Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 175 of 202
Found at i:54486129 original size:18 final size:18
Alignment explanation
Indices: 54486096--54486130 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54486086 ACCAGCAGAT
* *
54486096 GGCATACTGACTTGTTGG
1 GGCATACTAACCTGTTGG
54486114 GGCATACTAACCTGTTG
1 GGCATACTAACCTGTTG
54486131 TGGAGAGCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.31
Consensus pattern (18 bp):
GGCATACTAACCTGTTGG
Found at i:54487385 original size:15 final size:15
Alignment explanation
Indices: 54487365--54487395 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
54487355 CTATCATCTT
54487365 TAACTGCTAACAGAC
1 TAACTGCTAACAGAC
54487380 TAACTGCTAACAGAC
1 TAACTGCTAACAGAC
54487395 T
1 T
54487396 TACAACGGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.23
Consensus pattern (15 bp):
TAACTGCTAACAGAC
Found at i:54487429 original size:20 final size:20
Alignment explanation
Indices: 54487404--54487445 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
54487394 CTTACAACGG
*
54487404 TACAACGGTTTTGACTATAT
1 TACAACGGCTTTGACTATAT
*
54487424 TACAACTGCTTTGACTATAT
1 TACAACGGCTTTGACTATAT
54487444 TA
1 TA
54487446 ACTCTAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
TACAACGGCTTTGACTATAT
Found at i:54489905 original size:9 final size:9
Alignment explanation
Indices: 54489888--54489918 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
54489878 TCGAGTTGAT
54489888 TCGAATAAC
1 TCGAATAAC
*
54489897 TCGATTAAC
1 TCGAATAAC
54489906 TCGAATAAC
1 TCGAATAAC
54489915 TCGA
1 TCGA
54489919 TTTCTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:54493118 original size:24 final size:24
Alignment explanation
Indices: 54493086--54493137 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
54493076 AAGGCATCAA
* *
54493086 AGTTGATCTGAGCAAAATTTCAGC
1 AGTTAATCTGAGAAAAATTTCAGC
*
54493110 AGTTAATCTGAGAAAAATTTCAGT
1 AGTTAATCTGAGAAAAATTTCAGC
54493134 AGTT
1 AGTT
54493138 GTTGATTGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (24 bp):
AGTTAATCTGAGAAAAATTTCAGC
Found at i:54499664 original size:41 final size:41
Alignment explanation
Indices: 54499614--54499713 Score: 141
Period size: 41 Copynumber: 2.4 Consensus size: 41
54499604 GGCTTAGCAC
*
54499614 CTAGCAGGCTTATTGCC-AGTGAAACAATTCAGACTATATGT
1 CTAGCAGGCTTAATGCCGA-TGAAACAATTCAGACTATATGT
* *
54499655 CTAGTAGGCTTAATGCCGATGAAACATTTCAGACTATATGT
1 CTAGCAGGCTTAATGCCGATGAAACAATTCAGACTATATGT
54499696 CTAGCAGGC-TAAGTGCCG
1 CTAGCAGGCTTAA-TGCCG
54499714 GTGTATTGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
40 3 0.06
41 49 0.92
42 1 0.02
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGATGAAACAATTCAGACTATATGT
Found at i:54504090 original size:131 final size:131
Alignment explanation
Indices: 54503877--54504330 Score: 714
Period size: 131 Copynumber: 3.5 Consensus size: 131
54503867 CTGTAGTCTC
* * * * *
54503877 AGGG-AGATAAGATTCGCCGTATT-GATTTGCTCCGCTACTGCTTAGGGAGATAAGATCTGCAAT
1 AGGGAAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGCAAT
* * *
54503940 TTCCAACCTATTCCACTGCTGGTCAGGGACATAGAACTTGTGGCCTAAATCTGTTTCTCTACTCC
66 TTCCAACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCC
54504005 T
131 T
* * * *
54504006 AGGGAAGATAAGATTTGCCGTCTTCGATCTGCTCCATTATTGCTTAGGGAGACAAGATCTGCAAT
1 AGGGAAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGCAAT
54504071 TTCCAACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCC
66 TTCCAACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCC
54504136 T
131 T
* * * *
54504137 GGGGAAGATAAGATTCGTCATCTTCAATCTGCTCCACTATTGCTTAGGGAGACAAGATCTGCAAT
1 AGGGAAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGCAAT
54504202 TTCCAACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCC
66 TTCCAACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCC
54504267 T
131 T
* ** *
54504268 GGGGAAGATAAGATTCGCCATCTTCGATCTGCTCCGTTACTGCTTAGTGAGACAAGATCTGCA
1 AGGGAAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGCA
54504331 GTCTTTACTA
Statistics
Matches: 301, Mismatches: 22, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
129 4 0.01
130 17 0.06
131 280 0.93
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (131 bp):
AGGGAAGATAAGATTCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGCAAT
TTCCAACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCC
T
Found at i:54510548 original size:21 final size:20
Alignment explanation
Indices: 54510522--54510561 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
54510512 CTTCTACTGC
*
54510522 CTTCCATTTCCTCTGCTCTTT
1 CTTCCAATT-CTCTGCTCTTT
*
54510543 CTTCCAATTCTCTTCTCTT
1 CTTCCAATTCTCTGCTCTT
54510562 GACAATTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.07, C:0.38, G:0.03, T:0.53
Consensus pattern (20 bp):
CTTCCAATTCTCTGCTCTTT
Found at i:54519586 original size:17 final size:17
Alignment explanation
Indices: 54519554--54519588 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
54519544 AAGATATGAT
54519554 TCAACAACTTAATTAAC
1 TCAACAACTTAATTAAC
54519571 TCAA-AACTTAACTTAAC
1 TCAACAACTTAA-TTAAC
54519588 T
1 T
54519589 ATCTCAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (17 bp):
TCAACAACTTAATTAAC
Found at i:54521037 original size:3 final size:3
Alignment explanation
Indices: 54521029--54521081 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
54521019 AAAGCTTCTT
54521029 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54521077 TTA TT
1 TTA TT
54521082 TTGCATTCTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:54521473 original size:4 final size:4
Alignment explanation
Indices: 54521464--54521513 Score: 73
Period size: 4 Copynumber: 12.5 Consensus size: 4
54521454 ACAAAACGGC
* * *
54521464 TACA TACA TACA AACA TGCA TACA TACA TGCA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
54521512 TA
1 TA
54521514 TATATATGCA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.48, C:0.24, G:0.04, T:0.24
Consensus pattern (4 bp):
TACA
Found at i:54521837 original size:2 final size:2
Alignment explanation
Indices: 54521830--54521854 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54521820 TGCATGTATA
54521830 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
54521855 TTTCCTTTGG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:54524846 original size:4 final size:4
Alignment explanation
Indices: 54524839--54524889 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
54524829 CCTATCTGTT
54524839 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
1 TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC TATC
54524887 TAT
1 TAT
54524890 ATAGTAATCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.25, C:0.24, G:0.00, T:0.51
Consensus pattern (4 bp):
TATC
Found at i:54530225 original size:20 final size:22
Alignment explanation
Indices: 54530200--54530245 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
54530190 CCAAGCTCCC
54530200 ATTTGGGATCTC-AAA-TTTAG
1 ATTTGGGATCTCAAAATTTTAG
*
54530220 ATTT-GGATTTCAAAATTTTAG
1 ATTTGGGATCTCAAAATTTTAG
54530241 ATTTG
1 ATTTG
54530246 AAAATTATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 6 0.27
20 7 0.32
21 9 0.41
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (22 bp):
ATTTGGGATCTCAAAATTTTAG
Found at i:54531214 original size:2 final size:2
Alignment explanation
Indices: 54531207--54531238 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
54531197 ATTGACACAA
*
54531207 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54531239 TAAGTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:54533283 original size:3 final size:3
Alignment explanation
Indices: 54533275--54533327 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
54533265 ATACTAAATA
** * * *
54533275 AAT AAT AAT AGG AAA AAT AAAT AAT AAT AAT GAT AAT AAT AAT AAG
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
54533321 AAT AAT A
1 AAT AAT A
54533328 CGAAAAACAA
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:54535504 original size:18 final size:17
Alignment explanation
Indices: 54535471--54535509 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
54535461 TTTTATAAAT
54535471 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
54535489 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
54535506 TGTG
1 TGTG
54535510 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:54535759 original size:23 final size:23
Alignment explanation
Indices: 54535727--54535802 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
54535717 AGTGTTATTG
*
54535727 ATCAGGGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
54535750 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
54535773 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
54535796 ATCAGTG
1 ATCAGTG
54535803 TGGCACTTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:54535978 original size:38 final size:37
Alignment explanation
Indices: 54535932--54536004 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
54535922 ATGTGTGGAA
* *
54535932 TTGAATTGAATATTGACTTGAAAA-TGGAAAAGTGAATT
1 TTGAATTGAATAGTGA-TT-AAAAGTGAAAAAGTGAATT
54535970 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
54536005 ATTATGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.45, C:0.01, G:0.22, T:0.32
Consensus pattern (37 bp):
TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAATT
Found at i:54539314 original size:28 final size:28
Alignment explanation
Indices: 54539274--54539399 Score: 173
Period size: 28 Copynumber: 4.5 Consensus size: 28
54539264 TGACTTTCGA
*
54539274 CACTAAGTGTGCGAATTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
54539302 CACTAAGTGTGCGAGTTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* *
54539330 CACTAAGTGTGCGAGTTTAATGGCAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * * *
54539358 CACTAAGTGTGTGAGTTTGATTATTGAA-
1 CACTAAGTGTGCGAGTTTAATT-GTAAAG
54539386 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
54539400 ACTTATTGAA
Statistics
Matches: 87, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
28 85 0.98
29 2 0.02
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:54540163 original size:23 final size:23
Alignment explanation
Indices: 54540128--54540483 Score: 180
Period size: 23 Copynumber: 15.3 Consensus size: 23
54540118 TGGTGAACAA
*
54540128 ATGCTGTCCAATTTTGTATATAC
1 ATGCTGTCAAATTTTGTATATAC
* *
54540151 ATGCCGTCAAATTTTGTGTATA-
1 ATGCTGTCAAATTTTGTATATAC
* *
54540173 AGTGCTGTCCAAA--TTGCTACATAT
1 A-TGCTGT-CAAATTTTG-TATATAC
* * *
54540197 ATGCTGCCCAATTTTGGTGA-ATAA
1 ATGCTGTCAAATTTT-GT-ATATAC
*
54540221 ATGCTGTCCAATTTTGTATATAC
1 ATGCTGTCAAATTTTGTATATAC
*
54540244 ATGCTGTCAAATTTTGTGTATA-
1 ATGCTGTCAAATTTTGTATATAC
* *
54540266 ACTGCTGTCCAAA--TTGCTACATAT
1 A-TGCTGT-CAAATTTTG-TATATAC
* * *
54540290 ATGCTGCCCAATTTTGGTGA-ATAA
1 ATGCTGTCAAATTTT-GT-ATATAC
*
54540314 ATGCTGTCCAATTTTGTATATAC
1 ATGCTGTCAAATTTTGTATATAC
*
54540337 ATGCTGTCAAATTTTGTGTATA-
1 ATGCTGTCAAATTTTGTATATAC
* *
54540359 AGTGCTGTCCAAA-TTGGTATATAT
1 A-TGCTGT-CAAATTTTGTATATAC
* *** ** *
54540383 ATGCTGCCCCCTCTCCCCGTGA-ATAA
1 ATGCTGTCAAAT-T--TTGT-ATATAC
* *
54540409 ATGCTGTCCAATTTTTTATATAC
1 ATGCTGTCAAATTTTGTATATAC
*
54540432 ATGCTGTCAAATTTTGTGTATA-
1 ATGCTGTCAAATTTTGTATATAC
* *
54540454 AGTGCTATCCAAA-TTGGTATATAC
1 A-TGCTGT-CAAATTTTGTATATAC
54540478 ATGCTG
1 ATGCTG
54540484 CTTAATTTCT
Statistics
Matches: 258, Mismatches: 45, Indels: 60
0.71 0.12 0.17
Matches are distributed among these distances:
22 20 0.08
23 157 0.61
24 61 0.24
25 5 0.02
26 14 0.05
27 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (23 bp):
ATGCTGTCAAATTTTGTATATAC
Found at i:54540205 original size:93 final size:93
Alignment explanation
Indices: 54540090--54540484 Score: 637
Period size: 93 Copynumber: 4.2 Consensus size: 93
54540080 TAATGGTCTA
*
54540090 AAATTGGTATATATATGCTGCCCAATTTTGGTGAACAAATGCTGTCCAATTTTGTATATACATGC
1 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
*
54540155 CGTCAAATTTTGTGTATAAGTGCTGTCC
66 TGTCAAATTTTGTGTATAAGTGCTGTCC
* *
54540183 AAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
1 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
*
54540248 TGTCAAATTTTGTGTATAACTGCTGTCC
66 TGTCAAATTTTGTGTATAAGTGCTGTCC
* *
54540276 AAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
1 AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
54540341 TGTCAAATTTTGTGTATAAGTGCTGTCC
66 TGTCAAATTTTGTGTATAAGTGCTGTCC
** *** *
54540369 AAATTGGTATATATATGCTGCCCCCTCTCCCCGTGAATAAATGCTGTCCAATTTTTTATATACAT
1 AAATTGGTATATATATGCTGCCCAAT-T-TTGGTGAATAAATGCTGTCCAATTTTGTATATACAT
*
54540434 GCTGTCAAATTTTGTGTATAAGTGCTATCC
64 GCTGTCAAATTTTGTGTATAAGTGCTGTCC
*
54540464 AAATTGGTATATACATGCTGC
1 AAATTGGTATATATATGCTGC
54540485 TTAATTTCTG
Statistics
Matches: 284, Mismatches: 16, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
93 202 0.71
94 1 0.00
95 81 0.29
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (93 bp):
AAATTGGTATATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGC
TGTCAAATTTTGTGTATAAGTGCTGTCC
Found at i:54540210 original size:46 final size:45
Alignment explanation
Indices: 54540090--54540514 Score: 357
Period size: 46 Copynumber: 9.1 Consensus size: 45
54540080 TAATGGTCTA
* * * *
54540090 AAATTGGTATATATATGCTGCCCAATTTTGGTGAACAAATGCTGTCC
1 AAATT-GTATATACATGCTGCCAAATTTT-GTGTATAAATGCTGTCC
* * * *
54540137 AATTTTGTATATACATGCCGTCAAATTTTGTGTATAAGTGCTGTCC
1 AA-ATTGTATATACATGCTGCCAAATTTTGTGTATAAATGCTGTCC
* * * *
54540183 AAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCC
1 AAATTG-TATATACATGCTGCCAAATTTT-GTGTATAAATGCTGTCC
* * *
54540230 AATTTTGTATATACATGCTGTCAAATTTTGTGTATAACTGCTGTCC
1 AA-ATTGTATATACATGCTGCCAAATTTTGTGTATAAATGCTGTCC
* * * *
54540276 AAATTGCTACATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCC
1 AAATTG-TATATACATGCTGCCAAATTTT-GTGTATAAATGCTGTCC
* * *
54540323 AATTTTGTATATACATGCTGTCAAATTTTGTGTATAAGTGCTGTCC
1 AA-ATTGTATATACATGCTGCCAAATTTTGTGTATAAATGCTGTCC
* *** ** *
54540369 AAATTGGTATATATATGCTGCCCCCTCTCCCCGTGAATAAATGCTGTCC
1 AAATT-GTATATACATGCTGCCAAAT-T--TTGTGTATAAATGCTGTCC
* * * * *
54540418 AATTTTTTATATACATGCTGTCAAATTTTGTGTATAAGTGCTATCC
1 AA-ATTGTATATACATGCTGCCAAATTTTGTGTATAAATGCTGTCC
**
54540464 AAATTGGTATATACATGCTGCTTAATTTCTGATGTATAAGA-GCTGTCC
1 AAATT-GTATATACATGCTGCCAAATTT-TG-TGTATAA-ATGCTGTCC
54540512 AAA
1 AAA
54540515 CAGGGTAGAT
Statistics
Matches: 296, Mismatches: 66, Indels: 31
0.75 0.17 0.08
Matches are distributed among these distances:
45 10 0.03
46 134 0.45
47 94 0.32
48 25 0.08
49 31 0.10
50 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (45 bp):
AAATTGTATATACATGCTGCCAAATTTTGTGTATAAATGCTGTCC
Found at i:54543047 original size:6 final size:6
Alignment explanation
Indices: 54543031--54543062 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
54543021 TTTCGCCCTC
54543031 TTTAA- TTTAAT TTTAAT TTTAAT TTT-AT TTTA
1 TTTAAT TTTAAT TTTAAT TTTAAT TTTAAT TTTA
54543063 GTTTCCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTAAT
Found at i:54544318 original size:9 final size:9
Alignment explanation
Indices: 54544304--54544370 Score: 50
Period size: 9 Copynumber: 7.7 Consensus size: 9
54544294 AATTAAACCA
54544304 TTATGTAAG
1 TTATGTAAG
*
54544313 TTATGTAAT
1 TTATGTAAG
*
54544322 TTATGTAAT
1 TTATGTAAG
*
54544331 TTATGATATG
1 TTATG-TAAG
* * *
54544341 ATATAT-AT
1 TTATGTAAG
54544349 TTATGT-A-
1 TTATGTAAG
54544356 TTATGTAAG
1 TTATGTAAG
54544365 TTATGT
1 TTATGT
54544371 TCCAAAGTTT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
7 6 0.13
8 6 0.13
9 29 0.63
10 5 0.11
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (9 bp):
TTATGTAAG
Found at i:54549337 original size:27 final size:27
Alignment explanation
Indices: 54549305--54549378 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
54549295 GCAGAGGAGT
*
54549305 GTCGACGGCGATGCAACAGAGGGGATA
1 GTCGACGGCGATGCAACAGAGGGGACA
* *
54549332 GTCGACGGTGATGCAGCAGAGGGGACA
1 GTCGACGGCGATGCAACAGAGGGGACA
*
54549359 GTTGACGGCGATGCAACAGA
1 GTCGACGGCGATGCAACAGA
54549379 TGGCCGGGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.28, C:0.19, G:0.41, T:0.12
Consensus pattern (27 bp):
GTCGACGGCGATGCAACAGAGGGGACA
Found at i:54549613 original size:41 final size:41
Alignment explanation
Indices: 54549531--54549667 Score: 168
Period size: 41 Copynumber: 3.4 Consensus size: 41
54549521 AAAATGATAC
* * * *
54549531 TTTGCGGCGTTTTTCTTAT-AGCACCACTAATGCTTGACCT
1 TTTGCGGCGTTTTTCTCATAAACGCCGCTAATGCTTGACCT
54549571 TTTGCGGCGTTTTTCTCATAAACGCCGCTAATGCTTGACCT
1 TTTGCGGCGTTTTTCTCATAAACGCCGCTAATGCTTGACCT
* * * *
54549612 TTTGCAGCGTTTTTCTCATAAACGCTGCTACTGCTTTACCT
1 TTTGCGGCGTTTTTCTCATAAACGCCGCTAATGCTTGACCT
* * *
54549653 ATTGTGGCATTTTTC
1 TTTGCGGCGTTTTTC
54549668 CGTTAGTGCC
Statistics
Matches: 84, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
40 18 0.21
41 66 0.79
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.41
Consensus pattern (41 bp):
TTTGCGGCGTTTTTCTCATAAACGCCGCTAATGCTTGACCT
Found at i:54554552 original size:26 final size:27
Alignment explanation
Indices: 54554496--54554561 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 27
54554486 ATTGACGGAT
* * *
54554496 TTAAAAATAATTATAATTAACTTATTT
1 TTAAAAATAAATATAATTAACTAATTA
54554523 TTAAAAATAAATATTAATT-A-TAATTA
1 TTAAAAATAAATA-TAATTAACTAATTA
*
54554549 TTAAACATAAATA
1 TTAAAAATAAATA
54554562 AATACAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 16 0.47
27 13 0.38
28 5 0.15
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (27 bp):
TTAAAAATAAATATAATTAACTAATTA
Found at i:54554980 original size:17 final size:16
Alignment explanation
Indices: 54554949--54554995 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
54554939 CAAAAAATTA
54554949 TATTTTTCTATCTTTT
1 TATTTTTCTATCTTTT
*
54554965 TATTTTTTTATCCTTTT
1 TATTTTTCTAT-CTTTT
*
54554982 AATTTTTC-ATCTTT
1 TATTTTTCTATCTTT
54554996 CTAACATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 4 0.15
16 12 0.44
17 11 0.41
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (16 bp):
TATTTTTCTATCTTTT
Found at i:54560300 original size:15 final size:16
Alignment explanation
Indices: 54560266--54560305 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
54560256 AATAACAAGA
*
54560266 AAAATAATATAGATACT
1 AAAATAA-ATAGAAACT
54560283 AAAATAAA-AGAAACT
1 AAAATAAATAGAAACT
54560298 AAAATAAA
1 AAAATAAA
54560306 GTAATAAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 1 0.05
17 7 0.32
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (16 bp):
AAAATAAATAGAAACT
Found at i:54561863 original size:237 final size:237
Alignment explanation
Indices: 54561445--54561919 Score: 880
Period size: 237 Copynumber: 2.0 Consensus size: 237
54561435 CCAAAGCTCC
54561445 TCTTTCTCGTTATCAATTCTATGATCAAAATAAGGTTTAAGTCGAGTAATATTTACCTTAAATGT
1 TCTTTCTCGTTATCAATTCTATGATCAAAATAAGGTTTAAGTCGAGTAATATTTACCTTAAATGT
*
54561510 GTCAAGTTCAGAATTCATTAACTCGATTGTATCGTATAGAAAGACGTTCAGTATTGTAAAAGATT
66 GTCAAGTTCAGAATTCATTAACTCGATTGTACCGTATAGAAAGACGTTCAGTATTGTAAAAGATT
*
54561575 TTGATTTGTTTACATCCAGCTCTAAAGTGGCAATACATGGATCCGTTTTATCTAGTAGTACCTTA
131 TTGATTTGTTTACATCCAGCTCTAAAGTGGCAATACATGGATCCATTTTATCTAGTAGTACCTTA
*
54561640 TCTTTAACCTTGAATTGGTTCGTTCCATCCACATGCTCATCA
196 TCTTTAACCTTGAATTGGTTCATTCCATCCACATGCTCATCA
*
54561682 TCTTTCTTGTTATCAATTCTATGATCAAAATAAGGTTTAAGTCGAGTAATATTTACCTTAAATGT
1 TCTTTCTCGTTATCAATTCTATGATCAAAATAAGGTTTAAGTCGAGTAATATTTACCTTAAATGT
54561747 GTCAAGTTCAGAATT-AGTTAACTCGATTGTACCGTATAGAAAGACGTTCAGTATTGTAAAAGAT
66 GTCAAGTTCAGAATTCA-TTAACTCGATTGTACCGTATAGAAAGACGTTCAGTATTGTAAAAGAT
* *
54561811 TTTGATTTGTTTGCATCCAGCTCTAAAGTGGCAATACATGGATCTATTTTATCTAGTAGTACCTT
130 TTTGATTTGTTTACATCCAGCTCTAAAGTGGCAATACATGGATCCATTTTATCTAGTAGTACCTT
54561876 ATCTTTAACCTTGAATTGGTTCATTCCATCCACATGCTCATCA
195 ATCTTTAACCTTGAATTGGTTCATTCCATCCACATGCTCATCA
54561919 T
1 T
54561920 GGCGTCGCTT
Statistics
Matches: 231, Mismatches: 6, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
236 1 0.00
237 230 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (237 bp):
TCTTTCTCGTTATCAATTCTATGATCAAAATAAGGTTTAAGTCGAGTAATATTTACCTTAAATGT
GTCAAGTTCAGAATTCATTAACTCGATTGTACCGTATAGAAAGACGTTCAGTATTGTAAAAGATT
TTGATTTGTTTACATCCAGCTCTAAAGTGGCAATACATGGATCCATTTTATCTAGTAGTACCTTA
TCTTTAACCTTGAATTGGTTCATTCCATCCACATGCTCATCA
Found at i:54564389 original size:18 final size:18
Alignment explanation
Indices: 54564366--54564400 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54564356 CTTAGAATGT
* *
54564366 AAAAATTAAACTAAAAAC
1 AAAAATAAAAATAAAAAC
54564384 AAAAATAAAAATAAAAA
1 AAAAATAAAAATAAAAA
54564401 TGGCTAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.80, C:0.06, G:0.00, T:0.14
Consensus pattern (18 bp):
AAAAATAAAAATAAAAAC
Found at i:54567685 original size:19 final size:20
Alignment explanation
Indices: 54567644--54567693 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
54567634 ATTACAAAAT
*
54567644 AATTCAAAATATTTTTCAAA
1 AATTCAAAATATTTATCAAA
*
54567664 AATTGAAAATATTTAT-AAA
1 AATTCAAAATATTTATCAAA
54567683 AATTTCAAAAT
1 AA-TTCAAAAT
54567694 TTATATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (20 bp):
AATTCAAAATATTTATCAAA
Found at i:54567740 original size:29 final size:30
Alignment explanation
Indices: 54567702--54567760 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
54567692 ATTTATATTT
54567702 TAAAAAAATTATAAAA-ATTCTAAAA-AATA
1 TAAAAAAATTA-AAAATATTCTAAAATAATA
54567731 TAAAAAAATTAAAAATATTCTAAAATAATA
1 TAAAAAAATTAAAAATATTCTAAAATAATA
54567761 ATTTTGAGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.14
29 20 0.71
30 4 0.14
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (30 bp):
TAAAAAAATTAAAAATATTCTAAAATAATA
Found at i:54567743 original size:18 final size:19
Alignment explanation
Indices: 54567704--54567755 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
54567694 TTATATTTTA
*
54567704 AAAAAATTATAAAAATTCT
1 AAAAAATTATAAAAAATCT
54567723 AAAAAA-TATAAAAAAAT-T
1 AAAAAATTAT-AAAAAATCT
*
54567741 AAAAATATTCTAAAA
1 AAAAA-ATTATAAAA
54567756 TAATAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 9 0.32
19 17 0.61
20 2 0.07
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAAATTATAAAAAATCT
Found at i:54571259 original size:22 final size:21
Alignment explanation
Indices: 54571230--54571270 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
54571220 TTTTTCCCAT
**
54571230 GTTAGGTTTTTGGTTTTTAGG
1 GTTAGGTTTAAGGTTTTTAGG
54571251 GTTAGGGTTTAAGGTTTTTA
1 GTTA-GGTTTAAGGTTTTTA
54571271 AGATTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.15, C:0.00, G:0.32, T:0.54
Consensus pattern (21 bp):
GTTAGGTTTAAGGTTTTTAGG
Found at i:54571690 original size:124 final size:125
Alignment explanation
Indices: 54571395--54571711 Score: 458
Period size: 125 Copynumber: 2.5 Consensus size: 125
54571385 GATAAAATTA
* * * *
54571395 AAGCAGGATGCTTTATCAGAAGAATTTTTGAAGTCGCGCCGACGTGTACACGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTGTGAAATCGCGCCCACGTGGACACGCTTTTGCTACAGT
* * * *
54571460 AGGTTCTGTAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
66 AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAACAAATAGTATAAAAAACGCTTC
* * * *
54571520 AAGCAGGATGCTTTATAAGAAGAATTTGTGAAATCTCGACCTCGTGGACACGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATCAGAAGAATTTGTGAAATCGCGCCCACGTGGACACGCTTTTGCTACAGT
* *
54571585 AGG-CCTGGAAAAAATAATTTCGAGTTGATGTTTCTGAACAAATAGTAT-AAAAATGCTTC
66 AGGTCCT-GAAAAAATAATTTCGAGTTGACGTTTCTGAACAAATAGTATAAAAAACGCTTC
* *
54571644 AAGCAGGATGCTTTATCAGAAGAATTTGTGAAATCGCTCCCACGTGGACGCGCTTTTTGCTACAG
1 AAGCAGGATGCTTTATCAGAAGAATTTGTGAAATCGCGCCCACGTGGACACGC-TTTTGCTACAG
54571709 TAG
65 TAG
54571712 CATGTTTGGG
Statistics
Matches: 170, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
124 59 0.35
125 111 0.65
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (125 bp):
AAGCAGGATGCTTTATCAGAAGAATTTGTGAAATCGCGCCCACGTGGACACGCTTTTGCTACAGT
AGGTCCTGAAAAAATAATTTCGAGTTGACGTTTCTGAACAAATAGTATAAAAAACGCTTC
Found at i:54573699 original size:335 final size:335
Alignment explanation
Indices: 54573079--54573749 Score: 1137
Period size: 335 Copynumber: 2.0 Consensus size: 335
54573069 GATTCAGCTA
* *
54573079 TGTTAGTTAGCTTGATACTACCCACGGTGAAGGCAGACCTCAGGACTTCAATGCCGGTCTTAATT
1 TGTTAGCTAGCTTGATACTACCCACGGTGAAGGCAGACCTCAAGACTTCAATGCCGGTCTTAATT
54573144 ACCAATATTCGTAGCCAAATGGGGTACACGCCCTCTTACCGCAAGGCTTGGATAGCTAAGCAGAA
66 ACCAATATTCGTAGCCAAATGGGGTACACGCCCTCTTACCGCAAGGCTTGGATAGCTAAGCAGAA
54573209 GGCGTTGGAGAAGATGCATAGTGGGTGGGACGCTTCATATAATGAAATATGGCAGTGGTGTCAAG
131 GGCGTTGGAGAAGATGCATAGTGGGTGGGACGCTTCATATAATGAAATATGGCAGTGGTGTCAAG
* *
54573274 TGCTAGAGAGATACATTCCAGATGCTATCACAGACCTTGAAACGGAACATACGTACTACAACAGC
196 TGCTAGAGAGATACATCCCAGATGCCATCACAGACCTTGAAACGGAACATACGTACTACAACAGC
* * * *
54573339 CGATTGCTACATGGATGCCAAGTGTTCAAACGCCTATTTTGGACCTTTAAGCAATGCTGTGACGC
261 CGATTGCTACATGGATACCAAGTGTTCAAACGCCTATTTTGGACCTTTAAGCAATGCCGAGACAC
54573404 ATTTCCATAC
326 ATTTCCATAC
*
54573414 TGTTAGCTAGCTTGATACTACCCACGGTGAAGGCAGATCC-CAAGACTTCAGTGCCGGTCTTAAT
1 TGTTAGCTAGCTTGATACTACCCACGGTGAAGGCAGA-CCTCAAGACTTCAATGCCGGTCTTAAT
* *
54573478 TGCCAATATTCGTAGCCAAATGGGGTACACGCCCTCTTACCGCAATGCTTGGATAGCTAAGCAGA
65 TACCAATATTCGTAGCCAAATGGGGTACACGCCCTCTTACCGCAAGGCTTGGATAGCTAAGCAGA
54573543 AGGCGTTGGAGAAGATGCATAGTGGGTGGGACGCTTCATATAATGAAATATGGCAGTGGTGTCAA
130 AGGCGTTGGAGAAGATGCATAGTGGGTGGGACGCTTCATATAATGAAATATGGCAGTGGTGTCAA
* * * * *
54573608 GTGCTAGAGAGATATATCCCAGGTGCCATCACAGACCTTGAAACGGAACATGCGTACTATAACGG
195 GTGCTAGAGAGATACATCCCAGATGCCATCACAGACCTTGAAACGGAACATACGTACTACAACAG
* * * * *
54573673 CCGATTGCTACGTGGATACTAAGTGTTCAAATGCCTGTTTTGGACCTTTAAGCGATGCCGAGACA
260 CCGATTGCTACATGGATACCAAGTGTTCAAACGCCTATTTTGGACCTTTAAGCAATGCCGAGACA
54573738 CATTTCCATAC
325 CATTTCCATAC
54573749 T
1 T
54573750 ACAAGCCATT
Statistics
Matches: 314, Mismatches: 21, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
335 312 0.99
336 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (335 bp):
TGTTAGCTAGCTTGATACTACCCACGGTGAAGGCAGACCTCAAGACTTCAATGCCGGTCTTAATT
ACCAATATTCGTAGCCAAATGGGGTACACGCCCTCTTACCGCAAGGCTTGGATAGCTAAGCAGAA
GGCGTTGGAGAAGATGCATAGTGGGTGGGACGCTTCATATAATGAAATATGGCAGTGGTGTCAAG
TGCTAGAGAGATACATCCCAGATGCCATCACAGACCTTGAAACGGAACATACGTACTACAACAGC
CGATTGCTACATGGATACCAAGTGTTCAAACGCCTATTTTGGACCTTTAAGCAATGCCGAGACAC
ATTTCCATAC
Found at i:54575124 original size:22 final size:21
Alignment explanation
Indices: 54575097--54575155 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 21
54575087 TTAAGGTTAG
*
54575097 GGTTTTTAAGTTAAGAGTTTAT
1 GGTTTTTAAGTTAA-AGTTTAA
54575119 GGTTTTTAAGTTACAAGTTTAA
1 GGTTTTTAAGTTA-AAGTTTAA
54575141 GG-TTTTAAGTTAAAG
1 GGTTTTTAAGTTAAAG
54575156 GTTAGGCTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
20 3 0.09
21 10 0.29
22 21 0.60
23 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.46
Consensus pattern (21 bp):
GGTTTTTAAGTTAAAGTTTAA
Found at i:54575174 original size:14 final size:14
Alignment explanation
Indices: 54575157--54575215 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 14
54575147 AAGTTAAAGG
*
54575157 TTAGGCTTTAGGGT
1 TTAGGCTTAAGGGT
*
54575171 TTAGGGTTAAGGGT
1 TTAGGCTTAAGGGT
* *
54575185 TTAGGGTT-A-GGA
1 TTAGGCTTAAGGGT
* *
54575197 TTAGGGTTAGGGGT
1 TTAGGCTTAAGGGT
54575211 TTAGG
1 TTAGG
54575216 GTTAGTGGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
12 10 0.26
13 1 0.03
14 27 0.71
ACGTcount: A:0.19, C:0.02, G:0.42, T:0.37
Consensus pattern (14 bp):
TTAGGCTTAAGGGT
Found at i:54575200 original size:26 final size:26
Alignment explanation
Indices: 54575171--54575220 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
54575161 GCTTTAGGGT
54575171 TTAGGGTTAAGGGTTTAGGGTTAGGA
1 TTAGGGTTAAGGGTTTAGGGTTAGGA
*
54575197 TTAGGGTTAGGGGTTTAGGGTTAG
1 TTAGGGTTAAGGGTTTAGGGTTAG
54575221 TGGGTTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.20, C:0.00, G:0.44, T:0.36
Consensus pattern (26 bp):
TTAGGGTTAAGGGTTTAGGGTTAGGA
Found at i:54575210 original size:7 final size:6
Alignment explanation
Indices: 54575164--54575220 Score: 60
Period size: 7 Copynumber: 8.7 Consensus size: 6
54575154 AGGTTAGGCT
*
54575164 TTAGGG TTTAGGG TTAAGGG TTTAGGG TTAGGA TTAGGG TTAGGGG TTTAGGG
1 TTAGGG -TTAGGG TT-AGGG -TTAGGG TTAGGG TTAGGG TTA-GGG -TTAGGG
54575217 TTAG
1 TTAG
54575221 TGGGTTTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
6 19 0.43
7 20 0.45
8 5 0.11
ACGTcount: A:0.19, C:0.00, G:0.44, T:0.37
Consensus pattern (6 bp):
TTAGGG
Found at i:54575216 original size:14 final size:14
Alignment explanation
Indices: 54575167--54575227 Score: 81
Period size: 14 Copynumber: 4.4 Consensus size: 14
54575157 TTAGGCTTTA
*
54575167 GGGTTTAGGGTTAA
1 GGGTTTAGGGTTAG
54575181 GGGTTTAGGGTTA-
1 GGGTTTAGGGTTAG
*
54575194 -GGATTAGGGTTAG
1 GGGTTTAGGGTTAG
54575207 GGGTTTAGGGTTAG
1 GGGTTTAGGGTTAG
54575221 TGGGTTT
1 -GGGTTT
54575228 TTAAGTTAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
12 11 0.26
14 25 0.60
15 6 0.14
ACGTcount: A:0.16, C:0.00, G:0.46, T:0.38
Consensus pattern (14 bp):
GGGTTTAGGGTTAG
Found at i:54575285 original size:27 final size:27
Alignment explanation
Indices: 54575176--54575275 Score: 71
Period size: 26 Copynumber: 3.6 Consensus size: 27
54575166 AGGGTTTAGG
*
54575176 GTTAAGGGTTTAGGGTTA-GG--ATTAGG
1 GTTAAGGG-TTAGGGTTATGGTAATTA-A
* **
54575202 GTTAGGGGTTTAGGGTTAGTGGGTTTTTAA
1 GTTAAGGG-TTAGGGTTA-T-GGTAATTAA
**
54575232 GTTAAGGGTTAGGGTTATGGTTTTTAA
1 GTTAAGGGTTAGGGTTATGGTAATTAA
54575259 GTTAAGGGTTTAGGGTT
1 GTTAAGGG-TTAGGGTT
54575276 TGTCAATTAA
Statistics
Matches: 64, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
26 17 0.27
27 17 0.27
28 9 0.14
29 11 0.17
30 7 0.11
31 3 0.05
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (27 bp):
GTTAAGGGTTAGGGTTATGGTAATTAA
Found at i:54575843 original size:18 final size:18
Alignment explanation
Indices: 54575817--54575859 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
54575807 GACTTGGAAA
* *
54575817 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGCT
*
54575835 AGGATACATAAAAGGGCT
1 AGGAAACATAAAAGGGCT
54575853 AGGAAAC
1 AGGAAAC
54575860 GCACCTGGCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGAAACATAAAAGGGCT
Found at i:54576517 original size:7 final size:7
Alignment explanation
Indices: 54576507--54576532 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
54576497 TTATATACAT
54576507 AATACTA
1 AATACTA
54576514 AATACTA
1 AATACTA
54576521 AATACTA
1 AATACTA
54576528 AATAC
1 AATAC
54576533 CAATCGACTA
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:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:54577636 original size:30 final size:31
Alignment explanation
Indices: 54577594--54577654 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
54577584 GGGTTGGGAG
*
54577594 GGGAAGGGAGTAAAAGTTTTGGGGGAAAAGT
1 GGGAAGGGAGTAAAAGTTTTGAGGGAAAAGT
54577625 GGGAA-GGAGTAAAAGTTTTGAGGGAAAAGT
1 GGGAAGGGAGTAAAAGTTTTGAGGGAAAAGT
54577655 AAAAAGGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 24 0.83
31 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.43, T:0.20
Consensus pattern (31 bp):
GGGAAGGGAGTAAAAGTTTTGAGGGAAAAGT
Found at i:54577717 original size:9 final size:9
Alignment explanation
Indices: 54577703--54577739 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
54577693 TATAGTTTGA
54577703 TATTCGAAT
1 TATTCGAAT
54577712 TATTCGAAT
1 TATTCGAAT
*
54577721 TATTCGAGT
1 TATTCGAAT
54577730 TATTCGAAT
1 TATTCGAAT
54577739 T
1 T
54577740 CAAAAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:54579439 original size:11 final size:11
Alignment explanation
Indices: 54579423--54579447 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54579413 AAAGAATTAG
54579423 ATTATGACATC
1 ATTATGACATC
54579434 ATTATGACATC
1 ATTATGACATC
54579445 ATT
1 ATT
54579448 TATGCCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (11 bp):
ATTATGACATC
Found at i:54581691 original size:25 final size:25
Alignment explanation
Indices: 54581663--54581713 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
54581653 GTTTAATTTA
54581663 GGACATCGTTAGAGTCAATTGAATG
1 GGACATCGTTAGAGTCAATTGAATG
54581688 GGACATCGTTAGAGTCAATTGAATG
1 GGACATCGTTAGAGTCAATTGAATG
54581713 G
1 G
54581714 ACTAAACAAA
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:0.12, G:0.29, T:0.27
Consensus pattern (25 bp):
GGACATCGTTAGAGTCAATTGAATG
Found at i:54583639 original size:3 final size:3
Alignment explanation
Indices: 54583631--54583655 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
54583621 ATCAATTTCT
54583631 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
54583656 TATTTTGACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:54583869 original size:26 final size:25
Alignment explanation
Indices: 54583840--54583894 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
54583830 AGATTTATTC
54583840 TAGAGTTTAAAT-TTTTAAGTGTTAAA
1 TAGAGTTTAAATCTTTTAA--GTTAAA
* *
54583866 TAGATTTTAGATCTTTTAAGTTAAA
1 TAGAGTTTAAATCTTTTAAGTTAAA
54583891 TAGA
1 TAGA
54583895 TTGTGGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 10 0.38
26 10 0.38
27 6 0.23
ACGTcount: A:0.38, C:0.02, G:0.15, T:0.45
Consensus pattern (25 bp):
TAGAGTTTAAATCTTTTAAGTTAAA
Found at i:54589808 original size:20 final size:18
Alignment explanation
Indices: 54589764--54589811 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
54589754 AGCTTGAGAG
54589764 AAGAAA-AAAAAGAAATC
1 AAGAAAGAAAAAGAAATC
54589781 AA-ACAAGAAAAAGAAAGTGC
1 AAGA-AAGAAAAAGAAA-T-C
54589801 AAGAAAGAAAA
1 AAGAAAGAAAA
54589812 TTGAAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
17 4 0.15
18 9 0.35
19 1 0.04
20 10 0.38
21 1 0.04
ACGTcount: A:0.73, C:0.06, G:0.17, T:0.04
Consensus pattern (18 bp):
AAGAAAGAAAAAGAAATC
Found at i:54596111 original size:20 final size:20
Alignment explanation
Indices: 54596083--54596142 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
54596073 TAATTATTCT
*
54596083 TTTTTAATTAAATTTTAATC
1 TTTTAAATTAAATTTTAATC
*
54596103 TTTTAAATTTAAA-TTTATTC
1 TTTTAAA-TTAAATTTTAATC
* *
54596123 CTTTATATTAATATTTTAAT
1 TTTTAAATTAA-ATTTTAAT
54596143 TAAATTCTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 4 0.12
20 18 0.56
21 10 0.31
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTAAATTAAATTTTAATC
Found at i:54596126 original size:21 final size:21
Alignment explanation
Indices: 54596076--54596140 Score: 55
Period size: 20 Copynumber: 3.1 Consensus size: 21
54596066 TATTCTTTAA
* *
54596076 TTATTCTTTTTTAATTAAATT
1 TTATTCCTTTTAAATTAAATT
*
54596097 TTAAT-CTTTTAAATTTAAA-T
1 TTATTCCTTTTAAA-TTAAATT
*
54596117 TTATTCC-TTTATATTAATATT
1 TTATTCCTTTTAAATTAA-ATT
54596138 TTA
1 TTA
54596141 ATTAAATTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
19 4 0.11
20 17 0.49
21 14 0.40
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTCCTTTTAAATTAAATT
Found at i:54596172 original size:138 final size:134
Alignment explanation
Indices: 54596021--54596281 Score: 382
Period size: 134 Copynumber: 1.9 Consensus size: 134
54596011 GCCAATCAAG
* * * *
54596021 TTTTTAATTTTTTTTTGTTTCTTTAAATATTTCTTTATTTAGTTT-TATTCTTTAATTATTCTTT
1 TTTTTAATATTTTTTTATTTCTTGAAATATTTCTTTACTTAGTTTAT-TTCTTTAATTA----TT
* * *
54596085 TTTAATTAAATTTTAATCTTTTAAATTTAAATTTATTCCTTTATATTAATATTTTAATTAAATTC
61 TTTAATTAAATTTTAATCTTTTAAACTTAAATTTATTCATTTAAATTAAT-TTTTAATTAAATTC
54596150 TATGGTTTAT
125 TATGGTTTAT
54596160 TTTTTAA-ATTTTTTTATTTCTTGAAATATTTCTTTACTTAGTTTATTTCTTTAATTATTTTTAA
1 TTTTTAATATTTTTTTATTTCTTGAAATATTTCTTTACTTAGTTTATTTCTTTAATTATTTTTAA
*
54596224 TTAAATTTTATTCTTTTAAACTTAAATTTATTCATTTAAATTAATTTTTAATTAAATT
66 TTAAATTTTAATCTTTTAAACTTAAATTTATTCATTTAAATTAATTTTTAATTAAATT
54596282 TGATTATCGA
Statistics
Matches: 113, Mismatches: 8, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
133 13 0.12
134 48 0.42
138 44 0.39
139 8 0.07
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (134 bp):
TTTTTAATATTTTTTTATTTCTTGAAATATTTCTTTACTTAGTTTATTTCTTTAATTATTTTTAA
TTAAATTTTAATCTTTTAAACTTAAATTTATTCATTTAAATTAATTTTTAATTAAATTCTATGGT
TTAT
Found at i:54596190 original size:29 final size:28
Alignment explanation
Indices: 54596157--54596226 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 28
54596147 TTCTATGGTT
**
54596157 TATTTTTTAAATTTTTTTATTTCTTGAAA
1 TATTTTTT-AATTAGTTTATTTCTTGAAA
* * *
54596186 TATTTCTTTACTTAGTTTATTTCTTTAAT
1 TATTT-TTTAATTAGTTTATTTCTTGAAA
54596215 TA-TTTTTAATTA
1 TATTTTTTAATTA
54596227 AATTTTATTC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
27 7 0.21
28 2 0.06
29 22 0.65
30 3 0.09
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.66
Consensus pattern (28 bp):
TATTTTTTAATTAGTTTATTTCTTGAAA
Found at i:54596233 original size:21 final size:20
Alignment explanation
Indices: 54596213--54596273 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
54596203 TATTTCTTTA
*
54596213 ATTATTTTTAATTAAATTTT
1 ATTATTTTAAATTAAATTTT
*
54596233 ATTCTTTTAAACTTAAA-TTT
1 ATTATTTTAAA-TTAAATTTT
*
54596253 ATTCA-TTTAAATTAATTTTT
1 ATT-ATTTTAAATTAAATTTT
54596273 A
1 A
54596274 ATTAAATTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 4 0.12
20 25 0.74
21 5 0.15
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTATTTTAAATTAAATTTT
Found at i:54596253 original size:20 final size:20
Alignment explanation
Indices: 54596222--54596273 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
54596212 AATTATTTTT
*
54596222 AATTAAATTTTATTCTTTTA
1 AATTAAATTTTATTCATTTA
54596242 AACTTAAA-TTTATTCATTTA
1 AA-TTAAATTTTATTCATTTA
*
54596262 AATTAATTTTTA
1 AATTAAATTTTA
54596274 ATTAAATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 4 0.14
20 19 0.68
21 5 0.18
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (20 bp):
AATTAAATTTTATTCATTTA
Found at i:54609363 original size:97 final size:97
Alignment explanation
Indices: 54609187--54609379 Score: 316
Period size: 97 Copynumber: 2.0 Consensus size: 97
54609177 ACAATAAAAG
* *
54609187 TTTAAAAGAACATTCACTTATCCAAGCTTTAAGAAATCACACCCAATACGTTAGGGCAAGATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCAAGATTCC
* *
54609252 TCTAGAATCTCAAACTCGGAATATTTCCTTTC
66 TCTAAAATCACAAACTCGGAATATTTCCTTTC
54609284 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACA-ATTC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCA-AGATTC
* *
54609348 CTTTAAAATCACAAACTCTGAATATTTCCTTT
65 CTCTAAAATCACAAACTCGGAATATTTCCTTT
54609380 ATTATTTTAA
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
97 88 0.99
98 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.30
Consensus pattern (97 bp):
TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCAAGATTCC
TCTAAAATCACAAACTCGGAATATTTCCTTTC
Found at i:54609670 original size:9 final size:9
Alignment explanation
Indices: 54609656--54609680 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
54609646 TGCAAATGCT
54609656 ATAATAACA
1 ATAATAACA
54609665 ATAATAACA
1 ATAATAACA
54609674 ATAATAA
1 ATAATAA
54609681 ATACATCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (9 bp):
ATAATAACA
Found at i:54610223 original size:23 final size:22
Alignment explanation
Indices: 54610180--54610237 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
54610170 AAAGGGTATC
* *
54610180 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
54610201 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
54610224 TACATATCATATCT
1 TACAAATCATATCT
54610238 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:54610240 original size:19 final size:19
Alignment explanation
Indices: 54610193--54610309 Score: 126
Period size: 19 Copynumber: 5.8 Consensus size: 19
54610183 AAATTAAATC
*
54610193 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
54610213 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
54610235 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
54610256 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
* *
54610275 TCTAGGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
54610294 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
54610310 CTCAAAAATT
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
19 50 0.58
21 18 0.21
22 7 0.08
23 11 0.13
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:54610253 original size:21 final size:19
Alignment explanation
Indices: 54610216--54610309 Score: 152
Period size: 19 Copynumber: 4.8 Consensus size: 19
54610206 AATCATATCT
*
54610216 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
54610235 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
54610256 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
54610275 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
54610294 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
54610310 CTCAAAAATT
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
19 51 0.73
21 19 0.27
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:54610706 original size:132 final size:132
Alignment explanation
Indices: 54610538--54610838 Score: 430
Period size: 132 Copynumber: 2.3 Consensus size: 132
54610528 CTACAACTGC
* * * *
54610538 AGGGAGATAAGA-CTTACAATCTTCAACCTATTCCACTACTGACC-AGGG-AGATAGGATTA-TT
1 AGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTACTG-CCTAGGGAAG-TAGAATTACTA
*
54610599 GACTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTA
63 G-CTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTA
54610664 CTGCTT
127 CTGCTT
**
54610670 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCTAGGGAAGTAGAATTACTAGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTACTGCCTAGGGAAGTAGAATTACTAGCT
* * * *
54610735 TCAATGTACTTCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTTC
66 TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTACTGC
54610800 TT
131 TT
*
54610802 AGGCAGATAAGATCTGAAATCTTCAATCTATTCCACT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACT
54610839 GTAATGCCAA
Statistics
Matches: 153, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
131 2 0.01
132 144 0.94
133 7 0.05
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (132 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTACTGCCTAGGGAAGTAGAATTACTAGCT
TCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATCTACTCCACTACTGC
TT
Found at i:54611178 original size:132 final size:132
Alignment explanation
Indices: 54611008--54611515 Score: 553
Period size: 132 Copynumber: 3.8 Consensus size: 132
54610998 CTGTCAGTGC
54611008 AGGAAGACAGGACCTGCTAT-TTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTT
1 AGGAAGACAGGACCTGCTATCTTT-GATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTT
*
54611072 CTTCGATCTACTTCGCCACCAGTATGAGAAGATAAGATCTGCATCTTCGATCCACTTC-CTACCA
65 CTTCGATCTACTTC-CCACCAGTATGAGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCA
54611136 ATAT
129 ATAT
* * *
54611140 AGGTAGACAGGACCTGCTATCTTTGATCTAGTTCACGCCAATACATGAAGACAAGATCTGATTTC
1 AGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC
* * *
54611205 TTCGATCTACTTCACCTCCAGTATGGGAAGACAAGATCTGCATCCTCGATCCACTTCGCTACCAA
66 TTCGATCTACTTC-CCACCAGTATGAGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAA
54611270 TAT
130 TAT
* * * *
54611273 AGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAATATCTGC-ATC
1 AGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC
* * * * * * * * *
54611337 TTTGATCCACTTCCTACCAATAT-AGGAAGACAGGACCTGCTATCTTCGATCTACTTCAC-GCCA
66 TTCGATCTACTTCCCACCAGTATGA-GAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCA
*
54611400 ATAA
129 ATAT
* * * * * * * * *** *
54611404 ATGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACAAGATCTGC-AT
1 AGGAAGACAGGACCTGCTATCTTTGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTTT
* * * * *
54611468 CTTCGATCCACTTCCTACCAATAT-AGGAAGACAGGACCTGCTATCTTC
65 CTTCGATCTACTTCCCACCAGTATGA-GAAGACAAGATCTGC-ATCTTC
54611516 ACTGATCTGC
Statistics
Matches: 332, Mismatches: 39, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
131 56 0.17
132 208 0.63
133 68 0.20
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (132 bp):
AGGAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC
TTCGATCTACTTCCCACCAGTATGAGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAAT
AT
Found at i:54611377 original size:220 final size:220
Alignment explanation
Indices: 54611045--54611515 Score: 712
Period size: 220 Copynumber: 2.1 Consensus size: 220
54611035 CTACTTCACG
* * * * * * * *
54611045 CCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATGAGAAGATAAGAT
1 CCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCGACACCAATATCAGAAGACAAGAT
* * *
54611110 CTGCATCTTCGATCCACTTCCTACCAATATAGGTAGACAGGACCTGCTATCTTTGATCTAGTTCA
66 CTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCA
* * * *
54611175 CGCCAATACATGAAGACAAGATCTGATTTCTTCGATCTACTTCACCTCCAGTATGGGAAGACAAG
131 CGCCAATAAATGAAGACAAGATCTGATTTCTTCGATCTACTCCACCACCAATATGGGAAGACAAG
54611240 ATCTGCATCCTCGATCCACTTCGCTA
196 ATCTGCATCCTCGATCCACTTC-CTA
* *
54611266 CCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTC-ACGCCAATA-CATGAAGACAATA
1 CCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCGACACCAATATCA-GAAGACAAGA
*
54611329 TCTGCATCTTTGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTC
65 TCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTC
* *
54611394 ACGCCAATAAATGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAATATGGGAAGACAA
130 ACGCCAATAAATGAAGACAAGATCTGATTTCTTCGATCTACTCCACCACCAATATGGGAAGACAA
*
54611459 GATCTGCATCTTCGATCCACTTCCTA
195 GATCTGCATCCTCGATCCACTTCCTA
*
54611485 CCAATATAGGAAGACAGGACCTGCTATCTTC
1 CCAATATAGGAAGACAGGATCTGCTATCTTC
54611516 ACTGATCTGC
Statistics
Matches: 227, Mismatches: 22, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
219 34 0.15
220 156 0.69
221 37 0.16
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (220 bp):
CCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCGACACCAATATCAGAAGACAAGAT
CTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATCTTCGATCTACTTCA
CGCCAATAAATGAAGACAAGATCTGATTTCTTCGATCTACTCCACCACCAATATGGGAAGACAAG
ATCTGCATCCTCGATCCACTTCCTA
Found at i:54611514 original size:44 final size:45
Alignment explanation
Indices: 54611008--54611515 Score: 484
Period size: 44 Copynumber: 11.5 Consensus size: 45
54610998 CTGTCAGTGC
* * * * *
54611008 AGGAAGACAGGACCTGCTATTTTCGATCTACTTCAC-GCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACCAATAT
* * * * *
54611052 ATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACCAATAT
* *
54611097 -GAGAAGATAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATAT
1 AG-GAAGACAAGATCTGCTATCTTCGATCTACTTCACTACCAATAT
* * * * * * *
54611140 AGGTAGACAGGACCTGCTATCTTTGATCTAGTTCAC-GCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACCAATAT
* * * *
54611184 ATGAAGACAAGATCTGATTTCTTCGATCTACTTCACCT-CCAGTAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCA-CTACCAATAT
* * * *
54611229 GGGAAGACAAGATCTGC-ATCCTCGATCCACTTCGCTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACCAATAT
* * *
54611273 AGGAAGACAGGATCTGCTATCTTCGATCTACTTCAC-GCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACCAATAT
* * * *
54611317 ATGAAGACAATATCTGC-ATCTTTGATCCACTTC-CTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACCAATAT
* * * *
54611360 AGGAAGACAGGACCTGCTATCTTCGATCTACTTCAC-GCCAATAA
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACCAATAT
* * * * *
54611404 ATGAAGACAAGATCTGCTTTCTTCGATCTACTCCGCCACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACCAATAT
* *
54611449 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACCAATAT
* *
54611492 AGGAAGACAGGACCTGCTATCTTC
1 AGGAAGACAAGATCTGCTATCTTC
54611516 ACTGATCTGC
Statistics
Matches: 369, Mismatches: 81, Indels: 28
0.77 0.17 0.06
Matches are distributed among these distances:
42 1 0.00
43 77 0.21
44 214 0.58
45 77 0.21
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (45 bp):
AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACTACCAATAT
Found at i:54612743 original size:6 final size:6
Alignment explanation
Indices: 54612724--54612768 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
54612714 GGCCTCTCCA
*
54612724 TTTTC- TTTTAT TTTTC- TTTTCT TTTTCTT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT TTTTCT TTTT
54612769 ATCACTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
5 9 0.26
6 20 0.57
7 6 0.17
ACGTcount: A:0.02, C:0.13, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTCT
Found at i:54612758 original size:13 final size:13
Alignment explanation
Indices: 54612740--54612768 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54612730 TTTATTTTTC
54612740 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
54612753 TTTTCTTTTTCTT
1 TTTTCTTTTTCTT
54612766 TTT
1 TTT
54612769 ATCACTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTCTTTTTCTT
Found at i:54612767 original size:11 final size:11
Alignment explanation
Indices: 54612724--54612767 Score: 61
Period size: 11 Copynumber: 3.8 Consensus size: 11
54612714 GGCCTCTCCA
*
54612724 TTTTCTTTTAT
1 TTTTCTTTTCT
54612735 TTTTCTTTTCT
1 TTTTCTTTTCT
54612746 TTTTCTTTTTTCT
1 TTTTC--TTTTCT
54612759 TTTTCTTTT
1 TTTTCTTTT
54612768 TATCACTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 19 0.63
13 11 0.37
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:54617610 original size:23 final size:22
Alignment explanation
Indices: 54617580--54617622 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
54617570 ATTAAATCTC
54617580 TAAGATTACAAAATCATATCTTT
1 TAAGATTAC-AAATCATATCTTT
*
54617603 TAAGATTACATATCATATCT
1 TAAGATTACAAATCATATCT
54617623 AAGATTGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.40
Consensus pattern (22 bp):
TAAGATTACAAATCATATCTTT
Found at i:54617627 original size:19 final size:19
Alignment explanation
Indices: 54617578--54617694 Score: 126
Period size: 19 Copynumber: 5.8 Consensus size: 19
54617568 AAATTAAATC
*
54617578 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
54617598 TCTTTTAAGATTACATATCATA
1 TC---TAAGATTACATATCATA
*
54617620 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
54617641 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
* *
54617660 TCTAGGATTGCATATCATA
1 TCTAAGATTACATATCATA
*
54617679 TCTAAGATTGCATATC
1 TCTAAGATTACATATC
54617695 CTCAAAAATT
Statistics
Matches: 86, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
19 48 0.56
20 2 0.02
21 18 0.21
22 9 0.10
23 9 0.10
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:54617638 original size:21 final size:19
Alignment explanation
Indices: 54617603--54617694 Score: 148
Period size: 19 Copynumber: 4.7 Consensus size: 19
54617593 TCATATCTTT
*
54617603 TAAGATTACATATCATATC
1 TAAGATTGCATATCATATC
54617622 TAAGATTGCATATATCATATC
1 TAAGATTGC--ATATCATATC
54617643 TAAGATTGCATATCATATC
1 TAAGATTGCATATCATATC
*
54617662 TAGGATTGCATATCATATC
1 TAAGATTGCATATCATATC
54617681 TAAGATTGCATATC
1 TAAGATTGCATATC
54617695 CTCAAAAATT
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
19 49 0.72
21 19 0.28
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (19 bp):
TAAGATTGCATATCATATC
Found at i:54617655 original size:40 final size:38
Alignment explanation
Indices: 54617603--54617694 Score: 148
Period size: 40 Copynumber: 2.4 Consensus size: 38
54617593 TCATATCTTT
*
54617603 TAAGATTACATATCATATCTAAGATTGCATATATCATATC
1 TAAGATTGCATATCATATCTAAGATTGC--ATATCATATC
*
54617643 TAAGATTGCATATCATATCTAGGATTGCATATCATATC
1 TAAGATTGCATATCATATCTAAGATTGCATATCATATC
54617681 TAAGATTGCATATC
1 TAAGATTGCATATC
54617695 CTCAAAAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
38 24 0.48
40 26 0.52
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (38 bp):
TAAGATTGCATATCATATCTAAGATTGCATATCATATC
Found at i:54620521 original size:20 final size:18
Alignment explanation
Indices: 54620496--54620544 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
54620486 AATTTAGCCA
54620496 TTTTTTTATTTTAATATTT
1 TTTTTTTATTTTAAT-TTT
*
54620515 TTATTTTTAATTTAATTTT
1 TT-TTTTTATTTTAATTTT
54620534 TTTGTTTTATT
1 TTT-TTTTATT
54620545 CTTATAGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 1 0.04
19 13 0.50
20 12 0.46
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTTTTATTTTAATTTT
Found at i:54628852 original size:19 final size:19
Alignment explanation
Indices: 54628830--54628871 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
54628820 TTTAAAGCTA
*
54628830 GTTT-TTTTTCTCTTCTTTT
1 GTTTATTTTTC-CTTATTTT
54628849 GTTTATTTTTCCTTATTTT
1 GTTTATTTTTCCTTATTTT
54628868 GTTT
1 GTTT
54628872 CCTTCCTACC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.05, C:0.12, G:0.07, T:0.76
Consensus pattern (19 bp):
GTTTATTTTTCCTTATTTT
Found at i:54629645 original size:29 final size:29
Alignment explanation
Indices: 54629601--54629657 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 29
54629591 GAATATAAAC
54629601 TATATTTTTTATTTTTAAAATACACTACA
1 TATATTTTTTATTTTTAAAATACACTACA
54629630 TATATTTTTTTATTTTTAAAATACACTA
1 TATA-TTTTTTATTTTTAAAATACACTA
54629658 ATAGTAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (29 bp):
TATATTTTTTATTTTTAAAATACACTACA
Found at i:54638059 original size:43 final size:43
Alignment explanation
Indices: 54638011--54638255 Score: 427
Period size: 43 Copynumber: 5.7 Consensus size: 43
54638001 TTTTAGAAAA
* *
54638011 AAACGCCGCTAAAGACCAAGACCTTTAGCGGTGCTTCTCTCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
54638054 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
*
54638097 AAACGCCACTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
*
54638140 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCTCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
*
54638183 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
* *
54638226 AAACGCTGCTAAAGACCATGACCTTTAGCG
1 AAACGCCGCTAAAGACCAAGACCTTTAGCG
54638256 ACGTTTTTGC
Statistics
Matches: 193, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 193 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
Found at i:54638337 original size:22 final size:24
Alignment explanation
Indices: 54638311--54638354 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
54638301 TTGTTTTAAT
54638311 TAAATAATAT-TTAT-TTTTATGA
1 TAAATAATATATTATGTTTTATGA
*
54638333 TAAATATTATATTATGTTTTAT
1 TAAATAATATATTATGTTTTAT
54638355 TTTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 4 0.21
24 6 0.32
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (24 bp):
TAAATAATATATTATGTTTTATGA
Found at i:54641349 original size:11 final size:11
Alignment explanation
Indices: 54641333--54641357 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
54641323 GGAGAGCTTT
54641333 GGAGACGGAAA
1 GGAGACGGAAA
54641344 GGAGACGGAAA
1 GGAGACGGAAA
54641355 GGA
1 GGA
54641358 TCGAAGAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.48, T:0.00
Consensus pattern (11 bp):
GGAGACGGAAA
Found at i:54642367 original size:81 final size:84
Alignment explanation
Indices: 54642197--54642371 Score: 189
Period size: 81 Copynumber: 2.1 Consensus size: 84
54642187 CCTTAACTAC
* * *
54642197 TAACCCATAAACCTTATTTAATATATAAATTAAAAAAACACTAATTAATCTAAACCCTAAACCTT
1 TAACCCCTAAACCTTATTTAATATATAAATTAAAAAAACACTAATTAACCTAAACCCTAAACCCT
* * *
54642262 ATCCCAAATCCCTAACCCC
66 ATACCAAATCACTAACCCA
* * * *
54642281 TAACCCCTAAACCTTATTT-A-ATATAGATT-AAAACATACTAATTAACCTAAACCCTAAGCCCT
1 TAACCCCTAAACCTTATTTAATATATAAATTAAAAAAACACTAATTAACCTAAACCCTAAACCCT
* *
54642343 A-ACCTAA-CACTAAATCCA
66 ATACCAAATCACT-AACCCA
*
54642361 TAAACCCTAAA
1 TAACCCCTAAA
54642372 TATATCCCTA
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
79 3 0.04
80 18 0.23
81 29 0.38
82 8 0.10
83 1 0.01
84 18 0.23
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.26
Consensus pattern (84 bp):
TAACCCCTAAACCTTATTTAATATATAAATTAAAAAAACACTAATTAACCTAAACCCTAAACCCT
ATACCAAATCACTAACCCA
Found at i:54642369 original size:26 final size:24
Alignment explanation
Indices: 54642323--54642370 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
54642313 ACATACTAAT
* *
54642323 TAACCTAAACCCTAAGCCCTAACC
1 TAACCTAAACCATAAACCCTAACC
54642347 TAACACTAAATCCATAAACCCTAA
1 TAAC-CTAAA-CCATAAACCCTAA
54642371 ATATATCCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 5 0.25
26 11 0.55
ACGTcount: A:0.44, C:0.35, G:0.02, T:0.19
Consensus pattern (24 bp):
TAACCTAAACCATAAACCCTAACC
Found at i:54642446 original size:7 final size:7
Alignment explanation
Indices: 54642430--54642481 Score: 68
Period size: 7 Copynumber: 7.3 Consensus size: 7
54642420 CTTAAACCAG
*
54642430 AATCCCT
1 AATCCAT
54642437 AATCCAT
1 AATCCAT
54642444 AATCCAT
1 AATCCAT
54642451 AATCCAT
1 AATCCAT
*
54642458 AATCCCT
1 AATCCAT
54642465 AATTCCAT
1 AA-TCCAT
*
54642473 AATCTAT
1 AATCCAT
54642480 AA
1 AA
54642482 ACCTTAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
7 34 0.85
8 6 0.15
ACGTcount: A:0.40, C:0.29, G:0.00, T:0.31
Consensus pattern (7 bp):
AATCCAT
Found at i:54642935 original size:41 final size:41
Alignment explanation
Indices: 54642890--54643083 Score: 316
Period size: 41 Copynumber: 4.7 Consensus size: 41
54642880 AAATGTTTTT
* *
54642890 GCGGCGCTTTTTTAAAAACGCCGCTAAAGCCCCGAGCATTA
1 GCGGCGCTTTTTTAAAAACGCCGCTAAAGCTCTGAGCATTA
* ** *
54642931 GCGGCGCTTCTTGGAAAATGCCGCTAAAGCTCTGAGCATTA
1 GCGGCGCTTTTTTAAAAACGCCGCTAAAGCTCTGAGCATTA
*
54642972 GCGACGCTTTTTTAAAAACGCCGCTAAAGCTCTGAGCATTA
1 GCGGCGCTTTTTTAAAAACGCCGCTAAAGCTCTGAGCATTA
*
54643013 GCGGCGCTTTTTTAAAAACGCCACTAAAGCTCTGAGCATTA
1 GCGGCGCTTTTTTAAAAACGCCGCTAAAGCTCTGAGCATTA
54643054 GCGGCGCTTTTTTAAAAACGCCGCTAAAGC
1 GCGGCGCTTTTTTAAAAACGCCGCTAAAGC
54643084 CCTAGAAGGT
Statistics
Matches: 139, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 139 1.00
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (41 bp):
GCGGCGCTTTTTTAAAAACGCCGCTAAAGCTCTGAGCATTA
Found at i:54643162 original size:39 final size:39
Alignment explanation
Indices: 54643119--54643255 Score: 120
Period size: 40 Copynumber: 3.5 Consensus size: 39
54643109 TTGGGTTTAG
* *
54643119 ATTTTTTGTGGCGTTTTTCCAAGAACGCCGCTAATGCTC
1 ATTTTTAGCGGCGTTTTTCCAAGAACGCCGCTAATGCTC
* * * *
54643158 ATTTTTAGTGGCG-CTTTCCTGAA-AGCGCCGCTAATGCTTG
1 ATTTTTAGCGGCGTTTTTCC--AAGAACGCCGCTAATGC-TC
* *
54643198 ATCTTTAGCGGCGTTTTAT--GAGAAGCGCCGCTAATGCTCC
1 ATTTTTAGCGGCGTTTT-TCCAAGAA-CGCCGCTAATGCT-C
54643238 ATTTTTAGCGGCGTTTTT
1 ATTTTTAGCGGCGTTTTT
54643256 TGTCCAAACG
Statistics
Matches: 79, Mismatches: 11, Indels: 16
0.75 0.10 0.15
Matches are distributed among these distances:
38 6 0.08
39 28 0.35
40 42 0.53
41 2 0.03
42 1 0.01
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (39 bp):
ATTTTTAGCGGCGTTTTTCCAAGAACGCCGCTAATGCTC
Found at i:54643224 original size:40 final size:40
Alignment explanation
Indices: 54643140--54643254 Score: 146
Period size: 40 Copynumber: 2.9 Consensus size: 40
54643130 CGTTTTTCCA
* **
54643140 AGAA-CGCCGCTAATGC-TCATTTTTAGTGGCGCTTTCCTG
1 AGAAGCGCCGCTAATGCTTCATTTTTAGCGGCG-TTTTATG
* *
54643179 A-AAGCGCCGCTAATGCTTGATCTTTAGCGGCGTTTTATG
1 AGAAGCGCCGCTAATGCTTCATTTTTAGCGGCGTTTTATG
*
54643218 AGAAGCGCCGCTAATGCTCCATTTTTAGCGGCGTTTT
1 AGAAGCGCCGCTAATGCTTCATTTTTAGCGGCGTTTT
54643255 TTGTCCAAAC
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
38 2 0.03
39 19 0.29
40 44 0.68
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.33
Consensus pattern (40 bp):
AGAAGCGCCGCTAATGCTTCATTTTTAGCGGCGTTTTATG
Found at i:54643792 original size:3 final size:3
Alignment explanation
Indices: 54643784--54643811 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
54643774 GAGGGGAAGG
54643784 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
54643812 GCTGATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:54651561 original size:78 final size:78
Alignment explanation
Indices: 54651432--54651590 Score: 318
Period size: 78 Copynumber: 2.0 Consensus size: 78
54651422 GCTTTAAAGA
54651432 AGTCGACATCTAGTTAATTAGTAGGATGTCCACTATCCCATCTCCTATCAAACTCATTACATTGT
1 AGTCGACATCTAGTTAATTAGTAGGATGTCCACTATCCCATCTCCTATCAAACTCATTACATTGT
54651497 AGCTAATTATTAC
66 AGCTAATTATTAC
54651510 AGTCGACATCTAGTTAATTAGTAGGATGTCCACTATCCCATCTCCTATCAAACTCATTACATTGT
1 AGTCGACATCTAGTTAATTAGTAGGATGTCCACTATCCCATCTCCTATCAAACTCATTACATTGT
54651575 AGCTAATTATTAC
66 AGCTAATTATTAC
54651588 AGT
1 AGT
54651591 GTCCACTATC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 81 1.00
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.35
Consensus pattern (78 bp):
AGTCGACATCTAGTTAATTAGTAGGATGTCCACTATCCCATCTCCTATCAAACTCATTACATTGT
AGCTAATTATTAC
Found at i:54655722 original size:23 final size:23
Alignment explanation
Indices: 54655696--54655748 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
54655686 AAGGACAACT
*
54655696 AAATATTCATATTTATAC--TATTA
1 AAATATTAATATTT-TACATTA-TA
54655719 AAATATTAATATTTTACATTATA
1 AAATATTAATATTTTACATTATA
54655742 AAATATT
1 AAATATT
54655749 TATTGCTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 3 0.11
23 22 0.81
24 2 0.07
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (23 bp):
AAATATTAATATTTTACATTATA
Found at i:54662049 original size:42 final size:42
Alignment explanation
Indices: 54662003--54662203 Score: 219
Period size: 42 Copynumber: 4.8 Consensus size: 42
54661993 AAGCCCAAAG
* * *
54662003 GTTGAACAGAAGCTCATGAGAGCTAAATAGAAA-TGCATAAGG
1 GTTGAACAGAAGCTCATAAGAGCTAAACAGAAACT-CATAAGA
* * *
54662045 GTTGAACAGAAGCTCGTAAGAGCTAAACGGAAACTCATATGA
1 GTTGAACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGA
54662087 GTTGAACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGA
1 GTTGAACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGA
* * * *
54662129 GTTGAACAAAAGCTCGA-AAGAGTTGAAC-GAAAACTCATATGA
1 GTTGAACAGAAGCTC-ATAAGAGCTAAACAG-AAACTCATAAGA
* * * * *
54662171 GTTAAACAGAAACTCGTGAGAGCTAAATAGAAA
1 GTTGAACAGAAGCTCATAAGAGCTAAACAGAAA
54662204 GTAAACATGA
Statistics
Matches: 133, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
41 1 0.01
42 129 0.97
43 3 0.02
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.18
Consensus pattern (42 bp):
GTTGAACAGAAGCTCATAAGAGCTAAACAGAAACTCATAAGA
Found at i:54662064 original size:21 final size:21
Alignment explanation
Indices: 54661990--54662181 Score: 142
Period size: 21 Copynumber: 9.2 Consensus size: 21
54661980 ACATCATTTT
*
54661990 CAGAAGCCCA-AAG-GTTGAA
1 CAGAAGCTCATAAGAGTTGAA
* * *
54662009 CAGAAGCTCATGAGAGCTAAA
1 CAGAAGCTCATAAGAGTTGAA
* * *
54662030 TAGAA-ATGCATAAGGGTTGAA
1 CAGAAGCT-CATAAGAGTTGAA
* * *
54662051 CAGAAGCTCGTAAGAGCTAAA
1 CAGAAGCTCATAAGAGTTGAA
* * *
54662072 CGGAAACTCATATGAGTTGAA
1 CAGAAGCTCATAAGAGTTGAA
* *
54662093 CAGAAGCTCATAAGAGCTAAA
1 CAGAAGCTCATAAGAGTTGAA
*
54662114 CAGAAACTCATAAGAGTTGAA
1 CAGAAGCTCATAAGAGTTGAA
*
54662135 CAAAAGCTCGA-AAGAGTTGAA
1 CAGAAGCTC-ATAAGAGTTGAA
* * *
54662156 C-GAAAACTCATATGAGTTAAA
1 CAG-AAGCTCATAAGAGTTGAA
54662177 CAGAA
1 CAGAA
54662182 ACTCGTGAGA
Statistics
Matches: 129, Mismatches: 36, Indels: 14
0.72 0.20 0.08
Matches are distributed among these distances:
19 9 0.07
20 4 0.03
21 113 0.88
22 3 0.02
ACGTcount: A:0.45, C:0.16, G:0.22, T:0.17
Consensus pattern (21 bp):
CAGAAGCTCATAAGAGTTGAA
Found at i:54662144 original size:84 final size:84
Alignment explanation
Indices: 54662003--54662203 Score: 287
Period size: 84 Copynumber: 2.4 Consensus size: 84
54661993 AAGCCCAAAG
* * *
54662003 GTTGAACAGAAGCTCATGAGAGCTAAATAGAAATGCATAAGGGTTGAACAGAAGCTCGTAAGAGC
1 GTTGAACAGAAGCTCATGAGAGCTAAATAGAAATGCATAAGAGTTGAACAAAAGCTCGAAAGAGC
*
54662068 TAAACGGAAACTCATATGA
66 TAAACGAAAACTCATATGA
* *
54662087 GTTGAACAGAAGCTCATAAGAGCTAAACAGAAACT-CATAAGAGTTGAACAAAAGCTCGAAAGAG
1 GTTGAACAGAAGCTCATGAGAGCTAAATAGAAA-TGCATAAGAGTTGAACAAAAGCTCGAAAGAG
* *
54662151 TTGAACGAAAACTCATATGA
65 CTAAACGAAAACTCATATGA
* * *
54662171 GTTAAACAGAAACTCGTGAGAGCTAAATAGAAA
1 GTTGAACAGAAGCTCATGAGAGCTAAATAGAAA
54662204 GTAAACATGA
Statistics
Matches: 103, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
84 102 0.99
85 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.22, T:0.18
Consensus pattern (84 bp):
GTTGAACAGAAGCTCATGAGAGCTAAATAGAAATGCATAAGAGTTGAACAAAAGCTCGAAAGAGC
TAAACGAAAACTCATATGA
Found at i:54662183 original size:21 final size:21
Alignment explanation
Indices: 54662007--54662203 Score: 141
Period size: 21 Copynumber: 9.4 Consensus size: 21
54661997 CCAAAGGTTG
* * *
54662007 AACAGAAGCTCATGAGAGCTA
1 AACAGAAACTCATAAGAGTTA
* * *
54662028 AATAGAAA-TGCATAAGGGTTG
1 AACAGAAACT-CATAAGAGTTA
* * *
54662049 AACAGAAGCTCGTAAGAGCTA
1 AACAGAAACTCATAAGAGTTA
* * *
54662070 AACGGAAACTCATATGAGTTG
1 AACAGAAACTCATAAGAGTTA
* *
54662091 AACAGAAGCTCATAAGAGCTA
1 AACAGAAACTCATAAGAGTTA
*
54662112 AACAGAAACTCATAAGAGTTG
1 AACAGAAACTCATAAGAGTTA
*
54662133 AACA-AAAGCTCGA-AAGAGTTG
1 AACAGAAA-CTC-ATAAGAGTTA
*
54662154 AAC-GAAAACTCATATGAGTTA
1 AACAG-AAACTCATAAGAGTTA
* * *
54662175 AACAGAAACTCGTGAGAGCTA
1 AACAGAAACTCATAAGAGTTA
*
54662196 AATAGAAA
1 AACAGAAA
54662204 GTAAACATGA
Statistics
Matches: 135, Mismatches: 33, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
20 5 0.04
21 124 0.92
22 6 0.04
ACGTcount: A:0.46, C:0.15, G:0.22, T:0.18
Consensus pattern (21 bp):
AACAGAAACTCATAAGAGTTA
Found at i:54663075 original size:19 final size:18
Alignment explanation
Indices: 54663051--54663095 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
54663041 CTTCGTCTCC
54663051 TTCTTTCTTCCTTTTCCTT
1 TTCTTTCTTCC-TTTCCTT
* *
54663070 TTCTTTCTTTCTTTCTTT
1 TTCTTTCTTCCTTTCCTT
54663088 TTCTTTCT
1 TTCTTTCT
54663096 GTTTCGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (18 bp):
TTCTTTCTTCCTTTCCTT
Found at i:54663127 original size:35 final size:33
Alignment explanation
Indices: 54663055--54663128 Score: 78
Period size: 35 Copynumber: 2.2 Consensus size: 33
54663045 GTCTCCTTCT
* *
54663055 TTCTTCCTTTTCCTTTTCTTTCTTTCTTTCTTT
1 TTCTTTCTTTTCCTTTTCTTTCTTTCTTTCTTA
* *
54663088 TTCTTTCTGTTTCGTTTTGCTTTGTTTCTTT-TTAA
1 TTCTTTCT-TTTCCTTTT-CTTTCTTTCTTTCTT-A
54663123 TTCTTT
1 TTCTTT
54663129 TATTTTGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
33 7 0.21
34 10 0.29
35 17 0.50
ACGTcount: A:0.03, C:0.20, G:0.05, T:0.72
Consensus pattern (33 bp):
TTCTTTCTTTTCCTTTTCTTTCTTTCTTTCTTA
Found at i:54663139 original size:10 final size:10
Alignment explanation
Indices: 54663126--54663152 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
54663116 TTTTTAATTC
54663126 TTTTATTTTG
1 TTTTATTTTG
54663136 TTTTATTTTG
1 TTTTATTTTG
54663146 TTTTATT
1 TTTTATT
54663153 ATACATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.07, T:0.81
Consensus pattern (10 bp):
TTTTATTTTG
Found at i:54667827 original size:21 final size:22
Alignment explanation
Indices: 54667803--54667856 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
54667793 GTTAGCCAAC
54667803 AAAATATATAAATATAAATAA-
1 AAAATATATAAATATAAATAAT
* * *
54667824 AAAATATTTATATATATATAAT
1 AAAATATATAAATATAAATAAT
*
54667846 AAAATAAATAA
1 AAAATATATAA
54667857 TTTATATTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
AAAATATATAAATATAAATAAT
Found at i:54667842 original size:25 final size:27
Alignment explanation
Indices: 54667807--54667863 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 27
54667797 GCCAACAAAA
54667807 TATATAAATATAA-ATAAA-AAAT-ATT
1 TATATAAATATAATA-AAATAAATAATT
*
54667832 TATATATATATAATAAAATAAATAATT
1 TATATAAATATAATAAAATAAATAATT
54667859 TATAT
1 TATAT
54667864 TTAAATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 15 0.54
26 5 0.18
27 8 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (27 bp):
TATATAAATATAATAAAATAAATAATT
Found at i:54669089 original size:22 final size:22
Alignment explanation
Indices: 54669045--54669089 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
54669035 TTTATTAGGG
* *
54669045 GTTAAATTTAAATATTAATTAA
1 GTTAAATTTAAATATAAAATAA
* *
54669067 GTTAGATTTAATTATAAAATAA
1 GTTAAATTTAAATATAAAATAA
54669089 G
1 G
54669090 GGAAATTTTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (22 bp):
GTTAAATTTAAATATAAAATAA
Found at i:54676588 original size:82 final size:82
Alignment explanation
Indices: 54676463--54676757 Score: 254
Period size: 82 Copynumber: 3.5 Consensus size: 82
54676453 TATTGTTTGG
* * * *
54676463 AAACAAAATCAAAATAAAATATGTTAAGCGGCGGGAATAAATCCTGAAACAGGTTATTCAATCTA
1 AAACAAAATC-AAATAAAATCTGTTAAACGGCGGGAATAAATCCTGAAACAGATTATACAATCTA
54676528 AATCTAATTTGGGAAA-AA
65 AATCTAATTT-GGAAACAA
* ** * * * *
54676546 AAACAAAATCAAATAGAATCTGTTAAACAACGAGAATAAATCCCGAAACAGATTGTACAATTTAA
1 AAACAAAATCAAATAAAATCTGTTAAACGGCGGGAATAAATCCTGAAACAGATTATACAATCTAA
* *
54676611 TTCTAATTTGGAAACCA
66 ATCTAATTTGGAAACAA
** * * * ** *
54676628 AATTAAAATCGAATAAAATCTTTTAAACGGCGGGAATAAATCTTGAAACAGATTTTATTTAATTT
1 AAACAAAATCAAATAAAATCTGTTAAACGGCGGGAATAAATCCTGAAACAGA--TTATACAA-TC
*
54676693 TAATATTCT--TTTGGAAATAA
63 TAA-A-TCTAATTTGGAAACAA
* * *
54676713 AAACAAAATAGAGAATAAAATCTGTTGAACGGCAGGGAAAAAATC
1 AAACAAAAT-CA-AATAAAATCTGTTAAACGGC-GGGAATAAATC
54676758 TCAAAATAGA
Statistics
Matches: 167, Mismatches: 36, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
81 5 0.03
82 95 0.57
83 10 0.06
84 5 0.03
85 21 0.13
87 21 0.13
88 10 0.06
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.27
Consensus pattern (82 bp):
AAACAAAATCAAATAAAATCTGTTAAACGGCGGGAATAAATCCTGAAACAGATTATACAATCTAA
ATCTAATTTGGAAACAA
Found at i:54676800 original size:88 final size:87
Alignment explanation
Indices: 54676638--54676802 Score: 215
Period size: 88 Copynumber: 1.9 Consensus size: 87
54676628 AATTAAAATC
* * ** * *
54676638 GAATAAAATCTTTTAAACGGCGGGAATAAATCTTGAAACAGATTTTATTTAATTTTAATATTCTT
1 GAATAAAATCTGTTAAACGGCGGGAAAAAATCTCAAAACAGATTTTATTTAATTTAAATATTATT
*
54676703 TTGGAAATAAAAACAAAATAGA
66 TTCGAAATAAAAACAAAATAGA
* * *
54676725 GAATAAAATCTGTTGAACGGCAGGGAAAAAATCTCAAAATAGATTTTATTTAATTTAAAATTTTA
1 GAATAAAATCTGTTAAACGGC-GGGAAAAAATCTCAAAACAGATTTTATTTAATTT-AAATATTA
54676790 TTTTCG-AATAAAA
64 TTTTCGAAATAAAA
54676803 TATTTTTTTC
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
87 19 0.29
88 37 0.56
89 10 0.15
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.35
Consensus pattern (87 bp):
GAATAAAATCTGTTAAACGGCGGGAAAAAATCTCAAAACAGATTTTATTTAATTTAAATATTATT
TTCGAAATAAAAACAAAATAGA
Found at i:54676937 original size:24 final size:23
Alignment explanation
Indices: 54676909--54676958 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
54676899 ATACGTTAGC
54676909 AAACAAAAATATATAAATATAAAT
1 AAACAAAAATATATAAATAT-AAT
* * *
54676933 AAACAAATATTTATATATATAAT
1 AAACAAAAATATATAAATATAAT
54676956 AAA
1 AAA
54676959 ATAAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (23 bp):
AAACAAAAATATATAAATATAAT
Found at i:54676950 original size:22 final size:23
Alignment explanation
Indices: 54676915--54676958 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
54676905 TAGCAAACAA
54676915 AAATATATAAATATA-AATAAAC
1 AAATATATAAATATATAATAAAC
* *
54676937 AAATATTTATATATATAATAAA
1 AAATATATAAATATATAATAAA
54676959 ATAAATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
AAATATATAAATATATAATAAAC
Found at i:54676966 original size:22 final size:23
Alignment explanation
Indices: 54676909--54676967 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
54676899 ATACGTTAGC
*
54676909 AAACAAAAATATATAAATATAAAT
1 AAAC-AAAATTTATAAATATAAAT
*
54676933 AAACAAATATTTATATATAT-AAT
1 AAACAAA-ATTTATAAATATAAAT
54676956 AAA-ATAAATTTA
1 AAACA-AAATTTA
54676968 ATAATTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
22 6 0.19
23 11 0.35
24 14 0.45
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.32
Consensus pattern (23 bp):
AAACAAAATTTATAAATATAAAT
Found at i:54678158 original size:3 final size:3
Alignment explanation
Indices: 54678150--54678193 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
54678140 GTGAATAAAA
* *
54678150 TAT TAT TA- TAT GAT TAT TAT AAT ATAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TA
54678194 ACTAATGCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 2 0.06
3 31 0.89
4 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:54678186 original size:19 final size:22
Alignment explanation
Indices: 54678148--54678191 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
54678138 TTGTGAATAA
54678148 AATATTATTATATGATTATTAT
1 AATATTATTATATGATTATTAT
*
54678170 AATA-TATTATTATTATTATTAT
1 AATATTATTA-TATGATTATTAT
54678192 TAACTAATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
AATATTATTATATGATTATTAT
Found at i:54678273 original size:22 final size:22
Alignment explanation
Indices: 54678234--54678281 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
54678224 AACAAAAAGA
54678234 AAAAGAAACAAAAGAAGA-ACAG
1 AAAAGAAACAAAAGAAGAGAC-G
*
54678256 AAAAGAAAC-AGAGAAAGAGACG
1 AAAAGAAACAAAAG-AAGAGACG
54678278 AAAA
1 AAAA
54678282 CGGGGGAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 3 0.13
22 18 0.78
23 2 0.09
ACGTcount: A:0.71, C:0.08, G:0.21, T:0.00
Consensus pattern (22 bp):
AAAAGAAACAAAAGAAGAGACG
Found at i:54679238 original size:21 final size:21
Alignment explanation
Indices: 54679189--54679272 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
54679179 GCTTTGCCGA
*
54679189 TCAGGCAGTTTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGT-T
54679211 CTCAGGCACTTTATGTGTCGTT
1 -TCAGGCACTTTATGTGTCGTT
* **
54679233 TCAGGCACCTCGTGTGTCGTT
1 TCAGGCACTTTATGTGTCGTT
*
54679254 ACAGGCAC-TTATGTGTCGT
1 TCAGGCACTTTATGTGTCGT
54679273 ATACTAATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
20 9 0.17
21 25 0.46
22 1 0.02
23 19 0.35
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.37
Consensus pattern (21 bp):
TCAGGCACTTTATGTGTCGTT
Found at i:54682190 original size:77 final size:77
Alignment explanation
Indices: 54682107--54682361 Score: 198
Period size: 83 Copynumber: 3.2 Consensus size: 77
54682097 AAACCAAAAT
* * * *
54682107 CAAAATCAAAATCAATTCTGTTGAA-CGAC-AGGATTAAATCCCGAAATAGAATTATTTAATTAA
1 CAAAATCAAAATCAAATATGTT-AAGCGACGA-GAATAAATCCCGAAATAG-ATTATTCAATTAA
54682170 ATAT-T-ATTTGGAAA
63 AT-TCTAATTTGGAAA
* * *
54682184 CAAAATCAAAATAAAATATGTTAAGCGGCGAGAATAAATCCCGAAATAGATTATTCAATTTAATT
1 CAAAATCAAAATCAAATATGTTAAGCGACGAGAATAAATCCCGAAATAGATTATTCAATTAAATT
*
54682249 CTAATTTGGGAA
66 CTAATTTGGAAA
* * * * * * *
54682261 CAAAAAACAAAATCGAATATAACCGGTTAAACGGC-AGGAGTAAGTCCCGAAATAGATTATACAA
1 C-AAAATCAAAATC-AA-AT-A--TGTTAAGCGACGA-GAATAAATCCCGAAATAGATTATTCAA
*
54682325 TTTAATTCTAATTTGGAAA
59 TTAAATTCTAATTTGGAAA
* *
54682344 TC-AAATTAAAATCGAATA
1 -CAAAATCAAAATCAAATA
54682362 AAATTTGTTA
Statistics
Matches: 147, Mismatches: 19, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
75 1 0.01
76 16 0.11
77 48 0.33
78 11 0.07
79 3 0.02
80 4 0.03
81 2 0.01
82 10 0.07
83 51 0.35
84 1 0.01
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (77 bp):
CAAAATCAAAATCAAATATGTTAAGCGACGAGAATAAATCCCGAAATAGATTATTCAATTAAATT
CTAATTTGGAAA
Found at i:54682568 original size:86 final size:86
Alignment explanation
Indices: 54682358--54682667 Score: 354
Period size: 87 Copynumber: 3.6 Consensus size: 86
54682348 ATTAAAATCG
* * * * *
54682358 AATAAAATTTGTTAAACAGTGGGAATAAATCCCGAAATAGATTTTATTTAATTTTAATTTCTCGT
1 AATAAAATCTGTTGAACAGCGGGAATAAATCCCGAAACAGATTTTATTTAATTTTAA-TACTCGT
* ** *
54682423 TTGGCAACAAAATCGAGAATGA
65 TTGGAAACAAAATAAAAAATGA
* *
54682445 AATAAAATCTATTGAACAGCGGGAATAAATCCCGAAACAGATTTTATTTAATTTTAATACTCGCC
1 AATAAAATCTGTTGAACAGCGGGAATAAATCCCGAAACAGATTTTATTTAATTTTAATACTCG-T
* *
54682510 TTGGGAA-AAAATAAAAAATGG
65 TTGGAAACAAAATAAAAAATGA
* * ** *
54682531 AATAAAATATGTTGAACTGCGGGAATAAATCATGAAACAGATTTTATTTGATTTTAATACTCGTT
1 AATAAAATCTGTTGAACAGCGGGAATAAATCCCGAAACAGATTTTATTTAATTTTAATACTCG-T
* *
54682596 TTGAAAATAAAATAAAAAATGA
65 TTGGAAACAAAATAAAAAATGA
* * **
54682618 AATAAAATCCGTTGAACGGTAGGAATAAATCCCGAAAC-GAATTTTATTTA
1 AATAAAATCTGTTGAACAGCGGGAATAAATCCCGAAACAG-ATTTTATTTA
54682668 CTTTAAAATT
Statistics
Matches: 189, Mismatches: 31, Indels: 6
0.84 0.14 0.03
Matches are distributed among these distances:
86 78 0.41
87 111 0.59
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (86 bp):
AATAAAATCTGTTGAACAGCGGGAATAAATCCCGAAACAGATTTTATTTAATTTTAATACTCGTT
TGGAAACAAAATAAAAAATGA
Found at i:54682575 original size:173 final size:173
Alignment explanation
Indices: 54682351--54682667 Score: 413
Period size: 173 Copynumber: 1.8 Consensus size: 173
54682341 AAATCAAATT
* * * *
54682351 AAAATCGAATAAAATTTGTTAAACAGTGGGAATAAATCCCGAAATAGATTTTATTTAATTTTAAT
1 AAAATCGAATAAAATATGTTAAACAGCGGGAATAAATCACGAAACAGATTTTATTTAATTTTAA-
* ** ** * * *
54682416 TTCTCG-TTTGGCAACAAAATCGAGAATGAAATAAAATCTATTGAACAGCGGGAATAAATCCCGA
65 TACTCGTTTTGAAAACAAAATAAAAAATGAAATAAAATCCATTGAACAGCAGGAATAAATCCCGA
54682480 AAC-AGATTTTATTTAATTTTAATACTCGCCTTGGGAAAAAATAA
130 AACGA-ATTTTATTTAATTTTAATACTCGCCTTGGGAAAAAATAA
* * * * *
54682524 AAAATGGAATAAAATATGTTGAACTGCGGGAATAAATCATGAAACAGATTTTATTTGATTTTAAT
1 AAAATCGAATAAAATATGTTAAACAGCGGGAATAAATCACGAAACAGATTTTATTTAATTTTAAT
* * * *
54682589 ACTCGTTTTGAAAATAAAATAAAAAATGAAATAAAATCCGTTGAACGGTAGGAATAAATCCCGAA
66 ACTCGTTTTGAAAACAAAATAAAAAATGAAATAAAATCCATTGAACAGCAGGAATAAATCCCGAA
54682654 ACGAATTTTATTTA
131 ACGAATTTTATTTA
54682668 CTTTAAAATT
Statistics
Matches: 121, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
172 5 0.04
173 115 0.95
174 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.31
Consensus pattern (173 bp):
AAAATCGAATAAAATATGTTAAACAGCGGGAATAAATCACGAAACAGATTTTATTTAATTTTAAT
ACTCGTTTTGAAAACAAAATAAAAAATGAAATAAAATCCATTGAACAGCAGGAATAAATCCCGAA
ACGAATTTTATTTAATTTTAATACTCGCCTTGGGAAAAAATAA
Found at i:54682696 original size:87 final size:86
Alignment explanation
Indices: 54682440--54682675 Score: 217
Period size: 86 Copynumber: 2.7 Consensus size: 86
54682430 CAAAATCGAG
* * * * * * *
54682440 AATGAAATAAAAT-CTATTGAACAGCGGGAATAAATCCCGAAACAGATTTTATTTAATTTTAATA
1 AATGAAATAAAATAC-GTTGAACGGCAGGAATAAATCACGAAACAGATTTTATTTGACTTTAAAA
*** **
54682504 CTCGCCTTGGGAAAAAATAAAA
65 CTCATTTTGAAAAAAAATAAAA
* * * * * * *
54682526 AATGGAATAAAATATGTTGAACTGCGGGAATAAATCATGAAACAGATTTTATTTGATTTTAATAC
1 AATGAAATAAAATACGTTGAACGGCAGGAATAAATCACGAAACAGATTTTATTTGACTTTAAAAC
*
54682591 TCGTTTTGAAAATAAAATAAAA
66 TCATTTTGAAAA-AAAATAAAA
* * *
54682613 AATGAAATAAAATCCGTTGAACGGTAGGAATAAATCCCGAAAC-GAATTTTATTT-ACTTTAAAA
1 AATGAAATAAAATACGTTGAACGGCAGGAATAAATCACGAAACAG-ATTTTATTTGACTTTAAAA
54682676 TTTTATTTTC
Statistics
Matches: 126, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
86 73 0.58
87 53 0.42
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (86 bp):
AATGAAATAAAATACGTTGAACGGCAGGAATAAATCACGAAACAGATTTTATTTGACTTTAAAAC
TCATTTTGAAAAAAAATAAAA
Found at i:54682827 original size:20 final size:20
Alignment explanation
Indices: 54682802--54682853 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
54682792 CACGTTAGCG
54682802 AACAAAAATATATAAATATA
1 AACAAAAATATATAAATATA
* *
54682822 AACAAAAGAATATTTATATATA
1 AAC-AAA-AATATATAAATATA
*
54682844 TACAAAAATA
1 AACAAAAATA
54682854 AATTGAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 7 0.26
21 6 0.22
22 14 0.52
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (20 bp):
AACAAAAATATATAAATATA
Found at i:54684538 original size:83 final size:83
Alignment explanation
Indices: 54684309--54684542 Score: 210
Period size: 83 Copynumber: 2.9 Consensus size: 83
54684299 TATTGTTTGG
* * * * *** *
54684309 AAACAAAATCAAAATAAAATCTGTTAAGC-AGCGAGAATAAATCTTGAAATAGATTATTCAATTT
1 AAACAAAAGC-AAATAAAATATGTTAAACGA-CGGGAATAAATCCCAAAACAGATTATTCAATTT
*
54684373 AATTCTAATTTGGGAACGAA
64 AATTCTAATTTGGAAACGAA
* * * * * * *
54684393 AAACAAAATCAAATAGAATTTGTTAAACGACTGGAGTAAATCCCGAAACAGATTATACAATTTAA
1 AAACAAAAGCAAATAAAATATGTTAAACGACGGGAATAAATCCCAAAACAGATTATTCAATTTAA
*
54684458 TTCTAATTTGGAAAC-CA
66 TTCTAATTTGGAAACGAA
** * *
54684475 AATTAAAAGC-AATAAAATATGTTAAATGGCGGGAATAAATCCCAAAACAGATT-TT--ATTTAA
1 AAACAAAAGCAAATAAAATATGTTAAACGACGGGAATAAATCCCAAAACAGATTATTCAATTTAA
*
54684536 TTTTAAT
66 TTCTAAT
54684543 ACTCGTTTTA
Statistics
Matches: 125, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
78 12 0.10
80 1 0.01
81 36 0.29
82 8 0.06
83 57 0.46
84 11 0.09
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (83 bp):
AAACAAAAGCAAATAAAATATGTTAAACGACGGGAATAAATCCCAAAACAGATTATTCAATTTAA
TTCTAATTTGGAAACGAA
Found at i:54684660 original size:77 final size:76
Alignment explanation
Indices: 54684535--54684695 Score: 200
Period size: 77 Copynumber: 2.1 Consensus size: 76
54684525 ATTTTATTTA
* * * * **
54684535 ATTTTAATACTCGTTTTAGGAAAAAATAAAAAATGGAATAAAATCTGTTGAGCT-GTGGAATAAA
1 ATTTTATTACTCATTTTAGGAAAAAATAAAAAATGAAATAAAATCTGTTGAACTACAGGAATAAA
**
54684599 TCGTGAAACAG
66 TCACGAAACAG
54684610 ATTTTATTACTCATTTT-GGAACTAAAATAAAAAAATGAAATAAAATCTGTTGAACTACAGGAAT
1 ATTTTATTACTCATTTTAGGAA--AAAAT-AAAAAATGAAATAAAATCTGTTGAACTACAGGAAT
*
54684674 AAATCACGAAATAG
63 AAATCACGAAACAG
54684688 ATTTTATT
1 ATTTTATT
54684696 TGATTTTAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
74 4 0.05
75 15 0.21
76 5 0.07
77 25 0.34
78 24 0.33
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (76 bp):
ATTTTATTACTCATTTTAGGAAAAAATAAAAAATGAAATAAAATCTGTTGAACTACAGGAATAAA
TCACGAAACAG
Found at i:54684709 original size:88 final size:89
Alignment explanation
Indices: 54684609--54684795 Score: 252
Period size: 90 Copynumber: 2.1 Consensus size: 89
54684599 TCGTGAAACA
* * * *
54684609 GATTTTATTACTCATTTTGGAACTAAAAT-AAAAAAATGAAATAAAATCTGTTGAACTACAGGAA
1 GATTTTAATACTCATTTTGGAAATAAAATAAAAAAAATGAAATAAAATCTATTGAACGACAGGAA
* *
54684673 TAAATCACGAAATAGATTTTATTT
66 GAAATCACGAAACAGATTTTATTT
* *
54684697 GATTTTAATACTCATTTTGGAAATAAAATAAAAAAAAATGAAATAAAATCTATTGAACGGCGGGA
1 GATTTTAATACTCATTTTGGAAATAAAAT-AAAAAAAATGAAATAAAATCTATTGAACGACAGGA
* *
54684762 AGAAATCCCGAAACGGATTTTATTT
65 AGAAATCACGAAACAGATTTTATTT
54684787 -ACTTTTAAT
1 GA-TTTTAAT
54684796 TTGGAAACAA
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
88 27 0.31
89 1 0.01
90 58 0.67
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.33
Consensus pattern (89 bp):
GATTTTAATACTCATTTTGGAAATAAAATAAAAAAAATGAAATAAAATCTATTGAACGACAGGAA
GAAATCACGAAACAGATTTTATTT
Found at i:54687238 original size:2 final size:2
Alignment explanation
Indices: 54687219--54687262 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
54687209 ATAAAGAAAA
* *
54687219 AT AT AT AA AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54687260 AT A
1 AT A
54687263 ACATATGTGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:54687329 original size:2 final size:2
Alignment explanation
Indices: 54687322--54687358 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
54687312 GACATGTGCG
*
54687322 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54687359 TCATTAGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:54687575 original size:3 final size:3
Alignment explanation
Indices: 54687567--54687604 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
54687557 GCGCATGAAT
54687567 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
54687605 GATACAAGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.