Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2273
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: 65352
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:1793 original size:18 final size:18
Alignment explanation
Indices: 1770--1804 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1760 TATCATATGA
1770 TATTTATTACATTAATTC
1 TATTTATTACATTAATTC
1788 TATTTATTACATTAATT
1 TATTTATTACATTAATT
1805 TCATGTTTAT
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:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTATTACATTAATTC
Found at i:2302 original size:18 final size:18
Alignment explanation
Indices: 2279--2317 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2269 GTAACTTTTT
*
2279 ATTTTATGATTTTAAA-AA
1 ATTTTAT-ATTTAAAATAA
2297 ATTTTATATTTAAAATAA
1 ATTTTATATTTAAAATAA
2315 ATT
1 ATT
2318 AACTTTACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
ATTTTATATTTAAAATAA
Found at i:3863 original size:949 final size:952
Alignment explanation
Indices: 2091--3977 Score: 2567
Period size: 948 Copynumber: 2.0 Consensus size: 952
2081 GAATAAATTG
* * *
2091 CTCATTTATAAAAAATTTTGTATAACAAGATTTATATAACAATAACTAAAGATGATAAAAATACA
1 CTCAATTATAAAAAATTTTATATAACAAGATTTATATAACAATAACAAAAGATGATAAAAATACA
* *
2156 AGTATCTACCTTAAGAAAAGTCAAATATAATCCATGCAATGCATAAAAAAAACTATTTGAAAATA
66 AGTATCTACCTTAAGAAAAGTCAAACATAACCCATGCAATGCATAAAAAAAACTATTTGAAAATA
* * * *
2221 TATGCTTAAATAAGAAAGTGAGAACAAAGCTTATCTTGCTTTTGAGTTGTAACTTTTTATTTTAT
131 TATGCTTAAATAAGAAAGTGAGAACAAAGCTTATCTTGCCTTTAAGTTATAACTTTTCATTTTAT
* * *
2286 GATTTTAAAAAATTTTATATTTAAAATAAATTAACTTTACCTAATTTCAATTATTATAAATTAAA
196 GATTTTAAAAAATTTTATATTCAAAACAAATTAACTTTACCTAATTTCAATTACTATAAATTAAA
* * *
2351 TTATAAAGTCTAAATCTAAAAAATAAATAAAGTAAATAAATAAATAACATCCTATGTCAACAAGC
261 CTATAAAATCTAAATATAAAAAATAAATAAAGTAAATAAATAAATAACATCCTATGTCAACAAGC
* * *
2416 TAGTCTTGTAAACAAAGGAGAGAGAAGTGCTATTTTGACTTTTCAAAAATTGCCAAGGCTATTTT
326 AAGTCTTGTAAACAAAGGAGAGAGAAGAGC-----TGA-TTATCAAAAATTGCCAAGGCTATTTT
* * * *
2481 CTAGCACATGTCATCAACATTAAGTGGGCATTGTTATCAATTTTTTTTTTAATTTTTTACAAAAT
385 CTAGCACACGTCATCAACATTAAGTAGGCATTGTAATCAATTTTTTTTTTAATTTTCTACAAAAT
* * *
2546 AATAAGATTGAGAATCTAAATTAAAGTGAAAACAAACGTCAATAATATTTTAAATTCTCAATAAA
450 AATAAGATTAAAAATCTAAATTAAAGTGAAAACAAACGTCAATAATATTTAAAATTCTCAATAAA
*
2611 TCATATAAAATGACATCATTAATAGCAAACATTATAAAATTTTCAAAAAATTTTATTAAAGACAA
515 TCATATAAAATGACACCATTAATAGCAAACATTATAAAATTTTCAAAAAATTTTATTAAAGACAA
* *** *
2676 AATTAATATTATGTAAAACTTTTGGGAGGTATAGACTATTGTCCCTTTTTATTTTTCTTTCCAAC
580 AATCAATATTA-GTAAAACCGATGGGAGGCATAGACTATTGTCCCTTTTTATTTTTCTTTCCAAC
* *
2741 TATTTGATTTTTCCCTCGAACTTACAATAAAACTAAAGGGAAGATCAGAATTATGTTATGAAATT
644 TATTTGATTTTTCCCTCGAACCTACAATAAAACTAAAGGGAAGATCAAAATTATGTTATGAAATT
*
2806 GCAAGCTTATAGTTTTTGAGCTAAAAGCTGAACAGGACAATAGAGGTGCAACTGAGCTGAAAAAC
709 GCAAGCTTATAGTTTTTGAGCTAAAAGCTGAACAAGACAATAGAGGTGCAACTGAGCTGAAAAAC
* * *
2871 CAAGCTGGAAGCAAGAGTTGTAAGGAATATCGAGCTAAAAAAACAAGTTGGATATGACAATGAAT
774 CAAGCTAGAAGCAAGAGTTGTAAGGAATATCGAGCTAAAAAAACAAGCTGGATATG-CAATAAAT
* * * * *
2936 AGGAGGTTATAACCATTAGTCGAGGTAGCATTAGTTATTATTTCGTTTTCTTTGTTGATACAGTA
838 AGAAGATTATAACCATTAGCCGAGGTAGCAGTAGTTATTATTTCGTTTTCTTTGTTGATACAGCA
3001 AATA-AGATAGTTTACCATTCAGAGTCATCAGATGATCAACGAAGGAAAAC
903 AATAGA-ATAGTTTACCATTCAGAGTCATCAGATGATCAACGAAGGAAAAC
* *
3051 CTCAATTATAAAAAGA-TTTATATAATAA-ATTTTTATAACAATAACAAAAGATGATAAAAAAAT
1 CTCAATTATAAAAA-ATTTTATATAACAAGATTTATATAACAATAACAAAAGATGAT--AAAAAT
** * * *
3114 ATGAGTATCTACCTTAAAGAAAATGTCAAACATAACCCCTGCAATGCATGAAAGAAACTATTTGA
63 ACAAGTATCTACCTT-AAGAAAA-GTCAAACATAACCCATGCAATGCATAAAAAAAACTATTTGA
* * *
3179 AAATATATGTTTAAATAAGAAAGTGAGAATAAAGCTTATATTTGCCTTTAAGTTATAACCTTTTC
126 AAATATATGCTTAAATAAGAAAGTGAGAACAAAGCTTAT-CTTGCCTTTAAGTTATAA-CTTTTC
*
3244 ATTTTATGATTTT-AAAAATTTTATATTCAAAACAAATTAACTTTACCTAATTTTAATTACTATA
189 ATTTTATGATTTTAAAAAATTTTATATTCAAAACAAATTAACTTTACCTAATTTCAATTACTATA
* * *
3308 ATTTAAACTATAAAATCTAAATATAAAAAATAAATAAAGTAAATAAATAAATGATATCCTATGTC
254 AATTAAACTATAAAATCTAAATATAAAAAATAAATAAAGTAAATAAATAAATAACATCCTATGTC
* *
3373 AACAAGCAAGTCTTGTAAATAAAGG-GAGA-AA-AGC-G-TTATCAAAAA-TGCCAAGGTTACTT
319 AACAAGCAAGTCTTGTAAACAAAGGAGAGAGAAGAGCTGATTATCAAAAATTGCCAAGGCTA-TT
3432 TTCTAGCACACGTCATCAACATTAA-TAGGCATTGTAAT-AATTTTTTTTTGTAATTTTCTACAA
383 TTCTAGCACACGTCATCAACATTAAGTAGGCATTGTAATCAATTTTTTTTT-TAATTTTCTACAA
* * *
3495 AATAATATGATTAAAAAT-TCAAATTAAAGTGAAAAACAACCGTCAATAATATTTAAAATT-TTA
447 AATAATAAGATTAAAAATCT-AAATTAAAGTG-AAAACAAACGTCAATAATATTTAAAATTCTCA
* ** **** *
3558 ATAAATCGTATAAAATGATGCCATT-ATCA-CAAA-ATTATAAAAGATTTT-AAGGGGTTTTGTT
510 ATAAATCATATAAAATGACACCATTAAT-AGCAAACATTAT-AAA-ATTTTCAAAAAATTTTATT
** * *
3619 AGGGACAAAATCAATATTA-T-AAACCGATGGGAGGCGTAGATTATTGTCCCTTTTTATTTTTCT
572 AAAGACAAAATCAATATTAGTAAAACCGATGGGAGGCATAGACTATTGTCCCTTTTTATTTTTCT
* * * *
3682 TTCCAACTGTTTGATTTTTCTCTTC-AGCCTATAATAACAACTAAAGGGAAGATCAAAATTATGT
637 TTCCAACTATTTGATTTTTC-CCTCGAACCTACAATAA-AACTAAAGGGAAGATCAAAATTATGT
* * * * *
3746 TATGAAGTTGCAAGCTTATGGTTTTTGAGCTAAAAGCTGAACAAGACAATGGAGTTGCAGCTGAG
700 TATGAAATTGCAAGCTTATAGTTTTTGAGCTAAAAGCTGAACAAGACAATAGAGGTGCAACTGAG
* *
3811 CTGAAAAACCAAGCTAGAAGCAAGAGTTGTGAGGAATATTTGAGCT-AAAAAACAAGCTGGATAT
765 CTGAAAAACCAAGCTAGAAGCAAGAGTTGTAAGGAATA-TCGAGCTAAAAAAACAAGCTGGATAT
* * * *
3875 GGAATAAATAGAAGATTATAACCATTAGCCGAGTTGGCAGTAGTTGTTATTTCGTTTTCTTTGTT
829 GCAATAAATAGAAGATTATAACCATTAGCCGAGGTAGCAGTAGTTATTATTTCGTTTTCTTTGTT
* * *
3940 GGTATAGCAAATAGAATAGTTTACCATTTAGAGTCATC
894 GATACAGCAAATAGAATAGTTTACCATTCAGAGTCATC
3978 GGAGGATGAT
Statistics
Matches: 818, Mismatches: 91, Indels: 48
0.85 0.10 0.05
Matches are distributed among these distances:
948 152 0.19
949 143 0.17
950 11 0.01
951 45 0.06
952 88 0.11
953 61 0.07
955 1 0.00
959 25 0.03
960 23 0.03
961 22 0.03
962 9 0.01
963 77 0.09
964 143 0.17
965 18 0.02
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (952 bp):
CTCAATTATAAAAAATTTTATATAACAAGATTTATATAACAATAACAAAAGATGATAAAAATACA
AGTATCTACCTTAAGAAAAGTCAAACATAACCCATGCAATGCATAAAAAAAACTATTTGAAAATA
TATGCTTAAATAAGAAAGTGAGAACAAAGCTTATCTTGCCTTTAAGTTATAACTTTTCATTTTAT
GATTTTAAAAAATTTTATATTCAAAACAAATTAACTTTACCTAATTTCAATTACTATAAATTAAA
CTATAAAATCTAAATATAAAAAATAAATAAAGTAAATAAATAAATAACATCCTATGTCAACAAGC
AAGTCTTGTAAACAAAGGAGAGAGAAGAGCTGATTATCAAAAATTGCCAAGGCTATTTTCTAGCA
CACGTCATCAACATTAAGTAGGCATTGTAATCAATTTTTTTTTTAATTTTCTACAAAATAATAAG
ATTAAAAATCTAAATTAAAGTGAAAACAAACGTCAATAATATTTAAAATTCTCAATAAATCATAT
AAAATGACACCATTAATAGCAAACATTATAAAATTTTCAAAAAATTTTATTAAAGACAAAATCAA
TATTAGTAAAACCGATGGGAGGCATAGACTATTGTCCCTTTTTATTTTTCTTTCCAACTATTTGA
TTTTTCCCTCGAACCTACAATAAAACTAAAGGGAAGATCAAAATTATGTTATGAAATTGCAAGCT
TATAGTTTTTGAGCTAAAAGCTGAACAAGACAATAGAGGTGCAACTGAGCTGAAAAACCAAGCTA
GAAGCAAGAGTTGTAAGGAATATCGAGCTAAAAAAACAAGCTGGATATGCAATAAATAGAAGATT
ATAACCATTAGCCGAGGTAGCAGTAGTTATTATTTCGTTTTCTTTGTTGATACAGCAAATAGAAT
AGTTTACCATTCAGAGTCATCAGATGATCAACGAAGGAAAAC
Found at i:8014 original size:15 final size:12
Alignment explanation
Indices: 7977--8006 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
7967 TTAGTGCTAG
7977 CTTCCT-TCCTC
1 CTTCCTGTCCTC
7988 CTTCCTGTCCTC
1 CTTCCTGTCCTC
8000 CTTCCTG
1 CTTCCTG
8007 GTAGCCTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.00, C:0.50, G:0.07, T:0.43
Consensus pattern (12 bp):
CTTCCTGTCCTC
Found at i:11009 original size:41 final size:41
Alignment explanation
Indices: 10964--11146 Score: 111
Period size: 40 Copynumber: 4.6 Consensus size: 41
10954 GTATAATGAA
10964 AAATATTAATTAATATATTTATATAATATTTATATTATTTT
1 AAATATTAATTAATATATTTATATAATATTTATATTATTTT
* * *
11005 AAATAATAATT-ATAT-TTAAAATATATATTTAT-TTAAATTTT
1 AAATATTAATTAATATATTTATATA-ATATTTATATT--ATTTT
* * *
11046 AATAAATTAA-TAATTTATATTATA-AATTTTTATA-TA-TTT
1 AA-ATATTAATTAATATAT-TTATATAATATTTATATTATTTT
* * * * *
11085 --ATATTATATTTAT-TTTTTATATTATAATTATATTATAATT
1 AAATATTA-ATTAATATATTTATATAATATTTATATTAT-TTT
*
11125 -ATTATTAA-TAATATATTTATAT
1 AAATATTAATTAATATATTTATAT
11147 TTTTTATAAA
Statistics
Matches: 107, Mismatches: 19, Indels: 33
0.67 0.12 0.21
Matches are distributed among these distances:
36 10 0.09
37 10 0.09
38 5 0.05
39 14 0.13
40 24 0.22
41 23 0.21
42 16 0.15
43 2 0.02
44 3 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (41 bp):
AAATATTAATTAATATATTTATATAATATTTATATTATTTT
Found at i:11010 original size:21 final size:21
Alignment explanation
Indices: 10964--11020 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
10954 GTATAATGAA
*
10964 AAATATTAATTA-A-TATATTT
1 AAATAATAATTATATTAT-TTT
* *
10984 ATATAATATTTATATTATTTT
1 AAATAATAATTATATTATTTT
11005 AAATAATAATTATATT
1 AAATAATAATTATATT
11021 TAAAATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
20 9 0.30
21 18 0.60
22 3 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
AAATAATAATTATATTATTTT
Found at i:11089 original size:6 final size:6
Alignment explanation
Indices: 11078--11148 Score: 51
Period size: 6 Copynumber: 12.2 Consensus size: 6
11068 TAAATTTTTA
* * *
11078 TATATT TATA-T TATATT TAT-TT TTTATAT TATAAT TATA-T TATAAT
1 TATATT TATATT TATATT TATATT TATAT-T TATATT TATATT TATATT
* *
11124 TATTATT AATA-A TATATT TATATT T
1 TA-TATT TATATT TATATT TATATT T
11149 TTTATAAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
5 17 0.33
6 26 0.51
7 8 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TATATT
Found at i:11094 original size:11 final size:11
Alignment explanation
Indices: 10977--11147 Score: 82
Period size: 11 Copynumber: 15.1 Consensus size: 11
10967 TATTAATTAA
10977 TATATTTATAT
1 TATATTTATAT
*
10988 AATATTTATAT
1 TATATTTATAT
*
10999 TAT-TTTAAAT
1 TATATTTATAT
* *
11009 AATAATTATATT
1 TATATTTATA-T
* *
11021 TAAAATATATAT
1 T-ATATTTATAT
*
11033 T-TATTTAAAT
1 TATATTTATAT
* * *
11043 TTTA-ATAAAT
1 TATATTTATAT
11053 TAATAATTTATAT
1 T-AT-ATTTATAT
*
11066 TATAAATTTTTA-
1 TAT--ATTTATAT
11078 TATATTTATAT
1 TATATTTATAT
*
11089 TATATTTATTT
1 TATATTTATAT
*
11100 TTTATATTATAAT
1 TATAT-TTAT-AT
11113 TATA-TTATAAT
1 TATATTTAT-AT
* *
11124 TATTATTAATAA
1 TA-TATTTATAT
11136 TATATTTATAT
1 TATATTTATAT
11147 T
1 T
11148 TTTTATAAAA
Statistics
Matches: 120, Mismatches: 27, Indels: 26
0.69 0.16 0.15
Matches are distributed among these distances:
10 27 0.22
11 50 0.42
12 18 0.15
13 25 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TATATTTATAT
Found at i:11139 original size:29 final size:29
Alignment explanation
Indices: 11010--11147 Score: 100
Period size: 29 Copynumber: 5.0 Consensus size: 29
11000 ATTTTAAATA
*
11010 ATAATTA-TATTTAAAATATATATTTAT-TT
1 ATAATTATTA-TTAATA-ATATATTTATATT
*
11039 A-AATT-TTAATAAATTAATA-ATTTATATT
1 ATAATTATT-ATTAA-TAATATATTTATATT
11067 ATAA--ATT-TT--T-ATATATTTATATT
1 ATAATTATTATTAATAATATATTTATATT
* * * * *
11090 ATATTTATTTTTTATATTATAATTATATT
1 ATAATTATTATTAATAATATATTTATATT
11119 ATAATTATTATTAATAATATATTTATATT
1 ATAATTATTATTAATAATATATTTATATT
11148 TTTTATAAAA
Statistics
Matches: 85, Mismatches: 11, Indels: 26
0.70 0.09 0.21
Matches are distributed among these distances:
22 3 0.04
23 13 0.15
25 3 0.04
26 3 0.04
27 6 0.07
28 17 0.20
29 40 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
ATAATTATTATTAATAATATATTTATATT
Found at i:11403 original size:23 final size:23
Alignment explanation
Indices: 11372--11418 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
11362 GCCCTAACTT
11372 CCTTCCTCTTCCCTTCCTGCCGC
1 CCTTCCTCTTCCCTTCCTGCCGC
* * *
11395 CCTTTCTCTTCCTTTTCTGCCGC
1 CCTTCCTCTTCCCTTCCTGCCGC
11418 C
1 C
11419 GCCGCCGCCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.00, C:0.51, G:0.09, T:0.40
Consensus pattern (23 bp):
CCTTCCTCTTCCCTTCCTGCCGC
Found at i:13556 original size:24 final size:24
Alignment explanation
Indices: 13529--13791 Score: 295
Period size: 24 Copynumber: 10.8 Consensus size: 24
13519 TACAGCTGGA
13529 ATGCCTCCCAACAACATGGGAGGG
1 ATGCCTCCCAACAACATGGGAGGG
*
13553 ATGCCTCCCAACAACATGGGAAGG
1 ATGCCTCCCAACAACATGGGAGGG
*
13577 ATGCC-CTC--CAACATGGGAGGG
1 ATGCCTCCCAACAACATGGGAGGG
* *
13598 ATGCCACCTCCTAACAACATAGGAGGG
1 ATG---CCTCCCAACAACATGGGAGGG
*
13625 ATGCCTCCCAACAACATGGGAAGG
1 ATGCCTCCCAACAACATGGGAGGG
*
13649 ATGCCACCCAACAACATGGGAGGG
1 ATGCCTCCCAACAACATGGGAGGG
*
13673 ATGCCACCTCCTAACAACATGGGAGGG
1 ATG---CCTCCCAACAACATGGGAGGG
* *
13700 ATGCCACCGCCTAACAACATAGGAGGG
1 ATGCC-TC-CC-AACAACATGGGAGGG
*
13727 ATGCCCCCCAACAACATGGGAGGG
1 ATGCCTCCCAACAACATGGGAGGG
*
13751 ATGCC-CCC--TAACATGGGAGGG
1 ATGCCTCCCAACAACATGGGAGGG
*
13772 ATGCCACCCAACAACATGGG
1 ATGCCTCCCAACAACATGGG
13792 GAATATGGGG
Statistics
Matches: 205, Mismatches: 19, Indels: 30
0.81 0.07 0.12
Matches are distributed among these distances:
21 32 0.16
22 3 0.01
23 5 0.02
24 102 0.50
25 4 0.02
26 3 0.01
27 56 0.27
ACGTcount: A:0.31, C:0.30, G:0.27, T:0.12
Consensus pattern (24 bp):
ATGCCTCCCAACAACATGGGAGGG
Found at i:13608 original size:72 final size:73
Alignment explanation
Indices: 13532--13791 Score: 327
Period size: 72 Copynumber: 3.6 Consensus size: 73
13522 AGCTGGAATG
*
13532 CCTCCCAACAACATGGGAGGGATGCCTCCCAACAACATGGGAAGGATGCCCTC-CAACATGGGAG
1 CCTCCCAACAACATGGGAGGGATGCCTCCCAACAACATGGGAAGGATGCCCCCACAACATGGGAG
13596 GGATGCCA
66 GGATGCCA
* *
13604 CCTCCTAACAACATAGGAGGGATGCCTCCCAACAACATGGGAAGGATGCCACCCAACAACATGGG
1 CCTCCCAACAACATGGGAGGGATGCCTCCCAACAACATGGGAAGGATGCC-CCC-ACAACATGGG
13669 AGGGATGCCA
64 AGGGATGCCA
* * * *
13679 CCTCCTAACAACATGGGAGGGATGCCACCGCCTAACAACATAGGAGGGATGCCCCCCAACAACAT
1 CCTCCCAACAACATGGGAGGGATGCC-TC-CC-AACAACATGGGAAGGATG-CCCCC-ACAACAT
13744 GGGAGGGATG---
61 GGGAGGGATGCCA
* *
13754 CC-CCC--TAACATGGGAGGGATGCCACCCAACAACATGGG
1 CCTCCCAACAACATGGGAGGGATGCCTCCCAACAACATGGG
13792 GAATATGGGG
Statistics
Matches: 170, Mismatches: 11, Indels: 17
0.86 0.06 0.09
Matches are distributed among these distances:
69 10 0.06
70 2 0.01
71 1 0.01
72 65 0.38
73 2 0.01
74 2 0.01
75 46 0.27
76 1 0.01
77 2 0.01
78 37 0.22
79 2 0.01
ACGTcount: A:0.31, C:0.30, G:0.27, T:0.12
Consensus pattern (73 bp):
CCTCCCAACAACATGGGAGGGATGCCTCCCAACAACATGGGAAGGATGCCCCCACAACATGGGAG
GGATGCCA
Found at i:13645 original size:51 final size:50
Alignment explanation
Indices: 13529--13791 Score: 316
Period size: 51 Copynumber: 5.4 Consensus size: 50
13519 TACAGCTGGA
* *
13529 ATGCCTCCCAACAACATGGGAGGGATGCC-TCCC-AACAACATGGGAAGG
1 ATGCCTCCCAACAACATGGGAGGGATGCCACCCCTAACAACATGGGAGGG
* *
13577 ATGCC-CTC--CAACATGGGAGGGATGCCACCTCCTAACAACATAGGAGGG
1 ATGCCTCCCAACAACATGGGAGGGATGCCACC-CCTAACAACATGGGAGGG
*
13625 ATGCCTCCCAACAACATGGGAAGGATGCCA-CCC-AACAACATGGGAGGG
1 ATGCCTCCCAACAACATGGGAGGGATGCCACCCCTAACAACATGGGAGGG
* *
13673 ATGCCACCTCCTAACAACATGGGAGGGATGCCACCGCCTAACAACATAGGAGGG
1 ATG---CCTCCCAACAACATGGGAGGGATGCCACC-CCTAACAACATGGGAGGG
*
13727 ATGCCCCCCAACAACATGGGAGGGATG-C-CCCCT---AACATGGGAGGG
1 ATGCCTCCCAACAACATGGGAGGGATGCCACCCCTAACAACATGGGAGGG
*
13772 ATGCCACCCAACAACATGGG
1 ATGCCTCCCAACAACATGGG
13792 GAATATGGGG
Statistics
Matches: 189, Mismatches: 14, Indels: 27
0.82 0.06 0.12
Matches are distributed among these distances:
45 48 0.25
46 1 0.01
47 4 0.02
48 43 0.23
49 6 0.03
50 2 0.01
51 65 0.34
52 1 0.01
53 2 0.01
54 17 0.09
ACGTcount: A:0.31, C:0.30, G:0.27, T:0.12
Consensus pattern (50 bp):
ATGCCTCCCAACAACATGGGAGGGATGCCACCCCTAACAACATGGGAGGG
Found at i:14365 original size:2 final size:2
Alignment explanation
Indices: 14358--14393 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
14348 TTGGGGCAAA
14358 AT AT AT 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 AT AT AT
14394 CAGAACCCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18154 original size:25 final size:22
Alignment explanation
Indices: 18126--18189 Score: 56
Period size: 25 Copynumber: 2.6 Consensus size: 22
18116 ATTTTACTTG
18126 AATTTAAATTTAAATATTAATATAA
1 AATTTAAATTTAAATA-TAA-A-AA
*
18151 AATTTATATATATTTAATATAAAAA
1 AATTTA-A-AT-TTAAATATAAAAA
*
18176 TATTTAAATTTAAA
1 AATTTAAATTTAAA
18190 ATTTTATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
22 4 0.12
23 2 0.06
24 1 0.03
25 13 0.39
26 2 0.06
27 5 0.15
28 6 0.18
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTTAAATTTAAATATAAAAA
Found at i:18170 original size:22 final size:19
Alignment explanation
Indices: 18131--18174 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 19
18121 ACTTGAATTT
18131 AAATTTAAATATTAATATA
1 AAATTTAAATATTAATATA
18150 AAATTTATATATATTTAATATA
1 AAATTTA-A-ATA-TTAATATA
18172 AAA
1 AAA
18175 ATATTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.32
20 1 0.05
21 3 0.14
22 11 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAATTTAAATATTAATATA
Found at i:18188 original size:21 final size:22
Alignment explanation
Indices: 18133--18188 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
18123 TTGAATTTAA
*
18133 ATTTAAATATTAATATAAAATTT
1 ATTTAAAT-TTAATATAAAATAT
* *
18156 ATATATATTTAATATAAAA-AT
1 ATTTAAATTTAATATAAAATAT
18177 ATTTAAATTTAA
1 ATTTAAATTTAA
18189 AATTTTATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 11 0.39
22 11 0.39
23 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTTAAATTTAATATAAAATAT
Found at i:18828 original size:18 final size:20
Alignment explanation
Indices: 18795--18831 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
18785 TTTAAAGTTA
18795 AAATTATTTCTAATATTTAG
1 AAATTATTTCTAATATTTAG
18815 AAATT-TTT-TAATATTTA
1 AAATTATTTCTAATATTTA
18832 AAAAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (20 bp):
AAATTATTTCTAATATTTAG
Found at i:18840 original size:18 final size:18
Alignment explanation
Indices: 18800--18840 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
18790 AGTTAAAATT
* *
18800 ATTTCTAATATTTAGAAA
1 ATTTTTAATATTTAAAAA
*
18818 TTTTTTAATATTTAAAAA
1 ATTTTTAATATTTAAAAA
18836 ATTTT
1 ATTTT
18841 AAATTAAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTTTTAATATTTAAAAA
Found at i:18991 original size:14 final size:15
Alignment explanation
Indices: 18968--19008 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
18958 TTATTTTTAA
18968 ATTA-ATTAATATAT
1 ATTATATTAATATAT
*
18982 A-TATATTAATTTAT
1 ATTATATTAATATAT
*
18996 ATTATATAAATAT
1 ATTATATTAATAT
19009 TAAATCTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
13 2 0.09
14 11 0.50
15 9 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTATATTAATATAT
Found at i:19022 original size:14 final size:14
Alignment explanation
Indices: 18998--19041 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
18988 TAATTTATAT
18998 TATATAAATATTAAA
1 TATA-AAATATTAAA
*
19013 TCTAAAATATTATAA
1 TATAAAATATTA-AA
*
19028 TATAAAACATTAAA
1 TATAAAATATTAAA
19042 AATATATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (14 bp):
TATAAAATATTAAA
Found at i:19057 original size:61 final size:60
Alignment explanation
Indices: 18982--19101 Score: 147
Period size: 61 Copynumber: 2.0 Consensus size: 60
18972 ATTAATATAT
* * *
18982 ATATATTAATTTATAT-TATATAAATATTAAATCT-AAAATATTATAATA-TAAAACATTAAAA
1 ATATATTAAATTATATATATATAAAT-TT-AAT-TAAAAATATAAAAATATTAAAA-ATTAAAA
*
19043 ATATATTAAATTATATATTTATAAATTTAATTAAAAATATAAAAATATTAAAAATTAAA
1 ATATATTAAATTATATATATATAAATTTAATTAAAAATATAAAAATATTAAAAATTAAA
19102 TAAAAATAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
59 1 0.02
60 21 0.40
61 22 0.42
62 8 0.15
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (60 bp):
ATATATTAAATTATATATATATAAATTTAATTAAAAATATAAAAATATTAAAAATTAAAA
Found at i:19083 original size:18 final size:17
Alignment explanation
Indices: 19062--19103 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
19052 ATTATATATT
*
19062 TATAAATTTAATTAAAAA
1 TATAAATAT-ATTAAAAA
*
19080 TATAAAAATATTAAAAA
1 TATAAATATATTAAAAA
19097 T-TAAATA
1 TATAAATA
19104 AAAATAACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 5 0.24
17 9 0.43
18 7 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TATAAATATATTAAAAA
Found at i:19340 original size:18 final size:19
Alignment explanation
Indices: 19297--19343 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
19287 ACCACTTTCC
*
19297 ATTTATTTTATCTTAATTTT
1 ATTT-TTTTATCTTAATTCT
19317 AATTTTTTTATCTTAATTCT
1 -ATTTTTTTATCTTAATTCT
19337 -TTTTTTT
1 ATTTTTTT
19344 TCATAAGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 7 0.28
20 14 0.56
21 4 0.16
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.72
Consensus pattern (19 bp):
ATTTTTTTATCTTAATTCT
Found at i:19368 original size:10 final size:10
Alignment explanation
Indices: 19353--19391 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
19343 TTCATAAGAT
19353 ACACATATTC
1 ACACATATTC
19363 ACACATATTTTC
1 ACACATA--TTC
*
19375 ACAAATATTC
1 ACACATATTC
19385 ACACATA
1 ACACATA
19392 AATACCGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 16 0.64
12 9 0.36
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.31
Consensus pattern (10 bp):
ACACATATTC
Found at i:27355 original size:18 final size:18
Alignment explanation
Indices: 27330--27375 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
27320 AATAAATATT
27330 AATT-TAATATTTAATAA
1 AATTATAATATTTAATAA
*
27347 AATTATAATATATAATAA
1 AATTATAATATTTAATAA
27365 AA-TATAATATT
1 AATTATAATATT
27376 ATTATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTATAATATTTAATAA
Found at i:40223 original size:2 final size:2
Alignment explanation
Indices: 40218--40246 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40208 ACTTTCAGAC
40218 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40247 GTATGTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:42835 original size:6 final size:6
Alignment explanation
Indices: 42798--42848 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
42788 AATTCAACAC
* * * *
42798 TTTTAA TTTTCT TATTTAT TTATAT ATTTAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT T-TTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
42847 TT
1 TT
42849 CATCCTCACT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
6 32 0.86
7 5 0.14
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:43939 original size:3 final size:3
Alignment explanation
Indices: 43931--43972 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
43921 ATGAAATAGC
43931 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
43973 GGGATGAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:44029 original size:14 final size:14
Alignment explanation
Indices: 44010--44061 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
44000 CTAAGGAGGA
44010 TATTTTTTATAATT
1 TATTTTTTATAATT
*
44024 TATTTTTTA-AACTA
1 TATTTTTTATAA-TT
*
44038 TAATTTTTATTAATT
1 TATTTTTTA-TAATT
44053 TAATTTTTT
1 T-ATTTTTT
44062 TAAGTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
13 2 0.07
14 18 0.60
15 2 0.07
16 8 0.27
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTTTATAATT
Found at i:44064 original size:14 final size:15
Alignment explanation
Indices: 44011--44070 Score: 54
Period size: 15 Copynumber: 4.1 Consensus size: 15
44001 TAAGGAGGAT
44011 ATTTTTTATAA-TTT-
1 ATTTTTT-TAACTTTA
* *
44025 ATTTTTTAAACTATA
1 ATTTTTTTAACTTTA
44040 ATTTTTATTAA-TTTA
1 ATTTTT-TTAACTTTA
*
44055 ATTTTTTTAAGTTTA
1 ATTTTTTTAACTTTA
44070 A
1 A
44071 AAATATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
13 2 0.05
14 13 0.34
15 20 0.53
16 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (15 bp):
ATTTTTTTAACTTTA
Found at i:44134 original size:27 final size:29
Alignment explanation
Indices: 44102--44156 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
44092 GTTTTTCATA
44102 TTTATACT-ATAATAA-TACAT-ATATATT
1 TTTATA-TGATAATAATTACATAATATATT
44129 TTTATATGATAATAATTACATAATATAT
1 TTTATATGATAATAATTACATAATATAT
44157 AAAATAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 1 0.04
27 13 0.52
28 5 0.20
29 6 0.24
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.47
Consensus pattern (29 bp):
TTTATATGATAATAATTACATAATATATT
Found at i:45156 original size:2 final size:2
Alignment explanation
Indices: 45149--45180 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
45139 ACATGCCTTC
45149 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45181 ACTATTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:46818 original size:20 final size:20
Alignment explanation
Indices: 46768--46806 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
46758 GTATCCTTTC
46768 AAGTATCCCTCATCCCTCTT
1 AAGTATCCCTCATCCCTCTT
46788 AAGTATCCCTCATCCCTCT
1 AAGTATCCCTCATCCCTCT
46807 CTTGTATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.21, C:0.41, G:0.05, T:0.33
Consensus pattern (20 bp):
AAGTATCCCTCATCCCTCTT
Found at i:51254 original size:28 final size:28
Alignment explanation
Indices: 51222--51282 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
51212 AATGCCACCC
51222 TTTGTATTTGTCAAATATGGTGGTT-TCT
1 TTTGTATTTGTCAAATATGGTGGTTAT-T
51250 TTTGTATTTGTCAAATATGGTGGTTATT
1 TTTGTATTTGTCAAATATGGTGGTTATT
51278 TTTGT
1 TTTGT
51283 TTGTAAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 31 0.97
29 1 0.03
ACGTcount: A:0.18, C:0.05, G:0.21, T:0.56
Consensus pattern (28 bp):
TTTGTATTTGTCAAATATGGTGGTTATT
Found at i:51417 original size:20 final size:20
Alignment explanation
Indices: 51392--51448 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
51382 TCTCTTGTAT
51392 CCTCTCAAGTATCCCTCATC
1 CCTCTCAAGTATCCCTCATC
*
51412 CCTCTCAAGTATCCTTCATC
1 CCTCTCAAGTATCCCTCATC
**
51432 CCTCTCTTGTATCCCTC
1 CCTCTCAAGTATCCCTC
51449 TTCAATTCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.16, C:0.44, G:0.05, T:0.35
Consensus pattern (20 bp):
CCTCTCAAGTATCCCTCATC
Found at i:54145 original size:18 final size:18
Alignment explanation
Indices: 54091--54152 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
54081 ACAATTACGT
54091 AATATAAATACGAT-ATAAA
1 AATATAAATAC-ATAAT-AA
* *
54110 AATATGATATAAATAATAA
1 AATAT-AAATACATAATAA
54129 AATATAAATACATAATAA
1 AATATAAATACATAATAA
54147 AATATA
1 AATATA
54153 TAAATACAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 17 0.46
19 14 0.38
20 6 0.16
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
AATATAAATACATAATAA
Found at i:54155 original size:20 final size:19
Alignment explanation
Indices: 54091--54160 Score: 81
Period size: 19 Copynumber: 3.6 Consensus size: 19
54081 ACAATTACGT
54091 AATATAAATACGAT-ATAAA
1 AATATAAATAC-ATAATAAA
* *
54110 AATATGATATAAATAAT-AA
1 AATAT-AAATACATAATAAA
54129 AATATAAATACATAATAAA
1 AATATAAATACATAATAAA
54148 ATATATAAATACA
1 A-ATATAAATACA
54161 ACATTAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
18 9 0.21
19 17 0.40
20 17 0.40
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (19 bp):
AATATAAATACATAATAAA
Found at i:63684 original size:15 final size:13
Alignment explanation
Indices: 63640--63715 Score: 56
Period size: 13 Copynumber: 6.1 Consensus size: 13
63630 TTTCGACATG
63640 ATATAAAAA-AGTA
1 ATATAAAAATA-TA
63653 AT-T-AAAATATA
1 ATATAAAAATATA
63664 ATATAAAAATATA
1 ATATAAAAATATA
63677 CGATATAAAAA-AT-
1 --ATATAAAAATATA
*
63690 A-ATAAAAATATG
1 ATATAAAAATATA
* *
63702 ACATAAATATATA
1 ATATAAAAATATA
63715 A
1 A
63716 AAAATATTAA
Statistics
Matches: 53, Mismatches: 2, Indels: 16
0.75 0.03 0.23
Matches are distributed among these distances:
10 7 0.13
11 11 0.21
12 4 0.08
13 20 0.38
14 2 0.04
15 9 0.17
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.28
Consensus pattern (13 bp):
ATATAAAAATATA
Found at i:63698 original size:38 final size:39
Alignment explanation
Indices: 63639--63714 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 39
63629 TTTTCGACAT
* *
63639 GATATAAAAAAGTAATTAAAATATAATATAAAAATATAC
1 GATATAAAAAAGTAATAAAAATATAACATAAAAATATAC
* *
63678 GATATAAAAAA-TAATAAAAATATGACATAAATATATA
1 GATATAAAAAAGTAATAAAAATATAACATAAAAATATA
63715 AAAAATATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
38 22 0.67
39 11 0.33
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (39 bp):
GATATAAAAAAGTAATAAAAATATAACATAAAAATATAC
Done.