Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold147
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: 880509
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.26
Warning! 187686 characters in sequence are not A, C, G, or T
File 1 of 5
Found at i:20103 original size:59 final size:58
Alignment explanation
Indices: 20008--20226 Score: 169
Period size: 58 Copynumber: 3.8 Consensus size: 58
19998 GTGCAGATCT
* * * * *
20008 AGGTCGCCTTGATAGCGGTCTAAGTAT-AGGTTACTTGGTGTCACTTAGTGTG-GTAATC
1 AGGTCGCCTTGGTGGCGATCTAAGT-TCGGGTGACTTGGTGTCACTTAGTGTGTG-AATC
* **
20066 TAGGTCGCCTTGGTGGCGATCTAAGTTTGGGTGACTTGGCT-TCACCAAGTGTGTGAATC
1 -AGGTCGCCTTGGTGGCGATCTAAGTTCGGGTGACTTGG-TGTCACTTAGTGTGTGAATC
* * * * ** * * * *
20125 GGGTCACCCTGGCGATGATCTAAGTTCGAGTGACTCGGCGCCACTTAGTGTGTGAA-C
1 AGGTCGCCTTGGTGGCGATCTAAGTTCGGGTGACTTGGTGTCACTTAGTGTGTGAATC
* *
20182 CGTGTCGTCC-TGGTGGCGATCTAAGTTCCGGTGACTTGGTGTCAC
1 AG-GTCG-CCTTGGTGGCGATCTAAGTTCGGGTGACTTGGTGTCAC
20227 CCAGCGTGCG
Statistics
Matches: 124, Mismatches: 30, Indels: 13
0.74 0.18 0.08
Matches are distributed among these distances:
57 2 0.02
58 73 0.59
59 47 0.38
60 2 0.02
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.31
Consensus pattern (58 bp):
AGGTCGCCTTGGTGGCGATCTAAGTTCGGGTGACTTGGTGTCACTTAGTGTGTGAATC
Found at i:20158 original size:58 final size:58
Alignment explanation
Indices: 20083--20273 Score: 152
Period size: 58 Copynumber: 3.3 Consensus size: 58
20073 CCTTGGTGGC
* * *
20083 GATCTAAGTTTGGGTGACTTGGCTTCACCAAGTGTGTGAATCGGGTCACCCTGGCGAT
1 GATCTAAGTTCGAGTGACTTGGCTTCACCAAGTGTGTGAATCGGGTCACCCTGGCGGT
* ** ** * * ** * *
20141 GATCTAAGTTCGAGTGACTCGGCGCCACTTAGTGTGTGAACCGTGTCGTCCTGGTGGC
1 GATCTAAGTTCGAGTGACTTGGCTTCACCAAGTGTGTGAATCGGGTCACCCTGGCGGT
* * * * * *
20199 GATCTAAGTTCCG-GTGACTTGG-TGTCACCCAGCGTGCGGATCTGGTCACCTTGGCGGT
1 GATCTAAGTT-CGAGTGACTTGGCT-TCACCAAGTGTGTGAATCGGGTCACCCTGGCGGT
*
20257 GATCTAAGGTCGTAGTG
1 GATCTAAGTTCG-AGTG
20274 TGATAAAAAT
Statistics
Matches: 98, Mismatches: 31, Indels: 7
0.72 0.23 0.05
Matches are distributed among these distances:
57 2 0.02
58 91 0.93
59 5 0.05
ACGTcount: A:0.17, C:0.23, G:0.32, T:0.28
Consensus pattern (58 bp):
GATCTAAGTTCGAGTGACTTGGCTTCACCAAGTGTGTGAATCGGGTCACCCTGGCGGT
Found at i:27497 original size:34 final size:34
Alignment explanation
Indices: 27454--27520 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
27444 CTGAGTTAAT
*
27454 CATGAGAATTTTCATAGCTTGGAAGGGAAGGTAC
1 CATGAGAATTTTCATAGCTTGGAAGGAAAGGTAC
27488 CATGAGAATTTTCATAGCTTGGAAGGAAAGGTA
1 CATGAGAATTTTCATAGCTTGGAAGGAAAGGTA
27521 TGGGAAGGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.27
Consensus pattern (34 bp):
CATGAGAATTTTCATAGCTTGGAAGGAAAGGTAC
Found at i:34590 original size:2 final size:2
Alignment explanation
Indices: 34585--34612 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
34575 CTAGTTTAAA
34585 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
34613 GAACTAACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35145 original size:2 final size:2
Alignment explanation
Indices: 35138--35168 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
35128 CTAACTTTTC
35138 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 A
35169 GATGAGACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39019 original size:10 final size:10
Alignment explanation
Indices: 39004--39071 Score: 56
Period size: 10 Copynumber: 7.0 Consensus size: 10
38994 TATTTATTTC
39004 ATATATTTTT
1 ATATATTTTT
39014 ATATA--TTT
1 ATATATTTTT
39022 ATATATTTATT
1 ATATATTT-TT
*
39033 TTAT-TTTTT
1 ATATATTTTT
39042 AT-TAATTTTT
1 ATAT-ATTTTT
39052 AT-TATATTTT
1 ATATAT-TTTT
*
39062 AAATATTTTT
1 ATATATTTTT
39072 CATGTTATAT
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
8 9 0.19
9 5 0.10
10 26 0.54
11 8 0.17
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
ATATATTTTT
Found at i:39042 original size:20 final size:20
Alignment explanation
Indices: 38994--39071 Score: 76
Period size: 20 Copynumber: 4.0 Consensus size: 20
38984 TTTTTTTATG
*
38994 TATT-TATTTCATATATTTT
1 TATTATATTTTATATATTTT
39013 TA-TATA-TTTATATATTTAT
1 TATTATATTTTATATATTT-T
*
39032 T-TTATTTTTTAT-TAATTTT
1 TATTATATTTTATAT-ATTTT
*
39051 TATTATATTTTAAATATTTT
1 TATTATATTTTATATATTTT
39071 T
1 T
39072 CATGTTATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
18 11 0.23
19 12 0.25
20 24 0.50
21 1 0.02
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTATATTTTATATATTTT
Found at i:39051 original size:11 final size:12
Alignment explanation
Indices: 38978--39061 Score: 52
Period size: 12 Copynumber: 7.0 Consensus size: 12
38968 ATTTTAGGTA
38978 TTATTAT-TTTT
1 TTATTATATTTT
38989 TTATGTAT-TTATT
1 TTAT-TATATT-TT
*
39002 TCA-TATATTTT
1 TTATTATATTTT
* *
39013 TATATATTTATATAT
1 T-TAT-TATAT-TTT
*
39028 TTATTTTATTTT
1 TTATTATATTTT
39040 TTATTA-A-TTT
1 TTATTATATTTT
39050 TTATTATATTTT
1 TTATTATATTTT
39062 AAATATTTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
10 9 0.16
11 12 0.21
12 18 0.31
13 9 0.16
14 7 0.12
15 3 0.05
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (12 bp):
TTATTATATTTT
Found at i:39058 original size:31 final size:30
Alignment explanation
Indices: 38976--39060 Score: 84
Period size: 31 Copynumber: 2.8 Consensus size: 30
38966 AAATTTTAGG
* * *
38976 TATTATTATTTTTTTATGTATTTATTTCATA
1 TATTTTTATATTTTTATATATTTATTT-ATA
*
39007 TATTTTTATATATTTATATATTTATTT-TA
1 TATTTTTATATTTTTATATATTTATTTATA
39036 T-TTTTTATTAATTTTTATTATATTT
1 TATTTTTA-T-ATTTTTA-TATATTT
39061 TAAATATTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
28 6 0.13
29 4 0.09
30 6 0.13
31 30 0.65
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.71
Consensus pattern (30 bp):
TATTTTTATATTTTTATATATTTATTTATA
Found at i:42348 original size:14 final size:14
Alignment explanation
Indices: 42329--42363 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
42319 CCTTGAAAAA
42329 CAACTAAAGATATG
1 CAACTAAAGATATG
42343 CAACTAAAGATATG
1 CAACTAAAGATATG
42357 CAACTAA
1 CAACTAA
42364 GGCGATAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.20
Consensus pattern (14 bp):
CAACTAAAGATATG
Found at i:42616 original size:12 final size:13
Alignment explanation
Indices: 42589--42621 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
42579 GTTATTATAA
42589 TTTAGATTTTAA-T
1 TTTA-ATTTTAATT
42602 TTTAATTTTAATT
1 TTTAATTTTAATT
42615 TTTAATT
1 TTTAATT
42622 CGATTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (13 bp):
TTTAATTTTAATT
Found at i:44073 original size:12 final size:12
Alignment explanation
Indices: 44056--44081 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
44046 TATGGCGACC
44056 AAACCCATTACA
1 AAACCCATTACA
44068 AAACCCATTACA
1 AAACCCATTACA
44080 AA
1 AA
44082 GGTTATTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.31, G:0.00, T:0.15
Consensus pattern (12 bp):
AAACCCATTACA
Found at i:45205 original size:2 final size:2
Alignment explanation
Indices: 45198--45241 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
45188 AACAATGCGC
45198 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
45240 CT
1 CT
45242 ACGTGTGCGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:48349 original size:14 final size:13
Alignment explanation
Indices: 48324--48350 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
48314 TTGTTTTATG
48324 AAAAATAATTTTT
1 AAAAATAATTTTT
48337 AAAAATAATTTTT
1 AAAAATAATTTTT
48350 A
1 A
48351 TATTTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAAATAATTTTT
Found at i:48611 original size:11 final size:11
Alignment explanation
Indices: 48567--48612 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
48557 CTTTTAATTT
48567 TAAAAATATT-
1 TAAAAATATTA
*
48577 TAAAAAAATTA
1 TAAAAATATTA
*
48588 -AAATAATAATA
1 TAAA-AATATTA
48599 TAAAAATATTA
1 TAAAAATATTA
48610 TAA
1 TAA
48613 TTTTTAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
10 12 0.41
11 14 0.48
12 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAAATATTA
Found at i:48623 original size:15 final size:16
Alignment explanation
Indices: 48603--48640 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
48593 ATAATATAAA
*
48603 AATATTATA-ATTTTT
1 AATATTATATATTTTG
48618 AATATT-TATATTTTG
1 AATATTATATATTTTG
48633 AATATTAT
1 AATATTAT
48641 TAAACATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 17 0.85
16 1 0.05
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
AATATTATATATTTTG
Found at i:48686 original size:31 final size:31
Alignment explanation
Indices: 48620--48723 Score: 81
Period size: 31 Copynumber: 3.2 Consensus size: 31
48610 TAATTTTTAA
*
48620 TATTTATATTTTGAATATTATTAAACA-T-ATA-
1 TATTTATATTTT-AATAATA-TAAA-ATTAATAT
48651 TATTTATATTTTAATAATATAAAATTAATAT
1 TATTTATATTTTAATAATATAAAATTAATAT
*
48682 TATTTAT-TTTAATATAATTAATAAAATATAAATAT
1 TATTTATATTTTA-ATAA-T-ATAAAAT-T-AATAT
*
48717 AATTTAT
1 TATTTAT
48724 TGTTTTGATG
Statistics
Matches: 62, Mismatches: 3, Indels: 12
0.81 0.04 0.16
Matches are distributed among these distances:
28 1 0.02
29 5 0.08
30 13 0.21
31 23 0.37
32 1 0.02
33 7 0.11
34 1 0.02
35 11 0.18
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (31 bp):
TATTTATATTTTAATAATATAAAATTAATAT
Found at i:48845 original size:17 final size:17
Alignment explanation
Indices: 48799--48852 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
48789 AAACATTGCA
48799 AAAATAATATTTTAA-T
1 AAAATAATATTTTAATT
*
48815 --AATAATTATATTAATT
1 AAAATAA-TATTTTAATT
*
48831 AAAATAATATTTTAATA
1 AAAATAATATTTTAATT
48848 AAAAT
1 AAAAT
48853 GATAATGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
17 13 0.42
18 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAAATAATATTTTAATT
Found at i:49001 original size:15 final size:15
Alignment explanation
Indices: 48958--49008 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
48948 GAAATATATA
*
48958 AAATAATATTTCAAT
1 AAATAATATTTTAAT
* * *
48973 AATTATTATATTAAT
1 AAATAATATTTTAAT
48988 AAATAATATTTTAAT
1 AAATAATATTTTAAT
49003 -AATAAT
1 AAATAAT
49009 GGTAATATTT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
14 6 0.21
15 23 0.79
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
AAATAATATTTTAAT
Found at i:49406 original size:16 final size:16
Alignment explanation
Indices: 49385--49421 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
49375 CACAACTAAT
49385 AAATAACTTAAATATA
1 AAATAACTTAAATATA
* *
49401 AAATAATTTAAATTTA
1 AAATAACTTAAATATA
49417 AAATA
1 AAATA
49422 GTTTCAACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATAACTTAAATATA
Found at i:49897 original size:69 final size:69
Alignment explanation
Indices: 49824--49954 Score: 156
Period size: 69 Copynumber: 1.9 Consensus size: 69
49814 TCTCCTTTAT
* * * * * * *
49824 TCGATTAATTTTAATATTAAATTTGATCAATTCAAATTCAATAT-AATCTAAATTTAAAATAATT
1 TCGATCAATATTAATAGTAAACTTAATCAATTCAAATTCAAAATAAATC-AAAATTAAAATAATT
49888 CAAAC
65 CAAAC
** *
49893 TCGATCAATATTAATAGTAAACTTAATTGATTCAAATTTAAAATAAATCAAAATTAAAATAA
1 TCGATCAATATTAATAGTAAACTTAATCAATTCAAATTCAAAATAAATCAAAATTAAAATAA
49955 CTTAGATAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
69 47 0.92
70 4 0.08
ACGTcount: A:0.50, C:0.09, G:0.04, T:0.37
Consensus pattern (69 bp):
TCGATCAATATTAATAGTAAACTTAATCAATTCAAATTCAAAATAAATCAAAATTAAAATAATTC
AAAC
Found at i:49949 original size:16 final size:16
Alignment explanation
Indices: 49924--49954 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49914 CTTAATTGAT
*
49924 TCAAATTTAAAATAAA
1 TCAAAATTAAAATAAA
49940 TCAAAATTAAAATAA
1 TCAAAATTAAAATAA
49955 CTTAGATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
TCAAAATTAAAATAAA
Found at i:50251 original size:6 final size:6
Alignment explanation
Indices: 50237--50288 Score: 77
Period size: 6 Copynumber: 8.7 Consensus size: 6
50227 AATTGGCCTC
* * *
50237 TCAAAA TCAATA TCAAAA TCAAAA TCAAAA TTAAAA TCAAAT TCAAAA
1 TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA TCAAAA
50285 TCAA
1 TCAA
50289 CATGACATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (6 bp):
TCAAAA
Found at i:52833 original size:3 final size:3
Alignment explanation
Indices: 52825--52855 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
52815 TATCTGTTCT
52825 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
52856 GATGATGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:52860 original size:3 final size:3
Alignment explanation
Indices: 52854--52880 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
52844 TATTATTATT
52854 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
52881 TTGCATTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:54801 original size:2 final size:2
Alignment explanation
Indices: 54794--54837 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
54784 CGATCCATAC
54794 AT AT AT 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 AT AT AT
54836 AT
1 AT
54838 CTCCATGCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55043 original size:15 final size:15
Alignment explanation
Indices: 55023--55053 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
55013 GCTTTGATTG
55023 TTTTTATTACTATTA
1 TTTTTATTACTATTA
*
55038 TTTTTATTATTATTA
1 TTTTTATTACTATTA
55053 T
1 T
55054 GGATCTGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTTATTACTATTA
Found at i:56397 original size:12 final size:12
Alignment explanation
Indices: 56380--56419 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
56370 ACCAGAGAGC
*
56380 AAAAAGAGAACA
1 AAAAAGAGAAGA
56392 AAAAAGAG-AGA
1 AAAAAGAGAAGA
*
56403 AAAAAGAAAAGA
1 AAAAAGAGAAGA
56415 AAAAA
1 AAAAA
56420 ATAGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAGAGAAGA
Found at i:56399 original size:23 final size:23
Alignment explanation
Indices: 56360--56429 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
56350 GCTTTCAGCT
* *
56360 AAGAAAA-AAAACCAGAGAGCAAA
1 AAGAAAACAAAA-AAGAGAGAAAA
*
56383 AAGAGAACAAAAAAGAGAGAAAA
1 AAGAAAACAAAAAAGAGAGAAAA
* *
56406 AAGAAAAGAAAAAA-ATAGAAAA
1 AAGAAAACAAAAAAGAGAGAAAA
56428 AA
1 AA
56430 AATTAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
22 9 0.22
23 27 0.68
24 4 0.10
ACGTcount: A:0.76, C:0.06, G:0.17, T:0.01
Consensus pattern (23 bp):
AAGAAAACAAAAAAGAGAGAAAA
Found at i:56429 original size:12 final size:12
Alignment explanation
Indices: 56380--56464 Score: 55
Period size: 13 Copynumber: 6.5 Consensus size: 12
56370 ACCAGAGAGC
56380 AAAAAGAGAACAA
1 AAAAAGAGAA-AA
56393 AAAAGAGAGAAAA
1 AAAA-AGAGAAAA
56406 AAGAAA-AGAAAA
1 AA-AAAGAGAAAA
* *
56418 AAATAGAAAAAAA
1 AAAAAG-AGAAAA
*
56431 ATTAAAAAAGAAACA
1 A--AAAAGAGAAA-A
56446 AAAAGAGAGAAAA
1 AAAA-AGAGAAAA
*
56459 GAAAAG
1 AAAAAG
56465 CGATAGCTTC
Statistics
Matches: 57, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
11 2 0.04
12 10 0.18
13 22 0.39
14 18 0.32
15 5 0.09
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (12 bp):
AAAAAGAGAAAA
Found at i:57063 original size:21 final size:21
Alignment explanation
Indices: 57038--57078 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
57028 ACTAAATCAT
57038 TTTGTAATTTT-CAAGCATTTC
1 TTTGTAATTTTCCAAG-ATTTC
*
57059 TTTGTCATTTTCCAAGATTT
1 TTTGTAATTTTCCAAGATTT
57079 TGGTTTTCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.22, C:0.15, G:0.10, T:0.54
Consensus pattern (21 bp):
TTTGTAATTTTCCAAGATTTC
Found at i:57236 original size:58 final size:57
Alignment explanation
Indices: 57161--57435 Score: 232
Period size: 58 Copynumber: 4.7 Consensus size: 57
57151 CACCTTAGTA
* **
57161 ATTTTCTATGA-CTTAGAGATTTTTATGTAATTTTATATATGTTAAAGTCATTTAGGTC
1 ATTTTTTATGATC-TAGAGATTTTTATGTAATTTTATATATGTT-GGGTCATTTAGGTC
* * * *
57219 ATTTTTTATGATCTAGAGATTTTTATGTAATTTCATACATTTTTTTGGGTAATTTAGGTC
1 ATTTTTTATGATCTAGAGATTTTTATGTAATTT--TATA-TATGTTGGGTCATTTAGGTC
* ** * * * * * *
57279 GTTTTCCAT-TTCTAGAGACTTTTATGCAAATTTTATGTATGTTGGGATCATTTAAGTA
1 ATTTTTTATGATCTAGAGATTTTTATG-TAATTTTATATATGTTGGG-TCATTTAGGTC
** * *
57337 ATTTTTTATGATCTA-AGGATTTTTATACAAATTTTATGTATGTTGGGTCATTTAGATC
1 ATTTTTTATGATCTAGA-GATTTTTAT-GTAATTTTATATATGTTGGGTCATTTAGGTC
* * *
57395 ATTTTTAATGATCTAGGGATTTTTATGTAAATTTCATATAT
1 ATTTTTTATGATCTAGAGATTTTTATGT-AATTTTATATAT
57436 TTTGACTTTA
Statistics
Matches: 171, Mismatches: 35, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
57 7 0.04
58 88 0.51
59 47 0.27
60 25 0.15
61 4 0.02
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (57 bp):
ATTTTTTATGATCTAGAGATTTTTATGTAATTTTATATATGTTGGGTCATTTAGGTC
Found at i:57251 original size:29 final size:29
Alignment explanation
Indices: 57158--57251 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 29
57148 TGTCACCTTA
*
57158 GTAATTTTCTATGA-CTTAGAGATTTTTAT
1 GTAATTTTTTATGATC-TAGAGATTTTTAT
* * *
57187 GTAATTTTATATATG-T-TAAAG-TCATTTAG
1 GTAATTTT-T-TATGATCTAGAGAT-TTTTAT
*
57216 GTCATTTTTTATGATCTAGAGATTTTTAT
1 GTAATTTTTTATGATCTAGAGATTTTTAT
57245 GTAATTT
1 GTAATTT
57252 CATACATTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
27 4 0.08
28 3 0.06
29 37 0.76
30 1 0.02
31 4 0.08
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.52
Consensus pattern (29 bp):
GTAATTTTTTATGATCTAGAGATTTTTAT
Found at i:57390 original size:29 final size:29
Alignment explanation
Indices: 57299--57390 Score: 66
Period size: 29 Copynumber: 3.1 Consensus size: 29
57289 TCTAGAGACT
*
57299 TTTATGCAAATTTTATGTATGTTGGGATCA
1 TTTATACAAATTTTATGTATGTTGGG-TCA
** * *
57329 TTTA-AGTAATTTT-T-TATGATCTAAGGAT-T
1 TTTATACAAATTTTATGTATG-T-T--GGGTCA
57358 TTTATACAAATTTTATGTATGTTGGGTCA
1 TTTATACAAATTTTATGTATGTTGGGTCA
57387 TTTA
1 TTTA
57391 GATCATTTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 17
0.63 0.13 0.24
Matches are distributed among these distances:
27 4 0.09
28 5 0.11
29 15 0.33
30 13 0.29
31 4 0.09
32 4 0.09
ACGTcount: A:0.28, C:0.05, G:0.16, T:0.50
Consensus pattern (29 bp):
TTTATACAAATTTTATGTATGTTGGGTCA
Found at i:57514 original size:58 final size:58
Alignment explanation
Indices: 57289--57516 Score: 178
Period size: 59 Copynumber: 3.9 Consensus size: 58
57279 GTTTTCCATT
* * * * * *
57289 TCTAGAGACTTTTATGCAAATTTTATGTATGTTG-GGATCATTTAAGTAATTTTTTATGA
1 TCTAGGGATTTTTATGCAAA-TTTATGAATTTTGATG-TCATTTAAGTTATTTTTTATGA
* * * * * * *
57348 TCTAAGGATTTTTATACAAATTTTATGTATGTTG-GGTCATTT-AGATCATTTTTAATGA
1 TCTAGGGATTTTTATGCAAA-TTTATGAATTTTGATGTCATTTAAG-TTATTTTTTATGA
* * *
57406 TCTAGGGATTTTTATGTAAATTTCAT-ATATTTTGACT-TTATTTAAATTATTTTTTATGA
1 TCTAGGGATTTTTATGCAAATTT-ATGA-ATTTTGA-TGTCATTTAAGTTATTTTTTATGA
* * * *
57465 TTTAGGGACTTTGATGCAACTTTATGAATTTTGATGTCATTTAAGTTATTTT
1 TCTAGGGATTTTTATGCAAATTTATGAATTTTGATGTCATTTAAGTTATTTT
57517 CCATGATACA
Statistics
Matches: 138, Mismatches: 23, Indels: 17
0.78 0.13 0.10
Matches are distributed among these distances:
57 6 0.04
58 64 0.46
59 67 0.49
60 1 0.01
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (58 bp):
TCTAGGGATTTTTATGCAAATTTATGAATTTTGATGTCATTTAAGTTATTTTTTATGA
Found at i:57571 original size:48 final size:48
Alignment explanation
Indices: 57504--57596 Score: 127
Period size: 48 Copynumber: 1.9 Consensus size: 48
57494 TTTGATGTCA
* *
57504 TTTAAGTTATTTTCCATGATACAAG-GATTTTGGTGCAATTTCATAAAC
1 TTTAAGTCATTTTCCATGAT-CAAGAGATTTTGGTACAATTTCATAAAC
*
57552 TTTAATGTCATTTT-CATGATCTAGAGATTTTGGTACAATTTCATA
1 TTTAA-GTCATTTTCCATGATCAAGAGATTTTGGTACAATTTCATA
57597 TATTTTATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
47 3 0.08
48 30 0.75
49 7 0.17
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (48 bp):
TTTAAGTCATTTTCCATGATCAAGAGATTTTGGTACAATTTCATAAAC
Found at i:60267 original size:30 final size:30
Alignment explanation
Indices: 60231--60291 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
60221 TATAGGATTT
*
60231 TTTTCAGGGACAAGATTGTTGGTATTAGGC
1 TTTTCAGGAACAAGATTGTTGGTATTAGGC
* *
60261 TTTTCAGGAACAATATTTTTGGTATTAGGC
1 TTTTCAGGAACAAGATTGTTGGTATTAGGC
60291 T
1 T
60292 AATTAAGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.41
Consensus pattern (30 bp):
TTTTCAGGAACAAGATTGTTGGTATTAGGC
Found at i:60995 original size:43 final size:44
Alignment explanation
Indices: 60946--61044 Score: 112
Period size: 43 Copynumber: 2.2 Consensus size: 44
60936 ATTTATTATT
** *
60946 TATATTTTTATATATTATATTTATT-AAAAGTATA-TATATTTAA
1 TATATTTTTATATATTATATACATTAAAAATTATATTATA-TTAA
* *
60989 TATATTTATGTATATTATATACATTAAAAATTATATTATATTAA
1 TATATTTTTATATATTATATACATTAAAAATTATATTATATTAA
*
61033 AATTATTTTTAT
1 TA-TATTTTTAT
61045 GAATAAATTA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
43 21 0.47
44 13 0.29
45 11 0.24
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (44 bp):
TATATTTTTATATATTATATACATTAAAAATTATATTATATTAA
Found at i:61033 original size:17 final size:17
Alignment explanation
Indices: 61002--61061 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 17
60992 ATTTATGTAT
*
61002 ATTATA-TACATTAAAA
1 ATTATATTATATTAAAA
61018 ATTATATTATATT-AAA
1 ATTATATTATATTAAAA
* *
61034 ATTAT-TTTTATGAATAA
1 ATTATATTATATTAA-AA
*
61051 ATTATAATATA
1 ATTATATTATA
61062 ATTAGTTACA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
15 5 0.14
16 15 0.43
17 12 0.34
18 3 0.09
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (17 bp):
ATTATATTATATTAAAA
Found at i:63334 original size:2 final size:2
Alignment explanation
Indices: 63323--63368 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
63313 TGAAATTATC
*
63323 AT AT AT -T AT AT AT AT AG 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 AT AT AT
63364 AT AT A
1 AT AT A
63369 CTTCCTGCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:63386 original size:16 final size:17
Alignment explanation
Indices: 63367--63398 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
63357 TATATATATA
63367 TACTTC-CTGCTTTCAG
1 TACTTCTCTGCTTTCAG
63383 TACTTCTCTGCTTTCA
1 TACTTCTCTGCTTTCA
63399 CCATTGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.12, C:0.31, G:0.09, T:0.47
Consensus pattern (17 bp):
TACTTCTCTGCTTTCAG
Found at i:63432 original size:2 final size:2
Alignment explanation
Indices: 63425--63455 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
63415 CAATTTCTTT
63425 TA 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 TA T
63456 TCATATTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:63749 original size:2 final size:2
Alignment explanation
Indices: 63742--63782 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
63732 TTATTGCTTT
63742 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
63783 CTTAATTAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:65339 original size:36 final size:38
Alignment explanation
Indices: 65295--65390 Score: 90
Period size: 41 Copynumber: 2.5 Consensus size: 38
65285 ATATTAAAAA
*
65295 TAAA-TAATTTTTTATTTTTTAAATA-ATAT-TTTTAT
1 TAAATTAATTTTTTATTTTTTAAATATATATATTATAT
* * * *
65330 TTAATTAATTTATATATTTATGATAAATATTTATATTATAT
1 TAAATTAATTT-TTTATTT-T-TTAAATATATATATTATAT
*
65371 TAAATTTATTTTTTATTTTT
1 TAAATTAATTTTTTATTTTT
65391 ATTATTTTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
35 3 0.07
36 6 0.13
37 6 0.13
38 1 0.02
39 7 0.15
40 9 0.20
41 14 0.30
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (38 bp):
TAAATTAATTTTTTATTTTTTAAATATATATATTATAT
Found at i:65344 original size:21 final size:21
Alignment explanation
Indices: 65303--65393 Score: 53
Period size: 21 Copynumber: 4.4 Consensus size: 21
65293 AATAAATAAT
* * *
65303 TTTTTATTT-TTTAAATAATA
1 TTTTTATTTAATTAATTTATA
65323 TTTTTATTTAATTAATTTATA
1 TTTTTATTTAATTAATTTATA
* * *
65344 TATTTATGATAAAT-ATTTATA
1 TTTTTAT-TTAATTAATTTATA
* * * *
65365 -TTATATTAAATTTATTTTTTA
1 TTTTTATTTAA-TTAATTTATA
65386 TTTTTATT
1 TTTTTATT
65394 ATTTTTTATG
Statistics
Matches: 52, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
19 2 0.04
20 14 0.27
21 26 0.50
22 10 0.19
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (21 bp):
TTTTTATTTAATTAATTTATA
Found at i:66097 original size:22 final size:21
Alignment explanation
Indices: 66062--66113 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
66052 AATTTAATTT
* * *
66062 AAAATTAATTTTATATAAATA
1 AAAATAAAATTTATAAAAATA
*
66083 ATAACTAAAATTTATAAAAATA
1 A-AAATAAAATTTATAAAAATA
66105 AAAATAAAA
1 AAAATAAAA
66114 AAATAAAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATAAAATTTATAAAAATA
Found at i:66114 original size:22 final size:22
Alignment explanation
Indices: 66071--66113 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
66061 TAAAATTAAT
* *
66071 TTTATATAAATAATAACTAAAA
1 TTTATAAAAATAATAAATAAAA
66093 TTTATAAAAATAA-AAATAAAA
1 TTTATAAAAATAATAAATAAAA
66114 AAATAAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
TTTATAAAAATAATAAATAAAA
Found at i:66835 original size:2 final size:2
Alignment explanation
Indices: 66830--66870 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
66820 TTTTGTATGC
66830 AT 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 AT A
66871 AATTAAATTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:72967 original size:21 final size:20
Alignment explanation
Indices: 72934--72979 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
72924 GAGGTGTTGG
72934 ACATA-CTAAAAATGCATGAA
1 ACATAGCTAAAAATGCATG-A
*
72954 ACATAGCTTAAAATGCATGA
1 ACATAGCTAAAAATGCATGA
72974 ACATAG
1 ACATAG
72980 ATTGTTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.50, C:0.15, G:0.13, T:0.22
Consensus pattern (20 bp):
ACATAGCTAAAAATGCATGA
Found at i:73921 original size:15 final size:13
Alignment explanation
Indices: 73890--73914 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
73880 ACAAAACTTA
73890 TGTATCGATATAT
1 TGTATCGATATAT
73903 TGTATCGATATA
1 TGTATCGATATA
73915 AATTGTAAAA
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:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
TGTATCGATATAT
Found at i:74259 original size:3 final size:3
Alignment explanation
Indices: 74251--74293 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
74241 AACGTAATGT
74251 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
74294 AATTGTTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:75676 original size:2 final size:2
Alignment explanation
Indices: 75658--75698 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
75648 TTTGCTTTGC
* * *
75658 TA TA TA AA TA TA CA TA TA TA TG 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 TA TA TA TA TA TA T
75699 CTGAAGCTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:76084 original size:2 final size:2
Alignment explanation
Indices: 76077--76106 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
76067 TTAAGTATTG
76077 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
76107 TCTTGTGGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76971 original size:5 final size:5
Alignment explanation
Indices: 76961--76986 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
76951 GGTGTTGAGA
76961 TATAT TATAT TATAT TATAT TATAT T
1 TATAT TATAT TATAT TATAT TATAT T
76987 TAAAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TATAT
Found at i:77622 original size:2 final size:2
Alignment explanation
Indices: 77617--77648 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
77607 TACTTTTTTC
77617 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
77649 TGAGAAATGA
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):
AT
Found at i:80252 original size:79 final size:79
Alignment explanation
Indices: 80123--80280 Score: 298
Period size: 79 Copynumber: 2.0 Consensus size: 79
80113 ACTTATTTGG
* *
80123 CAACTTTGAAAATTGATGAGCTTCAAGAACCCATAGAAGAAGCCCTTTTGGAGGTGCTAGAGGTG
1 CAACTTTGAAAATTAATGAGCTTCAAGAACCCATAGAAGAAGCCCCTTTGGAGGTGCTAGAGGTG
80188 TTACAATCCTTCAA
66 TTACAATCCTTCAA
80202 CAACTTTGAAAATTAATGAGCTTCAAGAACCCATAGAAGAAGCCCCTTTGGAGGTGCTAGAGGTG
1 CAACTTTGAAAATTAATGAGCTTCAAGAACCCATAGAAGAAGCCCCTTTGGAGGTGCTAGAGGTG
80267 TTACAATCCTTCAA
66 TTACAATCCTTCAA
80281 TGATGTGATG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 77 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.26
Consensus pattern (79 bp):
CAACTTTGAAAATTAATGAGCTTCAAGAACCCATAGAAGAAGCCCCTTTGGAGGTGCTAGAGGTG
TTACAATCCTTCAA
Found at i:83504 original size:19 final size:19
Alignment explanation
Indices: 83471--83514 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
83461 TTCCTCTCTA
*
83471 TTTTTTTTAACCTCTAAGT
1 TTTTTTTTAACCTCTAAAT
83490 TTTTTGTTTAA-CTCTAAAT
1 TTTTT-TTTAACCTCTAAAT
83509 TTTTTT
1 TTTTTT
83515 AACTTTAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 17 0.74
20 5 0.22
ACGTcount: A:0.20, C:0.11, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTTTTTTAACCTCTAAAT
Found at i:83874 original size:2 final size:2
Alignment explanation
Indices: 83867--83893 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
83857 AAGATTTCAG
83867 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
83894 GATAAGGATG
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:85002 original size:2 final size:2
Alignment explanation
Indices: 84995--85023 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
84985 TGGGGCTTCG
84995 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 C
85024 ATCATCCACA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:85629 original size:2 final size:2
Alignment explanation
Indices: 85617--85653 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
85607 CTACCCTTAC
85617 AT AT A- 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 AT
85654 TAGACATTTC
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:112836 original size:20 final size:21
Alignment explanation
Indices: 112796--112836 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
112786 AACATCACTG
* *
112796 AATTTAAATTTTTTATAAAAA
1 AATTCAAATCTTTTATAAAAA
112817 AATTCAAATCTTTT-TAAAAA
1 AATTCAAATCTTTTATAAAAA
112837 TTTTATATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (21 bp):
AATTCAAATCTTTTATAAAAA
Found at i:112883 original size:23 final size:23
Alignment explanation
Indices: 112855--112923 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 23
112845 TCTATTTAAA
112855 ATTAAAATAATAATTTAAAAAAT
1 ATTAAAATAATAATTTAAAAAAT
* * *
112878 ATT-AAATAATTATTTTAAAATT
1 ATTAAAATAATAATTTAAAAAAT
* *
112900 TTATAAAATAA-AATTATAATAAAT
1 AT-TAAAATAATAATT-TAAAAAAT
112924 TATTTTATAA
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
22 17 0.49
23 7 0.20
24 11 0.31
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
ATTAAAATAATAATTTAAAAAAT
Found at i:112952 original size:23 final size:22
Alignment explanation
Indices: 112914--112972 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
112904 AAAATAAAAT
*
112914 TATAATAAAT-TA-TTTTATAA
1 TATAATAAATAAATTTTTATAA
*
112934 -ACTAAATAATTAAATTTTTATAA
1 TA-T-AATAAATAAATTTTTATAA
112957 TATAATAAATAAATTT
1 TATAATAAATAAATTT
112973 AAAATAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
19 1 0.03
20 1 0.03
21 6 0.19
22 13 0.42
23 9 0.29
24 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TATAATAAATAAATTTTTATAA
Found at i:114261 original size:1 final size:1
Alignment explanation
Indices: 114257--114290 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
114247 CGTTTTTCCC
114257 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
114291 ACTTTTCCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:114467 original size:3 final size:3
Alignment explanation
Indices: 114461--114485 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
114451 CATTATTAAC
114461 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
114486 TTTCGCTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:114935 original size:2 final size:2
Alignment explanation
Indices: 114928--114984 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
114918 TCTTTCTTCT
114928 TA TA TA TA TA 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 TA TA TA TA TA
114970 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
114985 TCCTTTGGCA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:116875 original size:3 final size:3
Alignment explanation
Indices: 116867--116891 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
116857 AATTTTGCAA
116867 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
116892 TTGATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:118423 original size:20 final size:21
Alignment explanation
Indices: 118386--118424 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
118376 CCTACCTTGC
*
118386 TTGTTGTAACAGGAATTTTGT
1 TTGTTGTAACAGCAATTTTGT
*
118407 TTGTT-TAACAGCTATTTT
1 TTGTTGTAACAGCAATTTT
118425 CTACCTTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.23, C:0.08, G:0.18, T:0.51
Consensus pattern (21 bp):
TTGTTGTAACAGCAATTTTGT
Found at i:123710 original size:28 final size:27
Alignment explanation
Indices: 123647--123719 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
123637 AAGTCACCCA
*
123647 TATATTTGTCAAAAATGGTGGTTATTT
1 TATATTTGTCAAAAATGATGGTTATTT
* *
123674 TGTGTTTGTCAAAAATGATGGTT-TCCTT
1 TATATTTGTCAAAAATGATGGTTAT--TT
*
123702 TATATTTGTCAAATATGA
1 TATATTTGTCAAAAATGA
123720 AAGCTTGTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.29, C:0.07, G:0.18, T:0.47
Consensus pattern (27 bp):
TATATTTGTCAAAAATGATGGTTATTT
Found at i:128304 original size:28 final size:27
Alignment explanation
Indices: 128246--128335 Score: 78
Period size: 28 Copynumber: 3.4 Consensus size: 27
128236 CACCCATATG
* * *
128246 TTTGTAAAAAATGGTGGTTATTTTGTG
1 TTTGTCAAAAATGGTGGTTATTTTATA
128273 TTTGTCAAAAATGGTGGTT-TCCTTTATA
1 TTTGTCAAAAATGGTGGTTAT--TTTATA
* * * *
128301 TTTGTCAAATATGGAGGCT-TGTT-TA
1 TTTGTCAAAAATGGTGGTTATTTTATA
128326 TTTGTCAAAA
1 TTTGTCAAAA
128336 TTTGTGGCTA
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
25 11 0.21
26 3 0.06
27 18 0.34
28 21 0.40
ACGTcount: A:0.27, C:0.07, G:0.21, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTATTTTATA
Found at i:128450 original size:25 final size:26
Alignment explanation
Indices: 128416--128465 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
128406 AAGTATCCCT
128416 CATTCCTCTCTTGTATC-TCTCTCAAG
1 CATTCCTCTCTTGTATCATCT-TCAAG
128442 CATT-CTCTCTTGTATCATCTTCAA
1 CATTCCTCTCTTGTATCATCTTCAA
128466 TTCTTTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.18, C:0.32, G:0.06, T:0.44
Consensus pattern (26 bp):
CATTCCTCTCTTGTATCATCTTCAAG
Found at i:129069 original size:2 final size:2
Alignment explanation
Indices: 129062--129097 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
129052 TATTACTTTC
129062 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
129098 CTTGGTAGAC
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:131454 original size:4 final size:4
Alignment explanation
Indices: 131445--131473 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
131435 ATAATCCAAC
131445 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
131474 TCAACATGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:133721 original size:2 final size:2
Alignment explanation
Indices: 133709--133740 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
133699 AACCTCAACC
133709 TA TA TA T- 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 TA TA T
133741 TAAGAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:142574 original size:24 final size:23
Alignment explanation
Indices: 142511--142574 Score: 58
Period size: 26 Copynumber: 2.6 Consensus size: 23
142501 GAAGCGGAGA
142511 TTAAT-ATAAATAATATATAATAT
1 TTAATAAT-AATAATATATAATAT
* *
142534 TATAATAGGATATTAATATAATTATAT
1 T-TAATA--ATAATAATAT-ATAATAT
142561 TTAATAATAATAAT
1 TTAATAATAATAAT
142575 TAAAAAATGG
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
23 1 0.03
24 11 0.33
26 12 0.36
27 9 0.27
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (23 bp):
TTAATAATAATAATATATAATAT
Found at i:143432 original size:16 final size:16
Alignment explanation
Indices: 143407--143452 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
143397 TAAATTGGTG
* *
143407 TATATGATAATATTAA
1 TATATAATAATAATAA
*
143423 TATATTATAATAATAA
1 TATATAATAATAATAA
143439 TA-ATAATAATAATA
1 TATATAATAATAATA
143453 GTAACAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
TATATAATAATAATAA
Found at i:143437 original size:3 final size:3
Alignment explanation
Indices: 143413--143452 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
143403 GGTGTATATG
* *
143413 ATA ATA TTA ATA TATT ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
143453 GTAACAAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 30 0.94
4 2 0.06
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:144645 original size:19 final size:18
Alignment explanation
Indices: 144588--144655 Score: 63
Period size: 19 Copynumber: 3.9 Consensus size: 18
144578 GATAATATCT
144588 AATAATATTATATTATT-
1 AATAATATTATATTATTA
* *
144605 GAT-ATA-TAAATATATTA
1 AATAATATTATAT-TATTA
144622 AATAATATTATATTATTAA
1 AATAATATTATATTATT-A
*
144641 AATAAAATTAT-TTAT
1 AATAATATTATATTAT
144656 ATTTTTTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
15 4 0.10
16 7 0.17
17 4 0.10
18 11 0.27
19 15 0.37
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (18 bp):
AATAATATTATATTATTA
Found at i:144722 original size:22 final size:22
Alignment explanation
Indices: 144697--144751 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
144687 CATTCGATTC
*
144697 ATTAATATATAAAAAATATATT
1 ATTAATATATAAAAAATAAATT
* * *
144719 ATTAATACATTAAATATAAATT
1 ATTAATATATAAAAAATAAATT
144741 -TT-ATATATAAA
1 ATTAATATATAAA
144752 TATGTGTATA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 7 0.26
21 2 0.07
22 18 0.67
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTAATATATAAAAAATAAATT
Found at i:144849 original size:17 final size:19
Alignment explanation
Indices: 144817--144855 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
144807 GTTATAGTAA
*
144817 ATTAAATAATATTATTT-T
1 ATTAAATAAAATTATTTAT
144835 ATTAAA-AAAATTATTTAT
1 ATTAAATAAAATTATTTAT
144853 ATT
1 ATT
144856 TATTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTAAATAAAATTATTTAT
Found at i:146769 original size:2 final size:2
Alignment explanation
Indices: 146762--146803 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
146752 TGAATACATC
146762 AT AT AT 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 AT AT AT
146804 TTGTGTTGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:147221 original size:2 final size:2
Alignment explanation
Indices: 147214--147242 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
147204 TATAAAGTAA
147214 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 A
147243 ATGGTTTCGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:148552 original size:5 final size:5
Alignment explanation
Indices: 148544--148586 Score: 68
Period size: 5 Copynumber: 8.6 Consensus size: 5
148534 ATAATAACCA
* *
148544 TTTCC TTTCT TTTCC TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
148587 TCCCCCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:151105 original size:2 final size:2
Alignment explanation
Indices: 151098--151139 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
151088 AATTCAAGTA
* *
151098 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
151140 CTCTTTGGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:153710 original size:5 final size:5
Alignment explanation
Indices: 153695--153731 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
153685 AATGTAGAGC
* *
153695 TGGGA TAGGA TGGGA TAGGA TGGGA TGGGA TGGGA TG
1 TGGGA TGGGA TGGGA TGGGA TGGGA TGGGA TGGGA TG
153732 CGAGGATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.24, C:0.00, G:0.54, T:0.22
Consensus pattern (5 bp):
TGGGA
Found at i:153731 original size:10 final size:10
Alignment explanation
Indices: 153695--153730 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
153685 AATGTAGAGC
153695 TGGGATAGGA
1 TGGGATAGGA
153705 TGGGATAGGA
1 TGGGATAGGA
*
153715 TGGGATGGGA
1 TGGGATAGGA
153725 TGGGAT
1 TGGGAT
153731 GCGAGGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.25, C:0.00, G:0.53, T:0.22
Consensus pattern (10 bp):
TGGGATAGGA
Found at i:154707 original size:16 final size:18
Alignment explanation
Indices: 154681--154714 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
154671 ATTTAGGTTG
154681 AATTATTTTAAG-TATTT
1 AATTATTTTAAGTTATTT
154698 AATT-TTTTAAGTTATTT
1 AATTATTTTAAGTTATTT
154715 TTAAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (18 bp):
AATTATTTTAAGTTATTT
Found at i:154938 original size:16 final size:16
Alignment explanation
Indices: 154917--154951 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
154907 ATTGAATTTG
154917 AATCATTCTAGATTCA
1 AATCATTCTAGATTCA
* *
154933 AATCATTTTAGATTTA
1 AATCATTCTAGATTCA
154949 AAT
1 AAT
154952 TAATTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (16 bp):
AATCATTCTAGATTCA
Found at i:155231 original size:16 final size:16
Alignment explanation
Indices: 155212--155288 Score: 100
Period size: 16 Copynumber: 4.8 Consensus size: 16
155202 TCGAAATAAA
155212 TCAAATTTGAAATGAT
1 TCAAATTTGAAATGAT
*
155228 TCAAATCTGAAATGAT
1 TCAAATTTGAAATGAT
* * * * *
155244 TTAAACTCGAAATAAA
1 TCAAATTTGAAATGAT
155260 TCAAATTTGAAATGAT
1 TCAAATTTGAAATGAT
155276 TCAAATTTGAAAT
1 TCAAATTTGAAAT
155289 AATTTAAACT
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 49 1.00
ACGTcount: A:0.47, C:0.09, G:0.10, T:0.34
Consensus pattern (16 bp):
TCAAATTTGAAATGAT
Found at i:155240 original size:32 final size:32
Alignment explanation
Indices: 155190--155306 Score: 103
Period size: 32 Copynumber: 3.7 Consensus size: 32
155180 TTGAATTTAT
* * *
155190 AATGATTTAAA-CTCGAAATAAATCAAATTTGA
1 AATGATTCAAATCT-GAAATGATTCAAATTTGA
* * *
155222 AATGATTCAAATCTGAAATGATTTAAACTCGA
1 AATGATTCAAATCTGAAATGATTCAAATTTGA
* * *
155254 AATAAATCAAATTTGAAATGATTCAAATTTGA
1 AATGATTCAAATCTGAAATGATTCAAATTTGA
* *
155286 AATAATTTAAA-CTCGAAATGA
1 AATGATTCAAATCT-GAAATGA
155307 CTTGAACAAT
Statistics
Matches: 68, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
31 1 0.01
32 65 0.96
33 2 0.03
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.32
Consensus pattern (32 bp):
AATGATTCAAATCTGAAATGATTCAAATTTGA
Found at i:155242 original size:48 final size:48
Alignment explanation
Indices: 155190--155304 Score: 212
Period size: 48 Copynumber: 2.4 Consensus size: 48
155180 TTGAATTTAT
155190 AATGATTTAAACTCGAAATAAATCAAATTTGAAATGATTCAAATCTGA
1 AATGATTTAAACTCGAAATAAATCAAATTTGAAATGATTCAAATCTGA
*
155238 AATGATTTAAACTCGAAATAAATCAAATTTGAAATGATTCAAATTTGA
1 AATGATTTAAACTCGAAATAAATCAAATTTGAAATGATTCAAATCTGA
*
155286 AATAATTTAAACTCGAAAT
1 AATGATTTAAACTCGAAAT
155305 GACTTGAACA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 65 1.00
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.32
Consensus pattern (48 bp):
AATGATTTAAACTCGAAATAAATCAAATTTGAAATGATTCAAATCTGA
Found at i:155303 original size:16 final size:16
Alignment explanation
Indices: 155198--155304 Score: 81
Period size: 16 Copynumber: 6.7 Consensus size: 16
155188 ATAATGATTT
*
155198 AAACTCGAAATAAATC
1 AAACTCGAAATAATTC
* * *
155214 AAATTTGAAATGATTC
1 AAACTCGAAATAATTC
* *
155230 AAA-TCTGAAATGATTT
1 AAACTC-GAAATAATTC
*
155246 AAACTCGAAATAAATC
1 AAACTCGAAATAATTC
* * *
155262 AAATTTGAAATGATTC
1 AAACTCGAAATAATTC
* * *
155278 AAATTTGAAATAATTT
1 AAACTCGAAATAATTC
155294 AAACTCGAAAT
1 AAACTCGAAAT
155305 GACTTGAACA
Statistics
Matches: 72, Mismatches: 17, Indels: 4
0.77 0.18 0.04
Matches are distributed among these distances:
15 1 0.01
16 69 0.96
17 2 0.03
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.31
Consensus pattern (16 bp):
AAACTCGAAATAATTC
Found at i:155514 original size:16 final size:16
Alignment explanation
Indices: 155474--155515 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
155464 GATTAACTTG
155474 AAATTTAAAATAATTC
1 AAATTTAAAATAATTC
* * *
155490 GAATCTAAAATAATTT
1 AAATTTAAAATAATTC
155506 AAATTTAAAA
1 AAATTTAAAA
155516 ATACTCAAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (16 bp):
AAATTTAAAATAATTC
Found at i:163683 original size:6 final size:6
Alignment explanation
Indices: 163672--163700 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
163662 ATTAGAATCA
163672 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC
163701 ACACGTCCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:163848 original size:44 final size:43
Alignment explanation
Indices: 163800--163889 Score: 153
Period size: 43 Copynumber: 2.1 Consensus size: 43
163790 AAAACTTTGT
163800 TTTTTTCCTTTTTCTTTTTTTTTTAAAAAAAAGAATTACAAAAC
1 TTTTTTCCTTTTT-TTTTTTTTTTAAAAAAAAGAATTACAAAAC
* *
163844 TTTTTTTCTTTTTTTTTTTTTTTTAAAAAAAGAATTACAAAAC
1 TTTTTTCCTTTTTTTTTTTTTTTAAAAAAAAGAATTACAAAAC
163887 TTT
1 TTT
163890 GTAAAGTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
43 32 0.73
44 12 0.27
ACGTcount: A:0.32, C:0.09, G:0.02, T:0.57
Consensus pattern (43 bp):
TTTTTTCCTTTTTTTTTTTTTTTAAAAAAAAGAATTACAAAAC
Found at i:164571 original size:2 final size:2
Alignment explanation
Indices: 164564--164596 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
164554 TTAGTAAGTT
164564 TA TA 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 TA TA T
164597 TTAAGACCTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:165803 original size:10 final size:9
Alignment explanation
Indices: 165790--165832 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
165780 GCCAAAAGAG
165790 AAAAGAACAA
1 AAAAGAA-AA
*
165800 AAAAGGAAA
1 AAAAGAAAA
165809 AAAA-AAAA
1 AAAAGAAAA
165817 AAAAGAAAGA
1 AAAAGAAA-A
165827 AAAAGA
1 AAAAGA
165833 TAAGCTTGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 7 0.24
9 9 0.31
10 13 0.45
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:165803 original size:17 final size:16
Alignment explanation
Indices: 165783--165830 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
165773 AAAAATGGCC
*
165783 AAAAGAGAAAAGAACAA
1 AAAAGAGAAAA-AAAAA
165800 AAAAG-GAAAAAAAAA
1 AAAAGAGAAAAAAAAA
*
165815 AAAAAAGAAAGAAAAA
1 AAAAGAGAAA-AAAAA
165831 GATAAGCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 8 0.30
16 9 0.33
17 10 0.37
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAGAGAAAAAAAAA
Found at i:168441 original size:34 final size:33
Alignment explanation
Indices: 168393--168613 Score: 257
Period size: 34 Copynumber: 6.5 Consensus size: 33
168383 TGGTAAAAAC
**
168393 CACCATTTAATCAACAATGACAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
168426 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
168460 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
168494 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
168528 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
168562 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
168596 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
168614 TCTCCCACTT
Statistics
Matches: 161, Mismatches: 18, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
33 23 0.14
34 132 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:168509 original size:68 final size:67
Alignment explanation
Indices: 168395--168613 Score: 287
Period size: 68 Copynumber: 3.2 Consensus size: 67
168385 GTAAAAACCA
* * * *
168395 CCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
168460 CAC
65 CAC
* * * *
168463 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
168528 CTC
65 CAC
* * * *
168531 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
168596 CA-
65 CAC
168598 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
168614 TCTCCCACTT
Statistics
Matches: 131, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
67 17 0.13
68 113 0.86
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:168537 original size:102 final size:101
Alignment explanation
Indices: 168393--168613 Score: 343
Period size: 102 Copynumber: 2.2 Consensus size: 101
168383 TGGTAAAAAC
* *
168393 CACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
168458 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
** ** * *
168494 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
168559 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
168596 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
168614 TCTCCCACTT
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 16 0.15
102 91 0.85
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGACAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:173069 original size:34 final size:33
Alignment explanation
Indices: 173021--173239 Score: 217
Period size: 34 Copynumber: 6.5 Consensus size: 33
173011 TGGTAAAAAC
*
173021 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
173054 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* *
173088 CACCCATTTAATCAATAATGGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
173122 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * * ** *
173156 CTCCCATTTAGTCAATAATGACAA-ATCACCAAAT
1 C-ACCATTTAATCAACAATGGTAACCT-ACCAAAT
* **
173190 CACCCATTTAATCAACAATGATAAATTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
173224 CACCATTTAATCAACA
1 CACCATTTAATCAACA
173240 TGTAATAGTA
Statistics
Matches: 157, Mismatches: 20, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 19 0.12
34 134 0.85
35 4 0.03
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.26
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:173137 original size:68 final size:66
Alignment explanation
Indices: 173023--173237 Score: 252
Period size: 68 Copynumber: 3.2 Consensus size: 66
173013 GTAAAAACCA
* * *
173023 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAATAATGGCAA-CTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
173088 CAC
64 CAC
* *
173091 CCATTTAATCAATAATGGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAATAATGGCAA-CTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
173156 CTC
64 CAC
* * * * * **
173159 CCATTTAGTCAATAATGACAAATCACCAAATCACCCATTTAATCAACAATGATAAATTACCAAAT
1 CCATTTAATCAATAATGGCAACT-ACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
173224 CA-
64 CAC
173226 CCATTTAATCAA
1 CCATTTAATCAA
173238 CATGTAATAG
Statistics
Matches: 126, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
67 14 0.11
68 111 0.88
69 1 0.01
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (66 bp):
CCATTTAATCAATAATGGCAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATCA
C
Found at i:173165 original size:102 final size:101
Alignment explanation
Indices: 173021--173239 Score: 303
Period size: 102 Copynumber: 2.2 Consensus size: 101
173011 TGGTAAAAAC
** *
173021 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGACAAACCACCAA
* * *
173086 ATCACCCATTTAATCAATAATGGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATGATAAACTACCAAAT
** * * * * *
173122 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAATAATGACAAATCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGACAAACCACCA
*
173187 AATCACCCATTTAATCAACAATGATAAATTACCAAAT
65 AATCACCCATTTAATCAACAATGATAAACTACCAAAT
173224 CACCATTTAATCAACA
1 CACCATTTAATCAACA
173240 TGTAATAGTA
Statistics
Matches: 101, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
101 14 0.14
102 87 0.86
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGACAAACCACCAA
ATCACCCATTTAATCAACAATGATAAACTACCAAAT
Found at i:173815 original size:12 final size:13
Alignment explanation
Indices: 173798--173827 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
173788 ATTTGATATC
173798 TTTTAA-TTAAAA
1 TTTTAATTTAAAA
173810 TTTTAATTTAAAA
1 TTTTAATTTAAAA
173823 TTTTA
1 TTTTA
173828 TAAATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTAATTTAAAA
Found at i:174352 original size:2 final size:2
Alignment explanation
Indices: 174345--174383 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
174335 AGAAGGTATG
*
174345 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
174384 GTCAACGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:175346 original size:2 final size:2
Alignment explanation
Indices: 175339--175376 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
175329 TTATTACCCC
175339 AT 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 AT
175377 CAAACTTGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:176215 original size:15 final size:16
Alignment explanation
Indices: 176188--176220 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
176178 TTTATTATTT
176188 TTTAATAATATTTATA
1 TTTAATAATATTTATA
*
176204 TTTAAT-ATATTTTTA
1 TTTAATAATATTTATA
176219 TT
1 TT
176221 AAATTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTAATAATATTTATA
Found at i:177123 original size:2 final size:2
Alignment explanation
Indices: 177116--177164 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
177106 GGACCCAAAC
177116 TA TA TA TA TA 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 TA TA TA TA TA
177158 TA TA TA T
1 TA TA TA T
177165 GTGCTTAATG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:177237 original size:2 final size:2
Alignment explanation
Indices: 177230--177278 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
177220 TGTATTTCCT
177230 TA TA TA TA TA 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 TA TA TA TA TA
177272 TA TA TA T
1 TA TA TA T
177279 GGAATCAGCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:181253 original size:110 final size:109
Alignment explanation
Indices: 180830--181233 Score: 576
Period size: 109 Copynumber: 3.7 Consensus size: 109
180820 TGAGAAATAA
* * * * *
180830 TATTCTTAATGCTTTTGTGATAACATTTATTTTTGTTAAGCATTTGACAAATATGTATTTTCACA
1 TATTCTTGATGCTTTTGTGATAACATCTATTTTTGTTAAGCATTTGATAAATGTATATTTTCACA
* *
180895 AATTTAAACAGTAAATAGAATAGGTATGAATGCTAATGGCTTAT
66 AATTTAATCAGTAAATAGAATAGGTAAGAATGCTAATGGCTTAT
* *
180939 TATTCTTGATGCTTTTGTGATAACATAC-ATTTTTGTTAAGCATTTGATAAATGTGTATTTTCAT
1 TATTCTTGATGCTTTTGTGATAACAT-CTATTTTTGTTAAGCATTTGATAAATGTATATTTTCAC
* ** * *
181003 GAATTTAATCAGTAAATAGAATATATATGAATACTAATGGCTTAT
65 AAATTTAATCAGTAAATAGAATAGGTAAGAATGCTAATGGCTTAT
* * *
181048 TATTCTTGATGCTTTTGTGATAACATTTATTTTTATTAAGCATTTGATAAATGTATATTTTTACA
1 TATTCTTGATGCTTTTGTGATAACATCTATTTTTGTTAAGCATTTGATAAATGTATATTTTCACA
*
181113 AATTTAATCAGTAAATAGAATAGGTAAGAATGCTAATGGCTTAC
66 AATTTAATCAGTAAATAGAATAGGTAAGAATGCTAATGGCTTAT
* * * * *
181157 TACTCTTGATGCTTTTGTGAGAACATCTATTTTTTGTTAAGCATGTGATAGATGTATATTTTCAA
1 TATTCTTGATGCTTTTGTGATAACATCTA-TTTTTGTTAAGCATTTGATAAATGTATATTTTCAC
181222 AAATTTAATCAG
65 AAATTTAATCAG
181234 CATATACACT
Statistics
Matches: 263, Mismatches: 29, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
109 221 0.84
110 42 0.16
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (109 bp):
TATTCTTGATGCTTTTGTGATAACATCTATTTTTGTTAAGCATTTGATAAATGTATATTTTCACA
AATTTAATCAGTAAATAGAATAGGTAAGAATGCTAATGGCTTAT
Found at i:181523 original size:110 final size:109
Alignment explanation
Indices: 181319--181549 Score: 266
Period size: 110 Copynumber: 2.1 Consensus size: 109
181309 TTATTGTTTC
* * * *
181319 AACATTTAGTTTTTGTCAAGCATTTGATATATTTGTATTTCCACAAACTTATTCAGTAAATAGAA
1 AACATTTA-TTTTTATCAAGCATTTGATAAATATGTATTTCCACAAACTTAATCAGTAAATAGAA
* * * * * *
181384 CATCTAAGACTGATAATGGCTAATTATTCTTGATGCTTTGGTTAT
65 CAGCAAAGAATGATAATAGCTAATCATTCTTGATGCTTTGGTGAT
* * * *
181429 AACATTTATTGTTTATTAAGCATTTGATAAATATGTATTTTCACAAATTTAATCAGTAAATAGAG
1 AACATTTATT-TTTATCAAGCATTTGATAAATATGTATTTCCACAAACTTAATCAGTAAATAGAA
* * * *
181494 TAGGAAAGAAT-ACTAATAGCTTATCATTCTTGATGCTTTTGTGAT
65 CAGCAAAGAATGA-TAATAGCTAATCATTCTTGATGCTTTGGTGAT
181539 AACATTTATTT
1 AACATTTATTT
181550 ACTTGATAAG
Statistics
Matches: 101, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
109 4 0.04
110 97 0.96
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (109 bp):
AACATTTATTTTTATCAAGCATTTGATAAATATGTATTTCCACAAACTTAATCAGTAAATAGAAC
AGCAAAGAATGATAATAGCTAATCATTCTTGATGCTTTGGTGAT
Found at i:182787 original size:44 final size:44
Alignment explanation
Indices: 182724--182809 Score: 163
Period size: 44 Copynumber: 2.0 Consensus size: 44
182714 CCTTTTAAAC
*
182724 TTGTCAATCGCTAAAGTTACTGATTACTAGAGATTTCACACAAA
1 TTGTCAATCGCTAAAGTTACCGATTACTAGAGATTTCACACAAA
182768 TTGTCAATCGCTAAAGTTACCGATTACTAGAGATTTCACACA
1 TTGTCAATCGCTAAAGTTACCGATTACTAGAGATTTCACACA
182810 TTGCAAACAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (44 bp):
TTGTCAATCGCTAAAGTTACCGATTACTAGAGATTTCACACAAA
Found at i:188897 original size:177 final size:178
Alignment explanation
Indices: 188601--188957 Score: 680
Period size: 177 Copynumber: 2.0 Consensus size: 178
188591 AAACCCAAAA
*
188601 TTAGTAGATAGATACCGAATTACTAACTATGCATCATTCTTGAAACCGAAACTGCACCACATATA
1 TTAGTAGATAGATACCGAATTACCAACTATGCATCATTCTTGAAACCGAAACTGCACCACATATA
*
188666 TATATAGCAGGAAGAATCCATGAAACTCAGGATGGATAGCGCCATAGATGATAGTTGAAACAACT
66 TATATAGCAGGAAGAATCCATGAAACTCAGGATGGATAGCGCCATAGATGATAGTTAAAACAACT
188731 ACAAATGGCGCTATCCCTCCTGAGCTTTACAGATT-CCCCATACTTGG
131 ACAAATGGCGCTATCCCTCCTGAGCTTTACAGATTCCCCCATACTTGG
188778 TTAGTAGATAGATACCGAATTACCAACTATGCATCATTCTTGAAACCGAAACTGCACCACATATA
1 TTAGTAGATAGATACCGAATTACCAACTATGCATCATTCTTGAAACCGAAACTGCACCACATATA
188843 TATATAGCAGGAAGAATCCATGAAACTCAGGATGGATAGCGCCATAGATGATAGTTAAAACAACT
66 TATATAGCAGGAAGAATCCATGAAACTCAGGATGGATAGCGCCATAGATGATAGTTAAAACAACT
*
188908 ACAGATGGCGCTATCCCTCCTGAGCTTTACAGATTCCCCCATACTTGG
131 ACAAATGGCGCTATCCCTCCTGAGCTTTACAGATTCCCCCATACTTGG
188956 TT
1 TT
188958 TACATGACGG
Statistics
Matches: 176, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
177 162 0.92
178 14 0.08
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.25
Consensus pattern (178 bp):
TTAGTAGATAGATACCGAATTACCAACTATGCATCATTCTTGAAACCGAAACTGCACCACATATA
TATATAGCAGGAAGAATCCATGAAACTCAGGATGGATAGCGCCATAGATGATAGTTAAAACAACT
ACAAATGGCGCTATCCCTCCTGAGCTTTACAGATTCCCCCATACTTGG
Found at i:194884 original size:68 final size:68
Alignment explanation
Indices: 194772--194929 Score: 219
Period size: 68 Copynumber: 2.3 Consensus size: 68
194762 GATAGGTTAT
* *
194772 TTGTTGGTTAAAT-GGTAATTTGATAATTTATTATTATTGATTAAATAAAAAATTTGATAATTTA
1 TTGTTGATTAAATGGGTAATTTGATAATTTATCATTATTGATTAAATAAAAAATTTGATAATTTA
194836 TTA
66 TTA
* * * * * *
194839 TTGTTGATTAAATGGGTAATTTGATAATTTATCATTGTTGGTTAAATGAAAGATTTGGTAGTTTA
1 TTGTTGATTAAATGGGTAATTTGATAATTTATCATTATTGATTAAATAAAAAATTTGATAATTTA
194904 TTA
66 TTA
* *
194907 TTGTTGATTAAATGAGTGATTTG
1 TTGTTGATTAAATGGGTAATTTG
194930 GTGATTTTTA
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 12 0.15
68 68 0.85
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.48
Consensus pattern (68 bp):
TTGTTGATTAAATGGGTAATTTGATAATTTATCATTATTGATTAAATAAAAAATTTGATAATTTA
TTA
Found at i:194931 original size:34 final size:34
Alignment explanation
Indices: 194772--194929 Score: 185
Period size: 34 Copynumber: 4.7 Consensus size: 34
194762 GATAGGTTAT
*
194772 TTGTTGGTTAAATG-GTAATTTGATAATTTATTA
1 TTGTTGATTAAATGAGTAATTTGATAATTTATTA
* * **
194805 TTATTGATTAAATAAAAAATTTGATAATTTATTA
1 TTGTTGATTAAATGAGTAATTTGATAATTTATTA
* *
194839 TTGTTGATTAAATGGGTAATTTGATAATTTATCA
1 TTGTTGATTAAATGAGTAATTTGATAATTTATTA
* * * *
194873 TTGTTGGTTAAATGA-AAGATTTGGTAGTTTATTA
1 TTGTTGATTAAATGAGTA-ATTTGATAATTTATTA
*
194907 TTGTTGATTAAATGAGTGATTTG
1 TTGTTGATTAAATGAGTAATTTG
194930 GTGATTTTTA
Statistics
Matches: 102, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
33 12 0.12
34 90 0.88
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.48
Consensus pattern (34 bp):
TTGTTGATTAAATGAGTAATTTGATAATTTATTA
Found at i:195263 original size:19 final size:19
Alignment explanation
Indices: 195239--195290 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
195229 TTATCGAGGT
*
195239 ACTATTCACGTATACATGC
1 ACTATTCACGTATACAGGC
* *
195258 ACTATTCACGTATACGGGT
1 ACTATTCACGTATACAGGC
195277 ACTATTCACGTATA
1 ACTATTCACGTATA
195291 TGATACTGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.23, G:0.13, T:0.33
Consensus pattern (19 bp):
ACTATTCACGTATACAGGC
Found at i:199406 original size:22 final size:22
Alignment explanation
Indices: 199378--199424 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
199368 GATTAAATAG
* *
199378 TGATTTGGTAGTTTGCCATTGT
1 TGATTTGGTAGTTTACCATTAT
*
199400 TGATTTGGTGGTTTACCATTAT
1 TGATTTGGTAGTTTACCATTAT
199422 TGA
1 TGA
199425 CTAAATGAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.09, G:0.26, T:0.49
Consensus pattern (22 bp):
TGATTTGGTAGTTTACCATTAT
Found at i:199454 original size:34 final size:34
Alignment explanation
Indices: 199401--199549 Score: 149
Period size: 34 Copynumber: 4.4 Consensus size: 34
199391 TGCCATTGTT
* *
199401 GATTTGGTGGTTTACCATTATTGACTAAATGAGA
1 GATTTGGTAGTTTGCCATTATTGACTAAATGAGA
* * * * *
199435 GATTTAGTAGTTTGTCATTATTGATTAAATGGGT
1 GATTTGGTAGTTTGCCATTATTGACTAAATGAGA
* *
199469 GATTTGGTGGTTTGCCATTGTTGACTAAATG-GAA
1 GATTTGGTAGTTTGCCATTATTGACTAAATGAG-A
* * *
199503 GATTTGGTAGTTTGCCATTGTTGATTAAAT-AGGT
1 GATTTGGTAGTTTGCCATTATTGACTAAATGA-GA
*
199537 GATTTTGTAGTTT
1 GATTTGGTAGTTT
199550 TTACCAAACC
Statistics
Matches: 95, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
33 1 0.01
34 93 0.98
35 1 0.01
ACGTcount: A:0.25, C:0.06, G:0.26, T:0.44
Consensus pattern (34 bp):
GATTTGGTAGTTTGCCATTATTGACTAAATGAGA
Found at i:199513 original size:68 final size:68
Alignment explanation
Indices: 199400--199541 Score: 214
Period size: 68 Copynumber: 2.1 Consensus size: 68
199390 TTGCCATTGT
*
199400 TGATTTGGTGGTTTACCATTATTGACTAAATGAGAGATTTAGTAGTTTGTCATTATTGATTAAAT
1 TGATTTGGTGGTTTACCATTATTGACTAAATGAGAGATTTAGTAGTTTGCCATTATTGATTAAAT
*
199465 GGG
66 AGG
* * * *
199468 TGATTTGGTGGTTTGCCATTGTTGACTAAATG-GAAGATTTGGTAGTTTGCCATTGTTGATTAAA
1 TGATTTGGTGGTTTACCATTATTGACTAAATGAG-AGATTTAGTAGTTTGCCATTATTGATTAAA
199532 TAGG
65 TAGG
199536 TGATTT
1 TGATTT
199542 TGTAGTTTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
67 1 0.01
68 66 0.99
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.43
Consensus pattern (68 bp):
TGATTTGGTGGTTTACCATTATTGACTAAATGAGAGATTTAGTAGTTTGCCATTATTGATTAAAT
AGG
Done.