Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015922.1 Corchorus olitorius cultivar O-4 contig15955, 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: 37905
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1423 original size:17 final size:17
Alignment explanation
Indices: 1401--1437 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
1391 ATTGAAGAGG
1401 AAAGAAGAAGCGAAAAA
1 AAAGAAGAAGCGAAAAA
*
1418 AAAGAAGAGGCGAAAAA
1 AAAGAAGAAGCGAAAAA
1435 AAA
1 AAA
1438 AAGCAGAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.70, C:0.05, G:0.24, T:0.00
Consensus pattern (17 bp):
AAAGAAGAAGCGAAAAA
Found at i:1993 original size:23 final size:23
Alignment explanation
Indices: 1967--2010 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1957 AATACAAAGG
*
1967 CAATCTTACATTGAATTGAAACA
1 CAATCTTACATTGAATCGAAACA
* *
1990 CAATTTTACATTTAATCGAAA
1 CAATCTTACATTGAATCGAAA
2011 TTACTAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (23 bp):
CAATCTTACATTGAATCGAAACA
Found at i:8209 original size:21 final size:22
Alignment explanation
Indices: 8185--8233 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
8175 AATACCATTT
8185 TAAAGT-CCAGTTCAATCATAA
1 TAAAGTGCCAGTTCAATCATAA
* *
8206 TAAAAATTGCTAGTTCAATCATAA
1 T--AAAGTGCCAGTTCAATCATAA
8230 TAAA
1 TAAA
8234 AATTGCTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
21 1 0.04
22 3 0.13
23 4 0.17
24 15 0.65
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (22 bp):
TAAAGTGCCAGTTCAATCATAA
Found at i:8220 original size:24 final size:24
Alignment explanation
Indices: 8193--8254 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
8183 TTTAAAGTCC
8193 AGTTCAATCATAATAAAAATTGCT
1 AGTTCAATCATAATAAAAATTGCT
8217 AGTTCAATCATAATAAAAATTGCT
1 AGTTCAATCATAATAAAAATTGCT
8241 AGTTCAATCA-AATA
1 AGTTCAATCATAATA
8255 TCATTGTTGC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 4 0.11
24 34 0.89
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (24 bp):
AGTTCAATCATAATAAAAATTGCT
Found at i:11987 original size:48 final size:49
Alignment explanation
Indices: 11915--12011 Score: 160
Period size: 48 Copynumber: 2.0 Consensus size: 49
11905 ATTTAGTTAA
*
11915 TAATGACAGAATTCTCTATTAAAGTAATAAAAATAGTTAATACAACTTG
1 TAATGACAAAATTCTCTATTAAAGTAATAAAAATAGTTAATACAACTTG
* *
11964 TAAT-ACAAAATTCTCTGTTAAAGTAATAAAAATAGTTAATACAGCTTG
1 TAATGACAAAATTCTCTATTAAAGTAATAAAAATAGTTAATACAACTTG
12012 GCGTGTGTAC
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 41 0.91
49 4 0.09
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (49 bp):
TAATGACAAAATTCTCTATTAAAGTAATAAAAATAGTTAATACAACTTG
Found at i:27645 original size:29 final size:29
Alignment explanation
Indices: 27589--27647 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
27579 CTCCAAATTA
* *
27589 ATTAAATTTTAATGTAATCATCATATATC
1 ATTAAATTTTAATATAATCATCAGATATC
* *
27618 ATTAGATTTTAATATAATCATCGGATATC
1 ATTAAATTTTAATATAATCATCAGATATC
27647 A
1 A
27648 AGATATTTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (29 bp):
ATTAAATTTTAATATAATCATCAGATATC
Found at i:27655 original size:29 final size:29
Alignment explanation
Indices: 27594--27655 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
27584 AATTAATTAA
* * **
27594 ATTTTAATGTAATCATCATATATCATTAG
1 ATTTTAATATAATCATCAGATATCAAGAG
* *
27623 ATTTTAATATAATCATCGGATATCAAGAT
1 ATTTTAATATAATCATCAGATATCAAGAG
27652 ATTT
1 ATTT
27656 GTAAAAATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.44
Consensus pattern (29 bp):
ATTTTAATATAATCATCAGATATCAAGAG
Found at i:32944 original size:21 final size:21
Alignment explanation
Indices: 32905--32953 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
32895 TCAATGCTTT
**
32905 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
32927 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
32948 A-GAAGC
1 AGGAAGC
32954 TACAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:35812 original size:16 final size:16
Alignment explanation
Indices: 35791--35822 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
35781 TTCCTTGATG
35791 TGCCGCCACCAATTTT
1 TGCCGCCACCAATTTT
35807 TGCCGCCACCAATTTT
1 TGCCGCCACCAATTTT
35823 CATCATAGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.38, G:0.12, T:0.31
Consensus pattern (16 bp):
TGCCGCCACCAATTTT
Done.