Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold197
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: 1875808
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 64134 characters in sequence are not A, C, G, or T
File 1 of 6
Found at i:1357 original size:7 final size:8
Alignment explanation
Indices: 1340--1369 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
1330 TAAAAATTGC
1340 AAAAAGAA
1 AAAAAGAA
1348 AAAAAGAA
1 AAAAAGAA
1356 AAAAAGAA
1 AAAAAGAA
1364 AGAAAA
1 A-AAAA
1370 TCTATAGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:8545 original size:103 final size:103
Alignment explanation
Indices: 8430--8651 Score: 327
Period size: 103 Copynumber: 2.2 Consensus size: 103
8420 ACATAGGTTA
* * * *
8430 GCTAGCTATTTGGGAGTTGTGAGCTTAACTCTTCCAACTCAGATAATTCAAATTGCAAGCTTAAC
1 GCTAGCTGTTTGGGAGTTGTGAGCTTAACTCTACCAACTCAAATAATTCAAATAGCAAGCTTAAC
*
8495 TCAGCTAACCTTTAAGTATCAGCTCGGAACGTAGGTCC
66 TCAACTAACCTTTAAGTATCAGCTCGGAACGTAGGTCC
* * *
8533 GCTAGCTGTTTGGGAGTTGTGAGCTTAACTCTACTAACTCAAATAATTCAGATAGCGAGCTTAAC
1 GCTAGCTGTTTGGGAGTTGTGAGCTTAACTCTACCAACTCAAATAATTCAAATAGCAAGCTTAAC
* * *
8598 TCAACTAACCTTTAAGTATCAGTTGGGACCGTAGGTCC
66 TCAACTAACCTTTAAGTATCAGCTCGGAACGTAGGTCC
* *
8636 GCTAGTTGTTTCGGAG
1 GCTAGCTGTTTGGGAG
8652 GTTGCGATCA
Statistics
Matches: 106, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.31
Consensus pattern (103 bp):
GCTAGCTGTTTGGGAGTTGTGAGCTTAACTCTACCAACTCAAATAATTCAAATAGCAAGCTTAAC
TCAACTAACCTTTAAGTATCAGCTCGGAACGTAGGTCC
Found at i:9058 original size:27 final size:27
Alignment explanation
Indices: 9028--9080 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
9018 TCTATTGCCG
*
9028 AATATTCCCATATTAATTATTAATTCA
1 AATATTCACATATTAATTATTAATTCA
*
9055 AATATTTACATATTAATTATTAATTC
1 AATATTCACATATTAATTATTAATTC
9081 TACACTAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (27 bp):
AATATTCACATATTAATTATTAATTCA
Found at i:10137 original size:2 final size:2
Alignment explanation
Indices: 10097--10129 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
10087 CCTTAAGCAA
10097 AT AT AT AT AT AT AT 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 AT A
10130 ACATATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10511 original size:41 final size:41
Alignment explanation
Indices: 10408--10516 Score: 128
Period size: 41 Copynumber: 2.7 Consensus size: 41
10398 CATCGACATA
* * * * ** *
10408 AAGCCTTCTAGGCACAAAACCAGATATGACACACCGGCACG
1 AAGCCTACTAGGCATAAAGCCTGATATGGTACACCAGCACG
* *
10449 AAGCCTGCTAGGCATATAGCCTGATATGGTACACCAGCACG
1 AAGCCTACTAGGCATAAAGCCTGATATGGTACACCAGCACG
*
10490 AAGCCTACTAGGTATAAAGCCTGATAT
1 AAGCCTACTAGGCATAAAGCCTGATAT
10517 AATTTACAGG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.34, C:0.27, G:0.21, T:0.18
Consensus pattern (41 bp):
AAGCCTACTAGGCATAAAGCCTGATATGGTACACCAGCACG
Found at i:12033 original size:68 final size:69
Alignment explanation
Indices: 11828--12071 Score: 251
Period size: 69 Copynumber: 3.6 Consensus size: 69
11818 GGGCTGTTAC
* * * * * * *
11828 ATAATATTAGTTGGGAACGTAGGTCCGCAAGCTGTGTTGGAGGCTGCAATCATAAACT-AGCAAG
1 ATAATATCAGCTGGGAATGTAGGTTCGCGAGCTGTGTTGGAGGCTGCGATCATAAACTGA-CGAG
*
11892 CTTTT
65 CCTTT
* * * * ** *
11897 ATAATATCATCTGGGAATGTAGGTCCGCGAGCTGTGTTGGAGCCTGCGATCATAAACCGGTGGGC
1 ATAATATCAGCTGGGAATGTAGGTTCGCGAGCTGTGTTGGAGGCTGCGATCATAAACTGACGAGC
11962 CTTT
66 CTTT
* * * *
11966 ATAATATCAGCTGGG-ATGTAGGTTCACGAGCTGTGTTTGAGGTTGCGATCATAAACTGACGATC
1 ATAATATCAGCTGGGAATGTAGGTTCGCGAGCTGTGTTGGAGGCTGCGATCATAAACTGACGAGC
12030 CTTT
66 CTTT
* * * *
12034 -TAATATTAGTTGGGAACGTAGGTTTGCGAGCTGTGTTG
1 ATAATATCAGCTGGGAATGTAGGTTCGCGAGCTGTGTTG
12072 AGTTGCGAGT
Statistics
Matches: 143, Mismatches: 30, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
67 12 0.08
68 62 0.43
69 69 0.48
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.31
Consensus pattern (69 bp):
ATAATATCAGCTGGGAATGTAGGTTCGCGAGCTGTGTTGGAGGCTGCGATCATAAACTGACGAGC
CTTT
Found at i:17822 original size:18 final size:19
Alignment explanation
Indices: 17788--17825 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
17778 AATTACAAAA
17788 AAAAAATTCAAATATTTAT
1 AAAAAATTCAAATATTTAT
*
17807 AAAAAATTTAAA-ATTTAT
1 AAAAAATTCAAATATTTAT
17825 A
1 A
17826 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAAATTCAAATATTTAT
Found at i:21366 original size:10 final size:10
Alignment explanation
Indices: 21348--21391 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
21338 GCACCAAAAC
*
21348 TTTATTTTAT
1 TTTAATTTAT
21358 TTTAATTTAT
1 TTTAATTTAT
*
21368 TTTATATTTAA
1 TTTA-ATTTAT
*
21379 TTTAATTTCT
1 TTTAATTTAT
21389 TTT
1 TTT
21392 CAAATTAGTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 20 0.69
11 9 0.31
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTAATTTAT
Found at i:21382 original size:21 final size:20
Alignment explanation
Indices: 21348--21391 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
21338 GCACCAAAAC
*
21348 TTTATTTTATTTTAATTTAT
1 TTTATTTTAATTTAATTTAT
*
21368 TTTATATTTAATTTAATTTCT
1 TTTAT-TTTAATTTAATTTAT
21389 TTT
1 TTT
21392 CAAATTAGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTATTTTAATTTAATTTAT
Found at i:21720 original size:116 final size:117
Alignment explanation
Indices: 21579--21814 Score: 465
Period size: 116 Copynumber: 2.0 Consensus size: 117
21569 AATTTAATAC
21579 TTAATTCAATAATTTCCTAAATTTTCTATTTAACCACTTATGTAATTATTTTCCTCATTTCGGCT
1 TTAATTCAATAATTTCCTAAATTTTCTATTTAACCACTTATGTAATTATTTTCCTCATTTCGGCT
21644 CCTATATTTTTCAAAATTTACTAAACAATCCCTATTTTTTAATATTAAATTT
66 CCTATATTTTTCAAAATTTACTAAACAATCCCTATTTTTTAATATTAAATTT
21696 TTAATTCAAT-ATTTCCTAAATTTTCTATTTAACCACTTATGTAATTATTTTCCTCATTTCGGCT
1 TTAATTCAATAATTTCCTAAATTTTCTATTTAACCACTTATGTAATTATTTTCCTCATTTCGGCT
21760 CCTATATTTTTCAAAATTTACTAAACAATCCCTATTTTTTAATATTAAATTT
66 CCTATATTTTTCAAAATTTACTAAACAATCCCTATTTTTTAATATTAAATTT
21812 TTA
1 TTA
21815 CATAACAATC
Statistics
Matches: 119, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
116 109 0.92
117 10 0.08
ACGTcount: A:0.31, C:0.17, G:0.03, T:0.49
Consensus pattern (117 bp):
TTAATTCAATAATTTCCTAAATTTTCTATTTAACCACTTATGTAATTATTTTCCTCATTTCGGCT
CCTATATTTTTCAAAATTTACTAAACAATCCCTATTTTTTAATATTAAATTT
Found at i:30064 original size:26 final size:26
Alignment explanation
Indices: 30035--30103 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 26
30025 TATACATAGT
*
30035 TGCTCACATGAGCTGTGAAATAGG-C
1 TGCTCACACGAGCTGTGAAATAGGAC
*
30060 ATGCTCACACGAGTTGTGAAATAGGAC
1 -TGCTCACACGAGCTGTGAAATAGGAC
30087 TGCTCACACGAGCTGTG
1 TGCTCACACGAGCTGTG
30104 GAGTACTTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
26 38 0.97
27 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.23
Consensus pattern (26 bp):
TGCTCACACGAGCTGTGAAATAGGAC
Found at i:31887 original size:3 final size:3
Alignment explanation
Indices: 31879--31966 Score: 158
Period size: 3 Copynumber: 29.0 Consensus size: 3
31869 NNNATAGTAT
31879 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
31927 TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
31967 AAGATGGTAA
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
3 79 0.96
4 3 0.04
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:32663 original size:16 final size:16
Alignment explanation
Indices: 32632--32676 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
32622 TGTTTTTCAA
*
32632 AAAAATAAATAAATAAAT
1 AAAAAT-AA-AAATAAAC
32650 AAAAATAAAAATAAAC
1 AAAAATAAAAATAAAC
*
32666 AACAATAAAAA
1 AAAAATAAAAA
32677 AGAGATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 17 0.68
17 2 0.08
18 6 0.24
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAATAAAAATAAAC
Found at i:33645 original size:44 final size:44
Alignment explanation
Indices: 33519--33649 Score: 158
Period size: 44 Copynumber: 3.0 Consensus size: 44
33509 CTATGGTAGA
* * ** *
33519 TTTAATCCGAC-CTACTGCAACTTCA-GAAGTATAGGATTCATCAT
1 TTTAATCCG-CTCCACTGCAACTTCAGGGAG-ATAGGATTTGTAAT
* *
33563 TTTAATCTGCTCCACTGCAACTTTAGGGAGATAGGATTTGTAAT
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTTGTAAT
*
33607 TTTAATCCGCTCCATTGCAACTTCAGGGAGATAGGATTTGTAA
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTTGTAA
33650 CTCTTCGTGG
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
43 1 0.01
44 71 0.95
45 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (44 bp):
TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTTGTAAT
Found at i:35001 original size:96 final size:96
Alignment explanation
Indices: 34837--35441 Score: 917
Period size: 96 Copynumber: 6.4 Consensus size: 96
34827 CGCTTAAATG
* ** ** *
34837 AAGATTCCCCGTTGTGGCTTCGATCTGATCTATTACAATGGGGAAGTGAGACTCGCCGTTGTAGC
1 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGACTCGCCGTTGTAGC
*
34902 TTCAATCTGTTTCGCTGCATCGCCTGAAAGT
66 TTCAATCTGTTCCGCTGCATCGCCTGAAAGT
* *
34933 AAGATTCGTCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGACTCACCGTTGTAGC
1 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGACTCGCCGTTGTAGC
*
34998 TTCAATCTGTTCCGCTGCATCGCCTGGAAGT
66 TTCAATCTGTTCCGCTGCATCGCCTGAAAGT
** *
35029 AAGATTCGCTATTGTGGCTTCGATC---T--ATTGCAATGGGGAAGTGAGACTCGCCTTTGTAGC
1 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGACTCGCCGTTGTAGC
* *
35089 TTCAATTTGTTCCGCTGCATCGCCTGGAAGT
66 TTCAATCTGTTCCGCTGCATCGCCTGAAAGT
* *
35120 AAGATTCGCCGTTGTGGCTTCGATC---T--ATTGCAATGGGGAAGGGAGACTCGCCCTTGTAGC
1 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGACTCGCCGTTGTAGC
*
35180 TTCAATTTGTTCCGCTGCATCGCCTGAAAGT
66 TTCAATCTGTTCCGCTGCATCGCCTGAAAGT
**
35211 AAGATTCGCCGTTGTGGCTTTAATCTTTTAAATTGCAATGGGGAAGTGAGACTCGCCGTTGTAGC
1 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGACTCGCCGTTGTAGC
* *
35276 TTCAATCTATTCCGCTGTATCGCCTGAAAGT
66 TTCAATCTGTTCCGCTGCATCGCCTGAAAGT
35307 AAGATTC-CTCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGACTCGCCGTTGTAG
1 AAGATTCGC-CGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGACTCGCCGTTGTAG
*
35371 CTTCAATTTGTTCCGCTGCATCGCCTGAAAGT
65 CTTCAATCTGTTCCGCTGCATCGCCTGAAAGT
35403 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT
1 AAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAAT
35442 CTATGGTTAC
Statistics
Matches: 469, Mismatches: 33, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
91 171 0.36
93 1 0.00
94 1 0.00
95 1 0.00
96 294 0.63
97 1 0.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (96 bp):
AAGATTCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGGGGAAGTGAGACTCGCCGTTGTAGC
TTCAATCTGTTCCGCTGCATCGCCTGAAAGT
Found at i:35091 original size:42 final size:42
Alignment explanation
Indices: 35023--35182 Score: 115
Period size: 42 Copynumber: 3.6 Consensus size: 42
35013 TGCATCGCCT
* *
35023 GGAAGTAAGATTCG-CTATTGTGGCTTCGATCTATTGCAATGG
1 GGAAGTAAGACTCGCCT-TTGTAGCTTCGATCTATTGCAATGG
* * * * * *
35065 GGAAGTGAGACTCGCCTTTGTAGCTTCAATTTGTTCCGCTGCATCGCCT
1 GGAAGTAAGACTCGCCTTTGTAGCTTCGATCTATT--GC--AAT-G--G
* * *
35114 GGAAGTAAGATTCGCCGTTGTGGCTTCGATCTATTGCAATGG
1 GGAAGTAAGACTCGCCTTTGTAGCTTCGATCTATTGCAATGG
** *
35156 GGAAGGGAGACTCGCCCTTGTAGCTTC
1 GGAAGTAAGACTCGCCTTTGTAGCTTC
35183 AATTTGTTCC
Statistics
Matches: 88, Mismatches: 22, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
42 48 0.55
43 2 0.02
44 3 0.03
45 2 0.02
46 2 0.02
47 3 0.03
49 28 0.32
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.31
Consensus pattern (42 bp):
GGAAGTAAGACTCGCCTTTGTAGCTTCGATCTATTGCAATGG
Found at i:37872 original size:6 final size:6
Alignment explanation
Indices: 37861--37921 Score: 79
Period size: 6 Copynumber: 10.0 Consensus size: 6
37851 TTGACCTCTC
* *
37861 CTTTTT CTTTTT CTTTTT ATTTTT CTTTTCT TTTTTT CTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTT-T CTTTTT CTTTTT CTTTTT
37910 -TTTTT CTATTTT
1 CTTTTT CT-TTTT
37922 GACTTTGATT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
5 5 0.10
6 34 0.71
7 9 0.19
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (6 bp):
CTTTTT
Found at i:37902 original size:25 final size:25
Alignment explanation
Indices: 37868--37921 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
37858 CTCCTTTTTC
*
37868 TTTTTCTTTTTATTTTTCTTTTCTT
1 TTTTTCTTTTTATTTTTCTTTTCTA
* *
37893 TTTTTCTTTTTCTTTTTTTTTTCTA
1 TTTTTCTTTTTATTTTTCTTTTCTA
37918 TTTT
1 TTTT
37922 GACTTTGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.85
Consensus pattern (25 bp):
TTTTTCTTTTTATTTTTCTTTTCTA
Found at i:38704 original size:17 final size:18
Alignment explanation
Indices: 38672--38708 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
38662 TCTGCACAGT
38672 ATGATTATGAATGAAAGA
1 ATGATTATGAATGAAAGA
*
38690 ATGATT-TGGATGAAAGA
1 ATGATTATGAATGAAAGA
38707 AT
1 AT
38709 AAAAGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (18 bp):
ATGATTATGAATGAAAGA
Found at i:42302 original size:3 final size:3
Alignment explanation
Indices: 42294--42329 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
42284 GAAATTGTAA
*
42294 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AA
42330 AAGATGGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:42887 original size:6 final size:6
Alignment explanation
Indices: 42876--42908 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
42866 CTGTTTTTCA
42876 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAA
42909 CAACAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:42921 original size:18 final size:18
Alignment explanation
Indices: 42876--42914 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
42866 CTGTTTTTCA
*
42876 AAAAATAAAAATAAAAAT
1 AAAAATAAAAATAAAAAC
42894 AAAAATAAAAATAAACAAC
1 AAAAATAAAAATAAA-AAC
42913 AA
1 AA
42915 TAAAAAAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.13
Consensus pattern (18 bp):
AAAAATAAAAATAAAAAC
Found at i:43548 original size:11 final size:11
Alignment explanation
Indices: 43532--43583 Score: 77
Period size: 11 Copynumber: 4.6 Consensus size: 11
43522 ACTACTGTAG
43532 ATATTAAAATA
1 ATATTAAAATA
43543 ATATTAAAATAA
1 ATATTAAAAT-A
*
43555 ATATTTAAATA
1 ATATTAAAATA
*
43566 ATATTTAAATA
1 ATATTAAAATA
43577 ATATTAA
1 ATATTAA
43584 CGAAATTCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
11 28 0.74
12 10 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATATTAAAATA
Found at i:43559 original size:23 final size:22
Alignment explanation
Indices: 43532--43583 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
43522 ACTACTGTAG
43532 ATATTAAAATAATATTAAAATAA
1 ATATTAAAATAATATTAAAAT-A
* *
43555 ATATTTAAATAATATTTAAATA
1 ATATTAAAATAATATTAAAATA
43577 ATATTAA
1 ATATTAA
43584 CGAAATTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATTAAAATAATATTAAAATA
Found at i:44952 original size:49 final size:49
Alignment explanation
Indices: 44899--44996 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
44889 CATGTTATTG
*
44899 ATTGTTGAAGTTTTTGTTTTTGCTAAATTCATTCATACATTTCATTTCA
1 ATTGTTGAAGTTTCTGTTTTTGCTAAATTCATTCATACATTTCATTTCA
44948 ATTGTTGAAGTTTCTGTTTTTGCTAAATTCATTCATACATTTCATTTCA
1 ATTGTTGAAGTTTCTGTTTTTGCTAAATTCATTCATACATTTCATTTCA
44997 TACTTCGTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.24, C:0.13, G:0.10, T:0.52
Consensus pattern (49 bp):
ATTGTTGAAGTTTCTGTTTTTGCTAAATTCATTCATACATTTCATTTCA
Found at i:52859 original size:17 final size:18
Alignment explanation
Indices: 52836--52880 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
52826 TAAAATATCT
**
52836 TAATAAAATATTATTTAA
1 TAATAAAATATTAAATAA
52854 -AATAAAA-ATTAAATAA
1 TAATAAAATATTAAATAA
52870 TAATAAAATAT
1 TAATAAAATAT
52881 CACCAACACC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 7 0.30
17 14 0.61
18 2 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAATAAAATATTAAATAA
Found at i:54652 original size:71 final size:71
Alignment explanation
Indices: 54565--54708 Score: 234
Period size: 71 Copynumber: 2.0 Consensus size: 71
54555 TTGGGTATTG
* *
54565 CGATACCCACCTGCCAAGGAGCACCCTATTTTAAGATTATCAACAATGTCGCAATATCCTACCCT
1 CGATACCCACCTGCCAAGGAGCACCCTATTTTAAAATTATCAACAACGTCGCAATATCCTACCCT
54630 GAGTAT
66 GAGTAT
* * * *
54636 CGATACCCACTTGCCAAGGAGCACCCTATTTTAAAATTGTCAACAACGTTGCAATATCTTACCCT
1 CGATACCCACCTGCCAAGGAGCACCCTATTTTAAAATTATCAACAACGTCGCAATATCCTACCCT
54701 GAGTAT
66 GAGTAT
54707 CG
1 CG
54709 CGATATCTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 67 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (71 bp):
CGATACCCACCTGCCAAGGAGCACCCTATTTTAAAATTATCAACAACGTCGCAATATCCTACCCT
GAGTAT
Found at i:56547 original size:2 final size:2
Alignment explanation
Indices: 56540--56576 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
56530 AAGGCTTTTG
56540 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
56577 ACATACGCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:59901 original size:2 final size:2
Alignment explanation
Indices: 59894--59922 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
59884 GCAACCTAAT
59894 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
59923 TGTAAAGACT
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:61846 original size:6 final size:6
Alignment explanation
Indices: 61847--61871 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
61837 TTAATATTAA
61847 ATTTAT ATTTAT ATTTAT ATTTAT A
1 ATTTAT ATTTAT ATTTAT ATTTAT A
61872 AAAAAAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATTTAT
Found at i:63040 original size:31 final size:31
Alignment explanation
Indices: 63005--63085 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
62995 GGCCATAACT
* * *
63005 TGGGAATATTTACCAAGTTTAGGCTTCAATA
1 TGGGAACAATTACCAAGTTTAAGCTTCAATA
* *
63036 TGGGAACAAGTGCCTAA-TTTAAGCTTCAATA
1 TGGGAACAATTACC-AAGTTTAAGCTTCAATA
*
63067 TGAGAACAATTACCAAGTT
1 TGGGAACAATTACCAAGTT
63086 CATGAACTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
30 2 0.05
31 36 0.90
32 2 0.05
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (31 bp):
TGGGAACAATTACCAAGTTTAAGCTTCAATA
Found at i:77152 original size:13 final size:13
Alignment explanation
Indices: 77134--77158 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
77124 GTTGATCTCC
77134 TAGTTTTTAATAA
1 TAGTTTTTAATAA
77147 TAGTTTTTAATA
1 TAGTTTTTAATA
77159 TCCACAATTG
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:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (13 bp):
TAGTTTTTAATAA
Found at i:87479 original size:13 final size:13
Alignment explanation
Indices: 87440--87479 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
87430 TTTAAACCAA
*
87440 ACTTTTCAAAAAC
1 ACTTTTCAAAAGC
* *
87453 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
87466 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
87479 A
1 A
87480 TTGCCAAACT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.28, G:0.05, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:89401 original size:15 final size:15
Alignment explanation
Indices: 89381--89422 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
89371 AATTAAGCAC
*
89381 TAATAAAAATGATGA
1 TAATAATAATGATGA
89396 TAATAATAATGATGA
1 TAATAATAATGATGA
*
89411 CAATAATAATGA
1 TAATAATAATGA
89423 AATGCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.57, C:0.02, G:0.12, T:0.29
Consensus pattern (15 bp):
TAATAATAATGATGA
Found at i:90673 original size:32 final size:32
Alignment explanation
Indices: 90636--90699 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
90626 GGCAGACGCA
* *
90636 CGACGGCCCGGAGACCAAGGGTCTGAAACAAG
1 CGACGGCCAGGAGACCAAAGGTCTGAAACAAG
*
90668 CGACGGCCAGGAGACCAAAGGTCTGAAGCAAG
1 CGACGGCCAGGAGACCAAAGGTCTGAAACAAG
90700 GTGCAGCGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.27, G:0.34, T:0.06
Consensus pattern (32 bp):
CGACGGCCAGGAGACCAAAGGTCTGAAACAAG
Found at i:93933 original size:11 final size:11
Alignment explanation
Indices: 93919--93949 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
93909 AAAGAAATAT
93919 GAATGAAAGTG
1 GAATGAAAGTG
93930 GAATGAAAGTG
1 GAATGAAAGTG
93941 GAATGAAAG
1 GAATGAAAG
93950 AGAATAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.35, T:0.16
Consensus pattern (11 bp):
GAATGAAAGTG
Found at i:95026 original size:2 final size:2
Alignment explanation
Indices: 95019--95045 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
95009 ATTCACAACT
95019 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
95046 TATACCATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:105294 original size:61 final size:60
Alignment explanation
Indices: 105189--105434 Score: 233
Period size: 68 Copynumber: 3.8 Consensus size: 60
105179 TTTGTTTTAT
* * * *
105189 TTATTTATTTATTATTCTGTTACTTTTTAAGTACCTAAAATTAATATTATTTATATTTATT-
1 TTATTTATTTATTATTCT-TTACTTTTTAAATACTTAAATTTAATATTATGTAT-TTTATTA
*
105250 TTATTTATTTATTTTTCTTTAGCTTTTTAAATACTTAAATTTAATATTATGTATTTTTTATTA
1 TTATTTATTTATTATTCTTTA-CTTTTTAAATACTTAAATTTAATATTATGTA--TTTTATTA
*
105313 TCTATTTATTCATTTATTATTCTTTTACTTCTTAAATACTTAAATTTAATATTATGTATTTTTTA
1 T-TA--T-TT-ATTTATTATTC-TTTACTTTTTAAATACTTAAATTTAATATTATGTA--TTTTA
105378 TTA
58 TTA
* * *
105381 TCTATTTATTCATTTATTATTCTTTTACTTTTTAAATATTTTAATTTGATATTA
1 T-TA--T-TT-ATTTATTATTC-TTTACTTTTTAAATACTTAAATTTAATATTA
105435 CTTATACTTC
Statistics
Matches: 164, Mismatches: 11, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
60 3 0.02
61 44 0.27
62 6 0.04
63 2 0.01
64 2 0.01
66 1 0.01
67 2 0.01
68 100 0.61
69 4 0.02
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (60 bp):
TTATTTATTTATTATTCTTTACTTTTTAAATACTTAAATTTAATATTATGTATTTTATTA
Found at i:105328 original size:68 final size:68
Alignment explanation
Indices: 105249--105434 Score: 302
Period size: 68 Copynumber: 2.7 Consensus size: 68
105239 TTATATTTAT
* *
105249 TTTATTTATTTATTTTTC-TTTAGCTTTTTAAATACTTAAATTTAATATTATGTATTTTTTATTA
1 TTTATTCATTTATTATTCTTTTA-CTTTTTAAATACTTAAATTTAATATTATGTATTTTTTATTA
105313 TCTA
65 TCTA
*
105317 TTTATTCATTTATTATTCTTTTACTTCTTAAATACTTAAATTTAATATTATGTATTTTTTATTAT
1 TTTATTCATTTATTATTCTTTTACTTTTTAAATACTTAAATTTAATATTATGTATTTTTTATTAT
105382 CTA
66 CTA
* * *
105385 TTTATTCATTTATTATTCTTTTACTTTTTAAATATTTTAATTTGATATTA
1 TTTATTCATTTATTATTCTTTTACTTTTTAAATACTTAAATTTAATATTA
105435 CTTATACTTC
Statistics
Matches: 110, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
68 106 0.96
69 4 0.04
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.62
Consensus pattern (68 bp):
TTTATTCATTTATTATTCTTTTACTTTTTAAATACTTAAATTTAATATTATGTATTTTTTATTAT
CTA
Found at i:109975 original size:24 final size:25
Alignment explanation
Indices: 109947--110000 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
109937 CATAACTTCG
*
109947 ATTTTTTA-A-TATATAATTTTTTTA
1 ATTTTTTAGATTATAT-ATATTTTTA
109971 ATTTTTTAGATTATATATATTTTTA
1 ATTTTTTAGATTATATATATTTTTA
109996 ATTTT
1 ATTTT
110001 CAAGTAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 8 0.30
25 14 0.52
26 5 0.19
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (25 bp):
ATTTTTTAGATTATATATATTTTTA
Found at i:111552 original size:18 final size:17
Alignment explanation
Indices: 111509--111543 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
111499 CAGTAAACCC
111509 TTTC-TTTCTTTTTTCT
1 TTTCTTTTCTTTTTTCT
111525 TTTCTTTTCTTTTTT-T
1 TTTCTTTTCTTTTTTCT
111541 TTT
1 TTT
111544 AACTTTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (17 bp):
TTTCTTTTCTTTTTTCT
Found at i:113131 original size:96 final size:96
Alignment explanation
Indices: 112888--113161 Score: 319
Period size: 94 Copynumber: 2.9 Consensus size: 96
112878 GTTTGTCAAT
* * **
112888 TAAATTAATTATAAATTTTT-TAAAATTGGATTA-GGTTTCGTGTTTATTGTTTTTTTAAGAAAA
1 TAAATTAATTATAAATTTTTATAAAATTAGATTAGGGTTTAGTGTTTA--GGGTTTTTAAG-AAA
* * *
112951 AAATCAATTAAATTAGGGTTTAGGGTTACTTGAG
63 AAATCAAATAAATTAGGGTTCACGGTTACTTGAG
* * * *
112985 TAATTTAA-T-T-AATTTTTAAAAAAATTAGATTAGGGTTTAGAGTTAAGGGTTTTTAACG-AAA
1 TAAATTAATTATAAATTTTT-ATAAAATTAGATTAGGGTTTAGTGTTTAGGGTTTTTAA-GAAAA
113046 AATCAAATAAATTAGGGTTCACGGTTACTTGAG
64 AATCAAATAAATTAGGGTTCACGGTTACTTGAG
113079 TAAATTAATTATAAATTTTTATAAAATTAGATTAGGGTTTAGTGTTTAGGG-TTTTAAGTAAAAA
1 TAAATTAATTATAAATTTTTATAAAATTAGATTAGGGTTTAGTGTTTAGGGTTTTTAAG-AAAAA
* *
113143 CCTTAAATAAATTAGGGTT
65 -ATCAAATAAATTAGGGTT
113162 TGGGGTTTAG
Statistics
Matches: 150, Mismatches: 17, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
94 48 0.32
95 16 0.11
96 46 0.31
97 40 0.27
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.42
Consensus pattern (96 bp):
TAAATTAATTATAAATTTTTATAAAATTAGATTAGGGTTTAGTGTTTAGGGTTTTTAAGAAAAAA
TCAAATAAATTAGGGTTCACGGTTACTTGAG
Found at i:113441 original size:126 final size:126
Alignment explanation
Indices: 113216--113491 Score: 489
Period size: 126 Copynumber: 2.2 Consensus size: 126
113206 ATCTCTCACG
* * *
113216 TGGACGCACTTTTGCTATAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTTCTGAGCAACTA
1 TGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTTCTGAGCAAATA
*
113281 GTGTCAAAAACGCTTTAAGCATGATGCTTTGTCAGCAGAAGTACTGAAAAAAGCTCCCACA
66 GTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAAAAGCTCCCACA
113342 TGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTTCTGAGCAAATA
1 TGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTTCTGAGCAAATA
* *
113407 GTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAGAAGCTCCCACG
66 GTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAAAAGCTCCCACA
*
113468 TGGATGCGCTTTTGCTACAGTAGC
1 TGGACGCGCTTTTGCTACAGTAGC
113492 ACATGTTTGG
Statistics
Matches: 143, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
126 143 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (126 bp):
TGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACGTTTCTGAGCAAATA
GTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAGAAGTACTGAAAAAAGCTCCCACA
Found at i:116442 original size:23 final size:23
Alignment explanation
Indices: 116406--116470 Score: 96
Period size: 23 Copynumber: 2.8 Consensus size: 23
116396 AGACTCACCA
116406 CAGCTCGTAT-GAGCTTACCGTTT
1 CAGCTC-TATAGAGCTTACCGTTT
116429 CAGCTCTATAGAGCTTACCGTTT
1 CAGCTCTATAGAGCTTACCGTTT
* *
116452 CAGCTCGATAGAGTTTACC
1 CAGCTCTATAGAGCTTACC
116471 ATTTATCAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
22 3 0.08
23 36 0.92
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.32
Consensus pattern (23 bp):
CAGCTCTATAGAGCTTACCGTTT
Found at i:116695 original size:20 final size:20
Alignment explanation
Indices: 116657--116695 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
116647 TATGGATGAA
* *
116657 TTACCGTTGATATGTATAAG
1 TTACCGTTGATACGGATAAG
*
116677 TTACGGTTGATACGGATAA
1 TTACCGTTGATACGGATAA
116696 ATTTCTGTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (20 bp):
TTACCGTTGATACGGATAAG
Found at i:119779 original size:30 final size:30
Alignment explanation
Indices: 119745--119812 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 30
119735 GTGCTATTGC
* *
119745 TGGGCTTGGTGATTGTATGGGTGATGATGA
1 TGGGCTTGGTGAATGTATGGGTCATGATGA
** * * *
119775 TGGGCCGGGTGAATGTCTGGGTCTTGTTGA
1 TGGGCTTGGTGAATGTATGGGTCATGATGA
119805 TGGGCTTG
1 TGGGCTTG
119813 CGTCGTCGTC
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.12, C:0.09, G:0.44, T:0.35
Consensus pattern (30 bp):
TGGGCTTGGTGAATGTATGGGTCATGATGA
Found at i:121510 original size:11 final size:11
Alignment explanation
Indices: 121496--121527 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
121486 TTTAAATAGA
121496 AATTTGAGAGG
1 AATTTGAGAGG
121507 AATTTGAGAGG
1 AATTTGAGAGG
121518 AATTTGAGAG
1 AATTTGAGAG
121528 AATATTAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (11 bp):
AATTTGAGAGG
Found at i:121546 original size:22 final size:21
Alignment explanation
Indices: 121486--121551 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
121476 TTAAAGCTCT
*
121486 TTTAAATAGAAATTTGAGAGGAA
1 TTTAAAGAGAAA-TTGAGA-GAA
* *
121509 TTT-GAGAGGAATTTGAGAGAA
1 TTTAAAGA-GAAATTGAGAGAA
121530 TATTAAAGAGAAATTGAGAGAA
1 T-TTAAAGAGAAATTGAGAGAA
121552 AGGATTTAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
21 4 0.11
22 22 0.63
23 9 0.26
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.27
Consensus pattern (21 bp):
TTTAAAGAGAAATTGAGAGAA
Found at i:121770 original size:40 final size:40
Alignment explanation
Indices: 121696--121771 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
121686 ACGTAGCAGG
*
121696 AAAACGCGTCCTTGAGGGAGCGATTTCTGTCCACGTAGGC
1 AAAACGCGTCCTTCAGGGAGCGATTTCTGTCCACGTAGGC
* *
121736 AAAACGCTTCC-TCAGGGACGCGTTTTCCTG-CCACGT
1 AAAACGCGTCCTTCAGGGA-GCGATTT-CTGTCCACGT
121772 CCCCTAACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
39 6 0.19
40 22 0.71
41 3 0.10
ACGTcount: A:0.21, C:0.29, G:0.26, T:0.24
Consensus pattern (40 bp):
AAAACGCGTCCTTCAGGGAGCGATTTCTGTCCACGTAGGC
Found at i:121945 original size:98 final size:98
Alignment explanation
Indices: 121770--121965 Score: 268
Period size: 98 Copynumber: 2.0 Consensus size: 98
121760 TTCCTGCCAC
** *
121770 GTCCCCTAACATCGCGCTGACATGGACGTGCTTTCGGGGAAATAAGGCCATTCCGGTAAATAATT
1 GTCCCCTAACATCGCGCTGACATGGACGCACTTTCGGAGAAATAAGGCCATTCCGGTAAATAATT
** *
121835 ATTTACCAGGCCCATTTCGGTAAATTTTTTAAAA
66 ATTTACCAGGCCCATTAAGGT-AATTTTTAAAAA
* * * **
121869 GTCCCCTGATATCGCGCTGACGTGGACGCACTTTC-GAGAAATTGGGCCATTCCGGTAAATAATT
1 GTCCCCTAACATCGCGCTGACATGGACGCACTTTCGGAGAAATAAGGCCATTCCGGTAAATAATT
*
121933 ATTTACCGGGCCCATTAAGGTAATTTTTAAAAA
66 ATTTACCAGGCCCATTAAGGTAATTTTTAAAAA
121966 AAAGAGCTTT
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
97 11 0.13
98 44 0.52
99 30 0.35
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (98 bp):
GTCCCCTAACATCGCGCTGACATGGACGCACTTTCGGAGAAATAAGGCCATTCCGGTAAATAATT
ATTTACCAGGCCCATTAAGGTAATTTTTAAAAA
Found at i:123151 original size:109 final size:109
Alignment explanation
Indices: 122932--123150 Score: 404
Period size: 109 Copynumber: 2.0 Consensus size: 109
122922 TAAAAAAAAA
*
122932 TTCGTATTCTGATATCTGATTCTGACACGAAAAAAGAGAATTTTTTTTTTAAATTGTACTGGGTG
1 TTCGTATACTGATATCTGATTCTGACACGAAAAAAGAGAATTTTTTTTTTAAATTGTACTGGGTG
*
122997 CCGGCCATTGACAGGCCCGCACCCAAAATTTTTTTTTTACTTTT
66 CCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTTACTTTT
*
123041 TTCGTATACTGATATCTGATTCTGACACGAAGAAAGAGAATTTTTTTTTTAAATTGTACTGGGTG
1 TTCGTATACTGATATCTGATTCTGACACGAAAAAAGAGAATTTTTTTTTTAAATTGTACTGGGTG
123106 CCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTT-CTTTT
66 CCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTTACTTTT
123149 TT
1 TT
123151 TTCCCCTTTT
Statistics
Matches: 107, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
108 7 0.07
109 100 0.93
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.40
Consensus pattern (109 bp):
TTCGTATACTGATATCTGATTCTGACACGAAAAAAGAGAATTTTTTTTTTAAATTGTACTGGGTG
CCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTTTACTTTT
Found at i:125648 original size:24 final size:24
Alignment explanation
Indices: 125585--125636 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
125575 TTTTTAGAAG
* * *
125585 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
125609 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
125633 ATTT
1 ATTT
125637 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:127802 original size:2 final size:2
Alignment explanation
Indices: 127748--127786 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
127738 ACACATTCGA
127748 AT AT AT AT AT AT AT AT AT AT 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 AT AT AT AT A
127787 ATTTTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:128482 original size:23 final size:23
Alignment explanation
Indices: 128433--128498 Score: 62
Period size: 23 Copynumber: 2.9 Consensus size: 23
128423 ACCCTATTTG
* * * *
128433 GACAGCTTTTATACATCAATTTG
1 GACAGCATTTATACACCAAATTA
*
128456 GACAGCATTTATATACCAAATTA
1 GACAGCATTTATACACCAAATTA
*
128479 GACAACATTT-TCACACCAAA
1 GACAGCATTTAT-ACACCAAA
128499 ATTTGGATAG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
22 1 0.03
23 34 0.97
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (23 bp):
GACAGCATTTATACACCAAATTA
Found at i:128533 original size:23 final size:23
Alignment explanation
Indices: 128498--128557 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
128488 TTCACACCAA
**
128498 AATTTGGATAGCATAAATACAAC
1 AATTTGGGCAGCATAAATACAAC
*
128521 AATTTGGGCAGCATATATACAAC
1 AATTTGGGCAGCATAAATACAAC
* *
128544 AGTTTGAGCAGCAT
1 AATTTGGGCAGCAT
128558 TTTTACGCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (23 bp):
AATTTGGGCAGCATAAATACAAC
Found at i:128583 original size:47 final size:46
Alignment explanation
Indices: 128529--128773 Score: 197
Period size: 47 Copynumber: 5.2 Consensus size: 46
128519 ACAATTTGGG
*
128529 CAGCATATATACAAC-AGTTTGAGCAGCATTTTTACGC-CAAAACTGGA
1 CAGCATATATACAACAAG-TTGAGCAGCA--TTTAAGCACAAAACTGGA
** * *
128576 CAGCATATATGTAACAAGTTGGGCAGCATTTAAGCATCAAAATTGGA
1 CAGCATATATACAACAAGTTGAGCAGCATTTAAGCA-CAAAACTGGA
** * * * * *
128623 CAGCATATATGTAACAAATTGGGCAGCATTTAAACATCAAAATTGAA
1 CAGCATATATACAACAAGTTGAGCAGCATTTAAGCA-CAAAACTGGA
** * * * *
128670 CAGCATATATGTAACAAATTGGGCAGCATTTAAACATCAAAATTGGA
1 CAGCATATATACAACAAGTTGAGCAGCATTTAAGCA-CAAAACTGGA
** * * * *
128717 CAGCATATATGTAACAAATTGGGCAGCACTTAAGCATCAAAATTGGA
1 CAGCATATATACAACAAGTTGAGCAGCATTTAAGCA-CAAAACTGGA
128764 CAGCATATAT
1 CAGCATATAT
128774 GTAACAAATT
Statistics
Matches: 184, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
45 6 0.03
47 176 0.96
48 2 0.01
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.25
Consensus pattern (46 bp):
CAGCATATATACAACAAGTTGAGCAGCATTTAAGCACAAAACTGGA
Found at i:128626 original size:24 final size:24
Alignment explanation
Indices: 128594--128769 Score: 151
Period size: 24 Copynumber: 7.5 Consensus size: 24
128584 ATGTAACAAG
*
128594 TTGGGCAGCATTTAAGCATCAAAA
1 TTGGACAGCATTTAAGCATCAAAA
* * * *
128618 TTGGACAGCATATATGTAAC-AAA
1 TTGGACAGCATTTAAGCATCAAAA
* *
128641 TTGGGCAGCATTTAAACATCAAAA
1 TTGGACAGCATTTAAGCATCAAAA
* * * * *
128665 TTGAACAGCATATATGTAAC-AAA
1 TTGGACAGCATTTAAGCATCAAAA
* *
128688 TTGGGCAGCATTTAAACATCAAAA
1 TTGGACAGCATTTAAGCATCAAAA
* * * *
128712 TTGGACAGCATATATGTAAC-AAA
1 TTGGACAGCATTTAAGCATCAAAA
* *
128735 TTGGGCAGCACTTAAGCATCAAAA
1 TTGGACAGCATTTAAGCATCAAAA
128759 TTGGACAGCAT
1 TTGGACAGCAT
128770 ATATGTAACA
Statistics
Matches: 110, Mismatches: 39, Indels: 6
0.71 0.25 0.04
Matches are distributed among these distances:
23 50 0.45
24 60 0.55
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (24 bp):
TTGGACAGCATTTAAGCATCAAAA
Found at i:128631 original size:94 final size:94
Alignment explanation
Indices: 128524--128785 Score: 348
Period size: 94 Copynumber: 2.8 Consensus size: 94
128514 ATACAACAAT
* ** ** * *
128524 TTGGGCAGCATATATACAACAGTTTGAGCAGCATTTTTACGCCAAAACTGGACAGCATATATGTA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTTTACGCCAAAATTGGACAGCATATATGTA
* *
128589 ACAAGTTGGGCAGCATTTAAGCATCAAAA
66 ACAAATTGGGCAGCATTTAAACATCAAAA
** ** *
128618 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAACATCAAAATTGAACAGCATATATGTA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTTTACGCCAAAATTGGACAGCATATATGTA
128683 ACAAATTGGGCAGCATTTAAACATCAAAA
66 ACAAATTGGGCAGCATTTAAACATCAAAA
* *
128712 TTGGACAGCATATATGTAACAAATTGGGCAGCA--CTTAAGCATCAAAATTGGACAGCATATATG
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTTTACGC--CAAAATTGGACAGCATATATG
128775 TAACAAATTGG
64 TAACAAATTGG
128786 TTCAACTCAT
Statistics
Matches: 145, Mismatches: 21, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
92 1 0.01
94 144 0.99
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (94 bp):
TTGGACAGCATATATGTAACAAATTGGGCAGCATTTTTACGCCAAAATTGGACAGCATATATGTA
ACAAATTGGGCAGCATTTAAACATCAAAA
Found at i:128774 original size:47 final size:47
Alignment explanation
Indices: 128566--128785 Score: 386
Period size: 47 Copynumber: 4.7 Consensus size: 47
128556 ATTTTTACGC
* * *
128566 CAAAACTGGACAGCATATATGTAACAAGTTGGGCAGCATTTAAGCAT
1 CAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAACAT
128613 CAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAACAT
1 CAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAACAT
*
128660 CAAAATTGAACAGCATATATGTAACAAATTGGGCAGCATTTAAACAT
1 CAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAACAT
* *
128707 CAAAATTGGACAGCATATATGTAACAAATTGGGCAGCACTTAAGCAT
1 CAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAACAT
128754 CAAAATTGGACAGCATATATGTAACAAATTGG
1 CAAAATTGGACAGCATATATGTAACAAATTGG
128786 TTCAACTCAT
Statistics
Matches: 166, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 166 1.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (47 bp):
CAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAACAT
Found at i:129710 original size:43 final size:43
Alignment explanation
Indices: 129622--129745 Score: 128
Period size: 43 Copynumber: 2.9 Consensus size: 43
129612 AACTCGTACA
* * * * * *
129622 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATA-CCG
1 ATGCCGACGTCCCAGACGTAGTCTTACACGAAAACACA-AGTCG
*
129665 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGAAAACACAAGTCG
1 ATGCCGAC-GTCCCAGAC-GTAGTCTTACACGAAAACACAAGTCG
*
129708 ATGCCGACGTCCCAGACGTAGTCTTACATGAAAACACA
1 ATGCCGACGTCCCAGACGTAGTCTTACACGAAAACACA
129746 TATTGGAGTC
Statistics
Matches: 70, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
42 4 0.06
43 63 0.90
44 3 0.04
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.19
Consensus pattern (43 bp):
ATGCCGACGTCCCAGACGTAGTCTTACACGAAAACACAAGTCG
Found at i:133461 original size:24 final size:24
Alignment explanation
Indices: 133427--133478 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
133417 TTTCTAGAAG
* **
133427 ATTTAGTATTTATGATTATAATAT
1 ATTTAGCATTTATGAGCATAATAT
*
133451 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATGAGCATAATAT
133475 ATTT
1 ATTT
133479 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATGAGCATAATAT
Found at i:133489 original size:24 final size:24
Alignment explanation
Indices: 133444--133495 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
133434 ATTTATGATT
*
133444 ATAATATATTTAGCATTTATTAGC
1 ATAATATATTTAGCATTTATTAGA
133468 ATAATATATTT-G-ACTTTGATTAGA
1 ATAATATATTTAGCA-TTT-ATTAGA
133492 ATAA
1 ATAA
133496 GGTTTTTTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 1 0.04
23 4 0.16
24 20 0.80
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (24 bp):
ATAATATATTTAGCATTTATTAGA
Found at i:141039 original size:19 final size:19
Alignment explanation
Indices: 141015--141051 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
141005 TTGTTAAGAG
*
141015 AAAAGAGCTATCATAAAAA
1 AAAAGAGCAATCATAAAAA
141034 AAAAGAGCAATCATAAAA
1 AAAAGAGCAATCATAAAA
141052 GAACAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.65, C:0.11, G:0.11, T:0.14
Consensus pattern (19 bp):
AAAAGAGCAATCATAAAAA
Found at i:142150 original size:19 final size:20
Alignment explanation
Indices: 142128--142175 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
142118 ATTACAAAAT
*
142128 AATTCAAAATAATTT-TCAA-
1 AATTCAAAAT-ATTTATAAAC
142147 AATTCAAAATATTTATAAAC
1 AATTCAAAATATTTATAAAC
142167 AATTCAAAA
1 AATTCAAAA
142176 GAAATATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 4 0.15
19 13 0.50
20 9 0.35
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.33
Consensus pattern (20 bp):
AATTCAAAATATTTATAAAC
Found at i:149243 original size:45 final size:45
Alignment explanation
Indices: 149176--149265 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
149166 ACACTAGTAT
*
149176 GGTGTGGATAAACCACTTATTGGTGCAAAAAAAAGCTACTAATAC
1 GGTGTGGATAAACCACTCATTGGTGCAAAAAAAAGCTACTAATAC
* ** * *
149221 GGTGTTGATAAACCACTCATTGGTTTAGATAAAAGCTACTAATAC
1 GGTGTGGATAAACCACTCATTGGTGCAAAAAAAAGCTACTAATAC
149266 AAGGTGGATT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (45 bp):
GGTGTGGATAAACCACTCATTGGTGCAAAAAAAAGCTACTAATAC
Found at i:149280 original size:45 final size:43
Alignment explanation
Indices: 149179--149281 Score: 116
Period size: 45 Copynumber: 2.3 Consensus size: 43
149169 CTAGTATGGT
*
149179 GTGGATAAACCACTTATTGGTGCAAAAAAAAGCTACTAATACG
1 GTGGATAAACCACTCATTGGTGCAAAAAAAAGCTACTAATACG
** * *
149222 GTGTTGATAAACCACTCATTGGTTTAGATAAAAGCTACTAATACAAG
1 GTG--GATAAACCACTCATTGGTGCAAAAAAAAGCTACTAATAC--G
*
149269 GTGGATTAACCAC
1 GTGGATAAACCAC
149282 CCATCAGTGT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
43 3 0.06
45 43 0.86
47 4 0.08
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.26
Consensus pattern (43 bp):
GTGGATAAACCACTCATTGGTGCAAAAAAAAGCTACTAATACG
Found at i:149295 original size:45 final size:44
Alignment explanation
Indices: 149206--149298 Score: 107
Period size: 45 Copynumber: 2.1 Consensus size: 44
149196 TGGTGCAAAA
* ** *
149206 AAAAGCTACTAATACGGTGTTGATAAACCACTCATTGGTTTAGAT
1 AAAAGCTACTAATACGGTG-TGATAAACCACCCATCAGTGTAGAT
*
149251 AAAAGCTACTAATACAAGGTG-GATTAACCACCCATCAGTGTAGAT
1 AAAAGCTACTAATAC--GGTGTGATAAACCACCCATCAGTGTAGAT
149296 AAA
1 AAA
149299 CTGCTCATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
45 37 0.90
47 4 0.10
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (44 bp):
AAAAGCTACTAATACGGTGTGATAAACCACCCATCAGTGTAGAT
Found at i:150856 original size:34 final size:34
Alignment explanation
Indices: 150813--150941 Score: 168
Period size: 34 Copynumber: 3.8 Consensus size: 34
150803 TGCCATATGG
* *
150813 CATGCTTATAATAGTTCAATATGGTAGCAATAAA
1 CATGCTTATAACAGATCAATATGGTAGCAATAAA
* *
150847 CATGCTTATAACAAATCAATACGGTAGCAATAAA
1 CATGCTTATAACAGATCAATATGGTAGCAATAAA
* * *
150881 CATGCTTATAACAGATCAATATGATAGTAATAGA
1 CATGCTTATAACAGATCAATATGGTAGCAATAAA
* * *
150915 CATGCTTATAACAAATCAGTACGGTAG
1 CATGCTTATAACAGATCAATATGGTAG
150942 AAAATCCATG
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 82 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (34 bp):
CATGCTTATAACAGATCAATATGGTAGCAATAAA
Found at i:150922 original size:68 final size:68
Alignment explanation
Indices: 150813--150941 Score: 204
Period size: 68 Copynumber: 1.9 Consensus size: 68
150803 TGCCATATGG
* * *
150813 CATGCTTATAATAGTTCAATATGGTAGCAATAAACATGCTTATAACAAATCAATACGGTAGCAAT
1 CATGCTTATAACAGATCAATATGATAGCAATAAACATGCTTATAACAAATCAATACGGTAGCAAT
150878 AAA
66 AAA
* * *
150881 CATGCTTATAACAGATCAATATGATAGTAATAGACATGCTTATAACAAATCAGTACGGTAG
1 CATGCTTATAACAGATCAATATGATAGCAATAAACATGCTTATAACAAATCAATACGGTAG
150942 AAAATCCATG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 55 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (68 bp):
CATGCTTATAACAGATCAATATGATAGCAATAAACATGCTTATAACAAATCAATACGGTAGCAAT
AAA
Found at i:165485 original size:101 final size:102
Alignment explanation
Indices: 165370--165554 Score: 293
Period size: 102 Copynumber: 1.8 Consensus size: 102
165360 AAAGTGATGG
* *
165370 TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTA-CCAG-AATGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACATGTATCCAGTAATGAT-GGTCACATGTGTAGT
165433 ACTATGTGCAGGCTACTATGCGTATCGGATAGCTTCGA
65 ACTATGTGCAGGCTACTATGCGTATCGGATAGCTTCGA
* ** *
165471 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTATCGGGTAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAAGCTACTACATGTATCCAGTAATGATGGTCACATGTGTAGTA
165536 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
165555 TGAACCGGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 35 0.46
102 36 0.47
103 5 0.07
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAAGCTACTACATGTATCCAGTAATGATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTATCGGATAGCTTCGA
Found at i:165492 original size:51 final size:50
Alignment explanation
Indices: 165370--165554 Score: 178
Period size: 51 Copynumber: 3.7 Consensus size: 50
165360 AAAGTGATGG
* * * * * * *
165370 TCACGTGTGTAGTACTATGTGCAAGCTACTACGTGTACCAGA-A-TGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGT-AT-GA
*
165420 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGCT-TCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAG-TAT-GA
* *** * *
165471 TCACGTGTGTAGTACTATGTGCAGGCTACTACATGTATCGGGTAGTGATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGT-ATGA
165522 TCACATGTGTAGTACTATGTGCAGGCTACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
165555 TGAACCGGTA
Statistics
Matches: 111, Mismatches: 19, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
50 36 0.32
51 73 0.66
52 1 0.01
53 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.31
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGTATGA
Found at i:165630 original size:46 final size:43
Alignment explanation
Indices: 165558--165642 Score: 107
Period size: 46 Copynumber: 1.9 Consensus size: 43
165548 TACTATGTGA
*
165558 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGTTGATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGTTGATCCC
* * *
165601 ACCGGATATCATTGATTACAAAGGGTGGTTGTTGTGTGTTGA
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGTTGA
165643 ATCCAACGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 5 0.14
44 11 0.31
45 2 0.06
46 17 0.49
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGTTGATCCC
Found at i:168578 original size:29 final size:29
Alignment explanation
Indices: 168536--168591 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
168526 TAAAAAAAAA
168536 TTAAATACGAAAATGGTATGTCAGTAGGG
1 TTAAATACGAAAATGGTATGTCAGTAGGG
*
168565 TTAAATACGAAAATGTTATGTCAGTAG
1 TTAAATACGAAAATGGTATGTCAGTAG
168592 CGATGGTGCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.30
Consensus pattern (29 bp):
TTAAATACGAAAATGGTATGTCAGTAGGG
Found at i:168804 original size:27 final size:27
Alignment explanation
Indices: 168773--168851 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
168763 AGGGGTGGTG
*
168773 CCTATTTGATAGGCAGGACCGGTGACC
1 CCTATCTGATAGGCAGGACCGGTGACC
*
168800 CCTATCTGATAGGC-GGCACTGGTGACC
1 CCTATCTGATAGGCAGG-ACCGGTGACC
* * * *
168827 TCTATCTAATAGGCAGCACCAGTGA
1 CCTATCTGATAGGCAGGACCGGTGA
168852 AGCAATTTTG
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
26 2 0.05
27 40 0.93
28 1 0.02
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.23
Consensus pattern (27 bp):
CCTATCTGATAGGCAGGACCGGTGACC
Found at i:169083 original size:10 final size:11
Alignment explanation
Indices: 169050--169095 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
169040 GTGTAGTTTG
*
169050 TTTATTGTTAT
1 TTTAATGTTAT
169061 TTT-ATGTTGAT
1 TTTAATGTT-AT
169072 TTTAAT-TTAT
1 TTTAATGTTAT
*
169082 TTTAAAGTTAT
1 TTTAATGTTAT
169093 TTT
1 TTT
169096 GTTAGTTACT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 11 0.37
11 17 0.57
12 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (11 bp):
TTTAATGTTAT
Found at i:169125 original size:25 final size:26
Alignment explanation
Indices: 169079--169127 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
169069 GATTTTAATT
*
169079 TATTTTAAAGTTATTTTGTTAGTTAC
1 TATTATAAAGTTATTTTGTTAGTTAC
169105 TATTATAAA-TTA-TTTGTTTAGTT
1 TATTATAAAGTTATTTTG-TTAGTT
169128 TAATATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 4 0.19
25 9 0.43
26 8 0.38
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (26 bp):
TATTATAAAGTTATTTTGTTAGTTAC
Found at i:169134 original size:26 final size:26
Alignment explanation
Indices: 169079--169134 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
169069 GATTTTAATT
* *
169079 TATTTTAAAGTTATTTTGTTAGTTAC
1 TATTATAAAGTTATTTTGTTAGTTAA
169105 TATTATAAA-TTA-TTTGTTTAGTTTAA
1 TATTATAAAGTTATTTTG-TTAG-TTAA
169131 TATT
1 TATT
169135 TATTGTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 4 0.15
25 7 0.27
26 15 0.58
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (26 bp):
TATTATAAAGTTATTTTGTTAGTTAA
Found at i:169193 original size:105 final size:107
Alignment explanation
Indices: 169071--169337 Score: 326
Period size: 115 Copynumber: 2.4 Consensus size: 107
169061 TTTATGTTGA
169071 TTTTAATTTATTTTAAAGTTATTTTGTTAGTTACTATTATAAATTATTTGTTTA-GTTTAAT-AT
1 TTTTAATTTATTTTAAAGTTATTTTGTTAGTTACTATTATAAATTATTTGTTTAGGTTT-ATGAT
*
169134 TTATTGTGATTTGTTAGGTTATGAATGTAAT-TTTTTACTGA-T
65 TTATTGTGATTTGTTAGGTTATGAATGTAATCTTTTTAAT-ATT
** * *
169176 TTTTAATTTATTTTAAAGTTATTTTGTCAGTAAGTTTTGTGATTAGGTTAATTGTTTGTTTAGGG
1 TTTTAATTTATTTTAAAGTTATTTTGT---T-AG-TTACT-ATTA--TAAATTATTTGTTTA-GG
*
169241 TTTATGGTTTATTGTGATTTGTTAGGTTATGAATGTAATCTTTTTAATATT
57 TTTATGATTTATTGTGATTTGTTAGGTTATGAATGTAATCTTTTTAATATT
* * *
169292 TTTTAATTTATTTGAAATTTATTTTGTTAGTAACTATTATAAATTA
1 TTTTAATTTATTTTAAAGTTATTTTGTTAGTTACTATTATAAATTA
169338 ATTATTAGTT
Statistics
Matches: 136, Mismatches: 13, Indels: 23
0.79 0.08 0.13
Matches are distributed among these distances:
105 27 0.20
108 6 0.04
109 2 0.01
110 7 0.05
111 6 0.04
112 2 0.01
113 14 0.10
114 2 0.01
115 37 0.27
116 33 0.24
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (107 bp):
TTTTAATTTATTTTAAAGTTATTTTGTTAGTTACTATTATAAATTATTTGTTTAGGTTTATGATT
TATTGTGATTTGTTAGGTTATGAATGTAATCTTTTTAATATT
Found at i:169244 original size:115 final size:114
Alignment explanation
Indices: 169112--169324 Score: 315
Period size: 116 Copynumber: 1.9 Consensus size: 114
169102 TACTATTATA
*
169112 AATTATTTGTTTAGTTTAAT-ATTTATTGTGATTTGTTAGGTTATGAATGTAAT-TTTTTACTGA
1 AATTATTTGTTTAGTTT-ATGATTTATTGTGATTTGTTAGGTTATGAATGTAATCTTTTTAAT-A
*
169175 -TTTTTAATTTATTTTAAAGTTATTTTGTCAGTAAGTTTTGTGATTAGGTT
64 TTTTTTAATTTATTTGAAAGTTATTTTGTCAGTAAGTTTTGTGATTAGGTT
* *
169225 AATTGTTTGTTTAGGGTTTATGGTTTATTGTGATTTGTTAGGTTATGAATGTAATCTTTTTAATA
1 AATTATTTGTTTA--GTTTATGATTTATTGTGATTTGTTAGGTTATGAATGTAATCTTTTTAATA
* *
169290 TTTTTTAATTTATTTGAAATTTATTTTGTTAGTAA
64 TTTTTTAATTTATTTGAAAGTTATTTTGTCAGTAA
169325 CTATTATAAA
Statistics
Matches: 89, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
113 12 0.13
114 2 0.02
115 37 0.42
116 38 0.43
ACGTcount: A:0.25, C:0.01, G:0.16, T:0.57
Consensus pattern (114 bp):
AATTATTTGTTTAGTTTATGATTTATTGTGATTTGTTAGGTTATGAATGTAATCTTTTTAATATT
TTTTAATTTATTTGAAAGTTATTTTGTCAGTAAGTTTTGTGATTAGGTT
Found at i:173246 original size:33 final size:33
Alignment explanation
Indices: 173200--173287 Score: 113
Period size: 33 Copynumber: 2.7 Consensus size: 33
173190 TGATGAACTT
*
173200 GAGCCGGGAGGAGTGGAGTACTGTGGTGGATAC
1 GAGCCGGGAGGAGTCGAGTACTGTGGTGGATAC
* * * * **
173233 GGGTCGGGAGGAGTCTAGTATTGTGGTGGATGT
1 GAGCCGGGAGGAGTCGAGTACTGTGGTGGATAC
173266 GAGCCGGGAGGAGTCGAGTACT
1 GAGCCGGGAGGAGTCGAGTACT
173288 TCGGTGGTAG
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.19, C:0.11, G:0.48, T:0.22
Consensus pattern (33 bp):
GAGCCGGGAGGAGTCGAGTACTGTGGTGGATAC
Found at i:174314 original size:22 final size:22
Alignment explanation
Indices: 174267--174329 Score: 58
Period size: 21 Copynumber: 2.9 Consensus size: 22
174257 ACATTTATAT
* *
174267 TATACATACAGTAAATAATACG
1 TATAAATATAGTAAATAATACG
174289 -ATAAATATAGTACAATAATA-G
1 TATAAATATAGTA-AATAATACG
* * *
174310 TATAATTATAATAAAAAATA
1 TATAAATATAGTAAATAATA
174330 TCTCATAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
21 17 0.50
22 17 0.50
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.30
Consensus pattern (22 bp):
TATAAATATAGTAAATAATACG
Found at i:174777 original size:109 final size:108
Alignment explanation
Indices: 174649--175036 Score: 566
Period size: 109 Copynumber: 3.6 Consensus size: 108
174639 AAATAACTTT
* *
174649 AAAATAAAAAAATTACATTCATAAAAAATCACAATAAACATTAAACTAAACACAAACAATTTATA
1 AAAACAAAAAAATTACATTCATAAAAAATCAC-A-AAACACTAAACTAAACACAAACAATTTATA
*
174714 ACCTAATAATAAATTACTAACAAAATAACTTTAAAATAA-TTAAA
64 ACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTAAA
* *
174758 AAAACAAAAAAAATACATTCATAAAAAATCACAATAAACACTAAATTAAACACAAACAATTTAT-
1 AAAACAAAAAAATTACATTCATAAAAAATCAC-A-AAACACTAAACTAAACACAAACAATTTATA
* * *
174822 ACCTAACCATAAATTACTAA-AAAATGACTTTAAAATAATTTTAA
64 ACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTAAA
* * *
174866 AAAATAAAAAATTTTACATTCATAAAAAAATCACAAAACACTAAATTAAACACAAACAATTTATA
1 AAAACAAAAAA-ATTACATTCAT-AAAAAATCACAAAACACTAAACTAAACACAAACAATTTATA
*
174931 ACCTAATCATAAATTACTAACAAAATAACTATAAAATAATTTAAA
64 ACCTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTAAA
* * *
174976 AAAACAAAAAAATTACATTCATAAAAGATCTCAAAACACTAAACTAAATACAAACAATTTA
1 AAAACAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTA
175037 GAATAATTAA
Statistics
Matches: 253, Mismatches: 21, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
107 17 0.07
108 96 0.38
109 99 0.39
110 41 0.16
ACGTcount: A:0.60, C:0.14, G:0.01, T:0.25
Consensus pattern (108 bp):
AAAACAAAAAAATTACATTCATAAAAAATCACAAAACACTAAACTAAACACAAACAATTTATAAC
CTAATCATAAATTACTAACAAAATAACTTTAAAATAATTTAAA
Found at i:175548 original size:18 final size:19
Alignment explanation
Indices: 175511--175548 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
175501 TTTTTAAAAA
*
175511 TATTTTTAATTACATTTAT
1 TATTTTTAATTACATATAT
175530 TATTTTTAATTA-ATATAT
1 TATTTTTAATTACATATAT
175548 T
1 T
175549 TTTCATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
TATTTTTAATTACATATAT
Found at i:179579 original size:79 final size:78
Alignment explanation
Indices: 179375--179616 Score: 267
Period size: 79 Copynumber: 3.1 Consensus size: 78
179365 AATTAAAGGT
* * * * *
179375 AAATAAAATTCATTTCGGGATTGGTTCCCGCCATTTAACGATTTTATTCCAAATTTTATTTTATT
1 AAATAAAATCCGTTTCGGGATTGATTCCCGCCATTCAACGATTTTATTCC-AATTTTGTTTTATT
*
179440 TCAAAAAACGAGTA
65 TCCAAAAACGAGTA
* ** *
179454 AAACT-AAATCTGTTTCAAGATTGATTCCCGCCATTCAACTATTTTATTCCAATTTTTGTTTTAT
1 AAA-TAAAATCCGTTTCGGGATTGATTCCCGCCATTCAACGATTTTATTCCAA-TTTTGTTTTAT
179518 TTCCAAAAACGAGTA
64 TTCCAAAAACGAGTA
* * * *
179533 AAATAAAATCCGTTTTGGGATTGATTCCCGCCGTTCAACGGA-TTTATTTC-ATTTTGATTTTGT
1 AAATAAAATCCGTTTCGGGATTGATTCCCGCCATTCAAC-GATTTTATTCCAATTTTG-TTTTAT
*
179596 TGCCAAAAACGAG-A
64 TTCCAAAAACGAGTA
*
179610 AATTAAA
1 AAATAAA
179617 TAAAATAAAA
Statistics
Matches: 138, Mismatches: 20, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
77 12 0.09
78 21 0.15
79 103 0.75
80 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (78 bp):
AAATAAAATCCGTTTCGGGATTGATTCCCGCCATTCAACGATTTTATTCCAATTTTGTTTTATTT
CCAAAAACGAGTA
Found at i:179639 original size:86 final size:85
Alignment explanation
Indices: 179533--180169 Score: 539
Period size: 86 Copynumber: 7.6 Consensus size: 85
179523 AAAACGAGTA
** * * * * *
179533 AAATAAAATCCGTTTTGGGATTGATTCCCGCCGTTCAAC-GGATTTATTTCATTTTGATTTTGTT
1 AAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTTAACAAGATTTATTTGATTTTGATTTTGTT
*
179597 GCCAAAAACGAGAAATTAAATA
66 GCCAAAAA--AGAAATTAAATT
* *
179619 AAATAAAATTTGTTTCGGGATTTATTCTCGCCGTTTAATAAGATTTATTTGA-TTTGATTTTGTT
1 AAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTTAACAAGATTTATTTGATTTTGATTTTGTT
* *
179683 GTCAAAAATGAGAAATCAAATT
66 GCCAAAAA--AGAAATTAAATT
* * * *
179705 AAATAAAATTTGTTTCAGAATTTATTCCCGTCGTTTAACAAGA--T-TTT-ATTTT-ATTTTATT
1 AAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTTAACAAGATTTATTTGATTTTGATTTTGTT
* *
179765 TCCAAATAAG-AATTAAATT
66 GCCAAAAAAGAAATTAAATT
* * ** *
179784 AAATAAAATCTATTTCGGGATTTATTCCTTCCGTTTAACAAGATTTTATTTGATATTG-TTTTGT
1 AAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTTAACAAGA-TTTATTTGATTTTGATTTTGT
** * *
179848 TTTCAAACAAAGATA-T-AATC
65 TGCCAAA-AAAGAAATTAAATT
*
179868 AAAT--AATTCTGTTTCGGGATTTATTCTCGCCGTTT-ACTAAGATTTATTTGA-TTTGATTTTG
1 AAATAAAATT-TGTTTCGGGATTTATTCCCGCCGTTTAAC-AAGATTTATTTGATTTTGATTTTG
*
179929 TAGCCAAAAATGAGAAATTAAATT
64 TTGCCAAAAA--AGAAATTAAATT
** * *
179953 AAATAAAATCTT-TTTCGGGATTTATTCCCGTTGTTTAACAAGATTTTATTTTATTTT-ATTTTA
1 AAATAAAAT-TTGTTTCGGGATTTATTCCCGCCGTTTAACAAGA-TTTATTTGATTTTGATTTTG
** *** *
180016 TTTTCAAATTCG-AATTGAATT
64 TTGCCAAAAAAGAAATTAAATT
* *
180037 AAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTTAACAAGATTTTATTCGATATTG-TTTTGT
1 AAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTTAACAAGA-TTTATTTGATTTTGATTTTGT
* ** *
180101 TTCCAAACAAAG-ACGT-AATC
65 TGCCAAA-AAAGAAATTAAATT
* *
180121 AAAT--AATTCTGTTTCGAGATTTATTCCCGTCGTTTAACAA-ATTTTATTT
1 AAATAAAATT-TGTTTCGGGATTTATTCCCGCCGTTTAACAAGA-TTTATTT
180170 TTGATTTAAT
Statistics
Matches: 449, Mismatches: 75, Indels: 58
0.77 0.13 0.10
Matches are distributed among these distances:
79 44 0.10
80 2 0.00
81 5 0.01
82 50 0.11
83 70 0.16
84 99 0.22
85 15 0.03
86 126 0.28
87 34 0.08
88 4 0.01
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (85 bp):
AAATAAAATTTGTTTCGGGATTTATTCCCGCCGTTTAACAAGATTTATTTGATTTTGATTTTGTT
GCCAAAAAAGAAATTAAATT
Found at i:179911 original size:248 final size:249
Alignment explanation
Indices: 179625--180157 Score: 802
Period size: 253 Copynumber: 2.1 Consensus size: 249
179615 AATAAAATAA
* *
179625 AATT-TGTTTCGGGATTTATTCTCGCCGTTTAATAAGATTTATTTGATTTGATTTTGTTGTCAAA
1 AATTCTGTTTCGGGATTTATTCTCGCCGTTTAATAAGATTTATTTGATTTGATTTTGTAGCCAAA
179689 AATGAGAAATCAAATTAAATAAAAT-TTGTTTCAGAATTTATTCCCGTCGTTTAACAAG-ATTTT
66 AATGAGAAATCAAATTAAATAAAATCTT-TTTCAGAATTTATTCCCGTCGTTTAACAAGTATTTT
**
179752 ATTTTATTTTATTTCCAAATAAGAATTAAATTAAATAAAATCTATTTCGGGATTTATTCCTTCCG
130 ATTTTATTTTATTTCCAAATAAGAATTAAATTAAATAAAATCTATTTCGGGATTTATTCCCGCCG
* * *
179817 TTTAACAAGATTTTATTTGATATTGTTTTGTTTTCAAACAAAGATATAATCAAAT
195 TTTAACAAGATTTTATTCGATATTGTTTTGTTTCCAAACAAAGACATAATCAAAT
*
179872 AATTCTGTTTCGGGATTTATTCTCGCCGTTTACTAAGATTTATTTGATTTGATTTTGTAGCCAAA
1 AATTCTGTTTCGGGATTTATTCTCGCCGTTTAATAAGATTTATTTGATTTGATTTTGTAGCCAAA
* * * *
179937 AATGAGAAATTAAATTAAATAAAATCTTTTTCGGGATTTATTCCCGTTGTTTAACAAGATTTTAT
66 AATGAGAAATCAAATTAAATAAAATCTTTTTCAGAATTTATTCCCGTCGTTTAACAAG----TAT
* ** * * *
180002 TTTATTTTATTTTATTTTCAAATTCGAATTGAATTAAATAAAATTTGTTTCGGGATTTATTCCCG
127 TTTATTTTATTTTATTTCCAAATAAGAATTAAATTAAATAAAATCTATTTCGGGATTTATTCCCG
*
180067 CCGTTTAACAAGATTTTATTCGATATTGTTTTGTTTCCAAACAAAGACGTAATCAAAT
192 CCGTTTAACAAGATTTTATTCGATATTGTTTTGTTTCCAAACAAAGACATAATCAAAT
* * *
180125 AATTCTGTTTCGAGATTTATTCCCGTCGTTTAA
1 AATTCTGTTTCGGGATTTATTCTCGCCGTTTAA
180158 CAAATTTTAT
Statistics
Matches: 256, Mismatches: 23, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
247 4 0.02
248 108 0.42
249 2 0.01
253 142 0.55
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.44
Consensus pattern (249 bp):
AATTCTGTTTCGGGATTTATTCTCGCCGTTTAATAAGATTTATTTGATTTGATTTTGTAGCCAAA
AATGAGAAATCAAATTAAATAAAATCTTTTTCAGAATTTATTCCCGTCGTTTAACAAGTATTTTA
TTTTATTTTATTTCCAAATAAGAATTAAATTAAATAAAATCTATTTCGGGATTTATTCCCGCCGT
TTAACAAGATTTTATTCGATATTGTTTTGTTTCCAAACAAAGACATAATCAAAT
Found at i:180005 original size:5 final size:5
Alignment explanation
Indices: 179995--180019 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
179985 GTTTAACAAG
179995 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
180020 CAAATTCGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:195685 original size:16 final size:16
Alignment explanation
Indices: 195666--195696 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
195656 TTATTAAGAG
195666 AAAAATAAAAATTAAT
1 AAAAATAAAAATTAAT
195682 AAAAATAAAAATTAA
1 AAAAATAAAAATTAA
195697 GATCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAATAAAAATTAAT
Found at i:196680 original size:23 final size:23
Alignment explanation
Indices: 196635--196681 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
196625 CTAAACTACG
* *
196635 ATTACAACTAAAAAGAAACCTAA
1 ATTACAAATAAAAAGAAAACTAA
* *
196658 ATTACAAATAGAAATAAAACTAA
1 ATTACAAATAAAAAGAAAACTAA
196681 A
1 A
196682 CAAGCAACCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.64, C:0.13, G:0.04, T:0.19
Consensus pattern (23 bp):
ATTACAAATAAAAAGAAAACTAA
Found at i:197579 original size:21 final size:21
Alignment explanation
Indices: 197555--197598 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
197545 TACAACATTT
*
197555 AAATATAGTATAGAAATTTGA
1 AAATATAGTATAAAAATTTGA
197576 AAATATAGTATAAAAATTTGA
1 AAATATAGTATAAAAATTTGA
197597 AA
1 AA
197599 CTGAAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (21 bp):
AAATATAGTATAAAAATTTGA
Found at i:197611 original size:20 final size:19
Alignment explanation
Indices: 197586--197638 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
197576 AAATATAGTA
197586 TAAAAATTTGAAACTGAAAT
1 TAAAAA-TTGAAACTGAAAT
*
197606 TAAAAATTGTAACTGAAAT
1 TAAAAATTGAAACTGAAAT
197625 AATAAAACATTGAA
1 --TAAAA-ATTGAA
197639 TTAATACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 12 0.43
20 6 0.21
21 5 0.18
22 5 0.18
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.28
Consensus pattern (19 bp):
TAAAAATTGAAACTGAAAT
Found at i:197619 original size:19 final size:20
Alignment explanation
Indices: 197586--197624 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
197576 AAATATAGTA
197586 TAAAAATTTGAAACTGAAAT
1 TAAAAATTTGAAACTGAAAT
*
197606 TAAAAA-TTGTAACTGAAAT
1 TAAAAATTTGAAACTGAAAT
197625 AATAAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (20 bp):
TAAAAATTTGAAACTGAAAT
Found at i:197745 original size:92 final size:91
Alignment explanation
Indices: 197619--197808 Score: 229
Period size: 92 Copynumber: 2.1 Consensus size: 91
197609 AAATTGTAAC
* * * ** * *
197619 TGAAATAATAAAACATTGAATTAATACATTCTACTATTAAAAATAATATAGGAATTTGTAACTTA
1 TGAAATAACAAAACATTGAATTAATACATACTACTATTAAAAATAATATAGAAACATGGAA-GTA
*
197684 AATTAAAAAAAAAACTATAATATT-AAA
65 AAAT-AAAAAAAAACTATAATATTAAAA
* * * * *
197711 TGAAATAACAAAATATTGTATTACTTCATACTACTATTAAAAATAATTTAGAAACATGGAAGTAA
1 TGAAATAACAAAACATTGAATTAATACATACTACTATTAAAAATAATATAGAAACATGGAAGTAA
*
197776 AATAAATAAAAACTATAATATTAAAA
66 AATAAAAAAAAACTATAATATTAAAA
197802 TGAAATA
1 TGAAATA
197809 TTAAAAAATT
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
90 18 0.22
91 15 0.18
92 50 0.60
ACGTcount: A:0.55, C:0.07, G:0.06, T:0.32
Consensus pattern (91 bp):
TGAAATAACAAAACATTGAATTAATACATACTACTATTAAAAATAATATAGAAACATGGAAGTAA
AATAAAAAAAAACTATAATATTAAAA
Found at i:198149 original size:27 final size:27
Alignment explanation
Indices: 198118--198177 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
198108 TAATTATACA
198118 TGGACATGAGCTCTATTTCACCTTAAT
1 TGGACATGAGCTCTATTTCACCTTAAT
198145 TGGACATGAGCTCTATTTCACCTTAAT
1 TGGACATGAGCTCTATTTCACCTTAAT
198172 TGGACA
1 TGGACA
198178 GCAAAGGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.35
Consensus pattern (27 bp):
TGGACATGAGCTCTATTTCACCTTAAT
Found at i:203007 original size:18 final size:19
Alignment explanation
Indices: 202984--203019 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
202974 TAATAATTAT
202984 AAATTA-AATTACTTTAAA
1 AAATTATAATTACTTTAAA
*
203002 AAATTATAATTATTTTAA
1 AAATTATAATTACTTTAA
203020 TATGACAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATTATAATTACTTTAAA
Found at i:203469 original size:226 final size:227
Alignment explanation
Indices: 203064--203520 Score: 907
Period size: 226 Copynumber: 2.0 Consensus size: 227
203054 ATATTCTTAA
203064 TGATTTAAAAGTTTCTCTAAACTCGTGTTATTATATATATATGTATATATAGTTATAGATATATC
1 TGATTTAAAAGTTTCTCTAAACTCGTGTTATTATATATATATGTATATATAGTTATAGATATATC
203129 TTAAGATATTTATATTCTTTTAAGGGATAGAGATATATAAGCATAGCCAAGGTTCAAACATGAAT
66 TTAAGATATTTATATTCTTTTAAGGGATAGAGATATATAAGCATAGCCAAGGTTCAAACATGAAT
203194 AGTTGGCTCGCCTTGGTTAAAAGGGTATAATATTCTTAGCAGTCCCTTTAAAATCCTTTTAGCCT
131 AGTTGGCTCGCCTTGGTTAAAAGGGTATAATATTCTTAGCAGTCCCTTTAAAATCCTTTTAGCCT
203259 TTTTCTAAATTTAAAAAAAATATATATGTTGG
196 TTTTCTAAATTTAAAAAAAATATATATGTTGG
203291 TGATTTAAAA-TTTCTCTAAACTCGTGTTATTATATATATATGTATATATAGTTATAGATATATC
1 TGATTTAAAAGTTTCTCTAAACTCGTGTTATTATATATATATGTATATATAGTTATAGATATATC
203355 TTAAGATATTTATATTCTTTTAAGGGATAGAGATATATAAGCATAGCCAAGGTTCAAACATGAAT
66 TTAAGATATTTATATTCTTTTAAGGGATAGAGATATATAAGCATAGCCAAGGTTCAAACATGAAT
203420 AGTTGGCTCGCCTTGGTTAAAAGGGTATAATATTCTTAGCAGTCCCTTTAAAATCCTTTTAGCCT
131 AGTTGGCTCGCCTTGGTTAAAAGGGTATAATATTCTTAGCAGTCCCTTTAAAATCCTTTTAGCCT
203485 TTTTCTAAATTTAAAAAAAATATATATGTTGG
196 TTTTCTAAATTTAAAAAAAATATATATGTTGG
203517 TGAT
1 TGAT
203521 GTTGCTTTTA
Statistics
Matches: 230, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
226 220 0.96
227 10 0.04
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (227 bp):
TGATTTAAAAGTTTCTCTAAACTCGTGTTATTATATATATATGTATATATAGTTATAGATATATC
TTAAGATATTTATATTCTTTTAAGGGATAGAGATATATAAGCATAGCCAAGGTTCAAACATGAAT
AGTTGGCTCGCCTTGGTTAAAAGGGTATAATATTCTTAGCAGTCCCTTTAAAATCCTTTTAGCCT
TTTTCTAAATTTAAAAAAAATATATATGTTGG
Found at i:217227 original size:3 final size:3
Alignment explanation
Indices: 217219--217252 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
217209 TATCAGTCAC
* *
217219 GAT GAT GAT GGT GAT GAT GAT GAT GAT GGT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
217253 CAGAGTCATG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.41, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:223279 original size:4 final size:4
Alignment explanation
Indices: 223270--223295 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
223260 TGAAAAAGGT
223270 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
223296 ACTAACGGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:234840 original size:29 final size:29
Alignment explanation
Indices: 234821--234878 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
234811 ATGTATTATA
*
234821 TAATAATGATAATAGTTATATAATAATAG
1 TAATAATGATAATAATTATATAATAATAG
*
234850 TTATAATGATAATAA-T-TATAATAATAG
1 TAATAATGATAATAATTATATAATAATAG
234877 TA
1 TA
234879 TAGCAAGTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 12 0.46
28 1 0.04
29 13 0.50
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.40
Consensus pattern (29 bp):
TAATAATGATAATAATTATATAATAATAG
Found at i:239885 original size:67 final size:67
Alignment explanation
Indices: 239685--239985 Score: 489
Period size: 67 Copynumber: 4.5 Consensus size: 67
239675 ATTTATGTAG
*
239685 TGAATTTTCATTCTTGTATCAACTTCAATTATTTACATATATTTGCATTATGTTTTTGTTTTTCT
1 TGAATTTTCATTCTTGTATCAACTTCAATTATTTACATATATTTGCATTATGTTTCTGTTTTTCT
239750 AT
66 AT
* * * *
239752 TGAACTTTCATTCTTGTATCAACTTAAATTA--TATATATATTTGCATTATGTTTCTATTTTTCT
1 TGAATTTTCATTCTTGTATCAACTTCAATTATTTACATATATTTGCATTATGTTTCTGTTTTTCT
239815 AT
66 AT
* * *
239817 TGAATTTTCATTCTTGTATCAACTTAAATTATTTACATATATTTTCATTATGTTTTTGTTTTTCT
1 TGAATTTTCATTCTTGTATCAACTTCAATTATTTACATATATTTGCATTATGTTTCTGTTTTTCT
239882 AT
66 AT
* * *
239884 TGAATTTCCATTCTTATATCAGCTTCAATTATTTACATATATTTGCATTATGTTTCTGTTTTTCT
1 TGAATTTTCATTCTTGTATCAACTTCAATTATTTACATATATTTGCATTATGTTTCTGTTTTTCT
239949 AT
66 AT
239951 TGAATTTTCATTCTTGTATCAACTTCAATTATTTA
1 TGAATTTTCATTCTTGTATCAACTTCAATTATTTA
239986 GATGAACTTG
Statistics
Matches: 213, Mismatches: 19, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
65 61 0.29
67 152 0.71
ACGTcount: A:0.26, C:0.13, G:0.07, T:0.55
Consensus pattern (67 bp):
TGAATTTTCATTCTTGTATCAACTTCAATTATTTACATATATTTGCATTATGTTTCTGTTTTTCT
AT
Found at i:242569 original size:72 final size:73
Alignment explanation
Indices: 242476--242620 Score: 283
Period size: 72 Copynumber: 2.0 Consensus size: 73
242466 AAATAATTAA
242476 CCATATTATTTATTTATTTTTTTGGATAATAAATTAAATAATAACTTCTTAATAAAAAAATACAA
1 CCATATTATTTATTTATTTTTTTGGATAATAAATTAAATAATAACTTCTTAATAAAAAAATACAA
242541 CATACTTT
66 CATACTTT
242549 CCATATTA-TTATTTATTTTTTTGGATAATAAATTAAATAATAACTTCTTAATAAAAAAATACAA
1 CCATATTATTTATTTATTTTTTTGGATAATAAATTAAATAATAACTTCTTAATAAAAAAATACAA
242613 CATACTTT
66 CATACTTT
242621 ATTTAACAAT
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
72 64 0.89
73 8 0.11
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (73 bp):
CCATATTATTTATTTATTTTTTTGGATAATAAATTAAATAATAACTTCTTAATAAAAAAATACAA
CATACTTT
Found at i:243327 original size:17 final size:17
Alignment explanation
Indices: 243305--243365 Score: 61
Period size: 17 Copynumber: 3.5 Consensus size: 17
243295 AATCTTAGAG
243305 TTTTAATTGTATACAGC
1 TTTTAATTGTATACAGC
* *
243322 TTTTAATTATAGCCTAGAG-
1 TTTTAATTGTA---TACAGC
*
243341 TTCTAATTGTATACAGC
1 TTTTAATTGTATACAGC
243358 TTTTAATT
1 TTTTAATT
243366 ATAGCCTTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
16 4 0.12
17 17 0.50
19 9 0.26
20 4 0.12
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (17 bp):
TTTTAATTGTATACAGC
Found at i:243340 original size:36 final size:36
Alignment explanation
Indices: 243300--243372 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
243290 TATTTAATCT
*
243300 TAGAGTTTTAATTGTATACAGCTTTTAATTATAGCC
1 TAGAGTTCTAATTGTATACAGCTTTTAATTATAGCC
243336 TAGAGTTCTAATTGTATACAGCTTTTAATTATAGCC
1 TAGAGTTCTAATTGTATACAGCTTTTAATTATAGCC
243372 T
1 T
243373 TTGATGTACT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (36 bp):
TAGAGTTCTAATTGTATACAGCTTTTAATTATAGCC
Found at i:249079 original size:36 final size:36
Alignment explanation
Indices: 249038--249108 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
249028 GATTATTTAA
*
249038 TCTTAGAGTTTTAATTGTATACAGCTTCTAATTATG
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
*
249074 TCTTAGAGTTCTAATTGTATACAGCTTTTAATTAT
1 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTAT
249109 AGCCTTTGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAGCTTCTAATTATG
Found at i:251644 original size:8 final size:8
Alignment explanation
Indices: 251631--251666 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
251621 AAATGTAACC
251631 AATACCAA
1 AATACCAA
251639 AATACCAA
1 AATACCAA
251647 AATACCAA
1 AATACCAA
251655 AATACCAA
1 AATACCAA
251663 AATA
1 AATA
251667 TCAACCTATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.64, C:0.22, G:0.00, T:0.14
Consensus pattern (8 bp):
AATACCAA
Found at i:256718 original size:79 final size:79
Alignment explanation
Indices: 256587--256741 Score: 220
Period size: 79 Copynumber: 2.0 Consensus size: 79
256577 GTGCACAGTT
* * * * * * * *
256587 ATAAATCAAAATCAGTAATAATCAATCTAACATATTTAGATATCGTATATTCTTTATCAATAGAG
1 ATAAATCAAAATCAGTAACAATAAATCTAAAATATTCAAATATCGCATATTCTTCATCAACAGAG
*
256652 TAACGTAGAGGGTG
66 TAACGCAGAGGGTG
256666 ATAAATCAAAATCAGTAACAATAAATCTAAAATATTCAAATATCGCATATTCTTCATCAACAGAG
1 ATAAATCAAAATCAGTAACAATAAATCTAAAATATTCAAATATCGCATATTCTTCATCAACAGAG
*
256731 TATCGCAGAGG
66 TAACGCAGAGG
256742 CGTACCATCA
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 66 1.00
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (79 bp):
ATAAATCAAAATCAGTAACAATAAATCTAAAATATTCAAATATCGCATATTCTTCATCAACAGAG
TAACGCAGAGGGTG
Found at i:261274 original size:17 final size:19
Alignment explanation
Indices: 261239--261291 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 19
261229 AGCTTTCTTC
*
261239 AATTTAAGCTTTCAATTTA
1 AATTTAAGTTTTCAATTTA
261258 AATTT-AGTTTT-AATTTA
1 AATTTAAGTTTTCAATTTA
*
261275 ATTTTAAGTTTTCAATT
1 AATTTAAGTTTTCAATT
261292 GCATACAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 10 0.33
18 11 0.37
19 9 0.30
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.55
Consensus pattern (19 bp):
AATTTAAGTTTTCAATTTA
Found at i:261850 original size:22 final size:22
Alignment explanation
Indices: 261794--261852 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
261784 TATGTCGATT
*
261794 TTGTAGAGATTAAAAAATTAAGA
1 TTGTAGAGATT-AAAAAGTAAGA
*
261817 TTG-A-AGAATAAAAAGT-AGA
1 TTGTAGAGATTAAAAAGTAAGA
261836 TTCGTAGAGATTAAAAA
1 TT-GTAGAGATTAAAAA
261853 AATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
19 5 0.17
20 7 0.23
21 5 0.17
22 10 0.33
23 3 0.10
ACGTcount: A:0.53, C:0.02, G:0.19, T:0.27
Consensus pattern (22 bp):
TTGTAGAGATTAAAAAGTAAGA
Found at i:264372 original size:28 final size:27
Alignment explanation
Indices: 264333--264610 Score: 216
Period size: 28 Copynumber: 9.7 Consensus size: 27
264323 TGAATCCATG
* *
264333 TTTTTAGATTTTACAATTTTACTCCTAT
1 TTTTTAGATTTTATAATTTT-CCCCTAT
*
264361 TTTTTAGATTTTTAAAATTTGTTACCCCTAT
1 TTTTTAGA-TTTTATAA-TT-TT-CCCCTAT
* * *
264392 TTTCTAGATTTTACAAAATTTCCCCTAT
1 TTTTTAGATTTTA-TAATTTTCCCCTAT
* *
264420 TTTTTAGATTTTGTAGTTTTCCCCTTATT
1 TTTTTAGATTTTATAATTTTCCCC-TA-T
* *
264449 TTTTTAGATTTTATAGGTTTGTCCCTTAT
1 TTTTTAGATTTTATA-ATTT-TCCCCTAT
* *
264478 TTTTTAGATTTTATAGTTTTGCCTCTAT
1 TTTTTAGATTTTATAATTTT-CCCCTAT
* * *
264506 TTTTAAGATTTTATAATTTTGCTCTTAT
1 TTTTTAGATTTTATAATTTT-CCCCTAT
* *
264534 TTTTCAGATTTTA-AAGTTTTACCCATATT
1 TTTTTAGATTTTATAA-TTTT-CCCCTA-T
*
264563 TTTTTAGATTTTATAGTTTTTCCCCTAT
1 TTTTTAGATTTTATA-ATTTTCCCCTAT
* * *
264591 TTTATAAATTTTATAGTTTT
1 TTTTTAGATTTTATAATTTT
264611 AACCCAGAAT
Statistics
Matches: 209, Mismatches: 28, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
27 15 0.07
28 94 0.45
29 58 0.28
30 19 0.09
31 23 0.11
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.58
Consensus pattern (27 bp):
TTTTTAGATTTTATAATTTTCCCCTAT
Found at i:264611 original size:57 final size:57
Alignment explanation
Indices: 264333--264616 Score: 250
Period size: 57 Copynumber: 4.9 Consensus size: 57
264323 TGAATCCATG
* * * * * * *
264333 TTTTTAGATTTTACAATTTTACTCCTATTTTTTAGATTTTTAAAATTTGTTACCCCTA-T
1 TTTTTAGATTTTATAGTTTTTCCCCTATTTTTTAGA-TTTT-ATAGTT-TTACCCATATT
* * *** * * *
264392 TTTCTAGATTTTACAAAATTTCCCCTATTTTTTAGATTTTGTAGTTTTCCCCTTATT
1 TTTTTAGATTTTATAGTTTTTCCCCTATTTTTTAGATTTTATAGTTTTACCCATATT
* * *
264449 TTTTTAGATTTTATAGGTTTGTCCCTTATTTTTTAGATTTTATAGTTTTGCCTC-TA-T
1 TTTTTAGATTTTATA-GTTTTTCCCCTATTTTTTAGATTTTATAGTTTTACC-CATATT
* * * * * * *
264506 TTTTAAGATTTTATAATTTTGCTCTTATTTTTCAGATTTTAAAGTTTTACCCATATT
1 TTTTTAGATTTTATAGTTTTTCCCCTATTTTTTAGATTTTATAGTTTTACCCATATT
* *
264563 TTTTTAGATTTTATAGTTTTTCCCCTATTTTATAAATTTTATAGTTTTAACCCA
1 TTTTTAGATTTTATAGTTTTTCCCCTATTTTTTAGATTTTATAGTTTT-ACCCA
264617 GAATTATATT
Statistics
Matches: 183, Mismatches: 36, Indels: 13
0.79 0.16 0.06
Matches are distributed among these distances:
55 1 0.01
56 38 0.21
57 72 0.39
58 40 0.22
59 32 0.17
ACGTcount: A:0.23, C:0.13, G:0.07, T:0.56
Consensus pattern (57 bp):
TTTTTAGATTTTATAGTTTTTCCCCTATTTTTTAGATTTTATAGTTTTACCCATATT
Found at i:264981 original size:34 final size:33
Alignment explanation
Indices: 264917--264981 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 33
264907 GCCATATTTG
* *
264917 ATCTGTTATAAGCATGTTATCCGTTTCCGTTTTA
1 ATCTGATATAAGCATGTTAT-CGTTACCGTTTTA
264951 ATCTGATATAAGCATGCTTTAT-GTTACCGTT
1 ATCTGATATAAGCATG--TTATCGTTACCGTT
264982 AAACCAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 23 0.85
36 4 0.15
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (33 bp):
ATCTGATATAAGCATGTTATCGTTACCGTTTTA
Found at i:288093 original size:20 final size:21
Alignment explanation
Indices: 288070--288108 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
288060 ACAAAAATGG
288070 TTGAA-TCAATAAAAAATTAA
1 TTGAACTCAATAAAAAATTAA
* *
288090 TTGAACTGAGTAAAAAATT
1 TTGAACTCAATAAAAAATT
288109 GGTTAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (21 bp):
TTGAACTCAATAAAAAATTAA
Found at i:291139 original size:43 final size:43
Alignment explanation
Indices: 291091--291214 Score: 135
Period size: 43 Copynumber: 2.9 Consensus size: 43
291081 AGCTCGTACA
* * * *
291091 ATGCCAACGTCCCAGACGTGGTCTTACATGTAAACATATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAAACCG
***
291134 ATGCCATTATCCCAGACAG-GGTCTTACACGTAAACACAAACCG
1 ATGCCAACGTCCCAGAC-GTGGTCTTACACGTAAACACAAACCG
* *
291177 ATGCCAACGTCCCAAACGTGGTCTTTCACG-ATAACACA
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTA-AACACA
291215 TATCGGAAAT
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
42 2 0.03
43 63 0.95
44 1 0.02
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAAACCG
Found at i:293816 original size:2 final size:2
Alignment explanation
Indices: 293809--293845 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
293799 TATAACTACC
293809 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
293846 CCTTGATTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:295592 original size:33 final size:32
Alignment explanation
Indices: 295554--295654 Score: 105
Period size: 33 Copynumber: 3.4 Consensus size: 32
295544 GGATATTATT
295554 ATGGGATATTATCTTTTAGCAATTTGATTCCTA
1 ATGGGATATTAT-TTTTAGCAATTTGATTCCTA
295587 ATGGGATATTA----TAG-AATATT-A-T--T-
1 ATGGGATATTATTTTTAGCAAT-TTGATTCCTA
295610 ATGGGATATTATTTCTTAGCAATTTGATTCCTA
1 ATGGGATATTATTT-TTAGCAATTTGATTCCTA
295643 ATGGGATATTAT
1 ATGGGATATTAT
295655 AGGATATTGT
Statistics
Matches: 56, Mismatches: 0, Indels: 24
0.70 0.00 0.30
Matches are distributed among these distances:
23 11 0.20
24 1 0.02
26 1 0.02
27 4 0.07
28 10 0.18
29 4 0.07
30 1 0.02
32 1 0.02
33 23 0.41
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.45
Consensus pattern (32 bp):
ATGGGATATTATTTTTAGCAATTTGATTCCTA
Found at i:295632 original size:56 final size:56
Alignment explanation
Indices: 295546--295698 Score: 263
Period size: 56 Copynumber: 2.7 Consensus size: 56
295536 TTTTGTAAGG
295546 ATATTATTATGGGATATTATCTTTTAGCAATTTGATTCCTAATGGGATATTATAGA
1 ATATTATTATGGGATATTATCTTTTAGCAATTTGATTCCTAATGGGATATTATAGA
*
295602 ATATTATTATGGGATATTAT-TTCTTAGCAATTTGATTCCTAATGGGATATTATAGG
1 ATATTATTATGGGATATTATCTT-TTAGCAATTTGATTCCTAATGGGATATTATAGA
* *
295658 ATATTGTCATGGGATATTATCTTTTAGCAATTTGATTCCTA
1 ATATTATTATGGGATATTATCTTTTAGCAATTTGATTCCTA
295699 CATAACTACT
Statistics
Matches: 92, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
55 2 0.02
56 88 0.96
57 2 0.02
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.45
Consensus pattern (56 bp):
ATATTATTATGGGATATTATCTTTTAGCAATTTGATTCCTAATGGGATATTATAGA
Found at i:303617 original size:6 final size:6
Alignment explanation
Indices: 303608--303701 Score: 179
Period size: 6 Copynumber: 15.7 Consensus size: 6
303598 TCTCATCTTG
303608 ACACAT ACACAT ACACAT ACACAT ACACAT ACACAT ACACAT ACACAT
1 ACACAT ACACAT ACACAT ACACAT ACACAT ACACAT ACACAT ACACAT
*
303656 AGACAT ACACAT ACACAT ACACAT ACACAT ACACAT ACACAT ACAC
1 ACACAT ACACAT ACACAT ACACAT ACACAT ACACAT ACACAT ACAC
303702 TTAACTATTA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 86 1.00
ACGTcount: A:0.50, C:0.33, G:0.01, T:0.16
Consensus pattern (6 bp):
ACACAT
Found at i:306395 original size:9 final size:9
Alignment explanation
Indices: 306381--306417 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
306371 TATAGTTTGA
306381 TATTCGAAT
1 TATTCGAAT
306390 TATTCGAAT
1 TATTCGAAT
* *
306399 TATTTGAGT
1 TATTCGAAT
306408 TATTCGAAT
1 TATTCGAAT
306417 T
1 T
306418 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:306489 original size:9 final size:9
Alignment explanation
Indices: 306472--306502 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
306462 TCGAGTTGAT
306472 TCGAATAAC
1 TCGAATAAC
*
306481 TCGATTAAC
1 TCGAATAAC
306490 TCGAATAAC
1 TCGAATAAC
306499 TCGA
1 TCGA
306503 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:307939 original size:6 final size:6
Alignment explanation
Indices: 307928--307954 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
307918 TCCTATTTTC
307928 AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAA
307955 CAACTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Done.