Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009582.1 Hibiscus syriacus cultivar Beakdansim tig00116959_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4978262
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 24
Found at i:3111035 original size:32 final size:32
Alignment explanation
Indices: 3110994--3111097 Score: 136
Period size: 32 Copynumber: 3.2 Consensus size: 32
3110984 ATCAAAATAA
* *
3110994 AATATTGACTCTATTGTGCATTATTTGAATGC
1 AATATTGACTCTATTATGCATTATCTGAATGC
* * *
3111026 AATACTGACTCTACTATGCATTATCTGATTGC
1 AATATTGACTCTATTATGCATTATCTGAATGC
* *
3111058 AATGTTGACTCTATTATGCATTATCTGAACGC
1 AATATTGACTCTATTATGCATTATCTGAATGC
*
3111090 AATGTTGA
1 AATATTGA
3111098 TACTACTATT
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 62 1.00
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.39
Consensus pattern (32 bp):
AATATTGACTCTATTATGCATTATCTGAATGC
Found at i:3111037 original size:64 final size:64
Alignment explanation
Indices: 3110944--3111092 Score: 154
Period size: 64 Copynumber: 2.3 Consensus size: 64
3110934 CTGACACTCG
* * ** *
3110944 TGTGCCTTATCTGAATGCAACACAAACTCTGTTATGTATTATCAAAATAAAATATTGACTCTAT
1 TGTGCATTATCTGAATGCAATACAAACTCTACTATGCATTATCAAAATAAAATATTGACTCTAT
* ** ** * ** *
3111008 TGTGCATTATTTGAATGCAATACTGACTCTACTATGCATTATCTGATTGCAATGTTGACTCTAT
1 TGTGCATTATCTGAATGCAATACAAACTCTACTATGCATTATCAAAATAAAATATTGACTCTAT
* *
3111072 TATGCATTATCTGAACGCAAT
1 TGTGCATTATCTGAATGCAAT
3111093 GTTGATACTA
Statistics
Matches: 68, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
64 68 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (64 bp):
TGTGCATTATCTGAATGCAATACAAACTCTACTATGCATTATCAAAATAAAATATTGACTCTAT
Found at i:3117356 original size:21 final size:21
Alignment explanation
Indices: 3117330--3117374 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
3117320 GTTATTGTTA
3117330 TTTCTCTTTTTATTGT-TTTTT
1 TTTCTCTTTTTATT-TCTTTTT
*
3117351 TTTCTCTTTTTGTTTCTTTTT
1 TTTCTCTTTTTATTTCTTTTT
3117372 TTT
1 TTT
3117375 AACTAAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.02, C:0.11, G:0.04, T:0.82
Consensus pattern (21 bp):
TTTCTCTTTTTATTTCTTTTT
Found at i:3117481 original size:44 final size:44
Alignment explanation
Indices: 3117429--3117549 Score: 145
Period size: 44 Copynumber: 2.8 Consensus size: 44
3117419 AAACGAACAG
* *
3117429 AATATTGATGTTGACCCAACTCTCTCTGTTATGGAATCAAGT-TA
1 AATATTGATGTTGACCCAACTCCCTCTGTTATGGAATCAA-TCGA
* * * *
3117473 AATGTTGATGTTGACTCAACTCCCTATATTATGGAATCAATCGA
1 AATATTGATGTTGACCCAACTCCCTCTGTTATGGAATCAATCGA
** *
3117517 AATATTGATGTTGATGCAATTCCCTCTGTTATG
1 AATATTGATGTTGACCCAACTCCCTCTGTTATG
3117550 AAATTGAGCA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 1 0.02
44 63 0.98
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (44 bp):
AATATTGATGTTGACCCAACTCCCTCTGTTATGGAATCAATCGA
Found at i:3117964 original size:42 final size:42
Alignment explanation
Indices: 3117899--3117990 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
3117889 GGATGGCCCA
* * *
3117899 AAGGACTTAATCACCATGTTCGAAAGACATACTAGTGACTTG
1 AAGGATTTAATCACCATGCTCGAAAGACATACTAGTGACTCG
* * * *
3117941 AAGGATTTAATCATCTTGCTCGAAAGACTTACTGGTGACTCG
1 AAGGATTTAATCACCATGCTCGAAAGACATACTAGTGACTCG
3117983 AAGGATTT
1 AAGGATTT
3117991 GCTCTTGCTT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (42 bp):
AAGGATTTAATCACCATGCTCGAAAGACATACTAGTGACTCG
Found at i:3118189 original size:129 final size:128
Alignment explanation
Indices: 3117939--3118248 Score: 395
Period size: 129 Copynumber: 2.4 Consensus size: 128
3117929 ACTAGTGACT
* * * * * *
3117939 TGAAGGATTTAATCATCTTGCTCGAAAGACTTACTGGTGACTCGAAGGATTTGCTCTTGCTTGGG
1 TGAAGGACTT-ATCACCCTGCTCGAAAGACTTA-TGATGACCCGAAGGATTTGCACTTGCTTGGG
* * * *
3118004 AATGCTTTCTTTCTTTTTAAGAATATCATGTGAAAACATCATACCTAAAGGACTTATAGATAGCC
64 AATACTTTATTTCTTTTCAAGAATATCATGTGAAAACATCATACCCAAAGGACTTATAGATAGCC
3118069 TGAAGGACTTATCACCCTGCTCGAAAGACTTATAGATGACCCGAAGGATTTGCACTTGCTTGGGA
1 TGAAGGACTTATCACCCTGCTCGAAAGACTTAT-GATGACCCGAAGGATTTGCACTTGCTTGGGA
* * * * * * *
3118134 ATATTTTATTTCTTTTCAAGAATATCATTTGAAAACATCATGCCCGAAGGTCTTATAGGTGGCC
65 ATACTTTATTTCTTTTCAAGAATATCATGTGAAAACATCATACCCAAAGGACTTATAGATAGCC
* * * *
3118198 CGAAGGACTTATCACCCTACTCGAAAGACTCACGGATGACCCGAAGGATTT
1 TGAAGGACTTATCACCCTGCTCGAAAGACTTA-TGATGACCCGAAGGATTT
3118249 AAACACCATG
Statistics
Matches: 157, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
128 1 0.01
129 147 0.94
130 9 0.06
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (128 bp):
TGAAGGACTTATCACCCTGCTCGAAAGACTTATGATGACCCGAAGGATTTGCACTTGCTTGGGAA
TACTTTATTTCTTTTCAAGAATATCATGTGAAAACATCATACCCAAAGGACTTATAGATAGCC
Found at i:3121709 original size:22 final size:23
Alignment explanation
Indices: 3121678--3121729 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
3121668 GATGAGTTCC
*
3121678 TATTTTTTAATTA-AAAATAT-A
1 TATTTTTTAATTATAAAAAATAA
3121699 TATTATTTTAATTATAAAAAATAA
1 TATT-TTTTAATTATAAAAAATAA
3121723 TATTTTT
1 TATTTTT
3121730 ATTTAAACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 4 0.15
22 9 0.33
23 9 0.33
24 5 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTTTTTAATTATAAAAAATAA
Found at i:3121716 original size:24 final size:21
Alignment explanation
Indices: 3121678--3121729 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 21
3121668 GATGAGTTCC
3121678 TATTTTTTAATT-AAAAATATA
1 TATTTTTTAATTAAAAAATA-A
3121699 TATTATTTTAATTATAAAAAATAA
1 TATT-TTTTAA-T-TAAAAAATAA
3121723 TATTTTT
1 TATTTTT
3121730 ATTTAAACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 4 0.15
22 6 0.22
23 4 0.15
24 6 0.22
25 7 0.26
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTTTTTAATTAAAAAATAA
Found at i:3122169 original size:44 final size:44
Alignment explanation
Indices: 3122106--3122192 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
3122096 TACAAAGTTA
3122106 AGTGATTAAATTTAAAAAAATAAAAGTGCAATAAATAAATAGGC
1 AGTGATTAAATTTAAAAAAATAAAAGTGCAATAAATAAATAGGC
3122150 AGTGATTAAATTTAAAAAAATAAAAGTGCAATAAATAAATAGG
1 AGTGATTAAATTTAAAAAAATAAAAGTGCAATAAATAAATAGG
3122193 AGAGAGCATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.57, C:0.03, G:0.14, T:0.25
Consensus pattern (44 bp):
AGTGATTAAATTTAAAAAAATAAAAGTGCAATAAATAAATAGGC
Found at i:3124876 original size:19 final size:20
Alignment explanation
Indices: 3124852--3124899 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
3124842 AACGATTTTC
*
3124852 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
3124871 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
3124891 TTTTGAAAA
1 TTTTGAAAA
3124900 AAGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:3126273 original size:34 final size:32
Alignment explanation
Indices: 3126234--3126303 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
3126224 TTTTGTAAAG
*
3126234 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
* *
3126268 GGGAAAGGTTCTAGTTTATCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
3126300 GGGA
1 GGGA
3126304 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:3126602 original size:23 final size:24
Alignment explanation
Indices: 3126570--3126620 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
3126560 CTCAAACCTC
3126570 AAAATTCCCAAAT-TCCTAATCCCT
1 AAAATTCCCAAATATCC-AATCCCT
*
3126594 AAAA-TCCCAAATATCCAATCTCT
1 AAAATTCCCAAATATCCAATCCCT
3126617 AAAA
1 AAAA
3126621 ATAGCCCTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAATTCCCAAATATCCAATCCCT
Found at i:3127442 original size:2 final size:2
Alignment explanation
Indices: 3127435--3127467 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3127425 ATTATGCAGA
3127435 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3127468 CTATTCAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3128477 original size:25 final size:26
Alignment explanation
Indices: 3128436--3128484 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
3128426 TTAAATATAT
*
3128436 TTTATAATTTTTTTAT-ATTATTTGA
1 TTTATAATTTTTATATAATTATTTGA
3128461 TTTATACA-TTTTATATAATTATTT
1 TTTATA-ATTTTTATATAATTATTT
3128485 TAAGTTTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTATAATTTTTATATAATTATTTGA
Found at i:3134175 original size:12 final size:12
Alignment explanation
Indices: 3134154--3134179 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3134144 TTGAGGAATA
3134154 GGAGGAGGATTT
1 GGAGGAGGATTT
3134166 GGAGGAGGATTT
1 GGAGGAGGATTT
3134178 GG
1 GG
3134180 TTGACGACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.54, T:0.23
Consensus pattern (12 bp):
GGAGGAGGATTT
Found at i:3134913 original size:20 final size:20
Alignment explanation
Indices: 3134884--3134921 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3134874 CCTCTTCAAA
*
3134884 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
3134904 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
3134922 TGCACCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:3153445 original size:26 final size:26
Alignment explanation
Indices: 3153416--3153465 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3153406 TATGATTTTG
3153416 CTTTAAAT-AATATTTTTATGAGATGA
1 CTTTAAATGAATATTTTTA-GAGATGA
* *
3153442 CTTTTAATGAATGTTTTTAGAGAT
1 CTTTAAATGAATATTTTTAGAGAT
3153466 AATTTCATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.34, C:0.04, G:0.14, T:0.48
Consensus pattern (26 bp):
CTTTAAATGAATATTTTTAGAGATGA
Found at i:3157882 original size:21 final size:21
Alignment explanation
Indices: 3157827--3157890 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
3157817 GATTCCCCTG
3157827 TGGGGGGAATCGGTTCCCATTCA
1 TGGGGGGAATCGGTTCCC--TCA
**
3157850 AAGGGGGAATCGGTTCCCTCA
1 TGGGGGGAATCGGTTCCCTCA
* *
3157871 TGGGGGGGATCGATTCCCTC
1 TGGGGGGAATCGGTTCCCTC
3157891 TGCACAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 19 0.54
23 16 0.46
ACGTcount: A:0.17, C:0.23, G:0.36, T:0.23
Consensus pattern (21 bp):
TGGGGGGAATCGGTTCCCTCA
Found at i:3164620 original size:23 final size:23
Alignment explanation
Indices: 3164580--3164655 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 23
3164570 CCACTAGGGG
*
3164580 CACATAGAATTTGTCCCGAAGGAC
1 CACATAGAA-ATGTCCCGAAGGAC
*
3164604 CGCATAGAAATGTCCCGAAGGAC
1 CACATAGAAATGTCCCGAAGGAC
* *
3164627 CACAT--ATATGTCCCGAATGAC
1 CACATAGAAATGTCCCGAAGGAC
3164648 CACATAGA
1 CACATAGA
3164656 TGTCCAAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
21 19 0.42
23 18 0.40
24 8 0.18
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.18
Consensus pattern (23 bp):
CACATAGAAATGTCCCGAAGGAC
Found at i:3164666 original size:21 final size:21
Alignment explanation
Indices: 3164624--3164671 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
3164614 TGTCCCGAAG
* **
3164624 GACCACATATATGTCCCGAAT
1 GACCACATAGATGTCCAAAAT
3164645 GACCACATAGATGTCCAAAAT
1 GACCACATAGATGTCCAAAAT
3164666 GACCAC
1 GACCAC
3164672 TCCTTAAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.29, G:0.15, T:0.19
Consensus pattern (21 bp):
GACCACATAGATGTCCAAAAT
Found at i:3164710 original size:21 final size:21
Alignment explanation
Indices: 3164677--3164772 Score: 104
Period size: 21 Copynumber: 4.6 Consensus size: 21
3164667 ACCACTCCTT
*
3164677 AAGGATCACATATATATTCCA
1 AAGGACCACATATATATTCCA
* *
3164698 AAGGACCAAATATGT-TTCCCA
1 AAGGACCACATATATATT-CCA
*
3164719 AAGAACCACATATATATTCCA
1 AAGGACCACATATATATTCCA
** * *
3164740 AAGGATTATATATATATCCCA
1 AAGGACCACATATATATTCCA
3164761 AAGGACCACATA
1 AAGGACCACATA
3164773 GAACCATCAA
Statistics
Matches: 59, Mismatches: 14, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
20 2 0.03
21 55 0.93
22 2 0.03
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (21 bp):
AAGGACCACATATATATTCCA
Found at i:3164730 original size:42 final size:42
Alignment explanation
Indices: 3164683--3164772 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
3164673 CCTTAAGGAT
* *
3164683 CACATATATATTCCAAAGGACCAAATATGTTTCCCAAAGAAC
1 CACATATATATTCCAAAGGACCAAATATATATCCCAAAGAAC
** * *
3164725 CACATATATATTCCAAAGGATTATATATATATCCCAAAGGAC
1 CACATATATATTCCAAAGGACCAAATATATATCCCAAAGAAC
3164767 CACATA
1 CACATA
3164773 GAACCATCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.43, C:0.22, G:0.09, T:0.26
Consensus pattern (42 bp):
CACATATATATTCCAAAGGACCAAATATATATCCCAAAGAAC
Found at i:3168822 original size:33 final size:31
Alignment explanation
Indices: 3168744--3168844 Score: 86
Period size: 33 Copynumber: 3.3 Consensus size: 31
3168734 TTAGCAACTC
*
3168744 AAAATATAATATATT-AAAATTTTACTTTTA
1 AAAATATAATATATTAAAAATTTTACTTTCA
*
3168774 AAAAAATAA-ATTATTAATAACATTTGTA-TTTCA
1 AAAATATAATA-TATTAA-AA-ATTT-TACTTTCA
* *
3168807 AAAATATAATATATT-AAGATTTTA-TTTTA
1 AAAATATAATATATTAAAAATTTTACTTTCA
*
3168836 AAAAAATAA
1 AAAATATAA
3168845 ATTATAAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
29 15 0.25
30 16 0.27
31 2 0.03
32 3 0.05
33 20 0.34
34 3 0.05
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (31 bp):
AAAATATAATATATTAAAAATTTTACTTTCA
Found at i:3168841 original size:31 final size:31
Alignment explanation
Indices: 3168744--3168843 Score: 109
Period size: 31 Copynumber: 3.2 Consensus size: 31
3168734 TTAGCAACTC
3168744 AAAATATAATATATTAAAATTTTACTTTTAAA
1 AAAATATAATATATTAAAATTTTA-TTTTAAA
*
3168776 AAAATA-AAT-TATTAATAACATTTGTA-TTT-CA
1 AAAATATAATATATT-A-AA-ATTT-TATTTTAAA
*
3168807 AAAATATAATATATTAAGATTTTATTTTAAA
1 AAAATATAATATATTAAAATTTTATTTTAAA
3168838 AAAATA
1 AAAATA
3168844 AATTATAAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
29 2 0.04
30 11 0.19
31 19 0.33
32 15 0.26
33 8 0.14
34 2 0.04
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (31 bp):
AAAATATAATATATTAAAATTTTATTTTAAA
Found at i:3168866 original size:62 final size:63
Alignment explanation
Indices: 3168744--3168866 Score: 194
Period size: 62 Copynumber: 2.0 Consensus size: 63
3168734 TTAGCAACTC
* **
3168744 AAAATATAATATATTAAAATTTTACTTTTAAAAAAATAAATTATTAATAACATTTGTATTTCA
1 AAAATATAATATATTAAAATTTTACTTTTAAAAAAATAAATTATAAATAACATTAATATTTCA
* *
3168807 AAAATATAATATATTAAGATTTTA-TTTTAAAAAAATAAATTATAAATAATATTAATATTT
1 AAAATATAATATATTAAAATTTTACTTTTAAAAAAATAAATTATAAATAACATTAATATTT
3168867 AAGTTGACTT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
62 32 0.58
63 23 0.42
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (63 bp):
AAAATATAATATATTAAAATTTTACTTTTAAAAAAATAAATTATAAATAACATTAATATTTCA
Found at i:3174430 original size:3 final size:3
Alignment explanation
Indices: 3174424--3174449 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3174414 TTGTTGTTGT
3174424 TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TG
3174450 GGTTGAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.35, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:3174639 original size:25 final size:24
Alignment explanation
Indices: 3174609--3174656 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
3174599 AGAAAGATAT
3174609 ATATATT-TATAAAATAAAATATTTG
1 ATATATTAT-TAAAA-AAAATATTTG
*
3174634 ATATATTATTATAAAAAATATTT
1 ATATATTATTAAAAAAAATATTT
3174657 TAATAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 11 0.52
26 1 0.05
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
ATATATTATTAAAAAAAATATTTG
Found at i:3175515 original size:3 final size:3
Alignment explanation
Indices: 3175507--3175536 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
3175497 ATATATTATG
*
3175507 TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3175537 ATAATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:3181090 original size:106 final size:106
Alignment explanation
Indices: 3180634--3182252 Score: 2389
Period size: 106 Copynumber: 15.4 Consensus size: 106
3180624 TCTAATTTCA
* * * * * *
3180634 TTCAGAGTCTATTTCAATTTCGCAGCGAAGAAAATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
3180699 CGACGAAGGGACCGCTGGTTGTTAATAAACAA-TTTTCCAA-
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCT-CAAT
* * *
3180739 TACTAGAGCCAATTTCAACTTCACAGCGAA-GATAGTGGACTCCAGACAACACAAGTTCAACTTC
1 TTC-AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTC
*
3180803 ACGACGAAGGGACCGCTGGTTGTCAATAAA-AACTTCCCAAT
65 ACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
* *
3180844 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCCA-ACAACGCATGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
3180908 CGACGAAGGGACCGCTGGTTGT-AACAAACAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
* *
3180948 TTCAGAGCCGATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
3181013 CGACGAAGGGACCGCTGGTTGTCAACAAA-AACCTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAA-CTTCTCAAT
* * * *
3181054 TTTAAAGCCAATTTCAACATCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
3181119 CGACAAAGGGACCGCTGGTTGTCAAT-AA-AACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
*
3181158 TTCAGAGCCAATTT-AACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
3181222 CGACGAAGGGACCGCTGGTTGTCAAACAAACTACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTC-AATAAACAACTTCTCAAT
*
3181264 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
3181329 CGACAAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
* * *
3181370 TTCAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCATGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
3181435 CGACGAAGGGACCGCTGGTT-TCAACAAACAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
*
3181475 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
3181540 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
* * *
3181581 TTCAGAGTCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
3181646 CGAAGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
* *
3181687 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCTAGACAACGTAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
3181752 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
* *
3181793 TTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCATACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
3181858 CGACGAAGGGACTGCTGGTTGTCAATAAACAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
* *
3181899 TTCAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
3181964 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
* * * *
3182005 TTCAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGGAC-CCAAGACAACACAAGCTCAACTTC
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTC
* *
3182069 ACGACGAAGGG-GCGACTGATTGTCAAT-AA-AA-TT-TC-A-
65 ACGACGAAGGGACCG-CTGGTTGTCAATAAACAACTTCTCAAT
* * * *
3182105 TTCAGAGTCAATTTTAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * * * * * **
3182170 CAACGAAGGGACGGCTGGTTGTTAACAAACAATTTCCCGGT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
*
3182211 TCCAGAGCCAATTTCAACTTCACGAAG-G-AGGATATTGGACTC
1 TTCAGAGCCAATTTCAACTTCAC--AGCGAAGGATATTGGACTC
3182253 AGAACAATGC
Statistics
Matches: 1392, Mismatches: 97, Indels: 49
0.91 0.06 0.03
Matches are distributed among these distances:
100 75 0.05
101 5 0.00
102 3 0.00
103 78 0.06
104 147 0.11
105 237 0.17
106 772 0.55
107 73 0.05
108 2 0.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (106 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAAT
Found at i:3185529 original size:3 final size:3
Alignment explanation
Indices: 3185523--3185558 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
3185513 AAAAAAAAAT
*
3185523 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTT TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TT
3185559 TTTGTAGCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:3190624 original size:64 final size:64
Alignment explanation
Indices: 3190523--3190817 Score: 428
Period size: 64 Copynumber: 4.6 Consensus size: 64
3190513 TGCAGCTTTT
* * *
3190523 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAATTTTATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* ** * *
3190587 AGAGTCAATTTCAACTTCACAGTGAATAATATTGGACTCAACAAACAACTTTCCAGTTTCGTTT
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * *
3190651 AGAGTAAATTTCAACTTCACAGCAAAGGATATTGGACTCAACAAACAACTTTTTCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAAC-TTTCCAGTTTCATTC
* * *
3190716 AGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAACAAACAACTTTCCAGTTTTATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * *
3190780 AGAGTCAATTTTAACTTCAGAGCGAAGGATAGTGGACT
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACT
3190818 TGAAACAATG
Statistics
Matches: 203, Mismatches: 27, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
64 146 0.72
65 57 0.28
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (64 bp):
AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
Found at i:3190770 original size:129 final size:128
Alignment explanation
Indices: 3190520--3190817 Score: 434
Period size: 129 Copynumber: 2.3 Consensus size: 128
3190510 TTTTGCAGCT
* *
3190520 TTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAATTTTAT
1 TTTAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAATTTCAT
* * * * *
3190585 TCAGAGTCAATTTCAACTTCACAGTGAATAATATTGGACTCAACAAACAACTTTCCAGTTTCG
66 TCAGAGCCAATTTCAACTTCACAGCGAAGAATATTAGACTCAACAAACAACTTTCCAGTTTCA
* * * *
3190648 TTTAGAGTAAATTTCAACTTCACAGCAAAGGATATTGGACTCAACAAACAACTTTTTCAGTTTCA
1 TTTAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAAC-TTTCCAATTTCA
* *
3190713 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAGACTCAACAAACAACTTTCCAGTTTTA
65 TTCAGAGCCAATTTCAACTTCACAGCGAAGAATATTAGACTCAACAAACAACTTTCCAGTTTCA
* * * *
3190777 TTCAGAGTCAATTTTAACTTCAGAGCGAAGGATAGTGGACT
1 TTTAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACT
3190818 TGAAACAATG
Statistics
Matches: 150, Mismatches: 19, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
128 49 0.33
129 101 0.67
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.31
Consensus pattern (128 bp):
TTTAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTCCAATTTCAT
TCAGAGCCAATTTCAACTTCACAGCGAAGAATATTAGACTCAACAAACAACTTTCCAGTTTCA
Found at i:3191040 original size:109 final size:109
Alignment explanation
Indices: 3190849--3191303 Score: 589
Period size: 109 Copynumber: 4.2 Consensus size: 109
3190839 AGATTGGATT
* * * *
3190849 TCAACTTCACAACGAATGAGCCATCCATGATTTCAACTTCACGACGAAGGATATCGTGCCAACAA
1 TCAACTTCACAACGAAGGAGCCATCCATGATTTCAACTTCACAACAAAGGATATCATGCCAACAA
** *
3190914 TACTTGGATTTGGACTTCACAACGAAGGATATCCAATTTAAAGC
66 TACTTGGATTTTAACTTCACAACGAAGGATATCCAATTCAAAGC
* * * * *
3190958 TCAACTTCACAATGAAGGAGTCATCCACGATTTCAACTTCACAACAAAGTATATCGTGCCAACAA
1 TCAACTTCACAACGAAGGAGCCATCCATGATTTCAACTTCACAACAAAGGATATCATGCCAACAA
* *
3191023 T-CTTTGGATTTTAACTTCACGATGAAGGATATCCAATTCAAAGC
66 TAC-TTGGATTTTAACTTCACAACGAAGGATATCCAATTCAAAGC
*
3191067 TCAACTTCACAACGAATGG-GCCATCCATGATTTCAATTTCACGAA-AAAGGATATCATGCCAAC
1 TCAACTTCACAACGAA-GGAGCCATCCATGATTTCAACTTCAC-AACAAAGGATATCATGCCAAC
* *
3191130 AATACTTGGATTTTAACTTCACAACGAAGGATATCTAATTCAAAGT
64 AATACTTGGATTTTAACTTCACAACGAAGGATATCCAATTCAAAGC
*
3191176 TCAACTTCAAAACGAAGG-GACCATCCATGATTTCAACTTCACAACGAAA-GATATCATGCCAAC
1 TCAACTTCACAACGAAGGAG-CCATCCATGATTTCAACTTCACAAC-AAAGGATATCATGCCAAC
* * ** * * *
3191239 AAT-CTTTGGATTTCAACTTAATGACAAAGGATATACAATTCAATGC
64 AATAC-TTGGATTTTAACTTCACAACGAAGGATATCCAATTCAAAGC
3191285 TCAACTTCACAACGAAGGA
1 TCAACTTCACAACGAAGGA
3191304 TATCGTGCCA
Statistics
Matches: 303, Mismatches: 34, Indels: 17
0.86 0.10 0.05
Matches are distributed among these distances:
108 7 0.02
109 288 0.95
110 8 0.03
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (109 bp):
TCAACTTCACAACGAAGGAGCCATCCATGATTTCAACTTCACAACAAAGGATATCATGCCAACAA
TACTTGGATTTTAACTTCACAACGAAGGATATCCAATTCAAAGC
Found at i:3191238 original size:218 final size:218
Alignment explanation
Indices: 3190849--3191300 Score: 674
Period size: 218 Copynumber: 2.1 Consensus size: 218
3190839 AGATTGGATT
** *
3190849 TCAACTTCACAACGAATGAGCCATCCATGATTTCAACTTCACGACGAAGGATATCGTGCCAACAA
1 TCAACTTCACAACGAATGAGCCATCCATGATTTCAACTTCACGAAAAAGGATATCATGCCAACAA
* * * * *
3190914 TACTTGGATTTGGACTTCACAACGAAGGATATCCAATTTAAAGCTCAACTTCACAATGAAGGAGT
66 TACTTGGATTTGAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCAAAACGAAGGAGC
* * *
3190979 CATCCACGATTTCAACTTCACAACAAAGTATATCGTGCCAACAATCTTTGGATTTTAACTTCACG
131 CATCCACGATTTCAACTTCACAACAAAGTATATCATGCCAACAATCTTTGGATTTCAACTTAACG
** *
3191044 ATGAAGGATATCCAATTCAAAGC
196 ACAAAGGATATACAATTCAAAGC
* *
3191067 TCAACTTCACAACGAATGGGCCATCCATGATTTCAATTTCACGAAAAAGGATATCATGCCAACAA
1 TCAACTTCACAACGAATGAGCCATCCATGATTTCAACTTCACGAAAAAGGATATCATGCCAACAA
* * *
3191132 TACTTGGATTTTAACTTCACAACGAAGGATATCTAATTCAAAGTTCAACTTCAAAACGAAGG-GA
66 TACTTGGATTTGAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCAAAACGAAGGAG-
*
3191196 CCATCCATGATTTCAACTTCACAACGAAAG-ATATCATGCCAACAATCTTTGGATTTCAACTTAA
130 CCATCCACGATTTCAACTTCACAAC-AAAGTATATCATGCCAACAATCTTTGGATTTCAACTTAA
* *
3191260 TGACAAAGGATATACAATTCAATGC
194 CGACAAAGGATATACAATTCAAAGC
3191285 TCAACTTCACAACGAA
1 TCAACTTCACAACGAA
3191301 GGATATCGTG
Statistics
Matches: 210, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
217 1 0.00
218 205 0.98
219 4 0.02
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (218 bp):
TCAACTTCACAACGAATGAGCCATCCATGATTTCAACTTCACGAAAAAGGATATCATGCCAACAA
TACTTGGATTTGAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCAAAACGAAGGAGC
CATCCACGATTTCAACTTCACAACAAAGTATATCATGCCAACAATCTTTGGATTTCAACTTAACG
ACAAAGGATATACAATTCAAAGC
Found at i:3191306 original size:77 final size:77
Alignment explanation
Indices: 3191208--3191377 Score: 277
Period size: 77 Copynumber: 2.2 Consensus size: 77
3191198 ATCCATGATT
3191208 TCAACTTCACAACGAAAGATATCATGCCAACAATCTTTGGATTTCAACTTAATGACAAAGGATAT
1 TCAACTTCACAACGAAAGATATCATGCCAACAATCTTTGGATTTCAACTTAATGACAAAGGATAT
3191273 ACAATTCAATGC
66 ACAATTCAATGC
* * * ***
3191285 TCAACTTCACAACGAAGGATATCGTGCCAACAATCTTTGGATTTTAACTTAATGGTGAAGGATAT
1 TCAACTTCACAACGAAAGATATCATGCCAACAATCTTTGGATTTCAACTTAATGACAAAGGATAT
*
3191350 CCAATTCAATGC
66 ACAATTCAATGC
3191362 TCAACTTCACAACGAA
1 TCAACTTCACAACGAA
3191378 TGAGCCACCT
Statistics
Matches: 86, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 86 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.28
Consensus pattern (77 bp):
TCAACTTCACAACGAAAGATATCATGCCAACAATCTTTGGATTTCAACTTAATGACAAAGGATAT
ACAATTCAATGC
Found at i:3191935 original size:3 final size:3
Alignment explanation
Indices: 3191916--3191972 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
3191906 ATACAAAAAA
3191916 ATT A-T ATT A-T ATT -TT ATT ATT ATT ATT ATT ATT ATT ATT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
* *
3191959 ATT TTT ATT TTT AT
1 ATT ATT ATT ATT AT
3191973 AGGCCCCATG
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 6 0.13
3 37 0.80
4 3 0.07
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
ATT
Found at i:3193367 original size:64 final size:65
Alignment explanation
Indices: 3193254--3193395 Score: 171
Period size: 64 Copynumber: 2.2 Consensus size: 65
3193244 TGCACTAAGA
* *
3193254 GTGCATCGATGCATCAAGTGCATTCGATGATTTAAAATAGCCAGAGTGCATCGATGCATGG-CTG
1 GTGCATCGATGCATCAAATGCATTCGATGATTCAAAATAGCCAGAGTGCATCGATGCATGGACTG
** ** ** *
3193318 GTGCATCGATGCATCAAATGCATTCGATG-TTCAATTTAATTCATTGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGATTCAAAAT-AGCCAGAGTGCATCGATGCATGGACT
3193382 G
65 G
*
3193383 GTGCATCGGTGCA
1 GTGCATCGATGCA
3193396 ATACTCTGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
63 5 0.08
64 47 0.71
65 14 0.21
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATCAAATGCATTCGATGATTCAAAATAGCCAGAGTGCATCGATGCATGGACTG
Found at i:3196077 original size:24 final size:24
Alignment explanation
Indices: 3196057--3196118 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
3196047 GTATCAACAT
3196057 GATGAATTGATGCACATTCAAAGG
1 GATGAATTGATGCACATTCAAAGG
*
3196081 GATGCATTGATGCACATTCAAAGG
1 GATGAATTGATGCACATTCAAAGG
* *
3196105 GATGCATCGATGCA
1 GATGAATTGATGCA
3196119 TTGTTAAGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (24 bp):
GATGAATTGATGCACATTCAAAGG
Found at i:3201959 original size:65 final size:64
Alignment explanation
Indices: 3201825--3201982 Score: 185
Period size: 65 Copynumber: 2.5 Consensus size: 64
3201815 TGCACTAAGA
* * * *
3201825 GTGCATCGATTCATCAAGTGCATTTGATGATTTAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGATTTAAAATAGCCACAGTGCATCGATGCATGGCTG
* * * *
3201889 GTGCATCGATGCATCAAATGCATTCGATGCTTTCATAAA-ATCCTCAGTGCATCGGTGCATGG-T
1 GTGCATCGATGCATCAAATGCATTCGATGATTT-A-AAATAGCCACAGTGCATCGATGCATGGCT
*
3201952 AT
64 -G
*
3201954 GTGCATCGATGCATGAAATGCATTCGATG
1 GTGCATCGATGCATCAAATGCATTCGATG
3201983 TTCAATTTAA
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
64 30 0.37
65 48 0.59
66 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGATTTAAAATAGCCACAGTGCATCGATGCATGGCTG
Found at i:3202023 original size:65 final size:63
Alignment explanation
Indices: 3201869--3202034 Score: 194
Period size: 65 Copynumber: 2.6 Consensus size: 63
3201859 AAATAGCCAG
*
3201869 AGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGCTTTCATAAAATCCTC
1 AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATGC-TTCATAAAAT-CTC
* * **
3201934 AGTGCATCGGTGCATGGTAT-GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAAT-TC
1 AGTGCATCGATGCATGGT-TGGTGCATCGATGCATCAAATGCATTCGATGCTTC-ATAAAATCTC
*
3201996 ATGGTGCATCGATGCATGGATTGGTGCATCGGTGCATCA
1 A--GTGCATCGATGCATGG-TTGGTGCATCGATGCATCA
3202035 CTCTGAAAAA
Statistics
Matches: 87, Mismatches: 8, Indels: 12
0.81 0.07 0.11
Matches are distributed among these distances:
62 3 0.03
63 3 0.03
64 21 0.24
65 59 0.68
66 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (63 bp):
AGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGCATTCGATGCTTCATAAAATCTC
Found at i:3204031 original size:30 final size:30
Alignment explanation
Indices: 3203995--3204070 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
3203985 CGAGTCAACT
* *
3203995 TGTTGACTTTAATCAAGTCAACCCATTGAC
1 TGTTGACTTTAACCAAGTCAACCCATTGAA
* * *
3204025 TGTTGACTTTGACCGAGTCAACCCGTTGAA
1 TGTTGACTTTAACCAAGTCAACCCATTGAA
*
3204055 TGTTGACTTTGACCAA
1 TGTTGACTTTAACCAA
3204071 AAAAGTCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.33
Consensus pattern (30 bp):
TGTTGACTTTAACCAAGTCAACCCATTGAA
Found at i:3211832 original size:21 final size:21
Alignment explanation
Indices: 3211791--3211832 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3211781 CTTTGTAATC
*
3211791 TGCCTCTTGGCTTCCCCAGCT
1 TGCCTCTTGGCTTCCACAGCT
*
3211812 TGCCTC-TGAGCTTCCATAGCT
1 TGCCTCTTG-GCTTCCACAGCT
3211833 AGTTGTTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.10, C:0.38, G:0.19, T:0.33
Consensus pattern (21 bp):
TGCCTCTTGGCTTCCACAGCT
Found at i:3216576 original size:16 final size:17
Alignment explanation
Indices: 3216545--3216579 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3216535 TCGGTAAGTC
*
3216545 TTTCTCTTCCTTTTTCT
1 TTTCTCTTCCTGTTTCT
3216562 TTTCTCTT-CTGTTTCT
1 TTTCTCTTCCTGTTTCT
3216578 TT
1 TT
3216580 GCTACTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.00, C:0.26, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTCTCTTCCTGTTTCT
Found at i:3217110 original size:3 final size:3
Alignment explanation
Indices: 3217102--3217229 Score: 211
Period size: 3 Copynumber: 42.3 Consensus size: 3
3217092 ATAATATATT
3217102 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
3217150 TATA TAA TGA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3217196 TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3217230 GATATGGGTA
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
3 113 0.97
4 3 0.03
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3217768 original size:113 final size:113
Alignment explanation
Indices: 3217549--3218308 Score: 1167
Period size: 113 Copynumber: 6.8 Consensus size: 113
3217539 GATAGAATTA
* *
3217549 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTAT
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTCTCATTAT
* * * * * * ** *
3217614 GAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAG
63 GAACT-TTCTCTGGAAAAGATAATCCATCAAATAATGAATTCAAGTAAAAGG
* *
3217665 TTGAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
3217730 TTTTCTCTGGAAAAGATAATCCATCAATTAATGAATTCAGGTAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAAATAATGAATTCAAGTAAAAGG
3217778 TTGAACAAA--CTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * *
3217840 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAAATAATGAATTCAAGTAAAAGG
3217888 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
3217953 CTTTCTCTGGAAAAGATAATCCATCAATTAATGAATTCAGGTAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAAATAATGAATTCAAGTAAAAGG
3218001 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * * *
3218066 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAAATAATGAATTCAAGTAAAAGG
3218114 TTGAACAAATTC-T-TCATTATGAACTTCTTCTTCCTTCTTCAGATGA-TTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
3218176 CTTTCTCTGGAAAAGATAATCCATCAATTAATGAATTCAGGT-AAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAAATAATGAATTCAAGTAAAAGG
3218223 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
3218288 CTTTCTCTGGAAAAGCTAATC
66 CTTTCTCTGGAAAAGATAATC
3218309 TTTCAAATGA
Statistics
Matches: 595, Mismatches: 42, Indels: 18
0.91 0.06 0.03
Matches are distributed among these distances:
109 17 0.03
110 133 0.22
111 88 0.15
112 62 0.10
113 254 0.43
114 1 0.00
116 40 0.07
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (113 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGGAAAAGATAATCCATCAAATAATGAATTCAAGTAAAAGG
Found at i:3217893 original size:223 final size:225
Alignment explanation
Indices: 3217549--3218300 Score: 1284
Period size: 223 Copynumber: 3.3 Consensus size: 225
3217539 GATAGAATTA
* *
3217549 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTAT
1 TTGAACAA-ATCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTCTCATTAT
* * * * ** * *
3217614 GAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCT
62 GAACT-TTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAATTCT
* *
3217678 TCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAATTTTCTCTGGAAA
126 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
3217743 AGATAATCCATCAATTAATGAATTCAGGTAAAAGG
191 AGATAATCCATCAATTAATGAATTCAGGTAAAAGG
3217778 TTGAACAAA-CTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAATCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
3217841 TTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCA
66 TTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCA
3217906 TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATA
131 TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATA
3217971 ATCCATCAATTAATGAATTCAGGTAAAAGG
196 ATCCATCAATTAATGAATTCAGGTAAAAGG
3218001 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAA-TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
3218066 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAATTC-T-TC
65 CTTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTC
3218129 ATTATGAACTTCTTCTTCCTTCTTCAGATGA-TTCTTCTCATTATGAACTTTCTCTGGAAAAGAT
130 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAT
3218193 AATCCATCAATTAATGAATTCAGGT-AAAGG
195 AATCCATCAATTAATGAATTCAGGTAAAAGG
3218223 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAA-TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
3218288 CTTTCTCTGGAAA
65 CTTTCTCTGGAAA
3218301 AGCTAATCTT
Statistics
Matches: 507, Mismatches: 12, Indels: 15
0.95 0.02 0.03
Matches are distributed among these distances:
222 85 0.17
223 237 0.47
224 34 0.07
225 24 0.05
226 97 0.19
227 22 0.04
229 8 0.02
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (225 bp):
TTGAACAAATCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
TTTCTCTGGAAATGATGATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAATTCTTCTCA
TTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATA
ATCCATCAATTAATGAATTCAGGTAAAAGG
Found at i:3218016 original size:336 final size:335
Alignment explanation
Indices: 3217549--3218308 Score: 1175
Period size: 336 Copynumber: 2.3 Consensus size: 335
3217539 GATAGAATTA
* *
3217549 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGATGAGTTCTTCTCATTAT
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCTTCTCATTAT
* * * * * * *
3217614 GAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAACAAAAAGTTGAACAAGTTCT
63 GAACT-TTCTCTGGAAAAGATAATCCATCAAATAATGAATTCAAACAAAAAGTTGAACAAATTCT
* *
3217678 TCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAATTTTCTCTGGAAA
127 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
* *
3217743 AGATAATCCATCAATTAATGAATTCAGGTAAAAGGTTGAACAAACTTC-TCATTATGAACTTCTT
192 AGATAATCCATCAAATAATGAATTCAAGTAAAAGGTTGAACAAA-TTCTTCATTATGAACTTCTT
* * *
3217807 CTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGA
256 CTTCCTTCTTCAGATGA-TTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCATCAAATAA
*
3217871 TGGATTCAAGTAAAAGG
320 TGAATTCAAGT-AAAGG
3217888 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *** *
3217953 CTTTCTCTGGAAAAGATAATCCATCAATTAATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTC
66 CTTTCTCTGGAAAAGATAATCCATCAAATAATGAATTCAAACAAAAAGTTGAACAAATTCTTCTC
*
3218018 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATGAT
131 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAT
* * *
3218083 GATCCATCAAATGATGGATTCAAGTAAAAGGTTGAACAAATTCTTCATTATGAACTTCTTCTTCC
196 AATCCATCAAATAATGAATTCAAGTAAAAGGTTGAACAAATTCTTCATTATGAACTTCTTCTTCC
*
3218148 TTCTTCAGATGATTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCATCAATTAATGAATT
261 TTCTTCAGATGATTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCATCAAATAATGAATT
*
3218213 CAGGTAAAGG
326 CAAGTAAAGG
3218223 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
3218288 CTTTCTCTGGAAAAGCTAATC
66 CTTTCTCTGGAAAAGATAATC
3218309 TTTCAAATGA
Statistics
Matches: 389, Mismatches: 29, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
335 95 0.24
336 240 0.62
337 14 0.04
339 40 0.10
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (335 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGGAAAAGATAATCCATCAAATAATGAATTCAAACAAAAAGTTGAACAAATTCTTCTC
ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAT
AATCCATCAAATAATGAATTCAAGTAAAAGGTTGAACAAATTCTTCATTATGAACTTCTTCTTCC
TTCTTCAGATGATTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCATCAAATAATGAATT
CAAGTAAAGG
Found at i:3219451 original size:83 final size:83
Alignment explanation
Indices: 3219111--3219643 Score: 710
Period size: 82 Copynumber: 6.4 Consensus size: 83
3219101 CTTATTTTTA
* * * * *
3219111 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGTTCATACCAAACCAGATAAC
1 CTATGAGCAAATTCATCTTCCCAATTCAATGATTGG--TTCT--GTCCA-ACCAGATCAGATAAC
3219176 TCAAAGAACACTTCCAGAAGATG
61 TCAAAGAACACTTCCAGAAGATG
* ** *
3219199 TTATTG-GCAAATTCATCTTCTAAACTCAATGATT-GTTCTGTCCAACCAGATCAGATAACTCAA
1 CTA-TGAGCAAATTCATCTTCCCAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAA
3219262 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* ** *
3219281 CTATTG-GCAAATTTATCTTCTAAACTCAATGATT-GTTCTGTCCAACCAGATCAGATAACTCAA
1 CTA-TGAGCAAATTCATCTTCCCAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAA
3219344 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
*
3219363 CTATGAGCACATTCATCTTCCCAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAA
1 CTATGAGCAAATTCATCTTCCCAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAA
* *
3219427 AGAACACTTCTAGAAAATG
65 AGAACACTTCCAGAAGATG
* *
3219446 TTATGAGCACATTCATCTTCCCAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAA
1 CTATGAGCAAATTCATCTTCCCAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAA
3219510 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* *
3219529 CTATTG-GCAAATTCATCTT-CCAGTT-AATGTTTGGTTCTGTCCAACCAGATCAGATAACTCAA
1 CTA-TGAGCAAATTCATCTTCCCAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAA
3219591 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
*
3219610 CTATGAGCAAATTCATCTT-CCAATT-AATGTTTGG
1 CTATGAGCAAATTCATCTTCCCAATTCAATGATTGG
3219644 ACTAAGATAT
Statistics
Matches: 414, Mismatches: 24, Indels: 21
0.90 0.05 0.05
Matches are distributed among these distances:
80 2 0.00
81 84 0.20
82 151 0.36
83 141 0.34
84 2 0.00
85 3 0.01
87 1 0.00
88 28 0.07
89 2 0.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (83 bp):
CTATGAGCAAATTCATCTTCCCAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:3219568 original size:247 final size:249
Alignment explanation
Indices: 3219111--3219643 Score: 776
Period size: 247 Copynumber: 2.1 Consensus size: 249
3219101 CTTATTTTTA
* * * *
3219111 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTTTGGGTTCATACCAAACCAGATAAC
1 CTATGAGCAAATTCATCTTCCCAATTCAATGATTGG-TTTCT-GGTCCAAACCAAACCAGATAAC
* *
3219176 TCAAAGAACACTTCCAGAAGATGTTATTGGCAAATTCATCTTCTAAACTCAATGATTGTTCTGTC
64 TCAAAGAACACTTCCAGAAAATGTTATTGGCAAATTCATCTTCCAAACTCAATGATTGTTCTGTC
*
3219241 CAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTTATCTTCTAAAC
129 CAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTC-AAAC
3219306 TCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
193 TCAATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
* * *
3219363 CTATGAGCACATTCATCTTCCCAATTCAATGATTGG-TTCT-G-CCAAACCAGATCAGATAACTC
1 CTATGAGCAAATTCATCTTCCCAATTCAATGATTGGTTTCTGGTCCAAACCAAACCAGATAACTC
* * * *
3219425 AAAGAACACTTCTAGAAAATGTTA-TGAGCACATTCATCTTCCCAATTCAATGATTGGTTCTG-C
66 AAAGAACACTTCCAGAAAATGTTATTG-GCAAATTCATCTTCCAAACTCAATGATT-GTTCTGTC
* *
3219488 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTC-CAG
129 C-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCAAAC
* *
3219552 TTAATGTTTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
193 TCAATGATT-GTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
*
3219610 CTATGAGCAAATTCATCTT-CCAATT-AATGTTTGG
1 CTATGAGCAAATTCATCTTCCCAATTCAATGATTGG
3219644 ACTAAGATAT
Statistics
Matches: 257, Mismatches: 20, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
245 8 0.03
246 16 0.06
247 131 0.51
248 65 0.25
250 3 0.01
252 34 0.13
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (249 bp):
CTATGAGCAAATTCATCTTCCCAATTCAATGATTGGTTTCTGGTCCAAACCAAACCAGATAACTC
AAAGAACACTTCCAGAAAATGTTATTGGCAAATTCATCTTCCAAACTCAATGATTGTTCTGTCCA
ACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCAAACTCA
ATGATTGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
Found at i:3220776 original size:10 final size:10
Alignment explanation
Indices: 3220763--3220789 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3220753 CCCCTTTTTC
3220763 TTTTTTTCTT
1 TTTTTTTCTT
3220773 TTTTTTTCTT
1 TTTTTTTCTT
3220783 TTTTTTT
1 TTTTTTT
3220790 TCTTCAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:3220779 original size:11 final size:11
Alignment explanation
Indices: 3220763--3220793 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3220753 CCCCTTTTTC
3220763 TTTTTTTC-TT
1 TTTTTTTCTTT
3220773 TTTTTTTCTTT
1 TTTTTTTCTTT
3220784 TTTTTTTCTT
1 TTTTTTTCTT
3220794 CAAGCATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.40
11 12 0.60
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:3233040 original size:16 final size:15
Alignment explanation
Indices: 3233019--3233054 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
3233009 CCTCGGTAAG
*
3233019 TCTTTCTCTTCCTTTT
1 TCTTTCTCTT-CTGTT
3233035 TCTTTCTCTTCTGTT
1 TCTTTCTCTTCTGTT
3233050 TCTTT
1 TCTTT
3233055 GCTACTGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.00, C:0.28, G:0.03, T:0.69
Consensus pattern (15 bp):
TCTTTCTCTTCTGTT
Found at i:3233598 original size:3 final size:3
Alignment explanation
Indices: 3233590--3233710 Score: 188
Period size: 3 Copynumber: 40.3 Consensus size: 3
3233580 TTAATATATT
*
3233590 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
3233638 TAA TGA TGA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
3233686 TAA TAA TAA TAA TAA TAA TGA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
3233711 GATATGGGTA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 108 1.00
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3235355 original size:30 final size:30
Alignment explanation
Indices: 3235321--3235448 Score: 161
Period size: 30 Copynumber: 4.3 Consensus size: 30
3235311 ACAGGTTGGG
* *
3235321 ACAGCTTGGTGGAGTATTTGGAAGACATAT
1 ACAGCTTAGTGGAGCATTTGGAAGACATAT
*
3235351 ACAGCTT-GATGGAGAATTTGGAAGACATAT
1 ACAGCTTAG-TGGAGCATTTGGAAGACATAT
*
3235381 ACAGCTTAGTGGAGCATTTGGAAGACATAA
1 ACAGCTTAGTGGAGCATTTGGAAGACATAT
* *
3235411 ACAACTTAGTGGAGCATTTAGG-AGACATAA
1 ACAGCTTAGTGGAGCATTT-GGAAGACATAT
*
3235441 ACAACTTA
1 ACAGCTTA
3235449 CAAACAACTC
Statistics
Matches: 91, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
29 1 0.01
30 87 0.96
31 3 0.03
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (30 bp):
ACAGCTTAGTGGAGCATTTGGAAGACATAT
Found at i:3239206 original size:127 final size:127
Alignment explanation
Indices: 3238980--3239215 Score: 472
Period size: 127 Copynumber: 1.9 Consensus size: 127
3238970 TCATTCAAAT
3238980 ATATGTTATGATTACATATCAATTCTTAGGATACTATTATTACATGTTTCCATTTATCATTTATT
1 ATATGTTATGATTACATATCAATTCTTAGGATACTATTATTACATGTTTCCATTTATCATTTATT
3239045 ACCATGATATTCATGCATACAACATATTCACATCTTTACAATAGATGCACATTGTCATTTAA
66 ACCATGATATTCATGCATACAACATATTCACATCTTTACAATAGATGCACATTGTCATTTAA
3239107 ATATGTTATGATTACATATCAATTCTTAGGATACTATTATTACATGTTTCCATTTATCATTTATT
1 ATATGTTATGATTACATATCAATTCTTAGGATACTATTATTACATGTTTCCATTTATCATTTATT
3239172 ACCATGATATTCATGCATACAACATATTCACATCTTTACAATAG
66 ACCATGATATTCATGCATACAACATATTCACATCTTTACAATAG
3239216 TCTTGCATTC
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 109 1.00
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.42
Consensus pattern (127 bp):
ATATGTTATGATTACATATCAATTCTTAGGATACTATTATTACATGTTTCCATTTATCATTTATT
ACCATGATATTCATGCATACAACATATTCACATCTTTACAATAGATGCACATTGTCATTTAA
Found at i:3239647 original size:30 final size:30
Alignment explanation
Indices: 3239495--3239643 Score: 192
Period size: 30 Copynumber: 5.0 Consensus size: 30
3239485 ACACGTTGGG
*
3239495 ACAACTT-GATGGAGCATTTGAAAGACATAT
1 ACAACTTAG-TGGAGCATTTGGAAGACATAT
* **
3239525 ACAACTTGGTGGAGCATTTAAAAGACATAT
1 ACAACTTAGTGGAGCATTTGGAAGACATAT
* *
3239555 ACAACTTGGTGGAGTATTTGGAAGACATAT
1 ACAACTTAGTGGAGCATTTGGAAGACATAT
* * *
3239585 ATAGCTTAGTGGAGCATTTGGAAGACATAA
1 ACAACTTAGTGGAGCATTTGGAAGACATAT
*
3239615 ACAACTTAGTGGAGCATTTGGGAGACATA
1 ACAACTTAGTGGAGCATTTGGAAGACATA
3239644 AACAGCTCAC
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
30 105 0.99
31 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (30 bp):
ACAACTTAGTGGAGCATTTGGAAGACATAT
Found at i:3246374 original size:22 final size:22
Alignment explanation
Indices: 3246333--3246375 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3246323 GTCAACAGAT
*
3246333 CTTGATTGTGTTTGTTTTTTTG
1 CTTGATTGTGTTTGTCTTTTTG
3246355 CTTGATTGTG-TTGTACTTTTT
1 CTTGATTGTGTTTGT-CTTTTT
3246376 TTCTCCATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.07, C:0.07, G:0.21, T:0.65
Consensus pattern (22 bp):
CTTGATTGTGTTTGTCTTTTTG
Found at i:3246755 original size:82 final size:81
Alignment explanation
Indices: 3246657--3247005 Score: 315
Period size: 83 Copynumber: 4.2 Consensus size: 81
3246647 TTAGCAGCGT
** * * * * * *
3246657 TTTTTCAATGAACGCCGCAATAGAGTGGTAATGTAGCGGCGTTTATACCTCAAACGTCGGAACAA
1 TTTTTCAACAAACGCCGCAATAGAGTAGTAATTTAGCGGCGTTTATA-CACAAACGCCGCAACAG
3246722 GGTTGTTTATAGTGGCG
65 GGTTGTTTATAGTGGCG
* * * *
3246739 TTTTTCAACAAACGCCGCAATAGAGTGGTAATTTAGTGGCGTTTTTATACAAACGCCGCAACAGG
1 TTTTTCAACAAACGCCGCAATAGAGTAGTAATTTAGCGGCGTTTATACACAAACGCCGCAACAGG
* *
3246804 GTTGTTTATATTGGTG
66 GTTGTTTATAGTGGCG
* * * * * * * * *
3246820 TTTGTCCAACAACCGGCGCTATAGAGAAGTAATTTAGCGGCGTTTATCAAACAAACGTCGTAATA
1 TTT-TTCAACAAACGCCGCAATAGAGTAGTAATTTAGCGGCGTTTAT-ACACAAACGCCGCAACA
*
3246885 GGGTTGTTTCTAGTGGCG
64 GGGTTGTTTATAGTGGCG
* * * * * *
3246903 TTTGTGCAA-AAAGCGCCACAATAGAGTAATAATTTAGCGGCGTTTGTACGACAAATGCCGCAAT
1 TTT-TTCAACAAA-CGCCGCAATAGAGTAGTAATTTAGCGGCGTTTATAC-ACAAACGCCGCAAC
* * *
3246967 ATGTTTGTTTATAGTGGCA
63 AGGGTTGTTTATAGTGGCG
*
3246986 TTTTT-ATAAAAACGCCGCAA
1 TTTTTCA-ACAAACGCCGCAA
3247006 AAACATGTAC
Statistics
Matches: 216, Mismatches: 45, Indels: 12
0.79 0.16 0.04
Matches are distributed among these distances:
81 31 0.14
82 89 0.41
83 96 0.44
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (81 bp):
TTTTTCAACAAACGCCGCAATAGAGTAGTAATTTAGCGGCGTTTATACACAAACGCCGCAACAGG
GTTGTTTATAGTGGCG
Found at i:3246776 original size:41 final size:42
Alignment explanation
Indices: 3246653--3246967 Score: 150
Period size: 41 Copynumber: 7.6 Consensus size: 42
3246643 TACTTTAGCA
* ** * * *
3246653 GCGTTTTTTCAATGAACGCCGCAATAGAGTGGTAATGTAGCG
1 GCGTTTGTTCAACAAACGCCGCAATAGAGTTGTAATTTAGTG
* * ** * * *
3246695 GCGTTTATACCTCAAACGTCGGAACA-AGGTTGT--TTATAGTG
1 GCGTTTGTTCAACAAACGCCGCAATAGA-GTTGTAATT-TAGTG
*
3246736 GCGTTT-TTCAACAAACGCCGCAATAGAGTGGTAATTTAGTG
1 GCGTTTGTTCAACAAACGCCGCAATAGAGTTGTAATTTAGTG
* * *
3246777 GCGTTT-TT-ATACAAACGCCGCAACAGGGTTGT--TTATATTG
1 GCGTTTGTTCA-ACAAACGCCGCAATAGAGTTGTAATT-TAGTG
* * * * * ** *
3246817 GTGTTTGTCCAACAACCGGCGCTATAGAGAAGTAATTTAGCG
1 GCGTTTGTTCAACAAACGCCGCAATAGAGTTGTAATTTAGTG
* * * *
3246859 GCGTTT-ATCAAACAAACGTCGTAATAGGGTTGT--TTCTAGTG
1 GCGTTTGTTC-AACAAACGCCGCAATAGAGTTGTAATT-TAGTG
* * ** *
3246900 GCGTTTGTGCAA-AAAGCGCCACAATAGAGTAATAATTTAGCG
1 GCGTTTGTTCAACAAA-CGCCGCAATAGAGTTGTAATTTAGTG
* * *
3246942 GCGTTTGTACGACAAATGCCGCAATA
1 GCGTTTGTTCAACAAACGCCGCAATA
3246968 TGTTTGTTTA
Statistics
Matches: 197, Mismatches: 58, Indels: 36
0.68 0.20 0.12
Matches are distributed among these distances:
39 2 0.01
40 33 0.17
41 84 0.43
42 71 0.36
43 7 0.04
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (42 bp):
GCGTTTGTTCAACAAACGCCGCAATAGAGTTGTAATTTAGTG
Found at i:3247437 original size:22 final size:22
Alignment explanation
Indices: 3247409--3247456 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
3247399 TGTTTTTCTT
3247409 CTTTCGAATAGAAAAATAATAG
1 CTTTCGAATAGAAAAATAATAG
*
3247431 CTTTCGAATAGGAAAATAATAG
1 CTTTCGAATAGAAAAATAATAG
3247453 CTTT
1 CTTT
3247457 TGAAAACGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (22 bp):
CTTTCGAATAGAAAAATAATAG
Found at i:3251860 original size:139 final size:137
Alignment explanation
Indices: 3251700--3252072 Score: 401
Period size: 139 Copynumber: 2.7 Consensus size: 137
3251690 CCTTGAACTT
* * * * *
3251700 TCTAATTTAGGGGAATTTTTTATTTGCTCATCGCATTTGTGCACGATGTTCCATTTCAATTATTC
1 TCTAATTTAGGAGAATTTTTTATTTGCTCATCGCACTTATGC-CGAGGTTCCATTTTAATTATTC
* * **
3251765 GATTCAATAATTGGATAAAATTTATTAGGATTAACAATTAGAGCCTCCATTTTAT-TTTAATTTC
65 GATTCAATAATTAGTTAAAATTTATTAGG-TTAA-AATTAGAGCCTCCACCTTATATTTAATTTC
*
3251829 ACTTTAGTTC
128 ACTTTAGTCC
* * * *
3251839 TCTAATTTAGGTGAATTTTTTATTTGATTC-TCACACTTAAGCTCGAGGTTCCATTTTAATTATT
1 TCTAATTTAGGAGAATTTTTTATTTG-CTCATCGCACTTATGC-CGAGGTTCCATTTTAATTATT
* * * * *
3251903 CG-TTCTAAGAATTAGTTAAAATTGATTATGGTTAATATTAGAGCTTTCACCTTATATTTAATTT
64 CGATTC-AATAATTAGTTAAAATTTATTA-GGTTAAAATTAGAGCCTCCACCTTATATTTAATTT
3251967 CACTTTAGTCC
127 CACTTTAGTCC
* * * * * * *
3251978 TTTAATTTAGGAGGATTTTTAATTTGGTCATCGTACTTATACCTGAGGTTCCATTTTAATTATTT
1 TCTAATTTAGGAGAATTTTTTATTTGCTCATCGCACTTATGCC-GAGGTTCCATTTTAATTATTC
* *
3252043 GATTCAATAATTTGTTAAAATTTGTTAGGT
65 GATTCAATAATTAGTTAAAATTTATTAGGT
3252073 CTTAATATTA
Statistics
Matches: 194, Mismatches: 33, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
138 24 0.12
139 163 0.84
140 7 0.04
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (137 bp):
TCTAATTTAGGAGAATTTTTTATTTGCTCATCGCACTTATGCCGAGGTTCCATTTTAATTATTCG
ATTCAATAATTAGTTAAAATTTATTAGGTTAAAATTAGAGCCTCCACCTTATATTTAATTTCACT
TTAGTCC
Found at i:3255233 original size:23 final size:23
Alignment explanation
Indices: 3255200--3255267 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
3255190 AACCTTATAT
3255200 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
3255223 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
3255246 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
3255268 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:3256611 original size:51 final size:51
Alignment explanation
Indices: 3256502--3256613 Score: 138
Period size: 51 Copynumber: 2.2 Consensus size: 51
3256492 AGGATTAGAT
* * * *
3256502 TTATTATTTTATTAAGAATTAAGATAGATTTAAAATATTATCTTTAGTTTA
1 TTATTATTTTATTAAGAATTAAGATAGAATCAAAATATTATATATAGTTTA
*
3256553 TTATTATTTTATTAGGAATTATA-ATAGAATCAAAATATTATATATAGCTTT-
1 TTATTATTTTATTAAGAATTA-AGATAGAATCAAAATATTATATATAG-TTTA
*
3256604 TTTTTATTTT
1 TTATTATTTT
3256614 TTTCAATAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
51 49 0.92
52 4 0.08
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (51 bp):
TTATTATTTTATTAAGAATTAAGATAGAATCAAAATATTATATATAGTTTA
Found at i:3266365 original size:6 final size:7
Alignment explanation
Indices: 3266341--3266370 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3266331 GACCCGACCC
3266341 GACCGTT
1 GACCGTT
3266348 GACCGTT
1 GACCGTT
3266355 GACCG-T
1 GACCGTT
3266361 GACCGTT
1 GACCGTT
3266368 GAC
1 GAC
3266371 TTCCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:3266365 original size:13 final size:14
Alignment explanation
Indices: 3266341--3266370 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3266331 GACCCGACCC
3266341 GACCGTTGACCGTT
1 GACCGTTGACCGTT
3266355 GACCG-TGACCGTT
1 GACCGTTGACCGTT
3266368 GAC
1 GAC
3266371 TTCCTTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.17, C:0.30, G:0.30, T:0.23
Consensus pattern (14 bp):
GACCGTTGACCGTT
Found at i:3270091 original size:3 final size:3
Alignment explanation
Indices: 3270083--3270146 Score: 51
Period size: 3 Copynumber: 21.3 Consensus size: 3
3270073 TAAAATTAGT
* * *
3270083 TAA TAA TAA T-A TCCAA TAA TAA TAA CAA CAA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA T--AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
3270129 T-A TAA TAG TAT TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
3270147 TAAACTATGG
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.08
3 46 0.88
5 2 0.04
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:3271039 original size:10 final size:9
Alignment explanation
Indices: 3271021--3271101 Score: 54
Period size: 10 Copynumber: 8.1 Consensus size: 9
3271011 GACATAAGAT
3271021 AAAATAAAA
1 AAAATAAAA
3271030 AAAATGAAAA
1 AAAAT-AAAA
* *
3271040 GAGATAAATA
1 AAAATAAA-A
3271050 AAAATAAATA
1 AAAATAAA-A
3271060 AAAATAAAA
1 AAAATAAAA
* *
3271069 TAAAGAAATA
1 AAAATAAA-A
3271079 AGAAGATAAAA
1 A-AA-ATAAAA
3271090 ACACAATAAAA
1 A-A-AATAAAA
3271101 A
1 A
3271102 CGAAAAAAGT
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
9 15 0.26
10 25 0.44
11 12 0.21
12 5 0.09
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (9 bp):
AAAATAAAA
Found at i:3271046 original size:29 final size:29
Alignment explanation
Indices: 3271009--3271068 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
3270999 GGCAAGTATG
3271009 AAGACATAAGAT-AAAATAAA-AAAAATGAA
1 AAGACATAA-ATAAAAATAAATAAAAAT-AA
*
3271038 AAGAGATAAATAAAAATAAATAAAAATAA
1 AAGACATAAATAAAAATAAATAAAAATAA
3271067 AA
1 AA
3271069 TAAAGAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 2 0.07
29 20 0.71
30 6 0.21
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (29 bp):
AAGACATAAATAAAAATAAATAAAAATAA
Found at i:3271051 original size:23 final size:25
Alignment explanation
Indices: 3271017--3271063 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
3271007 TGAAGACATA
*
3271017 AGATAAAATAAAAA-AAATGAAAAG
1 AGATAAAATAAAAATAAATAAAAAG
3271041 AGAT-AAATAAAAATAAATAAAAA
1 AGATAAAATAAAAATAAATAAAAA
3271064 TAAAATAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.15
Consensus pattern (25 bp):
AGATAAAATAAAAATAAATAAAAAG
Found at i:3271077 original size:29 final size:29
Alignment explanation
Indices: 3271021--3271090 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 29
3271011 GACATAAGAT
* *
3271021 AAAATAAAAAAAATGAAAAGAGATAAATA
1 AAAATAAAAAAAATGAAAAGAAAGAAATA
*
3271050 AAAATAAATAAAAAT-AAAATAAAGAAATA
1 AAAATAAA-AAAAATGAAAAGAAAGAAATA
3271079 AGAAGATAAAAA
1 A-AA-ATAAAAA
3271091 CACAATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 20 0.57
30 10 0.29
31 5 0.14
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (29 bp):
AAAATAAAAAAAATGAAAAGAAAGAAATA
Found at i:3271098 original size:38 final size:39
Alignment explanation
Indices: 3271021--3271101 Score: 96
Period size: 38 Copynumber: 2.1 Consensus size: 39
3271011 GACATAAGAT
*
3271021 AAAATAAAAAAAATGAAAAGAGATAAATAAAAATAAATA
1 AAAATAAAAAAAATGAAAAGAGATAAATAAAAACAAATA
* *
3271060 AAAATAAAATAAA-GAAATA-AGA-AGATAAAAACACAATA
1 AAAATAAAAAAAATGAAA-AGAGATAAATAAAAACA-AATA
3271098 AAAA
1 AAAA
3271102 CGAAAAAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
37 9 0.24
38 15 0.41
39 13 0.35
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (39 bp):
AAAATAAAAAAAATGAAAAGAGATAAATAAAAACAAATA
Found at i:3271206 original size:2 final size:2
Alignment explanation
Indices: 3271199--3271258 Score: 63
Period size: 2 Copynumber: 31.5 Consensus size: 2
3271189 GAATTAAATA
* * * *
3271199 AT AT AT AT AT AT AT AT AT GT A- AT A- AC GT AT AA AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3271238 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
3271259 AGTAATAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
1 3 0.06
2 45 0.94
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3271287 original size:43 final size:42
Alignment explanation
Indices: 3271193--3271276 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 42
3271183 TAATAAGAAT
* *
3271193 TAAATA-ATATATATATATATATATGTAATAACGTATAAATAA
1 TAAATATATATATATATATATATAAGTAATAAC-AATAAATAA
*
3271235 TATATATATATATATATATATATAAGTAATAA-AATAAGATAA
1 TAAATATATATATATATATATATAAGTAATAACAATAA-ATAA
3271277 ACGAATATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 4 0.11
42 9 0.24
43 24 0.65
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (42 bp):
TAAATATATATATATATATATATAAGTAATAACAATAAATAA
Found at i:3271297 original size:3 final size:3
Alignment explanation
Indices: 3271289--3271314 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3271279 GAATATATAC
3271289 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
3271315 CAGAGGGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3272366 original size:2 final size:2
Alignment explanation
Indices: 3272357--3272388 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3272347 ATATGTTTAT
3272357 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3272389 GTAATGTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3274284 original size:6 final size:6
Alignment explanation
Indices: 3274269--3274326 Score: 52
Period size: 6 Copynumber: 10.0 Consensus size: 6
3274259 ACCCACCTTA
* *
3274269 TTTTTC -TTTTC TTTTT- TTTTTC -TTTTG TTCTTC TTTCTAT- TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTT-T-TC TTTTTC
3274315 TTTTTC TTTTTC
1 TTTTTC TTTTTC
3274327 AATTTAAGGC
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
5 15 0.36
6 22 0.52
7 4 0.10
8 1 0.02
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:3274305 original size:15 final size:14
Alignment explanation
Indices: 3274285--3274324 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
3274275 TTTTCTTTTT
3274285 TTTTTCTTTTGTTC
1 TTTTTCTTTTGTTC
*
3274299 TTCTTTCTATTTTTTC
1 TT-TTTCT-TTTGTTC
3274315 TTTTTCTTTT
1 TTTTTCTTTT
3274325 TCAATTTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 5 0.22
15 10 0.43
16 8 0.35
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.80
Consensus pattern (14 bp):
TTTTTCTTTTGTTC
Found at i:3284694 original size:23 final size:22
Alignment explanation
Indices: 3284668--3284733 Score: 53
Period size: 24 Copynumber: 2.9 Consensus size: 22
3284658 ATGAAGACAT
3284668 AAGATAAAATAGAAAAAAATGAA
1 AAGATAAAATAGAAAAAAAT-AA
* *
3284691 AAGAGATAAATAAAAATAAAATAA
1 AAGATA-AAATAGAAA-AAAATAA
* *
3284715 AGAAATAAGA-AGAAAAAAA
1 A-AGATAAAATAGAAAAAAA
3284734 CACAATAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
22 4 0.12
23 9 0.26
24 13 0.38
25 8 0.24
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (22 bp):
AAGATAAAATAGAAAAAAATAA
Found at i:3284697 original size:25 final size:23
Alignment explanation
Indices: 3284669--3284733 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
3284659 TGAAGACATA
3284669 AGATAAAATAGAAAAAAATGAAAAG
1 AGATAAAATAGAAAAAAAT--AAAG
*
3284694 AGAT-AAATAAAAATAAAATAAAG
1 AGATAAAATAGAAA-AAAATAAAG
* *
3284717 AAATAAGA-AGAAAAAAA
1 AGATAAAATAGAAAAAAA
3284734 CACAATAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
22 4 0.12
23 11 0.32
24 10 0.29
25 9 0.26
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (23 bp):
AGATAAAATAGAAAAAAATAAAG
Found at i:3284720 original size:19 final size:18
Alignment explanation
Indices: 3284698--3284752 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
3284688 GAAAAGAGAT
* *
3284698 AAATAAAAATAAAATAAAG
1 AAATAAAAAGAAAA-AAAC
*
3284717 AAATAAGAAGAAAAAAAC
1 AAATAAAAAGAAAAAAAC
3284735 ACAATAAAAAAGAAAAAA
1 A-AAT-AAAAAGAAAAAA
3284753 TGAGGAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 4 0.13
19 15 0.50
20 11 0.37
ACGTcount: A:0.80, C:0.04, G:0.07, T:0.09
Consensus pattern (18 bp):
AAATAAAAAGAAAAAAAC
Found at i:3284816 original size:3 final size:3
Alignment explanation
Indices: 3284808--3284965 Score: 98
Period size: 3 Copynumber: 51.7 Consensus size: 3
3284798 CAAGATAAAA
*
3284808 AAT AAT AAT AAT AAT AAT AAT TA- AAT AA- AAT -AT ATAT ATAT ACAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT A-AT A-AT
* *
3284853 ATGT AAT AACGT -AT AAAT AAA AAT -AT ATAT ATAT AAT AAT AAGT AAT
1 A-AT AAT AA--T AAT -AAT AAT AAT AAT A-AT A-AT AAT AAT AA-T AAT
* ** *
3284900 AA- AAT AA- GAT AA- ACG AAT ATAT AAA AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
3284943 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
3284966 CATAGGGATT
Statistics
Matches: 125, Mismatches: 15, Indels: 30
0.74 0.09 0.18
Matches are distributed among these distances:
2 12 0.10
3 84 0.67
4 28 0.22
5 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3284861 original size:40 final size:39
Alignment explanation
Indices: 3284808--3284965 Score: 136
Period size: 40 Copynumber: 4.1 Consensus size: 39
3284798 CAAGATAAAA
*
3284808 AATAATAA-TAATAATAATAATTAAATAAAATATATATAT
1 AATAATAAGTAATAATAATAAATAAA-AAAATATATATAT
* *
3284847 -ATACATATGTAATAACGT-ATAAATAAAAATATATATATAT
1 AATA-ATAAGTAATAA--TAATAAATAAAAAAATATATATAT
** *
3284887 AATAATAAGTAATAA-AATAAGATAAACGAATATATA-AA
1 AATAATAAGTAATAATAATAA-ATAAAAAAATATATATAT
*
3284925 AATAATAA-TAATAATAAT-AATAATAATAATA-ATA-AT
1 AATAATAAGTAATAATAATAAATAA-AAAAATATATATAT
3284961 AATAA
1 AATAA
3284966 CATAGGGATT
Statistics
Matches: 99, Mismatches: 11, Indels: 21
0.76 0.08 0.16
Matches are distributed among these distances:
36 13 0.13
37 12 0.12
38 19 0.19
39 15 0.15
40 28 0.28
41 11 0.11
42 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (39 bp):
AATAATAAGTAATAATAATAAATAAAAAAATATATATAT
Found at i:3291679 original size:2 final size:2
Alignment explanation
Indices: 3291672--3291708 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
3291662 TCTTTAAAAC
3291672 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3291709 CCCCCATCCG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3291895 original size:24 final size:24
Alignment explanation
Indices: 3291868--3291974 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
3291858 AAACGGAGAT
*
3291868 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
3291892 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * * *
3291916 GTTAGGAATCATATCAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
3291940 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
3291964 ATCAGAAATCA
1 ATCAGAAATCA
3291975 GATAAAATAT
Statistics
Matches: 61, Mismatches: 22, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:3291974 original size:48 final size:48
Alignment explanation
Indices: 3291868--3291974 Score: 115
Period size: 48 Copynumber: 2.2 Consensus size: 48
3291858 AAACGGAGAT
* * *
3291868 ATCAGAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * * *
3291916 GTTAGGAATCATATCAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
3291964 ATCAGAAATCA
1 ATCAGAAATCA
3291975 GATAAAATAT
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.47, C:0.17, G:0.13, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:3296449 original size:17 final size:17
Alignment explanation
Indices: 3296376--3296451 Score: 62
Period size: 17 Copynumber: 4.4 Consensus size: 17
3296366 TACAACATAA
* *
3296376 AAAAGGAGTTGTAACCT
1 AAAATGAGTTGCAACCT
* * * *
3296393 ATAATGTGGTGCAAACT
1 AAAATGAGTTGCAACCT
* * *
3296410 AAAATGAGATACAGCCAT
1 AAAATGAGTTGCAACC-T
3296428 AAAATGAGTTGCAACCT
1 AAAATGAGTTGCAACCT
3296445 AAAATGA
1 AAAATGA
3296452 CAATCATAAA
Statistics
Matches: 43, Mismatches: 15, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
17 29 0.67
18 14 0.33
ACGTcount: A:0.45, C:0.13, G:0.20, T:0.22
Consensus pattern (17 bp):
AAAATGAGTTGCAACCT
Found at i:3296940 original size:37 final size:37
Alignment explanation
Indices: 3296890--3296964 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
3296880 TAAATATAAA
3296890 TTAAAAAGTTGCCCACAATCACATGGTCCTACAATGT
1 TTAAAAAGTTGCCCACAATCACATGGTCCTACAATGT
3296927 TTAAAAAGTTGCCCACAATCACATGGTCCTACAATGT
1 TTAAAAAGTTGCCCACAATCACATGGTCCTACAATGT
3296964 T
1 T
3296965 ATTATCTGGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (37 bp):
TTAAAAAGTTGCCCACAATCACATGGTCCTACAATGT
Found at i:3297228 original size:3 final size:3
Alignment explanation
Indices: 3297222--3297256 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3297212 AAATAATAAC
3297222 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3297257 GTATTAGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3300782 original size:18 final size:19
Alignment explanation
Indices: 3300756--3300794 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3300746 TCGGGTTTCA
*
3300756 TTTATTTTAA-ATTTTATT
1 TTTACTTTAAGATTTTATT
*
3300774 TTTACTTTAAGTTTTTATT
1 TTTACTTTAAGATTTTATT
3300793 TT
1 TT
3300795 CTTTTCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTACTTTAAGATTTTATT
Found at i:3306169 original size:21 final size:21
Alignment explanation
Indices: 3306143--3306194 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
3306133 GAAGTAAGTA
3306143 TCGATACTCATTTAAAGGGAG
1 TCGATACTCATTTAAAGGGAG
*
3306164 TCGATACTCATTTAATGGGAG
1 TCGATACTCATTTAAAGGGAG
3306185 TCGATACTCA
1 TCGATACTCA
3306195 GGGTCTGGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (21 bp):
TCGATACTCATTTAAAGGGAG
Found at i:3309862 original size:14 final size:14
Alignment explanation
Indices: 3309845--3309886 Score: 68
Period size: 14 Copynumber: 3.0 Consensus size: 14
3309835 TCGTTTCTTA
3309845 ATTT-TTTTTTTTGT
1 ATTTATTTTTTTT-T
3309859 ATTTATTTTTTTTT
1 ATTTATTTTTTTTT
3309873 ATTTATTTTTTTTT
1 ATTTATTTTTTTTT
3309887 CTTGAATTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 19 0.70
15 8 0.30
ACGTcount: A:0.12, C:0.00, G:0.02, T:0.86
Consensus pattern (14 bp):
ATTTATTTTTTTTT
Found at i:3309866 original size:18 final size:18
Alignment explanation
Indices: 3309845--3309886 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
3309835 TCGTTTCTTA
3309845 ATTTTTTTTT-TTGTATTT
1 ATTTTTTTTTATT-TATTT
3309863 ATTTTTTTTTATTTATTT
1 ATTTTTTTTTATTTATTT
3309881 -TTTTTT
1 ATTTTTT
3309887 CTTGAATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.26
18 15 0.65
19 2 0.09
ACGTcount: A:0.12, C:0.00, G:0.02, T:0.86
Consensus pattern (18 bp):
ATTTTTTTTTATTTATTT
Found at i:3309867 original size:32 final size:33
Alignment explanation
Indices: 3309828--3309895 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
3309818 CTAACCCCTT
* *
3309828 TTTATTTTCGTTTCTTAATTTTTTTTT-TTGTA
1 TTTATTTTCGTTTATTAATTTTTTTTTCTTGAA
** *
3309860 TTTATTTTTTTTTATTTATTTTTTTTTCTTGAA
1 TTTATTTTCGTTTATTAATTTTTTTTTCTTGAA
3309893 TTT
1 TTT
3309896 CAAGTCCCCG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 23 0.77
33 7 0.23
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.78
Consensus pattern (33 bp):
TTTATTTTCGTTTATTAATTTTTTTTTCTTGAA
Found at i:3314480 original size:20 final size:20
Alignment explanation
Indices: 3314455--3314503 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
3314445 CATGATGAAG
3314455 GTATCGATATTGTACCAGCA
1 GTATCGATATTGTACCAGCA
3314475 GTATCGATATTGTACCAGCA
1 GTATCGATATTGTACCAGCA
3314495 GTATCGATA
1 GTATCGATA
3314504 CTGACCCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATATTGTACCAGCA
Found at i:3314542 original size:19 final size:20
Alignment explanation
Indices: 3314494--3314542 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
3314484 TTGTACCAGC
*
3314494 AGTATCGATACTGACCCATG
1 AGTATCGATACTCACCCATG
* *
3314514 GGTATC-ATACTCACTC-TG
1 AGTATCGATACTCACCCATG
3314532 AGTATCGATAC
1 AGTATCGATAC
3314543 CAAATATAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 7 0.29
19 12 0.50
20 5 0.21
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (20 bp):
AGTATCGATACTCACCCATG
Found at i:3315896 original size:39 final size:39
Alignment explanation
Indices: 3315842--3315930 Score: 133
Period size: 39 Copynumber: 2.3 Consensus size: 39
3315832 GTAAGGACAA
* * * *
3315842 TAAGGACTTATCCTGAGCACAAAGCCGAGGAGCCTGCGG
1 TAAGGACTTACCCTGAGCACAAAGCCGAGGAACATGCAG
*
3315881 TAAGGACTTACCCTGAGCACAAAGCTGAGGAACATGCAG
1 TAAGGACTTACCCTGAGCACAAAGCCGAGGAACATGCAG
3315920 TAAGGACTTAC
1 TAAGGACTTAC
3315931 AAGTCATAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.33, C:0.24, G:0.27, T:0.17
Consensus pattern (39 bp):
TAAGGACTTACCCTGAGCACAAAGCCGAGGAACATGCAG
Found at i:3316359 original size:3 final size:3
Alignment explanation
Indices: 3316351--3316402 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
3316341 TCCTAATATG
3316351 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3316398 ATA AT
1 ATA AT
3316403 CCTTATTTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:3322650 original size:39 final size:39
Alignment explanation
Indices: 3322589--3322678 Score: 128
Period size: 39 Copynumber: 2.3 Consensus size: 39
3322579 TCATAATGCT
*
3322589 GTAAGAACTTACCCTAAGCACAAAGCCAAAGAGCCTGCG
1 GTAAGGACTTACCCTAAGCACAAAGCCAAAGAGCCTGCG
* * *
3322628 GTAAGGACTTACCCTGAA-CACAAAGCCGAGGAGCTTGCG
1 GTAAGGACTTACCCT-AAGCACAAAGCCAAAGAGCCTGCG
3322667 GTAAGGACTTAC
1 GTAAGGACTTAC
3322679 AAGTCATAGA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 44 0.96
40 2 0.04
ACGTcount: A:0.34, C:0.26, G:0.24, T:0.16
Consensus pattern (39 bp):
GTAAGGACTTACCCTAAGCACAAAGCCAAAGAGCCTGCG
Found at i:3327667 original size:29 final size:29
Alignment explanation
Indices: 3327625--3327695 Score: 108
Period size: 29 Copynumber: 2.4 Consensus size: 29
3327615 GTCCCGGGGG
3327625 TAGGTCGCCATGCACGCCC-GACGACCTAC
1 TAGGTCGCCATGCACGCCCAG-CGACCTAC
**
3327654 TAGGTCGCCATGCACGCCCAGCGACCTGG
1 TAGGTCGCCATGCACGCCCAGCGACCTAC
3327683 TAGGTCGCCATGC
1 TAGGTCGCCATGC
3327696 GTGCCATGCG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
29 38 0.97
30 1 0.03
ACGTcount: A:0.18, C:0.38, G:0.28, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCCCAGCGACCTAC
Found at i:3327706 original size:29 final size:28
Alignment explanation
Indices: 3327623--3327709 Score: 102
Period size: 29 Copynumber: 3.0 Consensus size: 28
3327613 CAGTCCCGGG
*
3327623 GGTAGGTCGCCATGCACGCCCGACGACCT
1 GGTAGGTCGCCATGCACGCCAG-CGACCT
**
3327652 ACTAGGTCGCCATGCACGCCCAGCGACCT
1 GGTAGGTCGCCATGCACG-CCAGCGACCT
**
3327681 GGTAGGTCGCCATGCGTGCCATGCGACCT
1 GGTAGGTCGCCATGCACGCCA-GCGACCT
3327710 ACCAGCACCT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
28 3 0.06
29 43 0.88
30 3 0.06
ACGTcount: A:0.17, C:0.37, G:0.30, T:0.16
Consensus pattern (28 bp):
GGTAGGTCGCCATGCACGCCAGCGACCT
Found at i:3327727 original size:10 final size:10
Alignment explanation
Indices: 3327720--3327815 Score: 106
Period size: 10 Copynumber: 9.3 Consensus size: 10
3327710 ACCAGCACCT
3327720 CCATGCACGC
1 CCATGCACGC
3327730 CCATGCACGC
1 CCATGCACGC
*
3327740 CCA-ACGAC-C
1 CCATGC-ACGC
3327749 TCCATGCACGC
1 -CCATGCACGC
3327760 CCATGCACGACC
1 CCATGCACG--C
3327772 TCCATGCACGC
1 -CCATGCACGC
3327783 CCATGCACGC
1 CCATGCACGC
*
3327793 CCAGGCACGC
1 CCATGCACGC
*
3327803 CCAGGCACGC
1 CCATGCACGC
3327813 CCA
1 CCA
3327816 ACGACCTCCA
Statistics
Matches: 76, Mismatches: 3, Indels: 14
0.82 0.03 0.15
Matches are distributed among these distances:
9 2 0.03
10 61 0.80
11 3 0.04
12 1 0.01
13 9 0.12
ACGTcount: A:0.22, C:0.50, G:0.20, T:0.08
Consensus pattern (10 bp):
CCATGCACGC
Found at i:3327753 original size:20 final size:21
Alignment explanation
Indices: 3327730--3327785 Score: 87
Period size: 23 Copynumber: 2.6 Consensus size: 21
3327720 CCATGCACGC
3327730 CCATGCACGCCCA-ACGACCT
1 CCATGCACGCCCACACGACCT
3327750 CCATGCACGCCCATGCACGACCT
1 CCATGCACGCCCA--CACGACCT
3327773 CCATGCACGCCCA
1 CCATGCACGCCCA
3327786 TGCACGCCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 13 0.39
23 20 0.61
ACGTcount: A:0.23, C:0.50, G:0.16, T:0.11
Consensus pattern (21 bp):
CCATGCACGCCCACACGACCT
Found at i:3327778 original size:13 final size:13
Alignment explanation
Indices: 3327743--3327781 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
3327733 TGCACGCCCA
3327743 ACGACCTCCATGC
1 ACGACCTCCATGC
3327756 ACG--C-CCATGC
1 ACGACCTCCATGC
3327766 ACGACCTCCATGC
1 ACGACCTCCATGC
3327779 ACG
1 ACG
3327782 CCCATGCACG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
10 9 0.39
11 1 0.04
12 1 0.04
13 12 0.52
ACGTcount: A:0.23, C:0.46, G:0.18, T:0.13
Consensus pattern (13 bp):
ACGACCTCCATGC
Found at i:3327938 original size:19 final size:19
Alignment explanation
Indices: 3327914--3327976 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 19
3327904 CATACAGTCC
3327914 ATGATTTAATAATTTAGTA
1 ATGATTTAATAATTTAGTA
*
3327933 ATGA-TT--TAA--TACTA
1 ATGATTTAATAATTTAGTA
* *
3327947 ATGATTTCATAATTTAGTG
1 ATGATTTAATAATTTAGTA
3327966 ATGATTTAATA
1 ATGATTTAATA
3327977 CTAATGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
14 8 0.23
15 2 0.06
16 3 0.09
17 3 0.09
18 2 0.06
19 17 0.49
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (19 bp):
ATGATTTAATAATTTAGTA
Found at i:3327950 original size:14 final size:14
Alignment explanation
Indices: 3327931--3328929 Score: 285
Period size: 14 Copynumber: 71.3 Consensus size: 14
3327921 AATAATTTAG
*
3327931 TAATGATTTAATAC
1 TAATGATTTAATAA
*
3327945 TAATGATTTCATAA
1 TAATGATTTAATAA
*
3327959 TTTAGTGATGATTTAATAC
1 --TA---ATGATTTAATAA
3327978 TAATGA-TT--TAA
1 TAATGATTTAATAA
** *
3327989 TAATGATTTGTTAC
1 TAATGATTTAATAA
3328003 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
3328014 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
3328030 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
3328049 TAATGATTTGATAA
1 TAATGATTTAATAA
*
3328063 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
3328075 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
3328089 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
3328101 T-ATTATTTAGTAA
1 TAATGATTTAATAA
3328114 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
3328124 TAATGATTTAATAC
1 TAATGATTTAATAA
3328138 TAATGATTTAATAATTTA
1 TAATGATTTAAT-A---A
*
3328156 GTAATGATTTAATAC
1 -TAATGATTTAATAA
*
3328171 TAATGATTTCATAA
1 TAATGATTTAATAA
*
3328185 TTTAGTGATGATTTAATAC
1 --TA---ATGATTTAATAA
3328204 TAATGA-TT--TAA
1 TAATGATTTAATAA
** *
3328215 TAATGATTTGTTAC
1 TAATGATTTAATAA
3328229 TAATGATTT-A-AA
1 TAATGATTTAATAA
*
3328241 -AATGATTTAAATATT
1 TAATGATTT-AATA-A
*
3328256 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
3328275 TAATGATTTGATAA
1 TAATGATTTAATAA
*
3328289 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
3328301 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
3328315 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
3328327 T-ATTATTTAGTAA
1 TAATGATTTAATAA
3328340 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
3328350 TAATGATTTAATAC
1 TAATGATTTAATAA
3328364 TAATGATTTAATAATTTA
1 TAATGATTTAAT-A---A
*
3328382 GTAATGATTTAATAC
1 -TAATGATTTAATAA
*
3328397 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
3328411 TTTAGTGATGATTTAATAC
1 --TA---ATGATTTAATAA
3328430 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
3328441 TAATGATTTAATAC
1 TAATGATTTAATAA
3328455 TAATGA-TT--TAA
1 TAATGATTTAATAA
*
3328466 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
3328482 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
3328501 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
3328515 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
3328527 TAATGATTTGATAA
1 TAATGATTTAATAA
*
3328541 TAATCA-TT-ATAA
1 TAATGATTTAATAA
* *
3328553 AAATGATTTAGTAA
1 TAATGATTTAATAA
*
3328567 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
3328579 AAATGA-TT--TAA
1 TAATGATTTAATAA
*
3328590 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
3328606 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
3328625 TAATGATTTGATAA
1 TAATGATTTAATAA
*
3328639 TAATTA-TT-ATAA
1 TAATGATTTAATAA
*
3328651 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
3328665 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
3328677 T-ATTATTTAGTAA
1 TAATGATTTAATAA
3328690 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
3328700 TAATGATTTAATAC
1 TAATGATTTAATAA
*
3328714 TAATGA-TT--TGA
1 TAATGATTTAATAA
*
3328725 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
3328741 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
3328760 TAATGATTTGATAA
1 TAATGATTTAATAA
*
3328774 TAATTA-TT-ATAA
1 TAATGATTTAATAA
*
3328786 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
3328800 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
3328812 T-ATTATTTAGTAA
1 TAATGATTTAATAA
3328825 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
3328835 TAATGATTTAATAC
1 TAATGATTTAATAA
*
3328849 TAATGATTTCATAATTTAG
1 TAATGA-TT--TAA--TAA
*
3328868 TAATGATTTAATAC
1 TAATGATTTAATAA
3328882 TAATGATTTAATAA
1 TAATGATTTAATAA
*
3328896 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
3328912 TAATGATTTAATAC
1 TAATGATTTAATAA
3328926 TAAT
1 TAAT
3328930 AATAATGATT
Statistics
Matches: 762, Mismatches: 101, Indels: 244
0.69 0.09 0.22
Matches are distributed among these distances:
10 16 0.02
11 119 0.16
12 88 0.12
13 59 0.08
14 254 0.33
15 19 0.02
16 72 0.09
17 9 0.01
18 9 0.01
19 107 0.14
20 10 0.01
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:3327959 original size:33 final size:33
Alignment explanation
Indices: 3327914--3327992 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
3327904 CATACAGTCC
3327914 ATGATTTAATAATTTAGTAATGATTTAATACTA
1 ATGATTTAATAATTTAGTAATGATTTAATACTA
* *
3327947 ATGATTTCATAATTTAGTGATGATTTAATACTA
1 ATGATTTAATAATTTAGTAATGATTTAATACTA
3327980 ATGATTTAATAAT
1 ATGATTTAATAAT
3327993 GATTTGTTAC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.46
Consensus pattern (33 bp):
ATGATTTAATAATTTAGTAATGATTTAATACTA
Found at i:3327986 original size:25 final size:25
Alignment explanation
Indices: 3327966--3328749 Score: 156
Period size: 25 Copynumber: 31.8 Consensus size: 25
3327956 TAATTTAGTG
3327966 ATGATTTAATACTAATGATTTAATA
1 ATGATTTAATACTAATGATTTAATA
**
3327991 ATGATTTGTTACTAATGATTTAATA
1 ATGATTTAATACTAATGATTTAATA
* *
3328016 ATGATTTAAATATTTAATGA-TT--TG
1 ATGATTT-AATA-CTAATGATTTAATA
* *
3328040 ATGA-TT--TAGTAATGATTTGATA
1 ATGATTTAATACTAATGATTTAATA
* * *
3328062 ATAATCATT-ATAATAATGATTTTATA
1 ATGAT--TTAATACTAATGATTTAATA
* * * * * *
3328088 AT-AATTATTTAGTTATTATTTAGTA
1 ATGATTTA-ATACTAATGATTTAATA
* *
3328113 ATTATTT-ATAATAATGATTTAATA
1 ATGATTTAATACTAATGATTTAATA
* * * * * *
3328137 CT-A-ATGAT-TTAATAATTTAGTA
1 ATGATTTAATACTAATGATTTAATA
*
3328159 ATGATTTAATACTAATGATTTCAT-
1 ATGATTTAATACTAATGATTTAATA
* *
3328183 A--A-TT--TAGTGATGATTTAATACTA
1 ATGATTTAATACTAATGATTT-A-A-TA
* * * *
3328206 ATGATTTAATAATGAT-TTGTTACTA
1 ATGATTTAATACTAATGAT-TTAATA
3328231 ATGATTTAA-A--AATGATTT-A-A
1 ATGATTTAATACTAATGATTTAATA
* * *
3328251 AT-ATTTAATGATTTGATGATTTAGTA
1 ATGATTTAAT-A-CTAATGATTTAATA
* * *
3328277 ATGATTTGATAATAATCATTATAATA
1 ATGATTTAATACTAATGATT-TAATA
* * * * *
3328303 ATGATTTTATAATAATTATTTAGTT
1 ATGATTTAATACTAATGATTTAATA
* * * *
3328328 ATTATTTAGTAATTAT--TTATAATA
1 ATGATTTAATACTAATGATT-TAATA
3328352 ATGATTTAATACTAATGATTTAAT-
1 ATGATTTAATACTAATGATTTAATA
*
3328376 A--A-TT--TAGTAATGATTTAATACTA
1 ATGATTTAATACTAATGATTT-A-A-TA
* *
3328399 ATGATTTAGTAATTTAGTGATGATTTAATACTA
1 ATGA-TT--TAA--TACTAATGATTT-A-A-TA
3328432 ATGATTT-A-A-TAATGATTTAATACTA
1 ATGATTTAATACTAATGATTT-A-A-TA
3328457 ATGATTT-A-A-TAATGATTT-A-A
1 ATGATTTAATACTAATGATTTAATA
* * *
3328477 AT-ATTTAATGATTTGATGATTTAGTA
1 ATGATTTAAT-A-CTAATGATTTAATA
* * * *
3328503 ATGATTTGATAATAATCATTATAGTA
1 ATGATTTAATACTAATGATT-TAATA
* * * *
3328529 ATGATTTGATAATAATCATTATAAAA
1 ATGATTTAATACTAATGATT-TAATA
* * * *
3328555 ATGATTTAGTAATAATCATTATAAAA
1 ATGATTTAATACTAATGATT-TAATA
3328581 ATGATTT-A-A-TAATGATTT-A-A
1 ATGATTTAATACTAATGATTTAATA
* * *
3328601 AT-ATTTAATGATTTGATGATTTAGTA
1 ATGATTTAAT-A-CTAATGATTTAATA
* * *
3328627 ATGATTTGATAATAATTATTATAATA
1 ATGATTTAATACTAATGATT-TAATA
* * * * *
3328653 ATGATTTGATAATAATTATTTAGTT
1 ATGATTTAATACTAATGATTTAATA
* * * *
3328678 ATTATTTAGTAATTAT--TTATAATA
1 ATGATTTAATACTAATGATT-TAATA
*
3328702 ATGATTTAATACTAATGATTTGATA
1 ATGATTTAATACTAATGATTTAATA
*
3328727 ATGATTTAAATATTTAATGATTT
1 ATGATTT-AATA-CTAATGATTT
3328750 GATGATTTAG
Statistics
Matches: 581, Mismatches: 102, Indels: 150
0.70 0.12 0.18
Matches are distributed among these distances:
19 41 0.07
20 16 0.03
21 8 0.01
22 29 0.05
23 22 0.04
24 78 0.13
25 164 0.28
26 152 0.26
27 36 0.06
28 8 0.01
29 2 0.00
30 1 0.00
32 2 0.00
33 22 0.04
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (25 bp):
ATGATTTAATACTAATGATTTAATA
Found at i:3327992 original size:11 final size:11
Alignment explanation
Indices: 3327978--3328896 Score: 170
Period size: 11 Copynumber: 76.4 Consensus size: 11
3327968 GATTTAATAC
3327978 TAATGATTTAA
1 TAATGATTTAA
*
3327989 TAATGATTTGTTAC
1 TAATGA--T-TTAA
3328003 TAATGATTTAA
1 TAATGATTTAA
3328014 TAATGATTT-A
1 TAATGATTTAA
3328024 -AAT-ATTTAA
1 TAATGATTTAA
*
3328033 TGATTTGATGATTTAG
1 T-A----ATGATTTAA
3328049 TAATGATTTGATAA
1 TAATGA-TT--TAA
*
3328063 TAATCATTATAA
1 TAATGATT-TAA
3328075 TAATGATTTTATAA
1 TAATGA--TT-TAA
* *
3328089 TAATTATTTAG
1 TAATGATTTAA
* * *
3328100 TTATTATTTAG
1 TAATGATTTAA
*
3328111 TAATTATTTATAA
1 TAATGA-TT-TAA
3328124 TAATGATTTAATA
1 TAATGATTT-A-A
3328137 CTAATGATTTAA
1 -TAATGATTTAA
*
3328149 T-A--ATTTAG
1 TAATGATTTAA
3328157 TAATGATTTAATA
1 TAATGATTT-A-A
*
3328170 CTAATGATTTCA
1 -TAATGATTTAA
*
3328182 T-A--ATTTAG
1 TAATGATTTAA
*
3328190 TGATGATTTAATA
1 TAATGATTT-A-A
3328203 CTAATGATTTAA
1 -TAATGATTTAA
*
3328215 TAATGATTTGTTAC
1 TAATGA--T-TTAA
3328229 TAATGATTTAA
1 TAATGATTTAA
*
3328240 AAATGATTT-A
1 TAATGATTTAA
3328250 -AAT-ATTTAA
1 TAATGATTTAA
*
3328259 TGATTTGATGATTTAG
1 T-A----ATGATTTAA
3328275 TAATGATTTGATAA
1 TAATGA-TT--TAA
*
3328289 TAATCATTATAA
1 TAATGATT-TAA
3328301 TAATGATTTTATAA
1 TAATGA--TT-TAA
* *
3328315 TAATTATTTAG
1 TAATGATTTAA
* * *
3328326 TTATTATTTAG
1 TAATGATTTAA
*
3328337 TAATTATTTATAA
1 TAATGA-TT-TAA
3328350 TAATGATTTAATA
1 TAATGATTT-A-A
3328363 CTAATGATTTAA
1 -TAATGATTTAA
*
3328375 T-A--ATTTAG
1 TAATGATTTAA
3328383 TAATGATTTAATA
1 TAATGATTT-A-A
*
3328396 CTAATGATTTAG
1 -TAATGATTTAA
*
3328408 T-A--ATTTAG
1 TAATGATTTAA
*
3328416 TGATGATTTAATA
1 TAATGATTT-A-A
3328429 CTAATGATTTAA
1 -TAATGATTTAA
3328441 TAATGATTTAATA
1 TAATGATTT-A-A
3328454 CTAATGATTTAA
1 -TAATGATTTAA
3328466 TAATGATTT-A
1 TAATGATTTAA
3328476 -AAT-ATTTAA
1 TAATGATTTAA
*
3328485 TGATTTGATGATTTAG
1 T-A----ATGATTTAA
3328501 TAATGATTTGATAA
1 TAATGA-TT--TAA
* *
3328515 TAATCATTATAG
1 TAATGATT-TAA
3328527 TAATGATTTGATAA
1 TAATGA-TT--TAA
*
3328541 TAATCATTATAA
1 TAATGATT-TAA
*
3328553 AAATGATTTAGTAA
1 TAATGA-TT--TAA
*
3328567 TAATCATTATAA
1 TAATGATT-TAA
*
3328579 AAATGATTTAA
1 TAATGATTTAA
3328590 TAATGATTT-A
1 TAATGATTTAA
3328600 -AAT-ATTTAA
1 TAATGATTTAA
*
3328609 TGATTTGATGATTTAG
1 T-A----ATGATTTAA
3328625 TAATGATTTGATAA
1 TAATGA-TT--TAA
*
3328639 TAATTATTATAA
1 TAATGATT-TAA
3328651 TAATGATTTGATAA
1 TAATGA-TT--TAA
* *
3328665 TAATTATTTAG
1 TAATGATTTAA
* * *
3328676 TTATTATTTAG
1 TAATGATTTAA
*
3328687 TAATTATTTATAA
1 TAATGA-TT-TAA
3328700 TAATGATTTAATA
1 TAATGATTT-A-A
*
3328713 CTAATGATTTGA
1 -TAATGATTTAA
3328725 TAATGATTT-A
1 TAATGATTTAA
3328735 -AAT-ATTTAA
1 TAATGATTTAA
*
3328744 TGATTTGATGATTTAG
1 T-A----ATGATTTAA
3328760 TAATGATTTGATAA
1 TAATGA-TT--TAA
*
3328774 TAATTATTATAA
1 TAATGATT-TAA
3328786 TAATGATTTTATAA
1 TAATGA--TT-TAA
* *
3328800 TAATTATTTAG
1 TAATGATTTAA
* * *
3328811 TTATTATTTAG
1 TAATGATTTAA
*
3328822 TAATTATTTATAA
1 TAATGA-TT-TAA
3328835 TAATGATTTAATA
1 TAATGATTT-A-A
*
3328848 CTAATGATTTCA
1 -TAATGATTTAA
*
3328860 T-A--ATTTAG
1 TAATGATTTAA
3328868 TAATGATTTAATA
1 TAATGATTT-A-A
3328881 CTAATGATTTAA
1 -TAATGATTTAA
3328893 TAAT
1 TAAT
3328897 AATGATTTAA
Statistics
Matches: 704, Mismatches: 78, Indels: 252
0.68 0.08 0.24
Matches are distributed among these distances:
8 49 0.07
9 25 0.04
10 10 0.01
11 199 0.28
12 114 0.16
13 64 0.09
14 198 0.28
15 15 0.02
16 30 0.04
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (11 bp):
TAATGATTTAA
Found at i:3328162 original size:19 final size:19
Alignment explanation
Indices: 3328138--3328202 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
3328128 GATTTAATAC
3328138 TAATGATTTAATAATTTAG
1 TAATGATTTAATAATTTAG
*
3328157 TAATGA-TT--TAA--TAC
1 TAATGATTTAATAATTTAG
*
3328171 TAATGATTTCATAATTTAG
1 TAATGATTTAATAATTTAG
*
3328190 TGATGATTTAATA
1 TAATGATTTAATA
3328203 CTAATGATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
14 8 0.22
15 2 0.05
16 3 0.08
17 3 0.08
18 2 0.05
19 19 0.51
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (19 bp):
TAATGATTTAATAATTTAG
Found at i:3328166 original size:135 final size:135
Alignment explanation
Indices: 3327986--3328879 Score: 604
Period size: 135 Copynumber: 6.4 Consensus size: 135
3327976 ACTAATGATT
** *
3327986 TAATAATGATTTGTTACTAATGATTTAATAATGATTTA-AAT-ATTTAATGATTTGATGATTTAG
1 TAATAATGATTTAATACTAATGATTTAATAAT--TTAATAATGATTTAATGATTTGATGATTTAG
*
3328049 TAATGATTTGATAATAATCATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAA
64 TAATGATTTGATAATAATGATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAA
3328114 TTATTTA
129 TTATTTA
* * *
3328121 TAATAATGATTTAATACTAATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTCATAAT
1 TAATAATGATTTAATACTAATGATTTAATAATTTAATAATGA--T--T--TAATGATTTGATGAT
* * * * * *** *
3328186 TTAGTGATGATTTAATACTAATGATT-TAATAATGATTTGT-TACTAATGATTTAAAAATGATTT
60 TTAGTAATGATTTGATAATAATGATTATAATAATGATTT-TATAATAATTATTTAGTTATTATTT
3328249 A--AA-TATTTAA
124 AGTAATTATTT-A
* * * * * * * * * * *
3328259 TGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTTAT-A-ATAATTAT
1 T-A-ATAATGATTTAATACT-A-ATGAT-TTAATAATT-TAATAATGATTTAATGATTTGATGAT
* * * * * * *
3328322 TTAGTTATTATTT-AGTAATTAT--TTATAATAATGATTTAATACTAATGATTTA---ATAATTT
60 TTAGTAATGATTTGA-TAATAATGATTATAATAATGATTTTATAATAATTATTTAGTTATTATTT
*
3328381 AGTAATGATTTAA
124 AGTAATTATTT-A
* * * * *
3328394 TACTAATGATTTAGTAATTTAGTGATGATTTAATACTAATGATTTAATAATGATTTAAT-A-CTA
1 TAATAATGA-TT--TAA--TACTAATGATTT-A-A-T-A--ATTTAATAATGATTTAATGATTTG
* * * * *
3328457 ATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCAT
55 ATGATTTAGTAATGATTT-GATA-ATAATGA-TT-AT-A---A-TAATGATTTTATAATAATTAT
* * *
3328522 TATAGTAATGATTT-GATAATAATCATTA
111 T-TAGTTATTATTTAG-TAATTAT--TTA
* * * * *
3328550 TAAAAATGATTTAGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTT
1 TAATAATGATTTAATACTAATGATT-T---AATAATTTAATAATG--------ATTTAATGATTT
* *
3328615 GATGATTTAGTAATGATTTGATAATAATTATTATAATAATGATTTGATAATAATTATTTAGTTAT
54 GATGATTTAGTAATGATTTGATAATAATGATTATAATAATGATTTTATAATAATTATTTAGTTAT
3328680 TATTTAGTAATTATTTA
119 TATTTAGTAATTATTTA
* *
3328697 TAATAATGATTTAATACTAATGATTTGATAATGATTTA-AAT-ATTTAATGATTTGATGATTTAG
1 TAATAATGATTTAATACTAATGATTTAATAAT--TTAATAATGATTTAATGATTTGATGATTTAG
*
3328760 TAATGATTTGATAATAATTATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAA
64 TAATGATTTGATAATAATGATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAA
3328825 TTATTTA
129 TTATTTA
* *
3328832 TAATAATGATTTAATACTAATGATTTCATAATTTAGTAATGATTTAAT
1 TAATAATGATTTAATACTAATGATTTAATAATTTAATAATGATTTAAT
3328880 ACTAATGATT
Statistics
Matches: 605, Mismatches: 84, Indels: 140
0.73 0.10 0.17
Matches are distributed among these distances:
132 7 0.01
133 9 0.01
134 13 0.02
135 196 0.32
136 28 0.05
137 8 0.01
138 11 0.02
139 2 0.00
140 74 0.12
141 42 0.07
142 9 0.01
143 11 0.02
144 11 0.02
145 5 0.01
146 3 0.00
147 25 0.04
149 27 0.04
150 23 0.04
151 28 0.05
152 4 0.01
153 3 0.00
154 4 0.01
155 16 0.03
156 10 0.02
157 14 0.02
158 4 0.01
159 18 0.03
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (135 bp):
TAATAATGATTTAATACTAATGATTTAATAATTTAATAATGATTTAATGATTTGATGATTTAGTA
ATGATTTGATAATAATGATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATT
ATTTA
Found at i:3328308 original size:226 final size:226
Alignment explanation
Indices: 3327914--3328591 Score: 1205
Period size: 226 Copynumber: 3.0 Consensus size: 226
3327904 CATACAGTCC
3327914 ATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTCATAATTTAGTGATGATTTAATACT
1 ATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTCATAATTTAGTGATGATTTAATACT
3327979 AATGATTTAATAATGATTTGTTACTAATGATTTAATAATGATTTAAATATTTAATGATTTGATGA
66 AATGATTTAATAATGATTTGTTACTAATGATTTAATAATGATTTAAATATTTAATGATTTGATGA
3328044 TTTAGTAATGATTTGATAATAATCATTATAATAATGATTTTATAATAATTATTTAGTTATTATTT
131 TTTAGTAATGATTTGATAATAATCATTATAATAATGATTTTATAATAATTATTTAGTTATTATTT
3328109 AGTAATTATTTATAATAATGATTTAATACTA
196 AGTAATTATTTATAATAATGATTTAATACTA
3328140 ATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTCATAATTTAGTGATGATTTAATACT
1 ATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTCATAATTTAGTGATGATTTAATACT
*
3328205 AATGATTTAATAATGATTTGTTACTAATGATTTAAAAATGATTTAAATATTTAATGATTTGATGA
66 AATGATTTAATAATGATTTGTTACTAATGATTTAATAATGATTTAAATATTTAATGATTTGATGA
3328270 TTTAGTAATGATTTGATAATAATCATTATAATAATGATTTTATAATAATTATTTAGTTATTATTT
131 TTTAGTAATGATTTGATAATAATCATTATAATAATGATTTTATAATAATTATTTAGTTATTATTT
3328335 AGTAATTATTTATAATAATGATTTAATACTA
196 AGTAATTATTTATAATAATGATTTAATACTA
3328366 ATGATTTAATAATTTAGTAATGATTTAATACTAATGATTT-AGTAATTTAGTGATGATTTAATAC
1 ATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTCA-TAATTTAGTGATGATTTAATAC
**
3328430 TAATGATTTAATAATGATTTAATACTAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
65 TAATGATTTAATAATGATTTGTTACTAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
* * * *** *
3328495 ATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAAAAATGAT
130 ATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTTATAATAATTATT-TAGTTATTAT
* *
3328560 TTAGTAATAATCATTATAAAAATGATTTAATA
194 TTAGTAATTAT--TTATAATAATGATTTAATA
3328592 ATGATTTAAA
Statistics
Matches: 435, Mismatches: 13, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
225 1 0.00
226 400 0.92
227 16 0.04
229 18 0.04
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (226 bp):
ATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTCATAATTTAGTGATGATTTAATACT
AATGATTTAATAATGATTTGTTACTAATGATTTAATAATGATTTAAATATTTAATGATTTGATGA
TTTAGTAATGATTTGATAATAATCATTATAATAATGATTTTATAATAATTATTTAGTTATTATTT
AGTAATTATTTATAATAATGATTTAATACTA
Found at i:3328388 original size:19 final size:19
Alignment explanation
Indices: 3328364--3328428 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 19
3328354 GATTTAATAC
3328364 TAATGATTTAATAATTTAG
1 TAATGATTTAATAATTTAG
*
3328383 TAATGA-TT--TAA--TAC
1 TAATGATTTAATAATTTAG
*
3328397 TAATGATTTAGTAATTTAG
1 TAATGATTTAATAATTTAG
*
3328416 TGATGATTTAATA
1 TAATGATTTAATA
3328429 CTAATGATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
14 8 0.22
15 2 0.05
16 3 0.08
17 3 0.08
18 2 0.05
19 19 0.51
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (19 bp):
TAATGATTTAATAATTTAG
Found at i:3328534 original size:26 final size:26
Alignment explanation
Indices: 3328498--3328676 Score: 153
Period size: 26 Copynumber: 7.2 Consensus size: 26
3328488 TTTGATGATT
3328498 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
3328524 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
**
3328550 TAAAAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
3328576 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
3328598 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
*
3328622 TAGTAATGATTTGATAATAATTATTA
1 TAGTAATGATTTGATAATAATCATTA
* *
3328648 TAATAATGATTTGATAATAATTATT-
1 TAGTAATGATTTGATAATAATCATTA
3328673 TAGT
1 TAGT
3328677 TATTATTTAG
Statistics
Matches: 132, Mismatches: 11, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
19 1 0.01
20 5 0.04
22 3 0.02
23 11 0.08
24 9 0.07
25 12 0.09
26 85 0.64
27 6 0.05
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.44
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:3328587 original size:124 final size:123
Alignment explanation
Indices: 3328456--3328847 Score: 522
Period size: 124 Copynumber: 3.1 Consensus size: 123
3328446 ATTTAATACT
*
3328456 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCA
1 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATTA
* * *
3328521 TTATAGTAATGATTTGATAATAATCATTATAAAAATGATTTAGTAATAATCATTATAAA
66 TTATAATAATGATTTGATAATAATTATTATAAAAATTATTTAGTAATAAT-ATTATAAA
3328580 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATTA
1 AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATTA
3328645 TTATAATAATGATTTGATAATAATTATTTAGTTATTATTTAGTAATTATTTA-TAATAATGATT-
66 TTATAATAATGATTTGATAATAATTA-TTA--TA--A---A--AATTATTTAGTAATAAT-ATTA
3328708 TAATA
120 TAA-A
*
3328713 CTAATGATTTGATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAAT
1 --AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAAT
* *** * *
3328778 TATTATAATAATGATTTTATAATAATTATT-TAGTTATTATTTAGTAATTAT-TTATAAT
64 TATTATAATAATGATTTGATAATAATTATTATAAAAATTATTTAGTAATAATATTATAAA
3328836 AATGATTTAATA
1 AATGATTTAATA
3328848 CTAATGATTT
Statistics
Matches: 240, Mismatches: 13, Indels: 33
0.84 0.05 0.12
Matches are distributed among these distances:
121 11 0.05
123 2 0.01
124 99 0.41
125 9 0.04
127 2 0.01
129 1 0.00
131 2 0.01
132 4 0.02
133 11 0.05
134 10 0.04
135 89 0.37
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47
Consensus pattern (123 bp):
AATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATTA
TTATAATAATGATTTGATAATAATTATTATAAAAATTATTTAGTAATAATATTATAAA
Found at i:3328596 original size:226 final size:226
Alignment explanation
Indices: 3327914--3328924 Score: 1150
Period size: 226 Copynumber: 4.5 Consensus size: 226
3327904 CATACAGTCC
3327914 ATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTCATAATTTAGTGATGATTTAATACT
1 ATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTCATAATTTAGTGATGATTTAATACT
**
3327979 AATGATTTAATAATGATTTGTTACTAATGATTTAATAATGATTTAAATATTTAATGATTTGATGA
66 AATGATTTAATAATGATTTAATACTAATGATTTAATAATGATTTAAATATTTAATGATTTGATGA
* * * *
3328044 TTTAGTAATGATTTGATAATAATCATTATAATAATGATTTTATAATAATTATTTAGTTATTATTT
131 TTTAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATTATTTAATAATGATTT
*
3328109 AGTAATTATTTATAATAATGATTTAATACTA
196 AGTAATAATTTATAATAATGATTTAATACTA
3328140 ATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTCATAATTTAGTGATGATTTAATACT
1 ATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTCATAATTTAGTGATGATTTAATACT
** *
3328205 AATGATTTAATAATGATTTGTTACTAATGATTTAAAAATGATTTAAATATTTAATGATTTGATGA
66 AATGATTTAATAATGATTTAATACTAATGATTTAATAATGATTTAAATATTTAATGATTTGATGA
* * * *
3328270 TTTAGTAATGATTTGATAATAATCATTATAATAATGATTTTATAATAATTATTTAGTTATTATTT
131 TTTAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATTATTTAATAATGATTT
*
3328335 AGTAATTATTTATAATAATGATTTAATACTA
196 AGTAATAATTTATAATAATGATTTAATACTA
3328366 ATGATTTAATAATTTAGTAATGATTTAATACTAATGATTT-AGTAATTTAGTGATGATTTAATAC
1 ATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTCA-TAATTTAGTGATGATTTAATAC
3328430 TAATGATTTAATAATGATTTAATACTAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
65 TAATGATTTAATAATGATTTAATACTAATGATTTAATAATGATTTAAATATTTAATGATTTGATG
* * *
3328495 ATTTAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAAAAATGAT
130 ATTTAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATTATT-TAATAATGAT
*
3328560 TTAGTAATAATCATTATAAAAATGATTT-A-A-TA
194 TTAGTAATAAT--TTATAATAATGATTTAATACTA
* * * * * * * * *
3328592 ATGATTTAA-ATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATTATTATAATAATG
1 ATGATTTAATA-ATTT-A-G---TAATGATTTAATACT-A-ATGAT-TTCATAATT-TAGTGATG
* * * * * * * * * *
3328656 ATTTGATAATAATTATTTAGTTATTATTTAGTAATTAT--TTATAATAATGATTT-AATA-CTAA
56 ATTTAATACTAATGATTTAATAATGATTTAATACTAATGATT-TAATAATGATTTAAATATTTAA
* * * * *
3328717 TGATTTGATAATGATTTA--AAT-ATTTAATGATTTGATGATT-TAGTAATGATTTGATAATAAT
120 TGATTTG---ATGATTTAGTAATGATTTGAT-A-ATAATCATTATAATAATGATTTGATAATAAT
* * * * *
3328778 TATTATAATAATGATTTTA-TAATAA-TTAT-TTAGTTA-TTATTTAGTA
180 TATT-TAATAATGA-TTTAGTAATAATTTATAATAATGATTTA-ATACTA
* *
3328824 ATTATTT-AT-A---A-TAATGATTTAATACTAATGATTTCATAATTTAGTAATGATTTAATACT
1 ATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTCATAATTTAGTGATGATTTAATACT
*
3328883 AATGATTTAATAATAATGATTTAAATATTTAATGATTTAATA
66 AATGA-TT--TAATAATGATTT-AATA-CTAATGATTTAATA
3328925 CTAATAATAA
Statistics
Matches: 691, Mismatches: 60, Indels: 71
0.84 0.07 0.09
Matches are distributed among these distances:
217 19 0.03
218 8 0.01
219 4 0.01
220 10 0.01
221 15 0.02
222 3 0.00
223 5 0.01
224 2 0.00
225 2 0.00
226 416 0.60
227 18 0.03
228 4 0.01
229 17 0.02
230 5 0.01
231 14 0.02
232 25 0.04
233 53 0.08
234 27 0.04
235 44 0.06
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (226 bp):
ATGATTTAATAATTTAGTAATGATTTAATACTAATGATTTCATAATTTAGTGATGATTTAATACT
AATGATTTAATAATGATTTAATACTAATGATTTAATAATGATTTAAATATTTAATGATTTGATGA
TTTAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATTATTTAATAATGATTT
AGTAATAATTTATAATAATGATTTAATACTA
Found at i:3328857 original size:124 final size:121
Alignment explanation
Indices: 3328229--3328847 Score: 341
Period size: 124 Copynumber: 5.1 Consensus size: 121
3328219 GATTTGTTAC
* *
3328229 TAATGATTTAAAAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATC
1 TAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATT
*
3328294 ATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTATTTATAA
66 ATTATAATAATGATTTGATAATAATTATTTAGTTATTATTTAGTAATTATTTATAA
*
3328350 TAATGATTTAATACTAATGATTT-AATAATTTAGTAATGATTTAATACTAATGATTTAGTAAT--
1 TAATGATTT-A-A-TAATGATTTAAAT-A-TT--TAATGA--T--T--TGATGATTTAGTAATGA
* * * * * * * * * * * * *
3328412 TTAG-TGATGATT-TAATACTAATGATTTAATAATGATT-TAATACTAATGATTTAATAATGATT
53 TTTGATAATAATTATTATAATAATGATTTGATAATAATTAT-TTAGTTATTATTTAGTAATTATT
*
3328474 TAAATATT
117 T--ATA-A
* * * * *
3328482 TAATGA-TT--TGATGATTTAGTAATGATTTGAT-A-ATAATCATTATAGTAATGATTTGATAAT
1 TAATGATTTAATAATGATTTA--AAT-ATTTAATGATTTGATGATT-TAGTAATGATTTGATAAT
* * * *** * * *
3328542 AATCATTATAAAAATGATTT-AGTAATAATCATTATAAAAATGATTTAATAATGA-TT-T-A
62 AATTATTATAATAATGATTTGA-TAATAATTATT-TAGTTATTATTTAGTAATTATTTATAA
* *
3328600 -AAT-A-TT--TAATGATTT-GATGATTTAGTAATGATTTGAT-A---A-TAATTA-TT-ATAAT
1 TAATGATTTAATAATGATTTAAAT-A-TT--TAATGATTTGATGATTTAGTAATGATTTGATAAT
* * *
3328652 AATGATTTGATAATAATTATTT-AGT--T-ATTATTTAGTAATTATTTA-TAATAATGATTTAAT
62 AATTA-TT-ATAATAATGATTTGA-TAATAATTATTTAGTTATTATTTAGTAAT--T-ATTT-AT
*
3328712 AC
120 AA
*
3328714 TAATGATTTGATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATT
1 TAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATT
*
3328779 ATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAATTATTTATAA
66 ATTATAATAATGATTTGATAATAATTATTTAGTTATTATTTAGTAATTATTTATAA
3328835 TAATGATTTAATA
1 TAATGATTTAATA
3328848 CTAATGATTT
Statistics
Matches: 381, Mismatches: 57, Indels: 120
0.68 0.10 0.22
Matches are distributed among these distances:
107 4 0.01
108 10 0.03
109 5 0.01
110 11 0.03
111 6 0.02
112 19 0.05
113 6 0.02
114 2 0.01
115 3 0.01
116 27 0.07
117 8 0.02
118 12 0.03
119 17 0.04
120 4 0.01
121 45 0.12
122 16 0.04
123 35 0.09
124 46 0.12
125 7 0.02
126 11 0.03
127 6 0.02
128 3 0.01
129 44 0.12
130 5 0.01
131 9 0.02
132 6 0.02
133 14 0.04
ACGTcount: A:0.42, C:0.01, G:0.10, T:0.47
Consensus pattern (121 bp):
TAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATT
ATTATAATAATGATTTGATAATAATTATTTAGTTATTATTTAGTAATTATTTATAA
Found at i:3328879 original size:8 final size:8
Alignment explanation
Indices: 3328868--3328923 Score: 50
Period size: 8 Copynumber: 7.5 Consensus size: 8
3328858 CATAATTTAG
3328868 TAATGATT
1 TAATGATT
*
3328876 TAAT-A-C
1 TAATGATT
3328882 TAATGATT
1 TAATGATT
*
3328890 TAAT-A-A
1 TAATGATT
3328896 TAATGATT
1 TAATGATT
3328904 TAAAT-ATT
1 T-AATGATT
3328912 TAATGATT
1 TAATGATT
3328920 TAAT
1 TAAT
3328924 ACTAATAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
6 8 0.21
7 7 0.18
8 20 0.53
9 3 0.08
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (8 bp):
TAATGATT
Found at i:3328900 original size:47 final size:45
Alignment explanation
Indices: 3328816--3328929 Score: 153
Period size: 47 Copynumber: 2.5 Consensus size: 45
3328806 TTTAGTTATT
* * *
3328816 ATTTAGTAATTATTT-ATAATAATGATTTAATACTAATGATTTCATA
1 ATTTAGTAATGATTTAATACTAATGATTTAATAATAATGATTT-A-A
3328862 ATTTAGTAATGATTTAATACTAATGATTTAATAATAATGATTTAA
1 ATTTAGTAATGATTTAATACTAATGATTTAATAATAATGATTTAA
3328907 ATATT--TAATGATTTAATACTAAT
1 AT-TTAGTAATGATTTAATACTAAT
3328930 AATAATGATT
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
44 18 0.29
45 3 0.05
46 17 0.27
47 25 0.40
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (45 bp):
ATTTAGTAATGATTTAATACTAATGATTTAATAATAATGATTTAA
Found at i:3328913 original size:36 final size:36
Alignment explanation
Indices: 3328835--3328940 Score: 98
Period size: 33 Copynumber: 3.0 Consensus size: 36
3328825 TTATTTATAA
* * *
3328835 TAATGATTTAATACTAATGATTTCATAAT--TTA-G
1 TAATGATTTAATACTAATGATTTAATAATAATGATT
3328868 TAATGATTTAATACTAATGATTTAATAATAATGATT
1 TAATGATTTAATACTAATGATTTAATAATAATGATT
* *
3328904 TAAAT-ATTTAATGATTTAAT-A-CTAATAATAATGATT
1 T-AATGATTTAAT-A-CTAATGATTTAATAATAATGATT
3328940 T
1 T
3328941 GATACTAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
33 28 0.45
35 2 0.03
36 23 0.37
37 5 0.08
38 4 0.06
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (36 bp):
TAATGATTTAATACTAATGATTTAATAATAATGATT
Found at i:3328937 original size:20 final size:20
Alignment explanation
Indices: 3328890--3328948 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
3328880 ACTAATGATT
3328890 TAATAATAATGATTTAA-A-
1 TAATAATAATGATTTAATAC
*
3328908 T-AT-TTAATGATTTAATAC
1 TAATAATAATGATTTAATAC
*
3328926 TAATAATAATGATTTGATAC
1 TAATAATAATGATTTAATAC
3328946 TAA
1 TAA
3328949 AAATCATTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 11 0.32
17 3 0.09
18 2 0.06
19 2 0.06
20 16 0.47
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (20 bp):
TAATAATAATGATTTAATAC
Done.