Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009888.1 Corchorus capsularis cultivar CVL-1 contig09909, 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: 72766
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:604 original size:22 final size:20
Alignment explanation
Indices: 579--619 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
569 GATGCCTTAT
579 AAAGTCAACCAAAGTCATTAAA
1 AAAGTC-ACCAAAGT-ATTAAA
*
601 AAAGTCACCATAGTATTAA
1 AAAGTCACCAAAGTATTAA
620 TGATATTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.51, C:0.17, G:0.10, T:0.22
Consensus pattern (20 bp):
AAAGTCACCAAAGTATTAAA
Found at i:3182 original size:12 final size:12
Alignment explanation
Indices: 3165--3189 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3155 AGCGATGCCT
3165 GGGAAAAGTGGG
1 GGGAAAAGTGGG
3177 GGGAAAAGTGGG
1 GGGAAAAGTGGG
3189 G
1 G
3190 CGAGAACGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.60, T:0.08
Consensus pattern (12 bp):
GGGAAAAGTGGG
Found at i:36606 original size:7 final size:8
Alignment explanation
Indices: 36572--36604 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
36562 ATCTTAATTT
36572 AACAAAAA
1 AACAAAAA
36580 AACAAAAA
1 AACAAAAA
36588 AACAAAAA
1 AACAAAAA
36596 AACAAAAA
1 AACAAAAA
36604 A
1 A
36605 CACACGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AACAAAAA
Found at i:43755 original size:27 final size:27
Alignment explanation
Indices: 43713--43770 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
43703 GAATGAACAG
*
43713 AAATGGCGGATTGTTCAAAATTACAAT
1 AAATGGCGGATCGTTCAAAATTACAAT
43740 AAATGGCGGATCGTTCAAAATTACAAT
1 AAATGGCGGATCGTTCAAAATTACAAT
43767 AAAT
1 AAAT
43771 TGAGAAGTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (27 bp):
AAATGGCGGATCGTTCAAAATTACAAT
Found at i:45478 original size:41 final size:41
Alignment explanation
Indices: 45421--45499 Score: 133
Period size: 41 Copynumber: 1.9 Consensus size: 41
45411 TATAACTATA
*
45421 GGCTAAATCTGGATTTAATTT-TTTACCTTAATTATTAGGGG
1 GGCTAAACCTGGATTTAATTTATTT-CCTTAATTATTAGGGG
45462 GGCTAAACCTGGATTTAATTTATTTCCTTAATTATTAG
1 GGCTAAACCTGGATTTAATTTATTTCCTTAATTATTAG
45500 AAGGGTCAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
41 33 0.92
42 3 0.08
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.44
Consensus pattern (41 bp):
GGCTAAACCTGGATTTAATTTATTTCCTTAATTATTAGGGG
Found at i:46502 original size:93 final size:93
Alignment explanation
Indices: 46342--46527 Score: 311
Period size: 93 Copynumber: 2.0 Consensus size: 93
46332 TTCCCGATTT
* *
46342 TCAATTAAGGACACAAGAGTTGCAAACGATGGATTTTGATCTATTTATGGCACCATATGGTTGGA
1 TCAATTAAGGACAC-AGAGTTGAAAACGATGGATTTTGATCGATTTATGGCACCATATGGTTGGA
*
46407 GCCAAATCCTAGAGTAATATTATTGGTTC
65 GCCAAATCCTAGAGTAATATTAATGGTTC
46436 TCAATTAAGGACAGC-GAGTTGAAAACGATGGATTTTGATCGATTTATGGCACCATATGGTTGGA
1 TCAATTAAGGACA-CAGAGTTGAAAACGATGGATTTTGATCGATTTATGGCACCATATGGTTGGA
*
46500 GCCATATCCTAGAGTAATATTAATGGTT
65 GCCAAATCCTAGAGTAATATTAATGGTT
46528 TTATGGCGTG
Statistics
Matches: 87, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
93 73 0.84
94 13 0.15
95 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (93 bp):
TCAATTAAGGACACAGAGTTGAAAACGATGGATTTTGATCGATTTATGGCACCATATGGTTGGAG
CCAAATCCTAGAGTAATATTAATGGTTC
Found at i:47157 original size:23 final size:22
Alignment explanation
Indices: 47126--47168 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
47116 TTCTTGTTTG
*
47126 ATCAACCTTGTTTTTACTTTTTC
1 ATCAACCTTGTTCTTA-TTTTTC
*
47149 ATCACCCTTGTTCTTATTTT
1 ATCAACCTTGTTCTTATTTT
47169 AAAGTTGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.16, C:0.23, G:0.05, T:0.56
Consensus pattern (22 bp):
ATCAACCTTGTTCTTATTTTTC
Found at i:58590 original size:15 final size:16
Alignment explanation
Indices: 58561--58590 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58551 TTTTGGGTCC
58561 TTTTTTTTCCTCTTTT
1 TTTTTTTTCCTCTTTT
58577 TTTTTTTTCC-CTTT
1 TTTTTTTTCCTCTTT
58591 CTATGTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTTTCCTCTTTT
Found at i:71146 original size:31 final size:29
Alignment explanation
Indices: 71071--71149 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 29
71061 ACTTATAGCG
* * *
71071 TTTGGATATTTTGCCCCATGGACTTCAAT
1 TTTGGACATTTTGCCCCCTGAACTTCAAT
71100 TTTGGACATTTTGCCCCCTGAACTTCAATT
1 TTTGGACATTTTGCCCCCTGAACTTCAA-T
*
71130 TTTGGGACGTTTTGCCCCCT
1 TTT-GGACATTTTGCCCCCT
71150 TAAGCTAACG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 25 0.57
30 4 0.09
31 15 0.34
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.41
Consensus pattern (29 bp):
TTTGGACATTTTGCCCCCTGAACTTCAAT
Found at i:71346 original size:29 final size:29
Alignment explanation
Indices: 71300--71371 Score: 110
Period size: 29 Copynumber: 2.4 Consensus size: 29
71290 TAGTCTAAAA
71300 GGCAAAACGTCCCAAAATTGAAGT-TGAGGG
1 GGCAAAACGT-CCAAAATTGAAGTCT-AGGG
*
71330 GGCAAAATGTCCAAAATTGAAGTCTAGGG
1 GGCAAAACGTCCAAAATTGAAGTCTAGGG
71359 GGCAAAACGTCCA
1 GGCAAAACGTCCA
71372 GACGCTACAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
29 29 0.74
30 10 0.26
ACGTcount: A:0.38, C:0.18, G:0.28, T:0.17
Consensus pattern (29 bp):
GGCAAAACGTCCAAAATTGAAGTCTAGGG
Found at i:72747 original size:1 final size:1
Alignment explanation
Indices: 72741--72766 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
72731 ACTGATATTT
72741 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.