Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022147.1 Corchorus olitorius cultivar O-4 contig22180, 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: 49980
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:19323 original size:109 final size:109
Alignment explanation
Indices: 19197--19405 Score: 391
Period size: 109 Copynumber: 1.9 Consensus size: 109
19187 TATATTATTG
*
19197 TTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGTACACATACCAAACAATACAAAATGC
1 TTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAAAATGC
19262 AATGAACTATTGGATTTAAAGAAAAATACAAGCACCTATTGTTA
66 AATGAACTATTGGATTTAAAGAAAAATACAAGCACCTATTGTTA
* *
19306 TTAATTGTGTTGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAAAGTGC
1 TTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAAAATGC
19371 AATGAACTATTGGATTTAAAGAAAAATACAAGCAC
66 AATGAACTATTGGATTTAAAGAAAAATACAAGCAC
19406 TAAAATGACT
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 97 1.00
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (109 bp):
TTAATTGTGTGGTTTATTCAATTGAACCTATTAAATAAGCACACATACCAAACAATACAAAATGC
AATGAACTATTGGATTTAAAGAAAAATACAAGCACCTATTGTTA
Found at i:30609 original size:50 final size:50
Alignment explanation
Indices: 30533--30627 Score: 172
Period size: 50 Copynumber: 1.9 Consensus size: 50
30523 TGTGATTTAG
* *
30533 CCTTTATTACGTGGTAACTCCTACAGACTCGAGTCTATACCATCAAATCA
1 CCTTTATTACGTGGTAACTCCCACAGACTCGAGTCCATACCATCAAATCA
30583 CCTTTATTACGTGGTAACTCCCACAGACTCGAGTCCATACCATCA
1 CCTTTATTACGTGGTAACTCCCACAGACTCGAGTCCATACCATCA
30628 CTCTGGTTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (50 bp):
CCTTTATTACGTGGTAACTCCCACAGACTCGAGTCCATACCATCAAATCA
Found at i:31066 original size:18 final size:19
Alignment explanation
Indices: 31043--31091 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
31033 CCCTAATTTT
*
31043 TCTCCAATC-CCAGCTCCA
1 TCTCCAATCTCCAACTCCA
31061 TCTCC-ATCTCCAACTCCA
1 TCTCCAATCTCCAACTCCA
*
31079 ACTCCAA-CTCCAA
1 TCTCCAATCTCCAA
31092 TCCTAAACCC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 3 0.11
18 23 0.85
19 1 0.04
ACGTcount: A:0.27, C:0.49, G:0.02, T:0.22
Consensus pattern (19 bp):
TCTCCAATCTCCAACTCCA
Found at i:31071 original size:12 final size:12
Alignment explanation
Indices: 31043--31090 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
31033 CCCTAATTTT
31043 TCTCCAA-TCCCA
1 TCTCCAACT-CCA
* *
31055 GCTCCATCTCCA
1 TCTCCAACTCCA
31067 TCTCCAACTCCA
1 TCTCCAACTCCA
*
31079 ACTCCAACTCCA
1 TCTCCAACTCCA
31091 ATCCTAAACC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
12 29 0.97
13 1 0.03
ACGTcount: A:0.25, C:0.50, G:0.02, T:0.23
Consensus pattern (12 bp):
TCTCCAACTCCA
Found at i:31091 original size:6 final size:6
Alignment explanation
Indices: 31056--31091 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
31046 CCAATCCCAG
* *
31056 CTCCAT CTCCAT CTCCAA CTCCAA CTCCAA CTCCAA
1 CTCCAA CTCCAA CTCCAA CTCCAA CTCCAA CTCCAA
31092 TCCTAAACCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.28, C:0.50, G:0.00, T:0.22
Consensus pattern (6 bp):
CTCCAA
Found at i:38529 original size:17 final size:16
Alignment explanation
Indices: 38483--38525 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
38473 TCAGATTACT
38483 AGTGATCTAAGATCACC
1 AGTGATC-AAGATCACC
38500 AGTGATGCAAGATCACC
1 AGTGAT-CAAGATCACC
*
38517 GGTGATCAA
1 AGTGATCAA
38526 AGATTACATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 20 0.83
18 1 0.04
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (16 bp):
AGTGATCAAGATCACC
Found at i:47907 original size:71 final size:74
Alignment explanation
Indices: 47783--47925 Score: 220
Period size: 71 Copynumber: 1.9 Consensus size: 74
47773 AAAGATACAA
*
47783 CAACAAGAAGCCATGTGAATCCTTGAAGTTGTTGGAACATTTTTCTAAATATCCAATAATTTCAA
1 CAACAAGAAGCCATGTGAATCCCTGAA--TGTTGGAACATTTTTCTAAATATCCAATAATTTCAA
47848 AATATCCTTGG
64 AATATCCTTGG
* *
47859 CAACAAGAAGCCAT-TTAATCCCTGAA-GTTGGAACA-TTTTCTAAATATCCAATAATTTGAAAA
1 CAACAAGAAGCCATGTGAATCCCTGAATGTTGGAACATTTTTCTAAATATCCAATAATTTCAAAA
47921 TATCC
66 TATCC
47926 AAAGGGATAT
Statistics
Matches: 64, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
71 31 0.48
72 9 0.14
75 10 0.16
76 14 0.22
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (74 bp):
CAACAAGAAGCCATGTGAATCCCTGAATGTTGGAACATTTTTCTAAATATCCAATAATTTCAAAA
TATCCTTGG
Found at i:48653 original size:22 final size:22
Alignment explanation
Indices: 48625--48667 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
48615 CATTAAATAC
48625 CATGCCATGAGGAATAACATGG
1 CATGCCATGAGGAATAACATGG
48647 CATGCCATGAGGAATAACATG
1 CATGCCATGAGGAATAACATG
48668 TACTGTACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.19
Consensus pattern (22 bp):
CATGCCATGAGGAATAACATGG
Done.