Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024108.1 Corchorus olitorius cultivar O-4 contig24141, 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: 27331
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.33
Found at i:4326 original size:28 final size:28
Alignment explanation
Indices: 4282--4335 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
4272 GAAGTTTTTG
* *
4282 CTAATTACCCGTTTACCTTCGACATGAC
1 CTAATTACCCGTCTACCTTCAACATGAC
4310 CTAATTACCCGTCTACCTTCAACATG
1 CTAATTACCCGTCTACCTTCAACATG
4336 GTGCTAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.26, C:0.33, G:0.09, T:0.31
Consensus pattern (28 bp):
CTAATTACCCGTCTACCTTCAACATGAC
Found at i:12457 original size:27 final size:27
Alignment explanation
Indices: 12415--12475 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
12405 TCCTCATTAT
* *
12415 AGGGGTAAAATCGTAATTTTATCAATC
1 AGGGGTAAAATAGTAAATTTATCAATC
* * *
12442 AGGGGTAATATAGTAAATTTGTCCATC
1 AGGGGTAAAATAGTAAATTTATCAATC
*
12469 ATGGGTA
1 AGGGGTA
12476 TTTTGGTAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.34, C:0.10, G:0.23, T:0.33
Consensus pattern (27 bp):
AGGGGTAAAATAGTAAATTTATCAATC
Found at i:17275 original size:28 final size:28
Alignment explanation
Indices: 17235--17291 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
17225 TGCAGTCTAT
17235 AACCATACTTTATAGGTCTAACGACGTG
1 AACCATACTTTATAGGTCTAACGACGTG
17263 AACCATACTTTATAGGTCTAACGACGTG
1 AACCATACTTTATAGGTCTAACGACGTG
17291 A
1 A
17292 TACATTATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (28 bp):
AACCATACTTTATAGGTCTAACGACGTG
Found at i:17299 original size:24 final size:25
Alignment explanation
Indices: 17239--17299 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 25
17229 GTCTATAACC
17239 ATACTTTATAGGTCTAACGACGTGAA
1 ATACTTTATAGGTCTAACGACGTG-A
17265 CCATACTTTATAGGTCTAACGACGTG-
1 --ATACTTTATAGGTCTAACGACGTGA
*
17291 ATACATTAT
1 ATACTTTAT
17300 TCTACTTGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 8 0.25
28 24 0.75
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (25 bp):
ATACTTTATAGGTCTAACGACGTGA
Found at i:18309 original size:38 final size:39
Alignment explanation
Indices: 18258--18336 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
18248 ATATTGTAAC
* *
18258 CTTTTCCATTGCTTTCT-TTTTTATGTATGGTTTTTTAG
1 CTTTTCCATTGCTTTCTCTTTTTATGTATAGCTTTTTAG
18296 CTTTTCCATTGCTTTCTCTTTTTATGTATAGCTTTTTAG
1 CTTTTCCATTGCTTTCTCTTTTTATGTATAGCTTTTTAG
18335 CT
1 CT
18337 GTTAAAGATT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 17 0.45
39 21 0.55
ACGTcount: A:0.11, C:0.16, G:0.11, T:0.61
Consensus pattern (39 bp):
CTTTTCCATTGCTTTCTCTTTTTATGTATAGCTTTTTAG
Found at i:18755 original size:11 final size:11
Alignment explanation
Indices: 18739--18764 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
18729 TTAGATGCAA
18739 AAAAAAAAAAC
1 AAAAAAAAAAC
18750 AAAAAAAAAAC
1 AAAAAAAAAAC
18761 AAAA
1 AAAA
18765 GCAAAGAGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:22564 original size:35 final size:34
Alignment explanation
Indices: 22524--22591 Score: 109
Period size: 35 Copynumber: 2.0 Consensus size: 34
22514 TTCGTTTATG
**
22524 TTCACGAACAGGCTCGTTTATTGTTCATTTAAGTA
1 TTCACGAACAAACTCGTTTATTGTTCA-TTAAGTA
22559 TTCACGAACAAACTCGTTTATTGTTCATTAAGT
1 TTCACGAACAAACTCGTTTATTGTTCATTAAGT
22592 GTTCGTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 6 0.19
35 25 0.81
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.40
Consensus pattern (34 bp):
TTCACGAACAAACTCGTTTATTGTTCATTAAGTA
Found at i:22660 original size:16 final size:16
Alignment explanation
Indices: 22639--22670 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
22629 TATAATTATT
22639 TATATATTAATAATAA
1 TATATATTAATAATAA
*
22655 TATATATTATTAATAA
1 TATATATTAATAATAA
22671 AAATTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATATTAATAATAA
Found at i:22665 original size:19 final size:19
Alignment explanation
Indices: 22623--22670 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
22613 GAACGTTCAT
* *
22623 TTATTATATAATTATTTATA
1 TTATTA-ATAATAATATATA
22643 -TATTAATAATAATATATA
1 TTATTAATAATAATATATA
22661 TTATTAATAA
1 TTATTAATAA
22671 AAATTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATTAATAATAATATATA
Found at i:22829 original size:18 final size:18
Alignment explanation
Indices: 22802--22836 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
22792 AATTATTACA
22802 TTGTTCATGAACAATTTT
1 TTGTTCATGAACAATTTT
*
22820 TTGTTTATGAACAATTT
1 TTGTTCATGAACAATTT
22837 CAATTTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (18 bp):
TTGTTCATGAACAATTTT
Found at i:25852 original size:41 final size:41
Alignment explanation
Indices: 25807--25894 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
25797 TTTTTCCGTT
* * * *
25807 TTCAATATAGTCCCTGATTTAGGTTTATACTTGTTAATTGA
1 TTCAATATAGTCCCTCATTAAGGGTAATACTTGTTAATTGA
* * *
25848 TTCAATTTTGTCCCTCATTAAGGGTAATATTTGTTAATTGA
1 TTCAATATAGTCCCTCATTAAGGGTAATACTTGTTAATTGA
25889 TTCAAT
1 TTCAAT
25895 TTCGCCCATG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (41 bp):
TTCAATATAGTCCCTCATTAAGGGTAATACTTGTTAATTGA
Done.