Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020447.1 Corchorus olitorius cultivar O-4 contig20480, 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: 56553
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:2389 original size:2 final size:2
Alignment explanation
Indices: 2382--2412 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2372 TTGCTAGTTA
*
2382 AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2413 AAGGGACACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3233 original size:92 final size:93
Alignment explanation
Indices: 3134--3302 Score: 277
Period size: 92 Copynumber: 1.8 Consensus size: 93
3124 TAGTAATATC
* *
3134 GTAAAAATAAAATAGGTATAAGGATATTAGATTTAACTAAA-AAAAATAGAGTTTTTAGTTGAGT
1 GTAAAAATAAAATAGGTATAAGAATATTAGATTTAACTAAATAAAAATAGAGTTTTTAGTTGACT
3198 AAAACTATAAAAGTAAAATGGTAAAATG
66 AAAACTATAAAAGTAAAATGGTAAAATG
* * * *
3226 GTAAAAATAAAATAGTTATAAGAATGTTAGATTTAATTAAATGAAAATAGAGTTTTTAGTTGACT
1 GTAAAAATAAAATAGGTATAAGAATATTAGATTTAACTAAATAAAAATAGAGTTTTTAGTTGACT
3291 AAAACTATAAAA
66 AAAACTATAAAA
3303 ATTTACACAA
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 37 0.53
93 33 0.47
ACGTcount: A:0.51, C:0.02, G:0.15, T:0.31
Consensus pattern (93 bp):
GTAAAAATAAAATAGGTATAAGAATATTAGATTTAACTAAATAAAAATAGAGTTTTTAGTTGACT
AAAACTATAAAAGTAAAATGGTAAAATG
Found at i:3373 original size:31 final size:31
Alignment explanation
Indices: 3338--3399 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
3328 ATATTCGAAA
**
3338 AATAAGGGTATAGTAGGCGATTCAAAAGTTT
1 AATAAGGGTATAACAGGCGATTCAAAAGTTT
3369 AATAAGGGTATAACAGGCGATTCAAAAGTTT
1 AATAAGGGTATAACAGGCGATTCAAAAGTTT
3400 TACAAAACTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.27
Consensus pattern (31 bp):
AATAAGGGTATAACAGGCGATTCAAAAGTTT
Found at i:5086 original size:167 final size:165
Alignment explanation
Indices: 4773--5268 Score: 645
Period size: 166 Copynumber: 2.9 Consensus size: 165
4763 GAATAAACAT
* * * * * *
4773 GTGGAATTACTAAAAGATCACCATCC-CGGATTAATGAGGAGCGAGAGAATTAATTTTTTTCGTC
1 GTGGAATTACTAAAAGATCCCCA-CCAAGGATTGATGATGAGCTAGAGAACTAATTTTTTTCGTC
* *
4837 TTTTCCCACTTGGCAGATTACTTAAATAAAATAACTGCCCTAATTTTTGATTCTTGAGGGGATTA
65 TTTTCCTACTTGGCAGATTAC-T---T-AAAT-A-T--CCTAACTTTTGATTCTTGAGGGGATTA
*
4902 AATAACTAGACTTTTTGGTCATTTCTCAATTGACTTTAATAGAGTA
121 AATAACTA-ACTTTTTGGTCATTTCTCAATTGACTTGAATAGAGTA
* * * ** * *
4948 GTGGAATTACTAAAAGATCCCTACCAAGGCTTGGTTTTGGAGTTAGAGAACTAATCTTTTTCGTC
1 GTGGAATTACTAAAAGATCCCCACCAAGGATTGATGAT-GAGCTAGAGAACTAATTTTTTTCGTC
* *
5013 TTTTTCTACTTGGCAGATTACTTAAATATCCTAACTTTTGATTCTTGAGGGGATTAAATAAGTAA
65 TTTTCCTACTTGGCAGATTACTTAAATATCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAA
*
5078 TCTTTTTGGTCATTTCTCAATGGACTTGAATAGAGTA
130 -CTTTTTGGTCATTTCTCAATTGACTTGAATAGAGTA
*
5115 GTGGAATTACTAAAAGATCCCCATCAAGGATTGATGATGAGCTATG-GAACTAATTTTTTTCGTC
1 GTGGAATTACTAAAAGATCCCCACCAAGGATTGATGATGAGCTA-GAGAACTAATTTTTTTCGTC
*
5179 TTTTCCTACTTGGCAGATTATTTAAATATCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAA
65 TTTTCCTACTTGGCAGATTACTTAAATATCCTAACTTTTGATTCTTGAGGGGATTAAATAACT-A
*
5244 ACTTTTTGGTTATTTCTCAATTGAC
129 ACTTTTTGGTCATTTCTCAATTGAC
5269 AAATGATTCA
Statistics
Matches: 284, Mismatches: 32, Indels: 19
0.85 0.10 0.06
Matches are distributed among these distances:
166 105 0.37
167 102 0.36
169 1 0.00
170 1 0.00
171 4 0.01
172 1 0.00
174 2 0.01
175 27 0.10
176 41 0.14
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (165 bp):
GTGGAATTACTAAAAGATCCCCACCAAGGATTGATGATGAGCTAGAGAACTAATTTTTTTCGTCT
TTTCCTACTTGGCAGATTACTTAAATATCCTAACTTTTGATTCTTGAGGGGATTAAATAACTAAC
TTTTTGGTCATTTCTCAATTGACTTGAATAGAGTA
Found at i:8452 original size:14 final size:14
Alignment explanation
Indices: 8433--8459 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8423 TCAACCAAAC
8433 CAAAAAAAAAAAAG
1 CAAAAAAAAAAAAG
8447 CAAAAAAAAAAAA
1 CAAAAAAAAAAAA
8460 TCGTTTCTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.07, G:0.04, T:0.00
Consensus pattern (14 bp):
CAAAAAAAAAAAAG
Found at i:11743 original size:20 final size:20
Alignment explanation
Indices: 11718--11755 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
11708 ATACTTATGT
11718 TTTCTTTTTAAGTTGCTTAA
1 TTTCTTTTTAAGTTGCTTAA
11738 TTTCTTTTTAAGTTGCTT
1 TTTCTTTTTAAGTTGCTT
11756 GATTATGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.16, C:0.11, G:0.11, T:0.63
Consensus pattern (20 bp):
TTTCTTTTTAAGTTGCTTAA
Found at i:14698 original size:19 final size:19
Alignment explanation
Indices: 14670--14716 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
14660 ATACTCAAAC
* *
14670 ACAAAAAATTTTAATTAAA
1 ACAAAAAATTGTAAGTAAA
*
14689 ACAAATAATTGTAAGTAAA
1 ACAAAAAATTGTAAGTAAA
*
14708 AAAAAAAAT
1 ACAAAAAAT
14717 GTCAAGTTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (19 bp):
ACAAAAAATTGTAAGTAAA
Found at i:15086 original size:26 final size:25
Alignment explanation
Indices: 15036--15085 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
15026 AAAACTTGAC
15036 CCTCCATTTTTACATAATTTATTTT
1 CCTCCATTTTTACATAATTTATTTT
* *
15061 CCTCCACTTTTT-TATAATTTGTTTT
1 CCTCCA-TTTTTACATAATTTATTTT
15086 TTATATAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.20, C:0.20, G:0.02, T:0.58
Consensus pattern (25 bp):
CCTCCATTTTTACATAATTTATTTT
Found at i:23402 original size:11 final size:12
Alignment explanation
Indices: 23381--23418 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
23371 TTAAATAAAC
23381 AATAAAGATAATA
1 AATAAA-ATAATA
*
23394 TAT-AAATAATA
1 AATAAAATAATA
23405 AATAAAATAATA
1 AATAAAATAATA
23417 AA
1 AA
23419 AGATGAGTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 8 0.36
12 12 0.55
13 2 0.09
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (12 bp):
AATAAAATAATA
Found at i:23402 original size:24 final size:23
Alignment explanation
Indices: 23372--23416 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
23362 TTTTGCTACT
23372 TAAATAA-ACAATAAAGATAATATA
1 TAAATAATA-AATAAA-ATAATATA
23396 TAAATAATAAATAAAATAATA
1 TAAATAATAAATAAAATAATA
23417 AAAGATGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 6 0.30
24 13 0.65
25 1 0.05
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (23 bp):
TAAATAATAAATAAAATAATATA
Found at i:23413 original size:20 final size:19
Alignment explanation
Indices: 23374--23418 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
23364 TTGCTACTTA
*
23374 AATAAACAATAAAGATAAT
1 AATAAACAATAAAGAAAAT
* *
23393 ATATAAATAATAAATAAAAT
1 A-ATAAACAATAAAGAAAAT
23413 AATAAA
1 AATAAA
23419 AGATGAGTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (19 bp):
AATAAACAATAAAGAAAAT
Found at i:24145 original size:7 final size:7
Alignment explanation
Indices: 24129--24159 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
24119 GAATGTAACG
*
24129 AGAAGTA
1 AGAAGCA
24136 AGAAGCA
1 AGAAGCA
24143 AGAAGCA
1 AGAAGCA
24150 AGAAGCA
1 AGAAGCA
24157 AGA
1 AGA
24160 TCTGAGCTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.58, C:0.10, G:0.29, T:0.03
Consensus pattern (7 bp):
AGAAGCA
Found at i:28781 original size:6 final size:6
Alignment explanation
Indices: 28781--28870 Score: 83
Period size: 6 Copynumber: 15.0 Consensus size: 6
28771 ACAACAGCAA
* * * * * * *
28781 CAACAG CATCCG CAGCAG CAGCAG CATCAG CATCAG CATCAG CAACAG
1 CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG CAACAG
* *
28829 CAACAG -AATCAG CATCAG CATCAG CAACAG CAACAG CAACAG
1 CAACAG CAA-CAG CAACAG CAACAG CAACAG CAACAG CAACAG
28871 TCTCAACAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
5 2 0.03
6 71 0.96
7 1 0.01
ACGTcount: A:0.40, C:0.33, G:0.19, T:0.08
Consensus pattern (6 bp):
CAACAG
Found at i:28799 original size:12 final size:12
Alignment explanation
Indices: 28784--28866 Score: 94
Period size: 12 Copynumber: 6.9 Consensus size: 12
28774 ACAGCAACAA
* *
28784 CAGCATCCGCAG
1 CAGCATCAGCAT
*
28796 CAGCAGCAGCAT
1 CAGCATCAGCAT
28808 CAGCATCAGCAT
1 CAGCATCAGCAT
* *
28820 CAGCAACAGCAA
1 CAGCATCAGCAT
*
28832 CAGAATCAGCAT
1 CAGCATCAGCAT
*
28844 CAGCATCAGCAA
1 CAGCATCAGCAT
*
28856 CAGCAACAGCA
1 CAGCATCAGCA
28867 ACAGTCTCAA
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 59 1.00
ACGTcount: A:0.39, C:0.34, G:0.19, T:0.08
Consensus pattern (12 bp):
CAGCATCAGCAT
Found at i:28803 original size:24 final size:24
Alignment explanation
Indices: 28775--28866 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
28765 TCAACGACAA
* * *
28775 CAGCAACAACAGCATCCGCAGCAG
1 CAGCAGCAACAGCATCAGCATCAG
*
28799 CAGCAGCATCAGCATCAGCATCAG
1 CAGCAGCAACAGCATCAGCATCAG
* *
28823 CAACAGCAACAGAATCAGCATCAG
1 CAGCAGCAACAGCATCAGCATCAG
* *
28847 CATCAGCAACAGCAACAGCA
1 CAGCAGCAACAGCATCAGCA
28867 ACAGTCTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.40, C:0.34, G:0.18, T:0.08
Consensus pattern (24 bp):
CAGCAGCAACAGCATCAGCATCAG
Found at i:28818 original size:30 final size:30
Alignment explanation
Indices: 28784--28866 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
28774 ACAGCAACAA
* * *
28784 CAGCATCCGCAGCAGCAGCAGCATCAGCAT
1 CAGCATCAGCAACAGCAACAGCATCAGCAT
*
28814 CAGCATCAGCAACAGCAACAGAATCAGCAT
1 CAGCATCAGCAACAGCAACAGCATCAGCAT
28844 CAGCATCAGCAACAGCAACAGCA
1 CAGCATCAGCAACAGCAACAGCA
28867 ACAGTCTCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.39, C:0.34, G:0.19, T:0.08
Consensus pattern (30 bp):
CAGCATCAGCAACAGCAACAGCATCAGCAT
Found at i:32770 original size:1 final size:1
Alignment explanation
Indices: 32764--32791 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
32754 CAAGGAAGGG
32764 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
32792 AATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:40831 original size:6 final size:6
Alignment explanation
Indices: 40823--40857 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
40813 TCTGAGAGGG
*
40823 ATTGGG ATTGGA ATTGGA ATTGGA ATTGGA ATTGG
1 ATTGGA ATTGGA ATTGGA ATTGGA ATTGGA ATTGG
40858 TCGGTCTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.34
Consensus pattern (6 bp):
ATTGGA
Found at i:42474 original size:17 final size:17
Alignment explanation
Indices: 42452--42490 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
42442 AAATTAAATA
**
42452 TTTTTATTTTAATATAT
1 TTTTTATTGAAATATAT
*
42469 TTTTTATTGAAATTTAT
1 TTTTTATTGAAATATAT
42486 TTTTT
1 TTTTT
42491 TTAATTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (17 bp):
TTTTTATTGAAATATAT
Found at i:43832 original size:12 final size:12
Alignment explanation
Indices: 43815--43841 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
43805 CATTTTAAAT
43815 TATAATATAATA
1 TATAATATAATA
43827 TATAATATAATA
1 TATAATATAATA
43839 TAT
1 TAT
43842 TTATAAATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TATAATATAATA
Found at i:44227 original size:178 final size:178
Alignment explanation
Indices: 43910--44368 Score: 514
Period size: 178 Copynumber: 2.6 Consensus size: 178
43900 CCGATCAAGG
* *
43910 TGATTTAAGTGTCTATTAAAAGGTTGTTCCATGATCTACAACTTTCATGAAAGACTCGAAAACTA
1 TGATTTAAGTGTCTATTAAAAGGTTGTTTCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
* * * *
43975 AATTTAATGTTTCAAGTATCAAAAAA-GCTTCTGAATAATTAGTTGTTTCGATTAATGGGAATGG
66 AATTTAATGTTTCAAGTAT-AAAAAATGCTTCTGAAAAATTAATTGTTTCGATTAACGGGAATGA
* * ****
44039 ACGATCCACTTAGTAAAACATTACTTTTACTCCAGATGTTTTCTTGAGC
130 ACGATCCACTTAATAAAACATAACTTTTACTCCAGATGTCCGATTGAGC
* * * *
44088 TGATTCAAGTGTCTCA-TAAAAGGTTATTTTATGATCTACAACTTTCATGCAGGACTCGAAAACT
1 TGATTTAAGTGTCT-ATTAAAAGGTTGTTTCATGATCTACAACTTTCATGAAGGACTCGAAAACT
* * *
44152 AAATTTAATGTTTCAAGTATAAAAAATGCTTCTAAAAAATTAATT-TCTTCGGTTACCGAGG-AT
65 AAATTTAATGTTTCAAGTATAAAAAATGCTTCTGAAAAATTAATTGT-TTCGATTAACG-GGAAT
* * * * * *
44215 GAACGGTCCACTTAATAATACATAATTTTTGCTCTAGATGTCCGATTGAGG
128 GAACGATCCACTTAATAAAACATAACTTTTACTCCAGATGTCCGATTGAGC
* * * * * * *
44266 TGATTTAAGTGTCTATTAAAAGGCTGTTTCGTGATCTTCAACTTTTATGTAGGACTTGAAAGCTA
1 TGATTTAAGTGTCTATTAAAAGGTTGTTTCATGATCTACAACTTTCATGAAGGACTCGAAAACT-
* * *
44331 AAATTTTATTTTTCAAATACT-AAAAATGCTTCTGAAAA
65 AAATTTAATGTTTCAAGTA-TAAAAAATGCTTCTGAAAA
44369 GTTTATATTT
Statistics
Matches: 235, Mismatches: 39, Indels: 13
0.82 0.14 0.05
Matches are distributed among these distances:
177 8 0.03
178 191 0.81
179 35 0.15
180 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Consensus pattern (178 bp):
TGATTTAAGTGTCTATTAAAAGGTTGTTTCATGATCTACAACTTTCATGAAGGACTCGAAAACTA
AATTTAATGTTTCAAGTATAAAAAATGCTTCTGAAAAATTAATTGTTTCGATTAACGGGAATGAA
CGATCCACTTAATAAAACATAACTTTTACTCCAGATGTCCGATTGAGC
Found at i:46683 original size:22 final size:22
Alignment explanation
Indices: 46655--46785 Score: 106
Period size: 22 Copynumber: 6.0 Consensus size: 22
46645 ATACATTGTG
46655 ATTTTGATAACCACACTATGAA
1 ATTTTGATAACCACACTATGAA
*** *
46677 ATTTTGATAATTTCCCTATGAA
1 ATTTTGATAACCACACTATGAA
*
46699 ATTTTGATAATCACACTAT-AA
1 ATTTTGATAACCACACTATGAA
* * * *
46720 A-ATTGGTAACCGCATTATGAAA
1 ATTTTGATAACCACACTATG-AA
* * *
46742 ATTTTGATAACCTC-TTCATAAA
1 ATTTTGATAACCACACT-ATGAA
*
46764 ATTTTGATAACCACACCATGAA
1 ATTTTGATAACCACACTATGAA
46786 GTTTCCCTTC
Statistics
Matches: 84, Mismatches: 20, Indels: 10
0.74 0.18 0.09
Matches are distributed among these distances:
20 12 0.14
21 3 0.04
22 58 0.69
23 11 0.13
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (22 bp):
ATTTTGATAACCACACTATGAA
Found at i:46933 original size:25 final size:26
Alignment explanation
Indices: 46885--46933 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
46875 ATTTTGTTAA
46885 CCTCCCTAGGAAACTTTGATAACCTC
1 CCTCCCTAGGAAACTTTGATAACCTC
* *
46911 CCTCCCTATG-AATTTTGATAACC
1 CCTCCCTAGGAAACTTTGATAACC
46934 ACACTATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.27, C:0.33, G:0.10, T:0.31
Consensus pattern (26 bp):
CCTCCCTAGGAAACTTTGATAACCTC
Found at i:47080 original size:44 final size:44
Alignment explanation
Indices: 47027--47125 Score: 110
Period size: 44 Copynumber: 2.2 Consensus size: 44
47017 GTAACGTCTG
* * ***
47027 TATGGAATTTTAAAAACTACACTATGACGTTTTGATAACC-TCC
1 TATGAAATTTTAAAAACCACACTATGAAAATTTGATAACCTTCC
**
47070 ATATGAAATTTTAGTAACCACACTATGAAAATTTGATAACCTTCC
1 -TATGAAATTTTAAAAACCACACTATGAAAATTTGATAACCTTCC
*
47115 TATGTAATTTT
1 TATGAAATTTT
47126 GGTTTGATTG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 43 0.93
45 3 0.07
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.37
Consensus pattern (44 bp):
TATGAAATTTTAAAAACCACACTATGAAAATTTGATAACCTTCC
Found at i:47081 original size:22 final size:22
Alignment explanation
Indices: 46830--47126 Score: 96
Period size: 22 Copynumber: 13.3 Consensus size: 22
46820 CTCTTTATTT
46830 AATTTTGATAACATCTCCATA--A
1 AATTTTGATAAC--CTCCATATGA
46852 AATTTTTG-TAACCTTCC-TATGA
1 AA-TTTTGATAACC-TCCATATGA
* * *
46874 AATTTTGTTAACCTCCCTAGGA
1 AATTTTGATAACCTCCATATGA
* *
46896 AACTTTGATAACCTCCCTCCCTATG-
1 AATTTTGATAA----CCTCCATATGA
*
46921 AATTTTGATAACC-ACACTAT-A
1 AATTTTGATAACCTCCA-TATGA
* * * *
46942 AATTTTAATAACCTTCGTATAA
1 AATTTTGATAACCTCCATATGA
* * *
46964 AATTTTGTTAACGACACTC-TAAGA
1 AATTTTGATAAC--CTC-CATATGA
*** *
46988 AATTTTGATAACCTTTTTATAA
1 AATTTTGATAACCTCCATATGA
* * ** *
47010 AATTTTGGTAACGTCTGTATGG
1 AATTTTGATAACCTCCATATGA
* * *
47032 AATTTT-AAAAACTACACTATGA
1 AATTTTGATAACCTCCA-TATGA
**
47054 CGTTTTGATAACCTCCATATGA
1 AATTTTGATAACCTCCATATGA
*
47076 AATTTT-AGTAACC-ACACTATGA
1 AATTTTGA-TAACCTCCA-TATGA
* *
47098 AAATTTGATAACCTTCC-TATGT
1 AATTTTGATAACC-TCCATATGA
47120 AATTTTG
1 AATTTTG
47127 GTTTGATTGA
Statistics
Matches: 202, Mismatches: 48, Indels: 50
0.67 0.16 0.17
Matches are distributed among these distances:
20 4 0.02
21 37 0.18
22 112 0.55
23 13 0.06
24 16 0.08
25 11 0.05
26 9 0.04
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (22 bp):
AATTTTGATAACCTCCATATGA
Found at i:47449 original size:2 final size:2
Alignment explanation
Indices: 47442--47533 Score: 175
Period size: 2 Copynumber: 46.0 Consensus size: 2
47432 AGGGTAAATT
47442 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
47484 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
47526 AT AC AC AC
1 AC AC AC AC
47534 CATGTGAACC
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 88 1.00
ACGTcount: A:0.50, C:0.49, G:0.00, T:0.01
Consensus pattern (2 bp):
AC
Found at i:48507 original size:16 final size:16
Alignment explanation
Indices: 48486--48520 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
48476 AACCTAGGAT
48486 ACACAAAGAGAGAGAC
1 ACACAAAGAGAGAGAC
48502 ACACAAAGAGAGAGAC
1 ACACAAAGAGAGAGAC
48518 ACA
1 ACA
48521 GATACGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.20, G:0.23, T:0.00
Consensus pattern (16 bp):
ACACAAAGAGAGAGAC
Found at i:55335 original size:13 final size:13
Alignment explanation
Indices: 55317--55341 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55307 TTTTGTGTTC
55317 GGTTCAATTTTTG
1 GGTTCAATTTTTG
55330 GGTTCAATTTTT
1 GGTTCAATTTTT
55342 AAGAAGAGGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.20, T:0.56
Consensus pattern (13 bp):
GGTTCAATTTTTG
Done.