Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 179 of 202
Found at i:55463633 original size:14 final size:13
Alignment explanation
Indices: 55463613--55463670 Score: 82
Period size: 13 Copynumber: 4.4 Consensus size: 13
55463603 TATTATGCCT
55463613 AAAAAAAACAAAA
1 AAAAAAAACAAAA
55463626 ACAAAAAAACAAAA
1 A-AAAAAAACAAAA
55463640 AAAACAAAAC-AAA
1 AAAA-AAAACAAAA
*
55463653 AAAACAAACAAAA
1 AAAAAAAACAAAA
55463666 AAAAA
1 AAAAA
55463671 TCAAGATGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
12 4 0.10
13 18 0.45
14 18 0.45
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAACAAAA
Found at i:55463670 original size:17 final size:16
Alignment explanation
Indices: 55463613--55463670 Score: 80
Period size: 17 Copynumber: 3.5 Consensus size: 16
55463603 TATTATGCCT
*
55463613 AAAAAAAACAAAAACA
1 AAAAAAAAAAAAAACA
55463629 AAAAAACAAAAAAAACA
1 AAAAAA-AAAAAAAACA
*
55463646 AAACAAAAAAACAAACA
1 AAA-AAAAAAAAAAACA
55463663 AAAAAAAA
1 AAAAAAAA
55463671 TCAAGATGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
16 11 0.29
17 24 0.63
18 3 0.08
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAACA
Found at i:55463683 original size:26 final size:22
Alignment explanation
Indices: 55463613--55463670 Score: 91
Period size: 22 Copynumber: 2.6 Consensus size: 22
55463603 TATTATGCCT
55463613 AAAAAAAACAAAAACAAAAAAAC
1 AAAAAAAAC-AAAACAAAAAAAC
55463636 AAAAAAAACAAAACAAAAAAAC
1 AAAAAAAACAAAACAAAAAAAC
55463658 AAACAAAAA-AAAA
1 AAA-AAAAACAAAA
55463671 TCAAGATGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
22 20 0.59
23 14 0.41
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (22 bp):
AAAAAAAACAAAACAAAAAAAC
Found at i:55464723 original size:79 final size:77
Alignment explanation
Indices: 55464544--55464972 Score: 614
Period size: 79 Copynumber: 5.5 Consensus size: 77
55464534 GTTTTTTTTT
* *
55464544 AAAATCAACTCATAATACAGAGATGAGTTGAGCCTCGGGTCACGCTGAGGTA-TTTTT-AATTTA
1 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTAAATTTC
*
55464607 TGTCTTTTTTTAA
66 TG-CTTTTTTCAA
55464620 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTAAAAATT
1 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTT--AAATT
55464685 TCTGCTTTTTTCAA
64 TCTGCTTTTTTCAA
*
55464699 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTTGGGTCACGCTGAGGTATTTTTTAAAATTT
1 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTT-AAATTT
*
55464764 CTGTTTTTTTCAAA
65 CTGCTTTTTTC-AA
*
55464778 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTTAATTTC
1 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTAAATTTC
55464843 TGCTTTTTTCAAA
66 TGCTTTTTTC-AA
** * *
55464856 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAATT
1 AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA-TT-TTTTAAATT
* *
55464921 TATG-TTTTTT-GA
64 TCTGCTTTTTTCAA
* * *
55464933 AAAATCAACTCATATTGCGAGAGGTGAGTCGAGCCTCGGG
1 AAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGG
55464973 GCACATGTCG
Statistics
Matches: 326, Mismatches: 19, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
76 51 0.16
77 22 0.07
78 102 0.31
79 133 0.41
80 18 0.06
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (77 bp):
AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTTAAATTTC
TGCTTTTTTCAA
Found at i:55465352 original size:16 final size:16
Alignment explanation
Indices: 55465333--55465365 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
55465323 TAAAATTTTG
55465333 AAAAAATAAAAAATAC
1 AAAAAATAAAAAATAC
*
55465349 AAAAAATAAAAATTAC
1 AAAAAATAAAAAATAC
55465365 A
1 A
55465366 TTTTGACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAAAATAAAAAATAC
Found at i:55466087 original size:11 final size:12
Alignment explanation
Indices: 55466071--55466117 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
55466061 CCCAAACAGT
55466071 AAAGAAG-AAAG
1 AAAGAAGAAAAG
55466082 AAAGAAGAAAAG
1 AAAGAAGAAAAG
55466094 AAAGATAGGAAAAGG
1 AAAGA-A-GAAAA-G
55466109 AAA-AAGAAA
1 AAAGAAGAAA
55466118 TAAAAAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
11 7 0.22
12 13 0.41
13 2 0.06
14 6 0.19
15 4 0.12
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (12 bp):
AAAGAAGAAAAG
Found at i:55466199 original size:14 final size:14
Alignment explanation
Indices: 55466156--55466190 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
55466146 TTTTGGCAGT
*
55466156 CCAGCAGCAGTCCA
1 CCAGCAGCAGCCCA
55466170 CCAGCAGCAGCCCA
1 CCAGCAGCAGCCCA
55466184 CCAGCAG
1 CCAGCAG
55466191 TGGCCCACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.29, C:0.46, G:0.23, T:0.03
Consensus pattern (14 bp):
CCAGCAGCAGCCCA
Found at i:55466316 original size:15 final size:15
Alignment explanation
Indices: 55466296--55466324 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55466286 CCAACAGCAG
55466296 CAGGCCACTGCCCAA
1 CAGGCCACTGCCCAA
55466311 CAGGCCACTGCCCA
1 CAGGCCACTGCCCA
55466325 GCCCAACGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.48, G:0.21, T:0.07
Consensus pattern (15 bp):
CAGGCCACTGCCCAA
Found at i:55466744 original size:20 final size:20
Alignment explanation
Indices: 55466716--55466753 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55466706 GAAAATATTC
*
55466716 AAAATTCCTCGTGTTTTAAT
1 AAAAATCCTCGTGTTTTAAT
55466736 AAAAATCCTCGTGTTTTA
1 AAAAATCCTCGTGTTTTA
55466754 TTAGAATCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
AAAAATCCTCGTGTTTTAAT
Found at i:55466899 original size:17 final size:17
Alignment explanation
Indices: 55466874--55466917 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
55466864 AAAAATCGTG
*
55466874 TTTCAAAAATTT-TCATG
1 TTTC-AAAATTTCTCATC
55466891 TCTTCAAAATTTCTCATC
1 T-TTCAAAATTTCTCATC
55466909 TTTCAAAAT
1 TTTCAAAAT
55466918 AATAATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.34, C:0.18, G:0.02, T:0.45
Consensus pattern (17 bp):
TTTCAAAATTTCTCATC
Found at i:55466979 original size:48 final size:50
Alignment explanation
Indices: 55466927--55467045 Score: 188
Period size: 48 Copynumber: 2.4 Consensus size: 50
55466917 TAATAATAAT
55466927 AAAATTTCCCGTGTTTCAAAAAAATATATTCGTGTTTC-TTTTTTTC-AA
1 AAAATTTCCCGTGTTTCAAAAAAATATATTCGTGTTTCTTTTTTTTCAAA
*
55466975 AAAATTTCCCATGTTTCAAAAAAATATATTCGTGTTTCTTTTTTTTCAAA
1 AAAATTTCCCGTGTTTCAAAAAAATATATTCGTGTTTCTTTTTTTTCAAA
** *
55467025 AAAAAATCTCGTGTTTCAAAA
1 AAAATTTCCCGTGTTTCAAAA
55467046 TTTTCGTTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
48 37 0.58
49 8 0.12
50 19 0.30
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (50 bp):
AAAATTTCCCGTGTTTCAAAAAAATATATTCGTGTTTCTTTTTTTTCAAA
Found at i:55467401 original size:42 final size:42
Alignment explanation
Indices: 55467354--55467436 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
55467344 CTTTTTTAGG
55467354 AAAATTTAAAAATAAATTTTTCTTCTAAAAAGAGAATTTATA
1 AAAATTTAAAAATAAATTTTTCTTCTAAAAAGAGAATTTATA
55467396 AAAATTTAAAAATAAATTTTTCTTCTAAAAAGAGAATTTAT
1 AAAATTTAAAAATAAATTTTTCTTCTAAAAAGAGAATTTAT
55467437 TAGGTGTCCG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (42 bp):
AAAATTTAAAAATAAATTTTTCTTCTAAAAAGAGAATTTATA
Found at i:55475523 original size:164 final size:164
Alignment explanation
Indices: 55475184--55475581 Score: 484
Period size: 164 Copynumber: 2.4 Consensus size: 164
55475174 TGGCAGCTTT
* * *
55475184 GACGTCGATTTCGCCTCCTTTTT-CTTCCCTACAATCCCACAACCAAAACCCCACCAAGAAAACA
1 GACGTCGATTCCGTCT-CTTTTTCCTTCCCTACAATCCCATAACCAAAACCCCACCAAG-AAA-A
* * * * *
55475248 GCATTATATATGCTTGTCAAACCCTAAAACAA---AGT-AAAAAACGGTAACCGAGTTAAGAACT
63 -C---A-ATGT-C-AGTCAAACTCTAAAA-AATTGAATAAAAAAACGATAACCGAGTTAAGAACT
* * ** * *
55475309 GAGTCACCTGTTTCTTCAGGTTCCCCTCTCGCAAATGGCAGTTTC
120 GACTCACCTGTTTCTTCAGGTTCCCCTATAACAAATGGCAATTGC
*
55475354 GACGTCGATTCCGTCTCTTCTTT-CTTCCCTATAATCCCATAACCAAAACCCCACCAAGAAAACA
1 GACGTCGATTCCGTCTCTT-TTTCCTTCCCTACAATCCCATAACCAAAACCCCACCAAGAAAACA
*
55475418 ATGTCAGTCAAACTCTAAAAAATTGAATAAAAAAACGATGACCGAGTTAAGAACTGACTCACCTG
65 ATGTCAGTCAAACTCTAAAAAATTGAATAAAAAAACGATAACCGAGTTAAGAACTGACTCACCTG
55475483 TTTCTTCAGGTTCCCCTATAACAAATGGCAATTGC
130 TTTCTTCAGGTTCCCCTATAACAAATGGCAATTGC
**
55475518 GACGTCGATTTTGTCTCTTTTTCCTTCCCTACAATCCCATAACCAAAACCCCACCAAGAAAACA
1 GACGTCGATTCCGTCTCTTTTTCCTTCCCTACAATCCCATAACCAAAACCCCACCAAGAAAACA
55475582 GCATTATATA
Statistics
Matches: 203, Mismatches: 19, Indels: 18
0.85 0.08 0.08
Matches are distributed among these distances:
160 2 0.01
161 13 0.06
162 1 0.00
163 8 0.04
164 121 0.60
167 1 0.00
168 1 0.00
169 6 0.03
170 50 0.25
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.26
Consensus pattern (164 bp):
GACGTCGATTCCGTCTCTTTTTCCTTCCCTACAATCCCATAACCAAAACCCCACCAAGAAAACAA
TGTCAGTCAAACTCTAAAAAATTGAATAAAAAAACGATAACCGAGTTAAGAACTGACTCACCTGT
TTCTTCAGGTTCCCCTATAACAAATGGCAATTGC
Found at i:55476811 original size:18 final size:20
Alignment explanation
Indices: 55476790--55476832 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
55476780 AAAATATATA
*
55476790 AAATAT-AAAATGTT-TAAT
1 AAATATGAAAATATTATAAT
*
55476808 AAATATGCAAATATTATAAT
1 AAATATGAAAATATTATAAT
55476828 AAATA
1 AAATA
55476833 CCAGTCATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 6 0.29
20 9 0.43
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (20 bp):
AAATATGAAAATATTATAAT
Found at i:55480299 original size:27 final size:26
Alignment explanation
Indices: 55480269--55480324 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
55480259 ATTTTTTACT
*
55480269 TTTAATAAT-TAATGAATTATTTTTAAA
1 TTTAATAATAT-ATGAAATA-TTTTAAA
*
55480296 TTTAATGATATATGAAATATTTTAAA
1 TTTAATAATATATGAAATATTTTAAA
55480322 TTT
1 TTT
55480325 TTAAATATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 10 0.38
27 15 0.58
28 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (26 bp):
TTTAATAATATATGAAATATTTTAAA
Found at i:55485968 original size:20 final size:20
Alignment explanation
Indices: 55485943--55485980 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
55485933 CGTGATCCGA
55485943 TTAAAACACGAGAATTTTTT
1 TTAAAACACGAGAATTTTTT
55485963 TTAAAACACGAGAATTTT
1 TTAAAACACGAGAATTTT
55485981 GGAAACACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (20 bp):
TTAAAACACGAGAATTTTTT
Found at i:55486012 original size:33 final size:35
Alignment explanation
Indices: 55485946--55486031 Score: 97
Period size: 33 Copynumber: 2.5 Consensus size: 35
55485936 GATCCGATTA
* * *
55485946 AAACACGAGAATTTTTTTTAAAACACGAGAATTT-TGG
1 AAACACGAG-A-TTTTTTAAAAAAACGAAAATTTAT-G
55485983 AAACAC-A-ATTTTTTAAAAAAACGAAAATTTATG
1 AAACACGAGATTTTTTAAAAAAACGAAAATTTATG
55486016 AAACACGAGATTTTTT
1 AAACACGAGATTTTTT
55486032 TTTGAAAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
33 26 0.60
34 3 0.07
35 7 0.16
36 1 0.02
37 6 0.14
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (35 bp):
AAACACGAGATTTTTTAAAAAAACGAAAATTTATG
Found at i:55486076 original size:18 final size:18
Alignment explanation
Indices: 55486054--55486109 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
55486044 AAAATTTTCA
55486054 AAACACCGA-AATTTTTG
1 AAACACCGAGAATTTTTG
*
55486071 ACAACA-CGAGGATTTTTG
1 A-AACACCGAGAATTTTTG
*
55486089 AAACA-CGGGAATTTTCTG
1 AAACACCGAGAATTTT-TG
55486107 AAA
1 AAA
55486110 ACATGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
17 16 0.48
18 17 0.52
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (18 bp):
AAACACCGAGAATTTTTG
Found at i:55486102 original size:17 final size:18
Alignment explanation
Indices: 55486063--55486109 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
55486053 AAAACACCGA
55486063 AATTTTTGACAACACGAGG
1 AATTTTTGA-AACACGAGG
55486082 -ATTTTTGAAACACG-GG
1 AATTTTTGAAACACGAGG
55486098 AATTTTCTGAAA
1 AATTTT-TGAAA
55486110 ACATGTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 2 0.08
17 11 0.42
18 13 0.50
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (18 bp):
AATTTTTGAAACACGAGG
Found at i:55486157 original size:17 final size:17
Alignment explanation
Indices: 55485945--55486158 Score: 94
Period size: 17 Copynumber: 11.9 Consensus size: 17
55485935 TGATCCGATT
*
55485945 AAAACACGAGAATTTTTTTT
1 AAAACACGA-AA--TTTTTG
55485965 AAAACACGAGAA-TTTTG
1 AAAACACGA-AATTTTTG
* * *
55485982 GAAACAC-AATTTTTTA
1 AAAACACGAAATTTTTG
* *
55485998 AAAAAACGAAAATTTATG
1 AAAACACG-AAATTTTTG
*
55486016 -AAACACGAGATTTTTTTTTG
1 AAAACACGA-A---ATTTTTG
* * *
55486036 AAAACACAAAAATTTTC
1 AAAACACGAAATTTTTG
55486053 AAAACACCGAAATTTTTG
1 AAAACA-CGAAATTTTTG
* *
55486071 ACAACACGAGGATTTTTG
1 AAAACACGA-AATTTTTG
*
55486089 -AAACACGGGAATTTTCTG
1 AAAACAC-GAAATTTT-TG
* *
55486107 AAAACATGTAAAATTTTG
1 AAAACACG-AAATTTTTG
*** *
55486125 AAAATTGGAATTTTTTG
1 AAAACACGAAATTTTTG
55486142 AAAACACGAAAATTTTT
1 AAAACACG-AAATTTTT
55486159 CTGATTTTTT
Statistics
Matches: 143, Mismatches: 36, Indels: 32
0.68 0.17 0.15
Matches are distributed among these distances:
15 1 0.01
16 11 0.08
17 52 0.36
18 44 0.31
19 10 0.07
20 18 0.13
21 7 0.05
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (17 bp):
AAAACACGAAATTTTTG
Found at i:55486297 original size:21 final size:18
Alignment explanation
Indices: 55486263--55486310 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 18
55486253 TCGTTACTTT
55486263 ATTTTTGAAAACACGAGAAA
1 ATTTTTGAAAACAC--GAAA
*
55486283 ATTTTTCGAAGACACGAAA
1 ATTTTT-GAAAACACGAAA
55486302 A-TTTTGAAA
1 ATTTTTGAAA
55486311 CCCGAGGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 3 0.12
18 4 0.16
19 5 0.20
20 6 0.24
21 7 0.28
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (18 bp):
ATTTTTGAAAACACGAAA
Found at i:55486673 original size:11 final size:11
Alignment explanation
Indices: 55486657--55486710 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
55486647 CAAATTGAAA
55486657 TTTTCTTTTCT
1 TTTTCTTTTCT
*
55486668 TTTTCTCTTCT
1 TTTTCTTTTCT
*
55486679 TTTT-TTCTTTT
1 TTTTCTT-TTCT
55486690 TTTTCTTTT-T
1 TTTTCTTTTCT
*
55486700 TCTT-TTTTCT
1 TTTTCTTTTCT
55486710 T
1 T
55486711 CTCTCTTCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
9 4 0.11
10 7 0.19
11 23 0.64
12 2 0.06
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTCT
Found at i:55486686 original size:24 final size:24
Alignment explanation
Indices: 55486657--55486707 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
55486647 CAAATTGAAA
55486657 TTTTCTTTTCTTTT-TCTCTTCTTT
1 TTTTCTTTT-TTTTCTCTCTTCTTT
* *
55486681 TTTTCTTTTTTTTCTTTTTTCTTT
1 TTTTCTTTTTTTTCTCTCTTCTTT
55486705 TTT
1 TTT
55486708 CTTCTCTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (24 bp):
TTTTCTTTTTTTTCTCTCTTCTTT
Found at i:55486691 original size:7 final size:7
Alignment explanation
Indices: 55486662--55486710 Score: 57
Period size: 7 Copynumber: 7.0 Consensus size: 7
55486652 TGAAATTTTC
55486662 TTTTCTT
1 TTTTCTT
55486669 TTTCTCTT
1 TTT-TCTT
55486677 CTTTT-TT
1 -TTTTCTT
*
55486684 TCTT-TT
1 TTTTCTT
55486690 TTTTCTT
1 TTTTCTT
55486697 TTTTCTT
1 TTTTCTT
55486704 TTTTCTT
1 TTTTCTT
55486711 CTCTCTTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
6 8 0.22
7 21 0.57
8 5 0.14
9 3 0.08
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTCTT
Found at i:55486695 original size:17 final size:18
Alignment explanation
Indices: 55486662--55486712 Score: 79
Period size: 16 Copynumber: 2.9 Consensus size: 18
55486652 TGAAATTTTC
55486662 TTTTCTTTTTCTCTTCTTT
1 TTTTCTTTTT-TCTTCTTT
55486681 TTTTCTTTTTT-TTC-TT
1 TTTTCTTTTTTCTTCTTT
55486697 TTTTCTTTTTTCTTCT
1 TTTTCTTTTTTCTTCT
55486713 CTCTTCTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 13 0.43
17 6 0.20
18 1 0.03
19 10 0.33
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTCTTTTTTCTTCTTT
Found at i:55486722 original size:28 final size:28
Alignment explanation
Indices: 55486663--55486723 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
55486653 GAAATTTTCT
* *
55486663 TTTCTTTTTCTCTTCTTTTTTTCTTTTT
1 TTTCTTTTTCTCTTCTTTTTTTCTCTTC
55486691 TTTCTTTTT-TCTT-TTTTCTTCTCTCTTC
1 TTTCTTTTTCTCTTCTTTT-TT-TCTCTTC
55486719 TTTCT
1 TTTCT
55486724 GGCCTGCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 4 0.14
27 6 0.21
28 19 0.66
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (28 bp):
TTTCTTTTTCTCTTCTTTTTTTCTCTTC
Found at i:55487044 original size:13 final size:13
Alignment explanation
Indices: 55487013--55487077 Score: 67
Period size: 13 Copynumber: 4.6 Consensus size: 13
55487003 AATTTTTATT
*
55487013 TTTTTATTTTTTC
1 TTTTTCTTTTTTC
55487026 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
55487039 TTTTTCTTCCTTCTTTC
1 TTTTTC-T--TT-TTTC
*
55487056 TTTCTCTTTTTTC
1 TTTTTCTTTTTTC
55487069 TTTCTTCTT
1 TTT-TTCTT
55487078 CTCCGATCGG
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
13 25 0.57
14 7 0.16
16 3 0.07
17 9 0.20
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:55487057 original size:17 final size:17
Alignment explanation
Indices: 55487035--55487079 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
55487025 CTTTTTCTTT
55487035 TTTCTTTTTCTTCCTTC
1 TTTCTTTTTCTTCCTTC
* **
55487052 TTTCTTTCTCTTTTTTC
1 TTTCTTTTTCTTCCTTC
*
55487069 TTTCTTCTTCT
1 TTTCTTTTTCT
55487080 CCGATCGGCC
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:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTCTTTTTCTTCCTTC
Found at i:55487070 original size:7 final size:7
Alignment explanation
Indices: 55487012--55487077 Score: 55
Period size: 7 Copynumber: 9.3 Consensus size: 7
55487002 TAATTTTTAT
*
55487012 TTTTTTA
1 TTTTTTC
55487019 TTTTTTC
1 TTTTTTC
55487026 -TTTTTC
1 TTTTTTC
55487032 TTTTTTC
1 TTTTTTC
55487039 TTTTTCTTCC
1 -TTTT-TT-C
*
55487049 TTCTTTC
1 TTTTTTC
*
55487056 -TTTCTC
1 TTTTTTC
55487062 TTTTTTC
1 TTTTTTC
*
55487069 TTTCTTC
1 TTTTTTC
55487076 TT
1 TT
55487078 CTCCGATCGG
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
6 10 0.21
7 26 0.54
8 6 0.12
9 5 0.10
10 1 0.02
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTTC
Found at i:55487485 original size:29 final size:29
Alignment explanation
Indices: 55487414--55487493 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
55487404 GAGTTTTGAG
* * *
55487414 AAAA-TTTAGGGGTTAAAATGTAATTTTA
1 AAAAGTTTAGTGGTCAAAATGTAATTTCA
*
55487442 AAAAG-TTGGTGGGTCAAAATGTAATTTCA
1 AAAAGTTTAGT-GGTCAAAATGTAATTTCA
55487471 AAAAGTTTAGTGGTCAAAATGTA
1 AAAAGTTTAGTGGTCAAAATGTA
55487494 TTTTTTTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 7 0.16
29 33 0.75
30 4 0.09
ACGTcount: A:0.41, C:0.04, G:0.21, T:0.34
Consensus pattern (29 bp):
AAAAGTTTAGTGGTCAAAATGTAATTTCA
Found at i:55487967 original size:76 final size:77
Alignment explanation
Indices: 55487717--55488402 Score: 1046
Period size: 77 Copynumber: 8.8 Consensus size: 77
55487707 CGCTCGGCAT
55487717 GTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGA-TTTT---AAAAAACAGAAATTTAA
1 GTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAAAACAGAAA-TT-A
* *
55487778 AAGAAATACTTCGGC
64 AA-AAATACCTCAGC
* ** * * * *
55487793 ATGTTTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTTATTTTTTTG-AAAAAAATAGAAATT
1 GTG-ACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGA--TTTTTGAAAAAAAACAGAAATT
55487857 AAAAAAAATACCTCAGC
63 --AAAAAATACCTCAGC
*
55487874 GTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAACAACAGAAATT-AA
1 GTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAAAACAGAAATTAAA
55487938 AAATACCTCAGC
66 AAATACCTCAGC
*
55487950 GTGACCCGAAGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAAAAACAGAAATTAA
1 GTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTG-AAAAAAAACAGAAATT--
*
55488015 AAAAAATACCTCAGT
63 AAAAAATACCTCAGC
55488030 GTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAAAAACAGAAATT-A
1 GTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTG-AAAAAAAACAGAAATTAA
55488094 AAAATACCTCAGC
65 AAAATACCTCAGC
*
55488107 GTGACTCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAAAAACAGAAATTAA
1 GTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTG-AAAAAAAACAGAAATTAA
55488172 AAAATACCTCAGC
65 AAAATACCTCAGC
*
55488185 GTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAACAACAGAAATT-AA
1 GTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAAAACAGAAATTAAA
55488249 AAATACCTCAGC
66 AAATACCTCAGC
*
55488261 GTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAAAATAGAAATTAAA
1 GTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAAAACAGAAATTAAA
55488326 AAATACCTCAGC
66 AAATACCTCAGC
* *
55488338 GTGACCCGAGGCACAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAACAACAGAAATTAAA
1 GTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAAAACAGAAATTAAA
55488403 TTAAAAAAAT
Statistics
Matches: 566, Mismatches: 30, Indels: 27
0.91 0.05 0.04
Matches are distributed among these distances:
76 135 0.24
77 213 0.38
78 65 0.11
79 13 0.02
80 111 0.20
81 14 0.02
82 15 0.03
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (77 bp):
GTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAAAACAGAAATTAAA
AAATACCTCAGC
Found at i:55488281 original size:311 final size:309
Alignment explanation
Indices: 55487716--55488402 Score: 1098
Period size: 311 Copynumber: 2.2 Consensus size: 309
55487706 TCGCTCGGCA
55487716 TGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGA-TTTT---AAAAAACAGAAATTTA
1 TGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAAAACAGAAA-TT-
* * ** * ***
55487777 AAAGAAATACTTCGGCATGTTTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTTATTTTTTTG
64 -AA-AAATACCTCAGCATGACTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
*
55487842 AAAAAAATAGAAATTAAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTAT
127 AAAAAAACAGAAATT-AAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTAT
55487907 GAGTTGATTTTTGAAAAACAACAGAAATTAAAAATACCTCAGCGTGACCCGAAGCTCAACTCACC
191 GAGTTGATTTTTGAAAAACAACAGAAATTAAAAATACCTCAGCGTGACCCGAAGCTCAACTCACC
55487972 TCTCGTATTATGAGTTGATTTTTGAAAAAAAAACAGAAATTAAAAAAAATACCTCAG
256 TCTCGTATTATGAGTTGATTTTTG-AAAAAAAACAGAAATT--AAAAAATACCTCAG
55488029 TGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAAAAACAGAAATTA
1 TGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTG-AAAAAAAACAGAAATTA
* * *
55488094 AAAATACCTCAGCGTGACT-CGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAA
65 AAAATACCTCAGCATGACTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAA
55488158 AAAACAGAAATT-AAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGT
130 AAAACAGAAATTAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGT
*
55488222 TGATTTTTGAAAAACAACAGAAATTAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTC
195 TGATTTTTGAAAAACAACAGAAATTAAAAATACCTCAGCGTGACCCGAAGCTCAACTCACCTCTC
*
55488287 GTATTATGAGTTGATTTTTGAAAAAAAATAGAAATTAAAAAATACCTCAG
260 GTATTATGAGTTGATTTTTGAAAAAAAACAGAAATTAAAAAATACCTCAG
* * *
55488337 CGTGACCCGAGGCACAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAACAACAGAAATTAA
1 TGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAAAACAGAAATTAA
55488402 A
66 A
55488403 TTAAAAAAAT
Statistics
Matches: 352, Mismatches: 17, Indels: 16
0.91 0.04 0.04
Matches are distributed among these distances:
307 18 0.05
308 59 0.17
310 15 0.04
311 136 0.39
313 91 0.26
314 17 0.05
315 2 0.01
317 2 0.01
318 12 0.03
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (309 bp):
TGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTTGATTTTTGAAAAAAAACAGAAATTAA
AAATACCTCAGCATGACTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAA
AAACAGAAATTAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTCGTATTATGAGTT
GATTTTTGAAAAACAACAGAAATTAAAAATACCTCAGCGTGACCCGAAGCTCAACTCACCTCTCG
TATTATGAGTTGATTTTTGAAAAAAAACAGAAATTAAAAAATACCTCAG
Found at i:55494342 original size:44 final size:44
Alignment explanation
Indices: 55494286--55494754 Score: 341
Period size: 44 Copynumber: 10.7 Consensus size: 44
55494276 TGATGCGATT
* * **
55494286 TGCTCCGCTGTAAACTCAGGGAGATAAGATCTCTGGCTTCAATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCTCTTTCTTCAATC
**
55494330 TGCTCCACTGTAACCTCAGGGAGATAAGATCT-TAAATTCTTCGGTC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCTCT---TTCTTCAATC
* * * * * *
55494376 TACTCCACCGTAACCTCAGGGAGATAAGA---CATTATGCGATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCTCTTTCTTCAATC
* * * * *
55494417 TACTCTACTGTAACTTCAGAGAGATAAGATCAT-TTAT-TTTAATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATC-TCTT-TCTTCAATC
* * *
55494461 CGCTCCACTGTAACCTCAGGGAGATAGGAT-TACTATCTTCAATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCT-CTTTCTTCAATC
* * * **
55494505 TGCTACGCTGTAATCTCAGGGAGATAAGATCTCTAATTCTTCGGTC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCTCT--TTCTTCAATC
* ** * *
55494551 TACTCCACTGTAACCTCAGGGAGATAAGA-C-C-TGATGCGATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCTCTTTCTTCAATC
* ** * * * *
55494592 TACTCTGCTGTAACTTCAGAGAGATAAGATC-CTTTATTTTAATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCTCTTT-CTTCAATC
* * ** * *
55494636 CGCTCCACTGTAACTTCAGGGAGATAAGAT-AGTGTCTTCGATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCTCTTTCTTCAATC
* * **
55494679 TGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATC
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCTCTTTCTTCAATC
*
55494723 TGCTCCACTGTAACCTCAGTGAGATAAGATCT
1 TGCTCCACTGTAACCTCAGGGAGATAAGATCT
55494755 AAAATATTCA
Statistics
Matches: 331, Mismatches: 74, Indels: 40
0.74 0.17 0.09
Matches are distributed among these distances:
41 63 0.19
42 3 0.01
43 34 0.10
44 163 0.49
45 3 0.01
46 65 0.20
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (44 bp):
TGCTCCACTGTAACCTCAGGGAGATAAGATCTCTTTCTTCAATC
Found at i:55494591 original size:175 final size:175
Alignment explanation
Indices: 55494287--55494751 Score: 679
Period size: 175 Copynumber: 2.7 Consensus size: 175
55494277 GATGCGATTT
* * * * *
55494287 GCTCCGCTGTAAACTCAGGGAGATAAGATCT-CTGGCTTCAATCTGCTCCACTGTAACCTCAGGG
1 GCTCCACTGTAACCTCAGGGAGATAAGAT-TACTGTCTTCAATCTGCTCCGCTGTAATCTCAGGG
* *
55494351 AGATAAGATCT-TAAATTCTTCGGTCTACTCCACCGTAACCTCAGGGAGATAAGACATTATGCGA
65 AGATAAGATCTCT-AATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACATGATGCGA
55494415 TCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCC
129 TCTACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCC
* * *
55494462 GCTCCACTGTAACCTCAGGGAGATAGGATTACTATCTTCAATCTGCTACGCTGTAATCTCAGGGA
1 GCTCCACTGTAACCTCAGGGAGATAAGATTACTGTCTTCAATCTGCTCCGCTGTAATCTCAGGGA
*
55494527 GATAAGATCTCTAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATC
66 GATAAGATCTCTAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACATGATGCGATC
* *
55494592 TACTCTGCTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCC
131 TACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCC
* * *
55494637 GCTCCACTGTAACTTCAGGGAGATAAGA-TAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGA
1 GCTCCACTGTAACCTCAGGGAGATAAGATTACTGTCTTCAATCTGCTCCGCTGTAATCTCAGGGA
** ** * *
55494701 GATAAGATCTCT--GGCTTCAATCTGCTCCACTGTAACCTCAGTGAGATAAGA
66 GATAAGATCTCTAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGA
55494752 TCTAAAATAT
Statistics
Matches: 263, Mismatches: 25, Indels: 7
0.89 0.08 0.02
Matches are distributed among these distances:
172 33 0.13
174 45 0.17
175 184 0.70
176 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (175 bp):
GCTCCACTGTAACCTCAGGGAGATAAGATTACTGTCTTCAATCTGCTCCGCTGTAATCTCAGGGA
GATAAGATCTCTAATTCTTCGGTCTACTCCACTGTAACCTCAGGGAGATAAGACATGATGCGATC
TACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCC
Found at i:55494678 original size:87 final size:87
Alignment explanation
Indices: 55494378--55494752 Score: 354
Period size: 87 Copynumber: 4.3 Consensus size: 87
55494368 CTTCGGTCTA
* * *
55494378 CTCCACCGTAACCTCAGGGAGATAAGACA-T-TATGCGATCTACTCTACTGTAA-CTTCAGAGAG
1 CTCCACTGTAACCTCAGGGAGATAAGATACTGTATGCGATCTACTCTGCTGTAATC-TCAGAGAG
55494440 ATAAGATCAT-TTATTTTAATCCG
65 ATAAGATC-TCTTATTTTAATCCG
* * * * * * *
55494463 CTCCACTGTAACCTCAGGGAGATAGGATTACTATCTTCAATCTGCTAC-GCTGTAATCTCAGGGA
1 CTCCACTGTAACCTCAGGGAGATAAGA-TACTGTATGCGATCTACT-CTGCTGTAATCTCAGAGA
* ** **
55494527 GATAAGATCTCTAATTCTTCGGTCTA
64 GATAAGATCTCTTATT-TT-AATCCG
*
55494553 CTCCACTGTAACCTCAGGGAGATAAGA-CCTG-ATGCGATCTACTCTGCTGTAA-CTTCAGAGAG
1 CTCCACTGTAACCTCAGGGAGATAAGATACTGTATGCGATCTACTCTGCTGTAATC-TCAGAGAG
55494615 ATAAGATC-CTTTATTTTAATCCG
65 ATAAGATCTC-TTATTTTAATCCG
* * * * * * *
55494638 CTCCACTGTAACTTCAGGGAGATAAGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGA
1 CTCCACTGTAACCTCAGGGAGATAAGATACTGTATGCGATCTACTCTGCTGTAATCTCAGAGAGA
*** * *
55494703 TAAGATCTCTGGCTTCAATCTG
66 TAAGATCTCTTATTTTAATCCG
*
55494725 CTCCACTGTAACCTCAGTGAGATAAGAT
1 CTCCACTGTAACCTCAGGGAGATAAGAT
55494753 CTAAAATATT
Statistics
Matches: 233, Mismatches: 42, Indels: 28
0.77 0.14 0.09
Matches are distributed among these distances:
85 53 0.23
86 8 0.03
87 102 0.44
88 38 0.16
89 4 0.02
90 28 0.12
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (87 bp):
CTCCACTGTAACCTCAGGGAGATAAGATACTGTATGCGATCTACTCTGCTGTAATCTCAGAGAGA
TAAGATCTCTTATTTTAATCCG
Found at i:55494734 original size:131 final size:127
Alignment explanation
Indices: 55494288--55494754 Score: 406
Period size: 131 Copynumber: 3.6 Consensus size: 127
55494278 ATGCGATTTG
*
55494288 CTCCGCTGTAAACTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
1 CTCCACTGT-AACTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
* ** * * * * * *
55494353 ATAAGATCTTAAATTCTTCGGTCTACTCCACCGTAACCTCAGGGAGATAAGACATTATGCGATCT
65 ATAAGATCTT-TATT-TT-AATCTGCTCCACTGTAACTTCAGGGAGATAAGATATTCTTCGATCT
55494418 A
127 A
* * *** * *
55494419 CTCTACTGTAACTTCAGAGAGATAAGATCAT-TTATTTTAATCCGCTCCACTGTAACCTCAGGGA
1 CTCCACTGTAAC-TCAGGGAGATAAGATC-TCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGA
* * * * *
55494483 GATAGGAT-TACTATCTTCAATCTGCTACGCTGTAA-TCTCAGGGAGATAAGATCTCTAATTCTT
64 GATAAGATCT-TTAT-TTTAATCTGCTCCACTGTAACT-TCAGGGAGATAAGA----T-ATTCTT
*
55494546 CGGTCTA
121 CGATCTA
* * * * ** * *
55494553 CTCCACTGTAACCTCAGGGAGATAAGA-C-CT-GATGCGATCTACTCTGCTGTAACTTCAGAGAG
1 CTCCACTGTAA-CTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
*
55494615 ATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAAGATAGTGTCTTCGATCT
65 ATAAGAT-CTTTATTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATA-T-TCTTCGATCT
*
55494680 G
127 A
* *
55494681 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGTGAG
1 CTCCACTGTAA-CTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAG
55494746 ATAAGATCT
65 ATAAGATCT
55494755 AAAATATTCA
Statistics
Matches: 262, Mismatches: 54, Indels: 41
0.73 0.15 0.11
Matches are distributed among these distances:
126 1 0.00
127 2 0.01
128 34 0.13
129 26 0.10
130 11 0.04
131 146 0.56
132 6 0.02
133 2 0.01
134 33 0.13
135 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (127 bp):
CTCCACTGTAACTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCTCAGGGAGA
TAAGATCTTTATTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATATTCTTCGATCTA
Found at i:55506888 original size:3 final size:3
Alignment explanation
Indices: 55506870--55506928 Score: 52
Period size: 3 Copynumber: 20.0 Consensus size: 3
55506860 AATATAAATA
* *
55506870 AAT AGAT AAC AAT AAT AAT AAT -GT AAT -AT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
55506914 ATT AA- AAT AACT AAT
1 AAT AAT AAT AA-T AAT
55506929 TTAATGATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
2 5 0.11
3 34 0.76
4 6 0.13
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:55506922 original size:25 final size:25
Alignment explanation
Indices: 55506875--55506922 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
55506865 AAATAAATAG
**
55506875 ATAACAATAATAATAATGTAATATA
1 ATAACAATAATAATAATAAAATATA
* *
55506900 ATAATAATAATAATATTAAAATA
1 ATAACAATAATAATAATAAAATA
55506923 ACTAATTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (25 bp):
ATAACAATAATAATAATAAAATATA
Found at i:55506933 original size:20 final size:17
Alignment explanation
Indices: 55506883--55506943 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 17
55506873 AGATAACAAT
55506883 AATAATAATGTAATATAA
1 AATAATAAT-TAATATAA
55506901 TAATAATAA-TAATATTAA
1 -AATAATAATTAATA-TAA
55506919 AATAACTAATTTAATGATAA
1 AATAA-TAA-TTAAT-ATAA
55506939 AATAA
1 AATAA
55506944 CTAAAATAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
17 10 0.27
18 6 0.16
19 8 0.22
20 12 0.32
21 1 0.03
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (17 bp):
AATAATAATTAATATAA
Found at i:55511250 original size:20 final size:20
Alignment explanation
Indices: 55511225--55511262 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
55511215 CGTAATCCGA
55511225 TTAAAACACGAGAATTTTTT
1 TTAAAACACGAGAATTTTTT
55511245 TTAAAACACGAGAATTTT
1 TTAAAACACGAGAATTTT
55511263 GGAAACAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (20 bp):
TTAAAACACGAGAATTTTTT
Found at i:55511300 original size:32 final size:32
Alignment explanation
Indices: 55511237--55511301 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
55511227 AAAACACGAG
* * * *
55511237 AATTTTTTTTAAAACACGAGAATTTTGGAAAC
1 AATTGTTTTAAAAAAACGAAAATTTTGGAAAC
55511269 AATTGTTTTAAAAAAACGAAAATTTAT-GAAAC
1 AATTGTTTTAAAAAAACGAAAATTT-TGGAAAC
55511301 A
1 A
55511302 CGAGATTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 27 0.96
33 1 0.04
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.34
Consensus pattern (32 bp):
AATTGTTTTAAAAAAACGAAAATTTTGGAAAC
Found at i:55511344 original size:18 final size:18
Alignment explanation
Indices: 55511274--55511438 Score: 117
Period size: 17 Copynumber: 9.2 Consensus size: 18
55511264 GAAACAATTG
* *
55511274 TTTTAAAAAAACGAAAAT
1 TTTTGAAAACACGAAAAT
* **
55511292 TTATG-AAACACGAGATTTT
1 TTTTGAAAACACGA-A-AAT
55511311 TTTTGAAAACACGAAAAT
1 TTTTGAAAACACGAAAAT
55511329 TTTT-AAAACACTG-AAAT
1 TTTTGAAAACAC-GAAAAT
**
55511346 TTTTGAAAACACGAGGAT
1 TTTTGAAAACACGAAAAT
*
55511364 TTTTG-AAACACGAGAAT
1 TTTTGAAAACACGAAAAT
*
55511381 TTTCTGAAAACATGAACAA-
1 TTT-TGAAAACACGAA-AAT
** * *
55511400 TTTTGAAAA-TTGGAATT
1 TTTTGAAAACACGAAAAT
55511417 TTTTGAAAACACGAAAAAT
1 TTTTGAAAACACG-AAAAT
55511436 TTT
1 TTT
55511439 CTGATTTTTT
Statistics
Matches: 115, Mismatches: 20, Indels: 23
0.73 0.13 0.15
Matches are distributed among these distances:
16 1 0.01
17 49 0.43
18 33 0.29
19 22 0.19
20 10 0.09
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.33
Consensus pattern (18 bp):
TTTTGAAAACACGAAAAT
Found at i:55511349 original size:35 final size:35
Alignment explanation
Indices: 55511274--55511438 Score: 140
Period size: 35 Copynumber: 4.6 Consensus size: 35
55511264 GAAACAATTG
* * * *
55511274 TTTTAAAAAAACGAAAATTTATGAAACAC-GAGATTTT
1 TTTTGAAAACACGAAAATTTTTGAAACACTGA-A--AT
*
55511311 TTTTGAAAACACGAAAATTTTTAAAACACTGAAAT
1 TTTTGAAAACACGAAAATTTTTGAAACACTGAAAT
**
55511346 TTTTGAAAACACGAGGATTTTTGAAACAC-GAGAAT
1 TTTTGAAAACACGAAAATTTTTGAAACACTGA-AAT
* * *
55511381 TTTCTGAAAACATGAACAA-TTTTGAAA-ATTGGAATT
1 TTT-TGAAAACACGAA-AATTTTTGAAACACT-GAAAT
*
55511417 TTTTGAAAACACGAAAAATTTT
1 TTTTGAAAACACGAAAATTTTT
55511439 CTGATTTTTT
Statistics
Matches: 107, Mismatches: 14, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
34 4 0.04
35 49 0.46
36 23 0.21
37 29 0.27
38 2 0.02
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.33
Consensus pattern (35 bp):
TTTTGAAAACACGAAAATTTTTGAAACACTGAAAT
Found at i:55511969 original size:24 final size:24
Alignment explanation
Indices: 55511937--55512010 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 24
55511927 ACAAATTGAA
*
55511937 TTTTACTTTTCTTTTTCTCTTCTT
1 TTTTTCTTTTCTTTTTCTCTTCTT
*
55511961 TTTTTCTTTTTTCTTTTT-TTTTC-T
1 TTTTTC--TTTTCTTTTTCTCTTCTT
55511985 TTTTTCTTTT-TTCTTCTCTCTTCTT
1 TTTTTCTTTTCTT-TT-TCTCTTCTT
55512010 T
1 T
55512011 CTGGCCTGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
21 2 0.05
22 6 0.15
23 1 0.02
24 16 0.39
25 6 0.15
26 10 0.24
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTTTCTTTTCTTTTTCTCTTCTT
Found at i:55511972 original size:7 final size:7
Alignment explanation
Indices: 55511943--55511999 Score: 57
Period size: 7 Copynumber: 8.0 Consensus size: 7
55511933 TGAATTTTAC
55511943 TTTTCTT
1 TTTTCTT
55511950 TTTCTCTT
1 TTT-TCTT
55511958 CTTTT-TT
1 -TTTTCTT
55511965 TCTTT-TT
1 T-TTTCTT
55511972 TCTTT-TT
1 T-TTTCTT
55511979 TTTTCTT
1 TTTTCTT
55511986 TTTTCTT
1 TTTTCTT
55511993 TTTTCTT
1 TTTTCTT
55512000 CTCTCTTCTT
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
6 4 0.09
7 34 0.74
8 5 0.11
9 3 0.07
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTCTT
Found at i:55511979 original size:17 final size:17
Alignment explanation
Indices: 55511943--55512001 Score: 91
Period size: 17 Copynumber: 3.4 Consensus size: 17
55511933 TGAATTTTAC
55511943 TTTTCTTTTTCTCTTCTTT
1 TTTTCTTTTT-TCTT-TTT
55511962 TTTTCTTTTTTCTTTTT
1 TTTTCTTTTTTCTTTTT
55511979 TTTTCTTTTTTCTTTTT
1 TTTTCTTTTTTCTTTTT
*
55511996 TCTTCT
1 TTTTCT
55512002 CTCTTCTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
17 25 0.64
18 4 0.10
19 10 0.26
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTCTTTTTTCTTTTT
Found at i:55511988 original size:11 final size:11
Alignment explanation
Indices: 55511937--55511996 Score: 57
Period size: 12 Copynumber: 5.1 Consensus size: 11
55511927 ACAAATTGAA
*
55511937 TTTTACTTTTCT
1 TTTTTCTTTT-T
*
55511949 TTTTCTCTTCTT
1 TTTT-TCTTTTT
55511961 TTTTTCTTTTT
1 TTTTTCTTTTT
*
55511972 TCTTTTTTTTTCT
1 T-TTTTCTTTT-T
55511985 TTTTTCTTTTT
1 TTTTTCTTTTT
55511996 T
1 T
55511997 CTTCTCTCTT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
11 9 0.22
12 25 0.62
13 6 0.15
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:55512006 original size:14 final size:14
Alignment explanation
Indices: 55511944--55512012 Score: 68
Period size: 14 Copynumber: 4.9 Consensus size: 14
55511934 GAATTTTACT
55511944 TTTCTTTTTCTCTTC
1 TTTCTTTTT-TCTTC
* *
55511959 TTTTTTTCTTTTTTC
1 TTTCTTT-TTTCTTC
*
55511974 TTT-TTTTTTCTTT
1 TTTCTTTTTTCTTC
55511987 TTTCTTTTTTCTTC
1 TTTCTTTTTTCTTC
* *
55512001 TCTCTTCTTTCT
1 TTTCTTTTTTCT
55512013 GGCCTGCTTC
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
13 8 0.18
14 22 0.49
15 13 0.29
16 2 0.04
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTCTTTTTTCTTC
Found at i:55512008 original size:17 final size:17
Alignment explanation
Indices: 55511952--55512010 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
55511942 CTTTTCTTTT
55511952 TCTCTTCTTTTTTTCTT-
1 TCTCTTC-TTTTTTCTTC
*
55511969 T-T-TTCTTTTTTTTTC
1 TCTCTTCTTTTTTCTTC
* *
55511984 TTTTTTCTTTTTTCTTC
1 TCTCTTCTTTTTTCTTC
55512001 TCTCTTCTTT
1 TCTCTTCTTT
55512011 CTGGCCTGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 8 0.23
15 4 0.11
16 2 0.06
17 21 0.60
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
TCTCTTCTTTTTTCTTC
Found at i:55512298 original size:6 final size:6
Alignment explanation
Indices: 55512287--55512350 Score: 60
Period size: 6 Copynumber: 10.3 Consensus size: 6
55512277 CTATTAATTA
* *
55512287 TTTTTC TTTTTC TTTTTC --TTTC TTCTTC TTTTTCC TTCTTTC TTTCTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT-C TT-TTTC TTTTTC
55512335 TTTTTTC TTTCTTC TT
1 -TTTTTC TTT-TTC TT
55512351 CTCTGATCGG
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
4 4 0.08
6 25 0.52
7 16 0.33
8 3 0.06
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (6 bp):
TTTTTC
Found at i:55512312 original size:13 final size:13
Alignment explanation
Indices: 55512287--55512350 Score: 66
Period size: 13 Copynumber: 5.2 Consensus size: 13
55512277 CTATTAATTA
55512287 TTTTTCTTT-TTC
1 TTTTTCTTTCTTC
55512299 TTTTTCTTTCTTC
1 TTTTTCTTTCTTC
*
55512312 TTCTT-TTTC--C
1 TTTTTCTTTCTTC
55512322 TTCTTTCTTTC-TC
1 TT-TTTCTTTCTTC
55512335 TTTTTTCTTTCTTC
1 -TTTTTCTTTCTTC
55512349 TT
1 TT
55512351 CTCTGATCGG
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
10 3 0.07
11 2 0.05
12 17 0.39
13 18 0.41
14 4 0.09
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTCTTTCTTC
Found at i:55512327 original size:20 final size:19
Alignment explanation
Indices: 55512299--55512354 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
55512289 TTTCTTTTTC
55512299 TTTTTCTTTCTTCTTCT-T
1 TTTTTCTTTCTTCTTCTCT
55512317 TTTCCTTCTTTC-T-TTCTCT
1 TTT--TTCTTTCTTCTTCTCT
55512336 TTTTTCTTTCTTCTTCTCT
1 TTTTTCTTTCTTCTTCTCT
55512355 GATCGGCCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
17 7 0.21
18 8 0.24
19 11 0.33
20 7 0.21
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTCTTTCTTCTTCTCT
Found at i:55512352 original size:10 final size:10
Alignment explanation
Indices: 55512290--55512352 Score: 57
Period size: 10 Copynumber: 6.7 Consensus size: 10
55512280 TTAATTATTT
55512290 TTCTT-TTTC
1 TTCTTCTTTC
*
55512299 TTTTTCTTTC
1 TTCTTCTTTC
55512309 TTCTTCTTT-
1 TTCTTCTTTC
55512318 TTCCTTCTTTC
1 TT-CTTCTTTC
55512329 -T-TTCTCTT-
1 TTCTTCT-TTC
55512337 TT-TTCTTTC
1 TTCTTCTTTC
55512346 TTCTTCT
1 TTCTTCT
55512353 CTGATCGGCC
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
8 6 0.13
9 15 0.33
10 24 0.53
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (10 bp):
TTCTTCTTTC
Found at i:55512709 original size:30 final size:29
Alignment explanation
Indices: 55512675--55512768 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 29
55512665 GGCTAAAACA
55512675 AATTTTGAGAAAATTTAGGGGTCAAAATGT
1 AATTTT-AGAAAATTTAGGGGTCAAAATGT
* *
55512705 AATTTT-GAAAAGTTGGTGGGTCAAAATGT
1 AATTTTAGAAAATTTAG-GGGTCAAAATGT
* * *
55512734 AATTTCA-AAAAGTTCAGTGGTCAAAATGT
1 AATTTTAGAAAA-TTTAGGGGTCAAAATGT
*
55512763 ATTTTT
1 AATTTT
55512769 TTGATTTTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
28 8 0.15
29 36 0.69
30 8 0.15
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.36
Consensus pattern (29 bp):
AATTTTAGAAAATTTAGGGGTCAAAATGT
Found at i:55512725 original size:29 final size:30
Alignment explanation
Indices: 55512693--55512768 Score: 102
Period size: 29 Copynumber: 2.6 Consensus size: 30
55512683 GAAAATTTAG
* *
55512693 GGGTCAAAATGTAATTTTGAAAAGTT-GGT
1 GGGTCAAAATGTAATTTTAAAAAGTTCAGT
*
55512722 GGGTCAAAATGTAATTTCAAAAAGTTCAGT
1 GGGTCAAAATGTAATTTTAAAAAGTTCAGT
*
55512752 -GGTCAAAATGTATTTTT
1 GGGTCAAAATGTAATTTT
55512769 TTGATTTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
29 39 0.95
30 2 0.05
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.36
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTAAAAAGTTCAGT
Found at i:55517459 original size:2 final size:2
Alignment explanation
Indices: 55517454--55517557 Score: 95
Period size: 2 Copynumber: 52.5 Consensus size: 2
55517444 CCCGTGTACC
* * * * *
55517454 TA TA TA TA TA T- TT TA TA CTT TA TA -A TT TA TA TA TA TA CA CA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
55517495 TA TG TC CA TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55517537 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
55517558 GTACATGCAT
Statistics
Matches: 83, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
1 2 0.02
2 80 0.96
3 1 0.01
ACGTcount: A:0.44, C:0.05, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55518147 original size:108 final size:110
Alignment explanation
Indices: 55517949--55518256 Score: 511
Period size: 108 Copynumber: 2.8 Consensus size: 110
55517939 CAAAAAACAA
55517949 AAAAATTTATAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
1 AAAAATTTATAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
55518014 GGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTT-TT
66 GGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTCTT
55518058 AAAAATTT-TAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
1 AAAAATTTATAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
55518122 GGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTCTT
66 GGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTCTT
** *
55518167 AAAAATTTCA-AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GGACGTGCCCTAAGGTGCT
1 AAAAATTT-ATAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
* * *
55518230 TGGTTTCGA--TTTCTCGTTTAACCAAAT
65 GGGTGTCGATTTTTCTCGTTCAACCAAAT
55518257 TGCCAAATAT
Statistics
Matches: 190, Mismatches: 6, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
107 17 0.09
108 98 0.52
109 41 0.22
110 34 0.18
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (110 bp):
AAAAATTTATAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
GGTGTCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTCTT
Found at i:55519521 original size:2 final size:2
Alignment explanation
Indices: 55519514--55519539 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55519504 AACTAAAATG
55519514 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
55519540 GTTTAATAAC
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:55523295 original size:15 final size:17
Alignment explanation
Indices: 55523274--55523314 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
55523264 AATCCCTTCA
55523274 AAAATTATA-AAATCAT
1 AAAATTATATAAATCAT
*
55523290 -AAATTA-ATAAATGAT
1 AAAATTATATAAATCAT
55523305 AAAATTATAT
1 AAAATTATAT
55523315 TTTCACCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
14 1 0.05
15 12 0.57
16 6 0.29
17 2 0.10
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (17 bp):
AAAATTATATAAATCAT
Found at i:55524739 original size:23 final size:23
Alignment explanation
Indices: 55524713--55524757 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
55524703 AGAAAGTAAG
55524713 ATGTGATGATCTTTATATCCTTT
1 ATGTGATGATCTTTATATCCTTT
55524736 ATGTGATGATCTTTATATCCTT
1 ATGTGATGATCTTTATATCCTT
55524758 CCCTAATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.13, G:0.13, T:0.51
Consensus pattern (23 bp):
ATGTGATGATCTTTATATCCTTT
Found at i:55533798 original size:20 final size:20
Alignment explanation
Indices: 55533775--55533812 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55533765 ATTAAATATA
55533775 TTAAGTAAA-ACTATGTGACT
1 TTAA-TAAATACTATGTGACT
*
55533795 TTAATAAATATTATGTGA
1 TTAATAAATACTATGTGA
55533813 AAATAGTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.39
Consensus pattern (20 bp):
TTAATAAATACTATGTGACT
Found at i:55535603 original size:4 final size:4
Alignment explanation
Indices: 55535594--55535624 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
55535584 TCCTGCTTAT
55535594 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
55535625 TATTTAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:55536266 original size:30 final size:30
Alignment explanation
Indices: 55536193--55536260 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 30
55536183 TTACAAAATG
*
55536193 GTCACTAAACTATTCAAAGTTTCCATTTAA
1 GTCACTGAACTATTCAAAGTTTCCATTTAA
* **
55536223 GTCATTGAACTATTCGAAAGTTTTTATTTAA
1 GTCACTGAACTATTC-AAAGTTTCCATTTAA
55536254 GTCACTG
1 GTCACTG
55536261 GCTATTAAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 13 0.41
31 19 0.59
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (30 bp):
GTCACTGAACTATTCAAAGTTTCCATTTAA
Found at i:55538388 original size:19 final size:22
Alignment explanation
Indices: 55538349--55538391 Score: 65
Period size: 19 Copynumber: 2.1 Consensus size: 22
55538339 TTAATATATA
55538349 TATTAATCAATTATATTTAATT
1 TATTAATCAATTATATTTAATT
55538371 TATTAA-CAA-TAT-TTTAATT
1 TATTAATCAATTATATTTAATT
55538390 TA
1 TA
55538392 CTTTACTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.43
20 3 0.14
21 3 0.14
22 6 0.29
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTAATCAATTATATTTAATT
Found at i:55548377 original size:2 final size:2
Alignment explanation
Indices: 55548372--55548405 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
55548362 TATATATATA
55548372 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
55548406 ATTAAGAGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:55555831 original size:8 final size:8
Alignment explanation
Indices: 55555795--55555865 Score: 54
Period size: 8 Copynumber: 8.4 Consensus size: 8
55555785 ATTGTTTTGA
55555795 AAATATAT
1 AAATATAT
55555803 AAA-ATAT
1 AAATATAT
*
55555810 AAACTTATAA
1 AAA--TATAT
*
55555820 AAATATTT
1 AAATATAT
55555828 AAATATAT
1 AAATATAT
*
55555836 AAAAACCTAT
1 AAATA--TAT
55555846 AATATATAT
1 AA-ATATAT
*
55555855 AAATTTAT
1 AAATATAT
55555863 AAA
1 AAA
55555866 AAATATATTA
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
7 7 0.14
8 25 0.50
9 5 0.10
10 11 0.22
11 2 0.04
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (8 bp):
AAATATAT
Found at i:55555863 original size:17 final size:17
Alignment explanation
Indices: 55555815--55555864 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
55555805 AATATAAACT
55555815 TATA-AAAATATTTA-AA
1 TATATAAAA-ATTTATAA
**
55555831 TATATAAAAACCTATAA
1 TATATAAAAATTTATAA
*
55555848 TATATATAAATTTATAA
1 TATATAAAAATTTATAA
55555865 AAAATATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 7 0.26
17 20 0.74
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (17 bp):
TATATAAAAATTTATAA
Found at i:55555885 original size:24 final size:21
Alignment explanation
Indices: 55555846--55555889 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 21
55555836 AAAAACCTAT
55555846 AATATATATAAATTTATAAAA
1 AATATATATAAATTTATAAAA
55555867 AATATATTATAAAATTTTATAAA
1 AATATA-TAT-AAA-TTTATAAA
55555890 TATATTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 3 0.15
23 3 0.15
24 8 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AATATATATAAATTTATAAAA
Found at i:55565751 original size:20 final size:20
Alignment explanation
Indices: 55565714--55565751 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55565704 AAGAGGTATG
*
55565714 ATTAAATTATTATTTTTATT
1 ATTAAATTATTATATTTATT
55565734 ATTAAATATATTA-ATTTA
1 ATTAAAT-TATTATATTTA
55565752 ATCCCGTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTAAATTATTATATTTATT
Found at i:55566674 original size:17 final size:18
Alignment explanation
Indices: 55566652--55566703 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
55566642 TTTTATTTTT
55566652 ATTTTTTAATTTTAAA-A
1 ATTTTTTAATTTTAAATA
*
55566669 ATTTTTTTATTTTTAAAATA
1 A-TTTTTTAATTTT-AAATA
55566689 ATTTTTTAATGTTTA
1 ATTTTTTAAT-TTTA
55566704 TTAAAAAATG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 1 0.03
18 11 0.38
19 12 0.41
20 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
ATTTTTTAATTTTAAATA
Found at i:55566676 original size:18 final size:19
Alignment explanation
Indices: 55566652--55566703 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
55566642 TTTTATTTTT
55566652 ATTTTTTAATTTTAAAA-A
1 ATTTTTTAATTTTAAAATA
* *
55566670 TTTTTTTATTTTTAAAATA
1 ATTTTTTAATTTTAAAATA
55566689 ATTTTTTAATGTTTA
1 ATTTTTTAAT-TTTA
55566704 TTAAAAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 15 0.54
19 9 0.32
20 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
ATTTTTTAATTTTAAAATA
Found at i:55567732 original size:14 final size:15
Alignment explanation
Indices: 55567699--55567734 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
55567689 AAATTTTAAG
55567699 AAAAATAAATATTGT
1 AAAAATAAATATTGT
* *
55567714 AAAAATAGATATTTT
1 AAAAATAAATATTGT
55567729 AAAAAT
1 AAAAAT
55567735 CTTACTTTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (15 bp):
AAAAATAAATATTGT
Found at i:55571822 original size:84 final size:85
Alignment explanation
Indices: 55571715--55571889 Score: 223
Period size: 84 Copynumber: 2.0 Consensus size: 85
55571705 GGATGGGATT
55571715 TGTGGTTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-G-ATGC-GATCTGCTCCAC
1 TGTGGTTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGTATGCTG-TCTGCTCCAC
55571777 TACTGCCTAGGGAGATAAGATC
64 TACTGCCTAGGGAGATAAGATC
* * * *
55571799 TGTGGTTTTAAT-TCGCTCCACTGCAACTTCAGGGAGATAGGATTGGTTTTTTTCTGTCTGCTCC
1 TGTGGTTTTAGTCT-GCTCCACTGCAACTTCAGGGAGATAAGATTGG---TATGCTGTCTGCTCC
*
55571863 ACTACTGCTTAGGGAGATAAGATC
62 ACTACTGCCTAGGGAGATAAGATC
55571887 TGT
1 TGT
55571890 AATCTTCAAT
Statistics
Matches: 79, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
83 3 0.04
84 39 0.49
88 36 0.46
89 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.33
Consensus pattern (85 bp):
TGTGGTTTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTATGCTGTCTGCTCCACTA
CTGCCTAGGGAGATAAGATC
Found at i:55571877 original size:44 final size:44
Alignment explanation
Indices: 55571767--55571889 Score: 126
Period size: 44 Copynumber: 2.8 Consensus size: 44
55571757 CTTGATGCGA
*
55571767 TCTGCTCCACTACTGCCTAGGGAGATAAGATCTGTGGTTTTAAT
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAAT
* ** * * **
55571811 TC-GCTCCACTGCAACTTCAGGGAGATAGGAT-TG-GTTTTTTTCT
1 TCTGCTCCACTACTGCTT-AGGGAGATAAGATCTGTG-GTTTTAAT
55571854 GTCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
1 -TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
55571890 AATCTTCAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 10
0.73 0.14 0.12
Matches are distributed among these distances:
42 1 0.02
43 18 0.30
44 28 0.46
45 14 0.23
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (44 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTTTAAT
Found at i:55571908 original size:44 final size:44
Alignment explanation
Indices: 55571859--55572524 Score: 274
Period size: 44 Copynumber: 15.5 Consensus size: 44
55571849 TTTCTGTCTG
*
55571859 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTA
1 CTCCACTACTGCTCAGGGAGATAAGATCTGTAATCTTCAATCTA
* * * * *****
55571903 TTCCACTGCTGCCCAGGGAGAT-AGAACTACCGGCTTCAA--TA
1 CTCCACTACTGCTCAGGGAGATAAGATCTGTAATCTTCAATCTA
* * * ** * * *
55571944 -T--A--A-T-CTCAGGGAGGTAAAATCCGCCATCTTCGACCTG
1 CTCCACTACTGCTCAGGGAGATAAGATCTGTAATCTTCAATCTA
* * *
55571981 CTCCACTATTGCTTAGGGAGATAAGATCTTTAATCTTCAATCTA
1 CTCCACTACTGCTCAGGGAGATAAGATCTGTAATCTTCAATCTA
* * * * * * * *
55572025 TTCCACTGCTGCCCATGGAGAT-AGA-CT-TGA--TGCGATCTG
1 CTCCACTACTGCTCAGGGAGATAAGATCTGTAATCTTCAATCTA
* *
55572064 CTCCACTA-TGCTTAGGGAGATAAGATCTGTAATCTTTAATCTA
1 CTCCACTACTGCTCAGGGAGATAAGATCTGTAATCTTCAATCTA
* * * * * *
55572107 TTCCACTGCTGCCCAGGGAGAT-AGAAC--TACTGGCTTCAATGTA
1 CTCCACTACTGCTCAGGGAGATAAGATCTGTAAT--CTTCAATCTA
* * * **** * * *
55572150 CTCCACTGAAAT-CTCAGGGAGGTAAAATCCACCATCTTCGACCTG
1 CTCCACT--ACTGCTCAGGGAGATAAGATCTGTAATCTTCAATCTA
* *
55572195 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTAAATCTA
1 CTCCACTACTGCTCAGGGAGATAAGATCTGTAATCTTCAATCTA
* * * * * *
55572239 TTCCACTGCTGCCCAGGGAGAT-AGAAC--TACTGGCTTCAATGTA
1 CTCCACTACTGCTCAGGGAGATAAGATCTGTAAT--CTTCAATCTA
* * * * ** * *
55572282 CTCCACCGTAAT-CTTAGGGAGGTAACATCTGCCATCTTCAACCTG
1 CTCCA-C-TACTGCTCAGGGAGATAAGATCTGTAATCTTCAATCTA
* *
55572327 CTCCACTACTGCTTAGGGAGATAATATCTGTAATCTTCAATCTA
1 CTCCACTACTGCTCAGGGAGATAAGATCTGTAATCTTCAATCTA
* * * * *
55572371 TTCCACTGCTGCTCAGGGAGAT-AGAAC--TACTGGCTTCAATGTA
1 CTCCACTACTGCTCAGGGAGATAAGATCTGTAAT--CTTCAATCTA
* * * * ** * *
55572414 CTCCACCGTAAT-CTCAGGGAGGTAAAATCCGCCATCTTCGATCTG
1 CTCCA-C-TACTGCTCAGGGAGATAAGATCTGTAATCTTCAATCTA
*
55572459 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAAT-TA
1 CTCCACTACTGCTCAGGGAGATAAGATCTGTAATCTTCAATCTA
* * * *
55572502 TTCCTCTGCTGCCCAGGGAGATA
1 CTCCACTACTGCTCAGGGAGATA
55572525 GAACTACTGG
Statistics
Matches: 435, Mismatches: 147, Indels: 81
0.66 0.22 0.12
Matches are distributed among these distances:
34 9 0.02
35 11 0.03
37 1 0.00
38 12 0.03
39 15 0.03
40 4 0.01
41 15 0.03
42 3 0.01
43 103 0.24
44 208 0.48
45 51 0.12
47 3 0.01
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (44 bp):
CTCCACTACTGCTCAGGGAGATAAGATCTGTAATCTTCAATCTA
Found at i:55572083 original size:82 final size:83
Alignment explanation
Indices: 55571978--55572131 Score: 274
Period size: 82 Copynumber: 1.9 Consensus size: 83
55571968 CATCTTCGAC
* *
55571978 CTGCTCCACTATTGCTTAGGGAGATAAGATCTTTAATCTTCAATCTATTCCACTGCTGCCCATGG
1 CTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGG
55572043 AGATAGACTTGATGCGAT
66 AGATAGACTTGATGCGAT
*
55572061 CTGCTCCACTA-TGCTTAGGGAGATAAGATCTGTAATCTTTAATCTATTCCACTGCTGCCCAGGG
1 CTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGG
55572125 AGATAGA
66 AGATAGA
55572132 ACTACTGGCT
Statistics
Matches: 68, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
82 57 0.84
83 11 0.16
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (83 bp):
CTGCTCCACTATTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGG
AGATAGACTTGATGCGAT
Found at i:55572124 original size:204 final size:211
Alignment explanation
Indices: 55571855--55572263 Score: 670
Period size: 214 Copynumber: 2.0 Consensus size: 211
55571845 TTTTTTTCTG
55571855 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGG
*
55571920 GAGATAGAACTACCGGCTTC-A-A-T-A-T-AATCTCAGGGAGGTAAAATCCGCCATCTTCGACC
66 GAGATAGAACTACCGGCTTCAATACTCACTAAATCTCAGGGAGGTAAAATCCACCATCTTCGACC
* * * *
55571979 TGCTCCACTATTGCTTAGGGAGATAAGATCTTTAATCTTCAATCTATTCCACTGCTGCCCATGGA
131 TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTAAATCTATTCCACTGCTGCCCAGGGA
55572044 GATAGACTTGATGCGA
196 GATAGACTTGATGCGA
*
55572060 TCTGCTCCACTA-TGCTTAGGGAGATAAGATCTGTAATCTTTAATCTATTCCACTGCTGCCCAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGG
*
55572124 GAGATAGAACTACTGGCTTCAATGTACTCCACTGAAATCTCAGGGAGGTAAAATCCACCATCTTC
66 GAGATAGAACTACCGGCTTCAA--TACT-CACT-AAATCTCAGGGAGGTAAAATCCACCATCTTC
55572189 GACCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTAAATCTATTCCACTGCTGCCCA
127 GACCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTAAATCTATTCCACTGCTGCCCA
55572254 GGGAGATAGA
192 GGGAGATAGA
55572264 ACTACTGGCT
Statistics
Matches: 187, Mismatches: 7, Indels: 11
0.91 0.03 0.05
Matches are distributed among these distances:
204 70 0.37
205 13 0.07
208 1 0.01
209 1 0.01
211 1 0.01
212 1 0.01
214 100 0.53
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (211 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGG
GAGATAGAACTACCGGCTTCAATACTCACTAAATCTCAGGGAGGTAAAATCCACCATCTTCGACC
TGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTAAATCTATTCCACTGCTGCCCAGGGA
GATAGACTTGATGCGA
Found at i:55572223 original size:132 final size:132
Alignment explanation
Indices: 55572061--55572620 Score: 953
Period size: 132 Copynumber: 4.3 Consensus size: 132
55572051 TTGATGCGAT
*
55572061 CTGCTCCACTA-TGCTTAGGGAGATAAGATCTGTAATCTTTAATCTATTCCACTGCTGCCCAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGG
* *
55572125 AGATAGAACTACTGGCTTCAATGTACTCCACTGAAATCTCAGGGAGGTAAAATCCACCATCTTCG
66 AGATAGAACTACTGGCTTCAATGTACTCCACCGTAATCTCAGGGAGGTAAAATCCACCATCTTCG
55572190 AC
131 AC
*
55572192 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTAAATCTATTCCACTGCTGCCCAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGG
* * ** *
55572257 AGATAGAACTACTGGCTTCAATGTACTCCACCGTAATCTTAGGGAGGTAACATCTGCCATCTTCA
66 AGATAGAACTACTGGCTTCAATGTACTCCACCGTAATCTCAGGGAGGTAAAATCCACCATCTTCG
55572322 AC
131 AC
* *
55572324 CTGCTCCACTACTGCTTAGGGAGATAATATCTGTAATCTTCAATCTATTCCACTGCTGCTCAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGG
*
55572389 AGATAGAACTACTGGCTTCAATGTACTCCACCGTAATCTCAGGGAGGTAAAATCCGCCATCTTCG
66 AGATAGAACTACTGGCTTCAATGTACTCCACCGTAATCTCAGGGAGGTAAAATCCACCATCTTCG
*
55572454 AT
131 AC
*
55572456 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAAT-TATTCCTCTGCTGCCCAGGG
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGG
* *
55572520 AGATAGAACTACTGGCTTCAATGTACTCCACCGTAATCTTAGGGAAGTAAAATCCACCATCTTCG
66 AGATAGAACTACTGGCTTCAATGTACTCCACCGTAATCTCAGGGAGGTAAAATCCACCATCTTCG
*
55572585 AT
131 AC
55572587 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
1 CTGCTCCACTACTGCTTAGGGAGATAAGATCTGT
55572621 TTTCTTTGAT
Statistics
Matches: 406, Mismatches: 22, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
131 127 0.31
132 279 0.69
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (132 bp):
CTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGG
AGATAGAACTACTGGCTTCAATGTACTCCACCGTAATCTCAGGGAGGTAAAATCCACCATCTTCG
AC
Found at i:55572700 original size:43 final size:45
Alignment explanation
Indices: 55572623--55572715 Score: 109
Period size: 43 Copynumber: 2.1 Consensus size: 45
55572613 AGATCTGTTT
* * * * *
55572623 TCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGC-A
1 TCTTCGATCCACTTCGCCACCAATATAGGAAGACAAGACCTGCTA
* *
55572667 TCTTCGATCCACTTC-CTACCAATATAGGAAGACATGACCTGCTA
1 TCTTCGATCCACTTCGCCACCAATATAGGAAGACAAGACCTGCTA
55572711 TCTTC
1 TCTTC
55572716 AATCTATTTC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 22 0.54
44 19 0.46
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (45 bp):
TCTTCGATCCACTTCGCCACCAATATAGGAAGACAAGACCTGCTA
Found at i:55573132 original size:24 final size:24
Alignment explanation
Indices: 55573100--55573145 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
55573090 ACCCTTACTG
*
55573100 TAATCTTCAAAGTTCAATCCATTA
1 TAATCTTCAAAGTTAAATCCATTA
*
55573124 TAATCTTCAAGGTTAAATCCAT
1 TAATCTTCAAAGTTAAATCCAT
55573146 GGTAATTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (24 bp):
TAATCTTCAAAGTTAAATCCATTA
Found at i:55573151 original size:24 final size:24
Alignment explanation
Indices: 55573099--55573151 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
55573089 TACCCTTACT
* *
55573099 GTAATCTTCAAAGTTCAATCCATT
1 GTAATCTTCAAAGTTAAATCCATG
* *
55573123 ATAATCTTCAAGGTTAAATCCATG
1 GTAATCTTCAAAGTTAAATCCATG
55573147 GTAAT
1 GTAAT
55573152 TTTGGGACAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (24 bp):
GTAATCTTCAAAGTTAAATCCATG
Found at i:55574142 original size:22 final size:23
Alignment explanation
Indices: 55574098--55574152 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
55574088 TTGGCCTCTC
* *
55574098 CTTTTTCTTTTTCACTCATTTTT
1 CTTTTTTTTTTTCACTCAATTTT
*
55574121 CTTTTTTTTTTTCA-TTAATTTT
1 CTTTTTTTTTTTCACTCAATTTT
*
55574143 ATTTTTTTTT
1 CTTTTTTTTT
55574153 CAAGTGAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 15 0.54
23 13 0.46
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (23 bp):
CTTTTTTTTTTTCACTCAATTTT
Found at i:55576950 original size:19 final size:20
Alignment explanation
Indices: 55576926--55576970 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
55576916 TGTGAAAATC
*
55576926 TAATGCATATG-ATGCAATG
1 TAATGCAAATGCATGCAATG
*
55576945 TAATGCAAATGCATGGAATG
1 TAATGCAAATGCATGCAATG
55576965 -AATGCA
1 TAATGCA
55576971 GAAAGAGACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.27
Consensus pattern (20 bp):
TAATGCAAATGCATGCAATG
Found at i:55582980 original size:106 final size:106
Alignment explanation
Indices: 55582782--55582993 Score: 282
Period size: 106 Copynumber: 2.0 Consensus size: 106
55582772 GGATTTTAGT
* * * *
55582782 AATTGGTGGTTTTAGCTGGATTTTAGTAATTGATAATGGGTTAATCAAATGGGGTTATTGTTGCT
1 AATTGGTGGTTTCAACTGGATTTTAGTAATTGATAATGGATTAATCAAATGGGGTTATTGTTGAT
* * * * *
55582847 GGTTAAACTATGTAGGAATTTTGTGGGTTTATAGCTTAAAA
66 GGTTAAACAATGTAAGAAATTTATGGGTTTACAGCTTAAAA
* * * *
55582888 AATTGGTGGTTTCAACTGGATTTTAGTAATTGCTAGTGGATTTATGAAATGGGGTTATTGTTGAT
1 AATTGGTGGTTTCAACTGGATTTTAGTAATTGATAATGGATTAATCAAATGGGGTTATTGTTGAT
*
55582953 TGTTAAACAAT-TGAAGAAATTTATGGGTTTACAGCTTAAAA
66 GGTTAAACAATGT-AAGAAATTTATGGGTTTACAGCTTAAAA
55582994 TTGGCAGATT
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
105 1 0.01
106 90 0.99
ACGTcount: A:0.29, C:0.05, G:0.25, T:0.41
Consensus pattern (106 bp):
AATTGGTGGTTTCAACTGGATTTTAGTAATTGATAATGGATTAATCAAATGGGGTTATTGTTGAT
GGTTAAACAATGTAAGAAATTTATGGGTTTACAGCTTAAAA
Found at i:55583866 original size:29 final size:30
Alignment explanation
Indices: 55583819--55583875 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
55583809 GTTAGCTGTT
55583819 TTAAAATTTAGAACTTAGG-TAAGTAATCC
1 TTAAAATTTAGAACTTAGGTTAAGTAATCC
*
55583848 TTAAAATTTAGGA-TCTAGGTTAAGTAAT
1 TTAAAATTTAGAACT-TAGGTTAAGTAAT
55583876 GTTGGTCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 1 0.04
29 16 0.64
30 8 0.32
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (30 bp):
TTAAAATTTAGAACTTAGGTTAAGTAATCC
Found at i:55585030 original size:106 final size:107
Alignment explanation
Indices: 55584897--55585200 Score: 448
Period size: 107 Copynumber: 2.8 Consensus size: 107
55584887 GAAATTCAAG
* * * * *
55584897 AGGATATTTGGTTGTTTGGTTAAACGAGAAATCGAAACCCAGCACATTAGGGCACG-CTCCTCGA
1 AGGATATTTAGCTATTTGGTTAAACGAGAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
**
55584961 ATTTCTGAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
66 ATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
* *
55585003 AGGATATTTAGCTATTTGGTTAAACGAGAAATCGAAACCCAGCACATTAGAGCACGTTTTCTCAA
1 AGGATATTTAGCTATTTGGTTAAACGAGAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
* *
55585068 ATTTCCAAATGCAAAACATTGCCCTATTTTGAAATTTTTAAA
66 ATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
* *
55585110 AGGATACTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTTAGCTATTTGGTTAAACGAG--AAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* *
55585175 GAATTTCCAAACGCTAAATATTGCCT
64 GAATTTCCAAACGCAAAACATTGCCT
55585201 CAATTAGAAA
Statistics
Matches: 176, Mismatches: 19, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
106 52 0.30
107 69 0.39
109 55 0.31
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (107 bp):
AGGATATTTAGCTATTTGGTTAAACGAGAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
ATTTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
Found at i:55585740 original size:21 final size:21
Alignment explanation
Indices: 55585715--55585754 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
55585705 TAACTATCAT
55585715 GAAATATAAA-AAATATATATA
1 GAAATATAAACAAAT-TATATA
*
55585736 GAAATGTAAACAAATTATA
1 GAAATATAAACAAATTATA
55585755 ATATATACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (21 bp):
GAAATATAAACAAATTATATA
Found at i:55585881 original size:17 final size:18
Alignment explanation
Indices: 55585842--55585887 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
55585832 ACATGTGTGT
*
55585842 ATAAAAATATGGAATATA
1 ATAAAAATATGCAATATA
*
55585860 A-AAAAATATTCAATA-A
1 ATAAAAATATGCAATATA
55585876 ATAAAAAGTATG
1 ATAAAAA-TATG
55585888 TACGTGTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 2 0.09
17 17 0.74
18 4 0.17
ACGTcount: A:0.63, C:0.02, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAAATATGCAATATA
Found at i:55586102 original size:18 final size:17
Alignment explanation
Indices: 55586065--55586131 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 17
55586055 CAAATAATAG
55586065 TAATAATAATAATAACA
1 TAATAATAATAATAACA
55586082 TAAGTAATAATAAT-ACAA
1 TAA-TAATAATAATAAC-A
** *
55586100 TAATAATAGCAATATCA
1 TAATAATAATAATAACA
*
55586117 GATATAATAATAATA
1 TA-ATAATAATAATA
55586132 GCGAAAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
17 15 0.38
18 25 0.62
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (17 bp):
TAATAATAATAATAACA
Found at i:55586126 original size:3 final size:3
Alignment explanation
Indices: 55586057--55586107 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
55586047 TAAATGAGCA
* * *
55586057 AAT AAT AGT AAT AAT AAT AAT AA- CAT AAGT AAT AAT AAT -AC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
55586101 AAT AAT A
1 AAT AAT A
55586108 GCAATATCAG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:55588060 original size:175 final size:175
Alignment explanation
Indices: 55587763--55588276 Score: 791
Period size: 175 Copynumber: 2.9 Consensus size: 175
55587753 CATGGTTTTA
* * * * *
55587763 GTCTGCTCCACTG-CAACGTCAGGGAGATAA-GACTGGATACGATCTGCTCTACTGCAACTTCAG
1 GTCTGCTCCACTGTC-ACCTCAGGGAGATAAGGCCT-GATGCGATCTACTCTACTGTAACTTCAG
* * *
55587826 AGGGATAAGATCCTTTATTTTAATCTGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGTTTC
64 AGAGATGAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGTTTC
*
55587891 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCG
129 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTAAAATTCTTCG
*
55587938 GTCTGGTCCACTGTCACCTCAGGGAGATAAGGCCTGATGCGATCTACTCTACTGTAACTTCAGAG
1 GTCTGCTCCACTGTCACCTCAGGGAGATAAGGCCTGATGCGATCTACTCTACTGTAACTTCAGAG
* *
55588003 AGATGAGATTCTTTATTGTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGTTTCAA
66 AGATGAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGTTTCAA
*
55588068 TCTGCTCCACTATAATCTCAGGGAGATAAGATCTAAAATTCTTCG
131 TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTAAAATTCTTCG
* * *
55588113 GTCTGCTCCACTGTAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTCCAGAG
1 GTCTGCTCCACTGTCACCTCAGGGAGATAAGGCCTGATGCGATCTACTCTACTGTAACTTCAGAG
* * *
55588178 AGATGAGATCCTTTATTTTAATCCGCTCTACTGTAA-CTTCAGAGAGATAGGATTACTAGCTTCA
66 AGATGAGATCCTTTATTTTAATCCGCTCCACTGTAATC-TCAGGGAGATAGGATTACTAGTTTCA
* *
55588242 ATCTACTCCGCTGTAATCTCAGGGAGATAAGATCT
130 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT
55588277 CTGGCTTCAA
Statistics
Matches: 311, Mismatches: 25, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
174 1 0.00
175 306 0.98
176 4 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (175 bp):
GTCTGCTCCACTGTCACCTCAGGGAGATAAGGCCTGATGCGATCTACTCTACTGTAACTTCAGAG
AGATGAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGTTTCAA
TCTGCTCCACTGTAATCTCAGGGAGATAAGATCTAAAATTCTTCG
Found at i:55588315 original size:44 final size:44
Alignment explanation
Indices: 55587847--55588320 Score: 280
Period size: 44 Copynumber: 10.8 Consensus size: 44
55587837 CCTTTATTTT
* *
55587847 AATCTGCTCCACTGTAATCTCAGGGAGATAGGAT-TACTAGTTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTACT-GCTTC
* *
55587891 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT--ACTGCTTC
** * * * * * *
55587937 GGTCTGGTCCACTGTCACCTCAGGGAGATAAG-GC--CTGATGC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTACTGCTTC
* * * * * *
55587978 GATCTACTCTACTGTAA-CTTCAGAGAGATGAGATTCTTTATTG--T-
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGA-TC--TACTGCTTC
* * *
55588022 AATCCGCTCCACTGTAATCTCAGGGAGATAGGAT-TACTAGTTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTACT-GCTTC
* * *
55588066 AATCTGCTCCACTATAATCTCAGGGAGATAAGATCTAAAATTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT--ACTGCTTC
** * * *
55588112 GGTCTGCTCCACTGTAACCTCAGGGAGATAAGA-C--CTGATGC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTACTGCTTC
* * * * * * ** *
55588153 GATCTACTCTACTGTAA-CTCCAGAGAGATGAGATCCT-TTATTTT
1 AATCTGCTCCACTGTAATCT-CAGGGAGATAAGAT-CTACTGCTTC
* * * *
55588197 AATCCGCTCTACTGTAA-CTTCAGAGAGATAGGAT-TACTAGCTTC
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTACT-GCTTC
* *
55588241 AATCTACTCCGCTGTAATCTCAGGGAGATAAGATCT-CTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTACT-GCTTC
* *
55588285 AATCTGCTCCACTGTAACCTTAGGGAGATAAGATCT
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT
55588321 GAAATATTCA
Statistics
Matches: 327, Mismatches: 76, Indels: 54
0.72 0.17 0.12
Matches are distributed among these distances:
40 6 0.02
41 55 0.17
42 1 0.00
43 5 0.02
44 184 0.56
45 8 0.02
46 62 0.19
47 6 0.02
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTACTGCTTC
Found at i:55600287 original size:109 final size:107
Alignment explanation
Indices: 55599986--55600288 Score: 455
Period size: 107 Copynumber: 2.8 Consensus size: 107
55599976 GAAATTCAAG
* * * * *
55599986 AGGATATTTGGCTGTTTGGTTAAACGAGAAATCGAAACCCAGCACATTAGGGGACG-CTCCTCGA
1 AGGATATTTAGCTATTTGGTTAAACGAGAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
** *
55600050 ATTTCTGAACGCAAAACATTGCCTTATTTTGAAATTTTTAAA
66 ATTTCCAAACGCAAAACATTGCCCTATTTTGAAATTTTTAAA
*
55600092 AGGATATTTAGCTATTTGGTTAAACGAGAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCAA
1 AGGATATTTAGCTATTTGGTTAAACGAGAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
*
55600157 ATTTCCAAATGCAAAACATTGCCCTATTTTGAAATTTTTAAA
66 ATTTCCAAACGCAAAACATTGCCCTATTTTGAAATTTTTAAA
* *
55600199 AGGATACTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTTAGCTATTTGGTTAAACGAG--AAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* *
55600264 GAATTTCCAAACGCTAAATATTGCC
64 GAATTTCCAAACGCAAAACATTGCC
55600289 TCAATTAGAA
Statistics
Matches: 178, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
106 53 0.30
107 69 0.39
109 56 0.31
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (107 bp):
AGGATATTTAGCTATTTGGTTAAACGAGAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGA
ATTTCCAAACGCAAAACATTGCCCTATTTTGAAATTTTTAAA
Found at i:55600887 original size:18 final size:18
Alignment explanation
Indices: 55600860--55600894 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
55600850 TACATAAAAC
55600860 ACATAAATATGTATATGT
1 ACATAAATATGTATATGT
*
55600878 ACATATATATGTATATG
1 ACATAAATATGTATATG
55600895 AACTAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (18 bp):
ACATAAATATGTATATGT
Found at i:55601193 original size:18 final size:17
Alignment explanation
Indices: 55601156--55601222 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 17
55601146 CAAATAATAG
55601156 TAATAATAATAATAACA
1 TAATAATAATAATAACA
55601173 TAAGTAATAATAAT-ACAA
1 TAA-TAATAATAATAAC-A
** *
55601191 TAATAATAGCAATATCA
1 TAATAATAATAATAACA
*
55601208 GATATAATAATAATA
1 TA-ATAATAATAATA
55601223 GCGAAAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
17 15 0.38
18 25 0.62
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.30
Consensus pattern (17 bp):
TAATAATAATAATAACA
Found at i:55601217 original size:3 final size:3
Alignment explanation
Indices: 55601148--55601198 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
55601138 TAAATGAGCA
* * *
55601148 AAT AAT AGT AAT AAT AAT AAT AA- CAT AAGT AAT AAT AAT -AC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
55601192 AAT AAT A
1 AAT AAT A
55601199 GCAATATCAG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:55603467 original size:24 final size:24
Alignment explanation
Indices: 55603408--55603472 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
55603398 AACAAATGGG
* *
55603408 CAGCATATACATACC-AAATTTAA
1 CAGCATATATACACCAAAATTTAA
*
55603431 CAGCACT-TTTACACCAAAATTTAA
1 CAGCA-TATATACACCAAAATTTAA
*
55603455 CAGCATATATACAGCAAA
1 CAGCATATATACACCAAA
55603473 TAGGCTTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
23 11 0.32
24 23 0.68
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.25
Consensus pattern (24 bp):
CAGCATATATACACCAAAATTTAA
Found at i:55603578 original size:2 final size:2
Alignment explanation
Indices: 55603571--55603596 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55603561 CTCAAACATC
55603571 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
55603597 CAAATAGATC
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:55604299 original size:41 final size:41
Alignment explanation
Indices: 55604254--55604396 Score: 178
Period size: 41 Copynumber: 3.5 Consensus size: 41
55604244 TTGTATAAAA
* * * * * *
55604254 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCGAGACATTT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
* * *
55604295 CACCGACACAAAGCCTGCTAGACATAAAGTCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
*
55604336 CACCGGCACAGAGCCTGCTAGGCATAAAGCCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
* *
55604377 CATCGGCATAAAGCCTGCTA
1 CACCGGCACAAAGCCTGCTA
55604397 AGCTGTAACA
Statistics
Matches: 86, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 86 1.00
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.19
Consensus pattern (41 bp):
CACCGGCACAAAGCCTGCTAGGCATAAAGCCTGATATAATT
Found at i:55614066 original size:41 final size:41
Alignment explanation
Indices: 55614009--55614222 Score: 329
Period size: 41 Copynumber: 5.2 Consensus size: 41
55613999 NNNNNNNNNN
55614009 TATGTGCCGGTGATTTGAATCGGGTTATAAACCTAGCAGGC
1 TATGTGCCGGTGATTTGAATCGGGTTATAAACCTAGCAGGC
* *
55614050 TATGTGCCGGTGATTTGAATTGTGTTATAAACCTAGCAGGC
1 TATGTGCCGGTGATTTGAATCGGGTTATAAACCTAGCAGGC
55614091 TATGTGCCGGTGATTTGAATCGGGTTATAAACCTAGCAGGC
1 TATGTGCCGGTGATTTGAATCGGGTTATAAACCTAGCAGGC
*
55614132 TACGTGCCGGTGATTTGAATCGGGTTATAAACCTAGCAGGC
1 TATGTGCCGGTGATTTGAATCGGGTTATAAACCTAGCAGGC
* * ** * ** *
55614173 TACGTGCCGGTGATCTGAATCAAGCTATAAGTCTAGCAGTC
1 TATGTGCCGGTGATTTGAATCGGGTTATAAACCTAGCAGGC
55614214 TATGTGCCG
1 TATGTGCCG
55614223 TTGAATCTAT
Statistics
Matches: 160, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 160 1.00
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.29
Consensus pattern (41 bp):
TATGTGCCGGTGATTTGAATCGGGTTATAAACCTAGCAGGC
Found at i:55617627 original size:27 final size:27
Alignment explanation
Indices: 55617594--55617666 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 27
55617584 TATGTCGAAT
55617594 TTGTTAGATATTGATTATGTTTTAAGC
1 TTGTTAGATATTGATTATGTTTTAAGC
*
55617621 TTGTTAGATATTGAATTTATTATGTTTTAATC
1 TTGTTAGATATTG-----ATTATGTTTTAAGC
*
55617653 TTGTTGGATATTGA
1 TTGTTAGATATTGA
55617667 AATGATTGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
27 14 0.36
32 25 0.64
ACGTcount: A:0.26, C:0.03, G:0.18, T:0.53
Consensus pattern (27 bp):
TTGTTAGATATTGATTATGTTTTAAGC
Found at i:55617646 original size:32 final size:32
Alignment explanation
Indices: 55617607--55617667 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
55617597 TTAGATATTG
55617607 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
1 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
* *
55617639 ATTATGTTTTAATCTTGTTGGATATTGAA
1 ATTATGTTTTAAGCTTGTTAGATATTGAA
55617668 ATGATTGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.03, G:0.16, T:0.52
Consensus pattern (32 bp):
ATTATGTTTTAAGCTTGTTAGATATTGAATTT
Found at i:55618926 original size:20 final size:20
Alignment explanation
Indices: 55618903--55618940 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55618893 AAAATTTAAA
*
55618903 ATATATATTTATTAATATGT
1 ATATAAATTTATTAATATGT
55618923 ATATAAATTTATTAATAT
1 ATATAAATTTATTAATAT
55618941 ATGTAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
ATATAAATTTATTAATATGT
Found at i:55619047 original size:19 final size:19
Alignment explanation
Indices: 55619023--55619080 Score: 98
Period size: 19 Copynumber: 3.0 Consensus size: 19
55619013 CATCCAAACA
55619023 CCAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
55619042 CCAGAAAAGTAAATCATTTT
1 CCAGAAAAGTAAATCA-TTT
*
55619062 CTAGAAAAGTAAATCATTT
1 CCAGAAAAGTAAATCATTT
55619081 TCTAGAAATC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
19 19 0.51
20 18 0.49
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (19 bp):
CCAGAAAAGTAAATCATTT
Found at i:55619067 original size:20 final size:20
Alignment explanation
Indices: 55619025--55619088 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
55619015 TCCAAACACC
*
55619025 AGAAAAGTAAATCA-TTTCC
1 AGAAAAGTAAATCATTTTCT
55619044 AGAAAAGTAAATCATTTTCT
1 AGAAAAGTAAATCATTTTCT
55619064 AGAAAAGTAAATCATTTTCT
1 AGAAAAGTAAATCATTTTCT
55619084 AGAAA
1 AGAAA
55619089 TCATTTTCCG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
19 14 0.33
20 29 0.67
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (20 bp):
AGAAAAGTAAATCATTTTCT
Found at i:55622757 original size:19 final size:18
Alignment explanation
Indices: 55622733--55622778 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
55622723 GACTGAATAT
55622733 ATCAATTATTGAGATGTTA
1 ATCAATTATTGAGAT-TTA
* **
55622752 ATCAATCATTGTTATTTA
1 ATCAATTATTGAGATTTA
55622770 ATCAATTAT
1 ATCAATTAT
55622779 CTTTTAACAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (18 bp):
ATCAATTATTGAGATTTA
Found at i:55622987 original size:10 final size:10
Alignment explanation
Indices: 55622974--55623006 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
55622964 TAAAATTATC
55622974 AAATTTTAAA
1 AAATTTTAAA
55622984 AAATTTTAAA
1 AAATTTTAAA
*
55622994 AAA-TATAAA
1 AAATTTTAAA
55623003 AAAT
1 AAAT
55623007 AAAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAATTTTAAA
Found at i:55624880 original size:14 final size:13
Alignment explanation
Indices: 55624852--55624877 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55624842 ATAATATATT
55624852 TATTAATTAAAAA
1 TATTAATTAAAAA
55624865 TATTAATTAAAAA
1 TATTAATTAAAAA
55624878 ATAACATGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TATTAATTAAAAA
Found at i:55625095 original size:134 final size:127
Alignment explanation
Indices: 55624924--55625169 Score: 321
Period size: 134 Copynumber: 1.9 Consensus size: 127
55624914 AAAATAATGG
* * * * *
55624924 AACCTGAGATTTAAGGATGTAATCGTAATTATCTAACCATCTAACGAAAAGAGTTAATATGTTAG
1 AACCAGAGATTTAAAGATGTAATCGTAACTATCTAACCATCTAAC-AAAAAAATTAATATGTTA-
* * *
55624989 AAATATTAATTAAAAAAAACTTGAAGTAACACGAAATAAAAAATACAAATGTGAATATGAAATGT
64 AAA-A--AATT--AAAAAACTTGAAGCAACACAAAATAAAAAATAAAAATGTGAATATGAAATGT
55625054 ATTA
124 ATTA
* * *
55625058 AACCAGAGATTTAAAGATGTAATTGTAACTATCTAACCATTTAACAAAAAAATTAGTATGTTAAA
1 AACCAGAGATTTAAAGATGTAATCGTAACTATCTAACCATCTAACAAAAAAATTAATATGTTAAA
*
55625123 AAAATTAAAAAACTTGAAGCAACATAAAATAAAAAATAAAAATGTGA
66 AAAATTAAAAAACTTGAAGCAACACAAAATAAAAAATAAAAATGTGA
55625170 GTAGGAAAAA
Statistics
Matches: 100, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
127 37 0.37
129 4 0.04
131 1 0.01
132 3 0.03
133 15 0.15
134 40 0.40
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.27
Consensus pattern (127 bp):
AACCAGAGATTTAAAGATGTAATCGTAACTATCTAACCATCTAACAAAAAAATTAATATGTTAAA
AAAATTAAAAAACTTGAAGCAACACAAAATAAAAAATAAAAATGTGAATATGAAATGTATTA
Found at i:55625185 original size:127 final size:132
Alignment explanation
Indices: 55624924--55625188 Score: 324
Period size: 127 Copynumber: 2.0 Consensus size: 132
55624914 AAAATAATGG
* * * * *
55624924 AACCTGAGATTTAAGGATGTAATCGTAATTATCTAACCATCTAACGAAAAGAGTTAATATGTTAG
1 AACCAGAGATTTAAAGATGTAATCGTAACTATCTAACCATCTAACGAAAAAAATTAATATGTTAG
* * * * ***
55624989 AAATATTAATTAAAAAAAACTTGAAGTAACACGAAATAAAAAATACAAATGTGAATATGAAATGT
66 AAATA-TAATT-AAAAAAACTTGAAGCAACACAAAATAAAAAATAAAAATGTGAATAGGAAAAAA
55625054 ATTA
129 ATTA
* * *
55625058 AACCAGAGATTTAAAGATGTAATTGTAACTATCTAACCATTTAAC-AAAAAAATTAGTATGTTA-
1 AACCAGAGATTTAAAGATGTAATCGTAACTATCTAACCATCTAACGAAAAAAATTAATATGTTAG
* *
55625121 AAA-A-AATT-AAAAAACTTGAAGCAACATAAAATAAAAAATAAAAATGTGAGTAGGAAAAAAAT
66 AAATATAATTAAAAAAACTTGAAGCAACACAAAATAAAAAATAAAAATGTGAATAGGAAAAAAAT
55625183 TA
131 TA
55625185 AACC
1 AACC
55625189 CAAGACTCAA
Statistics
Matches: 114, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
127 51 0.45
129 4 0.04
131 1 0.01
132 3 0.03
133 15 0.13
134 40 0.35
ACGTcount: A:0.52, C:0.09, G:0.12, T:0.26
Consensus pattern (132 bp):
AACCAGAGATTTAAAGATGTAATCGTAACTATCTAACCATCTAACGAAAAAAATTAATATGTTAG
AAATATAATTAAAAAAACTTGAAGCAACACAAAATAAAAAATAAAAATGTGAATAGGAAAAAAAT
TA
Found at i:55627596 original size:12 final size:12
Alignment explanation
Indices: 55627579--55627631 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 12
55627569 CCGATCTTCC
* *
55627579 TCTCCGACTGCA
1 TCTCCGTCTCCA
*
55627591 TCTCCGTCTCCG
1 TCTCCGTCTCCA
55627603 TCTCCGTCTCCA
1 TCTCCGTCTCCA
*
55627615 TCTCCATCTCCA
1 TCTCCGTCTCCA
55627627 TCTCC
1 TCTCC
55627632 ATCAATCCCA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.09, C:0.49, G:0.09, T:0.32
Consensus pattern (12 bp):
TCTCCGTCTCCA
Found at i:55627602 original size:6 final size:6
Alignment explanation
Indices: 55627589--55627634 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
55627579 TCTCCGACTG
* * *
55627589 CATCTC CGTCTC CGTCTC CGTCTC CATCTC CATCTC CATCTC CATC
1 CATCTC CATCTC CATCTC CATCTC CATCTC CATCTC CATCTC CATC
55627635 AATCCCAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.11, C:0.50, G:0.07, T:0.33
Consensus pattern (6 bp):
CATCTC
Found at i:55629328 original size:4 final size:4
Alignment explanation
Indices: 55629319--55629381 Score: 126
Period size: 4 Copynumber: 15.8 Consensus size: 4
55629309 TATGTTGTAT
55629319 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
55629367 ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATA
55629382 TATATACACT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:55631424 original size:45 final size:42
Alignment explanation
Indices: 55631368--55631476 Score: 119
Period size: 45 Copynumber: 2.5 Consensus size: 42
55631358 CTCCTATATT
* *
55631368 TATATGGCATGAAAGTCAACACCGGTACCTAATACCTACTGTATG
1 TATATGGCATGAAAGTCAACACCGATACATAATA-CT--TGTATG
* **
55631413 TATATGACATGAAAGTTGACACCGATACATAATACTTGTATG
1 TATATGGCATGAAAGTCAACACCGATACATAATACTTGTATG
* * *
55631455 TATACGGCATGATAGCCAACAC
1 TATATGGCATGAAAGTCAACAC
55631477 TAGTACATAG
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
42 22 0.42
44 2 0.04
45 29 0.55
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (42 bp):
TATATGGCATGAAAGTCAACACCGATACATAATACTTGTATG
Found at i:55631466 original size:42 final size:44
Alignment explanation
Indices: 55631368--55631502 Score: 125
Period size: 42 Copynumber: 3.1 Consensus size: 44
55631358 CTCCTATATT
* *
55631368 TATATGGCATGAAAGTCAACACCGGTACCTAATACCTACTGTATG
1 TATATGGCATGAAAGTCAACACCGATACATAATACCTA-TGTATG
* **
55631413 TATATGACATGAAAGTTGACACCGATACATAATA-CT-TGTATG
1 TATATGGCATGAAAGTCAACACCGATACATAATACCTATGTATG
* * * * * *
55631455 TATACGGCATGATAGCCAACA-CTAGTACATAGTACCTAT-TATA
1 TATATGGCATGAAAGTCAACACCGA-TACATAATACCTATGTATG
55631498 TATAT
1 TATAT
55631503 AGCCTAATTG
Statistics
Matches: 72, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
41 2 0.03
42 29 0.40
43 9 0.12
44 3 0.04
45 29 0.40
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (44 bp):
TATATGGCATGAAAGTCAACACCGATACATAATACCTATGTATG
Found at i:55632510 original size:16 final size:16
Alignment explanation
Indices: 55632468--55632510 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
55632458 ATCCTTAATC
*
55632468 TTTTTTTCT-TTCTTT
1 TTTTTTTCTATTCATT
55632483 TTTTTTTC-ATTCATT
1 TTTTTTTCTATTCATT
55632498 TTTTTTTCTATTC
1 TTTTTTTCTATTC
55632511 TCTTTCTCGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTTCTATTCATT
Found at i:55635839 original size:17 final size:17
Alignment explanation
Indices: 55635817--55635849 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
55635807 CTAAAAATTA
*
55635817 ATTAAATATTAAATAAT
1 ATTAAATATAAAATAAT
55635834 ATTAAATATAAAATAA
1 ATTAAATATAAAATAA
55635850 AAATTCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATTAAATATAAAATAAT
Found at i:55641047 original size:9 final size:9
Alignment explanation
Indices: 55640856--55641087 Score: 89
Period size: 9 Copynumber: 24.6 Consensus size: 9
55640846 GTTTAATACA
*
55640856 AAAAATTAA
1 AAAAATTAT
* *
55640865 AAAAATCAG
1 AAAAATTAT
55640874 AAAAATTAT
1 AAAAATTAT
55640883 AAAAATTA-
1 AAAAATTAT
55640891 AAAAA-TAT
1 AAAAATTAT
*
55640899 CAAAAGAATAT
1 -AAAA-ATTAT
* *
55640910 ATAAATGAT
1 AAAAATTAT
*
55640919 -TAAATGT-T
1 AAAAAT-TAT
*
55640927 AAAAACTAT
1 AAAAATTAT
*
55640936 GAAAATTGAT
1 AAAAATT-AT
55640946 ATAAATATTAT
1 A-AAA-ATTAT
*
55640957 AAATA-TAT
1 AAAAATTAT
* *
55640965 AAAATAATCT
1 AAAA-ATTAT
55640975 AATAAATTAT
1 AA-AAATTAT
55640985 -AAAATTAAT
1 AAAAATT-AT
*
55640994 AAAACATATTT
1 AAAA-AT-TAT
*
55641005 AAAATTTTAT
1 AAAA-ATTAT
**
55641015 AACAACGTATT
1 AA-AAATTA-T
*
55641026 AAAATTCTAT
1 AAAAAT-TAT
55641036 AAAAATTAT
1 AAAAATTAT
*
55641045 AAAAAGTAT
1 AAAAATTAT
*
55641054 TAAAATTAAT
1 AAAAATT-AT
*
55641064 ATAAACTTAT
1 A-AAAATTAT
55641074 AAAAATTAT
1 AAAAATTAT
55641083 AAAAA
1 AAAAA
55641088 CTTGAATTGG
Statistics
Matches: 168, Mismatches: 33, Indels: 44
0.69 0.13 0.18
Matches are distributed among these distances:
7 2 0.01
8 23 0.14
9 71 0.42
10 37 0.22
11 31 0.18
12 4 0.02
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:55641060 original size:29 final size:29
Alignment explanation
Indices: 55640926--55641087 Score: 84
Period size: 29 Copynumber: 5.5 Consensus size: 29
55640916 GATTAAATGT
* * *
55640926 TAAAAACTATGAAAATTGATATAAATATTA
1 TAAAAAGTATTAAAATTAATATAAA-ATTA
* *
55640956 TAAATA-TA-TAAAA-TAATCTAATAAATTA
1 TAAAAAGTATTAAAATTAATAT-A-AAATTA
* * * *
55640984 T-AAAATTAATAAAA-CATATTTAAAATTTTA
1 TAAAAAGTATTAAAATTA-ATATAAAA--TTA
* *
55641014 TAACAACGTATTAAAATT-CTATAAAAATTA
1 TAA-AAAGTATTAAAATTAATAT-AAAATTA
*
55641044 TAAAAAGTATTAAAATTAATATAAACTTA
1 TAAAAAGTATTAAAATTAATATAAAATTA
* *
55641073 TAAAAATTATAAAAA
1 TAAAAAGTATTAAAA
55641088 CTTGAATTGG
Statistics
Matches: 102, Mismatches: 18, Indels: 25
0.70 0.12 0.17
Matches are distributed among these distances:
27 7 0.07
28 15 0.15
29 43 0.42
30 21 0.21
31 3 0.03
32 13 0.13
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (29 bp):
TAAAAAGTATTAAAATTAATATAAAATTA
Found at i:55641088 original size:19 final size:19
Alignment explanation
Indices: 55641033--55641090 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
55641023 ATTAAAATTC
*
55641033 TATAAAAATTATAAAAA-G
1 TATAAAAATTATAAAAACT
* *
55641051 TATTAAAATTAATATAAACT
1 TATAAAAATT-ATAAAAACT
55641071 TATAAAAATTATAAAAACT
1 TATAAAAATTATAAAAACT
55641090 T
1 T
55641091 GAATTGGACC
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
18 9 0.27
19 15 0.45
20 9 0.27
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (19 bp):
TATAAAAATTATAAAAACT
Done.