Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 40 of 144
Found at i:12087623 original size:22 final size:22
Alignment explanation
Indices: 12087594--12087660 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
12087584 TGCACTAATG
12087594 AACAGAGAGCACTGAAGTGCTA
1 AACAGAGAGCACTGAAGTGCTA
* * * *
12087616 TACAGAGAGCACAGATGTTCTA
1 AACAGAGAGCACTGAAGTGCTA
*
12087638 AACAGAGAGCACTGACGTGCTA
1 AACAGAGAGCACTGAAGTGCTA
12087660 A
1 A
12087661 TAATCAGAGA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.16
Consensus pattern (22 bp):
AACAGAGAGCACTGAAGTGCTA
Found at i:12087671 original size:25 final size:24
Alignment explanation
Indices: 12087588--12087718 Score: 108
Period size: 25 Copynumber: 5.5 Consensus size: 24
12087578 TTATTATGCA
* *
12087588 CTAATGAACAGAGAGCACTGAAGTG
1 CTAAT-AACAGAGAGCACCGACGTG
* * *
12087613 CT-AT-ACAGAGAGCACAGATGTT
1 CTAATAACAGAGAGCACCGACGTG
*
12087635 CT-A-AACAGAGAGCACTGACGTG
1 CTAATAACAGAGAGCACCGACGTG
* *
12087657 CTAATAATCAGAGAGTACCAACGTG
1 CTAATAA-CAGAGAGCACCGACGTG
* *
12087682 CTAATAATCAAAGAGCACCAACGTG
1 CTAATAA-CAGAGAGCACCGACGTG
12087707 CTAATAATCAGA
1 CTAATAA-CAGA
12087719 TAGCGCGCTA
Statistics
Matches: 90, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
22 35 0.39
23 1 0.01
24 4 0.04
25 50 0.56
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.18
Consensus pattern (24 bp):
CTAATAACAGAGAGCACCGACGTG
Found at i:12091206 original size:5 final size:5
Alignment explanation
Indices: 12091196--12091229 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
12091186 ATTATTATAT
12091196 ATTTA ATTTA ATTTA ATTTA ATTTA ATTT- ATTTA
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA
12091230 TAAATAAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATTTA
Found at i:12091399 original size:19 final size:21
Alignment explanation
Indices: 12091371--12091414 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
12091361 TCAAACACCA
12091371 AAAAAGTAAATTATTTT-CAG
1 AAAAAGTAAATTATTTTCCAG
12091391 AAAAA-TAAATTATTTTCCAG
1 AAAAAGTAAATTATTTTCCAG
12091411 AAAA
1 AAAA
12091415 CATTTTACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.32
Consensus pattern (21 bp):
AAAAAGTAAATTATTTTCCAG
Found at i:12101125 original size:42 final size:42
Alignment explanation
Indices: 12101077--12101172 Score: 147
Period size: 42 Copynumber: 2.3 Consensus size: 42
12101067 TCGGTAGCAT
* *
12101077 ACACTTAGTGCCCGTTATTCAACATTGTCGTTTTAGTTTCGC
1 ACACTTAGTGCCCGTTATTCAACATTGTCATTTTAGTTTCAC
* * *
12101119 ACACTTAGTACTCGTTATTCACCATTGTCATTTTAGTTTCAC
1 ACACTTAGTGCCCGTTATTCAACATTGTCATTTTAGTTTCAC
12101161 ACACTTAGTGCC
1 ACACTTAGTGCC
12101173 ATTCGTATAG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.40
Consensus pattern (42 bp):
ACACTTAGTGCCCGTTATTCAACATTGTCATTTTAGTTTCAC
Found at i:12105034 original size:40 final size:40
Alignment explanation
Indices: 12104972--12105049 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
12104962 ATTAAATATA
12104972 ATTTAATAAAAATAAAAATAAATAAT-TTAATAATATTTTT
1 ATTTAATAAAAATAAAAATAAATAATATTAA-AATATTTTT
** * *
12105012 ATTTAATAAAAATATTATTAAATTATATTAAAATATTT
1 ATTTAATAAAAATAAAAATAAATAATATTAAAATATTT
12105050 CAAATGTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 29 0.88
41 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (40 bp):
ATTTAATAAAAATAAAAATAAATAATATTAAAATATTTTT
Found at i:12106394 original size:12 final size:12
Alignment explanation
Indices: 12106377--12106401 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12106367 TGGGGAATTT
12106377 AGTAATATATTG
1 AGTAATATATTG
12106389 AGTAATATATTG
1 AGTAATATATTG
12106401 A
1 A
12106402 AATGGATGGT
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:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (12 bp):
AGTAATATATTG
Found at i:12108712 original size:9 final size:9
Alignment explanation
Indices: 12108686--12108741 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 9
12108676 AAAACAGTAA
*
12108686 AAGAAGAAG
1 AAGAACAAG
*
12108695 -AGAAAAAG
1 AAGAACAAG
12108703 AAGAACAAG
1 AAGAACAAG
* *
12108712 AACAAAAACG
1 AAGAACAA-G
12108722 -AGAACAAG
1 AAGAACAAG
12108730 AAGAACAAG
1 AAGAACAAG
12108739 AAG
1 AAG
12108742 TGAAGAAATG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
8 8 0.21
9 29 0.76
10 1 0.03
ACGTcount: A:0.68, C:0.09, G:0.23, T:0.00
Consensus pattern (9 bp):
AAGAACAAG
Found at i:12110032 original size:26 final size:25
Alignment explanation
Indices: 12109981--12110042 Score: 115
Period size: 25 Copynumber: 2.4 Consensus size: 25
12109971 TTTAATATAT
12109981 AATATATATTTGATTAAAAATAAAA
1 AATATATATTTGATTAAAAATAAAA
12110006 AATATATATTTGATTAAAAATAAAAA
1 AATATATATTTGATTAAAAAT-AAAA
12110032 AATATATATTT
1 AATATATATTT
12110043 AATATATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 21 0.58
26 15 0.42
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (25 bp):
AATATATATTTGATTAAAAATAAAA
Found at i:12126068 original size:17 final size:18
Alignment explanation
Indices: 12126039--12126085 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
12126029 CAGAATTGGG
*
12126039 TTAA-TAAAATAATTTAA
1 TTAAGTAAATTAATTTAA
* *
12126056 TTGAG-AAATTAATTTAG
1 TTAAGTAAATTAATTTAA
12126073 TTAAGTAAATTAA
1 TTAAGTAAATTAA
12126086 ATAAATAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (18 bp):
TTAAGTAAATTAATTTAA
Found at i:12132949 original size:25 final size:25
Alignment explanation
Indices: 12132908--12132960 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
12132898 AAAGCTGTTG
*
12132908 AAAATTAAAAAGAAATTAGAAAATGT
1 AAAATTAAAAAGAAATTA-AAAAAGT
*
12132934 AAAATTAAAAA-TAATTAAAAAAGT
1 AAAATTAAAAAGAAATTAAAAAAGT
12132958 AAA
1 AAA
12132961 GAAGTTTCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 9 0.36
25 5 0.20
26 11 0.44
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.23
Consensus pattern (25 bp):
AAAATTAAAAAGAAATTAAAAAAGT
Found at i:12133380 original size:21 final size:21
Alignment explanation
Indices: 12133356--12133397 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
12133346 AATAATAATA
12133356 ATAATAATAACAATTGTTGTT
1 ATAATAATAACAATTGTTGTT
*
12133377 ATAATAATAATAATTGTTGTT
1 ATAATAATAACAATTGTTGTT
12133398 GTTGTTGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (21 bp):
ATAATAATAACAATTGTTGTT
Found at i:12144243 original size:31 final size:31
Alignment explanation
Indices: 12144202--12144378 Score: 216
Period size: 31 Copynumber: 5.7 Consensus size: 31
12144192 ATCCAATGCT
* *
12144202 CAAATC-AATTCGGCAATATATATCCATATA
1 CAAATCAAATTCGACAATGTATATCCATATA
* * *
12144232 TAAATCAAATTCGGCAATGAATATCCATATA
1 CAAATCAAATTCGACAATGTATATCCATATA
* * *
12144263 CAAATTAAATTTGACAATGTATAACCATATA
1 CAAATCAAATTCGACAATGTATATCCATATA
* *
12144294 CAAATCAAATTCGACAATGTATGGT-TATATA
1 CAAATCAAATTCGACAATGTAT-ATCCATATA
*
12144325 CAAATCAAATTCGACAATGTATATCTATATA
1 CAAATCAAATTCGACAATGTATATCCATATA
12144356 CAAATCAAATTC-AGCAATGTATA
1 CAAATCAAATTCGA-CAATGTATA
12144379 AAACATATAC
Statistics
Matches: 128, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
30 7 0.05
31 121 0.95
ACGTcount: A:0.45, C:0.16, G:0.08, T:0.31
Consensus pattern (31 bp):
CAAATCAAATTCGACAATGTATATCCATATA
Found at i:12144397 original size:62 final size:61
Alignment explanation
Indices: 12144208--12144398 Score: 204
Period size: 62 Copynumber: 3.1 Consensus size: 61
12144198 TGCTCAAATC
* * * * **
12144208 AATTCGGCAATATATATCCATATATAAATCAAATTCGGCAATGAATATCCATATACAAATTA
1 AATTCGACAATGTATATCCATATACAAATCAAATTC-GCAATGTATAAACATATACAAATTA
* * **** *
12144270 AATTTGACAATGTATAACCATATACAAATCAAATTCGACAATGTATGGTTATATACAAATCA
1 AATTCGACAATGTATATCCATATACAAATCAAATTCG-CAATGTATAAACATATACAAATTA
* *
12144332 AATTCGACAATGTATATCTATATACAAATCAAATTCAGCAATGTATAAAACATATAC-ATTTA
1 AATTCGACAATGTATATCCATATACAAATCAAATTC-GCAATGTAT-AAACATATACAAATTA
12144394 AATTC
1 AATTC
12144399 AAAAACATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
61 1 0.01
62 98 0.92
63 7 0.07
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (61 bp):
AATTCGACAATGTATATCCATATACAAATCAAATTCGCAATGTATAAACATATACAAATTA
Found at i:12146092 original size:76 final size:76
Alignment explanation
Indices: 12145963--12146113 Score: 266
Period size: 76 Copynumber: 2.0 Consensus size: 76
12145953 CGATGCAAAG
*
12145963 CCTGAACATCCCTACACAAGGCATCCATCTCGTTCTGCCACGGTTTTGCATGCATCCGAGAACCA
1 CCTGAACATCCCTACACAAGGCATCCATCTCGTTCTGCCACAGTTTTGCATGCATCCGAGAACCA
12146028 TCTTCACGCAA
66 TCTTCACGCAA
* * *
12146039 CCTGAACATCCCTACATAAGGCATCCATCTTGTTCTGCCACAGTTTTGTATGCATCCGAGAACCA
1 CCTGAACATCCCTACACAAGGCATCCATCTCGTTCTGCCACAGTTTTGCATGCATCCGAGAACCA
12146104 TCTTCACGCA
66 TCTTCACGCA
12146114 TGTCACTATT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 71 1.00
ACGTcount: A:0.25, C:0.34, G:0.15, T:0.26
Consensus pattern (76 bp):
CCTGAACATCCCTACACAAGGCATCCATCTCGTTCTGCCACAGTTTTGCATGCATCCGAGAACCA
TCTTCACGCAA
Found at i:12156215 original size:14 final size:14
Alignment explanation
Indices: 12156191--12156246 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
12156181 CTTTGTTTTT
12156191 TTTTTTAATTT-TTA
1 TTTTTT-ATTTGTTA
12156205 TTTATTTATTTGTTA
1 TTT-TTTATTTGTTA
*
12156220 TTTGTTATTTGTTA
1 TTTTTTATTTGTTA
* *
12156234 TTTATTCTTTGTT
1 TTTTTTATTTGTT
12156247 CTCAAATTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
14 28 0.76
15 9 0.24
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.75
Consensus pattern (14 bp):
TTTTTTATTTGTTA
Found at i:12156248 original size:7 final size:7
Alignment explanation
Indices: 12156210--12156246 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
12156200 TTTTATTTAT
12156210 TTATTTG
1 TTATTTG
12156217 TTATTTG
1 TTATTTG
12156224 TTATTTG
1 TTATTTG
*
12156231 TTATTTA
1 TTATTTG
*
12156238 TTCTTTG
1 TTATTTG
12156245 TT
1 TT
12156247 CTCAAATTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.14, C:0.03, G:0.11, T:0.73
Consensus pattern (7 bp):
TTATTTG
Found at i:12158826 original size:17 final size:17
Alignment explanation
Indices: 12158804--12158856 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
12158794 AAATCTCAGA
12158804 TTTTGATACCCATATCT
1 TTTTGATACCCATATCT
* *
12158821 TTTTGATACCTATATAT
1 TTTTGATACCCATATCT
* *
12158838 TTCTAATACCCATATCT
1 TTTTGATACCCATATCT
12158855 TT
1 TT
12158857 GACTTTCTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.26, C:0.21, G:0.04, T:0.49
Consensus pattern (17 bp):
TTTTGATACCCATATCT
Found at i:12168500 original size:17 final size:17
Alignment explanation
Indices: 12168478--12168514 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
12168468 TTGAAAAACC
12168478 CTTCTTGAGATTTCAAA
1 CTTCTTGAGATTTCAAA
**
12168495 CTTCTTGCTATTTCAAA
1 CTTCTTGAGATTTCAAA
12168512 CTT
1 CTT
12168515 GTACAAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.22, G:0.08, T:0.46
Consensus pattern (17 bp):
CTTCTTGAGATTTCAAA
Found at i:12169417 original size:32 final size:32
Alignment explanation
Indices: 12169372--12169453 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 32
12169362 TATAATTGGG
*
12169372 ACAAAGCCATCAATAGCAGTGATATGATC-AGC
1 ACAAAGCCATCAATAGCAGTAATATGATCGA-C
* * *
12169404 ACACAGCCATCAATAACGGTAATATGATCGAC
1 ACAAAGCCATCAATAGCAGTAATATGATCGAC
*
12169436 ACAAAGCCATCAGTAGCA
1 ACAAAGCCATCAATAGCA
12169454 TCGTAGCAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
32 40 0.98
33 1 0.02
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.17
Consensus pattern (32 bp):
ACAAAGCCATCAATAGCAGTAATATGATCGAC
Found at i:12169655 original size:24 final size:24
Alignment explanation
Indices: 12169622--12169703 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
12169612 CCATACTCAG
* * *
12169622 AATCAATCATACAAATAATAGACA
1 AATCAGTCATACAAATCACAGACA
* *
12169646 AATCAGTCATACCATTCACAGACA
1 AATCAGTCATACAAATCACAGACA
**
12169670 AATCAGTCATTTAAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
12169694 AATCAGTCAT
1 AATCAGTCAT
12169704 TTACACCACG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.48, C:0.22, G:0.07, T:0.23
Consensus pattern (24 bp):
AATCAGTCATACAAATCACAGACA
Found at i:12169731 original size:24 final size:24
Alignment explanation
Indices: 12169641--12169733 Score: 109
Period size: 24 Copynumber: 3.9 Consensus size: 24
12169631 TACAAATAAT
*
12169641 AGACAAATCAGTCA--TACCATTCAC
1 AGACAAATCAGTCATTTA-CA-CCAC
* *
12169665 AGACAAATCAGTCATTTAAATCAC
1 AGACAAATCAGTCATTTACACCAC
12169689 AGACAAATCAGTCATTTACACCAC
1 AGACAAATCAGTCATTTACACCAC
* *
12169713 GGACAAATCAATCATTTACAC
1 AGACAAATCAGTCATTTACAC
12169734 TTGAGAGGAA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
24 59 0.95
25 1 0.02
26 2 0.03
ACGTcount: A:0.43, C:0.26, G:0.09, T:0.23
Consensus pattern (24 bp):
AGACAAATCAGTCATTTACACCAC
Found at i:12169823 original size:54 final size:52
Alignment explanation
Indices: 12169749--12169977 Score: 169
Period size: 54 Copynumber: 4.2 Consensus size: 52
12169739 AGGAAAAATA
12169749 GTCATTTACCCTCCA-G-GGGTATTATGGTCATTTTACCTTACAGGAGTATTTCG
1 GTCATTTACCCT--ATGAGGGTATTATGGTCATTTTACCTTA-AGGAGTATTTCG
* * * *
12169802 GCCATTTAACCCTATGGGGGTATTATGGTTC-TTTTACCCTATGGAGGTATTTCG
1 GTCATTT-ACCCTATGAGGGTATTATGG-TCATTTTACCTTAAGGA-GTATTTCG
* * * * * *
12169856 ATCATTTTACCCTGTGAGGGTATTTTGGTTATTTTGCACTAATAAGG-GTATTTTG
1 GTCA-TTTACCCTATGAGGGTATTATGGTCATTTTAC-CT--TAAGGAGTATTTCG
* * * * *
12169911 GTCATTCTACCCTATGAGGGTATTTTAGTAATTTTACCTTATAGGGGTATTTCA
1 GTCATT-TACCCTATGAGGGTATTATGGTCATTTTACCTTA-AGGAGTATTTCG
*
12169965 GTAATTTTACCCT
1 GTCA-TTTACCCT
12169978 TCGGAGGTAT
Statistics
Matches: 141, Mismatches: 21, Indels: 27
0.75 0.11 0.14
Matches are distributed among these distances:
52 3 0.02
53 14 0.10
54 76 0.54
55 44 0.31
57 4 0.03
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.41
Consensus pattern (52 bp):
GTCATTTACCCTATGAGGGTATTATGGTCATTTTACCTTAAGGAGTATTTCG
Found at i:12169922 original size:55 final size:54
Alignment explanation
Indices: 12169847--12169963 Score: 144
Period size: 55 Copynumber: 2.1 Consensus size: 54
12169837 ACCCTATGGA
* * * * *
12169847 GGTATTTCGATCATTTTACCCTGTGAGGGTATTTTGGTTATTTTGCACTAATAAG
1 GGTATTTCGATCATTCTACCCTATGAGGGTATTTTAGTAATTTTAC-CTAATAAG
* * * *
12169902 GGTATTTTGGTCATTCTACCCTATGAGGGTATTTTAGTAATTTTACCTTATAGG
1 GGTATTTCGATCATTCTACCCTATGAGGGTATTTTAGTAATTTTACCTAATAAG
12169956 GGTATTTC
1 GGTATTTC
12169964 AGTAATTTTA
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
54 13 0.25
55 39 0.75
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.44
Consensus pattern (54 bp):
GGTATTTCGATCATTCTACCCTATGAGGGTATTTTAGTAATTTTACCTAATAAG
Found at i:12169962 original size:27 final size:27
Alignment explanation
Indices: 12169763--12170056 Score: 141
Period size: 27 Copynumber: 10.9 Consensus size: 27
12169753 TTTACCCTCC
* * *
12169763 AGGGGTATTATGGTCATTTTACCTTAC
1 AGGGGTATTTTGGTAATTTTACCTTAT
* * ** * *
12169790 AGGAGTATTTCGGCCATTTAACCCTAT
1 AGGGGTATTTTGGTAATTTTACCTTAT
* * ** *
12169817 GGGGGTATTATGGTTCTTTTACCCTAT
1 AGGGGTATTTTGGTAATTTTACCTTAT
* * * * *
12169844 -GGAGGTATTTCGATCATTTTACCCTGT
1 AGG-GGTATTTTGGTAATTTTACCTTAT
* * *
12169871 -GAGGGTATTTTGGTTATTTTGCACTAAT
1 AG-GGGTATTTTGGTAATTTTAC-CTTAT
* * * *
12169899 AAGGGTATTTTGGTCATTCTACCCTAT
1 AGGGGTATTTTGGTAATTTTACCTTAT
*
12169926 -GAGGGTATTTTAGTAATTTTACCTTAT
1 AG-GGGTATTTTGGTAATTTTACCTTAT
** *
12169953 AGGGGTATTTCAGTAATTTTACCCT-T
1 AGGGGTATTTTGGTAATTTTACCTTAT
* * *
12169979 CGGAGGTATTTCGGTAATTTTA-CTTTT
1 AGG-GGTATTTTGGTAATTTTACCTTAT
* * *
12170006 TGAGGGTATTTCGGTAATTTTACC-CATT
1 AG-GGGTATTTTGGTAATTTTACCTTA-T
* *
12170034 AGGGGTATTTCGATAATTTTACC
1 AGGGGTATTTTGGTAATTTTACC
12170057 CGTCGAGGGT
Statistics
Matches: 207, Mismatches: 49, Indels: 22
0.74 0.18 0.08
Matches are distributed among these distances:
26 7 0.03
27 175 0.85
28 25 0.12
ACGTcount: A:0.22, C:0.14, G:0.21, T:0.43
Consensus pattern (27 bp):
AGGGGTATTTTGGTAATTTTACCTTAT
Found at i:12170023 original size:81 final size:81
Alignment explanation
Indices: 12169925--12170079 Score: 217
Period size: 81 Copynumber: 1.9 Consensus size: 81
12169915 TTCTACCCTA
* * *
12169925 TGAGGGTATTTTAGTAATTTTA-CCTTATAGGGGTATTTC-AGTAATTTTACCCTTCG-GAGGTA
1 TGAGGGTATTTCAGTAATTTTACCCAT-TAGGGGTATTTCGA-TAATTTTACCCGTCGAG-GGTA
12169987 TTTCGGTAATTTTACTTTT
63 TTTCGGTAATTTTACTTTT
*
12170006 TGAGGGTATTTCGGTAATTTTACCCATTAGGGGTATTTCGATAATTTTACCCGTCGAGGGTATTT
1 TGAGGGTATTTCAGTAATTTTACCCATTAGGGGTATTTCGATAATTTTACCCGTCGAGGGTATTT
*
12170071 CGGTCATTT
66 CGGTAATTT
12170080 AACAACCTTT
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
81 61 0.92
82 5 0.08
ACGTcount: A:0.21, C:0.13, G:0.22, T:0.44
Consensus pattern (81 bp):
TGAGGGTATTTCAGTAATTTTACCCATTAGGGGTATTTCGATAATTTTACCCGTCGAGGGTATTT
CGGTAATTTTACTTTT
Found at i:12170079 original size:27 final size:27
Alignment explanation
Indices: 12169833--12170079 Score: 166
Period size: 27 Copynumber: 9.1 Consensus size: 27
12169823 ATTATGGTTC
* * *
12169833 TTTTACCCTATGGA-GGTATTTCGATCA
1 TTTTACCCT-TCGAGGGTATTTCGGTAA
* *
12169860 TTTTACCCTGT-GAGGGTATTTTGGTTA
1 TTTTACCCT-TCGAGGGTATTTCGGTAA
* * * * *
12169887 TTTTGCACTAAT-AAGGGTATTTTGGTCA
1 TTTTACCCT--TCGAGGGTATTTCGGTAA
* **
12169915 TTCTACCCTAT-GAGGGTATTTTAGTAA
1 TTTTACCCT-TCGAGGGTATTTCGGTAA
** *
12169942 TTTTA-CCTTATAGGGGTATTTCAGTAA
1 TTTTACCCTTCGA-GGGTATTTCGGTAA
12169969 TTTTACCCTTCG-GAGGTATTTCGGTAA
1 TTTTACCCTTCGAG-GGTATTTCGGTAA
** *
12169996 TTTTACTTTTTGAGGGTATTTCGGTAA
1 TTTTACCCTTCGAGGGTATTTCGGTAA
* *
12170023 TTTTACCCATTAG-GGGTATTTCGATAA
1 TTTTACCC-TTCGAGGGTATTTCGGTAA
* *
12170050 TTTTACCCGTCGAGGGTATTTCGGTCA
1 TTTTACCCTTCGAGGGTATTTCGGTAA
12170077 TTT
1 TTT
12170080 AACAACCTTT
Statistics
Matches: 179, Mismatches: 32, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
25 1 0.01
26 9 0.05
27 140 0.78
28 29 0.16
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.44
Consensus pattern (27 bp):
TTTTACCCTTCGAGGGTATTTCGGTAA
Found at i:12176697 original size:31 final size:31
Alignment explanation
Indices: 12176632--12176697 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
12176622 AGGAGTTTGG
* * *
12176632 TTTCTAGCATTTTTATTATTAATTATTTCTT
1 TTTCTAGCAATTTTATTATTAATTATTGCAT
12176663 TTTCTAGCAATTTTATTATTAATTATTGCAT
1 TTTCTAGCAATTTTATTATTAATTATTGCAT
12176694 TTTC
1 TTTC
12176698 AGTATTTAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.24, C:0.11, G:0.05, T:0.61
Consensus pattern (31 bp):
TTTCTAGCAATTTTATTATTAATTATTGCAT
Found at i:12180020 original size:19 final size:21
Alignment explanation
Indices: 12179976--12180022 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
12179966 AAGAAAATTT
* *
12179976 ATTGAAATCAACTTTCTATGG
1 ATTGAAACCAAATTTCTATGG
12179997 ATTGAAACCAAATTT-TAT-G
1 ATTGAAACCAAATTTCTATGG
12180016 ATTGAAA
1 ATTGAAA
12180023 AACAAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 8 0.33
20 3 0.12
21 13 0.54
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (21 bp):
ATTGAAACCAAATTTCTATGG
Found at i:12184877 original size:2 final size:2
Alignment explanation
Indices: 12184872--12184898 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
12184862 CCAAAAAACT
12184872 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
12184899 ATTTATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:12195484 original size:15 final size:15
Alignment explanation
Indices: 12195460--12195496 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
12195450 GCATAGGCAA
*
12195460 GGTTGCTATTTGAAT
1 GGTTGATATTTGAAT
12195475 GGTTGATATTTGAAT
1 GGTTGATATTTGAAT
12195490 GGTTGAT
1 GGTTGAT
12195497 TAGTTGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.22, C:0.03, G:0.30, T:0.46
Consensus pattern (15 bp):
GGTTGATATTTGAAT
Found at i:12198945 original size:23 final size:24
Alignment explanation
Indices: 12198919--12198963 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
12198909 TTGATTTCAA
*
12198919 AACCCTAA-AAGACAATTTTTGGG
1 AACCCTAAGAAGACAACTTTTGGG
*
12198942 AACCCTAAGAAGTCAACTTTTG
1 AACCCTAAGAAGACAACTTTTG
12198964 ATATTACCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.27
Consensus pattern (24 bp):
AACCCTAAGAAGACAACTTTTGGG
Found at i:12199771 original size:17 final size:17
Alignment explanation
Indices: 12199727--12199771 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
12199717 CTACAAAACA
*
12199727 TTTATTATTAATATATT
1 TTTATTATTAATAAATT
*
12199744 TATAATT-TTAATAAATT
1 T-TTATTATTAATAAATT
12199761 TTTATTATTAA
1 TTTATTATTAA
12199772 AATACTGAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 4 0.17
17 15 0.65
18 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTATTATTAATAAATT
Found at i:12201118 original size:87 final size:86
Alignment explanation
Indices: 12201018--12201187 Score: 218
Period size: 87 Copynumber: 2.0 Consensus size: 86
12201008 CTCGTTCGTT
* * *
12201018 CTTTTTTTTCACTCAATTAAGCA-TTTGAACTTTTAAAATACATCAAAAAGGC-CTTCAAACTTT
1 CTTTTTTTCCACTCAATTAAGCACTTT-AACTTTCAAAATACATCAAAAAGACTC-TCAAA-TTT
12201081 TTCAAAAAAAGCAATTAAGCCATG
63 TTCAAAAAAAGCAATTAAGCCATG
* * * *
12201105 CTTTTTTTCCACTCAATTGAGTACTTTAACTTTCAAAATGCATCAAAAAGACTCTCAAATTTTTT
1 CTTTTTTTCCACTCAATTAAGCACTTTAACTTTCAAAATACATCAAAAAGACTCTCAAATTTTTC
**
12201170 TTAAAAAGCAATTAAGCC
66 AAAAAAAGCAATTAAGCC
12201188 CCTGTTCTTA
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
86 21 0.29
87 47 0.65
88 4 0.06
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.36
Consensus pattern (86 bp):
CTTTTTTTCCACTCAATTAAGCACTTTAACTTTCAAAATACATCAAAAAGACTCTCAAATTTTTC
AAAAAAAGCAATTAAGCCATG
Found at i:12201236 original size:17 final size:18
Alignment explanation
Indices: 12201214--12201247 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12201204 ATTAGAAGAA
12201214 AAAATTT-TAAAAAATTT
1 AAAATTTATAAAAAATTT
*
12201231 AAAATTTATTAAAAATT
1 AAAATTTATAAAAAATT
12201248 AGAATTTTTT
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATTTATAAAAAATTT
Found at i:12201482 original size:28 final size:28
Alignment explanation
Indices: 12201434--12201493 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
12201424 GTACGATAAT
* *
12201434 TTTTATAATTTTTTTATATTTCTATATA
1 TTTTATAATTGTTTTAAATTTCTATATA
* *
12201462 TTTTATAA-TGTTTTACAATTTTTTTATA
1 TTTTATAATTGTTTTA-AATTTCTATATA
12201490 TTTT
1 TTTT
12201494 TTTTTCTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (28 bp):
TTTTATAATTGTTTTAAATTTCTATATA
Found at i:12201525 original size:20 final size:20
Alignment explanation
Indices: 12201502--12201547 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
12201492 TTTTTTTCTA
*
12201502 ATTT-TTAATAATTGAATATT
1 ATTTATTAA-AATTGAATAAT
*
12201522 ATTTATTAAAATTTAATAAT
1 ATTTATTAAAATTGAATAAT
12201542 ATTTAT
1 ATTTAT
12201548 AGCTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTTATTAAAATTGAATAAT
Found at i:12206547 original size:20 final size:20
Alignment explanation
Indices: 12206522--12206569 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
12206512 TATCAAGATT
12206522 TAATTATATGTAT-TTAAATA
1 TAATTATAT-TATATTAAATA
* *
12206542 TAATTATATTATATTATATT
1 TAATTATATTATATTAAATA
12206562 TAATTATA
1 TAATTATA
12206570 AGTGTTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
TAATTATATTATATTAAATA
Found at i:12206567 original size:10 final size:10
Alignment explanation
Indices: 12206519--12206569 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
12206509 CTTTATCAAG
12206519 ATTTAATTAT
1 ATTTAATTAT
* * *
12206529 ATGTATTTAA
1 ATTTAATTAT
*
12206539 ATATAATTAT
1 ATTTAATTAT
12206549 A-TTATATTAT
1 ATTTA-ATTAT
12206559 ATTTAATTAT
1 ATTTAATTAT
12206569 A
1 A
12206570 AGTGTTTGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
9 2 0.06
10 27 0.84
11 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (10 bp):
ATTTAATTAT
Found at i:12209934 original size:2 final size:2
Alignment explanation
Indices: 12209927--12209962 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12209917 TCCGTCCCTC
12209927 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12209963 ATATATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12210001 original size:17 final size:15
Alignment explanation
Indices: 12209981--12210015 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
12209971 ATATATATAT
*
12209981 ATATATAGCCTTAAG
1 ATATATAACCTTAAG
*
12209996 ATATATAATCTTAAG
1 ATATATAACCTTAAG
12210011 ATATA
1 ATATA
12210016 AAATTATGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (15 bp):
ATATATAACCTTAAG
Found at i:12210002 original size:2 final size:2
Alignment explanation
Indices: 12209962--12209987 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12209952 TCTCTCTCTC
12209962 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
12209988 GCCTTAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12212627 original size:21 final size:21
Alignment explanation
Indices: 12212601--12212640 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12212591 TTATTTTTTG
12212601 ATTATTTCTATTTTGGTCACA
1 ATTATTTCTATTTTGGTCACA
*
12212622 ATTATTTTTATTTTGGTCA
1 ATTATTTCTATTTTGGTCA
12212641 TTTCCCAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.57
Consensus pattern (21 bp):
ATTATTTCTATTTTGGTCACA
Found at i:12216207 original size:13 final size:14
Alignment explanation
Indices: 12216189--12216223 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
12216179 TGGGCCTTTC
12216189 ATTTTGGACTG-TA
1 ATTTTGGACTGTTA
12216202 ATTTTGGACTGTTTA
1 ATTTTGGACTG-TTA
12216217 ATTTTGG
1 ATTTTGG
12216224 GTTTTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 11 0.55
15 9 0.45
ACGTcount: A:0.20, C:0.06, G:0.23, T:0.51
Consensus pattern (14 bp):
ATTTTGGACTGTTA
Found at i:12221505 original size:9 final size:9
Alignment explanation
Indices: 12221491--12221516 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
12221481 ATAGTCGTAT
12221491 AATAATAAG
1 AATAATAAG
12221500 AATAATAAG
1 AATAATAAG
12221509 AATAATAA
1 AATAATAA
12221517 CAACAACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (9 bp):
AATAATAAG
Found at i:12226919 original size:101 final size:102
Alignment explanation
Indices: 12226802--12226986 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
12226792 AAAGTGATGG
* *
12226802 TCACGTGTGTACTACTATGTGCAGGCTACTACGTGTACCGAAATGAT-A-GGTCGCATGTGTAGT
1 TCACGTGTGTACTACTATGTGCAGGCTACTACGTGTACC-AAATGATAATGATCACATGTGTAGT
12226865 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
* * * *
12226903 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATGGTAATGATCACATGTGTAGTA
1 TCACGTGTGTACTACTATGTGCAGGCTACTACGTGTACCAAATGATAATGATCACATGTGTAGTA
12226968 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
12226987 TGAACCCAAT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
100 5 0.07
101 38 0.50
102 33 0.43
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTACTACTATGTGCAGGCTACTACGTGTACCAAATGATAATGATCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGTTTCGA
Found at i:12226932 original size:51 final size:50
Alignment explanation
Indices: 12226802--12226984 Score: 208
Period size: 51 Copynumber: 3.6 Consensus size: 50
12226792 AAAGTGATGG
* * * * *
12226802 TCACGTGTGTACTACTATGTGCAGGCTACTACGTGTACCGA-AATGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGATAGTAAT-GA
* * * *
12226852 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-TTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACC-GATAGTAAT-GA
* * *
12226903 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATGGTAATGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTA-CCGATAGTAATGA
12226954 TCACATGTGTAGTACTATGTGCAGGCTACTA
1 TCACATGTGTAGTACTATGTGCAGGCTACTA
12226985 TGTGAACCCA
Statistics
Matches: 112, Mismatches: 17, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
50 34 0.30
51 74 0.66
52 4 0.04
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.31
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGATAGTAATGA
Found at i:12226988 original size:26 final size:26
Alignment explanation
Indices: 12226908--12226988 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
12226898 TTCGATCACG
12226908 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * * * *
12226934 CGTGTA-T-CAGATG-GTAATGATCAC-A
1 TGTGTAGTAC-TATGTG-CAGGCT-ACTA
12226959 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
12226985 TGTG
1 TGTG
12226989 AACCCAATAT
Statistics
Matches: 38, Mismatches: 10, Indels: 14
0.61 0.16 0.23
Matches are distributed among these distances:
24 2 0.05
25 15 0.39
26 19 0.50
27 2 0.05
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:12237521 original size:21 final size:20
Alignment explanation
Indices: 12237497--12237535 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12237487 TTGGGTGTTT
*
12237497 TAGTTTTTTCAAGTGGTTTAC
1 TAGTGTTTT-AAGTGGTTTAC
*
12237518 TAGTGTTTTAAGTTGTTT
1 TAGTGTTTTAAGTGGTTT
12237536 TTGTATATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.18, C:0.05, G:0.21, T:0.56
Consensus pattern (20 bp):
TAGTGTTTTAAGTGGTTTAC
Found at i:12238895 original size:21 final size:20
Alignment explanation
Indices: 12238866--12238904 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12238856 ATGAACTCTA
*
12238866 TTTTCCCTTTTATTTTTTTAT
1 TTTTCCC-TTCATTTTTTTAT
*
12238887 TTTTTCCTTCATTTTTTT
1 TTTTCCCTTCATTTTTTT
12238905 CTTCCTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTCCCTTCATTTTTTTAT
Found at i:12239883 original size:26 final size:25
Alignment explanation
Indices: 12239850--12239899 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
12239840 TATATATACC
*
12239850 TTATTATAAATATCTTTATATCTTA
1 TTATTATAAATATCTATATATCTTA
* *
12239875 TTATGTATATATATCTATATCTCTT
1 TTAT-TATAAATATCTATATATCTT
12239900 TTTAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (25 bp):
TTATTATAAATATCTATATATCTTA
Found at i:12242321 original size:19 final size:19
Alignment explanation
Indices: 12242297--12242342 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
12242287 AACGTCTCTT
*
12242297 TTTGCATT-CATTTCATACA
1 TTTGCATTGCATTGCAT-CA
12242316 TTTGCATTGCATTGCATCA
1 TTTGCATTGCATTGCATCA
*
12242335 TATGCATT
1 TTTGCATT
12242343 AAATTTTCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.46
Consensus pattern (19 bp):
TTTGCATTGCATTGCATCA
Found at i:12245069 original size:17 final size:18
Alignment explanation
Indices: 12245047--12245083 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
12245037 AGTCAAAAAT
12245047 AAGAGAAAAA-AAAAGAA
1 AAGAGAAAAAGAAAAGAA
12245064 AAGAGAAAAAGAAAAGAA
1 AAGAGAAAAAGAAAAGAA
12245082 AA
1 AA
12245084 AGGAGAGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (18 bp):
AAGAGAAAAAGAAAAGAA
Found at i:12245072 original size:13 final size:12
Alignment explanation
Indices: 12245042--12245084 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
12245032 ATCAAAGTCA
12245042 AAAATAAGAGAAA-
1 AAAA-AAGA-AAAG
12245055 AAAAAAGAAAAG
1 AAAAAAGAAAAG
12245067 AGAAAAAGAAAAG
1 A-AAAAAGAAAAG
12245080 AAAAA
1 AAAAA
12245085 GGAGAGGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.11
12 9 0.32
13 16 0.57
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:12245892 original size:15 final size:15
Alignment explanation
Indices: 12245872--12245905 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
12245862 ACTTTGGGTC
12245872 AAAAAAATG-AAAAT
1 AAAAAAATGAAAAAT
12245886 AAAAAAATGAAAAAT
1 AAAAAAATGAAAAAT
12245901 AAAAA
1 AAAAA
12245906 TGGAGAGGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (15 bp):
AAAAAAATGAAAAAT
Found at i:12247799 original size:44 final size:43
Alignment explanation
Indices: 12247325--12248327 Score: 292
Period size: 44 Copynumber: 22.8 Consensus size: 43
12247315 AGACACAAAC
* * * * * *
12247325 CTATCACCCTAAACAGTAATGGAGTAGGTTGAAGATTGCATATT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATCGAAGATTG-AGATT
* * * *
12247369 CTATCACCCTAAGCAGTAGTGGAGCAGACCGAAGATGGTGAAT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATCGAAGATTGAGATT
* * * * * * ** *
12247412 CTTATCTTCCC-AATACAGTGGAGAAGCATATTTAAGCCATT-AG-TC
1 C-TATC-ACCCTAA-GCAGTAGTGGAGCAGATCGAAG--ATTGAGATT
* * *
12247457 CTATCACCCTAAGCAGTAGTGGAGTAGGTAGAAGATTGCAGATT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATCGAAGATTG-AGATT
* * * *
12247501 CTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAAT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATCGAAGATTGAGATT
* * * * * ** *
12247544 CTTATCTTCCC-AATACAGTGGAGAAGCAGATTTAAGCCATT-AG-TC
1 C-TATC-ACCCTAA-GCAGTAGTGGAGCAGATCGAAG--ATTGAGATT
** * * *
12247589 CTATCACCCTAAGCAGTAGTGGAATAGGTCAAAAATTGTAGATT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATCGAAGATTG-AGATT
* * ** * *
12247633 CTAT-ATCCCTAAGCAGTAGTGAAGCAGATCAAAGACGGTGAAT
1 CTATCA-CCCTAAGCAGTAGTGGAGCAGATCGAAGATTGAGATT
** * * * * * *
12247676 CTTATTTTCCC-AATACAGTGGAGAAGCATAT-GTAAGCCATT-AG-TC
1 C-TA-TCACCCTAA-GCAGTAGTGGAGCAGATCG-AAG--ATTGAGATT
* * * *
12247721 CAATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATCGAAGATTG-AGATT
* * * * *
12247765 CTGTCACCCTATGCAGTAGTGGAGCAGATCGAAGATGGTGAAT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATCGAAGATTGAGATT
* * * * ** *
12247808 CTTATCTTCCC-AATACAGTAGAGAAGCAGATTTAAGACATT-AG-TC
1 C-TATC-ACCCTAA-GCAGTAGTGGAGCAGATCGAAG--ATTGAGATT
** * * *
12247853 CTATCACCCTAAGCAGTAGTGGAATAGGTCAAAAATTGTAGATT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATCGAAGATTG-AGATT
* * ** * *
12247897 CTGT-ATCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAAT
1 CTATCA-CCCTAAGCAGTAGTGGAGCAGATCGAAGATTGAGATT
* * * * * ** *
12247940 CTTATCTTCCC-AATACAGTGGAGAAGCAGATTTAAGCCATT-AG-TC
1 C-TATC-ACCCTAA-GCAGTAGTGGAGCAGATCGAAG--ATTGAGATT
* *
12247985 CTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATCGAAGATTG-AGATT
* * * *
12248029 CTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAAT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATCGAAGATTGAGATT
* * * * * ** *
12248072 CTTATCTTCCC-AATACAGTGGAGAAGCAGATTTAAGCCATT-AG-TC
1 C-TATC-ACCCTAA-GCAGTAGTGGAGCAGATCGAAG--ATTGAGATT
* * *
12248117 CTATCACCCTAAGCAGTAGTGGAGTAGGTCAAAGATTGCAGATT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATCGAAGATTG-AGATT
* * * *
12248161 CTGTCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAAT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATCGAAGATTGAGATT
* * * * * * ** *
12248204 CTTATCTTCCC-AATACAGTGGAGAAGCAAATTTAAGTCATTG-G-TC
1 C-TATC-ACCCTAA-GCAGTAGTGGAGCAGATCGAAG--ATTGAGATT
** * *
12248249 CTATCACCCTAAGCAGTAGTGGAATAGGTCAAAGATTGTAGATT
1 CTATCACCCTAAGCAGTAGTGGAGCAGATCGAAGATTG-AGATT
* *
12248293 CTGT-ATCCCTAAGCAGTAGTGGAGCAGATCAAAGA
1 CTATCA-CCCTAAGCAGTAGTGGAGCAGATCGAAGA
12248328 CGGTGAATCT
Statistics
Matches: 666, Mismatches: 223, Indels: 140
0.65 0.22 0.14
Matches are distributed among these distances:
41 22 0.03
43 156 0.23
44 329 0.49
45 139 0.21
46 7 0.01
47 13 0.02
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (43 bp):
CTATCACCCTAAGCAGTAGTGGAGCAGATCGAAGATTGAGATT
Found at i:12248370 original size:132 final size:132
Alignment explanation
Indices: 12247324--12248348 Score: 1653
Period size: 132 Copynumber: 7.8 Consensus size: 132
12247314 AAGACACAAA
* * ** * *
12247324 CCTATCACCCTAAACAGTAATGGAGTAGGTTGAAGATTGCATATTCTATCACCCTAAGCAGTAGT
1 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCAAAGATTGCAGATTCTGTCACCCTAAGCAGTAGT
* *
12247389 GGAGCAGACCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCATATTTAAGCCATTA
66 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
12247454 GT
131 GT
12247456 CCTATCACCCTAAGCAGTAGTGGAGTAGGT-AGAAGATTGCAGATTCTGTCACCCTAAGCAGTAG
1 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCA-AAGATTGCAGATTCTGTCACCCTAAGCAGTAG
12247520 TGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATT
65 TGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATT
12247585 AGT
130 AGT
* * * *
12247588 CCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAAATTGTAGATTCTAT-ATCCCTAAGCAGTAG
1 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCAAAGATTGCAGATTCTGTCA-CCCTAAGCAGTAG
* * * * * *
12247652 TGAAGCAGATCAAAGACGGTGAATCTTATTTTCCCAATACAGTGGAGAAGCATATGTAAGCCATT
65 TGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATT
12247717 AGT
130 AGT
* ** *
12247720 CCAATCACCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCACCCTATGCAGTAGT
1 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCAAAGATTGCAGATTCTGTCACCCTAAGCAGTAGT
* *
12247785 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTAGAGAAGCAGATTTAAGACATTA
66 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
12247850 GT
131 GT
* * *
12247852 CCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAAATTGTAGATTCTGT-ATCCCTAAGCAGTAG
1 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCAAAGATTGCAGATTCTGTCA-CCCTAAGCAGTAG
* *
12247916 TGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATT
65 TGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATT
12247981 AGT
130 AGT
*
12247984 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTCTGTCACCCTAAGCAGTAGT
1 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCAAAGATTGCAGATTCTGTCACCCTAAGCAGTAGT
12248049 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
66 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
12248114 GT
131 GT
12248116 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCAAAGATTGCAGATTCTGTCACCCTAAGCAGTAGT
1 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCAAAGATTGCAGATTCTGTCACCCTAAGCAGTAGT
* * *
12248181 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAAATTTAAGTCATTG
66 GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
12248246 GT
131 GT
* *
12248248 CCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAGATTGTAGATTCTGT-ATCCCTAAGCAGTAG
1 CCTATCACCCTAAGCAGTAGTGGAGTAGGTCAAAGATTGCAGATTCTGTCA-CCCTAAGCAGTAG
* *
12248312 TGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAA
65 TGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAA
12248349 GATAGTAGGA
Statistics
Matches: 828, Mismatches: 58, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
131 3 0.00
132 822 0.99
133 3 0.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (132 bp):
CCTATCACCCTAAGCAGTAGTGGAGTAGGTCAAAGATTGCAGATTCTGTCACCCTAAGCAGTAGT
GGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
GT
Found at i:12248810 original size:55 final size:55
Alignment explanation
Indices: 12248726--12248835 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
12248716 AACTAAAAAA
12248726 ATTAACAGCAAACCCTAATCCCCCCTAACCCTAGGTGCGCCGCACCTAGGGCCTT
1 ATTAACAGCAAACCCTAATCCCCCCTAACCCTAGGTGCGCCGCACCTAGGGCCTT
* *
12248781 ATTAACAGCAAACCCTAATCCCCCCTAACCTTAGGTGCGTCGCACCTAGGGCCTT
1 ATTAACAGCAAACCCTAATCCCCCCTAACCCTAGGTGCGCCGCACCTAGGGCCTT
12248836 CTCACCAACT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.25, C:0.38, G:0.16, T:0.20
Consensus pattern (55 bp):
ATTAACAGCAAACCCTAATCCCCCCTAACCCTAGGTGCGCCGCACCTAGGGCCTT
Found at i:12249135 original size:21 final size:20
Alignment explanation
Indices: 12249109--12249147 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12249099 ATGAACTCTA
*
12249109 TTTTCCCTTTTATTTTTTTAT
1 TTTTCCC-TTCATTTTTTTAT
12249130 TTTTCCCTTCATTTTTTT
1 TTTTCCCTTCATTTTTTT
12249148 CTTCCTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTCCCTTCATTTTTTTAT
Found at i:12250601 original size:305 final size:306
Alignment explanation
Indices: 12250039--12250659 Score: 1217
Period size: 305 Copynumber: 2.0 Consensus size: 306
12250029 ACATATTTAC
*
12250039 ATATTTATATGCCATTTTTAATTTTCATATACATATATATATACCTTATTATAAATATCTTTATA
1 ATATATATATGCCATTTTTAATTTTCATATACATATATATATACCTTATTATAAATATCTTTATA
12250104 TATTGTTATGTATATATATCTATATCTCTTTTTAAATATTTTCTAGCTTATATATATACATACGT
66 TATTGTTATGTATATATATCTATATCTCTTTTTAAATATTTTCTAGCTTATATATATACATACGT
12250169 TTTGCTATATATATGTCTAGCTTCATTAAACATTTATATATATACGTCTATAAACTTTTATTTTA
131 TTTGCTATATATATGTCTAGCTTCATTAAACATTTATATATATACGTCTATAAACTTTTATTTTA
*
12250234 TTTTATTTATTTTCTATATATATATATACATACTTACATATATTATTATTTATACTTTATATATA
196 TTTTATTTATTTTCTATATATATATATACATACTTACATATATTATTATTTAAACTTTATATATA
12250299 CACCCGTATACACATACACACTTGCACATTTATATCTCAAGATTAA
261 CACCCGTATACACATACACACTTGCACATTTATATCTCAAGATTAA
12250345 ATATATATAT-CCATTTTTAATTTTCATATACATATATATATACCTTATTATAAATATCTTTATA
1 ATATATATATGCCATTTTTAATTTTCATATACATATATATATACCTTATTATAAATATCTTTATA
12250409 TATTGTTATGTATATATATCTATATCTCTTTTTAAATATTTTCTAGCTTATATATATACATACGT
66 TATTGTTATGTATATATATCTATATCTCTTTTTAAATATTTTCTAGCTTATATATATACATACGT
12250474 TTTGCTATATATATGTCTAGCTTCATTAAACATTTATATATATACGTCTATAAACTTTTATTTTA
131 TTTGCTATATATATGTCTAGCTTCATTAAACATTTATATATATACGTCTATAAACTTTTATTTTA
12250539 TTTTATTTATTTTCTATATATATATATACATACTTACATATATTATTATTTAAACTTTATATATA
196 TTTTATTTATTTTCTATATATATATATACATACTTACATATATTATTATTTAAACTTTATATATA
12250604 CACCCGTATACACATACACACTTGCACATTTATATCTCAAGATTAA
261 CACCCGTATACACATACACACTTGCACATTTATATCTCAAGATTAA
12250650 ATATATATAT
1 ATATATATAT
12250660 ATACATATGT
Statistics
Matches: 313, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
305 304 0.97
306 9 0.03
ACGTcount: A:0.35, C:0.13, G:0.04, T:0.48
Consensus pattern (306 bp):
ATATATATATGCCATTTTTAATTTTCATATACATATATATATACCTTATTATAAATATCTTTATA
TATTGTTATGTATATATATCTATATCTCTTTTTAAATATTTTCTAGCTTATATATATACATACGT
TTTGCTATATATATGTCTAGCTTCATTAAACATTTATATATATACGTCTATAAACTTTTATTTTA
TTTTATTTATTTTCTATATATATATATACATACTTACATATATTATTATTTAAACTTTATATATA
CACCCGTATACACATACACACTTGCACATTTATATCTCAAGATTAA
Found at i:12262490 original size:183 final size:183
Alignment explanation
Indices: 12262165--12262529 Score: 579
Period size: 183 Copynumber: 2.0 Consensus size: 183
12262155 CAACTTACCA
* *
12262165 CCAACGATAACCCTCCGTTTAACTATTGTTAAGACGAGAACACCGAATTCACCAGTCCGAGCCTC
1 CCAACGATAACCCTCCATTTAACTATTGTTAAGACGAGAACACCGAATTCACCAGTCCAAGCCTC
* * * *
12262230 TCCTTACGCCCAAATCGCAAAGAAAAAACATTATCACTTCAGTTGTTAAGAGATTCATGACAGAA
66 CCCCTACGCCCAAATCGCAAAGAAAAAACATTACCACTTCAGTCGTTAAGAGATTCATGACAGAA
* *
12262295 ACAAAAAGAAACACTTACCGAAACTAAGCGAGCACTAACCGCGTGTGAAAACG
131 ACAAAAAGAAACACTTACCGAAACTAAGCAAGCACTAACCGCGTGCGAAAACG
* *
12262348 CCAATGATAACCCTCCATTTAACTATTGTTAAGACGAGAACATCGAATTCACCAGTCCAAGCCTC
1 CCAACGATAACCCTCCATTTAACTATTGTTAAGACGAGAACACCGAATTCACCAGTCCAAGCCTC
* * *
12262413 CCCCTACGCCCAAA-CTGCAGAGAAAAAATATTACCACTTCAGTCGTTAAGAGATTCATGATAGA
66 CCCCTACGCCCAAATC-GCAAAGAAAAAACATTACCACTTCAGTCGTTAAGAGATTCATGACAGA
* *
12262477 AACGAAGAGAAACACTTACCGAAACTAAGCAAGCACTAACCGCGTGCGAAAAC
130 AACAAAAAGAAACACTTACCGAAACTAAGCAAGCACTAACCGCGTGCGAAAAC
12262530 AAAGGAAAAT
Statistics
Matches: 166, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
182 1 0.01
183 165 0.99
ACGTcount: A:0.38, C:0.27, G:0.16, T:0.19
Consensus pattern (183 bp):
CCAACGATAACCCTCCATTTAACTATTGTTAAGACGAGAACACCGAATTCACCAGTCCAAGCCTC
CCCCTACGCCCAAATCGCAAAGAAAAAACATTACCACTTCAGTCGTTAAGAGATTCATGACAGAA
ACAAAAAGAAACACTTACCGAAACTAAGCAAGCACTAACCGCGTGCGAAAACG
Found at i:12267682 original size:9 final size:9
Alignment explanation
Indices: 12267668--12267693 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
12267658 ATAGTCGTAT
12267668 AATAATAAG
1 AATAATAAG
12267677 AATAATAAG
1 AATAATAAG
12267686 AATAATAA
1 AATAATAA
12267694 CAACAACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (9 bp):
AATAATAAG
Found at i:12268697 original size:13 final size:13
Alignment explanation
Indices: 12268679--12268719 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
12268669 ACTCTTTCAC
12268679 ATCCTCTATACCA
1 ATCCTCTATACCA
* *
12268692 ATCCTCT-TTCCC
1 ATCCTCTATACCA
12268704 ATCCTCTATACCA
1 ATCCTCTATACCA
12268717 ATC
1 ATC
12268720 AGAGCCTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.24, C:0.41, G:0.00, T:0.34
Consensus pattern (13 bp):
ATCCTCTATACCA
Found at i:12268706 original size:25 final size:25
Alignment explanation
Indices: 12268670--12268719 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
12268660 TCCATTCCCA
12268670 CTCTTTCACATCCTCTATACCAATC
1 CTCTTTCACATCCTCTATACCAATC
*
12268695 CTCTTTCCCATCCTCTATACCAATC
1 CTCTTTCACATCCTCTATACCAATC
12268720 AGAGCCTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.22, C:0.42, G:0.00, T:0.36
Consensus pattern (25 bp):
CTCTTTCACATCCTCTATACCAATC
Found at i:12273159 original size:51 final size:51
Alignment explanation
Indices: 12273034--12273211 Score: 227
Period size: 51 Copynumber: 3.5 Consensus size: 51
12273024 GATGGTCATG
* * *
12273034 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-A-TGATAGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTAAT-GATCACA
* * * *
12273084 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-TTCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTAAT-GATCACA
* * *
12273135 TGTGTAGTACTATGTGCAGGCTACTACGTGTATCAGATGGTAATGATCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTAATGATCACA
12273186 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
12273212 TGTGAACCCA
Statistics
Matches: 111, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
50 35 0.32
51 74 0.67
52 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (51 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTAATGATCACA
Found at i:12273215 original size:26 final size:26
Alignment explanation
Indices: 12273135--12273215 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
12273125 TTCGATCACG
12273135 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
* * * * *
12273161 CGTGTA-T-CAGATG-GTAATGATCAC-A
1 TGTGTAGTAC-TATGTG-CAGGCT-ACTA
12273186 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
12273212 TGTG
1 TGTG
12273216 AACCCAATAT
Statistics
Matches: 38, Mismatches: 10, Indels: 14
0.61 0.16 0.23
Matches are distributed among these distances:
24 2 0.05
25 15 0.39
26 19 0.50
27 2 0.05
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:12283748 original size:21 final size:20
Alignment explanation
Indices: 12283724--12283762 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12283714 TTGGGTGTTT
*
12283724 TAGTTTTTTCAAGTGGTTTAC
1 TAGTGTTTT-AAGTGGTTTAC
*
12283745 TAGTGTTTTAAGTTGTTT
1 TAGTGTTTTAAGTGGTTT
12283763 TTGTATATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.18, C:0.05, G:0.21, T:0.56
Consensus pattern (20 bp):
TAGTGTTTTAAGTGGTTTAC
Found at i:12285422 original size:132 final size:132
Alignment explanation
Indices: 12285249--12285515 Score: 412
Period size: 132 Copynumber: 2.0 Consensus size: 132
12285239 TTGAAGAGAA
* *
12285249 TAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCAGATTCTGTCA-C
1 TAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAGATTGCAGATTCTGT-ATC
* * *
12285313 CCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGT-GGAGAAGCA
65 CCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGACAGTAGGA-AAGCA
12285377 AATT
129 AATT
* * *
12285381 TAAGTCATTGGTCCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAGATTGTAGATTCTGTATCC
1 TAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAGATTGCAGATTCTGTATCC
* *
12285446 CTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGATAGTAGGAAAGTAAA
66 CTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGACAGTAGGAAAGCAAA
12285511 TT
131 TT
12285513 TAA
1 TAA
12285516 ACCACCAACC
Statistics
Matches: 123, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
131 1 0.01
132 119 0.97
133 3 0.02
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (132 bp):
TAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAGATTGCAGATTCTGTATCC
CTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGACAGTAGGAAAGCAAA
TT
Found at i:12285645 original size:397 final size:397
Alignment explanation
Indices: 12284912--12285645 Score: 1387
Period size: 397 Copynumber: 1.8 Consensus size: 397
12284902 GTTGAAATGA
* *
12284912 TCACCCTAAGCAGTAGTGGAATAGGTCAAAGATGGTGAATCTTATCTTCCCAATACAGTAGAGAA
1 TCACCCTAAGCAGTAGTGGAACAGATCAAAGATGGTGAATCTTATCTTCCCAATACAGTAGAGAA
*
12284977 GCAGATTTAAGACATTAGTCCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAAATTGTAGATTC
66 GCAAATTTAAGACATTAGTCCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAAATTGTAGATTC
12285042 TGTATCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGATAGTAGGA
131 TGTATCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGATAGTAGGA
12285107 AAGTAAATTTAAACCACCAACCTCACCCTTTAAAGTTACAACAGAGTGGATTGAAGCTACAAGTC
196 AAGTAAATTTAAACCACCAACCTCACCCTTTAAAGTTACAACAGAGTGGATTGAAGCTACAAGTC
12285172 GTATCTCTCTGAAGTTGCAGTGGAATGGATCGAAGCAACAAGGCACAGTGGACTGGAGTGAAGCT
261 GTATCTCTCTGAAGTTGCAGTGGAATGGATCGAAGCAACAAGGCACAGTGGACTGGAGTGAAGCT
12285237 AATTGAAGAGAATAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCA
326 AATTGAAGAGAATAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCA
12285302 GATTCTG
391 GATTCTG
* * *
12285309 TCACCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAATCTTATCTTCCCAATACAGTGGAGAA
1 TCACCCTAAGCAGTAGTGGAACAGATCAAAGATGGTGAATCTTATCTTCCCAATACAGTAGAGAA
* * *
12285374 GCAAATTTAAGTCATTGGTCCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAGATTGTAGATTC
66 GCAAATTTAAGACATTAGTCCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAAATTGTAGATTC
12285439 TGTATCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGATAGTAGGA
131 TGTATCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGATAGTAGGA
12285504 AAGTAAATTTAAACCACCAACCTCACCCTTTAAAGTTACAACAGAGTGGATTGAAGCTACAAGTC
196 AAGTAAATTTAAACCACCAACCTCACCCTTTAAAGTTACAACAGAGTGGATTGAAGCTACAAGTC
12285569 GTATCTCTCTGAAGTTGCAGTGGAATGGATCGAAGCAACAAGGCACAGTGGACTGGAGTGAAGCT
261 GTATCTCTCTGAAGTTGCAGTGGAATGGATCGAAGCAACAAGGCACAGTGGACTGGAGTGAAGCT
12285634 AATTGAAGAGAA
326 AATTGAAGAGAA
12285646 GCGTCAAGAG
Statistics
Matches: 328, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
397 328 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.24
Consensus pattern (397 bp):
TCACCCTAAGCAGTAGTGGAACAGATCAAAGATGGTGAATCTTATCTTCCCAATACAGTAGAGAA
GCAAATTTAAGACATTAGTCCTATCACCCTAAGCAGTAGTGGAATAGGTCAAAAATTGTAGATTC
TGTATCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGATAGTAGGA
AAGTAAATTTAAACCACCAACCTCACCCTTTAAAGTTACAACAGAGTGGATTGAAGCTACAAGTC
GTATCTCTCTGAAGTTGCAGTGGAATGGATCGAAGCAACAAGGCACAGTGGACTGGAGTGAAGCT
AATTGAAGAGAATAAGCCATTAGTCCTATCACCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGCA
GATTCTG
Found at i:12286094 original size:141 final size:140
Alignment explanation
Indices: 12285841--12286119 Score: 513
Period size: 141 Copynumber: 2.0 Consensus size: 140
12285831 CAATATCTAG
12285841 GCCCAACAACAACAGCCCACAAACTAAAAAAAATTAACAGCAAACCCTAATCCCCCCTAACCCTA
1 GCCCAACAACAACAGCCCACAAACTAAAAAAAATTAACAGCAAACCCTAATCCCCCCTAACCCTA
*
12285906 GGTGCGTCGCACCTAGGGCCTTCTCACCAACTCCTCTGCTCCGCCGTTCACCTACTCTCTGCTTC
66 GGTGCGTCGCACCTAGGGCCTTCTCACCAACTCCTCTGCTCCGCCGTTCACCTACTCTCTGCTCC
12285971 ACTGCTCGTA
131 ACTGCTCGTA
*
12285981 GCCCAACAACAACAGCCCACAAACTAAAAAAAAATTAACAGCAAACCCTAATCCCCCCTAACCTT
1 GCCCAACAACAACAGCCCACAAACT-AAAAAAAATTAACAGCAAACCCTAATCCCCCCTAACCCT
* *
12286046 AGGTGCGTCGCACCTAGGGCCTTCTCACCAACTCCTTTGCTCCGCCGTTCACCTACTCTCTGGTC
65 AGGTGCGTCGCACCTAGGGCCTTCTCACCAACTCCTCTGCTCCGCCGTTCACCTACTCTCTGCTC
12286111 CACTGCTCG
130 CACTGCTCG
12286120 CCCTCTTGCC
Statistics
Matches: 134, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
140 25 0.19
141 109 0.81
ACGTcount: A:0.28, C:0.39, G:0.13, T:0.20
Consensus pattern (140 bp):
GCCCAACAACAACAGCCCACAAACTAAAAAAAATTAACAGCAAACCCTAATCCCCCCTAACCCTA
GGTGCGTCGCACCTAGGGCCTTCTCACCAACTCCTCTGCTCCGCCGTTCACCTACTCTCTGCTCC
ACTGCTCGTA
Found at i:12286278 original size:75 final size:75
Alignment explanation
Indices: 12286193--12286338 Score: 283
Period size: 75 Copynumber: 1.9 Consensus size: 75
12286183 AAAAGAGGAG
12286193 AGAAAAACAAACAAAAAGAGAGAGTTGTAAAATGACTATAAAAGCCATATCAAACATTGTAAAAG
1 AGAAAAACAAACAAAAAGAGAGAGTTGTAAAATGACTATAAAAGCCATATCAAACATTGTAAAAG
12286258 GGGTTCAGCT
66 GGGTTCAGCT
*
12286268 AGAAAAACAAACAAAAAGAGAGAGTTGTAAAATGGCTATAAAAGCCATATCAAACATTGTAAAAG
1 AGAAAAACAAACAAAAAGAGAGAGTTGTAAAATGACTATAAAAGCCATATCAAACATTGTAAAAG
12286333 GGGTTC
66 GGGTTC
12286339 GGCCCCCTCT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 70 1.00
ACGTcount: A:0.51, C:0.12, G:0.19, T:0.18
Consensus pattern (75 bp):
AGAAAAACAAACAAAAAGAGAGAGTTGTAAAATGACTATAAAAGCCATATCAAACATTGTAAAAG
GGGTTCAGCT
Found at i:12286446 original size:21 final size:20
Alignment explanation
Indices: 12286417--12286455 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12286407 ATGAACTCTA
*
12286417 TTTTCCCTTTTATTTTTTTAT
1 TTTTCCC-TTCATTTTTTTAT
*
12286438 TTTTTCCTTCATTTTTTT
1 TTTTCCCTTCATTTTTTT
12286456 CTTCCTTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTCCCTTCATTTTTTTAT
Found at i:12286668 original size:21 final size:20
Alignment explanation
Indices: 12286642--12286680 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12286632 ATGAACTCTA
*
12286642 TTTTCCCTTTTATTTTTTTAT
1 TTTTCCC-TTCATTTTTTTAT
12286663 TTTTCCCTTCATTTTTTT
1 TTTTCCCTTCATTTTTTT
12286681 CTTCCTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTCCCTTCATTTTTTTAT
Found at i:12286830 original size:224 final size:225
Alignment explanation
Indices: 12286407--12286855 Score: 828
Period size: 225 Copynumber: 2.0 Consensus size: 225
12286397 TTTTTTTGGT
*
12286407 ATGAACTCTATTTTCCCTTTTATTTTTTTATTTTTTCCTTCATTTTTTTCTTCCTTTTGAAACTG
1 ATGAACTCTATTTTCCCTTTTATTTTTTTATTTTTCCCTTCATTTTTTTCTTCCTTTTGAAACTG
12286472 TTTGTTTTCTCTATTTTTATTTTTCTTTTATTTTTAAAAACTATATAAATAACGTATAAACGTAA
66 TTTGTTTTCTCTATTTTTATTTTTCTTTTATTTTTAAAAACTATATAAATAACGTATAAACGTAA
*
12286537 AAAAAAGAAGCAAACTTTTACCTTTTTGAATTTTCCGGCCACCGCGCACGGTGGCCGGCATGACG
131 AAAAAAGAAGCAAACTTTTACCTTTTTGAATTTTCCGGCCACCGCGCACGGTGGCCGGCACGACG
12286602 GCGTCGACGGTGAAGCTTCACCGGACCCAG
196 GCGTCGACGGTGAAGCTTCACCGGACCCAG
12286632 ATGAACTCTATTTTCCCTTTTATTTTTTTATTTTTCCCTTCATTTTTTTCTTCCTTTTGAAACTG
1 ATGAACTCTATTTTCCCTTTTATTTTTTTATTTTTCCCTTCATTTTTTTCTTCCTTTTGAAACTG
*
12286697 TTTGTTTTCTCTATTTTTATTTTTCTTTTATTTTTAAAAACTATATATATAACGTATAAACGTAA
66 TTTGTTTTCTCTATTTTTATTTTTCTTTTATTTTTAAAAACTATATAAATAACGTATAAACGTAA
* * *
12286762 AACAAA-AAGCAAACTTTTACCTTTTTGAATTTTTCGGCCACCGCGCACGGTGGCCGGCGCGACG
131 AAAAAAGAAGCAAACTTTTACCTTTTTGAATTTTCCGGCCACCGCGCACGGTGGCCGGCACGACG
*
12286826 GCGTCGACGGTGACGCTTCACCGGACCCAG
196 GCGTCGACGGTGAAGCTTCACCGGACCCAG
12286856 GGCCGGAGTT
Statistics
Matches: 217, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
224 84 0.39
225 133 0.61
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.42
Consensus pattern (225 bp):
ATGAACTCTATTTTCCCTTTTATTTTTTTATTTTTCCCTTCATTTTTTTCTTCCTTTTGAAACTG
TTTGTTTTCTCTATTTTTATTTTTCTTTTATTTTTAAAAACTATATAAATAACGTATAAACGTAA
AAAAAAGAAGCAAACTTTTACCTTTTTGAATTTTCCGGCCACCGCGCACGGTGGCCGGCACGACG
GCGTCGACGGTGAAGCTTCACCGGACCCAG
Found at i:12287175 original size:133 final size:133
Alignment explanation
Indices: 12286937--12287201 Score: 485
Period size: 133 Copynumber: 2.0 Consensus size: 133
12286927 AGGGTTTTAA
12286937 AAAAAGAAATTTGGCTTTTATAATACTATTAAAACGGCGCCGTTTTGAGACCCCTTGACCCACGC
1 AAAAAGAAATTTGGCTTTTATAATACTATTAAAACGGCGCCGTTTTGAGACCCCTTGACCCACGC
* *
12287002 GGTGACCCGGCCCAGGGGGAAGGATCCGCGCATTTTGCCTTAGGGGGATATTTGTGCCATAGGTC
66 GGTGACCCGGCCCAGGGGGAAGGATCCACGCATTTTGCCTTAGGGAGATATTTGTGCCATAGGTC
12287067 CTT
131 CTT
* *
12287070 AAAAAGAAATTTGGCTTTTATAATACTATTAAAATGGCGCCGTTTTGAGACCCCTTGACCCGCGC
1 AAAAAGAAATTTGGCTTTTATAATACTATTAAAACGGCGCCGTTTTGAGACCCCTTGACCCACGC
*
12287135 GGTGACCCGGCCCAGGGGGAAGGATCCACGCGTTTTGCCTTAGGGAGATATTTGTGCCATAGGTC
66 GGTGACCCGGCCCAGGGGGAAGGATCCACGCATTTTGCCTTAGGGAGATATTTGTGCCATAGGTC
12287200 CT
131 CT
12287202 CAGGGGGAAG
Statistics
Matches: 127, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
133 127 1.00
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.26
Consensus pattern (133 bp):
AAAAAGAAATTTGGCTTTTATAATACTATTAAAACGGCGCCGTTTTGAGACCCCTTGACCCACGC
GGTGACCCGGCCCAGGGGGAAGGATCCACGCATTTTGCCTTAGGGAGATATTTGTGCCATAGGTC
CTT
Found at i:12287211 original size:55 final size:55
Alignment explanation
Indices: 12287147--12287256 Score: 193
Period size: 55 Copynumber: 2.0 Consensus size: 55
12287137 TGACCCGGCC
*
12287147 CAGGGGGAAGGATCCACGCGTTTTGCCTTAGGGAGATATTTGTGCCATAGGTCCT
1 CAGGGGGAAGGATCCACGCATTTTGCCTTAGGGAGATATTTGTGCCATAGGTCCT
* *
12287202 CAGGGGGAAGGATCCGCGCATTTTGCCTTAGGGGGATATTTGTGCCATAGGTCCT
1 CAGGGGGAAGGATCCACGCATTTTGCCTTAGGGAGATATTTGTGCCATAGGTCCT
12287257 TCCTCTTTTG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.19, C:0.20, G:0.34, T:0.27
Consensus pattern (55 bp):
CAGGGGGAAGGATCCACGCATTTTGCCTTAGGGAGATATTTGTGCCATAGGTCCT
Found at i:12287833 original size:22 final size:22
Alignment explanation
Indices: 12287803--12287859 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
12287793 TTAATTTTCA
*
12287803 TATACATATATATATACCTTAT
1 TATAAATATATATATACCTTAT
* * *
12287825 TATAAATATCTTTATATCTTAT
1 TATAAATATATATATACCTTAT
**
12287847 TATGTATATATAT
1 TATAAATATATAT
12287860 CTATATCTCT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.51
Consensus pattern (22 bp):
TATAAATATATATATACCTTAT
Found at i:12287854 original size:26 final size:25
Alignment explanation
Indices: 12287821--12287870 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
12287811 TATATATACC
*
12287821 TTATTATAAATATCTTTATATCTTA
1 TTATTATAAATATCTATATATCTTA
* *
12287846 TTATGTATATATATCTATATCTCTT
1 TTAT-TATAAATATCTATATATCTT
12287871 TTTAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (25 bp):
TTATTATAAATATCTATATATCTTA
Found at i:12290293 original size:19 final size:19
Alignment explanation
Indices: 12290269--12290314 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
12290259 AACGTCTCTT
*
12290269 TTTGCATT-CATTTCATACA
1 TTTGCATTGCATTGCAT-CA
12290288 TTTGCATTGCATTGCATCA
1 TTTGCATTGCATTGCATCA
*
12290307 TATGCATT
1 TTTGCATT
12290315 AAATTTTCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.46
Consensus pattern (19 bp):
TTTGCATTGCATTGCATCA
Found at i:12293041 original size:17 final size:18
Alignment explanation
Indices: 12293019--12293055 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
12293009 AGTCAAAAAT
12293019 AAGAGAAAAA-AAAAGAA
1 AAGAGAAAAAGAAAAGAA
12293036 AAGAGAAAAAGAAAAGAA
1 AAGAGAAAAAGAAAAGAA
12293054 AA
1 AA
12293056 AGGAGAGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (18 bp):
AAGAGAAAAAGAAAAGAA
Found at i:12293044 original size:13 final size:12
Alignment explanation
Indices: 12293014--12293056 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 12
12293004 ATCAAAGTCA
12293014 AAAATAAGAGAAA-
1 AAAA-AAGA-AAAG
12293027 AAAAAAGAAAAG
1 AAAAAAGAAAAG
12293039 AGAAAAAGAAAAG
1 A-AAAAAGAAAAG
12293052 AAAAA
1 AAAAA
12293057 GGAGAGGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.11
12 9 0.32
13 16 0.57
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (12 bp):
AAAAAAGAAAAG
Found at i:12293864 original size:15 final size:15
Alignment explanation
Indices: 12293844--12293877 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
12293834 ACTTTGGGTC
12293844 AAAAAAATG-AAAAT
1 AAAAAAATGAAAAAT
12293858 AAAAAAATGAAAAAT
1 AAAAAAATGAAAAAT
12293873 AAAAA
1 AAAAA
12293878 TGGAGAGGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (15 bp):
AAAAAAATGAAAAAT
Found at i:12296894 original size:21 final size:20
Alignment explanation
Indices: 12296868--12296906 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12296858 ATGAACTCTA
*
12296868 TTTTCCCTTTTATTTTTTTAT
1 TTTTCCC-TTCATTTTTTTAT
12296889 TTTTCCCTTCATTTTTTT
1 TTTTCCCTTCATTTTTTT
12296907 CTTCCTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTCCCTTCATTTTTTTAT
Found at i:12297860 original size:26 final size:25
Alignment explanation
Indices: 12297827--12297876 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
12297817 TATATATACC
*
12297827 TTATTATAAATATCTTTATATCTTA
1 TTATTATAAATATCTATATATCTTA
* *
12297852 TTATGTATATATATCTATATCTCTT
1 TTAT-TATAAATATCTATATATCTT
12297877 TTTAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (25 bp):
TTATTATAAATATCTATATATCTTA
Found at i:12312850 original size:13 final size:13
Alignment explanation
Indices: 12312832--12312856 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12312822 CAATCAAATG
12312832 CACACAAAATAAA
1 CACACAAAATAAA
12312845 CACACAAAATAA
1 CACACAAAATAA
12312857 TATTAATAAT
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:12313039 original size:53 final size:53
Alignment explanation
Indices: 12312959--12313064 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
12312949 TTTTTGTTTG
12312959 TAACATGCATATGTTTTGGGGGTGTCGTATAAATCTATTCTAAAACTAATTAT
1 TAACATGCATATGTTTTGGGGGTGTCGTATAAATCTATTCTAAAACTAATTAT
12313012 TAACATGCATATGTTTTGGGGGTGTCGTATAAATCTATTCTAAAACTAATTAT
1 TAACATGCATATGTTTTGGGGGTGTCGTATAAATCTATTCTAAAACTAATTAT
12313065 GTAATAAATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (53 bp):
TAACATGCATATGTTTTGGGGGTGTCGTATAAATCTATTCTAAAACTAATTAT
Found at i:12316802 original size:137 final size:135
Alignment explanation
Indices: 12316553--12316825 Score: 519
Period size: 137 Copynumber: 2.0 Consensus size: 135
12316543 TTTTTGTGTG
12316553 GGGTTTTATGATTCTCTGCCTCGACATGATTTTAAGCGAAAAAATCTTTCATCCCGACTTTCTAT
1 GGGTTTTATGATTCTCTGCCTCGACATGATTTTAAGCGAAAAAATCTTTCATCCCGACTTTCTAT
12316618 TGATTTTTTTTCTGTAATTTATAATTATTCCGCGATTGTAATGAAGCGAGCTAGGTTTGATTTCA
66 TGATTTTTTTTCTGTAATTTATAATTATTCCGCGATTGTAATGAAGCGAGCTAGGTTTGATTTCA
12316683 CAAAC
131 CAAAC
*
12316688 GGGTTTTTTGATTCTCTGCCTCGACATGATTTTAAGCGAAAAAAATCTTTCATCCCGACTTTCTA
1 GGGTTTTATGATTCTCTGCCTCGACATGATTTTAAGCG-AAAAAATCTTTCATCCCGACTTTCTA
12316753 TTGATTTTTTTTTCTGTAATTTATAATTATTCCGCGATTGTAATGAAGCGAGCTAGGTTTGATTT
65 TTGA-TTTTTTTTCTGTAATTTATAATTATTCCGCGATTGTAATGAAGCGAGCTAGGTTTGATTT
12316818 CACAAAC
129 CACAAAC
12316825 G
1 G
12316826 CCCAAAAAAT
Statistics
Matches: 135, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
135 37 0.27
136 30 0.22
137 68 0.50
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (135 bp):
GGGTTTTATGATTCTCTGCCTCGACATGATTTTAAGCGAAAAAATCTTTCATCCCGACTTTCTAT
TGATTTTTTTTCTGTAATTTATAATTATTCCGCGATTGTAATGAAGCGAGCTAGGTTTGATTTCA
CAAAC
Found at i:12320327 original size:139 final size:139
Alignment explanation
Indices: 12320077--12320357 Score: 544
Period size: 139 Copynumber: 2.0 Consensus size: 139
12320067 TTCTTATAAA
12320077 TTACTTTGAAGCTTAGGTTTACAAAGAACATATGCTATCATATCAGACATTATTATAATGGGCTA
1 TTACTTTGAAGCTTAGGTTTACAAAGAACATATGCTATCATATCAGACATTATTATAATGGGCTA
*
12320142 TCTTTCTTACTCGTCTTTTGTACGACATGAAGCATCCAAATTTACCATACTTCTGTCTCTAATAA
66 TCTTTCTTACTCGTCTTTTGTACGACATGAAGCATCAAAATTTACCATACTTCTGTCTCTAATAA
*
12320207 TCATGGTCT
131 TCATGGGCT
12320216 TTACTTTGAAGCTTAGGTTTACAAAGAACATATGCTATCATATCAGACATTATTATAATGGGCTA
1 TTACTTTGAAGCTTAGGTTTACAAAGAACATATGCTATCATATCAGACATTATTATAATGGGCTA
12320281 TCTTTCTTACTCGTCTTTTGTACGACATGAAGCATCAAAATTTACCATACTTCTGTCTCTAATAA
66 TCTTTCTTACTCGTCTTTTGTACGACATGAAGCATCAAAATTTACCATACTTCTGTCTCTAATAA
12320346 TCATGGGCT
131 TCATGGGCT
12320355 TTA
1 TTA
12320358 ATTAAACGGA
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 140 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (139 bp):
TTACTTTGAAGCTTAGGTTTACAAAGAACATATGCTATCATATCAGACATTATTATAATGGGCTA
TCTTTCTTACTCGTCTTTTGTACGACATGAAGCATCAAAATTTACCATACTTCTGTCTCTAATAA
TCATGGGCT
Found at i:12325169 original size:22 final size:22
Alignment explanation
Indices: 12325144--12325185 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12325134 TAATTAAATG
12325144 ATTTAAAGATT-ATAATATTTTT
1 ATTTAAA-ATTAATAATATTTTT
*
12325166 ATTTAAATTTAATAATATTT
1 ATTTAAAATTAATAATATTT
12325186 AATATATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
ATTTAAAATTAATAATATTTTT
Found at i:12351319 original size:42 final size:42
Alignment explanation
Indices: 12351273--12351367 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 42
12351263 TTAGCTTCTT
* * * *
12351273 TGAGCTTCTGTTTAACCTTTCTGGGTTTCCGTTCAGCTCCTA
1 TGAGCTTCTGTTCAACCCTTATGGGTTTCCGTTCAGCACCTA
** * *
12351315 TGAGCTTCCATTCAACCCTTATGGGTTTCCGTTTAGCACTTA
1 TGAGCTTCTGTTCAACCCTTATGGGTTTCCGTTCAGCACCTA
*
12351357 TGTGCTTCTGT
1 TGAGCTTCTGT
12351368 ATAGCCTTCG
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (42 bp):
TGAGCTTCTGTTCAACCCTTATGGGTTTCCGTTCAGCACCTA
Found at i:12351344 original size:21 final size:21
Alignment explanation
Indices: 12351294--12351344 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
12351284 TTAACCTTTC
* *
12351294 TGGGTTTCCGTTCAGCTCCTA
1 TGGGTTTCCATTCAACTCCTA
* *
12351315 TGAGCTTCCATTCAAC-CCTTA
1 TGGGTTTCCATTCAACTCC-TA
12351336 TGGGTTTCC
1 TGGGTTTCC
12351345 GTTTAGCACT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.14, C:0.29, G:0.20, T:0.37
Consensus pattern (21 bp):
TGGGTTTCCATTCAACTCCTA
Found at i:12355461 original size:22 final size:21
Alignment explanation
Indices: 12355436--12355486 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
12355426 TAATTTCAAA
12355436 ATTTATATTTACATATAA-ATAT
1 ATTTATATTT--ATATAACATAT
* *
12355458 ATTTACATGTATATAACATAT
1 ATTTATATTTATATAACATAT
12355479 ATTT-TATT
1 ATTTATATT
12355487 AAGAAACTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 8 0.33
21 8 0.33
22 8 0.33
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTTATATTTATATAACATAT
Found at i:12360581 original size:32 final size:33
Alignment explanation
Indices: 12360540--12360601 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
12360530 AATCAGTTGT
* *
12360540 AAAATTGTTTTAAAATATTA-AAATTTTTAATA
1 AAAATTGTTTAAAAAAATTATAAATTTTTAATA
*
12360572 AAAATTGTTTAAAAAAATTATAACTTTTTA
1 AAAATTGTTTAAAAAAATTATAAATTTTTA
12360602 CAATTACAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 18 0.69
33 8 0.31
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (33 bp):
AAAATTGTTTAAAAAAATTATAAATTTTTAATA
Found at i:12360824 original size:26 final size:27
Alignment explanation
Indices: 12360775--12360825 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
12360765 AATTGTTTTC
* *
12360775 AATAATAACAAAAAATTATCTGTGTCA
1 AATAATAACAAAAAATAAACTGTGTCA
*
12360802 AATAATAAC-AAAAATAAAGTGTGT
1 AATAATAACAAAAAATAAACTGTGT
12360826 TAGTAAGTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.55, C:0.08, G:0.10, T:0.27
Consensus pattern (27 bp):
AATAATAACAAAAAATAAACTGTGTCA
Found at i:12363801 original size:19 final size:18
Alignment explanation
Indices: 12363779--12363820 Score: 68
Period size: 17 Copynumber: 2.3 Consensus size: 18
12363769 TTATTTAAAC
12363779 AATATTTAACCAAATGTAT
1 AATATTT-ACCAAATGTAT
12363798 AATA-TTACCAAATGTAT
1 AATATTTACCAAATGTAT
12363815 AATATT
1 AATATT
12363821 ACTTGAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 15 0.68
18 3 0.14
19 4 0.18
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.38
Consensus pattern (18 bp):
AATATTTACCAAATGTAT
Found at i:12363809 original size:17 final size:17
Alignment explanation
Indices: 12363787--12363822 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
12363777 ACAATATTTA
12363787 ACCAAATGTATAATATT
1 ACCAAATGTATAATATT
12363804 ACCAAATGTATAATATT
1 ACCAAATGTATAATATT
12363821 AC
1 AC
12363823 TTGAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (17 bp):
ACCAAATGTATAATATT
Found at i:12364594 original size:2 final size:2
Alignment explanation
Indices: 12364587--12364628 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
12364577 ATTAATCTTT
12364587 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
12364629 CTTTGCCCAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:12371379 original size:210 final size:210
Alignment explanation
Indices: 12371017--12371438 Score: 844
Period size: 210 Copynumber: 2.0 Consensus size: 210
12371007 AACTGGAAGC
12371017 TTCTGATTTTGAGGTTGGTTTTCTCTTGTTCTTTCTGATCTATTGTTGGGTGTGTGATGCTTGTT
1 TTCTGATTTTGAGGTTGGTTTTCTCTTGTTCTTTCTGATCTATTGTTGGGTGTGTGATGCTTGTT
12371082 TCTGTTTCTCCTTGTTTGAATAAGCTGTTATTCTAAGTGAAACTAGATTGTATGTACAATTTTTT
66 TCTGTTTCTCCTTGTTTGAATAAGCTGTTATTCTAAGTGAAACTAGATTGTATGTACAATTTTTT
12371147 ATATGCATGATATCTTATCAACACAGTAAAATTAAGACTATTGTTGCTCTGCTATGCACTTGAAA
131 ATATGCATGATATCTTATCAACACAGTAAAATTAAGACTATTGTTGCTCTGCTATGCACTTGAAA
12371212 TCACTATTTAAATGA
196 TCACTATTTAAATGA
12371227 TTCTGATTTTGAGGTTGGTTTTCTCTTGTTCTTTCTGATCTATTGTTGGGTGTGTGATGCTTGTT
1 TTCTGATTTTGAGGTTGGTTTTCTCTTGTTCTTTCTGATCTATTGTTGGGTGTGTGATGCTTGTT
12371292 TCTGTTTCTCCTTGTTTGAATAAGCTGTTATTCTAAGTGAAACTAGATTGTATGTACAATTTTTT
66 TCTGTTTCTCCTTGTTTGAATAAGCTGTTATTCTAAGTGAAACTAGATTGTATGTACAATTTTTT
12371357 ATATGCATGATATCTTATCAACACAGTAAAATTAAGACTATTGTTGCTCTGCTATGCACTTGAAA
131 ATATGCATGATATCTTATCAACACAGTAAAATTAAGACTATTGTTGCTCTGCTATGCACTTGAAA
12371422 TCACTATTTAAATGA
196 TCACTATTTAAATGA
12371437 TT
1 TT
12371439 TTTTTTGCCA
Statistics
Matches: 212, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
210 212 1.00
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (210 bp):
TTCTGATTTTGAGGTTGGTTTTCTCTTGTTCTTTCTGATCTATTGTTGGGTGTGTGATGCTTGTT
TCTGTTTCTCCTTGTTTGAATAAGCTGTTATTCTAAGTGAAACTAGATTGTATGTACAATTTTTT
ATATGCATGATATCTTATCAACACAGTAAAATTAAGACTATTGTTGCTCTGCTATGCACTTGAAA
TCACTATTTAAATGA
Found at i:12374645 original size:6 final size:6
Alignment explanation
Indices: 12374636--12374674 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
12374626 AATGTTAACC
12374636 CACTTG CACTTG -AGCTTG CACTTG CACTTG CACTTG CAC
1 CACTTG CACTTG CA-CTTG CACTTG CACTTG CACTTG CAC
12374675 GGACCCTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 1 0.03
6 29 0.94
7 1 0.03
ACGTcount: A:0.18, C:0.33, G:0.18, T:0.31
Consensus pattern (6 bp):
CACTTG
Found at i:12379276 original size:21 final size:21
Alignment explanation
Indices: 12379250--12379291 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
12379240 AAGCATCCAC
12379250 ATTAGATGATACCCATAATAG
1 ATTAGATGATACCCATAATAG
12379271 ATTAGATGATACCCATAATAG
1 ATTAGATGATACCCATAATAG
12379292 CTCAGTCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (21 bp):
ATTAGATGATACCCATAATAG
Found at i:12400019 original size:23 final size:23
Alignment explanation
Indices: 12399971--12400021 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
12399961 ATAAACAATG
* *
12399971 TATACGAGGTTGCAAAAAAGCTA
1 TATACGAGGTTGCAAAAAAACCA
* *
12399994 TATATGAGGTTGTAAAAAAACCA
1 TATACGAGGTTGCAAAAAAACCA
12400017 TATAC
1 TATAC
12400022 AAGTTTTTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (23 bp):
TATACGAGGTTGCAAAAAAACCA
Found at i:12402073 original size:12 final size:12
Alignment explanation
Indices: 12402056--12402082 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12402046 TGTCCATCTT
12402056 TTCCTCTTCATC
1 TTCCTCTTCATC
12402068 TTCCTCTTCATC
1 TTCCTCTTCATC
12402080 TTC
1 TTC
12402083 AGCAACGCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.41, G:0.00, T:0.52
Consensus pattern (12 bp):
TTCCTCTTCATC
Found at i:12404982 original size:24 final size:23
Alignment explanation
Indices: 12404942--12404987 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
12404932 TAATTAAGAA
* *
12404942 AATTAATTAAATTTATTTTAATT
1 AATTAAATAAATATATTTTAATT
12404965 AATTAAATAAATAATATTTTAAT
1 AATTAAATAAAT-ATATTTTAAT
12404988 AAATAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AATTAAATAAATATATTTTAATT
Found at i:12404983 original size:28 final size:28
Alignment explanation
Indices: 12404930--12404983 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
12404920 GTGAAAATAA
*
12404930 TTTAATTAAGAAAATTAATTAAATTTAT
1 TTTAATTAAGAAAATTAAATAAATTTAT
**
12404958 TTTAATTAATTAAA-TAAATAATATTT
1 TTTAATTAAGAAAATTAAATAA-ATTT
12404984 TAATAAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
TTTAATTAAGAAAATTAAATAAATTTAT
Found at i:12405021 original size:22 final size:19
Alignment explanation
Indices: 12405002--12405038 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12404992 AGAAAATTAT
12405002 TTAT-TGAGTTGGATTAAA
1 TTATATGAGTTGGATTAAA
*
12405020 TTATATGAGTTGGTTTAAA
1 TTATATGAGTTGGATTAAA
12405039 GATCAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (19 bp):
TTATATGAGTTGGATTAAA
Found at i:12406999 original size:25 final size:25
Alignment explanation
Indices: 12406971--12407115 Score: 108
Period size: 25 Copynumber: 5.9 Consensus size: 25
12406961 TTAGCTTTCA
12406971 TGAGCATT-TCGATTAATGGCTCTCT
1 TGAGC-TTCTCGATTAATGGCTCTCT
* *
12406996 TGAGCTTCTCGA-TAATTGGTTCTCC
1 TGAGCTTCTCGATTAA-TGGCTCTCT
* *
12407021 GGAGCTTCCCGATTAATGGCTCTCT
1 TGAGCTTCTCGATTAATGGCTCTCT
* * *
12407046 AGAGCTTCTCGATGT--TGGCTCGCA
1 TGAGCTTCTCGAT-TAATGGCTCTCT
12407070 TGAGCTT-TCCGATT-ATGGCTCT-T
1 TGAGCTTCT-CGATTAATGGCTCTCT
*
12407093 ATGAGCTTCCCG-TTACATGGCTC
1 -TGAGCTTCTCGATTA-ATGGCTC
12407116 GAAAGAGCTT
Statistics
Matches: 96, Mismatches: 14, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
23 4 0.04
24 37 0.39
25 51 0.53
26 4 0.04
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.36
Consensus pattern (25 bp):
TGAGCTTCTCGATTAATGGCTCTCT
Found at i:12407055 original size:50 final size:49
Alignment explanation
Indices: 12406980--12407133 Score: 150
Period size: 49 Copynumber: 3.1 Consensus size: 49
12406970 ATGAGCATTT
* * * *
12406980 CGATTAATGGCTCTCTTGAGCTTCTCGATAATTGGTTCTCCGGAGCTTCC
1 CGATTAATGGCTCTCTAGAGCTTCTCGAT-ATTGGCTCGCAGGAGCTTCC
* * *
12407030 CGATTAATGGCTCTCTAGAGCTTCTCGATGTTGGCTCGCATGAGCTTTC
1 CGATTAATGGCTCTCTAGAGCTTCTCGATATTGGCTCGCAGGAGCTTCC
* * * * * *
12407079 CGATT-ATGGCTCT-TATGAGCTTCCCGTTACATGGCTCGAAAGAGCTTTC
1 CGATTAATGGCTCTCTA-GAGCTTCTCGATA-TTGGCTCGCAGGAGCTTCC
12407128 CGATTA
1 CGATTA
12407134 CATGCACTTA
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
47 2 0.02
48 18 0.20
49 40 0.45
50 28 0.32
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (49 bp):
CGATTAATGGCTCTCTAGAGCTTCTCGATATTGGCTCGCAGGAGCTTCC
Found at i:12407074 original size:24 final size:25
Alignment explanation
Indices: 12407022--12407133 Score: 78
Period size: 24 Copynumber: 4.6 Consensus size: 25
12407012 TGGTTCTCCG
*
12407022 GAGCTTC-CCGATTAATGGCTCTC-T
1 GAGCTTCTCCGATT-ATGGCTCGCAT
12407046 AGAGCTTCT-CGATGT-TGGCTCGCAT
1 -GAGCTTCTCCGAT-TATGGCTCGCAT
**
12407071 GAGCTT-TCCGATTATGGCTCTTAT
1 GAGCTTCTCCGATTATGGCTCGCAT
* *
12407095 GAGCTTC-CCG-TTACATGGCTCGAAA
1 GAGCTTCTCCGATT--ATGGCTCGCAT
12407120 GAGCTT-TCCGATTA
1 GAGCTTCTCCGATTA
12407134 CATGCACTTA
Statistics
Matches: 71, Mismatches: 6, Indels: 21
0.72 0.06 0.21
Matches are distributed among these distances:
23 4 0.06
24 35 0.49
25 29 0.41
26 3 0.04
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (25 bp):
GAGCTTCTCCGATTATGGCTCGCAT
Found at i:12411098 original size:37 final size:38
Alignment explanation
Indices: 12411045--12411121 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 38
12411035 TTTGAAGTAA
* * *
12411045 TAAATTGACACCCAGTGTCTCATCG-GCTAAACCGAAG
1 TAAATTGACACACAGTGCCTCATCGAACTAAACCGAAG
* *
12411082 TAAATTGGCACACAGTGCCTCATCGAACTAATCCGAAG
1 TAAATTGACACACAGTGCCTCATCGAACTAAACCGAAG
12411120 TA
1 TA
12411122 GTAAATTGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
37 22 0.65
38 12 0.35
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (38 bp):
TAAATTGACACACAGTGCCTCATCGAACTAAACCGAAG
Found at i:12411278 original size:16 final size:16
Alignment explanation
Indices: 12411257--12411300 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
12411247 TAATAATATC
*
12411257 CAATATCATATTTGCA
1 CAATATCATATTTACA
*
12411273 CAATATTATATTTACA
1 CAATATCATATTTACA
12411289 CATATATTCATA
1 CA-ATA-TCATA
12411301 ATATATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 16 0.70
17 3 0.13
18 4 0.17
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.41
Consensus pattern (16 bp):
CAATATCATATTTACA
Found at i:12412108 original size:12 final size:13
Alignment explanation
Indices: 12412091--12412151 Score: 56
Period size: 13 Copynumber: 4.7 Consensus size: 13
12412081 GTTCTTTCTA
12412091 TTCTTT-TTTATT
1 TTCTTTATTTATT
12412103 TTCTTTATTTA-T
1 TTCTTTATTTATT
*
12412115 TTCATTTACTTATT
1 TTC-TTTATTTATT
12412129 TAT-TTTATTATATT
1 T-TCTTTATT-TATT
*
12412143 TACTTTATT
1 TTCTTTATT
12412152 ATTATATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
12 10 0.25
13 16 0.40
14 13 0.32
15 1 0.03
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (13 bp):
TTCTTTATTTATT
Found at i:12412135 original size:22 final size:21
Alignment explanation
Indices: 12412106--12412172 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 21
12412096 TTTTATTTTC
12412106 TTTATTTATT-TCATTTACTTA
1 TTTATTTATTAT-ATTTACTTA
12412127 TTTATTTTATTATATTTACTT-
1 TTTA-TTTATTATATTTACTTA
12412148 TATTATTATATTATATATTTACTTA
1 T-TTATT-TA-T-TATATTTACTTA
12412173 AATATTAAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
21 7 0.18
22 19 0.49
23 2 0.05
24 11 0.28
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTATTTATTATATTTACTTA
Found at i:12412178 original size:24 final size:25
Alignment explanation
Indices: 12412128--12412179 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
12412118 ATTTACTTAT
* * *
12412128 TTATTTTATTATATTTACTTTATTA
1 TTATATTATTATATTTACTTAAATA
12412153 TTATATTA-TATATTTACTTAAATA
1 TTATATTATTATATTTACTTAAATA
12412177 TTA
1 TTA
12412180 AGTAATACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (25 bp):
TTATATTATTATATTTACTTAAATA
Found at i:12414395 original size:30 final size:30
Alignment explanation
Indices: 12414359--12414415 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
12414349 TCTTACAAAC
12414359 AATTTATA-TTAATTACATCAAAATATTTAA
1 AATTTATATTTAATT-CATCAAAATATTTAA
* *
12414389 AATTTATATTTCATTTATCAAAATATT
1 AATTTATATTTAATTCATCAAAATATT
12414416 AATAATATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 19 0.79
31 5 0.21
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (30 bp):
AATTTATATTTAATTCATCAAAATATTTAA
Found at i:12415512 original size:6 final size:6
Alignment explanation
Indices: 12415496--12415526 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
12415486 ATTGCTGTCA
*
12415496 TCAGTC CCAGTC TCAGTC TCAGTC TCAGTC T
1 TCAGTC TCAGTC TCAGTC TCAGTC TCAGTC T
12415527 ACCTGTGGCG
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:0.16, C:0.35, G:0.16, T:0.32
Consensus pattern (6 bp):
TCAGTC
Found at i:12419173 original size:20 final size:20
Alignment explanation
Indices: 12419148--12419188 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12419138 CACATTGACC
* *
12419148 ATGACATGGCAGATTCATCA
1 ATGACATAGCACATTCATCA
*
12419168 ATGACATAGCACATTGATCA
1 ATGACATAGCACATTCATCA
12419188 A
1 A
12419189 GTTGATTGTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (20 bp):
ATGACATAGCACATTCATCA
Found at i:12419312 original size:11 final size:9
Alignment explanation
Indices: 12419295--12419384 Score: 56
Period size: 10 Copynumber: 9.0 Consensus size: 9
12419285 ATGAAAAAGC
12419295 ATTTTAAAA
1 ATTTTAAAA
12419304 ATTAGTTAATAA
1 ATT--TTAA-AA
*
12419316 ATTTTAAATT
1 ATTTTAAA-A
*
12419326 TTATTTAAAA
1 AT-TTTAAAA
12419336 AGTTTTAAAAA
1 A-TTTT-AAAA
12419347 ATTGTTAAAA
1 ATT-TTAAAA
*
12419357 A-ATTAAAA
1 ATTTTAAAA
12419365 ATTTGTAAAA
1 ATTT-TAAAA
12419375 ATTTATAAAA
1 ATTT-TAAAA
12419385 TGTAAATTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 19
0.71 0.08 0.21
Matches are distributed among these distances:
8 7 0.11
9 5 0.08
10 29 0.45
11 18 0.28
12 5 0.08
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:12419319 original size:21 final size:20
Alignment explanation
Indices: 12419295--12419384 Score: 78
Period size: 21 Copynumber: 4.5 Consensus size: 20
12419285 ATGAAAAAGC
12419295 ATTTTAAAAATTAGTTAATAA
1 ATTTTAAAAATTAGTTAA-AA
** *
12419316 ATTTTAAATTTTATTTAAAA
1 ATTTTAAAAATTAGTTAAAA
12419336 AGTTTTAAAAAATT-GTTAAAA
1 A-TTTT-AAAAATTAGTTAAAA
* *
12419357 A-ATTAAAAATTTG-TAAAA
1 ATTTTAAAAATTAGTTAAAA
12419375 ATTTATAAAA
1 ATTT-TAAAA
12419385 TGTAAATTTT
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
18 13 0.23
19 4 0.07
20 8 0.14
21 26 0.46
22 5 0.09
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.42
Consensus pattern (20 bp):
ATTTTAAAAATTAGTTAAAA
Found at i:12419364 original size:19 final size:18
Alignment explanation
Indices: 12419340--12419390 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
12419330 TTAAAAAGTT
12419340 TTAAAAAATTGTTAAAAAA
1 TTAAAAAATTG-TAAAAAA
* *
12419359 TTAAAAATTTGTAAAAAT
1 TTAAAAAATTGTAAAAAA
*
12419377 TTATAAAA-TGTAAA
1 TTAAAAAATTGTAAA
12419391 TTTTGTTTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 6 0.21
18 12 0.43
19 10 0.36
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (18 bp):
TTAAAAAATTGTAAAAAA
Found at i:12419366 original size:18 final size:18
Alignment explanation
Indices: 12419340--12419385 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
12419330 TTAAAAAGTT
*
12419340 TTAAAAAATTGTTAAAAAA
1 TTAAAAATTTG-TAAAAAA
*
12419359 TTAAAAATTTGTAAAAAT
1 TTAAAAATTTGTAAAAAA
12419377 TTATAAAAT
1 TTA-AAAAT
12419386 GTAAATTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (18 bp):
TTAAAAATTTGTAAAAAA
Done.