Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 182 of 204
Found at i:53764591 original size:210 final size:210
Alignment explanation
Indices: 53764203--53764591 Score: 564
Period size: 210 Copynumber: 1.9 Consensus size: 210
53764193 CAATTGAAAT
* * * * ** *
53764203 AGGTAGCTCTTTAATGCCCGTCCCATCTAAATAAAGCTCTAGCAGGCATTCCATTTTTCCATCAA
1 AGGTAGCTCTTTAATGCCCGTCCCATCAAAACAAAGCTCCAACAAACATTCCATTTTCCCATCAA
*
53764268 TCTCTGGAAAGCTTTCAAGATTTGAGCAACCTGAAAGAATTAACTTTTCAAGAGATTCCATTCCA
66 TCTCTGGAAAGCTTTCAAGATTTGAGCAACCTGAAAGAATTAACCTTTCAAGAGATTCCATTCCA
* * * * **
53764333 ATTTTGATTGGAAGACCTTTAAGACTTTTGCAGTCTTTTAAATTCAAAACTTTAAGTCTTTTGAG
131 ATTCTGATTGGAAAACCTCTAAGACTTTTGCAGCCTCCTAAATTCAAAACTTTAAGTCTTTTGAG
53764398 ACTTCCGATCAAAGA
196 ACTTCCGATCAAAGA
***
53764413 AGGTAGCTCTTTAATGTTTGTCCCATCAAAACAAAGCTCCAACAAACATTCCATTTTCCCATCAA
1 AGGTAGCTCTTTAATGCCCGTCCCATCAAAACAAAGCTCCAACAAACATTCCATTTTCCCATCAA
* *
53764478 TCTCTGGAAAGCTTTCAAGTTTTGAGCAACCTGAAAGAGTTAACCTTTCAAGAGATTCCATTCCA
66 TCTCTGGAAAGCTTTCAAGATTTGAGCAACCTGAAAGAATTAACCTTTCAAGAGATTCCATTCCA
* * *
53764543 ATTCTGGTTGGAAAA-CTCCTCAGACTTTTGCAGCCTCCTAACTTCAAAA
131 ATTCTGATTGGAAAACCT-CTAAGACTTTTGCAGCCTCCTAAATTCAAAA
53764592 GCTTAAGCCT
Statistics
Matches: 156, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
209 2 0.01
210 154 0.99
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (210 bp):
AGGTAGCTCTTTAATGCCCGTCCCATCAAAACAAAGCTCCAACAAACATTCCATTTTCCCATCAA
TCTCTGGAAAGCTTTCAAGATTTGAGCAACCTGAAAGAATTAACCTTTCAAGAGATTCCATTCCA
ATTCTGATTGGAAAACCTCTAAGACTTTTGCAGCCTCCTAAATTCAAAACTTTAAGTCTTTTGAG
ACTTCCGATCAAAGA
Found at i:53765643 original size:42 final size:42
Alignment explanation
Indices: 53765591--53765675 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
53765581 AAAAAAAAAA
53765591 CAACAACATTAAAATTATATATAGATATATATGTCATCTTAC
1 CAACAACATTAAAATTATATATAGATATATATGTCATCTTAC
53765633 CAACAACATTAAAATTATATATAGATATATATGTCATCTTAC
1 CAACAACATTAAAATTATATATAGATATATATGTCATCTTAC
53765675 C
1 C
53765676 TTTTATTGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (42 bp):
CAACAACATTAAAATTATATATAGATATATATGTCATCTTAC
Found at i:53777571 original size:2 final size:2
Alignment explanation
Indices: 53777564--53777596 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
53777554 GAGAAACTTT
53777564 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53777597 CAATNNNNNN
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53778864 original size:90 final size:88
Alignment explanation
Indices: 53778756--53778959 Score: 241
Period size: 91 Copynumber: 2.3 Consensus size: 88
53778746 TCCTTAATTT
* * * *
53778756 TTTTAAAAAAAAGTAATTAAACACCT-CTATT-TTTTTTCCACTCAATTGAGCATTTGAACTTTC
1 TTTT-AAAAAAAGCAATTAAAC-CCTGCT-TTCTTTTTTCCACTCAATTGAGAACTTGAAATTTC
* * *
53778819 AAAATGCATCAAAAAGGCTCTCAAAC
63 AAAATGCATCAAAAAGACCCTCAAAA
* * *
53778845 TTCTTCAAAAAAAGCAATTAAGTCCCTGCTTTCTTTTTTTCACTCAATTGGGAACTTGAAATTTC
1 TT-TT-AAAAAAAGCAATTAA-ACCCTGCTTTCTTTTTTCCACTCAATTGAGAACTTGAAATTTC
53778910 AAAATGCATCAAAAAGACCCTCAAAA
63 AAAATGCATCAAAAAGACCCTCAAAA
*
53778936 TTTTAAAAAAATCAATTAAACCCT
1 TTTTAAAAAAAGCAATTAAACCCT
53778960 TGCTCTTATT
Statistics
Matches: 98, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
88 4 0.04
89 16 0.16
90 23 0.23
91 55 0.56
ACGTcount: A:0.40, C:0.20, G:0.08, T:0.33
Consensus pattern (88 bp):
TTTTAAAAAAAGCAATTAAACCCTGCTTTCTTTTTTCCACTCAATTGAGAACTTGAAATTTCAAA
ATGCATCAAAAAGACCCTCAAAA
Found at i:53778998 original size:18 final size:19
Alignment explanation
Indices: 53778975--53779014 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
53778965 TTATTAAGAA
53778975 TTAGAAAA-ATAATAAATT
1 TTAGAAAACATAATAAATT
* *
53778993 TTAGAAAACTTATTAAATT
1 TTAGAAAACATAATAAATT
53779012 TTA
1 TTA
53779015 ATACAAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (19 bp):
TTAGAAAACATAATAAATT
Found at i:53779127 original size:30 final size:29
Alignment explanation
Indices: 53778997--53779127 Score: 108
Period size: 30 Copynumber: 4.5 Consensus size: 29
53778987 TAAATTTTAG
* * *
53778997 AAAACTTATTAAATTTTAATACAAATAT-A
1 AAAAATTATAAAATTTT-ATAAAAATATAA
53779026 AAAAATT-TAAAA-TTTATTAAAAAT-TAGA
1 AAAAATTATAAAATTTTA-TAAAAATATA-A
* ** * *
53779054 AAAAAATATAAAAATCGTAAAAAAATAAAA
1 AAAAATTAT-AAAATTTTATAAAAATATAA
*
53779084 AAAAATTGTAAAATTTTATAAAAATCATAA
1 AAAAATTATAAAATTTTATAAAAAT-ATAA
53779114 AAAAATTATAAAAT
1 AAAAATTATAAAAT
53779128 GCATCAAAAA
Statistics
Matches: 79, Mismatches: 15, Indels: 15
0.72 0.14 0.14
Matches are distributed among these distances:
26 2 0.03
27 9 0.11
28 11 0.14
29 20 0.25
30 34 0.43
31 3 0.04
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (29 bp):
AAAAATTATAAAATTTTATAAAAATATAA
Found at i:53779137 original size:20 final size:20
Alignment explanation
Indices: 53779043--53779126 Score: 64
Period size: 19 Copynumber: 4.2 Consensus size: 20
53779033 TAAAATTTAT
* *
53779043 TAAAAATTAGAAAAAAA-TA
1 TAAAAATCATAAAAAAATTA
* *
53779062 TAAAAATCGTAAAAAAATAAA
1 TAAAAATCATAAAAAAAT-TA
* ** **
53779083 AAAAAATTGT-AAAATTTTA
1 TAAAAATCATAAAAAAATTA
53779102 TAAAAATCATAAAAAAATTA
1 TAAAAATCATAAAAAAATTA
53779122 TAAAA
1 TAAAA
53779127 TGCATCAAAA
Statistics
Matches: 48, Mismatches: 14, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
19 22 0.46
20 17 0.35
21 9 0.19
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (20 bp):
TAAAAATCATAAAAAAATTA
Found at i:53780888 original size:17 final size:16
Alignment explanation
Indices: 53780858--53780900 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
53780848 TATATTTTTC
53780858 TTATAAAAATATAAAA
1 TTATAAAAATATAAAA
*
53780874 TTATAAAATTCATAAAA
1 TTATAAAAAT-ATAAAA
*
53780891 ATATACAAAA
1 TTATA-AAAA
53780901 ACTTAACATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 9 0.41
17 10 0.45
18 3 0.14
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (16 bp):
TTATAAAAATATAAAA
Found at i:53782067 original size:26 final size:24
Alignment explanation
Indices: 53782038--53782102 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 24
53782028 TAAAATACAT
53782038 ATATATATTATAAAGA-ATGCATAAAC
1 ATATATATTATAAA-ATATG-A-AAAC
* * *
53782064 ATATAGACTATAAAATATGAAAAT
1 ATATATATTATAAAATATGAAAAC
*
53782088 ATAAATATTATAAAA
1 ATATATATTATAAAA
53782103 ATATAAATGT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
24 15 0.47
25 2 0.06
26 15 0.47
ACGTcount: A:0.58, C:0.05, G:0.06, T:0.31
Consensus pattern (24 bp):
ATATATATTATAAAATATGAAAAC
Found at i:53782088 original size:8 final size:7
Alignment explanation
Indices: 53782058--53782153 Score: 52
Period size: 8 Copynumber: 12.4 Consensus size: 7
53782048 TAAAGAATGC
53782058 ATAAACAT
1 ATAAA-AT
* *
53782066 ATAGACT
1 ATAAAAT
53782073 ATAAAAT
1 ATAAAAT
53782080 ATGAAAAT
1 AT-AAAAT
53782088 ATAAATATT
1 ATAAA-A-T
53782097 ATAAAAAT
1 AT-AAAAT
53782105 ATAAATGTAT
1 ATAAA---AT
53782115 ATAAAAT
1 ATAAAAT
53782122 ATAAAAACT
1 AT-AAAA-T
*
53782131 ATGAAA-
1 ATAAAAT
53782137 ATAAAAT
1 ATAAAAT
53782144 A-AAATAT
1 ATAAA-AT
53782151 ATA
1 ATA
53782154 CATACTATGT
Statistics
Matches: 70, Mismatches: 6, Indels: 24
0.70 0.06 0.24
Matches are distributed among these distances:
6 8 0.11
7 22 0.31
8 23 0.33
9 7 0.10
10 10 0.14
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (7 bp):
ATAAAAT
Found at i:53782105 original size:17 final size:17
Alignment explanation
Indices: 53782083--53782144 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
53782073 ATAAAATATG
*
53782083 AAAATATAAATATTATA
1 AAAATATAAATACTATA
*
53782100 AAAATATAAAT-GTATA
1 AAAATATAAATACTATA
* *
53782116 TAAAATATAAAAACTATG
1 -AAAATATAAATACTATA
53782134 AAAATA-AAATA
1 AAAATATAAATA
53782145 AAATATATAC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.21
17 27 0.71
18 3 0.08
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAATATAAATACTATA
Found at i:53782151 original size:34 final size:35
Alignment explanation
Indices: 53782073--53782151 Score: 90
Period size: 34 Copynumber: 2.3 Consensus size: 35
53782063 CATATAGACT
* *
53782073 ATAAAATATGAAAATATAAATATTATAAAAATATAA
1 ATAAAATAT-AAAATATAAAAACTATAAAAATATAA
** *
53782109 AT-GTATATAAAATATAAAAACTATGAAAATA-AA
1 ATAAAATATAAAATATAAAAACTATAAAAATATAA
53782142 ATAAAATATA
1 ATAAAATATA
53782152 TACATACTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
33 4 0.11
34 25 0.71
35 4 0.11
36 2 0.06
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.29
Consensus pattern (35 bp):
ATAAAATATAAAATATAAAAACTATAAAAATATAA
Found at i:53783701 original size:18 final size:17
Alignment explanation
Indices: 53783671--53783705 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
53783661 AACACACACT
53783671 TTTCCCTCCCCTTTTCC
1 TTTCCCTCCCCTTTTCC
*
53783688 TTTCCCTTCTCCTTTTCC
1 TTTCCC-TCCCCTTTTCC
53783706 ACCATCCACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTCCCTCCCCTTTTCC
Found at i:53784127 original size:18 final size:18
Alignment explanation
Indices: 53784106--53784162 Score: 86
Period size: 18 Copynumber: 3.4 Consensus size: 18
53784096 ACATTATCAT
53784106 TTATTTTTATTAAACTTA
1 TTATTTTTATTAAACTTA
53784124 TTATTTTTA-T---CTTA
1 TTATTTTTATTAAACTTA
53784138 TTATTTTTATTAAACTTA
1 TTATTTTTATTAAACTTA
53784156 TTATTTT
1 TTATTTT
53784163 CACTGCCCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
14 13 0.37
15 1 0.03
17 1 0.03
18 20 0.57
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATTTTTATTAAACTTA
Found at i:53784139 original size:14 final size:14
Alignment explanation
Indices: 53784120--53784147 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53784110 TTTTATTAAA
53784120 CTTATTATTTTTAT
1 CTTATTATTTTTAT
53784134 CTTATTATTTTTAT
1 CTTATTATTTTTAT
53784148 TAAACTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (14 bp):
CTTATTATTTTTAT
Found at i:53787310 original size:47 final size:47
Alignment explanation
Indices: 53787241--53787334 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
53787231 TCAGCAAAGT
*
53787241 CATGTCAAGCATATCCGATTGTCCATCATGATGAGTTAGTTGGAATC
1 CATGTCAAACATATCCGATTGTCCATCATGATGAGTTAGTTGGAATC
53787288 CATGTCAAACATATCCGATTGTCCATCATGATGAGTTAGTTGGAATC
1 CATGTCAAACATATCCGATTGTCCATCATGATGAGTTAGTTGGAATC
53787335 AGTCTATGCT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (47 bp):
CATGTCAAACATATCCGATTGTCCATCATGATGAGTTAGTTGGAATC
Found at i:53789998 original size:209 final size:207
Alignment explanation
Indices: 53789627--53790236 Score: 799
Period size: 209 Copynumber: 2.9 Consensus size: 207
53789617 TGCGAGGCTT
* * * * * *
53789627 AAGTTGTTGAATTTAAGAGGCTGCAAAAGTCTGAGGAGTTTTCCAACCAGAATTGGAATAGAATC
1 AAGTT-TTGAATTTAAAAGACTGCAAAAGTCT-AGGAGTCTTCCAATCAAAATTGGAATGGAATC
* * * *
53789692 TCTTGAAAAGTTGACTCTTTCAGGTTGCTCAAAACTTCAAAGCGTTCCAGAGATTGATGGGAAAA
64 TCTTGAAAAGTT-A-TCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGCAAAA
** * * * *
53789757 TGGAATGTTTGTTGGAGCTTTGTTTTGATGGGACAAACATTAAAGAGCTACCTTCTTCAATCGGA
127 TGGAATGCCTGCTAGAGCTTTATTTAGATGGGACAAACATTAAAGAGCTACCTTCTTCAATCGGA
53789822 AATCTCAGAA-ACTTA
192 AATCTCAGAAGACTTA
* *
53789837 AAGTTTTGAATTTAAAAGACTGCAAAAGTCGTAGGAGTCATCCAATCAAAATTGGAATGGGATCT
1 AAGTTTTGAATTTAAAAGACTGCAAAAGTC-TAGGAGTCTTCCAATCAAAATTGGAATGGAATCT
53789902 CTTGAAAAGTTAATTCTTTCAGGTTGCTTC-AATCTTAAAAGCTTTCCAGAGATTGATGGCAAAA
65 CTTGAAAAGTT-A-TCTTTCAGGTTGC-TCAAATCTTAAAAGCTTTCCAGAGATTGATGGCAAAA
* * *
53789966 TGGAATGCCTGCTAGTGCTTTATTTAGATGGGATAAACATTAAAGAGCTACCCTCTTCAATCGGA
127 TGGAATGCCTGCTAGAGCTTTATTTAGATGGGACAAACATTAAAGAGCTACCTTCTTCAATCGGA
53790031 AATCTCAGAAGACTTA
192 AATCTCAGAAGACTTA
*
53790047 AAGTTTTGAATTTAAAGGACTGCAAAAGTCTTAGGAGTCTTCCAATCAAAATTGGAATGGAATCT
1 AAGTTTTGAATTTAAAAGACTGCAAAAGTC-TAGGAGTCTTCCAATCAAAATTGGAATGGAATCT
*
53790112 CTTGAAAAG-------TCAGGTTGCTCAAATCTTAAAAGGTTTCCAGAGATTGATGGCAAAATGG
65 CTTGAAAAGTTATCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGCAAAATGG
* * ** * *
53790170 AATGCCTGCAAGAGCTTTCTTTAGATGGGACAGGCATTAAAGAGCTGCCTAT-TTCAATTGGAAA
130 AATGCCTGCTAGAGCTTTATTTAGATGGGACAAACATTAAAGAGCTACCT-TCTTCAATCGGAAA
53790234 TCT
194 TCT
53790237 GAGCAGTCTT
Statistics
Matches: 358, Mismatches: 37, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
200 2 0.01
201 101 0.28
202 1 0.00
209 171 0.48
210 83 0.23
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (207 bp):
AAGTTTTGAATTTAAAAGACTGCAAAAGTCTAGGAGTCTTCCAATCAAAATTGGAATGGAATCTC
TTGAAAAGTTATCTTTCAGGTTGCTCAAATCTTAAAAGCTTTCCAGAGATTGATGGCAAAATGGA
ATGCCTGCTAGAGCTTTATTTAGATGGGACAAACATTAAAGAGCTACCTTCTTCAATCGGAAATC
TCAGAAGACTTA
Found at i:53791048 original size:24 final size:25
Alignment explanation
Indices: 53791002--53791063 Score: 90
Period size: 24 Copynumber: 2.5 Consensus size: 25
53790992 TATTATATCT
*
53791002 ATAAAGTGTTTATTTTTTTAAAAATA
1 ATAAAGTGTTTA-TTTTTTAAAAAAA
53791028 ATAAAGTGTTTA-TTTTTAAAAAAA
1 ATAAAGTGTTTATTTTTTAAAAAAA
*
53791052 ATAAAATGTTTA
1 ATAAAGTGTTTA
53791064 ATTTAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 22 0.65
26 12 0.35
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (25 bp):
ATAAAGTGTTTATTTTTTAAAAAAA
Found at i:53791068 original size:23 final size:24
Alignment explanation
Indices: 53791018--53791070 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
53791008 TGTTTATTTT
* * *
53791018 TTTAAAAATAATAAAGTGTTTATT
1 TTTAAAAAAAATAAAATGTTTATA
53791042 TTTAAAAAAAATAAAATGTTTA-A
1 TTTAAAAAAAATAAAATGTTTATA
53791065 TTTAAA
1 TTTAAA
53791071 TATTGATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (24 bp):
TTTAAAAAAAATAAAATGTTTATA
Found at i:53795371 original size:3 final size:3
Alignment explanation
Indices: 53795363--53795397 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
53795353 ATTGAGAAGT
53795363 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
53795398 GAAGTCGGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:53797527 original size:28 final size:28
Alignment explanation
Indices: 53797488--53797553 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
53797478 CTATCAAATT
* *
53797488 AAAAATTATATTTTCATTTCATCATCCATA
1 AAAAATTAT-TTCT-ATTCCATCATCCATA
* *
53797518 AAAAATTATTTCTATTCCATCATCTATT
1 AAAAATTATTTCTATTCCATCATCCATA
53797546 AAAAATTA
1 AAAAATTA
53797554 ATCATATACT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 20 0.62
29 3 0.09
30 9 0.28
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (28 bp):
AAAAATTATTTCTATTCCATCATCCATA
Found at i:53797850 original size:9 final size:10
Alignment explanation
Indices: 53797827--53797852 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
53797817 AAAGACCCTA
53797827 AAAAATTTTC
1 AAAAATTTTC
53797837 AAAAATTTTC
1 AAAAATTTTC
53797847 AAAAAT
1 AAAAAT
53797853 GCAATTAAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAAATTTTC
Found at i:53797941 original size:31 final size:29
Alignment explanation
Indices: 53797884--53797942 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
53797874 AACAAAAAAA
*
53797884 TTATAAAAAATAAAAAAAAATGTAAAATT
1 TTATAAAAAATAAAAAAAAATATAAAATT
* *
53797913 TTATAAAAATCATAAAAAGAATTATAAAAT
1 TTATAAAAA--ATAAAAAAAAATATAAAAT
53797943 GCATCAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.36
31 16 0.64
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (29 bp):
TTATAAAAAATAAAAAAAAATATAAAATT
Found at i:53798247 original size:21 final size:19
Alignment explanation
Indices: 53798223--53798271 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 19
53798213 TATTTTTCTC
53798223 ATAAAAAAATACATAAAAATT
1 ATAAAAAAAT-CATAAAAA-T
*
53798244 ATAAAAATATCATAAAAAT
1 ATAAAAAAATCATAAAAAT
53798263 ATACAAAAA
1 ATA-AAAAA
53798272 CTTAACATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 12 0.48
21 9 0.36
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
ATAAAAAAATCATAAAAAT
Found at i:53798258 original size:11 final size:11
Alignment explanation
Indices: 53798221--53798264 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
53798211 TATATTTTTC
*
53798221 TCATAAAAAAA
1 TCATAAAAATA
53798232 TACATAAAAAT-
1 T-CATAAAAATA
53798243 T-ATAAAAATA
1 TCATAAAAATA
53798253 TCATAAAAATA
1 TCATAAAAATA
53798264 T
1 T
53798265 ACAAAAACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
9 8 0.28
10 1 0.03
11 12 0.41
12 8 0.28
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (11 bp):
TCATAAAAATA
Found at i:53799492 original size:3 final size:3
Alignment explanation
Indices: 53799486--53799564 Score: 88
Period size: 3 Copynumber: 25.7 Consensus size: 3
53799476 TTTTTTTTAG
53799486 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
* * * *
53799531 TTA CTTA GTA TTA TAA TTG TTAA TTA TTG TTA TT
1 TTA -TTA TTA TTA TTA TTA TT-A TTA TTA TTA TT
53799565 CCAATTTTAG
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.03
3 54 0.84
4 8 0.12
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:53817727 original size:18 final size:17
Alignment explanation
Indices: 53817704--53817737 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
53817694 CCGAAGATAG
53817704 CTTTCTTCTACTTTTTCC
1 CTTTCTT-TACTTTTTCC
*
53817722 CTTTCTTTTCTTTTTC
1 CTTTCTTTACTTTTTC
53817738 TTATGATAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (17 bp):
CTTTCTTTACTTTTTCC
Found at i:53824056 original size:40 final size:40
Alignment explanation
Indices: 53824012--53824102 Score: 112
Period size: 40 Copynumber: 2.3 Consensus size: 40
53824002 ACTTTTTAAC
* *
53824012 AAACGCCGCAATAGATCGAGAATTAGTGGTGCTTTCTAGG-
1 AAACGCCGCAATAGATCAAGAATTAGCGGTGCTTT-TAGGA
* * * *
53824052 AAACGCTGCTATAGATCAAGTATTAGCGGTGCTTTTCGGA
1 AAACGCCGCAATAGATCAAGAATTAGCGGTGCTTTTAGGA
53824092 AAACGCCGCAA
1 AAACGCCGCAA
53824103 AAAGATGAGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
39 3 0.07
40 39 0.93
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (40 bp):
AAACGCCGCAATAGATCAAGAATTAGCGGTGCTTTTAGGA
Found at i:53824405 original size:21 final size:21
Alignment explanation
Indices: 53824361--53824476 Score: 96
Period size: 21 Copynumber: 5.6 Consensus size: 21
53824351 AATATCTATA
* *
53824361 TTTAGGGTTTAGGGTGT-ATG
1 TTTAGGGTTTAGGGTTTAAGG
*
53824381 TTTATGGTTT-GAGGTTTAAGG
1 TTTAGGGTTTAG-GGTTTAAGG
53824402 TTTAGGGTTTAGGGTTTAAGG
1 TTTAGGGTTTAGGGTTTAAGG
*
53824423 TTTTAGGGTTTAGAGTTT-AGTG
1 -TTTAGGGTTTAGGGTTTAAG-G
* * * **
53824445 TTTACGGTGTA-TGTTTGTGG
1 TTTAGGGTTTAGGGTTTAAGG
53824465 TTTAGGGTTTAG
1 TTTAGGGTTTAG
53824477 TATTTAAGAT
Statistics
Matches: 78, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
19 1 0.01
20 27 0.35
21 32 0.41
22 18 0.23
ACGTcount: A:0.16, C:0.01, G:0.35, T:0.47
Consensus pattern (21 bp):
TTTAGGGTTTAGGGTTTAAGG
Found at i:53824432 original size:8 final size:7
Alignment explanation
Indices: 53824361--53824476 Score: 87
Period size: 7 Copynumber: 16.7 Consensus size: 7
53824351 AATATCTATA
53824361 TTTAGGG
1 TTTAGGG
53824368 TTTAGGG
1 TTTAGGG
* *
53824375 TGTA-TG
1 TTTAGGG
*
53824381 TTTATGG
1 TTTAGGG
53824388 TTT-GAGG
1 TTTAG-GG
*
53824395 TTTAAGG
1 TTTAGGG
53824402 TTTAGGG
1 TTTAGGG
53824409 TTTAGGG
1 TTTAGGG
*
53824416 TTTAAGGT
1 TTT-AGGG
53824424 TTTAGGG
1 TTTAGGG
*
53824431 TTTAGAG
1 TTTAGGG
*
53824438 TTTAGTG
1 TTTAGGG
*
53824445 TTTACGG
1 TTTAGGG
* *
53824452 TGTA-TG
1 TTTAGGG
53824458 TTT-GTGG
1 TTTAG-GG
53824465 TTTAGGG
1 TTTAGGG
53824472 TTTAG
1 TTTAG
53824477 TATTTAAGAT
Statistics
Matches: 85, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
6 7 0.08
7 71 0.84
8 7 0.08
ACGTcount: A:0.16, C:0.01, G:0.35, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:53824536 original size:7 final size:7
Alignment explanation
Indices: 53824524--53824706 Score: 74
Period size: 7 Copynumber: 26.0 Consensus size: 7
53824514 AATATCTATA
53824524 TTTAGGG
1 TTTAGGG
53824531 TTTAGGG
1 TTTAGGG
* *
53824538 TGTA-TG
1 TTTAGGG
*
53824544 TTTACGG
1 TTTAGGG
53824551 TTT-GAGG
1 TTTAG-GG
*
53824558 TTTAAGG
1 TTTAGGG
*
53824565 TTTAAGG
1 TTTAGGG
53824572 TTTAGGG
1 TTTAGGG
*
53824579 TTTTAAGG
1 -TTTAGGG
*
53824587 TTTAGAG
1 TTTAGGG
*
53824594 TTTAGTG
1 TTTAGGG
53824601 TTTAGGG
1 TTTAGGG
* *
53824608 TGTA-TG
1 TTTAGGG
53824614 TTT-GTGG
1 TTTAG-GG
53824621 TTT-GGG
1 TTTAGGG
53824627 TCTT-GGG
1 T-TTAGGG
53824634 TTTAGGG
1 TTTAGGG
* **
53824641 ATTAATG
1 TTTAGGG
*
53824648 TTTAGAAG
1 TTTAG-GG
*
53824656 TATAGAGG
1 TTTAG-GG
53824664 -TTAGGG
1 TTTAGGG
**
53824670 TTTAAAG
1 TTTAGGG
* *
53824677 TTTATGA
1 TTTAGGG
53824684 TTTAAGGG
1 TTT-AGGG
53824692 TTTTAGGG
1 -TTTAGGG
53824700 TTTAGGG
1 TTTAGGG
53824707 GGTTTTTGGT
Statistics
Matches: 132, Mismatches: 32, Indels: 24
0.70 0.17 0.13
Matches are distributed among these distances:
6 14 0.11
7 96 0.73
8 19 0.14
9 3 0.02
ACGTcount: A:0.20, C:0.01, G:0.34, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:53824586 original size:22 final size:22
Alignment explanation
Indices: 53824558--53824603 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
53824548 CGGTTTGAGG
53824558 TTTAAGGTTTA-AGGTTTAGGGT
1 TTTAAGGTTTAGA-GTTTAGGGT
*
53824580 TTTAAGGTTTAGAGTTTAGTGT
1 TTTAAGGTTTAGAGTTTAGGGT
53824602 TT
1 TT
53824604 AGGGTGTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (22 bp):
TTTAAGGTTTAGAGTTTAGGGT
Found at i:53824610 original size:156 final size:158
Alignment explanation
Indices: 53824294--53824627 Score: 548
Period size: 163 Copynumber: 2.1 Consensus size: 158
53824284 AATGTTTAGA
*
53824294 GTTTGGGGTTTAGGGTTTAGTATTTAAGATTCTTTTTTAATTAATTTTGTCCCCTATAATATCTA
1 GTTTGTGGTTTAGGGTTTAGTATTTAAGATTCTTTTTTAATTAATTTTGTCCCCTATAATATCTA
*
53824359 TATTTAGGGTTTAGGGTGTATGTTTATGGTTTGAGGTTTAAGGTTTAGGGTTTAGGGTTTAAGGT
66 TATTTAGGGTTTAGGGTGTATGTTTACGGTTTGAGGTTTAAGGTTTA--G---AGGGTTTAAGGT
*
53824424 TTTAGGGTTTAGAGTTTAGTGTTTACGGTGTAT
126 TTTAAGGTTTAGAGTTTAGTGTTTACGGTGTAT
*
53824457 GTTTGTGGTTTAGGGTTTAGTATTTAAGATTCTTTTTTAATTACTTTTGTCCCCTATAATATCTA
1 GTTTGTGGTTTAGGGTTTAGTATTTAAGATTCTTTTTTAATTAATTTTGTCCCCTATAATATCTA
*
53824522 TATTTAGGGTTTAGGGTGTATGTTTACGGTTTGAGGTTTAAGGTTTA-A-GGTTTAGGGTTTTAA
66 TATTTAGGGTTTAGGGTGTATGTTTACGGTTTGAGGTTTAAGGTTTAGAGGGTTTAAGGTTTTAA
*
53824585 GGTTTAGAGTTTAGTGTTTAGGGTGTAT
131 GGTTTAGAGTTTAGTGTTTACGGTGTAT
53824613 GTTTGTGGTTT-GGGT
1 GTTTGTGGTTTAGGGT
53824628 CTTGGGTTTA
Statistics
Matches: 165, Mismatches: 6, Indels: 8
0.92 0.03 0.04
Matches are distributed among these distances:
155 4 0.02
156 51 0.31
157 1 0.01
163 109 0.66
ACGTcount: A:0.19, C:0.04, G:0.27, T:0.49
Consensus pattern (158 bp):
GTTTGTGGTTTAGGGTTTAGTATTTAAGATTCTTTTTTAATTAATTTTGTCCCCTATAATATCTA
TATTTAGGGTTTAGGGTGTATGTTTACGGTTTGAGGTTTAAGGTTTAGAGGGTTTAAGGTTTTAA
GGTTTAGAGTTTAGTGTTTACGGTGTAT
Found at i:53825161 original size:39 final size:40
Alignment explanation
Indices: 53825105--53825182 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 40
53825095 CATTATATTC
*
53825105 AATTTTAAAATTGAACAA-T-AAAATAATGTCATATTAAA
1 AATTTTAAAATTGAACAATTAAAAAAAATGTCATATTAAA
*
53825143 AATTTTAAAAATTTAACAATTAAAAAAAATGTCATATTAA
1 AATTTT-AAAATTGAACAATTAAAAAAAATGTCATATTAA
53825183 TGTATCAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
38 6 0.17
39 11 0.31
40 1 0.03
41 17 0.49
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (40 bp):
AATTTTAAAATTGAACAATTAAAAAAAATGTCATATTAAA
Found at i:53825589 original size:125 final size:124
Alignment explanation
Indices: 53825279--53825677 Score: 480
Period size: 125 Copynumber: 3.2 Consensus size: 124
53825269 ATCTTTAGCA
* * * * *
53825279 GCGTTTTTCAT-AGAAACGCCACAAAAGGTAAACAATAGTGGCGTTTGGACTAAAAATGCCGCAA
1 GCGTTTTTC-TCAAAAACGCCGCAAAAGGTAAGCAATAGTGGCGTTTTGTCTAAAAATGCCGCAA
* * * ** *
53825343 CAATGTATTAAAAATTATACAAAACGGCGCCGTTTGGTTATTGGAATTTGATTTTTAGTG
65 CAATGTATTAAAAACTGTACAAAACGGCGCCATTTGGTTACAGGAATTTAATTTTTAGTG
* * * *
53825403 GCGTTTTTCTCCAAAACGCCGCAAAAGGTATGTAATAGTGGCG-TTTGTTCTAAAAACGCCGCAA
1 GCGTTTTTCTCAAAAACGCCGCAAAAGGTAAGCAATAGTGGCGTTTTG-TCTAAAAATGCCGCAA
* * *
53825467 CAATGTATTAAAAAGTGTACAAAATGACGCCATTTGGTTACAGGAATTTAACTTTTTAGTG
65 CAATGTATTAAAAACTGTACAAAACGGCGCCATTTGGTTACAGGAATTTAA-TTTTTAGTG
* * ** *
53825528 GCATTTTTCTCAAAAACGCCGCAAAAGGTAAGCATTAGCAGTGTTTTGTCTAAAAATGCCGCAAC
1 GCGTTTTTCTCAAAAACGCCGCAAAAGGTAAGCAATAGTGGCGTTTTGTCTAAAAATGCCGCAAC
* * *
53825593 AATGTATTAAAAACTGTACAAAACGGCGCCATTTTGTTTCAGGAAATTAATTTTGTAGTG
66 AATGTATTAAAAACTGTACAAAACGGCGCCATTTGGTTACAGGAATTTAATTTT-TAGTG
* *
53825653 TCGTTTTTGCT-GAAAACGCCGCAAA
1 GCGTTTTT-CTCAAAAACGCCGCAAA
53825678 TATTTCAATA
Statistics
Matches: 234, Mismatches: 35, Indels: 11
0.84 0.12 0.04
Matches are distributed among these distances:
123 4 0.02
124 96 0.41
125 128 0.55
126 6 0.03
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (124 bp):
GCGTTTTTCTCAAAAACGCCGCAAAAGGTAAGCAATAGTGGCGTTTTGTCTAAAAATGCCGCAAC
AATGTATTAAAAACTGTACAAAACGGCGCCATTTGGTTACAGGAATTTAATTTTTAGTG
Found at i:53828230 original size:5 final size:5
Alignment explanation
Indices: 53828220--53828244 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
53828210 AATAAGAACG
53828220 ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
53828245 CCATTTGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:53829989 original size:27 final size:27
Alignment explanation
Indices: 53829959--53830010 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
53829949 AAGGAAAGCC
53829959 TTTTAGAACGTCCTAGATTTTATAAAA
1 TTTTAGAACGTCCTAGATTTTATAAAA
53829986 TTTTAGAACGTCCTAGATTTTATAA
1 TTTTAGAACGTCCTAGATTTTATAA
53830011 TATTCAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (27 bp):
TTTTAGAACGTCCTAGATTTTATAAAA
Found at i:53837610 original size:24 final size:24
Alignment explanation
Indices: 53837582--53837666 Score: 71
Period size: 24 Copynumber: 3.3 Consensus size: 24
53837572 AAAAATTAAA
*
53837582 TTAGGGTATTATGTTTTTAATTGT
1 TTAGGGTATTAGGTTTTTAATTGT
* * **
53837606 TTAGGGTTTTAAGGTTTATGAAAAATTAAA
1 TTAGGGTATT-AGGTTT-T---TAATT-GT
53837636 TTAGGGTATTAGGTTTTTAATTGT
1 TTAGGGTATTAGGTTTTTAATTGT
53837660 TTAGGGT
1 TTAGGGT
53837667 TTCTGGGCTT
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
24 16 0.35
25 9 0.20
26 1 0.02
28 1 0.02
29 10 0.22
30 9 0.20
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.49
Consensus pattern (24 bp):
TTAGGGTATTAGGTTTTTAATTGT
Found at i:53837625 original size:54 final size:54
Alignment explanation
Indices: 53837566--53837734 Score: 203
Period size: 54 Copynumber: 2.9 Consensus size: 54
53837556 TTGATTAGGT
*
53837566 TTTATGAAAAATTAAATTAGGGTATTATGTTTTTAATTGTTTAGGGTTTTAAGG
1 TTTATGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAGGGTTTTAAGG
53837620 TTTATGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAGGGTTTCTGGGCTTGATTAGGG
1 TTTATGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAGGG--T-T----TT-A--A-GG
* * *
53837685 TTTAAGAAAAATTAAATCAAGGTATTAGGTTTTTAATTGTTTAGGGTTTT
1 TTTATGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAGGGTTTT
53837735 GGGGTTTGAT
Statistics
Matches: 100, Mismatches: 4, Indels: 18
0.82 0.03 0.15
Matches are distributed among these distances:
54 45 0.45
56 1 0.01
57 1 0.01
58 2 0.02
61 2 0.02
62 2 0.02
63 1 0.01
64 1 0.01
65 45 0.45
ACGTcount: A:0.30, C:0.02, G:0.22, T:0.46
Consensus pattern (54 bp):
TTTATGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAGGGTTTTAAGG
Found at i:53837694 original size:65 final size:65
Alignment explanation
Indices: 53837614--53837786 Score: 258
Period size: 65 Copynumber: 2.7 Consensus size: 65
53837604 GTTTAGGGTT
*
53837614 TTAAGGTTTATGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAGGGTTTCT-GGGCTTG
1 TTAAGGTTTAAGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAGGGTTT-TGGGGCTTG
53837678 A
65 A
* * * *
53837679 TTAGGGTTTAAGAAAAATTAAATCAAGGTATTAGGTTTTTAATTGTTTAGGGTTTTGGGGTTTGA
1 TTAAGGTTTAAGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAGGGTTTTGGGGCTTGA
* * *
53837744 TTAAGGTTTAGGAAAATTTAAATTAGGGTATTAAGTTTTTAAT
1 TTAAGGTTTAAGAAAAATTAAATTAGGGTATTAGGTTTTTAAT
53837787 AGGACTGAAG
Statistics
Matches: 96, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
64 1 0.01
65 95 0.99
ACGTcount: A:0.31, C:0.02, G:0.24, T:0.44
Consensus pattern (65 bp):
TTAAGGTTTAAGAAAAATTAAATTAGGGTATTAGGTTTTTAATTGTTTAGGGTTTTGGGGCTTGA
Found at i:53840837 original size:18 final size:17
Alignment explanation
Indices: 53840814--53840847 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
53840804 CCGAATATAG
53840814 CTTTCTTCTACTTTTTCC
1 CTTTCTT-TACTTTTTCC
*
53840832 CTTTCTTTTCTTTTTC
1 CTTTCTTTACTTTTTC
53840848 TTATGATAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (17 bp):
CTTTCTTTACTTTTTCC
Found at i:53865198 original size:28 final size:28
Alignment explanation
Indices: 53865144--53865220 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 28
53865134 CCCTAAACCG
* * *
53865144 GTTTAGGGTTTAAGGTCTAAGGAATAGA
1 GTTTACGGTTTAGGGTCTAGGGAATAGA
* *
53865172 GTTTACGGTTTAGGGTTTAGGGGATAGA
1 GTTTACGGTTTAGGGTCTAGGGAATAGA
* **
53865200 GGTTGTGGTTTAGGGTCTAGG
1 GTTTACGGTTTAGGGTCTAGG
53865221 TTATTTAGTA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.22, C:0.04, G:0.39, T:0.35
Consensus pattern (28 bp):
GTTTACGGTTTAGGGTCTAGGGAATAGA
Found at i:53867988 original size:18 final size:18
Alignment explanation
Indices: 53867965--53868009 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
53867955 AAACAATTTT
53867965 TAAATTATATAACTTACA
1 TAAATTATATAACTTACA
53867983 TAAATTATATAACTTACA
1 TAAATTATATAACTTACA
*
53868001 TAACTTATA
1 TAAATTATA
53868010 AATATTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATTATATAACTTACA
Found at i:53867994 original size:9 final size:9
Alignment explanation
Indices: 53867969--53868009 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
53867959 AATTTTTAAA
53867969 TTATATAAC
1 TTATATAAC
* *
53867978 TTACATAAA
1 TTATATAAC
53867987 TTATATAAC
1 TTATATAAC
*
53867996 TTACATAAC
1 TTATATAAC
53868005 TTATA
1 TTATA
53868010 AATATTTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (9 bp):
TTATATAAC
Found at i:53868145 original size:9 final size:9
Alignment explanation
Indices: 53868133--53868187 Score: 74
Period size: 9 Copynumber: 6.1 Consensus size: 9
53868123 ATAAACTTGC
53868133 ATAACTTAT
1 ATAACTTAT
*
53868142 ATAAATTAT
1 ATAACTTAT
*
53868151 ATAACTTAC
1 ATAACTTAT
*
53868160 ATAAATTAT
1 ATAACTTAT
*
53868169 ATAACTTAC
1 ATAACTTAT
53868178 ATAACTTAT
1 ATAACTTAT
53868187 A
1 A
53868188 AATATTTATA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (9 bp):
ATAACTTAT
Found at i:53868156 original size:18 final size:18
Alignment explanation
Indices: 53868133--53868187 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
53868123 ATAAACTTGC
*
53868133 ATAACTTATATAAATTAT
1 ATAACTTACATAAATTAT
53868151 ATAACTTACATAAATTAT
1 ATAACTTACATAAATTAT
*
53868169 ATAACTTACATAACTTAT
1 ATAACTTACATAAATTAT
53868187 A
1 A
53868188 AATATTTATA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAACTTACATAAATTAT
Found at i:53868156 original size:27 final size:27
Alignment explanation
Indices: 53868120--53868185 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
53868110 CATAAACTTA
* *
53868120 TATATAAACTTGCATAACTTATATAAAT
1 TATAT-AACTTACATAAATTATATAAAT
*
53868148 TATATAACTTACATAAATTATATAACT
1 TATATAACTTACATAAATTATATAAAT
*
53868175 TACATAACTTA
1 TATATAACTTA
53868186 TAAATATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 29 0.85
28 5 0.15
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (27 bp):
TATATAACTTACATAAATTATATAAAT
Found at i:53868162 original size:178 final size:179
Alignment explanation
Indices: 53867965--53868306 Score: 659
Period size: 179 Copynumber: 1.9 Consensus size: 179
53867955 AAACAATTTT
53867965 TAAATTATATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
1 TAAATTATATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
*
53868030 ATATAT-TTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTCA
66 ATAAATATTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTCA
53868094 AATTTATCAATCATATCATAAACTTATATATAAACTTGCATAACTTATA
131 AATTTATCAATCATATCATAAACTTATATATAAACTTGCATAACTTATA
53868143 TAAATTATATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
1 TAAATTATATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
*
53868208 ATAAATATTTTAAAATCTATATTTTTTTCAAAATTTATCAATGATAGCATAACTTACATAACTCA
66 ATAAATATTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTCA
53868273 AATTTATCAATCATATCATAAACTTATATATAAA
131 AATTTATCAATCATATCATAAACTTATATATAAA
53868307 TTATTTAAGT
Statistics
Matches: 161, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
178 70 0.43
179 91 0.57
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (179 bp):
TAAATTATATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
ATAAATATTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTCA
AATTTATCAATCATATCATAAACTTATATATAAACTTGCATAACTTATA
Found at i:53871259 original size:7 final size:7
Alignment explanation
Indices: 53871249--53871292 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
53871239 AACCCCTATC
53871249 CCCTAAA
1 CCCTAAA
53871256 CCCTAAA
1 CCCTAAA
*
53871263 CCGTAAA
1 CCCTAAA
* *
53871270 CTCTAGA
1 CCCTAAA
*
53871277 CCTTAAA
1 CCCTAAA
53871284 CCCTAAA
1 CCCTAAA
53871291 CC
1 CC
53871293 GATTTAGGGT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.39, C:0.39, G:0.05, T:0.18
Consensus pattern (7 bp):
CCCTAAA
Found at i:53871656 original size:14 final size:15
Alignment explanation
Indices: 53871632--53871667 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
53871622 AATCATAGAA
53871632 CATATAAACCCTAAAT
1 CATA-AAACCCTAAAT
53871648 C-TAAAACCCTAAAT
1 CATAAAACCCTAAAT
53871662 CATAAA
1 CATAAA
53871668 CATATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 12 0.63
15 6 0.32
16 1 0.05
ACGTcount: A:0.53, C:0.25, G:0.00, T:0.22
Consensus pattern (15 bp):
CATAAAACCCTAAAT
Found at i:53883550 original size:26 final size:26
Alignment explanation
Indices: 53883520--53883573 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
53883510 GTCTTGTTAC
*
53883520 TTAGTTGGATTTGAACTAAGTTGTCA
1 TTAGTTGAATTTGAACTAAGTTGTCA
*
53883546 TTAGTTTAATTTGAACTAAGTTGTCA
1 TTAGTTGAATTTGAACTAAGTTGTCA
53883572 TT
1 TT
53883574 GTACTTGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.46
Consensus pattern (26 bp):
TTAGTTGAATTTGAACTAAGTTGTCA
Found at i:53883703 original size:23 final size:23
Alignment explanation
Indices: 53883677--53883741 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
53883667 GTTTAGTTCC
53883677 CATGCAAAGGTGGCCATGCACGA
1 CATGCAAAGGTGGCCATGCACGA
53883700 CATGCAAAGGTGGCCATGCACGA
1 CATGCAAAGGTGGCCATGCACGA
*
53883723 CATGCAAAGGTGGTCATGC
1 CATGCAAAGGTGGCCATGC
53883742 TCGAAGAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.29, C:0.25, G:0.31, T:0.15
Consensus pattern (23 bp):
CATGCAAAGGTGGCCATGCACGA
Found at i:53898369 original size:5 final size:5
Alignment explanation
Indices: 53898359--53898402 Score: 88
Period size: 5 Copynumber: 8.8 Consensus size: 5
53898349 AAGAACGATT
53898359 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAAT
1 TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAATA TAAT
53898403 GTACCATTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:53912665 original size:5 final size:5
Alignment explanation
Indices: 53912655--53912679 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
53912645 AATAAGAACG
53912655 ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA
53912680 CCATTTGGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:53913565 original size:29 final size:31
Alignment explanation
Indices: 53913533--53913598 Score: 91
Period size: 29 Copynumber: 2.2 Consensus size: 31
53913523 GTCTAAATTT
*
53913533 AATTTTAAGAAATTTAGAGGTC-AAA-ATAA
1 AATTTTAAAAAATTTAGAGGTCAAAATATAA
* *
53913562 AATTTCAAAAAATTTGGAGGTCAAAATATAA
1 AATTTTAAAAAATTTAGAGGTCAAAATATAA
53913593 AATTTT
1 AATTTT
53913599 TTTTAAACAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 19 0.61
30 3 0.10
31 9 0.29
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.33
Consensus pattern (31 bp):
AATTTTAAAAAATTTAGAGGTCAAAATATAA
Found at i:53913572 original size:87 final size:88
Alignment explanation
Indices: 53913431--53913592 Score: 215
Period size: 87 Copynumber: 1.9 Consensus size: 88
53913421 GAAAAAAAAT
*
53913431 TAGGGGTCAAAATGTAATTTTAGAAAATTTTAAGGTTCAAAATAAAATTTAAAAAATAAGG-GGT
1 TAGGAGTCAAAATGTAATTTTAGAAAATTTTAAGGTTCAAAATAAAATTTAAAAAATAAGGAGGT
*
53913495 TAAAATATAATTTCATTAAAGTA
66 CAAAATATAATTTCATTAAAGTA
* * **
53913518 TAGGAGTCTAAATTTAATTTTA-AGAAA-TTTAGAGG-TCAAAATAAAATTTCAAAAAATTTGGA
1 TAGGAGTCAAAATGTAATTTTAGA-AAATTTTA-AGGTTCAAAATAAAATTT-AAAAAATAAGGA
53913580 GGTCAAAATATAA
63 GGTCAAAATATAA
53913593 AATTTTTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
86 19 0.29
87 34 0.52
88 12 0.18
ACGTcount: A:0.48, C:0.04, G:0.15, T:0.33
Consensus pattern (88 bp):
TAGGAGTCAAAATGTAATTTTAGAAAATTTTAAGGTTCAAAATAAAATTTAAAAAATAAGGAGGT
CAAAATATAATTTCATTAAAGTA
Found at i:53913597 original size:31 final size:29
Alignment explanation
Indices: 53913423--53913589 Score: 99
Period size: 29 Copynumber: 5.8 Consensus size: 29
53913413 GTAATTTTGA
* * ** *
53913423 AAAAAAATTAGGGGTCAAAATGTAATTTT
1 AAAAAATTTAGAGGTCAAAATAAAATTTC
*
53913452 AGAAAATTTTA-AGGTTCAAAATAAAATTT-
1 A-AAAAATTTAGAGG-TCAAAATAAAATTTC
* * * *
53913481 AAAAAA-TAAGGGGTTAAAATATAATTTC
1 AAAAAATTTAGAGGTCAAAATAAAATTTC
* * * * ** *
53913509 ATTAAAGTATAG-GAGTCTAAATTTAATTTT
1 A-AAAAATTTAGAG-GTCAAAATAAAATTTC
*
53913539 AAGAAATTTAGAGGTCAAAATAAAATTTC
1 AAAAAATTTAGAGGTCAAAATAAAATTTC
*
53913568 AAAAAATTTGGAGGTCAAAATA
1 AAAAAATTTAGAGGTCAAAATA
53913590 TAAAATTTTT
Statistics
Matches: 102, Mismatches: 28, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
27 14 0.14
28 7 0.07
29 46 0.45
30 35 0.34
ACGTcount: A:0.50, C:0.04, G:0.14, T:0.32
Consensus pattern (29 bp):
AAAAAATTTAGAGGTCAAAATAAAATTTC
Found at i:53917864 original size:114 final size:112
Alignment explanation
Indices: 53917660--53917946 Score: 439
Period size: 114 Copynumber: 2.5 Consensus size: 112
53917650 CTTTCAGAAA
* * * * *
53917660 TTTAGCGGCGTTTTTGAGAATGCGCCACAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTG
* * *
53917725 TCGGGGATTTAGTGGTGTTTTTAGGTAAGCGCCGCTAATGCTCAGGGC
66 TCGGGGATTTAGTGGCGCTTCTAGGTAAGCGCCGCTAATGCTCA-GGC
* * * *
53917773 TTTAGCTGTGTTTTTGGGAAAGCGTCGCAAAAATACCTAAGACCAACGACGCCGTTTTTTGAGCT
1 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAA-ACCTAAGCCCAACGACGCCGTTTTCTGAGCT
53917838 GTCGGGGATTTAGTGGCGCTTCTAGGTAAGCGCCGCTAATGCTCAGGC
65 GTCGGGGATTTAGTGGCGCTTCTAGGTAAGCGCCGCTAATGCTCAGGC
*
53917886 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAACCTTAGCCCAACGACGCCGTTTTCTGA
1 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGA
53917947 TCTTTCAGAT
Statistics
Matches: 156, Mismatches: 17, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
112 25 0.16
113 61 0.39
114 70 0.45
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (112 bp):
TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTG
TCGGGGATTTAGTGGCGCTTCTAGGTAAGCGCCGCTAATGCTCAGGC
Found at i:53917982 original size:113 final size:113
Alignment explanation
Indices: 53917660--53917995 Score: 467
Period size: 113 Copynumber: 3.0 Consensus size: 113
53917650 CTTTCAGAAA
* * * *
53917660 TTTAGCGGCGTTTTTGAGAATGCGCCACAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
*
53917725 TCGGGGATTTAGTGGTGTTTTTAGGTAAGCGCCGCTAATGCTCAGGGC
66 TCGGGGATTTAGTGGCGTTTTTAGGTAAGCGCCGCTAATGCTCAGGGC
* * * *
53917773 TTTAGCTGTGTTTTTGGGAAAGCGTCGCAAAAATACCTAAGACCAACGACGCCGTTTTTTGAGCT
1 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAA-ACCTAAGCCCAACGACGCCGTTTTCTGAGCT
* * *
53917838 GTCGGGGATTTAGTGGCGCTTCTAGGTAAGCGCCGCTAATGCTCA-GGC
65 TTCGGGGATTTAGTGGCGTTTTTAGGTAAGCGCCGCTAATGCTCAGGGC
* *
53917886 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAACCTTAGCCCAACGACGCCGTTTTCTGATCTT
1 TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
** * * * *
53917951 TCAGATGATTTAGCGGCGTTTTTCGGAAAGCGTCGCTAATGCTCA
66 TC-GGGGATTTAGTGGCGTTTTTAGGTAAGCGCCGCTAATGCTCA
53917996 AGGATTTAAA
Statistics
Matches: 194, Mismatches: 27, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
112 29 0.15
113 95 0.49
114 70 0.36
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (113 bp):
TTTAGCGGTGTTTTTGGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAGTGGCGTTTTTAGGTAAGCGCCGCTAATGCTCAGGGC
Found at i:53918302 original size:30 final size:31
Alignment explanation
Indices: 53918259--53918320 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
53918249 TATGCTTTAA
53918259 GGGTTAGTGGATTTAGGGGTAAGGGGTTAGG
1 GGGTTAGTGGATTTAGGGGTAAGGGGTTAGG
* * *
53918290 GGGTTA-TGGATTTAGGGTTTAGGGTTTAGG
1 GGGTTAGTGGATTTAGGGGTAAGGGGTTAGG
53918320 G
1 G
53918321 TTTCAACGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 22 0.79
31 6 0.21
ACGTcount: A:0.18, C:0.00, G:0.48, T:0.34
Consensus pattern (31 bp):
GGGTTAGTGGATTTAGGGGTAAGGGGTTAGG
Found at i:53918736 original size:7 final size:7
Alignment explanation
Indices: 53918674--53918741 Score: 50
Period size: 7 Copynumber: 9.4 Consensus size: 7
53918664 AAAGGGTTAG
53918674 GGGTTTA
1 GGGTTTA
*
53918681 GGGGTTA
1 GGGTTTA
*
53918688 CGAG-TTA
1 -GGGTTTA
*
53918695 CGGGTTAA
1 -GGGTTTA
53918703 GGG-TTA
1 GGGTTTA
53918709 GTGGTTTA
1 G-GGTTTA
*
53918717 GGATTTA
1 GGGTTTA
53918724 GGGTTTA
1 GGGTTTA
53918731 GGGTTTCA
1 GGGTTT-A
53918739 GGG
1 GGG
53918742 GTCGAATAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
6 3 0.06
7 34 0.69
8 12 0.24
ACGTcount: A:0.18, C:0.04, G:0.43, T:0.35
Consensus pattern (7 bp):
GGGTTTA
Found at i:53926622 original size:22 final size:21
Alignment explanation
Indices: 53926594--53926709 Score: 79
Period size: 18 Copynumber: 5.6 Consensus size: 21
53926584 ATTAGATTAC
53926594 TTACATTACTTACTAAAATATA
1 TTACATTACTTA-TAAAATATA
53926616 TTACATTAC-T-T-AAATATA
1 TTACATTACTTATAAAATATA
*
53926634 TTAC-TTAC-TA-AAATTTATAA
1 TTACATTACTTATAAA-ATAT-A
53926654 CTTACATTAC-T-T-AAATATA
1 -TTACATTACTTATAAAATATA
*
53926673 TTACATTACTTAAAATTTATATATA
1 TTACATTACTTATAA---A-ATATA
53926698 TTACATTACTTA
1 TTACATTACTTA
53926710 AATAAAAATT
Statistics
Matches: 77, Mismatches: 3, Indels: 25
0.73 0.03 0.24
Matches are distributed among these distances:
17 5 0.06
18 22 0.29
19 6 0.08
20 4 0.05
21 8 0.10
22 14 0.18
24 1 0.01
25 17 0.22
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (21 bp):
TTACATTACTTATAAAATATA
Found at i:53926630 original size:18 final size:18
Alignment explanation
Indices: 53926598--53926686 Score: 110
Period size: 18 Copynumber: 4.8 Consensus size: 18
53926588 GATTACTTAC
*
53926598 ATTAC-TTACTAAAATAT
1 ATTACATTACTTAAATAT
53926615 ATTACATTACTTAAATAT
1 ATTACATTACTTAAATAT
*
53926633 ATTAC-TTACTAAAATTTAT
1 ATTACATTACTTAAA--TAT
53926652 AACTTACATTACTTAAATAT
1 -A-TTACATTACTTAAATAT
53926672 ATTACATTACTTAAA
1 ATTACATTACTTAAA
53926687 ATTTATATAT
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
17 13 0.21
18 30 0.48
19 4 0.06
20 4 0.06
21 4 0.06
22 8 0.13
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTACATTACTTAAATAT
Found at i:53926642 original size:39 final size:39
Alignment explanation
Indices: 53926594--53926713 Score: 138
Period size: 39 Copynumber: 2.9 Consensus size: 39
53926584 ATTAGATTAC
53926594 TTACATTACTTACTAAA-ATATATTACATTACTTAAATATA
1 TTACATTACTTA--AAATATATATTACATTACTTAAATATA
*
53926634 TTAC-TTAC-TAAAATTTATAACTTACATTACTTAAATATA
1 TTACATTACTTAAAATATAT-A-TTACATTACTTAAATATA
53926673 TTACATTACTTAAAATTTATATATATTACATTACTTAAATA
1 TTACATTACTT-AAA---ATATATATTACATTACTTAAATA
53926714 AAAATTAGCT
Statistics
Matches: 69, Mismatches: 2, Indels: 15
0.80 0.02 0.17
Matches are distributed among these distances:
36 3 0.04
37 3 0.04
38 3 0.04
39 26 0.38
40 8 0.12
41 1 0.01
42 3 0.04
43 16 0.23
44 1 0.01
45 5 0.07
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (39 bp):
TTACATTACTTAAAATATATATTACATTACTTAAATATA
Found at i:53927017 original size:18 final size:18
Alignment explanation
Indices: 53926976--53927018 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
53926966 TTTTTTATGA
*
53926976 ATATTTTTAAATTTGTTG
1 ATATTTTAAAATTTGTTG
* *
53926994 AAATTTTAAAATTTTTTG
1 ATATTTTAAAATTTGTTG
*
53927012 TTATTTT
1 ATATTTT
53927019 TTCTGATTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (18 bp):
ATATTTTAAAATTTGTTG
Found at i:53927318 original size:9 final size:9
Alignment explanation
Indices: 53927304--53927509 Score: 86
Period size: 9 Copynumber: 23.3 Consensus size: 9
53927294 ATTAATATTA
53927304 TACATAACT
1 TACATAACT
53927313 TACATAA--
1 TACATAACT
53927320 TACATAA--
1 TACATAACT
53927327 TACATAACT
1 TACATAACT
*
53927336 TACATAAAT
1 TACATAACT
53927345 TACATAA--
1 TACATAACT
53927352 TACATAACT
1 TACATAACT
53927361 TACATAA--
1 TACATAACT
*
53927368 TACACAACT
1 TACATAACT
*
53927377 TA-ATTAATATT
1 TACA-T-A-ACT
53927388 ATACATAACT
1 -TACATAACT
*
53927398 TA-ATTACAAGTT
1 TACA-T--AA-CT
53927410 ATACATAACT
1 -TACATAACT
53927420 TACATAA--
1 TACATAACT
*
53927427 TACACAACT
1 TACATAACT
53927436 TACATAA--
1 TACATAACT
*
53927443 TACACAACT
1 TACATAACT
*
53927452 TA-ATTAATATT
1 TACA-T-A-ACT
*
53927463 ATACATAACA
1 -TACATAACT
*
53927473 TGCATAA--
1 TACATAACT
53927480 TACATAACT
1 TACATAACT
53927489 TACATAACT
1 TACATAACT
*
53927498 TACATAATT
1 TACATAACT
53927507 TAC
1 TAC
53927510 CTAATACATA
Statistics
Matches: 152, Mismatches: 17, Indels: 56
0.68 0.08 0.25
Matches are distributed among these distances:
7 45 0.30
8 3 0.02
9 75 0.49
10 6 0.04
11 10 0.07
12 7 0.05
13 5 0.03
14 1 0.01
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.33
Consensus pattern (9 bp):
TACATAACT
Found at i:53927324 original size:16 final size:16
Alignment explanation
Indices: 53927303--53927520 Score: 150
Period size: 16 Copynumber: 13.5 Consensus size: 16
53927293 AATTAATATT
53927303 ATACATAACTTACATA
1 ATACATAACTTACATA
53927319 ATACATAA--TACATA
1 ATACATAACTTACATA
*
53927333 ACTTACATAAATTACATA
1 A--TACATAACTTACATA
53927351 ATACATAACTTACATA
1 ATACATAACTTACATA
*
53927367 ATACACAACTTA-AT-
1 ATACATAACTTACATA
*
53927381 -TA-AT-ATTATACAT-
1 ATACATAACT-TACATA
* *
53927394 A-ACTTAA-TTACAAGTT
1 ATACATAACTTAC-A-TA
53927410 ATACATAACTTACATA
1 ATACATAACTTACATA
*
53927426 ATACACAACTTACATA
1 ATACATAACTTACATA
* *
53927442 ATACACAACTTAATTAATA
1 ATACATAACTT-A--CATA
* *
53927461 TTATACATAACATGCATA
1 --ATACATAACTTACATA
53927479 ATACATAACTTACATA
1 ATACATAACTTACATA
* *
53927495 ACTTACATAATTTACCTA
1 A--TACATAACTTACATA
53927513 ATACATAA
1 ATACATAA
53927521 ATATATATCA
Statistics
Matches: 164, Mismatches: 17, Indels: 42
0.74 0.08 0.19
Matches are distributed among these distances:
11 2 0.01
12 3 0.02
13 8 0.05
14 10 0.06
15 4 0.02
16 90 0.55
17 7 0.04
18 28 0.17
19 3 0.02
21 9 0.05
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.33
Consensus pattern (16 bp):
ATACATAACTTACATA
Found at i:53927354 original size:25 final size:24
Alignment explanation
Indices: 53927265--53927371 Score: 118
Period size: 23 Copynumber: 4.7 Consensus size: 24
53927255 TAATAAATAA
* * *
53927265 AACTTGCAT-AATTCATAATACAC
1 AACTTACATAAATACATAATACAT
* *
53927288 AACTTA-ATTAAT--ATTATACAT
1 AACTTACATAAATACATAATACAT
53927309 AACTTACAT-AATACATAATACAT
1 AACTTACATAAATACATAATACAT
53927332 AACTTACATAAATTACATAATACAT
1 AACTTACATAAA-TACATAATACAT
53927357 AACTTACAT-AATACA
1 AACTTACATAAATACA
53927372 CAACTTAATT
Statistics
Matches: 74, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
21 16 0.22
22 4 0.05
23 29 0.39
24 4 0.05
25 21 0.28
ACGTcount: A:0.50, C:0.17, G:0.01, T:0.33
Consensus pattern (24 bp):
AACTTACATAAATACATAATACAT
Found at i:53927414 original size:22 final size:21
Alignment explanation
Indices: 53927282--53927421 Score: 98
Period size: 21 Copynumber: 6.6 Consensus size: 21
53927272 ATAATTCATA
*
53927282 ATACACAACTTAATTAATATT
1 ATACATAACTTAATTAATATT
*
53927303 ATACATAACTTACA-TAATACATA
1 ATACATAACTTA-ATTAAT--ATT
53927326 ATACATAACTTACA-TAA-A-T
1 ATACATAACTTA-ATTAATATT
*
53927345 -TACATAATACATAACTTACATA--
1 ATACAT-A-ACTTAA-TTA-ATATT
*
53927367 ATACACAACTTAATTAATATT
1 ATACATAACTTAATTAATATT
53927388 ATACATAACTTAATTACA-AGTT
1 ATACATAACTTAATTA-ATA-TT
53927410 ATACATAACTTA
1 ATACATAACTTA
53927422 CATAATACAC
Statistics
Matches: 98, Mismatches: 7, Indels: 27
0.74 0.05 0.20
Matches are distributed among these distances:
18 5 0.05
19 5 0.05
20 8 0.08
21 38 0.39
22 18 0.18
23 24 0.24
ACGTcount: A:0.49, C:0.16, G:0.01, T:0.34
Consensus pattern (21 bp):
ATACATAACTTAATTAATATT
Found at i:53933037 original size:21 final size:22
Alignment explanation
Indices: 53933013--53933061 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
53933003 CTACAACTTA
53933013 AAGCAGAAG-CGGCAGCGAGGG
1 AAGCAGAAGACGGCAGCGAGGG
* *
53933034 AAGCA-ACGACTGCAGCGAGGG
1 AAGCAGAAGACGGCAGCGAGGG
53933055 AAGCAGA
1 AAGCAGA
53933062 GGCTACAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 2 0.08
21 21 0.88
22 1 0.04
ACGTcount: A:0.37, C:0.20, G:0.41, T:0.02
Consensus pattern (22 bp):
AAGCAGAAGACGGCAGCGAGGG
Found at i:53933449 original size:42 final size:42
Alignment explanation
Indices: 53933402--53933599 Score: 299
Period size: 42 Copynumber: 4.7 Consensus size: 42
53933392 TTTTGTATAA
53933402 AAATGCCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAAAG
1 AAATGCCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAAAG
* *
53933444 AAATGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGAAA-
1 AAATGCCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAAAG
*
53933485 AAATGCCGTTAAAGACCATGTTCTTTAGCGGCACTTAGAAAG
1 AAATGCCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAAAG
* ** * * *
53933527 AAACGCTACTAAAGACCATGTTCTTTAGCTGCGCTTAGAAAA
1 AAATGCCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAAAG
*
53933569 AAACGCCGCTAAAGACCATGTTCTTTAGCGG
1 AAATGCCGCTAAAGACCATGTTCTTTAGCGG
53933600 AGTTTTTTTC
Statistics
Matches: 140, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
41 38 0.27
42 102 0.73
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (42 bp):
AAATGCCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAAAG
Found at i:53933539 original size:83 final size:84
Alignment explanation
Indices: 53933400--53933599 Score: 348
Period size: 83 Copynumber: 2.4 Consensus size: 84
53933390 ATTTTTGTAT
*
53933400 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAAAGAAATGCCACTAAAGACCATGT
1 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAAAGAAACGCCACTAAAGACCATGT
53933465 TCTTTAGCGGCGCTTAG-A
66 TCTTTAGCGGCGCTTAGAA
* *
53933483 AAAAATGCCGTTAAAGACCATGTTCTTTAGCGGCACTTAGAAAGAAACGCTACTAAAGACCATGT
1 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAAAGAAACGCCACTAAAGACCATGT
*
53933548 TCTTTAGCTGCGCTTAGAA
66 TCTTTAGCGGCGCTTAGAA
*
53933567 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGG
1 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGG
53933600 AGTTTTTTTC
Statistics
Matches: 110, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
83 78 0.71
84 32 0.29
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (84 bp):
AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCACTTAGAAAGAAACGCCACTAAAGACCATGT
TCTTTAGCGGCGCTTAGAA
Found at i:53940294 original size:111 final size:110
Alignment explanation
Indices: 53940044--53940450 Score: 525
Period size: 110 Copynumber: 3.7 Consensus size: 110
53940034 GAAATTCAAG
* * * * *
53940044 AGGATATTTGGCTATTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGTACG-TTCCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGAAACCCAGCACCTTAGGGCACGTTTTCTC
* * ***
53940106 AAATTTTCAAACGCAAAACATTGCCTTATTTTGAAAAAAAAAATTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTG---AAAATTTTTAAA
* * * *
53940154 AGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGTACCTTAGGGCATGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGAAACCCAGCACCTTAGGGCACGTTTTCTC
*
53940219 GAATTTCCCAAACGCAAAGCATTGCCTTATTTTGAAAATTTTTAAA
66 GAATTT-CCAAACGCAAAACATTGCCTTATTTTGAAAATTTTTAAA
* * *
53940265 AGGATATTAAGCCATTTTGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGAAACCCAGCACCTTAGGGCACGTTTTCTC
53940330 GAATTTCCAAACGCAAAACATTGCCTTATTTT-AAAATTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATTTTTAAA
* * * * * *
53940374 AGGATATTTAGCTATTTGGTTGAACGAGAAGAGATCGAAACCCAACACATTAGGACACATTTTCT
1 AGGATATTTAGCCATTTGGTTGAACGAGAA-AAATCGAAACCCAGCACCTTAGGGCACGTTTTCT
53940439 CGAATTTCCAAA
65 CGAATTTCCAAA
53940451 TGGTAAATAT
Statistics
Matches: 262, Mismatches: 30, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
109 39 0.15
110 89 0.34
111 75 0.29
112 24 0.09
113 10 0.04
114 25 0.10
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (110 bp):
AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGAAACCCAGCACCTTAGGGCACGTTTTCTC
GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATTTTTAAA
Found at i:53941614 original size:82 final size:83
Alignment explanation
Indices: 53941519--53941770 Score: 380
Period size: 82 Copynumber: 3.0 Consensus size: 83
53941509 GTATCTTCGA
* *
53941519 CCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACGATCGAG
1 CCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGAG
53941584 AGAGGCAATGTTTGTGTT
66 AGAGGCAATGTTTGTGTT
*
53941602 -CTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGAG
1 CCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGAG
*
53941666 AGAGGCAAGGTTTGTGTCTT
66 AGAGGCAATGTTTGTG--TT
* * * *
53941686 CGACCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTATTATCTTCAACCAGCTCCACCACAACC
1 ---CCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACC
53941751 GAGAGAGGCAATGTTTGTGT
63 GAGAGAGGCAATGTTTGTGT
53941771 CTTCGATCTG
Statistics
Matches: 153, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
82 76 0.50
84 2 0.01
86 1 0.01
88 74 0.48
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (83 bp):
CCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGAG
AGAGGCAATGTTTGTGTT
Found at i:53941686 original size:43 final size:43
Alignment explanation
Indices: 53941637--53941774 Score: 120
Period size: 43 Copynumber: 3.2 Consensus size: 43
53941627 CAAGATCTGT
53941637 TGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTG
1 TGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTG
* * * * * * *
53941680 TGTCTTCGACCTGCTTCGCTGTCAATAC-AG-GAAGGCAAGATCTAT-
1 TGTCTTCAACCAGCTCCACT-ACAA-CCGAGAG-AGGCAAGGT-T-TG
* * *
53941725 TATCTTCAACCAGCTCCACCACAACCGAGAGAGGCAATGTTTG
1 TGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTG
53941768 TGTCTTC
1 TGTCTTC
53941775 GATCTGCTAC
Statistics
Matches: 69, Mismatches: 18, Indels: 16
0.67 0.17 0.16
Matches are distributed among these distances:
42 1 0.01
43 25 0.36
44 25 0.36
45 17 0.25
46 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (43 bp):
TGTCTTCAACCAGCTCCACTACAACCGAGAGAGGCAAGGTTTG
Found at i:53941740 original size:88 final size:88
Alignment explanation
Indices: 53941503--53941782 Score: 419
Period size: 88 Copynumber: 3.2 Consensus size: 88
53941493 TCAGGGGGTG
*
53941503 AGGTTTGTATCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
* *
53941568 CTCCACTACGATCGAGAGAGGCA
66 CTCCACTACAACCGAGAGAGGCA
* *
53941591 ATGTTTGTG--TT----CTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTGTTGTCTTCAACCAG
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
53941650 CTCCACTACAACCGAGAGAGGCA
66 CTCCACTACAACCGAGAGAGGCA
* * *
53941673 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAGGAAGGCAAGATCTATTATCTTCAACCAG
1 AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
*
53941738 CTCCACCACAACCGAGAGAGGCA
66 CTCCACTACAACCGAGAGAGGCA
* *
53941761 ATGTTTGTGTCTTCGATCTGCT
1 AGGTTTGTGTCTTCGACCTGCT
53941783 ACGCNNNNNN
Statistics
Matches: 173, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
82 76 0.44
84 2 0.01
86 2 0.01
88 93 0.54
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.28
Consensus pattern (88 bp):
AGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGTTGTCTTCAACCAG
CTCCACTACAACCGAGAGAGGCA
Found at i:53941760 original size:44 final size:43
Alignment explanation
Indices: 53941624--53941761 Score: 113
Period size: 44 Copynumber: 3.1 Consensus size: 43
53941614 CAATGTAGGA
*
53941624 AGGCAAGATCTGTTGTCTTCAACCAGCTCCACTACAACCGAGAG
1 AGGCAAGATCT-TTGTCTTCAACCAGCTCCACCACAACCGAGAG
* * * ** *
53941668 AGGCAAGGT-TTGTGTCTTCGACCTGCTTCGCTGTCA-ATACAG-GA-
1 AGGCAAGATCTT-TGTCTTCAACCAGC-TC-C-ACCACA-ACCGAGAG
*
53941712 AGGCAAGATCTATTATCTTCAACCAGCTCCACCACAACCGAGAG
1 AGGCAAGATCT-TTGTCTTCAACCAGCTCCACCACAACCGAGAG
53941756 AGGCAA
1 AGGCAA
53941762 TGTTTGTGTC
Statistics
Matches: 70, Mismatches: 14, Indels: 20
0.67 0.13 0.19
Matches are distributed among these distances:
42 6 0.09
43 17 0.24
44 26 0.37
45 16 0.23
46 5 0.07
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (43 bp):
AGGCAAGATCTTTGTCTTCAACCAGCTCCACCACAACCGAGAG
Found at i:53943038 original size:7 final size:7
Alignment explanation
Indices: 53943026--53943075 Score: 86
Period size: 7 Copynumber: 7.4 Consensus size: 7
53943016 TGGCCTCTCC
53943026 TTTTTCT
1 TTTTTCT
53943033 TTTTTCT
1 TTTTTCT
53943040 TTTTTCT
1 TTTTTCT
53943047 TTTTTC-
1 TTTTTCT
53943053 TTTTTCT
1 TTTTTCT
53943060 TTTTTCT
1 TTTTTCT
53943067 TTTTT-T
1 TTTTTCT
53943073 TTT
1 TTT
53943076 GAAATATTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 10 0.24
7 32 0.76
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:53943043 original size:13 final size:13
Alignment explanation
Indices: 53943025--53943075 Score: 86
Period size: 13 Copynumber: 3.9 Consensus size: 13
53943015 TTGGCCTCTC
53943025 CTTTTTCTTTTTT
1 CTTTTTCTTTTTT
53943038 CTTTTTTCTTTTTT
1 C-TTTTTCTTTTTT
53943052 CTTTTTCTTTTTT
1 CTTTTTCTTTTTT
53943065 CTTTTT-TTTTT
1 CTTTTTCTTTTT
53943076 GAAATATTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
12 5 0.14
13 19 0.51
14 13 0.35
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (13 bp):
CTTTTTCTTTTTT
Found at i:53943048 original size:20 final size:20
Alignment explanation
Indices: 53943026--53943075 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
53943016 TGGCCTCTCC
53943026 TTTTTCTTTTTTCTTTTTTCT
1 TTTTTC-TTTTTCTTTTTTCT
53943047 TTTTTCTTTTTCTTTTTTCT
1 TTTTTCTTTTTCTTTTTTCT
53943067 TTTTT-TTTT
1 TTTTTCTTTT
53943076 GAAATATTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 4 0.14
20 19 0.66
21 6 0.21
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (20 bp):
TTTTTCTTTTTCTTTTTTCT
Found at i:53946211 original size:110 final size:109
Alignment explanation
Indices: 53945996--53946425 Score: 551
Period size: 110 Copynumber: 3.9 Consensus size: 109
53945986 GAAATTCGAG
* * * * * *
53945996 AGGATATTTGGCTATTTGGTTAAACGAG--AAATCGAAACCCAGCACCTTAGGGTACG-TTCCTC
1 AGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGAAACCCAGCACCTTAGGGCACGTTTTCTC
* * **
53946058 AAATTTCCAAATGCAAAACATTGCCTTATTTTGAATTTTTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAA--AATTTTAAA
* * *
53946104 AGGATATTTAGCCATTTGATTGAATGAGAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGAAACCCAGCACCTTAGGGCACGTTTTCTC
53946169 GAATTTCCCAAACGCAAAACATTGCCTTATTTTGAAAATTTTAAA
66 GAATTT-CCAAACGCAAAACATTGCCTTATTTTGAAAATTTTAAA
* * *
53946214 AGGATATTAAGCCATTTGGTTGAATGAGAAAAATCGACACCCAGCACCTTAAGGCACGTTTTCTC
1 AGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGAAACCCAGCACCTTAGGGCACGTTTTCTC
*
53946279 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATTTTAAA
* * * * * *
53946323 AGGATATTTAGCTATTTGGTTGAACGAGAAGAGATCGAAACCCAACACATTAGGACACGTTTTCT
1 AGGATATTTAGCCATTTGGTTGAATGAGAA-AAATCGAAACCCAGCACCTTAGGGCACGTTTTCT
* * * * *
53946388 CGAATTTCCAAATGCTAAATATTGCCTCATTTAGAAAA
65 CGAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAA
53946426 AAATTCCTCT
Statistics
Matches: 284, Mismatches: 33, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
108 23 0.08
109 64 0.23
110 159 0.56
111 10 0.04
112 28 0.10
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.31
Consensus pattern (109 bp):
AGGATATTTAGCCATTTGGTTGAATGAGAAAAATCGAAACCCAGCACCTTAGGGCACGTTTTCTC
GAATTTCCAAACGCAAAACATTGCCTTATTTTGAAAATTTTAAA
Found at i:53946393 original size:220 final size:218
Alignment explanation
Indices: 53946024--53946425 Score: 572
Period size: 219 Copynumber: 1.8 Consensus size: 218
53946014 GTTAAACGAG
* * *
53946024 AAATCGAAACCCAGCACCTTAGGGTACGTTCCTCAAATTTCCAAATGCAAAACATTGCCTTATTT
1 AAATCGAAACCCAGCACCTTAAGGCACGTTCCTCAAATTTCCAAACGCAAAACATTGCCTTATTT
* * * * *
53946089 TGAATTTTTTTTAAAAGGATATTTAGCCATTTGATTGAATGAGAAAAATCGACACCCAGCACCTT
66 TGAA-TATTTTTAAAAGGATATTTAGCCATTTGATTGAACGAGAAAAATCGAAACCCAACACATT
* * * *
53946154 AGGGCATGTTTTCTCGAATTTCCCAAACGCAAAACATTGCCTTATTTTGAAAATTTTAAAAGGAT
130 AGGACACGTTTTCTCGAATTT-CCAAACGCAAAACATTGCCTCATTTAGAAAATTTTAAAAGGAT
53946219 ATTAAGCCATTTGGTTGAATGAGAA
194 ATTAAGCCATTTGGTTGAATGAGAA
* * *
53946244 AAATCGACACCCAGCACCTTAAGGCACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
1 AAATCGAAACCCAGCACCTTAAGGCACG-TTCCTCAAATTTCCAAACGCAAAACATTGCCTTATT
* * *
53946309 TTGAA-ATTTTTAAAAGGATATTTAGCTATTTGGTTGAACGAGAAGAGATCGAAACCCAACACAT
65 TTGAATATTTTTAAAAGGATATTTAGCCATTTGATTGAACGAGAA-AAATCGAAACCCAACACAT
* * *
53946373 TAGGACACGTTTTCTCGAATTTCCAAATGCTAAATATTGCCTCATTTAGAAAA
129 TAGGACACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTCATTTAGAAAA
53946426 AAATTCCTCT
Statistics
Matches: 159, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
219 61 0.38
220 60 0.38
221 38 0.24
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (218 bp):
AAATCGAAACCCAGCACCTTAAGGCACGTTCCTCAAATTTCCAAACGCAAAACATTGCCTTATTT
TGAATATTTTTAAAAGGATATTTAGCCATTTGATTGAACGAGAAAAATCGAAACCCAACACATTA
GGACACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTCATTTAGAAAATTTTAAAAGGATAT
TAAGCCATTTGGTTGAATGAGAA
Found at i:53946512 original size:18 final size:19
Alignment explanation
Indices: 53946489--53946524 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
53946479 TGATAATATG
*
53946489 AATG-AAAATAATATAAAA
1 AATGAAAAATAAGATAAAA
53946507 AATGAAAAATAAGATAAA
1 AATGAAAAATAAGATAAA
53946525 TCAATCATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (19 bp):
AATGAAAAATAAGATAAAA
Found at i:53946728 original size:28 final size:28
Alignment explanation
Indices: 53946696--53946756 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
53946686 ATATGTATGT
*
53946696 ATATACATA-AAATTATGAAAATATGAAA
1 ATATACATATAAATTAT-AAAATATAAAA
* * *
53946724 ATATATATATGAATTATAAGATATAAAA
1 ATATACATATAAATTATAAAATATAAAA
53946752 ATATA
1 ATATA
53946757 AGTACTTACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 22 0.79
29 6 0.21
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (28 bp):
ATATACATATAAATTATAAAATATAAAA
Found at i:53952582 original size:17 final size:17
Alignment explanation
Indices: 53952560--53952593 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
53952550 ATGATCCATA
53952560 GAAATTATATATATTGT
1 GAAATTATATATATTGT
53952577 GAAATTATATATATTGT
1 GAAATTATATATATTGT
53952594 CTGATTTTAG
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:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (17 bp):
GAAATTATATATATTGT
Found at i:53953268 original size:3 final size:3
Alignment explanation
Indices: 53953260--53953288 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
53953250 GTCAAGCATA
53953260 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
53953289 TTGTTACATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:53958988 original size:22 final size:20
Alignment explanation
Indices: 53958945--53958983 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
53958935 TAATTTAAAA
53958945 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
53958965 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
53958984 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:53959106 original size:20 final size:20
Alignment explanation
Indices: 53959081--53959120 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
53959071 AAATATTTTC
*
53959081 AGTAAATTATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
*
53959101 AGTAAATCATTTTTCAGAAA
1 AGTAAATCATTTTCCAGAAA
53959121 TCATTTTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (20 bp):
AGTAAATCATTTTCCAGAAA
Found at i:53970597 original size:81 final size:80
Alignment explanation
Indices: 53970499--53970657 Score: 264
Period size: 81 Copynumber: 2.0 Consensus size: 80
53970489 GTCAAAGGAT
* * *
53970499 TTGTTATGGCCAAGGAAATTTTGCTAGTCAAAATAGGCATATTGATGGTCAAAATTGGTGTGCTG
1 TTGTTATGGCCAAGGAAATTTTGCCAGTCAAAATAGGCATAGTCATGGTCAAAATTGGTGTGCTG
53970564 GCTTAAACAATGAAA
66 GCTTAAACAATGAAA
* *
53970579 TTGTTGATGGCCAAGGAAATTTTTCCAGTCAAAATAGGCATGGTCATGGTCAAAATTGGTGTGCT
1 TTGTT-ATGGCCAAGGAAATTTTGCCAGTCAAAATAGGCATAGTCATGGTCAAAATTGGTGTGCT
53970644 GGCTTAAACAATGA
65 GGCTTAAACAATGA
53970658 TCAATTGGCG
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
80 5 0.07
81 68 0.93
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.31
Consensus pattern (80 bp):
TTGTTATGGCCAAGGAAATTTTGCCAGTCAAAATAGGCATAGTCATGGTCAAAATTGGTGTGCTG
GCTTAAACAATGAAA
Found at i:53974590 original size:14 final size:14
Alignment explanation
Indices: 53974571--53974601 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
53974561 GGGTTAAAAC
53974571 TAAGCATTTTTGAA
1 TAAGCATTTTTGAA
53974585 TAAGCATTTTTGAA
1 TAAGCATTTTTGAA
53974599 TAA
1 TAA
53974602 TAAAAAGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (14 bp):
TAAGCATTTTTGAA
Found at i:53974819 original size:31 final size:29
Alignment explanation
Indices: 53974784--53974860 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
53974774 TTAACGACTC
*
53974784 AGTGACTAAAATATTACAACACGATAATATA
1 AGTGACTAAAATATAACAACAC-A-AATATA
* ***
53974815 AGTGACTAAAACATAACATTTCAAATATA
1 AGTGACTAAAATATAACAACACAAATATA
*
53974844 AGTGACTAAAATCTAAC
1 AGTGACTAAAATATAAC
53974861 CTGAGATAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
29 21 0.54
30 1 0.03
31 17 0.44
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (29 bp):
AGTGACTAAAATATAACAACACAAATATA
Found at i:53975302 original size:3 final size:3
Alignment explanation
Indices: 53975294--53975320 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
53975284 ATTGATCTTA
53975294 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
53975321 CCCATCCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:54003546 original size:4 final size:4
Alignment explanation
Indices: 54003537--54003595 Score: 52
Period size: 4 Copynumber: 14.5 Consensus size: 4
54003527 CAACCTAATT
*
54003537 TTTA TTTA TTTA TTTA -TTC TTTA CTTTA TTTA -TTA CTTTA TTTTA TTT-
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA -TTTA -TTTA TTTA
54003585 TATTA TTTA TT
1 T-TTA TTTA TT
54003596 ACTTATTTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
3 6 0.13
4 28 0.61
5 12 0.26
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:54003554 original size:12 final size:13
Alignment explanation
Indices: 54003537--54003603 Score: 58
Period size: 12 Copynumber: 5.5 Consensus size: 13
54003527 CAACCTAATT
54003537 TTTATTTATTTA-
1 TTTATTTATTTAC
*
54003549 TTTA-TTCTTTAC
1 TTTATTTATTTAC
54003561 TTTATTTA-TTAC
1 TTTATTTATTTAC
54003573 TTTATTTTATTT--
1 TTTA-TTTATTTAC
54003585 TATTATTTA-TTAC
1 T-TTATTTATTTAC
54003598 -TTATTT
1 TTTATTT
54003604 GGATATTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
11 14 0.30
12 21 0.46
13 9 0.20
14 2 0.04
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTTATTTAC
Found at i:54003566 original size:16 final size:16
Alignment explanation
Indices: 54003541--54003595 Score: 69
Period size: 17 Copynumber: 3.4 Consensus size: 16
54003531 CTAATTTTTA
54003541 TTTATTTATTTATT-C
1 TTTATTTATTTATTAC
54003556 TTTACTTTATTTATTAC
1 TTTA-TTTATTTATTAC
54003573 TTTATTTTATTTTATTA-
1 TTTA-TTTA-TTTATTAC
54003590 TTTATT
1 TTTATT
54003596 ACTTATTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
15 4 0.11
16 12 0.33
17 13 0.36
18 7 0.19
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTATTTATTTATTAC
Found at i:54014448 original size:18 final size:19
Alignment explanation
Indices: 54014425--54014460 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
54014415 GAATTATTTT
54014425 AGTTTACTTTT-TTTATTG
1 AGTTTACTTTTGTTTATTG
54014443 AGTTTACTTTTGTTTATT
1 AGTTTACTTTTGTTTATT
54014461 AATTTTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.17, C:0.06, G:0.11, T:0.67
Consensus pattern (19 bp):
AGTTTACTTTTGTTTATTG
Found at i:54014467 original size:19 final size:18
Alignment explanation
Indices: 54014425--54014467 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
54014415 GAATTATTTT
*
54014425 AGTTTACTTTTTTTATTG
1 AGTTTACTTTTTTTATTA
54014443 AGTTTACTTTTGTTTATTA
1 AGTTTACTTTT-TTTATTA
*
54014462 ATTTTA
1 AGTTTA
54014468 ATCAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.21, C:0.05, G:0.09, T:0.65
Consensus pattern (18 bp):
AGTTTACTTTTTTTATTA
Found at i:54016780 original size:4 final size:4
Alignment explanation
Indices: 54016773--54016801 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
54016763 TGAGATATTA
54016773 TATG TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG TATG T
54016802 TTTGAAGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:54019802 original size:6 final size:6
Alignment explanation
Indices: 54019791--54019823 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
54019781 CACGTTACCT
54019791 TTAGGA TTAGGA TTAGGA TTAGGA TTAGGA TTA
1 TTAGGA TTAGGA TTAGGA TTAGGA TTAGGA TTA
54019824 TATATTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.36
Consensus pattern (6 bp):
TTAGGA
Found at i:54024376 original size:21 final size:21
Alignment explanation
Indices: 54024350--54024392 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
54024340 TGATTTGATT
54024350 TTTTTTCCGAATCGAGTCGAG
1 TTTTTTCCGAATCGAGTCGAG
* *
54024371 TTTTTTCCGAATCTAGTTGAG
1 TTTTTTCCGAATCGAGTCGAG
54024392 T
1 T
54024393 GAAATGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (21 bp):
TTTTTTCCGAATCGAGTCGAG
Found at i:54024724 original size:9 final size:9
Alignment explanation
Indices: 54024710--54024739 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
54024700 AAAATATAAA
54024710 TTTTTTAAT
1 TTTTTTAAT
54024719 TTTTTTAAT
1 TTTTTTAAT
54024728 TTTTTTAAT
1 TTTTTTAAT
54024737 TTT
1 TTT
54024740 AAAATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:54027475 original size:41 final size:39
Alignment explanation
Indices: 54027412--54027584 Score: 150
Period size: 41 Copynumber: 4.2 Consensus size: 39
54027402 GAGGGCTTTC
* * *
54027412 GTGGCGTTTTTAAACAAACGCCGCTAATGTTATGGTTTTTA
1 GTGGCGTTTTT-TATAAGCGCCGCTAATGTTA-GGTTTTTA
* * *
54027453 GTGGCGTTTTTTCCTAAGCGCCGCTAATTTTAGGGCTTTTA
1 GTGGCGTTTTTT-ATAAGCGCCGCTAATGTTA-GGTTTTTA
* * *
54027494 GCGGCGTTTTTGATAATGCGCCGCTAAAGTTGAGGTTTTTA
1 GTGGCGTTTTTTATAA-GCGCCGCTAATGTT-AGGTTTTTA
* *
54027535 GTGGCGTTTGTTTATAAAGCGCCACTAATGTT-GGAGTTTTA
1 GTGGCGTTT-TTTAT-AAGCGCCGCTAATGTTAGG-TTTTTA
*
54027576 GCGGCGTTT
1 GTGGCGTTT
54027585 CGATGGAAAC
Statistics
Matches: 107, Mismatches: 19, Indels: 12
0.78 0.14 0.09
Matches are distributed among these distances:
40 5 0.05
41 83 0.78
42 17 0.16
43 2 0.02
ACGTcount: A:0.19, C:0.16, G:0.27, T:0.39
Consensus pattern (39 bp):
GTGGCGTTTTTTATAAGCGCCGCTAATGTTAGGTTTTTA
Found at i:54027519 original size:82 final size:82
Alignment explanation
Indices: 54027430--54027584 Score: 210
Period size: 82 Copynumber: 1.9 Consensus size: 82
54027420 TTTAAACAAA
* * * *
54027430 CGCCGCTAATGTT-ATGGTTTTTAGTGGCGTTT-TTTCCT-AAGCGCCGCTAATTTTAGG-GCTT
1 CGCCGCTAAAGTTGA-GGTTTTTAGTGGCGTTTGTTT-ATAAAGCGCCACTAATGTT-GGAG-TT
54027491 TTAGCGGCGTTTTTGATAATG
62 TTAGCGGCGTTTTTGATAATG
54027512 CGCCGCTAAAGTTGAGGTTTTTAGTGGCGTTTGTTTATAAAGCGCCACTAATGTTGGAGTTTTAG
1 CGCCGCTAAAGTTGAGGTTTTTAGTGGCGTTTGTTTATAAAGCGCCACTAATGTTGGAGTTTTAG
54027577 CGGCGTTT
66 CGGCGTTT
54027585 CGATGGAAAC
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
82 46 0.71
83 19 0.29
ACGTcount: A:0.17, C:0.16, G:0.27, T:0.39
Consensus pattern (82 bp):
CGCCGCTAAAGTTGAGGTTTTTAGTGGCGTTTGTTTATAAAGCGCCACTAATGTTGGAGTTTTAG
CGGCGTTTTTGATAATG
Found at i:54027598 original size:82 final size:81
Alignment explanation
Indices: 54027427--54027599 Score: 194
Period size: 82 Copynumber: 2.1 Consensus size: 81
54027417 GTTTTTAAAC
* * * *
54027427 AAACGCCGCTAATGTTATGGTTTTTAGTGGCGTTTTTTCCTAAGCGCCGCTAATTTTAGGGCTTT
1 AAACGCCGCTAAAGTTATGGTTTTTAGTGGCGTTTTTTCATAAGCGCCACTAATGTTAGGGCTTT
*
54027492 TAGCGGCGTTTTTGAT
66 TAGCGGCGTTTTCGAT
*
54027508 AATGCGCCGCTAAAGTTGA-GGTTTTTAGTGGCGTTTGTTT-ATAAAGCGCCACTAATGTT-GGA
1 AA-ACGCCGCTAAAGTT-ATGGTTTTTAGTGGCGTTT-TTTCAT-AAGCGCCACTAATGTTAGG-
54027570 G-TTTTAGCGGCG-TTTCGAT
61 GCTTTTAGCGGCGTTTTCGAT
54027589 GGAAACGCCGC
1 --AAACGCCGC
54027600 AAAATACATT
Statistics
Matches: 78, Mismatches: 7, Indels: 13
0.80 0.07 0.13
Matches are distributed among these distances:
81 8 0.10
82 49 0.63
83 21 0.27
ACGTcount: A:0.20, C:0.17, G:0.27, T:0.36
Consensus pattern (81 bp):
AAACGCCGCTAAAGTTATGGTTTTTAGTGGCGTTTTTTCATAAGCGCCACTAATGTTAGGGCTTT
TAGCGGCGTTTTCGAT
Found at i:54028206 original size:21 final size:20
Alignment explanation
Indices: 54028193--54028267 Score: 69
Period size: 23 Copynumber: 3.5 Consensus size: 20
54028183 GGGATTAAGG
54028193 TTTAGGGGTATGGGTTAGGAA
1 TTTAGGGGTATGGGTTAGG-A
*
54028214 TTTAGGGGTTAGGGGTTAGTGA
1 TTTAGGGG-TATGGGTTAG-GA
* *
54028236 TTTGGGGGGTTAGGGGTTAGGGA
1 TTT-AGGGG-TATGGGTTA-GGA
54028259 TTTAGGGGT
1 TTTAGGGGT
54028268 TAGGGTGTCA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
21 9 0.19
22 17 0.36
23 20 0.43
24 1 0.02
ACGTcount: A:0.17, C:0.00, G:0.48, T:0.35
Consensus pattern (20 bp):
TTTAGGGGTATGGGTTAGGA
Found at i:54028227 original size:7 final size:7
Alignment explanation
Indices: 54028215--54028272 Score: 53
Period size: 7 Copynumber: 7.9 Consensus size: 7
54028205 GGTTAGGAAT
54028215 TTAGGGG
1 TTAGGGG
54028222 TTAGGGG
1 TTAGGGG
**
54028229 TTAGTGAT
1 TTAG-GGG
*
54028237 TTGGGGGG
1 TT-AGGGG
54028245 TTAGGGG
1 TTAGGGG
*
54028252 TTAGGGAT
1 TTAGGG-G
54028260 TTAGGGG
1 TTAGGGG
54028267 TTAGGG
1 TTAGGG
54028273 TGTCAAGGGT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
7 27 0.68
8 12 0.30
9 1 0.03
ACGTcount: A:0.16, C:0.00, G:0.52, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:54028248 original size:23 final size:22
Alignment explanation
Indices: 54028193--54028272 Score: 108
Period size: 22 Copynumber: 3.6 Consensus size: 22
54028183 GGGATTAAGG
* *
54028193 TTTAGGGG-TATGGGTTAGGAA
1 TTTAGGGGTTAGGGGTTAGGGA
*
54028214 TTTAGGGGTTAGGGGTTAGTGA
1 TTTAGGGGTTAGGGGTTAGGGA
*
54028236 TTTGGGGGGTTAGGGGTTAGGGA
1 TTT-AGGGGTTAGGGGTTAGGGA
54028259 TTTAGGGGTTAGGG
1 TTTAGGGGTTAGGG
54028273 TGTCAAGGGT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.16
22 23 0.45
23 20 0.39
ACGTcount: A:0.17, C:0.00, G:0.49, T:0.34
Consensus pattern (22 bp):
TTTAGGGGTTAGGGGTTAGGGA
Found at i:54028265 original size:15 final size:15
Alignment explanation
Indices: 54028204--54028272 Score: 59
Period size: 15 Copynumber: 4.6 Consensus size: 15
54028194 TTAGGGGTAT
* *
54028204 GGGTTAGGAATTTAG
1 GGGTTAGGGAGTTAG
54028219 GGGTTAGGG-GTTAG
1 GGGTTAGGGAGTTAG
** * *
54028233 TGATTTGGGGGGTTAG
1 -GGGTTAGGGAGTTAG
*
54028249 GGGTTAGGGATTTAG
1 GGGTTAGGGAGTTAG
54028264 GGGTTAGGG
1 GGGTTAGGG
54028273 TGTCAAGGGT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
14 4 0.10
15 33 0.79
16 5 0.12
ACGTcount: A:0.17, C:0.00, G:0.51, T:0.32
Consensus pattern (15 bp):
GGGTTAGGGAGTTAG
Found at i:54029807 original size:24 final size:22
Alignment explanation
Indices: 54029778--54029823 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
54029768 ATCAGTTTTC
54029778 TCCCCAAAAATTCCCCCCAAATTT
1 TCCCCAAAAA-T-CCCCCAAATTT
54029802 TCCCCAAAAATCCCCCAAATTT
1 TCCCCAAAAATCCCCCAAATTT
54029824 AGAACCCTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 11 0.50
23 1 0.05
24 10 0.45
ACGTcount: A:0.35, C:0.41, G:0.00, T:0.24
Consensus pattern (22 bp):
TCCCCAAAAATCCCCCAAATTT
Found at i:54030846 original size:31 final size:32
Alignment explanation
Indices: 54030811--54030870 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
54030801 TTTTAGCTAG
* *
54030811 ATTTGGTCATTAACCTTTT-AAAAAGAGTCGA
1 ATTTGATCATCAACCTTTTAAAAAAGAGTCGA
*
54030842 ATTTGATTATCAACCTTTTAAAAAAGAGT
1 ATTTGATCATCAACCTTTTAAAAAAGAGT
54030871 TGAAGTTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 16 0.64
32 9 0.36
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (32 bp):
ATTTGATCATCAACCTTTTAAAAAAGAGTCGA
Found at i:54031631 original size:56 final size:56
Alignment explanation
Indices: 54031566--54031678 Score: 217
Period size: 56 Copynumber: 2.0 Consensus size: 56
54031556 GTCCTTAGTC
*
54031566 TAATCGAAAATGAGGAAATCACTTGAAAGACTAATATGTCATCTATCAAGTCCAAT
1 TAATCGAAAATGAGGAAATCAATTGAAAGACTAATATGTCATCTATCAAGTCCAAT
54031622 TAATCGAAAATGAGGAAATCAATTGAAAGACTAATATGTCATCTATCAAGTCCAAT
1 TAATCGAAAATGAGGAAATCAATTGAAAGACTAATATGTCATCTATCAAGTCCAAT
54031678 T
1 T
54031679 GGAGAGATGT
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.27
Consensus pattern (56 bp):
TAATCGAAAATGAGGAAATCAATTGAAAGACTAATATGTCATCTATCAAGTCCAAT
Found at i:54034622 original size:10 final size:11
Alignment explanation
Indices: 54034589--54034622 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
54034579 CGACCCGCCC
54034589 ATATTAATTTTT
1 ATATTAA-TTTT
54034601 ATATTAATTTT
1 ATATTAATTTT
54034612 ATATT-ATTTT
1 ATATTAATTTT
54034622 A
1 A
54034623 AAATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 6 0.27
11 9 0.41
12 7 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
ATATTAATTTT
Found at i:54034771 original size:30 final size:30
Alignment explanation
Indices: 54034735--54034797 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
54034725 CTTAAACAAG
54034735 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTTTAAAATAATAACAAAATTAA
54034765 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGTCTTTAAAATAATAACAAAATTAA
54034795 CAA
1 CAA
54034798 TAAAATAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.57, C:0.11, G:0.03, T:0.29
Consensus pattern (30 bp):
CAAATGTCTTTAAAATAATAACAAAATTAA
Found at i:54041660 original size:26 final size:24
Alignment explanation
Indices: 54041612--54041657 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
54041602 AATAAATTAT
*
54041612 ATATATAAATAGATTTAAAAGAAG
1 ATATATAAACAGATTTAAAAGAAG
*
54041636 ATATATAAACATATTTAAAAGA
1 ATATATAAACAGATTTAAAAGA
54041658 GAATTTAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (24 bp):
ATATATAAACAGATTTAAAAGAAG
Found at i:54041951 original size:28 final size:25
Alignment explanation
Indices: 54041911--54041972 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
54041901 AATCATAGAC
* *
54041911 GATAAATTTTAAA-ATAATAATACAT
1 GATAAA-TTTAAATAAAAAAATACAT
*
54041936 GATGAATTTAAATAAAAAAATACAT
1 GATAAATTTAAATAAAAAAATACAT
54041961 GATAAATTTAAA
1 GATAAATTTAAA
54041973 ATATGTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 6 0.19
25 26 0.81
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.32
Consensus pattern (25 bp):
GATAAATTTAAATAAAAAAATACAT
Found at i:54041987 original size:22 final size:23
Alignment explanation
Indices: 54041959--54042041 Score: 98
Period size: 22 Copynumber: 3.7 Consensus size: 23
54041949 AAAAAAATAC
*
54041959 ATGATAAATTTAAAAT-ATGTTT
1 ATGATAAATTTAAAATAATATTT
*
54041981 ATGATAAATTTAAAATAATAATAT
1 ATGATAAATTTAAAATAAT-ATTT
* *
54042005 ATTATAAA-TTAAAATAATATTG
1 ATGATAAATTTAAAATAATATTT
*
54042027 ATGATAATTTTAAAA
1 ATGATAAATTTAAAA
54042042 ATATATTAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
22 24 0.47
23 18 0.35
24 9 0.18
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (23 bp):
ATGATAAATTTAAAATAATATTT
Found at i:54042032 original size:46 final size:47
Alignment explanation
Indices: 54041911--54042042 Score: 133
Period size: 46 Copynumber: 2.8 Consensus size: 47
54041901 AATCATAGAC
* *
54041911 GATAAATTTTAAAATAATAATACATGATGAATTTAAATAAAAAAATACAT
1 GATAAA-TTTAAAATAAT-ATTCATGATAAATTTAAA-AAAAAAATACAT
* * * * *
54041961 GATAAATTTAAAAT-ATGTTTATGATAAATTTAAAATAATAATATAT
1 GATAAATTTAAAATAATATTCATGATAAATTTAAAAAAAAAATACAT
* * *
54042007 TATAAA-TTAAAATAATATTGATGATAATTTTAAAAA
1 GATAAATTTAAAATAATATTCATGATAAATTTAAAAA
54042043 TATATTAAGC
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
45 7 0.10
46 32 0.46
47 14 0.20
48 2 0.03
49 8 0.12
50 6 0.09
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (47 bp):
GATAAATTTAAAATAATATTCATGATAAATTTAAAAAAAAAATACAT
Found at i:54051019 original size:54 final size:54
Alignment explanation
Indices: 54050924--54051026 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 54
54050914 ACTCTCTGAA
* *
54050924 ATATTTTCAAACCATGGGATGGATGCCTCTAATCCATCAGGAACCTCAATGGTC
1 ATATTTTCAAACCATGGGATGGATGCATCTAATCCAGCAGGAACCTCAATGGTC
* ** *
54050978 ATATTTTCAAACCATGGGATGGATGTATCTTCTCCAGCAGGAAGCTCAA
1 ATATTTTCAAACCATGGGATGGATGCATCTAATCCAGCAGGAACCTCAA
54051027 CACCATTAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.28
Consensus pattern (54 bp):
ATATTTTCAAACCATGGGATGGATGCATCTAATCCAGCAGGAACCTCAATGGTC
Found at i:54055506 original size:52 final size:52
Alignment explanation
Indices: 54055449--54055555 Score: 196
Period size: 52 Copynumber: 2.1 Consensus size: 52
54055439 TATAATGTTG
*
54055449 CATTTTCAATTGGTATCAAAGCCATACACATAAAGCATTTTATGAGATCTTA
1 CATTTTCAATTGGTATCAAAGCCATACACATAAAGCATTTTATGAGATCTCA
*
54055501 CATTTTCAATTGGTATCAAAGCCATACACATAAAGTATTTTATGAGATCTCA
1 CATTTTCAATTGGTATCAAAGCCATACACATAAAGCATTTTATGAGATCTCA
54055553 CAT
1 CAT
54055556 CTGATAGCCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (52 bp):
CATTTTCAATTGGTATCAAAGCCATACACATAAAGCATTTTATGAGATCTCA
Found at i:54056389 original size:108 final size:108
Alignment explanation
Indices: 54056200--54056415 Score: 405
Period size: 108 Copynumber: 2.0 Consensus size: 108
54056190 GGACTGGACC
*
54056200 CAATAGTAGAATTTATATTGGATTTGTTTATGGATTTATTCACTTGTAGCGCTCATGGTGTGACT
1 CAATAGTAGAATTTATATTGGATTTGTTTATGGATTTATTCACTTGTAACGCTCATGGTGTGACT
54056265 TACCTCGATGCTGAGTAAGTAACTGACCATGTGTACCTAATAG
66 TACCTCGATGCTGAGTAAGTAACTGACCATGTGTACCTAATAG
*
54056308 CAATAGTAGAATTTATATTGGGTTTGTTTATGGATTTATTCACTTGTAACGCTCATGGTGTGACT
1 CAATAGTAGAATTTATATTGGATTTGTTTATGGATTTATTCACTTGTAACGCTCATGGTGTGACT
*
54056373 TACCTCGATTCTGAGTAAGTAACTGACCATGTGTACCTAATAG
66 TACCTCGATGCTGAGTAAGTAACTGACCATGTGTACCTAATAG
54056416 GGGTGAGCAA
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 105 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.38
Consensus pattern (108 bp):
CAATAGTAGAATTTATATTGGATTTGTTTATGGATTTATTCACTTGTAACGCTCATGGTGTGACT
TACCTCGATGCTGAGTAAGTAACTGACCATGTGTACCTAATAG
Done.