Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 128 of 325
Found at i:40897866 original size:22 final size:22
Alignment explanation
Indices: 40897811--40897866 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
40897801 TAGTAAGTTT
* *
40897811 ATATCTATTGATGCATAAGGTT
1 ATATCTATTGATGCATAAGATA
*
40897833 ATATCTATTGATGCATGAGATA
1 ATATCTATTGATGCATAAGATA
40897855 ATA-CTATATGAT
1 ATATCTAT-TGAT
40897867 TGATGTCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
ATATCTATTGATGCATAAGATA
Found at i:40899247 original size:217 final size:217
Alignment explanation
Indices: 40898872--40899276 Score: 711
Period size: 217 Copynumber: 1.9 Consensus size: 217
40898862 GTGAGACGTC
*
40898872 AAAAGCAACCTTCTTTAAATTGATGGATGAATGGTTTAGTGAATATATGAGAACAAATCCCTCTG
1 AAAAGCAACCTTCTTTAAATTGATGGATGAATGGTTTAGTGAATATATGAGAACAAATCCCGCTG
40898937 TTCAACAACCTCCCCCACATGCTTCACAACATGATGAAATGCCACAGGATGCTAGATATATTAGA
66 TTCAACAACCTCCCCCACATGCTTCACAACATGATGAAATGCCACAGGATGCTAGATATATTAGA
40899002 ATTGGTAAGGCTCCAGTAGATAAAATCAGAAAACATAGGGCTGAAGAATTTAGGGCTATGACCAA
131 ATTGGTAAGGCTCCAGTAGATAAAATCAGAAAACATAGGGCTGAAGAATTTAGGGCTATGACCAA
40899067 TAATGATCCAGTAGATAAAGTT
196 TAATGATCCAGTAGATAAAGTT
* *
40899089 AAAAGCAGCCTTCTTTGAATTGATGGATGAATGGTTTAGTGAATATATGAGAACAAATCCCGCTG
1 AAAAGCAACCTTCTTTAAATTGATGGATGAATGGTTTAGTGAATATATGAGAACAAATCCCGCTG
* * * * * *
40899154 TTCAACGACCTCCCCCACCTGCTTTACAACATGATGAAGTGCCACAGGATGCTAGATCTGTTAGA
66 TTCAACAACCTCCCCCACATGCTTCACAACATGATGAAATGCCACAGGATGCTAGATATATTAGA
* *
40899219 ATTGGTAAGGCTCTAGTAGATAAAATCAGAAAACATAGGGTTGAAGAATTTAGGGCTA
131 ATTGGTAAGGCTCCAGTAGATAAAATCAGAAAACATAGGGCTGAAGAATTTAGGGCTA
40899277 CGGCCGATGA
Statistics
Matches: 177, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
217 177 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (217 bp):
AAAAGCAACCTTCTTTAAATTGATGGATGAATGGTTTAGTGAATATATGAGAACAAATCCCGCTG
TTCAACAACCTCCCCCACATGCTTCACAACATGATGAAATGCCACAGGATGCTAGATATATTAGA
ATTGGTAAGGCTCCAGTAGATAAAATCAGAAAACATAGGGCTGAAGAATTTAGGGCTATGACCAA
TAATGATCCAGTAGATAAAGTT
Found at i:40905259 original size:40 final size:40
Alignment explanation
Indices: 40905147--40905277 Score: 127
Period size: 40 Copynumber: 3.3 Consensus size: 40
40905137 TTATTTGTGG
** * *
40905147 CACTTAGTGTGCGATAGGACATAGCTTCGACTATATATGG
1 CACTTAGTGTGCGATTCGACATAGCTTCGGCTATATATGA
*** * *
40905187 CACTTAGTGTATTATTCCACATAGCTTTGGCTATATATGA
1 CACTTAGTGTGCGATTCGACATAGCTTCGGCTATATATGA
* * * * *
40905227 CACTTAGTGTGCGATTTGAGATGGCTTCGGCTATGTACGA
1 CACTTAGTGTGCGATTCGACATAGCTTCGGCTATATATGA
*
40905267 AACTTAGTGTG
1 CACTTAGTGTG
40905278 TGAGATATTG
Statistics
Matches: 71, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
40 71 1.00
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (40 bp):
CACTTAGTGTGCGATTCGACATAGCTTCGGCTATATATGA
Found at i:40908137 original size:30 final size:30
Alignment explanation
Indices: 40908103--40908163 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
40908093 TCCTTAACTC
40908103 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
40908133 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
40908163 A
1 A
40908164 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:40909768 original size:30 final size:30
Alignment explanation
Indices: 40909734--40909794 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
40909724 TCCTTAACTC
40909734 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
40909764 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
40909794 A
1 A
40909795 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:40915054 original size:79 final size:81
Alignment explanation
Indices: 40914945--40915127 Score: 223
Period size: 79 Copynumber: 2.3 Consensus size: 81
40914935 TACTCGTTTA
* * *
40914945 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTTGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
40915008 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
40915025 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
40915088 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
40915104 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
40915128 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 58 0.65
80 28 0.31
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:40915127 original size:40 final size:40
Alignment explanation
Indices: 40914944--40915127 Score: 223
Period size: 40 Copynumber: 4.6 Consensus size: 40
40914934 CTACTCGTTT
* * *
40914944 AAATGCCTTCGGGACATAGCCCGGTTATAGTAACTTGCAC
1 AAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCAC
* *
40914984 AAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
1 AAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCAC
*
40915024 CAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCAC
1 AAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCAC
* * * *
40915063 AAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCAC
1 AAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCAC
40915104 AAA-GCCTTCGGGACTTAGCCCGGA
1 AAATGCCTTCGGGACTTAGCCCGGA
40915128 CATCATTCGA
Statistics
Matches: 124, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 78 0.63
41 12 0.10
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
AAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCAC
Found at i:40923838 original size:50 final size:50
Alignment explanation
Indices: 40923717--40923915 Score: 200
Period size: 50 Copynumber: 3.9 Consensus size: 50
40923707 ATTGTGAGAA
* * *** *
40923717 CACATGTGTAGTACTATGTGCAGGATACTATGTGTTTAAAATGGTTTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATGG--TTAGGT
** * *
40923769 CATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTGCCAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATGGTTAGGT
* * * * *
40923819 CGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAGCTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGAT-GGTTAGGT
* * **
40923870 CACATGTGTGGTACTAAGTGCAGGCCACTATGTGTAAGAGATGGTT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATGGTT
40923916 TTTATCACAA
Statistics
Matches: 121, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
50 45 0.37
51 41 0.34
52 35 0.29
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATGGTTAGGT
Found at i:40923923 original size:51 final size:50
Alignment explanation
Indices: 40923717--40923936 Score: 183
Period size: 51 Copynumber: 4.3 Consensus size: 50
40923707 ATTGTGAGAA
* * *
40923717 CACATGTGTAGTACTATGTGCAGGATACTATGTGTTTAA-A-ATGGTTTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTG--TAACAGATGG-TTT-GAT
** * ** * *
40923769 CATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTGCCAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTAACAGATGGTTTGAT
* * * * *
40923819 CGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAGCTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTAACAGAT-GGTTTGAT
* * * *
40923870 CACATGTGTGGTACTAAGTGCAGGCCACTATGTGTAAGAGATGGTTTTTAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTAACAGATGG-TTTGAT
* *
40923921 CACAAGTGTCGTACTA
1 CACATGTGTAGTACTA
40923937 TGCGAAGGCC
Statistics
Matches: 136, Mismatches: 28, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
50 41 0.30
51 62 0.46
52 33 0.24
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.32
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTAACAGATGGTTTGAT
Found at i:40925471 original size:13 final size:13
Alignment explanation
Indices: 40925453--40925482 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
40925443 GGTAAGGGGT
40925453 GTTGTATGATTGA
1 GTTGTATGATTGA
40925466 GTTGTATGATTGA
1 GTTGTATGATTGA
40925479 GTTG
1 GTTG
40925483 ATTTGTGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (13 bp):
GTTGTATGATTGA
Found at i:40930177 original size:83 final size:83
Alignment explanation
Indices: 40930078--40930254 Score: 336
Period size: 83 Copynumber: 2.1 Consensus size: 83
40930068 TGTGTGCCCT
**
40930078 GGCCGTGTGCGCCTAGATGAATGATGATGTCATAAACAAAATGTCTGGGTTTTTGGACATGGGCT
1 GGCCGTGTTAGCCTAGATGAATGATGATGTCATAAACAAAATGTCTGGGTTTTTGGACATGGGCT
40930143 ATGAAACGGGCGTGTCTA
66 ATGAAACGGGCGTGTCTA
40930161 GGCCGTGTTAGCCTAGATGAATGATGATGTCATAAACAAAATGTCTGGGTTTTTGGACATGGGCT
1 GGCCGTGTTAGCCTAGATGAATGATGATGTCATAAACAAAATGTCTGGGTTTTTGGACATGGGCT
40930226 ATGAAACGGGCGTGTCTA
66 ATGAAACGGGCGTGTCTA
40930244 GGCCGTGTTAG
1 GGCCGTGTTAG
40930255 GGAAACGGGA
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 92 1.00
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.28
Consensus pattern (83 bp):
GGCCGTGTTAGCCTAGATGAATGATGATGTCATAAACAAAATGTCTGGGTTTTTGGACATGGGCT
ATGAAACGGGCGTGTCTA
Found at i:40932679 original size:29 final size:27
Alignment explanation
Indices: 40932661--40932730 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
40932651 ATATTAAGTC
40932661 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
40932688 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
40932716 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
40932731 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:40932724 original size:28 final size:28
Alignment explanation
Indices: 40932661--40932758 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
40932651 ATATTAAGTC
*
40932661 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
40932688 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
40932716 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
40932745 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40932759 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:40935036 original size:46 final size:46
Alignment explanation
Indices: 40934969--40935137 Score: 193
Period size: 46 Copynumber: 3.7 Consensus size: 46
40934959 AACCCGCCCC
*
40934969 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACATCCA
*
40935015 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCACATCCA
* * * * *
40935063 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACATCCA
*
40935108 TAAGTGAACTTGGACTCAACTCAACGAGTT
1 TAAGTGAACTCGGACTCAACTCAACGAGTT
40935138 TGGATGCTCA
Statistics
Matches: 103, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 1 0.01
45 2 0.02
46 56 0.54
47 28 0.27
48 3 0.03
49 1 0.01
50 4 0.04
51 3 0.03
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCACATCCA
Found at i:40935081 original size:93 final size:93
Alignment explanation
Indices: 40934974--40935144 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
40934964 GCCCCTAAGT
* *
40934974 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
40935039 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* * *
40935067 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTTGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
*
40935132 CGAGTTTGGATGC
66 CGAGTTCGGATGC
40935145 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:40939836 original size:40 final size:40
Alignment explanation
Indices: 40939766--40939983 Score: 307
Period size: 40 Copynumber: 5.5 Consensus size: 40
40939756 AAGCCAGGTA
* * * *
40939766 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
40939805 CCTTCGGGACATAGCCCGGATGTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
40939845 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
40939885 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
40939925 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
40939965 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
40939984 TTATCATCCG
Statistics
Matches: 163, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
39 13 0.08
40 150 0.92
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40943848 original size:46 final size:46
Alignment explanation
Indices: 40943776--40943948 Score: 174
Period size: 46 Copynumber: 3.7 Consensus size: 46
40943766 AACCCGTCCC
* * *
40943776 TAAGTGAACTCGGACTCAACTAAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
* * * *
40943822 TAAGTGAACTTGGACTCAACTCAACGAGTTCAGATACCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-G-GA-C--GTTCGCATCCA
* * * *
40943870 TCA-CGAACTTGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
40943915 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40943949 TGCTCAACCA
Statistics
Matches: 102, Mismatches: 16, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 1 0.01
45 3 0.03
46 57 0.56
47 27 0.26
48 2 0.02
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCA
Found at i:40945980 original size:42 final size:42
Alignment explanation
Indices: 40945908--40946015 Score: 110
Period size: 42 Copynumber: 2.6 Consensus size: 42
40945898 TCGTATCAAT
* * * * *
40945908 GCCATATCTCAAATATGGTCTTACATGAAAT-ATCATATCGAC
1 GCCATATCCCAAAAATGGTCTTATACGAAATCA-CATACCGAC
* ** * *
40945950 GCCATGTCCCTGACATGGTCTTATACGAAATCACATACCGAT
1 GCCATATCCCAAAAATGGTCTTATACGAAATCACATACCGAC
40945992 GCCATATCCCAAAAATGGTCTTAT
1 GCCATATCCCAAAAATGGTCTTAT
40946016 TCGGAATCTC
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
42 51 0.98
43 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (42 bp):
GCCATATCCCAAAAATGGTCTTATACGAAATCACATACCGAC
Found at i:40950534 original size:49 final size:47
Alignment explanation
Indices: 40950465--40951040 Score: 810
Period size: 47 Copynumber: 12.1 Consensus size: 47
40950455 TGAATGATAG
40950465 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATTTATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA--TATGTGA
*
40950514 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
40950561 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40950608 TAAGGCCTAAT-G--GATGTGATGAATGTGAAAGTGTATATATAGATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATAT--ATGTGA
40950656 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
40950705 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
40950754 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
40950801 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGCGTATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40950848 TAA-GCCTAATGGCCGATGTGATGAATGTG-AAGTGTATATATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG------TATATATGTGA
*
40950899 TAGGGCCTAAT-GCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40950944 TAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTATAATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT-ATATGTGA
* * * * * * * *
40950991 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTG-
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40951037 TAAG
1 TAAG
40951041 TCCCGAAGGG
Statistics
Matches: 487, Mismatches: 22, Indels: 39
0.89 0.04 0.07
Matches are distributed among these distances:
44 21 0.04
45 34 0.07
46 51 0.10
47 140 0.29
48 40 0.08
49 132 0.27
50 8 0.02
51 54 0.11
52 7 0.01
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:40951036 original size:47 final size:47
Alignment explanation
Indices: 40950465--40951040 Score: 765
Period size: 49 Copynumber: 12.1 Consensus size: 47
40950455 TGAATGATAG
*
40950465 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATTTATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA--AATGTGA
* *
40950514 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAAATGTGA
* *
40950561 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAAATGTGA
40950608 TAAGGCCTAAT-G--GATGTGATGAATGTGAAAGTGTATATATAGATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA-A-ATGTGA
40950656 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA-A-ATGTGA
40950705 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA-A-ATGTGA
* *
40950754 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAAATGTGA
* * *
40950801 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGCGTATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAAATGTGA
40950848 TAA-GCCTAATGGCCGATGTGATGAATGTG-AAGTGTATATATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG----TATA-A-ATGTGA
* *
40950899 TAGGGCCTAAT-GCCGATGTG-TGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAAATGTGA
40950944 TAAGGCCTAAT-GCCGATGTGATGAATGTGAAAGTGTATAATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAA-ATGTGA
* * * * * * *
40950991 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTG-
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAAATGTGA
40951037 TAAG
1 TAAG
40951041 TCCCGAAGGG
Statistics
Matches: 482, Mismatches: 27, Indels: 39
0.88 0.05 0.07
Matches are distributed among these distances:
44 21 0.04
45 29 0.06
46 51 0.11
47 136 0.28
48 42 0.09
49 146 0.30
50 8 0.02
51 42 0.09
52 7 0.01
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAAATGTGA
Found at i:40951215 original size:37 final size:37
Alignment explanation
Indices: 40951159--40951237 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
40951149 CCGAGCTCTA
* * *
40951159 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
40951196 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
40951233 AAGAC
1 AAGAC
40951238 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:40951809 original size:14 final size:14
Alignment explanation
Indices: 40951790--40951817 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40951780 GTTAATGTAT
40951790 ATAGCCATGCGAAA
1 ATAGCCATGCGAAA
40951804 ATAGCCATGCGAAA
1 ATAGCCATGCGAAA
40951818 TGGCTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.14
Consensus pattern (14 bp):
ATAGCCATGCGAAA
Found at i:40953184 original size:29 final size:29
Alignment explanation
Indices: 40953152--40953225 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
40953142 GTTGTGAGAT
* *
40953152 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
40953181 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
40953210 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
40953226 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:40953696 original size:40 final size:40
Alignment explanation
Indices: 40953536--40953768 Score: 176
Period size: 40 Copynumber: 5.9 Consensus size: 40
40953526 TCGAATGATG
** *
40953536 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TATA
* ** *
40953576 TCCGGACTAAGAT-CCGAAG-GCATTTGTGCGAGT-ACTA-A
1 TCCGGGCTAAG-TCCCGAAGAGCATTCATGCTAGTGA-TATA
** * * *
40953614 TCCGGGCTAAG-CCCGAAG-GCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA-TATA
*
40953653 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * * * *
40953693 TCCGGGCTAAGTTCCGAAGAGCATTCGTACTGGTGTTATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * *
40953733 TCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
40953769 CGTGTATTCG
Statistics
Matches: 163, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.12
38 15 0.09
39 15 0.09
40 94 0.58
41 20 0.12
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
Found at i:40957710 original size:47 final size:47
Alignment explanation
Indices: 40957603--40958183 Score: 903
Period size: 47 Copynumber: 12.1 Consensus size: 47
40957593 GAAATGATAG
40957603 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
*
40957652 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
*
40957699 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40957746 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATAGATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATAT--ATGTGA
40957797 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
40957846 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG----TATATATGTGA
* *
40957897 TAAAGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATACGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* *
40957944 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGCGTATATATGAGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40957991 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
40958040 T-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40958086 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
* * * * * * * *
40958133 CAGGGCCGATTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40958180 TAAG
1 TAAG
40958184 TCCCGAAGGG
Statistics
Matches: 501, Mismatches: 22, Indels: 20
0.92 0.04 0.04
Matches are distributed among these distances:
46 12 0.02
47 265 0.53
48 34 0.07
49 94 0.19
51 96 0.19
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:40957995 original size:194 final size:190
Alignment explanation
Indices: 40957603--40958183 Score: 957
Period size: 194 Copynumber: 3.0 Consensus size: 190
40957593 GAAATGATAG
40957603 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
*
40957668 ATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
*
40957733 TGTATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATAGATGTGA
131 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT-GA---GA
40957797 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
*
40957862 ATGTGATGAATGTGAAAGTGTATATATATATGTGATAAAGCCTAATGGCCGATGTGATGAATGTG
66 ATGTGATGAATGTGAAAGTG----TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTG
* *
40957927 AAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGCGTATATATGAGA
127 AAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGAGA
40957991 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGAT-AGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
40958055 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
66 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
* * * * * * * * *
40958120 TGTATATATGTGACAGGGCCGATTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGA
131 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGAGA
40958180 TAAG
1 TAAG
40958184 TCCCGAAGGG
Statistics
Matches: 366, Mismatches: 17, Indels: 13
0.92 0.04 0.03
Matches are distributed among these distances:
189 97 0.27
193 34 0.09
194 137 0.37
197 2 0.01
198 96 0.26
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (190 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGAGA
Found at i:40958031 original size:245 final size:240
Alignment explanation
Indices: 40957603--40958128 Score: 975
Period size: 245 Copynumber: 2.2 Consensus size: 240
40957593 GAAATGATAG
*
40957603 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATATGTGATAAGGCCTAATGGC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGATAAAGCCTAATGGC
40957666 CGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
66 CGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
40957731 AGTGTATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATAGATGTG
131 AGCGTATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT--ATGTG
40957796 ATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
194 AT-AGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGA
40957846 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGATAAAGCCTAATGGC
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGATAAAGCCTAATGGC
40957911 CGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
66 CGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
40957976 AGCGTATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGAT
131 AGCGTATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGAT
40958041 AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
196 AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
40958086 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATAT
40958129 GTGACAGGGC
Statistics
Matches: 279, Mismatches: 2, Indels: 7
0.97 0.01 0.02
Matches are distributed among these distances:
240 54 0.19
242 34 0.12
243 43 0.15
245 148 0.53
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (240 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATATGTGATAAAGCCTAATGGC
CGATGTGATGAATGTGAAAGTGTATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
AGCGTATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGAT
AGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGA
Found at i:40958358 original size:37 final size:37
Alignment explanation
Indices: 40958302--40958380 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
40958292 CCGAGCTCTA
* * *
40958302 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
* *
40958339 AAGAGCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
40958376 AAGAC
1 AAGAC
40958381 TTCGTAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:40962426 original size:32 final size:30
Alignment explanation
Indices: 40962350--40962431 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 30
40962340 GTATACAATT
* *
40962350 GTAACATAAATATTTAATTACTTTTTATTTAA
1 GTAA-ATAGATATTT-ATTACTTATTATTTAA
40962382 GTAAATAGATATTTATTACTTATTATTATTAA
1 GTAAATAGATATTTATTACTTATTA-T-TTAA
*
40962414 GTTAAA-ATATATTTATTA
1 G-TAAATAGATATTTATTA
40962432 ATTAAATAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
30 10 0.23
31 10 0.23
32 20 0.45
33 4 0.09
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (30 bp):
GTAAATAGATATTTATTACTTATTATTTAA
Found at i:40962844 original size:3 final size:3
Alignment explanation
Indices: 40962838--40962865 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
40962828 AATAATAATA
40962838 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
40962866 ATTAGTGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:40962973 original size:17 final size:17
Alignment explanation
Indices: 40962951--40962987 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
40962941 AAAGAAAGAA
40962951 AAGAAAAAGGACAAACT
1 AAGAAAAAGGACAAACT
40962968 AAGAAAAAGGACAAACT
1 AAGAAAAAGGACAAACT
40962985 AAG
1 AAG
40962988 GGTTTAAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.65, C:0.11, G:0.19, T:0.05
Consensus pattern (17 bp):
AAGAAAAAGGACAAACT
Found at i:40971485 original size:44 final size:44
Alignment explanation
Indices: 40971401--40971485 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
40971391 TATGTAATCT
* * *
40971401 GAACTCATTGAGTTGTGTCTAAATTCATGATATTTGTGACATCA
1 GAACTCATTAAGTTGTGTCTAAATTCATGATATGTATGACATCA
* *
40971445 GAACTCATTAAGTTGTGTCTAAGTTCGTGATATGTATGACA
1 GAACTCATTAAGTTGTGTCTAAATTCATGATATGTATGACA
40971486 CATGTTTTGG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (44 bp):
GAACTCATTAAGTTGTGTCTAAATTCATGATATGTATGACATCA
Found at i:40973310 original size:32 final size:30
Alignment explanation
Indices: 40973234--40973315 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 30
40973224 GTATACAATT
* *
40973234 GTAACATAAATATTTAATTACTTTTTATTTAA
1 GTAA-ATAGATATTT-ATTACTTATTATTTAA
40973266 GTAAATAGATATTTATTACTTATTATTATTAA
1 GTAAATAGATATTTATTACTTATTA-T-TTAA
*
40973298 GTTAAA-ATATATTTATTA
1 G-TAAATAGATATTTATTA
40973316 ATTAAATAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
30 10 0.23
31 10 0.23
32 20 0.45
33 4 0.09
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (30 bp):
GTAAATAGATATTTATTACTTATTATTTAA
Found at i:40983635 original size:50 final size:50
Alignment explanation
Indices: 40983560--40983656 Score: 167
Period size: 50 Copynumber: 1.9 Consensus size: 50
40983550 ACTACTTGTG
* *
40983560 ATAGTTTGATATCTCTCAACGAAATTGTTTTACTAAGACAGAGATGAGTA
1 ATAGTGTGATATCTCTCAACGAAATTGTTTTACTAAGACAAAGATGAGTA
*
40983610 ATAGTGTGATATCTCTCAACGAAATTGTTTTGCTAAGACAAAGATGA
1 ATAGTGTGATATCTCTCAACGAAATTGTTTTACTAAGACAAAGATGA
40983657 CTTCCAACCG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (50 bp):
ATAGTGTGATATCTCTCAACGAAATTGTTTTACTAAGACAAAGATGAGTA
Found at i:40987707 original size:13 final size:13
Alignment explanation
Indices: 40987689--40987720 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
40987679 GTCCCATGGG
40987689 CATGTGGTCCGGT
1 CATGTGGTCCGGT
*
40987702 CATGTGGTCTGGT
1 CATGTGGTCCGGT
40987715 CATGTG
1 CATGTG
40987721 TCCTCTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.09, C:0.19, G:0.38, T:0.34
Consensus pattern (13 bp):
CATGTGGTCCGGT
Found at i:40993655 original size:27 final size:26
Alignment explanation
Indices: 40993625--40993688 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 26
40993615 TATTCAGTAT
* *
40993625 CAGTACAGTCTGGGCCTTAGCCCTATA
1 CAGTACAGTCT-GGCCTAAGCCCAATA
* *
40993652 CAGTAATAGTGTGGCCTAAGCCCAATA
1 CAGT-ACAGTCTGGCCTAAGCCCAATA
40993679 CAGTATCAGT
1 CAGTA-CAGT
40993689 ACCGTGTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
26 1 0.03
27 24 0.80
28 5 0.17
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (26 bp):
CAGTACAGTCTGGCCTAAGCCCAATA
Found at i:40993869 original size:27 final size:27
Alignment explanation
Indices: 40993839--40993903 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
40993829 AGCATAGCTG
40993839 CCAGAAACAGTAAATGTGGCAAAGCCA
1 CCAGAAACAGTAAATGTGGCAAAGCCA
* * * *
40993866 CCAGTAACAGTGAATGTGGCATAGTCA
1 CCAGAAACAGTAAATGTGGCAAAGCCA
*
40993893 CCA-ATACAGTA
1 CCAGAAACAGTA
40993904 CTTCCTCCAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 5 0.16
27 26 0.84
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.17
Consensus pattern (27 bp):
CCAGAAACAGTAAATGTGGCAAAGCCA
Found at i:40994090 original size:27 final size:27
Alignment explanation
Indices: 40994039--40994238 Score: 172
Period size: 27 Copynumber: 7.4 Consensus size: 27
40994029 GAGCATAATC
** **
40994039 GTCATTTTACCAAACAGGGATATTACA
1 GTCATTTTACCCTACAGGGGCATTACA
* * *
40994066 GTCATTTTATCCTACAAGGGCATTACG
1 GTCATTTTACCCTACAGGGGCATTACA
**
40994093 GTCATTTTACCCTACAGGGGCATTATG
1 GTCATTTTACCCTACAGGGGCATTACA
*
40994120 GTTATTTTACCCTACAGGGGCATTAC-
1 GTCATTTTACCCTACAGGGGCATTACA
* * **
40994146 GATCATTTTACCCTATAGGGGTAACACA
1 G-TCATTTTACCCTACAGGGGCATTACA
* * *
40994174 ATCATTTTACCCTACAAGGGCATTA-T
1 GTCATTTTACCCTACAGGGGCATTACA
* * *
40994200 GATCATTTTACCCTATAGGGGTATTA-T
1 G-TCATTTTACCCTACAGGGGCATTACA
40994227 GATCATTTTACC
1 G-TCATTTTACC
40994239 TATTTTGGGG
Statistics
Matches: 142, Mismatches: 28, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
26 1 0.01
27 141 0.99
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (27 bp):
GTCATTTTACCCTACAGGGGCATTACA
Found at i:40994100 original size:54 final size:54
Alignment explanation
Indices: 40994040--40994238 Score: 229
Period size: 54 Copynumber: 3.7 Consensus size: 54
40994030 AGCATAATCG
** * * *
40994040 TCATTTTACCAAACAGGGATATTACAGTCATTTTATCCTACAAGGGCATTACGG
1 TCATTTTACCCTACAGGGGTATTACAGTCATTTTACCCTACAAGGGCATTACGA
* ** * *
40994094 TCATTTTACCCTACAGGGGCATTATGGTTATTTTACCCTACAGGGGCATTACGA
1 TCATTTTACCCTACAGGGGTATTACAGTCATTTTACCCTACAAGGGCATTACGA
* ** * *
40994148 TCATTTTACCCTATAGGGGTAACACAATCATTTTACCCTACAAGGGCATTATGA
1 TCATTTTACCCTACAGGGGTATTACAGTCATTTTACCCTACAAGGGCATTACGA
* *
40994202 TCATTTTACCCTATAGGGGTATTA-TGATCATTTTACC
1 TCATTTTACCCTACAGGGGTATTACAG-TCATTTTACC
40994239 TATTTTGGGG
Statistics
Matches: 120, Mismatches: 24, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
54 120 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (54 bp):
TCATTTTACCCTACAGGGGTATTACAGTCATTTTACCCTACAAGGGCATTACGA
Found at i:40996914 original size:42 final size:45
Alignment explanation
Indices: 40996811--40996914 Score: 114
Period size: 44 Copynumber: 2.4 Consensus size: 45
40996801 TGTTATCGTG
* *
40996811 TAAGACCAC-GTCTGGGATGTTGGCATCGACTTATGATTTGCGTG
1 TAAGACCACTGTCTGGGATGTTGGCATCGACTTATGATTTGCCTA
*
40996855 TAAGACCACAT-T-TGGGATGTTGGCATCATAC-T-TGATTT-CCTA
1 TAAGACCAC-TGTCTGGGATGTTGGCATC-GACTTATGATTTGCCTA
40996897 TAAGACC-CTGTCTGGGAT
1 TAAGACCACTGTCTGGGAT
40996915 AGTGGTTTTG
Statistics
Matches: 52, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
40 1 0.02
41 2 0.04
42 15 0.29
43 6 0.12
44 25 0.48
45 3 0.06
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (45 bp):
TAAGACCACTGTCTGGGATGTTGGCATCGACTTATGATTTGCCTA
Found at i:40997953 original size:21 final size:21
Alignment explanation
Indices: 40997927--40997967 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
40997917 TTTCCCACAA
*
40997927 GGGCAGAGACACGGGTGTGTC
1 GGGCAGAGACACGGGCGTGTC
40997948 GGGCAGAGACACGGGCGTGT
1 GGGCAGAGACACGGGCGTGT
40997968 GTCTCAGCCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.20, G:0.49, T:0.12
Consensus pattern (21 bp):
GGGCAGAGACACGGGCGTGTC
Found at i:41005921 original size:49 final size:49
Alignment explanation
Indices: 41005865--41005963 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
41005855 GAGAGTTAAA
41005865 CTCTAATTATATTTTGAATCTGTGTATACAAGACTCACAAATGATAATC
1 CTCTAATTATATTTTGAATCTGTGTATACAAGACTCACAAATGATAATC
41005914 CTCTAATTATATTTTGAATCTGTGTATACAAGACTCACAAATGATAATC
1 CTCTAATTATATTTTGAATCTGTGTATACAAGACTCACAAATGATAATC
41005963 C
1 C
41005964 AACTAATGTC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.36
Consensus pattern (49 bp):
CTCTAATTATATTTTGAATCTGTGTATACAAGACTCACAAATGATAATC
Found at i:41010983 original size:20 final size:22
Alignment explanation
Indices: 41010958--41011010 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
41010948 ATGTTATGTA
41010958 GGTATCAATACTGCCTCT-A-T
1 GGTATCAATACTGCCTCTAAGT
* * *
41010978 GGTATCGATACTTCCTTTAAGT
1 GGTATCAATACTGCCTCTAAGT
41011000 GGTATCAATAC
1 GGTATCAATAC
41011011 CACGTGGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 15 0.56
21 1 0.04
22 11 0.41
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (22 bp):
GGTATCAATACTGCCTCTAAGT
Found at i:41014358 original size:29 final size:29
Alignment explanation
Indices: 41014326--41014407 Score: 103
Period size: 30 Copynumber: 2.8 Consensus size: 29
41014316 ATGGTCGCCC
* *
41014326 CCATCCTTTTTCATGTTCGATGGTCGAAA
1 CCATCCTTTTTCATATTCGATGGTCAAAA
* *
41014355 CCAT-CTCTTTTCTTTAATCGATGGTCAAAA
1 CCATCCT-TTTTC-ATATTCGATGGTCAAAA
41014385 CCATCCTTTTTCATATTCGATGG
1 CCATCCTTTTTCATATTCGATGG
41014408 GCATTGATAC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
28 2 0.05
29 18 0.41
30 22 0.50
31 2 0.05
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.40
Consensus pattern (29 bp):
CCATCCTTTTTCATATTCGATGGTCAAAA
Found at i:41023581 original size:20 final size:21
Alignment explanation
Indices: 41023542--41023581 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
41023532 AAGGACTATT
*
41023542 TTGTAAAGTTTGTAAAATAAG
1 TTGTAAAGTGTGTAAAATAAG
*
41023563 TTGTAAA-TGTGTGAAATAA
1 TTGTAAAGTGTGTAAAATAA
41023582 TTGAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (21 bp):
TTGTAAAGTGTGTAAAATAAG
Found at i:41033540 original size:110 final size:110
Alignment explanation
Indices: 41033354--41033577 Score: 236
Period size: 110 Copynumber: 2.0 Consensus size: 110
41033344 TGACCGTCCT
* ** * * * * *
41033354 ACTTGAAACGATAGATTATTCCTCTTCTGGCTATGGATTATGGATCCTTCCTATATCATATTTGG
1 ACTTGAAACGATAGATAATTCCTCTTCTAACTATGGATCATGGATCCTCCCGATACCATATTGGG
* * * *
41033419 ATCCTATATTCCACACCACTAGGGATAA-CCCCGATTGACCATCTC
66 ATCATAGATTCCACACCA-TAGGGATAACCCCCAATTAACCATCTC
* * *
41033464 ACTTGAACCGATAGATAATTCTTCTTCTAACTGTGGATCATGGATCCTCCCCGA-ACCATATTGG
1 ACTTGAAACGATAGATAATTCCTCTTCTAACTATGGATCATGGATCCT-CCCGATACCATATTGG
* * * * *
41033528 GTTCATAGATTCCACGCCATTGGGTTAACCCCCAATTAACCATCTT
65 GATCATAGATTCCACACCATAGGGATAACCCCCAATTAACCATCTC
41033574 ACTT
1 ACTT
41033578 AACATGATAG
Statistics
Matches: 92, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
109 7 0.08
110 82 0.89
111 3 0.03
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (110 bp):
ACTTGAAACGATAGATAATTCCTCTTCTAACTATGGATCATGGATCCTCCCGATACCATATTGGG
ATCATAGATTCCACACCATAGGGATAACCCCCAATTAACCATCTC
Found at i:41033663 original size:23 final size:20
Alignment explanation
Indices: 41033610--41033654 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
41033600 AGACTGCCTA
41033610 GGGATCGCATATCCTCCCTG
1 GGGATCGCATATCCTCCCTG
*
41033630 GGGATCGCATATCCTCCTTG
1 GGGATCGCATATCCTCCCTG
41033650 GGGAT
1 GGGAT
41033655 TAGCGCATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.27
Consensus pattern (20 bp):
GGGATCGCATATCCTCCCTG
Found at i:41043739 original size:22 final size:22
Alignment explanation
Indices: 41043711--41043754 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
41043701 TTTTGAACCA
41043711 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
41043733 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
41043755 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:41046190 original size:22 final size:22
Alignment explanation
Indices: 41046162--41046205 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
41046152 TTTTGAACCA
41046162 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
41046184 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
41046206 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:41048646 original size:22 final size:22
Alignment explanation
Indices: 41048618--41048661 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
41048608 TTTTGAACCA
41048618 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
41048640 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
41048662 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:41051103 original size:22 final size:22
Alignment explanation
Indices: 41051075--41051118 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
41051065 TTTTGAACCA
41051075 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
41051097 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
41051119 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:41057924 original size:17 final size:17
Alignment explanation
Indices: 41057904--41057945 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
41057894 TTAGATCTAA
*
41057904 TTACATTTTCCATTTTT
1 TTACATTTACCATTTTT
41057921 TTACA-TTACCATTTTT
1 TTACATTTACCATTTTT
41057937 TTATCATTT
1 TTA-CATTT
41057946 CAATTAATAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 13 0.59
17 7 0.32
18 2 0.09
ACGTcount: A:0.21, C:0.17, G:0.00, T:0.62
Consensus pattern (17 bp):
TTACATTTACCATTTTT
Found at i:41061745 original size:36 final size:36
Alignment explanation
Indices: 41061705--41061775 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
41061695 CCCAAGGCTG
*
41061705 AGCACCACCCAAAAATCCTACCAGAGGAAAAATATA
1 AGCACCACCCAAAAATCCTACAAGAGGAAAAATATA
* * *
41061741 AGCACCACCCAGAATTCCTAGAAGAGGAAAAATAT
1 AGCACCACCCAAAAATCCTACAAGAGGAAAAATAT
41061776 GCAAGGTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.48, C:0.25, G:0.14, T:0.13
Consensus pattern (36 bp):
AGCACCACCCAAAAATCCTACAAGAGGAAAAATATA
Found at i:41066217 original size:40 final size:40
Alignment explanation
Indices: 41066124--41066379 Score: 322
Period size: 40 Copynumber: 6.5 Consensus size: 40
41066114 AAGCCAAGTA
* * *
41066124 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * *
41066162 CCTTCAGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
41066202 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
41066242 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
41066282 CCTTCGGGACTTAGCCCGGATGTAATAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* ** *
41066322 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAACGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
41066362 CCTTCGGGACTTAGCCCG
1 CCTTCGGGACTTAGCCCG
41066380 ATTATCATCC
Statistics
Matches: 194, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
38 11 0.06
39 17 0.09
40 166 0.86
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:41069381 original size:18 final size:18
Alignment explanation
Indices: 41069331--41069382 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
41069321 GAAATTCTAT
41069331 ATCCTTCAAGGATTTTAA
1 ATCCTTCAAGGATTTTAA
* **
41069349 ACCCTT-TTGGAATTTTAA
1 ATCCTTCAAGG-ATTTTAA
41069367 ATCCTTCAAGGATTTT
1 ATCCTTCAAGGATTTT
41069383 CATATAAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
17 2 0.08
18 22 0.85
19 2 0.08
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (18 bp):
ATCCTTCAAGGATTTTAA
Found at i:41071383 original size:46 final size:46
Alignment explanation
Indices: 41071333--41071505 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
41071323 TGGTTGAGCA
41071333 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
41071379 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
41071424 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
41071472 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
41071506 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:41071489 original size:93 final size:93
Alignment explanation
Indices: 41071330--41071500 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
41071320 GGATGGTTGA
* *
41071330 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
41071395 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
41071423 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
41071488 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
41071501 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:41078944 original size:46 final size:46
Alignment explanation
Indices: 41078894--41079066 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
41078884 TGGTTGAGCA
41078894 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
41078940 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
41078985 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
41079033 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
41079067 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:41079050 original size:93 final size:93
Alignment explanation
Indices: 41078891--41079061 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
41078881 GGATGGTTGA
* *
41078891 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
41078956 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
41078984 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
41079049 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
41079062 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:41082573 original size:21 final size:20
Alignment explanation
Indices: 41082548--41082601 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
41082538 TTCGTTCAAA
*
41082548 CCTTATGGGTTTCTGTTTAG
1 CCTTATGGGCTTCTGTTTAG
*
41082568 CACTTATGTGCTTCTGTTTAG
1 C-CTTATGGGCTTCTGTTTAG
41082589 CCTT-TGGGCTTCT
1 CCTTATGGGCTTCT
41082602 AAAAACGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.27
20 4 0.13
21 18 0.60
ACGTcount: A:0.09, C:0.20, G:0.22, T:0.48
Consensus pattern (20 bp):
CCTTATGGGCTTCTGTTTAG
Found at i:41087105 original size:25 final size:25
Alignment explanation
Indices: 41087076--41087255 Score: 95
Period size: 25 Copynumber: 7.3 Consensus size: 25
41087066 CTCTCTCTAT
41087076 CGAGCCATATAACAGGAAGCTCATG
1 CGAGCCATATAACAGGAAGCTCATG
* ** *
41087101 TGAGCTGTATAACAGGAAGCTTAT-
1 CGAGCCATATAACAGGAAGCTCATG
* * ** *
41087125 CCAGGCTATATAATGGGAAGCTCATA
1 CGA-GCCATATAACAGGAAGCTCATG
** *
41087151 AAAGCCATA-ATCAGGAAGCTCATG
1 CGAGCCATATAACAGGAAGCTCATG
* *
41087175 CGAGCCA-ATAACGGGTAGCTC-TG
1 CGAGCCATATAACAGGAAGCTCATG
* * *
41087198 AAGAGCCAT-TAATCAAGACGCTC-TG
1 -CGAGCCATATAA-CAGGAAGCTCATG
* *
41087223 -GATAGCCATATATCGGGAAGCTCATG
1 CG--AGCCATATAACAGGAAGCTCATG
41087249 CGAGCCA
1 CGAGCCA
41087256 ATATCGAGAA
Statistics
Matches: 113, Mismatches: 31, Indels: 22
0.68 0.19 0.13
Matches are distributed among these distances:
23 4 0.04
24 35 0.31
25 68 0.60
26 5 0.04
27 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (25 bp):
CGAGCCATATAACAGGAAGCTCATG
Found at i:41087266 original size:24 final size:23
Alignment explanation
Indices: 41087165--41087269 Score: 68
Period size: 25 Copynumber: 4.3 Consensus size: 23
41087155 CCATAATCAG
* *
41087165 GAAGCTCATGCGAGCCAATAACGG
1 GAAGCTC-TGCGAGCCAATATCGA
* * * *
41087189 GTAGCTCTGAAGAGCCATTAATCAA
1 GAAGCTCTG-CGAGCCAAT-ATCGA
* *
41087214 GACGCTCTG-GATAGCCATATATCGG
1 GAAGCTCTGCG--AGCCA-ATATCGA
41087239 GAAGCTCATGCGAGCCAATATCGA
1 GAAGCTC-TGCGAGCCAATATCGA
41087263 GAAGCTC
1 GAAGCTC
41087270 CGGAGAACTA
Statistics
Matches: 61, Mismatches: 13, Indels: 14
0.69 0.15 0.16
Matches are distributed among these distances:
23 3 0.05
24 26 0.43
25 28 0.46
26 3 0.05
27 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (23 bp):
GAAGCTCTGCGAGCCAATATCGA
Found at i:41091385 original size:16 final size:16
Alignment explanation
Indices: 41091366--41091396 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41091356 CTTCTTCACT
41091366 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
41091382 TACTTACTTACTTAA
1 TACTCACTTACTTAA
41091397 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:41091402 original size:20 final size:20
Alignment explanation
Indices: 41091363--41091402 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
41091353 AAACTTCTTC
* *
41091363 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
41091383 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
41091403 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:41091735 original size:53 final size:55
Alignment explanation
Indices: 41091635--41091771 Score: 172
Period size: 53 Copynumber: 2.5 Consensus size: 55
41091625 ATCCTTTTGA
* * * *
41091635 AACTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTAT-G-
1 AACTTACCAATGCCATGTCTTGACATGGTCTTAAATGGGATCCTTGCCTTATGGT
* * *
41091688 AACTCACCAATGCCATGCCTTGGCATGGTCTTAAATGGGA-CCTTTGCCTTATGGT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTAAATGGGATCC-TTGCCTTATGGT
*
41091743 AACTTATCAATGCCATGTCTTGACATGGT
1 AACTTACCAATGCCATGTCTTGACATGGT
41091772 ATTACATGAT
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
52 2 0.03
53 42 0.60
54 1 0.01
55 25 0.36
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (55 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTAAATGGGATCCTTGCCTTATGGT
Found at i:41091794 original size:108 final size:110
Alignment explanation
Indices: 41091635--41091835 Score: 271
Period size: 108 Copynumber: 1.8 Consensus size: 110
41091625 ATCCTTTTGA
* * * * * *
41091635 AACTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATGAA-CTCACCAA-
1 AACTTACCAATGCCATGTCTCGACATGGTATTACATGATATACTTACCTTATAAACCTCACCAAT
*
41091698 TGCCATGCCTTGGCATGGTCTTAAATGGGACCTTTGCCTTATGGT
66 TGCCATGCCTTAGCATGGTCTTAAATGGGACCTTTGCCTTATGGT
* * * * *
41091743 AACTTATCAATGCCATGTCTTGACATGGTATTACATGATTTACTTATCTTATAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTCGACATGGTATTACATGATATACTTACCTTATAAACCTCACCAAT
*
41091808 TGCCATGCCTTAGCATGGTCTTACATGG
66 TGCCATGCCTTAGCATGGTCTTAAATGG
41091836 TATCCTTAAA
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
108 45 0.58
109 7 0.09
110 26 0.33
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTCGACATGGTATTACATGATATACTTACCTTATAAACCTCACCAAT
TGCCATGCCTTAGCATGGTCTTAAATGGGACCTTTGCCTTATGGT
Found at i:41100986 original size:13 final size:13
Alignment explanation
Indices: 41100968--41100992 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41100958 TATGTGATAT
41100968 GTGTGAAAATTTC
1 GTGTGAAAATTTC
41100981 GTGTGAAAATTT
1 GTGTGAAAATTT
41100993 TATTGTTTGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:41105511 original size:20 final size:21
Alignment explanation
Indices: 41105472--41105511 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
41105462 AAGGGCTATT
*
41105472 TTGTAAAGTTTGTAAAATAAG
1 TTGTAAAGTGTGTAAAATAAG
*
41105493 TTGTAAA-TGTGTGAAATAA
1 TTGTAAAGTGTGTAAAATAA
41105512 TTGAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (21 bp):
TTGTAAAGTGTGTAAAATAAG
Found at i:41106414 original size:49 final size:48
Alignment explanation
Indices: 41106349--41106476 Score: 132
Period size: 49 Copynumber: 2.6 Consensus size: 48
41106339 TGTTGTGCAT
* * * *
41106349 TAGTGTAAGACTTGTCTGGGACATGGCATCAACAC-CGATGGATGAGAG
1 TAGTGTAAGACCTGTCTGGGACATGGCATCAAC-CTCAATAGATGAAAG
* * ** *
41106397 CTAGTGTAAGACCTGTCTAGGACACGGCATTGACCTCAATATATGAAAG
1 -TAGTGTAAGACCTGTCTGGGACATGGCATCAACCTCAATAGATGAAAG
*
41106446 TCAATGTAAGACCTGTCTGGGACATGGCATC
1 T-AGTGTAAGACCTGTCTGGGACATGGCATC
41106477 GACTTTGATG
Statistics
Matches: 64, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
48 2 0.03
49 62 0.97
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.24
Consensus pattern (48 bp):
TAGTGTAAGACCTGTCTGGGACATGGCATCAACCTCAATAGATGAAAG
Found at i:41117525 original size:18 final size:18
Alignment explanation
Indices: 41117502--41117538 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
41117492 AAGGGAACCA
41117502 AAAGTACTAGTAATAACT
1 AAAGTACTAGTAATAACT
41117520 AAAGTACTAGTAATAACT
1 AAAGTACTAGTAATAACT
41117538 A
1 A
41117539 TCTTTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.11, G:0.11, T:0.27
Consensus pattern (18 bp):
AAAGTACTAGTAATAACT
Found at i:41118618 original size:10 final size:10
Alignment explanation
Indices: 41118605--41118646 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
41118595 ATTTGGTCCG
*
41118605 TTTTGTCTCT
1 TTTTGGCTCT
41118615 TTTTGGCTCTT
1 TTTTGGCTC-T
41118626 TTTTGGCTCT
1 TTTTGGCTCT
*
41118636 TTTTGACTCT
1 TTTTGGCTCT
41118646 T
1 T
41118647 GGTGCTCTCC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 19 0.66
11 10 0.34
ACGTcount: A:0.02, C:0.19, G:0.14, T:0.64
Consensus pattern (10 bp):
TTTTGGCTCT
Found at i:41118630 original size:11 final size:11
Alignment explanation
Indices: 41118605--41118639 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
41118595 ATTTGGTCCG
*
41118605 TTTTGTCTC-T
1 TTTTGGCTCTT
41118615 TTTTGGCTCTT
1 TTTTGGCTCTT
41118626 TTTTGGCTCTT
1 TTTTGGCTCTT
41118637 TTT
1 TTT
41118640 GACTCTTGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.00, C:0.17, G:0.14, T:0.69
Consensus pattern (11 bp):
TTTTGGCTCTT
Found at i:41118635 original size:21 final size:21
Alignment explanation
Indices: 41118605--41118646 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
41118595 ATTTGGTCCG
* *
41118605 TTTTGTCTCTTTTTGGCTCTT
1 TTTTGGCTCTTTTTGACTCTT
41118626 TTTTGGCTCTTTTTGACTCTT
1 TTTTGGCTCTTTTTGACTCTT
41118647 GGTGCTCTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.02, C:0.19, G:0.14, T:0.64
Consensus pattern (21 bp):
TTTTGGCTCTTTTTGACTCTT
Found at i:41119492 original size:48 final size:48
Alignment explanation
Indices: 41119362--41119587 Score: 223
Period size: 48 Copynumber: 4.8 Consensus size: 48
41119352 TTATGTATGG
* * * *
41119362 TCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCATTGATATGTA-A
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATAT-AAGA
** * *
41119410 TTTCGTGTAAGACCATAG-CTAGG-C-T---ATTGGCATCGATATAAGA
1 TCCCATGTAAGACCAT-GTCTGGGACATGGCATTGGCATCGATATAAGA
* * * *
41119453 TCCCATGTAAAACCATGTCTGAGACATGGCATTGGCATCGATCTACGA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATAAGA
* **
41119501 TCCAATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATTTGA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATAAGA
* * *
41119549 TCCCATGTAAGACCATATCCGGGATATGGCATTGGCATC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
41119588 CTACTATGTT
Statistics
Matches: 146, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
42 2 0.01
43 28 0.19
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 111 0.76
49 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (48 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATAAGA
Found at i:41131362 original size:19 final size:17
Alignment explanation
Indices: 41131322--41131365 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
41131312 TATATAATAG
*
41131322 AATTTTTTAAATTATTT
1 AATTTTTTAAATTATGT
*
41131339 TATTTTTATAAAATTATGT
1 AATTTTT-T-AAATTATGT
41131358 AATTTTTT
1 AATTTTTT
41131366 TTAATTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 6 0.27
18 2 0.09
19 14 0.64
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
AATTTTTTAAATTATGT
Found at i:41131392 original size:21 final size:21
Alignment explanation
Indices: 41131368--41131407 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
41131358 AATTTTTTTT
*
41131368 AATTTTATAAATATCTTAATC
1 AATTATATAAATATCTTAATC
* *
41131389 AATTATATAATTATTTTAA
1 AATTATATAAATATCTTAA
41131408 ATTATTTATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTATATAAATATCTTAATC
Found at i:41147592 original size:20 final size:20
Alignment explanation
Indices: 41147567--41147604 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41147557 GTTTAGTGGA
41147567 AAAAATTTTCT-AAGTTTTGT
1 AAAAATTTT-TAAAGTTTTGT
41147587 AAAAATTTTTAAAGTTTT
1 AAAAATTTTTAAAGTTTT
41147605 CGGTTTAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (20 bp):
AAAAATTTTTAAAGTTTTGT
Found at i:41153508 original size:14 final size:15
Alignment explanation
Indices: 41153477--41153509 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
41153467 ATTAAATTAT
41153477 TTATTTTGCTATATA
1 TTATTTTGCTATATA
*
41153492 TTATTTTTCTA-ATA
1 TTATTTTGCTATATA
41153506 TTAT
1 TTAT
41153510 ATATTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (15 bp):
TTATTTTGCTATATA
Found at i:41155526 original size:87 final size:87
Alignment explanation
Indices: 41155380--41155617 Score: 329
Period size: 87 Copynumber: 2.7 Consensus size: 87
41155370 TTTGAATTCA
* *
41155380 GTGAAT-TCATCAAGTCCATCTCAATAGGACTACCCAAACTCTGGGATATGAACTCATTAAGAGT
1 GTGAATAT-ATCAAGTTCATCTCAATAGGACCACCCAAACTCTGGGATATGAACTCATTAAGAGT
41155444 AATAAATTCAATCTCACATATTG
65 AATAAATTCAATCTCACATATTG
* *
41155467 GTGAATATATCAAGTTCATCTCAATAGGACCACCCAAACTTTGGGATATGAACTCATTAAGAGAA
1 GTGAATATATCAAGTTCATCTCAATAGGACCACCCAAACTCTGGGATATGAACTCATTAAGAGTA
*
41155532 ATAAATTCAATCTCACATGTTG
66 ATAAATTCAATCTCACATATTG
* * * * * *
41155554 GTGAATATATCAA-ATCTGTTTTAATAGGACCACCCAAA-TCCTAGGATATGAATTCATTAAGAG
1 GTGAATATATCAAGTTC-ATCTCAATAGGACCACCCAAACT-CTGGGATATGAACTCATTAAGAG
41155617 T
64 T
41155618 GAGAACTCAA
Statistics
Matches: 135, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
86 3 0.02
87 131 0.97
88 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.29
Consensus pattern (87 bp):
GTGAATATATCAAGTTCATCTCAATAGGACCACCCAAACTCTGGGATATGAACTCATTAAGAGTA
ATAAATTCAATCTCACATATTG
Found at i:41157949 original size:6 final size:6
Alignment explanation
Indices: 41157939--41157971 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
41157929 CAAGAGACGA
*
41157939 GAATAA GAATAG GAATAG GAATAG GAATAG GAA
1 GAATAG GAATAG GAATAG GAATAG GAATAG GAA
41157972 CGATAAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.30, T:0.15
Consensus pattern (6 bp):
GAATAG
Found at i:41158274 original size:3 final size:3
Alignment explanation
Indices: 41158268--41158296 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
41158258 TGAGGAGGAG
41158268 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
41158297 TTCTGATGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:41160938 original size:12 final size:11
Alignment explanation
Indices: 41160910--41160943 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
41160900 AGTCAAATTA
41160910 ATTATTTTA-T
1 ATTATTTTATT
41160920 ATTATTTTATT
1 ATTATTTTATT
41160931 ACTTATTTTATT
1 A-TTATTTTATT
41160943 A
1 A
41160944 GGAGAGGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.41
11 2 0.09
12 11 0.50
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:41161087 original size:177 final size:176
Alignment explanation
Indices: 41160791--41161142 Score: 623
Period size: 177 Copynumber: 2.0 Consensus size: 176
41160781 CAAAATCTGG
* * *
41160791 TCTCTCTTTCTCTCTCTTTCTGATGCGTTTGAGGTTTACATCATATTTTGTGATTTCTGTGAAGA
1 TCTCTCTTTCTCTCTCTCTCTAATGCATTTGAGGTTTACATCATATTTTGTGATTTCTGTGAAGA
*
41160856 GTTGAAATACTTCATTTCATCTAGGTGAAAGGTTTTATGCTAGAAGTCAAATTAATTATTTTATA
66 GTTGAAATACTTCATTTCATCTAGGTGAAAGGTTTTATGCTAGAAGTCAAATTAATTA-TTTAGA
* *
41160921 TTATTTTATTACTTATTTTATTAGGAGAGGTATTAGGAGTTCAATTC
130 TTAATTTATTACTTATTTTATTAGGAGAAGTATTAGGAGTTCAATTC
41160968 TCTCTCTTTCTCTCTCTCTCTAATGCATTTGAGGTTTACATCATATTTTGTGATTTCTGTGAAGA
1 TCTCTCTTTCTCTCTCTCTCTAATGCATTTGAGGTTTACATCATATTTTGTGATTTCTGTGAAGA
*
41161033 GTTGAAATACTTCATTTCATCTAGGTGAAAGGTTTTATGTTAGAAGTCAAATTAATTATTTAGAT
66 GTTGAAATACTTCATTTCATCTAGGTGAAAGGTTTTATGCTAGAAGTCAAATTAATTATTTAGAT
*
41161098 TAATTTATTACTTATTTTATTAGTAGAAGTATTAGGAGTTCAATT
131 TAATTTATTACTTATTTTATTAGGAGAAGTATTAGGAGTTCAATT
41161143 GAAAGTATCT
Statistics
Matches: 167, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
176 48 0.29
177 119 0.71
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.46
Consensus pattern (176 bp):
TCTCTCTTTCTCTCTCTCTCTAATGCATTTGAGGTTTACATCATATTTTGTGATTTCTGTGAAGA
GTTGAAATACTTCATTTCATCTAGGTGAAAGGTTTTATGCTAGAAGTCAAATTAATTATTTAGAT
TAATTTATTACTTATTTTATTAGGAGAAGTATTAGGAGTTCAATTC
Found at i:41168811 original size:14 final size:15
Alignment explanation
Indices: 41168792--41168820 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41168782 GTAAATACTT
41168792 CTATTTT-GAGAAGA
1 CTATTTTGGAGAAGA
41168806 CTATTTTGGAGAAGA
1 CTATTTTGGAGAAGA
41168821 AAATACTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (15 bp):
CTATTTTGGAGAAGA
Found at i:41173775 original size:23 final size:22
Alignment explanation
Indices: 41173724--41173775 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
41173714 CCTCGTCTTT
*
41173724 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
41173746 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
41173769 TTCTTTT
1 TTCTTTT
41173776 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:41177243 original size:33 final size:33
Alignment explanation
Indices: 41177205--41177334 Score: 233
Period size: 33 Copynumber: 3.9 Consensus size: 33
41177195 GACTGAGTGG
* *
41177205 GAGTGTTTGGTTGTTGGACAGGAGCTAGAATGT
1 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATGT
*
41177238 GAGTGTTTGGTTGCTGGAAAGGAGCTGGAATGT
1 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATGT
41177271 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATGT
1 GAGTGTTTGGTTGCTGGACAGGAGCTGGAATGT
41177304 GAGTGTTTGGTTGCTGGACAGGAGCTGGAAT
1 GAGTGTTTGGTTGCTGGACAGGAGCTGGAAT
41177335 CTCAAGAAGA
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 93 1.00
ACGTcount: A:0.20, C:0.08, G:0.42, T:0.31
Consensus pattern (33 bp):
GAGTGTTTGGTTGCTGGACAGGAGCTGGAATGT
Found at i:41179678 original size:19 final size:19
Alignment explanation
Indices: 41179654--41179694 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
41179644 CTTCCCTTCA
41179654 AGAATGTACGAACCAGTTG
1 AGAATGTACGAACCAGTTG
41179673 AGAATGTACGAACCAGTTG
1 AGAATGTACGAACCAGTTG
41179692 AGA
1 AGA
41179695 CTAATTCACG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.15, G:0.27, T:0.20
Consensus pattern (19 bp):
AGAATGTACGAACCAGTTG
Found at i:41186401 original size:23 final size:23
Alignment explanation
Indices: 41186366--41186440 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
41186356 AATTACTAAT
* * * *
41186366 TTGCACTGAAGTGTCACTTTCAA
1 TTGCACCGGAGTGCCACTGTCAA
* *
41186389 TTGCACCGGAGTGCCTCTGTCAG
1 TTGCACCGGAGTGCCACTGTCAA
41186412 TTGCACCGGAGTGCCA-TGATCAA
1 TTGCACCGGAGTGCCACTG-TCAA
41186435 TTGCAC
1 TTGCAC
41186441 AGAAATTTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
22 2 0.05
23 41 0.95
ACGTcount: A:0.21, C:0.27, G:0.24, T:0.28
Consensus pattern (23 bp):
TTGCACCGGAGTGCCACTGTCAA
Found at i:41191907 original size:26 final size:26
Alignment explanation
Indices: 41191871--41191924 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
41191861 CTAGTTCTAG
* *
41191871 AATGATTCAAAAGTCTGCTGAGTCAA
1 AATGATTCAAAAGTCTACTAAGTCAA
41191897 AATGATTCAAAAGTCTACTAAGTCAA
1 AATGATTCAAAAGTCTACTAAGTCAA
41191923 AA
1 AA
41191925 GCTGGATAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (26 bp):
AATGATTCAAAAGTCTACTAAGTCAA
Found at i:41192348 original size:27 final size:28
Alignment explanation
Indices: 41192288--41192351 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
41192278 TGGTTTTCTT
* *
41192288 ACACAAGTTGTGATACTTGAATTTGCTC
1 ACACAAGCTGTGATACTTGAAGTTGCTC
*
41192316 ACACAAGCTGTGATATTTG-AGTTGCTC
1 ACACAAGCTGTGATACTTGAAGTTGCTC
41192343 ACACAAGCT
1 ACACAAGCT
41192352 ATAGGTTAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 16 0.48
28 17 0.52
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (28 bp):
ACACAAGCTGTGATACTTGAAGTTGCTC
Found at i:41193507 original size:10 final size:10
Alignment explanation
Indices: 41193484--41193523 Score: 73
Period size: 10 Copynumber: 4.1 Consensus size: 10
41193474 TAATGAAGAA
41193484 AACACTTTTT
1 AACACTTTTT
41193494 -ACACTTTTT
1 AACACTTTTT
41193503 AACACTTTTT
1 AACACTTTTT
41193513 AACACTTTTT
1 AACACTTTTT
41193523 A
1 A
41193524 CCTTATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 9 0.31
10 20 0.69
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (10 bp):
AACACTTTTT
Found at i:41193508 original size:19 final size:20
Alignment explanation
Indices: 41193484--41193523 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
41193474 TAATGAAGAA
41193484 AACACTTTTT-ACACTTTTT
1 AACACTTTTTAACACTTTTT
41193503 AACACTTTTTAACACTTTTT
1 AACACTTTTTAACACTTTTT
41193523 A
1 A
41193524 CCTTATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (20 bp):
AACACTTTTTAACACTTTTT
Found at i:41195669 original size:20 final size:21
Alignment explanation
Indices: 41195644--41195687 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
41195634 TAGTTCAACG
*
41195644 GGTAAGAAAAGG-AATGGCAT
1 GGTAAGAAAAGGAAATGGAAT
*
41195664 GGTAAGTAAAGGAAATGGAAT
1 GGTAAGAAAAGGAAATGGAAT
41195685 GGT
1 GGT
41195688 TCATGATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.43, C:0.02, G:0.36, T:0.18
Consensus pattern (21 bp):
GGTAAGAAAAGGAAATGGAAT
Found at i:41204301 original size:23 final size:23
Alignment explanation
Indices: 41204270--41204318 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
41204260 AACGTAAGTA
*
41204270 AAAATGATGCATTATTTATATAC
1 AAAACGATGCATTATTTATATAC
41204293 AAAACGATGCATTATTTATATAC
1 AAAACGATGCATTATTTATATAC
41204316 AAA
1 AAA
41204319 CATATCTCGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (23 bp):
AAAACGATGCATTATTTATATAC
Found at i:41208053 original size:40 final size:40
Alignment explanation
Indices: 41207998--41208178 Score: 233
Period size: 40 Copynumber: 4.5 Consensus size: 40
41207988 TATTCGGATG
** *
41207998 ATATCCGGGCTAAGTCCCGAAGGCATTTGTG-TAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCT-AGTGACT
41208038 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
*
41208078 ATATCCGGGCTAAGTCTCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
* * ** *
41208118 ATATTCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAG-TGACT
*
41208158 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
41208179 ATACTTGGGT
Statistics
Matches: 126, Mismatches: 13, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 13 0.10
40 110 0.87
41 3 0.02
ACGTcount: A:0.25, C:0.23, G:0.25, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
Found at i:41211791 original size:43 final size:42
Alignment explanation
Indices: 41211669--41211791 Score: 131
Period size: 43 Copynumber: 2.9 Consensus size: 42
41211659 TACCGTACCA
* * * **
41211669 ATGCCATATCCCAGATATGGTCTTACATGTAATCTTGTATCG
1 ATGCCATATACCAGATATGGTCTTACACGAAATCTCATATCG
* *
41211711 ATGCCAATAGACCA-ACTATGGTCTTACACGAAGTCTCATATCG
1 ATGCC-ATATACCAGA-TATGGTCTTACACGAAATCTCATATCG
* *
41211754 ATGCCATATTCCAGATATAGTCTTACACGCAAATCTCA
1 ATGCCATATACCAGATATGGTCTTACACG-AAATCTCA
41211792 GTGACCCTAA
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
42 25 0.38
43 41 0.62
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (42 bp):
ATGCCATATACCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:41219166 original size:43 final size:43
Alignment explanation
Indices: 41219043--41219200 Score: 198
Period size: 43 Copynumber: 3.7 Consensus size: 43
41219033 ATGTGTTATT
* * *
41219043 GTGTAAAACCACGTCTGGGACGTTGGCATCGACT-TATGATTTGC
1 GTGTAAGACCACGTCTGGGACGTTGGCATCGA-TATTTGA-TTAC
* *
41219087 GTGTAAGACCACGTCTGGGACGTTGGGATCG-TATTTGATTCC
1 GTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTAC
41219129 GTGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATTTGATTAC
1 GTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATTTGATTAC
*
41219172 ATGTAAGACCACGTCTGGGACGTTGGCAT
1 GTGTAAGACCACGTCTGGGACGTTGGCAT
41219201 TTATGAGTTT
Statistics
Matches: 101, Mismatches: 7, Indels: 13
0.83 0.06 0.11
Matches are distributed among these distances:
41 1 0.01
42 31 0.31
43 39 0.39
44 30 0.30
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (43 bp):
GTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTAC
Found at i:41231233 original size:51 final size:51
Alignment explanation
Indices: 41231152--41231295 Score: 252
Period size: 51 Copynumber: 2.8 Consensus size: 51
41231142 GTGGCCTTCA
*
41231152 CCTTCACATAATACCACACTTGTGTCCAAAGCTATTATATTCACAAAGTGG
1 CCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAAGTGG
*
41231203 CCTTCACATAGTACCACACTTGTGTACAAAGCTATTATATTCACAAAGTGG
1 CCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAAGTGG
* *
41231254 CCTTCACATAGTACCACATTTGTGTCCAAAGCTATTTTATTC
1 CCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTC
41231296 CTAAGGTTCA
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 88 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (51 bp):
CCTTCACATAGTACCACACTTGTGTCCAAAGCTATTATATTCACAAAGTGG
Found at i:41231356 original size:28 final size:27
Alignment explanation
Indices: 41231319--41231410 Score: 129
Period size: 28 Copynumber: 3.4 Consensus size: 27
41231309 GGGAAATTTC
41231319 TCACTTAGCACAATGCCATGGACTTATT
1 TCACTTAGCAC-ATGCCATGGACTTATT
41231347 TCACTTAGCACATCGCCATGGACTTATT
1 TCACTTAGCACAT-GCCATGGACTTATT
41231375 TCACTTAG---ATGCCATGGTA-TTATT
1 TCACTTAGCACATGCCATGG-ACTTATT
41231399 TCACTTAGCACA
1 TCACTTAGCACA
41231411 ATGTCATATC
Statistics
Matches: 59, Mismatches: 0, Indels: 11
0.84 0.00 0.16
Matches are distributed among these distances:
24 20 0.34
25 3 0.05
27 3 0.05
28 33 0.56
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (27 bp):
TCACTTAGCACATGCCATGGACTTATT
Found at i:41232855 original size:46 final size:46
Alignment explanation
Indices: 41232710--41232973 Score: 186
Period size: 47 Copynumber: 5.7 Consensus size: 46
41232700 TGTGTGAGCT
*
41232710 AGTGTAAGA-CATGTCTA-GGACATGCATCGGC-CACATTATG-AGAGCC
1 AGTGTAAGACCATGTC-AGGGACATGCATCGGCTCA-A-GATGTA-AGCC
* * * * ** *
41232756 AGTATAATACCATGTCCGGGACATGGCATCGG--CATTGATACAAGTGCT
1 AGTGTAAGACCATGTCAGGGACAT-GCATCGGCTCA-AGATGTAA--GCC
* * *
41232804 AGTGTAAGA-TATGTCTGGGACATGCATCGGTCTCGAGATGTAAGCC
1 AGTGTAAGACCATGTCAGGGACATGCATCGG-CTCAAGATGTAAGCC
* *
41232850 AGTGTAAGA-CATATCAGGGACATGCATCGGCTACAAGATG-ATAGTC
1 AGTGTAAGACCATGTCAGGGACATGCATCGGCT-CAAGATGTA-AGCC
* * * *
41232896 AGTGTAAGACCATGTCAGGGACACGGCATCGACTTAAGATGTGAGCC
1 AGTGTAAGACCATGTCAGGGACA-TGCATCGGCTCAAGATGTAAGCC
*
41232943 AGTGTAAGACCATGTCTGGGACATGGCATCG
1 AGTGTAAGACCATGTCAGGGACAT-GCATCG
41232974 ACACCTTACC
Statistics
Matches: 173, Mismatches: 30, Indels: 29
0.75 0.13 0.12
Matches are distributed among these distances:
45 3 0.02
46 64 0.37
47 76 0.44
48 29 0.17
49 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACCATGTCAGGGACATGCATCGGCTCAAGATGTAAGCC
Found at i:41232962 original size:140 final size:141
Alignment explanation
Indices: 41232710--41232973 Score: 322
Period size: 140 Copynumber: 1.9 Consensus size: 141
41232700 TGTGTGAGCT
* ** * *
41232710 AGTGTAAGACATGTCTAGGACATGCATCGGCCACATTATGAGAGCCAGTATAATACCATGTCCGG
1 AGTGTAAGACATATCTAGGACATGCATCGGCCACAAGATGAGAGCCAGTATAAGACCATGTCAGG
* * * *
41232775 GACATGGCATCGGCATTGATACAAGTGCTAGTGTAAGATATGTCTGGGACAT-GCATCGGTCTCG
66 GACACGGCATCGACATTGATACAAGTGCCAGTGTAAGACATGTCTGGGACATGGCATCGGTCTCG
41232839 AGATGTAAGCC
131 AGATGTAAGCC
* * * *
41232850 AGTGTAAGACATATC-AGGGACATGCATCGGCTACAAGATGATAGTCAGTGTAAGACCATGTCAG
1 AGTGTAAGACATATCTA-GGACATGCATCGGCCACAAGATGAGAGCCAGTATAAGACCATGTCAG
* *
41232914 GGACACGGCATCGAC-TT-A-AGATGTGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCG
65 GGACACGGCATCGACATTGATACAAGT--GCCAGTGTAAGA-CATGTCTGGGACATGGCATCG
41232974 ACACCTTACC
Statistics
Matches: 104, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
137 4 0.04
138 1 0.01
139 14 0.13
140 79 0.76
141 6 0.06
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.23
Consensus pattern (141 bp):
AGTGTAAGACATATCTAGGACATGCATCGGCCACAAGATGAGAGCCAGTATAAGACCATGTCAGG
GACACGGCATCGACATTGATACAAGTGCCAGTGTAAGACATGTCTGGGACATGGCATCGGTCTCG
AGATGTAAGCC
Found at i:41239015 original size:40 final size:39
Alignment explanation
Indices: 41238978--41239200 Score: 256
Period size: 40 Copynumber: 5.7 Consensus size: 39
41238968 GCTACTCGTT
* * *
41238978 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAT-TAGTAACTCGCA
41239018 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGA-TTAGTAACTCGCA
41239058 CAAATGCCTTCGGGACTTAACCCGGATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTAGTAACTCGCA
** *
41239097 CAAATGCCTTC-GGATCTTAGTCCGGATTAGT-ACTCGTA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTAGTAACTCGCA
** * * *
41239135 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGAT-TAGTAAC-TCGCA
*
41239176 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
41239201 CATCATTCAA
Statistics
Matches: 167, Mismatches: 10, Indels: 12
0.88 0.05 0.06
Matches are distributed among these distances:
38 36 0.22
39 41 0.25
40 79 0.47
41 11 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAACCCGGATTAGTAACTCGCA
Found at i:41239099 original size:79 final size:78
Alignment explanation
Indices: 41238959--41239200 Score: 285
Period size: 79 Copynumber: 3.1 Consensus size: 78
41238949 CGGAATTTAA
** * *
41238959 CCGGATATAGCTACTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATG
1 CCGGAT-TAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
41239024 CCTTCGGGACTTAAC
64 CCTTCGGGACTTAGC
*
41239039 CCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT-TAGTAACTCGCACAAATG
1 CCGGA-TTAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
41239103 CCTTC-GGATCTTAGT
64 CCTTCGGGA-CTTAGC
* * * * *
41239118 CCGGATTAGTACTCGTACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-G
1 CCGGATTAGTACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCACAAATG
41239181 CCTTCGGGACTTAGC
64 CCTTCGGGACTTAGC
41239196 CCGGA
1 CCGGA
41239201 CATCATTCAA
Statistics
Matches: 141, Mismatches: 14, Indels: 16
0.82 0.08 0.09
Matches are distributed among these distances:
76 3 0.02
77 27 0.19
78 29 0.21
79 44 0.31
80 37 0.26
81 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CCGGATTAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCC
TTCGGGACTTAGC
Found at i:41239185 original size:117 final size:119
Alignment explanation
Indices: 41238978--41239200 Score: 285
Period size: 117 Copynumber: 1.9 Consensus size: 119
41238968 GCTACTCGTT
*
41238978 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
41239043 ATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTAGTAACTCGCA
66 ATATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGATTAGTAACTCGCA
* * * **
41239097 CAAATGCCTTC-GGATCTTAGTCCGGAT-TAGT-ACTCGTACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGA-CATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* * *
41239158 GGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
64 GGATATAGTAAC-TAGCACAAATGCCTTCGGGACTTAACCCGGA
41239201 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
116 3 0.03
117 52 0.58
118 15 0.17
119 20 0.22
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (119 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGATTAGTAACTCGCA
Found at i:41247004 original size:40 final size:39
Alignment explanation
Indices: 41246967--41247189 Score: 256
Period size: 40 Copynumber: 5.7 Consensus size: 39
41246957 GCTACTCGTT
* * *
41246967 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAT-TAGTAACTCGCA
41247007 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGA-TTAGTAACTCGCA
41247047 CAAATGCCTTCGGGACTTAACCCGGATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTAGTAACTCGCA
** *
41247086 CAAATGCCTTC-GGATCTTAGTCCGGATTAGT-ACTCGTA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTAGTAACTCGCA
** * * *
41247124 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGAT-TAGTAAC-TCGCA
*
41247165 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
41247190 CATCATTCAA
Statistics
Matches: 167, Mismatches: 10, Indels: 12
0.88 0.05 0.06
Matches are distributed among these distances:
38 36 0.22
39 41 0.25
40 79 0.47
41 11 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAACCCGGATTAGTAACTCGCA
Found at i:41247088 original size:79 final size:78
Alignment explanation
Indices: 41246948--41247189 Score: 285
Period size: 79 Copynumber: 3.1 Consensus size: 78
41246938 CGGAATTTAA
** * *
41246948 CCGGATATAGCTACTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATG
1 CCGGAT-TAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
41247013 CCTTCGGGACTTAAC
64 CCTTCGGGACTTAGC
*
41247028 CCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT-TAGTAACTCGCACAAATG
1 CCGGA-TTAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
41247092 CCTTC-GGATCTTAGT
64 CCTTCGGGA-CTTAGC
* * * * *
41247107 CCGGATTAGTACTCGTACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAA-G
1 CCGGATTAGTACTCGCACAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCACAAATG
41247170 CCTTCGGGACTTAGC
64 CCTTCGGGACTTAGC
41247185 CCGGA
1 CCGGA
41247190 CATCATTCAA
Statistics
Matches: 141, Mismatches: 14, Indels: 16
0.82 0.08 0.09
Matches are distributed among these distances:
76 3 0.02
77 27 0.19
78 29 0.21
79 44 0.31
80 37 0.26
81 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CCGGATTAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCC
TTCGGGACTTAGC
Found at i:41247174 original size:117 final size:119
Alignment explanation
Indices: 41246967--41247189 Score: 285
Period size: 117 Copynumber: 1.9 Consensus size: 119
41246957 GCTACTCGTT
*
41246967 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
41247032 ATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTAGTAACTCGCA
66 ATATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGATTAGTAACTCGCA
* * * **
41247086 CAAATGCCTTC-GGATCTTAGTCCGGAT-TAGT-ACTCGTACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGA-CATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
* * *
41247147 GGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
64 GGATATAGTAAC-TAGCACAAATGCCTTCGGGACTTAACCCGGA
41247190 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
116 3 0.03
117 52 0.58
118 15 0.17
119 20 0.22
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (119 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTAGCACAAATGCCTTCGGGACTTAACCCGGATTAGTAACTCGCA
Found at i:41252454 original size:760 final size:760
Alignment explanation
Indices: 41250966--41252485 Score: 2670
Period size: 760 Copynumber: 2.0 Consensus size: 760
41250956 TGAAAACTAT
*
41250966 TGTTATATTCAAATTCAATCAATGGCAAATACTTTTCCCACGTACCTTTGAACTTAATAATACAA
1 TGTTATATTCAAATTAAATCAATGGCAAATACTTTTCCCACGTACCTTTGAACTTAATAATACAA
41251031 CATCTCAACATATCCTCTAGTATCTGAATAATTCGCTCAGATTGACCATCCGTCTGCGGGTGAAA
66 CATCTCAACATATCCTCTAGTATCTGAATAATTCGCTCAGATTGACCATCCGTCTGCGGGTGAAA
* * *
41251096 CCCGATACTAAAATGTAACTTTGTACCCAGTGCATCTTGCAATTTCTTCCAAAATCATGATGTAA
131 CCAGATACTAAAATGAAACTTAGTACCCAGTGCATCTTGCAATTTCTTCCAAAATCATGATGTAA
*
41251161 ACCTCGGATCTCTATCCAAAACAATAGAAATAGGTACTCCGTGTAATCTCACAACCTCAAAGATA
196 ACCACGGATCTCTATCCAAAACAATAGAAATAGGTACTCCGTGTAATCTCACAACCTCAAAGATA
* * *
41251226 TACGATTCAGCTAACTTTTCTAATGAATAGTTTATTCGTACTGGAATGAAATGAGATGATTTTGT
261 TACGACTCAGCTAACTTTTCTAATGAATAGTCTATTCGTACTGGAATGAAATGAGATAATTTTGT
* *
41251291 CAACAAGTCAACAACAACCCAAATCGCATCTTTCTTTCTTGGAGATAGGGGCAAACCTGAAACAA
326 CAACAAGTCAACAACAACCCAAATCGCATCTTTCTTTCTCGGAGATAGGGGCAAACCCGAAACAA
*
41251356 AATCCATAGTTACTCTATCCCATTTCCACTCAGGAATCATAACCGGCTGCAATAAACCAAACGGT
391 AATCCATAGTTACTCTATCCCATTTCCACTCAGGAATCATAACCAGCTGCAATAAACCAAACGGT
* *
41251421 ACCTGATGCTCAGCTTTAACTTATTAACAAATCAAACATTTTGAAACAAATTCCAAAATATCATG
456 ACCTGATGCTCAGCTTTAACTTATTAACAAATCAAACATTTCGAAACAAATTCCAAAATATCACG
* *
41251486 TTTCATGCCATTCCACCAATAAAGCTGTTTCAATTCATTATACATTTTCTTCAATAGAGTCGCAA
521 TTTCATGCCATTCCACCAATAAAGCTGTTTCAAGTCATTATACATTTTCTTCAAGAGAGTCGCAA
*
41251551 TCATTGAAAAGCCTTTCACAAAACATCTATAATAACCAGCCAGTCCTAGAAAACTATAGACTTCA
586 TCATTGAAAAACCTTTCACAAAACATCTATAATAACCAGCCAGTCCTAGAAAACTATAGACTTCA
** * *
41251616 GATACATTTCTTTGAGGCTTCCAATCCATTTTTGCAGAAATCTTGTTTGGATCAACTCAAATACC
651 GATACATTTCTCCGAGGCTTCCAATCCATTATTGCAGAAATCTTGTTCGGATCAACTCAAATACC
* *
41251681 TGATGTGACACAATATGCCACAGAAAACCAACTTCACGCAACCAA
716 CGATGTAACACAATATGCCACAGAAAACCAACTTCACGCAACCAA
*
41251726 TGTTATATTCAAATTAAATCAATGGCAAATACTTTTCCCATGTACCTTTGAACTTAATAATACAA
1 TGTTATATTCAAATTAAATCAATGGCAAATACTTTTCCCACGTACCTTTGAACTTAATAATACAA
*
41251791 CATCTCAACATATCCTCTAGTATCTGAATAATTCGCTCGGATTGACCATCCGTCTGCGGGTGAAA
66 CATCTCAACATATCCTCTAGTATCTGAATAATTCGCTCAGATTGACCATCCGTCTGCGGGTGAAA
*
41251856 CGCAG-TACTAAAATGAAACTTAGTACCCAGTGCATCTTGCAGTTTCTTCCAAAATCATGATGTA
131 C-CAGATACTAAAATGAAACTTAGTACCCAGTGCATCTTGCAATTTCTTCCAAAATCATGATGTA
*
41251920 AACCACGGATCTCTATCCAAAACAATAGAAATAGGTACTCCGTGTAATCTCACAACCTCAGAGAT
195 AACCACGGATCTCTATCCAAAACAATAGAAATAGGTACTCCGTGTAATCTCACAACCTCAAAGAT
* *
41251985 ATACGACTCAGCTAACTTTTCTAATGAATAGTCTATTCGTACTGGAATGACATGAGCTAATTTTG
260 ATACGACTCAGCTAACTTTTCTAATGAATAGTCTATTCGTACTGGAATGAAATGAGATAATTTTG
41252050 TCAACAAGTCAACAACAACCCAAATCGCATCTTTCTTTCTCGGAGATAGGGGCAAACCCGAAACA
325 TCAACAAGTCAACAACAACCCAAATCGCATCTTTCTTTCTCGGAGATAGGGGCAAACCCGAAACA
*
41252115 AAATCCATAGTTACTCTATCCCATTTCCACTCAGGAATCATAATCAGCTGCAATAAACCAAACGG
390 AAATCCATAGTTACTCTATCCCATTTCCACTCAGGAATCATAACCAGCTGCAATAAACCAAACGG
41252180 TACCTGATGCTCAGCTTTAACTTATTAACAAATCAAACATTTCGAAACAAATTCCAAAATATCAC
455 TACCTGATGCTCAGCTTTAACTTATTAACAAATCAAACATTTCGAAACAAATTCCAAAATATCAC
*
41252245 GTTTCATGCCATTCCACCAATAAAGTTGTTTCAAGTCATTATACA-TTTCTTCAACGA-AGTCGC
520 GTTTCATGCCATTCCACCAATAAAGCTGTTTCAAGTCATTATACATTTTCTTCAA-GAGAGTCGC
* *
41252308 AATCATTGAAAAACCTTTCACAAAACGTCTATAATAACCAGCCAGT-CTCAGAAAACTGTAGACT
584 AATCATTGAAAAACCTTTCACAAAACATCTATAATAACCAGCCAGTCCT-AGAAAACTATAGACT
* *
41252372 TCAGATACATTTCTCCGAGGCTTCCAATCCATTATTGTAGAAATCTTGTTCGGATCAACTCGAAT
648 TCAGATACATTTCTCCGAGGCTTCCAATCCATTATTGCAGAAATCTTGTTCGGATCAACTCAAAT
41252437 ACCCGATGCTAACACAATATGCCACAGAAAACCAACTTCACGCAACCAA
713 ACCCGATG-TAACACAATATGCCACAGAAAACCAACTTCACGCAACCAA
41252486 AATTCACATT
Statistics
Matches: 722, Mismatches: 34, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
758 2 0.00
759 139 0.19
760 579 0.80
761 2 0.00
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.29
Consensus pattern (760 bp):
TGTTATATTCAAATTAAATCAATGGCAAATACTTTTCCCACGTACCTTTGAACTTAATAATACAA
CATCTCAACATATCCTCTAGTATCTGAATAATTCGCTCAGATTGACCATCCGTCTGCGGGTGAAA
CCAGATACTAAAATGAAACTTAGTACCCAGTGCATCTTGCAATTTCTTCCAAAATCATGATGTAA
ACCACGGATCTCTATCCAAAACAATAGAAATAGGTACTCCGTGTAATCTCACAACCTCAAAGATA
TACGACTCAGCTAACTTTTCTAATGAATAGTCTATTCGTACTGGAATGAAATGAGATAATTTTGT
CAACAAGTCAACAACAACCCAAATCGCATCTTTCTTTCTCGGAGATAGGGGCAAACCCGAAACAA
AATCCATAGTTACTCTATCCCATTTCCACTCAGGAATCATAACCAGCTGCAATAAACCAAACGGT
ACCTGATGCTCAGCTTTAACTTATTAACAAATCAAACATTTCGAAACAAATTCCAAAATATCACG
TTTCATGCCATTCCACCAATAAAGCTGTTTCAAGTCATTATACATTTTCTTCAAGAGAGTCGCAA
TCATTGAAAAACCTTTCACAAAACATCTATAATAACCAGCCAGTCCTAGAAAACTATAGACTTCA
GATACATTTCTCCGAGGCTTCCAATCCATTATTGCAGAAATCTTGTTCGGATCAACTCAAATACC
CGATGTAACACAATATGCCACAGAAAACCAACTTCACGCAACCAA
Found at i:41254654 original size:43 final size:43
Alignment explanation
Indices: 41254607--41254689 Score: 105
Period size: 43 Copynumber: 1.9 Consensus size: 43
41254597 ATGCGATTAC
* *
41254607 GTGTAAGACCAT-GCCTAGGAAATTGGCATCGTTATTTGATTTT
1 GTGTAAGACCATAG-CTAGGAAATTGGCATCGATATGTGATTTT
* **
41254650 GTGTAATACCATAGCTAGGCTATTGGCATCGATATGTGAT
1 GTGTAAGACCATAGCTAGGAAATTGGCATCGATATGTGAT
41254690 AACATGTAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 33 0.97
44 1 0.03
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (43 bp):
GTGTAAGACCATAGCTAGGAAATTGGCATCGATATGTGATTTT
Found at i:41258203 original size:20 final size:21
Alignment explanation
Indices: 41258174--41258221 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
41258164 AAATTTGTGC
* *
41258174 AATTTACTACCATAAA-TTCT
1 AATTTTCTACAATAAATTTCT
*
41258194 CATTTTCTACAATAAATTTCT
1 AATTTTCTACAATAAATTTCT
41258215 AATTTTC
1 AATTTTC
41258222 AGCATACAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTTTCTACAATAAATTTCT
Found at i:41259141 original size:39 final size:40
Alignment explanation
Indices: 41259089--41259172 Score: 125
Period size: 39 Copynumber: 2.1 Consensus size: 40
41259079 CGTTTGAATG
41259089 AAAAACGCCACTAAAGAACGAGCATTAGCGGCGC-TTTTT
1 AAAAACGCCACTAAAGAACGAGCATTAGCGGCGCTTTTTT
* ** *
41259128 AAAAACGCTACTAAAGATTGAGTATTAGCGGCGCTTTTTT
1 AAAAACGCCACTAAAGAACGAGCATTAGCGGCGCTTTTTT
41259168 AAAAA
1 AAAAA
41259173 TACCGCTCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 30 0.75
40 10 0.25
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (40 bp):
AAAAACGCCACTAAAGAACGAGCATTAGCGGCGCTTTTTT
Found at i:41259438 original size:126 final size:126
Alignment explanation
Indices: 41259258--41259605 Score: 536
Period size: 126 Copynumber: 2.8 Consensus size: 126
41259248 CACAACACCG
** * * *
41259258 TCGTTTTGTATTGAGCCTTTGGTGGCTTTAGCTGCGCTTTTTAAAAACGCCGCTAAAGATCGAGT
1 TCGTTTTGTATTGAGATTTTAGTGGCTTTAGCAGCGCTTTTTAAAAACGCCGCTAAAGATCAAGT
**
41259323 ATTAGCAGCGCTTTTTAGAAAACATTGCTAATGCTTGGCAAAATAATTTTGTAAAACGCCA
66 ATTAGCAGCGCTTTTTAGAAAACACCGCTAATGCTTGGCAAAATAATTTTGTAAAACGCCA
* * **
41259384 TTGTTTTGTATTGAGATTTTAGTGGCTTTAGCGGCGCTTTTTAAAAACAACGCTAAAGATCAAGT
1 TCGTTTTGTATTGAGATTTTAGTGGCTTTAGCAGCGCTTTTTAAAAACGCCGCTAAAGATCAAGT
*
41259449 ATTAGCGGCGCTTTTTAGAAAACACCGCTAATGCTTGGCAAAATAATTTTGTAAAACGCCA
66 ATTAGCAGCGCTTTTTAGAAAACACCGCTAATGCTTGGCAAAATAATTTTGTAAAACGCCA
41259510 TCGTTTTGTATTGAGATTTTAGTGGCTTTAGCAGCGCTTTTTAAAAACGCCGCTAAAGATCAAGT
1 TCGTTTTGTATTGAGATTTTAGTGGCTTTAGCAGCGCTTTTTAAAAACGCCGCTAAAGATCAAGT
* * *
41259575 ATTAACGGCACTTTTTTA-AGAAACACCGCTA
66 ATTAGCAGCGC-TTTTTAGA-AAACACCGCTA
41259606 TATGTACACC
Statistics
Matches: 203, Mismatches: 17, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
126 186 0.92
127 17 0.08
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (126 bp):
TCGTTTTGTATTGAGATTTTAGTGGCTTTAGCAGCGCTTTTTAAAAACGCCGCTAAAGATCAAGT
ATTAGCAGCGCTTTTTAGAAAACACCGCTAATGCTTGGCAAAATAATTTTGTAAAACGCCA
Found at i:41259659 original size:40 final size:38
Alignment explanation
Indices: 41259535--41259681 Score: 107
Period size: 40 Copynumber: 3.7 Consensus size: 38
41259525 ATTTTAGTGG
* * *
41259535 CTTTAGCAGCGCTTTTT-AAAAACGCCGCTAAAGATCAA
1 CTTTAGCAGCACTTTTTAAAAAACGCCGCTAATG-TCAT
* * * * * *
41259573 GTATTAACGGCACTTTTTTAAGAAACACCGCTATATGTACAC
1 CT-TTAGCAGCAC-TTTTTAAAAAACGCCGCTA-ATGT-CAT
*
41259615 CTTTAGCGGCACTTTTTAAAAAACGCCGCTAATGCTCGAT
1 CTTTAGCAGCACTTTTTAAAAAACGCCGCTAATG-TC-AT
** *
41259655 CTTTAGCAGCGTTTTTTGAAAAACGCC
1 CTTTAGCAGCACTTTTTAAAAAACGCC
41259682 ACAAAAAATG
Statistics
Matches: 85, Mismatches: 17, Indels: 12
0.75 0.15 0.11
Matches are distributed among these distances:
38 1 0.01
39 11 0.13
40 47 0.55
41 21 0.25
42 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (38 bp):
CTTTAGCAGCACTTTTTAAAAAACGCCGCTAATGTCAT
Found at i:41259916 original size:15 final size:15
Alignment explanation
Indices: 41259896--41259943 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
41259886 ACTATTGTAA
41259896 GGTTTATAGATTATG
1 GGTTTATAGATTATG
41259911 GGTTTA-AGGATTAT-
1 GGTTTATA-GATTATG
* *
41259925 GGTTTATGGTTTATG
1 GGTTTATAGATTATG
41259940 GGTT
1 GGTT
41259944 AAGGGTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.21, C:0.00, G:0.31, T:0.48
Consensus pattern (15 bp):
GGTTTATAGATTATG
Found at i:41259918 original size:22 final size:22
Alignment explanation
Indices: 41259893--41260002 Score: 84
Period size: 22 Copynumber: 5.1 Consensus size: 22
41259883 GTTACTATTG
*
41259893 TAAGGTTTATA-GATTATGGGTT
1 TAAGGTTTATAGGGTTA-GGGTT
* * *
41259915 TAAGGATTAT-GGTTTATGGTT
1 TAAGGTTTATAGGGTTAGGGTT
* *
41259936 TATGGGTTA-AGGGTTAGGGTT
1 TAAGGTTTATAGGGTTAGGGTT
* * *
41259957 TAAGTTTTAGATGGTTAGGGTT
1 TAAGGTTTATAGGGTTAGGGTT
*
41259979 TAAGGTTTA-GGGGTTAAGGGTT
1 TAAGGTTTATAGGGTT-AGGGTT
41260001 TA
1 TA
41260003 TGTTTTATGG
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
21 30 0.43
22 40 0.57
ACGTcount: A:0.24, C:0.00, G:0.34, T:0.43
Consensus pattern (22 bp):
TAAGGTTTATAGGGTTAGGGTT
Found at i:41259933 original size:7 final size:7
Alignment explanation
Indices: 41259896--41260026 Score: 66
Period size: 7 Copynumber: 18.3 Consensus size: 7
41259886 ACTATTGTAA
41259896 GGTTTAT
1 GGTTTAT
* *
41259903 AGATTAT
1 GGTTTAT
*
41259910 GGGTTTAA
1 -GGTTTAT
*
41259918 GGATTAT
1 GGTTTAT
41259925 GGTTTAT
1 GGTTTAT
41259932 GGTTTAT
1 GGTTTAT
* *
41259939 GGGTTAA
1 GGTTTAT
* *
41259946 GGGTTAG
1 GGTTTAT
*
41259953 GGTTTAA
1 GGTTTAT
*
41259960 GTTTTAGAT
1 GGTTT--AT
*
41259969 GG-TTAG
1 GGTTTAT
*
41259975 GGTTTAA
1 GGTTTAT
*
41259982 GGTTTAGG
1 GGTTTA-T
* *
41259990 GGTTAAG
1 GGTTTAT
41259997 GGTTTAT
1 GGTTTAT
*
41260004 GTTTTAT
1 GGTTTAT
*
41260011 GGTTTAA
1 GGTTTAT
41260018 GGTTTAT
1 GGTTTAT
41260025 GG
1 GG
41260027 GTTAGGAGTT
Statistics
Matches: 93, Mismatches: 26, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
6 3 0.03
7 77 0.83
8 11 0.12
9 2 0.02
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (7 bp):
GGTTTAT
Found at i:41260009 original size:22 final size:21
Alignment explanation
Indices: 41259932--41260053 Score: 100
Period size: 22 Copynumber: 5.7 Consensus size: 21
41259922 TATGGTTTAT
* *
41259932 GGTTTATGGGTTAAGGGTTAG
1 GGTTTATGGTTTAGGGGTTAG
* * *
41259953 GGTTTAAGTTTTAGATGGTTAG
1 GGTTTATGGTTTAG-GGGTTAG
*
41259975 GGTTTAAGGTTTAGGGGTTAAG
1 GGTTTATGGTTTAGGGGTT-AG
* * * *
41259997 GGTTTATGTTTTATGGTTTAA
1 GGTTTATGGTTTAGGGGTTAG
* *
41260018 GGTTTATGGGTTAGGAGTTAG
1 GGTTTATGGTTTAGGGGTTAG
*
41260039 GGATTTAGGGTTTAG
1 GG-TTTATGGTTTAG
41260054 ATTAATTAGT
Statistics
Matches: 78, Mismatches: 20, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
21 32 0.41
22 46 0.59
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (21 bp):
GGTTTATGGTTTAGGGGTTAG
Found at i:41260015 original size:36 final size:35
Alignment explanation
Indices: 41259911--41260030 Score: 107
Period size: 36 Copynumber: 3.4 Consensus size: 35
41259901 ATAGATTATG
* * * * *
41259911 GGTTTAAGGATTATGGTTTATGGTTTATGGGTTAA
1 GGTTTAGGGGTTAAGGTTTATGTTTTATGGTTTAA
* * * * *
41259946 GGGTTAGGGTTTAAGTTTTA-GATGGTTAGGGTTTAA
1 GGTTTAGGGGTTAAGGTTTATG-T-TTTATGGTTTAA
41259982 GGTTTAGGGGTTAAGGGTTTATGTTTTATGGTTTAA
1 GGTTTAGGGGTTAA-GGTTTATGTTTTATGGTTTAA
*
41260018 GGTTTATGGGTTA
1 GGTTTAGGGGTTA
41260031 GGAGTTAGGG
Statistics
Matches: 66, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
34 1 0.02
35 15 0.23
36 43 0.65
37 6 0.09
38 1 0.02
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (35 bp):
GGTTTAGGGGTTAAGGTTTATGTTTTATGGTTTAA
Found at i:41260052 original size:7 final size:7
Alignment explanation
Indices: 41259910--41260053 Score: 80
Period size: 7 Copynumber: 20.1 Consensus size: 7
41259900 TATAGATTAT
41259910 GGGTTTA
1 GGGTTTA
* *
41259917 AGGATTA
1 GGGTTTA
*
41259924 TGGTTTA
1 GGGTTTA
*
41259931 TGGTTTA
1 GGGTTTA
*
41259938 TGGGTTAA
1 -GGGTTTA
41259946 GGG-TTA
1 GGGTTTA
41259952 GGGTTTA
1 GGGTTTA
* *
41259959 AGTTTTA
1 GGGTTTA
41259966 GATGG-TTA
1 G--GGTTTA
41259974 GGGTTTA
1 GGGTTTA
*
41259981 AGGTTTA
1 GGGTTTA
*
41259988 GGGGTTAA
1 -GGGTTTA
41259996 GGGTTTA
1 GGGTTTA
* *
41260003 TGTTTTA
1 GGGTTTA
*
41260010 TGGTTTA
1 GGGTTTA
*
41260017 AGGTTTA
1 GGGTTTA
41260024 TGGG-TTA
1 -GGGTTTA
41260031 GGAG-TTA
1 GG-GTTTA
41260038 GGGATTTA
1 GGG-TTTA
41260046 GGGTTTA
1 GGGTTTA
41260053 G
1 G
41260054 ATTAATTAGT
Statistics
Matches: 107, Mismatches: 20, Indels: 20
0.73 0.14 0.14
Matches are distributed among these distances:
6 10 0.09
7 74 0.69
8 22 0.21
9 1 0.01
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.43
Consensus pattern (7 bp):
GGGTTTA
Found at i:41271256 original size:16 final size:16
Alignment explanation
Indices: 41271237--41271285 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
41271227 AAGCTATCTC
*
41271237 TATTGCGATCTATGTG
1 TATTGCGAACTATGTG
*
41271253 TATTGCAAACTATGCCT-
1 TATTGCGAACTATG--TG
41271270 TATTGCGAACTATGTG
1 TATTGCGAACTATGTG
41271286 AAATACGAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
15 1 0.04
16 12 0.44
17 13 0.48
18 1 0.04
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.39
Consensus pattern (16 bp):
TATTGCGAACTATGTG
Done.