Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020020.1 Corchorus olitorius cultivar O-4 contig20053, 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: 55695
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--48 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1 ACN
4 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
46 CT C
1 CT C
49 ATTTTCTGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1025 original size:29 final size:31
Alignment explanation
Indices: 990--1073 Score: 102
Period size: 29 Copynumber: 2.8 Consensus size: 31
980 GCAGATTTTG
*
990 AAAGGTTTAGGACCAATTTGAGCAAGTC-T-
1 AAAGGTTTAGGACCAAATTGAGCAAGTCGTC
* *
1019 AAAGGTTTAGAACCAAATTGAGC-ATTCGGTC
1 AAAGGTTTAGGACCAAATTGAGCAAGTC-GTC
*
1050 AAAGGTTTAGGGCCAAATTGAGCA
1 AAAGGTTTAGGACCAAATTGAGCA
1074 TTTAGCCCCA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 3 0.07
29 21 0.46
30 1 0.02
31 21 0.46
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAGGTTTAGGACCAAATTGAGCAAGTCGTC
Found at i:1057 original size:31 final size:31
Alignment explanation
Indices: 990--1075 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 31
980 GCAGATTTTG
*
990 AAAGGTTTAGGACCAATTTGAGCA--AGTCT
1 AAAGGTTTAGGACCAAATTGAGCATTAGTCT
* *
1019 AAAGGTTTAGAACCAAATTGAGCATTCGGTC-
1 AAAGGTTTAGGACCAAATTGAGCATT-AGTCT
*
1050 AAAGGTTTAGGGCCAAATTGAGCATT
1 AAAGGTTTAGGACCAAATTGAGCATT
1076 TAGCCCCAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 22 0.45
31 24 0.49
32 3 0.06
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (31 bp):
AAAGGTTTAGGACCAAATTGAGCATTAGTCT
Found at i:2407 original size:73 final size:73
Alignment explanation
Indices: 2274--2409 Score: 209
Period size: 73 Copynumber: 1.9 Consensus size: 73
2264 CAAACAAACT
* * *** *
2274 GTTATGAACTGAGAGCTATTACTGACCATTCAATTGTCACTCAAATTGTTTTTGAGCTATTACTG
1 GTTATGAACCGAGAGCTATTACTGACCATTCAATTGTCACTCAAACTGTTTGACACCTATTACTG
2339 AACTGGGA
66 AACTGGGA
*
2347 GTTATGAACCGGGAGCTATTACTGACCATTCAATTGTCACTCAAACTGTTTGACACCTATTAC
1 GTTATGAACCGAGAGCTATTACTGACCATTCAATTGTCACTCAAACTGTTTGACACCTATTAC
2410 GCTTTTGTGT
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
73 56 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (73 bp):
GTTATGAACCGAGAGCTATTACTGACCATTCAATTGTCACTCAAACTGTTTGACACCTATTACTG
AACTGGGA
Found at i:13451 original size:4 final size:4
Alignment explanation
Indices: 13436--13489 Score: 81
Period size: 4 Copynumber: 13.5 Consensus size: 4
13426 ACAGGATTGA
* *
13436 ATAT ACAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT GTAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
13484 GTAT AT
1 ATAT AT
13490 GCGTAATAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (4 bp):
ATAT
Found at i:13490 original size:6 final size:6
Alignment explanation
Indices: 13436--13489 Score: 81
Period size: 6 Copynumber: 9.0 Consensus size: 6
13426 ACAGGATTGA
* *
13436 ATATAC ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATGTAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
*
13484 GTATAT
1 ATATAT
13490 GCGTAATAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (6 bp):
ATATAT
Found at i:13490 original size:10 final size:10
Alignment explanation
Indices: 13436--13489 Score: 81
Period size: 10 Copynumber: 5.4 Consensus size: 10
13426 ACAGGATTGA
*
13436 ATATACATAT
1 ATATATATAT
13446 ATATATATAT
1 ATATATATAT
13456 ATATATATAT
1 ATATATATAT
13466 ATATATATAT
1 ATATATATAT
* *
13476 ATATGTATGT
1 ATATATATAT
13486 ATAT
1 ATAT
13490 GCGTAATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 41 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (10 bp):
ATATATATAT
Found at i:23250 original size:24 final size:24
Alignment explanation
Indices: 23222--23296 Score: 67
Period size: 24 Copynumber: 3.5 Consensus size: 24
23212 ATTAAAGTGC
*
23222 AACATATTTCATGTCCAACATAAA
1 AACATAATTCATGTCCAACATAAA
**
23246 AAC---A-TCAT-T-CAA-ATGCA
1 AACATAATTCATGTCCAACATAAA
23263 A-CATAATTCATGTCCAACATAAA
1 AACATAATTCATGTCCAACATAAA
23286 AACATAATTCA
1 AACATAATTCA
23297 AGTTCAGCAT
Statistics
Matches: 38, Mismatches: 5, Indels: 16
0.64 0.08 0.27
Matches are distributed among these distances:
16 1 0.03
17 4 0.11
18 3 0.08
19 2 0.05
20 8 0.21
21 1 0.03
22 3 0.08
23 4 0.11
24 12 0.32
ACGTcount: A:0.48, C:0.21, G:0.04, T:0.27
Consensus pattern (24 bp):
AACATAATTCATGTCCAACATAAA
Found at i:23273 original size:40 final size:41
Alignment explanation
Indices: 23176--23310 Score: 170
Period size: 40 Copynumber: 3.4 Consensus size: 41
23166 ATCAATTAAT
* * **
23176 AAAGTTCAACATAATTCATGTCCAACAT-GATTCATAATT-
1 AAAGTGCAACATAATTCATGTCCAACATAAAAACATAATTC
* *
23215 AAAGTGCAACATATTTCATGTCCAACATAAAAACATCATTC
1 AAAGTGCAACATAATTCATGTCCAACATAAAAACATAATTC
23256 AAA-TGCAACATAATTCATGTCCAACATAAAAACATAATTC
1 AAAGTGCAACATAATTCATGTCCAACATAAAAACATAATTC
* *
23296 -AAGTTCAGCATAATT
1 AAAGTGCAACATAATT
23311 TACACCAAAT
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 28 0.34
40 52 0.63
41 3 0.04
ACGTcount: A:0.44, C:0.19, G:0.07, T:0.29
Consensus pattern (41 bp):
AAAGTGCAACATAATTCATGTCCAACATAAAAACATAATTC
Found at i:23307 original size:24 final size:24
Alignment explanation
Indices: 23262--23308 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
23252 ATTCAAATGC
*
23262 AACATAATTCATGTCCAACATAAA
1 AACATAATTCAAGTCCAACATAAA
* *
23286 AACATAATTCAAGTTCAGCATAA
1 AACATAATTCAAGTCCAACATAA
23309 TTTACACCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.19, G:0.06, T:0.26
Consensus pattern (24 bp):
AACATAATTCAAGTCCAACATAAA
Found at i:25445 original size:51 final size:51
Alignment explanation
Indices: 25354--25500 Score: 143
Period size: 52 Copynumber: 2.8 Consensus size: 51
25344 ATCAACCTAA
* * *
25354 GCCATTCACACATCCAACCAAATATTAAGCAAAAAGGCATAAATCCA-TGTT
1 GCCATTCACA-ATCAAACCAAATATTAACCAAAAAGGCATAAATCCATTGCT
* ** ** **
25405 GTCATTCACTAATCAAACCAAATATTAACCAAAATTGCATATTTGTATTGCT
1 GCCATTCAC-AATCAAACCAAATATTAACCAAAAAGGCATAAATCCATTGCT
* * *
25457 GCCATTCACAAATCAAACCAAAGATTAACCAAACAGCCATAAAT
1 GCCATTCAC-AATCAAACCAAATATTAACCAAAAAGGCATAAAT
25501 TAGCTGCTGC
Statistics
Matches: 75, Mismatches: 19, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
51 36 0.48
52 39 0.52
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (51 bp):
GCCATTCACAATCAAACCAAATATTAACCAAAAAGGCATAAATCCATTGCT
Found at i:32428 original size:31 final size:31
Alignment explanation
Indices: 32393--32553 Score: 184
Period size: 31 Copynumber: 5.3 Consensus size: 31
32383 GGTGTCCGAC
*
32393 GTGGCATGCCATGTGTACCAAAAAGCGACAT
1 GTGGCACGCCATGTGTACCAAAAAGCGACAT
* * *
32424 GTGGCAAGCCACGTGTACCAAAAAGCGACAC
1 GTGGCACGCCATGTGTACCAAAAAGCGACAT
* *
32455 GTGGCACGCCACGTGTACCAAAAAGTGACAT
1 GTGGCACGCCATGTGTACCAAAAAGCGACAT
** *
32486 GTATCACGCCATGTGTACCAAAAAGTGACAT
1 GTGGCACGCCATGTGTACCAAAAAGCGACAT
* *
32517 GTGGCATGCC-TCGTGCA-CAAAAAG-GACAT
1 GTGGCACGCCAT-GTGTACCAAAAAGCGACAT
*
32546 GTGCCACG
1 GTGGCACG
32554 TGTCATTTTT
Statistics
Matches: 114, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
29 11 0.10
30 8 0.07
31 95 0.83
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.17
Consensus pattern (31 bp):
GTGGCACGCCATGTGTACCAAAAAGCGACAT
Found at i:49232 original size:40 final size:40
Alignment explanation
Indices: 49188--49267 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
49178 TTTCACATAA
* *
49188 ATGTTATGATAAATCCTATCCCCCTTAATTATCTAGAATT
1 ATGTTATAATAAATCATATCCCCCTTAATTATCTAGAATT
49228 ATGTTATAATAAATCATATCCCCCTTAATTATCTAGAATT
1 ATGTTATAATAAATCATATCCCCCTTAATTATCTAGAATT
49268 GTATCCTCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.40
Consensus pattern (40 bp):
ATGTTATAATAAATCATATCCCCCTTAATTATCTAGAATT
Found at i:49897 original size:38 final size:38
Alignment explanation
Indices: 49837--49912 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
49827 TTTGACTCCT
* *
49837 CTCCGATGCCTATGAACTGCAGAGGCCAATCCATCTTA
1 CTCCAATGCCTATGAACCGCAGAGGCCAATCCATCTTA
49875 CTCCAATGCCTATGAACCGCAGAGGCCAATCCATCTTA
1 CTCCAATGCCTATGAACCGCAGAGGCCAATCCATCTTA
49913 GATGCTGTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.28, C:0.33, G:0.17, T:0.22
Consensus pattern (38 bp):
CTCCAATGCCTATGAACCGCAGAGGCCAATCCATCTTA
Found at i:50799 original size:32 final size:31
Alignment explanation
Indices: 50762--50826 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 31
50752 TAAATACTTG
*
50762 ATACACAAATATATATTCAAACACTATTTGAT
1 ATACACAAATATATATTCAAA-AATATTTGAT
* *
50794 ATACACAAATATATGTTTAAAAATATTTGAT
1 ATACACAAATATATATTCAAAAATATTTGAT
50825 AT
1 AT
50827 CGTCTATCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 11 0.37
32 19 0.63
ACGTcount: A:0.48, C:0.11, G:0.05, T:0.37
Consensus pattern (31 bp):
ATACACAAATATATATTCAAAAATATTTGAT
Found at i:52546 original size:78 final size:78
Alignment explanation
Indices: 52452--52612 Score: 279
Period size: 78 Copynumber: 2.1 Consensus size: 78
52442 AGATTTATAG
* *
52452 TTTTACTCAACAAAAAACTCTATTTTTATTT-ATTTAAATCTAATATCTTTATAACTATTTTATT
1 TTTTACTCAACAAAAAACTCTATTTTTATTTGA-TTAAATCTAATATCTTTATAACTATTTCAGT
52516 TTACCATTTTACTA
65 TTACCATTTTACTA
*
52530 TTTTACTCAACTAAAAACTCTATTTTTATTTGATTAAATCTAATATCTTTATAACTATTTCAGTT
1 TTTTACTCAACAAAAAACTCTATTTTTATTTGATTAAATCTAATATCTTTATAACTATTTCAGTT
52595 TACCATTTTACTA
66 TACCATTTTACTA
52608 TTTTA
1 TTTTA
52613 AGTAGAAAAC
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
78 78 0.99
79 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.01, T:0.51
Consensus pattern (78 bp):
TTTTACTCAACAAAAAACTCTATTTTTATTTGATTAAATCTAATATCTTTATAACTATTTCAGTT
TACCATTTTACTA
Done.