Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012492.1 Corchorus olitorius cultivar O-4 contig12525, 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: 22645
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3823 original size:38 final size:38
Alignment explanation
Indices: 3772--3850 Score: 133
Period size: 38 Copynumber: 2.1 Consensus size: 38
3762 TCCAGATAAA
*
3772 ACAATACTAGCTCTTCCGGAG-CATTCAATCAAATTTGC
1 ACAATACTAGCTCTTCCAGAGCCA-TCAATCAAATTTGC
3810 ACAATACTAGCTCTTCCAGAGCCATCAATCAAATTTGC
1 ACAATACTAGCTCTTCCAGAGCCATCAATCAAATTTGC
3848 ACA
1 ACA
3851 CCCGATATAG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
38 37 0.95
39 2 0.05
ACGTcount: A:0.34, C:0.28, G:0.11, T:0.27
Consensus pattern (38 bp):
ACAATACTAGCTCTTCCAGAGCCATCAATCAAATTTGC
Found at i:5369 original size:33 final size:32
Alignment explanation
Indices: 5323--5399 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 32
5313 AATTTTTTTA
*
5323 ATGATAAAGAAAGGTAGAA-AGAGGAGATTATGC
1 ATGATAAATAAAGGTAGAAGA-AGG-GATTATGC
5356 ATGATAAATAAAGGTAGAAGAAGGGATTATGC
1 ATGATAAATAAAGGTAGAAGAAGGGATTATGC
*
5388 ATGTTAAATAAA
1 ATGATAAATAAA
5400 CTTTGTAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
32 19 0.46
33 21 0.51
34 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.26, T:0.22
Consensus pattern (32 bp):
ATGATAAATAAAGGTAGAAGAAGGGATTATGC
Found at i:5389 original size:32 final size:33
Alignment explanation
Indices: 5323--5399 Score: 113
Period size: 32 Copynumber: 2.4 Consensus size: 33
5313 AATTTTTTTA
*
5323 ATGATAAAGAAAGGTAGAAAGAGGAGATTATGC
1 ATGATAAATAAAGGTAGAAAGAGGAGATTATGC
5356 ATGATAAATAAAGGTAG-AAGAAGG-GATTATGC
1 ATGATAAATAAAGGTAGAAAG-AGGAGATTATGC
*
5388 ATGTTAAATAAA
1 ATGATAAATAAA
5400 CTTTGTAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
32 22 0.54
33 19 0.46
ACGTcount: A:0.49, C:0.03, G:0.26, T:0.22
Consensus pattern (33 bp):
ATGATAAATAAAGGTAGAAAGAGGAGATTATGC
Found at i:6367 original size:22 final size:22
Alignment explanation
Indices: 6339--6380 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
6329 GTTTATAATA
6339 TTCTTGGATCATCCGGGTTAAC
1 TTCTTGGATCATCCGGGTTAAC
* *
6361 TTCTTGGGTCATTCGGGTTA
1 TTCTTGGATCATCCGGGTTA
6381 CGGATTTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.40
Consensus pattern (22 bp):
TTCTTGGATCATCCGGGTTAAC
Found at i:12592 original size:139 final size:139
Alignment explanation
Indices: 12345--12619 Score: 514
Period size: 139 Copynumber: 2.0 Consensus size: 139
12335 AGGTGGACTT
12345 ATAAGAATCAGGAAGGACCAAAATTGGTCCTCCAAAACCCATGGACCAAATCTAATTTCCAAACC
1 ATAAGAATCAGGAAGGACCAAAATTGGTCCTCCAAAACCCATGGACCAAATCTAATTTCCAAACC
*
12410 AAACATGGGTCACTAATTAAAAGGACCTCTCGTCCCGTCCCGTCCCTTACTGGTCCCTCAATCCA
66 AAACATGGGTCACTAATTAAAAGGACCTCCCGTCCCGTCCCGTCCCTTACTGGTCCCTCAATCCA
12475 AACAGATTG
131 AACAGATTG
* * *
12484 ATAAGGATCAGGAAGGACCAAAATTGGTCCTCCAAAACCCATGGATCAAATCTAATTTCCAATCC
1 ATAAGAATCAGGAAGGACCAAAATTGGTCCTCCAAAACCCATGGACCAAATCTAATTTCCAAACC
12549 AAACATGGGTCACTAATTAAAAGGACCTCCCGTCCCGTCCCGTCCCTTACTGGTCCCTCAATCCA
66 AAACATGGGTCACTAATTAAAAGGACCTCCCGTCCCGTCCCGTCCCTTACTGGTCCCTCAATCCA
12614 AACAGA
131 AACAGA
12620 CTGTAAGTGT
Statistics
Matches: 132, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
139 132 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.21
Consensus pattern (139 bp):
ATAAGAATCAGGAAGGACCAAAATTGGTCCTCCAAAACCCATGGACCAAATCTAATTTCCAAACC
AAACATGGGTCACTAATTAAAAGGACCTCCCGTCCCGTCCCGTCCCTTACTGGTCCCTCAATCCA
AACAGATTG
Found at i:13183 original size:7 final size:7
Alignment explanation
Indices: 13171--13199 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
13161 CCACCCTTTC
13171 CTTTCGA
1 CTTTCGA
13178 CTTTCGA
1 CTTTCGA
13185 CTTTCGA
1 CTTTCGA
13192 CTTTCGA
1 CTTTCGA
13199 C
1 C
13200 GGCCGCGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.31, G:0.14, T:0.41
Consensus pattern (7 bp):
CTTTCGA
Found at i:21906 original size:12 final size:12
Alignment explanation
Indices: 21887--21940 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
21877 GGGGGGGGCG
21887 TGTATATATATA
1 TGTATATATATA
* *
21899 TATATATATGTA
1 TGTATATATATA
* *
21911 TGTATGTATGTA
1 TGTATATATATA
*
21923 TGTATATGTATA
1 TGTATATATATA
21935 TGTATA
1 TGTATA
21941 AACACATCGA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (12 bp):
TGTATATATATA
Found at i:22622 original size:2 final size:2
Alignment explanation
Indices: 22615--22644 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
22605 GTAGTATGTG
22615 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22645 G
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.