Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 117 of 196
Found at i:35372973 original size:23 final size:22
Alignment explanation
Indices: 35372940--35372982 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
35372930 AATAAAAAAT
35372940 ATTTTTAAAAAA-TAATATGATG
1 ATTTTTAAAAAAGTAA-ATGATG
35372962 ATTTTTAGAAAAAGTAAATGA
1 ATTTTTA-AAAAAGTAAATGA
35372983 GGTATCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 7 0.37
23 9 0.47
24 3 0.16
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (22 bp):
ATTTTTAAAAAAGTAAATGATG
Found at i:35376303 original size:54 final size:54
Alignment explanation
Indices: 35376212--35376321 Score: 168
Period size: 54 Copynumber: 2.0 Consensus size: 54
35376202 TCCCCCATAA
* *
35376212 TCCCTTAATTCACTCCTAAAATCGCTCCCTTACTTCCCACTACACATCCACCAC
1 TCCCCTAACTCACTCCTAAAATCGCTCCCTTACTTCCCACTACACATCCACCAC
* *
35376266 TCCCCTAACTCACTCCTAAAATCGCT-TCTTCACTTCCCACTATACATCCACCAC
1 TCCCCTAACTCACTCCTAAAATCGCTCCCTT-ACTTCCCACTACACATCCACCAC
35376320 TC
1 TC
35376322 ATAAACCCAG
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
53 3 0.06
54 48 0.94
ACGTcount: A:0.25, C:0.45, G:0.02, T:0.28
Consensus pattern (54 bp):
TCCCCTAACTCACTCCTAAAATCGCTCCCTTACTTCCCACTACACATCCACCAC
Found at i:35378350 original size:21 final size:21
Alignment explanation
Indices: 35378321--35378361 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
35378311 AGAACACGCC
35378321 AACAAAAGCTCATAAGAGCTA
1 AACAAAAGCTCATAAGAGCTA
* * *
35378342 AACAGAAGCTCGTGAGAGCT
1 AACAAAAGCTCATAAGAGCT
35378362 GATCCACCCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.15
Consensus pattern (21 bp):
AACAAAAGCTCATAAGAGCTA
Found at i:35380842 original size:38 final size:41
Alignment explanation
Indices: 35380783--35380868 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 41
35380773 AATTATATTT
* * *
35380783 AATACAATAAAATATTTATTATATTTAT-TT-GTGTTTTTC
1 AATATAATAAAATAATTATTATATTTATGTTAGTGTTTATC
35380822 AATATAATAAAA-AATTATTATATTTATGTTAGTGTTTATC
1 AATATAATAAAATAATTATTATATTTATGTTAGTGTTTATC
35380862 AATATAA
1 AATATAA
35380869 ATACTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 14 0.33
39 13 0.31
40 15 0.36
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (41 bp):
AATATAATAAAATAATTATTATATTTATGTTAGTGTTTATC
Found at i:35382514 original size:23 final size:22
Alignment explanation
Indices: 35382474--35382519 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
35382464 TTTTGACATA
*
35382474 TTAATAATTTTATACATAGATT
1 TTAATAATTTGATACATAGATT
* *
35382496 TTAATAAATTTGATTCATATATT
1 TTAAT-AATTTGATACATAGATT
35382519 T
1 T
35382520 CATATTAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (22 bp):
TTAATAATTTGATACATAGATT
Found at i:35385484 original size:9 final size:8
Alignment explanation
Indices: 35385470--35385513 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
35385460 TCAACTCTCT
35385470 TAAAAATAA
1 TAAAAAT-A
35385479 TAAAAATTA
1 TAAAAA-TA
35385488 TAAAAATA
1 TAAAAATA
*
35385496 TAAAATTA
1 TAAAAATA
*
35385504 TAAAATTA
1 TAAAAATA
35385512 TA
1 TA
35385514 TTTTTAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
8 19 0.58
9 13 0.39
10 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (8 bp):
TAAAAATA
Found at i:35385492 original size:8 final size:8
Alignment explanation
Indices: 35385481--35385513 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
35385471 AAAAATAATA
35385481 AAAATTAT
1 AAAATTAT
*
35385489 AAAAATAT
1 AAAATTAT
35385497 AAAATTAT
1 AAAATTAT
35385505 AAAATTAT
1 AAAATTAT
35385513 A
1 A
35385514 TTTTTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAATTAT
Found at i:35385502 original size:16 final size:16
Alignment explanation
Indices: 35385470--35385513 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 16
35385460 TCAACTCTCT
35385470 TAAAAATAATAAAAATTA
1 TAAAAAT-AT-AAAATTA
35385488 TAAAAATATAAAATTA
1 TAAAAATATAAAATTA
*
35385504 TAAAATTATA
1 TAAAAATATA
35385514 TTTTTAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 16 0.64
17 2 0.08
18 7 0.28
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TAAAAATATAAAATTA
Found at i:35387947 original size:18 final size:19
Alignment explanation
Indices: 35387912--35387948 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
35387902 TATATTATAT
*
35387912 TTAATAATTTTTTGACATA
1 TTAATAATTTTATGACATA
35387931 TTAATAATTTTAT-ACATA
1 TTAATAATTTTATGACATA
35387949 GATTTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (19 bp):
TTAATAATTTTATGACATA
Found at i:35390274 original size:25 final size:25
Alignment explanation
Indices: 35390216--35390271 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 25
35390206 ATGACTCTCT
* *
35390216 TGAGCTTCCCATTATTTGGCTTTCA
1 TGAGCTTCCCAATATTTGGCTTGCA
35390241 TGAGCTTCCCAATA-TTGGCTTGCA
1 TGAGCTTCCCAATATTTGGCTTGCA
35390265 TGAGCTT
1 TGAGCTT
35390272 TCCGATTACG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 16 0.55
25 13 0.45
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (25 bp):
TGAGCTTCCCAATATTTGGCTTGCA
Found at i:35390357 original size:25 final size:25
Alignment explanation
Indices: 35390288--35390382 Score: 84
Period size: 25 Copynumber: 3.8 Consensus size: 25
35390278 TACGGCTCTT
* * *
35390288 ATGAGCTTACCATTACATAGCTCAC
1 ATGAGATTCCCATTACATGGCTCAC
*
35390313 ATGAGATTCCCGTTACATGGCTCAC
1 ATGAGATTCCCATTACATGGCTCAC
* * *
35390338 ATGAGTTTCTCATTATATGGCTCGA-
1 ATGAGATTCCCATTACATGGCTC-AC
* *
35390363 AAGAGCTTCCCGATTACATG
1 ATGAGATTCCC-ATTACATG
35390383 CTCGTATGGG
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
25 48 0.86
26 8 0.14
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (25 bp):
ATGAGATTCCCATTACATGGCTCAC
Found at i:35393953 original size:20 final size:20
Alignment explanation
Indices: 35393916--35393954 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
35393906 CATTTTTTCT
*
35393916 TTACTTAAATTTCTTTTTAA
1 TTACTTAAATTACTTTTTAA
35393936 TTAC-TAAATTACTATTTTA
1 TTACTTAAATTACT-TTTTA
35393955 CCCTTATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (20 bp):
TTACTTAAATTACTTTTTAA
Found at i:35394687 original size:22 final size:22
Alignment explanation
Indices: 35394647--35394689 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
35394637 ATATATATTT
*
35394647 TTATATTATTAAAATAAAATAA
1 TTATATTATTAAAAAAAAATAA
35394669 TTATA-TATTAAATAAAAAATA
1 TTATATTATTAAA-AAAAAATA
35394690 GAACTTGACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTATATTATTAAAAAAAAATAA
Found at i:35397254 original size:35 final size:36
Alignment explanation
Indices: 35397205--35397280 Score: 104
Period size: 35 Copynumber: 2.1 Consensus size: 36
35397195 ACGTCATTAT
*
35397205 GTTATAATATATATAGT-TTTTATATTAT-TTATAAA
1 GTTATAATATATATA-TATATTATATTATATTATAAA
35397240 GCTTAT-ATATATATATATATTATATTATATTATAAA
1 G-TTATAATATATATATATATTATATTATATTATAAA
35397276 GTTAT
1 GTTAT
35397281 TATGATAATG
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
34 1 0.03
35 24 0.65
36 12 0.32
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (36 bp):
GTTATAATATATATATATATTATATTATATTATAAA
Found at i:35398241 original size:43 final size:43
Alignment explanation
Indices: 35398179--35398303 Score: 121
Period size: 43 Copynumber: 2.9 Consensus size: 43
35398169 GGATTCCGAT
35398179 ATGTGTTCT-CGTGTAAGACCACGTCTGGGACGTTGGCATCAAC
1 ATGTGTT-TACGTGTAAGACCACGTCTGGGACGTTGGCATCAAC
* * ***
35398222 CTGTGTTTACGTGTAAGACC-CTGTTTGGGACAG-TGGCATCGGT
1 ATGTGTTTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCAAC
* ** *
35398265 ATGTGATTACACGTAAGACCACGTCTGGGATGTTGGCAT
1 ATGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCAT
35398304 TGTACGAGCT
Statistics
Matches: 66, Mismatches: 11, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
42 3 0.05
43 61 0.92
44 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.30
Consensus pattern (43 bp):
ATGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCATCAAC
Found at i:35401668 original size:18 final size:17
Alignment explanation
Indices: 35401642--35401677 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
35401632 TTTGGTTATA
35401642 TTTAATTTTCGATATGTT
1 TTTAATTTT-GATATGTT
*
35401660 TTTATTTTTGATATGTT
1 TTTAATTTTGATATGTT
35401677 T
1 T
35401678 CATTTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTAATTTTGATATGTT
Found at i:35404534 original size:21 final size:21
Alignment explanation
Indices: 35404508--35404550 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
35404498 AATAGAAGTC
35404508 GATGCCAACGTCCCAGACGTG
1 GATGCCAACGTCCCAGACGTG
*
35404529 GATGCCAACGTCTCAGACGTG
1 GATGCCAACGTCCCAGACGTG
35404550 G
1 G
35404551 TCTTACACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.16
Consensus pattern (21 bp):
GATGCCAACGTCCCAGACGTG
Found at i:35406792 original size:7 final size:7
Alignment explanation
Indices: 35406780--35406807 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
35406770 TCACGAACAT
35406780 AAAAATA
1 AAAAATA
35406787 AAAAATA
1 AAAAATA
35406794 AAAAATA
1 AAAAATA
35406801 AAAAATA
1 AAAAATA
35406808 CAGAGATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:35407609 original size:8 final size:8
Alignment explanation
Indices: 35407596--35407621 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
35407586 TATTTCTCAC
35407596 TATTATAT
1 TATTATAT
35407604 TATTATAT
1 TATTATAT
35407612 TATTATAT
1 TATTATAT
35407620 TA
1 TA
35407622 GGCTATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTATAT
Found at i:35407892 original size:33 final size:35
Alignment explanation
Indices: 35407827--35407904 Score: 97
Period size: 35 Copynumber: 2.2 Consensus size: 35
35407817 ATATATATAC
* *
35407827 TTTATAATATATATATATATATAAACACGTAC-ATT
1 TTTATAATATATATACACATAT-AACACGTACAATT
*
35407862 TTTATAATATATATACACATAT-ACATGTACATATT
1 TTTATAATATATATACACATATAACACGTACA-ATT
35407897 TTTATAAT
1 TTTATAAT
35407905 CTATTTATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 7 0.18
35 31 0.82
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.45
Consensus pattern (35 bp):
TTTATAATATATATACACATATAACACGTACAATT
Found at i:35411548 original size:58 final size:57
Alignment explanation
Indices: 35411514--35411657 Score: 168
Period size: 58 Copynumber: 2.5 Consensus size: 57
35411504 TTAGTTCATA
35411514 TAATAATAATTATATTAAGAATTTTATAAAATTATATATTATTTTATTAAATTATATT
1 TAATAATAATTATATTAAGAATTTTATAAAATTATATATTATTTTATTAAATTATA-T
* ** * * *
35411572 TAATAATAATTATATTAA-AATATGGTTAAATTATTTATTATTTTTATTAAATTATTTT
1 TAATAATAATTATATTAAGAATTTTATAAAATTATATATTA-TTTTATTAAATTA-TAT
*
35411630 TAATAATAATCT-TATTAA-AATTTAATAA
1 TAATAATAAT-TATATTAAGAATTTTATAA
35411658 CAATAACAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
57 17 0.23
58 54 0.74
59 2 0.03
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (57 bp):
TAATAATAATTATATTAAGAATTTTATAAAATTATATATTATTTTATTAAATTATAT
Found at i:35411838 original size:16 final size:16
Alignment explanation
Indices: 35411817--35411872 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
35411807 TTGAATTACT
*
35411817 AATTACAACTCTATTC
1 AATTACAGCTCTATTC
35411833 AATTACAGCTCTATTC
1 AATTACAGCTCTATTC
*
35411849 AATTGCAGCTCTATTTC
1 AATTACAGCTCTA-TTC
35411866 -ATTACAG
1 AATTACAG
35411873 TGAACCAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 33 0.92
17 3 0.08
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (16 bp):
AATTACAGCTCTATTC
Found at i:35412796 original size:12 final size:12
Alignment explanation
Indices: 35412767--35412803 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
35412757 CTATTTATAA
35412767 TTTATATATTATT
1 TTTATATA-TATT
*
35412780 ATTATATATATT
1 TTTATATATATT
35412792 TTTATATATATT
1 TTTATATATATT
35412804 ATATATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 15 0.68
13 7 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTTATATATATT
Found at i:35412822 original size:19 final size:19
Alignment explanation
Indices: 35412784--35412878 Score: 75
Period size: 19 Copynumber: 4.8 Consensus size: 19
35412774 ATTATTATTA
* *
35412784 TATATATTTTTATATATAT
1 TATATATTTTTATTTCTAT
35412803 TATATATTTTTATTTCTAT
1 TATATATTTTTATTTCTAT
*
35412822 T-TAGTTATTATTTATTTAGTTAT
1 TATA--TATT-TTTATTT--CTAT
*
35412845 TATTTATTTTTATTTCTAT
1 TATATATTTTTATTTCTAT
* * *
35412864 TTTTTATTTCTATTT
1 TATATATTTTTATTT
35412879 AGTTATTATT
Statistics
Matches: 63, Mismatches: 7, Indels: 12
0.77 0.09 0.15
Matches are distributed among these distances:
18 2 0.03
19 34 0.54
20 4 0.06
21 14 0.22
22 4 0.06
23 4 0.06
24 1 0.02
ACGTcount: A:0.25, C:0.03, G:0.02, T:0.69
Consensus pattern (19 bp):
TATATATTTTTATTTCTAT
Found at i:35412830 original size:48 final size:45
Alignment explanation
Indices: 35412721--35412871 Score: 148
Period size: 48 Copynumber: 3.3 Consensus size: 45
35412711 TGGTTCATTA
* * * *
35412721 TTCTATCTATTATTATATTATCTATTATTATATTATCTATTTATAAT
1 TTCTATTTATTATTATATTAT-TTTTATTATATTATATATTT-TTAT
*
35412768 TTATATATTATTATTATATATATTTTTATATATATTATATATTTTTAT
1 TTCTAT-TTATTATTATAT-TATTTTTAT-TATATTATATATTTTTAT
* *
35412816 TTCTATTTAGTTATTAT-TTA--TTTAGT-TATTATTTATTTTTAT
1 TTCTATTTA-TTATTATATTATTTTTATTATATTATATATTTTTAT
*
35412858 TTCTATTTTTTATT
1 TTCTATTTATTATT
35412872 TCTATTTAGT
Statistics
Matches: 91, Mismatches: 9, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
41 5 0.05
42 23 0.25
43 1 0.01
44 4 0.04
46 2 0.02
47 9 0.10
48 31 0.34
49 16 0.18
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (45 bp):
TTCTATTTATTATTATATTATTTTTATTATATTATATATTTTTAT
Found at i:35412830 original size:51 final size:51
Alignment explanation
Indices: 35412728--35412913 Score: 170
Period size: 55 Copynumber: 3.6 Consensus size: 51
35412718 TTATTCTATC
* * * *
35412728 TATTATTATATTATCTA-TTAT-TATATTATCTATTTATAATT-TATATA-T
1 TATTATTATATTAT-TATTTATATATATTATATATTTTTATTTCTATTTAGT
35412776 TATTATTATATATATT-TTTATATATATTATATATTTTTATTTCTATTTAGT
1 TATTATTATAT-TATTATTTATATATATTATATATTTTTATTTCTATTTAGT
* * *
35412827 TATTATTTATTTAGTTATTATTTATTTTTATT-TCTATTTTTTATTTCTATTTAGT
1 TATTA-TTA--TA-TTATTATTTATATATATTATATA-TTTTTATTTCTATTTAGT
* *
35412882 TATTATT-TAGTTATTATTTATATTTAGTATAT
1 TATTATTATA-TTATTATTTATATATATTATAT
35412914 TTAGAATTTA
Statistics
Matches: 116, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
48 16 0.14
49 20 0.17
50 5 0.04
51 25 0.22
52 5 0.04
54 11 0.09
55 34 0.29
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (51 bp):
TATTATTATATTATTATTTATATATATTATATATTTTTATTTCTATTTAGT
Found at i:35412835 original size:11 final size:10
Alignment explanation
Indices: 35412728--35412902 Score: 104
Period size: 11 Copynumber: 16.3 Consensus size: 10
35412718 TTATTCTATC
35412728 TATTATTATAT
1 TATTATTAT-T
35412739 TATCTATTATT
1 TAT-TATTATT
35412750 ATATTATCTATT
1 -TATTAT-TATT
* *
35412762 TATAATTTATA
1 TATTA-TTATT
35412773 TATTATTATT
1 TATTATTATT
*
35412783 ATATATATTTTT
1 -TAT-TATTATT
*
35412795 ATATATATTATA
1 -TAT-TATTATT
*
35412807 TATTTTTATT
1 TATTATTATT
* *
35412817 T-CTATTTAGT
1 TATTA-TTATT
35412827 TATTATTTATT
1 TATTA-TTATT
35412838 TAGTTATTATT
1 TA-TTATTATT
*
35412849 TATTTTTATT
1 TATTATTATT
* *
35412859 T-CTATTTTT
1 TATTATTATT
35412868 TATT-TCTATT
1 TATTAT-TATT
35412878 TAGTTATTATT
1 TA-TTATTATT
35412889 TAGTTATTATT
1 TA-TTATTATT
35412900 TAT
1 TAT
35412903 ATTTAGTATA
Statistics
Matches: 131, Mismatches: 20, Indels: 27
0.74 0.11 0.15
Matches are distributed among these distances:
9 8 0.06
10 30 0.23
11 59 0.45
12 34 0.26
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (10 bp):
TATTATTATT
Found at i:35412851 original size:7 final size:7
Alignment explanation
Indices: 35412717--35412934 Score: 96
Period size: 7 Copynumber: 29.7 Consensus size: 7
35412707 CGACTGGTTC
35412717 ATTATTCT
1 ATTATT-T
35412725 ATCTA-TT
1 AT-TATTT
35412732 ATTATATT
1 ATTAT-TT
35412740 ATCTA-TT
1 AT-TATTT
35412747 ATTATATT
1 ATTAT-TT
35412755 ATCTATTT
1 AT-TATTT
*
35412763 ATAATTT
1 ATTATTT
35412770 A-TATATT
1 ATTAT-TT
35412777 ATTATTAT
1 ATTATT-T
35412785 ATATATTT
1 AT-TATTT
35412793 -TTATATAT
1 ATTAT-T-T
*
35412801 ATTATAT
1 ATTATTT
35412808 ATT-TTT
1 ATTATTT
*
35412814 ATT-TCT
1 ATTATTT
*
35412820 ATTTAGTT
1 A-TTATTT
35412828 ATTATTT
1 ATTATTT
*
35412835 ATTTAGTT
1 A-TTATTT
35412843 ATTATTT
1 ATTATTT
35412850 ATT-TTT
1 ATTATTT
35412856 ATTTCTATTT
1 A--T-TATTT
*
35412866 TTTATTT
1 ATTATTT
*
35412873 -CTATTT
1 ATTATTT
35412879 AGTTA-TT
1 A-TTATTT
*
35412886 ATTTAGTT
1 A-TTATTT
35412894 ATTATTT
1 ATTATTT
35412901 A-TATTT
1 ATTATTT
35412907 AGTATATTT
1 A-T-TATTT
**
35412916 AGAATTT
1 ATTATTT
35412923 ATTATTT
1 ATTATTT
35412930 ATTAT
1 ATTAT
35412935 AATATTTAAT
Statistics
Matches: 164, Mismatches: 19, Indels: 55
0.69 0.08 0.23
Matches are distributed among these distances:
6 32 0.20
7 69 0.42
8 38 0.23
9 22 0.13
10 3 0.02
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (7 bp):
ATTATTT
Found at i:35412852 original size:15 final size:14
Alignment explanation
Indices: 35412717--35412916 Score: 125
Period size: 15 Copynumber: 14.6 Consensus size: 14
35412707 CGACTGGTTC
*
35412717 ATTATTCTATCTATT
1 ATTATT-TATTTATT
*
35412732 ATTATATTATCTATT
1 ATTAT-TTATTTATT
*
35412747 ATTATATTATCTATTT
1 ATTAT-TTATTTA-TT
* *
35412763 ATAATTTATATATT
1 ATTATTTATTTATT
*
35412777 ATTA-TTATATA-T
1 ATTATTTATTTATT
*
35412789 ATT-TTTATATA-T
1 ATTATTTATTTATT
*
35412801 ATTATATATTT-TT
1 ATTATTTATTTATT
*
35412814 ATT-TCTATTTAGTT
1 ATTATTTATTTA-TT
35412828 ATTATTTATTTAGTT
1 ATTATTTATTTA-TT
35412843 ATTATTTATTT-TT
1 ATTATTTATTTATT
* *
35412856 ATT-TCTATTTTTT
1 ATTATTTATTTATT
*
35412869 ATT-TCTATTTAGTT
1 ATTATTTATTTA-TT
*
35412883 ATTATTTAGTTATT
1 ATTATTTATTTATT
* *
35412897 ATT-TATATTTAGT
1 ATTATTTATTTATT
35412910 A-TATTTA
1 ATTATTTA
35412917 GAATTTATTA
Statistics
Matches: 158, Mismatches: 15, Indels: 26
0.79 0.08 0.13
Matches are distributed among these distances:
12 28 0.18
13 44 0.28
14 20 0.13
15 59 0.37
16 7 0.04
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.65
Consensus pattern (14 bp):
ATTATTTATTTATT
Found at i:35412929 original size:51 final size:50
Alignment explanation
Indices: 35412826--35412934 Score: 121
Period size: 51 Copynumber: 2.1 Consensus size: 50
35412816 TTCTATTTAG
* * * ***
35412826 TTATTATTTATTTAGTTATTATTTATTTTTATTTCTATTTTTTATTTCTAT
1 TTATTA-TTATTTAGTTATTATTTATATTTATGTATATTTAGAATTTCTAT
*
35412877 TTAGTTATTATTTAGTTATTATTTATATTTA-GTATATTTAGAATTTATTAT
1 TTA-TTATTATTTAGTTATTATTTATATTTATGTATATTTAGAATTT-CTAT
35412928 TTATTAT
1 TTATTAT
35412935 AATATTTAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
50 14 0.29
51 32 0.65
52 3 0.06
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (50 bp):
TTATTATTATTTAGTTATTATTTATATTTATGTATATTTAGAATTTCTAT
Found at i:35412930 original size:29 final size:30
Alignment explanation
Indices: 35412808--35412931 Score: 99
Period size: 29 Copynumber: 4.4 Consensus size: 30
35412798 TATATTATAT
*
35412808 ATTT-TTATTTCTATTTAGTTATTATTT--
1 ATTTATTATTTATATTTAGTTATTATTTAG
* **
35412835 ATTTAGTTA--T-TATTTA-TTTTTATTTCT
1 ATTTA-TTATTTATATTTAGTTATTATTTAG
* *
35412862 ATTTTTTATTTCTATTTAGTTATTATTTAG
1 ATTTATTATTTATATTTAGTTATTATTTAG
35412892 --TTATTATTTATATTTAG-TA-TATTTAG
1 ATTTATTATTTATATTTAGTTATTATTTAG
35412918 AATTTATTATTTAT
1 -ATTTATTATTTAT
35412932 TATAATATTT
Statistics
Matches: 79, Mismatches: 7, Indels: 20
0.75 0.07 0.19
Matches are distributed among these distances:
25 8 0.10
26 16 0.20
27 11 0.14
28 16 0.20
29 20 0.25
30 8 0.10
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (30 bp):
ATTTATTATTTATATTTAGTTATTATTTAG
Found at i:35412959 original size:40 final size:40
Alignment explanation
Indices: 35412881--35412959 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
35412871 TTCTATTTAG
**
35412881 TTATTATTTAGTTATTATTTATATTTAGTATATTTAGAAT
1 TTATTATTTAGTTATTATTTATATTTAGTATAAATAGAAT
35412921 TTATTATTTA-TTATAATATTTA-ATTTAAGT-TAAATAGAA
1 TTATTATTTAGTTAT--TATTTATATTT-AGTATAAATAGAA
35412960 AAATTAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
39 4 0.12
40 21 0.62
41 9 0.26
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (40 bp):
TTATTATTTAGTTATTATTTATATTTAGTATAAATAGAAT
Found at i:35412997 original size:33 final size:31
Alignment explanation
Indices: 35412934--35413008 Score: 98
Period size: 33 Copynumber: 2.4 Consensus size: 31
35412924 TTATTTATTA
*
35412934 TAAT-ATTTAATTTAAGTTAAATAGAAAAAT
1 TAATAATTTAATTTAAGTTAAATAAAAAAAT
*
35412964 TAATAATTTAATTTAAGTATAATTAAAATAAAT
1 TAATAATTTAATTTAAGT-TAAATAAAA-AAAT
*
35412997 TATTAATTTAAT
1 TAATAATTTAAT
35413009 AATTTTTCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 4 0.10
31 13 0.33
32 7 0.18
33 15 0.38
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (31 bp):
TAATAATTTAATTTAAGTTAAATAAAAAAAT
Found at i:35421436 original size:24 final size:23
Alignment explanation
Indices: 35421408--35421455 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
35421398 AATTTAAAAA
35421408 ATAAAACATAATATAATATTT-ATT
1 ATAAAA-ATAA-ATAATATTTGATT
*
35421432 ATAAAAATAAATATTATTTGATT
1 ATAAAAATAAATAATATTTGATT
35421455 A
1 A
35421456 AAATAATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 8 0.36
24 6 0.27
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
ATAAAAATAAATAATATTTGATT
Found at i:35421527 original size:42 final size:43
Alignment explanation
Indices: 35421467--35421705 Score: 252
Period size: 43 Copynumber: 5.6 Consensus size: 43
35421457 AATAATTTTT
* * * * *
35421467 TAAAGATTAT-GTTTTTAGCGGCGTTTTTGCTAGAAGCGCCGC
1 TAAAGGTTATGGTCTTTAGCGGCGTTTGTGATAAAAGCGCCGC
* *
35421509 TAAAGGTT-TGTTCTTTAGCGGCGTTTGTGATAAAAGCGTCGC
1 TAAAGGTTATGGTCTTTAGCGGCGTTTGTGATAAAAGCGCCGC
* * * *
35421551 TAAAGGTCATGGTCTATAGCGGCGTTTGTGATAAAAGTGCCAC
1 TAAAGGTTATGGTCTTTAGCGGCGTTTGTGATAAAAGCGCCGC
* ** *
35421594 TAAAGGTCT-TGGTCTTTAGCGGCATTTGTGGGAAAAGTGCCGC
1 TAAAGGT-TATGGTCTTTAGCGGCGTTTGTGATAAAAGCGCCGC
* * **
35421637 TAAAGGTTGTGGTCTTTAGCGGCATTTGTGGGAAAAGCGCCGC
1 TAAAGGTTATGGTCTTTAGCGGCGTTTGTGATAAAAGCGCCGC
* *
35421680 TAAAGATTAT-GTTTTTAGCGGCGTTT
1 TAAAGGTTATGGTCTTTAGCGGCGTTT
35421706 TTTCCGGCAC
Statistics
Matches: 169, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.01
42 55 0.33
43 113 0.67
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.33
Consensus pattern (43 bp):
TAAAGGTTATGGTCTTTAGCGGCGTTTGTGATAAAAGCGCCGC
Found at i:35423029 original size:21 final size:22
Alignment explanation
Indices: 35422988--35423031 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
35422978 TATGATATGC
*
35422988 AATCTTAGAAGATATATTTTGT
1 AATCTTAGAAGATATAATTTGT
*
35423010 AATCTTAG-AGATTTAATTTGT
1 AATCTTAGAAGATATAATTTGT
35423031 A
1 A
35423032 GATATCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (22 bp):
AATCTTAGAAGATATAATTTGT
Found at i:35423265 original size:23 final size:23
Alignment explanation
Indices: 35423221--35423265 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
35423211 TCTTATTTTG
* *
35423221 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
35423244 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
35423266 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:35423611 original size:35 final size:39
Alignment explanation
Indices: 35423549--35423625 Score: 99
Period size: 37 Copynumber: 2.1 Consensus size: 39
35423539 CATACATACG
*
35423549 TTTTATAATATATACATATACGTACATA-TTTTTTA-ATT
1 TTTTATAATATATACATATACG-ACATAGTTTTATATATT
*
35423587 TTTTATAA-ATATATATATAC-ACATAGTTTTATATATT
1 TTTTATAATATATACATATACGACATAGTTTTATATATT
35423624 TT
1 TT
35423626 CTATGTTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
35 5 0.14
36 6 0.17
37 16 0.46
38 8 0.23
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (39 bp):
TTTTATAATATATACATATACGACATAGTTTTATATATT
Found at i:35439846 original size:23 final size:23
Alignment explanation
Indices: 35439819--35439865 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
35439809 AATTTAAAAA
35439819 ATAAACATAATATAA-TATTT-ATT
1 ATAAA-ATAA-ATAATTATTTGATT
35439842 ATAAAATAAATAATTATTTGATT
1 ATAAAATAAATAATTATTTGATT
35439865 A
1 A
35439866 AAATAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.18
22 9 0.41
23 9 0.41
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (23 bp):
ATAAAATAAATAATTATTTGATT
Found at i:35439962 original size:41 final size:42
Alignment explanation
Indices: 35439887--35440085 Score: 187
Period size: 42 Copynumber: 4.7 Consensus size: 42
35439877 AGATTATGTT
* * *
35439887 TTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGATA-AAGCGCCGCTAAAGGTCTTGGTC
* *
35439929 TTTAGCGGCGTTTGTGATAAAGCGTCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGATAAAGCGCCGCTAAAGGTCTTGGTC
* * *
35439971 TATAGCGGCGTTTGTGATAAAAG-TCCACTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGAT-AAAGCGCCGCTAAAGGTCTTGGTC
* *
35440013 TTTAGCGGCATTTGTGGA-AAAGTG-CGC-ATAAGGT-TGTGGTC
1 TTTAGCGGCGTTTGT-GATAAAGCGCCGCTA-AAGGTCT-TGGTC
*
35440054 TTTAGCGGCATTTGTGGGA-AAAGCGCCGCTAA
1 TTTAGCGGCGTTTGT--GATAAAGCGCCGCTAA
35440086 GATGTATTTT
Statistics
Matches: 133, Mismatches: 15, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
40 2 0.02
41 46 0.35
42 74 0.56
43 10 0.08
44 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGATAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:35440068 original size:83 final size:83
Alignment explanation
Indices: 35439915--35440069 Score: 199
Period size: 83 Copynumber: 1.9 Consensus size: 83
35439905 AGAAGCGCCG
* *
35439915 CTAAAGGTTTGTTCTTTAGCGGCGTTTGTGATAAAGCGTCGCTAAAGGTCATGGTCTATAGCGGC
1 CTAAAGGTTTGGTCTTTAGCGGCATTTGTGATAAAGCGTCGCTAAAGGTCATGGTCTATAGCGGC
*
35439980 GTTTGTGATAAAAGTCCA
66 ATTTGTGATAAAAGTCCA
* ** *
35439998 CTAAAGGTCTTGGTCTTTAGCGGCATTTGTGGA-AAAGTG-CGC-ATAAGGTTGTGGTCTTTAGC
1 CTAAAGGT-TTGGTCTTTAGCGGCATTTGT-GATAAAGCGTCGCTA-AAGGTCATGGTCTATAGC
35440060 GGCATTTGTG
63 GGCATTTGTG
35440070 GGAAAAGCGC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
82 1 0.02
83 35 0.56
84 24 0.39
85 2 0.03
ACGTcount: A:0.22, C:0.15, G:0.30, T:0.34
Consensus pattern (83 bp):
CTAAAGGTTTGGTCTTTAGCGGCATTTGTGATAAAGCGTCGCTAAAGGTCATGGTCTATAGCGGC
ATTTGTGATAAAAGTCCA
Found at i:35441354 original size:21 final size:21
Alignment explanation
Indices: 35441329--35441374 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
35441319 GATATGATTT
35441329 AGATATGA-TATGCAATCTTAG
1 AGATAT-ATTATGCAATCTTAG
* *
35441350 AGATATATTTTGTAATCTTAG
1 AGATATATTATGCAATCTTAG
35441371 AGAT
1 AGAT
35441375 TTAATTTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (21 bp):
AGATATATTATGCAATCTTAG
Found at i:35441382 original size:21 final size:21
Alignment explanation
Indices: 35441342--35441384 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
35441332 TATGATATGC
*
35441342 AATCTTAGAGATATATTTTGT
1 AATCTTAGAGATATAATTTGT
*
35441363 AATCTTAGAGATTTAATTTGT
1 AATCTTAGAGATATAATTTGT
35441384 A
1 A
35441385 GATATCCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.47
Consensus pattern (21 bp):
AATCTTAGAGATATAATTTGT
Found at i:35441646 original size:12 final size:12
Alignment explanation
Indices: 35441629--35441655 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
35441619 TTCCCTTTTT
35441629 ATTCATTTTCAA
1 ATTCATTTTCAA
35441641 ATTCATTTTCAA
1 ATTCATTTTCAA
35441653 ATT
1 ATT
35441656 AGTTTACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (12 bp):
ATTCATTTTCAA
Found at i:35448369 original size:56 final size:57
Alignment explanation
Indices: 35448256--35448389 Score: 152
Period size: 56 Copynumber: 2.4 Consensus size: 57
35448246 TTAGTTCATA
* *
35448256 TAATAATAATTATATTAAGAATTTTATAAAATTATATATTATTTATTAAATTATA-TT
1 TAATAATAATTATATTAA-AATATGATAAAATTATATATTATTTATTAAATTATATTT
* * *
35448313 TAATAATAATTATATTAAAATATGGTTAAATTATTTATTATTTTTATTAAA-T-TATTT
1 TAATAATAATTATATTAAAATATGATAAAATTATATATTA--TTTATTAAATTATATTT
35448370 TAAT-ATAATCT-TATTAAAAT
1 TAATAATAAT-TATATTAAAAT
35448390 TAATAACAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
56 33 0.49
57 26 0.38
58 9 0.13
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (57 bp):
TAATAATAATTATATTAAAATATGATAAAATTATATATTATTTATTAAATTATATTT
Found at i:35448575 original size:16 final size:16
Alignment explanation
Indices: 35448554--35448608 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
35448544 TTGAATTACT
*
35448554 AATTACAACTCTATTC
1 AATTACAGCTCTATTC
35448570 AATTACAGCTCTATTC
1 AATTACAGCTCTATTC
*
35448586 AATTGCAGCTCTATTC
1 AATTACAGCTCTATTC
35448602 -ATTACAG
1 AATTACAG
35448609 TGAACCAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
15 6 0.17
16 30 0.83
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (16 bp):
AATTACAGCTCTATTC
Found at i:35449463 original size:12 final size:12
Alignment explanation
Indices: 35449446--35449519 Score: 58
Period size: 12 Copynumber: 5.8 Consensus size: 12
35449436 CGACTGGTTC
*
35449446 ATTATTCTATCT
1 ATTATTATATCT
35449458 ATTATTATATCT
1 ATTATTATATCT
35449470 ATTATTATTTATCT
1 ATTATTA--TATCT
* * *
35449484 ATTTATAATTTAT
1 A-TTATTATATCT
*
35449497 ATTTATTATATAT
1 A-TTATTATATCT
*
35449510 ATTTTTATAT
1 ATTATTATAT
35449520 ATTATATATT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
12 26 0.50
13 15 0.29
14 6 0.12
15 5 0.10
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (12 bp):
ATTATTATATCT
Found at i:35449475 original size:15 final size:15
Alignment explanation
Indices: 35449446--35449526 Score: 64
Period size: 15 Copynumber: 5.5 Consensus size: 15
35449436 CGACTGGTTC
35449446 ATTAT-TCTATCTATT
1 ATTATATCTAT-TATT
35449461 ATTATATCTATTATT
1 ATTATATCTATTATT
*
35449476 ATT-TATCTATTTATA
1 ATTATATCTA-TTATT
*
35449491 ATT-TATAT-TTATT
1 ATTATATCTATTATT
*
35449504 ATATATAT-TTTTATAT
1 AT-TATATCTATTAT-T
35449520 ATTATAT
1 ATTATAT
35449527 ATTTATTTCT
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
13 6 0.11
14 8 0.14
15 35 0.61
16 8 0.14
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTATATCTATTATT
Found at i:35449501 original size:21 final size:21
Alignment explanation
Indices: 35449471--35449649 Score: 79
Period size: 22 Copynumber: 8.3 Consensus size: 21
35449461 ATTATATCTA
*
35449471 TTATTATTTATCTATTTATAAT
1 TTATTATTTATATATTTAT-AT
*
35449493 TTA-TATTTAT-TATATATAT
1 TTATTATTTATATATTTATAT
*
35449512 TTTTATATATTATATATTTAT-T
1 TTAT-TAT-TTATATATTTATAT
* *
35449534 TCTATTTAGTTAT-TATTTATTAG
1 T-TA-TTATTTATATATTTA-TAT
* *
35449557 TTATTATTTATTTTATTTCTAT
1 TTATTATTTA-TATATTTATAT
* * *
35449579 TTTTTA-TT-TCTA-TT-TAG
1 TTATTATTTATATATTTATAT
35449596 TTATTATTTAGTTATTATTTATAT
1 TTATTATTTA--TA-TATTTATAT
*
35449620 TTAGTATATTTAGA-ATTTATTAT
1 TTA-T-TATTTATATATTTA-TAT
35449643 TTATTAT
1 TTATTAT
35449650 AATATTTAAT
Statistics
Matches: 121, Mismatches: 16, Indels: 41
0.68 0.09 0.23
Matches are distributed among these distances:
17 7 0.06
18 4 0.03
19 7 0.06
20 6 0.05
21 28 0.23
22 32 0.26
23 23 0.19
24 7 0.06
25 1 0.01
26 6 0.05
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.65
Consensus pattern (21 bp):
TTATTATTTATATATTTATAT
Found at i:35449520 original size:12 final size:13
Alignment explanation
Indices: 35449459--35449657 Score: 65
Period size: 13 Copynumber: 15.2 Consensus size: 13
35449449 ATTCTATCTA
*
35449459 TTATTATATCTA-
1 TTATTATATATAT
*
35449471 TTATTATTTATCTAT
1 TTATTA--TATATAT
* *
35449486 TTATAATTTATAT
1 TTATTATATATAT
35449499 TTATTATATATAT
1 TTATTATATATAT
35449512 TT-TTATATATTAT
1 TTATTATATA-TAT
* * *
35449525 ATATTTATTTCTAT
1 TTA-TTATATATAT
*
35449539 TTAGT-TAT-TAT
1 TTATTATATATAT
35449550 TTATTAGT-TATTAT
1 TTATTA-TATA-TAT
* *
35449564 TTATTTTATTTCTAT
1 TTA--TTATATATAT
* * *
35449579 TTTTTATTTCTAT
1 TTATTATATATAT
* *
35449592 TTAGTTATTATTTAG
1 TTA-TTA-TATATAT
*
35449607 TTATTATTTATAT
1 TTATTATATATAT
* *
35449620 TTAGTATATTTA-
1 TTATTATATATAT
**
35449632 GAATT-TAT-TAT
1 TTATTATATATAT
35449643 TTATTATA-ATAT
1 TTATTATATATAT
35449655 TTA
1 TTA
35449658 ATTTAAGTTA
Statistics
Matches: 140, Mismatches: 29, Indels: 36
0.68 0.14 0.18
Matches are distributed among these distances:
10 2 0.01
11 13 0.09
12 26 0.19
13 49 0.35
14 23 0.16
15 23 0.16
16 4 0.03
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (13 bp):
TTATTATATATAT
Found at i:35449540 original size:40 final size:39
Alignment explanation
Indices: 35449455--35449628 Score: 133
Period size: 40 Copynumber: 4.4 Consensus size: 39
35449445 CATTATTCTA
* *
35449455 TCTA-TTATTATATCTATTATTATTTATCTATTTA-TAATT
1 TCTATTTATTATATATATTATTA-TTAT-TATTTATTTATT
* * *
35449494 TATATTTATTATATATATTTTTATATATTATATATTTATT
1 TCTATTTATTATATATATTATTAT-TATTATTTATTTATT
35449534 TCTATTTAGTTAT-TAT-TTATTAGTTATTATTTATTTTATT
1 TCTATTTA-TTATATATATTATTA-TTATTATTTA-TTTATT
* * * *
35449574 TCTATTTTTTATTTCTATTTAGTTATTATTTAGTTA-TTATT
1 TCTATTTATTATATATA-TTA-TTATTA-TTATTTATTTATT
* *
35449615 TATATTTAGTATAT
1 TCTATTTATTATAT
35449629 TTAGAATTTA
Statistics
Matches: 109, Mismatches: 15, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
39 26 0.24
40 49 0.45
41 19 0.17
42 6 0.06
43 9 0.08
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.65
Consensus pattern (39 bp):
TCTATTTATTATATATATTATTATTATTATTTATTTATT
Found at i:35449550 original size:11 final size:11
Alignment explanation
Indices: 35449536--35449616 Score: 66
Period size: 11 Copynumber: 7.5 Consensus size: 11
35449526 TATTTATTTC
35449536 TATTTAGTTAT
1 TATTTAGTTAT
35449547 TATTTATTAGTTAT
1 TA--T-TTAGTTAT
35449561 TATTTA-TT-T
1 TATTTAGTTAT
*
35449570 TATTT--CTAT
1 TATTTAGTTAT
*
35449579 TTTTTA-TT-T
1 TATTTAGTTAT
35449588 CTATTTAGTTAT
1 -TATTTAGTTAT
35449600 TATTTAGTTAT
1 TATTTAGTTAT
35449611 TATTTA
1 TATTTA
35449617 TATTTAGTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
8 1 0.02
9 12 0.21
10 8 0.14
11 24 0.41
12 2 0.03
13 1 0.02
14 10 0.17
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (11 bp):
TATTTAGTTAT
Found at i:35449555 original size:7 final size:7
Alignment explanation
Indices: 35449457--35449649 Score: 107
Period size: 7 Copynumber: 26.9 Consensus size: 7
35449447 TTATTCTATC
35449457 TATTATT
1 TATTATT
35449464 ATATCTA-T
1 -TAT-TATT
35449472 TATTATT
1 TATTATT
35449479 TATCTATT
1 TAT-TATT
*
35449487 TATAATT
1 TATTATT
35449494 TA-TATT
1 TATTATT
35449500 TATTATAT
1 TATTAT-T
35449508 ATATT-TT
1 -TATTATT
35449515 TA-TATAT
1 TATTAT-T
35449522 TATATATT
1 TAT-TATT
*
35449530 TATT-TC
1 TATTATT
*
35449536 TATTTAGT
1 TA-TTATT
35449544 TATTATT
1 TATTATT
*
35449551 TATTAGT
1 TATTATT
35449558 TATTATT
1 TATTATT
35449565 TATTTTATT
1 TA--TTATT
*
35449574 T-CTATT
1 TATTATT
*
35449580 TTTTATT
1 TATTATT
*
35449587 T-CTATT
1 TATTATT
35449593 TAGTTA-T
1 TA-TTATT
*
35449600 TATTTAGT
1 TA-TTATT
35449608 TATTATT
1 TATTATT
35449615 TA-TATT
1 TATTATT
35449621 TAGTATATT
1 TA-T-TATT
**
35449630 TAGAATT
1 TATTATT
35449637 TATTATT
1 TATTATT
35449644 TATTAT
1 TATTAT
35449650 AATATTTAAT
Statistics
Matches: 146, Mismatches: 18, Indels: 43
0.71 0.09 0.21
Matches are distributed among these distances:
5 1 0.01
6 29 0.20
7 71 0.49
8 24 0.16
9 21 0.14
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (7 bp):
TATTATT
Found at i:35449630 original size:50 final size:52
Alignment explanation
Indices: 35449528--35449630 Score: 149
Period size: 50 Copynumber: 2.0 Consensus size: 52
35449518 ATATTATATA
* *
35449528 TTTATTTCTATTTAGTTATTATTTATTAGTTATTATTTATTTTATTTCTATTT
1 TTTATTTCTATTTAGTTATTA-TTATTAGTTATTATTTATTTTATGTATATTT
35449581 TTTATTTCTATTTAGTTATTA-T-TTAGTTATTATTTATATTTA-GTATATTT
1 TTTATTTCTATTTAGTTATTATTATTAGTTATTATTTAT-TTTATGTATATTT
35449631 AGAATTTATT
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
50 21 0.45
51 5 0.11
53 21 0.45
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (52 bp):
TTTATTTCTATTTAGTTATTATTATTAGTTATTATTTATTTTATGTATATTT
Found at i:35449674 original size:40 final size:40
Alignment explanation
Indices: 35449596--35449674 Score: 92
Period size: 40 Copynumber: 2.0 Consensus size: 40
35449586 TTCTATTTAG
**
35449596 TTATTATTTAGTTATTATTTATATTTAGTATATTTAGAAT
1 TTATTATTTAGTTATTATTTATATTTAGTATAAATAGAAT
35449636 TTATTATTTA-TTATAATATTTA-ATTTAAGT-TAAATAGAA
1 TTATTATTTAGTTAT--TATTTATATTT-AGTATAAATAGAA
35449675 AAATTAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
39 4 0.12
40 21 0.62
41 9 0.26
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (40 bp):
TTATTATTTAGTTATTATTTATATTTAGTATAAATAGAAT
Found at i:35449712 original size:33 final size:31
Alignment explanation
Indices: 35449649--35449723 Score: 98
Period size: 33 Copynumber: 2.4 Consensus size: 31
35449639 TTATTTATTA
*
35449649 TAAT-ATTTAATTTAAGTTAAATAGAAAAAT
1 TAATAATTTAATTTAAGTTAAATAAAAAAAT
*
35449679 TAATAATTTAATTTAAGTATAATTAAAATAAAT
1 TAATAATTTAATTTAAGT-TAAATAAAA-AAAT
*
35449712 TATTAATTTAAT
1 TAATAATTTAAT
35449724 AATTTTTCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 4 0.10
31 13 0.33
32 7 0.18
33 15 0.38
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (31 bp):
TAATAATTTAATTTAAGTTAAATAAAAAAAT
Found at i:35453572 original size:19 final size:19
Alignment explanation
Indices: 35453548--35453584 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
35453538 TTAATGTGCG
*
35453548 AATATATGTATATGTGTGT
1 AATATATATATATGTGTGT
35453567 AATATATATATATGTGTG
1 AATATATATATATGTGTG
35453585 GATCGAACAA
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:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (19 bp):
AATATATATATATGTGTGT
Found at i:35453858 original size:41 final size:41
Alignment explanation
Indices: 35453796--35454053 Score: 408
Period size: 41 Copynumber: 6.3 Consensus size: 41
35453786 GTTTGGAATT
* *
35453796 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
35453837 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* * *
35453878 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
35453919 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* * *
35453960 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
35454001 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
35454042 GGTGATCCGAAT
1 GGTGATCTGAAT
35454054 ATGATGAATT
Statistics
Matches: 197, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 197 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.22
Consensus pattern (41 bp):
GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
Found at i:35453933 original size:82 final size:82
Alignment explanation
Indices: 35453796--35454047 Score: 495
Period size: 82 Copynumber: 3.1 Consensus size: 82
35453786 GTTTGGAATT
*
35453796 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCCGGTGATCTGAATCAGGCTATAAGC
35453861 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
35453878 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCCGGTGATCTGAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCCGGTGATCTGAATCAGGCTATAAGC
35453943 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
35453960 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCCGGTGATCTGAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCCGGTGATCTGAATCAGGCTATAAGC
35454025 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
35454042 GGTGAT
1 GGTGAT
35454048 CCGAATATGA
Statistics
Matches: 169, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 169 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (82 bp):
GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCCGGTGATCTGAATCAGGCTATAAGC
CTAGCAGGCTAAGTGCC
Found at i:35461281 original size:19 final size:19
Alignment explanation
Indices: 35461257--35461293 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
35461247 TTAATGTGCG
*
35461257 AATATATGTATATGTGTGT
1 AATATATATATATGTGTGT
35461276 AATATATATATATGTGTG
1 AATATATATATATGTGTG
35461294 GATCGAACAA
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:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (19 bp):
AATATATATATATGTGTGT
Found at i:35461567 original size:41 final size:41
Alignment explanation
Indices: 35461505--35461762 Score: 408
Period size: 41 Copynumber: 6.3 Consensus size: 41
35461495 GTTTGGAATT
* *
35461505 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
35461546 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* * *
35461587 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
35461628 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* * *
35461669 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
35461710 GGTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
35461751 GGTGATCCGAAT
1 GGTGATCTGAAT
35461763 ATGATGAATT
Statistics
Matches: 197, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 197 1.00
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.22
Consensus pattern (41 bp):
GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
Found at i:35461642 original size:82 final size:82
Alignment explanation
Indices: 35461505--35461756 Score: 495
Period size: 82 Copynumber: 3.1 Consensus size: 82
35461495 GTTTGGAATT
*
35461505 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCCGGTGATCTGAATCAGGCTATAAGC
35461570 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
35461587 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCCGGTGATCTGAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCCGGTGATCTGAATCAGGCTATAAGC
35461652 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
35461669 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCCGGTGATCTGAATCAGGCTATAAGC
1 GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCCGGTGATCTGAATCAGGCTATAAGC
35461734 CTAGCAGGCTAAGTGCC
66 CTAGCAGGCTAAGTGCC
35461751 GGTGAT
1 GGTGAT
35461757 CCGAATATGA
Statistics
Matches: 169, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 169 1.00
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (82 bp):
GGTGATATGAATCAGGTTATAAACCTAGCAGGCTAAGCGCCGGTGATCTGAATCAGGCTATAAGC
CTAGCAGGCTAAGTGCC
Found at i:35468028 original size:48 final size:48
Alignment explanation
Indices: 35467965--35468064 Score: 128
Period size: 48 Copynumber: 2.1 Consensus size: 48
35467955 CCTACCTACT
* * * * **
35467965 ATTCGGCCCATTATTCTGTCCACTAACAGGCCCAAGAGACTGGCCTGC
1 ATTCAGCCCACTATTCTATCCACTAACAGGCCCAAGAAACTAACCTGC
**
35468013 ATTCAGCCCACTATTCTATCCACTAGTAGGCCCAAGAAACTAACCTGC
1 ATTCAGCCCACTATTCTATCCACTAACAGGCCCAAGAAACTAACCTGC
35468061 ATTC
1 ATTC
35468065 TGTCTAAGGT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.27, C:0.33, G:0.16, T:0.24
Consensus pattern (48 bp):
ATTCAGCCCACTATTCTATCCACTAACAGGCCCAAGAAACTAACCTGC
Found at i:35471464 original size:18 final size:18
Alignment explanation
Indices: 35471411--35471464 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
35471401 AAATAGTGTC
* *
35471411 ATTCATTTCCAAAACATT
1 ATTCATTTACAAAACGTT
*
35471429 ATTCATTTACAAATCGTT
1 ATTCATTTACAAAACGTT
35471447 ATTCAATTT-CAAAACGTT
1 ATTC-ATTTACAAAACGTT
35471465 TTCTTATTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 27 0.87
19 4 0.13
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.41
Consensus pattern (18 bp):
ATTCATTTACAAAACGTT
Found at i:35475167 original size:69 final size:70
Alignment explanation
Indices: 35475085--35475227 Score: 261
Period size: 70 Copynumber: 2.1 Consensus size: 70
35475075 ATATTAAATC
**
35475085 ACAATTTCATACAATTT-TTCTTGTAAATTAAACGATGTTAAATATATAATTAGGGTTTGGCTGA
1 ACAATTTCATACAATTTCTTCTCCTAAATTAAACGATGTTAAATATATAATTAGGGTTTGGCTGA
35475149 TAAAA
66 TAAAA
35475154 ACAATTTCATACAATTTCTTCTCCTAAATTAAACGATGTTAAATATATAATTAGGGTTTGGCTGA
1 ACAATTTCATACAATTTCTTCTCCTAAATTAAACGATGTTAAATATATAATTAGGGTTTGGCTGA
35475219 TAAAA
66 TAAAA
35475224 ACAA
1 ACAA
35475228 CCGTACCGTA
Statistics
Matches: 71, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
69 17 0.24
70 54 0.76
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (70 bp):
ACAATTTCATACAATTTCTTCTCCTAAATTAAACGATGTTAAATATATAATTAGGGTTTGGCTGA
TAAAA
Found at i:35486910 original size:249 final size:248
Alignment explanation
Indices: 35486472--35486961 Score: 833
Period size: 249 Copynumber: 2.0 Consensus size: 248
35486462 TCTTCTCATG
35486472 GTAAGCATTTCATTGACATGGATTGCAGCATATGAACTTTGTTTGATTCGGTATTCACTCGTAGT
1 GTAAGCATTTCATTGACATGGATTGCAGCATATGAACTTTGTTTGATTCGGTATTCACTCGTAGT
* *
35486537 ATGCGATATCATTTTCCTAATTTTAAACCTGTCTTTAGTAGATGTTTTTGCCTACTTGATTCATA
66 ATGCGATATCATTTTCCTAATTCTAAACCTGTCTTTAGTAGATGTTTCTGCCTACTTGATTCATA
35486602 AATACATAAAATCTTGTTCTTGGTTCTTCATTGAGTATTTTGTCCCAGAAAGAATTTTAGATAGC
131 AATACATAAAATCTTGTTCTTGGTTCTTCATTGAGTATTTTGTCCCAGAAAGAATTTTAGATAGC
*
35486667 CGATTGAAG-TTTTCTGGGAAATAAGGTGTGAGACAAAAAAAGTATCATGGAGGT
196 CGATGGAAGTTTTTC-GGGAAATAAGGTGTGAGAC-AAAAAAGTATCATGGAGGT
*
35486721 GTAAGCATTTCATTGACATGGATTGCAGCATATGAACTTTGTTTGATTCGGTATTCAAC-CGTGG
1 GTAAGCATTTCATTGACATGGATTGCAGCATATGAACTTTGTTTGATTCGGTATTC-ACTCGTAG
35486785 TATGCGATATCATTTTCCTAATTCTAAACC-GCTCTTTAGTAGATGTTTCTGCCTACTTGATTCA
65 TATGCGATATCATTTTCCTAATTCTAAACCTG-TCTTTAGTAGATGTTTCTGCCTACTTGATTCA
* * * *
35486849 TAAATACATAAAATCTTGTTTTTGGTTCTTCATTGTGTATTTTGTCCCGGTAAGAATTTTAGATA
129 TAAATACATAAAATCTTGTTCTTGGTTCTTCATTGAGTATTTTGTCCCAGAAAGAATTTTAGATA
* *
35486914 GCTGATGGAAGTTTTTCGGGAAATAAGGTGTGAGACGAAAAAGTATCA
194 GCCGATGGAAGTTTTTCGGGAAATAAGGTGTGAGACAAAAAAGTATCA
35486962 CGGAAGCCCT
Statistics
Matches: 228, Mismatches: 10, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
248 12 0.05
249 209 0.92
250 7 0.03
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (248 bp):
GTAAGCATTTCATTGACATGGATTGCAGCATATGAACTTTGTTTGATTCGGTATTCACTCGTAGT
ATGCGATATCATTTTCCTAATTCTAAACCTGTCTTTAGTAGATGTTTCTGCCTACTTGATTCATA
AATACATAAAATCTTGTTCTTGGTTCTTCATTGAGTATTTTGTCCCAGAAAGAATTTTAGATAGC
CGATGGAAGTTTTTCGGGAAATAAGGTGTGAGACAAAAAAGTATCATGGAGGT
Found at i:35499253 original size:40 final size:40
Alignment explanation
Indices: 35499195--35499401 Score: 270
Period size: 40 Copynumber: 5.2 Consensus size: 40
35499185 AAATACTTTT
* * * *
35499195 TGAATGCACAAACGTGCCCCTGTTTGTACTTTGGTACCCT
1 TGAATGCACATACATGCCCCTGTTTGTACTTTGATACCCC
* ** *
35499235 TAAATGCACATACATGCCCCTGTTTGTACTTTTTTATCCC
1 TGAATGCACATACATGCCCCTGTTTGTACTTTGATACCCC
* *
35499275 TGAATGCACATACGTGCCCCTGTTTGTACTTCGATACCCC
1 TGAATGCACATACATGCCCCTGTTTGTACTTTGATACCCC
*
35499315 TGAATGCACATACATGCCCCTGTTTGTACTTTGATGCCCC
1 TGAATGCACATACATGCCCCTGTTTGTACTTTGATACCCC
** **
35499355 TGAATGCACATACATGCCATTGTTTGTACTTTGGCACCCCC
1 TGAATGCACATACATGCCCCTGTTTGTACTTTGATA-CCCC
35499396 TGAATG
1 TGAATG
35499402 TTTATAATGT
Statistics
Matches: 145, Mismatches: 21, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
40 135 0.93
41 10 0.07
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (40 bp):
TGAATGCACATACATGCCCCTGTTTGTACTTTGATACCCC
Found at i:35499295 original size:20 final size:20
Alignment explanation
Indices: 35499272--35499372 Score: 62
Period size: 20 Copynumber: 5.0 Consensus size: 20
35499262 ACTTTTTTAT
35499272 CCCTGAATGCACATACGTGC
1 CCCTGAATGCACATACGTGC
** * * *
35499292 CCCTGTTTGTAC-TTCGATAC
1 CCCTGAATGCACATACG-TGC
*
35499312 CCCTGAATGCACATACATGC
1 CCCTGAATGCACATACGTGC
** * **
35499332 CCCTGTTTGTAC-TTTGATGC
1 CCCTGAATGCACATACG-TGC
*
35499352 CCCTGAATGCACATACATGC
1 CCCTGAATGCACATACGTGC
35499372 C
1 C
35499373 ATTGTTTGTA
Statistics
Matches: 54, Mismatches: 23, Indels: 8
0.64 0.27 0.09
Matches are distributed among these distances:
19 4 0.07
20 47 0.87
21 3 0.06
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.29
Consensus pattern (20 bp):
CCCTGAATGCACATACGTGC
Found at i:35502150 original size:24 final size:24
Alignment explanation
Indices: 35502108--35502160 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
35502098 GCTAGGATAA
* *
35502108 TTAAAATATTATCTGTTAACATAT
1 TTAAAATATTATCTATTAACACAT
*
35502132 TTAAAATATTAT-TAATTAATACAT
1 TTAAAATATTATCT-ATTAACACAT
35502156 TTAAA
1 TTAAA
35502161 TGTTACGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (24 bp):
TTAAAATATTATCTATTAACACAT
Found at i:35503261 original size:69 final size:69
Alignment explanation
Indices: 35503181--35503321 Score: 255
Period size: 69 Copynumber: 2.0 Consensus size: 69
35503171 CAGTATCATA
35503181 TTAACATCATACTTCAAGCAAAAGAACTTTCTCAGGTCAAATTAATGTGTTTGAGCATATATATA
1 TTAACATCATACTTCAAGCAAAAGAACTTTCTCAGGTCAAATTAATGTGTTTGAGCATATATATA
35503246 CATC
66 CATC
* * *
35503250 TTAACATCATACTTCAAGCAAAAGATCTTTCTCAGGTCAACTTAATTTGTTTGAGCATATATATA
1 TTAACATCATACTTCAAGCAAAAGAACTTTCTCAGGTCAAATTAATGTGTTTGAGCATATATATA
35503315 CATC
66 CATC
35503319 TTA
1 TTA
35503322 TAGGAAACAA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (69 bp):
TTAACATCATACTTCAAGCAAAAGAACTTTCTCAGGTCAAATTAATGTGTTTGAGCATATATATA
CATC
Found at i:35513421 original size:3 final size:3
Alignment explanation
Indices: 35513413--35513439 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
35513403 TGAAGTTGAT
35513413 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
35513440 AATGGCCGAG
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:35513963 original size:21 final size:22
Alignment explanation
Indices: 35513937--35513979 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
35513927 CAGTTCTTTA
35513937 TTGCTT-AAAAAAAGTACTTCT
1 TTGCTTAAAAAAAAGTACTTCT
35513958 TTGCTTAAAAAAAAGTACTTCT
1 TTGCTTAAAAAAAAGTACTTCT
35513980 GACTCTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (22 bp):
TTGCTTAAAAAAAAGTACTTCT
Found at i:35514564 original size:13 final size:13
Alignment explanation
Indices: 35514548--35514598 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
35514538 TTTAAACTAA
35514548 ACTTTTCAAAATC
1 ACTTTTCAAAATC
* *
35514561 ACTTTTTTC-ATAGC
1 AC--TTTTCAAAATC
35514575 ACTTTTCAAAATC
1 ACTTTTCAAAATC
35514588 ACTTTTCAAAA
1 ACTTTTCAAAA
35514599 GCAATGAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
12 5 0.16
13 16 0.52
14 5 0.16
15 5 0.16
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.41
Consensus pattern (13 bp):
ACTTTTCAAAATC
Found at i:35519020 original size:25 final size:25
Alignment explanation
Indices: 35518979--35519056 Score: 104
Period size: 25 Copynumber: 3.2 Consensus size: 25
35518969 ACACCCAGCC
*
35518979 GTGTCCCA-GCCCATGTGCCAGGCT
1 GTGTCACACGCCCATGTGCCAGGCT
*
35519003 GTGTCACACGCCCGTGTGCCAGGCT
1 GTGTCACACGCCCATGTGCCAGGCT
* * *
35519028 ATGTCACACGCCCATGTGTCAGGCC
1 GTGTCACACGCCCATGTGCCAGGCT
35519053 GTGT
1 GTGT
35519057 AACTCTCGAA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
24 7 0.15
25 39 0.85
ACGTcount: A:0.14, C:0.35, G:0.29, T:0.22
Consensus pattern (25 bp):
GTGTCACACGCCCATGTGCCAGGCT
Found at i:35522214 original size:99 final size:98
Alignment explanation
Indices: 35522035--35522213 Score: 272
Period size: 99 Copynumber: 1.8 Consensus size: 98
35522025 TCTTAAAACC
* *
35522035 GAATGTATATTCACTATAAACATGAATAGTTGAATGCATATATACATATATGCTTAATAAATATT
1 GAATGTATATTCACTATAAACATGAATAGTCGAATGCATATATACA-ATATGCTTAACAAATATT
*
35522100 AGCTCCAAATGTATATACACTTTGAACATGAACT
65 AGCACCAAATGTATATACACTTTGAACATGAACT
* *
35522134 GAATGTATATTTACTATAAACGTGAATAGTCGAATGCATATATAC-ATATGCTTAACAAATATTA
1 GAATGTATATTCACTATAAACATGAATAGTCGAATGCATATATACAATATGCTTAACAAATATTA
*
35522198 -CAACCAATTGTATATA
66 GC-ACCAAATGTATATA
35522214 TGTATTTATC
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
96 1 0.01
97 30 0.41
99 42 0.58
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (98 bp):
GAATGTATATTCACTATAAACATGAATAGTCGAATGCATATATACAATATGCTTAACAAATATTA
GCACCAAATGTATATACACTTTGAACATGAACT
Found at i:35522268 original size:35 final size:35
Alignment explanation
Indices: 35522201--35522269 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 35
35522191 AATATTACAA
* * * *
35522201 CCAATTGTATATATGTATTTATCACCTGCATATAT
1 CCAATTGCATATATGTACTTAACACCTACATATAT
**
35522236 CCAATTGCATATATGTACTTAACATGTACATATA
1 CCAATTGCATATATGTACTTAACACCTACATATA
35522270 ACTAAACCTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (35 bp):
CCAATTGCATATATGTACTTAACACCTACATATAT
Found at i:35522688 original size:41 final size:41
Alignment explanation
Indices: 35522643--35522794 Score: 234
Period size: 41 Copynumber: 3.7 Consensus size: 41
35522633 TTCAGTACAT
* *
35522643 CGGCAATT-AGCCTACTAGACGTAAAGTCTGAAATATTTCAC
1 CGGC-ATTAAGCCTGCTAGACGTAAAGTCTGAAACATTTCAC
35522684 CGGCATTAAGCCTGCTAGACGTAAAGTCTGAAACATTTCAC
1 CGGCATTAAGCCTGCTAGACGTAAAGTCTGAAACATTTCAC
* * *
35522725 CAGCATTAAGCTTGCTAGACGTAAAGTCTAAAACATTTCAC
1 CGGCATTAAGCCTGCTAGACGTAAAGTCTGAAACATTTCAC
*
35522766 CGGCATCAAGCCTGCTAGACGTAAAGTCT
1 CGGCATTAAGCCTGCTAGACGTAAAGTCT
35522795 ATAAAATCCA
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
40 3 0.03
41 99 0.97
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (41 bp):
CGGCATTAAGCCTGCTAGACGTAAAGTCTGAAACATTTCAC
Found at i:35530954 original size:40 final size:40
Alignment explanation
Indices: 35530668--35531008 Score: 357
Period size: 40 Copynumber: 8.5 Consensus size: 40
35530658 AGCATGATTA
* * * * *
35530668 CTCTTCGGGACCTAGCCCAGATATAACACCAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
* ** * *
35530708 CTCTTTGGGGTTTAGCACGGATATATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
*
35530748 CTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
* * * *
35530788 CTCCTCGAGACTTAGCCCGGATATATCACTAGCATGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
* * *
35530828 CTCTTCGGAACTTAGCCTGGATACATCACTAGCATGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
* *
35530868 CTCTTCGGGACTTAGCCCGGATACATCGCTAGCATGAATG
1 CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
** * * *
35530908 CTCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACCAATG
1 CTCTTCGGGACTTAGCCCGGATACA-TCACTAGCACGAATG
* ** *
35530949 C-CTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC-AAAG
1 CTCTTCGGGA-CTTAGCCCGGATA-CATCAC-TAGCACGAATG
35530989 C-CTTCGGGACTTAGCCCGGA
1 CTCTTCGGGACTTAGCCCGGA
35531009 CATCATTTGA
Statistics
Matches: 254, Mismatches: 42, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
39 3 0.01
40 232 0.91
41 19 0.07
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATG
Found at i:35531353 original size:29 final size:29
Alignment explanation
Indices: 35531314--35531392 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
35531304 CTTAATAATC
*
35531314 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
35531344 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
35531373 AGCCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
35531393 ATCTCACAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 38 0.86
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:35531512 original size:43 final size:43
Alignment explanation
Indices: 35531374--35531603 Score: 437
Period size: 43 Copynumber: 5.4 Consensus size: 43
35531364 TGCATTTCAA
*
35531374 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTCTT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
35531417 GCCCGCA-ACTTAGTGCCAATCTCACAACCGTGAA-ACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
35531458 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
35531501 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
35531544 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
1 GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
35531587 GCCCGCACACTTAGTGC
1 GCCCGCACACTTAGTGC
35531604 TGAAAACCAA
Statistics
Matches: 184, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
41 13 0.07
42 54 0.29
43 117 0.64
ACGTcount: A:0.27, C:0.35, G:0.15, T:0.23
Consensus pattern (43 bp):
GCCCGCACACTTAGTGCCAATCTCACAACCGTGAACACTTATT
Found at i:35533515 original size:37 final size:37
Alignment explanation
Indices: 35533465--35533543 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
35533455 TTATTACGAA
* * *
35533465 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
35533502 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
35533539 GTCTT
1 GTCTT
35533544 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:35533697 original size:20 final size:21
Alignment explanation
Indices: 35533661--35533701 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
35533651 GCCCTTCGGG
35533661 ACTTATCACATTCATCACATC
1 ACTTATCACATTCATCACATC
35533682 ACTTATCACA-TCATCACATC
1 ACTTATCACATTCATCACATC
35533702 GGCCATTAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (21 bp):
ACTTATCACATTCATCACATC
Found at i:35533743 original size:47 final size:47
Alignment explanation
Indices: 35533681--35534041 Score: 681
Period size: 47 Copynumber: 7.7 Consensus size: 47
35533671 TTCATCACAT
*
35533681 CACTTATCACA-TCATCACATCGGCCATTAGGCCCTATCACATATATA
1 CACTT-TCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
35533728 CACTTTCACATTCATCACATCGGCCATTAGGCC-TATCACATATATA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
35533774 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
35533821 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
35533868 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
*
35533915 CACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
35533962 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
1 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
35534009 CACTTTCACATTCATCACATCGGCCATTAGGCC
1 CACTTTCACATTCATCACATCGGCCATTAGGCC
35534042 ATACTATCAT
Statistics
Matches: 310, Mismatches: 2, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
46 51 0.16
47 259 0.84
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (47 bp):
CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
Found at i:35539268 original size:46 final size:45
Alignment explanation
Indices: 35539200--35539324 Score: 169
Period size: 46 Copynumber: 2.7 Consensus size: 45
35539190 GCTATAACTC
*
35539200 AGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCACAACAA
1 AGTATGGTTTTCTT-ACTGAAATACCATACCTACTTTTCACAACAA
**
35539246 AGTATGGTTTTCGTTACTGAAATACCATACCTACTTTTCACAACTC
1 AGTATGGTTTTC-TTACTGAAATACCATACCTACTTTTCACAACAA
* * *
35539292 AGCATGGTTTTCTTTACTAAAATATCATACCTA
1 AGTATGGTTTTC-TTACTGAAATACCATACCTA
35539325 TGTTCCACAC
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
46 69 0.97
47 2 0.03
ACGTcount: A:0.31, C:0.23, G:0.10, T:0.36
Consensus pattern (45 bp):
AGTATGGTTTTCTTACTGAAATACCATACCTACTTTTCACAACAA
Found at i:35540437 original size:10 final size:10
Alignment explanation
Indices: 35540424--35540460 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
35540414 ATGACACTCC
35540424 ATAAATATTT
1 ATAAATATTT
35540434 ATAAAAATATTT
1 AT--AAATATTT
35540446 ATAAATATTT
1 ATAAATATTT
35540456 ATAAA
1 ATAAA
35540461 AATATTTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 15 0.60
12 10 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
ATAAATATTT
Found at i:35540443 original size:12 final size:12
Alignment explanation
Indices: 35540426--35540469 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
35540416 GACACTCCAT
35540426 AAATATTTATAA
1 AAATATTTATAA
35540438 AAATATTTAT--
1 AAATATTTATAA
35540448 AAATATTTATAA
1 AAATATTTATAA
35540460 AAATATTTAT
1 AAATATTTAT
35540470 GGCTCAGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.33
12 20 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
AAATATTTATAA
Found at i:35540452 original size:22 final size:22
Alignment explanation
Indices: 35540424--35540469 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
35540414 ATGACACTCC
35540424 ATAAATATTTATAAAAATATTT
1 ATAAATATTTATAAAAATATTT
35540446 ATAAATATTTATAAAAATATTT
1 ATAAATATTTATAAAAATATTT
35540468 AT
1 AT
35540470 GGCTCAGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATAAATATTTATAAAAATATTT
Found at i:35541869 original size:40 final size:41
Alignment explanation
Indices: 35541825--35541970 Score: 168
Period size: 41 Copynumber: 3.6 Consensus size: 41
35541815 AGGGGCACCA
* * *
35541825 AAGTACAAAAAGGGGCACGTATGTGCAATTTAGAAGTA-CG
1 AAGTACAAACAGGGGCACGTATGTGCAATTCAGAGGTACCG
* * * **
35541865 AAGTACAAACAGGGGCATGTCTGTGCAATTCAGGGGTATTG
1 AAGTACAAACAGGGGCACGTATGTGCAATTCAGAGGTACCG
** * *
35541906 AAGTACAAACAGGGGCATTTACGTACAATTCAGAGGTACCG
1 AAGTACAAACAGGGGCACGTATGTGCAATTCAGAGGTACCG
*
35541947 AAGTACAAACAGAGGCACGTATGT
1 AAGTACAAACAGGGGCACGTATGT
35541971 AAAACTCATA
Statistics
Matches: 87, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
40 32 0.37
41 55 0.63
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.21
Consensus pattern (41 bp):
AAGTACAAACAGGGGCACGTATGTGCAATTCAGAGGTACCG
Found at i:35541920 original size:20 final size:20
Alignment explanation
Indices: 35541895--35541958 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
35541885 CTGTGCAATT
35541895 CAGGGGTATTGAAGTACAAA
1 CAGGGGTATTGAAGTACAAA
* * * *
35541915 CAGGGGCATTTACGTACAATT
1 CAGGGGTATTGAAGTACAA-A
* **
35541936 CAGAGGTACCGAAGTACAAA
1 CAGGGGTATTGAAGTACAAA
35541956 CAG
1 CAG
35541959 AGGCACGTAT
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
20 19 0.59
21 13 0.41
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.19
Consensus pattern (20 bp):
CAGGGGTATTGAAGTACAAA
Found at i:35547038 original size:18 final size:17
Alignment explanation
Indices: 35547015--35547053 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
35547005 TGCTTTAATT
*
35547015 TTTTATTTGTTTATTTAC
1 TTTTATTTGTTGATTT-C
35547033 TTTTATTTGTTGATTTC
1 TTTTATTTGTTGATTTC
35547050 TTTT
1 TTTT
35547054 CATTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (17 bp):
TTTTATTTGTTGATTTC
Found at i:35547381 original size:109 final size:109
Alignment explanation
Indices: 35547168--35547480 Score: 440
Period size: 110 Copynumber: 2.9 Consensus size: 109
35547158 AACGAAAATT
*
35547168 TTTTCAAATAAGGCAATGTTTTGCG-TTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
1 TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
* * *
35547232 CGATTTCTCTCGTTCAACCAAATGACTTAATATCCTTTTC-AAAA
66 CGATTTTTCTCGTTCAACCAAATG-CTAAATAGCCTTTTCAAAAA
35547276 TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
1 TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
35547341 CGATTTTTTCTCGTTCAACCAAATAGCTAAATAGCC-TTTCAAAAA
66 CGA-TTTTTCTCGTTCAACCAAAT-GCTAAATAGCCTTTTCAAAAA
* * * * * *
35547386 TTTCAAAATAAGGCAATATTTTGCATTTGGGAAATTCGAG-GAACGTGCCCTAAGGTGCTGGGTT
1 TTTTAAAATAAGGCAATGTTTTGCGTTT-GGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
*
35547450 TCGA--TTTCTCGTTTAACCAAATTGCTAAATA
65 TCGATTTTTCTCGTTCAACCAAA-TGCTAAATA
35547481 TCCTCTTGAA
Statistics
Matches: 188, Mismatches: 11, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
107 24 0.13
108 25 0.13
109 46 0.24
110 81 0.43
111 12 0.06
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (109 bp):
TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
CGATTTTTCTCGTTCAACCAAATGCTAAATAGCCTTTTCAAAAA
Found at i:35550889 original size:8 final size:8
Alignment explanation
Indices: 35550873--35550912 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
35550863 GACTCGAAAG
35550873 AAAAAT-A
1 AAAAATCA
*
35550880 AAAAATTAA
1 AAAAA-TCA
35550889 AAAAATCA
1 AAAAATCA
35550897 AAAAATCA
1 AAAAATCA
35550905 AAAAATCA
1 AAAAATCA
35550913 TAAGAGAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
7 5 0.17
8 19 0.63
9 6 0.20
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.15
Consensus pattern (8 bp):
AAAAATCA
Found at i:35550912 original size:16 final size:17
Alignment explanation
Indices: 35550873--35550909 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
35550863 GACTCGAAAG
35550873 AAAAAT-AAAAAATTAA
1 AAAAATCAAAAAATTAA
*
35550889 AAAAATCAAAAAATCAA
1 AAAAATCAAAAAATTAA
35550906 AAAA
1 AAAA
35550910 TCATAAGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (17 bp):
AAAAATCAAAAAATTAA
Found at i:35550926 original size:6 final size:6
Alignment explanation
Indices: 35550917--35550955 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
35550907 AAATCATAAG
35550917 AGAAAA AGAAAGA AGAAAA A-AGAAA AGAAAA AGAAAA AG
1 AGAAAA AGAAA-A AGAAAA AGA-AAA AGAAAA AGAAAA AG
35550956 GAGAAGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 1 0.03
6 22 0.73
7 7 0.23
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:35552141 original size:43 final size:44
Alignment explanation
Indices: 35552071--35552186 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 44
35552061 CCCAAAAAGG
* * * *
35552071 GCGGCTCAAATTTTGAAACAAAATGGGGCACGG-AGTGATTAGA
1 GCGGCTCAAATTTTGGATCAAATTGGGGCACGGTAGTGATCAGA
* * *
35552114 GCGGCTTAAATTTTGGATCAAATTGGGGCATGGTGGTGATCAGA
1 GCGGCTCAAATTTTGGATCAAATTGGGGCACGGTAGTGATCAGA
* * *
35552158 GCAGCTCAAATTTT-GATCAGATCGGGGCA
1 GCGGCTCAAATTTTGGATCAAATTGGGGCA
35552187 TATGATGATC
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 41 0.67
44 20 0.33
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (44 bp):
GCGGCTCAAATTTTGGATCAAATTGGGGCACGGTAGTGATCAGA
Found at i:35553594 original size:100 final size:100
Alignment explanation
Indices: 35553311--35554444 Score: 1214
Period size: 100 Copynumber: 11.4 Consensus size: 100
35553301 AAACCATAGT
* * *
35553311 TTGCAATTC-AAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGTGGAGCAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTATTTCCCAGGCGATGCAGCGGAACAGA
35553375 TTGAAGCTACAACGGCGAATCTCACTTCCCTGACA
66 TTGAAGCTACAACGGCGAATCTCACTTCCCTGACA
* * * * *
35553410 TTGCAATTC-AAATATTGAAGCCACAACAGTGAATCTTA-CTCTCAGGCGATGCAGCAGAACAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTATTTCCCAGGCGATGCAGCGGAACAGA
*
35553473 TTGAAGCTACGACGGCGAATCTCACTTCCCTGACA
66 TTGAAGCTACAACGGCGAATCTCACTTCCCTGACA
* * * * ** ** *
35553508 TTGCAATTCAAAAGATTGAAGCTACAACAGCGAATCTAACCTCCTTGGTGATGCAGCGGAACAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTATTTCCCAGGCGATGCAGCGGAACAGA
* * *
35553573 TCGAAGCTACGACGGCGAATCTCACTTCCCCGACA
66 TTGAAGCTACAACGGCGAATCTCACTTCCCTGACA
* * * * * *
35553608 TTGCAATTCAAAATATTGAAGCCACAATGGTAAATCTTACTTT-CTAGGCGATGCAGGGGAGCAG
1 TTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTA-TTTCCCAGGCGATGCAGCGGAACAG
* * *
35553672 ATTGAAGCTACAACAGCAAATCTCACTTCCCCGACA
65 ATTGAAGCTACAACGGCGAATCTCACTTCCCTGACA
** * **
35553708 TTGCAATTCAAAAGATCAAAGCCACAACGGTGAATCTTATTTCCTAGGC-AGTGCAGTTGAACAG
1 TTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTATTTCCCAGGCGA-TGCAGCGGAACAG
* * * ** *
35553772 ATTGAAGCTACAACAGTGGATCTTGCTT-CCTCGATA
65 ATTGAAGCTACAACGGCGAATCTCACTTCCCT-GACA
* * * * * * *
35553808 TTGTAATTTAAAAGATCGAAGCCACAACAGTGAATCTTATTTCCCAGGCGATACAGCAGAATAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTATTTCCCAGGCGATGCAGCGGAACAGA
**
35553873 TTGAAGCTACAACGGCGAATCTCACTTCCCAAACA
66 TTGAAGCTACAACGGCGAATCTCACTTCCCTGACA
* * * * * *
35553908 TTGTAGTTTAAAAGATCGAAGCCACAACGGTGAATCGTATTTCCCAGGCGATGCAGCGGAATAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTATTTCCCAGGCGATGCAGCGGAACAGA
*
35553973 TTGAAGCTACGACGGCGAATCTCACTT-CCTCGACA
66 TTGAAGCTACAACGGCGAATCTCACTTCCCT-GACA
* * * * *
35554008 TTGCAATTTAAAAGATCGAAGCCACAATGGCGAATCTTATTTCCCAGGCGCTGCAGCGGAACAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTATTTCCCAGGCGATGCAGCGGAACAGA
* *
35554073 TTGAAGCTACGACGGTGAATCTCACTTTCCC-GACA
66 TTGAAGCTACAACGGCGAATCTCAC-TTCCCTGACA
* * ** *
35554108 TTGTAATTCAAAAGATTGAAGTCACAACGGCAAATCTCATTTCCCTA-GCGATGCAGCGGAACAG
1 TTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTATTTCCC-AGGCGATGCAGCGGAACAG
* * **
35554172 ATTGAAGCTACGATGGCGAATCTCACTTCCCCAACA
65 ATTGAAGCTACAACGGCGAATCTCACTTCCCTGACA
* * * * * *
35554208 TTACAATTCAAAAGATTGAAGCCACCAA-GGCGAATCTTACTTT-CCAGACGGTACAGTGGAACA
1 TTGCAATTCAAAAGATTGAAGCCA-CAACGGTGAATCTTA-TTTCCCAGGCGATGCAGCGGAACA
** *
35554271 GATTGAAGCTACAACGGCGAA-CTTTGCTTCCCCGACA
64 GATTGAAGCTACAACGGCGAATC-TCACTTCCCTGACA
* * * * * * *
35554308 TTGCGATTAAAAAGATTGAAGCCACAACGGTGAATCTTACTCCCCCGGCGGTGCAGCAGAACAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTATTTCCCAGGCGATGCAGCGGAACAGA
** * * *
35554373 TTGAAGCTACAACAACGAATTTTACTTCCTTGACA
66 TTGAAGCTACAACGGCGAATCTCACTTCCCTGACA
* * *
35554408 TTGCAATT-AAATAGATTGAAGCTACGACGGCGAATCT
1 TTGCAATTCAAA-AGATTGAAGCCACAACGGTGAATCT
35554445 CACTTCCCTG
Statistics
Matches: 884, Mismatches: 130, Indels: 41
0.84 0.12 0.04
Matches are distributed among these distances:
98 63 0.07
99 83 0.09
100 723 0.82
101 13 0.01
102 2 0.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (100 bp):
TTGCAATTCAAAAGATTGAAGCCACAACGGTGAATCTTATTTCCCAGGCGATGCAGCGGAACAGA
TTGAAGCTACAACGGCGAATCTCACTTCCCTGACA
Found at i:35554674 original size:50 final size:50
Alignment explanation
Indices: 35553311--35554910 Score: 536
Period size: 50 Copynumber: 32.1 Consensus size: 50
35553301 AAACCATAGT
* * * *
35553311 TTGCAATTC-AAAGATTGAAGCCACAACGGTGAATCTTACTT-CCCAGGCGA
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCA-AC-A
* ** ** **
35553361 -TGCAGTGGAGCAGATTGAAGCTACAACGGCGAATCTCACTTCCCTGACA
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACA
* * * * * * *
35553410 TTGCAATTC-AAATATTGAAGCCACAACAGTGAATCTTAC-T-CTCAGGCGA
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCA-AC-A
* * **
35553459 -TGC-A-GCAGAACAGATTGAAGCTACGACGGCGAATCTCACTTCCCTGACA
1 TTGCAATTCA-AA-AGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACA
* * * *****
35553508 TTGCAATTCAAAAGATTGAAGCTACAACAGCGAATCTAACCTCCTTGGTGA
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCC-CCAACA
**** * * * *
35553559 -TGCAGCGGAACAGATCGAAGCTACGACGGCGAATCTCACTTCCCCGACA
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACA
* * * ** * * * *
35553608 TTGCAATTCAAAATATTGAAGCCACAATGGTAAATCTTACTT-TCTAGGCGA
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCA-AC-A
**** ** * * *
35553659 -TGCAGGGGAGCAGATTGAAGCTACAACAGCAAATCTCACTTCCCCGACA
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACA
** * * * * * *
35553708 TTGCAATTCAAAAGATCAAAGCCACAACGGTGAATCTTA-TTTCCTAGGCA
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCA-ACA
* * * * * * * ** * * *
35553758 GTGCAGTTGAACAGATTGAAGCTACAACAGTGGATCTTGCTTCCTCGATA
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACA
* * * * * * * * *
35553808 TTGTAATTTAAAAGATCGAAGCCACAACAGTGAATCTTA-TTTCCCAGGCGA
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCA-AC-A
* * *
35553859 -TAC-A-GCAGAATAGATTGAAGCTACAACGGCGAATCTCACTTCCCAAACA
1 TTGCAATTCA-AA-AGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACA
* * * * * * * *
35553908 TTGTAGTTTAAAAGATCGAAGCCACAACGGTGAATCGT-A-TTTCCCAGGCGA
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATC-TCACTTCCCCA-AC-A
**** * * * *
35553959 -TGCAGCGGAATAGATTGAAGCTACGACGGCGAATCTCACTTCCTCGACA
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACA
* * * * * * * *
35554008 TTGCAATTTAAAAGATCGAAGCCACAATGGCGAATCTTA-TTTCCCAGGCG
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCA-ACA
* **** * * * * *
35554058 CTGCAGCGGAACAGATTGAAGCTACGACGGTGAATCTCACTTTCCCGACA
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACA
* * * * *
35554108 TTGTAATTCAAAAGATTGAAG-TCACAACGGCAAATCTCATTTCCCTAGCGA
1 TTGCAATTCAAAAGATTGAAGCT-ACAACGGCGAATCTCACTTCCCCAAC-A
**** * * *
35554159 -TGCAGCGGAACAGATTGAAGCTACGATGGCGAATCTCACTTCCCCAACA
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACA
* * * * *
35554208 TTACAATTCAAAAGATTGAAGCCACCAA-GGCGAATCTTACTT-TCCAGACG
1 TTGCAATTCAAAAGATTGAAGCTA-CAACGGCGAATCTCACTTCCCCA-ACA
* * * ** * ** *
35554258 GTACAGTGGAACAGATTGAAGCTACAACGGCGAA-CTTTGCTTCCCCGACA
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATC-TCACTTCCCCAACA
* * * * * * ** *
35554308 TTGCGATTAAAAAGATTGAAGCCACAACGGTGAATCTTACTCCCCCGGCG
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACA
* * ** * * ***
35554358 GTGC-A-GCAGAACAGATTGAAGCTACAACAACGAATTTTACTTCCTTGACA
1 TTGCAATTCA-AA-AGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACA
* **
35554408 TTGCAATT-AAATAGATTGAAGCTACGACGGCGAATCTCACTTCCCTGACA
1 TTGCAATTCAAA-AGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACA
* * * * * *
35554458 TTGCAATTTAAAAGATAGAAGCCACAACGGCGAATCTTA-TTTCCCAGGCGA
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCA-AC-A
* **** * * * *
35554509 -TGTAGCGGAACAGATTGAAGCTACGACGGCGAATCTCACTTTCCCGACA
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACA
* * * *
35554558 TTGCAATTCAAAAGATTGAAG-TCACAACGGCAAATCTCATTTCCCTAGCA
1 TTGCAATTCAAAAGATTGAAGCT-ACAACGGCGAATCTCACTTCCCCAACA
* * ** * * *
35554608 ATGCAGTGGAACAGATTGAAGCTACGATGGCGAATCTCACTTCCCCAACA
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACA
* * ** * * *
35554658 TTGCAATTCAAAAGATTAAAGCCACCAA-GGAAAATCTTACTT-TCC-AGA
1 TTGCAATTCAAAAGATTGAAGCTA-CAACGGCGAATCTCACTTCCCCAACA
* * ** * * ** **
35554706 TGGTACAGTGGAATAGATTGAAGCTACAACGGTGAATCTTGCTTCCCTGACA
1 T--TGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACA
* * * * * **
35554758 TTGCGATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTCCCCCAGTA
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACA
* **** * * * ** **
35554808 GTGCAGCGGAACAGATTGAAGCTACAACGGTGAATTTTGCTTCCTTAACA
1 TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACA
* * * *
35554858 TTGCAA-TCAAATAGATTGAAGCTACGACGGCGAATCTTACTTCCTCGACA
1 TTGCAATTCAAA-AGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACA
35554908 TTG
1 TTG
35554911 TAGTTAAACA
Statistics
Matches: 1086, Mismatches: 399, Indels: 130
0.67 0.25 0.08
Matches are distributed among these distances:
46 1 0.00
47 2 0.00
48 12 0.01
49 105 0.10
50 904 0.83
51 56 0.05
52 6 0.01
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (50 bp):
TTGCAATTCAAAAGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACA
Found at i:35554814 original size:450 final size:450
Alignment explanation
Indices: 35553967--35554910 Score: 1604
Period size: 450 Copynumber: 2.1 Consensus size: 450
35553957 GATGCAGCGG
*
35553967 AATAGATTGAAGCTACGACGGCGAATCTCACTTCCTCGACATTGCAATTTAAAAGATCGAAGCCA
1 AATAGATTGAAGCTACGACGGCGAATCTCACTTCCTCGACATTGCAATTTAAAAGATAGAAGCCA
* * *
35554032 CAATGGCGAATCTTATTTCCCAGGCGCTGCAGCGGAACAGATTGAAGCTACGACGGTGAATCTCA
66 CAACGGCGAATCTTATTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACGACGGCGAATCTCA
* *
35554097 CTTTCCCGACATTGTAATTCAAAAGATTGAAGTCACAACGGCAAATCTCATTTCCCTAGCGATGC
131 CTTTCCCGACATTGCAATTCAAAAGATTGAAGTCACAACGGCAAATCTCATTTCCCTAGCAATGC
*
35554162 AGCGGAACAGATTGAAGCTACGATGGCGAATCTCACTTCCCCAACATTACAATTCAAAAGATTGA
196 AGCGGAACAGATTGAAGCTACGATGGCGAATCTCACTTCCCCAACATTACAATTCAAAAGATTAA
**
35554227 AGCCACCAAGGCGAATCTTACTTTCCAGACGGTACAGTGGAACAGATTGAAGCTACAACGGCGAA
261 AGCCACCAAGGAAAATCTTACTTTCCAGACGGTACAGTGGAACAGATTGAAGCTACAACGGCGAA
* *
35554292 CTTTGCTTCCCCGACATTGCGATTAAAAAGATTGAAGCCACAACGGTGAATCTTACTCCCCCGGC
326 CTTTGCTTCCCCGACATTGCGATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTCCCCCAGC
* * *
35554357 GGTGCAGCAGAACAGATTGAAGCTACAACAACGAATTTTACTTCCTTGACATTGCAATTA
391 AGTGCAGCAGAACAGATTGAAGCTACAACAACGAATTTTACTTCCTTAACATTGCAATCA
35554417 AATAGATTGAAGCTACGACGGCGAATCTCACTTCC-CTGACATTGCAATTTAAAAGATAGAAGCC
1 AATAGATTGAAGCTACGACGGCGAATCTCACTTCCTC-GACATTGCAATTTAAAAGATAGAAGCC
*
35554481 ACAACGGCGAATCTTATTTCCCAGGCGATGTAGCGGAACAGATTGAAGCTACGACGGCGAATCTC
65 ACAACGGCGAATCTTATTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACGACGGCGAATCTC
35554546 ACTTTCCCGACATTGCAATTCAAAAGATTGAAGTCACAACGGCAAATCTCATTTCCCTAGCAATG
130 ACTTTCCCGACATTGCAATTCAAAAGATTGAAGTCACAACGGCAAATCTCATTTCCCTAGCAATG
* *
35554611 CAGTGGAACAGATTGAAGCTACGATGGCGAATCTCACTTCCCCAACATTGCAATTCAAAAGATTA
195 CAGCGGAACAGATTGAAGCTACGATGGCGAATCTCACTTCCCCAACATTACAATTCAAAAGATTA
* * *
35554676 AAGCCACCAAGGAAAATCTTACTTTCCAGATGGTACAGTGGAATAGATTGAAGCTACAACGGTGA
260 AAGCCACCAAGGAAAATCTTACTTTCCAGACGGTACAGTGGAACAGATTGAAGCTACAACGGCGA
*
35554741 A-TCTTGCTTCCCTGACATTGCGATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTCCCCCA
325 ACT-TTGCTTCCCCGACATTGCGATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTCCCCCA
* * *** *
35554805 GTAGTGCAGCGGAACAGATTGAAGCTACAACGGTGAATTTTGCTTCCTTAACATTGCAATCA
389 GCAGTGCAGCAGAACAGATTGAAGCTACAACAACGAATTTTACTTCCTTAACATTGCAATCA
*
35554867 AATAGATTGAAGCTACGACGGCGAATCTTACTTCCTCGACATTG
1 AATAGATTGAAGCTACGACGGCGAATCTCACTTCCTCGACATTG
35554911 TAGTTAAACA
Statistics
Matches: 463, Mismatches: 28, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
449 2 0.00
450 460 0.99
451 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (450 bp):
AATAGATTGAAGCTACGACGGCGAATCTCACTTCCTCGACATTGCAATTTAAAAGATAGAAGCCA
CAACGGCGAATCTTATTTCCCAGGCGATGCAGCGGAACAGATTGAAGCTACGACGGCGAATCTCA
CTTTCCCGACATTGCAATTCAAAAGATTGAAGTCACAACGGCAAATCTCATTTCCCTAGCAATGC
AGCGGAACAGATTGAAGCTACGATGGCGAATCTCACTTCCCCAACATTACAATTCAAAAGATTAA
AGCCACCAAGGAAAATCTTACTTTCCAGACGGTACAGTGGAACAGATTGAAGCTACAACGGCGAA
CTTTGCTTCCCCGACATTGCGATTAAAAAGATTGAAGCCACAACGGCGAATCTTACTCCCCCAGC
AGTGCAGCAGAACAGATTGAAGCTACAACAACGAATTTTACTTCCTTAACATTGCAATCA
Found at i:35554871 original size:150 final size:150
Alignment explanation
Indices: 35553372--35554910 Score: 715
Period size: 150 Copynumber: 10.3 Consensus size: 150
35553362 GCAGTGGAGC
* * * *
35553372 AGATTGAAGCTACAACGGCGAATCTCACTTCCCTGACATTGCAATT-CAAATATTGAAGCCACAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCGATTAAAAAGATTGAAGCCACAA
* * * * * *
35553436 CAGTGAATCTTACT--CTCAGGC-GATGCAGCAGAACAGATTGAAGCTACGACGGCGAATCTCAC
66 CGGCGAATCTTACTCCCCCA-GCAG-TGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTAC
*
35553498 TTCCCTGACATTGCAATTCAAA-
129 TTTCCTGACATTGCAA-TCAAAT
* * * * ** *** * * *
35553520 AGATTGAAGCTACAACAGCGAATCTAACCTCCTTGGTGA-TGC-AGCGGAACAGATCGAAGCTAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCT-GACATTGCGA-TTAAAAAGATTGAAGCCAC
* * * * **** * * * * **
35553583 GACGGCGAATCTCACTTCCCC-GACATTGCAATTCAAAATATTGAAGCCACAATGGTAAATCTTA
64 AACGGCGAATCTTACTCCCCCAG-CAGTGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTA
* **** **
35553647 CTTT-CTAGGCGA-TGCAGGGGAGC
128 CTTTCCT-GAC-ATTGCAATCAAAT
* * * * * * **
35553670 AGATTGAAGCTACAACAGCAAATCTCACTTCCCCGACATTGCAATTCAAAAGATCAAAGCCACAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCGATTAAAAAGATTGAAGCCACAA
* ** * ** * * * *
35553735 CGGTGAATCTTA-TTTCCTAGGCAGTGCAGTTGAACAGATTGAAGCTACAACAGTGGATCTTGC-
66 CGGCGAATCTTACTCCCCCA-GCAGTGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTACT
* * *
35553798 TTCCTCGATATTGTAATTTAAA-
130 TTCCT-GACATTGCAA-TCAAAT
* * * * * * * * ** * *
35553820 AGATCGAAGCCACAACAGTGAATCTTATTTCCCAGGCGA-TAC-AGCAGAATAGATTGAAGCTAC
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGAC-ATTGCGATTA-AAAAGATTGAAGCCAC
* * * * * * *** * * * * *
35553883 AACGGCGAATCTCACTTCCCAAACATTGTAGTTTAAAAGATCGAAGCCACAACGGTGAATCGTA-
64 AACGGCGAATCTTACTCCCCCAGCAGTGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTAC
* * * *
35553947 TTTCCCAGGCGA-TGC-AGCGGAAT
129 TTT-CCTGAC-ATTGCAATC-AAAT
* * * * *
35553970 AGATTGAAGCTACGACGGCGAATCTCACTT-CCTCGACATTGCAATTTAAAAGATCGAAGCCACA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCT-GACATTGCGATTAAAAAGATTGAAGCCACA
* ** * * *
35554034 ATGGCGAATCTTA-TTTCCCAGGC-GCTGCAGCGGAACAGATTGAAGCTACGACGGTGAATCTCA
65 ACGGCGAATCTTACTCCCCCA-GCAG-TGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTA
* *
35554097 CTTTCCCGACATTGTAATTCAAA-
128 CTTTCCTGACATTGCAA-TCAAAT
* * * *** * *
35554120 AGATTGAAG-TCACAACGGCAAATCTCATTTCCCT-AGCGA-TGC-AGCGGAACAGATTGAAGCT
1 AGATTGAAGCT-ACAACGGCGAATCTTACTTCCCTGA-C-ATTGCGA-TTAAAAAGATTGAAGCC
* * * * * * * **** * *
35554181 ACGATGGCGAATCTCACTTCCCCAACATTACAATTCAAAAGATTGAAGCCACCAA-GGCGAATCT
62 ACAACGGCGAATCTTACTCCCCCAGCAGTGCAGCGGAACAGATTGAAGCTA-CAACGGCGAATCT
* ** * * ** *
35554245 TACTTTCCAGACGGTACAGTGGAAC
126 TACTTTCCTGACATTGCAATCAAAT
* *
35554270 AGATTGAAGCTACAACGGCGAA-CTTTGCTTCCCCGACATTGCGATTAAAAAGATTGAAGCCACA
1 AGATTGAAGCTACAACGGCGAATC-TTACTTCCCTGACATTGCGATTAAAAAGATTGAAGCCACA
* * * * ** *
35554334 ACGGTGAATCTTACTCCCCCGGCGGTGCAGCAGAACAGATTGAAGCTACAACAACGAATTTTAC-
65 ACGGCGAATCTTACTCCCCCAGCAGTGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTACT
*
35554398 TTCCTTGACATTGCAATTAAAT
130 TTCC-TGACATTGCAATCAAAT
* * * * *
35554420 AGATTGAAGCTACGACGGCGAATCTCACTTCCCTGACATTGCAATTTAAAAGATAGAAGCCACAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCGATTAAAAAGATTGAAGCCACAA
** * * *
35554485 CGGCGAATCTTA-TTTCCCAGGC-GATGTAGCGGAACAGATTGAAGCTACGACGGCGAATCTCAC
66 CGGCGAATCTTACTCCCCCA-GCAG-TGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTAC
*
35554548 TTTCCCGACATTGCAATTCAAA-
129 TTTCCTGACATTGCAA-TCAAAT
* * * * ** * *
35554570 AGATTGAAG-TCACAACGGCAAATCTCATTTCCCT-AGCAATGC-AGTGGAACAGATTGAAGCTA
1 AGATTGAAGCT-ACAACGGCGAATCTTACTTCCCTGA-CATTGCGA-TTAAAAAGATTGAAGCCA
* * * * * * **** * * * **
35554632 CGATGGCGAATCTCACTTCCCCAACATTGCAATTCAAAAGATTAAAGCCACCAA-GGAAAATCTT
63 CAACGGCGAATCTTACTCCCCCAGCAGTGCAGCGGAACAGATTGAAGCTA-CAACGGCGAATCTT
* *** * * **
35554696 ACTTTCCAGATGGTACAGTGGAAT
127 ACTTTCCTGACATTGCAATCAAAT
* *
35554720 AGATTGAAGCTACAACGGTGAATCTTGCTTCCCTGACATTGCGATTAAAAAGATTGAAGCCACAA
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCGATTAAAAAGATTGAAGCCACAA
* * * *
35554785 CGGCGAATCTTACTCCCCCAGTAGTGCAGCGGAACAGATTGAAGCTACAACGGTGAATTTTGC-T
66 CGGCGAATCTTACTCCCCCAGCAGTGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTACTT
*
35554849 TCCTTAACATTGCAATCAAAT
131 TCC-TGACATTGCAATCAAAT
*
35554870 AGATTGAAGCTACGACGGCGAATCTTACTT-CCTCGACATTG
1 AGATTGAAGCTACAACGGCGAATCTTACTTCCCT-GACATTG
35554911 TAGTTAAACA
Statistics
Matches: 1008, Mismatches: 315, Indels: 134
0.69 0.22 0.09
Matches are distributed among these distances:
147 1 0.00
148 33 0.03
149 87 0.09
150 829 0.82
151 57 0.06
152 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (150 bp):
AGATTGAAGCTACAACGGCGAATCTTACTTCCCTGACATTGCGATTAAAAAGATTGAAGCCACAA
CGGCGAATCTTACTCCCCCAGCAGTGCAGCGGAACAGATTGAAGCTACAACGGCGAATCTTACTT
TCCTGACATTGCAATCAAAT
Found at i:35556576 original size:3 final size:3
Alignment explanation
Indices: 35556568--35556601 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
35556558 ATATTTTAGC
35556568 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
35556602 CGTACTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:35556975 original size:18 final size:17
Alignment explanation
Indices: 35556952--35556990 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
35556942 TGCTTTAATT
*
35556952 TTTTATTTGTTTATTTAC
1 TTTTATTTGTTGATTT-C
35556970 TTTTATTTGTTGATTTC
1 TTTTATTTGTTGATTTC
35556987 TTTT
1 TTTT
35556991 CATTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (17 bp):
TTTTATTTGTTGATTTC
Found at i:35557346 original size:110 final size:108
Alignment explanation
Indices: 35557106--35557418 Score: 445
Period size: 110 Copynumber: 2.9 Consensus size: 108
35557096 ACGAAAATTT
* *
35557106 TTTC-AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAATATGCCCTAAGGTGCTGGGTGT
1 TTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
* * * *
35557170 CGATTTCTCTCGTTCAACCAAATGACTTAATATCCTTTTAAAAA
66 CGATTTTTCTCGTTCAACCAAATG-CTAAATAGCCTTTCAAAAA
*
35557214 TTTTAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
1 TTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
35557279 CGATTTTTTCTCGTTCAACCAAATAGCTAAATAGCCTTTCAAAAA
66 CGA-TTTTTCTCGTTCAACCAAAT-GCTAAATAGCCTTTCAAAAA
* * *
35557324 TTTCAAAATAAGGCAATGTTTTGCATTTGGGAAATTCGAG-GAACGTGCCCTAAGGTGCTGGGTT
1 TTTCAAAATAAGGCAATGTTTTGCATTT-GGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
* *
35557388 TCGA--TTTCTCGTTTAACCAAATTGCCAAATA
65 TCGATTTTTCTCGTTCAACCAAA-TGCTAAATA
35557419 TCCTCTTGAA
Statistics
Matches: 187, Mismatches: 13, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
107 23 0.12
108 4 0.02
109 61 0.33
110 87 0.47
111 12 0.06
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (108 bp):
TTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
CGATTTTTCTCGTTCAACCAAATGCTAAATAGCCTTTCAAAAA
Found at i:35557824 original size:35 final size:35
Alignment explanation
Indices: 35557778--35557929 Score: 178
Period size: 35 Copynumber: 4.3 Consensus size: 35
35557768 CACTCTCTGT
35557778 TTGGTGTGTTTCGGAGGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGAGGGACTAGCTCTTATGAGCA
**
35557813 TTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGAGGGACTAGCTCTTATGAGCA
* ** **
35557848 TTGCTGTGTTTTAGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGAGGGACTAGCTCTTATGAGCA
* * * * * *
35557883 TTGCTGTGTTTTGGAGGGAATGGCTCGTGTGAGCA
1 TTGGTGTGTTTCGGAGGGACTAGCTCTTATGAGCA
35557918 TCTGGTGTGTTT
1 T-TGGTGTGTTT
35557930 TGGTTGGACT
Statistics
Matches: 103, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
35 94 0.91
36 9 0.09
ACGTcount: A:0.14, C:0.13, G:0.33, T:0.39
Consensus pattern (35 bp):
TTGGTGTGTTTCGGAGGGACTAGCTCTTATGAGCA
Found at i:35562645 original size:70 final size:72
Alignment explanation
Indices: 35562531--35562681 Score: 243
Period size: 71 Copynumber: 2.1 Consensus size: 72
35562521 GGGGAATCAT
* *
35562531 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTT-TCATTTCAAATATACAATG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
35562595 GATATCG
66 GATATCG
***
35562602 CACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
35562666 GATATCG
66 GATATCG
35562673 CACTTAGCA
1 CACTTAGCA
35562682 CCACCAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 28 0.38
71 46 0.62
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (72 bp):
CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATACAATG
GATATCG
Found at i:35562785 original size:104 final size:103
Alignment explanation
Indices: 35562601--35562823 Score: 367
Period size: 104 Copynumber: 2.2 Consensus size: 103
35562591 AATGGATATC
35562601 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
* *
35562666 GATATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GATATCGCACATAGCACCACCAATAAACCGGGGAATCA
35562704 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
35562769 GGATCA-CGCACATAGCACCACCCATAAATCGGGGAATCA
65 GGAT-ATCGCACATAGCACCACCAATAAACCGGGGAATCA
**
35562808 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
35562824 TTTATATACA
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 17 0.15
104 94 0.84
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (103 bp):
GCACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
GATATCGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:35563185 original size:29 final size:29
Alignment explanation
Indices: 35563152--35563215 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
35563142 TAATCCACCA
35563152 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
35563181 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
35563211 CCCAA
1 CCCAA
35563216 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:35563189 original size:30 final size:30
Alignment explanation
Indices: 35563159--35563215 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
35563149 CCACCCAACT
35563159 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
35563188 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
35563216 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:35570276 original size:104 final size:104
Alignment explanation
Indices: 35570154--35570377 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
35570144 AATGGATATC
35570154 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
35570219 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
35570258 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
35570323 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
35570362 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
35570378 TTTATATACA
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:35570739 original size:29 final size:29
Alignment explanation
Indices: 35570706--35570769 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
35570696 TAATCCACCA
35570706 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
35570735 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
35570765 CCCAA
1 CCCAA
35570770 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:35570743 original size:30 final size:30
Alignment explanation
Indices: 35570713--35570769 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
35570703 CCACCCAACT
35570713 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
35570742 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
35570770 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:35575159 original size:18 final size:17
Alignment explanation
Indices: 35575117--35575157 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
35575107 GAAAATATTA
35575117 ATAAAAATAGAATTTAG
1 ATAAAAATAGAATTTAG
*
35575134 ATAGAAATAGAATTTTAG
1 ATAAAAATAGAA-TTTAG
35575152 -TAAAAA
1 ATAAAAA
35575158 ATTTTAAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (17 bp):
ATAAAAATAGAATTTAG
Found at i:35575192 original size:34 final size:33
Alignment explanation
Indices: 35575153--35575217 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 33
35575143 GAATTTTAGT
35575153 AAAAAATTTTAAGAGAGAAT-TTGAGAGAAATTTG
1 AAAAAATTTT--GAGAGAATGTTGAGAGAAATTTG
*
35575187 AAAAAATTTTGAGAGAATGTTGTGAGAAATT
1 AAAAAATTTTGAGAGAATGTTGAGAGAAATT
35575218 AGTAGGGGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 8 0.28
33 11 0.38
34 10 0.34
ACGTcount: A:0.48, C:0.00, G:0.22, T:0.31
Consensus pattern (33 bp):
AAAAAATTTTGAGAGAATGTTGAGAGAAATTTG
Found at i:35576494 original size:35 final size:35
Alignment explanation
Indices: 35576448--35576514 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
35576438 TCTTTGTGTG
* *
35576448 AATGGTGGAAAAGAAGTTACAGATATAGGTATGTC
1 AATGGTAGAAAAGAAGTTACAAATATAGGTATGTC
35576483 AATGGTAGAAAAGAAGTTACAAATATAGGTAT
1 AATGGTAGAAAAGAAGTTACAAATATAGGTAT
35576515 TTTCTGAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.45, C:0.04, G:0.25, T:0.25
Consensus pattern (35 bp):
AATGGTAGAAAAGAAGTTACAAATATAGGTATGTC
Found at i:35588261 original size:12 final size:12
Alignment explanation
Indices: 35588244--35588281 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
35588234 TGCGAAGCCA
35588244 CACATGAGATCG
1 CACATGAGATCG
35588256 CACATGAGATCG
1 CACATGAGATCG
* *
35588268 CATATGAGACCG
1 CACATGAGATCG
35588280 CA
1 CA
35588282 TAAACACGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.34, C:0.26, G:0.24, T:0.16
Consensus pattern (12 bp):
CACATGAGATCG
Found at i:35592530 original size:21 final size:21
Alignment explanation
Indices: 35592504--35592544 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
35592494 ATCTGCTCAA
* *
35592504 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
35592525 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
35592545 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:35611394 original size:46 final size:46
Alignment explanation
Indices: 35611321--35611505 Score: 280
Period size: 46 Copynumber: 4.0 Consensus size: 46
35611311 ACAAGGCTAT
*
35611321 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
* * *
35611367 AACTCAGCATGGTTTTCTTTACCGAAATACCATACCTACTTTTTAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
* * *
35611413 AACTCAGTATGATTTTCTTTACCGAAATATCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
* * *
35611459 AACTCAGTATGGTTTTCTTCACTGGAATACCATACCTACGTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
35611505 A
1 A
35611506 CTTTTCCGTG
Statistics
Matches: 125, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 125 1.00
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
Found at i:35612780 original size:16 final size:17
Alignment explanation
Indices: 35612734--35612781 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
35612724 AAATTCTTTT
35612734 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
*
35612751 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAA
*
35612768 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
35612782 TTCTAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:35624446 original size:6 final size:6
Alignment explanation
Indices: 35624435--35624497 Score: 126
Period size: 6 Copynumber: 10.5 Consensus size: 6
35624425 AGTAGATGAT
35624435 GCTGAG GCTGAG GCTGAG GCTGAG GCTGAG GCTGAG GCTGAG GCTGAG
1 GCTGAG GCTGAG GCTGAG GCTGAG GCTGAG GCTGAG GCTGAG GCTGAG
35624483 GCTGAG GCTGAG GCT
1 GCTGAG GCTGAG GCT
35624498 AATTTTAATG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 57 1.00
ACGTcount: A:0.16, C:0.17, G:0.49, T:0.17
Consensus pattern (6 bp):
GCTGAG
Found at i:35638217 original size:62 final size:62
Alignment explanation
Indices: 35638120--35638239 Score: 231
Period size: 62 Copynumber: 1.9 Consensus size: 62
35638110 ATGTAATCCT
*
35638120 AGAAATAGGGCGACATAAATCTACCAGATTAGAGTCAAATCTAATAGTGGAATCCATAGATC
1 AGAAATAGGACGACATAAATCTACCAGATTAGAGTCAAATCTAATAGTGGAATCCATAGATC
35638182 AGAAATAGGACGACATAAATCTACCAGATTAGAGTCAAATCTAATAGTGGAATCCATA
1 AGAAATAGGACGACATAAATCTACCAGATTAGAGTCAAATCTAATAGTGGAATCCATA
35638240 AATCGAGTTA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.23
Consensus pattern (62 bp):
AGAAATAGGACGACATAAATCTACCAGATTAGAGTCAAATCTAATAGTGGAATCCATAGATC
Found at i:35648761 original size:36 final size:36
Alignment explanation
Indices: 35648714--35648794 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
35648704 GGCCCAAGTT
*
35648714 ACGCCCAAAAGGAGGCCTAAATCAGCGCTCCATATC
1 ACGCCCAAAAGGAGGCCCAAATCAGCGCTCCATATC
* * *
35648750 ACGCCCAAAAGGAGGCCCAAATCTGTGCTCTATATC
1 ACGCCCAAAAGGAGGCCCAAATCAGCGCTCCATATC
35648786 ACGCCCAAA
1 ACGCCCAAA
35648795 TACACGACCC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.33, C:0.33, G:0.19, T:0.15
Consensus pattern (36 bp):
ACGCCCAAAAGGAGGCCCAAATCAGCGCTCCATATC
Done.