Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 117 of 235
Found at i:39941882 original size:19 final size:19
Alignment explanation
Indices: 39941860--39941917 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
39941850 TTAGAATTTT
39941860 TTTAAAAAATTGTAAAAAA
1 TTTAAAAAATTGTAAAAAA
*
39941879 TTT-AAAAATTGT-AAAAT
1 TTTAAAAAATTGTAAAAAA
**
39941896 TTTATAAAAATCATAAAAAA
1 TTTA-AAAAATTGTAAAAAA
39941916 TT
1 TT
39941918 AACGACCCCT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
17 7 0.22
18 9 0.28
19 10 0.31
20 6 0.19
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (19 bp):
TTTAAAAAATTGTAAAAAA
Found at i:39942191 original size:25 final size:24
Alignment explanation
Indices: 39942162--39942217 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
39942152 CATAAAAAAA
39942162 CTAAAAACATT-AAAATAAATGTTTT
1 CTAAAAA-ATTGAAAATAAAT-TTTT
39942187 CTAAAAAATTGAAAATAAA-TTTT
1 CTAAAAAATTGAAAATAAATTTTT
39942210 -TAAAAAAT
1 CTAAAAAAT
39942218 ATGTATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.27
23 4 0.13
24 3 0.10
25 15 0.50
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (24 bp):
CTAAAAAATTGAAAATAAATTTTT
Found at i:39942752 original size:9 final size:8
Alignment explanation
Indices: 39942738--39942804 Score: 53
Period size: 9 Copynumber: 7.6 Consensus size: 8
39942728 CTTTATAAAA
39942738 TTTTATACT
1 TTTTATA-T
39942747 TTTTATAT
1 TTTTATAT
*
39942755 TTCTATAT
1 TTTTATAT
39942763 ATTTTATAATT
1 -TTTTAT-A-T
*
39942774 TTTTACAAT
1 TTTTA-TAT
39942783 TTTTATATT
1 TTTTATA-T
*
39942792 TTTTTTAT
1 TTTTATAT
39942800 TTTTA
1 TTTTA
39942805 ATAACTTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
8 14 0.30
9 25 0.53
10 7 0.15
11 1 0.02
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.70
Consensus pattern (8 bp):
TTTTATAT
Found at i:39942879 original size:37 final size:37
Alignment explanation
Indices: 39942783--39942882 Score: 98
Period size: 37 Copynumber: 2.7 Consensus size: 37
39942773 TTTTTACAAT
*
39942783 TTTTATATTTTTTTT-ATTTTTAATAACTTTTTAATAA
1 TTTTAT-TTTTTTTTAATTTTTAATAACTATTTAATAA
* * ** *
39942820 TTTAATTTTTTATTAAAATTTAATAA-TATTT-ATAGC
1 TTTTATTTTTTTTTAATTTTTAATAACTATTTAATA-A
39942856 TTTTATTTTTTTTCTAATTTTTAATAA
1 TTTTATTTTTTTT-TAATTTTTAATAA
39942883 AAGCAGGGCT
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
35 3 0.06
36 22 0.44
37 25 0.50
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (37 bp):
TTTTATTTTTTTTTAATTTTTAATAACTATTTAATAA
Found at i:39943005 original size:91 final size:91
Alignment explanation
Indices: 39942888--39943110 Score: 274
Period size: 91 Copynumber: 2.5 Consensus size: 91
39942878 AATAAAAGCA
* * *
39942888 GGGCTTAAATT-TTTTTTTGAAAAGGTTTGAGGGTCTTTTTGATGCATTTTGAAAGATCAAGT-G
1 GGGCTTAATTTCTTTTTTTGAAAAGGTTTGAGAG-CTTTTTGACGCATTTTGAAAGATCAAGTAG
*
39942951 CCTAATTGAGTGCAAAAAAAAA-AG-GG
65 CC-AAATGAGTGCAAAAAAAAAGAGTGG
* * *
39942977 GAGGCTTAATTTCTTTTTTTTAAAAGGTTTAAGAGCCTTTTTGACGCATTTTGAAAGTTCAAGTA
1 G-GGCTTAATTTCTTTTTTTGAAAAGGTTTGAGAG-CTTTTTGACGCATTTTGAAAGATCAAGTA
* *
39943042 TCCAAATGAGTGCAAAAAAAAAGAGTTG
64 GCCAAATGAGTGCAAAAAAAAAGAGTGG
* * *
39943070 GGGCTTAATTGCTTTTTTTGAAAATGTTTGAGTGCTTTTTG
1 GGGCTTAATTTCTTTTTTTGAAAAGGTTTGAGAGCTTTTTG
39943111 CACCCTTAAG
Statistics
Matches: 114, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
89 1 0.01
90 9 0.08
91 70 0.61
92 32 0.28
93 2 0.02
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.38
Consensus pattern (91 bp):
GGGCTTAATTTCTTTTTTTGAAAAGGTTTGAGAGCTTTTTGACGCATTTTGAAAGATCAAGTAGC
CAAATGAGTGCAAAAAAAAAGAGTGG
Found at i:39944056 original size:40 final size:40
Alignment explanation
Indices: 39943961--39944058 Score: 142
Period size: 40 Copynumber: 2.5 Consensus size: 40
39943951 CTTTTCAGGT
* * * *
39943961 CAAATCCTATCCACCTTAAGTTACTATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCAAGAA
* *
39944001 TAAATCCTATTCACTTTAAATTACCATAGTGAATCAAGAA
1 CAAATCCTATCCACTTTAAATTACCATAGTGAATCAAGAA
39944041 CAAATCCTATCCACTTTA
1 CAAATCCTATCCACTTTA
39944059 TATTCTCGAG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.31
Consensus pattern (40 bp):
CAAATCCTATCCACTTTAAATTACCATAGTGAATCAAGAA
Found at i:39945308 original size:22 final size:22
Alignment explanation
Indices: 39945282--39945328 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
39945272 ATTTTCTTTC
39945282 TCTACACTATTTCCCATTACAT
1 TCTACACTATTTCCCATTACAT
*
39945304 TCTACACTATTTCCCATTACTT
1 TCTACACTATTTCCCATTACAT
39945326 TCT
1 TCT
39945329 CTTATTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (22 bp):
TCTACACTATTTCCCATTACAT
Found at i:39951408 original size:46 final size:46
Alignment explanation
Indices: 39951353--39951568 Score: 407
Period size: 46 Copynumber: 4.7 Consensus size: 46
39951343 GGTTAAGCAT
*
39951353 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
39951399 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
39951445 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
39951491 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTAT-GATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
39951536 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
39951569 GGGGCGGGTT
Statistics
Matches: 167, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
45 43 0.26
46 124 0.74
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (46 bp):
CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:39962809 original size:79 final size:79
Alignment explanation
Indices: 39962676--39962896 Score: 318
Period size: 79 Copynumber: 2.8 Consensus size: 79
39962666 AAGTCACATC
** * * *
39962676 TCATGTAATAGTAGTAAATCAGGATTA-CCTTTTCAGGTCAAATCCTACCCACCTTAAGTTATCA
1 TCATGTAACCGTAGCAAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCA
*
39962740 TAAGGAATCATGTA
66 TAAGGAATCATATA
* * * *
39962754 TCGTGTAACCGTAGCGAATTAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAGGTTACCA
1 TCATGTAACCGTAGCAAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCA
*
39962819 TAATGAATCATATA
66 TAAGGAATCATATA
* *
39962833 TCATGTAACCGTAGCAAATCAAGATTACCCTTTTCAGGTCAAATCCTATCCGCCTTAAGTTACC
1 TCATGTAACCGTAGCAAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACC
39962897 GTAGTGAAAC
Statistics
Matches: 125, Mismatches: 17, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
78 21 0.17
79 104 0.83
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (79 bp):
TCATGTAACCGTAGCAAATCAGGATTACCCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCA
TAAGGAATCATATA
Found at i:39963055 original size:40 final size:40
Alignment explanation
Indices: 39962991--39963128 Score: 141
Period size: 40 Copynumber: 3.5 Consensus size: 40
39962981 CTTTTCAGGT
* * * *
39962991 CAAATCCTATTCGCCTTAAGTTACCGTAGTGAATCAAGAA
1 CAAATCCTATTCACTTTAAATTACCATAGTGAATCAAGAA
*
39963031 TAAATCCTATTCACTTTAAATTACCATAGTGAATCAAGAA
1 CAAATCCTATTCACTTTAAATTACCATAGTGAATCAAGAA
* * ** ** **
39963071 CAAATCCTATCCACTTTGAGGTATTATAGTGAATCGGGAA
1 CAAATCCTATTCACTTTAAATTACCATAGTGAATCAAGAA
* *
39963111 CGAATCCTATCCACTTTA
1 CAAATCCTATTCACTTTA
39963129 TATTCTCGAG
Statistics
Matches: 82, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (40 bp):
CAAATCCTATTCACTTTAAATTACCATAGTGAATCAAGAA
Found at i:39963066 original size:119 final size:119
Alignment explanation
Indices: 39962794--39963066 Score: 438
Period size: 119 Copynumber: 2.3 Consensus size: 119
39962784 TTTTCAGGTC
* * ** *
39962794 AAATCCTATCCACCTTAGGTTACCATAATGAATCATATATCATGTAACCGTAGCAAATCAAGATT
1 AAATCCTATTCACTTTAAATTACCATAATGAATCATATATCATGTAACCATAGCAAATCAAGATT
39962859 ACCCTTTTCAGGTCAAATCCTATCCGCCTTAAGTTACCGTAGTGAAACAAGAAT
66 ACCCTTTTCAGGTCAAATCCTATCCGCCTTAAGTTACCGTAGTGAAACAAGAAT
* * * *
39962913 AAATCCTATTCACTTTAAATTACCATAATAAATCATATATCATGTAACCATCGCGAATCAGGATT
1 AAATCCTATTCACTTTAAATTACCATAATGAATCATATATCATGTAACCATAGCAAATCAAGATT
* *
39962978 ACCCTTTTCAGGTCAAATCCTATTCGCCTTAAGTTACCGTAGTGAATCAAGAAT
66 ACCCTTTTCAGGTCAAATCCTATCCGCCTTAAGTTACCGTAGTGAAACAAGAAT
*
39963032 AAATCCTATTCACTTTAAATTACCATAGTGAATCA
1 AAATCCTATTCACTTTAAATTACCATAATGAATCA
39963067 AGAACAAATC
Statistics
Matches: 141, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
119 141 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (119 bp):
AAATCCTATTCACTTTAAATTACCATAATGAATCATATATCATGTAACCATAGCAAATCAAGATT
ACCCTTTTCAGGTCAAATCCTATCCGCCTTAAGTTACCGTAGTGAAACAAGAAT
Found at i:39964779 original size:11 final size:10
Alignment explanation
Indices: 39964763--39964796 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
39964753 TTATATATTA
39964763 AATAAATTAAT
1 AATAAA-TAAT
39964774 AATAAAATAAT
1 AAT-AAATAAT
39964785 AATAAATAAT
1 AATAAATAAT
39964795 AA
1 AA
39964797 AATATCTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.41
11 10 0.45
12 3 0.14
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AATAAATAAT
Found at i:39965623 original size:34 final size:34
Alignment explanation
Indices: 39965529--39965627 Score: 94
Period size: 34 Copynumber: 2.9 Consensus size: 34
39965519 AATATGACGC
* * * *
39965529 ATTGGCGTTGTGGCGAGATGTTGATTGAATGATGT
1 ATTGGTGTTGTGGCGAGATATTAATTGAA-GAAGT
** *
39965564 ATCAGTGTTGTGGTG-GA-ATGATAATTGAAGAAGT
1 ATTGGTGTTGTGGCGAGATAT--TAATTGAAGAAGT
39965598 ATTGGTGTTGTGGCGAGATATTAATTGAAG
1 ATTGGTGTTGTGGCGAGATATTAATTGAAG
39965628 GAGGACTAGA
Statistics
Matches: 50, Mismatches: 10, Indels: 9
0.72 0.14 0.13
Matches are distributed among these distances:
33 1 0.02
34 27 0.54
35 20 0.40
36 2 0.04
ACGTcount: A:0.26, C:0.04, G:0.34, T:0.35
Consensus pattern (34 bp):
ATTGGTGTTGTGGCGAGATATTAATTGAAGAAGT
Found at i:39968630 original size:50 final size:50
Alignment explanation
Indices: 39968576--39968677 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
39968566 CTGATCGATA
39968576 TGGGTTCTTGAAGTTGGTTTAAGGAAAAAACTTTTCTGTTTCTATCTTCT
1 TGGGTTCTTGAAGTTGGTTTAAGGAAAAAACTTTTCTGTTTCTATCTTCT
39968626 TGGGTTCTTGAAGTTGGTTTAAGGAAAAAACTTTTCTGTTTCTATCTTCT
1 TGGGTTCTTGAAGTTGGTTTAAGGAAAAAACTTTTCTGTTTCTATCTTCT
39968676 TG
1 TG
39968678 TTTTTGTATG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.22, C:0.12, G:0.21, T:0.46
Consensus pattern (50 bp):
TGGGTTCTTGAAGTTGGTTTAAGGAAAAAACTTTTCTGTTTCTATCTTCT
Found at i:39971064 original size:12 final size:12
Alignment explanation
Indices: 39971047--39971077 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
39971037 TAAGGGAAGA
39971047 GAGCCCAAGCAT
1 GAGCCCAAGCAT
39971059 GAGCCCAAGCAT
1 GAGCCCAAGCAT
39971071 GAGCCCA
1 GAGCCCA
39971078 GGTATGTCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.35, G:0.26, T:0.06
Consensus pattern (12 bp):
GAGCCCAAGCAT
Found at i:39975677 original size:3 final size:3
Alignment explanation
Indices: 39975669--39975710 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
39975659 TTGTGTCTAG
39975669 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39975711 ACTTGGAGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39982499 original size:3 final size:3
Alignment explanation
Indices: 39982491--39982522 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
39982481 TAACCATAGC
39982491 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
39982523 CAATTTCAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:39986766 original size:6 final size:6
Alignment explanation
Indices: 39986755--39986782 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
39986745 GCGGAAACGA
39986755 TGGCAG TGGCAG TGGCAG TGGCAG TGGC
1 TGGCAG TGGCAG TGGCAG TGGCAG TGGC
39986783 GTTTACCGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.18, G:0.50, T:0.18
Consensus pattern (6 bp):
TGGCAG
Found at i:39987116 original size:41 final size:40
Alignment explanation
Indices: 39987070--39987155 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 40
39987060 AAAAAATGGC
*
39987070 TTTTTGTGGTGTTCT-TAAAAAAAAAGCCACTACAGCTTAAT
1 TTTTTGTGGCGTT-TATAAAAAAAAAGCCACTACAGCTT-AT
** * *
39987111 TTTTTGTGGCGTTTATATTAAAAACGCCACTAGAGCTTAT
1 TTTTTGTGGCGTTTATAAAAAAAAAGCCACTACAGCTTAT
39987151 TTTTT
1 TTTTT
39987156 ATGCCATTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
40 8 0.21
41 31 0.79
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (40 bp):
TTTTTGTGGCGTTTATAAAAAAAAAGCCACTACAGCTTAT
Found at i:39987365 original size:14 final size:15
Alignment explanation
Indices: 39987330--39987365 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
39987320 TAAGTTCCTT
*
39987330 ATTTTTTAATTTTTA
1 ATTTTTTAATTTTAA
39987345 ATTTTTT-ATTTTAA
1 ATTTTTTAATTTTAA
39987359 ATTTTTT
1 ATTTTTT
39987366 TGAATATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (15 bp):
ATTTTTTAATTTTAA
Found at i:39987540 original size:22 final size:22
Alignment explanation
Indices: 39987510--39987554 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
39987500 ACATTAGTTG
* *
39987510 TTTAGATTTTTATATAGATGACA
1 TTTAGATTTTGATAGAGAT-ACA
39987533 TTTA-ATTTTGATAGAGATACA
1 TTTAGATTTTGATAGAGATACA
39987554 T
1 T
39987555 CTCAGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 12 0.60
23 4 0.20
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (22 bp):
TTTAGATTTTGATAGAGATACA
Found at i:39987832 original size:7 final size:7
Alignment explanation
Indices: 39987816--39987848 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
39987806 CAATTGCACA
*
39987816 CTAAATC
1 CTAAACC
39987823 CTAAACC
1 CTAAACC
39987830 CTAAACC
1 CTAAACC
39987837 CTAAACC
1 CTAAACC
39987844 CTAAA
1 CTAAA
39987849 TCATAAACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.18
Consensus pattern (7 bp):
CTAAACC
Found at i:39987855 original size:14 final size:14
Alignment explanation
Indices: 39987824--39987925 Score: 75
Period size: 14 Copynumber: 7.2 Consensus size: 14
39987814 CACTAAATCC
*
39987824 TAAACCCTAAACCC
1 TAAACCCTAAACCA
*
39987838 TAAACCCTAAATCA
1 TAAACCCTAAACCA
**
39987852 TAAACTTTAAA--A
1 TAAACCCTAAACCA
*
39987864 TAGTAACTCATAAA-CA
1 TA--AAC-CCTAAACCA
*
39987880 TTAAACCCTTAACCA
1 -TAAACCCTAAACCA
*
39987895 TATACCCTAAACCA
1 TAAACCCTAAACCA
*
39987909 TAAACCCTAAACTA
1 TAAACCCTAAACCA
39987923 TAA
1 TAA
39987926 TGATAATTAA
Statistics
Matches: 70, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
12 3 0.04
14 55 0.79
15 9 0.13
16 1 0.01
17 2 0.03
ACGTcount: A:0.48, C:0.27, G:0.01, T:0.24
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:39987855 original size:21 final size:21
Alignment explanation
Indices: 39987816--39987920 Score: 61
Period size: 21 Copynumber: 5.0 Consensus size: 21
39987806 CAATTGCACA
* *
39987816 CTAAATCCTAAACCCTAAACC
1 CTAAACCCTAAACCATAAACC
* *
39987837 CTAAACCCTAAATCATAAACT
1 CTAAACCCTAAACCATAAACC
* * *
39987858 TTAAA--ATAGTAACTCATAAACA
1 CTAAACCCTA--AAC-CATAAACC
* * *
39987880 TTAAACCCTTAACCATATACC
1 CTAAACCCTAAACCATAAACC
* *
39987901 CTAAACCATAAACCCTAAAC
1 CTAAACCCTAAACCATAAAC
39987921 TATAATGATA
Statistics
Matches: 62, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
19 2 0.03
21 44 0.71
22 15 0.24
24 1 0.02
ACGTcount: A:0.47, C:0.30, G:0.01, T:0.23
Consensus pattern (21 bp):
CTAAACCCTAAACCATAAACC
Found at i:39988146 original size:7 final size:7
Alignment explanation
Indices: 39988134--39988181 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
39988124 CCCCAACCCT
39988134 TAAACCA
1 TAAACCA
39988141 TAAACCA
1 TAAACCA
*
39988148 TAAATCA
1 TAAACCA
* *
39988155 TAATCCC
1 TAAACCA
39988162 TAAACCCA
1 TAAA-CCA
*
39988170 TAATCCA
1 TAAACCA
39988177 TAAAC
1 TAAAC
39988182 TTTAAAATAG
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
7 27 0.84
8 5 0.16
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCA
Found at i:39988702 original size:39 final size:39
Alignment explanation
Indices: 39988656--39988888 Score: 162
Period size: 39 Copynumber: 5.6 Consensus size: 39
39988646 TTTGCGACGT
39988656 TTTTTTAAAAAGCGCCGCTAAAGGTTACCTATAGCGGCG
1 TTTTTTAAAAAGCGCCGCTAAAGGTTACCTATAGCGGCG
* * * * *
39988695 TTTTTTAAAAAGCGCCGCTAATGCTTATCTTTAGAGGCG
1 TTTTTTAAAAAGCGCCGCTAAAGGTTACCTATAGCGGCG
* * *
39988734 -TTTTTCAAAAGCGCCGCTAAAGCCGCGGTAGTTTAGCATAATTTTTTGCGGCG
1 TTTTTTAAAAAGCGCCGCTAAA------G--G-TTA-CCT-A----TAGCGGCG
*
39988787 TTTTTTTAAAAAGCGCCGCTAAAGGTGACCTATAGCGGCG
1 TTTT-TTAAAAAGCGCCGCTAAAGGTTACCTATAGCGGCG
* * * * * *
39988827 TTTTTTAAAAAGCGCCGTTAATGCTTAATCTTTAGCGGCA
1 TTTTTTAAAAAGCGCCGCTAAAGGTT-ACCTATAGCGGCG
*
39988867 TTTTTCAAAAAGCGCCGCTAAA
1 TTTTTTAAAAAGCGCCGCTAAA
39988889 AACCTATTTT
Statistics
Matches: 149, Mismatches: 27, Indels: 35
0.71 0.13 0.17
Matches are distributed among these distances:
38 19 0.13
39 52 0.35
40 40 0.27
44 2 0.01
45 2 0.01
46 2 0.01
47 4 0.03
48 1 0.01
49 1 0.01
53 6 0.04
54 3 0.02
55 17 0.11
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (39 bp):
TTTTTTAAAAAGCGCCGCTAAAGGTTACCTATAGCGGCG
Found at i:39988777 original size:132 final size:132
Alignment explanation
Indices: 39988599--39988888 Score: 458
Period size: 132 Copynumber: 2.2 Consensus size: 132
39988589 AACTTTTTGC
* * * *
39988599 GGCGTTTTCCAAAAAACGCCGCAAAAGCCGCGCAGTTGGCATAATTTTTTGCGACGTTTTTTTAA
1 GGCGTTTTTCAAAAAGCGCCGCTAAAGCCGCGCAGTTAGCATAATTTTTTGCGACGTTTTTTTAA
*
39988664 AAAGCGCCGCTAAAGGTTACCTATAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTT-ATCTTTA
66 AAAGCGCCGCTAAAGGTGACCTATAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTTAATCTTTA
39988728 GA
131 GA
* *
39988730 GGCGTTTTTC-AAAAGCGCCGCTAAAGCCGCGGTAGTTTAGCATAATTTTTTGCGGCGTTTTTTT
1 GGCGTTTTTCAAAAAGCGCCGCTAAAGCCGC-GCAG-TTAGCATAATTTTTTGCGACGTTTTTTT
*
39988794 AAAAAGCGCCGCTAAAGGTGACCTATAGCGGCGTTTTTTAAAAAGCGCCGTTAATGCTTAATCTT
64 AAAAAGCGCCGCTAAAGGTGACCTATAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTTAATCTT
*
39988859 TAGC
129 TAGA
*
39988863 GGCATTTTTCAAAAAGCGCCGCTAAA
1 GGCGTTTTTCAAAAAGCGCCGCTAAA
39988889 AACCTATTTT
Statistics
Matches: 145, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
130 18 0.12
131 12 0.08
132 83 0.57
133 17 0.12
134 15 0.10
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (132 bp):
GGCGTTTTTCAAAAAGCGCCGCTAAAGCCGCGCAGTTAGCATAATTTTTTGCGACGTTTTTTTAA
AAAGCGCCGCTAAAGGTGACCTATAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTTAATCTTTA
GA
Found at i:39995351 original size:27 final size:27
Alignment explanation
Indices: 39995254--39995358 Score: 135
Period size: 27 Copynumber: 3.9 Consensus size: 27
39995244 AGGAAGCGTC
*
39995254 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
39995281 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
39995308 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
39995335 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
39995359 GCAGCCTCGC
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
26 9 0.13
27 61 0.86
28 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:39998358 original size:46 final size:48
Alignment explanation
Indices: 39998254--39998673 Score: 262
Period size: 50 Copynumber: 8.8 Consensus size: 48
39998244 GTTATTTGTG
* * * *
39998254 AGCCAATGTAAGACCATGTCTGGGACATGGAATCGGCATTGAGATG-A
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGTA
* * *
39998301 GAGCTAGTGTAATA-CATGTCTGGGACAT-GCATCGGCCTCGAGTTGTA
1 -AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGTA
* *
39998348 AGCCAGTGTAAGA-CATGTCTGGGACAT-GTATTGG-CTACGAGATGT-
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCT-CGAGATGTA
* *
39998393 -GTCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CACG-GATGTGTGA
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGA--TGT-A
* * * * * **
39998441 GAGCTAGGGTAAGACCATGTTTGGGACATGGCGTCAGCCTCGATTTCG-A
1 -AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGAT-GTA
* *
39998490 TAGTCAGTGTAAGACCATGTCTGGGACATGGCATCGG-CACG-GATGTGTGA
1 -AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGA--TGT-A
* * * * * **
39998540 GAGCTAGGGTAAGACCATGTTTGGGACATGGCGTCAGCCTCGATTTCG-A
1 -AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGAT-GTA
* * * * *
39998589 TAGTCAGTGTAAGACCATGTCTGGGACATGACATC-GACT-TA-ATGGATG
1 -AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGAT-G-TA
* * *
39998637 AGCTAGTGTAAGACCATGTTTGGGACATGACATCGGC
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
39998674 ATTATACCCT
Statistics
Matches: 288, Mismatches: 61, Indels: 46
0.73 0.15 0.12
Matches are distributed among these distances:
44 13 0.05
45 18 0.06
46 61 0.21
47 47 0.16
48 18 0.06
49 61 0.21
50 62 0.22
51 8 0.03
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.25
Consensus pattern (48 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGATGTA
Found at i:39998505 original size:99 final size:99
Alignment explanation
Indices: 39998393--39998665 Score: 464
Period size: 99 Copynumber: 2.8 Consensus size: 99
39998383 TACGAGATGT
39998393 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATGTGTGAGAGCTAGGGTAAGACCA
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATGTGTGAGAGCTAGGGTAAGACCA
39998458 TGTTTGGGACATGGCGTCAGCCTCGATTTCGATA
66 TGTTTGGGACATGGCGTCAGCCTCGATTTCGATA
39998492 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATGTGTGAGAGCTAGGGTAAGACCA
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATGTGTGAGAGCTAGGGTAAGACCA
39998557 TGTTTGGGACATGGCGTCAGCCTCGATTTCGATA
66 TGTTTGGGACATGGCGTCAGCCTCGATTTCGATA
* ** * *
39998591 GTCAGTGTAAGACCATGTCTGGGACATGACATC-G-ACTTA-ATG-GATGAGCTAGTGTAAGACC
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATGTGTGA-GAGCTAGGGTAAGACC
39998652 ATGTTTGGGACATG
65 ATGTTTGGGACATG
39998666 ACATCGGCAT
Statistics
Matches: 168, Mismatches: 5, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
95 2 0.01
96 31 0.18
97 3 0.02
98 1 0.01
99 131 0.78
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (99 bp):
GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGGATGTGTGAGAGCTAGGGTAAGACCA
TGTTTGGGACATGGCGTCAGCCTCGATTTCGATA
Found at i:39998558 original size:50 final size:50
Alignment explanation
Indices: 39998260--39998674 Score: 292
Period size: 49 Copynumber: 8.6 Consensus size: 50
39998250 TGTGAGCCAA
* ** *
39998260 TGTAAGACCATGTCTGGGACATGGAATCGGCATTGA-G-ATGAGAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCACCGATGTGTGAGAGCTAG
* *
39998308 TGTAATA-CATGTCTGGGACAT-GCATCGGC-CTCGA-GT-TGTA-AGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCAC-CGATGTGTG-AGAGCTAG
* * *
39998354 TGTAAGA-CATGTCTGGGACAT-GTATTGGCTA-CGA-GATGT--G-TC-AG
1 TGTAAGACCATGTCTGGGACATGGCATCGGC-ACCGATG-TGTGAGAGCTAG
*
39998398 TGTAAGACCATGTCTGGGACATGGCATCGGCACGGATGTGTGAGAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCACCGATGTGTGAGAGCTAG
* * * * *
39998448 GGTAAGACCATGTTTGGGACATGGCGTCAGC-CTCGAT-T-TCGATAG-TCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCAC-CGATGTGT-GAGAGCT-AG
*
39998497 TGTAAGACCATGTCTGGGACATGGCATCGGCACGGATGTGTGAGAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCACCGATGTGTGAGAGCTAG
* * * * *
39998547 GGTAAGACCATGTTTGGGACATGGCGTCAGC-CTCGAT-T-TCGATAG-TCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCAC-CGATGTGT-GAGAGCT-AG
* ** *
39998596 TGTAAGACCATGTCTGGGACATGACATC-G-ACTTA-ATG-GATGAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCACCGATGTGTGA-GAGCTAG
* *
39998643 TGTAAGACCATGTTTGGGACATGACATCGGCA
1 TGTAAGACCATGTCTGGGACATGGCATCGGCA
39998675 TTATACCCTA
Statistics
Matches: 295, Mismatches: 39, Indels: 65
0.74 0.10 0.16
Matches are distributed among these distances:
44 9 0.03
45 16 0.05
46 60 0.20
47 50 0.17
48 16 0.05
49 72 0.24
50 70 0.24
51 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (50 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCACCGATGTGTGAGAGCTAG
Found at i:40004125 original size:105 final size:105
Alignment explanation
Indices: 40003943--40004155 Score: 399
Period size: 105 Copynumber: 2.0 Consensus size: 105
40003933 AGAGAGAGAA
* *
40003943 GAAACTTTCATGGCTTAATTGGGTAAGTTTCCTTGTCCCGTTTTTAGTAATTTTGATATTTTTGA
1 GAAACTTTCATGGCTTAATTGGGTAAGTTTCCTCGTCCCATTTTTAGTAATTTTGATATTTTTGA
*
40004008 AACTGGGATAGCTTAATCTATCTATTTGAGGGATCAATTT
66 AACTGAGATAGCTTAATCTATCTATTTGAGGGATCAATTT
40004048 GAAACTTTCATGGCTTAATTGGGTAAGTTTCCTCGTCCCATTTTTAGTAATTTTGATATTTTTGA
1 GAAACTTTCATGGCTTAATTGGGTAAGTTTCCTCGTCCCATTTTTAGTAATTTTGATATTTTTGA
40004113 AACTGAGATAGCTTAATCTATCTATTTGAGGGATCAATTT
66 AACTGAGATAGCTTAATCTATCTATTTGAGGGATCAATTT
40004153 GAA
1 GAA
40004156 GAGTTAACAA
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 105 1.00
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.43
Consensus pattern (105 bp):
GAAACTTTCATGGCTTAATTGGGTAAGTTTCCTCGTCCCATTTTTAGTAATTTTGATATTTTTGA
AACTGAGATAGCTTAATCTATCTATTTGAGGGATCAATTT
Found at i:40004642 original size:17 final size:17
Alignment explanation
Indices: 40004620--40004653 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40004610 GCAGTATGAT
*
40004620 TTATAATTATGTGAATG
1 TTATAAATATGTGAATG
*
40004637 TTATAAATGTGTGAATG
1 TTATAAATATGTGAATG
40004654 AATATATGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (17 bp):
TTATAAATATGTGAATG
Found at i:40008423 original size:13 final size:13
Alignment explanation
Indices: 40008405--40008439 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
40008395 TTTAATTGGG
*
40008405 TAATTAATTTAGT
1 TAATTAATTTAAT
*
40008418 TAATTAAATTAAT
1 TAATTAATTTAAT
40008431 TAATTAATT
1 TAATTAATT
40008440 AATATTTATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (13 bp):
TAATTAATTTAAT
Found at i:40013429 original size:33 final size:32
Alignment explanation
Indices: 40013392--40013598 Score: 195
Period size: 33 Copynumber: 6.4 Consensus size: 32
40013382 TCTTTCTGAG
* *
40013392 TGGTACATACAAAATATACCTTTCCTTTTCATA
1 TGGTACACACAAAGTATACCTTTCCTTTTCA-A
* ** *
40013425 TGGTATACACAAAGTATACCTAACCTTTCCAA
1 TGGTACACACAAAGTATACCTTTCCTTTTCAA
* * **
40013457 -GCGTACACACAAAGTGTACATAACCTTTTCAA
1 TG-GTACACACAAAGTATACCTTTCCTTTTCAA
* * *
40013489 -GTGTACACATATAGTGTACCTTTCCTTTTCAA
1 TG-GTACACACAAAGTATACCTTTCCTTTTCAA
*
40013521 GTGGTATACACAAAGTATACCTTTCCTTTTCATA
1 -TGGTACACACAAAGTATACCTTTCCTTTTCA-A
* *
40013555 TGGTATACACAAAGTATACCCTTCCTTTTCAA
1 TGGTACACACAAAGTATACCTTTCCTTTTCAA
40013587 -GTGTACACACAA
1 TG-GTACACACAA
40013599 GGTGTACATA
Statistics
Matches: 147, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
31 2 0.01
32 63 0.43
33 80 0.54
34 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (32 bp):
TGGTACACACAAAGTATACCTTTCCTTTTCAA
Found at i:40013481 original size:32 final size:32
Alignment explanation
Indices: 40013394--40013618 Score: 177
Period size: 32 Copynumber: 6.9 Consensus size: 32
40013384 TTTCTGAGTG
* * **
40013394 GTACATACAAAATATACCTTTCCTTTTCATA-T
1 GTACACACAAAGTATACCTAACCTTTTCA-AGT
* * *
40013426 GGTATACACAAAGTATACCTAACCTTTCCAAGC
1 -GTACACACAAAGTATACCTAACCTTTTCAAGT
* *
40013459 GTACACACAAAGTGTACATAACCTTTTCAAGT
1 GTACACACAAAGTATACCTAACCTTTTCAAGT
* * * **
40013491 GTACACATATAGTGTACCTTTCCTTTTCAAGT
1 GTACACACAAAGTATACCTAACCTTTTCAAGT
* **
40013523 GGTATACACAAAGTATACCTTTCCTTTTCATA-T
1 -GTACACACAAAGTATACCTAACCTTTTCA-AGT
* *
40013556 GGTATACACAAAGTATACCCT-TCCTTTTCAAGT
1 -GTACACACAAAGTATA-CCTAACCTTTTCAAGT
* * *
40013589 GTACACACAAGGTGTACATAACCTTTTCAA
1 GTACACACAAAGTATACCTAACCTTTTCAA
40013619 ATTGTACCGT
Statistics
Matches: 160, Mismatches: 26, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
31 2 0.01
32 78 0.49
33 76 0.47
34 4 0.03
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.33
Consensus pattern (32 bp):
GTACACACAAAGTATACCTAACCTTTTCAAGT
Found at i:40014011 original size:27 final size:27
Alignment explanation
Indices: 40013981--40014034 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
40013971 TCATATAACC
* *
40013981 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
40014008 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
40014035 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:40016651 original size:249 final size:249
Alignment explanation
Indices: 40016213--40016709 Score: 949
Period size: 249 Copynumber: 2.0 Consensus size: 249
40016203 CTACTTCTGC
40016213 TGTCCAATATTGTTTTAGTTCAAGATGTTTATTACCATTTTTCCTCTAAATTTCAAAGGTCATAT
1 TGTCCAATATTGTTTTAGTTCAAGATGTTTATTACCATTTTTCCTCTAAATTTCAAAGGTCATAT
40016278 AATTCAGTCCTTGCTCAATTAGCCCATCTATTAAGCTAATTTTTCTCAATTCACATTTTATTCCA
66 AATTCAGTCCTTGCTCAATTAGCCCATCTATTAAGCTAATTTTTCTCAATTCACATTTTATTCCA
*
40016343 TCATTATAAACTATTACACAACCTTTGAAAATAATCATTTTAACACTAAACCTTAATTCACAACT
131 TCATTATAAACTATTACACAACCTTTGAAAATAATAATTTTAACACTAAACCTTAATTCACAACT
* *
40016408 TTTTCACAATTAGGTCCTAAAATCAATTTCTATTGAAATGACTTGATAAAATCG
196 TTTTCACAATTAGGTCCTAAAATCAATCTCTATTGAAATGACTTAATAAAATCG
40016462 TGTCCAATATTGTTTTAGTTCAAGATGTTTATTACCATTTTTCCTCTAAATTTCAAAGGTCATAT
1 TGTCCAATATTGTTTTAGTTCAAGATGTTTATTACCATTTTTCCTCTAAATTTCAAAGGTCATAT
40016527 AATTCAGTCCTTGCTCAATTAGCCCATCTATTAAGCTAATTTTTCTCAATTCACATTTTATTCCA
66 AATTCAGTCCTTGCTCAATTAGCCCATCTATTAAGCTAATTTTTCTCAATTCACATTTTATTCCA
*
40016592 TCATTATAAACTATTACACAACCTTTGAAAATCATAATTTTAACACTAAACCTTAATTCACAACT
131 TCATTATAAACTATTACACAACCTTTGAAAATAATAATTTTAACACTAAACCTTAATTCACAACT
*
40016657 TTTTCACAATTAGGTCCTAAAATCAATCTCTATTGAAATTACTTAATAAAATC
196 TTTTCACAATTAGGTCCTAAAATCAATCTCTATTGAAATGACTTAATAAAATC
40016710 ATCAGAAAAA
Statistics
Matches: 243, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
249 243 1.00
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.40
Consensus pattern (249 bp):
TGTCCAATATTGTTTTAGTTCAAGATGTTTATTACCATTTTTCCTCTAAATTTCAAAGGTCATAT
AATTCAGTCCTTGCTCAATTAGCCCATCTATTAAGCTAATTTTTCTCAATTCACATTTTATTCCA
TCATTATAAACTATTACACAACCTTTGAAAATAATAATTTTAACACTAAACCTTAATTCACAACT
TTTTCACAATTAGGTCCTAAAATCAATCTCTATTGAAATGACTTAATAAAATCG
Found at i:40026658 original size:90 final size:90
Alignment explanation
Indices: 40026550--40026729 Score: 351
Period size: 90 Copynumber: 2.0 Consensus size: 90
40026540 TAGCTACAGC
40026550 TAGTTTGTCCTCAATTTCAATATGAATGAAATTGACAAGACTCTGCCACAGCTGCTCAGTAAGTT
1 TAGTTTGTCCTCAATTTCAATATGAATGAAATTGACAAGACTCTGCCACAGCTGCTCAGTAAGTT
40026615 GTGAACTGCTGAAGGCAACATGAAA
66 GTGAACTGCTGAAGGCAACATGAAA
*
40026640 TAGTTTGTCCTCAATTTCAATATGAATGAAATTGACAAGACTCTGCCACAGTTGCTCAGTAAGTT
1 TAGTTTGTCCTCAATTTCAATATGAATGAAATTGACAAGACTCTGCCACAGCTGCTCAGTAAGTT
40026705 GTGAACTGCTGAAGGCAACATGAAA
66 GTGAACTGCTGAAGGCAACATGAAA
40026730 AAGGTTGGAC
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (90 bp):
TAGTTTGTCCTCAATTTCAATATGAATGAAATTGACAAGACTCTGCCACAGCTGCTCAGTAAGTT
GTGAACTGCTGAAGGCAACATGAAA
Found at i:40035541 original size:27 final size:27
Alignment explanation
Indices: 40035511--40035571 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
40035501 TCAGGAAATG
*
40035511 AAGCCTTTGTAGATAACTTTAAAAAGA
1 AAGCCTTTGTAGATAACTCTAAAAAGA
* * * *
40035538 AAGCCTTTGTGGCTAACTCTGAAAAGG
1 AAGCCTTTGTAGATAACTCTAAAAAGA
40035565 AAGCCTT
1 AAGCCTT
40035572 CATGTCAAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (27 bp):
AAGCCTTTGTAGATAACTCTAAAAAGA
Found at i:40044742 original size:40 final size:39
Alignment explanation
Indices: 40044682--40044823 Score: 196
Period size: 39 Copynumber: 3.6 Consensus size: 39
40044672 GAAAGATCTT
*
40044682 ATTCAGTATAATTAGTGGATAT-TGCTCATTTTGAGCAAAC
1 ATTCAGTATAATCAGTGGATATCT-CTCATTTT-AGCAAAC
* * *
40044722 ATTCTGTATAATCAGTGGATATCTCTCATTTCAGCAAAA
1 ATTCAGTATAATCAGTGGATATCTCTCATTTTAGCAAAC
* * *
40044761 ATTCAGTATGACCAGTGGATATCTCTCGTTTTAGCAAAC
1 ATTCAGTATAATCAGTGGATATCTCTCATTTTAGCAAAC
40044800 ATTCAGTATAATCAGTGGATATCT
1 ATTCAGTATAATCAGTGGATATCT
40044824 GTAACACCCC
Statistics
Matches: 89, Mismatches: 12, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
39 61 0.69
40 27 0.30
41 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (39 bp):
ATTCAGTATAATCAGTGGATATCTCTCATTTTAGCAAAC
Found at i:40046838 original size:4 final size:4
Alignment explanation
Indices: 40046831--40046870 Score: 62
Period size: 4 Copynumber: 10.0 Consensus size: 4
40046821 GTTTGTATGG
* *
40046831 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CATT CATT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT
40046871 TAATACTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.05, C:0.25, G:0.00, T:0.70
Consensus pattern (4 bp):
CTTT
Found at i:40048464 original size:58 final size:57
Alignment explanation
Indices: 40048384--40048524 Score: 151
Period size: 57 Copynumber: 2.5 Consensus size: 57
40048374 ATTATAGAAA
* * * *
40048384 GGATTTAG-CTCGGACGGGTAATCCTGATATAATCTCTCTCGGGCATATGTTACA-ATT
1 GGATTTAGCCT-GGACTGGTAATCCTGAT-TAAGCTCTCTCGAGCATATGTTACATAAT
* * * * *
40048441 AGGGTTTAGCCTGGACTGGTAATCCTAATTGAGCTCTTTTGAGCATATGTTACATAAT
1 -GGATTTAGCCTGGACTGGTAATCCTGATTAAGCTCTCTCGAGCATATGTTACATAAT
*
40048499 GGATTCAGCCTGGACTGGTAATCCTG
1 GGATTTAGCCTGGACTGGTAATCCTG
40048525 TAATACGATA
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
57 43 0.62
58 24 0.35
59 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (57 bp):
GGATTTAGCCTGGACTGGTAATCCTGATTAAGCTCTCTCGAGCATATGTTACATAAT
Found at i:40049709 original size:21 final size:21
Alignment explanation
Indices: 40049685--40049755 Score: 142
Period size: 21 Copynumber: 3.4 Consensus size: 21
40049675 GGACCACATA
40049685 GGCGTGTCCCAAGGTCACACG
1 GGCGTGTCCCAAGGTCACACG
40049706 GGCGTGTCCCAAGGTCACACG
1 GGCGTGTCCCAAGGTCACACG
40049727 GGCGTGTCCCAAGGTCACACG
1 GGCGTGTCCCAAGGTCACACG
40049748 GGCGTGTC
1 GGCGTGTC
40049756 TCTTGGACCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.17, C:0.32, G:0.35, T:0.15
Consensus pattern (21 bp):
GGCGTGTCCCAAGGTCACACG
Found at i:40049770 original size:22 final size:21
Alignment explanation
Indices: 40049659--40049798 Score: 136
Period size: 21 Copynumber: 6.5 Consensus size: 21
40049649 CGGCCTGCAG
**
40049659 CACGGGCGTGTCCCTTGGACCA
1 CACGGGCGTGTCCCAAGG-CCA
** *
40049681 CATAGGCGTGTCCCAAGGTCA
1 CACGGGCGTGTCCCAAGGCCA
*
40049702 CACGGGCGTGTCCCAAGGTCA
1 CACGGGCGTGTCCCAAGGCCA
*
40049723 CACGGGCGTGTCCCAAGGTCA
1 CACGGGCGTGTCCCAAGGCCA
* **
40049744 CACGGGCGTGTCTCTTGGACCA
1 CACGGGCGTGTCCCAAGG-CCA
* * *
40049766 CACGGGCATGTCCCTTAGACCA
1 CACGGGCGTGTCCC-AAGGCCA
40049788 CACGGGCGTGT
1 CACGGGCGTGT
40049799 AACTTAGAAA
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
21 57 0.57
22 41 0.41
23 2 0.02
ACGTcount: A:0.18, C:0.33, G:0.31, T:0.18
Consensus pattern (21 bp):
CACGGGCGTGTCCCAAGGCCA
Found at i:40050593 original size:75 final size:75
Alignment explanation
Indices: 40050464--40050881 Score: 440
Period size: 75 Copynumber: 5.7 Consensus size: 75
40050454 TACAATATCT
* * * *
40050464 CTCGTTTGAGCAACTTTTAG--T-AT-A-TAGACATTGCTCTTTTGAGCATGTTTAGTATAATCA
1 CTCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTTTTTTGAGCACGTTCAGTATAATCA
40050524 GTAGATATTG
66 GTAGATATTG
* * * *
40050534 CTTGTTTGAGCAACTTTCAATATAATCAGTAGACATTGCTTTTTTAAGCACGTTCAGTATAAACA
1 CTCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTTTTTTGAGCACGTTCAGTATAATCA
*
40050599 GTAGATATTC
66 GTAGATATTG
* * *
40050609 CTCGTTTGAGCAACTTTCAGTACAATCAATAGACATTG-TTCTTTTGAGCACGTTCAATATAATC
1 CTCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTT-TTTTGAGCACGTTCAGTATAATC
*
40050673 AGTAGATATTA
65 AGTAGATATTG
* * * * * * * * * *
40050684 CTCCTTTGAGC-GCATTGAATATAATCAGTAGATATTGCTTGTTTGAGCACATTTAGTATAACCA
1 CTCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTTTTTTGAGCACGTTCAGTATAATCA
*
40050748 GTAGATATTT
66 GTAGATATTG
** * * * *
40050758 CTTATTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTCTTTTGAACACATCCAGTATAATCA
1 CTCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTTTTTTGAGCACGTTCAGTATAATCA
40050823 GTAGATATTG
66 GTAGATATTG
* * * **
40050833 CTCGTCTGAGC-A-TATTCAGTATAATAAGTAGATATTGCTCATTTGAGCA
1 CTCGTTTGAGCAACT-TTCAGTATAATCAGTAGACATTGCTTTTTTGAGCA
40050882 TATTCAATAT
Statistics
Matches: 287, Mismatches: 52, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
70 17 0.06
72 1 0.00
73 3 0.01
74 91 0.32
75 175 0.61
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (75 bp):
CTCGTTTGAGCAACTTTCAGTATAATCAGTAGACATTGCTTTTTTGAGCACGTTCAGTATAATCA
GTAGATATTG
Found at i:40050707 original size:112 final size:112
Alignment explanation
Indices: 40050488--40050881 Score: 408
Period size: 112 Copynumber: 3.5 Consensus size: 112
40050478 TTTTAGTATA
* * * * *
40050488 TAGACATTGCTCTTTTGAGCA-TGTTTAGTATAATCAGTAGATATTGCTT-GTTTGAGCAACTTT
1 TAGATATTGCTCGTTTGAGCACT-TTCAGTATAATCAATAGATATTG-TTCTTTTGAGCAACTTT
* * * *
40050551 CAATATAATCAGTAGACATTGCTTTTTTAAGCACGTTCAGTATAAACAG
64 CAATATAATCAGTAGACATTGCTCTTTTGAGCACATTCAGTATAATCAG
* * * *
40050600 TAGATATTCCTCGTTTGAGCAACTTTCAGTACAATCAATAGACATTGTTCTTTTGAGC-ACGTTC
1 TAGATATTGCTCGTTTGAGC-ACTTTCAGTATAATCAATAGATATTGTTCTTTTGAGCAACTTTC
* * * * * *
40050664 AATATAATCAGTAGATATTACTCCTTTGAGCGCATTGAATATAATCAG
65 AATATAATCAGTAGACATTGCTCTTTTGAGCACATTCAGTATAATCAG
* * *
40050712 TAGATATTGCTTGTTTGAGCACATTT-AGTATAACCAGTAGATA-T-TTCTTATTTGAGCAACTT
1 TAGATATTGCTCGTTTGAGCAC-TTTCAGTATAATCAATAGATATTGTTC-T-TTTGAGCAACTT
* * *
40050774 TCAGTATAATCAGTAGACATTGCTCTTTTGAACACATCCAGTATAATCAG
63 TCAATATAATCAGTAGACATTGCTCTTTTGAGCACATTCAGTATAATCAG
* * *
40050824 TAGATATTGCTCGTCTGAGCA-TATTCAGTATAAT-AAGTAGATATTGCTCATTTGAGCA
1 TAGATATTGCTCGTTTGAGCACT-TTCAGTATAATCAA-TAGATATTGTTCTTTTGAGCA
40050882 TATTCAATAT
Statistics
Matches: 229, Mismatches: 41, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
109 3 0.01
110 3 0.01
111 25 0.11
112 167 0.73
113 28 0.12
114 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (112 bp):
TAGATATTGCTCGTTTGAGCACTTTCAGTATAATCAATAGATATTGTTCTTTTGAGCAACTTTCA
ATATAATCAGTAGACATTGCTCTTTTGAGCACATTCAGTATAATCAG
Found at i:40050882 original size:37 final size:37
Alignment explanation
Indices: 40050488--40050887 Score: 377
Period size: 37 Copynumber: 10.7 Consensus size: 37
40050478 TTTTAGTATA
* * ** *
40050488 TAGACATTGCTCTTTTGAGCATGTTTAGTATAATCAG
1 TAGATATTGCTCGTTTGAGCACATTCAGTATAATCAG
* * *
40050525 TAGATATTGCTTGTTTGAGCAACTTTCAATATAATCAG
1 TAGATATTGCTCGTTTGAGC-ACATTCAGTATAATCAG
* ** * * *
40050563 TAGACATTGCTTTTTTAAGCACGTTCAGTATAAACAG
1 TAGATATTGCTCGTTTGAGCACATTCAGTATAATCAG
* * * *
40050600 TAGATATTCCTCGTTTGAGCAACTTTCAGTACAATCAA
1 TAGATATTGCTCGTTTGAGC-ACATTCAGTATAATCAG
* * * * *
40050638 TAGACATTGTTCTTTTGAGCACGTTCAATATAATCAG
1 TAGATATTGCTCGTTTGAGCACATTCAGTATAATCAG
* * * * *
40050675 TAGATATTACTCCTTTGAGCGCATTGAATATAATCAG
1 TAGATATTGCTCGTTTGAGCACATTCAGTATAATCAG
* * *
40050712 TAGATATTGCTTGTTTGAGCACATTTAGTATAACCAG
1 TAGATATTGCTCGTTTGAGCACATTCAGTATAATCAG
* ** *
40050749 TAGATATTTCTTATTTGAGCAACTTTCAGTATAATCAG
1 TAGATATTGCTCGTTTGAGC-ACATTCAGTATAATCAG
* * * *
40050787 TAGACATTGCTCTTTTGAACACATCCAGTATAATCAG
1 TAGATATTGCTCGTTTGAGCACATTCAGTATAATCAG
* * *
40050824 TAGATATTGCTCGTCTGAGCATATTCAGTATAATAAG
1 TAGATATTGCTCGTTTGAGCACATTCAGTATAATCAG
* *
40050861 TAGATATTGCTCATTTGAGCATATTCA
1 TAGATATTGCTCGTTTGAGCACATTCA
40050888 ATATTTAACC
Statistics
Matches: 295, Mismatches: 65, Indels: 6
0.81 0.18 0.02
Matches are distributed among these distances:
37 207 0.70
38 88 0.30
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (37 bp):
TAGATATTGCTCGTTTGAGCACATTCAGTATAATCAG
Found at i:40053873 original size:30 final size:30
Alignment explanation
Indices: 40053824--40053897 Score: 125
Period size: 30 Copynumber: 2.5 Consensus size: 30
40053814 CTGGCACATG
40053824 GCCGTGTG-CCAGCCTGTGTGGCTCACACA
1 GCCGTGTGTCCAGCCTGTGTGGCTCACACA
40053853 GCCGTGTGTCCAG-CTCGTGTGGCTCACACA
1 GCCGTGTGTCCAGCCT-GTGTGGCTCACACA
40053883 GCCGTGTGTCCAGCC
1 GCCGTGTGTCCAGCC
40053898 CATGTGAGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
29 10 0.24
30 31 0.74
31 1 0.02
ACGTcount: A:0.12, C:0.35, G:0.31, T:0.22
Consensus pattern (30 bp):
GCCGTGTGTCCAGCCTGTGTGGCTCACACA
Found at i:40054798 original size:62 final size:59
Alignment explanation
Indices: 40054723--40054839 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 59
40054713 AGTGATTATC
* * * * *
40054723 TTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAATATTCTATTATTTTAATAAGAT
1 TTAACATTAAATTTAATCTAATATTTATC-T-TA-ATAAATATTATATTAATTTAATAAGAT
40054785 TTAACATTAAATTTAATCTAATATTTATCTTAATAAATATTATATTAATTTAATA
1 TTAACATTAAATTTAATCTAATATTTATCTTAATAAATATTATATTAATTTAATA
40054840 TTAAAGTGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 21 0.42
60 2 0.04
61 1 0.02
62 26 0.52
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.50
Consensus pattern (59 bp):
TTAACATTAAATTTAATCTAATATTTATCTTAATAAATATTATATTAATTTAATAAGAT
Found at i:40058261 original size:22 final size:22
Alignment explanation
Indices: 40058236--40058279 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
40058226 TAGTCATATA
40058236 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* *
40058258 ATAAATTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
40058280 TGTTTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:40058327 original size:16 final size:16
Alignment explanation
Indices: 40058306--40058339 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
40058296 TTTATTTTAG
40058306 TAATAAATTTTAAA-AA
1 TAAT-AATTTTAAATAA
40058322 TAATAATTTTAAATAA
1 TAATAATTTTAAATAA
40058338 TA
1 TA
40058340 TTATTCACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATTTTAAATAA
Found at i:40058392 original size:15 final size:15
Alignment explanation
Indices: 40058372--40058428 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
40058362 ATTCAATATT
40058372 AATATTTTAATAATA
1 AATATTTTAATAATA
*
40058387 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
40058406 AATATATTAATAATA
1 AATATTTTAATAATA
*
40058421 AATGTTTT
1 AATATTTT
40058429 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:40059934 original size:19 final size:20
Alignment explanation
Indices: 40059906--40059953 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
40059896 TATAAAAATT
* *
40059906 AAAATTATAA-AATTTATCA
1 AAAATAATAACAATTTATAA
**
40059925 AAAATAATAACTGTTTATAA
1 AAAATAATAACAATTTATAA
40059945 AAAATAATA
1 AAAATAATA
40059954 TTTTAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAATAATAACAATTTATAA
Found at i:40064904 original size:29 final size:30
Alignment explanation
Indices: 40064872--40064929 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
40064862 CTAGACCAAA
*
40064872 TTAATCCCTATACTATT-AAATGAATCAAT
1 TTAATCCCTATACTATTAAAAAGAATCAAT
* *
40064901 TTAATCCCTGTACTGTTAAAAAGAATCAA
1 TTAATCCCTATACTATTAAAAAGAATCAA
40064930 ATAAGGTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.34
Consensus pattern (30 bp):
TTAATCCCTATACTATTAAAAAGAATCAAT
Found at i:40085636 original size:21 final size:21
Alignment explanation
Indices: 40085590--40085662 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
40085580 GGCTTTGCCA
* *
40085590 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCACCTTGTGTGTCG--T
40085613 ATCAGGCACCTTGTGTGTCGT
1 ATCAGGCACCTTGTGTGTCGT
*
40085634 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACCTTGTGTGTCGT
*
40085655 TTCAGGCA
1 ATCAGGCA
40085663 TTTATTTGTC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 28 0.61
23 18 0.39
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (21 bp):
ATCAGGCACCTTGTGTGTCGT
Found at i:40096854 original size:16 final size:18
Alignment explanation
Indices: 40096823--40096855 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
40096813 GGTTACTATT
40096823 TTTTAGCCGATTTGATGC
1 TTTTAGCCGATTTGATGC
40096841 TTTTA-CCG-TTTGATG
1 TTTTAGCCGATTTGATG
40096856 AGTTTGATGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.48
Consensus pattern (18 bp):
TTTTAGCCGATTTGATGC
Found at i:40098630 original size:161 final size:156
Alignment explanation
Indices: 40098365--40098681 Score: 553
Period size: 161 Copynumber: 2.0 Consensus size: 156
40098355 ACTTATCCAA
40098365 TGAATCTTTTTAAGTATACCACTTACTTTATCAATTATTTCAACTTCATACTATATACCATTGCC
1 TGAATCTTTTTAAGTATACCACTTACTTTATCAATTATTTCAACTTCATACTATATACCATTGCC
* *
40098430 AACCATAATTTACTTATTTCATCAATACTTTCACAACCTAGATGACTCTCATAAGACGTCCTAGG
66 AACCATAATTTACTTATTTCATCAATACTTTCACAACCTAGATGACTCTCATAAGACATCCTAAG
40098495 TACATGCCATTACCAATACTCAACAT
131 TACATGCCATTACCAATACTCAACAT
*
40098521 NNNNNTGAATCTTTTTAAGTATATCACTTACTTTATCAATTATTTCAACTTCATACTATATACCA
1 -----TGAATCTTTTTAAGTATACCACTTACTTTATCAATTATTTCAACTTCATACTATATACCA
*
40098586 TTGCCAACCATAATTTACTTATTTCATCAATACTTTCACAACCTAGATGACTCTCATAAGATATC
61 TTGCCAACCATAATTTACTTATTTCATCAATACTTTCACAACCTAGATGACTCTCATAAGACATC
40098651 CTAAGTACATGCCATTACCAATACTCAACAT
126 CTAAGTACATGCCATTACCAATACTCAACAT
40098682 ACTTTACCTC
Statistics
Matches: 152, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
161 152 1.00
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.36
Consensus pattern (156 bp):
TGAATCTTTTTAAGTATACCACTTACTTTATCAATTATTTCAACTTCATACTATATACCATTGCC
AACCATAATTTACTTATTTCATCAATACTTTCACAACCTAGATGACTCTCATAAGACATCCTAAG
TACATGCCATTACCAATACTCAACAT
Found at i:40103374 original size:18 final size:18
Alignment explanation
Indices: 40103326--40103500 Score: 84
Period size: 18 Copynumber: 9.3 Consensus size: 18
40103316 TAATATTTAT
* *
40103326 TAACAATCAGTCAATCAG
1 TAACAATCAGTTATTCAG
*
40103344 -AACAAT-TGTTTATTCAG
1 TAACAATCAG-TTATTCAG
** *
40103361 TAACAGCCAGTTATTCGG
1 TAACAATCAGTTATTCAG
* *
40103379 TAACAATCAATTATTCAA
1 TAACAATCAGTTATTCAG
*
40103397 TAATAATCAGTTATTCAG
1 TAACAATCAGTTATTCAG
* *
40103415 TATCAATCAATTGATCGGTTATCCAG
1 --T-AA-C-A---ATCAGTTATTCAG
* *
40103441 TAACAGTCAATTATTCAG
1 TAACAATCAGTTATTCAG
* * *
40103459 TAAAAATCAGATATACAG
1 TAACAATCAGTTATTCAG
* *
40103477 TAACAATTAAATTATTCAG
1 TAACAA-TCAGTTATTCAG
40103496 TAACA
1 TAACA
40103501 GTCGATCTTT
Statistics
Matches: 113, Mismatches: 32, Indels: 23
0.67 0.19 0.14
Matches are distributed among these distances:
16 1 0.01
17 12 0.11
18 66 0.58
19 14 0.12
20 1 0.01
21 3 0.03
22 1 0.01
23 3 0.03
24 1 0.01
26 11 0.10
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (18 bp):
TAACAATCAGTTATTCAG
Found at i:40103393 original size:36 final size:36
Alignment explanation
Indices: 40103353--40103426 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 36
40103343 GAACAATTGT
* * *
40103353 TTATTCAGTAACAGCCAGTTATTCGGTAACAATCAA
1 TTATTCAATAACAACCAGTTATTCAGTAACAATCAA
* * *
40103389 TTATTCAATAATAATCAGTTATTCAGTATCAATCAA
1 TTATTCAATAACAACCAGTTATTCAGTAACAATCAA
40103425 TT
1 TT
40103427 GATCGGTTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.36
Consensus pattern (36 bp):
TTATTCAATAACAACCAGTTATTCAGTAACAATCAA
Found at i:40103693 original size:53 final size:53
Alignment explanation
Indices: 40103622--40103742 Score: 172
Period size: 53 Copynumber: 2.3 Consensus size: 53
40103612 CCAGAACAAT
* * * *
40103622 AACAGTGACAGTAGCAGTATGGTATACAGAGTACCTCATCAGAACAAATCC-A
1 AACAGTAACAGTAACAGTACGGTACACAGAGTACCTCATCAGAACAAATCCGA
* *
40103674 GAACGGTAACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
1 -AACAGTAACAGTAACAGTACGGTACACAGAGTACCTCATCAGAACAAATCCGA
40103728 AACAGTAACAGTAAC
1 AACAGTAACAGTAAC
40103743 GTTAACAGTA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
53 59 0.98
54 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.17
Consensus pattern (53 bp):
AACAGTAACAGTAACAGTACGGTACACAGAGTACCTCATCAGAACAAATCCGA
Found at i:40104081 original size:19 final size:19
Alignment explanation
Indices: 40104016--40104083 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 19
40104006 AAATATTTGG
* *
40104016 TTATCCAGTAACAGTC-AA
1 TTATTCAGTAACAATCAAA
* *
40104034 TTATTCAGTAAAAATCAGA
1 TTATTCAGTAACAATCAAA
* *
40104053 -TATACAGTAACAATTAAA
1 TTATTCAGTAACAATCAAA
40104071 TTATTCAGTAACA
1 TTATTCAGTAACA
40104084 GTCGATCTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
18 27 0.69
19 12 0.31
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.31
Consensus pattern (19 bp):
TTATTCAGTAACAATCAAA
Found at i:40131318 original size:18 final size:18
Alignment explanation
Indices: 40131291--40131325 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40131281 AGCACCAAAG
40131291 CTTTCATCCTCCTCCTCA
1 CTTTCATCCTCCTCCTCA
* *
40131309 CTTTCTTCCTCTTCCTC
1 CTTTCATCCTCCTCCTC
40131326 TTCTTCATTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.49, G:0.00, T:0.46
Consensus pattern (18 bp):
CTTTCATCCTCCTCCTCA
Found at i:40136324 original size:38 final size:36
Alignment explanation
Indices: 40136265--40136340 Score: 91
Period size: 38 Copynumber: 2.1 Consensus size: 36
40136255 AAACGCTACC
*
40136265 ATAAATATAAGAACTATTTTATTATATTAAAAATATAA
1 ATAAATATAAGAAATATTTTATTATATT--AAATATAA
* *
40136303 ATAAATATAATAAATGA-TTTATTGTATTAAATATAA
1 ATAAATATAAGAAAT-ATTTTATTATATTAAATATAA
40136339 AT
1 AT
40136341 TTTAAAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 10 0.29
38 23 0.68
39 1 0.03
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (36 bp):
ATAAATATAAGAAATATTTTATTATATTAAATATAA
Found at i:40141276 original size:18 final size:18
Alignment explanation
Indices: 40141255--40141290 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40141245 CAATTAAACC
40141255 ATTTGATTGATATATTTA
1 ATTTGATTGATATATTTA
* *
40141273 ATTTGATTTATTTATTTA
1 ATTTGATTGATATATTTA
40141291 TAATTAAGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (18 bp):
ATTTGATTGATATATTTA
Found at i:40141330 original size:18 final size:18
Alignment explanation
Indices: 40141267--40141332 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 18
40141257 TTGATTGATA
*
40141267 TATTTAATTTGATTTATT
1 TATTTAATTTAATTTATT
*
40141285 TATTTATAATTAAGTATTATTAT
1 TATTTA-ATTTAA-T-TTA-T-T
40141308 ATATTTAATTTAATTTATT
1 -TATTTAATTTAATTTATT
40141327 TATTTA
1 TATTTA
40141333 TAAATAAATC
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
18 12 0.31
19 5 0.13
20 2 0.05
21 6 0.15
22 2 0.05
23 6 0.15
24 6 0.15
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
TATTTAATTTAATTTATT
Found at i:40141392 original size:18 final size:18
Alignment explanation
Indices: 40141371--40141413 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
40141361 ATAATTTAAA
40141371 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
40141389 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
*
40141407 ATGTAAA
1 ATATAAA
40141414 AACAGTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATATAAATTTATTAATAT
Found at i:40141537 original size:14 final size:15
Alignment explanation
Indices: 40141518--40141555 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
40141508 CCAGAAATAT
40141518 AAATTATTTTTC-AA
1 AAATTATTTTTCGAA
40141532 AAATTATTTTTCGAA
1 AAATTATTTTTCGAA
40141547 AAA-TATTTT
1 AAATTATTTT
40141556 ACTGGCAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (15 bp):
AAATTATTTTTCGAA
Found at i:40143727 original size:12 final size:12
Alignment explanation
Indices: 40143710--40143748 Score: 78
Period size: 12 Copynumber: 3.2 Consensus size: 12
40143700 CCGAGCACTT
40143710 TATAAACCTTTC
1 TATAAACCTTTC
40143722 TATAAACCTTTC
1 TATAAACCTTTC
40143734 TATAAACCTTTC
1 TATAAACCTTTC
40143746 TAT
1 TAT
40143749 CTGAGGAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.44
Consensus pattern (12 bp):
TATAAACCTTTC
Found at i:40150611 original size:19 final size:18
Alignment explanation
Indices: 40150584--40150626 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
40150574 AAATTAACAA
*
40150584 AAAAATATATAATATTCAT
1 AAAAATATAAAATATTC-T
*
40150603 AAAATTATAAAATATTCT
1 AAAAATATAAAATATTCT
40150621 AAAAAT
1 AAAAAT
40150627 TTTAAATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAAATATAAAATATTCT
Found at i:40150627 original size:19 final size:18
Alignment explanation
Indices: 40150583--40150637 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
40150573 CAAATTAACA
* *
40150583 AAAAAATATATAATATTC
1 AAAAATTATAAAATATTC
40150601 ATAAAATTATAAAATATTC
1 A-AAAATTATAAAATATTC
*
40150620 TAAAAATTTTAAATATAT
1 -AAAAATTATAAA-ATAT
40150638 ATAATTCAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 1 0.03
19 25 0.81
20 5 0.16
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAATTATAAAATATTC
Found at i:40152810 original size:13 final size:13
Alignment explanation
Indices: 40152792--40152835 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
40152782 GATTTTGAAA
40152792 CAAAAAAAATAGT
1 CAAAAAAAATAGT
**
40152805 CAAAAAATTTAG-
1 CAAAAAAAATAGT
40152817 -AAAAAAAATAGT
1 CAAAAAAAATAGT
40152829 CAAAAAA
1 CAAAAAA
40152836 TTAAGGTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
11 9 0.36
13 16 0.64
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.16
Consensus pattern (13 bp):
CAAAAAAAATAGT
Found at i:40154777 original size:25 final size:25
Alignment explanation
Indices: 40154743--40154793 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
40154733 TATGAATATG
40154743 AATTGTATTAAACTGAGTTAAATTT
1 AATTGTATTAAACTGAGTTAAATTT
*
40154768 AATTGTATTAAATTGAGTTAAATTT
1 AATTGTATTAAACTGAGTTAAATTT
40154793 A
1 A
40154794 CTCGTATAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (25 bp):
AATTGTATTAAACTGAGTTAAATTT
Found at i:40154800 original size:25 final size:25
Alignment explanation
Indices: 40154747--40154800 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
40154737 AATATGAATT
*
40154747 GTATTAAACTGAGTTAAATTTAATT
1 GTATTAAACTGAGTTAAATTTAATC
* *
40154772 GTATTAAATTGAGTTAAATTTACTC
1 GTATTAAACTGAGTTAAATTTAATC
40154797 GTAT
1 GTAT
40154801 AGATCTAGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.06, G:0.13, T:0.44
Consensus pattern (25 bp):
GTATTAAACTGAGTTAAATTTAATC
Found at i:40155271 original size:26 final size:26
Alignment explanation
Indices: 40155231--40155290 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
40155221 CCCGATATAT
*
40155231 GGCTCTTCGTGAGCTTCCTAATTAAA
1 GGCTCTTCGTAAGCTTCCTAATTAAA
* * * *
40155257 GGCTCTTTGTAAGCTTTCTGATTAAT
1 GGCTCTTCGTAAGCTTCCTAATTAAA
40155283 GGCTCTTC
1 GGCTCTTC
40155291 AGAGCTTCCC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (26 bp):
GGCTCTTCGTAAGCTTCCTAATTAAA
Found at i:40155411 original size:24 final size:24
Alignment explanation
Indices: 40155384--40155442 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
40155374 TATTGGCTCG
40155384 TATGAGCTTCCTGGCTATGACTCT
1 TATGAGCTTCCTGGCTATGACTCT
40155408 TATGAGCTTCCTGGCTATGACTCT
1 TATGAGCTTCCTGGCTATGACTCT
40155432 TATGAGCTTCC
1 TATGAGCTTCC
40155443 CGTTATACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.37
Consensus pattern (24 bp):
TATGAGCTTCCTGGCTATGACTCT
Found at i:40156632 original size:12 final size:12
Alignment explanation
Indices: 40156615--40156647 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
40156605 TAGTTAGAAA
40156615 AAGAAATTATTG
1 AAGAAATTATTG
40156627 AAGAAATTATTG
1 AAGAAATTATTG
40156639 AAGAAATTA
1 AAGAAATTA
40156648 GGTAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (12 bp):
AAGAAATTATTG
Found at i:40174500 original size:14 final size:14
Alignment explanation
Indices: 40174481--40174508 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40174471 ACCCTAGTAG
40174481 TAATTAACAAGAAA
1 TAATTAACAAGAAA
40174495 TAATTAACAAGAAA
1 TAATTAACAAGAAA
40174509 GTCACTAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.07, T:0.21
Consensus pattern (14 bp):
TAATTAACAAGAAA
Found at i:40178260 original size:23 final size:22
Alignment explanation
Indices: 40178234--40178287 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
40178224 TATTATTATT
*
40178234 TAATATTTACAAGTCTAGTTTAG
1 TAATATTTA-AAGTATAGTTTAG
* *
40178257 TAATATATTAAATTATGGTTTAG
1 TAATAT-TTAAAGTATAGTTTAG
40178280 TAAT-TTTA
1 TAATATTTA
40178288 TTGAATTGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 3 0.11
22 1 0.04
23 20 0.74
24 3 0.11
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (22 bp):
TAATATTTAAAGTATAGTTTAG
Found at i:40178701 original size:27 final size:27
Alignment explanation
Indices: 40178663--40178715 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
40178653 TTTTTGTCTT
*
40178663 TGTCGGGTAAGTTCATATGAGACTTAA
1 TGTCAGGTAAGTTCATATGAGACTTAA
40178690 TGTCAGGTAAGTTCATATGAGACTTA
1 TGTCAGGTAAGTTCATATGAGACTTA
40178716 CTTTATTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (27 bp):
TGTCAGGTAAGTTCATATGAGACTTAA
Found at i:40185833 original size:49 final size:49
Alignment explanation
Indices: 40185761--40185859 Score: 171
Period size: 49 Copynumber: 2.0 Consensus size: 49
40185751 ATAAGTATAT
*
40185761 ATTCCTAACCGCTATCAGACGTACTAACGTCCAAAGTGTGAATACTGCA
1 ATTCCTAACCGCTATCAGACGTACTAAAGTCCAAAGTGTGAATACTGCA
* *
40185810 ATTCCTAACCGCTATCGGACGTACTAAAGTCCAGAGTGTGAATACTGCA
1 ATTCCTAACCGCTATCAGACGTACTAAAGTCCAAAGTGTGAATACTGCA
40185859 A
1 A
40185860 CTAAAGATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (49 bp):
ATTCCTAACCGCTATCAGACGTACTAAAGTCCAAAGTGTGAATACTGCA
Found at i:40190589 original size:54 final size:56
Alignment explanation
Indices: 40190498--40190628 Score: 167
Period size: 55 Copynumber: 2.4 Consensus size: 56
40190488 GGCTATGTGC
* * * *
40190498 GGCACTTAGTGTGTGAGACATTGATTATGGCACTTAGTTTGCGG-ACATTCATTAT
1 GGCACTTAGTATGCGAGACATTCATTATGGCACTTAGTATGCGGAACATTCATTAT
* * * *
40190553 GGCAGTTAGTATGC-AGACATTCATTATGGCATTTAGTATGCGGAACATTGATTGT
1 GGCACTTAGTATGCGAGACATTCATTATGGCACTTAGTATGCGGAACATTCATTAT
*
40190608 GGCACTTAGTCTGCGAGACAT
1 GGCACTTAGTATGCGAGACAT
40190629 CGAGTATGTG
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
54 26 0.41
55 32 0.50
56 6 0.09
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (56 bp):
GGCACTTAGTATGCGAGACATTCATTATGGCACTTAGTATGCGGAACATTCATTAT
Found at i:40190628 original size:28 final size:28
Alignment explanation
Indices: 40190498--40190628 Score: 151
Period size: 27 Copynumber: 4.8 Consensus size: 28
40190488 GGCTATGTGC
* * *
40190498 GGCACTTAGTGTGTGAGACATTGATTAT
1 GGCACTTAGTATGCGAGACATTCATTAT
*
40190526 GGCACTTAGTTTGCG-GACATTCATTAT
1 GGCACTTAGTATGCGAGACATTCATTAT
*
40190553 GGCAGTTAGTATGC-AGACATTCATTAT
1 GGCACTTAGTATGCGAGACATTCATTAT
* * *
40190580 GGCATTTAGTATGCG-GAACATTGATTGT
1 GGCACTTAGTATGCGAG-ACATTCATTAT
*
40190608 GGCACTTAGTCTGCGAGACAT
1 GGCACTTAGTATGCGAGACAT
40190629 CGAGTATGTG
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
27 49 0.55
28 39 0.44
29 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.26, T:0.34
Consensus pattern (28 bp):
GGCACTTAGTATGCGAGACATTCATTAT
Found at i:40192148 original size:20 final size:20
Alignment explanation
Indices: 40192123--40192170 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
40192113 CACCCGTGTG
* *
40192123 GTGGCCTGGGACATGCCTGT
1 GTGGCCTGGAACATGCCCGT
40192143 GTGGCCTGGAACATGCCCGT
1 GTGGCCTGGAACATGCCCGT
40192163 GTGGCCTG
1 GTGGCCTG
40192171 CCTATAGACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.10, C:0.27, G:0.40, T:0.23
Consensus pattern (20 bp):
GTGGCCTGGAACATGCCCGT
Found at i:40196203 original size:37 final size:39
Alignment explanation
Indices: 40196116--40196212 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 39
40196106 CACACCTGAA
*
40196116 TGGCAACCAACGTCTCATCGGATAGTTCGAAGCAAATAAG
1 TGGCAACCAACGTCTCATCGGATAGTCCGAAGC-AATAAG
* * *
40196156 TGACGACCAACGTCTCATCGGCTAAG-CCGAAGC-A-AAG
1 TGGCAACCAACGTCTCATCGGAT-AGTCCGAAGCAATAAG
*
40196193 TGGCAACCAACGCCTCATCG
1 TGGCAACCAACGTCTCATCG
40196213 AATCTATCCG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
37 20 0.41
38 1 0.02
40 26 0.53
41 2 0.04
ACGTcount: A:0.32, C:0.29, G:0.23, T:0.16
Consensus pattern (39 bp):
TGGCAACCAACGTCTCATCGGATAGTCCGAAGCAATAAG
Found at i:40197392 original size:3 final size:3
Alignment explanation
Indices: 40197378--40197422 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
40197368 TTATCTTAAT
40197378 TAA TAGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
40197423 GTAAGTAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:40200365 original size:14 final size:14
Alignment explanation
Indices: 40200337--40200370 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
40200327 ATGCCAAATG
*
40200337 TGCTG-AACAATCC
1 TGCTGAAACAACCC
40200350 TGCTGAAACAACCC
1 TGCTGAAACAACCC
40200364 TGCTGAA
1 TGCTGAA
40200371 GTAACTTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.21
Consensus pattern (14 bp):
TGCTGAAACAACCC
Found at i:40203435 original size:37 final size:39
Alignment explanation
Indices: 40203348--40203444 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 39
40203338 CACACCTGAA
*
40203348 TGGCGACCAACGTCTCATCGGATAGTTCGAAGCAAATAAG
1 TGGCGACCAACGTCTCATCGGATAGTCCGAAGC-AATAAG
* *
40203388 TGACGACCAACGTCTCATCGGCTAAG-CCGAAGC-A-AAG
1 TGGCGACCAACGTCTCATCGGAT-AGTCCGAAGCAATAAG
* *
40203425 TGGCAACCAACGCCTCATCG
1 TGGCGACCAACGTCTCATCG
40203445 AATCTATCCG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
37 20 0.40
38 1 0.02
40 27 0.54
41 2 0.04
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (39 bp):
TGGCGACCAACGTCTCATCGGATAGTCCGAAGCAATAAG
Found at i:40204624 original size:3 final size:3
Alignment explanation
Indices: 40204610--40204651 Score: 57
Period size: 3 Copynumber: 13.0 Consensus size: 3
40204600 TTATCTCAAT
40204610 TAA TAGA TAA TAA TAA TAA TAA TAA TAA TAA GTAAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA -T-AA TAA TAA
40204652 ATAAGTAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
3 29 0.81
4 5 0.14
5 2 0.06
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:40204654 original size:15 final size:14
Alignment explanation
Indices: 40204618--40204662 Score: 67
Period size: 15 Copynumber: 3.3 Consensus size: 14
40204608 ATTAATAGAT
40204618 AATAATAATAA-T-
1 AATAATAATAAGTA
40204630 AATAATAATAAGTA
1 AATAATAATAAGTA
40204644 AATAATAAATAAGTA
1 AATAAT-AATAAGTA
40204659 AATA
1 AATA
40204663 TATATTATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 11 0.37
13 1 0.03
14 6 0.20
15 12 0.40
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (14 bp):
AATAATAATAAGTA
Found at i:40206128 original size:22 final size:22
Alignment explanation
Indices: 40206085--40206129 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
40206075 ATCAATGAGT
* *
40206085 AAACCTTATCGATCATCGTCGA
1 AAACCTTATCAATCATCATCGA
*
40206107 AAACCTTATCAATCCTCATCGA
1 AAACCTTATCAATCATCATCGA
40206129 A
1 A
40206130 TAAATTCAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.29, G:0.09, T:0.27
Consensus pattern (22 bp):
AAACCTTATCAATCATCATCGA
Found at i:40206421 original size:13 final size:13
Alignment explanation
Indices: 40206403--40206432 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40206393 ACATCCCCAT
40206403 ACGGGCAGACCAC
1 ACGGGCAGACCAC
*
40206416 ACGGGCAGACTAC
1 ACGGGCAGACCAC
40206429 ACGG
1 ACGG
40206433 CCGTGTCCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.33, G:0.33, T:0.03
Consensus pattern (13 bp):
ACGGGCAGACCAC
Found at i:40215764 original size:59 final size:60
Alignment explanation
Indices: 40215693--40215809 Score: 146
Period size: 62 Copynumber: 1.9 Consensus size: 60
40215683 ATCACTTTAA
* * * *
40215693 TATTAAATTAATATAATATTTATC-AAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAAATAATAGAATATTTATCTAAGATAAACATTAAATTAAATTTAATATTAAATCT
* * *
40215752 TATTAAAATAATAGAATGTTTATCTTGTAGATACACATTAAATTAAATTTAATATTAA
1 TATTAAAATAATAGAATATTTATC-T-AAGATAAACATTAAATTAAATTTAATATTAA
40215810 TATAATCAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 21 0.44
62 27 0.56
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (60 bp):
TATTAAAATAATAGAATATTTATCTAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:40215834 original size:11 final size:11
Alignment explanation
Indices: 40215788--40215895 Score: 55
Period size: 11 Copynumber: 9.4 Consensus size: 11
40215778 GTAGATACAC
40215788 ATTAAATTAA-
1 ATTAAATTAAT
40215798 ATTTAATATTAAT
1 A-TTAA-ATTAAT
*
40215811 ATAATCAATTTAAT
1 AT--T-AAATTAAT
40215825 ATTAAATTAAT
1 ATTAAATTAAT
*
40215836 A--AAA-TACT
1 ATTAAATTAAT
*
40215844 ATTAAGATAAAT
1 ATTAA-ATTAAT
40215856 ATTAAATTAA-
1 ATTAAATTAAT
40215866 ATTTAATATTAGAAT
1 A-TTAA-ATT--AAT
*
40215881 ATTAAAATAAT
1 ATTAAATTAAT
40215892 ATTA
1 ATTA
40215896 TTTTTGAAAT
Statistics
Matches: 76, Mismatches: 7, Indels: 29
0.68 0.06 0.26
Matches are distributed among these distances:
8 4 0.05
9 3 0.04
10 4 0.05
11 28 0.37
12 17 0.22
13 3 0.04
14 14 0.18
15 3 0.04
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
ATTAAATTAAT
Found at i:40230883 original size:23 final size:23
Alignment explanation
Indices: 40230856--40230902 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
40230846 GTTAAATGTT
*
40230856 CACAAAAGTTGGGTGAACAATCA
1 CACAAAAGCTGGGTGAACAATCA
40230879 CACAAAAGCTGGGTGAACAATCA
1 CACAAAAGCTGGGTGAACAATCA
40230902 C
1 C
40230903 TGAGCATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.43, C:0.21, G:0.21, T:0.15
Consensus pattern (23 bp):
CACAAAAGCTGGGTGAACAATCA
Found at i:40235113 original size:45 final size:45
Alignment explanation
Indices: 40235062--40235217 Score: 201
Period size: 45 Copynumber: 3.5 Consensus size: 45
40235052 AGTTATGGTT
* *
40235062 GGTAAGCTCT-TTCGAGCTGAACAGTAAGCTCTATTGAGATGAAAC
1 GGTAAGCTCTATT-GAGCTGAACGGTAAGCTCTATTGAGCTGAAAC
* *
40235107 GGTAAGCTCTATTGAGCTGAATGGTAAGCT-TCAATGAGCTGAAAC
1 GGTAAGCTCTATTGAGCTGAACGGTAAGCTCT-ATTGAGCTGAAAC
*
40235152 AGTAAGCTCTATTGAGCTGAAACGGTAAGCTCTATTGAGCT-AAAC
1 GGTAAGCTCTATTGAGCTG-AACGGTAAGCTCTATTGAGCTGAAAC
* *
40235197 GGTAAGCTCCAATGAGCTGAA
1 GGTAAGCTCTATTGAGCTGAA
40235218 GTAGTAAGCT
Statistics
Matches: 97, Mismatches: 10, Indels: 9
0.84 0.09 0.08
Matches are distributed among these distances:
44 3 0.03
45 74 0.76
46 19 0.20
47 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (45 bp):
GGTAAGCTCTATTGAGCTGAACGGTAAGCTCTATTGAGCTGAAAC
Found at i:40235115 original size:23 final size:23
Alignment explanation
Indices: 40235062--40235217 Score: 196
Period size: 23 Copynumber: 6.9 Consensus size: 23
40235052 AGTTATGGTT
40235062 GGTAAGCTCT-TTCGAGCTG-AAC
1 GGTAAGCTCTATT-GAGCTGAAAC
* *
40235084 AGTAAGCTCTATTGAGATGAAAC
1 GGTAAGCTCTATTGAGCTGAAAC
*
40235107 GGTAAGCTCTATTGAGCTG-AAT
1 GGTAAGCTCTATTGAGCTGAAAC
*
40235129 GGTAAGCT-TCAATGAGCTGAAAC
1 GGTAAGCTCT-ATTGAGCTGAAAC
*
40235152 AGTAAGCTCTATTGAGCTGAAAC
1 GGTAAGCTCTATTGAGCTGAAAC
40235175 GGTAAGCTCTATTGAGCT-AAAC
1 GGTAAGCTCTATTGAGCTGAAAC
* *
40235197 GGTAAGCTCCAATGAGCTGAA
1 GGTAAGCTCTATTGAGCTGAA
40235218 GTAGTAAGCT
Statistics
Matches: 116, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
21 1 0.01
22 52 0.45
23 62 0.53
24 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (23 bp):
GGTAAGCTCTATTGAGCTGAAAC
Found at i:40235165 original size:68 final size:68
Alignment explanation
Indices: 40235075--40235228 Score: 247
Period size: 68 Copynumber: 2.3 Consensus size: 68
40235065 AAGCTCTTTC
* * *
40235075 GAGCTG-AACAGTAAGCTCTATTGAGATGAAACGGTAAGCTCTATTGAGCTGAATGGTAAGCTTC
1 GAGCTGAAACAGTAAGCTCTATTGAGATGAAACGGTAAGCTCTATTGAGCTAAACGGTAAGCTCC
40235139 AAT
66 AAT
*
40235142 GAGCTGAAACAGTAAGCTCTATTGAGCTGAAACGGTAAGCTCTATTGAGCTAAACGGTAAGCTCC
1 GAGCTGAAACAGTAAGCTCTATTGAGATGAAACGGTAAGCTCTATTGAGCTAAACGGTAAGCTCC
40235207 AAT
66 AAT
**
40235210 GAGCTGAAGTAGTAAGCTC
1 GAGCTGAAACAGTAAGCTC
40235229 ATACGAGCTG
Statistics
Matches: 80, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
67 6 0.08
68 74 0.93
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (68 bp):
GAGCTGAAACAGTAAGCTCTATTGAGATGAAACGGTAAGCTCTATTGAGCTAAACGGTAAGCTCC
AAT
Found at i:40235227 original size:23 final size:23
Alignment explanation
Indices: 40235063--40235251 Score: 183
Period size: 23 Copynumber: 8.3 Consensus size: 23
40235053 GTTATGGTTG
40235063 GTAAGCTCT-TTCGAGCTG-AACA
1 GTAAGCTCTATT-GAGCTGAAACA
* *
40235085 GTAAGCTCTATTGAGATGAAACG
1 GTAAGCTCTATTGAGCTGAAACA
**
40235108 GTAAGCTCTATTGAGCTG-AATG
1 GTAAGCTCTATTGAGCTGAAACA
*
40235130 GTAAGCT-TCAATGAGCTGAAACA
1 GTAAGCTCT-ATTGAGCTGAAACA
*
40235153 GTAAGCTCTATTGAGCTGAAACG
1 GTAAGCTCTATTGAGCTGAAACA
*
40235176 GTAAGCTCTATTGAGCT-AAACG
1 GTAAGCTCTATTGAGCTGAAACA
* * **
40235198 GTAAGCTCCAATGAGCTGAAGTA
1 GTAAGCTCTATTGAGCTGAAACA
* * *
40235221 GTAAGCTC-ATACGAGCTGTATCA
1 GTAAGCTCTAT-TGAGCTGAAACA
40235244 GTAAGCTC
1 GTAAGCTC
40235252 ATACGAGCTG
Statistics
Matches: 141, Mismatches: 19, Indels: 13
0.82 0.11 0.08
Matches are distributed among these distances:
21 1 0.01
22 53 0.38
23 86 0.61
24 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (23 bp):
GTAAGCTCTATTGAGCTGAAACA
Found at i:40235237 original size:45 final size:45
Alignment explanation
Indices: 40235062--40235238 Score: 184
Period size: 45 Copynumber: 3.9 Consensus size: 45
40235052 AGTTATGGTT
** *
40235062 GGTAAGCTCT-TTCGAGCTGAACAGTAAGCTC-TATTGAGATGAAAC
1 GGTAAGCTCTATT-GAGCTGAATGGTAAGCTCATA-TGAGCTGAAAC
40235107 GGTAAGCTCTATTGAGCTGAATGGTAAGCTTCA-ATGAGCTGAAAC
1 GGTAAGCTCTATTGAGCTGAATGGTAAGC-TCATATGAGCTGAAAC
* *
40235152 AGTAAGCTCTATTGAGCTGAAACGGTAAGCTC-TATTGAGCT-AAAC
1 GGTAAGCTCTATTGAGCTG-AATGGTAAGCTCATA-TGAGCTGAAAC
* * * *
40235197 GGTAAGCTCCAATGAGCTGAAGTAGTAAGCTCATACGAGCTG
1 GGTAAGCTCTATTGAGCTGAA-TGGTAAGCTCATATGAGCTG
40235239 TATCAGTAAG
Statistics
Matches: 112, Mismatches: 11, Indels: 17
0.80 0.08 0.12
Matches are distributed among these distances:
44 2 0.02
45 88 0.79
46 22 0.20
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (45 bp):
GGTAAGCTCTATTGAGCTGAATGGTAAGCTCATATGAGCTGAAAC
Found at i:40235248 original size:68 final size:68
Alignment explanation
Indices: 40235075--40235251 Score: 223
Period size: 68 Copynumber: 2.6 Consensus size: 68
40235065 AAGCTCTTTC
* * * * * *
40235075 GAGCTG-AACAGTAAGCTCTATTGAGATGAAACGGTAAGCTCTATTGAGCTGAATGGTAAGCTTC
1 GAGCTGAAACAGTAAGCTCTATCGAGCTGAAACAGTAAGCTCTATTGAGCTAAACGGTAAGCTCC
40235139 AAT
66 AAT
* *
40235142 GAGCTGAAACAGTAAGCTCTATTGAGCTGAAACGGTAAGCTCTATTGAGCTAAACGGTAAGCTCC
1 GAGCTGAAACAGTAAGCTCTATCGAGCTGAAACAGTAAGCTCTATTGAGCTAAACGGTAAGCTCC
40235207 AAT
66 AAT
** * *
40235210 GAGCTGAAGTAGTAAGCTC-ATACGAGCTGTATCAGTAAGCTC
1 GAGCTGAAACAGTAAGCTCTAT-CGAGCTGAAACAGTAAGCTC
40235252 ATACGAGCTG
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
67 8 0.08
68 90 0.92
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (68 bp):
GAGCTGAAACAGTAAGCTCTATCGAGCTGAAACAGTAAGCTCTATTGAGCTAAACGGTAAGCTCC
AAT
Found at i:40238105 original size:17 final size:17
Alignment explanation
Indices: 40238069--40238108 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
40238059 TTAAAAAAAA
* *
40238069 TAAAAACATAATGCTTT
1 TAAAAACATAATGATAT
*
40238086 TAAAAACATAATTATAT
1 TAAAAACATAATGATAT
40238103 TAAAAA
1 TAAAAA
40238109 TGTTATTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAAAACATAATGATAT
Found at i:40238382 original size:16 final size:16
Alignment explanation
Indices: 40238361--40238411 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
40238351 TGAATTATTG
40238361 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
* * **
40238377 ATTACAGCCCTATTAT
1 ATTACAACTCTATTCC
*
40238393 ATTACAACTGTATTCC
1 ATTACAACTCTATTCC
40238409 ATT
1 ATT
40238412 CTAACGAACC
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.39
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:40241474 original size:7 final size:7
Alignment explanation
Indices: 40241454--40241529 Score: 116
Period size: 7 Copynumber: 10.9 Consensus size: 7
40241444 GGTTTGTGGT
40241454 GTGATTG
1 GTGATTG
* *
40241461 CTCATTG
1 GTGATTG
*
40241468 ATGATTG
1 GTGATTG
40241475 GTGATTG
1 GTGATTG
40241482 GTGATTG
1 GTGATTG
40241489 GTGATTG
1 GTGATTG
*
40241496 GTAATTG
1 GTGATTG
40241503 GTGATTG
1 GTGATTG
40241510 GTGATTG
1 GTGATTG
40241517 GTGATTG
1 GTGATTG
40241524 GTGATT
1 GTGATT
40241530 AGTAAAAAGA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 62 1.00
ACGTcount: A:0.17, C:0.03, G:0.37, T:0.43
Consensus pattern (7 bp):
GTGATTG
Found at i:40246899 original size:34 final size:34
Alignment explanation
Indices: 40246856--40246924 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
40246846 AATAATCAGC
*
40246856 AAAGAATACTTCAGTGTCAAGAAACTAAGGTAGA
1 AAAGAATACTTCAATGTCAAGAAACTAAGGTAGA
40246890 AAAGAATACTTCAATGTCAAGAAACTAAGGTAGA
1 AAAGAATACTTCAATGTCAAGAAACTAAGGTAGA
40246924 A
1 A
40246925 TACTTGCTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.20
Consensus pattern (34 bp):
AAAGAATACTTCAATGTCAAGAAACTAAGGTAGA
Found at i:40251351 original size:149 final size:149
Alignment explanation
Indices: 40251081--40251384 Score: 572
Period size: 149 Copynumber: 2.0 Consensus size: 149
40251071 ATCAACTAAA
*
40251081 AACTAAATACATACACCTTTTAAGCTTGTTTCTCATTCATGGCCGTAACATCATAAATTTTCTTC
1 AACTAAATACATACACCTTTTAAGCTTGTTTCTCATTCATGGCCGTAACATCATAAACTTTCTTC
40251146 GCCATATATCAAGTTGATGAGTGACAAACCAGTTTTATTGTCTGGCCAACAGGTTGATTGTTAAG
66 GCCATATATCAAGTTGATGAGTGACAAACCAGTTTTATTGTCTGGCCAACAGGTTGATTGTTAAG
40251211 TACTTTGATAAATCAGAAC
131 TACTTTGATAAATCAGAAC
* * *
40251230 AACTAAATACGTACACCTTTTAAGCTTGTTTCTTATTCATGGCCGTAACATCATAAACTTTCTTT
1 AACTAAATACATACACCTTTTAAGCTTGTTTCTCATTCATGGCCGTAACATCATAAACTTTCTTC
40251295 GCCATATATCAAGTTGATGAGTGACAAACCAGTTTTATTGTCTGGCCAACAGGTTGATTGTTAAG
66 GCCATATATCAAGTTGATGAGTGACAAACCAGTTTTATTGTCTGGCCAACAGGTTGATTGTTAAG
40251360 TACTTTGATAAATCAGAAC
131 TACTTTGATAAATCAGAAC
40251379 AACTAA
1 AACTAA
40251385 TGAAGGTACA
Statistics
Matches: 151, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (149 bp):
AACTAAATACATACACCTTTTAAGCTTGTTTCTCATTCATGGCCGTAACATCATAAACTTTCTTC
GCCATATATCAAGTTGATGAGTGACAAACCAGTTTTATTGTCTGGCCAACAGGTTGATTGTTAAG
TACTTTGATAAATCAGAAC
Found at i:40255142 original size:26 final size:24
Alignment explanation
Indices: 40255112--40255161 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
40255102 AAATAAAAAA
*
40255112 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
40255138 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
40255162 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:40261963 original size:19 final size:18
Alignment explanation
Indices: 40261934--40261983 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
40261924 GTATATATTT
40261934 TAAATTTATTTAGGTAGA
1 TAAATTTATTTAGGTAGA
40261952 TAAATCTTATTTAGGTAGA
1 TAAAT-TTATTTAGGTAGA
*
40261971 TAAGTTTTATTTA
1 TAA-ATTTATTTA
40261984 TATTCTAGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 5 0.17
19 23 0.79
20 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.48
Consensus pattern (18 bp):
TAAATTTATTTAGGTAGA
Found at i:40262057 original size:42 final size:42
Alignment explanation
Indices: 40261998--40262088 Score: 155
Period size: 42 Copynumber: 2.2 Consensus size: 42
40261988 CTAGGAATAT
*
40261998 TTTTATTTTATCTTTTAGTAGTTTATTAGAATAAGAGAACTA
1 TTTTCTTTTATCTTTTAGTAGTTTATTAGAATAAGAGAACTA
* *
40262040 TTTTCTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAACTA
1 TTTTCTTTTATCTTTTAGTAGTTTATTAGAATAAGAGAACTA
40262082 TTTTCTT
1 TTTTCTT
40262089 AATTAGGATT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (42 bp):
TTTTCTTTTATCTTTTAGTAGTTTATTAGAATAAGAGAACTA
Found at i:40266741 original size:42 final size:43
Alignment explanation
Indices: 40266678--40266768 Score: 157
Period size: 42 Copynumber: 2.1 Consensus size: 43
40266668 ATTCTAGGAA
*
40266678 TATTTTTATTTTATCTTTTAGTAGTTTATTAGAATAAGAGAAC
1 TATTTTTATTTTATATTTTAGTAGTTTATTAGAATAAGAGAAC
*
40266721 TATTTTT-TTTTATATTTTAGTAGTTTATTAGAATAAGGGAAC
1 TATTTTTATTTTATATTTTAGTAGTTTATTAGAATAAGAGAAC
40266763 TATTTT
1 TATTTT
40266769 CTCAATTAGG
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 39 0.85
43 7 0.15
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.54
Consensus pattern (43 bp):
TATTTTTATTTTATATTTTAGTAGTTTATTAGAATAAGAGAAC
Found at i:40272607 original size:2 final size:2
Alignment explanation
Indices: 40272600--40272633 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
40272590 TGTTTCCATA
40272600 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40272634 AGAAATAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40277546 original size:24 final size:24
Alignment explanation
Indices: 40277514--40277563 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
40277504 AGAGGAACAG
40277514 TCGAGTACCAAGTAGTTTGAAAGT
1 TCGAGTACCAAGTAGTTTGAAAGT
40277538 TCGAGTACCAAGTAGTTTGAAAGT
1 TCGAGTACCAAGTAGTTTGAAAGT
40277562 TC
1 TC
40277564 TTGCCAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (24 bp):
TCGAGTACCAAGTAGTTTGAAAGT
Found at i:40281850 original size:14 final size:14
Alignment explanation
Indices: 40281831--40281866 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
40281821 TTAGTTTTTC
40281831 TTATTTTGATGACT
1 TTATTTTGATGACT
40281845 TTATTTTGATGACT
1 TTATTTTGATGACT
40281859 TTATTTTG
1 TTATTTTG
40281867 TTAATTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.19, C:0.06, G:0.14, T:0.61
Consensus pattern (14 bp):
TTATTTTGATGACT
Found at i:40283188 original size:30 final size:30
Alignment explanation
Indices: 40283152--40283209 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
40283142 TCGAGAAAGA
*
40283152 TCTTAAATATTAATATTGATTCTAAGTTAG
1 TCTTAAATATTAATATTGATACTAAGTTAG
40283182 TCTTAAATATTAATATTGATACTAAGTT
1 TCTTAAATATTAATATTGATACTAAGTT
40283210 TAATTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (30 bp):
TCTTAAATATTAATATTGATACTAAGTTAG
Found at i:40285109 original size:21 final size:20
Alignment explanation
Indices: 40285081--40285119 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
40285071 CAAACCATGT
40285081 ATCAAATTTCAAGTATATGA
1 ATCAAATTTCAAGTATATGA
*
40285101 ATCATAATTTCAATTATAT
1 ATCA-AATTTCAAGTATAT
40285120 TTTCATGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (20 bp):
ATCAAATTTCAAGTATATGA
Found at i:40286751 original size:19 final size:17
Alignment explanation
Indices: 40286707--40286758 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
40286697 ACCCAAAAAT
* * *
40286707 TATAAAATTATTTTTAC
1 TATAAATTTTTTTTTTC
40286724 TATAAATTTTTTTTTTC
1 TATAAATTTTTTTTTTC
40286741 TATAAATATTTTTATTTT
1 TATAAAT-TTTTT-TTTT
40286759 TCGAAACATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
17 21 0.70
18 5 0.17
19 4 0.13
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (17 bp):
TATAAATTTTTTTTTTC
Found at i:40288238 original size:34 final size:34
Alignment explanation
Indices: 40288165--40288243 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
40288155 GGACAAATCC
* ***
40288165 GTTATAAGCATATTAATTGTTGTTGTATCGAACT
1 GTTATAAGCATATTAATCGTTACCGTATCGAACT
* * *
40288199 ATTATAAGCATATTAATCGTTACCGTATTGATCT
1 GTTATAAGCATATTAATCGTTACCGTATCGAACT
40288233 GTTATAAGCAT
1 GTTATAAGCAT
40288244 GTCATACTGC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (34 bp):
GTTATAAGCATATTAATCGTTACCGTATCGAACT
Found at i:40291603 original size:11 final size:11
Alignment explanation
Indices: 40291587--40291629 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
40291577 TGAAATCAAT
40291587 TAATTCAACTA
1 TAATTCAACTA
*
40291598 TAATTCAATCAA
1 TAATTCAA-CTA
40291610 TTAATTCAACTA
1 -TAATTCAACTA
40291622 TAATTCAA
1 TAATTCAA
40291630 GAGATTTACC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 16 0.57
12 4 0.14
13 8 0.29
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (11 bp):
TAATTCAACTA
Found at i:40291610 original size:24 final size:24
Alignment explanation
Indices: 40291580--40291629 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
40291570 TAGTGATTGA
40291580 AATCAATTAATTCAACTATAATTC
1 AATCAATTAATTCAACTATAATTC
40291604 AATCAATTAATTCAACTATAATTC
1 AATCAATTAATTCAACTATAATTC
40291628 AA
1 AA
40291630 GAGATTTACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (24 bp):
AATCAATTAATTCAACTATAATTC
Found at i:40291852 original size:19 final size:20
Alignment explanation
Indices: 40291807--40291855 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
40291797 TATATTACTC
*
40291807 TAATAAAATAGTAAAATATT
1 TAATAATATAGTAAAATATT
40291827 TAATAATATAGT-AAAT-TT
1 TAATAATATAGTAAAATATT
40291845 TAATTAATATA
1 TAA-TAATATA
40291856 TAAGCTATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 5 0.19
19 11 0.41
20 11 0.41
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (20 bp):
TAATAATATAGTAAAATATT
Done.