Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 16 of 310
Found at i:4152101 original size:93 final size:93
Alignment explanation
Indices: 4151942--4152113 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
4151932 AGGATATTTG
* *
4151942 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
4152007 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
4152035 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
4152100 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
4152114 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:4155048 original size:15 final size:15
Alignment explanation
Indices: 4155009--4155087 Score: 65
Period size: 15 Copynumber: 5.4 Consensus size: 15
4154999 GTATCTTGGG
* *
4155009 TTTCTTTATCCTAGA
1 TTTCTTTATTCTGGA
*
4155024 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
4155039 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
4155054 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
4155069 TTT-TTTATTC-GGT
1 TTTCTTTATTCTGGA
4155082 TTTCTT
1 TTTCTT
4155088 GTTATCTTTG
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
13 5 0.10
14 7 0.14
15 38 0.76
ACGTcount: A:0.11, C:0.18, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:4157528 original size:46 final size:46
Alignment explanation
Indices: 4157475--4157634 Score: 284
Period size: 46 Copynumber: 3.5 Consensus size: 46
4157465 ATTTGGGCAT
4157475 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGC
4157521 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGC
* * *
4157567 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGC
*
4157613 CCGAGCTCGTTGAGTTGAGTCC
1 CCGAACTCGTTGAGTTGAGTCC
4157635 NNNNNNNNNN
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 110 1.00
ACGTcount: A:0.22, C:0.24, G:0.28, T:0.27
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGC
Found at i:4160889 original size:21 final size:21
Alignment explanation
Indices: 4160851--4160890 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4160841 TTGACCAACT
* *
4160851 TCCGGCAGGGGTTGTGGTTCC
1 TCCGGCAGGGGATCTGGTTCC
4160872 TCCGGCAGGGGATCTGGTT
1 TCCGGCAGGGGATCTGGTT
4160891 GTGGGTGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.23, G:0.42, T:0.28
Consensus pattern (21 bp):
TCCGGCAGGGGATCTGGTTCC
Found at i:4162938 original size:48 final size:46
Alignment explanation
Indices: 4162817--4162949 Score: 160
Period size: 47 Copynumber: 2.8 Consensus size: 46
4162807 ATGCAAACAT
** *
4162817 CATAAATGAAAAAAAATCAAGCAGTATTGAAATTTTAATTGTAATTG
1 CATAAATGAAAAAAAATCAAATAGTATTGAAA-TTTAATTGAAATTG
4162864 CATAAATGAAAAAAAATCAAATAGTATTGCAAATTTAATT-AAATTTG
1 CATAAATGAAAAAAAATCAAATAGTATTG-AAATTTAATTGAAA-TTG
* * *
4162911 CATAAATTAAGAAAATATCGAATAGTATTGAAAATTTAA
1 CATAAATGAA-AAAAAATCAAATAGTATTG-AAATTTAA
4162950 AATTTTCACT
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
46 2 0.03
47 46 0.61
48 28 0.37
ACGTcount: A:0.52, C:0.06, G:0.11, T:0.32
Consensus pattern (46 bp):
CATAAATGAAAAAAAATCAAATAGTATTGAAATTTAATTGAAATTG
Found at i:4164986 original size:25 final size:24
Alignment explanation
Indices: 4164935--4164985 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
4164925 TTGAATATTA
* *
4164935 TTTAATATTTTTTATTTATGTAAT
1 TTTAATAATTTTTATTTATATAAT
4164959 TTTAATTAATTTTTATTT-TATAAT
1 TTTAA-TAATTTTTATTTATATAAT
4164983 TTT
1 TTT
4164986 TTATAACAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTAATAATTTTTATTTATATAAT
Found at i:4165643 original size:19 final size:20
Alignment explanation
Indices: 4165619--4165662 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
4165609 CATAACGAGG
4165619 TAAAATTTA-TAT-TAGATT
1 TAAAATTTATTATGTAGATT
4165637 ATAAAA-TTATTATGTAGATT
1 -TAAAATTTATTATGTAGATT
4165657 TAAAAT
1 TAAAAT
4165663 ATAAATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.14
19 13 0.59
20 6 0.27
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
TAAAATTTATTATGTAGATT
Found at i:4166339 original size:63 final size:59
Alignment explanation
Indices: 4166222--4166343 Score: 138
Period size: 63 Copynumber: 2.0 Consensus size: 59
4166212 TTGTACAAAC
* ****
4166222 TATTTTTATATTGTTTCATTTAATAAAATAAAAGTTGTTTTGAATATTTTAATAGTAAAT
1 TATTTTTATATTGTTTCATTTAATAAAATAAAAGTTCTTTTGAATAAGGCAATAG-AAAT
*
4166282 TATTTTTATATT-TTGTCCTATTTAATAAAAATAGAAGTTCTTTTGAATAAGGCAATAGAAAT
1 TATTTTTATATTGTT-T-C-ATTTAAT-AAAATAAAAGTTCTTTTGAATAAGGCAATAGAAAT
4166344 AATGCAACAT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
59 2 0.04
60 13 0.25
61 1 0.02
62 11 0.21
63 25 0.48
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.48
Consensus pattern (59 bp):
TATTTTTATATTGTTTCATTTAATAAAATAAAAGTTCTTTTGAATAAGGCAATAGAAAT
Found at i:4169598 original size:126 final size:124
Alignment explanation
Indices: 4169368--4169761 Score: 513
Period size: 125 Copynumber: 3.1 Consensus size: 124
4169358 GCCAAGCAGG
* * * * * *
4169368 AACTACTGTATAAAAAGAGCGTCCACGTGAGAGTTTTTTTAGTAATTTTGCTGACAATGCATCCT
1 AACTACTGTAGAAAAAAAGCGTCCACGTGGGAGCTTTTTTAGTAATTTTGCTGACAGTGCATCTT
* * * *
4169433 GCTTGAAGCGTTTTTGACACCATTTTTTTTGAACTGTCTTCTCAAAATTATTTTTTTAGA
66 GCTTGAAGCATTTTTGACACTA-TTTTTTAGAACCGTCTTCTCAAAATTATTTTTTTAGA
* * *
4169493 AACTACTGTAGAAAAAAAGCGTCCACATGGGAGCTTTTTTCAGTAATTTTCCTGACAGCGCATCT
1 AACTACTGTAGAAAAAAAGCGTCCACGTGGGAGCTTTTTT-AGTAATTTTGCTGACAGTGCATCT
* *
4169558 TGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTAAGG
65 TGCTTGAAGCATTTTTGACACTATTTTTT-AGAACCGTCTTCTCAAAATTATTTTTTTAGA
** * *
4169619 AACTACTGTAGAAAAGGAGTGTCCACGTGGGAGCTTTTTTAGTAATTTTGCTGACAGTACAT-TC
1 AACTACTGTAGAAAAAAAGCGTCCACGTGGGAGCTTTTTTAGTAATTTTGCTGACAGTGCATCT-
** * *
4169683 TGCTTGAAATATTTTTGACATTATCTTTTTAGAACCATCTTCTCAAAATTAATTTTTTT-GA
65 TGCTTGAAGCATTTTTGACACTAT-TTTTTAGAACCGTCTTCTCAAAATT-ATTTTTTTAGA
4169744 AACTACTGTAGAAAAAAA
1 AACTACTGTAGAAAAAAA
4169762 AACAAAATCC
Statistics
Matches: 234, Mismatches: 30, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
124 1 0.00
125 117 0.50
126 116 0.50
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (124 bp):
AACTACTGTAGAAAAAAAGCGTCCACGTGGGAGCTTTTTTAGTAATTTTGCTGACAGTGCATCTT
GCTTGAAGCATTTTTGACACTATTTTTTAGAACCGTCTTCTCAAAATTATTTTTTTAGA
Found at i:4169907 original size:34 final size:34
Alignment explanation
Indices: 4169861--4169968 Score: 130
Period size: 33 Copynumber: 3.2 Consensus size: 34
4169851 TTTTTTTAAA
*
4169861 TAAACCAAAATTTAATTAATTTTATTAAAAACTC
1 TAAACCATAATTTAATTAATTTTATTAAAAACTC
* *
4169895 TAAACCATAATTTAATTAA-TTTATTTAAAACCC
1 TAAACCATAATTTAATTAATTTTATTAAAAACTC
* * *
4169928 TAAAACTTAATTTAATTACTTTT-TTACTAAAACTC
1 TAAACCATAATTTAATTAATTTTATTA--AAAACTC
4169963 TAAACC
1 TAAACC
4169969 TTAAATTTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
33 30 0.48
34 21 0.34
35 11 0.18
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (34 bp):
TAAACCATAATTTAATTAATTTTATTAAAAACTC
Found at i:4170350 original size:17 final size:18
Alignment explanation
Indices: 4170321--4170360 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
4170311 TAAAATTGGA
4170321 AAATAATTTTGAATGTTT
1 AAATAATTTTGAATGTTT
4170339 AAATAA-TTTGAATGTTT
1 AAATAATTTTGAATGTTT
4170356 AAATA
1 AAATA
4170361 GTACAAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (18 bp):
AAATAATTTTGAATGTTT
Found at i:4181462 original size:122 final size:122
Alignment explanation
Indices: 4181245--4181591 Score: 592
Period size: 122 Copynumber: 2.9 Consensus size: 122
4181235 TTGCTCACTA
4181245 GTCTATCATTTAATTTGCATTCTTAGGTTAGTTATCATATATTTCATGTTAAATCAAGTTATTAA
1 GTCTATCATTTAATTTGCATTCTTAGGTTAGTTATCATATATTTCATGTTAAATCAAGTTATTAA
4181310 GGAAACCCCATACCCATGACATTACTATGCTTATTCTCATGCTATTACCATGCCAAT
66 GGAAACCCCATACCCATGACATTACTATGCTTATTCTCATGCTATTACCATGCCAAT
4181367 GTCTATCATTTAATTTGCATTCTTAGGTTAGTTATCATATATTTCATGTTAAATCAAGTTATTAA
1 GTCTATCATTTAATTTGCATTCTTAGGTTAGTTATCATATATTTCATGTTAAATCAAGTTATTAA
4181432 GGAAACCCCATACCCATGACATTACTATGCTTATTCTCATGCTATTACCATGCCAAT
66 GGAAACCCCATACCCATGACATTACTATGCTTATTCTCATGCTATTACCATGCCAAT
* * * *
4181489 GTCTATCATTTAATTTGCATTCTTAGGTTAGTTATCATACATTCCGTGTTAAATCGAG--ATT-A
1 GTCTATCATTTAATTTGCATTCTTAGGTTAGTTATCATATATTTCATGTTAAATCAAGTTATTAA
* * * *
4181551 GGAAAACCTCATACCCATTACATTACTATTCTCATTCTCAT
66 GG-AAACCCCATACCCATGACATTACTATGCTTATTCTCAT
4181592 TGTTATTTTG
Statistics
Matches: 216, Mismatches: 8, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
119 3 0.01
120 37 0.17
122 176 0.81
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (122 bp):
GTCTATCATTTAATTTGCATTCTTAGGTTAGTTATCATATATTTCATGTTAAATCAAGTTATTAA
GGAAACCCCATACCCATGACATTACTATGCTTATTCTCATGCTATTACCATGCCAAT
Found at i:4186167 original size:24 final size:24
Alignment explanation
Indices: 4186135--4186182 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
4186125 TACATTAGGG
4186135 TTAGGGTGAAAATTAATGTCCAAA
1 TTAGGGTGAAAATTAATGTCCAAA
4186159 TTAGGGTGAAAATTAATGTCCAAA
1 TTAGGGTGAAAATTAATGTCCAAA
4186183 AACCCTTGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (24 bp):
TTAGGGTGAAAATTAATGTCCAAA
Found at i:4205197 original size:20 final size:20
Alignment explanation
Indices: 4205159--4205197 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
4205149 TATCAATAAT
*
4205159 TTAGAAAATTTTCAGAAAAC
1 TTAGAAAATTTTCACAAAAC
4205179 TTAGTAAAATTTTC-CAAAA
1 TTAG-AAAATTTTCACAAAA
4205198 ATAGGGGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (20 bp):
TTAGAAAATTTTCACAAAAC
Found at i:4208598 original size:30 final size:30
Alignment explanation
Indices: 4208514--4208582 Score: 138
Period size: 30 Copynumber: 2.3 Consensus size: 30
4208504 ACAATTAAAC
4208514 TTTATTTTATTTATGATTTGGCCCTATTAT
1 TTTATTTTATTTATGATTTGGCCCTATTAT
4208544 TTTATTTTATTTATGATTTGGCCCTATTAT
1 TTTATTTTATTTATGATTTGGCCCTATTAT
4208574 TTTATTTTA
1 TTTATTTTA
4208583 GTTTTAATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.62
Consensus pattern (30 bp):
TTTATTTTATTTATGATTTGGCCCTATTAT
Found at i:4209326 original size:63 final size:63
Alignment explanation
Indices: 4209248--4209372 Score: 241
Period size: 63 Copynumber: 2.0 Consensus size: 63
4209238 AAATATAAGT
4209248 GACTATCTTGGAATTGAAAAGTGATATGTCCTAACTTACTGGATGCAGCATTTTGCTGTTTCA
1 GACTATCTTGGAATTGAAAAGTGATATGTCCTAACTTACTGGATGCAGCATTTTGCTGTTTCA
*
4209311 GACTATCTTGGAATTGAAAAGTGATATGTCCTAACTTACTGGATGTAGCATTTTGCTGTTTC
1 GACTATCTTGGAATTGAAAAGTGATATGTCCTAACTTACTGGATGCAGCATTTTGCTGTTTC
4209373 GAGATAGGGA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (63 bp):
GACTATCTTGGAATTGAAAAGTGATATGTCCTAACTTACTGGATGCAGCATTTTGCTGTTTCA
Found at i:4212487 original size:19 final size:19
Alignment explanation
Indices: 4212451--4212489 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4212441 ATGCCTTTGA
*
4212451 TACATTCATACATTTGCAT
1 TACATTCATACATATGCAT
4212470 TACA-TCATATCATATGCAT
1 TACATTCATA-CATATGCAT
4212489 T
1 T
4212490 TAAGGTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (19 bp):
TACATTCATACATATGCAT
Found at i:4220730 original size:211 final size:211
Alignment explanation
Indices: 4220366--4220786 Score: 833
Period size: 211 Copynumber: 2.0 Consensus size: 211
4220356 GACACCTGAG
4220366 ATAGGGGTCATATTCACAGCACTTTGCATCATAACATGTTAAGGGCATTCGACTCATTTCAATTA
1 ATAGGGGTCATATTCACAGCACTTTGCATCATAACATGTTAAGGGCATTCGACTCATTTCAATTA
4220431 TAGCATACTTAGGCATAGGCACGTACTCATCTTACAGGTCATCAAAGATTTCAACATGGCAGCCC
66 TAGCATACTTAGGCATAGGCACGTACTCATCTTACAGGTCATCAAAGATTTCAACATGGCAGCCC
*
4220496 TATGCTTATGGGAAACAAATTGAAGACAGCAGATCTAGACTTCAGACATTTATGCTGAAGCAGAT
131 TATGCTTATGGGAAACAAATTGAAGACAGCAGATCTAGACTTCAGACATTTATACTGAAGCAGAT
4220561 CCAAGATGATTTGGTT
196 CCAAGATGATTTGGTT
4220577 ATAGGGGTCATATTCACAGCACTTTGCATCATAACATGTTAAGGGCATTCGACTCATTTCAATTA
1 ATAGGGGTCATATTCACAGCACTTTGCATCATAACATGTTAAGGGCATTCGACTCATTTCAATTA
4220642 TAGCATACTTAGGCATAGGCACGTACTCATCTTACAGGTCATCAAAGATTTCAACATGGCAGCCC
66 TAGCATACTTAGGCATAGGCACGTACTCATCTTACAGGTCATCAAAGATTTCAACATGGCAGCCC
4220707 TATGCTTATGGGAAACAAATTGAAGACAGCAGATCTAGACTTCAGACATTTATACTGAAGCAGAT
131 TATGCTTATGGGAAACAAATTGAAGACAGCAGATCTAGACTTCAGACATTTATACTGAAGCAGAT
4220772 CCAAGATGATTTGGT
196 CCAAGATGATTTGGT
4220787 ATTCTTGTGT
Statistics
Matches: 209, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
211 209 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (211 bp):
ATAGGGGTCATATTCACAGCACTTTGCATCATAACATGTTAAGGGCATTCGACTCATTTCAATTA
TAGCATACTTAGGCATAGGCACGTACTCATCTTACAGGTCATCAAAGATTTCAACATGGCAGCCC
TATGCTTATGGGAAACAAATTGAAGACAGCAGATCTAGACTTCAGACATTTATACTGAAGCAGAT
CCAAGATGATTTGGTT
Found at i:4221120 original size:118 final size:119
Alignment explanation
Indices: 4220736--4221205 Score: 791
Period size: 119 Copynumber: 4.0 Consensus size: 119
4220726 TTGAAGACAG
*
4220736 CAGATCTAGA-CTTCAGACATTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTTA
1 CAGATCTA-ACCTTCAGATATTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTTA
*
4220800 CAAGGAACAAATCGATGACATAGCAGATTTGACTCTCAGACGTTCTCAAATATAA
65 CAAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAATATAA
4220855 CAGATCTAACCTTCAGATATTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTTAC
1 CAGATCTAACCTTCAGATATTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTTAC
*
4220920 AAGGAACAAATCGATGACATAGCAGATTTGACTCTCAGACGTTCTCAAATATAA
66 AAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAATATAA
*
4220974 CAGATCTAACCTTCAGATATTTATACTGAAGCAGATCCAAGATGATTTGGTATT-TGGTGTTTAC
1 CAGATCTAACCTTCAGATATTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTTAC
* * * *
4221038 AAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGACATTTTCAAATATAG
66 AAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAATATAA
* *
4221092 CAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTCTAC
1 CAGATCTAACCTTCAGATATTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTTAC
* * * *
4221157 AAGGAACAAATCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAA
66 AAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAA
4221206 CAAACTCAAG
Statistics
Matches: 332, Mismatches: 17, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
118 112 0.34
119 220 0.66
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (119 bp):
CAGATCTAACCTTCAGATATTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTTAC
AAGGAACAAATCGAGGACATAGCAGATTTGACTCTCAGACGTTCTCAAATATAA
Found at i:4221152 original size:237 final size:238
Alignment explanation
Indices: 4220736--4221205 Score: 791
Period size: 237 Copynumber: 2.0 Consensus size: 238
4220726 TTGAAGACAG
*
4220736 CAGATCTAGACTTCAGACATTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTTAC
1 CAGATCTAGACTTCAGACATTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTGGTGTTTAC
* * *
4220801 AAGGAACAAATCGATGACATAGCAGATTTGACTCTCAGACGTTCTCAAATATAACAGATCTAACC
66 AAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGACATTCTCAAATATAACAGATCTAACC
*
4220866 TTCAGATATTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTTTACAAGGAACAAAT
131 TTCAGATATTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTCTACAAGGAACAAAT
* * *
4220931 CGATGACATAGCAGATTTGACTCTCAGACGTTCTCAAATATAA
196 CGAGGACATAGCAGATATGACTCTCAAACGTTCTCAAATATAA
*
4220974 CAGATCTA-ACCTTCAGATATTTATACTGAAGCAGATCCAAGATGATTTGGTATT-TGGTGTTTA
1 CAGATCTAGA-CTTCAGACATTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTGGTGTTTA
* *
4221037 CAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGACATTTTCAAATATAGCAGATCTAAC
65 CAAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGACATTCTCAAATATAACAGATCTAAC
*
4221102 CTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTCTACAAGGAACAAA
130 CTTCAGATATTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTCTACAAGGAACAAA
* *
4221167 TCGAGGACATTGCAGATATGACTCTCAAATGTTCTCAAA
195 TCGAGGACATAGCAGATATGACTCTCAAACGTTCTCAAA
4221206 CAAACTCAAG
Statistics
Matches: 217, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
237 166 0.76
238 51 0.24
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (238 bp):
CAGATCTAGACTTCAGACATTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTGGTGTTTAC
AAGAAACAAATCGAGGACATAGCAGATTTGACTCTCAGACATTCTCAAATATAACAGATCTAACC
TTCAGATATTTATACTGAAGCAGATCCAAGATGATTTGGTATTCTTGTGTCTACAAGGAACAAAT
CGAGGACATAGCAGATATGACTCTCAAACGTTCTCAAATATAA
Found at i:4222854 original size:43 final size:44
Alignment explanation
Indices: 4222748--4222863 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 44
4222738 TTTATTATTC
* * *
4222748 TATATATATATTATTATTTGTTTTATTTTAATTTTACTTTTATAT
1 TATATAT-TATTATTAATTATTTTATTATAATTTTACTTTTATAT
*
4222793 TATATATTA-TA-AAATTATTTTATTATAAGTTTTA-TTTTA-AT
1 TATATATTATTATTAATTATTTTATTATAA-TTTTACTTTTATAT
*
4222834 TATATATTATTATTACTTATTATGTATTAT
1 TATATATTATTATTAATTATT-T-TATTAT
4222864 TTTTCTTAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
41 11 0.18
42 20 0.33
43 13 0.22
44 3 0.05
45 13 0.22
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.62
Consensus pattern (44 bp):
TATATATTATTATTAATTATTTTATTATAATTTTACTTTTATAT
Found at i:4223046 original size:18 final size:17
Alignment explanation
Indices: 4223020--4223053 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
4223010 ATAATCTTTA
4223020 TTATGTTTTATTTTTATG
1 TTATGTTTT-TTTTTATG
*
4223038 TTATTTTTTTTTTTAT
1 TTATGTTTTTTTTTAT
4223054 ATATCATGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (17 bp):
TTATGTTTTTTTTTATG
Found at i:4223050 original size:17 final size:18
Alignment explanation
Indices: 4223020--4223053 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4223010 ATAATCTTTA
4223020 TTATGTTTTATTTTTATG
1 TTATGTTTTATTTTTATG
*
4223038 TTAT-TTTTTTTTTTAT
1 TTATGTTTTATTTTTAT
4223054 ATATCATGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (18 bp):
TTATGTTTTATTTTTATG
Found at i:4225938 original size:21 final size:20
Alignment explanation
Indices: 4225906--4225945 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4225896 AATTGATAAT
4225906 TTAGGAAATTTTCAAAAAAC
1 TTAGGAAATTTTCAAAAAAC
*
4225926 TTAGTAAAGTTTTCCAAAAA
1 TTAGGAAA-TTTT-CAAAAA
4225946 TAGGGGACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 4 0.24
22 6 0.35
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (20 bp):
TTAGGAAATTTTCAAAAAAC
Found at i:4230959 original size:47 final size:47
Alignment explanation
Indices: 4230808--4230938 Score: 154
Period size: 47 Copynumber: 2.8 Consensus size: 47
4230798 GTGCGAGTGA
* * * * * ** **
4230808 TACCTTGATTTTGCTACAGGCCATGGCATAGGTATTTCGGGGAGGAGT
1 TACCTTGAGTTGGCTACGGGCCATGGTATAGGTA-CTCCAGGATAAGT
*
4230856 TACCTTGATTTGGCTACGGGCCATGGTATAGGTACTCCAGGATAAGT
1 TACCTTGAGTTGGCTACGGGCCATGGTATAGGTACTCCAGGATAAGT
*
4230903 TACCTTGAGTTGGCTATGGGCCATGGTATAGGTACT
1 TACCTTGAGTTGGCTACGGGCCATGGTATAGGTACT
4230939 TATCGTATGA
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
47 42 0.58
48 31 0.42
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (47 bp):
TACCTTGAGTTGGCTACGGGCCATGGTATAGGTACTCCAGGATAAGT
Found at i:4233222 original size:63 final size:63
Alignment explanation
Indices: 4233098--4233242 Score: 168
Period size: 63 Copynumber: 2.3 Consensus size: 63
4233088 CCAAAGTAGG
* ** *
4233098 TTAACTACTCAATTTGTA-TTAGATAATGCAATTATTTAAGTTTATTTTTTATCAAACTAATAT
1 TTAAATACT-AATTTGTATTTAGATAATGCAATTATTTAACATTATTTTTTACCAAACTAATAT
* * * *
4233161 TTAAATACTAATTTATATTTAGATATTGTAATTATTTAACATTACTTTTTT-CCAAATTAATAT
1 TTAAATACTAATTTGTATTTAGATAATGCAATTATTTAACATTA-TTTTTTACCAAACTAATAT
* *
4233224 TTAGATACTAGTTTGTATT
1 TTAAATACTAATTTGTATT
4233243 AATTTACTAA
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
62 7 0.10
63 56 0.81
64 6 0.09
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (63 bp):
TTAAATACTAATTTGTATTTAGATAATGCAATTATTTAACATTATTTTTTACCAAACTAATAT
Found at i:4233370 original size:29 final size:30
Alignment explanation
Indices: 4233337--4233394 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
4233327 TTGATTTAAT
* *
4233337 GTGCAATTGTATACATG-AACTTTAATTTG
1 GTGCAATTATACACATGAAACTTTAATTTG
*
4233366 GTGCAATTATACACGTGAAACTTTAATTT
1 GTGCAATTATACACATGAAACTTTAATTT
4233395 CGGTTTAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.40
Consensus pattern (30 bp):
GTGCAATTATACACATGAAACTTTAATTTG
Found at i:4233505 original size:23 final size:23
Alignment explanation
Indices: 4233456--4233505 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
4233446 TTGGATAAAT
**
4233456 ATAATTATTTATGTATGCAATTT
1 ATAATTATTTATGTATGCAATAA
* *
4233479 ATAATTGTTTATGTATGTAATAA
1 ATAATTATTTATGTATGCAATAA
4233502 ATAA
1 ATAA
4233506 ATATAAAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (23 bp):
ATAATTATTTATGTATGCAATAA
Found at i:4233584 original size:30 final size:29
Alignment explanation
Indices: 4233550--4233613 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
4233540 AATTTACAAG
*
4233550 AATTGGATC-AAATCAAAATTTTATGTATAA
1 AATTGGA-CAAAATCAAAA-TTCATGTATAA
* *
4233580 AATTGTACAAAATCAAAATTCATGTATAC
1 AATTGGACAAAATCAAAATTCATGTATAA
4233609 AATTG
1 AATTG
4233614 CACATTAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.34
Consensus pattern (29 bp):
AATTGGACAAAATCAAAATTCATGTATAA
Found at i:4245225 original size:15 final size:15
Alignment explanation
Indices: 4245205--4245238 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
4245195 CCAATTTTGG
4245205 ACCCAAAACCCACTA
1 ACCCAAAACCCACTA
4245220 ACCCAAAACCCACTA
1 ACCCAAAACCCACTA
4245235 ACCC
1 ACCC
4245239 CTAAACAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (15 bp):
ACCCAAAACCCACTA
Found at i:4245611 original size:21 final size:21
Alignment explanation
Indices: 4245587--4245628 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4245577 TCGAAAGGTG
4245587 ATTATCATCGTAAAATTTCTT
1 ATTATCATCGTAAAATTTCTT
4245608 ATTATCATCGTAAAATTTCTT
1 ATTATCATCGTAAAATTTCTT
4245629 TCTTTTTTAT
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:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (21 bp):
ATTATCATCGTAAAATTTCTT
Found at i:4246370 original size:23 final size:22
Alignment explanation
Indices: 4246336--4246399 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
4246326 TTGTTATTAT
*
4246336 ATTAACTGTTATTATTATATTC
1 ATTAACTATTATTATTATATTC
* *
4246358 ATTAACATATTATTATTATTTTT
1 ATTAAC-TATTATTATTATATTC
*
4246381 ACTATACTATTATTATTAT
1 ATTA-ACTATTATTATTAT
4246400 TATATATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 6 0.17
23 28 0.78
24 2 0.06
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTAACTATTATTATTATATTC
Found at i:4246409 original size:23 final size:24
Alignment explanation
Indices: 4246344--4246428 Score: 77
Period size: 26 Copynumber: 3.4 Consensus size: 24
4246334 ATATTAACTG
4246344 TTATTATTATAT-TCATTAACATATTA
1 TTATTATTATATAT-A-T-ACATATTA
*
4246370 TTATTATT-TTTACTATAC-TATTA
1 TTATTATTATATA-TATACATATTA
*
4246393 TTATTATTATATATATACATATCTTT
1 TTATTATTATATATATACATA--TTA
4246419 TTATTATTAT
1 TTATTATTAT
4246429 TGTTTATATA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
23 18 0.36
24 7 0.14
25 3 0.06
26 21 0.42
27 1 0.02
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (24 bp):
TTATTATTATATATATACATATTA
Found at i:4246437 original size:23 final size:25
Alignment explanation
Indices: 4246365--4246439 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 25
4246355 TTCATTAACA
4246365 TATTATTATTATTTTTACTATACTAT
1 TATTATTATTATTTTTA-TATACTAT
*
4246391 TATTATTATTA--TATATATACATATCT
1 TATTATTATTATTTTTATATAC-TA--T
*
4246417 TTTTATTATTATTGTTTATATAC
1 TATTATTATTATT-TTTATATAC
4246440 ACATATTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
23 5 0.12
24 5 0.12
26 22 0.55
29 8 0.20
ACGTcount: A:0.32, C:0.07, G:0.01, T:0.60
Consensus pattern (25 bp):
TATTATTATTATTTTTATATACTAT
Found at i:4246448 original size:29 final size:29
Alignment explanation
Indices: 4246390--4246448 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
4246380 TACTATACTA
* *
4246390 TTATTATTATTATATATATACATATCTTT
1 TTATTATTATTATATATATACACATATTT
* *
4246419 TTATTATTATTGTTTATATACACATATTT
1 TTATTATTATTATATATATACACATATTT
4246448 T
1 T
4246449 AAAAAGTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (29 bp):
TTATTATTATTATATATATACACATATTT
Found at i:4247124 original size:3 final size:3
Alignment explanation
Indices: 4247118--4247152 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4247108 GTTATACTAC
4247118 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
4247153 CTTTCGTCAT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4249107 original size:30 final size:31
Alignment explanation
Indices: 4249070--4249153 Score: 134
Period size: 30 Copynumber: 2.7 Consensus size: 31
4249060 CACTCAACTT
* * *
4249070 TCAAAAAATAACAAATTAGTCACTAATGTTA
1 TCAAAAAGTAACAAATCAGTCACTAACGTTA
4249101 TCAAAAAGTAAC-AATCAGTCACTAACGTTA
1 TCAAAAAGTAACAAATCAGTCACTAACGTTA
4249131 TCAAAAAGTAACAAATCAGTCAC
1 TCAAAAAGTAACAAATCAGTCAC
4249154 CCATTAATAT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
30 28 0.57
31 21 0.43
ACGTcount: A:0.50, C:0.18, G:0.08, T:0.24
Consensus pattern (31 bp):
TCAAAAAGTAACAAATCAGTCACTAACGTTA
Found at i:4250594 original size:33 final size:31
Alignment explanation
Indices: 4250517--4250580 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
4250507 GTTGGTGTAA
4250517 TTTACCC-TTTTTTAAATTATGTATATATAT
1 TTTACCCTTTTTTTAAATTATGTATATATAT
4250547 TTTACCCTTTTTTTAAATTATGTATATATAT
1 TTTACCCTTTTTTTAAATTATGTATATATAT
4250578 TTT
1 TTT
4250581 TTCTTTACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 7 0.21
31 26 0.79
ACGTcount: A:0.28, C:0.09, G:0.03, T:0.59
Consensus pattern (31 bp):
TTTACCCTTTTTTTAAATTATGTATATATAT
Found at i:4254615 original size:19 final size:20
Alignment explanation
Indices: 4254593--4254636 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
4254583 ATTTTTATGT
*
4254593 TTTTATAAGTTTTTA-AGAA
1 TTTTATAAGTTTTTATAAAA
*
4254612 TTTTATATGTTTTTATAAAA
1 TTTTATAAGTTTTTATAAAA
4254632 TTTTA
1 TTTTA
4254637 AATATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (20 bp):
TTTTATAAGTTTTTATAAAA
Found at i:4254620 original size:29 final size:29
Alignment explanation
Indices: 4254574--4254655 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
4254564 ATTTTAATAT
* **
4254574 TTTTGAATCATTTT-TATGTTTTTATAAGT
1 TTTTAAAT-ATTTTATATGTTTTTATAAAA
4254603 TTTTAAGA-ATTTTATATGTTTTTATAAAA
1 TTTTAA-ATATTTTATATGTTTTTATAAAA
4254632 TTTTAAATATTTTAAATATGTTTT
1 TTTTAAATATTTT--ATATGTTTT
4254656 AGTTATTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
28 6 0.13
29 29 0.64
30 1 0.02
31 9 0.20
ACGTcount: A:0.32, C:0.01, G:0.07, T:0.60
Consensus pattern (29 bp):
TTTTAAATATTTTATATGTTTTTATAAAA
Found at i:4254680 original size:66 final size:64
Alignment explanation
Indices: 4254531--4254680 Score: 155
Period size: 66 Copynumber: 2.3 Consensus size: 64
4254521 TATGGTCCAG
* * *
4254531 TTTA-ATTTTTTATAATTTTATATGTTTATATTAATTTTAATATTTTTGAATCATTTTTATGTT
1 TTTATATTTTTTACAATTTTATATGTTTATATAAATTTTAATATTTTTAAATCATTTTTATGTT
* * *
4254594 TTTATAAGTTTTTAAGAATTTTATATGTTTTTATAAAATTTTAA-ATATTTTAAAT-ATGTTTTA
1 TTTAT-A-TTTTTTACAATTTTATATGTTTATAT-AAATTTTAATAT-TTTTAAATCAT-TTTTA
4254657 -GTTAT
61 TG-T-T
4254662 TTTATATTTTTTACAATTT
1 TTTATATTTTTTACAATTT
4254681 ATTTCGAGTT
Statistics
Matches: 72, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
63 4 0.06
65 1 0.01
66 39 0.54
67 22 0.31
68 6 0.08
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.62
Consensus pattern (64 bp):
TTTATATTTTTTACAATTTTATATGTTTATATAAATTTTAATATTTTTAAATCATTTTTATGTT
Found at i:4254750 original size:27 final size:25
Alignment explanation
Indices: 4254698--4254775 Score: 79
Period size: 25 Copynumber: 3.0 Consensus size: 25
4254688 GTTTATTAAG
4254698 TTTTTATTTTATAATATTTATAATT
1 TTTTTATTTTATAATATTTATAATT
* *
4254723 TTTTTATCTTATATAA-ATTTCT-ATA
1 TTTTTAT-TT-TATAATATTTATAATT
*
4254748 TTTTTATATTTAGTAATTTTTATAATT
1 TTTTTAT-TTTA-TAATATTTATAATT
4254775 T
1 T
4254776 AAATAGTCAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
24 2 0.05
25 21 0.50
26 11 0.26
27 8 0.19
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (25 bp):
TTTTTATTTTATAATATTTATAATT
Found at i:4254775 original size:25 final size:24
Alignment explanation
Indices: 4254689--4254775 Score: 70
Period size: 25 Copynumber: 3.4 Consensus size: 24
4254679 TTATTTCGAG
*
4254689 TTTATTAAGTTTTTAT-TTTATAATA
1 TTTA-TAA-TTTTTATATTTATAATT
*
4254714 TTTATAATTTTTTTATCTTATATAAATT
1 TTTATAA--TTTTTATATT-TAT-AATT
*
4254742 TCTAT-ATTTTTATATTTAGTAATT
1 TTTATAATTTTTATATTTA-TAATT
4254766 TTTATAATTT
1 TTTATAATTT
4254776 AAATAGTCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
24 13 0.25
25 25 0.49
26 2 0.04
27 4 0.08
28 7 0.14
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (24 bp):
TTTATAATTTTTATATTTATAATT
Found at i:4257235 original size:16 final size:17
Alignment explanation
Indices: 4257203--4257235 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4257193 TTTATAAGTA
*
4257203 TATATCAATCGTTTCAT
1 TATATCAATCATTTCAT
4257220 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
4257236 GTTTCATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:4257581 original size:46 final size:46
Alignment explanation
Indices: 4257521--4258391 Score: 1591
Period size: 46 Copynumber: 18.9 Consensus size: 46
4257511 TTTGACATGA
* * * * * * *
4257521 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTC-GTTTCATATCACGT
4257567 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
4257613 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
4257659 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
4257705 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
4257751 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
4257797 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
4257843 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
4257889 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
4257935 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
4257981 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
4258027 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
4258073 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
4258119 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
4258165 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
4258211 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
* *** *
4258257 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
4258303 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
** *
4258349 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCA
4258392 GAGAGCACAC
Statistics
Matches: 804, Mismatches: 20, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
45 4 0.00
46 800 1.00
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATTCGTTTCATATCACGT
Found at i:4263443 original size:40 final size:40
Alignment explanation
Indices: 4263399--4263477 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
4263389 CCTCTTTGAC
* * *
4263399 CTTTAATCTTTAACCTTATAAATTTAGACGAATTGTTGTA
1 CTTTAATATTTAACCTTACAAATTTAGACAAATTGTTGTA
* *
4263439 CTTTAATATTTAACCTTACAAATTTGGTCAAATTGTTGT
1 CTTTAATATTTAACCTTACAAATTTAGACAAATTGTTGT
4263478 TTATTGTGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.46
Consensus pattern (40 bp):
CTTTAATATTTAACCTTACAAATTTAGACAAATTGTTGTA
Found at i:4266709 original size:3 final size:3
Alignment explanation
Indices: 4266693--4266811 Score: 59
Period size: 3 Copynumber: 39.3 Consensus size: 3
4266683 CATATATGAA
* * * *
4266693 AAT AAT AGT GAT AAT AAT AAT -AT ATT AGAT AA- AAT AAT AAC AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
* * ** *
4266736 AAGT AGT AAT AAG AAT GGT AA- AAG AA- AAT AAT AAT AAT AAT AAT
1 AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
4266780 GAAGGT AAT AAT AAT AAT GAT AAT AAAT AAT A
1 -AA--T AAT AAT AAT AAT AAT AAT -AAT AAT A
4266812 GTAAAAAGAA
Statistics
Matches: 88, Mismatches: 17, Indels: 22
0.69 0.13 0.17
Matches are distributed among these distances:
2 10 0.11
3 67 0.76
4 8 0.09
5 2 0.02
6 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.11, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:4268195 original size:45 final size:45
Alignment explanation
Indices: 4268110--4269153 Score: 761
Period size: 45 Copynumber: 23.4 Consensus size: 45
4268100 TTTGATCCAC
* *
4268110 TCAGAGAGATAAGACTTG-TAGT-TTCAATCTGCTCCA--GCAACT
1 TCAGGGAGATAAGATTTGATA-TCTTCAATCTGCTCCACTGCAACT
* * * * *
4268152 TCAGGGAAATAAGGTTTGTTATCTTCGATCTACTCCACTGCAACT
1 TCAGGGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACT
* * * * * *
4268197 TCAGGGAGTTGAGATTCG-TAACTTCAACCTGCTCCAATGCAACT
1 TCAGGGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACT
* * * * * * *
4268241 TCAGGAAGATAAGGTTTG-TAACTTCAACCTACTCCACTGTATCT
1 TCAGGGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACT
* * * * *
4268285 TCAGGGGGATAAGGTTT-ATAGCTTTAACTCTGCTCTACTGCAACT
1 TCAGGGAGATAAGATTTGATATCTTCAA-TCTGCTCCACTGCAACT
* * * *
4268330 TCAGAGAGATAAGATTTGCTATCTTCGAT-TCGCTCTACTGCAACT
1 TCAGGGAGATAAGATTTGATATCTTCAATCT-GCTCCACTGCAACT
* * * * *
4268375 TCAGGGAGATAGGA-TTCATAACTTCAACCTGCTCCACTGTAACT
1 TCAGGGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACT
* * * * * *
4268419 TCAGGGGGATAAGGTTT-ATAGCTTTAACTCTACTCTACTGCAACT
1 TCAGGGAGATAAGATTTGATATCTTCAA-TCTGCTCCACTGCAACT
* * * *
4268464 TCAGAGAGATAAGATTTGCTATCTTCGAT-TCGCTCTACTGCAACT
1 TCAGGGAGATAAGATTTGATATCTTCAATCT-GCTCCACTGCAACT
* * * * * *
4268509 TCAGGGAGATAGGA-TTCATACCTTCAACCTGCTCCACTGTACCT
1 TCAGGGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACT
* * * * * *
4268553 TCAGGGGGATAAGGTTT-ATAGCTTTAACTCTACTCTACTGCAACT
1 TCAGGGAGATAAGATTTGATATCTTCAA-TCTGCTCCACTGCAACT
* * * *
4268598 TCAGAGAGATAAGATTTGCTATCTTCGAT-TCACTCCACTGCAACT
1 TCAGGGAGATAAGATTTGATATCTTCAATCT-GCTCCACTGCAACT
* * * * * * * *
4268643 TCAAGAAGATAGGACTCG-TAACTTCAACCTGCCCCACTGCAACT
1 TCAGGGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACT
* * * *
4268687 TCAAGGG-GATAAGGTTTGTGATTTGTAGCTTAAATCTGCCCCACTGCAACT
1 TC-AGGGAGATAA-GATT-TGA----TATCTTCAATCTGCTCCACTGCAACT
* *
4268738 TCAGGGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACT
1 TCAGGGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACT
* *
4268783 TCAGGGAGATAAGACTTG-TAAT-TTCAACCTGCTCCACTGCAACT
1 TCAGGGAGATAAGATTTGAT-ATCTTCAATCTGCTCCACTGCAACT
* ** * * * *
4268827 TCAGAGAGATAAGATCAGTTATCTTCAGTCTGCTCCTCTACAACT
1 TCAGGGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACT
* * * * *
4268872 TCAGGGAGATAAGATTCGCTATCTTCAGTCTACTCCACTACAACT
1 TCAGGGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACT
* * *
4268917 TCAGAGAGATAAGACTTG-TAAT-TTCAACCTGCTCCACTGCAACT
1 TCAGGGAGATAAGATTTGAT-ATCTTCAATCTGCTCCACTGCAACT
* * *
4268961 TCAGGGAGATAAGGTTTG-T-T-TT-GATCTGCTCTACTGCAACT
1 TCAGGGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACT
* ** * * * *
4269002 TCAGAGAGATAAGATCAGATGTCTTCAGTCTGCTCCTCTACAACT
1 TCAGGGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACT
* * * * *
4269047 TCAGGGAGATAAGACTCGCTATCTTCAGTCTACTCCACTGCAACT
1 TCAGGGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACT
* ** * * *
4269092 TCAGGGAGATAAGGTTT-ATGGCTTTAATCTACTCCACTGTAACT
1 TCAGGGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACT
4269136 TCAGGGAGATAAGATTTG
1 TCAGGGAGATAAGATTTG
4269154 CCGTGGTAGA
Statistics
Matches: 786, Mismatches: 179, Indels: 71
0.76 0.17 0.07
Matches are distributed among these distances:
41 30 0.04
42 19 0.02
43 15 0.02
44 296 0.38
45 368 0.47
46 19 0.02
49 2 0.00
50 7 0.01
51 30 0.04
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (45 bp):
TCAGGGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACT
Found at i:4268318 original size:89 final size:89
Alignment explanation
Indices: 4268132--4269153 Score: 586
Period size: 89 Copynumber: 11.5 Consensus size: 89
4268122 GACTTGTAGT
* *
4268132 TTCAA-TCTGCTCCA--GCAACTTCAGGGAA-ATAAGGTTTGTTATCTTCGATCTACTCCACTGC
1 TTCAACTCTGCTCCACTGCAACTTCA-GGAAGATAAGGTTTG-TATCTTCAACCTACTCCACTGC
* * * **
4268193 AACTTCAGGGAGTTGAGATTCGTAAC
64 AACTTCAGGGAGATAAGGTTTATAAC
* * * *
4268219 TTCAAC-CTGCTCCAATGCAACTTCAGGAAGATAAGGTTTGTAACTTCAACCTACTCCACTGTAT
1 TTCAACTCTGCTCCACTGCAACTTCAGGAAGATAAGGTTTGTATCTTCAACCTACTCCACTGCAA
* *
4268283 CTTCAGGGGGATAAGGTTTATAGC
66 CTTCAGGGAGATAAGGTTTATAAC
* * * * * * *
4268307 TTTAACTCTGCTCTACTGCAACTTCA-GAGAGATAAGATTTGCTATCTTCGA-TTCGCTCTACTG
1 TTCAACTCTGCTCCACTGCAACTTCAGGA-AGATAAGGTTTG-TATCTTCAACCT-ACTCCACTG
*
4268370 CAACTTCAGGGAGAT-AGGATTCATAAC
63 CAACTTCAGGGAGATAAGG-TTTATAAC
* ** * * * *
4268397 TTCAAC-CTGCTCCACTGTAACTTCAGGGGGATAAGGTTTATAGCTTTAACTCTACTCTACTGCA
1 TTCAACTCTGCTCCACTGCAACTTCAGGAAGATAAGGTTTGTATCTTCAAC-CTACTCCACTGCA
* * * *
4268461 ACTTCAGAGAGATAAGATTTGCTATC
65 ACTTCAGGGAGATAAGGTTT-ATAAC
* * * * ** * * *
4268487 TTCGATTC-GCTCTACTGCAACTTCAGGGAGAT-AGGATTCATACCTTCAACCTGCTCCACTGTA
1 TTCAACTCTGCTCCACTGCAACTTCAGGAAGATAAGG-TTTGTATCTTCAACCTACTCCACTGCA
* * *
4268550 CCTTCAGGGGGATAAGGTTTATAGC
65 ACTTCAGGGAGATAAGGTTTATAAC
* * * * * *
4268575 TTTAACTCTACTCTACTGCAACTTCA-GAGAGATAAGATTTGCTATCTTCGA-TTCACTCCACTG
1 TTCAACTCTGCTCCACTGCAACTTCAGGA-AGATAAGGTTTG-TATCTTCAACCT-ACTCCACTG
* * * **
4268638 CAACTTCAAGAAGAT-AGGACTCGTAAC
63 CAACTTCAGGGAGATAAGG-TTTATAAC
* * * * * *
4268665 TTCAAC-CTGCCCCACTGCAACTTCAAGG-GGATAAGGTTTGTGATTTGTAGCTTAAATCTGCCC
1 TTCAACTCTGCTCCACTGCAACTTC-AGGAAGATAAGGTTTGT-A----T--CTTCAACCTACTC
* * *
4268728 CACTGCAACTTCAGGGAGATAAGATTTGCTATC
58 CACTGCAACTTCAGGGAGATAAGGTTT-ATAAC
* * ** *
4268761 TTC-AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAAT-TTCAACCTGCTCCACTGCA
1 TTCAACTCTGCTCCACTGCAACTTCAGGAAGATAAGGTTTGT-ATCTTCAACCTACTCCACTGCA
* *
4268824 ACTTCAGAGAGATAAGATCAGTTAT--C
65 ACTTCAGGGAGATAAGGT---TTATAAC
* * * * * * ** *
4268850 TTC-AGTCTGCTCCTCTACAACTTCAGGGAGATAAGATTCGCTATCTTCAGTCTACTCCACTACA
1 TTCAACTCTGCTCCACTGCAACTTCAGGAAGATAAGGTTTG-TATCTTCAACCTACTCCACTGCA
* ** * *
4268914 ACTTCAGAGAGATAAGACTTGTAAT
65 ACTTCAGGGAGATAAGGTTTATAAC
* * * * *
4268939 TTCAAC-CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGT-T-TT-GATCTGCTCTACTGCAA
1 TTCAACTCTGCTCCACTGCAACTTCAGGAAGATAAGGTTTGTATCTTCAACCTACTCCACTGCAA
* * ** **
4269000 CTTCAGAGAGATAAGATCAGATGTC
66 CTTCAGGGAGATAAGGT-TTATAAC
* * * * ** * **
4269025 TTC-AGTCTGCTCCTCTACAACTTCAGGGAGATAAGACTCGCTATCTTCAGTCTACTCCACTGCA
1 TTCAACTCTGCTCCACTGCAACTTCAGGAAGATAAGGTTTG-TATCTTCAACCTACTCCACTGCA
**
4269089 ACTTCAGGGAGATAAGGTTTATGGC
65 ACTTCAGGGAGATAAGGTTTATAAC
* * * * *
4269114 TTTAA-TCTACTCCACTGTAACTTCAGGGAGATAAGATTTG
1 TTCAACTCTGCTCCACTGCAACTTCAGGAAGATAAGGTTTG
4269154 CCGTGGTAGA
Statistics
Matches: 724, Mismatches: 160, Indels: 100
0.74 0.16 0.10
Matches are distributed among these distances:
85 29 0.04
86 35 0.05
87 18 0.02
88 65 0.09
89 324 0.45
90 180 0.25
91 3 0.00
92 3 0.00
93 1 0.00
95 29 0.04
96 37 0.05
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (89 bp):
TTCAACTCTGCTCCACTGCAACTTCAGGAAGATAAGGTTTGTATCTTCAACCTACTCCACTGCAA
CTTCAGGGAGATAAGGTTTATAAC
Found at i:4268411 original size:134 final size:134
Alignment explanation
Indices: 4268132--4269154 Score: 1006
Period size: 134 Copynumber: 7.6 Consensus size: 134
4268122 GACTTGTAGT
* ** * * ** * *
4268132 TTCAATCTGCTCCA--GCAACTTCAGGGAAATAAGGTTTGTTATCTTCGA-TCTACTCCACTGCA
1 TTCAACCTGCTCCACTGCAACTTCAGGGGGATAAGGTTT-ATAGCTTTAACTCTGCTCTACTGCA
* * * * * ** * *
4268194 ACTTCAGGGAGTTGAGATTCG-TAACTTCAACCTGCTCCAATGCAACTTCAGGAAGATAAGG-TT
65 ACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGAT-AGGATT
*
4268257 TGTAAC
129 CGTAAC
* * *
4268263 TTCAACCTACTCCACTGTATCTTCAGGGGGATAAGGTTTATAGCTTTAACTCTGCTCTACTGCAA
1 TTCAACCTGCTCCACTGCAACTTCAGGGGGATAAGGTTTATAGCTTTAACTCTGCTCTACTGCAA
* *
4268328 CTTCAGAGAGATAAGATTTGCTATCTTCGATTC-GCTCTACTGCAACTTCAGGGAGATAGGATTC
66 CTTCAGAGAGATAAGATTTGCTATCTTC-AGTCTGCTCCACTGCAACTTCAGGGAGATAGGATTC
*
4268392 ATAAC
130 GTAAC
* *
4268397 TTCAACCTGCTCCACTGTAACTTCAGGGGGATAAGGTTTATAGCTTTAACTCTACTCTACTGCAA
1 TTCAACCTGCTCCACTGCAACTTCAGGGGGATAAGGTTTATAGCTTTAACTCTGCTCTACTGCAA
* *
4268462 CTTCAGAGAGATAAGATTTGCTATCTTCGATTC-GCTCTACTGCAACTTCAGGGAGATAGGATTC
66 CTTCAGAGAGATAAGATTTGCTATCTTC-AGTCTGCTCCACTGCAACTTCAGGGAGATAGGATTC
* *
4268526 ATACC
130 GTAAC
* * *
4268531 TTCAACCTGCTCCACTGTACCTTCAGGGGGATAAGGTTTATAGCTTTAACTCTACTCTACTGCAA
1 TTCAACCTGCTCCACTGCAACTTCAGGGGGATAAGGTTTATAGCTTTAACTCTGCTCTACTGCAA
* * * * *
4268596 CTTCAGAGAGATAAGATTTGCTATCTTCGATTC-ACTCCACTGCAACTTCAAGAAGATAGGACTC
66 CTTCAGAGAGATAAGATTTGCTATCTTC-AGTCTGCTCCACTGCAACTTCAGGGAGATAGGATTC
4268660 GTAAC
130 GTAAC
* * * * *
4268665 TTCAACCTGCCCCACTGCAACTTCAAGGGGATAAGGTTTGTGATTTGTAGC-TTAAATCTGCCCC
1 TTCAACCTGCTCCACTGCAACTTCAGGGGGATAAGG-TT-T-A----TAGCTTTAACTCTGCTCT
*
4268729 ACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATA
59 ACTGCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATA
* *
4268794 AGACTT-GTAAT
124 GGA-TTCGTAAC
* * * * *
4268805 TTCAACCTGCTCCACTGCAACTTCAGAGAGATAAGATCAGTTAT--C-TTCAGTCTGCTCCT-CT
1 TTCAACCTGCTCCACTGCAACTTCAGGGGGATAAGGT---TTATAGCTTTAACTCTGCT-CTACT
* * * * * * *
4268866 ACAACTTCAGGGAGATAAGATTCGCTATCTTCAGTCTACTCCACTACAACTTCAGAGAGATAAGA
62 GCAACTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAGGA
*
4268931 CTT-GTAAT
127 -TTCGTAAC
* * *
4268939 TTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGG-TT-T-GTTTTGA-TCTGCTCTACTGCAA
1 TTCAACCTGCTCCACTGCAACTTCAGGGGGATAAGGTTTATAGCTTTAACTCTGCTCTACTGCAA
** * * * * * *
4269000 CTTCAGAGAGATAAGATCAGATGTCTTCAGTCTGCTCCTCTACAACTTCAGGGAGATAAGACTCG
66 CTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAGGATTCG
*
4269065 CTATC
131 -TAAC
** * * * * * *
4269070 TTCAGTCTACTCCACTGCAACTTCAGGGAGATAAGGTTTATGGCTTTAA-TCTACTCCACTGTAA
1 TTCAACCTGCTCCACTGCAACTTCAGGGGGATAAGGTTTATAGCTTTAACTCTGCTCTACTGCAA
*
4269134 CTTCAGGGAGATAAGATTTGC
66 CTTCAGAGAGATAAGATTTGC
4269155 CGTGGTAGAT
Statistics
Matches: 771, Mismatches: 94, Indels: 51
0.84 0.10 0.06
Matches are distributed among these distances:
129 4 0.01
130 67 0.09
131 50 0.06
132 8 0.01
133 52 0.07
134 468 0.61
135 5 0.01
136 2 0.00
137 1 0.00
139 4 0.01
140 103 0.13
141 6 0.01
142 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (134 bp):
TTCAACCTGCTCCACTGCAACTTCAGGGGGATAAGGTTTATAGCTTTAACTCTGCTCTACTGCAA
CTTCAGAGAGATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAGGATTCG
TAAC
Found at i:4269327 original size:44 final size:43
Alignment explanation
Indices: 4268706--4269330 Score: 305
Period size: 44 Copynumber: 14.0 Consensus size: 43
4268696 TAAGGTTTGT
* * * *
4268706 GATTTGTAGCTTAAATCTGCCCCACTGCAACTTCAGGGAGATAA
1 GATTAGTAGCTTCAATCTACTCCACTGCAACTTCA-GGAGATAA
* * * *
4268750 GATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAA
1 GATTAG-TAGCTTCAATCTACTCCACTGCAACTTCA-GGAGATAA
** * *
4268795 GACTT-GTAATTTCAACCTGCTCCACTGCAACTTCAGAGAGATAA
1 GA-TTAGTAGCTTCAATCTACTCCACTGCAACTTCAG-GAGATAA
* * * * * *
4268839 GATCAGTTATCTTCAGTCTGCTCCTCTACAACTTCAGGGAGATAA
1 GATTAG-TAGCTTCAATCTACTCCACTGCAACTTCA-GGAGATAA
* * * *
4268884 GATTCGCTATCTTCAGTCTACTCCACTACAACTTCAGAGAGATAA
1 GATTAG-TAGCTTCAATCTACTCCACTGCAACTTCAG-GAGATAA
** * *
4268929 GACTT-GTAATTTCAACCTGCTCCACTGCAACTTCAGGGAGATAA
1 GA-TTAGTAGCTTCAATCTACTCCACTGCAACTTCA-GGAGATAA
* * ** * *
4268973 GGTT--T-GTTTTGATCTGCTCTACTGCAACTTCAGAGAGATAA
1 GATTAGTAGCTTCAATCTACTCCACTGCAACTTCAG-GAGATAA
* * * * *
4269014 GATCAG-ATGTCTTCAGTCTGCTCCTCTACAACTTCAGGGAGATAA
1 GATTAGTA-G-CTTCAATCTACTCCACTGCAACTTCA-GGAGATAA
* * * *
4269059 GACTCGCTATCTTCAGTCTACTCCACTGCAACTTCAGGGAGATAA
1 GATTAG-TAGCTTCAATCTACTCCACTGCAACTTCA-GGAGATAA
* * * *
4269104 GGTTTA-TGGCTTTAATCTACTCCACTGTAACTTCAGGGAGATAA
1 -GATTAGTAGCTTCAATCTACTCCACTGCAACTTCA-GGAGATAA
* * ** * * * *
4269148 GATTTGCCGTGGTAGATTTGATCCGAC-CTACTGCAACTTCAAAGG-TATAG
1 GA--T----TAGTAGCTTCAAT-CTACTCCACTGCAACTTC--AGGAGATAA
* * * * * * *
4269198 GACTCGTCGTTTTAATCTGCTCCACTGCAACTTCAGGAGATAG
1 GATTAGTAGCTTCAATCTACTCCACTGCAACTTCAGGAGATAA
* * * *
4269241 GATTAGTAGCTTCAATCTATTCCGCTGTAACTTCAAGCAGATAA
1 GATTAGTAGCTTCAATCTACTCCACTGCAACTTC-AGGAGATAA
* * * *
4269285 GATTGGTATCTTCAGTCTACTCCACTGCAACTTTAGGGAGATAA
1 GATTAGTAGCTTCAATCTACTCCACTGCAACTTCA-GGAGATAA
4269329 GA
1 GA
4269331 CTTGTAATTT
Statistics
Matches: 454, Mismatches: 94, Indels: 66
0.74 0.15 0.11
Matches are distributed among these distances:
40 1 0.00
41 31 0.07
42 4 0.01
43 37 0.08
44 171 0.38
45 171 0.38
46 8 0.02
47 1 0.00
49 1 0.00
50 23 0.05
51 5 0.01
52 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (43 bp):
GATTAGTAGCTTCAATCTACTCCACTGCAACTTCAGGAGATAA
Found at i:4278753 original size:19 final size:20
Alignment explanation
Indices: 4278731--4278776 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
4278721 GGTCTTTTCG
* *
4278731 TGAAATTTAATGCATATG-A
1 TGAAATGTAATGCAAATGAA
4278750 TGAAATGTAATGCAAATGAA
1 TGAAATGTAATGCAAATGAA
4278770 TGAAATG
1 TGAAATG
4278777 AATACAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (20 bp):
TGAAATGTAATGCAAATGAA
Found at i:4283171 original size:23 final size:23
Alignment explanation
Indices: 4283145--4283199 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
4283135 AGTAGTAGCG
*
4283145 AAAATAAAA-TAATATTAAAAGATA
1 AAAATAAAATTAATA--AAAACATA
4283169 AAAATAAAATTAATAAAAACAT-
1 AAAATAAAATTAATAAAAACATA
4283191 AAAATAAAA
1 AAAATAAAA
4283200 ATAAAAATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 9 0.31
23 6 0.21
24 9 0.31
25 5 0.17
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (23 bp):
AAAATAAAATTAATAAAAACATA
Found at i:4283177 original size:6 final size:6
Alignment explanation
Indices: 4283145--4283208 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
4283135 AGTAGTAGCG
* * * * *
4283145 AAAAT- AAAATA ATATTA AAAGATA AAAATA AAATTA ATAA-A AACAT-
1 AAAATA AAAATA AAAATA AAA-ATA AAAATA AAAATA AAAATA AAAATA
4283191 AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA
4283209 GATAAAATTA
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
5 12 0.27
6 28 0.62
7 5 0.11
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (6 bp):
AAAATA
Found at i:4283184 original size:28 final size:27
Alignment explanation
Indices: 4283152--4283219 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
4283142 GCGAAAATAA
* *
4283152 AATAATATTAAAAGATAAAAATAAAATT
1 AATAAAATTAAAA-ATAAAAATAAAAAT
**
4283180 AATAAAAACATAAAATAAAAATAAAAAT
1 AATAAAATTA-AAAATAAAAATAAAAAT
4283208 AGATAAAATTAA
1 A-ATAAAATTAA
4283220 GTATCATCAT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
28 22 0.69
29 10 0.31
ACGTcount: A:0.72, C:0.01, G:0.03, T:0.24
Consensus pattern (27 bp):
AATAAAATTAAAAATAAAAATAAAAAT
Found at i:4288897 original size:170 final size:170
Alignment explanation
Indices: 4288615--4288954 Score: 610
Period size: 170 Copynumber: 2.0 Consensus size: 170
4288605 TGTTTTAATT
*
4288615 AACTAATTAACTAAACTAAGAATTCACAGAAAATAGAATTGGGGAATTACTTTTGGGAAAACGAT
1 AACTAATTAACTAAACTAAGAATTCACAGAAAATAAAATTGGGGAATTACTTTTGGGAAAACGAT
* *
4288680 TGAATTAAGACAATATCTAAGGAAAAATCCACCTAGACTTCACTTGTTATTTTGGCTCCGAATC-
66 TGAATTAAGACAATACCTAAGGAAAAATCCACCTAGACTTAACTTGTTATTTTGGCTCCGAATCA
*
4288744 GAACGATTTATTCATTTAACTCGTTCCGTAGAGATCCCTAA
131 G-ACGATTTATTCATTTAACTCGTTCCATAGAGATCCCTAA
4288785 AACTAATTAACTAAACTAAGAATTCACAGAAAATAAAATTGGGGAATTACTTTTGGGAAAACGAT
1 AACTAATTAACTAAACTAAGAATTCACAGAAAATAAAATTGGGGAATTACTTTTGGGAAAACGAT
*
4288850 TGAATTAAGACAATACCTAAGGAAAAATCCACCTAGACTTAACTTGTTATTTTGGCTCTGAATCA
66 TGAATTAAGACAATACCTAAGGAAAAATCCACCTAGACTTAACTTGTTATTTTGGCTCCGAATCA
*
4288915 GACGATTTATTTATTTAACTCGTTCCATAGAGATCCCTAA
131 GACGATTTATTCATTTAACTCGTTCCATAGAGATCCCTAA
4288955 GTTATGTTAT
Statistics
Matches: 163, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
170 162 0.99
171 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.30
Consensus pattern (170 bp):
AACTAATTAACTAAACTAAGAATTCACAGAAAATAAAATTGGGGAATTACTTTTGGGAAAACGAT
TGAATTAAGACAATACCTAAGGAAAAATCCACCTAGACTTAACTTGTTATTTTGGCTCCGAATCA
GACGATTTATTCATTTAACTCGTTCCATAGAGATCCCTAA
Found at i:4292356 original size:3 final size:3
Alignment explanation
Indices: 4292348--4292605 Score: 131
Period size: 3 Copynumber: 85.3 Consensus size: 3
4292338 CATATATGAA
* * * *
4292348 AAT AAT AAT AAT -AT GAC AAT AAT AAT AAT AAT AAT AGT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
4292395 AAT AAAT AATT AAT GAT AAT AAA AAT AAT AGT AA- AGAA AAT AA- AGAT
1 AAT -AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT A-AT
* * * * *
4292442 AAG ATT AAT AAT GAT ACT AACT AAT -AT AAGT AAT AAT AGT AA- AAT
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT AA-T AAT AAT AAT AAT AAT
** * *
4292487 AAT AAT AAT AAT GGT AAT AAT -AT ATT AGAT AA- AAT AAT AAC AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
* * ** *
4292530 AAGT AGT AAT AAG AAT GGT AA- AAG AA- AAT AAT AAT AAT AAT AAT
1 AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
4292574 GAAGGT AAT AAT AAT AAT GAT AAT AAAT AAT A
1 -AA--T AAT AAT AAT AAT AAT AAT -AAT AAT A
4292606 GTAAAAAGAA
Statistics
Matches: 192, Mismatches: 41, Indels: 44
0.69 0.15 0.16
Matches are distributed among these distances:
2 18 0.09
3 149 0.78
4 22 0.11
5 2 0.01
6 1 0.01
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:4292361 original size:17 final size:17
Alignment explanation
Indices: 4292341--4292377 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
4292331 AATAAAACAT
4292341 ATATGAAAATAATAATA
1 ATATGAAAATAATAATA
*
4292358 ATATGACAATAATAATA
1 ATATGAAAATAATAATA
4292375 ATA
1 ATA
4292378 ATAATAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (17 bp):
ATATGAAAATAATAATA
Found at i:4292540 original size:32 final size:31
Alignment explanation
Indices: 4292470--4292541 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 31
4292460 AACTAATATA
*
4292470 AGTAATAATAGTAAAATAATAATAATAATGGT
1 AGTAATAATAGTAAAATAATAACAATAA-GGT
*
4292502 AATAATATATTAGATAAAATAATAACAA-AA-GT
1 AGTAATA-A-TAG-TAAAATAATAACAATAAGGT
4292534 AGTAATAA
1 AGTAATAA
4292542 GAATGGTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
31 1 0.03
32 14 0.41
33 1 0.03
34 5 0.15
35 13 0.38
ACGTcount: A:0.60, C:0.01, G:0.10, T:0.29
Consensus pattern (31 bp):
AGTAATAATAGTAAAATAATAACAATAAGGT
Found at i:4296615 original size:28 final size:28
Alignment explanation
Indices: 4296574--4296629 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
4296564 AAAGGGAAAG
* *
4296574 ATCACGCTGTAATATCTAGTGATTTGGC
1 ATCACGCTGCAATAACTAGTGATTTGGC
4296602 ATCACGCTGCAATAACTAGTGATTTGGC
1 ATCACGCTGCAATAACTAGTGATTTGGC
4296630 CAATATTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (28 bp):
ATCACGCTGCAATAACTAGTGATTTGGC
Found at i:4298247 original size:68 final size:65
Alignment explanation
Indices: 4298170--4298327 Score: 160
Period size: 71 Copynumber: 2.4 Consensus size: 65
4298160 ATACTATGTA
* *
4298170 GTAGTTAGGTCACATGTGTGATACGGGAAGTATC-CCATGTAGACAAGAGAGCTACGGGAGAGAT
1 GTAGCTAGGTCACATGTGTGATACGGGAAGGA-CACCATGTAGACAAGAGAGCTAC--GAGAGA-
4298234 AAAT
62 AAAT
* * * *
4298238 GTAGCTAGGTCGCATGTGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGATAA
1 GTAGCTAGGTCACATGTGTGA-T--ACGGGAAGGACACCATGTAGACAAGAGAGCTACGAGAGAA
4298303 AAT
63 AAT
* *
4298306 G--GCTAAGTCACATGGGTGATAC
1 GTAGCTAGGTCACATGTGTGATAC
4298328 TAAGTGTTCA
Statistics
Matches: 76, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
63 1 0.01
65 1 0.01
66 15 0.20
68 24 0.32
69 6 0.08
70 1 0.01
71 28 0.37
ACGTcount: A:0.34, C:0.15, G:0.30, T:0.22
Consensus pattern (65 bp):
GTAGCTAGGTCACATGTGTGATACGGGAAGGACACCATGTAGACAAGAGAGCTACGAGAGAAAAT
Found at i:4298729 original size:16 final size:17
Alignment explanation
Indices: 4298701--4298732 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4298691 TAGTAAGTAA
4298701 AGAAATCTTATATTTTG
1 AGAAATCTTATATTTTG
4298718 AGAAAT-TTATATTTT
1 AGAAATCTTATATTTT
4298733 AGTGAGACCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (17 bp):
AGAAATCTTATATTTTG
Found at i:4300298 original size:5 final size:5
Alignment explanation
Indices: 4300265--4300340 Score: 59
Period size: 5 Copynumber: 15.0 Consensus size: 5
4300255 AGGCAACCTA
* * *
4300265 ATTTT ATTTAT ATTTT -TTCTT TTTATT ATTTT ATATT -TTAT ATTTT
1 ATTTT ATTT-T ATTTT ATT-TT ATT-TT ATTTT ATTTT ATTTT ATTTT
*
4300311 ATTTT ATTTT ATATTT -TTCT ATTTT ATTTT
1 ATTTT ATTTT AT-TTT ATTTT ATTTT ATTTT
4300341 CTTACATGTT
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
4 6 0.11
5 37 0.65
6 14 0.25
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:4300301 original size:7 final size:7
Alignment explanation
Indices: 4300271--4300337 Score: 53
Period size: 7 Copynumber: 8.7 Consensus size: 7
4300261 CCTAATTTTA
4300271 TTTATAT
1 TTTATAT
* *
4300278 TTTTTCTT
1 TTTAT-AT
4300286 TTTATTAT
1 TTTA-TAT
4300294 TTTATAT
1 TTTATAT
4300301 TTTATAT
1 TTTATAT
4300308 TTTATTTTAT
1 TTTA---TAT
4300318 TTTATATT
1 TTTATA-T
*
4300326 TTTCTAT
1 TTTATAT
4300333 TTTAT
1 TTTAT
4300338 TTTCTTACAT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
7 25 0.52
8 15 0.31
9 1 0.02
10 7 0.15
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTATAT
Found at i:4300342 original size:12 final size:12
Alignment explanation
Indices: 4300265--4300327 Score: 64
Period size: 12 Copynumber: 5.4 Consensus size: 12
4300255 AGGCAACCTA
4300265 ATTTTA-TTTAT
1 ATTTTATTTTAT
4300276 ATTTT-TTCTT-T
1 ATTTTATT-TTAT
4300287 -TTATTATTTTAT
1 ATT-TTATTTTAT
4300299 ATTTTATATTT-T
1 ATTTTAT-TTTAT
4300311 ATTTTATTTTAT
1 ATTTTATTTTAT
4300323 ATTTT
1 ATTTT
4300328 TCTATTTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
10 2 0.05
11 14 0.32
12 23 0.52
13 5 0.11
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTTTATTTTAT
Found at i:4306236 original size:15 final size:16
Alignment explanation
Indices: 4306218--4306255 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
4306208 CTTTTACTCT
*
4306218 TTTATTTTC-TTATTA
1 TTTATTTTCTTTATAA
*
4306233 TTTACTTTCTTTATAA
1 TTTATTTTCTTTATAA
4306249 TTTATTT
1 TTTATTT
4306256 CATATCACGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTATTTTCTTTATAA
Found at i:4309340 original size:32 final size:33
Alignment explanation
Indices: 4309304--4309375 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
4309294 AACTTTTATG
*
4309304 AAATATTTT-CAGAAAATC-TGCCAAACAAC-AGA
1 AAATATTTTACACAAAATCAT-CCAAAC-ACTAGA
*
4309336 AAATATTTTACACAAATTCATCCAAACACTAGA
1 AAATATTTTACACAAAATCATCCAAACACTAGA
4309369 AAATATT
1 AAATATT
4309376 AGCTTTTCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 11 0.31
33 23 0.66
34 1 0.03
ACGTcount: A:0.50, C:0.18, G:0.06, T:0.26
Consensus pattern (33 bp):
AAATATTTTACACAAAATCATCCAAACACTAGA
Found at i:4310532 original size:24 final size:24
Alignment explanation
Indices: 4310517--4310568 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
4310507 AATCAATGTC
*
4310517 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
* *
4310541 AAATATATTATACTAATAATTACT
1 AAATATATTATACTAATAAATGCT
4310565 AAAT
1 AAAT
4310569 CTTATAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:4314973 original size:24 final size:24
Alignment explanation
Indices: 4314958--4315009 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
4314948 AATCAATGTC
4314958 AAATATATTATACTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
*
4314982 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATGCT
4315006 AAAT
1 AAAT
4315010 CTTCTAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:4315922 original size:128 final size:127
Alignment explanation
Indices: 4315694--4316008 Score: 522
Period size: 128 Copynumber: 2.5 Consensus size: 127
4315684 CATACGAGGA
* * *
4315694 AGGACACGATATTTTAAGCCTCCAAAAAATTGAGATCACCTCATGATTTCCAAAACACGCGAGAC
1 AGGACACGATATTTTAAGCCTCC-AAAAACTGAGATCACCTCATGATTTCCAAAACACGCAAAAC
4315759 AACTCAAGTTGGATTTTAAGATTCACTCGTTCCAAAGGAATAAAATAACACATCCAGCATGTT
65 AACTCAAGTTGGATTTTAAGATTCACTCGTTCCAAAGGAATAAAATAACACATCCAGCATGTT
* * *
4315822 AGGACACGATATTTTTAAGCCTTCAAAAACTGAGATCATCTCATGATTTCCAAAACATGCAAAAC
1 AGGACACGATA-TTTTAAGCCTCCAAAAACTGAGATCACCTCATGATTTCCAAAACACGCAAAAC
* *
4315887 AACTCAAGTTGGATTTTAAGATTCACTCGTTCCAAAGGAATAGAATACCACATCCAGCATGTT
65 AACTCAAGTTGGATTTTAAGATTCACTCGTTCCAAAGGAATAAAATAACACATCCAGCATGTT
* *
4315950 AGGACACGATATTTTAAGCCTCCAAAAACTGAAACCACCTCATGATTTCCAAAACACGC
1 AGGACACGATATTTTAAGCCTCCAAAAACTGAGATCACCTCATGATTTCCAAAACACGC
4316009 GACGAAAAAT
Statistics
Matches: 173, Mismatches: 13, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
127 43 0.25
128 119 0.69
129 11 0.06
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (127 bp):
AGGACACGATATTTTAAGCCTCCAAAAACTGAGATCACCTCATGATTTCCAAAACACGCAAAACA
ACTCAAGTTGGATTTTAAGATTCACTCGTTCCAAAGGAATAAAATAACACATCCAGCATGTT
Found at i:4316654 original size:31 final size:32
Alignment explanation
Indices: 4316614--4316679 Score: 82
Period size: 36 Copynumber: 2.0 Consensus size: 32
4316604 AGAGAAAACC
4316614 AAATTATAC-ATA-AATAAATTTAAAAGAAAA
1 AAATTATACAATATAATAAATTTAAAAGAAAA
4316644 AAATATATACATATATATAATAAATTTAAAAGAAAA
1 AAAT-TATAC--A-ATATAATAAATTTAAAAGAAAA
4316680 TATTTACATA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
30 4 0.13
31 5 0.17
35 3 0.10
36 18 0.60
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (32 bp):
AAATTATACAATATAATAAATTTAAAAGAAAA
Found at i:4316694 original size:29 final size:30
Alignment explanation
Indices: 4316614--4316695 Score: 80
Period size: 36 Copynumber: 2.6 Consensus size: 30
4316604 AGAGAAAACC
4316614 AAAT-TATACAT-AAATAAATTTAAAAGAAAA
1 AAATATATACATAAAATAAATTTAAAAG--AA
4316644 AAATATATACATATATATAATAAATTTAAAAG-A
1 AAATATATAC--ATA-A-AATAAATTTAAAAGAA
*
4316677 AAATATTTACATAAAATAA
1 AAATATATACATAAAATAA
4316696 TATGAAAACA
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
29 5 0.11
30 5 0.11
31 8 0.18
33 12 0.27
35 1 0.02
36 14 0.31
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (30 bp):
AAATATATACATAAAATAAATTTAAAAGAA
Found at i:4317997 original size:14 final size:14
Alignment explanation
Indices: 4317978--4318005 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4317968 GTCTCACATT
4317978 TATGTAGAAAAGAA
1 TATGTAGAAAAGAA
4317992 TATGTAGAAAAGAA
1 TATGTAGAAAAGAA
4318006 GCCATGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.21, T:0.21
Consensus pattern (14 bp):
TATGTAGAAAAGAA
Found at i:4318521 original size:83 final size:83
Alignment explanation
Indices: 4318397--4318728 Score: 655
Period size: 83 Copynumber: 4.0 Consensus size: 83
4318387 TTATTAATAT
*
4318397 TACCAGCCCTTTCAGATAAAACAAAATGGACTATTGTCACCACCACTGCTATTGGAGAACGCAAA
1 TACCAGCCCTTTCAGATAAAACAAATTGGACTATTGTCACCACCACTGCTATTGGAGAACGCAAA
4318462 ACAAATTTTATTTTTTGA
66 ACAAATTTTATTTTTTGA
4318480 TACCAGCCCTTTCAGATAAAACAAATTGGACTATTGTCACCACCACTGCTATTGGAGAACGCAAA
1 TACCAGCCCTTTCAGATAAAACAAATTGGACTATTGTCACCACCACTGCTATTGGAGAACGCAAA
4318545 ACAAATTTTATTTTTTGA
66 ACAAATTTTATTTTTTGA
4318563 TACCAGCCCTTTCAGATAAAACAAATTGGACTATTGTCACCACCACTGCTATTGGAGAACGCAAA
1 TACCAGCCCTTTCAGATAAAACAAATTGGACTATTGTCACCACCACTGCTATTGGAGAACGCAAA
4318628 ACAAATTTTATTTTTTGA
66 ACAAATTTTATTTTTTGA
4318646 TACCAGCCCTTTCAGATAAAACAAATTGGACTATTGTCACCACCACTGCTATTGGAGAACGCAAA
1 TACCAGCCCTTTCAGATAAAACAAATTGGACTATTGTCACCACCACTGCTATTGGAGAACGCAAA
4318711 ACAAATTTTATTTTTTGA
66 ACAAATTTTATTTTTTGA
4318729 CATGCTTTCC
Statistics
Matches: 248, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 248 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (83 bp):
TACCAGCCCTTTCAGATAAAACAAATTGGACTATTGTCACCACCACTGCTATTGGAGAACGCAAA
ACAAATTTTATTTTTTGA
Found at i:4325672 original size:70 final size:70
Alignment explanation
Indices: 4325552--4325690 Score: 242
Period size: 70 Copynumber: 2.0 Consensus size: 70
4325542 GCTTAAAATT
* *
4325552 GCATCGTTTTTAGATTAAGGATCTGCGCGCTGACCCGGTTACTCGAGGGGATCAGCGTGTTTTTA
1 GCATCGTTTTTAGATTAAGGATCCGCGCGCTGACCCGGTTACCCGAGGGGATCAGCGTGTTTTTA
4325617 AGGAG
66 AGGAG
* *
4325622 GCATCGTTTTTAGATTAAGGATCCGCGCGCTGACCCGGTTACCCGGGGGGATCCGCGTGTTTTTA
1 GCATCGTTTTTAGATTAAGGATCCGCGCGCTGACCCGGTTACCCGAGGGGATCAGCGTGTTTTTA
4325687 AGGA
66 AGGA
4325691 TTGGGTTAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.19, C:0.21, G:0.32, T:0.29
Consensus pattern (70 bp):
GCATCGTTTTTAGATTAAGGATCCGCGCGCTGACCCGGTTACCCGAGGGGATCAGCGTGTTTTTA
AGGAG
Found at i:4329145 original size:6 final size:7
Alignment explanation
Indices: 4329124--4329152 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
4329114 ACTTGAATTC
4329124 AACTAAA
1 AACTAAA
4329131 AACTAAA
1 AACTAAA
4329138 AACT-AA
1 AACTAAA
4329144 AACTAAA
1 AACTAAA
4329151 AA
1 AA
4329153 TACATGTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.72, C:0.14, G:0.00, T:0.14
Consensus pattern (7 bp):
AACTAAA
Found at i:4329147 original size:13 final size:14
Alignment explanation
Indices: 4329124--4329152 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
4329114 ACTTGAATTC
4329124 AACTAAAAACTAAA
1 AACTAAAAACTAAA
4329138 AACT-AAAACTAAA
1 AACTAAAAACTAAA
4329151 AA
1 AA
4329153 TACATGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.72, C:0.14, G:0.00, T:0.14
Consensus pattern (14 bp):
AACTAAAAACTAAA
Found at i:4338310 original size:20 final size:20
Alignment explanation
Indices: 4338285--4338324 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4338275 CGATTTTGGT
4338285 ATGGCTGGTTATATTGCAGG
1 ATGGCTGGTTATATTGCAGG
4338305 ATGGCTGGTTATATTGCAGG
1 ATGGCTGGTTATATTGCAGG
4338325 TTTTCCTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.35, T:0.35
Consensus pattern (20 bp):
ATGGCTGGTTATATTGCAGG
Found at i:4338989 original size:24 final size:24
Alignment explanation
Indices: 4338962--4339018 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
4338952 TACTCATTTT
4338962 ACTTTATCAATATTT-AAAATAAAC
1 ACTTTAT-AATATTTAAAAATAAAC
* *
4338986 ACTTTATTATTTTTAAAAATAAAC
1 ACTTTATAATATTTAAAAATAAAC
*
4339010 AGTTTATAA
1 ACTTTATAA
4339019 ATATAATAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (24 bp):
ACTTTATAATATTTAAAAATAAAC
Found at i:4350510 original size:30 final size:30
Alignment explanation
Indices: 4350449--4350511 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
4350439 ATTTATTTTA
*
4350449 TTGTTAATTTTCTTATTATTTTAAAGGCAT
1 TTGTTAATTTTCTTATTATTTTAAAGCCAT
*
4350479 TTGTTAATTTTTTTATTATTTTAGAA-CCAT
1 TTGTTAATTTTCTTATTATTTTA-AAGCCAT
4350509 TTG
1 TTG
4350512 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 28 0.93
31 2 0.07
ACGTcount: A:0.25, C:0.06, G:0.10, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTCTTATTATTTTAAAGCCAT
Found at i:4351767 original size:7 final size:7
Alignment explanation
Indices: 4351755--4351785 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
4351745 CATATACACT
4351755 TTTAATA
1 TTTAATA
4351762 TTTAATA
1 TTTAATA
4351769 TTTAATA
1 TTTAATA
4351776 TTTAATA
1 TTTAATA
4351783 TTT
1 TTT
4351786 TTTACCATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
TTTAATA
Found at i:4357310 original size:36 final size:36
Alignment explanation
Indices: 4357270--4357341 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
4357260 GATTCATAAG
4357270 ACTAAGCTTTTCACCATAGGGTGCTCTCATATTATT
1 ACTAAGCTTTTCACCATAGGGTGCTCTCATATTATT
* * *
4357306 ACTAAGCTTTTCACCGTGGGGTGCTCTCGTATTATT
1 ACTAAGCTTTTCACCATAGGGTGCTCTCATATTATT
4357342 TGTAAAGAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (36 bp):
ACTAAGCTTTTCACCATAGGGTGCTCTCATATTATT
Found at i:4363055 original size:14 final size:14
Alignment explanation
Indices: 4363000--4363055 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
4362990 AAATAAAAAT
4363000 ATATAATGATATA-A
1 ATATAAT-ATATATA
*
4363014 ATTATGAAAATATATA
1 A-TAT-AATATATATA
* *
4363030 ATACAATGTATATA
1 ATATAATATATATA
4363044 ATATAATATATA
1 ATATAATATATA
4363056 AAAATATCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
14 19 0.58
15 10 0.30
16 4 0.12
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (14 bp):
ATATAATATATATA
Found at i:4363495 original size:51 final size:51
Alignment explanation
Indices: 4363412--4363514 Score: 170
Period size: 51 Copynumber: 2.0 Consensus size: 51
4363402 TGATTGAAAT
*
4363412 GCGCGTTAAATTTAGAGGACTCAAAGGACAATTTAGCCCTAATCCTCAAAC
1 GCGCGTTAAATTTAGAGGACTCAAAGGACAATTTAGCCCTAATCCTAAAAC
** *
4363463 GCGCGTTAAATTTAGAGGACTCATTGGGCAATTTAGCCCTAATCCTAAAAC
1 GCGCGTTAAATTTAGAGGACTCAAAGGACAATTTAGCCCTAATCCTAAAAC
4363514 G
1 G
4363515 ACGTCGTTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 48 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (51 bp):
GCGCGTTAAATTTAGAGGACTCAAAGGACAATTTAGCCCTAATCCTAAAAC
Found at i:4365354 original size:207 final size:207
Alignment explanation
Indices: 4364924--4365479 Score: 839
Period size: 207 Copynumber: 2.7 Consensus size: 207
4364914 AATCTGCCTT
* *
4364924 CTTCGATTTGCTCTCT-ACCAATACAGAGATGCCAAGTCATCTTAGATTTGTTTCAGT-GTAAGC
1 CTTCGATTTGCTCTCTGA-CAATACAGAGATGCCAAATCATCTTAGATTTGCTTCA-TCGTAAGC
* * * * * * *
4364987 ATGCGAAAACCAAATCGGCTATGTCTTCGATTTGCTCCTTATAAGCACAAGGATACCAAACCATC
64 ACGTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATC
* * ** ** *
4365052 TTGGATC-TGCTTCAGTCTAGTCATCTGAAGGTTAGATCTGCTATGTGTCTACCCTCCGTCGAAT
129 TTGGATCTTGCTTCAATATAAACATCTGAAGGCCAGATCTGCTACGTGTCTACCCTCCGTCGAAT
4365116 ATGGAGACGCCAAA
194 ATGGAGACGCCAAA
* *
4365130 CTTCGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAACAC
1 CTTCGATTTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
* * *
4365195 GTGAAAGCCAAACCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAATGATGCCAAATCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
* *
4365260 GGATCTTGCTTCAATATAAACATCTGAAGGCCAGATCTGCTACGTGTCTGCTCTCCGTCGAATAT
131 GGATCTTGCTTCAATATAAACATCTGAAGGCCAGATCTGCTACGTGTCTACCCTCCGTCGAATAT
4365325 GGAGACGCCAAA
196 GGAGACGCCAAA
*
4365337 CTTCGATTTGCTCTCTGACAATACAGAGATGCTAAATCATCTTAGATTTGCTTCATCGTAAGCAC
1 CTTCGATTTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
* *
4365402 GTGAAAGCCAAATCAGCTATGACTTCGATTTGTTCCTTGTAAGCACAGGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
4365467 GGATCTTGCTTCA
131 GGATCTTGCTTCA
4365480 GCCAGATCTG
Statistics
Matches: 316, Mismatches: 31, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
205 1 0.00
206 117 0.37
207 198 0.63
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (207 bp):
CTTCGATTTGCTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCATCGTAAGCAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATGCCAAACCATCTT
GGATCTTGCTTCAATATAAACATCTGAAGGCCAGATCTGCTACGTGTCTACCCTCCGTCGAATAT
GGAGACGCCAAA
Found at i:4368354 original size:43 final size:43
Alignment explanation
Indices: 4368211--4368335 Score: 223
Period size: 43 Copynumber: 2.9 Consensus size: 43
4368201 GTTTATTAAA
* *
4368211 AAAAAGCGTCGCTAAAAGTCGTGGCCCTTAGCGGCGTTTGAAG
1 AAAAAGCGCCGCTAAAAGTCGTGGCCTTTAGCGGCGTTTGAAG
*
4368254 AAAAAGCGCCGCTAAAAGTCGTGGTCTTTAGCGGCGTTTGAAG
1 AAAAAGCGCCGCTAAAAGTCGTGGCCTTTAGCGGCGTTTGAAG
4368297 AAAAAGCGCCGCTAAAAGTCGTGGCCTTTAGCGGCGTTT
1 AAAAAGCGCCGCTAAAAGTCGTGGCCTTTAGCGGCGTTT
4368336 TTCCCACAAA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 78 1.00
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (43 bp):
AAAAAGCGCCGCTAAAAGTCGTGGCCTTTAGCGGCGTTTGAAG
Found at i:4368736 original size:21 final size:21
Alignment explanation
Indices: 4368710--4368749 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4368700 TCCTATGCTT
* *
4368710 TGCCTCTCTCGCTGTTGCCGC
1 TGCCTCCCTCGCTGCTGCCGC
4368731 TGCCTCCCTCGCTGCTGCC
1 TGCCTCCCTCGCTGCTGCC
4368750 TCCGCTCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.00, C:0.47, G:0.23, T:0.30
Consensus pattern (21 bp):
TGCCTCCCTCGCTGCTGCCGC
Found at i:4369186 original size:13 final size:14
Alignment explanation
Indices: 4369161--4369189 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
4369151 TGATGAATTG
4369161 AATTAAACAATTAT
1 AATTAAACAATTAT
4369175 AATTAAAC-ATTAT
1 AATTAAACAATTAT
4369188 AA
1 AA
4369190 ATATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACAATTAT
Found at i:4369393 original size:16 final size:17
Alignment explanation
Indices: 4369356--4369394 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
4369346 AAAATATTAT
*
4369356 TTAATATTAGAAAGTTA
1 TTAATATTAGAAAGTAA
*
4369373 TTAATATTTGAAAG-AA
1 TTAATATTAGAAAGTAA
4369389 TTAATA
1 TTAATA
4369395 AAACTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (17 bp):
TTAATATTAGAAAGTAA
Found at i:4374239 original size:9 final size:9
Alignment explanation
Indices: 4374225--4374414 Score: 107
Period size: 9 Copynumber: 20.6 Consensus size: 9
4374215 TATTTAAGTA
4374225 TTATGTAAG
1 TTATGTAAG
4374234 TTATGTAAG
1 TTATGTAAG
*
4374243 TTATGATATG
1 TTATG-TAAG
* * *
4374253 ATATAT-AT
1 TTATGTAAG
*
4374261 TTATGTAAA
1 TTATGTAAG
* *
4374270 TTATAT-AT
1 TTATGTAAG
*
4374278 TTATCTAAG
1 TTATGTAAG
*
4374287 TTATATAAG
1 TTATGTAAG
4374296 TTATGTAAG
1 TTATGTAAG
*
4374305 TTATGTAAA
1 TTATGTAAG
*
4374314 TTATGATATAAAA
1 TTATG---T-AAG
*
4374327 TATATTTAAG
1 T-TATGTAAG
4374337 TATTATGTAAG
1 --TTATGTAAG
4374348 TTATGTAAG
1 TTATGTAAG
* *
4374357 TTATAT-AT
1 TTATGTAAG
*
4374365 TTATCTAAG
1 TTATGTAAG
*
4374374 TTATATAAG
1 TTATGTAAG
*
4374383 TTATGTACG
1 TTATGTAAG
*
4374392 TTTTGTAAG
1 TTATGTAAG
* *
4374401 TTATATAAA
1 TTATGTAAG
4374410 TTATG
1 TTATG
4374415 ATATCAAATA
Statistics
Matches: 139, Mismatches: 31, Indels: 22
0.72 0.16 0.11
Matches are distributed among these distances:
8 16 0.12
9 98 0.71
10 8 0.06
11 8 0.06
12 2 0.01
13 4 0.03
14 3 0.02
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:4374307 original size:71 final size:69
Alignment explanation
Indices: 4374225--4374387 Score: 202
Period size: 71 Copynumber: 2.3 Consensus size: 69
4374215 TATTTAAGTA
* * * *
4374225 TTATGTAAGTTATGTAAGTTATGATATGATATATATTTATGTAAATTATAT-ATTTATCTAAGTT
1 TTATGTAAGTTATGTAAGTTATGATATAAAATATATTTAAGT--ATTATATAAGTTATCTAAGTT
4374289 ATATAAG
64 ATAT-AG
* * *
4374296 TTATGTAAGTTATGTAAATTATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTAT
1 TTATGTAAGTTATGTAAGTTATGATATAAAATATATTTAAGTATTATATAAGTTATCTAAGTTAT
*
4374361 ATAT
66 ATAG
* *
4374365 TTATCTAAGTTATATAAGTTATG
1 TTATGTAAGTTATGTAAGTTATG
4374388 TACGTTTTGT
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
69 27 0.34
70 15 0.19
71 38 0.47
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (69 bp):
TTATGTAAGTTATGTAAGTTATGATATAAAATATATTTAAGTATTATATAAGTTATCTAAGTTAT
ATAG
Found at i:4374363 original size:87 final size:90
Alignment explanation
Indices: 4374261--4374445 Score: 259
Period size: 96 Copynumber: 2.0 Consensus size: 90
4374251 TGATATATAT
*
4374261 TTATGTAAATTATATATTTATCTAAGTTATATAAG-T-TA-TGTAAGTTATGTAAATTATGATAT
1 TTATGTAAATTATATATTTATCTAAGTTATATAAGTTGTATTGTAAGTTATATAAATTATGATAT
4374323 AAAATATATTTAAGTATTATGTAAG
66 AAAATATATTTAAGTATTATGTAAG
*
4374348 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTACGTTTTGTAAGTTATATAAATTA
1 TTATGTAAATTATATATTTATCTAAGTTATATAAG-T-TGTA----TTGTAAGTTATATAAATTA
* *
4374413 TGATATCAAATATATTTATGTATTATGTAAG
60 TGATATAAAATATATTTAAGTATTATGTAAG
4374444 TT
1 TT
4374446 TTTTATTTCA
Statistics
Matches: 85, Mismatches: 4, Indels: 9
0.87 0.04 0.09
Matches are distributed among these distances:
87 34 0.40
90 1 0.01
91 2 0.02
96 48 0.56
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (90 bp):
TTATGTAAATTATATATTTATCTAAGTTATATAAGTTGTATTGTAAGTTATATAAATTATGATAT
AAAATATATTTAAGTATTATGTAAG
Found at i:4374401 original size:114 final size:114
Alignment explanation
Indices: 4374201--4374414 Score: 290
Period size: 114 Copynumber: 1.9 Consensus size: 114
4374191 ACTAGTTATG
* * * *
4374201 TATGATATGATATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGATATATATTTATG
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGATATATAGTTATA
*
4374266 TAAATTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAAT
66 TAAATTATATATTTATCTAAGTTATATAAATTATGTAAGTTATGTAAAT
* *
4374315 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTAT-ATAT-TTATCTAAGTTAT
1 TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGATATAT-AGTTAT
* * *
4374378 ATAAGTTATGTACGTTT-TGTAAGTTATATAAATTATG
65 ATAAATTATATA--TTTATCTAAGTTATATAAATTATG
4374415 ATATCAAATA
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
112 4 0.05
113 18 0.21
114 62 0.71
115 3 0.03
ACGTcount: A:0.38, C:0.01, G:0.13, T:0.47
Consensus pattern (114 bp):
TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGATATATAGTTATA
TAAATTATATATTTATCTAAGTTATATAAATTATGTAAGTTATGTAAAT
Found at i:4374453 original size:87 final size:87
Alignment explanation
Indices: 4374261--4374445 Score: 234
Period size: 87 Copynumber: 2.1 Consensus size: 87
4374251 TGATATATAT
*
4374261 TTATGTAAATTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAATTATGATATAAA
1 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAATTATGATATAAA
** *
4374326 ATATATTTAAGTATTATGTAAG
66 ATATATCAAAATATTATGTAAG
* * *
4374348 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTACGTTTTGTAAGTTAT-ATA-AAT
1 TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAATTATGATATAA-
*
4374411 TATGATATCAAATATATTTATGT-A-
65 AAT-ATATCAAA-ATA-TTATGTAAG
4374435 TTATGTAAGTT
1 TTATGTAAGTT
4374446 TTTTATTTCA
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
85 2 0.02
86 5 0.06
87 70 0.81
88 3 0.03
89 6 0.07
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (87 bp):
TTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATGTAAGTTATGTAAATTATGATATAAA
ATATATCAAAATATTATGTAAG
Found at i:4374539 original size:15 final size:15
Alignment explanation
Indices: 4374519--4374574 Score: 64
Period size: 15 Copynumber: 3.8 Consensus size: 15
4374509 AAGTAGCGGG
4374519 ATTAAATAATATTTA
1 ATTAAATAATATTTA
4374534 ATTAAATAATATTT-
1 ATTAAATAATATTTA
4374548 A-TAAA-AATTATTTTA
1 ATTAAATAA-TA-TTTA
*
4374563 ATTAAGTAATAT
1 ATTAAATAATAT
4374575 ACATGTCGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
12 2 0.06
13 6 0.17
14 4 0.11
15 16 0.46
16 5 0.14
17 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
ATTAAATAATATTTA
Found at i:4375596 original size:356 final size:358
Alignment explanation
Indices: 4374784--4375663 Score: 1629
Period size: 356 Copynumber: 2.5 Consensus size: 358
4374774 ATAAAACAGA
*
4374784 GAATTTTTTAAGATTCATCATACGCGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
1 GAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
*
4374849 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCGTATATACTTTGAATCTTTAAAATATTTAAAAT
66 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
4374914 AAGGTTGGAGAGAAGGTCAACCATTGTTGTAATTTTGATAAAAATTAGTTATAACTTTTAAAGAC
131 AAGGTTGGAGAGAAGGTCAACCATTGTTGTAATTTTGATAAAAATTAGTTATAACTTTTAAAGAC
4374979 ATTTAAAAATATTAAATATTAAAATCAAACATTATTAATGCAAAAAAATAGTAATTTGAATATAA
196 ATTTAAAAATATTAAATATTAAAATCAAACATTATTAATGCAAAAAAATAGTAATTTGAATATAA
4375044 TAATATAAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATATTCAATAGTAA
261 TAATATAAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATATTCAATAGTAA
*
4375109 ATGAGCTCGATAGAACTTTTTTCAAGTCTTTTT
326 ATGAACTCGATAGAACTTTTTTCAAGTCTTTTT
* * *
4375142 GAATTTTTTAAGATCCATCATATGTGACGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
1 GAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
4375207 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
66 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
*
4375272 AAGGTTGGAGAGAAGGTCAGCCATTGTTGTAATTTTGATAAAAATTAGTTATAACTTTTAAAGAC
131 AAGGTTGGAGAGAAGGTCAACCATTGTTGTAATTTTGATAAAAATTAGTTATAACTTTTAAAGAC
* *
4375337 ATTTAAAAGTATTAAATATTAAAATCAAACATTATTAATGC-AAAAATTAGTAATTTGAATATAA
196 ATTTAAAAATATTAAATATTAAAATCAAACATTATTAATGCAAAAAAATAGTAATTTGAATATAA
4375401 TAATAT-AAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATATTCAATAGTAA
261 TAATATAAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATATTCAATAGTAA
4375465 ATGAACTCGATAGAACTTTTTTCAAGTCTTTTT
326 ATGAACTCGATAGAACTTTTTTCAAGTCTTTTT
*
4375498 GAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTCCAG
1 GAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
4375563 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
66 CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
* * *
4375628 AAGGCTGGAGAGAAGGTCATCCATTGCTGTAATTTT
131 AAGGTTGGAGAGAAGGTCAACCATTGTTGTAATTTT
4375664 AATGGACAAG
Statistics
Matches: 506, Mismatches: 16, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
356 249 0.49
357 28 0.06
358 229 0.45
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (358 bp):
GAATTTTTTAAGATTCATCATACGTGGCGTTGTTACACCTAGGGAGGATCCATTATATCTTGCAG
CTCGATATAAGGCAACCCGTCAGGTTTCCAGCCTATATACTTTGAATCTTTAAAATATTTAAAAT
AAGGTTGGAGAGAAGGTCAACCATTGTTGTAATTTTGATAAAAATTAGTTATAACTTTTAAAGAC
ATTTAAAAATATTAAATATTAAAATCAAACATTATTAATGCAAAAAAATAGTAATTTGAATATAA
TAATATAAAAAAAGAATCGTAGTTTAATTTTTATAAGTAAATTGGAAATAAATATTCAATAGTAA
ATGAACTCGATAGAACTTTTTTCAAGTCTTTTT
Found at i:4375907 original size:15 final size:15
Alignment explanation
Indices: 4375887--4375915 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4375877 AGAATTTTGA
4375887 AATAAAACGTACCTT
1 AATAAAACGTACCTT
4375902 AATAAAACGTACCT
1 AATAAAACGTACCT
4375916 GGTCTACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.24
Consensus pattern (15 bp):
AATAAAACGTACCTT
Found at i:4376432 original size:183 final size:183
Alignment explanation
Indices: 4376117--4376483 Score: 689
Period size: 183 Copynumber: 2.0 Consensus size: 183
4376107 CCTAGAACAG
4376117 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATAAAAACTTTATCTAT
1 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATAAAAACTTTATCTAT
4376182 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAAGAGG
66 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAAGAGG
*
4376247 AGCAGGAAGCAGTAACTGAAATACATACAACATTAATTCACTAATACAGACAC
131 AGCAGGAAGCAGTAACTGAAACACATACAACATTAATTCACTAATACAGACAC
*
4376300 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATGAAAACTTTATCTAT
1 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATAAAAACTTTATCTAT
*
4376365 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
66 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAAGAGG
* *
4376430 AGCAGGAAGCAGTAACTGAAACATATACAACATTAATTCACTAATATAGACAC
131 AGCAGGAAGCAGTAACTGAAACACATACAACATTAATTCACTAATACAGACAC
4376483 A
1 A
4376484 AGGAACTATA
Statistics
Matches: 179, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
183 179 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (183 bp):
ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATAAAAACTTTATCTAT
ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAAGAGG
AGCAGGAAGCAGTAACTGAAACACATACAACATTAATTCACTAATACAGACAC
Found at i:4376575 original size:14 final size:13
Alignment explanation
Indices: 4376556--4376585 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
4376546 CAATATAATT
4376556 TTACTTCATATATA
1 TTACTTCATATA-A
4376570 TTACTTCATATAA
1 TTACTTCATATAA
4376583 TTA
1 TTA
4376586 TTATAGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (13 bp):
TTACTTCATATAA
Found at i:4379148 original size:15 final size:15
Alignment explanation
Indices: 4379128--4379176 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
4379118 GGTAAAAATT
4379128 TTGGGGGAGAAGAAG
1 TTGGGGGAGAAGAAG
*
4379143 TT-GGGG-G-A-AAT
1 TTGGGGGAGAAGAAG
*
4379154 TTGGAGGAGAAGAAG
1 TTGGGGGAGAAGAAG
4379169 TTGGGGGA
1 TTGGGGGA
4379177 AATTTGGTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
11 4 0.15
12 4 0.15
13 2 0.08
14 5 0.19
15 11 0.42
ACGTcount: A:0.31, C:0.00, G:0.51, T:0.18
Consensus pattern (15 bp):
TTGGGGGAGAAGAAG
Found at i:4379162 original size:26 final size:26
Alignment explanation
Indices: 4379127--4379183 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
4379117 GGGTAAAAAT
*
4379127 TTTGGGGGAGAAGAAGTTGGGGGAAA
1 TTTGGAGGAGAAGAAGTTGGGGGAAA
4379153 TTTGGAGGAGAAGAAGTTGGGGGAAA
1 TTTGGAGGAGAAGAAGTTGGGGGAAA
4379179 TTTGG
1 TTTGG
4379184 TGGAAATCGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (26 bp):
TTTGGAGGAGAAGAAGTTGGGGGAAA
Found at i:4379500 original size:28 final size:28
Alignment explanation
Indices: 4379468--4379525 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
4379458 AATCAAAACT
*
4379468 CTAT-ACCTTAAACCATTAAACTATATCC
1 CTATAACCTTAAACC-CTAAACTATATCC
* *
4379496 CTATAACCTTAATCCCTAAAGTATATCC
1 CTATAACCTTAAACCCTAAACTATATCC
4379524 CT
1 CT
4379526 TAAACCCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (28 bp):
CTATAACCTTAAACCCTAAACTATATCC
Found at i:4379526 original size:21 final size:21
Alignment explanation
Indices: 4379502--4379545 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
4379492 ATCCCTATAA
* *
4379502 CCTTAATCCCTAAAGTATATC
1 CCTTAAACCCTAAACTATATC
4379523 CCTTAAACCCTAAACTATATC
1 CCTTAAACCCTAAACTATATC
4379544 CC
1 CC
4379546 CTAACCATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.34, G:0.02, T:0.30
Consensus pattern (21 bp):
CCTTAAACCCTAAACTATATC
Found at i:4379815 original size:21 final size:22
Alignment explanation
Indices: 4379782--4379825 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
4379772 ACTAACCCTT
*
4379782 AACCCCTAACCCTTAAATCATA
1 AACCCCTAACCCTTAAACCATA
4379804 AACCCC-AACCCTTAAACCATA
1 AACCCCTAACCCTTAAACCATA
4379825 A
1 A
4379826 TACATAAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.43, C:0.39, G:0.00, T:0.18
Consensus pattern (22 bp):
AACCCCTAACCCTTAAACCATA
Found at i:4379956 original size:41 final size:41
Alignment explanation
Indices: 4379898--4380200 Score: 484
Period size: 41 Copynumber: 7.4 Consensus size: 41
4379888 AAACCCTAAA
* *
4379898 ATTTTTAGTGGCATTTTACCAAAAGCGCCGCTAATGCTCTT
1 ATTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTT
*
4379939 ATTTTTAGCGGCGTTTTACCAAAAGCGCTGCTAATGCTCTT
1 ATTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTT
*
4379980 ATTTTTAGCGGCGTTTTACCAAAAGCACCGCTAATGCTCTT
1 ATTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTT
* *
4380021 ATTTTTAGCGGTGCTTTACCAAAAGCGCCGCTAATGCTCTT
1 ATTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTT
* * *
4380062 ATTTTTAACGGCGTTTTACCAAAAGCGCCGCTATTGCT-TCG
1 ATTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCT-T
4380103 ATTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTT
1 ATTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTT
*
4380144 ATTTTTAGCGGCGTTTTACCAAAAGCGCCGCTATTGCTC-T
1 ATTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTT
*
4380184 GTTTTTAGCGGCGTTTT
1 ATTTTTAGCGGCGTTTT
4380201 TGGTAAAACG
Statistics
Matches: 242, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
40 18 0.07
41 223 0.92
42 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (41 bp):
ATTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTT
Found at i:4388668 original size:14 final size:14
Alignment explanation
Indices: 4388613--4388668 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
4388603 AAATAAAAAT
4388613 ATATAATGATATA-A
1 ATATAAT-ATATATA
*
4388627 ATTATGAAAATATATA
1 A-TAT-AATATATATA
* *
4388643 ATACAATGTATATA
1 ATATAATATATATA
4388657 ATATAATATATA
1 ATATAATATATA
4388669 AAAAATATCT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
14 19 0.58
15 10 0.30
16 4 0.12
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (14 bp):
ATATAATATATATA
Found at i:4390512 original size:14 final size:14
Alignment explanation
Indices: 4390495--4390548 Score: 81
Period size: 14 Copynumber: 3.9 Consensus size: 14
4390485 AATATTTTCC
4390495 GGAAAATGATTTTT
1 GGAAAATGATTTTT
4390509 GGAAAATGATTTTT
1 GGAAAATGATTTTT
* *
4390523 AGAAAATGATTTCT
1 GGAAAATGATTTTT
*
4390537 GAAAAATGATTT
1 GGAAAATGATTT
4390549 ACTTTTCTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.41, C:0.02, G:0.19, T:0.39
Consensus pattern (14 bp):
GGAAAATGATTTTT
Found at i:4390515 original size:28 final size:28
Alignment explanation
Indices: 4390483--4390548 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
4390473 GTTTGCAGGT
* * *
4390483 AAAAT-ATTTTCCGGAAAATGATTTTTGG
1 AAAATGATTTT-CAGAAAATGATTTCTGA
*
4390511 AAAATGATTTTTAGAAAATGATTTCTGA
1 AAAATGATTTTCAGAAAATGATTTCTGA
4390539 AAAATGATTT
1 AAAATGATTT
4390549 ACTTTTCTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 28 0.85
29 5 0.15
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.39
Consensus pattern (28 bp):
AAAATGATTTTCAGAAAATGATTTCTGA
Found at i:4390662 original size:18 final size:18
Alignment explanation
Indices: 4390639--4390678 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
4390629 CTGTTTTTAC
4390639 ATATATATTAATAAATTT
1 ATATATATTAATAAATTT
4390657 ATATATATTAATAAATTT
1 ATATATATTAATAAATTT
4390675 ATAT
1 ATAT
4390679 TTTAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATATATTAATAAATTT
Found at i:4390683 original size:16 final size:16
Alignment explanation
Indices: 4390640--4390683 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 16
4390630 TGTTTTTACA
*
4390640 TATATATTAATAAATT
1 TATATTTTAATAAATT
4390656 TATATATATTAATAAATT
1 TATAT-T-TTAATAAATT
4390674 TATATTTTAA
1 TATATTTTAA
4390684 ATTATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 9 0.36
17 1 0.04
18 15 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATATTTTAATAAATT
Found at i:4392274 original size:3 final size:3
Alignment explanation
Indices: 4392266--4392291 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4392256 TAAATGCAAA
4392266 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
4392292 ATTACCAACC
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4394543 original size:39 final size:36
Alignment explanation
Indices: 4394446--4394546 Score: 98
Period size: 39 Copynumber: 2.7 Consensus size: 36
4394436 CAGATCATTA
* * *
4394446 ATATAAAAATATATATTATAAT-AACATAATTGTAT
1 ATATAAATATATATATTATAATCTACATAATTATAT
4394481 ATATAAATACT-TATCATTAATAATCTACAATAATTATAT
1 ATATAAATA-TATAT-ATT-ATAATCTAC-ATAATTATAT
*
4394520 AATACTAACTATATATATTATAATCTA
1 -ATA-TAAATATATATATTATAATCTA
4394547 TCCTAAAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
35 11 0.20
36 4 0.07
37 5 0.09
38 2 0.04
39 17 0.31
40 7 0.13
41 8 0.15
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.41
Consensus pattern (36 bp):
ATATAAATATATATATTATAATCTACATAATTATAT
Found at i:4394807 original size:12 final size:12
Alignment explanation
Indices: 4394790--4394823 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
4394780 CGGCCCTCCC
4394790 ATATTAATTTTT
1 ATATTAATTTTT
*
4394802 ATATTATTTTTT
1 ATATTAATTTTT
4394814 ATA-TAATTTT
1 ATATTAATTTT
4394824 AAAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:4394983 original size:30 final size:30
Alignment explanation
Indices: 4394947--4395009 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
4394937 ACTTAACAAG
*
4394947 CAAATGT-TTCTAAAATAATAACAAAATTAA
1 CAAATGTCTT-TAAAATAATAAAAAAATTAA
4394977 CAAATGTCTTTAAAATAATAAAAAAATTAA
1 CAAATGTCTTTAAAATAATAAAAAAATTAA
4395007 CAA
1 CAA
4395010 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 29 0.94
31 2 0.06
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.29
Consensus pattern (30 bp):
CAAATGTCTTTAAAATAATAAAAAAATTAA
Found at i:4395074 original size:22 final size:22
Alignment explanation
Indices: 4395049--4395091 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
4395039 TATCCAAACA
4395049 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
4395071 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
4395092 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:4395095 original size:11 final size:11
Alignment explanation
Indices: 4395056--4395096 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
4395046 ACAATAACAA
4395056 CAAAATAGTAG
1 CAAAATAGTAG
* *
4395067 CAACATAATAG
1 CAAAATAGTAG
*
4395078 TAAAATAGTAG
1 CAAAATAGTAG
4395089 CAAAATAG
1 CAAAATAG
4395097 GGAGAAAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:4399996 original size:19 final size:19
Alignment explanation
Indices: 4399959--4399998 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4399949 TAAAAAATAT
*
4399959 AAATAATAAAAACTCATAA
1 AAATAATAAAAAATCATAA
* *
4399978 AAATTATAAAAAATTATAA
1 AAATAATAAAAAATCATAA
4399997 AA
1 AA
4399999 TACTCAGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (19 bp):
AAATAATAAAAAATCATAA
Found at i:4400193 original size:19 final size:19
Alignment explanation
Indices: 4400159--4400221 Score: 108
Period size: 19 Copynumber: 3.3 Consensus size: 19
4400149 TTGAAATATT
*
4400159 TAAAATTTTATACAAACTTA
1 TAAAATTCT-TACAAACTTA
4400179 TAAAATTCTTACAAACTTA
1 TAAAATTCTTACAAACTTA
4400198 TAAAATTCTTACAAACTTA
1 TAAAATTCTTACAAACTTA
4400217 TAAAA
1 TAAAA
4400222 ATTATTCAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
19 34 0.81
20 8 0.19
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAAATTCTTACAAACTTA
Found at i:4400231 original size:19 final size:19
Alignment explanation
Indices: 4400159--4400264 Score: 99
Period size: 19 Copynumber: 5.5 Consensus size: 19
4400149 TTGAAATATT
*
4400159 TAAAATTTTATACAAACTTA
1 TAAAATTAT-TACAAACTTA
*
4400179 TAAAATTCTTACAAACTTA
1 TAAAATTATTACAAACTTA
*
4400198 TAAAATTCTTACAAACTTA
1 TAAAATTATTACAAACTTA
**
4400217 TAAAAATTATT-CAAAAATA
1 T-AAAATTATTACAAACTTA
* *
4400236 TTAAAATTGA-TATAAACATA
1 -TAAAATT-ATTACAAACTTA
4400256 TAAAATTAT
1 TAAAATTAT
4400265 AAAAAAATCA
Statistics
Matches: 75, Mismatches: 6, Indels: 11
0.82 0.07 0.12
Matches are distributed among these distances:
18 1 0.01
19 50 0.67
20 24 0.32
ACGTcount: A:0.53, C:0.09, G:0.01, T:0.37
Consensus pattern (19 bp):
TAAAATTATTACAAACTTA
Found at i:4400241 original size:39 final size:38
Alignment explanation
Indices: 4400152--4400280 Score: 116
Period size: 39 Copynumber: 3.3 Consensus size: 38
4400142 AACATATTTG
* *
4400152 AAATATTTAAAATTTTATACAAACTTATAAAATTCTTACAA
1 AAATA-TTAAAATTCT-TACAAACTTATAAAATTATT-CAA
**
4400193 ACTTA-TAAAATTCTTACAAACTTATAAAAATTATTCAA
1 AAATATTAAAATTCTTACAAACTTAT-AAAATTATTCAA
** * * **
4400231 AAATATTAAAATTGATATAAACATATAAAATTATAAAA
1 AAATATTAAAATTCTTACAAACTTATAAAATTATTCAA
4400269 AAATCATTAAAA
1 AAAT-ATTAAAA
4400281 ATTATCTAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
38 31 0.42
39 39 0.53
41 3 0.04
ACGTcount: A:0.56, C:0.09, G:0.01, T:0.35
Consensus pattern (38 bp):
AAATATTAAAATTCTTACAAACTTATAAAATTATTCAA
Done.