Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 124 of 316
Found at i:39343410 original size:29 final size:29
Alignment explanation
Indices: 39343350--39343463 Score: 185
Period size: 29 Copynumber: 4.0 Consensus size: 29
39343340 CATACATGCT
* *
39343350 TATGGCCCACTAGGCCC-AATCTCATTCA
1 TATGGCCCACTAGGCCCAAATCACATTCG
39343378 TATGGCCCACTAGGCCCAAATCACATTCG
1 TATGGCCCACTAGGCCCAAATCACATTCG
*
39343407 TATGGCCCATTAGGCCCAAATCACATTCG
1 TATGGCCCACTAGGCCCAAATCACATTCG
*
39343436 TATGGCCCATTAGGCCCAAATCACATTC
1 TATGGCCCACTAGGCCCAAATCACATTC
39343464 ATATTCATAC
Statistics
Matches: 82, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
28 17 0.21
29 65 0.79
ACGTcount: A:0.27, C:0.33, G:0.16, T:0.24
Consensus pattern (29 bp):
TATGGCCCACTAGGCCCAAATCACATTCG
Found at i:39353031 original size:29 final size:30
Alignment explanation
Indices: 39352998--39353060 Score: 119
Period size: 29 Copynumber: 2.1 Consensus size: 30
39352988 TACTAGGCCA
39352998 TGTCCTCCACAAGGCTGAGACATACGG-CG
1 TGTCCTCCACAAGGCTGAGACATACGGTCG
39353027 TGTCCTCCACAAGGCTGAGACATACGGTCG
1 TGTCCTCCACAAGGCTGAGACATACGGTCG
39353057 TGTC
1 TGTC
39353061 TCTGCCCGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 27 0.82
30 6 0.18
ACGTcount: A:0.22, C:0.30, G:0.27, T:0.21
Consensus pattern (30 bp):
TGTCCTCCACAAGGCTGAGACATACGGTCG
Found at i:39353959 original size:47 final size:46
Alignment explanation
Indices: 39353890--39354066 Score: 180
Period size: 47 Copynumber: 3.8 Consensus size: 46
39353880 GGGAAGGTGC
39353890 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCCCAAG
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCCCAAG
* * **
39353936 TCGATGCCATGTCCCAGACATGGTCTTATACTGACT-ATCATCTCGTAG
1 -CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCA-CATC-CCAAG
* * * * * * *
39353984 CTGATG-CATGTCCTAGAAAT-ATCTTACACTAGCTCTCGTCTCAATG
1 C-GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCCCAA-G
39354030 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTC
1 -CGATGCCATGTCCCAGACATGGTCTTACACTGGCTC
39354067 TCATAATGTG
Statistics
Matches: 103, Mismatches: 19, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
45 1 0.01
46 19 0.18
47 63 0.61
48 20 0.19
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.28
Consensus pattern (46 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCCCAAG
Found at i:39354089 original size:47 final size:46
Alignment explanation
Indices: 39353890--39354103 Score: 172
Period size: 47 Copynumber: 4.6 Consensus size: 46
39353880 GGGAAGGTGC
*
39353890 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCCCAAGT-
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT--CAAGTG
* * * **
39353937 CGATGCCATGTCCCAGACATGGTCTTATACTGACTATCATCTCGTAG
1 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATCAAGT-G
* * * * *
39353984 CTGATG-CATGTCCTAGAAAT-ATCTTACACTAGCTCTCGTCTCAA-TG
1 C-GATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC--ATCAAGTG
39354030 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-AATGTGG
1 -CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATCAA-GT-G
* *
39354078 CCTATG-CATGTCCCAGAC-TTGTCTTA
1 -CGATGCCATGTCCCAGACATGGTCTTA
39354104 AACTAGCCAA
Statistics
Matches: 133, Mismatches: 23, Indels: 23
0.74 0.13 0.13
Matches are distributed among these distances:
45 5 0.04
46 25 0.19
47 76 0.57
48 27 0.20
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (46 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATCAAGTG
Found at i:39354103 original size:94 final size:93
Alignment explanation
Indices: 39353891--39354110 Score: 237
Period size: 94 Copynumber: 2.3 Consensus size: 93
39353881 GGAAGGTGCC
* * *
39353891 GATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATCCCAAGTCGATGCCATGTCCCAGACA
1 GATG-CATGTCCCAGAC-TTGTCTTACACTAGCTCACATCCCAAGCCGATGCCATGTCCCAGACA
* *
39353956 TGGTCTTATACTGACTATCATCTCGTAGCT
64 TGGTCTTACACTGACTATCATATCGTAGCT
* ** * * * *
39353986 GATGCATGTCCTAGAAATATCTTACACTAGCTCTCGTCTCAATGCCGATGCCATGTCCCAGACAT
1 GATGCATGTCCCAGACTTGTCTTACACTAGCTCACATCCCAA-GCCGATGCCATGTCCCAGACAT
* * *
39354051 GGTCTTACACTGGCTCTCATAAT-GTGGCCT
65 GGTCTTACACTGACTATCAT-ATCGTAG-CT
*
39354081 -ATGCATGTCCCAGACTTGTCTTAAACTAGC
1 GATGCATGTCCCAGACTTGTCTTACACTAGC
39354111 CAACAATAAC
Statistics
Matches: 102, Mismatches: 20, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
93 19 0.19
94 76 0.75
95 7 0.07
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.29
Consensus pattern (93 bp):
GATGCATGTCCCAGACTTGTCTTACACTAGCTCACATCCCAAGCCGATGCCATGTCCCAGACATG
GTCTTACACTGACTATCATATCGTAGCT
Found at i:39362069 original size:40 final size:42
Alignment explanation
Indices: 39361991--39362069 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
39361981 ATAGAGGTTT
* *
39361991 TCACCCGGCCAGACACACGGCCGTGTCATTGGCCCGTGTTCC
1 TCACACGGCCAGACACACGCCCGTGTCATTGGCCCGTGTTCC
* *
39362033 TCACACGGCCA-AGACACGCCCGTGT-GTTGGCCCGTGT
1 TCACACGGCCAGACACACGCCCGTGTCATTGGCCCGTGT
39362070 GAAAAAACCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 11 0.33
41 12 0.36
42 10 0.30
ACGTcount: A:0.15, C:0.38, G:0.28, T:0.19
Consensus pattern (42 bp):
TCACACGGCCAGACACACGCCCGTGTCATTGGCCCGTGTTCC
Found at i:39362864 original size:13 final size:13
Alignment explanation
Indices: 39362842--39362874 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
39362832 AAGGGTTTGT
39362842 TTAT-TAAACTAA
1 TTATCTAAACTAA
39362854 TTATCTAAACTAA
1 TTATCTAAACTAA
*
39362867 TTAACTAA
1 TTATCTAA
39362875 TTTAATTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:39365803 original size:6 final size:5
Alignment explanation
Indices: 39365774--39365846 Score: 57
Period size: 5 Copynumber: 14.8 Consensus size: 5
39365764 TATGTCTTTC
*
39365774 AAAAT AAAAT --AAT AAAATT GAAAT GAAAAT AAAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAA-T AAAAT -AAAAT -AAAAT AAAAT AAAAT
*
39365820 -AAAT -AAAT AAAA- ATAAT AAGAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AA-AAT AAAA
39365847 AGGTAGGAGG
Statistics
Matches: 56, Mismatches: 5, Indels: 14
0.75 0.07 0.19
Matches are distributed among these distances:
3 3 0.05
4 11 0.20
5 24 0.43
6 18 0.32
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:39370703 original size:27 final size:27
Alignment explanation
Indices: 39370667--39370856 Score: 173
Period size: 27 Copynumber: 7.3 Consensus size: 27
39370657 TACTGAAATG
*
39370667 CCCTCGATTTGTAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* * *
39370694 CCTTCAATTTATAGAATTACCATTTCA
1 CCCTCGATTTATAGAATTACCATTTTA
* * *
39370721 CCCTCGATTTACAAAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
39370748 CCCTCGATTTATAGAATTACCA---T-
1 CCCTCGATTTATAGAATTACCATTTTA
* *
39370771 ---T-GATTTATAAAATTACCGTTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* *
39370794 CCCTCGATTTACAAAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTTA
* * * *
39370821 CCCTC-AGTTTACAAAATTATCGTTTTA
1 CCCTCGA-TTTATAGAATTACCATTTTA
39370848 CCCTCGATT
1 CCCTCGATT
39370857 GTGAAATTAC
Statistics
Matches: 134, Mismatches: 19, Indels: 20
0.77 0.11 0.12
Matches are distributed among these distances:
19 15 0.11
20 1 0.01
22 1 0.01
24 1 0.01
26 2 0.01
27 113 0.84
28 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.39
Consensus pattern (27 bp):
CCCTCGATTTATAGAATTACCATTTTA
Found at i:39370739 original size:54 final size:53
Alignment explanation
Indices: 39370667--39370856 Score: 207
Period size: 54 Copynumber: 3.7 Consensus size: 53
39370657 TACTGAAATG
** * * * *
39370667 CCCTCGATTTGTAGAATTACCATTTTACCTTCAATTTATAGAATTACCATTTCA
1 CCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAGAATTACCATTT-A
39370721 CCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAGAATTACCA--T-
1 CCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAGAATTACCATTTA
* * *
39370771 ---T-GATTTATAAAATTACCGTTTTACCCTCGATTTACAAAATTACCATTTTA
1 CCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAGAATTACCA-TTTA
*
39370821 CCCTC-AGTTTACAAAATTATCGTTTTACCCTCGATT
1 CCCTCGA-TTTACAAAATTACCGTTTTACCCTCGATT
39370857 GTGAAATTAC
Statistics
Matches: 116, Mismatches: 11, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
46 41 0.35
47 1 0.01
49 1 0.01
52 1 0.01
53 2 0.02
54 70 0.60
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.39
Consensus pattern (53 bp):
CCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAGAATTACCATTTA
Found at i:39370783 original size:46 final size:46
Alignment explanation
Indices: 39370726--39370817 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
39370716 TTTCACCCTC
* *
39370726 GATTTACAAAATTACCGTTTTACCCTCGATTTATAGAATTACCATT
1 GATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTACCATT
*
39370772 GATTTATAAAATTACCGTTTTACCCTCGATTTACAAAATTACCATT
1 GATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTACCATT
39370818 TTACCCTCAG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.39
Consensus pattern (46 bp):
GATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTACCATT
Found at i:39370839 original size:73 final size:73
Alignment explanation
Indices: 39370700--39370839 Score: 210
Period size: 73 Copynumber: 1.9 Consensus size: 73
39370690 TTTACCTTCA
* * * *
39370700 ATTTATAGAATTACCATTTCACCCTCGATTTACAAAATTACCGTTTTACCCTCGATTTATAGAAT
1 ATTTATAAAATTACCATTTCACCCTCGATTTACAAAATTACCATTTTACCCTCGATTTACAAAAT
39370765 TACCATTG
66 TACCATTG
* *
39370773 ATTTATAAAATTACCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTC-AGTTTACAAAA
1 ATTTATAAAATTACCATTTCACCCTCGATTTACAAAATTACCATTTTACCCTCGA-TTTACAAAA
39370837 TTA
65 TTA
39370840 TCGTTTTACC
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
72 1 0.02
73 59 0.98
ACGTcount: A:0.34, C:0.21, G:0.06, T:0.39
Consensus pattern (73 bp):
ATTTATAAAATTACCATTTCACCCTCGATTTACAAAATTACCATTTTACCCTCGATTTACAAAAT
TACCATTG
Found at i:39370845 original size:100 final size:100
Alignment explanation
Indices: 39370672--39370856 Score: 273
Period size: 100 Copynumber: 1.9 Consensus size: 100
39370662 AAATGCCCTC
* * * * *
39370672 GATTTGTAGAATTACCATTTTACCTTCAATTTATAGAATTACCATTTCACCCTCGATTTACAAAA
1 GATTTATAAAATTACCATTTTACCCTCAATTTACAAAATTACCATTTCACCCTCGATTTACAAAA
39370737 TTACCGTTTTACCCTCGATTTATAGAATTACCATT
66 TTACCGTTTTACCCTCGATTTATAGAATTACCATT
* * *
39370772 GATTTATAAAATTACCGTTTTACCCTCGATTTACAAAATTACCATTTTACCCTC-AGTTTACAAA
1 GATTTATAAAATTACCATTTTACCCTCAATTTACAAAATTACCATTTCACCCTCGA-TTTACAAA
*
39370836 ATTATCGTTTTACCCTCGATT
65 ATTACCGTTTTACCCTCGATT
39370857 GTGAAATTAC
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
99 1 0.01
100 74 0.99
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.40
Consensus pattern (100 bp):
GATTTATAAAATTACCATTTTACCCTCAATTTACAAAATTACCATTTCACCCTCGATTTACAAAA
TTACCGTTTTACCCTCGATTTATAGAATTACCATT
Found at i:39370878 original size:27 final size:26
Alignment explanation
Indices: 39370848--39371038 Score: 154
Period size: 27 Copynumber: 7.1 Consensus size: 26
39370838 TATCGTTTTA
* *
39370848 CCCTCGATTGTGAAATTACTAAAATAC
1 CCCT-GATTGTAAAATTACCAAAATAC
* *
39370875 CCCTG-TAGGATAGAATTACCAAAATAC
1 CCCTGAT-TG-TAAAATTACCAAAATAC
*
39370902 CCCTAGTTTGTAAAATTACCAAAATAC
1 CCCT-GATTGTAAAATTACCAAAATAC
* *
39370929 CCCTAGTTTGTAAAATTACCGAAATAC
1 CCCT-GATTGTAAAATTACCAAAATAC
* * * *
39370956 CACTGGTTTGTGAAATTACCGAAATA-
1 CCCT-GATTGTAAAATTACCAAAATAC
*
39370982 CCCTCAATTTGTAAAATTACCAAAATAC
1 CCCT-GA-TTGTAAAATTACCAAAATAC
*
39371010 CCCTGATT-TACAAAATTACAAAAATAC
1 CCCTGATTGT--AAAATTACCAAAATAC
39371037 CC
1 CC
39371039 TTGACTTTCT
Statistics
Matches: 138, Mismatches: 18, Indels: 16
0.80 0.10 0.09
Matches are distributed among these distances:
25 2 0.01
26 7 0.05
27 122 0.88
28 6 0.04
29 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.28
Consensus pattern (26 bp):
CCCTGATTGTAAAATTACCAAAATAC
Found at i:39370929 original size:54 final size:52
Alignment explanation
Indices: 39370855--39371038 Score: 188
Period size: 54 Copynumber: 3.4 Consensus size: 52
39370845 TTACCCTCGA
* * ** *
39370855 TTGTGAAATTACTAAAATACCCCTGTAGGATAGAATTACCAAAATACCCCTAGT
1 TTGTAAAATTACCAAAATACCCCTGTTTG-TAAAATTACCAAAATACCCCT-GT
* *
39370909 TTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCGAAATACCACTGGT
1 TTGTAAAATTACCAAAATACCCCT-GTTTGTAAAATTACCAAAATACCCCT-GT
* * **
39370963 TTGTGAAATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGAT
1 TTGTAAAATTACCAAAATACCC-CTGTTTGTAAAATTACCAAAATACCCCTG-T
** *
39371017 TTACAAAATTACAAAAATACCC
1 TTGTAAAATTACCAAAATACCC
39371039 TTGACTTTCT
Statistics
Matches: 108, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
53 1 0.01
54 103 0.95
55 4 0.04
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (52 bp):
TTGTAAAATTACCAAAATACCCCTGTTTGTAAAATTACCAAAATACCCCTGT
Found at i:39371025 original size:81 final size:81
Alignment explanation
Indices: 39370888--39371037 Score: 214
Period size: 81 Copynumber: 1.9 Consensus size: 81
39370878 TGTAGGATAG
* ** **
39370888 AATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCGAAA
1 AATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCCTAGTTTACAAAATTACAAAAA
39370953 TACCACTGGTTTGTGA
66 TACCACTGGTTTGTGA
*
39370969 AATTACCGAAATA-CCCTCAATTTGTAAAATTACCAAAATACCCCT-GATTTACAAAATTACAAA
1 AATTACCAAAATACCCCT-AATTTGTAAAATTACCAAAATACCCCTAG-TTTACAAAATTACAAA
39371032 AATACC
64 AATACC
39371038 CTTGACTTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
80 5 0.08
81 56 0.92
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (81 bp):
AATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCCTAGTTTACAAAATTACAAAAA
TACCACTGGTTTGTGA
Found at i:39371039 original size:54 final size:54
Alignment explanation
Indices: 39370888--39371095 Score: 177
Period size: 54 Copynumber: 3.8 Consensus size: 54
39370878 TGTAGGATAG
* ** *
39370888 AATTACCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCC-CTAGTTTGTAA
1 AATTACCAAAATACCACTGA-TTTACAAAATTACCAAAATACCCTC-AATTTGTAA
* * *** *
39370942 AATTACCGAAATACCACTGGTTTGTGAAATTACCGAAATACCCTCAATTTGTAA
1 AATTACCAAAATACCACTGATTTACAAAATTACCAAAATACCCTCAATTTGTAA
* * * * *
39370996 AATTACCAAAATACCCCTGATTTACAAAATTACAAAAATACCCTTGACTTTCTAAA
1 AATTACCAAAATACCACTGATTTACAAAATTACCAAAATACCC-TCAATTTGT-AA
** * * **
39371052 AATTATAAAAATACCATTGGTTTACAAAATTACTGAAATACCCT
1 AATTACCAAAATACCACTGATTTACAAAATTACCAAAATACCCT
39371096 TGGTTTGTAG
Statistics
Matches: 126, Mismatches: 24, Indels: 7
0.80 0.15 0.04
Matches are distributed among these distances:
54 80 0.63
55 8 0.06
56 38 0.30
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.30
Consensus pattern (54 bp):
AATTACCAAAATACCACTGATTTACAAAATTACCAAAATACCCTCAATTTGTAA
Found at i:39371185 original size:27 final size:27
Alignment explanation
Indices: 39371155--39371215 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
39371145 ACCCTTAATA
39371155 GGTAAAAAGACCGTAA-AGCCCCTGTAG
1 GGTAAAAAGACCGTAATA-CCCCTGTAG
** * *
39371182 GGTAAAGTGACCGTAATACCCTTGTAT
1 GGTAAAAAGACCGTAATACCCCTGTAG
39371209 GGTAAAA
1 GGTAAAA
39371216 TGATGAATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (27 bp):
GGTAAAAAGACCGTAATACCCCTGTAG
Found at i:39372064 original size:25 final size:25
Alignment explanation
Indices: 39372030--39372099 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
39372020 AGGAAGTGCT
*
39372030 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
39372055 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
39372080 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
39372100 ATTAAAAGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.26
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:39372112 original size:24 final size:24
Alignment explanation
Indices: 39372029--39372112 Score: 107
Period size: 25 Copynumber: 3.4 Consensus size: 24
39372019 GAGGAAGTGC
*
39372029 TAAAAGGGCTTTGCCCCAGTTTACC
1 TAAAAGGGCTTTGCCCCAGTTTA-T
*
39372054 GAAAAGGGCTTTGCCCCAGTTTAT
1 TAAAAGGGCTTTGCCCCAGTTTAT
*
39372078 CAAAAAGGGCTTTGCCCCAG-TTAT
1 -TAAAAGGGCTTTGCCCCAGTTTAT
39372102 TAAAAGAGGCT
1 TAAAAG-GGCT
39372113 AGGCCTCCAG
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
23 5 0.09
24 8 0.15
25 40 0.75
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (24 bp):
TAAAAGGGCTTTGCCCCAGTTTAT
Found at i:39372123 original size:50 final size:50
Alignment explanation
Indices: 39372030--39372124 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
39372020 AGGAAGTGCT
**
39372030 AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
**
39372080 AAAAGGGCTTTGCCCCAG-TTA-TTAAAAGAGGCTAGGCCTCCAGTT
1 AAAAGGGCTTTGCCCCAGTTTACCGAAAAG-GGCTAGGCC-CCAGTT
39372125 ATATGATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
48 5 0.13
49 10 0.26
50 24 0.62
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.25
Consensus pattern (50 bp):
AAAAGGGCTTTGCCCCAGTTTACCGAAAAGGGCTAGGCCCCAGTTTATCA
Found at i:39372305 original size:42 final size:42
Alignment explanation
Indices: 39372246--39372337 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
39372236 TAGTCTCCCC
* ** *
39372246 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
39372288 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
39372330 AAATGGGC
1 AAATGGGC
39372338 CTAAAGGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:39372396 original size:31 final size:31
Alignment explanation
Indices: 39372361--39372444 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
39372351 CATTTACAGC
39372361 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
39372392 AAAGGCTACGGCCCAGTGATATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
39372423 AAATGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
39372445 TCAAGACTAA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 5 0.10
31 44 0.90
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:39374784 original size:13 final size:13
Alignment explanation
Indices: 39374762--39374794 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
39374752 AAGGGTTTGT
39374762 TTAT-TAAACTAA
1 TTATCTAAACTAA
39374774 TTATCTAAACTAA
1 TTATCTAAACTAA
*
39374787 TTAACTAA
1 TTATCTAA
39374795 TTTAATTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:39376436 original size:47 final size:45
Alignment explanation
Indices: 39376371--39376628 Score: 243
Period size: 46 Copynumber: 5.5 Consensus size: 45
39376361 GTGTCAATGC
*
39376371 CATGTCCCAGACATGGTCTTACACTGGCTCACATCTTAAGTCGATG
1 CATGTCCCAGACAT-GTCTTACACTGGCTCACATCTTAAGCCGATG
**
39376417 CCATGTCCCAGACATGGTCTTACACTAACT-ACCATCTCGT-AGCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTCA-CATCT--TAAGCCGATG
* * * *
39376465 CATGTCCCAAACATGTCTTACACTGGCTTACGTCTCAAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCACATCTTAA-GCCGATG
* * * * *
39376511 CATGTCCCAAACATGTCTTACACTAGCTCTCGTCTCAATGCCGATG
1 CATGTCCCAGACATGTCTTACACTGGCTCACATCTTAA-GCCGATG
* * * *
39376557 CCATGTCCCAGACATAGCCTTACACTGGCTCTCATAATGT-GGCCGATG
1 -CATGTCCCAGACAT-GTCTTACACTGGCTCACAT-CT-TAAGCCGATG
39376605 CATGTCCCAGACATGTCTTACACT
1 CATGTCCCAGACATGTCTTACACT
39376629 AGGCAACAAT
Statistics
Matches: 181, Mismatches: 20, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
45 1 0.01
46 75 0.41
47 73 0.40
48 30 0.17
49 2 0.01
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (45 bp):
CATGTCCCAGACATGTCTTACACTGGCTCACATCTTAAGCCGATG
Found at i:39376623 original size:140 final size:140
Alignment explanation
Indices: 39376371--39376628 Score: 351
Period size: 140 Copynumber: 1.8 Consensus size: 140
39376361 GTGTCAATGC
* * * * * *
39376371 CATGTCCCAGACATGGTCTTACACTGGCTCACATCTTAAGTCGATGCCATGTCCCAGACATGGTC
1 CATGTCCCAAACATGGTCTTACACTAGCTCACATCTCAAGCCGATGCCATGTCCCAGACATAGCC
*
39376436 TTACACTAACTACCATCTCGTAGCCGATGCATGTCCCAAACATGTCTTACACTGGCTTACGTCTC
66 TTACACTAACTACCATATCGTAGCCGATGCATGTCCCAAACATGTCTTACACTGGCTTACGTCTC
39376501 AAGGCCGATG
131 AAGGCCGATG
* *
39376511 CATGTCCCAAACAT-GTCTTACACTAGCTCTCGTCTCAATGCCGATGCCATGTCCCAGACATAGC
1 CATGTCCCAAACATGGTCTTACACTAGCTCACATCTCAA-GCCGATGCCATGTCCCAGACATAGC
** * *
39376575 CTTACACTGGCT-CTCATAAT-GTGGCCGATGCATGTCCCAGACATGTCTTACACT
65 CTTACACTAACTAC-CAT-ATCGTAGCCGATGCATGTCCCAAACATGTCTTACACT
39376629 AGGCAACAAT
Statistics
Matches: 102, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
139 21 0.21
140 80 0.78
141 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (140 bp):
CATGTCCCAAACATGGTCTTACACTAGCTCACATCTCAAGCCGATGCCATGTCCCAGACATAGCC
TTACACTAACTACCATATCGTAGCCGATGCATGTCCCAAACATGTCTTACACTGGCTTACGTCTC
AAGGCCGATG
Found at i:39380841 original size:125 final size:127
Alignment explanation
Indices: 39380683--39380959 Score: 459
Period size: 127 Copynumber: 2.2 Consensus size: 127
39380673 GAACATAGAC
*
39380683 ATAATTAATATATGAATTTGATTCATACAAAATATT-ATTATATATA-TTTGACTGAAATTAATT
1 ATAATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTTGACCGAAATTAATT
* * * *
39380746 AATATAATTAATTTTAGTCAAAATATAAAATACATGAAAATTTATATTTTTTTGGAAAGAAT
66 AATAAAATTAATTTTAGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAAGAAT
*
39380808 ATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTGACCGAAATTAATT
1 ATAATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTTGACCGAAATTAATT
* * *
39380873 AATAAAATTAATTTTGGTCAAAATATAAAAGAGATGGAAATTAATATTCTTTTGGAAAGAAT
66 AATAAAATTAATTTTAGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAAGAAT
39380935 ATAATTAATATATGAATTTGATTCA
1 ATAATTAATATATGAATTTGATTCA
39380960 AATAAATTTT
Statistics
Matches: 141, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
125 36 0.26
126 9 0.06
127 96 0.68
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (127 bp):
ATAATTAATATATGAATTTGATTCATACAAAATATTAATTATATATATTTTGACCGAAATTAATT
AATAAAATTAATTTTAGTCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGAAAGAAT
Found at i:39381001 original size:127 final size:126
Alignment explanation
Indices: 39380683--39381062 Score: 408
Period size: 127 Copynumber: 3.0 Consensus size: 126
39380673 GAACATAGAC
* *
39380683 ATAATTAATATATGAATTTGATTCATACAAAATATT-A-T-TATATATATTT-GACTGAAATTAA
1 ATAATTAATATATGAATTTGATTCATACAAAATATTAACTGTATATAT-TTTAAAC-AAAATTAA
* * * * *
39380744 TTAATATAATTAATTTTAGTCAAAATATAAAATACATGAAAATTTATATTTTTTTGGAAAGAAT
64 TTAATA-AATTAATTTTGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAGAAT
* * * *
39380808 ATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTGACCGAAATTAATT
1 ATAATTAATATATGAATTTGATTCATACAAAATATTAACTGTATATATTTTAAACAAAATTAATT
*
39380873 AATAAAATTAATTTTGGTCAAAATATAAAAGAGATGGAAATTAATATTCTTTTGGAAAGAAT
66 AAT-AAATTAATTTTGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAGAAT
* *
39380935 ATAATTAATATATGAATTTGATTCA-A-ATAAAT-TTTACTG-A-AT-TTGTTAATATAAACAGT
1 ATAATTAATATATGAATTTGATTCATACA-AAATATTAACTGTATATATT-TTAA-ACAAA-A-T
* * * * * *
39380994 T-A-T-ATTAATTAATTTCGATCAAAATATAGAAGACATAGAAATTAGTATTCTTTTGGAAAGAA
61 TAATTAATAAATTAATTTTGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAGAA
39381056 T
126 T
39381057 ATAATT
1 ATAATT
39381063 CATTTTTCTA
Statistics
Matches: 224, Mismatches: 21, Indels: 23
0.84 0.08 0.09
Matches are distributed among these distances:
122 59 0.26
123 7 0.03
124 4 0.02
125 44 0.20
126 8 0.04
127 93 0.42
128 9 0.04
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.40
Consensus pattern (126 bp):
ATAATTAATATATGAATTTGATTCATACAAAATATTAACTGTATATATTTTAAACAAAATTAATT
AATAAATTAATTTTGGTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGAAAGAAT
Found at i:39383657 original size:40 final size:39
Alignment explanation
Indices: 39383559--39383781 Score: 207
Period size: 40 Copynumber: 5.6 Consensus size: 39
39383549 TCCTCGTTCA
* * * *
39383559 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
39383598 CATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
39383637 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
39383677 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
39383717 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
39383758 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
39383782 CAGCATTCAA
Statistics
Matches: 155, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
39 39 0.25
40 104 0.67
41 12 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:39383741 original size:80 final size:79
Alignment explanation
Indices: 39383557--39383781 Score: 231
Period size: 80 Copynumber: 2.8 Consensus size: 79
39383547 GCTCCTCGTT
* * * * * *
39383557 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACCATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
39383621 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
39383636 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
39383701 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
39383716 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
39383780 GA
63 GA
39383782 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
78 1 0.01
79 38 0.31
80 69 0.57
81 13 0.11
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:39383790 original size:41 final size:41
Alignment explanation
Indices: 39383713--39383790 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
39383703 TTTGTATCTC
* * *
39383713 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
39383754 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
39383791 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:39396124 original size:13 final size:14
Alignment explanation
Indices: 39396106--39396160 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 14
39396096 CTAGTCTCTC
39396106 TTAATTTTTAATT-
1 TTAATTTTTAATTA
*
39396119 TTAA-TTTTATTTA
1 TTAATTTTTAATTA
39396132 TTAATTTTTCAATTAA
1 TTAATTTTT-AATT-A
*
39396148 TTGAATTATTAAT
1 TT-AATTTTTAAT
39396161 AATTTTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 7 0.21
13 8 0.24
14 4 0.12
15 3 0.09
16 6 0.18
17 6 0.18
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (14 bp):
TTAATTTTTAATTA
Found at i:39404121 original size:54 final size:54
Alignment explanation
Indices: 39404019--39404171 Score: 139
Period size: 54 Copynumber: 2.9 Consensus size: 54
39404009 AATACTTTAG
* ** * * * *
39404019 TTTACCAAATTACTGAAATACCC-CCAGTTGTGAAATTACC-AAAGTACCCCCGA
1 TTTACAAAATTACCCAAATACCCTCGATTTGTAAAATTACCGAAA-TACCCCCAA
* * * *
39404072 TTTATAAAATTACCCCAATATCCTCGATTTGTAAAATTACCGAAATACCCTCAA
1 TTTACAAAATTACCCAAATACCCTCGATTTGTAAAATTACCGAAATACCCCCAA
* *** *
39404126 TTTGCAAAATTATTGAAATACCCTCGATTTGTAAAATTACAGAAAT
1 TTTACAAAATTACCCAAATACCCTCGATTTGTAAAATTACCGAAAT
39404172 GTCCTCAACT
Statistics
Matches: 79, Mismatches: 19, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
53 17 0.22
54 59 0.75
55 3 0.04
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (54 bp):
TTTACAAAATTACCCAAATACCCTCGATTTGTAAAATTACCGAAATACCCCCAA
Found at i:39404228 original size:27 final size:27
Alignment explanation
Indices: 39404198--39404408 Score: 242
Period size: 27 Copynumber: 7.8 Consensus size: 27
39404188 ATTTCCAAAG
* * *
39404198 TACCATCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
39404225 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
39404252 TACTCTCGATTTATAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
39404279 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* **
39404306 TACCCTCGATTTATAGAATTACAATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
39404333 TACCCTTGATTTACAGAATTACCGTCT
1 TACCCTCGATTTACAGAATTACCGTTT
** * *
39404360 TACCCTAAATTTACAGAATTAACATTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
39404387 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
39404409 TAAAATACCC
Statistics
Matches: 158, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 158 1.00
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:39404417 original size:27 final size:27
Alignment explanation
Indices: 39404051--39404499 Score: 148
Period size: 27 Copynumber: 16.6 Consensus size: 27
39404041 CCCAGTTGTG
* * *
39404051 AAATTACCAAAGTACCCCCGATTTATA
1 AAATTACCAAAATACCCTCGATTTACA
** * **
39404078 AAATTACCCCAATATCCTCGATTTGTA
1 AAATTACCAAAATACCCTCGATTTACA
* * *
39404105 AAATTACCGAAATACCCTCAATTTGCA
1 AAATTACCAAAATACCCTCGATTTACA
*** **
39404132 AAATTATTGAAATACCCTCGATTTGTA
1 AAATTACCAAAATACCCTCGATTTACA
** * * **
39404159 AAATTA-CAGAAATGTCCTCAACTTGTA
1 AAATTACCA-AAATACCCTCGATTTACA
* * * *
39404186 AAATTTCCAAAGTACCATCGATTTATA
1 AAATTACCAAAATACCCTCGATTTACA
* ***** *
39404213 GAATTACTGTTTTACCCTTGATTTACA
1 AAATTACCAAAATACCCTCGATTTACA
* ***** * *
39404240 GAATTACTGTTTTACTCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTACA
**** *
39404267 AAATTACCGTTTTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTACA
* *** *
39404294 GAATTACCATTTTACCCTCGATTTATA
1 AAATTACCAAAATACCCTCGATTTACA
* ** *
39404321 GAATTA-CAATTTTACCCTTGATTTACA
1 AAATTACCAA-AATACCCTCGATTTACA
* **** **
39404348 GAATTACCGTCTTACCCTAAATTTACA
1 AAATTACCAAAATACCCTCGATTTACA
* * ***
39404375 GAATTAACATTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTACA
* * *
39404402 AAATTACTAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGATTTACA
* * ** *
39404429 ACATTACCAAAATACCCTTGATCAATA
1 AAATTACCAAAATACCCTCGATTTACA
* **
39404456 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTACA
39404483 AAATTACCAAAATACCC
1 AAATTACCAAAATACCC
39404500 CTGATTTGTA
Statistics
Matches: 337, Mismatches: 80, Indels: 10
0.79 0.19 0.02
Matches are distributed among these distances:
26 2 0.01
27 332 0.99
28 3 0.01
ACGTcount: A:0.36, C:0.22, G:0.08, T:0.34
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTACA
Found at i:39404418 original size:81 final size:80
Alignment explanation
Indices: 39404222--39404436 Score: 243
Period size: 81 Copynumber: 2.6 Consensus size: 80
39404212 AGAATTACTG
* ** * * * * **
39404222 TTTTACCCTTGATTTACAGAATTACTGTTTTACTCTCGATTTATAAAATTACCGTTTTACCCTCG
1 TTTTACCCTCGATTTACAGAATTACTAATTTACCCTTGATTTA-CAAATTACCGTCTTACCCTAA
* *
39404287 ATTTATAGAATTACCA
65 ATTTACAGAATTAACA
*
39404303 TTTTACCCTCGATTTATAGAATTAC-AATTTTACCCTTGATTTACAGAATTACCGTCTTACCCTA
1 TTTTACCCTCGATTTACAGAATTACTAA-TTTACCCTTGATTTACA-AATTACCGTCTTACCCTA
39404367 AATTTACAGAATTAACA
64 AATTTACAGAATTAACA
* ** *
39404384 TTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGGTTTACAACATTACC
1 TTTTACCCTCGATTTACAGAATTACTAATTTACCCTTGATTTACAA-ATTACC
39404437 AAAATACCCT
Statistics
Matches: 113, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
80 2 0.02
81 109 0.96
82 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.07, T:0.40
Consensus pattern (80 bp):
TTTTACCCTCGATTTACAGAATTACTAATTTACCCTTGATTTACAAATTACCGTCTTACCCTAAA
TTTACAGAATTAACA
Found at i:39404500 original size:27 final size:27
Alignment explanation
Indices: 39404389--39404515 Score: 137
Period size: 27 Copynumber: 4.7 Consensus size: 27
39404379 TAACATTTTA
* *
39404389 CCCTCGATTTACAAAATTACTAAAATAC
1 CCCT-GATTTATAAAATTACCAAAATAC
* * * *
39404417 CCTTGGTTTACAACATTACCAAAATAC
1 CCCTGATTTATAAAATTACCAAAATAC
* **
39404444 CCTTGATCAATAAAATTACCAAAATAC
1 CCCTGATTTATAAAATTACCAAAATAC
* *
39404471 CCCTGGTTTGTAAAATTACCAAAATAC
1 CCCTGATTTATAAAATTACCAAAATAC
*
39404498 CCCTGATTTGTAAAATTA
1 CCCTGATTTATAAAATTA
39404516 TCGACATACC
Statistics
Matches: 84, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
27 81 0.96
28 3 0.04
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (27 bp):
CCCTGATTTATAAAATTACCAAAATAC
Found at i:39404541 original size:27 final size:27
Alignment explanation
Indices: 39404457--39404776 Score: 324
Period size: 27 Copynumber: 11.6 Consensus size: 27
39404447 TGATCAATAA
* ** *
39404457 AATTACCAAAATACCCCTGGT-TTGTAA
1 AATTACCGAAATACCCCT-GTAGGGTAG
* ** *
39404484 AATTACCAAAATACCCCTG-ATTTGTAA
1 AATTACCGAAATACCCCTGTA-GGGTAG
* * *
39404511 AATTATCGACATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
39404538 AATTATTGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
39404565 AATTACCGAAATA-CCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
39404591 AATTATCGCAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
39404618 AATTACCGAAATACCCCTATAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
39404645 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
39404672 AATTACC-AGAATACCCTTGTAGGGTAG
1 AATTACCGA-AATACCCCTGTAGGGTAG
39404699 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
39404726 AATTACCGATTCTACCGAAATACCCCTGTAGGGTAG
1 ----A---A-T-TACCGAAATACCCCTGTAGGGTAG
39404762 AATTACCGAAATACC
1 AATTACCGAAATACC
39404777 TTGCGGGGTA
Statistics
Matches: 252, Mismatches: 26, Indels: 30
0.82 0.08 0.10
Matches are distributed among these distances:
26 24 0.10
27 196 0.78
28 3 0.01
29 1 0.00
31 1 0.00
32 1 0.00
34 1 0.00
35 1 0.00
36 24 0.10
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:39404749 original size:36 final size:36
Alignment explanation
Indices: 39404702--39404770 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
39404692 AGGGTAGAAT
39404702 TACCGAAATACCCCTGTAGGGTAGAATTACCGATTC
1 TACCGAAATACCCCTGTAGGGTAGAATTACCGATTC
39404738 TACCGAAATACCCCTGTAGGGTAGAATTACCGA
1 TACCGAAATACCCCTGTAGGGTAGAATTACCGA
39404771 AATACCTTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (36 bp):
TACCGAAATACCCCTGTAGGGTAGAATTACCGATTC
Found at i:39404792 original size:26 final size:27
Alignment explanation
Indices: 39404738--39404794 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
39404728 TTACCGATTC
* *
39404738 TACCGAAATACCCCTGTAGGGTAGAAT
1 TACCGAAATACCCCTGCAGGGTAAAAT
* *
39404765 TACCGAAATA-CCTTGCGGGGTAAAAT
1 TACCGAAATACCCCTGCAGGGTAAAAT
39404791 TACC
1 TACC
39404795 ATTTTGCCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (27 bp):
TACCGAAATACCCCTGCAGGGTAAAAT
Found at i:39405273 original size:22 final size:22
Alignment explanation
Indices: 39405221--39405274 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
39405211 TTAAAGCCTT
** *
39405221 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCACTGTGCCAAC
*
39405243 CT-ACATATGGCACTGTGCCAAC
1 CTGA-TTATGGCACTGTGCCAAC
39405265 CTGATTATGG
1 CTGATTATGG
39405275 TTGTGTGCCA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (22 bp):
CTGATTATGGCACTGTGCCAAC
Found at i:39405473 original size:27 final size:27
Alignment explanation
Indices: 39405443--39405544 Score: 116
Period size: 27 Copynumber: 3.8 Consensus size: 27
39405433 ATTCTGTTAA
* * *
39405443 GTGGCTTTGCCACATTATCTATTTCTG
1 GTGGCTATGCCACAATATCTGTTTCTG
39405470 GTGGCTATGCCACAAATATCTGTTT-TG
1 GTGGCTATGCCAC-AATATCTGTTTCTG
* *
39405497 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTATGCCACAATATCTGTTTCTG
* * *
39405524 GTGACTCTGTCACAATATCTG
1 GTGGCTATGCCACAATATCTG
39405545 ATAACTGAAC
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 10 0.15
27 47 0.71
28 9 0.14
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.37
Consensus pattern (27 bp):
GTGGCTATGCCACAATATCTGTTTCTG
Found at i:39405501 original size:54 final size:53
Alignment explanation
Indices: 39405443--39405544 Score: 132
Period size: 54 Copynumber: 1.9 Consensus size: 53
39405433 ATTCTGTTAA
* * * *
39405443 GTGGCTTTGCCACATTATCTATTTCTGGTGGCTATGCCACAAATATCTGTTTTG
1 GTGGCTCTGCCACAATATCTATATCTGGTGACTATGCCAC-AATATCTGTTTTG
* * *
39405497 GTGGCTCTGCCACAATATCTGTATCTGGTGACTCTGTCACAATATCTG
1 GTGGCTCTGCCACAATATCTATATCTGGTGACTATGCCACAATATCTG
39405545 ATAACTGAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 8 0.20
54 33 0.80
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.37
Consensus pattern (53 bp):
GTGGCTCTGCCACAATATCTATATCTGGTGACTATGCCACAATATCTGTTTTG
Found at i:39405749 original size:6 final size:6
Alignment explanation
Indices: 39405680--39405769 Score: 58
Period size: 6 Copynumber: 14.7 Consensus size: 6
39405670 ATTCACATTT
* * * * * *
39405680 TGATTT TGATTC TG-TTACC TGATAC TAATTT TGATTT TGATTC TGATACC
1 TGATTC TGATTC TGATT--C TGATTC TGATTC TGATTC TGATTC TGAT-TC
* *
39405730 TGATAC TAATTC TGATTC TGATTC TGATTC T-AGTTC TGAT
1 TGATTC TGATTC TGATTC TGATTC TGATTC TGA-TTC TGAT
39405770 AATGTTTCTT
Statistics
Matches: 66, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
5 3 0.05
6 53 0.80
7 9 0.14
8 1 0.02
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.49
Consensus pattern (6 bp):
TGATTC
Found at i:39405752 original size:37 final size:31
Alignment explanation
Indices: 39405676--39405757 Score: 137
Period size: 31 Copynumber: 2.6 Consensus size: 31
39405666 TTGCATTCAC
*
39405676 ATTTTGATTTTGATTCTGTTACCTGATACTA
1 ATTTTGATTTTGATTCTGATACCTGATACTA
39405707 ATTTTGATTTTGATTCTGATACCTGATACTA
1 ATTTTGATTTTGATTCTGATACCTGATACTA
* *
39405738 ATTCTGATTCTGATTCTGAT
1 ATTTTGATTTTGATTCTGAT
39405758 TCTAGTTCTG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.50
Consensus pattern (31 bp):
ATTTTGATTTTGATTCTGATACCTGATACTA
Found at i:39412690 original size:53 final size:53
Alignment explanation
Indices: 39412517--39412723 Score: 207
Period size: 53 Copynumber: 3.8 Consensus size: 53
39412507 ATTAGGGTTT
* * * * *
39412517 AAGGATACCAAGTAAGACCACGCCAAGACATGGCATTGGTAAGTTTTACAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAG-TTCATAAGGC
* * * * * * * * * *
39412571 AAGGAAATCATGGAAAACCATGTCAAGACATAGCATTGATAAACTACGATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGT-AAGTTC-ATAAGGC
* * * *
39412626 AAAGATCCCATGTAAGACCATGCCAAGGCATGGCAATGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
*
39412679 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATGGTAAGTT
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTT
39412724 TAAAAAGGAA
Statistics
Matches: 119, Mismatches: 32, Indels: 5
0.76 0.21 0.03
Matches are distributed among these distances:
53 47 0.39
54 35 0.29
55 37 0.31
ACGTcount: A:0.39, C:0.18, G:0.24, T:0.19
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCAATGGTAAGTTCATAAGGC
Found at i:39419513 original size:25 final size:26
Alignment explanation
Indices: 39419485--39419534 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
39419475 AAGCATCCCG
*
39419485 ATTAAA-GGCTCTTTGTGAGCTTCCT
1 ATTAAATGGCTCTTTATGAGCTTCCT
39419510 ATTAAATTGGCTCTTTATGAGCTTC
1 ATTAAA-TGGCTCTTTATGAGCTTC
39419535 TCAATAATGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.27
27 16 0.73
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (26 bp):
ATTAAATGGCTCTTTATGAGCTTCCT
Found at i:39423289 original size:43 final size:43
Alignment explanation
Indices: 39423147--39423297 Score: 157
Period size: 43 Copynumber: 3.5 Consensus size: 43
39423137 AGGTTACGAG
* *
39423147 ATGTGATTACATGGAAAACCATGTCTGGGACATTGGCAT-TGGAT
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCT--AT
* *
39423191 -TGTGATTACGTGTATGACCATGTCTGGGACATTGGCATCGT-T
1 ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATC-TAT
* * * *
39423233 AAT-CGATTTCATGTAAGACCCTGTCTGGGACAGTGGCATCTAT
1 -ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCTAT
*
39423276 ATGTGATAACATGTAAGACCAT
1 ATGTGATTACATGTAAGACCAT
39423298 ATTTGGGATA
Statistics
Matches: 87, Mismatches: 14, Indels: 13
0.76 0.12 0.11
Matches are distributed among these distances:
42 4 0.05
43 81 0.93
44 1 0.01
45 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (43 bp):
ATGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCTAT
Found at i:39450329 original size:19 final size:19
Alignment explanation
Indices: 39450305--39450344 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39450295 TATGGCCTGA
*
39450305 GGTCGAATTGGGCCATGTG
1 GGTCGAAATGGGCCATGTG
**
39450324 GGTCGAAATGGTTCATGTG
1 GGTCGAAATGGGCCATGTG
39450343 GG
1 GG
39450345 CTCCACGGGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.17, C:0.12, G:0.42, T:0.28
Consensus pattern (19 bp):
GGTCGAAATGGGCCATGTG
Found at i:39450625 original size:27 final size:27
Alignment explanation
Indices: 39450595--39450695 Score: 139
Period size: 27 Copynumber: 3.7 Consensus size: 27
39450585 CCCTAATTGA
*
39450595 TAAAATTACTATTTTGCCCTTATATGG
1 TAAAATGACTATTTTGCCCTTATATGG
* * *
39450622 TAAAATGACTGTTTTGCCTTATATATGA
1 TAAAATGACTATTTTGCCCT-TATATGG
*
39450650 TAAAATGACTATTTTGCCCTCATATGG
1 TAAAATGACTATTTTGCCCTTATATGG
*
39450677 TAAGATGACTATTTTGCCC
1 TAAAATGACTATTTTGCCC
39450696 ATATGTGAGG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
27 40 0.62
28 24 0.38
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (27 bp):
TAAAATGACTATTTTGCCCTTATATGG
Found at i:39451066 original size:18 final size:18
Alignment explanation
Indices: 39451025--39451069 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
39451015 TACTGTTTAA
39451025 ATTGTTACTGCACTGATT
1 ATTGTTACTGCACTGATT
* *
39451043 ACTGTTACTGTACT-ATTT
1 ATTGTTACTGCACTGA-TT
39451061 ATTGTTACT
1 ATTGTTACT
39451070 ACAATAGGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.49
Consensus pattern (18 bp):
ATTGTTACTGCACTGATT
Found at i:39455197 original size:48 final size:48
Alignment explanation
Indices: 39455079--39455339 Score: 317
Period size: 48 Copynumber: 5.4 Consensus size: 48
39455069 TGAGATTCCA
* * * * *
39455079 TGTAAGTCCGTGTCTGGGACATGGCATCGGCATCTAAGA-AGTGTGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCA-ATGATATA-TGTGCCAG
* * * *
39455128 TGTAAGTCTATGTCTGGGACATGGCATCGACAATGATATATGTGCCTG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCAATGATATATGTGCCAG
* *
39455176 TATAAGACCATGTTTGGGACATGGCATCGGCAATGATATATGTGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCAATGATATATGTGCCAG
** * *
39455224 TGTAAGACCATGTCTGGGACATGGCATCGGTGATAATATATATGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCAATGATATATGTGCCAG
* * * **
39455272 TGTAAGAGCATGTTTGGGACATGACATCGGCAATGATATATGTGCCTT
1 TGTAAGACCATGTCTGGGACATGGCATCGGCAATGATATATGTGCCAG
39455320 TGTAAGACCATGTCTGGGAC
1 TGTAAGACCATGTCTGGGAC
39455340 CTAGCATTGG
Statistics
Matches: 181, Mismatches: 30, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
48 151 0.83
49 30 0.17
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCAATGATATATGTGCCAG
Found at i:39455372 original size:144 final size:145
Alignment explanation
Indices: 39455072--39455394 Score: 363
Period size: 144 Copynumber: 2.2 Consensus size: 145
39455062 TGCTAAATGA
* * * * *
39455072 GATTCCATGTAAGTCCGTGTCTGGGACATGGCATCGGCATCTAAGAAGTGTGCCAGTGTAAGTCT
1 GATT-CATGTAAGACCATGTCTGGGACATGGCATCGG-ATATAAGAAGTATGCCAGTGTAAGGCT
* * *
39455137 ATGTCTGGGACATGGCATCGACAATGATATATGTGCCTGTATAAGACCATGTTTGGGACATGGCA
64 ATGTCTGGGACATGACATCGACAATGATATATGTGCCTGTATAAGACCATGTCTGGGACATAGCA
39455202 TCGGCAATGATATATGT
129 TCGGCAATGATATATGT
* *
39455219 G--CCAGTGTAAGACCATGTCTGGGACATGGCATCGG-TGATAATATA-TATGCCAGTGTAAGAG
1 GATTCA-TGTAAGACCATGTCTGGGACATGGCATCGGAT-ATAAGA-AGTATGCCAGTGTAAG-G
* * * * *
39455280 C-ATGTTTGGGACATGACATCGGCAATGATATATGTGCCTTTGTAAGACCATGTCTGGGACCTAG
62 CTATGTCTGGGACATGACATCGACAATGATATATGTGCCTGTATAAGACCATGTCTGGGACATAG
* *
39455344 CATTGGCGAT-A-ATATGT
127 CATCGGCAATGATATATGT
* *
39455361 GGATTCATGTAAGACCATGTCTAGGACGTGGCAT
1 -GATTCATGTAAGACCATGTCTGGGACATGGCAT
39455395 TGGTACTTTA
Statistics
Matches: 149, Mismatches: 20, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
142 6 0.04
143 3 0.02
144 107 0.72
145 32 0.21
147 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (145 bp):
GATTCATGTAAGACCATGTCTGGGACATGGCATCGGATATAAGAAGTATGCCAGTGTAAGGCTAT
GTCTGGGACATGACATCGACAATGATATATGTGCCTGTATAAGACCATGTCTGGGACATAGCATC
GGCAATGATATATGT
Found at i:39462820 original size:48 final size:48
Alignment explanation
Indices: 39462749--39462919 Score: 236
Period size: 48 Copynumber: 3.6 Consensus size: 48
39462739 TGAGATTCCA
* *
39462749 TGTAAGTCCATGTTTGGGACATGGCATCGGCGATGATATATGTGCCTG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATATGTGCCTG
* * *
39462797 TGTAAGACCATGTCTGGGACATGGCATCGGCGGTGACATATGTGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATATGTGCCTG
* ** *
39462845 TGTAAGACCATGTCTGGGACATGGCATCGACGATGATATATG-GATTCA
1 TGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATATGTGCCT-G
*
39462893 TGTAAGACCATGTCCGGGACATGGCAT
1 TGTAAGACCATGTCTGGGACATGGCAT
39462920 TGGTACTTTA
Statistics
Matches: 109, Mismatches: 13, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
47 1 0.01
48 108 0.99
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATATGTGCCTG
Found at i:39467201 original size:25 final size:27
Alignment explanation
Indices: 39467167--39467221 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
39467157 CTTTTGATCA
*
39467167 TCCCGATTAAA-GGCTCTTCGTGAGCT
1 TCCCGATTAAATGGCTCTTCATGAGCT
*
39467193 TCCCG-TTAAATTGGCTCTTTATGAGCT
1 TCCCGATTAAA-TGGCTCTTCATGAGCT
39467220 TC
1 TC
39467222 TCAATAATGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 5 0.20
26 5 0.20
27 15 0.60
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (27 bp):
TCCCGATTAAATGGCTCTTCATGAGCT
Found at i:39471400 original size:46 final size:46
Alignment explanation
Indices: 39471349--39471569 Score: 197
Period size: 46 Copynumber: 4.8 Consensus size: 46
39471339 ATGGTTGAGC
*
39471349 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA-ATG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA--GATGCAACAGG
* * *
39471396 -TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGAGATGTAACTAGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGATGCAAC-AGG
* * * * *
39471441 CATTCGAACTCGTTGAGTTGAGTCCGAG-TC-GTGAAATGTAACTAGG
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGATGCAAC-AGG
*
39471487 CATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC--G
1 -ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA--GATGC-AACAGG
* *
39471535 -CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTAG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAG
39471570 GGGTGGGTTA
Statistics
Matches: 150, Mismatches: 15, Indels: 21
0.81 0.08 0.11
Matches are distributed among these distances:
43 6 0.04
44 1 0.01
45 4 0.03
46 103 0.69
47 27 0.18
48 3 0.02
50 3 0.02
51 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGATGCAACAGG
Found at i:39471467 original size:47 final size:47
Alignment explanation
Indices: 39471396--39471517 Score: 210
Period size: 46 Copynumber: 2.6 Consensus size: 47
39471386 GATGCAAATG
*
39471396 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAGATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA
*
39471443 TTCGAACTCGTTGAGTTGAGTCCGAG-TCGTGAAATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA
*
39471489 TCCGAACTCATTGAGTTGAGTCCGAGTTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC
39471518 ACTTATGGAT
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
46 43 0.61
47 27 0.39
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (47 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCA
Found at i:39480299 original size:40 final size:40
Alignment explanation
Indices: 39480241--39480464 Score: 297
Period size: 40 Copynumber: 5.6 Consensus size: 40
39480231 AACCCAATTA
* * ** * *
39480241 CCTTCGGGATTTAGCCCGGATGTAACAACAAGCACAAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
* *
39480281 CCTTCGGGACTTAACCCGGAAATAGCAACCAGCATGAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
* *
39480321 CCTTCGGGACATAACCCGGAAATAATAACCAGCACGAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
* * *
39480361 CCTTCGGGACTTAACCCGGGAATAACAACCA-AACGAAAG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
* *
39480400 CCTTCGGGACTTAACCCGAAAATAACAACCAGCATGAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
*
39480440 CCTTCGGGACTTAACCCGGATATAA
1 CCTTCGGGACTTAACCCGGAAATAA
39480465 TCCTCAATTG
Statistics
Matches: 159, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
39 35 0.22
40 124 0.78
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (40 bp):
CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
Found at i:39480439 original size:79 final size:80
Alignment explanation
Indices: 39480263--39480464 Score: 289
Period size: 79 Copynumber: 2.5 Consensus size: 80
39480253 AGCCCGGATG
* * * * * *
39480263 TAACAACAAGCACAAATGCCTTCGGGACTTAACCCGGAAATAGCAACCAGCATGAATGCCTTCGG
1 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAATAACAACCAGAACGAAAGCCTTCGG
*
39480328 GACATAACCCGGAAA
66 GACATAACCCGAAAA
* *
39480343 TAATAACCAGCACGAATGCCTTCGGGACTTAACCCGGGAATAACAACCA-AACGAAAGCCTTCGG
1 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAATAACAACCAGAACGAAAGCCTTCGG
*
39480407 GACTTAACCCGAAAA
66 GACATAACCCGAAAA
* *
39480422 TAACAACCAGCATGAATGCCTTCGGGACTTAACCCGGATATAA
1 TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAATAA
39480465 TCCTCAATTG
Statistics
Matches: 108, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
79 64 0.59
80 44 0.41
ACGTcount: A:0.37, C:0.27, G:0.19, T:0.16
Consensus pattern (80 bp):
TAACAACCAGCACGAATGCCTTCGGGACTTAACCCGGAAATAACAACCAGAACGAAAGCCTTCGG
GACATAACCCGAAAA
Found at i:39488328 original size:40 final size:40
Alignment explanation
Indices: 39488284--39488501 Score: 321
Period size: 40 Copynumber: 5.5 Consensus size: 40
39488274 AACCCAATTA
* * ** *
39488284 CCTTCGGGATTTAGCCCGGATGTAACAACCAGCACAAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
*
39488324 CCTTCGGGACTTAACCCGGAAATAGCAACCAGCACGAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
*
39488364 CCTTCGGGACTTAACCCAGAAATAACAACCAGCACGAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
*
39488404 CCTTCGGGACTTAACCCAGG-AATAACAACTAGCACGAATG
1 CCTTCGGGACTTAACCC-GGAAATAACAACCAGCACGAATG
* *
39488444 CCTTCGGGACTTAACCCAGAAATAACAACCAGCATGAATG
1 CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
*
39488484 CCTTCGGGACATAACCCG
1 CCTTCGGGACTTAACCCG
39488502 AATATAATCC
Statistics
Matches: 161, Mismatches: 15, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
39 1 0.01
40 159 0.99
41 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.17
Consensus pattern (40 bp):
CCTTCGGGACTTAACCCGGAAATAACAACCAGCACGAATG
Found at i:39494310 original size:16 final size:16
Alignment explanation
Indices: 39494289--39494324 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
39494279 TATTTCTTGT
39494289 TTTTCGTTTTAGTTTA
1 TTTTCGTTTTAGTTTA
**
39494305 TTTTCGTTTTTTTTTA
1 TTTTCGTTTTAGTTTA
39494321 TTTT
1 TTTT
39494325 GGGTAGTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.08, C:0.06, G:0.08, T:0.78
Consensus pattern (16 bp):
TTTTCGTTTTAGTTTA
Found at i:39495035 original size:79 final size:79
Alignment explanation
Indices: 39494902--39495061 Score: 266
Period size: 79 Copynumber: 2.0 Consensus size: 79
39494892 TAATTTAGGA
* * * * *
39494902 GTAGATTTAATTTATTTTCTTTTCGGGTTTTCAATAATTTCTTGTTTTCTTCTTGACATAGGTTT
1 GTAGATTTAATTTATTTTCTTTTCAGCTTTTCAATAATTTCTTATTTTCATCTTGACATAAGTTT
39494967 TTATTCAAGAGTTT
66 TTATTCAAGAGTTT
*
39494981 GTAGATTTAATTTATTTTCTTTTCAGCTTTTCAATACTTTCTTATTTTCATCTTGACATAAGTTT
1 GTAGATTTAATTTATTTTCTTTTCAGCTTTTCAATAATTTCTTATTTTCATCTTGACATAAGTTT
39495046 TTATTCAAGAGTTT
66 TTATTCAAGAGTTT
39495060 GT
1 GT
39495062 TTATATAATT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
79 75 1.00
ACGTcount: A:0.22, C:0.11, G:0.12, T:0.55
Consensus pattern (79 bp):
GTAGATTTAATTTATTTTCTTTTCAGCTTTTCAATAATTTCTTATTTTCATCTTGACATAAGTTT
TTATTCAAGAGTTT
Found at i:39500289 original size:19 final size:20
Alignment explanation
Indices: 39500265--39500302 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
39500255 GGTACCACCA
39500265 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
39500284 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
39500303 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:39500600 original size:46 final size:46
Alignment explanation
Indices: 39500531--39500698 Score: 173
Period size: 46 Copynumber: 3.6 Consensus size: 46
39500521 CGCCCCTAAG
* *
39500531 TGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAA
1 TGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCATAAA
* * *
39500577 TAAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-T-CA
1 TGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATCCATAAA
* * * * *
39500624 CGAACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCATAAG
1 TGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCATAAA
39500670 TGAACTCGGACTCAACTCAACGAGTTCGG
1 TGAACTCGGACTCAACTCAACGAGTTCGG
39500699 ATGCTCAACC
Statistics
Matches: 98, Mismatches: 15, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 1 0.01
46 53 0.54
47 27 0.28
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (46 bp):
TGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCATAAA
Found at i:39500643 original size:93 final size:93
Alignment explanation
Indices: 39500532--39500702 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
39500522 GCCCCTAAGT
* *
39500532 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATAAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATAAACTCGGACTCAACTCAA
39500597 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * * * *
39500625 GAACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATAAACTCGGACTCAACTCAA
39500690 CGAGTTCGGATGC
66 CGAGTTCGGATGC
39500703 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.30, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATAAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:39500718 original size:46 final size:44
Alignment explanation
Indices: 39500579--39500718 Score: 124
Period size: 46 Copynumber: 3.0 Consensus size: 44
39500569 TCCATAAATA
*
39500579 AACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTA-CATCTCA-CG
1 AACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT-AGTG
* * * *
39500626 AACTCGGACTCAACTCAACGAGTTTGGACATTCGCATCCAT-AAGTG
1 AACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCTAGTG
39500672 AACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGTG
1 AACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CTAGTG
39500718 A
1 A
39500719 CATGTCACTT
Statistics
Matches: 76, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 32 0.42
47 29 0.38
49 4 0.05
50 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (44 bp):
AACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCTAGTG
Found at i:39501155 original size:30 final size:30
Alignment explanation
Indices: 39501121--39501180 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
39501111 ATTTAATACG
39501121 AACTTTAAAAAAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
*** *
39501151 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTAAAAAAATTACACTTTTGCCCCTA
39501181 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (30 bp):
AACTTTAAAAAAATTACACTTTTGCCCCTA
Found at i:39502491 original size:48 final size:46
Alignment explanation
Indices: 39502439--39502590 Score: 171
Period size: 48 Copynumber: 3.2 Consensus size: 46
39502429 CAAATTGCTA
* *
39502439 ATATCATGGCTCATAGCCAAATC-AGTGAAGCTCGCACCCGAAGTGCCG
1 ATATCATGGCTCA-AGCCAAATCAAGT-AA-CTCACACCCGAAGTGTCG
* * * *
39502487 ATATCATGACCCAAAGCCCAATCAAAGTAACTCACAGCCGAAGTGTCG
1 ATATCATGGCTC-AAGCCAAATC-AAGTAACTCACACCCGAAGTGTCG
*
39502535 ATATCATGGCTCGAAGCCAAATCAAAGTAACTCACACCCAAAGTGTCG
1 ATATCATGGCTC-AAGCCAAATC-AAGTAACTCACACCCGAAGTGTCG
39502583 ATATCATG
1 ATATCATG
39502591 TCCCCCGAAG
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
48 83 0.93
49 3 0.03
50 3 0.03
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.19
Consensus pattern (46 bp):
ATATCATGGCTCAAGCCAAATCAAGTAACTCACACCCGAAGTGTCG
Found at i:39509921 original size:23 final size:23
Alignment explanation
Indices: 39509894--39509941 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
39509884 TTAATACCCA
39509894 ATATCTCAGACATAGAGCATGCT
1 ATATCTCAGACATAGAGCATGCT
39509917 ATATCTCAGACATAGAGCATGCT
1 ATATCTCAGACATAGAGCATGCT
39509940 AT
1 AT
39509942 GTATGGATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (23 bp):
ATATCTCAGACATAGAGCATGCT
Found at i:39514619 original size:22 final size:23
Alignment explanation
Indices: 39514574--39514617 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
39514564 ACTGTAAACA
*
39514574 TTTTTCCTAGTTACCTTTGAAAT
1 TTTTTCCCAGTTACCTTTGAAAT
39514597 TTTTTCCCAGTTACCTTTGAA
1 TTTTTCCCAGTTACCTTTGAA
39514618 TTATAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.09, T:0.50
Consensus pattern (23 bp):
TTTTTCCCAGTTACCTTTGAAAT
Found at i:39519803 original size:17 final size:17
Alignment explanation
Indices: 39519758--39519803 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
39519748 ATTTATTTTA
39519758 TTGTTTATTTGTCATTAT
1 TTGTTTATTT-TCATTAT
* * *
39519776 TTATTTCTTTTCATTGT
1 TTGTTTATTTTCATTAT
39519793 TTGTTTATTTT
1 TTGTTTATTTT
39519804 TATCTCTTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.13, C:0.07, G:0.09, T:0.72
Consensus pattern (17 bp):
TTGTTTATTTTCATTAT
Found at i:39533349 original size:54 final size:54
Alignment explanation
Indices: 39533282--39533386 Score: 183
Period size: 54 Copynumber: 1.9 Consensus size: 54
39533272 ACTCATGAGT
*
39533282 TCATAATCACATAGTTCCTAGTGACATGTCACTTGTATCCTCAACTATTCCAAC
1 TCATAATCACATAGTTCCTAGTGACATGTCACTTGTATCCTAAACTATTCCAAC
**
39533336 TCATAATTGCATAGTTCCTAGTGACATGTCACTTGTATCCTAAACTATTCC
1 TCATAATCACATAGTTCCTAGTGACATGTCACTTGTATCCTAAACTATTCC
39533387 GAAGGTTCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (54 bp):
TCATAATCACATAGTTCCTAGTGACATGTCACTTGTATCCTAAACTATTCCAAC
Found at i:39551351 original size:21 final size:21
Alignment explanation
Indices: 39551327--39551370 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
39551317 GTTAAAACAA
39551327 AAAATACTAATCAAATGT-CCT
1 AAAATAC-AATCAAATGTACCT
* *
39551348 AAAATGCAATTAAATGTACCT
1 AAAATACAATCAAATGTACCT
39551369 AA
1 AA
39551371 GTATAGGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.50, C:0.16, G:0.07, T:0.27
Consensus pattern (21 bp):
AAAATACAATCAAATGTACCT
Found at i:39553680 original size:45 final size:45
Alignment explanation
Indices: 39553615--39553892 Score: 180
Period size: 47 Copynumber: 5.8 Consensus size: 45
39553605 ATTGACGGTT
39553615 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGGC
* * * * **
39553660 AAGGATCCCGTGTATGACCATGTCAAGACATGGCATTGGTATTGATT
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTA-AG-GC
* ** ** * *
39553707 AAGGACT-CTATGTAAGACCACATCAAGATGTAGCATTGGCACTAAGAC
1 AAGGA-TACCATGTAAGACCATGTCAAGACATGGCATTGG---TAAGGC
* *** **
39553755 AATGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAAGAT
1 AAGGATACCATGTAAGACCATGTCAAG-ACATGGCA-TTGGTAAGGC
* * *
39553802 AAGGATATCATGTAAGACCATTTCAAGGCATGGCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTG----G-----TAAGGC
* *
39553856 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATT
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATT
39553893 AATGAGTTAC
Statistics
Matches: 175, Mismatches: 40, Indels: 27
0.72 0.17 0.11
Matches are distributed among these distances:
45 41 0.23
46 8 0.05
47 56 0.32
48 19 0.11
49 7 0.04
50 6 0.03
54 38 0.22
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (45 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGGC
Found at i:39553838 original size:95 final size:92
Alignment explanation
Indices: 39553613--39553844 Score: 213
Period size: 95 Copynumber: 2.5 Consensus size: 92
39553603 GAATTGACGG
* * * * * * *
39553613 TTAAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGGCAAGGATCCCGTGTATGAC
1 TTAAGGATATCATGTAAGACCATATCAAGGCATGGCATTGGTAAGACAAGGATACCATGTAAGAC
*
39553678 CATGTCAAGACATGGCATTGGTATTGA
66 CATGTCAAGACATGGCATTGGTATAGA
* * *
39553705 TTAAGGA-CTCTATGTAAGACCACATCAA-G-ATGTAGCATTGGCACTAAGACAATGATACCATG
1 TTAAGGATATC-ATGTAAGACCATATCAAGGCATG--GCATTGG---TAAGACAAGGATACCATG
***
39553767 TAAGACCATGTTTGGAACATGGCATTTGGTA-AGA
60 TAAGACCATGTCAAG-ACATGGCA-TTGGTATAGA
* *
39553801 -TAAGGATATCATGTAAGACCATTTCAAGGCATGGCATTGATAAG
1 TTAAGGATATCATGTAAGACCATATCAAGGCATGGCATTGGTAAG
39553845 TTCTATAAGG
Statistics
Matches: 111, Mismatches: 18, Indels: 22
0.74 0.12 0.15
Matches are distributed among these distances:
90 3 0.03
91 1 0.01
92 33 0.30
95 52 0.47
96 13 0.12
97 9 0.08
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (92 bp):
TTAAGGATATCATGTAAGACCATATCAAGGCATGGCATTGGTAAGACAAGGATACCATGTAAGAC
CATGTCAAGACATGGCATTGGTATAGA
Found at i:39554000 original size:108 final size:107
Alignment explanation
Indices: 39553810--39554106 Score: 468
Period size: 108 Copynumber: 2.7 Consensus size: 107
39553800 ATAAGGATAT
** * * *
39553810 CATGTAAGACCATTTCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACC
1 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGGATA-CATGTAAGACC
*
39553875 ATGTCAAGACATGGCATTAATGAGTTACTATAAGGCAAAGGTTC
64 ATGTCAAGACATGGCATTAATGAGTTACTATAAGGCAAAGGTCC
* *
39553919 CATGTAAGACCATGCCAAGGTATGGCATTGGTGAGTTCATAAGGCAAGGATACAATGTAAGACGA
1 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGCAAGGATAC-ATGTAAGACCA
* *
39553984 TGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAATGTCC
65 TGTCAAGACATGGCATTAATGAGTTACTATAAGGCAAAGGTCC
39554027 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGCAAGGATACCATGTAAGACCA
1 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGCAAGGATA-CATGTAAGACCA
39554092 TGTCAAGACATGGCA
65 TGTCAAGACATGGCA
39554107 ATGGTAAGTT
Statistics
Matches: 174, Mismatches: 12, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
107 1 0.01
108 139 0.80
109 34 0.20
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.24
Consensus pattern (107 bp):
CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGCAAGGATACATGTAAGACCAT
GTCAAGACATGGCATTAATGAGTTACTATAAGGCAAAGGTCC
Found at i:39554118 original size:53 final size:54
Alignment explanation
Indices: 39553802--39554106 Score: 375
Period size: 55 Copynumber: 5.6 Consensus size: 54
39553792 TTGGTAAGAT
* * * *
39553802 AAGGATATCATGTAAGACCATTTCAAGGCATGGCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTCTATAAGGC
* * *
39553856 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTAATGAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTT-CTATAAGGC
* * ** *
39553911 AAAGG-TTCCATGTAAGACCATGCCAAGGTATGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTCTATAAGGC
* *
39553964 AAGGATACAATGTAAGACGATGTCAAGACATGGCATTGATGAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTT-CTATAAGGC
* * * * *
39554019 AAATG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTCTATAAGGC
39554072 AAGGATACCATGTAAGACCATGTCAAGACATGGCA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCA
39554107 ATGGTAAGTT
Statistics
Matches: 213, Mismatches: 31, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
52 7 0.03
53 74 0.35
54 43 0.20
55 82 0.38
56 7 0.03
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTCTATAAGGC
Found at i:39555466 original size:6 final size:6
Alignment explanation
Indices: 39555448--39555529 Score: 62
Period size: 6 Copynumber: 13.3 Consensus size: 6
39555438 AAGAAACATT
*
39555448 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGGTA A-CAGA ATCAAA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA
* * *
39555497 ATCAGT ATCAAGTA A-CAAA ATCAAA ATCAGA AT
1 ATCAGA ATC-AG-A ATCAGA ATCAGA ATCAGA AT
39555530 GTGAATGCAA
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
5 5 0.08
6 47 0.76
7 7 0.11
8 3 0.05
ACGTcount: A:0.52, C:0.16, G:0.13, T:0.18
Consensus pattern (6 bp):
ATCAGA
Found at i:39555493 original size:25 final size:26
Alignment explanation
Indices: 39555457--39555526 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 26
39555447 TATCAGAACT
*
39555457 AGAATCAGAATCAGAATCAGGTAAC-
1 AGAATCAAAATCAGAATCAGGTAACA
*
39555482 AGAATCAAAATCAGAATCA-GTATCA
1 AGAATCAAAATCAGAATCAGGTAACA
*
39555507 AGTAA-CAAAATCAAAATCAG
1 AG-AATCAAAATCAGAATCAG
39555527 AATGTGAATG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
24 4 0.10
25 33 0.85
26 2 0.05
ACGTcount: A:0.53, C:0.16, G:0.14, T:0.17
Consensus pattern (26 bp):
AGAATCAAAATCAGAATCAGGTAACA
Found at i:39555494 original size:31 final size:31
Alignment explanation
Indices: 39555459--39555529 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
39555449 TCAGAACTAG
* *
39555459 AATCAGAATCAGAATCAGGTAACAGAATCAA
1 AATCAGAATCAGAATCAAGTAACAAAATCAA
*
39555490 AATCAGAATCAGTATCAAGTAACAAAATCAA
1 AATCAGAATCAGAATCAAGTAACAAAATCAA
39555521 AATCAGAAT
1 AATCAGAAT
39555530 GTGAATGCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.54, C:0.15, G:0.13, T:0.18
Consensus pattern (31 bp):
AATCAGAATCAGAATCAAGTAACAAAATCAA
Found at i:39555703 original size:27 final size:26
Alignment explanation
Indices: 39555649--39555756 Score: 108
Period size: 27 Copynumber: 4.0 Consensus size: 26
39555639 AGCATGGCTG
** * *
39555649 CCAGAACAGATATTGTGATATAGTCA
1 CCAGAACAGATATTGTGGCAAAGCCA
* *
39555675 CCAGATACAAATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATTGTGGCAAAGCCA
*
39555702 CCAGAACAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-TTGTGGCAAAGCCA
* *
39555729 ACAGAAACAGATAATGTGGCAAAGCCA
1 CCAG-AACAGATATTGTGGCAAAGCCA
39555756 C
1 C
39555757 GTAACAGAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
26 11 0.16
27 49 0.72
28 8 0.12
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.19
Consensus pattern (26 bp):
CCAGAACAGATATTGTGGCAAAGCCA
Found at i:39555755 original size:54 final size:53
Alignment explanation
Indices: 39555649--39555756 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 53
39555639 AGCATGGCTG
* * * * * *
39555649 CCAGAACAGATATTGTGATATAGTCACCAGATACAAATATTGTGGCAGAGCCA
1 CCAGAACAGATATTGTGACATAGCCAACAGAAACAAATAATGTGGCAAAGCCA
* *
39555702 CCAGAACAGATATTTGTGGCATAGCCAACAGAAACAGATAATGTGGCAAAGCCA
1 CCAGAACAGATA-TTGTGACATAGCCAACAGAAACAAATAATGTGGCAAAGCCA
39555756 C
1 C
39555757 GTAACAGAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
53 12 0.26
54 34 0.74
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.19
Consensus pattern (53 bp):
CCAGAACAGATATTGTGACATAGCCAACAGAAACAAATAATGTGGCAAAGCCA
Found at i:39555952 original size:22 final size:22
Alignment explanation
Indices: 39555918--39555960 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
39555908 AATACGTTTG
*
39555918 GCACATAGACATAAT-TAGGTTC
1 GCACAGAGACAT-ATGTAGGTTC
*
39555940 GCACAGAGCCATATGTAGGTT
1 GCACAGAGACATATGTAGGTT
39555961 GGTGCAAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Consensus pattern (22 bp):
GCACAGAGACATATGTAGGTTC
Found at i:39556804 original size:27 final size:27
Alignment explanation
Indices: 39556391--39556797 Score: 537
Period size: 27 Copynumber: 15.1 Consensus size: 27
39556381 ACAAAGGTTC
*
39556391 TCGGTAATTCTATCCTACAGGGGTATT
1 TCGGTAATTCTACCCTACAGGGGTATT
* * *
39556418 TCAGTAATTCTACCCTATAAGGGTATT
1 TCGGTAATTCTACCCTACAGGGGTATT
* * * *
39556445 TCGATATTTTTACCCTACAAGGGTATAT
1 TCGGTAATTCTACCCTACAGGGGTAT-T
* * *
39556473 AC-ATAATTCTACCCTATAGGGGTATT
1 TCGGTAATTCTACCCTACAGGGGTATT
**
39556499 TTAGTAATTCTACCCTACAGGGGTATT
1 TCGGTAATTCTACCCTACAGGGGTATT
* *
39556526 TCGATAATTTTACCCTACAGGGGTATT
1 TCGGTAATTCTACCCTACAGGGGTATT
*
39556553 TCGATAATTCTACCCTACAGGGGTATT
1 TCGGTAATTCTACCCTACAGGGGTATT
39556580 TCGGTAATTCTACCCTACAGGGGTATT
1 TCGGTAATTCTACCCTACAGGGGTATT
*
39556607 TCGATAATTCTACCCTACAGGGGTATT
1 TCGGTAATTCTACCCTACAGGGGTATT
39556634 TCGGTAATTCTACCCTACAGGGGTATT
1 TCGGTAATTCTACCCTACAGGGGTATT
* *
39556661 CCGGTAATTCTACCTTACAGGGGTATT
1 TCGGTAATTCTACCCTACAGGGGTATT
*
39556688 TCGGTAATTCTACCCTATAGGGGTATT
1 TCGGTAATTCTACCCTACAGGGGTATT
* * *
39556715 TCGGTAATTCTATCCTACAAGGATATT
1 TCGGTAATTCTACCCTACAGGGGTATT
** * *
39556742 TTAGTATTTCTACCCTACAAGGGTATT
1 TCGGTAATTCTACCCTACAGGGGTATT
* *
39556769 TCGATAATTCTACCCTACATGGGTATT
1 TCGGTAATTCTACCCTACAGGGGTATT
39556796 TC
1 TC
39556798 AATAATTTTG
Statistics
Matches: 333, Mismatches: 45, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
26 1 0.00
27 330 0.99
28 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (27 bp):
TCGGTAATTCTACCCTACAGGGGTATT
Found at i:39557081 original size:27 final size:27
Alignment explanation
Indices: 39556849--39557095 Score: 212
Period size: 27 Copynumber: 9.2 Consensus size: 27
39556839 TTGGGGTTAC
** *
39556849 TTTGGTAATTTTACAAGTCGAGGGTAT
1 TTTGGTAATTTTACAAACCAAGGGTAT
* ** * *
39556876 GTCAGTAATTTTACAAATCGAGGGTAT
1 TTTGGTAATTTTACAAACCAAGGGTAT
** *
39556903 TTCAGTAATTTTACAAACTGAA-GGTAT
1 TTTGGTAATTTTACAAAC-CAAGGGTAT
* * * *
39556930 TTCGATAATTTTACAAATCGAGGGTAT
1 TTTGGTAATTTTACAAACCAAGGGTAT
* ***
39556957 TTTAGTAATTTTACAAA-TTGGGGTAT
1 TTTGGTAATTTTACAAACCAAGGGTAT
* *
39556983 TTTGGTGATTTTATAAACCAAGGGTAT
1 TTTGGTAATTTTACAAACCAAGGGTAT
* * *
39557010 TCTAGTAATTTTACAAACCAGGGGTAT
1 TTTGGTAATTTTACAAACCAAGGGTAT
* **
39557037 TTTGGTAATTCTGTAAACCAAGGGTAT
1 TTTGGTAATTTTACAAACCAAGGGTAT
39557064 TTTGGTAATTTTACAAACC-AGGGATAT
1 TTTGGTAATTTTACAAACCAAGGG-TAT
39557091 TTTGG
1 TTTGG
39557096 CTTGGTATTT
Statistics
Matches: 177, Mismatches: 39, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
26 25 0.14
27 151 0.85
28 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (27 bp):
TTTGGTAATTTTACAAACCAAGGGTAT
Found at i:39557103 original size:40 final size:40
Alignment explanation
Indices: 39557059--39557135 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
39557049 GTAAACCAAG
39557059 GGTATTTTGGTAATTTTACAAACCAGGGATATTTTGGCTT
1 GGTATTTTGGTAATTTTACAAACCAGGGATATTTTGGCTT
*
39557099 GGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGG
1 GGTATTTTGGTAATTTTACAAACCAGGGATATTTTGG
39557136 TGATTTGGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.42
Consensus pattern (40 bp):
GGTATTTTGGTAATTTTACAAACCAGGGATATTTTGGCTT
Found at i:39559061 original size:6 final size:6
Alignment explanation
Indices: 39559043--39559136 Score: 86
Period size: 6 Copynumber: 15.3 Consensus size: 6
39559033 AAGAAACATT
*
39559043 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATCAAA ATCAGGTA A-CAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA
* * *
39559092 ATCAAA ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
39559137 GTGAATGCAA
Statistics
Matches: 72, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
5 5 0.07
6 58 0.81
7 6 0.08
8 3 0.04
ACGTcount: A:0.51, C:0.16, G:0.15, T:0.18
Consensus pattern (6 bp):
ATCAGA
Found at i:39559095 original size:31 final size:31
Alignment explanation
Indices: 39559057--39559136 Score: 133
Period size: 31 Copynumber: 2.6 Consensus size: 31
39559047 GAACTAGAAT
*
39559057 CAGAATCAGAATCAGAATCAAAATCAGGTAA
1 CAGAATCAAAATCAGAATCAAAATCAGGTAA
**
39559088 CAGAATCAAAATCAGAATCAGTATCAGGTAA
1 CAGAATCAAAATCAGAATCAAAATCAGGTAA
39559119 CAGAATCAAAATCAGAAT
1 CAGAATCAAAATCAGAAT
39559137 GTGAATGCAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.51, C:0.16, G:0.15, T:0.17
Consensus pattern (31 bp):
CAGAATCAAAATCAGAATCAAAATCAGGTAA
Found at i:39559348 original size:27 final size:27
Alignment explanation
Indices: 39559254--39559358 Score: 87
Period size: 27 Copynumber: 4.1 Consensus size: 27
39559244 CAGCATGGCT
*
39559254 ACCAG-AACAGATATTGTGAC-AA---
1 ACCAGAAACAGATATTGTGGCAAAGCC
* * *
39559276 ACCAGATACAAATATTGTGGCAGAGCC
1 ACCAGAAACAGATATTGTGGCAAAGCC
* *
39559303 ACTAG-AACAGATATTTGTGGCATAGCC
1 ACCAGAAACAGATA-TTGTGGCAAAGCC
* *
39559330 ACCAGAAACAGATAATGTGGTAAAGCC
1 ACCAGAAACAGATATTGTGGCAAAGCC
39559357 AC
1 AC
39559359 TTAACAGAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
22 5 0.08
23 12 0.19
24 1 0.02
26 6 0.09
27 32 0.50
28 8 0.12
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.19
Consensus pattern (27 bp):
ACCAGAAACAGATATTGTGGCAAAGCC
Found at i:39559545 original size:22 final size:22
Alignment explanation
Indices: 39559517--39559580 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
39559507 GCAAATACGT
*
39559517 TTGGCACATAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
39559539 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
39559561 TTAGG-ACAAAGCCATAATCA
1 TT-GGCACAAAGCCATAATCA
39559581 AAATAATTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 2 0.06
22 29 0.83
23 4 0.11
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.22
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:39559958 original size:27 final size:27
Alignment explanation
Indices: 39559896--39559958 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 27
39559886 CAGTCACTTG
*
39559896 CCCACAA-GGGCAAAATAGTCATTTCA
1 CCCACAAGGGGCAAAATAGTAATTTCA
* *** *
39559922 CACTGTAGGGGCAAAATAGTAATTTTA
1 CCCACAAGGGGCAAAATAGTAATTTCA
39559949 CCCACAAGGG
1 CCCACAAGGG
39559959 TATCTCAGTA
Statistics
Matches: 26, Mismatches: 10, Indels: 1
0.70 0.27 0.03
Matches are distributed among these distances:
26 3 0.12
27 23 0.88
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (27 bp):
CCCACAAGGGGCAAAATAGTAATTTCA
Found at i:39560029 original size:54 final size:54
Alignment explanation
Indices: 39559941--39560179 Score: 300
Period size: 54 Copynumber: 4.4 Consensus size: 54
39559931 GGCAAAATAG
* * * *
39559941 TAATTTTACCC-ACAAGGGTATCTCAGTAATTCTACCCTATAGGGATATTTTGA
1 TAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTATAGGGGTATTTCGA
* * * *
39559994 TAATTCTACCCTACAGGGGTACTTCGGTAATTCTACCCTATAGGGGTATTTCGG
1 TAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTATAGGGGTATTTCGA
* * * *
39560048 TAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCCTACAGGGGTATTTCGG
1 TAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTATAGGGGTATTTCGA
* * * * * * *
39560102 TAATTCTATCCTATAAGGGTATTTCAGTATTTCGACCCAACAAGGGTATTTCGA
1 TAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTATAGGGGTATTTCGA
39560156 TAATTCTACCCTACAAGGGTATTT
1 TAATTCTACCCTACAAGGGTATTT
39560180 TAATAATTTT
Statistics
Matches: 162, Mismatches: 23, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
53 10 0.06
54 152 0.94
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (54 bp):
TAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTATAGGGGTATTTCGA
Found at i:39560071 original size:81 final size:81
Alignment explanation
Indices: 39559940--39560176 Score: 316
Period size: 81 Copynumber: 2.9 Consensus size: 81
39559930 GGGCAAAATA
* * * * *
39559940 GTAATTTTACCC-ACAAGGGTATCTCAGTAATTCTACCCTATAGGGATATTTTGATAATTCTACC
1 GTAATTCTACCCTATAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTTGATAATTCTACC
39560004 CTACAGGGGTACTTCG
66 CTACAGGGGTACTTCG
* *
39560020 GTAATTCTACCCTATAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTT-AGTAATTCTAC
1 GTAATTCTACCCTATAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTTGA-TAATTCTAC
*
39560084 CCTACAGGGGTATTTCG
65 CCTACAGGGGTACTTCG
* * * * * *
39560101 GTAATTCTATCCTATAAGGGTATTTCAGTATTTCGACCCAACAAGGGTATTTCGATAATTCTACC
1 GTAATTCTACCCTATAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTTGATAATTCTACC
*
39560166 CTACAAGGGTA
66 CTACAGGGGTA
39560177 TTTTAATAAT
Statistics
Matches: 137, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
80 12 0.09
81 124 0.91
82 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (81 bp):
GTAATTCTACCCTATAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTTGATAATTCTACC
CTACAGGGGTACTTCG
Found at i:39560187 original size:27 final size:27
Alignment explanation
Indices: 39559940--39560179 Score: 268
Period size: 27 Copynumber: 8.9 Consensus size: 27
39559930 GGGCAAAATA
* * *
39559940 GTAATTTTACCC-ACAAGGGTATCTCA
1 GTAATTCTACCCTACAAGGGTATTTCG
* *
39559966 GTAATTCTACCCTA-TAGGGATATTTTG
1 GTAATTCTACCCTACAAGGG-TATTTCG
* * *
39559993 ATAATTCTACCCTACAGGGGTACTTCG
1 GTAATTCTACCCTACAAGGGTATTTCG
* *
39560020 GTAATTCTACCCTATAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCG
* **
39560047 GTAATTCTACCCTACAGGGGTATTTTA
1 GTAATTCTACCCTACAAGGGTATTTCG
*
39560074 GTAATTCTACCCTACAGGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCG
* * *
39560101 GTAATTCTATCCTATAAGGGTATTTCA
1 GTAATTCTACCCTACAAGGGTATTTCG
* * *
39560128 GTATTTCGACCCAACAAGGGTATTTCG
1 GTAATTCTACCCTACAAGGGTATTTCG
*
39560155 ATAATTCTACCCTACAAGGGTATTT
1 GTAATTCTACCCTACAAGGGTATTT
39560180 TAATAATTTT
Statistics
Matches: 179, Mismatches: 32, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
26 15 0.08
27 161 0.90
28 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (27 bp):
GTAATTCTACCCTACAAGGGTATTTCG
Found at i:39560201 original size:27 final size:27
Alignment explanation
Indices: 39560171--39560350 Score: 118
Period size: 27 Copynumber: 6.7 Consensus size: 27
39560161 CTACCCTACA
* *
39560171 AGGGTATTTTAATAATTTTGTAAATCG
1 AGGGTATTTCAGTAATTTTGTAAATCG
*** *
39560198 AGGGTAAAAC-GATAATTCTGTAAATC-
1 AGGGTATTTCAG-TAATTTTGTAAATCG
* ** *
39560224 AGGGGTACTTT-GGTAATTTTACAAGTCG
1 A-GGGTA-TTTCAGTAATTTTGTAAATCG
**
39560252 AGGGTATTTCAGTAATTTTAAAAATCG
1 AGGGTATTTCAGTAATTTTGTAAATCG
*
39560279 AAGGTATTTCAGTAATTTTGTAAA-CTG
1 AGGGTATTTCAGTAATTTTGTAAATC-G
* * ** *
39560306 AGGGTATTTCGGCAA-TTTAAAAATTG
1 AGGGTATTTCAGTAATTTTGTAAATCG
*
39560332 AGGGTATTTTAGTAATTTT
1 AGGGTATTTCAGTAATTTT
39560351 ACAAATTGGG
Statistics
Matches: 116, Mismatches: 28, Indels: 18
0.72 0.17 0.11
Matches are distributed among these distances:
26 24 0.21
27 90 0.78
28 2 0.02
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.38
Consensus pattern (27 bp):
AGGGTATTTCAGTAATTTTGTAAATCG
Found at i:39560202 original size:54 final size:54
Alignment explanation
Indices: 39560037--39560203 Score: 148
Period size: 54 Copynumber: 3.1 Consensus size: 54
39560027 TACCCTATAG
* * **
39560037 GGGTATTTCGGTAATTCTACCCTACAGGGGTATTTTAGTAA--TTCTACCCTACA
1 GGGTATTTCGGTAATTCTACCCTACAAGGGTATTTTAGTAATTTTGTACAAT-CA
* * * *
39560090 GGGGTATTTCGGTAATTCTATCCTATAAGGGTATTTCAGT-ATTTCG-ACCCAA-CAA
1 -GGGTATTTCGGTAATTCTACCCTACAAGGGTATTTTAGTAATTTTGTA--CAATC-A
* *
39560145 GGGTATTTCGATAATTCTACCCTACAAGGGTATTTTAATAATTTTGTA-AATCGA
1 GGGTATTTCGGTAATTCTACCCTACAAGGGTATTTTAGTAATTTTGTACAATC-A
39560199 GGGTA
1 GGGTA
39560204 AAACGATAAT
Statistics
Matches: 90, Mismatches: 15, Indels: 16
0.74 0.12 0.13
Matches are distributed among these distances:
53 3 0.03
54 78 0.87
55 7 0.08
56 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.36
Consensus pattern (54 bp):
GGGTATTTCGGTAATTCTACCCTACAAGGGTATTTTAGTAATTTTGTACAATCA
Found at i:39560294 original size:54 final size:52
Alignment explanation
Indices: 39560236--39560354 Score: 141
Period size: 53 Copynumber: 2.2 Consensus size: 52
39560226 GGGTACTTTG
* *
39560236 GTAATTTTACAAGTCGAGGGTATTTCAGTAATTTTAAAAATCGAAGGTATTTCA
1 GTAATTTTACAACT-GAGGGTATTTCAGCAA-TTTAAAAATCGAAGGTATTTCA
* * * *
39560290 GTAATTTTGTA-AACTGAGGGTATTTCGGCAATTTAAAAATTGAGGGTATTTTA
1 GTAA-TTT-TACAACTGAGGGTATTTCAGCAATTTAAAAATCGAAGGTATTTCA
39560343 GTAATTTTACAA
1 GTAATTTTACAA
39560355 ATTGGGGTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
51 2 0.04
52 5 0.09
53 23 0.41
54 18 0.32
55 6 0.11
56 2 0.04
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.39
Consensus pattern (52 bp):
GTAATTTTACAACTGAGGGTATTTCAGCAATTTAAAAATCGAAGGTATTTCA
Found at i:39560348 original size:53 final size:53
Alignment explanation
Indices: 39560226--39560463 Score: 194
Period size: 54 Copynumber: 4.5 Consensus size: 53
39560216 TGTAAATCAG
* * * *
39560226 GGGTACTTTGGTAATTTTAC-AAGTCGAGGGTATTTCAGTAATTTTAAAAATCGA
1 GGGTATTTTAGTAATTTTACAAACT-GAGGGTATTTCGGTAA-TTTAAAAATCGA
* * ** * *
39560280 AGGTATTTCAGTAATTTTGTAAACTGAGGGTATTTCGGCAATTTAAAAATTGA
1 GGGTATTTTAGTAATTTTACAAACTGAGGGTATTTCGGTAATTTAAAAATCGA
* * * * *
39560333 GGGTATTTTAGTAATTTTACAAATTG-GGGTATTTTGGTGATTTAAGAAACCAA
1 GGGTATTTTAGTAATTTTACAAACTGAGGGTATTTCGGTAATTTAA-AAATCGA
* * * * ** * *
39560386 GGGTATTCTAGTAATTTTACAAAC-CAGAGGTATTTTGTTAATTTTGTAAACCAA
1 GGGTATTTTAGTAATTTTACAAACTGAG-GGTATTTCGGTAA-TTTAAAAATCGA
*
39560440 GGGTATTTTGGTAATTTTACAAAC
1 GGGTATTTTAGTAATTTTACAAAC
39560464 CAGGGGTATT
Statistics
Matches: 149, Mismatches: 30, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
52 16 0.11
53 59 0.40
54 68 0.46
55 6 0.04
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (53 bp):
GGGTATTTTAGTAATTTTACAAACTGAGGGTATTTCGGTAATTTAAAAATCGA
Found at i:39560367 original size:26 final size:27
Alignment explanation
Indices: 39560226--39560462 Score: 140
Period size: 27 Copynumber: 8.9 Consensus size: 27
39560216 TGTAAATCAG
* * * *
39560226 GGGTACTTTGGTAATTTTACAAGTCGA
1 GGGTATTTTAGTAATTTTACAAATTGA
* * *
39560253 GGGTATTTCAGTAATTTTAAAAATCGA
1 GGGTATTTTAGTAATTTTACAAATTGA
* * ** *
39560280 AGGTATTTCAGTAATTTTGTAAACTGA
1 GGGTATTTTAGTAATTTTACAAATTGA
** * *
39560307 GGGTATTTCGGCAA-TTTAAAAATTGA
1 GGGTATTTTAGTAATTTTACAAATTGA
39560333 GGGTATTTTAGTAATTTTACAAATTG-
1 GGGTATTTTAGTAATTTTACAAATTGA
* * * * ***
39560359 GGGTATTTTGGTGATTTAAGAAACCAA
1 GGGTATTTTAGTAATTTTACAAATTGA
* **
39560386 GGGTATTCTAGTAATTTTACAAA-CCA
1 GGGTATTTTAGTAATTTTACAAATTGA
** ***
39560412 GAGGTATTTT-GTTAATTTTGTAAACCAA
1 G-GGTATTTTAG-TAATTTTACAAATTGA
*
39560440 GGGTATTTTGGTAATTTTACAAA
1 GGGTATTTTAGTAATTTTACAAA
39560463 CCAGGGGTAT
Statistics
Matches: 165, Mismatches: 39, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
26 43 0.26
27 118 0.72
28 4 0.02
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (27 bp):
GGGTATTTTAGTAATTTTACAAATTGA
Found at i:39560442 original size:54 final size:54
Alignment explanation
Indices: 39560332--39560490 Score: 214
Period size: 54 Copynumber: 3.0 Consensus size: 54
39560322 TTAAAAATTG
**
39560332 AGGGTATTTTAGTAATTTTACAAA-TTGGGGTATTTTGGTGATTTAAG-AAACCA
1 AGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTGATTT-AGTAAACCA
* * * * *
39560385 AGGGTATTCTAGTAATTTTACAAACCAGAGGTATTTTGTTAATTTTGTAAACCA
1 AGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTGATTTAGTAAACCA
* *
39560439 AGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTGATTTGGTAAAC
1 AGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTGATTTAGTAAAC
39560491 TAAAGTATTC
Statistics
Matches: 91, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
53 24 0.26
54 67 0.74
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (54 bp):
AGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTGATTTAGTAAACCA
Found at i:39560475 original size:27 final size:27
Alignment explanation
Indices: 39560333--39560483 Score: 160
Period size: 27 Copynumber: 5.6 Consensus size: 27
39560323 TAAAAATTGA
* **
39560333 GGGTATTTTAGTAATTTTACAAA-TTG
1 GGGTATTTTGGTAATTTTACAAACCAG
* * * *
39560359 GGGTATTTTGGTGATTTAAGAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAG
* *
39560386 GGGTATTCTAGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
* * ** *
39560413 AGGTATTTTGTTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAG
39560440 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAG
*
39560467 GGGTATTTTGGTGATTT
1 GGGTATTTTGGTAATTT
39560484 GGTAAACTAA
Statistics
Matches: 98, Mismatches: 26, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
26 19 0.19
27 79 0.81
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAG
Found at i:39562874 original size:15 final size:15
Alignment explanation
Indices: 39562848--39562899 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
39562838 GGCAGTTTCA
*
39562848 TCTTTCTCTTCTTCT
1 TCTTTCTTTTCTTCT
*
39562863 TCTTTTTTTTCTTCT
1 TCTTTCTTTTCTTCT
39562878 TCTTTCTTTTCTTCT
1 TCTTTCTTTTCTTCT
*
39562893 TCATTCT
1 TCTTTCT
39562900 CACTGTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (15 bp):
TCTTTCTTTTCTTCT
Found at i:39563261 original size:28 final size:28
Alignment explanation
Indices: 39563176--39563262 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 28
39563166 ATCTCTTCAG
*
39563176 TTAGTTAATTGCTTGTACTTGAGAAAAA
1 TTAGTTAATTGCTTGTACTTGAGTAAAA
* * * *
39563204 TTAGTTATAATT-C--ATACTT--TTAGAC
1 TTAG-T-TAATTGCTTGTACTTGAGTAAAA
39563229 TTAGTTAATTGCTTGTACTTGAGTAAAA
1 TTAGTTAATTGCTTGTACTTGAGTAAAA
39563257 TTAGTT
1 TTAGTT
39563263 TCCTTTTAGG
Statistics
Matches: 43, Mismatches: 9, Indels: 14
0.65 0.14 0.21
Matches are distributed among these distances:
23 5 0.12
24 2 0.05
25 6 0.14
26 5 0.12
27 5 0.12
28 13 0.30
29 2 0.05
30 5 0.12
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.45
Consensus pattern (28 bp):
TTAGTTAATTGCTTGTACTTGAGTAAAA
Found at i:39574655 original size:44 final size:43
Alignment explanation
Indices: 39574512--39574668 Score: 140
Period size: 43 Copynumber: 3.7 Consensus size: 43
39574502 AGCTTGTACA
* * * * *
39574512 ATGCCAACGTCCTAGACATGGTCTTCCATGT-AATCACATAACG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCA-AAAACG
* * * * *
39574555 ATGCCACTGTCCCAGGCAAGGTCTTACAC--AAATCAAATACA
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCAAAAACG
* * *
39574596 ATGTCGATGTCCCAGACATGGTCTTACACGTAAATCAAAAATTG
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCAAAAA-CG
* *
39574640 ATGCCAATGTCCCAGACGTAGTCTTACAC
1 ATGCCAATGTCCCAGACATGGTCTTACAC
39574669 ATAATCACAT
Statistics
Matches: 88, Mismatches: 22, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
41 27 0.31
42 5 0.06
43 31 0.35
44 25 0.28
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCAAAAACG
Found at i:39581289 original size:20 final size:20
Alignment explanation
Indices: 39581264--39581302 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
39581254 AAGATATGTG
*
39581264 TTTATATAGATGAACTACTA
1 TTTATACAGATGAACTACTA
*
39581284 TTTATACGGATGAACTACT
1 TTTATACAGATGAACTACT
39581303 GGTTATATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (20 bp):
TTTATACAGATGAACTACTA
Found at i:39581308 original size:20 final size:20
Alignment explanation
Indices: 39581272--39581331 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
39581262 TGTTTATATA
*
39581272 GATGAACTACTATTTATACG
1 GATGAACTACTAGTTATACG
* *
39581292 GATGAACTACTGGTTATATG
1 GATGAACTACTAGTTATACG
* *
39581312 AATGAATTA-TAGTTTATACG
1 GATGAACTACTAG-TTATACG
39581332 AATAGAAATG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (20 bp):
GATGAACTACTAGTTATACG
Found at i:39593777 original size:46 final size:47
Alignment explanation
Indices: 39593711--39593831 Score: 217
Period size: 47 Copynumber: 2.6 Consensus size: 47
39593701 GCATTGGCAC
39593711 TAAGATAAGGATACCATGTAAGACCATGTTTGG-ACATGGCATTTGG
1 TAAGATAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
*
39593757 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGATAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
*
39593804 TAAGATAAGGATATCATGTAAGACCATG
1 TAAGATAAGGATACCATGTAAGACCATG
39593832 CCAAGGCTTG
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
46 32 0.45
47 39 0.55
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (47 bp):
TAAGATAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:39593874 original size:54 final size:54
Alignment explanation
Indices: 39593810--39593976 Score: 221
Period size: 55 Copynumber: 3.1 Consensus size: 54
39593800 TTGGTAAGAT
* * * *
39593810 AAGGATATCATGTAAGACCATGCCAAGGCTTGACATTGATAAGTTCTATAAGGC
1 AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTTCTATAAGGC
* *
39593864 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGC
1 AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTT-CTATAAGGC
** *
39593919 AAAGG-ACCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTTCTATAAGGC
39593972 AAGGA
1 AAGGA
39593977 TACCACGTAA
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
52 4 0.04
53 7 0.07
54 40 0.40
55 44 0.44
56 4 0.04
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (54 bp):
AAGGAAATCATGTAAGACCATGCCAAGGCATGGCATTGATGAGTTCTATAAGGC
Found at i:39593938 original size:55 final size:53
Alignment explanation
Indices: 39593818--39594006 Score: 218
Period size: 55 Copynumber: 3.5 Consensus size: 53
39593808 ATAAGGATAT
* * * * *
39593818 CATGTAAGACCATGCCAAGGCTTGACATTGATAAGTTCTATAAGGCAAGGAAAT
1 CATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGCAAGG-AAC
* *
39593872 CATGTAAGACCATGTCAAGACATGGCATTGATGAGTTACTATAAGGCAAAGGACC
1 CATGTAAGACCATGCCAAGACATGGCATTGATGAGTT-CTATAAGGC-AAGGAAC
* *
39593927 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGGATAC
1 CATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGCAAGGA-AC
* * * *
39593980 CACGTAAGAACGTGTCAAGACATGGCA
1 CATGTAAGACCATGCCAAGACATGGCA
39594007 ATGGTAAGTT
Statistics
Matches: 116, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
52 5 0.04
53 30 0.26
54 33 0.28
55 44 0.38
56 4 0.03
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (53 bp):
CATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGCAAGGAAC
Found at i:39594139 original size:16 final size:17
Alignment explanation
Indices: 39594120--39594152 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
39594110 CTTATTTATT
39594120 ATTGAGATTAT-AAGTA
1 ATTGAGATTATCAAGTA
39594136 ATTGAGATTATCAAGTA
1 ATTGAGATTATCAAGTA
39594153 TTAAGTAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.36
Consensus pattern (17 bp):
ATTGAGATTATCAAGTA
Found at i:39597994 original size:28 final size:30
Alignment explanation
Indices: 39597933--39597994 Score: 76
Period size: 28 Copynumber: 2.1 Consensus size: 30
39597923 AATAAACATT
* *
39597933 GTTGAATTTGAATTTGTATGATTTTTATAT
1 GTTGAATTTGAATTTGTATGATTTCTATAG
39597963 GTTGAATTT-AA-TTGTATGGATTTCTAT-G
1 GTTGAATTTGAATTTGTAT-GATTTCTATAG
39597991 GTTG
1 GTTG
39597995 GAGCCGAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 10 0.34
29 10 0.34
30 9 0.31
ACGTcount: A:0.24, C:0.02, G:0.21, T:0.53
Consensus pattern (30 bp):
GTTGAATTTGAATTTGTATGATTTCTATAG
Found at i:39598134 original size:42 final size:43
Alignment explanation
Indices: 39598087--39598198 Score: 176
Period size: 41 Copynumber: 2.7 Consensus size: 43
39598077 TAACAGTGAT
39598087 ATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCGGTGTA-TG
1 ATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCGGTGTATTG
39598129 ATATCAGGCTTATTGCCTAGCAGGCTTT-ATGCCGGTGTATTG
1 ATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCGGTGTATTG
* * *
39598171 A-ATCAAGTTTATTACCTAGCAGGCTTTG
1 ATATCAGGCTTATTGCCTAGCAGGCTTTG
39598199 TACGATGTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
41 34 0.52
42 31 0.48
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (43 bp):
ATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCGGTGTATTG
Found at i:39601363 original size:29 final size:29
Alignment explanation
Indices: 39601305--39601461 Score: 221
Period size: 29 Copynumber: 5.5 Consensus size: 29
39601295 ATAGTAAGTC
*
39601305 CGCACACTTAGTG-TTATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
39601333 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
39601362 CGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
*
39601391 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACT
* * * * *
39601419 TGCACACTTAGTGCTATGCA-ATTTAAACC
1 CGCACACTTAGTGCT-TACATAATCAAACT
39601448 CGCACACTTAGTGC
1 CGCACACTTAGTGC
39601462 CAATCTCATG
Statistics
Matches: 117, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
28 39 0.33
29 76 0.65
30 2 0.02
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTTACATAATCAAACT
Found at i:39601412 original size:57 final size:58
Alignment explanation
Indices: 39601305--39601461 Score: 221
Period size: 57 Copynumber: 2.7 Consensus size: 58
39601295 ATAGTAAGTC
*
39601305 CGCACACTTAGTG-TTATATAATCAAACTCGCACACTTAGTGCTTACATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACTCGCACACTTAGTGCTTACATAATCAAACT
*
39601362 CGCACACTTAGTGCTTACATAATCAAACTCGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTACATAATCAAACTCGCACACTTAGTGCTTACATAATCAAACT
* * * * *
39601419 TGCACACTTAGTGCTATGCA-ATTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCT-TACATAATCAAACTCGCACACTTAGTGC
39601462 CAATCTCATG
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
57 60 0.66
58 31 0.34
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (58 bp):
CGCACACTTAGTGCTTACATAATCAAACTCGCACACTTAGTGCTTACATAATCAAACT
Found at i:39601925 original size:12 final size:12
Alignment explanation
Indices: 39601908--39601932 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39601898 ATGGGCATAC
39601908 ATATGTATATAT
1 ATATGTATATAT
39601920 ATATGTATATAT
1 ATATGTATATAT
39601932 A
1 A
39601933 CTTCCGAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATATGTATATAT
Found at i:39608672 original size:40 final size:40
Alignment explanation
Indices: 39608628--39608889 Score: 328
Period size: 39 Copynumber: 6.7 Consensus size: 40
39608618 GCTCCTCGTT
* *
39608628 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
39608668 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
*
39608708 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
39608747 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
39608786 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
39608825 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
39608866 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39608890 CATCATTCAA
Statistics
Matches: 203, Mismatches: 11, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
38 2 0.01
39 126 0.62
40 64 0.32
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:39615887 original size:40 final size:39
Alignment explanation
Indices: 39615843--39615985 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 39
39615833 GCTCCTCGTT
*
39615843 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAATTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGTTATAGTAATTCGCA
* *
39615883 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGG-TTATAGTAATTCGCA
*
39615923 CAAATGCCTTCGGGCTTAGCCCGG-AATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGTTA-TAGTAAT-TCGCA
39615962 CAAATGCCTTCGGGCTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGG
39615986 AAATGCCTTC
Statistics
Matches: 93, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.01
39 42 0.45
40 48 0.52
41 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGTTATAGTAATTCGCA
Found at i:39615960 original size:39 final size:40
Alignment explanation
Indices: 39615843--39615987 Score: 199
Period size: 39 Copynumber: 3.7 Consensus size: 40
39615833 GCTCCTCGTT
* *
39615843 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
39615883 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
39615923 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
39615962 CAAATGCCTTCGGG-CTTAGCCCGGAA
1 CAAATGCCTTCGGGACTTAGCCCGGAA
39615988 ATGCCTTCGG
Statistics
Matches: 97, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
39 49 0.51
40 46 0.47
41 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:39615993 original size:23 final size:23
Alignment explanation
Indices: 39615963--39616010 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
39615953 TATCTCGCAC
39615963 AAATGCCTTCGGGCTTAGCCCGG
1 AAATGCCTTCGGGCTTAGCCCGG
39615986 AAATGCCTTCGGGCTTAGCCCGG
1 AAATGCCTTCGGGCTTAGCCCGG
39616009 AA
1 AA
39616011 TTAGTATCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.29, G:0.29, T:0.21
Consensus pattern (23 bp):
AAATGCCTTCGGGCTTAGCCCGG
Found at i:39616072 original size:101 final size:103
Alignment explanation
Indices: 39615884--39616088 Score: 278
Period size: 101 Copynumber: 2.0 Consensus size: 103
39615874 TAATTCGCAC
*
39615884 AAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 AAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
*
39615949 TTAGTATCTCGCACAAATGCCTTCGGG-CTTAGCCCGG
66 TTAGTATCTAGCACAAATGCCTTCGGGACTTAGCCCGG
* * * *
39615986 AAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACAAATGCCTTCGG-GCTTAGCCCGGA
39616050 TATT-GTCA-CTTAGCAC-AA-GCCTTCGGGACTTAGCCCGG
65 -ATTAGT-ATC-TAGCACAAATGCCTTCGGGACTTAGCCCGG
39616088 A
1 A
39616089 CATCATTCAA
Statistics
Matches: 92, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
101 44 0.48
102 39 0.42
103 9 0.10
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.25
Consensus pattern (103 bp):
AAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
TTAGTATCTAGCACAAATGCCTTCGGGACTTAGCCCGG
Done.