Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 106 of 145
Found at i:35641934 original size:24 final size:24
Alignment explanation
Indices: 35641906--35641961 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
35641896 ATGCCGAATC
*
35641906 GGAAGAACCACAACCACCACCGGA
1 GGAAGAACCACAACCACCACCAGA
* * *
35641930 GGAAGTACCACAATCAGCACCAGA
1 GGAAGAACCACAACCACCACCAGA
35641954 GGAAGAAC
1 GGAAGAAC
35641962 AACCGCCGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.30, G:0.23, T:0.04
Consensus pattern (24 bp):
GGAAGAACCACAACCACCACCAGA
Found at i:35642198 original size:29 final size:27
Alignment explanation
Indices: 35642191--35642274 Score: 114
Period size: 29 Copynumber: 3.0 Consensus size: 27
35642181 AAAACCCTAA
35642191 CCTAACCCTAACCTAAATTAATTAAAAAC
1 CCTAA-CCTAACCTAAATTAATT-AAAAC
*
35642220 CCTAAACCTAACCTAAATTAACTAACAAC
1 CCT-AACCTAACCTAAATTAATTAA-AAC
*
35642249 CCTAATCTAACCTAAATTAATTAAAA
1 CCTAACCTAACCTAAATTAATTAAAA
35642275 NNNNNNNNNN
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.04
28 21 0.42
29 25 0.50
30 2 0.04
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (27 bp):
CCTAACCTAACCTAAATTAATTAAAAC
Found at i:35642235 original size:34 final size:34
Alignment explanation
Indices: 35642168--35642260 Score: 106
Period size: 29 Copynumber: 2.9 Consensus size: 34
35642158 AAATAAAAAC
* *
35642168 CCTAATTTAATTGAAAACCCTAACCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACCTAACCCTAA
35642202 CCTAAATTAATTAAAAACCCT-A---AA-CCTAA
1 CCTAAATTAATTAAAAACCCTAACCTAACCCTAA
* * *
35642231 CCTAAATTAACTAACAACCCTAATCTAACC
1 CCTAAATTAATTAAAAACCCTAACCTAACC
35642261 TAAATTAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
29 24 0.48
30 3 0.06
33 3 0.06
34 20 0.40
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (34 bp):
CCTAAATTAATTAAAAACCCTAACCTAACCCTAA
Found at i:35661060 original size:7 final size:7
Alignment explanation
Indices: 35661048--35661079 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
35661038 ATTTAATATT
35661048 AAATTTA
1 AAATTTA
35661055 AAATTTA
1 AAATTTA
35661062 AAATTTA
1 AAATTTA
35661069 AAA-TTA
1 AAATTTA
35661075 AAATT
1 AAATT
35661080 AGAAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATTTA
Found at i:35661075 original size:13 final size:13
Alignment explanation
Indices: 35661037--35661079 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
35661027 TTTTAATTTT
*
35661037 AATTTAATATT-A
1 AATTTAAAATTAA
35661049 AATTTAAAATTTAA
1 AATTTAAAA-TTAA
35661063 AATTTAAAATTAA
1 AATTTAAAATTAA
35661076 AATT
1 AATT
35661080 AGAAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 8 0.29
13 10 0.36
14 10 0.36
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTTAAAATTAA
Found at i:35661519 original size:20 final size:18
Alignment explanation
Indices: 35661477--35661519 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
35661467 AACTTTTTTC
*
35661477 ATTTTTATAAAATTTTCA
1 ATTTTTATAAAATTATCA
*
35661495 ATTTTTATACAATATTATGA
1 ATTTTTATA-AA-ATTATCA
35661515 ATTTT
1 ATTTT
35661520 AAAATTTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 2 0.10
20 10 0.48
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTTTTATAAAATTATCA
Found at i:35664680 original size:194 final size:190
Alignment explanation
Indices: 35664340--35664752 Score: 537
Period size: 194 Copynumber: 2.2 Consensus size: 190
35664330 GTTTTAATCC
* * * * *
35664340 GCTCCACTACAACTTTAGGGAGAT-AGGATTGGTCGCTTCAATCTACTTCACTGCAACTTCAGGA
1 GCTCCACTACAACTTCAGGGAGATAAAGACTGGTCGCGTCAATCTACTCCACTGCAACTTCAGGA
* * *
35664404 AGATAAGATCTGCCATAATTTGTAGGTTTAATCTATTCCACTGCAACGCCAGGGAAATAAGATTC
66 AGATAAGATCTGCCATAATTTGTAGCTTTAATATATTACACTGCAACGCCAGGGAAATAAGATTC
* * *
35664469 GCTGCCTTCAACTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCACTGTTTTCAGTCT
131 GCTGCCTTCAACTTTAATCTGTTCCACCGCAACGCC-----AATAAGATTCACTATCTTCAGTCT
* * * *
35664534 GCTCCACTCCAACTTCAGGGAGATAAAG-CTGGTGGCGTCAATCTGCTCCACTGTAACTTCAGGA
1 GCTCCACTACAACTTCAGGGAGATAAAGACTGGTCGCGTCAATCTACTCCACTGCAACTTCAGGA
* * *
35664598 AGATAAGGT-TCGCCATAATTTGTAGCTTTAATATGTTACACTGCAACGTCAGGGAAATAAGATT
66 AGATAAGATCT-GCCATAATTTGTAGCTTTAATATATTACACTGCAACGCCAGGGAAATAAGATT
* * * *
35664662 CGTTGTCTTCAGCTTTAATCTGTTCCACCGCAACGCCAATAAGATTCGCTATCTTCAGTCT
130 CGCTGCCTTCAACTTTAATCTGTTCCACCGCAACGCCAATAAGATTCACTATCTTCAGTCT
*
35664723 GCTCCACTGCAACTTCAGGGAGAT-AAGACT
1 GCTCCACTACAACTTCAGGGAGATAAAGACT
35664753 TGTTATGGTA
Statistics
Matches: 193, Mismatches: 23, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
188 3 0.02
189 46 0.24
193 1 0.01
194 141 0.73
195 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (190 bp):
GCTCCACTACAACTTCAGGGAGATAAAGACTGGTCGCGTCAATCTACTCCACTGCAACTTCAGGA
AGATAAGATCTGCCATAATTTGTAGCTTTAATATATTACACTGCAACGCCAGGGAAATAAGATTC
GCTGCCTTCAACTTTAATCTGTTCCACCGCAACGCCAATAAGATTCACTATCTTCAGTCT
Found at i:35664865 original size:44 final size:44
Alignment explanation
Indices: 35664817--35665648 Score: 330
Period size: 44 Copynumber: 18.7 Consensus size: 44
35664807 GTTTTAATTC
* * * *
35664817 GCTCCTCTACAACTTCAGGGAGATAGGATTAGTAGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAACCT
* *
35664861 GCTCCACTGCAACTTCAGGGAGATAAGATTGGTATCTTCAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAACCT
* * * * *
35664905 ACTCCACTGCAACTTCAGGGAGATAAGGTT--T-GATAT-GATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCT-TCAACCT
* * * * * * * **
35664946 TCTCTACTGCAAATTCAGAGAGATAAGATCTGTAATTTATAGATTAAATTT
1 GCTCCACTGCAACTTCAGGGAGATAAGA--T-T-A---GTAGCTTCAACCT
* * * * ** * **
35664997 GTTCCACTGCAACTTTAGGGAAATAAGATTCGCTATTTTTATTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAG-TAGCTTCAACCT
* * * *
35665042 GCTCCACTGTAACTTTAGGGAGATAAGACTT-GTAACTTTAATCC-
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTAGTAGCTTCAA-CCT
* * * * *
35665086 GTTCCACTGCAACTTTAGGGAGATAAGATTATTGGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAACCT
* * ** * **
35665130 GTTCCACTGCAACTTCAGGGAAATAAGATTCTCTATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATT-AGTAGCTTCAACCT
* * * *
35665175 TCTCCACTGTAACTTCATGGG-GATAAGACTT-GTAACTTTAATCC-
1 GCTCCACTGCAACTTCA-GGGAGATAAGA-TTAGTAGCTTCAA-CCT
* * * * **
35665219 ACTCCACTGCAACTTCAGGGAGATAGGATT-GTTGGCTTTAATAT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAG-TAGCTTCAACCT
* * * * * * **
35665263 GTTCCACTACAACTTCAGGGAGATAAGATTTGCCACCTTTAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAG-TAGCTTCAACCT
* * * * ** **
35665308 GCCCCACTGTAACTTTAGGGGGATAAGACTT-GCTTTCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTAG-TAGCTTCAACCT
* * * * *
35665353 GCTCCACTGCAATTTTAGGGAGATGAGACTT-GTAACTTTAATCC-
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTAGTAGCTTCAA-CCT
* * * * * * *
35665397 GCTCCACTGCAACTTCAAGAAGATAGGATTATTGGCTTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAACCT
** * * ** * **
35665441 TTTCTACTGCAACTTTAGGGAGATAAGATTCACCATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATT-AGTAGCTTCAACCT
** **
35665486 G-TCCCACTGCAACTTCAGGGAGATAAGACTT-GCTCTCTTCAGTCT
1 GCT-CCACTGCAACTTCAGGGAGATAAGA-TTAG-TAGCTTCAACCT
* * ** * *
35665531 GCTCTACTGTAACTTCAAAGAGATAAGACTT-GTAACTTTAATCC-
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTAGTAGCTTCAA-CCT
* * * * * *
35665575 GCTCCACTGTAACTTCAGGGAGATAGGATTATTGGCTTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAACCT
35665619 GCTCCACTGCAACTTCAGGGAGATAAGATT
1 GCTCCACTGCAACTTCAGGGAGATAAGATT
35665649 CACCATCTTC
Statistics
Matches: 603, Mismatches: 148, Indels: 74
0.73 0.18 0.09
Matches are distributed among these distances:
41 27 0.04
42 2 0.00
43 16 0.03
44 315 0.52
45 200 0.33
46 12 0.02
48 1 0.00
49 1 0.00
50 2 0.00
51 27 0.04
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGCTTCAACCT
Found at i:35665153 original size:133 final size:132
Alignment explanation
Indices: 35664996--35665376 Score: 492
Period size: 133 Copynumber: 2.9 Consensus size: 132
35664986 AGATTAAATT
* * *
35664996 TGTTCCACTGCAACTTTAGGGAAATAAGATTCGCTATTTTTATTCTGCTCCACTGTAACTTTAGG
1 TGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTTAGTCTGCTCCACTGTAACTTTAGG
*
35665061 GAGATAAGACTTGTAACTTTAATCCGTTCCACTGCAACTTTAGGGAGATAAGATTATTGGCTTCA
66 G-GATAAGACTTGTAACTTTAATCCGCTCCACTGCAACTTTAGGGAGATAAGATTATTGGCTTCA
*
35665126 ATC
130 ATA
* * * *
35665129 TGTTCCACTGCAACTTCAGGGAAATAAGATTCTCTATCTTCAGTCTTCTCCACTGTAACTTCATG
1 TGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTTAGTCTGCTCCACTGTAACTTTA-G
* * * * *
35665194 GGGATAAGACTTGTAACTTTAATCCACTCCACTGCAACTTCAGGGAGATAGGATTGTTGGCTTTA
65 GGGATAAGACTTGTAACTTTAATCCGCTCCACTGCAACTTTAGGGAGATAAGATTATTGGCTTCA
35665259 ATA
130 ATA
* * * * * *
35665262 TGTTCCACTACAACTTCAGGGAGATAAGATTTGCCACCTTTAGTCTGCCCCACTGTAACTTTAGG
1 TGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTTAGTCTGCTCCACTGTAACTTTA-G
** * * * *
35665327 GGGATAAGACTTGCTTTCTTCAGTCTGCTCCACTGCAATTTTAGGGAGAT
65 GGGATAAGACTTG-TAACTTTAATCCGCTCCACTGCAACTTTAGGGAGAT
35665377 GAGACTTGTA
Statistics
Matches: 213, Mismatches: 33, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
133 182 0.85
134 31 0.15
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (132 bp):
TGTTCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTTAGTCTGCTCCACTGTAACTTTAGG
GGATAAGACTTGTAACTTTAATCCGCTCCACTGCAACTTTAGGGAGATAAGATTATTGGCTTCAA
TA
Found at i:35665404 original size:178 final size:178
Alignment explanation
Indices: 35665042--35665658 Score: 758
Period size: 178 Copynumber: 3.5 Consensus size: 178
35665032 TTTTTATTCT
* * * * ** * *
35665042 GCTCCACTGTAACTTTAGGGAGATAAGACTT-GTAACTTTAATCCGTTCCACTGCAACTTTAGGG
1 GCTCCACTGCAACTTCAGGGAGATAGGA-TTATTGGCTTTAATCTGTTCCACTGCAACTTCAGGG
**** * ** *
35665106 AGATAAGATT-ATTGGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGA-TT-CTCTATCT
65 AGATAAGATTCACCACCTTCAGTCTGCCCCACTGCAACTTCAGGGAGATAAGACTTGCTC--TCT
*
35665168 TCAGTCTTCTCCACTGTAACTTCATGGG-GATAAGACTTGTAACTTTAATCC
128 TCAGTCTGCTCCACTGTAACTTCA-GGGAGATAAGACTTGTAACTTTAATCC
* * * *
35665219 ACTCCACTGCAACTTCAGGGAGATAGGATTGTTGGCTTTAATATGTTCCACTACAACTTCAGGGA
1 GCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGTTCCACTGCAACTTCAGGGA
** * * * * *
35665284 GATAAGATTTGCCACCTTTAGTCTGCCCCACTGTAACTTTAGGGGGATAAGACTTGCTTTCTTCA
66 GATAAGATTCACCACCTTCAGTCTGCCCCACTGCAACTTCAGGGAGATAAGACTTGCTCTCTTCA
* * * *
35665349 GTCTGCTCCACTGCAATTTTAGGGAGATGAGACTTGTAACTTTAATCC
131 GTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGTAACTTTAATCC
* * * * *
35665397 GCTCCACTGCAACTTCAAGAAGATAGGATTATTGGCTTTAATCTTTTCTACTGCAACTTTAGGGA
1 GCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGTTCCACTGCAACTTCAGGGA
* *
35665462 GATAAGATTCACCATCTTCAGTCTGTCCCACTGCAACTTCAGGGAGATAAGACTTGCTCTCTTCA
66 GATAAGATTCACCACCTTCAGTCTGCCCCACTGCAACTTCAGGGAGATAAGACTTGCTCTCTTCA
* **
35665527 GTCTGCTCTACTGTAACTTCAAAGAGATAAGACTTGTAACTTTAATCC
131 GTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGTAACTTTAATCC
* *
35665575 GCTCCACTGTAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGCAACTTCAGGGA
1 GCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGTTCCACTGCAACTTCAGGGA
*
35665640 GATAAGATTCACCATCTTC
66 GATAAGATTCACCACCTTC
35665659 TTCAATCCAT
Statistics
Matches: 373, Mismatches: 62, Indels: 9
0.84 0.14 0.02
Matches are distributed among these distances:
176 2 0.01
177 63 0.17
178 304 0.82
179 2 0.01
180 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (178 bp):
GCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGTTCCACTGCAACTTCAGGGA
GATAAGATTCACCACCTTCAGTCTGCCCCACTGCAACTTCAGGGAGATAAGACTTGCTCTCTTCA
GTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGTAACTTTAATCC
Found at i:35667880 original size:11 final size:11
Alignment explanation
Indices: 35667864--35667911 Score: 52
Period size: 10 Copynumber: 4.8 Consensus size: 11
35667854 CTTTGGTTTC
35667864 TCCTTTTTCTT
1 TCCTTTTTCTT
35667875 TCC-TTTTCTT
1 TCCTTTTTCTT
*
35667885 T-CTTCTTC--
1 TCCTTTTTCTT
35667893 T-CTTTTTCTT
1 TCCTTTTTCTT
35667903 TCCTTTTTC
1 TCCTTTTTC
35667912 CATCATTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
8 7 0.23
9 1 0.03
10 13 0.42
11 10 0.32
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (11 bp):
TCCTTTTTCTT
Found at i:35679123 original size:41 final size:41
Alignment explanation
Indices: 35679034--35679172 Score: 201
Period size: 41 Copynumber: 3.4 Consensus size: 41
35679024 TTGATCTCGA
* *
35679034 TTTCGCACACTTAGTGCCCGTTATT-AACAT-AATTATTTGG
1 TTTCGCACACTTAGTGCTCGTTATTCAACATCAA-TATTTAG
*
35679074 TTTCGCACACTTAGTGCTCGTTATTCAACATCAATACTTAG
1 TTTCGCACACTTAGTGCTCGTTATTCAACATCAATATTTAG
* * *
35679115 TTTTGCACACTTAGTGCTCGTTATTCAACATCATTATTTAA
1 TTTCGCACACTTAGTGCTCGTTATTCAACATCAATATTTAG
35679156 TTTCGCACACTTAGTGC
1 TTTCGCACACTTAGTGC
35679173 CAATCATATA
Statistics
Matches: 89, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
40 24 0.27
41 63 0.71
42 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (41 bp):
TTTCGCACACTTAGTGCTCGTTATTCAACATCAATATTTAG
Found at i:35684271 original size:40 final size:40
Alignment explanation
Indices: 35684227--35684363 Score: 193
Period size: 41 Copynumber: 3.4 Consensus size: 40
35684217 TTGATATTGA
* * *
35684227 TTTCGCACACTTAGTGCCCGTTATTAACATAATTATTTGG
1 TTTCGCACACTTAGTGCTCGTTATTAACATCATTATTTAG
* * *
35684267 TTTCGCACACTTTAGTGCTCGTAATCAACATCATTACTTAG
1 TTTCGCACAC-TTAGTGCTCGTTATTAACATCATTATTTAG
*
35684308 TTTCGCACACTTAGTGCTCGTTATTCAACATCATTATTTAA
1 TTTCGCACACTTAGTGCTCGTTATT-AACATCATTATTTAG
35684349 TTTCGCACACTTAGT
1 TTTCGCACACTTAGT
35684364 ACCAATCATA
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
40 23 0.27
41 62 0.73
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.39
Consensus pattern (40 bp):
TTTCGCACACTTAGTGCTCGTTATTAACATCATTATTTAG
Found at i:35687805 original size:41 final size:41
Alignment explanation
Indices: 35687622--35687797 Score: 246
Period size: 41 Copynumber: 4.3 Consensus size: 41
35687612 AATTCAGACT
35687622 CGTCTAGCAGGCTTGATGCCGGTGAAATATTTCAGACTTTA
1 CGTCTAGCAGGCTTGATGCCGGTGAAATATTTCAGACTTTA
* * * * *
35687663 GGTCTAGCAAGCTTGATGTCGGTGAAATATTTGAAACTTTA
1 CGTCTAGCAGGCTTGATGCCGGTGAAATATTTCAGACTTTA
* *
35687704 TGCCTAGCAGGCTTGATGCCGGTGAAATATTTCAGA-TTTA
1 CGTCTAGCAGGCTTGATGCCGGTGAAATATTTCAGACTTTA
* * **
35687744 CGTCTAGCAGGCTTAATGCCGTTGAAATATTTTGGACTTTA
1 CGTCTAGCAGGCTTGATGCCGGTGAAATATTTCAGACTTTA
35687785 CGTCTAGCAGGCT
1 CGTCTAGCAGGCT
35687798 AATTGCCGGT
Statistics
Matches: 117, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
40 34 0.29
41 83 0.71
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (41 bp):
CGTCTAGCAGGCTTGATGCCGGTGAAATATTTCAGACTTTA
Found at i:35687808 original size:81 final size:82
Alignment explanation
Indices: 35687622--35687797 Score: 257
Period size: 81 Copynumber: 2.2 Consensus size: 82
35687612 AATTCAGACT
* * *
35687622 CGTCTAGCAGGCTTGATGCCGGTGAAATATTTCAGACTTTAGGTCTAGCAAGCTTGATGTCGGTG
1 CGTCTAGCAGGCTTGATGCCGGTGAAATATTTCAGACTTTACGTCTAGCAAGCTTAATGCCGGTG
35687687 AAATATTTGAAACTTTA
66 AAATATTTGAAACTTTA
* * * *
35687704 TGCCTAGCAGGCTTGATGCCGGTGAAATATTTCAGA-TTTACGTCTAGCAGGCTTAATGCCGTTG
1 CGTCTAGCAGGCTTGATGCCGGTGAAATATTTCAGACTTTACGTCTAGCAAGCTTAATGCCGGTG
*
35687768 AAATATTTTG-GACTTTA
66 AAATA-TTTGAAACTTTA
35687785 CGTCTAGCAGGCT
1 CGTCTAGCAGGCT
35687798 AATTGCCGGT
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
81 45 0.54
82 38 0.46
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (82 bp):
CGTCTAGCAGGCTTGATGCCGGTGAAATATTTCAGACTTTACGTCTAGCAAGCTTAATGCCGGTG
AAATATTTGAAACTTTA
Found at i:35689269 original size:89 final size:87
Alignment explanation
Indices: 35689176--35689340 Score: 267
Period size: 87 Copynumber: 1.9 Consensus size: 87
35689166 TTTATATAAA
*
35689176 AAATAATAATGAAAAAAATAAAAATTTCATATAAAAATTTTAACTTTATCAAATATTACATTATT
1 AAATAATAATGAAAAAAATAAAAATTTCATATAAAAA--TTAACTTTATCAAATATTACAATATT
35689241 TTCATAAAAATAAAAAAATCATAT
64 TTCATAAAAATAAAAAAATCATAT
* * *
35689265 AAATAATAATGAAAATAATAATAATTTCATATAAAAATTCACTTTATCAAATATTACAATATTTT
1 AAATAATAATGAAAAAAATAAAAATTTCATATAAAAATTAACTTTATCAAATATTACAATATTTT
*
35689330 CATATAAATAA
66 CATAAAAATAA
35689341 TAATGAAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
87 36 0.51
89 35 0.49
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.36
Consensus pattern (87 bp):
AAATAATAATGAAAAAAATAAAAATTTCATATAAAAATTAACTTTATCAAATATTACAATATTTT
CATAAAAATAAAAAAATCATAT
Found at i:35689336 original size:70 final size:71
Alignment explanation
Indices: 35689259--35689398 Score: 241
Period size: 70 Copynumber: 2.0 Consensus size: 71
35689249 AATAAAAAAA
35689259 TCATATAAATAATAATGAAAATAATAATAATTTCATAT-AAAAA-TTCACTTTATCA-AATATTA
1 TCATATAAATAATAATGAAAA-AATAATAATTTCATATAAAAAATTTCACTTTAT-ATAATATTA
35689321 CAATATTT
64 CAATATTT
35689329 TCATATAAATAATAATGAAAAAATAATAATTTCATATAAAAAATTTCACTTTATATAATATTACA
1 TCATATAAATAATAATGAAAAAATAATAATTTCATATAAAAAATTTCACTTTATATAATATTACA
35689394 ATATT
66 ATATT
35689399 CACGAGTATT
Statistics
Matches: 67, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
69 16 0.24
70 27 0.40
71 24 0.36
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (71 bp):
TCATATAAATAATAATGAAAAAATAATAATTTCATATAAAAAATTTCACTTTATATAATATTACA
ATATTT
Found at i:35695184 original size:28 final size:28
Alignment explanation
Indices: 35695152--35695206 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
35695142 CACTTTCTGA
35695152 TCATACTTTTGGCAGACACCCTTACTGG
1 TCATACTTTTGGCAGACACCCTTACTGG
* *
35695180 TCATACTTTTGGCGGATACCCTTACTG
1 TCATACTTTTGGCAGACACCCTTACTG
35695207 ATCTTGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (28 bp):
TCATACTTTTGGCAGACACCCTTACTGG
Found at i:35695766 original size:24 final size:24
Alignment explanation
Indices: 35695730--35695783 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
35695720 AAAATTTCAC
* * *
35695730 AAAGGCCATATCAGAATACGCCAT
1 AAAGGCAAGATCACAATACGCCAT
* *
35695754 AAAGGCAAGATCACAGTATGCCAT
1 AAAGGCAAGATCACAATACGCCAT
35695778 AAAGGC
1 AAAGGC
35695784 CAGCAAAATG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.15
Consensus pattern (24 bp):
AAAGGCAAGATCACAATACGCCAT
Found at i:35700164 original size:20 final size:21
Alignment explanation
Indices: 35700129--35700168 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
35700119 GTGTTTTATT
35700129 TAATTTATAAAAATAAAAATC
1 TAATTTATAAAAATAAAAATC
*
35700150 TAATTT-TATAAATAAAAAT
1 TAATTTATAAAAATAAAAAT
35700169 TCATTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATTTATAAAAATAAAAATC
Found at i:35702454 original size:19 final size:20
Alignment explanation
Indices: 35702415--35702455 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
35702405 TACAACACAA
35702415 TTCAATTTCATATTGAATAT
1 TTCAATTTCATATTGAATAT
35702435 TTCAATTTTCAT-TT-AATAT
1 TTCAA-TTTCATATTGAATAT
35702454 TT
1 TT
35702456 GCCTAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.35
20 7 0.35
21 6 0.30
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (20 bp):
TTCAATTTCATATTGAATAT
Found at i:35704566 original size:137 final size:137
Alignment explanation
Indices: 35704320--35704596 Score: 554
Period size: 137 Copynumber: 2.0 Consensus size: 137
35704310 TTTTTAACAC
35704320 TTTAACCAACGGTTCTTGGATCTTTAAGACATCAACAACCTTTTTCCTTAAGTCACTTGAGTTAA
1 TTTAACCAACGGTTCTTGGATCTTTAAGACATCAACAACCTTTTTCCTTAAGTCACTTGAGTTAA
35704385 TGACTTCAGTCATTTCTAGTCCAGTTGGTTTTCTTGCATATGTGGACCTTTTCCATGCTGAAGAA
66 TGACTTCAGTCATTTCTAGTCCAGTTGGTTTTCTTGCATATGTGGACCTTTTCCATGCTGAAGAA
35704450 GTCACCA
131 GTCACCA
35704457 TTTAACCAACGGTTCTTGGATCTTTAAGACATCAACAACCTTTTTCCTTAAGTCACTTGAGTTAA
1 TTTAACCAACGGTTCTTGGATCTTTAAGACATCAACAACCTTTTTCCTTAAGTCACTTGAGTTAA
35704522 TGACTTCAGTCATTTCTAGTCCAGTTGGTTTTCTTGCATATGTGGACCTTTTCCATGCTGAAGAA
66 TGACTTCAGTCATTTCTAGTCCAGTTGGTTTTCTTGCATATGTGGACCTTTTCCATGCTGAAGAA
35704587 GTCACCA
131 GTCACCA
35704594 TTT
1 TTT
35704597 CCTTTAGTGC
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
137 140 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.38
Consensus pattern (137 bp):
TTTAACCAACGGTTCTTGGATCTTTAAGACATCAACAACCTTTTTCCTTAAGTCACTTGAGTTAA
TGACTTCAGTCATTTCTAGTCCAGTTGGTTTTCTTGCATATGTGGACCTTTTCCATGCTGAAGAA
GTCACCA
Found at i:35706143 original size:34 final size:34
Alignment explanation
Indices: 35706100--35706231 Score: 131
Period size: 34 Copynumber: 3.8 Consensus size: 34
35706090 AATATTCACC
* *
35706100 AAAATGAAACAAAAATGATAAGGCTTAAAACTAA
1 AAAATGAAACAAAAATAATAAGACTTAAAACTAA
35706134 AAAATGAAACAAAAATAATAAGACTTAAAACTCTAA
1 AAAATGAAACAAAAATAATAAGACTTAAAA--CTAA
** ****
35706170 CAGCA-GAAACACTGCTAATAAGACTTAAAACTAA
1 -AAAATGAAACAAAAATAATAAGACTTAAAACTAA
* *
35706204 AAAATGGAAAAAAAAATTATAAGACTTA
1 AAAAT-GAAACAAAAATAATAAGACTTA
35706232 TAATTAATAA
Statistics
Matches: 77, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
33 2 0.03
34 32 0.42
35 16 0.21
36 25 0.32
37 2 0.03
ACGTcount: A:0.60, C:0.11, G:0.10, T:0.19
Consensus pattern (34 bp):
AAAATGAAACAAAAATAATAAGACTTAAAACTAA
Found at i:35706271 original size:40 final size:40
Alignment explanation
Indices: 35706215--35706301 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 40
35706205 AAATGGAAAA
* *
35706215 AAAAATTATAAGACTTATAATTAATAATACAAAAGATTCAC
1 AAAAA-TATAAAACTTATAATTAACAATACAAAAGATTCAC
* * * *
35706256 AAAAATATAAAACTTATAATTCACACTACAAAATATTTAC
1 AAAAATATAAAACTTATAATTAACAATACAAAAGATTCAC
35706296 AAAAAT
1 AAAAAT
35706302 TTAGATAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 35 0.88
41 5 0.12
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.29
Consensus pattern (40 bp):
AAAAATATAAAACTTATAATTAACAATACAAAAGATTCAC
Found at i:35711098 original size:3 final size:3
Alignment explanation
Indices: 35711085--35711115 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
35711075 GTCAATGGCC
35711085 AGA AG- AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
35711116 TTTACAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:35712157 original size:22 final size:22
Alignment explanation
Indices: 35712112--35712175 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
35712102 TCCAAACAAC
* * * *
35712112 AACAACAAAATAGTAGTAATAT
1 AACAGCAAAATGGTAGCAAAAT
* *
35712134 AATAGCAGAATGGTAGCAAAAT
1 AACAGCAAAATGGTAGCAAAAT
*
35712156 AACATCAAAATGGTAGCAAA
1 AACAGCAAAATGGTAGCAAA
35712176 CAACAACAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.55, C:0.11, G:0.16, T:0.19
Consensus pattern (22 bp):
AACAGCAAAATGGTAGCAAAAT
Found at i:35713692 original size:20 final size:21
Alignment explanation
Indices: 35713641--35713694 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
35713631 AAAAATGTTG
35713641 ATATATAATAATACATGTAATA
1 ATATATAAT-ATACATGTAATA
* * *
35713663 ATAATTTAATATATAT-TTATA
1 AT-ATATAATATACATGTAATA
35713684 ATATATAATAT
1 ATATATAATAT
35713695 TTATCANNNN
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 8 0.30
21 6 0.22
22 7 0.26
23 6 0.22
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (21 bp):
ATATATAATATACATGTAATA
Found at i:35714229 original size:16 final size:17
Alignment explanation
Indices: 35714199--35714239 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
35714189 AAATGTGGGT
35714199 TAAAAATA-ACTTTATA
1 TAAAAATATACTTTATA
35714215 TAAAAATATAC-TTATA
1 TAAAAATATACTTTATA
*
35714231 -AAATATATA
1 TAAAAATATA
35714240 TTCATCAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 8 0.35
16 13 0.57
17 2 0.09
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAAAATATACTTTATA
Found at i:35715765 original size:17 final size:17
Alignment explanation
Indices: 35715727--35715766 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
35715717 ATTTATAATG
*
35715727 ATAAAAACACCCTTAAA
1 ATAATAACACCCTTAAA
35715744 ATAATAACA-CCTTCAAA
1 ATAATAACACCCTT-AAA
35715761 ATAATA
1 ATAATA
35715767 TGATTTGTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.23
Consensus pattern (17 bp):
ATAATAACACCCTTAAA
Found at i:35717565 original size:19 final size:19
Alignment explanation
Indices: 35717507--35717568 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
35717497 AATGTTTAAT
*
35717507 TTTTATATCTTTTTAATAA
1 TTTTATATTTTTTTAATAA
**
35717526 TTTTA-ATTTTTAAAAATAA
1 TTTTATATTTTT-TTAATAA
35717545 TTTATATATTTTTTTAA-AA
1 TTT-TATATTTTTTTAATAA
35717564 TTTTA
1 TTTTA
35717569 AAAAATTAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
18 7 0.20
19 18 0.51
20 4 0.11
21 6 0.17
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTATATTTTTTTAATAA
Found at i:35717717 original size:94 final size:95
Alignment explanation
Indices: 35717610--35717798 Score: 371
Period size: 94 Copynumber: 2.0 Consensus size: 95
35717600 TTTCTTCATG
35717610 ATTTGACAAAAAAATATAAATTTAATAATTAAAAAGTATAAAAAAAAATTAAATGAAGTATGAAA
1 ATTTGACAAAAAAATATAAATTTAATAATTAAAAAGTATAAAAAAAAATTAAATGAAGTATGAAA
35717675 TAAGTAATTATGTCAAAAATTGACGCATCA
66 TAAGTAATTATGTCAAAAATTGACGCATCA
35717705 ATTTGAC-AAAAAATATAAATTTAATAATTAAAAAGTATAAAAAAAAATTAAATGAAGTATGAAA
1 ATTTGACAAAAAAATATAAATTTAATAATTAAAAAGTATAAAAAAAAATTAAATGAAGTATGAAA
35717769 TAAGTAATTATGTCAAAAATTGACGCATCA
66 TAAGTAATTATGTCAAAAATTGACGCATCA
35717799 CAGATGACTC
Statistics
Matches: 94, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
94 87 0.93
95 7 0.07
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.29
Consensus pattern (95 bp):
ATTTGACAAAAAAATATAAATTTAATAATTAAAAAGTATAAAAAAAAATTAAATGAAGTATGAAA
TAAGTAATTATGTCAAAAATTGACGCATCA
Found at i:35723852 original size:17 final size:18
Alignment explanation
Indices: 35723826--35723861 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
35723816 TCTTTTTCTC
35723826 TCTGCATTTTTTTCTTTA
1 TCTGCATTTTTTTCTTTA
35723844 TCTGC-TTTTTTTCTTTA
1 TCTGCATTTTTTTCTTTA
35723861 T
1 T
35723862 TATTATTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.08, C:0.17, G:0.06, T:0.69
Consensus pattern (18 bp):
TCTGCATTTTTTTCTTTA
Found at i:35724498 original size:3 final size:3
Alignment explanation
Indices: 35724483--35724542 Score: 54
Period size: 3 Copynumber: 20.7 Consensus size: 3
35724473 TAATCACTTA
* * *
35724483 ATT ATT TTT ATT ATT ATT -TG A-T ATT ATT ATT ATT -TT ACT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
*
35724526 ATT ATT GTT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
35724543 ATTTGATTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
2 4 0.09
3 39 0.87
4 2 0.04
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:35724552 original size:16 final size:17
Alignment explanation
Indices: 35724490--35724552 Score: 66
Period size: 16 Copynumber: 4.1 Consensus size: 17
35724480 TTAATTATTT
35724490 TTATTATTATTTGA-TA
1 TTATTATTATTTGATTA
* *
35724506 TTATTATTATTTTACTA
1 TTATTATTATTTGATTA
35724523 -T-TTATTA-TTG-TTA
1 TTATTATTATTTGATTA
35724536 TTATTA-TATTTGATTA
1 TTATTATTATTTGATTA
35724552 T
1 T
35724553 ATTTACCTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 2 0.05
14 5 0.13
15 12 0.31
16 18 0.46
17 2 0.05
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.65
Consensus pattern (17 bp):
TTATTATTATTTGATTA
Found at i:35724555 original size:24 final size:24
Alignment explanation
Indices: 35724483--35724555 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 24
35724473 TAATCACTTA
* *
35724483 ATTATTTTTATTATTATTTGATATT
1 ATTATTATTATTACTATTTGATA-T
35724508 ATTATTATT-TTACTATTT-AT-T
1 ATTATTATTATTACTATTTGATAT
*
35724529 ATTGTTATTATTA-TATTTGATTAT
1 ATTATTATTATTACTATTTGA-TAT
35724553 ATT
1 ATT
35724556 TACCTATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
21 14 0.34
22 4 0.10
23 3 0.07
24 12 0.29
25 8 0.20
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (24 bp):
ATTATTATTATTACTATTTGATAT
Found at i:35727526 original size:26 final size:26
Alignment explanation
Indices: 35727497--35727550 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
35727487 CCAAAGACAG
35727497 AAACCACCAGACATCAGAGTCCTTTA
1 AAACCACCAGACATCAGAGTCCTTTA
35727523 AAACCACCAGACATCAGAGTCCTTTA
1 AAACCACCAGACATCAGAGTCCTTTA
35727549 AA
1 AA
35727551 GCGAGAATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (26 bp):
AAACCACCAGACATCAGAGTCCTTTA
Found at i:35731675 original size:88 final size:88
Alignment explanation
Indices: 35731393--35731676 Score: 385
Period size: 88 Copynumber: 3.2 Consensus size: 88
35731383 CAAAGCCTTA
*
35731393 TCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGTCCTATCTCCCTGACCAGCAGTGGAA
1 TCTCCCTAACCAGCAGTGGAATAGGTTGAAGATTGCAAGTCCTATCTCCCTGACCAGCAGTGGAA
* *
35731458 T-GTGTTGAGGATTGCAAGTCCTG
66 TAG-GTTGAAGATTGTAAGTCCTG
* *
35731481 TCTCTCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGTCCTATCTCCCTGACCAGCAGTGGAA
1 TCTCCCTAACCAGCAGTGGAATAGGTTGAAGATTGCAAGTCCTATCTCCCTGACCAGCAGTGGAA
* *
35731546 TAGGTGGAAGATTGTAAGTCCTA
66 TAGGTTGAAGATTGTAAGTCCTG
* * * * * *
35731569 TCTCCCTGAA-CAACAGTGGAATAGGTGGAAGATTGTATGTCCTATCTCCTTGAACAGCAGTGGA
1 TCTCCCT-AACCAGCAGTGGAATAGGTTGAAGATTGCAAGTCCTATCTCCCTGACCAGCAGTGGA
35731633 ATAGGTTGAAGATTGT-AGATCCTG
65 ATAGGTTGAAGATTGTAAG-TCCTG
* *
35731657 TCTCCCTAAGCAGTAGTGGA
1 TCTCCCTAACCAGCAGTGGA
35731677 GCAGATCGAA
Statistics
Matches: 175, Mismatches: 17, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
87 4 0.02
88 169 0.97
89 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.27
Consensus pattern (88 bp):
TCTCCCTAACCAGCAGTGGAATAGGTTGAAGATTGCAAGTCCTATCTCCCTGACCAGCAGTGGAA
TAGGTTGAAGATTGTAAGTCCTG
Found at i:35731676 original size:44 final size:44
Alignment explanation
Indices: 35731391--35731647 Score: 390
Period size: 44 Copynumber: 5.8 Consensus size: 44
35731381 CACAAAGCCT
35731391 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGTCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGTCC
*
35731435 TATCTCCCTGACCAGCAGTGGAAT-GTGTTGAGGATTGCAAGTCC
1 TATCTCCCTGACCAGCAGTGGAATAG-GTTGAAGATTGCAAGTCC
* *
35731479 TGTCTCTCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGTCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGTCC
* *
35731523 TATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTAAGTCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGTCC
* * * * *
35731567 TATCTCCCTGAACAACAGTGGAATAGGTGGAAGATTGTATGTCC
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGTCC
* *
35731611 TATCTCCTTGAACAGCAGTGGAATAGGTTGAAGATTG
1 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTG
35731648 TAGATCCTGT
Statistics
Matches: 197, Mismatches: 14, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
43 1 0.01
44 195 0.99
45 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (44 bp):
TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGTCC
Found at i:35731688 original size:132 final size:132
Alignment explanation
Indices: 35731391--35731688 Score: 350
Period size: 132 Copynumber: 2.3 Consensus size: 132
35731381 CACAAAGCCT
* * * * * *
35731391 TATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGTCCTATCTCCCTGACCAGCAGTGG
1 TATCTCCCTAACCAGCAGTGGAACAGATCGAAGATTGCAAGTCCTATCTCCCTGAACAACAGTGG
* * * *
35731456 AATGTGTTGAGGATTGCAAGTCCTGTCTCTCTGACCAGCAGTGGAATAGGTTGAAGATTGCAAGT
66 AATGTGTGGAAGATTGCAAGTCCTATCTCTCTGAACAGCAGTGGAATAGGTTGAAGATTGCAAGT
35731521 CC
131 CC
* * * * *
35731523 TATCTCCCTGACCAGCAGTGGAATAGGTGGAAGATTGTAAGTCCTATCTCCCTGAACAACAGTGG
1 TATCTCCCTAACCAGCAGTGGAACAGATCGAAGATTGCAAGTCCTATCTCCCTGAACAACAGTGG
* * *
35731588 AATAG-GTGGAAGATTGTATGTCCTATCTC-CTTGAACAGCAGTGGAATAGGTTGAAGATTG-TA
66 AAT-GTGTGGAAGATTGCAAGTCCTATCTCTC-TGAACAGCAGTGGAATAGGTTGAAGATTGCAA
35731650 GATCC
129 G-TCC
* * * *
35731655 TGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA
1 TATCTCCCTAACCAGCAGTGGAACAGATCGAAGA
35731689 CGGCGAATCT
Statistics
Matches: 144, Mismatches: 19, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
131 3 0.02
132 140 0.97
133 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (132 bp):
TATCTCCCTAACCAGCAGTGGAACAGATCGAAGATTGCAAGTCCTATCTCCCTGAACAACAGTGG
AATGTGTGGAAGATTGCAAGTCCTATCTCTCTGAACAGCAGTGGAATAGGTTGAAGATTGCAAGT
CC
Found at i:35733296 original size:21 final size:21
Alignment explanation
Indices: 35733272--35733320 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
35733262 TTTTATTTGA
35733272 TATTATTATTATT-TTACTATT
1 TATTATTATTATTATTA-TATT
*
35733293 TATTATTGTTATTATTATATT
1 TATTATTATTATTATTATATT
35733314 TGATTAT
1 T-ATTAT
35733321 ATTTACCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (21 bp):
TATTATTATTATTATTATATT
Found at i:35733299 original size:24 final size:22
Alignment explanation
Indices: 35733251--35733317 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 22
35733241 TAATCACTTA
*
35733251 ATTATTTTTATTTTTATTTGAT
1 ATTATTATTATTTTTATTTGAT
35733273 ATTATTATTATTTTACTATTT-ATT
1 ATTATTATTATTTT--TATTTGA-T
* *
35733297 ATTGTTATTA-TTATATTTGAT
1 ATTATTATTATTTTTATTTGAT
35733318 TATATTTACC
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
21 6 0.16
22 14 0.37
23 3 0.08
24 15 0.39
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.67
Consensus pattern (22 bp):
ATTATTATTATTTTTATTTGAT
Found at i:35733323 original size:24 final size:22
Alignment explanation
Indices: 35733253--35733323 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
35733243 ATCACTTAAT
*
35733253 TATTTTTATTTT-TATTTGATA
1 TATTATTATTTTATATTTGATA
35733274 TTATTATTATTTTACTATTT-AT-
1 -TATTATTATTTTA-TATTTGATA
*
35733296 TATTGTTATTATTATATTTGATTA
1 TATTATTATT-TTATATTTGA-TA
35733320 TATT
1 TATT
35733324 TACCTATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
21 14 0.34
22 15 0.37
23 3 0.07
24 9 0.22
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.68
Consensus pattern (22 bp):
TATTATTATTTTATATTTGATA
Found at i:35738160 original size:26 final size:24
Alignment explanation
Indices: 35738105--35738160 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
35738095 ACACACAGAA
35738105 TTTTTTTTTATTTTTTTCATATTT
1 TTTTTTTTTATTTTTTTCATATTT
* *
35738129 TATTTTTTTGTACTTTTTT-ATCACTT
1 T-TTTTTTT-TATTTTTTTCAT-ATTT
35738155 TTTTTT
1 TTTTTT
35738161 GTGAGAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 1 0.04
25 14 0.52
26 12 0.44
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (24 bp):
TTTTTTTTTATTTTTTTCATATTT
Found at i:35739228 original size:17 final size:17
Alignment explanation
Indices: 35739206--35739238 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
35739196 TGATGTGTAC
35739206 GACCATGGATGAAAGAA
1 GACCATGGATGAAAGAA
35739223 GACCATGGATGAAAGA
1 GACCATGGATGAAAGA
35739239 CTCCATGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.45, C:0.12, G:0.30, T:0.12
Consensus pattern (17 bp):
GACCATGGATGAAAGAA
Found at i:35741725 original size:25 final size:25
Alignment explanation
Indices: 35741694--35741748 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
35741684 CCCCAAATCG
35741694 TTTTCCCCAAATACCTAACTTAGTT
1 TTTTCCCCAAATACCTAACTTAGTT
* *
35741719 TTTTCCCTAAATCCCTAACTTAGTT
1 TTTTCCCCAAATACCTAACTTAGTT
35741744 TTTTC
1 TTTTC
35741749 TTTCCCATCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.24, C:0.27, G:0.04, T:0.45
Consensus pattern (25 bp):
TTTTCCCCAAATACCTAACTTAGTT
Found at i:35746691 original size:21 final size:21
Alignment explanation
Indices: 35746667--35746716 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
35746657 CTTAAAGCGT
*
35746667 AGGCAACAGCGAGGGAAGCAG
1 AGGCAACAGCAAGGGAAGCAG
* * *
35746688 AGGCAGCAGCAATGGCAGCAG
1 AGGCAACAGCAAGGGAAGCAG
*
35746709 AGGTAACA
1 AGGCAACA
35746717 AGAAAATATG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.20, G:0.38, T:0.04
Consensus pattern (21 bp):
AGGCAACAGCAAGGGAAGCAG
Found at i:35751767 original size:27 final size:26
Alignment explanation
Indices: 35751726--35751780 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 26
35751716 AATACACATA
35751726 TTTATATAATTAAAATAT-TCATATT
1 TTTATATAATTAAAATATGTCATATT
35751751 TTTATATTAGATTAAAATATGTCATATT
1 TTTATA-TA-ATTAAAATATGTCATATT
35751779 TT
1 TT
35751781 GTTAAATTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 6 0.22
26 2 0.07
27 10 0.37
28 9 0.33
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (26 bp):
TTTATATAATTAAAATATGTCATATT
Found at i:35752864 original size:24 final size:22
Alignment explanation
Indices: 35752839--35752911 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 22
35752829 TGGCTATATA
35752839 AAAAATTAATATATAAAATTATT
1 AAAAATTAA-ATATAAAATTATT
* * *
35752862 AAATATTAAAT-TAATATTAAT
1 AAAAATTAAATATAAAATTATT
* *
35752883 ATAAATATAAATATAAATATTTTT
1 AAAAAT-TAAATATAAA-ATTATT
35752907 AAAAA
1 AAAAA
35752912 ATCTAAAAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
21 12 0.32
22 7 0.18
23 11 0.29
24 8 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAAATTAAATATAAAATTATT
Found at i:35752881 original size:18 final size:19
Alignment explanation
Indices: 35752858--35752903 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
35752848 TATATAAAAT
35752858 TATTAAATATTAAAT-TAA
1 TATTAAATATTAAATATAA
35752876 TATT-AATA-TAAATATAA
1 TATTAAATATTAAATATAA
35752893 -ATATAAATATT
1 TAT-TAAATATT
35752904 TTTAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 7 0.29
17 8 0.33
18 8 0.33
19 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TATTAAATATTAAATATAA
Found at i:35752889 original size:12 final size:12
Alignment explanation
Indices: 35752843--35752903 Score: 65
Period size: 12 Copynumber: 5.2 Consensus size: 12
35752833 TATATAAAAA
*
35752843 ATTAATATATAAA
1 ATTAATATA-AAT
35752856 ATT-AT-TAAAT
1 ATTAATATAAAT
*
35752866 ATTAA-ATTAAT
1 ATTAATATAAAT
35752877 ATTAATATAAAT
1 ATTAATATAAAT
*
35752889 ATAAATATAAAT
1 ATTAATATAAAT
35752901 ATT
1 ATT
35752904 TTTAAAAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
10 5 0.12
11 12 0.30
12 20 0.50
13 3 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
ATTAATATAAAT
Found at i:35754766 original size:25 final size:27
Alignment explanation
Indices: 35754726--35754784 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 27
35754716 GTAATATTAT
*
35754726 TATTACTGTTATTATTTTCTTTGTATA
1 TATTACTGTTATTATTTTATTTGTATA
*
35754753 TATT-CTGTT-TTATTTTATTTTTATA
1 TATTACTGTTATTATTTTATTTGTATA
*
35754778 TTTTACT
1 TATTACT
35754785 ATTTTTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 17 0.61
26 7 0.25
27 4 0.14
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (27 bp):
TATTACTGTTATTATTTTATTTGTATA
Found at i:35762448 original size:41 final size:41
Alignment explanation
Indices: 35762366--35762473 Score: 119
Period size: 41 Copynumber: 2.7 Consensus size: 41
35762356 AAGTGATCGA
* * * * *
35762366 ATATAATACAGACTTTACGTC-AGCAGGCTTGATGCCGGTG
1 ATATAATTCAGACTTTACGTCTAGCAGACTTAATACCAGTG
35762406 ATATAATTCAGACTTTACGTCTAGCAGACTTAATACCAGTG
1 ATATAATTCAGACTTTACGTCTAGCAGACTTAATACCAGTG
* * * * *
35762447 ATACATTTCGGACTATAGGTCTAGCAG
1 ATATAATTCAGACTTTACGTCTAGCAG
35762474 GCTAAAAGCC
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
40 20 0.35
41 37 0.65
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (41 bp):
ATATAATTCAGACTTTACGTCTAGCAGACTTAATACCAGTG
Found at i:35774759 original size:3 final size:3
Alignment explanation
Indices: 35774751--35774776 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35774741 ATTTAGAATT
35774751 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
35774777 CAGTGAGGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:35779460 original size:13 final size:12
Alignment explanation
Indices: 35779433--35779457 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35779423 TTTCCATCTA
35779433 TCTTCTTTATTT
1 TCTTCTTTATTT
35779445 TCTTCTTTATTT
1 TCTTCTTTATTT
35779457 T
1 T
35779458 TCTAATCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCTTCTTTATTT
Found at i:35781985 original size:16 final size:16
Alignment explanation
Indices: 35781955--35781996 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
35781945 AAAAATTATA
35781955 AATTAA-TTT-TAATT
1 AATTAATTTTCTAATT
35781969 AATTAATTTTCTAATT
1 AATTAATTTTCTAATT
*
35781985 AAATAATTTTCT
1 AATTAATTTTCT
35781997 CAACTTGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 3 0.12
16 16 0.64
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTAATTTTCTAATT
Found at i:35783972 original size:37 final size:37
Alignment explanation
Indices: 35783922--35783997 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
35783912 TTTAGTCACG
*
35783922 AAGTCATCCACTATAGAATCGTGACTGAGCTTTCCCT
1 AAGTCATCCACTATAGAATCGTGACTGAGCTCTCCCT
*
35783959 AAGTCATCCACTATAGTATCGTGACTGAGCTCTCCCT
1 AAGTCATCCACTATAGAATCGTGACTGAGCTCTCCCT
35783996 AA
1 AA
35783998 TGATAAACCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.29
Consensus pattern (37 bp):
AAGTCATCCACTATAGAATCGTGACTGAGCTCTCCCT
Found at i:35785398 original size:2 final size:2
Alignment explanation
Indices: 35785391--35785432 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
35785381 AAATTGAGAG
35785391 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
35785433 TGCTTGTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:35787973 original size:40 final size:36
Alignment explanation
Indices: 35787929--35788027 Score: 110
Period size: 40 Copynumber: 2.6 Consensus size: 36
35787919 AAATTATATC
*
35787929 AAATTATTAATTATTAATTGTTACTAACATTTCTTTAGTA
1 AAATTATTAATTATTAATTGTTA-TAA-A-TT-GTTAGTA
* *
35787969 AAATTATTAATTGTTAATTG-TATTAATTGTTAGTA
1 AAATTATTAATTATTAATTGTTATAAATTGTTAGTA
*
35788004 AAATTATCAAATTATTAATTGTTA
1 AAATTAT-TAATTATTAATTGTTA
35788028 ATTGTTTTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
35 13 0.25
36 13 0.25
37 3 0.06
38 2 0.04
39 2 0.04
40 19 0.37
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.49
Consensus pattern (36 bp):
AAATTATTAATTATTAATTGTTATAAATTGTTAGTA
Found at i:35787994 original size:16 final size:16
Alignment explanation
Indices: 35787973--35788042 Score: 60
Period size: 16 Copynumber: 4.7 Consensus size: 16
35787963 TTAGTAAAAT
35787973 TATTAATTGTTAATTG
1 TATTAATTGTTAATTG
35787989 TATTAATTGTT-A--G
1 TATTAATTGTTAATTG
* * * *
35788002 TA-AAATTATCAAAT-
1 TATTAATTGTTAATTG
35788016 TATTAATTGTTAATTG
1 TATTAATTGTTAATTG
*
35788032 TTTTAATTGTT
1 TATTAATTGTT
35788043 GTAACAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
12 5 0.12
13 4 0.10
14 2 0.05
15 9 0.22
16 21 0.51
ACGTcount: A:0.34, C:0.01, G:0.10, T:0.54
Consensus pattern (16 bp):
TATTAATTGTTAATTG
Found at i:35788108 original size:23 final size:22
Alignment explanation
Indices: 35788082--35788127 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
35788072 AACTTAAAAC
* *
35788082 AAAACTAAAACTAGTATAT-TTT
1 AAAAATAAAAATA-TATATATTT
35788104 AAAAATAAAAATATATATATTT
1 AAAAATAAAAATATATATATTT
35788126 AA
1 AA
35788128 TATATTTTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (22 bp):
AAAAATAAAAATATATATATTT
Found at i:35788773 original size:21 final size:21
Alignment explanation
Indices: 35788749--35788790 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
35788739 ATAAAATTGG
35788749 GATAGTTTAACCTTAGGTGGT
1 GATAGTTTAACCTTAGGTGGT
35788770 GATAGTTTAACCTTAGGTGGT
1 GATAGTTTAACCTTAGGTGGT
35788791 AAAATGACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.10, G:0.29, T:0.38
Consensus pattern (21 bp):
GATAGTTTAACCTTAGGTGGT
Found at i:35793347 original size:17 final size:17
Alignment explanation
Indices: 35793325--35793377 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 17
35793315 ATTAAAAAAT
35793325 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
* *
35793342 CATATCATATCTACGATTG
1 CATATC-T-TCTAAGATTA
*
35793361 CATATCTTCAAAGATTA
1 CATATCTTCTAAGATTA
35793378 TGTTTCCATA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 13 0.45
18 2 0.07
19 14 0.48
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.38
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:35793348 original size:22 final size:22
Alignment explanation
Indices: 35793296--35793353 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
35793286 AAAAGGTATC
* *
35793296 TACAGATCAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
*
35793317 TAAAAAATCATATCTTCTAAGAT
1 T-ACAAATCATATCTTCTAAGAT
*
35793340 TACATATCATATCT
1 TACAAATCATATCT
35793354 ACGATTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 1 0.03
22 20 0.67
23 9 0.30
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.34
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:35798476 original size:23 final size:22
Alignment explanation
Indices: 35798431--35798488 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
35798421 AAAAGGTATC
* * *
35798431 TACAAATAAAATC-TCTAATAT
1 TACAAATCATATCTTCTAAGAT
35798452 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
35798475 TACATATCATATCT
1 TACAAATCATATCT
35798489 ACGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:35798482 original size:17 final size:17
Alignment explanation
Indices: 35798460--35798512 Score: 52
Period size: 19 Copynumber: 3.0 Consensus size: 17
35798450 ATTACAAAAT
35798460 CATATCTTCTAAGATTA
1 CATATCTTCTAAGATTA
* *
35798477 CATATCATATCTACGATTG
1 CATATC-T-TCTAAGATTA
* *
35798496 CATATCCTCGAAGATTA
1 CATATCTTCTAAGATTA
35798513 TGTTTCCATA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
17 13 0.46
18 1 0.04
19 14 0.50
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (17 bp):
CATATCTTCTAAGATTA
Found at i:35818839 original size:41 final size:41
Alignment explanation
Indices: 35818794--35818877 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
35818784 TACTTTTCCC
35818794 AATTTCAATAAGTAGAAATCAAGATATAATAAAACAAGATT
1 AATTTCAATAAGTAGAAATCAAGATATAATAAAACAAGATT
*
35818835 AATTTCAATAAGTAGAAATCAAGATATAATAAAACAAGCTT
1 AATTTCAATAAGTAGAAATCAAGATATAATAAAACAAGATT
35818876 AA
1 AA
35818878 GGATCATTCG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.26
Consensus pattern (41 bp):
AATTTCAATAAGTAGAAATCAAGATATAATAAAACAAGATT
Found at i:35829220 original size:56 final size:56
Alignment explanation
Indices: 35829151--35829300 Score: 167
Period size: 56 Copynumber: 2.6 Consensus size: 56
35829141 ATTCGAGTTT
* * * * **
35829151 TGGTCTGTTAATGGTAGGCACCAGAGTACGAAAAAAA-GAAAAAAAATTTTGGGTGC
1 TGGTCTGTCAATGGCAGACACC-CAGTACGAAAAAAAGGAAAAAAAAAATTGGGTGC
*
35829207 TGGTCTGTCAATGGCCGACACCCAGTACGAAAAAAAGGAAAAAAAAAATTGGGTGC
1 TGGTCTGTCAATGGCAGACACCCAGTACGAAAAAAAGGAAAAAAAAAATTGGGTGC
* * * *
35829263 TAGCCTGTCAATGGCCGGCACCCAGTACAGTAAAAAAA
1 TGGTCTGTCAATGGCAGACACCCAGTAC-G-AAAAAAA
35829301 TTCGAGTTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
55 13 0.16
56 60 0.74
57 1 0.01
58 7 0.09
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (56 bp):
TGGTCTGTCAATGGCAGACACCCAGTACGAAAAAAAGGAAAAAAAAAATTGGGTGC
Found at i:35829894 original size:13 final size:13
Alignment explanation
Indices: 35829876--35829900 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35829866 TTAAGAAAGT
35829876 AAAAATTAAAATA
1 AAAAATTAAAATA
35829889 AAAAATTAAAAT
1 AAAAATTAAAAT
35829901 TGTCGCGATC
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATTAAAATA
Found at i:35834005 original size:52 final size:52
Alignment explanation
Indices: 35833946--35834117 Score: 238
Period size: 53 Copynumber: 3.2 Consensus size: 52
35833936 CTGACACTCT
*
35833946 CTTTTTTTCATTCAGTCTCATTTATTTAAAATTTTTTTCCTACAAT-TAACACC
1 CTTTTTTTCATTCAATCTCATTTATTTAAAA-TTTTTTCCTAC-ATCTAACACC
* * *
35833999 CTTTTTTTTTCATTCAATCTCATATATTTTAAATTTTTTCCCACATCTAACACC
1 C--TTTTTTTCATTCAATCTCATTTATTTAAAATTTTTTCCTACATCTAACACC
* *
35834053 ATTTTTTTCATTCAATCTCATTTATTTCAAAATTTTTTCCTACATCTAGCACC
1 CTTTTTTTCATTCAATCTCATTTATTT-AAAATTTTTTCCTACATCTAACACC
35834106 CTTTTTTTCATT
1 CTTTTTTTCATT
35834118 TTCGTTTCTA
Statistics
Matches: 105, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
52 25 0.24
53 36 0.34
54 17 0.16
55 27 0.26
ACGTcount: A:0.25, C:0.22, G:0.01, T:0.52
Consensus pattern (52 bp):
CTTTTTTTCATTCAATCTCATTTATTTAAAATTTTTTCCTACATCTAACACC
Found at i:35834890 original size:113 final size:112
Alignment explanation
Indices: 35834687--35834905 Score: 307
Period size: 113 Copynumber: 1.9 Consensus size: 112
35834677 AGCATCCGAA
*
35834687 ATTTTTTTCCCCCAAAAAGGTGGTGCCGGCCAATTGGCAGGCCACCACAAAAAAATTTACTTTTT
1 ATTTTTTTCCCCAAAAAAGGTGGTGCCGGCCAATTGGCAGGCCACCACAAAAAAATTTACTTTTT
* *
35834752 TCGTATACTGATACCTGCTATTGACAC-AAAAAAAGTAAAAAAAAAT
66 TCGTATACTGATACCTGATACTGACACGAAAAAAAGTAAAAAAAAAT
* *****
35834798 ATTTTTTTCCACCAAAAAAGGTGGTGCCGGCC-ATTGGCAGGCCACCTCAATTTTTTTTTTACTT
1 ATTTTTTTCC-CCAAAAAAGGTGGTGCCGGCCAATTGGCAGGCCACCACAA--AAAAATTTACTT
*
35834862 TTTTCGTATGCTGATACCTGATACTGACACGAAAAAAAGTAAAA
63 TTTTCGTATACTGATACCTGATACTGACACGAAAAAAAGTAAAA
35834906 TTTTTTTTAC
Statistics
Matches: 94, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
111 27 0.29
112 20 0.21
113 34 0.36
114 13 0.14
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.30
Consensus pattern (112 bp):
ATTTTTTTCCCCAAAAAAGGTGGTGCCGGCCAATTGGCAGGCCACCACAAAAAAATTTACTTTTT
TCGTATACTGATACCTGATACTGACACGAAAAAAAGTAAAAAAAAAT
Found at i:35834968 original size:56 final size:56
Alignment explanation
Indices: 35834908--35835016 Score: 139
Period size: 56 Copynumber: 1.9 Consensus size: 56
35834898 AAGTAAAATT
* * *
35834908 TTTTTTACTGTACT-GGGTGCCGGTCATTGACAGGCCAACACCCAAATTTTTTTTTC
1 TTTTTTAC-GTACTCGGGTGCCGGCCATTGACAGACCAAAACCCAAATTTTTTTTTC
* * * *
35834964 TTTTTTTCGTACTCTGGTGCCGGCCATTGACAGACCAAAACTCGAATTTTTTT
1 TTTTTTACGTACTCGGGTGCCGGCCATTGACAGACCAAAACCCAAATTTTTTT
35835017 ACCCAAATTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
55 5 0.11
56 40 0.89
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.39
Consensus pattern (56 bp):
TTTTTTACGTACTCGGGTGCCGGCCATTGACAGACCAAAACCCAAATTTTTTTTTC
Found at i:35836374 original size:36 final size:36
Alignment explanation
Indices: 35836287--35836375 Score: 87
Period size: 36 Copynumber: 2.5 Consensus size: 36
35836277 TTATTATAAA
* *
35836287 TATATTAAATAAT-TTGTTAAAATATTAAATCATAT
1 TATATTAAATAATATTATTAAAATATTAAATAATAT
*
35836322 T-TATTACATATTATATTATT-AAATA-TAAATAAATAT
1 TATATTA-A-ATAATATTATTAAAATATTAAAT-AATAT
35836358 GTATATTAAATAATATTA
1 -TATATTAAATAATATTA
35836376 AGCTTAATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
34 5 0.11
35 7 0.16
36 21 0.48
37 6 0.14
38 5 0.11
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (36 bp):
TATATTAAATAATATTATTAAAATATTAAATAATAT
Found at i:35843807 original size:20 final size:20
Alignment explanation
Indices: 35843763--35843831 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
35843753 AAAATTACAA
*
35843763 AAAAAAATCAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
*
35843783 CAAAAATTCAAAAT-ATTTAT
1 AAAAAATTCAAAATAATTT-T
*
35843803 AAAAATTTCAAAATTTATATTTT
1 AAAAAATTCAAAA--TA-ATTTT
35843826 AAAAAA
1 AAAAAA
35843832 ATATAAAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 4 0.10
20 24 0.62
22 1 0.03
23 6 0.15
24 4 0.10
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTTT
Found at i:35846874 original size:19 final size:19
Alignment explanation
Indices: 35846836--35846875 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
35846826 AAAATATCAT
*
35846836 ATTAATTTTAATTAATTTG
1 ATTAATTTTAATTAACTTG
35846855 ATTAA-TTTAATTATACTTG
1 ATTAATTTTAATTA-ACTTG
35846874 AT
1 AT
35846876 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (19 bp):
ATTAATTTTAATTAACTTG
Found at i:35857180 original size:24 final size:24
Alignment explanation
Indices: 35857153--35857199 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
35857143 ATTGAAATGG
35857153 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
35857177 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
35857200 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:35857197 original size:15 final size:15
Alignment explanation
Indices: 35857177--35857226 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 15
35857167 TGATGAATTT
35857177 ATTGAATTTATATTG
1 ATTGAATTTATATTG
35857192 ATTGAATTGGTATATAT-
1 ATTGAATT--TATAT-TG
*
35857209 ATTGAATATATATTG
1 ATTGAATTTATATTG
35857224 ATT
1 ATT
35857227 ATTTGAATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
17 12 0.40
18 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:35857404 original size:41 final size:40
Alignment explanation
Indices: 35857359--35857468 Score: 127
Period size: 37 Copynumber: 2.8 Consensus size: 40
35857349 ACTTCGAGTT
* **
35857359 GATGAGACACTTGGTGTCAAATTATTACTTCGGATATATTC
1 GATGAGACACTGGGTGTCAAATTATTACTTCGG-TATAGCC
* * * *
35857400 GATGAGGCGCTGGGTG-CCAA-T-TTACTTCGGTTTAGCC
1 GATGAGACACTGGGTGTCAAATTATTACTTCGGTATAGCC
35857437 GATGAGACACTGGGTGTCAAATTATTACTTCG
1 GATGAGACACTGGGTGTCAAATTATTACTTCG
35857469 AATTATTTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 7
0.77 0.14 0.10
Matches are distributed among these distances:
37 18 0.32
38 12 0.21
39 2 0.04
40 11 0.20
41 13 0.23
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
GATGAGACACTGGGTGTCAAATTATTACTTCGGTATAGCC
Found at i:35859430 original size:4 final size:4
Alignment explanation
Indices: 35859421--35859446 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
35859411 GATCCATCGG
35859421 AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA
35859447 ATTAATTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:35866760 original size:9 final size:9
Alignment explanation
Indices: 35866745--35866785 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
35866735 TTTTGGTTAA
35866745 GAATTAACC
1 GAATTAACC
*
35866754 AAATTAACC
1 GAATTAACC
35866763 GAATTAACC
1 GAATTAACC
*
35866772 GAATTACCC
1 GAATTAACC
35866781 GAATT
1 GAATT
35866786 GAATCACTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.44, C:0.22, G:0.10, T:0.24
Consensus pattern (9 bp):
GAATTAACC
Found at i:35866815 original size:17 final size:17
Alignment explanation
Indices: 35866793--35866853 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
35866783 ATTGAATCAC
35866793 TACATAATTAAAAATAT
1 TACATAATTAAAAATAT
*** *
35866810 TACATAAGTCTTTGAATCAC
1 TACATAA-T-TAAAAAT-AT
*
35866830 TACATAATTAAAAACAT
1 TACATAATTAAAAATAT
35866847 TACATAA
1 TACATAA
35866854 GTCTTGAAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 6
0.68 0.19 0.13
Matches are distributed among these distances:
17 15 0.47
18 4 0.12
19 5 0.16
20 8 0.25
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (17 bp):
TACATAATTAAAAATAT
Found at i:35866831 original size:37 final size:37
Alignment explanation
Indices: 35866784--35866858 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
35866774 ATTACCCGAA
*
35866784 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
35866821 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAGTCT
35866858 T
1 T
35866859 GAAATTAACA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAGTCT
Found at i:35866872 original size:37 final size:37
Alignment explanation
Indices: 35866784--35866875 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 37
35866774 ATTACCCGAA
* *
35866784 TTGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATAACTACATAATTAAAAACATTACATAAGTCT
*
35866821 TTGAATCACTACATAATTAAAAACATTACATAAGTC-
1 TTGAATAACTACATAATTAAAAACATTACATAAGTCT
35866857 TTGAAATTAAC-ACATAATT
1 TTG-AA-TAACTACATAATT
35866876 GAAATGTAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
36 3 0.06
37 45 0.88
38 3 0.06
ACGTcount: A:0.47, C:0.14, G:0.05, T:0.34
Consensus pattern (37 bp):
TTGAATAACTACATAATTAAAAACATTACATAAGTCT
Found at i:35867031 original size:38 final size:38
Alignment explanation
Indices: 35866987--35867102 Score: 196
Period size: 38 Copynumber: 3.0 Consensus size: 38
35866977 GACTTAGAGT
* *
35866987 TAGACTTTAGTTTTATTTTTATTGGGTTGATAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGG
35867025 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTT-GGTAATTGGG
*
35867064 TAAACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGG
35867102 T
1 T
35867103 TGGGTAATTG
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
38 38 0.51
39 36 0.49
ACGTcount: A:0.20, C:0.03, G:0.27, T:0.51
Consensus pattern (38 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGG
Found at i:35867071 original size:39 final size:38
Alignment explanation
Indices: 35866990--35867102 Score: 190
Period size: 39 Copynumber: 2.9 Consensus size: 38
35866980 TTAGAGTTAG
* * *
35866990 ACTTTAGTTTTATTTTTATTGGGTTGATAATTGGGTAG
1 ACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGGTAA
35867028 ACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGGTAA
1 ACTTTAGTTTTAGTTTTATTGGGTT-GGTAATTGGGTAA
35867067 ACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGGT
1 ACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGGT
35867103 TGGGTAATTG
Statistics
Matches: 71, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
38 35 0.49
39 36 0.51
ACGTcount: A:0.19, C:0.03, G:0.27, T:0.51
Consensus pattern (38 bp):
ACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGGTAA
Found at i:35867110 original size:13 final size:13
Alignment explanation
Indices: 35867084--35867120 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
35867074 TTTTAGTTTT
35867084 ATTGGGTT-GGTA
1 ATTGGGTTGGGTA
35867096 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
*
35867109 ATTGAGTTGGGT
1 ATTGGGTTGGGT
35867121 TGGATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.16, C:0.00, G:0.43, T:0.41
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:35867855 original size:6 final size:6
Alignment explanation
Indices: 35867839--35867878 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
35867829 AAGAAAGCCC
* * *
35867839 AGACGA TGACGA AGACGA CGACGA AGACGA AGAAGA AGAC
1 AGACGA AGACGA AGACGA AGACGA AGACGA AGACGA AGAC
35867879 AGTAACCAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.47, C:0.17, G:0.33, T:0.03
Consensus pattern (6 bp):
AGACGA
Found at i:35874926 original size:41 final size:42
Alignment explanation
Indices: 35874881--35874983 Score: 142
Period size: 40 Copynumber: 2.5 Consensus size: 42
35874871 CAAAAATTAA
*
35874881 AAAAAGTATTGTAAAATTAAAAAAAATT-AAAAAAGTATTTT
1 AAAAAGTATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTT
* * *
35874922 AAAAA-AATTTTAAAATTTAAAAAATTTAAAAAAAGTATTTT
1 AAAAAGTATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTT
35874963 -AAAAGTATTTTAAAA-TAAAAA
1 AAAAAGTATTTTAAAATTAAAAA
35874984 TATTTATTAT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
40 27 0.50
41 27 0.50
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (42 bp):
AAAAAGTATTTTAAAATTAAAAAAAATTAAAAAAAGTATTTT
Found at i:35874930 original size:32 final size:33
Alignment explanation
Indices: 35874854--35874926 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 33
35874844 ACCAAAAATT
*
35874854 TATTTTAAAAATTAAAACAAAAATTAAAAAAAG
1 TATTGTAAAAATTAAAACAAAAATTAAAAAAAG
35874887 TATTGT-AAAATT-AAA-AAAAATT-AAAAAAG
1 TATTGTAAAAATTAAAACAAAAATTAAAAAAAG
*
35874916 TATTTTAAAAA
1 TATTGTAAAAA
35874927 AATTTTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
29 12 0.32
30 11 0.30
31 3 0.08
32 6 0.16
33 5 0.14
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (33 bp):
TATTGTAAAAATTAAAACAAAAATTAAAAAAAG
Found at i:35874937 original size:30 final size:29
Alignment explanation
Indices: 35874903--35874966 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 29
35874893 AAAATTAAAA
*
35874903 AAAATTAAAAAAGTATTTTAAAAAA-ATTTT
1 AAAATTAAAAAA--ATTTAAAAAAAGATTTT
*
35874933 AAAATTTAAAAAATTTAAAAAAAGTATTTT
1 AAAATTAAAAAAATTTAAAAAAAG-ATTTT
35874963 AAAA
1 AAAA
35874967 GTATTTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 10 0.33
30 20 0.67
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATTAAAAAAATTTAAAAAAAGATTTT
Found at i:35874953 original size:10 final size:10
Alignment explanation
Indices: 35874893--35874955 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
35874883 AAAGTATTGT
35874893 AAAA-TTAAA
1 AAAATTTAAA
*
35874902 AAAAATTAAA
1 AAAATTTAAA
35874912 AAAGTATTTTAAA
1 AAA--A-TTTAAA
*
35874925 AAAATTT--T
1 AAAATTTAAA
35874933 AAAATTT-AA
1 AAAATTTAAA
35874942 AAAATTTAAA
1 AAAATTTAAA
35874952 AAAA
1 AAAA
35874956 GTATTTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
8 7 0.16
9 11 0.24
10 17 0.38
11 1 0.02
12 1 0.02
13 8 0.18
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:35874989 original size:40 final size:40
Alignment explanation
Indices: 35874882--35874989 Score: 139
Period size: 41 Copynumber: 2.7 Consensus size: 40
35874872 AAAAATTAAA
* *
35874882 AAAAGTATTGTAAAATTAAAAAAAATT-AAAAAAGTATTTT
1 AAAAGTATTTTAAAATT-AAAAAATTTAAAAAAAGTATTTT
**
35874922 AAAAAAATTTTAAAATTTAAAAAATTTAAAAAAAGTATTTT
1 AAAAGTATTTTAAAA-TTAAAAAATTTAAAAAAAGTATTTT
35874963 AAAAGTATTTTAAAA-TAAAAATATTTA
1 AAAAGTATTTTAAAATTAAAAA-ATTTA
35874990 TTATATTCGG
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
39 6 0.10
40 25 0.42
41 28 0.47
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (40 bp):
AAAAGTATTTTAAAATTAAAAAATTTAAAAAAAGTATTTT
Found at i:35878218 original size:52 final size:52
Alignment explanation
Indices: 35878140--35878243 Score: 165
Period size: 52 Copynumber: 2.0 Consensus size: 52
35878130 TGAACGACAG
* * *
35878140 GGAAGCCTTTGGGACTGCACACACCATTGGTACTGTCTAAGGTACGTTGCGT
1 GGAAGCCTCTGAGACTGCACACACCATTGGTACTGTCTAAGGCACGTTGCGT
35878192 GGAAGCCTCTGAGACCT-CACACACCATTGGTACTGTCTAAGGCACGTTGCGT
1 GGAAGCCTCTGAGA-CTGCACACACCATTGGTACTGTCTAAGGCACGTTGCGT
35878244 CTAACTATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
52 46 0.96
53 2 0.04
ACGTcount: A:0.22, C:0.26, G:0.27, T:0.25
Consensus pattern (52 bp):
GGAAGCCTCTGAGACTGCACACACCATTGGTACTGTCTAAGGCACGTTGCGT
Found at i:35879304 original size:32 final size:32
Alignment explanation
Indices: 35879267--35879338 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
35879257 CAGTTCTATA
* * *
35879267 AAATGATAACTAATATCACCTTTTCA-TTTGTG
1 AAATGATAACAAATATCAAC-TTTAATTTTGTG
*
35879299 AAATGATAACAAATATCAACTTTAATTTTGTT
1 AAATGATAACAAATATCAACTTTAATTTTGTG
35879331 AAATGATA
1 AAATGATA
35879339 CAATATTCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 4 0.11
32 31 0.89
ACGTcount: A:0.42, C:0.11, G:0.08, T:0.39
Consensus pattern (32 bp):
AAATGATAACAAATATCAACTTTAATTTTGTG
Found at i:35884215 original size:21 final size:21
Alignment explanation
Indices: 35884177--35884224 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
35884167 ATGAATTATT
35884177 TTGAAAGAGTTTTGATCTTAG
1 TTGAAAGAGTTTTGATCTTAG
* *
35884198 TTGATAGA-TTTTGAATCTTTG
1 TTGAAAGAGTTTTG-ATCTTAG
35884219 TTGAAA
1 TTGAAA
35884225 AATAAACAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.46
Consensus pattern (21 bp):
TTGAAAGAGTTTTGATCTTAG
Found at i:35885714 original size:20 final size:20
Alignment explanation
Indices: 35885689--35885728 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
35885679 CATTTCATTT
*
35885689 ATGCAATTGCTTTATCCATA
1 ATGCAATTACTTTATCCATA
35885709 ATGCAATTACTTTATCCATA
1 ATGCAATTACTTTATCCATA
35885729 CCATATTCAA
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:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCAATTACTTTATCCATA
Found at i:35885979 original size:38 final size:39
Alignment explanation
Indices: 35885930--35886005 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
35885920 GTCACATTGG
*
35885930 TTAAACCGAAG-TAAATTGGCACCTAGTGCCTCATCGAA
1 TTAAACCGAAGTTAAATTGACACCTAGTGCCTCATCGAA
* *
35885968 TTAATCCGAAGTTAAATTGACACCTAGTGTCTCATCGA
1 TTAAACCGAAGTTAAATTGACACCTAGTGCCTCATCGA
35886006 CTTGAAGTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 10 0.29
39 24 0.71
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (39 bp):
TTAAACCGAAGTTAAATTGACACCTAGTGCCTCATCGAA
Found at i:35886206 original size:24 final size:24
Alignment explanation
Indices: 35886161--35886207 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
35886151 TATATATTCC
35886161 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
35886185 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
35886208 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:35887247 original size:25 final size:24
Alignment explanation
Indices: 35887219--35887286 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
35887209 TATAACAAGA
*
35887219 AGCTCACAAAAAGC-CTATAACGGGT
1 AGCTC-CAAAAAGCAAT-TAACGGGT
*
35887244 AGCTCCAAAGAGCAATTAACGGGT
1 AGCTCCAAAAAGCAATTAACGGGT
** *
35887268 AGCTCTGAAGAGCAATTAA
1 AGCTCCAAAAAGCAATTAA
35887287 TGGGAAGCAC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 32 0.84
25 6 0.16
ACGTcount: A:0.40, C:0.21, G:0.22, T:0.18
Consensus pattern (24 bp):
AGCTCCAAAAAGCAATTAACGGGT
Found at i:35887263 original size:24 final size:24
Alignment explanation
Indices: 35887236--35887286 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
35887226 AAAAAGCCTA
35887236 TAACGGGTAGCTCCAAAGAGCAAT
1 TAACGGGTAGCTCCAAAGAGCAAT
**
35887260 TAACGGGTAGCTCTGAAGAGCAAT
1 TAACGGGTAGCTCCAAAGAGCAAT
35887284 TAA
1 TAA
35887287 TGGGAAGCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (24 bp):
TAACGGGTAGCTCCAAAGAGCAAT
Found at i:35887861 original size:21 final size:21
Alignment explanation
Indices: 35887835--35887878 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35887825 TATTCGAGTA
*
35887835 AATTTAACA-TCAATTTAATAC
1 AATTT-ACATTCAATTCAATAC
35887856 AATTTACATTCAATTCAATAC
1 AATTTACATTCAATTCAATAC
35887877 AA
1 AA
35887879 GTCACATCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (21 bp):
AATTTACATTCAATTCAATAC
Found at i:35887885 original size:21 final size:21
Alignment explanation
Indices: 35887844--35887885 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
35887834 AAATTTAACA
* * *
35887844 TCAATTTAATACAATTTACAT
1 TCAATTCAATACAAGTCACAT
35887865 TCAATTCAATACAAGTCACAT
1 TCAATTCAATACAAGTCACAT
35887886 CTTAGGTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.19, G:0.02, T:0.36
Consensus pattern (21 bp):
TCAATTCAATACAAGTCACAT
Found at i:35888441 original size:22 final size:24
Alignment explanation
Indices: 35888397--35888442 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
35888387 TTTTTCATGT
35888397 TTTATTTTTACACTCCATAACAAC
1 TTTATTTTTACACTCCATAACAAC
*
35888421 TTTATTTTT-CA-TCTATAACAAC
1 TTTATTTTTACACTCCATAACAAC
35888443 AACTATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 2 0.10
24 9 0.43
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.46
Consensus pattern (24 bp):
TTTATTTTTACACTCCATAACAAC
Found at i:35888549 original size:7 final size:7
Alignment explanation
Indices: 35888537--35888561 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
35888527 TTCCTAAGTG
35888537 AAATAAT
1 AAATAAT
35888544 AAATAAT
1 AAATAAT
35888551 AAATAAT
1 AAATAAT
35888558 AAAT
1 AAAT
35888562 TTTAATCAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATAAT
Found at i:35889775 original size:31 final size:29
Alignment explanation
Indices: 35889737--35889835 Score: 101
Period size: 31 Copynumber: 3.3 Consensus size: 29
35889727 ACTACCAAAA
*
35889737 TAGTCACTTTTGTTTGACTCAA-GTTACATTT
1 TAGTCACTTATGTTTGA---AATGTTACATTT
*
35889768 TAGTCACTTATGTTTGAAATGTTACGTTT
1 TAGTCACTTATGTTTGAAATGTTACATTT
* * *
35889797 TAGTCACTTATGTTATCATATTGTAACATTT
1 TAGTCACTTATGTT-TGA-AATGTTACATTT
35889828 TAGTCACT
1 TAGTCACT
35889836 GAGCCGTTAG
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
28 2 0.03
29 22 0.37
30 2 0.03
31 33 0.56
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.47
Consensus pattern (29 bp):
TAGTCACTTATGTTTGAAATGTTACATTT
Found at i:35889801 original size:29 final size:29
Alignment explanation
Indices: 35889737--35889810 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
35889727 ACTACCAAAA
*
35889737 TAGTCACTTTTGTTTGACTCAAGTTACATTT
1 TAGTCACTTATGTTTGA--CAAGTTACATTT
*
35889768 TAGTCACTTATGTTTGA-AATGTTACGTTT
1 TAGTCACTTATGTTTGACAA-GTTACATTT
35889797 TAGTCACTTATGTT
1 TAGTCACTTATGTT
35889811 ATCATATTGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 2 0.05
29 22 0.55
31 16 0.40
ACGTcount: A:0.23, C:0.14, G:0.15, T:0.49
Consensus pattern (29 bp):
TAGTCACTTATGTTTGACAAGTTACATTT
Found at i:35890442 original size:31 final size:29
Alignment explanation
Indices: 35890378--35890446 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
35890368 ACGATAACGT
* *
35890378 AAGTGACTAAAACGTAACATTTCAAACAT
1 AAGTGACTAAAACGTAACATGTCAAACAA
* *
35890407 AAGTGACTAAAATGTAACCTGAGTCAAACAA
1 AAGTGACTAAAACGTAACAT--GTCAAACAA
35890438 AAGTGACTA
1 AAGTGACTA
35890447 TTTTGATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAACGTAACATGTCAAACAA
Found at i:35895455 original size:31 final size:32
Alignment explanation
Indices: 35895398--35895473 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
35895388 AAAAACTTGT
* *
35895398 ATAGTTTAGTAACTTAAAATGAAAACTT-TTGA
1 ATAGTTTAGTGACTTAAAATGAAAACTTAAT-A
*
35895430 ATAGTTGAGTGAC-TAAAAT-ATAAACTTAATA
1 ATAGTTTAGTGACTTAAAATGA-AAACTTAATA
35895461 ATAGTTTAGTGAC
1 ATAGTTTAGTGAC
35895474 CTTGAGTGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
30 1 0.03
31 25 0.66
32 12 0.32
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (32 bp):
ATAGTTTAGTGACTTAAAATGAAAACTTAATA
Found at i:35900726 original size:20 final size:20
Alignment explanation
Indices: 35900701--35900741 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
35900691 CCCTAAAATG
35900701 GGACCGTGTCATTTCGGGTT
1 GGACCGTGTCATTTCGGGTT
*
35900721 GGACCGTGTCATTTTGGGTT
1 GGACCGTGTCATTTCGGGTT
35900741 G
1 G
35900742 AACACATGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.17, G:0.37, T:0.37
Consensus pattern (20 bp):
GGACCGTGTCATTTCGGGTT
Found at i:35901089 original size:116 final size:116
Alignment explanation
Indices: 35900885--35901123 Score: 478
Period size: 116 Copynumber: 2.1 Consensus size: 116
35900875 GAGTGAAAAG
35900885 TATTGAAGTAAAAGTGTGAAAATTAAAAAGAAGAAATGACTTGATTAGATAAATGAGAAATAGAG
1 TATTGAAGTAAAAGTGTGAAAATTAAAAAGAAGAAATGACTTGATTAGATAAATGAGAAATAGAG
35900950 GAAGGACTAGAAGGGCAATAATATGAAAAGAGTAGAATAAATAGTGGAGGA
66 GAAGGACTAGAAGGGCAATAATATGAAAAGAGTAGAATAAATAGTGGAGGA
35901001 TATTGAAGTAAAAGTGTGAAAATTAAAAAGAAGAAATGACTTGATTAGATAAATGAGAAATAGAG
1 TATTGAAGTAAAAGTGTGAAAATTAAAAAGAAGAAATGACTTGATTAGATAAATGAGAAATAGAG
35901066 GAAGGACTAGAAGGGCAATAATATGAAAAGAGTAGAATAAATAGTGGAGGA
66 GAAGGACTAGAAGGGCAATAATATGAAAAGAGTAGAATAAATAGTGGAGGA
35901117 TATTGAA
1 TATTGAA
35901124 ATTGAGTGTA
Statistics
Matches: 123, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 123 1.00
ACGTcount: A:0.51, C:0.03, G:0.26, T:0.21
Consensus pattern (116 bp):
TATTGAAGTAAAAGTGTGAAAATTAAAAAGAAGAAATGACTTGATTAGATAAATGAGAAATAGAG
GAAGGACTAGAAGGGCAATAATATGAAAAGAGTAGAATAAATAGTGGAGGA
Found at i:35902795 original size:22 final size:23
Alignment explanation
Indices: 35902767--35902822 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
35902757 CTATCTTCAA
* *
35902767 TGTCACGACATTC-GACCCTCAG
1 TGTCACGACATTCTAACCCCCAG
*
35902789 TGTCACGATA-TCTAACCCCCAG
1 TGTCACGACATTCTAACCCCCAG
*
35902811 TGTCGCGACATT
1 TGTCACGACATT
35902823 GGAGCAGGGG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
21 2 0.07
22 24 0.89
23 1 0.04
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.25
Consensus pattern (23 bp):
TGTCACGACATTCTAACCCCCAG
Found at i:35909583 original size:24 final size:22
Alignment explanation
Indices: 35909556--35909603 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
35909546 ATTATTAGTG
*
35909556 AAACAAATAATTTAATTATATTCT
1 AAACAAA-AATTTAA-AATATTCT
*
35909580 AAACTAAAATTTAAAATATTCT
1 AAACAAAAATTTAAAATATTCT
35909602 AA
1 AA
35909604 GTAATAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 9 0.41
23 7 0.32
24 6 0.27
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (22 bp):
AAACAAAAATTTAAAATATTCT
Found at i:35916705 original size:28 final size:28
Alignment explanation
Indices: 35916618--35916715 Score: 99
Period size: 28 Copynumber: 3.5 Consensus size: 28
35916608 AAATTAGCGC
* * *
35916618 GCTTATCG-TATTATTTCGCGCTTCGGT
1 GCTTATCGTTATTATTTTGCACTTTGGT
** * *
35916645 GCTTATCGTTGTAAAAATTTGTACTTTGGT
1 GCTTATCG-T-TATTATTTTGCACTTTGGT
*
35916675 GCTTATCGTTATTATTTTGCACTTTGAT
1 GCTTATCGTTATTATTTTGCACTTTGGT
35916703 GCTTATCGTTATT
1 GCTTATCGTTATT
35916716 TGAAATTTGT
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
27 8 0.14
28 27 0.48
29 1 0.02
30 20 0.36
ACGTcount: A:0.17, C:0.15, G:0.18, T:0.49
Consensus pattern (28 bp):
GCTTATCGTTATTATTTTGCACTTTGGT
Found at i:35922289 original size:184 final size:184
Alignment explanation
Indices: 35921980--35922347 Score: 664
Period size: 184 Copynumber: 2.0 Consensus size: 184
35921970 TTGGGTGTAT
*
35921980 AGCAGCTCTCCATCAAGCCAAAATCTTCTCGTTTTTCCCTCCTTGGCCAACTCCGTCAGATTATT
1 AGCAGCTCTCCATCAAGCCAAAATCTTCTCGTTTTTCCCTCCTTGGCCAACTCCGTCAAATTATT
*
35922045 GGCTGTGGGATCATGGGACAATCCTTCTGGAATACGTTCCAACAAGGAACCATCAGGTTGGCTAA
66 GGCTGTGGGATCATGGGACAATCCTTCTCGAATACGTTCCAACAAGGAACCATCAGGTTGGCTAA
* * *
35922110 TTGCCGCAAATTCCATCTTTCGACTCAGTGCGTCGGCTACAATGTTGGCACTCC
131 GTACCGCAAATTCCATCTTTCGACTCAGTGCGTCGGCCACAATGTTGGCACTCC
*
35922164 AGCAGCTCTCCATCAAGCCAAAATCTTCTCGTTTTTCCCTCCTTGGCCAACTCCGTCAAATTTTT
1 AGCAGCTCTCCATCAAGCCAAAATCTTCTCGTTTTTCCCTCCTTGGCCAACTCCGTCAAATTATT
*
35922229 GGTTGTGGGATCATGGGACAATCCTTCTCGAATACGTTCCAACAAGGAACCATCAGGTTGGCTAA
66 GGCTGTGGGATCATGGGACAATCCTTCTCGAATACGTTCCAACAAGGAACCATCAGGTTGGCTAA
*
35922294 GTACCGCAAATTCCATCTTTTGACTCAGTGCGTCGGCCACAATGTTGGCACTCC
131 GTACCGCAAATTCCATCTTTCGACTCAGTGCGTCGGCCACAATGTTGGCACTCC
35922348 CCGGCTTATA
Statistics
Matches: 176, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
184 176 1.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (184 bp):
AGCAGCTCTCCATCAAGCCAAAATCTTCTCGTTTTTCCCTCCTTGGCCAACTCCGTCAAATTATT
GGCTGTGGGATCATGGGACAATCCTTCTCGAATACGTTCCAACAAGGAACCATCAGGTTGGCTAA
GTACCGCAAATTCCATCTTTCGACTCAGTGCGTCGGCCACAATGTTGGCACTCC
Found at i:35925736 original size:35 final size:36
Alignment explanation
Indices: 35925696--35925767 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
35925686 TCTAGGATCA
35925696 CATATC-TCAAAAGATCACCTTCCATATTTGCCAAG
1 CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
* * *
35925731 CATATCTTCATAAGATCACTTTCCTTATTTGCCAAG
1 CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
35925767 C
1 C
35925768 TCCGGAGATG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 6 0.18
36 27 0.82
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (36 bp):
CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
Found at i:35927120 original size:41 final size:40
Alignment explanation
Indices: 35927063--35927203 Score: 212
Period size: 41 Copynumber: 3.5 Consensus size: 40
35927053 GACTTTAAGT
* *
35927063 CTAGCAGGCTAAGTGCCGGTGGTCTGAACCAGGCTATGAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTAT-AAC
*
35927104 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTAT-AAC
35927145 CTAGCAGGCTACA-TGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTA-AGTGCCGGTGATCTGAATCAGGCTATAA-C
35927186 CTAGCAGGCTAAGTGCCG
1 CTAGCAGGCTAAGTGCCG
35927204 TGAATATGTT
Statistics
Matches: 92, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
40 3 0.03
41 88 0.96
42 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.21
Consensus pattern (40 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAC
Found at i:35929759 original size:19 final size:19
Alignment explanation
Indices: 35929735--35929799 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 19
35929725 TTTGAATAAA
*
35929735 TTTTTAATCAAGTCAAAAT
1 TTTTTAATCAAGTTAAAAT
35929754 TTTTTAAATCAAGTTAAACA-
1 TTTTT-AATCAAGTTAAA-AT
*
35929774 TTTTCAATCAAAGTTAAAAT
1 TTTTTAATC-AAGTTAAAAT
35929794 TATTTT
1 T-TTTT
35929800 TAAAAAAGTC
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 10 0.26
20 24 0.63
21 4 0.11
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.45
Consensus pattern (19 bp):
TTTTTAATCAAGTTAAAAT
Found at i:35932401 original size:29 final size:30
Alignment explanation
Indices: 35932368--35932435 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 30
35932358 TTTTTTTAAA
*
35932368 TAAAATAACTAAG-ACTAATTTTTAAAAAT
1 TAAAATAACTAAGCACTAAATTTTAAAAAT
*
35932397 TAAAAGTAA--ATGCACTAAATTTTAAAAAT
1 TAAAA-TAACTAAGCACTAAATTTTAAAAAT
*
35932426 TCAAA-AACTA
1 TAAAATAACTA
35932436 TTGAGGCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
27 2 0.06
28 2 0.06
29 25 0.78
30 3 0.09
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (30 bp):
TAAAATAACTAAGCACTAAATTTTAAAAAT
Found at i:35937832 original size:14 final size:15
Alignment explanation
Indices: 35937809--35937846 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
35937799 TATTAGTTAC
35937809 TTATTATTTTATTT-A
1 TTATT-TTTTATTTCA
*
35937824 TTCTTTTTTATTTCA
1 TTATTTTTTATTTCA
35937839 TTATTTTT
1 TTATTTTT
35937847 ATTCAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (15 bp):
TTATTTTTTATTTCA
Found at i:35938649 original size:26 final size:25
Alignment explanation
Indices: 35938604--35938657 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 25
35938594 TTTAAATTAT
*
35938604 TAAAATTATAATTTATTATTTTAATA
1 TAAAATTATAATTTATTA-TTCAATA
35938630 TAAAATTATAAGTTTA-TATTCAATA
1 TAAAATTATAA-TTTATTATTCAATA
35938655 TAA
1 TAA
35938658 TTTAATACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 9 0.35
26 13 0.50
27 4 0.15
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (25 bp):
TAAAATTATAATTTATTATTCAATA
Found at i:35940286 original size:15 final size:15
Alignment explanation
Indices: 35940262--35940307 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
35940252 GAAGAAAAAG
35940262 AATA-AATAAAATGA
1 AATATAATAAAATGA
35940276 AATATAATAAAA-GA
1 AATATAATAAAATGA
*
35940290 AATAATAATAAAGTGA
1 AAT-ATAATAAAATGA
35940306 AA
1 AA
35940308 AAAAATGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 9 0.32
15 15 0.54
16 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.22
Consensus pattern (15 bp):
AATATAATAAAATGA
Done.