Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 36 of 345
Found at i:10105812 original size:72 final size:72
Alignment explanation
Indices: 10105695--10105833 Score: 199
Period size: 72 Copynumber: 1.9 Consensus size: 72
10105685 CGTTACACCA
* * *
10105695 ATTGCTCGTCCAAGCTGAATATACTCCTGTCAGGTTACCAATCCAAGCTAAACATTTATAATGAC
1 ATTGCTCGTCCAAGCTGAATATACTCATGTCAGGTTACCAATCCAAGCTAAACATTTAAAACGAC
10105760 ATGTTTG
66 ATGTTTG
* * * *
10105767 ATTGCTTGTCCAAGCTGAATATA-TACATGTTAGGTTACCAGTCCAAGCTAAACCTTTAAAACGA
1 ATTGCTCGTCCAAGCTGAATATACT-CATGTCAGGTTACCAATCCAAGCTAAACATTTAAAACGA
10105831 CAT
65 CAT
10105834 CAGGTTACCA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
71 1 0.02
72 58 0.98
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (72 bp):
ATTGCTCGTCCAAGCTGAATATACTCATGTCAGGTTACCAATCCAAGCTAAACATTTAAAACGAC
ATGTTTG
Found at i:10112102 original size:167 final size:167
Alignment explanation
Indices: 10111826--10112159 Score: 632
Period size: 167 Copynumber: 2.0 Consensus size: 167
10111816 ATAGTAGGGG
*
10111826 GAGTTGGGATTTTATTCTGAATTAAATTTTTGTAATTTTATTTTGTTTTGTTTTCTTCCCAAAAA
1 GAGTTGGGATTTTATTCTGAATTAAATTTTTATAATTTTATTTTGTTTTGTTTTCTTCCCAAAAA
* * *
10111891 TCCCTTTTCTTTTCTGATGTTCTTCCCTTTCCTCTCTTTGCAAGTTTCTTTTTGTTTTCTTCTTC
66 TCCCTTTTCTTTTCTGATGTTCTTCCATTTCCTCTCTCTGCAAGTTTCTTTTTGTTTTCATCTTC
10111956 TATCCTGTTCACAATCATTCGTTTTTATCACTGTGTT
131 TATCCTGTTCACAATCATTCGTTTTTATCACTGTGTT
10111993 GAGTTGGGATTTTATTCTGAATTAAATTTTTATAATTTTATTTTGTTTTGTTTTCTTCCCAAAAA
1 GAGTTGGGATTTTATTCTGAATTAAATTTTTATAATTTTATTTTGTTTTGTTTTCTTCCCAAAAA
10112058 TCCCTTTTCTTTTCTGATGTTCTTCCATTTCCTCTCTCTGCAAGTTTCTTTTTGTTTTCATCTTC
66 TCCCTTTTCTTTTCTGATGTTCTTCCATTTCCTCTCTCTGCAAGTTTCTTTTTGTTTTCATCTTC
10112123 TATCCTGTTCACAATCATTCGTTTTTATCACTGTGTT
131 TATCCTGTTCACAATCATTCGTTTTTATCACTGTGTT
10112160 TTGGATTTTC
Statistics
Matches: 163, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
167 163 1.00
ACGTcount: A:0.16, C:0.19, G:0.10, T:0.54
Consensus pattern (167 bp):
GAGTTGGGATTTTATTCTGAATTAAATTTTTATAATTTTATTTTGTTTTGTTTTCTTCCCAAAAA
TCCCTTTTCTTTTCTGATGTTCTTCCATTTCCTCTCTCTGCAAGTTTCTTTTTGTTTTCATCTTC
TATCCTGTTCACAATCATTCGTTTTTATCACTGTGTT
Found at i:10123561 original size:19 final size:19
Alignment explanation
Indices: 10123539--10123583 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
10123529 TATAATTTTA
*
10123539 TTATTACTAATTAAAAATT
1 TTATTAATAATTAAAAATT
* *
10123558 TTATAAATTATTAAAAATT
1 TTATTAATAATTAAAAATT
*
10123577 TAATTAA
1 TTATTAA
10123584 AAAAATTCTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (19 bp):
TTATTAATAATTAAAAATT
Found at i:10123778 original size:6 final size:6
Alignment explanation
Indices: 10123761--10123791 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
10123751 AAAAACAAGC
10123761 GGAAATG GGAAAG GGAAAG GGAAAG GGAAAG
1 GGAAA-G GGAAAG GGAAAG GGAAAG GGAAAG
10123792 ATAATTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.79
7 5 0.21
ACGTcount: A:0.48, C:0.00, G:0.48, T:0.03
Consensus pattern (6 bp):
GGAAAG
Found at i:10134524 original size:90 final size:90
Alignment explanation
Indices: 10134357--10134603 Score: 273
Period size: 90 Copynumber: 2.7 Consensus size: 90
10134347 TGCAACTCTA
* * * *
10134357 GTGGTTCATCCACAAATTATT-TGGCAACT-TTTATCTGCAAAAAATGTTGTGCATTCACAACCA
1 GTGGTTCATCCACCAATT-TTCTGGCAGCTCTTT-TTTGC-AAATATGTTGTGCATTCACAACCA
** * * *
10134420 TCTGGTAGCGTATTAACCTAAAACATTG
63 TCTGACAACATATTAACCTAAAACACTG
* *
10134448 GTGGTTCATCCACCCATTTTCTGGCAGCTCTTTTTTGCAAATATGTTGTGTATTCACAACCATCT
1 GTGGTTCATCCACCAATTTTCTGGCAGCTCTTTTTTGCAAATATGTTGTGCATTCACAACCATCT
* **
10134513 GACAACATATTAACTTGCAACACTG
66 GACAACATATTAACCTAAAACACTG
** ** **
10134538 GTGGTTCATCCACCAAGATTCAAGCAGCTCTCATTTGCAAATATGTTGTGCATTCACAACCATCT
1 GTGGTTCATCCACCAATTTTCTGGCAGCTCTTTTTTGCAAATATGTTGTGCATTCACAACCATCT
10134603 G
66 G
10134604 GTAGTGTATT
Statistics
Matches: 132, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
90 102 0.77
91 27 0.20
92 3 0.02
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.33
Consensus pattern (90 bp):
GTGGTTCATCCACCAATTTTCTGGCAGCTCTTTTTTGCAAATATGTTGTGCATTCACAACCATCT
GACAACATATTAACCTAAAACACTG
Found at i:10134632 original size:90 final size:90
Alignment explanation
Indices: 10134400--10134639 Score: 300
Period size: 90 Copynumber: 2.7 Consensus size: 90
10134390 TCTGCAAAAA
** * *
10134400 ATGTTGTGCATTCACAACCATCTGGTAGCGTATTAACCTAAAACATTGGTGGTTCATCCACCCAT
1 ATGTTGTGCATTCACAACCATCTGGTAGCGTATTAACCTGCAACATTGGTGGTTCATCCACCAAG
* ** **
10134465 TTTCTGGCAGCTCTTTTTTGCAAAT
66 ATTCAAGCAGCTCTCATTTGCAAAT
* ** * * * *
10134490 ATGTTGTGTATTCACAACCATCTGACAACATATTAACTTGCAACACTGGTGGTTCATCCACCAAG
1 ATGTTGTGCATTCACAACCATCTGGTAGCGTATTAACCTGCAACATTGGTGGTTCATCCACCAAG
10134555 ATTCAAGCAGCTCTCATTTGCAAAT
66 ATTCAAGCAGCTCTCATTTGCAAAT
* * * *
10134580 ATGTTGTGCATTCACAACCATCTGGTAGTGTATTAACCTGCAACTTTTGTGGTTTATCCA
1 ATGTTGTGCATTCACAACCATCTGGTAGCGTATTAACCTGCAACATTGGTGGTTCATCCA
10134640 AAACCCGGTG
Statistics
Matches: 123, Mismatches: 27, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
90 123 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (90 bp):
ATGTTGTGCATTCACAACCATCTGGTAGCGTATTAACCTGCAACATTGGTGGTTCATCCACCAAG
ATTCAAGCAGCTCTCATTTGCAAAT
Found at i:10142163 original size:18 final size:18
Alignment explanation
Indices: 10142137--10142184 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 18
10142127 CCTATAATGA
*
10142137 GATTGTTTAAAAAAAGTC
1 GATTCTTTAAAAAAAGTC
10142155 GATTCTTTATAAAAAAAAGTC
1 GATTC-TT-T-AAAAAAAGTC
10142176 GATTCTTTA
1 GATTCTTTA
10142185 TGAATTTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 5 0.19
19 3 0.12
20 3 0.12
21 15 0.58
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (18 bp):
GATTCTTTAAAAAAAGTC
Found at i:10142171 original size:21 final size:21
Alignment explanation
Indices: 10142145--10142185 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
10142135 GAGATTGTTT
10142145 AAAAAAAGTCGATTCTTTATA
1 AAAAAAAGTCGATTCTTTATA
10142166 AAAAAAAGTCGATTCTTTAT
1 AAAAAAAGTCGATTCTTTAT
10142186 GAATTTCAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.34
Consensus pattern (21 bp):
AAAAAAAGTCGATTCTTTATA
Found at i:10142995 original size:31 final size:31
Alignment explanation
Indices: 10142960--10143051 Score: 82
Period size: 31 Copynumber: 3.0 Consensus size: 31
10142950 ATTTTTAGAG
10142960 TTAGGACTAAATTGATAGATTTTGTAAATAT
1 TTAGGACTAAATTGATAGATTTTGTAAATAT
* * * *
10142991 TTAGGGCCAAATTTATTGAATTTT-TAAA-A-
1 TTAGGACTAAATTGATAG-ATTTTGTAAATAT
* * * *
10143020 TTAGAACTAAAATGACAAATTTTGTAAATAT
1 TTAGGACTAAATTGATAGATTTTGTAAATAT
10143051 T
1 T
10143052 GATGGCTAAA
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
28 5 0.11
29 14 0.31
30 2 0.04
31 19 0.42
32 5 0.11
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.40
Consensus pattern (31 bp):
TTAGGACTAAATTGATAGATTTTGTAAATAT
Found at i:10143042 original size:60 final size:60
Alignment explanation
Indices: 10142949--10143075 Score: 164
Period size: 60 Copynumber: 2.1 Consensus size: 60
10142939 GTATAGTTTT
* * * * * * *
10142949 AATTTTTAGAGTTAGGACTAAATTGATAGATTTTGTAAATATTTAGGGCCAAATTTATTG
1 AATTTTTAAAATTAGAACTAAAATGACAAATTTTGTAAATATTGAGGGCCAAATTTATTG
* * *
10143009 AATTTTTAAAATTAGAACTAAAATGACAAATTTTGTAAATATTGATGGCTAAATTTGTTG
1 AATTTTTAAAATTAGAACTAAAATGACAAATTTTGTAAATATTGAGGGCCAAATTTATTG
10143069 AATTTTT
1 AATTTTT
10143076 TATATTTAGG
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.43
Consensus pattern (60 bp):
AATTTTTAAAATTAGAACTAAAATGACAAATTTTGTAAATATTGAGGGCCAAATTTATTG
Found at i:10148294 original size:34 final size:34
Alignment explanation
Indices: 10148256--10148327 Score: 126
Period size: 34 Copynumber: 2.1 Consensus size: 34
10148246 ATCACAACCA
10148256 CTTATTTACCATCCTTAGTTCTTAAAACAACACT
1 CTTATTTACCATCCTTAGTTCTTAAAACAACACT
**
10148290 CTTATTTACCATCCTTAGTTCTTAAAATGACACT
1 CTTATTTACCATCCTTAGTTCTTAAAACAACACT
10148324 CTTA
1 CTTA
10148328 GTCACACAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (34 bp):
CTTATTTACCATCCTTAGTTCTTAAAACAACACT
Found at i:10153779 original size:19 final size:19
Alignment explanation
Indices: 10153738--10153795 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
10153728 GCATTACTTT
* * *
10153738 CACACAAAGTGCATCTTGA
1 CACACAAGGTGCATCCTGG
*
10153757 CACACAAGGTGCATCGTGG
1 CACACAAGGTGCATCCTGG
**
10153776 CACATGAGGTGCATCCTGG
1 CACACAAGGTGCATCCTGG
10153795 C
1 C
10153796 GGATAAGCGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (19 bp):
CACACAAGGTGCATCCTGG
Found at i:10155416 original size:43 final size:43
Alignment explanation
Indices: 10155368--10155460 Score: 132
Period size: 43 Copynumber: 2.2 Consensus size: 43
10155358 ATTACCGAGA
*
10155368 TGTGATTACATGTAAGACTATGTCCGAGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCCGAGACATTGGCATTGTAT
** * *
10155411 TGTGATTACATGTAAGACCATGTTTGGGACATTGGCATTGTTT
1 TGTGATTACATGTAAGACCATGTCCGAGACATTGGCATTGTAT
*
10155454 TATGATT
1 TGTGATT
10155461 TTGCATAAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.39
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCCGAGACATTGGCATTGTAT
Found at i:10159638 original size:5 final size:5
Alignment explanation
Indices: 10159603--10159631 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
10159593 GTATTTGTGA
10159603 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
10159632 AATAAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:10166252 original size:19 final size:18
Alignment explanation
Indices: 10166228--10166277 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 18
10166218 AGTAATTTTA
10166228 AATTTTTATAACATT-TAAT
1 AATTTTTATAAC-TTAT-AT
10166247 AATTTTTAATAACTTATAT
1 AATTTTT-ATAACTTATAT
10166266 ATATTTTTATAA
1 A-ATTTTTATAA
10166278 TTTTCTAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTTTTATAACTTATAT
Found at i:10166278 original size:29 final size:27
Alignment explanation
Indices: 10166240--10166317 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 27
10166230 TTTTTATAAC
* *
10166240 ATTTAATAATTTTTAATAACTTATATAT
1 ATTTTATAATTTTTAATAAATTAT-TAT
*
10166268 ATTTTTATAATTTTCTAAAGAAATTATTAT
1 A-TTTTATAATTTT-T-AATAAATTATTAT
*
10166298 ATTTTATTAATTTCTAATAA
1 ATTTTA-TAATTTTTAATAA
10166318 TTTTTAATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
28 5 0.12
29 17 0.41
30 11 0.27
31 8 0.20
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (27 bp):
ATTTTATAATTTTTAATAAATTATTAT
Found at i:10166796 original size:36 final size:38
Alignment explanation
Indices: 10166753--10166835 Score: 116
Period size: 36 Copynumber: 2.2 Consensus size: 38
10166743 TAACATATTA
* *
10166753 ATAAATTTTATAATATTTAATAGTTTT-TATATTTTTT
1 ATAAATTTTATAATATTTAATAATTTTATAGATTTTTT
*
10166790 A-AAATTTTATGATATTTAATAATTTTGATAGATTTTTT
1 ATAAATTTTATAATATTTAATAATTTT-ATAGATTTTTT
10166828 ATAAATTT
1 ATAAATTT
10166836 CAAAATTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
36 23 0.57
37 1 0.03
38 10 0.25
39 6 0.15
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (38 bp):
ATAAATTTTATAATATTTAATAATTTTATAGATTTTTT
Found at i:10166895 original size:23 final size:24
Alignment explanation
Indices: 10166841--10166908 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 24
10166831 AATTTCAAAA
*
10166841 TTTTAAATATTTTAATGAATTTTAG
1 TTTTAATTATTTTAAT-AATTTTAG
* *
10166866 CTATAATTATTTTAAT-ATTTTAG
1 TTTTAATTATTTTAATAATTTTAG
*
10166889 TTTTAATT-TTAT-ATAATTTT
1 TTTTAATTATTTTAATAATTTT
10166909 CTATAATTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
21 2 0.06
22 8 0.22
23 13 0.36
25 13 0.36
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTTAATTATTTTAATAATTTTAG
Found at i:10167036 original size:18 final size:18
Alignment explanation
Indices: 10167013--10167057 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
10167003 ATTAAAAAAA
10167013 ATCAATTAAGCCCTCCAT
1 ATCAATTAAGCCCTCCAT
10167031 ATCAATTAAGCCCTCCAT
1 ATCAATTAAGCCCTCCAT
10167049 ATCAATTAA
1 ATCAATTAA
10167058 ACCACATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.29
Consensus pattern (18 bp):
ATCAATTAAGCCCTCCAT
Found at i:10174603 original size:18 final size:17
Alignment explanation
Indices: 10174582--10174649 Score: 73
Period size: 18 Copynumber: 3.8 Consensus size: 17
10174572 TAACAGTTAG
10174582 TTATTCAGTAACAATCAA
1 TTATTCAGTAACAAT-AA
* *
10174600 TTATTCAATAATAATAA
1 TTATTCAGTAACAATAA
*
10174617 GTTACTCAGTAACAATTAAA
1 -TTATTCAGTAACAA-T-AA
10174637 TTATTCAGTAACA
1 TTATTCAGTAACA
10174650 GTCGATCTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
17 2 0.05
18 24 0.59
19 13 0.32
20 2 0.05
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (17 bp):
TTATTCAGTAACAATAA
Found at i:10174604 original size:36 final size:37
Alignment explanation
Indices: 10174564--10174651 Score: 106
Period size: 36 Copynumber: 2.4 Consensus size: 37
10174554 GAACGATTAT
* * * *
10174564 TTATTCTGTAACAGTTAGTTATTCAGTAACAA-TCAA
1 TTATTCAGTAACAGTAAGTTACTCAGTAACAATTAAA
* * *
10174600 TTATTCAATAATAATAAGTTACTCAGTAACAATTAAA
1 TTATTCAGTAACAGTAAGTTACTCAGTAACAATTAAA
10174637 TTATTCAGTAACAGT
1 TTATTCAGTAACAGT
10174652 CGATCTTTCC
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
36 26 0.63
37 15 0.37
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (37 bp):
TTATTCAGTAACAGTAAGTTACTCAGTAACAATTAAA
Found at i:10174846 original size:47 final size:47
Alignment explanation
Indices: 10174777--10174893 Score: 173
Period size: 47 Copynumber: 2.5 Consensus size: 47
10174767 CAGTAACAGT
* ***
10174777 AACAGTAGCAATACGGTACACAGAGTACCTCATCGGAACAAATCTGG
1 AACAGTAACAATACGGTACACAGAGTACCTCATCGGAACAAATCCAA
10174824 AACAGTAACAATACGGTACACAGAGTACCTCATCGGAACAAATCCAA
1 AACAGTAACAATACGGTACACAGAGTACCTCATCGGAACAAATCCAA
*
10174871 AACAGTAACAGTAACGGTA-ACAG
1 AACAGTAACAAT-ACGGTACACAG
10174894 TAACAATATC
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
47 58 0.91
48 6 0.09
ACGTcount: A:0.43, C:0.23, G:0.19, T:0.15
Consensus pattern (47 bp):
AACAGTAACAATACGGTACACAGAGTACCTCATCGGAACAAATCCAA
Found at i:10175104 original size:20 final size:20
Alignment explanation
Indices: 10175076--10175128 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
10175066 CTTTTCAGTT
10175076 TTCAATTAATTTATATTTT-AA
1 TTCAATTAATTT-T-TTTTCAA
10175097 TT-AATTAATTTTTTTTCAA
1 TTCAATTAATTTTTTTTCAA
10175116 TTCAATATAATTT
1 TTCAAT-TAATTT
10175129 CATTCACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 4 0.14
19 5 0.17
20 12 0.41
21 8 0.28
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (20 bp):
TTCAATTAATTTTTTTTCAA
Found at i:10176559 original size:16 final size:17
Alignment explanation
Indices: 10176530--10176569 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
10176520 TTTCGTTTCA
* *
10176530 TTCTGTTTCTTTTCTTT
1 TTCTTTTTCATTTCTTT
10176547 TT-TTTTTCATTTCTTT
1 TTCTTTTTCATTTCTTT
10176563 TTCTTTT
1 TTCTTTT
10176570 GTTTTACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.80
Consensus pattern (17 bp):
TTCTTTTTCATTTCTTT
Found at i:10176733 original size:31 final size:31
Alignment explanation
Indices: 10176677--10176766 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 31
10176667 CACACTTGTC
*
10176677 ATAATTTAATATATTTATTACATAAAAATC-TT
1 ATAATATAA-ATATTTATTA-ATAAAAATCTTT
*
10176709 ATAATATAAATATTTAATTAATAAATATCTTTT
1 ATAATATAAATATTT-ATTAATAAAAATC-TTT
*
10176742 ATAAATAATAAATATCTATTAATAA
1 AT-AAT-ATAAATATTTATTAATAA
10176767 TTAAATATAC
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
31 14 0.28
32 12 0.24
33 4 0.08
34 11 0.22
35 9 0.18
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (31 bp):
ATAATATAAATATTTATTAATAAAAATCTTT
Found at i:10178727 original size:26 final size:26
Alignment explanation
Indices: 10178662--10178728 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 26
10178652 TGTTTAATAT
10178662 GAAAAAAAAAGAATGAGAGAAAAAA-
1 GAAAAAAAAAGAATGAGAGAAAAAAG
**
10178687 GAAAAAAAATCAA-GAGAGATAGTAAAGAG
1 GAAAAAAAAAGAATGAGAGA-A--AAA-AG
10178716 GAAAAAAAAAGAA
1 GAAAAAAAAAGAA
10178729 AGAATAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
24 6 0.18
25 12 0.36
27 3 0.09
28 1 0.03
29 11 0.33
ACGTcount: A:0.72, C:0.01, G:0.21, T:0.06
Consensus pattern (26 bp):
GAAAAAAAAAGAATGAGAGAAAAAAG
Found at i:10180285 original size:27 final size:27
Alignment explanation
Indices: 10180255--10180336 Score: 78
Period size: 27 Copynumber: 3.1 Consensus size: 27
10180245 ATGGCAACTA
* * *
10180255 GGGTAGTTTTTCGGGATGGTAAACACG
1 GGGTAGTTTGTCAGGACGGTAAACACG
**
10180282 GGGTAGTTTGTCAGGACGGTAAACATA
1 GGGTAGTTTGTCAGGACGGTAAACACG
* * *
10180309 AGG-A-TATGTCGGGACGGTAAACACG
1 GGGTAGTTTGTCAGGACGGTAAACACG
10180334 GGG
1 GGG
10180337 AAGTCTGCCA
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
25 19 0.43
26 1 0.02
27 24 0.55
ACGTcount: A:0.27, C:0.12, G:0.38, T:0.23
Consensus pattern (27 bp):
GGGTAGTTTGTCAGGACGGTAAACACG
Found at i:10186408 original size:44 final size:45
Alignment explanation
Indices: 10186346--10186430 Score: 127
Period size: 44 Copynumber: 1.9 Consensus size: 45
10186336 CTATACGCCT
* *
10186346 AAAATGAGTAATACCATAACTGAAAGATATTATAGCATCATGATA
1 AAAAGGAGTAATACCATAACTGAAAGACATTATAGCATCATGATA
* *
10186391 AAAAGGAGTAA-ACCATAATTGAAAGACGTTATAGCATCAT
1 AAAAGGAGTAATACCATAACTGAAAGACATTATAGCATCAT
10186431 AAGTAAGCAC
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 26 0.72
45 10 0.28
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (45 bp):
AAAAGGAGTAATACCATAACTGAAAGACATTATAGCATCATGATA
Found at i:10193283 original size:45 final size:45
Alignment explanation
Indices: 10193182--10193286 Score: 140
Period size: 45 Copynumber: 2.3 Consensus size: 45
10193172 AAGGGTAGCA
* *
10193182 GTAACAATAACAGTAACAGTATTCAACACACAAAGTGCTAAATCT
1 GTAACAATAACGGTAACAGTATTCAACACACAAAGTGCTAAATCG
* * *
10193227 GTACCAATAACGGTAACAGTATTCGACACACAAAGTG-TCGAATCG
1 GTAACAATAACGGTAACAGTATTCAACACACAAAGTGCT-AAATCG
*
10193272 GTAACAGTAACGGTA
1 GTAACAATAACGGTA
10193287 GTCGGCACAT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
44 1 0.02
45 51 0.98
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (45 bp):
GTAACAATAACGGTAACAGTATTCAACACACAAAGTGCTAAATCG
Found at i:10193701 original size:24 final size:24
Alignment explanation
Indices: 10193669--10193716 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
10193659 GATAAAGTTT
10193669 GAATTATAGTGATACAAACCAGAA
1 GAATTATAGTGATACAAACCAGAA
*
10193693 GAATTATAGTGATACAAACTAGAA
1 GAATTATAGTGATACAAACCAGAA
10193717 TTCTCTTCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (24 bp):
GAATTATAGTGATACAAACCAGAA
Found at i:10198483 original size:27 final size:27
Alignment explanation
Indices: 10198453--10198506 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
10198443 ATAAGGTGTA
*
10198453 AGTGAATCTACAAGAGGAAAGAAATGC
1 AGTGAATCTACAAGAGGAAAAAAATGC
*
10198480 AGTGAATTTACAAGAGGAAAAAAATGC
1 AGTGAATCTACAAGAGGAAAAAAATGC
10198507 GAAAGGGTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.50, C:0.09, G:0.24, T:0.17
Consensus pattern (27 bp):
AGTGAATCTACAAGAGGAAAAAAATGC
Found at i:10200694 original size:26 final size:26
Alignment explanation
Indices: 10200656--10200712 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
10200646 CATTTTAACA
* *
10200656 TAATGTTTGTCTTA-TTGTGGTCACTC
1 TAATTTTTGTCTTAGTT-TAGTCACTC
*
10200682 TAATTTTTTTCTTAGTTTAGTCACTC
1 TAATTTTTGTCTTAGTTTAGTCACTC
*
10200708 CAATT
1 TAATT
10200713 AAGATAATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.19, C:0.16, G:0.12, T:0.53
Consensus pattern (26 bp):
TAATTTTTGTCTTAGTTTAGTCACTC
Found at i:10202698 original size:21 final size:21
Alignment explanation
Indices: 10202664--10202703 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
10202654 AAAAAAACCC
10202664 GTAAAATTCTTAAAAGTTTTGA
1 GTAAAATTCTTAAAA-TTTTGA
*
10202686 GTAAACTTC-TAAAATTTT
1 GTAAAATTCTTAAAATTTT
10202704 CTAAAAAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 5 0.29
22 8 0.47
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.42
Consensus pattern (21 bp):
GTAAAATTCTTAAAATTTTGA
Found at i:10217641 original size:53 final size:52
Alignment explanation
Indices: 10217515--10217697 Score: 191
Period size: 53 Copynumber: 3.6 Consensus size: 52
10217505 TGCGCCCATT
* ** ** *
10217515 TAAGACCATAGTTGGGCTATAGCATCGGTGCAATGTGATATGTGTTTCCGTA
1 TAAGACCATAGTTGGGCTATGGCATCGGTGTGACATGATATGTGATTCCGTA
10217567 TAAGACCATAGTTGGGCTATGGCATCGGTGTGACATGATAATGTGATTCCGTA
1 TAAGACCATAGTTGGGCTATGGCATCGGTGTGACATGAT-ATGTGATTCCGTA
* *
10217620 TAAGACCATA-TCTGGGATATGGCATCGGTGTG---TG--ATGTGA-TCCGTG
1 TAAGACCATAGT-TGGGCTATGGCATCGGTGTGACATGATATGTGATTCCGTA
*** *
10217666 TAAGACCATAGCACGGCTATGGCTTCGGTGTG
1 TAAGACCATAGTTGGGCTATGGCATCGGTGTG
10217698 TGATATGTGA
Statistics
Matches: 115, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
46 31 0.27
47 6 0.05
50 2 0.02
52 35 0.30
53 41 0.36
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (52 bp):
TAAGACCATAGTTGGGCTATGGCATCGGTGTGACATGATATGTGATTCCGTA
Found at i:10224025 original size:9 final size:9
Alignment explanation
Indices: 10224011--10224044 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
10224001 TGATTTGCTG
10224011 ATTAGTTAA
1 ATTAGTTAA
10224020 ATTAGTTAA
1 ATTAGTTAA
10224029 ATTAGTTAA
1 ATTAGTTAA
10224038 ATTAGTT
1 ATTAGTT
10224045 TTAACAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (9 bp):
ATTAGTTAA
Found at i:10224331 original size:17 final size:18
Alignment explanation
Indices: 10224299--10224333 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
10224289 ATAATTTTTA
10224299 AATGTGTCTAAATTAATT
1 AATGTGTCTAAATTAATT
*
10224317 AATGTGT-TGAATTAATT
1 AATGTGTCTAAATTAATT
10224334 TGTGTGTACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (18 bp):
AATGTGTCTAAATTAATT
Found at i:10224429 original size:24 final size:24
Alignment explanation
Indices: 10224400--10224461 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
10224390 ACAGCATGCC
*
10224400 TGGACAGATTTAATGAGCTGCTGG
1 TGGACAGATTTAATGAGCTACTGG
* *
10224424 TTGACAAATTTAATGAGCTACTGG
1 TGGACAGATTTAATGAGCTACTGG
10224448 TGGAC-GAATTTAAT
1 TGGACAG-ATTTAAT
10224462 ATGTCCTAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.32
Consensus pattern (24 bp):
TGGACAGATTTAATGAGCTACTGG
Found at i:10227855 original size:53 final size:52
Alignment explanation
Indices: 10227713--10227911 Score: 187
Period size: 52 Copynumber: 3.9 Consensus size: 52
10227703 GAAAAGATGA
* ** **
10227713 GATATGTG-TGTCCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGT
1 GATATGTGAT-TCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGACAT
* * *
10227765 GATATGTGTTTTCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGGCAT
1 GATATGTGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGACAT
* * *
10227817 GATAATGTGATTCCGTATAAGACCATATCTGAGATATGGCATCGGTGTG---T
1 GAT-ATGTGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGACAT
* ** * *
10227867 G--ATGTGA-TCCGTGTAAGACCATAGCACGGCTATGACTTCGGTGTG
1 GATATGTGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTG
10227912 TGATATGTGA
Statistics
Matches: 125, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
46 30 0.24
47 6 0.05
50 2 0.02
52 46 0.37
53 41 0.33
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.31
Consensus pattern (52 bp):
GATATGTGATTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTGTGACAT
Found at i:10230217 original size:50 final size:51
Alignment explanation
Indices: 10230140--10230268 Score: 199
Period size: 50 Copynumber: 2.5 Consensus size: 51
10230130 GACCATGGCA
10230140 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGA-AAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAA-TG
*
10230191 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
* * *
10230241 ACAAGTGAAAAGTGGTAGCTTCAGCTAC
1 ACAAGTGATAAGTGATAGCTTCGGCTAC
10230269 CTGATCAGTG
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
50 45 0.62
51 27 0.38
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:10230416 original size:31 final size:31
Alignment explanation
Indices: 10230244--10230419 Score: 271
Period size: 31 Copynumber: 5.7 Consensus size: 31
10230234 ACAAATGACA
* *
10230244 AGTGAAAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
* *
10230275 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
*
10230306 AGTGAAAAGTGGTAGTTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
10230337 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
* *
10230368 CGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
* *
10230399 AGTGAATAGTGTTAGCTCCGG
1 AGTGAAAAGTGGTAGCTCCGG
10230420 TTACAAGTGA
Statistics
Matches: 134, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 134 1.00
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
Found at i:10230559 original size:46 final size:47
Alignment explanation
Indices: 10230442--10230564 Score: 158
Period size: 47 Copynumber: 2.6 Consensus size: 47
10230432 AGTGATTTCC
* * *
10230442 GTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTACT
1 GTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATACT
* * *
10230489 GTATAAGACCATATCTGGGATATGGCATCAGTGAGATGTGTGATTC-
1 GTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATACT
* * *
10230535 GTGTAAGACCATAGCTGGGCTATGGCATCA
1 GTATAAGACCATATCTGGGATATGGCATCA
10230565 TTATGTGAAG
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
46 27 0.40
47 40 0.60
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (47 bp):
GTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATACT
Found at i:10236755 original size:29 final size:29
Alignment explanation
Indices: 10236708--10236792 Score: 95
Period size: 28 Copynumber: 3.0 Consensus size: 29
10236698 ACGAGATGCA
* *
10236708 AAAGTGCAAGTCAAAGTGGCAGG-CAATCC
1 AAAGTACAAGCCAAAGTGGC-GGACAATCC
*
10236737 AAAGTACAAGCCAAGGTGGCGGACAAT-C
1 AAAGTACAAGCCAAAGTGGCGGACAATCC
*
10236765 TAAGTGA-AAGCCAAAGTGGCGGACAATC
1 AAAGT-ACAAGCCAAAGTGGCGGACAATC
10236793 TAACTGCGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
28 26 0.54
29 22 0.46
ACGTcount: A:0.39, C:0.20, G:0.28, T:0.13
Consensus pattern (29 bp):
AAAGTACAAGCCAAAGTGGCGGACAATCC
Found at i:10241160 original size:20 final size:20
Alignment explanation
Indices: 10241135--10241175 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
10241125 AGATGATGAC
10241135 ATTCATGTTTTACTAATTTA
1 ATTCATGTTTTACTAATTTA
10241155 ATTCATGTTTTACTAATTTA
1 ATTCATGTTTTACTAATTTA
10241175 A
1 A
10241176 CATATTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.10, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTCATGTTTTACTAATTTA
Found at i:10253810 original size:30 final size:31
Alignment explanation
Indices: 10253776--10253838 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
10253766 CGTTATACAC
* *
10253776 ATGAAACTTA-ATTATAATTCAATTGTATAT
1 ATGAAACTTAGATTATAATTAAATTATATAT
*
10253806 ATGAAACTTAGATTTTAATTAAATTATATAT
1 ATGAAACTTAGATTATAATTAAATTATATAT
10253837 AT
1 AT
10253839 TTAAAGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 10 0.34
31 19 0.66
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (31 bp):
ATGAAACTTAGATTATAATTAAATTATATAT
Found at i:10255664 original size:38 final size:38
Alignment explanation
Indices: 10255613--10255693 Score: 162
Period size: 38 Copynumber: 2.1 Consensus size: 38
10255603 TTAAGGATTA
10255613 TGAAATCATATTTGAAGAAAAAATAAATCATAACAAAC
1 TGAAATCATATTTGAAGAAAAAATAAATCATAACAAAC
10255651 TGAAATCATATTTGAAGAAAAAATAAATCATAACAAAC
1 TGAAATCATATTTGAAGAAAAAATAAATCATAACAAAC
10255689 TGAAA
1 TGAAA
10255694 GTAATACATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.58, C:0.10, G:0.09, T:0.23
Consensus pattern (38 bp):
TGAAATCATATTTGAAGAAAAAATAAATCATAACAAAC
Found at i:10255681 original size:22 final size:22
Alignment explanation
Indices: 10255615--10255682 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 22
10255605 AAGGATTATG
10255615 AAATCATATTTGAAGAAAAAAT
1 AAATCATATTTGAAGAAAAAAT
* *
10255637 AAATC--A--T--A-ACAAACT
1 AAATCATATTTGAAGAAAAAAT
10255652 GAAATCATATTTGAAGAAAAAAT
1 -AAATCATATTTGAAGAAAAAAT
10255675 AAATCATA
1 AAATCATA
10255683 ACAAACTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 16
0.63 0.07 0.30
Matches are distributed among these distances:
15 5 0.15
16 6 0.18
18 2 0.06
20 2 0.06
22 14 0.41
23 5 0.15
ACGTcount: A:0.59, C:0.09, G:0.07, T:0.25
Consensus pattern (22 bp):
AAATCATATTTGAAGAAAAAAT
Found at i:10263222 original size:25 final size:24
Alignment explanation
Indices: 10263194--10263253 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
10263184 ATATAAAAAA
* *
10263194 ATTTTTGATTTTTAAAATTCTTTTT
1 ATTTTT-ATTATTAAAATTCTTTAT
*
10263219 ATTTTATATTATTAAAATTGTTTAT
1 ATTTT-TATTATTAAAATTCTTTAT
10263244 ATTTTT-TTAT
1 ATTTTTATTAT
10263254 AAATCTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
23 4 0.13
24 1 0.03
25 25 0.81
26 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (24 bp):
ATTTTTATTATTAAAATTCTTTAT
Found at i:10270818 original size:33 final size:30
Alignment explanation
Indices: 10270756--10270819 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 30
10270746 ATAAGTTTGA
10270756 TTATTATTTATAAAATAATTTAAATATATT
1 TTATTATTTATAAAATAATTTAAATATATT
10270786 TTATTATTTATTATGAATATAATTTAAA-ATATT
1 TTATTATTTA-TA--AA-ATAATTTAAATATATT
10270819 T
1 T
10270820 AAATTTTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
30 10 0.33
31 2 0.07
33 8 0.27
34 10 0.33
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (30 bp):
TTATTATTTATAAAATAATTTAAATATATT
Found at i:10271136 original size:39 final size:39
Alignment explanation
Indices: 10271082--10271161 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
10271072 CTACTGTGTG
10271082 ATAGATTGATAAAACTATTAATTTGCTTGTAGTAATGTA
1 ATAGATTGATAAAACTATTAATTTGCTTGTAGTAATGTA
10271121 ATAGATTGATAAAACTATTAATTTGCTTGTAGTAATGTA
1 ATAGATTGATAAAACTATTAATTTGCTTGTAGTAATGTA
10271160 AT
1 AT
10271162 GTATCTATGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (39 bp):
ATAGATTGATAAAACTATTAATTTGCTTGTAGTAATGTA
Found at i:10276257 original size:11 final size:11
Alignment explanation
Indices: 10276241--10276273 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
10276231 TTTTTATGGA
10276241 GAATTGCAAGG
1 GAATTGCAAGG
10276252 GAATTGCAAGG
1 GAATTGCAAGG
10276263 GAATTGCAAGG
1 GAATTGCAAGG
10276274 CAACAAGTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.36, T:0.18
Consensus pattern (11 bp):
GAATTGCAAGG
Found at i:10285188 original size:32 final size:32
Alignment explanation
Indices: 10285147--10285210 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
10285137 ATAAAGCCAA
*
10285147 ACATAAATCTTTTGCCTAAAGACCTCCCGATT
1 ACATAAATCTTTTGCCCAAAGACCTCCCGATT
10285179 ACATAAATCTTTTGCCCAAAGACCTCCCGATT
1 ACATAAATCTTTTGCCCAAAGACCTCCCGATT
10285211 CGATTTGATC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.31, C:0.30, G:0.09, T:0.30
Consensus pattern (32 bp):
ACATAAATCTTTTGCCCAAAGACCTCCCGATT
Found at i:10293072 original size:14 final size:14
Alignment explanation
Indices: 10293053--10293084 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
10293043 GTCAGACACC
10293053 TGTACGTGTCTGAT
1 TGTACGTGTCTGAT
10293067 TGTACGTGTCTGAT
1 TGTACGTGTCTGAT
10293081 TGTA
1 TGTA
10293085 TTTGGAGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.16, C:0.12, G:0.28, T:0.44
Consensus pattern (14 bp):
TGTACGTGTCTGAT
Found at i:10301376 original size:23 final size:24
Alignment explanation
Indices: 10301350--10301400 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
10301340 TACATGTTTA
10301350 TTTTTTG-TTTTCAGTTTG-TTTTG
1 TTTTTTGCTTTT-AGTTTGTTTTTG
*
10301373 TTTTTTGCTTTTATTTTGTTTTTG
1 TTTTTTGCTTTTAGTTTGTTTTTG
10301397 TTTT
1 TTTT
10301401 GCTTGCTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.04, C:0.04, G:0.14, T:0.78
Consensus pattern (24 bp):
TTTTTTGCTTTTAGTTTGTTTTTG
Found at i:10302907 original size:16 final size:16
Alignment explanation
Indices: 10302886--10302917 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
10302876 GGACACCGCC
10302886 GACTTAATTTTATATT
1 GACTTAATTTTATATT
10302902 GACTTAATTTTATATT
1 GACTTAATTTTATATT
10302918 TTTTCATATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.56
Consensus pattern (16 bp):
GACTTAATTTTATATT
Found at i:10304015 original size:12 final size:12
Alignment explanation
Indices: 10303998--10304023 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10303988 GTAACCATTG
10303998 TTATTGAATTCT
1 TTATTGAATTCT
10304010 TTATTGAATTCT
1 TTATTGAATTCT
10304022 TT
1 TT
10304024 TAAAATTGTA
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:0.08, G:0.08, T:0.62
Consensus pattern (12 bp):
TTATTGAATTCT
Found at i:10305825 original size:21 final size:21
Alignment explanation
Indices: 10305799--10305858 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
10305789 TTCTCTAACC
10305799 ATGGTCAAAATTATTTTGAAA
1 ATGGTCAAAATTATTTTGAAA
** *
10305820 ATGGTCAAAATTATAATGGAA
1 ATGGTCAAAATTATTTTGAAA
* *
10305841 GTGGTCAGAATTATTTTG
1 ATGGTCAAAATTATTTTG
10305859 CTGGTCAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.37
Consensus pattern (21 bp):
ATGGTCAAAATTATTTTGAAA
Found at i:10316089 original size:42 final size:42
Alignment explanation
Indices: 10316029--10316129 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 42
10316019 ATGGTTATGT
* * *
10316029 GTGATTTCGTGTAAGACCATATCTGGGATATGCCATCGATAT
1 GTGATTTCGTGTAAGACCATATATGGGACATGCCATCGATAC
* *
10316071 TTGATTTCGTGTAAGACCATATATGGGACATGGCATCGATAC
1 GTGATTTCGTGTAAGACCATATATGGGACATGCCATCGATAC
* *
10316113 GAGATATCGTGTAAGAC
1 GTGATTTCGTGTAAGAC
10316130 TATAGCTAGG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (42 bp):
GTGATTTCGTGTAAGACCATATATGGGACATGCCATCGATAC
Found at i:10324795 original size:13 final size:13
Alignment explanation
Indices: 10324763--10324808 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
10324753 TGTTTGGCAA
*
10324763 TGCTTTTGAAAAG
1 TGCTTTTGAGAAG
**
10324776 TAATTTTGAGAAG
1 TGCTTTTGAGAAG
10324789 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
10324802 TGCTTTT
1 TGCTTTT
10324809 AAAATTTTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.26, C:0.07, G:0.24, T:0.43
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:10327147 original size:72 final size:71
Alignment explanation
Indices: 10326874--10327156 Score: 338
Period size: 72 Copynumber: 3.9 Consensus size: 71
10326864 ATAATTTAGT
* * * * *
10326874 ATAAATAAGTAGAACATAAATTTAATATCCAAAAAGCAAACATAATCAATTATGGATAAAAACTA
1 ATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTGAT-AAAACTA
*
10326939 G-TCCTAAGC
65 GATAC--A-C
* * * * *
10326948 ATAAATAAGTAGACCATAAATTCAATATCCAAAGACCAAACATAAACAACTATTAACAAAACAAG
1 ATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAG
*
10327013 ATTTCAC
66 A-TACAC
* *
10327020 ATAAATAAGTCA-AACATAAATTCAATATCCAAAAATCAAACATAAACAACCATTGATAAAACTA
1 ATAAATAAGT-AGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTGATAAAACTA
10327084 GATGACAC
65 GAT-ACAC
*
10327092 ATAAATAAGTAGAACATAAAATT-AATATCCAAAAACCAAACATAAATAACTATTGATAAAACTA
1 ATAAATAAGTAGAACAT-AAATTCAATATCCAAAAACCAAACATAAACAACTATTGATAAAACTA
10327156 G
65 G
10327157 TTTAGCATTG
Statistics
Matches: 181, Mismatches: 22, Indels: 14
0.83 0.10 0.06
Matches are distributed among these distances:
71 2 0.01
72 115 0.64
73 14 0.08
74 48 0.27
75 2 0.01
ACGTcount: A:0.55, C:0.16, G:0.07, T:0.22
Consensus pattern (71 bp):
ATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTGATAAAACTAG
ATACAC
Found at i:10327153 original size:144 final size:145
Alignment explanation
Indices: 10326874--10327145 Score: 374
Period size: 146 Copynumber: 1.9 Consensus size: 145
10326864 ATAATTTAGT
* * **
10326874 ATAAATAAGTAGAACATAAATTTAATATCCAAAAAGCAAACATAATCAATTATGGATAAAAACTA
1 ATAAATAAGTAGAACATAAATTCAATATCCAAAAAGCAAACATAAACAACCATGGATAAAAACTA
* * *
10326939 GTCCTAAGCATAAATAAGTAGACCATAAATTCAATATCCAAAGACCAAACATAAACAACTATTAA
66 GTAC-AAGCATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTAA
10327004 CAAAACAAGATTTCAC
130 CAAAACAAGATTTCAC
* *
10327020 ATAAATAAGTCA-AACATAAATTCAATATCCAAAAATCAAACATAAACAACCATTGAT-AAAACT
1 ATAAATAAGT-AGAACATAAATTCAATATCCAAAAAGCAAACATAAACAACCATGGATAAAAACT
*
10327083 AGATGAC-A-CATAAATAAGTAGAACATAAAATT-AATATCCAAAAACCAAACATAAATAACTAT
65 AG-T-ACAAGCATAAATAAGTAGAACAT-AAATTCAATATCCAAAAACCAAACATAAACAACTAT
10327145 T
127 T
10327146 GATAAAACTA
Statistics
Matches: 112, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
144 46 0.41
145 14 0.12
146 50 0.45
147 2 0.02
ACGTcount: A:0.55, C:0.16, G:0.06, T:0.22
Consensus pattern (145 bp):
ATAAATAAGTAGAACATAAATTCAATATCCAAAAAGCAAACATAAACAACCATGGATAAAAACTA
GTACAAGCATAAATAAGTAGAACATAAATTCAATATCCAAAAACCAAACATAAACAACTATTAAC
AAAACAAGATTTCAC
Found at i:10327608 original size:18 final size:18
Alignment explanation
Indices: 10327585--10327632 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
10327575 TCCATCAATT
* *
10327585 TGAACACCATTTGAAATG
1 TGAACATCATTTAAAATG
10327603 TGAACATCATTTAAAATG
1 TGAACATCATTTAAAATG
10327621 TGAACATCATTT
1 TGAACATCATTT
10327633 CTCACATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (18 bp):
TGAACATCATTTAAAATG
Found at i:10330296 original size:9 final size:9
Alignment explanation
Indices: 10330272--10330312 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
10330262 TTTGAATTTT
*
10330272 ATAATTTAA
1 ATAATTCAA
*
10330281 ATTATTCAA
1 ATAATTCAA
*
10330290 ATAATTCGA
1 ATAATTCAA
10330299 ATAATTCAA
1 ATAATTCAA
10330308 ATAAT
1 ATAAT
10330313 AAATTGATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.39
Consensus pattern (9 bp):
ATAATTCAA
Found at i:10330419 original size:12 final size:12
Alignment explanation
Indices: 10330404--10330444 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
10330394 TTCAAAAAAT
10330404 AAAATATTTATA
1 AAAATATTTATA
*
10330416 AAAATATTT-TCC
1 AAAATATTTAT-A
10330428 AAAAT-TTTATA
1 AAAATATTTATA
10330439 AAAATA
1 AAAATA
10330445 AATATAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (12 bp):
AAAATATTTATA
Found at i:10330684 original size:52 final size:52
Alignment explanation
Indices: 10330584--10330685 Score: 150
Period size: 52 Copynumber: 2.0 Consensus size: 52
10330574 ATCATACTAA
* * *
10330584 TTTTGTTTTATTTTATTCTAAAAGAATTTTCAAATAGAGATGGCATTTATTT
1 TTTTCTTTTATTTTATTCTAAAAGAATTTTCAAATACAGATGACATTTATTT
* * *
10330636 TTTTCTTTTATTTTATTCTAAAAGAATTTTTAAATACATATGATATTTAT
1 TTTTCTTTTATTTTATTCTAAAAGAATTTTCAAATACAGATGACATTTAT
10330686 ATTCAAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.32, C:0.06, G:0.08, T:0.54
Consensus pattern (52 bp):
TTTTCTTTTATTTTATTCTAAAAGAATTTTCAAATACAGATGACATTTATTT
Found at i:10331289 original size:2 final size:2
Alignment explanation
Indices: 10331282--10331324 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
10331272 GGCTTCTTCT
10331282 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
10331324 T
1 T
10331325 TTTGCTATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:10336534 original size:25 final size:25
Alignment explanation
Indices: 10336500--10336555 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
10336490 AGAGCAAAGA
10336500 AAGTTT-CCAAGGGCAAGGTTTGCC
1 AAGTTTACCAAGGGCAAGGTTTGCC
10336524 AAGTTTACCAAGGGCAAGGTTTGCC
1 AAGTTTACCAAGGGCAAGGTTTGCC
10336549 AAGTTTA
1 AAGTTTA
10336556 GGTTCCATGG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 6 0.19
25 25 0.81
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (25 bp):
AAGTTTACCAAGGGCAAGGTTTGCC
Found at i:10337759 original size:59 final size:59
Alignment explanation
Indices: 10337686--10337798 Score: 199
Period size: 59 Copynumber: 1.9 Consensus size: 59
10337676 GTGTCTCCAT
10337686 AGATTAAGTCGAGATGAGTTAAGCCTATATCAATGGGCTTTTCATATAGAATACAAGTA
1 AGATTAAGTCGAGATGAGTTAAGCCTATATCAATGGGCTTTTCATATAGAATACAAGTA
* * *
10337745 AGATTAGGTCGAGATGAGTTAAGCCTATATTAATGGGGTTTTCATATAGAATAC
1 AGATTAAGTCGAGATGAGTTAAGCCTATATCAATGGGCTTTTCATATAGAATAC
10337799 GTAAGAAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (59 bp):
AGATTAAGTCGAGATGAGTTAAGCCTATATCAATGGGCTTTTCATATAGAATACAAGTA
Found at i:10356346 original size:21 final size:21
Alignment explanation
Indices: 10356320--10356360 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10356310 ATCTGCTCAA
* *
10356320 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
10356341 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
10356361 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:10364663 original size:25 final size:25
Alignment explanation
Indices: 10364635--10364685 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
10364625 TGCCCGCAAG
10364635 GTTTGTACTGATATTTGAAGAAGTA
1 GTTTGTACTGATATTTGAAGAAGTA
10364660 GTTTGTACTGATATTTGAAGAAGTA
1 GTTTGTACTGATATTTGAAGAAGTA
10364685 G
1 G
10364686 AACTAGACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.25, T:0.39
Consensus pattern (25 bp):
GTTTGTACTGATATTTGAAGAAGTA
Found at i:10366082 original size:3 final size:3
Alignment explanation
Indices: 10366074--10366107 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
10366064 CAATTTTACA
10366074 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
10366108 TGTGAGTAAG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:10366846 original size:14 final size:13
Alignment explanation
Indices: 10366825--10366854 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
10366815 GTAAAATGTT
10366825 TTTCGGAAAATAA
1 TTTCGGAAAATAA
10366838 TTTCTGGAAAATAA
1 TTTC-GGAAAATAA
10366852 TTT
1 TTT
10366855 ACTTTTCTAA
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:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (13 bp):
TTTCGGAAAATAA
Found at i:10366988 original size:20 final size:20
Alignment explanation
Indices: 10366963--10367002 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
10366953 CTGTTTTTAC
10366963 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
10366983 ATATATTAATAAATTTATAT
1 ATATATTAATAAATTTATAT
10367003 TTTAAATTGT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATATTAATAAATTTATAT
Found at i:10367007 original size:16 final size:18
Alignment explanation
Indices: 10366958--10367002 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
10366948 AAAAGCTGTT
* *
10366958 TTTACATATATTAATAAA
1 TTTATATATTTTAATAAA
10366976 TTTATATATATATTAATAAA
1 TTTATATAT-T-TTAATAAA
10366996 TTTATAT
1 TTTATAT
10367003 TTTAAATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATATATTTTAATAAA
Found at i:10367684 original size:54 final size:54
Alignment explanation
Indices: 10367620--10367727 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
10367610 TGTGCCAGAT
10367620 GAAGATACTTTTGTTCTTACCTCTTCAGTCTCTTCATTGTCCCAGTCTATATGC
1 GAAGATACTTTTGTTCTTACCTCTTCAGTCTCTTCATTGTCCCAGTCTATATGC
10367674 GAAGATACTTTTGTTCTTACCTCTTCAGTCTCTTCATTGTCCCAGTCTATATGC
1 GAAGATACTTTTGTTCTTACCTCTTCAGTCTCTTCATTGTCCCAGTCTATATGC
10367728 ACTGAATCTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.19, C:0.26, G:0.13, T:0.43
Consensus pattern (54 bp):
GAAGATACTTTTGTTCTTACCTCTTCAGTCTCTTCATTGTCCCAGTCTATATGC
Found at i:10368361 original size:32 final size:32
Alignment explanation
Indices: 10368315--10368394 Score: 90
Period size: 32 Copynumber: 2.5 Consensus size: 32
10368305 TGTCAATCAT
*
10368315 TTCAATATCCAACAAGCTT-AAAACATAATAAA
1 TTCAATATCCAACAA-ATTCAAAACATAATAAA
** * *
10368347 TTCAATATGTAACAAATTCAAGACATAATAAT
1 TTCAATATCCAACAAATTCAAAACATAATAAA
*
10368379 TTCAAAATCCAACAAA
1 TTCAATATCCAACAAA
10368395 CTAAAATTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 2 0.05
32 37 0.95
ACGTcount: A:0.53, C:0.17, G:0.04, T:0.26
Consensus pattern (32 bp):
TTCAATATCCAACAAATTCAAAACATAATAAA
Found at i:10370682 original size:2 final size:2
Alignment explanation
Indices: 10370677--10370719 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
10370667 ATATCTATTT
* * *
10370677 AC AC AC AT AC AC AT AC AC AT AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
10370719 A
1 A
10370720 TATATATATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.42, G:0.00, T:0.07
Consensus pattern (2 bp):
AC
Found at i:10370696 original size:12 final size:12
Alignment explanation
Indices: 10370677--10370721 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
10370667 ATATCTATTT
10370677 ACACACATACAC
1 ACACACATACAC
*
10370689 ATACACATACAC
1 ACACACATACAC
*
10370701 ACACACACACAC
1 ACACACATACAC
10370713 ACACACATA
1 ACACACATA
10370722 TATATATATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.51, C:0.40, G:0.00, T:0.09
Consensus pattern (12 bp):
ACACACATACAC
Found at i:10379596 original size:57 final size:58
Alignment explanation
Indices: 10379524--10379644 Score: 167
Period size: 57 Copynumber: 2.1 Consensus size: 58
10379514 TTTCAGGTCT
* * * *
10379524 TTTTCATTTTTATTTTGGAGATAACCA-CATCCATTTCCAAATGATTT-C-ATTTCTCTA
1 TTTTCATTTTCATTTTGGAGAAAACCATAAT-CATTTCCAAATG-TTTCCTATTTCTCCA
10379581 TTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCCTATTTCTCCA
1 TTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCCTATTTCTCCA
10379639 TTTTCA
1 TTTTCA
10379645 CTATTTCTAT
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
56 3 0.05
57 38 0.67
58 16 0.28
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.47
Consensus pattern (58 bp):
TTTTCATTTTCATTTTGGAGAAAACCATAATCATTTCCAAATGTTTCCTATTTCTCCA
Found at i:10385804 original size:17 final size:17
Alignment explanation
Indices: 10385782--10385815 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
10385772 CCTTAGACTA
10385782 CTATTTATATACTATTT
1 CTATTTATATACTATTT
10385799 CTATTTATATACTATTT
1 CTATTTATATACTATTT
10385816 AATGATGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (17 bp):
CTATTTATATACTATTT
Found at i:10386256 original size:5 final size:5
Alignment explanation
Indices: 10386248--10386275 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
10386238 AATATAGTGG
10386248 TAAAA TAAAA TAAAA TAAAA TAAAA TAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAA
10386276 GAATCCATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:10390942 original size:5 final size:5
Alignment explanation
Indices: 10390932--10390959 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
10390922 TTGTGTGTTC
10390932 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
10390960 CACAGAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:10396510 original size:7 final size:6
Alignment explanation
Indices: 10396488--10396531 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
10396478 TTAGAATTTA
* * *
10396488 AAAAAT AAAAAT AAAACT AAAAAT ATCAAAT TAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A-AAAAT AAAAAT AAAAAT A
10396532 TTAAATCTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
6 27 0.87
7 4 0.13
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAAAT
Found at i:10396537 original size:19 final size:20
Alignment explanation
Indices: 10396486--10396537 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
10396476 TTTTAGAATT
*
10396486 TAAAAA-ATAAAAATAAAAC
1 TAAAAATATAAAATTAAAAC
*
10396505 TAAAAATATCAAATTAAAA-
1 TAAAAATATAAAATTAAAAC
*
10396524 TAAAAATATTAAAT
1 TAAAAATATAAAAT
10396538 CTAATTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (20 bp):
TAAAAATATAAAATTAAAAC
Found at i:10405519 original size:6 final size:6
Alignment explanation
Indices: 10405501--10405556 Score: 85
Period size: 6 Copynumber: 9.3 Consensus size: 6
10405491 ATATGAAGAC
* *
10405501 AAAATA AACATA AAAATA AAAATA AAAATA AAAATA AAAATA AACATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
*
10405549 AAGATA AA
1 AAAATA AA
10405557 TGGACTCAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:10405524 original size:18 final size:18
Alignment explanation
Indices: 10405501--10405556 Score: 94
Period size: 18 Copynumber: 3.1 Consensus size: 18
10405491 ATATGAAGAC
10405501 AAAATAAACATAAAAATA
1 AAAATAAACATAAAAATA
*
10405519 AAAATAAAAATAAAAATA
1 AAAATAAACATAAAAATA
*
10405537 AAAATAAACATAAAGATA
1 AAAATAAACATAAAAATA
10405555 AA
1 AA
10405557 TGGACTCAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.79, C:0.04, G:0.02, T:0.16
Consensus pattern (18 bp):
AAAATAAACATAAAAATA
Found at i:10407320 original size:15 final size:15
Alignment explanation
Indices: 10407290--10407331 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
10407280 TGCAAGAATC
10407290 AAAATAAAAT-AATT
1 AAAATAAAATAAATT
*
10407304 AAACTAAAATAAATT
1 AAAATAAAATAAATT
*
10407319 AAAAGAAAATAAA
1 AAAATAAAATAAA
10407332 AAGAATAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.21
Consensus pattern (15 bp):
AAAATAAAATAAATT
Found at i:10407340 original size:9 final size:9
Alignment explanation
Indices: 10407320--10407355 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
10407310 AAATAAATTA
10407320 AAAGAAAAT
1 AAAGAAAAT
10407329 AAA-AAGAAT
1 AAAGAA-AAT
10407338 AAAGAAAAT
1 AAAGAAAAT
10407347 AAAGAAAAT
1 AAAGAAAAT
10407356 GGAGAACAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 2 0.08
9 21 0.84
10 2 0.08
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (9 bp):
AAAGAAAAT
Found at i:10408005 original size:71 final size:71
Alignment explanation
Indices: 10407921--10408074 Score: 218
Period size: 71 Copynumber: 2.2 Consensus size: 71
10407911 GGTCGTATCG
* *** * *
10407921 CACGGCCGTGTGTAATGTTGTTCGCTTTTCCTTTGCTCGTGTGACTTCCCACATGCCCGTGTGTC
1 CACGGCCGTGTGTAATGTTGTTCGCTTCTCCTCCACTCGTGTGACTTCCCACACGCCCGTCTGTC
10407986 TGAACA
66 TGAACA
* * *
10407992 CACGGCCATGTGTAATGTTGTTCGCTTCTCCTCCACTCGTGTGGCTTCCCACACGCCCGTCTGTT
1 CACGGCCGTGTGTAATGTTGTTCGCTTCTCCTCCACTCGTGTGACTTCCCACACGCCCGTCTGTC
10408057 TGAACA
66 TGAACA
*
10408063 CATGGCCGTGTG
1 CACGGCCGTGTG
10408075 CCTCGCCTGT
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 72 1.00
ACGTcount: A:0.13, C:0.31, G:0.24, T:0.32
Consensus pattern (71 bp):
CACGGCCGTGTGTAATGTTGTTCGCTTCTCCTCCACTCGTGTGACTTCCCACACGCCCGTCTGTC
TGAACA
Found at i:10408794 original size:27 final size:27
Alignment explanation
Indices: 10408746--10408797 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
10408736 GGCTATCCTG
* * * *
10408746 TGTTTAACTTTCCGTCAGACTATCTCA
1 TGTTTAACGTCCCATCAAACTATCTCA
10408773 TGTTTAACGTCCCATCAAACTATCT
1 TGTTTAACGTCCCATCAAACTATCT
10408798 ATGATGTCGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.25, C:0.27, G:0.10, T:0.38
Consensus pattern (27 bp):
TGTTTAACGTCCCATCAAACTATCTCA
Found at i:10411581 original size:9 final size:9
Alignment explanation
Indices: 10411567--10411593 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
10411557 AACCAAGTTT
10411567 TTCAATTTA
1 TTCAATTTA
10411576 TTCAATTTA
1 TTCAATTTA
10411585 TTCAATTTA
1 TTCAATTTA
10411594 GTCCCTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (9 bp):
TTCAATTTA
Found at i:10411869 original size:45 final size:44
Alignment explanation
Indices: 10411818--10411946 Score: 120
Period size: 45 Copynumber: 2.9 Consensus size: 44
10411808 ACTATCAAAG
*
10411818 GATGCCATAATTCCTTTCAGCCATAGTTTTACTCATTTTCA-TCAT
1 GATGCCATAATTCCTTTCAGCTAT-GTTTTACTCATTTTCATTC-T
* * *
10411863 GATGCCATAGCA-T-CTTTTAGCTATGGTCTTACTCATTTCCATTCT
1 GATGCCATA--ATTCCTTTCAGCTAT-GTTTTACTCATTTTCATTCT
* * *
10411908 GATGCCATAGTACCTTTCGGCTATGATTTTACTCATTTT
1 GATGCCATAATTCCTTTCAGCTATG-TTTTACTCATTTT
10411947 AGGCATATAG
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
44 1 0.01
45 62 0.93
46 3 0.04
47 1 0.01
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.43
Consensus pattern (44 bp):
GATGCCATAATTCCTTTCAGCTATGTTTTACTCATTTTCATTCT
Found at i:10425236 original size:26 final size:25
Alignment explanation
Indices: 10425154--10425236 Score: 71
Period size: 25 Copynumber: 3.3 Consensus size: 25
10425144 GGCTCTCACA
* * *
10425154 AGCTTCCCGTTACATGGTTC-ACATG
1 AGCTTCCCATTATATGGCTCGA-ATG
*
10425179 AGCTTCCCATTATATGGCTCGAAAG
1 AGCTTCCCATTATATGGCTCGAATG
* *
10425204 AGCTTCCCGTT-TATGTGCTCGTATG
1 AGCTTCCCATTATATG-GCTCGAATG
10425229 AGCATTCC
1 AGC-TTCC
10425237 TGAATATGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
24 4 0.08
25 39 0.81
26 5 0.10
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (25 bp):
AGCTTCCCATTATATGGCTCGAATG
Found at i:10431499 original size:30 final size:30
Alignment explanation
Indices: 10431464--10431521 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
10431454 CAAGCACTTC
* **
10431464 CACACGGGTAAACCACTTGCCCGTGTGTGA
1 CACACGGGCAAACCACACGCCCGTGTGTGA
*
10431494 CACACGGGCAAGCCACACGCCCGTGTGT
1 CACACGGGCAAACCACACGCCCGTGTGT
10431522 CATGGCCCTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.22, C:0.34, G:0.28, T:0.16
Consensus pattern (30 bp):
CACACGGGCAAACCACACGCCCGTGTGTGA
Found at i:10436385 original size:3 final size:3
Alignment explanation
Indices: 10436377--10436425 Score: 66
Period size: 3 Copynumber: 16.7 Consensus size: 3
10436367 ACCCTTCCCA
*
10436377 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GA-A ATT ATT ATT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT
10436421 ATT AT
1 ATT AT
10436426 GCATTTTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 3 0.07
3 37 0.90
4 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:10442277 original size:13 final size:13
Alignment explanation
Indices: 10442259--10442311 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 13
10442249 TATGGTGCAC
10442259 ACGGCCGTGTCGA
1 ACGGCCGTGTCGA
*
10442272 ACGGCCGTGTGGTGCA
1 ACGGCCGTGT--CG-A
10442288 CACGGCCGTGTCGA
1 -ACGGCCGTGTCGA
10442302 ACGGCCGTGT
1 ACGGCCGTGT
10442312 GCACTGTCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
13 20 0.59
14 1 0.03
15 2 0.06
16 1 0.03
17 10 0.29
ACGTcount: A:0.13, C:0.30, G:0.40, T:0.17
Consensus pattern (13 bp):
ACGGCCGTGTCGA
Found at i:10442285 original size:30 final size:30
Alignment explanation
Indices: 10442245--10442312 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
10442235 ATGTCCCCAA
*
10442245 GCCGTATGGTGCACACGGCCGTGTCGAACG
1 GCCGTGTGGTGCACACGGCCGTGTCGAACG
10442275 GCCGTGTGGTGCACACGGCCGTGTCGAACG
1 GCCGTGTGGTGCACACGGCCGTGTCGAACG
10442305 GCCGTGTG
1 GCCGTGTG
10442313 CACTGTCATT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.13, C:0.29, G:0.40, T:0.18
Consensus pattern (30 bp):
GCCGTGTGGTGCACACGGCCGTGTCGAACG
Found at i:10442294 original size:17 final size:17
Alignment explanation
Indices: 10442245--10442298 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
10442235 ATGTCCCCAA
*
10442245 GCCGTATGGTGCACACG
1 GCCGTGTGGTGCACACG
*
10442262 GCCGTGT--CG-A-ACG
1 GCCGTGTGGTGCACACG
10442275 GCCGTGTGGTGCACACG
1 GCCGTGTGGTGCACACG
10442292 GCCGTGT
1 GCCGTGT
10442299 CGAACGGCCG
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
13 10 0.33
14 1 0.03
15 2 0.07
16 1 0.03
17 16 0.53
ACGTcount: A:0.13, C:0.30, G:0.39, T:0.19
Consensus pattern (17 bp):
GCCGTGTGGTGCACACG
Found at i:10446993 original size:13 final size:13
Alignment explanation
Indices: 10446975--10447008 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
10446965 TCTTCTTTAT
10446975 CAGCTTCTGGTTG
1 CAGCTTCTGGTTG
10446988 CAGCTTCTGGTTG
1 CAGCTTCTGGTTG
10447001 CAGCTTCT
1 CAGCTTCT
10447009 TTTCATATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.09, C:0.26, G:0.26, T:0.38
Consensus pattern (13 bp):
CAGCTTCTGGTTG
Found at i:10448763 original size:49 final size:49
Alignment explanation
Indices: 10448697--10448792 Score: 156
Period size: 49 Copynumber: 2.0 Consensus size: 49
10448687 TATAGTTATG
* *
10448697 GGGAAACCGGAAATGTCGTATCCACGAGGCCTAAAAGTACTAGTAATTA
1 GGGAAACCAGAAATGTCGTATCCACGAGGACTAAAAGTACTAGTAATTA
* *
10448746 GGGAGACCAGAAATGTCGTATCCATGAGGACTAAAAGTACTAGTAAT
1 GGGAAACCAGAAATGTCGTATCCACGAGGACTAAAAGTACTAGTAAT
10448793 CACTATCTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.21
Consensus pattern (49 bp):
GGGAAACCAGAAATGTCGTATCCACGAGGACTAAAAGTACTAGTAATTA
Found at i:10450545 original size:6 final size:6
Alignment explanation
Indices: 10450536--10450591 Score: 60
Period size: 6 Copynumber: 9.2 Consensus size: 6
10450526 TCATTATTAC
* * *
10450536 TATTTT TATTTT TATTTT TATTTT TCTTTT TCTTTT T-CTTT TACTTATT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TA-TT-TT
10450585 TATTTT T
1 TATTTT T
10450592 GAAGACTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
5 4 0.09
6 33 0.75
7 3 0.07
8 4 0.09
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.80
Consensus pattern (6 bp):
TATTTT
Found at i:10450571 original size:18 final size:18
Alignment explanation
Indices: 10450536--10450591 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
10450526 TCATTATTAC
*
10450536 TATTTTTATTTTTATTTT
1 TATTTTTCTTTTTATTTT
*
10450554 TATTTTTCTTTTTCTTTT
1 TATTTTTCTTTTTATTTT
* *
10450572 TCTTTTACTTATTTATTTT
1 TATTTTTCTT-TTTATTTT
10450591 T
1 T
10450592 GAAGACTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 24 0.75
19 8 0.25
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.80
Consensus pattern (18 bp):
TATTTTTCTTTTTATTTT
Found at i:10455911 original size:25 final size:26
Alignment explanation
Indices: 10455869--10455917 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
10455859 AGTTGTAAAT
10455869 CAGAAAAATATCTCTAGA-AATTTTC
1 CAGAAAAATATCTCTAGAGAATTTTC
* * *
10455894 CAGAATAATCTCTTTAGAGAATTT
1 CAGAAAAATATCTCTAGAGAATTT
10455918 CCTTTTACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (26 bp):
CAGAAAAATATCTCTAGAGAATTTTC
Found at i:10456609 original size:19 final size:19
Alignment explanation
Indices: 10456576--10456615 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
10456566 AAAATATCAT
*
10456576 ATTAATTTTAATTTATTTG
1 ATTAATTTTAATTTACTTG
10456595 ATTAA-TTTAATTTTACTTG
1 ATTAATTTTAA-TTTACTTG
10456614 AT
1 AT
10456616 CAAAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
ATTAATTTTAATTTACTTG
Found at i:10466251 original size:17 final size:16
Alignment explanation
Indices: 10466206--10466255 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 16
10466196 GCATATATAA
10466206 TTTTTTAT-ATTACTTC
1 TTTTTTATAATTA-TTC
10466222 TTTTTAATATAATTATTC
1 TTTTT--TATAATTATTC
10466240 TTATTTTATAATTATT
1 TT-TTTTATAATTATT
10466256 TGTAAATTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.17
17 10 0.33
18 8 0.27
19 7 0.23
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTTATAATTATTC
Found at i:10474222 original size:17 final size:17
Alignment explanation
Indices: 10474196--10474236 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
10474186 ATATACATAA
10474196 TTTATCATTT-TAAATAT
1 TTTATCATTTATAAA-AT
*
10474213 TTTATTATTTATAAAA-
1 TTTATCATTTATAAAAT
10474229 TTTATCAT
1 TTTATCAT
10474237 AAAAACTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 7 0.33
17 10 0.48
18 4 0.19
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTATCATTTATAAAAT
Found at i:10474527 original size:17 final size:18
Alignment explanation
Indices: 10474505--10474550 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
10474495 TTTTTAATTA
10474505 TTTATATAATAAAT-AAT
1 TTTATATAATAAATAAAT
* *
10474522 TTTATATTATATATAAAT
1 TTTATATAATAAATAAAT
10474540 TTTATA-AATAA
1 TTTATATAATAA
10474551 TGCACTACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTATATAATAAATAAAT
Found at i:10475064 original size:6 final size:6
Alignment explanation
Indices: 10475053--10475094 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
10475043 TAATTATTTG
10475053 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
10475095 ATTACGTACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTATAT
Found at i:10480847 original size:9 final size:8
Alignment explanation
Indices: 10480826--10480860 Score: 52
Period size: 9 Copynumber: 4.1 Consensus size: 8
10480816 TACATTTCAC
10480826 AAAATAAA
1 AAAATAAA
10480834 AAAATAATA
1 AAAATAA-A
10480843 AAAATAAA
1 AAAATAAA
10480851 AAACATAAA
1 AAA-ATAAA
10480860 A
1 A
10480861 TGCAGGAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 11 0.44
9 14 0.56
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (8 bp):
AAAATAAA
Found at i:10495056 original size:21 final size:21
Alignment explanation
Indices: 10495030--10495070 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10495020 AGACGAGCAA
* *
10495030 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
10495051 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
10495071 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:10504093 original size:71 final size:71
Alignment explanation
Indices: 10504016--10504167 Score: 173
Period size: 71 Copynumber: 2.1 Consensus size: 71
10504006 TTTAGTGAGC
* * * * * *
10504016 AACATCGAATTATATTTTAGT-ATTTGCTGAGATCTT-GCATAAGTTGCGTATTCTCGATAGCTT
1 AACATCGAATTATACTTTAGTGA-TGGCTGAGAT-TTAGCACAAGTTACGGATTCACGATAGCTT
10504079 GAGTAAGT
64 GAGTAAGT
* * *
10504087 AGCATCGAATTATACTTTATTGATGGCTGAGATTTAGCACATGTTACGGATTCACGATAGCTTGA
1 AACATCGAATTATACTTTAGTGATGGCTGAGATTTAGCACAAGTTACGGATTCACGATAGCTTGA
*
10504152 GTGAGT
66 GTAAGT
*
10504158 AACATTGAAT
1 AACATCGAAT
10504168 AAAACTTATT
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
70 2 0.03
71 64 0.96
72 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.36
Consensus pattern (71 bp):
AACATCGAATTATACTTTAGTGATGGCTGAGATTTAGCACAAGTTACGGATTCACGATAGCTTGA
GTAAGT
Found at i:10511048 original size:30 final size:30
Alignment explanation
Indices: 10511012--10511072 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
10511002 CATGGGCTGG
* *
10511012 CACATGGGCGTGTAG-CCTGCCCGTGTGGAT
1 CACATGGGCATGT-GCCCAGCCCGTGTGGAT
10511042 CACATGGGCATGTGCCCAGCCCGTGTGGAT
1 CACATGGGCATGTGCCCAGCCCGTGTGGAT
10511072 C
1 C
10511073 CTGAAAACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.04
30 27 0.96
ACGTcount: A:0.15, C:0.30, G:0.34, T:0.21
Consensus pattern (30 bp):
CACATGGGCATGTGCCCAGCCCGTGTGGAT
Found at i:10512893 original size:12 final size:11
Alignment explanation
Indices: 10512850--10512927 Score: 53
Period size: 10 Copynumber: 7.5 Consensus size: 11
10512840 AGTTGAAGAG
10512850 AAAAAAA-ATA
1 AAAAAAATATA
* *
10512860 AAACAACTA-A
1 AAAAAAATATA
*
10512870 AACAAAAT-TA
1 AAAAAAATATA
10512880 AAAAGAAATATA
1 AAAA-AAATATA
10512892 AAAAATAATA-A
1 AAAAA-AATATA
*
10512903 TAAAAAA-AT-
1 AAAAAAATATA
10512912 AAAAAAATA-A
1 AAAAAAATATA
10512922 AAAAAA
1 AAAAAA
10512928 TAAACTCAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
9 7 0.13
10 24 0.46
11 11 0.21
12 10 0.19
ACGTcount: A:0.81, C:0.04, G:0.01, T:0.14
Consensus pattern (11 bp):
AAAAAAATATA
Found at i:10512908 original size:14 final size:15
Alignment explanation
Indices: 10512886--10512930 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
10512876 ATTAAAAAGA
10512886 AATATAAAAAATAAT
1 AATATAAAAAATAAT
*
10512901 AATA-AAAAAATAAA
1 AATATAAAAAATAAT
*
10512915 AAAATAAAAAA-AAT
1 AATATAAAAAATAAT
10512929 AA
1 AA
10512931 ACTCAATGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (15 bp):
AATATAAAAAATAAT
Found at i:10512916 original size:9 final size:9
Alignment explanation
Indices: 10512850--10512931 Score: 67
Period size: 9 Copynumber: 8.3 Consensus size: 9
10512840 AGTTGAAGAG
10512850 AAAAAAAAT
1 AAAAAAAAT
* *
10512859 AAAACAACT
1 AAAAAAAAT
10512868 AAAACAAAATT
1 AAAA-AAAA-T
10512879 AAAAAGAAATAT
1 -AAAA-AAA-AT
10512891 AAAAAATAAT
1 AAAAAA-AAT
10512901 AATAAAAAA-
1 AA-AAAAAAT
10512910 ATAAAAAAAT
1 A-AAAAAAAT
10512920 AAAAAAAAT
1 AAAAAAAAT
10512929 AAA
1 AAA
10512932 CTCAATGATA
Statistics
Matches: 60, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
9 29 0.48
10 12 0.20
11 10 0.17
12 8 0.13
13 1 0.02
ACGTcount: A:0.80, C:0.04, G:0.01, T:0.15
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:10513053 original size:16 final size:16
Alignment explanation
Indices: 10513032--10513079 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
10513022 GCAAAATAAA
*
10513032 ATATAATAA-TAAAAGT
1 ATATAAAAATTAAAA-T
10513048 ATATAAAAATTAAAAT
1 ATATAAAAATTAAAAT
*
10513064 ATAAAAAAATTAAAAT
1 ATATAAAAATTAAAAT
10513080 TAAAAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 24 0.83
17 5 0.17
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (16 bp):
ATATAAAAATTAAAAT
Found at i:10513065 original size:14 final size:14
Alignment explanation
Indices: 10513024--10513086 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 14
10513014 TAGAAATAGC
10513024 AAAA-TAAAATATA
1 AAAATTAAAATATA
* *
10513037 ATAATAAAAGTATATA
1 AAAATTAAA--ATATA
10513053 AAAATTAAAATATAAA
1 AAAATTAAAATAT--A
10513069 AAAATTAAAAT-TA
1 AAAATTAAAATATA
10513082 AAAAT
1 AAAAT
10513087 ATAAGTATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
13 9 0.22
14 7 0.17
15 1 0.02
16 24 0.59
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (14 bp):
AAAATTAAAATATA
Found at i:10513085 original size:16 final size:16
Alignment explanation
Indices: 10513041--10513085 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
10513031 AATATAATAA
*
10513041 TAAAAGTATATAAAAAT
1 TAAAA-TATAAAAAAAT
10513058 TAAAATATAAAAAAAT
1 TAAAATATAAAAAAAT
10513074 TAAAAT-TAAAAA
1 TAAAATATAAAAA
10513086 TATAAGTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 6 0.22
16 16 0.59
17 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (16 bp):
TAAAATATAAAAAAAT
Found at i:10513159 original size:22 final size:20
Alignment explanation
Indices: 10513129--10513180 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 20
10513119 AATTAATTAG
*
10513129 TAAAATAAAAATAAATAATA
1 TAAAATAAAAATAAATAAAA
10513149 TAACAATTAAAAATAAATAAAA
1 TAA-AA-TAAAAATAAATAAAA
10513171 TAAAATAAAA
1 TAAAATAAAA
10513181 TTGGGGTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 8 0.28
21 4 0.14
22 17 0.59
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (20 bp):
TAAAATAAAAATAAATAAAA
Found at i:10515950 original size:31 final size:31
Alignment explanation
Indices: 10515909--10515971 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
10515899 GCCTTATTTC
10515909 TCAACAAGAAGGGGAATAATCCAAATGAGTA
1 TCAACAAGAAGGGGAATAATCCAAATGAGTA
*
10515940 TCAACGAGAAGGGGAATAATCCAAATGAGTA
1 TCAACAAGAAGGGGAATAATCCAAATGAGTA
10515971 T
1 T
10515972 TTGGGTCTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.46, C:0.13, G:0.24, T:0.17
Consensus pattern (31 bp):
TCAACAAGAAGGGGAATAATCCAAATGAGTA
Found at i:10517255 original size:26 final size:30
Alignment explanation
Indices: 10517196--10517255 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
10517186 CCATATTATA
10517196 AATTGATTGGTTAATGATTTTCAATGGATG
1 AATTGATTGGTTAATGATTTTCAATGGATG
*
10517226 AATTGTTTGG-TAA-GATTTT-AATGGAT-
1 AATTGATTGGTTAATGATTTTCAATGGATG
10517252 AATT
1 AATT
10517256 TGAATGGTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 4 0.14
27 7 0.24
28 6 0.21
29 3 0.10
30 9 0.31
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.45
Consensus pattern (30 bp):
AATTGATTGGTTAATGATTTTCAATGGATG
Done.