Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 27 of 199
Found at i:11356948 original size:43 final size:43
Alignment explanation
Indices: 11356884--11357191 Score: 375
Period size: 43 Copynumber: 7.2 Consensus size: 43
11356874 GCGTTTTTAG
* *
11356884 CGCCGCTAAAGATCAGGACCTTTAGCGGCGCTTTTCTCACAAA
1 CGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAA
** *
11356927 CGCCGCTATAGATCAAAACCTTTAACGGCGC-TTTCCCACAAA
1 CGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAA
* * *
11356969 TGCCGCTATATATCAGGATCTTTAGCGGCGCTTTTCCCACAAA
1 CGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAA
* *
11357012 CGCCGCTATAGATCAGGACCTTTAGCGACACTTTTCCCACAAA
1 CGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAA
* ** *
11357055 CGCCACTATAGATCAGGACCTTTAGCAACGCTTTTCCTACAAA
1 CGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAA
* * * * *
11357098 CGCCGCTATAGATTAAGACCTTTAGCGACGCTTCTCTCACAAA
1 CGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAA
* ** * **
11357141 CGCCGCTATAAATCATAACTTTTAGCGGCGCTTTTTTCACAAA
1 CGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAA
*
11357184 CACCGCTA
1 CGCCGCTA
11357192 AAAGTGCCAT
Statistics
Matches: 228, Mismatches: 36, Indels: 2
0.86 0.14 0.01
Matches are distributed among these distances:
42 35 0.15
43 193 0.85
ACGTcount: A:0.28, C:0.31, G:0.16, T:0.26
Consensus pattern (43 bp):
CGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAA
Found at i:11360827 original size:22 final size:24
Alignment explanation
Indices: 11360802--11360845 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
11360792 AATCAAACAC
*
11360802 CAAATTA-AAAAA-AAATTAATAA
1 CAAATTAGAAAAATAAAATAATAA
11360824 CAAATTAGAAAAATAAAATAAT
1 CAAATTAGAAAAATAAAATAAT
11360846 TAAGAGTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 5 0.26
24 7 0.37
ACGTcount: A:0.70, C:0.05, G:0.02, T:0.23
Consensus pattern (24 bp):
CAAATTAGAAAAATAAAATAATAA
Found at i:11360843 original size:21 final size:20
Alignment explanation
Indices: 11360782--11360844 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
11360772 CTTAAGTACT
* * *
11360782 AAATTAAAAAAATCAAACACC
1 AAATT-AAAAAATAAAATAAC
*
11360803 AAATTAAAAAAAAATTAATAAC
1 AAATTAAAAAATAA--AATAAC
11360825 AAATTAGAAAAATAAAATAA
1 AAATTA-AAAAATAAAATAA
11360845 TTAAGAGTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
20 7 0.21
21 10 0.29
22 10 0.29
23 7 0.21
ACGTcount: A:0.71, C:0.08, G:0.02, T:0.19
Consensus pattern (20 bp):
AAATTAAAAAATAAAATAAC
Found at i:11361018 original size:5 final size:5
Alignment explanation
Indices: 11361010--11361061 Score: 104
Period size: 5 Copynumber: 10.4 Consensus size: 5
11361000 ATAATTATTT
11361010 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
11361060 TT
1 TT
11361062 GATTGGTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 47 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:11363374 original size:27 final size:27
Alignment explanation
Indices: 11363339--11363395 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
11363329 AAGCATTCTT
*
11363339 TTTTTTTGTTTACATTCCCTTAATTAA
1 TTTTCTTGTTTACATTCCCTTAATTAA
11363366 TTTTCTTGTTTACATTCCCTTAATTAA
1 TTTTCTTGTTTACATTCCCTTAATTAA
11363393 TTT
1 TTT
11363396 CAACATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.16, G:0.04, T:0.60
Consensus pattern (27 bp):
TTTTCTTGTTTACATTCCCTTAATTAA
Found at i:11364011 original size:7 final size:7
Alignment explanation
Indices: 11364001--11364075 Score: 53
Period size: 7 Copynumber: 10.7 Consensus size: 7
11363991 CTTAACCTCC
*
11364001 AACCCCT
1 AACCCCA
11364008 AACCCCA
1 AACCCCA
*
11364015 AATCCCA
1 AACCCCA
*
11364022 AACCCCT
1 AACCCCA
11364029 AACCCCA
1 AACCCCA
*
11364036 AA-CCTA
1 AACCCCA
*
11364042 TAACCCTA
1 -AACCCCA
* *
11364050 AATCGCA
1 AACCCCA
*
11364057 AACACCA
1 AACCCCA
*
11364064 AAACCCA
1 AACCCCA
11364071 AACCC
1 AACCC
11364076 ATAACTACTA
Statistics
Matches: 51, Mismatches: 15, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
6 3 0.06
7 44 0.86
8 4 0.08
ACGTcount: A:0.43, C:0.47, G:0.01, T:0.09
Consensus pattern (7 bp):
AACCCCA
Found at i:11364071 original size:35 final size:35
Alignment explanation
Indices: 11364001--11364080 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
11363991 CTTAACCTCC
* * * *
11364001 AACCCCTAACCCCAAATCCCAAACCCCTAACCCCA
1 AACCCATAACCCCAAATCCCAAACACCAAAACCCA
* * *
11364036 AACCTATAACCCTAAATCGCAAACACCAAAACCCA
1 AACCCATAACCCCAAATCCCAAACACCAAAACCCA
11364071 AACCCATAAC
1 AACCCATAAC
11364081 TACTAACCCC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.44, C:0.45, G:0.01, T:0.10
Consensus pattern (35 bp):
AACCCATAACCCCAAATCCCAAACACCAAAACCCA
Found at i:11364160 original size:13 final size:13
Alignment explanation
Indices: 11364135--11364184 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 13
11364125 AATTAATCTA
11364135 AACCCTAAACCCT
1 AACCCTAAACCCT
11364148 AACCC-AAATCCCT
1 AACCCTAAA-CCCT
11364161 AATCCCT-AACACCT
1 AA-CCCTAAAC-CCT
11364175 AACCCCTAAA
1 AA-CCCTAAA
11364185 TCACAACCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 3 0.10
13 12 0.39
14 14 0.45
15 2 0.06
ACGTcount: A:0.40, C:0.44, G:0.00, T:0.16
Consensus pattern (13 bp):
AACCCTAAACCCT
Found at i:11364162 original size:20 final size:21
Alignment explanation
Indices: 11364137--11364184 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
11364127 TTAATCTAAA
*
11364137 CCCTAAACCCTAAC-CCAAAT
1 CCCTAAACCCTAACACCAAAC
* *
11364157 CCCTAATCCCTAACACCTAAC
1 CCCTAAACCCTAACACCAAAC
11364178 CCCTAAA
1 CCCTAAA
11364185 TCACAACCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.17
Consensus pattern (21 bp):
CCCTAAACCCTAACACCAAAC
Found at i:11364684 original size:41 final size:41
Alignment explanation
Indices: 11364625--11364776 Score: 218
Period size: 41 Copynumber: 3.7 Consensus size: 41
11364615 AAATGTTTTT
11364625 GCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCTAAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCTAAGCATTA
* ** *
11364666 GCGGCGCTTCTTGGAAAACGCCGCTAAA-GCCCAGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCTA-AGCATTA
* * *
11364707 GTGGCGCTTTTTCAAAAACGCCGCTAAAAGCCTGAGCATTA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCTAAGCATTA
11364748 GCGGCGC-TTTTCAAAAACGCCGCTAAAGG
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGG
11364777 GTTGGGCTTA
Statistics
Matches: 97, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
40 25 0.26
41 69 0.71
42 3 0.03
ACGTcount: A:0.28, C:0.27, G:0.24, T:0.20
Consensus pattern (41 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCTAAGCATTA
Found at i:11364843 original size:39 final size:39
Alignment explanation
Indices: 11364789--11364924 Score: 157
Period size: 39 Copynumber: 3.4 Consensus size: 39
11364779 TGGGCTTAGG
11364789 TTTTTAGCGGCGTTTTTCAAAAAACGCCGCTAATGCTCA
1 TTTTTAGCGGCGTTTTTCAAAAAACGCCGCTAATGCTCA
* * ** *
11364828 TTTTTGGCGGCGTTTTCCTGAAAGCGCCGCTAATGCTCA
1 TTTTTAGCGGCGTTTTTCAAAAAACGCCGCTAATGCTCA
* * * *
11364867 GTCTTTAGCGGCG-CTTTAAATAAAACGCCGCTAATGCTTGA
1 -TTTTTAGCGGCGTTTTTCAA-AAAACGCCGCTAATGC-TCA
11364908 TTTTTAGCGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
11364925 TGTCCAAACG
Statistics
Matches: 77, Mismatches: 16, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
39 36 0.47
40 36 0.47
41 5 0.06
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTTCAAAAAACGCCGCTAATGCTCA
Found at i:11364896 original size:40 final size:38
Alignment explanation
Indices: 11364791--11364922 Score: 122
Period size: 40 Copynumber: 3.3 Consensus size: 38
11364781 GGCTTAGGTT
* *
11364791 TTTAGCGGCGTTTTTCAA-AAAACGCCGCTAATGCTCATT
1 TTTAGCGGCG--TTTAAATAAAACGCCGCTAATGCTCATC
* *** *
11364830 TTTGGCGGCGTTTTCCTGAAAGCGCCGCTAATGCTCAGTC
1 TTTAGCGGCGTTTAAAT-AAAACGCCGCTAATGCTCA-TC
* *
11364870 TTTAGCGGCGCTTTAAATAAAACGCCGCTAATGCTTGATT
1 TTTAGCGGCG-TTTAAATAAAACGCCGCTAATGC-TCATC
11364910 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
11364923 TTTGTCCAAA
Statistics
Matches: 75, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
37 3 0.04
39 30 0.40
40 36 0.48
41 6 0.08
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (38 bp):
TTTAGCGGCGTTTAAATAAAACGCCGCTAATGCTCATC
Found at i:11369003 original size:13 final size:13
Alignment explanation
Indices: 11368985--11369009 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11368975 TAATTTATAT
11368985 GTGTGAAAATTTC
1 GTGTGAAAATTTC
11368998 GTGTGAAAATTT
1 GTGTGAAAATTT
11369010 TATCGTTGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:11370933 original size:41 final size:41
Alignment explanation
Indices: 11370804--11370914 Score: 204
Period size: 41 Copynumber: 2.7 Consensus size: 41
11370794 GACTATATGT
*
11370804 CTAGCAGGCTAAGTGCCGGTGAACCGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
11370845 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
*
11370886 CTAGCAGGCTAAGTGCCAGTGAACTGAAT
1 CTAGCAGGCTAAGTGCCGGTGAACTGAAT
11370915 TAGATTTTAA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.30, C:0.23, G:0.29, T:0.19
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGC
Found at i:11370941 original size:41 final size:41
Alignment explanation
Indices: 11370776--11370949 Score: 152
Period size: 41 Copynumber: 4.2 Consensus size: 41
11370766 TCGGACTTAT
* * * *** *
11370776 TGCCAGTGAAATTATTCAGACTATATGTCTAGCAGGCTAAG
1 TGCCAGTGAACTGAATCAGACTATAAACCTAGCAGGATAAG
* * * * *
11370817 TGCCGGTGAACCGAATCAGGCTATAAGCCTAGCAGGCTAAG
1 TGCCAGTGAACTGAATCAGACTATAAACCTAGCAGGATAAG
* * * *
11370858 TGCCGGTGAACTGAATCAGGCTATAAGCCTAGCAGGCTAAG
1 TGCCAGTGAACTGAATCAGACTATAAACCTAGCAGGATAAG
* * *
11370899 TGCCAGTGAACTGAATTAGATTTTAAACCTAGCA-GATGAAG
1 TGCCAGTGAACTGAATCAGACTATAAACCTAGCAGGAT-AAG
*
11370940 TGCTAGTGAA
1 TGCCAGTGAA
11370950 TCTGTTTAAA
Statistics
Matches: 115, Mismatches: 17, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
40 2 0.02
41 113 0.98
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.24
Consensus pattern (41 bp):
TGCCAGTGAACTGAATCAGACTATAAACCTAGCAGGATAAG
Found at i:11376045 original size:20 final size:20
Alignment explanation
Indices: 11376004--11376063 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
11375994 TTTTTTAAAA
* *
11376004 TTTTAAAAATAAAAAAAATAT
1 TTTTAAAAAT-TAAAAATTAT
11376025 TTTTAAAAATTAAAAATTA-
1 TTTTAAAAATTAAAAATTAT
*
11376044 -TTTAAAGTATTAAAAATTAT
1 TTTTAAA-AATTAAAAATTAT
11376064 AAAAAATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 6 0.18
19 11 0.32
20 7 0.21
21 10 0.29
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (20 bp):
TTTTAAAAATTAAAAATTAT
Found at i:11376054 original size:29 final size:28
Alignment explanation
Indices: 11376025--11376104 Score: 69
Period size: 28 Copynumber: 2.9 Consensus size: 28
11376015 AAAAAAATAT
11376025 TTTTAAAAATTAAAAATTATTTAAAGTA
1 TTTTAAAAATTAAAAATTATTTAAAGTA
* *
11376053 --TTAAAAATTATAAAAAATATTT-TAG-A
1 TTTTAAAAA-T-TAAAAATTATTTAAAGTA
*
11376079 CTTTTAAAATATTAAAAATTAATTAA
1 -TTTTAAAA-ATTAAAAATTATTTAA
11376105 TTACCAACGT
Statistics
Matches: 40, Mismatches: 5, Indels: 13
0.69 0.09 0.22
Matches are distributed among these distances:
26 8 0.20
27 3 0.08
28 21 0.52
29 7 0.17
30 1 0.03
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (28 bp):
TTTTAAAAATTAAAAATTATTTAAAGTA
Found at i:11376104 original size:19 final size:18
Alignment explanation
Indices: 11376027--11376104 Score: 61
Period size: 19 Copynumber: 4.2 Consensus size: 18
11376017 AAAAATATTT
11376027 TTAAAA-ATTAAAAATTA
1 TTAAAATATTAAAAATTA
*
11376044 TTTAAAGTATTAAAAATTA
1 -TTAAAATATTAAAAATTA
* * * *
11376063 TAAAAAATATTTTAGACTT-
1 T-TAAAATA-TTAAAAATTA
11376082 TTAAAATATTAAAAATTAA
1 TTAAAATATTAAAAATT-A
11376101 TTAA
1 TTAA
11376105 TTACCAACGT
Statistics
Matches: 45, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
17 6 0.13
18 12 0.27
19 21 0.47
20 6 0.13
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (18 bp):
TTAAAATATTAAAAATTA
Found at i:11377253 original size:11 final size:11
Alignment explanation
Indices: 11377237--11377305 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
11377227 TGTTTCTTAA
11377237 AATTTTTAAAT
1 AATTTTTAAAT
*
11377248 AA-TTTTAATT
1 AATTTTTAAAT
* *
11377258 AAGCTCTCTAAAT
1 AA--TTTTTAAAT
11377271 AATTTTTAAAT
1 AATTTTTAAAT
11377282 AA-TTTT---T
1 AATTTTTAAAT
11377289 AATTTTTAAAT
1 AATTTTTAAAT
11377300 AATTTT
1 AATTTT
11377306 GAAAATTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
7 3 0.07
8 4 0.09
10 13 0.29
11 18 0.40
13 7 0.16
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (11 bp):
AATTTTTAAAT
Found at i:11377293 original size:18 final size:18
Alignment explanation
Indices: 11377270--11377305 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
11377260 GCTCTCTAAA
11377270 TAATTTTTAAATAATTTT
1 TAATTTTTAAATAATTTT
11377288 TAATTTTTAAATAATTTT
1 TAATTTTTAAATAATTTT
11377306 GAAAATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TAATTTTTAAATAATTTT
Found at i:11378541 original size:27 final size:27
Alignment explanation
Indices: 11378511--11378574 Score: 69
Period size: 31 Copynumber: 2.3 Consensus size: 27
11378501 ATTATTACAC
11378511 TGTTAACGATAAT-TAACATAACTAAAA
1 TGTTAACGATAATATAA-ATAACTAAAA
11378538 TGTTAAAATTCGATAATATAAATAACTAAAA
1 TGTT--AA--CGATAATATAAATAACTAAAA
11378569 T-TTAAC
1 TGTTAAC
11378575 ATGAAGTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
26 1 0.03
27 4 0.12
28 2 0.06
29 2 0.06
30 2 0.06
31 18 0.56
32 3 0.09
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (27 bp):
TGTTAACGATAATATAAATAACTAAAA
Found at i:11378922 original size:24 final size:25
Alignment explanation
Indices: 11378862--11378923 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
11378852 CTGTTAGCTT
11378862 ATTATTTTTAATTCATAAATTTAAAA
1 ATTATTTTTAA-TCATAAATTTAAAA
** *
11378888 AACATTATTAAT-AT-AATTTAAACA
1 ATTATTTTTAATCATAAATTTAAA-A
11378912 ATTATTTTTAAT
1 ATTATTTTTAAT
11378924 TTATTGTATA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
23 8 0.28
24 12 0.41
25 1 0.03
26 8 0.28
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (25 bp):
ATTATTTTTAATCATAAATTTAAAA
Found at i:11383363 original size:5 final size:5
Alignment explanation
Indices: 11383355--11383380 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
11383345 GACAAGACTT
11383355 TCTAA TCTAA TCTAA TCTAA TCTAA T
1 TCTAA TCTAA TCTAA TCTAA TCTAA T
11383381 TCCATTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.42
Consensus pattern (5 bp):
TCTAA
Found at i:11400723 original size:18 final size:19
Alignment explanation
Indices: 11400700--11400737 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
11400690 GGAAGCAGGC
*
11400700 AATGATTGAAGA-AATCAG
1 AATGATTGAAAAGAATCAG
11400718 AATGATTGAAAAGAATCAG
1 AATGATTGAAAAGAATCAG
11400737 A
1 A
11400738 CCTATAGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
AATGATTGAAAAGAATCAG
Found at i:11407004 original size:6 final size:6
Alignment explanation
Indices: 11406993--11407018 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
11406983 TTATTGTTTA
11406993 CCCTAT CCCTAT CCCTAT CCCTAT CC
1 CCCTAT CCCTAT CCCTAT CCCTAT CC
11407019 ACTCAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.54, G:0.00, T:0.31
Consensus pattern (6 bp):
CCCTAT
Found at i:11409141 original size:21 final size:21
Alignment explanation
Indices: 11409112--11409155 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
11409102 AATTGCAGTG
*
11409112 GCTGCTGCCACCGCAGCTGCA
1 GCTGATGCCACCGCAGCTGCA
* **
11409133 GCTGATGCCGCCGTGGCTGCA
1 GCTGATGCCACCGCAGCTGCA
11409154 GC
1 GC
11409156 AAAGGCGGCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.11, C:0.39, G:0.34, T:0.16
Consensus pattern (21 bp):
GCTGATGCCACCGCAGCTGCA
Found at i:11411258 original size:14 final size:14
Alignment explanation
Indices: 11411239--11411278 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
11411229 TTGATTGCCA
11411239 GTAAAATGTTTTCT
1 GTAAAATGTTTTCT
*
11411253 GTAAAATGATTTCT
1 GTAAAATGTTTTCT
*
11411267 GAAAAATGTTTT
1 GTAAAATGTTTT
11411279 ACTTTTCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (14 bp):
GTAAAATGTTTTCT
Found at i:11411287 original size:20 final size:20
Alignment explanation
Indices: 11411262--11411301 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
11411252 TGTAAAATGA
*
11411262 TTTCTGAAAAATGTTTTACT
1 TTTCTGAAAAATGATTTACT
*
11411282 TTTCTGTAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
11411302 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:11411290 original size:34 final size:35
Alignment explanation
Indices: 11411247--11411313 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
11411237 CAGTAAAATG
*
11411247 TTTTCTGTAAAATGATTT-CTGAAAAATGTTTTAC
1 TTTTCTGTAAAATGATTTACTGAAAAATATTTTAC
*
11411281 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
11411314 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 18 0.60
35 12 0.40
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (35 bp):
TTTTCTGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:11411317 original size:14 final size:15
Alignment explanation
Indices: 11411241--11411317 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
11411231 GATTGCCAGT
*
11411241 AAAATG-TTTTCTGT
1 AAAATGATTTTCTGG
*
11411255 AAAATGA-TTTCTGA
1 AAAATGATTTTCTGG
*
11411269 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
11411289 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
11411304 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
11411318 TGTTTGATTG
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
14 26 0.51
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:11414133 original size:18 final size:18
Alignment explanation
Indices: 11414112--11414162 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
11414102 AGGAATGAAG
11414112 GAAGGGAGAAGAATGGAT
1 GAAGGGAGAAGAATGGAT
*** *
11414130 GAAGGGAGCTTACTGGAT
1 GAAGGGAGAAGAATGGAT
11414148 GAAGGGAGAAGAATG
1 GAAGGGAGAAGAATG
11414163 CCTGAAAGCT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.43, T:0.14
Consensus pattern (18 bp):
GAAGGGAGAAGAATGGAT
Found at i:11427286 original size:50 final size:55
Alignment explanation
Indices: 11427206--11427341 Score: 165
Period size: 56 Copynumber: 2.5 Consensus size: 55
11427196 CCCTATACAT
* **
11427206 GCCATGTCCTAGACATGGTCTTACGGGGGACCTCTC-T-CCTC-A-G-TGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATACCTCAATGATGCCAAC
* * *
11427256 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAGTCTCAATGATGCTAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA-CCTCAATGATGCCAAC
*
11427312 GCCATGTCCCAGATATGGTCTTACATGGGA
1 GCCATGTCCCAGACATGGTCTTACATGGGA
11427342 TCTCATCACC
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
50 33 0.45
51 1 0.01
53 3 0.04
54 1 0.01
55 1 0.01
56 34 0.47
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.26
Consensus pattern (55 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATACCTCAATGATGCCAAC
Found at i:11427322 original size:56 final size:50
Alignment explanation
Indices: 11427204--11427341 Score: 159
Period size: 50 Copynumber: 2.6 Consensus size: 50
11427194 GTCCCTATAC
* **
11427204 ATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCTCCTCAGTGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCTCCTCAGTGCCA
* * *
11427254 ACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAGTCTCAATGATGCTA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC-T--CCTC-A-G-TGCCA
*
11427310 ATGCCATGTCCCAGATATGGTCTTACATGGGA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGA
11427342 TCTCATCACC
Statistics
Matches: 74, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
50 34 0.46
51 1 0.01
53 3 0.04
54 1 0.01
55 1 0.01
56 34 0.46
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.27
Consensus pattern (50 bp):
ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCTCCTCAGTGCCA
Found at i:11429723 original size:24 final size:24
Alignment explanation
Indices: 11429677--11429721 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
11429667 AAAGAAATAT
*
11429677 AAAAAATGCTTTACAATTATTTAA
1 AAAAAATGCTTGACAATTATTTAA
*
11429701 AAAAAATTCTTGAC-ATTATTT
1 AAAAAATGCTTGACAATTATTT
11429722 TATTAAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (24 bp):
AAAAAATGCTTGACAATTATTTAA
Found at i:11448874 original size:20 final size:19
Alignment explanation
Indices: 11448825--11448874 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
11448815 TCTAGGCACC
11448825 TTTTATATAA-TTCTATGAT
1 TTTTATA-AATTTCTATGAT
* *
11448844 TTTAATTAATTTCTAATGAT
1 TTTTATAAATTTCT-ATGAT
11448864 TTTTATAAATT
1 TTTTATAAATT
11448875 ATTTTATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 2 0.08
19 9 0.36
20 14 0.56
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (19 bp):
TTTTATAAATTTCTATGAT
Found at i:11451495 original size:39 final size:37
Alignment explanation
Indices: 11451428--11451520 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
11451418 ACCAGAATGG
* *
11451428 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
11451467 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
11451504 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
11451521 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:11451884 original size:3 final size:3
Alignment explanation
Indices: 11451876--11451911 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
11451866 ATTCCCACTC
* *
11451876 ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA CTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11451912 CTTACCTCAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11451893 original size:12 final size:12
Alignment explanation
Indices: 11451876--11451911 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
11451866 ATTCCCACTC
*
11451876 ATAATAATAATA
1 ATAATACTAATA
11451888 ATAATACTAATA
1 ATAATACTAATA
11451900 ATAATACTAATA
1 ATAATACTAATA
11451912 CTTACCTCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAATACTAATA
Found at i:11452636 original size:16 final size:16
Alignment explanation
Indices: 11452617--11452651 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11452607 TTCTTTGTTC
11452617 TTTCTATTCTGTTTCT
1 TTTCTATTCTGTTTCT
* *
11452633 TTTCTGTTTTGTTTCT
1 TTTCTATTCTGTTTCT
11452649 TTT
1 TTT
11452652 ATATATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.14, G:0.09, T:0.74
Consensus pattern (16 bp):
TTTCTATTCTGTTTCT
Found at i:11467641 original size:18 final size:17
Alignment explanation
Indices: 11467618--11467651 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
11467608 TTTTAATTGA
*
11467618 TTATTTGTAATTTGTAAT
1 TTATTTATAA-TTGTAAT
11467636 TTATTTATAATTGTAA
1 TTATTTATAATTGTAA
11467652 CTCTAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (17 bp):
TTATTTATAATTGTAAT
Found at i:11468551 original size:6 final size:6
Alignment explanation
Indices: 11468540--11468590 Score: 102
Period size: 6 Copynumber: 8.5 Consensus size: 6
11468530 GAGATGTGTG
11468540 GGGTAA GGGTAA GGGTAA GGGTAA GGGTAA GGGTAA GGGTAA GGGTAA
1 GGGTAA GGGTAA GGGTAA GGGTAA GGGTAA GGGTAA GGGTAA GGGTAA
11468588 GGG
1 GGG
11468591 GCCAAAGGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.31, C:0.00, G:0.53, T:0.16
Consensus pattern (6 bp):
GGGTAA
Found at i:11475273 original size:78 final size:78
Alignment explanation
Indices: 11475181--11475337 Score: 296
Period size: 78 Copynumber: 2.0 Consensus size: 78
11475171 ATCTAAAGCA
*
11475181 AGCAAAGTTCGAGGAAAAACAAAGGCAAACACTATCAAAGCTAAAAAGTAAAACCCCAAACGGAT
1 AGCAAAGTTCGAGGAAAAACAAAGGCAAACACTACCAAAGCTAAAAAGTAAAACCCCAAACGGAT
11475246 ACTCAACATTTCC
66 ACTCAACATTTCC
*
11475259 AGCAAAGTTCGAGGAAAAACTAAGGCAAACACTACCAAAGCTAAAAAGTAAAACCCCAAACGGAT
1 AGCAAAGTTCGAGGAAAAACAAAGGCAAACACTACCAAAGCTAAAAAGTAAAACCCCAAACGGAT
11475324 ACTCAACATTTCC
66 ACTCAACATTTCC
11475337 A
1 A
11475338 TCCAAACCAA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.48, C:0.24, G:0.14, T:0.14
Consensus pattern (78 bp):
AGCAAAGTTCGAGGAAAAACAAAGGCAAACACTACCAAAGCTAAAAAGTAAAACCCCAAACGGAT
ACTCAACATTTCC
Found at i:11479222 original size:58 final size:58
Alignment explanation
Indices: 11479152--11479267 Score: 232
Period size: 58 Copynumber: 2.0 Consensus size: 58
11479142 AAGTTTCACA
11479152 AAATTCCAACATTGTGCGAGTGTGCTGAGACGTAGAATGTCAATAGAAAGGAATAGTT
1 AAATTCCAACATTGTGCGAGTGTGCTGAGACGTAGAATGTCAATAGAAAGGAATAGTT
11479210 AAATTCCAACATTGTGCGAGTGTGCTGAGACGTAGAATGTCAATAGAAAGGAATAGTT
1 AAATTCCAACATTGTGCGAGTGTGCTGAGACGTAGAATGTCAATAGAAAGGAATAGTT
11479268 CTTTGTGATA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.26
Consensus pattern (58 bp):
AAATTCCAACATTGTGCGAGTGTGCTGAGACGTAGAATGTCAATAGAAAGGAATAGTT
Found at i:11479743 original size:22 final size:22
Alignment explanation
Indices: 11479718--11479759 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
11479708 AATAAATACC
11479718 AAAAATTTTATTTTAAAAATTA
1 AAAAATTTTATTTTAAAAATTA
11479740 AAAAATTTTATTTTAAAAAT
1 AAAAATTTTATTTTAAAAAT
11479760 ATTTTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAAATTTTATTTTAAAAATTA
Found at i:11479749 original size:17 final size:16
Alignment explanation
Indices: 11479727--11479858 Score: 71
Period size: 17 Copynumber: 8.1 Consensus size: 16
11479717 CAAAAATTTT
11479727 ATTTTAAAAATTAAAAA
1 ATTTT-AAAATTAAAAA
**
11479744 ATTTT-ATTTTAAAAA
1 ATTTTAAAATTAAAAA
11479759 TATTTTAAAATTAAAAAA
1 -ATTTTAAAATT-AAAAA
*
11479777 ATTTAAAAATGTATTTTAAAA
1 ATTTTAAAAT-TA----AAAA
*
11479798 ATATT----TTAAAAA
1 ATTTTAAAATTAAAAA
11479810 TATTTTAAAATTAAAAA
1 -ATTTTAAAATTAAAAA
* **
11479827 AATTTAAAA--AAAGT
1 ATTTTAAAATTAAAAA
11479841 ATTTTAAAATTAAAAA
1 ATTTTAAAATTAAAAA
11479857 AT
1 AT
11479859 AAAAATATTT
Statistics
Matches: 86, Mismatches: 14, Indels: 31
0.66 0.11 0.24
Matches are distributed among these distances:
12 4 0.05
13 4 0.05
14 11 0.13
15 8 0.09
16 20 0.23
17 26 0.30
18 6 0.07
21 7 0.08
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (16 bp):
ATTTTAAAATTAAAAA
Found at i:11479764 original size:11 final size:11
Alignment explanation
Indices: 11479748--11479819 Score: 75
Period size: 11 Copynumber: 6.9 Consensus size: 11
11479738 TAAAAAATTT
11479748 TATTTTAAAAA
1 TATTTTAAAAA
11479759 TATTTT--AAA
1 TATTTTAAAAA
11479768 -A--TTAAAAA
1 TATTTTAAAAA
*
11479776 -AATTTAAAAA
1 TATTTTAAAAA
11479786 TGTATTTTAAAAA
1 --TATTTTAAAAA
11479799 TATTTTAAAAA
1 TATTTTAAAAA
11479810 TATTTTAAAA
1 TATTTTAAAA
11479820 TTAAAAAAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 14
0.78 0.01 0.21
Matches are distributed among these distances:
6 2 0.04
8 5 0.09
9 3 0.06
10 7 0.13
11 27 0.51
13 9 0.17
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:11479792 original size:40 final size:41
Alignment explanation
Indices: 11479732--11479808 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 41
11479722 ATTTTATTTT
*
11479732 AAAAATTAAAAAATTTTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTAAAAAATTGTATTTTAAAAATATTTTAAAATTAA
*
11479773 AAAAATTTAAAAA-TGTATTTTAAAAATATTTTAAAA
1 AAAAATTAAAAAATTGTATTTTAAAAATATTTTAAAA
11479809 ATATTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 22 0.65
41 12 0.35
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (41 bp):
AAAAATTAAAAAATTGTATTTTAAAAATATTTTAAAATTAA
Found at i:11479813 original size:51 final size:52
Alignment explanation
Indices: 11479748--11479849 Score: 188
Period size: 51 Copynumber: 2.0 Consensus size: 52
11479738 TAAAAAATTT
*
11479748 TATTTTAAAAATATTTTAAAATTAAAAAAATTT-AAAAATGTATTTTAAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAA
11479799 TATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAA
11479850 TTAAAAAATA
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 33 0.67
52 16 0.33
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (52 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAATTTAAAAAAAGTATTTTAAAAA
Found at i:11479828 original size:30 final size:30
Alignment explanation
Indices: 11479792--11479857 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
11479782 AAAATGTATT
* *
11479792 TTAAAAATATTT-TAAAAA-TATTTTAAAA
1 TTAAAAAAATTTAAAAAAAGTATTTTAAAA
11479820 TTAAAAAAATTTAAAAAAAGTATTTTAAAA
1 TTAAAAAAATTTAAAAAAAGTATTTTAAAA
11479850 TTAAAAAA
1 TTAAAAAA
11479858 TAAAAATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 11 0.32
29 5 0.15
30 18 0.53
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (30 bp):
TTAAAAAAATTTAAAAAAAGTATTTTAAAA
Found at i:11486289 original size:14 final size:13
Alignment explanation
Indices: 11486253--11486285 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
11486243 AAAATTTGTC
*
11486253 TAATATTT-TTCT
1 TAATATTTATTTT
11486265 TAATATTTATTTT
1 TAATATTTATTTT
11486278 TAATATTT
1 TAATATTT
11486286 TATTAGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (13 bp):
TAATATTTATTTT
Found at i:11493381 original size:21 final size:23
Alignment explanation
Indices: 11493357--11493403 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
11493347 AAGTAAACCT
11493357 TAAT-TTTTTTTCT-TA-ATTAAA
1 TAATCTTTTTTT-TATATATTAAA
11493378 TAATCCTTTTTTTTATATATTAAA
1 TAAT-CTTTTTTTTATATATTAAA
11493402 TA
1 TA
11493404 GAGTATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
21 4 0.18
22 1 0.05
23 9 0.41
24 8 0.36
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (23 bp):
TAATCTTTTTTTTATATATTAAA
Found at i:11500331 original size:21 final size:22
Alignment explanation
Indices: 11500295--11500344 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
11500285 TGAAAATTAC
*
11500295 TACATAATTGTTAAAACTTATA
1 TACAAAATTGTTAAAACTTATA
*
11500317 TACAAAATT-TTAAAATTTATA
1 TACAAAATTGTTAAAACTTATA
*
11500338 TAAAAAA
1 TACAAAA
11500345 CATAAATTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (22 bp):
TACAAAATTGTTAAAACTTATA
Found at i:11521948 original size:6 final size:6
Alignment explanation
Indices: 11521928--11521976 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
11521918 CTGTCGCTTC
* * *
11521928 CACTGT CACTG- --CTGT CACTGT CACTAT CACTAT CACTGC CACTGT
1 CACTGT CACTGT CACTGT CACTGT CACTGT CACTGT CACTGT CACTGT
11521973 CACT
1 CACT
11521977 AGCACTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 3 0.08
6 33 0.92
ACGTcount: A:0.20, C:0.37, G:0.12, T:0.31
Consensus pattern (6 bp):
CACTGT
Found at i:11521965 original size:18 final size:18
Alignment explanation
Indices: 11521942--11521982 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
11521932 GTCACTGCTG
*
11521942 TCACTGTCACTATCACTA
1 TCACTGCCACTATCACTA
*
11521960 TCACTGCCACTGTCACTA
1 TCACTGCCACTATCACTA
*
11521978 GCACT
1 TCACT
11521983 ATTTGCTTGC
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:0.24, C:0.37, G:0.10, T:0.29
Consensus pattern (18 bp):
TCACTGCCACTATCACTA
Found at i:11529190 original size:20 final size:19
Alignment explanation
Indices: 11529150--11529198 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
11529140 AATTAAGTTT
*
11529150 ATTTAAATAAAAATATTAA
1 ATTTAAATAAAAATATGAA
11529169 ATTTAAATTAAAAA-ATAGAA
1 ATTTAAA-TAAAAATAT-GAA
11529189 ATTTATAATA
1 ATTTA-AATA
11529199 TTAAATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 9 0.35
20 15 0.58
21 2 0.08
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
ATTTAAATAAAAATATGAA
Found at i:11529409 original size:15 final size:14
Alignment explanation
Indices: 11529373--11529419 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
11529363 TACAATATAT
11529373 AATATATAATTTAA
1 AATATATAATTTAA
11529387 AA-ACTATAATTCTAA
1 AATA-TATAATT-TAA
*
11529402 AATATATAATTTTA
1 AATATATAATTTAA
11529416 AATA
1 AATA
11529420 GTTAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 1 0.03
14 15 0.52
15 12 0.41
16 1 0.03
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATATAATTTAA
Found at i:11529583 original size:19 final size:19
Alignment explanation
Indices: 11529549--11529612 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 19
11529539 AAATAATTTT
11529549 TATTTTTA-AACTTTTTTAAC
1 TATTTTTACAA-TTTTTT-AC
11529569 TATTTTTACAATTTTTTA-
1 TATTTTTACAATTTTTTAC
*
11529587 TAGTTTTTACATTTTTTTAC
1 TA-TTTTTACAATTTTTTAC
11529607 -ATTTTT
1 TATTTTT
11529613 GTAACAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
18 7 0.17
19 17 0.43
20 14 0.35
21 2 0.05
ACGTcount: A:0.25, C:0.08, G:0.02, T:0.66
Consensus pattern (19 bp):
TATTTTTACAATTTTTTAC
Found at i:11529603 original size:10 final size:10
Alignment explanation
Indices: 11529571--11529612 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
11529561 TTTTTAACTA
*
11529571 TTTTTACAAT
1 TTTTTACATT
* *
11529581 TTTTTATA-G
1 TTTTTACATT
11529590 TTTTTACATT
1 TTTTTACATT
11529600 TTTTTACATT
1 TTTTTACATT
11529610 TTT
1 TTT
11529613 GTAACAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.26
10 20 0.74
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.69
Consensus pattern (10 bp):
TTTTTACATT
Found at i:11530567 original size:13 final size:13
Alignment explanation
Indices: 11530542--11530587 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
11530532 GAAAAAAAAA
*
11530542 TTTAAAAATACTT
1 TTTAAAAACACTT
* *
11530555 TTTCACAACACTT
1 TTTAAAAACACTT
11530568 TTTAAAAACACTT
1 TTTAAAAACACTT
*
11530581 TTCAAAA
1 TTTAAAA
11530588 GTATTACTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.39
Consensus pattern (13 bp):
TTTAAAAACACTT
Found at i:11530917 original size:40 final size:40
Alignment explanation
Indices: 11530859--11530939 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
11530849 TATAAATCAT
*
11530859 TAACACTATTATTAATATAACATCATTTCACATTAACATA
1 TAACACAATTATTAATATAACATCATTTCACATTAACATA
* * *
11530899 TAACACAATTATTGATATAACGTCATTTTACATTAACATA
1 TAACACAATTATTAATATAACATCATTTCACATTAACATA
11530939 T
1 T
11530940 TGCGTACATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.43, C:0.16, G:0.02, T:0.38
Consensus pattern (40 bp):
TAACACAATTATTAATATAACATCATTTCACATTAACATA
Found at i:11533162 original size:22 final size:21
Alignment explanation
Indices: 11533108--11533163 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
11533098 TTCATCAATG
*
11533108 TTTTATTGTTATTTGCTACTA
1 TTTTGTTGTTATTTGCTACTA
* * *
11533129 TTTTGCTATTATATTGTTACTA
1 TTTTGTTGTTAT-TTGCTACTA
11533151 TTTTGTTGTTATT
1 TTTTGTTGTTATT
11533164 ATTTGGATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
21 10 0.36
22 18 0.64
ACGTcount: A:0.18, C:0.07, G:0.11, T:0.64
Consensus pattern (21 bp):
TTTTGTTGTTATTTGCTACTA
Found at i:11538179 original size:40 final size:39
Alignment explanation
Indices: 11538135--11538211 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 39
11538125 CTCAAGAAAG
*
11538135 CACTTT-GTCCACGTGGACAGAAAACGCTTCCTTGAGGGCA
1 CACTTTAGTCCACGT-GA-ACAAAACGCTTCCTTGAGGGCA
* *
11538175 CACTTTGAGTTCACGTGAACAAAGCGCTTCCTTGAGG
1 CACTTT-AGTCCACGTGAACAAAACGCTTCCTTGAGG
11538212 AATTACTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 23 0.72
41 2 0.06
42 7 0.22
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.25
Consensus pattern (39 bp):
CACTTTAGTCCACGTGAACAAAACGCTTCCTTGAGGGCA
Found at i:11539079 original size:96 final size:95
Alignment explanation
Indices: 11538962--11539272 Score: 323
Period size: 83 Copynumber: 3.4 Consensus size: 95
11538952 AACAACTAGT
* *
11538962 TTTATTTGA-TTTTTCCTTTAAAACCTTAAATACTAAACCCCAATCTATTTTTTTAAAAATTTTT
1 TTTATTTGATTTTTTCC-TTAAAACCTTAAATACTAAACCCTAATCTATTTTTTT-AAAATTTAT
*
11539026 AATTAATTTACTCAAATAATCCTAAACCCTAA
64 AATTAATTTACTCAAATAAACCTAAACCCTAA
11539058 TTTATTTGATTTTTTCCTT---A----AAA-A-T----CCTAATCTAATTTTTTTAAAATTTATA
1 TTTATTTGATTTTTTCCTTAAAACCTTAAATACTAAACCCTAATCT-ATTTTTTTAAAATTTATA
* * *
11539110 ATTAATTTACTCAAGTAACCCTAAACCTTAA
65 ATTAATTTACTCAAATAAACCTAAACCCTAA
* * *
11539141 TTTATTTGATTTTTTCCTTAAAAACCATAAACACTAAACCCTAATCTAATTTTTTAAAATTTATA
1 TTTATTTGATTTTTTCCTT-AAAACCTTAAATACTAAACCCTAATCTATTTTTTTAAAATTTATA
* * *
11539206 ATTAATTTAATTAAA-AAACCTTAAACCCTTA
65 ATTAATTTACTCAAATAAACC-TAAACCCTAA
* *
11539237 TTTATTT-AATTTTTCCTTAAAACTCTAAAAT-CTAAA
1 TTTATTTGATTTTTTCCTTAAAAC-CTTAAATACTAAA
11539273 AACTCAAAAA
Statistics
Matches: 181, Mismatches: 16, Indels: 38
0.77 0.07 0.16
Matches are distributed among these distances:
83 63 0.35
84 8 0.04
87 2 0.01
88 1 0.01
89 3 0.02
91 3 0.02
92 1 0.01
93 2 0.01
94 10 0.06
95 18 0.10
96 55 0.30
97 15 0.08
ACGTcount: A:0.39, C:0.16, G:0.01, T:0.44
Consensus pattern (95 bp):
TTTATTTGATTTTTTCCTTAAAACCTTAAATACTAAACCCTAATCTATTTTTTTAAAATTTATAA
TTAATTTACTCAAATAAACCTAAACCCTAA
Found at i:11543786 original size:35 final size:35
Alignment explanation
Indices: 11543747--11543813 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
11543737 GTTCAAATAA
11543747 AAATATGGCATGTGACTGATTCAAATAGAGAAAAC
1 AAATATGGCATGTGACTGATTCAAATAGAGAAAAC
* *
11543782 AAATATGGCTTGTGATTGATTCAAATAGAGAA
1 AAATATGGCATGTGACTGATTCAAATAGAGAA
11543814 CGTCATAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (35 bp):
AAATATGGCATGTGACTGATTCAAATAGAGAAAAC
Found at i:11556485 original size:6 final size:6
Alignment explanation
Indices: 11556468--11556510 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
11556458 ACCTTCTTCT
*
11556468 TTCCCC TT-CCC TTCCCC TTCCCC TTCCCT TTCCCC TTCCCC TT
1 TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TT
11556511 GGGTTGCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (6 bp):
TTCCCC
Found at i:11556598 original size:25 final size:25
Alignment explanation
Indices: 11556570--11556619 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
11556560 CAGGTAAGGC
11556570 TCCTTCTCCTTCTTCCGTTCTTCAT
1 TCCTTCTCCTTCTTCCGTTCTTCAT
* *
11556595 TCCTTTTTCTTCTTCCGTTCTTCAT
1 TCCTTCTCCTTCTTCCGTTCTTCAT
11556620 CTTCTCTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.04, C:0.36, G:0.04, T:0.56
Consensus pattern (25 bp):
TCCTTCTCCTTCTTCCGTTCTTCAT
Found at i:11559519 original size:21 final size:21
Alignment explanation
Indices: 11559495--11559550 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
11559485 CACCGCTGTT
*
11559495 TCTAATCTCACTGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
11559516 TCTAATCTCACCGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
*
11559537 ACTAATCTCACCGC
1 TCTAATCTCACCGC
11559551 CACCGCTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.29, C:0.34, G:0.09, T:0.29
Consensus pattern (21 bp):
TCTAATCTCACCGCTACAGTA
Found at i:11561144 original size:17 final size:17
Alignment explanation
Indices: 11561120--11561153 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11561110 GTATTTAATA
11561120 AATTACAC-AAATTTAT
1 AATTACACTAAATTTAT
11561136 AATTAACACTAAATTTAT
1 AATT-ACACTAAATTTAT
11561154 TCCATAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 4 0.25
18 8 0.50
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTACACTAAATTTAT
Found at i:11564142 original size:28 final size:29
Alignment explanation
Indices: 11564111--11564171 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
11564101 GAAATTAATT
*
11564111 CTATCTAATTTTAA-AATCAATTTTTACA
1 CTATCTAATTTTAACAAACAATTTTTACA
**
11564139 CTAT-TTTTTTTAACAAACAATTTTTACA
1 CTATCTAATTTTAACAAACAATTTTTACA
11564167 CTATC
1 CTATC
11564172 ATAAATGGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (29 bp):
CTATCTAATTTTAACAAACAATTTTTACA
Found at i:11568784 original size:16 final size:16
Alignment explanation
Indices: 11568747--11568777 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11568737 GTTGGGTTAG
11568747 GGTTTTATGGATTTTA
1 GGTTTTATGGATTTTA
*
11568763 GGTTTTATGGGTTTT
1 GGTTTTATGGATTTT
11568778 GAGTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.29, T:0.58
Consensus pattern (16 bp):
GGTTTTATGGATTTTA
Found at i:11568808 original size:20 final size:18
Alignment explanation
Indices: 11568784--11568837 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 18
11568774 TTTTGAGTTT
11568784 TTTTTATATATATTTTTTA
1 TTTTT-TATATATTTTTTA
11568803 TGTTTTGTATATATATTTTTA
1 T-TTTT-TATATAT-TTTTTA
11568824 TTTTTT-TATATTTT
1 TTTTTTATATATTTT
11568838 CTTGAGATGT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 3 0.09
18 5 0.16
19 2 0.06
20 15 0.47
21 7 0.22
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (18 bp):
TTTTTTATATATTTTTTA
Found at i:11568808 original size:22 final size:20
Alignment explanation
Indices: 11568782--11568834 Score: 79
Period size: 22 Copynumber: 2.5 Consensus size: 20
11568772 GGTTTTGAGT
11568782 TTTTTTTATATATATTTTTTA
1 TTTTTTTATATATA-TTTTTA
*
11568803 TGTTTTGTATATATATTTTTA
1 T-TTTTTTATATATATTTTTA
11568824 TTTTTTTATAT
1 TTTTTTTATAT
11568835 TTTCTTGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 9 0.31
21 8 0.28
22 12 0.41
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.74
Consensus pattern (20 bp):
TTTTTTTATATATATTTTTA
Found at i:11568892 original size:15 final size:15
Alignment explanation
Indices: 11568872--11568904 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
11568862 TTTAATTTGA
11568872 TATTTACAACC-ATCG
1 TATTTAC-ACCAATCG
11568887 TATTTACACCAATCG
1 TATTTACACCAATCG
11568902 TAT
1 TAT
11568905 ATTTGAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.33, C:0.24, G:0.06, T:0.36
Consensus pattern (15 bp):
TATTTACACCAATCG
Found at i:11571329 original size:26 final size:26
Alignment explanation
Indices: 11571293--11571344 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
11571283 CACCACTGAA
* *
11571293 TCGGGGAATCATCACTTAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
11571319 TCGGGGAATCAGCACATAGCAACCCC
1 TCGGGGAATCAGCACATAGCAACCCC
11571345 CTTTTCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.35, G:0.21, T:0.15
Consensus pattern (26 bp):
TCGGGGAATCAGCACATAGCAACCCC
Found at i:11571421 original size:70 final size:71
Alignment explanation
Indices: 11571305--11571455 Score: 241
Period size: 72 Copynumber: 2.1 Consensus size: 71
11571295 GGGGAATCAT
*
11571305 CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTT-CATTTCAAATATACAATGG
1 CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTTACATTTCAAAGATACAATGG
11571369 ATATCG
66 ATATCG
* ***
11571375 CACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTG
1 CACTTAGCAACCCCTC-GGGGAATCAGCACATAGCAACCCCCTTTTACATTTCAAAGATACAATG
11571440 GATATCG
65 GATATCG
11571447 CACTTAGCA
1 CACTTAGCA
11571456 CCACCAATGA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 16 0.22
71 28 0.38
72 30 0.41
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (71 bp):
CACTTAGCAACCCCTCGGGGAATCAGCACATAGCAACCCCCTTTTACATTTCAAAGATACAATGG
ATATCG
Found at i:11571498 original size:104 final size:104
Alignment explanation
Indices: 11571374--11571597 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
11571364 AATGGATATC
11571374 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
11571439 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGGAATCA
11571478 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
11571543 GGATCACGCACATAGCACCACCCATAAATCGGGGAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
**
11571582 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
11571598 TTTATATACA
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGGAATCA
Found at i:11571958 original size:29 final size:29
Alignment explanation
Indices: 11571925--11571988 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
11571915 TAATCCACCA
11571925 CCCAACTTTTTG-AAAATTACAATTTTGCC
1 CCCAAC-TTTTGCAAAATTACAATTTTGCC
* * *
11571954 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGCAAAATTACAATTTTGCC
11571984 CCCAA
1 CCCAA
11571989 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.33
30 20 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (29 bp):
CCCAACTTTTGCAAAATTACAATTTTGCC
Found at i:11571962 original size:30 final size:30
Alignment explanation
Indices: 11571932--11571988 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
11571922 CCACCCAACT
11571932 TTTTG-AAAATTACAATTTTGCCCCCAAAC
1 TTTTGCAAAATTACAATTTTGCCCCCAAAC
* * *
11571961 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGCAAAATTACAATTTTGCCCCCAA
11571989 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
TTTTGCAAAATTACAATTTTGCCCCCAAAC
Found at i:11574140 original size:37 final size:38
Alignment explanation
Indices: 11574081--11574194 Score: 124
Period size: 37 Copynumber: 3.0 Consensus size: 38
11574071 TGTCAATTTA
* *
11574081 TTACTTCGGATTTATTCGATGAGGCACTGGGTGCCAAC
1 TTACTTCTGATTTAATCGATGAGGCACTGGGTGCCAAC
* * *
11574119 TTACTTCTG-TTTAATCGATGAGACACTGGGTGTCAAT
1 TTACTTCTGATTTAATCGATGAGGCACTGGGTGCCAAC
* *
11574156 TTACTACTTCGAATT-ATCCGATGAGGCACTGGGTGCCAA
1 TTACTTC-T-GATTTAAT-CGATGAGGCACTGGGTGCCAA
11574195 ATTGGTGTGT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
37 30 0.48
38 9 0.14
39 3 0.05
40 21 0.33
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (38 bp):
TTACTTCTGATTTAATCGATGAGGCACTGGGTGCCAAC
Found at i:11580640 original size:26 final size:25
Alignment explanation
Indices: 11580610--11580670 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
11580600 TATTATTTTT
11580610 ATATAAAAATAAATTTTAAAAATA-TA
1 ATATAAAAATAAA--TTAAAAATATTA
* *
11580636 ATATATTAAATACATTAAAAATATTA
1 ATATA-AAAATAAATTAAAAATATTA
*
11580662 AAATAAAAA
1 ATATAAAAA
11580671 ATTCAACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 12 0.41
26 11 0.38
27 6 0.21
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (25 bp):
ATATAAAAATAAATTAAAAATATTA
Found at i:11587374 original size:10 final size:10
Alignment explanation
Indices: 11587359--11587386 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
11587349 ACTATTTTTT
11587359 TTATTTTACA
1 TTATTTTACA
11587369 TTATTTTACA
1 TTATTTTACA
11587379 TTATTTTA
1 TTATTTTA
11587387 GTACATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (10 bp):
TTATTTTACA
Found at i:11587818 original size:20 final size:20
Alignment explanation
Indices: 11587793--11587840 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
11587783 CGAACTTTTT
* *
11587793 GGGTAATTTTTGGGTAATTA
1 GGGTAATTTTCGAGTAATTA
11587813 GGGTAATTTTCGAGTAATTA
1 GGGTAATTTTCGAGTAATTA
*
11587833 GGTTAATT
1 GGGTAATT
11587841 CGATTAATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.44
Consensus pattern (20 bp):
GGGTAATTTTCGAGTAATTA
Found at i:11587839 original size:9 final size:9
Alignment explanation
Indices: 11587827--11587875 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
11587817 AATTTTCGAG
*
11587827 TAATTAGGT
1 TAATTCGGT
*
11587836 TAATTCGAT
1 TAATTCGGT
11587845 TAATTCGGT
1 TAATTCGGT
*
11587854 TAA-TCGGG
1 TAATTCGGT
*
11587862 TAATTCGGG
1 TAATTCGGT
11587871 TAATT
1 TAATT
11587876 TTTAACCAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
8 7 0.20
9 28 0.80
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (9 bp):
TAATTCGGT
Found at i:11587848 original size:18 final size:18
Alignment explanation
Indices: 11587806--11587866 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
11587796 TAATTTTTGG
*
11587806 GTAATTAGGGTAATTTTCGA
1 GTAATTAGGTTAA--TTCGA
11587826 GTAATTAGGTTAATTCGA
1 GTAATTAGGTTAATTCGA
* * *
11587844 TTAATTCGGTTAA-TCGG
1 GTAATTAGGTTAATTCGA
11587861 GTAATT
1 GTAATT
11587867 CGGGTAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
17 8 0.22
18 16 0.44
20 12 0.33
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.41
Consensus pattern (18 bp):
GTAATTAGGTTAATTCGA
Found at i:11587867 original size:17 final size:17
Alignment explanation
Indices: 11587822--11587874 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
11587812 AGGGTAATTT
*
11587822 TCGAGTAATTAGGTTAA
1 TCGAGTAATTCGGTTAA
*
11587839 TTCGATTAATTCGGTTAA
1 -TCGAGTAATTCGGTTAA
* *
11587857 TCGGGTAATTCGGGTAA
1 TCGAGTAATTCGGTTAA
11587874 T
1 T
11587875 TTTTAACCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 15 0.50
18 15 0.50
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.38
Consensus pattern (17 bp):
TCGAGTAATTCGGTTAA
Found at i:11588212 original size:8 final size:8
Alignment explanation
Indices: 11588199--11588234 Score: 54
Period size: 8 Copynumber: 4.2 Consensus size: 8
11588189 TTAAAAAATA
11588199 TATTATTT
1 TATTATTT
11588207 TATTATTT
1 TATTATTT
11588215 TATTATTT
1 TATTATTT
11588223 TACATTATTT
1 T--ATTATTT
11588233 TA
1 TA
11588235 GTACATTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 18 0.69
10 8 0.31
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (8 bp):
TATTATTT
Found at i:11588563 original size:14 final size:15
Alignment explanation
Indices: 11588538--11588566 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
11588528 TATAATGTAC
11588538 TAAAATAATTTAAAA
1 TAAAATAATTTAAAA
11588553 TAAAA-AATTTAAAA
1 TAAAATAATTTAAAA
11588567 AATAGTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAATAATTTAAAA
Found at i:11588697 original size:155 final size:153
Alignment explanation
Indices: 11588298--11588771 Score: 683
Period size: 151 Copynumber: 3.1 Consensus size: 153
11588288 AAAATCCGAG
* * * *
11588298 AAAAAATACGAACAAAAGGCTGAAATAAGAGTTTTTTTAAAATTTATTTAAAAAACACACTAAAT
1 AAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTTAAATTTATTTAAAAAACACACTAAAT
*
11588363 TAATACATTTCAAATATGATGTACTAAAATAATGTAAAATAATAAAA-TACAAAAATAATATATT
66 TAATACATTTCAAATATGATGTACTAAAATAATGTAAAATAA-AAAATTA-AAAAATAGTATA-T
* *
11588427 TTTATTGAAAGTAATAAAATCCGGG--
128 TTT-TTAAAAGTAATAAAATTCGGGAA
*
11588452 AAAAAATACGAACAAAGGGCCGAAATAA-GG-ATTTTTT-AATTTATTTAAAAAACACACTAAAT
1 AAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTTAAATTTATTTAAAAAACACACTAAAT
* *
11588514 TAATACATTTCAAATATAATGTACTAAAATAATTTAAAATAAAAAATTTAAAAAATAGTATATTT
66 TAATACATTTCAAATATGATGTACTAAAATAATGTAAAATAAAAAA-TTAAAAAATAGTATATTT
11588579 TTTAAAAGTAATAAAATTCGGGAA
130 TTTAAAAGTAATAAAATTCGGGAA
** * * *
11588603 AAAAAATATTAACATAGGGTCGAAATAAGGGTTTTTTTTTAAATTTATTTAAAAAACACAGTAAA
1 AAAAAATACGAACAAAGGGCCGAAATAAGGG-TTTTTTTTAAATTTATTTAAAAAACACACTAAA
*
11588668 TTAATACATTTCAAATATGATATACTAAAATAATGTAAAATTAAAAAATTAAAAAATAGTATATT
65 TTAATACATTTCAAATATGATGTACTAAAATAATGTAAAA-TAAAAAATTAAAAAATAGTATATT
*
11588733 TTTTAAAAGTAATAAAA-TCTGGAA
129 TTTTAAAAGTAATAAAATTCGGGAA
11588757 AAAAAATACGAACAA
1 AAAAAATACGAACAA
11588772 TTGGTGCCAC
Statistics
Matches: 288, Mismatches: 23, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
149 19 0.07
150 8 0.03
151 100 0.35
152 9 0.03
153 1 0.00
154 50 0.17
155 94 0.33
156 7 0.02
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.31
Consensus pattern (153 bp):
AAAAAATACGAACAAAGGGCCGAAATAAGGGTTTTTTTTAAATTTATTTAAAAAACACACTAAAT
TAATACATTTCAAATATGATGTACTAAAATAATGTAAAATAAAAAATTAAAAAATAGTATATTTT
TTAAAAGTAATAAAATTCGGGAA
Found at i:11590282 original size:8 final size:9
Alignment explanation
Indices: 11590263--11590301 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
11590253 ATATAAAATT
11590263 ATTTTTTAA
1 ATTTTTTAA
11590272 ATTTTTTAA
1 ATTTTTTAA
*
11590281 TTTTTTTAA
1 ATTTTTTAA
**
11590290 AAATTTTAA
1 ATTTTTTAA
11590299 ATT
1 ATT
11590302 AATAAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (9 bp):
ATTTTTTAA
Found at i:11592027 original size:22 final size:24
Alignment explanation
Indices: 11591994--11592040 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
11591984 TATAAAAATA
11591994 TTATTAATTTT-ACAATATATTTT
1 TTATTAATTTTAACAATATATTTT
*
11592017 TTATT-ATTTTAATAATATATTTT
1 TTATTAATTTTAACAATATATTTT
11592040 T
1 T
11592041 ACATATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (24 bp):
TTATTAATTTTAACAATATATTTT
Found at i:11592047 original size:23 final size:24
Alignment explanation
Indices: 11592007--11592055 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
11591997 TTAATTTTAC
*
11592007 AATATATTTTTTATTATTTTA-AT
1 AATATATTTTTTAATATTTTATAT
11592030 AATATA-TTTTTACATATTTTATAT
1 AATATATTTTTTA-ATATTTTATAT
11592054 AA
1 AA
11592056 AAAATAAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 13 0.57
24 4 0.17
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
AATATATTTTTTAATATTTTATAT
Found at i:11593569 original size:17 final size:17
Alignment explanation
Indices: 11593544--11593577 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11593534 GAATTTGATG
* *
11593544 AAAATAATTTATTAAAT
1 AAAAAAATTTACTAAAT
11593561 AAAAAAATTTACTAAAT
1 AAAAAAATTTACTAAAT
11593578 TTGATGAGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
AAAAAAATTTACTAAAT
Found at i:11594878 original size:13 final size:13
Alignment explanation
Indices: 11594862--11594940 Score: 71
Period size: 13 Copynumber: 6.5 Consensus size: 13
11594852 AATTTTGAAT
11594862 TATTTAATGATAA
1 TATTTAATGATAA
*
11594875 TATTTAA--A-AT
1 TATTTAATGATAA
*
11594885 TATTTAACGATAA
1 TATTTAATGATAA
*
11594898 TATTTAA--A-AT
1 TATTTAATGATAA
*
11594908 TATTTAGTGATAA
1 TATTTAATGATAA
*
11594921 TATTTAGTGATAA
1 TATTTAATGATAA
11594934 TATTTAA
1 TATTTAA
11594941 AAAACAATCT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
10 15 0.28
11 2 0.04
12 2 0.04
13 35 0.65
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.47
Consensus pattern (13 bp):
TATTTAATGATAA
Found at i:11594879 original size:23 final size:23
Alignment explanation
Indices: 11594859--11594926 Score: 118
Period size: 23 Copynumber: 3.0 Consensus size: 23
11594849 TTAAATTTTG
11594859 AATTATTTAATGATAATATTTAA
1 AATTATTTAATGATAATATTTAA
*
11594882 AATTATTTAACGATAATATTTAA
1 AATTATTTAATGATAATATTTAA
*
11594905 AATTATTTAGTGATAATATTTA
1 AATTATTTAATGATAATATTTA
11594927 GTGATAATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (23 bp):
AATTATTTAATGATAATATTTAA
Found at i:11609952 original size:31 final size:29
Alignment explanation
Indices: 11609882--11609952 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
11609872 AAATCAAAAT
** *
11609882 TTCATGTATAAAATTACACAAAATTAAAT
1 TTCATGTATAAAATTACACAAAAGCAAAG
*
11609911 TTCATATATAAAATTACA-AGTTAAAGCAAAG
1 TTCATGTATAAAATTACACA---AAAGCAAAG
11609942 TTCATGTATAA
1 TTCATGTATAA
11609953 TTTTGAGATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
28 1 0.03
29 17 0.50
31 16 0.47
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (29 bp):
TTCATGTATAAAATTACACAAAAGCAAAG
Found at i:11615753 original size:5 final size:5
Alignment explanation
Indices: 11615743--11615767 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
11615733 AGAAAGAAAG
11615743 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
11615768 GCGTATTTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:11624741 original size:29 final size:30
Alignment explanation
Indices: 11624707--11624801 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
11624697 TGTATATGAT
*
11624707 ACATG-AACTTTAATTTGGTGT-AATTATAC
1 ACATGAAACTTTAATTTGGT-TCAAATATAC
* *
11624736 ACATGAAACTTTGATTGTGGTTCAAATATAT
1 ACATGAAACTTTAATT-TGGTTCAAATATAC
* *
11624767 AAATGAAACTTTAATTTTGATTC-AATCATAC
1 ACATGAAACTTTAA-TTTGGTTCAAAT-ATAC
11624798 ACAT
1 ACAT
11624802 TTAATGAAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
29 5 0.09
30 13 0.25
31 33 0.62
32 2 0.04
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.39
Consensus pattern (30 bp):
ACATGAAACTTTAATTTGGTTCAAATATAC
Found at i:11639429 original size:24 final size:24
Alignment explanation
Indices: 11639387--11639435 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
11639377 ACAGTAATCC
* *
11639387 TTTATTTTATCTTATCTTATTTTA
1 TTTACTTTATCTTATCTTAATTTA
11639411 TTTACTTTATCTT-TGCTTAATTTA
1 TTTACTTTATCTTAT-CTTAATTTA
11639435 T
1 T
11639436 AGGATTTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.20, C:0.10, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTACTTTATCTTATCTTAATTTA
Found at i:11644278 original size:58 final size:58
Alignment explanation
Indices: 11644208--11644321 Score: 194
Period size: 58 Copynumber: 2.0 Consensus size: 58
11644198 TTTCAAGGTT
*
11644208 AGCCAGTTTCCGTCCATC-AACAGGGTTTCATTGTATTCAATTTAGTAGTGTGATTGTC
1 AGCCAGTTTCCGTCCATCGAA-AGGGTTTCATTGTATTCAATTTAATAGTGTGATTGTC
*
11644266 AGCCAGTTTCCGTCCATCGAAAGGGTTTCTTTGTATTCAATTTAATAGTGTGATTG
1 AGCCAGTTTCCGTCCATCGAAAGGGTTTCATTGTATTCAATTTAATAGTGTGATTG
11644322 AATATCAGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
58 51 0.96
59 2 0.04
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.39
Consensus pattern (58 bp):
AGCCAGTTTCCGTCCATCGAAAGGGTTTCATTGTATTCAATTTAATAGTGTGATTGTC
Found at i:11660084 original size:22 final size:23
Alignment explanation
Indices: 11660055--11660129 Score: 75
Period size: 22 Copynumber: 3.3 Consensus size: 23
11660045 ATTAAATTGA
11660055 TTAT-ATAATTTATTAAAAT-AT
1 TTATAATAATTTATTAAAATAAT
**
11660076 TTATAATAAAATATTAGAAGATACAT
1 TTATAATAATTTATTA-AA-ATA-AT
*
11660102 TT-TAATAATTTATTAAATTAAT
1 TTATAATAATTTATTAAAATAAT
11660124 TTATAA
1 TTATAA
11660130 ATTCACATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
21 4 0.09
22 13 0.30
23 7 0.16
24 4 0.09
25 11 0.26
26 4 0.09
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (23 bp):
TTATAATAATTTATTAAAATAAT
Found at i:11662682 original size:6 final size:6
Alignment explanation
Indices: 11662671--11662705 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
11662661 TTTAGATATC
11662671 AAAATT AAAATT AAAATT AAAATT AAAATT AAAAT
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAAT
11662706 CCACTTCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:11671908 original size:21 final size:22
Alignment explanation
Indices: 11671882--11671928 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
11671872 CTCTGCTCAA
*
11671882 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
11671903 ACTCCACCTGCTGCGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
11671925 ACTC
1 ACTC
11671929 ACTCCTTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.21
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:11680517 original size:2 final size:2
Alignment explanation
Indices: 11680504--11680537 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
11680494 CTCATCCACA
*
11680504 TC TC TC TT 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 TC TC TC TC
11680538 CCACTCTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:11680937 original size:14 final size:15
Alignment explanation
Indices: 11680913--11680946 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
11680903 TGTCTTTGGA
*
11680913 TTTTCTTTTTT-CCT
1 TTTTTTTTTTTCCCT
11680927 TTTTTTTTTTTCCCT
1 TTTTTTTTTTTCCCT
11680942 TTTTT
1 TTTTT
11680947 GGTTTGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTTTCCCT
Found at i:11681405 original size:6 final size:7
Alignment explanation
Indices: 11681388--11681412 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
11681378 TCTTGGTGGG
11681388 TTTTTTA
1 TTTTTTA
11681395 TTTTTTA
1 TTTTTTA
11681402 TTTTTTA
1 TTTTTTA
11681409 TTTT
1 TTTT
11681413 GAATCATACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:11687169 original size:19 final size:19
Alignment explanation
Indices: 11687147--11687184 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
11687137 CTATATTTTG
*
11687147 AAATATAATT-TATATAAAA
1 AAATACAATTATA-ATAAAA
11687166 AAATACAATTATAATAAAA
1 AAATACAATTATAATAAAA
11687185 CATTACATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATACAATTATAATAAAA
Found at i:11688923 original size:13 final size:13
Alignment explanation
Indices: 11688902--11688934 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
11688892 GAGAGTATTG
*
11688902 CATGCGCCCTCTA
1 CATGGGCCCTCTA
11688915 CATGGGCCCTCTA
1 CATGGGCCCTCTA
11688928 CATGGGC
1 CATGGGC
11688935 TTCTGCCTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.39, G:0.24, T:0.21
Consensus pattern (13 bp):
CATGGGCCCTCTA
Found at i:11697732 original size:26 final size:26
Alignment explanation
Indices: 11697702--11697752 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
11697692 TTCAAAGAAT
*
11697702 TTTGATCTCTGTTGAAAAATAATTCA
1 TTTGATATCTGTTGAAAAATAATTCA
*
11697728 TTTGATATCTGTTGACAAATAATTC
1 TTTGATATCTGTTGAAAAATAATTC
11697753 TTAAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (26 bp):
TTTGATATCTGTTGAAAAATAATTCA
Found at i:11715733 original size:21 final size:21
Alignment explanation
Indices: 11715709--11715749 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
11715699 ACCTTTTCTA
*
11715709 AAGTTAAAAGTCAAAACTATC
1 AAGTTAAAAGGCAAAACTATC
*
11715730 AAGTTAAAAGGCAAATCTAT
1 AAGTTAAAAGGCAAAACTAT
11715750 GTTGTTCTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.24
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACTATC
Found at i:11717219 original size:20 final size:21
Alignment explanation
Indices: 11717196--11717234 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
11717186 ACTAAAAAAA
11717196 TTAAATAATAAAAT-AAAAGT
1 TTAAATAATAAAATGAAAAGT
*
11717216 TTAAATATTAAAATGAAAA
1 TTAAATAATAAAATGAAAA
11717235 AAATAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (21 bp):
TTAAATAATAAAATGAAAAGT
Found at i:11719648 original size:32 final size:32
Alignment explanation
Indices: 11719611--11719675 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
11719601 AACTTATGAA
11719611 ATTACAATGATAAACACCTATTAAAACATCTT
1 ATTACAATGATAAACACCTATTAAAACATCTT
11719643 ATTACAATGATAAACACCTATTAAAACATCTT
1 ATTACAATGATAAACACCTATTAAAACATCTT
11719675 A
1 A
11719676 CTCATCGCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.48, C:0.18, G:0.03, T:0.31
Consensus pattern (32 bp):
ATTACAATGATAAACACCTATTAAAACATCTT
Found at i:11726779 original size:21 final size:20
Alignment explanation
Indices: 11726750--11726798 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 20
11726740 TCTCTAAAAT
11726750 TTTGATAAA-TATTTATATTTA
1 TTTG-TAAAGTATTT-TATTTA
11726771 TCTTGTAAATGTATTTTATTTA
1 T-TTGTAAA-GTATTTTATTTA
11726793 TTTGTA
1 TTTGTA
11726799 GAGGCAACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 10 0.40
22 10 0.40
23 5 0.20
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (20 bp):
TTTGTAAAGTATTTTATTTA
Found at i:11727532 original size:24 final size:24
Alignment explanation
Indices: 11727504--11727552 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
11727494 AAATTATGTC
11727504 AATCTTCTTATTAGTCTTCAATAA
1 AATCTTCTTATTAGTCTTCAATAA
11727528 AATCTTCTTATTAGTCTTCAATAA
1 AATCTTCTTATTAGTCTTCAATAA
11727552 A
1 A
11727553 GGGATAACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.04, T:0.45
Consensus pattern (24 bp):
AATCTTCTTATTAGTCTTCAATAA
Found at i:11733196 original size:12 final size:12
Alignment explanation
Indices: 11733179--11733212 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
11733169 TCTTATATAG
11733179 ATATATAATTTT
1 ATATATAATTTT
*
11733191 ATATATAACTTT
1 ATATATAATTTT
*
11733203 ATATAAAATT
1 ATATATAATT
11733213 ATTTTATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (12 bp):
ATATATAATTTT
Found at i:11736809 original size:21 final size:22
Alignment explanation
Indices: 11736785--11736857 Score: 71
Period size: 23 Copynumber: 3.4 Consensus size: 22
11736775 TTTAACAAAG
11736785 TTATAATATTTTTTTATAA-TT
1 TTATAATATTTTTTTATAATTT
*
11736806 TTAT-ATA-ATTTTTATAATTTT
1 TTATAATATTTTTTTATAA-TTT
* *
11736827 TTATAATATTTTTCATATTATTT
1 TTATAATATTTTT-TTATAATTT
*
11736850 TTAAAATA
1 TTATAATA
11736858 CAAATTTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
19 9 0.21
20 3 0.07
21 10 0.24
22 3 0.07
23 13 0.31
24 4 0.10
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (22 bp):
TTATAATATTTTTTTATAATTT
Found at i:11736819 original size:19 final size:18
Alignment explanation
Indices: 11736795--11736936 Score: 82
Period size: 17 Copynumber: 7.7 Consensus size: 18
11736785 TTATAATATT
11736795 TTTTTATAATTTTATATAA
1 TTTTTATAATTTTATA-AA
11736814 TTTTTATAATTTTTTATAATA
1 TTTTTATAA--TTTTATAA-A
11736835 TTTTTCATATTATTTT-TAAA
1 TTTTT-ATA--ATTTTATAAA
* **
11736855 -ATACA-AATTTTATAAA
1 TTTTTATAATTTTATAAA
*
11736871 TTTTCTATAATTTTCA-CAA
1 TTTT-TATAATTTT-ATAAA
* *
11736890 TTTTTA-ATTTATTAT-AT
1 TTTTTATAATT-TTATAAA
*
11736907 TTTTTATAAATTTA-AAA
1 TTTTTATAATTTTATAAA
11736924 TTTTTATAATTTT
1 TTTTTATAATTTT
11736937 TTTCTATATT
Statistics
Matches: 95, Mismatches: 13, Indels: 32
0.68 0.09 0.23
Matches are distributed among these distances:
15 5 0.05
16 4 0.04
17 29 0.31
18 8 0.08
19 22 0.23
20 3 0.03
21 16 0.17
22 7 0.07
24 1 0.01
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTTTATAATTTTATAAA
Found at i:11736821 original size:9 final size:9
Alignment explanation
Indices: 11736795--11736937 Score: 76
Period size: 10 Copynumber: 14.6 Consensus size: 9
11736785 TTATAATATT
11736795 TTTTTATAA
1 TTTTTATAA
11736804 TTTTATATAA
1 TTTT-TATAA
11736814 TTTTTATAA
1 TTTTTATAA
11736823 TTTTTTATAATA
1 -TTTTTAT-A-A
11736835 TTTTTCATATTA
1 TTTTT-ATA--A
11736847 TTTTTAAAATACAA
1 TTTTT---AT--AA
*
11736861 ATTTTATAAA
1 TTTTTAT-AA
11736871 TTTTCTATAA
1 TTTT-TATAA
* *
11736881 TTTTCACAA
1 TTTTTATAA
11736890 -TTTT-TAA
1 TTTTTATAA
*
11736897 TTTATTATAT
1 TTT-TTATAA
11736907 TTTTTATAA
1 TTTTTATAA
* *
11736916 -ATTTAAAA
1 TTTTTATAA
11736924 TTTTTATAA
1 TTTTTATAA
11736933 TTTTT
1 TTTTT
11736938 TTCTATATTG
Statistics
Matches: 105, Mismatches: 14, Indels: 30
0.70 0.09 0.20
Matches are distributed among these distances:
7 2 0.02
8 11 0.10
9 30 0.29
10 32 0.30
11 12 0.11
12 10 0.10
14 7 0.07
16 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:11736899 original size:35 final size:34
Alignment explanation
Indices: 11736863--11736929 Score: 82
Period size: 35 Copynumber: 2.0 Consensus size: 34
11736853 AAATACAAAT
* *
11736863 TTTA-TAAATTTTCTATAATTTTCACAATTTTTAA
1 TTTATTAAATTTTCTATAAATTT-AAAATTTTTAA
* *
11736897 TTTATTATATTTTTTATAAATTTAAAATTTTTA
1 TTTATTAAATTTTCTATAAATTTAAAATTTTTA
11736930 TAATTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 13 0.46
35 15 0.54
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (34 bp):
TTTATTAAATTTTCTATAAATTTAAAATTTTTAA
Found at i:11736937 original size:26 final size:25
Alignment explanation
Indices: 11736863--11736937 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 25
11736853 AAATACAAAT
* *
11736863 TTTATAAATTTTCTATAATTTTCACAA
1 TTTA-AAATTTT-TATAATTTTTAAAA
** *
11736890 TTTTTAATTTATTATATTTTTTATAAA
1 TTTAAAATTT-TTATAATTTTTA-AAA
11736917 TTTAAAATTTTTATAATTTTT
1 TTTAAAATTTTTATAATTTTT
11736938 TTCTATATTG
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
26 24 0.63
27 14 0.37
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTAAAATTTTTATAATTTTTAAAA
Found at i:11737023 original size:31 final size:31
Alignment explanation
Indices: 11736988--11737047 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
11736978 TGTTAAAAAT
*
11736988 TCTTATAAAATAA-TTAAAAACTCAATTAAGA
1 TCTTAAAAAATAATTTAAAAA-TCAATTAAGA
11737019 TCTTAAAAAATAATTTAAAAATCAATTAA
1 TCTTAAAAAATAATTTAAAAATCAATTAA
11737048 ACAGTCACGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.57, C:0.08, G:0.02, T:0.33
Consensus pattern (31 bp):
TCTTAAAAAATAATTTAAAAATCAATTAAGA
Done.