Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022856.1 Corchorus olitorius cultivar O-4 contig22889, 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: 45393
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Found at i:329 original size:16 final size:16
Alignment explanation
Indices: 308--398 Score: 96
Period size: 16 Copynumber: 5.7 Consensus size: 16
298 CTTCCCGAGA
308 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
324 CCGAACCCG-ACATAAC
1 CCGAACCCGAAAAT-AC
* *
340 CCGATCTCGAAAATAC
1 CCGAACCCGAAAATAC
**
356 CCGAACCCG-ACTTAAC
1 CCGAACCCGAAAAT-AC
*
372 CCGAGCCCGAAAATAC
1 CCGAACCCGAAAATAC
388 CCGAACCCGAA
1 CCGAACCCGAA
399 CCTGCCCGAG
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
15 5 0.08
16 49 0.83
17 5 0.08
ACGTcount: A:0.37, C:0.40, G:0.14, T:0.09
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:412 original size:32 final size:32
Alignment explanation
Indices: 308--397 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
298 CTTCCCGAGA
*
308 CCGAACCCGAAAATACCCGAACCCGACATAAC
1 CCGAGCCCGAAAATACCCGAACCCGACATAAC
* * *
340 CCGATCTCGAAAATACCCGAACCCGACTTAAC
1 CCGAGCCCGAAAATACCCGAACCCGACATAAC
372 CCGAGCCCGAAAATACCCGAACCCGA
1 CCGAGCCCGAAAATACCCGAACCCGA
398 ACCTGCCCGA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.37, C:0.40, G:0.14, T:0.09
Consensus pattern (32 bp):
CCGAGCCCGAAAATACCCGAACCCGACATAAC
Found at i:3705 original size:15 final size:15
Alignment explanation
Indices: 3668--3706 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
3658 AAAGGTGTGG
*
3668 ACGGGATTCAGGCTT
1 ACGGGATTCAGGATT
* *
3683 ATGAGATTCAGGATT
1 ACGGGATTCAGGATT
3698 ACGGGATTC
1 ACGGGATTC
3707 CTAGCATCGG
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (15 bp):
ACGGGATTCAGGATT
Found at i:11491 original size:14 final size:14
Alignment explanation
Indices: 11474--11501 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
11464 TCCGGCGCCT
11474 CCACCGACGGGCCC
1 CCACCGACGGGCCC
11488 CCACCGACGGGCCC
1 CCACCGACGGGCCC
11502 TCAAAATTTT
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:0.14, C:0.57, G:0.29, T:0.00
Consensus pattern (14 bp):
CCACCGACGGGCCC
Found at i:18802 original size:27 final size:27
Alignment explanation
Indices: 18772--18892 Score: 91
Period size: 27 Copynumber: 4.9 Consensus size: 27
18762 TTTGGTAAGA
*
18772 AAAAATGGAATTTGGTAATTAAAGAGT
1 AAAAATGGAATTTGGTAACTAAAGAGT
* *
18799 AAAAGTGAAATTTGGTAACT-AAG-GT
1 AAAAATGGAATTTGGTAACTAAAGAGT
* * *
18824 -TAAATGGTATATGG----T-AAGA--
1 AAAAATGGAATTTGGTAACTAAAGAGT
*
18843 AAAAATGGAATTTGGTAATTAAAGAGT
1 AAAAATGGAATTTGGTAACTAAAGAGT
* *
18870 AAAAGTGAAATTTGGTAACTAAA
1 AAAAATGGAATTTGGTAACTAAA
18893 TTCAGTTAAA
Statistics
Matches: 71, Mismatches: 14, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
20 15 0.21
24 10 0.14
25 6 0.08
26 3 0.04
27 37 0.52
ACGTcount: A:0.47, C:0.02, G:0.22, T:0.29
Consensus pattern (27 bp):
AAAAATGGAATTTGGTAACTAAAGAGT
Found at i:18816 original size:71 final size:71
Alignment explanation
Indices: 18725--18891 Score: 316
Period size: 71 Copynumber: 2.4 Consensus size: 71
18715 AAAAGGGTAA
* *
18725 AGTAAAAATGAAATTTGGTAACTAAGGTTAAATGGTATTTGGTAAGAAAAAATGGAATTTGGTAA
1 AGTAAAAGTGAAATTTGGTAACTAAGGTTAAATGGTATATGGTAAGAAAAAATGGAATTTGGTAA
18790 TTAAAG
66 TTAAAG
18796 AGTAAAAGTGAAATTTGGTAACTAAGGTTAAATGGTATATGGTAAGAAAAAATGGAATTTGGTAA
1 AGTAAAAGTGAAATTTGGTAACTAAGGTTAAATGGTATATGGTAAGAAAAAATGGAATTTGGTAA
18861 TTAAAG
66 TTAAAG
18867 AGTAAAAGTGAAATTTGGTAACTAA
1 AGTAAAAGTGAAATTTGGTAACTAA
18892 ATTCAGTTAA
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 94 1.00
ACGTcount: A:0.46, C:0.02, G:0.23, T:0.30
Consensus pattern (71 bp):
AGTAAAAGTGAAATTTGGTAACTAAGGTTAAATGGTATATGGTAAGAAAAAATGGAATTTGGTAA
TTAAAG
Found at i:19733 original size:16 final size:17
Alignment explanation
Indices: 19700--19733 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
19690 ACATTTTCCA
19700 TCAAATTCATCAAATTT
1 TCAAATTCATCAAATTT
*
19717 TCAAATT-ATCAAGTTT
1 TCAAATTCATCAAATTT
19733 T
1 T
19734 GGAGAAGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (17 bp):
TCAAATTCATCAAATTT
Found at i:36701 original size:15 final size:16
Alignment explanation
Indices: 36677--36716 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
36667 AGAGGTTGAA
*
36677 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
36692 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
36708 AGAAAACAA
1 AGAAAACAA
36717 AACAAACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:39039 original size:18 final size:19
Alignment explanation
Indices: 39018--39055 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
39008 TCTTGAAATT
*
39018 AATCTTC-AATGGTCTTCA
1 AATCTTCAAATAGTCTTCA
39036 AATCTTCAAATAGTCTTCA
1 AATCTTCAAATAGTCTTCA
39055 A
1 A
39056 TAAGTCTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (19 bp):
AATCTTCAAATAGTCTTCA
Found at i:41932 original size:11 final size:12
Alignment explanation
Indices: 41916--41948 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
41906 GATGGCTCGG
41916 GTGGCCGGGC-T
1 GTGGCCGGGCAT
41927 GTGGCCGGGCAT
1 GTGGCCGGGCAT
41939 GTGGCTCGGG
1 GTGGC-CGGG
41949 ACGGCTTGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 6 0.30
13 4 0.20
ACGTcount: A:0.03, C:0.24, G:0.55, T:0.18
Consensus pattern (12 bp):
GTGGCCGGGCAT
Found at i:45211 original size:15 final size:16
Alignment explanation
Indices: 45187--45226 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
45177 AGAGGTTGAA
*
45187 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
45202 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
45218 AGAAAACAA
1 AGAAAACAA
45227 AACAAACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Done.