Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018112.1 Corchorus olitorius cultivar O-4 contig18145, 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: 15919
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Found at i:1195 original size:27 final size:27
Alignment explanation
Indices: 1165--1240 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 27
1155 AGTGAACTTG
*
1165 AAATGACCAAAATGCCCCT-GAATGCGC
1 AAATGACTAAAATGCCCCTAG-ATGCGC
*
1192 AAATGACTAAAATGCCCCCTAGATGTGC
1 AAATGACTAAAATG-CCCCTAGATGCGC
1220 AAATGACTAAAATGCCCCTAG
1 AAATGACTAAAATGCCCCTAG
1241 TTTTTTTTGG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
27 20 0.44
28 24 0.53
29 1 0.02
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.18
Consensus pattern (27 bp):
AAATGACTAAAATGCCCCTAGATGCGC
Found at i:1413 original size:21 final size:21
Alignment explanation
Indices: 1387--1441 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1377 CGGCCATTCA
**
1387 CCGTGCCACCACCGGTTAAGC
1 CCGTGCCACCACCGGCCAAGC
*
1408 CCGTGCCACCACCGGCCATGC
1 CCGTGCCACCACCGGCCAAGC
*
1429 CCGTGCCATCACC
1 CCGTGCCACCACC
1442 ATTCCAAGCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.13
Consensus pattern (21 bp):
CCGTGCCACCACCGGCCAAGC
Found at i:1814 original size:15 final size:14
Alignment explanation
Indices: 1794--1823 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1784 ATCTTTTTAA
1794 TTTTCCTTGCATTAT
1 TTTTCCTTG-ATTAT
1809 TTTTCCTTGATTAT
1 TTTTCCTTGATTAT
1823 T
1 T
1824 GCTTTGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCCTTGATTAT
Found at i:2035 original size:18 final size:18
Alignment explanation
Indices: 2012--2046 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2002 TCTGCATGCA
2012 TCATAATCTTAAAATATG
1 TCATAATCTTAAAATATG
2030 TCATAATCTTAAAATAT
1 TCATAATCTTAAAATAT
2047 ACCATAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.40
Consensus pattern (18 bp):
TCATAATCTTAAAATATG
Found at i:2052 original size:18 final size:18
Alignment explanation
Indices: 2013--2054 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2003 CTGCATGCAT
**
2013 CATAATCTTAAAATATGT
1 CATAATCTTAAAATATAC
2031 CATAATCTTAAAATATAC
1 CATAATCTTAAAATATAC
2049 CATAAT
1 CATAAT
2055 TTTTTCGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (18 bp):
CATAATCTTAAAATATAC
Found at i:8075 original size:21 final size:19
Alignment explanation
Indices: 8049--8106 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
8039 ACTGCTCTAT
8049 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
8070 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
8089 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
8107 TGCTAAACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:8881 original size:69 final size:69
Alignment explanation
Indices: 8766--8898 Score: 175
Period size: 69 Copynumber: 1.9 Consensus size: 69
8756 CAACTAAGGA
* * *
8766 AAGGAAAAATGGTGGGAGCACCATTTAAATACATCTCAATGTTAAAATTA-GATATAAAGACAAT
1 AAGGAAAAATGGTAGGAACACCATTTAAATACATCTCAATGCTAAAATTACG-TATAAAGACAAT
8830 ACACT
65 ACACT
8835 AAGGAAAAAATGGTAGGAACACCA-TT-AATCACATC-CAAATGCTAAAATTACGTATAAAGACA
1 AAGG-AAAAATGGTAGGAACACCATTTAAAT-ACATCTC-AATGCTAAAATTACGTATAAAGACA
8897 AT
63 AT
8899 GCATTTCAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
68 4 0.07
69 35 0.61
70 18 0.32
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.23
Consensus pattern (69 bp):
AAGGAAAAATGGTAGGAACACCATTTAAATACATCTCAATGCTAAAATTACGTATAAAGACAATA
CACT
Found at i:9936 original size:2 final size:2
Alignment explanation
Indices: 9931--9968 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
9921 TATAACTTAA
*
9931 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9969 TAACCTAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11421 original size:37 final size:37
Alignment explanation
Indices: 11371--11523 Score: 191
Period size: 37 Copynumber: 4.0 Consensus size: 37
11361 AATTAAAATC
11371 TAAAAGCTT-ATGGGAACTTTCCCAATTTGAAAACTTT
1 TAAAA-CTTGATGGGAACTTTCCCAATTTGAAAACTTT
* *
11408 TAAAACTTTATGGGAACTTTCCTAATTTGAAAACTTT
1 TAAAACTTGATGGGAACTTTCCCAATTTGAAAACTTT
* **
11445 GAAGGCTTGATGGGAACTTTCCCAATTTGAAAACTTTTT
1 TAAAACTTGATGGGAACTTTCCCAATTTGAAAAC--TTT
*
11484 TAAAAAAACTTGATGGGAACTTTCCCGATTTGAAAACTTT
1 T---AAAACTTGATGGGAACTTTCCCAATTTGAAAACTTT
11524 GATGGAAGTG
Statistics
Matches: 100, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
36 3 0.03
37 61 0.61
39 3 0.03
40 3 0.03
42 30 0.30
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (37 bp):
TAAAACTTGATGGGAACTTTCCCAATTTGAAAACTTT
Found at i:11458 original size:74 final size:75
Alignment explanation
Indices: 11376--11525 Score: 223
Period size: 79 Copynumber: 2.0 Consensus size: 75
11366 AAATCTAAAA
* *
11376 GCTTATGGGAACTTTCCCAATTTGAAAAC-TTTT-AAAACTTTATGGGAACTTTCCTAATTTGAA
1 GCTTATGGGAACTTTCCCAATTTGAAAACTTTTTAAAAACTTGATGGGAACTTTCCCAATTTGAA
11439 AACTTTGAAG
66 AACTTTGAAG
*
11449 GCTTGATGGGAACTTTCCCAATTTGAAAACTTTTTTAAAAAAACTTGATGGGAACTTTCCCGATT
1 GCTT-ATGGGAACTTTCCCAATTTGAAAAC-TTTTT--AAAAACTTGATGGGAACTTTCCCAATT
11514 TGAAAACTTTGA
62 TGAAAACTTTGA
11526 TGGAAGTGTC
Statistics
Matches: 68, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
73 4 0.06
74 25 0.37
76 4 0.06
79 35 0.51
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (75 bp):
GCTTATGGGAACTTTCCCAATTTGAAAACTTTTTAAAAACTTGATGGGAACTTTCCCAATTTGAA
AACTTTGAAG
Found at i:14311 original size:21 final size:21
Alignment explanation
Indices: 14285--14326 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
14275 ACACAAAGAA
*
14285 GTTTCAGGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
14306 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
14327 CCTAAGGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (21 bp):
GTTTCAAGCTCATCGGAGTTG
Done.