Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 127 of 175
Found at i:39711040 original size:25 final size:25
Alignment explanation
Indices: 39711001--39711085 Score: 75
Period size: 25 Copynumber: 3.4 Consensus size: 25
39710991 ATATGTCATT
* *
39711001 GGGAAGCTCATGAGAGCCGTAAATC
1 GGGAAGCTCAAGAGAGCCATAAATC
* * *
39711026 GGGTAGCTCAAGAGAGCTATTAATC
1 GGGAAGCTCAAGAGAGCCATAAATC
*
39711051 GGGAAGCTCATACA-AGCCA-AATATC
1 GGGAAGCTCA-AGAGAGCCATAA-ATC
*
39711076 AGGAAGCTCA
1 GGGAAGCTCA
39711086 TGAGTACTGT
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
24 1 0.02
25 45 0.94
26 2 0.04
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (25 bp):
GGGAAGCTCAAGAGAGCCATAAATC
Found at i:39718262 original size:71 final size:71
Alignment explanation
Indices: 39718057--39718262 Score: 234
Period size: 71 Copynumber: 2.9 Consensus size: 71
39718047 AGACTGCCTT
* * * *
39718057 CGATGTCACGACACAGCCCTGAAGACACGCCCAAGCTAGTAAGTTGCCTTCGGTGCCATGACACA
1 CGATGTCACGACACAGCCCTAAAGACTCGCCCAAGCTAGTAAATTGCCTTCGGTGTCATGACACA
*
39718122 GCCAAA
66 ACCAAA
* * * * *
39718128 CGATGTCACGACAGAGCCCTAAAGACAT-GCCCAAGCTAGTAGACTACCTTCGGTGTCACGACAC
1 CGATGTCACGACACAGCCCTAAAGAC-TCGCCCAAGCTAGTAAATTGCCTTCGGTGTCATGACAC
39718192 AACCAAA
65 AACCAAA
* ** * * * * *
39718199 GGATGTTGCGACACAGCCCTAAAGACTCACCCAAGTTAGTAAATTGCCATCAGTGTCGTGACAC
1 CGATGTCACGACACAGCCCTAAAGACTCGCCCAAGCTAGTAAATTGCCTTCGGTGTCATGACAC
39718263 CGACGTGACA
Statistics
Matches: 110, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
70 1 0.01
71 109 0.99
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.17
Consensus pattern (71 bp):
CGATGTCACGACACAGCCCTAAAGACTCGCCCAAGCTAGTAAATTGCCTTCGGTGTCATGACACA
ACCAAA
Found at i:39721176 original size:10 final size:10
Alignment explanation
Indices: 39721161--39721198 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
39721151 ATCGAAAATG
39721161 ATCAAAATTA
1 ATCAAAATTA
39721171 ATCAAAATTA
1 ATCAAAATTA
*
39721181 ATTAAAATTA
1 ATCAAAATTA
*
39721191 ATTAAAAT
1 ATCAAAAT
39721199 CCAACATGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (10 bp):
ATCAAAATTA
Found at i:39726922 original size:102 final size:101
Alignment explanation
Indices: 39726746--39727086 Score: 472
Period size: 102 Copynumber: 3.4 Consensus size: 101
39726736 CGATGAACAT
*
39726746 GTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAA
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAA
*
39726811 GTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCAC
66 GTGAAGGCTACTATGTGTACCGA-AAGCTTTGGTCAC
* *
39726848 GTGTGTAGTACTATGTGAAGGCTACTACGTGGATCGATAAATGATGGTCACATGTGTAGTACTAA
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAA
*
39726913 GTGAAGGCTATTATGTGTACCGAAAAGCTTTGGTCAC
66 GTGAAGGCTACTATGTGTACCG-AAAGCTTTGGTCAC
* * * * * * *
39726950 GTGTGTAGTACTATGTGAAGGCTACTATGTGAACCG-TAAA-ACTTGATAACGTGTGTAGTACTA
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATA-ATGGTCACATGTGTAGTACTA
* * * * *
39727013 TGTGAAGGCTACTACGTGAACCGTAAAAC-TTGATCAC
65 AGTGAAGGCTACTATGTGTACCG-AAAGCTTTGGTCAC
39727050 GTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
39727087 ATGATAAAAG
Statistics
Matches: 213, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
100 40 0.19
101 44 0.21
102 128 0.60
103 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.30
Consensus pattern (101 bp):
GTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAA
GTGAAGGCTACTATGTGTACCGAAAGCTTTGGTCAC
Found at i:39727013 original size:50 final size:50
Alignment explanation
Indices: 39726746--39727082 Score: 383
Period size: 51 Copynumber: 6.7 Consensus size: 50
39726736 CGATGAACAT
* * *
39726746 GTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATA-ATGGTCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTACCG-TAAA-ACTTGGTCAC
* * * * *
39726797 ATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCG-AGAAGCTTTGGTCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGTA-AAAC-TTGGTCAC
* * ***
39726848 GTGTGTAGTACTATGTGAAGGCTACTACGTGGATCGATAAATGATGGTCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTACCG-TAAAACTTGGTCAC
* * * *
39726899 ATGTGTAGTACTAAGTGAAGGCTATTATGTGTACCG-AAAAGCTTTGGTCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGTAAAA-C-TTGGTCAC
* * * *
39726950 GTGTGTAGTACTATGTGAAGGCTACTATGTGAACCGTAAAACTTGATAAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGTAAAACTTGGTCAC
* *
39727000 GTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGTAAAACTTGGTCAC
39727050 GTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTA
39727083 TCGAATGATA
Statistics
Matches: 243, Mismatches: 35, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
49 4 0.02
50 88 0.36
51 144 0.59
52 6 0.02
53 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.30
Consensus pattern (50 bp):
GTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGTAAAACTTGGTCAC
Found at i:39730314 original size:25 final size:23
Alignment explanation
Indices: 39730270--39730316 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
39730260 GGAATAGGGA
39730270 AGAAAATGAAGAACAATGAAGAG
1 AGAAAATGAAGAACAATGAAGAG
39730293 AGAAAAGTGAAAGAA-AAGTGAAGA
1 AGAAAA-TG-AAGAACAA-TGAAGA
39730317 ATGAATGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.29
24 4 0.19
25 11 0.52
ACGTcount: A:0.62, C:0.02, G:0.28, T:0.09
Consensus pattern (23 bp):
AGAAAATGAAGAACAATGAAGAG
Found at i:39732801 original size:13 final size:13
Alignment explanation
Indices: 39732783--39732809 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39732773 CTTTTATAAT
39732783 ATCAATTCAATTC
1 ATCAATTCAATTC
39732796 ATCAATTCAATTC
1 ATCAATTCAATTC
39732809 A
1 A
39732810 AACGACATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.37
Consensus pattern (13 bp):
ATCAATTCAATTC
Found at i:39733511 original size:31 final size:31
Alignment explanation
Indices: 39733452--39733515 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
39733442 TTTTAGAAAA
* * *
39733452 TAAATGAGGTATTTATTTTTTAATTAAGTGT
1 TAAATGAGGTATTGATTTGTTAACTAAGTGT
**
39733483 TAAATGAGGTATTGATTTGTTGGCTAAGTGT
1 TAAATGAGGTATTGATTTGTTAACTAAGTGT
39733514 TA
1 TA
39733516 GTGAAATGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.30, C:0.02, G:0.22, T:0.47
Consensus pattern (31 bp):
TAAATGAGGTATTGATTTGTTAACTAAGTGT
Found at i:39738875 original size:31 final size:31
Alignment explanation
Indices: 39738837--39738899 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
39738827 GAACGATTGT
*
39738837 ACGTACGGTTCACATCGATATAGTGTAAGGA
1 ACGTACGGTTCACATCGATATAATGTAAGGA
39738868 ACGTACGGTTCACATCGATATAATGTAAGGA
1 ACGTACGGTTCACATCGATATAATGTAAGGA
39738899 A
1 A
39738900 TCTAACTAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (31 bp):
ACGTACGGTTCACATCGATATAATGTAAGGA
Found at i:39742228 original size:20 final size:20
Alignment explanation
Indices: 39742195--39742234 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
39742185 ACTGATCCAA
*
39742195 TATCGATACTTTTCTTAAGG
1 TATCGATACTTTTCCTAAGG
39742215 TATCGATA-TATTTCCTAAGG
1 TATCGATACT-TTTCCTAAGG
39742235 CATTGATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
TATCGATACTTTTCCTAAGG
Found at i:39742242 original size:20 final size:20
Alignment explanation
Indices: 39742196--39742243 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
39742186 CTGATCCAAT
* *
39742196 ATCGATACT-TTTCTTAAGGT
1 ATCGATA-TATTTCCTAAGGC
39742216 ATCGATATATTTCCTAAGGC
1 ATCGATATATTTCCTAAGGC
*
39742236 ATTGATAT
1 ATCGATAT
39742244 TTCTGCTCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
ATCGATATATTTCCTAAGGC
Found at i:39743187 original size:22 final size:22
Alignment explanation
Indices: 39743162--39743205 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
39743152 TTAATGGTTT
*
39743162 ATATATATGTATTAATA-ATTAA
1 ATATAAAT-TATTAATATATTAA
*
39743184 ATATAAATTGTTAATATATTAA
1 ATATAAATTATTAATATATTAA
39743206 CAGTTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (22 bp):
ATATAAATTATTAATATATTAA
Found at i:39743717 original size:16 final size:17
Alignment explanation
Indices: 39743698--39743730 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39743688 AATTTTATAG
39743698 ATTTTA-ATAATTATTA
1 ATTTTATATAATTATTA
*
39743714 ATTTTATATATTTATTA
1 ATTTTATATAATTATTA
39743731 TACATATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTATATAATTATTA
Found at i:39743727 original size:24 final size:24
Alignment explanation
Indices: 39743668--39743727 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
39743658 TGTTATGTTA
*
39743668 TTATATATTTTATAAATTTAAATT
1 TTATATATTTAATAAATTTAAATT
* *
39743692 TTATAGATTTTAAT-AATTATTAATT
1 TTATATA-TTTAATAAATT-TAAATT
39743717 TTATATATTTA
1 TTATATATTTA
39743728 TTATACATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
24 14 0.47
25 16 0.53
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TTATATATTTAATAAATTTAAATT
Found at i:39753794 original size:21 final size:20
Alignment explanation
Indices: 39753768--39753819 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
39753758 ATTCAATTTT
39753768 TAAAAATTAT-TATAAAAGTTA
1 TAAAAATTATAT-TAAAAG-TA
*
39753789 TAAAAATTATATTATAAGTA
1 TAAAAATTATATTAAAAGTA
39753809 TAAAAA-TATAT
1 TAAAAATTATAT
39753820 GGGTGTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 5 0.17
20 8 0.28
21 15 0.52
22 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (20 bp):
TAAAAATTATATTAAAAGTA
Found at i:39758271 original size:113 final size:111
Alignment explanation
Indices: 39758055--39758969 Score: 1063
Period size: 113 Copynumber: 8.3 Consensus size: 111
39758045 TTTTTTCATT
* * * * *
39758055 TCAGAGTCAGATATAAATATACGGAAAAAATTTAAAAAAAA--ATTTTGGTTGGTGGCCTGTTAA
1 TCAGAGTCAGATATAAATATACGAAAAAAATTTAAAAAAAATTTTTTTGGGTGCTGGCCTGTCAA
* *
39758118 TGGCCGGCACCTAGTAC-AA-TTT-AAAAAAATTTCTTTTTTTTTGTG
66 TGGCCGGCACCCAGTACAAATTTTAAAAAAAAATTC--TTTTTTTGTG
* *
39758163 TCAAAGTCAGATATAAATATACGAAAAAAATTTAAAAAAAAAAGTTTTTTTTGGGTG-TTGCCTG
1 TCAGAGTCAGATATAAATATACGAAAAAAATTT--AAAAAAAA--TTTTTTTGGGTGCTGGCCTG
39758227 TCAATGGCCGGCACCCAGTACAAATTTTAAAAAAAAATTCTTTTTTTTTGTG
62 TCAATGGCCGGCACCCAGTACAAATTTTAAAAAAAAATTC--TTTTTTTGTG
*
39758279 TCAGAGTCAGATATAAATATACGAAAAAAA-TTAAAAAAAATTTTTTTGGGTGCAGGCCTGTCAA
1 TCAGAGTCAGATATAAATATACGAAAAAAATTTAAAAAAAATTTTTTTGGGTGCTGGCCTGTCAA
* *
39758343 TGGCCGGCACCCAGTACAAA-TTT--AAAAATATT-TTTTTTCGTG
66 TGGCCGGCACCCAGTACAAATTTTAAAAAAAAATTCTTTTTTTGTG
* *
39758385 TCAGAGTCAGATATAAATATACGAAAAAAATTTTAAAAAAATTTTTTTGGGGTGTTGGCCTGTCA
1 TCAGAGTCAGATATAAATATACGAAAAAAATTTAAAAAAAATTTTTTT-GGGTGCTGGCCTGTCA
* *** *
39758450 ATGGCCGGCACCCAGTACAAATTTAAAAAAAAAACTAAATTTTTCGTG
65 ATGGCCGGCACCCAGTACAAATTTTAAAAAAAAA-TTCTTTTTTTGTG
** **
39758498 TCAGAGTCAGATATAAATATACGAAAAGATTTTTTAAAAAAAAAATTTTT-GGTGCTGGCCTGTC
1 TCAGAGTCAGATATAAATATACGAAAA-A-AATTTAAAAAAAATTTTTTTGGGTGCTGGCCTGTC
* * * *
39758562 AATGGCTGGCACCCAATACAAATTTTAAAAAAAATTTCTTTTTTTTTTGTA
64 AATGGCCGGCACCCAGTACAAATTTTAAAAAAAAATTC---TTTTTTTGTG
* * * *
39758613 TCATAGTCAGATATAAATATATGAAAAAAATTTAAAAAAAA--ATTTTGGGTGCTGGCCTATCAA
1 TCAGAGTCAGATATAAATATACGAAAAAAATTTAAAAAAAATTTTTTTGGGTGCTGGCCTGTCAA
* *
39758676 TGGTCAGCACCCAGTACAAA--TTAAAAAAAAATTCTTTTTTTTTCGTG
66 TGGCCGGCACCCAGTACAAATTTTAAAAAAAAATTC--TTTTTTT-GTG
* * *
39758723 TTAGAGTCAGATATAAATATACGAAAAAAATTTAAAAAAAATTTTTTTTTGGTGCTGGCTTGTCA
1 TCAGAGTCAGATATAAATATACGAAAAAAATTTAAAAAAAA-TTTTTTTGGGTGCTGGCCTGTCA
* *
39758788 ATGGCCGGCACCCAGTACAAATTTAAAAAAAAAATTCTTTTTTTTTTCCTG
65 ATGGCCGGCACCCAGTACAAATTTTAAAAAAAAATTC---TTTTTTT-GTG
* *
39758839 TCAGAGTCAAATATAAATATATGAAAAAAATTT-AAAAAAATTTTTTTGGGTGCTGGCCTGTCAA
1 TCAGAGTCAGATATAAATATACGAAAAAAATTTAAAAAAAATTTTTTTGGGTGCTGGCCTGTCAA
*
39758903 TGGCCGGCACCCAGTACAAA--TT------AGATT-TTTTTTTCGTG
66 TGGCCGGCACCCAGTACAAATTTTAAAAAAAAATTCTTTTTTT-GTG
39758941 TCAGAGTCAGATATAAATATACGAAAAAA
1 TCAGAGTCAGATATAAATATACGAAAAAA
39758970 TTAAATTTTT
Statistics
Matches: 709, Mismatches: 68, Indels: 66
0.84 0.08 0.08
Matches are distributed among these distances:
102 37 0.05
106 43 0.06
107 16 0.02
108 66 0.09
109 19 0.03
110 61 0.09
111 25 0.04
112 63 0.09
113 160 0.23
114 54 0.08
115 72 0.10
116 93 0.13
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (111 bp):
TCAGAGTCAGATATAAATATACGAAAAAAATTTAAAAAAAATTTTTTTGGGTGCTGGCCTGTCAA
TGGCCGGCACCCAGTACAAATTTTAAAAAAAAATTCTTTTTTTGTG
Found at i:39758720 original size:225 final size:221
Alignment explanation
Indices: 39758043--39758971 Score: 1119
Period size: 225 Copynumber: 4.2 Consensus size: 221
39758033 AAAATTTTAC
* *
39758043 TTTTTTTTCATTTCAGAGTCAGATATAAATATACGGAAAAAATTT-AAAAAAAAA-TTTTGGTTG
1 TTTTTTTTCGTGTCAGAGTCAGATATAAATATAC-GAAAAAATTTAAAAAAAAAATTTTTGG-TG
* * * *
39758106 GTGGCCTGTTAATGGCCGGCACCTAGTAC-AATTTAAAAAAATTTC-TTTTTTTTTGTGTCAAAG
64 CTGGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAATTTCTTTTTTTTTTGTGTCAGAG
* *
39758169 TCAGATATAAATATACGAAAAAAATTTAAAAAAAAAAGTTTTTTTTGGGTG-TTGCCTGTCAATG
129 TCAGATATAAATATACGAAAAAAATTTAAAAAAATAA-----TTTTGGGTGCTGGCCTGTCAATG
39758233 GCCGGCACCCAGTACAAATTTTAAAAAAAAATTCT
189 GCCGGCACCCAGTACAAA-TTTAAAAAAAAA-TCT
* **
39758268 TTTTTTTT-GTGTCAGAGTCAGATATAAATATACGAAAAAAATTAAAAAAAATTTTTTTGGGTGC
1 TTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAATTTAAAAAAAAAATTTTT-GGTGC
* * *
39758332 AGGCCTGTCAATGGCCGGCACCCAGTACAAATTT--AAAAA--T-ATTTTTTTTCGTGTCAGAGT
65 TGGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAATTTCTTTTTTTTTTGTGTCAGAGT
** *
39758392 CAGATATAAATATACGAAAAAAATTTTAAAAAAATTTTTTTGGGGTGTTGGCCTGTCAATGGCCG
130 CAGATATAAATATACGAAAAAAA-TTTAAAAAAATAATTTT-GGGTGCTGGCCTGTCAATGGCCG
*
39758457 GCACCCAGTACAAATTTAAAAAAAAAACT
193 GCACCCAGTACAAATTTAAAAAAAAATCT
*** *
39758486 AAATTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAGATTTTTTAAAAAAAAAATTTTTGGT
1 TTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAA-A--ATTTAAAAAAAAAATTTTTGGT
* * *
39758551 GCTGGCCTGTCAATGGCTGGCACCCAATACAAATTTTAAAAAAAATTTCTTTTTTTTTTGTATCA
63 GCTGGCCTGTCAATGGCCGGCACCCAGTACAAA-TTT-AAAAAAATTTCTTTTTTTTTTGTGTCA
* * * *
39758616 TAGTCAGATATAAATATATGAAAAAAATTTAAAAAAA-AATTTTGGGTGCTGGCCTATCAATGGT
126 GAGTCAGATATAAATATACGAAAAAAATTTAAAAAAATAATTTTGGGTGCTGGCCTGTCAATGGC
*
39758680 CAGCACCCAGTACAAA-TTAAAAAAAAATTCT
191 CGGCACCCAGTACAAATTTAAAAAAAAA-TCT
* **
39758711 TTTTTTTTCGTGTTAGAGTCAGATATAAATATACGAAAAAAATTTAAAAAAAATTTTTTTTTGGT
1 TTTTTTTTCGTGTCAGAGTCAGATATAAATATACG-AAAAAATTTAAAAAAAA--AATTTTTGGT
* * *
39758776 GCTGGCTTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAAAAATTCTTTTTTTTTTCCTGTC
63 GCTGGCCTGTCAATGGCCGGCACCCAGTACAAATTT--AAAAAAATTTCTTTTTTTTTT-GTGTC
* * **
39758841 AGAGTCAAATATAAATATATGAAAAAAATTTAAAAAAATTTTTTTGGGTGCTGGCCTGTCAATGG
125 AGAGTCAGATATAAATATACGAAAAAAATTTAAAAAAATAATTTTGGGTGCTGGCCTGTCAATGG
*
39758906 CCGGCACCCAGTACAAA-TT------AGA--T
190 CCGGCACCCAGTACAAATTTAAAAAAAAATCT
39758929 TTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAATT
1 TTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAATT
39758972 AAATTTTTTT
Statistics
Matches: 618, Mismatches: 60, Indels: 60
0.84 0.08 0.08
Matches are distributed among these distances:
217 8 0.01
218 46 0.07
219 47 0.08
220 31 0.05
221 35 0.06
222 59 0.10
223 30 0.05
224 49 0.08
225 170 0.28
226 54 0.09
227 51 0.08
228 38 0.06
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (221 bp):
TTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAATTTAAAAAAAAAATTTTTGGTGCT
GGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAATTTCTTTTTTTTTTGTGTCAGAGTC
AGATATAAATATACGAAAAAAATTTAAAAAAATAATTTTGGGTGCTGGCCTGTCAATGGCCGGCA
CCCAGTACAAATTTAAAAAAAAATCT
Found at i:39759177 original size:113 final size:112
Alignment explanation
Indices: 39758964--39759268 Score: 354
Period size: 113 Copynumber: 2.7 Consensus size: 112
39758954 TAAATATACG
*
39758964 AAAAAATTAAATTTTTTTTTAAATTTGTACT--G-GCGGCCATTGACAGGCCAGCACCCAAACAA
1 AAAAAAGTAAATTTTTTTTTAAA-TTGTACTGGGTGCGGCCATTGACAGGCCAGCACCC--A-AA
* ** *
39759026 AAATTTTTTAAAATTTTTTTCGTATAATTATATCTGACTCTGAAACGAAAA
62 AATTTTTTTTTAATTTTTTTCCTATAATTATATCTGACTCTGAAACGAAAA
* *
39759077 AAGAAAG-AATATTTTTTTTTAAATTGTACTGGGTGCCTGCCATTGACAGGCCAGCACCCAAAAA
1 AAAAAAGTAA-ATTTTTTTTTAAATTGTACTGGGTG-CGGCCATTGACAGGCCAGCACCCAAAAA
* * * *
39759141 TTTTTTTTTTATTTTTTTCCTATATTTATATTTGACTCTGACACGAAAA
64 TTTTTTTTTAATTTTTTTCCTATAATTATATCTGACTCTGAAACGAAAA
* * *
39759190 AAAAAAGTAAATTTTTTTTT-TACTGT--TGGGTGTCGGCCATTGACAGGCCTGCACCCAAAAAT
1 AAAAAAGTAAATTTTTTTTTAAATTGTACTGGGTG-CGGCCATTGACAGGCCAGCACCCAAAAAT
**
39759252 TTTTTTTTCCTTTTTTT
65 TTTTTTTTAATTTTTTT
39759269 TTCTTTTTCG
Statistics
Matches: 167, Mismatches: 19, Indels: 15
0.83 0.09 0.07
Matches are distributed among these distances:
110 48 0.29
112 13 0.08
113 79 0.47
114 4 0.02
115 1 0.01
116 22 0.13
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (112 bp):
AAAAAAGTAAATTTTTTTTTAAATTGTACTGGGTGCGGCCATTGACAGGCCAGCACCCAAAAATT
TTTTTTTAATTTTTTTCCTATAATTATATCTGACTCTGAAACGAAAA
Found at i:39760018 original size:213 final size:214
Alignment explanation
Indices: 39759651--39760078 Score: 804
Period size: 213 Copynumber: 2.0 Consensus size: 214
39759641 TTCCAAATGG
* *
39759651 GGAATATTTGGAACCGTGCTATATTAAACCTGATGATGGTATGCATATTGTTTGCTTCATTCCTT
1 GGAATATTTGGAACCGTGCTATATTAAACCTGATAATGGTATGCATATTGTTTGCTTCATCCCTT
* *
39759716 TGTCATGATGTAATTTCGTTACAGGCATTAATTGATGCTACATCCTCCGACAGCGACCTTGAAAA
66 TGTCATGATGTAATTTCATTACAGGCATTAATTGATGCTACATCCTCCGACAGCGACCCTGAAAA
39759781 TGAGAGTGGTGTTAGAATGGTGGCATTGTTTGATCATGAGGAGGTTGGATCTAATTCAGCACAAG
131 TGAGAGTGGTGTTAGAATGGTGGCATTGTTTGATCATGAGGAGGTTGGATCTAATTCAGCACAAG
39759846 GAGC-GGATCTCCTGCAAT
196 GAGCGGGATCTCCTGCAAT
*
39759864 GGAATATTTGGAACCGTGCTATATTAAACCTGATAATGGTATGCATATTTTTTGCTTCATCCCTT
1 GGAATATTTGGAACCGTGCTATATTAAACCTGATAATGGTATGCATATTGTTTGCTTCATCCCTT
39759929 TGTCATGATGTAATTTCATTACAGGCATTAATTGATGCTACATCCTCCGACAGCGACCCTGAAAA
66 TGTCATGATGTAATTTCATTACAGGCATTAATTGATGCTACATCCTCCGACAGCGACCCTGAAAA
39759994 TGAGAGTGGTGTTAGAATGGTGGCATTGTTTGATCATGAGGAGGTTGGATCTAATTCAGCACAAG
131 TGAGAGTGGTGTTAGAATGGTGGCATTGTTTGATCATGAGGAGGTTGGATCTAATTCAGCACAAG
39760059 GAGCGGGATCTCCTGCAAT
196 GAGCGGGATCTCCTGCAAT
39760078 G
1 G
39760079 TTAGATGCTC
Statistics
Matches: 209, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
213 194 0.93
214 15 0.07
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (214 bp):
GGAATATTTGGAACCGTGCTATATTAAACCTGATAATGGTATGCATATTGTTTGCTTCATCCCTT
TGTCATGATGTAATTTCATTACAGGCATTAATTGATGCTACATCCTCCGACAGCGACCCTGAAAA
TGAGAGTGGTGTTAGAATGGTGGCATTGTTTGATCATGAGGAGGTTGGATCTAATTCAGCACAAG
GAGCGGGATCTCCTGCAAT
Found at i:39769631 original size:20 final size:20
Alignment explanation
Indices: 39769608--39769654 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
39769598 GTGAATCAGG
*
39769608 TTAAATAACAAAGAATAGAT
1 TTAAACAACAAAGAATAGAT
* * *
39769628 TTAAACAATAATGAATCGAT
1 TTAAACAACAAAGAATAGAT
39769648 TTAAACA
1 TTAAACA
39769655 TAACGACAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.28
Consensus pattern (20 bp):
TTAAACAACAAAGAATAGAT
Found at i:39769669 original size:21 final size:20
Alignment explanation
Indices: 39769620--39769660 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
39769610 AAATAACAAA
* *
39769620 GAATAGATTTAAACAATAAT
1 GAATCGATTTAAACAATAAC
39769640 GAATCGATTTAAAC-ATAAC
1 GAATCGATTTAAACAATAAC
39769659 GA
1 GA
39769661 CAATCGATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.27
Consensus pattern (20 bp):
GAATCGATTTAAACAATAAC
Found at i:39770960 original size:24 final size:24
Alignment explanation
Indices: 39770933--39770994 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
39770923 GGTGTCGATT
*
39770933 CCTCCTATTCATCTTGATCTCAAC
1 CCTCATATTCATCTTGATCTCAAC
* * *
39770957 CCTCATCTTCATCTTTATCTCCAC
1 CCTCATATTCATCTTGATCTCAAC
* *
39770981 CCTCGTTTTCATCT
1 CCTCATATTCATCT
39770995 CCATCTCTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.16, C:0.39, G:0.03, T:0.42
Consensus pattern (24 bp):
CCTCATATTCATCTTGATCTCAAC
Found at i:39771000 original size:24 final size:24
Alignment explanation
Indices: 39770940--39771001 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
39770930 ATTCCTCCTA
*
39770940 TTCATCTTGATCTCAACCCTCATC
1 TTCATCTTCATCTCAACCCTCATC
* * * *
39770964 TTCATCTTTATCTCCACCCTCGTT
1 TTCATCTTCATCTCAACCCTCATC
*
39770988 TTCATCTCCATCTC
1 TTCATCTTCATCTC
39771002 TTTCTTTTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.16, C:0.39, G:0.03, T:0.42
Consensus pattern (24 bp):
TTCATCTTCATCTCAACCCTCATC
Found at i:39773672 original size:22 final size:22
Alignment explanation
Indices: 39773641--39773694 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
39773631 GTAGAAGCGA
39773641 TGTCGTGACACATCAGGTCTTG
1 TGTCGTGACACATCAGGTCTTG
*
39773663 TGTCGCGACACATCAGGTCTTG
1 TGTCGTGACACATCAGGTCTTG
39773685 TGTCGTGACA
1 TGTCGTGACA
39773695 TCGAGGGCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.19, C:0.24, G:0.28, T:0.30
Consensus pattern (22 bp):
TGTCGTGACACATCAGGTCTTG
Found at i:39779644 original size:124 final size:126
Alignment explanation
Indices: 39779215--39779686 Score: 815
Period size: 126 Copynumber: 3.8 Consensus size: 126
39779205 CGAGTTGAAT
*
39779215 TTTCTGATCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCG
1 TTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCG
*
39779280 CGCCCTCGTGGACGCGCTTTTGCTACAGTATGTCACGGAAGAAATAATTATTTTTTTGACG
66 CGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTTTTGACG
* *
39779341 TTTCTTAGCAAATAGTATAAAATCACTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCG
1 TTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCG
*
39779406 CGCCTTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTTTTGACG
66 CGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTTTTGACG
*
39779467 TTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGGGAAGAATTTGTGAAATCG
1 TTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCG
* * *
39779532 CGGCCTCGT-GAGCGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAA-T-TTTTTTTGACG
66 CGCCCTCGTGGA-CGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTTTTGACG
*
39779591 TTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGGGAAATCG
1 TTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCG
*
39779656 CGCCCTCGTGGATGCGCTTTTGCTACAGTAG
66 CGCCCTCGTGGACGCGCTTTTGCTACAGTAG
39779687 CATGTTTGGG
Statistics
Matches: 328, Mismatches: 16, Indels: 6
0.94 0.05 0.02
Matches are distributed among these distances:
124 100 0.30
125 5 0.02
126 223 0.68
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (126 bp):
TTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCG
CGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTTTTGACG
Found at i:39781931 original size:116 final size:116
Alignment explanation
Indices: 39781800--39782039 Score: 426
Period size: 116 Copynumber: 2.1 Consensus size: 116
39781790 TGATAAATTG
39781800 TATTAACTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
1 TATTAACTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
* *
39781865 TAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAAT
66 TAGTACCAGTCAAAACAGTTTTCCAAATCTAACATTACGTGAATGTAAAAT
* * *
39781916 TATTAACTCTAAAAATTTTATTAATGGTTCGTAAAATTATCAAATTATATAAAATTATTAATTGT
1 TATTAACTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
*
39781981 TAGTAGCAGTCAAAACAGTTTTCCAAATCTAACATTACGTGAATGTAAAAT
66 TAGTACCAGTCAAAACAGTTTTCCAAATCTAACATTACGTGAATGTAAAAT
39782032 TATTAACT
1 TATTAACT
39782040 TAGTTTAGGG
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
116 118 1.00
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (116 bp):
TATTAACTCAAAAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGT
TAGTACCAGTCAAAACAGTTTTCCAAATCTAACATTACGTGAATGTAAAAT
Found at i:39782089 original size:20 final size:20
Alignment explanation
Indices: 39782064--39782125 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 20
39782054 TAATTAAATT
39782064 AAGTTAGGAG-TAGGGTTTTA
1 AAGTTAGG-GTTAGGGTTTTA
39782084 AAGTTAAGGGTTAGGGTTTTA
1 AAGTT-AGGGTTAGGGTTTTA
39782105 AAGTTAAAGGGTTAGGGTTTT
1 AAGTT--AGGGTTAGGGTTTT
39782126 TAATTAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
20 6 0.15
21 18 0.46
22 15 0.38
ACGTcount: A:0.29, C:0.00, G:0.34, T:0.37
Consensus pattern (20 bp):
AAGTTAGGGTTAGGGTTTTA
Found at i:39782117 original size:22 final size:22
Alignment explanation
Indices: 39782074--39782133 Score: 97
Period size: 21 Copynumber: 2.8 Consensus size: 22
39782064 AAGTTAGGAG
39782074 TAGGGTTTTAAAGTT-AAGGGT
1 TAGGGTTTTAAAGTTAAAGGGT
39782095 TAGGGTTTTAAAGTTAAAGGGT
1 TAGGGTTTTAAAGTTAAAGGGT
*
39782117 TAGGGTTTTTAA-TTAAA
1 TAGGGTTTTAAAGTTAAA
39782134 TTAGGTTAGG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
21 20 0.54
22 17 0.46
ACGTcount: A:0.32, C:0.00, G:0.28, T:0.40
Consensus pattern (22 bp):
TAGGGTTTTAAAGTTAAAGGGT
Found at i:39782144 original size:29 final size:29
Alignment explanation
Indices: 39782112--39782488 Score: 269
Period size: 29 Copynumber: 13.4 Consensus size: 29
39782102 TTAAAGTTAA
39782112 AGGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
39782141 AGGGTTAGGGTTTTTAATT-AA--A--TT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
*
39782165 A-GGTTAGGGTTTTT-A--AAGTTAAGGTTT
1 AGGGTTAGGGTTTTTAATTAAATT-AGG-TT
* **
39782192 AGGGTT----TTTAATAAAATTAGGTTAGG--
1 AGGGTTAGGGTTT--T-TAATTAAATTAGGTT
39782218 ---GTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
*
39782244 AGAGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
*
39782273 AGGGTTTA-GGTTTTTTATTAAATTAGGTT
1 AGGG-TTAGGGTTTTTAATTAAATTAGGTT
* *
39782302 AGGGCTAGGGTTTTTAATGAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
39782331 AGGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
** * * **
39782360 AGGGTT-TTGTATTAAATTAGGTTAGGATTTTT
1 AGGGTTAGGGTTTTTAATTAAATTAGG----TT
** * **** * *
39782392 AAAGTTAAGGTTTAGGGTT--TTTAAGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
*
39782419 AGGGTTAGGG-TTTTAATTAAATTAAGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
39782447 AGGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTT
*
39782476 AGAGTTTAGGGTT
1 AG-GGTTAGGGTT
39782489 AAATTAGGTT
Statistics
Matches: 274, Mismatches: 40, Indels: 67
0.72 0.10 0.18
Matches are distributed among these distances:
21 1 0.00
22 1 0.00
23 16 0.06
24 17 0.06
25 1 0.00
26 6 0.02
27 15 0.05
28 40 0.15
29 146 0.53
30 16 0.06
31 4 0.01
32 6 0.02
33 5 0.02
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (29 bp):
AGGGTTAGGGTTTTTAATTAAATTAGGTT
Found at i:39782252 original size:58 final size:58
Alignment explanation
Indices: 39782190--39782488 Score: 311
Period size: 58 Copynumber: 5.1 Consensus size: 58
39782180 AAGTTAAGGT
* *
39782190 TTAGGGTTTTTAATAAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGAG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
*
39782248 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTA-GGTTTTTTATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGG
* *
39782306 CTAGGGTTTTTAATGAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
** * * ** ** * **** * *
39782364 TT-TTGTATTAAATTAGGTTAGGATTTTTAAAGTTAAGGTTTAGGGTT--TTTAAGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGG----TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
* *
39782423 TTAGGG-TTTTAATTAAATTAAGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGAGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAG-GG
39782481 TTAGGGTT
1 TTAGGGTT
39782489 AAATTAGGTT
Statistics
Matches: 190, Mismatches: 40, Indels: 21
0.76 0.16 0.08
Matches are distributed among these distances:
55 14 0.07
57 24 0.13
58 110 0.58
59 27 0.14
60 1 0.01
61 14 0.07
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.45
Consensus pattern (58 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGG
Found at i:39782298 original size:87 final size:88
Alignment explanation
Indices: 39782182--39782366 Score: 309
Period size: 87 Copynumber: 2.1 Consensus size: 88
39782172 GGTTTTTAAA
* * *
39782182 GTTAAGGTTTAGGGTTTTTAATAAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGA
1 GTTAGGGTTTAGGGTTTTTAATAAAATTAGGTTAGGGCTAGGGTTTTTAATGAAATTAGGTTAGA
39782247 GTTAGGGTTTTTAATTAAATTAG
66 GTTAGGGTTTTTAATTAAATTAG
* * *
39782270 GTTAGGGTTTA-GGTTTTTTATTAAATTAGGTTAGGGCTAGGGTTTTTAATGAAATTAGGTTAGG
1 GTTAGGGTTTAGGGTTTTTAATAAAATTAGGTTAGGGCTAGGGTTTTTAATGAAATTAGGTTAGA
39782334 GTTAGGGTTTTTAATTAAATTAG
66 GTTAGGGTTTTTAATTAAATTAG
39782357 GTTAGGGTTT
1 GTTAGGGTTT
39782367 TGTATTAAAT
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
87 81 0.89
88 10 0.11
ACGTcount: A:0.28, C:0.01, G:0.27, T:0.45
Consensus pattern (88 bp):
GTTAGGGTTTAGGGTTTTTAATAAAATTAGGTTAGGGCTAGGGTTTTTAATGAAATTAGGTTAGA
GTTAGGGTTTTTAATTAAATTAG
Found at i:39782329 original size:116 final size:115
Alignment explanation
Indices: 39782112--39782488 Score: 377
Period size: 116 Copynumber: 3.4 Consensus size: 115
39782102 TTAAAGTTAA
*
39782112 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTA--G---
1 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
*
39782172 -GG-TTTTTA--AAGTTAAGGTT----TAGGGTTTTTAATAAAATTAGGTT
66 AGGTTTTTTATTAAATT-AGGTTAGGGTAGGGTTTTTAATAAAATTAGGTT
39782215 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
*
39782280 AGGTTTTTTATTAAATTAGGTTAGGGCTAGGGTTTTTAATGAAATTAGGTT
66 AGGTTTTTTATTAAATTAGGTTAGGG-TAGGGTTTTTAATAAAATTAGGTT
*
39782331 AGGGTTAGGGTTTTTAATT-AA--A--TTAG-GTTAGGGTTTTGT-ATTAAATTAGGTTAGGATT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTT-TAATTAAATTAGGTTAGG--G
* * * * * *
39782389 TTTAAAGTTAAGGTTTAGGGTT--TTTAAGTTAGGGTTAGGG-TTTTAATTAAATTAAGTT
63 TTT-AGGTT---TTTTA---TTAAATTAGGTTAGGG-TAGGGTTTTTAATAAAATTAGGTT
39782447 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTTAGGGTT
1 AGGGTTAGGGTTTTTAATTAAATTAGGTTAGAG-TTAGGGTT
39782489 AAATTAGGTT
Statistics
Matches: 232, Mismatches: 11, Indels: 42
0.81 0.04 0.15
Matches are distributed among these distances:
103 58 0.25
105 1 0.00
109 2 0.01
110 33 0.14
111 10 0.04
112 7 0.03
113 5 0.02
115 2 0.01
116 81 0.35
117 17 0.07
119 3 0.01
121 4 0.02
122 1 0.00
123 8 0.03
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (115 bp):
AGGGTTAGGGTTTTTAATTAAATTAGGTTAGAGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
AGGTTTTTTATTAAATTAGGTTAGGGTAGGGTTTTTAATAAAATTAGGTT
Found at i:39782412 original size:21 final size:20
Alignment explanation
Indices: 39782371--39782434 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
39782361 GGGTTTTGTA
*
39782371 TTAAA-TTA-GGTTAGGATTT
1 TTAAAGTTAGGGTTAGG-GTT
*
39782390 TTAAAGTTAAGGTTTAGGGTT
1 TTAAAGTT-AGGGTTAGGGTT
*
39782411 TTTAAGTTAGGGTTAGGGTT
1 TTAAAGTTAGGGTTAGGGTT
39782431 TTAA
1 TTAA
39782435 TTAAATTAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
19 5 0.14
20 16 0.43
21 10 0.27
22 6 0.16
ACGTcount: A:0.28, C:0.00, G:0.27, T:0.45
Consensus pattern (20 bp):
TTAAAGTTAGGGTTAGGGTT
Found at i:39782428 original size:20 final size:22
Alignment explanation
Indices: 39782379--39782432 Score: 76
Period size: 20 Copynumber: 2.5 Consensus size: 22
39782369 TATTAAATTA
*
39782379 GGTTAGGATTTTTAAAGTTAAG
1 GGTTAGGGTTTTTAAAGTTAAG
*
39782401 GTTTAGGGTTTTT-AAGTT-AG
1 GGTTAGGGTTTTTAAAGTTAAG
39782421 GGTTAGGGTTTT
1 GGTTAGGGTTTT
39782433 AATTAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 13 0.45
21 5 0.17
22 11 0.38
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.46
Consensus pattern (22 bp):
GGTTAGGGTTTTTAAAGTTAAG
Found at i:39782491 original size:116 final size:116
Alignment explanation
Indices: 39782168--39782508 Score: 386
Period size: 116 Copynumber: 2.9 Consensus size: 116
39782158 TTAAATTAGG
*
39782168 TTAGGGTTTTTAAAGTTAAGGTTTAGGGTTTTTAATAAAATTAGGTTAGGGTTAGGGTTTTTAAT
1 TTAGGGTTTTT-AAGTT-AGGGTTAGGGTTTTTAATAAAATTAGGTTAGGGTTAGGGTTTTTAAT
* ** ** *
39782233 TAAATTAGGTTAGAG-TTAGGGTTTTTAATTAAATTAGG---TTAGGGTTTAGGT
64 TAAATTAGGTTAGAGTTTAGGG--TTAAATTAGGTTAGGTTTTTAAAGTTAAGGT
**** * * * *
39782284 TTTTTATTAAATTAGGTTAGGGCTAGGGTTTTTAATGAAATTAGGTTAGGGTTAGGGTTTTTAAT
1 TTAGGGTT--TTTAAGTTAGGGTTAGGGTTTTTAATAAAATTAGGTTAGGGTTAGGGTTTTTAAT
* * **
39782349 TAAATTAGGTTAGGGTTTTGTATTAAATTAGGTTAGGATTTTTAAAGTTAAGGT
64 TAAATTAGGTTAGAGTTTAGGGTTAAATTAGGTTAGG-TTTTTAAAGTTAAGGT
* *
39782403 TTAGGGTTTTTAAGTTAGGGTTAGGG-TTTTAATTAAATTAAGTTAGGGTTAGGGTTTTTAATTA
1 TTAGGGTTTTTAAGTTAGGGTTAGGGTTTTTAATAAAATTAGGTTAGGGTTAGGGTTTTTAATTA
39782467 AATTAGGTTAGAGTTTAGGGTTAAATTAGGTTAGGGTTTTTA
66 AATTAGGTTAGAGTTTAGGGTTAAATTAGGTTA-GGTTTTTA
39782509 TTACATCAAA
Statistics
Matches: 185, Mismatches: 32, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
115 12 0.06
116 133 0.72
117 24 0.13
118 2 0.01
119 14 0.08
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.45
Consensus pattern (116 bp):
TTAGGGTTTTTAAGTTAGGGTTAGGGTTTTTAATAAAATTAGGTTAGGGTTAGGGTTTTTAATTA
AATTAGGTTAGAGTTTAGGGTTAAATTAGGTTAGGTTTTTAAAGTTAAGGT
Found at i:39782532 original size:25 final size:25
Alignment explanation
Indices: 39782504--39782665 Score: 221
Period size: 25 Copynumber: 6.7 Consensus size: 25
39782494 AGGTTAGGGT
39782504 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
39782529 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
*
39782554 TTTTATTACATCAAATAAATTTCTA
1 TTTTATTACATCAAATAAACTTCTA
39782579 TTTTATTACATCAAAT-AA-TATC-A
1 TTTTATTACATCAAATAAACT-TCTA
** * *
39782602 --AAATAAC-TCAAA-AAATTTCTA
1 TTTTATTACATCAAATAAACTTCTA
39782623 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
39782648 TTTTATTACATCAAATAA
1 TTTTATTACATCAAATAA
39782666 TATCAAAATA
Statistics
Matches: 121, Mismatches: 8, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
20 9 0.07
21 6 0.05
23 6 0.05
24 9 0.07
25 91 0.75
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (25 bp):
TTTTATTACATCAAATAAACTTCTA
Found at i:39782635 original size:69 final size:69
Alignment explanation
Indices: 39782539--39782710 Score: 290
Period size: 69 Copynumber: 2.5 Consensus size: 69
39782529 TTTTATTACA
* *
39782539 TCAAATAAACTTCTATTTTATTACATCAAATAAATTTCTATTTTATTACATCAAATAATATCAAA
1 TCAAA-AAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAA
39782604 ATAAC
65 ATAAC
39782609 TCAAAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAA
1 TCAAAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAA
39782674 TAAC
66 TAAC
* *
39782678 TCAAAAAATTTCTATTTTTTTTACATAAAATAA
1 TCAAAAAATTTCTA-TTTTATTACATCAAATAA
39782711 TATCAAAATA
Statistics
Matches: 97, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
69 76 0.78
70 21 0.22
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (69 bp):
TCAAAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAA
TAAC
Found at i:39782702 original size:45 final size:45
Alignment explanation
Indices: 39782633--39782720 Score: 133
Period size: 45 Copynumber: 2.0 Consensus size: 45
39782623 TTTTATTACA
*
39782633 TCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAAC
1 TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
* *
39782678 TCAAA-AAATTTCTATTTTTTTTACATAAAATAATATCAAAATA
1 TCAAATAAACTTCTA-TTTTATTACATAAAATAATATCAAAATA
39782721 TTCAAAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
44 8 0.21
45 31 0.79
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (45 bp):
TCAAATAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
Found at i:39783166 original size:18 final size:18
Alignment explanation
Indices: 39783143--39783177 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39783133 CGGAAAAGGA
*
39783143 TACATATAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
39783161 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
39783178 AAACGCACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:39783839 original size:7 final size:7
Alignment explanation
Indices: 39783829--39783853 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
39783819 TTATATACAT
39783829 AATACTA
1 AATACTA
39783836 AATACTA
1 AATACTA
39783843 AATACTA
1 AATACTA
39783850 AATA
1 AATA
39783854 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:39784061 original size:20 final size:20
Alignment explanation
Indices: 39784024--39784061 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39784014 TTTATTTTTA
39784024 AAAATCTAAATAATAATTGT
1 AAAATCTAAATAATAATTGT
*
39784044 AAAATGTAATATAA-AATT
1 AAAATCTAA-ATAATAATT
39784062 TATCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAATCTAAATAATAATTGT
Found at i:39785030 original size:29 final size:29
Alignment explanation
Indices: 39784998--39785086 Score: 86
Period size: 29 Copynumber: 3.3 Consensus size: 29
39784988 AAAAAGGAAA
39784998 TTGAGAGAAAATTGAAATTAAATATGGAT
1 TTGAGAGAAAATTGAAATTAAATATGGAT
** *
39785027 TTGAGAGAATTTTGGAAA-GAAAT-T-GA-
1 TTGAGAGAAAATT-GAAATTAAATATGGAT
39785053 --GAG-G-AAATTGAAATTAAATATGGAT
1 TTGAGAGAAAATTGAAATTAAATATGGAT
39785078 TTGAGAGAA
1 TTGAGAGAA
39785087 TTTTGAAAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
21 4 0.09
22 7 0.16
23 2 0.04
24 5 0.11
27 5 0.11
28 2 0.04
29 16 0.36
30 4 0.09
ACGTcount: A:0.46, C:0.00, G:0.25, T:0.29
Consensus pattern (29 bp):
TTGAGAGAAAATTGAAATTAAATATGGAT
Found at i:39785049 original size:51 final size:51
Alignment explanation
Indices: 39784990--39785101 Score: 199
Period size: 51 Copynumber: 2.2 Consensus size: 51
39784980 TTATTTTAAA
39784990 AAAGGAAATTGAGAGAAAATTGAAATTAAATATGGATTTGAGAGAATTTTGG
1 AAAGGAAATTGAGAGAAAATTGAAATTAAATATGGATTTGAGAGAATTTT-G
*
39785042 AAA-GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTG
1 AAAGGAAATTGAGAGAAAATTGAAATTAAATATGGATTTGAGAGAATTTTG
39785092 AAAGGAAATT
1 AAAGGAAATT
39785102 TTTGAGAATT
Statistics
Matches: 58, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
50 4 0.07
51 51 0.88
52 3 0.05
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (51 bp):
AAAGGAAATTGAGAGAAAATTGAAATTAAATATGGATTTGAGAGAATTTTG
Found at i:39792023 original size:19 final size:19
Alignment explanation
Indices: 39791999--39792039 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
39791989 ATCTCATTTC
39791999 ATTCA-TTGCATTTAGATTA
1 ATTCATTTGCATTTA-ATTA
*
39792018 ATTCATTTTCATTTAATTA
1 ATTCATTTGCATTTAATTA
39792037 ATT
1 ATT
39792040 TACTTTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.32, C:0.10, G:0.05, T:0.54
Consensus pattern (19 bp):
ATTCATTTGCATTTAATTA
Found at i:39792617 original size:30 final size:32
Alignment explanation
Indices: 39792564--39792626 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 32
39792554 GTTTCTTTCT
39792564 AGTTTATTCTAGACTTAGGTTATTTTCATTTGTA
1 AGTTTATTCTAGACTT--GTTATTTTCATTTGTA
39792598 AGTTTATTCTAGA-TT-TTATTTTCATTTGT
1 AGTTTATTCTAGACTTGTTATTTTCATTTGT
39792627 CGAGGAACTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 14 0.48
33 2 0.07
34 13 0.45
ACGTcount: A:0.22, C:0.08, G:0.13, T:0.57
Consensus pattern (32 bp):
AGTTTATTCTAGACTTGTTATTTTCATTTGTA
Found at i:39799241 original size:50 final size:50
Alignment explanation
Indices: 39799099--39799395 Score: 218
Period size: 50 Copynumber: 5.8 Consensus size: 50
39799089 GAATATAACA
* * * * ** * * * *
39799099 TGCCAAAGCTATGTCCCAGACATAGTCTTACATAGGATGTTTCTTGTA-C
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* * * * * **
39799148 TGCCAATGTCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* * * * ** * *
39799198 TGCCCATGCCATGTCCTAGACATAGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* * * * * *
39799248 TGCCAACGCTATGTCCCAGACATGGTCTTACATGCGACCTTTTATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
*
39799298 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--T--A-GG
* * *
39799354 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
39799396 TTACCCAAAT
Statistics
Matches: 193, Mismatches: 48, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
49 35 0.18
50 117 0.61
53 1 0.01
56 40 0.21
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.30
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
Found at i:39799273 original size:100 final size:102
Alignment explanation
Indices: 39799148--39799387 Score: 254
Period size: 100 Copynumber: 2.3 Consensus size: 102
39799138 TTTCTTGTAC
* * * * * *
39799148 TGCCAATGTCATATCCCAGATATGGTCTTACATGAGA-GTTCTCATATAGGTGCCCATGCCATGT
1 TGCCAACGTCATGTCCCAGACATGGTCTTACATGAGACCTT-TCATATAGGTGCCAACGCCATGT
* * *
39799212 CCTAGACATAGTCTTACGGGGGACCTCTC-ATCT-TGG
65 CCCAGACATAGTCTTACAGGGGACCTCTCAATCTATGA
* * * *
39799248 TGCCAACG-CTATGTCCCAGACATGGTCTTACATGCGACCTTTTATCTCGGTGCCAACGCCATGT
1 TGCCAACGTC-ATGTCCCAGACATGGTCTTACATGAGACCTTTCATATAGGTGCCAACGCCATGT
* *
39799312 CCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
65 CCCAGACATAGTCTTACAGGGGACCTCTC--AATCT--ATGA
*
39799354 TGCCAATGTCATGTCCCAGACATGGTCTTACATG
1 TGCCAACGTCATGTCCCAGACATGGTCTTACATG
39799388 GGATCTCTTT
Statistics
Matches: 115, Mismatches: 16, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
99 1 0.01
100 74 0.64
101 2 0.02
103 4 0.03
106 33 0.29
107 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (102 bp):
TGCCAACGTCATGTCCCAGACATGGTCTTACATGAGACCTTTCATATAGGTGCCAACGCCATGTC
CCAGACATAGTCTTACAGGGGACCTCTCAATCTATGA
Found at i:39802389 original size:17 final size:17
Alignment explanation
Indices: 39802362--39802396 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
39802352 TTTTTTTAAA
39802362 AAAAATACATTACAAAAT
1 AAAAATACATTA-AAAAT
39802380 AAAAAT-CATTAAAAAT
1 AAAAATACATTAAAAAT
39802396 A
1 A
39802397 TATATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 5 0.29
18 6 0.35
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAATACATTAAAAAT
Found at i:39803116 original size:21 final size:22
Alignment explanation
Indices: 39803090--39803133 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
39803080 ACGAACATCG
39803090 AAGAAA-CAAAAAGAAAAAAAA
1 AAGAAATCAAAAAGAAAAAAAA
*
39803111 AAGAAATCGAAAAGAAAAAAAA
1 AAGAAATCAAAAAGAAAAAAAA
39803133 A
1 A
39803134 TCAGATTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.82, C:0.05, G:0.11, T:0.02
Consensus pattern (22 bp):
AAGAAATCAAAAAGAAAAAAAA
Found at i:39803128 original size:17 final size:17
Alignment explanation
Indices: 39803102--39803135 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39803092 GAAACAAAAA
*
39803102 GAAAAAAAAAAGAAATC
1 GAAAAAAAAAAAAAATC
*
39803119 GAAAAGAAAAAAAAATC
1 GAAAAAAAAAAAAAATC
39803136 AGATTTCAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.06, G:0.12, T:0.06
Consensus pattern (17 bp):
GAAAAAAAAAAAAAATC
Found at i:39803928 original size:44 final size:44
Alignment explanation
Indices: 39803863--39803967 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 44
39803853 GATCTAACCT
* * * *
39803863 ACTGCAACTTCAGAGG-TATAGGATTCATTG-TTTTAATCCGCTCC
1 ACTGCAACTTCAG-GGAGATAGGATT-AGTGACTTCAATCCGCTCC
* *
39803907 ACTGCAACTTCAGGGAGATAGGATTGGTGACTTCAATCTGCTCC
1 ACTGCAACTTCAGGGAGATAGGATTAGTGACTTCAATCCGCTCC
39803951 ACTGCAACTTCAGGGAG
1 ACTGCAACTTCAGGGAG
39803968 CTAAGATTTG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
43 4 0.08
44 49 0.92
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.29
Consensus pattern (44 bp):
ACTGCAACTTCAGGGAGATAGGATTAGTGACTTCAATCCGCTCC
Found at i:39804209 original size:143 final size:143
Alignment explanation
Indices: 39804029--39804288 Score: 396
Period size: 143 Copynumber: 1.8 Consensus size: 143
39804019 TGATTTGTAT
* * *
39804029 CTTTAATCTGTTCCACTACGACGCCAGGGAAATAAGA-TCTGCTGTCTTCAGTCTGCTCCGCTGC
1 CTTTAATCTGTTCAACTACAACACCAGGGAAATAAGATTC-GCTGTCTTCAGTCTGCTCCGCTGC
* **
39804093 AACTTTAGGAAGATAAGGCTGGTGGCTTCAATCTGCTCTACTGCAACTTCAGGAAGGCAAGATCC
65 AACTTTAGGAAGATAAGACTGGTAACTTCAATCTGCTCTACTGCAACTTCAGGAAGGCAAGATCC
39804158 GACATAATTTATAG
130 GACATAATTTATAG
* *
39804172 CTTTAATCTGTTCAACTGCAACACCGGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCA
1 CTTTAATCTGTTCAACTACAACACCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCA
* * * *
39804237 ACTTTAGGGAGATAAGACTTGTAACTTTAATCTGCTCTACTGTAACTTCAGG
66 ACTTTAGGAAGATAAGACTGGTAACTTCAATCTGCTCTACTGCAACTTCAGG
39804289 GAGATAGGAT
Statistics
Matches: 104, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
143 102 0.98
144 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (143 bp):
CTTTAATCTGTTCAACTACAACACCAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTCCGCTGCA
ACTTTAGGAAGATAAGACTGGTAACTTCAATCTGCTCTACTGCAACTTCAGGAAGGCAAGATCCG
ACATAATTTATAG
Found at i:39814089 original size:13 final size:13
Alignment explanation
Indices: 39814051--39814089 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
39814041 CTGTAGACTA
39814051 TTTAA-ATTTGGT
1 TTTAATATTTGGT
39814063 TTTAATATTT-GT
1 TTTAATATTTGGT
*
39814075 TTTAGTATTTGGT
1 TTTAATATTTGGT
39814088 TT
1 TT
39814090 GGGCCCCAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 16 0.67
13 8 0.33
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.64
Consensus pattern (13 bp):
TTTAATATTTGGT
Found at i:39841495 original size:13 final size:13
Alignment explanation
Indices: 39841477--39841502 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39841467 CAAGCAACAT
39841477 AAATAAAAATGAC
1 AAATAAAAATGAC
39841490 AAATAAAAATGAC
1 AAATAAAAATGAC
39841503 GACCCTTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (13 bp):
AAATAAAAATGAC
Found at i:39864290 original size:21 final size:21
Alignment explanation
Indices: 39864264--39864303 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
39864254 AATAAATACC
39864264 AAAAAATTATTTTAAAAATTA
1 AAAAAATTATTTTAAAAATTA
39864285 AAAAAATTATTTTAAAAAT
1 AAAAAATTATTTTAAAAAT
39864304 ATTTTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAAATTATTTTAAAAATTA
Found at i:39864337 original size:41 final size:42
Alignment explanation
Indices: 39864277--39864403 Score: 188
Period size: 41 Copynumber: 3.1 Consensus size: 42
39864267 AAATTATTTT
* *
39864277 AAAAATTAAAAAAATTATTTTAAAAATATTTTAAAATTAAAA
1 AAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
39864319 AAAAATTTAAAAAA-TATTTTAAAAATATTTTAAAATT--AA
1 AAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
* *
39864358 AAAATTTTAAAAAAAGTATTTTAAAAGTATTTTAAAATTAAAA
1 AAAAATTT-AAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
39864401 AAA
1 AAA
39864404 TAAAAATATT
Statistics
Matches: 78, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
39 9 0.12
40 6 0.08
41 45 0.58
42 13 0.17
43 5 0.06
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (42 bp):
AAAAATTTAAAAAAGTATTTTAAAAATATTTTAAAATTAAAA
Found at i:39864342 original size:10 final size:11
Alignment explanation
Indices: 39864265--39864394 Score: 75
Period size: 11 Copynumber: 12.4 Consensus size: 11
39864255 ATAAATACCA
39864265 AAAAATTATTTT
1 AAAAA-TATTTT
**
39864277 -AAAA-ATTAA
1 AAAAATATTTT
39864286 AAAAATTATTTT
1 AAAAA-TATTTT
39864298 AAAAATATTTT
1 AAAAATATTTT
**
39864309 --AAA-ATTAA
1 AAAAATATTTT
* *
39864317 AAAAAAATTTA
1 AAAAATATTTT
39864328 AAAAATATTTT
1 AAAAATATTTT
39864339 AAAAATATTTT
1 AAAAATATTTT
39864350 --AAA-A--TT
1 AAAAATATTTT
39864356 AAAAA-ATTTT
1 AAAAATATTTT
39864366 AAAAAAAGTATTTT
1 --AAAAA-TATTTT
*
39864380 AAAAGTATTTT
1 AAAAATATTTT
39864391 AAAA
1 AAAA
39864395 TTAAAAAAAT
Statistics
Matches: 94, Mismatches: 10, Indels: 29
0.71 0.08 0.22
Matches are distributed among these distances:
6 2 0.02
8 8 0.09
9 9 0.10
10 9 0.10
11 44 0.47
12 17 0.18
14 5 0.05
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:39864354 original size:30 final size:30
Alignment explanation
Indices: 39864293--39864383 Score: 87
Period size: 30 Copynumber: 3.0 Consensus size: 30
39864283 TAAAAAAATT
* * ****
39864293 ATTTTAAAAATATTTTAAAATTAAAAAAAA
1 ATTTAAAAAATATTTTAAAAATATTTTAAA
39864323 ATTTAAAAAATATTTTAAAAATATTTTAAA
1 ATTTAAAAAATATTTTAAAAATATTTTAAA
*
39864353 A-TTAAAAAAT-TTTAAAAAAAGTATTTTAAA
1 ATTTAAAAAATATTT-TAAAAA-TATTTTAAA
39864383 A
1 A
39864384 GTATTTTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 3 0.06
29 14 0.27
30 35 0.67
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (30 bp):
ATTTAAAAAATATTTTAAAAATATTTTAAA
Found at i:39864370 original size:17 final size:17
Alignment explanation
Indices: 39864296--39864369 Score: 60
Period size: 19 Copynumber: 4.0 Consensus size: 17
39864286 AAAAATTATT
39864296 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
* *
39864313 TTAAAAAAAAATTTAAAAAATA
1 TT--AAAAATATTT--TAAA-A
39864335 TTTTAAAAATATTTTAAAA
1 --TTAAAAATATTTTAAAA
39864354 TTAAAAA-ATTTTAAAA
1 TTAAAAATATTTTAAAA
39864370 AAAGTATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
16 9 0.20
17 9 0.20
19 10 0.22
20 3 0.07
21 3 0.07
22 10 0.22
24 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:39866046 original size:21 final size:19
Alignment explanation
Indices: 39866020--39866063 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
39866010 TGATTTCAAA
39866020 ATAATAATTATATGGAAAAAC
1 ATAAT-ATTATAT-GAAAAAC
* *
39866041 ATAATATTTTATTAAAAAC
1 ATAATATTATATGAAAAAC
39866060 ATAA
1 ATAA
39866064 AACTAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.48
20 6 0.29
21 5 0.24
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.34
Consensus pattern (19 bp):
ATAATATTATATGAAAAAC
Found at i:39871584 original size:14 final size:15
Alignment explanation
Indices: 39871565--39871597 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
39871555 TTTTAATATC
39871565 TTTAGG-TTTAAGGT
1 TTTAGGTTTTAAGGT
39871579 TTTAGGTTTTTAAGGT
1 TTTAGG-TTTTAAGGT
39871595 TTT
1 TTT
39871598 CGATTGGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
16 11 0.65
ACGTcount: A:0.18, C:0.00, G:0.24, T:0.58
Consensus pattern (15 bp):
TTTAGGTTTTAAGGT
Found at i:39878552 original size:15 final size:14
Alignment explanation
Indices: 39878500--39878554 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 14
39878490 AAGTTGCAAA
39878500 AAAAATGTGAAAAAAT
1 AAAAATG-G-AAAAAT
*
39878516 AAAAATAGAAAAAT
1 AAAAATGGAAAAAT
39878530 GAAAAATGGAAAAAGT
1 -AAAAATGGAAAAA-T
39878546 AAAAATGGA
1 AAAAATGGA
39878555 GAGGCTAAGG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
14 6 0.17
15 22 0.63
16 7 0.20
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.15
Consensus pattern (14 bp):
AAAAATGGAAAAAT
Found at i:39880044 original size:88 final size:88
Alignment explanation
Indices: 39879824--39880045 Score: 356
Period size: 88 Copynumber: 2.5 Consensus size: 88
39879814 CAGACTGAAG
* * *
39879824 ATAGCAGATCTTGCCTTCCTGTACTGATAGAGAAGTAGATCGAAAATACCAGCCTTGTCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGAGAAGTAGATCGAAGATACCAGCCTTGTCTCCCTA
* *
39879889 GGCAGTAGTGGAGTAGGTTAAAA
66 GGCAGCAGTGGAGTAGGTCAAAA
*
39879912 ATAGCAGATCTTGCCTTCCTGTACTGACAGAGAAGCAGATCGAAGATACCAGCCTTGTCTCCCTA
1 ATAGCAGATCTTGCCTTCCTGTACTGACAGAGAAGTAGATCGAAGATACCAGCCTTGTCTCCCTA
39879977 GGCAGCAGTGGAGTAGGTCAAAA
66 GGCAGCAGTGGAGTAGGTCAAAA
* *
39880000 AT-GACAGATCTTGCCTTCCTGTACTGGCAGTGAAGTAGATCGAAGA
1 ATAG-CAGATCTTGCCTTCCTGTACTGACAGAGAAGTAGATCGAAGA
39880046 CATCATTCTT
Statistics
Matches: 124, Mismatches: 9, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
87 1 0.01
88 123 0.99
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.24
Consensus pattern (88 bp):
ATAGCAGATCTTGCCTTCCTGTACTGACAGAGAAGTAGATCGAAGATACCAGCCTTGTCTCCCTA
GGCAGCAGTGGAGTAGGTCAAAA
Found at i:39880356 original size:50 final size:50
Alignment explanation
Indices: 39880243--39880672 Score: 292
Period size: 50 Copynumber: 8.6 Consensus size: 50
39880233 TATTACAGTG
* * * * * *
39880243 GAAAAGATTGAAGCCACAGCGGCGGATCTTACTT-CCTGGCAGTGCAGTG
1 GAAAAGATTGAAGCCACAACGGCGGATCTTATTTCCCCGGCATTGCAATT
** * * * *
39880292 GAAAAGATTGAAGCCATGATGGCGGATCTGATTTCCCCGACATTGTAATT
1 GAAAAGATTGAAGCCACAACGGCGGATCTTATTTCCCCGGCATTGCAATT
* * * * * * * *
39880342 GAAAAGATTGAAGCCACAGCGACGAATCTTACTTCCCTGGCAGTGCAGTA
1 GAAAAGATTGAAGCCACAACGGCGGATCTTATTTCCCCGGCATTGCAATT
* * *
39880392 GAAAAGATTGAAGCCACGATGGCGGATCTAATTTCCCCGGCATTGCAATT
1 GAAAAGATTGAAGCCACAACGGCGGATCTTATTTCCCCGGCATTGCAATT
* * * * * * * ***
39880442 AAAAAAATTGAAGCCATAACAGCGGATCTTACTTCCCTGGCAGTGCAGCG
1 GAAAAGATTGAAGCCACAACGGCGGATCTTATTTCCCCGGCATTGCAATT
* **
39880492 GAACAGATTGAAGCCACAACGGC-GAGTCTTATTTCCCCAACATTGCAATT
1 GAAAAGATTGAAGCCACAACGGCGGA-TCTTATTTCCCCGGCATTGCAATT
* * * * * * * ** *
39880542 TAAAAGATTGAAGCCACAACGACAGATCTTATCTCTCTGACGGTGCAGA-G
1 GAAAAGATTGAAGCCACAACGGCGGATCTTATTTCCCCGGCATTGCA-ATT
* * * * * * * *
39880592 GAACAGATTGAAGCTACGACGGCGGATC-TAGTTTTCTCGACATTACGATT
1 GAAAAGATTGAAGCCACAACGGCGGATCTTA-TTTCCCCGGCATTGCAATT
* * *
39880642 TAAAAGATTAAAGCCACAACGACGGATCTTA
1 GAAAAGATTGAAGCCACAACGGCGGATCTTA
39880673 CCTCTCTGGC
Statistics
Matches: 279, Mismatches: 95, Indels: 12
0.72 0.25 0.03
Matches are distributed among these distances:
49 33 0.12
50 241 0.86
51 5 0.02
ACGTcount: A:0.32, C:0.22, G:0.23, T:0.23
Consensus pattern (50 bp):
GAAAAGATTGAAGCCACAACGGCGGATCTTATTTCCCCGGCATTGCAATT
Found at i:39880549 original size:200 final size:199
Alignment explanation
Indices: 39880244--39880738 Score: 559
Period size: 200 Copynumber: 2.5 Consensus size: 199
39880234 ATTACAGTGG
* *
39880244 AAAAGATTGAAGCCACAGCGGCGGATCTTACTT-CCTGGCAGTGCAGTGGAAAAGATTGAAGCCA
1 AAAAGATTGAAGCCACAAC-GCGGATCTTACTTCCCTGGCAGTGCAGCGGAAAAGATTGAAGCCA
* * * * *
39880308 TGATGGCG-GATCTGATTTCCCCGACATTGTAATTGAAAAGATTGAAGCCACAGCGAC-GAATCT
65 TGACGGCGAG-TCTTATTTCCCCAACATTGCAATTGAAAAGATTGAAGCCACAACGACAG-ATCT
* * *
39880371 TA-CTTCCCTGGCAGTGCAGTA-GAAAAGATTGAAGCCACGATGGCGGATCTAATTTCCCCGGCA
128 TATC-TCCCTGACAGTGCAG-AGGAAAAGATTGAAGCCACGACGGCGGATCTAATTTCCCCGACA
*
39880434 TTGCAATTA
191 TTACAATTA
* * *
39880443 AAAAAATTGAAGCCATAACAGCGGATCTTACTTCCCTGGCAGTGCAGCGGAACAGATTGAAGCCA
1 AAAAGATTGAAGCCACAAC-GCGGATCTTACTTCCCTGGCAGTGCAGCGGAAAAGATTGAAGCCA
** *
39880508 CAACGGCGAGTCTTATTTCCCCAACATTGCAATTTAAAAGATTGAAGCCACAACGACAGATCTTA
65 TGACGGCGAGTCTTATTTCCCCAACATTGCAATTGAAAAGATTGAAGCCACAACGACAGATCTTA
* * * * * * *
39880573 TCTCTCTGACGGTGCAGAGGAACAGATTGAAGCTACGACGGCGGATCTAGTTTTCTCGACATTAC
130 TCTCCCTGACAGTGCAGAGGAAAAGATTGAAGCCACGACGGCGGATCTAATTTCCCCGACATTAC
* *
39880638 GATTT
195 AATTA
* * * * * * *
39880643 AAAAGATTAAAGCCACAACGACGGATCTTACCTCTCTGGCGGTGTAGCGGAATAGATTGAAGTCA
1 AAAAGATTGAAGCCACAACG-CGGATCTTACTTCCCTGGCAGTGCAGCGGAAAAGATTGAAGCCA
* * * *
39880708 TGACGGTGAATCTTGTTTTCCCAACATTGCA
65 TGACGGCGAGTCTTATTTCCCCAACATTGCA
39880739 GTTAAATAAA
Statistics
Matches: 248, Mismatches: 42, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
199 31 0.12
200 214 0.86
201 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (199 bp):
AAAAGATTGAAGCCACAACGCGGATCTTACTTCCCTGGCAGTGCAGCGGAAAAGATTGAAGCCAT
GACGGCGAGTCTTATTTCCCCAACATTGCAATTGAAAAGATTGAAGCCACAACGACAGATCTTAT
CTCCCTGACAGTGCAGAGGAAAAGATTGAAGCCACGACGGCGGATCTAATTTCCCCGACATTACA
ATTA
Found at i:39880726 original size:100 final size:100
Alignment explanation
Indices: 39880244--39880738 Score: 505
Period size: 100 Copynumber: 5.0 Consensus size: 100
39880234 ATTACAGTGG
* * *
39880244 AAAAGATTGAAGCCACAGCGGCGGATCTTACTT-CCTGGCAGTGCAGTGGAAAAGATTGAAGCCA
1 AAAAGATTGAAGCCACAACGACGGATCTTACTTCCCTGGCAGTGCAGCGGAAAAGATTGAAGCCA
* * * *
39880308 TGATGGCGGATC-TGATTTCCCCGACATTGTAATTG
66 CGACGGCGGATCTTG-TTTCCCCGACATTGCAATTT
* * **
39880343 AAAAGATTGAAGCCACAGCGACGAATCTTACTTCCCTGGCAGTGCAGTAGAAAAGATTGAAGCCA
1 AAAAGATTGAAGCCACAACGACGGATCTTACTTCCCTGGCAGTGCAGCGGAAAAGATTGAAGCCA
* ** * *
39880408 CGATGGCGGATCTAATTTCCCCGGCATTGCAATTA
66 CGACGGCGGATCTTGTTTCCCCGACATTGCAATTT
* * *
39880443 AAAAAATTGAAGCCATAAC-AGCGGATCTTACTTCCCTGGCAGTGCAGCGGAACAGATTGAAGCC
1 AAAAGATTGAAGCCACAACGA-CGGATCTTACTTCCCTGGCAGTGCAGCGGAAAAGATTGAAGCC
* * *
39880507 ACAACGGC-GAGTCTTATTTCCCCAACATTGCAATTT
65 ACGACGGCGGA-TCTTGTTTCCCCGACATTGCAATTT
* * * * * * *
39880543 AAAAGATTGAAGCCACAACGACAGATCTTA-TCTCTCTGACGGTGCAGAGGAACAGATTGAAGCT
1 AAAAGATTGAAGCCACAACGACGGATCTTACT-TCCCTGGCAGTGCAGCGGAAAAGATTGAAGCC
* * * * *
39880607 ACGACGGCGGATCTAGTTTTCTCGACATTACGATTT
65 ACGACGGCGGATCTTGTTTCCCCGACATTGCAATTT
* * * * * * *
39880643 AAAAGATTAAAGCCACAACGACGGATCTTACCTCTCTGGCGGTGTAGCGGAATAGATTGAAGTCA
1 AAAAGATTGAAGCCACAACGACGGATCTTACTTCCCTGGCAGTGCAGCGGAAAAGATTGAAGCCA
* * * * *
39880708 TGACGGTGAATCTTGTTTTCCCAACATTGCA
66 CGACGGCGGATCTTGTTTCCCCGACATTGCA
39880739 GTTAAATAAA
Statistics
Matches: 333, Mismatches: 55, Indels: 15
0.83 0.14 0.04
Matches are distributed among these distances:
99 35 0.11
100 295 0.89
101 3 0.01
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (100 bp):
AAAAGATTGAAGCCACAACGACGGATCTTACTTCCCTGGCAGTGCAGCGGAAAAGATTGAAGCCA
CGACGGCGGATCTTGTTTCCCCGACATTGCAATTT
Found at i:39886799 original size:9 final size:9
Alignment explanation
Indices: 39886785--39886857 Score: 51
Period size: 9 Copynumber: 8.1 Consensus size: 9
39886775 GAACAAGAGC
39886785 TTGAGAAAA
1 TTGAGAAAA
*
39886794 TTGAGAGAA
1 TTGAGAAAA
*
39886803 TTTAGAAAA
1 TTGAGAAAA
*
39886812 TTGAGAGAA
1 TTGAGAAAA
* * *
39886821 TTTAGAGAG
1 TTGAGAAAA
*
39886830 TTGAGAGAA
1 TTGAGAAAA
39886839 -T-AGAAAGA
1 TTGAGAAA-A
39886847 TTTGAGAAAA
1 -TTGAGAAAA
39886857 T
1 T
39886858 AGAAAGATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
7 4 0.08
8 2 0.04
9 37 0.74
10 2 0.04
11 5 0.10
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (9 bp):
TTGAGAAAA
Found at i:39886811 original size:18 final size:18
Alignment explanation
Indices: 39886788--39886839 Score: 86
Period size: 18 Copynumber: 2.9 Consensus size: 18
39886778 CAAGAGCTTG
39886788 AGAAAATTGAGAGAATTT
1 AGAAAATTGAGAGAATTT
39886806 AGAAAATTGAGAGAATTT
1 AGAAAATTGAGAGAATTT
* *
39886824 AGAGAGTTGAGAGAAT
1 AGAAAATTGAGAGAAT
39886840 AGAAAGATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.48, C:0.00, G:0.27, T:0.25
Consensus pattern (18 bp):
AGAAAATTGAGAGAATTT
Found at i:39886851 original size:18 final size:18
Alignment explanation
Indices: 39886794--39886877 Score: 91
Period size: 18 Copynumber: 4.7 Consensus size: 18
39886784 CTTGAGAAAA
39886794 TTGAGAGAATTTAGAAA-A-
1 TTGAGAGAA--TAGAAAGAT
** * *
39886812 TTGAGAGAATTTAGAGAG
1 TTGAGAGAATAGAAAGAT
39886830 TTGAGAGAATAGAAAGAT
1 TTGAGAGAATAGAAAGAT
*
39886848 TTGAGAAAATAGAAAGAT
1 TTGAGAGAATAGAAAGAT
39886866 TTGAGAGAATAG
1 TTGAGAGAATAG
39886878 GATGTGAGTG
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
16 3 0.05
17 1 0.02
18 51 0.93
ACGTcount: A:0.48, C:0.00, G:0.27, T:0.25
Consensus pattern (18 bp):
TTGAGAGAATAGAAAGAT
Found at i:39896474 original size:43 final size:43
Alignment explanation
Indices: 39896333--39896488 Score: 160
Period size: 43 Copynumber: 3.7 Consensus size: 43
39896323 GGCTCGTACA
* **
39896333 ATGCCAACGTCCCAGACGTGGTCTTACATGTA-ATCAC-ATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACACATATA-CACAAT-TCG
* * * * *
39896376 ATGCC-ACTATCCTAGACAGGGTCTTACACAAAT-CA-AATACG
1 ATGCCAAC-GTCCCAGACATGGTCTTACACATATACACAATTCG
*
39896417 ATGCCAATGTCCCAGACATGGTCTTACACATATACACAATTCG
1 ATGCCAACGTCCCAGACATGGTCTTACACATATACACAATTCG
*
39896460 ATGCCAACGTCCCAGACGTGGTCTTACAC
1 ATGCCAACGTCCCAGACATGGTCTTACAC
39896489 GAAAATACAT
Statistics
Matches: 91, Mismatches: 16, Indels: 12
0.76 0.13 0.10
Matches are distributed among these distances:
41 28 0.31
42 9 0.10
43 54 0.59
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACACATATACACAATTCG
Found at i:39896483 original size:84 final size:84
Alignment explanation
Indices: 39896333--39896488 Score: 194
Period size: 84 Copynumber: 1.9 Consensus size: 84
39896323 GGCTCGTACA
* ** *
39896333 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCGATGCCACTATCCTAGACAGGGT
1 ATGCCAACGTCCCAGACATGGTCTTACACATAATCACATATCGATGCCACTATCCCAGACAGGGT
39896398 CTTACACAAATCAAATACG
66 CTTACACAAATCAAATACG
* *
39896417 ATGCCAATGTCCCAGACATGGTCTTACACAT-ATACACA-ATTCGATGCCAAC-GTCCCAGAC-G
1 ATGCCAACGTCCCAGACATGGTCTTACACATAAT-CACATA-TCGATGCC-ACTATCCCAGACAG
39896478 TGGTCTTACAC
63 -GGTCTTACAC
39896489 GAAAATACAT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
83 4 0.06
84 56 0.90
85 2 0.03
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (84 bp):
ATGCCAACGTCCCAGACATGGTCTTACACATAATCACATATCGATGCCACTATCCCAGACAGGGT
CTTACACAAATCAAATACG
Found at i:39907808 original size:82 final size:82
Alignment explanation
Indices: 39907671--39907903 Score: 457
Period size: 82 Copynumber: 2.8 Consensus size: 82
39907661 TCATTAACCT
39907671 AAAACAATGTGTTCATTAACCTAAAGGTCCTAACGCTTCCCAACAAATACCACTTGAACACATGT
1 AAAACAATGTGTTCATTAACCTAAAGGTCCTAACGCTTCCCAACAAATACCACTTGAACACATGT
39907736 TCTATAAAGCCCTCCCC
66 TCTATAAAGCCCTCCCC
39907753 AAAACAATGTGTTCATTAACCTAAAGGTCCTAACGCTTCCCAACAAATACCACTTGAACACATGT
1 AAAACAATGTGTTCATTAACCTAAAGGTCCTAACGCTTCCCAACAAATACCACTTGAACACATGT
39907818 TCTATAAAGCCCTCCCC
66 TCTATAAAGCCCTCCCC
*
39907835 AAAACAATGTGTTCATTAACCTAAAGGTCCTAACGCTTCCCAACAAATACCACTTGAACACATGC
1 AAAACAATGTGTTCATTAACCTAAAGGTCCTAACGCTTCCCAACAAATACCACTTGAACACATGT
39907900 TCTA
66 TCTA
39907904 CAAATGAGAC
Statistics
Matches: 150, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 150 1.00
ACGTcount: A:0.36, C:0.30, G:0.10, T:0.24
Consensus pattern (82 bp):
AAAACAATGTGTTCATTAACCTAAAGGTCCTAACGCTTCCCAACAAATACCACTTGAACACATGT
TCTATAAAGCCCTCCCC
Found at i:39925318 original size:41 final size:39
Alignment explanation
Indices: 39925273--39925404 Score: 151
Period size: 40 Copynumber: 3.3 Consensus size: 39
39925263 AGCGGCATTT
**
39925273 TTAGCGGCGTTTGGATAAAAAACGCCGCTAAAGATCGAGCA
1 TTAGCGGCGTTT--ATGGAAAACGCCGCTAAAGATCGAGCA
* *
39925314 TTAGCGGCGCTTCT-TGGAAAATGCCGCTAAAGATCGAGTA
1 TTAGCGGCG-TT-TATGGAAAACGCCGCTAAAGATCGAGCA
* *
39925354 TTAGCGGCGCTTTATGGAAAACGCCGCTAAA-AACAAGCA
1 TTAGCGGCG-TTTATGGAAAACGCCGCTAAAGATCGAGCA
39925393 TTAGCGGCGTTT
1 TTAGCGGCGTTT
39925405 CTCGAAAGCG
Statistics
Matches: 80, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
38 3 0.04
39 15 0.19
40 50 0.62
41 9 0.11
42 2 0.03
43 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (39 bp):
TTAGCGGCGTTTATGGAAAACGCCGCTAAAGATCGAGCA
Found at i:39925345 original size:40 final size:41
Alignment explanation
Indices: 39925291--39925406 Score: 166
Period size: 40 Copynumber: 2.9 Consensus size: 41
39925281 GTTTGGATAA
39925291 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTCT-TGG
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTCTATGG
* *
39925331 AAAATGCCGCTAAAGATCGAGTATTAGCGGCGCTT-TATGG
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTCTATGG
* * *
39925371 AAAACGCCGCTAAA-AACAAGCATTAGCGGCGTTTCT
1 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTCT
39925407 CGAAAGCGCC
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
39 17 0.25
40 50 0.75
ACGTcount: A:0.31, C:0.22, G:0.25, T:0.22
Consensus pattern (41 bp):
AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTCTATGG
Found at i:39925569 original size:41 final size:41
Alignment explanation
Indices: 39925504--39925758 Score: 225
Period size: 41 Copynumber: 6.2 Consensus size: 41
39925494 AGCTGCTTTA
*
39925504 AATGCTCAGGGTTTTAGCGGCGTTTTTGGAAAAGCGCCGCT
1 AATGCTCAGAGTTTTAGCGGCGTTTTTGGAAAAGCGCCGCT
* * * *
39925545 AATGCTCAGAGTTTTAACGACGTTTTTGGGAAAGCGCTGCT
1 AATGCTCAGAGTTTTAGCGGCGTTTTTGGAAAAGCGCCGCT
* * *
39925586 AATGCTCA-AGGCTTTAGCGGCGTTTTTGGGAAAGTGCCGCT
1 AATGCTCAGA-GTTTTAGCGGCGTTTTTGGAAAAGCGCCGCT
* * * * *
39925627 AATTCTTAGGGCTTTAGCGGCGTTTTTAGG-AAAGCGTCGCT
1 AATGCTCAGAGTTTTAGCGGCGTTTTT-GGAAAAGCGCCGCT
* * * * *
39925668 AATTCTTAGGGCTTTTAGCAGCGTTTTT-GATAAAACGCCG-T
1 AATGCTCAGAG-TTTTAGCGGCGTTTTTGGA-AAAGCGCCGCT
* * *
39925709 GAATGCTC-TATTTTTAGCGGCGTTTTCT-AAAAAGCGCCGCT
1 -AATGCTCAGAGTTTTAGCGGCGTTTT-TGGAAAAGCGCCGCT
39925750 AATGCTCAG
1 AATGCTCAG
39925759 GGATTTAAAA
Statistics
Matches: 176, Mismatches: 28, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
40 31 0.18
41 117 0.66
42 28 0.16
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (41 bp):
AATGCTCAGAGTTTTAGCGGCGTTTTTGGAAAAGCGCCGCT
Found at i:39925747 original size:40 final size:40
Alignment explanation
Indices: 39925680--39925756 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
39925670 TTCTTAGGGC
39925680 TTTTAGCAGCGTTTTTGATAAAACGCCG-TGAATGCTCTAT
1 TTTTAGCAGCGTTTTTGATAAAACGCCGCT-AATGCTCTAT
*
39925720 TTTTAGCGGCGTTTTCT-A-AAAAGCGCCGCTAATGCTC
1 TTTTAGCAGCGTTTT-TGATAAAA-CGCCGCTAATGCTC
39925757 AGGGATTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
39 4 0.12
40 27 0.82
41 2 0.06
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (40 bp):
TTTTAGCAGCGTTTTTGATAAAACGCCGCTAATGCTCTAT
Found at i:39925985 original size:7 final size:7
Alignment explanation
Indices: 39925940--39926093 Score: 116
Period size: 7 Copynumber: 21.7 Consensus size: 7
39925930 TATCACTATA
*
39925940 GTTTAGG
1 GTTTATG
*
39925947 GTTTTTG
1 GTTTATG
*
39925954 GTTTAAG
1 GTTTATG
*
39925961 GTATATG
1 GTTTATG
39925968 GTTTA-G
1 GTTTATG
39925974 AGTTTATG
1 -GTTTATG
39925982 GTTTATG
1 GTTTATG
*
39925989 GATTATG
1 GTTTATG
*
39925996 AGTTTAGG
1 -GTTTATG
*
39926004 GGTTATG
1 GTTTATG
39926011 GTTTATG
1 GTTTATG
39926018 GTTTATG
1 GTTTATG
39926025 GTTTATG
1 GTTTATG
*
39926032 GTTTAAAG
1 GTTT-ATG
*
39926040 GTTGA-G
1 GTTTATG
*
39926046 GTTTAAG
1 GTTTATG
39926053 GTTTA-G
1 GTTTATG
*
39926059 AGGTTATG
1 -GTTTATG
* *
39926067 TGTTAAGG
1 -GTTTATG
39926075 GTTTATG
1 GTTTATG
*
39926082 GTTTAGG
1 GTTTATG
39926089 GTTTA
1 GTTTA
39926094 GATTAACTAG
Statistics
Matches: 116, Mismatches: 24, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
6 7 0.06
7 93 0.80
8 16 0.14
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.47
Consensus pattern (7 bp):
GTTTATG
Found at i:39926030 original size:14 final size:14
Alignment explanation
Indices: 39925940--39926093 Score: 141
Period size: 14 Copynumber: 10.9 Consensus size: 14
39925930 TATCACTATA
*
39925940 GTTTAGGGTTTTTG
1 GTTTAGGGTTTATG
* *
39925954 GTTTAAGGTATATG
1 GTTTAGGGTTTATG
*
39925968 GTTTAGAGTTTATG
1 GTTTAGGGTTTATG
* *
39925982 GTTTATGGATTATG
1 GTTTAGGGTTTATG
*
39925996 AGTTTAGGGGTTATG
1 -GTTTAGGGTTTATG
*
39926011 GTTTATGGTTTATG
1 GTTTAGGGTTTATG
* *
39926025 GTTTATGGTTTAAAG
1 GTTTAGGGTTT-ATG
* *
39926040 GTTGA-GGTTTAAG
1 GTTTAGGGTTTATG
39926053 GTTTAGAGG-TTATG
1 GTTTAG-GGTTTATG
*
39926067 TGTTAAGGGTTTATG
1 -GTTTAGGGTTTATG
39926082 GTTTAGGGTTTA
1 GTTTAGGGTTTA
39926094 GATTAACTAG
Statistics
Matches: 115, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
13 7 0.06
14 78 0.68
15 30 0.26
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.47
Consensus pattern (14 bp):
GTTTAGGGTTTATG
Found at i:39926367 original size:14 final size:15
Alignment explanation
Indices: 39926341--39926378 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
39926331 AATAATTATA
39926341 TATGGATTTAGGGAT
1 TATGGATTTAGGGAT
39926356 TATGGA-TTAGGGAT
1 TATGGATTTAGGGAT
39926370 TATGG-TTTA
1 TATGGATTTA
39926379 AGGGTTGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (15 bp):
TATGGATTTAGGGAT
Found at i:39926399 original size:21 final size:21
Alignment explanation
Indices: 39926365--39926439 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
39926355 TTATGGATTA
*
39926365 GGGA-TTATGGTTTAAGGGTT
1 GGGATTTAAGGTTTAAGGGTT
39926385 GGGATTTAAGGTTTAAGGGTT
1 GGGATTTAAGGTTTAAGGGTT
* * *
39926406 AGGATTTAGGGGTTT-AGGATTT
1 GGGATTTA-AGGTTTAAGG-GTT
39926428 AGGGATTTAAGG
1 -GGGATTTAAGG
39926440 GTTGGGTTAG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
20 4 0.09
21 25 0.56
22 9 0.20
23 7 0.16
ACGTcount: A:0.24, C:0.00, G:0.39, T:0.37
Consensus pattern (21 bp):
GGGATTTAAGGTTTAAGGGTT
Found at i:39926413 original size:14 final size:15
Alignment explanation
Indices: 39926396--39926428 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
39926386 GGATTTAAGG
39926396 TTTAAGGG-TTAGGA
1 TTTAAGGGTTTAGGA
*
39926410 TTTAGGGGTTTAGGA
1 TTTAAGGGTTTAGGA
39926425 TTTA
1 TTTA
39926429 GGGATTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.42
Consensus pattern (15 bp):
TTTAAGGGTTTAGGA
Found at i:39926424 original size:15 final size:15
Alignment explanation
Indices: 39926404--39926436 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
39926394 GGTTTAAGGG
*
39926404 TTAGGATTTAGGGGT
1 TTAGGATTTAGGGAT
39926419 TTAGGATTTAGGGAT
1 TTAGGATTTAGGGAT
39926434 TTA
1 TTA
39926437 AGGGTTGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.42
Consensus pattern (15 bp):
TTAGGATTTAGGGAT
Found at i:39926458 original size:7 final size:7
Alignment explanation
Indices: 39926347--39926463 Score: 66
Period size: 7 Copynumber: 16.7 Consensus size: 7
39926337 TATATATGGA
39926347 TTTAGGG
1 TTTAGGG
* *
39926354 ATTATGG
1 TTTAGGG
*
39926361 ATTAGGG
1 TTTAGGG
* *
39926368 ATTATGG
1 TTTAGGG
39926375 TTTAAGGG
1 TTT-AGGG
39926383 -TT-GGG
1 TTTAGGG
*
39926388 ATTTAAGG
1 -TTTAGGG
39926396 TTTAAGGG
1 TTT-AGGG
*
39926404 -TTAGGA
1 TTTAGGG
39926410 TTTAGGGG
1 TTTA-GGG
*
39926418 TTTAGGA
1 TTTAGGG
39926425 TTTAGGG
1 TTTAGGG
39926432 ATTTAAGGG
1 -TTT-AGGG
39926441 -TT-GGG
1 TTTAGGG
39926446 -TTAGGG
1 TTTAGGG
39926452 TTTAGGG
1 TTTAGGG
39926459 TTTAG
1 TTTAG
39926464 ATTAATTAGT
Statistics
Matches: 87, Mismatches: 12, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
5 8 0.09
6 6 0.07
7 52 0.60
8 17 0.20
9 4 0.05
ACGTcount: A:0.22, C:0.00, G:0.38, T:0.39
Consensus pattern (7 bp):
TTTAGGG
Found at i:39930463 original size:27 final size:26
Alignment explanation
Indices: 39930433--39930489 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
39930423 AATTTCGAGG
*
39930433 TTTACAATTTT-TAATTTTTATTAATT
1 TTTAC-ATTTTCTAACTTTTATTAATT
* *
39930459 ATTTACGTTTTCTCACTTTTATTAATT
1 -TTTACATTTTCTAACTTTTATTAATT
39930486 TTTA
1 TTTA
39930490 TTATTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.26, C:0.09, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTACATTTTCTAACTTTTATTAATT
Found at i:39930783 original size:43 final size:43
Alignment explanation
Indices: 39930695--39930859 Score: 188
Period size: 43 Copynumber: 3.8 Consensus size: 43
39930685 TTTTTGCGAG
* * * * * * *
39930695 AAGCGTCGCTAAAGGT-TTGTTCTATAGTGGTGTTTGTGATAAA
1 AAGCGTCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGCGA-CAA
*
39930738 AAGTGTCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGCGACAA
1 AAGCGTCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGCGACAA
* * * **
39930781 AAGCGTCGCTAAAGGTCGTGGTCTTTAGTGGCGTTTGTGGGAA
1 AAGCGTCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGCGACAA
*
39930824 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTT
1 AAGCGTCGCTAAAGGTCATGGTCTTTAGCGGCGTTT
39930860 ATTTCTAGAA
Statistics
Matches: 104, Mismatches: 17, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
43 87 0.84
44 17 0.16
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.31
Consensus pattern (43 bp):
AAGCGTCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGCGACAA
Found at i:39930793 original size:86 final size:86
Alignment explanation
Indices: 39930695--39930859 Score: 242
Period size: 86 Copynumber: 1.9 Consensus size: 86
39930685 TTTTTGCGAG
* * * * * *
39930695 AAGCGTCGCTAAAGGT-TTGTTCTATAGTGGTGTTTGTGATAAAAAGTGTCGCTAAAGGTCATGG
1 AAGCGTCGCTAAAGGTCGTGGTCTATAGTGGCGTTTGTG-GAAAAAGCGCCGCTAAAGGTCATGG
39930759 TCTTTAGCGGCGTTTGCGACAA
65 TCTTTAGCGGCGTTTGCGACAA
* *
39930781 AAGCGTCGCTAAAGGTCGTGGTCTTTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGT
1 AAGCGTCGCTAAAGGTCGTGGTCTATAGTGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGT
39930846 CTTTAGCGGCGTTT
66 CTTTAGCGGCGTTT
39930860 ATTTCTAGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
86 52 0.74
87 18 0.26
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.31
Consensus pattern (86 bp):
AAGCGTCGCTAAAGGTCGTGGTCTATAGTGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGT
CTTTAGCGGCGTTTGCGACAA
Found at i:39937199 original size:26 final size:26
Alignment explanation
Indices: 39937161--39937266 Score: 77
Period size: 26 Copynumber: 3.9 Consensus size: 26
39937151 GGACTGTATT
* *
39937161 TTTCAGTTGTTAAGGGGTCAAAAGAA
1 TTTCAATTTTTAAGGGGTCAAAAGAA
* * * *
39937187 TTTGAACTTTTAAAGGGTAAAAAGAAA
1 TTTCAATTTTTAAGGGGTCAAAAG-AA
* *
39937214 TTTATCAATTTTTAAGGAGTCTAAAAACAA
1 -TT-TCAATTTTTAAGGGGTC--AAAAGAA
* *
39937244 TTTTAATTTTTAAGGGCTCAAAA
1 TTTCAATTTTTAAGGGGTCAAAA
39937267 TTTTTTTTTA
Statistics
Matches: 60, Mismatches: 15, Indels: 10
0.71 0.18 0.12
Matches are distributed among these distances:
26 22 0.37
27 2 0.03
28 16 0.27
29 14 0.23
30 2 0.03
31 4 0.07
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.35
Consensus pattern (26 bp):
TTTCAATTTTTAAGGGGTCAAAAGAA
Found at i:39937230 original size:28 final size:26
Alignment explanation
Indices: 39937170--39937266 Score: 70
Period size: 28 Copynumber: 3.5 Consensus size: 26
39937160 TTTTCAGTTG
* * * *
39937170 TTAAGGGGTCAAAAGAATTTGAACTTT
1 TTAAGGGCTAAAAAAAATTTTAA-TTT
*
39937197 TAAAGGG-TAAAAAGAAATTTATCAATTT
1 TTAAGGGCTAAAAA-AAATTT-T-AATTT
*
39937225 TTAAGGAGTCTAAAAACAATTTTAATTT
1 TTAAGG-G-CTAAAAAAAATTTTAATTT
*
39937253 TTAAGGGCTCAAAA
1 TTAAGGGCTAAAAA
39937267 TTTTTTTTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
26 11 0.19
27 12 0.21
28 19 0.33
29 4 0.07
30 5 0.09
31 6 0.11
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.33
Consensus pattern (26 bp):
TTAAGGGCTAAAAAAAATTTTAATTT
Found at i:39938200 original size:33 final size:33
Alignment explanation
Indices: 39938158--39938227 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
39938148 CGTCTCGGTT
* * *
39938158 GGTGGAGATATGACTTGCAAGGCTCACAAGAGA
1 GGTGGAGATATAACCTGCAAGGCTCACAAGAAA
*
39938191 GGTGGAGATATAACCTGCAAGGCTCATAAGAAA
1 GGTGGAGATATAACCTGCAAGGCTCACAAGAAA
39938224 GGTG
1 GGTG
39938228 TCAATATAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.14, G:0.33, T:0.19
Consensus pattern (33 bp):
GGTGGAGATATAACCTGCAAGGCTCACAAGAAA
Found at i:39938235 original size:33 final size:33
Alignment explanation
Indices: 39938158--39938235 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
39938148 CGTCTCGGTT
* * * *
39938158 GGTGGAGATATGACTTGCAAGGCTCACAAGAGA
1 GGTGCAGATATAACCTGCAAGGCTCACAAGAAA
* *
39938191 GGTGGAGATATAACCTGCAAGGCTCATAAGAAA
1 GGTGCAGATATAACCTGCAAGGCTCACAAGAAA
39938224 GGTGTCA-ATATA
1 GGTG-CAGATATA
39938236 GTGCCTATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 38 0.97
34 1 0.03
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (33 bp):
GGTGCAGATATAACCTGCAAGGCTCACAAGAAA
Found at i:39939161 original size:19 final size:18
Alignment explanation
Indices: 39939137--39939213 Score: 57
Period size: 19 Copynumber: 4.1 Consensus size: 18
39939127 CAAAATTATT
39939137 ATTTTAGAAATTTTTTAAA
1 ATTTT-GAAATTTTTTAAA
* *
39939156 ATTTT-AACTTTATTTATAT
1 ATTTTGAAATTT-TTTA-AA
*
39939175 ATTTTTAGAATTTTTTAAAA
1 ATTTTGA-AATTTTTT-AAA
* *
39939195 AATTTGTAATTTTTTAAA
1 ATTTTGAAATTTTTTAAA
39939213 A
1 A
39939214 ATATAAATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
17 5 0.11
18 8 0.17
19 19 0.41
20 9 0.20
21 5 0.11
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (18 bp):
ATTTTGAAATTTTTTAAA
Found at i:39939272 original size:20 final size:18
Alignment explanation
Indices: 39939145--39939272 Score: 64
Period size: 20 Copynumber: 6.4 Consensus size: 18
39939135 TTATTTTAGA
39939145 AATTTTTT-AAA-ATTTT
1 AATTTTTTAAAATATTTT
*
39939161 AACTTTATTT-ATATATTTTT
1 AA-TTT-TTTAAAATA-TTTT
*
39939181 AGAATTTTTTAAAAAATTTGT
1 --AATTTTTTAAAATATTT-T
39939202 AATTTTTTAAAAATATAAATTTT
1 AATTTTTT--AAA-AT--ATTTT
*
39939225 GAATTTTTTATAAATATTGTG
1 -AATTTTTTA-AAATATT-TT
*
39939246 AATTTTTGAAAATTATTTT
1 AATTTTTTAAAA-TATTTT
39939265 AATTTTTT
1 AATTTTTT
39939273 TGTAATTTTT
Statistics
Matches: 87, Mismatches: 8, Indels: 31
0.69 0.06 0.25
Matches are distributed among these distances:
16 2 0.02
17 3 0.03
18 5 0.06
19 20 0.23
20 25 0.29
21 11 0.13
22 6 0.07
23 3 0.03
24 12 0.14
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.57
Consensus pattern (18 bp):
AATTTTTTAAAATATTTT
Found at i:39940187 original size:96 final size:96
Alignment explanation
Indices: 39939980--39940296 Score: 467
Period size: 96 Copynumber: 3.3 Consensus size: 96
39939970 TAAATAAGAG
* * * *
39939980 ATTAGGGTTTAGGGTTTCTTAATTAAATTAATTATAAATTTTT-CAAAATTAGATTAGGGTTTTG
1 ATTAGGGTTTAGGGTTACTTAAGTAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAG
* *
39940044 TGTTTATGG-TTTTAAGGAAAAATCAATTAA
66 TGTTTAAGGTTTTTAAGGAAAAATCAAATAA
* * *
39940074 ATTAGGGTTTAGGGTTACTTGAGTAATTTAATTATAAATTTTTAAAAAATCAGATTAGGGTTTAG
1 ATTAGGGTTTAGGGTTACTTAAGTAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAG
*
39940139 TGTTAAAGGTTTTTAAGGAAAAATCAAATAA
66 TGTTTAAGGTTTTTAAGGAAAAATCAAATAA
** *
39940170 ATTAGGGTTTAAAGTTACTTAAGTAAATTAATTATAAATTTTAAAAAAATTAGATTAGGGTTTAG
1 ATTAGGGTTTAGGGTTACTTAAGTAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAG
* *
39940235 TGTTTAGGGTTTTTAAGGAAAAACTAAAATAA
66 TGTTTAAGGTTTTTAAGGAAAAA-TCAAATAA
*
39940267 ATTAGGGTTTAGGGTTACTTAATTAAATTA
1 ATTAGGGTTTAGGGTTACTTAAGTAAATTA
39940297 TTTGTTAATA
Statistics
Matches: 198, Mismatches: 22, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
94 39 0.20
95 25 0.13
96 100 0.51
97 34 0.17
ACGTcount: A:0.39, C:0.03, G:0.18, T:0.41
Consensus pattern (96 bp):
ATTAGGGTTTAGGGTTACTTAAGTAAATTAATTATAAATTTTTAAAAAATTAGATTAGGGTTTAG
TGTTTAAGGTTTTTAAGGAAAAATCAAATAA
Found at i:39940598 original size:126 final size:126
Alignment explanation
Indices: 39940331--39940598 Score: 383
Period size: 126 Copynumber: 2.1 Consensus size: 126
39940321 CGTGGACTTT
* * * * *
39940331 TTTGCTACAGTAGTTACTTAAAAAATGATTTTGAGAAGACGTTTTTGAGCAAATAATGGCAAAAA
1 TTTGCTACAGTAGTTCCTGAAAAAATAATTTCGAGAAGACGTTTCTGAGCAAATAATGGCAAAAA
*
39940396 CACTTTAAGCAGGATGCATTGTCAACAAAAGTACTAAAAGAAGCTCCCACGTGACCGCTCT
66 CACTTTAAGCAGGATGCATTGTCAACAAAAGTACTAAAAGAAGCTCCCACGTGACCGCTCC
* * *
39940457 TTTGCTACAGTAGTTCCTGAAAGAATAATTTCGAGAAGACGTTTCTGAGCAAATAGTGTCAAAAA
1 TTTGCTACAGTAGTTCCTGAAAAAATAATTTCGAGAAGACGTTTCTGAGCAAATAATGGCAAAAA
* * * * * ** *
39940522 CGCTTTAAGTAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAGCTCCCACGTGGGCGTTCC
66 CACTTTAAGCAGGATGCATTGTCAACAAAAGTACTAAAAGAAGCTCCCACGTGACCGCTCC
39940583 TTTGCTACAGTAGTTC
1 TTTGCTACAGTAGTTC
39940599 ATATTTGGCT
Statistics
Matches: 125, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
126 125 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (126 bp):
TTTGCTACAGTAGTTCCTGAAAAAATAATTTCGAGAAGACGTTTCTGAGCAAATAATGGCAAAAA
CACTTTAAGCAGGATGCATTGTCAACAAAAGTACTAAAAGAAGCTCCCACGTGACCGCTCC
Found at i:39943776 original size:30 final size:33
Alignment explanation
Indices: 39943735--39943837 Score: 124
Period size: 34 Copynumber: 3.2 Consensus size: 33
39943725 TTACCTTATT
*
39943735 TAAAAGAATTTCTATTTTATTA-A-AAAT-ATA
1 TAAAATAATTTCTATTTTATTACAGAAATAATA
* *
39943765 -AAAGTAAATTTCTATATTATTACATGAAATAATA
1 TAAAAT-AATTTCTATTTTATTACA-GAAATAATA
39943799 TAAAATAATTTCTATTTTATTACATGAAATAATA
1 TAAAATAATTTCTATTTTATTACA-GAAATAATA
39943833 TAAAA
1 TAAAA
39943838 ATATTCAAAA
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
29 3 0.05
30 15 0.24
31 1 0.02
33 4 0.06
34 35 0.56
35 4 0.06
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (33 bp):
TAAAATAATTTCTATTTTATTACAGAAATAATA
Found at i:39943799 original size:111 final size:108
Alignment explanation
Indices: 39943576--39943774 Score: 317
Period size: 111 Copynumber: 1.8 Consensus size: 108
39943566 TGTATTATTT
* *
39943576 ATATTTTTTAAATGAAAAATATAAAAATATTCAAAATATTGCTTTATTTAAAAGAATTTCTATTT
1 ATATTTTTTAAATGAAAAATATAAAAATATTCAAAATATTACCTTATTTAAAAGAATTTCTATTT
*
39943641 TATTAAAAATATTAAAGTAAATTGCAATTACTTTATTCAAAACA
66 TATTAAAAATATAAAAGTAAATTGCAATTAC-TTATTCAAAACA
* * *
39943685 ATATTTTATTGAATGAAATAATATAGAAATATTTAAAATATTACCTTATTTAAAAGAATTTCTAT
1 ATATTTT-TTAAATGAAA-AATATAAAAATATTCAAAATATTACCTTATTTAAAAGAATTTCTAT
39943750 TTTATTAAAAATATAAAAGTAAATT
64 TTTATTAAAAATATAAAAGTAAATT
39943775 TCTATATTAT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
109 7 0.09
110 9 0.11
111 66 0.80
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (108 bp):
ATATTTTTTAAATGAAAAATATAAAAATATTCAAAATATTACCTTATTTAAAAGAATTTCTATTT
TATTAAAAATATAAAAGTAAATTGCAATTACTTATTCAAAACA
Found at i:39943813 original size:34 final size:36
Alignment explanation
Indices: 39943759--39943837 Score: 135
Period size: 34 Copynumber: 2.2 Consensus size: 36
39943749 TTTTATTAAA
39943759 AATATAAAAGTAAATTTCTATATTATTACATGAAAT
1 AATATAAAAGTAAATTTCTATATTATTACATGAAAT
*
39943795 AATATAAAA-T-AATTTCTATTTTATTACATGAAAT
1 AATATAAAAGTAAATTTCTATATTATTACATGAAAT
39943829 AATATAAAA
1 AATATAAAA
39943838 ATATTCAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
34 32 0.76
35 1 0.02
36 9 0.21
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (36 bp):
AATATAAAAGTAAATTTCTATATTATTACATGAAAT
Found at i:39944270 original size:18 final size:18
Alignment explanation
Indices: 39944244--39944286 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
39944234 GACTAGAAAA
* * *
39944244 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
39944262 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
39944280 AGGATAC
1 AGGATAC
39944287 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:39946103 original size:11 final size:11
Alignment explanation
Indices: 39946089--39946147 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
39946079 GAGACCTTTA
*
39946089 AGAGGAATTTG
1 AGAGGAATATG
39946100 AGAGGAATATG
1 AGAGGAATATG
39946111 AGA-GAATACTGG
1 AGAGGAATA-T-G
* *
39946123 AGAGAAATACG
1 AGAGGAATATG
*
39946134 AGA-GAATTTG
1 AGAGGAATATG
39946144 AGAG
1 AGAG
39946148 AAAGGATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
10 12 0.32
11 18 0.47
12 4 0.11
13 4 0.11
ACGTcount: A:0.44, C:0.03, G:0.34, T:0.19
Consensus pattern (11 bp):
AGAGGAATATG
Found at i:39946146 original size:21 final size:21
Alignment explanation
Indices: 39946093--39946150 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 21
39946083 CCTTTAAGAG
* *
39946093 GAATTTGAGAGGAATATGAGA
1 GAATTTGAGAGAAATACGAGA
*
39946114 GAATACTGGAGAGAAATACGAGA
1 GAAT--TTGAGAGAAATACGAGA
39946137 GAATTTGAGAGAAA
1 GAATTTGAGAGAAA
39946151 GGATTTAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 13 0.42
23 18 0.58
ACGTcount: A:0.47, C:0.03, G:0.31, T:0.19
Consensus pattern (21 bp):
GAATTTGAGAGAAATACGAGA
Found at i:39950006 original size:18 final size:17
Alignment explanation
Indices: 39949978--39950012 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39949968 TTGTCTAAGA
*
39949978 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39949995 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39950013 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39950126 original size:18 final size:17
Alignment explanation
Indices: 39950098--39950132 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39950088 ATTATTAAGA
*
39950098 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39950115 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39950133 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39950186 original size:120 final size:120
Alignment explanation
Indices: 39949973--39950989 Score: 1998
Period size: 120 Copynumber: 8.5 Consensus size: 120
39949963 GGCAGTTGTC
39949973 TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
1 TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
39950038 TTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
66 TTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
39950093 TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
1 TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
39950158 TTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
66 TTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
39950213 TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
1 TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
39950278 TTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
66 TTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
39950333 TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
1 TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
39950398 TTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
66 TTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
39950453 TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
1 TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
39950518 TTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
66 TTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
*
39950573 TAATAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
1 TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
39950638 TTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
66 TTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
**
39950693 TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTACATTAATTTATA
1 TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
39950758 TTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
66 TTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
*
39950813 TAAGAATTTTACTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
1 TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
39950878 TTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
66 TTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
39950933 TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
39950990 TAAATATGAT
Statistics
Matches: 889, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 889 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (120 bp):
TAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATA
TTTTACAGTATCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTAT
Found at i:39950246 original size:18 final size:17
Alignment explanation
Indices: 39950218--39950252 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39950208 ATTATTAAGA
*
39950218 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39950235 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39950253 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39950366 original size:18 final size:17
Alignment explanation
Indices: 39950338--39950372 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39950328 ATTATTAAGA
*
39950338 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39950355 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39950373 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39950486 original size:18 final size:17
Alignment explanation
Indices: 39950458--39950492 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39950448 ATTATTAAGA
*
39950458 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39950475 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39950493 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39950602 original size:47 final size:42
Alignment explanation
Indices: 39950551--39950882 Score: 124
Period size: 44 Copynumber: 8.1 Consensus size: 42
39950541 TTTCAGTAAA
* *
39950551 TTAATATAAGAATATTAATTATTAATAATTTTATTAAATTATATATT
1 TTAAT-TAA-AATA-TAATTAATAATAATTATATT-AATT-TATATT
* *
39950598 TTAATTAAAATATATTTAATAATAATTATGTTAATTTATATT
1 TTAATTAAAATATAATTAATAATAATTATATTAATTTATATT
* ** * * * *
39950640 TTACAGTATCATAT-ATT-ATGAT--TT-CAGTAAATTA-A-T
1 TTA-ATTAAAATATAATTAATAATAATTATATTAATTTATATT
* * * * * *
39950676 ATAA-GAATAT-TAATTATTAAGAATTTTATTAAATTATATATT
1 TTAATTAAAATATAATTAATAATAATTATATT-AATT-TATATT
* *
39950718 TTAATTAAAATATATTTAATAATAATTACATTAATTTATATT
1 TTAATTAAAATATAATTAATAATAATTATATTAATTTATATT
* ** * * * *
39950760 TTACAGTATCATAT-ATT-ATGAT--TT-CAGTAAATTA-A-T
1 TTA-ATTAAAATATAATTAATAATAATTATATTAATTTATATT
* * * * * * *
39950796 ATAA-GAATAT-TAATTATTAAGAATTTTACTAAATTATATATT
1 TTAATTAAAATATAATTAATAATAATTATA-TTAATT-TATATT
* *
39950838 TTAATTAAAATATATTTAATAATAATTATGTTAATTTATATT
1 TTAATTAAAATATAATTAATAATAATTATATTAATTTATATT
39950880 TTA
1 TTA
39950883 CAGTATCATA
Statistics
Matches: 203, Mismatches: 58, Indels: 53
0.65 0.18 0.17
Matches are distributed among these distances:
33 2 0.01
34 12 0.06
35 6 0.03
36 6 0.03
37 6 0.03
38 17 0.08
39 10 0.05
40 4 0.02
41 10 0.05
42 39 0.19
43 35 0.17
44 44 0.22
45 4 0.02
46 3 0.01
47 5 0.02
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (42 bp):
TTAATTAAAATATAATTAATAATAATTATATTAATTTATATT
Found at i:39950606 original size:18 final size:17
Alignment explanation
Indices: 39950578--39950612 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39950568 ATTATTAATA
*
39950578 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39950595 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39950613 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39950726 original size:18 final size:17
Alignment explanation
Indices: 39950698--39950732 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39950688 ATTATTAAGA
*
39950698 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39950715 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39950733 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39950966 original size:18 final size:17
Alignment explanation
Indices: 39950938--39950972 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39950928 ATTATTAAGA
*
39950938 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39950955 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39950973 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39951229 original size:16 final size:16
Alignment explanation
Indices: 39951208--39951275 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
39951198 GATTTGCTAT
39951208 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
39951224 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
39951240 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
39951256 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
39951272 TACA
1 TACA
39951276 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.26
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:39959393 original size:18 final size:17
Alignment explanation
Indices: 39959372--39959406 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39959362 TTATTATTAA
*
39959372 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
39959390 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
39959407 TCTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:39963040 original size:20 final size:20
Alignment explanation
Indices: 39963015--39963053 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
39963005 TAAAACCCCA
39963015 AAATACCTATTACAACTGCG
1 AAATACCTATTACAACTGCG
39963035 AAATACCTATTACAACTGC
1 AAATACCTATTACAACTGC
39963054 TGAGGGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.26, G:0.08, T:0.26
Consensus pattern (20 bp):
AAATACCTATTACAACTGCG
Found at i:39970926 original size:18 final size:19
Alignment explanation
Indices: 39970886--39970928 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
39970876 TAATTAATGA
*
39970886 TTAATTAAATTATCAAATC
1 TTAATTAAATTAACAAATC
39970905 TTAATT-AATTAACATAAT-
1 TTAATTAAATTAACA-AATC
39970923 TTAATT
1 TTAATT
39970929 TTGAACTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATTAAATTAACAAATC
Found at i:39973420 original size:43 final size:43
Alignment explanation
Indices: 39973360--39973451 Score: 166
Period size: 43 Copynumber: 2.1 Consensus size: 43
39973350 TAGAAATGAG
*
39973360 TTTTTCAATAAAATATGAAACTAATTATTCAAGCTCAATAAAT
1 TTTTTTAATAAAATATGAAACTAATTATTCAAGCTCAATAAAT
*
39973403 TTTTTTAATAGAATATGAAACTAATTATTCAAGCTCAATAAAT
1 TTTTTTAATAAAATATGAAACTAATTATTCAAGCTCAATAAAT
39973446 TTTTTT
1 TTTTTT
39973452 TCTCTTTTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (43 bp):
TTTTTTAATAAAATATGAAACTAATTATTCAAGCTCAATAAAT
Found at i:39973497 original size:17 final size:16
Alignment explanation
Indices: 39973444--39973507 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
39973434 AGCTCAATAA
39973444 ATTTTTTTTCTCTTTT-
1 ATTTTTTTT-TCTTTTC
*
39973460 -TTATGTTTTTCTTTTC
1 ATT-TTTTTTTCTTTTC
*
39973476 TTTTTTTTTTCTTTTC
1 ATTTTTTTTTCTTTTC
*
39973492 GATTTTTTATTCTTTT
1 -ATTTTTTTTTCTTTT
39973508 TTTAGAACAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 8 0.20
16 17 0.43
17 15 0.38
ACGTcount: A:0.06, C:0.11, G:0.03, T:0.80
Consensus pattern (16 bp):
ATTTTTTTTTCTTTTC
Found at i:39974523 original size:25 final size:25
Alignment explanation
Indices: 39974486--39974535 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
39974476 AAACAAAAAC
*
39974486 AAAATTACAAAAAAATAAAAATAAA
1 AAAATAACAAAAAAATAAAAATAAA
* * *
39974511 AAAATAACTAAAATATAAAACTAAA
1 AAAATAACAAAAAAATAAAAATAAA
39974536 TGAAATCACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (25 bp):
AAAATAACAAAAAAATAAAAATAAA
Found at i:39981282 original size:154 final size:163
Alignment explanation
Indices: 39981040--39981405 Score: 475
Period size: 154 Copynumber: 2.3 Consensus size: 163
39981030 TTAGATTTGA
39981040 AATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAA-AGCCTGATGCGATCTACTCTACTGT
1 AATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGAGCCTGATGCGATCTACTCTACTGT
* * *
39981104 AATTTCAGAGAGATAAGATCCTTTTAATCCGCT-C-C-A-CT-G-T-G-TTATTAACTTCAATCT
66 AACTTCAGAGAGATAAGATCCTTTTAATACACTCCACTATCTGGATAGATTATTAACTTCAATCT
* *
39981161 ACTTCGCTGTAATCTCAGGGAGATAAGATCTGT
131 ACTCCGCTGTAATCTCAGGAAGATAAGATCTGT
* *
39981194 AATTCTTCGGTCTATTCCACTGTAATCTAAGCGAGATAAGA-CCTGATGCGATCTACTCTACTGT
1 AATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGAGCCTGATGCGATCTACTCTACTGT
*
39981258 AACCTT-AGAGAGATAAGATCCTTTTAATACACTCCACTGTAATCTCAGGGAGATAGGATTATTG
66 AA-CTTCAGAGAGATAAGATCCTTTTAATACACTCCAC--T-ATCT----G-GATA-GATTATTA
*
39981322 ACTTTAATCTACTCCGCTGTAATCTCAGGAAGATAAGATCTGT
121 ACTTCAATCTACTCCGCTGTAATCTCAGGAAGATAAGATCTGT
*
39981365 AATTCTTCGGTTTATTCCACTGTAATCTCAGGGAGATAAGA
1 AATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGA
39981406 TCTTTTAATC
Statistics
Matches: 181, Mismatches: 12, Indels: 21
0.85 0.06 0.10
Matches are distributed among these distances:
154 87 0.48
155 4 0.02
156 1 0.01
160 1 0.01
161 2 0.01
167 1 0.01
168 1 0.01
170 1 0.01
171 83 0.46
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (163 bp):
AATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGAGCCTGATGCGATCTACTCTACTGT
AACTTCAGAGAGATAAGATCCTTTTAATACACTCCACTATCTGGATAGATTATTAACTTCAATCT
ACTCCGCTGTAATCTCAGGAAGATAAGATCTGT
Found at i:39981342 original size:44 final size:42
Alignment explanation
Indices: 39981244--39981619 Score: 180
Period size: 44 Copynumber: 8.9 Consensus size: 42
39981234 ACCTGATGCG
* * * * *
39981244 ATCTACTCTACTGTAACCTTAGAGAGATAAGA-TCCT-TTTA
1 ATCTACTCCACTGTAATCTCAGGGAGATAAGATTACTCTTTA
* *
39981284 ATAC-ACTCCACTGTAATCTCAGGGAGATAGGATTATTGACTTTA
1 AT-CTACTCCACTGTAATCTCAGGGAGATAAGATTACT--CTTTA
* * * **
39981328 ATCTACTCCGCTGTAATCTCAGGAAGATAAGATCTGTAATTCTTCG
1 ATCTACTCCACTGTAATCTCAGGGAGATAAGA--T-T-ACTCTTTA
* * *
39981374 GTTTATTCCACTGTAATCTCAGGGAGATAAGA-T-CT-TTTA
1 ATCTACTCCACTGTAATCTCAGGGAGATAAGATTACTCTTTA
*** * * *
39981413 ATCCGTTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCA
1 ATCTACTCCACTGTAATCTCAGGGAGATAAGATTACT--CTTTA
* * * * *
39981457 ATCTGCTTCGCTGTAATCTCAGGGAGATAAGATTTGAATCTTTTCG
1 ATCTACTCCACTGTAATCTCAGGGAGATAAGA-TT-ACTC-TTT-A
* * * * ***
39981503 GTCTATTCCACTGTAATCTCAGGGAGATAAGA--CCTGATGCG
1 ATCTACTCCACTGTAATCTCAGGGAGATAAGATTACT-CTTTA
* * * * *
39981544 ATCTACTCTACTGTAATTTCAGAGAGAAAAGA-TCCT-TTTA
1 ATCTACTCCACTGTAATCTCAGGGAGATAAGATTACTCTTTA
* *
39981584 AT-TCGCTCCACTGTAATCTCAGGGAGATAGGATTAC
1 ATCT-ACTCCACTGTAATCTCAGGGAGATAAGATTAC
39981620 CGACTTCAAT
Statistics
Matches: 251, Mismatches: 62, Indels: 45
0.70 0.17 0.13
Matches are distributed among these distances:
39 29 0.12
40 52 0.21
41 34 0.14
42 6 0.02
43 1 0.00
44 61 0.24
45 4 0.02
46 60 0.24
47 1 0.00
48 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (42 bp):
ATCTACTCCACTGTAATCTCAGGGAGATAAGATTACTCTTTA
Found at i:39981429 original size:129 final size:130
Alignment explanation
Indices: 39981253--39981534 Score: 397
Period size: 129 Copynumber: 2.2 Consensus size: 130
39981243 GATCTACTCT
* * * *
39981253 ACTGTAACCTTAGAGAGATAAGATCCTTTTAATACACTCCACTGTAATCTCAGGGAGATAGGATT
1 ACTGTAATCTCAGGGAGATAAGATCCTTTTAATACACTCCACTGTAATCTCAGGGAAATAGGATT
* * *
39981318 ATTGACTTTAATCTACTCCGCTGTAATCTCAGGAAGATAAGATCTGTAAT-TCTTCGGTTTATTC
66 ACTGACTTCAATCTACTCCGCTGTAATCTCAGGAAGATAAGATCTG-AATCTCTTCGGTCTATTC
39981382 C
130 C
* **
39981383 ACTGTAATCTCAGGGAGATAAGAT-CTTTTAATCCGTTCCACTGTAATCTCAGGGAAATAGGATT
1 ACTGTAATCTCAGGGAGATAAGATCCTTTTAATACACTCCACTGTAATCTCAGGGAAATAGGATT
* * * * * *
39981447 ACTGGCTTCAATCTGCTTCGCTGTAATCTCAGGGAGATAAGATTTGAATCTTTTCGGTCTATTCC
66 ACTGACTTCAATCTACTCCGCTGTAATCTCAGGAAGATAAGATCTGAATCTCTTCGGTCTATTCC
39981512 ACTGTAATCTCAGGGAGATAAGA
1 ACTGTAATCTCAGGGAGATAAGA
39981535 CCTGATGCGA
Statistics
Matches: 135, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
128 3 0.02
129 111 0.82
130 21 0.16
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (130 bp):
ACTGTAATCTCAGGGAGATAAGATCCTTTTAATACACTCCACTGTAATCTCAGGGAAATAGGATT
ACTGACTTCAATCTACTCCGCTGTAATCTCAGGAAGATAAGATCTGAATCTCTTCGGTCTATTCC
Done.