Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 11 of 91
Found at i:3189009 original size:47 final size:46
Alignment explanation
Indices: 3188940--3189340 Score: 368
Period size: 47 Copynumber: 8.6 Consensus size: 46
3188930 GTGACACGAT
* *
3188940 TGTGACATGGCAAGGTTTAGAGTTTGTGACACTCCATGGAGGGAATC
1 TGTGACATAGC-AGGTTTAGAGTTTGTGACACGCCATGGAGGGAATC
3188987 TGTGACATAGCAGTGTTTAGAGTTTGTGACACGCCATGGAGGGAATC
1 TGTGACATAGCAG-GTTTAGAGTTTGTGACACGCCATGGAGGGAATC
* ** * *
3189034 TATGACACGGCAGGGTTCAGAGTTTGTGACATGCCATGGAGGGAATC
1 TGTGACATAGCA-GGTTTAGAGTTTGTGACACGCCATGGAGGGAATC
* * * * *
3189081 TGTGACAT-GCCAGCATTCAGAGTTTGTGACACGGCATGGAAGGAATT
1 TGTGACATAG-CAG-GTTTAGAGTTTGTGACACGCCATGGAGGGAATC
* * * * *
3189128 TATTACAAAACAGGATTTAGAGTTTATGACACGCCATGGAGGGAATC
1 TGTGACATAGCAGG-TTTAGAGTTTGTGACACGCCATGGAGGGAATC
* *
3189175 TGTGACATGGCAGTGTTTAGAG-TTGTGACACGCTATGGAGGGAATC
1 TGTGACATAGCAG-GTTTAGAGTTTGTGACACGCCATGGAGGGAATC
*
3189221 TGTGACACGTCAGCA--TTTAGAGTTTGTGACACGCCATGGAGGGAATT
1 TGTGACA--T-AGCAGGTTTAGAGTTTGTGACACGCCATGGAGGGAATC
* * * * * * *
3189268 TGTAACA-CGACAAGGTTCAGAGTTTGTCAGACTCCAT--AGAG-ATC
1 TGTGACATAG-C-AGGTTTAGAGTTTGTGACACGCCATGGAGGGAATC
* *
3189312 TGTGACATAGCAGGGTTTATAGTGTGTGA
1 TGTGACATAGCA-GGTTTAGAGTTTGTGA
3189341 TACAGTATGG
Statistics
Matches: 289, Mismatches: 48, Indels: 37
0.77 0.13 0.10
Matches are distributed among these distances:
43 2 0.01
44 22 0.08
45 5 0.02
46 40 0.14
47 214 0.74
48 3 0.01
49 3 0.01
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (46 bp):
TGTGACATAGCAGGTTTAGAGTTTGTGACACGCCATGGAGGGAATC
Found at i:3189103 original size:94 final size:93
Alignment explanation
Indices: 3188942--3189266 Score: 420
Period size: 94 Copynumber: 3.5 Consensus size: 93
3188932 GACACGATTG
* *
3188942 TGACATGGCAAGG-TTTAGAGTTTGTGACACTCCATGGAGGGAATCTGTGACATAGCAGTGTTTA
1 TGACACGGC-AGGATTTAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACAT-GCAGTGTTTA
3189006 GAGTTTGTGACACGCCATGGAGGGAATCTA
64 GAGTTTGTGACACGCCATGGAGGGAATCTA
* * * ** *
3189036 TGACACGGCAGGGTTCAGAGTTTGTGACATGCCATGGAGGGAATCTGTGACATGCCAGCATTCAG
1 TGACACGGCAGGATTTAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACATG-CAGTGTTTAG
* * *
3189101 AGTTTGTGACACGGCATGGAAGGAATTTA
65 AGTTTGTGACACGCCATGGAGGGAATCTA
* *** *
3189130 TTACAAAACAGGATTTAGAGTTTATGACACGCCATGGAGGGAATCTGTGACATGGCAGTGTTTAG
1 TGACACGGCAGGATTTAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACAT-GCAGTGTTTAG
* *
3189195 AG-TTGTGACACGCTATGGAGGGAATCTG
65 AGTTTGTGACACGCCATGGAGGGAATCTA
* *
3189223 TGACACGTCAGCATTTAGAGTTTGTGACACGCCATGGAGGGAAT
1 TGACACGGCAGGATTTAGAGTTTGTGACACGCCATGGAGGGAAT
3189267 TTGTAACACG
Statistics
Matches: 196, Mismatches: 32, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
93 63 0.32
94 132 0.67
95 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (93 bp):
TGACACGGCAGGATTTAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACATGCAGTGTTTAGA
GTTTGTGACACGCCATGGAGGGAATCTA
Found at i:3189197 original size:141 final size:140
Alignment explanation
Indices: 3188958--3189268 Score: 435
Period size: 141 Copynumber: 2.2 Consensus size: 140
3188948 GGCAAGGTTT
* * * * * *
3188958 AGAGTTTGTGACACTCCATGGAGGGAATCTGTGACATAGCAGTGTTTAGAGTTTGTGACACGCCA
1 AGAGTTTGTGACACGCCATGGAGGGAATTTATGACAAAACAGTGTTTAGAGTTTATGACACGCCA
*
3189023 TGGAGGGAATCTATGACACGGCAGGGTTCAGAGTTTGTGACATGCCATGGAGGGAATCTGTGACA
66 TGGAGGGAATCTATGACACGGCAGGGTTCAGAG-TTGTGACACGCCATGGAGGGAATCTGTGACA
*
3189088 TGCCAGCATTC
130 CGCCAGCATTC
* * *
3189099 AGAGTTTGTGACACGGCATGGAAGGAATTTATTACAAAACAG-GATTTAGAGTTTATGACACGCC
1 AGAGTTTGTGACACGCCATGGAGGGAATTTATGACAAAACAGTG-TTTAGAGTTTATGACACGCC
* * * * *
3189163 ATGGAGGGAATCTGTGACATGGCAGTGTTTAGAGTTGTGACACGCTATGGAGGGAATCTGTGACA
65 ATGGAGGGAATCTATGACACGGCAGGGTTCAGAGTTGTGACACGCCATGGAGGGAATCTGTGACA
* *
3189228 CGTCAGCATTT
130 CGCCAGCATTC
3189239 AGAGTTTGTGACACGCCATGGAGGGAATTT
1 AGAGTTTGTGACACGCCATGGAGGGAATTT
3189269 GTAACACGAC
Statistics
Matches: 149, Mismatches: 20, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
140 66 0.44
141 83 0.56
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (140 bp):
AGAGTTTGTGACACGCCATGGAGGGAATTTATGACAAAACAGTGTTTAGAGTTTATGACACGCCA
TGGAGGGAATCTATGACACGGCAGGGTTCAGAGTTGTGACACGCCATGGAGGGAATCTGTGACAC
GCCAGCATTC
Found at i:3190023 original size:31 final size:31
Alignment explanation
Indices: 3189985--3190094 Score: 114
Period size: 31 Copynumber: 3.5 Consensus size: 31
3189975 GTGTTAGTGT
*
3189985 TGGCGTGTAATAACATTTGAC-TTGATACGCA
1 TGGCGTGTAACAACATTTGACGTT-ATACGCA
* * *
3190016 TGGCGTGTTACAACATTTTACGTTATATGCA
1 TGGCGTGTAACAACATTTGACGTTATACGCA
* * * *
3190047 TGGCGTATTACAACATTTTACGTTATATGCA
1 TGGCGTGTAACAACATTTGACGTTATACGCA
* *
3190078 TGGCATGTTACAACATT
1 TGGCGTGTAACAACATT
3190095 ATGGGTTAAC
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
31 69 0.97
32 2 0.03
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (31 bp):
TGGCGTGTAACAACATTTGACGTTATACGCA
Found at i:3191769 original size:145 final size:145
Alignment explanation
Indices: 3191518--3191789 Score: 359
Period size: 145 Copynumber: 1.9 Consensus size: 145
3191508 ACGGTTTGTG
*
3191518 TTCAACAATTCCATATGTGATTATCGAATAACATATCTGTGTTTGCAGTTGCACCATGTGACGAT
1 TTCAACAATTCCATATGTGATTATCGAATAACATATCTGTGTTTGCAGTTGCACCATGCGACGAT
** * * *
3191583 AACTCCACAACCATGGAAAGGCCCTTTTCAGACTCACAGTGCTAACAACCCGTCGGTAAGATCGA
66 AACTCCACAACCATCCAAAGGCCCCTTTCAGACACACAGTGCTAACAACCCGTCGATAAGATCGA
3191648 TTATAATAGTTTCTA
131 TTATAATAGTTTCTA
* * * * *
3191663 TTCAACAATTCCATATGTGATTATCGGATAGCATATTTGTGTTTGTAGTTGGACCATGCGACGAT
1 TTCAACAATTCCATATGTGATTATCGAATAACATATCTGTGTTTGCAGTTGCACCATGCGACGAT
* * * * * *
3191728 AGCTCCTCAACTA-CCAAGAGGTCCCCTTT-AGACACATAGTGCTAACGACCCGTTGATAAGAT
66 AACTCCACAACCATCCAA-AGG-CCCCTTTCAGACACACAGTGCTAACAACCCGTCGATAAGAT
3191790 TAGTTTTAAT
Statistics
Matches: 108, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
144 2 0.02
145 100 0.93
146 6 0.06
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (145 bp):
TTCAACAATTCCATATGTGATTATCGAATAACATATCTGTGTTTGCAGTTGCACCATGCGACGAT
AACTCCACAACCATCCAAAGGCCCCTTTCAGACACACAGTGCTAACAACCCGTCGATAAGATCGA
TTATAATAGTTTCTA
Found at i:3191805 original size:145 final size:144
Alignment explanation
Indices: 3191518--3191842 Score: 354
Period size: 145 Copynumber: 2.2 Consensus size: 144
3191508 ACGGTTTGTG
*
3191518 TTCAACAATTCCATATGTGATTATCGAATAACATATCTGTGTTTGCAGTTGCACCATGTGACGAT
1 TTCAACAATTCCATATGTGATTATCGAATAACATATCTGTGTTTGCAGTTGCACCATGCGACGAT
** * * * *
3191583 AACTCCACAACCATGGAAAGGCCCTTTTCAGACTCACAGTGCTAACAACCCGTCGGTAAGATCGA
66 AACTCCACAACCATCCAAAGGCCCCTTTCAGACACACAGTGCTAACAACCCGTCGATAAGATAGA
3191648 TTATAATAGTTTCT
131 TTATAATAGTTTCT
* * * * *
3191662 ATTCAACAATTCCATATGTGATTATCGGATAGCATATTTGTGTTTGTAGTTGGACCATGCGACGA
1 -TTCAACAATTCCATATGTGATTATCGAATAACATATCTGTGTTTGCAGTTGCACCATGCGACGA
* * * * * *
3191727 TAGCTCCTCAACTA-CCAAGAGGTCCCCTTT-AGACACATAGTGCTAACGACCCGTTGATAAGAT
65 TAACTCCACAACCATCCAA-AGG-CCCCTTTCAGACACACAGTGCTAACAACCCGTCGATAAGA-
* *
3191790 TAG-TTTTAATGGTTTCT
127 TAGATTATAATAGTTTCT
* *
3191807 TCTCAACATTTTCACATATGT--TTATCGAGTAACATA
1 T-TCAACA-ATTC-CATATGTGATTATCGAATAACATA
3191843 CTAATTTCTG
Statistics
Matches: 150, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
144 3 0.02
145 129 0.86
146 11 0.07
147 7 0.05
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (144 bp):
TTCAACAATTCCATATGTGATTATCGAATAACATATCTGTGTTTGCAGTTGCACCATGCGACGAT
AACTCCACAACCATCCAAAGGCCCCTTTCAGACACACAGTGCTAACAACCCGTCGATAAGATAGA
TTATAATAGTTTCT
Found at i:3194089 original size:62 final size:62
Alignment explanation
Indices: 3193974--3194091 Score: 164
Period size: 62 Copynumber: 1.9 Consensus size: 62
3193964 GTCACCCTTG
* ** * * *
3193974 AATACTGCAACAAGTCAACGTGTCACGCCATGTATCTGCTTTCACGCAGCGTGTCACCCCAC
1 AATACTACAACAAGTCAACGTGTCACGCCATAAATCGGCTTCCACGCAACGTGTCACCCCAC
* *
3194036 AATACTACAACAAGTCAGCGTGTCACGCCATAAATCGGCTTCCACTCAACGTGTCA
1 AATACTACAACAAGTCAACGTGTCACGCCATAAATCGGCTTCCACGCAACGTGTCA
3194092 ACACAATTGA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 48 1.00
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (62 bp):
AATACTACAACAAGTCAACGTGTCACGCCATAAATCGGCTTCCACGCAACGTGTCACCCCAC
Found at i:3194135 original size:87 final size:86
Alignment explanation
Indices: 3194021--3194357 Score: 433
Period size: 87 Copynumber: 3.9 Consensus size: 86
3194011 GCTTTCACGC
*
3194021 AGCGTGTCACCCCACAATACTACAACAAGTCAGCGTGTCACGCCATAAATCGGCTTCCACTCAAC
1 AGCGTGTCACCCCACAATACTGCAACAAGTCAGCGTGTCACGCCATAAATCGGCTTCCACTCAAC
* *
3194086 GTGTCAACACAATTGATATTG
66 ATGTCAACACAATTGGTATTG
* * * * *
3194107 AAGCGTGTCACCCCATAAAATTGCAACAAGTCACCGTGTCACACCATAAATCGGCTTCCACTCAA
1 -AGCGTGTCACCCCACAATACTGCAACAAGTCAGCGTGTCACGCCATAAATCGGCTTCCACTCAA
* *
3194172 CGTGTCAACACAGTTGGTATTGG
65 CATGTCAACACAATTGGTATT-G
* * * *
3194195 GGCGTGTCACCCCACAATACTGCAACAAGTCCGCATGTCACGCCATAAATCTGCTTCCACTCAAC
1 AGCGTGTCACCCCACAATACTGCAACAAGTCAGCGTGTCACGCCATAAATCGGCTTCCACTCAAC
* * **
3194260 ACGTCAACATAATTGGGGTGTG
66 ATGTCAACACAATTGGTAT-TG
* * * *
3194282 -GCGTGTCACCCCACAATATTGCAACCAGTCAGCGTGTCACGCTATAAATCTGCTTCCACTCAAC
1 AGCGTGTCACCCCACAATACTGCAACAAGTCAGCGTGTCACGCCATAAATCGGCTTCCACTCAAC
*
3194346 ATGTCACCACAA
66 ATGTCAACACAA
3194358 AATGTCATTA
Statistics
Matches: 217, Mismatches: 31, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
86 68 0.31
87 147 0.68
88 2 0.01
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (86 bp):
AGCGTGTCACCCCACAATACTGCAACAAGTCAGCGTGTCACGCCATAAATCGGCTTCCACTCAAC
ATGTCAACACAATTGGTATTG
Found at i:3197905 original size:31 final size:31
Alignment explanation
Indices: 3197857--3198027 Score: 220
Period size: 31 Copynumber: 5.5 Consensus size: 31
3197847 ATTTTCAGTC
* * *
3197857 ATGTTGTTACACACCATGCATATAACATAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
3197888 ATGTTGTAACACGCCATGCATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
* *
3197919 ATCTTGTAACACTCCATGCATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
* *
3197950 ATGTTGTAACACGCCATGCGTATCAA-GTCAA
1 ATGTTGTAACACGCCATGCATAT-AACGTAAA
* *
3197981 ATGTTGTTACACGCCATGCATATCAA-GTCAA
1 ATGTTGTAACACGCCATGCATAT-AACGTAAA
*
3198012 ATGTTGTTACACGCCA
1 ATGTTGTAACACGCCA
3198028 ACGCTGACAC
Statistics
Matches: 128, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
31 126 0.98
32 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.28
Consensus pattern (31 bp):
ATGTTGTAACACGCCATGCATATAACGTAAA
Found at i:3200588 original size:2 final size:2
Alignment explanation
Indices: 3200581--3200605 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3200571 CGTTCCTACC
3200581 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 T
3200606 GCACCTCCAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3201945 original size:2 final size:2
Alignment explanation
Indices: 3201938--3201988 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
3201928 AGACACCTAA
*
3201938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT -T A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3201978 AT AT AT AT AT A
1 AT AT AT AT AT A
3201989 NCCTCGTCGG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3202918 original size:7 final size:7
Alignment explanation
Indices: 3202906--3202991 Score: 57
Period size: 7 Copynumber: 11.3 Consensus size: 7
3202896 AAAAAAATTT
3202906 TAAAAAA
1 TAAAAAA
3202913 TAAAAAA
1 TAAAAAA
*
3202920 TAAAAAG
1 TAAAAAA
3202927 TAAAAAAA
1 T-AAAAAA
3202935 TATAAAAA
1 TA-AAAAA
*
3202943 -AATGATAA
1 TAA--AAAA
3202951 TAATAAAA
1 TAA-AAAA
*
3202959 TGAAAAA
1 TAAAAAA
3202966 TAAATAAA
1 TAAA-AAA
3202974 TAATAATAA
1 TAA-AA-AA
*
3202983 TAAATAA
1 TAAAAAA
3202990 TA
1 TA
3202992 TAATTGGAAC
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
6 1 0.02
7 27 0.43
8 27 0.43
9 8 0.13
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.22
Consensus pattern (7 bp):
TAAAAAA
Found at i:3202943 original size:32 final size:32
Alignment explanation
Indices: 3202895--3202989 Score: 86
Period size: 32 Copynumber: 2.9 Consensus size: 32
3202885 TTATATTTTT
* *
3202895 TAAAAAAATTTTAAAAAATAAAAAATAAAAAG
1 TAAAAAAATATAAAAAAATAAAAAATAAAAAG
* *
3202927 TAAAAAAATATAAAAAAATGATAATAATAAAATG
1 TAAAAAAATATAAAAAAAT-A-AAAAATAAAAAG
*
3202961 -AAAAATAA-ATAAATAATAATAATAAATAA
1 TAAAAA-AATATAAA-AA-AATAAAAAATAA
3202990 TATAATTGGA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
32 17 0.33
33 17 0.33
34 15 0.29
35 3 0.06
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (32 bp):
TAAAAAAATATAAAAAAATAAAAAATAAAAAG
Found at i:3202958 original size:26 final size:27
Alignment explanation
Indices: 3202907--3202994 Score: 78
Period size: 29 Copynumber: 3.4 Consensus size: 27
3202897 AAAAAATTTT
*
3202907 AAAAA-AT-AAAAAATAA-AA-AGTAA
1 AAAAATATAAAAAAATAATAATAATAA
*
3202930 AAAAATATAAAAAAATGATAATAATAA
1 AAAAATATAAAAAAATAATAATAATAA
* *
3202957 AATGAAAAATAAATAAATAATAATAAT-A
1 AA--AAATATAAAAAAATAATAATAATAA
*
3202985 AATAATATAA
1 AAAAATATAA
3202995 TTGGAACAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
23 5 0.10
24 2 0.04
25 8 0.15
26 8 0.15
27 6 0.12
28 3 0.06
29 20 0.38
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (27 bp):
AAAAATATAAAAAAATAATAATAATAA
Found at i:3206169 original size:18 final size:18
Alignment explanation
Indices: 3206144--3206188 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
3206134 TCTTTTCATT
*
3206144 TTCATTTTTCT-TTATTA
1 TTCATTTTTTTATTATTA
* *
3206161 TTTATTTTTTTATTTTTA
1 TTCATTTTTTTATTATTA
3206179 TTCATTTTTT
1 TTCATTTTTT
3206189 GTTTTATGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.78
Consensus pattern (18 bp):
TTCATTTTTTTATTATTA
Found at i:3206193 original size:22 final size:21
Alignment explanation
Indices: 3206154--3206195 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3206144 TTCATTTTTC
3206154 TTTATTATTTATTTTTTTATT
1 TTTATTATTTATTTTTTTATT
3206175 TTTATTCATTT-TTTGTTTTAT
1 TTTATT-ATTTATTT-TTTTAT
3206196 GATTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTATTATTTATTTTTTTATT
Found at i:3206193 original size:25 final size:25
Alignment explanation
Indices: 3206142--3206202 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
3206132 TTTCTTTTCA
* *
3206142 TTTTCATTTTTCTTTATTATTTATT
1 TTTTCATTTTTATTCATTATTTATT
* * *
3206167 TTTTTATTTTTATTCATTTTTTGTT
1 TTTTCATTTTTATTCATTATTTATT
* *
3206192 TTATGATTTTT
1 TTTTCATTTTT
3206203 TTTAATTAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (25 bp):
TTTTCATTTTTATTCATTATTTATT
Found at i:3206416 original size:15 final size:16
Alignment explanation
Indices: 3206390--3206419 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3206380 TATTTTTGTT
3206390 CTTTTTTGTTCTTTTC
1 CTTTTTTGTTCTTTTC
3206406 CTTTTTT-TTCTTTT
1 CTTTTTTGTTCTTTT
3206420 TTTTCTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (16 bp):
CTTTTTTGTTCTTTTC
Found at i:3206419 original size:24 final size:25
Alignment explanation
Indices: 3206382--3206430 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
3206372 CGTCAACTTA
3206382 TTTTTGTTCTTTTTTGTTCTTTTCC
1 TTTTTGTTCTTTTTTGTTCTTTTCC
*
3206407 TTTTTTTTCTTTTTT-TTCTTTTCC
1 TTTTTGTTCTTTTTTGTTCTTTTCC
3206431 AATTTCCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (25 bp):
TTTTTGTTCTTTTTTGTTCTTTTCC
Found at i:3208906 original size:41 final size:42
Alignment explanation
Indices: 3208855--3208940 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 42
3208845 TTTTATCGTG
* *
3208855 TTTCATGTCTTAATCATGTT-GACACGGTTTAAACACGAAAA
1 TTTCATGTCTTAATCATGTTAGACACGATTAAAACACGAAAA
* * *
3208896 TTTCTTGTCTTAATCATGTTAGACATGATTAAAACACGATAA
1 TTTCATGTCTTAATCATGTTAGACACGATTAAAACACGAAAA
3208938 TTT
1 TTT
3208941 TGTGTCAAAC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 19 0.49
42 20 0.51
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (42 bp):
TTTCATGTCTTAATCATGTTAGACACGATTAAAACACGAAAA
Found at i:3211668 original size:15 final size:15
Alignment explanation
Indices: 3211648--3211684 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
3211638 GGTCCGGCAG
*
3211648 AATTCAATCCTTATC
1 AATTCAATACTTATC
3211663 AATTCAATACTTATC
1 AATTCAATACTTATC
*
3211678 AAGTCAA
1 AATTCAA
3211685 GATGATGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.35
Consensus pattern (15 bp):
AATTCAATACTTATC
Found at i:3214640 original size:26 final size:27
Alignment explanation
Indices: 3214591--3214643 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
3214581 AGAAAATAGA
3214591 TAATTTTATTAATTATTAATTATTTTT
1 TAATTTTATTAATTATTAATTATTTTT
*
3214618 TAATTTT-TTAATT-TTTATATATTTTT
1 TAATTTTATTAATTATTAAT-TATTTTT
3214644 AATATAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 13 0.54
27 7 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (27 bp):
TAATTTTATTAATTATTAATTATTTTT
Found at i:3224325 original size:38 final size:39
Alignment explanation
Indices: 3224241--3224344 Score: 140
Period size: 38 Copynumber: 2.7 Consensus size: 39
3224231 CCGGCTCATT
*
3224241 TACATCCCCCCACATCGTGCACATAGCCGGCACCATCGTG
1 TACATCCCCCCACATCGTGCACATAGCAGG-ACCATCGTG
* * *
3224281 TGCATCCCCCCACATCGTGCACA-ATCAGTG-TCATCGTG
1 TACATCCCCCCACATCGTGCACATAGCAG-GACCATCGTG
3224319 TACATCCCCCCACATCGTGCACATAG
1 TACATCCCCCCACATCGTGCACATAG
3224345 GCACTATCAT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
38 29 0.52
39 4 0.07
40 23 0.41
ACGTcount: A:0.23, C:0.40, G:0.16, T:0.20
Consensus pattern (39 bp):
TACATCCCCCCACATCGTGCACATAGCAGGACCATCGTG
Found at i:3225258 original size:19 final size:21
Alignment explanation
Indices: 3225219--3225258 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3225209 GAAGAAGACC
3225219 AGCTGCTGGAAAATCTCTAGA
1 AGCTGCTGGAAAATCTCTAGA
3225240 AGCTGCTGG-AAAT-TCTAGA
1 AGCTGCTGGAAAATCTCTAGA
3225259 TATTTATAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 4 0.21
21 9 0.47
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (21 bp):
AGCTGCTGGAAAATCTCTAGA
Found at i:3226907 original size:36 final size:35
Alignment explanation
Indices: 3226838--3226908 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
3226828 TTTAACCCTT
* * *
3226838 CTACCTTTCCAGTGGTTAAGGTTTAACCACTCAAA
1 CTACCTTTCAAGTGGTTAAGGATAAACCACTCAAA
3226873 CTACCTTTCAAG-GGTTAAGGGATAACACCACTCAAA
1 CTACCTTTCAAGTGGTTAA-GGATAA-ACCACTCAAA
3226909 TGTATAATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 6 0.19
35 15 0.48
36 10 0.32
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.27
Consensus pattern (35 bp):
CTACCTTTCAAGTGGTTAAGGATAAACCACTCAAA
Found at i:3231449 original size:43 final size:43
Alignment explanation
Indices: 3231399--3231484 Score: 138
Period size: 43 Copynumber: 2.0 Consensus size: 43
3231389 TATATGTCAA
3231399 ATAGGGATGGTAGTGTTGTTACC-ACCTATAAGTTATAGCCCAT
1 ATAGGGATGGTAGTGTTGTT-CCTACCTATAAGTTATAGCCCAT
* *
3231442 ATAGGGATGGTGGTGTTGTTCCTACCTGTAAGTTATAGCCCAT
1 ATAGGGATGGTAGTGTTGTTCCTACCTATAAGTTATAGCCCAT
3231485 GTTAGGACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 2 0.05
43 38 0.95
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (43 bp):
ATAGGGATGGTAGTGTTGTTCCTACCTATAAGTTATAGCCCAT
Found at i:3231499 original size:43 final size:43
Alignment explanation
Indices: 3231411--3231509 Score: 121
Period size: 43 Copynumber: 2.3 Consensus size: 43
3231401 AGGGATGGTA
***
3231411 GTGTTGTTACC-ACCTATAAGTTATAGCCCATATAGGGATGGTG
1 GTGTTGTT-CCTACCTATAAGTTATAGCCCATATAGGGACAATG
* *
3231454 GTGTTGTTCCTACCTGTAAGTTATAGCCCATGTTA-GGACAATG
1 GTGTTGTTCCTACCTATAAGTTATAGCCCAT-ATAGGGACAATG
3231497 GTGTTGTTCCTAC
1 GTGTTGTTCCTAC
3231510 TTGCAATTCA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
42 2 0.04
43 45 0.92
44 2 0.04
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (43 bp):
GTGTTGTTCCTACCTATAAGTTATAGCCCATATAGGGACAATG
Found at i:3233659 original size:153 final size:153
Alignment explanation
Indices: 3233366--3233674 Score: 435
Period size: 153 Copynumber: 2.0 Consensus size: 153
3233356 AACACTTTGC
* * * *
3233366 AAACATGGATCTCACATAATATCAAGTTCAATTTTATCAATCTTGAATAATTAAATCCGTCTTTA
1 AAACATGGATCTCACATAATATCAAGTTCAATGTCATCAATCTTAAATAATTAAATCCATCTTTA
* * *
3233431 GGATCAACAGATGAGTTAAGGAAAAAACGAAAAAAAAGAAAAGAAAAATAATTCTAAAATTTGGG
66 GGATCAACAGATGAGTTAAGGAAAAAACGAAAAAAAAGAAAAGAAAAATAATTCCAAAACTTAGG
**
3233496 CCTACTTGAGCTAAGGAAAAAAA
131 CCTAAATGAGCTAAGGAAAAAAA
*
3233519 AAACATGGATCTCGCATAATATCAAGTTCAATGTCATCAATCTTAAATAATTAAATCCATCTTTA
1 AAACATGGATCTCACATAATATCAAGTTCAATGTCATCAATCTTAAATAATTAAATCCATCTTTA
* ** * *
3233584 GGATCAA-ATTATGAGTTAAGGAAAAAAATTAAAACAAAA-ATAATAAAAATAATTCCAAAACTT
66 GGATCAACA-GATGAGTTAAGG-AAAAAACGAAAA-AAAAGAAAAGAAAAATAATTCCAAAACTT
3233647 AGG-CTAAATGAGCTAAGGAAAAAAA
128 AGGCCTAAATGAGCTAAGGAAAAAAA
3233672 AAA
1 AAA
3233675 GAAATATAAT
Statistics
Matches: 138, Mismatches: 15, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
152 1 0.01
153 101 0.73
154 32 0.23
155 4 0.03
ACGTcount: A:0.50, C:0.12, G:0.13, T:0.26
Consensus pattern (153 bp):
AAACATGGATCTCACATAATATCAAGTTCAATGTCATCAATCTTAAATAATTAAATCCATCTTTA
GGATCAACAGATGAGTTAAGGAAAAAACGAAAAAAAAGAAAAGAAAAATAATTCCAAAACTTAGG
CCTAAATGAGCTAAGGAAAAAAA
Found at i:3238001 original size:32 final size:32
Alignment explanation
Indices: 3237965--3238070 Score: 99
Period size: 32 Copynumber: 3.2 Consensus size: 32
3237955 TTGTAGATTA
*
3237965 TGGTTGAGCCTTTGAAAAGCCACTTTGAGTTT
1 TGGTTGAGCCTTTGAAAAACCACTTTGAGTTT
* * *
3237997 TGGTTAAG-CTCATGAAAAACCA-TTGTGAAAGGTTA
1 TGGTTGAGCCT-TTGAAAAACCACTT-TG--A-GTTT
* *
3238032 GGGTTGAGCCTTTGAAAAACCACTTTGGGTTT
1 TGGTTGAGCCTTTGAAAAACCACTTTGAGTTT
3238064 TGGTTGA
1 TGGTTGA
3238071 TCCCGGTAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
31 4 0.07
32 27 0.47
34 1 0.02
35 21 0.37
36 4 0.07
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.34
Consensus pattern (32 bp):
TGGTTGAGCCTTTGAAAAACCACTTTGAGTTT
Found at i:3238095 original size:67 final size:67
Alignment explanation
Indices: 3237925--3238097 Score: 206
Period size: 67 Copynumber: 2.6 Consensus size: 67
3237915 AGTTTTTGCA
* * * * *
3237925 TTTTGGTTAATCCCGTGAGAAAAACCATTGTTG-TAGATTATGGTTGAGCCTTTGAAAAGCCACT
1 TTTTGGTTAATCCCG-G-TAAAAACCATTG-TGAAAGGTTAGGGTTGAGCCTTTGAAAAACCACT
3237989 TTGAG
63 TTGAG
* * *
3237994 TTTTGGTTAAGCTC-ATGAAAAACCATTGTGAAAGGTTAGGGTTGAGCCTTTGAAAAACCACTTT
1 TTTTGGTTAATCCCGGT-AAAAACCATTGTGAAAGGTTAGGGTTGAGCCTTTGAAAAACCACTTT
*
3238058 GGG
65 GAG
*
3238061 TTTTGGTTGATCCCGGTAAAAACCATTGTGAAAGGTT
1 TTTTGGTTAATCCCGGTAAAAACCATTGTGAAAGGTT
3238098 TTGGCTAAGC
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
66 2 0.02
67 73 0.83
68 1 0.01
69 12 0.14
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (67 bp):
TTTTGGTTAATCCCGGTAAAAACCATTGTGAAAGGTTAGGGTTGAGCCTTTGAAAAACCACTTTG
AG
Found at i:3244845 original size:73 final size:71
Alignment explanation
Indices: 3244715--3244903 Score: 197
Period size: 73 Copynumber: 2.6 Consensus size: 71
3244705 GAGGATTGAG
* * * *
3244715 AGACAGAGA-AGACTTAGTCGACCAAGCAGTAAGTTAGTCGACTAAAAGCTTATTGCCAAAAATC
1 AGACAGAGACA-ACTTAGTCGACTAAG-AGGAAGTTAGTCGACTAAAAGCTCACTGCCAAAAA-C
3244779 T-GGAATTT-A
63 TAGG--TTTAA
* * *
3244788 AGATAGA-ACCAACTTAATCGACTAAGAAGGAAGTTAGTCGACTAAGAGCTCACTGCCAAAAACT
1 AGACAGAGA-CAACTTAGTCGACTAAG-AGGAAGTTAGTCGACTAAAAGCTCACTGCCAAAAACT
3244852 AGGTTTAGA
64 AGGTTTA-A
*
3244861 AGACAGAGACAACTTAGTCGACTAAGAGTGCAGTTAGTCGACT
1 AGACAGAGACAACTTAGTCGACTAAGAG-GAAGTTAGTCGACT
3244904 GAGATCATTC
Statistics
Matches: 98, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
71 3 0.03
72 5 0.05
73 88 0.90
74 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (71 bp):
AGACAGAGACAACTTAGTCGACTAAGAGGAAGTTAGTCGACTAAAAGCTCACTGCCAAAAACTAG
GTTTAA
Found at i:3245344 original size:35 final size:35
Alignment explanation
Indices: 3245302--3245412 Score: 95
Period size: 35 Copynumber: 3.3 Consensus size: 35
3245292 GATCCCGTGA
3245302 GAAAAACCATTATTTTAGGTTATGGTTGAGCCTTT
1 GAAAAACCATTATTTTAGGTTATGGTTGAGCCTTT
* * * **
3245337 GAAAAACC---ACTTTGGGTTTTGGTTGAGCCCGT
1 GAAAAACCATTATTTTAGGTTATGGTTGAGCCTTT
* *** *
3245369 GAAAAA-CAGTTGTGAAAGGTTGTGGTTGAGCCTTT
1 GAAAAACCA-TTATTTTAGGTTATGGTTGAGCCTTT
3245404 GAAAAACCA
1 GAAAAACCA
3245413 CTTTGGGTTT
Statistics
Matches: 57, Mismatches: 14, Indels: 9
0.71 0.17 0.11
Matches are distributed among these distances:
31 1 0.02
32 25 0.44
35 29 0.51
36 2 0.04
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.32
Consensus pattern (35 bp):
GAAAAACCATTATTTTAGGTTATGGTTGAGCCTTT
Found at i:3245364 original size:32 final size:32
Alignment explanation
Indices: 3245319--3245432 Score: 140
Period size: 32 Copynumber: 3.5 Consensus size: 32
3245309 CATTATTTTA
*
3245319 GGTTATGGTTGAGCCTTTGAAAAACCACTTTG
1 GGTTTTGGTTGAGCCTTTGAAAAACCACTTTG
** *
3245351 GGTTTTGGTTGAGCCCGTGAAAAA-CAGTTGTG
1 GGTTTTGGTTGAGCCTTTGAAAAACCACTT-TG
*
3245383 AAAGGTTGTGGTTGAGCCTTTGAAAAACCACTTTG
1 ---GGTTTTGGTTGAGCCTTTGAAAAACCACTTTG
3245418 GGTTTTGGTTGAGCC
1 GGTTTTGGTTGAGCC
3245433 CAATAAAAAC
Statistics
Matches: 68, Mismatches: 9, Indels: 10
0.78 0.10 0.11
Matches are distributed among these distances:
31 4 0.06
32 37 0.54
35 23 0.34
36 4 0.06
ACGTcount: A:0.23, C:0.14, G:0.30, T:0.33
Consensus pattern (32 bp):
GGTTTTGGTTGAGCCTTTGAAAAACCACTTTG
Found at i:3245400 original size:67 final size:67
Alignment explanation
Indices: 3245318--3245456 Score: 228
Period size: 67 Copynumber: 2.1 Consensus size: 67
3245308 CCATTATTTT
*
3245318 AGGTTATGGTTGAGCCTTTGAAAAACCACTTTGGGTTTTGGTTGAGCCC-GTGAAAAA-CAGTTG
1 AGGTTATGGTTGAGCCTTTGAAAAACCACTTTGGGTTTTGGTTGAGCCCAAT-AAAAACCA-TTG
3245381 TGAA
64 TGAA
*
3245385 AGGTTGTGGTTGAGCCTTTGAAAAACCACTTTGGGTTTTGGTTGAGCCCAATAAAAACCATTGTG
1 AGGTTATGGTTGAGCCTTTGAAAAACCACTTTGGGTTTTGGTTGAGCCCAATAAAAACCATTGTG
3245450 AA
66 AA
3245452 AGGTT
1 AGGTT
3245457 TTAGCTAAGC
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
67 65 0.96
68 3 0.04
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (67 bp):
AGGTTATGGTTGAGCCTTTGAAAAACCACTTTGGGTTTTGGTTGAGCCCAATAAAAACCATTGTG
AA
Found at i:3262447 original size:48 final size:48
Alignment explanation
Indices: 3262391--3262487 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
3262381 GATATGGGTG
3262391 TGGTGGATCTTTTTCTAGGGATAAGAATAACGAGAGACAATAATGGCC
1 TGGTGGATCTTTTTCTAGGGATAAGAATAACGAGAGACAATAATGGCC
3262439 TGGTGGATCTTTTTCTAGGGATAAGAATAACGAGAGACAATAATGGCC
1 TGGTGGATCTTTTTCTAGGGATAAGAATAACGAGAGACAATAATGGCC
3262487 T
1 T
3262488 AACATTATCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (48 bp):
TGGTGGATCTTTTTCTAGGGATAAGAATAACGAGAGACAATAATGGCC
Found at i:3268134 original size:60 final size:59
Alignment explanation
Indices: 3268016--3268136 Score: 136
Period size: 60 Copynumber: 2.0 Consensus size: 59
3268006 TAATTGATAA
* * * *
3268016 TAAAGGGAGACCTGAAGCCTCGACTCATATTTAGTGGCGTGGGGAGTTTCCATGAGTAGG
1 TAAAGGGAGACCTAAAGCCCCGACTCATATTTAGTGACGTGGGAAGTTTCCA-GAGTAGG
* * * *
3268076 TAAAGGGGGACCTAAAGCCCCGACTTATATTTGGTGATGTGGGAAGTTCTCACA-AGTAGG
1 TAAAGGGAGACCTAAAGCCCCGACTCATATTTAGTGACGTGGGAAGTT-TC-CAGAGTAGG
3268136 T
1 T
3268137 GTTGATGTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
60 47 0.92
61 2 0.04
62 2 0.04
ACGTcount: A:0.26, C:0.17, G:0.31, T:0.26
Consensus pattern (59 bp):
TAAAGGGAGACCTAAAGCCCCGACTCATATTTAGTGACGTGGGAAGTTTCCAGAGTAGG
Found at i:3275517 original size:31 final size:31
Alignment explanation
Indices: 3275431--3275517 Score: 81
Period size: 31 Copynumber: 2.8 Consensus size: 31
3275421 TGGTACCAAT
*
3275431 ATGAATTTAGCCCAATTAAGTTG-GC-ACAAG
1 ATGATTTTAGCCCAATTAAG-TGAGCAACAAG
* ** * *
3275461 A-GATTGTAAGCAAAATTTAGCGAGCAACAAG
1 ATGATT-TTAGCCCAATTAAGTGAGCAACAAG
3275492 ATGATTTTAGCCCAATTAAGTGAGCA
1 ATGATTTTAGCCCAATTAAGTGAGCA
3275518 CTAAAGAGTT
Statistics
Matches: 42, Mismatches: 11, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
29 4 0.10
30 13 0.31
31 21 0.50
32 4 0.10
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (31 bp):
ATGATTTTAGCCCAATTAAGTGAGCAACAAG
Found at i:3275553 original size:61 final size:60
Alignment explanation
Indices: 3275407--3275711 Score: 231
Period size: 61 Copynumber: 5.0 Consensus size: 60
3275397 AAGAGAGTCC
* * * * * * *
3275407 AAGCCTAATCTAGCTGGTACCAATATGAATTTAGCCCAATTAAGTTGGCA-CAAGAGATTGT
1 AAGCCCAATCTAGCTAGCACCAAGATGAATTAAGCCCAATTAAGCTGGCATAAAGAG-TT-T
** * * * * *
3275468 AAGCAAAATTTAGCGAGCAACAAGATGATTTTAGCCCAATTAAG-TGAGCACTAAAGAGTTT
1 AAGCCCAATCTAGCTAGCACCAAGATGAATTAAGCCCAATTAAGCTG-GCA-TAAAGAGTTT
* * * * * *
3275529 AAGCCCAATCT-GACTAACACCAAGATGAATTAAGCCCCATTAAGTTGGCAT-GAGAACTTCC
1 AAGCCCAATCTAG-CTAGCACCAAGATGAATTAAGCCCAATTAAGCTGGCATAAAG-AGTT-T
* * * * * *
3275590 AAGCCCCATCTAGCTGGCAACAAGATGAATTAAGCCCAATTAAGCTGACACGAAAGATTTT
1 AAGCCCAATCTAGCTAGCACCAAGATGAATTAAGCCCAATTAAGCTGGCA-TAAAGAGTTT
* * * *
3275651 AAGCCTAATCTAGCTAGCACCAAGATGATTTAAGCCTAGTTAAGCTGGCATGAAAGAGTTT
1 AAGCCCAATCTAGCTAGCACCAAGATGAATTAAGCCCAATTAAGCTGGCAT-AAAGAGTTT
3275712 TAAAATTTTA
Statistics
Matches: 190, Mismatches: 43, Indels: 22
0.75 0.17 0.09
Matches are distributed among these distances:
59 2 0.01
60 7 0.04
61 166 0.87
62 8 0.04
63 7 0.04
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (60 bp):
AAGCCCAATCTAGCTAGCACCAAGATGAATTAAGCCCAATTAAGCTGGCATAAAGAGTTT
Found at i:3275571 original size:122 final size:122
Alignment explanation
Indices: 3275407--3275700 Score: 299
Period size: 122 Copynumber: 2.4 Consensus size: 122
3275397 AAGAGAGTCC
* *** * * **
3275407 AAGCCTAATCTAGCTGGTACCAATATGAATTTAGCCCAATTAAGTTGGCACAAGAGA-TTGTAAG
1 AAGCCCAATCTAGCTAACACCAAGATGAATTAAGCCCAATTAAGTTGGCACAAGA-ACTTCCAAG
* * * *
3275471 CAAAATTTAGC-GAGCAACAAGATGATTTTAGCCCAATTAAG-TGAGCACTAAAGAGTTT
65 CAAAATCTAGCTG-GCAACAAGATGAATTAAGCCCAATTAAGCTGA-CACGAAAGAGTTT
* **
3275529 AAGCCCAATCT-GACTAACACCAAGATGAATTAAGCCCCATTAAGTTGGCATGAGAACTTCCAAG
1 AAGCCCAATCTAG-CTAACACCAAGATGAATTAAGCCCAATTAAGTTGGCACAAGAACTTCCAAG
*** *
3275593 CCCCATCTAGCTGGCAACAAGATGAATTAAGCCCAATTAAGCTGACACGAAAGATTTT
65 CAAAATCTAGCTGGCAACAAGATGAATTAAGCCCAATTAAGCTGACACGAAAGAGTTT
* * * * * *
3275651 AAGCCTAATCTAGCTAGCACCAAGATGATTTAAGCCTAGTTAAGCTGGCA
1 AAGCCCAATCTAGCTAACACCAAGATGAATTAAGCCCAATTAAGTTGGCA
3275701 TGAAAGAGTT
Statistics
Matches: 141, Mismatches: 26, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
121 2 0.01
122 134 0.95
123 5 0.04
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.24
Consensus pattern (122 bp):
AAGCCCAATCTAGCTAACACCAAGATGAATTAAGCCCAATTAAGTTGGCACAAGAACTTCCAAGC
AAAATCTAGCTGGCAACAAGATGAATTAAGCCCAATTAAGCTGACACGAAAGAGTTT
Found at i:3275701 original size:122 final size:122
Alignment explanation
Indices: 3275484--3275703 Score: 311
Period size: 122 Copynumber: 1.8 Consensus size: 122
3275474 AATTTAGCGA
* * *
3275484 GCAACAAGATGATTTTAGCCCAATTAAGTGAGCACTAAAGAGTTTAAGCCCAATCTGACTAACAC
1 GCAACAAGATGAATTAAGCCCAATTAAGTGAGCACGAAAGAGTTTAAGCCCAATCTGACTAACAC
*
3275549 CAAGATGAATTAAGCCCCATTAAGTTGGCATGAGAACTTCCAAGCCCCATCTAGCTG
66 CAAGATGAATTAAGCCCCATTAAGCTGGCATGAGAACTTCCAAGCCCCATCTAGCTG
* * *
3275606 GCAACAAGATGAATTAAGCCCAATTAAGCTGA-CACGAAAGATTTTAAGCCTAATCT-AGCTAGC
1 GCAACAAGATGAATTAAGCCCAATTAAG-TGAGCACGAAAGAGTTTAAGCCCAATCTGA-CTAAC
* *
3275669 ACCAAGATGATTTAAG-CCTAGTTAAGCTGGCATGA
64 ACCAAGATGAATTAAGCCCCA-TTAAGCTGGCATGA
3275704 AAGAGTTTTA
Statistics
Matches: 86, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
121 4 0.05
122 79 0.92
123 3 0.03
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (122 bp):
GCAACAAGATGAATTAAGCCCAATTAAGTGAGCACGAAAGAGTTTAAGCCCAATCTGACTAACAC
CAAGATGAATTAAGCCCCATTAAGCTGGCATGAGAACTTCCAAGCCCCATCTAGCTG
Found at i:3275714 original size:31 final size:30
Alignment explanation
Indices: 3275619--3275714 Score: 79
Period size: 31 Copynumber: 3.1 Consensus size: 30
3275609 ACAAGATGAA
* *
3275619 TTAAGCCCAATTAAGCTGACACGAAAGA-TT
1 TTAAGCCTAATTAAGCTGGCA-GAAAGAGTT
* ** *
3275649 TTAAGCCTAATCT-AGCTAGCACCAAGATGAT
1 TTAAGCCTAAT-TAAGCTGGCAGAAAGA-GTT
*
3275680 TTAAGCCTAGTTAAGCTGGCATGAAAGAGTT
1 TTAAGCCTAATTAAGCTGGCA-GAAAGAGTT
3275711 TTAA
1 TTAA
3275715 AATTTTACAT
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
29 4 0.08
30 17 0.34
31 25 0.50
32 4 0.08
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (30 bp):
TTAAGCCTAATTAAGCTGGCAGAAAGAGTT
Found at i:3275808 original size:60 final size:60
Alignment explanation
Indices: 3275717--3277980 Score: 735
Period size: 60 Copynumber: 37.9 Consensus size: 60
3275707 AGTTTTAAAA
* * * * * * *
3275717 TTTTACATTGAACTTATTTTGAGATAAGTTGAGGT-TATATTAAGTTTAGGAGTTTCAAAT
1 TTTTAAATTGAACTTGTTTTGAGATAGGTTGA-GTCTAGATTAAGTCTAAGAATTTCAAAT
* * * * *
3275777 TTTTAAATTAAACTTGTTTTGGGATAGGTTGAGTCTTGATTAAGTCCAAGAACTTC-AAT
1 TTTTAAATTGAACTTGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAATTTCAAAT
* * * * * * *
3275836 TTTTAAATGGAACCTGTTTTGACATAGGTTGAATCTAGATTAAGTTTAGGAATTTTAAAT
1 TTTTAAATTGAACTTGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAATTTCAAAT
* * * * * *
3275896 TTTTAAATTGAACCTATTTTGATATAGGTAGAGCCTAGATTAAGTCTAAGAACTTCAAATT
1 TTTTAAATTGAACTTGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAATTTCAAA-T
* *** * * * *
3275957 TTTTAAATCGAACTTGTTTTGAGATAGGGCAAGCCTAGATTAAGTCTAGGTACTT-AAAT
1 TTTTAAATTGAACTTGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAATTTCAAAT
* * * * * * * *
3276016 TTCTTAAA-TCAAATGAGTTTTGAAAAAAGTCGAGCCTAGATTAAGTCTAAGAAATTT-AAAT
1 TT-TTAAATTGAACT-TGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAG-AATTTCAAAT
* * * * ** *
3276077 TCTTAAATCGAACCTATTTTGAGATAGGACGAGCCTA-AGTTAAGTCT-AGAAATTTCAAAT
1 TTTTAAATTGAACTTGTTTTGAGATAGGTTGAGTCTAGA-TTAAGTCTAAG-AATTTCAAAT
* * * * * * * * * * *
3276137 TTCTTAAATCGAACCTATTTT-ATAATAAGTCGAGCCTGGATTAAGTTTAA-AATTTTAATTT
1 TT-TTAAATTGAACTTGTTTTGA-GATAGGTTGAGTCTAGATTAAGTCTAAGAATTTCAA-AT
** * * * *
3276198 TTTTAAATCAAACCTATTTTGAGATAAGTTGAGCCTAGATTAAGTCTAAGAATTT-AAACT
1 TTTTAAATTGAACTTGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAATTTCAAA-T
** * * ** **
3276258 TTTT-AATCAAACATGTTTTGATATAGGTCAAGTCTAGATTAAGTCTAAGAATTTTGTAAT
1 TTTTAAATTGAACTTGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAA-TTTCAAAT
* * * ** * *
3276318 TTTTAAAGTTGAACTTGTTTTAAGATAAGTCGAACCTACATTAAGTCTAGGAATTTCAAAT
1 TTTTAAA-TTGAACTTGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAATTTCAAAT
* * * * * *
3276379 TTTCAAATCGAAACTAT-TTTT-AGATAGGTCGAGCCTAGATTAAATGT-AGAAACTTT-AAATT
1 TTTTAAATTG-AACT-TGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAG-AA-TTTCAAA-T
*** * * * * *
3276440 TTTTAAACAAAACCTGTTTTGAAATAGGTCGAGCCTAGATTAAGTCTATGAA-TT-AAA-
1 TTTTAAATTGAACTTGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAATTTCAAAT
* * * * * *
3276497 GTTTAAATCGAA-TCTATTTTGAGATAGGTCGAGCCTAGACTAAGTCTAAGAA-TT-ATAA-
1 TTTTAAATTGAACT-TGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAATTTCA-AAT
* * * * * * *
3276555 GTTTAAATCGAA-TCTATTTTAAGATAGGTCGAGCCTAGATTAAG-CTTAAGACTTTC-AA-
1 TTTTAAATTGAACT-TGTTTTGAGATAGGTTGAGTCTAGATTAAGTC-TAAGAATTTCAAAT
* * ** * * * * *
3276613 TCTTAAATTGAA-TCTATTTT-AGGATAGGTCAAGCCTAAATTAAGTATAGGAATTACAAGA-
1 TTTTAAATTGAACT-TGTTTTGA-GATAGGTTGAGTCTAGATTAAGTCTAAGAATTTCAA-AT
* * * * * * *
3276673 --TTAAATCGAA-TCTATTTTAAGATAAGTCGAGCCTAGATTAAGTCTAGGAATTAT-AAA-
1 TTTTAAATTGAACT-TGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAATT-TCAAAT
* * * ** * * *
3276730 -ATTAAA-TCAAATCAATTTTGAGATAGGTTGAGCCTAAATTAAGTCTAGGAA-TT-ATAA-
1 TTTTAAATTGAACT-TGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAATTTCA-AAT
* * ** * * * * * *
3276787 GTTTAAATCGAA-TCAATTATGAGATAGCTTAAGCCTAGATTAAGTCTAGGAGTTTC-AA-
1 TTTTAAATTGAACT-TGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAATTTCAAAT
* * * * * *
3276845 TCTTAAATTGAA-TCTATTTTGACATAGGTTGAGCCTAGATTAAGTCTAGGAATTAC-AA-
1 TTTTAAATTGAACT-TGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAATTTCAAAT
* * * * * * * * *
3276903 GTTTAAATTGAA-TCTATTTTAAGATAAGTCGAGCCT-GAATTAAGTATAAGAGTCTC-AA-
1 TTTTAAATTGAACT-TGTTTTGAGATAGGTTGAGTCTAG-ATTAAGTCTAAGAATTTCAAAT
* * * ** * * *
3276961 TCTTAAATTGAA-TCTATTTTAAGATAGGTCAAGCCTAAATTAAGTCT-AGAAATTT-TAAT
1 TTTTAAATTGAACT-TGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAG-AATTTCAAAT
* * ** * *
3277020 TTTTTAATTGAACATGTTTTGAGATAGACTGAGCCTAGATTAAGTCTAAGAGTTTCAAAT
1 TTTTAAATTGAACTTGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAATTTCAAAT
* ** * * * * * *
3277080 TTTTAAGTCAAACCTGCTTTGAGATAAGTCGAG-CTTAGATTAAGTCTCAGAATTTCAATT
1 TTTTAAATTGAACTTGTTTTGAGATAGGTTGAGTC-TAGATTAAGTCTAAGAATTTCAAAT
* * ** * * * * * * *
3277140 TTTTAAATAGAACATGTTTCAACATAAGTCGAGCCTAAACTAAGTAT-AGAAATTTCAAAT
1 TTTTAAATTGAACTTGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAG-AATTTCAAAT
** * * * * * * * * *
3277200 TTTTAAATCAAACCTATTTTAATATAGGTCGAGCCTTGATTAAG-CCAAGCAACTTCAAATT
1 TTTTAAATTGAACTTGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAG-AATTTCAAA-T
** * * * ** *
3277261 TTTTAAATCAAACATGTTTTAAGATAAGTCAAGCCTAGATTAAGTCTAAGAATTT-AAATT
1 TTTTAAATTGAACTTGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAATTTCAAA-T
* * * * * ***** * * * * *
3277321 TTTTAAATCGAACCTATTTTGAAAAATACCAAGCCTAGATTATGTCTAAAAAATTCAATT
1 TTTTAAATTGAACTTGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAATTTCAAAT
** ** * ** * *
3277381 TTCTTAAATCAAACCGGTTTTAAGATAGGTCAAGCCTAGATTAAGTCTGACG-ATTT-AAATT
1 TT-TTAAATTGAACTTGTTTTGAGATAGGTTGAGTCTAGATTAAGTCT-AAGAATTTCAAA-T
* *** * **** * * * *
3277442 TTTTAAATCGAACCAATTTTGAGAAAGACCAAGCCTAGATTATGTTTAAGAAATTCAAAT
1 TTTTAAATTGAACTTGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAATTTCAAAT
* * * * **
3277502 TTCTTAAATCGAACCTGTTTTGAGATA-GTTCGAGGCTAGGTTAAGTCT-AGAAATTTTTAAT
1 TT-TTAAATTGAACTTGTTTTGAGATAGGTT-GAGTCTAGATTAAGTCTAAG-AATTTCAAAT
* * * * * * *
3277563 TTCTTAAATCGAATTTGTTTTAAGATAAGTCGAGTCTAGGTTAAGTCT-AGAAATTT-TAAT
1 TT-TTAAATTGAACTTGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAG-AATTTCAAAT
* * * * * * **
3277623 TTCTTAAA-TCAAATCTGTTTTAAGATAAGTCGAGTCTAGATTAAGTCTAAGAATTTTATTTT
1 TT-TTAAATTGAACT-TGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAATTTCA-AAT
* * * * * * * *
3277685 TTTTAAATCGAACCTATTTTAAAATAGGTTGAG-CATAGATTAAATCTAGGAATTTAAAAT
1 TTTTAAATTGAACTTGTTTTGAGATAGGTTGAGTC-TAGATTAAGTCTAAGAATTTCAAAT
* ** * * * * * * *
3277745 TTTTTAATCAAACCTATTTTAAGATAGGTCGAGTTTAGATTAAGTCTAAAAATTTCTAAT
1 TTTTAAATTGAACTTGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAATTTCAAAT
* * * * * * **
3277805 TTTCAAAGTCGAAAC-TATTTTAAGATTGGTCGAACCTAGATTAAGTCT-AGTAATTTCAAAT
1 TTTTAAA-TTG-AACTTGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAG-AATTTCAAAT
* * * * * *
3277866 TTTCAAATTGAA-TCTGTTTCT-AGATAAGTCGAGCCTAAATTAAGTCT-AGAAACTTCAAATT
1 TTTTAAATTGAACT-TGTTT-TGAGATAGGTTGAGTCTAGATTAAGTCTAAG-AATTTCAAA-T
* * * * * * * *
3277927 TTTTAAA-TCAAATCTATTTTGAGTTAGGTTAAGGCTAGATTAAGACTAGGAATT
1 TTTTAAATTGAACT-TGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAATT
3277981 ACAAGTTTAA
Statistics
Matches: 1752, Mismatches: 364, Indels: 175
0.76 0.16 0.08
Matches are distributed among these distances:
56 2 0.00
57 56 0.03
58 362 0.21
59 169 0.10
60 646 0.37
61 463 0.26
62 54 0.03
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.37
Consensus pattern (60 bp):
TTTTAAATTGAACTTGTTTTGAGATAGGTTGAGTCTAGATTAAGTCTAAGAATTTCAAAT
Found at i:3276023 original size:121 final size:120
Alignment explanation
Indices: 3275755--3278549 Score: 1655
Period size: 121 Copynumber: 23.5 Consensus size: 120
3275745 TTGAGGTTAT
* * ** * * * * * *
3275755 ATTAAGTTTAGGAGTTTCAAATTTTTAAATTAAACTTGTTTTGGGATAGGTTGAGTCTTGATTAA
1 ATTAAGTCTAGGAATTT-AAATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATTAA
* * * * * * **
3275820 GTCCAAGAACTTC-AA-TTTTTAAATGGAACCTGTTTTGACATAGGTTGAATCTAG
65 GTCTAAGAAATTCAAATTTTTTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAG
* * * *
3275874 ATTAAGTTTAGGAATTTTAAATTTTTAAATTGAACCTATTTTGATATAGGTAGAGCCTAGATTAA
1 ATTAAGTCTAGGAA-TTTAAATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATTAA
* * * * *
3275939 GTCTAAGAACTTCAAATTTTTTAAATCGAACTTGTTTTGAGATAGGGCAAGCCTAG
65 GTCTAAGAAATTCAAATTTTTTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAG
* * * * * *
3275995 ATTAAGTCTAGGTACTTAAATTTCTTAAATC-AA-ATGAGTTTTGAAAAAAGTCGAGCCTAGATT
1 ATTAAGTCTAGGAATTTAAATTT-TTAAATCGAACCT-A-TTTTGAGATAGGTCGAGCCTAGATT
* * * * *
3276058 AAGTCTAAGAAATTTAAA-TTCTTAAATCGAACCTATTTTGAGATAGGACGAGCCTA-
63 AAGTCTAAGAAATTCAAATTTTTTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAG
* * * *
3276114 AGTTAAGTCTAGAAATTTCAAATTTCTTAAATCGAACCTATTTT-ATAATAAGTCGAGCCTGGAT
1 A-TTAAGTCTAGGAATTT-AAATTT-TTAAATCGAACCTATTTTGA-GATAGGTCGAGCCTAGAT
* * * * * * * * *
3276178 TAAGTTTAA-AATTTTAATTTTTTTAAATCAAACCTATTTTGAGATAAGTTGAGCCTAG
62 TAAGTCTAAGAAATTCAAATTTTTTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAG
* * * * * * *
3276236 ATTAAGTCTAAGAATTTAAACTTTTT-AATCAAACATGTTTTGATATAGGTCAAGTCTAGATTAA
1 ATTAAGTCTAGGAATTTAAA-TTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATTAA
* ** * * * * *
3276300 GTCTAAGAATTTTGTAA-TTTTTAAAGTTGAACTTGTTTTAAGATAAGTCGAACCTAC
65 GTCTAAGAA-ATTCAAATTTTTTAAA-TCGAACCTGTTTTAAGATAGGTCGAGCCTAG
* * *
3276357 ATTAAGTCTAGGAATTTCAAATTTTCAAATCGAAACTATTTTTAGATAGGTCGAGCCTAGATTAA
1 ATTAAGTCTAGGAATTT-AAATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATTAA
* * * *
3276422 ATGT-AGAAACTTTAAATTTTTTAAA-CAAAACCTGTTTTGAA-ATAGGTCGAGCCTAG
65 GTCTAAGAAA-TTCAAATTTTTTAAATC-GAACCTGTTTT-AAGATAGGTCGAGCCTAG
* * * *
3276478 ATTAAGTCTATGAA-TTAAA-GTTTAAATCGAATCTATTTTGAGATAGGTCGAGCCTAGACTAAG
1 ATTAAGTCTAGGAATTTAAATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATTAAG
* * *
3276541 TCTAAG-AATT-ATAA--GTTTAAATCGAATCTATTTTAAGATAGGTCGAGCCTAG
66 TCTAAGAAATTCA-AATTTTTTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAG
* * * * * * * *
3276593 ATTAAG-CTTAAGACTTTCAA-TCTTAAATTGAATCTATTTT-AGGATAGGTCAAGCCTAAATTA
1 ATTAAGTC-TAGGAATTTAAATTTTTAAATCGAACCTATTTTGA-GATAGGTCGAGCCTAGATTA
* * * * *
3276655 AGTAT-AGGAATTACAAGA----TTAAATCGAATCTATTTTAAGATAAGTCGAGCCTAG
64 AGTCTAAGAAATT-CAA-ATTTTTTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAG
* * * * * *
3276709 ATTAAGTCTAGGAATTATAAA--ATTAAATCAAATCAATTTTGAGATAGGTTGAGCCTAAATTAA
1 ATTAAGTCTAGGAATT-TAAATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATTAA
* * * ** * * * **
3276772 GTCT-AGGAATT-ATAA--GTTTAAATCGAATCAATTATGAGATAGCTTAAGCCTAG
65 GTCTAAGAAATTCA-AATTTTTTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAG
* * * * * * *
3276825 ATTAAGTCTAGGAGTTTCAA-TCTTAAATTGAATCTATTTTGACATAGGTTGAGCCTAGATTAAG
1 ATTAAGTCTAGGAATTTAAATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATTAAG
* * * * * *
3276889 TCT-AGGAATT-ACAA--GTTTAAATTGAATCTATTTTAAGATAAGTCGAGCCT-G
66 TCTAAGAAATTCA-AATTTTTTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAG
* * * * * * * * * * *
3276940 AATTAAGTATAAGAGTCTCAA-TCTTAAATTGAATCTATTTTAAGATAGGTCAAGCCTAAATTAA
1 -ATTAAGTCTAGGAATTTAAATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATTAA
** * * * *
3277004 GTCT-AGAAATTTTAATTTTTT-AATTGAACATGTTTTGAGATA-GACTGAGCCTAG
65 GTCTAAGAAATTCAAATTTTTTAAATCGAACCTGTTTTAAGATAGGTC-GAGCCTAG
* * * * ** * *
3277058 ATTAAGTCTAAGAGTTTCAAATTTTTAAGTCAAACCTGCTTTGAGATAAGTCGAGCTTAGATTAA
1 ATTAAGTCTAGGAATTT-AAATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATTAA
* * * * * * * *
3277123 GTCTCAGAATTTC-AATTTTTTAAATAGAACATGTTTCAACATAAGTCGAGCCTAA
65 GTCTAAGAAATTCAAATTTTTTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAG
* * * * * * *
3277178 ACTAAGTATAGAAATTTCAAATTTTTAAATCAAACCTATTTTAATATAGGTCGAGCCTTGATTAA
1 ATTAAGTCTAGGAATTT-AAATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATTAA
* * * * * *
3277243 G-CCAAGCAACTTCAAATTTTTTAAATCAAACATGTTTTAAGATAAGTCAAGCCTAG
65 GTCTAAG-AAATTCAAATTTTTTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAG
* * * *** * *
3277299 ATTAAGTCTAAGAATTTAAATTTTTTAAATCGAACCTATTTTGAAAAATACCAAGCCTAGATTAT
1 ATTAAGTCTAGGAATTTAAA-TTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATTAA
* * * *
3277364 GTCTAAAAAATTC-AATTTTCTTAAATCAAACCGGTTTTAAGATAGGTCAAGCCTAG
65 GTCTAAGAAATTCAAATTTT-TTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAG
* * * ** *
3277420 ATTAAGTCTGACG-ATTTAAATTTTTTAAATCGAACCAATTTTGAGAAAGACCAAGCCTAGATTA
1 ATTAAGTCT-AGGAATTTAAA-TTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATTA
* * * * * *
3277484 TGTTTAAGAAATTCAAATTTCTTAAATCGAACCTGTTTTGAGATAGTTCGAGGCTAG
64 AGTCTAAGAAATTCAAATTTTTTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAG
* * * ** * * * * *
3277541 GTTAAGTCTAGAAATTTTTAATTTCTTAAATCGAATTTGTTTTAAGATAAGTCGAGTCTAGGTTA
1 ATTAAGTCTAGGAA-TTTAAATTT-TTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATTA
** * * * * *
3277606 AGTCT-AGAAATTTTAATTTCTTAAATCAAATCTGTTTTAAGATAAGTCGAGTCTAG
64 AGTCTAAGAAATTCAAATTTTTTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAG
* ** * * * *
3277662 ATTAAGTCTAAGAATTTTATTTTTTTTAAATCGAACCTATTTTAAAATAGGTTGAGCATAGATTA
1 ATTAAGTCTAGGAA-TTTA-AATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATTA
* * * * * * **
3277727 AATCTAGGAATTTAAAATTTTTT-AATCAAACCTATTTTAAGATAGGTCGAGTTTAG
64 AGTCTAAGAAATTCAAATTTTTTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAG
** * * * * * *
3277783 ATTAAGTCTAAAAATTTCTAATTTTCAAAGTCGAAACTATTTTAAGATTGGTCGAACCTAGATTA
1 ATTAAGTCTAGGAATTT-AAATTTTTAAA-TCGAACCTATTTTGAGATAGGTCGAGCCTAGATTA
* * * * * *
3277848 AGTCT-AGTAATTTCAAA-TTTTCAAATTGAATCTGTTTCT-AGATAAGTCGAGCCTAA
64 AGTCTAAG-AAATTCAAATTTTTTAAATCGAACCTGTTT-TAAGATAGGTCGAGCCTAG
* * * * * ** *
3277904 ATTAAGTCTAGAAACTTCAAATTTTTTAAATCAAATCTATTTTGAGTTAGGTTAAGGCTAGATTA
1 ATTAAGTCTAGGAA-TTTAAA-TTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATTA
* * * * * *
3277969 AGACT-AGGAATT-ACAA--GTTTAAATCAAATCTATTTTAAGATAGGTCGAGCCTAG
64 AGTCTAAGAAATTCA-AATTTTTTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAG
* * * * * * *
3278023 ATTAAGTTTTGGAA-TTATAA-GTTTAAATCAAATCTATTTTAAGATAGGTCAAGCCTAGATTAA
1 ATTAAGTCTAGGAATTTA-AATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATTAA
* * * ** * * * * *
3278086 GT-TTAGGAGTTTTAA--TCTTAAATTGAATCTATTTTAAGATAGGTCAAGCCTAG
65 GTCTAAGAAATTCAAATTTTTTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAG
** * * * * * *
3278139 ATTAAGTCTAGGAA-TTACAA-GATTAAATCCAATCTATTGTGAAATAAGTCAAGCCTAGATTAA
1 ATTAAGTCTAGGAATTTA-AATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATTAA
** * * * ** *
3278202 GTCTAAG-AATTGTAA--GTTTAAAACAAATATATTTTAAGATAGGTCGAGCCTAG
65 GTCTAAGAAATTCAAATTTTTTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAG
* * * * * *
3278255 ATTAACTCTA-AAAGTTTCAA-TCTTAAATCGAATCC-ATTTTAAGATAGGTCAAGCCTAGATTA
1 ATTAAGTCTAGGAA-TTTAAATTTTTAAATCGAA-CCTATTTTGAGATAGGTCGAGCCTAGATTA
* * ** * * * *
3278317 AGTCT-AGGAATTACAAA---TTTAAATTGAATATATTTTGAGATAGGTCAAGCCTAA
64 AGTCTAAGAAATT-CAAATTTTTTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAG
* * * * * * * * **
3278371 ATTATGTCTA-GAAGTCT-CAGTCTTAAATCGAATCTGTTTTGAGATAAGTCGAGTATAGATTAA
1 ATTAAGTCTAGGAA-TTTAAATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATTAA
** * * *
3278434 GTCTAAG-AA-T-AACA-AGTTTAAATCGAATCTATTTTAAGATAGGTCGAGTCTAG
65 GTCTAAGAAATTCAA-ATTTTTTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAG
* * ** ** ** * *
3278487 ATTAAGTCTAGGAGTTTCAA-GCTTAAATATAATTTATCTTGAGATAGGTCGAGCCTAAATTAA
1 ATTAAGTCTAGGAATTTAAATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATTAA
3278550 ATTTAGGAAC
Statistics
Matches: 2159, Mismatches: 426, Indels: 185
0.78 0.15 0.07
Matches are distributed among these distances:
113 2 0.00
114 6 0.00
115 55 0.03
116 714 0.33
117 63 0.03
118 53 0.02
119 191 0.09
120 206 0.10
121 748 0.35
122 120 0.06
123 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (120 bp):
ATTAAGTCTAGGAATTTAAATTTTTAAATCGAACCTATTTTGAGATAGGTCGAGCCTAGATTAAG
TCTAAGAAATTCAAATTTTTTAAATCGAACCTGTTTTAAGATAGGTCGAGCCTAG
Found at i:3276583 original size:58 final size:58
Alignment explanation
Indices: 3275799--3278549 Score: 1492
Period size: 58 Copynumber: 46.4 Consensus size: 58
3275789 CTTGTTTTGG
* * * * * * * * *
3275799 GATAGGTTGAGTCTTGATTAAGTCCAAGAACTTCA-ATTTTTAAATGGAACCTGTTTTGA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAA-TT-ATAATTTTAAATCGAATCTATTTTAA
* * ** * * * * * *
3275858 CATAGGTTGAATCTAGATTAAGTTTAGGAATTTTAAATTTTTAAATTGAACCTATTTTGA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTAT-AA-TTTTAAATCGAATCTATTTTAA
* * * *
3275918 TATAGGTAGAGCCTAGATTAAGTCTAAGAACTTCA-AATTTTTTAAATCGAA-CTTGTTTTGA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAA-TT-ATAA--TTTTAAATCGAATC-TATTTTAA
* * * * * *
3275979 GATAGGGCAAGCCTAGATTAAGTCTAGGTACTTA-AATTTCTTAAATCAAAT-GAGTTTTGAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAG-AATTATAA-TT-TTAAATCGAATCTA-TTTT-AA
* * * *
3276040 -AAAAGTCGAGCCTAGATTAAGTCTAAGAAATT-TAAATTCTTAAATCGAACCTATTTTGA
1 GATAGGTCGAGCCTAGATTAAGTCTAAG-AATTAT-AATT-TTAAATCGAATCTATTTTAA
* *
3276099 GATAGGACGAGCCTA-AGTTAAGTCT-AGAAATT-TCAAATTTCTTAAATCGAACCTATTTTATA
1 GATAGGTCGAGCCTAGA-TTAAGTCTAAG-AATTAT--AA-TT-TTAAATCGAATCTATTTTA-A
* * * * * * *
3276161 -ATAAGTCGAGCCTGGATTAAGTTTAA-AATTTTAATTTTTTTAAATCAAACCTATTTTGA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTATAA---TTTTAAATCGAATCTATTTTAA
* * * * * *
3276220 GATAAGTTGAGCCTAGATTAAGTCTAAGAATT-TAAACTTTTTAATC-AAACATGTTTTGA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTAT-AA-TTTTAAATCGAATC-TATTTTAA
* * * * * *
3276279 TATAGGTCAAGTCTAGATTAAGTCTAAGAATTTTGTAATTTTTAAAGTTGAA-CTTGTTTTAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAA--TTATAA-TTTTAAA-TCGAATC-TATTTTAA
* * * * * *
3276341 GATAAGTCGAACCTACATTAAGTCTAGGAATT-TCAAATTTTCAAATCGAAACTATTTTTA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTAT--AATTTT-AAATCGAATCTATTTTAA
* * * * *
3276401 GATAGGTCGAGCCTAGATTAAATGT-AGAAACTT-TAAATTTTTTAAA-CAAAACCTGTTTTGAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAG-AA-TTAT-AA--TTTTAAATC-GAATCTATTTT-AA
* * *
3276463 -ATAGGTCGAGCCTAGATTAAGTCTATGAATTA-AAGTTTAAATCGAATCTATTTTGA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTATAATTTTAAATCGAATCTATTTTAA
* *
3276519 GATAGGTCGAGCCTAGACTAAGTCTAAGAATTATAAGTTTAAATCGAATCTATTTTAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTATAATTTTAAATCGAATCTATTTTAA
* * * *
3276577 GATAGGTCGAGCCTAGATTAAG-CTTAAGACTT-TCAATCTTAAATTGAATCTATTTTAG
1 GATAGGTCGAGCCTAGATTAAGTC-TAAGAATTAT-AATTTTAAATCGAATCTATTTTAA
* * * * * **
3276635 GATAGGTCAAGCCTAAATTAAGTATAGGAATTACAAGATTAAATCGAATCTATTTTAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTATAATTTTAAATCGAATCTATTTTAA
* * ** * * *
3276693 GATAAGTCGAGCCTAGATTAAGTCTAGGAATTATAAAATTAAATCAAATCAATTTTGA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTATAATTTTAAATCGAATCTATTTTAA
* * * * * * *
3276751 GATAGGTTGAGCCTAAATTAAGTCTAGGAATTATAAGTTTAAATCGAATCAATTATGA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTATAATTTTAAATCGAATCTATTTTAA
* ** * * * * *
3276809 GATAGCTTAAGCCTAGATTAAGTCTAGGAGTT-TCAATCTTAAATTGAATCTATTTTGA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTAT-AATTTTAAATCGAATCTATTTTAA
* * * * * *
3276867 CATAGGTTGAGCCTAGATTAAGTCTAGGAATTACAAGTTTAAATTGAATCTATTTTAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTATAATTTTAAATCGAATCTATTTTAA
* * * * * *
3276925 GATAAGTCGAGCCT-GAATTAAGTATAAGAGTCT-CAATCTTAAATTGAATCTATTTTAA
1 GATAGGTCGAGCCTAG-ATTAAGTCTAAGAAT-TATAATTTTAAATCGAATCTATTTTAA
* * * * * * *
3276983 GATAGGTCAAGCCTAAATTAAGTCT-AGAAATTTTAATTTTTTAATTGAA-CATGTTTTGA
1 GATAGGTCGAGCCTAGATTAAGTCTAAG-AATTATAA-TTTTAAATCGAATC-TATTTTAA
* * * * * ** *
3277042 GATA-GACTGAGCCTAGATTAAGTCTAAGAGTT-TCAAATTTTTAAGTCAAACCTGCTTTGA
1 GATAGGTC-GAGCCTAGATTAAGTCTAAGAATTAT--AA-TTTTAAATCGAATCTATTTTAA
* * * *
3277102 GATAAGTCGAGCTTAGATTAAGTCTCAGAATT-TCAATTTTTTAAATAGAA-C-ATGTTTCAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTAT-AA--TTTTAAATCGAATCTAT-TTT-AA
* * * * * * *
3277162 CATAAGTCGAGCCTAAACTAAGTAT-AGAAATT-TCAAATTTTTAAATCAAACCTATTTTAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAG-AATTAT--AA-TTTTAAATCGAATCTATTTTAA
* * * * *
3277222 TATAGGTCGAGCCTTGATTAAG-CCAAGCAACTTCA-AATTTTTTAAATC-AAACATGTTTTAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAG-AA-TT-ATAA--TTTTAAATCGAATC-TATTTTAA
* * *
3277283 GATAAGTCAAGCCTAGATTAAGTCTAAGAATT-TAAATTTTTTAAATCGAACCTATTTTGAAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTAT-AA--TTTTAAATCGAATCTATTTT--AA
* * * * * * * * **
3277345 AATA--CCAAGCCTAGATTATGTCTAAAAAATTCA-ATTTTCTTAAATCAAACCGGTTTTAA
1 GATAGGTCGAGCCTAGATTAAGTCT-AAGAATT-ATA-ATT-TTAAATCGAATCTATTTTAA
* * * * * *
3277404 GATAGGTCAAGCCTAGATTAAGTCTGACGATTTA-AATTTTTTAAATCGAACCAATTTTGA
1 GATAGGTCGAGCCTAGATTAAGTCT-AAGAATTATAA--TTTTAAATCGAATCTATTTTAA
* ** * * * * * *
3277464 GAAAGACCAAGCCTAGATTATGTTTAAGAAATTCA-AATTTCTTAAATCGAACCTGTTTTGA
1 GATAGGTCGAGCCTAGATTAAGTCTAAG-AATT-ATAA-TT-TTAAATCGAATCTATTTTAA
* * * * * *
3277525 GATAGTTCGAGGCTAGGTTAAGTCT-AGAAATTTTTAATTTCTTAAATCGAATTTGTTTTAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAG-AA-TTATAA-TT-TTAAATCGAATCTATTTTAA
* * * * * *
3277586 GATAAGTCGAGTCTAGGTTAAGTCT-AGAAATTTTAATTTCTTAAATCAAATCTGTTTTAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAG-AATTATAA-TT-TTAAATCGAATCTATTTTAA
* * ** *
3277646 GATAAGTCGAGTCTAGATTAAGTCTAAGAATTTTATTTTTTTTAAATCGAACCTATTTTAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAA--TTA-TAATTTTAAATCGAATCTATTTTAA
* * * * * * * * *
3277707 AATAGGTTGAGCATAGATTAAATCTAGGAATTTAAAATTTTTTAATCAAACCTATTTTAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAA-TTATAA-TTTTAAATCGAATCTATTTTAA
** * * *
3277767 GATAGGTCGAGTTTAGATTAAGTCTAAAAATTTCTAATTTTCAAAGTCGAAACTATTTTAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAA-TTATAATTTT-AAA-TCGAATCTATTTTAA
* * * *
3277828 GATTGGTCGAACCTAGATTAAGTCT-AGTAATT-TCAAATTTTCAAATTGAATCTGTTTCT-A
1 GATAGGTCGAGCCTAGATTAAGTCTAAG-AATTAT--AATTTT-AAATCGAATCTATTT-TAA
* * * *
3277888 GATAAGTCGAGCCTAAATTAAGTCT-AGAAACTTCA-AATTTTTTAAATCAAATCTATTTTGA
1 GATAGGTCGAGCCTAGATTAAGTCTAAG-AA-TT-ATAA--TTTTAAATCGAATCTATTTTAA
* ** * * * * * *
3277949 GTTAGGTTAAGGCTAGATTAAGACTAGGAATTACAAGTTTAAATCAAATCTATTTTAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTATAATTTTAAATCGAATCTATTTTAA
* ** * *
3278007 GATAGGTCGAGCCTAGATTAAGTTTTGGAATTATAAGTTTAAATCAAATCTATTTTAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTATAATTTTAAATCGAATCTATTTTAA
* * * * * * *
3278065 GATAGGTCAAGCCTAGATTAAGTTTAGGAGTTTTAATCTTAAATTGAATCTATTTTAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTATAATTTTAAATCGAATCTATTTTAA
* * * ** * *
3278123 GATAGGTCAAGCCTAGATTAAGTCTAGGAATTACAAGATTAAATCCAATCTATTGTGAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTATAATTTTAAATCGAATCTATT-TTAA
* * * * * * *
3278182 -ATAAGTCAAGCCTAGATTAAGTCTAAGAATTGTAAGTTTAAAACAAATATATTTTAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTATAATTTTAAATCGAATCTATTTTAA
* * *
3278239 GATAGGTCGAGCCTAGATTAACTCTAA-AAGTT-TCAATCTTAAATCGAATCCATTTTAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAA-TTAT-AATTTTAAATCGAATCTATTTTAA
* * * * * * *
3278297 GATAGGTCAAGCCTAGATTAAGTCTAGGAATTACAAATTTAAATTGAATATATTTTGA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTATAATTTTAAATCGAATCTATTTTAA
* * * * * * * * *
3278355 GATAGGTCAAGCCTAAATTATGTCT-AGAAGTCTCAGTCTTAAATCGAATCTGTTTTGA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTAT-AATTTTAAATCGAATCTATTTTAA
* ** * * *
3278413 GATAAGTCGAGTATAGATTAAGTCTAAGAATAACAAGTTTAAATCGAATCTATTTTAA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTATAATTTTAAATCGAATCTATTTTAA
* * * ** ** * * *
3278471 GATAGGTCGAGTCTAGATTAAGTCTAGGAGTT-TCAAGCTTAAATATAATTTATCTTGA
1 GATAGGTCGAGCCTAGATTAAGTCTAAGAATTAT-AATTTTAAATCGAATCTATTTTAA
*
3278529 GATAGGTCGAGCCTAAATTAA
1 GATAGGTCGAGCCTAGATTAA
3278550 ATTTAGGAAC
Statistics
Matches: 2156, Mismatches: 407, Indels: 259
0.76 0.14 0.09
Matches are distributed among these distances:
56 1 0.00
57 61 0.03
58 834 0.39
59 154 0.07
60 577 0.27
61 463 0.21
62 63 0.03
63 3 0.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (58 bp):
GATAGGTCGAGCCTAGATTAAGTCTAAGAATTATAATTTTAAATCGAATCTATTTTAA
Found at i:3278680 original size:18 final size:18
Alignment explanation
Indices: 3278657--3278692 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3278647 ATTAATCATT
3278657 TTTTTATT-TACATTTTTA
1 TTTTTATTAT-CATTTTTA
3278675 TTTTTATTATCATTTTTA
1 TTTTTATTATCATTTTTA
3278693 CCATTTGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTATTATCATTTTTA
Found at i:3281176 original size:2 final size:2
Alignment explanation
Indices: 3281171--3281211 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3281161 GTTTTTTTAA
3281171 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3281212 NNNNNNNNNN
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3281633 original size:36 final size:35
Alignment explanation
Indices: 3281578--3281672 Score: 111
Period size: 35 Copynumber: 2.7 Consensus size: 35
3281568 TAACGGGCTT
* * *
3281578 AAGCACAACCCTCATAATGCCTTTTTTATGGGAAC
1 AAGCACAACCCTCACAATGCCTTTTTCATAGGAAC
*
3281613 AAGCACAACCCTCAACAATGCC-TTTTCATAGGAGC
1 AAGCACAACCCTC-ACAATGCCTTTTTCATAGGAAC
* *
3281648 AAGAACAACCCTTACAAATGCCTTT
1 AAGCACAACCCTCAC-AATGCCTTT
3281673 CATGGGAGCA
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
34 2 0.04
35 40 0.78
36 9 0.18
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.24
Consensus pattern (35 bp):
AAGCACAACCCTCACAATGCCTTTTTCATAGGAAC
Found at i:3281681 original size:34 final size:34
Alignment explanation
Indices: 3281605--3281709 Score: 113
Period size: 35 Copynumber: 3.0 Consensus size: 34
3281595 TGCCTTTTTT
* * *
3281605 ATGGGAACAAGCACAACCCTCA-ACAATGCCTTTTC
1 ATGGGAGCAAGAACAACCCTTACA-AATGCC-TTTC
*
3281640 ATAGGAGCAAGAACAACCCTTACAAATGCCTTTC
1 ATGGGAGCAAGAACAACCCTTACAAATGCCTTTC
* * *
3281674 ATGGGAGCAAGTACAATCCTTACAAATAGCTTTTC
1 ATGGGAGCAAGAACAACCCTTACAAAT-GCCTTTC
3281709 A
1 A
3281710 AGGTTAAGCT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
34 28 0.47
35 31 0.52
36 1 0.02
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (34 bp):
ATGGGAGCAAGAACAACCCTTACAAATGCCTTTC
Found at i:3284133 original size:16 final size:16
Alignment explanation
Indices: 3284091--3284134 Score: 63
Period size: 16 Copynumber: 2.7 Consensus size: 16
3284081 ACACATCCAA
3284091 AAAATATAATAATGAAT
1 AAAATA-AATAATGAAT
3284108 AATAAT-AATAATGAAT
1 AA-AATAAATAATGAAT
3284124 AAAATAAATAA
1 AAAATAAATAA
3284135 ATAGTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.12
16 17 0.68
17 2 0.08
18 3 0.12
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (16 bp):
AAAATAAATAATGAAT
Found at i:3291803 original size:564 final size:565
Alignment explanation
Indices: 3290735--3291860 Score: 2204
Period size: 564 Copynumber: 2.0 Consensus size: 565
3290725 CTGTACTCAG
3290735 TGAGGCAATAGCTTTGGTGAAGGATATTGGTTACTTGAAAGATATTTTCCCTTTCCATGTAAGTT
1 TGAGGCAATAGCTTTGGTGAAGGATATTGGTTACTTGAAAGATATTTTCCCTTTCCATGTAAGTT
3290800 AAGTTGGCATCTATGACTTGTATGTATGCTATCCATGTAGAAAATTCTATGTTATGTATGAACAG
66 AAGTTGGCATCTATGACTTGTATGTATGCTATCCATGTAGAAAATTCTATGTTATGTATGAACAG
3290865 CATTAGAGTGAAACTAAGGGATATCCGACTTATCCATTTTGGCTCCGTACAAGAAAACTTTTATC
131 CATTAGAGTGAAACTAAGGGATATCCGACTTATCCATTTTGGCTCCGTACAAGAAAACTTTTATC
3290930 AAGCCATACGCAGGGGTCCATACATCAAAGCATAGGAGCATGAAATTTTAGATGTGACACTCTCA
196 AAGCCATACGCAGGGGTCCATACATCAAAGCATAGGAGCATGAAATTTTAGATGTGACACTCTCA
3290995 TTTCTTTCTTATATGATGCAATCTCTTTCGTATCATAGTATTAACACCAGTATTTCTACTTTACC
261 TTTCTTTCTTATATGATGCAATCTCTTTCGTATCATAGTATTAACACCAGTATTTCTACTTTACC
3291060 CTGTTAGACTTTCTGATTGACAGAAAGAGATGATGAGGGTTTGAATTGGACATGGCTAGAATGCC
326 CTGTTAGACTTTCTGATTGACAGAAAGAGATGATGAGGGTTTGAATTGGACATGGCTAGAATGCC
3291125 AGACTATTCCACAAGGGATAGGAGCCATAGCTTTCCTTCTTCTTCTCTCTTTTTTCTTTTTGTTT
391 AGACTATTCCACAAGGGATAGGAGCCATAGCTTTCCTTCTTCTTCTCTCTTTTTTCTTTTTGTTT
*
3291190 TTCAGAAGGAGCCATAGGTTTAATACAGGATGTAAATTGAAAGTGCCATTATAGGATAACTCAGC
456 TCCAGAAGGAGCCATAGGTTTAATACAGGATGTAAATTGAAAGTGCCATTATAGGATAACTCAGC
3291255 TCACCCTTGTATATTTTTGCTCTCC-CTCTCT-CTCTCTCTCACA
521 TCACCCTTGTATATTTTTGCTCTCCTCTCTCTCCTCTCTCTCACA
3291298 NTGAGGCAATAGCTTTGGTGAAGGATATTGGTTACTTGAAAGATATTTTCCCTTTCCATGTAAGT
1 -TGAGGCAATAGCTTTGGTGAAGGATATTGGTTACTTGAAAGATATTTTCCCTTTCCATGTAAGT
3291363 TAAGTTGGCATCTATGACTTGTATGTATGCTATCCATGTAGAAAATTCTATGTTATGTATGAACA
65 TAAGTTGGCATCTATGACTTGTATGTATGCTATCCATGTAGAAAATTCTATGTTATGTATGAACA
3291428 GCATTAGAGTGAAACTAAGGGATATCCGACTTATCCATTTTGGCTCCGTACAAGAAAACTTTTAT
130 GCATTAGAGTGAAACTAAGGGATATCCGACTTATCCATTTTGGCTCCGTACAAGAAAACTTTTAT
3291493 CAAGCCATACGCAGGGGTCCATACATCAAAGCATAGGAGCATGAAATTTTAGATGTGACACTCTC
195 CAAGCCATACGCAGGGGTCCATACATCAAAGCATAGGAGCATGAAATTTTAGATGTGACACTCTC
3291558 ATTTCTTTCTTATATGATGCAATCTCTTTCGTATCATAGTATTAACACCAGTATTTCTACTTTAC
260 ATTTCTTTCTTATATGATGCAATCTCTTTCGTATCATAGTATTAACACCAGTATTTCTACTTTAC
3291623 CCTGTTAGACTTTCTGATTGACAGAAAGAGATGATGAGGGTTTGAATTGGACATGGCTAGAATGC
325 CCTGTTAGACTTTCTGATTGACAGAAAGAGATGATGAGGGTTTGAATTGGACATGGCTAGAATGC
3291688 CAGACTATTCCACAAGGGATAGGAGCCATAGCTTTCCTTCTTCTTCTTCTCTTTTTTCTTTTT-T
390 CAGACTATTCCACAAGGGATAGGAGCCATAGCTTTCCTTCTTCTTC-TCTCTTTTTTCTTTTTGT
3291752 TTTCCAGAAGGAGCCATAGGTTTAATACAGGATGTAAATTGAAAGTGCCATTATAGGATAACTCA
454 TTTCCAGAAGGAGCCATAGGTTTAATACAGGATGTAAATTGAAAGTGCCATTATAGGATAACTCA
3291817 GCTCACCCTTGTATATTTTTGCTCTCCTCTCTCTCCTCTCTCTC
519 GCTCACCCTTGTATATTTTTGCTCTCCTCTCTCTCCTCTCTCTC
3291861 TCTCTCTCTC
Statistics
Matches: 558, Mismatches: 1, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
564 527 0.94
565 22 0.04
566 9 0.02
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (565 bp):
TGAGGCAATAGCTTTGGTGAAGGATATTGGTTACTTGAAAGATATTTTCCCTTTCCATGTAAGTT
AAGTTGGCATCTATGACTTGTATGTATGCTATCCATGTAGAAAATTCTATGTTATGTATGAACAG
CATTAGAGTGAAACTAAGGGATATCCGACTTATCCATTTTGGCTCCGTACAAGAAAACTTTTATC
AAGCCATACGCAGGGGTCCATACATCAAAGCATAGGAGCATGAAATTTTAGATGTGACACTCTCA
TTTCTTTCTTATATGATGCAATCTCTTTCGTATCATAGTATTAACACCAGTATTTCTACTTTACC
CTGTTAGACTTTCTGATTGACAGAAAGAGATGATGAGGGTTTGAATTGGACATGGCTAGAATGCC
AGACTATTCCACAAGGGATAGGAGCCATAGCTTTCCTTCTTCTTCTCTCTTTTTTCTTTTTGTTT
TCCAGAAGGAGCCATAGGTTTAATACAGGATGTAAATTGAAAGTGCCATTATAGGATAACTCAGC
TCACCCTTGTATATTTTTGCTCTCCTCTCTCTCCTCTCTCTCACA
Found at i:3291850 original size:2 final size:2
Alignment explanation
Indices: 3291838--3291891 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
3291828 TATATTTTTG
3291838 CT CT C- CT CT CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3291878 CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT
3291892 ATATATATAT
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:3291896 original size:2 final size:2
Alignment explanation
Indices: 3291891--3291919 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3291881 TCTCTCTCTC
3291891 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 T
3291920 GGACATCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3304571 original size:20 final size:20
Alignment explanation
Indices: 3304546--3304593 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
3304536 TGTCAGAATG
3304546 ACCTGAATTTGAAATGACCC
1 ACCTGAATTTGAAATGACCC
3304566 ACCTGAATTTGAAATGACCC
1 ACCTGAATTTGAAATGACCC
3304586 ACACTGAA
1 AC-CTGAA
3304594 GATGACCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.38, C:0.25, G:0.15, T:0.23
Consensus pattern (20 bp):
ACCTGAATTTGAAATGACCC
Found at i:3307687 original size:17 final size:17
Alignment explanation
Indices: 3307665--3307699 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3307655 GCCTGAAAAG
3307665 GACAAATGACAATAAAT
1 GACAAATGACAATAAAT
*
3307682 GACAAATGACGATAAAT
1 GACAAATGACAATAAAT
3307699 G
1 G
3307700 GATGCCTTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (17 bp):
GACAAATGACAATAAAT
Found at i:3309770 original size:15 final size:16
Alignment explanation
Indices: 3309741--3309773 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3309731 AATTCGTTAA
*
3309741 ATTTATAAAATAATAC
1 ATTTATAAAAAAATAC
3309757 ATTTA-AAAAAAATAC
1 ATTTATAAAAAAATAC
3309772 AT
1 AT
3309774 AAGTCTCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTTATAAAAAAATAC
Found at i:3326993 original size:83 final size:84
Alignment explanation
Indices: 3326848--3327008 Score: 202
Period size: 83 Copynumber: 1.9 Consensus size: 84
3326838 TTTAAATACA
* * *
3326848 TTATTATAAATATTAATAGGATTTATCTAATTTGTTAAATAAAAACTCTAAAGCAAATAATGACT
1 TTATTATAAATATCAATAAGATTTATCCAATTTGTTAAATAAAAACTCTAAAGCAAATAATGACT
*
3326913 TTCTTTAA-AAATATTATT
66 TTCATTAACAAATATTATT
* * * * *
3326931 TTATTATAAATATCAATAAGATTTATCCAATTTG-TAAATAAGAATTTTAATTGC-ATTGAATGA
1 TTATTATAAATATCAATAAGATTTATCCAATTTGTTAAATAAAAACTCTAA-AGCAAAT-AATGA
3326994 CTTTCATTAACAAAT
64 CTTTCATTAACAAAT
3327009 GACAAGATTA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
82 15 0.23
83 47 0.71
84 4 0.06
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (84 bp):
TTATTATAAATATCAATAAGATTTATCCAATTTGTTAAATAAAAACTCTAAAGCAAATAATGACT
TTCATTAACAAATATTATT
Found at i:3330893 original size:16 final size:16
Alignment explanation
Indices: 3330874--3330904 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3330864 TTGTTTGGAG
3330874 TTTGGATCATTTTAGA
1 TTTGGATCATTTTAGA
*
3330890 TTTGGATCCTTTTAG
1 TTTGGATCATTTTAG
3330905 GTTCATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (16 bp):
TTTGGATCATTTTAGA
Found at i:3333091 original size:54 final size:54
Alignment explanation
Indices: 3333024--3333251 Score: 186
Period size: 54 Copynumber: 4.2 Consensus size: 54
3333014 AAGAGTCCAA
* * * * ****
3333024 GGGTGTTCCAAGCACAGAAACGCCCATAGGCGTTCCAAGCGTAGAAGTGTTCAG
1 GGGTGTTCCAAGCACAGAAGCGCCCAAAGGTGTTCCAAGCGTGGAAGCACCCAG
* * * * *
3333078 GGGTGTTCTAAGCACAGAAGCGTCCAAAGGTGTTTCAAACATGGAAGCACCCAG
1 GGGTGTTCCAAGCACAGAAGCGCCCAAAGGTGTTCCAAGCGTGGAAGCACCCAG
* * ** *
3333132 GGGTGTTCCAAGTACAGAAGCGCCCAGAGGTGTTCCAAGCGTGGAAGCACATAA
1 GGGTGTTCCAAGCACAGAAGCGCCCAAAGGTGTTCCAAGCGTGGAAGCACCCAG
* * * ** ** * * * *
3333186 GAGTGTTCTAAGTACAGAAGCATCCAAAGGCATTCCAAGCGTAGAAGCGCTCAA
1 GGGTGTTCCAAGCACAGAAGCGCCCAAAGGTGTTCCAAGCGTGGAAGCACCCAG
*
3333240 AGGTGTTCCAAG
1 GGGTGTTCCAAG
3333252 TGTGAAAGCA
Statistics
Matches: 137, Mismatches: 37, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
54 137 1.00
ACGTcount: A:0.31, C:0.22, G:0.29, T:0.18
Consensus pattern (54 bp):
GGGTGTTCCAAGCACAGAAGCGCCCAAAGGTGTTCCAAGCGTGGAAGCACCCAG
Found at i:3333109 original size:27 final size:27
Alignment explanation
Indices: 3333018--3333251 Score: 114
Period size: 27 Copynumber: 8.7 Consensus size: 27
3333008 GAGCAAAAGA
* *
3333018 GTCCAAGGGTGTTCCAAGCACAGAAAC
1 GTCCAAAGGTGTTCCAAGCACAGAAGC
* * * ** *
3333045 GCCCATAGGCGTTCCAAGCGTAGAAGT
1 GTCCAAAGGTGTTCCAAGCACAGAAGC
* ** *
3333072 GTTCAGGGGTGTTCTAAGCACAGAAGC
1 GTCCAAAGGTGTTCCAAGCACAGAAGC
* * **
3333099 GTCCAAAGGTGTTTCAAACATGGAAGC
1 GTCCAAAGGTGTTCCAAGCACAGAAGC
** ** *
3333126 ACCCAGGGGTGTTCCAAGTACAGAAGC
1 GTCCAAAGGTGTTCCAAGCACAGAAGC
* * ***
3333153 GCCCAGAGGTGTTCCAAGCGTGGAAGC
1 GTCCAAAGGTGTTCCAAGCACAGAAGC
* * *
3333180 --ACATAAGAGTGTTCTAAGTACAGAAGC
1 GTCCA-AAG-GTGTTCCAAGCACAGAAGC
* ** **
3333207 ATCCAAAGGCATTCCAAGCGTAGAAGC
1 GTCCAAAGGTGTTCCAAGCACAGAAGC
3333234 G-CTCAAAGGTGTTCCAAG
1 GTC-CAAAGGTGTTCCAAG
3333252 TGTGAAAGCA
Statistics
Matches: 145, Mismatches: 57, Indels: 10
0.68 0.27 0.05
Matches are distributed among these distances:
25 2 0.01
26 3 0.02
27 135 0.93
28 3 0.02
29 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (27 bp):
GTCCAAAGGTGTTCCAAGCACAGAAGC
Found at i:3333233 original size:108 final size:108
Alignment explanation
Indices: 3333020--3333252 Score: 252
Period size: 108 Copynumber: 2.2 Consensus size: 108
3333010 GCAAAAGAGT
* * *** * *
3333020 CCAAGGGTGTTCCAAGCACAGAAACGCCCATAGGCGTTCCAAGCGTAGAAGTGTTCAGGGGTGTT
1 CCAAGGGTGTTCCAAGTACAGAAACGCCCAGAGGCGTTCCAAGCGTAGAAGACATCAAGAGTGTT
* ** * *
3333085 CTAAGCACAGAAGCGTCCAAAGGTGTTTCAAACATGGAAGCAC
66 CTAAGCACAGAAGCATCCAAAGGCATTCCAAACATAGAAGCAC
* * * *
3333128 CCAGGGGTGTTCCAAGTACAGAAGCGCCCAGAGGTGTTCCAAGCGTGGAAGCACAT-AAGAGTGT
1 CCAAGGGTGTTCCAAGTACAGAAACGCCCAGAGGCGTTCCAAGCGTAGAAG-ACATCAAGAGTGT
* * * *
3333192 TCTAAGTACAGAAGCATCCAAAGGCATTCCAAGCGTAGAAGCGC
65 TCTAAGCACAGAAGCATCCAAAGGCATTCCAAACATAGAAGCAC
* *
3333236 TCAAAGGTGTTCCAAGT
1 CCAAGGGTGTTCCAAGT
3333253 GTGAAAGCAC
Statistics
Matches: 101, Mismatches: 23, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
108 100 0.99
109 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (108 bp):
CCAAGGGTGTTCCAAGTACAGAAACGCCCAGAGGCGTTCCAAGCGTAGAAGACATCAAGAGTGTT
CTAAGCACAGAAGCATCCAAAGGCATTCCAAACATAGAAGCAC
Found at i:3333329 original size:28 final size:27
Alignment explanation
Indices: 3333278--3333330 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
3333268 GGTGTTCCAA
* * *
3333278 GCCCAAGGACGTTCCAAGCGCAGAAAC
1 GCCCAAGGACATTACAAGCACAGAAAC
3333305 GCCCAAGGAGCATTACAAGCACAGAA
1 GCCCAAGGA-CATTACAAGCACAGAA
3333331 GCACCTAGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.38, C:0.30, G:0.25, T:0.08
Consensus pattern (27 bp):
GCCCAAGGACATTACAAGCACAGAAAC
Found at i:3334406 original size:25 final size:25
Alignment explanation
Indices: 3334378--3334461 Score: 71
Period size: 25 Copynumber: 3.3 Consensus size: 25
3334368 CACTCATTTC
*
3334378 TTGGCCATAGTTTGTTATTTACATA
1 TTGGCCATAGTTTGTTATTCACATA
* *** * *
3334403 TTGGCCGCA-AGCTTTATCGCTCACTTC
1 TTGG-C-CATAG-TTTGTTATTCACATA
3334430 TTGGCCATAGTTTGTTATTCACATA
1 TTGGCCATAGTTTGTTATTCACATA
3334455 TTGGCCA
1 TTGGCCA
3334462 CAAGCTTTAT
Statistics
Matches: 42, Mismatches: 13, Indels: 8
0.67 0.21 0.13
Matches are distributed among these distances:
25 22 0.52
26 6 0.14
27 14 0.33
ACGTcount: A:0.20, C:0.21, G:0.18, T:0.40
Consensus pattern (25 bp):
TTGGCCATAGTTTGTTATTCACATA
Found at i:3334412 original size:52 final size:52
Alignment explanation
Indices: 3334349--3334554 Score: 270
Period size: 52 Copynumber: 4.0 Consensus size: 52
3334339 AATATTACGC
* * * * *
3334349 TATTGGTCGCAACCTTTATCACTCATTTCTTGGCCATAGTTTGTTATTTACA
1 TATTGGCCGCAAGCTTTATCGCTCACTTCTTGGCCATAGTTTGTTATTCACA
3334401 TATTGGCCGCAAGCTTTATCGCTCACTTCTTGGCCATAGTTTGTTATTCACA
1 TATTGGCCGCAAGCTTTATCGCTCACTTCTTGGCCATAGTTTGTTATTCACA
* * ** *
3334453 TATTGGCCACAAGCTTTATTGCTCACTTCTTAACCATAGTTTGCTATTCACA
1 TATTGGCCGCAAGCTTTATCGCTCACTTCTTGGCCATAGTTTGTTATTCACA
* * * *
3334505 AATTGGCTGCAAGCTTTATTGCTCACTTCTTGGCCATGGTTT-TCTATTCA
1 TATTGGCCGCAAGCTTTATCGCTCACTTCTTGGCCATAGTTTGT-TATTCA
3334555 TAGAAAGGCC
Statistics
Matches: 136, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
52 136 1.00
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (52 bp):
TATTGGCCGCAAGCTTTATCGCTCACTTCTTGGCCATAGTTTGTTATTCACA
Found at i:3334581 original size:104 final size:104
Alignment explanation
Indices: 3334382--3334582 Score: 244
Period size: 104 Copynumber: 1.9 Consensus size: 104
3334372 CATTTCTTGG
* * *
3334382 CCATAGTTTGTTATTTACATATTGGCCGCAAGCTTTATCGCTCACTTCTTGGCCATAGTTTGTTA
1 CCATAGTTTGCTATTCACAAATTGGCCGCAAGCTTTATCGCTCACTTCTTGGCCATAGTTTGTTA
* ** * **
3334447 TTCACATATTGGCCACAAGCTTTATTGCTCACTTCTTAA
66 TTCACAGAAAGGCCACAAGCTTAAACGCTCACTTCTTAA
* * *
3334486 CCATAGTTTGCTATTCACAAATTGGCTGCAAGCTTTATTGCTCACTTCTTGGCCATGGTTT-TCT
1 CCATAGTTTGCTATTCACAAATTGGCCGCAAGCTTTATCGCTCACTTCTTGGCCATAGTTTGT-T
* *
3334550 ATTCATAGAAAGGCCGCAA-CATTAAACGCTCAC
65 ATTCACAGAAAGGCCACAAGC-TTAAACGCTCAC
3334583 GTAATATGTC
Statistics
Matches: 81, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
103 2 0.02
104 79 0.98
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (104 bp):
CCATAGTTTGCTATTCACAAATTGGCCGCAAGCTTTATCGCTCACTTCTTGGCCATAGTTTGTTA
TTCACAGAAAGGCCACAAGCTTAAACGCTCACTTCTTAA
Found at i:3335891 original size:20 final size:20
Alignment explanation
Indices: 3335863--3335909 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3335853 TCATTGGACT
* *
3335863 CATGGTTATTCGTGTGGTCA
1 CATGATTATTCATGTGGTCA
*
3335883 CATGATTATTTATGTGGTCA
1 CATGATTATTCATGTGGTCA
3335903 CATGATT
1 CATGATT
3335910 CTTTTTCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.43
Consensus pattern (20 bp):
CATGATTATTCATGTGGTCA
Found at i:3338473 original size:15 final size:15
Alignment explanation
Indices: 3338453--3338484 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3338443 ACATATACAT
*
3338453 AAGAAAAAAAAGAGA
1 AAGAAAAAAAAAAGA
3338468 AAGAAAAAAAAAAGA
1 AAGAAAAAAAAAAGA
3338483 AA
1 AA
3338485 CAAACACAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAAAGA
Found at i:3338552 original size:21 final size:20
Alignment explanation
Indices: 3338528--3338571 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
3338518 GTTCAAAATT
*
3338528 TTAAGGAAGAACTTTTGAGAA
1 TTAAGG-AGAACCTTTGAGAA
*
3338549 TTAAGGAGAGCCTTTGAGAA
1 TTAAGGAGAACCTTTGAGAA
3338569 TTA
1 TTA
3338572 TCTCATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.30
Consensus pattern (20 bp):
TTAAGGAGAACCTTTGAGAA
Found at i:3338859 original size:2 final size:2
Alignment explanation
Indices: 3338842--3338886 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
3338832 NTACATACAT
3338842 TA TA TA T- TA TA T- TA TA TA TA TA TA T- TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3338880 TA TA TA T
1 TA TA TA T
3338887 CCAGTGTGCT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 4 0.10
2 35 0.90
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3338867 original size:13 final size:13
Alignment explanation
Indices: 3338840--3338886 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
3338830 GCNTACATAC
3338840 ATTATATAT-TAT
1 ATTATATATATAT
3338852 ATTATATATATAT
1 ATTATATATATAT
3338865 ATTATATATATAT
1 ATTATATATATAT
*
3338878 AATATATAT
1 ATTATATAT
3338887 CCAGTGTGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 9 0.27
13 24 0.73
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTATATATATAT
Found at i:3338870 original size:11 final size:11
Alignment explanation
Indices: 3338840--3338886 Score: 58
Period size: 11 Copynumber: 4.0 Consensus size: 11
3338830 GCNTACATAC
3338840 ATTATATATTAT
1 ATTATATA-TAT
3338852 ATTATATATATAT
1 A-T-TATATATAT
3338865 ATTATATATAT
1 ATTATATATAT
*
3338876 ATAATATATAT
1 ATTATATATAT
3338887 CCAGTGTGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
11 19 0.59
12 2 0.06
13 5 0.16
14 6 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATTATATATAT
Found at i:3339462 original size:27 final size:27
Alignment explanation
Indices: 3339423--3339598 Score: 122
Period size: 27 Copynumber: 6.5 Consensus size: 27
3339413 AAATTACATC
*
3339423 AGGGATGTTCCAAG-AGCAGAAGTGCCCA
1 AGGG-TGTTCCAAGCA-CAGAAGCGCCCA
* * *
3339451 AGGGTGTTCCAAGTATAGAAACGCCCA
1 AGGGTGTTCCAAGCACAGAAGCGCCCA
* **
3339478 TA-GGTGTTTCAAGTGCAGAAGCGCCCA
1 -AGGGTGTTCCAAGCACAGAAGCGCCCA
* *
3339505 AGGGTGTTCCAAGCACAGAAGCACTCA
1 AGGGTGTTCCAAGCACAGAAGCGCCCA
* ** * *
3339532 AGGATGTTCCAAATATAGAAGCGTCCA
1 AGGGTGTTCCAAGCACAGAAGCGCCCA
** * * * *
3339559 AAAGCGTTCCAAGCATAGCAGCGTCCA
1 AGGGTGTTCCAAGCACAGAAGCGCCCA
*
3339586 AAGGTGTTCCAAG
1 AGGGTGTTCCAAG
3339599 TGTGAAAGCA
Statistics
Matches: 117, Mismatches: 28, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
26 1 0.01
27 110 0.94
28 6 0.05
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.18
Consensus pattern (27 bp):
AGGGTGTTCCAAGCACAGAAGCGCCCA
Found at i:3339666 original size:27 final size:27
Alignment explanation
Indices: 3339618--3339717 Score: 94
Period size: 27 Copynumber: 3.7 Consensus size: 27
3339608 ACCAAATGGT
* *
3339618 GTTCCAAGCG-AGGAAACACTCAGGGGC
1 GTTCCAAGCGTA-GAAGCGCTCAGGGGC
** *
3339645 GTTCCAAGCACAGAAGCGCTCAGGGGT
1 GTTCCAAGCGTAGAAGCGCTCAGGGGC
* * * *
3339672 GTTCTAAGCGTAGAAGAGCCCAGGAGC
1 GTTCCAAGCGTAGAAGCGCTCAGGGGC
*
3339699 ATTCCAAGCGTAGAAGCGC
1 GTTCCAAGCGTAGAAGCGC
3339718 CTAAAGGCGT
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
27 57 0.98
28 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.32, T:0.14
Consensus pattern (27 bp):
GTTCCAAGCGTAGAAGCGCTCAGGGGC
Found at i:3339733 original size:27 final size:28
Alignment explanation
Indices: 3339703--3339762 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
3339693 AGGAGCATTC
* * * *
3339703 CAAGCGTAGAAGCGCCTAAAG-GCGTTT
1 CAAGCGCACAAGCGCCCAAAGAGCGTTA
*
3339730 CAAGTGCACAAGCGCCCAAAGAGCGTTA
1 CAAGCGCACAAGCGCCCAAAGAGCGTTA
3339758 CAAGC
1 CAAGC
3339763 ACAGAAGCAC
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 17 0.65
28 9 0.35
ACGTcount: A:0.33, C:0.27, G:0.27, T:0.13
Consensus pattern (28 bp):
CAAGCGCACAAGCGCCCAAAGAGCGTTA
Found at i:3339770 original size:28 final size:27
Alignment explanation
Indices: 3339710--3339770 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
3339700 TTCCAAGCGT
* * **
3339710 AGAAGCGCCTAAAGGCGTTTCAAGTGC
1 AGAAGCGCCCAAAGGCGTTACAAGCAC
*
3339737 ACAAGCGCCCAAAGAGCGTTACAAGCAC
1 AGAAGCGCCCAAAG-GCGTTACAAGCAC
3339765 AGAAGC
1 AGAAGC
3339771 ACTCAGGAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 12 0.44
28 15 0.56
ACGTcount: A:0.36, C:0.26, G:0.26, T:0.11
Consensus pattern (27 bp):
AGAAGCGCCCAAAGGCGTTACAAGCAC
Found at i:3353169 original size:208 final size:208
Alignment explanation
Indices: 3352790--3353182 Score: 601
Period size: 208 Copynumber: 1.9 Consensus size: 208
3352780 AAGTTTTGTG
* ** * *
3352790 AGTGATAAAGATTTAATAACTAATTTTGTAGGTCCAGAATATTGTAATAGAAAGAATACAGATAT
1 AGTGACAAAGATTTAATAACTAATTTTGTACCTCCACAATATTGTAATAAAAAGAATACAGATAT
* * *
3352855 AATAGGAATTAAATAAAAGTAATAGTGATATAAGGGTCATCTAGACCTAAATTTCTTTTAATACT
66 AATAGAAATGAAATAAAAGTAATAGTGATATAAGGGTCATCTAGACCCAAATTTCTTTTAATACT
* * *
3352920 TTTTGTAAATCATGTTGTAGTTATGTTATGATAGCAAGAATAAGGATATAATAGGGATCAAATAT
131 TTTTGTAAATCATGTTGCAATTATGTTATGATAGAAAGAATAAGGATATAATAGGGATCAAATAT
3352985 AATTTTTTTTTGC
196 AATTTTTTTTTGC
*
3352998 AGTGACAAAGATTTAATAACTAATCTTTGTTCCTCCACAATATTGTAATAAAAAGAATA-AGGAT
1 AGTGACAAAGATTTAATAACTAAT-TTTGTACCTCCACAATATTGTAATAAAAAGAATACA-GAT
* **
3353062 ATAATAGAAATGAAATAAAAGTAATGGTGATATAAGGGTTGTCTAGACCCAAATTT-TTTTAATA
64 ATAATAGAAATGAAATAAAAGTAATAGTGATATAAGGGTCATCTAGACCCAAATTTCTTTTAATA
* *
3353126 TTTTTTGTGAATCATGTTGCAATTATGTTATGATAGAAAGAATAAGGATATAATAGG
129 CTTTTTGTAAATCATGTTGCAATTATGTTATGATAGAAAGAATAAGGATATAATAGG
3353183 AATTAAATTT
Statistics
Matches: 166, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
208 84 0.51
209 82 0.49
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (208 bp):
AGTGACAAAGATTTAATAACTAATTTTGTACCTCCACAATATTGTAATAAAAAGAATACAGATAT
AATAGAAATGAAATAAAAGTAATAGTGATATAAGGGTCATCTAGACCCAAATTTCTTTTAATACT
TTTTGTAAATCATGTTGCAATTATGTTATGATAGAAAGAATAAGGATATAATAGGGATCAAATAT
AATTTTTTTTTGC
Found at i:3355784 original size:221 final size:224
Alignment explanation
Indices: 3355381--3355824 Score: 555
Period size: 221 Copynumber: 2.0 Consensus size: 224
3355371 TTAAGACTCA
* * * * *
3355381 ATATTTACATATCTAGTTTTTCATGTAGAAGAAGTGAAGTGTTGTTCTTTATTAGTTTTTTTTTT
1 ATATTTACATATCTACTTTTTCACGTAGAAGAAGTCAAGTGTTGTTCTTTATTAG-ATTTTTATT
* *
3355446 TTGAAATATTTATGTTTTTATTGTAATTTCCTTTCTAAAATGGACAACCATGGTTTCATTAAAGT
65 TTGAAATATTTATGTTTTTATTATAATTTCCTTTCTAAAAGGGACAACCATGGTTTCATTAAAGT
* * *
3355511 TATATCTATTTATCATGTCTTCCTCATTTGGTTGGAGAGAGAATGGTGATATTCACTATCTGCTC
130 TATATCTAGTTATCATGTCTTCCTCATTTGGTTGGAGAGAGAATGATGATATTCACTAACTGCTC
*
3355576 TTCGAT-TTTG-TCACCCTTCTTTCCTTCTTT
195 TT--ATGTTTGTTCACCCTCCTTTCCTTCTTT
* * *
3355606 ATATTTGCA-ATCTACTTTTTCACG-AGGAAGGAGTCAAGTTTTGTTCTTTATTA-ATTTTTATT
1 ATATTTACATATCTACTTTTTCACGTA-GAAGAAGTCAAGTGTTGTTCTTTATTAGATTTTTATT
* * * * *
3355668 TTGAAATATTCTTATGTTTTTGTTATATTTTCC-TT-T-AGAGGGACAGCCATGGTTTCATTGAA
65 TTGAAATA-T-TTATGTTTTTATTATAATTTCCTTTCTAAAAGGGACAACCATGGTTTCATTAAA
* * *
3355730 GTTATATCTAGTTATTATGTCTTGCTCATTTGGTTGGAGAGAGGAA-GATGATATTCATTAACTG
128 GTTATATCTAGTTATCATGTCTTCCTCATTTGGTTGGAGAGA-GAATGATGATATTCACTAACTG
*
3355794 CTCTTTTGTTTGTTCACCCTCCTTTCCTTCT
192 CTCTTATGTTTGTTCACCCTCCTTTCCTTCT
3355825 CCATTTACAA
Statistics
Matches: 190, Mismatches: 23, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
219 1 0.01
220 4 0.02
221 98 0.52
222 19 0.10
223 4 0.02
224 56 0.29
225 8 0.04
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.48
Consensus pattern (224 bp):
ATATTTACATATCTACTTTTTCACGTAGAAGAAGTCAAGTGTTGTTCTTTATTAGATTTTTATTT
TGAAATATTTATGTTTTTATTATAATTTCCTTTCTAAAAGGGACAACCATGGTTTCATTAAAGTT
ATATCTAGTTATCATGTCTTCCTCATTTGGTTGGAGAGAGAATGATGATATTCACTAACTGCTCT
TATGTTTGTTCACCCTCCTTTCCTTCTTT
Found at i:3365628 original size:135 final size:135
Alignment explanation
Indices: 3365384--3365649 Score: 433
Period size: 135 Copynumber: 2.0 Consensus size: 135
3365374 ATTTAAGATA
* * *
3365384 AAATTGTGAGAAATAACCTGTTTTGATAAAAATATTTTAAAAGTAACTATCAAAATAAATTTAAC
1 AAATTGTGAGAAATAACATGTTTTGATAAAAACATTTTAAAAGTAACCATCAAAATAAATTTAAC
* * *
3365449 TGTTTTTAGTCATATTTAGTCATGACTTAACGAAAATACTCTTTAAACTATTTCAAATAAATTAA
66 TGTTTTTAGTCATATTTAATCATGACTTAACAAAAATACCCTTTAAACTATTTCAAATAAATTAA
3365514 AGAGG
131 AGAGG
* * *
3365519 AAATTGTGAGAAATGACATTTTTTGATAAAAACATTTTAAAAGTAACCATCAAAATAAGTTTAAC
1 AAATTGTGAGAAATAACATGTTTTGATAAAAACATTTTAAAAGTAACCATCAAAATAAATTTAAC
* *
3365584 TGTTTTTAGTCATATTTAATCATGACTTGATAAAAATACCCTTTAAACTATTTCAAATAAATTAA
66 TGTTTTTAGTCATATTTAATCATGACTTAACAAAAATACCCTTTAAACTATTTCAAATAAATTAA
3365649 A
131 A
3365650 CCATTTATCA
Statistics
Matches: 120, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
135 120 1.00
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.36
Consensus pattern (135 bp):
AAATTGTGAGAAATAACATGTTTTGATAAAAACATTTTAAAAGTAACCATCAAAATAAATTTAAC
TGTTTTTAGTCATATTTAATCATGACTTAACAAAAATACCCTTTAAACTATTTCAAATAAATTAA
AGAGG
Found at i:3371833 original size:25 final size:24
Alignment explanation
Indices: 3371805--3371851 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
3371795 TATTCTTTCA
3371805 ATTTATATTATCATTTATATTTGTT
1 ATTTATATTATCATTT-TATTTGTT
* * *
3371830 ATTTTTATTTTTATTTTATTTG
1 ATTTATATTATCATTTTATTTG
3371852 CTCATATGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 6 0.32
25 13 0.68
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.70
Consensus pattern (24 bp):
ATTTATATTATCATTTTATTTGTT
Found at i:3372197 original size:22 final size:23
Alignment explanation
Indices: 3372172--3372215 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
3372162 ATTTAGTTGA
3372172 AAGA-AAATTATCTTGAGTATAT
1 AAGAGAAATTATCTTGAGTATAT
3372194 AAGAGGAAATTATCTTGAGTAT
1 AAGA-GAAATTATCTTGAGTAT
3372216 TTAGTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.20
24 16 0.80
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.34
Consensus pattern (23 bp):
AAGAGAAATTATCTTGAGTATAT
Found at i:3377811 original size:30 final size:30
Alignment explanation
Indices: 3377775--3377836 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
3377765 ATCTCTTTGT
3377775 TTGGTTGTCACATGTTCCAGGGAATAATCA
1 TTGGTTGTCACATGTTCCAGGGAATAATCA
3377805 TTGGTTGTCACATGTTCCAGGGAATAATCA
1 TTGGTTGTCACATGTTCCAGGGAATAATCA
3377835 TT
1 TT
3377837 CTTTCAAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (30 bp):
TTGGTTGTCACATGTTCCAGGGAATAATCA
Found at i:3378086 original size:20 final size:22
Alignment explanation
Indices: 3378013--3378117 Score: 57
Period size: 21 Copynumber: 5.0 Consensus size: 22
3378003 ATTTTAATTC
3378013 TAATAACAT-TTAA-ATTATAAA
1 TAATAA-ATATTAAGATTATAAA
*
3378034 T-A-AAATATTAAGATTTTAAA
1 TAATAAATATTAAGATTATAAA
* *
3378054 -ATATTAATGTTAA-ATTATAAA
1 TA-ATAAATATTAAGATTATAAA
*
3378075 TAATAAAT-TTAATATT-TAAA
1 TAATAAATATTAAGATTATAAA
* * *
3378095 TGATCAATTATTAAAATT-TAAA
1 TAAT-AAATATTAAGATTATAAA
3378117 T
1 T
3378118 TAATTATAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
18 2 0.03
19 6 0.09
20 19 0.28
21 20 0.30
22 20 0.30
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (22 bp):
TAATAAATATTAAGATTATAAA
Found at i:3378133 original size:26 final size:29
Alignment explanation
Indices: 3378049--3378141 Score: 90
Period size: 26 Copynumber: 3.4 Consensus size: 29
3378039 TATTAAGATT
*
3378049 TTAAAATATTAAT-GTTAAATTATAAA-TA
1 TTAAAAT-TTAATATTTAAATTATAAATTA
* * *
3378077 AT-AAATTTAATATTTAAATGATCAATTA
1 TTAAAATTTAATATTTAAATTATAAATTA
3378105 TTAAAATTTAA-A-TT-AATTATAAATTA
1 TTAAAATTTAATATTTAAATTATAAATTA
*
3378131 TTAATATTTAA
1 TTAAAATTTAA
3378142 CAAATAAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
26 25 0.46
27 16 0.30
28 5 0.09
29 8 0.15
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (29 bp):
TTAAAATTTAATATTTAAATTATAAATTA
Found at i:3382752 original size:24 final size:25
Alignment explanation
Indices: 3382691--3382754 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 25
3382681 ACACTATCTA
* * *
3382691 TTTCCAATAGTCATAATTGTTGGTT
1 TTTCAAATAGACATAATTATTGGTT
*
3382716 TTTCAACA-A-ACATGATTATTGG-T
1 TTTCAA-ATAGACATAATTATTGGTT
3382739 TTTCAAATAGACATAA
1 TTTCAAATAGACATAA
3382755 ATGTTTGTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
22 1 0.03
23 8 0.26
24 15 0.48
25 6 0.19
26 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (25 bp):
TTTCAAATAGACATAATTATTGGTT
Found at i:3383884 original size:30 final size:31
Alignment explanation
Indices: 3383849--3383907 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3383839 AAGCCTTTTT
*
3383849 TTTTATTTTGAACT-AAATAAGCTCTTATAC
1 TTTTATTTTGAACTCAAATAAGCACTTATAC
* *
3383879 TTTTATTTTTAAGTCAAATAAGCACTTAT
1 TTTTATTTTGAACTCAAATAAGCACTTAT
3383908 GACTAATGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (31 bp):
TTTTATTTTGAACTCAAATAAGCACTTATAC
Found at i:3385011 original size:30 final size:30
Alignment explanation
Indices: 3384951--3385012 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
3384941 AAAGCCATTG
*
3384951 TATTTTTATTTTGAACCAAATACATTTTTA
1 TATTTTTATTTTGAACCAAATACATCTTTA
* **
3384981 TATTTTTGTTTTGAGTCAAATA-AGTCTTTA
1 TATTTTTATTTTGAACCAAATACA-TCTTTA
3385011 TA
1 TA
3385013 ACTAATGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 1 0.04
30 26 0.96
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (30 bp):
TATTTTTATTTTGAACCAAATACATCTTTA
Found at i:3388334 original size:19 final size:19
Alignment explanation
Indices: 3388310--3388346 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3388300 CTTCTAAACT
3388310 TCAAATCATACTCAAATAC
1 TCAAATCATACTCAAATAC
*
3388329 TCAAATCATACTCCAATA
1 TCAAATCATACTCAAATA
3388347 AGTTAAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (19 bp):
TCAAATCATACTCAAATAC
Found at i:3399472 original size:87 final size:87
Alignment explanation
Indices: 3399314--3399488 Score: 325
Period size: 87 Copynumber: 2.0 Consensus size: 87
3399304 TTTAGCAACT
*
3399314 GAGATGTGATTAATGACATTGTGATGCAAGGATATATAGTATAATAAAATTCAAGCATATAATTG
1 GAGAAGTGATTAATGACATTGTGATGCAAGGATATATAGTATAATAAAATTCAAGCATATAATTG
3399379 GAAATGATATAAACGATATGCA
66 GAAATGATATAAACGATATGCA
3399401 GNAGAAGTGATT-ATGACATTGTGATGCAAGGATATATAGTATAATAAAATTCAAGCATATAATT
1 G-AGAAGTGATTAATGACATTGTGATGCAAGGATATATAGTATAATAAAATTCAAGCATATAATT
3399465 GGAAATGATATAAACGATATGCA
65 GGAAATGATATAAACGATATGCA
3399488 G
1 G
3399489 TTATGCATAG
Statistics
Matches: 86, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
87 77 0.90
88 9 0.10
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.29
Consensus pattern (87 bp):
GAGAAGTGATTAATGACATTGTGATGCAAGGATATATAGTATAATAAAATTCAAGCATATAATTG
GAAATGATATAAACGATATGCA
Found at i:3400860 original size:66 final size:66
Alignment explanation
Indices: 3400691--3400874 Score: 235
Period size: 66 Copynumber: 2.8 Consensus size: 66
3400681 TTAATTGTTA
**
3400691 GGTTTTGGTTGATCCCGTGAAAAACTATTGTTGCAGGTTATGGTTGAGCCTTGAAAAAACCACTT
1 GGTTTTGGTTGATCCCGTGAAAAACTATTG-TAAAGGTTATGGTTGAGCCTTGAAAAAACCACTT
3400756 TG
65 TG
* * * * * * *
3400758 GGTTTTAGTTTAACCCGTGAAAAACTAGTGTAAAAGGTTGTGGTTGAGCCTTG-AAAAACTATTT
1 GGTTTTGGTTGATCCCGTGAAAAACTATTGT-AAAGGTTATGGTTGAGCCTTGAAAAAACCACTT
3400822 TG
65 TG
* *
3400824 GGTTTTGGTTGATCCCGTGAAAAACCATTGCTAAAGGTTATGGCTGAGCCT
1 GGTTTTGGTTGATCCCGTGAAAAACTATTG-TAAAGGTTATGGTTGAGCCT
3400875 GCGAAAAGCC
Statistics
Matches: 99, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
66 54 0.55
67 45 0.45
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.34
Consensus pattern (66 bp):
GGTTTTGGTTGATCCCGTGAAAAACTATTGTAAAGGTTATGGTTGAGCCTTGAAAAAACCACTTT
G
Found at i:3419419 original size:66 final size:66
Alignment explanation
Indices: 3419331--3419582 Score: 319
Period size: 66 Copynumber: 3.8 Consensus size: 66
3419321 AAGTTAGTTG
* * * ***
3419331 TTGGGTTTTGGTTGATCCCGTGAAAAACCATTGTTGCAGGTTGTGGTTGA-CCTTAGAAAAACCA
1 TTGGGTTTTAGTTGAGCCCGTGAAAAACCAGTGTAAAAGGTTGTGGTTGAGCCTT-GAAAAACCA
3419395 CT
65 CT
* * * *
3419397 TTGGGTTTTAGTTTAGCTCGTGAAAAACTAGTGTAAAAGGTTGTGGTTGAGCCTTGAAAAATCAC
1 TTGGGTTTTAGTTGAGCCCGTGAAAAACCAGTGTAAAAGGTTGTGGTTGAGCCTTGAAAAACCAC
3419462 T
66 T
* * *
3419463 TTGGGTTTTAGTTTAGCCTGTGAAAAACTAGTGTAAAAGGTTGTGGTTGAGCCTTGAAAAACCAC
1 TTGGGTTTTAGTTGAGCCCGTGAAAAACCAGTGTAAAAGGTTGTGGTTGAGCCTTGAAAAACCAC
3419528 T
66 T
* * * *
3419529 TTGGGTTTTGGTTGATCCCGTGAAAAACCATTGCT-AAAGGTTGTGGCTGAGCCT
1 TTGGGTTTTAGTTGAGCCCGTGAAAAACCAGTG-TAAAAGGTTGTGGTTGAGCCT
3419583 GCGAAAAGCC
Statistics
Matches: 164, Mismatches: 20, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
66 159 0.97
67 5 0.03
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.34
Consensus pattern (66 bp):
TTGGGTTTTAGTTGAGCCCGTGAAAAACCAGTGTAAAAGGTTGTGGTTGAGCCTTGAAAAACCAC
T
Found at i:3419521 original size:34 final size:34
Alignment explanation
Indices: 3419417--3419524 Score: 116
Period size: 34 Copynumber: 3.2 Consensus size: 34
3419407 GTTTAGCTCG
3419417 TGAAAAACTAGTGTAAAAGGTTGTGGTTGAGCCT
1 TGAAAAACTAGTGTAAAAGGTTGTGGTTGAGCCT
* ** * * *
3419451 TGAAAAA-TCACT-T--TGGGTTTTAGTTTAGCCT
1 TGAAAAACT-AGTGTAAAAGGTTGTGGTTGAGCCT
3419482 GTGAAAAACTAGTGTAAAAGGTTGTGGTTGAGCCT
1 -TGAAAAACTAGTGTAAAAGGTTGTGGTTGAGCCT
3419517 TGAAAAAC
1 TGAAAAAC
3419525 CACTTTGGGT
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
31 13 0.23
32 9 0.16
33 4 0.07
34 17 0.30
35 13 0.23
ACGTcount: A:0.32, C:0.10, G:0.26, T:0.31
Consensus pattern (34 bp):
TGAAAAACTAGTGTAAAAGGTTGTGGTTGAGCCT
Found at i:3421319 original size:23 final size:24
Alignment explanation
Indices: 3421283--3421328 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
3421273 ATGAAATCAA
3421283 GTTTTCTTCACTTTCCTT-TCCAT
1 GTTTTCTTCACTTTCCTTCTCCAT
** *
3421306 GTTTTCTTTTCTTTTCTTCTCCA
1 GTTTTCTTCACTTTCCTTCTCCA
3421329 AACTTCTTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.07, C:0.28, G:0.04, T:0.61
Consensus pattern (24 bp):
GTTTTCTTCACTTTCCTTCTCCAT
Found at i:3445092 original size:22 final size:22
Alignment explanation
Indices: 3445049--3445115 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
3445039 TTAGATTGGT
3445049 ATCAGAGCTTTTGGTTTTTAAAG
1 ATCAGAGCTTTTGG-TTTTAAAG
*
3445072 GTCAGAGCTTTTGGTTTTAAAG
1 ATCAGAGCTTTTGGTTTTAAAG
* *
3445094 ATCAGAGTTTTTGGGTTTAAAG
1 ATCAGAGCTTTTGGTTTTAAAG
3445116 TTGTTTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 27 0.68
23 13 0.32
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.42
Consensus pattern (22 bp):
ATCAGAGCTTTTGGTTTTAAAG
Found at i:3445195 original size:5 final size:5
Alignment explanation
Indices: 3445155--3445194 Score: 53
Period size: 5 Copynumber: 8.0 Consensus size: 5
3445145 CCCCAAGTCC
** *
3445155 AGTTA AGTTA AAATA AGTTA AGTTA AGTTA AGTTA GGTTA
1 AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA AGTTA
3445195 GATTGAATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.20, T:0.38
Consensus pattern (5 bp):
AGTTA
Found at i:3449289 original size:2 final size:2
Alignment explanation
Indices: 3449282--3449310 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3449272 GCATAAAATA
3449282 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3449311 CACCATTGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3449564 original size:34 final size:33
Alignment explanation
Indices: 3449526--3449618 Score: 150
Period size: 34 Copynumber: 2.7 Consensus size: 33
3449516 CCATTTAAGG
3449526 GCTGGTTTTGGAGGCTAAATAGTGCCATTTTTTT
1 GCTGGTTTTGGAGGCTAAA-AGTGCCATTTTTTT
3449560 GCTGGTTTTGGAGGCTGAAAAGTGCCATTTTTTT
1 GCTGGTTTTGGAGGCT-AAAAGTGCCATTTTTTT
*
3449594 GCTGGTTTTGGAGGCCAAAAAGTGC
1 GCTGGTTTTGGAGG-CTAAAAGTGC
3449619 AAAATTTTGC
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
34 52 0.93
35 4 0.07
ACGTcount: A:0.19, C:0.13, G:0.30, T:0.38
Consensus pattern (33 bp):
GCTGGTTTTGGAGGCTAAAAGTGCCATTTTTTT
Found at i:3449755 original size:35 final size:35
Alignment explanation
Indices: 3449710--3449796 Score: 117
Period size: 34 Copynumber: 2.5 Consensus size: 35
3449700 AGGGAAAGGT
*
3449710 GCAGCTTAGCTGCTGAAATTTT-AAGGAAAAATAAA
1 GCAGCTTAGCTGCTGAAATTTTGAAGCAAAAAT-AA
*
3449745 GCAGCATAGCTGCTG--ATTTTGAAGCAAAAATAA
1 GCAGCTTAGCTGCTGAAATTTTGAAGCAAAAATAA
3449778 GCAGCCTTAGCTGCTGAAA
1 GCAG-CTTAGCTGCTGAAA
3449797 AATTAAAAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
33 11 0.24
34 19 0.42
35 14 0.31
36 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (35 bp):
GCAGCTTAGCTGCTGAAATTTTGAAGCAAAAATAA
Found at i:3449941 original size:5 final size:5
Alignment explanation
Indices: 3449931--3449989 Score: 93
Period size: 5 Copynumber: 11.8 Consensus size: 5
3449921 GAGAAAGAAA
*
3449931 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA- AAAGAG AAAAG AAACG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA-AG AAAAG AAAAG
3449981 AAAAG AAAA
1 AAAAG AAAA
3449990 TAACAAGGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
4 3 0.06
5 44 0.88
6 3 0.06
ACGTcount: A:0.80, C:0.02, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:3450080 original size:25 final size:24
Alignment explanation
Indices: 3450024--3450080 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
3450014 AACAAGCAAC
*
3450024 AAAATGTACATGGTCTAATAAAGA
1 AAAATGGACATGGTCTAATAAAGA
3450048 AAATATGGACATGGTCTAATTAAA-A
1 AAA-ATGGACATGGTCTAA-TAAAGA
3450073 AGAAATGG
1 A-AAATGG
3450081 GAGAAGTCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 3 0.10
25 20 0.69
26 6 0.21
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (24 bp):
AAAATGGACATGGTCTAATAAAGA
Found at i:3451779 original size:372 final size:373
Alignment explanation
Indices: 3451073--3451823 Score: 1100
Period size: 372 Copynumber: 2.0 Consensus size: 373
3451063 TTCACGTCAT
* ** * * *
3451073 GCCGAACCACTTTGTGATGATGAACTCCGCTAACACCAAGGAATGGCTATGTTTTTCAAACTAAA
1 GCCGAACCACCTCATGATGAGGAACTCAGCTAACACCAAGGAATGACTATGTTTTTCAAACTAAA
* **
3451138 AATATGTTTTACGTGTATACAAAATTTTAACAGCCTTGGCGGGCTTGAGTGTACGCCTCTAATCA
66 AATATGTTTTACGTGTATACAAAATTTTAACAACCTTGGCGGGCTCAAGTGTACGCCTCTAATCA
* *
3451203 AGGTGTCGTCAAATACTATTTGATGGCATGAGCCAAATGTTTATAGAAGTCATTAGCTTAAATGA
131 AGGTGTCATCAAATACTATTTGAT-GC---AG---AATGTTTATAGAAGTCATAAGCTTAAATGA
* *
3451268 GAAATTAAATGAAATACAACCATTTGCATGGGTTGGGATAAATTTTTAAATTGTGAAATACTTAA
189 GAAATTAAATGAAATACAACCATTTGCATGGGTTGGGATAAATTTTCAAATTATGAAATACTTAA
*
3451333 AAATGATGGGATATTTTAATTGTCTCATTTTACTCAGCTTTAGCTAATTTAAATGATGTTTGTTT
254 AAATGATGGGAAATTTTAATTGTCTCATTTTACTCAGCTTTAGCTAATTTAAATGATGTTTGTTT
*
3451398 ACTCACTGGGATTTTATAATCTCACCACCCTCCTTTCCACCCATTTCAGGCTNCAC
319 ACTCACTGGGATTTTATAATCTCACCACCCTCATTTCCACCCATTTCAGGCT-CAC
* *
3451454 GCCGAACCACCTCATGATGAGGAACTCAGCTAACGCCAAGGAATGACTGTGTTTTTCAAACTAAA
1 GCCGAACCACCTCATGATGAGGAACTCAGCTAACACCAAGGAATGACTATGTTTTTCAAACTAAA
* * *
3451519 AATATGTTTTACGTGTATACGAAACTTTTTAACAACCTTGGTGGGCTCAAGTGTACGCCTCTGAT
66 AATATGTTTTACGTGTATAC-AAA-ATTTTAACAACCTTGGCGGGCTCAAGTGTACGCCTCTAAT
* *
3451584 CAAGGTGTCATCGAGTACTATTTGAT-C-G-ATGTTTAT-GAAAGTCATAAGCCTT-AATGAGAA
129 CAAGGTGTCATCAAATACTATTTGATGCAGAATGTTTATAG-AAGTCATAAG-CTTAAATGAGAA
* *
3451644 ATTAAATGAAATACAACCGTTTGCATGGGTTGGGATGAATTTTCAAATTATGAAATACTT-AAAA
192 ATTAAATGAAATACAACCATTTGCATGGGTTGGGATAAATTTTCAAATTATGAAATACTTAAAAA
* * *
3451708 TGATGGGAAATTTTAATTGTCTCCTTTTACTCGGCTTTAGCTGATTTAAATGATGTTTGTTTACT
257 TGATGGGAAATTTTAATTGTCTCATTTTACTCAGCTTTAGCTAATTTAAATGATGTTTGTTTACT
*
3451773 CACTGGGATTTTATAATCTCACCACCCTCATTTTCACCCATTTCAGGCTCA
322 CACTGGGATTTTATAATCTCACCACCCTCATTTCCACCCATTTCAGGCTCA
3451824 GAGTAGGCTG
Statistics
Matches: 338, Mismatches: 28, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
371 2 0.01
372 113 0.33
373 81 0.24
374 3 0.01
377 1 0.00
381 78 0.23
382 3 0.01
383 57 0.17
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (373 bp):
GCCGAACCACCTCATGATGAGGAACTCAGCTAACACCAAGGAATGACTATGTTTTTCAAACTAAA
AATATGTTTTACGTGTATACAAAATTTTAACAACCTTGGCGGGCTCAAGTGTACGCCTCTAATCA
AGGTGTCATCAAATACTATTTGATGCAGAATGTTTATAGAAGTCATAAGCTTAAATGAGAAATTA
AATGAAATACAACCATTTGCATGGGTTGGGATAAATTTTCAAATTATGAAATACTTAAAAATGAT
GGGAAATTTTAATTGTCTCATTTTACTCAGCTTTAGCTAATTTAAATGATGTTTGTTTACTCACT
GGGATTTTATAATCTCACCACCCTCATTTCCACCCATTTCAGGCTCAC
Found at i:3454241 original size:1 final size:1
Alignment explanation
Indices: 3454237--3454284 Score: 69
Period size: 1 Copynumber: 48.0 Consensus size: 1
3454227 TTTTTCCATC
* * *
3454237 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTTTTTGTTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3454285 CTAAACCAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.02, C:0.00, G:0.04, T:0.94
Consensus pattern (1 bp):
T
Found at i:3454750 original size:5 final size:6
Alignment explanation
Indices: 3454732--3454757 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3454722 TGGTGGGTTA
3454732 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
3454758 TTGGAGCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:3456201 original size:24 final size:21
Alignment explanation
Indices: 3456159--3456203 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 21
3456149 AGATTCTTCA
*
3456159 TTTTCTATTTTTTCTTATTGT
1 TTTTCTATTTTTTATTATTGT
3456180 TTTTGCTATTTTTTTATGTATTGT
1 TTTT-CTA-TTTTTTAT-TATTGT
3456204 GGTTAATGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 3 0.15
23 7 0.35
24 6 0.30
ACGTcount: A:0.11, C:0.07, G:0.09, T:0.73
Consensus pattern (21 bp):
TTTTCTATTTTTTATTATTGT
Found at i:3457087 original size:94 final size:94
Alignment explanation
Indices: 3456937--3457194 Score: 358
Period size: 94 Copynumber: 2.7 Consensus size: 94
3456927 CACGTCAACG
* * * * * * *
3456937 TTCAAAGTTAGTGAGATGCCATGGAGGGAATCTATGACATG-TCAGTGTTAAGAGTTGGTGACAC
1 TTCAGAGTTAGTGAGACGCCATGGAGGGAATCTGTGACACGCT-AGAGTTCAGAGTTGGTGACAT
3457001 GCCATGGTA-GGAATCTGTGACACGCCAGCA
65 GCCATGG-AGGGAATCTGTGACACGCCAGCA
* * *
3457031 TTCAGAGTTGGTGAGACACCATGGAGGGAATCTGTGACACGCTAGAGTTCAGAGTTGGTAACATG
1 TTCAGAGTTAGTGAGACGCCATGGAGGGAATCTGTGACACGCTAGAGTTCAGAGTTGGTGACATG
* * *
3457096 GCATGGAGGGAATCTGTGACACGCTAGCG
66 CCATGGAGGGAATCTGTGACACGCCAGCA
*
3457125 TTCAGAGTTCGTGAGACGCCATGGAGGGAATCTGTGACACGCTAGAGTTCAGAGTTGGTGACATG
1 TTCAGAGTTAGTGAGACGCCATGGAGGGAATCTGTGACACGCTAGAGTTCAGAGTTGGTGACATG
3457190 CCATG
66 CCATG
3457195 TTTAGAGTGT
Statistics
Matches: 145, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
93 1 0.01
94 143 0.99
95 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (94 bp):
TTCAGAGTTAGTGAGACGCCATGGAGGGAATCTGTGACACGCTAGAGTTCAGAGTTGGTGACATG
CCATGGAGGGAATCTGTGACACGCCAGCA
Found at i:3457208 original size:23 final size:23
Alignment explanation
Indices: 3457182--3457257 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
3457172 TTCAGAGTTG
*
3457182 GTGACATGCCATGTTTAGAGTGT
1 GTGACACGCCATGTTTAGAGTGT
* * * **
3457205 GTGACACGACATTGCTTAAACAGT
1 GTGACACGCCA-TGTTTAGAGTGT
3457229 -TGACACGCCATGGTTTAGAGTGT
1 GTGACACGCCAT-GTTTAGAGTGT
3457252 GTGACA
1 GTGACA
3457258 TGGCATTGAA
Statistics
Matches: 39, Mismatches: 11, Indels: 5
0.71 0.20 0.09
Matches are distributed among these distances:
22 1 0.03
23 25 0.64
24 13 0.33
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.29
Consensus pattern (23 bp):
GTGACACGCCATGTTTAGAGTGT
Found at i:3457208 original size:94 final size:93
Alignment explanation
Indices: 3456921--3457212 Score: 334
Period size: 94 Copynumber: 3.1 Consensus size: 93
3456911 TGTGACAAAG
* * * * * * * *
3456921 CTGTTACACGTCAACGTTCAAAGTTAGTGAGATGCCATGGAGGGAATCTATGACATG-TCAGTGT
1 CTGTGACACGCCAGCGTTCAGAGTTAGTGAGACGCCATGGAGGGAATCTGTGACACGCT-AGAGT
* * *
3456985 TAAGAGTTGGTGACACGCCATGGTAGGAAT
65 TCAGAGTTGGTGACATGCCATGATA-GAAT
* * *
3457015 CTGTGACACGCCAGCATTCAGAGTTGGTGAGACACCATGGAGGGAATCTGTGACACGCTAGAGTT
1 CTGTGACACGCCAGCGTTCAGAGTTAGTGAGACGCCATGGAGGGAATCTGTGACACGCTAGAGTT
* * **
3457080 CAGAGTTGGTAACATGGCATGGAGGGAAT
66 CAGAGTTGGTGACATGCCAT-GATAGAAT
* *
3457109 CTGTGACACGCTAGCGTTCAGAGTTCGTGAGACGCCATGGAGGGAATCTGTGACACGCTAGAGTT
1 CTGTGACACGCCAGCGTTCAGAGTTAGTGAGACGCCATGGAGGGAATCTGTGACACGCTAGAGTT
* *
3457174 CAGAGTTGGTGACATGCCATGTTTAGAGT
66 CAGAGTTGGTGACATGCCATG-ATAGAAT
*
3457203 GTGTGACACG
1 CTGTGACACG
3457213 ACATTGCTTA
Statistics
Matches: 166, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
93 1 0.01
94 163 0.98
95 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (93 bp):
CTGTGACACGCCAGCGTTCAGAGTTAGTGAGACGCCATGGAGGGAATCTGTGACACGCTAGAGTT
CAGAGTTGGTGACATGCCATGATAGAAT
Found at i:3457212 original size:47 final size:47
Alignment explanation
Indices: 3456936--3457194 Score: 308
Period size: 47 Copynumber: 5.5 Consensus size: 47
3456926 ACACGTCAAC
* * * * * *
3456936 GTTCAAAGTTAGTGAGATGCCATGGAGGGAATCTATGACATG-TCAGT
1 GTTCAGAGTTGGTGACATGCCATGGAGGGAATCTGTGACACGCT-AGA
* * *
3456983 GTTAAGAGTTGGTGACACGCCATGGTA-GGAATCTGTGACACGCCAGCA
1 GTTCAGAGTTGGTGACATGCCATGG-AGGGAATCTGTGACACGCTAG-A
* **
3457031 -TTCAGAGTTGGTGAGACACCATGGAGGGAATCTGTGACACGCTAGA
1 GTTCAGAGTTGGTGACATGCCATGGAGGGAATCTGTGACACGCTAGA
* * *
3457077 GTTCAGAGTTGGTAACATGGCATGGAGGGAATCTGTGACACGCTAGC
1 GTTCAGAGTTGGTGACATGCCATGGAGGGAATCTGTGACACGCTAGA
* * *
3457124 GTTCAGAGTTCGTGAGACGCCATGGAGGGAATCTGTGACACGCTAGA
1 GTTCAGAGTTGGTGACATGCCATGGAGGGAATCTGTGACACGCTAGA
3457171 GTTCAGAGTTGGTGACATGCCATG
1 GTTCAGAGTTGGTGACATGCCATG
3457195 TTTAGAGTGT
Statistics
Matches: 179, Mismatches: 28, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
46 2 0.01
47 176 0.98
48 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (47 bp):
GTTCAGAGTTGGTGACATGCCATGGAGGGAATCTGTGACACGCTAGA
Found at i:3457245 original size:47 final size:47
Alignment explanation
Indices: 3457183--3457335 Score: 172
Period size: 47 Copynumber: 3.4 Consensus size: 47
3457173 TCAGAGTTGG
* * *
3457183 TGACATGCCAT-GTTTAGAGTGTGTGACACGACATTGCTTAAACAGT
1 TGACACGCCATGGTTTAGAGTGTGTGACATGGCATTGCTTAAACAGT
*
3457229 TGACACGCCATGGTTTAGAGTGTGTGACATGGCATTG---AAA-AGC
1 TGACACGCCATGGTTTAGAGTGTGTGACATGGCATTGCTTAAACAGT
* * * *
3457272 TGATACGCCATGGTTTAAAGTGTGTGAGATGGCATTGCTTGAACAGT
1 TGACACGCCATGGTTTAGAGTGTGTGACATGGCATTGCTTAAACAGT
* **
3457319 TGAGACATCATGGTTTA
1 TGACACGCCATGGTTTA
3457336 AAATAGAGAG
Statistics
Matches: 90, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
43 36 0.40
44 3 0.03
46 12 0.13
47 39 0.43
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (47 bp):
TGACACGCCATGGTTTAGAGTGTGTGACATGGCATTGCTTAAACAGT
Found at i:3457294 original size:43 final size:45
Alignment explanation
Indices: 3457183--3457308 Score: 150
Period size: 43 Copynumber: 2.8 Consensus size: 45
3457173 TCAGAGTTGG
* * * *
3457183 TGACATGCCAT-GTTTAGAGTGTGTGACACGACATTGCTTAAACAGT
1 TGACACGCCATGGTTTAGAGTGTGTGACATGGCATTG--TAAACAGC
3457229 TGACACGCCATGGTTTAGAGTGTGTGACATGGCATTG-AAA-AGC
1 TGACACGCCATGGTTTAGAGTGTGTGACATGGCATTGTAAACAGC
* * *
3457272 TGATACGCCATGGTTTAAAGTGTGTGAGATGGCATTG
1 TGACACGCCATGGTTTAGAGTGTGTGACATGGCATTG
3457309 CTTGAACAGT
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
43 36 0.50
44 3 0.04
46 10 0.14
47 23 0.32
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (45 bp):
TGACACGCCATGGTTTAGAGTGTGTGACATGGCATTGTAAACAGC
Found at i:3457846 original size:31 final size:31
Alignment explanation
Indices: 3457799--3457969 Score: 218
Period size: 31 Copynumber: 5.5 Consensus size: 31
3457789 GTCAGTGTTA
*
3457799 GCGTGTGACAACATTTGACTCGATATGCATG
1 GCGTGTCACAACATTTGACTCGATATGCATG
*
3457830 GCGTGTCACAATATTTGACTCGATATGCATG
1 GCGTGTCACAACATTTGACTCGATATGCATG
*
3457861 GCGTGTCACAACATTTTACTCGATATGCATG
1 GCGTGTCACAACATTTGACTCGATATGCATG
* * * * *
3457892 ACGTGTCACAATATTTTACTTGTTATGCATG
1 GCGTGTCACAACATTTGACTCGATATGCATG
* *
3457923 GCGTGTCACAACATTTTG-CTTGCTATGCATG
1 GCGTGTCACAACA-TTTGACTCGATATGCATG
* *
3457954 GCATGTCACATCATTT
1 GCGTGTCACAACATTT
3457970 ATTCCTTAAT
Statistics
Matches: 125, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
30 3 0.02
31 119 0.95
32 3 0.02
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (31 bp):
GCGTGTCACAACATTTGACTCGATATGCATG
Found at i:3457897 original size:62 final size:62
Alignment explanation
Indices: 3457799--3457963 Score: 240
Period size: 62 Copynumber: 2.7 Consensus size: 62
3457789 GTCAGTGTTA
* *
3457799 GCGTGTGACAACATTTGACTCGATATGCATGGCGTGTCACAATATTTGACTCGATATGCATG
1 GCGTGTCACAACATTTTACTCGATATGCATGGCGTGTCACAATATTTGACTCGATATGCATG
* * * *
3457861 GCGTGTCACAACATTTTACTCGATATGCATGACGTGTCACAATATTTTACTTGTTATGCATG
1 GCGTGTCACAACATTTTACTCGATATGCATGGCGTGTCACAATATTTGACTCGATATGCATG
* * * *
3457923 GCGTGTCACAACATTTTGCTTGCTATGCATGGCATGTCACA
1 GCGTGTCACAACATTTTACTCGATATGCATGGCGTGTCACA
3457964 TCATTTATTC
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 92 1.00
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (62 bp):
GCGTGTCACAACATTTTACTCGATATGCATGGCGTGTCACAATATTTGACTCGATATGCATG
Found at i:3458733 original size:31 final size:31
Alignment explanation
Indices: 3458684--3458982 Score: 400
Period size: 31 Copynumber: 9.6 Consensus size: 31
3458674 GTCAGCGTTA
*
3458684 GCGTGTGACAACATTTTACTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * *
3458715 GCGTGTCAGAACAATTTACTTATTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * *
3458746 GCATGTCACAACCTTTAACTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * * * *
3458777 GCATGTCAGAACATTTTGCTTATTATCCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* *
3458808 GCATGTCACAACATTTTGCTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* *
3458839 GCGTGTCAAAACATTTTGCTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
* * *
3458870 GCGTGTCATAACGTTTTACTTGTTATCCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
**
3458901 GCGTGTCACAATGTTTTACTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
*
3458932 GTGTGTCACAACATTTTACTTGTTATGCATG
1 GCGTGTCACAACATTTTACTTGTTATGCATG
3458963 GCGTGTCACAACATTTTACT
1 GCGTGTCACAACATTTTACT
3458983 GGTTGTGGTT
Statistics
Matches: 236, Mismatches: 32, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 236 1.00
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.39
Consensus pattern (31 bp):
GCGTGTCACAACATTTTACTTGTTATGCATG
Found at i:3460547 original size:17 final size:16
Alignment explanation
Indices: 3460527--3460599 Score: 62
Period size: 16 Copynumber: 4.6 Consensus size: 16
3460517 TGTACATTTT
*
3460527 TTTTGTATACAGAATTA
1 TTTT-TATACATAATTA
3460544 TTTTTAT--ATAATTA
1 TTTTTATACATAATTA
* *
3460558 ATTTTATACATAATTT
1 TTTTTATACATAATTA
*
3460574 TTTTGTATACACAATT-
1 TTTT-TATACATAATTA
*
3460590 TATTTATACA
1 TTTTTATACA
3460600 ATTCATTGTA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
14 12 0.26
15 6 0.13
16 15 0.32
17 14 0.30
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (16 bp):
TTTTTATACATAATTA
Found at i:3460570 original size:16 final size:16
Alignment explanation
Indices: 3460532--3460658 Score: 59
Period size: 16 Copynumber: 8.1 Consensus size: 16
3460522 ATTTTTTTTG
*
3460532 TATACAGAATT-ATTT
1 TATACATAATTAATTT
*
3460547 T-TATATAATTAATTT
1 TATACATAATTAATTT
**
3460562 TATACATAATTTTTTT
1 TATACATAATTAATTT
* *
3460578 GTATACACAATTTA-TT
1 -TATACATAATTAATTT
* *
3460594 TATAC--AATTCATTG
1 TATACATAATTAATTT
*
3460608 TATACAGAATTAATTCT
1 TATACATAATTAATT-T
** *
3460625 TATTGTATACA-CAATTT
1 TA-TACATA-ATTAATTT
*
3460642 TTTACATAATTAATTT
1 TATACATAATTAATTT
3460658 T
1 T
3460659 TTGCCTATAC
Statistics
Matches: 83, Mismatches: 19, Indels: 19
0.69 0.16 0.16
Matches are distributed among these distances:
13 5 0.06
14 13 0.16
15 12 0.14
16 30 0.36
17 15 0.18
18 7 0.08
19 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.50
Consensus pattern (16 bp):
TATACATAATTAATTT
Found at i:3460612 original size:46 final size:47
Alignment explanation
Indices: 3460524--3460656 Score: 135
Period size: 46 Copynumber: 2.7 Consensus size: 47
3460514 GTCTGTACAT
* * *
3460524 TTTTTTTGTATACAGAATTATTTTTATATAATTAATTTTATAC-A-TAA
1 TTTTTTTGTATACACAA-T-TTTTTATACAATTAATTGTATACAATTAA
*
3460571 TTTTTTTGTATACACAATTTATTTATACAATTCATTGTATACAGAATTAA
1 TTTTTTTGTATACACAATTT-TTTATACAATTAATTGTATAC--AATTAA
* * *
3460621 TTCTTATTGTATACACAATTTTTTACATAATTAATT
1 TT-TTTTTGTATACACAATTTTTTATACAATTAATT
3460657 TTTTGCCTAT
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
45 2 0.03
46 19 0.26
47 16 0.22
49 1 0.01
50 17 0.24
51 17 0.24
ACGTcount: A:0.35, C:0.08, G:0.05, T:0.52
Consensus pattern (47 bp):
TTTTTTTGTATACACAATTTTTTATACAATTAATTGTATACAATTAA
Found at i:3460654 original size:34 final size:33
Alignment explanation
Indices: 3460610--3460674 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
3460600 ATTCATTGTA
3460610 TACAGAATTAATTCTTATTG-TATACACAATTTTT
1 TACAGAATTAATT-TT-TTGCTATACACAATTTTT
*
3460644 TACATAATTAATTTTTTGCCTATACACAATT
1 TACAGAATTAATTTTTTG-CTATACACAATT
3460675 AATTTTATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 3 0.11
33 2 0.07
34 23 0.82
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (33 bp):
TACAGAATTAATTTTTTGCTATACACAATTTTT
Found at i:3461715 original size:31 final size:31
Alignment explanation
Indices: 3461679--3461940 Score: 344
Period size: 31 Copynumber: 8.5 Consensus size: 31
3461669 TGGCATGTTA
* * *
3461679 GTGTGACAACATTTCACTTGATATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* * * *
3461710 ATGTGACAACATTTGACTTGTTATGCATGAC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* *
3461741 GTGTCAGAACATTTTACTTGTTATGCATGAC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* * * *
3461772 GTGTCACAAAAATTTACGTGTTATGCATGCC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* * *
3461803 ATGTCACAGCATTTTACTTGCTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
* *
3461834 GTGTCAGAACATTTTACTTGTTATGCACGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
*
3461865 GTGTCACAACATTTTACTTGTTATGCATGGT
1 GTGTCACAACATTTTACTTGTTATGCATGGC
*
3461896 GTGTCACAACATTTTGCTTGTTATGCATGGC
1 GTGTCACAACATTTTACTTGTTATGCATGGC
3461927 GTGTCACAACATTT
1 GTGTCACAACATTT
3461941 ATTCCTTATT
Statistics
Matches: 201, Mismatches: 30, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 201 1.00
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (31 bp):
GTGTCACAACATTTTACTTGTTATGCATGGC
Found at i:3466257 original size:31 final size:31
Alignment explanation
Indices: 3466209--3466451 Score: 285
Period size: 31 Copynumber: 7.8 Consensus size: 31
3466199 TTTGTCAGTC
* *
3466209 ATGTTGTTACACACCATGCATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
* * *
3466240 ATGTAGTAACACGCCATGTATAAAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
* *
3466271 ATG-TGCTAACACGCCATGCAAATAACATAAA
1 ATGTTG-TAACACGCCATGCATATAACGTAAA
*
3466302 ATGTTGTAACACGCCATGCATATAATAG-AAA
1 ATGTTGTAACACGCCATGCATATAA-CGTAAA
* * * *
3466333 ATG-CGATAACACACCATGCATATAATGTTAA
1 ATGTTG-TAACACGCCATGCATATAACGTAAA
** * *
3466364 ATGCAGTAACACGCCATGCATATAACATTAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
3466395 ATGTTGTAACACGCCATGCATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAACGTAAA
*
3466426 ATATTGTAACACGCCATGCATATAAC
1 ATGTTGTAACACGCCATGCATATAAC
3466452 CAATGTCGTG
Statistics
Matches: 180, Mismatches: 26, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
30 3 0.02
31 174 0.97
32 3 0.02
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.25
Consensus pattern (31 bp):
ATGTTGTAACACGCCATGCATATAACGTAAA
Found at i:3478802 original size:254 final size:254
Alignment explanation
Indices: 3478353--3478859 Score: 768
Period size: 254 Copynumber: 2.0 Consensus size: 254
3478343 CCTATAATTT
* * * * *
3478353 AAATTAAATAAAATCATTATCAAAACACTCTTTCAAAATATACACAAATTAAAAGGATGAAAGTA
1 AAATTAAATAAAATCATAATCAAAACACTCTGTCAAAATATACAAAAATTAAAAAGATGAAAGCA
* *
3478418 AGCCAAAATCTGCTTTGATACCATTGTTGGTAGGTGGGCTTACCTTTTCAGATAAATAATTCACT
66 AGCCAAAATCTGCTTTGACACCACTGTTGGTAGGTGGGCTTACCTTTTCAGATAAATAATTCACT
* * * * *
3478483 CCCTTTCTGATTGAGGAAGCTGGCCTTACAAATTCTCCTTCGTGCACATAATAATTTCTTCACTC
131 CCCTTTCTAATCGAAGAAGCTGACCTTACAAATTCTCCTTCGTGCACACAATAATTTCTTCACTC
* *
3478548 TCATTGTTATGGAGTGGCTACTAGAGTCCTCCACAAGGAATTACACGTTCCAAAACCCA
196 TCATTGTTAAGGAGTGGCTACTAGAGTCCTCCACAAAGAATTACACGTTCCAAAACCCA
3478607 AAATTAAATAAAATCATAATCAAAACACTCTGTCAAAATATACAAAAATTAAAAAGATGAAAGCA
1 AAATTAAATAAAATCATAATCAAAACACTCTGTCAAAATATACAAAAATTAAAAAGATGAAAGCA
*
3478672 AGCCAAAA-CTTGCTTTGACACCACTGTTGGTAGGTGGGCTTACCTTCTT-AGATAAATATTTCA
66 AGCCAAAATC-TGCTTTGACACCACTGTTGGTAGGTGGGCTTACCTT-TTCAGATAAATAATTCA
* * * *
3478735 CTCCTTTTCTAATCGAATAAGCTTACCTTACAAA-TCTTCCTTCTTGCACACAATAATTTCTTCA
129 CTCCCTTTCTAATCGAAGAAGCTGACCTTACAAATTC-TCCTTCGTGCACACAATAATTTCTTCA
* * *
3478799 CTCTCGTTGTTAAGGAGTGGCTACTAGAGTCCTTCGCAAAGAATTACACGTTCCAAAACCC
193 CTCTCATTGTTAAGGAGTGGCTACTAGAGTCCTCCACAAAGAATTACACGTTCCAAAACCC
3478860 TCTGACCTTG
Statistics
Matches: 228, Mismatches: 22, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
253 3 0.01
254 223 0.98
255 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.30
Consensus pattern (254 bp):
AAATTAAATAAAATCATAATCAAAACACTCTGTCAAAATATACAAAAATTAAAAAGATGAAAGCA
AGCCAAAATCTGCTTTGACACCACTGTTGGTAGGTGGGCTTACCTTTTCAGATAAATAATTCACT
CCCTTTCTAATCGAAGAAGCTGACCTTACAAATTCTCCTTCGTGCACACAATAATTTCTTCACTC
TCATTGTTAAGGAGTGGCTACTAGAGTCCTCCACAAAGAATTACACGTTCCAAAACCCA
Found at i:3479056 original size:21 final size:20
Alignment explanation
Indices: 3479026--3479104 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 20
3479016 GAGATAGGAT
3479026 ATTATATTTAAATTTAAACAA
1 ATTA-ATTTAAATTTAAACAA
* **
3479047 ATTAATTTTAAATGTAATTAA
1 ATTAA-TTTAAATTTAAACAA
* *
3479068 TCTTTATTTAAATTTAAACAA
1 -ATTAATTTAAATTTAAACAA
3479089 ATTAAATTTAAATTTA
1 ATT-AATTTAAATTTA
3479105 TCCTATCTCA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
20 3 0.07
21 39 0.87
22 3 0.07
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (20 bp):
ATTAATTTAAATTTAAACAA
Found at i:3484910 original size:47 final size:47
Alignment explanation
Indices: 3484785--3484965 Score: 249
Period size: 47 Copynumber: 3.9 Consensus size: 47
3484775 TGCATACAAG
* * *
3484785 TTTACTTAACAAATAAGTAAAATAATTGCACTATGCATTTTATAAAT
1 TTTACTTAACAAATAAGTAAAATAAATACATTATGCATTTTATAAAT
* ** *
3484832 TTTGCCTTTTCAAATAAGTAAAATAATTACATTATGCATTTTATAAAT
1 TTT-ACTTAACAAATAAGTAAAATAAATACATTATGCATTTTATAAAT
* *
3484880 TTTACGTAACAAATAAGTAAAATAAATACATCATGCATTTTATAAAT
1 TTTACTTAACAAATAAGTAAAATAAATACATTATGCATTTTATAAAT
*
3484927 TTTACCTAACAAATAAGTAAAATAAATACA-TA-GCATTTT
1 TTTACTTAACAAATAAGTAAAATAAATACATTATGCATTTT
3484966 TACAACATAT
Statistics
Matches: 120, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
45 7 0.06
46 1 0.01
47 70 0.58
48 42 0.35
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (47 bp):
TTTACTTAACAAATAAGTAAAATAAATACATTATGCATTTTATAAAT
Done.