Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017837.1 Corchorus olitorius cultivar O-4 contig17870, 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: 40630
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:8084 original size:1 final size:1
Alignment explanation
Indices: 8078--8103 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
8068 GTTACAAGGG
8078 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
8104 CTGAATTTGT
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
Found at i:21923 original size:22 final size:22
Alignment explanation
Indices: 21896--21976 Score: 108
Period size: 22 Copynumber: 3.7 Consensus size: 22
21886 ATTCTCTCAT
*
21896 TAAGCTCTATTATGATCTACGC
1 TAAGCTCTATTATGTTCTACGC
* *
21918 TGAGCTCTATTATGTTCTATGC
1 TAAGCTCTATTATGTTCTACGC
* *
21940 TAAGATTTATTATGTTCTACGC
1 TAAGCTCTATTATGTTCTACGC
*
21962 TAAACTCTATTATGT
1 TAAGCTCTATTATGT
21977 GAGGTCACAC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (22 bp):
TAAGCTCTATTATGTTCTACGC
Found at i:22434 original size:7 final size:7
Alignment explanation
Indices: 22422--22446 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
22412 TTTGAAGCCA
22422 TCATCAT
1 TCATCAT
22429 TCATCAT
1 TCATCAT
22436 TCATCAT
1 TCATCAT
22443 TCAT
1 TCAT
22447 TTTAGGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (7 bp):
TCATCAT
Found at i:24414 original size:13 final size:13
Alignment explanation
Indices: 24385--24425 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
24375 GGTGTTTCAA
*
24385 ATAATATTTAGTAT
1 ATAATATATA-TAT
24399 ATAATATATATAT
1 ATAATATATATAT
24412 ATAATATATATAT
1 ATAATATATATAT
24425 A
1 A
24426 CTCCCTCAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 17 0.65
14 9 0.35
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (13 bp):
ATAATATATATAT
Found at i:26060 original size:7 final size:7
Alignment explanation
Indices: 26048--26072 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
26038 AAGGAAAAGG
26048 AAAGTCC
1 AAAGTCC
26055 AAAGTCC
1 AAAGTCC
26062 AAAGTCC
1 AAAGTCC
26069 AAAG
1 AAAG
26073 AGCTTATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.24, G:0.16, T:0.12
Consensus pattern (7 bp):
AAAGTCC
Found at i:34095 original size:6 final size:6
Alignment explanation
Indices: 34084--34109 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
34074 TATGGGGGAA
34084 ACCAAC ACCAAC ACCAAC ACCAAC AC
1 ACCAAC ACCAAC ACCAAC ACCAAC AC
34110 AGGTACGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (6 bp):
ACCAAC
Found at i:37370 original size:21 final size:21
Alignment explanation
Indices: 37329--37372 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
37319 TTATTAGTGG
* *
37329 TATTATAATTATTAAACTTAT
1 TATTATAATTAATAAAATTAT
37350 TATTATAA-TAATAATAATTAT
1 TATTATAATTAATAA-AATTAT
37371 TA
1 TA
37373 GTGGTATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTATAATTAATAAAATTAT
Found at i:37372 original size:30 final size:27
Alignment explanation
Indices: 37287--37369 Score: 112
Period size: 30 Copynumber: 3.0 Consensus size: 27
37277 GTTAATTTAG
37287 ACTTATTATTATTATAATAATTATTAA
1 ACTTATTATTATTATAATAATTATTAA
*
37314 ACTTATTATTAGTGGTATTATAATTATTAA
1 ACTTATTATTA-T--TATAATAATTATTAA
* *
37344 ACTTATTATTATAATAATAATAATTA
1 ACTTATTATTATTATAATAATTATTA
37370 TTAGTGGTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
27 22 0.45
28 1 0.02
29 1 0.02
30 25 0.51
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (27 bp):
ACTTATTATTATTATAATAATTATTAA
Found at i:40497 original size:18 final size:18
Alignment explanation
Indices: 40474--40512 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
40464 TACAGATTAA
40474 TATGCGATTTATTATTTT
1 TATGCGATTTATTATTTT
40492 TATGCGATTTATTATTTT
1 TATGCGATTTATTATTTT
40510 TAT
1 TAT
40513 TTAGTTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.05, G:0.10, T:0.62
Consensus pattern (18 bp):
TATGCGATTTATTATTTT
Done.