Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018927.1 Corchorus olitorius cultivar O-4 contig18960, 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: 13237
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:2086 original size:33 final size:33
Alignment explanation
Indices: 2033--2134 Score: 161
Period size: 33 Copynumber: 3.1 Consensus size: 33
2023 GCTCTTACAA
2033 ACAATGAAGTT-ACGGGCCTTCATCACGCCGTT
1 ACAATGAAGTTCACGGGCCTTCATCACGCCGTT
* *
2065 CCAATGAAGTTCACGGGCCTTCATCACGCCTTT
1 ACAATGAAGTTCACGGGCCTTCATCACGCCGTT
* *
2098 ACAATGAAGTTCACGGGCCTTCATCATGCCTTT
1 ACAATGAAGTTCACGGGCCTTCATCACGCCGTT
2131 ACAA
1 ACAA
2135 GTTGAGCAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 10 0.15
33 55 0.85
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.26
Consensus pattern (33 bp):
ACAATGAAGTTCACGGGCCTTCATCACGCCGTT
Found at i:3155 original size:15 final size:15
Alignment explanation
Indices: 3135--3176 Score: 66
Period size: 17 Copynumber: 2.7 Consensus size: 15
3125 TGGAGTCAAC
3135 AATTTTAACTATTGG
1 AATTTTAACTATTGG
3150 AATTTTATCACTATTGG
1 AATTTTA--ACTATTGG
3167 AATTTTAACT
1 AATTTTAACT
3177 TGTTGATGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.40
17 15 0.60
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (15 bp):
AATTTTAACTATTGG
Found at i:4404 original size:27 final size:26
Alignment explanation
Indices: 4349--4404 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
4339 AATATAAGTG
* *
4349 AAATTACCATTTTACCCTTAGTGGGA
1 AAATTACCATTTTACCCTAAGTGCGA
* *
4375 AAATTACGATTTTACCCCTAAGTGCTA
1 AAATTACCATTTTA-CCCTAAGTGCGA
4402 AAA
1 AAA
4405 AATGCCGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (26 bp):
AAATTACCATTTTACCCTAAGTGCGA
Found at i:7968 original size:24 final size:25
Alignment explanation
Indices: 7922--7972 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
7912 ATTGGAGTAT
*
7922 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
7947 TTATTT-TCTTGTTTATTTATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
7971 TT
1 TT
7973 GTTCACATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.18, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:11835 original size:112 final size:112
Alignment explanation
Indices: 11638--11851 Score: 331
Period size: 112 Copynumber: 1.9 Consensus size: 112
11628 TCCGTCACCC
*
11638 GAAATCTGGTCCTAGATCCTCTTAGCCTTGCTCGATTTTTGTAGATCTAAGCTACCCAAAACCAT
1 GAAATCTGGTCCTAGATCCTCTTAACCTTGCTCGATTTTTGTAGATCTAAGCTACCCAAAACCAT
* *
11703 ATGCCCAAATCATATCTACCAAAATCCGATCTACATCCTCTGTATCT
66 ATGCCCAAATCAGATATACCAAAATCCGATCTACATCCTCTGTATCT
* * * * * *
11750 GAAATCTGTTCCTAGATTCTTTTAACCTTGCTCGATTTTCT-TATATTTAAGTTACCCAAAACCA
1 GAAATCTGGTCCTAGATCCTCTTAACCTTGCTCGATTTT-TGTAGATCTAAGCTACCCAAAACCA
11814 TATGCCCAAATCAGATATACCAAAATCCGATCTACATC
65 TATGCCCAAATCAGATATACCAAAATCCGATCTACATC
11852 TTTCACTACC
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
112 91 0.99
113 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (112 bp):
GAAATCTGGTCCTAGATCCTCTTAACCTTGCTCGATTTTTGTAGATCTAAGCTACCCAAAACCAT
ATGCCCAAATCAGATATACCAAAATCCGATCTACATCCTCTGTATCT
Found at i:12450 original size:20 final size:19
Alignment explanation
Indices: 12422--12463 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
12412 TAAAACATAG
12422 TTTAATTTTTCTTT-TTTCTT
1 TTTAATTTTT-TTTGTTT-TT
*
12442 TTTACTTTTTTTTGTTTTT
1 TTTAATTTTTTTTGTTTTT
12461 TTT
1 TTT
12464 CCTGTTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.07, C:0.07, G:0.02, T:0.83
Consensus pattern (19 bp):
TTTAATTTTTTTTGTTTTT
Found at i:13184 original size:2 final size:2
Alignment explanation
Indices: 13177--13213 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
13167 TGGTAGATTT
13177 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
13214 TATATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:13218 original size:2 final size:2
Alignment explanation
Indices: 13213--13237 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13203 ACACACACAC
13213 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.