Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 176 of 182
Found at i:53295746 original size:3 final size:3
Alignment explanation
Indices: 53295738--53295771 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
53295728 ACACCAGTAT
53295738 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
53295772 CTTCGCCTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:53304624 original size:31 final size:32
Alignment explanation
Indices: 53304584--53304671 Score: 101
Period size: 33 Copynumber: 2.8 Consensus size: 32
53304574 TTAGACCCCT
53304584 AAAATTTTTAGAAATTTAAATTAAG-CCTTCC
1 AAAATTTTTAGAAATTTAAATTAAGACCTTCC
* *
53304615 AAAAGTTTTAGAAATTTTAAAATT-AGATCTTCC
1 AAAATTTTTAGAAA-TTT-AAATTAAGACCTTCC
*
53304648 AAAATTTTTGGAAATTCT-AATTAA
1 AAAATTTTTAGAAATT-TAAATTAA
53304672 TCCTCTCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
31 17 0.35
32 8 0.17
33 23 0.48
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (32 bp):
AAAATTTTTAGAAATTTAAATTAAGACCTTCC
Found at i:53304647 original size:33 final size:32
Alignment explanation
Indices: 53304584--53304685 Score: 104
Period size: 31 Copynumber: 3.2 Consensus size: 32
53304574 TTAGACCCCT
53304584 AAAATTTTTAGAAA-TTTAAATTAAGCCTTCC
1 AAAATTTTTAGAAATTTTAAATTAAGCCTTCC
* *
53304615 AAAAGTTTTAGAAATTTTAAAATT-AGATCTTCC
1 AAAATTTTTAGAAATTTT-AAATTAAG-CCTTCC
* * *
53304648 AAAATTTTTGGAAATTCT-AATTAATCC-TCTC
1 AAAATTTTTAGAAATTTTAAATTAAGCCTTC-C
53304679 AAAATTT
1 AAAATTT
53304686 CCCAAAACAT
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
30 2 0.03
31 26 0.44
32 6 0.10
33 25 0.42
ACGTcount: A:0.41, C:0.12, G:0.07, T:0.40
Consensus pattern (32 bp):
AAAATTTTTAGAAATTTTAAATTAAGCCTTCC
Found at i:53304970 original size:17 final size:17
Alignment explanation
Indices: 53304912--53304970 Score: 52
Period size: 16 Copynumber: 3.6 Consensus size: 17
53304902 ATTATCCAAA
*
53304912 AACTCAAAAT-GATTTG
1 AACTCAAAATAGACTTG
* *
53304928 AACTTAAAATA-CCTTG
1 AACTCAAAATAGACTTG
*
53304944 AAC-CACAAATAGACTCG
1 AACTCA-AAATAGACTTG
53304961 AACTCAAAAT
1 AACTCAAAAT
53304971 TGATCAACCG
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
15 1 0.03
16 20 0.61
17 10 0.30
18 2 0.06
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.24
Consensus pattern (17 bp):
AACTCAAAATAGACTTG
Found at i:53322266 original size:20 final size:20
Alignment explanation
Indices: 53322241--53322293 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
53322231 ATGACTAGTT
*
53322241 TATAAAATTTAATTTAAATA
1 TATAAAATATAATTTAAATA
* *
53322261 TATAAACTATATTTTAAATA
1 TATAAAATATAATTTAAATA
*
53322281 T-TAAAAAATAATT
1 TATAAAATATAATT
53322294 AATACAAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
TATAAAATATAATTTAAATA
Found at i:53323337 original size:36 final size:36
Alignment explanation
Indices: 53323290--53323364 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
53323280 GCATTGCCTA
53323290 AAACAAATTGGCAATAAGTGACTGTAATACCAGAGC
1 AAACAAATTGGCAATAAGTGACTGTAATACCAGAGC
53323326 AAACAAATTGGCAATAAGTGACTGTAATACCAGAGC
1 AAACAAATTGGCAATAAGTGACTGTAATACCAGAGC
53323362 AAA
1 AAA
53323365 TTGTAAGTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.19
Consensus pattern (36 bp):
AAACAAATTGGCAATAAGTGACTGTAATACCAGAGC
Found at i:53327124 original size:50 final size:50
Alignment explanation
Indices: 53327049--53327148 Score: 182
Period size: 50 Copynumber: 2.0 Consensus size: 50
53327039 TGAGCTTGAA
*
53327049 AAGGTAAATTTTTAATTTGGGTTGGCTTGAGCTGATTCAAATTAAAGTTT
1 AAGGTAAATTTTTAATTCGGGTTGGCTTGAGCTGATTCAAATTAAAGTTT
*
53327099 AAGGTAAATTTTTAATTCGGGTTGGCTTGAGCTGGTTCAAATTAAAGTTT
1 AAGGTAAATTTTTAATTCGGGTTGGCTTGAGCTGATTCAAATTAAAGTTT
53327149 TAATAATAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.29, C:0.07, G:0.23, T:0.41
Consensus pattern (50 bp):
AAGGTAAATTTTTAATTCGGGTTGGCTTGAGCTGATTCAAATTAAAGTTT
Found at i:53327165 original size:50 final size:49
Alignment explanation
Indices: 53327061--53327165 Score: 122
Period size: 50 Copynumber: 2.1 Consensus size: 49
53327051 GGTAAATTTT
* ****
53327061 TAATTTGGGTTGGCTTGAGCTGATTCAAATTAAAGTTTAAGGTAAATTTT
1 TAATTCGGGTTGGCTTGAGCTGATTCAAATTAAAGTTTAA-GTAAAAAAC
*
53327111 TAATTCGGGTTGGCTTGAGCTGGTTCAAATTAAAGTTTTAA-TAATAAAAC
1 TAATTCGGGTTGGCTTGAGCTGATTCAAATTAAAG-TTTAAGTAA-AAAAC
53327161 TAATT
1 TAATT
53327166 TTGCTTGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
49 3 0.06
50 39 0.83
51 5 0.11
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (49 bp):
TAATTCGGGTTGGCTTGAGCTGATTCAAATTAAAGTTTAAGTAAAAAAC
Found at i:53328283 original size:50 final size:52
Alignment explanation
Indices: 53328202--53328300 Score: 114
Period size: 50 Copynumber: 1.9 Consensus size: 52
53328192 ACCTTAAATG
* * *
53328202 ACCCAACTGAGATACTCAAAATGATCTTGAATGGA-CTTTAACCCGAAATGAT
1 ACCCAACTGACATACTCAAAACGATCTTGAATGGATC-TGAACCCGAAATGAT
* * *
53328254 ACCCAACTGACATA-TCCAAACGGTC-TGAATTGATCTGAACCCGAAAT
1 ACCCAACTGACATACTCAAAACGATCTTGAATGGATCTGAACCCGAAAT
53328301 AAAATTATCT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
50 18 0.45
51 9 0.22
52 13 0.32
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.23
Consensus pattern (52 bp):
ACCCAACTGACATACTCAAAACGATCTTGAATGGATCTGAACCCGAAATGAT
Found at i:53330933 original size:19 final size:19
Alignment explanation
Indices: 53330884--53330941 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
53330874 TAATGATAAA
* * *
53330884 TTTAGTTTTTAATGTTTATA
1 TTTATTTTTTAAT-TTAATT
*
53330904 TTT-TTTGTTAATTTAATT
1 TTTATTTTTTAATTTAATT
*
53330922 TTTATTTTTTAATTAAATT
1 TTTATTTTTTAATTTAATT
53330941 T
1 T
53330942 AACTCTTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 7 0.23
19 21 0.68
20 3 0.10
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (19 bp):
TTTATTTTTTAATTTAATT
Found at i:53330940 original size:24 final size:24
Alignment explanation
Indices: 53330891--53330943 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
53330881 AAATTTAGTT
*
53330891 TTTAATGTTTATATTTTTTGTTAA
1 TTTAATGTTTATATTTTTTATTAA
53330915 TTTAAT-TTT-TATTTTTTAATTAAA
1 TTTAATGTTTATATTTTTT-ATT-AA
53330939 TTTAA
1 TTTAA
53330944 CTCTTAAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 8 0.31
23 5 0.19
24 13 0.50
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (24 bp):
TTTAATGTTTATATTTTTTATTAA
Found at i:53331115 original size:17 final size:17
Alignment explanation
Indices: 53331088--53331134 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
53331078 TTATGAACAT
53331088 TTTTGTTTGAAATTTTAA
1 TTTT-TTTGAAATTTTAA
* *
53331106 TTTTTTTGAATTTTTTA
1 TTTTTTTGAAATTTTAA
*
53331123 TATTTTT-AAATT
1 TTTTTTTGAAATT
53331135 ATTTATTGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 4 0.16
17 17 0.68
18 4 0.16
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (17 bp):
TTTTTTTGAAATTTTAA
Found at i:53341080 original size:13 final size:13
Alignment explanation
Indices: 53341057--53341090 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
53341047 ATGATTTAGA
53341057 TAAAAATATAAATT
1 TAAAAA-ATAAATT
53341071 TAAAAAATAAATT
1 TAAAAAATAAATT
53341084 TAAAAAA
1 TAAAAAA
53341091 ATATGTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.70
14 6 0.30
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
TAAAAAATAAATT
Found at i:53343762 original size:38 final size:38
Alignment explanation
Indices: 53343708--53343784 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
53343698 TAACGATTTA
53343708 ACTATCGGTATAGTGGATCAATACCCATAAAAGAGTAG
1 ACTATCGGTATAGTGGATCAATACCCATAAAAGAGTAG
* *
53343746 ACTATCGGTATGGTGGATCAATACCCATCAAAGAGTAG
1 ACTATCGGTATAGTGGATCAATACCCATAAAAGAGTAG
53343784 A
1 A
53343785 ACATGTTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (38 bp):
ACTATCGGTATAGTGGATCAATACCCATAAAAGAGTAG
Found at i:53348298 original size:46 final size:46
Alignment explanation
Indices: 53348231--53348323 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
53348221 TTTTATGTGT
53348231 TGTATAGGACTAGAATTACACCATGTTTTACTTACTTTAGGAAAGG
1 TGTATAGGACTAGAATTACACCATGTTTTACTTACTTTAGGAAAGG
53348277 TGTATAGGACTAGAATTACACCATGTTTTACTTACTTTAGGAAAGG
1 TGTATAGGACTAGAATTACACCATGTTTTACTTACTTTAGGAAAGG
53348323 T
1 T
53348324 TTATTCATGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (46 bp):
TGTATAGGACTAGAATTACACCATGTTTTACTTACTTTAGGAAAGG
Found at i:53356291 original size:234 final size:230
Alignment explanation
Indices: 53355755--53356312 Score: 820
Period size: 234 Copynumber: 2.4 Consensus size: 230
53355745 TGATTTTTTT
* * * * * * *
53355755 AATTATGTTGTTTCATGTTGATCACTGGTTTAAACTT-GTTGTGATCGGTGAAATTAGATGAA-T
1 AATTACGTTGTTTCATGCTGATCACTGCTTTAAA-TTAGTAGTGCTAGATGAAATTAGAT-AACT
* * *
53355818 TTGAGGCAGTTTAATGTTTTG-TTTAATCGAATCTTGTGTTTGCATGATCATATAATCGAGTTTT
64 TTGAGGCAATTTAATCTCTTGTTTTAATCGAATCTTGTGTTTGCATGATCATATAATCGAGTTTT
* *
53355882 GTTTGTCAAAGTTTTTTCTCCCTTATTTGATAAATTTGATGTTCTATTATTGGAAAAAAATGATT
129 GTTTGTCAAAGTTTTTTCCCCCTTATTTGAAAAATTTGATGTTCTATTATTGGAAAAAAATGATT
*
53355947 AGGAAAATGAAAGATGAATAATTGTGGAAAATTCTTT
194 AGGAAAATGAAAGATGAATAATTGTGGAAAATTCTTC
* *
53355984 AATTACGTTGTTTCATGCAGATCACTGCTTTAAATTAGTAGTGCTAGATGAAATTAGATGACTTT
1 AATTACGTTGTTTCATGCTGATCACTGCTTTAAATTAGTAGTGCTAGATGAAATTAGATAACTTT
* *
53356049 GAGGCAATTTAATCTCTTGTTTTGATCTAATCTTGTGTTTGCATGATCATATAATCGAGTTTTGT
66 GAGGCAATTTAATCTCTTGTTTTAATCGAATCTTGTGTTTGCATGATCATATAATCGAGTTTTGT
*
53356114 TTGTCAAGGTTCTTTTTCCCCCTTATTTGAAAAATTTG-TGGTTCTATTATTGGAAAAAAATGAT
131 TTGTCAAAG-T-TTTTTCCCCCTTATTTGAAAAATTTGAT-GTTCTATTATTGGAAAAAAATGAT
*
53356178 TAGGAAAATGAAAAGATTAATAATTGTAGG-AAATTCTTC
193 TAGGAAAATG-AAAGATGAATAATTGT-GGAAAATTCTTC
*
53356217 AATTACGTTGTTTCATGCTGATCAATTGCTTTAAATTAGTAGTGCTAGATGAAATTAGATAACTT
1 AATTACGTTGTTTCATGCTGATC-ACTGCTTTAAATTAGTAGTGCTAGATGAAATTAGATAACTT
*
53356282 TGAGGCAATTTAATCTCTTATTTTAATCGAA
65 TGAGGCAATTTAATCTCTTGTTTTAATCGAA
53356313 CCCAAATTTT
Statistics
Matches: 295, Mismatches: 25, Indels: 13
0.89 0.08 0.04
Matches are distributed among these distances:
228 3 0.01
229 67 0.23
230 51 0.17
231 2 0.01
232 58 0.20
233 45 0.15
234 69 0.23
ACGTcount: A:0.30, C:0.10, G:0.18, T:0.42
Consensus pattern (230 bp):
AATTACGTTGTTTCATGCTGATCACTGCTTTAAATTAGTAGTGCTAGATGAAATTAGATAACTTT
GAGGCAATTTAATCTCTTGTTTTAATCGAATCTTGTGTTTGCATGATCATATAATCGAGTTTTGT
TTGTCAAAGTTTTTTCCCCCTTATTTGAAAAATTTGATGTTCTATTATTGGAAAAAAATGATTAG
GAAAATGAAAGATGAATAATTGTGGAAAATTCTTC
Found at i:53356721 original size:228 final size:231
Alignment explanation
Indices: 53356319--53356849 Score: 635
Period size: 228 Copynumber: 2.3 Consensus size: 231
53356309 CGAACCCAAA
* * *
53356319 TTTTGTTTGTCAAGTTATTTTTTTCCTTATTTAATAATTTTGCTGTTAAATTTTTGATGAAAAAT
1 TTTTGTTTGTAAATTTATTTTTTT-CTTATTTAATAATTTTGCTGTTAAATTATTGATG-AAAAT
* * ** * *
53356384 TT-ATCAGTAAAAAGAGAAGATGAGTAATTGTTGAAATTTTTTTAATTATGTTGTTTCATGTGGA
64 TTGATCAGGAAAAAGAAAAGATGAACAATTGTTGAAATTTCTTTAATTATATTGTTTCATGTGGA
** * ** *
53356448 TCACTGCTTTAAACTCGTAGTGTTTTATGAAATTAAATGACTTTGAGGTGATTTAATCTATTGTT
129 TCACTGCTTTAAACTCGTAGTGTTAGATGAAATTAAATAACTTTGAGGCAACTTAATCTATTGTT
*
53356513 TTAAT-TGAATCTTGTGTTTGCATGATCAAATAATCAAG
194 TTAATCT-AATCTTGTGCTTGCATGATCAAATAATCAAG
* * * *
53356551 TTTTGTTTGTAAATTTA-TTTTTT-TTGTTTGATAGTTTTGATGTTAAATTATTGATGAAAATTT
1 TTTTGTTTGTAAATTTATTTTTTTCTTATTTAATAATTTTGCTGTTAAATTATTGATGAAAATTT
* * *
53356614 GATCAGGGAAAAGAAAAGATGAACAGTTGTTGAGAA-TTCTTT-CTTATATTGTTTCATGTTGG-
66 GATCAGGAAAAAGAAAAGATGAACAATTGTTGA-AATTTCTTTAATTATATTGTTTCATG-TGGA
* * *
53356676 TCACTGCTTTAAACTTGTAGTGTTAGATGAAATTAGATAACTTTGAGGCAACTTAATCTCTTGTT
129 TCACTGCTTTAAACTCGTAGTGTTAGATGAAATTAAATAACTTTGAGGCAACTTAATCTATTGTT
*
53356741 TTAATCTAATCTTGTGCTTGCATGATCATATAATCAAG
194 TTAATCTAATCTTGTGCTTGCATGATCAAATAATCAAG
* * * * *
53356779 TTCTTGTCTGCCAAGTTAAATTCTTTTTCTTATTTTATAATTTTGCTGTTAAATTATTGATGAAA
1 TT-TTGTTTG-TAAATT-TATT-TTTTTCTTATTTAATAATTTTGCTGTTAAATTATTGATGAAA
*
53356844 AATTGA
62 ATTTGA
53356850 GAGTGAATTG
Statistics
Matches: 253, Mismatches: 36, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
228 113 0.45
229 69 0.27
230 6 0.02
231 7 0.03
232 16 0.06
233 5 0.02
234 37 0.15
ACGTcount: A:0.30, C:0.08, G:0.16, T:0.46
Consensus pattern (231 bp):
TTTTGTTTGTAAATTTATTTTTTTCTTATTTAATAATTTTGCTGTTAAATTATTGATGAAAATTT
GATCAGGAAAAAGAAAAGATGAACAATTGTTGAAATTTCTTTAATTATATTGTTTCATGTGGATC
ACTGCTTTAAACTCGTAGTGTTAGATGAAATTAAATAACTTTGAGGCAACTTAATCTATTGTTTT
AATCTAATCTTGTGCTTGCATGATCAAATAATCAAG
Found at i:53361976 original size:39 final size:39
Alignment explanation
Indices: 53361933--53362011 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
53361923 AAGAAATTAG
53361933 TATGATTGTATAGACGTATTTATGTTAAATTTTAATGAC
1 TATGATTGTATAGACGTATTTATGTTAAATTTTAATGAC
53361972 TATGATTGTATAGACGTATTTATGTTAAATTTTAATGAC
1 TATGATTGTATAGACGTATTTATGTTAAATTTTAATGAC
53362011 T
1 T
53362012 CGAAGAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (39 bp):
TATGATTGTATAGACGTATTTATGTTAAATTTTAATGAC
Found at i:53365269 original size:198 final size:197
Alignment explanation
Indices: 53364931--53365330 Score: 773
Period size: 198 Copynumber: 2.0 Consensus size: 197
53364921 CCATATTAAT
*
53364931 GCCATACATAGTTTTGTATAAGAATCGACTAAATGATATCTCTAGACTATTCTACTTCCCCAAGT
1 GCCATACATAGTTTTGTATAAGAATAGACTAAATGATATCTCTAGACTATTCTACTTCCCCAAGT
53364996 CCCACATGAAGCACATTGTGTATGACGAACAAAAGATAGCAACATTCAATCAAACATATACTTTA
66 CCCACATGAAGCACATTGTGTATGACGAACAAAAGATAGCAACATTCAATCAAACATATACTTTA
*
53365061 TAAAATTACGTGCAGGTATAAAAAGTATATATATCTAAAGCATTACCTGTTGCTTTTCAACACGT
131 TAAAATTACGTGCAGGAAT-AAAAGTATATATATCTAAAGCATTACCTGTTGCTTTTCAACACGT
53365126 AAA
195 AAA
53365129 GCCATACATAGTTTTGTATAAGAATAGACTAAATGATATCTCTAGACTATTCTACTTCCCCAAGT
1 GCCATACATAGTTTTGTATAAGAATAGACTAAATGATATCTCTAGACTATTCTACTTCCCCAAGT
53365194 CCCACATGAAGCACATTGTGTATGACGAACAAAAGATAGCAACATTCAATCAAACATATACTTTA
66 CCCACATGAAGCACATTGTGTATGACGAACAAAAGATAGCAACATTCAATCAAACATATACTTTA
53365259 TAAAATTACGTGCAGGAATAAAAGTATATATATCTAAAGCATTACCTGTTGCTTTTCAACACGTA
131 TAAAATTACGTGCAGGAATAAAAGTATATATATCTAAAGCATTACCTGTTGCTTTTCAACACGTA
53365324 AA
196 AA
53365326 GCCAT
1 GCCAT
53365331 GGTCTTGATG
Statistics
Matches: 200, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
197 53 0.26
198 147 0.74
ACGTcount: A:0.39, C:0.19, G:0.13, T:0.29
Consensus pattern (197 bp):
GCCATACATAGTTTTGTATAAGAATAGACTAAATGATATCTCTAGACTATTCTACTTCCCCAAGT
CCCACATGAAGCACATTGTGTATGACGAACAAAAGATAGCAACATTCAATCAAACATATACTTTA
TAAAATTACGTGCAGGAATAAAAGTATATATATCTAAAGCATTACCTGTTGCTTTTCAACACGTA
AA
Found at i:53378373 original size:218 final size:223
Alignment explanation
Indices: 53377852--53378890 Score: 1012
Period size: 235 Copynumber: 4.6 Consensus size: 223
53377842 TGGGTGCTTA
* * ** * *
53377852 TATATATCATTGTTTTGAGTGATGTAATTGGTAAAGAATCTATGCTTTTTAGAGGCTTATGATGA
1 TATATAGCTTTGTTTTGAGTGATGTAATTATTAATGAATCTACGC-TTTTAGAGGCTTATGATGA
* **
53377917 TTAAGAATTGCCTACATTGTCAGACCTTCAGTTTGATGACAACAAAAAC-TACAAATCTGAGGCC
65 TTAAGAATTGCCTACATTGTCAGACCTTCAGTCTGATGA-AATTAAAACTTACAAATCTGAGGCC
*** * * * * *
53377981 TAAAGTCAATGATCGTAACTTAAAAACTTATTTTTTGTTGGT-AGACCA-AC-C-AATATC-A-T
129 TAAAGTTTCTGATCGTAACTT-AAAACTTA-TTTGTGATGGTGTGACCATACTCGATTGTCAACT
* * *
53378040 TTTCT--C--CTTATATCATGC-ATGTACTCTG
192 TTTCTCCCTACTTAAAACATGCGA-GTAGTCTG
* * * * * *
53378068 TGTATTGCTTTGTTTTGAGTGATGTAATTAGTGAA-GGACCTATGCTTTTAGAGGCTTATGATGA
1 TATATAGCTTTGTTTTGAGTGATGTAATTA-TTAATGAATCTACGCTTTTAGAGGCTTATGATGA
*
53378132 TTAAGAATTGCCTACATTGTCAGACCTAT-AGTCTGATGAAAATAGAAA-TTACAAATCTGAGGC
65 TTAAGAATTGCCTACATTGTCAGACCT-TCAGTCTGATGAAATTA-AAACTTACAAATCTGAGGC
* *
53378195 CTAAAGTTGCTGATCATAACTTAAAACTTATTTGTGATGGTG-GACCA-AC-CGATT-TC-A-TT
128 CTAAAGTTTCTGATCGTAACTTAAAACTTATTTGTGATGGTGTGACCATACTCGATTGTCAACTT
*
53378254 TTCTCCCTACATTAAAACATG-TATGTAGTCTG
193 TTCTCCCTAC-TTAAAACATGCGA-GTAGTCTG
53378286 TATATAGCTTTGTTTTGAGTGATGTAATTATTAATGAATCTACGCTTTTAGAGGCTTATGATGAT
1 TATATAGCTTTGTTTTGAGTGATGTAATTATTAATGAATCTACGCTTTTAGAGGCTTATGATGAT
*
53378351 TAAGAATTGCCTACATTGTCAGACCTTCAGTCTGATGAGATTAAAACTTACAAATCTGAGGCCTA
66 TAAGAATTGCCTACATTGTCAGACCTTCAGTCTGATGAAATTAAAACTTACAAATCTGAGGCCTA
* * * * ** * * *
53378416 ACGTTTCTGGTTGTAACTTAAAAGTTATTTGTGATGGTGTTGGTCATGCTTGATGGGCATGGACC
131 AAGTTTCTGATCGTAACTTAAAACTTATTTGTGATGGTG-TGACCATACTCGAT-----T-G-TC
*
53378481 AACTGTTTTCTCCCTATTTTAAAACATGCGAGTAGTCTG
188 AAC--TTTTCTCCCTA-CTTAAAACATGCGAGTAGTCTG
* * * * *
53378520 TATATGGCTTTGTTTTGAGTGATGT-ATCTATTAATGAATCTATGGATTTAAGAGGCTCATGATG
1 TATATAGCTTTGTTTTGAGTGATGTAAT-TATTAATGAATCTA-CGCTTTTAGAGGCTTATGATG
53378584 ATTAAGAATTGCCTACATTGTCAGACCTTCAGTCTGATGAAATTAAAACTTACAAATCTGAGGCC
64 ATTAAGAATTGCCTACATTGTCAGACCTTCAGTCTGATGAAATTAAAACTTACAAATCTGAGGCC
* * * ** * *
53378649 TAAAGTTTCTGGTTC-TAACTTAAAATTTAATTGTGATGGTGGTGGTCATGCTTG-TTGGGCATG
129 TAAAGTTTCT-GATCGTAACTTAAAACTTATTTGTGATGGT-GTGACCATACTCGATT--G--T-
* *
53378712 GACCAACCGTTTTCTCCCTATGTTAAAACATGCGAGTAGCCTG
187 ---CAA-C-TTTTCTCCCTA-CTTAAAACATGCGAGTAGTCTG
* * * * *
53378755 TATATGGCTTTGTTTTGAGTGATGTAACTATTAATGAATCTACGGATTTAAGAGGCTCATGATGA
1 TATATAGCTTTGTTTTGAGTGATGTAATTATTAATGAATCTAC-GCTTTTAGAGGCTTATGATGA
* *
53378820 TTAAGAATTGCCTACATTGTCAGACCTTCAGTCTGATGAAATTAAAAGTTATAAATCTGAGGCCT
65 TTAAGAATTGCCTACATTGTCAGACCTTCAGTCTGATGAAATTAAAACTTACAAATCTGAGGCCT
53378885 AAAGTT
130 AAAGTT
53378891 AAAACTTGGA
Statistics
Matches: 716, Mismatches: 61, Indels: 73
0.84 0.07 0.09
Matches are distributed among these distances:
213 26 0.04
214 13 0.02
215 91 0.13
216 34 0.05
217 10 0.01
218 162 0.23
220 3 0.00
221 1 0.00
222 3 0.00
227 1 0.00
229 1 0.00
230 3 0.00
231 2 0.00
233 2 0.00
234 68 0.09
235 291 0.41
236 5 0.01
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (223 bp):
TATATAGCTTTGTTTTGAGTGATGTAATTATTAATGAATCTACGCTTTTAGAGGCTTATGATGAT
TAAGAATTGCCTACATTGTCAGACCTTCAGTCTGATGAAATTAAAACTTACAAATCTGAGGCCTA
AAGTTTCTGATCGTAACTTAAAACTTATTTGTGATGGTGTGACCATACTCGATTGTCAACTTTTC
TCCCTACTTAAAACATGCGAGTAGTCTG
Found at i:53378662 original size:235 final size:234
Alignment explanation
Indices: 53378252--53378890 Score: 1039
Period size: 235 Copynumber: 2.7 Consensus size: 234
53378242 ACCGATTTCA
* * *
53378252 TTTTCTCCCTACATTAAAACATG-TATGTAGTCTGTATATAGCTTTGTTTTGAGTGATGTAAT-T
1 TTTTCTCCCTATATTAAAACATGCGA-GTAGTCTGTATATGGCTTTGTTTTGAGTGATGT-ATCT
* * * *
53378315 ATTAATGAATCTACGCTTTTAGAGGCTTATGATGATTAAGAATTGCCTACATTGTCAGACCTTCA
64 ATTAATGAATCTAGGATTTAAGAGGCTCATGATGATTAAGAATTGCCTACATTGTCAGACCTTCA
* * * *
53378380 GTCTGATGAGATTAAAACTTACAAATCTGAGGCCTAACGTTTCTGGTTGTAACTTAAAAGTTATT
129 GTCTGATGAAATTAAAACTTACAAATCTGAGGCCTAAAGTTTCTGGTTCTAACTTAAAAGTTAAT
* *
53378445 TGTGATGGTGTTGGTCATGCTTGATGGGCATGGACCAACTG
194 TGTGATGGTGGTGGTCATGCTTGATGGGCATGGACCAACCG
*
53378486 TTTTCTCCCTATTTTAAAACATGCGAGTAGTCTGTATATGGCTTTGTTTTGAGTGATGTATCTAT
1 TTTTCTCCCTATATTAAAACATGCGAGTAGTCTGTATATGGCTTTGTTTTGAGTGATGTATCTAT
53378551 TAATGAATCTATGGATTTAAGAGGCTCATGATGATTAAGAATTGCCTACATTGTCAGACCTTCAG
66 TAATGAATCTA-GGATTTAAGAGGCTCATGATGATTAAGAATTGCCTACATTGTCAGACCTTCAG
*
53378616 TCTGATGAAATTAAAACTTACAAATCTGAGGCCTAAAGTTTCTGGTTCTAACTTAAAATTTAATT
130 TCTGATGAAATTAAAACTTACAAATCTGAGGCCTAAAGTTTCTGGTTCTAACTTAAAAGTTAATT
*
53378681 GTGATGGTGGTGGTCATGCTTGTTGGGCATGGACCAACCG
195 GTGATGGTGGTGGTCATGCTTGATGGGCATGGACCAACCG
* * *
53378721 TTTTCTCCCTATGTTAAAACATGCGAGTAGCCTGTATATGGCTTTGTTTTGAGTGATGTAACTAT
1 TTTTCTCCCTATATTAAAACATGCGAGTAGTCTGTATATGGCTTTGTTTTGAGTGATGTATCTAT
53378786 TAATGAATCTACGGATTTAAGAGGCTCATGATGATTAAGAATTGCCTACATTGTCAGACCTTCAG
66 TAATGAATCTA-GGATTTAAGAGGCTCATGATGATTAAGAATTGCCTACATTGTCAGACCTTCAG
* *
53378851 TCTGATGAAATTAAAAGTTATAAATCTGAGGCCTAAAGTT
130 TCTGATGAAATTAAAACTTACAAATCTGAGGCCTAAAGTT
53378891 AAAACTTGGA
Statistics
Matches: 380, Mismatches: 22, Indels: 5
0.93 0.05 0.01
Matches are distributed among these distances:
233 2 0.01
234 67 0.18
235 311 0.82
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (234 bp):
TTTTCTCCCTATATTAAAACATGCGAGTAGTCTGTATATGGCTTTGTTTTGAGTGATGTATCTAT
TAATGAATCTAGGATTTAAGAGGCTCATGATGATTAAGAATTGCCTACATTGTCAGACCTTCAGT
CTGATGAAATTAAAACTTACAAATCTGAGGCCTAAAGTTTCTGGTTCTAACTTAAAAGTTAATTG
TGATGGTGGTGGTCATGCTTGATGGGCATGGACCAACCG
Found at i:53394163 original size:42 final size:42
Alignment explanation
Indices: 53394116--53394201 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
53394106 TGCACTTCTA
53394116 AACTTGAACATGTGTCCTATGGTATATTTCCCTAATAAGGCT
1 AACTTGAACATGTGTCCTATGGTATATTTCCCTAATAAGGCT
53394158 AACTTGAACATGTGTCCTATGGTATATTTCCCTAATAAGGCT
1 AACTTGAACATGTGTCCTATGGTATATTTCCCTAATAAGGCT
53394200 AA
1 AA
53394202 AGATAGTTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (42 bp):
AACTTGAACATGTGTCCTATGGTATATTTCCCTAATAAGGCT
Found at i:53401662 original size:14 final size:15
Alignment explanation
Indices: 53401643--53401677 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
53401633 TTAGTTTTTC
53401643 CATTTTTC-AAAATT
1 CATTTTTCAAAAATT
53401657 CATTTTTCAAAAATT
1 CATTTTTCAAAAATT
53401672 -ATTTTT
1 CATTTTT
53401678 AATTAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 14 0.70
15 6 0.30
ACGTcount: A:0.34, C:0.11, G:0.00, T:0.54
Consensus pattern (15 bp):
CATTTTTCAAAAATT
Found at i:53401955 original size:19 final size:21
Alignment explanation
Indices: 53401917--53401955 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
53401907 TTTTTAAAAA
*
53401917 AATATTTATATTATATTTTTT
1 AATATTTATATTAAATTTTTT
53401938 AATATTTA-A-TAAATTTTT
1 AATATTTATATTAAATTTTT
53401956 ACATTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 1 0.06
21 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
AATATTTATATTAAATTTTTT
Found at i:53402139 original size:10 final size:10
Alignment explanation
Indices: 53402124--53402148 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
53402114 AAACGAGCCG
53402124 GGCTAAGCTA
1 GGCTAAGCTA
53402134 GGCTAAGCTA
1 GGCTAAGCTA
53402144 GGCTA
1 GGCTA
53402149 GGCTTGAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.20, G:0.32, T:0.20
Consensus pattern (10 bp):
GGCTAAGCTA
Found at i:53406232 original size:32 final size:33
Alignment explanation
Indices: 53406170--53406232 Score: 76
Period size: 32 Copynumber: 1.9 Consensus size: 33
53406160 GAGGAATTCA
**
53406170 AAAAAAACGCTTCCACATAGGAGCTTTTTTCCC
1 AAAAAAACGCTTCCACATAGGAGCACTTTTCCC
*
53406203 AAAAATAC-CTTCCACAT-GGAAGCACTTTTC
1 AAAAAAACGCTTCCACATAGG-AGCACTTTTC
53406233 TTCGTGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
31 2 0.08
32 17 0.65
33 7 0.27
ACGTcount: A:0.35, C:0.27, G:0.11, T:0.27
Consensus pattern (33 bp):
AAAAAAACGCTTCCACATAGGAGCACTTTTCCC
Found at i:53406776 original size:15 final size:14
Alignment explanation
Indices: 53406753--53406803 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 14
53406743 TGTGAAAGTT
53406753 TTTTAAAAATAAAA
1 TTTTAAAAATAAAA
53406767 TTTTATAAAATAAAA
1 TTTTA-AAAATAAAA
*
53406782 TCTTAAAAATAATTAA
1 TTTTAAAAATAA--AA
53406798 TTTTAA
1 TTTTAA
53406804 TAACCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 12 0.38
15 13 0.41
16 7 0.22
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTTAAAAATAAAA
Found at i:53407705 original size:29 final size:29
Alignment explanation
Indices: 53407663--53407720 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
53407653 TGATGAGGAT
* * * *
53407663 TGGATTAAATTAGTTTCTCTATTATTAAA
1 TGGATCAAATTAGTCTTTATATTATTAAA
*
53407692 TGGATCAATTTAGTCTTTATATTATTAAA
1 TGGATCAAATTAGTCTTTATATTATTAAA
53407721 AAGATTGAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.34, C:0.07, G:0.10, T:0.48
Consensus pattern (29 bp):
TGGATCAAATTAGTCTTTATATTATTAAA
Found at i:53417197 original size:26 final size:26
Alignment explanation
Indices: 53417142--53417204 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
53417132 CTGAAGAAAT
* * *
53417142 TATTGAATTAGCTCGTAAGAACGATG
1 TATTGAACTGGCTCGTAAGAACGATA
*
53417168 TATTGAACTGGCTCGTAA-AAGTGATA
1 TATTGAACTGGCTCGTAAGAA-CGATA
*
53417194 TATTGTACTGG
1 TATTGAACTGG
53417205 GAGCGATGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 2 0.06
26 29 0.94
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (26 bp):
TATTGAACTGGCTCGTAAGAACGATA
Found at i:53417248 original size:45 final size:45
Alignment explanation
Indices: 53417163--53417248 Score: 118
Period size: 45 Copynumber: 1.9 Consensus size: 45
53417153 CTCGTAAGAA
* * ***
53417163 CGATGTATTGAACTGGCTCGTAAAAGTGATATATTGTACTGGGAG
1 CGATGTATTGAACTGGCTCATAAAAGCGATATACCATACTGGGAG
*
53417208 CGATGTATTGAACTGGCTCATAAGAGCGATATACCATACTG
1 CGATGTATTGAACTGGCTCATAAAAGCGATATACCATACTG
53417249 ACTCTCAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 35 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (45 bp):
CGATGTATTGAACTGGCTCATAAAAGCGATATACCATACTGGGAG
Found at i:53423465 original size:19 final size:18
Alignment explanation
Indices: 53423441--53423480 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
53423431 TTTTATACTA
53423441 TAATTAAAATT-AATTAAGC
1 TAATT-AAATTAAATTAA-C
53423460 TAATTAAATTAAATTAAC
1 TAATTAAATTAAATTAAC
53423478 TAA
1 TAA
53423481 ACTTTGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (18 bp):
TAATTAAATTAAATTAAC
Found at i:53424104 original size:21 final size:21
Alignment explanation
Indices: 53424080--53424138 Score: 82
Period size: 21 Copynumber: 2.7 Consensus size: 21
53424070 TATTCACATG
53424080 CCAACCAACCAATTTATGATT
1 CCAACCAACCAATTTATGATT
*
53424101 CCAACCAACCAATTTATTATT
1 CCAACCAACCAATTTATGATT
*
53424122 CACATGCCAACCAATTT
1 C-CA-ACCAACCAATTT
53424139 GTTTTATTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 21 0.62
22 2 0.06
23 11 0.32
ACGTcount: A:0.37, C:0.31, G:0.03, T:0.29
Consensus pattern (21 bp):
CCAACCAACCAATTTATGATT
Found at i:53429893 original size:308 final size:308
Alignment explanation
Indices: 53429335--53429952 Score: 1236
Period size: 308 Copynumber: 2.0 Consensus size: 308
53429325 TTTTTTCATG
53429335 ATATTGCTACTATAAGAGCACATTCGAATCATGAAAAACTAAATAAGTTCTCTCCTATAAGGTTC
1 ATATTGCTACTATAAGAGCACATTCGAATCATGAAAAACTAAATAAGTTCTCTCCTATAAGGTTC
53429400 TCATCAGTAATATTTTTCCAAGTACTTTTAATTGAGAACTTATTTTGAATACTGTAAAGTTATAC
66 TCATCAGTAATATTTTTCCAAGTACTTTTAATTGAGAACTTATTTTGAATACTGTAAAGTTATAC
53429465 TCACAGTTTTTAAAACTTGCAACTTCAGGTGCATCCAACCATAACGAGCTTTTAGATAGAATTAC
131 TCACAGTTTTTAAAACTTGCAACTTCAGGTGCATCCAACCATAACGAGCTTTTAGATAGAATTAC
53429530 CATATTCTATTGCTCATATTTTTCCTTCCACAATTTAAGTAGATATTTCACAGTCAAATATTTTG
196 CATATTCTATTGCTCATATTTTTCCTTCCACAATTTAAGTAGATATTTCACAGTCAAATATTTTG
53429595 ACTTTAACCCCTTAATGAGAATAATGATAAAAGAATATCACAAAGATA
261 ACTTTAACCCCTTAATGAGAATAATGATAAAAGAATATCACAAAGATA
53429643 ATATTGCTACTATAAGAGCACATTCGAATCATGAAAAACTAAATAAGTTCTCTCCTATAAGGTTC
1 ATATTGCTACTATAAGAGCACATTCGAATCATGAAAAACTAAATAAGTTCTCTCCTATAAGGTTC
53429708 TCATCAGTAATATTTTTCCAAGTACTTTTAATTGAGAACTTATTTTGAATACTGTAAAGTTATAC
66 TCATCAGTAATATTTTTCCAAGTACTTTTAATTGAGAACTTATTTTGAATACTGTAAAGTTATAC
53429773 TCACAGTTTTTAAAACTTGCAACTTCAGGTGCATCCAACCATAACGAGCTTTTAGATAGAATTAC
131 TCACAGTTTTTAAAACTTGCAACTTCAGGTGCATCCAACCATAACGAGCTTTTAGATAGAATTAC
53429838 CATATTCTATTGCTCATATTTTTCCTTCCACAATTTAAGTAGATATTTCACAGTCAAATATTTTG
196 CATATTCTATTGCTCATATTTTTCCTTCCACAATTTAAGTAGATATTTCACAGTCAAATATTTTG
53429903 ACTTTAACCCCTTAATGAGAATAATGATAAAAGAATATCACAAAGATA
261 ACTTTAACCCCTTAATGAGAATAATGATAAAAGAATATCACAAAGATA
53429951 AT
1 AT
53429953 CATAATCAAT
Statistics
Matches: 310, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
308 310 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (308 bp):
ATATTGCTACTATAAGAGCACATTCGAATCATGAAAAACTAAATAAGTTCTCTCCTATAAGGTTC
TCATCAGTAATATTTTTCCAAGTACTTTTAATTGAGAACTTATTTTGAATACTGTAAAGTTATAC
TCACAGTTTTTAAAACTTGCAACTTCAGGTGCATCCAACCATAACGAGCTTTTAGATAGAATTAC
CATATTCTATTGCTCATATTTTTCCTTCCACAATTTAAGTAGATATTTCACAGTCAAATATTTTG
ACTTTAACCCCTTAATGAGAATAATGATAAAAGAATATCACAAAGATA
Found at i:53439152 original size:15 final size:15
Alignment explanation
Indices: 53439132--53439169 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
53439122 ACAAAACGAT
53439132 AACATAAATAATTAA
1 AACATAAATAATTAA
* *
53439147 AACAT-AATATTTCA
1 AACATAAATAATTAA
53439161 AACATAAAT
1 AACATAAAT
53439170 GACTAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.61, C:0.11, G:0.00, T:0.29
Consensus pattern (15 bp):
AACATAAATAATTAA
Found at i:53443102 original size:19 final size:19
Alignment explanation
Indices: 53443074--53443110 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
53443064 GTGAAGGTTC
53443074 TTGATGAATATTTATATAA
1 TTGATGAATATTTATATAA
* *
53443093 TTGATTAATATTTTTATA
1 TTGATGAATATTTATATA
53443111 TTTAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (19 bp):
TTGATGAATATTTATATAA
Found at i:53443139 original size:33 final size:35
Alignment explanation
Indices: 53443080--53443155 Score: 113
Period size: 34 Copynumber: 2.2 Consensus size: 35
53443070 GTTCTTGATG
53443080 AATATTTATATAATTGATTAATATTTTTATAT-TTA
1 AATATTTATATAATT-ATTAATATTTTTATATATTA
53443115 AA-ATTTATATAATCT-TTAATATTTTTATATATTA
1 AATATTTATATAAT-TATTAATATTTTTATATATTA
53443149 AATATTT
1 AATATTT
53443156 TAAAAATCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
33 15 0.39
34 16 0.42
35 7 0.18
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (35 bp):
AATATTTATATAATTATTAATATTTTTATATATTA
Found at i:53443154 original size:17 final size:16
Alignment explanation
Indices: 53443099--53443156 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 16
53443089 ATAATTGATT
53443099 AATATTTTTATATTTA
1 AATATTTTTATATTTA
* *
53443115 AA-ATTTATATAATCTTT
1 AATATTTTTAT-AT-TTA
53443132 AATATTTTTATATATTA
1 AATATTTTTATAT-TTA
53443149 AATATTTT
1 AATATTTT
53443157 AAAAATCTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
15 7 0.21
16 4 0.12
17 16 0.47
18 7 0.21
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
AATATTTTTATATTTA
Found at i:53443164 original size:35 final size:33
Alignment explanation
Indices: 53443097--53443160 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
53443087 ATATAATTGA
*
53443097 TTAATATTTTTATATTTAAAATTTATATAATCT
1 TTAATATTTTTATATTTAAAATTTATAAAATCT
53443130 TTAATATTTTTATATATTAAATATTT-TAAAA
1 TTAATATTTTTATAT-TTAAA-ATTTATAAAA
53443161 ATCTATCGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 15 0.54
34 9 0.32
35 4 0.14
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (33 bp):
TTAATATTTTTATATTTAAAATTTATAAAATCT
Found at i:53445545 original size:47 final size:48
Alignment explanation
Indices: 53445491--53445588 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 48
53445481 AAGAATCAAA
*
53445491 CCAGACTTGTAGGC-GCGGTTGGACAAAGAATCAAGTAAGGTATTGGT
1 CCAGACTTGTAGGCAGCGGTTGGACAAAGAATCAAATAAGGTATTGGT
*
53445538 CCAGACTTGTAGGCAGGGGTTGGACAAAGAATCAAATAAGGTATTGGT
1 CCAGACTTGTAGGCAGCGGTTGGACAAAGAATCAAATAAGGTATTGGT
53445586 CCA
1 CCA
53445589 CAATAAGGCG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 14 0.29
48 34 0.71
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.22
Consensus pattern (48 bp):
CCAGACTTGTAGGCAGCGGTTGGACAAAGAATCAAATAAGGTATTGGT
Found at i:53446764 original size:20 final size:22
Alignment explanation
Indices: 53446730--53446780 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
53446720 TGTAATATCT
53446730 TTTAATATTTATATTT-TTTTAA
1 TTTAAT-TTTATATTTGTTTTAA
53446752 TTTAATTTT-TATTTGTTTTAA
1 TTTAATTTTATATTTGTTTTAA
*
53446773 TTAAATTT
1 TTTAATTT
53446781 AATTTTCCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 5 0.19
21 16 0.59
22 6 0.22
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTAATTTTATATTTGTTTTAA
Found at i:53446785 original size:20 final size:20
Alignment explanation
Indices: 53446730--53446786 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
53446720 TGTAATATCT
53446730 TTTAATATTTATATTTTTTTAA
1 TTTAA-ATTTA-ATTTTTTTAA
* *
53446752 TTTAATTTTTATTTGTTTTAA
1 TTTAAATTTAATTT-TTTTAA
53446773 -TTAAATTTAATTTT
1 TTTAAATTTAATTTT
53446787 CCATATTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 1 0.03
20 15 0.50
21 9 0.30
22 5 0.17
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTAAATTTAATTTTTTTAA
Found at i:53450163 original size:252 final size:250
Alignment explanation
Indices: 53449819--53450289 Score: 665
Period size: 252 Copynumber: 1.9 Consensus size: 250
53449809 ATTTGATCAA
** * * *
53449819 AAATTATTGAAAATACATAAAAATAAAAATTGAAAAAAAATTTTAAATAGTTCAATATCTAGTTC
1 AAATTATTGAAAATACATAAAAATAAAAATTGAAAAAAAATAATAAATACTCCAATATCTAGCTC
* * ** *
53449884 TATGAATGGTTCCAAAAATCACGAGGATAAAAAAATGTATTTTATAAAATACCAACATCTTTGCA
66 TATGAATGGTTCCAAAAATCACGAGGATAAAAAAATGTATTTCATAAAATACAAACAAATATGCA
* * * *
53449949 TCTCCATTTTGTCCCTAAATTTCTCTTTAGTGGCACACATAAAATTTTAAAGGGAGTTGTCCAAA
131 TCTCCATTTTGTCCCTAAACTTCTCTTTAGTGCCACACA-AAAAGTTTAAAAGGAGTTGTCCAAA
53450014 TAAACATCTTTCACTTGCTTCCCTAAAACCACGAACCTGGATGAATTCTATTACTG
195 TAAACATCTTTCACTTGCTTCCCTAAAACCACGAACCTGGATGAATTCTATTACTG
* *
53450070 AAATTATTGAAAATACATAAAAATAAAAAAATTGAAAAAAAA-AATAATTACTCCAATATCTTGC
1 AAATTATTGAAAATACATAAAAAT--AAAAATTGAAAAAAAATAATAAATACTCCAATATCTAGC
* * *
53450134 TCTATGAATGGTTCCAAAAATCTCGAGGATAACAAAATGTATTTCATAAAATACAAATAAATATG
64 TCTATGAATGGTTCCAAAAATCACGAGGATAAAAAAATGTATTTCATAAAATACAAACAAATATG
* * * * ** *
53450199 TATCTCCATTTTGTCTCTAAACTTCTTTTTGGTGCCACACACCACGTTTAAAAGGAGTTGTCCAA
129 CATCTCCATTTTGTCCCTAAACTTCTCTTTAGTGCCACACAAAAAGTTTAAAAGGAGTTGTCCAA
*
53450264 ATAAAGATCTTTCACTTGCTTCCCTA
194 ATAAACATCTTTCACTTGCTTCCCTA
53450290 GAAGCTTGAA
Statistics
Matches: 191, Mismatches: 27, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
251 68 0.36
252 107 0.56
253 16 0.08
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (250 bp):
AAATTATTGAAAATACATAAAAATAAAAATTGAAAAAAAATAATAAATACTCCAATATCTAGCTC
TATGAATGGTTCCAAAAATCACGAGGATAAAAAAATGTATTTCATAAAATACAAACAAATATGCA
TCTCCATTTTGTCCCTAAACTTCTCTTTAGTGCCACACAAAAAGTTTAAAAGGAGTTGTCCAAAT
AAACATCTTTCACTTGCTTCCCTAAAACCACGAACCTGGATGAATTCTATTACTG
Found at i:53454629 original size:33 final size:33
Alignment explanation
Indices: 53454565--53454629 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
53454555 ACCATGAACA
**
53454565 ACAAGCAGGGCACCTTATTAACCCATTTTCATT
1 ACAAGCAGGGCACCTTATTAACCCACCTTCATT
* * *
53454598 ACAATCAGGGCACCTTCTTAACCTACCTTCAT
1 ACAAGCAGGGCACCTTATTAACCCACCTTCAT
53454630 CTTCTTCAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.29, C:0.31, G:0.11, T:0.29
Consensus pattern (33 bp):
ACAAGCAGGGCACCTTATTAACCCACCTTCATT
Found at i:53457304 original size:2 final size:2
Alignment explanation
Indices: 53457297--53457321 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53457287 TGAAATAAAA
53457297 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
53457322 AATCAATCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:53465751 original size:15 final size:16
Alignment explanation
Indices: 53465731--53465764 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
53465721 AATTAACTTT
*
53465731 ATTTTTTTATATTTTA
1 ATTTTTATATATTTTA
53465747 ATTTTTGATATATTTTA
1 ATTTTT-ATATATTTTA
53465764 A
1 A
53465765 AATTTTCTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
ATTTTTATATATTTTA
Found at i:53469900 original size:23 final size:22
Alignment explanation
Indices: 53469873--53469923 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
53469863 AAAATATAAA
*
53469873 AATATATTA-AAAATGTTATGATG
1 AATATATTATAAAA-GTT-TAATG
53469896 AATATA-TATAAAAGTTTAATG
1 AATATATTATAAAAGTTTAATG
53469917 AATATAT
1 AATATAT
53469924 ATTAAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 10 0.40
22 5 0.20
23 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (22 bp):
AATATATTATAAAAGTTTAATG
Found at i:53479751 original size:21 final size:21
Alignment explanation
Indices: 53479725--53479768 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
53479715 GTTAACAAAC
* *
53479725 TTTAAGCTGAAATT-GATTATT
1 TTTAAG-TAAAATTCGAGTATT
53479746 TTTAAGTAAAATTCGAGTATT
1 TTTAAGTAAAATTCGAGTATT
53479767 TT
1 TT
53479769 GGATACAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.48
Consensus pattern (21 bp):
TTTAAGTAAAATTCGAGTATT
Found at i:53488184 original size:61 final size:59
Alignment explanation
Indices: 53488007--53488188 Score: 138
Period size: 61 Copynumber: 3.0 Consensus size: 59
53487997 AAAATTTAGA
* * * * * * *
53488007 AATAAATTTGACCCTCTAACAATTA-TATATTTTTCAATTTAATTTAAAATATAAAAAATT
1 AATAAATTT-ACCCTTTAACATTTACAAAATTTATCAATTTAATTTTAAAT-TTAAAAATT
* *** ** * *
53488067 AGTAAATTTAGTTTTTAATTTTTACAAAATTTGT-AATTTTAA--TTGAATTCTAAAAAATT
1 AATAAATTTACCCTTTAACATTTACAAAATTTATCAA-TTTAATTTTAAATT-T-AAAAATT
53488126 CAATAAATTTAACCCTTTAACATTTACAAAATTTATCAATTTAATTTTAAATTTAAAAATT
1 -AATAAATTT-ACCCTTTAACATTTACAAAATTTATCAATTTAATTTTAAATTTAAAAATT
53488187 AA
1 AA
53488189 AAAAAAACAT
Statistics
Matches: 91, Mismatches: 22, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
57 1 0.01
58 4 0.04
59 17 0.19
60 29 0.32
61 31 0.34
62 3 0.03
63 6 0.07
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (59 bp):
AATAAATTTACCCTTTAACATTTACAAAATTTATCAATTTAATTTTAAATTTAAAAATT
Found at i:53492397 original size:17 final size:17
Alignment explanation
Indices: 53492371--53492403 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
53492361 AAGTATGTAA
53492371 AATTACTTTAGTTTTAC
1 AATTACTTTAGTTTTAC
*
53492388 AATTATTTTAGTTTTA
1 AATTACTTTAGTTTTA
53492404 TATTATGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (17 bp):
AATTACTTTAGTTTTAC
Found at i:53499907 original size:17 final size:17
Alignment explanation
Indices: 53499885--53499922 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
53499875 AATAAAAAAA
53499885 ATAATGAGTAACATAAT
1 ATAATGAGTAACATAAT
53499902 ATAATGAGTAACATAAT
1 ATAATGAGTAACATAAT
53499919 ATAA
1 ATAA
53499923 GCATGTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.29
Consensus pattern (17 bp):
ATAATGAGTAACATAAT
Found at i:53503070 original size:7 final size:7
Alignment explanation
Indices: 53503057--53503096 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
53503047 TAAATATAAT
53503057 AAAAAAG
1 AAAAAAG
*
53503064 GAAAAAG
1 AAAAAAG
53503071 AAAAAAG
1 AAAAAAG
53503078 AAAAAAG
1 AAAAAAG
53503085 AAAAAAG
1 AAAAAAG
53503092 AAAAA
1 AAAAA
53503097 TGCACTGCAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:53504634 original size:12 final size:12
Alignment explanation
Indices: 53504617--53504642 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53504607 TATTCATAAA
53504617 CCCACTCCCAAT
1 CCCACTCCCAAT
53504629 CCCACTCCCAAT
1 CCCACTCCCAAT
53504641 CC
1 CC
53504643 GATGCTTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.62, G:0.00, T:0.15
Consensus pattern (12 bp):
CCCACTCCCAAT
Found at i:53508310 original size:35 final size:35
Alignment explanation
Indices: 53508220--53508302 Score: 123
Period size: 35 Copynumber: 2.4 Consensus size: 35
53508210 TTAACGTCAA
* * *
53508220 TGAATT-AAAGAGGCCATTAAACCTAAATTGATGTG
1 TGAATTAAAAGA-GACATTAAACCCAAATTGATGTC
53508255 TGAATTAAAAGAGACATTAAACCCAAATTGATGTC
1 TGAATTAAAAGAGACATTAAACCCAAATTGATGTC
53508290 TGAATTAAAAGAG
1 TGAATTAAAAGAG
53508303 TTATTAAATC
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
35 39 0.89
36 5 0.11
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.27
Consensus pattern (35 bp):
TGAATTAAAAGAGACATTAAACCCAAATTGATGTC
Found at i:53511493 original size:29 final size:29
Alignment explanation
Indices: 53511461--53511531 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 29
53511451 AAAATTACAT
* *
53511461 TTTAATCCCTCAAAATGATAAAAATTTGA
1 TTTAATCCCTAAAAATGATAAAAATTTAA
** *
53511490 TTTAATCTTTTAAAAATTATAAAAATTTAA
1 TTTAATC-CCTAAAAATGATAAAAATTTAA
53511520 TTTAA-CCCTAAA
1 TTTAATCCCTAAA
53511532 CCAAATTATC
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
28 4 0.12
29 8 0.24
30 22 0.65
ACGTcount: A:0.46, C:0.11, G:0.03, T:0.39
Consensus pattern (29 bp):
TTTAATCCCTAAAAATGATAAAAATTTAA
Found at i:53517184 original size:20 final size:22
Alignment explanation
Indices: 53517159--53517200 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
53517149 AAATAATTTT
53517159 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
53517179 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
53517201 TCATTTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:53517188 original size:29 final size:31
Alignment explanation
Indices: 53517119--53517197 Score: 128
Period size: 29 Copynumber: 2.6 Consensus size: 31
53517109 TTGAAAATTC
53517119 AAATAA-TTTAATAATTTTATTATTTCAAAA
1 AAATAATTTTAATAATTTTATTATTTCAAAA
*
53517149 AAATAATTTTAATAATTTTA-TATTT-TAAA
1 AAATAATTTTAATAATTTTATTATTTCAAAA
53517178 AAATAATTTTAATAATTTTA
1 AAATAATTTTAATAATTTTA
53517198 AAATCATTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
29 23 0.49
30 11 0.23
31 13 0.28
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (31 bp):
AAATAATTTTAATAATTTTATTATTTCAAAA
Found at i:53517201 original size:20 final size:20
Alignment explanation
Indices: 53517150--53517206 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
53517140 ATTTCAAAAA
53517150 AATAATTTT--AATAATTTT
1 AATAATTTTAAAATAATTTT
53517168 -AT-ATTTTAAAAAATAATTTT
1 AATAATTTT--AAAATAATTTT
*
53517188 AATAATTTTAAAATCATTT
1 AATAATTTTAAAATAATTT
53517207 ATTGACGTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 5 0.16
17 2 0.06
20 18 0.56
21 2 0.06
22 5 0.16
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
AATAATTTTAAAATAATTTT
Found at i:53526950 original size:2 final size:2
Alignment explanation
Indices: 53526943--53526981 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
53526933 AGCAACATAC
*
53526943 AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53526982 AAGTTAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:53534796 original size:6 final size:6
Alignment explanation
Indices: 53534780--53534823 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
53534770 TATTCAGCAA
*
53534780 CCCAAT TCCAAT CCCAAT CCCAAT CCCAAT CCCAAT CCCAAT CC
1 CCCAAT CCCAAT CCCAAT CCCAAT CCCAAT CCCAAT CCCAAT CC
53534824 GATGCTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (6 bp):
CCCAAT
Found at i:53545744 original size:30 final size:30
Alignment explanation
Indices: 53545690--53545777 Score: 99
Period size: 30 Copynumber: 2.9 Consensus size: 30
53545680 AATTTATGGT
*
53545690 AAAATTATATATTGATCCCTTTAAAGATGAAA
1 AAAATTATAT-TTGATCTCTTTAAAGAT-AAA
* * *
53545722 AAAATT-TATTTAATCTCTTTAAAAATAAT
1 AAAATTATATTTGATCTCTTTAAAGATAAA
53545751 AAAATTATATTTGGATCTC-TTAAAGAT
1 AAAATTATATTT-GATCTCTTTAAAGAT
53545778 TTTATAATTC
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
29 8 0.17
30 26 0.54
31 8 0.17
32 6 0.12
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (30 bp):
AAAATTATATTTGATCTCTTTAAAGATAAA
Found at i:53564549 original size:6 final size:6
Alignment explanation
Indices: 53564534--53564565 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
53564524 CATTCAGCAA
*
53564534 CCCAAT CCCAAC CCCAAT CCCAAT CCCAAT CC
1 CCCAAT CCCAAT CCCAAT CCCAAT CCCAAT CC
53564566 GATGCTTCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.31, C:0.56, G:0.00, T:0.12
Consensus pattern (6 bp):
CCCAAT
Found at i:53569576 original size:18 final size:17
Alignment explanation
Indices: 53569555--53569619 Score: 53
Period size: 18 Copynumber: 3.8 Consensus size: 17
53569545 AAGTTTACAC
53569555 TTTTTTAATTTTTGATAA
1 TTTTTTAATTTTT-ATAA
* *
53569573 TTTTTAAATATTTTAAAA
1 TTTTTTAAT-TTTTATAA
* *
53569591 TTTTCATAAATTTTAT-A
1 TTTT-TTAATTTTTATAA
53569608 -TTTTTAATTTTT
1 TTTTTTAATTTTT
53569620 TTTAAAATTA
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
15 7 0.19
16 3 0.08
17 1 0.03
18 20 0.54
19 6 0.16
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTTTAATTTTTATAA
Found at i:53569999 original size:59 final size:60
Alignment explanation
Indices: 53569907--53570094 Score: 218
Period size: 59 Copynumber: 3.1 Consensus size: 60
53569897 TTAATATAAT
* * * *
53569907 ATTTGGTGTTTGAATTTAATATTTTTTTTTAATTTGATATCTAAACTTTTTTT-GATTCA
1 ATTTGGTATTTGAATTTGATATTTTTTTCTAATTTGATACCTAAACTTTTTTTAGATTCA
* * **
53569966 ATTTGGTATTTGAATTTGACATTTTTTTCTAATTT-AGTACCTAAACTTTTTTTGGACCCA
1 ATTTGGTATTTGAATTTGATATTTTTTTCTAATTTGA-TACCTAAACTTTTTTTAGATTCA
* * * * * *
53570026 ATTTGGTATTTAAACTTGGTATTTTTTCCTAATTTGGTACCTAAGCTTTGTTTTAGATTCA
1 ATTTGGTATTTGAATTTGATATTTTTTTCTAATTTGATACCTAAACTTT-TTTTAGATTCA
53570087 ATTTGGTA
1 ATTTGGTA
53570095 CCTAAATTTA
Statistics
Matches: 108, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
58 1 0.01
59 46 0.43
60 45 0.42
61 16 0.15
ACGTcount: A:0.24, C:0.10, G:0.13, T:0.53
Consensus pattern (60 bp):
ATTTGGTATTTGAATTTGATATTTTTTTCTAATTTGATACCTAAACTTTTTTTAGATTCA
Found at i:53570030 original size:60 final size:58
Alignment explanation
Indices: 53569907--53570094 Score: 214
Period size: 60 Copynumber: 3.1 Consensus size: 58
53569897 TTAATATAAT
* * * *
53569907 ATTTGGTGTTTGAATTTAATATTTTTTTTTAATTTGATATCTAAACTTTTTTTGATTCA
1 ATTTGGTATTTGAATTTGATATTTTTTTCTAATTTG-TACCTAAACTTTTTTTGATTCA
* **
53569966 ATTTGGTATTTGAATTTGACATTTTTTTCTAATTTAGTACCTAAACTTTTTTTGGACCCA
1 ATTTGGTATTTGAATTTGATATTTTTTTCTAATTT-GTACCTAAACTTTTTTT-GATTCA
* * * * *
53570026 ATTTGGTATTTAAACTTGGTATTTTTTCCTAATTTGGTACCTAAGCTTTGTTTTAGATTCA
1 ATTTGGTATTTGAATTTGATATTTTTTTCTAATTT-GTACCTAAACTTT-TTTT-GATTCA
53570087 ATTTGGTA
1 ATTTGGTA
53570095 CCTAAATTTA
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
59 46 0.42
60 47 0.43
61 16 0.15
ACGTcount: A:0.24, C:0.10, G:0.13, T:0.53
Consensus pattern (58 bp):
ATTTGGTATTTGAATTTGATATTTTTTTCTAATTTGTACCTAAACTTTTTTTGATTCA
Found at i:53570389 original size:32 final size:31
Alignment explanation
Indices: 53570300--53570382 Score: 105
Period size: 32 Copynumber: 2.7 Consensus size: 31
53570290 TGGACCTCAA
* *
53570300 AAGTTTAAGTACCAACTTA-AAAAAAGTGTT
1 AAGTTTAAGTACCAAATTAGAAAAAAGTGTC
* * *
53570330 AAATTTAGGTACCAAATTAAGAAAAAAATGTC
1 AAGTTTAAGTACCAAATT-AGAAAAAAGTGTC
53570362 AAGTTTAAGTACCAAATTAGA
1 AAGTTTAAGTACCAAATTAGA
53570383 CCAAAAAAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 15 0.34
31 4 0.09
32 25 0.57
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAGAAAAAAGTGTC
Found at i:53570416 original size:28 final size:29
Alignment explanation
Indices: 53570333--53570416 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 29
53570323 AAGTGTTAAA
*
53570333 TTTAGGTACCAAATTAAGAAAAAAATGTCAAG
1 TTTAGATACCAAATTAAGAAAAAAA--T-AAG
* *
53570365 TTTA-AGTACCAAATT-AGACCAAAAA-AAT
1 TTTAGA-TACCAAATTAAGA-AAAAAATAAG
53570393 TTTAGATACCAAATTAAGAAAAAA
1 TTTAGATACCAAATTAAGAAAAAA
53570417 TATCACCAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
28 19 0.43
29 4 0.09
31 3 0.07
32 18 0.41
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.25
Consensus pattern (29 bp):
TTTAGATACCAAATTAAGAAAAAAATAAG
Found at i:53580837 original size:17 final size:17
Alignment explanation
Indices: 53580815--53580853 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
53580805 AGGTGGAGAA
*
53580815 CTTGTTCGTTGAGAATT
1 CTTGTTCGTAGAGAATT
53580832 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
53580849 CTTGT
1 CTTGT
53580854 CAAGGTGGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:53581224 original size:17 final size:16
Alignment explanation
Indices: 53581193--53581226 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
53581183 TTTCTTTACG
*
53581193 TTTTCTTTGCGATATT
1 TTTTCATTGCGATATT
53581209 TTTTCATTGTCGATATT
1 TTTTCATTG-CGATATT
53581226 T
1 T
53581227 AATTTTATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.15, C:0.12, G:0.12, T:0.62
Consensus pattern (16 bp):
TTTTCATTGCGATATT
Found at i:53605491 original size:12 final size:13
Alignment explanation
Indices: 53605474--53605506 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
53605464 CCGAAAATTT
53605474 AAATATG-TCAAA
1 AAATATGCTCAAA
53605486 AAATATGGCTCAAA
1 AAATAT-GCTCAAA
53605500 AAATATG
1 AAATATG
53605507 GTTATTTCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 2 0.11
14 11 0.58
ACGTcount: A:0.55, C:0.09, G:0.12, T:0.24
Consensus pattern (13 bp):
AAATATGCTCAAA
Found at i:53605500 original size:14 final size:14
Alignment explanation
Indices: 53605481--53605507 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
53605471 TTTAAATATG
53605481 TCAAAAAATATGGC
1 TCAAAAAATATGGC
53605495 TCAAAAAATATGG
1 TCAAAAAATATGG
53605508 TTATTTCTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.11, G:0.15, T:0.22
Consensus pattern (14 bp):
TCAAAAAATATGGC
Found at i:53607085 original size:6 final size:6
Alignment explanation
Indices: 53607074--53607113 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
53607064 ACTGATTATA
53607074 CTCCAT CTCCAT CTCCAT CTCCAT CTCCAT CTCCAT CTCC
1 CTCCAT CTCCAT CTCCAT CTCCAT CTCCAT CTCCAT CTCC
53607114 GTTCCTTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.15, C:0.53, G:0.00, T:0.33
Consensus pattern (6 bp):
CTCCAT
Found at i:53620798 original size:25 final size:23
Alignment explanation
Indices: 53620770--53620816 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
53620760 AGTTGGATCC
53620770 GAATTAAATTCTAAAAAGATAATTA
1 GAATTAAA-TCTAAAAA-ATAATTA
*
53620795 GAATTAAATCTAAACAATAATT
1 GAATTAAATCTAAAAAATAATT
53620817 TCCTAATTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 7 0.33
25 8 0.38
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (23 bp):
GAATTAAATCTAAAAAATAATTA
Found at i:53620905 original size:13 final size:13
Alignment explanation
Indices: 53620884--53620917 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
53620874 ATATAACAAT
53620884 AATAATAATCCTA
1 AATAATAATCCTA
*
53620897 AATATTAATCCTA
1 AATAATAATCCTA
*
53620910 AAAAATAA
1 AATAATAA
53620918 AATTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:53622467 original size:68 final size:70
Alignment explanation
Indices: 53622383--53622514 Score: 205
Period size: 68 Copynumber: 1.9 Consensus size: 70
53622373 GCTTGTTGAG
* * *
53622383 AAGGTAGCAGCAACTCAACTCTATGAGACTCCCAAACAAGC-T-ATAAGCTGAAGGAGGAGTTCC
1 AAGGCAGCAGCAACTCAACCCTATAAGACTCCCAAACAAGCTTAATAAGCTGAAGGAGGAGTTCC
53622446 AAGGT
66 AAGGT
*
53622451 AAGGCAGCAGCAACTCAACCCTGTAAGACTCCCAAACAAGCTTAGATAAGCTGAAGGAGGAGTT
1 AAGGCAGCAGCAACTCAACCCTATAAGACTCCCAAACAAGCTTA-ATAAGCTGAAGGAGGAGTT
53622515 GATGGAGCAT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
68 37 0.65
69 1 0.02
71 19 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (70 bp):
AAGGCAGCAGCAACTCAACCCTATAAGACTCCCAAACAAGCTTAATAAGCTGAAGGAGGAGTTCC
AAGGT
Found at i:53626553 original size:11 final size:11
Alignment explanation
Indices: 53626539--53626610 Score: 62
Period size: 11 Copynumber: 6.8 Consensus size: 11
53626529 TAATTTAGAG
*
53626539 TTAAATTGATT
1 TTAAATTTATT
53626550 TTAAATTTA-T
1 TTAAATTTATT
*
53626560 TTAAATTTATC
1 TTAAATTTATT
*
53626571 TTAAATTTAAAT
1 TTAAATTT-ATT
53626583 TT-AA-TTA-T
1 TTAAATTTATT
**
53626591 TTAAATTTACC
1 TTAAATTTATT
53626602 TTAAATTTA
1 TTAAATTTA
53626611 AATTAAAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
8 3 0.06
9 3 0.06
10 15 0.29
11 27 0.53
12 3 0.06
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.54
Consensus pattern (11 bp):
TTAAATTTATT
Found at i:53626567 original size:6 final size:6
Alignment explanation
Indices: 53626549--53626631 Score: 59
Period size: 6 Copynumber: 14.0 Consensus size: 6
53626539 TTAAATTGAT
53626549 TTTAAA TTT--A TTTAAA TTT--A TCTTAAA TTTAAA TTTAATTA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAA--A TTTAAA
* * * *
53626596 TTT-AC CTTAAA TTTAAA TTAAAA TACTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
53626632 CATTAAAAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
4 6 0.10
5 5 0.08
6 37 0.62
7 6 0.10
8 6 0.10
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:53626594 original size:31 final size:31
Alignment explanation
Indices: 53626556--53626614 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
53626546 GATTTTAAAT
*
53626556 TTATTTAAATTTATCTTAAATTTAAATTTAA
1 TTATTTAAATTTACCTTAAATTTAAATTTAA
53626587 TTATTTAAATTTACCTTAAATTTAAATT
1 TTATTTAAATTTACCTTAAATTTAAATT
53626615 AAAATACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (31 bp):
TTATTTAAATTTACCTTAAATTTAAATTTAA
Found at i:53626616 original size:11 final size:11
Alignment explanation
Indices: 53626550--53626617 Score: 52
Period size: 11 Copynumber: 6.5 Consensus size: 11
53626540 TAAATTGATT
*
53626550 TTAAATTT-AT
1 TTAAATTTAAA
**
53626560 TTAAATTTATC
1 TTAAATTTAAA
53626571 TTAAATTTAAA
1 TTAAATTTAAA
* *
53626582 TTTAA-TT-AT
1 TTAAATTTAAA
**
53626591 TTAAATTTACC
1 TTAAATTTAAA
53626602 TTAAATTTAAA
1 TTAAATTTAAA
53626613 TTAAA
1 TTAAA
53626618 ATACTAAATT
Statistics
Matches: 44, Mismatches: 11, Indels: 5
0.73 0.18 0.08
Matches are distributed among these distances:
9 5 0.11
10 12 0.27
11 27 0.61
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:53627356 original size:13 final size:13
Alignment explanation
Indices: 53627338--53627362 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53627328 ATAAGAAGGT
53627338 TTTATTAATAATA
1 TTTATTAATAATA
53627351 TTTATTAATAAT
1 TTTATTAATAAT
53627363 TAATAATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTATTAATAATA
Found at i:53628505 original size:59 final size:58
Alignment explanation
Indices: 53628439--53628690 Score: 274
Period size: 59 Copynumber: 4.3 Consensus size: 58
53628429 CCAAATAGTT
* * * ** * *
53628439 CAAAAATT-GCATTTTGACCCCAAAATTTTAGAAAATTATATTTTTAACCTCGATTTCAT
1 CAAAAATTACCATTTT-ACCCCCAAACTTTCCAAAATT-TATTTTTAACCTCAATTTCAC
* * *
53628498 CAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCAATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATT-TATTTTTAACCTCAATTTCAC
53628557 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTTCATTTTTTAACCTCAATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTT-A-TTTTTAACCTCAATTTCAC
** * * * **
53628617 CAAAAATTACCATTTTACCCCTGAACTCTCTAAAATTCCATTTTTAACCTTGATTTCAC
1 CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATT-TATTTTTAACCTCAATTTCAC
*
53628676 C-GAAATTACCATTTT
1 CAAAAATTACCATTTT
53628691 GCCCTCGGGT
Statistics
Matches: 167, Mismatches: 22, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
58 13 0.08
59 96 0.57
60 58 0.35
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.37
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTTATTTTTAACCTCAATTTCAC
Found at i:53628631 original size:60 final size:59
Alignment explanation
Indices: 53628478--53628690 Score: 311
Period size: 59 Copynumber: 3.6 Consensus size: 59
53628468 AGAAAATTAT
* *
53628478 ATTTTTAACCTCGATTTCATCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCC
1 ATTTTTAACCTCAATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCC
* * *
53628537 ATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTTC
1 ATTTTTAACCTCAATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCC
* * *
53628596 ATTTTTTAACCTCAATTTCACCAAAAATTACCATTTTACCCCTGAACTCTCTAAAATTCC
1 A-TTTTTAACCTCAATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCC
** *
53628656 ATTTTTAACCTTGATTTCACC-GAAATTACCATTTT
1 ATTTTTAACCTCAATTTCACCAAAAATTACCATTTT
53628691 GCCCTCGGGT
Statistics
Matches: 139, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
58 13 0.09
59 73 0.53
60 53 0.38
ACGTcount: A:0.33, C:0.28, G:0.02, T:0.37
Consensus pattern (59 bp):
ATTTTTAACCTCAATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCC
Found at i:53654362 original size:16 final size:16
Alignment explanation
Indices: 53654343--53654373 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53654333 TCCTTTGTTT
*
53654343 ATATATTTATTTTAAA
1 ATATATTTATATTAAA
53654359 ATATATTTATATTAA
1 ATATATTTATATTAA
53654374 TAAAAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATATTTATATTAAA
Found at i:53654618 original size:6 final size:6
Alignment explanation
Indices: 53654619--53654646 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
53654609 TTTAAATTTA
53654619 AAAATT AAAATT AAAATT AAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAA
53654647 CAAAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:53654632 original size:13 final size:13
Alignment explanation
Indices: 53654610--53654646 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
53654600 ATAAAGGGGT
*
53654610 TTAAATTTAAAAA
1 TTAAAATTAAAAA
53654623 TTAAAATT-AAAA
1 TTAAAATTAAAAA
53654635 TTAAAATTAAAA
1 TTAAAATTAAAA
53654647 CAAAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TTAAAATTAAAAA
Found at i:53682198 original size:21 final size:19
Alignment explanation
Indices: 53682158--53682199 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
53682148 ACATCATAAC
*
53682158 CAAACAAGTTAACAAGTTA
1 CAAACAAATTAACAAGTTA
53682177 CAAACTAAATTAACATAGTTA
1 CAAAC-AAATTAACA-AGTTA
53682198 CA
1 CA
53682200 TTAAAAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 8 0.40
21 7 0.35
ACGTcount: A:0.52, C:0.17, G:0.07, T:0.24
Consensus pattern (19 bp):
CAAACAAATTAACAAGTTA
Found at i:53691513 original size:85 final size:85
Alignment explanation
Indices: 53691368--53691530 Score: 245
Period size: 85 Copynumber: 1.9 Consensus size: 85
53691358 TCGCTTCATT
* * * *
53691368 GATTTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACCGCTTCATTGATTTAATCCACTTCTC
1 GATTTGGCCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTTAACCCACTTCTC
53691433 TATATCTCATCAGAAAGGCG
66 TATATCTCATCAGAAAGGCG
* * * *
53691453 GATTTGGCCCACTTCTTTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTC
1 GATTTGGCCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTTAACCCACTTCTC
*
53691518 TGTATCTCATCAG
66 TATATCTCATCAG
53691531 GAAGATGACC
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
85 69 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (85 bp):
GATTTGGCCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTCATTGATTTAACCCACTTCTC
TATATCTCATCAGAAAGGCG
Found at i:53691531 original size:48 final size:48
Alignment explanation
Indices: 53691455--53691585 Score: 235
Period size: 48 Copynumber: 2.7 Consensus size: 48
53691445 GAAAGGCGGA
* *
53691455 TTTGGCCCACTTCTTTGTATCTCATCAGGAAGATGACCACTTTATTGC
1 TTTGACCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGC
53691503 TTTGACCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGC
1 TTTGACCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGC
*
53691551 TTTGACCCACTTCTCTGTATCTTATCAGGAAGATG
1 TTTGACCCACTTCTCTGTATCTCATCAGGAAGATG
53691586 GGGTTTGAAG
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 80 1.00
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (48 bp):
TTTGACCCACTTCTCTGTATCTCATCAGGAAGATGACCACTTTATTGC
Found at i:53691674 original size:48 final size:48
Alignment explanation
Indices: 53691618--53691709 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
53691608 TGAGCTTCGC
* * *
53691618 TTCATTGATTTGGTCTATTTCTCTGTATCTCATCA-AGAAGATGACCGT
1 TTCATTGATTTGATCCACTTCTCTGTATCTCATCAGA-AAGATGACCGT
53691666 TTCATTGATTTGATCCACTTCTCTGTATCTCATCAGAAAGATGA
1 TTCATTGATTTGATCCACTTCTCTGTATCTCATCAGAAAGATGA
53691710 TCGCTTTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 39 0.98
49 1 0.03
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (48 bp):
TTCATTGATTTGATCCACTTCTCTGTATCTCATCAGAAAGATGACCGT
Found at i:53691732 original size:48 final size:48
Alignment explanation
Indices: 53691636--53691747 Score: 129
Period size: 48 Copynumber: 2.3 Consensus size: 48
53691626 TTTGGTCTAT
* *
53691636 TTCTCTGTATCTCATCAAGAAGATGACCGTTTCATTGATTTGATCCAC
1 TTCTCTGTATCTCATCAAGAAGATGACCGTTTCATTGATTTAACCCAC
* *
53691684 TTCTCTGTATCTCATC-AGAAAGATGATCGCTTT-ATTGTTTTAACCCAC
1 TTCTCTGTATCTCATCAAG-AAGATGACCG-TTTCATTGATTTAACCCAC
* * *
53691732 TTTTTTATATCTCATC
1 TTCTCTGTATCTCATC
53691748 GGGAAGATAG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
47 2 0.04
48 50 0.91
49 3 0.05
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (48 bp):
TTCTCTGTATCTCATCAAGAAGATGACCGTTTCATTGATTTAACCCAC
Found at i:53691755 original size:171 final size:169
Alignment explanation
Indices: 53691463--53691879 Score: 564
Period size: 171 Copynumber: 2.4 Consensus size: 169
53691453 GATTTGGCCC
* *
53691463 ACTTCTTTGTATCTCATCAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTGTATCTCAT
1 ACTTCTCTGTATCTCATCAAGAAGATGACC-CTTTATTGCTTTGA-CCACTTCTCTGTATCTCAT
* * * * *
53691528 CAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTCTGTATCTTATCAGGAAGATGGGGTTTG
64 CAGAAAGATGACCACTTTATTGCTTTAACCCACTTCTCTATATCTCATCAGGAAGATAGGGTTTG
* * *
53691593 AAGTCTCACTCGTATTGAGCTTCGCTTCATTGATTTGGTCT
129 AAATCTCACTCATATTGAGCTTCGCTTCATTGATTTGATCT
* * *
53691634 ATTTCTCTGTATCTCATCAAGAAGATGACCGTTTCATTGATTTGATCCACTTCTCTGTATCTCAT
1 ACTTCTCTGTATCTCATCAAGAAGATGACCCTTT-ATTGCTTTGA-CCACTTCTCTGTATCTCAT
* * * * * *
53691699 CAGAAAGATGATCGCTTTATTGTTTTAACCCACTTTTTTATATCTCATCGGGAAGATAGGGTTTG
64 CAGAAAGATGACCACTTTATTGCTTTAACCCACTTCTCTATATCTCATCAGGAAGATAGGGTTTG
* *
53691764 AAATCTCATTCATATTGAGCTTTGCTTCATTGATTTGATCT
129 AAATCTCACTCATATTGAGCTTCGCTTCATTGATTTGATCT
* * *
53691805 ACTTCTCTGTATCTCATCAAAAAGATAACACCTTTATTGCTTTGACTCACTTCTTTGTATCTCAT
1 ACTTCTCTGTATCTCATCAAGAAGATGAC-CCTTTATTGCTTTGAC-CACTTCTCTGTATCTCAT
53691870 CAGAAAGATG
64 CAGAAAGATG
53691880 GGGTTTGAAG
Statistics
Matches: 215, Mismatches: 28, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
170 4 0.02
171 207 0.96
172 4 0.02
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (169 bp):
ACTTCTCTGTATCTCATCAAGAAGATGACCCTTTATTGCTTTGACCACTTCTCTGTATCTCATCA
GAAAGATGACCACTTTATTGCTTTAACCCACTTCTCTATATCTCATCAGGAAGATAGGGTTTGAA
ATCTCACTCATATTGAGCTTCGCTTCATTGATTTGATCT
Found at i:53691987 original size:123 final size:122
Alignment explanation
Indices: 53691666--53691989 Score: 427
Period size: 123 Copynumber: 2.6 Consensus size: 122
53691656 AGATGACCGT
* * *
53691666 TTCATTGATTTGATCCACTTCTCTGTATCTCATC-AGAAAGATGATCGCTTTATTGTTTTAACCC
1 TTCATTGATTTGATCTACTTCTCTGTATCTCATCAAG-AAGATGACCGCTTTATTGATTTAA-CC
* * * * *
53691730 ACTTTTTTATATCTCATCGGGAAGATAGGGTTTGAAATCTCATTCATATTGAGCTTTGC
64 ACTTCTTTGTATCTCATCAGAAAGATAGGGTTTGAAATCTCATTCATATTAAGCTTTGC
* * * *
53691789 TTCATTGATTTGATCTACTTCTCTGTATCTCATCAAAAAGATAACAC-CTTTATTGCTTTGACTC
1 TTCATTGATTTGATCTACTTCTCTGTATCTCATCAAGAAGATGAC-CGCTTTATTGATTTAAC-C
* *
53691853 ACTTCTTTGTATCTCATCAGAAAGATGGGGTTTGAAGTCTCATTCATATTAAGCTTTGC
64 ACTTCTTTGTATCTCATCAGAAAGATAGGGTTTGAAATCTCATTCATATTAAGCTTTGC
* * *
53691912 TTCATTGATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCCTCATTGATTTAATCCA
1 TTCATTGATTTGATCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTTATTGATTTAA-CCA
*
53691977 CTTCTCTGTATCT
65 CTTCTTTGTATCT
53691990 AGTCAAGAAG
Statistics
Matches: 175, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
122 2 0.01
123 170 0.97
124 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.41
Consensus pattern (122 bp):
TTCATTGATTTGATCTACTTCTCTGTATCTCATCAAGAAGATGACCGCTTTATTGATTTAACCAC
TTCTTTGTATCTCATCAGAAAGATAGGGTTTGAAATCTCATTCATATTAAGCTTTGC
Found at i:53692063 original size:85 final size:85
Alignment explanation
Indices: 53691918--53692074 Score: 224
Period size: 85 Copynumber: 1.8 Consensus size: 85
53691908 TTGCTTCATT
* * * *
53691918 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATGACCGCCTCATTGATTTAATCCACTTCTC
1 GATTTGGTCCACTTCTCTATATCTCATCAAGAAGATGACCACCTCATTGATTTAACCCACTTCTC
53691983 TGTATCTAGTCAAGAAGGCG
66 TGTATCTAGTCAAGAAGGCG
* * * * * *
53692003 GATTTGGTCCACTTCTCTATATCTCATTAGGAAGATGACCACTTTATTGCTTTGACCCACTTCTC
1 GATTTGGTCCACTTCTCTATATCTCATCAAGAAGATGACCACCTCATTGATTTAACCCACTTCTC
53692068 TGTATCT
66 TGTATCT
53692075 CATCAGGAAG
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
85 62 1.00
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.37
Consensus pattern (85 bp):
GATTTGGTCCACTTCTCTATATCTCATCAAGAAGATGACCACCTCATTGATTTAACCCACTTCTC
TGTATCTAGTCAAGAAGGCG
Found at i:53692252 original size:159 final size:159
Alignment explanation
Indices: 53692059--53692366 Score: 447
Period size: 159 Copynumber: 1.9 Consensus size: 159
53692049 TTGCTTTGAC
* * *
53692059 CCACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCGTATTGAGCTTCGCTTCA
1 CCACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCATATTAAGCTTCGCCTCA
* * * * *
53692124 TTGATTTGGTCTACTTCTCTGTAT-TCATCAAGAAGATGACTGCCTCATTGTTTCAATCCACTTC
66 TTGATTTGGTATACTTCTCTATATCTCATCAAGAAGATGACAGCCTCATTGTCT-AACCCACTTC
*
53692188 TCTGTATCTCATCAGGAAGACAGATTTGGT
130 TCTATATCTCATCAGGAAGACAGATTTGGT
* * *
53692218 CCACTTCTTTGTATCTCATCAGGAAGATGGGGTTTGAAGTCTCATTCATATTAAGCTTTGCCTCA
1 CCACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCATATTAAGCTTCGCCTCA
* * * *
53692283 TTGATTTGGTATACTTCTTTATATCTCATCAAGAAGATGACAGCTTCGTTGTCTGACCCACTTCT
66 TTGATTTGGTATACTTCTCTATATCTCATCAAGAAGATGACAGCCTCATTGTCTAACCCACTTCT
*
53692348 CTATATCTCATCATGAAGA
131 CTATATCTCATCAGGAAGA
53692367 TGGGGTTTGA
Statistics
Matches: 131, Mismatches: 17, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
159 106 0.81
160 25 0.19
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (159 bp):
CCACTTCTCTGTATCTCATCAGGAAGATGAGGTTTGAAGTCTCATTCATATTAAGCTTCGCCTCA
TTGATTTGGTATACTTCTCTATATCTCATCAAGAAGATGACAGCCTCATTGTCTAACCCACTTCT
CTATATCTCATCAGGAAGACAGATTTGGT
Found at i:53692447 original size:46 final size:46
Alignment explanation
Indices: 53692382--53692569 Score: 217
Period size: 46 Copynumber: 4.2 Consensus size: 46
53692372 TTTGATCTAT
53692382 CCCTCTTGAC-TAGGGGTAAAAGATCAGAATGTGGCTTCAATCTGC
1 CCCTCTTGACTTAGGGGTAAAAGATCAGAATGTGGCTTCAATCTGC
* ** *
53692427 CTCTCTTGACTTAGGGGTAAAAGATTGGAATGTGGCTTCAATCTGT
1 CCCTCTTGACTTAGGGGTAAAAGATCAGAATGTGGCTTCAATCTGC
* * *
53692473 CTCTCTTAACTT-GGGGTAAATGA-CTAG-ATGATGGCTTCAATCTGC
1 CCCTCTTGACTTAGGGGTAAAAGATC-AGAATG-TGGCTTCAATCTGC
* * * *
53692518 CCCTCTTGACTTAAGGATAAAAGAT-TGAATGT-TCTTCAATCTGC
1 CCCTCTTGACTTAGGGGTAAAAGATCAGAATGTGGCTTCAATCTGC
53692562 CCCTCTTG
1 CCCTCTTG
53692570 GATGGTCTTC
Statistics
Matches: 121, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
44 22 0.18
45 45 0.37
46 54 0.45
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (46 bp):
CCCTCTTGACTTAGGGGTAAAAGATCAGAATGTGGCTTCAATCTGC
Found at i:53692896 original size:49 final size:49
Alignment explanation
Indices: 53692720--53692967 Score: 187
Period size: 49 Copynumber: 5.0 Consensus size: 49
53692710 TCTTTCTAAA
* * *
53692720 GGTACCGGGTTCACCGTTGTGACCTCAACCTTTCCTTTCATATCTTCAT
1 GGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCAT
* * ** * * * * * * *
53692769 GGTATCGGATTCATTGCTGCGACCTCGATCC-TCCCCATCACATCTTCTAA
1 GGTACCGGGTTCACCGTTGCGGCCTC-AACCTTTCCCTTCATATCTTC-AT
* * * * *
53692819 GGTACCGGGTTCGCTGTTGTGGCTTCAACCTTTCCCTTCATGTCTTCAT
1 GGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCAT
* * *
53692868 GGTACCGGGTTCATCATTGCGGCCTCAACCTTTCCCATCTCAT-T-TTCTAA
1 GGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCC-T-TCATATCTTC-AT
* * * * *
53692918 GGTACCGAGTTCGCCGTTACGGCCTCAACATTTCCCTTCAAATCTTCAT
1 GGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCAT
53692967 G
1 G
53692968 TTTTCTTAGT
Statistics
Matches: 150, Mismatches: 41, Indels: 16
0.72 0.20 0.08
Matches are distributed among these distances:
48 3 0.02
49 73 0.49
50 70 0.47
51 4 0.03
ACGTcount: A:0.17, C:0.31, G:0.18, T:0.34
Consensus pattern (49 bp):
GGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCAT
Found at i:53692905 original size:99 final size:99
Alignment explanation
Indices: 53692713--53692967 Score: 296
Period size: 99 Copynumber: 2.6 Consensus size: 99
53692703 TCTTTAATCT
* * * *
53692713 TTCTAAAGGTACCGGGTTCACCGTTGTGACCTCAACCTTTCCTTTCATATCTTCATGGTATCGGA
1 TTCT-AAGGTACCGGGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGA
** *
53692778 TTCATTGCTGCGACCTCGATCCTCCCCATCACATC
65 TTCATCACTGCGACCTCGAACCTCCCCATCACATC
* * * *
53692813 TTCTAAGGTACCGGGTTCGCTGTTGTGGCTTCAACCTTTCCCTTCATGTCTTCATGGTACCGGGT
1 TTCTAAGGTACCGGGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGAT
* * * * *
53692878 TCATCATTGCGGCCTC-AACCTTTCCCATCTCATT
66 TCATCACTGCGACCTCGAACC-TCCCCATCACATC
* ** * *
53692912 TTCTAAGGTACCGAGTTCGCCGTTACGGCCTCAACATTTCCCTTCAAATCTTCATG
1 TTCTAAGGTACCGGGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATG
53692968 TTTTCTTAGT
Statistics
Matches: 130, Mismatches: 24, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
98 3 0.02
99 123 0.95
100 4 0.03
ACGTcount: A:0.18, C:0.31, G:0.17, T:0.34
Consensus pattern (99 bp):
TTCTAAGGTACCGGGTTCGCCGTTGTGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGGAT
TCATCACTGCGACCTCGAACCTCCCCATCACATC
Found at i:53692941 original size:50 final size:50
Alignment explanation
Indices: 53692802--53692953 Score: 157
Period size: 50 Copynumber: 3.1 Consensus size: 50
53692792 CTCGATCCTC
* * * * *
53692802 CCCATCACATCTTCTAAGGTACCGGGTTCGCTGTTGTGGCTTCAACCTTT
1 CCCATCTCATTTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTT
* ** *
53692852 CCC-T-TCATGTCTTC-ATGGTACCGGGTTCATCATTGCGGCCTCAACCTTT
1 CCCATCTCAT-T-TTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTT
* * *
53692901 CCCATCTCATTTTCTAAGGTACCGAGTTCGCCGTTACGGCCTCAACATTT
1 CCCATCTCATTTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTT
53692951 CCC
1 CCC
53692954 TTCAAATCTT
Statistics
Matches: 81, Mismatches: 16, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
48 3 0.04
49 35 0.43
50 39 0.48
51 4 0.05
ACGTcount: A:0.16, C:0.33, G:0.18, T:0.33
Consensus pattern (50 bp):
CCCATCTCATTTTCTAAGGTACCGGGTTCGCCGTTGCGGCCTCAACCTTT
Found at i:53693950 original size:17 final size:17
Alignment explanation
Indices: 53693912--53693949 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
53693902 TCTCCTTTTC
*
53693912 TTTTTCCCTTTTTTCCT
1 TTTTTCCCTTTTTTACT
*
53693929 TTTTTCTCTTTTTTA-T
1 TTTTTCCCTTTTTTACT
53693945 TTTTT
1 TTTTT
53693950 TTATTTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCCCTTTTTTACT
Found at i:53708895 original size:68 final size:69
Alignment explanation
Indices: 53708771--53708902 Score: 194
Period size: 68 Copynumber: 1.9 Consensus size: 69
53708761 ATGCTCCATC
* * *
53708771 AACTCCTCCTTCAGCTTATCCAAGCTTGTTTGGGAGTCTTATAGCGGTGAGCTACTGCTGCCTTA
1 AACTCCTCCTTCAGCTTAT-C-AGCTTGTTTGGGAGTCTCATAGAGGTGAGCTACTGCTACCTTA
53708836 CCTTGG
64 CCTTGG
* *
53708842 AACTCCTCCTTCAGCTTAT-AGCTTGTTTGGGAGTCTCATAGAGTTGAGTTACTGCTACCTT
1 AACTCCTCCTTCAGCTTATCAGCTTGTTTGGGAGTCTCATAGAGGTGAGCTACTGCTACCTT
53708903 CTCAACAAAC
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
68 37 0.66
71 19 0.34
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (69 bp):
AACTCCTCCTTCAGCTTATCAGCTTGTTTGGGAGTCTCATAGAGGTGAGCTACTGCTACCTTACC
TTGG
Found at i:53720334 original size:2 final size:2
Alignment explanation
Indices: 53720327--53720380 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
53720317 GTATGGGTTA
53720327 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
53720369 AT AT AT AT AT AT
1 AT AT AT AT AT AT
53720381 GACCGTCCAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53720437 original size:22 final size:22
Alignment explanation
Indices: 53720412--53720458 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
53720402 AAATGTAGAA
* *
53720412 TTAAGATTTAAATTTTAAAATT
1 TTAAAATTTAAAGTTTAAAATT
*
53720434 TTAAAATTTAAGGTTTAAAATT
1 TTAAAATTTAAAGTTTAAAATT
53720456 TTA
1 TTA
53720459 CGGTTATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (22 bp):
TTAAAATTTAAAGTTTAAAATT
Found at i:53721631 original size:58 final size:58
Alignment explanation
Indices: 53721561--53721680 Score: 188
Period size: 58 Copynumber: 2.1 Consensus size: 58
53721551 AAAAGGAGTT
* *
53721561 GTTTATGAGTGTTATTT-AGGAATAAAATTATATTTGGGTTTAAAAATATTTGAGTTTA
1 GTTTATAAGTGTT-TTTGAAGAATAAAATTATATTTGGGTTTAAAAATATTTGAGTTTA
* *
53721619 GTTTATAAGTGTTTTTGAAGAATGAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 GTTTATAAGTGTTTTTGAAGAATAAAATTATATTTGGGTTTAAAAATATTTGAGTTTA
53721677 GTTT
1 GTTT
53721681 GTTGATGGGT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
57 3 0.05
58 54 0.95
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (58 bp):
GTTTATAAGTGTTTTTGAAGAATAAAATTATATTTGGGTTTAAAAATATTTGAGTTTA
Found at i:53721932 original size:23 final size:23
Alignment explanation
Indices: 53721888--53721933 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
53721878 GAAAAAAATT
**
53721888 TAACTCGATTCGTTTAACTTGAA
1 TAACTCGATTCGAATAACTTGAA
*
53721911 TAACTCGATTCGAATAATTTGAA
1 TAACTCGATTCGAATAACTTGAA
53721934 ATTCAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (23 bp):
TAACTCGATTCGAATAACTTGAA
Found at i:53725551 original size:25 final size:25
Alignment explanation
Indices: 53725500--53725551 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
53725490 ATAAGATTCG
**
53725500 TTGACTCGACTCGATTCGAAATTTT
1 TTGACTCGACTCGATTCGAAAAATT
*
53725525 TTGACTCGATTCGATTCGAAAAATT
1 TTGACTCGACTCGATTCGAAAAATT
53725550 TT
1 TT
53725552 TAAATTGAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.40
Consensus pattern (25 bp):
TTGACTCGACTCGATTCGAAAAATT
Found at i:53729977 original size:20 final size:20
Alignment explanation
Indices: 53729933--53729980 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
53729923 GGAAAGTACC
53729933 AAAAAATT-TAAGGAAATAT
1 AAAAAATTATAAGGAAATAT
** *
53729952 CGAAAATTATAAGGAAGTAT
1 AAAAAATTATAAGGAAATAT
53729972 AAAAAATTA
1 AAAAAATTA
53729981 GGAGGGAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.60, C:0.02, G:0.12, T:0.25
Consensus pattern (20 bp):
AAAAAATTATAAGGAAATAT
Found at i:53730378 original size:20 final size:20
Alignment explanation
Indices: 53730355--53730427 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
53730345 AAAAAGTACT
53730355 TAAAATATGAGAGAATACAA
1 TAAAATATGAGAGAATACAA
* * * *
53730375 TAAATTATGAAAAAATATAA
1 TAAAATATGAGAGAATACAA
* * *
53730395 GAAATTTATGAGAGAATACCGA
1 TAAA-ATATGAGAGAATA-CAA
53730417 -AAAATATGAGA
1 TAAAATATGAGA
53730428 ATGTACCAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 26 0.63
21 14 0.34
22 1 0.02
ACGTcount: A:0.58, C:0.04, G:0.15, T:0.23
Consensus pattern (20 bp):
TAAAATATGAGAGAATACAA
Found at i:53730412 original size:21 final size:20
Alignment explanation
Indices: 53730360--53730413 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
53730350 GTACTTAAAA
*
53730360 TATGAGAGAATACAATAAAT
1 TATGAGAGAATACAAGAAAT
* * *
53730380 TATGAAAAAATATAAGAAATT
1 TATGAGAGAATACAAGAAA-T
53730401 TATGAGAGAATAC
1 TATGAGAGAATAC
53730414 CGAAAAATAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.56, C:0.04, G:0.15, T:0.26
Consensus pattern (20 bp):
TATGAGAGAATACAAGAAAT
Found at i:53730446 original size:21 final size:20
Alignment explanation
Indices: 53730411--53730466 Score: 78
Period size: 21 Copynumber: 2.8 Consensus size: 20
53730401 TATGAGAGAA
*
53730411 TACCGAAAAATATGAGAAT-G
1 TACCAAAAAATATGAG-ATGG
53730431 TACCAAAAACATATGAGATGG
1 TACCAAAAA-ATATGAGATGG
53730452 TACCAAAAAATATGA
1 TACCAAAAAATATGA
53730467 TGAGTTCGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.52, C:0.12, G:0.16, T:0.20
Consensus pattern (20 bp):
TACCAAAAAATATGAGATGG
Found at i:53732117 original size:25 final size:26
Alignment explanation
Indices: 53732089--53732139 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
53732079 AATAAATATA
* *
53732089 AAAAATTATTAAGATTA-TAAAAAAT
1 AAAAATTATAAAAATTATTAAAAAAT
*
53732114 AAAATTTATAAAAATTATTAAAAAAT
1 AAAAATTATAAAAATTATTAAAAAAT
53732140 TAATTAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
AAAAATTATAAAAATTATTAAAAAAT
Found at i:53734253 original size:26 final size:26
Alignment explanation
Indices: 53734206--53734262 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
53734196 AAAATGAATG
*
53734206 TATAAAATTTTCAATAAATAAAA-ATA
1 TATAAAATTTTAAATAAATAAAATA-A
*
53734232 TATAAAATTATTAAAT-ATTAAAATAA
1 TATAAAATT-TTAAATAAATAAAATAA
53734258 TATAA
1 TATAA
53734263 TTTAAATATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 21 0.78
27 6 0.22
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
TATAAAATTTTAAATAAATAAAATAA
Found at i:53739984 original size:25 final size:24
Alignment explanation
Indices: 53739942--53740001 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 24
53739932 AAAATTTATC
*
53739942 ATTTAATATAATAAATAATTATAAAT
1 ATTT-ATAAAATAAATAATTA-AAAT
53739968 GA-TTATAAAATAAATAATTAAAAT
1 -ATTTATAAAATAAATAATTAAAAT
53739992 ATTTATAAAA
1 ATTTATAAAA
53740002 ATATGATGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
23 1 0.03
24 12 0.39
25 15 0.48
26 2 0.06
27 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
ATTTATAAAATAAATAATTAAAAT
Found at i:53740004 original size:25 final size:25
Alignment explanation
Indices: 53739951--53740001 Score: 79
Period size: 24 Copynumber: 2.1 Consensus size: 25
53739941 CATTTAATAT
53739951 AATAAATAATTATAAATGATTATAA
1 AATAAATAATTATAAATGATTATAA
53739976 AATAAATAATTA-AAAT-ATTTATAA
1 AATAAATAATTATAAATGA-TTATAA
53740000 AA
1 AA
53740002 ATATGATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 1 0.04
24 12 0.48
25 12 0.48
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
AATAAATAATTATAAATGATTATAA
Found at i:53746221 original size:28 final size:29
Alignment explanation
Indices: 53746189--53746245 Score: 98
Period size: 30 Copynumber: 2.0 Consensus size: 29
53746179 TTTTTTATTC
53746189 AAAGTAACTC-ATTTTTTAATTATTTACG
1 AAAGTAACTCGATTTTTTAATTATTTACG
53746217 AAAGTAACTCGTATTTTTTAATTATTTAC
1 AAAGTAACTCG-ATTTTTTAATTATTTAC
53746246 TAAAATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 10 0.37
30 17 0.63
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (29 bp):
AAAGTAACTCGATTTTTTAATTATTTACG
Found at i:53746955 original size:22 final size:22
Alignment explanation
Indices: 53746900--53746956 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
53746890 TGGATCACTC
* *
53746900 AAATTTCAGCTAATTTAAATCG
1 AAATTTCAGCTCACTTAAATCG
*
53746922 AAATTTCAGCTCACTTAAATCT
1 AAATTTCAGCTCACTTAAATCG
53746944 AAATTTCAGCTCA
1 AAATTTCAGCTCA
53746957 TCACCACTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.35
Consensus pattern (22 bp):
AAATTTCAGCTCACTTAAATCG
Found at i:53747830 original size:7 final size:7
Alignment explanation
Indices: 53747831--53747856 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
53747821 TTTTATATTT
53747831 TTTTAAA
1 TTTTAAA
53747838 TTTTAAA
1 TTTTAAA
53747845 TTTTAAA
1 TTTTAAA
53747852 TTTTA
1 TTTTA
53747857 TTATTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTTAAA
Found at i:53747835 original size:24 final size:24
Alignment explanation
Indices: 53747808--53747865 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
53747798 TTATTAGGGA
** *
53747808 TTTAATTTTTCGATTTTATATTTT
1 TTTAATTTTTAAATTTTAAATTTT
*
53747832 TTTAAATTTTAAATTTTAAATTTT
1 TTTAATTTTTAAATTTTAAATTTT
*
53747856 ATT-ATTTTTA
1 TTTAATTTTTA
53747866 TTATAATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTAATTTTTAAATTTTAAATTTT
Found at i:53748237 original size:20 final size:21
Alignment explanation
Indices: 53748199--53748237 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
53748189 AAAAATAAAA
*
53748199 TTTTGATATTTTTATAAATGT
1 TTTTGATATTTTTAGAAATGT
*
53748220 TTTTTATATTTTT-GAAAT
1 TTTTGATATTTTTAGAAAT
53748238 ATAAAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (21 bp):
TTTTGATATTTTTAGAAATGT
Found at i:53748237 original size:142 final size:138
Alignment explanation
Indices: 53748021--53748311 Score: 426
Period size: 142 Copynumber: 2.1 Consensus size: 138
53748011 TTTATTTTAG
*
53748021 GAATGTTTTTATATATTTTTGAATTTTTTTAAAAAAATTTGATATTTTTCACAAATTTTTTTATA
1 GAAT-TTTTTATATATTTTTGAATTTTTTAAAAAAAATTTGATATTTTTCACAAATTTTTTTATA
**
53748086 TTTTCGAAATATAAAAAATA-ATTTTCGTAATATTTTTTTACAAATAAAAAATTTGATATTTTTT
65 TTTTCGAAATATAAAAAATATATTTTCAAAATATTTTTTTACAAATAAAAAATTTGATATTTTTT
*
53748150 TTCTATTTTT
130 TAC-ATTTTT
*
53748160 GACATATTTTT-TATATTTTTGAATTTTTTAAAAATAAAATTTTGATATTTTT-ATAAATGTTTT
1 GA-AT-TTTTTATATATTTTTGAATTTTTT-AAAA-AAAA-TTTGATATTTTTCACAAAT-TTTT
* *
53748223 TTATATTTTTGAAATATAAAAAATATTTTTTCAAAATATTTTTTTACAAATAAAAAATTTGATAT
60 TTATATTTTCGAAATATAAAAAATATATTTTCAAAATATTTTTTTACAAATAAAAAATTTGATAT
53748288 TTTTTTACATTTTT
125 TTTTTTACATTTTT
53748302 GAATTTTTTA
1 GAATTTTTTA
53748312 ATTAAATTCA
Statistics
Matches: 137, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
139 20 0.15
140 15 0.11
141 11 0.08
142 48 0.35
143 43 0.31
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (138 bp):
GAATTTTTTATATATTTTTGAATTTTTTAAAAAAAATTTGATATTTTTCACAAATTTTTTTATAT
TTTCGAAATATAAAAAATATATTTTCAAAATATTTTTTTACAAATAAAAAATTTGATATTTTTTT
ACATTTTT
Found at i:53748274 original size:14 final size:13
Alignment explanation
Indices: 53748242--53748266 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
53748232 TGAAATATAA
53748242 AAAATATTTTTTC
1 AAAATATTTTTTC
53748255 AAAATATTTTTT
1 AAAATATTTTTT
53748267 TACAAATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
AAAATATTTTTTC
Found at i:53751690 original size:51 final size:52
Alignment explanation
Indices: 53751617--53751716 Score: 116
Period size: 52 Copynumber: 1.9 Consensus size: 52
53751607 ATAAATAGGT
* * * * *
53751617 GGTGTCGGTCATGACATGGTC-A-ATACCAATTTTTTTTATTTGATAAAATGA
1 GGTGTCGCTCATGACATAGTCAACATA-AAAATTTTTTTATTTGACAAAATGA
53751668 GGTGTCGCTCATG-CAATAGTCAACATAAAAATTTTTTTATTTGACAAAA
1 GGTGTCGCTCATGAC-ATAGTCAACATAAAAATTTTTTTATTTGACAAAA
53751717 AAAAGTGTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
50 1 0.02
51 17 0.41
52 20 0.49
53 3 0.07
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (52 bp):
GGTGTCGCTCATGACATAGTCAACATAAAAATTTTTTTATTTGACAAAATGA
Done.