Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 125 of 276
Found at i:40290557 original size:11 final size:11
Alignment explanation
Indices: 40290541--40290578 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
40290531 ATCATTCAAG
40290541 CCATCCCTCAT
1 CCATCCCTCAT
40290552 CCATCCC-CTAT
1 CCATCCCTC-AT
40290563 CCATCCCTCATT
1 CCATCCCTCA-T
40290575 CCAT
1 CCAT
40290579 AACATTCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.04
11 17 0.71
12 6 0.25
ACGTcount: A:0.18, C:0.53, G:0.00, T:0.29
Consensus pattern (11 bp):
CCATCCCTCAT
Found at i:40292189 original size:11 final size:11
Alignment explanation
Indices: 40292173--40292210 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
40292163 ATCATTCAAG
40292173 CCATCCCTCAT
1 CCATCCCTCAT
40292184 CCATCCC-CTAT
1 CCATCCCTC-AT
40292195 CCATCCCTCATT
1 CCATCCCTCA-T
40292207 CCAT
1 CCAT
40292211 AACATTCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 1 0.04
11 17 0.71
12 6 0.25
ACGTcount: A:0.18, C:0.53, G:0.00, T:0.29
Consensus pattern (11 bp):
CCATCCCTCAT
Found at i:40296192 original size:33 final size:33
Alignment explanation
Indices: 40296155--40296221 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
40296145 GATTGGACTT
40296155 TATAAGTGTGACTATTCCATGACTTGTGTCCAA
1 TATAAGTGTGACTATTCCATGACTTGTGTCCAA
40296188 TATAAGTGTGACTATTCCATGACTTGTGTCCAA
1 TATAAGTGTGACTATTCCATGACTTGTGTCCAA
40296221 T
1 T
40296222 CTAGATATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (33 bp):
TATAAGTGTGACTATTCCATGACTTGTGTCCAA
Found at i:40302072 original size:23 final size:22
Alignment explanation
Indices: 40302029--40302082 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
40302019 CAAGCTAATG
**
40302029 AACAGTAAGTTCTATTGAGCTGA
1 AACAGTAAGTTCTATCAAGCT-A
*
40302052 AACGGTAAGTTCTATCAAGCTA
1 AACAGTAAGTTCTATCAAGCTA
40302074 AACAGTAAG
1 AACAGTAAG
40302083 CTCATACGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (22 bp):
AACAGTAAGTTCTATCAAGCTA
Found at i:40302156 original size:26 final size:24
Alignment explanation
Indices: 40302074--40302238 Score: 95
Period size: 24 Copynumber: 6.8 Consensus size: 24
40302064 TATCAAGCTA
* *
40302074 AACAGTAAGCTCATACGAGTTG-G
1 AACAGTAAGCTCATACGAGATGAT
* * **
40302097 AACGGTAAGCTCCA-ATGATCTGAT
1 AACAGTAAGCT-CATACGAGATGAT
*
40302121 AACAGTAAGCTCTTACGAGATGAT
1 AACAGTAAGCTCATACGAGATGAT
* * *
40302145 ATATTAGTAAGCTCATACGAGTTG-G
1 A-A-CAGTAAGCTCATACGAGATGAT
* * * **
40302170 AACGGTAGGCTCCA-ATGATCTGAT
1 AACAGTAAGCT-CATACGAGATGAT
*
40302194 AACAGTAAGCTCTTACGAGATGAT
1 AACAGTAAGCTCATACGAGATGAT
*
40302218 ATATTAGTAAGCTCATACGAG
1 A-A-CAGTAAGCTCATACGAG
40302239 CTGTGGTGAG
Statistics
Matches: 103, Mismatches: 29, Indels: 17
0.69 0.19 0.11
Matches are distributed among these distances:
23 28 0.27
24 40 0.39
25 3 0.03
26 32 0.31
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (24 bp):
AACAGTAAGCTCATACGAGATGAT
Found at i:40302164 original size:73 final size:73
Alignment explanation
Indices: 40302077--40302238 Score: 315
Period size: 73 Copynumber: 2.2 Consensus size: 73
40302067 CAAGCTAAAC
40302077 AGTAAGCTCATACGAGTTGGAACGGTAAGCTCCAATGATCTGATAACAGTAAGCTCTTACGAGAT
1 AGTAAGCTCATACGAGTTGGAACGGTAAGCTCCAATGATCTGATAACAGTAAGCTCTTACGAGAT
40302142 GATATATT
66 GATATATT
*
40302150 AGTAAGCTCATACGAGTTGGAACGGTAGGCTCCAATGATCTGATAACAGTAAGCTCTTACGAGAT
1 AGTAAGCTCATACGAGTTGGAACGGTAAGCTCCAATGATCTGATAACAGTAAGCTCTTACGAGAT
40302215 GATATATT
66 GATATATT
40302223 AGTAAGCTCATACGAG
1 AGTAAGCTCATACGAG
40302239 CTGTGGTGAG
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 88 1.00
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.27
Consensus pattern (73 bp):
AGTAAGCTCATACGAGTTGGAACGGTAAGCTCCAATGATCTGATAACAGTAAGCTCTTACGAGAT
GATATATT
Found at i:40302578 original size:23 final size:23
Alignment explanation
Indices: 40302538--40302614 Score: 102
Period size: 24 Copynumber: 3.3 Consensus size: 23
40302528 TACATTCTAT
*
40302538 CGAGCTG-AACAGTGAGCTCATA
1 CGAGCTGAAACAGTAAGCTCATA
* *
40302560 CGAGCTGAAACAATAAGCTCTTA
1 CGAGCTGAAACAGTAAGCTCATA
*
40302583 CGAGCTGTTAACAGTAAGCTCATA
1 CGAGCTG-AAACAGTAAGCTCATA
40302607 CGAGCTGA
1 CGAGCTGA
40302615 TATATCACCT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
22 7 0.15
23 19 0.41
24 20 0.43
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.21
Consensus pattern (23 bp):
CGAGCTGAAACAGTAAGCTCATA
Found at i:40310378 original size:30 final size:30
Alignment explanation
Indices: 40310324--40310381 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
40310314 GGGCTGGCAT
* *
40310324 ATGGGCGTGTGGCCTGCCCGTGTGGATCAC
1 ATGGGCGTGTGCCCAGCCCGTGTGGATCAC
* *
40310354 ATGGGCGTGTGCCCAGTCCTTGTGGATC
1 ATGGGCGTGTGCCCAGCCCGTGTGGATC
40310382 CTGAAAACTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.10, C:0.26, G:0.38, T:0.26
Consensus pattern (30 bp):
ATGGGCGTGTGCCCAGCCCGTGTGGATCAC
Found at i:40311181 original size:10 final size:10
Alignment explanation
Indices: 40311166--40311209 Score: 58
Period size: 9 Copynumber: 4.7 Consensus size: 10
40311156 CATATATGTA
40311166 TTTTTTT-AC
1 TTTTTTTGAC
40311175 TTTTTTTGAC
1 TTTTTTTGAC
40311185 -TTTTTT-AC
1 TTTTTTTGAC
*
40311193 TTATTTTGAC
1 TTTTTTTGAC
40311203 TTTTTTT
1 TTTTTTT
40311210 AGAACAATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 2 0.07
9 18 0.60
10 10 0.33
ACGTcount: A:0.11, C:0.09, G:0.05, T:0.75
Consensus pattern (10 bp):
TTTTTTTGAC
Found at i:40311190 original size:18 final size:18
Alignment explanation
Indices: 40311167--40311208 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
40311157 ATATATGTAT
*
40311167 TTTTTTACTTTTTTTGAC
1 TTTTTTACTTATTTTGAC
40311185 TTTTTTACTTATTTTGAC
1 TTTTTTACTTATTTTGAC
40311203 TTTTTT
1 TTTTTT
40311209 TAGAACAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.12, C:0.10, G:0.05, T:0.74
Consensus pattern (18 bp):
TTTTTTACTTATTTTGAC
Found at i:40312311 original size:19 final size:19
Alignment explanation
Indices: 40312295--40312333 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
40312285 AAAAAAAACC
40312295 AAAGAGAAA-AG-AAAAAA
1 AAAGAGAAATAGCAAAAAA
40312312 AAAGAGAAATAGCAAAAAA
1 AAAGAGAAATAGCAAAAAA
40312331 AAA
1 AAA
40312334 TTAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.45
18 2 0.10
19 9 0.45
ACGTcount: A:0.79, C:0.03, G:0.15, T:0.03
Consensus pattern (19 bp):
AAAGAGAAATAGCAAAAAA
Found at i:40312440 original size:22 final size:20
Alignment explanation
Indices: 40312396--40312447 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
40312386 AATTAATTAG
*
40312396 TAAAATAAGAATAAATAATA
1 TAAAATAAAAATAAATAATA
40312416 TAACAATTAAAAATAAATCAA-A
1 TAA-AA-TAAAAATAAAT-AATA
40312438 TAAAATAAAA
1 TAAAATAAAA
40312448 TTGGGGAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 8 0.29
21 4 0.14
22 14 0.50
23 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (20 bp):
TAAAATAAAAATAAATAATA
Found at i:40321926 original size:27 final size:27
Alignment explanation
Indices: 40321896--40321963 Score: 111
Period size: 27 Copynumber: 2.5 Consensus size: 27
40321886 CAAATTACCA
*
40321896 TTTTACCCTCGATTTGTAGAATTA-TCG
1 TTTTACCCTCGATTTATAGAATTACT-G
40321923 TTTTACCCTCGATTTATAGAATTACTG
1 TTTTACCCTCGATTTATAGAATTACTG
40321950 TTTTACCCTCGATT
1 TTTTACCCTCGATT
40321964 GTGAAATTAC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 38 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.46
Consensus pattern (27 bp):
TTTTACCCTCGATTTATAGAATTACTG
Found at i:40321985 original size:27 final size:26
Alignment explanation
Indices: 40321955--40322097 Score: 103
Period size: 27 Copynumber: 5.3 Consensus size: 26
40321945 TACTGTTTTA
**
40321955 CCCTCGATTGTGAAATTACTGAAATAC
1 CCCT-GATTGTGAAATTACCAAAATAC
*
40321982 CCCT-ATAG-GATAGAATTACCAAAATAC
1 CCCTGATTGTG--A-AATTACCAAAATAC
* *
40322009 CCCTAGTTTGTAAAATTACCAAAATAC
1 CCCT-GATTGTGAAATTACCAAAATAC
* * *
40322036 CACTGGTTTGTGAAATTACCGAAATA-
1 CCCT-GATTGTGAAATTACCAAAATAC
* *
40322062 CCCTCAATTTGTAAAATTACCAAAATAC
1 CCCT-GA-TTGTGAAATTACCAAAATAC
40322090 CCCTGATT
1 CCCTGATT
40322098 TACAAAATTA
Statistics
Matches: 91, Mismatches: 17, Indels: 17
0.73 0.14 0.14
Matches are distributed among these distances:
24 1 0.01
25 3 0.03
26 6 0.07
27 74 0.81
28 5 0.05
29 2 0.02
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (26 bp):
CCCTGATTGTGAAATTACCAAAATAC
Found at i:40322098 original size:27 final size:27
Alignment explanation
Indices: 40321995--40322132 Score: 138
Period size: 27 Copynumber: 5.1 Consensus size: 27
40321985 TATAGGATAG
40321995 AATTACCAAAATACCCCT-AGTTTGTAA
1 AATTACCAAAATACCCCTGA-TTTGTAA
* * *
40322022 AATTACCAAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTGATTTGTAA
* *
40322049 AATTACCGAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-GATTTGTAA
**
40322076 AATTACCAAAATACCCCTGATTTACAA
1 AATTACCAAAATACCCCTGATTTGTAA
* *
40322103 AATTA-CAGAAATACCCTTGACTTTCTAA
1 AATTACCA-AAATACCCCTGA-TTTGTAA
40322131 AA
1 AA
40322133 ATTATAGAAA
Statistics
Matches: 91, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
26 5 0.05
27 75 0.82
28 11 0.12
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (27 bp):
AATTACCAAAATACCCCTGATTTGTAA
Found at i:40322105 original size:81 final size:81
Alignment explanation
Indices: 40321962--40322117 Score: 201
Period size: 81 Copynumber: 1.9 Consensus size: 81
40321952 TTACCCTCGA
* * * **
40321962 TTGTGAAATTACTGAAATACCCCTATAGGATAGAATTACCAAAATACCCCTAGTTTGTAAAATTA
1 TTGTGAAATTACCGAAATACCCCAATAGGATAAAATTACCAAAATACCCCTAGTTTACAAAATTA
40322027 CCA-AAATACCACTGGT
66 -CAGAAATACCACTGGT
**
40322043 TTGTGAAATTACCGAAATACCCTCAATTTG-TAAAATTACCAAAATACCCCT-GATTTACAAAAT
1 TTGTGAAATTACCGAAATACCC-CAATAGGATAAAATTACCAAAATACCCCTAG-TTTACAAAAT
40322106 TACAGAAATACC
64 TACAGAAATACC
40322118 CTTGACTTTC
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
80 3 0.05
81 58 0.89
82 4 0.06
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (81 bp):
TTGTGAAATTACCGAAATACCCCAATAGGATAAAATTACCAAAATACCCCTAGTTTACAAAATTA
CAGAAATACCACTGGT
Found at i:40322106 original size:54 final size:54
Alignment explanation
Indices: 40321995--40322175 Score: 186
Period size: 54 Copynumber: 3.3 Consensus size: 54
40321985 TATAGGATAG
* * ***
40321995 AATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCACTGGTTTGTGA
1 AATTACCGAAATACCCTC-AATTTGTAAAATTACCAAAATACCACTGGTTTACAA
* *
40322049 AATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCCCTGATTTACAA
1 AATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCACTGGTTTACAA
* * * * * *
40322103 AATTACAGAAATACCCTTGACTTTCTAAAAATTA-TAGAAATACCATTGGTTTACAA
1 AATTACCGAAATACCC-TCAATTTGT-AAAATTACCA-AAATACCACTGGTTTACAA
*
40322159 AATTACTGAAATACCCT
1 AATTACCGAAATACCCT
40322176 TGGTTTGTAG
Statistics
Matches: 107, Mismatches: 16, Indels: 7
0.82 0.12 0.05
Matches are distributed among these distances:
54 60 0.56
55 9 0.08
56 38 0.36
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.30
Consensus pattern (54 bp):
AATTACCGAAATACCCTCAATTTGTAAAATTACCAAAATACCACTGGTTTACAA
Found at i:40322169 original size:27 final size:27
Alignment explanation
Indices: 40322074--40322181 Score: 103
Period size: 27 Copynumber: 3.9 Consensus size: 27
40322064 CTCAATTTGT
** * *
40322074 AAAATTACCAAAATACCCCTGATTTAC
1 AAAATTACTGAAATACCCTTGGTTTAC
* *
40322101 AAAATTACAGAAATACCCTTGACTTT-C
1 AAAATTACTGAAATACCCTTG-GTTTAC
*
40322128 TAAAAATTA-TAGAAATACCATTGGTTTAC
1 --AAAATTACT-GAAATACCCTTGGTTTAC
40322157 AAAATTACTGAAATACCCTTGGTTT
1 AAAATTACTGAAATACCCTTGGTTT
40322182 GTAGATTTAC
Statistics
Matches: 67, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
27 41 0.61
28 7 0.10
29 19 0.28
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (27 bp):
AAAATTACTGAAATACCCTTGGTTTAC
Found at i:40322265 original size:27 final size:27
Alignment explanation
Indices: 40322222--40322295 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 27
40322212 AAATGACTAA
*
40322222 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
**
40322249 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
* *
40322276 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
40322296 TGACGAATAT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
26 3 0.08
27 34 0.89
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:40322299 original size:27 final size:27
Alignment explanation
Indices: 40322235--40322299 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
40322225 ACCCCTAATA
*
40322235 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* * *
40322262 GGTAAAGTGACCGTAATA-CCCTTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
40322289 GGTAAAATGAC
1 GGTAAAATGAC
40322300 GAATATGCCC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:40323147 original size:25 final size:24
Alignment explanation
Indices: 40323109--40323172 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 24
40323099 AGGAAGTGCT
*
40323109 AAAAGGGCTCTGCCCCAGTTTACC
1 AAAAGGGCTTTGCCCCAGTTTACC
*
40323133 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTACC
40323158 AGAAAGGGCTTTGCC
1 A-AAAGGGCTTTGCC
40323173 TTAGTTATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 1 0.03
25 35 0.97
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTACC
Found at i:40323385 original size:42 final size:42
Alignment explanation
Indices: 40323326--40323417 Score: 175
Period size: 42 Copynumber: 2.2 Consensus size: 42
40323316 TAGTCTCCCC
*
40323326 AAATGGGCTTGCATACATTCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
40323368 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
40323410 AAATGGGC
1 AAATGGGC
40323418 CTAAGGGCCA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
Found at i:40323476 original size:31 final size:31
Alignment explanation
Indices: 40323441--40323586 Score: 258
Period size: 31 Copynumber: 4.7 Consensus size: 31
40323431 CGTTTACAGT
40323441 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
40323472 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
40323503 AAAGGTTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
40323534 AAAGGCTTCAGCCCAGTGATATGATTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
40323565 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
40323587 TCAAGACTAA
Statistics
Matches: 110, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
30 5 0.05
31 105 0.95
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:40330878 original size:23 final size:22
Alignment explanation
Indices: 40330799--40330901 Score: 93
Period size: 23 Copynumber: 4.5 Consensus size: 22
40330789 CAAGCTGATG
40330799 AACAGTAAGCTCTACTGAGCTGA
1 AACAGTAAGCTCTA-TGAGCTGA
* * *
40330822 AA-TGATAAGCTCTATCAAGC-GG
1 AACAG-TAAGCTCTAT-GAGCTGA
40330844 AACAGTAAGCTCATATGAGCTGA
1 AACAGTAAGCTC-TATGAGCTGA
* *
40330867 AACGGTAAGCTCCAATGAGCTGA
1 AACAGTAAGCT-CTATGAGCTGA
40330890 TAACAGTAAGCT
1 -AACAGTAAGCT
40330902 TCTACGATCT
Statistics
Matches: 64, Mismatches: 9, Indels: 13
0.74 0.10 0.15
Matches are distributed among these distances:
22 15 0.23
23 38 0.59
24 11 0.17
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.21
Consensus pattern (22 bp):
AACAGTAAGCTCTATGAGCTGA
Found at i:40331579 original size:32 final size:32
Alignment explanation
Indices: 40331543--40331613 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
40331533 ATCTATCCTT
40331543 AAACATTTAACTACTCAATCATTCAACAATGG
1 AAACATTTAACTACTCAATCATTCAACAATGG
40331575 AAACATTTAACTACTCAATCATTCAACAATGG
1 AAACATTTAACTACTCAATCATTCAACAATGG
*
40331607 AATCATT
1 AAACATT
40331614 CAAAATCTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.30
Consensus pattern (32 bp):
AAACATTTAACTACTCAATCATTCAACAATGG
Found at i:40331581 original size:16 final size:16
Alignment explanation
Indices: 40331559--40331616 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
40331549 TTAACTACTC
40331559 AATCATTCAACAATGG
1 AATCATTCAACAATGG
* * * *
40331575 AAACATTTAACTACT-C
1 AATCATTCAAC-AATGG
40331591 AATCATTCAACAATGG
1 AATCATTCAACAATGG
40331607 AATCATTCAA
1 AATCATTCAA
40331617 AATCTATAAC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 2 0.06
16 28 0.88
17 2 0.06
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.28
Consensus pattern (16 bp):
AATCATTCAACAATGG
Found at i:40333128 original size:22 final size:19
Alignment explanation
Indices: 40333098--40333144 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
40333088 AAAGATGATA
40333098 ATTATTAATATATAATTATATCT
1 ATTA-TAATATAT-ATTA-AT-T
40333121 ATTATAATATATATTAATT
1 ATTATAATATATATTAATT
40333140 ATTAT
1 ATTAT
40333145 CAACTTTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 4 0.17
22 8 0.33
23 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTATAATATATATTAATT
Found at i:40333140 original size:16 final size:15
Alignment explanation
Indices: 40333100--40333141 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
40333090 AGATGATAAT
40333100 TATTAATATATAATTA
1 TATTAAT-TATAATTA
40333116 TATCT-ATTATAATATA
1 TAT-TAATTATAAT-TA
40333132 TATTAATTAT
1 TATTAATTAT
40333142 TATCAACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 7 0.30
16 15 0.65
17 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTAATTATAATTA
Found at i:40339667 original size:6 final size:6
Alignment explanation
Indices: 40339658--40339717 Score: 50
Period size: 6 Copynumber: 10.0 Consensus size: 6
40339648 ATGGGGTGGT
* * ** * *
40339658 GATGAA GATGAA GATGAA GGTTG-A GATGAA GATGAA CATGGG GGTCAA
1 GATGAA GATGAA GATGAA -GATGAA GATGAA GATGAA GATGAA GATGAA
40339706 GATGAA GATGAA
1 GATGAA GATGAA
40339718 TATGGGGGTT
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
5 3 0.08
6 34 0.85
7 3 0.08
ACGTcount: A:0.42, C:0.03, G:0.37, T:0.18
Consensus pattern (6 bp):
GATGAA
Found at i:40339690 original size:24 final size:23
Alignment explanation
Indices: 40339633--40339724 Score: 94
Period size: 24 Copynumber: 3.9 Consensus size: 23
40339623 ACCATGGAAG
* *
40339633 GAGATAAAGATGAAGATGGGGTG
1 GAGATGAAGATGAAGATGGGGTC
* * *
40339656 GTGATGAAGATGAAGATGAAGGTT
1 GAGATGAAGATGAAGATG-GGGTC
*
40339680 GAGATGAAGATGAACATGGGGGTC
1 GAGATGAAGATGAAGAT-GGGGTC
* *
40339704 AAGATGAAGATGAATATGGGG
1 GAGATGAAGATGAAGATGGGG
40339725 GTTAAGGTGA
Statistics
Matches: 57, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
23 20 0.35
24 36 0.63
25 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.40, T:0.20
Consensus pattern (23 bp):
GAGATGAAGATGAAGATGGGGTC
Found at i:40339725 original size:24 final size:24
Alignment explanation
Indices: 40339658--40339741 Score: 96
Period size: 24 Copynumber: 3.5 Consensus size: 24
40339648 ATGGGGTGGT
* ** *
40339658 GATGAAGATGAAGATGAAGGTTGA
1 GATGAAGATGAACATGGGGGTTAA
*
40339682 GATGAAGATGAACATGGGGGTCAA
1 GATGAAGATGAACATGGGGGTTAA
*
40339706 GATGAAGATGAATATGGGGGTTAA
1 GATGAAGATGAACATGGGGGTTAA
* *
40339730 GGTGAAGGTGAA
1 GATGAAGATGAA
40339742 GACGATGAAG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.38, C:0.02, G:0.39, T:0.20
Consensus pattern (24 bp):
GATGAAGATGAACATGGGGGTTAA
Found at i:40344312 original size:17 final size:18
Alignment explanation
Indices: 40344290--40344323 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40344280 CATATTGAAG
40344290 TGTTTT-AGTGAAAACCT
1 TGTTTTCAGTGAAAACCT
*
40344307 TGTTTTCATTGAAAACC
1 TGTTTTCAGTGAAAACC
40344324 CTTCCACAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (18 bp):
TGTTTTCAGTGAAAACCT
Found at i:40345460 original size:28 final size:27
Alignment explanation
Indices: 40345406--40345464 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
40345396 ACATACATGC
* *
40345406 ATATGGCCCACTAGGCCTAATCTCATTT
1 ATATGGCCCACTAGCCCAAATCTCA-TT
*
40345434 ATATGGCCCATTCAGCCCAAATC-CATT
1 ATATGGCCCACT-AGCCCAAATCTCATT
40345461 ATAT
1 ATAT
40345465 CCATGCTCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.22
28 13 0.48
29 8 0.30
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.31
Consensus pattern (27 bp):
ATATGGCCCACTAGCCCAAATCTCATT
Found at i:40345716 original size:16 final size:16
Alignment explanation
Indices: 40345676--40345718 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
40345666 GTAGCCAAAC
40345676 TTTCAGCTTTTCGACA
1 TTTCAGCTTTTCGACA
**
40345692 TTTTGGCTTTTCGACA
1 TTTCAGCTTTTCGACA
40345708 TTTCAGCTTTT
1 TTTCAGCTTTT
40345719 GCCGATCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.51
Consensus pattern (16 bp):
TTTCAGCTTTTCGACA
Found at i:40347731 original size:40 final size:40
Alignment explanation
Indices: 40347676--40348047 Score: 638
Period size: 40 Copynumber: 9.3 Consensus size: 40
40347666 TATTCGGATG
* *
40347676 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
40347716 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTCCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
40347756 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
40347796 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
40347836 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
40347876 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
40347916 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
** * *
40347956 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * *
40347996 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
40348036 ATATCC-GGCTAA
1 ATATCCGGGCTAA
40348048 ATTTCGAAGA
Statistics
Matches: 317, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
39 6 0.02
40 311 0.98
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:40352853 original size:46 final size:46
Alignment explanation
Indices: 40352784--40352875 Score: 148
Period size: 46 Copynumber: 2.0 Consensus size: 46
40352774 NNNNNNNGTT
** * *
40352784 ACATCTCACGAACTTGGACTCAACTCAACGAGTTCGGACGTTCGCA
1 ACATCTCACGAACTCAGAATCAACTCAACGAGTTCAGACGTTCGCA
40352830 ACATCTCACGAACTCAGAATCAACTCAACGAGTTCAGACGTTCGCA
1 ACATCTCACGAACTCAGAATCAACTCAACGAGTTCAGACGTTCGCA
40352876 TCCATAAGTG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (46 bp):
ACATCTCACGAACTCAGAATCAACTCAACGAGTTCAGACGTTCGCA
Found at i:40352889 original size:46 final size:45
Alignment explanation
Indices: 40352803--40352911 Score: 130
Period size: 46 Copynumber: 2.4 Consensus size: 45
40352793 GAACTTGGAC
* *
40352803 TCAACTCAACGAGTTCGGACGTTCGCAACATCTCACGAACTCAGAA
1 TCAACTCAACGAGTTCAGACGTTCGCAACA-CTAACGAACTCAGAA
* * * *
40352849 TCAACTCAACGAGTTCAGACGTTCGCATC-CATAAGTGAACTCGGAC
1 TCAACTCAACGAGTTCAGACGTTCGCAACAC-TAA-CGAACTCAGAA
40352895 TCAACTCAACGAGTTCA
1 TCAACTCAACGAGTTCA
40352912 ATGCCCAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
44 1 0.02
45 2 0.04
46 52 0.95
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.21
Consensus pattern (45 bp):
TCAACTCAACGAGTTCAGACGTTCGCAACACTAACGAACTCAGAA
Found at i:40355288 original size:40 final size:40
Alignment explanation
Indices: 40355233--40355407 Score: 341
Period size: 40 Copynumber: 4.4 Consensus size: 40
40355223 TATGTGCATA
40355233 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
40355273 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
40355313 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
40355353 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
1 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
*
40355393 GCATTCGTGCTGGTT
1 GCATTCGTGCGGGTT
40355408 GTTACATCCG
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 134 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (40 bp):
GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAG
Found at i:40355431 original size:80 final size:80
Alignment explanation
Indices: 40355233--40355431 Score: 272
Period size: 80 Copynumber: 2.5 Consensus size: 80
40355223 TATGTGCATA
* * ** *
40355233 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAACCG
1 GCATTCGTGCGGGTTATTACAACCGAGCCAAATCCCGAAGGCATTCGTGCGGGTTATTATAACCG
40355298 GGTTAAGTCCCGAAG
66 GGTTAAGTCCCGAAG
* * ** *
40355313 GCATTCGTGCGGGTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGGGTTATTATAACCG
1 GCATTCGTGCGGGTTATTACAACCGAGCCAAATCCCGAAGGCATTCGTGCGGGTTATTATAACCG
40355378 GGTTAAGTCCCGAAG
66 GGTTAAGTCCCGAAG
* * * *
40355393 GCATTCGTGCTGGTTGTTACATCCGAGCCAAATTCCGAA
1 GCATTCGTGCGGGTTATTACAACCGAGCCAAATCCCGAA
40355432 AGTATTTATG
Statistics
Matches: 110, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 110 1.00
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.28
Consensus pattern (80 bp):
GCATTCGTGCGGGTTATTACAACCGAGCCAAATCCCGAAGGCATTCGTGCGGGTTATTATAACCG
GGTTAAGTCCCGAAG
Found at i:40358529 original size:45 final size:49
Alignment explanation
Indices: 40358412--40358595 Score: 182
Period size: 50 Copynumber: 3.8 Consensus size: 49
40358402 GATACTAGGG
*
40358412 AGATATGAGAGTTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTC
1 AGATATGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTC
*
40358461 GAGATATGAGAGCTAGCGTAAGACCATGTTTGGGACATGGCATCGG-CT-
1 -AGATATGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTC
* * * * * * *
40358509 TGATATGTG-TC-AGTGTAAGACCATGTCTAGGACATGGTATCGACAC-C
1 AGATATGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGC-CTC
* * *
40358556 -GATAGATAAGAGCCAGTGTAAGACCATGTCTGGGACATGG
1 AGAT--ATGAGAGCTAGTGTAAGACCATGTTTGGGACATGG
40358596 AATCTGTAAC
Statistics
Matches: 113, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
45 27 0.24
46 4 0.04
47 8 0.07
48 3 0.03
49 3 0.03
50 68 0.60
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.24
Consensus pattern (49 bp):
AGATATGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTC
Found at i:40364564 original size:23 final size:23
Alignment explanation
Indices: 40364538--40364611 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
40364528 GTCCTTCGGG
40364538 ACTTATCACAGTTATACACTTCC
1 ACTTATCACAGTTATACACTTCC
* *
40364561 ACTTCCATCCCA-TT-GAC-CATTCGGC
1 ACTT--ATCACAGTTATACAC-TTC--C
40364586 -CTTATCACAGTTATACACTTCC
1 ACTTATCACAGTTATACACTTCC
40364608 ACTT
1 ACTT
40364612 CCATCCCATT
Statistics
Matches: 38, Mismatches: 4, Indels: 18
0.63 0.07 0.30
Matches are distributed among these distances:
22 7 0.18
23 14 0.37
24 10 0.26
25 7 0.18
ACGTcount: A:0.26, C:0.34, G:0.07, T:0.34
Consensus pattern (23 bp):
ACTTATCACAGTTATACACTTCC
Found at i:40364602 original size:47 final size:47
Alignment explanation
Indices: 40364551--40364951 Score: 601
Period size: 47 Copynumber: 8.4 Consensus size: 47
40364541 TATCACAGTT
* * * *
40364551 ATACACTTCCAC-TTCCATCCCATTGACCATTCGGCCTTATCACAGT-T
1 ATACACTTTCACATT-CATCACATTGGCCATTCGGCCTTATCACA-TAC
* * *
40364598 ATACACTTCCAC-TTCCATCCCATTGGCCATTCGGCCATATCACATAC
1 ATACACTTTCACATT-CATCACATTGGCCATTCGGCCTTATCACATAC
40364645 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATAC
40364692 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATAC
*
40364741 ATACACTTTCACATTCATCACATTGGTCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATAC
* *
40364790 ATACACTTTCAAATTCATCACATTGGCCATTCGGCCTTTTCACATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATAC
*
40364837 ATACACTTTCACATTCATCAGATTGGCCATTCGGCCTTATCACATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATAC
40364884 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
1 ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATAC
40364933 ATACACTTTCACATTCATC
1 ATACACTTTCACATTCATC
40364952 GTAACAAAAT
Statistics
Matches: 334, Mismatches: 14, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
46 1 0.00
47 216 0.65
48 2 0.01
49 115 0.34
ACGTcount: A:0.27, C:0.32, G:0.08, T:0.32
Consensus pattern (47 bp):
ATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATAC
Found at i:40364760 original size:27 final size:27
Alignment explanation
Indices: 40364730--40364812 Score: 70
Period size: 27 Copynumber: 3.3 Consensus size: 27
40364720 ATTCGGCCTT
40364730 ATCACATATACATACACTTTCACATTC
1 ATCACATATACATACACTTTCACATTC
** * *
40364757 ATCACAT-T-GGT-CA--TTCGGCCTT-
1 ATCACATATACATACACTTTC-ACATTC
*
40364779 ATCACATATACATACACTTTCAAATTC
1 ATCACATATACATACACTTTCACATTC
40364806 ATCACAT
1 ATCACAT
40364813 TGGCCATTCG
Statistics
Matches: 40, Mismatches: 9, Indels: 14
0.63 0.14 0.22
Matches are distributed among these distances:
22 10 0.25
23 4 0.10
24 3 0.08
25 3 0.08
26 3 0.08
27 17 0.43
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.34
Consensus pattern (27 bp):
ATCACATATACATACACTTTCACATTC
Found at i:40364876 original size:192 final size:190
Alignment explanation
Indices: 40364551--40364951 Score: 646
Period size: 192 Copynumber: 2.1 Consensus size: 190
40364541 TATCACAGTT
* * * *
40364551 ATACACTTCCAC-TTCCATCCCATTGACCATTCGGCCTTATCACAGTTATACACTTCCACTTCCA
1 ATACACTTTCACATT-CATCACATTGACCATTCGGCCTTATCACAGTTATACACTTCAAATTCCA
*
40364615 TCCCATTGGCCATTCGGCCATATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGC
65 TCACATTGGCCATTCGGCCATATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGC
40364680 CTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
130 CTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
**
40364741 ATACACTTTCACATTCATCACATTGGTCATTCGGCCTTATCACA-TATACATACACTTTCAAATT
1 ATACACTTTCACATTCATCACATTGACCATTCGGCCTTATCACAGT-T--ATACAC-TTCAAATT
* * *
40364805 -CATCACATTGGCCATTCGGCCTTTTCACATACATACACTTTCACATTCATCAGATTGGCCATTC
62 CCATCACATTGGCCATTCGGCCATATCACATACATACACTTTCACATTCATCACATTGGCCATTC
40364869 GGCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
127 GGCCTTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
40364933 ATACACTTTCACATTCATC
1 ATACACTTTCACATTCATC
40364952 GTAACAAAAT
Statistics
Matches: 196, Mismatches: 10, Indels: 8
0.92 0.05 0.04
Matches are distributed among these distances:
189 1 0.01
190 38 0.19
191 2 0.01
192 149 0.76
193 6 0.03
ACGTcount: A:0.27, C:0.32, G:0.08, T:0.32
Consensus pattern (190 bp):
ATACACTTTCACATTCATCACATTGACCATTCGGCCTTATCACAGTTATACACTTCAAATTCCAT
CACATTGGCCATTCGGCCATATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCC
TTATCACATACATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATAC
Found at i:40367102 original size:113 final size:110
Alignment explanation
Indices: 40366913--40367124 Score: 289
Period size: 113 Copynumber: 1.9 Consensus size: 110
40366903 TGAAAAAATG
* * * *
40366913 TTTCAAAATAGGCATTTTCATCGAATAATAATAAAAGCTTTAGAGGTGTGCAAAAACATGTTTTA
1 TTTCAAAAGAGGCATTTTCATCGAATAAAAATAAAAGCTTTAGAGGTGCGCAAAAACATGTTTCA
* *
40366978 GTAGACACATTTTCATCGAATAGTAATAATGAAATTGAAAACTCA
66 GCAGACACATTTTCATCGAATACTAATAATGAAATTGAAAACTCA
* * * **
40367023 TTTCAGAAGAGGCGTTTTCATCGAATAACAAAAATGAAAGCTTTAGAGGTGCGTGAAAACATGTT
1 TTTCAAAAGAGGCATTTTCATCGAAT---AAAAATAAAAGCTTTAGAGGTGCGCAAAAACATGTT
*
40367088 TCAGCAGACGCATTTTCATCGAATACTAATAATGAAA
63 TCAGCAGACACATTTTCATCGAATACTAATAATGAAA
40367125 AGGTCTTATT
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
110 23 0.26
113 64 0.74
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (110 bp):
TTTCAAAAGAGGCATTTTCATCGAATAAAAATAAAAGCTTTAGAGGTGCGCAAAAACATGTTTCA
GCAGACACATTTTCATCGAATACTAATAATGAAATTGAAAACTCA
Found at i:40373462 original size:43 final size:43
Alignment explanation
Indices: 40373415--40373528 Score: 140
Period size: 43 Copynumber: 2.7 Consensus size: 43
40373405 GAGGCCACTA
* *
40373415 TCCTAGACAGGGTCTTACATGAAATCACAATACAATGCCAAAT-
1 TCCTAGACATGGTCTTACATGAAATCACAATACAATACC-AATG
* * *
40373458 TCCTAGATATGGTCTTACACGTAATCACAATACAATACCAATG
1 TCCTAGACATGGTCTTACATGAAATCACAATACAATACCAATG
* * *
40373501 TCCCAAACATGGTCTTACATGCAATCAC
1 TCCTAGACATGGTCTTACATGAAATCAC
40373529 TGTAACACCC
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 3 0.05
43 57 0.95
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.25
Consensus pattern (43 bp):
TCCTAGACATGGTCTTACATGAAATCACAATACAATACCAATG
Found at i:40374379 original size:2 final size:2
Alignment explanation
Indices: 40374374--40374402 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40374364 AATATATATA
40374374 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
40374403 AACATGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:40401423 original size:29 final size:29
Alignment explanation
Indices: 40401281--40401427 Score: 156
Period size: 29 Copynumber: 5.1 Consensus size: 29
40401271 ACATACATGC
*
40401281 ATATGGCCCA-CTAGGCCC-AATCTCATTT
1 ATATGGCCCATC-AGGCCCAAATCACATTT
* * * *
40401309 ATATGGCCCATCCGACCCAATTCACATTC
1 ATATGGCCCATCAGGCCCAAATCACATTT
* *
40401338 ATATGGCCCATCAGGCCCAATTCACATTC
1 ATATGGCCCATCAGGCCCAAATCACATTT
* * *
40401367 ATATGGCCCATTAGGCCCCAATCTCATTT
1 ATATGGCCCATCAGGCCCAAATCACATTT
* *
40401396 ATATGGCCCATCCGGCCCAAATGACA-TT
1 ATATGGCCCATCAGGCCCAAATCACATTT
40401424 ATAT
1 ATAT
40401428 TCATGCTCAC
Statistics
Matches: 100, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
28 20 0.20
29 80 0.80
ACGTcount: A:0.27, C:0.33, G:0.14, T:0.27
Consensus pattern (29 bp):
ATATGGCCCATCAGGCCCAAATCACATTT
Found at i:40401670 original size:16 final size:16
Alignment explanation
Indices: 40401645--40401681 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
40401635 AAACTTTTGG
40401645 CTTTTCGGCATTTCAA
1 CTTTTCGGCATTTCAA
* *
40401661 CTTTTTGGCATTTCAG
1 CTTTTCGGCATTTCAA
40401677 CTTTT
1 CTTTT
40401682 GCAGATCTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.14, C:0.22, G:0.14, T:0.51
Consensus pattern (16 bp):
CTTTTCGGCATTTCAA
Found at i:40407110 original size:14 final size:15
Alignment explanation
Indices: 40407091--40407123 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
40407081 CAAGAAAATG
*
40407091 ATGATACATGAAAA-
1 ATGATAAATGAAAAC
40407105 ATGATAAATGAAAAC
1 ATGATAAATGAAAAC
40407120 ATGA
1 ATGA
40407124 GATGATGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.58, C:0.06, G:0.15, T:0.21
Consensus pattern (15 bp):
ATGATAAATGAAAAC
Found at i:40408395 original size:26 final size:26
Alignment explanation
Indices: 40408321--40408395 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
40408311 ACCAATATCA
*
40408321 CAGCAAAGCTGCCAGTAATTA-TATCG
1 CAGCAAAGCTGCCAGT-ATTAGTAACG
* * **
40408347 CAGCAGAGCTGTCAGTAACAGTAACG
1 CAGCAAAGCTGCCAGTATTAGTAACG
40408373 CAGCAAAGCTGCCAGTATTAGTA
1 CAGCAAAGCTGCCAGTATTAGTA
40408396 TATGTGGCAA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
25 2 0.05
26 37 0.95
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.20
Consensus pattern (26 bp):
CAGCAAAGCTGCCAGTATTAGTAACG
Found at i:40414476 original size:68 final size:67
Alignment explanation
Indices: 40414404--40414553 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
40414394 CATCATGTGT
* * * *
40414404 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
40414466 ATGTAG
62 ATGTAG
** * *
40414472 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
40414537 AG
66 AG
40414539 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
40414554 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:40414509 original size:64 final size:64
Alignment explanation
Indices: 40414428--40414611 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
40414418 AGACATTATG
* *
40414428 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
40414492 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
40414557 AA
63 AA
* * * *
40414559 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
40414612 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:40418923 original size:68 final size:67
Alignment explanation
Indices: 40418851--40419000 Score: 171
Period size: 67 Copynumber: 2.2 Consensus size: 67
40418841 CATCATGTGT
* * * *
40418851 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACC
40418913 ATGTAG
62 ATGTAG
** * *
40418919 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
40418984 AG
66 AG
40418986 ACAAGAGAGCTACGA
1 ACAAGAGAGCTACGA
40419001 GATAAACTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
64 20 0.29
65 7 0.10
66 4 0.06
67 26 0.37
68 13 0.19
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:40418956 original size:64 final size:64
Alignment explanation
Indices: 40418875--40419058 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
40418865 AGACATTATG
* *
40418875 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
40418939 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
40419004 AA
63 AA
* * * *
40419006 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
40419059 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:40421694 original size:29 final size:30
Alignment explanation
Indices: 40421652--40421717 Score: 107
Period size: 29 Copynumber: 2.2 Consensus size: 30
40421642 GCACTTGTGT
40421652 TAGTTTAGCCTGAATCAGGTAAGGAA-TTA
1 TAGTTTAGCCTGAATCAGGTAAGGAATTTA
*
40421681 TAGTTTAGCCTGAATCGGGTAAGGAATTTA
1 TAGTTTAGCCTGAATCAGGTAAGGAATTTA
*
40421711 TAATTTA
1 TAGTTTA
40421718 CAGTGATGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 25 0.74
30 9 0.26
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.35
Consensus pattern (30 bp):
TAGTTTAGCCTGAATCAGGTAAGGAATTTA
Found at i:40426033 original size:21 final size:21
Alignment explanation
Indices: 40426009--40426058 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
40425999 CGGCCTATAG
*
40426009 CACGGGCATGT-TATAGGACCA
1 CACGGGCATGTCCAT-GGACCA
40426030 CACGGGCATGTCCCATGGACCA
1 CACGGGCATGT-CCATGGACCA
40426052 CACGGGC
1 CACGGGC
40426059 GTGTGAGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 11 0.42
22 13 0.50
23 2 0.08
ACGTcount: A:0.24, C:0.32, G:0.30, T:0.14
Consensus pattern (21 bp):
CACGGGCATGTCCATGGACCA
Found at i:40430375 original size:15 final size:15
Alignment explanation
Indices: 40430355--40430384 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40430345 ATTATGAAAG
40430355 ATATGTTTTGGATTA
1 ATATGTTTTGGATTA
*
40430370 ATATGTTTTGTATTA
1 ATATGTTTTGGATTA
40430385 GAATTTTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.17, T:0.57
Consensus pattern (15 bp):
ATATGTTTTGGATTA
Found at i:40431029 original size:43 final size:43
Alignment explanation
Indices: 40430980--40431120 Score: 128
Period size: 43 Copynumber: 3.3 Consensus size: 43
40430970 AGAAAACATT
*
40430980 TGGGACATTGGCATCAATATGTGATTGCGCGTAAGACCATGTC
1 TGGGACATTGGCATCAATATGTGATTGCGTGTAAGACCATGTC
* * * * *
40431023 TAGGACATCGACATCGCAT-T-TGATT-TGTGTAAGACTC-TGTC
1 TGGGACATTGGCATC-AATATGTGATTGCGTGTAAGAC-CATGTC
* * * * *
40431064 TGGGACAGTGGCATCGATATGTGATAGCATGTAAGACCACGTC
1 TGGGACATTGGCATCAATATGTGATTGCGTGTAAGACCATGTC
*
40431107 TGGGACGTTGGCAT
1 TGGGACATTGGCAT
40431121 TGTACGATAC
Statistics
Matches: 75, Mismatches: 17, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
40 2 0.03
41 24 0.32
42 11 0.15
43 36 0.48
44 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.28
Consensus pattern (43 bp):
TGGGACATTGGCATCAATATGTGATTGCGTGTAAGACCATGTC
Found at i:40435178 original size:37 final size:37
Alignment explanation
Indices: 40435128--40435206 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
40435118 TTATTACGAA
* * *
40435128 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
40435165 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
40435202 GTCTT
1 GTCTT
40435207 TAGAGCTCGG
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:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:40441218 original size:56 final size:56
Alignment explanation
Indices: 40441132--40441363 Score: 437
Period size: 56 Copynumber: 4.1 Consensus size: 56
40441122 ACAAGGGATG
40441132 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
40441188 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
40441244 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
* *
40441300 ATGGGCAAAACATGTCATCAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
40441356 ATGGGCAA
1 ATGGGCAA
40441364 TAAACTAATA
Statistics
Matches: 172, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 172 1.00
ACGTcount: A:0.45, C:0.09, G:0.22, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:40455114 original size:231 final size:231
Alignment explanation
Indices: 40454711--40455174 Score: 910
Period size: 231 Copynumber: 2.0 Consensus size: 231
40454701 TCCAAACATC
40454711 GAACCTTCTACTGAGCATCACCTGAAAATAAAATAAAAGAGGGGGTGAGTTTTCTTAAACTCAGT
1 GAACCTTCTACTGAGCATCACCTGAAAATAAAATAAAAGAGGGGGTGAGTTTTCTTAAACTCAGT
40454776 GTGTACAACCCTCAGCAAAAACAAGCATTCAAAAGGAAAAAAAAAACATCATTCATCAATCATGC
66 GTGTACAACCCTCAGCAAAAACAAGCATTCAAAAGGAAAAAAAAAACATCATTCATCAATCATGC
40454841 AATGCAATCCCATCCAAATTATCCATCCGCTACACACCAGCTCCGTCCCTGGTCACACCATGTGG
131 AATGCAATCCCATCCAAATTATCCATCCGCTACACACCAGCTCCGTCCCTGGTCACACCATGTGG
40454906 GGATATAAATATCAACCCACCCAGCCCACACACCAT
196 GGATATAAATATCAACCCACCCAGCCCACACACCAT
40454942 GAACCTTCTACTGAGCATCACCTGAAAATAAAATAAAAGAGGGGGTGAGTTTTCTTAAACTCAGT
1 GAACCTTCTACTGAGCATCACCTGAAAATAAAATAAAAGAGGGGGTGAGTTTTCTTAAACTCAGT
40455007 GTGTACAACCCTCAGCAAAAACAAGCATTCAAAAGGAAAAAAAAAACATCATTCATCAATCATGC
66 GTGTACAACCCTCAGCAAAAACAAGCATTCAAAAGGAAAAAAAAAACATCATTCATCAATCATGC
* *
40455072 AATGCAATCCCATCCAAATTATCCATCCGCTACACACCAGCTCGGTCCCTGGTCACACCGTGTGG
131 AATGCAATCCCATCCAAATTATCCATCCGCTACACACCAGCTCCGTCCCTGGTCACACCATGTGG
40455137 GGATATAAATATCAACCCACCCAGCCCACACACCAT
196 GGATATAAATATCAACCCACCCAGCCCACACACCAT
40455173 GA
1 GA
40455175 TAGCCCGGTT
Statistics
Matches: 231, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
231 231 1.00
ACGTcount: A:0.38, C:0.28, G:0.14, T:0.20
Consensus pattern (231 bp):
GAACCTTCTACTGAGCATCACCTGAAAATAAAATAAAAGAGGGGGTGAGTTTTCTTAAACTCAGT
GTGTACAACCCTCAGCAAAAACAAGCATTCAAAAGGAAAAAAAAAACATCATTCATCAATCATGC
AATGCAATCCCATCCAAATTATCCATCCGCTACACACCAGCTCCGTCCCTGGTCACACCATGTGG
GGATATAAATATCAACCCACCCAGCCCACACACCAT
Found at i:40455753 original size:29 final size:29
Alignment explanation
Indices: 40455687--40455797 Score: 102
Period size: 29 Copynumber: 3.9 Consensus size: 29
40455677 AATTTCACAT
* *
40455687 ACCTGTATCTGGCCCATTAAGCCC-AATC
1 ACCTATATATGGCCCATTAAGCCCAAATC
*
40455715 A--TATTCATATGGCCCATTAGGCCCAAATC
1 ACCTA-T-ATATGGCCCATTAAGCCCAAATC
*
40455744 ACCTATATATGGCCCATTAAGACCAAATC
1 ACCTATATATGGCCCATTAAGCCCAAATC
* * * * *
40455773 ACATTTATATAGCCCGTTAGGCCCA
1 ACCTATATATGGCCCATTAAGCCCA
40455798 GACACATTCA
Statistics
Matches: 67, Mismatches: 11, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
26 1 0.01
27 1 0.01
28 17 0.25
29 45 0.67
30 1 0.01
31 2 0.03
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.26
Consensus pattern (29 bp):
ACCTATATATGGCCCATTAAGCCCAAATC
Found at i:40455764 original size:57 final size:58
Alignment explanation
Indices: 40455687--40455797 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
40455677 AATTTCACAT
* * * * *
40455687 ACCTGTATCTGGCCCATTAAG-CCCAATCATATTCATATGGCCCATTAGGCCCAAATC
1 ACCTATATATGGCCCATTAAGACCAAATCACATTCATATAGCCCATTAGGCCCAAATC
* *
40455744 ACCTATATATGGCCCATTAAGACCAAATCACATTTATATAGCCCGTTAGGCCCA
1 ACCTATATATGGCCCATTAAGACCAAATCACATTCATATAGCCCATTAGGCCCA
40455798 GACACATTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 19 0.41
58 27 0.59
ACGTcount: A:0.31, C:0.30, G:0.14, T:0.26
Consensus pattern (58 bp):
ACCTATATATGGCCCATTAAGACCAAATCACATTCATATAGCCCATTAGGCCCAAATC
Found at i:40456107 original size:21 final size:21
Alignment explanation
Indices: 40456083--40456148 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
40456073 CCAAACCTAC
40456083 AATCGATATCACTCAAAGATT
1 AATCGATATCACTCAAAGATT
* * **
40456104 AATC-TTA-CA-TACTAACCTAT
1 AATCGATATCACT-CAAAGAT-T
40456124 AATCGATATCACTCAAAGATT
1 AATCGATATCACTCAAAGATT
40456145 AATC
1 AATC
40456149 TTACATACTC
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
18 1 0.03
19 6 0.19
20 7 0.22
21 11 0.34
22 6 0.19
23 1 0.03
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.30
Consensus pattern (21 bp):
AATCGATATCACTCAAAGATT
Found at i:40456133 original size:41 final size:41
Alignment explanation
Indices: 40456076--40456157 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
40456066 CTTTACCCCA
40456076 AACCTACAATCGATATCACTCAAAGATTAATCTTACATACT
1 AACCTACAATCGATATCACTCAAAGATTAATCTTACATACT
*
40456117 AACCTATAATCGATATCACTCAAAGATTAATCTTACATACT
1 AACCTACAATCGATATCACTCAAAGATTAATCTTACATACT
40456158 CATCGAATAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.30
Consensus pattern (41 bp):
AACCTACAATCGATATCACTCAAAGATTAATCTTACATACT
Found at i:40456158 original size:21 final size:21
Alignment explanation
Indices: 40456093--40456159 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
40456083 AATCGATATC
40456093 ACTCAAAGATTAATCTTACAT
1 ACTCAAAGATTAATCTTACAT
** * *
40456114 ACT--AACCTATAATC-GATAT
1 ACTCAAAGAT-TAATCTTACAT
40456133 CACTCAAAGATTAATCTTACAT
1 -ACTCAAAGATTAATCTTACAT
40456155 ACTCA
1 ACTCA
40456160 TCGAATACTT
Statistics
Matches: 33, Mismatches: 8, Indels: 10
0.65 0.16 0.20
Matches are distributed among these distances:
19 6 0.18
20 8 0.24
21 13 0.39
22 6 0.18
ACGTcount: A:0.42, C:0.22, G:0.04, T:0.31
Consensus pattern (21 bp):
ACTCAAAGATTAATCTTACAT
Found at i:40468209 original size:21 final size:20
Alignment explanation
Indices: 40468180--40468232 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
40468170 AATAATAAAA
*
40468180 TAAATAAATAATTCATGAAGT
1 TAAAAAAATAATTC-TGAAGT
* *
40468201 TAAAAAAATAATTCTTAATT
1 TAAAAAAATAATTCTGAAGT
40468221 TAAAGAAAATAA
1 TAAA-AAAATAA
40468233 AGTAATTATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 8 0.29
21 20 0.71
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (20 bp):
TAAAAAAATAATTCTGAAGT
Found at i:40479380 original size:74 final size:74
Alignment explanation
Indices: 40479259--40479410 Score: 268
Period size: 74 Copynumber: 2.1 Consensus size: 74
40479249 GAAGCAAGAA
* * *
40479259 GGCAAAGTGATAGCTTATTCCTTGAGACAGTTAAAGCCTCATGAAAAGAACTATCTGCCACACGA
1 GGCAAAGTGATAGCTTATTCCTCGAGACAGTTAAAGCCTCATGAAAAGAACTATCCGACACACGA
40479324 CCTAGAGTT
66 CCTAGAGTT
*
40479333 GGCAAAGTGATAGCTTATTCCTCGAGACAGTTAAAGCCTCATGAAAAGAACTATCCGACACATGA
1 GGCAAAGTGATAGCTTATTCCTCGAGACAGTTAAAGCCTCATGAAAAGAACTATCCGACACACGA
40479398 CCTAGAGTT
66 CCTAGAGTT
40479407 GGCA
1 GGCA
40479411 GCCATTGTGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (74 bp):
GGCAAAGTGATAGCTTATTCCTCGAGACAGTTAAAGCCTCATGAAAAGAACTATCCGACACACGA
CCTAGAGTT
Found at i:40488573 original size:16 final size:16
Alignment explanation
Indices: 40488526--40488573 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
40488516 ATTTTTAAAA
*
40488526 TTTTAGTTTATATATT
1 TTTTATTTTATATATT
** *
40488542 TTGAATTTTAAATATT
1 TTTTATTTTATATATT
*
40488558 TTTTATTTTATCTATT
1 TTTTATTTTATATATT
40488574 AAATTGCTCA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (16 bp):
TTTTATTTTATATATT
Found at i:40496695 original size:25 final size:25
Alignment explanation
Indices: 40496667--40496720 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
40496657 AGCTCTTCCA
*
40496667 AGCTAAATAGCAGGAAGCTCATGCG
1 AGCTAAATAACAGGAAGCTCATGCG
* * * *
40496692 AGCTGAATAACGGGAAGCTTATGTG
1 AGCTAAATAACAGGAAGCTCATGCG
40496717 AGCT
1 AGCT
40496721 GAGTATCGGG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.20
Consensus pattern (25 bp):
AGCTAAATAACAGGAAGCTCATGCG
Found at i:40496721 original size:25 final size:25
Alignment explanation
Indices: 40496679--40496737 Score: 82
Period size: 25 Copynumber: 2.4 Consensus size: 25
40496669 CTAAATAGCA
40496679 GGAAGCTCATGCGAGCTGAATAACG
1 GGAAGCTCATGCGAGCTGAATAACG
* * * *
40496704 GGAAGCTTATGTGAGCTGAGTATCG
1 GGAAGCTCATGCGAGCTGAATAACG
40496729 GGAAGCTCA
1 GGAAGCTCA
40496738 GAAGAGCAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.34, T:0.20
Consensus pattern (25 bp):
GGAAGCTCATGCGAGCTGAATAACG
Found at i:40509717 original size:22 final size:22
Alignment explanation
Indices: 40509692--40509750 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
40509682 TAACTCGTAT
*
40509692 GAGCTTACTC-TTCAGCTCGATA
1 GAGCTTAC-CATTCAGCTCAATA
40509714 GAGCTTACCATTTCAGCTCAATA
1 GAGCTTACCA-TTCAGCTCAATA
*
40509737 GAGCTTACCGTTCA
1 GAGCTTACCATTCA
40509751 TCAGCTCAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 1 0.03
22 12 0.36
23 20 0.61
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (22 bp):
GAGCTTACCATTCAGCTCAATA
Found at i:40509732 original size:23 final size:23
Alignment explanation
Indices: 40509702--40509759 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 23
40509692 GAGCTTACTC
*
40509702 TTCAGCTCGATAGAGCTTACCAT
1 TTCAGCTCAATAGAGCTTACCAT
*
40509725 TTCAGCTCAATAGAGCTTACCGT
1 TTCAGCTCAATAGAGCTTACCAT
40509748 TCATCAGCTCAA
1 T--TCAGCTCAA
40509760 GATGAGTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 22 0.71
25 9 0.29
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.29
Consensus pattern (23 bp):
TTCAGCTCAATAGAGCTTACCAT
Found at i:40509777 original size:26 final size:25
Alignment explanation
Indices: 40509703--40509777 Score: 73
Period size: 23 Copynumber: 3.0 Consensus size: 25
40509693 AGCTTACTCT
* * *
40509703 TCAGCTCGATAGAGCTTACC-AT-T
1 TCAGCTCAAGAGAGCTTACCGATCA
* *
40509726 TCAGCTCAATAGAGCTTACCGTTCA
1 TCAGCTCAAGAGAGCTTACCGATCA
*
40509751 TCAGCTCAAGATGAGTTTACCGATCA
1 TCAGCTCAAGA-GAGCTTACCGATCA
40509777 T
1 T
40509778 GGCTCGAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
23 19 0.44
24 1 0.02
25 10 0.23
26 13 0.30
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (25 bp):
TCAGCTCAAGAGAGCTTACCGATCA
Found at i:40511719 original size:29 final size:29
Alignment explanation
Indices: 40511677--40511801 Score: 146
Period size: 29 Copynumber: 4.4 Consensus size: 29
40511667 ACATGCAATG
*
40511677 CAATTCACGTTCATATGGCCCATCAGGCC
1 CAATTCACATTCATATGGCCCATCAGGCC
* ** *
40511706 CAATTCACGTTCATATCACACATCAGGCC
1 CAATTCACATTCATATGGCCCATCAGGCC
*
40511735 CAATTCACATTCATATGGCCCAT-TGGCC
1 CAATTCACATTCATATGGCCCATCAGGCC
* * *
40511763 CAA-TCCCATTTATATGGCCCATCCGGCC
1 CAATTCACATTCATATGGCCCATCAGGCC
*
40511791 CAAATCACATT
1 CAATTCACATT
40511802 ATAATCATGC
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
27 17 0.21
28 14 0.17
29 51 0.62
ACGTcount: A:0.27, C:0.34, G:0.13, T:0.26
Consensus pattern (29 bp):
CAATTCACATTCATATGGCCCATCAGGCC
Found at i:40511801 original size:56 final size:58
Alignment explanation
Indices: 40511681--40511801 Score: 138
Period size: 56 Copynumber: 2.1 Consensus size: 58
40511671 GCAATGCAAT
* * *
40511681 TCACGTTCATATGGCCCATCAGGCCCAATTCACGTTCATATCACACATCAGGCCCAAT
1 TCACATTCATATGGCCCATCAGGCCCAATTCACATTCATATCACACATCAGGCCCAAA
* * * ** * *
40511739 TCACATTCATATGGCCCAT-TGGCCCAA-TCCCATTTATATGGCCCATCCGGCCCAAA
1 TCACATTCATATGGCCCATCAGGCCCAATTCACATTCATATCACACATCAGGCCCAAA
40511795 TCACATT
1 TCACATT
40511802 ATAATCATGC
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
56 28 0.53
57 7 0.13
58 18 0.34
ACGTcount: A:0.26, C:0.35, G:0.13, T:0.26
Consensus pattern (58 bp):
TCACATTCATATGGCCCATCAGGCCCAATTCACATTCATATCACACATCAGGCCCAAA
Found at i:40512041 original size:16 final size:16
Alignment explanation
Indices: 40512017--40512051 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
40512007 GTAGCCAAAC
*
40512017 TTTTGGCTTTTCGGCA
1 TTTTAGCTTTTCGGCA
40512033 TTTTAGCTTTTCGGCA
1 TTTTAGCTTTTCGGCA
40512049 TTT
1 TTT
40512052 CGGCTTTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.09, C:0.17, G:0.20, T:0.54
Consensus pattern (16 bp):
TTTTAGCTTTTCGGCA
Found at i:40512053 original size:24 final size:22
Alignment explanation
Indices: 40512016--40512059 Score: 61
Period size: 24 Copynumber: 1.9 Consensus size: 22
40512006 CGTAGCCAAA
*
40512016 CTTTTGGCTTTTCGGCATTTTAG
1 CTTTTGGCATTTCGGC-TTTTAG
40512039 CTTTTCGGCATTTCGGCTTTT
1 CTTTT-GGCATTTCGGCTTTT
40512060 GCCGATCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.07, C:0.20, G:0.20, T:0.52
Consensus pattern (22 bp):
CTTTTGGCATTTCGGCTTTTAG
Found at i:40512057 original size:16 final size:16
Alignment explanation
Indices: 40512021--40512059 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
40512011 CCAAACTTTT
*
40512021 GGCTTTTCGGCATTTT
1 GGCTTTTCGGCATTTC
*
40512037 AGCTTTTCGGCATTTC
1 GGCTTTTCGGCATTTC
40512053 GGCTTTT
1 GGCTTTT
40512060 GCCGATCTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.08, C:0.21, G:0.23, T:0.49
Consensus pattern (16 bp):
GGCTTTTCGGCATTTC
Found at i:40513663 original size:51 final size:49
Alignment explanation
Indices: 40513538--40513678 Score: 176
Period size: 51 Copynumber: 2.8 Consensus size: 49
40513528 GAAGGTATCT
* *
40513538 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCT
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCG
*** * *
40513587 GGTACATGTAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCG
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAG---TCG
*
40513638 GGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 GGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACC
40513679 TCACAATAGA
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
48 4 0.05
49 35 0.46
51 37 0.49
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (49 bp):
GGTACGCATAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCG
Found at i:40520747 original size:13 final size:13
Alignment explanation
Indices: 40520729--40520760 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
40520719 TCTTCTCCCT
40520729 CGGCCCGATCATA
1 CGGCCCGATCATA
40520742 CGGCCCGATCATA
1 CGGCCCGATCATA
40520755 CGGCCC
1 CGGCCC
40520761 AGTCCCAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.19, C:0.44, G:0.25, T:0.12
Consensus pattern (13 bp):
CGGCCCGATCATA
Found at i:40522521 original size:29 final size:28
Alignment explanation
Indices: 40522475--40522666 Score: 203
Period size: 29 Copynumber: 6.7 Consensus size: 28
40522465 AATCTCATTA
*
40522475 ATATGGCCCATTCA-GCCCGATTCACGTTC
1 ATATGGCCCA-TCAGGCCCAATTCAC-TTC
40522504 ATATGGCCCATCAGGCCCAATTCACATTC
1 ATATGGCCCATCAGGCCCAATTCAC-TTC
* * *
40522533 ATATGGCCCATTAGGCCCAAACTCA-TTT
1 ATATGGCCCATCAGGCCC-AATTCACTTC
*
40522561 ATATGGCCCATCCA-GCCCATTTCACGTTC
1 ATATGGCCCAT-CAGGCCCAATTCAC-TTC
*
40522590 ATATGACCCATCAGGCCCAATTCACATTC
1 ATATGGCCCATCAGGCCCAATTCAC-TTC
* *
40522619 ATATGGCCCATTAGGCCCAATCTCA-TTT
1 ATATGGCCCATCAGGCCCAAT-TCACTTC
*
40522647 ATATGGCCCATCCGGCCCAA
1 ATATGGCCCATCAGGCCCAA
40522667 ATTACATTAT
Statistics
Matches: 139, Mismatches: 17, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
27 4 0.03
28 42 0.30
29 85 0.61
30 8 0.06
ACGTcount: A:0.26, C:0.34, G:0.15, T:0.26
Consensus pattern (28 bp):
ATATGGCCCATCAGGCCCAATTCACTTC
Found at i:40522558 original size:86 final size:86
Alignment explanation
Indices: 40522441--40522665 Score: 344
Period size: 86 Copynumber: 2.6 Consensus size: 86
40522431 ACCCCTACAT
* * ** * * *
40522441 ACATGCATATGGCCCACTACACACAATCTCATTAATATGGCCCATTCAGCCCGA-TTCACGTTCA
1 ACATTCATATGGCCCATTAGGCCCAATCTCATTTATATGGCCCATCCAGCCC-ATTTCACGTTCA
*
40522505 TATGGCCCATCAGGCCCAATTC
65 TATGACCCATCAGGCCCAATTC
*
40522527 ACATTCATATGGCCCATTAGGCCCAAACTCATTTATATGGCCCATCCAGCCCATTTCACGTTCAT
1 ACATTCATATGGCCCATTAGGCCCAATCTCATTTATATGGCCCATCCAGCCCATTTCACGTTCAT
40522592 ATGACCCATCAGGCCCAATTC
66 ATGACCCATCAGGCCCAATTC
*
40522613 ACATTCATATGGCCCATTAGGCCCAATCTCATTTATATGGCCCATCCGGCCCA
1 ACATTCATATGGCCCATTAGGCCCAATCTCATTTATATGGCCCATCCAGCCCA
40522666 AATTACATTA
Statistics
Matches: 127, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
85 1 0.01
86 126 0.99
ACGTcount: A:0.27, C:0.34, G:0.14, T:0.26
Consensus pattern (86 bp):
ACATTCATATGGCCCATTAGGCCCAATCTCATTTATATGGCCCATCCAGCCCATTTCACGTTCAT
ATGACCCATCAGGCCCAATTC
Found at i:40522674 original size:57 final size:56
Alignment explanation
Indices: 40522464--40522678 Score: 206
Period size: 57 Copynumber: 3.8 Consensus size: 56
40522454 CCACTACACA
* * *
40522464 CAATCTCATTAATATGGCCCATTCA-GCCCGATTCACGTTCATATGGCCCATCAGGCC
1 CAATCTCATTCATATGGCCCA-TCAGGCCCAATT-ACATTCATATGGCCCATCAGGCC
* * * *
40522521 CAATTCACATTCATATGGCCCATTAGGCCCAAACT-CATTTATATGGCCCATCCA-GCC
1 CAA-TCTCATTCATATGGCCCATCAGGCCC-AATTACATTCATATGGCCCAT-CAGGCC
* * *
40522578 C-ATTTCACGTTCATATGACCCATCAGGCCCAATTCACATTCATATGGCCCATTAGGCC
1 CAATCTCA--TTCATATGGCCCATCAGGCCCAATT-ACATTCATATGGCCCATCAGGCC
* *
40522636 CAATCTCATTTATATGGCCCATCCGGCCCAAATTACATT-ATAT
1 CAATCTCATTCATATGGCCCATCAGGCCC-AATTACATTCATAT
40522679 TCATGCTCAC
Statistics
Matches: 129, Mismatches: 18, Indels: 23
0.76 0.11 0.14
Matches are distributed among these distances:
55 3 0.02
56 8 0.06
57 66 0.51
58 45 0.35
59 7 0.05
ACGTcount: A:0.27, C:0.32, G:0.13, T:0.28
Consensus pattern (56 bp):
CAATCTCATTCATATGGCCCATCAGGCCCAATTACATTCATATGGCCCATCAGGCC
Found at i:40526664 original size:56 final size:56
Alignment explanation
Indices: 40526577--40526957 Score: 568
Period size: 56 Copynumber: 6.8 Consensus size: 56
40526567 ACATTTTTTA
* *
40526577 GTTGGCATCAATATGTGATT-TAGATATGTGTGTGTGAGTAAGACCACGTTTAATAC
1 GTTGGCATCGATATGTGATTCT-GATATGTGTGTGCGAGTAAGACCACGTTTAATAC
* *
40526633 ATTGGCATCGATATGTGATTCTGATATGTGTGTGCGAGTAAGACCACATTTAATAC
1 GTTGGCATCGATATGTGATTCTGATATGTGTGTGCGAGTAAGACCACGTTTAATAC
*
40526689 GTTGGCATCGATATGTGATT-TCGATATGTGTGTGTGAGTAAGACCACGTTTAATAC
1 GTTGGCATCGATATGTGATTCT-GATATGTGTGTGCGAGTAAGACCACGTTTAATAC
* * *
40526745 GTTGGCATCGATATGTGATTTTGATATGTGTGTGCAAGTAAGACAACGTTTAATAC
1 GTTGGCATCGATATGTGATTCTGATATGTGTGTGCGAGTAAGACCACGTTTAATAC
* * * *
40526801 GTTGGCATCAATATGTGATTCAGATATGTGTGTGAGAGTAAGACCACGTTTAATAT
1 GTTGGCATCGATATGTGATTCTGATATGTGTGTGCGAGTAAGACCACGTTTAATAC
*
40526857 GTTGGCATCAATATGTGATTCTGATATGTGTGTGCGAGTAAGACCACGTTTAATAC
1 GTTGGCATCGATATGTGATTCTGATATGTGTGTGCGAGTAAGACCACGTTTAATAC
* * * * *
40526913 GTTGGCATTGATATGTGATTTTGATACGTGTTTACGAGTAAGACC
1 GTTGGCATCGATATGTGATTCTGATATGTGTGTGCGAGTAAGACC
40526958 CTGTTTGGGA
Statistics
Matches: 296, Mismatches: 26, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
55 1 0.00
56 293 0.99
57 2 0.01
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (56 bp):
GTTGGCATCGATATGTGATTCTGATATGTGTGTGCGAGTAAGACCACGTTTAATAC
Found at i:40532148 original size:31 final size:31
Alignment explanation
Indices: 40532105--40532187 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
40532095 TCTGTCTCAA
40532105 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
* *
40532135 CATATCACTGGGCCAAAGCTTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
* *
40532166 TATATCACT-GACCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
40532188 ACTATAAGCG
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 15 0.33
31 31 0.67
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:40535228 original size:24 final size:24
Alignment explanation
Indices: 40535196--40535257 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
40535186 TTCATAAGAG
* *
40535196 CCATAATCAGGAAGTTCACAAATAA
1 CCAT-ATCAAGAAGTTCACAAAAAA
*
40535221 CCTTATCAAGAAGTTCACAAAAAA
1 CCATATCAAGAAGTTCACAAAAAA
*
40535245 CCATATCGAGAAG
1 CCATATCAAGAAG
40535258 CTCCGGATAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 29 0.91
25 3 0.09
ACGTcount: A:0.47, C:0.21, G:0.13, T:0.19
Consensus pattern (24 bp):
CCATATCAAGAAGTTCACAAAAAA
Found at i:40536235 original size:50 final size:50
Alignment explanation
Indices: 40536174--40536325 Score: 270
Period size: 50 Copynumber: 3.0 Consensus size: 50
40536164 TAGATTTAAC
*
40536174 TATCCCGATCTCAAAAATATAAAAATTACTAAAAACGAGACAAGAAAACA
1 TATCCCAATCTCAAAAATATAAAAATTACTAAAAACGAGACAAGAAAACA
40536224 TATCCCAATCTCAAAAATATAAAAATTACTAAAAACGAGACAAGAAAACA
1 TATCCCAATCTCAAAAATATAAAAATTACTAAAAACGAGACAAGAAAACA
*
40536274 TATCCCAATCTCAAAAATATAAAAATTACTAAAAAC-AGGACAAGAAATCA
1 TATCCCAATCTCAAAAATATAAAAATTACTAAAAACGA-GACAAGAAAACA
40536324 TA
1 TA
40536326 CCTAATTAAC
Statistics
Matches: 99, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
49 1 0.01
50 98 0.99
ACGTcount: A:0.57, C:0.18, G:0.07, T:0.19
Consensus pattern (50 bp):
TATCCCAATCTCAAAAATATAAAAATTACTAAAAACGAGACAAGAAAACA
Found at i:40538141 original size:25 final size:25
Alignment explanation
Indices: 40538084--40538156 Score: 85
Period size: 25 Copynumber: 2.9 Consensus size: 25
40538074 GTGAGATAAC
* * *
40538084 TAATGGAAAGCTCATGCGAGCTAAA
1 TAATGGGAAGCTCATACGAGCTGAA
*
40538109 TAATGGGAAGCTCATACGAGCTGAG
1 TAATGGGAAGCTCATACGAGCTGAA
*
40538134 T-ATCGGGAAGCTCATAAGAGCTG
1 TAAT-GGGAAGCTCATACGAGCTG
40538157 TGGTGTGTCC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
24 2 0.05
25 40 0.95
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (25 bp):
TAATGGGAAGCTCATACGAGCTGAA
Found at i:40551081 original size:11 final size:11
Alignment explanation
Indices: 40551065--40551090 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40551055 CGTTACTTGT
40551065 GTTATAAAATG
1 GTTATAAAATG
40551076 GTTATAAAATG
1 GTTATAAAATG
40551087 GTTA
1 GTTA
40551091 ACTATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.38
Consensus pattern (11 bp):
GTTATAAAATG
Found at i:40552792 original size:26 final size:25
Alignment explanation
Indices: 40552757--40552821 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 25
40552747 CTCATATTCA
* * *
40552757 TCATATTTTCACTTCTTATTTCGAT
1 TCATAATTTCACTTCATATTTCAAT
* *
40552782 ATCTTAATTTCAATTCATATTTCAAT
1 -TCATAATTTCACTTCATATTTCAAT
40552808 TCATAATTTCACTT
1 TCATAATTTCACTT
40552822 TCTCATACTT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 12 0.38
26 20 0.62
ACGTcount: A:0.28, C:0.18, G:0.02, T:0.52
Consensus pattern (25 bp):
TCATAATTTCACTTCATATTTCAAT
Found at i:40552818 original size:13 final size:13
Alignment explanation
Indices: 40552786--40552818 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
40552776 TTCGATATCT
40552786 TAATTTCAATTCA
1 TAATTTCAATTCA
40552799 T-ATTTCAATTCA
1 TAATTTCAATTCA
40552811 TAATTTCA
1 TAATTTCA
40552819 CTTTCTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATTTCAATTCA
Found at i:40553728 original size:34 final size:34
Alignment explanation
Indices: 40553690--40553755 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
40553680 AGTAACAGTC
40553690 CAGTAACAGT-TAGGGCCTTAGCCCAATACAGTGT
1 CAGTAACAGTGT-GGGCCTTAGCCCAATACAGTGT
* * *
40553724 CAGTAGCAGTGTGGGCTTTAGCCCATTACAGT
1 CAGTAACAGTGTGGGCCTTAGCCCAATACAGT
40553756 AATAGTAGCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 27 0.96
35 1 0.04
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (34 bp):
CAGTAACAGTGTGGGCCTTAGCCCAATACAGTGT
Found at i:40553763 original size:34 final size:34
Alignment explanation
Indices: 40553702--40553766 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
40553692 GTAACAGTTA
*
40553702 GGGCCTTAGCCCAATACAGTGTCAGTAGCAGTGT
1 GGGCCTTAGCCCAATACAGTATCAGTAGCAGTGT
* *
40553736 GGGCTTTAGCCCATTACAGTAAT-AGTAGCAG
1 GGGCCTTAGCCCAATACAGT-ATCAGTAGCAG
40553767 AAATACAATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
34 26 0.96
35 1 0.04
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (34 bp):
GGGCCTTAGCCCAATACAGTATCAGTAGCAGTGT
Found at i:40553827 original size:22 final size:23
Alignment explanation
Indices: 40553788--40553830 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
40553778 GGTGTCCTAC
*
40553788 CCATCCATCCTCTACACTCCACT
1 CCATCCAGCCTCTACACTCCACT
40553811 CCATCCAGCC-CTACACTCCA
1 CCATCCAGCCTCTACACTCCA
40553831 TGTGGGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.23, C:0.53, G:0.02, T:0.21
Consensus pattern (23 bp):
CCATCCAGCCTCTACACTCCACT
Found at i:40567185 original size:41 final size:37
Alignment explanation
Indices: 40567085--40567186 Score: 87
Period size: 41 Copynumber: 2.6 Consensus size: 37
40567075 AGTTCAAAGC
* * *
40567085 AAAGTTGACAGCCAGTGTCTCTTCGACCTAGCCGAAGT
1 AAAG-TGACACCCAGTGTCTCATCAACCTAGCCGAAGT
* * ** *
40567123 AAAGTGATACCCAATACCTCATCAAACCTATCCGAAGT
1 AAAGTGACACCCAGTGTCTCATC-AACCTAGCCGAAGT
40567161 AAAATAGTGACACCCAGTGTCTCATC
1 --AA-AGTGACACCCAGTGTCTCATC
40567187 GACTTAAGGT
Statistics
Matches: 48, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
37 13 0.27
38 16 0.33
40 2 0.04
41 17 0.35
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (37 bp):
AAAGTGACACCCAGTGTCTCATCAACCTAGCCGAAGT
Found at i:40569555 original size:753 final size:753
Alignment explanation
Indices: 40568204--40569710 Score: 3014
Period size: 753 Copynumber: 2.0 Consensus size: 753
40568194 AAACCTCAAT
40568204 TTAATTTCATCAAAACTTTGTTCTAAAGCTTTTAAAACATCAAAATTAAGAGAAAGGACTTGATT
1 TTAATTTCATCAAAACTTTGTTCTAAAGCTTTTAAAACATCAAAATTAAGAGAAAGGACTTGATT
40568269 GACTTACCTTTTAAAATTTAAAGCTTCAAATCCCTAATTTTTCATTTTCTTTTCTTTTTCTCCTT
66 GACTTACCTTTTAAAATTTAAAGCTTCAAATCCCTAATTTTTCATTTTCTTTTCTTTTTCTCCTT
40568334 CCTTTCTTTCTTCCTTTCCTGTTTTGCTCTCTGTAACTTTCTTTCTTTTTCTTTTATGTTTCATC
131 CCTTTCTTTCTTCCTTTCCTGTTTTGCTCTCTGTAACTTTCTTTCTTTTTCTTTTATGTTTCATC
40568399 TTTGTTTCTTTTATAATATATATATTCGTTTATATTGATAATTGTTTTTATAAAAATCTATTTAA
196 TTTGTTTCTTTTATAATATATATATTCGTTTATATTGATAATTGTTTTTATAAAAATCTATTTAA
40568464 TAACAAATATAATTAATGCAATTGTACAATCATATAATTTACATTTGTCTCTATTTAATTTGTTT
261 TAACAAATATAATTAATGCAATTGTACAATCATATAATTTACATTTGTCTCTATTTAATTTGTTT
40568529 ACCTCATAAAAAACTTATAATTAATTAATTATCAAATAAACATCTTTTATTTAATAATAATAAAT
326 ACCTCATAAAAAACTTATAATTAATTAATTATCAAATAAACATCTTTTATTTAATAATAATAAAT
40568594 AATAAATATCTATTTAATTACTAATATTTGTATTACAAATGTTTTTATTTTAATTAATACACATG
391 AATAAATATCTATTTAATTACTAATATTTGTATTACAAATGTTTTTATTTTAATTAATACACATG
40568659 GACTTTATCTCAACCATACATTTGTCATAAATCTAATTTATTTATCAACTAAAAATCTCCTATTG
456 GACTTTATCTCAACCATACATTTGTCATAAATCTAATTTATTTATCAACTAAAAATCTCCTATTG
40568724 TAATTATTTAATTAATAATTATCTTTTACTTAATAAATATAAATACTAAATATCTATTTACTAAT
521 TAATTATTTAATTAATAATTATCTTTTACTTAATAAATATAAATACTAAATATCTATTTACTAAT
40568789 TAATTATTTATATTACAATTGTATACATATATTTTTCTACATTTGTCTATTTTTATCACCTTACA
586 TAATTATTTATATTACAATTGTATACATATATTTTTCTACATTTGTCTATTTTTATCACCTTACA
40568854 CTTGTCATATTCTAATTTATTTTTCTAATATAATAATAATAATAATAATAAAATTTCTAGACGTT
651 CTTGTCATATTCTAATTTATTTTTCTAATATAATAATAATAATAATAATAAAATTTCTAGACGTT
40568919 TCCTTATATGCCGCCTCAACCTCCAAATGTGACTTAAC
716 TCCTTATATGCCGCCTCAACCTCCAAATGTGACTTAAC
40568957 TTAATTTCATCAAAACTTTGTTCTAAAGCTTTTAAAACATCAAAATTAAGAGAAAGGACTTGATT
1 TTAATTTCATCAAAACTTTGTTCTAAAGCTTTTAAAACATCAAAATTAAGAGAAAGGACTTGATT
40569022 GACTTACCTTTTAAAATTTAAAGCTTCAAATCCCTAATTTTTCATTTTCTTTTCTTTTTCTCCTT
66 GACTTACCTTTTAAAATTTAAAGCTTCAAATCCCTAATTTTTCATTTTCTTTTCTTTTTCTCCTT
40569087 CCTTTCTTTCTTCCTTTCCTGTTTTGCTCTCTGTAACTTTCTTTCTTTTTCTTTTATGTTTCATC
131 CCTTTCTTTCTTCCTTTCCTGTTTTGCTCTCTGTAACTTTCTTTCTTTTTCTTTTATGTTTCATC
40569152 TTTGTTTCTTTTATAATATATATATTCGTTTATATTGATAATTGTTTTTATAAAAATCTATTTAA
196 TTTGTTTCTTTTATAATATATATATTCGTTTATATTGATAATTGTTTTTATAAAAATCTATTTAA
40569217 TAACAAATATAATTAATGCAATTGTACAATCATATAATTTACATTTGTCTCTATTTAATTTGTTT
261 TAACAAATATAATTAATGCAATTGTACAATCATATAATTTACATTTGTCTCTATTTAATTTGTTT
40569282 ACCTCATAAAAAACTTATAATTAATTAATTATCAAATAAACATCTTTTATTTAATAATAATAAAT
326 ACCTCATAAAAAACTTATAATTAATTAATTATCAAATAAACATCTTTTATTTAATAATAATAAAT
40569347 AATAAATATCTATTTAATTACTAATATTTGTATTACAAATGTTTTTATTTTAATTAATACACATG
391 AATAAATATCTATTTAATTACTAATATTTGTATTACAAATGTTTTTATTTTAATTAATACACATG
40569412 GACTTTATCTCAACCATACATTTGTCATAAATCTAATTTATTTATCAACTAAAAATCTCCTATTG
456 GACTTTATCTCAACCATACATTTGTCATAAATCTAATTTATTTATCAACTAAAAATCTCCTATTG
40569477 TAATTATTTAATTAATAATTATCTTTTACTTAATAAATATAAATACTAAATATCTATTTACTAAT
521 TAATTATTTAATTAATAATTATCTTTTACTTAATAAATATAAATACTAAATATCTATTTACTAAT
40569542 TAATTATTTATATTACAATTGTATACATATATTTTTCTACATTTGTCTATTTTTATCACCTTACA
586 TAATTATTTATATTACAATTGTATACATATATTTTTCTACATTTGTCTATTTTTATCACCTTACA
40569607 CTTGTCATATTCTAATTTATTTTTCTAATATAATAATAATAATAATAATAAAATTTCTAGACGTT
651 CTTGTCATATTCTAATTTATTTTTCTAATATAATAATAATAATAATAATAAAATTTCTAGACGTT
40569672 TCCTTATATGCCGCCTCAACCTCCAAATGTGACTTAAC
716 TCCTTATATGCCGCCTCAACCTCCAAATGTGACTTAAC
40569710 T
1 T
40569711 GCCCATTTGG
Statistics
Matches: 754, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
753 754 1.00
ACGTcount: A:0.34, C:0.14, G:0.05, T:0.47
Consensus pattern (753 bp):
TTAATTTCATCAAAACTTTGTTCTAAAGCTTTTAAAACATCAAAATTAAGAGAAAGGACTTGATT
GACTTACCTTTTAAAATTTAAAGCTTCAAATCCCTAATTTTTCATTTTCTTTTCTTTTTCTCCTT
CCTTTCTTTCTTCCTTTCCTGTTTTGCTCTCTGTAACTTTCTTTCTTTTTCTTTTATGTTTCATC
TTTGTTTCTTTTATAATATATATATTCGTTTATATTGATAATTGTTTTTATAAAAATCTATTTAA
TAACAAATATAATTAATGCAATTGTACAATCATATAATTTACATTTGTCTCTATTTAATTTGTTT
ACCTCATAAAAAACTTATAATTAATTAATTATCAAATAAACATCTTTTATTTAATAATAATAAAT
AATAAATATCTATTTAATTACTAATATTTGTATTACAAATGTTTTTATTTTAATTAATACACATG
GACTTTATCTCAACCATACATTTGTCATAAATCTAATTTATTTATCAACTAAAAATCTCCTATTG
TAATTATTTAATTAATAATTATCTTTTACTTAATAAATATAAATACTAAATATCTATTTACTAAT
TAATTATTTATATTACAATTGTATACATATATTTTTCTACATTTGTCTATTTTTATCACCTTACA
CTTGTCATATTCTAATTTATTTTTCTAATATAATAATAATAATAATAATAAAATTTCTAGACGTT
TCCTTATATGCCGCCTCAACCTCCAAATGTGACTTAAC
Found at i:40576122 original size:16 final size:15
Alignment explanation
Indices: 40576101--40576130 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40576091 CAAAATATAC
40576101 TATATTAAAATAAATT
1 TATATTAAAA-AAATT
40576117 TATATTAAAAAAAT
1 TATATTAAAAAAAT
40576131 CCCATAGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TATATTAAAAAAATT
Found at i:40576231 original size:23 final size:25
Alignment explanation
Indices: 40576188--40576237 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 25
40576178 CACATGGTGC
*
40576188 ATTTTGAACAAAAAATTTACAGGGT
1 ATTTTGAACAAAAAATATACAGGGT
*
40576213 ATTTTGAA-AAAAAA-ATACATGGT
1 ATTTTGAACAAAAAATATACAGGGT
40576236 AT
1 AT
40576238 ATTAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 9 0.39
24 6 0.26
25 8 0.35
ACGTcount: A:0.48, C:0.06, G:0.14, T:0.32
Consensus pattern (25 bp):
ATTTTGAACAAAAAATATACAGGGT
Found at i:40578354 original size:21 final size:21
Alignment explanation
Indices: 40578329--40578371 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
40578319 ACATTCATGA
40578329 AGTAAATTAATAAAGTTGTCT
1 AGTAAATTAATAAAGTTGTCT
40578350 AGTAAATTAATAAAGTTGTCT
1 AGTAAATTAATAAAGTTGTCT
40578371 A
1 A
40578372 TGCGCTGAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (21 bp):
AGTAAATTAATAAAGTTGTCT
Found at i:40578435 original size:15 final size:15
Alignment explanation
Indices: 40578415--40578445 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40578405 CTGACTTGGA
40578415 CAAGATTTTTAATAT
1 CAAGATTTTTAATAT
40578430 CAAGATTTTTAATAT
1 CAAGATTTTTAATAT
40578445 C
1 C
40578446 CTAAGTCAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (15 bp):
CAAGATTTTTAATAT
Found at i:40578716 original size:19 final size:17
Alignment explanation
Indices: 40578664--40578724 Score: 50
Period size: 19 Copynumber: 3.3 Consensus size: 17
40578654 AATTCTTCGA
40578664 ATTTTTATATTTTTCAAAT
1 ATTTTTAT-TTTTT-AAAT
**
40578683 ATTTTTAATCATTTAAAGTT
1 ATTTTT-ATTTTTTAAA--T
*
40578703 ATTTTTATTTTTTAAAA
1 ATTTTTATTTTTTAAAT
40578720 ATTTT
1 ATTTT
40578725 AAAGAGTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
17 5 0.15
18 3 0.09
19 17 0.50
20 9 0.26
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (17 bp):
ATTTTTATTTTTTAAAT
Found at i:40585187 original size:46 final size:47
Alignment explanation
Indices: 40585007--40585312 Score: 211
Period size: 47 Copynumber: 6.5 Consensus size: 47
40584997 TTTGTGTGCT
* * * * *
40585007 AGTGTAAGA-CATGTCTGGGGCATGCATCGGCCACATTATGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCTATATGATGAGAGCC
* * * * * * *
40585053 AGCGTAAGACCATGTCTAGGACATGGCATCGAC-ATTAAGACGATAGCT
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCTA-TATGATGAGAGCC
* * **
40585101 AGTGTAAGA-CATGTCTAGGACATGCATCAGCCTCGA-GATGTA-AGCC
1 AGTGTAAGACCATGTCTGGGACATGCATC-GGCTATATGATG-AGAGCC
* *
40585147 AGTGTAAGA-CATGTCTGGGACATGCATCGGCTATATGAT--GTGTC
1 AGTGTAAGACCATGTCTGGGACATGCATCGGCTATATGATGAGAGCC
* * * *
40585191 AGTGTAAGACCATGTCTGAGACTTGGCATCGGCACAGATAT-ATGAGAGTC
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGG--C-TATATGATGAGAGCC
* * *
40585241 AGTGTAAGACCATGTTTGGGACATGGCATCGACT-TAACG-TGAGAGCC
1 AGTGTAAGACCATGTCTGGGACAT-GCATCGGCTAT-ATGATGAGAGCC
*
40585288 AGTGTAAGACCATGTCTAGGACATG
1 AGTGTAAGACCATGTCTGGGACATG
40585313 GCATTGGCAT
Statistics
Matches: 209, Mismatches: 34, Indels: 34
0.75 0.12 0.12
Matches are distributed among these distances:
44 11 0.05
45 16 0.08
46 58 0.28
47 61 0.29
48 27 0.13
49 4 0.02
50 32 0.15
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGCATCGGCTATATGATGAGAGCC
Found at i:40586450 original size:30 final size:30
Alignment explanation
Indices: 40586416--40586478 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
40586406 TAATAACAAG
*
40586416 CAAATGCATCTAAAATAATAACAAAATTAA
1 CAAATACATCTAAAATAATAACAAAATTAA
* *
40586446 CAAATACCTTTAAAATAATAACAAAATTAA
1 CAAATACATCTAAAATAATAACAAAATTAA
40586476 CAA
1 CAA
40586479 TAAAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (30 bp):
CAAATACATCTAAAATAATAACAAAATTAA
Found at i:40594630 original size:13 final size:13
Alignment explanation
Indices: 40594612--40594636 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40594602 AAGTAATCGA
40594612 ACACGGGCGTGTT
1 ACACGGGCGTGTT
40594625 ACACGGGCGTGT
1 ACACGGGCGTGT
40594637 CTCTGCCGAG
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:0.16, C:0.24, G:0.40, T:0.20
Consensus pattern (13 bp):
ACACGGGCGTGTT
Found at i:40596037 original size:20 final size:20
Alignment explanation
Indices: 40596012--40596051 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
40596002 CAATTGCGGT
40596012 TAATCAAAATCCTGCTCCAC
1 TAATCAAAATCCTGCTCCAC
*
40596032 TAATCAAAATCCTGTTCCAC
1 TAATCAAAATCCTGCTCCAC
40596052 ATATTATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.33, G:0.05, T:0.28
Consensus pattern (20 bp):
TAATCAAAATCCTGCTCCAC
Found at i:40598448 original size:38 final size:38
Alignment explanation
Indices: 40598406--40598506 Score: 175
Period size: 38 Copynumber: 2.7 Consensus size: 38
40598396 AGGCGTGTGA
40598406 CACGCCCGTGTGGAAGACCCGTGGTTGAAACTGAGAAT
1 CACGCCCGTGTGGAAGACCCGTGGTTGAAACTGAGAAT
40598444 CACGCCCGTGTGGAAGACCCGTGGTTGAAACTGAGAAT
1 CACGCCCGTGTGGAAGACCCGTGGTTGAAACTGAGAAT
** *
40598482 CACGCCCGTGTCTAACACCCGTGGT
1 CACGCCCGTGTGGAAGACCCGTGGT
40598507 CGAACCTGTT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 60 1.00
ACGTcount: A:0.24, C:0.28, G:0.30, T:0.19
Consensus pattern (38 bp):
CACGCCCGTGTGGAAGACCCGTGGTTGAAACTGAGAAT
Found at i:40602406 original size:13 final size:13
Alignment explanation
Indices: 40602388--40602412 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40602378 AAGTAATCGA
40602388 ACACGGGCGTGTT
1 ACACGGGCGTGTT
40602401 ACACGGGCGTGT
1 ACACGGGCGTGT
40602413 CTCTACCGAG
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:0.16, C:0.24, G:0.40, T:0.20
Consensus pattern (13 bp):
ACACGGGCGTGTT
Found at i:40614709 original size:57 final size:58
Alignment explanation
Indices: 40614590--40614720 Score: 167
Period size: 57 Copynumber: 2.3 Consensus size: 58
40614580 TCATACAGAA
* * * * *
40614590 AGGATTTAGCCTGGACTGGTAATCCTGATATAAACTCTCTTGAGCATATGTTATAGAT
1 AGGATTTAGCATGGACGGGTAATCCTGATATAAACTCTCTTGAGCATATGTTAGAAAC
* *
40614648 AGGATTTGGCATGGACGGGTAATCCTGAT-TAAACTCT-TATGAGCATATGTTGGAAAC
1 AGGATTTAGCATGGACGGGTAATCCTGATATAAACTCTCT-TGAGCATATGTTAGAAAC
*
40614705 AGGATTTAGCTTGGAC
1 AGGATTTAGCATGGAC
40614721 AAGTAATCTT
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
56 1 0.02
57 36 0.57
58 26 0.41
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (58 bp):
AGGATTTAGCATGGACGGGTAATCCTGATATAAACTCTCTTGAGCATATGTTAGAAAC
Found at i:40628828 original size:40 final size:40
Alignment explanation
Indices: 40628779--40628999 Score: 363
Period size: 40 Copynumber: 5.5 Consensus size: 40
40628769 ACTCACTCAT
* *
40628779 TGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAA
*
40628819 TGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAA
*
40628859 TGCCTTCGGGACTTAGCCCGGATGTAGTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAA
40628899 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAA
* * *
40628939 TGCCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAA
1 TGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAA
40628979 TGCCTTCGGGACTTAGCCCGG
1 TGCCTTCGGGACTTAGCCCGG
40629000 TTATCATCCG
Statistics
Matches: 171, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
39 1 0.01
40 170 0.99
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (40 bp):
TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAA
Found at i:40630369 original size:25 final size:25
Alignment explanation
Indices: 40630335--40630383 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
40630325 TACGAGTTAG
40630335 TTTTAAAGACTCACCATAGACTCAA
1 TTTTAAAGACTCACCATAGACTCAA
*
40630360 TTTTAGAGACTCACCATAGACTCA
1 TTTTAAAGACTCACCATAGACTCA
40630384 CCTTTACTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (25 bp):
TTTTAAAGACTCACCATAGACTCAA
Found at i:40630389 original size:25 final size:25
Alignment explanation
Indices: 40630336--40630389 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
40630326 ACGAGTTAGT
*
40630336 TTTAAAGACTCACCATAGACTCAAT
1 TTTAAAGACTCACCATAGACTCAAC
* *
40630361 TTTAGAGACTCACCATAGACTCACC
1 TTTAAAGACTCACCATAGACTCAAC
40630386 TTTA
1 TTTA
40630390 CTTTGGCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (25 bp):
TTTAAAGACTCACCATAGACTCAAC
Found at i:40636170 original size:3 final size:3
Alignment explanation
Indices: 40636162--40636198 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
40636152 CCAAAAGTTC
40636162 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
40636199 TTTTTTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:40649402 original size:39 final size:39
Alignment explanation
Indices: 40649285--40649585 Score: 407
Period size: 39 Copynumber: 7.6 Consensus size: 39
40649275 GCTCCTCGTT
* *
40649285 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
40649325 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
40649365 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
40649404 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
40649443 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
40649482 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
* * *
40649521 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGT-ATC-TCGCA
40649562 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
40649586 CATCATTCAA
Statistics
Matches: 243, Mismatches: 11, Indels: 15
0.90 0.04 0.06
Matches are distributed among these distances:
39 171 0.70
40 61 0.25
41 11 0.05
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:40658708 original size:40 final size:40
Alignment explanation
Indices: 40658664--40658925 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
40658654 GCTCCTCGTT
* *
40658664 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
40658704 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
40658744 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
40658783 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
40658822 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
40658861 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
40658902 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40658926 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:40663668 original size:43 final size:41
Alignment explanation
Indices: 40663604--40663733 Score: 134
Period size: 43 Copynumber: 3.0 Consensus size: 41
40663594 CATAGGATTT
*
40663604 TCGATATGTGATTACTTGTAAGACGACGTCTGGGACGTTGGCA
1 TCGATATGTGATTAC-AGTAAGAC-ACGTCTGGGACGTTGGCA
* * ** *
40663647 TCGATATGTGTTTACGAGTAAGACCCTGTCTGGGACAATGGCT
1 TCGATATGTGATTAC-AGTAAGACAC-GTCTGGGACGTTGGCA
* *
40663690 TCGATATGTGATTACATGTTAGACCACGTCTAGGACGTTGGCA
1 TCGATATGTGATTACA-GTAAGA-CACGTCTGGGACGTTGGCA
40663733 T
1 T
40663734 TGTACGATAT
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
42 2 0.03
43 66 0.94
44 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.31
Consensus pattern (41 bp):
TCGATATGTGATTACAGTAAGACACGTCTGGGACGTTGGCA
Found at i:40665789 original size:48 final size:48
Alignment explanation
Indices: 40665718--40666038 Score: 346
Period size: 48 Copynumber: 6.7 Consensus size: 48
40665708 TATAATGTGT
*
40665718 GCTAGTGTAAGACCATGTCTGGGACATGGCATTGGCCACATTATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGA
** *** * *
40665766 GCTAGTGTAAGACCATGTCTGGGACATGGCATTAGCGTTGA-TATGTGT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CACATTATGAGA
* *
40665814 GCTAGTGTAAGACCATGTCCGGGACATGGCATCGGCCACATTAAGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGA
* * **** * *
40665862 GCCAGTGTAAGACCATGTCTGGTACATGGCATCGGTGTTGA-TATGTGT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGG-CCACATTATGAGA
**
40665910 GCTAGTGTAAGACCATGTCTGGGACATGAAATCGGCCACATTATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGA
* * *
40665958 GCCAATGTAAGACCATGTCTGGGACATGGCATCGG---CATTGAGATGAAA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATT---ATGAGA
*
40666006 GCTAGTGTAAGACCATGTCTAGGACATGGCATC
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATC
40666039 TGCAATTTAC
Statistics
Matches: 223, Mismatches: 43, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
45 4 0.02
47 2 0.01
48 215 0.96
49 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (48 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGA
Found at i:40665876 original size:96 final size:96
Alignment explanation
Indices: 40665712--40666038 Score: 501
Period size: 96 Copynumber: 3.4 Consensus size: 96
40665702 GGGTGTTATA
* *
40665712 ATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATTGGCCACATTATGAGAGCTAGTGTAAG
1 ATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCCAGTGTAAG
**
40665777 ACCATGTCTGGGACATGGCATTAGCGTTGAT
66 ACCATGTCTGGGACATGGCATCGGCGTTGAT
* *
40665808 ATGTGTGCTAGTGTAAGACCATGTCCGGGACATGGCATCGGCCACATTAAGAGAGCCAGTGTAAG
1 ATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCCAGTGTAAG
* *
40665873 ACCATGTCTGGTACATGGCATCGGTGTTGAT
66 ACCATGTCTGGGACATGGCATCGGCGTTGAT
** *
40665904 ATGTGTGCTAGTGTAAGACCATGTCTGGGACATGAAATCGGCCACATTATGAGAGCCAATGTAAG
1 ATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCCAGTGTAAG
* *
40665969 ACCATGTCTGGGACATGGCATCGGCATTGAG
66 ACCATGTCTGGGACATGGCATCGGCGTTGAT
*** *
40666000 ATGAAAGCTAGTGTAAGACCATGTCTAGGACATGGCATC
1 ATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATC
40666039 TGCAATTTAC
Statistics
Matches: 208, Mismatches: 23, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
96 208 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.25
Consensus pattern (96 bp):
ATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCACATTATGAGAGCCAGTGTAAG
ACCATGTCTGGGACATGGCATCGGCGTTGAT
Found at i:40668886 original size:59 final size:59
Alignment explanation
Indices: 40668814--40668935 Score: 235
Period size: 59 Copynumber: 2.1 Consensus size: 59
40668804 TTATGGATAC
40668814 TTTACGATGAGTACAAGTATGTATGCTAAACTTATGAGTAATGCTTTAATAAAGATCGA
1 TTTACGATGAGTACAAGTATGTATGCTAAACTTATGAGTAATGCTTTAATAAAGATCGA
*
40668873 TTTACGATGAGTACAGGTATGTATGCTAAACTTATGAGTAATGCTTTAATAAAGATCGA
1 TTTACGATGAGTACAAGTATGTATGCTAAACTTATGAGTAATGCTTTAATAAAGATCGA
40668932 TTTA
1 TTTA
40668936 TGTCCGTATG
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (59 bp):
TTTACGATGAGTACAAGTATGTATGCTAAACTTATGAGTAATGCTTTAATAAAGATCGA
Done.