Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022085.1 Corchorus olitorius cultivar O-4 contig22118, 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: 23111
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:2200 original size:24 final size:23
Alignment explanation
Indices: 2168--2224 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 23
2158 GCCTTATACA
**
2168 CAAACTAATGATATGTTTAGGATT
1 CAAACTAATGATATGTACA-GATT
2192 CAAACTAATG---TGTACAGATT
1 CAAACTAATGATATGTACAGATT
2212 CAAACTAATGATA
1 CAAACTAATGATA
2225 AACAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 14 0.50
21 4 0.14
24 10 0.36
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (23 bp):
CAAACTAATGATATGTACAGATT
Found at i:4484 original size:6 final size:6
Alignment explanation
Indices: 4473--4513 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
4463 CATTCATTTC
4473 TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TT-TTT TT-TTT T
1 TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT TTGTTT T
4514 GTAAAATTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 9 0.26
6 26 0.74
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTGTTT
Found at i:14590 original size:9 final size:9
Alignment explanation
Indices: 14576--14614 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
14566 ACTAAAAATA
14576 ATATATAGT
1 ATATATAGT
14585 ATATATA--
1 ATATATAGT
*
14592 CTATATAGT
1 ATATATAGT
14601 ATATATAGT
1 ATATATAGT
14610 ATATA
1 ATATA
14615 ATAATTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 6 0.23
9 20 0.77
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (9 bp):
ATATATAGT
Found at i:14598 original size:16 final size:16
Alignment explanation
Indices: 14577--14614 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
14567 CTAAAAATAA
14577 TATATAGTATATATAC
1 TATATAGTATATATAC
*
14593 TATATAGTATATATAG
1 TATATAGTATATATAC
14609 TATATA
1 TATATA
14615 ATAATTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (16 bp):
TATATAGTATATATAC
Found at i:15716 original size:74 final size:74
Alignment explanation
Indices: 15586--15813 Score: 343
Period size: 74 Copynumber: 3.1 Consensus size: 74
15576 TAAGCAAATA
* * *
15586 CACATATTTTTACTAATGTTTCATATAGAT-CAA-TGAACACTTAACATGGTTTAATCCAATTGA
1 CACA-ATTTTTACTAATGTTTCATATGGGTCCAATTGGACACTTAACATGGTTTAATCCAATTGA
15649 GGTGGACACT
65 GGTGGACACT
15659 CACAATTTTTACTAATGTTTCATATGGGTCCAATTGGACACTTAACATGGTTTAATCCAATTGAG
1 CACAATTTTTACTAATGTTTCATATGGGTCCAATTGGACACTTAACATGGTTTAATCCAATTGAG
*
15724 ATGGACACT
66 GTGGACACT
* * * * *
15733 CACAATTTTTACTAATGTTTCATATGGGGCCAATTGGATACTTAACATGGTTTAATTCAACTGGG
1 CACAATTTTTACTAATGTTTCATATGGGTCCAATTGGACACTTAACATGGTTTAATCCAATTGAG
*
15798 GTGGGCACT
66 GTGGACACT
15807 CACAATT
1 CACAATT
15814 ATTTTGGGTG
Statistics
Matches: 142, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
72 23 0.16
73 7 0.05
74 112 0.79
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (74 bp):
CACAATTTTTACTAATGTTTCATATGGGTCCAATTGGACACTTAACATGGTTTAATCCAATTGAG
GTGGACACT
Found at i:16156 original size:21 final size:20
Alignment explanation
Indices: 16122--16161 Score: 55
Period size: 19 Copynumber: 1.9 Consensus size: 20
16112 TTTGAATTTC
16122 TAAATTGTATATTT-TTTTA
1 TAAATTGTATATTTCTTTTA
16141 TAAATTGTAAATATTTCTTTT
1 TAAATTGT--ATATTTCTTTT
16162 TATTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.44
21 6 0.33
22 4 0.22
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (20 bp):
TAAATTGTATATTTCTTTTA
Found at i:18248 original size:31 final size:30
Alignment explanation
Indices: 18168--18263 Score: 124
Period size: 30 Copynumber: 3.2 Consensus size: 30
18158 TGTAAATTTC
*
18168 ATTGGGCCTCT-TTGAGTGTGTGTGAAGTAT
1 ATTGGGCCACTATT-AGTGTGTGTGAAGTAT
18198 ATTGGGCCACTATTAGTGTGTGTGAAGTAT
1 ATTGGGCCACTATTAGTGTGTGTGAAGTAT
*
18228 ATTGGG-CAGCTTTTTAGTGTGTGTGAAGTAT
1 ATTGGGCCA-C-TATTAGTGTGTGTGAAGTAT
*
18259 GTTGG
1 ATTGG
18264 TGGCCCCTAT
Statistics
Matches: 60, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
29 2 0.03
30 33 0.55
31 25 0.42
ACGTcount: A:0.19, C:0.08, G:0.33, T:0.40
Consensus pattern (30 bp):
ATTGGGCCACTATTAGTGTGTGTGAAGTAT
Found at i:18550 original size:25 final size:26
Alignment explanation
Indices: 18501--18552 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
18491 AGAAAACTAG
18501 TCTTTTAATATTTCTTTTTTGGTACA
1 TCTTTTAATATTTCTTTTTTGGTACA
18527 TCTTTTAATATTTC-TTTTTGGTACA
1 TCTTTTAATATTTCTTTTTTGGTACA
18552 T
1 T
18553 TAGTCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.19, C:0.12, G:0.08, T:0.62
Consensus pattern (26 bp):
TCTTTTAATATTTCTTTTTTGGTACA
Done.