Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 127 of 182
Found at i:40392214 original size:21 final size:19
Alignment explanation
Indices: 40392190--40392244 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
40392180 CTTATTGTCA
40392190 TTAATTAGGAAAAATTAAAGG
1 TTAATTAGGAAAAATT-AA-G
**
40392211 TTAATTAAGTGATTAATTAAG
1 TTAATT-AG-GAAAAATTAAG
40392232 TTAATTAGGAAAA
1 TTAATTAGGAAAA
40392245 GTCTTAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
19 3 0.11
20 2 0.07
21 13 0.46
22 4 0.14
23 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (19 bp):
TTAATTAGGAAAAATTAAG
Found at i:40398308 original size:23 final size:22
Alignment explanation
Indices: 40398282--40398427 Score: 175
Period size: 23 Copynumber: 6.4 Consensus size: 22
40398272 AGCACTAGCA
*
40398282 TGCTTACTGATCAACACTGTGTG
1 TGCTTACTGATC-GCACTGTGTG
* *
40398305 TGCTTACTGATTCGCACTATATG
1 TGCTTACTGA-TCGCACTGTGTG
40398328 TGCTTACTGATTCGCACTGTGTG
1 TGCTTACTGA-TCGCACTGTGTG
* *
40398351 TGCTTACTGATTGCACTATGTG
1 TGCTTACTGATCGCACTGTGTG
*
40398373 TGCTTACTGATCAGCATTGTGTG
1 TGCTTACTGATC-GCACTGTGTG
* *
40398396 TGCTTACTAGATTGCACTGTTTG
1 TGCTTACT-GATCGCACTGTGTG
40398419 TGCTTACTG
1 TGCTTACTG
40398428 TTGCCCAGCA
Statistics
Matches: 107, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
22 22 0.21
23 80 0.75
24 5 0.05
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.40
Consensus pattern (22 bp):
TGCTTACTGATCGCACTGTGTG
Found at i:40398346 original size:46 final size:45
Alignment explanation
Indices: 40398282--40398427 Score: 213
Period size: 46 Copynumber: 3.2 Consensus size: 45
40398272 AGCACTAGCA
*
40398282 TGCTTACTGATCAACACTGTGTGTGCTTACTGATTCGCACTATATG
1 TGCTTACTGATCAGCACTGTGTGTGCTTACTGATT-GCACTATATG
*
40398328 TGCTTACTGATTC-GCACTGTGTGTGCTTACTGATTGCACTATGTG
1 TGCTTACTGA-TCAGCACTGTGTGTGCTTACTGATTGCACTATATG
* * *
40398373 TGCTTACTGATCAGCATTGTGTGTGCTTACTAGATTGCACTGTTTG
1 TGCTTACTGATCAGCACTGTGTGTGCTTACT-GATTGCACTATATG
40398419 TGCTTACTG
1 TGCTTACTG
40398428 TTGCCCAGCA
Statistics
Matches: 92, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
44 2 0.02
45 36 0.39
46 52 0.57
47 2 0.02
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.40
Consensus pattern (45 bp):
TGCTTACTGATCAGCACTGTGTGTGCTTACTGATTGCACTATATG
Found at i:40398382 original size:68 final size:68
Alignment explanation
Indices: 40398282--40398431 Score: 189
Period size: 68 Copynumber: 2.2 Consensus size: 68
40398272 AGCACTAGCA
** *
40398282 TGCTTACTGATCAACACTGTGTGTGCTTACTGATTC-GCACTATATGTGCTTACT-GATTCGCAC
1 TGCTTACTGAT-TGCACTATGTGTGCTTACTGA-TCAGCACTATATGTGCTTACTAGATT-GCAC
40398345 TGTGTG
63 TGTGTG
* * *
40398351 TGCTTACTGATTGCACTATGTGTGCTTACTGATCAGCATTGTGTGTGCTTACTAGATTGCACTGT
1 TGCTTACTGATTGCACTATGTGTGCTTACTGATCAGCACTATATGTGCTTACTAGATTGCACTGT
*
40398416 TTG
66 GTG
40398419 TGCTTACTG-TTGC
1 TGCTTACTGATTGC
40398432 CCAGCACTTA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
67 6 0.08
68 51 0.71
69 15 0.21
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.40
Consensus pattern (68 bp):
TGCTTACTGATTGCACTATGTGTGCTTACTGATCAGCACTATATGTGCTTACTAGATTGCACTGT
GTG
Found at i:40401976 original size:39 final size:39
Alignment explanation
Indices: 40401929--40402037 Score: 137
Period size: 39 Copynumber: 2.8 Consensus size: 39
40401919 ACATCGAAGA
* * *
40401929 TATACTGAACTGGCAGTGACACTGTAAACATTGCAATGT
1 TATACTGAACTGGCAGTGACACTGTAAACACTACAATAT
****
40401968 TATACTGAACCAATAGTGACACTGTAAACACTACAATAT
1 TATACTGAACTGGCAGTGACACTGTAAACACTACAATAT
* *
40402007 AATACTAAACTGGCAGTGACACTGTAAACAC
1 TATACTGAACTGGCAGTGACACTGTAAACAC
40402038 CGCAACGCTA
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (39 bp):
TATACTGAACTGGCAGTGACACTGTAAACACTACAATAT
Found at i:40404909 original size:21 final size:21
Alignment explanation
Indices: 40404885--40404924 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
40404875 AACTACCTAC
40404885 TACTAACAAAATAAAATTACT
1 TACTAACAAAATAAAATTACT
*
40404906 TACTAACAAAATTAAATTA
1 TACTAACAAAATAAAATTA
40404925 AATTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (21 bp):
TACTAACAAAATAAAATTACT
Found at i:40409237 original size:21 final size:21
Alignment explanation
Indices: 40409211--40409349 Score: 96
Period size: 21 Copynumber: 6.8 Consensus size: 21
40409201 TGATAAAAAC
40409211 AGAATTCTGAGGAAGAATTTG
1 AGAATTCTGAGGAAGAATTTG
*
40409232 AGAATTCTGAGGAAGAATATG
1 AGAATTCTGAGGAAGAATTTG
* * *
40409253 TA-AATTTTGTGGAAGAATATATT
1 -AGAATTCTGAGGAAGAAT-T-TG
* * *
40409276 A-ATTTTCTCA--AAGAATCTG
1 AGA-ATTCTGAGGAAGAATTTG
*
40409295 AGAA---TGAGGAAGAATCTG
1 AGAATTCTGAGGAAGAATTTG
*
40409313 AGAATTTTGAGGAAGAATCTTG
1 AGAATTCTGAGGAAGAAT-TTG
40409335 A-AATTCTGAGGAAGA
1 AGAATTCTGAGGAAGA
40409350 TCAAAGCAAT
Statistics
Matches: 92, Mismatches: 15, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
16 2 0.02
18 13 0.14
19 2 0.02
20 1 0.01
21 64 0.70
22 6 0.07
23 4 0.04
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.29
Consensus pattern (21 bp):
AGAATTCTGAGGAAGAATTTG
Found at i:40409309 original size:18 final size:19
Alignment explanation
Indices: 40409286--40409332 Score: 69
Period size: 18 Copynumber: 2.4 Consensus size: 19
40409276 AATTTTCTCA
40409286 AAGAATCTGAGAA-TGAGG
1 AAGAATCTGAGAATTGAGG
40409304 AAGAATCTGAGAATTTTGAGG
1 AAGAATCTGAGAA--TTGAGG
40409325 AAGAATCT
1 AAGAATCT
40409333 TGAAATTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.50
21 13 0.50
ACGTcount: A:0.43, C:0.06, G:0.28, T:0.23
Consensus pattern (19 bp):
AAGAATCTGAGAATTGAGG
Found at i:40410781 original size:30 final size:30
Alignment explanation
Indices: 40410719--40410783 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
40410709 ACTTATTTTA
* * ***
40410719 TTGTTAATTTTGTTATTATTTTAGAGGTAT
1 TTGTTAATTTTGTTACTATTTTAAACACAT
40410749 TTGTTAATTTTGTTACTATTTTAAACACAT
1 TTGTTAATTTTGTTACTATTTTAAACACAT
40410779 TTGTT
1 TTGTT
40410784 TATTAAGTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.25, C:0.05, G:0.12, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAAACACAT
Found at i:40411704 original size:18 final size:17
Alignment explanation
Indices: 40411678--40411716 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
40411668 CCCATTTTGG
40411678 ATTTATTTTAAATTTAA
1 ATTTATTTTAAATTTAA
*
40411695 ATTTATTTTTAAATTTGA
1 ATTTA-TTTTAAATTTAA
40411713 ATTT
1 ATTT
40411717 GTTAAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTTATTTTAAATTTAA
Found at i:40413909 original size:91 final size:88
Alignment explanation
Indices: 40413813--40414108 Score: 329
Period size: 91 Copynumber: 3.3 Consensus size: 88
40413803 ATGTACTTTC
*
40413813 TTTTTTTAAATAAATAAGTGGGGAGGGGCATGTTCACTCGAACTTTAACTCTTTTTTTTTAAATA
1 TTTTTTTAAATAAACAAGTGGGG-GGGGCATGTTCACTCGAACTTTAA--CTTTTTTTTTAAATA
40413878 AACAAGTGGGTGGCATGTTCACTCGAA
63 AACAAGTGGG-GGCATGTTCACTCGAA
* * *
40413905 TTTTTTTTTTAAATAAACAA-TTGAGGGGGCATGTGCACTCGAACTTTAACTTTTTTTTTAAATA
1 ---TTTTTTTAAATAAACAAGTGGGGGGGGCATGTTCACTCGAACTTTAACTTTTTTTTTAAATA
*
40413969 AACAAGTGGGGGTATGTTCACTCGAA
63 AACAAGTGGGGGCATGTTCACTCGAA
*
40413995 CTTTTTTTTTTAAATAAACAAGTGGGGGAGGACATGTTCACTC---C---AACTTTTTTTTTAAA
1 ----TTTTTTTAAATAAACAAGTGGGGG-GGGCATGTTCACTCGAACTTTAACTTTTTTTTTAAA
40414054 TAAACAAGTGGGGGGCATGTTCACTCCGAA
61 TAAACAAGT-GGGGGCATGTTCACT-CGAA
40414084 CTTTCTTTTTAAATAAACAAG-GGGG
1 --TT-TTTTTAAATAAACAAGTGGGG
40414109 CATGTTCACT
Statistics
Matches: 184, Mismatches: 11, Indels: 20
0.86 0.05 0.09
Matches are distributed among these distances:
87 31 0.17
88 30 0.16
89 4 0.02
90 16 0.09
91 45 0.24
92 4 0.02
93 35 0.19
94 3 0.02
95 16 0.09
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.37
Consensus pattern (88 bp):
TTTTTTTAAATAAACAAGTGGGGGGGGCATGTTCACTCGAACTTTAACTTTTTTTTTAAATAAAC
AAGTGGGGGCATGTTCACTCGAA
Found at i:40413922 original size:42 final size:42
Alignment explanation
Indices: 40413859--40414145 Score: 341
Period size: 42 Copynumber: 6.6 Consensus size: 42
40413849 CTCGAACTTT
40413859 AACTCTTTTTTTTTAAATAAACAAGTGGGTGGCATGTTCACTCG
1 AACT-TTTTTTTTTAAATAAACAAGTGGG-GGCATGTTCACTCG
* *
40413903 AA-TTTTTTTTTTAAATAAACAATTGAGGGGGCATGTGCACTCG
1 AACTTTTTTTTTTAAATAAACAA--GTGGGGGCATGTTCACTCG
*
40413946 AACTTTAACTTTTTTTTTAAATAAACAAGTGGGGGTATGTTCACTCG
1 AAC--T---TTTTTTTTTAAATAAACAAGTGGGGGCATGTTCACTCG
*
40413993 AACTTTTTTTTTTAAATAAACAAGTGGGGGAGGACATGTTCACTCC
1 AACTTTTTTTTTTAAATAAACAAGT--GGG-GG-CATGTTCACTCG
40414039 AAC-TTTTTTTTTAAATAAACAAGTGGGGGGCATGTTCACTCCG
1 AACTTTTTTTTTTAAATAAACAAGT-GGGGGCATGTTCACT-CG
* *
40414082 AAC-TTTCTTTTTAAATAAACAA--GGGGGCATGTTCACTCC
1 AACTTTTTTTTTTAAATAAACAAGTGGGGGCATGTTCACTCG
*
40414121 AACTTTTTTTTTTAAATAAAGAAGT
1 AACTTTTTTTTTTAAATAAACAAGT
40414146 TGCATTTCAT
Statistics
Matches: 215, Mismatches: 12, Indels: 34
0.82 0.05 0.13
Matches are distributed among these distances:
39 4 0.02
40 32 0.15
42 50 0.23
43 40 0.19
44 13 0.06
45 24 0.11
46 14 0.07
47 19 0.09
49 19 0.09
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (42 bp):
AACTTTTTTTTTTAAATAAACAAGTGGGGGCATGTTCACTCG
Found at i:40414064 original size:87 final size:83
Alignment explanation
Indices: 40413863--40414145 Score: 358
Period size: 91 Copynumber: 3.3 Consensus size: 83
40413853 AACTTTAACT
40413863 CTTTTTTTTTAAATAAACAAGTGGGTGGCATGTTCACTCGAA-TTTTTTTTTTAAATAAACAATT
1 CTTTTTTTTTAAATAAACAAGTGGG-GGCATGTTCACTCGAACTTTTTTTTTTAAATAAACAA-T
*
40413927 GAGGGGGCATGTGCACTCGAACTTTAA
64 G-GGGGGCATGTTCACTC---C---AA
*
40413954 CTTTTTTTTTAAATAAACAAGTGGGGGTATGTTCACTCGAACTTTTTTTTTTAAATAAACAAGTG
1 CTTTTTTTTTAAATAAACAAGTGGGGGCATGTTCACTCGAACTTTTTTTTTTAAATAAACAA-T-
40414019 GGGGAGGACATGTTCACTCCAA
64 GGGG-GG-CATGTTCACTCCAA
*
40414041 CTTTTTTTTTAAATAAACAAGTGGGGGGCATGTTCACTCCGAAC-TTTCTTTTTAAATAAACAA-
1 CTTTTTTTTTAAATAAACAAGT-GGGGGCATGTTCACT-CGAACTTTTTTTTTTAAATAAACAAT
40414104 -GGGGGCATGTTCACTCCAA
64 GGGGGGCATGTTCACTCCAA
*
40414123 CTTTTTTTTTTAAATAAAGAAGT
1 C-TTTTTTTTTAAATAAACAAGT
40414146 TGCATTTCAT
Statistics
Matches: 179, Mismatches: 6, Indels: 22
0.86 0.03 0.11
Matches are distributed among these distances:
82 15 0.08
83 22 0.12
84 3 0.02
87 24 0.13
88 32 0.18
89 5 0.03
90 16 0.09
91 49 0.27
92 3 0.02
93 10 0.06
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (83 bp):
CTTTTTTTTTAAATAAACAAGTGGGGGCATGTTCACTCGAACTTTTTTTTTTAAATAAACAATGG
GGGGCATGTTCACTCCAA
Found at i:40418160 original size:33 final size:33
Alignment explanation
Indices: 40418103--40418168 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
40418093 AATGTCCAAA
*
40418103 CCTTACCTTTTTCTCTATGCTTAACAAGGATTC
1 CCTTACCTTTTTCTATATGCTTAACAAGGATTC
* *
40418136 CCTTTCCTTTTTCTATATGGTTAACAAGGATTC
1 CCTTACCTTTTTCTATATGCTTAACAAGGATTC
40418169 TTGTTTGACA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44
Consensus pattern (33 bp):
CCTTACCTTTTTCTATATGCTTAACAAGGATTC
Found at i:40425413 original size:26 final size:26
Alignment explanation
Indices: 40425377--40425431 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
40425367 TTTCTTACTT
* *
40425377 TCAATAAGATATGTTCTTCCTTTATC
1 TCAATAAGATACGTTCTTCCTTCATC
40425403 TCAATAAGATACGTTCTTCCTTCATC
1 TCAATAAGATACGTTCTTCCTTCATC
40425429 TCA
1 TCA
40425432 TGTTTTAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.27, C:0.24, G:0.07, T:0.42
Consensus pattern (26 bp):
TCAATAAGATACGTTCTTCCTTCATC
Found at i:40426367 original size:24 final size:21
Alignment explanation
Indices: 40426311--40426380 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 21
40426301 TCACATCAAC
* *
40426311 AAATAATTTT-AAATTTATTA
1 AAATTATTTTAAAATTAATTA
40426331 AAATTATTTTAAAATTAATTTA
1 AAATTATTTTAAAATTAA-TTA
40426353 AAATTATATTTTAAAA-T-A-TA
1 AAA-T-TATTTTAAAATTAATTA
40426373 AAATTATT
1 AAATTATT
40426381 AAAATAATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
18 4 0.09
19 1 0.02
20 14 0.32
21 6 0.14
22 7 0.16
23 2 0.05
24 10 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAATTATTTTAAAATTAATTA
Found at i:40426372 original size:12 final size:11
Alignment explanation
Indices: 40426311--40426369 Score: 59
Period size: 11 Copynumber: 5.4 Consensus size: 11
40426301 TCACATCAAC
*
40426311 AAATAATTTT-
1 AAATTATTTTA
*
40426321 AAATT-TATTA
1 AAATTATTTTA
40426331 AAATTATTTTA
1 AAATTATTTTA
*
40426342 AAATTAATTTA
1 AAATTATTTTA
40426353 AAATTATATTTTA
1 AAA-T-TATTTTA
40426366 AAAT
1 AAAT
40426370 ATAAAATTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
9 3 0.08
10 9 0.22
11 17 0.43
12 2 0.05
13 9 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:40427072 original size:17 final size:18
Alignment explanation
Indices: 40427046--40427100 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 18
40427036 GGGGTAATGA
*
40427046 TTATAATTTAAAA-AATT
1 TTATATTTTAAAATAATT
40427063 TTATATTTTAAAATAATT
1 TTATATTTTAAAATAATT
40427081 AATTA-ATTTTAAAATAATT
1 --TTATATTTTAAAATAATT
40427100 T
1 T
40427101 AAAATGTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 13 0.38
18 4 0.12
19 14 0.41
20 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATATTTTAAAATAATT
Found at i:40427953 original size:21 final size:21
Alignment explanation
Indices: 40427914--40427954 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40427904 TGATTTTGTG
* * *
40427914 TGAAATGTTATTGATGATAAT
1 TGAAATGTTAATAAAGATAAT
40427935 TGAAATGTTAATAAAGATAA
1 TGAAATGTTAATAAAGATAA
40427955 ATTAAATTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (21 bp):
TGAAATGTTAATAAAGATAAT
Found at i:40428204 original size:21 final size:21
Alignment explanation
Indices: 40428162--40428207 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
40428152 AGGTTGGACC
*
40428162 AATATTGAATTGTGGATGTTG
1 AATATTGAATTGTAGATGTTG
*
40428183 AATATTGAATTTTAGA-GTTTG
1 AATATTGAATTGTAGATG-TTG
40428204 AATA
1 AATA
40428208 ATGTAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (21 bp):
AATATTGAATTGTAGATGTTG
Found at i:40430162 original size:29 final size:28
Alignment explanation
Indices: 40430116--40430214 Score: 92
Period size: 29 Copynumber: 3.4 Consensus size: 28
40430106 GAAATAATAT
* * *
40430116 AGATACAATTACACATACAATCATGTCA
1 AGATACAGTTACAAATACAGTCATGTCA
*
40430144 GAGATACAGTTACAAATACAGTCGA-ATCA
1 -AGATACAGTTACAAATACAGTC-ATGTCA
* *
40430173 ACGATACAGTTACAGATGCAGTCATGTCA
1 A-GATACAGTTACAAATACAGTCATGTCA
*
40430202 CAGATATAGTTAC
1 -AGATACAGTTAC
40430215 GGATGAAGAC
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.03
29 54 0.93
30 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.24
Consensus pattern (28 bp):
AGATACAGTTACAAATACAGTCATGTCA
Found at i:40430219 original size:29 final size:29
Alignment explanation
Indices: 40430175--40430260 Score: 111
Period size: 29 Copynumber: 3.0 Consensus size: 29
40430165 TCGAATCAAC
* *
40430175 GATACAGTTACAGATGCAGTCATG-TCACA
1 GATATAGTTACAGATGCAGACATGAT-ACA
* *
40430204 GATATAGTTACGGATGAAGACATGATACA
1 GATATAGTTACAGATGCAGACATGATACA
*
40430233 TATATAGTTACAGATGCAGACATGATAC
1 GATATAGTTACAGATGCAGACATGATAC
40430261 CTCCATCCGT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
29 48 0.98
30 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (29 bp):
GATATAGTTACAGATGCAGACATGATACA
Found at i:40430918 original size:53 final size:51
Alignment explanation
Indices: 40430821--40430980 Score: 155
Period size: 53 Copynumber: 3.0 Consensus size: 51
40430811 GTGTCTGAAA
* * *
40430821 ACCATGTACCTA-CACCATGTGTCAGCCCATGTTCCCAAAACAGTATACACAC
1 ACCATGTACC-AGC-CCATGTGTCAGCTCGTGTCCCCAAAACAGTATACACAC
*
40430873 ACCTTGATACGC-GCCCATGTGTCAGCTCGTGTGCCCCAAAACAGTATACACAC
1 ACCATG-TAC-CAGCCCATGTGTCAGCTCGTGT-CCCCAAAACAGTATACACAC
* * * *
40430926 AACCATGTGCCAGCCCGTATGCCAGCTCGTGTACCTCC-AAACAGTATACACAC
1 -ACCATGTACCAGCCCATGTGTCAGCTCGTGT-CC-CCAAAACAGTATACACAC
40430979 AC
1 AC
40430981 ACCCTTACAT
Statistics
Matches: 91, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
52 24 0.26
53 59 0.65
54 8 0.09
ACGTcount: A:0.29, C:0.35, G:0.16, T:0.20
Consensus pattern (51 bp):
ACCATGTACCAGCCCATGTGTCAGCTCGTGTCCCCAAAACAGTATACACAC
Found at i:40433004 original size:13 final size:13
Alignment explanation
Indices: 40432986--40433011 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40432976 GTCCTAAATT
40432986 GCACCATTTAACA
1 GCACCATTTAACA
40432999 GCACCATTTAACA
1 GCACCATTTAACA
40433012 ACTATTATCT
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:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (13 bp):
GCACCATTTAACA
Found at i:40435978 original size:2 final size:2
Alignment explanation
Indices: 40435971--40435995 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
40435961 CATTTTATTC
40435971 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
40435996 ACTATAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40442609 original size:43 final size:44
Alignment explanation
Indices: 40442532--40442620 Score: 117
Period size: 43 Copynumber: 2.0 Consensus size: 44
40442522 TTTAAAATAA
* * ** *
40442532 AATAGAAGTTACGATAACTATATATTTAGCAATAATTATAATTT
1 AATAGAAGTTACAAAAACTATATATTTAAAAATAATTAGAATTT
*
40442576 AATAGAAGTTA-AAAAATTATATATTTAAAAATAATTAGAATTT
1 AATAGAAGTTACAAAAACTATATATTTAAAAATAATTAGAATTT
40442619 AA
1 AA
40442621 GTTATAATCA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
43 28 0.72
44 11 0.28
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.37
Consensus pattern (44 bp):
AATAGAAGTTACAAAAACTATATATTTAAAAATAATTAGAATTT
Found at i:40443034 original size:14 final size:15
Alignment explanation
Indices: 40443012--40443109 Score: 60
Period size: 15 Copynumber: 6.5 Consensus size: 15
40443002 CTAGTTTGAA
*
40443012 TAAATAATTAA-TAT
1 TAAAAAATTAATTAT
40443026 TAAAAAATTAGATTAT
1 TAAAAAATTA-ATTAT
* * **
40443042 T-GAAATTTAAAAAAT
1 TAAAAAATT-AATTAT
40443057 T-AAAAATTAATTAT
1 TAAAAAATTAATTAT
* *
40443071 AAAAAAATAAATATAT
1 TAAAAAATTAAT-TAT
*
40443087 T-AAAAATTAACTAT
1 TAAAAAATTAATTAT
40443101 ATAAAAAAT
1 -TAAAAAAT
40443110 ATTCAATATG
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
14 16 0.25
15 33 0.52
16 14 0.22
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (15 bp):
TAAAAAATTAATTAT
Found at i:40443077 original size:16 final size:16
Alignment explanation
Indices: 40443058--40443109 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
40443048 TTAAAAAATT
40443058 AAAAATT-AAT-TATA
1 AAAAATTAAATATATA
* *
40443072 AAAAAATAAATATATT
1 AAAAATTAAATATATA
*
40443088 AAAAATTAACTATATA
1 AAAAATTAAATATATA
40443104 AAAAAT
1 AAAAAT
40443110 ATTCAATATG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 6 0.19
15 3 0.10
16 22 0.71
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAAATTAAATATATA
Found at i:40443088 original size:23 final size:22
Alignment explanation
Indices: 40443010--40443089 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 22
40443000 TACTAGTTTG
40443010 AATAAATAATTAA-TATTAAAAA
1 AATAAATAATTAATTA-TAAAAA
* * *
40443032 ATTAGATTATTGAAATT-TAAAAA
1 AATAAATAATT--AATTATAAAAA
*
40443055 ATTAAA-AATTAATTATAAAAA
1 AATAAATAATTAATTATAAAAA
40443076 AATAAATATATTAA
1 AATAAATA-ATTAA
40443090 AAATTAACTA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
20 4 0.09
21 11 0.24
22 12 0.26
23 16 0.35
24 2 0.04
25 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (22 bp):
AATAAATAATTAATTATAAAAA
Found at i:40447369 original size:21 final size:23
Alignment explanation
Indices: 40447343--40447384 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
40447333 TAATACAATA
40447343 AACACAAAGAC-A-CCTAAGATT
1 AACACAAAGACAATCCTAAGATT
40447364 AACACAAAGACAATCCTAAGA
1 AACACAAAGACAATCCTAAGA
40447385 AATAACCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.58
22 1 0.05
23 7 0.37
ACGTcount: A:0.55, C:0.24, G:0.10, T:0.12
Consensus pattern (23 bp):
AACACAAAGACAATCCTAAGATT
Found at i:40452857 original size:24 final size:24
Alignment explanation
Indices: 40452830--40452879 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
40452820 TGGATCTGTC
40452830 AAGTACACATCCGCAACAATCTAG
1 AAGTACACATCCGCAACAATCTAG
40452854 AAGTACACATCCGCAACAATCTAG
1 AAGTACACATCCGCAACAATCTAG
40452878 AA
1 AA
40452880 ATGAAGATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.28, G:0.12, T:0.16
Consensus pattern (24 bp):
AAGTACACATCCGCAACAATCTAG
Found at i:40453589 original size:25 final size:24
Alignment explanation
Indices: 40453532--40453590 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
40453522 AAAAGTAGGT
* *
40453532 TATA-TATTATTTTTCTAATATTA
1 TATATTATAATTTTTCTAATATCA
40453555 TATATTATAATTTTTACTAAT-TCA
1 TATATTATAATTTTT-CTAATATCA
*
40453579 TATTTTAATAAT
1 TATATT-ATAAT
40453591 AATTATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 4 0.13
24 16 0.53
25 10 0.33
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (24 bp):
TATATTATAATTTTTCTAATATCA
Found at i:40453609 original size:26 final size:26
Alignment explanation
Indices: 40453578--40453661 Score: 69
Period size: 29 Copynumber: 3.0 Consensus size: 26
40453568 TTACTAATTC
40453578 ATATTTTAATAATAATTATATTAAAA
1 ATATTTTAATAATAATTATATTAAAA
* *
40453604 ATATTTTTAAATTATATATTATTTTATTAAA
1 ATA-TTTT-AATAATA-ATTATATTA--AAA
* * *
40453635 TTGTATTTAATAATAATTATGTTAAAA
1 ATAT-TTTAATAATAATTATATTAAAA
40453662 TATAATTAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
26 3 0.07
27 7 0.15
28 6 0.13
29 16 0.35
30 7 0.15
31 7 0.15
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
ATATTTTAATAATAATTATATTAAAA
Found at i:40453652 original size:58 final size:58
Alignment explanation
Indices: 40453564--40453709 Score: 181
Period size: 58 Copynumber: 2.5 Consensus size: 58
40453554 ATATATTATA
* ** *
40453564 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATATTTTTAAATT-ATATATT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAATTAAT-TAAT
* *
40453624 A-TTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATTAATTAAT
1 ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAAT
40453681 ATTTTTATTAAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
40453710 CATTAAAATT
Statistics
Matches: 76, Mismatches: 7, Indels: 8
0.84 0.08 0.09
Matches are distributed among these distances:
57 18 0.24
58 45 0.59
59 8 0.11
60 5 0.07
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAAT
Found at i:40453900 original size:16 final size:16
Alignment explanation
Indices: 40453879--40453934 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
40453869 TGAATTACTG
40453879 ATTACAG-TCCTATTCT
1 ATTACAGCT-CTATTCT
*
40453895 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCT
* *
40453911 ATTATAGCTTTATTCT
1 ATTACAGCTCTATTCT
40453927 ATTACAGC
1 ATTACAGC
40453935 AAATCAAACG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
16 33 0.97
17 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.07, T:0.43
Consensus pattern (16 bp):
ATTACAGCTCTATTCT
Found at i:40456550 original size:12 final size:12
Alignment explanation
Indices: 40456533--40456576 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
40456523 TTAACTTAAT
40456533 CGAACATATTCA
1 CGAACATATTCA
**
40456545 CGAACAT-TAAA
1 CGAACATATTCA
40456556 CGAACATATTCA
1 CGAACATATTCA
*
40456568 TGAACATAT
1 CGAACATAT
40456577 AATTGAACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.45, C:0.20, G:0.09, T:0.25
Consensus pattern (12 bp):
CGAACATATTCA
Found at i:40456554 original size:23 final size:23
Alignment explanation
Indices: 40456528--40456597 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
40456518 TTCATTTAAC
40456528 TTAATCGAACATATTCACGAACA
1 TTAATCGAACATATTCACGAACA
* *
40456551 TTAAACGAACATATTCATGAACA
1 TTAATCGAACATATTCACGAACA
* *
40456574 TATAATTGAACATGTTCACGAACA
1 T-TAATCGAACATATTCACGAACA
40456598 ATGTTAATGA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 22 0.55
24 18 0.45
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (23 bp):
TTAATCGAACATATTCACGAACA
Found at i:40456735 original size:17 final size:16
Alignment explanation
Indices: 40456712--40456790 Score: 79
Period size: 17 Copynumber: 4.8 Consensus size: 16
40456702 CCCAAACCAT
*
40456712 TTTAAATTTACTTTGAA
1 TTTAAATTTAATTT-AA
* *
40456729 ATTAAATTCAATTTTAA
1 TTTAAATTTAA-TTTAA
40456746 TTTAAATTTGAATTTAA
1 TTTAAATTT-AATTTAA
*
40456763 TTTAAATTTAATAT-A
1 TTTAAATTTAATTTAA
40456778 TTGTAAATTTAAT
1 TT-TAAATTTAAT
40456791 AAATATCCAT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
15 3 0.06
16 14 0.26
17 31 0.58
18 5 0.09
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.52
Consensus pattern (16 bp):
TTTAAATTTAATTTAA
Found at i:40456753 original size:6 final size:6
Alignment explanation
Indices: 40456712--40456773 Score: 51
Period size: 6 Copynumber: 10.8 Consensus size: 6
40456702 CCCAAACCAT
* * * *
40456712 TTTAAA TTT-AC TTTGAAA -TTAAA -TTCAA TTTTAA TTTAAA TTTGAA
1 TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
40456758 TTT-AA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAA
40456774 TATATTGTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 16 0.35
6 29 0.63
7 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:40456764 original size:11 final size:11
Alignment explanation
Indices: 40456712--40456790 Score: 56
Period size: 11 Copynumber: 7.1 Consensus size: 11
40456702 CCCAAACCAT
*
40456712 TTTAAATTTAC
1 TTTAAATTTAA
*
40456723 TTTGAAATTAAA
1 TTT-AAATTTAA
* *
40456735 TTCAATTTTAA
1 TTTAAATTTAA
40456746 TTTAAATTTGAA
1 TTTAAATTT-AA
40456758 TTT-AATTTAAA
1 TTTAAATTT-AA
*
40456769 TTT-AATAT-A
1 TTTAAATTTAA
40456778 TTGTAAATTTAA
1 TT-TAAATTTAA
40456790 T
1 T
40456791 AAATATCCAT
Statistics
Matches: 53, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
9 3 0.06
10 1 0.02
11 34 0.64
12 15 0.28
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.52
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:40458853 original size:60 final size:59
Alignment explanation
Indices: 40458735--40459146 Score: 369
Period size: 59 Copynumber: 6.9 Consensus size: 59
40458725 CCCTGAAGGT
* * * * **
40458735 CCCT-AAACTATCCAAAACTTGTATTTTAACCCCCAAACTTCTTTAAAATTACA-TTTTGA
1 CCCTAAAACT-TCCAAAAATTATATTTTTACCCTCAAACTT-TCAAAAATTACATTTTTGA
* * *
40458794 CCCTAAAACTTATCCAAAAAGTATATTTTTGCCCTCAAACTTTCAAAAATTCCA-TTTTGA
1 CCCTAAAAC-T-TCCAAAAATTATATTTTTACCCTCAAACTTTCAAAAATTACATTTTTGA
* * * * *
40458854 CCCTGAAACTTCCCAAAAAATTACATTTTAACCCTAAAACTTTCAAAAAATTACATTTTTAA
1 CCCTAAAACTT-CC-AAAAATTATATTTTTACCCTCAAACTTTC-AAAAATTACATTTTTGA
* *
40458916 CCCTAAAACTTCCAAAAATTACATTTTTACCC-CAAACTTCCAAAAATTACATTTTTGA
1 CCCTAAAACTTCCAAAAATTATATTTTTACCCTCAAACTTTCAAAAATTACATTTTTGA
* * * * * * *
40458974 CCCCAAAACTTCCCAAAATTATGTTTTTACCTTCGAAC-TTCTAGAAATTCCATTTTTGA
1 CCCTAAAACTTCCAAAAATTATATTTTTACCCTCAAACTTTC-AAAAATTACATTTTTGA
* * *
40459033 CCCCAAAACTTCCAAAAATTATATTTTTACCC-CTAAACTTTCAAAAAATT-TATTTTTAA
1 CCCTAAAACTTCCAAAAATTATATTTTTACCCTC-AAACTTTC-AAAAATTACATTTTTGA
* * *
40459092 CCC-CAAATTTCCAAAAATTCA-ATTTTTGACCCTGAAAC-TTC-AAAATTACCATTTT
1 CCCTAAAACTTCCAAAAATT-ATATTTTT-ACCCTCAAACTTTCAAAAATTA-CATTTT
40459147 ACCCCCGAAT
Statistics
Matches: 295, Mismatches: 43, Indels: 31
0.80 0.12 0.08
Matches are distributed among these distances:
56 6 0.02
58 75 0.25
59 84 0.28
60 78 0.26
61 37 0.13
62 15 0.05
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (59 bp):
CCCTAAAACTTCCAAAAATTATATTTTTACCCTCAAACTTTCAAAAATTACATTTTTGA
Found at i:40459080 original size:30 final size:30
Alignment explanation
Indices: 40458779--40459151 Score: 278
Period size: 30 Copynumber: 12.6 Consensus size: 30
40458769 AAACTTCTTT
*
40458779 AAAATTACATTTTGA-CCCTAAAACTTATCCA
1 AAAATTACATTTTTACCCCTAAAAC-T-TCCA
* * * * *
40458810 AAAAGTATATTTTT-GCCCTCAAACTTTCA
1 AAAATTACATTTTTACCCCTAAAACTTCCA
* * *
40458839 AAAATTCCATTTTGA-CCCTGAAACTTCCCAA
1 AAAATTACATTTTTACCCCTAAAACTT-CC-A
* *
40458870 AAAATTACA-TTTTAACCCTAAAACTTTCAA
1 AAAATTACATTTTTACCCCTAAAAC-TTCCA
*
40458900 AAAATTACATTTTTAACCCTAAAACTTCCA
1 AAAATTACATTTTTACCCCTAAAACTTCCA
40458930 AAAATTACATTTTTACCCC--AAACTTCCA
1 AAAATTACATTTTTACCCCTAAAACTTCCA
*
40458958 AAAATTACATTTTTGACCCC-AAAACTTCCC
1 AAAATTACATTTTT-ACCCCTAAAACTTCCA
** * ** *
40458988 AAAATTATGTTTTTA-CCTTCGAACTTCTA
1 AAAATTACATTTTTACCCCTAAAACTTCCA
* *
40459017 GAAATTCCATTTTTGACCCC-AAAACTTCCA
1 AAAATTACATTTTT-ACCCCTAAAACTTCCA
* *
40459047 AAAATTATATTTTTACCCCT-AAACTTTCAA
1 AAAATTACATTTTTACCCCTAAAAC-TTCCA
* *
40459077 AAAATT-TATTTTTAACCCC--AAATTTCCA
1 AAAATTACATTTTT-ACCCCTAAAACTTCCA
*
40459105 AAAATT-CAATTTTTGA-CCCTGAAACTT-C-
1 AAAATTAC-ATTTTT-ACCCCTAAAACTTCCA
40459133 AAAATTACCA-TTTTACCCC
1 AAAATTA-CATTTTTACCCC
40459152 CGAATGTCCA
Statistics
Matches: 279, Mismatches: 42, Indels: 45
0.76 0.11 0.12
Matches are distributed among these distances:
27 1 0.00
28 51 0.18
29 73 0.26
30 98 0.35
31 54 0.19
32 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTTACCCCTAAAACTTCCA
Found at i:40466413 original size:50 final size:51
Alignment explanation
Indices: 40466333--40466437 Score: 140
Period size: 50 Copynumber: 2.1 Consensus size: 51
40466323 AGAAGATGCC
* *
40466333 AAGGGAAAGATCTAAGACCACAACGACGGATCCAATACCGCAAAGATACAA
1 AAGGGAAAGATCTAAGACCACAACGACGGATCCAATACCGCAAAAAGACAA
* * * * *
40466384 AAGGGAAAGTTCTAAG-TCGCAACGGCGGATCCAGTACCGCAAAAAGACAA
1 AAGGGAAAGATCTAAGACCACAACGACGGATCCAATACCGCAAAAAGACAA
40466434 AAGG
1 AAGG
40466438 CAAAAGTCTT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
50 32 0.68
51 15 0.32
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (51 bp):
AAGGGAAAGATCTAAGACCACAACGACGGATCCAATACCGCAAAAAGACAA
Found at i:40466552 original size:92 final size:92
Alignment explanation
Indices: 40466441--40467586 Score: 2143
Period size: 92 Copynumber: 12.5 Consensus size: 92
40466431 CAAAAGGCAA
*
40466441 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCTTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCCT
40466506 CTTGAAGTTGTAGTAAAGTTGGATAGC
66 CTTGAAGTTGTAGTAAAGTTGGATAGC
40466533 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCCT
*
40466598 CTTGAAGTTGTAGTAAAGTTGGATAGT
66 CTTGAAGTTGTAGTAAAGTTGGATAGC
40466625 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCCT
40466690 CTTGAAGTTGTAGTAAAGTTGGATAGC
66 CTTGAAGTTGTAGTAAAGTTGGATAGC
40466717 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCCT
40466782 CTTGAAGTTGTAGTAAAGTTGGATAGC
66 CTTGAAGTTGTAGTAAAGTTGGATAGC
*
40466809 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCTTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCCT
40466874 CTTGAAGTTGTAGTAAAGTTGGATAGC
66 CTTGAAGTTGTAGTAAAGTTGGATAGC
40466901 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCCT
40466966 CTTGAAGTTGTAGTAAAGTTGGATAGC
66 CTTGAAGTTGTAGTAAAGTTGGATAGC
40466993 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCCT
40467058 CTTGAAGTTGTAGTAAAGTTGGATAGC
66 CTTGAAGTTGTAGTAAAGTTGGATAGC
*
40467085 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACCTCAATTCCTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCCT
*
40467150 CTTGAAGTTGTAGTAAAGTTGGATGGC
66 CTTGAAGTTGTAGTAAAGTTGGATAGC
*
40467177 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTCAAACATCAATTCCTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCCT
*
40467242 CTTGACGTTGTAGTAAAGTTGGATAGC
66 CTTGAAGTTGTAGTAAAGTTGGATAGC
*
40467269 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATACT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCCT
40467334 CTTGAAGTTGTAGTAAAGTTGGATAGC
66 CTTGAAGTTGTAGTAAAGTTGGATAGC
*
40467361 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCCATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCCT
40467426 CTTGAAGTTGTAGTAAAGTTGGATAGC
66 CTTGAAGTTGTAGTAAAGTTGGATAGC
* *
40467453 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTAAAACATCAATTCCTATCCT
1 AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCCT
*
40467518 CTTGAAGTTGTGGTAAAG--GGATAGC
66 CTTGAAGTTGTAGTAAAGTTGGATAGC
*
40467543 AAGTCTTTATCTCTCTCTGAAATTGTAGTAAGAGCAAGATGAAG
1 AAGTCTTTA--TCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAG
40467587 CCTCGACATC
Statistics
Matches: 1031, Mismatches: 21, Indels: 4
0.98 0.02 0.00
Matches are distributed among these distances:
90 16 0.02
92 1015 0.98
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (92 bp):
AAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGTTTCAAACATCAATTCCTATCCT
CTTGAAGTTGTAGTAAAGTTGGATAGC
Found at i:40467863 original size:17 final size:16
Alignment explanation
Indices: 40467841--40467882 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
40467831 CCAAACCATT
40467841 TTAAATTTACTTTGAAA
1 TTAAATTTA-TTTGAAA
*
40467858 TTAAATTTATTTTAAA
1 TTAAATTTATTTGAAA
*
40467874 TTCAATTTA
1 TTAAATTTA
40467883 AATTTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.52
Consensus pattern (16 bp):
TTAAATTTATTTGAAA
Found at i:40467870 original size:28 final size:28
Alignment explanation
Indices: 40467838--40467894 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
40467828 GGCCCAAACC
* *
40467838 ATTTTAAATTTACTTTGAAA-TTAAATTT
1 ATTTTAAATTCAATTT-AAATTTAAATTT
40467866 ATTTTAAATTCAATTTAAATTTAAATTT
1 ATTTTAAATTCAATTTAAATTTAAATTT
40467894 A
1 A
40467895 ATATCATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.53
Consensus pattern (28 bp):
ATTTTAAATTCAATTTAAATTTAAATTT
Found at i:40467874 original size:11 final size:11
Alignment explanation
Indices: 40467858--40467913 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
40467848 TACTTTGAAA
*
40467858 TTAAATTTATT
1 TTAAATTTAAT
*
40467869 TTAAATTCAAT
1 TTAAATTTAAT
40467880 TTAAATTTAAAT
1 TTAAATTT-AAT
* *
40467892 TT-AATATCAT
1 TTAAATTTAAT
40467902 TGTAAATTTAAT
1 T-TAAATTTAAT
40467914 AAATATCCAT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
10 3 0.09
11 21 0.60
12 11 0.31
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.52
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:40469750 original size:59 final size:59
Alignment explanation
Indices: 40469657--40470058 Score: 342
Period size: 59 Copynumber: 6.9 Consensus size: 59
40469647 GAGGTCCCTT
* * ** * *
40469657 AACTATCCAGAAATTATA-TTTTGACCCTGAAACTTCCAAAAATTACATTTTTTCCCTCG
1 AACT-TCCAAAAATTACATTTTTGACCCCAAAACTTCCAAAAATTACATTTTTACCCTCA
* ** * *
40469716 AACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCTTAAAATTATATTTTTACCCTTA
1 AACTTCCAAAAATTACATTTTTGACCCCAAAACTTCCAAAAATTACATTTTTACCCTCA
* * * * *
40469775 AACTTCTAAAAATTACA-TTTTGACCCTAAAACTTTCAAAAAATTACATTTTAACCCTAA
1 AACTTCCAAAAATTACATTTTTGACCCCAAAAC-TTCCAAAAATTACATTTTTACCCTCA
* * * * * **
40469834 AACTCCCAAAACTTACATTTTT-ACCCCCAAACTTCCAAAAATTACATTTTGATCCAAA
1 AACTTCCAAAAATTACATTTTTGACCCCAAAACTTCCAAAAATTACATTTTTACCCTCA
* ** * *
40469892 AACTTCCCAAAATTATGTTTTT-ACCCTC-AAACTTCTAAAAATTTCATTTTTGA-CCTCGA
1 AACTTCCAAAAATTACATTTTTGACCC-CAAAACTTCCAAAAATTACATTTTT-ACCCTC-A
* *
40469951 AACTTCCAAAAATTATATTTTTG-CCCC-AAACTTTCAAAAAAATT--ATTTTTGACCC-CA
1 AACTTCCAAAAATTACATTTTTGACCCCAAAAC-TTC-CAAAAATTACATTTTT-ACCCTCA
* * *
40470008 AACTTCCAAAAATTCCATTTTTGACCTCAAAACTGCC-AAAATTACCATTTT
1 AACTTCCAAAAATTACATTTTTGACCCCAAAACTTCCAAAAATTA-CATTTT
40470059 ACCTCCGGAT
Statistics
Matches: 282, Mismatches: 46, Indels: 30
0.79 0.13 0.08
Matches are distributed among these distances:
56 6 0.02
57 22 0.08
58 108 0.38
59 135 0.48
60 11 0.04
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.35
Consensus pattern (59 bp):
AACTTCCAAAAATTACATTTTTGACCCCAAAACTTCCAAAAATTACATTTTTACCCTCA
Found at i:40469758 original size:30 final size:30
Alignment explanation
Indices: 40469657--40470058 Score: 323
Period size: 29 Copynumber: 13.7 Consensus size: 30
40469647 GAGGTCCCTT
* * **
40469657 AACTATCCAGAAATTATA-TTTTGACCCTGA
1 AACT-TCCAAAAATTACATTTTTGACCCCAA
* *
40469687 AACTTCCAAAAATTACATTTTT-TCCCTC-G
1 AACTTCCAAAAATTACATTTTTGACCC-CAA
*
40469716 AACTTCCAAAAATTCCATTTTTGACCCCAA
1 AACTTCCAAAAATTACATTTTTGACCCCAA
** * **
40469746 AACTTCTTAAAATTATATTTTT-ACCCTTA
1 AACTTCCAAAAATTACATTTTTGACCCCAA
* *
40469775 AACTTCTAAAAATTACA-TTTTGACCCTAA
1 AACTTCCAAAAATTACATTTTTGACCCCAA
* * *
40469804 AACTTTCAAAAAATTACA-TTTTAACCCTAA
1 AAC-TTCCAAAAATTACATTTTTGACCCCAA
* * *
40469834 AACTCCCAAAACTTACATTTTT-ACCCCCA
1 AACTTCCAAAAATTACATTTTTGACCCCAA
* *
40469863 AACTTCCAAAAATTACA-TTTTGATCCAAA
1 AACTTCCAAAAATTACATTTTTGACCCCAA
* **
40469892 AACTTCCCAAAATTATGTTTTT-ACCCTC-A
1 AACTTCCAAAAATTACATTTTTGACCC-CAA
* * * *
40469921 AACTTCTAAAAATTTCATTTTTGACCTCGA
1 AACTTCCAAAAATTACATTTTTGACCCCAA
*
40469951 AACTTCCAAAAATTATATTTTTG-CCCC-A
1 AACTTCCAAAAATTACATTTTTGACCCCAA
*
40469979 AACTTTCAAAAAAATT--ATTTTTGACCCC-A
1 AAC-TTC-CAAAAATTACATTTTTGACCCCAA
* *
40470008 AACTTCCAAAAATTCCATTTTTGACCTCAA
1 AACTTCCAAAAATTACATTTTTGACCCCAA
*
40470038 AACTGCC-AAAATTACCATTTT
1 AACTTCCAAAAATTA-CATTTT
40470059 ACCTCCGGAT
Statistics
Matches: 304, Mismatches: 49, Indels: 38
0.78 0.13 0.10
Matches are distributed among these distances:
27 7 0.02
28 22 0.07
29 167 0.55
30 108 0.36
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.35
Consensus pattern (30 bp):
AACTTCCAAAAATTACATTTTTGACCCCAA
Found at i:40469836 original size:88 final size:87
Alignment explanation
Indices: 40469667--40470021 Score: 308
Period size: 88 Copynumber: 4.1 Consensus size: 87
40469657 AACTATCCAG
* ** ** * *
40469667 AAATTATATTTTGACCCTGAAACTTCCAAAAATTACATTTTTTCCCTCGAACTTCCAAAAATTCC
1 AAATTATATTTTTACCCTGAAACTTCCAAAAATTACATTTTGACCCTAAAACTTCAAAAAATTAC
* * *
40469732 ATTTTTGACCCCAAAACTTCTTA
66 A-TTTTAACCCTAAAACTTCTAA
* *
40469755 AAATTATATTTTTACCCTTAAACTTCTAAAAATTACATTTTGACCCTAAAACTTTCAAAAAATTA
1 AAATTATATTTTTACCCTGAAACTTCCAAAAATTACATTTTGACCCTAAAAC-TTCAAAAAATTA
* *
40469820 CATTTTAACCCTAAAACTCCCAA
65 CATTTTAACCCTAAAACTTCTAA
* * ** * * ** *
40469843 AACTTACATTTTTACCCCCAAACTTCCAAAAATTACATTTTGATCCAAAAACTTCCCAAAATTAT
1 AAATTATATTTTTACCCTGAAACTTCCAAAAATTACATTTTGACCCTAAAACTTCAAAAAATTAC
* * *
40469908 GTTTTTACCCTCAAACTTCTAA
66 ATTTTAACCCTAAAACTTCTAA
* *
40469930 AAATT-TCATTTTTGA-CCTCGAAACTTCCAAAAATTATATTTTTG-CCC-CAAACTTTCAAAAA
1 AAATTAT-ATTTTT-ACCCT-GAAACTTCCAAAAATTACA-TTTTGACCCTAAAAC-TTC-AAAA
* * * *
40469991 AATTA-TTTTTGACCC-CAAACTTCCAA
60 AATTACATTTTAACCCTAAAACTTCTAA
40470017 AAATT
1 AAATT
40470022 CCATTTTTGA
Statistics
Matches: 219, Mismatches: 41, Indels: 15
0.80 0.15 0.05
Matches are distributed among these distances:
87 58 0.26
88 137 0.63
89 24 0.11
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (87 bp):
AAATTATATTTTTACCCTGAAACTTCCAAAAATTACATTTTGACCCTAAAACTTCAAAAAATTAC
ATTTTAACCCTAAAACTTCTAA
Found at i:40470203 original size:84 final size:84
Alignment explanation
Indices: 40470104--40470285 Score: 328
Period size: 84 Copynumber: 2.2 Consensus size: 84
40470094 GATTTTTCTA
*
40470104 AAAATTATCATTTTGCCAAAATGTCTAAAATGTCTTTTTTAACCTAAAATTTTCCCAAAATTACC
1 AAAATTACCATTTTGCCAAAATGTCTAAAATGTCTTTTTTAACCTAAAATTTTCCCAAAATTACC
*
40470169 ATTTTGCCCCTGAGAGTCC
66 ATTTTGCCCCTGAAAGTCC
40470188 AAAATTACCATTTTGCCAAAATGTCTAAAATGTCTTTTTTAACCTAAAATTTTCCCAAAATTACC
1 AAAATTACCATTTTGCCAAAATGTCTAAAATGTCTTTTTTAACCTAAAATTTTCCCAAAATTACC
* *
40470253 ATTTTGTCCTTGAAAGTCC
66 ATTTTGCCCCTGAAAGTCC
40470272 AAAATTACCATTTT
1 AAAATTACCATTTT
40470286 ACCTCCGGGT
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 94 1.00
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (84 bp):
AAAATTACCATTTTGCCAAAATGTCTAAAATGTCTTTTTTAACCTAAAATTTTCCCAAAATTACC
ATTTTGCCCCTGAAAGTCC
Found at i:40473030 original size:59 final size:60
Alignment explanation
Indices: 40472969--40473220 Score: 238
Period size: 58 Copynumber: 4.3 Consensus size: 60
40472959 ATCCCGAGGT
*
40472969 AAAATGGTAATTTTTGGAAAAAATCG-GTGTCAAAAATGGGATTTTGA-AAAGTTTGGGGTA
1 AAAAT-GTAATTTTTGGAAAAAATCGAG-GTCAAAAATGGAATTTTGAGAAAGTTTGGGGTA
* ** ** * *
40473029 AAAATATAATTTTTGG-TGAAATCG-GGTTTAAAATGGAATTTTG-GGAAGTTTAGGGT-
1 AAAATGTAATTTTTGGAAAAAATCGAGGTCAAAAATGGAATTTTGAGAAAGTTTGGGGTA
*
40473085 AAAATGGTAATTTTT-GATAAAATCGAGGTCAAAAATGGAATTTT-AGAAAGTTTGGGGGTA
1 AAAAT-GTAATTTTTGGAAAAAATCGAGGTCAAAAATGGAATTTTGAGAAAGTTT-GGGGTA
** * * *
40473145 AAAATGTAA-TTTTGG-AAAGTTCGAGTGT-AAAAATGTAATTTTTAGAAAGTTTGAGGGTC
1 AAAATGTAATTTTTGGAAAAAATCGAG-GTCAAAAATGGAATTTTGAGAAAGTTTG-GGGTA
*
40473204 AAAATATAATTTTTGGA
1 AAAATGTAATTTTTGGA
40473221 TTGTTTAGAG
Statistics
Matches: 159, Mismatches: 20, Indels: 25
0.78 0.10 0.12
Matches are distributed among these distances:
56 6 0.04
57 40 0.25
58 55 0.35
59 42 0.26
60 16 0.10
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.35
Consensus pattern (60 bp):
AAAATGTAATTTTTGGAAAAAATCGAGGTCAAAAATGGAATTTTGAGAAAGTTTGGGGTA
Found at i:40473042 original size:29 final size:29
Alignment explanation
Indices: 40473010--40473218 Score: 110
Period size: 29 Copynumber: 7.2 Consensus size: 29
40473000 AAAAATGGGA
*
40473010 TTTTGAAAAGTTTGGGGTAAAAATATAAT
1 TTTTGAAAAGTTTGGGGTAAAAATGTAAT
* * * * *
40473039 TTTTGGTGAAA--TCGGGTTTAAAATGGAA-
1 TTTT-G-AAAAGTTTGGGGTAAAAATGTAAT
** *
40473067 TTTTGGGAAGTTTAGGGT-AAAATGGTAAT
1 TTTTGAAAAGTTTGGGGTAAAAAT-GTAAT
* * * *
40473096 TTTTGATAAA-ATCGAGGTCAAAAATGGAAT
1 TTTTGA-AAAGTTTGGGGT-AAAAATGTAAT
*
40473126 TTTAG-AAAGTTTGGGGGTAAAAATGTAA-
1 TTTTGAAAAGTTT-GGGGTAAAAATGTAAT
* * *
40473154 TTTTGGAAAGTTCGAGTGTAAAAATGTAAT
1 TTTTGAAAAGTTTG-GGGTAAAAATGTAAT
* *
40473184 TTTT-AGAAAGTTTGAGGGTCAAAATATAAT
1 TTTTGA-AAAGTTTG-GGGTAAAAATGTAAT
40473214 TTTTG
1 TTTTG
40473219 GATTGTTTAG
Statistics
Matches: 133, Mismatches: 31, Indels: 30
0.69 0.16 0.15
Matches are distributed among these distances:
26 3 0.02
27 6 0.05
28 19 0.14
29 54 0.41
30 43 0.32
31 8 0.06
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.36
Consensus pattern (29 bp):
TTTTGAAAAGTTTGGGGTAAAAATGTAAT
Found at i:40473195 original size:30 final size:30
Alignment explanation
Indices: 40473080--40473217 Score: 124
Period size: 29 Copynumber: 4.7 Consensus size: 30
40473070 TGGGAAGTTT
**
40473080 AGGGT-AAAATGGTAATTTTT-GATAAAATCG
1 AGGGTAAAAAT-GTAATTTTTAGA-AAGTTCG
* *
40473110 A-GGTCAAAAATGGAA-TTTTAGAAAGTTTG
1 AGGGT-AAAAATGTAATTTTTAGAAAGTTCG
* *
40473139 GGGGTAAAAATGTAA-TTTTGGAAAGTTCG
1 AGGGTAAAAATGTAATTTTTAGAAAGTTCG
* *
40473168 AGTGTAAAAATGTAATTTTTAGAAAGTTTG
1 AGGGTAAAAATGTAATTTTTAGAAAGTTCG
* *
40473198 AGGGTCAAAATATAATTTTT
1 AGGGTAAAAATGTAATTTTT
40473218 GGATTGTTTA
Statistics
Matches: 88, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
29 45 0.51
30 38 0.43
31 5 0.06
ACGTcount: A:0.39, C:0.03, G:0.23, T:0.35
Consensus pattern (30 bp):
AGGGTAAAAATGTAATTTTTAGAAAGTTCG
Found at i:40474344 original size:9 final size:9
Alignment explanation
Indices: 40474330--40474361 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
40474320 GTTAAAAAAG
40474330 TATTATTAA
1 TATTATTAA
40474339 TATTATTAA
1 TATTATTAA
40474348 TATTTATTAA
1 TA-TTATTAA
40474358 TATT
1 TATT
40474362 CATTTAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATTAA
Found at i:40474832 original size:25 final size:25
Alignment explanation
Indices: 40474797--40474853 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
40474787 ATGTAGTGGC
*
40474797 GGTGGCAGAGCATGTTGAAGCTGGT
1 GGTGGCAGAGCAAGTTGAAGCTGGT
*
40474822 GGTGGCTGAGCAAGTTGAAGCTGGT
1 GGTGGCAGAGCAAGTTGAAGCTGGT
*
40474847 GATGGCA
1 GGTGGCA
40474854 TTATCGATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.21, C:0.12, G:0.44, T:0.23
Consensus pattern (25 bp):
GGTGGCAGAGCAAGTTGAAGCTGGT
Found at i:40475124 original size:17 final size:17
Alignment explanation
Indices: 40475085--40475178 Score: 118
Period size: 17 Copynumber: 5.5 Consensus size: 17
40475075 ACTTTTCTTT
*
40475085 AATTTAAATCTAGAAA-A
1 AATTTAAATTTA-AAATA
*
40475102 ATTTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
* *
40475119 AATTTAAACTTAAATTA
1 AATTTAAATTTAAAATA
*
40475136 AATTTAAACTTTAAAACA
1 AATTTAAA-TTTAAAATA
40475154 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAATA
40475171 AATTTAAA
1 AATTTAAA
40475179 GAAAACTGGG
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
16 3 0.05
17 49 0.74
18 14 0.21
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:40475149 original size:35 final size:34
Alignment explanation
Indices: 40475104--40475178 Score: 114
Period size: 35 Copynumber: 2.2 Consensus size: 34
40475094 CTAGAAAAAT
* *
40475104 TTTAAATTTAAAATAAATTTAAACTTAAATTAAA
1 TTTAAATTTAAAACAAATTTAAACTTAAAATAAA
*
40475138 TTTAAACTTTAAAACAAATTTAAATTTAAAATAAA
1 TTTAAA-TTTAAAACAAATTTAAACTTAAAATAAA
40475173 TTTAAA
1 TTTAAA
40475179 GAAAACTGGG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
34 6 0.16
35 31 0.84
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (34 bp):
TTTAAATTTAAAACAAATTTAAACTTAAAATAAA
Found at i:40475867 original size:206 final size:204
Alignment explanation
Indices: 40475513--40476101 Score: 749
Period size: 206 Copynumber: 2.9 Consensus size: 204
40475503 TTCACTTGGC
* * * ** * * * * *
40475513 CTTCTTCTCAGTATCTCATCAAGAAGATAATCGCATCACTTGTTTTGATCCACTTCTCTGTGTTT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATTCGCTTCCCTGTATCT
* * * * *
40475578 CATCAGGAAGACGGATTTGGTTCACTTCTCCGTATCTCATCAAGAAGCTAACCACTTTATTGTTT
66 CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTT
*
40475643 CGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCGT-GA
131 CGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACATCGAGCGTCGA
*
40475707 GTTTG-ATTCA
196 GTTGGTA-T-A
*
40475717 GTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTATTTCAATTCGCTTCCCTGTAT
1 --CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATTCGCTTCCCTGTAT
* *
40475782 CTCATGAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGC
64 CTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGC
* * * *
40475847 TTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCAAAGATTTGGTCGCATTGAGCGTC
129 TTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACATCGAGCGTC
40475912 GAGTTGGTATA
194 GAGTTGGTATA
* * **
40475923 CTTC-TCT--GTATCTCATCAGGAAGATGACAGCCTCACTTGTTTCAATTCGTCTTCTTGATGAT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATTCG-CTTC--CCTG-T
* * * * *
40475985 ATCTCATCAAGAAGACGAATTTGGTTGATTTCTTAGTATCTCATCAGGAAGCTAACCTTTTTATT
62 ATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATT
*
40476050 GCTTC-ACACTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCAAAGATTTG
127 GCTTCGAC-CTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTG
40476102 TTCGCATTGA
Statistics
Matches: 338, Mismatches: 38, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
201 39 0.12
202 4 0.01
203 3 0.01
204 8 0.02
205 106 0.31
206 170 0.50
207 7 0.02
208 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.35
Consensus pattern (204 bp):
CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATTCGCTTCCCTGTATCT
CATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTT
CGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACATCGAGCGTCGA
GTTGGTATA
Found at i:40476305 original size:78 final size:78
Alignment explanation
Indices: 40476212--40476365 Score: 200
Period size: 78 Copynumber: 2.0 Consensus size: 78
40476202 TGGTTGACGG
* ** * * * * *
40476212 TGATCTGCCCCAAGCTCGGGGTAAAAGATTGAATGGTTATAATCTGTCCCTGGCTCGGGGTAAGA
1 TGATCTGCCCCAAGCTCAGGGTAAAAGATCAAATGGCTACAATCTGCCCCAGGCTCAGGGTAAGA
*
40476277 TATTAGTTGACAA
66 AATTAGTTGACAA
* *
40476290 TGATCTGCCCTAAGCTCAGGGTAAAAGATCAAATGGCTGCAATCTGCCCCAGGCTCAGGGTAAGA
1 TGATCTGCCCCAAGCTCAGGGTAAAAGATCAAATGGCTACAATCTGCCCCAGGCTCAGGGTAAGA
*
40476355 AATTGGTTGAC
66 AATTAGTTGAC
40476366 GATGTAACTT
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
78 64 1.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (78 bp):
TGATCTGCCCCAAGCTCAGGGTAAAAGATCAAATGGCTACAATCTGCCCCAGGCTCAGGGTAAGA
AATTAGTTGACAA
Found at i:40493219 original size:9 final size:9
Alignment explanation
Indices: 40493173--40493211 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
40493163 ACGCCAAAAC
40493173 AAAGAAATA
1 AAAGAAATA
**
40493182 AAAGAAGCA
1 AAAGAAATA
*
40493191 AAACAAATA
1 AAAGAAATA
40493200 AAAGAAATA
1 AAAGAAATA
40493209 AAA
1 AAA
40493212 AATATAAAGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.77, C:0.05, G:0.10, T:0.08
Consensus pattern (9 bp):
AAAGAAATA
Found at i:40494681 original size:28 final size:28
Alignment explanation
Indices: 40494640--40494740 Score: 87
Period size: 28 Copynumber: 3.5 Consensus size: 28
40494630 CGGAGGGGGC
* *
40494640 AAAATGGTATTTTTAGACACTCGAGGGT
1 AAAATGGTAATTTTAGACACTTGAGGGT
* *
40494668 AAAATGGTAATTTTGGAAAAGCTTG-GGGT
1 AAAATGGTAATTTTAG-ACA-CTTGAGGGT
* * * *
40494697 CAAAATTGAAATTTTTAAACATTTGAGGGT
1 -AAAATGGTAA-TTTTAGACACTTGAGGGT
40494727 AAAATGGTAATTTT
1 AAAATGGTAATTTT
40494741 TAGGAAAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
28 18 0.32
29 17 0.30
30 17 0.30
31 4 0.07
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.35
Consensus pattern (28 bp):
AAAATGGTAATTTTAGACACTTGAGGGT
Found at i:40494741 original size:29 final size:29
Alignment explanation
Indices: 40494640--40494742 Score: 104
Period size: 29 Copynumber: 3.6 Consensus size: 29
40494630 CGGAGGGGGC
* *
40494640 AAAATGGT-ATTTTTAGACACTCGAGGGT
1 AAAATGGTAATTTTTAAACACTTGAGGGT
*
40494668 AAAATGGTAATTTTGGAAA-AGCTTG-GGGT
1 AAAATGGTAATTTT-TAAACA-CTTGAGGGT
* * *
40494697 CAAAATTGAAATTTTTAAACATTTGAGGGT
1 -AAAATGGTAATTTTTAAACACTTGAGGGT
40494727 AAAATGGTAATTTTTA
1 AAAATGGTAATTTTTA
40494743 GGAAAAAACG
Statistics
Matches: 60, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
28 8 0.13
29 30 0.50
30 22 0.37
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (29 bp):
AAAATGGTAATTTTTAAACACTTGAGGGT
Found at i:40494823 original size:30 final size:31
Alignment explanation
Indices: 40494660--40494966 Score: 152
Period size: 30 Copynumber: 10.4 Consensus size: 31
40494650 TTTTAGACAC
*
40494660 TCGAGGGT-AAAATGGTAA-TTTTGGAAAAGC
1 TCGAGGGTAAAAATGGTAATTTTTGGAAAA-A
* * * * *
40494690 TTG-GGGTCAAAATTGAAATTTTT--AAACAT
1 TCGAGGGTAAAAATGGTAATTTTTGGAAA-AA
*
40494719 TTGAGGGT-AAAATGGTAATTTTTAGGAAAAA
1 TCGAGGGTAAAAATGGTAATTTTT-GGAAAAA
* * *
40494750 ACGA-GGTCAAAAATGG-AGTTTTTGG--AGA
1 TCGAGGGT-AAAAATGGTAATTTTTGGAAAAA
* * * *
40494778 TCCCAAGCT-AAAATGGTAATTTTTGAAAAAA
1 T-CGAGGGTAAAAATGGTAATTTTTGGAAAAA
**
40494809 TCG-GGGTAAAAATGG-AATTTTTGGAAAGT
1 TCGAGGGTAAAAATGGTAATTTTTGGAAAAA
* * **
40494838 TCGAGGGTACAAAT-ATAATTTTTGGTTAAA
1 TCGAGGGTAAAAATGGTAATTTTTGGAAAAA
* **
40494868 TC-AGAGTTAAAAATGG-AA-TTTTGGAAAGT
1 TCGAG-GGTAAAAATGGTAATTTTTGGAAAAA
*
40494897 TCGAGGGT-AAAATGGTAATTTTTGGTAAAA
1 TCGAGGGTAAAAATGGTAATTTTTGGAAAAA
* * **
40494927 TTGAGGTTAAAAAT-GT-A-TTTTGGAAAGT
1 TCGAGGGTAAAAATGGTAATTTTTGGAAAAA
*
40494955 TTGAGGGTAAAA
1 TCGAGGGTAAAA
40494967 TATAATTTTC
Statistics
Matches: 208, Mismatches: 46, Indels: 48
0.69 0.15 0.16
Matches are distributed among these distances:
28 35 0.17
29 64 0.31
30 78 0.38
31 21 0.10
32 10 0.05
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (31 bp):
TCGAGGGTAAAAATGGTAATTTTTGGAAAAA
Found at i:40494844 original size:119 final size:117
Alignment explanation
Indices: 40494667--40494975 Score: 297
Period size: 118 Copynumber: 2.6 Consensus size: 117
40494657 CACTCGAGGG
* ** * * *
40494667 TAAAATGGTAATTTTGGAAAAGCTTGGGGTCAAAATTGAAATTTTT--AAACATTTGAGGGTAAA
1 TAAAATGGTAATTTTTGAAAAAATTGGGGT-AAAAATGGAATTTTTGGAAA-GTTTGAGGGTAAA
* * *
40494730 ATGGTAATTTTTAGGAAAAAAC-GAGGTCAAAAATGGAGTTTTTGGAGA-TCCCAAGC
64 AT-ATAATTTTT-GGAAAAAACAGA-GTCAAAAATGGA-ATTTTGGAAAGTCCCAAGC
* *
40494786 TAAAATGGTAATTTTTGAAAAAATCGGGGTAAAAATGGAATTTTTGGAAAGTTCGAGGGTACAAA
1 TAAAATGGTAATTTTTGAAAAAATTGGGGTAAAAATGGAATTTTTGGAAAGTTTGAGGGTA-AAA
** * * * * * *
40494851 TATAATTTTTGGTTAAATCAGAGTTAAAAATGGAATTTTGGAAAGTTCGAGGG
65 TATAATTTTTGGAAAAAACAGAGTCAAAAATGGAATTTTGGAAAGTCCCAAGC
** * *
40494904 TAAAATGGTAATTTTTGGTAAAATTGAGGTTAAAAAT-GTA-TTTTGGAAAGTTTGAGGGTAAAA
1 TAAAATGGTAATTTTTGAAAAAATTG-GGGTAAAAATGGAATTTTTGGAAAGTTTGAGGGTAAAA
40494967 TATAATTTT
65 TATAATTTT
40494976 CAAAAAGTTC
Statistics
Matches: 159, Mismatches: 25, Indels: 15
0.80 0.13 0.08
Matches are distributed among these distances:
116 12 0.08
117 27 0.17
118 59 0.37
119 54 0.34
120 7 0.04
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (117 bp):
TAAAATGGTAATTTTTGAAAAAATTGGGGTAAAAATGGAATTTTTGGAAAGTTTGAGGGTAAAAT
ATAATTTTTGGAAAAAACAGAGTCAAAAATGGAATTTTGGAAAGTCCCAAGC
Found at i:40494890 original size:59 final size:58
Alignment explanation
Indices: 40494815--40494975 Score: 227
Period size: 59 Copynumber: 2.7 Consensus size: 58
40494805 AAAATCGGGG
*
40494815 TAAAAATGGAATTTTTGGAAAGTTCGAGGGTACAAATATAATTTTTGGTTAAATCAGA-GT
1 TAAAAATGGAA-TTTTGGAAAGTTCGAGGGTA-AAATATAATTTTTGGTAAAAT-AGAGGT
* *
40494875 TAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTAAAATTGAGGT
1 TAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAAT-ATAATTTTTGGTAAAATAGAGGT
* *
40494934 TAAAAAT-GTATTTTGGAAAGTTTGAGGGTAAAATATAATTTT
1 TAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATATAATTTT
40494976 CAAAAAGTTC
Statistics
Matches: 93, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
57 7 0.08
58 31 0.33
59 44 0.47
60 11 0.12
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (58 bp):
TAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATATAATTTTTGGTAAAATAGAGGT
Found at i:40494958 original size:28 final size:29
Alignment explanation
Indices: 40494875--40494966 Score: 100
Period size: 28 Copynumber: 3.2 Consensus size: 29
40494865 AAATCAGAGT
* *
40494875 TAAAAATGGAATTTTGGAAAGTTCGAGGG
1 TAAAAATGGTATTTTGGAAAGTTTGAGGG
* *
40494904 T-AAAATGGTAATTTTTGGTAAA-ATTGAGGT
1 TAAAAATGGT-A-TTTTGG-AAAGTTTGAGGG
40494934 TAAAAAT-GTATTTTGGAAAGTTTGAGGG
1 TAAAAATGGTATTTTGGAAAGTTTGAGGG
40494962 TAAAA
1 TAAAA
40494967 TATAATTTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
27 3 0.06
28 24 0.46
29 3 0.06
30 14 0.27
31 8 0.15
ACGTcount: A:0.39, C:0.01, G:0.26, T:0.34
Consensus pattern (29 bp):
TAAAAATGGTATTTTGGAAAGTTTGAGGG
Found at i:40496121 original size:9 final size:9
Alignment explanation
Indices: 40496107--40496138 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
40496097 GTTAAAAAAG
40496107 TATTATTAA
1 TATTATTAA
40496116 TATTATTAA
1 TATTATTAA
40496125 TATTTATTAA
1 TA-TTATTAA
40496135 TATT
1 TATT
40496139 CATTTAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 13 0.59
10 9 0.41
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATTATTAA
Found at i:40496609 original size:25 final size:25
Alignment explanation
Indices: 40496574--40496630 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 25
40496564 ATGCAGTGGC
*
40496574 GGTGGCAGAGCAGGTTGAAGCTGGT
1 GGTGGCAGAGCAAGTTGAAGCTGGT
* *
40496599 GGTGGCTGAGCAAGTTGAAGTTGGT
1 GGTGGCAGAGCAAGTTGAAGCTGGT
*
40496624 GATGGCA
1 GGTGGCA
40496631 TTATCGATGA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.21, C:0.11, G:0.46, T:0.23
Consensus pattern (25 bp):
GGTGGCAGAGCAAGTTGAAGCTGGT
Found at i:40496901 original size:17 final size:17
Alignment explanation
Indices: 40496881--40496956 Score: 89
Period size: 17 Copynumber: 4.4 Consensus size: 17
40496871 CTAGAAAAAT
*
40496881 TTTAAACTTCAAATAAA
1 TTTAAACTTAAAATAAA
*
40496898 TTTAAACTTAAATTAAA
1 TTTAAACTTAAAATAAA
* *
40496915 TTTAAATTTTAAAAACAAA
1 TTTAAA-CTT-AAAATAAA
*
40496934 TTTAAATTTAAAATAAA
1 TTTAAACTTAAAATAAA
40496951 TTTAAA
1 TTTAAA
40496957 GAAAAGTGGG
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
17 34 0.67
18 5 0.10
19 12 0.24
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (17 bp):
TTTAAACTTAAAATAAA
Found at i:40496927 original size:7 final size:6
Alignment explanation
Indices: 40496894--40496956 Score: 58
Period size: 6 Copynumber: 10.7 Consensus size: 6
40496884 AAACTTCAAA
* ** *
40496894 TAAATT TAAACT TAAA-T TAAATT TAAATTT TAAAAA CAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAA-TT TAAATT TAAATT TAAATT
*
40496942 TAAA-A TAAATT TAAA
1 TAAATT TAAATT TAAA
40496957 GAAAAGTGGG
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
5 9 0.20
6 30 0.67
7 6 0.13
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (6 bp):
TAAATT
Found at i:40496936 original size:19 final size:17
Alignment explanation
Indices: 40496862--40496956 Score: 75
Period size: 17 Copynumber: 5.5 Consensus size: 17
40496852 ACTTCTCTTT
*
40496862 AATTTAAATCTAGAAA-A
1 AATTTAAATTTA-AAACA
* * * *
40496879 ATTTTAAACTTCAAATA
1 AATTTAAATTTAAAACA
* **
40496896 AATTTAAACTTAAATTA
1 AATTTAAATTTAAAACA
40496913 AATTTAAATTTTAAAAACA
1 AATTTAAA-TTT-AAAACA
*
40496932 AATTTAAATTTAAAATA
1 AATTTAAATTTAAAACA
40496949 AATTTAAA
1 AATTTAAA
40496957 GAAAAGTGGG
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
16 3 0.05
17 44 0.69
18 5 0.08
19 12 0.19
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (17 bp):
AATTTAAATTTAAAACA
Found at i:40497844 original size:23 final size:23
Alignment explanation
Indices: 40497781--40497861 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 23
40497771 ACATTGCTCT
*
40497781 TGAACATGTTCAATTATATGTTCA
1 TGAACATGTTCGATTA-ATGTTCA
* * * *
40497805 TGAACTTGTTTGTTTAATGTTCG
1 TGAACATGTTCGATTAATGTTCA
*
40497828 TGAACATGTTCGATTAA-GTTAAA
1 TGAACATGTTCGATTAATGTT-CA
*
40497851 TGTACATGTTC
1 TGAACATGTTC
40497862 ATAAACATTA
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
22 3 0.07
23 30 0.67
24 12 0.27
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.43
Consensus pattern (23 bp):
TGAACATGTTCGATTAATGTTCA
Found at i:40506367 original size:49 final size:48
Alignment explanation
Indices: 40506298--40506394 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 48
40506288 AATTGAGTTA
* * * *
40506298 ATACGATTAAATCACGCTAATGATTGTTTAATTATATTTTTTTATCACT
1 ATACGAGTAAAGCACACTAATGATTATTTAATTATA-TTTTTTATCACT
40506347 ATACGAGTAAAGCACACTAATGATTATTTAATTATATTTTTTATCACT
1 ATACGAGTAAAGCACACTAATGATTATTTAATTATATTTTTTATCACT
40506395 TAATTATTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 12 0.27
49 32 0.73
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.44
Consensus pattern (48 bp):
ATACGAGTAAAGCACACTAATGATTATTTAATTATATTTTTTATCACT
Found at i:40508794 original size:12 final size:12
Alignment explanation
Indices: 40508775--40508815 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
40508765 AAATGAAGGC
*
40508775 TCTTGCTTCTTT
1 TCTTGCTTCTAT
*
40508787 TTTTGCTTCTAT
1 TCTTGCTTCTAT
40508799 TCTTGCTTCTAT
1 TCTTGCTTCTAT
40508811 TCTTG
1 TCTTG
40508816 AATCTCTTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.05, C:0.22, G:0.10, T:0.63
Consensus pattern (12 bp):
TCTTGCTTCTAT
Found at i:40522329 original size:231 final size:231
Alignment explanation
Indices: 40522052--40522547 Score: 654
Period size: 231 Copynumber: 2.1 Consensus size: 231
40522042 TCTCATATTT
* * * ** *
40522052 CTGCTCATACTGTTTTACATTAACTTCAAGATCTCTACAACGTTCTTTGAAAGCCTTCTCTTCCC
1 CTGCTCACATTGTTTTACACTAACTTCAAGATCTCTACAACGTTCTTCCAAAGCCTTCTCTTCCA
* * * *
40522117 TCTCAAACTCCATATAACGCTTCACAAAACTCTTCTCTTTCAACTCAAATTGTTCTTCTTTCAAC
66 ACTCAAACTCCATACAACGCTTCACAAAACTCTTCTCTTTCAACCCAAATTGTTCTTCTCTCAAC
* * * * * ** *
40522182 TCATACTCGCTCAAGCACTTCTCCAAAT-ATTTCTCTTTCACCCCAACTTCCTTGAACTTATCTT
131 ACATAATCCCTCAAGCAATTCTCCAAATCA-TTCTCTTTCAACCCAACTTCCTCCAACTTATCAT
*
40522246 TTA-CTGATTTCTCCATCAACTTAAACTCTTCACATTG
195 TTACCAG-TTTCTCCATCAACTTAAACTCTTCACATTG
* * *
40522283 CTGCTCACATTGTTTTACACTAACTTCAAGATCTCTGCGACGTTCTTCCAAAGCCTTTTCTTCCA
1 CTGCTCACATTGTTTTACACTAACTTCAAGATCTCTACAACGTTCTTCCAAAGCCTTCTCTTCCA
* * * *
40522348 ACTCAAATTCCATACACCGCTTCTCAAAACTCTTCTCTTTCAACCCAAATTGTTGTTCTCTCAAC
66 ACTCAAACTCCATACAACGCTTCACAAAACTCTTCTCTTTCAACCCAAATTGTTCTTCTCTCAAC
* * *
40522413 ACATAATCCCTCAAGCAATTCTCCAAATCATTCTCTTTTAATCCAATTTCCTCCAACTTATCATT
131 ACATAATCCCTCAAGCAATTCTCCAAATCATTCTCTTTCAACCCAACTTCCTCCAACTTATCATT
* *
40522478 TACCAGTTTCTCCATCAACTTAACCTCTTTACATTG
196 TACCAGTTTCTCCATCAACTTAAACTCTTCACATTG
* * *
40522514 CTGCTCACATTGTTCTACACTAAATTGAAGATCT
1 CTGCTCACATTGTTTTACACTAACTTCAAGATCT
40522548 TTACGACTGC
Statistics
Matches: 229, Mismatches: 34, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
231 226 0.99
232 3 0.01
ACGTcount: A:0.26, C:0.31, G:0.06, T:0.37
Consensus pattern (231 bp):
CTGCTCACATTGTTTTACACTAACTTCAAGATCTCTACAACGTTCTTCCAAAGCCTTCTCTTCCA
ACTCAAACTCCATACAACGCTTCACAAAACTCTTCTCTTTCAACCCAAATTGTTCTTCTCTCAAC
ACATAATCCCTCAAGCAATTCTCCAAATCATTCTCTTTCAACCCAACTTCCTCCAACTTATCATT
TACCAGTTTCTCCATCAACTTAAACTCTTCACATTG
Found at i:40522584 original size:231 final size:231
Alignment explanation
Indices: 40522052--40522615 Score: 636
Period size: 231 Copynumber: 2.4 Consensus size: 231
40522042 TCTCATATTT
* * * * * * * ** * *
40522052 CTGCTCATACTGTTTTACATTAACTTCAAGATCTCTACAACGTTCTTTGAAAGCCTTCTCTTCCC
1 CTGCTCACATTGTTCTACACTAAATTCAAGATCTCTACGACGTGCTTCCAAAGCCTTTTCTTCCA
* * * * * *
40522117 TCTCAAACTCCATATAACGCTTCACAAAACTCTTCTCTTTCAACTCAAATTGTTCTTCTTTCAAC
66 ACTCAAAATCCATACAACGCTTCTCAAAACTCTTCTCTTTCAACCCAAATTGTTCTTCTCTCAAC
* * * * * ** *
40522182 TCATACTCGCTCAAGCACTTCTCCAAATATTTCTCTTTCACCCCAACTTCCTTGAACTTATCTTT
131 ACATAATCCCTCAAGCAATTCTCCAAATATTTCTCTTTCAACCCAACTTCCTCCAACTTATCATT
*
40522247 TACTGATTTCTCCATCAACTTAAACTCTTCACATTG
196 TACAGATTTCTCCATCAACTTAAACTCTTCACATTG
* * * *
40522283 CTGCTCACATTGTTTTACACTAACTTCAAGATCTCTGCGACGTTCTTCCAAAGCCTTTTCTTCCA
1 CTGCTCACATTGTTCTACACTAAATTCAAGATCTCTACGACGTGCTTCCAAAGCCTTTTCTTCCA
* * *
40522348 ACTCAAATTCCATACACCGCTTCTCAAAACTCTTCTCTTTCAACCCAAATTGTTGTTCTCTCAAC
66 ACTCAAAATCCATACAACGCTTCTCAAAACTCTTCTCTTTCAACCCAAATTGTTCTTCTCTCAAC
* * *
40522413 ACATAATCCCTCAAGCAATTCTCCAAATCA-TTCTCTTTTAATCCAATTTCCTCCAACTTATCAT
131 ACATAATCCCTCAAGCAATTCTCCAAAT-ATTTCTCTTTCAACCCAACTTCCTCCAACTTATCAT
* *
40522477 TTACCAG-TTTCTCCATCAACTTAACCTCTTTACATTG
195 TTA-CAGATTTCTCCATCAACTTAAACTCTTCACATTG
* * *
40522514 CTGCTCACATTGTTCTACACTAAATTGAAGATCTTTACGAC-TGCGTT-CAAGATCCTTCTTC-T
1 CTGCTCACATTGTTCTACACTAAATTCAAGATCTCTACGACGTGC-TTCCAA-AGCCTT-TTCTT
* * *
40522576 CTAACTCAAAATCCCTACAACACTTCTCAAAAGC-CTTCTC
63 CCAACTCAAAATCCATACAACGCTTCTCAAAA-CTCTTCTC
40522616 CTTTAACACA
Statistics
Matches: 284, Mismatches: 43, Indels: 12
0.84 0.13 0.04
Matches are distributed among these distances:
230 5 0.02
231 272 0.96
232 7 0.02
ACGTcount: A:0.26, C:0.31, G:0.06, T:0.36
Consensus pattern (231 bp):
CTGCTCACATTGTTCTACACTAAATTCAAGATCTCTACGACGTGCTTCCAAAGCCTTTTCTTCCA
ACTCAAAATCCATACAACGCTTCTCAAAACTCTTCTCTTTCAACCCAAATTGTTCTTCTCTCAAC
ACATAATCCCTCAAGCAATTCTCCAAATATTTCTCTTTCAACCCAACTTCCTCCAACTTATCATT
TACAGATTTCTCCATCAACTTAAACTCTTCACATTG
Found at i:40523157 original size:6 final size:6
Alignment explanation
Indices: 40523146--40523174 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
40523136 TGTCTTTAAG
40523146 GGAGAC GGAGAC GGAGAC GGAGAC GGAGA
1 GGAGAC GGAGAC GGAGAC GGAGAC GGAGA
40523175 GAGATGAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.52, T:0.00
Consensus pattern (6 bp):
GGAGAC
Found at i:40523641 original size:47 final size:49
Alignment explanation
Indices: 40523544--40523644 Score: 116
Period size: 48 Copynumber: 2.1 Consensus size: 49
40523534 ATATCTGAAA
* * *
40523544 AAAAAAATTGAGTCTTGATTTTGTGGCGGTCGGCACCATTATTTGATTT
1 AAAAAAATTGAGTCTTAATTTTATGGCGGTCGACACCATTATTTGATTT
* * * * *
40523593 AAAAAAATTGA-TTTTAATTTTATGGTGGTTGACATCATT-TTTTATTT
1 AAAAAAATTGAGTCTTAATTTTATGGCGGTCGACACCATTATTTGATTT
40523640 AAAAA
1 AAAAA
40523645 TAATCTTTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
47 12 0.27
48 21 0.48
49 11 0.25
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.43
Consensus pattern (49 bp):
AAAAAAATTGAGTCTTAATTTTATGGCGGTCGACACCATTATTTGATTT
Found at i:40526614 original size:59 final size:58
Alignment explanation
Indices: 40526412--40526696 Score: 218
Period size: 59 Copynumber: 4.9 Consensus size: 58
40526402 AAAACGATAA
* * * * * *
40526412 TTTTAGACACTTCGAGGGTAAAAAGGTAATTTTTGGAAATTTCAAGGTCAAAATAGAAT
1 TTTTAGACA-TCCAAGGGTAAAATGGTAATTTTTGGAAGTTTCAGGGTCAAAATGGAAT
* * ** * *** ** *
40526471 TTTTGGACATTCGGGGGTAAGATGGTAATTTTCAAAAGTTTTGGGGTTAAAAATGGAAT
1 TTTTAGACATCCAAGGGTAAAATGGTAATTTTTGGAAGTTTCAGGG-TCAAAATGGAAT
* * * *
40526530 TTTTGGACATCTAAGGGTAAAATGGTAATTTTTGGAGGGTTCAGGGTCAAAATGGAAT
1 TTTTAGACATCCAAGGGTAAAATGGTAATTTTTGGAAGTTTCAGGGTCAAAATGGAAT
** *
40526588 TTTTAGACATCCAAGGGTAAAAATGGTAATTTTTGGAA-TTTTTGAGGTCAAAAAT-GAAA
1 TTTTAGACATCCAAGGGT-AAAATGGTAATTTTTGGAAGTTTCAG-GGTC-AAAATGGAAT
* * * ** * *
40526647 TTTTGGATATTCGGGGGTAGAACGGTAATTTTTGGAAG-TTCAGGGT-AAAA
1 TTTTAGACATCCAAGGGTAAAATGGTAATTTTTGGAAGTTTCAGGGTCAAAA
40526697 CTATAATTTT
Statistics
Matches: 179, Mismatches: 42, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
55 4 0.02
57 3 0.02
58 77 0.43
59 90 0.50
60 5 0.03
ACGTcount: A:0.34, C:0.07, G:0.26, T:0.34
Consensus pattern (58 bp):
TTTTAGACATCCAAGGGTAAAATGGTAATTTTTGGAAGTTTCAGGGTCAAAATGGAAT
Found at i:40526651 original size:117 final size:116
Alignment explanation
Indices: 40526410--40526707 Score: 296
Period size: 117 Copynumber: 2.5 Consensus size: 116
40526400 GTAAAACGAT
* * * *
40526410 AATTTTAGACACTTCGAGGGTAAAAAGGTAATTTTTGGAAATTTCAAGGTCAAAATAGAATTTTT
1 AATTTTGGACA-TTCAAGGGTAAAAAGGTAATTTTTGG-AAGTTCAGGGTCAAAATAGAATTTTT
* * ** * * *
40526475 GGACATTCGGGGGTAAGATGGTAATTTTCAAAAGTTTTGGGGTTAAAAATGGA
64 AGACATCCAAGGGTAAAATGGTAATTTTCAAAAGTTTTGAGGTCAAAAATGGA
* * * *
40526528 ATTTTTGGACA-TCTAAGGGTAAAATGGTAATTTTTGGAGGGTTCAGGGTCAAAATGGAATTTTT
1 AATTTTGGACATTC-AAGGGTAAAAAGGTAATTTTTGGA-AGTTCAGGGTCAAAATAGAATTTTT
*** *
40526592 AGACATCCAAGGGTAAAAATGGTAATTTTTGGAATTTTTGAGGTCAAAAAT-GA
64 AGACATCCAAGGGT-AAAATGGTAATTTTCAAAAGTTTTGAGGTCAAAAATGGA
* ** * * *
40526645 AATTTTGGATATTCGGGGGTAGAACGGTAATTTTTGGAAGTTCAGGGT-AAAACTATAATTTTT
1 AATTTTGGACATTCAAGGGTAAAAAGGTAATTTTTGGAAGTTCAGGGTCAAAA-TAGAATTTTT
40526708 TGGAAAGTTT
Statistics
Matches: 147, Mismatches: 28, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
115 4 0.03
116 20 0.14
117 83 0.56
118 40 0.27
ACGTcount: A:0.34, C:0.07, G:0.25, T:0.35
Consensus pattern (116 bp):
AATTTTGGACATTCAAGGGTAAAAAGGTAATTTTTGGAAGTTCAGGGTCAAAATAGAATTTTTAG
ACATCCAAGGGTAAAATGGTAATTTTCAAAAGTTTTGAGGTCAAAAATGGA
Found at i:40526738 original size:30 final size:28
Alignment explanation
Indices: 40526426--40526856 Score: 203
Period size: 29 Copynumber: 14.8 Consensus size: 28
40526416 AGACACTTCG
* *
40526426 AGGGTAAAAAGGTAATTTTTGGAAATTTC
1 AGGGTAAAAATGTAATTTTTGG-AAGTTC
* *
40526455 AAGGTCAAAATAG-AATTTTTGGACA-TTC
1 AGGGTAAAAAT-GTAATTTTTGGA-AGTTC
* * *** *
40526483 GGGGGT-AAGATGGTAATTTTCAAAAGTTTT
1 -AGGGTAAAAAT-GTAATTTTTGGAAG-TTC
* * *
40526513 GGGGTTAAAAATGGAATTTTTGGACA-TCTA
1 AGGG-TAAAAATGTAATTTTTGGA-AGT-TC
*
40526543 AGGGT-AAAATGGTAATTTTTGGAGGGTTC
1 AGGGTAAAAAT-GTAATTTTTGGA-AGTTC
* * * *
40526572 AGGGTCAAAATGGAATTTTTAGACA-TCC
1 AGGGTAAAAATGTAATTTTTGGA-AGTTC
* *
40526600 AAGGGTAAAAATGGTAATTTTTGGAATTTT
1 -AGGGTAAAAAT-GTAATTTTTGGAAGTTC
* *
40526630 TGAGGTCAAAAATG-AAATTTTGGATA-TTC
1 AG-GGT-AAAAATGTAATTTTTGGA-AGTTC
* * **
40526659 GGGGGTAGAACGGTAATTTTTGGAAGTTC
1 -AGGGTAAAAATGTAATTTTTGGAAGTTC
* * *
40526688 AGGGTAAAACTATAATTTTTTGGAAAGTTT
1 AGGGTAAAAATGTAA-TTTTTGG-AAGTTC
* *
40526718 ATGGTCAAAAATGTAATTTTTGGAGGTTC
1 AGGGT-AAAAATGTAATTTTTGGAAGTTC
* * *
40526747 AGGGGTAAAAATATAATTTTTAGAAAATTC
1 A-GGGTAAAAATGTAATTTTT-GGAAGTTC
* * *
40526777 AAGGTCAAAAATGTAATTTTTGAAAGTTT
1 AGGGT-AAAAATGTAATTTTTGGAAGTTC
*
40526806 AGGGTAAAAATGTAATTTTTGTGAAGTTT
1 AGGGTAAAAATGTAATTTTTG-GAAGTTC
* * *
40526835 AGAAGTCAAAATGCAATTTTTG
1 AG-GGTAAAAATGTAATTTTTG
40526857 AAAACTTCGA
Statistics
Matches: 308, Mismatches: 64, Indels: 59
0.71 0.15 0.14
Matches are distributed among these distances:
28 49 0.16
29 146 0.47
30 94 0.31
31 19 0.06
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.35
Consensus pattern (28 bp):
AGGGTAAAAATGTAATTTTTGGAAGTTC
Found at i:40526741 original size:59 final size:59
Alignment explanation
Indices: 40526671--40526825 Score: 213
Period size: 59 Copynumber: 2.6 Consensus size: 59
40526661 GGGTAGAACG
* * * * *
40526671 GTAATTTTTGGAAGTTCAGGGTAAAACTATAATTTTTTGGAAAGTTTATGGTCAAAAAT
1 GTAATTTTTGGAAGTTCAGGGTAAAAATATAATTTTTTAGAAAATTCAAGGTCAAAAAT
*
40526730 GTAATTTTTGGAGGTTCAGGGGTAAAAATATAA-TTTTTAGAAAATTCAAGGTCAAAAAT
1 GTAATTTTTGGAAGTTCA-GGGTAAAAATATAATTTTTTAGAAAATTCAAGGTCAAAAAT
* * *
40526789 GTAATTTTTGAAAGTTTAGGGTAAAAATGTAATTTTT
1 GTAATTTTTGGAAGTTCAGGGTAAAAATATAATTTTT
40526826 GTGAAGTTTA
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
58 13 0.15
59 58 0.69
60 13 0.15
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (59 bp):
GTAATTTTTGGAAGTTCAGGGTAAAAATATAATTTTTTAGAAAATTCAAGGTCAAAAAT
Found at i:40526843 original size:59 final size:58
Alignment explanation
Indices: 40526671--40526859 Score: 190
Period size: 59 Copynumber: 3.2 Consensus size: 58
40526661 GGGTAGAACG
* *
40526671 GTAATTTTTGGAAGTTCAGGGTAAAACTATAATTTTT-TGGAAAGTTTATG-GTCAAAAAT
1 GTAATTTTTGAAAGTTCAGGGTAAAAATATAATTTTTGT-G-AAGTTTA-GAGTCAAAAAT
* * * * *
40526730 GTAATTTTTGGAGGTTCAGGGGTAAAAATATAATTTTTAG-AAAATTCA-AGGTCAAAAAT
1 GTAATTTTTGAAAGTTCA-GGGTAAAAATATAATTTTT-GTGAAGTTTAGA-GTCAAAAAT
* *
40526789 GTAATTTTTGAAAGTTTAGGGTAAAAATGTAATTTTTGTGAAGTTTAGAAGTC-AAAAT
1 GTAATTTTTGAAAGTTCAGGGTAAAAATATAATTTTTGTGAAGTTTAG-AGTCAAAAAT
*
40526847 GCAATTTTTGAAA
1 GTAATTTTTGAAA
40526860 ACTTCGAGGG
Statistics
Matches: 109, Mismatches: 13, Indels: 17
0.78 0.09 0.12
Matches are distributed among these distances:
57 1 0.01
58 40 0.37
59 49 0.45
60 19 0.17
ACGTcount: A:0.38, C:0.04, G:0.20, T:0.38
Consensus pattern (58 bp):
GTAATTTTTGAAAGTTCAGGGTAAAAATATAATTTTTGTGAAGTTTAGAGTCAAAAAT
Found at i:40526884 original size:118 final size:118
Alignment explanation
Indices: 40526671--40526888 Score: 257
Period size: 118 Copynumber: 1.8 Consensus size: 118
40526661 GGGTAGAACG
* * *
40526671 GTAATTTTTGGAAGTTCAGGGTAAAACTATAATTTTTTGGAAAGTTTATGGTCAAAAATGTAATT
1 GTAATTTTTGAAAGTTCAGGGTAAAAATATAATTTTTTGGAAAGTTTATGGTCAAAAATGCAATT
* **
40526736 TTTGGAGGTTCAGGGGTAAAAATATAATTTTTAGAAAATTCAAGGTCAAAAAT
66 TTTGAAACTTCAGGGGTAAAAATATAATTTTTAGAAAATTCAAGGTCAAAAAT
* *
40526789 GTAATTTTTGAAAGTTTAGGGTAAAAATGTAA-TTTTTGTG-AAGTTTA-GAAGTC-AAAATGCA
1 GTAATTTTTGAAAGTTCAGGGTAAAAATATAATTTTTTG-GAAAGTTTATG--GTCAAAAATGCA
* * *
40526850 ATTTTTGAAAACTTC-GAGGGTCAGAATATGATTTTTAGA
63 ATTTTTG-AAACTTCAG-GGGTAAAAATATAATTTTTAGA
40526889 CAGTTCAGGG
Statistics
Matches: 84, Mismatches: 11, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
116 1 0.01
117 28 0.33
118 55 0.65
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (118 bp):
GTAATTTTTGAAAGTTCAGGGTAAAAATATAATTTTTTGGAAAGTTTATGGTCAAAAATGCAATT
TTTGAAACTTCAGGGGTAAAAATATAATTTTTAGAAAATTCAAGGTCAAAAAT
Found at i:40528672 original size:11 final size:10
Alignment explanation
Indices: 40528648--40528686 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
40528638 TGGACTTTTT
40528648 AATTTAAATA
1 AATTTAAATA
40528658 AATTTAAACTA
1 AATTTAAA-TA
40528669 AATTTATAAT-
1 AATTTA-AATA
40528679 AATTTAAA
1 AATTTAAA
40528687 CCTAAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 2 0.07
10 14 0.52
11 9 0.33
12 2 0.07
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (10 bp):
AATTTAAATA
Found at i:40528672 original size:21 final size:22
Alignment explanation
Indices: 40528648--40528692 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
40528638 TGGACTTTTT
40528648 AATTTA-AATAAATTTAAA-CTA
1 AATTTATAAT-AATTTAAACCTA
40528669 AATTTATAATAATTTAAACCTA
1 AATTTATAATAATTTAAACCTA
40528691 AA
1 AA
40528693 ATAAATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.38
Consensus pattern (22 bp):
AATTTATAATAATTTAAACCTA
Found at i:40529353 original size:208 final size:207
Alignment explanation
Indices: 40528996--40529373 Score: 528
Period size: 208 Copynumber: 1.8 Consensus size: 207
40528986 GTTTGGTGTT
** *
40528996 ATTGATTTGGTCTACTTCTCAGTATCTCATCAGAAGATGATTGCATCACTTGTTTTGATCCACTT
1 ATTGATTTGGTCTACTTCTCAGTATCTCATCAGAAGATGACCGCATCACTTGTTTTAATCCACTT
* * * * * * *
40529061 TTTTGTGTCTTATCAAGAAGACGGATCTGGTTAACTTCTCTGTATCTCATCAAGAAGGTAACCGC
66 CTTTGTATCTCATCAAGAAGACGAATCTGGTTAACTTCTCAGTATCTCATCAAGAAGCTAACCAC
*
40529126 TTTATTTATTCGACCTGCTTCTCAATATCTCATCAGGAAGTTAGGTTCGAAGATTTGCTCACTTT
131 TTTATTTATTCGACCTGCTTCTCAATATCTCATCAAGAAGTTAGGTTCGAAGATTTGCTCACTTT
40529191 GAGCCTGGCTTC
196 GAGCCTGGCTTC
* * *
40529203 ATTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATTAC-TGTTTTCAATCCGC
1 ATTGATTTGGTCTACTTCTCAGTATCTCATCA-GAAGATGACCGCATCACTTGTTTT-AATCCAC
* * *
40529267 TTCTTTGTATCTCATCAGGAAGACGAATTTGGTCT-GCTTCTCAGTATCTCATCAAGAAGCTAAC
64 TTCTTTGTATCTCATCAAGAAGACGAATCTGGT-TAACTTCTCAGTATCTCATCAAGAAGCTAAC
* *
40529331 CATTTTA-TTACTTCGACCTGCTTCTCAGTATCTCATCAAGAAG
128 CACTTTATTTA-TTCGACCTGCTTCTCAATATCTCATCAAGAAG
40529374 CTTATTCATC
Statistics
Matches: 148, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
207 40 0.27
208 107 0.72
209 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (207 bp):
ATTGATTTGGTCTACTTCTCAGTATCTCATCAGAAGATGACCGCATCACTTGTTTTAATCCACTT
CTTTGTATCTCATCAAGAAGACGAATCTGGTTAACTTCTCAGTATCTCATCAAGAAGCTAACCAC
TTTATTTATTCGACCTGCTTCTCAATATCTCATCAAGAAGTTAGGTTCGAAGATTTGCTCACTTT
GAGCCTGGCTTC
Found at i:40537639 original size:59 final size:57
Alignment explanation
Indices: 40537568--40537846 Score: 215
Period size: 59 Copynumber: 4.7 Consensus size: 57
40537558 ACCCAGGGGT
* * *
40537568 AAAATGGTAATTTTATATAGTTCGAGGGTAAAAAGGTAATTTTTGGAAATTTTGAGGTTA
1 AAAATGG-AATTTT-TATA-TTCGAGGGTAAAATGGTAATTTTTGGAAATTTTGGGGTCA
* * * * * *
40537628 AAAATGGAATTTTTGGACATCCGGGGGTAAGATGGTAATTTTTAGAAGTTTTGGGGTCA
1 AAAATGGAATTTTT--ATATTCGAGGGTAAAATGGTAATTTTTGGAAATTTTGGGGTCA
* * * * * * *
40537687 AAAATGAAAGTTTTGGACATT-TAGGGGTAAAATAGTAATTTTTGGAGGA-TTAGGGGTCA
1 AAAATGGAA-TTTT-TATATTCGA-GGGTAAAATGGTAATTTTTGGA-AATTTTGGGGTCA
* * *
40537746 AAAATAGAATTTTTAGATATCCGAGGGTAAAATGGTAATTTTTGGAATTTTTGGGGT-A
1 AAAATGGAATTTTT--ATATTCGAGGGTAAAATGGTAATTTTTGGAAATTTTGGGGTCA
* *
40537804 AAAATGAAATTTTTGGATATTTCGA-GATAAAATGGTAATTTTT
1 AAAATGGAATTTTT--ATA-TTCGAGGGTAAAATGGTAATTTTT
40537847 AGATGTTTAG
Statistics
Matches: 173, Mismatches: 35, Indels: 24
0.75 0.15 0.10
Matches are distributed among these distances:
58 39 0.23
59 120 0.69
60 14 0.08
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.37
Consensus pattern (57 bp):
AAAATGGAATTTTTATATTCGAGGGTAAAATGGTAATTTTTGGAAATTTTGGGGTCA
Found at i:40537640 original size:88 final size:86
Alignment explanation
Indices: 40537548--40537822 Score: 227
Period size: 88 Copynumber: 3.1 Consensus size: 86
40537538 AAAAAACGTG
40537548 ATTTTTGGATACCCAGGGGTAAAATGGTAATTTTATATAGTTCGAGGGTAAAAAGGTAATTTTTG
1 ATTTTTGGATA-CCAGGGGTAAAATGGTAATTTTATATAGTTCGAGGGTAAAAAGGTAATTTTTG
* *
40537613 GAAATTTTGAGGTTAAAAATGGA
65 GAAATTTTG-GGGTAAAAATGAA
* * * * * * * *
40537636 ATTTTTGGACATCCGGGGGTAAGATGGTAATTTT-TAGAAGTTTTG-GGGTCAAAAATGAAAGTT
1 ATTTTTGGATA-CCAGGGGTAAAATGGTAATTTTATA-TAG-TTCGAGGGT-AAAAAGGTAATTT
* * *
40537699 TTGGACATTTAGGGGT-AAAATAGTA
62 TTGGAAATTTTGGGGTAAAAAT-GAA
* ** * * * *
40537724 ATTTTTGGAGGATTAGGGGTCAAAAATAG-AATTTTTAGATA-TCCGAGGGTAAAATGGTAATTT
1 ATTTTTGGA-TACCAGGGGT--AAAATGGTAA-TTTTATATAGTTCGAGGGTAAAAAGGTAATTT
*
40537787 TTGGAATTTTTGGGGTAAAAATGAA
62 TTGGAAATTTTGGGGTAAAAATGAA
40537812 ATTTTTGGATA
1 ATTTTTGGATA
40537823 TTTCGAGATA
Statistics
Matches: 144, Mismatches: 32, Indels: 23
0.72 0.16 0.12
Matches are distributed among these distances:
87 8 0.06
88 90 0.62
89 35 0.24
90 10 0.07
91 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (86 bp):
ATTTTTGGATACCAGGGGTAAAATGGTAATTTTATATAGTTCGAGGGTAAAAAGGTAATTTTTGG
AAATTTTGGGGTAAAAATGAA
Found at i:40537730 original size:29 final size:30
Alignment explanation
Indices: 40537593--40538023 Score: 162
Period size: 29 Copynumber: 14.7 Consensus size: 30
40537583 TATAGTTCGA
* *
40537593 GGGTAAAA-AGGTAATTTTTGGAAATTTTG
1 GGGTAAAATATGTAATTTTTGGAAATTTAG
* * * ***
40537622 AGGTTAAAA-ATGGAATTTTTGGACATCCGG
1 -GGGTAAAATATGTAATTTTTGGAAATTTAG
* * * * *
40537652 GGGTAAGAT-GGTAATTTTTAGAAGTTTTG
1 GGGTAAAATATGTAATTTTTGGAAATTTAG
* * *
40537681 GGGTCAAAA-ATGAAAGTTTTGGACATTTAG
1 GGGT-AAAATATGTAATTTTTGGAAATTTAG
*
40537711 GGGTAAAATA-GTAATTTTTGGAGGA-TTAG
1 GGGTAAAATATGTAATTTTTGGA-AATTTAG
* * **
40537740 GGGTCAAAA-ATAG-AATTTTTAGATA-TCCG
1 GGGT-AAAATAT-GTAATTTTTGGAAATTTAG
* * *
40537769 AGGGTAAAAT-GGTAATTTTTGGAATTTTTG
1 -GGGTAAAATATGTAATTTTTGGAAATTTAG
* * *
40537799 GGGTAAAA-ATGAAATTTTTGGATATTTCG
1 GGGTAAAATATGTAATTTTTGGAAATTTAG
* * * * **
40537828 AGATAAAAT-GGTAATTTTTAGATGTTTAG
1 GGGTAAAATATGTAATTTTTGGAAATTTAG
** *
40537857 GGG-GGAA-ATGTAATTTTTAGAAAAGTTTAG
1 GGGTAAAATATGTAATTTTT-GGAAA-TTTAG
* * *
40537887 GGTTAAAA-ATGTAATTTTTTGGAAAGTTCG
1 GGGTAAAATATGTAA-TTTTTGGAAATTTAG
* * ** * *
40537917 AGGTAAAAAATGTAA-TTTTGGAGGTTCAA
1 GGGTAAAATATGTAATTTTTGGAAATTTAG
* * * *
40537946 GGGTAAAAAATGTAATTTTTAGAAAGTTAA
1 GGGTAAAATATGTAATTTTTGGAAATTTAG
* * *
40537976 GGGTCAAA-ATGTAATTTTT-AAAAGTTTGG
1 GGGTAAAATATGTAATTTTTGGAAA-TTTAG
*
40538005 GGGTAAAA-ATATAATTTTT
1 GGGTAAAATATGTAATTTTT
40538024 ATGAAGTTTA
Statistics
Matches: 293, Mismatches: 86, Indels: 45
0.69 0.20 0.11
Matches are distributed among these distances:
28 15 0.05
29 159 0.54
30 95 0.32
31 19 0.06
32 5 0.02
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (30 bp):
GGGTAAAATATGTAATTTTTGGAAATTTAG
Found at i:40537756 original size:118 final size:117
Alignment explanation
Indices: 40537593--40537846 Score: 314
Period size: 118 Copynumber: 2.2 Consensus size: 117
40537583 TATAGTTCGA
* * * * *
40537593 GGGTAAAA-AGGTAATTTTTGGAAATTTTGAGGTTAAAAATGGAATTTTTGGACATCCGGGGGTA
1 GGGTAAAATA-GTAATTTTTGGAAATTTAGAGGTCAAAAATAGAATTTTTAGACATCCGAGGGTA
*
40537657 AGATGGTAATTTTTAGAAGTTTTGGGGTCAAAAATGAAAGTTTTGGACATTTAG
65 AAATGGTAATTTTTAGAAGTTTTGGGGT-AAAAATGAAAGTTTTGGACATTTAG
* * *
40537711 GGGTAAAATAGTAATTTTTGGAGGA-TTAGGGGTCAAAAATAGAATTTTTAGATATCCGAGGGTA
1 GGGTAAAATAGTAATTTTTGGA-AATTTAGAGGTCAAAAATAGAATTTTTAGACATCCGAGGGTA
* * * * *
40537775 AAATGGTAATTTTTGGAATTTTTGGGGTAAAAATGAAATTTTTGGATATTTCG
65 AAATGGTAATTTTTAGAAGTTTTGGGGTAAAAATGAAAGTTTTGGACATTTAG
* * *
40537828 AGATAAAATGGTAATTTTT
1 GGGTAAAATAGTAATTTTT
40537847 AGATGTTTAG
Statistics
Matches: 117, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
117 38 0.32
118 77 0.66
119 2 0.02
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (117 bp):
GGGTAAAATAGTAATTTTTGGAAATTTAGAGGTCAAAAATAGAATTTTTAGACATCCGAGGGTAA
AATGGTAATTTTTAGAAGTTTTGGGGTAAAAATGAAAGTTTTGGACATTTAG
Found at i:40537924 original size:89 final size:88
Alignment explanation
Indices: 40537799--40537994 Score: 211
Period size: 89 Copynumber: 2.2 Consensus size: 88
40537789 GGAATTTTTG
* * * * * *
40537799 GGGTAAAAATG-AAATTTTTGGATATTTCGAGAT-AAAATGGTAATTTTTAGATGTT-TAGGG-G
1 GGGTAAAAATGTAATTTTTTGGAAAGTTCGAGATAAAAAT-GTAA-TTTTAGAGGTTCAAGGGTA
** *
40537860 GGAAATGTAATTTTTAGAAAAGTTTA
64 AAAAATGTAATTTTTAG-AAAGTTAA
* *
40537886 GGGTTAAAAATGTAATTTTTTGGAAAGTTCGAGGTAAAAAATGTAATTTTGGAGGTTCAAGGGTA
1 GGG-TAAAAATGTAATTTTTTGGAAAGTTCGAGAT-AAAAATGTAATTTTAGAGGTTCAAGGGTA
40537951 AAAAATGTAATTTTTAGAAAGTTAA
64 AAAAATGTAATTTTTAGAAAGTTAA
*
40537976 GGGTCAAAATGTAATTTTT
1 GGGTAAAAATGTAATTTTT
40537995 AAAAGTTTGG
Statistics
Matches: 91, Mismatches: 12, Indels: 10
0.81 0.11 0.09
Matches are distributed among these distances:
87 3 0.03
88 8 0.09
89 42 0.46
90 18 0.20
91 20 0.22
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (88 bp):
GGGTAAAAATGTAATTTTTTGGAAAGTTCGAGATAAAAATGTAATTTTAGAGGTTCAAGGGTAAA
AAATGTAATTTTTAGAAAGTTAA
Found at i:40538009 original size:59 final size:57
Alignment explanation
Indices: 40537862--40538053 Score: 158
Period size: 59 Copynumber: 3.2 Consensus size: 57
40537852 TTTAGGGGGG
* * *
40537862 AAATGTAATTTTTAGAAAAGTTTAGGGTTAAAAATGTAATTTTTTGGAAAGTT-CGAGGTAAA
1 AAATGTAATTTTT--AAAAGTTTAGGG-TAAAAATGTAA-TTTTTAGAAAGTTAAG-GGT-CA
** * *
40537924 AAATGTAA-TTTTGGAGGTTCAAGGGTAAAAAATGTAATTTTTAGAAAGTTAAGGGTCA
1 AAATGTAATTTTTAAAAGTT-TAGGGT-AAAAATGTAATTTTTAGAAAGTTAAGGGTCA
* * *
40537982 AAATGTAATTTTTAAAAGTTTGGGGGTAAAAATATAATTTTTATG-AAGTTTAAGAGTCA
1 AAATGTAATTTTTAAAAGTTT-AGGGTAAAAATGTAATTTTTA-GAAAG-TTAAGGGTCA
40538041 AAAT-TCAATTTTT
1 AAATGT-AATTTTT
40538054 GGAAACTCTA
Statistics
Matches: 108, Mismatches: 14, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
58 28 0.26
59 53 0.49
60 15 0.14
61 4 0.04
62 8 0.07
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.38
Consensus pattern (57 bp):
AAATGTAATTTTTAAAAGTTTAGGGTAAAAATGTAATTTTTAGAAAGTTAAGGGTCA
Found at i:40538024 original size:29 final size:29
Alignment explanation
Indices: 40537862--40538058 Score: 145
Period size: 29 Copynumber: 6.6 Consensus size: 29
40537852 TTTAGGGGGG
*
40537862 AAATGTAATTTTTAGAAAAGTTTAGGGTTAA
1 AAATGTAATTTTTAG-AAAGTTAAGGG-TAA
* *
40537893 AAATGTAATTTTTTGGAAAGTT-CGAGGTAAA
1 AAATGTAA-TTTTTAGAAAGTTAAG-GGT-AA
* *
40537924 AAATGTAA-TTTT-GGAGGTTCAAGGGTAAA
1 AAATGTAATTTTTAGAAAGTT-AAGGGT-AA
*
40537953 AAATGTAATTTTTAGAAAGTTAAGGGTCA
1 AAATGTAATTTTTAGAAAGTTAAGGGTAA
**
40537982 AAATGTAATTTTTA-AAAGTTTGGGGGTAA
1 AAATGTAATTTTTAGAAAG-TTAAGGGTAA
* * *
40538011 AAATATAATTTTTATG-AAGTTTAAGAGTCA
1 AAATGTAATTTTTA-GAAAG-TTAAGGGTAA
*
40538041 AAAT-TCAATTTTTGGAAA
1 AAATGT-AATTTTTAGAAA
40538059 CTCTAGGGAG
Statistics
Matches: 137, Mismatches: 17, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
28 9 0.07
29 55 0.40
30 36 0.26
31 31 0.23
32 6 0.04
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.37
Consensus pattern (29 bp):
AAATGTAATTTTTAGAAAGTTAAGGGTAA
Found at i:40539175 original size:20 final size:20
Alignment explanation
Indices: 40539145--40539215 Score: 63
Period size: 20 Copynumber: 3.4 Consensus size: 20
40539135 TATTATTTAA
40539145 TATTAAAATTATATATATTAT
1 TATT-AAATTATATATATTAT
* *
40539166 TATTAAATTAGATTTATTAT
1 TATTAAATTATATATATTAT
* *
40539186 TACT-AATAATATTAGTATTATT
1 TATTAAATTATA-TA-TATTA-T
40539208 TATTAAAT
1 TATTAAAT
40539216 ACGTTTTGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
19 5 0.13
20 18 0.46
21 9 0.23
22 4 0.10
23 3 0.08
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (20 bp):
TATTAAATTATATATATTAT
Found at i:40539892 original size:11 final size:10
Alignment explanation
Indices: 40539857--40539931 Score: 62
Period size: 11 Copynumber: 6.8 Consensus size: 10
40539847 GGACTTTTTT
40539857 ATTTAAATAA
1 ATTTAAATAA
40539867 ATTTAAACTTAA
1 ATTTAAA--TAA
40539879 ATTTATAATAA
1 ATTTA-AATAA
40539890 ATTTAAACCTAA
1 ATTTAAA--TAA
*
40539902 A-ATAAATTTAA
1 ATTTAAA--TAA
40539913 ATTTAAAATAA
1 ATTT-AAATAA
40539924 ATTTAAAT
1 ATTTAAAT
40539932 TTTATTGGAC
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
10 13 0.24
11 23 0.43
12 13 0.24
13 5 0.09
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (10 bp):
ATTTAAATAA
Found at i:40539892 original size:23 final size:22
Alignment explanation
Indices: 40539857--40539931 Score: 82
Period size: 23 Copynumber: 3.4 Consensus size: 22
40539847 GGACTTTTTT
*
40539857 ATTTAAATAAATTTAAACTTAA
1 ATTTAAATAAATTTAAACCTAA
40539879 ATTTATAATAAATTTAAACCTAA
1 ATTTA-AATAAATTTAAACCTAA
* *
40539902 A-ATAAATTTAAATTTAAA-ATAA
1 ATTTAAA--TAAATTTAAACCTAA
40539924 ATTTAAAT
1 ATTTAAAT
40539932 TTTATTGGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
21 3 0.07
22 11 0.24
23 31 0.69
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
ATTTAAATAAATTTAAACCTAA
Found at i:40539895 original size:17 final size:17
Alignment explanation
Indices: 40539870--40539933 Score: 92
Period size: 17 Copynumber: 3.8 Consensus size: 17
40539860 TAAATAAATT
* *
40539870 TAAACTTAAATTTATAA
1 TAAATTTAAATTTAAAA
**
40539887 TAAATTTAAACCTAAAA
1 TAAATTTAAATTTAAAA
40539904 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
40539921 TAAATTTAAATTT
1 TAAATTTAAATTT
40539934 TATTGGACCC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:40539935 original size:7 final size:6
Alignment explanation
Indices: 40539864--40539933 Score: 58
Period size: 6 Copynumber: 12.2 Consensus size: 6
40539854 TTTATTTAAA
* ** *
40539864 TAAATT TAAACT TAAATT TATAA-- TAAATT TAAACC TAAA-A TAAATT
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT TAAATT
*
40539910 TAAATT TAAA-A TAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT T
40539934 TATTGGACCC
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
4 2 0.04
5 10 0.20
6 37 0.73
7 2 0.04
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (6 bp):
TAAATT
Found at i:40545123 original size:37 final size:36
Alignment explanation
Indices: 40545063--40545192 Score: 161
Period size: 37 Copynumber: 3.6 Consensus size: 36
40545053 ACAAAACCTG
* *
40545063 CTAGGCACATAGCTTGAATACACCAGCACGAAGCTTA
1 CTAGGCACATAGCCTGAATACACC-GCACAAAGCTTA
*
40545100 CTAGGCACATAGCCTGAAGACACCGGCACAAAGCTTA
1 CTAGGCACATAGCCTGAATACACC-GCACAAAGCTTA
* * * * * *
40545137 TTAGGCACATAGCTTGAATACACCGCATAAAACCTG
1 CTAGGCACATAGCCTGAATACACCGCACAAAGCTTA
40545173 CTAGGCACATAGCCTGAATA
1 CTAGGCACATAGCCTGAATA
40545193 TTTAGATGAA
Statistics
Matches: 80, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
36 26 0.32
37 54 0.68
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.18
Consensus pattern (36 bp):
CTAGGCACATAGCCTGAATACACCGCACAAAGCTTA
Found at i:40550678 original size:17 final size:18
Alignment explanation
Indices: 40550656--40550691 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
40550646 ATTAAAACAT
*
40550656 AATAAATTCA-ATTTGTA
1 AATAAATTAATATTTGTA
40550673 AATAAATTAATATTTGTA
1 AATAAATTAATATTTGTA
40550691 A
1 A
40550692 CGAGTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.42
Consensus pattern (18 bp):
AATAAATTAATATTTGTA
Found at i:40557932 original size:23 final size:23
Alignment explanation
Indices: 40557906--40557992 Score: 86
Period size: 23 Copynumber: 3.8 Consensus size: 23
40557896 TCGGGCTCGA
* *
40557906 TTCGTTTTGCGTTCACGAACATG
1 TTCGTTTTACGTTCGCGAACATG
* *
40557929 TTCGTTTAACGTTCGCAAACATG
1 TTCGTTTTACGTTCGCGAACATG
* * *
40557952 TTTGTTTATATGTTCGTGAACATG
1 TTCGTTT-TACGTTCGCGAACATG
*
40557976 TTCGTTTT-TGTTCGCGA
1 TTCGTTTTACGTTCGCGA
40557993 GTATTAATTA
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
22 8 0.15
23 26 0.50
24 18 0.35
ACGTcount: A:0.18, C:0.17, G:0.21, T:0.44
Consensus pattern (23 bp):
TTCGTTTTACGTTCGCGAACATG
Found at i:40557973 original size:24 final size:24
Alignment explanation
Indices: 40557916--40557992 Score: 88
Period size: 23 Copynumber: 3.3 Consensus size: 24
40557906 TTCGTTTTGC
* *
40557916 GTTCACGAACATGTTCGTTTA-AC
1 GTTCGCGAACATGTTCGTTTATAT
* *
40557939 GTTCGCAAACATGTTTGTTTATAT
1 GTTCGCGAACATGTTCGTTTATAT
*
40557963 GTTCGTGAACATGTTCGTTT-T-T
1 GTTCGCGAACATGTTCGTTTATAT
40557985 GTTCGCGA
1 GTTCGCGA
40557993 GTATTAATTA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
22 8 0.18
23 19 0.42
24 18 0.40
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.42
Consensus pattern (24 bp):
GTTCGCGAACATGTTCGTTTATAT
Found at i:40570600 original size:20 final size:20
Alignment explanation
Indices: 40570575--40570683 Score: 68
Period size: 20 Copynumber: 5.5 Consensus size: 20
40570565 ATTCAACAGG
40570575 TATCGATACCGTTTT-AAAAT
1 TATCGATA-CGTTTTAAAAAT
*
40570595 TATCGATA-ATTTTCAAAAAT
1 TATCGATACGTTTT-AAAAAT
* *
40570615 TATTGATACCCG-TTT-AAAAG
1 TATCGATA--CGTTTTAAAAAT
*
40570635 TATCGATA-TTTTTCAAAAAT
1 TATCGATACGTTTT-AAAAAT
**
40570655 TATCGATAC-TTGGGAAAAAT
1 TATCGATACGTT-TTAAAAAT
40570675 TATCGATAC
1 TATCGATAC
40570684 CTTCTGGCCT
Statistics
Matches: 70, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
18 7 0.10
20 60 0.86
22 3 0.04
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.38
Consensus pattern (20 bp):
TATCGATACGTTTTAAAAAT
Found at i:40570610 original size:40 final size:40
Alignment explanation
Indices: 40570574--40570663 Score: 119
Period size: 40 Copynumber: 2.2 Consensus size: 40
40570564 AATTCAACAG
*
40570574 GTATCGATA-CCGTTTTAAAATTATCGATAATTTTCAAAAA
1 GTATCGATACCCG-TTTAAAAGTATCGATAATTTTCAAAAA
* * *
40570614 TTATTGATACCCGTTTAAAAGTATCGATATTTTTCAAAAA
1 GTATCGATACCCGTTTAAAAGTATCGATAATTTTCAAAAA
*
40570654 TTATCGATAC
1 GTATCGATAC
40570664 TTGGGAAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 41 0.93
41 3 0.07
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.39
Consensus pattern (40 bp):
GTATCGATACCCGTTTAAAAGTATCGATAATTTTCAAAAA
Found at i:40570679 original size:40 final size:40
Alignment explanation
Indices: 40570590--40570682 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 40
40570580 ATACCGTTTT
* ***
40570590 AAAATTATCGATAATTTTCAAAAATTATTGATACCCGTTT
1 AAAATTATCGATAATTTTCAAAAATTATCGATACCCGGGA
* * **
40570630 AAAAGTATCGATATTTTTCAAAAATTATCGATACTTGGGA
1 AAAATTATCGATAATTTTCAAAAATTATCGATACCCGGGA
40570670 AAAATTATCGATA
1 AAAATTATCGATA
40570683 CCTTCTGGCC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (40 bp):
AAAATTATCGATAATTTTCAAAAATTATCGATACCCGGGA
Found at i:40573157 original size:20 final size:21
Alignment explanation
Indices: 40573132--40573182 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
40573122 TAAAGGATTT
*
40573132 TATCGATACCCT-CTTAAAAG
1 TATCGATACCCTCCTTAAAAA
***
40573152 TATCGATAATTTCCTTAAAAA
1 TATCGATACCCTCCTTAAAAA
40573173 TATCGATACC
1 TATCGATACC
40573183 AAAATTCTGA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.37, C:0.22, G:0.08, T:0.33
Consensus pattern (21 bp):
TATCGATACCCTCCTTAAAAA
Found at i:40573329 original size:20 final size:20
Alignment explanation
Indices: 40573285--40573329 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
40573275 ATATCGATTC
* *
40573285 GGTATCGATACTTTTTGAAA
1 GGTATCGATAATTTCTGAAA
* *
40573305 AGTATCGATAATTTCTGTAA
1 GGTATCGATAATTTCTGAAA
40573325 GGTAT
1 GGTAT
40573330 TGATTATTTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (20 bp):
GGTATCGATAATTTCTGAAA
Found at i:40574205 original size:28 final size:28
Alignment explanation
Indices: 40574163--40574222 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
40574153 GTAAAAGATA
40574163 GTTTCTTGCTCTAAGATTATTGGGTTTT
1 GTTTCTTGCTCTAAGATTATTGGGTTTT
*
40574191 GTTTCTTGCTTTAAGATTATTGGGTTTT
1 GTTTCTTGCTCTAAGATTATTGGGTTTT
40574219 GTTT
1 GTTT
40574223 AATTATAGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.13, C:0.08, G:0.22, T:0.57
Consensus pattern (28 bp):
GTTTCTTGCTCTAAGATTATTGGGTTTT
Found at i:40576640 original size:21 final size:21
Alignment explanation
Indices: 40576590--40576638 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
40576580 ATCTAATTAC
40576590 AAATATTTAATAATTATATTT
1 AAATATTTAATAATTATATTT
40576611 AAATATTTAA-AA-TATAGTTT
1 AAATATTTAATAATTATA-TTT
*
40576631 ATATATTT
1 AAATATTT
40576639 TAATTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 4 0.15
20 12 0.46
21 10 0.38
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
AAATATTTAATAATTATATTT
Found at i:40577687 original size:10 final size:10
Alignment explanation
Indices: 40577672--40577696 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
40577662 TACAGAAATG
40577672 TAAAAAATTA
1 TAAAAAATTA
40577682 TAAAAAATTA
1 TAAAAAATTA
40577692 TAAAA
1 TAAAA
40577697 TTCTAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:40577716 original size:15 final size:15
Alignment explanation
Indices: 40577685--40577726 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
40577675 AAAATTATAA
40577685 AAAATTATAAAATTCT
1 AAAATTAT-AAATTCT
40577701 AAAATATATAAA-TCT
1 AAAAT-TATAAATTCT
40577716 AAAATTATAAA
1 AAAATTATAAA
40577727 AAGGTAGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.24
15 8 0.32
16 8 0.32
17 3 0.12
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (15 bp):
AAAATTATAAATTCT
Found at i:40577862 original size:22 final size:24
Alignment explanation
Indices: 40577817--40577874 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
40577807 TTATTTTGAC
* *
40577817 TTTTTAAAA-TTTATAATGATATA
1 TTTTTAAAATTTTATAATAAAATA
40577840 -TTTTAAAATTTTATAA-AAAATA
1 TTTTTAAAATTTTATAATAAAATA
*
40577862 TTTTTAAACTTTT
1 TTTTTAAAATTTT
40577875 TATTAACAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 12 0.40
23 18 0.60
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTTTAAAATTTTATAATAAAATA
Found at i:40582929 original size:18 final size:18
Alignment explanation
Indices: 40582908--40582954 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
40582898 TGAATTTTCG
*
40582908 AATTTAAATAACTCGAAA
1 AATTTAAATAACACGAAA
** *
40582926 AATTCGAATAACACGAAT
1 AATTTAAATAACACGAAA
40582944 AATTTAAATAA
1 AATTTAAATAA
40582955 ACTGAATATC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (18 bp):
AATTTAAATAACACGAAA
Found at i:40582961 original size:18 final size:18
Alignment explanation
Indices: 40582908--40582962 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
40582898 TGAATTTTCG
*
40582908 AATTTAAAT-AACTCGAAA
1 AATTTAAATAAACT-GAAT
**
40582926 AATTCGAATAACAC-GAAT
1 AATTTAAATAA-ACTGAAT
40582944 AATTTAAATAAACTGAAT
1 AATTTAAATAAACTGAAT
40582962 A
1 A
40582963 TCAAATTATA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
17 2 0.07
18 24 0.83
19 1 0.03
20 2 0.07
ACGTcount: A:0.55, C:0.11, G:0.07, T:0.27
Consensus pattern (18 bp):
AATTTAAATAAACTGAAT
Found at i:40591815 original size:30 final size:30
Alignment explanation
Indices: 40591779--40591844 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
40591769 ATTTATAAAA
*
40591779 ATAAAATTGTATTTTAATTC-TCTAAAAATT
1 ATAAAATTGTAATTTAA-TCATCTAAAAATT
* *
40591809 ATAAAATTTTAATTTAATCATTTAAAAATT
1 ATAAAATTGTAATTTAATCATCTAAAAATT
40591839 ATAAAA
1 ATAAAA
40591845 ATATAGACTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 2 0.06
30 30 0.94
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (30 bp):
ATAAAATTGTAATTTAATCATCTAAAAATT
Found at i:40594009 original size:53 final size:52
Alignment explanation
Indices: 40593920--40594019 Score: 141
Period size: 52 Copynumber: 1.9 Consensus size: 52
40593910 AAGGTTTTGG
*
40593920 AAGAAGTAAAAGTTTTTGGACAAACCAAAAGGAAAAAAAATTGGAGGTTCGA
1 AAGAAATAAAAGTTTTTGGACAAACCAAAAGGAAAAAAAATTGGAGGTTCGA
* **
40593972 AAGAAATAAAAG-TTTTGAGATAAAGTAAAAGGAAAAAAAATTGG-GGTT
1 AAGAAATAAAAGTTTTTG-GACAAACCAAAAGGAAAAAAAATTGGAGGTT
40594020 TAAGGAGAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
51 9 0.21
52 34 0.79
ACGTcount: A:0.52, C:0.04, G:0.23, T:0.21
Consensus pattern (52 bp):
AAGAAATAAAAGTTTTTGGACAAACCAAAAGGAAAAAAAATTGGAGGTTCGA
Found at i:40594363 original size:22 final size:22
Alignment explanation
Indices: 40594316--40594360 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
40594306 AAACAAAACT
**
40594316 AATAAATAATAATTTTAATATG
1 AATAAATAATAATAATAATATG
*
40594338 AATAAATAATAA-AATATTATG
1 AATAAATAATAATAATAATATG
40594359 AA
1 AA
40594361 ATATCTACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (22 bp):
AATAAATAATAATAATAATATG
Found at i:40614251 original size:20 final size:22
Alignment explanation
Indices: 40614221--40614262 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
40614211 AGAAATCATA
40614221 GTATATTGTTT-CAAGATTCTT
1 GTATATTGTTTGCAAGATTCTT
*
40614242 GTAT-TTGTTTGTAAGATTCTT
1 GTATATTGTTTGCAAGATTCTT
40614263 TCATCTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.21, C:0.07, G:0.17, T:0.55
Consensus pattern (22 bp):
GTATATTGTTTGCAAGATTCTT
Done.