Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 57 of 135
Found at i:19666154 original size:16 final size:16
Alignment explanation
Indices: 19666133--19666241 Score: 60
Period size: 16 Copynumber: 6.2 Consensus size: 16
19666123 AGTAAAAAAA
* *
19666133 TTTAAAAATTCTAATT
1 TTTAAAAATTATAAAT
19666149 TTTAAAAATTATAAAT
1 TTTAAAAATTATAAAT
*
19666165 TATAAAAATATTATTAGGAAT
1 T-TTAAAA-ATTA-TA--AAT
19666186 TTATAAAAATTATTAAAAAT
1 TT-TAAAAATTA-T--AAAT
* *
19666206 TATTAAAAA-AATTAATT
1 T-TTAAAAATTA-TAAAT
19666223 TTTAAAAA-TATAAAT
1 TTTAAAAATTATAAAT
19666238 TTTA
1 TTTA
19666242 TTAAACTATT
Statistics
Matches: 76, Mismatches: 8, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
15 8 0.11
16 23 0.30
17 9 0.12
18 4 0.05
19 5 0.07
20 17 0.22
21 9 0.12
22 1 0.01
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (16 bp):
TTTAAAAATTATAAAT
Found at i:19666219 original size:12 final size:10
Alignment explanation
Indices: 19666145--19666214 Score: 58
Period size: 10 Copynumber: 7.2 Consensus size: 10
19666135 TAAAAATTCT
*
19666145 AATTTTTAAA
1 AATTATTAAA
19666155 AATTA-T--A
1 AATTATTAAA
*
19666162 AATTATAAAA
1 AATTATTAAA
**
19666172 ATATTATTAGG
1 A-ATTATTAAA
19666183 AATT-TATAAA
1 AATTAT-TAAA
19666193 AATTATTAAA
1 AATTATTAAA
19666203 AATTATTAAA
1 AATTATTAAA
19666213 AA
1 AA
19666215 AATTAATTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
7 6 0.13
9 2 0.04
10 31 0.66
11 8 0.17
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (10 bp):
AATTATTAAA
Found at i:19666636 original size:19 final size:20
Alignment explanation
Indices: 19666600--19666652 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
19666590 TACAAAATAA
19666600 TCAAAATAATTT-TAAAAAGT
1 TCAAAAT-ATTTATAAAAAGT
*
19666620 TCAAAATATTTATAAAAATT
1 TCAAAATATTTATAAAAAGT
19666640 TCAAAA-ATTTATA
1 TCAAAATATTTATA
19666653 TATATATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 11 0.35
20 20 0.65
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.38
Consensus pattern (20 bp):
TCAAAATATTTATAAAAAGT
Found at i:19667406 original size:17 final size:16
Alignment explanation
Indices: 19667384--19667433 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
19667374 TGATTTTTAA
19667384 TATTTTAATAAATTTTT
1 TATTTT-ATAAATTTTT
19667401 TATTTTATAAAATTTTAT
1 TATTTTAT-AAATTTT-T
19667419 T-TTTT-TAAATTTTT
1 TATTTTATAAATTTTT
19667433 T
1 T
19667434 TTGTAATTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
14 2 0.06
15 7 0.23
16 3 0.10
17 17 0.55
18 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTTATAAATTTTT
Found at i:19667416 original size:16 final size:16
Alignment explanation
Indices: 19667384--19667432 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
19667374 TGATTTTTAA
*
19667384 TATTTTAATAAATTTTT
1 TATTTT-ATAAAATTTT
19667401 TATTTTATAAAA-TTT
1 TATTTTATAAAATTTT
* *
19667416 TATTTTTTTAAATTTT
1 TATTTTATAAAATTTT
19667432 T
1 T
19667433 TTTGTAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 13 0.46
16 9 0.32
17 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTTATAAAATTTT
Found at i:19671862 original size:51 final size:53
Alignment explanation
Indices: 19671802--19671906 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
19671792 ATGGCATTAT
19671802 TTCACAAAAAATACATGTAATTTTA-T-TTTTAACAATTTAGTCCTTAAACCC
1 TTCACAAAAAATACATGTAATTTTATTGTTTTAACAATTTAGTCCTTAAACCC
*
19671853 TTCACAAAAAATACATGTACTTTTATTGTTTTAACAATTTAGTCCTTAAACCC
1 TTCACAAAAAATACATGTAATTTTATTGTTTTAACAATTTAGTCCTTAAACCC
19671906 T
1 T
19671907 AAAATCATCA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 24 0.47
52 1 0.02
53 26 0.51
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (53 bp):
TTCACAAAAAATACATGTAATTTTATTGTTTTAACAATTTAGTCCTTAAACCC
Found at i:19675263 original size:33 final size:33
Alignment explanation
Indices: 19675215--19675393 Score: 223
Period size: 33 Copynumber: 5.4 Consensus size: 33
19675205 TACTGTTGAT
* * * * *
19675215 TGATGAGGAGAGTGATGTTGAAGGAGCAGAAGC
1 TGATGGGGAGGGTGATGTTGAAGGGGTACAAGC
19675248 TGATGGGGAGGGTGATGTTGAAGGGGTACAAGC
1 TGATGGGGAGGGTGATGTTGAAGGGGTACAAGC
* * * **
19675281 TGATGAGAAGGATGATGTAAAAGGGGTACAAGC
1 TGATGGGGAGGGTGATGTTGAAGGGGTACAAGC
**
19675314 TGATGGGGAGGGTGATGTAAAAGGGGTACAAGC
1 TGATGGGGAGGGTGATGTTGAAGGGGTACAAGC
* *
19675347 TGATGGGGAAGGTGATGTTGAAGGGGTAGAAGC
1 TGATGGGGAGGGTGATGTTGAAGGGGTACAAGC
*
19675380 TGATAGGGAGGGTG
1 TGATGGGGAGGGTG
19675394 TGACTGCTAC
Statistics
Matches: 127, Mismatches: 19, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 127 1.00
ACGTcount: A:0.30, C:0.05, G:0.45, T:0.20
Consensus pattern (33 bp):
TGATGGGGAGGGTGATGTTGAAGGGGTACAAGC
Found at i:19677812 original size:28 final size:28
Alignment explanation
Indices: 19677780--19678062 Score: 109
Period size: 28 Copynumber: 9.8 Consensus size: 28
19677770 TTGACTTTTG
19677780 GGGGTAAAAATGGAATTTTGGCAAAATTA
1 GGGGTAAAAATGGAATTTTGG-AAAATTA
*
19677809 -GGGTTAAAATAGG-ATTTT-GAAAAGTTTA
1 GGGGTAAAAAT-GGAATTTTGGAAAA--TTA
*
19677837 GGGGT-AAAATGGTAATTTTTGGTGAAATT-
1 GGGGTAAAAATGG-AA-TTTTGG-AAAATTA
* *
19677866 GGGGTCAAAAATGGGATTTTGGAAAGTTTA
1 GGGGT-AAAAATGGAATTTTGGAAA-ATTA
* * *
19677896 GGGGT-AAAATGGTGATTTTTGGTGAAATCA
1 GGGGTAAAAAT-G-GAATTTTGG-AAAATTA
* *
19677926 -AGGTCAAAAATGGAATTTTGGAAAGTTTA
1 GGGGT-AAAAATGGAATTTTGGAAA-ATTA
* * * **
19677955 CGGGT-AAAATAGTAATTTTTGGTGAAA-CC
1 GGGGTAAAAAT-GGAA-TTTTGG-AAAATTA
** *
19677984 GGGGTTAAAAATGGAATTTTGGGAAGTTTG
1 GGGG-TAAAAATGGAATTTT-GGAAAATTA
* * ** *
19678014 GGGGTAAATA-GTAATTTTTGGAAGTTTC
1 GGGGTAAAAATGGAA-TTTTGGAAAATTA
*
19678042 GGGGTTAAAATGGAATTTTGG
1 GGGGTAAAAATGGAATTTTGG
19678063 GAAGTTTGAG
Statistics
Matches: 191, Mismatches: 34, Indels: 59
0.67 0.12 0.21
Matches are distributed among these distances:
26 4 0.02
27 3 0.02
28 61 0.32
29 57 0.30
30 41 0.21
31 22 0.12
32 3 0.02
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (28 bp):
GGGGTAAAAATGGAATTTTGGAAAATTA
Found at i:19677885 original size:30 final size:31
Alignment explanation
Indices: 19677842--19678003 Score: 89
Period size: 30 Copynumber: 5.5 Consensus size: 31
19677832 GTTTAGGGGT
19677842 AAAATGGTAATTTTTGGTGAAATTGGGGTCA
1 AAAATGGTAATTTTTGGTGAAATTGGGGTCA
*
19677873 AAAATGG-GA-TTTT-G-GAAAGTTTAGGGGT--
1 AAAATGGTAATTTTTGGTGAAA--TT-GGGGTCA
* ***
19677901 AAAATGGTGATTTTTGGTGAAATCAAGGTCA
1 AAAATGGTAATTTTTGGTGAAATTGGGGTCA
*
19677932 AAAATGG-AA-TTTT-G-GAAAGTTTACGGGT--
1 AAAATGGTAATTTTTGGTGAAA--TT-GGGGTCA
* ** *
19677960 AAAATAGTAATTTTTGGTGAAACCGGGGTTA
1 AAAATGGTAATTTTTGGTGAAATTGGGGTCA
19677991 AAAATGG-AATTTT
1 AAAATGGTAATTTT
19678004 GGGAAGTTTG
Statistics
Matches: 100, Mismatches: 13, Indels: 37
0.67 0.09 0.25
Matches are distributed among these distances:
27 8 0.08
28 15 0.15
29 22 0.22
30 25 0.25
31 22 0.22
32 8 0.08
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.33
Consensus pattern (31 bp):
AAAATGGTAATTTTTGGTGAAATTGGGGTCA
Found at i:19677892 original size:59 final size:59
Alignment explanation
Indices: 19677780--19678034 Score: 295
Period size: 59 Copynumber: 4.4 Consensus size: 59
19677770 TTGACTTTTG
** * * *
19677780 GGGGTAAAAATGG-AA-TTTTGGCAAAATTAGGGT-TAAAATAGG-ATTTTGAAAAGTTTA
1 GGGGT-AAAATGGTAATTTTTGGTGAAATCAGGGTCAAAAAT-GGAATTTTGGAAAGTTTA
** *
19677837 GGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTCAAAAATGGGATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTTA
* *
19677896 GGGGTAAAATGGTGATTTTTGGTGAAATCAAGGTCAAAAATGGAATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTTA
* * * * * * *
19677955 CGGGTAAAATAGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTGGGAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTTA
*
19678014 GGGGT-AAATAGTAATTTTTGG
1 GGGGTAAAATGGTAATTTTTGG
19678035 AAGTTTCGGG
Statistics
Matches: 174, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
56 7 0.04
57 7 0.04
58 33 0.19
59 127 0.73
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.33
Consensus pattern (59 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTCAAAAATGGAATTTTGGAAAGTTTA
Found at i:19677937 original size:31 final size:31
Alignment explanation
Indices: 19677842--19677938 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 31
19677832 GTTTAGGGGT
* **
19677842 AAAATGGTAATTTTTGGTGAAATTGGGGTCA
1 AAAATGGTGATTTTTGGTGAAATTAAGGTCA
* ***
19677873 AAAATGG-GA-TTTT-G-GAAAGTTTAGGGGT
1 AAAATGGTGATTTTTGGTGAAA-TTAAGGTCA
*
19677901 AAAATGGTGATTTTTGGTGAAATCAAGGTCA
1 AAAATGGTGATTTTTGGTGAAATTAAGGTCA
19677932 AAAATGG
1 AAAATGG
19677939 AATTTTGGAA
Statistics
Matches: 50, Mismatches: 11, Indels: 10
0.70 0.15 0.14
Matches are distributed among these distances:
27 4 0.08
28 12 0.24
29 6 0.12
30 5 0.10
31 19 0.38
32 4 0.08
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (31 bp):
AAAATGGTGATTTTTGGTGAAATTAAGGTCA
Found at i:19677963 original size:29 final size:29
Alignment explanation
Indices: 19677780--19678069 Score: 137
Period size: 29 Copynumber: 10.0 Consensus size: 29
19677770 TTGACTTTTG
*
19677780 GGGGTAAAAATGGAATTTTGGCAAA-ATTA
1 GGGGTAAAAATGGAATTTTGG-AAAGTTTA
* *
19677809 -GGGTTAAAATAGG-ATTTTGAAAAGTTTA
1 GGGGTAAAAAT-GGAATTTTGGAAAGTTTA
19677837 GGGGT-AAAATGGTAATTTTTGGTGAAA--TT-
1 GGGGTAAAAATGG-AA-TTTT-G-GAAAGTTTA
*
19677866 GGGGTCAAAAATGGGATTTTGGAAAGTTTA
1 GGGGT-AAAAATGGAATTTTGGAAAGTTTA
* *
19677896 GGGGT-AAAATGGTGATTTTTGGTGAAA--TCA
1 GGGGTAAAAAT-G-GAATTTT-G-GAAAGTTTA
*
19677926 -AGGTCAAAAATGGAATTTTGGAAAGTTTA
1 GGGGT-AAAAATGGAATTTTGGAAAGTTTA
* * **
19677955 CGGGT-AAAATAGTAATTTTTGGTGAAA---CC
1 GGGGTAAAAAT-GGAA-TTTT-G-GAAAGTTTA
* *
19677984 GGGGTTAAAAATGGAATTTTGGGAAGTTTG
1 GGGG-TAAAAATGGAATTTTGGAAAGTTTA
* * *
19678014 GGGGTAAATA-GTAATTTTTGG-AAGTTTC
1 GGGGTAAAAATGGAA-TTTTGGAAAGTTTA
* *
19678042 GGGGTTAAAATGGAATTTTGGGAAGTTT
1 GGGGTAAAAATGGAATTTTGGAAAGTTT
19678070 GAGGACTATA
Statistics
Matches: 201, Mismatches: 26, Indels: 68
0.68 0.09 0.23
Matches are distributed among these distances:
27 16 0.08
28 59 0.29
29 60 0.30
30 35 0.17
31 20 0.10
32 11 0.05
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTGGAAAGTTTA
Found at i:19679070 original size:20 final size:20
Alignment explanation
Indices: 19679045--19679086 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
19679035 CTTTTTCTTT
19679045 TTTATTAAAAATTAATATTA
1 TTTATTAAAAATTAATATTA
* * *
19679065 TTTATTAATATTTATTATTA
1 TTTATTAAAAATTAATATTA
19679085 TT
1 TT
19679087 ACCGTTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTATTAAAAATTAATATTA
Found at i:19679894 original size:17 final size:16
Alignment explanation
Indices: 19679877--19679949 Score: 76
Period size: 17 Copynumber: 4.4 Consensus size: 16
19679867 TTAATACAAT
19679877 TTTAAATTAAATTAAA
1 TTTAAATTAAATTAAA
* *
19679893 TTCAAATTTAAAGTAAA
1 TTTAAA-TTAAATTAAA
*
19679910 TTTAAATTTAAAATAAA
1 TTTAAA-TTAAATTAAA
19679927 TTTAAGA-TAAATTTAAA
1 TTTAA-ATTAAA-TTAAA
19679944 TTTAAA
1 TTTAAA
19679950 AATAAATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
16 10 0.20
17 38 0.78
18 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (16 bp):
TTTAAATTAAATTAAA
Found at i:19679899 original size:11 final size:11
Alignment explanation
Indices: 19679877--19679961 Score: 66
Period size: 11 Copynumber: 7.5 Consensus size: 11
19679867 TTAATACAAT
19679877 TTTAAATTAAA
1 TTTAAATTAAA
19679888 -TTAAATTCAAA
1 TTTAAATT-AAA
*
19679899 TTTAAAGTAAA
1 TTTAAATTAAA
19679910 TTTAAATTTAAA
1 TTTAAA-TTAAA
* *
19679922 -ATAAATTTAA
1 TTTAAATTAAA
**
19679932 GATAAATTTAAA
1 TTTAAA-TTAAA
*
19679944 TTTAAAAATAAA
1 TTT-AAATTAAA
19679956 TTTAAA
1 TTTAAA
19679962 ACCAATTTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
10 11 0.18
11 24 0.40
12 22 0.37
13 3 0.05
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.40
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:19679902 original size:22 final size:22
Alignment explanation
Indices: 19679859--19679949 Score: 69
Period size: 22 Copynumber: 4.1 Consensus size: 22
19679849 TCTTTCATCT
* * * *
19679859 AATTAAGTTTAATACAATTTTA
1 AATTAAATTAAATTCAAATTTA
19679881 AATTAAATTAAATTCAAATTTA
1 AATTAAATTAAATTCAAATTTA
* * *
19679903 AAGTAAATTTAAATTTAAA-ATA
1 AATTAAA-TTAAATTCAAATTTA
*
19679925 AATTTAAGA-TAAATTTAAATTTA
1 AA-TTAA-ATTAAATTCAAATTTA
19679948 AA
1 AA
19679950 AATAAATTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
22 38 0.68
23 17 0.30
24 1 0.02
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (22 bp):
AATTAAATTAAATTCAAATTTA
Found at i:19679915 original size:6 final size:6
Alignment explanation
Indices: 19679877--19679961 Score: 74
Period size: 6 Copynumber: 15.0 Consensus size: 6
19679867 TTAATACAAT
* *
19679877 TTTAAA -TTAAA -TTAAA TTCAAA TTTAAA -GTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* **
19679922 -ATAAA TTTAAGA --TAAA TTTAAA TTTAAA AATAAA TTTAAA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
19679962 ACCAATTTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
4 1 0.02
5 21 0.33
6 40 0.63
7 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.40
Consensus pattern (6 bp):
TTTAAA
Found at i:19679927 original size:28 final size:29
Alignment explanation
Indices: 19679879--19679961 Score: 111
Period size: 28 Copynumber: 2.9 Consensus size: 29
19679869 AATACAATTT
*
19679879 TAAA-TTAAA-TTAAATTCAAATTTAAAG-
1 TAAATTTAAATTTAAAAT-AAATTTAAAGA
19679906 TAAATTTAAATTTAAAATAAATTT-AAGA
1 TAAATTTAAATTTAAAATAAATTTAAAGA
19679934 TAAATTTAAATTTAAAAATAAATTTAAA
1 TAAATTTAAATTT-AAAATAAATTTAAA
19679962 ACCAATTTAA
Statistics
Matches: 50, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
27 7 0.14
28 24 0.48
29 17 0.34
30 2 0.04
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (29 bp):
TAAATTTAAATTTAAAATAAATTTAAAGA
Found at i:19679968 original size:29 final size:28
Alignment explanation
Indices: 19679883--19679972 Score: 101
Period size: 29 Copynumber: 3.2 Consensus size: 28
19679873 CAATTTTAAA
* **
19679883 TTAAA-TTAAATTCAAATTTAAAGTAAAT
1 TTAAATTTAAAAT-AAATTTAAAACAAAT
* *
19679911 TTAAATTTAAAATAAATTTAAGATAAAT
1 TTAAATTTAAAATAAATTTAAAACAAAT
*
19679939 TTAAATTTAAAAATAAATTTAAAACCAAT
1 TTAAATTT-AAAATAAATTTAAAACAAAT
19679968 TTAAA
1 TTAAA
19679973 CCTCAATTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 3
0.86 0.10 0.05
Matches are distributed among these distances:
28 26 0.48
29 28 0.52
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (28 bp):
TTAAATTTAAAATAAATTTAAAACAAAT
Found at i:19689223 original size:29 final size:29
Alignment explanation
Indices: 19689191--19689499 Score: 150
Period size: 29 Copynumber: 10.5 Consensus size: 29
19689181 CTTCCGAGGG
*
19689191 TAAAAATGGAATTTTGGTGAAACTGGGGT
1 TAAAAATGGAATTTTGGTGAAATTGGGGT
19689220 TAAAAAT-GATATTTT-G-GAAAGTTCGAGGG-
1 TAAAAATGGA-ATTTTGGTGAAA-TT-G-GGGT
19689249 T-AAAATGGTAATTTTTGGTGAAATTGGGGT
1 TAAAAATGG-AA-TTTTGGTGAAATTGGGGT
* * * *
19689279 CAAAAATGGGATTTT--AGAAAGTTTGGGGG
1 TAAAAATGGAATTTTGGTGAAA--TTGGGGT
* * *
19689308 T-AAAATGGGGATTTTTGGTGAAACTGGAGT
1 TAAAAAT--GGAATTTTGGTGAAATTGGGGT
*
19689338 TAAAAATGGGATTTT-G-GAAAGTTTAGGGG-
1 TAAAAATGGAATTTTGGTGAAA--TT-GGGGT
* *
19689367 T-AAAATGGTGATTTTTTGTGAAATTGGGGT
1 TAAAAAT-G-GAATTTTGGTGAAATTGGGGT
* *
19689397 CAAAAAAGGAATTTT-G-GAAAGTTTAGGGG-
1 TAAAAATGGAATTTTGGTGAAA--TT-GGGGT
19689426 T-AAAATGGTAATTTTTGGTGAAATTGGGGT
1 TAAAAATGG-AA-TTTTGGTGAAATTGGGGT
* * *
19689456 TAAAAAAGGAATTTTGG-GAAGTTTGGGGA
1 TAAAAATGGAATTTTGGTGAA-ATTGGGGT
19689485 T-AAAATGGTAATTTT
1 TAAAAATGG-AATTTT
19689500 TAGAAGTTTC
Statistics
Matches: 215, Mismatches: 27, Indels: 76
0.68 0.08 0.24
Matches are distributed among these distances:
27 16 0.07
28 36 0.17
29 75 0.35
30 45 0.21
31 27 0.13
32 16 0.07
ACGTcount: A:0.34, C:0.02, G:0.31, T:0.34
Consensus pattern (29 bp):
TAAAAATGGAATTTTGGTGAAATTGGGGT
Found at i:19689285 original size:59 final size:57
Alignment explanation
Indices: 19689186--19689500 Score: 330
Period size: 59 Copynumber: 5.4 Consensus size: 57
19689176 TTTTACTTCC
* *
19689186 GAGGGTAAAAATGG-AA-TTTTGGTGAAACTGGGGTTAAAAATGATATTTTGGAAAGTT
1 GAGGGT-AAAATGGTAATTTTTGGTGAAATTGGGGTCAAAAATGA-ATTTTGGAAAGTT
* *
19689243 CGAGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTCAAAAATGGGATTTTAGAAAGTTT
1 -GAGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTCAAAAAT-GAATTTTGGAAAG-TT
* ** * * * *
19689303 GGGGGTAAAATGGGGATTTTTGGTGAAACTGGAGTTAAAAATGGGATTTTGGAAAGTT
1 GAGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTCAAAAAT-GAATTTTGGAAAGTT
* * * *
19689361 TAGGGGTAAAATGGTGATTTTTTGTGAAATTGGGGTCAAAAAAGGAATTTTGGAAAGTT
1 GA-GGGTAAAATGGTAATTTTTGGTGAAATTGGGGTC-AAAAATGAATTTTGGAAAGTT
* * * *
19689420 TAGGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAAAGGAATTTTGGGAAGTTT
1 GA-GGGTAAAATGGTAATTTTTGGTGAAATTGGGG-TCAAAAATGAATTTTGGAAAG-TT
19689480 G-GGGATAAAATGGTAATTTTT
1 GAGGG-TAAAATGGTAATTTTT
19689501 AGAAGTTTCA
Statistics
Matches: 223, Mismatches: 25, Indels: 17
0.84 0.09 0.06
Matches are distributed among these distances:
57 7 0.03
58 13 0.06
59 192 0.86
60 11 0.05
ACGTcount: A:0.34, C:0.02, G:0.31, T:0.33
Consensus pattern (57 bp):
GAGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTCAAAAATGAATTTTGGAAAGTT
Found at i:19689519 original size:118 final size:115
Alignment explanation
Indices: 19689188--19689500 Score: 414
Period size: 118 Copynumber: 2.7 Consensus size: 115
19689178 TTACTTCCGA
* *
19689188 GGGTAAAAATGGAA-TTTTGGTGAAACTGGGGTT-AAAAATGATATTTTGGAAAGTTCGAGGGTA
1 GGGT-AAAATGGAATTTTTGGTGAAACTGGGGTTAAAAAAGGA-ATTTTGGAAAGTTTG-GGGTA
* * *
19689251 AAATGGTAATTTTTGGTGAAATTGGGGTCAAAAATGGGATTTTAGAAAGTTTGG
63 AAATGGTAATTTTT-GTGAAATTGGGGTCAAAAATGGAATTTTGGAAAGTTTAG
* * * *
19689305 GGGTAAAATGGGGATTTTTGGTGAAACTGGAGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAA
1 GGGTAAAAT-GGAATTTTTGGTGAAACTGGGGTTAAAAAAGGAATTTTGGAAAGTTT-GGGGTAA
* *
19689370 AATGGTGATTTTTTGTGAAATTGGGGTCAAAAAAGGAATTTTGGAAAGTTTAG
64 AATGGT-AATTTTTGTGAAATTGGGGTCAAAAATGGAATTTTGGAAAGTTTAG
* *
19689423 GGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAAAGGAATTTTGGGAAGTTTGGGGATAA
1 GGGTAAAATGG-AATTTTTGGTGAAACTGGGGTTAAAAAAGGAATTTTGGAAAGTTTGGGG-TAA
19689488 AATGGTAATTTTT
64 AATGGTAATTTTT
19689501 AGAAGTTTCA
Statistics
Matches: 171, Mismatches: 18, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
116 5 0.03
117 19 0.11
118 135 0.79
119 12 0.07
ACGTcount: A:0.34, C:0.02, G:0.31, T:0.34
Consensus pattern (115 bp):
GGGTAAAATGGAATTTTTGGTGAAACTGGGGTTAAAAAAGGAATTTTGGAAAGTTTGGGGTAAAA
TGGTAATTTTTGTGAAATTGGGGTCAAAAATGGAATTTTGGAAAGTTTAG
Found at i:19689538 original size:58 final size:57
Alignment explanation
Indices: 19689217--19689538 Score: 236
Period size: 59 Copynumber: 5.5 Consensus size: 57
19689207 GTGAAACTGG
* * * * **
19689217 GGTT-AAAAATGATATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAAATTGG
1 GGTTAAAAAAGGA-ATTTTGGGAAGTTTG-GGGTAAAATGGTAATTTTT-GAGAAATTCA
* * * * * ** * * *
19689276 GGTCAAAAATGGGATTTTAGAAAGTTTGGGGGTAAAATGGGGATTTTTGGTGAAACT-G
1 GGTTAAAAAAGGAATTTTGGGAAGTTT-GGGGTAAAATGGTAATTTTT-GAGAAATTCA
* * * * * **
19689334 GAGTTAAAAATGGGATTTTGGAAAGTTTAGGGGTAAAATGGTGATTTTTTGTGAAATTGG
1 G-GTTAAAAAAGGAATTTTGGGAAGTTT-GGGGTAAAATGGT-AATTTTTGAGAAATTCA
* * * **
19689394 GGTCAAAAAAGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGTGAAATTGG
1 GGTTAAAAAAGGAATTTTGGGAAGTTT-GGGGTAAAATGGTAATTTTT-GAGAAATTCA
*
19689453 GGTTAAAAAAGGAATTTTGGGAAGTTTGGGGATAAAATGGTAATTTTT-AGAAGTTTCA
1 GGTTAAAAAAGGAATTTTGGGAAGTTTGGGG-TAAAATGGTAATTTTTGAGAA-ATTCA
* *
19689511 GGTTCAAAATGGAATTTTGGGAAGTTTG
1 GGTTAAAAAAGGAATTTTGGGAAGTTTG
19689539 AGGACTAGAG
Statistics
Matches: 227, Mismatches: 28, Indels: 17
0.83 0.10 0.06
Matches are distributed among these distances:
57 3 0.01
58 40 0.18
59 171 0.75
60 13 0.06
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.34
Consensus pattern (57 bp):
GGTTAAAAAAGGAATTTTGGGAAGTTTGGGGTAAAATGGTAATTTTTGAGAAATTCA
Found at i:19690529 original size:20 final size:20
Alignment explanation
Indices: 19690504--19690545 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
19690494 TTTTTTTCTT
19690504 TTTATTAAAAATTAATATTA
1 TTTATTAAAAATTAATATTA
* * *
19690524 TTTATTAATATTTATTATTA
1 TTTATTAAAAATTAATATTA
19690544 TT
1 TT
19690546 ACCGTTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTATTAAAAATTAATATTA
Found at i:19691346 original size:6 final size:6
Alignment explanation
Indices: 19691337--19691413 Score: 62
Period size: 6 Copynumber: 14.0 Consensus size: 6
19691327 TTAATACAAT
* *
19691337 TTTAAA TTT-AA -TTAAA TTCAAA TTTAAA -GTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
19691382 -ATAAA --TAAA TTTAAA TTTAAGA --TAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA
19691414 ACCAATTTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
4 7 0.12
5 15 0.26
6 35 0.60
7 1 0.02
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:19691354 original size:17 final size:15
Alignment explanation
Indices: 19691321--19691380 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 15
19691311 TTTCATCTAA
*
19691321 TTAAGTTTAATACAATT
1 TTAAATTTAATA-AA-T
19691338 TTAAATTTAATTAAAT
1 TTAAATTTAA-TAAAT
*
19691354 TCAAATTTAAAGTAAAT
1 TTAAATTT-AA-TAAAT
19691371 TTAAATTTAA
1 TTAAATTTAA
19691381 AATAAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
16 10 0.27
17 25 0.68
18 2 0.05
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (15 bp):
TTAAATTTAATAAAT
Found at i:19691360 original size:11 final size:11
Alignment explanation
Indices: 19691337--19691398 Score: 58
Period size: 11 Copynumber: 5.7 Consensus size: 11
19691327 TTAATACAAT
*
19691337 TTTAAATTTAA
1 TTTAAATTAAA
19691348 -TTAAATTCAAA
1 TTTAAATT-AAA
*
19691359 TTTAAAGTAAA
1 TTTAAATTAAA
19691370 TTTAAATTTAAA
1 TTTAAA-TTAAA
*
19691382 -ATAAA-TAAA
1 TTTAAATTAAA
19691391 TTTAAATT
1 TTTAAATT
19691399 TAAGATAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
9 4 0.10
10 11 0.27
11 16 0.39
12 10 0.24
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:19691381 original size:17 final size:17
Alignment explanation
Indices: 19691337--19691413 Score: 75
Period size: 17 Copynumber: 4.4 Consensus size: 17
19691327 TTAATACAAT
*
19691337 TTTAAATTT-AATTAAA
1 TTTAAATTTAAAATAAA
* *
19691353 TTCAAATTTAAAGTAAA
1 TTTAAATTTAAAATAAA
19691370 TTTAAATTTAAAATAAATAAA
1 TTTAAATTT---A-AAATAAA
*
19691391 TTTAAATTTAAGATAAA
1 TTTAAATTTAAAATAAA
19691408 TTTAAA
1 TTTAAA
19691414 ACCAATTTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
16 8 0.16
17 26 0.51
18 1 0.02
20 1 0.02
21 15 0.29
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:19691392 original size:21 final size:21
Alignment explanation
Indices: 19691361--19691408 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
19691351 AATTCAAATT
19691361 TAAAGTAAATTTAAATTTAAAA
1 TAAA-TAAATTTAAATTTAAAA
*
19691383 TAAATAAATTTAAATTTAAGA
1 TAAATAAATTTAAATTTAAAA
19691404 TAAAT
1 TAAAT
19691409 TTAAAACCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (21 bp):
TAAATAAATTTAAATTTAAAA
Found at i:19693283 original size:51 final size:51
Alignment explanation
Indices: 19693223--19693325 Score: 161
Period size: 51 Copynumber: 2.0 Consensus size: 51
19693213 CTAAGCTAAA
* *
19693223 TTAAATTACATAAACAACAACCAAAATTAATCATTAGTCCCAAGCATAATG
1 TTAAATTACATAAACAACAACAAAAATTAATCATTAGTCCAAAGCATAATG
** *
19693274 TTAAATTACATAAACAACAACAAAAATTGGTCATTAGTTCAAAGCATAATG
1 TTAAATTACATAAACAACAACAAAAATTAATCATTAGTCCAAAGCATAATG
19693325 T
1 T
19693326 ATATCAAGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 47 1.00
ACGTcount: A:0.49, C:0.17, G:0.08, T:0.27
Consensus pattern (51 bp):
TTAAATTACATAAACAACAACAAAAATTAATCATTAGTCCAAAGCATAATG
Found at i:19696209 original size:26 final size:26
Alignment explanation
Indices: 19696154--19696209 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
19696144 CAATTAACTT
* * *
19696154 ATTTATTATCAAATAAATATTTACTT
1 ATTTATTATCAAATAAATAATGACTC
*
19696180 ATTTATTATCAAATAAGTAAATGA-TC
1 ATTTATTATCAAATAAAT-AATGACTC
19696206 ATTT
1 ATTT
19696210 TAAAAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 22 0.88
27 3 0.12
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (26 bp):
ATTTATTATCAAATAAATAATGACTC
Found at i:19712185 original size:42 final size:42
Alignment explanation
Indices: 19712103--19712226 Score: 117
Period size: 42 Copynumber: 2.9 Consensus size: 42
19712093 AAGGAGGAAG
19712103 TTTTGACAGTTTATCTACACTACTGGTGGATTGTCCACATAT
1 TTTTGACAGTTTATCTACACTACTGGTGGATTGTCCACATAT
* * * *
19712145 TTTTGGCAGTTTATCTGCA-TATCTGGTGGTTTG-CTTACATAT
1 TTTTGACAGTTTATCTACACTA-CTGGTGGATTGTC-CACATAT
* * * * * *
19712187 CTATGATAGTTTATCTACAAATACTAGTGGCTTGTCCACA
1 TTTTGACAGTTTATCTAC-ACTACTGGTGGATTGTCCACA
19712227 ACGCGGTGTG
Statistics
Matches: 65, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
41 3 0.05
42 46 0.71
43 13 0.20
44 3 0.05
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (42 bp):
TTTTGACAGTTTATCTACACTACTGGTGGATTGTCCACATAT
Found at i:19713029 original size:24 final size:24
Alignment explanation
Indices: 19712992--19713055 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
19712982 TGTTCAACCT
*
19712992 TTCACCTTTTATCTCCCTTAACAT-
1 TTCACCTTTCATCTCCCTTAAC-TC
* *
19713016 TTTACCTTTCATCTTCCTTAACTC
1 TTCACCTTTCATCTCCCTTAACTC
19713040 TTCACCTTTCATCTCC
1 TTCACCTTTCATCTCC
19713056 TTGTAAACTC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 1 0.03
24 33 0.97
ACGTcount: A:0.17, C:0.36, G:0.00, T:0.47
Consensus pattern (24 bp):
TTCACCTTTCATCTCCCTTAACTC
Found at i:19716383 original size:25 final size:27
Alignment explanation
Indices: 19716355--19716413 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
19716345 AAAGCTACCT
*
19716355 AAATAACTTTGCCAC-TAGG-TTTTCC
1 AAATAACTATGCCACGTAGGTTTTTCC
* *
19716380 AAATAA-TATGTCACGTAGGTTTTTTC
1 AAATAACTATGCCACGTAGGTTTTTCC
19716406 AAATAACT
1 AAATAACT
19716414 CACCATTTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 6 0.21
25 10 0.36
26 11 0.39
27 1 0.04
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (27 bp):
AAATAACTATGCCACGTAGGTTTTTCC
Found at i:19716476 original size:50 final size:50
Alignment explanation
Indices: 19716375--19716525 Score: 142
Period size: 50 Copynumber: 3.0 Consensus size: 50
19716365 GCCACTAGGT
* * ** * ***
19716375 TTTCCAAATAATATGTCACGTAGGTTTTTTCAAATAACTCACCA-TTTGGC
1 TTTCCAAAAAATATGTCACATAGG-CCTTTCAAATAACTCGCCACAAAGGC
19716425 TTTCCAAAAAATATGTCACATAGGCCTTTCAAATAACTCGCCACAAAGGC
1 TTTCCAAAAAATATGTCACATAGGCCTTTCAAATAACTCGCCACAAAGGC
* * * * * * * *
19716475 TTTCTAGACAATATGCCATATAGGCCTTTTAGATAACTTGCCACAAAGGC
1 TTTCCAAAAAATATGTCACATAGGCCTTTCAAATAACTCGCCACAAAGGC
19716525 T
1 T
19716526 CTGTTTGGTT
Statistics
Matches: 84, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
49 16 0.19
50 68 0.81
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (50 bp):
TTTCCAAAAAATATGTCACATAGGCCTTTCAAATAACTCGCCACAAAGGC
Found at i:19716492 original size:25 final size:24
Alignment explanation
Indices: 19716459--19716525 Score: 64
Period size: 25 Copynumber: 2.7 Consensus size: 24
19716449 CCTTTCAAAT
*
19716459 AACTCGCCACAAAGGCTTTCTAGAC
1 AACTTGCCACAAAGGCTTT-TAGAC
* * *
19716484 AA-TATGCCATATAGGCCTTTTAGAT
1 AACT-TGCCACAAAGG-CTTTTAGAC
19716509 AACTTGCCACAAAGGCT
1 AACTTGCCACAAAGGCT
19716526 CTGTTTGGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
24 3 0.09
25 25 0.76
26 5 0.15
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (24 bp):
AACTTGCCACAAAGGCTTTTAGAC
Found at i:19719467 original size:23 final size:25
Alignment explanation
Indices: 19719437--19719490 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
19719427 CAGAATTCAG
19719437 AATATCGC-C-CACGAGCCAGACAA
1 AATATCGCTCTCACGAGCCAGACAA
* * *
19719460 AATATCGCTCTTACGAGCTAGACAG
1 AATATCGCTCTCACGAGCCAGACAA
19719485 AATATC
1 AATATC
19719491 TTCATCGTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 8 0.31
24 1 0.04
25 17 0.65
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.19
Consensus pattern (25 bp):
AATATCGCTCTCACGAGCCAGACAA
Found at i:19722576 original size:30 final size:30
Alignment explanation
Indices: 19722540--19722621 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 30
19722530 TTATAAGTTA
19722540 TTTTTTTATCAATTTTTAAGGGTCCCAAATT
1 TTTTTTTATCAATTTTTAAGGG-CCCAAATT
* * *
19722571 TTTTTTTTTTAGTTTTTAAGGGCCCAAATTT
1 TTTTTTTATCAATTTTTAAGGGCCCAAA-TT
*
19722602 ATTGTTTTTATCAACTTTTA
1 -TT-TTTTTATCAATTTTTA
19722622 GAAGACCTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
30 6 0.15
31 21 0.51
32 2 0.05
33 12 0.29
ACGTcount: A:0.23, C:0.11, G:0.10, T:0.56
Consensus pattern (30 bp):
TTTTTTTATCAATTTTTAAGGGCCCAAATT
Found at i:19722587 original size:31 final size:30
Alignment explanation
Indices: 19722552--19722611 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
19722542 TTTTTATCAA
* *
19722552 TTTTTAAGGGTCCCAAATTTTTTTTTTTTAG
1 TTTTTAAGGG-CCCAAATTTATTGTTTTTAG
19722583 TTTTTAAGGGCCCAAATTTATTGTTTTTA
1 TTTTTAAGGGCCCAAATTTATTGTTTTTA
19722612 TCAACTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 17 0.63
31 10 0.37
ACGTcount: A:0.22, C:0.10, G:0.13, T:0.55
Consensus pattern (30 bp):
TTTTTAAGGGCCCAAATTTATTGTTTTTAG
Found at i:19723601 original size:19 final size:20
Alignment explanation
Indices: 19723568--19723627 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 20
19723558 TCTCAACAAA
19723568 AATTATAAAATAATTCAAAAT
1 AATTATAAAA-AATTCAAAAT
*
19723589 AATT-TCAAAAATTTC-AAAT
1 AATTAT-AAAAAATTCAAAAT
*
19723608 ATTTATAAAAAATTCAAAAT
1 AATTATAAAAAATTCAAAAT
19723628 TGATATTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 15 0.45
20 10 0.30
21 8 0.24
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (20 bp):
AATTATAAAAAATTCAAAAT
Found at i:19727221 original size:45 final size:45
Alignment explanation
Indices: 19727120--19727271 Score: 173
Period size: 45 Copynumber: 3.4 Consensus size: 45
19727110 AGCATCAAGA
* * * * * * *
19727120 AAACTTCTTGTTTCCTATATCTATATCCTGTTT--GACACCAAGG
1 AAACTTCTTGTTTCCTGTATCCATAGCATGTTTCCGGCTCCAGGG
* * * *
19727163 AAGCTCCTTGTTTCCTGTATCCGTAGCATGTTTCCGGCTCCATGG
1 AAACTTCTTGTTTCCTGTATCCATAGCATGTTTCCGGCTCCAGGG
* *
19727208 AAACTTCTTGTTTCCTGTATCCATAGCCTGTTTCCGGCTTCAGGG
1 AAACTTCTTGTTTCCTGTATCCATAGCATGTTTCCGGCTCCAGGG
19727253 AAACTTCTTGTTTCCTGTA
1 AAACTTCTTGTTTCCTGTA
19727272 CATGTAGTTT
Statistics
Matches: 91, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
43 26 0.29
45 65 0.71
ACGTcount: A:0.18, C:0.26, G:0.17, T:0.39
Consensus pattern (45 bp):
AAACTTCTTGTTTCCTGTATCCATAGCATGTTTCCGGCTCCAGGG
Found at i:19729474 original size:12 final size:12
Alignment explanation
Indices: 19729459--19729522 Score: 83
Period size: 12 Copynumber: 5.3 Consensus size: 12
19729449 AACAACAAAT
*
19729459 AACAAGAATAGC
1 AACAAAAATAGC
*
19729471 AACAAGAATAGC
1 AACAAAAATAGC
*
19729483 AACAAAAATAAC
1 AACAAAAATAGC
*
19729495 AGCAAAAATAGC
1 AACAAAAATAGC
*
19729507 AACAAAAATAAC
1 AACAAAAATAGC
19729519 AACA
1 AACA
19729523 TCAAAACAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.66, C:0.17, G:0.09, T:0.08
Consensus pattern (12 bp):
AACAAAAATAGC
Found at i:19729487 original size:24 final size:24
Alignment explanation
Indices: 19729459--19729522 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
19729449 AACAACAAAT
* * *
19729459 AACAAGAATAGCAACAAGAATAGC
1 AACAAAAATAACAACAAAAATAGC
*
19729483 AACAAAAATAACAGCAAAAATAGC
1 AACAAAAATAACAACAAAAATAGC
19729507 AACAAAAATAACAACA
1 AACAAAAATAACAACA
19729523 TCAAAACAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.66, C:0.17, G:0.09, T:0.08
Consensus pattern (24 bp):
AACAAAAATAACAACAAAAATAGC
Found at i:19729538 original size:25 final size:22
Alignment explanation
Indices: 19729510--19729561 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
19729500 AAATAGCAAC
*
19729510 AAAAATAACAACATCAAAACAAT
1 AAAAA-AATAACATCAAAACAAT
* *
19729533 AAAAAAATAGCATCAAAACAGT
1 AAAAAAATAACATCAAAACAAT
19729555 AAAAAAA
1 AAAAAAA
19729562 CCGAAACAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.71, C:0.13, G:0.04, T:0.12
Consensus pattern (22 bp):
AAAAAAATAACATCAAAACAAT
Found at i:19729594 original size:22 final size:22
Alignment explanation
Indices: 19729560--19729621 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
19729550 ACAGTAAAAA
*
19729560 AACCGAAACAGTAAAATAACAAC
1 AACCAAAACAGTAAAA-AACAAC
* *
19729583 -ACCAAAATAGTAAAAAACAGC
1 AACCAAAACAGTAAAAAACAAC
19729604 AACCAAAACAGTAAAAAA
1 AACCAAAACAGTAAAAAA
19729622 AAAAAAAGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 5 0.15
22 29 0.85
ACGTcount: A:0.65, C:0.19, G:0.08, T:0.08
Consensus pattern (22 bp):
AACCAAAACAGTAAAAAACAAC
Found at i:19731148 original size:2 final size:2
Alignment explanation
Indices: 19731143--19731168 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19731133 CCACCCTTAA
19731143 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
19731169 TTAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19732475 original size:36 final size:36
Alignment explanation
Indices: 19732423--19732494 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
19732413 AAAGTTAAGG
19732423 TAGTGGAGTAGACATTTGGGGCTAAACCACTCTAAA
1 TAGTGGAGTAGACATTTGGGGCTAAACCACTCTAAA
* *
19732459 TAGTGGAGTGGGCATTTGGGGCTAAACCACTCTAAA
1 TAGTGGAGTAGACATTTGGGGCTAAACCACTCTAAA
19732495 CTCTTTGTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (36 bp):
TAGTGGAGTAGACATTTGGGGCTAAACCACTCTAAA
Found at i:19735224 original size:19 final size:19
Alignment explanation
Indices: 19735200--19735237 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
19735190 TGGTTAAGTG
19735200 TTAGTGAATTTGTCATTGA
1 TTAGTGAATTTGTCATTGA
19735219 TTAGTGAATTTGTCATTGA
1 TTAGTGAATTTGTCATTGA
19735238 AACCCAAGTT
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:0.26, C:0.05, G:0.21, T:0.47
Consensus pattern (19 bp):
TTAGTGAATTTGTCATTGA
Found at i:19736558 original size:17 final size:18
Alignment explanation
Indices: 19736526--19736559 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19736516 ATTTATTAAG
*
19736526 AATTTATTATATATTTTA
1 AATTTATTAAATATTTTA
19736544 AATTT-TTAAATATTTT
1 AATTTATTAAATATTTT
19736560 TTAATATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
AATTTATTAAATATTTTA
Found at i:19753833 original size:14 final size:16
Alignment explanation
Indices: 19753803--19753834 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
19753793 TTTACACTCG
19753803 AATTAAACTATTAAAC
1 AATTAAACTATTAAAC
19753819 AATTAAA-TA-TAAAC
1 AATTAAACTATTAAAC
19753833 AA
1 AA
19753835 AATAGGTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (16 bp):
AATTAAACTATTAAAC
Found at i:19758802 original size:15 final size:15
Alignment explanation
Indices: 19758782--19758838 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
19758772 ATTCAGTAGT
19758782 AATATTTTAATAATA
1 AATATTTTAATAATA
*
19758797 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
19758816 AATATATTAATAATA
1 AATATTTTAATAATA
19758831 AATATTTT
1 AATATTTT
19758839 GTAGTATGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:19760935 original size:30 final size:30
Alignment explanation
Indices: 19760899--19761178 Score: 120
Period size: 30 Copynumber: 9.5 Consensus size: 30
19760889 TCTCGATGGC
*
19760899 AAAAATGTAATTTTAGGAAAATTCGGGGTT
1 AAAAATGTAATTTTAGGAAAATTTGGGGTT
* * *
19760929 AAAAATGGAATCTT-GGAAATTTTAGGGG-T
1 AAAAATGTAATTTTAGGAAAATTT-GGGGTT
* * * *
19760958 -AAAATGGTAATTTTTGGTGAAA-TCGAGGTT
1 AAAAAT-GTAATTTTAGG-AAAATTTGGGGTT
** * *
19760988 AAAAATGGGATTTT-GGAAAGTTTGGGGGT
1 AAAAATGTAATTTTAGGAAAATTTGGGGTT
* * *
19761017 -AAAATGGTAATTTTTGGTGAAA-TTAGGGTT
1 AAAAAT-GTAATTTTAGG-AAAATTTGGGGTT
** * * * *
19761047 AAAAATGGGATTTT-GGAAAGTTAGGAGCT
1 AAAAATGTAATTTTAGGAAAATTTGGGGTT
*
19761076 -AAAATAGTAATTTTAGGTAAAA-TTAGGGTT
1 AAAAAT-GTAATTTTAGG-AAAATTTGGGGTT
** *
19761106 AAAAATGGGATTTTA-GAAAGTTTGAGGG-T
1 AAAAATGTAATTTTAGGAAAATTTG-GGGTT
* **
19761135 -AAAATAGTAATTTTTGGAAGTTTTGGGG-T
1 AAAAAT-GTAATTTTAGGAAAATTTGGGGTT
*
19761164 CAAAATGTAATTTTA
1 AAAAATGTAATTTTA
19761179 TGAAGTTTTG
Statistics
Matches: 181, Mismatches: 48, Indels: 43
0.67 0.18 0.16
Matches are distributed among these distances:
28 27 0.15
29 64 0.35
30 68 0.38
31 22 0.12
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.35
Consensus pattern (30 bp):
AAAAATGTAATTTTAGGAAAATTTGGGGTT
Found at i:19760969 original size:59 final size:59
Alignment explanation
Indices: 19760900--19761151 Score: 307
Period size: 59 Copynumber: 4.3 Consensus size: 59
19760890 CTCGATGGCA
* * * * *
19760900 AAAAT-GTAATTTTAGG-AAAATTCGGGGTTAAAAATGGAATCTTGGAAATTTTAGGGGT
1 AAAATAGTAATTTTTGGTAAAATT-AGGGTTAAAAATGGGATTTTGGAAAGTTTAGGGGT
* * * *
19760958 AAAATGGTAATTTTTGGTGAAA-TCGAGGTTAAAAATGGGATTTTGGAAAGTTTGGGGGT
1 AAAATAGTAATTTTTGGTAAAATTAG-GGTTAAAAATGGGATTTTGGAAAGTTTAGGGGT
* * *
19761017 AAAATGGTAATTTTTGGTGAAATTAGGGTTAAAAATGGGATTTTGGAAAG-TTAGGAGCT
1 AAAATAGTAATTTTTGGTAAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTTAGG-GGT
* *
19761076 AAAATAGTAATTTTAGGTAAAATTAGGGTTAAAAATGGGATTTTAGAAAGTTT-GAGGGT
1 AAAATAGTAATTTTTGGTAAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTTAG-GGGT
19761135 AAAATAGTAATTTTTGG
1 AAAATAGTAATTTTTGG
19761152 AAGTTTTGGG
Statistics
Matches: 171, Mismatches: 16, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
58 10 0.06
59 153 0.89
60 8 0.05
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (59 bp):
AAAATAGTAATTTTTGGTAAAATTAGGGTTAAAAATGGGATTTTGGAAAGTTTAGGGGT
Found at i:19761183 original size:29 final size:30
Alignment explanation
Indices: 19761126--19761209 Score: 95
Period size: 29 Copynumber: 2.8 Consensus size: 30
19761116 TTTTAGAAAG
19761126 TTTGAGGGT-AAAATAGTAATTTTTGGAAGT
1 TTTG-GGGTCAAAATAGTAATTTTTGGAAGT
19761156 TTTGGGGTCAAAAT-GTAATTTTAT-GAAGT
1 TTTGGGGTCAAAATAGTAATTTT-TGGAAGT
* *
19761185 TTTGGGATCATAAATA-TCATTTTTG
1 TTTGGGGTCA-AAATAGTAATTTTTG
19761210 AATAGTTTAG
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
29 27 0.57
30 20 0.43
ACGTcount: A:0.31, C:0.04, G:0.23, T:0.43
Consensus pattern (30 bp):
TTTGGGGTCAAAATAGTAATTTTTGGAAGT
Found at i:19762341 original size:28 final size:25
Alignment explanation
Indices: 19762291--19762352 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
19762281 TTTGTTTGTT
19762291 TTACTATTATTAATGATATTATTAA
1 TTACTATTATTAATGATATTATTAA
* *
19762316 TTACTATTATTTATGATATT-TTTA
1 TTACTATTATTAATGATATTATTAA
19762340 TTA--ATTATTAATG
1 TTACTATTATTAATG
19762353 TAATTTATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 9 0.26
24 6 0.18
25 19 0.56
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.56
Consensus pattern (25 bp):
TTACTATTATTAATGATATTATTAA
Found at i:19763173 original size:23 final size:22
Alignment explanation
Indices: 19763143--19763191 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
19763133 GTATTTGGAC
* *
19763143 ATTTAATTTATATTTATTTTAA
1 ATTTAATTTATATTAAGTTTAA
19763165 ATTTCAATTTATATTAAGTTTAA
1 ATTT-AATTTATATTAAGTTTAA
19763188 ATTT
1 ATTT
19763192 TGGAAAAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
ATTTAATTTATATTAAGTTTAA
Found at i:19763174 original size:17 final size:17
Alignment explanation
Indices: 19763147--19763191 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
19763137 TTGGACATTT
* *
19763147 AATTTATATTTATTTTA
1 AATTTAAATTTATATTA
*
19763164 AATTTCAATTTATATTA
1 AATTTAAATTTATATTA
*
19763181 AGTTTAAATTT
1 AATTTAAATTT
19763192 TGGAAAAACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (17 bp):
AATTTAAATTTATATTA
Found at i:19763880 original size:12 final size:12
Alignment explanation
Indices: 19763863--19763888 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19763853 TGTATCTCAT
19763863 CAGGAAACTAAC
1 CAGGAAACTAAC
19763875 CAGGAAACTAAC
1 CAGGAAACTAAC
19763887 CA
1 CA
19763889 TGTTATTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.27, G:0.15, T:0.08
Consensus pattern (12 bp):
CAGGAAACTAAC
Found at i:19764036 original size:196 final size:189
Alignment explanation
Indices: 19763875--19764585 Score: 822
Period size: 201 Copynumber: 3.6 Consensus size: 189
19763865 GGAAACTAAC
*
19763875 CAGGAAACTAACCATGTTATTGTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGA
1 CAGGAAGCTAACCATGTTATTGTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGA
19763940 AGATTTGCTCGCGTTGAGC-A-TT-G-A-GTATCTCATCAGGAAGATGACCGCCTCTGTTGTTTT
66 AGATTTGCTCGCGTTGAGCTAGTTGGTATGTATCTCATCAGGAAGATGACCGCCTCTGTTGTTTT
* * *
19764000 AATTTGCTTATCTGGATCTCCTTAGGAAGACAAATTTGGTCCACTTCTCTGTATCTCAT
131 AATTCGCTTCTCTGGATCTCCTCAGGAAGACAAATTTGGTCCACTTCTCTGTATCTCAT
* * *
19764059 CAGGAAACTAACCATGTTATTGTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGTTGGGTACGA
1 CAGGAAGCTAACCATGTTATTGTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGA
* * * *
19764124 AGATTTGCTCGCTTTGAGCGTTGATTTGGTATTCTTCTCTGTGTCTCATCAGGAAGATGACTGCC
66 AGATTTGCTCGCGTTGAGC--T-AGTTGGTA--------TGTATCTCATCAGGAAGATGACCGCC
* * *
19764189 TC-GCTTGTTTTAATTCGCTCCTTTGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTA
120 TCTG-TTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACAAATTTGGTCCACTTCTCTGTA
19764253 TCTCAT
184 TCTCAT
* * * *
19764259 CAGGAAGCTAACCATTTTATTGTTTCGGCCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACAA
1 CAGGAAGCTAACCATGTTATTGTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGA
* *
19764324 AGATTTGCTCGCTTTGAGCGTTTGAGTTGGTATTCTTCTCTGTATCTCATCAGGAAGATAACCGC
66 AGATTTGCTCGCGTTGAGC---T-AGTTGGTA--------TGTATCTCATCAGGAAGATGACCGC
* ** * * * *
19764389 ATCACTTGTTTTAATTCACTTCTCTGGATCTCCTTAGGAAGACGAATTTGGTCCACTTCTCTATA
119 CTCTGTTGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGACAAATTTGGTCCACTTCTCTGTA
19764454 TCTCAT
184 TCTCAT
* * *
19764460 CAGGAAGCTAACCATTTTATTGTTTTGACCTGCTTCTCAGTGTCTCATCAGGAAGCTTGGTTCGA
1 CAGGAAGCTAACCATGTTATTGTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGA
** *
19764525 AGATTTGCTCGTTTTGAGTGTTGAGTTGGTATCTGTATCTCATCAGGAAGATGACCGCCTC
66 AGATTTGCTCGCGTTGA--GCT-AGTTGGTA--TGTATCTCATCAGGAAGATGACCGCCTC
19764586 GCTGTCTTGT
Statistics
Matches: 469, Mismatches: 37, Indels: 32
0.87 0.07 0.06
Matches are distributed among these distances:
184 81 0.17
188 1 0.00
189 2 0.00
190 1 0.00
191 1 0.00
194 28 0.06
199 1 0.00
200 174 0.37
201 179 0.38
203 1 0.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (189 bp):
CAGGAAGCTAACCATGTTATTGTTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTTCGA
AGATTTGCTCGCGTTGAGCTAGTTGGTATGTATCTCATCAGGAAGATGACCGCCTCTGTTGTTTT
AATTCGCTTCTCTGGATCTCCTCAGGAAGACAAATTTGGTCCACTTCTCTGTATCTCAT
Found at i:19764238 original size:200 final size:200
Alignment explanation
Indices: 19763964--19764588 Score: 960
Period size: 201 Copynumber: 3.1 Consensus size: 200
19763954 TGAGCATTGA
* *
19763964 GTATCTCATCAGGAAGATGACCGCCTCTG-TTGTTTTAATTTGCTTATCTGGATCTCCTTAGGAA
1 GTATCTCATCAGGAAGATGACCGCCTC-GCTTGTTTTAATTCGCTTCTCTGGATCTCCTTAGGAA
* * *
19764028 GACAAATTTGGTCCACTTCTCTGTATCTCATCAGGAAACTAACCATGTTATTGTTTCGACCTGCT
65 GACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTGCT
*
19764093 TCTCAGTGTCTCATCAGGAAGTTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGATTTGGTATTC
130 TCTCAGTGTCTCATCAGGAAGTTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGAGTTGGTATTC
19764158 TTCTCT
195 TTCTCT
* * * * *
19764164 GTGTCTCATCAGGAAGATGACTGCCTCGCTTGTTTTAATTCGCTCCTTTGGATCTCCTCAGGAAG
1 GTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTCTCTGGATCTCCTTAGGAAG
*
19764229 ACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGGCCTGCTT
66 ACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTGCTT
* *
19764294 CTCAGTGTCTCATCAGGAAGCTGGGTACAAAGATTTGCTCGCTTTGAGCGTTTGAGTTGGTATTC
131 CTCAGTGTCTCATCAGGAAGTTGGGTACGAAGATTTGCTCGCTTTGAGCG-TTGAGTTGGTATTC
19764359 TTCTCT
195 TTCTCT
* * * *
19764365 GTATCTCATCAGGAAGATAACCGCATCACTTGTTTTAATTCACTTCTCTGGATCTCCTTAGGAAG
1 GTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTCTCTGGATCTCCTTAGGAAG
* *
19764430 ACGAATTTGGTCCACTTCTCTATATCTCATCAGGAAGCTAACCATTTTATTGTTTTGACCTGCTT
66 ACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTGCTT
* * *
19764495 CTCAGTGTCTCATCAGGAAGCTT-GGTTCGAAGATTTGCTCGTTTTGAGTGTTGAGTTGGTA---
131 CTCAGTGTCTCATCAGGAAG-TTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGAGTTGGTATTC
19764556 ---TCT
195 TTCTCT
19764559 GTATCTCATCAGGAAGATGACCGCCTCGCT
1 GTATCTCATCAGGAAGATGACCGCCTCGCT
19764589 GTCTTGTTAA
Statistics
Matches: 388, Mismatches: 34, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
194 30 0.08
199 1 0.00
200 176 0.45
201 180 0.46
202 1 0.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (200 bp):
GTATCTCATCAGGAAGATGACCGCCTCGCTTGTTTTAATTCGCTTCTCTGGATCTCCTTAGGAAG
ACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTGTTTCGACCTGCTT
CTCAGTGTCTCATCAGGAAGTTGGGTACGAAGATTTGCTCGCTTTGAGCGTTGAGTTGGTATTCT
TCTCT
Found at i:19776789 original size:28 final size:28
Alignment explanation
Indices: 19776758--19776858 Score: 84
Period size: 28 Copynumber: 3.5 Consensus size: 28
19776748 TTTGGTAAAA
*
19776758 TCGAGGTTAAAATGAGATTTTAGAAAGT
1 TCGAGGGTAAAATGAGATTTTAGAAAGT
19776786 TCGAGGGTAAAAT-AGTAATTTTAGGTGAAA-T
1 TCGAGGGTAAAATGAG--ATTTTA---GAAAGT
*
19776817 T-G-GGGTTAAAAATGGGATTTTAGAAAGT
1 TCGAGGG-T-AAAATGAGATTTTAGAAAGT
*
19776845 TCGGGGGTAAAATG
1 TCGAGGGTAAAATG
19776859 GTAATTTTTG
Statistics
Matches: 60, Mismatches: 2, Indels: 22
0.71 0.02 0.26
Matches are distributed among these distances:
27 6 0.10
28 20 0.33
29 11 0.18
30 11 0.18
31 7 0.12
32 5 0.08
ACGTcount: A:0.37, C:0.03, G:0.30, T:0.31
Consensus pattern (28 bp):
TCGAGGGTAAAATGAGATTTTAGAAAGT
Found at i:19776851 original size:117 final size:118
Alignment explanation
Indices: 19776696--19776925 Score: 322
Period size: 117 Copynumber: 2.0 Consensus size: 118
19776686 AATTTCGAGA
* * * *
19776696 AAATTCGGGGTTAAAATGGAATCTTGGAAAGTTTGGGGGTAAATTGGTAATTTTTGGTAAAATC-
1 AAATTCGGGGTTAAAATGGAATCTTAGAAAGTTCGGGGGTAAAATGGTAATTTTTGATAAAATCA
19776760 GAGGTT-AAAATGAGATTTTAGAAAGTTCGAGGGTAAAATAGTAATTTTAGGTG
66 G-GGTTAAAAATGAGATTTTAGAAAGTTCGAGGGTAAAATAGTAATTTTAGGTG
* *
19776813 AAATT-GGGGTTAAAAATGGGATTTTAGAAAGTTCGGGGGTAAAATGGTAATTTTTGATAAAATC
1 AAATTCGGGGTT-AAAATGGAATCTTAGAAAGTTCGGGGGTAAAATGGTAATTTTTGATAAAATC
* * * * *
19776877 AGGGTTAAAAATGGGATTTTGGAAAGTTCGGGGGTAAAGTGGTAATTTT
65 AGGGTTAAAAATGAGATTTTAGAAAGTTCGAGGGTAAAATAGTAATTTT
19776926 TGGAAGTTTC
Statistics
Matches: 99, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
116 6 0.06
117 55 0.56
118 38 0.38
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (118 bp):
AAATTCGGGGTTAAAATGGAATCTTAGAAAGTTCGGGGGTAAAATGGTAATTTTTGATAAAATCA
GGGTTAAAAATGAGATTTTAGAAAGTTCGAGGGTAAAATAGTAATTTTAGGTG
Found at i:19776852 original size:30 final size:30
Alignment explanation
Indices: 19776818--19776911 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
19776808 AGGTGAAATT
19776818 GGGGTTAAAAATGGGATTTTAGAAAGTTCG
1 GGGGTTAAAAATGGGATTTTAGAAAGTTCG
* * **
19776848 GGGG-T-AAAATGGTAATTTTTGATAAAATC-
1 GGGGTTAAAAATGG-GATTTTAGA-AAGTTCG
* *
19776877 AGGGTTAAAAATGGGATTTTGGAAAGTTCG
1 GGGGTTAAAAATGGGATTTTAGAAAGTTCG
19776907 GGGGT
1 GGGGT
19776912 AAAGTGGTAA
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
28 7 0.14
29 15 0.31
30 20 0.41
31 7 0.14
ACGTcount: A:0.33, C:0.03, G:0.33, T:0.31
Consensus pattern (30 bp):
GGGGTTAAAAATGGGATTTTAGAAAGTTCG
Found at i:19776853 original size:59 final size:58
Alignment explanation
Indices: 19776695--19776928 Score: 297
Period size: 59 Copynumber: 4.0 Consensus size: 58
19776685 TAATTTCGAG
* * * * *
19776695 AAAATTCGGGGTTAAAATGGAATCTTGGAAAGTTTGGGGGTAAATTGGTAATTTTTGGT
1 AAAA-TCGGGGTTAAAATGGGATTTTAGAAAGTTCGGGGGTAAAATGGTAATTTTTGGT
* * * * *
19776754 AAAATCGAGGTTAAAATGAGATTTTAGAAAGTTCGAGGGTAAAATAGTAATTTTAGGT
1 AAAATCGGGGTTAAAATGGGATTTTAGAAAGTTCGGGGGTAAAATGGTAATTTTTGGT
* * *
19776812 GAAATTGGGGTTAAAAATGGGATTTTAGAAAGTTCGGGGGTAAAATGGTAATTTTTGAT
1 AAAATCGGGGTT-AAAATGGGATTTTAGAAAGTTCGGGGGTAAAATGGTAATTTTTGGT
* * *
19776871 AAAATCAGGGTTAAAAATGGGATTTTGGAAAGTTCGGGGGTAAAGTGGTAATTTTTGG
1 AAAATCGGGGTT-AAAATGGGATTTTAGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
19776929 AAGTTTCAAG
Statistics
Matches: 150, Mismatches: 24, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
58 53 0.35
59 97 0.65
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (58 bp):
AAAATCGGGGTTAAAATGGGATTTTAGAAAGTTCGGGGGTAAAATGGTAATTTTTGGT
Found at i:19776932 original size:29 final size:29
Alignment explanation
Indices: 19776699--19776933 Score: 108
Period size: 29 Copynumber: 8.1 Consensus size: 29
19776689 TTCGAGAAAA
* *
19776699 TTCGGGGTTAAAATGG-AA-TCTTGGAAAG
1 TTCGGGGGTAAAATGGTAATTTTTGG-AAG
* * *
19776727 TTTGGGGGTAAATTGGTAATTTTTGGTAAA
1 TTCGGGGGTAAAATGGTAATTTTTGG-AAG
* * * * *
19776757 ATCGAGGTTAAAAT-G-AGATTTTAGAAAG
1 TTCGGGGGTAAAATGGTA-ATTTTTGGAAG
* * * *
19776785 TTCGAGGGTAAAATAGTAATTTTAGGTGAAA
1 TTCGGGGGTAAAATGGTAATTTT-TG-GAAG
* * * *
19776816 TT-GGGGTTAAAAATGG-GATTTTAGAAAG
1 TTCGGGGGT-AAAATGGTAATTTTTGGAAG
* *
19776844 TTCGGGGGTAAAATGGTAATTTTTGATAAA
1 TTCGGGGGTAAAATGGTAATTTTTG-GAAG
* * * *
19776874 ATCAGGGTTAAAAATGG-GA-TTTTGGAAAG
1 TTCGGGGGT-AAAATGGTAATTTTTGG-AAG
*
19776903 TTCGGGGGTAAAGTGGTAATTTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAG
19776932 TT
1 TT
19776934 TCAAGGTCAA
Statistics
Matches: 150, Mismatches: 42, Indels: 29
0.68 0.19 0.13
Matches are distributed among these distances:
28 45 0.30
29 46 0.31
30 42 0.28
31 17 0.11
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.34
Consensus pattern (29 bp):
TTCGGGGGTAAAATGGTAATTTTTGGAAG
Found at i:19778100 original size:25 final size:25
Alignment explanation
Indices: 19778071--19778133 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
19778061 TTTATTTGTT
19778071 TTACTATTATTAATGATATTATTAA
1 TTACTATTATTAATGATATTATTAA
* * *
19778096 TTACTATTATTTATGATATTTTTTA
1 TTACTATTATTAATGATATTATTAA
19778121 TTA--ATTATTAATG
1 TTACTATTATTAATG
19778134 TAATTTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 9 0.26
25 25 0.74
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (25 bp):
TTACTATTATTAATGATATTATTAA
Found at i:19778138 original size:12 final size:13
Alignment explanation
Indices: 19778075--19778135 Score: 51
Period size: 12 Copynumber: 5.0 Consensus size: 13
19778065 TTTGTTTTAC
19778075 TATTATTAATG-A
1 TATTATTAATGTA
19778087 TATTATTAAT-TA
1 TATTATTAATGTA
*
19778099 CTATTATTTATG-A
1 -TATTATTAATGTA
* *
19778112 TATTTTTTAT-TA
1 TATTATTAATGTA
19778124 -ATTATTAATGTA
1 TATTATTAATGTA
19778136 ATTTATTACC
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
11 7 0.17
12 23 0.57
13 10 0.25
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (13 bp):
TATTATTAATGTA
Found at i:19779423 original size:29 final size:30
Alignment explanation
Indices: 19779360--19779439 Score: 108
Period size: 29 Copynumber: 2.6 Consensus size: 30
19779350 ATACCAAAAC
* *
19779360 TATACACGAACTATGATTTAATGTGCAATTG
1 TATACATGAACTTTGATTT-ATGTGCAATTG
19779391 TATACATGAACTTTGATTT-TGTGCAATTG
1 TATACATGAACTTTGATTTATGTGCAATTG
*
19779420 TATACATGAAATTTTGATTT
1 TATACATG-AACTTTGATTT
19779440 GATTCAATTC
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
29 18 0.40
30 10 0.22
31 17 0.38
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (30 bp):
TATACATGAACTTTGATTTATGTGCAATTG
Found at i:19779665 original size:29 final size:30
Alignment explanation
Indices: 19779633--19779692 Score: 68
Period size: 31 Copynumber: 2.0 Consensus size: 30
19779623 TCACGTGTAT
* *
19779633 AATTGCAC-CAAATTAAAATTCATGTATAA
1 AATTACACACAAATCAAAATTCATGTATAA
* *
19779662 AATTACACATTAAATCAAAGTTCATGTATAA
1 AATTACACA-CAAATCAAAATTCATGTATAA
19779693 TTTTGAGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 7 0.28
31 18 0.72
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.32
Consensus pattern (30 bp):
AATTACACACAAATCAAAATTCATGTATAA
Found at i:19794028 original size:37 final size:37
Alignment explanation
Indices: 19793985--19794056 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
19793975 TGGCACTTTA
* *
19793985 ATGCATTTCATTTTGGAGTGTAGGTTGGATCACTTCG
1 ATGCATTTCATTTTGGAGTGTAGGTTAGAGCACTTCG
19794022 ATGCATTTCATTTTGGAGTGTAGGTTAGAGCACTT
1 ATGCATTTCATTTTGGAGTGTAGGTTAGAGCACTT
19794057 TAGTACGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.40
Consensus pattern (37 bp):
ATGCATTTCATTTTGGAGTGTAGGTTAGAGCACTTCG
Found at i:19805788 original size:24 final size:24
Alignment explanation
Indices: 19805772--19805822 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
19805762 AGTTTGACTT
19805772 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* *
19805796 AAACAAATAAATAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
19805820 AAA
1 AAA
19805823 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.57, C:0.08, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:19818190 original size:24 final size:24
Alignment explanation
Indices: 19818151--19818213 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
19818141 TAAACTAATA
* *
19818151 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
19818175 AGAGTTTAATTGAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
19818199 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
19818214 GGTTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:19819506 original size:3 final size:3
Alignment explanation
Indices: 19819498--19819530 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
19819488 GTGTAAAATA
19819498 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19819531 TAAGAAGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19819886 original size:13 final size:11
Alignment explanation
Indices: 19819858--19819900 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
19819848 AGTTAAATAT
19819858 TATTTTATTAA
1 TATTTTATTAA
19819869 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
19819882 TA-TTTATTAT
1 TATTTTATTAA
19819892 TATTTTATT
1 TATTTTATT
19819901 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:19819887 original size:23 final size:23
Alignment explanation
Indices: 19819861--19819904 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
19819851 TAAATATTAT
19819861 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
19819884 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
19819905 AAATGGTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:19820919 original size:26 final size:26
Alignment explanation
Indices: 19820885--19820938 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
19820875 CACCCAGGAA
*
19820885 TGTCACTGCATGAATATGTACAGAAT
1 TGTCACTGCATGAACATGTACAGAAT
* * *
19820911 TGTCGCTGCATGAACGTGTAGAGAAT
1 TGTCACTGCATGAACATGTACAGAAT
19820937 TG
1 TG
19820939 CACCCAGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (26 bp):
TGTCACTGCATGAACATGTACAGAAT
Found at i:19834829 original size:3 final size:3
Alignment explanation
Indices: 19834821--19834884 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
19834811 GCCTTATTGC
19834821 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
19834869 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
19834885 TTGTTTTGTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:19837955 original size:29 final size:29
Alignment explanation
Indices: 19837922--19837986 Score: 116
Period size: 27 Copynumber: 2.3 Consensus size: 29
19837912 TTTAATGCAT
19837922 AACTTGTGTTGGTTGTGTTTGAGACATTA
1 AACTTGTGTTGGTTGTGTTTGAGACATTA
19837951 AAC-T-TGTTGGTTGTGTTTGAGACATTA
1 AACTTGTGTTGGTTGTGTTTGAGACATTA
19837978 AACTTGTGT
1 AACTTGTGT
19837987 CTTGGCATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
27 26 0.76
28 2 0.06
29 6 0.18
ACGTcount: A:0.22, C:0.08, G:0.26, T:0.45
Consensus pattern (29 bp):
AACTTGTGTTGGTTGTGTTTGAGACATTA
Found at i:19843004 original size:78 final size:78
Alignment explanation
Indices: 19842867--19843112 Score: 219
Period size: 78 Copynumber: 3.2 Consensus size: 78
19842857 ATTGCAGTAA
* * * * ** *
19842867 GCAAATTGAAGACACACTG-ATCTCTTA-CCCAGATCATGAGGCAAACAGAAGCATCCAATCTTT
1 GCAAATTAAAGACACAC-GAATCACTTACCCCA-ATCACGGGGCAAATTGAAACATCCAATCTTT
19842930 TACCCTAATAAAAGG
64 TACCCTAATAAAAGG
* * *
19842945 G-AAGATTAAAGACACACTAATCACTTATCCTAATCACGGGGCAAATTGAAACATCCAATCTTTT
1 GCAA-ATTAAAGACACACGAATCACTTACCCCAATCACGGGGCAAATTGAAACATCCAATCTTTT
* *
19843009 ACCCTAATCAGAGG
65 ACCCTAATAAAAGG
** * * * * * * *
19843023 GCAAATTGCAGACACTCGGATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTA
1 GCAAATTAAAGACACACGAATCACTTACCCCAATCACGGGGCAAATTGAAACATCCAATCTTTTA
* * *
19843088 CCTTAATCAGAGG
66 CCCTAATAAAAGG
*
19843101 GCAAATTGAAGA
1 GCAAATTAAAGA
19843113 TATCATCCAA
Statistics
Matches: 139, Mismatches: 25, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
77 2 0.01
78 132 0.95
79 5 0.04
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (78 bp):
GCAAATTAAAGACACACGAATCACTTACCCCAATCACGGGGCAAATTGAAACATCCAATCTTTTA
CCCTAATAAAAGG
Found at i:19843016 original size:38 final size:39
Alignment explanation
Indices: 19842918--19843534 Score: 170
Period size: 42 Copynumber: 15.4 Consensus size: 39
19842908 CAAACAGAAG
* *
19842918 CATCCAATCTTTTACCCTAATAAAAGGG-AAGATT-AAAGA
1 CATCCAATCTTTTACCCTAATCAGAGGGCAA-ATTGAAA-A
** *
19842957 CA-CACTAATCACTTATCCTAATCACG-GGGCAAATTG-AAA
1 CATC-C-AATCTTTTACCCTAATCA-GAGGGCAAATTGAAAA
* *
19842996 CATCCAATCTTTTACCCTAATCAGAGGGCAAATTGCAGA
1 CATCCAATCTTTTACCCTAATCAGAGGGCAAATTGAAAA
** * ** * *
19843035 CACTCGGATCTCTTACCCCGATCATG-GGGCAGATTG-AAG
1 CA-TCCAATCTTTTACCCTAATCA-GAGGGCAAATTGAAAA
*
19843074 CATCCAATCTTTTACCTTAATCAGAGGGCAAATTGAAGATA
1 CATCCAATCTTTTACCCTAATCAGAGGGCAAATTGAA-A-A
** * * * *
19843115 TCATCCAATCTTTTACCCCGATCATAAGGTAGATTGAAGACA
1 -CATCCAATCTTTTACCCTAATCAGAGGGCAAATTGAA-A-A
* * * * * *
19843157 TCATCCAATCTCTTACCTTGATCATAGGGCAGATTG-AAG
1 -CATCCAATCTTTTACCCTAATCAGAGGGCAAATTGAAAA
* * ** *
19843196 CACCCAATCTTTTTCCCCGATCATG-GGGCATATTGAAGACA
1 CATCCAATCTTTTACCCTAATCA-GAGGGCAAATTGAA-A-A
* ** * * * **
19843237 TCATCCAATCTCTTACCCCGACCATAGGGCAGATTGAAGC
1 -CATCCAATCTTTTACCCTAATCAGAGGGCAAATTGAAAA
* * ** * *
19843277 CATTCAATCTCTTA-CCTCGGTCATGA-GGCAGATTG-AAG
1 CATCCAATCTTTTACCCT-AATCA-GAGGGCAAATTGAAAA
* * *
19843315 TATCCAATCTTTTATCCTAATCAGAGGG-AAGATTAAAGATA
1 CATCCAATCTTTTACCCTAATCAGAGGGCAA-ATTGAA-A-A
** ** * * * *
19843356 TCATCCAATCTCCTACCCCGATCATAAGGTAGATTGAAGACA
1 -CATCCAATCTTTTACCCTAATCAGAGGGCAAATTGAA-A-A
* ** * * **
19843398 TCATCCAATCTCTTACCCCGACCATG-GGGCAGATTGAAGC
1 -CATCCAATCTTTTACCCTAATCA-GAGGGCAAATTGAAAA
* ** * *
19843438 CATCCAAT-TTCTTGCCCCGATCATG-GGGCAGATT-AAAG
1 CATCCAATCTT-TTACCCTAATCA-GAGGGCAAATTGAAAA
* * *
19843476 CATCCAATCTTTTACCCTAATCAGAGAGTAGATTGAAGACA
1 CATCCAATCTTTTACCCTAATCAGAGGGCAAATTGAA-A-A
*
19843517 TCATCCAATCTCTTACCC
1 -CATCCAATCTTTTACCC
19843535 CGATCATGGG
Statistics
Matches: 439, Mismatches: 100, Indels: 75
0.71 0.16 0.12
Matches are distributed among these distances:
37 6 0.01
38 126 0.29
39 78 0.18
40 54 0.12
41 4 0.01
42 170 0.39
43 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (39 bp):
CATCCAATCTTTTACCCTAATCAGAGGGCAAATTGAAAA
Found at i:19843377 original size:161 final size:161
Alignment explanation
Indices: 19842996--19843600 Score: 586
Period size: 161 Copynumber: 3.8 Consensus size: 161
19842986 CAAATTGAAA
* ** ** *
19842996 CATCCAATCTTTTACCCTAATCAGAGGGCAA-ATTGCAGACA-C-TCGGATCTCTTACCCCGATC
1 CATCCAATCTTTTACCCTAATCAGAGAG-AAGATTAAAGACATCATCCAATCTCCTACCCCGATC
* * *** * * *
19843058 ATGGGGCAGATTGAAG----CATCCAATCTTTTACCTTAATCA-GAGGGCAAATTGAAGATATCA
65 ATGGGGTAGATTGAAGACATCATCCAATCTCTTACCCCGACCATG-GGGCAGATTGAAG---CCA
* * * *
19843118 TCCAATCTTTTACCCCGATCATAAGGTAGATTGAAGACAT
126 TCCAATCTCTTACCCCGATCATGAGGCAGATT--A-A-AG
* * * * * * * ** *
19843158 CATCCAATCTCTTACCTTGATCATAGGGCAGATTGAAG-CA-C--CCAATCTTTTTCCCCGATCA
1 CATCCAATCTTTTACCCTAATCAGAGAGAAGATTAAAGACATCATCCAATCTCCTACCCCGATCA
* * * *
19843219 TGGGGCATATTGAAGACATCATCCAATCTCTTACCCCGACCATAGGGCAGATTGAAGCCATTCAA
66 TGGGGTAGATTGAAGACATCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAA
* * *
19843284 TCTCTTACCTCGGTCATGAGGCAGATTGAAG
131 TCTCTTACCCCGATCATGAGGCAGATTAAAG
* * * *
19843315 TATCCAATCTTTTATCCTAATCAGAGGGAAGATTAAAGATATCATCCAATCTCCTACCCCGATCA
1 CATCCAATCTTTTACCCTAATCAGAGAGAAGATTAAAGACATCATCCAATCTCCTACCCCGATCA
**
19843380 TAAGGTAGATTGAAGACATCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAA
66 TGGGGTAGATTGAAGACATCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAA
* * *
19843445 TTTCTTGCCCCGATCATGGGGCAGATTAAAG
131 TCTCTTACCCCGATCATGAGGCAGATTAAAG
* * *
19843476 CATCCAATCTTTTACCCTAATCAGAGAGTAGATTGAAGACATCATCCAATCTCTTACCCCGATCA
1 CATCCAATCTTTTACCCTAATCAGAGAGAAGATTAAAGACATCATCCAATCTCCTACCCCGATCA
* * * *
19843541 TGGGGTAGATTGAAGACATCATCCAATCTCTTACCTCGATCATGGGGAATATTGAAGCCA
66 TGGGGTAGATTGAAGACATCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCA
19843601 CTATCTAATC
Statistics
Matches: 369, Mismatches: 64, Indels: 21
0.81 0.14 0.05
Matches are distributed among these distances:
157 31 0.08
158 2 0.01
159 1 0.00
160 30 0.08
161 245 0.66
162 30 0.08
164 30 0.08
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (161 bp):
CATCCAATCTTTTACCCTAATCAGAGAGAAGATTAAAGACATCATCCAATCTCCTACCCCGATCA
TGGGGTAGATTGAAGACATCATCCAATCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAA
TCTCTTACCCCGATCATGAGGCAGATTAAAG
Found at i:19843528 original size:241 final size:239
Alignment explanation
Indices: 19842977--19843560 Score: 759
Period size: 241 Copynumber: 2.4 Consensus size: 239
19842967 ACTTATCCTA
* * * *
19842977 ATCACGGGGCAAATTGAAACATCCAATCTTTTACCCTAATCAGAGGGCAAATTGCAGACAC-TCG
1 ATCATGGGGCAAATTGAAACATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACACATCC
*
19843041 GATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAGGGCAAA
66 AATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAGGGCAAA
* **
19843106 TTGAAGATATCATCCAATCTTTTACCCCGATCATAAGGTAGATTGAAGACATCATCCAATCTCTT
131 TTAAAGATATCATCCAATCTCCTACCCCGATCATAAGGTAGATTGAAGACATCATCCAATCTCTT
** * *
19843171 ACCTTGATCATAGGGCAGATTGAAGCACCCAATCTTTTTCCCCG
196 ACCCCGACCATAGGGCAGATTGAAGCACCCAATCTTTTGCCCCG
* * ** * *
19843215 ATCATGGGGCATATTGAAGACATCATCCAATCTCTTACCCCGACCATAGGGCAGATTGAAG-C-C
1 ATCATGGGGCAAATTG-A-A-A-CATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACAC
* * * * *
19843278 ATTCAATCTCTTACCTCGGTCATGAGGCAGATTGAAGTATCCAATCTTTTATCC-TAATCAGAGG
62 ATCCAATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTA-CCTTAATCAGAGG
19843342 G-AAGATTAAAGATATCATCCAATCTCCTACCCCGATCATAAGGTAGATTGAAGACATCATCCAA
126 GCAA-ATTAAAGATATCATCCAATCTCCTACCCCGATCATAAGGTAGATTGAAGACATCATCCAA
* *
19843406 TCTCTTACCCCGACCATGGGGCAGATTGAAGCCATCCAAT-TTCTTGCCCCG
190 TCTCTTACCCCGACCATAGGGCAGATTGAAG-CACCCAATCTT-TTGCCCCG
* * *
19843457 ATCATGGGGCAGATT-AAAGCATCCAATCTTTTACCCTAATCAGAGAGTAGATTGAAGACATCAT
1 ATCATGGGGCAAATTGAAA-CATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACA-CAT
*
19843521 CCAATCTCTTACCCCGATCATGGGGTAGATTGAAGACATC
64 CCAATCTCTTACCCCGATCATGGGGCAGATTGAAG-CATC
19843561 ATCCAATCTC
Statistics
Matches: 293, Mismatches: 40, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
238 46 0.16
239 3 0.01
240 5 0.02
241 175 0.60
242 64 0.22
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (239 bp):
ATCATGGGGCAAATTGAAACATCCAATCTTTTACCCTAATCAGAGGGCAGATTGAAGACACATCC
AATCTCTTACCCCGATCATGGGGCAGATTGAAGCATCCAATCTTTTACCTTAATCAGAGGGCAAA
TTAAAGATATCATCCAATCTCCTACCCCGATCATAAGGTAGATTGAAGACATCATCCAATCTCTT
ACCCCGACCATAGGGCAGATTGAAGCACCCAATCTTTTGCCCCG
Found at i:19843583 original size:42 final size:42
Alignment explanation
Indices: 19843042--19843597 Score: 496
Period size: 42 Copynumber: 13.8 Consensus size: 42
19843032 AGACACTCGG
19843042 ATCTCTTACCCCGATCATGGGGCAGATTGAAG----CATCCA
1 ATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
* *** * *
19843080 ATCTTTTACCTTAATCA-GAGGGCAAATTGAAGATATCATCCA
1 ATCTCTTACCCCGATCATG-GGGCAGATTGAAGACATCATCCA
* ** *
19843122 ATCTTTTACCCCGATCATAAGGTAGATTGAAGACATCATCCA
1 ATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
** *
19843164 ATCTCTTACCTTGATCATAGGGCAGATTGAAG-CA-C--CCA
1 ATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
* * *
19843202 ATCTTTTTCCCCGATCATGGGGCATATTGAAGACATCATCCA
1 ATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
* * *
19843244 ATCTCTTACCCCGACCATAGGGCAGATTGAAG-C--CATTCA
1 ATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
* * *
19843283 ATCTCTTACCTCGGTCATGAGGCAGATTGAAG---T-ATCCA
1 ATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
* * ** * * *
19843321 ATCTTTTATCCTAATCA-GAGGGAAGATTAAAGATATCATCCA
1 ATCTCTTACCCCGATCATG-GGGCAGATTGAAGACATCATCCA
* ** *
19843363 ATCTCCTACCCCGATCATAAGGTAGATTGAAGACATCATCCA
1 ATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
*
19843405 ATCTCTTACCCCGACCATGGGGCAGATTGAAG-C--CATCCA
1 ATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
* * *
19843444 ATTTCTTGCCCCGATCATGGGGCAGATT--A-A-AGCATCCA
1 ATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
* ** * *
19843482 ATCTTTTACCCTAATCA-GAGAGTAGATTGAAGACATCATCCA
1 ATCTCTTACCCCGATCATG-GGGCAGATTGAAGACATCATCCA
*
19843524 ATCTCTTACCCCGATCATGGGGTAGATTGAAGACATCATCCA
1 ATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
* * *
19843566 ATCTCTTACCTCGATCATGGGGAATATTGAAG
1 ATCTCTTACCCCGATCATGGGGCAGATTGAAG
19843598 CCACTATCTA
Statistics
Matches: 414, Mismatches: 78, Indels: 48
0.77 0.14 0.09
Matches are distributed among these distances:
37 4 0.01
38 104 0.25
39 65 0.16
40 3 0.01
41 6 0.01
42 231 0.56
43 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (42 bp):
ATCTCTTACCCCGATCATGGGGCAGATTGAAGACATCATCCA
Found at i:19854530 original size:2 final size:2
Alignment explanation
Indices: 19854525--19854560 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
19854515 AGTAAATTAA
19854525 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19854561 CAGAGTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19854739 original size:38 final size:39
Alignment explanation
Indices: 19854680--19854761 Score: 114
Period size: 38 Copynumber: 2.1 Consensus size: 39
19854670 TATATGGCGA
19854680 ATATATACATACTATATATATAAAG-AATAAACTATATAT
1 ATATATACATACTATATATAT-AAGTAATAAACTATATAT
* *
19854719 ATATATATATA-TATATATATAAGTAATAAATTATATAT
1 ATATATACATACTATATATATAAGTAATAAACTATATAT
*
19854757 GTATA
1 ATATA
19854762 ATCTAAGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
37 3 0.08
38 26 0.67
39 10 0.26
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (39 bp):
ATATATACATACTATATATATAAGTAATAAACTATATAT
Found at i:19854756 original size:2 final size:2
Alignment explanation
Indices: 19854680--19854739 Score: 59
Period size: 2 Copynumber: 29.5 Consensus size: 2
19854670 TATATGGCGA
* * * *
19854680 AT AT AT AC AT ACT AT AT AT AT AA AG A- AT AA ACT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
19854723 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
19854740 AGTAATAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
1 1 0.02
2 45 0.92
3 3 0.06
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (2 bp):
AT
Found at i:19856547 original size:40 final size:39
Alignment explanation
Indices: 19856483--19856813 Score: 305
Period size: 40 Copynumber: 8.4 Consensus size: 39
19856473 ATAACTTTAG
* * *
19856483 GGGTAAATGATTAGATTG-CTTCAATCTGTCCCATGGTCA
1 GGGTAAAAGATTGGATGGTCTTCAATCTG-CCCATGGTCA
* * *
19856522 GGGTAAAAGATCGGATGGTCTTCAATCTGCCCTCTGGTTA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCC-ATGGTCA
* * *
19856562 GGGTAAAAGATTGAATTG-CTTCAACCTGCCCCATGGTCA
1 GGGTAAAAGATTGGATGGTCTTCAATCTG-CCCATGGTCA
* * * * * *
19856601 GGGTAAGAGATCGGATGGTCATCAATTTGCCCTCTGGTTA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCC-ATGGTCA
* *
19856641 GGGTAAAAGATTGGATTG-CTTCAATCTGCCCCATGGTCG
1 GGGTAAAAGATTGGATGGTCTTCAATCTG-CCCATGGTCA
* * * *
19856680 GGGTAAGAGATCGGATGGTTTTCAATCTGCACTC-TGGTTA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGC-C-CATGGTCA
*
19856720 GGGTAAAAGATTGGATTG-CTTCAATCTGCCCATGGTCA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCATGGTCA
* * * *
19856758 AGGTAAGAGATTGAATGGTCTTCAATCTGTCCTC-TGGTTA
1 GGGTAAAAGATTGGATGGTCTTCAATCTG-CC-CATGGTCA
19856798 GGGTAAAAGATTGGAT
1 GGGTAAAAGATTGGAT
19856814 TACTTCAATT
Statistics
Matches: 231, Mismatches: 48, Indels: 25
0.76 0.16 0.08
Matches are distributed among these distances:
37 1 0.00
38 20 0.09
39 96 0.42
40 112 0.48
41 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (39 bp):
GGGTAAAAGATTGGATGGTCTTCAATCTGCCCATGGTCA
Found at i:19856595 original size:79 final size:79
Alignment explanation
Indices: 19856483--19856822 Score: 529
Period size: 79 Copynumber: 4.3 Consensus size: 79
19856473 ATAACTTTAG
* * * *
19856483 GGGTAAATGATTAGATTGCTTCAATCTGTCCCATGGTCAGGGTAAAAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATCGGATGGTCTTCAAT
19856548 CTGCCCTCTGGTTA
66 CTGCCCTCTGGTTA
* * *
19856562 GGGTAAAAGATTGAATTGCTTCAACCTGCCCCATGGTCAGGGTAAGAGATCGGATGGTCATCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATCGGATGGTCTTCAAT
*
19856627 TTGCCCTCTGGTTA
66 CTGCCCTCTGGTTA
* *
19856641 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTTTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATCGGATGGTCTTCAAT
*
19856706 CTGCACTCTGGTTA
66 CTGCCCTCTGGTTA
* * *
19856720 GGGTAAAAGATTGGATTGCTTCAATCTG-CCCATGGTCAAGGTAAGAGATTGAATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATCGGATGGTCTTCAAT
*
19856784 CTGTCCTCTGGTTA
66 CTGCCCTCTGGTTA
*
19856798 GGGTAAAAGATTGGATTACTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAAT
19856823 TGGCCCTATT
Statistics
Matches: 238, Mismatches: 23, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
78 67 0.28
79 171 0.72
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (79 bp):
GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCAGGGTAAGAGATCGGATGGTCTTCAAT
CTGCCCTCTGGTTA
Found at i:19857045 original size:50 final size:50
Alignment explanation
Indices: 19856936--19857045 Score: 116
Period size: 50 Copynumber: 2.2 Consensus size: 50
19856926 CTTTAGGTGA
* * * * *
19856936 ATGAGATTCGTCATTGCGGCTTCAATCTGTCCCTTTACAGTTTTAGGCGT
1 ATGAGATTTGCCATTGCGGCTTCAATCTATCCCTCTACAGTTTAAGGCGT
* * *
19856986 ATGAGATTTGCCATTGTGGCTTCAATCTATTCCTCTGCAGCTTTAAGG-GT
1 ATGAGATTTGCCATTGCGGCTTCAATCTATCCCTCTACAG-TTTAAGGCGT
19857036 AT-AGAATTTG
1 ATGAG-ATTTG
19857046 TCGTTCTATC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
49 2 0.04
50 42 0.84
51 6 0.12
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (50 bp):
ATGAGATTTGCCATTGCGGCTTCAATCTATCCCTCTACAGTTTAAGGCGT
Found at i:19858527 original size:17 final size:18
Alignment explanation
Indices: 19858502--19858556 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
19858492 AATTAGTAGT
*
19858502 CAAATTAATATA-ATATA
1 CAAAATAATATATATATA
19858519 CAAAATAATATATATATA
1 CAAAATAATATATATATA
* *
19858537 TATATATATATATATATATA
1 CA-AAATA-ATATATATATA
19858557 AGCTATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 11 0.34
18 6 0.19
19 4 0.12
20 11 0.34
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (18 bp):
CAAAATAATATATATATA
Found at i:19858533 original size:2 final size:2
Alignment explanation
Indices: 19858526--19858575 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
19858516 ATACAAAATA
* *
19858526 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AG CT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
19858567 AT AC AT AT A
1 AT AT AT AT A
19858576 ATTTTACATA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:19860560 original size:39 final size:39
Alignment explanation
Indices: 19860501--19860721 Score: 225
Period size: 39 Copynumber: 5.6 Consensus size: 39
19860491 AAGAGATCGG
*
19860501 ATCTGCCCTC-TGGTTAGGGTAAAAGATTGGATTGCTTCA
1 ATCTGCCC-CATGGTTGGGGTAAAAGATTGGATTGCTTCA
* * * *
19860540 ATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCA
1 ATCTGCCCCATGGTTGGGGTAAAAGATTGGATTG-CTTCA
* * *
19860580 ATCTACCATC-TGGTTAGGGTAAAAGATTGGATTGCTTCA
1 ATCTGCC-CCATGGTTGGGGTAAAAGATTGGATTGCTTCA
* * * * *
19860619 ATCTGCTCCATGGTCGGGGTAAGAGATCGGATGGTCTTCA
1 ATCTGCCCCATGGTTGGGGTAAAAGATTGGATTG-CTTCA
* *
19860659 ATCTACCCTC-TGGTTAGGGTAAAAGATTGGATTGCTTCA
1 ATCTGCCC-CATGGTTGGGGTAAAAGATTGGATTGCTTCA
19860698 AT-TGGCCCCATGGTTGGGGTAAAA
1 ATCT-GCCCCATGGTTGGGGTAAAA
19860722 TACTCGGGGT
Statistics
Matches: 145, Mismatches: 29, Indels: 16
0.76 0.15 0.08
Matches are distributed among these distances:
38 4 0.03
39 79 0.54
40 60 0.41
41 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.30
Consensus pattern (39 bp):
ATCTGCCCCATGGTTGGGGTAAAAGATTGGATTGCTTCA
Found at i:19860600 original size:40 final size:38
Alignment explanation
Indices: 19860507--19860699 Score: 199
Period size: 40 Copynumber: 4.9 Consensus size: 38
19860497 TCGGATCTGC
*
19860507 CCTCTGGTTAGGGTAAAAGATTGGATTGCTTCAATCTG
1 CCTCTGGTTAGGGTAAAAGATTGGATTGCTTCAATCTA
* ** * * *
19860545 CCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAATCTA
1 CCTC-TGGTTAGGGTAAAAGATTGGATTG-CTTCAATCTA
19860585 CCATCTGGTTAGGGTAAAAGATTGGATTGCTTCAATCT-
1 CC-TCTGGTTAGGGTAAAAGATTGGATTGCTTCAATCTA
* ** * * *
19860623 GCTCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAATCTA
1 CCT-C-TGGTTAGGGTAAAAGATTGGATTG-CTTCAATCTA
19860664 CCCTCTGGTTAGGGTAAAAGATTGGATTGCTTCAAT
1 -CCTCTGGTTAGGGTAAAAGATTGGATTGCTTCAAT
19860700 TGGCCCCATG
Statistics
Matches: 122, Mismatches: 25, Indels: 15
0.75 0.15 0.09
Matches are distributed among these distances:
37 1 0.01
38 5 0.04
39 54 0.44
40 58 0.48
41 2 0.02
42 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (38 bp):
CCTCTGGTTAGGGTAAAAGATTGGATTGCTTCAATCTA
Found at i:19860640 original size:79 final size:79
Alignment explanation
Indices: 19860509--19860719 Score: 379
Period size: 79 Copynumber: 2.7 Consensus size: 79
19860499 GGATCTGCCC
19860509 TCTGGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGG
1 TCTGGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGG
19860574 TCTTCAATCTACCA
66 TCTTCAATCTACCA
*
19860588 TCTGGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCTCCATGGTCGGGGTAAGAGATCGGATGG
1 TCTGGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGG
*
19860653 TCTTCAATCTACCC
66 TCTTCAATCTACCA
*
19860667 TCTGGTTAGGGTAAAAGATTGGATTGCTTCAAT-TGGCCCCATGGTTGGGGTAA
1 TCTGGTTAGGGTAAAAGATTGGATTGCTTCAATCT-GCCCCATGGTCGGGGTAA
19860720 AATACTCGGG
Statistics
Matches: 127, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
78 1 0.01
79 126 0.99
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (79 bp):
TCTGGTTAGGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGG
TCTTCAATCTACCA
Found at i:19860840 original size:50 final size:50
Alignment explanation
Indices: 19860780--19860911 Score: 131
Period size: 50 Copynumber: 2.6 Consensus size: 50
19860770 TCATCCTTGA
* * * **
19860780 GACTTTAATCTGTTCCTTTACAGCTTTAGGGGAATGAGCTTCGTCATTGT
1 GACTTCAATCTGTTCCTTTACAGCTTTAGGGGAATGAGATTCGCCATTAC
* * * * *
19860830 GGCTTCAATCTG-CCTCTTTACAGCTTTAGGTGTATGAGATTTGCCATTAC
1 GACTTCAATCTGTTC-CTTTACAGCTTTAGGGGAATGAGATTCGCCATTAC
* * *
19860880 GACTTCAATCTATTCCTCTACAGTTTTAGGGG
1 GACTTCAATCTGTTCCTTTACAGCTTTAGGGG
19860912 TATAGAATTT
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
49 1 0.02
50 62 0.97
51 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (50 bp):
GACTTCAATCTGTTCCTTTACAGCTTTAGGGGAATGAGATTCGCCATTAC
Found at i:19861981 original size:17 final size:19
Alignment explanation
Indices: 19861955--19861993 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
19861945 TTGGCATCCA
*
19861955 TTTGCCTAGG-AAG-TCTT
1 TTTGCATAGGAAAGATCTT
19861972 TTTGCATAGGAAAGATCTT
1 TTTGCATAGGAAAGATCTT
19861991 TTT
1 TTT
19861994 CAACACTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 3 0.16
19 7 0.37
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.44
Consensus pattern (19 bp):
TTTGCATAGGAAAGATCTT
Found at i:19867819 original size:58 final size:58
Alignment explanation
Indices: 19867757--19867876 Score: 195
Period size: 58 Copynumber: 2.1 Consensus size: 58
19867747 ACCCATCAAC
**
19867757 AAACTAAACCCAAATATTTTTAAAGTCAAATATAATTTTATTCGTAAAAAACACTCAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCGTAAAAAACACTCAT
* * *
19867815 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCTTAAATAACACTTAT
1 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCGTAAAAAACACTCAT
19867873 AAAC
1 AAAC
19867877 AACTCCTTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.48, C:0.17, G:0.02, T:0.33
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTTATTCGTAAAAAACACTCAT
Found at i:19871788 original size:224 final size:224
Alignment explanation
Indices: 19871397--19871844 Score: 716
Period size: 224 Copynumber: 2.0 Consensus size: 224
19871387 GGGATGAGCT
* *
19871397 GTCTTGATCGATACTATCTCATTACTAACAAAGGAGCATATCCCATAACTCCTCATACCCCTAAT
1 GTCTTGACCGATACTATCTCATTACTAACAAAGGAGCATATCCCACAACTCCTCATACCCCTAAT
* * *
19871462 AAAGGAACCCAATCGAAATCACCACATCGATAAATAATATCATCGGGAATGTACCACGGTGCTGG
66 AAAGGAACCCAATCGAAATCACCACATCGATAAATAATATCACCGGGAATGTACCACGATGCTCG
19871527 CCATTCTATGTCTTCGTCTCAAAGACTATGAAGTATTGCCATCCATTTTTCCTCAGAAATATCCT
131 CCATTCTATGTCTTCGTCTCAAAGACTATGAAGTATTGCCATCCATTTTTCCTCAGAAATATCCT
* *
19871592 CTCGTCTTTATGTAGCAACAAATTCTCTC
196 CTCATCTTTATGTAGCAACAAATTATCTC
* *
19871621 GTCTTGACCGATACTATCTTATTACTAACAAAGGAGCATATCCCACAACTCCTCATATCCCTAAT
1 GTCTTGACCGATACTATCTCATTACTAACAAAGGAGCATATCCCACAACTCCTCATACCCCTAAT
* * ** *
19871686 AAGGGAACCCAGTCGAAATCACCGTATCGATAAATAATTTCACCGGGAATGTACCACGATGCTCG
66 AAAGGAACCCAATCGAAATCACCACATCGATAAATAATATCACCGGGAATGTACCACGATGCTCG
* * * * *
19871751 CCATTCTATGTCTTTGTCTCAAAGGCTATGGAGTATTGTCATCCATTTTTCCTCAGAAATATTCT
131 CCATTCTATGTCTTCGTCTCAAAGACTATGAAGTATTGCCATCCATTTTTCCTCAGAAATATCCT
*
19871816 CTCATCTTTGTGTAGCAACAAATTATCTC
196 CTCATCTTTATGTAGCAACAAATTATCTC
19871845 AAAGGAGAAT
Statistics
Matches: 204, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
224 204 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (224 bp):
GTCTTGACCGATACTATCTCATTACTAACAAAGGAGCATATCCCACAACTCCTCATACCCCTAAT
AAAGGAACCCAATCGAAATCACCACATCGATAAATAATATCACCGGGAATGTACCACGATGCTCG
CCATTCTATGTCTTCGTCTCAAAGACTATGAAGTATTGCCATCCATTTTTCCTCAGAAATATCCT
CTCATCTTTATGTAGCAACAAATTATCTC
Found at i:19874158 original size:13 final size:13
Alignment explanation
Indices: 19874131--19874167 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
19874121 AAATAGGTTA
*
19874131 TTAGCGGC-ATTT
1 TTAGCGGCGTTTT
19874143 TTAGCGGCGTTTT
1 TTAGCGGCGTTTT
19874156 TTAGCGGCGTTT
1 TTAGCGGCGTTT
19874168 GGATAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 8 0.35
13 15 0.65
ACGTcount: A:0.11, C:0.16, G:0.30, T:0.43
Consensus pattern (13 bp):
TTAGCGGCGTTTT
Found at i:19874293 original size:41 final size:41
Alignment explanation
Indices: 19874191--19874677 Score: 661
Period size: 41 Copynumber: 11.9 Consensus size: 41
19874181 CACAAAAACT
* * * *
19874191 AGAGCAATAGCGGCGCTTATAGAAAAGCGCCACTAAAAGT-
1 AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTC
* *
19874231 GGAGCAATAGCGGCGCTTATGGGTAAGCGCCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTC
* *
19874272 AGAGAAATACCGGCGCTTATGGGAAAGCGCCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTC
* *
19874313 AGAGCAATAGCGGCGCTTATGAGCAAGCGCCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTC
*
19874354 AGAGCAATAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTC
*
19874395 AGAGCAATAGCGGCGCTTATGGAAAAGCGCCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTC
* * *
19874436 AGACCAATAGCGGCGCTTATGGGAAAACACCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTC
* * * * *
19874477 AGAGCAATAGCGACGCTTATGAGCAAGCGTCGCTAAAGGTT
1 AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTC
* * * * *
19874518 AAAGCAATAACGGCGCTTATAGAAAATCGCCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTC
* *
19874559 AGAGCAATAGCGGCGCTTATGAGAAAGCGCCGCTAAAGGTT
1 AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTC
* ***
19874600 AAAGCAATAGCGGCGCTTATAAAAAAGCGCCGCTAAAGGTC
1 AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTC
* * *
19874641 AGAGCAATAGCGACGCTTATAGAAAAGCGCCGCTAAA
1 AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAA
19874678 AGTTGAGTTT
Statistics
Matches: 393, Mismatches: 53, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
40 34 0.09
41 359 0.91
ACGTcount: A:0.34, C:0.22, G:0.29, T:0.16
Consensus pattern (41 bp):
AGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTC
Found at i:19874329 original size:24 final size:24
Alignment explanation
Indices: 19874297--19874411 Score: 87
Period size: 24 Copynumber: 5.4 Consensus size: 24
19874287 CTTATGGGAA
19874297 AGCGCCGCTAAAGGTCAGAGCAAT
1 AGCGCCGCTAAAGGTCAGAGCAAT
* *
19874321 AGCGGCGCT-TA--T--GAGC-A-
1 AGCGCCGCTAAAGGTCAGAGCAAT
19874338 AGCGCCGCTAAAGGTCAGAGCAAT
1 AGCGCCGCTAAAGGTCAGAGCAAT
* *
19874362 AGCGGCGCT-TA--T--GAG-AA-
1 AGCGCCGCTAAAGGTCAGAGCAAT
19874379 AGCGCCGCTAAAGGTCAGAGCAAT
1 AGCGCCGCTAAAGGTCAGAGCAAT
*
19874403 AGCGGCGCT
1 AGCGCCGCT
19874412 TATGGAAAAG
Statistics
Matches: 68, Mismatches: 9, Indels: 28
0.65 0.09 0.27
Matches are distributed among these distances:
17 16 0.24
18 5 0.07
19 7 0.10
20 2 0.03
21 2 0.03
22 7 0.10
23 5 0.07
24 24 0.35
ACGTcount: A:0.30, C:0.24, G:0.32, T:0.14
Consensus pattern (24 bp):
AGCGCCGCTAAAGGTCAGAGCAAT
Found at i:19876631 original size:2 final size:2
Alignment explanation
Indices: 19876626--19876651 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19876616 TATTGCTCAT
19876626 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
19876652 ATCCTGTGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:19878156 original size:43 final size:43
Alignment explanation
Indices: 19878028--19878337 Score: 392
Period size: 43 Copynumber: 7.3 Consensus size: 43
19878018 TTTATTAGTG
*
19878028 TTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * *
19878071 TTAGCGGCGTTTTTGGG-AAAGCGTCGCTAAAGACCATATTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* *
19878113 TTAGCGGCGTTTGTGGGTAAAGCGCCGCTAAA-AGCAATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGA-CCATGTTCT
* * * *
19878156 TTAGTGGCATTTGTGTGAAAAGCGCCGCTGAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
** *
19878199 TTAGCGGTATTTGTGGAAAAAGCGCCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * *
19878242 TTAGCTGCGTTTTTGAG-AAAGCGCCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* * * *
19878284 TTAGCGGCGTTTTTGTGAAAAGTGCCGCTAAAAACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
* *
19878327 ATAGCAGCGTT
1 TTAGCGGCGTT
19878338 ATCTTTAGCG
Statistics
Matches: 232, Mismatches: 31, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
42 80 0.34
43 151 0.65
44 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.29
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCT
Found at i:19878305 original size:85 final size:86
Alignment explanation
Indices: 19878028--19878337 Score: 391
Period size: 85 Copynumber: 3.6 Consensus size: 86
19878018 TTTATTAGTG
* *
19878028 TTAGCGGCGTTTGTG-GAAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTTTGGGAAAG
1 TTAGCGGCGTTTGTGTGAAAAAGCGCCGCTAAAGACCATGTTCTTTAGCTGCGTTTTTGAGAAAG
* *
19878092 CGTCGCTAAAGACCATATTCT
66 CGCCGCTAAAGACCATGTTCT
** * *
19878113 TTAGCGGCGTTTGTG-GGTAAAGCGCCGCTAAA-AGCAATGTTCTTTAG-TGGCATTTGTGTGA-
1 TTAGCGGCGTTTGTGTGAAAAAGCGCCGCTAAAGA-CCATGTTCTTTAGCT-GCGTTT-T-TGAG
*
19878174 AAAGCGCCGCTGAAGACCATGTTCT
62 AAAGCGCCGCTAAAGACCATGTTCT
**
19878199 TTAGCGGTATTTGTG-GAAAAAGCGCCGCTAAAGACCATGTTCTTTAGCTGCGTTTTTGAGAAAG
1 TTAGCGGCGTTTGTGTGAAAAAGCGCCGCTAAAGACCATGTTCTTTAGCTGCGTTTTTGAGAAAG
19878263 CGCCGCTAAAGACCATGTTCT
66 CGCCGCTAAAGACCATGTTCT
* * * * *
19878284 TTAGCGGCGTTTTTGTG-AAAAGTGCCGCTAAAAACCATGTTCTATAGCAGCGTT
1 TTAGCGGCGTTTGTGTGAAAAAGCGCCGCTAAAGACCATGTTCTTTAGCTGCGTT
19878338 ATCTTTAGCG
Statistics
Matches: 194, Mismatches: 23, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
84 4 0.02
85 117 0.60
86 69 0.36
87 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.29
Consensus pattern (86 bp):
TTAGCGGCGTTTGTGTGAAAAAGCGCCGCTAAAGACCATGTTCTTTAGCTGCGTTTTTGAGAAAG
CGCCGCTAAAGACCATGTTCT
Found at i:19878513 original size:17 final size:18
Alignment explanation
Indices: 19878488--19878524 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
19878478 AATTAGTAGT
*
19878488 CAAATTAATATA-ATATA
1 CAAAATAATATATATATA
19878505 CAAAATAATATATATATA
1 CAAAATAATATATATATA
19878523 CA
1 CA
19878525 TACATTCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.32
Consensus pattern (18 bp):
CAAAATAATATATATATA
Found at i:19879920 original size:4 final size:4
Alignment explanation
Indices: 19879909--19879937 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
19879899 TTTATTTATA
19879909 AAAT -AAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
19879938 CAAAATTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:19888692 original size:29 final size:30
Alignment explanation
Indices: 19888639--19888722 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
19888629 AAATTTTAAA
19888639 TTAATAATGAT-AAAA-TTACACTTTAACCCC
1 TTAA-AATGATAAAAATTTACA-TTTAACCCC
* *
19888669 TTAAAATGATAAAAATTTA-ATTTAATCCT
1 TTAAAATGATAAAAATTTACATTTAACCCC
* *
19888698 TTAAAAATAATAAAGATTTACATTT
1 TT-AAAATGATAAAAATTTACATTT
19888723 GTACTATCGT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 15 0.33
30 24 0.52
31 7 0.15
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.38
Consensus pattern (30 bp):
TTAAAATGATAAAAATTTACATTTAACCCC
Found at i:19896359 original size:24 final size:24
Alignment explanation
Indices: 19896331--19896395 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
19896321 TAGACTAATA
* *
19896331 AGAGTTTGACTCAAATAAATAAAC
1 AGAGTTTAACTGAAATAAATAAAC
* *
19896355 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAATAAATAAAC
19896379 AGAGTTTAACTGAAATA
1 AGAGTTTAACTGAAATA
19896396 TTATTTCTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.51, C:0.09, G:0.14, T:0.26
Consensus pattern (24 bp):
AGAGTTTAACTGAAATAAATAAAC
Found at i:19898344 original size:24 final size:24
Alignment explanation
Indices: 19898283--19898345 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
19898273 TAGACTAATA
* * *
19898283 AGAGTTTGACTCAAACAAATAAAT
1 AGAGTTTAACTGAAACAAATAAAC
*
19898307 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
19898331 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
19898346 GATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.51, C:0.10, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:19898861 original size:92 final size:94
Alignment explanation
Indices: 19898709--19898900 Score: 325
Period size: 92 Copynumber: 2.1 Consensus size: 94
19898699 TTATGCCTTT
19898709 TTTATTCAATCAATCATTTAAGAAAAAAAATTTACCATAAAAATACTAAATCCAATCAATCATAT
1 TTTATTCAATCAATCATTTAAGAAAAAAAATTTACCATAAAAATACTAAATCCAATCAATCATAT
* *
19898774 TTAATAAAGTTGCCTAAATTAATTTATTA
66 TTAATAAAGTTACCTAAATTAACTTATTA
* *
19898803 TTTATTCAATCAATCATTT-A-AAAAAACATTTACGATAAAAATACTAAATCCAATCAATCATAT
1 TTTATTCAATCAATCATTTAAGAAAAAAAATTTACCATAAAAATACTAAATCCAATCAATCATAT
*
19898866 TTAATAAAGTTACCTCAATTAACTTATTA
66 TTAATAAAGTTACCTAAATTAACTTATTA
19898895 TTTATT
1 TTTATT
19898901 AAATATGATC
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
92 73 0.78
93 1 0.01
94 19 0.20
ACGTcount: A:0.46, C:0.14, G:0.03, T:0.38
Consensus pattern (94 bp):
TTTATTCAATCAATCATTTAAGAAAAAAAATTTACCATAAAAATACTAAATCCAATCAATCATAT
TTAATAAAGTTACCTAAATTAACTTATTA
Found at i:19898868 original size:46 final size:44
Alignment explanation
Indices: 19898731--19898869 Score: 106
Period size: 46 Copynumber: 3.0 Consensus size: 44
19898721 ATCATTTAAG
19898731 AAAAAAAATTTACCATAAAAATACTAAATCCAATCAATCATATTT
1 AAAAAAAATTTA-CATAAAAATACTAAATCCAATCAATCATATTT
* * * * * * *
19898776 --AATAAAGTTGCCTAAATTAATTTATTATTTATTCAATCAATC--ATTT
1 AAAAAAAATTTACATAAA--AA--TACTA--AATCCAATCAATCATATTT
19898822 AAAAAAACATTTACGATAAAAATACTAAATCCAATCAATCATATTT
1 AAAAAAA-ATTTAC-ATAAAAATACTAAATCCAATCAATCATATTT
19898868 AA
1 AA
19898870 TAAAGTTACC
Statistics
Matches: 68, Mismatches: 14, Indels: 23
0.65 0.13 0.22
Matches are distributed among these distances:
42 5 0.07
43 7 0.10
44 13 0.19
46 18 0.26
48 17 0.25
49 4 0.06
50 4 0.06
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.34
Consensus pattern (44 bp):
AAAAAAAATTTACATAAAAATACTAAATCCAATCAATCATATTT
Found at i:19899767 original size:24 final size:24
Alignment explanation
Indices: 19899740--19899789 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
19899730 GAATTAATCC
* *
19899740 TTCAGTTAAACTCTGTTTATTTGT
1 TTCAATTAAACTCTATTTATTTGT
19899764 TTCAATTAAACTCTATTTATTTGT
1 TTCAATTAAACTCTATTTATTTGT
19899788 TT
1 TT
19899790 GAGTCAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.56
Consensus pattern (24 bp):
TTCAATTAAACTCTATTTATTTGT
Found at i:19909980 original size:12 final size:13
Alignment explanation
Indices: 19909959--19909996 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
19909949 AAAGGTGGAT
19909959 AAGAAGAAAGAGA
1 AAGAAGAAAGAGA
19909972 AAG-AGAAAG-GA
1 AAGAAGAAAGAGA
*
19909983 AAGAAAAAAGAGA
1 AAGAAGAAAGAGA
19909996 A
1 A
19909997 GCAAGAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 5 0.23
12 11 0.50
13 6 0.27
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAGAGA
Found at i:19910556 original size:18 final size:18
Alignment explanation
Indices: 19910532--19910572 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
19910522 ACCTAAAAAG
*
19910532 AAGAAGGAAAATGAGGAA
1 AAGAAGGAAAAAGAGGAA
*
19910550 GAGAAGGAAAAAGAGGAA
1 AAGAAGGAAAAAGAGGAA
19910568 AAGAA
1 AAGAA
19910573 TGAAGAGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.34, T:0.02
Consensus pattern (18 bp):
AAGAAGGAAAAAGAGGAA
Found at i:19918109 original size:24 final size:23
Alignment explanation
Indices: 19918061--19918113 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
19918051 AGTGTTTTTG
*
19918061 AAAACATAAAGTAAAAAGACAAA
1 AAAAAATAAAGTAAAAAGACAAA
* *
19918084 AATAAAATAAAGTAAATAAAAGAAA
1 AA-AAAATAAAGTAAA-AAGACAAA
19918109 AAAAA
1 AAAAA
19918114 CTTGAGTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.08
24 15 0.60
25 8 0.32
ACGTcount: A:0.77, C:0.04, G:0.08, T:0.11
Consensus pattern (23 bp):
AAAAAATAAAGTAAAAAGACAAA
Found at i:19926452 original size:24 final size:24
Alignment explanation
Indices: 19926419--19926697 Score: 353
Period size: 24 Copynumber: 11.6 Consensus size: 24
19926409 TAAGTTTCAG
19926419 TTACGTTTATGCTCGTCAGCCACT
1 TTACGTTTATGCTCGTCAGCCACT
* * * *
19926443 ATACGTTTATGCTAGCCAACCACT
1 TTACGTTTATGCTCGTCAGCCACT
**
19926467 TTACGTTTATGCTCGTCAATCACT
1 TTACGTTTATGCTCGTCAGCCACT
**
19926491 TTACGTTTATGCTCACCAGCCACT
1 TTACGTTTATGCTCGTCAGCCACT
* *
19926515 TTACGTTTATGCTCGCCATCCACT
1 TTACGTTTATGCTCGTCAGCCACT
*
19926539 TTACGTTTATGCTCATCAGCCACT
1 TTACGTTTATGCTCGTCAGCCACT
*
19926563 TTACGTTTATGCT-ATCCAGCCACT
1 TTACGTTTATGCTCGT-CAGCCACT
* * *
19926587 TTATGTTTATGCTCGCCATCCACT
1 TTACGTTTATGCTCGTCAGCCACT
*
19926611 TTGCGTTTATGCTCGTCAGCCACT
1 TTACGTTTATGCTCGTCAGCCACT
*
19926635 TTACGTTTATGATCGTCAGCCACT
1 TTACGTTTATGCTCGTCAGCCACT
* * *
19926659 TTACATTTATGCTCATCAGTCACT
1 TTACGTTTATGCTCGTCAGCCACT
*
19926683 TTACGTTTACGCTCG
1 TTACGTTTATGCTCG
19926698 CCATCTAATA
Statistics
Matches: 219, Mismatches: 34, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
23 2 0.01
24 217 0.99
ACGTcount: A:0.20, C:0.29, G:0.14, T:0.38
Consensus pattern (24 bp):
TTACGTTTATGCTCGTCAGCCACT
Found at i:19930839 original size:17 final size:17
Alignment explanation
Indices: 19930798--19930840 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
19930788 ACGAAATTAA
*
19930798 AATTTGATTGAAAAAAT
1 AATTTAATTGAAAAAAT
* **
19930815 AATATAATTGAAAATTT
1 AATTTAATTGAAAAAAT
19930832 AATTTAATT
1 AATTTAATT
19930841 AATTAAACTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (17 bp):
AATTTAATTGAAAAAAT
Found at i:19941629 original size:27 final size:27
Alignment explanation
Indices: 19941591--19941646 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
19941581 AATAACATCC
19941591 TAGTACATGTCATAAAACCAAGTGATG
1 TAGTACATGTCATAAAACCAAGTGATG
19941618 TAGTACATGTCATAAAACCAAGTGATG
1 TAGTACATGTCATAAAACCAAGTGATG
19941645 TA
1 TA
19941647 AAGTTTACCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (27 bp):
TAGTACATGTCATAAAACCAAGTGATG
Found at i:19942991 original size:23 final size:24
Alignment explanation
Indices: 19942960--19943004 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
19942950 TCTTTCATCA
*
19942960 TTAAGCTTTAATTAA-CTATTTTT
1 TTAACCTTTAATTAACCTATTTTT
*
19942983 TTAACCTTTATTTAACCTATTT
1 TTAACCTTTAATTAACCTATTT
19943005 ATAAACAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.29, C:0.13, G:0.02, T:0.56
Consensus pattern (24 bp):
TTAACCTTTAATTAACCTATTTTT
Found at i:19950175 original size:328 final size:327
Alignment explanation
Indices: 19949577--19950211 Score: 970
Period size: 328 Copynumber: 1.9 Consensus size: 327
19949567 TTTTATTATT
*
19949577 GGTAAAAGCATGATTTGTTTCGGTAGAAGTGACACATATATCGGTAGAACTATCTCAAGTATCAG
1 GGTAAAAGCATGATTTATTTCGGTAGAAGTGACACATATATCGGTAGAACTATCTCAAGTATCAG
* * *
19949642 TAGAAATCTACACGATTTTTGAATTTCTTACTAATATGACTACTACCGATACCCTTGCAACCGGT
66 TAGAAATCTACACGATTTTTGAATTTCTTACTAACATGACTACTACCGATA-CCTTACAACAGGT
* *
19949707 ATTAGTAGAAGTCTCCAAAAATCATGAAAATGACATATTTTCCCTTTTTAAGTTGTGTTGGTATT
130 ATCAGTAGAAGTCTCCAAAAATCATGAAAATGACATATTTTCCCTTTTTAAGTTGTGTTGATATT
** * *
19949772 CAATTGATTATTCATGCCATGCTTATTGCATTACCTTATTAAAATATGATTAAATGAAATAGTAA
195 CAACCGATAATTCATGCCATGCTTATTGCATCACCTTATTAAAATATGATTAAATGAAATAGTAA
19949837 TGTAAGATAAACTGCGACAAATGATCTGAAGGACATCGAGACCCTAATTGGTGACAATATCGAGT
260 TGTAAGATAAACTGCGACAAATGATCTGAAGGACATCGAGACCCTAATTGGTGACAATATCGAGT
19949902 TTA
325 TTA
* * *
19949905 GGTAAAAGCATGATTTATTTCTGTAGAAGTGACACATGTATCGGTAGAACTATCTCAAGTATCGG
1 GGTAAAAGCATGATTTATTTCGGTAGAAGTGACACATATATCGGTAGAACTATCTCAAGTATCAG
* * *
19949970 TAGAAATTTATACGATTTTTGAATTTCTTACTAACATGACTACTATCGATA-CTTAACTAACAGG
66 TAGAAATCTACACGATTTTTGAATTTCTTACTAACATGACTACTACCGATACCTT-AC-AACAGG
* *
19950034 TATCAGTGGAAGTCTCCAAAAATCAT-AGAAATGACAT-TTTTGCCCTTTTTGAGTTGTGTTGAT
129 TATCAGTAGAAGTCTCCAAAAATCATGA-AAATGACATATTTT-CCCTTTTTAAGTTGTGTTGAT
* * *
19950097 ATTCAACCGATAATTCATGTCGTGCTTATTGCATCACCTTATTAAGATATGATTAAATGAAATAG
192 ATTCAACCGATAATTCATGCCATGCTTATTGCATCACCTTATTAAAATATGATTAAATGAAATAG
* * * * *
19950162 TAATGTGAGATAAACTGCGATATATTATCTGAAGGACATCGGGACCCTAA
257 TAATGTAAGATAAACTGCGACAAATGATCTGAAGGACATCGAGACCCTAA
19950212 CCAGTAACTG
Statistics
Matches: 277, Mismatches: 26, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
326 3 0.01
327 6 0.02
328 268 0.97
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (327 bp):
GGTAAAAGCATGATTTATTTCGGTAGAAGTGACACATATATCGGTAGAACTATCTCAAGTATCAG
TAGAAATCTACACGATTTTTGAATTTCTTACTAACATGACTACTACCGATACCTTACAACAGGTA
TCAGTAGAAGTCTCCAAAAATCATGAAAATGACATATTTTCCCTTTTTAAGTTGTGTTGATATTC
AACCGATAATTCATGCCATGCTTATTGCATCACCTTATTAAAATATGATTAAATGAAATAGTAAT
GTAAGATAAACTGCGACAAATGATCTGAAGGACATCGAGACCCTAATTGGTGACAATATCGAGTT
TA
Done.