Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 156 of 185
Found at i:47063416 original size:19 final size:18
Alignment explanation
Indices: 47063383--47063444 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 18
47063373 GGGATACAAA
*
47063383 TTTTAGTAATTTTTTTGCAT
1 TTTTA-TAA-TTTTTTGTAT
* *
47063403 TTTTATATTGTTTTTGTAA
1 TTTTATAAT-TTTTTGTAT
47063422 TTTTATAATTTTTTGTAT
1 TTTTATAATTTTTTGTAT
47063440 TTTTA
1 TTTTA
47063445 AATATATTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 14 0.39
19 17 0.47
20 5 0.14
ACGTcount: A:0.21, C:0.02, G:0.08, T:0.69
Consensus pattern (18 bp):
TTTTATAATTTTTTGTAT
Found at i:47063424 original size:20 final size:19
Alignment explanation
Indices: 47063391--47063464 Score: 64
Period size: 18 Copynumber: 3.9 Consensus size: 19
47063381 AATTTTAGTA
*
47063391 ATTTTTTTG-CATTTTTAT
1 ATTTTTTTGTAATTTTTAT
47063409 ATTGTTTTTGTAA-TTTTAT
1 ATT-TTTTTGTAATTTTTAT
*
47063428 AATTTTTTGT-ATTTTTAAAT
1 ATTTTTTTGTAATTTTT--AT
* *
47063448 ATATTTTTATAATTTTT
1 ATTTTTTTGTAATTTTT
47063465 TTTGTAATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
17 1 0.02
18 14 0.31
19 14 0.31
20 10 0.22
21 6 0.13
ACGTcount: A:0.24, C:0.01, G:0.05, T:0.69
Consensus pattern (19 bp):
ATTTTTTTGTAATTTTTAT
Found at i:47063433 original size:38 final size:39
Alignment explanation
Indices: 47063381--47063463 Score: 107
Period size: 37 Copynumber: 2.2 Consensus size: 39
47063371 AGGGGATACA
* * *
47063381 AATTTTAGTAATTTTTTTGCATTTTTATAT-TGTTTTTGT
1 AATTTTAGTAA-TTTTTTGCATTTTTAAATATATTTTTAT
*
47063420 AATTTTA-TAATTTTTTGTATTTTTAAATATATTTTTAT
1 AATTTTAGTAATTTTTTGCATTTTTAAATATATTTTTAT
47063458 AATTTT
1 AATTTT
47063464 TTTTGTAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
37 16 0.41
38 16 0.41
39 7 0.18
ACGTcount: A:0.27, C:0.01, G:0.06, T:0.66
Consensus pattern (39 bp):
AATTTTAGTAATTTTTTGCATTTTTAAATATATTTTTAT
Found at i:47065243 original size:7 final size:7
Alignment explanation
Indices: 47065231--47065258 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
47065221 TTTTGGTACT
47065231 CTTTCCA
1 CTTTCCA
47065238 CTTTCCA
1 CTTTCCA
47065245 CTTTCCA
1 CTTTCCA
47065252 CTTTCCA
1 CTTTCCA
47065259 ATCCTTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.43, G:0.00, T:0.43
Consensus pattern (7 bp):
CTTTCCA
Found at i:47069071 original size:14 final size:15
Alignment explanation
Indices: 47069047--47069082 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
47069037 TATTATTGAA
47069047 AAATA-TTCAAT-AT
1 AAATATTTCAATAAT
47069060 AAATATTTCAATAAT
1 AAATATTTCAATAAT
47069075 AAATATTT
1 AAATATTT
47069083 ATTATAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.24
14 6 0.29
15 10 0.48
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATATTTCAATAAT
Found at i:47070033 original size:14 final size:15
Alignment explanation
Indices: 47070002--47070039 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
47069992 ATTTGCCATT
47070002 AAAAT-ATTTTTCAG
1 AAAATAATTTTTCAG
*
47070016 AAAATAATTTTTGA-
1 AAAATAATTTTTCAG
47070030 AAAATAATTT
1 AAAATAATTT
47070040 ATTTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 15 0.68
15 7 0.32
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (15 bp):
AAAATAATTTTTCAG
Found at i:47070069 original size:19 final size:20
Alignment explanation
Indices: 47070031--47070069 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
47070021 AATTTTTGAA
*
47070031 AAATAATTTATTTTTTTTAG
1 AAATAATTTATTTATTTTAG
*
47070051 AAATGATTTA-TTATTTTAG
1 AAATAATTTATTTATTTTAG
47070070 TGTTTGAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (20 bp):
AAATAATTTATTTATTTTAG
Found at i:47070914 original size:18 final size:18
Alignment explanation
Indices: 47070891--47070927 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
47070881 GGTTTATGCA
47070891 AAACCAAATATAGCATCT
1 AAACCAAATATAGCATCT
47070909 AAACCAAATATAGCATCT
1 AAACCAAATATAGCATCT
47070927 A
1 A
47070928 TTGATCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.22, G:0.05, T:0.22
Consensus pattern (18 bp):
AAACCAAATATAGCATCT
Found at i:47075877 original size:5 final size:5
Alignment explanation
Indices: 47075867--47075906 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
47075857 TTCTTCGTGT
*
47075867 TTTTA TTTTA TTTTA -TTTA TTTTA TCTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
47075907 ATATATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:47075891 original size:19 final size:19
Alignment explanation
Indices: 47075867--47075903 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
47075857 TTCTTCGTGT
*
47075867 TTTTATTTTATTTTATTTA
1 TTTTATCTTATTTTATTTA
47075886 TTTTATCTTATTTTATTT
1 TTTTATCTTATTTTATTT
47075904 TATATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTATCTTATTTTATTTA
Found at i:47076773 original size:16 final size:18
Alignment explanation
Indices: 47076742--47076776 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
47076732 AGAAGAAAAG
47076742 AAGGAGGAAGGAAGGAGA
1 AAGGAGGAAGGAAGGAGA
47076760 AAGG-GGAA-GAAGGAGA
1 AAGGAGGAAGGAAGGAGA
47076776 A
1 A
47076777 GAAGAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 4 0.24
18 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (18 bp):
AAGGAGGAAGGAAGGAGA
Found at i:47077074 original size:26 final size:26
Alignment explanation
Indices: 47077039--47077097 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
47077029 AGCAGGCCAG
* *
47077039 CCAGCAGGCCCAGATTCG-GCAGCAGC
1 CCAGCAGGCCCAG-TCCGCCCAGCAGC
47077065 CCAGCAGGCCCAGTCCGCCCAGCAGC
1 CCAGCAGGCCCAGTCCGCCCAGCAGC
47077091 CCAGCAG
1 CCAGCAG
47077098 TGCAGCAGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 3 0.10
26 27 0.90
ACGTcount: A:0.22, C:0.44, G:0.29, T:0.05
Consensus pattern (26 bp):
CCAGCAGGCCCAGTCCGCCCAGCAGC
Found at i:47077077 original size:9 final size:8
Alignment explanation
Indices: 47077058--47077097 Score: 53
Period size: 8 Copynumber: 4.8 Consensus size: 8
47077048 CCAGATTCGG
47077058 CAGCAGCC
1 CAGCAGCC
47077066 CAGCAGGCC
1 CAGCA-GCC
*
47077075 CAGTCCGCC
1 CAG-CAGCC
47077084 CAGCAGCC
1 CAGCAGCC
47077092 CAGCAG
1 CAGCAG
47077098 TGCAGCAGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 15 0.54
9 12 0.43
10 1 0.04
ACGTcount: A:0.23, C:0.47, G:0.28, T:0.03
Consensus pattern (8 bp):
CAGCAGCC
Found at i:47077691 original size:17 final size:17
Alignment explanation
Indices: 47077647--47077694 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 17
47077637 AAAAAAAAAA
*
47077647 TCGTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTC
*
47077664 TCATGTCTTCAAAAATTC
1 TCGTGT-TTCAAAAATTC
47077682 TCGTGTTTCAAAA
1 TCGTGTTTCAAAA
47077695 CAATAATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTC
Found at i:47077810 original size:35 final size:35
Alignment explanation
Indices: 47077770--47077863 Score: 125
Period size: 35 Copynumber: 2.6 Consensus size: 35
47077760 TATTATTGTG
47077770 TTTCAAAAATTCTCGTGAATAAAAAAATTTCGTGT
1 TTTCAAAAATTCTCGTGAATAAAAAAATTTCGTGT
* ** *
47077805 TTTCAAAAATTCCCGTGTTTAAAAAATTTTCGTGT
1 TTTCAAAAATTCTCGTGAATAAAAAAATTTCGTGT
47077840 TTTCACAAAAAATTCTCGTGAATA
1 TTT--C-AAAAATTCTCGTGAATA
47077864 TTTTTTTGGT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
35 34 0.69
37 1 0.02
38 14 0.29
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (35 bp):
TTTCAAAAATTCTCGTGAATAAAAAAATTTCGTGT
Found at i:47077812 original size:17 final size:17
Alignment explanation
Indices: 47077792--47077849 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
47077782 TCGTGAATAA
47077792 AAAAATTTCGTGTTTTC
1 AAAAATTTCGTGTTTTC
* *
47077809 AAAAATTCCCGTG-TTTA
1 AAAAATT-TCGTGTTTTC
47077826 AAAAATTTTCGTGTTTTC
1 AAAAA-TTTCGTGTTTTC
47077844 ACAAAA
1 A-AAAA
47077850 AATTCTCGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 19 0.58
18 10 0.30
19 4 0.12
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (17 bp):
AAAAATTTCGTGTTTTC
Found at i:47077960 original size:18 final size:17
Alignment explanation
Indices: 47077939--47077987 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
47077929 AAAAAATTCG
47077939 TGTTTCCAAAAATTTTCA
1 TGTTTCC-AAAATTTTCA
* *
47077957 TGTTTTCAAAATTTTCG
1 TGTTTCCAAAATTTTCA
*
47077974 TGTTT-TAAAATTTT
1 TGTTTCCAAAATTTT
47077988 TTTCGTGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 8 0.29
17 14 0.50
18 6 0.21
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (17 bp):
TGTTTCCAAAATTTTCA
Found at i:47077967 original size:17 final size:16
Alignment explanation
Indices: 47077947--47078037 Score: 83
Period size: 17 Copynumber: 5.2 Consensus size: 16
47077937 CGTGTTTCCA
*
47077947 AAAATTTTCATGTTTT
1 AAAATTTTCGTGTTTT
47077963 CAAAATTTTCGTGTTTT
1 -AAAATTTTCGTGTTTT
47077980 AAAATTTTTTTCGTGTTATT
1 AAAA---TTTTCGTGTT-TT
* * *
47078000 AAAATTCTCATGTATTG
1 AAAATTTTCGTGT-TTT
47078017 AAAATTTTCGTGTTTT
1 AAAATTTTCGTGTTTT
47078033 CAAAA
1 -AAAA
47078038 AAATTCTGTG
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
16 6 0.10
17 38 0.62
18 1 0.02
19 10 0.16
20 6 0.10
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.51
Consensus pattern (16 bp):
AAAATTTTCGTGTTTT
Found at i:47077992 original size:19 final size:20
Alignment explanation
Indices: 47077968--47078005 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
47077958 GTTTTCAAAA
47077968 TTTTCGTGTT-TTAAAATTT
1 TTTTCGTGTTATTAAAATTT
47077987 TTTTCGTGTTATTAAAATT
1 TTTTCGTGTTATTAAAATT
47078006 CTCATGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.24, C:0.05, G:0.11, T:0.61
Consensus pattern (20 bp):
TTTTCGTGTTATTAAAATTT
Found at i:47078004 original size:36 final size:37
Alignment explanation
Indices: 47077951--47078024 Score: 89
Period size: 36 Copynumber: 2.0 Consensus size: 37
47077941 TTTCCAAAAA
* * *
47077951 TTTTCATGTTTTCAAAATTTTCGTGT-TTTAAAATTT
1 TTTTCATGTTTTCAAAATTCTCATGTATTGAAAATTT
*
47077987 TTTTCGTGTTATT-AAAATTCTCATGTATTGAAAATTT
1 TTTTCATGTT-TTCAAAATTCTCATGTATTGAAAATTT
47078024 T
1 T
47078025 CGTGTTTTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
36 20 0.62
37 12 0.38
ACGTcount: A:0.27, C:0.08, G:0.09, T:0.55
Consensus pattern (37 bp):
TTTTCATGTTTTCAAAATTCTCATGTATTGAAAATTT
Found at i:47078042 original size:20 final size:20
Alignment explanation
Indices: 47078017--47078095 Score: 119
Period size: 19 Copynumber: 4.1 Consensus size: 20
47078007 TCATGTATTG
47078017 AAAATTTTCGTGTTTTCAAA
1 AAAATTTTCGTGTTTTCAAA
*
47078037 AAAATTCT-GTGTTTTCAAA
1 AAAATTTTCGTGTTTTCAAA
47078056 AAAA-TTTCGTG-TTTCAAA
1 AAAATTTTCGTGTTTTCAAA
*
47078074 AAAATCTTCGTGTTTTCAAA
1 AAAATTTTCGTGTTTTCAAA
47078094 AA
1 AA
47078096 TTATTATTGT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
18 13 0.25
19 24 0.45
20 16 0.30
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.41
Consensus pattern (20 bp):
AAAATTTTCGTGTTTTCAAA
Found at i:47078049 original size:53 final size:53
Alignment explanation
Indices: 47077910--47078114 Score: 141
Period size: 53 Copynumber: 3.7 Consensus size: 53
47077900 TTGTTTGACG
* *
47077910 AATTTTCGTGTTTTCAAAAAAAAAATTC-GTGTTTCCAAAAATTTTCATGTTTTCAA
1 AATTTTCGTGTTTTC---AAAAAAATTCTGTGTTT-CAAAAATTCTCATGTATTCAA
*** * * *
47077966 AATTTTCGTGTTTT-AAAATTTTTTTCGTGTTAT-TAAAATTCTCATGTATTGAA
1 AATTTTCGTGTTTTCAAAAAAATTCT-GTGTT-TCAAAAATTCTCATGTATTCAA
*
47078019 AATTTTCGTGTTTTCAAAAAAATTCTGTGTTTTCAAAAAAATT-TCGTGT-TTCAAAAA
1 AATTTTCGTGTTTTCAAAAAAATTCTGTG-TTTC--AAAAATTCTCATGTATTC---AA
* * *
47078076 AATCTTCGTGTTTTCAAAAATTATTATTGTGTTTCAAAA
1 AATTTTCGTGTTTTCAAAAA-AATT-CTGTGTTTCAAAA
47078115 TCTCGTGTTT
Statistics
Matches: 118, Mismatches: 18, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
52 6 0.05
53 34 0.29
54 16 0.14
55 6 0.05
56 24 0.20
57 21 0.18
58 7 0.06
59 4 0.03
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.46
Consensus pattern (53 bp):
AATTTTCGTGTTTTCAAAAAAATTCTGTGTTTCAAAAATTCTCATGTATTCAA
Found at i:47078067 original size:38 final size:38
Alignment explanation
Indices: 47078017--47078114 Score: 119
Period size: 38 Copynumber: 2.5 Consensus size: 38
47078007 TCATGTATTG
*
47078017 AAAATTTTCGTGTTTTCAAAAAAA--TTCTGTGTTTTCAA
1 AAAAATTTCGTG-TTTCAAAAAAATCTTC-GTGTTTTCAA
47078055 AAAAATTTCGTGTTTCAAAAAAATCTTCGTGTTTTCAA
1 AAAAATTTCGTGTTTCAAAAAAATCTTCGTGTTTTCAA
* *
47078093 AAATTATTATTGTGTTTCAAAA
1 AAA-AATT-TCGTGTTTCAAAA
47078115 TCTCGTGTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
37 11 0.21
38 24 0.45
39 6 0.11
40 12 0.23
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (38 bp):
AAAAATTTCGTGTTTCAAAAAAATCTTCGTGTTTTCAA
Found at i:47079546 original size:18 final size:18
Alignment explanation
Indices: 47079506--47079543 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
47079496 ATAATAAATT
47079506 TAAA-ATTTATATTAATA
1 TAAATATTTATATTAATA
*
47079523 TTAATATTTATATTAA-A
1 TAAATATTTATATTAATA
47079540 TAAA
1 TAAA
47079544 ATAAAAACCC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TAAATATTTATATTAATA
Found at i:47080631 original size:6 final size:6
Alignment explanation
Indices: 47080615--47080665 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
47080605 TTTTTTTTTT
**
47080615 TTAATA TTTAATA TTAATA -TAATCA TTTTTA CTTAATA TTAATA TTAATA
1 TTAATA -TTAATA TTAATA TTAAT-A TTAATA -TTAATA TTAATA TTAATA
47080665 T
1 T
47080666 ACAATTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
5 4 0.11
6 21 0.57
7 12 0.32
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (6 bp):
TTAATA
Found at i:47080763 original size:50 final size:49
Alignment explanation
Indices: 47080670--47080769 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 49
47080660 TAATATACAA
* * * *
47080670 TTTAAATTTATTATCAGTGTTTGAAAATATCTATCTATTTTTATCTATT
1 TTTAAATCTATTATCAGTGTTTGAAAATATCTATATATATTTATATATT
* * *
47080719 TTTAAATCTATTATTATGTTTTTGAAAATATTTATATATATTTATATATT
1 TTTAAATCTATTATCA-GTGTTTGAAAATATCTATATATATTTATATATT
47080769 T
1 T
47080770 ATTTGATTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
49 14 0.33
50 29 0.67
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (49 bp):
TTTAAATCTATTATCAGTGTTTGAAAATATCTATATATATTTATATATT
Found at i:47092797 original size:16 final size:18
Alignment explanation
Indices: 47092764--47092814 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
47092754 ATTCTCTTTC
47092764 ATCCTCTTTCTCAACAAA
1 ATCCTCTTTCTCAACAAA
*
47092782 ATCCT-TTTCTC-CCAAA
1 ATCCTCTTTCTCAACAAA
**
47092798 ATTTATCTTTCTCAACA
1 A-TCCTCTTTCTCAACA
47092815 GTATTCTCCT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
16 5 0.19
17 8 0.31
18 11 0.42
19 2 0.08
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.39
Consensus pattern (18 bp):
ATCCTCTTTCTCAACAAA
Found at i:47108557 original size:27 final size:28
Alignment explanation
Indices: 47108527--47108579 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
47108517 TTTTAATTTT
*
47108527 TTTTAAATTACTTTTTATA-ATTTTTAA
1 TTTTAAAATACTTTTTATATATTTTTAA
*
47108554 TTTTAAAATATTTTTTATATATTTTT
1 TTTTAAAATACTTTTTATATATTTTT
47108580 TTAATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (28 bp):
TTTTAAAATACTTTTTATATATTTTTAA
Found at i:47112051 original size:29 final size:30
Alignment explanation
Indices: 47111996--47112057 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
47111986 GTTATATATA
*
47111996 AACTTTGATTTAATGTGTAATGTCATACATG
1 AACTTTGATTT-ATGTGTAATGTCATAAATG
* *
47112027 AACTTTGATTT-TGTGTGATTTCATAAATG
1 AACTTTGATTTATGTGTAATGTCATAAATG
47112056 AA
1 AA
47112058 ATTTTGCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 17 0.61
31 11 0.39
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (30 bp):
AACTTTGATTTATGTGTAATGTCATAAATG
Found at i:47135163 original size:19 final size:20
Alignment explanation
Indices: 47135136--47135177 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
47135126 ATTAGAAATG
* *
47135136 AAATAATCATAAA-CTTTTA
1 AAATAATCACAAATCTATTA
*
47135155 AAATTATCACAAATCTATTA
1 AAATAATCACAAATCTATTA
47135175 AAA
1 AAA
47135178 ACAAATATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATAATCACAAATCTATTA
Found at i:47135292 original size:14 final size:14
Alignment explanation
Indices: 47135273--47135300 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
47135263 GAAAAAGAAA
47135273 GGATTCCACTGTTT
1 GGATTCCACTGTTT
47135287 GGATTCCACTGTTT
1 GGATTCCACTGTTT
47135301 TTCCACCGAG
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:0.14, C:0.21, G:0.21, T:0.43
Consensus pattern (14 bp):
GGATTCCACTGTTT
Found at i:47147627 original size:14 final size:15
Alignment explanation
Indices: 47147597--47147646 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
47147587 ATAACTTAAA
47147597 TTCAACACTTAATTT
1 TTCAACACTTAATTT
* *
47147612 TTCAACATTTATTTT
1 TTCAACACTTAATTT
** *
47147627 TTGGACACTTGATTT
1 TTCAACACTTAATTT
47147642 TTCAA
1 TTCAA
47147647 TTTATCAAGC
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.28, C:0.16, G:0.06, T:0.50
Consensus pattern (15 bp):
TTCAACACTTAATTT
Found at i:47167453 original size:19 final size:18
Alignment explanation
Indices: 47167426--47167465 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
47167416 TATTATCAAA
* *
47167426 AAAATAAATCCAATTACT
1 AAAATAAATCAAAATACT
47167444 AAAATGAAATCAAAATACT
1 AAAAT-AAATCAAAATACT
47167463 AAA
1 AAA
47167466 CCGAAGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.62, C:0.12, G:0.03, T:0.23
Consensus pattern (18 bp):
AAAATAAATCAAAATACT
Found at i:47170740 original size:23 final size:23
Alignment explanation
Indices: 47170714--47170766 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
47170704 AAATTAAAAC
47170714 AAATATTCAT-ATTTATATTATTA
1 AAATATTCATCATTTATATTA-TA
* *
47170737 AAATCTTCATCTTTTATATTATA
1 AAATATTCATCATTTATATTATA
47170760 AAATATT
1 AAATATT
47170767 TATAAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.51
Consensus pattern (23 bp):
AAATATTCATCATTTATATTATA
Found at i:47172674 original size:20 final size:20
Alignment explanation
Indices: 47172649--47172686 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
47172639 GGTAAAATGA
*
47172649 TTTCTGGAAAATGTTTTATT
1 TTTCTGGAAAATGATTTATT
*
47172669 TTTCTGTAAAATGATTTA
1 TTTCTGGAAAATGATTTA
47172687 CTAGAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTATT
Found at i:47172678 original size:34 final size:35
Alignment explanation
Indices: 47172634--47172700 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
47172624 CAGTAAAAAG
* *
47172634 TTTTCGGTAAAATGATTT-CTGGAAAATGTTTTAT
1 TTTTCGGTAAAATGATTTACTAGAAAATATTTTAT
*
47172668 TTTTCTGTAAAATGATTTACTAGAAAATATTTT
1 TTTTCGGTAAAATGATTTACTAGAAAATATTTT
47172701 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (35 bp):
TTTTCGGTAAAATGATTTACTAGAAAATATTTTAT
Found at i:47175146 original size:28 final size:27
Alignment explanation
Indices: 47175109--47175176 Score: 88
Period size: 25 Copynumber: 2.6 Consensus size: 27
47175099 AAGCTTTGAG
*
47175109 GAATGAAAAATGTCTGCTGCTTAGA-AGA
1 GAATGGAAAATGTCT-CTGCTTAGAGA-A
47175137 GAATGGAAAATG--TCTGCTTAGAGAA
1 GAATGGAAAATGTCTCTGCTTAGAGAA
47175162 GAATGGAAAATGTCT
1 GAATGGAAAATGTCT
47175177 TACCAATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
25 22 0.61
26 2 0.06
27 1 0.03
28 11 0.31
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.25
Consensus pattern (27 bp):
GAATGGAAAATGTCTCTGCTTAGAGAA
Found at i:47176065 original size:11 final size:11
Alignment explanation
Indices: 47176062--47176129 Score: 51
Period size: 11 Copynumber: 6.5 Consensus size: 11
47176052 TTTTTTTAAA
47176062 TTTTAAAATTT
1 TTTTAAAATTT
47176073 TTTTAAAATACTT
1 TTTTAAAAT--TT
47176086 TTTT--AATTT
1 TTTTAAAATTT
47176095 TTTT--AA---
1 TTTTAAAATTT
*
47176101 TTTTAAAATAT
1 TTTTAAAATTT
47176112 TTTTAAAATATT
1 TTTTAAAAT-TT
47176124 TTTTAA
1 TTTTAA
47176130 TTTTTGTTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 15
0.75 0.02 0.23
Matches are distributed among these distances:
6 4 0.08
8 2 0.04
9 8 0.17
11 21 0.44
12 7 0.15
13 6 0.12
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATTT
Found at i:47176076 original size:22 final size:22
Alignment explanation
Indices: 47176019--47176076 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
47176009 CCGAATATAA
*
47176019 TAAATATTTTTATTTTTTTAATTT
1 TAAA-ATTTTT-TTTTTTAAATTT
**
47176043 TAAAATACTTTTTTTTAAATTT
1 TAAAATTTTTTTTTTTAAATTT
47176065 TAAAATTTTTTT
1 TAAAATTTTTTT
47176077 AAAATACTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 21 0.72
23 4 0.14
24 4 0.14
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (22 bp):
TAAAATTTTTTTTTTTAAATTT
Found at i:47176096 original size:39 final size:38
Alignment explanation
Indices: 47176053--47176134 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 38
47176043 TAAAATACTT
*
47176053 TTTTTTAAATTTTAAAATTTTTTTAAAATACTTTTTTAA
1 TTTTTTAAATTTTAAAATATTTTTAAAATA-TTTTTTAA
*
47176092 TTTTTTTAATTTTAAAATATTTTTAAAATATTTTTTAA
1 TTTTTTAAATTTTAAAATATTTTTAAAATATTTTTTAA
47176130 TTTTT
1 TTTTT
47176135 GTTTTAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 13 0.32
39 28 0.68
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (38 bp):
TTTTTTAAATTTTAAAATATTTTTAAAATATTTTTTAA
Found at i:47181808 original size:22 final size:22
Alignment explanation
Indices: 47181763--47181808 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
47181753 AAAATATTAA
* *
47181763 TTTTTTATTTCAAAAATTAATT
1 TTTTTTATTCCAAAAACTAATT
*
47181785 TTTTTTATTCCAAAACCT-ATT
1 TTTTTTATTCCAAAAACTAATT
47181806 TTT
1 TTT
47181809 AAAAGCATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTTTATTCCAAAAACTAATT
Found at i:47188186 original size:41 final size:40
Alignment explanation
Indices: 47188118--47188205 Score: 131
Period size: 41 Copynumber: 2.2 Consensus size: 40
47188108 GGTGCCAATT
47188118 TACTTCGGTTTAACCGATGAGACACTGGGTATCAATTTAC
1 TACTTCGGTTTAACCGATGAGACACTGGGTATCAATTTAC
** * *
47188158 TACTTCGGATTTATTCGATGAGATACTGGGTGTCAATTTAC
1 TACTTCGG-TTTAACCGATGAGACACTGGGTATCAATTTAC
47188199 TACTTCG
1 TACTTCG
47188206 AATTATCCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 8 0.19
41 35 0.81
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (40 bp):
TACTTCGGTTTAACCGATGAGACACTGGGTATCAATTTAC
Found at i:47189269 original size:17 final size:17
Alignment explanation
Indices: 47189240--47189283 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
47189230 GAATTTGGAA
47189240 GAATTTT-TGAATTAGT
1 GAATTTTGTGAATTAGT
*
47189256 GAATTTTGTGAATTATT
1 GAATTTTGTGAATTAGT
47189273 GAATTTTGTGA
1 GAATTTTGTGA
47189284 TTTAAAAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 7 0.27
17 19 0.73
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (17 bp):
GAATTTTGTGAATTAGT
Found at i:47190151 original size:46 final size:46
Alignment explanation
Indices: 47190034--47190309 Score: 455
Period size: 46 Copynumber: 6.0 Consensus size: 46
47190024 CATGGCAAAG
* * *
47190034 TGTGAAATGTAGGTATGATATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
*
47190080 TGTG-AAAGTATGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
* *
47190125 TGTGAAAAGTAAGTATGGTGTTTCAGTGAAGAAAACCATACTGAAT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
*
47190171 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAAT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
*
47190217 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACTATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
* *
47190263 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
47190309 T
1 T
47190310 ATAGCAATGT
Statistics
Matches: 217, Mismatches: 12, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
45 41 0.19
46 176 0.81
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.30
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
Found at i:47193105 original size:20 final size:20
Alignment explanation
Indices: 47193082--47193128 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
47193072 GGGTTAAGAT
*
47193082 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
47193102 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
47193122 TGAGCTG
1 TGAGCTG
47193129 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:47198242 original size:11 final size:10
Alignment explanation
Indices: 47198206--47198244 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
47198196 AATAAAAAGG
47198206 AAAGAAAGAA
1 AAAGAAAGAA
*
47198216 AAGAGAAAGAG
1 AA-AGAAAGAA
47198227 AAAGAAAGAA
1 AAAGAAAGAA
47198237 AGAAGAAA
1 A-AAGAAA
47198245 CGCAAGGGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 10 0.40
11 15 0.60
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:47198242 original size:17 final size:17
Alignment explanation
Indices: 47198199--47198240 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
47198189 AAAACGAAAT
*
47198199 AAAAAGGAA-AGAAAGA
1 AAAAAGAAAGAGAAAGA
*
47198215 AAAGAGAAAGAGAAAGA
1 AAAAAGAAAGAGAAAGA
47198232 AAGAAAGAA
1 AA-AAAGAA
47198241 GAAACGCAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 7 0.33
17 9 0.43
18 5 0.24
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAGAGAAAGA
Found at i:47199164 original size:37 final size:40
Alignment explanation
Indices: 47199122--47199252 Score: 117
Period size: 41 Copynumber: 3.3 Consensus size: 40
47199112 GTTGATTAGG
47199122 CACTAGGTGTCAA-TT-TACTTCGG-TTTAACCGATGAGA
1 CACTAGGTGTCAATTTATACTTCGGATTTAACCGATGAGA
* **
47199159 CACTAGGTATCAATTTACTACTTCGGATTTATTCGATGAGA
1 CACTAGGTGTCAATTTA-TACTTCGGATTTAACCGATGAGA
* * * * * * *
47199200 CACTCGGTGTTATTTTAGTACTTC-GAATTATCCAATGAGG
1 CACTAGGTGTCAATTTA-TACTTCGGATTTAACCGATGAGA
*
47199240 CACTGGGTGTCAA
1 CACTAGGTGTCAA
47199253 ACTGGTGTGT
Statistics
Matches: 75, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
37 12 0.16
38 2 0.03
40 30 0.40
41 31 0.41
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (40 bp):
CACTAGGTGTCAATTTATACTTCGGATTTAACCGATGAGA
Found at i:47207568 original size:17 final size:17
Alignment explanation
Indices: 47207542--47207580 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
47207532 AACAGAAAAA
47207542 CATG-AGCATAGAAGAG
1 CATGAAGCATAGAAGAG
47207558 CATGAAGCATAGAAGAG
1 CATGAAGCATAGAAGAG
47207575 CATGAA
1 CATGAA
47207581 AAAGGTTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.46, C:0.13, G:0.28, T:0.13
Consensus pattern (17 bp):
CATGAAGCATAGAAGAG
Found at i:47208996 original size:20 final size:20
Alignment explanation
Indices: 47208971--47209008 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
47208961 TTAATTTTAT
47208971 TTAATTTTCA-TTTTTTTAAA
1 TTAATTTT-AGTTTTTTTAAA
47208991 TTAATTTTAGTTTTTTTA
1 TTAATTTTAGTTTTTTTA
47209009 TTTTATAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (20 bp):
TTAATTTTAGTTTTTTTAAA
Found at i:47211054 original size:17 final size:18
Alignment explanation
Indices: 47211034--47211072 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
47211024 ATGTTTTTTT
47211034 TCTTTTTC-ATTTTAATA
1 TCTTTTTCTATTTTAATA
47211051 TC-TTTTCTATTTTAATA
1 TCTTTTTCTATTTTAATA
47211068 -CTTTT
1 TCTTTT
47211073 CATATCCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.67
Consensus pattern (18 bp):
TCTTTTTCTATTTTAATA
Found at i:47211056 original size:16 final size:15
Alignment explanation
Indices: 47211037--47211075 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
47211027 TTTTTTTTCT
47211037 TTTTCATTTTAATATC
1 TTTTCATTTTAATA-C
47211053 TTTTCTATTTTAATAC
1 TTTTC-ATTTTAATAC
47211069 TTTTCAT
1 TTTTCAT
47211076 ATCCATGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 2 0.09
16 11 0.50
17 9 0.41
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTCATTTTAATAC
Found at i:47215803 original size:21 final size:21
Alignment explanation
Indices: 47215713--47215814 Score: 82
Period size: 21 Copynumber: 5.0 Consensus size: 21
47215703 CAATTACGCA
47215713 AACAGAAGCTCG-AA-AGCTG
1 AACAGAAGCTCGTAAGAGCTG
* * ** *
47215732 AGCAGAAGATTATAAAAGCTG
1 AACAGAAGCTCGTAAGAGCTG
* * *
47215753 AACAGAAACTCATAAGAGTTG
1 AACAGAAGCTCGTAAGAGCTG
* *
47215774 AACAAAAGCTCGTAAGAGCTT
1 AACAGAAGCTCGTAAGAGCTG
* *
47215795 AACAGAAGCTTGAAAGAGCT
1 AACAGAAGCTCGTAAGAGCT
47215815 AAAGAAAAAG
Statistics
Matches: 63, Mismatches: 18, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
19 8 0.13
20 2 0.03
21 53 0.84
ACGTcount: A:0.45, C:0.16, G:0.23, T:0.17
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTG
Found at i:47217297 original size:31 final size:33
Alignment explanation
Indices: 47217235--47217297 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
47217225 ATAACAATAT
*
47217235 AGTGACTTAAATAAAAAAATATTTGAATAGTTC
1 AGTGACTTAAATAAAAAAATATTCGAATAGTTC
* *
47217268 AGTGACTTAAAT-GAAAACT-TTCGAATAGTT
1 AGTGACTTAAATAAAAAAATATTCGAATAGTT
47217298 TAATGACTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 10 0.37
32 5 0.19
33 12 0.44
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.33
Consensus pattern (33 bp):
AGTGACTTAAATAAAAAAATATTCGAATAGTTC
Found at i:47219534 original size:20 final size:21
Alignment explanation
Indices: 47219504--47219552 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
47219494 CATGTTTTTA
47219504 AAATG-ATTTGA-TTTATATC-
1 AAATGTATTTGAGTTTAT-TCT
47219523 AAATGTATTTGAGTTTATTCT
1 AAATGTATTTGAGTTTATTCT
47219544 AAAT-TATTT
1 AAATGTATTT
47219553 TAAAGAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 5 0.19
20 13 0.48
21 9 0.33
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.51
Consensus pattern (21 bp):
AAATGTATTTGAGTTTATTCT
Found at i:47221463 original size:21 final size:21
Alignment explanation
Indices: 47221417--47221474 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
47221407 CTAGGAGGGT
* *
47221417 AAAGTGTCAATACTTGATCTT
1 AAAGTATCAATACTTGATCTA
*
47221438 GAAGTATCAATACTT-ACTCTA
1 AAAGTATCAATACTTGA-TCTA
**
47221459 AAAGTATTTATACTTG
1 AAAGTATCAATACTTG
47221475 CCTTAAAGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (21 bp):
AAAGTATCAATACTTGATCTA
Found at i:47228678 original size:20 final size:20
Alignment explanation
Indices: 47228655--47228695 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
47228645 ACAAAAAGTG
47228655 GGAAAACAACAACAAAACAT
1 GGAAAACAACAACAAAACAT
*
47228675 GGAAAACAACATCAAAACAT
1 GGAAAACAACAACAAAACAT
47228695 G
1 G
47228696 AAGGGGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.61, C:0.20, G:0.12, T:0.07
Consensus pattern (20 bp):
GGAAAACAACAACAAAACAT
Found at i:47233005 original size:167 final size:162
Alignment explanation
Indices: 47232708--47233038 Score: 563
Period size: 167 Copynumber: 2.0 Consensus size: 162
47232698 ATGACATTAA
*
47232708 CAACCTCAAGACTGTTCGATTGAATTAAACCTCTTTGAATCGCCTATCCAAAATAAGCTTCAACC
1 CAACATCAAGACTGTTCGATTGAATTAAACCTCTTTGAATCGCCTATCCAAAATAAGCTTCAACC
* *
47232773 TATATGCCCCAAAGCTCAACTTTCATCACCGTGCAATTTACTAAGTATTTGCAGAACCCAATGAT
66 TAGATGCCCCAAAGCTCAACTTTCATCACCGTGCAATTTACTAAGTATCTGCAGAACCCAATGAT
*
47232838 CCACCCACCATTATGATCTCGCACTAATCCTT
131 CCACCCACCATTATGATCCCGCACTAATCCTT
47232870 CAACATCAAGACTGTTCGATTGAATTAAACCTCTTTGAATCGCCTATCCAAAATAAGCTTCAACC
1 CAACATCAAGACTGTTCGATTGAATTAAACCTCTTTGAATCGCCTATCCAAAATAAGCTTCAA-C
* *
47232935 CATCCAAGATGCCCCAAAGCTCAACTTTCGTCACCGTGCAATTTCCTAAGTATCTGCAGAACCCA
65 C-T---AGATGCCCCAAAGCTCAACTTTCATCACCGTGCAATTTACTAAGTATCTGCAGAACCCA
47233000 ATGATCCACCCACCATTATGATCCCGCACTAATCCTT
126 ATGATCCACCCACCATTATGATCCCGCACTAATCCTT
47233037 CA
1 CA
47233039 GCAGCAGTGA
Statistics
Matches: 158, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
162 62 0.39
163 2 0.01
164 1 0.01
167 93 0.59
ACGTcount: A:0.31, C:0.31, G:0.11, T:0.27
Consensus pattern (162 bp):
CAACATCAAGACTGTTCGATTGAATTAAACCTCTTTGAATCGCCTATCCAAAATAAGCTTCAACC
TAGATGCCCCAAAGCTCAACTTTCATCACCGTGCAATTTACTAAGTATCTGCAGAACCCAATGAT
CCACCCACCATTATGATCCCGCACTAATCCTT
Found at i:47234641 original size:31 final size:31
Alignment explanation
Indices: 47234582--47234641 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
47234572 AGTCACAAAT
* * ***
47234582 GTTTTCGATCATTTCTATTTTGGTCACTCAC
1 GTTTTAGATCATTTCTAGTTTAACCACTCAC
47234613 GTTTTAGATCATTTCTAGTTTAACCACTC
1 GTTTTAGATCATTTCTAGTTTAACCACTC
47234642 TCCTTTTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.12, T:0.47
Consensus pattern (31 bp):
GTTTTAGATCATTTCTAGTTTAACCACTCAC
Found at i:47240303 original size:39 final size:39
Alignment explanation
Indices: 47240251--47240331 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
47240241 AGTTTGATGA
* * * *
47240251 AATAATGCGAATACATAGTTGAGCGAGAGATATAGCAAT
1 AATAATGCAAATACATAGATAAGCAAGAGATATAGCAAT
*
47240290 AATAATGTAAATACATAGATAAGCAAGAGATATAGCAAT
1 AATAATGCAAATACATAGATAAGCAAGAGATATAGCAAT
47240329 AAT
1 AAT
47240332 TAAATTAGTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.49, C:0.09, G:0.19, T:0.23
Consensus pattern (39 bp):
AATAATGCAAATACATAGATAAGCAAGAGATATAGCAAT
Found at i:47246497 original size:19 final size:19
Alignment explanation
Indices: 47246473--47246510 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
47246463 GTCAAATCTA
47246473 TTTAATTTTATATTTAATT
1 TTTAATTTTATATTTAATT
47246492 TTTAATTTTATATTTAATT
1 TTTAATTTTATATTTAATT
47246511 ATTGTTGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTAATTTTATATTTAATT
Found at i:47253528 original size:15 final size:15
Alignment explanation
Indices: 47253508--47253555 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
47253498 TGGGTCTTTT
47253508 ACAAAAATAATACAA
1 ACAAAAATAATACAA
*
47253523 ACAAAAATAAAACAAA
1 ACAAAAATAATAC-AA
* *
47253539 ACTAAAATAATATAA
1 ACAAAAATAATACAA
47253554 AC
1 AC
47253556 TTTTTTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.73, C:0.12, G:0.00, T:0.15
Consensus pattern (15 bp):
ACAAAAATAATACAA
Found at i:47256984 original size:38 final size:38
Alignment explanation
Indices: 47256926--47257002 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
47256916 CGTATAATGC
* * *
47256926 AATGCTTGATTGTGTTTGTAAGCTTTGTGGGGAAAAAG
1 AATGCTTGATTGTATATGTAAGCTTTGTAGGGAAAAAG
47256964 AATGCTTGATTGTATATGTAAGCTTTGTAGGGAAAAAG
1 AATGCTTGATTGTATATGTAAGCTTTGTAGGGAAAAAG
47257002 A
1 A
47257003 TCCATTTCGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35
Consensus pattern (38 bp):
AATGCTTGATTGTATATGTAAGCTTTGTAGGGAAAAAG
Found at i:47260066 original size:17 final size:17
Alignment explanation
Indices: 47260036--47260069 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
47260026 TTTGTCACCC
*
47260036 ACCATATGGGTCTCATT
1 ACCATATGGATCTCATT
*
47260053 ACCATTTGGATCTCATT
1 ACCATATGGATCTCATT
47260070 GGTTTTTGTC
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:0.24, C:0.24, G:0.15, T:0.38
Consensus pattern (17 bp):
ACCATATGGATCTCATT
Found at i:47261921 original size:20 final size:19
Alignment explanation
Indices: 47261898--47261941 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
47261888 ATATGCTTTC
*
47261898 AAAATTAAATTTTGATATGA
1 AAAATCAAATTTTGATAT-A
* *
47261918 AAAATCAATTTTTGGTATA
1 AAAATCAAATTTTGATATA
47261937 AAAAT
1 AAAAT
47261942 ACCATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (19 bp):
AAAATCAAATTTTGATATA
Found at i:47263830 original size:16 final size:18
Alignment explanation
Indices: 47263793--47263827 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
47263783 AATACTAAGA
47263793 ATTT-TATTAAATTATAT
1 ATTTATATTAAATTATAT
47263810 ATTTATATTAAATTATAT
1 ATTTATATTAAATTATAT
47263828 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATATTAAATTATAT
Found at i:47263839 original size:16 final size:17
Alignment explanation
Indices: 47263800--47263845 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
47263790 AGAATTTTAT
* *
47263800 TAAATTATATATTTATAT
1 TAAATTATAT-TTAATAA
47263818 TAAATTATATTTAATAA
1 TAAATTATATTTAATAA
47263835 T-AATTAT-TTTA
1 TAAATTATATTTA
47263846 GATTATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 4 0.15
16 6 0.23
17 6 0.23
18 10 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAAATTATATTTAATAA
Found at i:47263841 original size:26 final size:25
Alignment explanation
Indices: 47263812--47263989 Score: 77
Period size: 26 Copynumber: 7.2 Consensus size: 25
47263802 AATTATATAT
47263812 TTATATTAAATTATATTTAATAATAA
1 TTATATTAAATTATATTTAATAAT-A
* * * *
47263838 TTATTTTAGATTATATTTTATAGTA
1 TTATATTAAATTATATTTAATAATA
*
47263863 TTATA-T--ATTATGATTTTAGTAA-A
1 TTATATTAAATTAT-A-TTTAATAATA
* *
47263886 TTCATA-TAAGAATAT-TTTAATATTA
1 TT-ATATTAA-ATTATATTTAATAATA
** ** * * *
47263911 AGA-ATTTTATTA-AATT-ATATTT
1 TTATATTAAATTATATTTAATAATA
*
47263933 TTTTATTAAATTATATTTAATAATTA
1 TTATATTAAATTATATTTAATAA-TA
* * *
47263959 TTATTTTAAATTATATTTTATACTA
1 TTATATTAAATTATATTTAATAATA
47263984 TTATAT
1 TTATAT
47263990 ATTATAATTT
Statistics
Matches: 108, Mismatches: 31, Indels: 27
0.65 0.19 0.16
Matches are distributed among these distances:
22 10 0.09
23 17 0.16
24 21 0.19
25 16 0.15
26 40 0.37
27 4 0.04
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.55
Consensus pattern (25 bp):
TTATATTAAATTATATTTAATAATA
Found at i:47263936 original size:18 final size:18
Alignment explanation
Indices: 47263915--47263950 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
47263905 ATATTAAGAA
47263915 TTTTATTAAATTATATTT
1 TTTTATTAAATTATATTT
47263933 TTTTATTAAATTATATTT
1 TTTTATTAAATTATATTT
47263951 AATAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTATTAAATTATATTT
Found at i:47263957 original size:13 final size:13
Alignment explanation
Indices: 47263941--47263998 Score: 64
Period size: 13 Copynumber: 4.3 Consensus size: 13
47263931 TTTTTTATTA
*
47263941 AATTATATTTAAT
1 AATTATATTTTAT
47263954 AATTATTATTTTA-
1 AATTA-TATTTTAT
47263967 AATTATATTTTAT
1 AATTATATTTTAT
*
47263980 ACTATTATATATTAT
1 A--ATTATATTTTAT
47263995 AATT
1 AATT
47263999 TTAGTAAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
12 7 0.18
13 14 0.36
14 6 0.15
15 12 0.31
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (13 bp):
AATTATATTTTAT
Found at i:47263958 original size:18 final size:18
Alignment explanation
Indices: 47263919--47263958 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
47263909 TAAGAATTTT
** *
47263919 ATTAAATTATATTTTTTT
1 ATTAAATTATATTTAATA
47263937 ATTAAATTATATTTAATA
1 ATTAAATTATATTTAATA
47263955 ATTA
1 ATTA
47263959 TTATTTTAAA
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:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTAAATTATATTTAATA
Found at i:47263966 original size:121 final size:120
Alignment explanation
Indices: 47263723--47264023 Score: 514
Period size: 121 Copynumber: 2.5 Consensus size: 120
47263713 CCTTAGTTTN
*
47263723 TTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCGTATAAGAATATTTAATAC
1 TTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATAC
47263788 TAAGAATTTTATTAAATTATATATTTATATTAAATTATATTTAATAATAATTATT
66 TAAGAATTTTATTAAATTATATATTTATATTAAATTATATTTAATAATAATTATT
47263843 TTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTTAATA
1 TTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATA-TTTAATA
* * * *
47263908 TTAAGAATTTTATTAAATTATATTTTTTTATTAAATTATATTTAATAATTATTATT
65 CTAAGAATTTTATTAAATTATATATTTATATTAAATTATATTTAATAATAATTATT
* * *
47263964 TTAAATTATATTTTATACTATTATATATTATAATTTTAGTAAATTCATATAAGAAT-TTTA
1 TTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTA
47264024 TTAAATTATA
Statistics
Matches: 172, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
119 4 0.02
120 56 0.33
121 112 0.65
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (120 bp):
TTAGATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATAC
TAAGAATTTTATTAAATTATATATTTATATTAAATTATATTTAATAATAATTATT
Found at i:47264290 original size:45 final size:44
Alignment explanation
Indices: 47264204--47264294 Score: 119
Period size: 45 Copynumber: 2.0 Consensus size: 44
47264194 ACCTCTATTC
* *
47264204 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCATTA
*** *
47264248 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTAATCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTAATCCATTA
47264293 CA
1 CA
47264295 CCTCTATTCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 16 0.40
45 24 0.60
ACGTcount: A:0.35, C:0.29, G:0.05, T:0.31
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCATTA
Found at i:47264294 original size:16 final size:16
Alignment explanation
Indices: 47264273--47264326 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
47264263 TTGATTTGCT
47264273 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
47264289 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
*
47264305 ATTACGCCTCTAATCC
1 ATTACACCTCTAATCC
*
47264321 AATACA
1 ATTACA
47264327 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.31, C:0.35, G:0.02, T:0.31
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:47271841 original size:56 final size:56
Alignment explanation
Indices: 47271755--47271886 Score: 228
Period size: 56 Copynumber: 2.4 Consensus size: 56
47271745 GGAGCAAGGC
* *
47271755 AAATTAAAGATACAAGGTAGTGAATCTGATATCTCAGCTCATTTTCAGAGAAAACA
1 AAATTAAAGATATAAGGTAGTGAATCTGATATCTCAGCTCATTTTCACAGAAAACA
* *
47271811 AAATTAAAGATATAAGTTAGTGAATCTGATATCTCAGCTCATTTTTACAGAAAACA
1 AAATTAAAGATATAAGGTAGTGAATCTGATATCTCAGCTCATTTTCACAGAAAACA
47271867 AAATTAAAGATATAAGGTAG
1 AAATTAAAGATATAAGGTAG
47271887 CTCTCTTGTA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 71 1.00
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (56 bp):
AAATTAAAGATATAAGGTAGTGAATCTGATATCTCAGCTCATTTTCACAGAAAACA
Found at i:47273768 original size:9 final size:10
Alignment explanation
Indices: 47273750--47273801 Score: 61
Period size: 10 Copynumber: 5.1 Consensus size: 10
47273740 TTCTTTAAAT
47273750 AAAAGCAAAA
1 AAAAGCAAAA
*
47273760 AAAAGAAAAAAA
1 AAAAG--CAAAA
47273772 AAAAGC-AAA
1 AAAAGCAAAA
*
47273781 AACAGCAAAA
1 AAAAGCAAAA
47273791 AAAAGCAAAA
1 AAAAGCAAAA
47273801 A
1 A
47273802 GCGCAAAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 8 0.23
10 18 0.51
12 9 0.26
ACGTcount: A:0.81, C:0.10, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAGCAAAA
Found at i:47273781 original size:19 final size:19
Alignment explanation
Indices: 47273759--47273802 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
47273749 TAAAAGCAAA
47273759 AAAAAGAAAAAAAAAAAGC
1 AAAAAGAAAAAAAAAAAGC
* **
47273778 AAAAACAGCAAAAAAAAGC
1 AAAAAGAAAAAAAAAAAGC
47273797 AAAAAG
1 AAAAAG
47273803 CGCAAAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.80, C:0.09, G:0.11, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAAAAAAAAGC
Found at i:47273807 original size:19 final size:18
Alignment explanation
Indices: 47273768--47273846 Score: 85
Period size: 19 Copynumber: 4.4 Consensus size: 18
47273758 AAAAAAGAAA
47273768 AAAAAAAAGCAAAAACAGC
1 AAAAAAAAGCAAAAAC-GC
47273787 AAAAAAAAGCAAAAAGCGC
1 AAAAAAAAGCAAAAA-CGC
* *
47273806 -AAAAGAA--AAAAA-GA
1 AAAAAAAAGCAAAAACGC
47273820 AAAAAAAAGCAAAAAGCGC
1 AAAAAAAAGCAAAAA-CGC
47273839 AAAAAAAA
1 AAAAAAAA
47273847 AAGTTGCCTA
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
14 1 0.02
15 6 0.12
16 5 0.10
17 5 0.10
18 6 0.12
19 26 0.52
20 1 0.02
ACGTcount: A:0.76, C:0.11, G:0.13, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGCAAAAACGC
Found at i:47279818 original size:23 final size:23
Alignment explanation
Indices: 47279728--47279819 Score: 89
Period size: 23 Copynumber: 3.9 Consensus size: 23
47279718 GAGCCATGAT
*
47279728 CGGTAAGCTCATTCCGAGCTGATAAA
1 CGGTAAGCTCA-TACGAGCTG--AAA
47279754 CGGTAAGCTC-TATCGAGCTGAAA
1 CGGTAAGCTCATA-CGAGCTGAAA
* *
47279777 CGGTAAGGTCCGTA-GAGCTGAAA
1 CGGTAAGCT-CATACGAGCTGAAA
*
47279800 CGGTAAGCTCATACAAGCTG
1 CGGTAAGCTCATACGAGCTG
47279820 TGGTGAGTCC
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
22 3 0.05
23 33 0.58
24 2 0.04
25 9 0.16
26 10 0.18
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.21
Consensus pattern (23 bp):
CGGTAAGCTCATACGAGCTGAAA
Found at i:47280107 original size:29 final size:29
Alignment explanation
Indices: 47280074--47280129 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
47280064 TATAATGTAT
47280074 ATAGTATTTGTAACATTTCATTTGCATAA
1 ATAGTATTTGTAACATTTCATTTGCATAA
47280103 ATAGTATTTGTAACATTTCATTTGCAT
1 ATAGTATTTGTAACATTTCATTTGCAT
47280130 TCATGTAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (29 bp):
ATAGTATTTGTAACATTTCATTTGCATAA
Found at i:47287652 original size:19 final size:19
Alignment explanation
Indices: 47287607--47287646 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
47287597 AGTTCATGTT
* *
47287607 TTCATTTCACATTTTCATA
1 TTCAATTCACATTTTCAAA
47287626 TTCAATTCACATTTTCAAA
1 TTCAATTCACATTTTCAAA
47287645 TT
1 TT
47287647 ATATTCCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.20, G:0.00, T:0.50
Consensus pattern (19 bp):
TTCAATTCACATTTTCAAA
Found at i:47287908 original size:44 final size:44
Alignment explanation
Indices: 47287840--47287998 Score: 186
Period size: 44 Copynumber: 3.7 Consensus size: 44
47287830 AGCAGTAACA
* * * *
47287840 GTAATAGTATTCAACACACAAAGTGTCGACTCTGTAATAGTACG
1 GTAACAGTATTCGACACACAAAGTGCCGAATCTGTAATAGTACG
*
47287884 GTAACAGTATTCGACACACAAAGTGCCGAAT-TGGTAACAGTAACG
1 GTAACAGTATTCGACACACAAAGTGCCGAATCT-GTAATAGT-ACG
* * *
47287929 GTAACCGTATTCGAAACACAAAGTGCCGAATC-G--ATA--ACA
1 GTAACAGTATTCGACACACAAAGTGCCGAATCTGTAATAGTACG
47287968 GTAACAGTATTCGACACACAAAGTGCCGAAT
1 GTAACAGTATTCGACACACAAAGTGCCGAAT
47287999 TAGTAACAGT
Statistics
Matches: 101, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
39 31 0.31
42 2 0.02
43 1 0.01
44 35 0.35
45 32 0.32
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.21
Consensus pattern (44 bp):
GTAACAGTATTCGACACACAAAGTGCCGAATCTGTAATAGTACG
Found at i:47287927 original size:39 final size:39
Alignment explanation
Indices: 47287834--47288015 Score: 175
Period size: 39 Copynumber: 4.4 Consensus size: 39
47287824 AACGGTAGCA
* * * *
47287834 GTAACAGTAATAGTATTCAACACACAAAGTGTCGACTCTG
1 GTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT-TG
* *
47287874 TAATAGTACGGTAACAGTATTCGACACACAAAGTGCCGAATTG
1 --GTA--ACAGTAACAGTATTCGACACACAAAGTGCCGAATTG
* *
47287917 GTAACAGTAACGGTAACCGTATTCGAAACACAAAGTGCCGAATCG
1 GTAACAGTAAC----A--GTATTCGACACACAAAGTGCCGAATTG
* *
47287962 ATAACAGTAACAGTATTCGACACACAAAGTGCCGAATTA
1 GTAACAGTAACAGTATTCGACACACAAAGTGCCGAATTG
47288001 GTAACAGTAACAGTA
1 GTAACAGTAACAGTA
47288016 GTCGGCTTAT
Statistics
Matches: 117, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
39 45 0.38
41 3 0.03
42 2 0.02
43 3 0.03
44 29 0.25
45 35 0.30
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (39 bp):
GTAACAGTAACAGTATTCGACACACAAAGTGCCGAATTG
Found at i:47288012 original size:45 final size:44
Alignment explanation
Indices: 47287832--47288015 Score: 209
Period size: 45 Copynumber: 4.2 Consensus size: 44
47287822 GTAACGGTAG
* * * *
47287832 CAGTAACAGTAATAGTATTCAACACACAAAGTGTCGACTCTGTAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT-TGTAA
* *
47287877 TAGT-ACGGTAACAGTATTCGACACACAAAGTGCCGAATTGGTAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATT-GTAA
* * * *
47287921 CAGTAACGGTAACCGTATTCGAAACACAAAGTGCCGAATCG---
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATTGTAA
47287962 -A-TAACAGTAACAGTATTCGACACACAAAGTGCCGAATTAGTAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATT-GTAA
47288005 CAGTAACAGTA
1 CAGTAACAGTA
47288016 GTCGGCTTAT
Statistics
Matches: 117, Mismatches: 14, Indels: 16
0.80 0.10 0.11
Matches are distributed among these distances:
39 33 0.28
40 2 0.02
43 1 0.01
44 38 0.32
45 43 0.37
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (44 bp):
CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATTGTAA
Found at i:47291680 original size:5 final size:5
Alignment explanation
Indices: 47291670--47291696 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
47291660 ACTACACGAT
47291670 GAAAA GAAAA GAAAA GAAAA GAAAA GA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GA
47291697 TTATATATTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:47296790 original size:22 final size:22
Alignment explanation
Indices: 47296765--47296828 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
47296755 TCTCCGATTA
47296765 TTAGCACATTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
* *
47296787 TTAGCACATTTGTGCTCTATGT
1 TTAGCACATTAGTGCTCTCTGT
* *
47296809 ATAGCACTTTAGTGCTCTCT
1 TTAGCACATTAGTGCTCTCT
47296829 ATTCAATAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCTGT
Found at i:47311085 original size:7 final size:6
Alignment explanation
Indices: 47311066--47311101 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
47311056 TGCAGTGAAT
*
47311066 ATAAATA ATAAAA ATAAAA ATAAAA ATAAAA GTAAA
1 ATAAA-A ATAAAA ATAAAA ATAAAA ATAAAA ATAAA
47311102 GGTATAGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:47311866 original size:35 final size:35
Alignment explanation
Indices: 47311820--47311889 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
47311810 ACTACTGTTG
47311820 GAGTTTTCAATTGAGATTAAAAAGTGAAATTTGAA
1 GAGTTTTCAATTGAGATTAAAAAGTGAAATTTGAA
47311855 GAGTTTTCAATTGAGATTAAAAAGTGAAATTTGAA
1 GAGTTTTCAATTGAGATTAAAAAGTGAAATTTGAA
47311890 TGGGAAAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.03, G:0.20, T:0.34
Consensus pattern (35 bp):
GAGTTTTCAATTGAGATTAAAAAGTGAAATTTGAA
Found at i:47315194 original size:47 final size:47
Alignment explanation
Indices: 47315143--47315239 Score: 194
Period size: 47 Copynumber: 2.1 Consensus size: 47
47315133 CATCAACCTT
47315143 ATTATCATTTCACGTACCAAGGGTCGCTAAAACCACGTTCTAATTGC
1 ATTATCATTTCACGTACCAAGGGTCGCTAAAACCACGTTCTAATTGC
47315190 ATTATCATTTCACGTACCAAGGGTCGCTAAAACCACGTTCTAATTGC
1 ATTATCATTTCACGTACCAAGGGTCGCTAAAACCACGTTCTAATTGC
47315237 ATT
1 ATT
47315240 CCTCTGCCTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (47 bp):
ATTATCATTTCACGTACCAAGGGTCGCTAAAACCACGTTCTAATTGC
Found at i:47322189 original size:17 final size:17
Alignment explanation
Indices: 47322162--47322195 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
47322152 CGATTCAAAG
47322162 TAAATAAATTATTAAAAA
1 TAAATAAATTA-TAAAAA
47322180 TAAA-AAATTATAAAAA
1 TAAATAAATTATAAAAA
47322196 CCAAATCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 6 0.38
18 4 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAATAAATTATAAAAA
Found at i:47327370 original size:16 final size:16
Alignment explanation
Indices: 47327322--47327370 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
47327312 TCAAGAATAC
47327322 TTATATTTAGAACAA-
1 TTATATTTAGAACAAT
* * *
47327337 CTATTATTTGGAAAAAT
1 TTA-TATTTAGAACAAT
47327354 TTATATTTAGAACAAT
1 TTATATTTAGAACAAT
47327370 T
1 T
47327371 GTGTTTTTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
15 2 0.08
16 22 0.85
17 2 0.08
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (16 bp):
TTATATTTAGAACAAT
Found at i:47329902 original size:4 final size:4
Alignment explanation
Indices: 47329895--47329948 Score: 108
Period size: 4 Copynumber: 13.5 Consensus size: 4
47329885 CATAACATTA
47329895 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
47329943 TATG TA
1 TATG TA
47329949 AAGGTGTCAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:47330098 original size:17 final size:17
Alignment explanation
Indices: 47330076--47330108 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
47330066 GCCCATCTCC
47330076 GAAGCTTGGCAAATATG
1 GAAGCTTGGCAAATATG
47330093 GAAGCTTGGCAAATAT
1 GAAGCTTGGCAAATAT
47330109 AATCTTTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.24
Consensus pattern (17 bp):
GAAGCTTGGCAAATATG
Found at i:47339706 original size:18 final size:19
Alignment explanation
Indices: 47339670--47339707 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
47339660 ATAAAAACAA
*
47339670 AAATTGAATATTGCAAAAT
1 AAATTGAATAATGCAAAAT
47339689 AAATTGAATAAT-CAAAAT
1 AAATTGAATAATGCAAAAT
47339707 A
1 A
47339708 GTCTCACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.58, C:0.05, G:0.08, T:0.29
Consensus pattern (19 bp):
AAATTGAATAATGCAAAAT
Found at i:47346049 original size:2 final size:2
Alignment explanation
Indices: 47346042--47346079 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
47346032 ACCTTTATAA
* *
47346042 GT GT GT GT GT GT GT GT CT GT GT GT GT GT GT TT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
47346080 ATAATTTTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.03, G:0.45, T:0.53
Consensus pattern (2 bp):
GT
Found at i:47351661 original size:3 final size:3
Alignment explanation
Indices: 47351653--47351680 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
47351643 CTTTACCATC
47351653 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
47351681 TTGATTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:47354159 original size:16 final size:17
Alignment explanation
Indices: 47354133--47354169 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
47354123 GTTTTTTCCG
*
47354133 GGAGAAGTGGGAAAGGA
1 GGAGAAGTGGGAAAGCA
47354150 GGAG-AGTGGGAAAGCA
1 GGAGAAGTGGGAAAGCA
47354166 GGAG
1 GGAG
47354170 TTGAAGAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.38, C:0.03, G:0.54, T:0.05
Consensus pattern (17 bp):
GGAGAAGTGGGAAAGCA
Found at i:47359284 original size:24 final size:24
Alignment explanation
Indices: 47359257--47359308 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
47359247 TTTCTAGAAG
* **
47359257 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
47359281 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
47359305 ATTT
1 ATTT
47359309 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:47368327 original size:3 final size:3
Alignment explanation
Indices: 47368319--47368356 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
47368309 ATCACGTGTT
47368319 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
47368357 TTGATTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:47373730 original size:9 final size:9
Alignment explanation
Indices: 47373716--47373740 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
47373706 TTGACATGAC
47373716 TTTGTCATT
1 TTTGTCATT
47373725 TTTGTCATT
1 TTTGTCATT
47373734 TTTGTCA
1 TTTGTCA
47373741 CATTTGCAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.64
Consensus pattern (9 bp):
TTTGTCATT
Found at i:47376757 original size:33 final size:33
Alignment explanation
Indices: 47376714--47376781 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
47376704 CAAAGTTACC
* *
47376714 TTCACGAGCAACGACATCATCTTAGTGGAAACA
1 TTCACAAGCAACGACATCATCTCAGTGGAAACA
47376747 TTCACAAGCAACGACATCATCTCAGTGGAAACA
1 TTCACAAGCAACGACATCATCTCAGTGGAAACA
47376780 TT
1 TT
47376782 GCTAAAGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (33 bp):
TTCACAAGCAACGACATCATCTCAGTGGAAACA
Found at i:47382128 original size:12 final size:12
Alignment explanation
Indices: 47382111--47382171 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
47382101 AGGCAACCCA
47382111 ATTTTTATTTTT
1 ATTTTTATTTTT
47382123 ATTTTTA--TTT
1 ATTTTTATTTTT
47382133 ATTTTT-TTCTTT
1 ATTTTTATT-TTT
*
47382145 A-CTTTATTTATT
1 ATTTTTATTT-TT
47382157 A-TTTTA-TTTT
1 ATTTTTATTTTT
47382167 ATTTT
1 ATTTT
47382172 ACTTATTTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
10 12 0.29
11 9 0.22
12 20 0.49
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (12 bp):
ATTTTTATTTTT
Found at i:47382145 original size:22 final size:20
Alignment explanation
Indices: 47382111--47382179 Score: 75
Period size: 22 Copynumber: 3.2 Consensus size: 20
47382101 AGGCAACCCA
47382111 ATTTTTATTTTTATTTTTATTT
1 ATTTTT-TTTTTA-TTTTATTT
*
47382133 ATTTTTTTCTTTACTTTATTT
1 ATTTTTTT-TTTATTTTATTT
*
47382154 ATTATTTTATTTTATTTTACTT
1 ATT-TTTT-TTTTATTTTATTT
47382176 ATTT
1 ATTT
47382180 GGATATTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 13 0.32
22 27 0.66
23 1 0.02
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (20 bp):
ATTTTTTTTTTATTTTATTT
Found at i:47382150 original size:17 final size:15
Alignment explanation
Indices: 47382114--47382171 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 15
47382104 CAACCCAATT
47382114 TTTATTTTTATTTTTA
1 TTTATTTTT-TTTTTA
47382130 TTTATTTTTTTCTTTA
1 TTTATTTTTTT-TTTA
*
47382146 CTTTATTTATTATTTTA
1 -TTTATTT-TTTTTTTA
47382163 TTTTATTTT
1 -TTTATTTT
47382172 ACTTATTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
15 2 0.05
16 14 0.38
17 18 0.49
18 3 0.08
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTATTTTTTTTTTA
Found at i:47382413 original size:12 final size:12
Alignment explanation
Indices: 47382396--47382456 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
47382386 AGGCAACCCA
47382396 ATTTTTATTTTT
1 ATTTTTATTTTT
47382408 ATTTTTA--TTT
1 ATTTTTATTTTT
47382418 ATTTTT-TTCTTT
1 ATTTTTATT-TTT
*
47382430 A-CTTTATTTATT
1 ATTTTTATTT-TT
47382442 A-TTTTA-TTTT
1 ATTTTTATTTTT
47382452 ATTTT
1 ATTTT
47382457 ACTTATTTGG
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
10 12 0.29
11 9 0.22
12 20 0.49
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (12 bp):
ATTTTTATTTTT
Found at i:47382430 original size:22 final size:20
Alignment explanation
Indices: 47382396--47382464 Score: 75
Period size: 22 Copynumber: 3.2 Consensus size: 20
47382386 AGGCAACCCA
47382396 ATTTTTATTTTTATTTTTATTT
1 ATTTTT-TTTTTA-TTTTATTT
*
47382418 ATTTTTTTCTTTACTTTATTT
1 ATTTTTTT-TTTATTTTATTT
*
47382439 ATTATTTTATTTTATTTTACTT
1 ATT-TTTT-TTTTATTTTATTT
47382461 ATTT
1 ATTT
47382465 GGATATTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 13 0.32
22 27 0.66
23 1 0.02
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (20 bp):
ATTTTTTTTTTATTTTATTT
Found at i:47382435 original size:17 final size:15
Alignment explanation
Indices: 47382399--47382456 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 15
47382389 CAACCCAATT
47382399 TTTATTTTTATTTTTA
1 TTTATTTTT-TTTTTA
47382415 TTTATTTTTTTCTTTA
1 TTTATTTTTTT-TTTA
*
47382431 CTTTATTTATTATTTTA
1 -TTTATTT-TTTTTTTA
47382448 TTTTATTTT
1 -TTTATTTT
47382457 ACTTATTTGG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
15 2 0.05
16 14 0.38
17 18 0.49
18 3 0.08
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTATTTTTTTTTTA
Found at i:47382598 original size:285 final size:284
Alignment explanation
Indices: 47382088--47382657 Score: 1122
Period size: 285 Copynumber: 2.0 Consensus size: 284
47382078 AAGTTAAACA
47382088 AACGCTTGTTGGGAGGCAACCCAATTTTTATTTTTATTTTTATTTATTTTTTTCTTTACTTTATT
1 AACGCTTGTTGGGAGGCAACCCAATTTTTATTTTTATTTTTATTTATTTTTTTCTTTACTTTATT
47382153 TATTATTTTATTTTATTTTACTTATTTGGATATTAATAAATTTTTCTTCTTTTGCTTAGATAAAA
66 TATTATTTTATTTTATTTTACTTATTTGGATATTAATAAATTTTTCTTCTTTTGCTTAGATAAAA
47382218 CAGAGCAAAAATGCGAAGAAAACCGTTGAGCAACGCTTAGAGTGCATTATGGCCCGACTTGAAAC
131 CAGAGCAAAAATGCGAAGAAAACCGTTGAGCAACGCTTAGAGTGCATTATGGCCCGACTTGAAAC
47382283 CTTTGGCCAGCAACTGACCAAGCTCATTGCCATCATTTGTGATCGACAGTAACAACACGGGGAGC
196 CTTTGGCCAGCAACTGACCAAGCTCATTGCCATCATTTGTGATCGACAGTAACAACACGGGGAGC
47382348 TTTTCTAAACTTTTCTACCTATTT
261 TTTTCTAAACTTTTCTACCTATTT
47382372 NAACGCTTGTTGGGAGGCAACCCAATTTTTATTTTTATTTTTATTTATTTTTTTCTTTACTTTAT
1 -AACGCTTGTTGGGAGGCAACCCAATTTTTATTTTTATTTTTATTTATTTTTTTCTTTACTTTAT
47382437 TTATTATTTTATTTTATTTTACTTATTTGGATATTAATAAATTTTTCTTCTTTTGCTTAGATAAA
65 TTATTATTTTATTTTATTTTACTTATTTGGATATTAATAAATTTTTCTTCTTTTGCTTAGATAAA
47382502 ACAGAGCAAAAATGCGAAGAAAACCGTTGAGCAACGCTTAGAGTGCATTATGGCCCGACTTGAAA
130 ACAGAGCAAAAATGCGAAGAAAACCGTTGAGCAACGCTTAGAGTGCATTATGGCCCGACTTGAAA
47382567 CCTTTGGCCAGCAACTGACCAAGCTCATTGCCATCATTTGTGATCGACAGTAACAACACGGGGAG
195 CCTTTGGCCAGCAACTGACCAAGCTCATTGCCATCATTTGTGATCGACAGTAACAACACGGGGAG
*
47382632 TTTTTCTAAACTTTTCTACCTATTT
260 CTTTTCTAAACTTTTCTACCTATTT
47382657 A
1 A
47382658 TTTCTTTTCG
Statistics
Matches: 284, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
284 1 0.00
285 283 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (284 bp):
AACGCTTGTTGGGAGGCAACCCAATTTTTATTTTTATTTTTATTTATTTTTTTCTTTACTTTATT
TATTATTTTATTTTATTTTACTTATTTGGATATTAATAAATTTTTCTTCTTTTGCTTAGATAAAA
CAGAGCAAAAATGCGAAGAAAACCGTTGAGCAACGCTTAGAGTGCATTATGGCCCGACTTGAAAC
CTTTGGCCAGCAACTGACCAAGCTCATTGCCATCATTTGTGATCGACAGTAACAACACGGGGAGC
TTTTCTAAACTTTTCTACCTATTT
Found at i:47383503 original size:20 final size:20
Alignment explanation
Indices: 47383478--47383516 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
47383468 CCTAAAGCAT
*
47383478 AAAAAAATGAGAAAAAAAAC
1 AAAAAAAAGAGAAAAAAAAC
*
47383498 AAAAAAAAGATAAAAAAAA
1 AAAAAAAAGAGAAAAAAAA
47383517 ATAATTTGGG
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:0.85, C:0.03, G:0.08, T:0.05
Consensus pattern (20 bp):
AAAAAAAAGAGAAAAAAAAC
Found at i:47383520 original size:10 final size:10
Alignment explanation
Indices: 47383478--47383520 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
47383468 CCTAAAGCAT
47383478 AAAAAAATGAGA
1 AAAAAAAT-A-A
*
47383490 AAAAAAACAA
1 AAAAAAATAA
47383500 AAAAAAGATAA
1 AAAAAA-ATAA
47383511 AAAAAAATAA
1 AAAAAAATAA
47383521 TTTGGGAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 11 0.39
11 10 0.36
12 7 0.25
ACGTcount: A:0.84, C:0.02, G:0.07, T:0.07
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:47386075 original size:10 final size:10
Alignment explanation
Indices: 47386060--47386084 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
47386050 ATAATCAATA
47386060 TTTTTTTATT
1 TTTTTTTATT
47386070 TTTTTTTATT
1 TTTTTTTATT
47386080 TTTTT
1 TTTTT
47386085 GAACAATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:47387265 original size:23 final size:21
Alignment explanation
Indices: 47387245--47387311 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 21
47387235 TCCATTTACC
47387245 TTTTTTATATATATTATTTTA
1 TTTTTTATATATATTATTTTA
*
47387266 TTTTATTATGTACTATTATTTTAA
1 TTTT-TTATATA-TATTATTTT-A
47387290 TTCTTTT-TATCATA-TATTTTA
1 TT-TTTTATAT-ATATTATTTTA
47387311 T
1 T
47387312 CTAGTTTCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 6 0.15
22 12 0.31
23 13 0.33
24 6 0.15
25 2 0.05
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.67
Consensus pattern (21 bp):
TTTTTTATATATATTATTTTA
Found at i:47387531 original size:25 final size:23
Alignment explanation
Indices: 47387493--47387551 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 23
47387483 TAATAAACTA
* *
47387493 TTTTTAT-TCTACATACATATCT
1 TTTTTATATATACATACATATAT
*
47387515 TTGATTTATATATACATACTTATAT
1 TT--TTTATATATACATACATATAT
47387540 TTTTTATATATA
1 TTTTTATATATA
47387552 TTTTATAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 2 0.06
23 10 0.32
24 5 0.16
25 14 0.45
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTTTATATATACATACATATAT
Found at i:47387557 original size:20 final size:20
Alignment explanation
Indices: 47387523--47387572 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
47387513 CTTTGATTTA
* *
47387523 TATATACATA-CTTATATTT
1 TATATACATATTTTATAATT
* *
47387542 TTTATATATATTTTATAATT
1 TATATACATATTTTATAATT
47387562 TATATACATAT
1 TATATACATAT
47387573 ACATATATAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (20 bp):
TATATACATATTTTATAATT
Found at i:47396614 original size:24 final size:24
Alignment explanation
Indices: 47396576--47396827 Score: 123
Period size: 24 Copynumber: 10.8 Consensus size: 24
47396566 TGAATTGGAT
* *
47396576 AATTTACAATAAATAATATATAATA
1 AATTTAAAAT-AATAATATATGATA
* *
47396601 AATTTGAAATAATAATACAT-ATAA
1 AATTTAAAATAATAATATATGAT-A
** *
47396625 AATTT-AAA-AATTTTGT-TGAT-
1 AATTTAAAATAATAATATATGATA
* * **
47396645 AATTCTAGAATAATCATACGTGATA
1 AATT-TAAAATAATAATATATGATA
** * *
47396670 AATCCAAAATAATAGTATATAATA
1 AATTTAAAATAATAATATATGATA
* *
47396694 AATTT-AAA-AATATTA-AGGATA
1 AATTTAAAATAATAATATATGATA
* *
47396715 AATTTGAAATAGAT-ATACATGATA
1 AATTTAAAATA-ATAATATATGATA
** ** *
47396739 AATTTAAAATAATGTTA-ACAATG
1 AATTTAAAATAATAATATATGATA
47396762 AATTTAAAATAATAATAT-TGATA
1 AATTTAAAATAATAATATATGATA
* *
47396785 AA-TTACAAATAATAAAACATGATA
1 AATTTA-AAATAATAATATATGATA
* *
47396809 AATCTAAAATAATGATATA
1 AATTTAAAATAATAATATA
47396828 AAATACACTT
Statistics
Matches: 168, Mismatches: 43, Indels: 33
0.69 0.18 0.14
Matches are distributed among these distances:
20 4 0.02
21 11 0.07
22 20 0.12
23 49 0.29
24 71 0.42
25 13 0.08
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (24 bp):
AATTTAAAATAATAATATATGATA
Found at i:47398508 original size:15 final size:15
Alignment explanation
Indices: 47398488--47398540 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
47398478 ACCGTTGAAA
*
47398488 CCCTAAATCTCAAAC
1 CCCTAAATCTCTAAC
47398503 CCCTAAA-CATCTAAC
1 CCCTAAATC-TCTAAC
*
47398518 CCCTAAACCTCTAAC
1 CCCTAAATCTCTAAC
47398533 CCCTAAAT
1 CCCTAAAT
47398541 TAACCTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
14 1 0.03
15 32 0.94
16 1 0.03
ACGTcount: A:0.38, C:0.42, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCTCTAAC
Found at i:47399149 original size:41 final size:41
Alignment explanation
Indices: 47399104--47399504 Score: 287
Period size: 41 Copynumber: 9.8 Consensus size: 41
47399094 AGGCAGGAGA
* *
47399104 ATTAGTGGCGCTCAGATAAAAACGCCACTAAAGATCCAAGT
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCAAGT
* * *
47399145 ATTAGCAGCGCTTAAATAAAACCGCCACTAAAGATCCAAGT
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCAAGT
* ** * *
47399186 ATTAGCGGCGCTGAAATAAAGTCGCCGCTAAAGA-CCTGAGCT
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCC-AAG-T
* * * * * *
47399228 TTTA-CGGCGTTCATATAATAACACCACTAAAGATCTAAGT
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCAAGT
* * * * *
47399268 ATTAGCGTCGCTAAAATAAAATCGCCGCTAAAGA-CCTGAGCT
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCC-AAG-T
* * * *
47399310 -TTTGCGGCGTTCATATAAAAACGCCACTAAAGAT-TAGAG-
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCA-AGT
* * *
47399349 ATTTAGCGGCGCTCAGATAAAAATGCCACTAAAGAT-CAGAGA
1 A-TTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCA-AGT
** * * *** *
47399391 ATTAGCCACGCCCAGATAAAAACGCCACTAAAGATAGGAGA
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCAAGT
* ** *
47399432 ATTAGCGGCGCT-AAGATAAAAACGCCACTATAGATCCGTGC
1 ATTAGCGGCGCTCAA-ATAAAAACGCCACTAAAGATCCAAGT
* * *
47399473 ATTAGTGGCGCACAAATAAAAACGCCGCTAAA
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAA
47399505 TGTTTAAAAA
Statistics
Matches: 280, Mismatches: 66, Indels: 28
0.75 0.18 0.07
Matches are distributed among these distances:
40 8 0.03
41 263 0.94
42 9 0.03
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.20
Consensus pattern (41 bp):
ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCAAGT
Found at i:47406219 original size:7 final size:6
Alignment explanation
Indices: 47406199--47406249 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
47406189 GTTTCCCTGC
* * * *
47406199 AAAATA AAAATA AAAATT AAAATA AATAATA AGAA-A AAATTA AAATTA
1 AAAATA AAAATA AAAATA AAAATA AA-AATA AAAATA AAAATA AAAATA
47406247 AAA
1 AAA
47406250 TGTGTATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
5 3 0.08
6 30 0.79
7 5 0.13
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (6 bp):
AAAATA
Found at i:47427072 original size:18 final size:19
Alignment explanation
Indices: 47427027--47427072 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
47427017 TGTAATTAGA
*
47427027 AAAATGAATAAAAACTATT
1 AAAATAAATAAAAACTATT
*
47427046 ATAAA-AAAT-AAAACTTTT
1 A-AAATAAATAAAAACTATT
47427064 AAAATAAAT
1 AAAATAAAT
47427073 TCAAAAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 3 0.13
18 13 0.57
19 4 0.17
20 3 0.13
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATAAATAAAAACTATT
Found at i:47441593 original size:20 final size:21
Alignment explanation
Indices: 47441568--47441607 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
47441558 CCACACTTCC
47441568 AATTGTATGTACTT-ATCTTT
1 AATTGTATGTACTTAATCTTT
*
47441588 AATTGTATGTGCTTAATCTT
1 AATTGTATGTACTTAATCTT
47441608 GTTTATCCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.25, C:0.10, G:0.12, T:0.53
Consensus pattern (21 bp):
AATTGTATGTACTTAATCTTT
Done.