Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 97 of 163
Found at i:27488996 original size:25 final size:25
Alignment explanation
Indices: 27488961--27489014 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
27488951 AAATAATTAT
*
27488961 TTTTATATTAAATTATACTAAAATA
1 TTTTATATTAAATTATATTAAAATA
* *
27488986 TTTTATTTTAAATTATATTACAATA
1 TTTTATATTAAATTATATTAAAATA
27489011 TTTT
1 TTTT
27489015 TTAGTTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTTATATTAAATTATATTAAAATA
Found at i:27489095 original size:28 final size:30
Alignment explanation
Indices: 27488979--27489098 Score: 83
Period size: 28 Copynumber: 4.1 Consensus size: 30
27488969 TAAATTATAC
*
27488979 TAAAATATTTTATTTTAAATTATA-TTACAA
1 TAAAATA-TTTATTTTAAATTATATTTAAAA
* * * * * *
27489009 T--ATTTTTTAGTTTTATATTA-AATTATAT
1 TAAAATATTTA-TTTTAAATTATATTTAAAA
27489037 TAAAATATTTAATTTTAAATTATATTTTAAAA
1 TAAAATATTT-ATTTTAAATTATA-TTTAAAA
27489069 TAAAATATTT-TTGTTAAATT-TA-TTAAAA
1 TAAAATATTTATT-TTAAATTATATTTAAAA
27489097 TA
1 TA
27489099 TTTCAAACAA
Statistics
Matches: 71, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
27 5 0.07
28 24 0.34
30 19 0.27
31 9 0.13
32 14 0.20
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (30 bp):
TAAAATATTTATTTTAAATTATATTTAAAA
Found at i:27493932 original size:21 final size:21
Alignment explanation
Indices: 27493906--27493945 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27493896 GATACTTGAT
*
27493906 AAAAGGTATCGATACTTTTGG
1 AAAAGGTATCAATACTTTTGG
*
27493927 AAAAGGTATCAATTCTTTT
1 AAAAGGTATCAATACTTTT
27493946 TGTCATTGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (21 bp):
AAAAGGTATCAATACTTTTGG
Found at i:27494876 original size:17 final size:17
Alignment explanation
Indices: 27494851--27494925 Score: 98
Period size: 17 Copynumber: 4.5 Consensus size: 17
27494841 ACCCATTTCT
*
27494851 TTTAGATTTATTTTAAG
1 TTTAAATTTATTTTAAG
*
27494868 TTTAAATTTGTTTTAA-
1 TTTAAATTTATTTTAAG
*
27494884 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAG
* *
27494901 TTTAAATTTATTCTAAA
1 TTTAAATTTATTTTAAG
27494918 TTTAAATT
1 TTTAAATT
27494926 AATAATGTCC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
16 14 0.28
17 36 0.72
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAG
Found at i:27494899 original size:33 final size:34
Alignment explanation
Indices: 27494851--27494925 Score: 107
Period size: 33 Copynumber: 2.2 Consensus size: 34
27494841 ACCCATTTCT
* * * *
27494851 TTTAGATTTATTTTAAGTTTAAATTTGTT-TTAA
1 TTTAAATTTAATTTAAGTTTAAATTTATTCTAAA
27494884 TTTAAATTTAATTTAAGTTTAAATTTATTCTAAA
1 TTTAAATTTAATTTAAGTTTAAATTTATTCTAAA
27494918 TTTAAATT
1 TTTAAATT
27494926 AATAATGTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 26 0.70
34 11 0.30
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.57
Consensus pattern (34 bp):
TTTAAATTTAATTTAAGTTTAAATTTATTCTAAA
Found at i:27496775 original size:29 final size:29
Alignment explanation
Indices: 27496671--27497011 Score: 234
Period size: 30 Copynumber: 11.7 Consensus size: 29
27496661 CTGAACTATC
* * *
27496671 CAAAAATAACATTTTAAACCCTACACTTTT
1 CAAAAATTACATTTT-AACCCTAAACTTCT
* * * * *
27496701 CCAAAATCATATTTTGACCCTCGAACTTCT
1 CAAAAATTACATTTTAACCCT-AAACTTCT
* * *
27496731 CGAAAATTATATTTTTACCTCTAAACTTCT
1 CAAAAATTACATTTTAACC-CTAAACTTCT
* * *
27496761 CAAAAATCACATTTTGACCTTCAAACTTCT
1 CAAAAATTACATTTTAACCCT-AAACTTCT
27496791 CAAAAATTACATTTT--CCCTTAAACTTC-
1 CAAAAATTACATTTTAACCC-TAAACTTCT
* * *
27496818 CAAAAATTATATTTCTACCCCCAAACTTCT
1 CAAAAATTACATTT-TAACCCTAAACTTCT
*
27496848 -AAAAATCACATTTTAACCCCTAAACTTCT
1 CAAAAATTACATTTTAA-CCCTAAACTTCT
*
27496877 CAAAAATTACATTTTTAACCATAAACTTCT
1 CAAAAATTACA-TTTTAACCCTAAACTTCT
* * *
27496907 TAAAAATTACATTTT-TCCCTCGAACTTC-
1 CAAAAATTACATTTTAACCCT-AAACTTCT
* *
27496935 CAAAAA-T-CATGTTTTACCCTAAA-TTTT
1 CAAAAATTACAT-TTTAACCCTAAACTTCT
* * * *
27496962 CCCAAAATGACATTTTTACCTTCAAAACTT-T
1 -CAAAAATTACATTTTAACC--CTAAACTTCT
*
27496993 CCAAAATTACATTTTAACC
1 CAAAAATTACATTTTAACC
27497012 TCAAACTCTC
Statistics
Matches: 251, Mismatches: 39, Indels: 42
0.76 0.12 0.13
Matches are distributed among these distances:
26 5 0.02
27 19 0.08
28 29 0.12
29 53 0.21
30 130 0.52
31 13 0.05
32 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (29 bp):
CAAAAATTACATTTTAACCCTAAACTTCT
Found at i:27496953 original size:116 final size:116
Alignment explanation
Indices: 27496699--27497036 Score: 323
Period size: 116 Copynumber: 2.9 Consensus size: 116
27496689 CCCTACACTT
* * * * * * *
27496699 TTCC-AAAATCATATTTTGACCCTCGAACTTCTCGAAAATTATATTTTTACCTCTAAACTTCTCA
1 TTCCAAAAATCATATTTT-ACCCCCAAACTTCTCAAAAATCACATTTTAACCCCTAAACTTCTCA
* * *
27496763 AAAATCACATTTTGACCTTCAAACTTCTCAAAAATTACATTTTCCCTTAAAC
65 AAAATCACATTTTAACCATCAAACTTCTCAAAAATTACATTTTCCCTCAAAC
*
27496815 TTCCAAAAATTATATTTCTACCCCCAAACTTCT-AAAAATCACATTTTAACCCCTAAACTTCTCA
1 TTCCAAAAATCATATTT-TACCCCCAAACTTCTCAAAAATCACATTTTAACCCCTAAACTTCTCA
* * *
27496879 AAAATTACATTTTTAACCAT-AAACTTCTTAAAAATTACATTTTTCCCTCGAAC
65 AAAATCACA-TTTTAACCATCAAACTTCTCAAAAATTACA-TTTTCCCTCAAAC
* * * * * * * *
27496932 TTCCAAAAATCATGTTTTA-CCCTAAA-TTTTCCCAAAATGACATTTTTACCTTCAAAACTT-TC
1 TTCCAAAAATCATATTTTACCCCCAAACTTCT-CAAAAATCACATTTTAACC-CCTAAACTTCTC
* * ** *
27496994 CAAAATTACATTTTAACC-TCAAAC-TCTCTGAAATTTCATTTTC
64 AAAAATCACATTTTAACCATCAAACTTCTCAAAAATTACATTTTC
27497037 GACCCAATTT
Statistics
Matches: 186, Mismatches: 28, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
113 5 0.03
114 14 0.08
115 18 0.10
116 84 0.45
117 64 0.34
118 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (116 bp):
TTCCAAAAATCATATTTTACCCCCAAACTTCTCAAAAATCACATTTTAACCCCTAAACTTCTCAA
AAATCACATTTTAACCATCAAACTTCTCAAAAATTACATTTTCCCTCAAAC
Found at i:27497146 original size:14 final size:15
Alignment explanation
Indices: 27497107--27497154 Score: 64
Period size: 14 Copynumber: 3.3 Consensus size: 15
27497097 TAATTTTCTC
27497107 ATTTATTTTTTCGTAT
1 ATTTA-TTTTTCGTAT
*
27497123 -TTTATTTTTCTTAT
1 ATTTATTTTTCGTAT
27497137 ATTTA-TTTTCGTAT
1 ATTTATTTTTCGTAT
27497151 ATTT
1 ATTT
27497155 GTTCGTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 21 0.72
15 8 0.28
ACGTcount: A:0.19, C:0.06, G:0.04, T:0.71
Consensus pattern (15 bp):
ATTTATTTTTCGTAT
Found at i:27497386 original size:97 final size:97
Alignment explanation
Indices: 27497277--27497470 Score: 309
Period size: 97 Copynumber: 2.0 Consensus size: 97
27497267 AAAATATTTA
* * *
27497277 AAATCGAGGCAATATTCTTTTATTTC-GGATTTTGAAAATTCGTGCCTTAACTTACTAGGCATGA
1 AAATCGAAGCAATATTCCTTTATTTCAGG-TTTTGAAAATTCGTGCCTTAACTTACTAGGCACGA
* *
27497341 TTTTTCTTCAAACCGGGATAATCGAATACCCTT
65 CTTTTCTTCAAACCGAGATAATCGAATACCCTT
*
27497374 AAATCGAAGCAATATTCCTTTATTTCAGGTTTTGAAAATTTGTGCCTTAACTTACTAGGCACGAC
1 AAATCGAAGCAATATTCCTTTATTTCAGGTTTTGAAAATTCGTGCCTTAACTTACTAGGCACGAC
*
27497439 TTTTCTTCAAACTGAGATAATCGAATACCCTT
66 TTTTCTTCAAACCGAGATAATCGAATACCCTT
27497471 TTTCAAGGTT
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
97 87 0.98
98 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (97 bp):
AAATCGAAGCAATATTCCTTTATTTCAGGTTTTGAAAATTCGTGCCTTAACTTACTAGGCACGAC
TTTTCTTCAAACCGAGATAATCGAATACCCTT
Found at i:27504650 original size:14 final size:14
Alignment explanation
Indices: 27504631--27504658 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
27504621 GGCTATAATG
27504631 ATCACTAATGTGAA
1 ATCACTAATGTGAA
27504645 ATCACTAATGTGAA
1 ATCACTAATGTGAA
27504659 TTTTTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
ATCACTAATGTGAA
Found at i:27510880 original size:24 final size:24
Alignment explanation
Indices: 27510844--27510889 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
27510834 ACATTCATCC
* *
27510844 AATTCATGCATTA-GCATTCAAAAG
1 AATTCAAGAATTACGCA-TCAAAAG
27510868 AATTCAAGAATTACGCATCAAA
1 AATTCAAGAATTACGCATCAAA
27510890 TGAAAAATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (24 bp):
AATTCAAGAATTACGCATCAAAAG
Found at i:27525939 original size:21 final size:21
Alignment explanation
Indices: 27525860--27525949 Score: 92
Period size: 21 Copynumber: 4.2 Consensus size: 21
27525850 AGCATTGTTG
* * * *
27525860 TTGTTGTTGTTGCTATTTTTG
1 TTGTAGTTGTTGTTGTTTTTA
*
27525881 TTGTAGTTGTTG-TGTTTTTG
1 TTGTAGTTGTTGTTGTTTTTA
*
27525901 TTGTTGATATTGTTGTTGTTTTTA
1 TTG-T-A-GTTGTTGTTGTTTTTA
27525925 TTGTAGTTGTTGTTGTTTTTA
1 TTGTAGTTGTTGTTGTTTTTA
27525946 TTGT
1 TTGT
27525950 TACTGTTGTT
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
20 10 0.17
21 31 0.52
22 2 0.03
23 7 0.12
24 10 0.17
ACGTcount: A:0.08, C:0.01, G:0.24, T:0.67
Consensus pattern (21 bp):
TTGTAGTTGTTGTTGTTTTTA
Found at i:27525956 original size:21 final size:21
Alignment explanation
Indices: 27525911--27525959 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
27525901 TTGTTGATAT
*
27525911 TGTTGTTGTTTTTATTGTAGT
1 TGTTGTTGTTTTTATTGTAGC
27525932 TGTTGTTGTTTTTATTGTTA-C
1 TGTTGTTGTTTTTATTG-TAGC
27525953 TGTTGTT
1 TGTTGTT
27525960 ATGGCTGCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.08, C:0.02, G:0.22, T:0.67
Consensus pattern (21 bp):
TGTTGTTGTTTTTATTGTAGC
Found at i:27525959 original size:3 final size:3
Alignment explanation
Indices: 27525854--27525941 Score: 79
Period size: 3 Copynumber: 29.7 Consensus size: 3
27525844 AGATCTAGCA
* * * * *
27525854 TTG TTG TTG TTG TTG TTG CTA TTT TTG TTG TAG TTG TTG -TG TTT TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
* * * * *
27525901 TTG TTG ATA TTG TTG TTG TTT TTA TTG TAG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
27525942 TTTATTGTTA
Statistics
Matches: 66, Mismatches: 18, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
2 2 0.03
3 64 0.97
ACGTcount: A:0.07, C:0.01, G:0.26, T:0.66
Consensus pattern (3 bp):
TTG
Found at i:27526007 original size:18 final size:18
Alignment explanation
Indices: 27525970--27526008 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
27525960 ATGGCTGCAA
* *
27525970 CTTGTTTTTTAAATTTTT
1 CTTGTTTTTGAAATTGTT
*
27525988 CTTGTTTTTGAAGTTGTT
1 CTTGTTTTTGAAATTGTT
27526006 CTT
1 CTT
27526009 ACTGTTATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.08, G:0.13, T:0.67
Consensus pattern (18 bp):
CTTGTTTTTGAAATTGTT
Found at i:27526045 original size:3 final size:3
Alignment explanation
Indices: 27526039--27526145 Score: 90
Period size: 3 Copynumber: 35.7 Consensus size: 3
27526029 GCTGCTGCTA
* * * * * * *
27526039 TTG TTG TTA TTG TTG TTG TTG TTG TGG TTG TTA TTA TTG ATG TAG TTA
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
* * * * *
27526087 TTG TTG TAG TTG TTC TTT TTA TTG TTG TTT TTG TTG TTG TTG CTT-
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG -TTG
27526132 TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TT
27526146 ATAGCTATTT
Statistics
Matches: 82, Mismatches: 20, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
2 2 0.02
3 78 0.95
4 2 0.02
ACGTcount: A:0.07, C:0.02, G:0.25, T:0.65
Consensus pattern (3 bp):
TTG
Found at i:27526051 original size:9 final size:9
Alignment explanation
Indices: 27526037--27526176 Score: 69
Period size: 9 Copynumber: 15.9 Consensus size: 9
27526027 TTGCTGCTGC
27526037 TATTGTTGT
1 TATTGTTGT
27526046 TATTGTTGT
1 TATTGTTGT
*
27526055 TGTTGTTGT
1 TATTGTTGT
** *
27526064 GGTTGTTAT
1 TATTGTTGT
27526073 TATTGATGTAGT
1 TATTG-T-T-GT
27526085 TATTGTTG-
1 TATTGTTGT
27526093 TA--GTTGT
1 TATTGTTGT
*
27526100 T-CT-TT-T
1 TATTGTTGT
27526106 TATTGTTGT
1 TATTGTTGT
*
27526115 TTTTGTTGT
1 TATTGTTGT
*
27526124 TGTTGCTT-T
1 TATTG-TTGT
*
27526133 TGTTGTTGT
1 TATTGTTGT
* * * *
27526142 TGTTATAGC
1 TATTGTTGT
* *
27526151 TATTTTTAT
1 TATTGTTGT
27526160 TATTGTTGT
1 TATTGTTGT
27526169 TATTGTTG
1 TATTGTTG
27526177 CTGATGATGT
Statistics
Matches: 101, Mismatches: 19, Indels: 22
0.71 0.13 0.15
Matches are distributed among these distances:
6 6 0.06
7 4 0.04
8 6 0.06
9 73 0.72
10 4 0.04
11 2 0.02
12 6 0.06
ACGTcount: A:0.11, C:0.02, G:0.23, T:0.64
Consensus pattern (9 bp):
TATTGTTGT
Found at i:27526056 original size:12 final size:12
Alignment explanation
Indices: 27526039--27526176 Score: 82
Period size: 12 Copynumber: 11.2 Consensus size: 12
27526029 GCTGCTGCTA
27526039 TTGTTGTTATTG
1 TTGTTGTTATTG
*
27526051 TTGTTGTTGTTG
1 TTGTTGTTATTG
* *
27526063 TGGTTGTTATTA
1 TTGTTGTTATTG
* *
27526075 TTGATG-TAGTTA
1 TTGTTGTTA-TTG
27526087 TTGTTG-TAGTTG
1 TTGTTGTTA-TTG
* *
27526099 TTCTTTTTATTG
1 TTGTTGTTATTG
* *
27526111 TTGTTTTTGTTG
1 TTGTTGTTATTG
*
27526123 TTGTTGCTTTTGTTG
1 TTGTTG---TTATTG
*
27526138 TTGTTGTTATAG
1 TTGTTGTTATTG
* * * *
27526150 CTATTTTTATTA
1 TTGTTGTTATTG
27526162 TTGTTGTTATTG
1 TTGTTGTTATTG
27526174 TTG
1 TTG
27526177 CTGATGATGT
Statistics
Matches: 97, Mismatches: 24, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
11 2 0.02
12 81 0.84
13 2 0.02
15 12 0.12
ACGTcount: A:0.10, C:0.02, G:0.23, T:0.64
Consensus pattern (12 bp):
TTGTTGTTATTG
Found at i:27526283 original size:21 final size:21
Alignment explanation
Indices: 27526234--27526284 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
27526224 ATTGCTGTAA
*
27526234 TTTTTGTTGCTGCTACTATTG
1 TTTTTGTTGATGCTACTATTG
** * *
27526255 TTGATGTTGATGTTGCTATTG
1 TTTTTGTTGATGCTACTATTG
27526276 TTTTTGTTG
1 TTTTTGTTG
27526285 TTGTAGCAAT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.10, C:0.08, G:0.24, T:0.59
Consensus pattern (21 bp):
TTTTTGTTGATGCTACTATTG
Found at i:27533457 original size:19 final size:19
Alignment explanation
Indices: 27533433--27533538 Score: 115
Period size: 19 Copynumber: 5.6 Consensus size: 19
27533423 AATATATTGA
*
27533433 ACTGGCTCATAAGAGCAAT
1 ACTGGCTCGTAAGAGCAAT
*
27533452 ACTGGCTCGTGAGAGCAAT
1 ACTGGCTCGTAAGAGCAAT
* *
27533471 ACTGGCTCGTGAGAGTAAT
1 ACTGGCTCGTAAGAGCAAT
* * *
27533490 ACAGACTCGTAGGAGCAAT
1 ACTGGCTCGTAAGAGCAAT
*
27533509 ACTGGCTCGTGAGTA-CAAT
1 ACTGGCTCGTAAG-AGCAAT
*
27533528 ATTGGCTCGTA
1 ACTGGCTCGTA
27533539 TGGTTTGATA
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
19 71 0.99
20 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (19 bp):
ACTGGCTCGTAAGAGCAAT
Found at i:27533537 original size:38 final size:39
Alignment explanation
Indices: 27533433--27533538 Score: 128
Period size: 38 Copynumber: 2.8 Consensus size: 39
27533423 AATATATTGA
* *
27533433 ACTGGCTCATAAGAGCAATACTGGCTCGT-GAGAGCAAT
1 ACTGGCTCGTGAGAGCAATACTGGCTCGTAGAGAGCAAT
* * *
27533471 ACTGGCTCGTGAGAGTAATACAGACTCGTAG-GAGCAAT
1 ACTGGCTCGTGAGAGCAATACTGGCTCGTAGAGAGCAAT
*
27533509 ACTGGCTCGTGAGTA-CAATATTGGCTCGTA
1 ACTGGCTCGTGAG-AGCAATACTGGCTCGTA
27533539 TGGTTTGATA
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 55 0.96
39 2 0.04
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (39 bp):
ACTGGCTCGTGAGAGCAATACTGGCTCGTAGAGAGCAAT
Found at i:27535289 original size:11 final size:11
Alignment explanation
Indices: 27535273--27535299 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
27535263 TGAAATCAAG
27535273 TATTTTCATAA
1 TATTTTCATAA
27535284 TATTTTCATAA
1 TATTTTCATAA
27535295 TATTT
1 TATTT
27535300 AGTGAGATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (11 bp):
TATTTTCATAA
Found at i:27536702 original size:33 final size:32
Alignment explanation
Indices: 27536655--27536770 Score: 83
Period size: 33 Copynumber: 3.5 Consensus size: 32
27536645 GCTGCTATTA
* * *
27536655 TTGTTGATGTTATTGCTATTACTATTATTTTTG
1 TTGTTGTTGCTATTGATATTACT-TTATTTTTG
*
27536688 TTGTTGTTGCTATTGATATTGA-TGTT-TTTGTTA
1 TTGTTGTTGCTATTGATATT-ACT-TTATTT-TTG
* * * * * *
27536721 TTGTTGTAGCTACTGTTATTGCTTCTAATGTTG
1 TTGTTGTTGCTATTGATATTACTT-TATTTTTG
27536754 TTGTTGTTGCTATTGAT
1 TTGTTGTTGCTATTGAT
27536771 GGTGTTGTTA
Statistics
Matches: 63, Mismatches: 15, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
32 4 0.06
33 57 0.90
34 2 0.03
ACGTcount: A:0.16, C:0.07, G:0.20, T:0.58
Consensus pattern (32 bp):
TTGTTGTTGCTATTGATATTACTTTATTTTTG
Found at i:27536707 original size:27 final size:27
Alignment explanation
Indices: 27536649--27536701 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
27536639 GTCACTGCTG
* * *
27536649 CTATTATTGTTGATGTTATTGCTATTA
1 CTATTATTTTTGTTGTTGTTGCTATTA
27536676 CTATTATTTTTGTTGTTGTTGCTATT
1 CTATTATTTTTGTTGTTGTTGCTATT
27536702 GATATTGATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.17, C:0.08, G:0.15, T:0.60
Consensus pattern (27 bp):
CTATTATTTTTGTTGTTGTTGCTATTA
Found at i:27536718 original size:27 final size:27
Alignment explanation
Indices: 27536649--27536723 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 27
27536639 GTCACTGCTG
*
27536649 CTATTAT-TGTTGATGTTATTGCTATTA
1 CTATTATGT-TTGTTGTTATTGCTATTA
* *
27536676 CTATTATTTTTGTTGTTGTTGCTATTGA
1 CTATTATGTTTGTTGTTATTGCTATT-A
27536704 -TATTGATGTTT-TTGTTATTG
1 CTATT-ATGTTTGTTGTTATTG
27536724 TTGTAGCTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 34 0.83
28 7 0.17
ACGTcount: A:0.17, C:0.05, G:0.17, T:0.60
Consensus pattern (27 bp):
CTATTATGTTTGTTGTTATTGCTATTA
Found at i:27536788 original size:33 final size:33
Alignment explanation
Indices: 27536679--27536788 Score: 98
Period size: 33 Copynumber: 3.3 Consensus size: 33
27536669 GCTATTACTA
*
27536679 TTATTTTTGTTGTTGTTGCTATTGATATTGATG
1 TTATTTTTGTTGTTGTTGCTATTGATATTGTTG
* * * *
27536712 TT-TTTGTTATTGTTGTAGCTACTGTTATTGCTT-
1 TTATTT-TTGTTGTTGTTGCTATTGATATTG-TTG
* * * **
27536745 CTAATGTTGTTGTTGTTGCTATTGATGGTGTTG
1 TTATTTTTGTTGTTGTTGCTATTGATATTGTTG
27536778 TTATTTTTGTT
1 TTATTTTTGTT
27536789 ATAGATTTTA
Statistics
Matches: 56, Mismatches: 17, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
32 5 0.09
33 49 0.88
34 2 0.04
ACGTcount: A:0.13, C:0.05, G:0.22, T:0.60
Consensus pattern (33 bp):
TTATTTTTGTTGTTGTTGCTATTGATATTGTTG
Found at i:27536868 original size:21 final size:21
Alignment explanation
Indices: 27536814--27536869 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
27536804 GATATTGTAT
* *
27536814 TATTGTTGATTTTGTTGTTAC
1 TATTATTGATGTTGTTGTTAC
*
27536835 TATTATT-ATTGTTGTTGTT-T
1 TATTATTGA-TGTTGTTGTTAC
27536855 TAGTTATTGATGTTG
1 TA-TTATTGATGTTG
27536870 CTACTACTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 3 0.10
21 25 0.86
22 1 0.03
ACGTcount: A:0.16, C:0.02, G:0.20, T:0.62
Consensus pattern (21 bp):
TATTATTGATGTTGTTGTTAC
Found at i:27536957 original size:21 final size:20
Alignment explanation
Indices: 27536933--27536985 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
27536923 ATTATTACTA
*
27536933 TTGTTACTATTTTTATTGATG
1 TTGTTA-TATTATTATTGATG
* *
27536954 TTGTTATGTCTATTATTGTTG
1 TTGTTATAT-TATTATTGATG
27536975 TTGTTAATATT
1 TTGTT-ATATT
27536986 GTTGTTGCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 2 0.08
21 21 0.81
22 3 0.12
ACGTcount: A:0.19, C:0.04, G:0.15, T:0.62
Consensus pattern (20 bp):
TTGTTATATTATTATTGATG
Found at i:27537002 original size:15 final size:15
Alignment explanation
Indices: 27536963--27537132 Score: 78
Period size: 15 Copynumber: 11.1 Consensus size: 15
27536953 GTTGTTATGT
27536963 CTATTATTGTTGTTG
1 CTATTATTGTTGTTG
* *
27536978 TTAATATTGTTGTTG
1 CTATTATTGTTGTTG
* *
27536993 CTATTGTTGTTGGTG
1 CTATTATTGTTGTTG
*
27537008 GTGATGGTGA-TGTTGTTG
1 CT-AT--T-ATTGTTGTTG
**
27537026 CTGCTATTGTTGTTG
1 CTATTATTGTTGTTG
* * *
27537041 ATATTATTGTTATTA
1 CTATTATTGTTGTTG
* *
27537056 TTGATGT-TT-TTGTTA
1 CT-AT-TATTGTTGTTG
* *
27537071 CTACTATAGTTGTTG
1 CTATTATTGTTGTTG
*
27537086 TTATTGA-TGTTGTTG
1 CTATT-ATTGTTGTTG
* * *
27537101 CTAATATTGTTGCTA
1 CTATTATTGTTGTTG
*
27537116 TTATTATTGTTGTTG
1 CTATTATTGTTGTTG
27537131 CT
1 CT
27537133 GCTGTTATTT
Statistics
Matches: 109, Mismatches: 35, Indels: 22
0.66 0.21 0.13
Matches are distributed among these distances:
13 1 0.01
14 4 0.04
15 87 0.80
16 7 0.06
17 1 0.01
18 9 0.08
ACGTcount: A:0.16, C:0.05, G:0.23, T:0.56
Consensus pattern (15 bp):
CTATTATTGTTGTTG
Found at i:27537004 original size:12 final size:12
Alignment explanation
Indices: 27536972--27537051 Score: 61
Period size: 12 Copynumber: 6.7 Consensus size: 12
27536962 TCTATTATTG
*
27536972 TTGTTGTTAATA
1 TTGTTGTTGATA
*
27536984 TTGTTGTTGCTA
1 TTGTTGTTGATA
* *
27536996 TTGTTGTTGGTG
1 TTGTTGTTGATA
* * * *
27537008 GTGATGGTGATG
1 TTGTTGTTGATA
* *
27537020 TTGTTGCTGCTA
1 TTGTTGTTGATA
27537032 TTGTTGTTGATA
1 TTGTTGTTGATA
*
27537044 TTATTGTT
1 TTGTTGTT
27537052 ATTATTGATG
Statistics
Matches: 52, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 52 1.00
ACGTcount: A:0.12, C:0.04, G:0.29, T:0.55
Consensus pattern (12 bp):
TTGTTGTTGATA
Found at i:27537128 original size:18 final size:18
Alignment explanation
Indices: 27537107--27537192 Score: 54
Period size: 18 Copynumber: 4.8 Consensus size: 18
27537097 GTTGCTAATA
27537107 TTGTTGCTATTATTATTG
1 TTGTTGCTATTATTATTG
*
27537125 TTGTTGCTGCTGTTATT-TGTG
1 TTG-T--TGCTATTATTAT-TG
** *
27537146 TTGTTGCTGCTGTTATTG
1 TTGTTGCTATTATTATTG
* *
27537164 TTGTAG---TTATTGTTG
1 TTGTTGCTATTATTATTG
27537179 TTGTTGCTATTATT
1 TTGTTGCTATTATT
27537193 TTTATTGTAA
Statistics
Matches: 52, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
15 11 0.21
18 23 0.44
19 2 0.04
20 2 0.04
21 14 0.27
ACGTcount: A:0.10, C:0.07, G:0.23, T:0.59
Consensus pattern (18 bp):
TTGTTGCTATTATTATTG
Found at i:27537140 original size:21 final size:20
Alignment explanation
Indices: 27537111--27537167 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 20
27537101 CTAATATTGT
*
27537111 TGCTATTATTATTGTTGTTGC
1 TGCTGTTATT-TTGTTGTTGC
27537132 TGCTGTTATTTGTGTTGTTGC
1 TGCTGTTATTT-TGTTGTTGC
27537153 TGCTGTTATTGTTGT
1 TGCTGTTATT-TTGT
27537168 AGTTATTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.09, C:0.09, G:0.25, T:0.58
Consensus pattern (20 bp):
TGCTGTTATTTTGTTGTTGC
Found at i:27537200 original size:18 final size:18
Alignment explanation
Indices: 27537156--27537200 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
27537146 TTGTTGCTGC
27537156 TGTTATTGTTGTAGTTAT
1 TGTTATTGTTGTAGTTAT
*
27537174 TGTTGTTGTTGCTA-TTAT
1 TGTTATTGTTG-TAGTTAT
*
27537192 TTTTATTGT
1 TGTTATTGT
27537201 AATTTTTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.13, C:0.02, G:0.20, T:0.64
Consensus pattern (18 bp):
TGTTATTGTTGTAGTTAT
Found at i:27537534 original size:3 final size:3
Alignment explanation
Indices: 27537505--27537594 Score: 58
Period size: 3 Copynumber: 30.3 Consensus size: 3
27537495 TTGCTATTGA
* * * * * * *
27537505 TGT TAT TGT TTT TGT TGT AGAT T-T TGT TGT TAT TAT TAT TGT TGA
1 TGT TGT TGT TGT TGT TGT TG-T TGT TGT TGT TGT TGT TGT TGT TGT
* * * *
27537550 TGA TGT TAT TGT TAT TAT TGT TG- TGT TGT TGT TGT TGT TGT TGT T
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT T
27537595 ATTAATGTTG
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
2 4 0.06
3 65 0.93
4 1 0.01
ACGTcount: A:0.12, C:0.00, G:0.23, T:0.64
Consensus pattern (3 bp):
TGT
Found at i:27537546 original size:24 final size:24
Alignment explanation
Indices: 27537502--27537570 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 24
27537492 TTGTTGCTAT
* * *
27537502 TGATGTTATTGTTTTTGTTGTAGA
1 TGATGTTATTATTATTATTGTAGA
** * *
27537526 TTTTGTTGTTATTATTATTGTTGA
1 TGATGTTATTATTATTATTGTAGA
*
27537550 TGATGTTATTGTTATTATTGT
1 TGATGTTATTATTATTATTGT
27537571 TGTGTTGTTG
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.17, C:0.00, G:0.20, T:0.62
Consensus pattern (24 bp):
TGATGTTATTATTATTATTGTAGA
Found at i:27537741 original size:27 final size:26
Alignment explanation
Indices: 27537662--27537747 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 26
27537652 GTTTTTGTTT
* *
27537662 TTGTTGTTGTTGTT-AT-TGCTACTA
1 TTGTTGTTGTAGTTAATGTGCTGCTA
* *
27537686 TTGTTGTTG-ATGTTATTGTGTCTGTTA
1 TTGTTGTTGTA-GTTAATGTG-CTGCTA
27537713 TTGTTGTTGTAGTTAATGCTGCTGCTA
1 TTGTTGTTGTAGTTAATG-TGCTGCTA
*
27537740 TTGCTGTT
1 TTGTTGTT
27537748 ATTTTTGTTG
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
24 12 0.24
25 1 0.02
26 2 0.04
27 31 0.63
28 3 0.06
ACGTcount: A:0.12, C:0.08, G:0.24, T:0.56
Consensus pattern (26 bp):
TTGTTGTTGTAGTTAATGTGCTGCTA
Found at i:27537785 original size:12 final size:12
Alignment explanation
Indices: 27537768--27537792 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27537758 ATGTTGTTAC
27537768 TATTGCTATTGT
1 TATTGCTATTGT
27537780 TATTGCTATTGT
1 TATTGCTATTGT
27537792 T
1 T
27537793 GTTGTTGTTG
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:0.16, T:0.60
Consensus pattern (12 bp):
TATTGCTATTGT
Found at i:27537888 original size:15 final size:15
Alignment explanation
Indices: 27537870--27537918 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
27537860 TTGTTGTTGA
*
27537870 TGTTGTTGCTACTAT
1 TGTTGTTGCTATTAT
** *
27537885 TGTTGTTATTGTTAT
1 TGTTGTTGCTATTAT
27537900 TGTTGTTGCTATTAT
1 TGTTGTTGCTATTAT
27537915 TGTT
1 TGTT
27537919 ACTGTTGTTA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.12, C:0.06, G:0.20, T:0.61
Consensus pattern (15 bp):
TGTTGTTGCTATTAT
Found at i:27537919 original size:27 final size:27
Alignment explanation
Indices: 27537872--27537924 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
27537862 GTTGTTGATG
* *
27537872 TTGTTGCTACTATTGTTGTTATTGTTA
1 TTGTTGCTACTATTATTGTTACTGTTA
* *
27537899 TTGTTGTTGCTATTATTGTTACTGTT
1 TTGTTGCTACTATTATTGTTACTGTT
27537925 GTTATTGATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.13, C:0.08, G:0.19, T:0.60
Consensus pattern (27 bp):
TTGTTGCTACTATTATTGTTACTGTTA
Found at i:27537927 original size:30 final size:30
Alignment explanation
Indices: 27537840--27537931 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
27537830 TTGTAGTTAA
* * *
27537840 TGTTGTTACTATTTTTACTGTTGTTGTTGATGT
1 TGTTGCTACTATTGTTACTGTTGTT-AT--TGT
** *
27537873 TGTTGCTACTATTGTTGTTATTGTTATTGT
1 TGTTGCTACTATTGTTACTGTTGTTATTGT
*
27537903 TGTTGCTATTATTGTTACTGTTGTTATTG
1 TGTTGCTACTATTGTTACTGTTGTTATTG
27537932 ATATTTTTGT
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
30 28 0.57
32 1 0.02
33 20 0.41
ACGTcount: A:0.13, C:0.07, G:0.21, T:0.60
Consensus pattern (30 bp):
TGTTGCTACTATTGTTACTGTTGTTATTGT
Found at i:27537972 original size:18 final size:18
Alignment explanation
Indices: 27537744--27537972 Score: 64
Period size: 18 Copynumber: 12.9 Consensus size: 18
27537734 CTGCTATTGC
* *
27537744 TGTTATTTTTGTTGATGT
1 TGTTATTATTGTTGTTGT
* * *
27537762 TGTTACTATTGCTATTGT
1 TGTTATTATTGTTGTTGT
* **
27537780 TATTGCTATTGTTGTTGT
1 TGTTATTATTGTTGTTGT
*
27537798 TGTTGATGA-TGTTGTTG-
1 TGTT-ATTATTGTTGTTGT
* * *
27537815 TGTTTGTTATTATCGTTGT
1 TG-TTATTATTGTTGTTGT
* **
27537834 AGTTA--A-TGTTGTTAC
1 TGTTATTATTGTTGTTGT
* * *
27537849 TATTTTTACTGTTGTTGT
1 TGTTATTATTGTTGTTGT
* * * *
27537867 TGATGTTGTTGCTACTATTGT
1 TGTTATTATTG-T--TGTTGT
* *
27537888 TGTTATTGTTATTGTTGT
1 TGTTATTATTGTTGTTGT
* **
27537906 TGCTATTATTGTTACTGT
1 TGTTATTATTGTTGTTGT
27537924 TGTTATTGATAT-TT-TTG-
1 TGTTATT-AT-TGTTGTTGT
*
27537941 T-TTA-TATTGATGTTGT
1 TGTTATTATTGTTGTTGT
*
27537957 TGTTATTAATGTTGTT
1 TGTTATTATTGTTGTT
27537973 ACCGCTACTA
Statistics
Matches: 146, Mismatches: 48, Indels: 34
0.64 0.21 0.15
Matches are distributed among these distances:
13 1 0.01
14 3 0.02
15 11 0.08
16 5 0.03
17 9 0.06
18 95 0.65
19 7 0.05
20 2 0.01
21 13 0.09
ACGTcount: A:0.15, C:0.04, G:0.21, T:0.60
Consensus pattern (18 bp):
TGTTATTATTGTTGTTGT
Found at i:27538074 original size:9 final size:9
Alignment explanation
Indices: 27538060--27538094 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
27538050 TGCTATTACT
27538060 GTTGTTGTA
1 GTTGTTGTA
27538069 GTTGTTGTA
1 GTTGTTGTA
*
27538078 GTTGTAGTA
1 GTTGTTGTA
*
27538087 GTTATTGT
1 GTTGTTGT
27538095 TGCTATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.31, T:0.54
Consensus pattern (9 bp):
GTTGTTGTA
Found at i:27538186 original size:3 final size:3
Alignment explanation
Indices: 27538178--27539976 Score: 266
Period size: 3 Copynumber: 604.3 Consensus size: 3
27538168 TTTTTATTGG
* * * * * *
27538178 TGT TGT TGT TAT TGT TGT TGCT AG- TGC TAT TGT CGT TGCT TCT T-T
1 TGT TGT TGT TGT TGT TGT TG-T TGT TGT TGT TGT TGT TG-T TGT TGT
* * * * *
27538223 TGT TGT TGT TGT TGT TGT T-T T-T TGT TTT TGC TAT TGC TGT TGT TGC
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
* * * ** * *
27538269 TGA TAT TGT TGT TGT TGC TGT TAC TAT TGT TGT T-C TGT T-T ATGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT -TGT
* ** * ** * * *
27538313 TGT TGT TGT TAT TCC TAT TGT TAA TGT GGT TGT TGT TTT TGT TTT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
* * * * * * * * *
27538361 TGT AGC TAT TGT TGT TGT TGA TGA TGA TGT TCT TAT TGT TACT CTGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT T-GT -TGT
* * * * * * * ** * * *
27538408 TAT TGT TGT TAT TAT TGT TGT TGA TGC TGC TAT TGT TAA TGA TGG TGA
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
* * * * * * *
27538456 TGT TGT TAT TGC TAT TTT TAT T-T TTT TGT TAG- TGT T-T CTAT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT T-GT TGT TGT -TGT TGT
* * * * * * *
27538500 TAT TGC TAT TGT TGT T-T T-T TGT AGA TGT TGT TGT TGT TGT TGC TAT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
* * *
27538546 TGT T-T TGT TGT TGT TGT TTT TGT AGT AGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
* * * * * * *
27538593 TAT T-T TTT TTT TGT TAT TGT TGT TGT TGT TGT T-T TGT AGT AGT AGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
* * * * * * * * * *
27538639 AGT AGT AGT AGT AG- TGT TGT TGT TGT TGT TGT TGC TAT TGC TAT TTT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
* * * * ** *
27538686 ATGT TGT TGT TGC TAT TAT TAT TAC TGT TGT TGCT T-T TGT AGT TGT
1 -TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG-T TGT TGT TGT TGT
* * * * *
27538732 TGT TGG TGG TGT TGG TGG TGT T-T TGGT TGT TGT TGT TGT GGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT T-GT TGT TGT TGT TGT TGT TGT
* * * * * *
27538777 TGT TGT AGT TAT TTT TTT TGT TGT TGT TAT TGT TGA TGCT T-T TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG-T TGT TGT
** * *** * ** * ** ** **
27538822 TGT TAC TGT TGT TGC AAC TGC AAT TTT TGT TAA TGT TGT TGT TAC TAC
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
*** * * ** * * *
27538870 TGT TGCAT T-T ACAA T-T TCT TGT TGA TAC TAT TAT TGA TGT TGT TGT
1 TGT TG--T TGT -TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
* * * * ** * * * *
27538916 TGT TGA TGT TCT TGT TGT TAT TGC TCC TGT TAT TAT TGT TGC TCT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
* * ** * * *
27538964 TAT TGT TCT TGT TGT TAC TAT TGT TGT TGT TGC TAT TGCT T-T T-T
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG-T TGT TGT
* * * *
27539008 TGGT T-T TGT TGC T-T TGT TGT TGT TGT TGC TAT TGT TAT TGT TGT
1 T-GT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
** * * * * * * *
27539052 TAC TAT TAT TGCT CG- TGT T-T ATGT TTT TGT TAT TGT TGT TAT AGT
1 TGT TGT TGT TG-T TGT TGT TGT -TGT TGT TGT TGT TGT TGT TGT TGT
* * * * *
27539097 TGT TGT TGT TGT TGT AT-T TGT TAT TAT TGC TAT TGT TGT TGT TCT
1 TGT TGT TGT TGT TGT -TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
* * ** * * ** **
27539142 TTT TGC AAT TAT TGT TGT TGT TGC TGCT ACT ACT T-T TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TG-T TGT TGT TGT TGT TGT TGT
* * ** * * *
27539187 TAT TAT TGT TGT TGT TGT TGT TGT TGT TGT TCC TGT TGC TAT TGT TAT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
* * * * * * *
27539235 TGT TGT TGT TAT TGT TGC TGT TGT TAT TTT TAT AGT TGT TGT TTT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
* * * * * * * * ** *
27539283 TGC TGC TAT TGT TAT TCT TGT TGT TGT TAT TTT TAT AAT TGT TGT TGC
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
** * * * * *
27539331 TGT TAC TAT TGT TGT TAT T-T CTAT TGT TGT TAT TACT TG- TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT -TGT TGT TGT TGT T-GT TGT TGT TGT
* * *
27539376 TTT TGT TGT T-T TGT T-T GTGT TGT TGT TGT TG- TGT TGT TAT TCT
1 TGT TGT TGT TGT TGT TGT -TGT TGT TGT TGT TGT TGT TGT TGT TGT
* * * * ** *
27539419 TGT TGT TGC TAT TGT TGT TGT T-T CTGC TGT TGT TAT TAC TGT TAT
1 TGT TGT TGT TGT TGT TGT TGT TGT -TGT TGT TGT TGT TGT TGT TGT
* * * * * * * * * *
27539464 TGT AGT TGT AGT T-T TTT TGT TAT TTT TCT TAT T-T T-T TCT TTT TTT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
* *** * * * * * * *
27539509 TAGT TGC TGT AAC TAT TTT TGA TGT TAT TGT TAT TAT TGT TGA TGT
1 T-GT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
* * * * * * * * * * *
27539555 TGT AGT TGT TGT TGC TGC TGC TAT TGT TGC TGT TAT TGC TAT TAT TTT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
** * ** * * * * * * *
27539603 TGT TAC TGC TAC TAT TTT TAG- TGT TGC TAT TGT TGG TGT AGT AGT
1 TGT TGT TGT TGT TGT TGT T-GT TGT TGT TGT TGT TGT TGT TGT TGT
* * * * * * * * *
27539648 TGT TGT AGC TAT TGT TCT TGC TGC TAT TGT TAT TGA TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
* ** * * * *
27539696 TGT TGT TGT TGT TGA TGT TAC TAT TAT TGT TGT TGT TGT TGT TGC TAT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
* * * * * * * *
27539744 TGT TGT TGT TAT T-T TCGT TGT AGC TAT TGT TAT TGT TGC TGC TAT
1 TGT TGT TGT TGT TGT T-GT TGT TGT TGT TGT TGT TGT TGT TGT TGT
* * * * * * * * * *
27539789 TAT TGT TGA TGC TGC GGC TGT TGC TAT TGA TGT TGT TAT T-T TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
** * * * * * * *
27539836 ACAT T-T TGT TGT TGG TAT TGT TAT TTT TGT TAT TAT TGT TAT TGT
1 -TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
* * * * *
27539881 TG- GGTT TGT TGT TGT TGC TGC TGT TGGT GGT T-C TGT TGT TGT TGT
1 TGT TG-T TGT TGT TGT TGT TGT TGT T-GT TGT TGT TGT TGT TGT TGT
*
27539926 TGT TGT TG- TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT CGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
27539973 TGT T
1 TGT T
27539977 ATTGCTACTA
Statistics
Matches: 1283, Mismatches: 443, Indels: 140
0.69 0.24 0.08
Matches are distributed among these distances:
2 70 0.05
3 1174 0.92
4 36 0.03
5 3 0.00
ACGTcount: A:0.10, C:0.06, G:0.23, T:0.60
Consensus pattern (3 bp):
TGT
Found at i:27538263 original size:22 final size:22
Alignment explanation
Indices: 27538220--27538263 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
27538210 TCGTTGCTTC
* * *
27538220 TTTTGTTGTTGTTGTTGTTGTT
1 TTTTGTTGTTGCTATTGCTGTT
*
27538242 TTTTGTTTTTGCTATTGCTGTT
1 TTTTGTTGTTGCTATTGCTGTT
27538264 GTTGCTGATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.02, C:0.05, G:0.23, T:0.70
Consensus pattern (22 bp):
TTTTGTTGTTGCTATTGCTGTT
Found at i:27538607 original size:50 final size:49
Alignment explanation
Indices: 27538488--27538618 Score: 156
Period size: 50 Copynumber: 2.7 Consensus size: 49
27538478 TTTTTGTTAG
* * *
27538488 TGTTTCTATTGTTATTGCTATTGTTGTTTTT-TGTAGATGTTGTTGTTGT
1 TGTTGCTATTGTT-TTGTTGTTGTTGTTTTTGTGTAGATGTTGTTGTTGT
*
27538537 TGTTGCTATTGTTTTGTTGTTGTTGTTTTTGTAGTAGTTGTTGTTGTTGT
1 TGTTGCTATTGTTTTGTTGTTGTTGTTTTTGT-GTAGATGTTGTTGTTGT
* * * * *
27538587 TGTTGTTATTTTTTTTTTGTTATTGTTGTTGT
1 TGTTGCTATTGTTTTGTTGTTGTTGTTTTTGT
27538619 TGTTGTTTTG
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
48 15 0.21
49 13 0.18
50 43 0.61
ACGTcount: A:0.08, C:0.02, G:0.24, T:0.66
Consensus pattern (49 bp):
TGTTGCTATTGTTTTGTTGTTGTTGTTTTTGTGTAGATGTTGTTGTTGT
Found at i:27539389 original size:14 final size:14
Alignment explanation
Indices: 27539367--27539413 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
27539357 TTGTTATTAC
* *
27539367 TTGTGTTGTTTTTG
1 TTGTTTTGTTTGTG
27539381 TTGTTTTGTTTGTG
1 TTGTTTTGTTTGTG
27539395 TTGTTGTTG-TTGTG
1 TTGTT-TTGTTTGTG
27539409 TTGTT
1 TTGTT
27539414 ATTCTTGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 27 0.90
15 3 0.10
ACGTcount: A:0.00, C:0.00, G:0.30, T:0.70
Consensus pattern (14 bp):
TTGTTTTGTTTGTG
Found at i:27539397 original size:23 final size:23
Alignment explanation
Indices: 27539367--27539426 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
27539357 TTGTTATTAC
* *
27539367 TTGTGTTGTTTTTGTTGTTTTGT
1 TTGTGTTGTTGTTGTTGTGTTGT
27539390 TTGTGTTGTTGTTGTTGTGTTGT
1 TTGTGTTGTTGTTGTTGTGTTGT
*
27539413 TAT-TCTTGTTGTTG
1 T-TGTGTTGTTGTTG
27539427 CTATTGTTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 32 0.97
24 1 0.03
ACGTcount: A:0.02, C:0.02, G:0.28, T:0.68
Consensus pattern (23 bp):
TTGTGTTGTTGTTGTTGTGTTGT
Found at i:27539401 original size:20 final size:20
Alignment explanation
Indices: 27539373--27539410 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
27539363 TTACTTGTGT
* *
27539373 TGTTTTTGTTGTTTTGTTTG
1 TGTTGTTGTTGTTGTGTTTG
27539393 TGTTGTTGTTGTTGTGTT
1 TGTTGTTGTTGTTGTGTT
27539411 GTTATTCTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (20 bp):
TGTTGTTGTTGTTGTGTTTG
Found at i:27541981 original size:15 final size:15
Alignment explanation
Indices: 27541958--27542047 Score: 60
Period size: 15 Copynumber: 5.9 Consensus size: 15
27541948 TGACCAAATG
*
27541958 TATTATTGTTGATGC
1 TATTGTTGTTGATGC
*
27541973 TATTGTTGTTGTTGC
1 TATTGTTGTTGATGC
*
27541988 TACTGCTATTGTTGATGC
1 TA-T--TGTTGTTGATGC
* *
27542006 AATTTTTTGTTGATG-
1 TA-TTGTTGTTGATGC
* *
27542021 -A-TGTTGTTGTTGT
1 TATTGTTGTTGATGC
27542034 TATTGTTGTTGATG
1 TATTGTTGTTGATG
27542048 TTGTTATTTC
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
12 9 0.15
14 2 0.03
15 25 0.42
16 11 0.19
18 12 0.20
ACGTcount: A:0.14, C:0.06, G:0.24, T:0.56
Consensus pattern (15 bp):
TATTGTTGTTGATGC
Found at i:27542099 original size:24 final size:24
Alignment explanation
Indices: 27542072--27542194 Score: 99
Period size: 24 Copynumber: 5.2 Consensus size: 24
27542062 GCTATTATTA
27542072 TTGTTGTTGCTCTTGTTACTGTTG
1 TTGTTGTTGCTCTTGTTACTGTTG
* *
27542096 TTGTTGTTGCTCTTGTTGCTATTG
1 TTGTTGTTGCTCTTGTTACTGTTG
* ** * * * *
27542120 TTGTTGGTATTGTAGTTATTGCTG
1 TTGTTGTTGCTCTTGTTACTGTTG
* * *
27542144 TTGTTGTTG-AC--GCTACTATTG
1 TTGTTGTTGCTCTTGTTACTGTTG
* *
27542165 TTGTTGTTTCTCTTGTTGCTGTTG
1 TTGTTGTTGCTCTTGTTACTGTTG
27542189 TTGTTG
1 TTGTTG
27542195 ACGTTGCTAT
Statistics
Matches: 72, Mismatches: 24, Indels: 6
0.71 0.24 0.06
Matches are distributed among these distances:
21 14 0.19
22 1 0.01
24 57 0.79
ACGTcount: A:0.07, C:0.11, G:0.26, T:0.57
Consensus pattern (24 bp):
TTGTTGTTGCTCTTGTTACTGTTG
Found at i:27542172 original size:3 final size:3
Alignment explanation
Indices: 27542012--27542152 Score: 59
Period size: 3 Copynumber: 47.0 Consensus size: 3
27542002 ATGCAATTTT
* * * * * *
27542012 TTG TTG ATG ATG TTG TTG TTG TTA TTG TTG TTG ATG TTG TTA TT- TCTA
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T-TG
* * * * * * * * * *
27542060 TTG CTA TTA TTA TTG TTG TTG CTC TTG TTA CTG TTG TTG TTG TTG CTC
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
* * * * * * *
27542108 TTG TTG CTA TTG TTG TTG GTA TTG TAG TTA TTG CTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
27542153 ACGCTACTAT
Statistics
Matches: 98, Mismatches: 38, Indels: 4
0.70 0.27 0.03
Matches are distributed among these distances:
2 1 0.01
3 96 0.98
4 1 0.01
ACGTcount: A:0.10, C:0.06, G:0.25, T:0.59
Consensus pattern (3 bp):
TTG
Found at i:27542205 original size:42 final size:44
Alignment explanation
Indices: 27542110--27542212 Score: 129
Period size: 42 Copynumber: 2.4 Consensus size: 44
27542100 TGTTGCTCTT
* *
27542110 GTTGCTATTGTTGTTGGTATTGTAGTTATTGCTGTTGTTGTTGAC
1 GTTGCTATTGTTGTT-GTATTCTACTTATTGCTGTTGTTGTTGAC
* * *
27542155 GCTACTATTGTTGTTGT-TTCT-CTTGTTGCTGTTGTTGTTGAC
1 GTTGCTATTGTTGTTGTATTCTACTTATTGCTGTTGTTGTTGAC
*
27542197 GTTGCTATTATTGTTG
1 GTTGCTATTGTTGTTG
27542213 CTCTTATTTC
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
42 32 0.64
43 3 0.06
44 2 0.04
45 13 0.26
ACGTcount: A:0.10, C:0.10, G:0.26, T:0.54
Consensus pattern (44 bp):
GTTGCTATTGTTGTTGTATTCTACTTATTGCTGTTGTTGTTGAC
Found at i:27542318 original size:69 final size:69
Alignment explanation
Indices: 27542187--27542319 Score: 171
Period size: 69 Copynumber: 1.9 Consensus size: 69
27542177 TTGTTGCTGT
* * *
27542187 TGTTGTTGACGTTGCTATTATTGTTGCTCTTATTTCTGTTGTTGCTGCTGGTATTATAGTTATTA
1 TGTTGTTGACGTTGCTATTATTGCTGCTCTTATTTCTGTTGTTGATGATGGTATTATAGTTATTA
27542252 TTCA
66 TTCA
* * * *
27542256 TGTTGTTGACGTTGCTATTGTTGCTGCTCTTGTTAT-TGTTGTTGAT-ATTGTAGTTATTGTTAT
1 TGTTGTTGACGTTGCTATTATTGCTGCTCTTATT-TCTGTTGTTGATGATGGTA-TTATAGTTAT
27542319 T
64 T
27542320 GCTGCTACTG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
68 4 0.07
69 50 0.91
70 1 0.02
ACGTcount: A:0.14, C:0.10, G:0.22, T:0.55
Consensus pattern (69 bp):
TGTTGTTGACGTTGCTATTATTGCTGCTCTTATTTCTGTTGTTGATGATGGTATTATAGTTATTA
TTCA
Found at i:27542441 original size:60 final size:60
Alignment explanation
Indices: 27542336--27542448 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
27542326 ACTGCGATTG
** * *
27542336 TTATTGTTATTGTTTTTGTTACTCCTGTTGCTATTTTTGTAGTTGTTGTTGCTATTGCTA
1 TTATTGTTATTACTTTTGTTACTACTGTTACTATTTTTGTAGTTGTTGTTGCTATTGCTA
* * *
27542396 TTATTGTTATTACTTTTGTTACTATTGTTATTCTTATTTGT-GTTGTTGTTGCT
1 TTATTGTTATTACTTTTGTTACTACTGTTACTATT-TTTGTAGTTGTTGTTGCT
27542449 GTTGTTGTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
60 40 0.89
61 5 0.11
ACGTcount: A:0.12, C:0.09, G:0.17, T:0.62
Consensus pattern (60 bp):
TTATTGTTATTACTTTTGTTACTACTGTTACTATTTTTGTAGTTGTTGTTGCTATTGCTA
Found at i:27542605 original size:18 final size:18
Alignment explanation
Indices: 27542584--27544040 Score: 131
Period size: 18 Copynumber: 81.4 Consensus size: 18
27542574 GCTCTTTTTA
27542584 TTGTTGTTGCTATTGTTG
1 TTGTTGTTGCTATTGTTG
* *
27542602 TTGTTGCTT-TTTTTGTTG
1 TTGTTG-TTGCTATTGTTG
*
27542620 TTGTTGTT--TGTTGTTG
1 TTGTTGTTGCTATTGTTG
* * * **
27542636 CTATTGTTTCGGTTGTTG
1 TTGTTGTTGCTATTGTTG
* * * *
27542654 CAATTTTTGTTACTATTATTA
1 ---TTGTTGTTGCTATTGTTG
*
27542675 TTGCTGTTGCTATTGTTG
1 TTGTTGTTGCTATTGTTG
27542693 TTGTTGTTGCTATTGCTT-
1 TTGTTGTTGCTATTG-TTG
* *
27542711 TTGTTGCTGCTATATTATTG
1 TTGTTGTTGC--TATTGTTG
* * *
27542731 TTGCTGCTGTCTTTACTATTATTA
1 TTG-T--TG---TTGCTATTGTTG
*
27542755 TTGTTGTTGCTCTTGTTG
1 TTGTTGTTGCTATTGTTG
* *
27542773 TTGTTGTTTTGTTTTTGTTG
1 TTGTTG--TTGCTATTGTTG
* * *
27542793 TTATTTTTGTTATTGTTG
1 TTGTTGTTGCTATTGTTG
*
27542811 TTATTGTTGC---TGTTG
1 TTGTTGTTGCTATTGTTG
*
27542826 TTGCTGTTGCTATTG--G
1 TTGTTGTTGCTATTGTTG
* *
27542842 TGGTGGTT-CTATTGTTG
1 TTGTTGTTGCTATTGTTG
*
27542859 TTGTTG-T--TA---TCG
1 TTGTTGTTGCTATTGTTG
* *
27542871 TTGTTGTTGCTATTATTT
1 TTGTTGTTGCTATTGTTG
*
27542889 TTGTTGATGC--TT-TTG
1 TTGTTGTTGCTATTGTTG
* *
27542904 TTATTGTTGTTATTGTTG
1 TTGTTGTTGCTATTGTTG
* **
27542922 TTATT-TCTATTATTGTTG
1 TTGTTGT-TGCTATTGTTG
* **** *
27542940 TTGATGTCGTTGTTACCCCTC
1 TTG-T-T-GTTGCTATTGTTG
* *
27542961 TTGTTGCTGCAATT-TATAG
1 TTGTTGTTGCTATTGT-T-G
** *
27542980 TTGTTGTTATTGTTGTTG
1 TTGTTGTTGCTATTGTTG
* ** *
27542998 TTGATGTTGTTCTTATCATTA
1 TTGTTGTTG--C-TATTGTTG
* * *
27543019 TTATTGCTGC-AAT-TTG
1 TTGTTGTTGCTATTGTTG
* **
27543035 TTGTTGATATTATTGTTG
1 TTGTTGTTGCTATTGTTG
* *
27543053 CTGCTGTTG-T-TT-TT-
1 TTGTTGTTGCTATTGTTG
* * *
27543067 TCTATTGTTACAATT--TG
1 T-TGTTGTTGCTATTGTTG
* *
27543084 TTGTTGATGTTATTGTTG
1 TTGTTGTTGCTATTGTTG
* *
27543102 TTGCTGCTGCTATTGTTG
1 TTGTTGTTGCTATTGTTG
* * * **
27543120 CTGTTGTTGTTGTTGTAA
1 TTGTTGTTGCTATTGTTG
*
27543138 TTGTTGTTGTTATTGTTG
1 TTGTTGTTGCTATTGTTG
* ** *
27543156 TTGTTGTTACTGCTATTG
1 TTGTTGTTGCTATTGTTG
* *
27543174 TTGCTATTGCTA---TTG
1 TTGTTGTTGCTATTGTTG
* * *
27543189 TTGTTGCTGCTACTATTG
1 TTGTTGTTGCTATTGTTG
*
27543207 TTGTTGTTGCTCTTGTTG
1 TTGTTGTTGCTATTGTTG
* *
27543225 TTGTGGTTG--A-TGATG
1 TTGTTGTTGCTATTGTTG
* *
27543240 TTGCTGTTG---TTGTGG
1 TTGTTGTTGCTATTGTTG
*
27543255 TTGTTGTTGTTATTGTTG
1 TTGTTGTTGCTATTGTTG
* * *
27543273 TTGCTATTG-TTTCTGTT-
1 TTGTTGTTGCTAT-TGTTG
* ** *
27543290 TCTGTTGTTGTTCCTGTTC
1 T-TGTTGTTGCTATTGTTG
* *
27543309 TTATTATTGCTATTGTTG
1 TTGTTGTTGCTATTGTTG
* * * *
27543327 TTATTTTTGTTGTTGTTG
1 TTGTTGTTGCTATTGTTG
* *
27543345 TTATTATTGTTCTTATTGTTAG
1 TTGTTGTTG--C-TATTGTT-G
*
27543367 -TGCTGTTG-TAGTTGTTG
1 TTGTTGTTGCTA-TTGTTG
* * *
27543384 TTGTAGTTGCTGTTGTTA
1 TTGTTGTTGCTATTGTTG
* *
27543402 TTGTAGCTGCTATTGTTG
1 TTGTTGTTGCTATTGTTG
* * *
27543420 TTAATGTTATTGTTACTGTTG
1 -T--TGTTGTTGCTATTGTTG
* * *
27543441 TTGCTGCTGCAATTTGTT-
1 TTGTTGTTGCTA-TTGTTG
* * * *
27543459 TTTTATATTG-TGTTGTTT
1 TTGT-TGTTGCTATTGTTG
* * * *
27543477 TTATTTTTGATATTATTG
1 TTGTTGTTGCTATTGTTG
* * * * **
27543495 TTTTTGATGTTCTTACTG
1 TTGTTGTTGCTATTGTTG
* **
27543513 TTATTGTTATTATTGTT-
1 TTGTTGTTGCTATTGTTG
*
27543530 TCTGTT-TCT-CTTATTGCTG
1 T-TGTTGT-TGC-TATTGTTG
** *
27543549 TTGTTGTTGCTGCTGTTTC
1 TTGTTGTTGCTATTG-TTG
* * *
27543568 TCTATTGTTGTTATTATT-
1 T-TGTTGTTGCTATTGTTG
*
27543586 TTTTCTGTT--T-TT-TTG
1 TTGT-TGTTGCTATTGTTG
27543601 TTGTTGTTG-TA--GTTG
1 TTGTTGTTGCTATTGTTG
* *
27543616 TTGTAGTTTCTATTGTTG
1 TTGTTGTTGCTATTGTTG
* * *
27543634 TTGTTGTTGTAGCTATCGATA
1 TTGTTG-T-T-GCTATTGTTG
* * *
27543655 TTGCTATTACTATTGTTG
1 TTGTTGTTGCTATTGTTG
*
27543673 TTGATGTTGCTATTGTTGTTG
1 TTGTTGTTGCTA---TTGTTG
* **
27543694 TTGTTGTTGCTATCGTAA
1 TTGTTGTTGCTATTGTTG
* ** * *
27543712 TTTTTGTTATTGTTGATG
1 TTGTTGTTGCTATTGTTG
*
27543730 TTGTTG-TGTCTATTACTATTG
1 TTGTTGTTG-CTA-T--TGTTG
* *
27543751 TTGTTGTAGCTATTGATG
1 TTGTTGTTGCTATTGTTG
* * *
27543769 TTGATGCTGTTATTGTTG
1 TTGTTGTTGCTATTGTTG
* *
27543787 TTGATGTTG---TTGTTA
1 TTGTTGTTGCTATTGTTG
**
27543802 TTGTTGTAACTATTGTTG
1 TTGTTGTTGCTATTGTTG
* ** *
27543820 TTGTTGCTATTATTTTTG
1 TTGTTGTTGCTATTGTTG
* *
27543838 TTGATATTGTTACTATTGTTC
1 TTG---TTGTTGCTATTGTTG
* *
27543859 TTGTTGTTGTTGA-TGATG
1 TTGTTGTTGCT-ATTGTTG
27543877 TTG-TGTTTGCTATTGTTG
1 TTGTTG-TTGCTATTGTTG
* *
27543895 TTGTT-TT--TA---ATA
1 TTGTTGTTGCTATTGTTG
**
27543907 TTGTTACTGCTATTGTTG
1 TTGTTGTTGCTATTGTTG
* * **
27543925 ATGTTGTTGCAATTACTG
1 TTGTTGTTGCTATTGTTG
*
27543943 TTGTTGTTG---TTGATG
1 TTGTTGTTGCTATTGTTG
* * *
27543958 TAGTTGCTGCTATTGTTTCCA
1 TTGTTGTTGCTATTG-TT--G
* *
27543979 TTGTTGTT-ATTTGTGTTG
1 TTGTTGTTGCTAT-TGTTG
* *
27543997 TTGTTGTTGTTATTGTTT
1 TTGTTGTTGCTATTGTTG
*
27544015 TTTTTGTTGCTATTGTTG
1 TTGTTGTTGCTATTGTTG
27544033 TTGTTGTT
1 TTGTTGTT
27544041 ATTGTAGTAG
Statistics
Matches: 1002, Mismatches: 310, Indels: 254
0.64 0.20 0.16
Matches are distributed among these distances:
12 14 0.01
13 2 0.00
14 6 0.01
15 115 0.11
16 44 0.04
17 42 0.04
18 559 0.56
19 45 0.04
20 41 0.04
21 116 0.12
22 3 0.00
23 3 0.00
24 10 0.01
26 2 0.00
ACGTcount: A:0.11, C:0.07, G:0.22, T:0.59
Consensus pattern (18 bp):
TTGTTGTTGCTATTGTTG
Found at i:27542653 original size:3 final size:3
Alignment explanation
Indices: 27542584--27542635 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
27542574 GCTCTTTTTA
* * *
27542584 TTG TTG TTG CTA TTG TTG TTG TTG CTT- TTT TTG TTG TTG TTG TTTG
1 TTG TTG TTG TTG TTG TTG TTG TTG -TTG TTG TTG TTG TTG TTG -TTG
27542630 TTG TTG
1 TTG TTG
27542636 CTATTGTTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
2 2 0.05
3 34 0.83
4 5 0.12
ACGTcount: A:0.02, C:0.04, G:0.27, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:27542697 original size:15 final size:15
Alignment explanation
Indices: 27542584--27543355 Score: 168
Period size: 15 Copynumber: 51.3 Consensus size: 15
27542574 GCTCTTTTTA
27542584 TTGTTGTTGCTATTG
1 TTGTTGTTGCTATTG
27542599 TTGTTGTTGCT-TT-
1 TTGTTGTTGCTATTG
* *
27542612 TT-TTGTTGTTGTTG
1 TTGTTGTTGCTATTG
27542626 TTTGTTGTTGCTATTG
1 -TTGTTGTTGCTATTG
* *
27542642 TTTCGGTTGTTGCAATTT
1 -TT--GTTGTTGCTATTG
** ** *
27542660 TTGTTACTATTATTA
1 TTGTTGTTGCTATTG
*
27542675 TTGCTGTTGCTATTGTTG
1 TTGTTGTTGCTA---TTG
27542693 TTGTTGTTGCTATTG
1 TTGTTGTTGCTATTG
* *
27542708 CTT-TTGTTGCTGCTATA
1 -TTGTTGTTGCT-AT-TG
* **
27542725 TTATTGTTGCTGCTG
1 TTGTTGTTGCTATTG
** ** *
27542740 TCT-TTACTATTATTA
1 T-TGTTGTTGCTATTG
*
27542755 TTGTTGTTGCTCTTG
1 TTGTTGTTGCTATTG
*
27542770 TTGTTGTTG-TTTTG
1 TTGTTGTTGCTATTG
* * *
27542784 TTTTTGTTGTTATTT
1 TTGTTGTTGCTATTG
*
27542799 TTGTTATTG---TTG
1 TTGTTGTTGCTATTG
* *
27542811 TTATTGTTGCTGTTG
1 TTGTTGTTGCTATTG
*
27542826 TTGCTGTTGCTATTGG
1 TTGTTGTTGCTATT-G
* *
27542842 TGGTGGTT-CTATTG
1 TTGTTGTTGCTATTG
* *
27542856 TTGTTGTTGTTATCG
1 TTGTTGTTGCTATTG
*
27542871 TTGTTGTTGCTATTATTT
1 TTGTTGTTGC---TATTG
* *
27542889 TTGTTGATGCTTTTG
1 TTGTTGTTGCTATTG
* *
27542904 TTATTGTTGTTATTG
1 TTGTTGTTGCTATTG
* * *
27542919 TTGTTATTTCTATTA
1 TTGTTGTTGCTATTG
27542934 TTGTTGTTG--A-TG
1 TTGTTGTTGCTATTG
* * *** *
27542946 TCGTTGTTACCCCTC
1 TTGTTGTTGCTATTG
* *
27542961 TTGTTGCTGCAATT-
1 TTGTTGTTGCTATTG
*
27542975 TATAGTTGTTGTTATTG
1 T-T-GTTGTTGCTATTG
27542992 TTGTTGTTG--A-TG
1 TTGTTGTTGCTATTG
* * *
27543004 TTGTTCTT-ATCATTA
1 TTGTTGTTGCT-ATTG
* * *
27543019 TTATTGCTGC-AAT-
1 TTGTTGTTGCTATTG
* *
27543032 TTGTTGTTGATATTA
1 TTGTTGTTGCTATTG
* *
27543047 TTGTTGCTGCTGTTG
1 TTGTTGTTGCTATTG
27543062 TT-TT-TT-CTATTG
1 TTGTTGTTGCTATTG
* * *
27543074 TTACAATTTGTTGTTGATGTTA
1 -------TTGTTGTTGCTATTG
**
27543096 TTGTTGTTGCTGCTG
1 TTGTTGTTGCTATTG
* * *
27543111 CTATTGTTGCTGTTG
1 TTGTTGTTGCTATTG
27543126 TTGTTGTTG-TAATTG
1 TTGTTGTTGCT-ATTG
** *
27543141 TTGTTGTTATTGTTG
1 TTGTTGTTGCTATTG
27543156 TTGTTGTTACTGCTATTG
1 TTGTTG-T--TGCTATTG
* *
27543174 TTGCTATTGCTATTG
1 TTGTTGTTGCTATTG
*
27543189 TTGTTGCTGCTACTATTG
1 TTGTTG-T--TGCTATTG
*
27543207 TTGTTGTTGCTCTTG
1 TTGTTGTTGCTATTG
* *
27543222 TTGTTGTGGTTGA-TG
1 TTGTTGTTGCT-ATTG
* * * *
27543237 ATGTTGCTGTTGTTG
1 TTGTTGTTGCTATTG
* * * *
27543252 TGGTTGTTGTTGTTA
1 TTGTTGTTGCTATTG
27543267 TTGTTGTTGCTATTG
1 TTGTTGTTGCTATTG
*
27543282 TT-TCTGTT--T-CTG
1 TTGT-TGTTGCTATTG
* * *
27543294 TTGTTGTTCCTGTTC
1 TTGTTGTTGCTATTG
* *
27543309 TTATTATTGCTATTG
1 TTGTTGTTGCTATTG
*
27543324 TTGTTATT--T-TTG
1 TTGTTGTTGCTATTG
* *
27543336 TTGTTGTTGTTATTA
1 TTGTTGTTGCTATTG
27543351 TTGTT
1 TTGTT
27543356 CTTATTGTTA
Statistics
Matches: 539, Mismatches: 153, Indels: 130
0.66 0.19 0.16
Matches are distributed among these distances:
12 56 0.10
13 17 0.03
14 34 0.06
15 313 0.58
16 38 0.07
17 14 0.03
18 58 0.11
19 2 0.00
20 2 0.00
21 2 0.00
22 3 0.01
ACGTcount: A:0.10, C:0.08, G:0.23, T:0.59
Consensus pattern (15 bp):
TTGTTGTTGCTATTG
Found at i:27542905 original size:48 final size:48
Alignment explanation
Indices: 27542853--27542945 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
27542843 GGTGGTTCTA
* * *
27542853 TTGTTGTTGTTGTTATCGTTGTTGTTGCTATTATTTTTGTTGATGCTT
1 TTGTTATTGTTGTTATCGTTGTTATTGCTATTATTGTTGTTGATGCTT
* *
27542901 TTGTTATTGTTGTTATTGTTGTTATTTCTATTATTGTTGTTGATG
1 TTGTTATTGTTGTTATCGTTGTTATTGCTATTATTGTTGTTGATG
27542946 TCGTTGTTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.11, C:0.04, G:0.22, T:0.63
Consensus pattern (48 bp):
TTGTTATTGTTGTTATCGTTGTTATTGCTATTATTGTTGTTGATGCTT
Found at i:27542942 original size:3 final size:3
Alignment explanation
Indices: 27542755--27542923 Score: 83
Period size: 3 Copynumber: 56.7 Consensus size: 3
27542745 ACTATTATTA
* * * * *
27542755 TTG TTG TTG CTC TTG TTG TTG TTG TT- TTG TTT TTG TTG TTA TTT TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
* * * * * * * *
27542802 TTA TTG TTG TTA TTG TTG CTG TTG TTG CTG TTG CTA TTGG TGG TGG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT-G TTG TTG
* * * * * * * *
27542848 TT- CTA TTG TTG TTG TTG TTA TCG TTG TTG TTG CTA TTA TTT TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
* * *
27542895 ATG CTT- TTG TTA TTG TTG TTA TTG TTG TT
1 TTG -TTG TTG TTG TTG TTG TTG TTG TTG TT
27542924 ATTTCTATTA
Statistics
Matches: 120, Mismatches: 41, Indels: 10
0.70 0.24 0.06
Matches are distributed among these distances:
2 5 0.04
3 113 0.94
4 2 0.02
ACGTcount: A:0.07, C:0.05, G:0.25, T:0.63
Consensus pattern (3 bp):
TTG
Found at i:27543132 original size:6 final size:6
Alignment explanation
Indices: 27543081--27543405 Score: 143
Period size: 6 Copynumber: 54.2 Consensus size: 6
27543071 TTGTTACAAT
* * * * * * *
27543081 TTGTTG TTGATG TTATTG TTGTTG CTGCTG CTATTG TTGCTG TTGTTG
1 TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG
** * * * * *
27543129 TTGTTG TAATTG TTGTTG TTATTG TTGTTG TTGTTA CTGCTA TTGTTG
1 TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG
* * * * * * * * * * *
27543177 CTATTG CTATTG TTGTTG CTGCTA CTATTG TTGTTG TTGCTC TTGTTG
1 TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG
* * * * * *
27543225 TTGTGG TTGATG ATGTTG CTGTTG TTGTGG TTGTTG TTGTTA TTGTTG
1 TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG
* * * * * * * * *
27543273 TTGCTA TTGTT- TCTGTT- TCTGTTG TTGTTC CTGTTC TTATTA TTGCTA
1 TTGTTG TTGTTG T-TGTTG T-TGTTG TTGTTG TTGTTG TTGTTG TTGTTG
* * * * * *
27543321 TTGTTG TTATTT TTGTTG TTGTTG TTATTA TTGTTC TTATTG TTAG-TG
1 TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG TT-GTTG
* * * * *
27543369 CTGTTG TAGTTG TTGTTG TAGTTG CTGTTG TTATTG T
1 TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG TTGTTG T
27543406 AGCTGCTATT
Statistics
Matches: 232, Mismatches: 83, Indels: 8
0.72 0.26 0.02
Matches are distributed among these distances:
5 2 0.01
6 229 0.99
7 1 0.00
ACGTcount: A:0.08, C:0.07, G:0.26, T:0.59
Consensus pattern (6 bp):
TTGTTG
Found at i:27543662 original size:33 final size:33
Alignment explanation
Indices: 27543598--27543662 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
27543588 TTCTGTTTTT
* * * *
27543598 TTGTTGTTGTTGTAGTTGTTGTAGTTTCTATTG
1 TTGTTGTTGTTGTAGCTATCGTAGTTGCTATTG
27543631 TTGTTGTTGTTGTAGCTATCGATA-TTGCTATT
1 TTGTTGTTGTTGTAGCTATCG-TAGTTGCTATT
27543663 ACTATTGTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 25 0.93
34 2 0.07
ACGTcount: A:0.12, C:0.06, G:0.25, T:0.57
Consensus pattern (33 bp):
TTGTTGTTGTTGTAGCTATCGTAGTTGCTATTG
Found at i:27543732 original size:57 final size:57
Alignment explanation
Indices: 27543624--27543763 Score: 149
Period size: 57 Copynumber: 2.5 Consensus size: 57
27543614 TGTTGTAGTT
*
27543624 TCTATTGTTGTTGTTGTTGTAGCTATCGATATTGCTATTACTATTGTTGTTGATGT-
1 TCTATTGTTGTTGTTGTTGTAGCTATCGATATTGCTATTACTATTGATGTTGATGTG
* ** * * * *
27543680 TGCTATTGTTGTTGTTGTTGTTGCTATCG-TAATTTTTGTTATTGTTGATGTTGTTGTG
1 T-CTATTGTTGTTGTTGTTGTAGCTATCGAT-ATTGCTATTACTATTGATGTTGATGTG
** *
27543738 TCTATTACTATTGTTGTTGTAGCTAT
1 TCTATTGTTGTTGTTGTTGTAGCTAT
27543764 TGATGTTGAT
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
56 2 0.03
57 66 0.96
58 1 0.01
ACGTcount: A:0.14, C:0.08, G:0.22, T:0.56
Consensus pattern (57 bp):
TCTATTGTTGTTGTTGTTGTAGCTATCGATATTGCTATTACTATTGATGTTGATGTG
Found at i:27543809 original size:51 final size:51
Alignment explanation
Indices: 27543751--27543857 Score: 142
Period size: 51 Copynumber: 2.1 Consensus size: 51
27543741 ATTACTATTG
* * * **
27543751 TTGTTGTAGCTATTGATGTTGATGCTGTTATTGTTGTTGATGTTGTTGTTA
1 TTGTTGTAACTATTGATGTTGATGCTATTATTGTTGTTGATATTGTTACTA
* * *
27543802 TTGTTGTAACTATTGTTGTTGTTGCTATTATTTTTGTTGATATTGTTACTA
1 TTGTTGTAACTATTGATGTTGATGCTATTATTGTTGTTGATATTGTTACTA
27543853 TTGTT
1 TTGTT
27543858 CTTGTTGTTG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.15, C:0.05, G:0.22, T:0.58
Consensus pattern (51 bp):
TTGTTGTAACTATTGATGTTGATGCTATTATTGTTGTTGATATTGTTACTA
Found at i:27544011 original size:39 final size:39
Alignment explanation
Indices: 27543968--27544045 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
27543958 TAGTTGCTGC
* *
27543968 TATTGTTTCCATTGTTGTTATT-TGTGTTGTTGTTGTTGT
1 TATTGTTTCCATTGTTGCTATTGT-TGTTGTTGTTATTGT
***
27544007 TATTGTTTTTTTTGTTGCTATTGTTGTTGTTGTTATTGT
1 TATTGTTTCCATTGTTGCTATTGTTGTTGTTGTTATTGT
27544046 AGTAGTTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
39 32 0.97
40 1 0.03
ACGTcount: A:0.08, C:0.04, G:0.22, T:0.67
Consensus pattern (39 bp):
TATTGTTTCCATTGTTGCTATTGTTGTTGTTGTTATTGT
Found at i:27544012 original size:27 final size:27
Alignment explanation
Indices: 27543979--27544070 Score: 105
Period size: 27 Copynumber: 3.4 Consensus size: 27
27543969 ATTGTTTCCA
*
27543979 TTGTTGTTATTTGTGTTGTTGTTGTTG
1 TTGTTGTTATTTGTGTTGTTATTGTTG
* * * *
27544006 TTATTGTTTTTTTTGTTGCTATTGTTG
1 TTGTTGTTATTTGTGTTGTTATTGTTG
*
27544033 TTGTTGTTA-TTGTAGTAGTTATTGTTG
1 TTGTTGTTATTTGT-GTTGTTATTGTTG
*
27544060 CTGTTGTTATT
1 TTGTTGTTATT
27544071 GCTACTGCTG
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
26 3 0.06
27 48 0.92
28 1 0.02
ACGTcount: A:0.09, C:0.02, G:0.24, T:0.65
Consensus pattern (27 bp):
TTGTTGTTATTTGTGTTGTTATTGTTG
Found at i:27544065 original size:33 final size:31
Alignment explanation
Indices: 27543978--27544102 Score: 85
Period size: 33 Copynumber: 3.9 Consensus size: 31
27543968 TATTGTTTCC
*
27543978 ATTGT-TGTTATTTG-TGTTGTTGTTGTTGTT
1 ATTGTGTGTTA-TTGTTGCTGTTGTTGTTGTT
* *
27544008 ATTGT-TTTTTTTGTTGCTATTGTTGTTGTTGTT
1 ATTGTGTGTTATTGTTGC---TGTTGTTGTTGTT
* *
27544041 ATTGTAGTAGTTATTGTTGCTGTTGTTATTGCT
1 ATTGT-GT-GTTATTGTTGCTGTTGTTGTTGTT
* * *
27544074 ACTGCTGTTGTTATTATTACTGTTGTTGT
1 ATTG-TG-TGTTATTGTTGCTGTTGTTGT
27544103 GGTTGCAGTT
Statistics
Matches: 75, Mismatches: 11, Indels: 15
0.74 0.11 0.15
Matches are distributed among these distances:
29 3 0.04
30 10 0.13
33 50 0.67
34 2 0.03
35 1 0.01
36 9 0.12
ACGTcount: A:0.10, C:0.05, G:0.23, T:0.62
Consensus pattern (31 bp):
ATTGTGTGTTATTGTTGCTGTTGTTGTTGTT
Found at i:27544070 original size:15 final size:15
Alignment explanation
Indices: 27544019--27544100 Score: 62
Period size: 15 Copynumber: 5.5 Consensus size: 15
27544009 TTGTTTTTTT
* *
27544019 TGTTGCTATTGTTGT
1 TGTTGTTATTGTTGC
27544034 TGTTGTTATTG-T--
1 TGTTGTTATTGTTGC
* *
27544046 AGTAGTTATTGTTGC
1 TGTTGTTATTGTTGC
27544061 TGTTGTTATTGCTACTGC
1 TGTTGTTATTG-T--TGC
* *
27544079 TGTTGTTATTATTAC
1 TGTTGTTATTGTTGC
27544094 TGTTGTT
1 TGTTGTT
27544101 GTGGTTGCAG
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
12 9 0.17
13 1 0.02
14 1 0.02
15 28 0.52
16 1 0.02
17 1 0.02
18 13 0.24
ACGTcount: A:0.12, C:0.07, G:0.23, T:0.57
Consensus pattern (15 bp):
TGTTGTTATTGTTGC
Found at i:27544081 original size:18 final size:18
Alignment explanation
Indices: 27544058--27544102 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
27544048 TAGTTATTGT
*
27544058 TGCTGTTGTTATTGCTAC
1 TGCTGTTGTTATTACTAC
*
27544076 TGCTGTTGTTATTATTAC
1 TGCTGTTGTTATTACTAC
*
27544094 TGTTGTTGT
1 TGCTGTTGT
27544103 GGTTGCAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.11, C:0.11, G:0.22, T:0.56
Consensus pattern (18 bp):
TGCTGTTGTTATTACTAC
Found at i:27544085 original size:3 final size:3
Alignment explanation
Indices: 27543667--27544067 Score: 72
Period size: 3 Copynumber: 133.7 Consensus size: 3
27543657 GCTATTACTA
* * * * * * ** *
27543667 TTG TTG TTG ATG TTG CTA TTG TTG TTG TTG TTG TTG CTA TCG TAA TTT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
* * * * * * *
27543715 TTG TTA TTG TTG ATG TTG TTG -TG TCTA TTA CTA TTG TTG TTG TAG
1 TTG TTG TTG TTG TTG TTG TTG TTG T-TG TTG TTG TTG TTG TTG TTG
* * * * * * * *
27543760 CTA TTG ATG TTG ATG CTG TTA TTG TTG TTG ATG TTG TTG TTA TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
** * * * * * * * * * * *
27543808 TAA CTA TTG TTG TTG TTG CTA TTA TTT TTG TTG ATA TTG TTA CTA TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
* * * * * *
27543856 TTC TTG TTG TTG TTG ATG ATG TTG -TG TTTG CTA TTG TTG TTG TTT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG -TTG TTG TTG TTG TTG TTG
* * * * * * * * *** * *
27543901 TTA ATA TTG TTA CTG CTA TTG TTG ATG TTG TTG CAA TTA CTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
* * * * * ** *
27543949 TTG TTG ATG TAG TTG CTG CTA TTG TT- TCCA TTG TTG TTA TT- TGTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T-TG TTG TTG TTG TTG T-TG
* * * * * *
27543994 TTG TTG TTG TTG TTA TTG TTT TTT TTG TTG CTA TTG TTG TTG TTG TTA
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
* * * *
27544042 TTG TAG TAG TTA TTG TTG CTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
27544068 ATTGCTACTG
Statistics
Matches: 273, Mismatches: 117, Indels: 16
0.67 0.29 0.04
Matches are distributed among these distances:
2 6 0.02
3 261 0.96
4 6 0.02
ACGTcount: A:0.12, C:0.05, G:0.24, T:0.59
Consensus pattern (3 bp):
TTG
Found at i:27544269 original size:21 final size:21
Alignment explanation
Indices: 27544232--27544273 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
27544222 GTAACTATTT
*
27544232 TTGATGTTGCTGTTATTGTTG
1 TTGATGTTGCTGCTATTGTTG
27544253 TTGATGTTG-TAGCTATTGTTG
1 TTGATGTTGCT-GCTATTGTTG
27544274 CTGCTGCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.12, C:0.05, G:0.29, T:0.55
Consensus pattern (21 bp):
TTGATGTTGCTGCTATTGTTG
Found at i:27544317 original size:18 final size:18
Alignment explanation
Indices: 27544268--27544327 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
27544258 GTTGTAGCTA
*
27544268 TTGTTGCTGCTGCTATTT
1 TTGTTGCTGCTACTATTT
* *
27544286 TTGCTATTGTTGCTATTATTT
1 TTG---TTGCTGCTACTATTT
27544307 TTGTTGCTGCTACTATTT
1 TTGTTGCTGCTACTATTT
27544325 TTG
1 TTG
27544328 ATGTTATTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 19 0.56
21 15 0.44
ACGTcount: A:0.10, C:0.13, G:0.18, T:0.58
Consensus pattern (18 bp):
TTGTTGCTGCTACTATTT
Found at i:27544332 original size:21 final size:20
Alignment explanation
Indices: 27544269--27544332 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 20
27544259 TTGTAGCTAT
*
27544269 TGTTGCTGCTGCTATTTTTG
1 TGTTGCTGCTACTATTTTTG
* * *
27544289 CTATTGTTGCTATTA-TTTT-
1 -TGTTGCTGCTACTATTTTTG
27544308 TGTTGCTGCTACTATTTTTG
1 TGTTGCTGCTACTATTTTTG
27544328 ATGTT
1 -TGTT
27544333 ATTGTTGTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 11 0.33
19 4 0.12
20 4 0.12
21 14 0.42
ACGTcount: A:0.11, C:0.12, G:0.19, T:0.58
Consensus pattern (20 bp):
TGTTGCTGCTACTATTTTTG
Found at i:27544381 original size:15 final size:15
Alignment explanation
Indices: 27544292--27544405 Score: 68
Period size: 15 Copynumber: 7.4 Consensus size: 15
27544282 ATTTTTGCTA
** *
27544292 TTGTTGCTATTATTT
1 TTGTTGCTGCTATTG
* *
27544307 TTGTTGCTGCTACTA
1 TTGTTGCTGCTATTG
* * *
27544322 TTTTTGATGTTATTG
1 TTGTTGCTGCTATTG
*
27544337 TTGTTGCTGTAGTAGTTG
1 TTGTTGCTG--CTA-TTG
27544355 TTGTTG-TAGCTATTG
1 TTGTTGCT-GCTATTG
27544370 TTGTTGCTGCTATTG
1 TTGTTGCTGCTATTG
* * * *
27544385 TTATTGATGTTGTTG
1 TTGTTGCTGCTATTG
27544400 TTGTTG
1 TTGTTG
27544406 TCGTTAATAT
Statistics
Matches: 76, Mismatches: 18, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
15 60 0.79
16 3 0.04
17 3 0.04
18 10 0.13
ACGTcount: A:0.11, C:0.07, G:0.25, T:0.57
Consensus pattern (15 bp):
TTGTTGCTGCTATTG
Found at i:27544441 original size:15 final size:15
Alignment explanation
Indices: 27544421--27544534 Score: 59
Period size: 15 Copynumber: 7.4 Consensus size: 15
27544411 AATATTGCAA
27544421 CAACAATAGCAACAT
1 CAACAATAGCAACAT
* *
27544436 CAACAACAACAACAT
1 CAACAATAGCAACAT
* *
27544451 CAATAACAATAGCAGCAA
1 C---AACAATAGCAACAT
* *
27544469 CAACAATAGCTACAA
1 CAACAATAGCAACAT
* * * *
27544484 CAAGTACTA-CTACAG
1 CAA-CAATAGCAACAT
*
27544499 CAACAACAGCAACAT
1 CAACAATAGCAACAT
* * *
27544514 CAAAAATAGTAACAG
1 CAACAATAGCAACAT
27544529 CAACAA
1 CAACAA
27544535 AAATAATAGC
Statistics
Matches: 73, Mismatches: 21, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
14 2 0.03
15 57 0.78
16 3 0.04
18 11 0.15
ACGTcount: A:0.54, C:0.26, G:0.08, T:0.11
Consensus pattern (15 bp):
CAACAATAGCAACAT
Found at i:27544542 original size:21 final size:21
Alignment explanation
Indices: 27544502--27544548 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
27544492 ACTACAGCAA
*
27544502 CAACAGCAACATCAAAAATAG
1 CAACAGCAACATAAAAAATAG
*
27544523 TAACAGCAACA-AAAATAATAG
1 CAACAGCAACATAAAA-AATAG
27544544 CAACA
1 CAACA
27544549 ACCGCAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.60, C:0.21, G:0.09, T:0.11
Consensus pattern (21 bp):
CAACAGCAACATAAAAAATAG
Found at i:27544550 original size:18 final size:18
Alignment explanation
Indices: 27544506--27544550 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
27544496 CAGCAACAAC
* *
27544506 AGCAACATCAAAAATAGT
1 AGCAACAACAAAAATAAT
* *
27544524 AACAGCAACAAAAATAAT
1 AGCAACAACAAAAATAAT
27544542 AGCAACAAC
1 AGCAACAAC
27544551 CGCAAAAATA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.60, C:0.20, G:0.09, T:0.11
Consensus pattern (18 bp):
AGCAACAACAAAAATAAT
Found at i:27544698 original size:21 final size:21
Alignment explanation
Indices: 27544674--27544724 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
27544664 AAAAATAATT
*
27544674 ACAACAATAATAAAAGCCACA
1 ACAACAATAATAAAAGCAACA
* **
27544695 ACAACAACAATAGCAGCAACA
1 ACAACAATAATAAAAGCAACA
*
27544716 ATAACAATA
1 ACAACAATA
27544725 CAACAATAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.61, C:0.24, G:0.06, T:0.10
Consensus pattern (21 bp):
ACAACAATAATAAAAGCAACA
Found at i:27544793 original size:21 final size:21
Alignment explanation
Indices: 27544768--27544912 Score: 105
Period size: 21 Copynumber: 6.6 Consensus size: 21
27544758 ATTGCAATCA
* *
27544768 CAACAACAATAATAATAACAG
1 CAACAACAACAATAACAACAG
** *
27544789 CAACAGTAGCAATAACAACAG
1 CAACAACAACAATAACAACAG
*
27544810 CAACAACAAGAACAACT-ACAATAG
1 CAACAAC---AACAA-TAACAACAG
* *
27544834 CAACAACAACAATAGCAACAAAAA
1 CAACAACAACAAT---AACAACAG
* *
27544858 AAACAACAACAATAACAACAA
1 CAACAACAACAATAACAACAG
*
27544879 CAACAACAACAAAAACAACA-
1 CAACAACAACAATAACAACAG
27544899 CAAACAACAACAAT
1 C-AACAACAACAAT
27544913 GGGAACAATA
Statistics
Matches: 99, Mismatches: 16, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
20 2 0.02
21 62 0.63
24 34 0.34
25 1 0.01
ACGTcount: A:0.63, C:0.25, G:0.05, T:0.07
Consensus pattern (21 bp):
CAACAACAACAATAACAACAG
Found at i:27544811 original size:12 final size:12
Alignment explanation
Indices: 27544810--27545126 Score: 89
Period size: 12 Copynumber: 26.2 Consensus size: 12
27544800 ATAACAACAG
*
27544810 CAACAACAAGAA
1 CAACAACAATAA
*
27544822 CAACTACAATAGCAA
1 CAACAACAAT---AA
*
27544837 CAACAACAATAG
1 CAACAACAATAA
* *
27544849 CAACAAAAAAAA
1 CAACAACAATAA
27544861 CAACAACAATAA
1 CAACAACAATAA
*
27544873 CAACAACAACAA
1 CAACAACAATAA
* *
27544885 CAACAAAAACAA
1 CAACAACAATAA
*
27544897 C-ACAAACAACAA
1 CAAC-AACAATAA
* *
27544909 CAATGGGAACAATAG
1 CAA---CAACAATAA
*
27544924 CAGCAAC--T-A
1 CAACAACAATAA
*
27544933 CATCAACAATAA
1 CAACAACAATAA
** *
27544945 CAACTGCAATTA
1 CAACAACAATAA
27544957 CAACAAC-ATCAA
1 CAACAACAAT-AA
*
27544969 CAATAAC-ATCAA
1 CAACAACAAT-AA
* * *
27544981 CAATAGCAGTAA
1 CAACAACAATAA
* ** *
27544993 CAATATTAAAAA
1 CAACAACAATAA
*
27545005 CAACAACAATAG
1 CAACAACAATAA
* *
27545017 CAA-ACACAACAT
1 CAACA-ACAATAA
* *
27545029 CATCAACAACAA
1 CAACAACAATAA
* *
27545041 CAAGAACAATAG
1 CAACAACAATAA
* *
27545053 TAACAA-TATCAA
1 CAACAACAAT-AA
* **
27545065 CAAAAATAGCAGCAA
1 C-AACA-A-CAATAA
*
27545080 CAACAACAATAG
1 CAACAACAATAA
*
27545092 CTACAACAATAA
1 CAACAACAATAA
27545104 CAACAAC-AT--
1 CAACAACAATAA
27545113 CAACAACAATAA
1 CAACAACAATAA
27545125 CA
1 CA
27545127 GCATCAACAT
Statistics
Matches: 220, Mismatches: 62, Indels: 46
0.67 0.19 0.14
Matches are distributed among these distances:
9 13 0.06
10 3 0.01
11 10 0.05
12 161 0.73
13 7 0.03
14 4 0.02
15 22 0.10
ACGTcount: A:0.60, C:0.25, G:0.05, T:0.10
Consensus pattern (12 bp):
CAACAACAATAA
Found at i:27544830 original size:15 final size:15
Alignment explanation
Indices: 27544802--27545154 Score: 116
Period size: 15 Copynumber: 23.5 Consensus size: 15
27544792 CAGTAGCAAT
*
27544802 AACAACAGCAACAAC
1 AACAACAACAACAAC
* * *
27544817 AAGAACAACTACAAT
1 AACAACAACAACAAC
* *
27544832 AGCAACAACAACAAT
1 AACAACAACAACAAC
* * *
27544847 AGCAACAAAAAAAAC
1 AACAACAACAACAAC
*
27544862 AACAACAATAACAAC
1 AACAACAACAACAAC
*
27544877 AACAACAACAACAAA
1 AACAACAACAACAAC
27544892 AACAAC-ACAAACAAC
1 AACAACAAC-AACAAC
**** *
27544907 AACAATGGGAACAAT
1 AACAACAACAACAAC
* * * *
27544922 AGCAGCAACTACATC
1 AACAACAACAACAAC
* **
27544937 AACAATAACAACTGC
1 AACAACAACAACAAC
** *
27544952 AATTACAACAACATC
1 AACAACAACAACAAC
* *
27544967 AACAATAACATCAAC
1 AACAACAACAACAAC
* * ** *
27544982 AATAGCAGTAACAAT
1 AACAACAACAACAAC
** *
27544997 ATTAAAAACAACAAC
1 AACAACAACAACAAC
* *
27545012 AATAGCAA-ACACAAC
1 AACAACAACA-ACAAC
* *
27545027 ATCATCAACAACAAC
1 AACAACAACAACAAC
* * **
27545042 AAGAACAATAGTAAC
1 AACAACAACAACAAC
* * * *
27545057 AATATCAACAAAAAT
1 AACAACAACAACAAC
* *
27545072 AGCAGCAACAACAAC
1 AACAACAACAACAAC
* * * *
27545087 AATAGCTACAACAAT
1 AACAACAACAACAAC
*
27545102 AACAACAACATCAAC
1 AACAACAACAACAAC
* * *
27545117 AACAATAACAGCATC
1 AACAACAACAACAAC
* * * *
27545132 AACATCAATAGCTAC
1 AACAACAACAACAAC
27545147 AACAACAA
1 AACAACAA
27545155 TAGTAGGAGC
Statistics
Matches: 235, Mismatches: 99, Indels: 8
0.69 0.29 0.02
Matches are distributed among these distances:
14 3 0.01
15 231 0.98
16 1 0.00
ACGTcount: A:0.59, C:0.25, G:0.06, T:0.10
Consensus pattern (15 bp):
AACAACAACAACAAC
Found at i:27544886 original size:24 final size:24
Alignment explanation
Indices: 27544768--27545286 Score: 109
Period size: 24 Copynumber: 21.4 Consensus size: 24
27544758 ATTGCAATCA
* * *
27544768 CAACAACAATAATAATAACAGCAA
1 CAACAACAACAACAATAACAACAA
** * * * *
27544792 CAGTAGCAATAACAACAGCAACAA
1 CAACAACAACAACAATAACAACAA
* * *
27544816 CAAGAACAACTACAATAGCAACAA
1 CAACAACAACAACAATAACAACAA
* *
27544840 CAACAATAGCAACAA-AA-AA-AA
1 CAACAACAACAACAATAACAACAA
* *
27544861 CAACAACAATAACAACAACAACAA
1 CAACAACAACAACAATAACAACAA
*
27544885 CAACAAAAACAACACA-AACAACAA
1 CAACAACAACAACA-ATAACAACAA
**** * ** * *
27544909 CAATGGGAACAATAGCAGCAACTA
1 CAACAACAACAACAATAACAACAA
* * * **
27544933 CATCAACAATAACAACT-GCAATTA
1 CAACAACAACAACAA-TAACAACAA
* *
27544957 CAACAACATCAACAATAACATCAA
1 CAACAACAACAACAATAACAACAA
* * ** ** *
27544981 CAATAGCAGTAACAATATTAAAAA
1 CAACAACAACAACAATAACAACAA
* * *
27545005 CAACAACAATAGCAA-ACACAACAT
1 CAACAACAACAACAATA-ACAACAA
* * * *
27545029 CATCAACAACAACAAGAACAATAG
1 CAACAACAACAACAATAACAACAA
* * * * * * *
27545053 TAACAATATCAACAAAAATAGCAG
1 CAACAACAACAACAATAACAACAA
* *
27545077 CAACAACAACAATAGCT-ACAACAA
1 CAACAACAACAACA-ATAACAACAA
* * * *
27545101 TAACAACAACATCAACAACAATAA
1 CAACAACAACAACAATAACAACAA
* * * * *
27545125 CAGCATCAACATCAATAGCTACAA
1 CAACAACAACAACAATAACAACAA
* * * ** *
27545149 CAACAATAGTAGGAGCAGCAACAACTA
1 CAACAACA--A-CAACAATAACAACAA
* * *
27545176 CAACAACAACAATAGTAATAGAC-A
1 CAACAACAACAACAATAACA-ACAA
* *
27545200 CAACAACATCAACAATAACAAAAATTA
1 CAACAACAACAACAATAAC-AACA--A
* ** * *
27545227 CGATAGCAACAATAACAATAGTAATAG
1 C-A-A-CAACAACAACAATAACAACAA
* *
27545254 CAACAACAACAACAATAGCAACAT
1 CAACAACAACAACAATAACAACAA
27545278 CAACAACAA
1 CAACAACAA
27545287 TAGTAGTAGC
Statistics
Matches: 343, Mismatches: 130, Indels: 44
0.66 0.25 0.09
Matches are distributed among these distances:
21 14 0.04
22 4 0.01
23 5 0.01
24 276 0.80
25 7 0.02
26 2 0.01
27 18 0.05
28 1 0.00
29 4 0.01
30 12 0.03
ACGTcount: A:0.58, C:0.24, G:0.07, T:0.11
Consensus pattern (24 bp):
CAACAACAACAACAATAACAACAA
Found at i:27544895 original size:9 final size:9
Alignment explanation
Indices: 27544838--27544908 Score: 70
Period size: 9 Copynumber: 7.9 Consensus size: 9
27544828 CAATAGCAAC
*
27544838 AACAACAAT
1 AACAACAAA
*
27544847 AGCAACAAA
1 AACAACAAA
* *
27544856 AAAAACAAC
1 AACAACAAA
* *
27544865 AACAATAAC
1 AACAACAAA
*
27544874 AACAACAAC
1 AACAACAAA
27544883 AACAACAAA
1 AACAACAAA
*
27544892 AACAACACA
1 AACAACAAA
27544901 AACAACAA
1 AACAACAA
27544909 CAATGGGAAC
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.70, C:0.25, G:0.01, T:0.03
Consensus pattern (9 bp):
AACAACAAA
Found at i:27545057 original size:21 final size:21
Alignment explanation
Indices: 27545032--27545126 Score: 61
Period size: 21 Copynumber: 4.7 Consensus size: 21
27545022 ACAACATCAT
* *
27545032 CAACAACAACAAGAACAATAG
1 CAACAACAACAACAAAAATAG
* * *
27545053 TAACAATATCAACAAAAATAG
1 CAACAACAACAACAAAAATAG
*
27545074 CAGCAACAACAAC---AATAG
1 CAACAACAACAACAAAAATAG
* * * * *
27545092 CTACAACAATAACAACAACAT
1 CAACAACAACAACAAAAATAG
*
27545113 CAACAACAATAACA
1 CAACAACAACAACA
27545127 GCATCAACAT
Statistics
Matches: 56, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
18 15 0.27
21 41 0.73
ACGTcount: A:0.60, C:0.24, G:0.05, T:0.11
Consensus pattern (21 bp):
CAACAACAACAACAAAAATAG
Found at i:27545098 original size:18 final size:17
Alignment explanation
Indices: 27545003--27545154 Score: 78
Period size: 18 Copynumber: 8.5 Consensus size: 17
27544993 CAATATTAAA
27545003 AACAACAACAATAGCA-
1 AACAACAACAATAGCAC
*
27545019 AAC-ACAACATCATCAACAAC
1 AACAACAACA--AT-AGC-AC
* *
27545039 AACAAGAACAATAGTAAC
1 AACAACAACAATAG-CAC
*
27545057 AATATCAACAAAAATAGCAGC
1 -A-A-CAACAACAATAGCA-C
27545078 AACAACAACAATAGCTAC
1 AACAACAACAATAGC-AC
* *
27545096 AACAATAACAACA--AC
1 AACAACAACAATAGCAC
* *
27545111 ATCAACAACAATAACAGC
1 AACAACAACAATAGCA-C
* *
27545129 ATCAACATCAATAGCTAC
1 AACAACAACAATAGC-AC
27545147 AACAACAA
1 AACAACAA
27545155 TAGTAGGAGC
Statistics
Matches: 103, Mismatches: 17, Indels: 30
0.69 0.11 0.20
Matches are distributed among these distances:
15 18 0.17
16 3 0.03
17 3 0.03
18 50 0.49
19 7 0.07
20 6 0.06
21 16 0.16
ACGTcount: A:0.58, C:0.26, G:0.05, T:0.11
Consensus pattern (17 bp):
AACAACAACAATAGCAC
Found at i:27545100 original size:51 final size:51
Alignment explanation
Indices: 27545045--27545151 Score: 151
Period size: 51 Copynumber: 2.1 Consensus size: 51
27545035 CAACAACAAG
** * *
27545045 AACAATAGTAACAATATCAACAAAAATAGCAGCAACAACAACAATAGCTAC
1 AACAATAACAACAACATCAACAAAAATAACAGCAACAACAACAATAGCTAC
* * *
27545096 AACAATAACAACAACATCAACAACAATAACAGCATCAACATCAATAGCTAC
1 AACAATAACAACAACATCAACAAAAATAACAGCAACAACAACAATAGCTAC
27545147 AACAA
1 AACAA
27545152 CAATAGTAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.57, C:0.24, G:0.06, T:0.13
Consensus pattern (51 bp):
AACAATAACAACAACATCAACAAAAATAACAGCAACAACAACAATAGCTAC
Found at i:27545204 original size:33 final size:33
Alignment explanation
Indices: 27545145--27545220 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
27545135 ATCAATAGCT
*
27545145 ACAACAACAATAGTAGGAGCAGCAACAAC-TACA
1 ACAACAACAATAGTAAGAGCAGCAACAACAT-CA
*
27545178 ACAACAACAATAGTAATAGACA-CAACAACATCA
1 ACAACAACAATAGTAAGAG-CAGCAACAACATCA
*
27545211 ACAATAACAA
1 ACAACAACAA
27545221 AAATTACGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 35 0.92
34 3 0.08
ACGTcount: A:0.57, C:0.24, G:0.09, T:0.11
Consensus pattern (33 bp):
ACAACAACAATAGTAAGAGCAGCAACAACATCA
Found at i:27545270 original size:18 final size:18
Alignment explanation
Indices: 27545249--27545289 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
27545239 TAACAATAGT
27545249 AATAGCAACAACAACAAC
1 AATAGCAACAACAACAAC
*
27545267 AATAGCAACATCAACAAC
1 AATAGCAACAACAACAAC
27545285 AATAG
1 AATAG
27545290 TAGTAGCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.59, C:0.24, G:0.07, T:0.10
Consensus pattern (18 bp):
AATAGCAACAACAACAAC
Found at i:27545352 original size:15 final size:15
Alignment explanation
Indices: 27545308--27545352 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
27545298 ATTCGATAGC
*
27545308 TACAACGACAAC-AA
1 TACAACAACAACAAA
*
27545322 TAGCAACTACAACAAA
1 TA-CAACAACAACAAA
27545338 TACAACAACAACAAA
1 TACAACAACAACAAA
27545353 ACAGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 21 0.78
16 4 0.15
ACGTcount: A:0.60, C:0.27, G:0.04, T:0.09
Consensus pattern (15 bp):
TACAACAACAACAAA
Found at i:27545546 original size:6 final size:6
Alignment explanation
Indices: 27545535--27545811 Score: 99
Period size: 6 Copynumber: 46.2 Consensus size: 6
27545525 AATAGCAGCT
* * * * ** *
27545535 ACAACA ACAACA ACTACA ACAGCA CCAACA ATAGGA ACAATA ACAACA
1 ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA
* * * * * * * **
27545583 ACAGCA ACAAAA ATAACA ACAATA GCAATA ACAAGA ACAGGA ACAACA
1 ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA
* * * ** * *
27545631 GCAGA-A ACAGA-A ACAATA GCAACA ACAATT ATAACA ACAACA ACCACA
1 ACA-ACA ACA-ACA ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA
* * * ** * * * * *
27545679 ACAATA GCAACA ACAACA ATAGTA GCAGCA ACAACA ATAACA ATAGCA
1 ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA
* ** * * * **
27545727 ACAATA GTAGCA ACAACA ATAACA ATAACA ATTACA ACAACA ACAACA
1 ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA
* * * ** *
27545775 GCAATA GCAACA ACAACA ACAATG ACATCA ACAACA A
1 ACAACA ACAACA ACAACA ACAACA ACAACA ACAACA A
27545812 ATTGTAGCAA
Statistics
Matches: 192, Mismatches: 77, Indels: 4
0.70 0.28 0.01
Matches are distributed among these distances:
5 1 0.01
6 190 0.99
7 1 0.01
ACGTcount: A:0.59, C:0.25, G:0.08, T:0.09
Consensus pattern (6 bp):
ACAACA
Found at i:27545553 original size:9 final size:9
Alignment explanation
Indices: 27545535--27545811 Score: 99
Period size: 9 Copynumber: 30.8 Consensus size: 9
27545525 AATAGCAGCT
27545535 ACAACAACA
1 ACAACAACA
*
27545544 ACAACTACA
1 ACAACAACA
* *
27545553 ACAGCACCA
1 ACAACAACA
* **
27545562 ACAATAGGA
1 ACAACAACA
*
27545571 ACAATAACA
1 ACAACAACA
*
27545580 ACAACAGCA
1 ACAACAACA
* *
27545589 ACAAAAATA
1 ACAACAACA
*
27545598 ACAACAATA
1 ACAACAACA
* *
27545607 GCAATAACA
1 ACAACAACA
* **
27545616 AGAACAGGA
1 ACAACAACA
*
27545625 ACAACAGCA
1 ACAACAACA
27545634 GA-AACAGA-A
1 -ACAACA-ACA
* *
27545643 ACAATAGCA
1 ACAACAACA
**
27545652 ACAACAATT
1 ACAACAACA
*
27545661 ATAACAACA
1 ACAACAACA
*
27545670 ACAACCACA
1 ACAACAACA
* *
27545679 ACAATAGCA
1 ACAACAACA
27545688 ACAACAACA
1 ACAACAACA
* ** *
27545697 ATAGTAGCA
1 ACAACAACA
*
27545706 GCAACAACA
1 ACAACAACA
* *
27545715 ATAACAATA
1 ACAACAACA
* *
27545724 GCAACAATA
1 ACAACAACA
** *
27545733 GTAGCAACA
1 ACAACAACA
*
27545742 ACAATAACA
1 ACAACAACA
* **
27545751 ATAACAATT
1 ACAACAACA
27545760 ACAACAACA
1 ACAACAACA
*
27545769 ACAACAGCA
1 ACAACAACA
* *
27545778 ATAGCAACA
1 ACAACAACA
27545787 ACAACAACA
1 ACAACAACA
** *
27545796 ATGACATCA
1 ACAACAACA
27545805 ACAACAA
1 ACAACAA
27545812 ATTGTAGCAA
Statistics
Matches: 181, Mismatches: 83, Indels: 8
0.67 0.31 0.03
Matches are distributed among these distances:
8 1 0.01
9 179 0.99
10 1 0.01
ACGTcount: A:0.59, C:0.25, G:0.08, T:0.09
Consensus pattern (9 bp):
ACAACAACA
Found at i:27545600 original size:27 final size:27
Alignment explanation
Indices: 27545511--27545601 Score: 65
Period size: 27 Copynumber: 3.3 Consensus size: 27
27545501 AACAGTAACG
* * * * *
27545511 ATAACATTAACAACAATAGCAGCTACA
1 ATAACAATAACAACAACAGCAACAAAA
* * * *
27545538 ACAACAACAACTACAACAGCACCAACAA
1 ATAACAATAACAACAACAGCAACAA-AA
*
27545566 TAGGAACAATAACAACAACAGCAACAAAA
1 -A-TAACAATAACAACAACAGCAACAAAA
27545595 ATAACAA
1 ATAACAA
27545602 CAATAGCAAT
Statistics
Matches: 48, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
27 23 0.48
28 2 0.04
29 3 0.06
30 20 0.42
ACGTcount: A:0.58, C:0.25, G:0.07, T:0.10
Consensus pattern (27 bp):
ATAACAATAACAACAACAGCAACAAAA
Found at i:27545621 original size:21 final size:21
Alignment explanation
Indices: 27545570--27545811 Score: 89
Period size: 21 Copynumber: 11.2 Consensus size: 21
27545560 CAACAATAGG
27545570 AACAATAACAACAACAGCAAC
1 AACAATAACAACAACAGCAAC
* * *
27545591 AAAAATAACAACAATAGCAAT
1 AACAATAACAACAACAGCAAC
*
27545612 AACAAGAACAGGAACAACAGCAGA-
1 AACAATAAC---AACAACAGCA-AC
* * *
27545636 AACAGA-AACAATAGCAACAAC
1 AACA-ATAACAACAACAGCAAC
** * *
27545657 AATTATAACAACAACAACCAC
1 AACAATAACAACAACAGCAAC
*
27545678 AACAATAGCAAC-A-A-CAAC
1 AACAATAACAACAACAGCAAC
* * * * * *
27545696 AATAGTAGCAGCAACAACAAT
1 AACAATAACAACAACAGCAAC
* *
27545717 AACAATAGCAACAATAGTAGCAAC
1 AACAATAACAAC-A-A-CAGCAAC
* *
27545741 AACAATAACAATAACAATTACAAC
1 AACAATAACAACAAC-A--GCAAC
* * *
27545765 AACAACAACAGCAATAGCAAC
1 AACAATAACAACAACAGCAAC
* ** *
27545786 AACAACAACAATGACATCAAC
1 AACAATAACAACAACAGCAAC
27545807 AACAA
1 AACAA
27545812 ATTGTAGCAA
Statistics
Matches: 163, Mismatches: 42, Indels: 32
0.69 0.18 0.14
Matches are distributed among these distances:
18 12 0.07
19 2 0.01
20 4 0.02
21 92 0.56
22 3 0.02
23 3 0.02
24 45 0.28
25 2 0.01
ACGTcount: A:0.60, C:0.24, G:0.08, T:0.09
Consensus pattern (21 bp):
AACAATAACAACAACAGCAAC
Found at i:27545689 original size:18 final size:18
Alignment explanation
Indices: 27545519--27545811 Score: 110
Period size: 18 Copynumber: 15.3 Consensus size: 18
27545509 CGATAACATT
27545519 AACAACAATAGCAGCTACAAC
1 AACAACAATAGCA---ACAAC
*
27545540 AACAACAACTA-CAACAGC
1 AACAACAA-TAGCAACAAC
* * *
27545558 ACCAACAATAGGAACAAT
1 AACAACAATAGCAACAAC
* *
27545576 AACAACAACAGCAACAAAAAT
1 AACAACAATAGCAAC---AAC
*
27545597 AACAACAATAGCAATAACAAG
1 AACAACAATAGC---AACAAC
*
27545618 AACAGGAACAACAGCAGA-AAC
1 AAC---AACAATAGCA-ACAAC
27545639 AGA-AACAATAGCAACAAC
1 A-ACAACAATAGCAACAAC
** * * *
27545657 AATTATAACAACAACAAC
1 AACAACAATAGCAACAAC
*
27545675 CACAACAATAGCAACAAC
1 AACAACAATAGCAACAAC
* *
27545693 AACAATAGTAGCAGCAACAAC
1 AACAACA--A-TAGCAACAAC
* *
27545714 AATAACAATAGCAACAAT
1 AACAACAATAGCAACAAC
** * * * *
27545732 AGTAGCAACAACAATAAC
1 AACAACAATAGCAACAAC
*
27545750 AATAACAATTA-CAACAAC
1 AACAACAA-TAGCAACAAC
27545768 AACAACAGCAATAGCAACAAC
1 AAC-A-A-CAATAGCAACAAC
*
27545789 AACAACAAT-GACATCAAC
1 AACAACAATAG-CAACAAC
27545807 AACAA
1 AACAA
27545812 ATTGTAGCAA
Statistics
Matches: 206, Mismatches: 42, Indels: 51
0.69 0.14 0.17
Matches are distributed among these distances:
17 5 0.02
18 117 0.57
19 4 0.02
20 5 0.02
21 60 0.29
22 4 0.02
24 11 0.05
ACGTcount: A:0.58, C:0.25, G:0.08, T:0.09
Consensus pattern (18 bp):
AACAACAATAGCAACAAC
Found at i:27545698 original size:15 final size:15
Alignment explanation
Indices: 27545671--27545793 Score: 84
Period size: 15 Copynumber: 7.8 Consensus size: 15
27545661 ATAACAACAA
*
27545671 CAACCACAACAATAG
1 CAACAACAACAATAG
27545686 CAACAACAACAATAGTAG
1 CAACAACAAC-A-A-TAG
* *
27545704 CAGCAACAACAATAA
1 CAACAACAACAATAG
* *
27545719 CAATAGCAACAATAG
1 CAACAACAACAATAG
* * *
27545734 TAGCAACAACAATAA
1 CAACAACAACAATAG
* * *
27545749 CAATAACAATTACAACAA
1 CAACAAC-A--ACAATAG
*
27545767 CAACAACAGCAATAG
1 CAACAACAACAATAG
27545782 CAACAACAACAA
1 CAACAACAACAA
27545794 CAATGACATC
Statistics
Matches: 81, Mismatches: 21, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
15 51 0.63
16 3 0.04
17 3 0.04
18 24 0.30
ACGTcount: A:0.58, C:0.25, G:0.07, T:0.10
Consensus pattern (15 bp):
CAACAACAACAATAG
Found at i:27545711 original size:30 final size:31
Alignment explanation
Indices: 27545676--27545757 Score: 112
Period size: 33 Copynumber: 2.6 Consensus size: 31
27545666 AACAACAACC
* *
27545676 ACAACAATAGCAACAACAACAATAGTAGCAGCA
1 ACAACAATAACAATAACAACAATAGTAGCA--A
*
27545709 ACAACAATAACAATAGCAACAATAGTAGC-A
1 ACAACAATAACAATAACAACAATAGTAGCAA
27545739 ACAACAATAACAATAACAA
1 ACAACAATAACAATAACAA
27545758 TTACAACAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
30 19 0.42
33 26 0.58
ACGTcount: A:0.59, C:0.22, G:0.09, T:0.11
Consensus pattern (31 bp):
ACAACAATAACAATAACAACAATAGTAGCAA
Found at i:27545713 original size:33 final size:33
Alignment explanation
Indices: 27545671--27545793 Score: 108
Period size: 33 Copynumber: 3.8 Consensus size: 33
27545661 ATAACAACAA
* *
27545671 CAACCACAACAATAGCAACAACAACAATAGTAG
1 CAACAACAACAATAACAACAACAACAATAGTAG
* * *
27545704 CAGCAACAACAATAACAATAGCAACAATAGTAG
1 CAACAACAACAATAACAACAACAACAATAGTAG
* * * ** *
27545737 CAACAACAATAACAATAACAATTACAACA--A-
1 CAACAACAACAATAACAACAACAACAATAGTAG
* *
27545767 CAACAACAGCAATAGCAACAACAACAA
1 CAACAACAACAATAACAACAACAACAA
27545794 CAATGACATC
Statistics
Matches: 69, Mismatches: 21, Indels: 3
0.74 0.23 0.03
Matches are distributed among these distances:
30 20 0.29
31 1 0.01
33 48 0.70
ACGTcount: A:0.58, C:0.25, G:0.07, T:0.10
Consensus pattern (33 bp):
CAACAACAACAATAACAACAACAACAATAGTAG
Found at i:27545841 original size:19 final size:21
Alignment explanation
Indices: 27545817--27545857 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
27545807 AACAAATTGT
27545817 AGCAATAG-AA-AAAAACAAC
1 AGCAATAGCAACAAAAACAAC
*
27545836 AGCAATAGCAACAACAACAAC
1 AGCAATAGCAACAAAAACAAC
27545857 A
1 A
27545858 ATGACATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 2 0.11
21 9 0.47
ACGTcount: A:0.63, C:0.22, G:0.10, T:0.05
Consensus pattern (21 bp):
AGCAATAGCAACAAAAACAAC
Found at i:27545850 original size:62 final size:61
Alignment explanation
Indices: 27545768--27545900 Score: 257
Period size: 62 Copynumber: 2.2 Consensus size: 61
27545758 TTACAACAAC
27545768 AACAACAGCAATAGCAACAACAACAACAATGACATCAACAACAAATTGTAGCAATAGAAAAA
1 AACAACAGCAATAGCAACAACAACAACAATGACATCAACAACAAATTGTAGCAATAG-AAAA
27545830 AACAACAGCAATAGCAACAACAACAACAATGACATCAACAACAAATTGTAGCAATAGAAAA
1 AACAACAGCAATAGCAACAACAACAACAATGACATCAACAACAAATTGTAGCAATAGAAAA
27545891 AACAACAGCA
1 AACAACAGCA
27545901 GCAACAATAA
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
61 14 0.20
62 57 0.80
ACGTcount: A:0.58, C:0.22, G:0.10, T:0.11
Consensus pattern (61 bp):
AACAACAGCAATAGCAACAACAACAACAATGACATCAACAACAAATTGTAGCAATAGAAAA
Found at i:27545980 original size:21 final size:21
Alignment explanation
Indices: 27545941--27545980 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
27545931 AATAGTAATG
*
27545941 ATAAGAACAACATCAATAACA
1 ATAAGAACAACAACAATAACA
* *
27545962 ATAATAACAACAACTATAA
1 ATAAGAACAACAACAATAA
27545981 ATTGCAGCAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.62, C:0.17, G:0.03, T:0.17
Consensus pattern (21 bp):
ATAAGAACAACAACAATAACA
Found at i:27546224 original size:3 final size:3
Alignment explanation
Indices: 27546075--27546204 Score: 86
Period size: 3 Copynumber: 43.7 Consensus size: 3
27546065 ACAATAGTAG
* * * * *
27546075 CAA CAA CAG CGA CAA CAA CAA CAA CAA CAA CAA CAGA -AC CAC CAC
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA-A CAA CAA CAA
* * * * *
27546120 CAA CAG CAA CAA CAA CAA -ACC CAA CAA TAA CAA CAA TAA -AA AAA
1 CAA CAA CAA CAA CAA CAA CA-A CAA CAA CAA CAA CAA CAA CAA CAA
* * * * *
27546164 TAA CAA CAA AAA CAA CAA CAA CAA GAG CAA CAA CAA TAA CA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CA
27546205 GTAGTAAAGA
Statistics
Matches: 99, Mismatches: 23, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
2 3 0.03
3 94 0.95
4 2 0.02
ACGTcount: A:0.62, C:0.30, G:0.05, T:0.03
Consensus pattern (3 bp):
CAA
Found at i:27546240 original size:33 final size:35
Alignment explanation
Indices: 27546191--27546273 Score: 98
Period size: 36 Copynumber: 2.4 Consensus size: 35
27546181 ACAACAAGAG
* *
27546191 CAACAACAATAACAGTAG-TAAAG-ACAGCAACAA
1 CAACAACAATAGCAGTAGCAAAAGAACAGCAACAA
* *
27546224 CAATAACAATAGCAGTAGCAAAAGCAATAGCAACAA
1 CAACAACAATAGCAGTAGCAAAAG-AACAGCAACAA
*
27546260 TAACAACAATAGCA
1 CAACAACAATAGCA
27546274 ACAACAATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
33 16 0.39
34 4 0.10
36 21 0.51
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.11
Consensus pattern (35 bp):
CAACAACAATAGCAGTAGCAAAAGAACAGCAACAA
Found at i:27546266 original size:9 final size:9
Alignment explanation
Indices: 27546248--27546277 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
27546238 GTAGCAAAAG
27546248 CAATAGCAA
1 CAATAGCAA
*
27546257 CAATAACAA
1 CAATAGCAA
27546266 CAATAGCAA
1 CAATAGCAA
27546275 CAA
1 CAA
27546278 CAATAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.60, C:0.23, G:0.07, T:0.10
Consensus pattern (9 bp):
CAATAGCAA
Found at i:27546285 original size:15 final size:15
Alignment explanation
Indices: 27546221--27546465 Score: 91
Period size: 15 Copynumber: 15.6 Consensus size: 15
27546211 AAGACAGCAA
*
27546221 CAACAATAACAATAG
1 CAACAACAACAATAG
27546236 CAGTAGCAA-AAGCAATAG
1 CA--A-CAACAA-CAATAG
27546254 CAACAATAACAACAATAG
1 CAAC---AACAACAATAG
* *
27546272 CAACAACAATAATAA
1 CAACAACAACAATAG
* ** * *
27546287 TAGTAACAAAAATTG
1 CAACAACAACAATAG
27546302 CAACAACCGAAACAATAG
1 CAACAA-C--AACAATAG
* * *
27546320 CAGCAACAAAAATAA
1 CAACAACAACAATAG
* * *
27546335 CAACAATAAAAAAAG
1 CAACAACAACAATAG
*
27546350 CAATAACAACAATAG
1 CAACAACAACAATAG
* *
27546365 CAACAACAATAAAAAG
1 CAACAACAA-CAATAG
* *
27546381 -AGCAACAACAA-AA
1 CAACAACAACAATAG
* * * *
27546394 AAATAACAATAATAA
1 CAACAACAACAATAG
* *
27546409 TAATAACGATAGCAATAG
1 CAACAAC-A-A-CAATAG
* *
27546427 CAACAACAACAACAA
1 CAACAACAACAATAG
*
27546442 CAACAAAAACAATAG
1 CAACAACAACAATAG
27546457 CAACAACAA
1 CAACAACAA
27546466 TAACTACAAT
Statistics
Matches: 169, Mismatches: 44, Indels: 34
0.68 0.18 0.14
Matches are distributed among these distances:
13 1 0.01
14 10 0.06
15 99 0.59
16 8 0.05
17 6 0.04
18 43 0.25
19 2 0.01
ACGTcount: A:0.62, C:0.19, G:0.08, T:0.11
Consensus pattern (15 bp):
CAACAACAACAATAG
Found at i:27546360 original size:33 final size:33
Alignment explanation
Indices: 27546323--27546408 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
27546313 ACAATAGCAG
*
27546323 CAACAAAAATAACAACAATAAAAAAAGCAATAA
1 CAACAAAAATAACAACAATAAAAAAAGCAACAA
* ** *
27546356 CAACAATAGCAACAACAATAAAAAGAGCAACAA
1 CAACAAAAATAACAACAATAAAAAAAGCAACAA
*
27546389 CAA-AAAAATAACAATAATAA
1 CAACAAAAATAACAACAATAA
27546409 TAATAACGAT
Statistics
Matches: 44, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 13 0.30
33 31 0.70
ACGTcount: A:0.70, C:0.16, G:0.05, T:0.09
Consensus pattern (33 bp):
CAACAAAAATAACAACAATAAAAAAAGCAACAA
Found at i:27546433 original size:3 final size:3
Alignment explanation
Indices: 27546427--27546530 Score: 73
Period size: 3 Copynumber: 34.7 Consensus size: 3
27546417 ATAGCAATAG
* * * * *
27546427 CAA CAA CAA CAA CAA CAA CAA AAA CAA TAG CAA CAA CAA TAA CTA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
* * * * * * * * *
27546475 TAG CAA CAA CAA TAA CTA CAA CAG CAA CAA CAC CAC CAG CAA CAA TAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
*
27546523 TAA CAA CA
1 CAA CAA CA
27546531 CAAACATGAA
Statistics
Matches: 76, Mismatches: 25, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.60, C:0.29, G:0.04, T:0.08
Consensus pattern (3 bp):
CAA
Found at i:27546460 original size:21 final size:21
Alignment explanation
Indices: 27546436--27546506 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
27546426 GCAACAACAA
* **
27546436 CAACAACAACAAAAACAATAG
1 CAACAACAATAACTACAATAG
27546457 CAACAACAATAACTACAATAG
1 CAACAACAATAACTACAATAG
*
27546478 CAACAACAATAACTACAACAG
1 CAACAACAATAACTACAATAG
27546499 CAACAACA
1 CAACAACA
27546507 CCACCAGCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.61, C:0.27, G:0.04, T:0.08
Consensus pattern (21 bp):
CAACAACAATAACTACAATAG
Found at i:27546562 original size:18 final size:18
Alignment explanation
Indices: 27546539--27546582 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
27546529 CACAAACATG
*
27546539 AACAGCAATAGTAATAAC
1 AACAGCAATAGTAACAAC
27546557 AACAGCAATAGTAACAAC
1 AACAGCAATAGTAACAAC
27546575 AACAGCAA
1 AACAGCAA
27546583 CAACAACACA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.57, C:0.20, G:0.11, T:0.11
Consensus pattern (18 bp):
AACAGCAATAGTAACAAC
Found at i:27546777 original size:69 final size:69
Alignment explanation
Indices: 27546704--27546839 Score: 168
Period size: 69 Copynumber: 2.0 Consensus size: 69
27546694 TCGCAGCAGC
* * * * *
27546704 AACAATAACAATAACTA-CAATATCAGCAATA-ACAACAAGAGCAACAACAATAGCAACGTCAAT
1 AACAATAACAATAA-TACCAATAGCAACAACAGA-AACAAGAGCAACAACAACAGCAACGTCAAC
27546767 AACATT
64 AACATT
* * *
27546773 AACAATAACTATAATACCAGTAGCAACAACAGAAACAAGAGCAACAATAACAGCAACGTCAACAA
1 AACAATAACAATAATACCAATAGCAACAACAGAAACAAGAGCAACAACAACAGCAACGTCAACAA
27546838 CA
66 CA
27546840 ACAGCAACAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
68 2 0.04
69 54 0.95
70 1 0.02
ACGTcount: A:0.55, C:0.23, G:0.09, T:0.13
Consensus pattern (69 bp):
AACAATAACAATAATACCAATAGCAACAACAGAAACAAGAGCAACAACAACAGCAACGTCAACAA
CATT
Found at i:27546857 original size:21 final size:21
Alignment explanation
Indices: 27546796--27546863 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
27546786 ATACCAGTAG
*
27546796 CAACAACAGAAACAAGAGCAA
1 CAACAACAGCAACAAGAGCAA
* *
27546817 CAATAACAGCAAC--G-TCAA
1 CAACAACAGCAACAAGAGCAA
*
27546835 CAACAACAGCAACAAGAGAAA
1 CAACAACAGCAACAAGAGCAA
27546856 CAACAACA
1 CAACAACA
27546864 ATGGTAGTGT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
18 15 0.39
19 1 0.03
20 1 0.03
21 21 0.55
ACGTcount: A:0.59, C:0.26, G:0.12, T:0.03
Consensus pattern (21 bp):
CAACAACAGCAACAAGAGCAA
Found at i:27546880 original size:3 final size:3
Alignment explanation
Indices: 27546874--27546948 Score: 78
Period size: 3 Copynumber: 25.0 Consensus size: 3
27546864 ATGGTAGTGT
* * * * *
27546874 CAA CAA CAA CAA CAA TAA CTA CAA TAC CAA CAA CAA CAA CAG CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA
* * *
27546922 GAG CAA CAA CAA CAA CAA CAG CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
27546949 TAATAATAAC
Statistics
Matches: 56, Mismatches: 16, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.60, C:0.31, G:0.05, T:0.04
Consensus pattern (3 bp):
CAA
Found at i:27546937 original size:24 final size:24
Alignment explanation
Indices: 27546832--27546938 Score: 79
Period size: 24 Copynumber: 4.5 Consensus size: 24
27546822 ACAGCAACGT
*
27546832 CAACAACAACAGCAACAAGAGAAA
1 CAACAACAACAGCAACAAGAGCAA
** * ***** *
27546856 CAACAACAATGGTAGTGTCAACAA
1 CAACAACAACAGCAACAAGAGCAA
* * * * *
27546880 CAACAACAATAACTACAATACCAA
1 CAACAACAACAGCAACAAGAGCAA
27546904 CAACAACAACAGCAACAAGAGCAA
1 CAACAACAACAGCAACAAGAGCAA
27546928 CAACAACAACA
1 CAACAACAACA
27546939 ACAGCAACAA
Statistics
Matches: 58, Mismatches: 25, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.57, C:0.27, G:0.09, T:0.07
Consensus pattern (24 bp):
CAACAACAACAGCAACAAGAGCAA
Found at i:27546989 original size:18 final size:18
Alignment explanation
Indices: 27546894--27546992 Score: 74
Period size: 18 Copynumber: 5.5 Consensus size: 18
27546884 AACAATAACT
* * *
27546894 ACAATACCAACAACAACA
1 ACAATAACAACAGCAATA
** * *
27546912 ACAGCAACAAGAGCAACA
1 ACAATAACAACAGCAATA
* *
27546930 ACAACAACAACAGCAACA
1 ACAATAACAACAGCAATA
* *
27546948 ATAATAATAACAGCAATA
1 ACAATAACAACAGCAATA
*
27546966 GA-AATAACAACATCAATA
1 -ACAATAACAACAGCAATA
27546984 ACAATAACA
1 ACAATAACA
27546993 CTAACAACAT
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
17 1 0.02
18 64 0.97
19 1 0.02
ACGTcount: A:0.61, C:0.24, G:0.06, T:0.09
Consensus pattern (18 bp):
ACAATAACAACAGCAATA
Found at i:27549211 original size:19 final size:19
Alignment explanation
Indices: 27549187--27549224 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
27549177 TTTGTTGTTT
27549187 GAGTTTAAGAAACAAATGG
1 GAGTTTAAGAAACAAATGG
27549206 GAGTTTAAGAAACAAATGG
1 GAGTTTAAGAAACAAATGG
27549225 AAAGTGTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.26, T:0.21
Consensus pattern (19 bp):
GAGTTTAAGAAACAAATGG
Found at i:27556355 original size:13 final size:12
Alignment explanation
Indices: 27556326--27556354 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
27556316 TCCCAACTTT
27556326 AAAAATTTTAAA
1 AAAAATTTTAAA
27556338 AAAAATTTTAAA
1 AAAAATTTTAAA
27556350 AAAAA
1 AAAAA
27556355 ACATTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
AAAAATTTTAAA
Found at i:27556831 original size:7 final size:7
Alignment explanation
Indices: 27556818--27556852 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
27556808 CGAAAAAGTA
27556818 CTTGTGC
1 CTTGTGC
*
27556825 TTTGTGC
1 CTTGTGC
27556832 CTTGTGC
1 CTTGTGC
27556839 CTTGTGC
1 CTTGTGC
27556846 CTTGTGC
1 CTTGTGC
27556853 GATATGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.00, C:0.26, G:0.29, T:0.46
Consensus pattern (7 bp):
CTTGTGC
Found at i:27561519 original size:6 final size:6
Alignment explanation
Indices: 27561510--27561598 Score: 89
Period size: 6 Copynumber: 15.2 Consensus size: 6
27561500 TTAAATTGAT
27561510 TTTAAA TTT--A TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTAATTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAA--A
* * *
27561557 TTTAAA TTT-AC TTTAAA TTTAAA TTTAAA TTAAAA TTAAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T
27561599 ACTAAACATT
Statistics
Matches: 72, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
4 6 0.08
5 6 0.08
6 52 0.72
7 2 0.03
8 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:27561519 original size:17 final size:16
Alignment explanation
Indices: 27561510--27561583 Score: 107
Period size: 17 Copynumber: 4.6 Consensus size: 16
27561500 TTAAATTGAT
27561510 TTTAAATTTATTTAAA
1 TTTAAATTTATTTAAA
27561526 TTTAAATTTATCTTAAA
1 TTTAAATTTAT-TTAAA
*
27561543 TTTAAATTTAATT--A
1 TTTAAATTTATTTAAA
27561557 TTTAAATTTACTTTAAA
1 TTTAAATTTA-TTTAAA
27561574 TTTAAATTTA
1 TTTAAATTTA
27561584 AATTAAAATT
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
14 11 0.21
15 2 0.04
16 13 0.25
17 26 0.50
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:27561563 original size:37 final size:36
Alignment explanation
Indices: 27561517--27561587 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 36
27561507 GATTTTAAAT
27561517 TTATTTAAATTTAAATTT-ATCTTAAATTTAAATTTAA
1 TTATTTAAATTT-AATTTAAT-TTAAATTTAAATTTAA
*
27561554 TTATTTAAATTTACTTTAAATTTAAATTTAAATT
1 TTATTTAAATTTAATTT-AATTTAAATTTAAATT
27561588 AAAATTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 4 0.13
37 25 0.81
38 2 0.06
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (36 bp):
TTATTTAAATTTAATTTAATTTAAATTTAAATTTAA
Found at i:27561589 original size:11 final size:11
Alignment explanation
Indices: 27561499--27561596 Score: 72
Period size: 11 Copynumber: 8.5 Consensus size: 11
27561489 GACTTTTTGT
* *
27561499 TTTAAATTGAT
1 TTTAAATTAAA
*
27561510 TTTAAATT-TA
1 TTTAAATTAAA
27561520 TTTAAATTTAAA
1 TTTAAA-TTAAA
**
27561532 TTTATCTTAAA
1 TTTAAATTAAA
27561543 TTTAAATTTAATTA
1 TTTAAA-TTAA--A
* *
27561557 TTTAAATTTAC
1 TTTAAATTAAA
27561568 TTTAAATTTAAA
1 TTTAAA-TTAAA
27561580 TTTAAATTAAA
1 TTTAAATTAAA
*
27561591 ATTAAA
1 TTTAAA
27561597 ATACTAAACA
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
10 6 0.09
11 35 0.51
12 18 0.26
13 3 0.04
14 7 0.10
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:27561589 original size:17 final size:17
Alignment explanation
Indices: 27561499--27561596 Score: 96
Period size: 17 Copynumber: 6.0 Consensus size: 17
27561489 GACTTTTTGT
* *
27561499 TTTAAATTGATTTTAAA
1 TTTAAATTAAATTTAAA
*
27561516 TTT-ATTTAAATTTAAA
1 TTTAAATTAAATTTAAA
**
27561532 TTTATCTTAAATTTAAA
1 TTTAAATTAAATTTAAA
27561549 TTT-AATT--ATTTAAA
1 TTTAAATTAAATTTAAA
**
27561563 TTTACTTTAAATTTAAA
1 TTTAAATTAAATTTAAA
*
27561580 TTTAAATTAAAATTAAA
1 TTTAAATTAAATTTAAA
27561597 ATACTAAACA
Statistics
Matches: 65, Mismatches: 12, Indels: 8
0.76 0.14 0.09
Matches are distributed among these distances:
14 10 0.15
15 2 0.03
16 15 0.23
17 38 0.58
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (17 bp):
TTTAAATTAAATTTAAA
Done.