCGA
12854 GGTATCGATG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
12 29 0.71
13 12 0.29
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:12834 original size:25 final size:25
Alignment explanation
Indices: 12799--12853 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
12789 TTAATACAGG
*
12799 TATCG-ACGGATGTATCGACGGATA
1 TATCGAACGGATATATCGACGGATA
12823 TATCGAACGGATATATCGACGGATA
1 TATCGAACGGATATATCGACGGATA
12848 TATCGA
1 TATCGA
12854 GGTATCGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 5 0.17
25 24 0.83
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (25 bp):
TATCGAACGGATATATCGACGGATA
Found at i:13602 original size:3 final size:3
Alignment explanation
Indices: 13594--13629 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
13584 TCATTCCCCC
*
13594 CAT CAT CAT CAT CAT TAT CAT CAT CAT CAT CA- CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
13630 TTCCGTGAGC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:14361 original size:12 final size:12
Alignment explanation
Indices: 14344--14382 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
14334 GTACAGATAT
14344 CGGATATATCGA
1 CGGATATATCGA
14356 CGGATATATCGA
1 CGGATATATCGA
14368 -GG---TATCGA
1 CGGATATATCGA
14376 CGGATAT
1 CGGATAT
14383 TTAATTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
11 2 0.09
12 13 0.57
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (12 bp):
CGGATATATCGA
Found at i:25125 original size:9 final size:8
Alignment explanation
Indices: 25080--25115 Score: 54
Period size: 9 Copynumber: 4.2 Consensus size: 8
25070 AGGAAAAAAG
25080 AAGAAGAA
1 AAGAAGAA
25088 AAGAAGGAA
1 AAGAA-GAA
25097 AAGAAGAA
1 AAGAAGAA
25105 AAGGAAGAA
1 AA-GAAGAA
25114 AA
1 AA
25116 AAAGGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 10 0.38
9 16 0.62
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (8 bp):
AAGAAGAA
Found at i:25936 original size:35 final size:35
Alignment explanation
Indices: 25894--26404 Score: 726
Period size: 35 Copynumber: 14.7 Consensus size: 35
25884 AGTAATAAGT
* *
25894 AACTTAATTCAGGGCAATTAACTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
* *
25929 AACTTAATTCATGGTAATTAAGTGAGTCAGTAATA
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
*
25964 AACTTAATTCAGAGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
*
25999 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
* * *
26034 AACTTAATTCAGGGTAATTAAGTAAGTAAGTAATA
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
* * *
26069 AACTTAATTTAGGGTAATTATGTGAGTCAGTAATA
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
26104 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
* *
26139 AACTTAATTCAGGGTAATTAAGTAACTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
* * *
26174 AACTTAATTCAGGGTAATTAAGTAAGTAAGTAATA
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
*
26209 AACTTAATTCAGGGTAATTGAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
* *
26244 AACTTAATTCAGGGTAATTAAGTAATTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
26279 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
* ** *
26314 AACTTTAATTCGGGGTAATTAAGTGA-TTTG-AGT-
1 AAC-TTAATTCAGGGTAATTAAGTGAGTCAGTAATC
*
26347 AACTTAATTCAGGGTAATTAAGT-AGTTCAATAAGT-
1 AACTTAATTCAGGGTAATTAAGTGAG-TCAGTAA-TC
*
26382 AACTTAATTTAGGGTAATTAAGT
1 AACTTAATTCAGGGTAATTAAGT
26405 TTAGTAAGAA
Statistics
Matches: 429, Mismatches: 42, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
31 1 0.00
32 19 0.04
33 4 0.01
34 3 0.01
35 381 0.89
36 21 0.05
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (35 bp):
AACTTAATTCAGGGTAATTAAGTGAGTCAGTAATC
Found at i:28666 original size:19 final size:19
Alignment explanation
Indices: 28642--28679 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
28632 CTTAGAATTA
28642 GAGTAG-TCTTGTAACTTAG
1 GAGTAGTTCTT-TAACTTAG
28661 GAGTAGTTCTTTAACTTAG
1 GAGTAGTTCTTTAACTTAG
28680 CATTTTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (19 bp):
GAGTAGTTCTTTAACTTAG
Found at i:34094 original size:33 final size:33
Alignment explanation
Indices: 34047--34116 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
34037 AGGATTTTTA
34047 TAAAATAGATAAAGTTGAAGGGCTAAATCAAGT
1 TAAAATAGATAAAGTTGAAGGGCTAAATCAAGT
*
34080 TAAAGTAGATAAAGTTGAAGGGCTAAATCAAGT
1 TAAAATAGATAAAGTTGAAGGGCTAAATCAAGT
34113 TAAA
1 TAAA
34117 TGAAATAGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.49, C:0.06, G:0.21, T:0.24
Consensus pattern (33 bp):
TAAAATAGATAAAGTTGAAGGGCTAAATCAAGT
Found at i:34619 original size:2 final size:2
Alignment explanation
Indices: 34614--34649 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
34604 GTTCCATATA
34614 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
34650 ATATATAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:35656 original size:12 final size:12
Alignment explanation
Indices: 35629--35662 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
35619 CGATTAAAAG
35629 TATAAT-ATAA-
1 TATAATAATAAT
35639 TATAATAATAAT
1 TATAATAATAAT
35651 TATAATAATAAT
1 TATAATAATAAT
35663 ATATCATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 6 0.27
11 4 0.18
12 12 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TATAATAATAAT
Found at i:39518 original size:12 final size:13
Alignment explanation
Indices: 39503--39532 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
39493 GAAAAATATC
39503 AAAAAAA-TAAAA
1 AAAAAAACTAAAA
39515 AAAAAAACTAAAA
1 AAAAAAACTAAAA
39528 AAAAA
1 AAAAA
39533 TTTCGACCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.90, C:0.03, G:0.00, T:0.07
Consensus pattern (13 bp):
AAAAAAACTAAAA
Found at i:42799 original size:17 final size:18
Alignment explanation
Indices: 42766--42799 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
42756 AAATTTATGG
*
42766 ATGTTTGATGTTGGTTTT
1 ATGTTTGATGATGGTTTT
42784 ATGTTT-ATGATGGTTT
1 ATGTTTGATGATGGTTT
42800 GGGGTTGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.15, C:0.00, G:0.26, T:0.59
Consensus pattern (18 bp):
ATGTTTGATGATGGTTTT
Found at i:49264 original size:10 final size:10
Alignment explanation
Indices: 49247--49281 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
49237 CTGAGAAAGA
49247 AAAGAGAGAG
1 AAAGAGAGAG
*
49257 AGAGAGAGAG
1 AAAGAGAGAG
*
49267 AAAAAGAGAG
1 AAAGAGAGAG
49277 AAAGA
1 AAAGA
49282 TTTTGCTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (10 bp):
AAAGAGAGAG
Found at i:50466 original size:28 final size:27
Alignment explanation
Indices: 50405--50472 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 27
50395 ATCCCTTCTG
*
50405 GGTAAAATTACAATGTTACCCTCGATT
1 GGTAAAATTACAATGTTACCCTCGAAT
* *
50432 GGTTAAAATTACCATTTTACCCTCGAAT
1 GG-TAAAATTACAATGTTACCCTCGAAT
50460 GAGT-AAATTACAA
1 G-GTAAAATTACAA
50473 CTTTGCCCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 10 0.29
28 24 0.69
29 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (27 bp):
GGTAAAATTACAATGTTACCCTCGAAT
Found at i:50842 original size:13 final size:14
Alignment explanation
Indices: 50819--50856 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
50809 TTACTCTGGT
*
50819 TTATGACTTTGATA
1 TTATGATTTTGATA
50833 -TATGATTTTGATA
1 TTATGATTTTGATA
50846 TTAATGATTTT
1 TT-ATGATTTT
50857 CTTGTATTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 12 0.57
14 1 0.05
15 8 0.38
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.55
Consensus pattern (14 bp):
TTATGATTTTGATA
Found at i:53116 original size:16 final size:16
Alignment explanation
Indices: 53076--53109 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
53066 TCAACCAATT
53076 TGAAAATTTTGGACTA
1 TGAAAATTTTGGACTA
53092 TGAAAATTTTGGACTA
1 TGAAAATTTTGGACTA
53108 TG
1 TG
53110 GTAATTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (16 bp):
TGAAAATTTTGGACTA
Found at i:55183 original size:30 final size:30
Alignment explanation
Indices: 55147--55251 Score: 106
Period size: 30 Copynumber: 3.5 Consensus size: 30
55137 TAATAGCCGG
*
55147 ATGTACATCCTGCGGCAATGGAATATATGC
1 ATGTACATCCTGCGGCAATGGAACATATGC
* *
55177 ATGTACATCCTGCAGCAGA-GGAACATCA-GT
1 ATGTACATCCTGCGGCA-ATGGAACAT-ATGC
* * * *
55207 TTGTAAATCCTACGGCAATGGAACATCTGC
1 ATGTACATCCTGCGGCAATGGAACATATGC
*
55237 CTGTACATCCTGCGG
1 ATGTACATCCTGCGG
55252 TTGAGCCGGA
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
29 1 0.02
30 56 0.95
31 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGTACATCCTGCGGCAATGGAACATATGC
Found at i:56157 original size:31 final size:33
Alignment explanation
Indices: 56119--56185 Score: 93
Period size: 34 Copynumber: 2.1 Consensus size: 33
56109 TCCCACTTTT
*
56119 TTTTTTTTTTTTG-C-AATCTTTGCAACCCTTG
1 TTTTTTTTTTTTGACAAATCTTTCCAACCCTTG
*
56150 TTTTTTTTTTTTGACAGAATCTTTCCCACCCTTG
1 TTTTTTTTTTTTGACA-AATCTTTCCAACCCTTG
56184 TT
1 TT
56186 AGAAAGCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 13 0.42
32 1 0.03
34 17 0.55
ACGTcount: A:0.13, C:0.21, G:0.09, T:0.57
Consensus pattern (33 bp):
TTTTTTTTTTTTGACAAATCTTTCCAACCCTTG
Done.