Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 97 of 206
Found at i:28348073 original size:138 final size:137
Alignment explanation
Indices: 28347827--28348377 Score: 846
Period size: 138 Copynumber: 4.0 Consensus size: 137
28347817 TAGGAAAAGG
* *
28347827 AATTATATTCTTTCCAAAAAA-ATTAATTTCCATATCTTTTATATTTTG-GCCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAAATATTAATTTCCATGTCTTTTATATTTTGAG-CAAAATTAATTAA
*
28347890 TATAACTGTTTATAATAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
65 TATAACTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
28347955 CATATATT
130 CATATATT
28347963 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGAGCAAAATTAATTAA
1 AATTATATTCTTTCCAAAA-AATATTAATTTCCATGTCTTTTATATTTTGAGCAAAATTAATTAA
* * * *
28348028 TATAATTGCTTATATTAATAAATTC-GATCAAATATATACAATTAATATTTTTTATGAATCAAAT
65 TATAACTGTTTATATTAATAAATTCAG-TAAAATATATACAATTAATATTTTGTATGAATCAAAT
*
28348092 TCTTATATT
129 TCATATATT
*
28348101 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGA-CTGAAATTAATTA
1 AATTATATTCTTTCCAAAA-AATATTAATTTCCATGTCTTTTATATTTTGAGC-AAAATTAATTA
*
28348165 ATATAACTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATGAAAT
64 ATATAACTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
28348230 TCATATATT
129 TCATATATT
* * ** *
28348239 AATTATATTCATTCCAAAAAAAAAAAATTT-CATGTCTTTTATATTTTGATCAAAATTAATTAAT
1 AATTATATTCTTTCCAAAAAATATTAATTTCCATGTCTTTTATATTTTGAGCAAAATTAATTAAT
* *
28348303 ATAACTG-TTATATTAATAAA-TCTAATGAAATATATACAATTAATATTTTGTATGAATCAAATT
66 ATAACTGTTTATATTAATAAATTC-AGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
28348366 CATATATT
130 CATATATT
28348374 AATT
1 AATT
28348378 TTATCTATGT
Statistics
Matches: 384, Mismatches: 23, Indels: 17
0.91 0.05 0.04
Matches are distributed among these distances:
134 2 0.01
135 62 0.16
136 57 0.15
137 13 0.03
138 248 0.65
139 2 0.01
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (137 bp):
AATTATATTCTTTCCAAAAAATATTAATTTCCATGTCTTTTATATTTTGAGCAAAATTAATTAAT
ATAACTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATTC
ATATATT
Found at i:28354289 original size:25 final size:25
Alignment explanation
Indices: 28354252--28354305 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
28354242 TTTTCTCAAA
* * *
28354252 AATTTAATTAATATAAAATATTA-AT
1 AATTCAATAAATAGAAAA-ATTAGAT
28354277 AATTCAATAAATAGAAAAATTAGAT
1 AATTCAATAAATAGAAAAATTAGAT
28354302 AATT
1 AATT
28354306 AAATTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (25 bp):
AATTCAATAAATAGAAAAATTAGAT
Found at i:28355035 original size:30 final size:30
Alignment explanation
Indices: 28354978--28355037 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
28354968 TCTTTTTAAA
* *
28354978 AATATTTACAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAGAGGCACCAAATTTTT
28355008 AATATTTACAAAAAGA-GCAACCAAATTTTT
1 AATATTTACAAAAAGAGGC-ACCAAATTTTT
28355038 GAAAATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 25 0.93
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCACCAAATTTTT
Found at i:28362018 original size:18 final size:19
Alignment explanation
Indices: 28361992--28362028 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
28361982 AATTTTGGAA
28361992 TGGAAAGAAGAGA-GAAAG
1 TGGAAAGAAGAGAGGAAAG
*
28362010 TGGAGAGAAGAGAGGAAAG
1 TGGAAAGAAGAGAGGAAAG
28362029 ATGTGAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.43, T:0.05
Consensus pattern (19 bp):
TGGAAAGAAGAGAGGAAAG
Found at i:28362890 original size:12 final size:12
Alignment explanation
Indices: 28362849--28362891 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
28362839 AGTTAATTGC
28362849 TATATTAGTATG
1 TATATTAGTATG
* *
28362861 TCTGTTATGTATG
1 TATATTA-GTATG
28362874 TATATTAGTATG
1 TATATTAGTATG
*
28362886 GATATT
1 TATATT
28362892 TTGTATGTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
12 15 0.60
13 10 0.40
ACGTcount: A:0.28, C:0.02, G:0.19, T:0.51
Consensus pattern (12 bp):
TATATTAGTATG
Found at i:28362896 original size:25 final size:25
Alignment explanation
Indices: 28362849--28362899 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
28362839 AGTTAATTGC
** *
28362849 TATATTAGTATGTCTGTTATGTATG
1 TATATTAGTATGGATATTATGTATG
*
28362874 TATATTAGTATGGATATTTTGTATG
1 TATATTAGTATGGATATTATGTATG
28362899 T
1 T
28362900 TATGTATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.25, C:0.02, G:0.20, T:0.53
Consensus pattern (25 bp):
TATATTAGTATGGATATTATGTATG
Found at i:28362920 original size:16 final size:16
Alignment explanation
Indices: 28362899--28362948 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
28362889 ATTTTGTATG
28362899 TTATGTATATTACTAT
1 TTATGTATATTACTAT
*
28362915 TTATGTAT-GT--TAT
1 TTATGTATATTACTAT
*
28362928 GTA-GTATATTACTAT
1 TTATGTATATTACTAT
28362943 TTATGT
1 TTATGT
28362949 CATGTATGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
12 4 0.15
13 6 0.23
15 6 0.23
16 10 0.38
ACGTcount: A:0.28, C:0.04, G:0.12, T:0.56
Consensus pattern (16 bp):
TTATGTATATTACTAT
Found at i:28362929 original size:9 final size:9
Alignment explanation
Indices: 28362857--28362930 Score: 50
Period size: 9 Copynumber: 8.7 Consensus size: 9
28362847 GCTATATTAG
*
28362857 TATGTCTGT
1 TATGTATGT
28362866 TATGTATGT
1 TATGTATGT
28362875 ATAT-TA-G-
1 -TATGTATGT
* *
28362882 TATGGATAT
1 TATGTATGT
*
28362891 TTTGTATGT
1 TATGTATGT
*
28362900 TATGTATAT
1 TATGTATGT
*
28362909 TA-CTAT-T
1 TATGTATGT
28362916 TATGTATGT
1 TATGTATGT
28362925 TATGTA
1 TATGTA
28362931 GTATATTACT
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
6 3 0.06
7 4 0.08
8 7 0.14
9 32 0.65
10 3 0.06
ACGTcount: A:0.26, C:0.03, G:0.18, T:0.54
Consensus pattern (9 bp):
TATGTATGT
Found at i:28362943 original size:28 final size:27
Alignment explanation
Indices: 28362888--28362963 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 27
28362878 TTAGTATGGA
28362888 TATTT-TGTATGTTA--TGTATATTAC
1 TATTTATGTATGTTATGTGTATATTAC
28362912 TATTTATGTATGTTATGTAGTATATTAC
1 TATTTATGTATGTTATGT-GTATATTAC
28362940 TATTTATGTCATG-TATGT-TATATT
1 TATTTATGT-ATGTTATGTGTATATT
28362964 TATTACTGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
24 5 0.11
25 9 0.19
26 6 0.13
27 1 0.02
28 23 0.49
29 3 0.06
ACGTcount: A:0.26, C:0.04, G:0.13, T:0.57
Consensus pattern (27 bp):
TATTTATGTATGTTATGTGTATATTAC
Found at i:28362956 original size:58 final size:59
Alignment explanation
Indices: 28362857--28362998 Score: 146
Period size: 58 Copynumber: 2.4 Consensus size: 59
28362847 GCTATATTAG
* * ** *
28362857 TATGTCTGTTATGTATGTATATTAGTATGGATATTTTGTATGTTATGTATATTACTATT
1 TATGTATGTTATGTATGTATATTACTATGGATATCATGTATGTTATATATATTACTATT
** * * *
28362916 TATGTATGTTATGTA-GTATATTACTATTTATGTCATGTATGTTATATTTATTACTGTT
1 TATGTATGTTATGTATGTATATTACTATGGATATCATGTATGTTATATATATTACTATT
28362974 TCCAT-TATG-TATGTTATGTATATTA
1 T--ATGTATGTTATG-TATGTATATTA
28362999 TTGTTTATAT
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
58 39 0.57
59 20 0.29
60 10 0.14
ACGTcount: A:0.26, C:0.05, G:0.15, T:0.54
Consensus pattern (59 bp):
TATGTATGTTATGTATGTATATTACTATGGATATCATGTATGTTATATATATTACTATT
Found at i:28362967 original size:24 final size:24
Alignment explanation
Indices: 28362870--28362966 Score: 87
Period size: 24 Copynumber: 4.1 Consensus size: 24
28362860 GTCTGTTATG
* *
28362870 TATGTATATTA-GTATG-GATATT
1 TATGTATGTTATGTATGTTATATT
*
28362892 T-TGTATGTTATGTATATTACTATT
1 TATGTATGTTATGTATGTTA-TATT
28362916 TATGTATGTTATGTA-G-TATATT
1 TATGTATGTTATGTATGTTATATT
* *
28362938 ACTATTTATGTCATGTATGTTATATT
1 --TATGTATGTTATGTATGTTATATT
28362964 TAT
1 TAT
28362967 TACTGTTTCC
Statistics
Matches: 61, Mismatches: 6, Indels: 14
0.75 0.07 0.17
Matches are distributed among these distances:
21 8 0.13
22 9 0.15
23 3 0.05
24 21 0.34
25 14 0.23
26 6 0.10
ACGTcount: A:0.28, C:0.03, G:0.14, T:0.55
Consensus pattern (24 bp):
TATGTATGTTATGTATGTTATATT
Found at i:28363011 original size:30 final size:30
Alignment explanation
Indices: 28362866--28363014 Score: 135
Period size: 30 Copynumber: 5.1 Consensus size: 30
28362856 GTATGTCTGT
* ** *
28362866 TATG-TATGTATATTAGTATGGATATTTTG
1 TATGTTATGTATATTACTATTTATATTATG
*
28362895 TATGTTATGTATATTACTATTTAT-GTATG
1 TATGTTATGTATATTACTATTTATATTATG
* *
28362924 TTATG-TA-GTATATTACTATTTATGTCATG
1 -TATGTTATGTATATTACTATTTATATTATG
* * * **
28362953 TATGTTATATTTATTACTGTTTCCATTATG
1 TATGTTATGTATATTACTATTTATATTATG
* *
28362983 TATGTTATGTATATTATTGTTTATATTATG
1 TATGTTATGTATATTACTATTTATATTATG
28363013 TA
1 TA
28363015 ACTAACTTTA
Statistics
Matches: 96, Mismatches: 19, Indels: 9
0.77 0.15 0.07
Matches are distributed among these distances:
28 20 0.21
29 14 0.15
30 62 0.65
ACGTcount: A:0.27, C:0.04, G:0.14, T:0.55
Consensus pattern (30 bp):
TATGTTATGTATATTACTATTTATATTATG
Found at i:28364457 original size:39 final size:39
Alignment explanation
Indices: 28364413--28364552 Score: 221
Period size: 39 Copynumber: 3.6 Consensus size: 39
28364403 CATATTCACT
* *
28364413 TTTAAGCATATGTCACATTA-TACATATAATCACATAACA
1 TTTAAGCATATATCACAATACT-CATATAATCACATAACA
*
28364452 TTTAAGCATATATCACAATACTCGTATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
28364491 TTCAAGCATATATCACAATACTCATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
28364530 -TTAAGCATATATCACAATACTCA
1 TTTAAGCATATATCACAATACTCA
28364553 AAAACATGTT
Statistics
Matches: 94, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
38 22 0.23
39 71 0.76
40 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.31
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAACA
Found at i:28364466 original size:22 final size:21
Alignment explanation
Indices: 28364427--28364545 Score: 73
Period size: 22 Copynumber: 5.9 Consensus size: 21
28364417 AGCATATGTC
28364427 ACATTATA-CATATAATCACATA
1 ACATTA-AGCATAT-ATCACATA
28364449 ACATTTAAGCATATATCACA-A
1 ACA-TTAAGCATATATCACATA
* *
28364470 TAC--T-CGTATA-ATCACATA
1 -ACATTAAGCATATATCACATA
28364488 ACATTCAAGCATATATCACA-A
1 ACATT-AAGCATATATCACATA
28364509 TAC--T---CATATAATCACATA
1 -ACATTAAGCATAT-ATCACATA
28364527 ACATTAAGCATATATCACA
1 ACATTAAGCATATATCACA
28364546 ATACTCAAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 35
0.66 0.03 0.30
Matches are distributed among these distances:
16 5 0.07
17 16 0.21
18 6 0.08
19 3 0.04
20 1 0.01
21 12 0.16
22 25 0.33
23 8 0.11
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.29
Consensus pattern (21 bp):
ACATTAAGCATATATCACATA
Found at i:28369796 original size:26 final size:27
Alignment explanation
Indices: 28369759--28369922 Score: 95
Period size: 29 Copynumber: 5.9 Consensus size: 27
28369749 AATTTACATC
28369759 AAAGG-ATGCCTTTGTGGCTATCTCTG-
1 AAAGGAAT-CCTTTGTGGCTATCTCTGT
*
28369785 AAAGGAATCCTTTGTGGCGATCTCTGTT
1 AAAGGAATCCTTTGTGGCTATCTCTG-T
*
28369813 AAAAGGAAGCCTTTGTGG-TAATCTCTGTT
1 -AAAGGAATCCTTTGTGGCT-ATCTCTG-T
* ** * *
28369842 AAAAAGAAGACTTTATGGCGATCTCTGCT
1 -AAAGGAATCCTTTGTGGCTATCTCTG-T
* *
28369871 AAATGG-ATGCCTTTGTGGCGAGACTCTG-
1 AAA-GGAAT-CCTTTGTGGCTA-TCTCTGT
* *
28369899 AAAGGAAAGCCTCTGTGGCTATCT
1 AAAGG-AATCCTTTGTGGCTATCT
28369923 TTGGAAAAAA
Statistics
Matches: 110, Mismatches: 17, Indels: 21
0.74 0.11 0.14
Matches are distributed among these distances:
26 22 0.20
27 6 0.05
28 17 0.15
29 60 0.55
30 5 0.05
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (27 bp):
AAAGGAATCCTTTGTGGCTATCTCTGT
Found at i:28369827 original size:29 final size:29
Alignment explanation
Indices: 28369759--28369891 Score: 146
Period size: 29 Copynumber: 4.7 Consensus size: 29
28369749 AATTTACATC
* *
28369759 AAAGGATGCCTTTGTGGCTATCTCTG---
1 AAAGGAAGCCTTTGTGGCGATCTCTGTTA
*
28369785 AAAGGAATCCTTTGTGGCGATCTCTGTTA
1 AAAGGAAGCCTTTGTGGCGATCTCTGTTA
**
28369814 AAAGGAAGCCTTTGTGGTAATCTCTGTTA
1 AAAGGAAGCCTTTGTGGCGATCTCTGTTA
* * * *
28369843 AAAAGAAGACTTTATGGCGATCTCTGCTA
1 AAAGGAAGCCTTTGTGGCGATCTCTGTTA
* *
28369872 AATGGATGCCTTTGTGGCGA
1 AAAGGAAGCCTTTGTGGCGA
28369892 GACTCTGAAA
Statistics
Matches: 87, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
26 23 0.26
29 64 0.74
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (29 bp):
AAAGGAAGCCTTTGTGGCGATCTCTGTTA
Found at i:28373066 original size:40 final size:40
Alignment explanation
Indices: 28373022--28373098 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
28373012 CTACCTCTAA
28373022 TGTAATGACTAAGGATAAAAGATGGATTAAGGCCTAAAGG
1 TGTAATGACTAAGGATAAAAGATGGATTAAGGCCTAAAGG
28373062 TGTAATGACTAAGGATAAAAGATGGATTAAGGCCTAA
1 TGTAATGACTAAGGATAAAAGATGGATTAAGGCCTAA
28373099 GGGTATGTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.43, C:0.08, G:0.26, T:0.23
Consensus pattern (40 bp):
TGTAATGACTAAGGATAAAAGATGGATTAAGGCCTAAAGG
Found at i:28378083 original size:68 final size:67
Alignment explanation
Indices: 28377974--28378314 Score: 405
Period size: 68 Copynumber: 5.0 Consensus size: 67
28377964 CTTAAAATCG
* * * *
28377974 GGAGTCTGCCAGGACATCAAACATGAGGTTAAATTGTGTAAGACCATAACTCGGCTATGGCAACA
1 GGAGTCTGCCAGGACATTAAACATG-GGTTACATTGTGTAAGACCATAGCTCGACTATGGCAACA
28378039 TAT
65 TAT
* * *
28378042 GGAGTCTGCCAAGACATTAAACATAGGGTTATATTGTGTAAGACCATAGCTCGACTATGGAAACA
1 GGAGTCTGCCAGGACATTAAACAT-GGGTTACATTGTGTAAGACCATAGCTCGACTATGGCAACA
28378107 TAT
65 TAT
* * *
28378110 GGAGTCCGCCAGGACATTAAACATGAGGTTACATTGTGTAAGACCATAGCTCAAATATGGCAACA
1 GGAGTCTGCCAGGACATTAAACATG-GGTTACATTGTGTAAGACCATAGCTCGACTATGGCAACA
28378175 TAT
65 TAT
** * * * * * * * *
28378178 GGAGTCCACTAAGACATTAAACATGGGGTTACATTATGTCATACCAAAGCTCGACTATTGCAACG
1 GGAGTCTGCCAGGACATTAAACAT-GGGTTACATTGTGTAAGACCATAGCTCGACTATGGCAACA
28378243 TAT
65 TAT
* * * *
28378246 GGAGTCTTCTAGGACATTAAACATGGGGTTACGTTGTGTAAGACCATAGCTC-AGCTATGGTAAC
1 GGAGTCTGCCAGGACATTAAACAT-GGGTTACATTGTGTAAGACCATAGCTCGA-CTATGGCAAC
28378310 ATAT
64 ATAT
28378314 G
1 G
28378315 AAGTTTGCGA
Statistics
Matches: 235, Mismatches: 34, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
67 2 0.01
68 231 0.98
69 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (67 bp):
GGAGTCTGCCAGGACATTAAACATGGGTTACATTGTGTAAGACCATAGCTCGACTATGGCAACAT
AT
Found at i:28378229 original size:136 final size:136
Alignment explanation
Indices: 28377974--28378314 Score: 466
Period size: 136 Copynumber: 2.5 Consensus size: 136
28377964 CTTAAAATCG
* * * *
28377974 GGAGTCTGCCAGGACATCAAACATGAGGTTAAATTGTGTAAGACCATAACTCGGCTATGGCAACA
1 GGAGTCTGCCAGGACATTAAACATGAGGTTACATTGTGTAAGACCATAGCTCAGCTATGGCAACA
** * * *
28378039 TATGGAGTCTGCCAAGACATTAAACATAGGGTTATATTGTGTAAGACCATAGCTCGACTATGGAA
66 TATGGAGTCCACCAAGACATTAAACATAGGGTTACATTATGTAAGACCAAAGCTCGACTATGGAA
28378104 ACATAT
131 ACATAT
* **
28378110 GGAGTCCGCCAGGACATTAAACATGAGGTTACATTGTGTAAGACCATAGCTCAAATATGGCAACA
1 GGAGTCTGCCAGGACATTAAACATGAGGTTACATTGTGTAAGACCATAGCTCAGCTATGGCAACA
* * * * * *
28378175 TATGGAGTCCACTAAGACATTAAACATGGGGTTACATTATGTCATACCAAAGCTCGACTATTGCA
66 TATGGAGTCCACCAAGACATTAAACATAGGGTTACATTATGTAAGACCAAAGCTCGACTATGGAA
*
28378240 ACGTAT
131 ACATAT
* * * * *
28378246 GGAGTCTTCTAGGACATTAAACATGGGGTTACGTTGTGTAAGACCATAGCTCAGCTATGGTAACA
1 GGAGTCTGCCAGGACATTAAACATGAGGTTACATTGTGTAAGACCATAGCTCAGCTATGGCAACA
28378311 TATG
66 TATG
28378315 AAGTTTGCGA
Statistics
Matches: 178, Mismatches: 27, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
136 178 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (136 bp):
GGAGTCTGCCAGGACATTAAACATGAGGTTACATTGTGTAAGACCATAGCTCAGCTATGGCAACA
TATGGAGTCCACCAAGACATTAAACATAGGGTTACATTATGTAAGACCAAAGCTCGACTATGGAA
ACATAT
Found at i:28381532 original size:30 final size:30
Alignment explanation
Indices: 28381498--28381585 Score: 113
Period size: 30 Copynumber: 2.9 Consensus size: 30
28381488 GGTGTCCTCG
* *
28381498 CATCATAAGATAGCCACAGAGGCATCCATA
1 CATCATTAGATAGCCACAAAGGCATCCATA
* **
28381528 CATCATTAGATAGCCAGAAAGGTGTCCATA
1 CATCATTAGATAGCCACAAAGGCATCCATA
* *
28381558 CATCATTAGATAGCCATAAAGGCGTCCA
1 CATCATTAGATAGCCACAAAGGCATCCA
28381586 AACAAAAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (30 bp):
CATCATTAGATAGCCACAAAGGCATCCATA
Found at i:28383649 original size:29 final size:30
Alignment explanation
Indices: 28383580--28383659 Score: 101
Period size: 29 Copynumber: 2.7 Consensus size: 30
28383570 CATAATTTGA
*
28383580 TCGTCGCCATCCCTTTTCATAGTTCAATGG
1 TCGTCACCATCCCTTTTCATAGTTCAATGG
* *
28383610 TCGTCAACATCCCTTTTCATTG-T-AGATGG
1 TCGTCACCATCCCTTTTCATAGTTCA-ATGG
*
28383639 TCGTCACCATCCATTTTCATA
1 TCGTCACCATCCCTTTTCATA
28383660 ATCAATAGCC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
28 1 0.02
29 23 0.53
30 19 0.44
ACGTcount: A:0.20, C:0.29, G:0.14, T:0.38
Consensus pattern (30 bp):
TCGTCACCATCCCTTTTCATAGTTCAATGG
Found at i:28383679 original size:29 final size:28
Alignment explanation
Indices: 28383647--28383716 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
28383637 GGTCGTCACC
28383647 ATCCATTTTCATAATCAATAGCCGAAGCT
1 ATCC-TTTTCATAATCAATAGCCGAAGCT
* * * **
28383676 ATCCCTTTCTGTATTTGATAGCCGAAGCT
1 ATCCTTTTC-ATAATCAATAGCCGAAGCT
28383705 ATCCCTTTTCAT
1 AT-CCTTTTCAT
28383717 TTGTTGATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
28 4 0.12
29 22 0.69
30 6 0.19
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.37
Consensus pattern (28 bp):
ATCCTTTTCATAATCAATAGCCGAAGCT
Found at i:28383837 original size:41 final size:41
Alignment explanation
Indices: 28383780--28383863 Score: 152
Period size: 41 Copynumber: 2.0 Consensus size: 41
28383770 TTTTACACAA
28383780 TAGTAGCATTCAAATCATGAAATAAAAA-AGAAACTTAAATG
1 TAGTAGCATTCAAATCATGAAATAAAAACA-AAACTTAAATG
28383821 TAGTAGCATTCAAATCATGAAATAAAAACAAAACTTAAATG
1 TAGTAGCATTCAAATCATGAAATAAAAACAAAACTTAAATG
28383862 TA
1 TA
28383864 CAAACTTACT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 41 0.98
42 1 0.02
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.25
Consensus pattern (41 bp):
TAGTAGCATTCAAATCATGAAATAAAAACAAAACTTAAATG
Found at i:28389221 original size:28 final size:28
Alignment explanation
Indices: 28389189--28389247 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
28389179 TTATAAGAAC
**
28389189 TTAATGTCTTTTTCAACATAATATCATT
1 TTAATGTCACTTTCAACATAATATCATT
28389217 TTAATGTCACTTTCAACATAATATCATT
1 TTAATGTCACTTTCAACATAATATCATT
28389245 TTA
1 TTA
28389248 GTTCCAAACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.34, C:0.15, G:0.03, T:0.47
Consensus pattern (28 bp):
TTAATGTCACTTTCAACATAATATCATT
Found at i:28389260 original size:28 final size:28
Alignment explanation
Indices: 28389201--28389260 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
28389191 AATGTCTTTT
***
28389201 TCAACATAATATCATTTTAATGTCACTT
1 TCAACATAATATCATTTTAATGTCAAAC
*
28389229 TCAACATAATATCATTTTAGT-TCCAAAC
1 TCAACATAATATCATTTTAATGT-CAAAC
28389257 TCAA
1 TCAA
28389261 AACTAACTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.38, C:0.20, G:0.03, T:0.38
Consensus pattern (28 bp):
TCAACATAATATCATTTTAATGTCAAAC
Found at i:28390631 original size:22 final size:22
Alignment explanation
Indices: 28390606--28390649 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
28390596 TGAAAGAGTA
28390606 GGCTTTGAAGAGGGCAAGTCCT
1 GGCTTTGAAGAGGGCAAGTCCT
28390628 GGCTTTGAAGAGGGCAAGTCCT
1 GGCTTTGAAGAGGGCAAGTCCT
28390650 TTGTATTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23
Consensus pattern (22 bp):
GGCTTTGAAGAGGGCAAGTCCT
Found at i:28408399 original size:20 final size:18
Alignment explanation
Indices: 28408347--28408393 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
28408337 AAAAAACAAA
*
28408347 ATATAATAAT-TATTAAT
1 ATATAATTATATATTAAT
*
28408364 ATACAATTATATATTAAT
1 ATATAATTATATATTAAT
28408382 ATATAATTATAT
1 ATATAATTATAT
28408394 CCATTATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATAATTATATATTAAT
Found at i:28427049 original size:18 final size:18
Alignment explanation
Indices: 28427026--28427063 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
28427016 TTTATTTTAC
28427026 TTAGTTAAAATCCTAGTT
1 TTAGTTAAAATCCTAGTT
28427044 TTAGTTAAAATCCTAGTT
1 TTAGTTAAAATCCTAGTT
28427062 TT
1 TT
28427064 TAATCACCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (18 bp):
TTAGTTAAAATCCTAGTT
Found at i:28428586 original size:39 final size:39
Alignment explanation
Indices: 28428543--28428621 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
28428533 CCATAGAATA
28428543 AGTAAATTTCTCACATACAAACATATCATTTAATTTATC
1 AGTAAATTTCTCACATACAAACATATCATTTAATTTATC
28428582 AGTAAATTTCTCACATACAAACATATCATTTAATTTATC
1 AGTAAATTTCTCACATACAAACATATCATTTAATTTATC
28428621 A
1 A
28428622 ATCTCTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.38
Consensus pattern (39 bp):
AGTAAATTTCTCACATACAAACATATCATTTAATTTATC
Found at i:28428652 original size:17 final size:17
Alignment explanation
Indices: 28428630--28428662 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28428620 CAATCTCTTT
28428630 TTACATATAATATCATG
1 TTACATATAATATCATG
*
28428647 TTACATATGATATCAT
1 TTACATATAATATCAT
28428663 CCATAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (17 bp):
TTACATATAATATCATG
Found at i:28437191 original size:141 final size:141
Alignment explanation
Indices: 28436943--28437245 Score: 398
Period size: 141 Copynumber: 2.1 Consensus size: 141
28436933 AACACCCAAT
* * *
28436943 AGTTTATTGATTTACGATCT-TGAACGATTCATTCATAGCTTGTCGATTACAATCGTAGCTTCAT
1 AGTTCATTGATTTACGAT-TATAAACAATTCATTCATAGCTTGTCGATTACAATCGTAGCTTCAT
* ** *
28437007 TTAAACAGTCTATTGATTTATGATCACAATGGATATTTCTAGAGTTTGTTGATTTAAGATCATAG
65 TTAAACAGTCTATTGATTTACGATCACAATGGATATTTCTAGAGCCTGTTGATGTAAGATCATAG
28437072 CTCCACTCAACA
130 CTCCACTCAACA
* * *
28437084 A-TTCATTGATTTATGATTATAAACAATTCATTTATAGCTTGTCGATTTACGATCGTAGCTTCAT
1 AGTTCATTGATTTACGATTATAAACAATTCATTCATAGCTTGTCGA-TTACAATCGTAGCTTCAT
* * * *
28437148 TTAAATAGTC-AGTTTATTTACGATCACAACT-GATATTTTTAGAGCCTGTTGATGTAAGATCGT
65 TTAAACAGTCTA-TTGATTTACGATCACAA-TGGATATTTCTAGAGCCTGTTGATGTAAGATCAT
**
28437211 AGCTCCACTCAGTA
128 AGCTCCACTCAACA
28437225 AGTTCATTGATTTACGATTAT
1 AGTTCATTGATTTACGATTAT
28437246 GAATGACTAT
Statistics
Matches: 140, Mismatches: 17, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
139 1 0.01
140 38 0.27
141 82 0.59
142 19 0.14
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.40
Consensus pattern (141 bp):
AGTTCATTGATTTACGATTATAAACAATTCATTCATAGCTTGTCGATTACAATCGTAGCTTCATT
TAAACAGTCTATTGATTTACGATCACAATGGATATTTCTAGAGCCTGTTGATGTAAGATCATAGC
TCCACTCAACA
Found at i:28437589 original size:68 final size:69
Alignment explanation
Indices: 28437479--28437660 Score: 330
Period size: 68 Copynumber: 2.7 Consensus size: 69
28437469 TGATAATACA
*
28437479 TAAGTATTTGTTAACCGATGATAACTTTCCTTTATTTTATGGTGAAAAGATTGGCTTTTGTTTAT
1 TAAGTATTTGTTAACCGATGATAACTTTCCTTTATTTTATGGTGAAAAGATTGGCTTTTGGTTAT
28437544 GCCT
66 GCCT
*
28437548 TAAGTA-TTGTTAACTGATGATAACTTTCCTTTATTTTATGGTGAAAAGATTGGCTTTTGGTTAT
1 TAAGTATTTGTTAACCGATGATAACTTTCCTTTATTTTATGGTGAAAAGATTGGCTTTTGGTTAT
28437612 GCCT
66 GCCT
*
28437616 TAAGTATTTGTTAACCGATGATAACTTTCGTTTATTTTATGGTGA
1 TAAGTATTTGTTAACCGATGATAACTTTCCTTTATTTTATGGTGA
28437661 TAAATTATTA
Statistics
Matches: 108, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
68 66 0.61
69 42 0.39
ACGTcount: A:0.25, C:0.10, G:0.18, T:0.46
Consensus pattern (69 bp):
TAAGTATTTGTTAACCGATGATAACTTTCCTTTATTTTATGGTGAAAAGATTGGCTTTTGGTTAT
GCCT
Found at i:28439615 original size:99 final size:100
Alignment explanation
Indices: 28439420--28439760 Score: 458
Period size: 99 Copynumber: 3.4 Consensus size: 100
28439410 TATCGATGAA
*
28439420 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGTTGGTCACATGTGTAGTTC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAA--TTGGTCACATGTGTAGTAC
* *
28439485 TAAGTGAACGCTACAATGTGTATCGAGAAGCTTTGGT
64 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
*
28439522 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAA-TGGTCACTTGTGTAGTACTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATTGGTCACATGTGTAGTACTA
28439586 AGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 AGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
* * *
28439621 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAACCG-TAAAACTTGATCACGTGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGAT-AAA-TTGGTCACATGTGTAGTAC
* * * * *
28439685 TATA-TGAAGGCTACTACGTGAACCGTA-AAAC-TTGAT
64 TA-AGTGAAGGCTACAATGTGTACCG-AGAAGCTTTGGT
* * *
28439721 CATGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGA
28439761 ATGATAAAAG
Statistics
Matches: 217, Mismatches: 16, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
98 1 0.00
99 92 0.42
100 39 0.18
101 39 0.18
102 46 0.21
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (100 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATTGGTCACATGTGTAGTACTA
AGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
Found at i:28439693 original size:50 final size:50
Alignment explanation
Indices: 28439420--28439754 Score: 354
Period size: 51 Copynumber: 6.7 Consensus size: 50
28439410 TATCGATGAA
* * * *
28439420 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAGAAA-CTTGGT
* * * * * * * * *
28439471 CACATGTGTAGTTCTAAGTGAACGCTACAATGTGTATCGAGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAGAAAC-TTGGT
* * *
28439522 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAA--TGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAGAAACTTGGT
* * * * * *
28439570 CACTTGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAGAAAC-TTGGT
* *
28439621 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAACCGTA-AAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-AGAAACTTGGT
* *
28439671 CACGTGTGTAGTACTATATGAAGGCTACTACGTGAACCGTA-AAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-AGAAACTTGGT
*
28439721 CATGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
28439755 TATCGAATGA
Statistics
Matches: 237, Mismatches: 42, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
48 39 0.16
50 84 0.35
51 113 0.48
52 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAGAAACTTGGT
Found at i:28439793 original size:151 final size:149
Alignment explanation
Indices: 28439521--28439793 Score: 336
Period size: 151 Copynumber: 1.8 Consensus size: 149
28439511 GAAGCTTTGG
* * * *
28439521 TCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGGTCACTTGTGTAGTACTA
1 TCACGTGTGTAGTACTATATGAAGGCTACTACGTGAACCGATAAATGATCACTTGTGTAGTACTA
* * *** * * *
28439586 AGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTA
66 AGTGAAGGCTACAACGTGTACCGAGAAGATAAAGTAACATGGGTAGTACTGTGTGAAGGCTACTA
28439651 CGTGAACCGTAAAACTTGA
131 CGTGAACCGTAAAACTTGA
28439670 TCACGTGTGTAGTACTATATGAAGGCTACTACGTGAACCG-TAAAACTTGATCA-TGTGTGTAGT
1 TCACGTGTGTAGTACTATATGAAGGCTACTACGTGAACCGAT-AAA--TGATCACT-TGTGTAGT
* * * *
28439733 ACTATGTGAAGGCTACTACGTGTATCGA-ATGATAAAAGTAACATGGGTAGTACTGTGTGAA
62 ACTAAGTGAAGGCTACAACGTGTACCGAGAAGAT-AAAGTAACATGGGTAGTACTGTGTGAA
28439794 AAACCTCAAA
Statistics
Matches: 103, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
148 1 0.01
149 40 0.39
150 4 0.04
151 58 0.56
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (149 bp):
TCACGTGTGTAGTACTATATGAAGGCTACTACGTGAACCGATAAATGATCACTTGTGTAGTACTA
AGTGAAGGCTACAACGTGTACCGAGAAGATAAAGTAACATGGGTAGTACTGTGTGAAGGCTACTA
CGTGAACCGTAAAACTTGA
Found at i:28441646 original size:15 final size:15
Alignment explanation
Indices: 28441626--28441654 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28441616 CCTCAAGGTT
28441626 TGGGGCTGAAGAATA
1 TGGGGCTGAAGAATA
28441641 TGGGGCTGAAGAAT
1 TGGGGCTGAAGAAT
28441655 TTAGAGCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.07, G:0.41, T:0.21
Consensus pattern (15 bp):
TGGGGCTGAAGAATA
Found at i:28450229 original size:20 final size:20
Alignment explanation
Indices: 28450194--28450242 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
28450184 ATCATGGTCT
*
28450194 TTGCTT-CTTCTTTACTTAC
1 TTGCTTACTTGTTTACTTAC
28450213 TCT-CTTACTTGTTTACTTAC
1 T-TGCTTACTTGTTTACTTAC
28450233 TTGCTTACTT
1 TTGCTTACTT
28450243 AAAAAACTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.57
Consensus pattern (20 bp):
TTGCTTACTTGTTTACTTAC
Found at i:28450551 original size:50 final size:50
Alignment explanation
Indices: 28450471--28450603 Score: 122
Period size: 50 Copynumber: 2.7 Consensus size: 50
28450461 CAATGCCACA
** * * *
28450471 TCCCAGATATGGTCTTACAAGGGAGTTCTCATATCGATGCCCATGCAATG
1 TCCCAGATATGGTCTTACAAGGGACCTCTCATATAGATGCCAACGCAATG
*** * *
28450521 TCCCAGATATGGTCTTATGGGGGACCTCTCATCTAGATGCCAACGCCATG
1 TCCCAGATATGGTCTTACAAGGGACCTCTCATATAGATGCCAACGCAATG
* * * * * *
28450571 TCCCAAACAAGATCCTACATGGGACCTCTCATA
1 TCCCAGATATGGTCTTACAAGGGACCTCTCATA
28450604 ACCTCAATAA
Statistics
Matches: 64, Mismatches: 19, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
50 64 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (50 bp):
TCCCAGATATGGTCTTACAAGGGACCTCTCATATAGATGCCAACGCAATG
Found at i:28452605 original size:20 final size:20
Alignment explanation
Indices: 28452571--28452614 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
28452561 GTCTTAACCG
28452571 AATTAATTAGTTCTTAG-TTT
1 AATTAATTAGTTCTT-GTTTT
28452591 AATTAATT-GTATCTTGTTTT
1 AATTAATTAGT-TCTTGTTTT
28452611 AATT
1 AATT
28452615 TAAGACGTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.57
Consensus pattern (20 bp):
AATTAATTAGTTCTTGTTTT
Found at i:28453932 original size:18 final size:18
Alignment explanation
Indices: 28453909--28453950 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
28453899 GAAATTTTTT
28453909 AAAAAA-GTGAATTGAAAA
1 AAAAAACGTGAATT-AAAA
28453927 AAAAAATCGTGAATTAAAA
1 AAAAAA-CGTGAATTAAAA
28453946 AAAAA
1 AAAAA
28453951 GGTGTTGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.27
19 9 0.41
20 7 0.32
ACGTcount: A:0.69, C:0.02, G:0.12, T:0.17
Consensus pattern (18 bp):
AAAAAACGTGAATTAAAA
Found at i:28454305 original size:14 final size:14
Alignment explanation
Indices: 28454286--28454315 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28454276 TTCGAAAGAT
*
28454286 TTGTGAGGTTTTTG
1 TTGTGAGGTCTTTG
28454300 TTGTGAGGTCTTTG
1 TTGTGAGGTCTTTG
28454314 TT
1 TT
28454316 TTCATGTCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.03, G:0.33, T:0.57
Consensus pattern (14 bp):
TTGTGAGGTCTTTG
Found at i:28466678 original size:50 final size:50
Alignment explanation
Indices: 28466543--28466680 Score: 161
Period size: 49 Copynumber: 2.8 Consensus size: 50
28466533 TACCGACAAT
* * ** * *
28466543 GCCATATCCCAAATATGGTCTTACATGGGAATTCTCATATCGGTGCCCAT
1 GCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAC
* ** * *
28466593 GCCATGTCCCAG-CATGGTCTTACGGGGGACCTCTCATCTTGGTGCCAAC
1 GCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAC
*
28466642 GCCATATCCCAGAGATGGTCTTACATGGGACCTCTCATA
1 GCCATATCCCAGACATGGTCTTACATGGGACCTCTCATA
28466681 ACCTTAATAA
Statistics
Matches: 71, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
49 39 0.55
50 32 0.45
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
GCCATATCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAC
Found at i:28476738 original size:48 final size:48
Alignment explanation
Indices: 28476686--28476796 Score: 132
Period size: 48 Copynumber: 2.3 Consensus size: 48
28476676 AAGGTCATAG
* * * **
28476686 ATAAACTACCATATAATTAGAATCGTGAACAACATCACATTAATGCAC
1 ATAAACTGCCATATAATCAGAATCATGAACAACATCACATTAACACAC
* *** *
28476734 ATAAACTGCCATATAATCAGATTCATGAACAGTGTCACATTAACACAG
1 ATAAACTGCCATATAATCAGAATCATGAACAACATCACATTAACACAC
28476782 ATAAACTGCCATATA
1 ATAAACTGCCATATA
28476797 CTTCCACCTT
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (48 bp):
ATAAACTGCCATATAATCAGAATCATGAACAACATCACATTAACACAC
Found at i:28480669 original size:55 final size:56
Alignment explanation
Indices: 28480562--28480670 Score: 157
Period size: 56 Copynumber: 2.0 Consensus size: 56
28480552 ATTTATAGCT
*
28480562 GACACCCTTGTACCAAATTTTAAAAAAAAATATTGGGTGTTAGGACAATGATGGTC
1 GACACCCTCGTACCAAATTTTAAAAAAAAATATTGGGTGTTAGGACAATGATGGTC
* ** * *
28480618 GACACCCTCGTACCAGATTTTTTAAAAAAA-ATTGGGTGTTGGGACATTGATGG
1 GACACCCTCGTACCAAATTTTAAAAAAAAATATTGGGTGTTAGGACAATGATGG
28480671 CCATCACCTC
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
55 21 0.45
56 26 0.55
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (56 bp):
GACACCCTCGTACCAAATTTTAAAAAAAAATATTGGGTGTTAGGACAATGATGGTC
Found at i:28480686 original size:55 final size:56
Alignment explanation
Indices: 28480563--28480695 Score: 155
Period size: 55 Copynumber: 2.4 Consensus size: 56
28480553 TTTATAGCTG
* * *
28480563 ACACCCTTGTACCAAATTTTAAAAAAAAATATTGGGTGTTAGGACAATGATGGTCG
1 ACACCCTCGTACCAGATTTTAAAAAAAAATATTGGGTGTTAGGACAATGATGGTCC
** * *
28480619 ACACCCTCGTACCAGATTTTTTAAAAAAA-ATTGGGTGTTGGGACATTGATGG-CC
1 ACACCCTCGTACCAGATTTTAAAAAAAAATATTGGGTGTTAGGACAATGATGGTCC
*
28480673 ATCA-CCTCAGTACCAGAATTTAA
1 A-CACCCTC-GTACCAGATTTTAA
28480696 TTAAAAAGTA
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
54 6 0.09
55 34 0.52
56 25 0.38
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (56 bp):
ACACCCTCGTACCAGATTTTAAAAAAAAATATTGGGTGTTAGGACAATGATGGTCC
Found at i:28480840 original size:69 final size:70
Alignment explanation
Indices: 28480687--28481012 Score: 482
Period size: 70 Copynumber: 4.6 Consensus size: 70
28480677 CCTCAGTACC
*
28480687 AGAATTTAATTAAAAAGTAAAT-ATTGAAGGATAAATTAATTTAAAGGAATAAATTTAAATTTTA
1 AGAATTTAATTAAAAAG-AAATAATTAAAGGATAAATTAATTTAAAGGAATAAATTTAAATTTTA
28480751 AAAAAT
65 AAAAAT
* *
28480757 AGAATTTAATTAAAAATAAATAATTAATGGATAAA-TATATTTAAAGGAATAAATTTAAATTTT-
1 AGAATTTAATTAAAAAGAAATAATTAAAGGATAAATTA-ATTTAAAGGAATAAATTTAAATTTTA
28480820 AAAAAT
65 AAAAAT
* * *
28480826 AGAATTTAACTAAAAACAAATAATTAAAGGATAAATCT-ATTTAAAGGAATAAATTCAAATTTTA
1 AGAATTTAATTAAAAAGAAATAATTAAAGGATAAAT-TAATTTAAAGGAATAAATTTAAATTTTA
28480890 AAAAAT
65 AAAAAT
* *
28480896 AGAATTTAATTAAAGAAAGAAATAATTAAAGGGTAAATTAATTTAAAGGGATAAATTTAAA-TTT
1 AGAATTTAATT-AA-AAAGAAATAATTAAAGGATAAATTAATTTAAAGGAATAAATTTAAATTTT
28480960 AAAAAAT
64 AAAAAAT
*
28480967 AGAATTTAAATAAAAAAGAAATAATTAAAGGATAAATTAATTTAAA
1 AGAATTT-AATTAAAAAGAAATAATTAAAGGATAAATTAATTTAAA
28481013 TAAATAGAAA
Statistics
Matches: 233, Mismatches: 14, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
69 68 0.29
70 99 0.42
71 23 0.10
72 43 0.18
ACGTcount: A:0.57, C:0.01, G:0.09, T:0.32
Consensus pattern (70 bp):
AGAATTTAATTAAAAAGAAATAATTAAAGGATAAATTAATTTAAAGGAATAAATTTAAATTTTAA
AAAAT
Found at i:28480937 original size:16 final size:18
Alignment explanation
Indices: 28480921--28480962 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
28480911 AAAGAAATAA
28480921 TTAAAGGG-TAAATTAAT
1 TTAAAGGGATAAATTAAT
28480938 TTAAAGGGATAAATTTAAAT
1 TTAAAGGGATAAA-TT-AAT
28480958 TTAAA
1 TTAAA
28480963 AAATAGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.36
18 4 0.18
19 2 0.09
20 8 0.36
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (18 bp):
TTAAAGGGATAAATTAAT
Found at i:28481042 original size:17 final size:17
Alignment explanation
Indices: 28481020--28481053 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28481010 AAATAAATAG
28481020 AAATTAAAAAAAGAAAA
1 AAATTAAAAAAAGAAAA
*
28481037 AAATTAGAAAAAGAAAA
1 AAATTAAAAAAAGAAAA
28481054 GAGGATGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (17 bp):
AAATTAAAAAAAGAAAA
Found at i:28481054 original size:70 final size:69
Alignment explanation
Indices: 28480699--28481055 Score: 167
Period size: 70 Copynumber: 5.1 Consensus size: 69
28480689 AATTTAATTA
* ** ** * *
28480699 AAAAGTAAAT-ATTGAAGGATAAATTAATTTAAAGGAATAAATTTAAATTTTAAAAAATAGAATT
1 AAAAG-AAATAATTAAAGGATAAATTAATTTAAA-G-ATAAATAGAAATTAAAAAAAAAAAAATT
* **
28480763 TAATTA-
63 AAAAAAG
* * ** ** * *
28480769 AAAATAAATAATTAATGGATAAA-TATATTTAAAGGAATAAATTTAAATT-TTAAAAATAGAATT
1 AAAAGAAATAATTAAAGGATAAATTA-ATTTAAA-G-ATAAATAGAAATTAAAAAAAAAAAAATT
* **
28480832 TAACTA-
63 AAAAAAG
* ** * * * *
28480838 AAAACAAATAATTAAAGGATAAATCT-ATTTAAAGGAATAAATTCAAATTTTAAAAAATAGAATT
1 AAAAGAAATAATTAAAGGATAAAT-TAATTTAAA-G-ATAAATAGAAA-TTAAAAAAAAAAAAAT
*
28480902 TAATTAAAG
62 TAA-AAAAG
* ** * * * *
28480911 -AAAGAAATAATTAAAGGGTAAATTAATTTAAAGGGATAAATTTAAATTTAAAAAATAGAATTTA
1 AAAAGAAATAATTAAAGGATAAATTAATTTAAA--GATAAATAGAAATTAAAAAAAAAAAAATTA
*
28480975 AATAA-
64 AAAAAG
28480980 AAAAGAAATAATTAAAGGATAAATTAATTT-AA-ATAAATAGAAATTAAAAAAAGAAAAAAATTA
1 AAAAGAAATAATTAAAGGATAAATTAATTTAAAGATAAATAGAAATT-AAAAAA-AAAAAAATTA
28481043 GAAAAAG
64 -AAAAAG
28481050 AAAAGA
1 AAAAGA
28481056 GGATGAGAAT
Statistics
Matches: 240, Mismatches: 32, Indels: 30
0.79 0.11 0.10
Matches are distributed among these distances:
66 11 0.05
67 5 0.02
68 7 0.03
69 71 0.30
70 76 0.32
71 29 0.12
72 39 0.16
73 2 0.01
ACGTcount: A:0.60, C:0.01, G:0.10, T:0.30
Consensus pattern (69 bp):
AAAAGAAATAATTAAAGGATAAATTAATTTAAAGATAAATAGAAATTAAAAAAAAAAAAATTAAA
AAAG
Found at i:28481919 original size:6 final size:6
Alignment explanation
Indices: 28481910--28481941 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
28481900 ATATTTTCCC
28481910 TTTCTT TTTCTT TTTCTT TTTCTT TTTACTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT TTT-CTT T
28481942 GTCGTGTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.84
7 4 0.16
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTCTT
Found at i:28487557 original size:3 final size:3
Alignment explanation
Indices: 28487543--28487601 Score: 100
Period size: 3 Copynumber: 19.3 Consensus size: 3
28487533 TCTTGTTATC
*
28487543 TTA TTGA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28487589 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
28487602 ATTTCTATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:28488244 original size:72 final size:71
Alignment explanation
Indices: 28488127--28488269 Score: 250
Period size: 72 Copynumber: 2.0 Consensus size: 71
28488117 TCTTTTCAAA
** *
28488127 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAGGGATCGTGTCCTAACTTACTGGGCATGATCCC
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGCGTCCTAACTTACTGGGCATGATCCC
28488192 ATTTTTT
66 -TTTTTT
28488199 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGCGTCCTAACTTACTGGGCATGATCCC
1 CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGCGTCCTAACTTACTGGGCATGATCCC
28488264 TTTTTT
66 TTTTTT
28488270 AAATCCGAGA
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
71 6 0.09
72 62 0.91
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (71 bp):
CTCAAGTTTTAAACGATCTCGGGAATTAAGAAAAGATCGCGTCCTAACTTACTGGGCATGATCCC
TTTTTT
Found at i:28491499 original size:2 final size:2
Alignment explanation
Indices: 28491494--28491535 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
28491484 TATTGAATTC
28491494 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28491536 TAAAAGCAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28492369 original size:2 final size:2
Alignment explanation
Indices: 28492362--28492388 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28492352 TAGAAGGGAA
28492362 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
28492389 ATATTTGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:28499243 original size:20 final size:21
Alignment explanation
Indices: 28499202--28499245 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
28499192 AAATCAAGTT
*
28499202 TTATACTTAACATTTCATAAC
1 TTATACTTAAAATTTCATAAC
28499223 TTATA-TTAAAATTTCCA-AAC
1 TTATACTTAAAATTT-CATAAC
28499243 TTA
1 TTA
28499246 CAAAATTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (21 bp):
TTATACTTAAAATTTCATAAC
Found at i:28500091 original size:25 final size:25
Alignment explanation
Indices: 28500048--28500101 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
28500038 GCTCTCTCTC
*
28500048 GAGCCATATAACGGAAAGCTCATGT
1 GAGCCATATAACGGAAAGCTCATGA
* * *
28500073 GAGCCATGTAATGGGAAGCTCATGA
1 GAGCCATATAACGGAAAGCTCATGA
28500098 GAGC
1 GAGC
28500102 TGTAATCAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.19, G:0.30, T:0.19
Consensus pattern (25 bp):
GAGCCATATAACGGAAAGCTCATGA
Found at i:28500833 original size:20 final size:20
Alignment explanation
Indices: 28500795--28500832 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28500785 CCATGTATTT
*
28500795 CATAAAATTTATAATTTTTC
1 CATAAAATTTACAATTTTTC
*
28500815 CATAAATTTTAC-ATTTTT
1 CATAAAATTTACAATTTTT
28500833 TTCAATTTAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.53
Consensus pattern (20 bp):
CATAAAATTTACAATTTTTC
Found at i:28501208 original size:31 final size:30
Alignment explanation
Indices: 28501172--28501233 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 30
28501162 ATTTTTAATT
*
28501172 AATTTA-TCATCTTT-TATTATTTCATCTTTCC
1 AATTTATTCAT-TTTCT-TTATTTAAT-TTTCC
28501203 AATTTATTCATTTTCTTTATTTAATTTTCC
1 AATTTATTCATTTTCTTTATTTAATTTTCC
28501233 A
1 A
28501234 TTGATGAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 6 0.21
31 17 0.61
32 5 0.18
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (30 bp):
AATTTATTCATTTTCTTTATTTAATTTTCC
Found at i:28504435 original size:27 final size:27
Alignment explanation
Indices: 28504381--28504471 Score: 123
Period size: 27 Copynumber: 3.4 Consensus size: 27
28504371 GCGATCCAAT
* * *
28504381 ATCGGGAAGCTC-TG-AAGAGCCATGA
1 ATCGGGAAGCTCATGAAAAAGCCTTTA
*
28504406 ATCGGAAAGCTCATGAAAAAGCCTTTA
1 ATCGGGAAGCTCATGAAAAAGCCTTTA
*
28504433 ATCGGGAAGCTCATGAAATAGCCTTTA
1 ATCGGGAAGCTCATGAAAAAGCCTTTA
28504460 ATCGGGAAGCTC
1 ATCGGGAAGCTC
28504472 CGGAGAGCCA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
25 11 0.19
26 2 0.03
27 45 0.78
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (27 bp):
ATCGGGAAGCTCATGAAAAAGCCTTTA
Found at i:28508735 original size:13 final size:13
Alignment explanation
Indices: 28508719--28508771 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
28508709 TTTAAACCAA
28508719 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
28508732 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
*
28508745 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
28508758 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
28508771 A
1 A
28508772 ATGAAGAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 3 0.09
13 27 0.79
14 4 0.12
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:28508737 original size:26 final size:26
Alignment explanation
Indices: 28508708--28508763 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
28508698 AACACTCAAA
28508708 TTTTAAACCAA-ACTTTTCAAAAGCAC
1 TTTTAAA-CAACACTTTTCAAAAGCAC
** *
28508734 TTTTCCACAACACTTTTTAAAAGCAC
1 TTTTAAACAACACTTTTCAAAAGCAC
28508760 TTTT
1 TTTT
28508764 CAAAAGCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 3 0.12
26 23 0.88
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.38
Consensus pattern (26 bp):
TTTTAAACAACACTTTTCAAAAGCAC
Found at i:28513266 original size:67 final size:66
Alignment explanation
Indices: 28513159--28513302 Score: 225
Period size: 67 Copynumber: 2.2 Consensus size: 66
28513149 TGGCCTTGCC
* * *
28513159 ATGGTCTTACATTTGTAGTGCCATAACCTAGTTATGGTCTTATCATCAGAATGCCATAGCCCAGC
1 ATGGTCTTACATTTGTAGTGCCATAACCCAATTATGGTCTTATCATCAAAATGCCATAGCCCAGC
28513224 T
66 T
* *
28513225 ATGGTCTTACATTTTGTATTGTCATAACCCAATTATGGTCTTATCATCAAAATGCCATAGCCCAG
1 ATGGTCTTACA-TTTGTAGTGCCATAACCCAATTATGGTCTTATCATCAAAATGCCATAGCCCAG
28513290 CT
65 CT
*
28513292 GTGGTCTTACA
1 ATGGTCTTACA
28513303 CATGTATCTA
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
66 11 0.15
67 60 0.85
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (66 bp):
ATGGTCTTACATTTGTAGTGCCATAACCCAATTATGGTCTTATCATCAAAATGCCATAGCCCAGC
T
Found at i:28513267 original size:34 final size:33
Alignment explanation
Indices: 28513159--28513302 Score: 112
Period size: 33 Copynumber: 4.3 Consensus size: 33
28513149 TGGCCTTGCC
* *
28513159 ATGGTCTTACATTTGTAGTGCCATAACCTAGTT
1 ATGGTCTTACATTTGTAATGCCATAACCCAGTT
** * *
28513192 ATGGTCTTATCATCAG-AATGCCATAGCCCAGCT
1 ATGGTCTTA-CATTTGTAATGCCATAACCCAGTT
* * *
28513225 ATGGTCTTACATTTTGTATTGTCATAACCCAATT
1 ATGGTCTTACA-TTTGTAATGCCATAACCCAGTT
*** * *
28513259 ATGGTCTTATCA-TCAAAATGCCATAGCCCAGCT
1 ATGGTCTTA-CATTTGTAATGCCATAACCCAGTT
*
28513292 GTGGTCTTACA
1 ATGGTCTTACA
28513303 CATGTATCTA
Statistics
Matches: 85, Mismatches: 22, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
32 4 0.05
33 54 0.64
34 25 0.29
35 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (33 bp):
ATGGTCTTACATTTGTAATGCCATAACCCAGTT
Found at i:28513413 original size:33 final size:33
Alignment explanation
Indices: 28513159--28513440 Score: 111
Period size: 33 Copynumber: 8.3 Consensus size: 33
28513149 TGGCCTTGCC
** * * * *
28513159 ATGGTCTTACATTTGTAGTGCCATAACCTAGTT
1 ATGGTCTTACATTTAAAATGCCATAGCCCAGCT
* *
28513192 ATGGTCTTATCA-TCAGAATGCCATAGCCCAGCT
1 ATGGTCTTA-CATTTAAAATGCCATAGCCCAGCT
** * * * **
28513225 ATGGTCTTACATTTTGTATTGTCATAACCCAATT
1 ATGGTCTTACA-TTTAAAATGCCATAGCCCAGCT
*
28513259 ATGGTCTTATCA-TCAAAATGCCATAGCCCAGCT
1 ATGGTCTTA-CATTTAAAATGCCATAGCCCAGCT
* * * * * * *
28513292 GTGGTCTTACACATGTATCTATATTGCCATGGTCCAACC
1 ATGGTCTT--ACA--T-T-TAAAATGCCATAGCCCAGCT
* * ** * * *
28513331 ATGGTCTTACGTTCAAGGTGCCATAACTCAGTT
1 ATGGTCTTACATTTAAAATGCCATAGCCCAGCT
* *
28513364 ATGGTCTTTTCA-TTAAAATGTCATAGCCCAGCT
1 ATGGTC-TTACATTTAAAATGCCATAGCCCAGCT
* * * *
28513397 ATGGTCTTACATTTAAACATTGCTATGGTCCAGCC
1 ATGGTCTTACATTTAAA-A-TGCCATAGCCCAGCT
28513432 ATGGTCTTA
1 ATGGTCTTA
28513441 TTTTTCAATT
Statistics
Matches: 175, Mismatches: 59, Indels: 28
0.67 0.23 0.11
Matches are distributed among these distances:
32 6 0.03
33 92 0.53
34 31 0.18
35 23 0.13
37 2 0.01
38 1 0.01
39 20 0.11
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (33 bp):
ATGGTCTTACATTTAAAATGCCATAGCCCAGCT
Found at i:28515298 original size:15 final size:15
Alignment explanation
Indices: 28515278--28515307 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28515268 TTCATCTAAT
28515278 ATTATAACTATTCAA
1 ATTATAACTATTCAA
28515293 ATTATAACTATTCAA
1 ATTATAACTATTCAA
28515308 GTAATATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTATAACTATTCAA
Found at i:28515602 original size:16 final size:18
Alignment explanation
Indices: 28515576--28515608 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28515566 TTTACATTTG
28515576 TTACAATATT-AATTTAT
1 TTACAATATTAAATTTAT
28515593 TTACAA-ATTAAATTTA
1 TTACAATATTAAATTTA
28515609 CTATTGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (18 bp):
TTACAATATTAAATTTAT
Found at i:28520318 original size:20 final size:20
Alignment explanation
Indices: 28520293--28520331 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28520283 CGTAAAATGA
*
28520293 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
28520313 TTTCTGTAAAATGATTTAC
1 TTTCTGGAAAATGATTTAC
28520332 AGAAAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:28520337 original size:34 final size:33
Alignment explanation
Indices: 28520279--28520343 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
28520269 AGTAAAATAT
* *
28520279 TTTTCGTAAAATGATTTCTGGAAAATGTTTTAC
1 TTTTCGTAAAATGATTTCTAGAAAATATTTTAC
28520312 TTTTCTGTAAAATGATTTAC-AGAAAATATTTT
1 TTTTC-GTAAAATGATTT-CTAGAAAATATTTT
28520344 CTAGTATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 5 0.18
34 22 0.79
35 1 0.04
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.46
Consensus pattern (33 bp):
TTTTCGTAAAATGATTTCTAGAAAATATTTTAC
Found at i:28520998 original size:5 final size:5
Alignment explanation
Indices: 28520988--28521018 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
28520978 AATAAATAAT
28520988 ATATA ATATA ATATA TATATA ATATA ATATA
1 ATATA ATATA ATATA -ATATA ATATA ATATA
28521019 TATGGTCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:28521005 original size:16 final size:16
Alignment explanation
Indices: 28520978--28521021 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
28520968 CACTCAAGCC
28520978 AATA-AATA-ATATAT
1 AATATAATATATATAT
28520992 AATATAATATATATAT
1 AATATAATATATATAT
28521008 AATATAATATATAT
1 AATATAATATATAT
28521022 GGTCCTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.14
15 4 0.14
16 20 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATAATATATATAT
Found at i:28532693 original size:45 final size:45
Alignment explanation
Indices: 28532638--28532850 Score: 257
Period size: 45 Copynumber: 4.7 Consensus size: 45
28532628 CCAGAAACGT
* * * *
28532638 GTAAGACCATGACTAAAAGACGTTTTGTCATCACAATTCTATCGA
1 GTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCGA
* * * *
28532683 GTAAAACCATGACTGAAAGATGTTATGGCATCATGATTCTATTGA
1 GTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCGA
** * *
28532728 GTAAGACTGTGACTCAAAGACGTTATGGCATCACGATTCTATCAA
1 GTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCGA
* * * *
28532773 ATAAGACCATGATTGAAAGACGTTATGGCATCACGATCCTATTGA
1 GTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCGA
*
28532818 GTAAGACCAT-AGCTGAAAGACGCTATGGCATCA
1 GTAAGACCATGA-CTGAAAGACGTTATGGCATCA
28532851 TGAATCAAAG
Statistics
Matches: 140, Mismatches: 27, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
44 1 0.01
45 139 0.99
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (45 bp):
GTAAGACCATGACTGAAAGACGTTATGGCATCACGATTCTATCGA
Found at i:28532865 original size:90 final size:90
Alignment explanation
Indices: 28532638--28532892 Score: 255
Period size: 90 Copynumber: 2.8 Consensus size: 90
28532628 CCAGAAACGT
* * * * * * * * * *
28532638 GTAAGACCATGACTAAAAGACGTTTTGTCATCAC-AATTCTATCGAGTAAAACCATGACTGAAAG
1 GTAAGACCATGACTCAAAGACGCTATGGCATCACGAA-TCAAACAAATAAGACCATGATTGAAAG
* * *
28532702 ATGTTATGGCATCATGATTCTATTGA
65 ACGTTATGGCATCACGATCCTATTGA
** * * * *
28532728 GTAAGACTGTGACTCAAAGACGTTATGGCATCACGATTCTATCAAATAAGACCATGATTGAAAGA
1 GTAAGACCATGACTCAAAGACGCTATGGCATCACGAATCAAACAAATAAGACCATGATTGAAAGA
28532793 CGTTATGGCATCACGATCCTATTGA
66 CGTTATGGCATCACGATCCTATTGA
* * *
28532818 GTAAGACCAT-AGCTGAAAGACGCTATGGCATCATGAATCAAAGAAATAAGACCAT-AGTTGAAA
1 GTAAGACCATGA-CTCAAAGACGCTATGGCATCACGAATCAAACAAATAAGACCATGA-TTGAAA
*
28532881 GACATTATGGCA
64 GACGTTATGGCA
28532893 AGAAGATGAA
Statistics
Matches: 139, Mismatches: 23, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
89 2 0.01
90 136 0.98
91 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (90 bp):
GTAAGACCATGACTCAAAGACGCTATGGCATCACGAATCAAACAAATAAGACCATGATTGAAAGA
CGTTATGGCATCACGATCCTATTGA
Found at i:28532974 original size:45 final size:44
Alignment explanation
Indices: 28532819--28532985 Score: 156
Period size: 45 Copynumber: 3.7 Consensus size: 44
28532809 TCCTATTGAG
* * * *
28532819 TAAGACCATAGCTGAAAGACGCTATGGCATCATGAATC-AAAGAAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCAAG-A-CGAAAAAAA
* ** *
28532864 TAAGACCATAGTTGAAAGACATTATGGCAAGAAGATGAAAAAAAAGAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCAAGACG---AAAAA-AA
* *
28532912 TAAGACCATGGTTGAAAGACACTATGGCATCAAGACGAGAATAAA
1 TAAGACCATAGTTGAAAGACACTATGGCATCAAGACGA-AAAAAA
* *
28532957 TAAAACCATAGTTGAAAGACACCATGGCA
1 TAAGACCATAGTTGAAAGACACTATGGCA
28532986 CAGTCCCATC
Statistics
Matches: 99, Mismatches: 17, Indels: 12
0.77 0.13 0.09
Matches are distributed among these distances:
44 1 0.01
45 57 0.58
46 3 0.03
47 4 0.04
48 34 0.34
ACGTcount: A:0.47, C:0.15, G:0.20, T:0.17
Consensus pattern (44 bp):
TAAGACCATAGTTGAAAGACACTATGGCATCAAGACGAAAAAAA
Found at i:28536147 original size:37 final size:37
Alignment explanation
Indices: 28536089--28536189 Score: 95
Period size: 37 Copynumber: 2.7 Consensus size: 37
28536079 AAAAATAGTA
*
28536089 TTATTTTAATAGTTTAATATTAGATTTAAT-TTAATAC
1 TTATCTTAATAGTTTAATATTA-ATTTAATATTAATAC
*
28536126 TTATCTTAATAGTATT-TTATTAATTTAATATTAAAGTGA-
1 TTATCTTAATAGT-TTAATATTAATTTAATATT-AA-T-AC
*
28536165 TTATCTTAATA-TTAAAT-TTAATTTA
1 TTATCTTAATAGTTTAATATTAATTTA
28536190 GATAAACATT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
36 7 0.13
37 28 0.52
38 6 0.11
39 12 0.22
40 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (37 bp):
TTATCTTAATAGTTTAATATTAATTTAATATTAATAC
Found at i:28540591 original size:43 final size:44
Alignment explanation
Indices: 28540510--28540646 Score: 131
Period size: 43 Copynumber: 3.2 Consensus size: 44
28540500 CACTAACTTG
** * * *
28540510 TGTAAGACCACATC-GGGAC-GTTGGAATCGATTTGAGATTTACA
1 TGTAAGACCATGTCTGGGACAG-TGGCATCGATATAAGATTTACA
* * *
28540553 TGTAAGACCATGTCTGGGACATTGGTATCG-TATAAGATTT-CG
1 TGTAAGACCATGTCTGGGACAGTGGCATCGATATAAGATTTACA
* **
28540595 TGTAAGACCCTGTCTGGGACAGTGGCATCGATATTGGA-TTACA
1 TGTAAGACCATGTCTGGGACAGTGGCATCGATATAAGATTTACA
28540638 TGTAAGACC
1 TGTAAGACC
28540647 TCGTATGGGG
Statistics
Matches: 77, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
42 30 0.39
43 35 0.45
44 12 0.16
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (44 bp):
TGTAAGACCATGTCTGGGACAGTGGCATCGATATAAGATTTACA
Found at i:28540609 original size:42 final size:43
Alignment explanation
Indices: 28540544--28540646 Score: 129
Period size: 42 Copynumber: 2.4 Consensus size: 43
28540534 AATCGATTTG
* *
28540544 AGATTTACATGTAAGACCATGTCTGGGACATTGGTATCGTATA
1 AGATTTACATGTAAGACCATGTCTGGGACAGTGGCATCGTATA
* * *
28540587 AGATTT-CGTGTAAGACCCTGTCTGGGACAGTGGCATCGATATT
1 AGATTTACATGTAAGACCATGTCTGGGACAGTGGCATCG-TATA
*
28540630 GGA-TTACATGTAAGACC
1 AGATTTACATGTAAGACC
28540647 TCGTATGGGG
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
42 30 0.59
43 21 0.41
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (43 bp):
AGATTTACATGTAAGACCATGTCTGGGACAGTGGCATCGTATA
Found at i:28543417 original size:15 final size:15
Alignment explanation
Indices: 28543399--28543428 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28543389 TTTACTATTA
*
28543399 TGTCTTTTGTATTTT
1 TGTCTTTTATATTTT
28543414 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
28543429 GCATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.07, G:0.10, T:0.73
Consensus pattern (15 bp):
TGTCTTTTATATTTT
Found at i:28545400 original size:2 final size:2
Alignment explanation
Indices: 28545395--28545421 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28545385 TATATAATTA
28545395 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
28545422 GGCTTGCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28552620 original size:53 final size:53
Alignment explanation
Indices: 28552531--28552641 Score: 145
Period size: 53 Copynumber: 2.1 Consensus size: 53
28552521 TACCACTAAA
* * *
28552531 TGTAACACCCTAACCCATCTCCATCGCCGAATTAGAGTTACAGAGTATTA-TG
1 TGTAACACCCTAACCCATATCCATCGCCGAATTAGAGTTACAAAGCATTACTG
* *
28552583 TGTAACACCCCTAACCCATATCCATTGTCGGAA-TAGAGTTACAAAGCATTACTG
1 TGTAACA-CCCTAACCCATATCCATCG-CCGAATTAGAGTTACAAAGCATTACTG
28552637 TGTAA
1 TGTAA
28552642 ACGCCTCTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
52 7 0.14
53 33 0.65
54 11 0.22
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.27
Consensus pattern (53 bp):
TGTAACACCCTAACCCATATCCATCGCCGAATTAGAGTTACAAAGCATTACTG
Found at i:28557871 original size:42 final size:43
Alignment explanation
Indices: 28557776--28557872 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 43
28557766 ACGGCTAAGC
* ** *
28557776 CACACGCCCGTATGCTAGGCTGTGTAAATCTTGAAATAGCCAT
1 CACACGCCCGTGTGCTAGGCCATGTAAATCTCGAAATAGCCAT
** * *
28557819 -ACACATCCGTGTGCTAGGCCATGTAACTCTCGAAATGGCC-T
1 CACACGCCCGTGTGCTAGGCCATGTAAATCTCGAAATAGCCAT
28557860 CACACGCCCGTGT
1 CACACGCCCGTGT
28557873 ACCAGGCCGT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
41 1 0.02
42 42 0.98
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (43 bp):
CACACGCCCGTGTGCTAGGCCATGTAAATCTCGAAATAGCCAT
Found at i:28558881 original size:41 final size:41
Alignment explanation
Indices: 28558778--28558970 Score: 181
Period size: 41 Copynumber: 4.7 Consensus size: 41
28558768 ACCAGAGTGT
* * * * **
28558778 AAACCGGGGCACGTATGTGTAGTTCGGGGGTTTCGAAGTAC
1 AAACAGGGGCACGTATGTGCAATTCAGGGGTACCGAAGTAC
* * * * * * *
28558819 GAACAGGGGCA-TTAATATGCAATTTAAGGGTACTGACGTAC
1 AAACAGGGGCACGT-ATGTGCAATTCAGGGGTACCGAAGTAC
*
28558860 AAACAGGGGCACGTATGTGCAATTCAGGGGTACCAAAGTAC
1 AAACAGGGGCACGTATGTGCAATTCAGGGGTACCGAAGTAC
* * * *
28558901 AAATAGGGGCACATATGTGTAATTCAGGGGTACCGAAGTAT
1 AAACAGGGGCACGTATGTGCAATTCAGGGGTACCGAAGTAC
* * *
28558942 AAACAGGGGCATGTATGTGTAATTTAGGG
1 AAACAGGGGCACGTATGTGCAATTCAGGG
28558971 ATTAACTAAC
Statistics
Matches: 120, Mismatches: 30, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
40 1 0.01
41 118 0.98
42 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (41 bp):
AAACAGGGGCACGTATGTGCAATTCAGGGGTACCGAAGTAC
Found at i:28558889 original size:21 final size:21
Alignment explanation
Indices: 28558863--28558930 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
28558853 GACGTACAAA
*
28558863 CAGGGGCACGTATGTGCAATT
1 CAGGGGCACATATGTGCAATT
* * * *
28558884 CAGGGGTACCA-AAGTACAAAT
1 CAGGGGCA-CATATGTGCAATT
*
28558905 -AGGGGCACATATGTGTAATT
1 CAGGGGCACATATGTGCAATT
28558925 CAGGGG
1 CAGGGG
28558931 TACCGAAGTA
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
19 2 0.06
20 12 0.35
21 19 0.56
22 1 0.03
ACGTcount: A:0.31, C:0.16, G:0.32, T:0.21
Consensus pattern (21 bp):
CAGGGGCACATATGTGCAATT
Found at i:28559213 original size:17 final size:17
Alignment explanation
Indices: 28559193--28559230 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
28559183 TCAATCTCAA
28559193 AATTCA-ATTTAATCCAT
1 AATTCACATTT-ATCCAT
*
28559210 AATTCACATTTATTCAT
1 AATTCACATTTATCCAT
28559227 AATT
1 AATT
28559231 ATAATTTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTCACATTTATCCAT
Found at i:28560200 original size:12 final size:12
Alignment explanation
Indices: 28560183--28560225 Score: 56
Period size: 11 Copynumber: 3.8 Consensus size: 12
28560173 AACTAATCCT
28560183 CTCTCAAATTTC
1 CTCTCAAATTTC
28560195 CTCTCAAA-TTC
1 CTCTCAAATTTC
28560206 CT-TCAAAATTT-
1 CTCTC-AAATTTC
28560217 CTCTCAAAT
1 CTCTCAAAT
28560226 CCATATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
10 2 0.07
11 14 0.50
12 12 0.43
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:28561407 original size:7 final size:7
Alignment explanation
Indices: 28561395--28561427 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
28561385 TAGTCGATTG
28561395 GTATTTA
1 GTATTTA
28561402 GTATTTA
1 GTATTTA
28561409 GTATTTA
1 GTATTTA
28561416 GTATTTA
1 GTATTTA
28561423 GTATT
1 GTATT
28561428 ATGTATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:28562056 original size:18 final size:18
Alignment explanation
Indices: 28562029--28562068 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28562019 TAGGTGCGTT
* *
28562029 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
*
28562047 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTA
28562065 TCCT
1 TCCT
28562069 TTTTCGAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.30, G:0.07, T:0.45
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:28562367 original size:21 final size:21
Alignment explanation
Indices: 28562327--28562373 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
28562317 ATGCCCTACT
*
28562327 GGAAGAACCAGAATCCCCGCC
1 GGAAGAACCACAATCCCCGCC
28562348 GGAAGAACCACAA-CCGCCGCC
1 GGAAGAACCACAATCC-CCGCC
*
28562369 AGAAG
1 GGAAG
28562374 CTGGACAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.36, C:0.36, G:0.26, T:0.02
Consensus pattern (21 bp):
GGAAGAACCACAATCCCCGCC
Found at i:28562644 original size:21 final size:22
Alignment explanation
Indices: 28562610--28563207 Score: 653
Period size: 22 Copynumber: 27.0 Consensus size: 22
28562600 TTTAATTGAC
* *
28562610 AAACCTTAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
*
28562632 AAACCCTAACCCTAACCCTTAAATTAA
1 AAACCCT-A----AACCCTTAACTTAA
* * *
28562659 AAAACCTAACCCCTTAACTTTA
1 AAACCCTAAACCCTTAACTTAA
*
28562681 AAACCCTAAACCCTTAACCTAAAA
1 AAACCCTAAACCCTTAA-CT-TAA
* *
28562705 ACCCTAACCCTAAACACTTAACCTAA
1 A----AACCCTAAACCCTTAACTTAA
*
28562731 AAACCCT-AACCCATTAACCTAA
1 AAACCCTAAACCC-TTAACTTAA
28562753 AAACCCT-AACCCTTAACATTAA
1 AAACCCTAAACCCTTAAC-TTAA
* * *
28562775 CAA-TCTAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
* *
28562796 TAAACCCTAAACTCTTAAATTAA
1 -AAACCCTAAACCCTTAACTTAA
*
28562819 AAACCCTAAACCCTTAAATTAA
1 AAACCCTAAACCCTTAACTTAA
*
28562841 AAACCCTAAATCCTTAAAC-TAA
1 AAACCCTAAACCCTT-AACTTAA
* *
28562863 AAACCCT-AATCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
*
28562884 AAACCCT-AACCCTTAACTTTA
1 AAACCCTAAACCCTTAACTTAA
28562905 AAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
28562927 AAACCATAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
28562949 AAACCCT-AACCCTTAAATTAA
1 AAACCCTAAACCCTTAACTTAA
*
28562970 AAACCCTAAACCCTTAACAT-A
1 AAACCCTAAACCCTTAACTTAA
* *
28562991 AAACCAT-AACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
*
28563012 AAACCCTAAACCC-TAACTTTA
1 AAACCCTAAACCCTTAACTTAA
*
28563033 AAACCCTAGACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
28563055 AAACACTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
* *
28563077 AAACCCT-AACCTTTAAATTAA
1 AAACCCTAAACCCTTAACTTAA
* *
28563098 AAACCCTAAACCCTAAACCTAA
1 AAACCCTAAACCCTTAACTTAA
* *
28563120 AAACCCTAAACCTTTAACTTTA
1 AAACCCTAAACCCTTAACTTAA
*
28563142 AAACCCTAAACCCTTAACTTTA
1 AAACCCTAAACCCTTAACTTAA
28563164 AAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
28563186 AAATCCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
28563207 A
1 A
28563208 TATAATTTGA
Statistics
Matches: 493, Mismatches: 59, Indels: 49
0.82 0.10 0.08
Matches are distributed among these distances:
20 14 0.03
21 135 0.27
22 285 0.58
23 19 0.04
24 2 0.00
26 4 0.01
27 19 0.04
28 15 0.03
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.23
Consensus pattern (22 bp):
AAACCCTAAACCCTTAACTTAA
Found at i:28562686 original size:43 final size:43
Alignment explanation
Indices: 28562639--28563207 Score: 639
Period size: 43 Copynumber: 13.0 Consensus size: 43
28562629 TAAAAACCCT
* * * *
28562639 AACCCTAACCCTTAAATTAAAAAACCTAACCCCTTAACTTTAA
1 AACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
* * *
28562682 AACCCTAAACCCTTAACCTAAAAACCCTAACCCTAAACACTTAACCTAAA
1 AACCCT-AACCCTTAA-CT-TAAA----AACCCTAAACCCTTAACTTAAA
* *
28562732 AACCCTAACCCATTAACCTAAAAACCCT-AACCCTTAACATTAAC
1 AACCCTAACCC-TTAACTTAAAAACCCTAAACCCTTAAC-TTAAA
* * * *
28562776 AA-TCTAAACCCTTAACCTAATAAACCCTAAACTCTTAAATTAAA
1 AACCCT-AACCCTTAACTTAA-AAACCCTAAACCCTTAACTTAAA
* *
28562820 AACCCTAAACCCTTAAATTAAAAACCCTAAATCCTTAAAC-TAAA
1 AACCCT-AACCCTTAACTTAAAAACCCTAAACCCTT-AACTTAAA
* * *
28562864 AACCCTAATCCTTAACCTAAAAACCCT-AACCCTTAACTTTAA
1 AACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
*
28562906 AACCCTAAACCCTTAACTTAAAAACCATAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
* *
28562950 AACCCTAACCCTTAAATTAAAAACCCTAAACCCTTAACAT-AA
1 AACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
* * *
28562992 AACCATAACCCTTAACCTAAAAACCCTAAACCC-TAACTTTAA
1 AACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
*
28563034 AACCCTAGACCCTTAACTTAAAAACACTAAACCCTTAACTTAAA
1 AACCCTA-ACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
* * * *
28563078 AACCCTAACCTTTAAATTAAAAACCCTAAACCCTAAACCTAAA
1 AACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
* * *
28563121 AACCCTAAACCTTTAACTTTAAAACCCTAAACCCTTAACTTTAA
1 AACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
*
28563165 AACCCTAAACCCTTAACTTAAAAATCCT-AACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
28563208 TATAATTTGA
Statistics
Matches: 449, Mismatches: 56, Indels: 42
0.82 0.10 0.08
Matches are distributed among these distances:
41 8 0.02
42 55 0.12
43 168 0.37
44 153 0.34
45 26 0.06
46 3 0.01
48 3 0.01
49 6 0.01
50 27 0.06
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (43 bp):
AACCCTAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAA
Found at i:28562703 original size:13 final size:13
Alignment explanation
Indices: 28562685--28562731 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
28562675 ACTTTAAAAC
28562685 CCTAAACCCTTAA
1 CCTAAACCCTTAA
28562698 CCTAAAAACCC-TAA
1 CCT--AAACCCTTAA
*
28562712 CCCTAAACACTTAA
1 -CCTAAACCCTTAA
28562726 CCTAAA
1 CCTAAA
28562732 AACCCTAACC
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
13 14 0.48
14 6 0.21
15 9 0.31
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.19
Consensus pattern (13 bp):
CCTAAACCCTTAA
Found at i:28562712 original size:14 final size:14
Alignment explanation
Indices: 28562688--28562741 Score: 65
Period size: 14 Copynumber: 3.8 Consensus size: 14
28562678 TTAAAACCCT
28562688 AAACCCTTAACCTAA
1 AAACCC-TAACCTAA
28562703 AAACCCTAACCCTAA
1 AAACCCTAA-CCTAA
* *
28562718 ACA-CTTAACCTAA
1 AAACCCTAACCTAA
28562731 AAACCCTAACC
1 AAACCCTAACC
28562742 CATTAACCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
13 7 0.21
14 13 0.39
15 13 0.39
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
AAACCCTAACCTAA
Found at i:28562713 original size:28 final size:27
Alignment explanation
Indices: 28562682--28562775 Score: 117
Period size: 28 Copynumber: 3.6 Consensus size: 27
28562672 TTAACTTTAA
28562682 AACCCTAAACCCTTAACCTAAAAACCCT
1 AACCCTAAA-CCTTAACCTAAAAACCCT
28562710 AACCCTAAACACTTAACCTAAAAACCCT
1 AACCCTAAAC-CTTAACCTAAAAACCCT
28562738 AACCC---A--TTAACCTAAAAACCCT
1 AACCCTAAACCTTAACCTAAAAACCCT
* *
28562760 AACCCTTAACATTAAC
1 AACCCTAAACCTTAAC
28562776 AATCTAAACC
Statistics
Matches: 60, Mismatches: 0, Indels: 13
0.82 0.00 0.18
Matches are distributed among these distances:
22 21 0.35
25 2 0.03
27 6 0.10
28 31 0.52
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.19
Consensus pattern (27 bp):
AACCCTAAACCTTAACCTAAAAACCCT
Found at i:28563120 original size:6 final size:7
Alignment explanation
Indices: 28563098--28563177 Score: 54
Period size: 7 Copynumber: 11.0 Consensus size: 7
28563088 TTTAAATTAA
28563098 AAACCCT
1 AAACCCT
28563105 AAACCCT
1 AAACCCT
28563112 AAA-CCT
1 AAACCCT
28563118 AAAAACCCT
1 --AAACCCT
*
28563127 AAACCTT
1 AAACCCT
* **
28563134 TAACTTT
1 AAACCCT
28563141 AAAACCCT
1 -AAACCCT
28563149 AAACCCT
1 AAACCCT
* **
28563156 TAACTTT
1 AAACCCT
28563163 AAAACCCT
1 -AAACCCT
28563171 AAACCCT
1 AAACCCT
28563178 TAACTTAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
6 3 0.05
7 39 0.70
8 11 0.20
9 3 0.05
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.23
Consensus pattern (7 bp):
AAACCCT
Found at i:28566584 original size:125 final size:125
Alignment explanation
Indices: 28566185--28566649 Score: 587
Period size: 125 Copynumber: 3.7 Consensus size: 125
28566175 CATGTTACTA
* * * * **
28566185 TAGCAAAAGCGCGTCCACGTGAGTGTGATTTCACAAATTCTTCTCATAAAGCATCCTGCAAGAAG
1 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAG
** * * * *
28566250 CG-ACTTTATACTATTTGCTCAGAAACGTCAAGTTGAAATTATTTTTCTAGGACCAACTG
66 CGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCAACTG
* * *
28566309 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTTA-AATAGCATGCTGCTTGTA
1 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGCTTGAA
* * * *
28566373 GCGTTGTTTTATACTATTTGCTCAGAAATGTCAACTCAAAATTA-TTTTCTCAGGACCTACTG
65 GCGTT-TTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTC-CAGGACCAACTG
* * * * * *
28566435 TAGCAAAAGCGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTTATAAAGCATCTTTCTTTAAG
1 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAG
*
28566500 CGTTTTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTCCAGGA-CAACTG
66 CGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGACCAACTG
* * *
28566560 TAGTAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCACAAAGCATCCTACTTGAAG
1 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAG
* *
28566625 CATTTTTTAAACTAGTTGCTCAGAA
66 CGTTTTTTAAACTATTTGCTCAGAA
28566650 GCGACTTCAA
Statistics
Matches: 294, Mismatches: 40, Indels: 13
0.85 0.12 0.04
Matches are distributed among these distances:
123 2 0.01
124 55 0.19
125 123 0.42
126 109 0.37
127 5 0.02
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (125 bp):
TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAG
CGTTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCAACTG
Found at i:28572667 original size:59 final size:63
Alignment explanation
Indices: 28572604--28572745 Score: 175
Period size: 70 Copynumber: 2.2 Consensus size: 63
28572594 ATTTAAAGGG
*
28572604 AAGCAAAGACATG-AATTAA-A-T-CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTA
1 AAGCATAGACATGCAATTAAGATTACAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTA
*
28572663 AAGCATAGACATGCATTTAAGGTGATGTTCAACAGCAGCAATAAAGGAGGTGTTGGCCGAATTTA
1 AAGCATAGACATGCAATTAA---GA--TT--ACAGCAGCAATAAAGGAGGTGTTGGCCGAATTTA
28572728 ATGTA
59 ATGTA
28572733 AAGCATAGACATG
1 AAGCATAGACATG
28572746 TATTTAAGGT
Statistics
Matches: 70, Mismatches: 2, Indels: 11
0.84 0.02 0.13
Matches are distributed among these distances:
59 12 0.17
60 5 0.07
64 1 0.01
67 1 0.01
70 51 0.73
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.23
Consensus pattern (63 bp):
AAGCATAGACATGCAATTAAGATTACAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTA
Found at i:28572708 original size:70 final size:70
Alignment explanation
Indices: 28572625--28572761 Score: 256
Period size: 70 Copynumber: 2.0 Consensus size: 70
28572615 TGAATTAAAT
28572625 CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
1 CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
28572690 TTCAA
66 TTCAA
* *
28572695 CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGTATTTAAGGTGCTG
1 CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
28572760 TT
66 TT
28572762 GGGCATGCAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.34, C:0.12, G:0.26, T:0.27
Consensus pattern (70 bp):
CAGCAGCAATAAAGGAGGTGTTGGCCGAATTTAATGTAAAGCATAGACATGCATTTAAGGTGATG
TTCAA
Found at i:28584451 original size:61 final size:58
Alignment explanation
Indices: 28584340--28584471 Score: 183
Period size: 61 Copynumber: 2.2 Consensus size: 58
28584330 ATTACTTTAA
* * * *
28584340 TATTAAATTAATATAATACTTATTAAGATAAATATTAGATTAAATTTAATATTAAATC
1 TATTAAATTAATAGAATACTTATTAAGATAAATATTAAATTAAATGTAATATTAAAAC
*
28584398 TATTAAATTGATAGAATACTTATCTATAAGATAAATATTAAATTAAATGTAATATTAAAAC
1 TATTAAATTAATAGAATACTTA--T-TAAGATAAATATTAAATTAAATGTAATATTAAAAC
*
28584459 TATTAAAATAATA
1 TATTAAATTAATA
28584472 TTATTTTTGG
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
58 20 0.31
60 1 0.02
61 43 0.67
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.40
Consensus pattern (58 bp):
TATTAAATTAATAGAATACTTATTAAGATAAATATTAAATTAAATGTAATATTAAAAC
Found at i:28586189 original size:22 final size:22
Alignment explanation
Indices: 28586127--28586212 Score: 118
Period size: 22 Copynumber: 3.9 Consensus size: 22
28586117 ATTGTTCAAA
* **
28586127 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
28586149 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
28586171 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
* * *
28586193 CATGAGGGTTTAGTTCGTTA
1 CATGAGAGCTTAGTACGTTA
28586213 AACAATTTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:28596291 original size:30 final size:30
Alignment explanation
Indices: 28596234--28596292 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
28596224 GCCTTTTGAA
* *
28596234 AATATTTACAAAAAGAGACATCTAATTTTT
1 AATATTTACAAAAAGAGACACCAAATTTTT
28596264 AATATTTACAAAAAGAGTA-ACCAAATTTT
1 AATATTTACAAAAAGAG-ACACCAAATTTT
28596293 GAAAATAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (30 bp):
AATATTTACAAAAAGAGACACCAAATTTTT
Found at i:28603406 original size:26 final size:25
Alignment explanation
Indices: 28603351--28603406 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
28603341 TAATAAAAAT
28603351 TTATTATAAATTAATTAAATTCAAC
1 TTATTATAAATTAATTAAATTCAAC
* * *
28603376 ATATTAATAATTTAATTACAATTTAA-
1 TTATT-ATAAATTAATTA-AATTCAAC
28603402 TTATT
1 TTATT
28603407 TTATAATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
25 4 0.16
26 15 0.60
27 6 0.24
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.48
Consensus pattern (25 bp):
TTATTATAAATTAATTAAATTCAAC
Found at i:28608688 original size:125 final size:125
Alignment explanation
Indices: 28608532--28608789 Score: 455
Period size: 125 Copynumber: 2.1 Consensus size: 125
28608522 TAATAAATTT
*
28608532 TTAATAAAACCAACCCACCATCACCCATCAACATTTAATTAGTGGTGTAATTACTACTTTAGTCC
1 TTAAT-AAACCAACCCACCATCACCCATCAACATTTAATTAGTGGTGTAATTACTACTTTACTCC
28608597 TTTTAATTAATTTCAATCTATAATTCAACTTTTAGCACTTACGCGATTTAGTCCATGTACA
65 TTTTAATTAATTTCAATCTATAATTCAACTTTTAGCACTTACGCGATTTAGTCCATGTACA
*
28608658 TTAATAAACCAACCCACTATCGA-CCATCAACATTTAATTAGTGGTGTAATTACTACTTTACTCC
1 TTAATAAACCAACCCACCATC-ACCCATCAACATTTAATTAGTGGTGTAATTACTACTTTACTCC
* *
28608722 TTTTAATTAATTTCAATCTATAATTCAACTTTTAGCTCTTACGTGATTTAGTCCATGTACA
65 TTTTAATTAATTTCAATCTATAATTCAACTTTTAGCACTTACGCGATTTAGTCCATGTACA
28608783 TTAATAA
1 TTAATAA
28608790 CTCCTAATTC
Statistics
Matches: 127, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
125 121 0.95
126 6 0.05
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (125 bp):
TTAATAAACCAACCCACCATCACCCATCAACATTTAATTAGTGGTGTAATTACTACTTTACTCCT
TTTAATTAATTTCAATCTATAATTCAACTTTTAGCACTTACGCGATTTAGTCCATGTACA
Found at i:28611130 original size:64 final size:64
Alignment explanation
Indices: 28611058--28611248 Score: 305
Period size: 64 Copynumber: 3.0 Consensus size: 64
28611048 AAAATTGGAG
28611058 ACTCAATCTCAGTCACTTAATCTGAAATACTTACAACAGTCAATTCCCAAAACTATCGACAAAA
1 ACTCAATCTCAGTCACTTAATCTGAAATACTTACAACAGTCAATTCCCAAAACTATCGACAAAA
* * * *
28611122 ACTCAATCTCAGTCATTTAATCTGAATTACTTACAACAGTCAATTCCTAAAACTATCGACGAAA
1 ACTCAATCTCAGTCACTTAATCTGAAATACTTACAACAGTCAATTCCCAAAACTATCGACAAAA
*
28611186 ACTCAATCTCAATCACTTAATCT-AAATTACTTACAATC-GTCAATTCCCAAAACTATCGACAAA
1 ACTCAATCTCAGTCACTTAATCTGAAA-TACTTACAA-CAGTCAATTCCCAAAACTATCGACAAA
28611249 CTTACCTCGC
Statistics
Matches: 116, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
63 2 0.02
64 113 0.97
65 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.06, T:0.28
Consensus pattern (64 bp):
ACTCAATCTCAGTCACTTAATCTGAAATACTTACAACAGTCAATTCCCAAAACTATCGACAAAA
Found at i:28615494 original size:41 final size:41
Alignment explanation
Indices: 28615387--28615544 Score: 167
Period size: 41 Copynumber: 3.8 Consensus size: 41
28615377 GATATGTATT
*
28615387 TTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACT-TGTGTA
1 TTCGTGTAAGACCACGTCTGGGACATTGGCATC-A-TATGTG-A
* * * *
28615430 TACGTGTAAGACCATGTCCGGGACATTGGCATCATATTTGA
1 TTCGTGTAAGACCACGTCTGGGACATTGGCATCATATGTGA
* *
28615471 TTTGTGTAAGACC-CTGTCTGGGACAGTGGCATCATATGTGA
1 TTCGTGTAAGACCAC-GTCTGGGACATTGGCATCATATGTGA
* * *
28615512 TTACATGTAAGACCACGTCTGTGACGTTGGCAT
1 TT-CGTGTAAGACCACGTCTGGGACATTGGCAT
28615545 TGTACGAGCC
Statistics
Matches: 95, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
41 38 0.40
42 27 0.28
43 30 0.32
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (41 bp):
TTCGTGTAAGACCACGTCTGGGACATTGGCATCATATGTGA
Found at i:28615735 original size:16 final size:17
Alignment explanation
Indices: 28615706--28615737 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
28615696 TGAATTGATG
28615706 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
28615723 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
28615738 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:28616919 original size:16 final size:15
Alignment explanation
Indices: 28616898--28616967 Score: 60
Period size: 16 Copynumber: 4.9 Consensus size: 15
28616888 TTTGTAAGTT
28616898 CAGGCTTTATGCCTAG
1 CAGGCTTTATGCCT-G
28616914 CAGGCTTTATGCC-G
1 CAGGCTTTATGCCTG
* **
28616928 -ATGAATTATG--T-
1 CAGGCTTTATGCCTG
28616939 CAGGCTTTATGCCTAG
1 CAGGCTTTATGCCT-G
28616955 CAGGCTTTATGCC
1 CAGGCTTTATGCC
28616968 GGTGAATTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
12 7 0.17
13 7 0.17
14 2 0.05
16 26 0.62
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (15 bp):
CAGGCTTTATGCCTG
Found at i:28616954 original size:41 final size:41
Alignment explanation
Indices: 28616897--28617050 Score: 186
Period size: 41 Copynumber: 3.8 Consensus size: 41
28616887 TTTTGTAAGT
*
28616897 TCAGGCTTTATGCCTAGCAGGCTTTATGCCGATGAATTATG
1 TCAGGCTTTATGCCTAGCAGGCTTTATGCCGATGAATTATA
*
28616938 TCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGGCTTTATGCCGATGAATTATA
* * * * * *
28616979 TCAGACTTTATGTCTAGTAGGCTTTGTGCC-AGTGAAATGTA
1 TCAGGCTTTATGCCTAGCAGGCTTTATGCCGA-TGAATTATA
**
28617020 TC-GAGCTTGGTGCCTAGCAGGCTTTATGCCG
1 TCAG-GCTTTATGCCTAGCAGGCTTTATGCCG
28617051 GTGTTATATA
Statistics
Matches: 95, Mismatches: 15, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
40 1 0.01
41 94 0.99
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (41 bp):
TCAGGCTTTATGCCTAGCAGGCTTTATGCCGATGAATTATA
Found at i:28630131 original size:136 final size:136
Alignment explanation
Indices: 28629905--28630456 Score: 908
Period size: 136 Copynumber: 4.1 Consensus size: 136
28629895 TATCACTTTA
* * *
28629905 ACATTTTAGTCTTTTAACATTAAAATTACTAAAAATTAC-TTACAAAATAGTCTTATTGAACAAT
1 ACATTTTAATCCTTTAACATTAAAATTACTAAAAATTACTTTACAAAATAGTCTTATTTAACAAT
* *
28629969 AAAACTTAATAATTTATCATAAAACTTCAAAAACATACTAAAATCATCAATTACATAATCCATAA
66 AAAGCTTAATAATTTATCATAAAACTTCAAAAACATACTAAACTCATCAATTACATAATCCATAA
*
28630034 CACTTG
131 CATTTG
* *
28630040 ACATTTTAATCCTTTAACATTAAAATTGCTAAAAATTACTTTACTAAATAGTCTTATTTAACAAT
1 ACATTTTAATCCTTTAACATTAAAATTACTAAAAATTACTTTACAAAATAGTCTTATTTAACAAT
* *
28630105 AAAGCTTAATAATTTATAATAAAACTTCAAAAACATACTAAACTCATCAATTACATAATCCAGAA
66 AAAGCTTAATAATTTATCATAAAACTTCAAAAACATACTAAACTCATCAATTACATAATCCATAA
28630170 CATTTG
131 CATTTG
* * * *
28630176 ACATTTTAGTCCTTTAACATTAAAATTGCTAAAAATTACTTTGCAAAATAGTCTTATTCAACAAT
1 ACATTTTAATCCTTTAACATTAAAATTACTAAAAATTACTTTACAAAATAGTCTTATTTAACAAT
* *
28630241 AAAGCTTACTAATTTATCATAAAACTTCAAAAACACACTAAACTCATCAATTACATAATCCATAA
66 AAAGCTTAATAATTTATCATAAAACTTCAAAAACATACTAAACTCATCAATTACATAATCCATAA
28630306 CATTTG
131 CATTTG
*
28630312 ACATTTTAATCCTTTAACATTAAAATTACTAAAAATTACTTTACAAAATAGTCTTATTTAATAAT
1 ACATTTTAATCCTTTAACATTAAAATTACTAAAAATTACTTTACAAAATAGTCTTATTTAACAAT
* * *
28630377 AAAGCTTAATAATTTATCATAAAACTTAAAAAAAATACTAAACTCATCAGTTACATAATCCATAA
66 AAAGCTTAATAATTTATCATAAAACTTCAAAAACATACTAAACTCATCAATTACATAATCCATAA
28630442 CATTTG
131 CATTTG
28630448 ACAGTTTTA
1 ACA-TTTTA
28630457 CAAATTAGTT
Statistics
Matches: 387, Mismatches: 28, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
135 36 0.09
136 346 0.89
137 5 0.01
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.35
Consensus pattern (136 bp):
ACATTTTAATCCTTTAACATTAAAATTACTAAAAATTACTTTACAAAATAGTCTTATTTAACAAT
AAAGCTTAATAATTTATCATAAAACTTCAAAAACATACTAAACTCATCAATTACATAATCCATAA
CATTTG
Found at i:28634390 original size:20 final size:20
Alignment explanation
Indices: 28634290--28634390 Score: 71
Period size: 20 Copynumber: 5.0 Consensus size: 20
28634280 ACTTGTTGTT
*
28634290 TGAATGCACATTCGTACCCC
1 TGAATGCACATTCGTGCCCC
** * *
28634310 TGTTTGTAC-TTCGGTACCCC
1 TGAATGCACATTC-GTGCCCC
*
28634330 TGAATGCACATTTGTGCCCC
1 TGAATGCACATTCGTGCCCC
** * *
28634350 TGTTTGTAC-TTCGGTGACCC
1 TGAATGCACATTC-GTGCCCC
*
28634370 TGAATGCACATGCGTGCCCC
1 TGAATGCACATTCGTGCCCC
28634390 T
1 T
28634391 ATTTGTACTT
Statistics
Matches: 59, Mismatches: 18, Indels: 8
0.69 0.21 0.09
Matches are distributed among these distances:
19 5 0.08
20 50 0.85
21 4 0.07
ACGTcount: A:0.17, C:0.31, G:0.21, T:0.32
Consensus pattern (20 bp):
TGAATGCACATTCGTGCCCC
Found at i:28634420 original size:40 final size:40
Alignment explanation
Indices: 28634290--28634409 Score: 179
Period size: 40 Copynumber: 3.0 Consensus size: 40
28634280 ACTTGTTGTT
*
28634290 TGAATGCACATTCGTACCCCTGTTTGTACTTCGGTACCCC
1 TGAATGCACATTCGTGCCCCTGTTTGTACTTCGGTACCCC
*
28634330 TGAATGCACATTTGTGCCCCTGTTTGTACTTCGGTGA-CCC
1 TGAATGCACATTCGTGCCCCTGTTTGTACTTCGGT-ACCCC
* * *
28634370 TGAATGCACATGCGTGCCCCTATTTGTACTTCAGTACCCC
1 TGAATGCACATTCGTGCCCCTGTTTGTACTTCGGTACCCC
28634410 CGAACACACA
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
39 1 0.01
40 70 0.97
41 1 0.01
ACGTcount: A:0.17, C:0.31, G:0.19, T:0.33
Consensus pattern (40 bp):
TGAATGCACATTCGTGCCCCTGTTTGTACTTCGGTACCCC
Found at i:28644586 original size:18 final size:17
Alignment explanation
Indices: 28644548--28644588 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
28644538 ATCTTGTTCG
*
28644548 TATTTTTAGAAAAAACT
1 TATTTTTAGAAAAAACA
*
28644565 TATTTTTAGTAAAAATCA
1 TATTTTTAG-AAAAAACA
28644583 TATTTT
1 TATTTT
28644589 CAGCCAACCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (17 bp):
TATTTTTAGAAAAAACA
Found at i:28651749 original size:40 final size:40
Alignment explanation
Indices: 28651705--28651782 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
28651695 TTAATAAAAG
28651705 AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTAAT
1 AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTAAT
* * * *
28651745 AAAGTCCAGCAACTCATTTATTACCTAAGATGAGTTTA
1 AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTA
28651783 TTTAAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (40 bp):
AAAGTCCAACAACTCAATTACTAACTAAGATGAGTTTAAT
Found at i:28657663 original size:40 final size:40
Alignment explanation
Indices: 28657619--28657696 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
28657609 TAAATAAAAG
28657619 AAAGTCCAACAACTCAATTACTAACTAAAATGAGTTTAAT
1 AAAGTCCAACAACTCAATTACTAACTAAAATGAGTTTAAT
* * * * *
28657659 AAAGTCCAGCAACTTATTTATTAACTAAGATGAGTTTA
1 AAAGTCCAACAACTCAATTACTAACTAAAATGAGTTTA
28657697 TTTAAATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (40 bp):
AAAGTCCAACAACTCAATTACTAACTAAAATGAGTTTAAT
Found at i:28659374 original size:13 final size:15
Alignment explanation
Indices: 28659346--28659377 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
28659336 TTACAGATAA
28659346 ATATGTCAGAATCAG
1 ATATGTCAGAATCAG
28659361 ATATG-CAGAA-CAG
1 ATATGTCAGAATCAG
28659374 ATAT
1 ATAT
28659378 ACAAAATTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 5 0.29
15 5 0.29
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (15 bp):
ATATGTCAGAATCAG
Found at i:28669338 original size:45 final size:45
Alignment explanation
Indices: 28669287--28669374 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
28669277 TGTGAACCGA
* * *
28669287 ACATCATTGATTAGTAAGGTGGTTGTTATGTGCTGATTCCACCAG
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCAG
*
28669332 ACATCATTGATTAATAAGGTGGTTGCTATGTGTTGAATCCACC
1 ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACC
28669375 GAGTATATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.35
Consensus pattern (45 bp):
ACATCATTGATTAATAAGGTGGTTGCTATGTGCTGAATCCACCAG
Found at i:28676188 original size:24 final size:25
Alignment explanation
Indices: 28676152--28676203 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
28676142 ATTGTTTAAA
*
28676152 TTTATCATATATTATCATTTTAAGT
1 TTTATCATATATTATCATTCTAAGT
* *
28676177 TTTAT-ATGTATTATTATTCTAAGT
1 TTTATCATATATTATCATTCTAAGT
28676201 TTT
1 TTT
28676204 CATGTGTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.60
Consensus pattern (25 bp):
TTTATCATATATTATCATTCTAAGT
Found at i:28676267 original size:24 final size:21
Alignment explanation
Indices: 28676212--28676267 Score: 51
Period size: 23 Copynumber: 2.5 Consensus size: 21
28676202 TTCATGTGTA
*
28676212 ATTACTTT-TTTTAATTTATC
1 ATTATTTTATTTTAATTTATC
28676232 ATATATTCTTATTTTAATTTCCATC
1 AT-TATT-TTATTTTAATTT--ATC
28676257 TATTATTTTAT
1 -ATTATTTTAT
28676268 ATAGTTGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
20 2 0.07
21 3 0.10
22 2 0.07
23 9 0.31
24 4 0.14
25 7 0.24
26 2 0.07
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTATTTTATTTTAATTTATC
Found at i:28686094 original size:143 final size:143
Alignment explanation
Indices: 28685837--28686487 Score: 964
Period size: 143 Copynumber: 4.6 Consensus size: 143
28685827 ATTGAAGTCA
* * * *
28685837 TTACGGTGAATCTTATCTTTCTAAAGTTGCAGCGGAGCAGA-TGAATCCACCAGCCTTATCTCAC
1 TTACGGTGAATCTTATCTTCCTGAAGTTGCAGCGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
* * *
28685901 TGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGGCGTTACAATGGAACAGA
66 TGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTACAGTGGAACAGA
28685966 TTAAAGCTACAAG
131 TTAAAGCTACAAG
* *
28685979 TTACGGCGAATCTTATCTTCCTGAAGTTACAGCGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
1 TTACGGTGAATCTTATCTTCCTGAAGTTGCAGCGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
* * **
28686044 TGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCTCTGGCGTTGTAGTGGAACAGA
66 TGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTACAGTGGAACAGA
28686109 TTAAAGCTACAAG
131 TTAAAGCTACAAG
** * ** * *
28686122 TTACATTGAATCTTATCTTCCTAAAGTTATAGCGGAGCAGATTGAAGTCACTAGCCTTATCTCCC
1 TTACGGTGAATCTTATCTTCCTGAAGTTGCAGCGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
* * * *
28686187 TAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGGCATTACAGTGGAACAGA
66 TGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTACAGTGGAACAGA
28686252 TTAAAGCTACAAG
131 TTAAAGCTACAAG
* * *
28686265 TTATGGTGAATCTTATCTT-CTGAAATTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
1 TTACGGTGAATCTTATCTTCCTGAAGTTGCAGCGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
* * * * **
28686329 TAAAGTTGTAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGACGTTGTAGTGGAACAGA
66 TGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTACAGTGGAACAGA
28686394 TTAAAGCTACAAG
131 TTAAAGCTACAAG
* * *
28686407 TTATGGTGAATCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACCAGCCTTATCTCCC
1 TTACGGTGAATCTTATCTTCCTGAAGTTGCAGCGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
28686472 TGAAGTTGCAGCGGAG
66 TGAAGTTGCAGCGGAG
28686488 TAGATCGAAG
Statistics
Matches: 459, Mismatches: 48, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
142 164 0.36
143 295 0.64
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (143 bp):
TTACGGTGAATCTTATCTTCCTGAAGTTGCAGCGGAGCAGATTGAAGCCACCAGCCTTATCTCCC
TGAAGTTGCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCGTTACAGTGGAACAGA
TTAAAGCTACAAG
Found at i:28686365 original size:285 final size:286
Alignment explanation
Indices: 28685837--28686487 Score: 1011
Period size: 285 Copynumber: 2.3 Consensus size: 286
28685827 ATTGAAGTCA
* * *
28685837 TTACGGTGAATCTTATCTTTCTAAAGTTGCAGCGGAGCAGA-TGAA-TCCACCAGCCTTATCTCA
1 TTACAGTGAATCTTATCTTCCTAAAGTTGCAGCGGAGCAGATTGAAGT-CACCAGCCTTATCTCC
*
28685900 CTGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGGCGTTACAATGGAACAG
65 CTGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGGCATTACAATGGAACAG
*
28685965 ATTAAAGCTACAAGTTACGGCGAATCTTATCTTCCTGAAGTTACAGCGGAGCAGATTGAAGCCAC
130 ATTAAAGCTACAAGTTACGGCGAATCTTATCTTCCTGAAATTACAGCGGAGCAGATTGAAGCCAC
* * * * *
28686030 CAGCCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATCTTATTTCTCTGGCGT
195 CAGCCTTATCTCCCTAAAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGACGT
28686095 TGTAGTGGAACAGATTAAAGCTACAAG
260 TGTAGTGGAACAGATTAAAGCTACAAG
* ** *
28686122 TTACATTGAATCTTATCTTCCTAAAGTTATAGCGGAGCAGATTGAAGTCACTAGCCTTATCTCCC
1 TTACAGTGAATCTTATCTTCCTAAAGTTGCAGCGGAGCAGATTGAAGTCACCAGCCTTATCTCCC
* * * *
28686187 TAAAGTTGCAGTGGAGCAGACTGAAGATAGCGAATCTTATTTCCCTGGCATTACAGTGGAACAGA
66 TGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGGCATTACAATGGAACAGA
* * * *
28686252 TTAAAGCTACAAGTTATGGTGAATCTTATCTT-CTGAAATTGCAGTGGAGCAGATTGAAGCCACC
131 TTAAAGCTACAAGTTACGGCGAATCTTATCTTCCTGAAATTACAGCGGAGCAGATTGAAGCCACC
*
28686316 AGCCTTATCTCCCTAAAGTTGTAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGACGTT
196 AGCCTTATCTCCCTAAAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGACGTT
28686381 GTAGTGGAACAGATTAAAGCTACAAG
261 GTAGTGGAACAGATTAAAGCTACAAG
** * * * *
28686407 TTATGGTGAATCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACCAGCCTTATCTCCC
1 TTACAGTGAATCTTATCTTCCTAAAGTTGCAGCGGAGCAGATTGAAGTCACCAGCCTTATCTCCC
28686472 TGAAGTTGCAGCGGAG
66 TGAAGTTGCAGCGGAG
28686488 TAGATCGAAG
Statistics
Matches: 329, Mismatches: 35, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
285 219 0.67
286 109 0.33
287 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (286 bp):
TTACAGTGAATCTTATCTTCCTAAAGTTGCAGCGGAGCAGATTGAAGTCACCAGCCTTATCTCCC
TGAAGTTGCAGCGGAGCAGACTGAAGATAGCAAATCTTATTTCCCTGGCATTACAATGGAACAGA
TTAAAGCTACAAGTTACGGCGAATCTTATCTTCCTGAAATTACAGCGGAGCAGATTGAAGCCACC
AGCCTTATCTCCCTAAAGTTGCAGCGGAGCAGACTGAAGACAACGAATCTTATTTCCCTGACGTT
GTAGTGGAACAGATTAAAGCTACAAG
Found at i:28686514 original size:44 final size:44
Alignment explanation
Indices: 28686417--28686519 Score: 125
Period size: 44 Copynumber: 2.3 Consensus size: 44
28686407 TTATGGTGAA
* * * *
28686417 TCTTATCTTCCTGAAGTTGCAGTGGAGTAGATTGAAGCCACCAG
1 TCTTATCTCCCTGAAGTTGCAGCGGAGTAGATCGAAGCCACAAG
* **
28686461 CCTTATCTCCCTGAAGTTGCAGCGGAGTAGATCGAAGTTACAAG
1 TCTTATCTCCCTGAAGTTGCAGCGGAGTAGATCGAAGCCACAAG
* *
28686505 TCTTTTCTCCTTGAA
1 TCTTATCTCCCTGAA
28686520 ATTACATTGG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 49 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGCGGAGTAGATCGAAGCCACAAG
Found at i:28686974 original size:23 final size:23
Alignment explanation
Indices: 28686944--28686991 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
28686934 CACAAGGTGG
28686944 CCCAAATTCAAGTTTCCAGAAAC
1 CCCAAATTCAAGTTTCCAGAAAC
28686967 CCCAAATTCAAGTTTCCAGAAAC
1 CCCAAATTCAAGTTTCCAGAAAC
28686990 CC
1 CC
28686992 TTAGGGTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.33, G:0.08, T:0.21
Consensus pattern (23 bp):
CCCAAATTCAAGTTTCCAGAAAC
Done.