Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013327.1 Corchorus olitorius cultivar O-4 contig13360, 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: 47490
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8206 original size:28 final size:28
Alignment explanation
Indices: 8174--8246 Score: 146
Period size: 28 Copynumber: 2.6 Consensus size: 28
8164 TAAATGGTTC
8174 ATTTTGGCATTATAATTTTTTTAGATCA
1 ATTTTGGCATTATAATTTTTTTAGATCA
8202 ATTTTGGCATTATAATTTTTTTAGATCA
1 ATTTTGGCATTATAATTTTTTTAGATCA
8230 ATTTTGGCATTATAATT
1 ATTTTGGCATTATAATT
8247 AGTCGCATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.53
Consensus pattern (28 bp):
ATTTTGGCATTATAATTTTTTTAGATCA
Found at i:8378 original size:23 final size:23
Alignment explanation
Indices: 8348--8394 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
8338 ATATTATTAC
8348 ACCATTATCTTCAAATATAATTG
1 ACCATTATCTTCAAATATAATTG
*
8371 ACCATTATCTTCAAATGTAATTG
1 ACCATTATCTTCAAATATAATTG
8394 A
1 A
8395 ACTACTAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.38
Consensus pattern (23 bp):
ACCATTATCTTCAAATATAATTG
Found at i:9661 original size:16 final size:15
Alignment explanation
Indices: 9637--9686 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
9627 TTTATTTTTA
9637 TTTTT-TCTTTTTCT
1 TTTTTCTCTTTTTCT
*
9651 CTTTTTCTCTTTTTACG
1 -TTTTTCTCTTTTT-CT
9668 TTTTTCT-TTTTTCT
1 TTTTTCTCTTTTTCT
9682 TTTTT
1 TTTTT
9687 TTTCCCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 6 0.19
15 10 0.32
16 14 0.45
17 1 0.03
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTTCTCTTTTTCT
Found at i:9687 original size:8 final size:7
Alignment explanation
Indices: 9631--9686 Score: 67
Period size: 7 Copynumber: 7.7 Consensus size: 7
9621 TTGGGTTTTA
*
9631 TTTTTAT
1 TTTTTCT
9638 TTTTTCT
1 TTTTTCT
9645 TTTTCTCT
1 TTTT-TCT
9653 TTTTCTCT
1 TTTT-TCT
* *
9661 TTTTACG
1 TTTTTCT
9668 TTTTTCT
1 TTTTTCT
9675 TTTTTCT
1 TTTTTCT
9682 TTTTT
1 TTTTT
9687 TTTCCCATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
7 28 0.65
8 15 0.35
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.80
Consensus pattern (7 bp):
TTTTTCT
Found at i:9856 original size:31 final size:31
Alignment explanation
Indices: 9813--9915 Score: 92
Period size: 31 Copynumber: 3.4 Consensus size: 31
9803 GTCAAATTTT
9813 GGCCCAATTTGGTGCAATTTGCTAAGGTTTA
1 GGCCCAATTTGGTGCAATTTGCTAAGGTTTA
*
9844 GGCCCAAGTTGGT-C-ATGTT--TAAAGGTTTA
1 GGCCCAATTTGGTGCAAT-TTGCT-AAGGTTTA
* * *
9873 -GCCTCAAATT-GAGCAAGTTTGCAAAGGTTTA
1 GGCC-CAATTTGGTGCAA-TTTGCTAAGGTTTA
9904 GGCCCAATTTGG
1 GGCCCAATTTGG
9916 ACCTTAGGCC
Statistics
Matches: 57, Mismatches: 5, Indels: 19
0.70 0.06 0.23
Matches are distributed among these distances:
28 5 0.09
29 16 0.28
30 6 0.11
31 26 0.46
32 4 0.07
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (31 bp):
GGCCCAATTTGGTGCAATTTGCTAAGGTTTA
Found at i:18094 original size:21 final size:21
Alignment explanation
Indices: 18068--18108 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
18058 TTCTTCTCTG
18068 CGTTTT-TGAAAAAAAAAATTA
1 CGTTTTCT-AAAAAAAAAATTA
18089 CGTTTTCTAAAAAAAAAATT
1 CGTTTTCTAAAAAAAAAATT
18109 TGTTTCTGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.34
Consensus pattern (21 bp):
CGTTTTCTAAAAAAAAAATTA
Found at i:21040 original size:42 final size:42
Alignment explanation
Indices: 20988--21068 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
20978 CTACCAGCCA
* *
20988 CGCCACCTGCTTGGCCATGCCTGGCCAAC-TCCGCGCCATCCG
1 CGCCACCTGCTCGGCCATG-CTAGCCAACATCCGCGCCATCCG
* *
21030 CGCCACCTGCTCGGTCATGCTAGCCATCATCCGCGCCAT
1 CGCCACCTGCTCGGCCATGCTAGCCAACATCCGCGCCAT
21069 TCCATGCTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 7 0.21
42 27 0.79
ACGTcount: A:0.14, C:0.46, G:0.22, T:0.19
Consensus pattern (42 bp):
CGCCACCTGCTCGGCCATGCTAGCCAACATCCGCGCCATCCG
Found at i:22272 original size:319 final size:319
Alignment explanation
Indices: 21693--22326 Score: 1232
Period size: 319 Copynumber: 2.0 Consensus size: 319
21683 TAAATAAACC
21693 ACATGAGCATGAGTAATATCAATTGTTTGTGTTAATTTCTTATATGTTTTCACACTGAGGACAAT
1 ACATGAGCATGAGTAATATCAATTGTTTGTGTTAATTTCTTATATGTTTTCACACTGAGGACAAT
*
21758 GTGTCTTTTCAGTGTGGGGGAGAGAGTCTAGTCTAATAGAGAGTTTACATGCATATTGATCATAA
66 ATGTCTTTTCAGTGTGGGGGAGAGAGTCTAGTCTAATAGAGAGTTTACATGCATATTGATCATAA
*
21823 TCTTAATTAATGCCATAATTTTTTTTGGAAAATTTTGAAAATTGTGCATGTATTGAGTGATTTGA
131 TCTTAATTAATGCCATAATTTTTTTTCGAAAATTTTGAAAATTGTGCATGTATTGAGTGATTTGA
21888 TTTAATTATGATTGAAGAATGCTTAGAATTTTTAAGAATGTTTTATTTGATTGATTGATTTTTAG
196 TTTAATTATGATTGAAGAATGCTTAGAATTTTTAAGAATGTTTTATTTGATTGATTGATTTTTAG
21953 CATGATATCTTATTTCTTAGAATTAGGTATAATTAGAGTTTTGTGATAAAAGCATGTAA
261 CATGATATCTTATTTCTTAGAATTAGGTATAATTAGAGTTTTGTGATAAAAGCATGTAA
*
22012 ACATGAGCATGAGTAATATCAATTGTTTGTGTTAATTTCTTATATGTTTTCACATTGAGGACAAT
1 ACATGAGCATGAGTAATATCAATTGTTTGTGTTAATTTCTTATATGTTTTCACACTGAGGACAAT
22077 ATGTCTTTTCAGTGTGGGGGAGAGAGTCTAGTCTAATAGAGAGTTTACATGCATATTGATCATAA
66 ATGTCTTTTCAGTGTGGGGGAGAGAGTCTAGTCTAATAGAGAGTTTACATGCATATTGATCATAA
22142 TCTTAATTAATGCCATAATTTTTTTTCGAAAATTTTGAAAATTGTGCATGTATTGAGTGATTTGA
131 TCTTAATTAATGCCATAATTTTTTTTCGAAAATTTTGAAAATTGTGCATGTATTGAGTGATTTGA
22207 TTTAATTATGATTGAAGAATGCTTAGAATTTTTAAGAATGTTTTATTTGATTGATTGATTTTTAG
196 TTTAATTATGATTGAAGAATGCTTAGAATTTTTAAGAATGTTTTATTTGATTGATTGATTTTTAG
*
22272 CATGATATCTTATTTTTTAGAATTAGGTATAATTAGAGTTTTGTGATAAAAGCAT
261 CATGATATCTTATTTCTTAGAATTAGGTATAATTAGAGTTTTGTGATAAAAGCAT
22327 ATTGTTCATT
Statistics
Matches: 311, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
319 311 1.00
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (319 bp):
ACATGAGCATGAGTAATATCAATTGTTTGTGTTAATTTCTTATATGTTTTCACACTGAGGACAAT
ATGTCTTTTCAGTGTGGGGGAGAGAGTCTAGTCTAATAGAGAGTTTACATGCATATTGATCATAA
TCTTAATTAATGCCATAATTTTTTTTCGAAAATTTTGAAAATTGTGCATGTATTGAGTGATTTGA
TTTAATTATGATTGAAGAATGCTTAGAATTTTTAAGAATGTTTTATTTGATTGATTGATTTTTAG
CATGATATCTTATTTCTTAGAATTAGGTATAATTAGAGTTTTGTGATAAAAGCATGTAA
Found at i:31970 original size:32 final size:33
Alignment explanation
Indices: 31909--31989 Score: 146
Period size: 32 Copynumber: 2.5 Consensus size: 33
31899 ATTTCTAATG
*
31909 AAACTGATTCATACCTTTTCTTTTTTTCCAAAA
1 AAACTGATTCATACCTTCTCTTTTTTTCCAAAA
31942 AAACTGATTCATACCTTCT-TTTTTTTCCAAAA
1 AAACTGATTCATACCTTCTCTTTTTTTCCAAAA
31974 AAACTGATTCATACCT
1 AAACTGATTCATACCT
31990 AAGTCGTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.62
33 18 0.38
ACGTcount: A:0.32, C:0.22, G:0.04, T:0.42
Consensus pattern (33 bp):
AAACTGATTCATACCTTCTCTTTTTTTCCAAAA
Found at i:39294 original size:3 final size:3
Alignment explanation
Indices: 39286--39313 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
39276 GCAAAATCCC
39286 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
39314 GTTAATACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:41194 original size:20 final size:21
Alignment explanation
Indices: 41169--41207 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
41159 TGATTTGCTA
*
41169 ATTGATTTAGTAAA-ATTGGG
1 ATTGATATAGTAAATATTGGG
41189 ATTGATATAGTAAATATTG
1 ATTGATATAGTAAATATTG
41208 AAAAGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (21 bp):
ATTGATATAGTAAATATTGGG
Found at i:41270 original size:14 final size:14
Alignment explanation
Indices: 41251--41278 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41241 GAATAAGCAC
41251 TATAAATAATAATT
1 TATAAATAATAATT
41265 TATAAATAATAATT
1 TATAAATAATAATT
41279 AATGAATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TATAAATAATAATT
Done.