Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014444.1 Corchorus olitorius cultivar O-4 contig14477, 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: 55730
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:4191 original size:25 final size:25
Alignment explanation
Indices: 4163--4212 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
4153 CTCACTTCAT
4163 ACCCTATTCATCAAATTATGCCATG
1 ACCCTATTCATCAAATTATGCCATG
4188 ACCCTATTCATCAAATTATGCCATG
1 ACCCTATTCATCAAATTATGCCATG
4213 TGTCCATAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (25 bp):
ACCCTATTCATCAAATTATGCCATG
Found at i:6389 original size:22 final size:20
Alignment explanation
Indices: 6342--6390 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
6332 ATATAGAATG
* *
6342 TTATTATTTAGTATTTTTAT
1 TTATTATTTAGTACTGTTAT
6362 TT-TTATTTAGTAACTGTTATT
1 TTATTATTTAGT-ACTGTTA-T
6383 TTATTATT
1 TTATTATT
6391 ATTATAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 9 0.38
20 7 0.29
21 3 0.12
22 5 0.21
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.67
Consensus pattern (20 bp):
TTATTATTTAGTACTGTTAT
Found at i:11012 original size:24 final size:25
Alignment explanation
Indices: 10984--11034 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
10974 AAAGACTAAC
* *
10984 AATAAAATAAATAAGCAAGA-AAAT
1 AATAAAATAAAGAAACAAGATAAAT
*
11008 AATAAAATTAAGAAACAAGATAAAT
1 AATAAAATAAAGAAACAAGATAAAT
11033 AA
1 AA
11035 ATACTCCAAT
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:0.71, C:0.04, G:0.08, T:0.18
Consensus pattern (25 bp):
AATAAAATAAAGAAACAAGATAAAT
Found at i:13205 original size:27 final size:27
Alignment explanation
Indices: 13174--13230 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
13164 CAATTTCCGC
13174 CAAAGTTCCCGCAGCAAACCAAAATTG
1 CAAAGTTCCCGCAGCAAACCAAAATTG
** *
13201 CAAAGTTGTCGCAGCAACCCAAAATTG
1 CAAAGTTCCCGCAGCAAACCAAAATTG
13228 CAA
1 CAA
13231 TATTGCCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.28, G:0.16, T:0.16
Consensus pattern (27 bp):
CAAAGTTCCCGCAGCAAACCAAAATTG
Found at i:13276 original size:27 final size:27
Alignment explanation
Indices: 13182--13279 Score: 99
Period size: 27 Copynumber: 3.6 Consensus size: 27
13172 GCCAAAGTTC
* *
13182 CCGCAGCAAACCAAAATTGCAAAGTTG
1 CCGCAGCAACCCAAAATTGCAAAATTG
* *
13209 TCGCAGCAACCCAAAATTGCAATATTG
1 CCGCAGCAACCCAAAATTGCAAAATTG
* * *
13236 CCACAAG-TACCCAAAATTGAAAAATTG
1 CCGC-AGCAACCCAAAATTGCAAAATTG
* *
13263 CCGCAGCGAGCCAAAAT
1 CCGCAGCAACCCAAAAT
13280 CACCAAGGCA
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
26 2 0.04
27 53 0.93
28 2 0.04
ACGTcount: A:0.41, C:0.27, G:0.16, T:0.16
Consensus pattern (27 bp):
CCGCAGCAACCCAAAATTGCAAAATTG
Found at i:14123 original size:26 final size:23
Alignment explanation
Indices: 14086--14135 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 23
14076 ACATGAAAAG
14086 AAATAAAAGAGTAATAAAAAGGGGAA
1 AAATAAAAGAGT--T-AAAAGGGGAA
*
14112 AAATAAAGGAGTTAAAAGGGGAA
1 AAATAAAAGAGTTAAAAGGGGAA
14135 A
1 A
14136 GATGAAGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 11 0.48
24 1 0.04
26 11 0.48
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.12
Consensus pattern (23 bp):
AAATAAAAGAGTTAAAAGGGGAA
Found at i:22792 original size:18 final size:18
Alignment explanation
Indices: 22771--22806 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
22761 CGAAGGAAGA
22771 AGAAGAAACGAAAAGGGG
1 AGAAGAAACGAAAAGGGG
**
22789 AGAAGAAATTAAAAGGGG
1 AGAAGAAACGAAAAGGGG
22807 TTGTTTCACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.03, G:0.36, T:0.06
Consensus pattern (18 bp):
AGAAGAAACGAAAAGGGG
Found at i:23825 original size:34 final size:34
Alignment explanation
Indices: 23786--23997 Score: 192
Period size: 34 Copynumber: 5.9 Consensus size: 34
23776 GAGTCAAGTT
*
23786 TTTAAGTTTTCAAATTGGGAAAGTTCCCATCGGG
1 TTTAAGTTTTCAAATTGGGAAAGTTCCCATCAGG
* *
23820 TTTAAGTTTTCAAACTGGGAAAGTTCCCACCAGG
1 TTTAAGTTTTCAAATTGGGAAAGTTCCCATCAGG
* ** *
23854 TTTTAGTTTTCAAATTGGGAAAGTTCCCAAAAAGTTTT
1 TTTAAGTTTTCAAATTGGGAAAGTTCCC-ATCAG---G
* *
23892 TTTAAGTTTTTAAATTGGAAAAGTTCCCATCAGG
1 TTTAAGTTTTCAAATTGGGAAAGTTCCCATCAGG
* * *
23926 TTTTAGTTTTCAATTTATGGAAAGTTCCCGTCATTTTCA-G
1 TTTAAGTTTTCAAATT-GGGAAAGTT-CC--CA---TCAGG
* *
23966 TTTTAGTTTTCAAAGTGGGAAAGTTCCCATCA
1 TTTAAGTTTTCAAATTGGGAAAGTTCCCATCA
23998 AAAGCATTTT
Statistics
Matches: 145, Mismatches: 22, Indels: 23
0.76 0.12 0.12
Matches are distributed among these distances:
33 3 0.02
34 70 0.48
35 10 0.07
36 4 0.03
37 3 0.02
38 29 0.20
39 8 0.06
40 15 0.10
41 3 0.02
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (34 bp):
TTTAAGTTTTCAAATTGGGAAAGTTCCCATCAGG
Found at i:23926 original size:72 final size:73
Alignment explanation
Indices: 23820--23954 Score: 209
Period size: 72 Copynumber: 1.9 Consensus size: 73
23810 TCCCATCGGG
*
23820 TTTAAGTTTTCAAACTGGGAAAGTTCCCACCAGGTTTTAGTTTTCAAATT-GGGAAAGTTCCCAA
1 TTTAAGTTTTCAAACTGGAAAAGTTCCCACCAGGTTTTAGTTTTCAAATTAGGGAAAGTTCCCAA
23884 AAAGTTTT
66 AAAGTTTT
* * * * *
23892 TTTAAGTTTTTAAATTGGAAAAGTTCCCATCAGGTTTTAGTTTTCAATTTATGGAAAGTTCCC
1 TTTAAGTTTTCAAACTGGAAAAGTTCCCACCAGGTTTTAGTTTTCAAATTAGGGAAAGTTCCC
23955 GTCATTTTCA
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
72 45 0.80
73 11 0.20
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (73 bp):
TTTAAGTTTTCAAACTGGAAAAGTTCCCACCAGGTTTTAGTTTTCAAATTAGGGAAAGTTCCCAA
AAAGTTTT
Found at i:35973 original size:21 final size:20
Alignment explanation
Indices: 35942--35986 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
35932 TCTTTTTCTT
35942 TTTCTTTCTTT-AATTTTCGA
1 TTTCTTTCTTTCAA-TTTCGA
35962 TTTCTTTACTTTCAATTTCGA
1 TTTCTTT-CTTTCAATTTCGA
35983 TTTC
1 TTTC
35987 AATTGTGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.30
21 14 0.61
22 2 0.09
ACGTcount: A:0.16, C:0.18, G:0.04, T:0.62
Consensus pattern (20 bp):
TTTCTTTCTTTCAATTTCGA
Found at i:45591 original size:3 final size:3
Alignment explanation
Indices: 45583--45607 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
45573 TGCCTCCCCT
45583 TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG T
45608 AAATGAGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (3 bp):
TGG
Found at i:46642 original size:11 final size:11
Alignment explanation
Indices: 46628--46655 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
46618 TTTTAGGTCG
46628 ATTTTTTTTAT
1 ATTTTTTTTAT
46639 ATTTTTTTTAT
1 ATTTTTTTTAT
46650 ATTTTT
1 ATTTTT
46656 CGATCTAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
ATTTTTTTTAT
Done.