Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168004.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_26, whole genome shotgun sequence
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: 16099665
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 13 of 77
Found at i:2134686 original size:2 final size:2
Alignment explanation
Indices: 2134681--2134709 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2134671 ATTTTTTAAG
2134681 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2134710 AACATAAACT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2135438 original size:8 final size:8
Alignment explanation
Indices: 2135425--2135460 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
2135415 TTAAAACAAA
2135425 TTATATAT
1 TTATATAT
2135433 TTATATAT
1 TTATATAT
*
2135441 TTAAATAT
1 TTATATAT
2135449 TTATAATAT
1 TTAT-ATAT
2135458 TTA
1 TTA
2135461 ATTTATGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
8 18 0.72
9 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
TTATATAT
Found at i:2138297 original size:130 final size:129
Alignment explanation
Indices: 2138048--2138289 Score: 285
Period size: 130 Copynumber: 1.9 Consensus size: 129
2138038 TTTTTAGTAG
* * *
2138048 AAAATACCTTTAATAATTTATAAAAAAATATGAAACAAATTCTTGAAGGTGATTTTGGCCGAAAG
1 AAAATACCTTTAATAATTTACAAAAAAATATGAAACAAATTCTTGAAGGTGATTTTGCCCAAAAG
** * *
2138113 TGCCTTTAATAATCCATTCAATTAATTTTTAGGTCGTATTATTGAAAGAGATTTTTTTTTAAAAA
66 T-CCTTTAATAATCCACACAATAAATTTTTAGGTCGGATTATTGAAAGAGATTTTTTTTTAAAAA
*** *
2138178 AAAATACCTTTAATAATCTATACAAAAAAAGT-TGAAATGGATTCTTGAAGGT-TTTTTGCCCAA
1 AAAATACCTTTAATAAT-T-TACAAAAAAA-TATGAAACAAATTCTTGAAGGTGATTTTGCCCAA
* * *
2138241 AACGT-CTTTAATATTTCACACAATAAATTTTTAGGTGGGATTATT-AAAG
63 AA-GTCCTTTAATAATCCACACAATAAATTTTTAGGTCGGATTATTGAAAG
2138290 GTGATTTTGG
Statistics
Matches: 94, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
129 4 0.04
130 50 0.53
131 11 0.12
132 28 0.30
133 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (129 bp):
AAAATACCTTTAATAATTTACAAAAAAATATGAAACAAATTCTTGAAGGTGATTTTGCCCAAAAG
TCCTTTAATAATCCACACAATAAATTTTTAGGTCGGATTATTGAAAGAGATTTTTTTTTAAAAA
Found at i:2138586 original size:305 final size:303
Alignment explanation
Indices: 2137743--2138679 Score: 991
Period size: 305 Copynumber: 3.1 Consensus size: 303
2137733 TTTTTGGCAG
* * * *
2137743 AAAATGCTCTTAATAATCCATTGAAAAAATATGAAACCGATTCTTGAAAGCGTTTTTTGG-TCAA
1 AAAATGCCCTTAATAATCCATAGAAAAAATATGAAACAGATTCTTGAAGGCG-TTTTTGGCT-AA
* ** *
2137807 ACTCGCCTTTAATAATTCCAAGCAATAAATTTTTAGTTGGGATTATTAAAGGTGATTTTTG-CAA
64 ACGCGCCTTTAATAA-TCCAATTAATAAATTTTTAGTTGGGATTATTGAAGGTGATTTTTGTC-A
* * * *
2137871 AAAATGCCTTCAATAATCCATACACAAAAA-TTGGAACGGACTT-TTGAATGTGTTTTTGGCTCA
127 AAAATACCTTCAATAATCCATACA-AAAAAGTTGAAACGGA-TTCTTGAAGGTGTTTTT-GCCCA
* ** ** ** * *
2137934 AAACGCCTTTAATATTCTACATGATAATTTAAATGGTCTGATTATTGAAAATAATTTTGGTCAAA
189 AAACGCCTTTAATATTCCACACAATAATTTTTA-GGTGGGATTATTGAAAGTGATTTTGGTCAAA
* * *
2137999 AACGCCTTCAATAACA-TTTGTCAGGGATTATTCAAGGTATTTT-TAG-TA
253 AATGCCTTCAATAACATTTTGTTAGGGATTATTCAAGGTATTTTCTTGTTA
* * ** * * * *
2138047 GAAAATACCTTTAATAATTTATA-AAAAAATATGAAACAAATTCTTGAAGGTGATTTTGGCCGAA
1 -AAAATGCCCTTAATAATCCATAGAAAAAATATGAAACAGATTCTTGAAGGCGTTTTTGG-CTAA
* * * * * * * *
2138111 A-GTGCCTTTAATAATCC-ATTCAATTAATTTTTAGGTCGTATTATTGAAAGAGATTTTTTTTTA
64 ACGCGCCTTTAATAATCCAATT-AATAAATTTTTAGTTGGGATTATTGAAGGTGA--TTTTTGT-
* * * *
2138174 AAAAAAAATACCTTTAATAATCTATACAAAAAAAGTTGAAATGGATTCTTGAAGGT-TTTTTGCC
125 --CAAAAATACCTTCAATAATCCATAC-AAAAAAGTTGAAACGGATTCTTGAAGGTGTTTTTGCC
* *
2138238 CAAAACGTCTTTAATATTTCACACAATAAATTTTTAGGTGGGATTATT-AAAGGTGATTTTGGTC
187 CAAAACGCCTTTAATATTCCACACAAT-AATTTTTAGGTGGGATTATTGAAA-GTGATTTTGGTC
* * * *
2138302 AAAAATACCTTCAATAACATTTTGTTATGGATTATTTAAGGCATTTTCTTGTTA
250 AAAAATGCCTTCAATAACATTTTGTTAGGGATTATTCAAGGTATTTTCTTGTTA
* * * *
2138356 AATATGCCCTTAATAAACCATAGAAAAAATATGGAACGGATTCTT-AAGTGCGTTTTTGGCTAAA
1 AAAATGCCCTTAATAATCCATAGAAAAAATATGAAACAGATTCTTGAAG-GCGTTTTTGGCTAAA
* *
2138420 CGCACCTTCAATAATCCAATTAATAAATTTTTAGTTGGGATTATTGAAGGTGATTTTTGTCAAAA
65 CGCGCCTTTAATAATCCAATTAATAAATTTTTAGTTGGGATTATTGAAGGTGATTTTTGTCAAAA
* *
2138485 ATACCTTCAATAATCCATACAAAAAAGTTGAAACGGATTCTTAAAGGTGTTTTTATCCCAAAACG
130 ATACCTTCAATAATCCATACAAAAAAGTTGAAACGGATTCTTGAAGGTGTTTTT-GCCCAAAACG
* *
2138550 CCTTTAATATTCCACACAATATATTTTTAGGTGGGATTATTGAAAGCGATTTTAGTCAAAAATGC
194 CCTTTAATATTCCACACAATA-ATTTTTAGGTGGGATTATTGAAAGTGATTTTGGTCAAAAATGC
* * *
2138615 CTTCAATAGCATTTTGTTAGGGATAAATCAAGGTATTTTCTTGTTA
258 CTTCAATAACATTTTGTTAGGGATTATTCAAGGTATTTTCTTGTTA
* * *
2138661 AAAAAGCCTTTATTAATCC
1 AAAATGCCCTTAATAATCC
2138680 CATCAAAAAA
Statistics
Matches: 513, Mismatches: 94, Indels: 50
0.78 0.14 0.08
Matches are distributed among these distances:
301 1 0.00
302 28 0.05
303 43 0.08
304 61 0.12
305 136 0.27
306 64 0.12
307 68 0.13
308 41 0.08
309 68 0.13
310 3 0.01
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (303 bp):
AAAATGCCCTTAATAATCCATAGAAAAAATATGAAACAGATTCTTGAAGGCGTTTTTGGCTAAAC
GCGCCTTTAATAATCCAATTAATAAATTTTTAGTTGGGATTATTGAAGGTGATTTTTGTCAAAAA
TACCTTCAATAATCCATACAAAAAAGTTGAAACGGATTCTTGAAGGTGTTTTTGCCCAAAACGCC
TTTAATATTCCACACAATAATTTTTAGGTGGGATTATTGAAAGTGATTTTGGTCAAAAATGCCTT
CAATAACATTTTGTTAGGGATTATTCAAGGTATTTTCTTGTTA
Found at i:2138782 original size:35 final size:35
Alignment explanation
Indices: 2138713--2138782 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
2138703 TGCATATGTC
* *
2138713 AAGTCAGTTGTAGGTTTATGCCCATAAAACATTTG
1 AAGTCAGTTGTAGATTTATGCCCAGAAAACATTTG
* * *
2138748 AAGTCAGTTGTATATTTATGCCTAGAAAATATTTG
1 AAGTCAGTTGTAGATTTATGCCCAGAAAACATTTG
2138783 GTTTATATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (35 bp):
AAGTCAGTTGTAGATTTATGCCCAGAAAACATTTG
Found at i:2142010 original size:24 final size:25
Alignment explanation
Indices: 2141974--2142039 Score: 116
Period size: 24 Copynumber: 2.7 Consensus size: 25
2141964 TAGCAATGTG
2141974 TTCAGAAACACCTTTCAGTAAATCA
1 TTCAGAAACACCTTTCAGTAAATCA
2141999 TTCAG-AACACCTTTCAGTAAATCA
1 TTCAGAAACACCTTTCAGTAAATCA
*
2142023 TTCAGAAACACCATTCA
1 TTCAGAAACACCTTTCA
2142040 ACATATGATT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
24 24 0.62
25 15 0.38
ACGTcount: A:0.39, C:0.26, G:0.08, T:0.27
Consensus pattern (25 bp):
TTCAGAAACACCTTTCAGTAAATCA
Found at i:2142082 original size:28 final size:28
Alignment explanation
Indices: 2142019--2142115 Score: 94
Period size: 28 Copynumber: 3.6 Consensus size: 28
2142009 CTTTCAGTAA
*
2142019 ATCATTCAG-AAACACCAT-TCA-AC-AT
1 ATCATTCAGCAAAC-CAATATCATACAAT
* *
2142044 ATGATTCAGCACACCAATATCATACAAT
1 ATCATTCAGCAAACCAATATCATACAAT
**
2142072 ATCATTCAGCAAAATAATATCATACAAT
1 ATCATTCAGCAAACCAATATCATACAAT
* *
2142100 ACCATTAAGCAAACCA
1 ATCATTCAGCAAACCA
2142116 TAATATTTAA
Statistics
Matches: 57, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
25 11 0.19
26 6 0.11
27 2 0.04
28 38 0.67
ACGTcount: A:0.46, C:0.25, G:0.05, T:0.24
Consensus pattern (28 bp):
ATCATTCAGCAAACCAATATCATACAAT
Found at i:2143150 original size:187 final size:184
Alignment explanation
Indices: 2142835--2143490 Score: 831
Period size: 187 Copynumber: 3.5 Consensus size: 184
2142825 TCTTTAAAAT
* * ** *
2142835 TATTGAAGGTATTTTATACTAAAAGATGCC-TTAATAATCTAAAAAATTTTTAAAAGAAAATTAT
1 TATTGAAGGTGTTTT-TACTAGAAGACACCTTTAATAATCTCAAAAATTTTTAAAAGAAAATTAT
* *
2142899 TGAAGGTATTTGTTCTTAAAAAATACCTTCAATAATTATGTACAAAAATTAAAAGGAATTAGTGA
65 TAAAGG--TTTGTTCTTAAAAAATACCTTCAATAATTATGTATAAAAATTAAAAGGAATTAGTGA
* *
2142964 ATGCATTTTTCTAGAATAAACTCCTTCACTAACCATTTTAAAATTTGAAGTAGTAAAA
128 A-GCATTTTTCTAGAATAAACTCCTTCACTAACCATCTTAAAATTTGAAGTAGTGAAA
*
2143022 TATTGAAGGTGTTTTCACTAGAAGACACCTATTAATAATCTCAAAAATTTTTAAAAGAAAATTAT
1 TATTGAAGGTGTTTTTACTAGAAGACACCT-TTAATAATCTCAAAAATTTTTAAAAGAAAATTAT
* *
2143087 TAAAGCGTTTGTTCTCAAAAAATTCCTTCAATAATTATGTATAAAAATTAAAAGGAATTAGTGAA
65 TAAAG-GTTTGTTCTTAAAAAATACCTTCAATAATTATGTATAAAAATTAAAAGGAATTAGTGAA
* * * *
2143152 GACATTTTTAT-GAAATAAACGCCTTCACTAACCGTCTTAAAATTT-AAGTAGTGCAA
129 G-CATTTTTCTAG-AATAAACTCCTTCACTAACCATCTTAAAATTTGAAGTAGTGAAA
* * * * *
2143208 TATTGAAAGCGTTTTTACTAGAAGACGCCTTTAGTAATCTTAAAAATTTTTAAAAGAAAATTATT
1 TATTGAAGGTGTTTTTACTAGAAGACACCTTTAATAATCTCAAAAATTTTTAAAAGAAAATTATT
* * *
2143273 GAAGGTGGTTGTTCTTAAAAAATGCCTTCAATAATTATGTATAAAAATTAAAAAAGAATTAGTGA
66 AAAGGT--TTGTTCTTAAAAAATACCTTCAATAATTATGTATAAAAATT-AAAAGGAATTAGTGA
* *
2143338 AGGCGTTTTTCTAGAATAAA-TGCCTTCACTAATCATCTTAAAATTTG-AGTAGTGAAA
128 A-GCATTTTTCTAGAATAAACT-CCTTCACTAACCATCTTAAAATTTGAAGTAGTGAAA
* *
2143395 TATTGAAGATGTTTTTTACTAGAAGACACCTTCAATAATCTCAAACAATTTTTAAAA-AAAATTA
1 TATTGAAGGTG-TTTTTACTAGAAGACACCTTTAATAATCTCAAA-AATTTTTAAAAGAAAATTA
**
2143459 TTAAAGACGTTT-TTAGTAAAAAATCACCTTCA
64 TTAAAG--GTTTGTTCTTAAAAAAT-ACCTTCA
2143491 CTGATATTCA
Statistics
Matches: 409, Mismatches: 43, Indels: 33
0.84 0.09 0.07
Matches are distributed among these distances:
184 2 0.00
185 36 0.09
186 86 0.21
187 183 0.45
188 88 0.22
189 12 0.03
190 2 0.00
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (184 bp):
TATTGAAGGTGTTTTTACTAGAAGACACCTTTAATAATCTCAAAAATTTTTAAAAGAAAATTATT
AAAGGTTTGTTCTTAAAAAATACCTTCAATAATTATGTATAAAAATTAAAAGGAATTAGTGAAGC
ATTTTTCTAGAATAAACTCCTTCACTAACCATCTTAAAATTTGAAGTAGTGAAA
Found at i:2150030 original size:20 final size:21
Alignment explanation
Indices: 2149986--2150030 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2149976 TGAGTGCCAA
* *
2149986 AATTGAGGAAGAACGTGCTAG
1 AATTGAGGAAAAACGTACTAG
*
2150007 AATTGAGTAAAAACGTAC-AG
1 AATTGAGGAAAAACGTACTAG
2150027 AATT
1 AATT
2150031 TCAACAGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.44, C:0.09, G:0.24, T:0.22
Consensus pattern (21 bp):
AATTGAGGAAAAACGTACTAG
Found at i:2150735 original size:34 final size:34
Alignment explanation
Indices: 2150691--2150788 Score: 119
Period size: 34 Copynumber: 2.9 Consensus size: 34
2150681 AATAGAGGCG
* * *
2150691 TTTTCTAAATACAAACGCCGTTAATATAGTAGCAT-
1 TTTTCTAAATACAAACGTCGCTAATATAGCA--ATA
*
2150726 TTTTC-AAATACAAATGTCGCTAATATAGCAATA
1 TTTTCTAAATACAAACGTCGCTAATATAGCAATA
*
2150759 TTTTCTAGATACAAACGTCGCTAATATAGC
1 TTTTCTAAATACAAACGTCGCTAATATAGC
2150789 GGCGTTTTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
32 2 0.04
33 5 0.09
34 43 0.78
35 5 0.09
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (34 bp):
TTTTCTAAATACAAACGTCGCTAATATAGCAATA
Found at i:2152221 original size:26 final size:26
Alignment explanation
Indices: 2152191--2152242 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
2152181 CTTGTTTTAA
* * *
2152191 AAGTTTAATAGTTGTAAAGATTTATT
1 AAGTTTAATAATTATAAAAATTTATT
2152217 AAGTTTAATAATTATAAAAATTTATT
1 AAGTTTAATAATTATAAAAATTTATT
2152243 TTATTAGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (26 bp):
AAGTTTAATAATTATAAAAATTTATT
Found at i:2154683 original size:8 final size:9
Alignment explanation
Indices: 2154656--2154691 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
2154646 ACTATTACTC
2154656 TTTCATTATT
1 TTTCATT-TT
*
2154666 TTTAATTTT
1 TTTCATTTT
2154675 TTTCATTTT
1 TTTCATTTT
2154684 TTTCATTT
1 TTTCATTT
2154692 AAATTTATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 18 0.75
10 6 0.25
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTCATTTT
Found at i:2158621 original size:30 final size:30
Alignment explanation
Indices: 2158563--2158623 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
2158553 ATCAAAGCTC
*
2158563 CGTTTGATAAACGTTATACTTTTCTTTTTT
1 CGTTTGATAAACGTTATACATTTCTTTTTT
* *
2158593 CGTTTGATAAACGTTTATTCATTTTTTTTTT
1 CGTTTGATAAACG-TTATACATTTCTTTTTT
2158624 ACAAACTTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.20, C:0.11, G:0.10, T:0.59
Consensus pattern (30 bp):
CGTTTGATAAACGTTATACATTTCTTTTTT
Found at i:2164342 original size:15 final size:15
Alignment explanation
Indices: 2164322--2164357 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2164312 GGTGTAACTC
* *
2164322 TTTATCTATGTTTAT
1 TTTATCGATATTTAT
2164337 TTTATCGATATTTAT
1 TTTATCGATATTTAT
2164352 TTTATC
1 TTTATC
2164358 AAACTTGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.22, C:0.08, G:0.06, T:0.64
Consensus pattern (15 bp):
TTTATCGATATTTAT
Found at i:2164844 original size:48 final size:48
Alignment explanation
Indices: 2164755--2164859 Score: 124
Period size: 48 Copynumber: 2.2 Consensus size: 48
2164745 TAAGAAAATT
** * * * *
2164755 AAAAAA-TACAAGTTTATACTAACGGATGTTAAGTGTTGGTATGGGTA
1 AAAAAATTACAAGTTTATACTAACAAACGTTAAGTATCGGTATAGGTA
2164802 AAAAAATTACAAGTTTATACTAACAAACGTTAA-TCATCGGTATAGGTA
1 AAAAAATTACAAGTTTATACTAACAAACGTTAAGT-ATCGGTATAGGTA
2164850 AGAAAAATTA
1 A-AAAAATTA
2164860 AAATATATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
47 7 0.14
48 34 0.69
49 8 0.16
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.30
Consensus pattern (48 bp):
AAAAAATTACAAGTTTATACTAACAAACGTTAAGTATCGGTATAGGTA
Found at i:2165049 original size:55 final size:54
Alignment explanation
Indices: 2164903--2165049 Score: 149
Period size: 51 Copynumber: 2.7 Consensus size: 54
2164893 GGTATATGTG
* * * *
2164903 AGAAAATTAAAACATACAAATCTATATTGATGGGCTTTAAGGGTCAATATAGGTA
1 AGAAAATTAAAACATACAAGTCTATATTGACGGG-TTTAACGGTCAATATAGGCA
* * * ** *
2164958 A-AAAA--AAAA-TTACAAGTCTATACTAACGAGCATTAACTGTCAATATAGGCA
1 AGAAAATTAAAACATACAAGTCTATATTGACG-GGTTTAACGGTCAATATAGGCA
2165009 AGAAAATTAAAACATACAAGTCTATATTGACGGGTGTTAAC
1 AGAAAATTAAAACATACAAGTCTATATTGACGGGT-TTAAC
2165050 CGTCGGTAAA
Statistics
Matches: 71, Mismatches: 15, Indels: 12
0.72 0.15 0.12
Matches are distributed among these distances:
51 31 0.44
52 9 0.13
54 9 0.13
55 22 0.31
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.27
Consensus pattern (54 bp):
AGAAAATTAAAACATACAAGTCTATATTGACGGGTTTAACGGTCAATATAGGCA
Found at i:2169201 original size:18 final size:18
Alignment explanation
Indices: 2169178--2169230 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
2169168 CGAGCCGCTC
2169178 TTTATTT-TGGTATTTTTG
1 TTTATTTAT-GTATTTTTG
*
2169196 TTTATTTATTTATTTTTG
1 TTTATTTATGTATTTTTG
2169214 TTTTATGTTAT-TATTTT
1 -TTTAT-TTATGTATTTT
2169231 GAACAAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 15 0.48
19 12 0.39
20 4 0.13
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.75
Consensus pattern (18 bp):
TTTATTTATGTATTTTTG
Found at i:2169231 original size:18 final size:18
Alignment explanation
Indices: 2169188--2169230 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
2169178 TTTATTTTGG
2169188 TATTTTTGTTTATTTATT
1 TATTTTTGTTTATTTATT
2169206 TATTTTTGTTTTATGTTA-T
1 TATTTTTG-TTTAT-TTATT
2169225 TATTTT
1 TATTTT
2169231 GAACAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.35
19 12 0.52
20 3 0.13
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.77
Consensus pattern (18 bp):
TATTTTTGTTTATTTATT
Found at i:2171202 original size:17 final size:19
Alignment explanation
Indices: 2171176--2171217 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2171166 CCAATAATAG
*
2171176 TTTTTGTTTTC-A-TGTTT
1 TTTTTTTTTTCAATTGTTT
2171193 TTTTTTTTTTCAATTGTTT
1 TTTTTTTTTTCAATTGTTT
2171212 TTTTTT
1 TTTTTT
2171218 AATGTATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.45
18 1 0.05
19 11 0.50
ACGTcount: A:0.07, C:0.05, G:0.07, T:0.81
Consensus pattern (19 bp):
TTTTTTTTTTCAATTGTTT
Found at i:2172906 original size:3 final size:3
Alignment explanation
Indices: 2172898--2172962 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
2172888 ATTTTAATAC
2172898 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2172946 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
2172963 CACAAATGGC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2188094 original size:89 final size:90
Alignment explanation
Indices: 2187991--2188190 Score: 248
Period size: 87 Copynumber: 2.3 Consensus size: 90
2187981 ATGGTATTAG
* * * * *
2187991 TTGAAACTATACTATGAAAAAAAATT-ATTTTTTAGAATTCTA-AGTTTCAACCAAAAACAATGT
1 TTGAAACTATACTATGAAAAAAAATTCATTGTTCAGAATTATATAATTTCAA-CAAAAACAATAT
* *
2188054 TCTTAAAATTAAAAATGTGGTTTTTA
65 TCTTAAAATTAAAAATGTAGTATTTA
* *
2188080 TTGAAAATATACTATG---AAAAATTCATTGTTCAGAATTATATAATTTCAATAAAAACAATATT
1 TTGAAACTATACTATGAAAAAAAATTCATTGTTCAGAATTATATAATTTCAACAAAAACAATATT
*
2188142 TTTAAAATTAAAAATGTAGTATTTA
66 CTTAAAATTAAAAATGTAGTATTTA
* *
2188167 TTGAAACTATATTATAAAAAAAAA
1 TTGAAACTATACTATGAAAAAAAA
2188191 AAGTTATTTT
Statistics
Matches: 93, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
86 7 0.08
87 59 0.63
88 7 0.08
89 15 0.16
90 5 0.05
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (90 bp):
TTGAAACTATACTATGAAAAAAAATTCATTGTTCAGAATTATATAATTTCAACAAAAACAATATT
CTTAAAATTAAAAATGTAGTATTTA
Found at i:2188288 original size:13 final size:12
Alignment explanation
Indices: 2188269--2188300 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
2188259 AAAATGTAGT
2188269 TTATTATGAAAA
1 TTATTATGAAAA
2188281 TATATTATGAAAA
1 T-TATTATGAAAA
2188294 TTATTAT
1 TTATTAT
2188301 AATATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (12 bp):
TTATTATGAAAA
Found at i:2188605 original size:21 final size:20
Alignment explanation
Indices: 2188579--2188619 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
2188569 AATAAATAAA
2188579 TAAATAAATAATTTAACATAT
1 TAAATAAATAATTTAA-ATAT
*
2188600 TAAATAAGTAATTTAAATAT
1 TAAATAAATAATTTAAATAT
2188620 ATATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (20 bp):
TAAATAAATAATTTAAATAT
Found at i:2191920 original size:22 final size:22
Alignment explanation
Indices: 2191895--2191936 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2191885 TTTTGTTTTG
*
2191895 TTTTGTT-AGATTTATAAATAAT
1 TTTTGTTGAAATTT-TAAATAAT
2191917 TTTTGTTGAAATTTTAAATA
1 TTTTGTTGAAATTTTAAATA
2191937 TATCATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.36, C:0.00, G:0.10, T:0.55
Consensus pattern (22 bp):
TTTTGTTGAAATTTTAAATAAT
Found at i:2192963 original size:26 final size:26
Alignment explanation
Indices: 2192918--2192974 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
2192908 AATCAACCAA
* *
2192918 AATTATTATAATATTCTTTTTATCAT
1 AATTATTAAAATATTATTTTTATCAT
*
2192944 AATTATTAAAATGTTATTTTTATCAT
1 AATTATTAAAATATTATTTTTATCAT
2192970 AATTA
1 AATTA
2192975 CGAAAATGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (26 bp):
AATTATTAAAATATTATTTTTATCAT
Found at i:2196010 original size:207 final size:201
Alignment explanation
Indices: 2195569--2196074 Score: 493
Period size: 207 Copynumber: 2.5 Consensus size: 201
2195559 TTTTTATAAT
* * *
2195569 ATATAAGTATGTTATATACCAAAGGTATTATTGTAACCATCAATATAAGCTCCAAACAAAAAAAA
1 ATATAAGTATGTTATATACCAAAGTTATTATTGTAACCATCAGTATAAGCTACAAAC-AAAAAAA
* * * * * *
2195634 ATTACCAACCTTTATCTGAGAAAAAAAAAGTTACGGTGTATTGATGGATTTTTTATACCATTAGA
65 ATTACCAACCTCTATTTGAG-AAAAAAAAGTTACGATATATTGATGGATTTTTAATACCATTAAA
* * * ** * * *
2195699 ATATACAATATCTAGATTTGTATAATTATTGATACAGATAAACTTTTTTTTTAAGGTATATGAAT
129 ATATACAATATCAACATTTGTATAACTACCGATACAGATAAACTTTTTTCTGAAGATATATGAAT
2195764 ATTCGTCA
194 ATTCGTCA
* * * * * *
2195772 ATATAGGTGTGTTATATATCGATAA-TTATTATTCTAA-TAGTCAGTATAAGCTTCAAAC-AAAA
1 ATATAAGTATGTTATATA-CCA-AAGTTATTATTGTAACCA-TCAGTATAAGCTACAAACAAAAA
* * * *
2195834 AAATTACCAACCTCTATTTGAGAAAAAAAAGTTATGATATATTTATGGATTTTTAATATCGTTAA
63 AAATTACCAACCTCTATTTGAGAAAAAAAAGTTACGATATATTGATGGATTTTTAATACCATTAA
* **
2195899 AATATACAATAACTATATCAACACTTTGTATAGCTACCGATTTAGATAAAC-TTTTTCTGACA-A
128 AATATAC----A--ATATCAACA-TTTGTATAACTACCGATACAGATAAACTTTTTTCTGA-AGA
2195962 TATATGAATATTCGTCA
185 TATATGAATATTCGTCA
* * * * * *
2195979 GTATAAGTATGTTATATACTAAAGCTTATTATTGTAACCATTAGTATAAG-AACCAACTAAAAAA
1 ATATAAGTATGTTATATACCAAAG-TTATTATTGTAACCATCAGTATAAGCTACAAACAAAAAAA
* * *
2196043 ATTATCAACCTCTATTTGGGAAAAGAAAGTTA
65 ATTACCAACCTCTATTTGAGAAAAAAAAGTTA
2196075 GGGCTTAAAT
Statistics
Matches: 246, Mismatches: 42, Indels: 26
0.78 0.13 0.08
Matches are distributed among these distances:
201 42 0.17
202 24 0.10
203 17 0.07
204 28 0.11
205 5 0.02
206 6 0.02
207 101 0.41
208 23 0.09
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (201 bp):
ATATAAGTATGTTATATACCAAAGTTATTATTGTAACCATCAGTATAAGCTACAAACAAAAAAAA
TTACCAACCTCTATTTGAGAAAAAAAAGTTACGATATATTGATGGATTTTTAATACCATTAAAAT
ATACAATATCAACATTTGTATAACTACCGATACAGATAAACTTTTTTCTGAAGATATATGAATAT
TCGTCA
Found at i:2196169 original size:24 final size:24
Alignment explanation
Indices: 2196137--2196200 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
2196127 ACCACCTCTA
*
2196137 CATCTTCAAATCCTATCAGTACCC
1 CATCTTCAAATCCTATCAGCACCC
* * *
2196161 CATCTTCAAATCCCATCGGCACCT
1 CATCTTCAAATCCTATCAGCACCC
* *
2196185 GATCTTTAAATCCTAT
1 CATCTTCAAATCCTAT
2196201 TGCTTCTACA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.28, C:0.34, G:0.06, T:0.31
Consensus pattern (24 bp):
CATCTTCAAATCCTATCAGCACCC
Found at i:2196970 original size:38 final size:38
Alignment explanation
Indices: 2196919--2196996 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
2196909 GTTTTCCTAG
2196919 TAAATCCAAACTATTTCTAATAAAATTTCACAACTTGA
1 TAAATCCAAACTATTTCTAATAAAATTTCACAACTTGA
2196957 TAAATCCAAACTATTTCTAATAAAATTTCACAACTTGA
1 TAAATCCAAACTATTTCTAATAAAATTTCACAACTTGA
2196995 TA
1 TA
2196997 GCTTAGCATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.35
Consensus pattern (38 bp):
TAAATCCAAACTATTTCTAATAAAATTTCACAACTTGA
Found at i:2203945 original size:31 final size:31
Alignment explanation
Indices: 2203907--2203970 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
2203897 GCGTGAAGAG
2203907 TAAGAAGAGCTTTCCTTAAACTTAAAAAACT
1 TAAGAAGAGCTTTCCTTAAACTTAAAAAACT
2203938 TAAGAAGAGCTTTCCTTAAACTTAAAAAACT
1 TAAGAAGAGCTTTCCTTAAACTTAAAAAACT
2203969 TA
1 TA
2203971 GCTCAGACTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.30
Consensus pattern (31 bp):
TAAGAAGAGCTTTCCTTAAACTTAAAAAACT
Found at i:2205971 original size:19 final size:20
Alignment explanation
Indices: 2205943--2205988 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
2205933 AATGAAGAAA
2205943 TTAT-TTTTTTTATT-ATTT
1 TTATCTTTTTTTATTGATTT
2205961 TTATCTTTTTTTATTGATTT
1 TTATCTTTTTTTATTGATTT
2205981 TT-TCTTTT
1 TTATCTTTT
2205989 AAGTGGGAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.15
19 16 0.62
20 6 0.23
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.80
Consensus pattern (20 bp):
TTATCTTTTTTTATTGATTT
Found at i:2216108 original size:3 final size:3
Alignment explanation
Indices: 2216092--2216197 Score: 62
Period size: 3 Copynumber: 36.0 Consensus size: 3
2216082 ATAGTATGTC
* *
2216092 ATT ATT ATAC ATT ATT A-T ACT A-T ATTT ATT ATT ATT ATT ATT -TT
1 ATT ATT AT-T ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT
* * * * *
2216136 CATT ATC ATT ATC ATT ATC ATT ATT ATT ATT CTT ATT -TT TTT GATT
1 -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT
*
2216182 -TT ATT -TT ATT CTT ATT
1 ATT ATT ATT ATT ATT ATT
2216198 TTTCTTTTGT
Statistics
Matches: 80, Mismatches: 13, Indels: 20
0.71 0.12 0.18
Matches are distributed among these distances:
2 12 0.15
3 59 0.74
4 9 0.11
ACGTcount: A:0.28, C:0.08, G:0.01, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:2216970 original size:15 final size:14
Alignment explanation
Indices: 2216950--2217001 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 14
2216940 GCGCAAGGTT
2216950 TTTTTTTATTTTTAA
1 TTTTTTTATTTTT-A
*
2216965 TTTTTTAATTTTTA
1 TTTTTTTATTTTTA
2216979 TTTTTTTACTCATTTTA
1 TTTTTTTA-T--TTTTA
2216996 TTTTTT
1 TTTTTT
2217002 AGTTTTTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 8 0.25
15 13 0.41
17 11 0.34
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTTATTTTTA
Found at i:2216984 original size:7 final size:7
Alignment explanation
Indices: 2216951--2217009 Score: 55
Period size: 7 Copynumber: 7.9 Consensus size: 7
2216941 CGCAAGGTTT
2216951 TTTTTTA
1 TTTTTTA
*
2216958 TTTTTAA
1 TTTTTTA
2216965 TTTTTTA
1 TTTTTTA
*
2216972 ATTTTTA
1 TTTTTTA
2216979 TTTTTTTA
1 -TTTTTTA
*
2216987 CTCATTTTA
1 -T-TTTTTA
2216996 TTTTTTA
1 TTTTTTA
2217003 GTTTTTT
1 -TTTTTT
2217010 TCTCATTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
7 23 0.55
8 14 0.33
9 5 0.12
ACGTcount: A:0.17, C:0.03, G:0.02, T:0.78
Consensus pattern (7 bp):
TTTTTTA
Found at i:2216994 original size:24 final size:24
Alignment explanation
Indices: 2216967--2217026 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
2216957 ATTTTTAATT
*
2216967 TTTTAATTTTTA-TTTTTTTACTCA
1 TTTTATTTTTTAGTTTTTTT-CTCA
2216991 TTTTATTTTTTAGTTTTTTTCTCA
1 TTTTATTTTTTAGTTTTTTTCTCA
2217015 TTATTATTTTTT
1 TT-TTATTTTTT
2217027 GATCTTCTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 17 0.52
25 16 0.48
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.75
Consensus pattern (24 bp):
TTTTATTTTTTAGTTTTTTTCTCA
Found at i:2216994 original size:25 final size:25
Alignment explanation
Indices: 2216966--2217026 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
2216956 TATTTTTAAT
*
2216966 TTTTTAATTTTTA-TTTTTTTACTCA
1 TTTTTATTTTTTAGTTTTTTT-CTCA
2216991 -TTTTATTTTTTAGTTTTTTTCTCA
1 TTTTTATTTTTTAGTTTTTTTCTCA
*
2217015 TTATTATTTTTT
1 TTTTTATTTTTT
2217027 GATCTTCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
24 15 0.47
25 17 0.53
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (25 bp):
TTTTTATTTTTTAGTTTTTTTCTCA
Found at i:2217089 original size:3 final size:3
Alignment explanation
Indices: 2217081--2217115 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2217071 ATTTTTGCAA
2217081 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2217116 ATCTTCTCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2217814 original size:43 final size:43
Alignment explanation
Indices: 2217767--2217848 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
2217757 AAATTTGAGG
* * *
2217767 TTTTTCATTGCTTATGCTTGCTTAATTATTTATTTATTTTACT
1 TTTTTCATTACTTATACTTGCTTAATTAATTATTTATTTTACT
2217810 TTTTTCATTACTTATACTTGCTTAATTAATTATTTATTT
1 TTTTTCATTACTTATACTTGCTTAATTAATTATTTATTT
2217849 ATTATATGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.22, C:0.11, G:0.05, T:0.62
Consensus pattern (43 bp):
TTTTTCATTACTTATACTTGCTTAATTAATTATTTATTTTACT
Found at i:2227578 original size:66 final size:65
Alignment explanation
Indices: 2227442--2227565 Score: 187
Period size: 66 Copynumber: 1.9 Consensus size: 65
2227432 CTTTGCTTTT
* * *
2227442 AAAAAAAAAAAAAAAAAGTTCAAGTTGAAAACCTGAAAAGGTAACTTTAACCAAAAAACAAAACA
1 AAAAAAAAAAAAAAAAAGTTCAAGTTGAAAAACTGAAAAGGCAACTTGAACCAAAAAACAAAACA
*
2227507 AAAAAAAAAGAAAAAAAAGTTCAAGTT-AAAAACTTAAAAGGGCAACTTGAACCAAAAAA
1 AAAAAAAAA-AAAAAAAAGTTCAAGTTGAAAAACTGAAAA-GGCAACTTGAACCAAAAAA
2227566 TTTTAAAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
65 19 0.36
66 34 0.64
ACGTcount: A:0.65, C:0.11, G:0.10, T:0.14
Consensus pattern (65 bp):
AAAAAAAAAAAAAAAAAGTTCAAGTTGAAAAACTGAAAAGGCAACTTGAACCAAAAAACAAAACA
Found at i:2227648 original size:53 final size:54
Alignment explanation
Indices: 2227517--2227633 Score: 162
Period size: 54 Copynumber: 2.1 Consensus size: 54
2227507 AAAAAAAAAG
* ** * * *
2227517 AAAAAAAAGTTCAAGTTAAAAACTTAAAAGGGCAACTTGAACCAAAAAATTTTA
1 AAAAAAAAGTACAAGTTAAAAACCCAAAAGGGCAACTTAAACCAAAAAATATCA
*
2227571 AAAAAAAAGTACAAGTTAAAAACCCAAAAGGGTAACTTAAACCAAAAAATAATCA
1 AAAAAAAAGTACAAGTTAAAAACCCAAAAGGGCAACTTAAACCAAAAAAT-ATCA
2227626 AAAAAAAA
1 AAAAAAAA
2227634 TTTGAGTTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
54 45 0.82
55 10 0.18
ACGTcount: A:0.62, C:0.12, G:0.09, T:0.17
Consensus pattern (54 bp):
AAAAAAAAGTACAAGTTAAAAACCCAAAAGGGCAACTTAAACCAAAAAATATCA
Found at i:2229041 original size:692 final size:692
Alignment explanation
Indices: 2227718--2229103 Score: 2691
Period size: 692 Copynumber: 2.0 Consensus size: 692
2227708 GAAAGGCACA
*
2227718 CTAGGGGTAATGAATTTCAAAGAGCTCCAAGGTGTTAGGACATCATGTTTTGATTGAATTTTTCA
1 CTAGGGGTAATGAATTTCAAAGAGCTCCAAGGTGTTAGGACATCATGTTTTAATTGAATTTTTCA
2227783 AAAAAATTCAAGATTTGTTGTCATGATTATTTGATTGTTTGTTTTGGGGCATTGCCATCCCTAAA
66 AAAAAATTCAAGATTTGTTGTCATGATTATTTGATTGTTTGTTTTGGGGCATTGCCATCCCTAAA
2227848 TGGTCACCTTTATACATATTCATTTTATTTCTGGCCATCATTTGTAATTTATCGCTTACCTAAAT
131 TGGTCACCTTTATACATATTCATTTTATTTCTGGCCATCATTTGTAATTTATCGCTTACCTAAAT
*
2227913 AAACGATATTTGTCTTATTTTTCACTTTTGATATAGTTTCTTGCTCTTTATGCCTTGTTATGAAT
196 AAACGATATTTGTCTTATTTTTCACTTTTGATATAGTTTCTTACTCTTTATGCCTTGTTATGAAT
2227978 AGAAGAAGTGCATAGCTTGCATCTTATATTTTGAAATTGAGATAATGATTAATAATGGAATGAAG
261 AGAAGAAGTGCATAGCTTGCATCTTATATTTTGAAATTGAGATAATGATTAATAATGGAATGAAG
*
2228043 TTATAAGAAATTATTTGTTACTTTGAGAGAATTGAAAGAGACAAGGGCCAAAGATGAACTCTTTT
326 TTATAAGAAATTATGTGTTACTTTGAGAGAATTGAAAGAGACAAGGGCCAAAGATGAACTCTTTT
*
2228108 GAATAAAAGAGAATCAATAGCTTTCCTTAGGACAAAAATAAATGCATATTTGAGATGATGATGAT
391 GAATAAAAGAGAATCAAAAGCTTTCCTTAGGACAAAAATAAATGCATATTTGAGATGATGATGAT
2228173 AGTTTCCTTGCTAGAAAAGTGCAAAAAGATGAAAGCTATAGAAGCCTTAGTACCACAATGAATGC
456 AGTTTCCTTGCTAGAAAAGTGCAAAAAGATGAAAGCTATAGAAGCCTTAGTACCACAATGAATGC
* *
2228238 ATCCTAAATAGGGTATACATTCATATCATTGCATGCTCATCACATGTTTTGATTTCGTCTCAGAT
521 ATCCTAAATAGGGTATACATTCATATCATTGCATGCTCATCACAGGTCTTGATTTCGTCTCAGAT
2228303 CAAATCATCTTCAGACTCGCGGTATCAATCCAGTCATTTGTCTATGACCTTGACTCGATTTTAAT
586 CAAATCATCTTCAGACTCGCGGTATCAATCCAGTCATTTGTCTATGACCTTGACTCGATTTTAAT
*
2228368 CATCTTTAGACTCATGACATCAATCAATCATTTATCCAGGAC
651 CATCTTTAGACTCATGACATCAATCAATCATTTATCCAAGAC
2228410 CTAGGGGTAATGAATTTCAAAGAGCTCCAAGGTGTTAGGACATCATGTTTTAATTGAATTTTTCA
1 CTAGGGGTAATGAATTTCAAAGAGCTCCAAGGTGTTAGGACATCATGTTTTAATTGAATTTTTCA
2228475 AAAAAATTCAAGATTTGTTGTCATGATTATTTGATTGTTTGTTTTGGGGCATTGCCATCCCTAAA
66 AAAAAATTCAAGATTTGTTGTCATGATTATTTGATTGTTTGTTTTGGGGCATTGCCATCCCTAAA
2228540 TGGTCACCTTTATACATATTCATTTTATTTCTGGCCATCATTTGTAATTTATCGCTTACCTAAAT
131 TGGTCACCTTTATACATATTCATTTTATTTCTGGCCATCATTTGTAATTTATCGCTTACCTAAAT
2228605 AAACGATATTTGTCTTATTTTTCACTTTTGATATAGTTTCTTACTCTTTATGCCTTGTTATGAAT
196 AAACGATATTTGTCTTATTTTTCACTTTTGATATAGTTTCTTACTCTTTATGCCTTGTTATGAAT
2228670 AGAAGAAGTGCATAGCTTGCATCTTATATTTTGAAATTGAGATAATGATTAATAATGGAATGAAG
261 AGAAGAAGTGCATAGCTTGCATCTTATATTTTGAAATTGAGATAATGATTAATAATGGAATGAAG
2228735 TTATAAGAAATTATGTGTTACTTTGAGAGAATTGAAAGAGACAAGGGCCAAAGATGAACTCTTTT
326 TTATAAGAAATTATGTGTTACTTTGAGAGAATTGAAAGAGACAAGGGCCAAAGATGAACTCTTTT
*
2228800 GAATAAAAGAGAATTAAAAGCTTTCCTTAGGACAAAAATAAATGCATATTTGAGATGATGATGAT
391 GAATAAAAGAGAATCAAAAGCTTTCCTTAGGACAAAAATAAATGCATATTTGAGATGATGATGAT
2228865 AGTTTCCTTGCTAGAAAAGTGCAAAAAGATGAAAGCTATAGAAGCCTTAGTACCACAATGAATGC
456 AGTTTCCTTGCTAGAAAAGTGCAAAAAGATGAAAGCTATAGAAGCCTTAGTACCACAATGAATGC
2228930 ATCCTAAATAGGGTATACATTCATATCATTGCATGCTCATCACAGGTCTTGATTTCGTCTCAGAT
521 ATCCTAAATAGGGTATACATTCATATCATTGCATGCTCATCACAGGTCTTGATTTCGTCTCAGAT
*
2228995 CAAATCATCTTCAGACTCGCGGTATCAATCCGGTCATTTGTCTATGACCTTGACTCGATTTTAAT
586 CAAATCATCTTCAGACTCGCGGTATCAATCCAGTCATTTGTCTATGACCTTGACTCGATTTTAAT
2229060 CATCTTTAGACTCATGACATCAATCAATCATTTATCCAAGAC
651 CATCTTTAGACTCATGACATCAATCAATCATTTATCCAAGAC
2229102 CT
1 CT
2229104 CGACTCGATC
Statistics
Matches: 685, Mismatches: 9, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
692 685 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (692 bp):
CTAGGGGTAATGAATTTCAAAGAGCTCCAAGGTGTTAGGACATCATGTTTTAATTGAATTTTTCA
AAAAAATTCAAGATTTGTTGTCATGATTATTTGATTGTTTGTTTTGGGGCATTGCCATCCCTAAA
TGGTCACCTTTATACATATTCATTTTATTTCTGGCCATCATTTGTAATTTATCGCTTACCTAAAT
AAACGATATTTGTCTTATTTTTCACTTTTGATATAGTTTCTTACTCTTTATGCCTTGTTATGAAT
AGAAGAAGTGCATAGCTTGCATCTTATATTTTGAAATTGAGATAATGATTAATAATGGAATGAAG
TTATAAGAAATTATGTGTTACTTTGAGAGAATTGAAAGAGACAAGGGCCAAAGATGAACTCTTTT
GAATAAAAGAGAATCAAAAGCTTTCCTTAGGACAAAAATAAATGCATATTTGAGATGATGATGAT
AGTTTCCTTGCTAGAAAAGTGCAAAAAGATGAAAGCTATAGAAGCCTTAGTACCACAATGAATGC
ATCCTAAATAGGGTATACATTCATATCATTGCATGCTCATCACAGGTCTTGATTTCGTCTCAGAT
CAAATCATCTTCAGACTCGCGGTATCAATCCAGTCATTTGTCTATGACCTTGACTCGATTTTAAT
CATCTTTAGACTCATGACATCAATCAATCATTTATCCAAGAC
Found at i:2229421 original size:114 final size:113
Alignment explanation
Indices: 2229160--2229431 Score: 255
Period size: 114 Copynumber: 2.4 Consensus size: 113
2229150 TCTAATTTTG
* * * *
2229160 ACTCAGGTCAGATCATCTTCAAACTCGTAGCATCAGTCCAATCATTTATCTATGACCTCGACTTA
1 ACTCAGGTCAGATCAT-TTCAGACTCATAGCATCAGTCCAATCATTTACCTACGACCTCGACTTA
* **
2229225 GTCTTGATCATCTTTAGACTCGTAGTATCATCCCAGTCATCTGATCTTG
65 GTCTTGATCATCTTTAGACTCGTAATATCATCCCAGTCATCTGATCTCA
* * * **** *
2229274 ACTCAAGTCAGATCATTTTTAGACTTACT-GCATCAGTTTGGTCATTTACCTACGACCTTGACTT
1 ACTCAGGTCAGATCA-TTTCAGACTCA-TAGCATCAGTCCAATCATTTACCTACGACCTCGACTT
* * * * *
2229338 GGTCTTGGTCA-CTTTTTGACTCGTAATATTATCTCAGTCAT-TCGATCTCA
64 AGTCTTGATCATC-TTTAGACTCGTAATATCATCCCAGTCATCT-GATCTCA
* *
2229388 ATTTAGGTCAGATCACTTTCAGACTCATAGCATCA-TCCCAATCA
1 ACTCAGGTCAGATCA-TTTCAGACTCATAGCATCAGT-CCAATCA
2229432 CTCAATCTTG
Statistics
Matches: 122, Mismatches: 30, Indels: 12
0.74 0.18 0.07
Matches are distributed among these distances:
113 4 0.03
114 116 0.95
115 2 0.02
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (113 bp):
ACTCAGGTCAGATCATTTCAGACTCATAGCATCAGTCCAATCATTTACCTACGACCTCGACTTAG
TCTTGATCATCTTTAGACTCGTAATATCATCCCAGTCATCTGATCTCA
Found at i:2229700 original size:10 final size:10
Alignment explanation
Indices: 2229685--2229725 Score: 82
Period size: 10 Copynumber: 4.1 Consensus size: 10
2229675 TATAGTATGT
2229685 CATTATTATA
1 CATTATTATA
2229695 CATTATTATA
1 CATTATTATA
2229705 CATTATTATA
1 CATTATTATA
2229715 CATTATTATA
1 CATTATTATA
2229725 C
1 C
2229726 TATAGTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (10 bp):
CATTATTATA
Found at i:2229702 original size:3 final size:3
Alignment explanation
Indices: 2229686--2229805 Score: 56
Period size: 3 Copynumber: 40.0 Consensus size: 3
2229676 ATAGTATGTC
* * * *
2229686 ATT ATT ATAC ATT ATT ATAC ATT ATT ATAC ATT ATT A-T ACT A-T AGTT
1 ATT ATT AT-T ATT ATT AT-T ATT ATT AT-T ATT ATT ATT ATT ATT A-TT
* * *
2229733 ATT ATT ATT ATT ATT A-T AGT ATAT GTT ATAT ACT A-T AGTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT AT-T ATT ATT A-TT ATT ATT
*
2229779 ATT ATT -TT ATT -TT ATT -TT ATT CTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2229806 GTTTTGGTCA
Statistics
Matches: 91, Mismatches: 12, Indels: 28
0.69 0.09 0.21
Matches are distributed among these distances:
2 14 0.15
3 63 0.69
4 14 0.15
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:2229778 original size:31 final size:26
Alignment explanation
Indices: 2229706--2229780 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 26
2229696 ATTATTATAC
*
2229706 ATTATTATACATTATTATACTATAGTT
1 ATTATTAT-TATTATTATACTATAGTT
*
2229733 ATTATTATTATTATTATAGTATATGTT
1 ATTATTATTATTATTATACTATA-GTT
2229760 ATATACTATAGTTATTATTAT
1 AT-TA-T-TA-TTATTATTAT
2229781 TATTTTATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
26 13 0.32
27 13 0.32
28 2 0.05
29 1 0.02
30 2 0.05
31 10 0.24
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (26 bp):
ATTATTATTATTATTATACTATAGTT
Found at i:2230582 original size:14 final size:14
Alignment explanation
Indices: 2230565--2230666 Score: 73
Period size: 14 Copynumber: 7.2 Consensus size: 14
2230555 TCTTTTTCTA
2230565 TTTTATTTTTATTT
1 TTTTATTTTTATTT
***
2230579 TTTTATTCCAATTT
1 TTTTATTTTTATTT
*
2230593 TTTTATTTTCATTT
1 TTTTATTTTTATTT
2230607 TTTTACTCATTTTA-TT
1 TTTTA-T--TTTTATTT
* *
2230623 TTTTAGTTTT-TGT
1 TTTTATTTTTATTT
* * *
2230636 TCTCATTATTATTT
1 TTTTATTTTTATTT
*
2230650 TTTTATCTTTATTT
1 TTTTATTTTTATTT
2230664 TTT
1 TTT
2230667 AAGAAATTTT
Statistics
Matches: 65, Mismatches: 18, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
13 11 0.17
14 42 0.65
15 1 0.02
16 7 0.11
17 4 0.06
ACGTcount: A:0.16, C:0.08, G:0.02, T:0.75
Consensus pattern (14 bp):
TTTTATTTTTATTT
Found at i:2230623 original size:23 final size:24
Alignment explanation
Indices: 2230593--2230650 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
2230583 ATTCCAATTT
2230593 TTTTATTTTCA-TTTTT-TTACTCA
1 TTTTATTTTCAGTTTTTGTT-CTCA
*
2230616 TTTTATTTTTTAGTTTTTGTTCTCA
1 TTTTA-TTTTCAGTTTTTGTTCTCA
2230641 TTATTATTTT
1 TT-TTATTTT
2230651 TTTATCTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 5 0.17
24 5 0.17
25 15 0.50
26 5 0.17
ACGTcount: A:0.16, C:0.09, G:0.03, T:0.72
Consensus pattern (24 bp):
TTTTATTTTCAGTTTTTGTTCTCA
Found at i:2230624 original size:28 final size:29
Alignment explanation
Indices: 2230563--2230624 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
2230553 TTTCTTTTTC
* *
2230563 TATTTTATTTTTATTTTTTTATTCCAATT
1 TATTTTATTTTCATTTTTTTACTCCAATT
*
2230592 T-TTTTATTTTCATTTTTTTACT-CATTT
1 TATTTTATTTTCATTTTTTTACTCCAATT
2230619 TATTTT
1 TATTTT
2230625 TTAGTTTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 5 0.17
28 23 0.79
29 1 0.03
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (29 bp):
TATTTTATTTTCATTTTTTTACTCCAATT
Found at i:2230712 original size:3 final size:3
Alignment explanation
Indices: 2230704--2230738 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2230694 ATTTTTACAA
2230704 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2230739 ATCTTCTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2235066 original size:29 final size:30
Alignment explanation
Indices: 2235029--2235108 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 30
2235019 AATTAATAAA
2235029 TTTATAATTTAAATATTATATTAAA-AATT
1 TTTATAATTTAAATATTATATTAAATAATT
* * *
2235058 TTTAAAATTTATATATTATATTAAATATTT
1 TTTATAATTTAAATATTATATTAAATAATT
*
2235088 TATTATAATTTAAAAATTATA
1 T-TTATAATTTAAATATTATA
2235109 AGTGACATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 23 0.53
30 4 0.09
31 16 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
TTTATAATTTAAATATTATATTAAATAATT
Found at i:2237041 original size:2 final size:2
Alignment explanation
Indices: 2237034--2237084 Score: 50
Period size: 2 Copynumber: 25.0 Consensus size: 2
2237024 TTTACGTGAA
* * *
2237034 AT AT AT AT AT AT AT AT AT AT AT AT TT TT CAT TT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
2237076 ACT AT AT AT
1 A-T AT AT AT
2237085 TTTATATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
1 1 0.02
2 38 0.90
3 3 0.07
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2237093 original size:27 final size:27
Alignment explanation
Indices: 2237034--2237093 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
2237024 TTTACGTGAA
*
2237034 ATATATATATATATATATATATATTTT
1 ATATTTATATATATATATATATATTTT
2237061 -TCATTTATATATA-ATACTATATATTTT
1 AT-ATTTATATATATATA-TATATATTTT
2237088 ATATTT
1 ATATTT
2237094 TATTAAGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
26 4 0.14
27 24 0.83
28 1 0.03
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (27 bp):
ATATTTATATATATATATATATATTTT
Found at i:2238047 original size:2 final size:2
Alignment explanation
Indices: 2238042--2238067 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2238032 TTTTTTAATA
2238042 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2238068 TAGACCTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2238277 original size:24 final size:24
Alignment explanation
Indices: 2238243--2238302 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
2238233 TTTAACTACA
* *
2238243 TTATATATATATATA-TATTGTATT
1 TTATATTTATATATACTA-TATATT
2238267 TTATATTTATATATACTATATATT
1 TTATATTTATATATACTATATATT
2238291 TTATA-TTATATA
1 TTATATTTATATA
2238303 AAGGATAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
23 7 0.21
24 24 0.73
25 2 0.06
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
TTATATTTATATATACTATATATT
Found at i:2238286 original size:7 final size:7
Alignment explanation
Indices: 2238246--2238302 Score: 53
Period size: 7 Copynumber: 7.9 Consensus size: 7
2238236 AACTACATTA
2238246 TATATAT
1 TATATAT
2238253 ATATATAT
1 -TATATAT
* *
2238261 TGTATTT
1 TATATAT
2238268 TATAT-T
1 TATATAT
2238274 TATATAT
1 TATATAT
2238281 ACTATATAT
1 --TATATAT
*
2238290 TTTATAT
1 TATATAT
2238297 TATATA
1 TATATA
2238303 AAGGATAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
6 6 0.15
7 21 0.51
8 7 0.17
9 7 0.17
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (7 bp):
TATATAT
Found at i:2240403 original size:19 final size:20
Alignment explanation
Indices: 2240365--2240403 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2240355 TATTACTTGA
* *
2240365 GATTTAAAATCATTTTATTT
1 GATTAAAAATCATTTAATTT
2240385 GATTAAAAATCA-TTAATTT
1 GATTAAAAATCATTTAATTT
2240404 TTAATAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (20 bp):
GATTAAAAATCATTTAATTT
Found at i:2242212 original size:22 final size:22
Alignment explanation
Indices: 2242169--2242212 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
2242159 TGGCAAAAAA
*
2242169 GAAATTTTAAAATTTCAGGTTT
1 GAAATTTTAAAATTTCAAGTTT
* * *
2242191 GAAATTTTTAGATTTTAAGTTT
1 GAAATTTTAAAATTTCAAGTTT
2242213 ACGTTCTTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.50
Consensus pattern (22 bp):
GAAATTTTAAAATTTCAAGTTT
Found at i:2243005 original size:20 final size:20
Alignment explanation
Indices: 2242980--2243018 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2242970 GAGTTAGGAC
2242980 TTGAGGCTTAAATCCCATGT
1 TTGAGGCTTAAATCCCATGT
2243000 TTGAGGCTTAAATCCCATG
1 TTGAGGCTTAAATCCCATG
2243019 CTTCTTCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (20 bp):
TTGAGGCTTAAATCCCATGT
Found at i:2245937 original size:9 final size:10
Alignment explanation
Indices: 2245923--2245968 Score: 76
Period size: 10 Copynumber: 4.6 Consensus size: 10
2245913 TTCATTTTTC
2245923 TTTTTTCCTT-
1 TTTTTT-CTTA
2245933 TTTTTTCTTA
1 TTTTTTCTTA
2245943 TTTTTTCTTA
1 TTTTTTCTTA
2245953 TTTTTTCTTA
1 TTTTTTCTTA
2245963 TTTTTT
1 TTTTTT
2245969 ATACATCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
9 3 0.09
10 32 0.91
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTCTTA
Found at i:2245988 original size:11 final size:11
Alignment explanation
Indices: 2245934--2246005 Score: 60
Period size: 10 Copynumber: 6.7 Consensus size: 11
2245924 TTTTTCCTTT
2245934 TTTTTCTTAT-
1 TTTTTCTTATC
2245944 TTTTTCTTAT-
1 TTTTTCTTATC
2245954 TTTTTCTTAT-
1 TTTTTCTTATC
* *
2245964 TTTTTATACATC
1 TTTTTCT-TATC
*
2245976 TTTTTCTTTTC
1 TTTTTCTTATC
* *
2245987 TTTTCCTTCTC
1 TTTTTCTTATC
*
2245998 ATTTTCTT
1 TTTTTCTT
2246006 TTCCTTTAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
10 26 0.51
11 19 0.37
12 6 0.12
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTCTTATC
Found at i:2246309 original size:24 final size:25
Alignment explanation
Indices: 2246282--2246339 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
2246272 TTTTTTTTCA
*
2246282 TTTCTCTTTGTCTTCAT-TTTTCTT
1 TTTCTCTTTGTCTTCATATTTTCCT
* * *
2246306 TTTCTATTTTTTTTCATATTTTCCT
1 TTTCTCTTTGTCTTCATATTTTCCT
*
2246331 TTTCACTTT
1 TTTCTCTTT
2246340 TGATTTTTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 14 0.52
25 13 0.48
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTCTCTTTGTCTTCATATTTTCCT
Found at i:2249352 original size:21 final size:20
Alignment explanation
Indices: 2249328--2249381 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
2249318 TAGAGATAAT
2249328 AATAAAAAAACA-AATTAAAAA
1 AATAAAAAAA-ATAA-TAAAAA
2249349 AATAATAAAAAATAATAAAAA
1 AATAA-AAAAAATAATAAAAA
*
2249370 AAGAAAAAAAAT
1 AATAAAAAAAAT
2249382 TGAAATTGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 7 0.23
21 16 0.53
22 7 0.23
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (20 bp):
AATAAAAAAAATAATAAAAA
Found at i:2249358 original size:10 final size:10
Alignment explanation
Indices: 2249345--2249370 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2249335 AAACAAATTA
2249345 AAAAAATAAT
1 AAAAAATAAT
2249355 AAAAAATAAT
1 AAAAAATAAT
2249365 AAAAAA
1 AAAAAA
2249371 AGAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (10 bp):
AAAAAATAAT
Found at i:2254335 original size:24 final size:24
Alignment explanation
Indices: 2254308--2254354 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
2254298 AGTATAATGG
2254308 TTCTTAAATTATATGACATGTTGC
1 TTCTTAAATTATATGACATGTTGC
2254332 TTCTTAAATTATATGACATGTTG
1 TTCTTAAATTATATGACATGTTG
2254355 TAATGCAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.11, G:0.13, T:0.47
Consensus pattern (24 bp):
TTCTTAAATTATATGACATGTTGC
Found at i:2259663 original size:15 final size:15
Alignment explanation
Indices: 2259643--2259674 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2259633 ACAAAATTAG
2259643 ATTAATCCTTATAAA
1 ATTAATCCTTATAAA
2259658 ATTAATCCTTATAAA
1 ATTAATCCTTATAAA
2259673 AT
1 AT
2259675 CCATGTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTAATCCTTATAAA
Found at i:2264887 original size:12 final size:12
Alignment explanation
Indices: 2264861--2264907 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
2264851 AAGCTGCTTC
*
2264861 TATTTTTTTA-G
1 TATTTTTTTATT
2264872 TATTTTTTTATT
1 TATTTTTTTATT
*
2264884 TATTTTATTTAGT
1 TATTTT-TTTATT
*
2264897 TATTTATTTAT
1 TATTTTTTTAT
2264908 GTGTTTGATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
11 10 0.33
12 10 0.33
13 10 0.33
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.74
Consensus pattern (12 bp):
TATTTTTTTATT
Found at i:2266640 original size:24 final size:24
Alignment explanation
Indices: 2266613--2266660 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
2266603 ATATCAAAAC
*
2266613 ATCATTAAATTTTCATACCAATAT
1 ATCATCAAATTTTCATACCAATAT
2266637 ATCATCAAATTTTCATACCAATAT
1 ATCATCAAATTTTCATACCAATAT
2266661 TTCTCTCCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.40
Consensus pattern (24 bp):
ATCATCAAATTTTCATACCAATAT
Found at i:2266771 original size:13 final size:13
Alignment explanation
Indices: 2266753--2266778 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2266743 ATCATTAAGC
2266753 CACACAACAATAG
1 CACACAACAATAG
2266766 CACACAACAATAG
1 CACACAACAATAG
2266779 AATGAAAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.31, G:0.08, T:0.08
Consensus pattern (13 bp):
CACACAACAATAG
Found at i:2273040 original size:21 final size:21
Alignment explanation
Indices: 2272998--2273040 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
2272988 TTTTGCTAGG
* *
2272998 GGATCGATCCCTTCCCTTAAA
1 GGATCGATCCCTTCCATCAAA
2273019 GGATCGATCCCTTCCATCAAA
1 GGATCGATCCCTTCCATCAAA
2273040 G
1 G
2273041 CTTGTACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.26
Consensus pattern (21 bp):
GGATCGATCCCTTCCATCAAA
Found at i:2278285 original size:17 final size:17
Alignment explanation
Indices: 2278263--2278334 Score: 74
Period size: 17 Copynumber: 4.0 Consensus size: 17
2278253 AAAAAAATGA
*
2278263 AAAAAAAAAGAAGAAAG
1 AAAAAAAAAGAAAAAAG
*
2278280 AAAAAAAATTA-AAAAATTAA
1 AAAAAAAA--AGAAAAA--AG
2278300 AAAAAAAAAGAAAAAAG
1 AAAAAAAAAGAAAAAAG
2278317 AAAAAAAAAGGAAAAAAG
1 AAAAAAAAA-GAAAAAAG
2278335 GGAAAGAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
17 18 0.39
18 13 0.28
19 6 0.13
20 9 0.20
ACGTcount: A:0.83, C:0.00, G:0.11, T:0.06
Consensus pattern (17 bp):
AAAAAAAAAGAAAAAAG
Found at i:2278303 original size:37 final size:37
Alignment explanation
Indices: 2278253--2278324 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
2278243 GAATGGATGA
* *
2278253 AAAAAAATGAAAAAAAAAAGAAGAAAGAAAAAAAATT
1 AAAAAAATAAAAAAAAAAAGAAAAAAGAAAAAAAATT
*
2278290 AAAAAATTAAAAAAAAAAAGAAAAAAGAAAAAAAA
1 AAAAAAATAAAAAAAAAAAGAAAAAAGAAAAAAAA
2278325 AGGAAAAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.07
Consensus pattern (37 bp):
AAAAAAATAAAAAAAAAAAGAAAAAAGAAAAAAAATT
Found at i:2278325 original size:24 final size:24
Alignment explanation
Indices: 2278263--2278348 Score: 64
Period size: 27 Copynumber: 3.3 Consensus size: 24
2278253 AAAAAAATGA
* *
2278263 AAAAAAAAAGAAGAAAGAAAAAAAATT
1 AAAAAAAAAGAA-AAA-AAGAAAAA-G
*
2278290 AAAAAATTAAAAAAAAAAAGAAAAAAG
1 AAAAAA--AAAGAAAAAAAG-AAAAAG
* **
2278317 AAAAAAAAAGGAAAAAAGGGAAAG
1 AAAAAAAAAGAAAAAAAGAAAAAG
2278341 AAAAAAAA
1 AAAAAAAA
2278349 TTTTAAACAA
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
24 12 0.24
25 10 0.20
27 14 0.29
28 8 0.16
29 5 0.10
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.05
Consensus pattern (24 bp):
AAAAAAAAAGAAAAAAAGAAAAAG
Found at i:2278332 original size:37 final size:37
Alignment explanation
Indices: 2278253--2278333 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
2278243 GAATGGATGA
* * * **
2278253 AAAAAAATGAAAAAAAAAAGAAGAAAGAAAAAAAATT
1 AAAAAATTAAAAAAAAAAAGAAAAAAGAAAAAAAAAG
2278290 AAAAAATTAAAAAAAAAAAGAAAAAAGAAAAAAAAAGG
1 AAAAAATTAAAAAAAAAAAGAAAAAAGAAAAAAAAA-G
2278328 AAAAAA
1 AAAAAA
2278334 GGGAAAGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
37 32 0.84
38 6 0.16
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (37 bp):
AAAAAATTAAAAAAAAAAAGAAAAAAGAAAAAAAAAG
Found at i:2279789 original size:21 final size:21
Alignment explanation
Indices: 2279765--2279827 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
2279755 GACAAGATTG
*
2279765 TGAATTTCATATGAGAATCTT
1 TGAATTTCAAATGAGAATCTT
*
2279786 TGAATTTCAAATGTGAATCTT
1 TGAATTTCAAATGAGAATCTT
* *
2279807 TGAGTTTTAAATGAGAATCTT
1 TGAATTTCAAATGAGAATCTT
2279828 CAAGGAATGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (21 bp):
TGAATTTCAAATGAGAATCTT
Found at i:2280393 original size:44 final size:44
Alignment explanation
Indices: 2280321--2280651 Score: 299
Period size: 44 Copynumber: 7.5 Consensus size: 44
2280311 GTCGAGAAGC
* * * *
2280321 GCTTTATTTATTTTTTCAAAGTCATTGAGCCTCTGCTTAGAGGA
1 GCTTTGTTTATTTTTCCAAAGTTATTGAGCCTCTACTTAGAGGA
* * *
2280365 GCCTTGTTTATTTTTCCAAAGTTGTTGAGCCTCTGA-TTACAGGA
1 GCTTTGTTTATTTTTCCAAAGTTATTGAGCCTCT-ACTTAGAGGA
* *
2280409 GCTTTGTTTATTTTTCCAAAGTCATTGACCCTCTACTTAGAGGA
1 GCTTTGTTTATTTTTCCAAAGTTATTGAGCCTCTACTTAGAGGA
* * * * * * *
2280453 GCCTTGTTTA-TTTTCTCAAAGTCATTAAGCCTCTGCTTAAAAGT
1 GCTTTGTTTATTTTTC-CAAAGTTATTGAGCCTCTACTTAGAGGA
* * * * * *
2280497 GCTTTATTTATCTTTCCAAAGTTGTTAAACCTTTACTTAGAGGA
1 GCTTTGTTTATTTTTCCAAAGTTATTGAGCCTCTACTTAGAGGA
* * ** * *
2280541 TCTTTATTTATTTTTTTAAAGTTGTTGAGCCTCTATTTAGAGGA
1 GCTTTGTTTATTTTTCCAAAGTTATTGAGCCTCTACTTAGAGGA
* * **
2280585 GGTTTGTTTATTTTT-CAGAAGTTATTGAGCCTCTATTTAGAATA
1 GCTTTGTTTATTTTTCCA-AAGTTATTGAGCCTCTACTTAGAGGA
* * *
2280629 GCCTTATTTATTTTTCGAAAGTT
1 GCTTTGTTTATTTTTCCAAAGTT
2280652 GTAAAACCTC
Statistics
Matches: 232, Mismatches: 49, Indels: 12
0.79 0.17 0.04
Matches are distributed among these distances:
43 7 0.03
44 220 0.95
45 5 0.02
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (44 bp):
GCTTTGTTTATTTTTCCAAAGTTATTGAGCCTCTACTTAGAGGA
Found at i:2280423 original size:88 final size:88
Alignment explanation
Indices: 2280321--2280653 Score: 339
Period size: 88 Copynumber: 3.8 Consensus size: 88
2280311 GTCGAGAAGC
* * *
2280321 GCTTTATTTATTTTTTCAAAGTCATTGAGCCTCTGCTTAGAGGAGCCTTGTTTATTTTTCCAAAG
1 GCTTTATTTATTTTTCCAAAGTCATTGAGCCTCTACTTAGAGGAGCCTTATTTATTTTTCCAAAG
*
2280386 TTGTTGAGCCTCTGATTACAGGA
66 TTGTTGAGCCTCTGATTAAAGGA
* * *
2280409 GCTTTGTTTATTTTTCCAAAGTCATTGACCCTCTACTTAGAGGAGCCTTGTTTA-TTTTCTCAAA
1 GCTTTATTTATTTTTCCAAAGTCATTGAGCCTCTACTTAGAGGAGCCTTATTTATTTTTC-CAAA
** * * * *
2280473 GTCATTAAGCCTCTGCTTAAAAGT
65 GTTGTTGAGCCTCTGATTAAAGGA
* ** * * * * * **
2280497 GCTTTATTTATCTTTCCAAAGTTGTTAAACCTTTACTTAGAGGATCTTTATTTATTTTTTTAAAG
1 GCTTTATTTATTTTTCCAAAGTCATTGAGCCTCTACTTAGAGGAGCCTTATTTATTTTTCCAAAG
*
2280562 TTGTTGAGCCTCT-ATTTAGAGGA
66 TTGTTGAGCCTCTGA-TTAAAGGA
* * * * ** *
2280585 GGTTTGTTTATTTTT-CAGAAGTTATTGAGCCTCTATTTAGAATAGCCTTATTTATTTTTCGAAA
1 GCTTTATTTATTTTTCCA-AAGTCATTGAGCCTCTACTTAGAGGAGCCTTATTTATTTTTCCAAA
2280649 GTTGT
65 GTTGT
2280654 AAAACCTCTA
Statistics
Matches: 197, Mismatches: 44, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
87 7 0.04
88 186 0.94
89 4 0.02
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.45
Consensus pattern (88 bp):
GCTTTATTTATTTTTCCAAAGTCATTGAGCCTCTACTTAGAGGAGCCTTATTTATTTTTCCAAAG
TTGTTGAGCCTCTGATTAAAGGA
Found at i:2280669 original size:132 final size:130
Alignment explanation
Indices: 2280327--2280686 Score: 389
Period size: 132 Copynumber: 2.7 Consensus size: 130
2280317 AAGCGCTTTA
** * *
2280327 TTTATTTTTTCAAAGTCATTGAGCCTCTGCTTAGAGGAGCCTTGTTTATTTTTCCAAAGTTGTTG
1 TTTA-TTTTTCAAAGTCATTGAGCCTCTGCTTAGAATAGCCTTATTTATTTTTCCAAAGTTGTTA
* * * *
2280392 AGCCTCTGATTACAGGAGCTTTGTTTATTTTTCCAAAGTCATTGACCCTCTACTTAGAGGAGCCT
65 AACCTCT-ATTAGAGGATCTTTATTTATTTTTCCAAAGTCATTGACCCTCTACTTAGAGGAGCCT
2280457 TG
129 TG
* * * *
2280459 TTTATTTTCTCAAAGTCATTAAGCCTCTGCTTAAAAGT-GCTTTATTTATCTTTCCAAAGTTGTT
1 TTTATTTT-TCAAAGTCATTGAGCCTCTGCTTAGAA-TAGCCTTATTTATTTTTCCAAAGTTGTT
* ** ** * * **
2280523 AAACCTTTACTTAGAGGATCTTTATTTATTTTTTTAAAGTTGTTGAGCCTCTATTTAGAGGAGGT
64 AAACCTCTA-TTAGAGGATCTTTATTTATTTTTCCAAAGTCATTGACCCTCTACTTAGAGGAGCC
2280588 TTG
128 TTG
* ** * *
2280591 TTTATTTTTCAGAAGTTATTGAGCCTCTATTTAGAATAGCCTTATTTATTTTTCGAAAGTTGTAA
1 TTTATTTTTCA-AAGTCATTGAGCCTCTGCTTAGAATAGCCTTATTTATTTTTCCAAAGTTGTTA
*
2280656 AACCTCTATTTAGAGGAGTTTTTATGTTATT
65 AACCTCTA-TTAGAGGA-TCTTTAT-TTATT
2280687 CAAGAAGTCT
Statistics
Matches: 188, Mismatches: 33, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
131 9 0.05
132 168 0.89
133 6 0.03
134 5 0.03
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (130 bp):
TTTATTTTTCAAAGTCATTGAGCCTCTGCTTAGAATAGCCTTATTTATTTTTCCAAAGTTGTTAA
ACCTCTATTAGAGGATCTTTATTTATTTTTCCAAAGTCATTGACCCTCTACTTAGAGGAGCCTTG
Found at i:2280861 original size:12 final size:11
Alignment explanation
Indices: 2280833--2280871 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
2280823 TTTTGCTAAT
2280833 AAAAAAAAA-G
1 AAAAAAAAATG
*
2280843 AATAAAAAATTG
1 AA-AAAAAAATG
2280855 AAAAAAAAATG
1 AAAAAAAAATG
2280866 AAAAAA
1 AAAAAA
2280872 TAGGTAGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 2 0.08
11 20 0.80
12 3 0.12
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (11 bp):
AAAAAAAAATG
Found at i:2281188 original size:30 final size:31
Alignment explanation
Indices: 2281148--2281212 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
2281138 AAATTTCCAG
*
2281148 TTTTCGATGAG-TTTTTAACATCGATTGAAT
1 TTTTCAATGAGTTTTTTAACATCGATTGAAT
**
2281178 TTTTCAATGAGTTTTTTTGCATCGATTGAAT
1 TTTTCAATGAGTTTTTTAACATCGATTGAAT
2281209 TTTT
1 TTTT
2281213 TGGTAGGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 10 0.32
31 21 0.68
ACGTcount: A:0.23, C:0.09, G:0.15, T:0.52
Consensus pattern (31 bp):
TTTTCAATGAGTTTTTTAACATCGATTGAAT
Found at i:2283757 original size:15 final size:16
Alignment explanation
Indices: 2283734--2283770 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
2283724 GAAACATTAT
2283734 CAATAATTTGA-AAAC
1 CAATAATTTGATAAAC
*
2283749 CAATTATTTGATAAAC
1 CAATAATTTGATAAAC
2283765 C-ATAAT
1 CAATAAT
2283771 ATTAGACAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (16 bp):
CAATAATTTGATAAAC
Found at i:2288416 original size:33 final size:33
Alignment explanation
Indices: 2288374--2288481 Score: 216
Period size: 33 Copynumber: 3.3 Consensus size: 33
2288364 ACTCTATCAC
2288374 ATAATTTTAGTATTTATATTCACATAAACAATT
1 ATAATTTTAGTATTTATATTCACATAAACAATT
2288407 ATAATTTTAGTATTTATATTCACATAAACAATT
1 ATAATTTTAGTATTTATATTCACATAAACAATT
2288440 ATAATTTTAGTATTTATATTCACATAAACAATT
1 ATAATTTTAGTATTTATATTCACATAAACAATT
2288473 ATAATTTTA
1 ATAATTTTA
2288482 AAGTAAAAAT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 75 1.00
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (33 bp):
ATAATTTTAGTATTTATATTCACATAAACAATT
Found at i:2289638 original size:2 final size:2
Alignment explanation
Indices: 2289631--2289664 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2289621 ATAGCTATTC
2289631 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2289665 TCTACTCTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2292549 original size:26 final size:26
Alignment explanation
Indices: 2292520--2292571 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
2292510 GCATCATTGG
2292520 CATATTATCAATCAAATCCAATTAAA
1 CATATTATCAATCAAATCCAATTAAA
2292546 CATATTATCAATCAAATCCAATTAAA
1 CATATTATCAATCAAATCCAATTAAA
2292572 TTCAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (26 bp):
CATATTATCAATCAAATCCAATTAAA
Found at i:2297923 original size:19 final size:19
Alignment explanation
Indices: 2297901--2297941 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2297891 TTTAATTATT
* *
2297901 ATTTTTTTGTTTTTTCTTC
1 ATTTTTTTGTTTCTTCTAC
2297920 ATTTTTTTGTTTCTTCTAC
1 ATTTTTTTGTTTCTTCTAC
2297939 ATT
1 ATT
2297942 ACCATGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.10, C:0.12, G:0.05, T:0.73
Consensus pattern (19 bp):
ATTTTTTTGTTTCTTCTAC
Found at i:2298530 original size:22 final size:23
Alignment explanation
Indices: 2298486--2298532 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2298476 GAAATTACAC
2298486 AAACAAAATGTGAATGAAGATTG
1 AAACAAAATGTGAATGAAGATTG
2298509 AAACAAAAT-TGAAATGAA-ATTG
1 AAACAAAATGTG-AATGAAGATTG
2298531 AA
1 AA
2298533 GTTTTAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.57, C:0.04, G:0.17, T:0.21
Consensus pattern (23 bp):
AAACAAAATGTGAATGAAGATTG
Found at i:2301217 original size:21 final size:21
Alignment explanation
Indices: 2301193--2301258 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
2301183 TTTTACTTTT
*
2301193 TTTTATTTGAT-TTTTTAATTA
1 TTTTATTTGATATTATT-ATTA
2301214 TTTT-TTATGATATTATTATTA
1 TTTTATT-TGATATTATTATTA
* *
2301235 TTATTATTTTATGTTATTATTA
1 TT-TTATTTGATATTATTATTA
2301257 TT
1 TT
2301259 ATTCATTCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 2 0.05
21 14 0.37
22 20 0.53
23 2 0.05
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (21 bp):
TTTTATTTGATATTATTATTA
Found at i:2301232 original size:3 final size:3
Alignment explanation
Indices: 2301224--2301261 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
2301214 TTTTTTATGA
*
2301224 TAT TAT TAT TAT TAT TAT T-T TA- TGT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2301262 CATTCTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 3 0.10
3 28 0.90
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2301252 original size:25 final size:24
Alignment explanation
Indices: 2301210--2301271 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 24
2301200 TGATTTTTTA
2301210 ATTATTTTTTATGATATTATTATT
1 ATTATTTTTTATGATATTATTATT
*
2301234 ATTATTATTTTATGTTATTATTATT
1 ATTATT-TTTTATGATATTATTATT
2301259 ATTCATTCTTTTA
1 ATT-ATT-TTTTA
2301272 GAGATAAGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 6 0.18
25 20 0.59
26 8 0.24
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.66
Consensus pattern (24 bp):
ATTATTTTTTATGATATTATTATT
Found at i:2301672 original size:24 final size:24
Alignment explanation
Indices: 2301633--2301694 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
2301623 AGATTTATTT
2301633 AAATAAT-AAAAAATAA-ATGAAA
1 AAATAATAAAAAAATAATATGAAA
* *
2301655 ATAATGATAAAAAAATAATGTGAAA
1 A-AATAATAAAAAAATAATATGAAA
2301680 AAATAATAAATAAAA
1 AAATAATAAA-AAAA
2301695 ATTAAATAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
22 1 0.03
23 5 0.15
24 17 0.52
25 10 0.30
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (24 bp):
AAATAATAAAAAAATAATATGAAA
Found at i:2301680 original size:13 final size:14
Alignment explanation
Indices: 2301652--2301686 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
2301642 AAAATAAATG
2301652 AAAATAATGATAAA
1 AAAATAATGATAAA
*
2301666 AAAATAATG-TGAA
1 AAAATAATGATAAA
2301679 AAAATAAT
1 AAAATAAT
2301687 AAATAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (14 bp):
AAAATAATGATAAA
Found at i:2301879 original size:55 final size:56
Alignment explanation
Indices: 2301787--2301907 Score: 156
Period size: 55 Copynumber: 2.2 Consensus size: 56
2301777 TTATCATCAA
* *
2301787 GAAAAATAATTTTTTAGGATTTCGCCAAAGAATTGGGATAATCATAAAATTAGTTT
1 GAAAAATAATTTTTTAGGATTTCGCCAAAAAATTGGGATAATCATAAAATCAGTTT
* * *
2301843 GAAAAATGA-TTTTT-GGATTTTGCCAAAAAAATTGGGATAATCCTAAAATCAGTTT
1 GAAAAATAATTTTTTAGGATTTCGCC-AAAAAATTGGGATAATCATAAAATCAGTTT
*
2301898 TAATAAATAA
1 GAA-AAATAA
2301908 ATAAAAATAT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
54 9 0.16
55 34 0.61
56 13 0.23
ACGTcount: A:0.43, C:0.07, G:0.15, T:0.35
Consensus pattern (56 bp):
GAAAAATAATTTTTTAGGATTTCGCCAAAAAATTGGGATAATCATAAAATCAGTTT
Found at i:2304880 original size:7 final size:7
Alignment explanation
Indices: 2304860--2304892 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
2304850 TGAAAAAGAA
2304860 AAAAAAT
1 AAAAAAT
*
2304867 -AAGAAT
1 AAAAAAT
2304873 AAAAAAT
1 AAAAAAT
2304880 AAAAAAT
1 AAAAAAT
2304887 AAAAAA
1 AAAAAA
2304893 AAGATAGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:2304948 original size:3 final size:3
Alignment explanation
Indices: 2304942--2305067 Score: 82
Period size: 3 Copynumber: 46.3 Consensus size: 3
2304932 CAACAACAAC
* *
2304942 AAT AAT AAT AAT -AT AAT AAT AAT AA- CAT AAT AAT -AT AAT -AT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
2304986 -AT AAT -AT AAT -AT ACT GAT -AT ACT -AT ACT -AT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
2305028 AAT AAT -AT ACT -AT AAT AAAT AAT AAT -AT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT A
2305068 CAATACAATA
Statistics
Matches: 95, Mismatches: 13, Indels: 30
0.69 0.09 0.22
Matches are distributed among these distances:
2 23 0.24
3 69 0.73
4 3 0.03
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:2304959 original size:5 final size:5
Alignment explanation
Indices: 2304943--2305084 Score: 98
Period size: 5 Copynumber: 27.6 Consensus size: 5
2304933 AACAACAACA
*
2304943 ATAAT AATAAT ATAAT AATAAT A-ACAT AATAAT ATAAT ATACT ATAAT
1 ATAAT -ATAAT ATAAT -ATAAT ATA-AT -ATAAT ATAAT ATAAT ATAAT
* * *
2304991 ATAAT ATACTGAT ATACT ATACT AT-A- ATAAT AATAAT AATAAT ATACT
1 ATAAT ATA---AT ATAAT ATAAT ATAAT ATAAT -ATAAT -ATAAT ATAAT
* *
2305039 ATAAT A-AAT AATAAT ATAAT A-AA- ATAAT ACAAT ACAAT ATAAT ATA
1 ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
2305085 CTAGATTGTA
Statistics
Matches: 114, Mismatches: 8, Indels: 29
0.75 0.05 0.19
Matches are distributed among these distances:
3 3 0.03
4 9 0.08
5 69 0.61
6 27 0.24
7 1 0.01
8 5 0.04
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.35
Consensus pattern (5 bp):
ATAAT
Found at i:2304959 original size:8 final size:8
Alignment explanation
Indices: 2304946--2305067 Score: 91
Period size: 8 Copynumber: 15.8 Consensus size: 8
2304936 AACAACAATA
2304946 ATAATAAT
1 ATAATAAT
2304954 ATAAT-A-
1 ATAATAAT
*
2304960 ATAATAAC
1 ATAATAAT
2304968 ATAATAAT
1 ATAATAAT
2304976 ATAAT-AT
1 ATAATAAT
2304983 ACT-ATAAT
1 A-TAATAAT
2304991 ATAAT-AT
1 ATAATAAT
*
2304998 ACTGAT-AT
1 A-TAATAAT
*
2305006 ACT-ATACT
1 A-TAATAAT
2305014 ATAATAAT
1 ATAATAAT
2305022 AATAATAAT
1 -ATAATAAT
*
2305031 A-ATATACT
1 ATA-ATAAT
2305039 ATAATAA-
1 ATAATAAT
2305046 ATAATAAT
1 ATAATAAT
*
2305054 ATAATAAA
1 ATAATAAT
2305062 ATAATA
1 ATAATA
2305068 CAATACAATA
Statistics
Matches: 95, Mismatches: 7, Indels: 24
0.75 0.06 0.19
Matches are distributed among these distances:
6 5 0.05
7 22 0.23
8 59 0.62
9 9 0.09
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (8 bp):
ATAATAAT
Found at i:2305125 original size:20 final size:20
Alignment explanation
Indices: 2305076--2305137 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
2305066 TACAATACAA
*
2305076 TATAATATACTAGATTGTA-
1 TATAATATACTAAATTGTAC
* * *
2305095 -ACAATAAACTATATTGTAC
1 TATAATATACTAAATTGTAC
*
2305114 TATAATATACTAAATTATAC
1 TATAATATACTAAATTGTAC
2305134 TATA
1 TATA
2305138 CTAGTAATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
18 15 0.44
20 19 0.56
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.39
Consensus pattern (20 bp):
TATAATATACTAAATTGTAC
Found at i:2305842 original size:55 final size:55
Alignment explanation
Indices: 2305656--2305862 Score: 163
Period size: 55 Copynumber: 3.8 Consensus size: 55
2305646 GAGACAAAAT
* * * * * * *
2305656 CACAAGTTTGAAAAATGATCTGGATTAAGCCAAGATCAAATAACCAT-GACGAAAT
1 CACAAGTCTGAAAAATGATTTGGACTAAGCCAAGATTAAATGACC-TGGACTAAAC
* * * *
2305711 CATAAGTCTGAAAAATGATTTAGACTGAGCCAAGATT-GATGA-CTGGGA-TAGAAC
1 CACAAGTCTGAAAAATGATTTGGACTAAGCCAAGATTAAATGACCT-GGACTA-AAC
* * * *
2305765 CATAAGTCT-AGAAAATGGTTTGGACTAACCCAAGATTAAATGACCTGGACTAAGC
1 CACAAGTCTGA-AAAATGATTTGGACTAAGCCAAGATTAAATGACCTGGACTAAAC
* * * * *
2305820 CACAAGTTTGAAAAATGATTTGGATTGAGTCAAGATAAAATGA
1 CACAAGTCTGAAAAATGATTTGGACTAAGCCAAGATTAAATGA
2305863 TTGGGATGAA
Statistics
Matches: 119, Mismatches: 25, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
52 1 0.01
53 3 0.03
54 38 0.32
55 72 0.61
56 5 0.04
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (55 bp):
CACAAGTCTGAAAAATGATTTGGACTAAGCCAAGATTAAATGACCTGGACTAAAC
Found at i:2310636 original size:20 final size:19
Alignment explanation
Indices: 2310598--2310636 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2310588 TTCGAAAAAG
* *
2310598 ATTTTTTTATTTTTTATTT
1 ATTTTTTTATTTATCATTT
2310617 ATTTTATTTATTTATCATTT
1 ATTTT-TTTATTTATCATTT
2310637 CTTAGAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (19 bp):
ATTTTTTTATTTATCATTT
Found at i:2311594 original size:16 final size:16
Alignment explanation
Indices: 2311573--2311616 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2311563 ATTATCACAG
2311573 ATAAAAAAAAAGAATA
1 ATAAAAAAAAAGAATA
2311589 ATAAAAATAAAA-AATA
1 ATAAAAA-AAAAGAATA
*
2311605 A-AATAAAAAAGA
1 ATAAAAAAAAAGA
2311617 TAGTAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 4 0.16
15 5 0.20
16 12 0.48
17 4 0.16
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.14
Consensus pattern (16 bp):
ATAAAAAAAAAGAATA
Found at i:2311602 original size:21 final size:20
Alignment explanation
Indices: 2311573--2311614 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
2311563 ATTATCACAG
*
2311573 ATAAAAAAAAAGAATAATAAAA
1 ATAAAAAATAA-AATAA-AAAA
2311595 ATAAAAAATAAAATAAAAAA
1 ATAAAAAATAAAATAAAAAA
2311615 GATAGTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 5 0.26
22 10 0.53
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.14
Consensus pattern (20 bp):
ATAAAAAATAAAATAAAAAA
Found at i:2311657 original size:3 final size:3
Alignment explanation
Indices: 2311651--2311777 Score: 69
Period size: 3 Copynumber: 45.3 Consensus size: 3
2311641 CAACAACAAC
* * *
2311651 AAT AAT AAT AAT AAT AAT AAT -AT AGT AGT AA- CAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
2311696 -AT ACT -AT AAT -AT AAT -GT ACT GAT ATAT TAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
* *
2311738 AAT AAT -AT ACT -AC AAT AAAT AAT AAT -AT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT A
2311778 TACTACAACA
Statistics
Matches: 94, Mismatches: 17, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
2 17 0.18
3 72 0.77
4 5 0.05
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:2311745 original size:23 final size:24
Alignment explanation
Indices: 2311652--2311777 Score: 102
Period size: 25 Copynumber: 5.2 Consensus size: 24
2311642 AACAACAACA
2311652 ATAATAATAATAATAATAATATAGT
1 ATAATAATAATAATAATAATATA-T
*
2311677 AGTAA-CATAATAAT-ATAATATACT
1 A-TAATAATAATAATAATAATATA-T
* * *
2311701 ATAAT-ATAAT-GTACTGATATATT
1 ATAATAATAATAATAATAATATA-T
2311724 ATAATAATAATAATAATAATATACT
1 ATAATAATAATAATAATAATATA-T
* *
2311749 ACAATAAATAATAAT-ATAATA-AA
1 ATAAT-AATAATAATAATAATATAT
2311772 ATAATA
1 ATAATA
2311778 TACTACAACA
Statistics
Matches: 82, Mismatches: 13, Indels: 15
0.75 0.12 0.14
Matches are distributed among these distances:
22 2 0.02
23 24 0.29
24 16 0.20
25 28 0.34
26 12 0.15
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.35
Consensus pattern (24 bp):
ATAATAATAATAATAATAATATAT
Found at i:2311774 original size:20 final size:20
Alignment explanation
Indices: 2311723--2311775 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
2311713 ACTGATATAT
2311723 TATAATAATAAT-AATAATAA
1 TATAATAA-AATAAATAATAA
* *
2311743 TATACTACAATAAATAATAA
1 TATAATAAAATAAATAATAA
2311763 TATAATAAAATAA
1 TATAATAAAATAA
2311776 TATACTACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (20 bp):
TATAATAAAATAAATAATAA
Found at i:2311790 original size:20 final size:18
Alignment explanation
Indices: 2311732--2311785 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 18
2311722 TTATAATAAT
2311732 AATAATAATAATATACTAC
1 AATAA-AATAATATACTAC
*
2311751 AAT-AAATAATA-A-TAT
1 AATAAAATAATATACTAC
2311766 AATAAAATAATATACTAC
1 AATAAAATAATATACTAC
2311784 AA
1 AA
2311786 CATAATATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
15 5 0.17
16 9 0.30
17 8 0.27
18 5 0.17
19 3 0.10
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (18 bp):
AATAAAATAATATACTAC
Found at i:2311801 original size:78 final size:77
Alignment explanation
Indices: 2311651--2311811 Score: 193
Period size: 78 Copynumber: 2.1 Consensus size: 77
2311641 CAACAACAAC
* * * * *
2311651 AATAATAATAATAATAATAATATAGTAGTAACATAATAATATAATATACTATAATATAATGTACT
1 AATAATAATAATAATAATAATATAATAATAACATAATAAAATAATATACTACAACATAA-GTACT
2311716 GATATATTATAAT
65 GATATATTATAAT
*
2311729 AATAATAATAATAATATACTACA-ATAAATAATAATATAATAAAATAATATACTACAACATAA-T
1 AATAATAATAATAATA-A-TA-ATAT-AATAATAACATAATAAAATAATATACTACAACATAAGT
*
2311792 A-TGCTATATTATAAT
62 ACTGATATATTATAAT
2311807 AATAA
1 AATAA
2311812 ACTATACTAT
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
78 34 0.47
79 3 0.04
80 4 0.06
81 31 0.43
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.35
Consensus pattern (77 bp):
AATAATAATAATAATAATAATATAATAATAACATAATAAAATAATATACTACAACATAAGTACTG
ATATATTATAAT
Found at i:2311808 original size:33 final size:33
Alignment explanation
Indices: 2311724--2311815 Score: 96
Period size: 33 Copynumber: 2.7 Consensus size: 33
2311714 CTGATATATT
*
2311724 ATAATAATAATAATAATAATATACTACAATAAATA
1 ATAAT-ATAAT-ATAATAATATACTACAACAAATA
*
2311759 ATAATATAATAAAATAATATACTACAACATAAT-
1 ATAATATAATATAATAATATACTACAACA-AATA
** * *
2311792 ATGCTATATTATAATAATAAACTA
1 ATAATATAATATAATAATATACTA
2311816 TACTATAGTA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
33 36 0.73
34 8 0.16
35 5 0.10
ACGTcount: A:0.59, C:0.08, G:0.01, T:0.33
Consensus pattern (33 bp):
ATAATATAATATAATAATATACTACAACAAATA
Found at i:2311843 original size:25 final size:23
Alignment explanation
Indices: 2311795--2311847 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 23
2311785 ACATAATATG
*
2311795 CTATATTATAATAATAAACTATA
1 CTATAGTATAATAATAAACTATA
*
2311818 CTATAGTATAATATACTAAATTATA
1 CTATAGTATAATA-A-TAAACTATA
2311843 CTATA
1 CTATA
2311848 CTAGTAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 12 0.46
24 1 0.04
25 13 0.50
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (23 bp):
CTATAGTATAATAATAAACTATA
Found at i:2311931 original size:19 final size:19
Alignment explanation
Indices: 2311907--2311945 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2311897 GGTATCTACA
2311907 ATACCAATTGATAAAAAAT
1 ATACCAATTGATAAAAAAT
* *
2311926 ATACCAATTGTTAGAAAAT
1 ATACCAATTGATAAAAAAT
2311945 A
1 A
2311946 AATTTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (19 bp):
ATACCAATTGATAAAAAAT
Found at i:2313884 original size:36 final size:35
Alignment explanation
Indices: 2313836--2313913 Score: 86
Period size: 36 Copynumber: 2.2 Consensus size: 35
2313826 CTCACTTCTA
* *
2313836 TGTTTTTGGTTTTTCCATCTTTGT-TTTCTATCTTT
1 TGTTTTTAGTTTTTCCATATTT-TCTTTCTATCTTT
* * *
2313871 TGTTTATTAGTTTTTTCATATTTTCTTTTTCTCTTT
1 TGTTT-TTAGTTTTTCCATATTTTCTTTCTATCTTT
2313907 TGTTTTT
1 TGTTTTT
2313914 CTATTTTGGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
35 8 0.22
36 28 0.78
ACGTcount: A:0.08, C:0.12, G:0.09, T:0.72
Consensus pattern (35 bp):
TGTTTTTAGTTTTTCCATATTTTCTTTCTATCTTT
Found at i:2313921 original size:13 final size:13
Alignment explanation
Indices: 2313882--2313921 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
2313872 GTTTATTAGT
*
2313882 TTTTTCATATTTTC
1 TTTTTC-TATTTTG
*
2313896 TTTTTCTCTTTTG
1 TTTTTCTATTTTG
2313909 TTTTTCTATTTTG
1 TTTTTCTATTTTG
2313922 GCATCGTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 17 0.74
14 6 0.26
ACGTcount: A:0.07, C:0.12, G:0.05, T:0.75
Consensus pattern (13 bp):
TTTTTCTATTTTG
Found at i:2329922 original size:16 final size:16
Alignment explanation
Indices: 2329896--2329945 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
2329886 CATAATCCCA
*
2329896 TAATTATTTTAAATTT
1 TAATTAATTTAAATTT
* *
2329912 TGATTAATTTAAAATT
1 TAATTAATTTAAATTT
* *
2329928 AAATTAAATTAAATTT
1 TAATTAATTTAAATTT
2329944 TA
1 TA
2329946 TAAAGAATAA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
TAATTAATTTAAATTT
Found at i:2330190 original size:27 final size:26
Alignment explanation
Indices: 2330151--2330244 Score: 77
Period size: 27 Copynumber: 3.5 Consensus size: 26
2330141 TCAAAATAAA
2330151 TAAA-TAAATAAATACTTAATTTAATAT
1 TAAATTAAA-AAATA-TTAATTTAATAT
* *
2330178 TAAATTAAAAAATTTTAATTAAATATT
1 TAAATTAAAAAATATTAATTTAATA-T
**
2330205 TAAATTATAAATTTATTAA-TTAATA-
1 TAAATTA-AAAAATATTAATTTAATAT
2330230 TAATATTTAAAAAAT
1 TAA-A-TTAAAAAAT
2330245 TATTTGAATC
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
25 3 0.06
26 15 0.28
27 24 0.44
28 12 0.22
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (26 bp):
TAAATTAAAAAATATTAATTTAATAT
Found at i:2330247 original size:27 final size:26
Alignment explanation
Indices: 2330166--2330248 Score: 89
Period size: 27 Copynumber: 3.1 Consensus size: 26
2330156 AAATAAATAC
2330166 TTAATTTAATATTAAATTAAAAAATT-
1 TTAA-TTAATATTAAATTAAAAAATTA
* *
2330192 TTAATTAAATATTTAAATTATAAATTTA
1 TTAATT-AATA-TTAAATTAAAAAATTA
2330220 TTAATTAATA-TAATATTTAAAAAATTA
1 TTAATTAATATTAA-A-TTAAAAAATTA
2330247 TT
1 TT
2330249 TGAATCATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
25 5 0.10
26 9 0.19
27 28 0.58
28 6 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (26 bp):
TTAATTAATATTAAATTAAAAAATTA
Found at i:2330302 original size:18 final size:18
Alignment explanation
Indices: 2330279--2330316 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2330269 AAAATTAATA
2330279 ATATT-ATAAATAAATATT
1 ATATTAATAAATAAAT-TT
*
2330297 ATATTAATTAATAAATTT
1 ATATTAATAAATAAATTT
2330315 AT
1 AT
2330317 GAGTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTAATAAATAAATTT
Found at i:2334116 original size:2 final size:2
Alignment explanation
Indices: 2334111--2334157 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
2334101 ATTCACACAC
* * *
2334111 AT AT AT AT AT AT AT AT AA AT AG AT A- AT TT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2334152 AT AT AT
1 AT AT AT
2334158 GTGAATTTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2335333 original size:17 final size:16
Alignment explanation
Indices: 2335311--2335342 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2335301 TTTTATTTAA
2335311 ATATTTTTTATAAAAAT
1 ATATTTTTT-TAAAAAT
2335328 ATATTTTTTTAAAAA
1 ATATTTTTTTAAAAA
2335343 ATAATAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATTTTTTTAAAAAT
Found at i:2335667 original size:11 final size:13
Alignment explanation
Indices: 2335634--2335667 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
2335624 CTTCTTCCAT
2335634 TTATTTCTCTACC
1 TTATTTCTCTACC
2335647 TTATTTCTCT-CC
1 TTATTTCTCTACC
2335659 TTA-TTCTCT
1 TTATTTCTCT
2335668 GTAAAGTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 6 0.29
12 5 0.24
13 10 0.48
ACGTcount: A:0.12, C:0.29, G:0.00, T:0.59
Consensus pattern (13 bp):
TTATTTCTCTACC
Found at i:2336216 original size:3 final size:3
Alignment explanation
Indices: 2336210--2336260 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
2336200 TTTTTTAATT
2336210 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2336258 TTA
1 TTA
2336261 CTAAAAAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2336485 original size:31 final size:31
Alignment explanation
Indices: 2336390--2336487 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
2336380 TTGAAACCCA
* * *
2336390 AGATT-AAATTACAAACCTCGAACGAAACTCG
1 AGATTCAAA-TACAAACCTTGAAAGAAACTTG
** * *
2336421 AGATTCAAATATGAACCCT-AGATGAAA-TCTG
1 AGATTCAAATACAAACCTTGA-AAGAAACT-TG
2336452 AGATTCAAATACAAACCTTGAAAGAAACTTG
1 AGATTCAAATACAAACCTTGAAAGAAACTTG
2336483 AGATT
1 AGATT
2336488 TGATTATGGA
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
30 2 0.04
31 45 0.87
32 5 0.10
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.23
Consensus pattern (31 bp):
AGATTCAAATACAAACCTTGAAAGAAACTTG
Found at i:2353122 original size:9 final size:9
Alignment explanation
Indices: 2353108--2353133 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2353098 AGTTTTTATA
2353108 ATATAAAAT
1 ATATAAAAT
2353117 ATATAAAAT
1 ATATAAAAT
2353126 ATATAAAA
1 ATATAAAA
2353134 ATTTTGAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
ATATAAAAT
Found at i:2357707 original size:40 final size:40
Alignment explanation
Indices: 2357630--2357708 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
2357620 AGAATTTAAT
*
2357630 AAAAATGACATTTTTAAATTAAAAAATGTAGTCTTTGTTG
1 AAAAATGACATTTCTAAATTAAAAAATGTAGTCTTTGTTG
*
2357670 AAAAGATGACATTTCTAAGA-T-AAAAATGTAGTTTTTGTT
1 AAAA-ATGACATTTCTAA-ATTAAAAAATGTAGTCTTTGTT
2357709 TGTAAACATG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 21 0.60
41 13 0.37
42 1 0.03
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (40 bp):
AAAAATGACATTTCTAAATTAAAAAATGTAGTCTTTGTTG
Done.