Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 10 of 161
Found at i:3369727 original size:27 final size:27
Alignment explanation
Indices: 3369646--3369734 Score: 108
Period size: 27 Copynumber: 3.3 Consensus size: 27
3369636 ATATTCGTCA
* * *
3369646 CTTTACCATACAAGGG-TATTACGGTCA
1 CTTTACCCTACAGGGGCT-TTACGGTCT
3369673 CTTTACCCTACAGGGGGCTTTACGGTCT
1 CTTTACCCTACA-GGGGCTTTACGGTCT
*
3369701 CTTTACCCTACAGGGGCTTTACAGTCT
1 CTTTACCCTACAGGGGCTTTACGGTCT
*
3369728 TTTTACC
1 CTTTACC
3369735 TAATAGGGGT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
27 31 0.56
28 23 0.42
29 1 0.02
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.34
Consensus pattern (27 bp):
CTTTACCCTACAGGGGCTTTACGGTCT
Found at i:3370017 original size:27 final size:27
Alignment explanation
Indices: 3369765--3370030 Score: 178
Period size: 27 Copynumber: 9.8 Consensus size: 27
3369755 TTTCATCCTA
* * * *
3369765 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTCGGTAATTTTACAAAC
* * **
3369792 CAATGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTCGGTAATTTTACAAAC
* ** * *
3369819 CAATGGTATTTCCATAATTTTTAGAAAGT
1 CAAGGGTATTTCGGTAA-TTTTACAAA-C
* * ** *
3369848 CAAGGGTATTTCTGTAACTTTGTAAAT
1 CAAGGGTATTTCGGTAATTTTACAAAC
* * *
3369875 TAGGGGTA-TTCTGGTAATTTTACAAAT
1 CAAGGGTATTTC-GGTAATTTTACAAAC
** *
3369902 TGAGGGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTCGGTAATTTTACAAAC
*
3369929 C-AGTGGTATTTTGGTAATTTTACAAAC
1 CAAG-GGTATTTCGGTAATTTTACAAAC
* * * *
3369956 TAGGGGTATTTTGGTAATTTTACAAATT
1 CAAGGGTATTTCGGTAATTTTACAAA-C
*
3369984 GAA-GGTATTTCGGTAATTTTACAAAC
1 CAAGGGTATTTCGGTAATTTTACAAAC
**
3370010 CAAGGGTATTTTAGTAATTTT
1 CAAGGGTATTTCGGTAATTTT
3370031 GTAAATCGAG
Statistics
Matches: 189, Mismatches: 42, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
26 7 0.04
27 150 0.79
28 18 0.10
29 14 0.07
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTCGGTAATTTTACAAAC
Found at i:3370042 original size:27 final size:27
Alignment explanation
Indices: 3369796--3370191 Score: 192
Period size: 27 Copynumber: 14.6 Consensus size: 27
3369786 ACAAACCAAT
* * * * *
3369796 GGTATTTCAGTAATTTTGTAAACCAAT
1 GGTATTTCGGTAATTTTATAAATCGAG
** * *
3369823 GGTATTTCCATAATTTTTAGAAAGTCAAG
1 GGTATTTCGGTAA-TTTTATAAA-TCGAG
* * * *
3369852 GGTATTTCTGTAACTTTGTAAAT-TAGG
1 GGTATTTCGGTAATTTTATAAATCGA-G
* *
3369879 GGTA-TTCTGGTAATTTTACAAATTGAG
1 GGTATTTC-GGTAATTTTATAAATCGAG
* * *
3369906 GGTATTTCGGTAATTTCACAAA-CCAG
1 GGTATTTCGGTAATTTTATAAATCGAG
* * *
3369932 TGGTATTTTGGTAATTTTACAAA-CTAGG
1 -GGTATTTCGGTAATTTTATAAATCGA-G
* * * *
3369960 GGTATTTTGGTAATTTTACAAATTGAA
1 GGTATTTCGGTAATTTTATAAATCGAG
* * *
3369987 GGTATTTCGGTAATTTTACAAACCAAG
1 GGTATTTCGGTAATTTTATAAATCGAG
** *
3370014 GGTATTTTAGTAATTTTGTAAATCGAG
1 GGTATTTCGGTAATTTTATAAATCGAG
*** * ** *
3370041 GGTAAAACAGTAAGGTTGTAAATCGAG
1 GGTATTTCGGTAATTTTATAAATCGAG
** *
3370068 GGTAAAAT-GGTAATTCTATAAATCGAG
1 GGT-ATTTCGGTAATTTTATAAATCGAG
*** * *
3370095 GGTAAAACGGTAATTCTGTAAATCGAG
1 GGTATTTCGGTAATTTTATAAATCGAG
*** *
3370122 GGTAAAACGGTAATTCTATAAATCGAG
1 GGTATTTCGGTAATTTTATAAATCGAG
* *
3370149 GGTACTTT-GGTAATTTTACAAATTGAG
1 GGTA-TTTCGGTAATTTTATAAATCGAG
* *
3370176 GGCATTTCAGTAATTT
1 GGTATTTCGGTAATTT
3370192 GGTAAACTAA
Statistics
Matches: 296, Mismatches: 60, Indels: 26
0.77 0.16 0.07
Matches are distributed among these distances:
26 12 0.04
27 248 0.84
28 22 0.07
29 14 0.05
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.36
Consensus pattern (27 bp):
GGTATTTCGGTAATTTTATAAATCGAG
Found at i:3370044 original size:81 final size:81
Alignment explanation
Indices: 3369848--3370042 Score: 270
Period size: 81 Copynumber: 2.4 Consensus size: 81
3369838 TTTAGAAAGT
* *
3369848 CAAGGGTATTTCTGTAACTTTGTAAAT-TAGGGGTATTCTGGTAATTTTACAAATTGAGGGTATT
1 CAAGGGTATTT-TGTAATTTTGTAAATCTAGGGGTATTCTGGTAATTTTACAAATTGAAGGTATT
3369912 TCGGTAATTTCACAAAC
65 TCGGTAATTTCACAAAC
** *
3369929 C-AGTGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAATTGAAGGTAT
1 CAAG-GGTATTTT-GTAATTTTGTAAATCTAGGGGTATTCTGGTAATTTTACAAATTGAAGGTAT
*
3369992 TTCGGTAATTTTACAAAC
64 TTCGGTAATTTCACAAAC
*
3370010 CAAGGGTATTTTAGTAATTTTGTAAATCGAGGG
1 CAAGGGTATTTT-GTAATTTTGTAAATCTAGGG
3370043 TAAAACAGTA
Statistics
Matches: 99, Mismatches: 10, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
80 3 0.03
81 89 0.90
82 7 0.07
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (81 bp):
CAAGGGTATTTTGTAATTTTGTAAATCTAGGGGTATTCTGGTAATTTTACAAATTGAAGGTATTT
CGGTAATTTCACAAAC
Found at i:3370080 original size:81 final size:81
Alignment explanation
Indices: 3369995--3370197 Score: 219
Period size: 81 Copynumber: 2.5 Consensus size: 81
3369985 AAGGTATTTC
* * * *
3369995 GGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACAGTAAGGT-TG
1 GGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTGTAAATCGAGGGTAAAACAGTAA-GTCTA
3370059 TAAATCGAGGGTAAAAT
65 TAAATCGAGGGTAAAAT
* * *** * * * *
3370076 GGTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTAT
1 GGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTGTAAATCGAGGGTAAAACAGTAAGTCTAT
***
3370141 AAATCGAGGGTACTTT
66 AAATCGAGGGTAAAAT
* * *
3370157 GGTAATTTTACAAATTGAGGGCATTTCAGTAATTTGGTAAA
1 GGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTGTAAA
3370198 CTAAAGTATT
Statistics
Matches: 95, Mismatches: 26, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
80 1 0.01
81 94 0.99
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (81 bp):
GGTAATTTTACAAATCGAGGGTATTTCAGTAATTTTGTAAATCGAGGGTAAAACAGTAAGTCTAT
AAATCGAGGGTAAAAT
Found at i:3375328 original size:21 final size:21
Alignment explanation
Indices: 3375298--3375338 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3375288 GTAATGTTGT
3375298 TTGGACTGAAGAACGCAGGGA
1 TTGGACTGAAGAACGCAGGGA
*
3375319 TTGGATTGAAGAACGCAGGG
1 TTGGACTGAAGAACGCAGGG
3375339 GCAACCTACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.12, G:0.39, T:0.17
Consensus pattern (21 bp):
TTGGACTGAAGAACGCAGGGA
Found at i:3378121 original size:19 final size:19
Alignment explanation
Indices: 3378071--3378123 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
3378061 TTTCGAAAAT
3378071 CAAAAAAAGAAAAAAACAAA
1 CAAAAAAA-AAAAAAACAAA
* *
3378091 CAGAAAAGAAAAAAACAAA
1 CAAAAAAAAAAAAAACAAA
3378110 -AAACAAAAAAAAAA
1 CAAA-AAAAAAAAAA
3378124 GAGAGAGAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 2 0.07
19 20 0.71
20 6 0.21
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (19 bp):
CAAAAAAAAAAAAAACAAA
Found at i:3379369 original size:206 final size:205
Alignment explanation
Indices: 3379002--3379379 Score: 569
Period size: 206 Copynumber: 1.8 Consensus size: 205
3378992 ATGACCGCAG
** * * *
3379002 CATAGAGATCTGGCCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGTAT
1 CATAGAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGATTTGGCATCCTTGTAC
* *
3379067 TTACAAGGAACAAATTGAAATCATAGCTAATTTAGCTTTCACGTGCTTACGCTGAAGCAAGTCTA
66 TTACAAGGAACAAATCGAAATCATAGCTAATTTAGCTTTCACGTGCTTACGCTGAAGCAAATCTA
3379132 AGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTTGACGG
131 AGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTTGACGG
3379197 AGGGCAGACA
196 AGGGCAGACA
* * *
3379207 CATAGCAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGGTTTGGTATCCTTGTG
1 CATAG-AGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGATTTGGCATCCTTGTA
* * * * * *
3379272 CTTACAAGGAGCAAATCGAAGA-CATAGCTGATTTGGTTTTCGCGTGCTTATGCTGAAGCAAATC
65 CTTACAAGGAACAAATCGAA-ATCATAGCTAATTTAGCTTTCACGTGCTTACGCTGAAGCAAATC
* *
3379336 TAAGATGATTTGGCATTTCTGTATTGTCAGAGAACAAATTGAAG
129 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAG
3379380 AAGCAGACTT
Statistics
Matches: 153, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
205 5 0.03
206 147 0.96
207 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (205 bp):
CATAGAGATCTAACCTTCAGATGATTAGACTGAAGCAGATCCAAGATGATTTGGCATCCTTGTAC
TTACAAGGAACAAATCGAAATCATAGCTAATTTAGCTTTCACGTGCTTACGCTGAAGCAAATCTA
AGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTTGACGG
AGGGCAGACA
Found at i:3381014 original size:26 final size:27
Alignment explanation
Indices: 3380985--3381057 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 27
3380975 CCTTTATCCC
*
3380985 TTTTAAAATTATTTATA-ACTTA-TTTA
1 TTTTAAAATTATATATATA-TTATTTTA
*
3381011 TTTT-AAATTGTATATATATTATTTTA
1 TTTTAAAATTATATATATATTATTTTA
* *
3381037 TTTTAATA-TATATATGTATTA
1 TTTTAAAATTATATATATATTA
3381058 GATATTATAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
25 13 0.33
26 24 0.62
27 2 0.05
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (27 bp):
TTTTAAAATTATATATATATTATTTTA
Found at i:3381125 original size:25 final size:24
Alignment explanation
Indices: 3381021--3381177 Score: 89
Period size: 25 Copynumber: 6.5 Consensus size: 24
3381011 TTTTAAATTG
* *
3381021 TATA-TATATTA-TTTTATTTTAA
1 TATATTATATTACTTATATTTTAT
* *
3381043 TATA-TATATGTA-TTAGATATTA-
1 TATATTATAT-TACTTATATTTTAT
3381065 TATATTATTATTTACTTATATTTTAT
1 TATATTA-TA-TTACTTATATTTTAT
3381091 TATATTATATTACTTCATATTTT-T
1 TATATTATATTACTT-ATATTTTAT
* *
3381115 CTAT-TTCATATTAATATATATTTTAA
1 -TATATT-ATATTACT-TATATTTTAT
* *
3381141 CATA-TATCAGTACTTAT-TATTTAT
1 TATATTAT-ATTACTTATAT-TTTAT
3381165 TATAATTATATTA
1 TAT-ATTATATTA
3381178 TTTTACATTT
Statistics
Matches: 106, Mismatches: 13, Indels: 29
0.72 0.09 0.20
Matches are distributed among these distances:
22 13 0.12
23 12 0.11
24 24 0.23
25 46 0.43
26 11 0.10
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (24 bp):
TATATTATATTACTTATATTTTAT
Found at i:3381214 original size:41 final size:41
Alignment explanation
Indices: 3381116--3381214 Score: 96
Period size: 41 Copynumber: 2.4 Consensus size: 41
3381106 CATATTTTTC
* * *
3381116 TATTTCATATTAATATATATTTTAACATATATCAGTACTTAT
1 TATTTCATATTATTATATATTTTAACATATAACAG-ACATAT
* *
3381158 TATTT-ATTATAATTATATTATTTT-ACATTTTAACA-ACATAT
1 TATTTCA-TATTATTATA-TATTTTAACA-TATAACAGACATAT
3381199 TATTTCATATTATTAT
1 TATTTCATATTATTAT
3381215 CATCTATTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
41 19 0.40
42 17 0.36
43 11 0.23
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.54
Consensus pattern (41 bp):
TATTTCATATTATTATATATTTTAACATATAACAGACATAT
Found at i:3381419 original size:21 final size:22
Alignment explanation
Indices: 3381385--3381428 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3381375 TATTTCAAAA
*
3381385 TTCATTATTAATT-ACTATGTT
1 TTCATTATTAATTAAATATGTT
3381406 TTCATGTATT-ATTAAATATGTT
1 TTCAT-TATTAATTAAATATGTT
3381428 T
1 T
3381429 ATTATCTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (22 bp):
TTCATTATTAATTAAATATGTT
Found at i:3389131 original size:66 final size:67
Alignment explanation
Indices: 3389002--3389131 Score: 174
Period size: 66 Copynumber: 1.9 Consensus size: 67
3388992 GGGATGTATC
*
3389002 CCATGTAGACAAGAGAGCTACGTGAGAGATAAATGTAGCTAGGTCGCATGAGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTAC--G-GAGATAAATG-AGCTAGGTCGCATGAGTGATACCAAGTGA
3389067 AGGACA
62 AGGACA
* *
3389073 CCATGTAGACAAGAGAGCTAC-GAGATAAATCG-GCTAGGTCGCATGAGTGGTACTAAGTG
1 CCATGTAGACAAGAGAGCTACGGAGATAAAT-GAGCTAGGTCGCATGAGTGATACCAAGTG
3389132 TTCACCATGT
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
66 24 0.44
67 9 0.16
68 1 0.02
71 21 0.38
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (67 bp):
CCATGTAGACAAGAGAGCTACGGAGATAAATGAGCTAGGTCGCATGAGTGATACCAAGTGAAGGA
CA
Found at i:3394931 original size:29 final size:28
Alignment explanation
Indices: 3394895--3394972 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
3394885 TCATGAGATT
3394895 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
3394925 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
3394952 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
3394973 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:3395190 original size:174 final size:174
Alignment explanation
Indices: 3394925--3395252 Score: 629
Period size: 174 Copynumber: 1.9 Consensus size: 174
3394915 AAATTGTACA
3394925 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
*
3394990 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCGA
3395055 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* *
3395099 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
3395164 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCGA
3395229 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
3395253 ACCTTGAGTT
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
174 151 1.00
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCGA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:3400003 original size:644 final size:644
Alignment explanation
Indices: 3398775--3400063 Score: 2578
Period size: 644 Copynumber: 2.0 Consensus size: 644
3398765 GCAGAATATC
3398775 ATATGTATGCAGTAGATATGCATGTCACATCCATAAAACTTACATTCAACACCTAAGGGTATTTT
1 ATATGTATGCAGTAGATATGCATGTCACATCCATAAAACTTACATTCAACACCTAAGGGTATTTT
3398840 AGTCATTTTCATCTTTAGGGGCATTTCGATAATTTTCCTATTATTACAATTTTCACTTACCTTGG
66 AGTCATTTTCATCTTTAGGGGCATTTCGATAATTTTCCTATTATTACAATTTTCACTTACCTTGG
3398905 CCCGTTAACAAATCCTGTGAGCTAAGATGAATGAATACTATGCACCAGGTAGGATTCCAGAGAAG
131 CCCGTTAACAAATCCTGTGAGCTAAGATGAATGAATACTATGCACCAGGTAGGATTCCAGAGAAG
3398970 AGGAGGTGAGTCATTAAGATTGCTTAAGTACCAACCTCTCCCTAGATCCAATCCTAGACATGCAT
196 AGGAGGTGAGTCATTAAGATTGCTTAAGTACCAACCTCTCCCTAGATCCAATCCTAGACATGCAT
3399035 ATACCTGTTGCCACACCTTAACCCTATGACTTGTCCACGGTCGCTGTAACACCCCAAACCCGGCC
261 ATACCTGTTGCCACACCTTAACCCTATGACTTGTCCACGGTCGCTGTAACACCCCAAACCCGGCC
3399100 CAGACGTTATGGCCGAATCTGGCGTGTTACATTGAAGTGTTTTAGAGAAAACCATGTTTTCATTG
326 CAGACGTTATGGCCGAATCTGGCGTGTTACATTGAAGTGTTTTAGAGAAAACCATGTTTTCATTG
3399165 AAAACTCTTCTTAAAAAAACCCTAATTAACTAAAAAAGAAACCTTTTAGTTACGAAAGCCTTGTT
391 AAAACTCTTCTTAAAAAAACCCTAATTAACTAAAAAAGAAACCTTTTAGTTACGAAAGCCTTGTT
3399230 TAAATCATTTGATATTTTTTTAAAAAAAATTAGTTGCGGAAACATAGAAAACATAATATAATTTA
456 TAAATCATTTGATATTTTTTTAAAAAAAATTAGTTGCGGAAACATAGAAAACATAATATAATTTA
3399295 AGAAATCTATGTTCAACTTCTCGTAATTACAATGAAAATAATAATAATAATTCAAGTAGTAATTG
521 AGAAATCTATGTTCAACTTCTCGTAATTACAATGAAAATAATAATAATAATTCAAGTAGTAATTG
3399360 AAAACCTTATTACAATCTGGTCTGAACACACTTAAAAAGAAATAAAAAATTAAATGCTT
586 AAAACCTTATTACAATCTGGTCTGAACACACTTAAAAAGAAATAAAAAATTAAATGCTT
3399419 ATATGTATGCAGTAGATATGCATGTCACATCCATAAAACTTACATTCAACACCTAAGGGTATTTT
1 ATATGTATGCAGTAGATATGCATGTCACATCCATAAAACTTACATTCAACACCTAAGGGTATTTT
3399484 AGTCATTTTCATCTTTAGGGGCATTTCGATAATTTTCCTATTATTACAATTTTCACTTACCTTGG
66 AGTCATTTTCATCTTTAGGGGCATTTCGATAATTTTCCTATTATTACAATTTTCACTTACCTTGG
3399549 CCCGTTAACAAATCCTGTGAGCTAAGATGAATGAATACTATGCACCAGGTAGGATTCCAGAGAAG
131 CCCGTTAACAAATCCTGTGAGCTAAGATGAATGAATACTATGCACCAGGTAGGATTCCAGAGAAG
3399614 AGGAGGTGAGTCATTAAGATTGCTTAAGTACCAACCTCTCCCTAGATCCAATCCTAGACATGCAT
196 AGGAGGTGAGTCATTAAGATTGCTTAAGTACCAACCTCTCCCTAGATCCAATCCTAGACATGCAT
3399679 ATACCTGTTGCCACACCTTAACCCTATGACTTGTCCACGGTCGCTGTAACACCCCAAACCCGGCC
261 ATACCTGTTGCCACACCTTAACCCTATGACTTGTCCACGGTCGCTGTAACACCCCAAACCCGGCC
3399744 CAGACGTTATGGCCGAATCTGGCGTGTTACATTGAAGTGTTTTAGAGAAAACCATGTTTTCATTG
326 CAGACGTTATGGCCGAATCTGGCGTGTTACATTGAAGTGTTTTAGAGAAAACCATGTTTTCATTG
3399809 AAAACTCTTCTTAAAAAAACCCTAATTAACTAAAAAAGAAACCTTTTAGTTACGAAAGCCTTGTT
391 AAAACTCTTCTTAAAAAAACCCTAATTAACTAAAAAAGAAACCTTTTAGTTACGAAAGCCTTGTT
3399874 TAAATCATTTGATATTTTTTTAAAAAAAATTAGTTGCGGAAACATAGAAAACATAATATAATTTA
456 TAAATCATTTGATATTTTTTTAAAAAAAATTAGTTGCGGAAACATAGAAAACATAATATAATTTA
3399939 AGAAATCTATGTTCAACTTCTCGTAATTACAATGAAAATAATAATAATAATTCAAGTAGTAATTG
521 AGAAATCTATGTTCAACTTCTCGTAATTACAATGAAAATAATAATAATAATTCAAGTAGTAATTG
3400004 AAAACCTTATTACAATCTGGTCTGAACACACTTAAAAAGAAATAAAAAATTAAATGCTT
586 AAAACCTTATTACAATCTGGTCTGAACACACTTAAAAAGAAATAAAAAATTAAATGCTT
3400063 A
1 A
3400064 AAAAAACCAA
Statistics
Matches: 645, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
644 645 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (644 bp):
ATATGTATGCAGTAGATATGCATGTCACATCCATAAAACTTACATTCAACACCTAAGGGTATTTT
AGTCATTTTCATCTTTAGGGGCATTTCGATAATTTTCCTATTATTACAATTTTCACTTACCTTGG
CCCGTTAACAAATCCTGTGAGCTAAGATGAATGAATACTATGCACCAGGTAGGATTCCAGAGAAG
AGGAGGTGAGTCATTAAGATTGCTTAAGTACCAACCTCTCCCTAGATCCAATCCTAGACATGCAT
ATACCTGTTGCCACACCTTAACCCTATGACTTGTCCACGGTCGCTGTAACACCCCAAACCCGGCC
CAGACGTTATGGCCGAATCTGGCGTGTTACATTGAAGTGTTTTAGAGAAAACCATGTTTTCATTG
AAAACTCTTCTTAAAAAAACCCTAATTAACTAAAAAAGAAACCTTTTAGTTACGAAAGCCTTGTT
TAAATCATTTGATATTTTTTTAAAAAAAATTAGTTGCGGAAACATAGAAAACATAATATAATTTA
AGAAATCTATGTTCAACTTCTCGTAATTACAATGAAAATAATAATAATAATTCAAGTAGTAATTG
AAAACCTTATTACAATCTGGTCTGAACACACTTAAAAAGAAATAAAAAATTAAATGCTT
Found at i:3401094 original size:712 final size:712
Alignment explanation
Indices: 3399731--3401157 Score: 2854
Period size: 712 Copynumber: 2.0 Consensus size: 712
3399721 GCTGTAACAC
3399731 CCCAAACCCGGCCCAGACGTTATGGCCGAATCTGGCGTGTTACATTGAAGTGTTTTAGAGAAAAC
1 CCCAAACCCGGCCCAGACGTTATGGCCGAATCTGGCGTGTTACATTGAAGTGTTTTAGAGAAAAC
3399796 CATGTTTTCATTGAAAACTCTTCTTAAAAAAACCCTAATTAACTAAAAAAGAAACCTTTTAGTTA
66 CATGTTTTCATTGAAAACTCTTCTTAAAAAAACCCTAATTAACTAAAAAAGAAACCTTTTAGTTA
3399861 CGAAAGCCTTGTTTAAATCATTTGATATTTTTTTAAAAAAAATTAGTTGCGGAAACATAGAAAAC
131 CGAAAGCCTTGTTTAAATCATTTGATATTTTTTTAAAAAAAATTAGTTGCGGAAACATAGAAAAC
3399926 ATAATATAATTTAAGAAATCTATGTTCAACTTCTCGTAATTACAATGAAAATAATAATAATAATT
196 ATAATATAATTTAAGAAATCTATGTTCAACTTCTCGTAATTACAATGAAAATAATAATAATAATT
3399991 CAAGTAGTAATTGAAAACCTTATTACAATCTGGTCTGAACACACTTAAAAAGAAATAAAAAATTA
261 CAAGTAGTAATTGAAAACCTTATTACAATCTGGTCTGAACACACTTAAAAAGAAATAAAAAATTA
3400056 AATGCTTAAAAAAACCAAGTCCAAATTATCTTGCTAGCCAGCCACCCAGAGTCCCTCCAAACATC
326 AATGCTTAAAAAAACCAAGTCCAAATTATCTTGCTAGCCAGCCACCCAGAGTCCCTCCAAACATC
3400121 AAACCTTCTATTGAGCATCACCTGAAAATAAAATAAAAGAGCGGGTGAGTTTTCCCAAACCGAGT
391 AAACCTTCTATTGAGCATCACCTGAAAATAAAATAAAAGAGCGGGTGAGTTTTCCCAAACCGAGT
3400186 GTGTACAACCCTCGACAAAAACAAGCATTCAAAAAAAACATCATTCATCAATCATGTCATGCAAT
456 GTGTACAACCCTCGACAAAAACAAGCATTCAAAAAAAACATCATTCATCAATCATGTCATGCAAT
3400251 ACCATCCAAATTATCCATCCGCTACGCACCAGCTCCGTCCCCTGTCACACCATGTGGGGATATGA
521 ACCATCCAAATTATCCATCCGCTACGCACCAGCTCCGTCCCCTGTCACACCATGTGGGGATATGA
3400316 GTATCGACCCACCCAGCCCACACACCATGGTAGCCCGATTGCGGAACTACTGTCATTTACATATT
586 GTATCGACCCACCCAGCCCACACACCATGGTAGCCCGATTGCGGAACTACTGTCATTTACATATT
3400381 GGGCTTTAAAAGCCGTCGGTGAATCCACGATTGTCAAGCAACCATGCGATCCTCGTATACGT
651 GGGCTTTAAAAGCCGTCGGTGAATCCACGATTGTCAAGCAACCATGCGATCCTCGTATACGT
3400443 CCCAAACCCGGCCCAGACGTTATGGCCGAATCTGGCGTGTTACATTGAAGTGTTTTAGAGAAAAC
1 CCCAAACCCGGCCCAGACGTTATGGCCGAATCTGGCGTGTTACATTGAAGTGTTTTAGAGAAAAC
3400508 CATGTTTTCATTGAAAACTCTTCTTAAAAAAACCCTAATTAACTAAAAAAGAAACCTTTTAGTTA
66 CATGTTTTCATTGAAAACTCTTCTTAAAAAAACCCTAATTAACTAAAAAAGAAACCTTTTAGTTA
3400573 CGAAAGCCTTGTTTAAATCATTTGATATTTTTTTAAAAAAAATTAGTTGCGGAAACATAGAAAAC
131 CGAAAGCCTTGTTTAAATCATTTGATATTTTTTTAAAAAAAATTAGTTGCGGAAACATAGAAAAC
3400638 ATAATATAATTTAAGAAATCTATGTTCAACTTCTCGTAATTACAATGAAAATAATAATAATAATT
196 ATAATATAATTTAAGAAATCTATGTTCAACTTCTCGTAATTACAATGAAAATAATAATAATAATT
3400703 CAAGTAGTAATTGAAAACCTTATTACAATCTGGTCTGAACACACTTAAAAAGAAATAAAAAATTA
261 CAAGTAGTAATTGAAAACCTTATTACAATCTGGTCTGAACACACTTAAAAAGAAATAAAAAATTA
3400768 AATGCTTAAAAAAACCAAGTCCAAATTATCTTGCTAGCCAGCCACCCAGAGTCCCTCCAAACATC
326 AATGCTTAAAAAAACCAAGTCCAAATTATCTTGCTAGCCAGCCACCCAGAGTCCCTCCAAACATC
3400833 AAACCTTCTATTGAGCATCACCTGAAAATAAAATAAAAGAGCGGGTGAGTTTTCCCAAACCGAGT
391 AAACCTTCTATTGAGCATCACCTGAAAATAAAATAAAAGAGCGGGTGAGTTTTCCCAAACCGAGT
3400898 GTGTACAACCCTCGACAAAAACAAGCATTCAAAAAAAACATCATTCATCAATCATGTCATGCAAT
456 GTGTACAACCCTCGACAAAAACAAGCATTCAAAAAAAACATCATTCATCAATCATGTCATGCAAT
3400963 ACCATCCAAATTATCCATCCGCTACGCACCAGCTCCGTCCCCTGTCACACCATGTGGGGATATGA
521 ACCATCCAAATTATCCATCCGCTACGCACCAGCTCCGTCCCCTGTCACACCATGTGGGGATATGA
3401028 GTATCGACCCACCCAGCCCACACACCATGGTAGCCCGATTGCGGAACTACTGTCATTTACATATT
586 GTATCGACCCACCCAGCCCACACACCATGGTAGCCCGATTGCGGAACTACTGTCATTTACATATT
3401093 GGGCTTTAAAAGCCGTCGGTGAATCCACGATTGTCAAGCAACCATGCGATCCTCGTATACGT
651 GGGCTTTAAAAGCCGTCGGTGAATCCACGATTGTCAAGCAACCATGCGATCCTCGTATACGT
3401155 CCC
1 CCC
3401158 CCGTTCCATA
Statistics
Matches: 715, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
712 715 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (712 bp):
CCCAAACCCGGCCCAGACGTTATGGCCGAATCTGGCGTGTTACATTGAAGTGTTTTAGAGAAAAC
CATGTTTTCATTGAAAACTCTTCTTAAAAAAACCCTAATTAACTAAAAAAGAAACCTTTTAGTTA
CGAAAGCCTTGTTTAAATCATTTGATATTTTTTTAAAAAAAATTAGTTGCGGAAACATAGAAAAC
ATAATATAATTTAAGAAATCTATGTTCAACTTCTCGTAATTACAATGAAAATAATAATAATAATT
CAAGTAGTAATTGAAAACCTTATTACAATCTGGTCTGAACACACTTAAAAAGAAATAAAAAATTA
AATGCTTAAAAAAACCAAGTCCAAATTATCTTGCTAGCCAGCCACCCAGAGTCCCTCCAAACATC
AAACCTTCTATTGAGCATCACCTGAAAATAAAATAAAAGAGCGGGTGAGTTTTCCCAAACCGAGT
GTGTACAACCCTCGACAAAAACAAGCATTCAAAAAAAACATCATTCATCAATCATGTCATGCAAT
ACCATCCAAATTATCCATCCGCTACGCACCAGCTCCGTCCCCTGTCACACCATGTGGGGATATGA
GTATCGACCCACCCAGCCCACACACCATGGTAGCCCGATTGCGGAACTACTGTCATTTACATATT
GGGCTTTAAAAGCCGTCGGTGAATCCACGATTGTCAAGCAACCATGCGATCCTCGTATACGT
Found at i:3401997 original size:664 final size:664
Alignment explanation
Indices: 3400729--3402057 Score: 2658
Period size: 664 Copynumber: 2.0 Consensus size: 664
3400719 ACCTTATTAC
3400729 AATCTGGTCTGAACACACTTAAAAAGAAATAAAAAATTAAATGCTTAAAAAAACCAAGTCCAAAT
1 AATCTGGTCTGAACACACTTAAAAAGAAATAAAAAATTAAATGCTTAAAAAAACCAAGTCCAAAT
3400794 TATCTTGCTAGCCAGCCACCCAGAGTCCCTCCAAACATCAAACCTTCTATTGAGCATCACCTGAA
66 TATCTTGCTAGCCAGCCACCCAGAGTCCCTCCAAACATCAAACCTTCTATTGAGCATCACCTGAA
3400859 AATAAAATAAAAGAGCGGGTGAGTTTTCCCAAACCGAGTGTGTACAACCCTCGACAAAAACAAGC
131 AATAAAATAAAAGAGCGGGTGAGTTTTCCCAAACCGAGTGTGTACAACCCTCGACAAAAACAAGC
3400924 ATTCAAAAAAAACATCATTCATCAATCATGTCATGCAATACCATCCAAATTATCCATCCGCTACG
196 ATTCAAAAAAAACATCATTCATCAATCATGTCATGCAATACCATCCAAATTATCCATCCGCTACG
3400989 CACCAGCTCCGTCCCCTGTCACACCATGTGGGGATATGAGTATCGACCCACCCAGCCCACACACC
261 CACCAGCTCCGTCCCCTGTCACACCATGTGGGGATATGAGTATCGACCCACCCAGCCCACACACC
3401054 ATGGTAGCCCGATTGCGGAACTACTGTCATTTACATATTGGGCTTTAAAAGCCGTCGGTGAATCC
326 ATGGTAGCCCGATTGCGGAACTACTGTCATTTACATATTGGGCTTTAAAAGCCGTCGGTGAATCC
3401119 ACGATTGTCAAGCAACCATGCGATCCTCGTATACGTCCCCCGTTCCATAATTCCCACCCATATGC
391 ACGATTGTCAAGCAACCATGCGATCCTCGTATACGTCCCCCGTTCCATAATTCCCACCCATATGC
3401184 AACCTAAGCAAAATATCATATGTATGCATGTCACATCCATAAAACTTACATTCTACACCTAGGGG
456 AACCTAAGCAAAATATCATATGTATGCATGTCACATCCATAAAACTTACATTCTACACCTAGGGG
3401249 TATTTTGGTCATTTTCGCCCTTAGGGGCATTTCGATAATTTTCCCACAATTACAGTTTTCACTTA
521 TATTTTGGTCATTTTCGCCCTTAGGGGCATTTCGATAATTTTCCCACAATTACAGTTTTCACTTA
3401314 CCTTGGCCCGTTAACGAGTCCCGTGAGCTAAGATGAATGAATACTATGCACCAGGTAGGATTCCA
586 CCTTGGCCCGTTAACGAGTCCCGTGAGCTAAGATGAATGAATACTATGCACCAGGTAGGATTCCA
3401379 GAAAAGAGGAGGTA
651 GAAAAGAGGAGGTA
3401393 AATCTGGTCTGAACACACTTAAAAAGAAATAAAAAATTAAATGCTTAAAAAAACCAAGTCCAAAT
1 AATCTGGTCTGAACACACTTAAAAAGAAATAAAAAATTAAATGCTTAAAAAAACCAAGTCCAAAT
3401458 TATCTTGCTAGCCAGCCACCCAGAGTCCCTCCAAACATCAAACCTTCTATTGAGCATCACCTGAA
66 TATCTTGCTAGCCAGCCACCCAGAGTCCCTCCAAACATCAAACCTTCTATTGAGCATCACCTGAA
3401523 AATAAAATAAAAGAGCGGGTGAGTTTTCCCAAACCGAGTGTGTACAACCCTCGACAAAAACAAGC
131 AATAAAATAAAAGAGCGGGTGAGTTTTCCCAAACCGAGTGTGTACAACCCTCGACAAAAACAAGC
3401588 ATTCAAAAAAAACATCATTCATCAATCATGTCATGCAATACCATCCAAATTATCCATCCGCTACG
196 ATTCAAAAAAAACATCATTCATCAATCATGTCATGCAATACCATCCAAATTATCCATCCGCTACG
3401653 CACCAGCTCCGTCCCCTGTCACACCATGTGGGGATATGAGTATCGACCCACCCAGCCCACACACC
261 CACCAGCTCCGTCCCCTGTCACACCATGTGGGGATATGAGTATCGACCCACCCAGCCCACACACC
3401718 ATGGTAGCCCGATTGCGGAACTACTGTCATTTACATATTGGGCTTTAAAAGCCGTCGGTGAATCC
326 ATGGTAGCCCGATTGCGGAACTACTGTCATTTACATATTGGGCTTTAAAAGCCGTCGGTGAATCC
3401783 ACGATTGTCAAGCAACCATGCGATCCTCGTATACGTCCCCCGTTCCATAATTCCCACCCATATGC
391 ACGATTGTCAAGCAACCATGCGATCCTCGTATACGTCCCCCGTTCCATAATTCCCACCCATATGC
3401848 AACCTAAGCAAAATATCATATGTATGCATGTCACATCCATAAAACTTACATTCTACACCTAGGGG
456 AACCTAAGCAAAATATCATATGTATGCATGTCACATCCATAAAACTTACATTCTACACCTAGGGG
3401913 TATTTTGGTCATTTTCGCCCTTAGGGGCATTTCGATAATTTTCCCACAATTACAGTTTTCACTTA
521 TATTTTGGTCATTTTCGCCCTTAGGGGCATTTCGATAATTTTCCCACAATTACAGTTTTCACTTA
3401978 CCTTGGCCCGTTAACGAGTCCCGTGAGCTAAGATGAATGAATACTATGCACCAGGTAGGATTCCA
586 CCTTGGCCCGTTAACGAGTCCCGTGAGCTAAGATGAATGAATACTATGCACCAGGTAGGATTCCA
3402043 GAAAAGAGGAGGTA
651 GAAAAGAGGAGGTA
3402057 A
1 A
3402058 GTCATTAAGA
Statistics
Matches: 665, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
664 665 1.00
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (664 bp):
AATCTGGTCTGAACACACTTAAAAAGAAATAAAAAATTAAATGCTTAAAAAAACCAAGTCCAAAT
TATCTTGCTAGCCAGCCACCCAGAGTCCCTCCAAACATCAAACCTTCTATTGAGCATCACCTGAA
AATAAAATAAAAGAGCGGGTGAGTTTTCCCAAACCGAGTGTGTACAACCCTCGACAAAAACAAGC
ATTCAAAAAAAACATCATTCATCAATCATGTCATGCAATACCATCCAAATTATCCATCCGCTACG
CACCAGCTCCGTCCCCTGTCACACCATGTGGGGATATGAGTATCGACCCACCCAGCCCACACACC
ATGGTAGCCCGATTGCGGAACTACTGTCATTTACATATTGGGCTTTAAAAGCCGTCGGTGAATCC
ACGATTGTCAAGCAACCATGCGATCCTCGTATACGTCCCCCGTTCCATAATTCCCACCCATATGC
AACCTAAGCAAAATATCATATGTATGCATGTCACATCCATAAAACTTACATTCTACACCTAGGGG
TATTTTGGTCATTTTCGCCCTTAGGGGCATTTCGATAATTTTCCCACAATTACAGTTTTCACTTA
CCTTGGCCCGTTAACGAGTCCCGTGAGCTAAGATGAATGAATACTATGCACCAGGTAGGATTCCA
GAAAAGAGGAGGTA
Found at i:3402300 original size:29 final size:28
Alignment explanation
Indices: 3402234--3402310 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 28
3402224 AATTTCACAT
* * *
3402234 ACCTGTATCTGGCCCATTAAGCCCAATC
1 ACCTGTATATGGCCCATTAGGCCAAATC
**
3402262 ATAT-TCATATGGCCCATTAGGCCTAAATC
1 ACCTGT-ATATGGCCCATTAGGCC-AAATC
*
3402291 ACCTGTATATCGCCCATTAG
1 ACCTGTATATGGCCCATTAG
3402311 CCCCAAGTCA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
27 1 0.03
28 17 0.45
29 19 0.50
30 1 0.03
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.29
Consensus pattern (28 bp):
ACCTGTATATGGCCCATTAGGCCAAATC
Found at i:3402321 original size:29 final size:28
Alignment explanation
Indices: 3402245--3402338 Score: 75
Period size: 29 Copynumber: 3.3 Consensus size: 28
3402235 CCTGTATCTG
* *
3402245 GCCCATTAAG-CCC-AATCATATTCATATG
1 GCCCATT-AGCCCCAAATCACATT-ATATA
* * * *
3402273 GCCCATTAGGCCTAAATCACCTGTATATC
1 GCCCATTAGCCCCAAATCACAT-TATATA
*
3402302 GCCCATTAGCCCCAAGTCACATTATATA
1 GCCCATTAGCCCCAAATCACATTATATA
*
3402330 GCCCGTTAG
1 GCCCATTAG
3402339 GTCCAGTCAC
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
27 2 0.04
28 22 0.42
29 28 0.53
30 1 0.02
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.27
Consensus pattern (28 bp):
GCCCATTAGCCCCAAATCACATTATATA
Found at i:3402338 original size:28 final size:27
Alignment explanation
Indices: 3402296--3402356 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
3402286 AAATCACCTG
*
3402296 TATATCGCCCATTAGCCCCAAGTCACAT
1 TATATAGCCCATTAGCCCC-AGTCACAT
* **
3402324 TATATAGCCCGTTAGGTCCAGTCACAT
1 TATATAGCCCATTAGCCCCAGTCACAT
3402351 TCATAT
1 T-ATAT
3402357 TCATGCTCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 9 0.32
28 19 0.68
ACGTcount: A:0.28, C:0.30, G:0.13, T:0.30
Consensus pattern (27 bp):
TATATAGCCCATTAGCCCCAGTCACAT
Found at i:3402603 original size:16 final size:16
Alignment explanation
Indices: 3402582--3402616 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
3402572 TTTTTTGGCA
3402582 TTTCGGCATTTCAGCT
1 TTTCGGCATTTCAGCT
*
3402598 TTTCGGCATTTCTGCT
1 TTTCGGCATTTCAGCT
3402614 TTT
1 TTT
3402617 GCCGATACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.09, C:0.23, G:0.17, T:0.51
Consensus pattern (16 bp):
TTTCGGCATTTCAGCT
Found at i:3403880 original size:29 final size:29
Alignment explanation
Indices: 3403847--3403933 Score: 133
Period size: 29 Copynumber: 3.1 Consensus size: 29
3403837 TTATATTCAC
*
3403847 ATGGCTCATTAGGCCCACATCACATTTAT
1 ATGGCTCATTAGGCCCAAATCACATTTAT
* *
3403876 ATGGCTCTTTAGGCCTAAATCACATTTAT
1 ATGGCTCATTAGGCCCAAATCACATTTAT
3403905 ATGGC-CATTAGGCCCAAATCACA-TTAT
1 ATGGCTCATTAGGCCCAAATCACATTTAT
3403932 AT
1 AT
3403934 TCATGCTCAC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
27 6 0.11
28 16 0.30
29 31 0.58
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (29 bp):
ATGGCTCATTAGGCCCAAATCACATTTAT
Found at i:3406587 original size:20 final size:21
Alignment explanation
Indices: 3406549--3406587 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3406539 GAATTAATTT
3406549 CACACGGGCGTGCTGCCCTTC
1 CACACGGGCGTGCTGCCCTTC
3406570 CACACGGGCGTG-TGCCCT
1 CACACGGGCGTGCTGCCCT
3406588 GTTTCAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.10, C:0.41, G:0.31, T:0.18
Consensus pattern (21 bp):
CACACGGGCGTGCTGCCCTTC
Found at i:3415584 original size:47 final size:45
Alignment explanation
Indices: 3415531--3415651 Score: 167
Period size: 47 Copynumber: 2.6 Consensus size: 45
3415521 CTTGTGTGAA
3415531 CTAGTGTAAGACATGTCTGGGACATGGCATCGGCATTGA-GACGA-GTG
1 CTAGTGTAAGACATGTCTGGGACATGGCATCGGC--T-ACGA-GATGTG
3415578 CTAGTGTAAGACATGTCTGGGACAT-GCATCGGCTACGAGATGTG
1 CTAGTGTAAGACATGTCTGGGACATGGCATCGGCTACGAGATGTG
*
3415622 CCAGTGTAAGACCATGTCTGGGACATGGCA
1 CTAGTGTAAGA-CATGTCTGGGACATGGCA
3415652 ACGACACAGA
Statistics
Matches: 69, Mismatches: 1, Indels: 9
0.87 0.01 0.11
Matches are distributed among these distances:
43 3 0.04
44 16 0.23
45 14 0.20
46 11 0.16
47 25 0.36
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.23
Consensus pattern (45 bp):
CTAGTGTAAGACATGTCTGGGACATGGCATCGGCTACGAGATGTG
Found at i:3424655 original size:40 final size:40
Alignment explanation
Indices: 3424559--3424819 Score: 370
Period size: 40 Copynumber: 6.5 Consensus size: 40
3424549 TTGAATGATG
* * *
3424559 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-A
** *
3424598 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
3424638 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
3424678 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
3424718 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
3424758 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
3424799 -CCGGGCTATGTCCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCA
3424820 CTTGAACGAG
Statistics
Matches: 206, Mismatches: 10, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
39 19 0.09
40 177 0.86
41 10 0.05
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:3424841 original size:120 final size:119
Alignment explanation
Indices: 3424559--3424856 Score: 356
Period size: 120 Copynumber: 2.5 Consensus size: 119
3424549 TTGAATGATG
** * *
3424559 TCCGGGCTAAGTCCCGAAGG--CTTGTGCTAAGTGAC-AATATCCGGACTAAGAT-CCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCACTTGAAC-GAGTGACTAA-ATCCGG-TTAA-ATCCCGAAGGCA
* *
3424620 TTTGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
62 TTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAAA
* * ** * *
3424678 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCACTTGAACGAGTGACTAAATCC-GGTTAAATCCCGAAGGCATTT
3424743 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
65 GTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTA-AA
* * *
3424799 -CCGGGCTATGTCCCGAAGGCACTTGAACGAG-GAGCTATATCCGGTTAAATTCCGAAGG
1 TCCGGGCTAAGTCCCGAAGGCACTTGAACGAGTGA-CTAAATCCGGTTAAATCCCGAAGG
3424857 TACGTGATTT
Statistics
Matches: 155, Mismatches: 17, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
119 35 0.23
120 108 0.70
121 12 0.08
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (119 bp):
TCCGGGCTAAGTCCCGAAGGCACTTGAACGAGTGACTAAATCCGGTTAAATCCCGAAGGCATTTG
TGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTAAA
Found at i:3427275 original size:7 final size:7
Alignment explanation
Indices: 3427263--3427293 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3427253 GTTGTTAAAT
3427263 GATGAAA
1 GATGAAA
3427270 GATGAAA
1 GATGAAA
3427277 GATGAAA
1 GATGAAA
*
3427284 AATGAAA
1 GATGAAA
3427291 GAT
1 GAT
3427294 ATGTGATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.26, T:0.16
Consensus pattern (7 bp):
GATGAAA
Found at i:3427867 original size:40 final size:41
Alignment explanation
Indices: 3427804--3427895 Score: 127
Period size: 40 Copynumber: 2.3 Consensus size: 41
3427794 TTATGTACGA
*
3427804 CACTAAGTGTG-AGATTAGAAATAGCTTCGGCTATA-AATGG
1 CACTAAGTGTGCAAATTAGAAATAGCTTCGGCTATATAA-GG
* *
3427844 CACTAAGTGTGCAAATT-GGAATAGCTTCGGCTATATGAGG
1 CACTAAGTGTGCAAATTAGAAATAGCTTCGGCTATATAAGG
3427884 CACTAAGTGTGC
1 CACTAAGTGTGC
3427896 GATACCAAGA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
40 42 0.89
41 5 0.11
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (41 bp):
CACTAAGTGTGCAAATTAGAAATAGCTTCGGCTATATAAGG
Found at i:3428863 original size:31 final size:31
Alignment explanation
Indices: 3428819--3428897 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
3428809 TTTAACGGTT
3428819 ACTGGGCCGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
** *
3428850 ACTGGGCTAAAGCCTTTTCATAAATCATTTC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
3428881 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
3428898 ACTATAAACG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:3428980 original size:43 final size:42
Alignment explanation
Indices: 3428924--3429013 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 42
3428914 CCCATAGGCT
* ** * *
3428924 CATTTCAATATCATACGTAATGTCAATGGATGTATGCAAGCC
1 CATTTCAATATCATACGAAATACCAATGAATGTATGCAAACC
*
3428966 CATTTCATATATCATATGAAATACCAATGAATGTATGCAAACC
1 CATTTCA-ATATCATACGAAATACCAATGAATGTATGCAAACC
3429009 CATTT
1 CATTT
3429014 GAGGAGACTA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
42 7 0.17
43 34 0.83
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (42 bp):
CATTTCAATATCATACGAAATACCAATGAATGTATGCAAACC
Found at i:3429229 original size:26 final size:26
Alignment explanation
Indices: 3429145--3429280 Score: 208
Period size: 26 Copynumber: 5.3 Consensus size: 26
3429135 CTAGAGGCCT
3429145 AGCCTCTTTT-AAT-AACTGGGGCA-A
1 AGCC-CTTTTCAATAAACTGGGGCATA
**
3429169 AGCCCTTTTCGGTAAACTGGGGCA-A
1 AGCCCTTTTCAATAAACTGGGGCATA
3429194 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
3429220 AGCCCTTTTCAATAAACTGGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
*
3429246 AGCCCTTTTCAATAAACTAGGGCATA
1 AGCCCTTTTCAATAAACTGGGGCATA
3429272 AGCCCTTTT
1 AGCCCTTTT
3429281 GCACTTCATC
Statistics
Matches: 104, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.05
24 5 0.05
25 33 0.32
26 61 0.59
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (26 bp):
AGCCCTTTTCAATAAACTGGGGCATA
Found at i:3429351 original size:20 final size:20
Alignment explanation
Indices: 3429326--3429390 Score: 121
Period size: 20 Copynumber: 3.2 Consensus size: 20
3429316 TTATGAATAC
3429326 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
3429346 ATCATGTGCATTTCATACAT
1 ATCATGTGCATTTCATACAT
*
3429366 ATCATGTGCATTTTATACAT
1 ATCATGTGCATTTCATACAT
3429386 ATCAT
1 ATCAT
3429391 ATCAATCATG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (20 bp):
ATCATGTGCATTTCATACAT
Found at i:3436760 original size:15 final size:15
Alignment explanation
Indices: 3436735--3436792 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
3436725 TCATATATAT
3436735 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
3436751 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
3436766 AATAATTTCAATCAA
1 TATAAATTCAATCAA
3436781 TATAAATTCAAT
1 TATAAATTCAAT
3436793 AAATTCATCG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:3437302 original size:23 final size:24
Alignment explanation
Indices: 3437265--3437319 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
3437255 CATCCCCTGC
*
3437265 TATTCTGTTTCTTTCCTTCTTTT-
1 TATTCTTTTTCTTTCCTTCTTTTG
* *
3437288 TATTCTTTTTGTTTCTTTCTTTTG
1 TATTCTTTTTCTTTCCTTCTTTTG
3437312 T-TTCTTTT
1 TATTCTTTT
3437320 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 27 0.96
24 1 0.04
ACGTcount: A:0.04, C:0.16, G:0.05, T:0.75
Consensus pattern (24 bp):
TATTCTTTTTCTTTCCTTCTTTTG
Found at i:3437312 original size:13 final size:13
Alignment explanation
Indices: 3437294--3437318 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3437284 TTTTTATTCT
3437294 TTTTGTTTCTTTC
1 TTTTGTTTCTTTC
3437307 TTTTGTTTCTTT
1 TTTTGTTTCTTT
3437319 TATATATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (13 bp):
TTTTGTTTCTTTC
Found at i:3437495 original size:31 final size:32
Alignment explanation
Indices: 3437437--3437500 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
3437427 CATACATTTG
*
3437437 TCATAATTTAATATATTTATTACATAAAAATC
1 TCATAATATAATATATTTATTACATAAAAATC
*
3437469 TCATAATATAAT-TATTTAATTA-ATAAATATC
1 TCATAATATAATATATTT-ATTACATAAAAATC
3437500 T
1 T
3437501 TATTTAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 14 0.48
32 15 0.52
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (32 bp):
TCATAATATAATATATTTATTACATAAAAATC
Found at i:3438031 original size:13 final size:14
Alignment explanation
Indices: 3438013--3438041 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3438003 GATTAACTTC
3438013 ATAAATATTTT-TA
1 ATAAATATTTTCTA
3438026 ATAAATATTTTCTA
1 ATAAATATTTTCTA
3438040 AT
1 AT
3438042 CCATTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATATTTTCTA
Found at i:3442923 original size:23 final size:23
Alignment explanation
Indices: 3442845--3442927 Score: 66
Period size: 21 Copynumber: 3.8 Consensus size: 23
3442835 ATCAGTATAT
*
3442845 GACACATAAAGTGCCT-AAA-AT
1 GACACATAAAGTGCCTGAAATAC
** * *
3442866 GACACACGAGGTGCCTG--ATTC
1 GACACATAAAGTGCCTGAAATAC
* * *
3442887 AACACATGAGGTGCCTGAAATAC
1 GACACATAAAGTGCCTGAAATAC
3442910 GACACATAAAGTGCCTGA
1 GACACATAAAGTGCCTGA
3442928 TCGGTATAGC
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
20 1 0.02
21 28 0.60
23 18 0.38
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (23 bp):
GACACATAAAGTGCCTGAAATAC
Found at i:3444305 original size:23 final size:23
Alignment explanation
Indices: 3444253--3444298 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3444243 CGTCCCCTGC
*
3444253 TATTCTGTTTCTTTCCTTCTTTT
1 TATTCTTTTTCTTTCCTTCTTTT
* *
3444276 TATTCTTTTTGTTTCTTTCTTTT
1 TATTCTTTTTCTTTCCTTCTTTT
3444299 GTTTCTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.74
Consensus pattern (23 bp):
TATTCTTTTTCTTTCCTTCTTTT
Found at i:3444980 original size:13 final size:14
Alignment explanation
Indices: 3444962--3444990 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3444952 GATTAACTTC
3444962 ATAAATATTTT-TA
1 ATAAATATTTTCTA
3444975 ATAAATATTTTCTA
1 ATAAATATTTTCTA
3444989 AT
1 AT
3444991 CCATTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATATTTTCTA
Found at i:3451811 original size:31 final size:31
Alignment explanation
Indices: 3451776--3451839 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
3451766 CCTTTTCATA
3451776 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
** *
3451807 TTTCATATTTCATATTACTGGGCTGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
3451838 TT
1 TT
3451840 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:3452109 original size:23 final size:23
Alignment explanation
Indices: 3452054--3452173 Score: 177
Period size: 23 Copynumber: 5.1 Consensus size: 23
3452044 CCTAGCCTCT
*
3452054 TTTAATAACTGGGGCAAAAAGCCC
1 TTTAATAACTGGGGC-ACAAGCCC
*
3452078 TTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCACAAGCCC
*
3452102 TTTAATAACTAGGGCACAAGCCC
1 TTTAATAACTGGGGCACAAGCCC
*
3452125 TTTAATAACTAGGGCACAAGCCC
1 TTTAATAACTGGGGCACAAGCCC
*
3452148 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCACAAGCCC
3452171 TTT
1 TTT
3452174 TTCACTTCCT
Statistics
Matches: 90, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
23 68 0.76
24 7 0.08
25 15 0.17
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.26
Consensus pattern (23 bp):
TTTAATAACTGGGGCACAAGCCC
Found at i:3452249 original size:20 final size:20
Alignment explanation
Indices: 3452224--3452290 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
3452214 TTATGCATAC
3452224 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
3452244 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
3452264 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
3452284 ACCATGT
1 ATCATGT
3452291 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:3452255 original size:11 final size:11
Alignment explanation
Indices: 3452224--3452279 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
3452214 TTATGCATAC
3452224 ATCATGTGCAT
1 ATCATGTGCAT
*
3452235 ATCA--TACAT
1 ATCATGTGCAT
3452244 ATCATGTGCAT
1 ATCATGTGCAT
*
3452255 ATCA--TACAT
1 ATCATGTGCAT
*
3452264 GTCATGTGCAT
1 ATCATGTGCAT
3452275 ATCAT
1 ATCAT
3452280 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:3452359 original size:25 final size:25
Alignment explanation
Indices: 3452327--3452374 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3452317 ATACATAAAC
* * *
3452327 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
3452352 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
3452375 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:3455127 original size:77 final size:77
Alignment explanation
Indices: 3455000--3455156 Score: 287
Period size: 77 Copynumber: 2.0 Consensus size: 77
3454990 GGCACCCTAT
* *
3455000 GCAACCGTACTATTTCCGTCACATACAATTTGGCCAACTTCTGAAGTGAGTAATCGGTTCGGACA
1 GCAACCGTACTATTTCCGCCACATACAATTTGGCCAACTTCTGAAGTGAGTAATCAGTTCGGACA
3455065 GGTATGAAATGA
66 GGTATGAAATGA
*
3455077 GCAACCGTACTATTTCTGCCACATACAATTTGGCCAACTTCTGAAGTGAGTAATCAGTTCGGACA
1 GCAACCGTACTATTTCCGCCACATACAATTTGGCCAACTTCTGAAGTGAGTAATCAGTTCGGACA
3455142 GGTATGAAATGA
66 GGTATGAAATGA
3455154 GCA
1 GCA
3455157 GATTTCGTCA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (77 bp):
GCAACCGTACTATTTCCGCCACATACAATTTGGCCAACTTCTGAAGTGAGTAATCAGTTCGGACA
GGTATGAAATGA
Found at i:3459970 original size:31 final size:31
Alignment explanation
Indices: 3459929--3459992 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
3459919 CCTTTTCATA
*
3459929 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
3459960 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
3459991 TT
1 TT
3459993 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:3460295 original size:46 final size:47
Alignment explanation
Indices: 3460207--3460302 Score: 149
Period size: 46 Copynumber: 2.1 Consensus size: 47
3460197 CCTTGCCTCT
*
3460207 TTTAATAACTGGGACAAAAGCCTTTTTTATAACTAGGGCATAAGCCC
1 TTTAATAACTGGGACAAAAGCCTCTTTTATAACTAGGGCATAAGCCC
* * *
3460254 TTTAATAACTGGGGCATAAGCC-CTTTTATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGACAAAAGCCTCTTTTATAACTAGGGCATAAGCCC
3460300 TTT
1 TTT
3460303 TGCACTTCCT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
46 25 0.56
47 20 0.44
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (47 bp):
TTTAATAACTGGGACAAAAGCCTCTTTTATAACTAGGGCATAAGCCC
Found at i:3460303 original size:23 final size:23
Alignment explanation
Indices: 3460205--3460303 Score: 135
Period size: 23 Copynumber: 4.2 Consensus size: 23
3460195 GGCCTTGCCT
* *
3460205 CTTTTAATAACTGGGACAAAAGCC
1 CTTTT-ATAACTGGGGCATAAGCC
* *
3460229 TTTTTTATAACTAGGGCATAAGCC
1 -CTTTTATAACTGGGGCATAAGCC
*
3460253 CTTTAATAACTGGGGCATAAGCC
1 CTTTTATAACTGGGGCATAAGCC
3460276 CTTTTATAACTGGGGCATAAGCC
1 CTTTTATAACTGGGGCATAAGCC
3460299 CTTTT
1 CTTTT
3460304 GCACTTCCTC
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
23 47 0.71
24 15 0.23
25 4 0.06
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (23 bp):
CTTTTATAACTGGGGCATAAGCC
Found at i:3460378 original size:20 final size:20
Alignment explanation
Indices: 3460353--3460419 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
3460343 TTATGAATAC
3460353 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
3460373 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
3460393 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
3460413 ACCATGT
1 ATCATGT
3460420 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:3460384 original size:11 final size:11
Alignment explanation
Indices: 3460353--3460408 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
3460343 TTATGAATAC
3460353 ATCATGTGCAT
1 ATCATGTGCAT
*
3460364 ATCA--TACAT
1 ATCATGTGCAT
3460373 ATCATGTGCAT
1 ATCATGTGCAT
*
3460384 ATCA--TACAT
1 ATCATGTGCAT
*
3460393 GTCATGTGCAT
1 ATCATGTGCAT
3460404 ATCAT
1 ATCAT
3460409 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:3460488 original size:25 final size:25
Alignment explanation
Indices: 3460456--3460503 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3460446 ATACATAAAC
* * *
3460456 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
3460481 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
3460504 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:3462303 original size:28 final size:27
Alignment explanation
Indices: 3462195--3462306 Score: 113
Period size: 27 Copynumber: 4.1 Consensus size: 27
3462185 AGCATGGCTG
* *
3462195 CCAGAACAGATA-ATGTGACAGAGTCA
1 CCAGAACAGATATATGTGGCAGAGCCA
*
3462221 CCAGATATAGA-A-ATCGTGGCAGAGCCA
1 CCAGA-ACAGATATAT-GTGGCAGAGCCA
3462248 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATATATGTGGCAGAGCCA
* * * *
3462275 CCAGATCAGATAATTTGTGGCATAACCA
1 CCAGAACAGAT-ATATGTGGCAGAGCCA
3462303 CCAG
1 CCAG
3462307 GACGCTTCCT
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
26 12 0.16
27 42 0.58
28 19 0.26
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (27 bp):
CCAGAACAGATATATGTGGCAGAGCCA
Found at i:3465950 original size:38 final size:38
Alignment explanation
Indices: 3465902--3465977 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
3465892 TTCTGTAGTA
*
3465902 TCCTGCCAATCCTAGAAAACTCTGTATTTCCGACACTG
1 TCCTGCCAATCCTAGAAAACTCCGTATTTCCGACACTG
*
3465940 TCCTGCCAATCCTAGAAAACTCCGTATTTTCGACACTG
1 TCCTGCCAATCCTAGAAAACTCCGTATTTCCGACACTG
3465978 ACCTAGGCGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.26, C:0.32, G:0.13, T:0.29
Consensus pattern (38 bp):
TCCTGCCAATCCTAGAAAACTCCGTATTTCCGACACTG
Found at i:3469790 original size:27 final size:27
Alignment explanation
Indices: 3469752--3469864 Score: 124
Period size: 27 Copynumber: 4.1 Consensus size: 27
3469742 AACATGGCTG
* *
3469752 CCAGA-ACAGATAATGTGACAGAGTCA
1 CCAGATACAGATAATGTGGCAGAGCCA
*
3469778 CCAGATATAGATAATCGTGGCAGAGCCA
1 CCAGATACAGATAAT-GTGGCAGAGCCA
3469806 CCAGA-ACAGATATATGTGGCAGAGCCA
1 CCAGATACAGATA-ATGTGGCAGAGCCA
* *
3469833 CCAGAT-CAAATAATTTGTGGCATAGCCA
1 CCAGATACAGATAA--TGTGGCAGAGCCA
3469861 CCAG
1 CCAG
3469865 GACGCTTCCT
Statistics
Matches: 75, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
26 6 0.08
27 36 0.48
28 33 0.44
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (27 bp):
CCAGATACAGATAATGTGGCAGAGCCA
Found at i:3469807 original size:28 final size:26
Alignment explanation
Indices: 3469759--3469864 Score: 108
Period size: 28 Copynumber: 3.9 Consensus size: 26
3469749 CTGCCAGAAC
* *
3469759 AGATAATGTGACAGAGTCACCAGATA
1 AGATAATGTGGCAGAGCCACCAGATA
3469785 TAGATAATCGTGGCAGAGCCACCAGA-A
1 -AGATAAT-GTGGCAGAGCCACCAGATA
3469812 CAGATATATGTGGCAGAGCCACCAGATCA
1 -AGATA-ATGTGGCAGAGCCACCAGAT-A
*
3469841 A-ATAATTTGTGGCATAGCCACCAG
1 AGATAA--TGTGGCAGAGCCACCAG
3469865 GACGCTTCCT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
26 1 0.01
27 33 0.48
28 34 0.49
29 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.19
Consensus pattern (26 bp):
AGATAATGTGGCAGAGCCACCAGATA
Found at i:3469835 original size:55 final size:54
Alignment explanation
Indices: 3469752--3469864 Score: 149
Period size: 55 Copynumber: 2.1 Consensus size: 54
3469742 AACATGGCTG
*
3469752 CCAGAACAGATAATGTGACAGAGTCACCAGAT-ATAGATAA-TCGTGGCAGAGCCA
1 CCAGAACAGATAATGTGACAGAGCCACCAGATCA-A-ATAATTCGTGGCAGAGCCA
* * *
3469806 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAAATAATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGACAGAGCCACCAGATCAAATAATTCGTGGCAGAGCCA
3469861 CCAG
1 CCAG
3469865 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
54 16 0.31
55 35 0.67
56 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (54 bp):
CCAGAACAGATAATGTGACAGAGCCACCAGATCAAATAATTCGTGGCAGAGCCA
Found at i:3474022 original size:17 final size:17
Alignment explanation
Indices: 3473979--3474025 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
3473969 TTCAATTCAA
* *
3473979 CAATATATTTCAATTATT
1 CAATATAATTC-ATAATT
3473997 CACAT-TAATTCATAATT
1 CA-ATATAATTCATAATT
3474014 CAATATAATTCA
1 CAATATAATTCA
3474026 ATTCACTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 2 0.08
17 14 0.56
18 7 0.28
19 2 0.08
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.43
Consensus pattern (17 bp):
CAATATAATTCATAATT
Found at i:3474613 original size:51 final size:52
Alignment explanation
Indices: 3474513--3474634 Score: 135
Period size: 51 Copynumber: 2.4 Consensus size: 52
3474503 CCCAAATTTT
* * * *
3474513 CTTCATACTTT-ATCCGGA-ATTATTACTTTGTTGTTCTGGCTTCATCAAGAA
1 CTTCATA-TTTCATCCGGATATTATTACTTTATTGCTCTAGCTTCAACAAGAA
* *
3474564 C-TCTATATTTCATCCGGATA-TATTACTTTATTGCTCTAGTTTCAACAAGAG
1 CTTC-ATATTTCATCCGGATATTATTACTTTATTGCTCTAGCTTCAACAAGAA
*
3474615 CTTCATATTTCATCCAGATA
1 CTTCATATTTCATCCGGATA
3474635 ATTTAGTTCT
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
50 5 0.08
51 52 0.87
52 3 0.05
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.42
Consensus pattern (52 bp):
CTTCATATTTCATCCGGATATTATTACTTTATTGCTCTAGCTTCAACAAGAA
Found at i:3474693 original size:27 final size:28
Alignment explanation
Indices: 3474663--3474721 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
3474653 TTCCTGTGTG
3474663 AAAAA-CCAATAAAACTCTTGCTAGTTA
1 AAAAACCCAATAAAACTCTTGCTAGTTA
*
3474690 AAAAACCCAATAAAACTCTTGCTAGTTG
1 AAAAACCCAATAAAACTCTTGCTAGTTA
3474718 AAAA
1 AAAA
3474722 TTCATATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 5 0.17
28 25 0.83
ACGTcount: A:0.49, C:0.19, G:0.08, T:0.24
Consensus pattern (28 bp):
AAAAACCCAATAAAACTCTTGCTAGTTA
Found at i:3475179 original size:23 final size:23
Alignment explanation
Indices: 3475127--3475172 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3475117 CGTCCCCTGC
*
3475127 TATTCTGTTTCTTTCCTTCTTTT
1 TATTCTTTTTCTTTCCTTCTTTT
* *
3475150 TATTCTTTTTGTTTCTTTCTTTT
1 TATTCTTTTTCTTTCCTTCTTTT
3475173 GTTTCTTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.04, C:0.17, G:0.04, T:0.74
Consensus pattern (23 bp):
TATTCTTTTTCTTTCCTTCTTTT
Found at i:3475853 original size:13 final size:14
Alignment explanation
Indices: 3475835--3475863 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3475825 GATTAACTTC
3475835 ATAAATATTTT-TA
1 ATAAATATTTTCTA
3475848 ATAAATATTTTCTA
1 ATAAATATTTTCTA
3475862 AT
1 AT
3475864 CCATTTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATATTTTCTA
Found at i:3484777 original size:13 final size:13
Alignment explanation
Indices: 3484759--3484799 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
3484749 TTGAAGCACT
3484759 TCACACGGGCGTG
1 TCACACGGGCGTG
*
3484772 TCACACGAGCGTG
1 TCACACGGGCGTG
*
3484785 TCACACGGGCATG
1 TCACACGGGCGTG
3484798 TC
1 TC
3484800 TCTGTCGGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.20, C:0.32, G:0.32, T:0.17
Consensus pattern (13 bp):
TCACACGGGCGTG
Found at i:3487106 original size:24 final size:24
Alignment explanation
Indices: 3487077--3487135 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
3487067 AACCGAATTT
* * *
3487077 GCACACATAGTG-CTTATTACACTC
1 GCACACATAGTGCCATAGTAAAC-C
3487101 GCACACATAGTGCCATAGTAAACC
1 GCACACATAGTGCCATAGTAAACC
3487125 GCACACATAGT
1 GCACACATAGT
3487136 CATTGGATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
24 24 0.77
25 7 0.23
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (24 bp):
GCACACATAGTGCCATAGTAAACC
Found at i:3491276 original size:20 final size:20
Alignment explanation
Indices: 3491251--3491290 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3491241 ACATGAAATA
3491251 TGCATTCTTTAGATGTAATT
1 TGCATTCTTTAGATGTAATT
*
3491271 TGCATTTTTTAGATGTAATT
1 TGCATTCTTTAGATGTAATT
3491291 CTATATTACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.07, G:0.15, T:0.53
Consensus pattern (20 bp):
TGCATTCTTTAGATGTAATT
Found at i:3494640 original size:18 final size:17
Alignment explanation
Indices: 3494613--3494650 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
3494603 ATTTTACTTT
3494613 TTTTTATTTCTATTTTTA
1 TTTTTATTTCTA-TTTTA
*
3494631 TTTTTGTTTCTATTTTA
1 TTTTTATTTCTATTTTA
3494648 TTT
1 TTT
3494651 CAAATTCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTTATTTCTATTTTA
Found at i:3498718 original size:49 final size:49
Alignment explanation
Indices: 3498643--3498845 Score: 343
Period size: 49 Copynumber: 4.1 Consensus size: 49
3498633 GTGAACATGC
* *
3498643 ATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTAT
*
3498692 ATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAATGTAT
1 ATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTAT
* *
3498741 ATACATGTGATAAGGCCTAATAACCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTAT
* *
3498790 ATATACGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
1 ATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTAT
3498839 ATATATG
1 ATATATG
3498846 NNNNNNNNNN
Statistics
Matches: 143, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 143 1.00
ACGTcount: A:0.35, C:0.09, G:0.26, T:0.30
Consensus pattern (49 bp):
ATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTAT
Found at i:3500701 original size:29 final size:29
Alignment explanation
Indices: 3500659--3500716 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
3500649 TCTGGGATTT
3500659 TTTGGTTTCTTTATGTTTTGTTATTATTA
1 TTTGGTTTCTTTATGTTTTGTTATTATTA
3500688 TTTGGTTTCTTTATGTTTTGTTATTATTA
1 TTTGGTTTCTTTATGTTTTGTTATTATTA
3500717 CTCTTCTGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.14, C:0.03, G:0.14, T:0.69
Consensus pattern (29 bp):
TTTGGTTTCTTTATGTTTTGTTATTATTA
Found at i:3500723 original size:26 final size:28
Alignment explanation
Indices: 3500665--3500723 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
3500655 ATTTTTTGGT
* *
3500665 TTCTTTATGTTTTGTTATTATTATTTGGT
1 TTCTTTATGTTTTGTTATTATTATCT-GC
3500694 TTCTTTATGTTTTGTTATTATTA-CT-C
1 TTCTTTATGTTTTGTTATTATTATCTGC
3500720 TTCT
1 TTCT
3500724 GAGATGTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 4 0.14
28 1 0.04
29 23 0.82
ACGTcount: A:0.14, C:0.08, G:0.10, T:0.68
Consensus pattern (28 bp):
TTCTTTATGTTTTGTTATTATTATCTGC
Found at i:3510055 original size:40 final size:40
Alignment explanation
Indices: 3509957--3510259 Score: 380
Period size: 40 Copynumber: 7.6 Consensus size: 40
3509947 TCCTCGTTCA
* * * ** *
3509957 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
3509996 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
3510036 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
3510076 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
3510116 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
3510156 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
3510196 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
3510236 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
3510260 CAGCATTCAA
Statistics
Matches: 239, Mismatches: 20, Indels: 9
0.89 0.07 0.03
Matches are distributed among these distances:
39 37 0.15
40 194 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:3519626 original size:39 final size:39
Alignment explanation
Indices: 3519581--3519701 Score: 215
Period size: 39 Copynumber: 3.1 Consensus size: 39
3519571 AAGCAAGACA
* *
3519581 CTGGAAATGTATCCGGGCTAAAGACCTGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
3519620 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
*
3519659 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
3519698 CTGG
1 CTGG
3519702 TAACATAATT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 79 1.00
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.24
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:3529895 original size:20 final size:20
Alignment explanation
Indices: 3529870--3529912 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
3529860 GCTATAAAGC
3529870 TTAGTAAGCTCATATGAATA
1 TTAGTAAGCTCATATGAATA
3529890 TTAGTAAGCTCATATGAATA
1 TTAGTAAGCTCATATGAATA
3529910 TTA
1 TTA
3529913 AACTCATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (20 bp):
TTAGTAAGCTCATATGAATA
Found at i:3529920 original size:17 final size:19
Alignment explanation
Indices: 3529870--3529921 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
3529860 GCTATAAAGC
3529870 TTAGTAAGCTCATATGAATA
1 TTAG-AAGCTCATATGAATA
3529890 TTAGTAAGCTCATATGAATA
1 TTAG-AAGCTCATATGAATA
3529910 TTA-AA-CTCATAT
1 TTAGAAGCTCATAT
3529922 ATCAAATAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.22
18 2 0.06
20 23 0.72
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (19 bp):
TTAGAAGCTCATATGAATA
Found at i:3530613 original size:47 final size:47
Alignment explanation
Indices: 3530542--3530671 Score: 170
Period size: 47 Copynumber: 2.8 Consensus size: 47
3530532 TCAATCGATA
* * * * * *
3530542 AGTACTTATACCATGGTCCGTAGCCAACTTAAGGTAACTTATCCCGG
1 AGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCCCGG
* * *
3530589 AGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCCTCTCTG
1 AGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCCCGG
*
3530636 AATACCTATACCATGGCCCATAGCCAAATCAAGGTA
1 AGTACCTATACCATGGCCCATAGCCAAATCAAGGTA
3530672 TTTTTCGCAC
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 73 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (47 bp):
AGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCCCGG
Found at i:3534456 original size:19 final size:20
Alignment explanation
Indices: 3534427--3534464 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3534417 TTCTGAATAA
*
3534427 TTTTAATTTTTTATTTTTAG
1 TTTTAATTTTTCATTTTTAG
3534447 TTTT-ATTTTTCATTTTTA
1 TTTTAATTTTTCATTTTTA
3534465 TCTTTGTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (20 bp):
TTTTAATTTTTCATTTTTAG
Found at i:3534476 original size:25 final size:25
Alignment explanation
Indices: 3534424--3534486 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
3534414 AATTTCTGAA
*
3534424 TAATTTTAATTTTTTATTTTTAGTTT
1 TAATTTTAA-TTTTTATCTTTAGTTT
* *
3534450 TATTTTTCATTTTTATCTTT-GTCTT
1 TAATTTTAATTTTTATCTTTAGT-TT
3534475 TAATTTTAATTT
1 TAATTTTAATTT
3534487 GTTTATGTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 2 0.06
25 22 0.71
26 7 0.23
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (25 bp):
TAATTTTAATTTTTATCTTTAGTTT
Found at i:3535743 original size:15 final size:16
Alignment explanation
Indices: 3535723--3535756 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3535713 AAGTCGTGTT
*
3535723 TTATTATTTAATTA-A
1 TTATTATATAATTACA
3535738 TTATTATATAATTACA
1 TTATTATATAATTACA
3535754 TTA
1 TTA
3535757 GAGTCGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATTATATAATTACA
Found at i:3536825 original size:40 final size:39
Alignment explanation
Indices: 3536770--3537011 Score: 229
Period size: 40 Copynumber: 6.1 Consensus size: 39
3536760 ACAATTATTG
* * *
3536770 CCTGAATGCACATACGTGCGCCTGTTAGTACTTTGATATC
1 CCTGAATGCACATACGTGCCCCTGTTTGTACTTTGGTA-C
*
3536810 CCTGAATGCACATACGTGCCCCTATTTGTACTTTGGTACC
1 CCTGAATGCACATACGTGCCCCTGTTTGTACTTTGGTA-C
* *** *
3536850 CCTGAATG-A-ACA-GTGCTGTTGTTTGTACTCTGGTAC
1 CCTGAATGCACATACGTGCCCCTGTTTGTACTTTGGTAC
* *
3536886 CCTTGAATGCACATATGTGCCCCTGTTTGTACTTCGGTACC
1 CC-TGAATGCACATACGTGCCCCTGTTTGTACTTTGGTA-C
* * * *
3536927 CCTGAATGTACATACATGCCCCTATTTGTACTTTGATAC
1 CCTGAATGCACATACGTGCCCCTGTTTGTACTTTGGTAC
* * * * *
3536966 CTCTGAATGCATATACGTGCTCTTGATTGTACTATGGTAC
1 C-CTGAATGCACATACGTGCCCCTGTTTGTACTTTGGTAC
3537006 CTCTGA
1 C-CTGA
3537012 GAACATCATA
Statistics
Matches: 164, Mismatches: 32, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
36 3 0.02
37 24 0.15
38 3 0.02
39 5 0.03
40 126 0.77
41 3 0.02
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (39 bp):
CCTGAATGCACATACGTGCCCCTGTTTGTACTTTGGTAC
Found at i:3540796 original size:25 final size:25
Alignment explanation
Indices: 3540767--3540814 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
3540757 TTATAACATG
* * *
3540767 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
3540792 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
3540815 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:3540880 original size:20 final size:20
Alignment explanation
Indices: 3540851--3540897 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
3540841 ATTTTGATAA
*
3540851 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
3540871 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
3540891 ACATGAT
1 ACATGAT
3540898 GTAATCATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:3541026 original size:24 final size:24
Alignment explanation
Indices: 3540946--3541050 Score: 151
Period size: 23 Copynumber: 4.4 Consensus size: 24
3540936 GGAGGAAGTG
* *
3540946 TAAAAGGACATATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
3540970 T-AAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
3540993 T-AAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
* *
3541016 TAAAAGGGCTTTTACCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
3541040 TAAAAGAGGCT
1 TAAAAG-GGCT
3541051 AGGCATCCAA
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
23 44 0.59
24 27 0.36
25 4 0.05
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:3541267 original size:31 final size:31
Alignment explanation
Indices: 3541232--3541295 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
3541222 CGTTTACAGT
3541232 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
3541263 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
3541294 AA
1 AA
3541296 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:3548918 original size:11 final size:11
Alignment explanation
Indices: 3548882--3548937 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
3548872 CATGGTATGT
3548882 ATGATATGCAC
1 ATGATATGCAC
* *
3548893 ATGACATG--T
1 ATGATATGCAC
3548902 ATGATATGCAC
1 ATGATATGCAC
*
3548913 ATGATATG--T
1 ATGATATGCAC
3548922 ATGATATGCAC
1 ATGATATGCAC
3548933 ATGAT
1 ATGAT
3548938 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:3548937 original size:20 final size:20
Alignment explanation
Indices: 3548871--3548937 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
3548861 ATTTTGATAA
*
3548871 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
3548891 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
3548911 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
3548931 ACATGAT
1 ACATGAT
3548938 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:3549021 original size:23 final size:23
Alignment explanation
Indices: 3548988--3549060 Score: 110
Period size: 23 Copynumber: 3.1 Consensus size: 23
3548978 AGGAAGTGTA
*
3548988 AAAGGGTTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
3549011 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
* *
3549034 AAAAGGGCTTTTGCCCCATTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
3549058 AAA
1 AAA
3549061 AGAGGCTAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 25 0.54
24 21 0.46
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:3549081 original size:25 final size:24
Alignment explanation
Indices: 3548986--3549081 Score: 124
Period size: 24 Copynumber: 4.0 Consensus size: 24
3548976 AGAGGAAGTG
*
3548986 TAAAAGGGTTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
3549010 T-AAAGGGCTTATGCCCCAGTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
* *
3549033 TAAAAGGGCTTTTGCCCCATTTAT
1 TAAAAGGGCTTATGCCCCAGTTAT
*
3549057 TAAAAGAGGC-TAGGCCTCCAGTTAT
1 TAAAAG-GGCTTATGCC-CCAGTTAT
3549082 ATGATCAAGA
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
23 22 0.35
24 31 0.49
25 10 0.16
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (24 bp):
TAAAAGGGCTTATGCCCCAGTTAT
Found at i:3550374 original size:12 final size:12
Alignment explanation
Indices: 3550357--3550381 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3550347 ATATGGTAAT
3550357 TGATAATTAAAA
1 TGATAATTAAAA
3550369 TGATAATTAAAA
1 TGATAATTAAAA
3550381 T
1 T
3550382 AAGAAAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (12 bp):
TGATAATTAAAA
Found at i:3554296 original size:47 final size:48
Alignment explanation
Indices: 3554231--3554590 Score: 229
Period size: 46 Copynumber: 7.6 Consensus size: 48
3554221 TTTGTATGCT
3554231 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCAC-ATTATGAAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAG-CACGATTATGAAAGCC
*
3554277 AGTGTAAGACCATGTCTGGGACATGGCATC-G-AC-ATTGA-GACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCACGATT-ATGA--A-AGCC
* * * *
3554325 AGTGTAAGA-CATGTTTGGGACAT-GCATCAGCTTCGA-GATGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGC-ACGATTATGAAAGCC
* * * * * *
3554371 ATTATAAGA-CATGTCTGGGACAT-GCATCAACTACGA-GATG--TGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGC-ACGATTATGAAAGCC
** * *
3554415 AGTGTAAGACCATGTCTGGGACATCACATCAGCACGGATATGTGAAAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCAC-GAT-TATGAAAGCC
* * * * *
3554465 AGTGTAAGATCATGTCTGGGACATGGCATTC-GCATCAATTTTGATAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCA-TCAGCA-CGATTATGAAAGCC
* * *
3554514 AGTGTAAGACCAGGTCTGGGATATGGCATCA--AC--TTAATGGATGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCACGATT-AT-GA-AAGCC
* *
3554561 AGTGTAAGACCAGGTCTGGGACATGTCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
3554591 GGTATTATAC
Statistics
Matches: 252, Mismatches: 38, Indels: 47
0.75 0.11 0.14
Matches are distributed among these distances:
44 11 0.04
45 24 0.10
46 64 0.25
47 63 0.25
48 22 0.09
49 33 0.13
50 32 0.13
51 3 0.01
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAGCACGATTATGAAAGCC
Found at i:3554531 original size:49 final size:47
Alignment explanation
Indices: 3554465--3554590 Score: 130
Period size: 47 Copynumber: 2.6 Consensus size: 47
3554455 TGTGAAAGCT
* * * * *
3554465 AGTGTAAGATCATGTCTGGGACATGGCATTC-GCATCAATTTTGAT-AGTC
1 AGTGTAAGACCAGGTCTGGGACATGGCA-TCAAC-TCAA--TGGATGAGCC
* *
3554514 AGTGTAAGACCAGGTCTGGGATATGGCATCAACTTAATGGATGAGCC
1 AGTGTAAGACCAGGTCTGGGACATGGCATCAACTCAATGGATGAGCC
*
3554561 AGTGTAAGACCAGGTCTGGGACATGTCATC
1 AGTGTAAGACCAGGTCTGGGACATGGCATC
3554591 GGTATTATAC
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
46 4 0.06
47 31 0.47
48 5 0.08
49 26 0.39
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (47 bp):
AGTGTAAGACCAGGTCTGGGACATGGCATCAACTCAATGGATGAGCC
Found at i:3559033 original size:5 final size:5
Alignment explanation
Indices: 3559025--3559051 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3559015 CAAAAATAAA
3559025 ATTTT ATTTT ATTTT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT AT
3559052 GGTTGGTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
ATTTT
Found at i:3562774 original size:43 final size:43
Alignment explanation
Indices: 3562723--3562830 Score: 130
Period size: 43 Copynumber: 2.5 Consensus size: 43
3562713 TATCTGAGAT
* **
3562723 ATGGTCTTACATGTTATCACATATTGATGCCAATAG-CCTAG-C
1 ATGGTCTTACATGTAATCACATAACGATGCCAAT-GTCCTAGAC
* *
3562765 TATTGTCTTACATGAAATCACATAACGATGCCAATGTCCTAGAC
1 -ATGGTCTTACATGTAATCACATAACGATGCCAATGTCCTAGAC
*
3562809 ATGGTCTTACACGTAATCACAT
1 ATGGTCTTACATGTAATCACAT
3562831 CTCGGTAATT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
42 1 0.02
43 53 0.96
44 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.31
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCACATAACGATGCCAATGTCCTAGAC
Found at i:3563764 original size:32 final size:32
Alignment explanation
Indices: 3563723--3563783 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
3563713 CGGCTTATAG
*
3563723 CCATCAGTAGCGGTAATTTGATCGGCACAAAT
1 CCATCAGTAGCGGTAATATGATCGGCACAAAT
* *
3563755 CCATCAGTAGCTGTAATATGATTGGCACA
1 CCATCAGTAGCGGTAATATGATCGGCACA
3563784 CAGCCATGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (32 bp):
CCATCAGTAGCGGTAATATGATCGGCACAAAT
Found at i:3564315 original size:27 final size:27
Alignment explanation
Indices: 3564275--3564395 Score: 152
Period size: 27 Copynumber: 4.5 Consensus size: 27
3564265 TCATTTTGCC
* * *
3564275 CTACAAGGGAATTTTGGTAATTTTACA
1 CTACAGGGGTATTTCGGTAATTTTACA
* *
3564302 CTATAGGGGTATTTCGATAATTTTACA
1 CTACAGGGGTATTTCGGTAATTTTACA
* *
3564329 TTACAGGGCTATTTCGGTAATTTTACA
1 CTACAGGGGTATTTCGGTAATTTTACA
* *
3564356 CTACAGGGGTATTTCAGTACTTTTACA
1 CTACAGGGGTATTTCGGTAATTTTACA
*
3564383 CTATAGGGGTATT
1 CTACAGGGGTATT
3564396 GTGACGCCCC
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 80 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (27 bp):
CTACAGGGGTATTTCGGTAATTTTACA
Found at i:3566345 original size:42 final size:41
Alignment explanation
Indices: 3566265--3566414 Score: 162
Period size: 41 Copynumber: 3.6 Consensus size: 41
3566255 GAGCTTGGTC
3566265 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
1 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
* *
3566306 TCGAAGGGCTTTTTAGAGCCAGTG-TCATAACCGGACTTAGTT
1 TCGAAGGGC-TTTT-GAGCCAGTGCTAATAACCGAACTTAGTT
* * * * * *
3566348 CCGAAGGGCCTTCGAGCCAGTAGTCTAAT--CCGAGCTTGGTC
1 TCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGTT
*
3566389 TCGAAGGGCTTTTGAGCCGGTGCTAA
1 TCGAAGGGCTTTTGAGCCAGTGCTAA
3566415 GAGTCGGACT
Statistics
Matches: 90, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
39 4 0.04
40 9 0.10
41 37 0.41
42 28 0.31
43 12 0.13
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (41 bp):
TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
Found at i:3566397 original size:41 final size:40
Alignment explanation
Indices: 3566245--3566414 Score: 161
Period size: 41 Copynumber: 4.2 Consensus size: 40
3566235 GCTAATCGGG
*
3566245 GTCTAAATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCAGT
1 GTCT-AATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT
* *
3566286 G-CTAATAACCGAACTTAGTTTCGAAGGGCTTTTTAGAGCCAGT
1 GTCTAAT--CCGAGCTTAGTCTCGAAGGGC-TTTT-GAGCCAGT
* *
3566329 GTCATAA-CCG-GACTTAGT-TCCGAAGGGCCTTCGAGCCAGT
1 GTC-TAATCCGAG-CTTAGTCT-CGAAGGGCTTTTGAGCCAGT
* *
3566369 AGTCTAATCCGAGCTTGGTCTCGAAGGGCTTTTGAGCCGGT
1 -GTCTAATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT
3566410 G-CTAA
1 GTCTAA
3566415 GAGTCGGACT
Statistics
Matches: 107, Mismatches: 10, Indels: 26
0.75 0.07 0.18
Matches are distributed among these distances:
39 7 0.07
40 14 0.13
41 50 0.47
42 23 0.21
43 9 0.08
44 1 0.01
45 3 0.03
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (40 bp):
GTCTAATCCGAGCTTAGTCTCGAAGGGCTTTTGAGCCAGT
Found at i:3568712 original size:31 final size:31
Alignment explanation
Indices: 3568672--3568811 Score: 208
Period size: 31 Copynumber: 4.5 Consensus size: 31
3568662 TTTAACGGTT
* *
3568672 ACTGGGCCGAAGCCTTTTCATAAATCACATC
1 ACTGGGCCGAAGCCTTATCATAAATCATATC
* *
3568703 ATTGGGCCGAAGCCTTATCATAAATCTTATC
1 ACTGGGCCGAAGCCTTATCATAAATCATATC
*
3568734 ACTAGGCCGAAGCCTTATCATAAATCATATC
1 ACTGGGCCGAAGCCTTATCATAAATCATATC
*
3568765 ACTAGGCCGAAGCCTTATCATAAATCATATC
1 ACTGGGCCGAAGCCTTATCATAAATCATATC
**
3568796 TTTGGGCCGAAGCCTT
1 ACTGGGCCGAAGCCTT
3568812 TACTGTAAAT
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 99 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTATCATAAATCATATC
Found at i:3569791 original size:27 final size:27
Alignment explanation
Indices: 3569761--3569825 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
3569751 GGGCATATTC
*
3569761 GTCATTTTACCATACAGGGGTTTTACG
1 GTCATTTTACCATACAGGGGCTTTACG
* *
3569788 GTCACTTTACCCTACAGGGGCTTTACG
1 GTCATTTTACCATACAGGGGCTTTACG
*
3569815 GTCTTTTTACC
1 GTCATTTTACC
3569826 TAATAGGGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGCTTTACG
Found at i:3569909 original size:27 final size:27
Alignment explanation
Indices: 3569879--3570162 Score: 173
Period size: 27 Copynumber: 10.4 Consensus size: 27
3569869 GTAAATCTAC
* *
3569879 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAGGGTATTTTAGTAATTTTAT
* *
3569906 AAACCAATGGTATTTCTA-TAATTTTTAG
1 AAACCAAGGGTATTT-TAGTAA-TTTTAT
* * *
3569934 AAAGTCTAAGGGTATTTTTA-CAATTTTGT
1 AAA--CCAAGGGTA-TTTTAGTAATTTTAT
* *
3569963 AAATC-AGTGGTATTTTAGTAATTTTAC
1 AAACCAAG-GGTATTTTAGTAATTTTAT
*** * * *
3569990 AAATTGAGGGTATTTCAGTAATTTCAC
1 AAACCAAGGGTATTTTAGTAATTTTAT
* * *
3570017 AAA-CTAGTGGTATTTTGGTAATTTTAC
1 AAACCAAG-GGTATTTTAGTAATTTTAT
* * * *
3570044 AAACTAGGGGTATTTTGGTAATTTTAC
1 AAACCAAGGGTATTTTAGTAATTTTAT
* * * *
3570071 AAACCAGGGGCATTTTAGCAAATTTAT
1 AAACCAAGGGTATTTTAGTAATTTTAT
* * * *
3570098 AGA-CTAGGGTATTTTGGTAATTTTGT
1 AAACCAAGGGTATTTTAGTAATTTTAT
*
3570124 AAACCAAGGGTATTTTAGTAATTTTGT
1 AAACCAAGGGTATTTTAGTAATTTTAT
**
3570151 AAGTCAAGGGTA
1 AAACCAAGGGTA
3570163 AAACAGTAAT
Statistics
Matches: 202, Mismatches: 44, Indels: 22
0.75 0.16 0.08
Matches are distributed among these distances:
26 27 0.13
27 143 0.71
28 11 0.05
29 7 0.03
30 11 0.05
31 3 0.01
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (27 bp):
AAACCAAGGGTATTTTAGTAATTTTAT
Found at i:3570179 original size:54 final size:54
Alignment explanation
Indices: 3570114--3570246 Score: 167
Period size: 54 Copynumber: 2.5 Consensus size: 54
3570104 GGGTATTTTG
* * *** * * *
3570114 GTAATTTTGTAAACCAAGGGTATTTTAGTAATTTTGTAAGTCAAGGGTAAAACA
1 GTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCAAGGGTAAAACA
* *
3570168 GTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCAAGGGTAAAACA
*
3570222 GTAATTCTGTAAATCGAGGGTAAAA
1 GTAATTCTGTAAATCAAGGGTAAAA
3570247 CGGTAATTAT
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 68 1.00
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (54 bp):
GTAATTCTGTAAATCAAGGGTAAAATAGTAATTCTATAAATCAAGGGTAAAACA
Found at i:3570264 original size:27 final size:27
Alignment explanation
Indices: 3570140--3570270 Score: 172
Period size: 27 Copynumber: 4.9 Consensus size: 27
3570130 AGGGTATTTT
* * *
3570140 AGTAATTTTGTAAGTCAAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
3570167 AGTAATTCTGTAAATCAAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
3570194 AGTAATTCTATAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
3570221 GGTAATTCTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* * *
3570248 GGTAATTATGTAAATCGGGGGTA
1 AGTAATTCTGTAAATCGAGGGTA
3570271 CTTTGGTAAT
Statistics
Matches: 94, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 94 1.00
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:3578573 original size:49 final size:48
Alignment explanation
Indices: 3578514--3578703 Score: 186
Period size: 50 Copynumber: 3.8 Consensus size: 48
3578504 GTAGACAAGG
*
3578514 TTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCAACCAA
1 TTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATG-AACCAA
* *
3578563 TTATCCGGTACACGTAGTAGCCTGCACTTAGTACTATACACATG-ACCTAA
1 TTATCTGGTACACATAGTAGCCTGCACTTAGTAC--TACACATGAACC-AA
** * * * * *
3578613 CCATCTGATACACGTAGTAGCCTGCACTTAGTACTACAAACGTGATCGAA
1 TTATCTGGTACACATAGTAGCCTGCACTTAGTACTAC--ACATGAACCAA
* *
3578663 GTT-TTTGGGTACGCATAGTAGCCTGCACTTAGTACTACACA
1 -TTATCT-GGTACACATAGTAGCCTGCACTTAGTACTACACA
3578704 CATGACTCAC
Statistics
Matches: 116, Mismatches: 17, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
48 3 0.03
49 36 0.31
50 40 0.34
51 37 0.32
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.27
Consensus pattern (48 bp):
TTATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGAACCAA
Found at i:3584491 original size:49 final size:49
Alignment explanation
Indices: 3584432--3584670 Score: 253
Period size: 49 Copynumber: 4.8 Consensus size: 49
3584422 GTAGACAAGG
* * *
3584432 TTATCTGGTACGCATAGTAGCCTGCACTTAGTATTACACATGCGACCAA
1 TTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
* * * *
3584481 TTATCCGGTACACGTAGTAGCCTACACTTAGTACTACACATGTGTCCTAA
1 TTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACC-AA
** * * * * * *
3584531 CCATCTGATACACGTAGTAGCCTGCACTTATTACTACACATGTGATCGAA
1 TTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA
* ** * *
3584581 GTTATCAGGTATGCATAGTAGCCTGTACATAGTACTACACATGCGACCAA
1 -TTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
* *
3584631 TTGTCCGGTACACTTAGTAGCCTGCACTTAGTACTACACA
1 TTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACA
3584671 CGTGACTCAC
Statistics
Matches: 153, Mismatches: 34, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
49 73 0.48
50 45 0.29
51 35 0.23
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (49 bp):
TTATCCGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAA
Found at i:3587277 original size:50 final size:49
Alignment explanation
Indices: 3587104--3587335 Score: 248
Period size: 49 Copynumber: 4.7 Consensus size: 49
3587094 TCTATTGTGA
* *
3587104 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATTATT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATCATT
* * * ** ** * *
3587153 GGTCGCATGTGTAGTACTAAGTGTAGGCTACTTTGCATACCCGATAACTTT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGAT--CATT
* * *** *
3587204 GATCATGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATTAGATCGTT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATCATT
* *
3587253 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATT
1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATCATT
* *
3587303 GGTCACATGTGTAGTACTAAGTGCAAGCTACTA
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTA
3587336 TGCGTACCAG
Statistics
Matches: 148, Mismatches: 32, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
49 70 0.47
50 43 0.29
51 35 0.24
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (49 bp):
GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATCATT
Found at i:3587378 original size:150 final size:150
Alignment explanation
Indices: 3587103--3587381 Score: 391
Period size: 150 Copynumber: 1.9 Consensus size: 150
3587093 ATCTATTGTG
* *
3587103 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATTATTGGTCGCATGTGTAGT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAATTGGTCACATGTGTAGT
* * * * * * *
3587168 ACTAAGTGTAGGCTACTTTGCATACCCGATAACTTTGATCATGTGTGTAGTACTAAGTGCAGGCT
66 ACTAAGTGCAAGCTACTATGCATACCAGATAACTTTGATCAAGTGTGTAGAAATAAGTGCAGGCT
3587233 ACTACGTGTATTAGATCGTT
131 ACTACGTGTATTAGATCGTT
* *
3587253 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACTGGATAATTGGTCACATGTGTAGT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAATTGGTCACATGTGTAGT
* * * *
3587318 ACTAAGTGCAAGCTACTATGCGTACCAGATAGCTTTGGCTACAAGTGTG-A-AAATATGTGCAGG
66 ACTAAGTGCAAGCTACTATGCATACCAGATAACTTT-GAT-CAAGTGTGTAGAAATAAGTGCAGG
3587381 C
129 C
3587382 AACTGAGTAT
Statistics
Matches: 112, Mismatches: 15, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
150 102 0.91
151 3 0.03
152 7 0.06
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (150 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCGGATAATTGGTCACATGTGTAGT
ACTAAGTGCAAGCTACTATGCATACCAGATAACTTTGATCAAGTGTGTAGAAATAAGTGCAGGCT
ACTACGTGTATTAGATCGTT
Found at i:3592187 original size:9 final size:10
Alignment explanation
Indices: 3592180--3592247 Score: 59
Period size: 11 Copynumber: 6.5 Consensus size: 10
3592170 AAGAGAAAAC
3592180 AAAGAAAAGA
1 AAAGAAAAGA
3592190 AAAGAAAAAGA
1 AAAG-AAAAGA
*
3592201 AAA-AGCAAGA
1 AAAGA-AAAGA
*
3592211 GAAGAAAAAGA
1 AAAG-AAAAGA
3592222 AAATGAAATA-A
1 AAA-GAAA-AGA
3592233 AAAGAAAAGA
1 AAAGAAAAGA
3592243 AAAGA
1 AAAGA
3592248 GAGGCAAGAG
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
9 2 0.04
10 20 0.43
11 22 0.47
12 3 0.06
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.03
Consensus pattern (10 bp):
AAAGAAAAGA
Found at i:3592190 original size:5 final size:5
Alignment explanation
Indices: 3592180--3592247 Score: 59
Period size: 5 Copynumber: 13.0 Consensus size: 5
3592170 AAGAGAAAAC
* *
3592180 AAAGA AAAGA AAAGAA AAAGA AAA-A GCAAGA GAAGAA AAAGA AAATGA
1 AAAGA AAAGA AAAG-A AAAGA AAAGA -AAAGA AAAG-A AAAGA AAA-GA
3592228 AATA-A AAAGA AAAGA AAAGA
1 AA-AGA AAAGA AAAGA AAAGA
3592248 GAGGCAAGAG
Statistics
Matches: 53, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
4 2 0.04
5 36 0.68
6 14 0.26
7 1 0.02
ACGTcount: A:0.76, C:0.01, G:0.19, T:0.03
Consensus pattern (5 bp):
AAAGA
Found at i:3592200 original size:6 final size:6
Alignment explanation
Indices: 3592180--3592245 Score: 52
Period size: 6 Copynumber: 11.3 Consensus size: 6
3592170 AAGAGAAAAC
*
3592180 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATG--
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
*
3592227 AAATAA AAAG-A AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AA
3592246 GAGAGGCAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
4 2 0.04
5 14 0.28
6 25 0.50
7 3 0.06
8 3 0.06
9 3 0.06
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (6 bp):
AAAGAA
Found at i:3592221 original size:37 final size:37
Alignment explanation
Indices: 3592170--3592240 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
3592160 CATTCTTGTA
3592170 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
3592207 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
3592241 GAAAAGAGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:3592248 original size:37 final size:37
Alignment explanation
Indices: 3592169--3592249 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
3592159 ACATTCTTGT
3592169 AAAGAGAAAACAAAGAAAAGAAAAGAAAAAGAAAAAG
1 AAAGAGAAAACAAAGAAAAGAAAAGAAAAAGAAAAAG
* *
3592206 CAAGAGAAGAA-AAAGAAAATG-AAATAAAAAG-AAAAG
1 AAAGAGAA-AACAAAGAAAA-GAAAAGAAAAAGAAAAAG
3592242 AAAAGAGA
1 -AAAGAGA
3592250 GGCAAGAGGC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
36 5 0.13
37 30 0.79
38 3 0.08
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.02
Consensus pattern (37 bp):
AAAGAGAAAACAAAGAAAAGAAAAGAAAAAGAAAAAG
Found at i:3592327 original size:11 final size:12
Alignment explanation
Indices: 3592295--3592325 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3592285 TTGAGAGAAC
3592295 TTGAAAAAGCCT
1 TTGAAAAAGCCT
3592307 TTGAAAAAGCCT
1 TTGAAAAAGCCT
3592319 TTGAAAA
1 TTGAAAA
3592326 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:3594540 original size:30 final size:29
Alignment explanation
Indices: 3594506--3594608 Score: 93
Period size: 30 Copynumber: 3.5 Consensus size: 29
3594496 AGCTCACTCC
3594506 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAA-CT
* * * * *
3594536 TAGCTCAACTTCAGCTTAGGAGTTTAGACT
1 TAGCTCAACTTTAGCTCACGAG-CTAAACT
* *
3594566 CAGCTCAACTTTAGCTCATGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAA-CT
3594596 TAGCTCAA-TTTAG
1 TAGCTCAACTTTAG
3594609 TTTAAACTCG
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
29 9 0.16
30 46 0.79
31 3 0.05
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (29 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACT
Found at i:3598254 original size:68 final size:64
Alignment explanation
Indices: 3598047--3598299 Score: 212
Period size: 68 Copynumber: 3.8 Consensus size: 64
3598037 ATATAGTTTG
* *
3598047 GCTCTCTTGTACACATGGTGAACACTTAGTACCACCCATGTGACCTAG-T-CAGTTTA-TCTCGT
1 GCTCTCTTGTACACATGGTGTACAC-TAGTACCACCCATGTGACCTAGCTACA-TATATTCTCGT
3598109 A
64 A
* * * * * *
3598110 GCTCTCTTAT-CTACATGGTGTCCTTCACCTGGAACCACGCATGCGACCTAGCTACATATATTC-
1 GCTCTCTTGTAC-ACATGGTG---TACA-CTAGTACCACCCATGTGACCTAGCTACATATATTCT
3598173 CGTA
61 CGTA
*
3598177 GCTCTCTTGT-CTACATGGTGTACACATAGTATCACCCATGTGACCTAGCTACATCATAATGTCT
1 GCTCTCTTGTAC-ACATGGTGTACAC-TAGTACCACCCATGTGACCTAGCTACAT-AT-AT-TCT
*
3598241 TGTA
61 CGTA
* * * **
3598245 GCTCTCTTGTACACATGATGTGCACTCAGCACCATACATGTGACCTAGCTACATA
1 GCTCTCTTGTACACATGGTGTACACT-AGTACCACCCATGTGACCTAGCTACATA
3598300 CCATCTGTAT
Statistics
Matches: 153, Mismatches: 22, Indels: 26
0.76 0.11 0.13
Matches are distributed among these distances:
62 1 0.01
63 18 0.12
64 26 0.17
65 2 0.01
66 22 0.14
67 32 0.21
68 51 0.33
69 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (64 bp):
GCTCTCTTGTACACATGGTGTACACTAGTACCACCCATGTGACCTAGCTACATATATTCTCGTA
Found at i:3599008 original size:30 final size:30
Alignment explanation
Indices: 3598960--3599020 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3598950 TCCTTAATTC
*
3598960 AAACTTTTGAAAAATTACAATTTTTCCCCT
1 AAACTTTTGAAAAATTACAATTTTGCCCCT
* * * *
3598990 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTTGAAAAATTACAATTTTGCCCCT
3599020 A
1 A
3599021 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (30 bp):
AAACTTTTGAAAAATTACAATTTTGCCCCT
Found at i:3601373 original size:101 final size:100
Alignment explanation
Indices: 3601183--3601708 Score: 605
Period size: 101 Copynumber: 5.3 Consensus size: 100
3601173 GTAAGATCAT
* * * * * * *
3601183 GTGTGTAGTACTAAGCGCAGGCTACTACGTGTACCGGATTA-TT-GGCCGCATGTGTAGTACTAA
1 GTGTGTAGTACTAAGTGCAGGCTACTACCTGAACCAGA-TAGTTAGGTCACGTGTGTAGTACTAA
* * * *
3601246 GTGCAGGCTACTATGCGTACCCGATAACTTTGATCAC
65 GTGCAGGCTACTACGTGTACCAGATAA-TTTGGTCAC
** *
3601283 GTGTGTAGTACTAAGTGCAGGCTACTACCTGAATGAGATGGTTAGGTCACGTGTGTAGTACTAAG
1 GTGTGTAGTACTAAGTGCAGGCTACTACCTGAACCAGATAGTTAGGTCACGTGTGTAGTACTAAG
3601348 TGCAGGCTACTACGTGTACCAGATAA-TTGGTCAC
66 TGCAGGCTACTACGTGTACCAGATAATTTGGTCAC
* * * * * * *
3601382 ATGTGTAGTACTAAGTGCAGGCTACTATGC-GTACCCGATAACTTTGATCACGTGTGTAGTACTA
1 GTGTGTAGTACTAAGTGCAGGCTACTA-CCTGAACCAGAT-AGTTAGGTCACGTGTGTAGTACTA
* * ** ** *
3601446 AGTGCAGGCTACTACCTGAATGAGATGGTTAGGTCAC
64 AGTGCAGGCTACTACGTGTACCAGATAATTTGGTCAC
* * * *
3601483 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT-GGTCACATGTGTAGTACTAAG
1 GTGTGTAGTACTAAGTGCAGGCTACTACCTGAACCAGATAGTTAGGTCACGTGTGTAGTACTAAG
* * * *
3601547 TGCAGGCTACTATGCGTACCCGATAACTTTGATCAC
66 TGCAGGCTACTACGTGTACCAGATAA-TTTGGTCAC
** *
3601583 GTGTGTAGTACTAAGTGCAGGCTACTACCTGAATGAGATGGTTAGGTCACGTGTGTAGTACTAAG
1 GTGTGTAGTACTAAGTGCAGGCTACTACCTGAACCAGATAGTTAGGTCACGTGTGTAGTACTAAG
3601648 TGCAGGCTACTACGTGTACCAGATAA-TTGGTCAC
66 TGCAGGCTACTACGTGTACCAGATAATTTGGTCAC
*
3601682 ATGTGTAGTACTAAGTGCAGGCTACTA
1 GTGTGTAGTACTAAGTGCAGGCTACTA
3601709 TGCGTACTAG
Statistics
Matches: 357, Mismatches: 61, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
99 108 0.30
100 124 0.35
101 125 0.35
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (100 bp):
GTGTGTAGTACTAAGTGCAGGCTACTACCTGAACCAGATAGTTAGGTCACGTGTGTAGTACTAAG
TGCAGGCTACTACGTGTACCAGATAATTTGGTCAC
Found at i:3601721 original size:49 final size:49
Alignment explanation
Indices: 3601183--3601721 Score: 598
Period size: 49 Copynumber: 10.8 Consensus size: 49
3601173 GTAAGATCAT
* * * * * *
3601183 GTGTGTAGTACTAAGCGCAGGCTACTACGTGTACCGGATTATTGGCCGC
1 GTGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATTGGTCAC
* * * *
3601232 ATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTTGATCAC
1 GTGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAA--TTGGTCAC
* ** **
3601283 GTGTGTAGTACTAAGTGCAGGCTACTAC-CTGAATGAGATGGTTAGGTCAC
1 GTGTGTAGTACTAAGTGCAGGCTACTACGC-GTACCAGATAATT-GGTCAC
*
3601333 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCAC
1 GTGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATTGGTCAC
* * * *
3601382 ATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTTGATCAC
1 GTGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAA--TTGGTCAC
* ** **
3601433 GTGTGTAGTACTAAGTGCAGGCTACTAC-CTGAATGAGATGGTTAGGTCAC
1 GTGTGTAGTACTAAGTGCAGGCTACTACGC-GTACCAGATAATT-GGTCAC
*
3601483 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCAC
1 GTGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATTGGTCAC
* * * *
3601532 ATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTTGATCAC
1 GTGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAA--TTGGTCAC
* ** **
3601583 GTGTGTAGTACTAAGTGCAGGCTACTAC-CTGAATGAGATGGTTAGGTCAC
1 GTGTGTAGTACTAAGTGCAGGCTACTACGC-GTACCAGATAATT-GGTCAC
*
3601633 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCAC
1 GTGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATTGGTCAC
* * *
3601682 ATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTAGATA
1 GTGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATA
3601722 GCTTTGGCTA
Statistics
Matches: 407, Mismatches: 68, Indels: 30
0.81 0.13 0.06
Matches are distributed among these distances:
49 169 0.42
50 126 0.31
51 112 0.28
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (49 bp):
GTGTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATAATTGGTCAC
Found at i:3601754 original size:150 final size:150
Alignment explanation
Indices: 3601183--3601715 Score: 1021
Period size: 150 Copynumber: 3.6 Consensus size: 150
3601173 GTAAGATCAT
* * * * *
3601183 GTGTGTAGTACTAAGCGCAGGCTACTACGTGTACCGGATTATTGGCCGCATGTGTAGTACTAAGT
1 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACATGTGTAGTACTAAGT
3601248 GCAGGCTACTATGCGTACCCGATAACTTTGATCACGTGTGTAGTACTAAGTGCAGGCTACTACCT
66 GCAGGCTACTATGCGTACCCGATAACTTTGATCACGTGTGTAGTACTAAGTGCAGGCTACTACCT
3601313 GAATGAGATGGTTAGGTCAC
131 GAATGAGATGGTTAGGTCAC
3601333 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACATGTGTAGTACTAAGT
1 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACATGTGTAGTACTAAGT
3601398 GCAGGCTACTATGCGTACCCGATAACTTTGATCACGTGTGTAGTACTAAGTGCAGGCTACTACCT
66 GCAGGCTACTATGCGTACCCGATAACTTTGATCACGTGTGTAGTACTAAGTGCAGGCTACTACCT
3601463 GAATGAGATGGTTAGGTCAC
131 GAATGAGATGGTTAGGTCAC
3601483 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACATGTGTAGTACTAAGT
1 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACATGTGTAGTACTAAGT
3601548 GCAGGCTACTATGCGTACCCGATAACTTTGATCACGTGTGTAGTACTAAGTGCAGGCTACTACCT
66 GCAGGCTACTATGCGTACCCGATAACTTTGATCACGTGTGTAGTACTAAGTGCAGGCTACTACCT
3601613 GAATGAGATGGTTAGGTCAC
131 GAATGAGATGGTTAGGTCAC
3601633 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACATGTGTAGTACTAAGT
1 GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACATGTGTAGTACTAAGT
3601698 GCAGGCTACTATGCGTAC
66 GCAGGCTACTATGCGTAC
3601716 TAGATAGCTT
Statistics
Matches: 378, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 378 1.00
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (150 bp):
GTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCACATGTGTAGTACTAAGT
GCAGGCTACTATGCGTACCCGATAACTTTGATCACGTGTGTAGTACTAAGTGCAGGCTACTACCT
GAATGAGATGGTTAGGTCAC
Found at i:3606551 original size:46 final size:46
Alignment explanation
Indices: 3606498--3606712 Score: 158
Period size: 46 Copynumber: 4.6 Consensus size: 46
3606488 TTCGTGTGCT
* * *
3606498 AGTGTAAGATATGTCTGGAACATGCATCGGCCACATTATGAGACCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
* * *
3606544 AGTGTAAGACCATGTCTAGGACATGGCATC-G--ACATTGAGACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATT---ATGAGAGCC
* * *
3606592 AGTGTAAGACATGTCTGGGACATGCATCAGCCTCGA-GATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATG-AGAGCC
* * * **
3606638 AGTGTAAGACATGTATGGGACATGCATCGGCTAC--TA-GATGTGTT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGA-GAGCC
3606682 AGTGTAAGACCATGTCTGGGACATGGCATCG
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCG
3606713 ACTTGATCGA
Statistics
Matches: 135, Mismatches: 20, Indels: 28
0.74 0.11 0.15
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 11 0.08
45 18 0.13
46 55 0.41
47 27 0.20
48 20 0.15
49 1 0.01
50 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
Found at i:3611424 original size:27 final size:27
Alignment explanation
Indices: 3611393--3611446 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
3611383 TAGAGATGTG
3611393 AGAAAAAGACTGATGACTAAACCTTAT
1 AGAAAAAGACTGATGACTAAACCTTAT
3611420 AGAAAAAGACTGATGACTAAACCTTAT
1 AGAAAAAGACTGATGACTAAACCTTAT
3611447 TATTCTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (27 bp):
AGAAAAAGACTGATGACTAAACCTTAT
Found at i:3615849 original size:27 final size:27
Alignment explanation
Indices: 3615819--3615969 Score: 160
Period size: 27 Copynumber: 5.6 Consensus size: 27
3615809 ATATTGAGTC
* *
3615819 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
3615846 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
3615873 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
3615901 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
3615928 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
3615955 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
3615970 GTACAATTCA
Statistics
Matches: 106, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
27 83 0.78
28 23 0.22
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Done.