Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008065.1 Corchorus capsularis cultivar CVL-1 contig08086, 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: 40320
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--38 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
39 ATCAAAGCAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5255 original size:2 final size:2
Alignment explanation
Indices: 5248--5275 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5238 TTGCAAATTA
5248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5276 TCTACGTAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8290 original size:3 final size:3
Alignment explanation
Indices: 8282--8321 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
8272 GTGGACAATA
8282 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
8322 GCGGTCTATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:17967 original size:20 final size:21
Alignment explanation
Indices: 17942--17987 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
17932 AATTAAAGTT
* *
17942 TCAACCACCTTAATTGA-CAC
1 TCAACCACCTAAATTAATCAC
17962 TCAACCACCTAAATTAATCAC
1 TCAACCACCTAAATTAATCAC
17983 TCAAC
1 TCAAC
17988 AAGGGGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.39, C:0.35, G:0.02, T:0.24
Consensus pattern (21 bp):
TCAACCACCTAAATTAATCAC
Found at i:19068 original size:1 final size:1
Alignment explanation
Indices: 19062--19086 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
19052 ACACTGAGGG
19062 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
19087 GAAACTAGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19568 original size:20 final size:20
Alignment explanation
Indices: 19543--19581 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
19533 GCGTACGCAA
19543 GGTCTCGAACCTAAGACCTG
1 GGTCTCGAACCTAAGACCTG
*
19563 GGTCTCGAACCTGAGACCT
1 GGTCTCGAACCTAAGACCT
19582 TAAGCTGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.21
Consensus pattern (20 bp):
GGTCTCGAACCTAAGACCTG
Found at i:23886 original size:29 final size:29
Alignment explanation
Indices: 23826--23889 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
23816 TTTCATTTTA
* * *
23826 ATATATATAGCTACTTTTTTTTTGGCAGT
1 ATATATATAGCTACTTTTTTGTGGGCACT
23855 ATATATATAGCTAC-TTTTTGTGGGCAACT
1 ATATATATAGCTACTTTTTTGTGGGC-ACT
23884 ATATAT
1 ATATAT
23890 TGAATAATTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (29 bp):
ATATATATAGCTACTTTTTTGTGGGCACT
Found at i:24510 original size:32 final size:32
Alignment explanation
Indices: 24468--24555 Score: 133
Period size: 32 Copynumber: 2.8 Consensus size: 32
24458 TGATGTCGCT
24468 AACGTGGCAATGCCACGTCATCGGTTTGGA-CC
1 AACGTGGCAATGCCACGTCATCGGTTT-GATCC
* * *
24500 GACGTGGCAATGTCACGTCATCGGTTTGATCT
1 AACGTGGCAATGCCACGTCATCGGTTTGATCC
24532 AACGTGGCAATGCCACGTCATCGG
1 AACGTGGCAATGCCACGTCATCGG
24556 CATGACGGTG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
31 2 0.04
32 48 0.96
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.24
Consensus pattern (32 bp):
AACGTGGCAATGCCACGTCATCGGTTTGATCC
Found at i:24664 original size:29 final size:30
Alignment explanation
Indices: 24594--24664 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 30
24584 GAGAGGGGGT
* *
24594 AAAACGTCCAAAATTGAGAATTTAGGAGGT
1 AAAACGTCCAAAATTGAGAATTCAGGAGGC
** *
24624 AAAGTGTTCAAAATTGA-AATTCAGGAGGC
1 AAAACGTCCAAAATTGAGAATTCAGGAGGC
*
24653 AAAACATCCAAA
1 AAAACGTCCAAA
24665 CGTTACAAGT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
29 18 0.56
30 14 0.44
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.21
Consensus pattern (30 bp):
AAAACGTCCAAAATTGAGAATTCAGGAGGC
Found at i:26290 original size:29 final size:31
Alignment explanation
Indices: 26257--26327 Score: 85
Period size: 29 Copynumber: 2.3 Consensus size: 31
26247 TATTGGGTCG
*
26257 AGGACGTTTTGTCC-CATGAACTT-CAAA-TC
1 AGGACATTTTG-CCTCATGAACTTCCAAATTC
*
26286 AGGACATTTTGCCTCCTGAACTTCCCAAATTC
1 AGGACATTTTGCCTCATGAACTT-CCAAATTC
26318 AGGACATTTT
1 AGGACATTTT
26328 ACCCCTTGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
28 2 0.06
29 18 0.50
31 4 0.11
32 12 0.33
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.32
Consensus pattern (31 bp):
AGGACATTTTGCCTCATGAACTTCCAAATTC
Found at i:34574 original size:3 final size:3
Alignment explanation
Indices: 34566--34591 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
34556 ATCCCTTTTC
34566 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
34592 CTTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:36237 original size:26 final size:29
Alignment explanation
Indices: 36185--36239 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 29
36175 TAATTGGAAT
*
36185 CAACTTAAGCTTTATTTAATCTTCAGGTTG
1 CAACTTAAGC-TTATTTAATCTACAGGTTG
36215 CAACTTAAGC-T-TTT-ATCTACAGGTT
1 CAACTTAAGCTTATTTAATCTACAGGTT
36240 TTGATATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 10 0.42
27 3 0.12
28 1 0.04
30 10 0.42
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (29 bp):
CAACTTAAGCTTATTTAATCTACAGGTTG
Found at i:40028 original size:32 final size:32
Alignment explanation
Indices: 39987--40206 Score: 415
Period size: 32 Copynumber: 6.9 Consensus size: 32
39977 AGGGCTAATT
39987 TGAATTAAGGCAAGTTCAATGTCATTTGGATG
1 TGAATTAAGGCAAGTTCAATGTCATTTGGATG
40019 TGAATTAAGGCAAGTTCAATGTCATTTGGATG
1 TGAATTAAGGCAAGTTCAATGTCATTTGGATG
40051 TGAATTAAGGCAAGTTCAATGTCATTTGGATG
1 TGAATTAAGGCAAGTTCAATGTCATTTGGATG
*
40083 TGGATTAAGGCAAGTTCAATGTCATTTGGATG
1 TGAATTAAGGCAAGTTCAATGTCATTTGGATG
*
40115 TGGATTAAGGCAAGTTCAATGTCATTTGGATG
1 TGAATTAAGGCAAGTTCAATGTCATTTGGATG
40147 TG-ATTAAGGCAAGTTCAATGTCATTTGGATG
1 TGAATTAAGGCAAGTTCAATGTCATTTGGATG
40178 TGAATTAAGGCAAGTTCAATGTCATTTGG
1 TGAATTAAGGCAAGTTCAATGTCATTTGG
40207 GAAAGTTGAA
Statistics
Matches: 186, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
31 31 0.17
32 155 0.83
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.35
Consensus pattern (32 bp):
TGAATTAAGGCAAGTTCAATGTCATTTGGATG
Done.