Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 4 of 325
Found at i:998646 original size:18 final size:17
Alignment explanation
Indices: 998618--998652 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
998608 ATTATTAAGA
*
998618 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
998635 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
998653 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:999060 original size:16 final size:17
Alignment explanation
Indices: 999009--999078 Score: 117
Period size: 17 Copynumber: 4.2 Consensus size: 17
998999 GATTAGCTAT
999009 TACACCTCTAATCCCAA
1 TACACCTCTAATCCCAA
999026 TACACCTCTAATCCCAA
1 TACACCTCTAATCCCAA
999043 TACACCTCTAAT-CCAA
1 TACACCTCTAATCCCAA
*
999059 TACGCCTCTAAT-CCAA
1 TACACCTCTAATCCCAA
999075 TACA
1 TACA
999079 GTGAACCAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
16 22 0.43
17 29 0.57
ACGTcount: A:0.36, C:0.39, G:0.01, T:0.24
Consensus pattern (17 bp):
TACACCTCTAATCCCAA
Found at i:999067 original size:33 final size:33
Alignment explanation
Indices: 999009--999078 Score: 115
Period size: 33 Copynumber: 2.1 Consensus size: 33
998999 GATTAGCTAT
999009 TACACCTCTAATCCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCCAATACACCTCTAAT-CCAA
*
999043 TACACCTCTAAT-CCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCCAATACACCTCTAATCCAA
999075 TACA
1 TACA
999079 GTGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 8 0.23
33 15 0.43
34 12 0.34
ACGTcount: A:0.36, C:0.39, G:0.01, T:0.24
Consensus pattern (33 bp):
TACACCTCTAATCCCAATACACCTCTAATCCAA
Found at i:1003028 original size:14 final size:15
Alignment explanation
Indices: 1003005--1003033 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1002995 TTTTATTTAA
1003005 TTTAATAAAAATTAT
1 TTTAATAAAAATTAT
1003020 TTTAA-AAAAATTAT
1 TTTAATAAAAATTAT
1003034 GATTTTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTAATAAAAATTAT
Found at i:1005876 original size:105 final size:105
Alignment explanation
Indices: 1005694--1005962 Score: 459
Period size: 105 Copynumber: 2.6 Consensus size: 105
1005684 TAACCGTTAT
* **
1005694 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1005759 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
*
1005799 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1005864 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
* **
1005904 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
1005963 TTATATACAA
Statistics
Matches: 155, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
105 154 0.99
106 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (105 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
Found at i:1006324 original size:29 final size:29
Alignment explanation
Indices: 1006291--1006354 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
1006281 TAATCCACCA
1006291 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
1006320 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
1006350 CCCAA
1 CCCAA
1006355 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:1006328 original size:30 final size:30
Alignment explanation
Indices: 1006298--1006354 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1006288 CCACCCAACT
1006298 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
1006327 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
1006355 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:1013356 original size:104 final size:105
Alignment explanation
Indices: 1013176--1013443 Score: 450
Period size: 104 Copynumber: 2.6 Consensus size: 105
1013166 TAACCGTTAT
* **
1013176 TGGTGGATCTCGCACTTAGCACCACCGCTGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1013241 AATCAGCACATAGCAACCCCC-TTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
*
1013280 TGGTGGATATCGCACTTAGCACCACCAATGAACCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1013345 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
66 AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
* **
1013385 TGGTGGATCA-CGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 TGGTGGAT-ATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
1013444 TTATATACAA
Statistics
Matches: 154, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
104 82 0.53
105 71 0.46
106 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.21, T:0.19
Consensus pattern (105 bp):
TGGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGG
AATCAGCACATAGCAACCCCCTTTTCACATTTCAAAGATA
Found at i:1013804 original size:29 final size:29
Alignment explanation
Indices: 1013771--1013834 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
1013761 TAATCCACCA
1013771 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
1013800 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
1013830 CCCAA
1 CCCAA
1013835 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:1013808 original size:30 final size:30
Alignment explanation
Indices: 1013778--1013834 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1013768 CCACCCAACT
1013778 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
1013807 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
1013835 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:1018170 original size:20 final size:20
Alignment explanation
Indices: 1018133--1018170 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1018123 TGATGAGGAG
*
1018133 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
1018153 CAAGAA-ATCGAAGCTGGA
1 CAAGAATATC-AAGCTGGA
1018171 GGAGAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:1020068 original size:46 final size:46
Alignment explanation
Indices: 1020016--1020243 Score: 332
Period size: 46 Copynumber: 5.0 Consensus size: 46
1020006 AGTGTGCTCT
*
1020016 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1020062 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
1020108 CTGATATGAAATGTGTAAGCCCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* ***
1020154 GTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
1020200 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
1020244 TCATGTCAAA
Statistics
Matches: 167, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 1 0.01
46 166 0.99
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:1030483 original size:24 final size:24
Alignment explanation
Indices: 1030456--1030511 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 24
1030446 AAATTTGGTG
*
1030456 TAATTAAAAGATTAAAATATTAAA
1 TAATTAAAAGAATAAAATATTAAA
* * * *
1030480 TAATAAAAATAATAAAATTTTATA
1 TAATTAAAAGAATAAAATATTAAA
1030504 T-ATTAAAA
1 TAATTAAAA
1030512 ATTTATTTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
TAATTAAAAGAATAAAATATTAAA
Found at i:1030512 original size:24 final size:24
Alignment explanation
Indices: 1030468--1030513 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1030458 ATTAAAAGAT
1030468 TAAAATATTAAATAATAAAAATAA
1 TAAAATATTAAATAATAAAAATAA
* * *
1030492 TAAAATTTTATATATTAAAAAT
1 TAAAATATTAAATAATAAAAAT
1030514 TTATTTTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
TAAAATATTAAATAATAAAAATAA
Found at i:1034268 original size:17 final size:17
Alignment explanation
Indices: 1034232--1034265 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1034222 ATTATTTCAA
1034232 AAAAAATTAAAAAAATT
1 AAAAAATTAAAAAAATT
*
1034249 AAAAAATATAAATAAAT
1 AAAAAAT-TAAAAAAAT
1034266 AAATTTAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAAATTAAAAAAATT
Found at i:1042766 original size:16 final size:17
Alignment explanation
Indices: 1042729--1042766 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1042719 TGATAATTAG
1042729 ATTTTTTATTATTTGGT
1 ATTTTTTATTATTTGGT
* *
1042746 TTTTTTTA-TATTTTGT
1 ATTTTTTATTATTTGGT
1042762 ATTTT
1 ATTTT
1042767 GGTTCTTCTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (17 bp):
ATTTTTTATTATTTGGT
Found at i:1049092 original size:84 final size:85
Alignment explanation
Indices: 1048951--1049119 Score: 304
Period size: 84 Copynumber: 2.0 Consensus size: 85
1048941 TTAGAGGGAG
* *
1048951 TAGATAGGTTGGCCCTCTCTTAAATAAAAAATTATGTTGTGGTCCCTTAATAAATTAT-AGAAAA
1 TAGATAGGTTGGCCCTCTCTTAAATAAAAAATTATGTTGTGGTCACTTAATAAATTATAAAAAAA
1049015 TAAAAGTTATGGTGAAAAAA
66 TAAAAGTTATGGTGAAAAAA
1049035 TAGATAGGTTGGCCCTCTCTTAAATAAAAAATTATGTTGTGGTCACTTAATAAATTATAAAAAAA
1 TAGATAGGTTGGCCCTCTCTTAAATAAAAAATTATGTTGTGGTCACTTAATAAATTATAAAAAAA
*
1049100 TAAAAGTTATTGTGAAAAAA
66 TAAAAGTTATGGTGAAAAAA
1049120 AATGCATTTT
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
84 57 0.70
85 24 0.30
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (85 bp):
TAGATAGGTTGGCCCTCTCTTAAATAAAAAATTATGTTGTGGTCACTTAATAAATTATAAAAAAA
TAAAAGTTATGGTGAAAAAA
Found at i:1051667 original size:41 final size:41
Alignment explanation
Indices: 1051622--1051733 Score: 188
Period size: 41 Copynumber: 2.7 Consensus size: 41
1051612 CACAAGGCAA
* * *
1051622 TAGCGGCACTTTTGATAAAATGCCGCTAAAGACCAGAGCAT
1 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAGACCAGAGCAT
*
1051663 TAGCGGCGCTTTTGGTGAAACGCCGCTAAAGACCAGAGCAT
1 TAGCGGCGCTTTTGGTAAAACGCCGCTAAAGACCAGAGCAT
1051704 TAGCGGCGCTTTTGGTAAAACGCCGCTAAA
1 TAGCGGCGCTTTTGGTAAAACGCCGCTAAA
1051734 AGTCATGTAA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 66 1.00
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.21
Consensus pattern (41 bp):
TAGCGGCGCTTTTGGTAAAACGCCGCTAAAGACCAGAGCAT
Found at i:1052377 original size:24 final size:24
Alignment explanation
Indices: 1052350--1052398 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1052340 CATATATTTA
1052350 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTTTATATAAAAATTAAT
1052374 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTTTATATAAAAATTAAT
1052398 T
1 T
1052399 GTTATTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (24 bp):
TTAAAAGTTTATATAAAAATTAAT
Found at i:1053263 original size:14 final size:13
Alignment explanation
Indices: 1053214--1053265 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
1053204 TTAATTTTTT
1053214 TATTTATAAAAACCA
1 TATTTATAAAAA--A
1053229 -ATTTATAAAAAA
1 TATTTATAAAAAA
* *
1053241 TAGTAATAAAAAA
1 TATTTATAAAAAA
1053254 TATTTTATAAAA
1 TA-TTTATAAAA
1053266 TCACTTAACT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
12 1 0.03
13 12 0.39
14 18 0.58
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (13 bp):
TATTTATAAAAAA
Found at i:1055988 original size:18 final size:18
Alignment explanation
Indices: 1055963--1056037 Score: 107
Period size: 18 Copynumber: 4.2 Consensus size: 18
1055953 ATCGTTTACG
1055963 GTACTATTCACGTATACA
1 GTACTATTCACGTATACA
*
1055981 GCACTATTCACGTATAC-
1 GTACTATTCACGTATACA
*
1055998 GATACTATTCACGTATACG
1 G-TACTATTCACGTATACA
*
1056017 GTACTGTTCACGTATACA
1 GTACTATTCACGTATACA
1056035 GTA
1 GTA
1056038 GTTGGGATTG
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
17 1 0.02
18 49 0.96
19 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.32
Consensus pattern (18 bp):
GTACTATTCACGTATACA
Found at i:1062677 original size:43 final size:43
Alignment explanation
Indices: 1062629--1062811 Score: 251
Period size: 43 Copynumber: 4.3 Consensus size: 43
1062619 AATCATTATT
* * * * *
1062629 TTTAGCGGCGTTTGTGAGAAAAGTGCCGTTAAATGTTATGATC
1 TTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCATGATC
* *
1062672 TTTAGCGGCGTTTGTG-AAAAACCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCATGATC
* * * *
1062714 TTTAGCGGCGTTTGAGAAAAAAGCACCGCTAAAGGTTATGGTC
1 TTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCATGATC
*
1062757 TTTAGCGGCGTTTGCGAAAAAAGCGCCGCTAAAGGTCATGATC
1 TTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCATGATC
1062800 TTTAGCGGCGTT
1 TTTAGCGGCGTT
1062812 GCATATAGCG
Statistics
Matches: 124, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
42 34 0.27
43 90 0.73
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCATGATC
Found at i:1062776 original size:85 final size:86
Alignment explanation
Indices: 1062629--1062811 Score: 269
Period size: 85 Copynumber: 2.1 Consensus size: 86
1062619 AATCATTATT
* * ** * * *
1062629 TTTAGCGGCGTTTGTGAGAAAAGTGCCGTTAAATGTTATGATCTTTAGCGGCGTTTGTG-AAAAA
1 TTTAGCGGCGTTTGAGAAAAAAGCACCGCTAAAGGTTATGATCTTTAGCGGCGTTTGCGAAAAAA
*
1062693 CCGCCGCTAAAGGTCATGGTC
66 CCGCCGCTAAAGGTCATGATC
*
1062714 TTTAGCGGCGTTTGAGAAAAAAGCACCGCTAAAGGTTATGGTCTTTAGCGGCGTTTGCGAAAAAA
1 TTTAGCGGCGTTTGAGAAAAAAGCACCGCTAAAGGTTATGATCTTTAGCGGCGTTTGCGAAAAAA
*
1062779 GCGCCGCTAAAGGTCATGATC
66 CCGCCGCTAAAGGTCATGATC
1062800 TTTAGCGGCGTT
1 TTTAGCGGCGTT
1062812 GCATATAGCG
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
85 51 0.59
86 36 0.41
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (86 bp):
TTTAGCGGCGTTTGAGAAAAAAGCACCGCTAAAGGTTATGATCTTTAGCGGCGTTTGCGAAAAAA
CCGCCGCTAAAGGTCATGATC
Found at i:1066711 original size:30 final size:30
Alignment explanation
Indices: 1066675--1066734 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1066665 TATCGGTGTT
* *
1066675 AGTTTTATATGTGGGGACAAAAATAGCTAA
1 AGTTTTATATGAGGAGACAAAAATAGCTAA
1066705 AGTTTTATATGAGGAGACAAAAATAGCTAA
1 AGTTTTATATGAGGAGACAAAAATAGCTAA
1066735 TGTATGACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.28
Consensus pattern (30 bp):
AGTTTTATATGAGGAGACAAAAATAGCTAA
Found at i:1067327 original size:157 final size:157
Alignment explanation
Indices: 1067111--1067416 Score: 395
Period size: 157 Copynumber: 1.9 Consensus size: 157
1067101 TCACATGAAT
* **
1067111 GAGGAGTACTTGCTTTGCAAACTGAAATTATGGCTAAAATAGTGTTTGAAACTGACATCATAATT
1 GAGGAGTACTTGCTTTGCAAACAGAAACGATGGCTAAAATAGTGTTTGAAACTGACATCATAATT
* * * *
1067176 TTAACCACGAAA-TAAAAAAAAAACATGAACAATAGTAAAAATGAACCCCAAGATTGA-ATATGC
66 TTAACAACGAAATTAAAAAAAAAA-ATCAACAAAAGTAAAAATGAACACCAAGATT-ATATATGC
*
1067239 AGTTCAACCTTAGTCTATGTCAACGGAAC
129 AGTTCAACCTCAGTCTATGTCAACGGAAC
* * * *
1067268 GAGGGGTACTTGCTTTGCAAACAGAAACGGTCGG-TAAAATAGTGTTTGGAACT-ATCATCATAG
1 GAGGAGTACTTGCTTTGCAAACAGAAACGAT-GGCTAAAATAGTGTTTGAAACTGA-CATCATAA
* * * * *
1067331 TTTTAACAATGAAATTAAAAAAAAAAGTCCACAAAAGTTAAAATGAACACCAAGATTATTTATGC
64 TTTTAACAACGAAATTAAAAAAAAAAATCAACAAAAGTAAAAATGAACACCAAGATTATATATGC
1067396 AGTTCAACCTCAGTCTATGTC
129 AGTTCAACCTCAGTCTATGTC
1067417 TGCAACGCCT
Statistics
Matches: 128, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
156 2 0.02
157 113 0.88
158 13 0.10
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (157 bp):
GAGGAGTACTTGCTTTGCAAACAGAAACGATGGCTAAAATAGTGTTTGAAACTGACATCATAATT
TTAACAACGAAATTAAAAAAAAAAATCAACAAAAGTAAAAATGAACACCAAGATTATATATGCAG
TTCAACCTCAGTCTATGTCAACGGAAC
Found at i:1067481 original size:27 final size:27
Alignment explanation
Indices: 1067451--1067505 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
1067441 ACACATATCT
* *
1067451 TTCTCAGAGTACAACCAATTATTTAAG
1 TTCTCAGAGTACAACCAATGAATTAAG
*
1067478 TTCTCAGAGTACAGCCAATGAATTAAG
1 TTCTCAGAGTACAACCAATGAATTAAG
1067505 T
1 T
1067506 CCTAATACTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (27 bp):
TTCTCAGAGTACAACCAATGAATTAAG
Found at i:1068834 original size:24 final size:24
Alignment explanation
Indices: 1068783--1068838 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
1068773 TTACTTTATT
** * *
1068783 ATATTTTATAAGGGAAACGTGCAT
1 ATATTTTATAAGAAAAACGTACAC
*
1068807 ATATTTTATAAGAAAAATGTACAC
1 ATATTTTATAAGAAAAACGTACAC
1068831 ATATTTTA
1 ATATTTTA
1068839 CTTTATATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (24 bp):
ATATTTTATAAGAAAAACGTACAC
Found at i:1079595 original size:25 final size:28
Alignment explanation
Indices: 1079552--1079602 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
1079542 TTATTAAAAC
1079552 TCTTCTAAAAGAAAACTC-AAGAGAAAT
1 TCTTCTAAAAGAAAACTCAAAGAGAAAT
1079579 TCTT-TAAAA-AAAACTCAAAGAGAA
1 TCTTCTAAAAGAAAACTCAAAGAGAA
1079603 TTTTATTAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 7 0.30
26 12 0.52
27 4 0.17
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.22
Consensus pattern (28 bp):
TCTTCTAAAAGAAAACTCAAAGAGAAAT
Found at i:1081341 original size:5 final size:5
Alignment explanation
Indices: 1081331--1081372 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
1081321 CATTGGTTGT
1081331 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TT
1081373 TCAGCTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:1083143 original size:20 final size:18
Alignment explanation
Indices: 1083115--1083153 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
1083105 TGCTTATTAT
*
1083115 TTAAGAAATAATAATTATAA
1 TTAAAAAAT-ATAA-TATAA
1083135 TTAAAAAATATAATATAA
1 TTAAAAAATATAATATAA
1083153 T
1 T
1083154 AATATAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TTAAAAAATATAATATAA
Found at i:1085910 original size:47 final size:47
Alignment explanation
Indices: 1085758--1085934 Score: 204
Period size: 47 Copynumber: 3.8 Consensus size: 47
1085748 TGTAACCCGC
* *
1085758 CCATAAGTGAACTCGGACTCAACTCAACGAGCTT-GGGC-GTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACAGTTCACAT
*
1085804 CCATAAGTGAACTCGGACTTAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-AGTTCACAT
* * *
1085854 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACAGTTCACAT
*
1085898 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1085935 TGTTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
43 3 0.03
44 5 0.05
45 3 0.03
46 34 0.31
47 56 0.50
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (47 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACAGTTCACAT
Found at i:1085926 original size:94 final size:93
Alignment explanation
Indices: 1085766--1085936 Score: 272
Period size: 94 Copynumber: 1.8 Consensus size: 93
1085756 GCCCATAAGT
* * * *
1085766 GAACTCGGACTCAACTCAACGAGCTTGGGCGTTCGCATCCATAAGTGAACTCGGACTTAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTTGGACGTTCACATCCATAAGTGAACTCAGACTCAACTCAA
1085831 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
1085859 GAACTCGGACTCAACTCAACGAG-TTCGGACATTTCACATCCATAAGTGAACTCAGACTCAACTC
1 GAACTCGGACTCAACTCAACGAGCTT-GGAC-GTTCACATCCATAAGTGAACTCAGACTCAACTC
1085923 AACGAGTTCGGATG
64 AACGAGTTCGGATG
1085937 TTCAACCATC
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
92 2 0.03
93 26 0.37
94 43 0.61
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTTGGACGTTCACATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:1086390 original size:30 final size:30
Alignment explanation
Indices: 1086356--1086415 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1086346 CCTTAATACG
1086356 AACTTTGGCAAAATTAC-CATTTTGCCCCTA
1 AACTTTGGCAAAATTACAC-TTTTGCCCCTA
* *
1086386 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
1086416 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.27, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:1090142 original size:52 final size:52
Alignment explanation
Indices: 1090063--1090233 Score: 270
Period size: 52 Copynumber: 3.2 Consensus size: 52
1090053 TACTTCTGAT
* *
1090063 CAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACATTTATCTGATCAAGTGA
1 CAAGTGA-AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
*
1090116 CAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
* *
1090168 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGA
1 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
*
1090220 CAAAGTGATAAGTG
1 C-AAGTGAAAAGTG
1090234 GCTACACTTA
Statistics
Matches: 110, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
52 93 0.85
53 17 0.15
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (52 bp):
CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
Found at i:1090243 original size:37 final size:37
Alignment explanation
Indices: 1090196--1090305 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
1090186 TGATAGCTTC
*
1090196 GGCTATACTTATCTGATCAAGAGACAAAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
* *
1090233 GGCTACACTTATCTGATCAAGAAACAAAGTGATAGGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
*
1090270 GGCTACACTTATCTGATC-AGGGAC-AAGTGATAAGT
1 GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
1090305 G
1 G
1090306 ATCATACGTA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 11 0.16
36 4 0.06
37 52 0.78
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.25
Consensus pattern (37 bp):
GGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
Found at i:1096334 original size:16 final size:16
Alignment explanation
Indices: 1096313--1096343 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1096303 AATCGGACTC
1096313 AACTCAACGAGTTCGG
1 AACTCAACGAGTTCGG
1096329 AACTCAACGAGTTCG
1 AACTCAACGAGTTCG
1096344 ACATTTCACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (16 bp):
AACTCAACGAGTTCGG
Found at i:1098204 original size:41 final size:42
Alignment explanation
Indices: 1098130--1098209 Score: 119
Period size: 41 Copynumber: 1.9 Consensus size: 42
1098120 ATTTTGAGTC
*
1098130 CACACGGCTTGTCACACGGGCGTGTGATCAGACCATGTGAGA
1 CACACGGCTTGTCACACGGGCATGTGATCAGACCATGTGAGA
*
1098172 CACACGGCTTG-CACACGGGCATGTTGAT-AGACCGTGTG
1 CACACGGCTTGTCACACGGGCATG-TGATCAGACCATGTG
1098210 TCCCCTGCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
41 20 0.57
42 15 0.43
ACGTcount: A:0.23, C:0.26, G:0.31, T:0.20
Consensus pattern (42 bp):
CACACGGCTTGTCACACGGGCATGTGATCAGACCATGTGAGA
Found at i:1102401 original size:4 final size:4
Alignment explanation
Indices: 1102392--1102418 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1102382 GATTTAATCT
1102392 AAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAA
1102419 AACCCAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:1103086 original size:19 final size:19
Alignment explanation
Indices: 1103040--1103086 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1103030 TTTTATATAT
*
1103040 TATATAATTTATAATAAAA
1 TATATAATATATAATAAAA
* *
1103059 AAT-TAAATATATAATAATA
1 TATAT-AATATATAATAAAA
1103078 TATATAATA
1 TATATAATA
1103087 CTATTATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
18 1 0.05
19 20 0.91
20 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TATATAATATATAATAAAA
Found at i:1112634 original size:42 final size:43
Alignment explanation
Indices: 1112551--1112635 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
1112541 ATATAAAAAA
* * *
1112551 GTCATTATGGATTTAATGCTTGAGTGACTAAAATGAAAGCATT
1 GTCATTAGGGATTTAATACTTGAGTAACTAAAATGAAAGCATT
1112594 GTCATTAGGGATTTAATACTTG-GTAACTAAAATGAAAGCATT
1 GTCATTAGGGATTTAATACTTGAGTAACTAAAATGAAAGCATT
1112636 CTTTAACAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 19 0.49
43 20 0.51
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.34
Consensus pattern (43 bp):
GTCATTAGGGATTTAATACTTGAGTAACTAAAATGAAAGCATT
Found at i:1114473 original size:11 final size:11
Alignment explanation
Indices: 1114457--1114512 Score: 60
Period size: 11 Copynumber: 5.2 Consensus size: 11
1114447 CTTTATATAC
1114457 TAATAAAATAA
1 TAATAAAATAA
1114468 TAATAAAATAA
1 TAATAAAATAA
* **
1114479 TAA-AATATCT
1 TAATAAAATAA
* *
1114489 TATTAAAATAT
1 TAATAAAATAA
1114500 TAATAAAATAA
1 TAATAAAATAA
1114511 TA
1 TA
1114513 TTTATCTAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
10 6 0.17
11 30 0.83
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:1114528 original size:43 final size:41
Alignment explanation
Indices: 1114457--1114540 Score: 96
Period size: 43 Copynumber: 2.0 Consensus size: 41
1114447 CTTTATATAC
*
1114457 TAATAAAATAATAATAAAATAATAAAATATCTTATTAAAATAT
1 TAATAAAATAATAATAAAATAATAAAATA-ATTA-TAAAATAT
* * ** *
1114500 TAATAAAATAATATTTATCTAATTAAATAATTATAAAATAT
1 TAATAAAATAATAATAAAATAATAAAATAATTATAAAATAT
1114541 CAAAATATCT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
41 8 0.23
42 3 0.09
43 24 0.69
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (41 bp):
TAATAAAATAATAATAAAATAATAAAATAATTATAAAATAT
Found at i:1117761 original size:26 final size:26
Alignment explanation
Indices: 1117725--1117834 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
1117715 TGATACAAAT
1117725 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
1117751 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
1117777 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* * *
1117803 TGATAGTGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
1117829 TGATAA
1 TGATAA
1117835 GAATTTCATG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:1119461 original size:27 final size:27
Alignment explanation
Indices: 1119420--1119559 Score: 176
Period size: 27 Copynumber: 5.2 Consensus size: 27
1119410 GAGGAAGCGT
*
1119420 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
1119447 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
*
1119474 TCTGGTGGCTCTGCCACATATATCT-A
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
1119500 TTCTGGTGGCTCTGCCACGATTATCTGTA
1 -TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
1119529 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
1119555 TCTGG
1 TCTGG
1119560 CAGCCATGCT
Statistics
Matches: 102, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
26 6 0.06
27 80 0.78
28 15 0.15
29 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:1121368 original size:19 final size:19
Alignment explanation
Indices: 1121344--1121381 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1121334 AGTCTAATGA
*
1121344 TAGGTTTAGATGGGTGGTG
1 TAGGTTTAGATGGATGGTG
1121363 TAGGTTTAGATGGATGGTG
1 TAGGTTTAGATGGATGGTG
1121382 CATTTATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.45, T:0.37
Consensus pattern (19 bp):
TAGGTTTAGATGGATGGTG
Found at i:1126411 original size:28 final size:27
Alignment explanation
Indices: 1126350--1126412 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 27
1126340 AATTTTAAGG
*
1126350 TTAAAATTTTCTATTAGTCCTTGTACT
1 TTAAAATTTTATATTAGTCCTTGTACT
1126377 TTGAAAATTTTGATATTTAGTCCTTGTAC-
1 TT-AAAATTTT-ATA-TTAGTCCTTGTACT
1126406 TTAAAAT
1 TTAAAAT
1126413 GATAAAATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 2 0.06
28 13 0.41
29 4 0.12
30 13 0.41
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (27 bp):
TTAAAATTTTATATTAGTCCTTGTACT
Found at i:1128772 original size:4 final size:4
Alignment explanation
Indices: 1128763--1128809 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
1128753 ATCAATGAAC
1128763 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
1128810 CTCCATTGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:1128938 original size:4 final size:4
Alignment explanation
Indices: 1128929--1128968 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
1128919 ATGAACTTTC
*
1128929 ACAT ACAT ACAT ACAT ACAT ACAT ACAT GCAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1128969 TTCCATTGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:1129036 original size:159 final size:160
Alignment explanation
Indices: 1128729--1129087 Score: 490
Period size: 159 Copynumber: 2.2 Consensus size: 160
1128719 CCTCCCGGAG
* * * *
1128729 TTCATCACATAATCATAGCATTTAATCAATGAACCATACATACATACATACATACATACATACAT
1 TTCATCACATAACCATAGCATTGAATC-ATGAA-CTTTCA-ACATACATACATACATACATACAT
*
1128794 ACATACATACATACATCTCCATTGTTTCCTTCCCAATCAAAACCTGAAATTCAACACAAACCAAT
63 ACATACATACATACATCTCCATTGCTTCCTTCCCAATCAAAACCTGAAATTCAACACAAACCAAT
* * *
1128859 CTTTTGCACCCATATTTTTTTTCCTTCCCCTAA
128 CCTTTACACCCATATTTTTTTCCCTTCCCCTAA
1128892 TTCATCACATAACCATAGCATTGAATCATGAACTTTC-ACATACATACATACATACATACATACA
1 TTCATCACATAACCATAGCATTGAATCATGAACTTTCAACATACATACATACATACATACATACA
* * *
1128956 TGCATACATACATTTCCATTGCTTCC-T-CCAATCAGAACCTGAAATTCAACACCACAACCAATC
66 TACATACATACATCTCCATTGCTTCCTTCCCAATCAAAACCTGAAATTCAACA-CA-AACCAATC
* *
1129019 CTTTACACCTATATTTTTTTCCCTTCCCCTAG
129 CTTTACACCCATATTTTTTTCCCTTCCCCTAA
* * * *
1129051 TTCATCATATAACAATAGAACTGAATCATGGAACTTT
1 TTCATCACATAACCATAGCATTGAATCAT-GAACTTT
1129088 GAACTTTCCC
Statistics
Matches: 176, Mismatches: 17, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
157 23 0.13
158 3 0.02
159 110 0.62
160 7 0.04
161 3 0.02
162 5 0.03
163 25 0.14
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.31
Consensus pattern (160 bp):
TTCATCACATAACCATAGCATTGAATCATGAACTTTCAACATACATACATACATACATACATACA
TACATACATACATCTCCATTGCTTCCTTCCCAATCAAAACCTGAAATTCAACACAAACCAATCCT
TTACACCCATATTTTTTTCCCTTCCCCTAA
Found at i:1129329 original size:13 final size:14
Alignment explanation
Indices: 1129304--1129332 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1129294 CAATCAAAAC
1129304 AACCCACAAACAAA
1 AACCCACAAACAAA
1129318 AACCCA-AAACAAA
1 AACCCACAAACAAA
1129331 AA
1 AA
1129333 AAAATTCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (14 bp):
AACCCACAAACAAA
Found at i:1133516 original size:69 final size:69
Alignment explanation
Indices: 1133403--1133566 Score: 229
Period size: 69 Copynumber: 2.4 Consensus size: 69
1133393 GGGTACATCA
* * * * * * *
1133403 GGTGAAAGATCCTATCTATAGTAAAGTTAAGCTCTTTCATCAAATGACTCAACCATCTAACAACA
1 GGTGAAAGGTCCTCTCTTTAATAAAGTCAAGCTCTGTCATCAAATGACTCAACCATCTAACAAAA
1133468 ATTG
66 ATTG
* *
1133472 GGTGAAAGGTCCTCTCTTTAATAGAGTCAAGCTCTGTCATCAAATGACTCAACCATCTAATAAAA
1 GGTGAAAGGTCCTCTCTTTAATAAAGTCAAGCTCTGTCATCAAATGACTCAACCATCTAACAAAA
1133537 ATTG
66 ATTG
*
1133541 GGTGAAAAGGTCCTCTCTTTAGTAAA
1 GGTG-AAAGGTCCTCTCTTTAATAAA
1133567 TTATCCAACT
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
69 64 0.77
70 19 0.23
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (69 bp):
GGTGAAAGGTCCTCTCTTTAATAAAGTCAAGCTCTGTCATCAAATGACTCAACCATCTAACAAAA
ATTG
Found at i:1134742 original size:30 final size:29
Alignment explanation
Indices: 1134662--1134748 Score: 88
Period size: 30 Copynumber: 2.9 Consensus size: 29
1134652 TACGTGGTTC
* * *
1134662 TACTTTTTGTAATTTTAAAACTTAGTCTTAA
1 TACTTTTTAT-ATTTTAAAATTTAAT-TTAA
*
1134693 TAC-TTTTAT-TTTTAGAAATTTAATTTACT
1 TACTTTTTATATTTTA-AAATTTAATTTA-A
1134722 TACTTTTTATATTTTAAAATTTAATTT
1 TACTTTTTATATTTTAAAATTTAATTT
1134749 TAACTATTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
28 8 0.17
29 10 0.21
30 22 0.46
31 8 0.17
ACGTcount: A:0.32, C:0.07, G:0.03, T:0.57
Consensus pattern (29 bp):
TACTTTTTATATTTTAAAATTTAATTTAA
Found at i:1144761 original size:24 final size:21
Alignment explanation
Indices: 1144705--1144754 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
1144695 AAGCAAATTA
1144705 GGACCAAAATCATCATTTTTG
1 GGACCAAAATCATCATTTTTG
1144726 GGACCAAAATCATCATTTTTG
1 GGACCAAAATCATCATTTTTG
1144747 GGACCAAA
1 GGACCAAA
1144755 CAAATCACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (21 bp):
GGACCAAAATCATCATTTTTG
Found at i:1150872 original size:78 final size:79
Alignment explanation
Indices: 1150738--1150890 Score: 281
Period size: 78 Copynumber: 1.9 Consensus size: 79
1150728 GAGTCACATC
*
1150738 TCATGTAACTGTAGTGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAGGTTACCA
1 TCATGTAACTGTAGTGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCA
1150803 TAATGAATCATATA
66 TAATGAATCATATA
1150817 TCATGTAACTGTAGTGAATCAGGATTA-CCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCA
1 TCATGTAACTGTAGTGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCA
*
1150881 TAGTGAATCA
66 TAATGAATCA
1150891 AGAATAAATC
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
78 45 0.62
79 27 0.38
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (79 bp):
TCATGTAACTGTAGTGAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCA
TAATGAATCATATA
Found at i:1150919 original size:40 final size:40
Alignment explanation
Indices: 1150855--1150992 Score: 186
Period size: 40 Copynumber: 3.5 Consensus size: 40
1150845 CTTTTCAGGT
* *
1150855 CAAATCCTATCCACCTTAAGTTACCATAGTGAATCAAGAA
1 CAAATCCTATCCACTTTAAGTTACCATAGTGAATCAGGAA
* * *
1150895 TAAATCCTATTCACTTTAAATTACCATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAGTTACCATAGTGAATCAGGAA
* * **
1150935 CAAATCCTATCCACTTTGAGGTATTATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAGTTACCATAGTGAATCAGGAA
*
1150975 CGAATCCTATCCACTTTA
1 CAAATCCTATCCACTTTA
1150993 TATTCTCGAG
Statistics
Matches: 84, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 84 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.30
Consensus pattern (40 bp):
CAAATCCTATCCACTTTAAGTTACCATAGTGAATCAGGAA
Found at i:1155771 original size:12 final size:12
Alignment explanation
Indices: 1155754--1155779 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1155744 AATCAATTTC
1155754 TATATATATATT
1 TATATATATATT
1155766 TATATATATATT
1 TATATATATATT
1155778 TA
1 TA
1155780 AATGTCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TATATATATATT
Found at i:1162250 original size:6 final size:6
Alignment explanation
Indices: 1162239--1162263 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1162229 AAGAAAAGAG
1162239 AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA A
1162264 GAACACACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:1169351 original size:19 final size:20
Alignment explanation
Indices: 1169319--1169361 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1169309 TCTTTTTGAA
* *
1169319 TTCATTCATTTGCATTACAT
1 TTCATTCATATGCATTAAAT
1169339 TTCA-TCATATGCATTAAAT
1 TTCATTCATATGCATTAAAT
1169358 TTCA
1 TTCA
1169362 CGAAAAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.30, C:0.19, G:0.05, T:0.47
Consensus pattern (20 bp):
TTCATTCATATGCATTAAAT
Found at i:1176511 original size:27 final size:29
Alignment explanation
Indices: 1176470--1176523 Score: 94
Period size: 27 Copynumber: 1.9 Consensus size: 29
1176460 CAGGCACGAC
1176470 TTTTTTAATATTAAAATATTATTTTTTTG
1 TTTTTTAATATTAAAATATTATTTTTTTG
1176499 TTTTTTAA-A-TAAAATATTATTTTTT
1 TTTTTTAATATTAAAATATTATTTTTT
1176524 ATTTTTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 16 0.64
28 1 0.04
29 8 0.32
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (29 bp):
TTTTTTAATATTAAAATATTATTTTTTTG
Found at i:1176537 original size:25 final size:25
Alignment explanation
Indices: 1176478--1176541 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 25
1176468 ACTTTTTTAA
1176478 TATT-AAAATATTATTTTTTTGTTT
1 TATTAAAAATATTATTTTTTTGTTT
1176502 T-TTAAATAAAATATTATTTTTTAT-TTT
1 TATT--A-AAAATATTATTTTTT-TGTTT
1176529 TATTAAAAATATT
1 TATTAAAAATATT
1176542 TAAATTTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
23 2 0.06
24 1 0.03
25 8 0.24
26 1 0.03
27 19 0.56
28 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TATTAAAAATATTATTTTTTTGTTT
Found at i:1176834 original size:3 final size:3
Alignment explanation
Indices: 1176826--1176922 Score: 176
Period size: 3 Copynumber: 31.7 Consensus size: 3
1176816 ATAAGCATGA
1176826 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1176874 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAAG AAAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG -AAG -AAG AAG
1176921 AA
1 AA
1176923 AAAAAGGTAA
Statistics
Matches: 93, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 86 0.92
4 7 0.08
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1178021 original size:60 final size:60
Alignment explanation
Indices: 1177905--1178036 Score: 156
Period size: 60 Copynumber: 2.2 Consensus size: 60
1177895 ATGTAGTTTT
* * * * *
1177905 TTTTTGTTTTTATAATAATTTTAAAATTAATTTGCTAGTAATTTAAAATTATGTTATTAA
1 TTTTTGTGTTTATAATAATTTTAAAAATAATTTACTAGTAATTTAAAATTACGTTATAAA
* * * **
1177965 TTTTTGTGTTTGTAATTATTTTAAAAATAATTTATTAGTAATTTAGGATTACGTTATAAA
1 TTTTTGTGTTTATAATAATTTTAAAAATAATTTACTAGTAATTTAAAATTACGTTATAAA
* *
1178025 TTATTGCGTTTA
1 TTTTTGTGTTTA
1178037 ATTTAGTATT
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (60 bp):
TTTTTGTGTTTATAATAATTTTAAAAATAATTTACTAGTAATTTAAAATTACGTTATAAA
Found at i:1178161 original size:28 final size:28
Alignment explanation
Indices: 1178122--1178199 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 28
1178112 GGACAGATGT
*
1178122 TTAAGCTCATTTAATTTTTTTAGGTTGTTG
1 TTAA-CTCATTTAATTTTTTTA-GTTGCTG
* * **
1178152 TTAAGT-ATTTATATGTTAATAGTTGCTG
1 TTAACTCATTTA-ATTTTTTTAGTTGCTG
1178180 TTAACTCATTTAATTTTTTT
1 TTAACTCATTTAATTTTTTT
1178200 TATGTCAACT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
28 21 0.57
29 12 0.32
30 4 0.11
ACGTcount: A:0.24, C:0.06, G:0.13, T:0.56
Consensus pattern (28 bp):
TTAACTCATTTAATTTTTTTAGTTGCTG
Found at i:1184095 original size:24 final size:23
Alignment explanation
Indices: 1184063--1184108 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
1184053 TTTCCGTTCA
*
1184063 ACTAAATTTTGTGTCTGTTGCTCT
1 ACTAAATTTTGTGTATG-TGCTCT
1184087 ACTAAATTTTGTGTATGTGCTC
1 ACTAAATTTTGTGTATGTGCTC
1184109 ATTTGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.20, C:0.15, G:0.17, T:0.48
Consensus pattern (23 bp):
ACTAAATTTTGTGTATGTGCTCT
Found at i:1184209 original size:27 final size:27
Alignment explanation
Indices: 1184168--1184247 Score: 88
Period size: 27 Copynumber: 3.0 Consensus size: 27
1184158 CCTGTGGGCC
*
1184168 TTTGTGCCTCTGAGATAGGCACAACCA
1 TTTGCGCCTCTGAGATAGGCACAACCA
* * * *
1184195 TTTGCGCCTCAGAGAAAGGCTCAACTA
1 TTTGCGCCTCTGAGATAGGCACAACCA
* * *
1184222 GTCGCGCCTCTGAGATAGGCGCAACC
1 TTTGCGCCTCTGAGATAGGCACAACC
1184248 TATATTCGTA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.21
Consensus pattern (27 bp):
TTTGCGCCTCTGAGATAGGCACAACCA
Found at i:1184313 original size:27 final size:27
Alignment explanation
Indices: 1184283--1184340 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
1184273 TACTGATCCG
* *
1184283 AAAATAAAAAAATAATATTTT-ATTTAA
1 AAAACAAAAAAAT-ATATTTTAATATAA
1184310 AAAACAAAAAAATATATTTTAATATAA
1 AAAACAAAAAAATATATTTTAATATAA
1184337 AAAA
1 AAAA
1184341 AAGAGTCGCG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (27 bp):
AAAACAAAAAAATATATTTTAATATAA
Found at i:1185121 original size:16 final size:16
Alignment explanation
Indices: 1185096--1185127 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1185086 TAACTCAAAC
1185096 AACTCAAAATTCGATT
1 AACTCAAAATTCGATT
*
1185112 AACTCGAAATTCGATT
1 AACTCAAAATTCGATT
1185128 TTTTTCGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (16 bp):
AACTCAAAATTCGATT
Found at i:1185484 original size:17 final size:18
Alignment explanation
Indices: 1185462--1185519 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 18
1185452 ATTTAATTAC
1185462 ATAAAA-TATAAAATATT
1 ATAAAACTATAAAATATT
*
1185479 ATAAAATTATAAAATTATT
1 ATAAAACTATAAAA-TATT
* *
1185498 AAAAAACTAATAAAATTTT
1 ATAAAACT-ATAAAATATT
1185517 ATA
1 ATA
1185520 CAACACAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
17 6 0.18
18 7 0.21
19 15 0.44
20 6 0.18
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAAAACTATAAAATATT
Found at i:1195229 original size:68 final size:68
Alignment explanation
Indices: 1195115--1195411 Score: 389
Period size: 68 Copynumber: 4.4 Consensus size: 68
1195105 TTCAATCTAC
* * * * * *
1195115 TCCGCTGAAACTTAAAGGAGATCCGTTGTGGCTT-TGAGCCGCTCCAATGTCGTTTCAGGGAGAA
1 TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCT-AGCCGCTCCAACGCCATTTCAGGGAGAA
1195179 GAGA
65 GAGA
* * **
1195183 TCCGTTGAAACTTTAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGACAGAAG
1 TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAG
1195248 AGA
66 AGA
* * * * * *
1195251 TCCGTTGAAACTTTAAGGAGATCTACTGTGGCTTCTAGCCGCTCCAACTCTATTTCAGGTAGAAG
1 TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAG
1195316 AGA
66 AGA
* *
1195319 TCCGCTGAAACTTCAAGGAGATCTGTTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAG
1 TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAG
*
1195384 GGA
66 AGA
* *
1195387 TCCGCTAAAACTTCAAGAAGATCTG
1 TCCGCTGAAACTTCAAGGAGATCTG
1195412 ACTTGTAATT
Statistics
Matches: 203, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
68 202 1.00
69 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (68 bp):
TCCGCTGAAACTTCAAGGAGATCTGCTGTGGCTTCTAGCCGCTCCAACGCCATTTCAGGGAGAAG
AGA
Found at i:1195619 original size:78 final size:75
Alignment explanation
Indices: 1195537--1195959 Score: 315
Period size: 78 Copynumber: 5.4 Consensus size: 75
1195527 AAACTGACGT
* * * * * *
1195537 TCAACTCATCTCTCGTATTATGAGTTAATTTTTGAAAAAAGTGAAAAATTGAAAACATCTCAGTA
1 TCAACTCACCTCTCGTAATATGAGTTAATTTTTG-AAAAA-T-AAAAACTAAAAACACCTCAGCA
1195602 TGTGACCTGAGGC
63 TGTGACCTGAGGC
* * * *
1195615 TCAACTCACCTCTTGTAATATGAGTTGATTTTTTTGAAAAATAGAAACTAAAAACACCTCAGCGT
1 TCAACTCACCTCTCGTAATATGAGTT-A-ATTTTTGAAAAATAAAAACTAAAAACACCTCAGCAT
1195680 GTGACCTGAGGC
64 GTGACCTGAGGC
* * * * * *
1195692 TCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTGAAAAATAGAAACTAAAGATACCTCAGC
1 TCAACTCACCTCTCGTAATATGAGTT-A---ATTTTTGAAAAATAAAAACTAAAAACACCTCAGC
* * *
1195757 GTGTGACTTGAGGT
62 ATGTGACCTGAGGC
* * **** * * * * * **
1195771 TCAACTCACTTCTCGCAATATGAGTTGAATTTTTTTTTGAATCAGAAATTGAAAATACCTTAGTG
1 TCAACTCACCTCTCGTAATATGAGTT-AA-TTTTTGAAAAAT-AAAAACTAAAAACACCTCAGCA
* **
1195836 CGTGATTTGAGGC
63 TGTGACCTGAGGC
* * ** * * *
1195849 TCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAATAGGAACTAAAGATACCTCAGCG
1 TCAACTCACCTCTCGTAATATGAGTT-A-ATTTTTG-AAAAATAAAAACTAAAAACACCTCAGCA
*
1195914 TGTGACCCGAGGC
63 TGTGACCTGAGGC
*
1195927 TCAACTCACCTCTCGCAATATGAGTTAATTTTT
1 TCAACTCACCTCTCGTAATATGAGTTAATTTTT
1195960 TTAAAACAGA
Statistics
Matches: 288, Mismatches: 49, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
76 5 0.02
77 63 0.22
78 134 0.47
79 80 0.28
80 6 0.02
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (75 bp):
TCAACTCACCTCTCGTAATATGAGTTAATTTTTGAAAAATAAAAACTAAAAACACCTCAGCATGT
GACCTGAGGC
Found at i:1195769 original size:79 final size:79
Alignment explanation
Indices: 1195602--1195961 Score: 475
Period size: 78 Copynumber: 4.6 Consensus size: 79
1195592 CATCTCAGTA
* *
1195602 TGTGACCTGAGGCTCAACTCACCTCTTGTAATATGAGTTGA--TTTTTTTGAAAAATAGAAACTA
1 TGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAAATAGAAACTA
* *
1195665 AAAACACCTCAGCG
66 AAGATACCTCAGCG
*
1195679 TGTGACCTGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTTTGAAAAATAGAAACTA
1 TGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAAATAGAAACTA
1195744 AAGATACCTCAGCG
66 AAGATACCTCAGCG
* * * *
1195758 TGTGACTTGAGGTTCAACTCACTTCTCGCAATATGAGTTGAATTTTTTTTTG---AATCAGAAAT
1 TGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTTTTTTGAAAAAT-AGAAAC
* *
1195820 TGAAA-ATACCTTAGTG
64 T-AAAGATACCTCAGCG
* ** *
1195836 CGTGATTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAAAAATAGGAACT
1 TGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTG-AAAAATAGAAACT
1195899 AAAGATACCTCAGCG
65 AAAGATACCTCAGCG
* *
1195914 TGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTT
1 TGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
1195962 AAAACAGAAA
Statistics
Matches: 246, Mismatches: 25, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
75 8 0.03
77 45 0.18
78 101 0.41
79 76 0.31
80 16 0.07
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (79 bp):
TGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAAATAGAAACTA
AAGATACCTCAGCG
Found at i:1206131 original size:31 final size:32
Alignment explanation
Indices: 1206072--1206141 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
1206062 TTAGAATAAA
* * *
1206072 AATAACAATAATATAATAAAGAAAATA-TTCT
1 AATAATAATAATAAAAGAAAGAAAATATTTCT
* * *
1206103 AATAATAATAATAAAAGAAATAATATATTTGT
1 AATAATAATAATAAAAGAAAGAAAATATTTCT
1206135 AATAATA
1 AATAATA
1206142 GTAGAAAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 22 0.69
32 10 0.31
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.31
Consensus pattern (32 bp):
AATAATAATAATAAAAGAAAGAAAATATTTCT
Found at i:1206302 original size:17 final size:17
Alignment explanation
Indices: 1206280--1206367 Score: 65
Period size: 18 Copynumber: 4.8 Consensus size: 17
1206270 TATAGTACCT
1206280 AAAATATAATAATAATG
1 AAAATATAATAATAATG
1206297 AAAATATAAATAGATAA-G
1 AAAATAT-AATA-ATAATG
*
1206315 AAATATAATAGATGAGTAATAAG
1 AAA-AT-ATA-AT-AATAAT--G
1206338 AAAATA-AAT-ATAGATG
1 AAAATATAATAATA-ATG
1206354 AAAATATAATAATA
1 AAAATATAATAATA
1206368 GTCATAATAC
Statistics
Matches: 57, Mismatches: 2, Indels: 23
0.70 0.02 0.28
Matches are distributed among these distances:
16 7 0.12
17 12 0.21
18 13 0.23
19 9 0.16
20 8 0.14
21 2 0.04
22 2 0.04
23 4 0.07
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (17 bp):
AAAATATAATAATAATG
Found at i:1206335 original size:16 final size:17
Alignment explanation
Indices: 1206281--1206327 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
1206271 ATAGTACCTA
1206281 AAATAT-AATA-ATAATG
1 AAATATAAATAGATAA-G
1206297 AAAATATAAATAGATAAG
1 -AAATATAAATAGATAAG
1206315 AAATAT-AATAGAT
1 AAATATAAATAGAT
1206328 GAGTAATAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 7 0.25
17 12 0.43
18 5 0.18
19 4 0.14
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.28
Consensus pattern (17 bp):
AAATATAAATAGATAAG
Found at i:1206367 original size:3 final size:3
Alignment explanation
Indices: 1206359--1206841 Score: 113
Period size: 3 Copynumber: 163.7 Consensus size: 3
1206349 AGATGAAAAT
* * * * * * * *
1206359 ATA ATA ATA GTC ATA AT- ACA ATA GTA ATA GTA ATT ACA AAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * ** *
1206406 ATA GTA ATA AAA ATA A-G ATA ATA ATA ATA ACA ATA ATA ATA ACC GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
1206453 GTA GTG ATA AAA AT- ATA ATA GTA ATA ATA ATG ATA ATAA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
* * * ** ** * **
1206497 GTA ATT ATA ATA ATA GTA A-A A-A AGG ATA ATA AGG ATA GTA GCA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * ** * * *
1206543 ATA ATG GTA AGA ACG ATA ATAA ATA ATA GTA GTAA ATA ATA ATA AAA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA AT-A ATA ATA ATA ATA
* * *
1206590 ATA ATA ATA GTA ATA ATA ATA ATGA A-A ATA GTGA A-A ATA ATA ATG
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA AT-A ATA ATA ATA ATA
* * * * * *
1206635 GTA AT- ATA ATA GTA ATA ATA ACA ATA ATG GTA ATA AAA ATA A-A A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
1206680 ATA AAA ATA ATG GTA ACA A-A ATA A-A ATTA ATG AT- GTA ATA AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA
* * * *
1206722 GTA ATA ATA ATA A-A ATA AGT- ATGA AGA GAAA AT- ATA ATC ATA ATA
1 ATA ATA ATA ATA ATA ATA A-TA AT-A ATA -ATA ATA ATA ATA ATA ATA
* * * * * * * * *
1206767 ATA ATA GTT GTA GTA ATA ATA ATA AGA AGA AGA AGA ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
1206815 ATGA AT- ATAA ATA ATA GTA AAA ATA AT
1 AT-A ATA AT-A ATA ATA ATA ATA ATA AT
1206842 GAAATTAACT
Statistics
Matches: 338, Mismatches: 114, Indels: 56
0.67 0.22 0.11
Matches are distributed among these distances:
2 32 0.09
3 284 0.84
4 22 0.07
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:1206376 original size:41 final size:41
Alignment explanation
Indices: 1206288--1206364 Score: 97
Period size: 41 Copynumber: 1.9 Consensus size: 41
1206278 CTAAAATATA
*
1206288 ATAATAATGAAAATATAAATAGATAAGAAATATAATAGATG
1 ATAATAATGAAAATATAAATAGATAAGAAATATAATAGATC
*
1206329 AGTAATAA-GAAAATA-AATATAGATGA-AAATATAATA
1 A-TAATAATGAAAATATAA-ATAGATAAGAAATATAATA
1206365 ATAGTCATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
40 12 0.36
41 15 0.45
42 6 0.18
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (41 bp):
ATAATAATGAAAATATAAATAGATAAGAAATATAATAGATC
Found at i:1206404 original size:41 final size:41
Alignment explanation
Indices: 1206354--1206447 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
1206344 AATATAGATG
* * *
1206354 AAAATATAATAATAGTCATAATACAAT-AG-TAATAGTAATTAC
1 AAAA-ATAATAATAGTAATAA-A-AATAAGATAATAATAATAAC
1206396 AAAAATAATAATAGTAATAAAAATAAGATAATAATAATAAC
1 AAAAATAATAATAGTAATAAAAATAAGATAATAATAATAAC
*
1206437 AATAATAATAA
1 AAAAATAATAA
1206448 CCGTAGTAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
39 3 0.07
40 3 0.07
41 36 0.78
42 4 0.09
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (41 bp):
AAAAATAATAATAGTAATAAAAATAAGATAATAATAATAAC
Found at i:1206428 original size:20 final size:20
Alignment explanation
Indices: 1206403--1206441 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1206393 TACAAAAATA
*
1206403 ATAATAGTAATAAAAATAAG
1 ATAATAATAATAAAAATAAG
*
1206423 ATAATAATAATAACAATAA
1 ATAATAATAATAAAAATAA
1206442 TAATAACCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.26
Consensus pattern (20 bp):
ATAATAATAATAAAAATAAG
Found at i:1206691 original size:28 final size:27
Alignment explanation
Indices: 1206628--1206705 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 27
1206618 TAGTGAAAAT
* * *
1206628 AATAATGGTAATATAATAGTAATAATAAC
1 AATAATGGTAATAAAATA--AAAAATAAA
1206657 AATAATGGTAATAAAAATAAAAAATAAA
1 AATAATGGTAAT-AAAATAAAAAATAAA
*
1206685 AATAATGGTAACAAAATAAAA
1 AATAATGGTAATAAAATAAAA
1206706 TTAATGATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.20
28 18 0.41
29 12 0.27
30 5 0.11
ACGTcount: A:0.64, C:0.03, G:0.09, T:0.24
Consensus pattern (27 bp):
AATAATGGTAATAAAATAAAAAATAAA
Found at i:1208980 original size:20 final size:23
Alignment explanation
Indices: 1208941--1208983 Score: 65
Period size: 20 Copynumber: 2.0 Consensus size: 23
1208931 CCCTAAAAGC
1208941 ATATATTAATAAATAATATTAAA
1 ATATATTAATAAATAATATTAAA
1208964 ATAT-TTAA-AAA-AATATTAAA
1 ATATATTAATAAATAATATTAAA
1208984 GGCGGAATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.45
21 3 0.15
22 4 0.20
23 4 0.20
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
ATATATTAATAAATAATATTAAA
Found at i:1211788 original size:46 final size:46
Alignment explanation
Indices: 1211721--1211825 Score: 183
Period size: 46 Copynumber: 2.3 Consensus size: 46
1211711 ACAAATAGGG
*
1211721 AGAAAGAACAATGCCTTAAGTAGAGAATGGCAAATGTGGGATGATT
1 AGAAAGAACAATGCCTTAAGTAGAGAATGGCAAATGTGAGATGATT
1211767 AGAAAGAACAATGCCTTAAGTAGAGAATGGCAAATGTGAGATGATT
1 AGAAAGAACAATGCCTTAAGTAGAGAATGGCAAATGTGAGATGATT
* *
1211813 AGAATGAGCAATG
1 AGAAAGAACAATG
1211826 GTTAGGCCTA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 56 1.00
ACGTcount: A:0.43, C:0.09, G:0.28, T:0.21
Consensus pattern (46 bp):
AGAAAGAACAATGCCTTAAGTAGAGAATGGCAAATGTGAGATGATT
Found at i:1211984 original size:11 final size:11
Alignment explanation
Indices: 1211967--1212002 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
1211957 AGATATGGGT
1211967 AGGTATGGG-A
1 AGGTATGGGCA
1211977 ATGGTATGGGCA
1 A-GGTATGGGCA
1211989 AGGTATGGGCA
1 AGGTATGGGCA
1212000 AGG
1 AGG
1212003 AATGTGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 1 0.04
11 21 0.88
12 2 0.08
ACGTcount: A:0.28, C:0.06, G:0.47, T:0.19
Consensus pattern (11 bp):
AGGTATGGGCA
Found at i:1215218 original size:12 final size:12
Alignment explanation
Indices: 1215201--1215225 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1215191 CTTTTTCATC
1215201 TATTTTCTTTAT
1 TATTTTCTTTAT
1215213 TATTTTCTTTAT
1 TATTTTCTTTAT
1215225 T
1 T
1215226 GTTCTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTTCTTTAT
Found at i:1215258 original size:13 final size:12
Alignment explanation
Indices: 1215233--1215291 Score: 61
Period size: 13 Copynumber: 4.9 Consensus size: 12
1215223 ATTGTTCTAA
*
1215233 TATTTAATTTAT
1 TATTTATTTTAT
1215245 TATTCTA--TT-T
1 TATT-TATTTTAT
1215255 TATTTATTTTAAT
1 TATTTATTTT-AT
1215268 TATTTATTTTAAT
1 TATTTATTTT-AT
1215281 TATTTATTTTA
1 TATTTATTTTA
1215292 ATTTTTGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
9 2 0.05
10 5 0.12
11 4 0.10
12 5 0.12
13 26 0.62
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (12 bp):
TATTTATTTTAT
Found at i:1215259 original size:17 final size:17
Alignment explanation
Indices: 1215213--1215262 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 17
1215203 TTTTCTTTAT
* *
1215213 TATTTTCTTTATTGTTC
1 TATTTTATTTATTATTC
1215230 TAATATTTAATTTATTATTC
1 T-AT-TTT-ATTTATTATTC
1215250 TATTTTATTTATT
1 TATTTTATTTATT
1215263 TTAATTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 8 0.29
18 5 0.18
19 5 0.18
20 10 0.36
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.68
Consensus pattern (17 bp):
TATTTTATTTATTATTC
Found at i:1215263 original size:26 final size:27
Alignment explanation
Indices: 1215235--1215295 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
1215225 TGTTCTAATA
*
1215235 TTTAATTTA-TTATTCTATTTTATTTAT
1 TTTAATTTATTTATTCTA-ATTATTTAT
*
1215262 TTTAA-TTATTTATTTTAATTATTTAT
1 TTTAATTTATTTATTCTAATTATTTAT
1215288 TTTAATTT
1 TTTAATTT
1215296 TTGATTCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 16 0.53
27 14 0.47
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTAATTTATTTATTCTAATTATTTAT
Found at i:1215265 original size:22 final size:22
Alignment explanation
Indices: 1215233--1215285 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
1215223 ATTGTTCTAA
*
1215233 TATTTAATTT-ATTATTCTATTT
1 TATTTATTTTAATTATT-TATTT
1215255 TATTTATTTTAATTATTTATTT
1 TATTTATTTTAATTATTTATTT
*
1215277 TAATTATTT
1 TATTTATTT
1215286 ATTTTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 22 0.79
23 6 0.21
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
TATTTATTTTAATTATTTATTT
Found at i:1215292 original size:13 final size:13
Alignment explanation
Indices: 1215254--1215294 Score: 82
Period size: 13 Copynumber: 3.2 Consensus size: 13
1215244 TTATTCTATT
1215254 TTATTTATTTTAA
1 TTATTTATTTTAA
1215267 TTATTTATTTTAA
1 TTATTTATTTTAA
1215280 TTATTTATTTTAA
1 TTATTTATTTTAA
1215293 TT
1 TT
1215295 TTTGATTCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTTATTTTAA
Found at i:1220751 original size:86 final size:86
Alignment explanation
Indices: 1220647--1220831 Score: 244
Period size: 86 Copynumber: 2.2 Consensus size: 86
1220637 TTATTCGAAA
* * * * *
1220647 AAACACCGCTATAGAACATGATCTTTAGCGGGGCTTTACCCAAAAATGCCACAATAGAACATGAC
1 AAACACCGCTATAAAACATGACCTTTAGCGGAGCTTTACCCAAAAACGCCACAATAGAACATAAC
1220712 ATTTAACGGCGCTTTTCCCAC
66 ATTTAACGGCGCTTTTCCCAC
* * * * ***
1220733 AAACGCCGCTATAAAACATGACCTTTAGTGGAGCTTTTCCCACAAACGCCGTTATAGAACATAAC
1 AAACACCGCTATAAAACATGACCTTTAGCGGAGCTTTACCCAAAAACGCCACAATAGAACATAAC
* *
1220798 CTTTAATGGCGCTTTTCCCAC
66 ATTTAACGGCGCTTTTCCCAC
1220819 AAACACCGCTATA
1 AAACACCGCTATA
1220832 GAACGTGAGC
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (86 bp):
AAACACCGCTATAAAACATGACCTTTAGCGGAGCTTTACCCAAAAACGCCACAATAGAACATAAC
ATTTAACGGCGCTTTTCCCAC
Found at i:1220783 original size:43 final size:43
Alignment explanation
Indices: 1220647--1220835 Score: 216
Period size: 43 Copynumber: 4.4 Consensus size: 43
1220637 TTATTCGAAA
* * * * * *
1220647 AAACACCGCTATAGAACATGATCTTTAGCGGGGCTTTACCCAA
1 AAACGCCGCTATAGAACATGACCTTTAACGGCGCTTTTCCCAC
* * * *
1220690 AAATGCCACAATAGAACATGACATTTAACGGCGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAACGGCGCTTTTCCCAC
* ** *
1220733 AAACGCCGCTATAAAACATGACCTTTAGTGGAGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAACGGCGCTTTTCCCAC
* * *
1220776 AAACGCCGTTATAGAACATAACCTTTAATGGCGCTTTTCCCAC
1 AAACGCCGCTATAGAACATGACCTTTAACGGCGCTTTTCCCAC
*
1220819 AAACACCGCTATAGAAC
1 AAACGCCGCTATAGAAC
1220836 GTGAGCTCGA
Statistics
Matches: 121, Mismatches: 25, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 121 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTATAGAACATGACCTTTAACGGCGCTTTTCCCAC
Found at i:1223282 original size:22 final size:23
Alignment explanation
Indices: 1223237--1223284 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1223227 ACAACGTACT
*
1223237 AACCATTAAACCATAAACCCTAA
1 AACCATTAAACCAGAAACCCTAA
* *
1223260 AACCA-TAAACCAGAGACCTTAA
1 AACCATTAAACCAGAAACCCTAA
1223282 AAC
1 AAC
1223285 TTAAACATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.52, C:0.29, G:0.04, T:0.15
Consensus pattern (23 bp):
AACCATTAAACCAGAAACCCTAA
Found at i:1225092 original size:12 final size:12
Alignment explanation
Indices: 1225075--1225099 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1225065 CTTTTCCATC
1225075 TATTTTCTTTAT
1 TATTTTCTTTAT
1225087 TATTTTCTTTAT
1 TATTTTCTTTAT
1225099 T
1 T
1225100 GTTCTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTTCTTTAT
Found at i:1227018 original size:19 final size:19
Alignment explanation
Indices: 1226972--1227025 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1226962 CCACTAAATT
*
1226972 AACAG-CCCACTAACCCATC
1 AACAGACCCACT-ACCCAAC
1226991 AA-A-ACCCACTACCCAAC
1 AACAGACCCACTACCCAAC
1227008 AACAGACCCACTACCCAA
1 AACAGACCCACTACCCAA
1227026 TTGACTCTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 8 0.26
18 8 0.26
19 15 0.48
ACGTcount: A:0.43, C:0.46, G:0.04, T:0.07
Consensus pattern (19 bp):
AACAGACCCACTACCCAAC
Found at i:1228191 original size:14 final size:14
Alignment explanation
Indices: 1228153--1228194 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1228143 TTTAGTTATT
*
1228153 TTATTATTTAAGT-
1 TTATTATTTTAGTA
* *
1228166 TAATTATCTTAGTA
1 TTATTATTTTAGTA
1228180 TTATTATTTTAGTA
1 TTATTATTTTAGTA
1228194 T
1 T
1228195 CTAATATTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (14 bp):
TTATTATTTTAGTA
Found at i:1236273 original size:19 final size:19
Alignment explanation
Indices: 1236249--1236322 Score: 58
Period size: 21 Copynumber: 3.7 Consensus size: 19
1236239 GTGGGGGTCT
1236249 ACACACCCATGTGAAGGCCAC
1 ACACACCCATGTGAAGG-C-C
* *
1236270 ACACACCCGTATGAAGGCC
1 ACACACCCATGTGAAGGCC
* * *
1236289 ACATCGCCCATGTGGAGGCG
1 ACA-CACCCATGTGAAGGCC
* *
1236309 GCACACCCGTGTGA
1 ACACACCCATGTGA
1236323 GTAGCCCGTG
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
19 12 0.29
20 14 0.34
21 15 0.37
ACGTcount: A:0.27, C:0.35, G:0.26, T:0.12
Consensus pattern (19 bp):
ACACACCCATGTGAAGGCC
Found at i:1236275 original size:21 final size:21
Alignment explanation
Indices: 1236249--1236291 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1236239 GTGGGGGTCT
*
1236249 ACACACCCATGTGAAGGCCAC
1 ACACACCCATATGAAGGCCAC
*
1236270 ACACACCCGTATGAAGGCCAC
1 ACACACCCATATGAAGGCCAC
1236291 A
1 A
1236292 TCGCCCATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.35, C:0.37, G:0.19, T:0.09
Consensus pattern (21 bp):
ACACACCCATATGAAGGCCAC
Found at i:1236722 original size:30 final size:30
Alignment explanation
Indices: 1236688--1236749 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
1236678 ACTTAGTTTA
1236688 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
1236718 TTGTTAATTTTGTTATTATTTTAGAGATAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
1236748 TT
1 TT
1236750 ACTCGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:1238389 original size:21 final size:21
Alignment explanation
Indices: 1238365--1238428 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
1238355 AGGGTTGAAC
*
1238365 GGAAGCTCATAAAAGCTAAAT
1 GGAAGCTCATAAGAGCTAAAT
* * *
1238386 GGAAACTCAT--GAGTTAACT
1 GGAAGCTCATAAGAGCTAAAT
*
1238405 -GAAGCTCATAAGACCTAAAT
1 GGAAGCTCATAAGAGCTAAAT
1238425 GGAA
1 GGAA
1238429 AGCAAACACG
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 8 0.25
19 6 0.19
20 6 0.19
21 12 0.38
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (21 bp):
GGAAGCTCATAAGAGCTAAAT
Found at i:1258271 original size:6 final size:6
Alignment explanation
Indices: 1258262--1258312 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
1258252 ATTTATATAC
* * *
1258262 ATATGT ATATGG ATATGG ATATGG ATATGT ATATGT ATATGT ATATGT
1 ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT ATATGT
1258310 ATA
1 ATA
1258313 ATCATAATAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (6 bp):
ATATGT
Found at i:1258277 original size:18 final size:18
Alignment explanation
Indices: 1258256--1258308 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
1258246 TTATATATTT
*
1258256 ATATACATATGTATATGG
1 ATATGCATATGTATATGG
* * *
1258274 ATATGGATATGGATATGT
1 ATATGCATATGTATATGG
*
1258292 ATATGTATATGTATATG
1 ATATGCATATGTATATG
1258309 TATAATCATA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.42
Consensus pattern (18 bp):
ATATGCATATGTATATGG
Found at i:1258397 original size:3 final size:3
Alignment explanation
Indices: 1258389--1258415 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1258379 TTTATTGTTG
1258389 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1258416 TTATTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1258420 original size:3 final size:3
Alignment explanation
Indices: 1258414--1258456 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
1258404 ATAATAATAA
*
1258414 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1258457 TTGAACATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1258917 original size:24 final size:23
Alignment explanation
Indices: 1258873--1258937 Score: 77
Period size: 19 Copynumber: 3.0 Consensus size: 23
1258863 AAAAATAAAT
1258873 AAATATTTATTATTATATTTTAA
1 AAATATTTATTATTATATTTTAA
1258896 AAATATTTATTTATTCAT-TTTT--
1 AAATATTTA-TTATT-ATATTTTAA
1258918 -AA-ATTTATTATTATATTTTA
1 AAATATTTATTATTATATTTTA
1258938 TTGAAACTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
18 2 0.05
19 9 0.24
20 5 0.13
21 2 0.05
23 9 0.24
24 9 0.24
25 2 0.05
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
AAATATTTATTATTATATTTTAA
Found at i:1261345 original size:22 final size:22
Alignment explanation
Indices: 1261307--1261348 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1261297 AGAGAGTTAA
*
1261307 AAATGTAATTTTGTTATTATAT
1 AAATGTAAATTTGTTATTATAT
1261329 AAATGTAAAATTT-TTATTAT
1 AAATGT-AAATTTGTTATTAT
1261349 TTTCACGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
AAATGTAAATTTGTTATTATAT
Found at i:1267696 original size:26 final size:26
Alignment explanation
Indices: 1267660--1267712 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
1267650 GGTCAAATAG
*
1267660 ATTCTATAGTTAATCTTTCTCGTATA
1 ATTCTATAGTTAATCTTTCTCATATA
1267686 ATTCTATAGTTAATCTTTCTCATATA
1 ATTCTATAGTTAATCTTTCTCATATA
1267712 A
1 A
1267713 GTCATGTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.15, G:0.06, T:0.49
Consensus pattern (26 bp):
ATTCTATAGTTAATCTTTCTCATATA
Found at i:1284972 original size:4 final size:4
Alignment explanation
Indices: 1284963--1285003 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
1284953 TCATGTAATA
1284963 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
1285004 ACTGATGATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:1285318 original size:26 final size:26
Alignment explanation
Indices: 1285262--1285318 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
1285252 AGATCATGTC
*
1285262 AATTTAAATTTTCAAAGTTCTTGGAT
1 AATTTAAATTTTCAAAGTTCTTGAAT
* *
1285288 AATTTAAGATTTTTAGAGTT-TTGAAT
1 AATTTAA-ATTTTCAAAGTTCTTGAAT
*
1285314 TATTT
1 AATTT
1285319 GGGGTTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (26 bp):
AATTTAAATTTTCAAAGTTCTTGAAT
Found at i:1285356 original size:32 final size:33
Alignment explanation
Indices: 1285290--1285357 Score: 93
Period size: 32 Copynumber: 2.1 Consensus size: 33
1285280 TCTTGGATAA
* * *
1285290 TTTAAGATTTTTAGAGTTTTGAATTATTTGGGG
1 TTTAAAATTTTTAAAGTTTTGAATCATTTGGGG
*
1285323 TTTAAAATTTTTAAAG-TTTGAATCATTTTGGG
1 TTTAAAATTTTTAAAGTTTTGAATCATTTGGGG
1285355 TTT
1 TTT
1285358 GGATAGTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 17 0.55
33 14 0.45
ACGTcount: A:0.26, C:0.01, G:0.19, T:0.53
Consensus pattern (33 bp):
TTTAAAATTTTTAAAGTTTTGAATCATTTGGGG
Found at i:1293796 original size:30 final size:30
Alignment explanation
Indices: 1293762--1293854 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
1293752 GTTGATCTCT
1293762 ATTGAAGATTAAACAAGCAGGCAAGGTTTC
1 ATTGAAGATTAAACAAGCAGGCAAGGTTTC
* * *
1293792 ATTGAAG--T-AA-ATGAATG-AA--TTAATC
1 ATTGAAGATTAAACAAGCAGGCAAGGTT--TC
1293817 TATTGAAGATTAAACAAGCAGGCAAGGTTTC
1 -ATTGAAGATTAAACAAGCAGGCAAGGTTTC
1293848 ATTGAAG
1 ATTGAAG
1293855 TAAATGAATG
Statistics
Matches: 47, Mismatches: 6, Indels: 20
0.64 0.08 0.27
Matches are distributed among these distances:
23 2 0.04
25 4 0.09
26 11 0.23
27 2 0.04
28 2 0.04
29 2 0.04
30 18 0.38
31 4 0.09
33 2 0.04
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.27
Consensus pattern (30 bp):
ATTGAAGATTAAACAAGCAGGCAAGGTTTC
Found at i:1293845 original size:56 final size:56
Alignment explanation
Indices: 1293759--1293873 Score: 230
Period size: 56 Copynumber: 2.1 Consensus size: 56
1293749 CAGGTTGATC
1293759 TCTATTGAAGATTAAACAAGCAGGCAAGGTTTCATTGAAGTAAATGAATGAATTAA
1 TCTATTGAAGATTAAACAAGCAGGCAAGGTTTCATTGAAGTAAATGAATGAATTAA
1293815 TCTATTGAAGATTAAACAAGCAGGCAAGGTTTCATTGAAGTAAATGAATGAATTAA
1 TCTATTGAAGATTAAACAAGCAGGCAAGGTTTCATTGAAGTAAATGAATGAATTAA
1293871 TCT
1 TCT
1293874 TGTGATATGC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.30
Consensus pattern (56 bp):
TCTATTGAAGATTAAACAAGCAGGCAAGGTTTCATTGAAGTAAATGAATGAATTAA
Found at i:1296399 original size:6 final size:6
Alignment explanation
Indices: 1296388--1296418 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1296378 TGAATACTCC
*
1296388 CTTCAT CTTCAT CTTCAT CTTCTT CTTCAT C
1 CTTCAT CTTCAT CTTCAT CTTCAT CTTCAT C
1296419 CTTTTCCTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.13, C:0.35, G:0.00, T:0.52
Consensus pattern (6 bp):
CTTCAT
Found at i:1297344 original size:12 final size:12
Alignment explanation
Indices: 1297327--1297352 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1297317 CTCTAAATTT
1297327 GGATTCCATTGA
1 GGATTCCATTGA
1297339 GGATTCCATTGA
1 GGATTCCATTGA
1297351 GG
1 GG
1297353 TAAGATGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (12 bp):
GGATTCCATTGA
Found at i:1298108 original size:24 final size:24
Alignment explanation
Indices: 1298076--1298138 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
1298066 AAGTAGTCTC
1298076 TTTTTTTTGTTAAAATTTCATTCA
1 TTTTTTTTGTTAAAATTTCATTCA
**
1298100 TTTTTTTTGTTAAAATTTTGTTCA
1 TTTTTTTTGTTAAAATTTCATTCA
*
1298124 TTTCTTTTGTTAAAA
1 TTTTTTTTGTTAAAA
1298139 GATAGTCTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.63
Consensus pattern (24 bp):
TTTTTTTTGTTAAAATTTCATTCA
Found at i:1299513 original size:87 final size:87
Alignment explanation
Indices: 1299367--1299542 Score: 352
Period size: 87 Copynumber: 2.0 Consensus size: 87
1299357 TAATCAATTT
1299367 TGAAAACAAATATGGTTCAGTTTATTTGATTTTCGAGACTTAATCGATTTCTTTGATTATCGATA
1 TGAAAACAAATATGGTTCAGTTTATTTGATTTTCGAGACTTAATCGATTTCTTTGATTATCGATA
1299432 TTAAAAACCCGAACCAATCAAA
66 TTAAAAACCCGAACCAATCAAA
1299454 TGAAAACAAATATGGTTCAGTTTATTTGATTTTCGAGACTTAATCGATTTCTTTGATTATCGATA
1 TGAAAACAAATATGGTTCAGTTTATTTGATTTTCGAGACTTAATCGATTTCTTTGATTATCGATA
1299519 TTAAAAACCCGAACCAATCAAA
66 TTAAAAACCCGAACCAATCAAA
1299541 TG
1 TG
1299543 TCCACCTGAT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 89 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (87 bp):
TGAAAACAAATATGGTTCAGTTTATTTGATTTTCGAGACTTAATCGATTTCTTTGATTATCGATA
TTAAAAACCCGAACCAATCAAA
Found at i:1303980 original size:16 final size:16
Alignment explanation
Indices: 1303959--1303992 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
1303949 TGGGCTTTCC
1303959 TTCTTATAAGATACTG
1 TTCTTATAAGATACTG
1303975 TTCTTATAAGATACTG
1 TTCTTATAAGATACTG
1303991 TT
1 TT
1303993 AAATAGGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (16 bp):
TTCTTATAAGATACTG
Found at i:1311313 original size:46 final size:46
Alignment explanation
Indices: 1311237--1311642 Score: 535
Period size: 46 Copynumber: 8.8 Consensus size: 46
1311227 TGATGTCATA
* * * *
1311237 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATATCATGTTGCCATG
* * *
1311283 GTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCATGTTGCCATG
* *
1311330 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATG
*
1311376 GTATCTTTCAACCATGGTCTTATTCATTTCATATCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATG
* * **
1311422 GTATCTTTTAACCATGGTCTTACACATTTCATATCACATTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATG
* ***
1311468 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCATGTTGCCATG
* * *
1311515 GTATCTTTCAACCATGGTCTTACTCATTTTATATCAAGTTGCCATT
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATG
* * * *
1311561 GTATGTTTCAATCATGGTCTTACACATTTCATATCAAGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATG
* *
1311607 GTATCTTTCAACCATGGTCTTACACATTCCATATCA
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCA
1311643 GAGAGCACAC
Statistics
Matches: 319, Mismatches: 38, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
46 239 0.75
47 80 0.25
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATG
Found at i:1311510 original size:139 final size:137
Alignment explanation
Indices: 1311237--1311634 Score: 546
Period size: 139 Copynumber: 2.9 Consensus size: 137
1311227 TGATGTCATA
* * * *
1311237 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATGGTATCTTTCAACCATGGT
1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGT
** * * * *
1311301 CTTATTCATTTTCCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGTCA
65 CTTACACA-TTTCATATCA-ATTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCACGTCA
1311366 GGTTGCCATG
128 GGTTGCCATG
* *
1311376 GTATCTTTCAACCATGGTCTTATTCATTTCATATCATGTTGCCATGGTATCTTTTAACCATGGTC
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTC
* * *
1311441 TTACACATTTCATATCACATTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCAT
66 TTACACATTTCATATCA-ATTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCACGTCAG
1311506 GTTGCCATG
129 GTTGCCATG
* * * * *
1311515 GTATCTTTCAACCATGGTCTTACTCATTTTATATCAAGTTGCCATTGTATGTTTCAATCATGGTC
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTC
*
1311580 TTACACATTTCATATCAAGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT
66 TTACACATTTCATATCAA-TTGCCATGGTATCTTTCAACCATGGTCTTACTCATT
1311635 CCATATCAGA
Statistics
Matches: 231, Mismatches: 25, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
138 48 0.21
139 183 0.79
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (137 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATATCATGTTGCCATGGTATCTTTCAACCATGGTC
TTACACATTTCATATCAATTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCACGTCAGGT
TGCCATG
Found at i:1311558 original size:185 final size:185
Alignment explanation
Indices: 1311275--1311642 Score: 628
Period size: 185 Copynumber: 2.0 Consensus size: 185
1311265 TTCTGTCATG
*
1311275 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCCTGTCATGTTGCCATGGTATCTTTCA
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATGGTATCTTTCA
* * **
1311340 ACCATGGTCTTACTCATTTCATGTCAGGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTT
66 ACCATGGTCTTACTCATTTCATATCAAGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTT
* * *
1311405 CATATCATGTTGCCATGGTATCTTTTAACCATGGTCTTACACATTTCATATCACA
131 CATATCAAGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTCCATATCACA
1311460 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATGGTATCTTTCA
1 TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATGGTATCTTTCA
* * * *
1311525 ACCATGGTCTTACTCATTTTATATCAAGTTGCCATTGTATGTTTCAATCATGGTCTTACACATTT
66 ACCATGGTCTTACTCATTTCATATCAAGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTT
1311590 CATATCAAGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTCCATATCA
131 CATATCAAGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTCCATATCA
1311643 GAGAGCACAC
Statistics
Matches: 171, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
185 171 1.00
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (185 bp):
TTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATGGTATCTTTCA
ACCATGGTCTTACTCATTTCATATCAAGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTT
CATATCAAGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTCCATATCACA
Found at i:1316590 original size:13 final size:13
Alignment explanation
Indices: 1316572--1316596 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1316562 TTGAGAGATA
1316572 AAAATTTAATATT
1 AAAATTTAATATT
1316585 AAAATTTAATAT
1 AAAATTTAATAT
1316597 AAACACTCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAATTTAATATT
Found at i:1318513 original size:18 final size:18
Alignment explanation
Indices: 1318490--1318525 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1318480 CCAAAACTTA
1318490 CAGGATCAGCATCATGAT
1 CAGGATCAGCATCATGAT
1318508 CAGGATCAGCATCATGAT
1 CAGGATCAGCATCATGAT
1318526 GACTCTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (18 bp):
CAGGATCAGCATCATGAT
Done.