Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022973.1 Corchorus olitorius cultivar O-4 contig23006, 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: 51648
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:4099 original size:11 final size:11
Alignment explanation
Indices: 4083--4108 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4073 AGATAATTTC
4083 TTTTCTTCTAG
1 TTTTCTTCTAG
4094 TTTTCTTCTAG
1 TTTTCTTCTAG
4105 TTTT
1 TTTT
4109 TTAGGCAAGG
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:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:7733 original size:21 final size:21
Alignment explanation
Indices: 7707--7760 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
7697 GCCCATTCAT
**
7707 CGTGCCACCACCGGTTAAGCC
1 CGTGCCACCACCGGCCAAGCC
*
7728 CGTGCCACCACCGGCCATGCC
1 CGTGCCACCACCGGCCAAGCC
*
7749 CGTGCCATCACC
1 CGTGCCACCACC
7761 ATTCCATGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.48, G:0.22, T:0.13
Consensus pattern (21 bp):
CGTGCCACCACCGGCCAAGCC
Found at i:10249 original size:11 final size:11
Alignment explanation
Indices: 10233--10258 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
10223 AGATAATTTA
10233 TTTTCTTCTAG
1 TTTTCTTCTAG
10244 TTTTCTTCTAG
1 TTTTCTTCTAG
10255 TTTT
1 TTTT
10259 TTAGGCAAGG
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:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:11899 original size:72 final size:72
Alignment explanation
Indices: 11628--11913 Score: 378
Period size: 72 Copynumber: 4.0 Consensus size: 72
11618 AAAAGTAGTG
* * * * * * *
11628 AGGATTGTGCGAAGGACTGCGAAATGTGCGAACTGCCTCGGCTATAGTCGCAAGGAGGAAGATGA
1 AGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGAAGAGGA
*
11693 TTATGTA
66 TCATGTA
* ** **
11700 AGGATTGTGCGAAGGACTGCCAAATGTGGGAACAGCCTCGGCTTTAATCGCAATGAA-AGAGATT
1 AGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGA-AGAGG
11764 ATCATGTA
65 ATCATGTA
*
11772 AGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATGGCAATGAAGAAGAGGA
1 AGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGAAGAGGA
11837 TCATGTA
66 TCATGTA
* * *
11844 AGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCAAG-TACGATCGTAATGAAGAAGAGG
1 AGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTC-GGCTACAATCGCAATGAAGAAGAGG
*
11908 ACCATG
65 ATCATG
11914 GGATGGGTTG
Statistics
Matches: 191, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
71 1 0.01
72 188 0.98
73 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (72 bp):
AGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGAAGAGGA
TCATGTA
Found at i:12124 original size:11 final size:11
Alignment explanation
Indices: 12108--12144 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
12098 CCAGATAGTG
12108 GGTCATGTGGT
1 GGTCATGTGGT
12119 GGTCATGTGGT
1 GGTCATGTGGT
**
12130 GGAGATGTGGT
1 GGTCATGTGGT
12141 GGTC
1 GGTC
12145 CATTACCCAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.11, C:0.08, G:0.49, T:0.32
Consensus pattern (11 bp):
GGTCATGTGGT
Found at i:12355 original size:35 final size:35
Alignment explanation
Indices: 12314--12409 Score: 156
Period size: 35 Copynumber: 2.7 Consensus size: 35
12304 TATAACATAG
12314 CCCCAAGTGTTGAATGATGAAGGAATTGCTAGAGT
1 CCCCAAGTGTTGAATGATGAAGGAATTGCTAGAGT
* * *
12349 CCCCAAGTATTGAATGATGAAGGAATTGTTGGAGT
1 CCCCAAGTGTTGAATGATGAAGGAATTGCTAGAGT
*
12384 CCCCAAGTGTTGAATCATGAAGGAAT
1 CCCCAAGTGTTGAATGATGAAGGAAT
12410 ATGTTGTACT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 56 1.00
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (35 bp):
CCCCAAGTGTTGAATGATGAAGGAATTGCTAGAGT
Found at i:15331 original size:26 final size:26
Alignment explanation
Indices: 15247--15335 Score: 115
Period size: 27 Copynumber: 3.3 Consensus size: 26
15237 ATTTAATTGG
* *
15247 GGTCATTTGCACGTCCATGTGCATTTT
1 GGTCATTTCCACGTCCA-GGGCATTTT
* *
15274 GGTCATTTGCATGTCCAGGGGCATTTT
1 GGTCATTTCCACGTCCA-GGGCATTTT
*
15301 GGTCATTTCCACGTCCAGGCCATTTT
1 GGTCATTTCCACGTCCAGGGCATTTT
15327 GGTCATTTC
1 GGTCATTTC
15336 AAGTACACTT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
26 17 0.30
27 39 0.70
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.38
Consensus pattern (26 bp):
GGTCATTTCCACGTCCAGGGCATTTT
Found at i:20065 original size:15 final size:15
Alignment explanation
Indices: 20045--20093 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
20035 AAGTAAATCC
20045 AAAAGAAGATTTTGG
1 AAAAGAAGATTTTGG
**
20060 AAAAGAAG-TTAATTCC
1 AAAAGAAGATT--TTGG
20076 AAAAGAAGATTTTGG
1 AAAAGAAGATTTTGG
20091 AAA
1 AAA
20094 TTAATAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 2 0.07
15 13 0.48
16 10 0.37
17 2 0.07
ACGTcount: A:0.51, C:0.04, G:0.20, T:0.24
Consensus pattern (15 bp):
AAAAGAAGATTTTGG
Found at i:20921 original size:27 final size:27
Alignment explanation
Indices: 20891--20942 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
20881 ATCTAAAATA
20891 TTAACTGAGAATAAAATATTAAATTGT
1 TTAACTGAGAATAAAATATTAAATTGT
20918 TTAACTGAGAATAAAATATTAAATT
1 TTAACTGAGAATAAAATATTAAATT
20943 CATCTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.37
Consensus pattern (27 bp):
TTAACTGAGAATAAAATATTAAATTGT
Found at i:23930 original size:17 final size:16
Alignment explanation
Indices: 23876--23926 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
23866 ATCACCCCCC
*
23876 AGATCACTAGTGATCTA
1 AGATCACCAGTGATC-A
*
23893 AGGTCACCAGTGATGCA
1 AGATCACCAGTGAT-CA
*
23910 AGATCACCGGTGATCA
1 AGATCACCAGTGATCA
23926 A
1 A
23927 AGATTACATG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Found at i:26637 original size:18 final size:19
Alignment explanation
Indices: 26614--26650 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
26604 TAAATTTCAG
*
26614 AAAATT-CCAATTGGAAAC
1 AAAATTCCCAATTGAAAAC
26632 AAAATTCCCAATTGAAAAC
1 AAAATTCCCAATTGAAAAC
26651 TCCTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.51, C:0.19, G:0.08, T:0.22
Consensus pattern (19 bp):
AAAATTCCCAATTGAAAAC
Found at i:34907 original size:40 final size:40
Alignment explanation
Indices: 34852--34934 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
34842 ATGGGATCCA
34852 ATTGTTTCCTCACAATATCATCAAATGACTTAAACAACCC
1 ATTGTTTCCTCACAATATCATCAAATGACTTAAACAACCC
34892 ATTGTTTCCTCACAATATCATCAAATGACTTAAACAACCC
1 ATTGTTTCCTCACAATATCATCAAATGACTTAAACAACCC
34932 ATT
1 ATT
34935 CTCTACAGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.31
Consensus pattern (40 bp):
ATTGTTTCCTCACAATATCATCAAATGACTTAAACAACCC
Found at i:35126 original size:30 final size:30
Alignment explanation
Indices: 35092--35150 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
35082 GATTTTGTTC
35092 TGTCAGTAAAAGTGAAATCAAGTAATCTGA
1 TGTCAGTAAAAGTGAAATCAAGTAATCTGA
35122 TGTCAGTAAAAGTGAAATCAAGTAATCTG
1 TGTCAGTAAAAGTGAAATCAAGTAATCTG
35151 CACACCATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.27
Consensus pattern (30 bp):
TGTCAGTAAAAGTGAAATCAAGTAATCTGA
Found at i:36196 original size:2 final size:2
Alignment explanation
Indices: 36189--36218 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
36179 GAGCCTTCAG
36189 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36219 TTTTCGAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:37025 original size:15 final size:15
Alignment explanation
Indices: 37007--37070 Score: 56
Period size: 15 Copynumber: 4.0 Consensus size: 15
36997 CCCAACCCGA
*
37007 AACCGAAACTGACCC
1 AACCGAAAATGACCC
*
37022 AACCCAAAAATGACCC
1 AA-CCGAAAATGACCC
*
37038 GAAAACCGAAACTGACCC
1 ---AACCGAAAATGACCC
*
37056 AACCCAAAATGACCC
1 AACCGAAAATGACCC
37071 GAATCCCCCA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
15 15 0.38
16 11 0.28
18 11 0.28
19 2 0.05
ACGTcount: A:0.45, C:0.38, G:0.11, T:0.06
Consensus pattern (15 bp):
AACCGAAAATGACCC
Found at i:37065 original size:33 final size:34
Alignment explanation
Indices: 37001--37073 Score: 132
Period size: 34 Copynumber: 2.2 Consensus size: 34
36991 AATCCGCCCA
37001 ACCCG-AAACCGAAACTGACCCAACCCAAAAATG
1 ACCCGAAAACCGAAACTGACCCAACCCAAAAATG
37034 ACCCGAAAACCGAAACTGACCCAACCC-AAAATG
1 ACCCGAAAACCGAAACTGACCCAACCCAAAAATG
37067 ACCCGAA
1 ACCCGAA
37074 TCCCCCAACA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 18 0.46
34 21 0.54
ACGTcount: A:0.45, C:0.37, G:0.12, T:0.05
Consensus pattern (34 bp):
ACCCGAAAACCGAAACTGACCCAACCCAAAAATG
Found at i:38889 original size:22 final size:22
Alignment explanation
Indices: 38864--38908 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
38854 TTTCAACAAA
38864 TCAAGTTCTGGGAAGAAATTGT
1 TCAAGTTCTGGGAAGAAATTGT
* * *
38886 TCAAGTTTTGGGCAGAAGTTGT
1 TCAAGTTCTGGGAAGAAATTGT
38908 T
1 T
38909 TTGCATTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.09, G:0.29, T:0.36
Consensus pattern (22 bp):
TCAAGTTCTGGGAAGAAATTGT
Found at i:41452 original size:26 final size:26
Alignment explanation
Indices: 41422--41473 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
41412 TTCATCAAAG
*
41422 GATAAAAAGTATTAAGAATTTTGCTC
1 GATAAAAAGTATTAAGAATTTAGCTC
*
41448 GATAAGAAGTATTAAGAATTTAGCTC
1 GATAAAAAGTATTAAGAATTTAGCTC
41474 CTCATGGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.33
Consensus pattern (26 bp):
GATAAAAAGTATTAAGAATTTAGCTC
Found at i:51268 original size:28 final size:28
Alignment explanation
Indices: 51229--51299 Score: 124
Period size: 28 Copynumber: 2.5 Consensus size: 28
51219 GTCACTTAAG
* *
51229 GGGGCATTTTGGTCATTTTGCATATCTA
1 GGGGCATTTTGGTCATTTTACACATCTA
51257 GGGGCATTTTGGTCATTTTACACATCTA
1 GGGGCATTTTGGTCATTTTACACATCTA
51285 GGGGCATTTTGGTCA
1 GGGGCATTTTGGTCA
51300 CTTCAAGTGC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.18, C:0.15, G:0.27, T:0.39
Consensus pattern (28 bp):
GGGGCATTTTGGTCATTTTACACATCTA
Done.