Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 34 of 132
Found at i:9214925 original size:43 final size:42
Alignment explanation
Indices: 9214789--9214934 Score: 165
Period size: 40 Copynumber: 3.5 Consensus size: 42
9214779 TTATGCTCTA
* * *
9214789 TCGAGTCATAAGTCTTCCTTTA-ACTATATTCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTTATACAAT-TTCTCATTCTCATC
*
9214831 TCGAGACATGAGTCTTCC-TTACT-C-ATGTCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTTA-TACAATTTCTCATTCTCATC
* * *
9214871 TCGATAAATGAGTCTTCCATTTATACAATTTCTCATTCTCAAC
1 TCGAGACATGAGTCTTCC-TTTATACAATTTCTCATTCTCATC
*
9214914 CCGAGACATGAGTCTTCCTTT
1 TCGAGACATGAGTCTTCCTTT
9214935 TTATACACCA
Statistics
Matches: 88, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
40 29 0.33
41 6 0.07
42 24 0.27
43 29 0.33
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (42 bp):
TCGAGACATGAGTCTTCCTTTATACAATTTCTCATTCTCATC
Found at i:9220682 original size:26 final size:26
Alignment explanation
Indices: 9220613--9220732 Score: 140
Period size: 26 Copynumber: 4.7 Consensus size: 26
9220603 AAAGTTTTTT
9220613 AGACAATCTAATGTGGAAGTCTGCCA
1 AGACAATCTAATGTGGAAGTCTGCCA
* *
9220639 AGA-AGA-ATAATGTGGAAGTCTGTCA
1 AGACA-ATCTAATGTGGAAGTCTGCCA
*
9220664 AGACAATTTAATGTGGAAGTCCT-CCA
1 AGACAATCTAATGTGGAAGT-CTGCCA
* *
9220690 AGACGATCTAATGTGGAAGT-TCGTCA
1 AGACAATCTAATGTGGAAGTCT-GCCA
9220716 AGACAATCTAATGTGGA
1 AGACAATCTAATGTGGA
9220733 GTTTCGCTAG
Statistics
Matches: 80, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
24 1 0.01
25 22 0.28
26 55 0.69
27 2 0.03
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (26 bp):
AGACAATCTAATGTGGAAGTCTGCCA
Found at i:9220750 original size:52 final size:52
Alignment explanation
Indices: 9220613--9220757 Score: 174
Period size: 52 Copynumber: 2.8 Consensus size: 52
9220603 AAAGTTTTTT
*
9220613 AGACAATCTAATGTGGAAGTCT-GCCAAGAAGA-ATAATGTGGAAGTCTGTCA
1 AGACAATCTAATGTGGAAGTCTCG-CAAGAAGATCTAATGTGGAAGTCTGTCA
* *
9220664 AGACAATTTAATGTGGAAGTCCTC-CAAGACGATCTAATGTGGAAGT-TCGTCA
1 AGACAATCTAATGTGGAAGT-CTCGCAAGAAGATCTAATGTGGAAGTCT-GTCA
* *
9220716 AGACAATCTAATGTGG-AGTTTCGCTAGAATGATCTAATGTGG
1 AGACAATCTAATGTGGAAGTCTCGCAAGAA-GATCTAATGTGG
9220758 GAGTATGTAA
Statistics
Matches: 81, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
50 2 0.02
51 34 0.42
52 45 0.56
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (52 bp):
AGACAATCTAATGTGGAAGTCTCGCAAGAAGATCTAATGTGGAAGTCTGTCA
Found at i:9224123 original size:38 final size:38
Alignment explanation
Indices: 9224069--9224442 Score: 435
Period size: 38 Copynumber: 9.8 Consensus size: 38
9224059 TTAGTATTTA
* *
9224069 TCGCTCGTTTGAGCAAACATTCAGTAAAATCAGTGGAT
1 TCGCTCGTTTGAGCAAACATTCAGTATAATCAATGGAT
* * * *
9224107 TCGTTTGTTTGAGCAAACATTTAGTAAAATCAATGGAT
1 TCGCTCGTTTGAGCAAACATTCAGTATAATCAATGGAT
* *
9224145 TCGCTCGTTTGAGCAATCATTCAGTATAATTAATGGAT
1 TCGCTCGTTTGAGCAAACATTCAGTATAATCAATGGAT
* * *
9224183 TCGCTCATTTGAGCAAACATTTAGTAAAATCAATGGAT
1 TCGCTCGTTTGAGCAAACATTCAGTATAATCAATGGAT
* *
9224221 TC-CTTCGTTTGAGCAAACATTCAATATAATCATTGGAT
1 TCGC-TCGTTTGAGCAAACATTCAGTATAATCAATGGAT
* * * * *
9224259 TCGCTCATTTGAGTAATCATTCAATATAATCAGTGGAT
1 TCGCTCGTTTGAGCAAACATTCAGTATAATCAATGGAT
* * *
9224297 TCGCTCGTTTGATCGAACATTCAGTATAATCAGTGGAT
1 TCGCTCGTTTGAGCAAACATTCAGTATAATCAATGGAT
* * * *
9224335 TCACTCATTTTAGCAAACATTCAGTATATTCAATGGAT
1 TCGCTCGTTTGAGCAAACATTCAGTATAATCAATGGAT
* ** * **
9224373 TCACTCAATTGAGTAGTCATTCAGTATAATCAATGGAT
1 TCGCTCGTTTGAGCAAACATTCAGTATAATCAATGGAT
* *
9224411 TCGCTCGTTTGAGCAAAGATTCGGTATAATCA
1 TCGCTCGTTTGAGCAAACATTCAGTATAATCA
9224443 GTGTTCCACC
Statistics
Matches: 283, Mismatches: 51, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
37 1 0.00
38 281 0.99
39 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (38 bp):
TCGCTCGTTTGAGCAAACATTCAGTATAATCAATGGAT
Found at i:9224220 original size:114 final size:114
Alignment explanation
Indices: 9224069--9224445 Score: 502
Period size: 114 Copynumber: 3.3 Consensus size: 114
9224059 TTAGTATTTA
* * * *
9224069 TCGCTCGTTTGAGCAAACATTCAGTAAAATCAGTGGATTCGTTTGTTTGAGCAAACATTTAGTAA
1 TCGCTCGTTTGAGCAAACATTCAGTAAAATCAGTGGATTCATTCGTTTGAGCAAACATTCAGTAT
* * *
9224134 AATCAATGGATTCGCTCGTTTGAGCAATCATTCAGTATAATTAATGGAT
66 AATCAATGGATTCGCTCATTTGAGTAATCATTCAGTATAATCAATGGAT
* * * * *
9224183 TCGCTCATTTGAGCAAACATTTAGTAAAATCAATGGATTCCTTCGTTTGAGCAAACATTCAATAT
1 TCGCTCGTTTGAGCAAACATTCAGTAAAATCAGTGGATTCATTCGTTTGAGCAAACATTCAGTAT
* * *
9224248 AATCATTGGATTCGCTCATTTGAGTAATCATTCAATATAATCAGTGGAT
66 AATCAATGGATTCGCTCATTTGAGTAATCATTCAGTATAATCAATGGAT
* * * * * *
9224297 TCGCTCGTTTGATCGAACATTCAGTATAATCAGTGGATTCACTCATTTTAGCAAACATTCAGTAT
1 TCGCTCGTTTGAGCAAACATTCAGTAAAATCAGTGGATTCATTCGTTTGAGCAAACATTCAGTAT
* * * *
9224362 ATTCAATGGATTCACTCAATTGAGTAGTCATTCAGTATAATCAATGGAT
66 AATCAATGGATTCGCTCATTTGAGTAATCATTCAGTATAATCAATGGAT
* * *
9224411 TCGCTCGTTTGAGCAAAGATTCGGTATAATCAGTG
1 TCGCTCGTTTGAGCAAACATTCAGTAAAATCAGTG
9224446 TTCCACCTTT
Statistics
Matches: 227, Mismatches: 36, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
114 227 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (114 bp):
TCGCTCGTTTGAGCAAACATTCAGTAAAATCAGTGGATTCATTCGTTTGAGCAAACATTCAGTAT
AATCAATGGATTCGCTCATTTGAGTAATCATTCAGTATAATCAATGGAT
Found at i:9226231 original size:17 final size:17
Alignment explanation
Indices: 9226211--9226244 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
9226201 GGTAACTCAT
9226211 TAAACTATCGAA-CTTAC
1 TAAACTAT-GAAGCTTAC
9226228 TAAACTATGAAGCTTAC
1 TAAACTATGAAGCTTAC
9226245 CAAAGAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (17 bp):
TAAACTATGAAGCTTAC
Found at i:9241873 original size:17 final size:16
Alignment explanation
Indices: 9241846--9241880 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
9241836 GTACCCAAAA
*
9241846 AAATTATATATTTTTT
1 AAATTATATATATTTT
9241862 AAATTAATATATATTTT
1 AAATT-ATATATATTTT
9241879 AA
1 AA
9241881 TTTTGAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATTATATATATTTT
Found at i:9243912 original size:32 final size:33
Alignment explanation
Indices: 9243867--9243928 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
9243857 ATAAATGAGA
* *
9243867 TTTTATGTTTCTTAAAA-ATCGGAAAAAAACTT
1 TTTTAAGTGTCTTAAAAGATCGGAAAAAAACTT
*
9243899 TTTTAAGTGTCTTAAAAGATCGTAAAAAAA
1 TTTTAAGTGTCTTAAAAGATCGGAAAAAAA
9243929 AATTTGACCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 15 0.58
33 11 0.42
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (33 bp):
TTTTAAGTGTCTTAAAAGATCGGAAAAAAACTT
Found at i:9244662 original size:6 final size:6
Alignment explanation
Indices: 9244645--9244702 Score: 71
Period size: 6 Copynumber: 9.2 Consensus size: 6
9244635 TCCCCCTTCC
* *
9244645 CCCTTT CTCCTTT CCCTTT CCCTTT CCCTTT CCCTTCC CCCTTT GTCCTTT
1 CCCTTT C-CCTTT CCCTTT CCCTTT CCCTTT CCCTT-T CCCTTT -CCCTTT
9244696 CCCTTT C
1 CCCTTT C
9244703 TCGTTTTCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
6 29 0.64
7 16 0.36
ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48
Consensus pattern (6 bp):
CCCTTT
Found at i:9244670 original size:12 final size:12
Alignment explanation
Indices: 9244645--9244702 Score: 71
Period size: 13 Copynumber: 4.6 Consensus size: 12
9244635 TCCCCCTTCC
9244645 CCCTTTCTCCTTT
1 CCCTTTC-CCTTT
9244658 CCCTTTCCCTTT
1 CCCTTTCCCTTT
*
9244670 CCCTTTCCCTTCC
1 CCCTTTCCCTT-T
*
9244683 CCCTTTGTCCTTT
1 CCCTTT-CCCTTT
9244696 CCCTTTC
1 CCCTTTC
9244703 TCGTTTTCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
12 16 0.41
13 19 0.49
14 4 0.10
ACGTcount: A:0.00, C:0.50, G:0.02, T:0.48
Consensus pattern (12 bp):
CCCTTTCCCTTT
Found at i:9244683 original size:38 final size:39
Alignment explanation
Indices: 9244628--9244702 Score: 125
Period size: 38 Copynumber: 1.9 Consensus size: 39
9244618 CTCTCCCCCA
9244628 TTTCCCTTCCCCCTTCCCCCTTTCTCCTTTCCCTTTCCC
1 TTTCCCTTCCCCCTTCCCCCTTTCTCCTTTCCCTTTCCC
* *
9244667 TTTCCCTT-TCCCTTCCCCCTTTGTCCTTTCCCTTTC
1 TTTCCCTTCCCCCTTCCCCCTTTCTCCTTTCCCTTTC
9244703 TCGTTTTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 26 0.76
39 8 0.24
ACGTcount: A:0.00, C:0.52, G:0.01, T:0.47
Consensus pattern (39 bp):
TTTCCCTTCCCCCTTCCCCCTTTCTCCTTTCCCTTTCCC
Found at i:9247171 original size:14 final size:14
Alignment explanation
Indices: 9247152--9247187 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
9247142 GAAAAGTAAT
9247152 TCATTTTCCAGAAA-
1 TCATTTTCC-GAAAG
9247166 TCATTTTCCGAAAG
1 TCATTTTCCGAAAG
9247180 TCATTTTC
1 TCATTTTC
9247188 AGTCAAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.19
14 17 0.81
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (14 bp):
TCATTTTCCGAAAG
Found at i:9255118 original size:28 final size:28
Alignment explanation
Indices: 9255084--9255190 Score: 196
Period size: 28 Copynumber: 3.8 Consensus size: 28
9255074 GAGCATTATT
*
9255084 ACCTTTGGATCAACAGGGAGTAAGCATG
1 ACCTTTGGGTCAACAGGGAGTAAGCATG
9255112 ACCTTTGGGTCAACAGGGAGTAAGCATG
1 ACCTTTGGGTCAACAGGGAGTAAGCATG
9255140 ACCTTTGGGTCAACAGGGAGTAAGCATG
1 ACCTTTGGGTCAACAGGGAGTAAGCATG
*
9255168 ACCTTTGGGTCAACAAGGAGTAA
1 ACCTTTGGGTCAACAGGGAGTAA
9255191 ATCAAATATC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 77 1.00
ACGTcount: A:0.31, C:0.18, G:0.30, T:0.21
Consensus pattern (28 bp):
ACCTTTGGGTCAACAGGGAGTAAGCATG
Found at i:9259874 original size:3 final size:3
Alignment explanation
Indices: 9259823--9259895 Score: 53
Period size: 3 Copynumber: 25.3 Consensus size: 3
9259813 TTTAAGGTTT
* * * * * * *
9259823 AAG AAG -AG AAA AAG TAG AA- AAG AAT AAA AAG AAA AAG AA- TAG GAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
9259868 AAG AAG AAG AAG AAG AAG AAG GAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
9259896 GAAAAAATAG
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
2 5 0.09
3 48 0.91
ACGTcount: A:0.67, C:0.00, G:0.29, T:0.04
Consensus pattern (3 bp):
AAG
Found at i:9262128 original size:23 final size:21
Alignment explanation
Indices: 9262080--9262135 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
9262070 ATTCCAACTG
9262080 AAATAAAATA--ATTTGAAAA
1 AAATAAAATATTATTTGAAAA
*
9262099 CAA-AAAATATTATTTGAAGAA
1 AAATAAAATATTATTTGAA-AA
9262120 TAAATAAAAT-TTATTT
1 -AAATAAAATATTATTT
9262136 CTAGTTGGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 6 0.20
19 2 0.07
20 7 0.23
21 2 0.07
22 8 0.27
23 5 0.17
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (21 bp):
AAATAAAATATTATTTGAAAA
Found at i:9262375 original size:16 final size:17
Alignment explanation
Indices: 9262337--9262376 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
9262327 TGGAATTGAA
9262337 TTTTTT-ATAAAAATAT
1 TTTTTTGATAAAAATAT
*
9262353 TTTTTTGATAGAAAT-T
1 TTTTTTGATAAAAATAT
9262369 TTTTTTGA
1 TTTTTTGA
9262377 CTAATTGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.68
17 7 0.32
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (17 bp):
TTTTTTGATAAAAATAT
Found at i:9265246 original size:26 final size:26
Alignment explanation
Indices: 9265217--9265283 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 26
9265207 CTTAATGCAT
9265217 ATTTTAATTTTT-AAATCATTTTT-CTC
1 ATTTTAATTTTTAAAAT--TTTTTACTC
**
9265243 ATTTCGATTTTTAAAATTTTTTGACTC
1 ATTTTAATTTTTAAAATTTTTT-ACTC
*
9265270 AATTTAATTTTTAA
1 ATTTTAATTTTTAA
9265284 CTTCTTCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
25 5 0.15
26 10 0.30
27 18 0.55
ACGTcount: A:0.30, C:0.09, G:0.03, T:0.58
Consensus pattern (26 bp):
ATTTTAATTTTTAAAATTTTTTACTC
Found at i:9272873 original size:22 final size:22
Alignment explanation
Indices: 9272821--9272919 Score: 90
Period size: 23 Copynumber: 4.3 Consensus size: 22
9272811 CATCCAAATA
* *
9272821 ACCAAAATAACAATCAAAATAGC
1 ACCAAAATAATAA-AAAAATAGC
* * *
9272844 AGCAAAAATAATAGAAAAATAAC
1 A-CCAAAATAATAAAAAAATAGC
* *
9272867 AACAAAAATAAAAATAAAAATAGC
1 -ACCAAAATAATAA-AAAAATAGC
*
9272891 ACCAAAATAGTAAAAAAATAGC
1 ACCAAAATAATAAAAAAATAGC
9272913 ACCAAAA
1 ACCAAAA
9272920 CAGCAACCAA
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
22 16 0.26
23 28 0.45
24 18 0.29
ACGTcount: A:0.68, C:0.14, G:0.06, T:0.12
Consensus pattern (22 bp):
ACCAAAATAATAAAAAAATAGC
Found at i:9272874 original size:12 final size:12
Alignment explanation
Indices: 9272824--9272888 Score: 53
Period size: 12 Copynumber: 5.5 Consensus size: 12
9272814 CCAAATAACC
9272824 AAAATAACAATC-
1 AAAATAACAA-CA
* *
9272836 AAAATAGCAGCA
1 AAAATAACAACA
* *
9272848 AAAATAA-TAGA
1 AAAATAACAACA
9272859 AAAATAACAACA
1 AAAATAACAACA
* *
9272871 AAAATAAAAATA
1 AAAATAACAACA
9272883 AAAATA
1 AAAATA
9272889 GCACCAAAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
11 9 0.22
12 32 0.78
ACGTcount: A:0.72, C:0.09, G:0.05, T:0.14
Consensus pattern (12 bp):
AAAATAACAACA
Found at i:9272897 original size:11 final size:11
Alignment explanation
Indices: 9272883--9272931 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
9272873 AATAAAAATA
9272883 AAAATAGCACC
1 AAAATAGCACC
* **
9272894 AAAATAGTAAA
1 AAAATAGCACC
9272905 AAAATAGCACC
1 AAAATAGCACC
*
9272916 AAAACAGCAACC
1 AAAATAGC-ACC
9272928 AAAA
1 AAAA
9272932 CAGTAAAAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
11 23 0.77
12 7 0.23
ACGTcount: A:0.63, C:0.20, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAATAGCACC
Found at i:9272942 original size:23 final size:23
Alignment explanation
Indices: 9272916--9273018 Score: 103
Period size: 22 Copynumber: 4.8 Consensus size: 23
9272906 AAATAGCACC
*
9272916 AAAACAGCAACCAAAACAG--TA
1 AAAACAGCAACCAAAACAGCAAA
* *
9272937 AAAA-A--AATCAAAACAGTAAA
1 AAAACAGCAACCAAAACAGCAAA
* *
9272957 AACACAAC-ACCAAAACAGCAAA
1 AAAACAGCAACCAAAACAGCAAA
*
9272979 AAAATAGCAACCAAAACAGCAAA
1 AAAACAGCAACCAAAACAGCAAA
9273002 AAAACAGC-ACCAAAACA
1 AAAACAGCAACCAAAACA
9273019 ACAATATAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
18 10 0.15
20 5 0.07
21 5 0.07
22 26 0.39
23 21 0.31
ACGTcount: A:0.66, C:0.23, G:0.07, T:0.04
Consensus pattern (23 bp):
AAAACAGCAACCAAAACAGCAAA
Found at i:9272987 original size:11 final size:11
Alignment explanation
Indices: 9272968--9273010 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
9272958 ACACAACACC
9272968 AAAACAGCAAA
1 AAAACAGCAAA
* *
9272979 AAAATAGCAACC
1 AAAACAGCAA-A
9272991 AAAACAGCAAA
1 AAAACAGCAAA
9273002 AAAACAGCA
1 AAAACAGCA
9273011 CCAAAACAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.67, C:0.21, G:0.09, T:0.02
Consensus pattern (11 bp):
AAAACAGCAAA
Found at i:9273016 original size:11 final size:11
Alignment explanation
Indices: 9272905--9273018 Score: 58
Period size: 11 Copynumber: 10.5 Consensus size: 11
9272895 AAATAGTAAA
*
9272905 AAAATAGCACC
1 AAAACAGCACC
9272916 AAAACAGCAACC
1 AAAACAGC-ACC
*
9272928 AAAACAGTA--
1 AAAACAGCACC
* *
9272937 AAAA-A-AATC
1 AAAACAGCACC
* *
9272946 AAAACAGTA-A
1 AAAACAGCACC
*
9272956 AAACACAACACC
1 AAA-ACAGCACC
**
9272968 AAAACAGCAAA
1 AAAACAGCACC
*
9272979 AAAATAGCAACC
1 AAAACAGC-ACC
**
9272991 AAAACAGCAAA
1 AAAACAGCACC
9273002 AAAACAGCACC
1 AAAACAGCACC
9273013 AAAACA
1 AAAACA
9273019 ACAATATAAT
Statistics
Matches: 76, Mismatches: 19, Indels: 16
0.68 0.17 0.14
Matches are distributed among these distances:
7 1 0.01
8 1 0.01
9 8 0.11
10 4 0.05
11 41 0.54
12 21 0.28
ACGTcount: A:0.65, C:0.24, G:0.07, T:0.04
Consensus pattern (11 bp):
AAAACAGCACC
Found at i:9273885 original size:20 final size:20
Alignment explanation
Indices: 9273862--9273901 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
9273852 TATAATTATT
9273862 TATGTATTTTTAAATGTTGA
1 TATGTATTTTTAAATGTTGA
9273882 TATGTATTTTTAAATGTTGA
1 TATGTATTTTTAAATGTTGA
9273902 GGGCTAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (20 bp):
TATGTATTTTTAAATGTTGA
Found at i:9274410 original size:14 final size:15
Alignment explanation
Indices: 9274393--9274425 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
9274383 ATAATGATAA
9274393 AATTA-ATTTTTAAT
1 AATTATATTTTTAAT
*
9274407 AATTATATTTTTATT
1 AATTATATTTTTAAT
9274422 AATT
1 AATT
9274426 TGACTCTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
AATTATATTTTTAAT
Found at i:9275068 original size:29 final size:30
Alignment explanation
Indices: 9275035--9275091 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
9275025 TGGTTTAATA
9275035 TGTAATTTTATATAT-AAATTTTGATTTTG
1 TGTAATTTTATATATGAAATTTTGATTTTG
*
9275064 TGTAATTTTATATATGAAATTTTTATTT
1 TGTAATTTTATATATGAAATTTTGATTT
9275092 GATTCAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (30 bp):
TGTAATTTTATATATGAAATTTTGATTTTG
Found at i:9276282 original size:11 final size:11
Alignment explanation
Indices: 9276263--9276295 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
9276253 TTAGGATATT
9276263 ATTTATATTTA
1 ATTTATATTTA
*
9276274 ATTTGTATTTA
1 ATTTATATTTA
9276285 ATTTATATTTA
1 ATTTATATTTA
9276296 TCTTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (11 bp):
ATTTATATTTA
Found at i:9276323 original size:14 final size:14
Alignment explanation
Indices: 9276286--9276315 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
9276276 TTGTATTTAA
*
9276286 TTTATATTTATCTT
1 TTTAAATTTATCTT
9276300 TTTAAATTTATCTT
1 TTTAAATTTATCTT
9276314 TT
1 TT
9276316 AGAGTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTAAATTTATCTT
Found at i:9279037 original size:24 final size:24
Alignment explanation
Indices: 9278971--9279042 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
9278961 TTGACTCAAG
* *
9278971 CAAATAAACAAAGTTTAATTAAAA
1 CAAATAAACAGAGTTTAATTGAAA
9278995 CAAATAAACAGAGTTTAATTGAAA
1 CAAATAAACAGAGTTTAATTGAAA
*
9279019 CAATTAAACAGAGTTTAATTGAAA
1 CAAATAAACAGAGTTTAATTGAAA
9279043 GATTATTTCT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.26
Consensus pattern (24 bp):
CAAATAAACAGAGTTTAATTGAAA
Found at i:9280882 original size:13 final size:13
Alignment explanation
Indices: 9280864--9280890 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9280854 AGTTCTAAAC
9280864 TCTAATGAGTGTA
1 TCTAATGAGTGTA
9280877 TCTAATGAGTGTA
1 TCTAATGAGTGTA
9280890 T
1 T
9280891 TTTCTAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (13 bp):
TCTAATGAGTGTA
Found at i:9281007 original size:24 final size:24
Alignment explanation
Indices: 9280979--9281047 Score: 86
Period size: 24 Copynumber: 2.9 Consensus size: 24
9280969 AGTTTGACTC
9280979 AAACAAATAAACAGAATTTAATTA
1 AAACAAATAAACAGAATTTAATTA
* * *
9281003 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAACAGAATTTAATTA
*
9281027 AAACAATTAAACA-AAGTTTAA
1 AAACAAATAAACAGAA-TTTAA
9281048 CTGAAAGATT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 1 0.03
24 37 0.97
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.26
Consensus pattern (24 bp):
AAACAAATAAACAGAATTTAATTA
Found at i:9281052 original size:24 final size:24
Alignment explanation
Indices: 9280969--9281053 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
9280959 GACTAATAAG
* *
9280969 AGTTTGACTCAAACAAATAAACAGA
1 AGTTTAACTGAAACAAATAAACA-A
* * * *
9280994 A-TTTAATTAAAACAAATAAATAG
1 AGTTTAACTGAAACAAATAAACAA
* *
9281017 AGTTTAATTGAAACAATTAAACAA
1 AGTTTAACTGAAACAAATAAACAA
9281041 AGTTTAACTGAAA
1 AGTTTAACTGAAA
9281054 GATTATTTCT
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 1 0.02
24 47 0.96
25 1 0.02
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.27
Consensus pattern (24 bp):
AGTTTAACTGAAACAAATAAACAA
Found at i:9283114 original size:21 final size:21
Alignment explanation
Indices: 9283090--9283139 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
9283080 CCTATAACAG
* * *
9283090 TTCTACCGATACAAGTGAAGC
1 TTCTACCGAAACAAATCAAGC
*
9283111 TTCTACCGAAACAAATCATGC
1 TTCTACCGAAACAAATCAAGC
9283132 TTCTACCG
1 TTCTACCG
9283140 GTACTAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (21 bp):
TTCTACCGAAACAAATCAAGC
Found at i:9284278 original size:195 final size:193
Alignment explanation
Indices: 9283894--9284341 Score: 535
Period size: 195 Copynumber: 2.3 Consensus size: 193
9283884 TACCAGTACT
* * ** *
9283894 CGATGCTTCTCACACAAGTTATCGAGGACTCGCAATGTATGCGGTATCC-CAGCCATCGGTACGG
1 CGATG-TTCTCACACGAGTTGTCGAGGACTCGCAAAATATGCGGTA-CCTCAGCCATCGATACGG
* * * *
9283958 TGCCTGTCTGTACTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAGTATGCAT
64 TACCTG-CTGCACTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTATCGAGAATATGCAT
* *
9284023 AAAGCATAATCTCAGCCATCATAGGGCCTGTAATCCATTTAGGATCCATATATCTTTCCCGAGTC
128 AAAGCATAATCTCAGCCATCATAAGGCCTGTAATCCATTTAGGATCCATATATCTTTCCCGACTC
9284088 A
193 A
*
9284089 CGATGTTGCTCACACGAGTTGTTGAGGACTCGCAAAATATGCGGTACCTCAGCCATCGATACGGT
1 CGATGTT-CTCACACGAGTTGTCGAGGACTCGCAAAATATGCGGTACCTCAGCCATCGATACGGT
* * *
9284154 ATCTG-TGCA-TAT-AACTGTTCCCTAACGATGCTGCTCACATGAGCTATCGAGAATATGCACTT
65 ACCTGCTGCACTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTATCGAGAATATGCA-TA
* * * * * * * *
9284216 ATGCATAAATCTCAGTCATCGTAAGGCCTGTAATCCATTTTTGGATTCGTTTCTCATTTCCCGAC
129 AAGCAT-AATCTCAGCCATCATAAGGCCTGTAATCCA-TTTAGGATCCATATATC-TTTCCCGAC
9284281 TCA
191 TCA
* * * * *
9284284 CGATGCTACTCACACGAGCTGTCGAGGACTCGCAACATATGCTGTACCTCAACCATCG
1 CGATG-TTCTCACACGAGTTGTCGAGGACTCGCAAAATATGCGGTACCTCAGCCATCG
9284342 CATTGGTTTC
Statistics
Matches: 217, Mismatches: 29, Indels: 14
0.83 0.11 0.05
Matches are distributed among these distances:
191 44 0.20
192 9 0.04
193 30 0.14
194 16 0.07
195 117 0.54
196 1 0.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (193 bp):
CGATGTTCTCACACGAGTTGTCGAGGACTCGCAAAATATGCGGTACCTCAGCCATCGATACGGTA
CCTGCTGCACTATAAACTGTTCCCTAACGATGCTGCTCACACGAGCTATCGAGAATATGCATAAA
GCATAATCTCAGCCATCATAAGGCCTGTAATCCATTTAGGATCCATATATCTTTCCCGACTCA
Found at i:9291686 original size:96 final size:96
Alignment explanation
Indices: 9291512--9291693 Score: 242
Period size: 96 Copynumber: 1.9 Consensus size: 96
9291502 AAGGATGTTC
* *
9291512 GATTATCTCGATTTGAAGAAAGGATACACCTAGTAAGTTAAGGCACAAATTTTCAAAATCGAAGA
1 GATTATCTCGATTTGAAGAAAAGATACACCTAATAAGTTAAGGCACAAATTTTCAAAATCGAAGA
*
9291577 TAAGGAAACATTGCCTCGATTAAGGGTATTT
66 TAAAGAAACATTGCCTCGATTAAGGGTATTT
* * * * * *
9291608 GATTATTTCGATTTGAAGAAAAGTTGCACCTAATAAGTTAAGGCGCAAATTTTTGAAACTCGAA-
1 GATTATCTCGATTTGAAGAAAAGATACACCTAATAAGTTAAGGCACAAA-TTTTCAAAATCGAAG
*
9291672 ATAAA-AGAATATTGCCTCGATT
65 ATAAAGA-AACATTGCCTCGATT
9291694 TTAAAGTTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
95 1 0.01
96 61 0.82
97 12 0.16
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (96 bp):
GATTATCTCGATTTGAAGAAAAGATACACCTAATAAGTTAAGGCACAAATTTTCAAAATCGAAGA
TAAAGAAACATTGCCTCGATTAAGGGTATTT
Found at i:9291952 original size:28 final size:28
Alignment explanation
Indices: 9291912--9291973 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
9291902 AAATGAGACT
* *
9291912 TTTTGGATACTCGGGGGTAAAATAGTAA
1 TTTTGGATACTCGAGGGCAAAATAGTAA
*
9291940 TTTTGGACT-CTCGAGGGCAAAATGGTAA
1 TTTTGGA-TACTCGAGGGCAAAATAGTAA
9291968 TTTTGG
1 TTTTGG
9291974 GAAAATTTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.27, C:0.10, G:0.29, T:0.34
Consensus pattern (28 bp):
TTTTGGATACTCGAGGGCAAAATAGTAA
Found at i:9292086 original size:29 final size:27
Alignment explanation
Indices: 9292047--9292226 Score: 139
Period size: 29 Copynumber: 6.2 Consensus size: 27
9292037 ATGGGGATCA
9292047 AAAATGGAATTTTTGGATA-TCTCAGGGT
1 AAAATGGAATTTTTGGA-AGT-TCAGGGT
* *
9292075 AAAATGGTAATTTTTGAAAGTTTCAAGGT
1 AAAATGG-AATTTTTGGAAG-TTCAGGGT
9292104 CAAAAATGGAA-TTTTGGAAGTTCGAGGGT
1 --AAAATGGAATTTTTGGAAGTTC-AGGGT
* **
9292133 AAAATGGTAATTTTTAGAAGTTTTGGGGT
1 AAAATGG-AATTTTTGGAAG-TTCAGGGT
*
9292162 CAAAAATGGAATTTTTGGAAGTTTAAGGGT
1 --AAAATGGAATTTTTGGAAG-TTCAGGGT
* *
9292192 AAAAATGTAATTTTTGGAAAGTTTAGGGT
1 -AAAATGGAATTTTTGG-AAGTTCAGGGT
9292221 CAAAAT
1 -AAAAT
9292227 ATAATTTTGG
Statistics
Matches: 127, Mismatches: 13, Indels: 23
0.78 0.08 0.14
Matches are distributed among these distances:
27 7 0.06
28 13 0.10
29 67 0.53
30 26 0.20
31 14 0.11
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (27 bp):
AAAATGGAATTTTTGGAAGTTCAGGGT
Found at i:9292136 original size:117 final size:113
Alignment explanation
Indices: 9291940--9292238 Score: 316
Period size: 117 Copynumber: 2.6 Consensus size: 113
9291930 AAAATAGTAA
* * * * ** *
9291940 TTTTGGACTCTCGAGGGCAAAATGGTAATTTTGGGAAAATTTAGGGTTTAAAATGAAATTTTAGA
1 TTTTGGAATCTC-AGGGTAAAATGGTAATTTT-TGAAAGTTTAGGGTCAAAAATG-AATTTTGGA
*
9292005 TATTCGGGGGTAAAACGGTAA-TTTTAGAAAAAATGGGGATCAAAAATGGAAT
63 -ATTCGAGGGTAAAACGGTAATTTTTAGAAAAAATGGGG-TCAAAAATGGAAT
*
9292057 TTTTGGATATCTCAGGGTAAAATGGTAATTTTTGAAAGTTTCAAGGTCAAAAATGGAATTTTGGA
1 TTTTGGA-ATCTCAGGGTAAAATGGTAATTTTTGAAAGTTT-AGGGTCAAAAAT-GAATTTTGGA
* ****
9292122 AGTTCGAGGGTAAAATGGTAATTTTTAGAAGTTTTGGGGTCAAAAATGGAAT
63 A-TTCGAGGGTAAAACGGTAATTTTTAGAAAAAATGGGGTCAAAAATGGAAT
* *
9292174 TTTTGGAAGTTTAAGGGTAAAAAT-GTAATTTTTGGAAAGTTTAGGGTCAAAATAT-AATTTTGG
1 TTTTGGAA-TCTCAGGGT-AAAATGGTAATTTTT-GAAAGTTTAGGGTCAAAA-ATGAATTTTGG
9292237 AA
62 AA
9292239 AAGTTTAGGG
Statistics
Matches: 156, Mismatches: 17, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
116 19 0.12
117 104 0.67
118 33 0.21
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (113 bp):
TTTTGGAATCTCAGGGTAAAATGGTAATTTTTGAAAGTTTAGGGTCAAAAATGAATTTTGGAATT
CGAGGGTAAAACGGTAATTTTTAGAAAAAATGGGGTCAAAAATGGAAT
Found at i:9292145 original size:58 final size:57
Alignment explanation
Indices: 9291953--9292344 Score: 243
Period size: 59 Copynumber: 6.7 Consensus size: 57
9291943 TGGACTCTCG
* * * ** * *
9291953 AGGGCAAAATGGTAATTTTGGGAAAATTTAGGGTTTAAAAT-GAAATTTTAGATA-TTC
1 AGGGTAAAATGGTAATTTT-TGAAAGTTTAGGGTCAAAAATGGAATTTTTGGA-AGTTC
* * * *** *
9292010 GGGGGTAAAACGGTAATTTTAGAAAAAATGGGGATCAAAAATGGAATTTTTGGATA-TCTC
1 -AGGGTAAAATGGTAATTTTTGAAAGTTTAGGG-TCAAAAATGGAATTTTTGGA-AGT-TC
*
9292070 AGGGTAAAATGGTAATTTTTGAAAGTTTCAAGGTCAAAAATGGAA-TTTTGGAAGTTC
1 AGGGTAAAATGGTAATTTTTGAAAGTTT-AGGGTCAAAAATGGAATTTTTGGAAGTTC
* *
9292127 GAGGGTAAAATGGTAATTTTT-AGAAGTTTTGGGGTCAAAAATGGAATTTTTGGAAGTTTA
1 -AGGGTAAAATGGTAATTTTTGA-AAG-TTTAGGGTCAAAAATGGAATTTTTGGAAG-TTC
*
9292187 AGGGTAAAAAT-GTAATTTTTGGAAAGTTTAGGGTCAAAATAT--AA-TTTTGGAAAAGTTT
1 AGGGT-AAAATGGTAATTTTT-GAAAGTTTAGGGTCAAAA-ATGGAATTTTTGG--AAGTTC
* * * * * *
9292245 AGGGGTTAAAAT-ATAATTTTGGAAAATTTAGGGGTCAAAATAT--AATTTTAGAAAAGTTTA
1 A-GGG-TAAAATGGTAATTTTTGAAAGTTTA-GGGTCAAAA-ATGGAATTTTTG-GAAG-TTC
*
9292305 AGGGTCAAAAT-GTAATTTTGGAAAAGTTTAGGGGTCAAAA
1 AGGGT-AAAATGGTAATTTTTG-AAAGTTTA-GGGTCAAAA
9292345 TATGATTTTT
Statistics
Matches: 278, Mismatches: 32, Indels: 46
0.78 0.09 0.13
Matches are distributed among these distances:
57 19 0.07
58 81 0.29
59 136 0.49
60 41 0.15
61 1 0.00
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (57 bp):
AGGGTAAAATGGTAATTTTTGAAAGTTTAGGGTCAAAAATGGAATTTTTGGAAGTTC
Found at i:9292231 original size:29 final size:29
Alignment explanation
Indices: 9292082--9292367 Score: 225
Period size: 30 Copynumber: 9.7 Consensus size: 29
9292072 GGTAAAATGG
*
9292082 TAATTTTT-GAAAGTTTCAAGGTCAAAA-A
1 TAATTTTTGGAAAGTTT-AGGGTCAAAATA
* *
9292110 TGGAA-TTTTGG-AAGTTCGAGGGT-AAAATGG
1 T--AATTTTTGGAAAGTT-TAGGGTCAAAAT-A
* *
9292140 TAATTTTTAG-AAGTTTTGGGGTCAAAA-A
1 TAATTTTTGGAAAG-TTTAGGGTCAAAATA
* *
9292168 TGGAATTTTTGG-AAGTTTAAGGGTAAAAATG
1 T--AATTTTTGGAAAGTTT-AGGGTCAAAATA
9292199 TAATTTTTGGAAAGTTTAGGGTCAAAATA
1 TAATTTTTGGAAAGTTTAGGGTCAAAATA
*
9292228 TAA-TTTTGGAAAAGTTTAGGGGTTAAAATA
1 TAATTTTTGG-AAAGTTTA-GGGTCAAAATA
*
9292258 TAA-TTTTGGAAAATTTAGGGGTCAAAATA
1 TAATTTTTGGAAAGTTTA-GGGTCAAAATA
* * *
9292287 TAATTTTAGAAAAGTTTAAGGGTCAAAATG
1 TAATTTTTGGAAAGTTT-AGGGTCAAAATA
9292317 TAA-TTTTGGAAAAGTTTAGGGGTCAAAATA
1 TAATTTTTGG-AAAGTTTA-GGGTCAAAATA
* * *
9292347 TGATTTTTAGATAGTTTAGGG
1 TAATTTTTGGAAAGTTTAGGG
9292368 ACATTTAAGG
Statistics
Matches: 211, Mismatches: 26, Indels: 41
0.76 0.09 0.15
Matches are distributed among these distances:
28 14 0.07
29 87 0.41
30 103 0.49
31 7 0.03
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (29 bp):
TAATTTTTGGAAAGTTTAGGGTCAAAATA
Found at i:9292258 original size:30 final size:30
Alignment explanation
Indices: 9292150--9292353 Score: 249
Period size: 30 Copynumber: 6.9 Consensus size: 30
9292140 TAATTTTTAG
*
9292150 AAGTTTTGGGGTCAAAA-ATGGAATTTTTGG--
1 AAGTTTAGGGGTCAAAATAT--AA-TTTTGGAA
* * *
9292180 AAGTTTAAGGGTAAAAATGTAATTTTTGG-A
1 AAGTTTAGGGGTCAAAATATAA-TTTTGGAA
9292210 AAGTTTA-GGGTCAAAATATAATTTTGGAA
1 AAGTTTAGGGGTCAAAATATAATTTTGGAA
*
9292239 AAGTTTAGGGGTTAAAATATAATTTTGGAA
1 AAGTTTAGGGGTCAAAATATAATTTTGGAA
*
9292269 AA-TTTAGGGGTCAAAATATAATTTTAGAA
1 AAGTTTAGGGGTCAAAATATAATTTTGGAA
* *
9292298 AAGTTTAAGGGTCAAAATGTAATTTTGGAA
1 AAGTTTAGGGGTCAAAATATAATTTTGGAA
*
9292328 AAGTTTAGGGGTCAAAATATGATTTT
1 AAGTTTAGGGGTCAAAATATAATTTT
9292354 TAGATAGTTT
Statistics
Matches: 154, Mismatches: 15, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
28 6 0.04
29 56 0.36
30 91 0.59
31 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (30 bp):
AAGTTTAGGGGTCAAAATATAATTTTGGAA
Found at i:9292617 original size:17 final size:17
Alignment explanation
Indices: 9292597--9292631 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
9292587 TTAAAGCAAA
*
9292597 TTAAGATAAATTTAAAT
1 TTAAAATAAATTTAAAT
9292614 TTAAAATAAATTTAAAT
1 TTAAAATAAATTTAAAT
9292631 T
1 T
9292632 AATTTAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
TTAAAATAAATTTAAAT
Found at i:9292624 original size:27 final size:27
Alignment explanation
Indices: 9292567--9292639 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
9292557 AAATCAATTT
* * *
9292567 AAATTTAATTAAATTCAAATTTAAAGC
1 AAATTTAAATAAATTTAAATTTAAAAC
*
9292594 AAA-TTAAGATAAATTTAAATTTAAAAT
1 AAATTTAA-ATAAATTTAAATTTAAAAC
*
9292621 AAATTTAAATTAATTTAAA
1 AAATTTAAATAAATTTAAA
9292640 CCTAATTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
26 4 0.10
27 31 0.79
28 4 0.10
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (27 bp):
AAATTTAAATAAATTTAAATTTAAAAC
Found at i:9295564 original size:18 final size:19
Alignment explanation
Indices: 9295522--9295564 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
9295512 GCCTTTCATG
9295522 CTTTTCTCATCTCTCGCTT
1 CTTTTCTCATCTCTCGCTT
* **
9295541 CCTTTCT-ATCTCTTTCTT
1 CTTTTCTCATCTCTCGCTT
9295559 CTTTTC
1 CTTTTC
9295565 CTTCTCATCT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.05, C:0.35, G:0.02, T:0.58
Consensus pattern (19 bp):
CTTTTCTCATCTCTCGCTT
Found at i:9302722 original size:3 final size:3
Alignment explanation
Indices: 9302716--9302781 Score: 51
Period size: 3 Copynumber: 21.3 Consensus size: 3
9302706 TTTTTATAAA
* * ** * *
9302716 TAT TAT TAT TAT TAT TAT TAAT CAT TAA TGC TATT TAT TAT AAA TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TA-T TAT TAT TAT TAT
*
9302763 TAT TAT TAT TAT TAA TAT T
1 TAT TAT TAT TAT TAT TAT T
9302782 TAGTAATATT
Statistics
Matches: 48, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
3 44 0.92
4 4 0.08
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:9303566 original size:17 final size:17
Alignment explanation
Indices: 9303546--9303580 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
9303536 TTAAAGCAAA
*
9303546 TTAAGATAAATTTAAAT
1 TTAAAATAAATTTAAAT
9303563 TTAAAATAAATTTAAAT
1 TTAAAATAAATTTAAAT
9303580 T
1 T
9303581 AATTTAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
TTAAAATAAATTTAAAT
Found at i:9303573 original size:27 final size:27
Alignment explanation
Indices: 9303516--9303588 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 27
9303506 AAATCAATTT
* * *
9303516 AAATTTAATTAAATTCAAATTTAAAGC
1 AAATTTAAATAAATTTAAATTTAAAAC
*
9303543 AAA-TTAAGATAAATTTAAATTTAAAAT
1 AAATTTAA-ATAAATTTAAATTTAAAAC
*
9303570 AAATTTAAATTAATTTAAA
1 AAATTTAAATAAATTTAAA
9303589 CCTAATTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
26 4 0.10
27 31 0.79
28 4 0.10
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (27 bp):
AAATTTAAATAAATTTAAATTTAAAAC
Found at i:9305312 original size:17 final size:17
Alignment explanation
Indices: 9305290--9305327 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
9305280 CCTTAACCTT
9305290 GTTGCTTCAACAAGAAC
1 GTTGCTTCAACAAGAAC
9305307 GTTGCTTCAACAAGAAC
1 GTTGCTTCAACAAGAAC
9305324 GTTG
1 GTTG
9305328 TACGTCTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (17 bp):
GTTGCTTCAACAAGAAC
Found at i:9306568 original size:13 final size:13
Alignment explanation
Indices: 9306546--9306580 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
9306536 TTGTCAAGAA
*
9306546 TACCTTAAAGTTC
1 TACCTCAAAGTTC
9306559 TACCTCAAAGTTC
1 TACCTCAAAGTTC
9306572 TACCTCAAA
1 TACCTCAAA
9306581 AGGCAAGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.34, C:0.29, G:0.06, T:0.31
Consensus pattern (13 bp):
TACCTCAAAGTTC
Found at i:9310297 original size:14 final size:11
Alignment explanation
Indices: 9310259--9310289 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
9310249 ATAAATGTTA
9310259 AATATTAAAAT
1 AATATTAAAAT
9310270 AATATTAAAAT
1 AATATTAAAAT
9310281 AATATTAAA
1 AATATTAAA
9310290 TCACTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AATATTAAAAT
Found at i:9313337 original size:126 final size:127
Alignment explanation
Indices: 9313120--9313348 Score: 318
Period size: 126 Copynumber: 1.8 Consensus size: 127
9313110 GATGCAGACG
* * *
9313120 AGCTGCCATATGGTTGAGGATCCACAACCTGTCGAAGATAAAAGCTATCAGAGAAAGTTGTGAAT
1 AGCTGCCATATGATTGAGGATCCACAACCTCTCGAAGATAAAAGCTATCACAGAAAGTTGTGAAT
* * *
9313185 ACTTCGTATAAAAGTCGTAGTTGGAATCTGC-TAAGCTATGAATACACAGATGGTGCAGATA
66 ACTCCGTACAAAAGTCGCAGTTGGAATCTGCTTAAGCTATGAATACACAGATGGTGCAGATA
* ** * *
9313246 AGCTGCCGTATGATTGAGGATCCACAATTTCTCGCAGATGAAAGCTATCACAGAAA-TTGTGAAT
1 AGCTGCCATATGATTGAGGATCCACAACCTCTCGAAGATAAAAGCTATCACAGAAAGTTGTGAAT
* *
9313310 GCTCCGTACATATAGTCGCAGTTGGAATCTGCTTAAGCT
66 ACTCCGTACA-AAAGTCGCAGTTGGAATCTGCTTAAGCT
9313349 GTGGGTACAA
Statistics
Matches: 88, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
125 15 0.17
126 67 0.76
127 6 0.07
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (127 bp):
AGCTGCCATATGATTGAGGATCCACAACCTCTCGAAGATAAAAGCTATCACAGAAAGTTGTGAAT
ACTCCGTACAAAAGTCGCAGTTGGAATCTGCTTAAGCTATGAATACACAGATGGTGCAGATA
Found at i:9313958 original size:49 final size:45
Alignment explanation
Indices: 9313850--9314413 Score: 282
Period size: 45 Copynumber: 13.9 Consensus size: 45
9313840 ATCATATGTG
* * *
9313850 TCGTATAGTATAATCAATTAAATAATATTTACCATATCATATATA
1 TCGTATAGCATAATCAATCAAATAATATTTACCATATCATACATA
*
9313895 TCGTATAGCATAATCAATCAAATAATATTTACCATGTCATACATA
1 TCGTATAGCATAATCAATCAAATAATATTTACCATATCATACATA
* * *
9313940 TCGTATAG-AGTACTTAATCACATAATA--T----T-T-AT-CATA
1 TCGTATAGCA-TAATCAATCAAATAATATTTACCATATCATACATA
* * *
9313976 TCATATAGCATAATCAATCAAATAACATTTA-C----CGT--AT-
1 TCGTATAGCATAATCAATCAAATAATATTTACCATATCATACATA
* *
9314013 T-GTATAGCATAATCAATCAAATAATATTTACCATGTCATGCATA
1 TCGTATAGCATAATCAATCAAATAATATTTACCATATCATACATA
* * * * * **
9314057 TCGTATAGAATACTTAATAAAATAATATTTACTATATCATGTATA
1 TCGTATAGCATAATCAATCAAATAATATTTACCATATCATACATA
* *
9314102 TTGTATAGCATAGTCAATCAAATAATA-TT----TA-C---CATA
1 TCGTATAGCATAATCAATCAAATAATATTTACCATATCATACATA
* ** *
9314138 TCGTATAGCATAATCAATAAAATATCATTTACCG---------TA
1 TCGTATAGCATAATCAATCAAATAATATTTACCATATCATACATA
* * *
9314174 TCGTATAGCATAATTAATCAAATAATAATTACC--AT-GT---TA
1 TCGTATAGCATAATCAATCAAATAATATTTACCATATCATACATA
*
9314213 T-GCATA-CATAATCAATCAAATAATA-TT----TA-C---CATA
1 TCGTATAGCATAATCAATCAAATAATATTTACCATATCATACATA
*
9314247 TCGTATAGCATAATCAATCAAATAATA--T----T-T-AT-CGTA
1 TCGTATAGCATAATCAATCAAATAATATTTACCATATCATACATA
* * * *
9314283 TCGTATAGCATAATTAATCAAATAATATTTATCATGTCATGCATA
1 TCGTATAGCATAATCAATCAAATAATATTTACCATATCATACATA
* * * * * *
9314328 TCGTATAGAATACTTAATCAAATAATATTTATCATATCATGCACA
1 TCGTATAGCATAATCAATCAAATAATATTTACCATATCATACATA
* ** *
9314373 CCGTATAGCATCGTTAATCAAATAATATTTACCATATCATA
1 TCGTATAGCATAATCAATCAAATAATATTTACCATATCATA
9314414 TAGCATAACC
Statistics
Matches: 421, Mismatches: 55, Indels: 86
0.75 0.10 0.15
Matches are distributed among these distances:
34 4 0.01
35 6 0.01
36 156 0.37
37 25 0.06
38 9 0.02
39 6 0.01
40 2 0.00
41 2 0.00
42 1 0.00
43 4 0.01
44 6 0.01
45 200 0.48
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (45 bp):
TCGTATAGCATAATCAATCAAATAATATTTACCATATCATACATA
Found at i:9313995 original size:36 final size:36
Alignment explanation
Indices: 9313955--9314519 Score: 416
Period size: 36 Copynumber: 14.7 Consensus size: 36
9313945 TAGAGTACTT
* *
9313955 AATCACATAATATTTATCATATCATATAGCATAATC
1 AATCAAATAATATTTACCATATCATATAGCATAATC
* * **
9313991 AATCAAATAACATTTACCGTATTGTATAGCATAATC
1 AATCAAATAATATTTACCATATCATATAGCATAATC
* *
9314027 AATCAAATAATATTTACCATGTCATGCATATCGTATAGAATAC
1 AATCAAATAATATTTACCA--T-AT-CATATAGCAT--AAT-C
* * *
9314070 TTAATAAAATAATATTTACTATATCATGTATATTGTATAGCATAGTC
1 --AATCAAATAATATTTACCATATC------A---TATAGCATAATC
*
9314117 AATCAAATAATATTTACCATATCGTATAGCATAATC
1 AATCAAATAATATTTACCATATCATATAGCATAATC
* * * *
9314153 AATAAAAT-ATCATTTACCGTATCGTATAGCATAATT
1 AATCAAATAAT-ATTTACCATATCATATAGCATAATC
* * *
9314189 AATCAAATAATAATTACCATGTTATGCATA-CATAATC
1 AATCAAATAATATTTACCATATCAT--ATAGCATAATC
*
9314226 AATCAAATAATATTTACCATATCGTATAGCATAATC
1 AATCAAATAATATTTACCATATCATATAGCATAATC
* * * *
9314262 AATCAAATAATATTTATCGTATCGTATAGCATAATT
1 AATCAAATAATATTTACCATATCATATAGCATAATC
* * *
9314298 AATCAAATAATATTTATCATGTCATGCATATCGTATAGAATAC
1 AATCAAATAATATTTACCA--T-AT-CATATAGCAT--AAT-C
* * *
9314341 TTAATCAAATAATATTTATCATATCATGCACACCGTATAGCATC
1 --AATCAAATAATATTTACCATATCAT--ATA--GCATA--ATC
*
9314385 GTTAATCAAATAATATTTACCATATCATATAGCATAACC
1 ---AATCAAATAATATTTACCATATCATATAGCATAATC
* * * *
9314424 AATC-AATAACATTTACCATACCGTATAGCATAATT
1 AATCAAATAATATTTACCATATCATATAGCATAATC
*
9314459 AATCAAATAATATTTACCATATCGTATAGCATAATC
1 AATCAAATAATATTTACCATATCATATAGCATAATC
* *
9314495 AATCAAATAAAATTTATCATATCAT
1 AATCAAATAATATTTACCATATCAT
9314520 GCATATCGTA
Statistics
Matches: 429, Mismatches: 60, Indels: 80
0.75 0.11 0.14
Matches are distributed among these distances:
35 35 0.08
36 216 0.50
37 29 0.07
38 5 0.01
39 6 0.01
40 13 0.03
41 8 0.02
42 10 0.02
43 7 0.02
44 1 0.00
45 89 0.21
47 2 0.00
48 2 0.00
50 6 0.01
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.35
Consensus pattern (36 bp):
AATCAAATAATATTTACCATATCATATAGCATAATC
Found at i:9314122 original size:126 final size:110
Alignment explanation
Indices: 9313979--9314510 Score: 419
Period size: 126 Copynumber: 4.6 Consensus size: 110
9313969 TATCATATCA
* * *
9313979 TATAGCATAATCAATCAAATAACATTTACCGTATTGTATAGCATAATCAATCAAATAATATTTAC
1 TATAGCATAATCAATCAAATAATATTTACCATATCGTATAGCATAATCAATCAAATAATATTTA-
* *
9314044 CATGTCATGCATATCGTATAGAATACTTAATAAAATAATATTTACTATATCATGTATATTG
65 C----C--G--TATCGTATAGAATAATTAATAAAATAATA---A-T-TACCATGT-TA-TG
* *
9314105 TATAGCATAGTCAATCAAATAATATTTACCATATCGTATAGCATAATCAATAAAAT-ATCATTTA
1 TATAGCATAATCAATCAAATAATATTTACCATATCGTATAGCATAATCAATCAAATAAT-ATTTA
* *
9314169 CCGTATCGTATAGCATAATTAATCAAATAATAATTACCATGTTATG
65 CCGTATCGTATAGAATAATTAATAAAATAATAATTACCATGTTATG
* *
9314215 CATA-CATAATCAATCAAATAATATTTACCATATCGTATAGCATAATCAATCAAATAATATTTAT
1 TATAGCATAATCAATCAAATAATATTTACCATATCGTATAGCATAATCAATCAAATAATATTTAC
* * * *
9314279 CGTATCGTATAGCATAATTAATCAAATAATATTTATCATGTCATGCATATCG
66 CGTATCGTATAGAATAATTAATAAAATAATAATTA-C----CATG-TTAT-G
* * * * ** *
9314331 TATAGAATACTTAATCAAATAATATTTATCATATCATGCACACCGTATAGCATCGTTAATCAAAT
1 TATAGCATAATCAATCAAATAATATTTA-C----CAT----ATCGTATAGCATAATCAATCAAAT
* * * ** * * * *
9314396 AATATTTACCATATCATATAGCATAACCAAT-CAATAACATTTACCA---TACCG
57 AATATTTACCGTATCGTATAGAATAATTAATAAAATAATAATTACCATGTTA-TG
* *
9314447 TATAGCATAATTAATCAAATAATATTTACCATATCGTATAGCATAATCAATCAAATAAAATTTA
1 TATAGCATAATCAATCAAATAATATTTACCATATCGTATAGCATAATCAATCAAATAATATTTA
9314511 TCATATCATG
Statistics
Matches: 348, Mismatches: 38, Indels: 59
0.78 0.09 0.13
Matches are distributed among these distances:
107 27 0.08
109 88 0.25
110 8 0.02
111 5 0.01
112 7 0.02
113 1 0.00
114 5 0.01
115 4 0.01
116 33 0.09
117 46 0.13
118 1 0.00
119 1 0.00
120 2 0.01
121 1 0.00
122 3 0.01
124 1 0.00
125 13 0.04
126 102 0.29
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (110 bp):
TATAGCATAATCAATCAAATAATATTTACCATATCGTATAGCATAATCAATCAAATAATATTTAC
CGTATCGTATAGAATAATTAATAAAATAATAATTACCATGTTATG
Found at i:9314129 original size:162 final size:157
Alignment explanation
Indices: 9313850--9314551 Score: 659
Period size: 162 Copynumber: 4.5 Consensus size: 157
9313840 ATCATATGTG
* * ** * * *
9313850 TCGTATAGTATAATCAATTAAATAATATTTACCATATCATATATATCGTATAGCATAATCAATCA
1 TCGTATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAGAAT-CTTAATCA
* * * * *
9313915 AATAATATTTACCATGTCATACATATCGTATAG-AGTACTTAATCACATAATATTTATCATATCA
65 AATAATATTTACCA--T-AT-CATATCGTATAGCA-TAATCAATCAAATAATATTTACCATATCG
9313979 TATAGCATAATCAATCAAATAACATTTACCGTA
125 TATAGCATAATCAATCAAATAACATTTACCGTA
* * *
9314012 TTGTATAGCATAATCAATCAAATAATATTTACCATGTCATGCATATCGTATAGAATACTTAATAA
1 TCGTATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAGAAT-CTTAATCA
* * *
9314077 AATAATATTTACTATATCATGTATATTGTATAGCATAGTCAATCAAATAATATTTACCATATCGT
65 AATAATATTTACCATATC----ATATCGTATAGCATAATCAATCAAATAATATTTACCATATCGT
* *
9314142 ATAGCATAATCAATAAAATATCATTTACCGTA
126 ATAGCATAATCAATCAAATAACATTTACCGTA
* * * *
9314174 TCGTATAGCATAATTAATCAAATAATAATTACCATGTTATGCATA-C--AT--AATC--AATCAA
1 TCGTATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAGAATCTTAATCAA
* *
9314232 ATAATATTTA-C----CATATCGTATAGCATAATCAATCAAATAATATTTATCGTATCGTATAGC
66 ATAATATTTACCATATCATATCGTATAGCATAATCAATCAAATAATATTTACCATATCGTATAGC
* *
9314292 ATAATTAATCAAATAATATTTATCATGTCATGCATA
131 ATAATCAATCAAATAACATTTA-C----C--G--TA
* * * * * * *
9314328 TCGTATAGAATACTTAATCAAATAATATTTATCATATCATGCACACCGTATAGCATCGTTAATCA
1 TCGTATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAGAATC-TTAATCA
* * *
9314393 AATAATATTTACCATATC--A---TATAGCATAACCAATC-AATAACATTTACCATACCGTATAG
65 AATAATATTTACCATATCATATCGTATAGCATAATCAATCAAATAATATTTACCATATCGTATAG
* * *
9314452 CATAATTAATCAAATAATATTTACCATA
130 CATAATCAATCAAATAACATTTACCGTA
* * * * *
9314480 TCGTATAGCATAATCAATCAAATAAAATTTATCATATCATGCATATCGTATAGCATGCTCAACCA
1 TCGTATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAGAAT-CTTAATCA
9314545 AATAATA
65 AATAATA
9314552 ATCATATTAT
Statistics
Matches: 457, Mismatches: 55, Indels: 66
0.79 0.10 0.11
Matches are distributed among these distances:
145 62 0.14
146 1 0.00
149 1 0.00
150 1 0.00
152 65 0.14
153 1 0.00
154 55 0.12
155 1 0.00
156 2 0.00
157 5 0.01
158 1 0.00
159 7 0.02
160 2 0.00
161 44 0.10
162 205 0.45
163 2 0.00
165 1 0.00
167 1 0.00
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.35
Consensus pattern (157 bp):
TCGTATAGCATAATCAATCAAATAATATTTACCATATCATGCATATCGTATAGAATCTTAATCAA
ATAATATTTACCATATCATATCGTATAGCATAATCAATCAAATAATATTTACCATATCGTATAGC
ATAATCAATCAAATAACATTTACCGTA
Found at i:9314244 original size:109 final size:110
Alignment explanation
Indices: 9314055--9314510 Score: 429
Period size: 109 Copynumber: 4.0 Consensus size: 110
9314045 ATGTCATGCA
* * * * *
9314055 TATCGTATAGAATACTTAATAAAATAATATTTACTATATCATGTATATTGTATAGCATAGTCAAT
1 TATCGTATAGCATAATTAATCAAATAATATTTAC-----CATGT-TA-TGCATAGCATAATCAAT
*
9314120 CAAATAATATTTACCATATCGTATAGCATAATCAATAAAAT-ATCATTTACCG
59 CAAATAATATTTACCATATCGTATAGCATAATCAATCAAATAAT-ATTTACCG
*
9314172 TATCGTATAGCATAATTAATCAAATAATAATTACCATGTTATGCATA-CATAATCAATCAAATAA
1 TATCGTATAGCATAATTAATCAAATAATATTTACCATGTTATGCATAGCATAATCAATCAAATAA
*
9314236 TATTTACCATATCGTATAGCATAATCAATCAAATAATATTTATCG
66 TATTTACCATATCGTATAGCATAATCAATCAAATAATATTTACCG
* * *
9314281 TATCGTATAGCATAATTAATCAAATAATATTTATCATGTCATGCATATCGTATAGAATACTTAAT
1 TATCGTATAGCATAATTAATCAAATAATATTTACCATGTTATGCATA--GCAT--AAT-C--AAT
* ** * *
9314346 CAAATAATATTTATCATATCATGCACACCGTATAGCATCGTTAATCAAATAATATTTACCA
59 CAAATAATATTTA-C----CAT----ATCGTATAGCATAATCAATCAAATAATATTTACCG
* ** * * * *
9314407 TATCATATAGCATAACCAATC-AATAACATTTACCA---TACCGTATAGCATAATTAATCAAATA
1 TATCGTATAGCATAATTAATCAAATAATATTTACCATGTTA-TGCATAGCATAATCAATCAAATA
*
9314468 ATATTTACCATATCGTATAGCATAATCAATCAAATAAAATTTA
65 ATATTTACCATATCGTATAGCATAATCAATCAAATAATATTTA
9314511 TCATATCATG
Statistics
Matches: 287, Mismatches: 33, Indels: 48
0.78 0.09 0.13
Matches are distributed among these distances:
107 27 0.09
109 100 0.35
110 7 0.02
111 5 0.02
112 7 0.02
114 3 0.01
115 2 0.01
116 16 0.06
117 46 0.16
118 1 0.00
119 3 0.01
121 3 0.01
122 4 0.01
123 4 0.01
125 12 0.04
126 47 0.16
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (110 bp):
TATCGTATAGCATAATTAATCAAATAATATTTACCATGTTATGCATAGCATAATCAATCAAATAA
TATTTACCATATCGTATAGCATAATCAATCAAATAATATTTACCG
Found at i:9314394 original size:271 final size:271
Alignment explanation
Indices: 9313892--9314519 Score: 879
Period size: 271 Copynumber: 2.3 Consensus size: 271
9313882 CATATCATAT
* * * *
9313892 ATATCGTATAGCATAATCAATCAAATAATATTTACCATGTCATACATATCGTATAGAGTACTTAA
1 ATATCGTATAGCATAATTAATCAAATAATATTTACCATGTTATGCATA--GCATA-A-T-C--AA
* *
9313957 TCACATAATATTTATCATATCATATAGCATAATCAATCAAATAACATTTACCGTATTGTATAGCA
59 TCAAATAATATTTATCATATCATATAGCATAATCAATCAAATAACATTTACCGTATCGTATAGCA
9314022 TAATCAATCAAATAATATTTACCATGTCATGCATATCGTATAGAATACTTAATAAAATAATATTT
124 TAATCAATCAAATAATATTTACCATGTCATGCATATCGTATAGAATACTTAATAAAATAATATTT
* * ** * *
9314087 ACTATATCATGTATATTGTATAGCATAGTCAATCAAATAATATTTACCATATCGTATAGCATAAT
189 ACTATATCATGCACACCGTATAGCATAGTCAATCAAATAATATTTACCATATCATATAGCATAAC
*
9314152 CAATAAAATATCATTTACC
254 CAAT-AAATAACATTTACC
* *
9314171 GTATCGTATAGCATAATTAATCAAATAATAATTACCATGTTATGCATA-CATAATCAATCAAATA
1 ATATCGTATAGCATAATTAATCAAATAATATTTACCATGTTATGCATAGCATAATCAATCAAATA
* * * * *
9314235 ATATTTACCATATCGTATAGCATAATCAATCAAATAATATTTATCGTATCGTATAGCATAATTAA
66 ATATTTATCATATCATATAGCATAATCAATCAAATAACATTTACCGTATCGTATAGCATAATCAA
* *
9314300 TCAAATAATATTTATCATGTCATGCATATCGTATAGAATACTTAATCAAATAATATTTA-TCATA
131 TCAAATAATATTTACCATGTCATGCATATCGTATAGAATACTTAATAAAATAATATTTACT-ATA
* * *
9314364 TCATGCACACCGTATAGCATCGTTAATCAAATAATATTTACCATATCATATAGCATAACCAATCA
195 TCATGCACACCGTATAGCATAGTCAATCAAATAATATTTACCATATCATATAGCATAACCAATAA
9314429 ATAACATTTACC
260 ATAACATTTACC
* *
9314441 ATACCGTATAGCATAATTAATCAAATAATATTTACCA---TATCGTATAGCATAATCAATCAAAT
1 ATATCGTATAGCATAATTAATCAAATAATATTTACCATGTTAT-GCATAGCATAATCAATCAAAT
*
9314503 AAAATTTATCATATCAT
65 AATATTTATCATATCAT
9314520 GCATATCGTA
Statistics
Matches: 314, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
267 3 0.01
268 4 0.01
269 29 0.09
270 47 0.15
271 182 0.58
273 1 0.00
274 1 0.00
275 1 0.00
276 3 0.01
279 43 0.14
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.35
Consensus pattern (271 bp):
ATATCGTATAGCATAATTAATCAAATAATATTTACCATGTTATGCATAGCATAATCAATCAAATA
ATATTTATCATATCATATAGCATAATCAATCAAATAACATTTACCGTATCGTATAGCATAATCAA
TCAAATAATATTTACCATGTCATGCATATCGTATAGAATACTTAATAAAATAATATTTACTATAT
CATGCACACCGTATAGCATAGTCAATCAAATAATATTTACCATATCATATAGCATAACCAATAAA
TAACATTTACC
Found at i:9314466 original size:197 final size:198
Alignment explanation
Indices: 9314175--9314551 Score: 560
Period size: 197 Copynumber: 1.9 Consensus size: 198
9314165 TTTACCGTAT
* * * *
9314175 CGTATAGCATAATTAATCAAATAATAATTACCATGTTATGCATACATAATCAATCAAATAATATT
1 CGTATAGCATAATTAATCAAATAATAATTACCATATCAT-CATACATAACCAATCAAATAACATT
* * * *
9314240 TACCATATCGTATAGCATAATCAATCAAATAATATTTATCGTATCGTATAGCATAATTAATCAAA
65 TACCATACCGTATAGCATAATCAATCAAATAATATTTACCATATCGTATAGCATAATCAATCAAA
* * * *
9314305 TAATATTTATCATGTCATGCATATCGTATAGAATACTTAATCAAATAATATTTATCATATCATGC
130 TAAAATTTATCATATCATGCATATCGTATAGAATACTCAACCAAATAATATTTATCATATCATGC
9314370 ACAC
195 ACAC
** *
9314374 CGTATAGCATCGTTAATCAAATAATATTTACCATATCAT-ATAGCATAACCAATC-AATAACATT
1 CGTATAGCATAATTAATCAAATAATAATTACCATATCATCATA-CATAACCAATCAAATAACATT
*
9314437 TACCATACCGTATAGCATAATTAATCAAATAATATTTACCATATCGTATAGCATAATCAATCAAA
65 TACCATACCGTATAGCATAATCAATCAAATAATATTTACCATATCGTATAGCATAATCAATCAAA
* *
9314502 TAAAATTTATCATATCATGCATATCGTATAGCATGCTCAACCAAATAATA
130 TAAAATTTATCATATCATGCATATCGTATAGAATACTCAACCAAATAATA
9314552 ATCATATTAT
Statistics
Matches: 159, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
197 115 0.72
198 10 0.06
199 34 0.21
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (198 bp):
CGTATAGCATAATTAATCAAATAATAATTACCATATCATCATACATAACCAATCAAATAACATTT
ACCATACCGTATAGCATAATCAATCAAATAATATTTACCATATCGTATAGCATAATCAATCAAAT
AAAATTTATCATATCATGCATATCGTATAGAATACTCAACCAAATAATATTTATCATATCATGCA
CAC
Found at i:9314488 original size:71 final size:72
Alignment explanation
Indices: 9314372--9314515 Score: 227
Period size: 71 Copynumber: 2.0 Consensus size: 72
9314362 TATCATGCAC
** *
9314372 ACCGTATAGCATCGTTAATCAAATAATATTTACCATATCATATAGCATAACCAATC-AATAACAT
1 ACCGTATAGCATAATTAATCAAATAATATTTACCATATCATATAGCATAACCAATCAAATAAAAT
9314436 TTACCAT
66 TTACCAT
* *
9314443 ACCGTATAGCATAATTAATCAAATAATATTTACCATATCGTATAGCATAATCAATCAAATAAAAT
1 ACCGTATAGCATAATTAATCAAATAATATTTACCATATCATATAGCATAACCAATCAAATAAAAT
*
9314508 TTATCAT
66 TTACCAT
9314515 A
1 A
9314516 TCATGCATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
71 52 0.79
72 14 0.21
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (72 bp):
ACCGTATAGCATAATTAATCAAATAATATTTACCATATCATATAGCATAACCAATCAAATAAAAT
TTACCAT
Found at i:9314563 original size:45 final size:44
Alignment explanation
Indices: 9314476--9314564 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 44
9314466 TAATATTTAC
* *
9314476 CATATCGTATAGCATAATCAATCAAATAAAATTTATCATATCATG
1 CATATCGTATAGCATAATCAACCAAATAAAATATAT-ATATCATG
**
9314521 CATATCGTATAGCATGCTCAACCAAATAATAATCATAT-TATCAT
1 CATATCGTATAGCATAATCAACCAAATAA-AAT-ATATATATCAT
9314565 TCATGCCATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
45 32 0.84
46 3 0.08
47 3 0.08
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (44 bp):
CATATCGTATAGCATAATCAACCAAATAAAATATATATATCATG
Found at i:9315563 original size:39 final size:39
Alignment explanation
Indices: 9315459--9315572 Score: 111
Period size: 39 Copynumber: 2.9 Consensus size: 39
9315449 CGGTATAACT
* * * *
9315459 TTACGGTGTTTACAGTGTCACCATCAGTTCAGTATTTCA
1 TTACGGTATTTACAGTGTTACCGTCAATTCAGTATTTCA
* * * ** ** *
9315498 GTACGGTATTTTCAATGTTATTGTCAATTTTGTATTTCC
1 TTACGGTATTTACAGTGTTACCGTCAATTCAGTATTTCA
*
9315537 TTACGGTATTTACAGTGTTACCGTCAACTCAGTATT
1 TTACGGTATTTACAGTGTTACCGTCAATTCAGTATT
9315573 GTTTCGCAGT
Statistics
Matches: 55, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
39 55 1.00
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.43
Consensus pattern (39 bp):
TTACGGTATTTACAGTGTTACCGTCAATTCAGTATTTCA
Found at i:9316846 original size:55 final size:54
Alignment explanation
Indices: 9316757--9316958 Score: 183
Period size: 55 Copynumber: 3.6 Consensus size: 54
9316747 ACAAAAACTA
* * *
9316757 TAAAATTTGAAAAACCAGTAGAAAAACTGTAAAATCT-GTAAAAGTGGTAAAATTG
1 TAAAATTTG-AAAACCAGTGGCAAAACTGTAAAATCTAG-AAAAGTGGCAAAATTG
** * *** *
9316812 TAAAATTTAGAAAACCAGTGGCAAAACTACAAAATCTGGAAAACCAACAGCAAAACTG
1 TAAAATTT-GAAAACCAGTGGCAAAACTGTAAAATCTAG-AAA--AGTGGCAAAATTG
* * *
9316870 TAAAATATTGAAAA-CAGTGGTAAAACTGTAAAATATAGAACAGTGGCAAAATTG
1 TAAAAT-TTGAAAACCAGTGGCAAAACTGTAAAATCTAGAAAAGTGGCAAAATTG
* *
9316924 TAAAATTTGGAAAATCAGTGGCAGAACTGTAAAAT
1 TAAAATTT-GAAAACCAGTGGCAAAACTGTAAAAT
9316959 AGTGGCAGTT
Statistics
Matches: 118, Mismatches: 22, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
53 2 0.02
54 20 0.17
55 49 0.42
56 7 0.06
57 19 0.16
58 19 0.16
59 2 0.02
ACGTcount: A:0.50, C:0.11, G:0.17, T:0.22
Consensus pattern (54 bp):
TAAAATTTGAAAACCAGTGGCAAAACTGTAAAATCTAGAAAAGTGGCAAAATTG
Found at i:9316920 original size:26 final size:27
Alignment explanation
Indices: 9316750--9316959 Score: 145
Period size: 29 Copynumber: 7.5 Consensus size: 27
9316740 GGGCGTTACA
* * * *
9316750 AAAACTATAAAATTTGAAAAACCAGTAGA
1 AAAACTGTAAAATATG-AAAA-CAGTGGC
* * *
9316779 AAAACTGTAAAATCTGTAAA-AGTGGT
1 AAAACTGTAAAATATGAAAACAGTGGC
* *
9316805 AAAATTGTAAAATTTAGAAAACCAGTGGC
1 AAAACTGTAAAATAT-GAAAA-CAGTGGC
** * ***
9316834 AAAACTACAAAATCTGGAAAACCAACAGC
1 AAAACTGTAAAATAT-GAAAA-CAGTGGC
*
9316863 AAAACTGTAAAATATTGAAAACAGTGGT
1 AAAACTGTAAAATA-TGAAAACAGTGGC
*
9316891 AAAACTGTAAAATAT-AGAACAGTGGC
1 AAAACTGTAAAATATGAAAACAGTGGC
* *
9316917 AAAATTGTAAAATTTGGAAAATCAGTGGC
1 AAAACTGTAAAATAT-GAAAA-CAGTGGC
*
9316946 AGAACTGTAAAATA
1 AAAACTGTAAAATA
9316960 GTGGCAGTTT
Statistics
Matches: 142, Mismatches: 32, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
26 39 0.27
27 5 0.04
28 23 0.16
29 74 0.52
30 1 0.01
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.22
Consensus pattern (27 bp):
AAAACTGTAAAATATGAAAACAGTGGC
Found at i:9317389 original size:13 final size:12
Alignment explanation
Indices: 9317350--9317431 Score: 78
Period size: 12 Copynumber: 6.8 Consensus size: 12
9317340 TTAGTGCTGC
9317350 TTTTGCTGTTAT
1 TTTTGCTGTTAT
9317362 TTTTG-TGGTTAT
1 TTTTGCT-GTTAT
9317374 TTTTGCTGTTATT
1 TTTTGCTGTTA-T
* *
9317387 TTTTGTTGTT-G
1 TTTTGCTGTTAT
**
9317398 TTTTGCTAATAT
1 TTTTGCTGTTAT
*
9317410 TTTTGCTGTTGT
1 TTTTGCTGTTAT
*
9317422 TTTTGTTGTT
1 TTTTGCTGTT
9317432 TGGATGTTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
11 8 0.14
12 37 0.66
13 11 0.20
ACGTcount: A:0.07, C:0.05, G:0.20, T:0.68
Consensus pattern (12 bp):
TTTTGCTGTTAT
Found at i:9317401 original size:24 final size:23
Alignment explanation
Indices: 9317350--9317424 Score: 87
Period size: 24 Copynumber: 3.2 Consensus size: 23
9317340 TTAGTGCTGC
* *
9317350 TTTTGCTGTTATTTTTGTGGTTAT
1 TTTTGCTGTTATTTTTGTTGTT-G
9317374 TTTTGCTGTTATTTTTTGTTGTTG
1 TTTTGCTGTTA-TTTTTGTTGTTG
** *
9317398 TTTTGCTAATATTTTTGCTGTTG
1 TTTTGCTGTTATTTTTGTTGTTG
9317421 TTTT
1 TTTT
9317425 TGTTGTTTGG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 15 0.33
24 20 0.44
25 10 0.22
ACGTcount: A:0.08, C:0.05, G:0.19, T:0.68
Consensus pattern (23 bp):
TTTTGCTGTTATTTTTGTTGTTG
Found at i:9317425 original size:24 final size:23
Alignment explanation
Indices: 9317336--9317431 Score: 86
Period size: 24 Copynumber: 4.0 Consensus size: 23
9317326 TTTTTTTTAC
* * *
9317336 TATTTTAGTGCTGCTTTTGCTGT
1 TATTTTTGTGTTGTTTTTGCTGT
*
9317359 TATTTTTGTGGTTATTTTTGCTGT
1 TATTTTTGT-GTTGTTTTTGCTGT
**
9317383 TATTTTT-TGTTGTTGTTTTGCTAA
1 TATTTTTGTGTTG-T-TTTTGCTGT
*
9317407 TATTTTTGCTGTTGTTTTTGTTGT
1 TATTTTTG-TGTTGTTTTTGCTGT
9317431 T
1 T
9317432 TGGATGTTAT
Statistics
Matches: 58, Mismatches: 10, Indels: 9
0.75 0.13 0.12
Matches are distributed among these distances:
22 3 0.05
23 10 0.17
24 39 0.67
25 1 0.02
26 5 0.09
ACGTcount: A:0.08, C:0.06, G:0.20, T:0.66
Consensus pattern (23 bp):
TATTTTTGTGTTGTTTTTGCTGT
Found at i:9317634 original size:26 final size:25
Alignment explanation
Indices: 9317557--9317635 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 25
9317547 AATATAAAGA
* * *
9317557 ATTTTTAATGTATTTTAAATTTGTTT
1 ATTTTTAATGTATTTTATA-TTATAT
*
9317583 ATTTTTAATGT-TTGT-T-TTA-AT
1 ATTTTTAATGTATTTTATATTATAT
*
9317604 GTTTTTAAGTGTATTTTATATTATAT
1 ATTTTTAA-TGTATTTTATATTATAT
9317630 ATTTTT
1 ATTTTT
9317636 TAATTTTGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
21 8 0.20
22 5 0.12
23 3 0.07
24 1 0.02
25 6 0.15
26 18 0.44
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (25 bp):
ATTTTTAATGTATTTTATATTATAT
Found at i:9319432 original size:18 final size:17
Alignment explanation
Indices: 9319402--9319435 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9319392 GATTTAAACT
*
9319402 ATATACTTTATTTTTTG
1 ATATAATTTATTTTTTG
9319419 ATATAATTTGATTTTTT
1 ATATAATTT-ATTTTTT
9319436 TAATTTTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (17 bp):
ATATAATTTATTTTTTG
Found at i:9326222 original size:21 final size:21
Alignment explanation
Indices: 9326172--9326223 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
9326162 GGAGTTTTTA
*
9326172 GTATCGGTAGAAGCATGACAT
1 GTATCGGTAGAAGCATCACAT
* * *
9326193 GTTTTGGTAGAAGTC-TCACTT
1 GTATCGGTAGAAG-CATCACAT
9326214 GTATCGGTAG
1 GTATCGGTAG
9326224 TATTGTCTCA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAAGCATCACAT
Found at i:9334699 original size:6 final size:6
Alignment explanation
Indices: 9334688--9334713 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
9334678 CAAAAGCACC
9334688 TCTCTT TCTCTT TCTCTT TCTCTT TC
1 TCTCTT TCTCTT TCTCTT TCTCTT TC
9334714 CATGGACTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (6 bp):
TCTCTT
Found at i:9337203 original size:27 final size:27
Alignment explanation
Indices: 9337165--9337220 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
9337155 AAATCATAGT
9337165 ACCTTCAAACTTTTAATGAATTGTAGC
1 ACCTTCAAACTTTTAATGAATTGTAGC
9337192 ACCTTCAAACTTTTAATGAATTGTAGC
1 ACCTTCAAACTTTTAATGAATTGTAGC
9337219 AC
1 AC
9337221 AAGCAAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.36
Consensus pattern (27 bp):
ACCTTCAAACTTTTAATGAATTGTAGC
Found at i:9337227 original size:27 final size:27
Alignment explanation
Indices: 9337170--9337227 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
9337160 ATAGTACCTT
***
9337170 CAAACTTTTAATGAATTGTAGCACCTT
1 CAAACTTTTAATGAATTGTAGCACAAG
9337197 CAAACTTTTAATGAATTGTAGCACAAG
1 CAAACTTTTAATGAATTGTAGCACAAG
9337224 CAAA
1 CAAA
9337228 ATGTGAATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (27 bp):
CAAACTTTTAATGAATTGTAGCACAAG
Found at i:9343001 original size:37 final size:37
Alignment explanation
Indices: 9342950--9343026 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
9342940 ATTAACTTAA
9342950 CAAAAAAAAATTTCTATTTGTAAGTAAAGAATATAAT
1 CAAAAAAAAATTTCTATTTGTAAGTAAAGAATATAAT
*
9342987 CAAAAAAAATTTTCTATTTGTAAGTAAAGAATATAAT
1 CAAAAAAAAATTTCTATTTGTAAGTAAAGAATATAAT
9343024 CAA
1 CAA
9343027 CATTTCTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.32
Consensus pattern (37 bp):
CAAAAAAAAATTTCTATTTGTAAGTAAAGAATATAAT
Found at i:9344903 original size:5 final size:5
Alignment explanation
Indices: 9344893--9344930 Score: 76
Period size: 5 Copynumber: 7.6 Consensus size: 5
9344883 ATTCTTGTTA
9344893 CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC CTT
1 CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC CTT
9344931 TTTTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (5 bp):
CTTCC
Found at i:9354793 original size:15 final size:15
Alignment explanation
Indices: 9354773--9354804 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
9354763 TATTTTGTTG
9354773 GATTCAGAAAGAGTA
1 GATTCAGAAAGAGTA
*
9354788 GATTCAGATAGAGTA
1 GATTCAGAAAGAGTA
9354803 GA
1 GA
9354805 AAGAGACAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.28, T:0.22
Consensus pattern (15 bp):
GATTCAGAAAGAGTA
Found at i:9388865 original size:21 final size:20
Alignment explanation
Indices: 9388823--9388867 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
9388813 GGAAAAACTT
*
9388823 AAATTAATTCTTAAAAATTA
1 AAATTAATTCTTAAAAAGTA
*
9388843 AAATTAATTTTTAAAAAGGTA
1 AAATTAATTCTTAAAAA-GTA
9388864 AAAT
1 AAAT
9388868 GAGTGATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (20 bp):
AAATTAATTCTTAAAAAGTA
Found at i:9395180 original size:21 final size:21
Alignment explanation
Indices: 9395147--9395186 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
9395137 ATAAACTTCA
* *
9395147 AGATTCGAGGTTCAAGGTTTG
1 AGATTCAAAGTTCAAGGTTTG
*
9395168 AGATTCAAAGTTCGAGGTT
1 AGATTCAAAGTTCAAGGTT
9395187 CTGGGTAAAA
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:0.28, C:0.10, G:0.30, T:0.33
Consensus pattern (21 bp):
AGATTCAAAGTTCAAGGTTTG
Found at i:9395300 original size:17 final size:18
Alignment explanation
Indices: 9395278--9395326 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
9395268 GTATTTATAA
9395278 TTTAAA-AAATTAATTAT
1 TTTAAATAAATTAATTAT
* *
9395295 TTTAAATAATTTAATTAAA
1 TTTAAATAAATTAATT-AT
9395314 TTTAAATTAAATT
1 TTTAAA-TAAATT
9395327 GAAGAAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 6 0.23
18 8 0.31
19 7 0.27
20 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTAAATAAATTAATTAT
Found at i:9396871 original size:13 final size:11
Alignment explanation
Indices: 9396843--9396885 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
9396833 AGTTTAATAT
9396843 TATTTTATTAA
1 TATTTTATTAA
9396854 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
9396867 TA-TTTATTAT
1 TATTTTATTAA
9396877 TATTTTATT
1 TATTTTATT
9396886 TATAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:9396885 original size:11 final size:11
Alignment explanation
Indices: 9396830--9396885 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
9396820 TTATTAATTA
* *
9396830 ATTAGTTTAAT
1 ATTATTTTATT
9396841 ATTATTTTATT
1 ATTATTTTATT
*
9396852 AATATTTTACTT
1 ATTATTTTA-TT
*
9396864 A-GATATTTATT
1 ATTAT-TTTATT
9396875 ATTATTTTATT
1 ATTATTTTATT
9396886 TATAAAATGG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
11 28 0.76
12 9 0.24
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:9410556 original size:12 final size:13
Alignment explanation
Indices: 9410533--9410567 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
9410523 CCCAAGTGTT
9410533 TTTACTTTTATTTA
1 TTTAC-TTTATTTA
9410547 TTTA-TTTATTTA
1 TTTACTTTATTTA
9410559 TTTACTTTA
1 TTTACTTTA
9410568 CTTTTATGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 12 0.60
13 4 0.20
14 4 0.20
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTACTTTATTTA
Found at i:9410663 original size:17 final size:16
Alignment explanation
Indices: 9410642--9410680 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
9410632 ATTTATTTCA
*
9410642 TTTTTAGTTTTAGTTT
1 TTTTTAGTTTTAATTT
*
9410658 TATTTTATTTTTAATTT
1 T-TTTTAGTTTTAATTT
9410675 TTTTTA
1 TTTTTA
9410681 ATTATACACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.77
Consensus pattern (16 bp):
TTTTTAGTTTTAATTT
Found at i:9411666 original size:17 final size:17
Alignment explanation
Indices: 9411611--9411667 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
9411601 ATTATTTAGA
* *
9411611 AAAAGAAAAAAAAAGTC
1 AAAAGAAGAAAAAAGAC
* *
9411628 GAAAA-AATGAAAAAATAG
1 -AAAAGAA-GAAAAAAGAC
9411646 AAAAGAAGAAAAAAGAC
1 AAAAGAAGAAAAAAGAC
9411663 AAAAG
1 AAAAG
9411668 TGTGTTTGAG
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
17 19 0.61
18 12 0.39
ACGTcount: A:0.75, C:0.04, G:0.16, T:0.05
Consensus pattern (17 bp):
AAAAGAAGAAAAAAGAC
Found at i:9412723 original size:23 final size:25
Alignment explanation
Indices: 9412697--9412742 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
9412687 CCAATTAGTA
9412697 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
9412720 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
9412743 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:9421754 original size:24 final size:24
Alignment explanation
Indices: 9421735--9421796 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
9421725 ACTTAGCCCA
* *
9421735 TACGAGCCCAGAATGTTTAGCTCT
1 TACGAGCCTAGAATGGTTAGCTCT
9421759 TACGAGCCTAGAATGGTTAGCTCT
1 TACGAGCCTAGAATGGTTAGCTCT
9421783 TACGAGCCTAGAAT
1 TACGAGCCTAGAAT
9421797 CAAAATAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (24 bp):
TACGAGCCTAGAATGGTTAGCTCT
Found at i:9424272 original size:27 final size:28
Alignment explanation
Indices: 9424242--9424317 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
9424232 TGAATCGAAC
9424242 TCGTTGACTGTTGACCGTTGACC-TTGA
1 TCGTTGACTGTTGACCGTTGACCGTTGA
*
9424269 TCGTTGACTGTTGACCGTTAACCGTTGA
1 TCGTTGACTGTTGACCGTTGACCGTTGA
* * *
9424297 CCATTGACT-TTGACTGTTGAC
1 TCGTTGACTGTTGACCGTTGAC
9424318 TGTTTTCTCT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 32 0.74
28 11 0.26
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (28 bp):
TCGTTGACTGTTGACCGTTGACCGTTGA
Found at i:9424282 original size:34 final size:34
Alignment explanation
Indices: 9424244--9424321 Score: 113
Period size: 34 Copynumber: 2.3 Consensus size: 34
9424234 AATCGAACTC
*
9424244 GTTGACTGTTGACCGTTGACC-TTGATCGTTGACT
1 GTTGACTGTTAACCGTTGACCATTGA-CGTTGACT
* *
9424278 GTTGACCGTTAACCGTTGACCATTGACTTTGACT
1 GTTGACTGTTAACCGTTGACCATTGACGTTGACT
9424312 GTTGACTGTT
1 GTTGACTGTT
9424322 TTCTCTGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 35 0.90
35 4 0.10
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (34 bp):
GTTGACTGTTAACCGTTGACCATTGACGTTGACT
Found at i:9424311 original size:6 final size:7
Alignment explanation
Indices: 9424244--9424321 Score: 63
Period size: 7 Copynumber: 11.4 Consensus size: 7
9424234 AATCGAACTC
9424244 GTTGACT
1 GTTGACT
*
9424251 GTTGACC
1 GTTGACT
9424258 GTTGAC-
1 GTTGACT
*
9424264 CTTGA-T
1 GTTGACT
9424270 CGTTGACT
1 -GTTGACT
*
9424278 GTTGACC
1 GTTGACT
* *
9424285 GTTAACC
1 GTTGACT
*
9424292 GTTGACC
1 GTTGACT
*
9424299 ATTGACT
1 GTTGACT
9424306 -TTGACT
1 GTTGACT
9424312 GTTGACT
1 GTTGACT
9424319 GTT
1 GTT
9424322 TTCTCTGTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
6 10 0.17
7 48 0.81
8 1 0.02
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (7 bp):
GTTGACT
Found at i:9425357 original size:23 final size:22
Alignment explanation
Indices: 9425304--9425358 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
9425294 TTGTAAATAC
*
9425304 ATTTTATTTTGGGGATTTTGAT
1 ATTTTATTTTGGGGATTTAGAT
9425326 ATTTTATTTTGGGAGATTTAG-T
1 ATTTTATTTTGGG-GATTTAGAT
9425348 ATTTTAATTTT
1 ATTTT-ATTTT
9425359 ATTAGAGACT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.22, C:0.00, G:0.18, T:0.60
Consensus pattern (22 bp):
ATTTTATTTTGGGGATTTAGAT
Found at i:9431387 original size:27 final size:27
Alignment explanation
Indices: 9431346--9431409 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
9431336 AACCGAACCC
*
9431346 GTTGACCGTTGACTTCGACCATTGACT
1 GTTGACCGTTCACTTCGACCATTGACT
* * * *
9431373 GTTGATCGTTCACTTTGACCGTTGACC
1 GTTGACCGTTCACTTCGACCATTGACT
*
9431400 GTTTACCGTT
1 GTTGACCGTT
9431410 TACCTTTACT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.38
Consensus pattern (27 bp):
GTTGACCGTTCACTTCGACCATTGACT
Found at i:9431435 original size:13 final size:13
Alignment explanation
Indices: 9431347--9431431 Score: 66
Period size: 13 Copynumber: 6.4 Consensus size: 13
9431337 ACCGAACCCG
9431347 TTGACCGTTGACT
1 TTGACCGTTGACT
* *
9431360 TCGACCATTGACT
1 TTGACCGTTGACT
* *
9431373 GTTGATCGTTCACT
1 -TTGACCGTTGACT
9431387 TTGACCGTTGACCGT
1 TTGACCGTTGA-C-T
*
9431402 TT-ACCGTTTACCT
1 TTGACCGTTGA-CT
*
9431415 TT-ACTGTTGACT
1 TTGACCGTTGACT
9431427 TTGAC
1 TTGAC
9431432 TGTTATGTAA
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
12 4 0.07
13 31 0.54
14 19 0.33
15 3 0.05
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.40
Consensus pattern (13 bp):
TTGACCGTTGACT
Found at i:9432717 original size:20 final size:21
Alignment explanation
Indices: 9432665--9432717 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
9432655 ATGTTACACG
* *
9432665 TTGACCGTTGA-CTTTTACTA
1 TTGACCGTTGACCATTAACTA
*
9432685 TTGACCGTCGACCATTAACT-
1 TTGACCGTTGACCATTAACTA
9432705 TTGACCGTTGACC
1 TTGACCGTTGACC
9432718 GTTCACTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (21 bp):
TTGACCGTTGACCATTAACTA
Found at i:9433126 original size:15 final size:14
Alignment explanation
Indices: 9433087--9433126 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
9433077 GTGAGCTAGG
9433087 GTTTAAGGTTTCGA
1 GTTTAAGGTTTCGA
9433101 GTTTAAGGTTTCGA
1 GTTTAAGGTTTCGA
*
9433115 GTCTTGAGGTTT
1 GT-TTAAGGTTT
9433127 TGTTATAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.17, C:0.07, G:0.30, T:0.45
Consensus pattern (14 bp):
GTTTAAGGTTTCGA
Found at i:9433239 original size:14 final size:15
Alignment explanation
Indices: 9433220--9433249 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9433210 TTAAATCTTT
9433220 AAAA-CCTTAAAATC
1 AAAACCCTTAAAATC
9433234 AAAACCCTTAAAATC
1 AAAACCCTTAAAATC
9433249 A
1 A
9433250 CAAAACGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.57, C:0.23, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAACCCTTAAAATC
Found at i:9433293 original size:8 final size:8
Alignment explanation
Indices: 9433273--9433381 Score: 50
Period size: 8 Copynumber: 13.4 Consensus size: 8
9433263 TCATCACTTT
9433273 AAACCTT-
1 AAACCTTA
9433280 AAACCTTA
1 AAACCTTA
9433288 AAACCTT-
1 AAACCTTA
*
9433295 AAA-CTCA
1 AAACCTTA
9433302 AAATCCTTA
1 AAA-CCTTA
*
9433311 AAA-ATCTA
1 AAACCT-TA
*
9433319 AAACCCTAA
1 AAA-CCTTA
*
9433328 ACTAATCACTTT
1 A--AA-C-CTTA
*
9433340 AAATCTTA
1 AAACCTTA
*
9433348 AATCCTTA
1 AAACCTTA
9433356 AAACCTT-
1 AAACCTTA
9433363 AAA-CTTA
1 AAACCTTA
9433370 AAACCCTTA
1 AAA-CCTTA
9433379 AAA
1 AAA
9433382 ATATGATATT
Statistics
Matches: 76, Mismatches: 13, Indels: 24
0.67 0.12 0.21
Matches are distributed among these distances:
6 5 0.07
7 20 0.26
8 27 0.36
9 15 0.20
10 3 0.04
11 3 0.04
12 3 0.04
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.28
Consensus pattern (8 bp):
AAACCTTA
Found at i:9433293 original size:15 final size:15
Alignment explanation
Indices: 9433273--9433380 Score: 58
Period size: 15 Copynumber: 6.7 Consensus size: 15
9433263 TCATCACTTT
9433273 AAACCTTAAACCTTA
1 AAACCTTAAACCTTA
*
9433288 AAACCTTAAA-CTCA
1 AAACCTTAAACCTTA
**
9433302 AAATCCTTAAAAATCTA
1 AAA-CCTTAAACCT-TA
* *
9433319 AAACCCTAAACTAATCACTTT
1 AAA-CCT----TAAAC-CTTA
*
9433340 AAATCTTAAATCCTTA
1 AAACCTTAAA-CCTTA
9433356 AAACCTTAAA-CTTA
1 AAACCTTAAACCTTA
9433370 AAACCCTTAAA
1 AAA-CCTTAAA
9433381 AATATGATAT
Statistics
Matches: 71, Mismatches: 12, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
14 13 0.18
15 24 0.34
16 16 0.23
17 8 0.11
20 2 0.03
21 7 0.10
22 1 0.01
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (15 bp):
AAACCTTAAACCTTA
Found at i:9433311 original size:23 final size:23
Alignment explanation
Indices: 9433283--9433381 Score: 62
Period size: 23 Copynumber: 4.3 Consensus size: 23
9433273 AAACCTTAAA
9433283 CCTTAAAACCTTAAACTCAAAAT
1 CCTTAAAACCTTAAACTCAAAAT
* * * *
9433306 CCTTAAAAATCTAAAACCCTAAA-
1 CCTT-AAAACCTTAAACTCAAAAT
* * *
9433329 -C-TAATCACTTTAAATCTTAAA-T
1 CCTTAA-AACCTTAAA-CTCAAAAT
* *
9433351 CCTTAAAACCTTAAACTTAAAAC
1 CCTTAAAACCTTAAACTCAAAAT
9433374 CCTTAAAA
1 CCTTAAAA
9433382 ATATGATATT
Statistics
Matches: 55, Mismatches: 14, Indels: 14
0.66 0.17 0.17
Matches are distributed among these distances:
20 2 0.04
21 6 0.11
22 10 0.18
23 20 0.36
24 17 0.31
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.28
Consensus pattern (23 bp):
CCTTAAAACCTTAAACTCAAAAT
Found at i:9433367 original size:68 final size:69
Alignment explanation
Indices: 9433204--9433383 Score: 267
Period size: 67 Copynumber: 2.7 Consensus size: 69
9433194 TCCAAAACCC
* * * *
9433204 TAAACCTTAAATCTTTAAAACCTTAAAATCAAAACCCTT-AAAATCACAAAACGCTAAACTCATC
1 TAAACCTTAAATCCTTAAAACCTTAAACTCAAAACCCTTAAAAATCACAAAACCCTAAACTAATC
9433268 ACTT
66 ACTT
* *
9433272 TAAACCTTAAA-CCTTAAAACCTTAAACTCAAAATCCTTAAAAATC-TAAAACCCTAAACTAATC
1 TAAACCTTAAATCCTTAAAACCTTAAACTCAAAACCCTTAAAAATCACAAAACCCTAAACTAATC
9433335 ACTT
66 ACTT
* *
9433339 TAAATCTTAAATCCTTAAAACCTTAAACTTAAAACCCTTAAAAAT
1 TAAACCTTAAATCCTTAAAACCTTAAACTCAAAACCCTTAAAAAT
9433384 ATGATATTAT
Statistics
Matches: 101, Mismatches: 9, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
67 53 0.52
68 48 0.48
ACGTcount: A:0.48, C:0.24, G:0.01, T:0.28
Consensus pattern (69 bp):
TAAACCTTAAATCCTTAAAACCTTAAACTCAAAACCCTTAAAAATCACAAAACCCTAAACTAATC
ACTT
Found at i:9437007 original size:52 final size:52
Alignment explanation
Indices: 9436880--9437116 Score: 305
Period size: 52 Copynumber: 4.5 Consensus size: 52
9436870 TTCATTTAAA
* ** * * **
9436880 ACTCACGATGACA-TATAGTCATCGGACCTCTTGTTCCGTAAAAGAATTTATGC
1 ACTCACGATGACACT-TAGTCATCGGACCTCATAATCCGT-AAAGGATTCATAT
* * * *
9436933 ACTCATGATGACACTTAGTCATCGGACCTCACAATCCATAAAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTCATAATCCGTAAAGGATTCATAT
* *
9436985 ACTCACGATAACACTTAATCATCGGACCTCATAATCCGTAAAGGATTCATAT
1 ACTCACGATGACACTTAGTCATCGGACCTCATAATCCGTAAAGGATTCATAT
* *
9437037 ACTCACGATGACACTTAGTCATCAGACCTCATAATCCGTAAAGGATTCATAC
1 ACTCACGATGACACTTAGTCATCGGACCTCATAATCCGTAAAGGATTCATAT
*
9437089 ACTCACGATGACACTTATTCATCGGACC
1 ACTCACGATGACACTTAGTCATCGGACC
9437117 CTTTTTCATT
Statistics
Matches: 161, Mismatches: 22, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
52 129 0.80
53 31 0.19
54 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (52 bp):
ACTCACGATGACACTTAGTCATCGGACCTCATAATCCGTAAAGGATTCATAT
Found at i:9438996 original size:26 final size:27
Alignment explanation
Indices: 9438967--9439025 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
9438957 CATAACCAGT
* *
9438967 AGGCACCATTGGTG-CTCCTATCCAAA
1 AGGCACCATTGGTGCCGCCTACCCAAA
* *
9438993 AGGCACCGTTGGTGCCGCCTACCCCAA
1 AGGCACCATTGGTGCCGCCTACCCAAA
9439020 AGGCAC
1 AGGCAC
9439026 TACCCTCCCG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 13 0.46
27 15 0.54
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.17
Consensus pattern (27 bp):
AGGCACCATTGGTGCCGCCTACCCAAA
Found at i:9439507 original size:9 final size:9
Alignment explanation
Indices: 9439495--9439521 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
9439485 ATTAATTTTA
9439495 TTTTTTAAT
1 TTTTTTAAT
9439504 TTTTTTAAT
1 TTTTTTAAT
9439513 TTTTTTAAT
1 TTTTTTAAT
9439522 ATTAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:9441465 original size:9 final size:9
Alignment explanation
Indices: 9441447--9441490 Score: 52
Period size: 10 Copynumber: 4.6 Consensus size: 9
9441437 AAAAAAAATC
9441447 AAAACATTAT
1 AAAA-ATTAT
*
9441457 AAAAGTTAT
1 AAAAATTAT
9441466 AAAAAATTAT
1 -AAAAATTAT
9441476 AAAAATTATT
1 AAAAATTA-T
9441486 AAAAA
1 AAAAA
9441491 AAATCTACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
9 12 0.40
10 18 0.60
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:9441469 original size:19 final size:20
Alignment explanation
Indices: 9441368--9441491 Score: 83
Period size: 19 Copynumber: 6.2 Consensus size: 20
9441358 AAAAATATGT
* *
9441368 AAAATCATAAAAATTATTCA
1 AAAATTATAAAAATTATTAA
* *
9441388 AAAATTA-CAAAACTA-TAA
1 AAAATTATAAAAATTATTAA
* * *
9441406 ACAAATTATGAAATTTATAAAA
1 A-AAATTATAAAAATTAT-TAA
* ** *
9441428 AAAATGTAAAAAAAAAATCAA
1 AAAAT-TATAAAAATTATTAA
* *
9441449 AACATTATAAAAGTTA-TAA
1 AAAATTATAAAAATTATTAA
9441468 AAAATTATAAAAATTATTAA
1 AAAATTATAAAAATTATTAA
9441488 AAAA
1 AAAA
9441492 AATCTACAAT
Statistics
Matches: 76, Mismatches: 22, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
18 3 0.04
19 28 0.37
20 25 0.33
21 10 0.13
22 10 0.13
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (20 bp):
AAAATTATAAAAATTATTAA
Found at i:9441689 original size:17 final size:17
Alignment explanation
Indices: 9441655--9441689 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
9441645 TACAGTTTGC
*
9441655 TATATTTTTTTGTAATT
1 TATATTTTTTTCTAATT
*
9441672 TATATTTTTTTCTTATT
1 TATATTTTTTTCTAATT
9441689 T
1 T
9441690 TCTACTATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (17 bp):
TATATTTTTTTCTAATT
Found at i:9441744 original size:9 final size:9
Alignment explanation
Indices: 9441727--9441797 Score: 65
Period size: 9 Copynumber: 7.8 Consensus size: 9
9441717 CAATTATCTA
*
9441727 TATATTTAT
1 TATAATTAT
9441736 TATAATTATT
1 TATAATTA-T
*
9441746 TTTAATTTAT
1 TATAA-TTAT
9441756 TATAATTTAT
1 TATAA-TTAT
9441766 TATAATTA-
1 TATAATTAT
*
9441774 TAT-ATTTT
1 TATAATTAT
*
9441782 TATAATTTT
1 TATAATTAT
9441791 TATAATT
1 TATAATT
9441798 TTTTTTACAA
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
7 3 0.06
8 6 0.11
9 22 0.41
10 20 0.37
11 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
TATAATTAT
Found at i:9441761 original size:10 final size:10
Alignment explanation
Indices: 9441720--9441798 Score: 80
Period size: 10 Copynumber: 8.2 Consensus size: 10
9441710 TTTTCTACAA
9441720 TTATCTATATAT
1 TTAT-TATA-AT
9441732 TTATTATAA-
1 TTATTATAAT
*
9441741 TTATTTTTAAT
1 TTA-TTATAAT
9441752 TTATTATAAT
1 TTATTATAAT
9441762 TTATTATAA-
1 TTATTATAAT
9441771 TTA-TAT-AT
1 TTATTATAAT
9441779 TT-TTATAAT
1 TTATTATAAT
9441788 TT-TTATAAT
1 TTATTATAAT
9441797 TT
1 TT
9441799 TTTTTACAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 13
0.80 0.03 0.17
Matches are distributed among these distances:
7 1 0.02
8 8 0.13
9 19 0.32
10 21 0.35
11 7 0.12
12 4 0.07
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (10 bp):
TTATTATAAT
Found at i:9441775 original size:16 final size:17
Alignment explanation
Indices: 9441725--9441788 Score: 77
Period size: 16 Copynumber: 4.1 Consensus size: 17
9441715 TACAATTATC
9441725 TATATATTTATTATAAT
1 TATATATTTATTATAAT
9441742 TAT-T-TTTAATT-T-AT
1 TATATATTT-ATTATAAT
9441756 TATA-ATTTATTATAAT
1 TATATATTTATTATAAT
9441772 TATATATTT-TTATAAT
1 TATATATTTATTATAAT
9441788 T
1 T
9441789 TTTATAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
14 8 0.20
15 8 0.20
16 18 0.44
17 7 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATATTTATTATAAT
Found at i:9441800 original size:10 final size:10
Alignment explanation
Indices: 9441560--9441801 Score: 76
Period size: 10 Copynumber: 24.7 Consensus size: 10
9441550 CTTTGATTTT
9441560 ATTTTTTA-A
1 ATTTTTTATA
*
9441569 AATTTTTATA
1 ATTTTTTATA
*
9441579 TAGTTTTTATA
1 -ATTTTTTATA
* *
9441590 ATATTTGATA
1 ATTTTTTATA
* *
9441600 ATATTTTGTA
1 ATTTTTTATA
* * *
9441610 AATTTTAATT
1 ATTTTTTATA
9441620 ATTTTTTATA
1 ATTTTTTATA
*
9441630 TTTTTTTAT-
1 ATTTTTTATA
* *
9441639 ACTTTTTACA
1 ATTTTTTATA
* **
9441649 GTTTGCTATA
1 ATTTTTTATA
* *
9441659 TTTTTTTGTA
1 ATTTTTTATA
9441669 A---TTTATA
1 ATTTTTTATA
* * *
9441676 TTTTTTTCTT
1 ATTTTTTATA
*
9441686 ATTTTCTACT-
1 ATTTTTTA-TA
9441696 ATTTTGTTAGTA
1 ATTTT-TTA-TA
* *
9441708 TTTTTTCTACA
1 ATTTTT-TATA
* *
9441719 ATTATCTATA
1 ATTTTTTATA
*
9441729 TATTTATTATA
1 -ATTTTTTATA
9441740 ATTATTTT-TA
1 ATT-TTTTATA
*
9441750 ATTTATTATA
1 ATTTTTTATA
*
9441760 ATTTATTATA
1 ATTTTTTATA
*
9441770 A--TTATAT-
1 ATTTTTTATA
9441777 A-TTTTTATA
1 ATTTTTTATA
9441786 A-TTTTTATA
1 ATTTTTTATA
9441795 ATTTTTT
1 ATTTTTT
9441802 TTACAATTTT
Statistics
Matches: 165, Mismatches: 52, Indels: 31
0.67 0.21 0.12
Matches are distributed among these distances:
7 6 0.04
8 9 0.05
9 26 0.16
10 90 0.55
11 28 0.17
12 6 0.04
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:9441822 original size:21 final size:21
Alignment explanation
Indices: 9441778--9441822 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
9441768 TAATTATATA
* *
9441778 TTTTTATAATTTTTATAATTT
1 TTTTTACAATTTTTATAATGT
9441799 TTTTTACAATTTTCTAT-ATGT
1 TTTTTACAATTTT-TATAATGT
9441820 TTT
1 TTT
9441823 ACGATTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTTACAATTTTTATAATGT
Found at i:9442572 original size:22 final size:20
Alignment explanation
Indices: 9442537--9442578 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
9442527 TCATTGTTGA
*
9442537 GAAATTGATGAATTAGGCTT
1 GAAATTGATGAATTAAGCTT
9442557 GAAATTGATAGAAATTAAGCTT
1 GAAATTGAT-G-AATTAAGCTT
9442579 AGATAATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 1 0.05
22 9 0.47
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.33
Consensus pattern (20 bp):
GAAATTGATGAATTAAGCTT
Found at i:9448114 original size:29 final size:29
Alignment explanation
Indices: 9448074--9448129 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
9448064 TAAATTGATA
*
9448074 TATGATCTTTTGCATTTTCTATGAAATAT
1 TATGATCCTTTGCATTTTCTATGAAATAT
9448103 TATGATCCTTTGCATTTTCTATGAAAT
1 TATGATCCTTTGCATTTTCTATGAAAT
9448130 GACATGACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.11, T:0.50
Consensus pattern (29 bp):
TATGATCCTTTGCATTTTCTATGAAATAT
Found at i:9449550 original size:36 final size:36
Alignment explanation
Indices: 9449503--9449574 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
9449493 AATCCAACTT
9449503 TTAATGGTTTCATATTTGGAAAGGAGGACATGATAC
1 TTAATGGTTTCATATTTGGAAAGGAGGACATGATAC
9449539 TTAATGGTTTCATATTTGGAAAGGAGGACATGATAC
1 TTAATGGTTTCATATTTGGAAAGGAGGACATGATAC
9449575 CCCAATAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.33
Consensus pattern (36 bp):
TTAATGGTTTCATATTTGGAAAGGAGGACATGATAC
Found at i:9451432 original size:54 final size:54
Alignment explanation
Indices: 9451366--9451490 Score: 173
Period size: 53 Copynumber: 2.3 Consensus size: 54
9451356 GAGGAGATAA
*
9451366 AAAAAAGTAGAAAAGAAAGAAAAGGTCAAAATGAAAACCCGCAAAGGGCATCTTTT
1 AAAAAAG-AGAAAAGAAAGAAAAGGTCAAAATGAAAACCCACAAAGGGCATC-TTT
* **
9451422 AAAAAA-AG-AAAGAAAGAAAAGGTCAAGATGAAAATTCACAAAGGGCATCTTT
1 AAAAAAGAGAAAAGAAAGAAAAGGTCAAAATGAAAACCCACAAAGGGCATCTTT
*
9451474 AAAAAAGAAAAAAGAAA
1 AAAAAAGAGAAAAGAAA
9451491 AAAGAAAAGA
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
52 9 0.15
53 38 0.61
54 9 0.15
56 6 0.10
ACGTcount: A:0.59, C:0.10, G:0.18, T:0.13
Consensus pattern (54 bp):
AAAAAAGAGAAAAGAAAGAAAAGGTCAAAATGAAAACCCACAAAGGGCATCTTT
Found at i:9451486 original size:7 final size:7
Alignment explanation
Indices: 9451474--9451515 Score: 66
Period size: 7 Copynumber: 5.7 Consensus size: 7
9451464 GGGCATCTTT
9451474 AAAAAAG
1 AAAAAAG
9451481 AAAAAAG
1 AAAAAAG
9451488 AAAAAAG
1 AAAAAAG
9451495 AAAAGAAG
1 AAAA-AAG
9451503 AAGAAAAG
1 AA-AAAAG
9451511 AAAAA
1 AAAAA
9451516 GGAAGTCAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 21 0.64
8 10 0.30
9 2 0.06
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:9451492 original size:8 final size:8
Alignment explanation
Indices: 9451474--9451515 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
9451464 GGGCATCTTT
9451474 AAAAAAG-
1 AAAAAAGA
9451481 AAAAAAG-
1 AAAAAAGA
9451488 AAAAAAGA
1 AAAAAAGA
*
9451496 AAAGAAGA
1 AAAAAAGA
*
9451504 AGAAAAGA
1 AAAAAAGA
9451512 AAAA
1 AAAA
9451516 GGAAGTCAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
7 14 0.47
8 16 0.53
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:9451526 original size:23 final size:23
Alignment explanation
Indices: 9451474--9451515 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
9451464 GGGCATCTTT
9451474 AAAA-AAGAA-AAAAGAAAAAAG
1 AAAACAAGAAGAAAAGAAAAAAG
*
9451495 AAAAGAAGAAGAAAAGAAAAA
1 AAAACAAGAAGAAAAGAAAAA
9451516 GGAAGTCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 5 0.26
23 10 0.53
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (23 bp):
AAAACAAGAAGAAAAGAAAAAAG
Found at i:9453472 original size:98 final size:98
Alignment explanation
Indices: 9453303--9454063 Score: 618
Period size: 98 Copynumber: 7.8 Consensus size: 98
9453293 CAGGTTTCAT
* * * * *
9453303 TACCACAAGGATATGGAGGGAAAGGTTTAAGTCGCAACGGTGAACCTTGTACCTCAAAAGCATAA
1 TACCACGAGGATATAGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGA
* *
9453368 AGGGAAA-ATTTTAAGCCACAACGGTGAATCCAG
66 AGGGAAAGA-TTTAAGCCGCAACGGCGAATCCAG
* * *
9453401 TACCACGAGGATATAGAGGCAAAGGTTTAAGTCGCAACGGCTAACCTTATACCTCAGAAGCATGA
1 TACCACGAGGATATAGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGA
** * * *
9453466 AGGGAAAGATTTAATTCGTAACGGTGAATCCAA
66 AGGGAAAGATTTAAGCCGCAACGGCGAATCCAG
* *
9453499 TACCACAAGGATATAGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA
1 TACCACGAGGATATAGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGA
* *
9453564 AGGGAAAGATTCAAGTCGCAACGGCGAATCCAG
66 AGGGAAAGATTTAAGCCGCAACGGCGAATCCAG
* * *
9453597 TACCATGAGGATATGGAGGGAAAGGTTTATGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGA
1 TACCACGAGGATATAGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGA
* *
9453662 AGGGAAAGATTTAAGCCGCAACGACGAATCTAG
66 AGGGAAAGATTTAAGCCGCAACGGCGAATCCAG
* * * * * * * *
9453695 TACCACGAAGATAT-GAAGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACA-AAGATATG
1 TACCACGAGGATATAGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAG-CATG
* * * * * *
9453758 GAGAGAAAGGTTTAAGTCGCAACAGCGAA-CCTTG
65 AAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AG
* * * * * * * * *
9453792 TACCTC-A-GAAACATGAAGGGAAAGATTTAAGCCGCAACAGCGAATCTAGTACCACA-AAG-AT
1 TACCACGAGGATATA-G-AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA-
* * *
9453853 TTGAAGGGAAAGGTTTAAGTCGCAACGGCGAA-CCTTG
63 -TGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AG
* * * ** * * * *
9453890 TACCTC-A-GAAACATGAAGGGAAAAATTTAAGCCGCAACGGCGAATCTAGTACCAC-GAAG-AT
1 TACCACGAGGATATA-G-AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCA-
* * *
9453951 TTGAAGGGAAAGGTTTAAGTCGCAACGGCGAA-CCTTG
63 -TGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AG
* * * * * * * ** *
9453988 TACCTC-AGAAACATAAAGGGAAA-GTTTAAGGTAGCCACGGCAAACCCAGTACCTTAGAAGCAT
1 TACCACGAG-GATATAGAGGGAAAGGTTTAA-GTCGCAACGGCGAACCTTGTACCTCAGAAGCAT
*
9454051 GACGGGAAAGATT
64 GAAGGGAAAGATT
9454064 GAATCCGTAA
Statistics
Matches: 574, Mismatches: 75, Indels: 28
0.85 0.11 0.04
Matches are distributed among these distances:
95 3 0.01
96 6 0.01
97 72 0.13
98 484 0.84
99 5 0.01
100 4 0.01
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (98 bp):
TACCACGAGGATATAGAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGA
AGGGAAAGATTTAAGCCGCAACGGCGAATCCAG
Found at i:9453479 original size:49 final size:48
Alignment explanation
Indices: 9453319--9454063 Score: 498
Period size: 49 Copynumber: 15.2 Consensus size: 48
9453309 AAGGATATGG
* * * * *
9453319 AGGGAAAGGTTTAAGTCGCAACGGTGAACCTTGTACCTCAAAAGCATAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACC-TATACCTCAGAAGCATGA
* * * * *
9453368 AGGGAAA-ATTTTAAGCCACAACGGTGAATCC-AGTACCAC-G-AGGAT-A
1 AGGGAAAGA-TTTAAGTCGCAACGGCGAA-CCTA-TACCTCAGAAGCATGA
* *
9453414 TAGAGGCAAAGGTTTAAGTCGCAACGGCTAACCTTATACCTCAGAAGCATGA
1 -AG-GG-AAAGATTTAAGTCGCAACGGCGAACC-TATACCTCAGAAGCATGA
* * * * * * *
9453466 AGGGAAAGATTTAATTCGTAACGGTGAATCCAATA-C-CACAAGGATATA
1 AGGGAAAGATTTAAGTCGCAACGGCGAA-CCTATACCTCAGAAGCAT-GA
* * *
9453514 GAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGA
1 -AGGGAAAGATTTAAGTCGCAACGGCGAACC-TATACCTCAGAAGCATGA
* * * * *
9453564 AGGGAAAGATTCAAGTCGCAACGGCGAATCC-AGTACCATGAGGA-TATGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAA-CCTA-TACC-TCAGAAGCATGA
* * *
9453613 AGGGAAAGGTTTATGTCGCAACGGCGAACCTTGTACCTCAGAAGCATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACC-TATACCTCAGAAGCATGA
* * * * *
9453662 AGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAC-GAAGATATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTA-TACCTCAGAAG-CATGA
* * * * *
9453711 A-GGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACA-AAGATATGG
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTA-TACCTCAGAAG-CATGA
* * * * *
9453759 AGAGAAAGGTTTAAGTCGCAACAGCGAACCTTGTACCTCAGAAACATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACC-TATACCTCAGAAGCATGA
* * * *
9453808 AGGGAAAGATTTAAGCCGCAACAGCGAATCTAGTACCACA-AAG-ATTTGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTA-TACCTCAGAAGCA--TGA
* * *
9453857 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACC-TATACCTCAGAAGCATGA
* * * *
9453906 AGGGAAAAATTTAAGCCGCAACGGCGAATCTAGTACCAC-GAAG-ATTTGA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTA-TACCTCAGAAGCA--TGA
* * * *
9453955 AGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACC-TATACCTCAGAAGCATGA
* * * * *
9454004 AGGGAAAG-TTTAAGGTAGCCACGGCAAACCCAGTACCTTAGAAGCATGA
1 AGGGAAAGATTTAA-GTCGCAACGGCGAACCTA-TACCTCAGAAGCATGA
*
9454053 CGGGAAAGATT
1 AGGGAAAGATT
9454064 GAATCCGTAA
Statistics
Matches: 544, Mismatches: 107, Indels: 89
0.74 0.14 0.12
Matches are distributed among these distances:
46 1 0.00
47 15 0.03
48 76 0.14
49 408 0.75
50 28 0.05
51 15 0.03
52 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (48 bp):
AGGGAAAGATTTAAGTCGCAACGGCGAACCTATACCTCAGAAGCATGA
Found at i:9453789 original size:244 final size:245
Alignment explanation
Indices: 9453462--9453991 Score: 794
Period size: 244 Copynumber: 2.2 Consensus size: 245
9453452 CCTCAGAAGC
* * * * * * *
9453462 ATGAAGGGAAAGATTTAATTCGTAACGGTGAATCCAATACCACAAGGATATAGAGGGAAAGGTTT
1 ATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGTACCACAAAGATATAGAGAGAAAGGTTT
* * *
9453527 AAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTCAAGTCGCAACGGCGAA
66 AAGTCGCAACGACGAACCTTGTACCTCAGAAACATGAAGGGAAAGATTCAAGCCGCAACAGCGAA
** * * * *
9453592 TCCAGTACCATGAGGATATGGAGGGAAAGGTTTATGTCGCAACGGCGAACCTTGTACCTCAGAAG
131 TCCAGTACCACAAAGATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAA
*
9453657 CATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACGAAGAT
196 CATGAAGGGAAAAATTTAAGCCGCAACGACGAATCTAGTACCACGAAGAT
* *
9453707 ATGAA-GGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACAAAGATATGGAGAGAAAGGTTT
1 ATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGTACCACAAAGATATAGAGAGAAAGGTTT
*
9453771 AAGTCGCAAC-AGCGAACCTTGTACCTCAGAAACATGAAGGGAAAGATTTAAGCCGCAACAGCGA
66 AAGTCGCAACGA-CGAACCTTGTACCTCAGAAACATGAAGGGAAAGATTCAAGCCGCAACAGCGA
* *
9453835 ATCTAGTACCACAAAGATTTGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAA
130 ATCCAGTACCACAAAGATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAA
*
9453900 ACATGAAGGGAAAAATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGAT
195 ACATGAAGGGAAAAATTTAAGCCGCAACGACGAATCTAGTACCACGAAGAT
* * * *
9453951 TTGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACC
1 ATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGTACC
9453992 TCAGAAACAT
Statistics
Matches: 255, Mismatches: 28, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
243 1 0.00
244 218 0.85
245 36 0.14
ACGTcount: A:0.37, C:0.19, G:0.26, T:0.18
Consensus pattern (245 bp):
ATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAGTACCACAAAGATATAGAGAGAAAGGTTT
AAGTCGCAACGACGAACCTTGTACCTCAGAAACATGAAGGGAAAGATTCAAGCCGCAACAGCGAA
TCCAGTACCACAAAGATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAA
CATGAAGGGAAAAATTTAAGCCGCAACGACGAATCTAGTACCACGAAGAT
Found at i:9454009 original size:342 final size:341
Alignment explanation
Indices: 9453377--9454017 Score: 953
Period size: 342 Copynumber: 1.9 Consensus size: 341
9453367 AAGGGAAAAT
* * * *
9453377 TTTAAGCCACAACGGTGAATCCAGTACCACGAGGATATAGAGGCAAAGGTTTAAGTCGCAACGGC
1 TTTAAGCCACAACGGCGAATCCAGTACCACAAAGATATAGAGGCAAAGGTTTAAGTCGCAACAGC
* * ** * * *
9453442 TAACCTTATACCTCAGAAGCATGAAGGGAAAGATTTAATTCGTAACGGTGAATCCAATACCACAA
66 GAACCTTATACCTCAGAAACATGAAGGGAAAGATTTAAGCCGCAACAGCGAATCCAATACCACAA
* * *
9453507 GGATATAGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAGCATGAAGGGAAAG
131 AGATATAGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAACATGAAGGGAAAA
* * * * *
9453572 ATTCAAGTCGCAACGGCGAATCCAGTACCATGAGGATATGGAGGGAAAGGTTTATGTCGCAACGG
196 ATTCAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAACGG
* *
9453637 CGAACCTTGTACCTCAGAAGCATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCACG
261 CGAACCTTGTACCTCAGAAACATAAAGGGAAAG-TTTAAGCCGCAACGACGAATCTAGTACCACG
9453702 AAGATATGAAGGAAAGA
325 AAGATATGAAGGAAAGA
* * *
9453719 TTTAAGCCGCAACGGCGAATCTAGTACCACAAAGATATGGAGAG-AAAGGTTTAAGTCGCAACAG
1 TTTAAGCCACAACGGCGAATCCAGTACCACAAAGATATAGAG-GCAAAGGTTTAAGTCGCAACAG
* * *
9453783 CGAACCTTGTACCTCAGAAACATGAAGGGAAAGATTTAAGCCGCAACAGCGAATCTAGTACCACA
65 CGAACCTTATACCTCAGAAACATGAAGGGAAAGATTTAAGCCGCAACAGCGAATCCAATACCACA
* *
9453848 AAGAT-TTGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGGGAA
130 AAGATATAG-AGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAACATGAAGGGAA
* * *
9453912 AAATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATTTGAAGGGAAAGGTTTAAGTCGCAAC
194 AAATTCAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAAC
9453977 GGCGAACCTTGTACCTCAGAAACATAAAGGGAAAGTTTAAG
259 GGCGAACCTTGTACCTCAGAAACATAAAGGGAAAGTTTAAG
9454018 GTAGCCACGG
Statistics
Matches: 265, Mismatches: 32, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
341 8 0.03
342 256 0.97
343 1 0.00
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (341 bp):
TTTAAGCCACAACGGCGAATCCAGTACCACAAAGATATAGAGGCAAAGGTTTAAGTCGCAACAGC
GAACCTTATACCTCAGAAACATGAAGGGAAAGATTTAAGCCGCAACAGCGAATCCAATACCACAA
AGATATAGAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAACATGAAGGGAAAA
ATTCAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAACGG
CGAACCTTGTACCTCAGAAACATAAAGGGAAAGTTTAAGCCGCAACGACGAATCTAGTACCACGA
AGATATGAAGGAAAGA
Done.