Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 139 of 230
Found at i:40883243 original size:11 final size:11
Alignment explanation
Indices: 40883227--40883253 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
40883217 CAATTCAATA
40883227 TGTTTGACATG
1 TGTTTGACATG
40883238 TGTTTGACATG
1 TGTTTGACATG
40883249 TGTTT
1 TGTTT
40883254 AGGAGATCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.07, G:0.26, T:0.52
Consensus pattern (11 bp):
TGTTTGACATG
Found at i:40884558 original size:22 final size:23
Alignment explanation
Indices: 40884504--40884558 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 23
40884494 ATTTTTTTCA
40884504 TTTTCATTTTTGATTTTGATGACT
1 TTTTC-TTTTTGATTTTGATGACT
* *
40884528 TTTT-ATTTTGATTTTGATG-TT
1 TTTTCTTTTTGATTTTGATGACT
40884549 TTTTCTTTTT
1 TTTTCTTTTT
40884559 TTTTTCCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 5 0.19
22 18 0.67
24 4 0.15
ACGTcount: A:0.13, C:0.05, G:0.11, T:0.71
Consensus pattern (23 bp):
TTTTCTTTTTGATTTTGATGACT
Found at i:40888243 original size:24 final size:24
Alignment explanation
Indices: 40888205--40888504 Score: 142
Period size: 24 Copynumber: 12.8 Consensus size: 24
40888195 TGAATTAGAT
* *
40888205 AATTTACAATAAATAATATATAATA
1 AATTTAAAAT-AATAATATATGATA
* *
40888230 AATTTGAAATAATAATACAT-ATAA
1 AATTTAAAATAATAATATATGAT-A
* *
40888254 AATTT-AAA-AAT-TTTTATGAT-
1 AATTTAAAATAATAATATATGATA
* * * *
40888274 GATTCTATAATAATCATACATGATA
1 AATT-TAAAATAATAATATATGATA
** * * *
40888299 AATCCAAAATGATAGTATATAATA
1 AATTTAAAATAATAATATATGATA
*
40888323 AATTT-AAA-AATATTA-ATGATA
1 AATTTAAAATAATAATATATGATA
* * *
40888344 AATTTGAAATAA-ATATACAGGATA
1 AATTTAAAATAATA-ATATATGATA
** * *
40888368 AATTTAAAATAATGTTA-ACGATG
1 AATTTAAAATAATAATATATGATA
40888391 AATTTAAAATAATAATAT-TGATA
1 AATTTAAAATAATAATATATGATA
* *
40888414 AA-TTACAAATAATAAAACATGATA
1 AATTTA-AAATAATAATATATGATA
* **
40888438 AATCTAAAATAATAATATACAATA
1 AATTTAAAATAATAATATATGATA
* * * *
40888462 AACTT-AGATAATATTA-ATGATT
1 AATTTAAAATAATAATATATGATA
*
40888484 AATTTAATGATAATAAGTATA
1 AATTTAA-AATAATAA-TATA
40888505 AACATTCAAA
Statistics
Matches: 203, Mismatches: 52, Indels: 39
0.69 0.18 0.13
Matches are distributed among these distances:
20 3 0.01
21 14 0.07
22 26 0.13
23 59 0.29
24 86 0.42
25 14 0.07
26 1 0.00
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (24 bp):
AATTTAAAATAATAATATATGATA
Found at i:40888473 original size:70 final size:69
Alignment explanation
Indices: 40888282--40888487 Score: 182
Period size: 70 Copynumber: 3.0 Consensus size: 69
40888272 ATGATTCTAT
* * * * * * *
40888282 AATAATCATACATGATAAATCCAAAATGATAGTATATAATAAATTTAAAAATATTAATGATAAAT
1 AATAATAATACATGATAAATCTAAAATAATAATATACAATAAATTTAATAATAATAATGATAAAT
**
40888347 TTGA
66 TACA
* * ** * * *
40888351 AATAA-ATATACAGGATAAATTTAAAATAATGTTA-ACGATGAATTTAAAATAATAATATTGATA
1 AATAATA-ATACATGATAAATCTAAAATAATAATATACAATAAATTT--AATAATAATAATGATA
40888414 AATTACA
63 AATTACA
* * * *
40888421 AATAATAAAACATGATAAATCTAAAATAATAATATACAATAAACTTAGATAATATTAATGATTAA
1 AATAATAATACATGATAAATCTAAAATAATAATATACAATAAATTTA-ATAATAATAATGATAAA
40888486 TT
65 TT
40888488 TAATGATAAT
Statistics
Matches: 105, Mismatches: 26, Indels: 11
0.74 0.18 0.08
Matches are distributed among these distances:
68 8 0.08
69 27 0.26
70 61 0.58
71 9 0.09
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (69 bp):
AATAATAATACATGATAAATCTAAAATAATAATATACAATAAATTTAATAATAATAATGATAAAT
TACA
Found at i:40889294 original size:20 final size:20
Alignment explanation
Indices: 40889261--40889323 Score: 83
Period size: 19 Copynumber: 3.1 Consensus size: 20
40889251 TTTTTGATTT
40889261 TTTTTCTTCCCTTTACACTGA
1 TTTTT-TTCCCTTTACACTGA
*
40889282 TTTTTTTCTCTTTACACTGA
1 TTTTTTTCCCTTTACACTGA
* *
40889302 -CTTTTCCCCTTTACACTGA
1 TTTTTTTCCCTTTACACTGA
40889321 TTT
1 TTT
40889324 CCTCCCTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.44
20 15 0.42
21 5 0.14
ACGTcount: A:0.14, C:0.27, G:0.05, T:0.54
Consensus pattern (20 bp):
TTTTTTTCCCTTTACACTGA
Found at i:40889330 original size:19 final size:20
Alignment explanation
Indices: 40889263--40889332 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
40889253 TTTGATTTTT
* *
40889263 TTTCTTCCCTTTACACTGAT
1 TTTCCTCCCTTTACACTGAC
** *
40889283 TTTTTTCTCTTTACACTGAC
1 TTTCCTCCCTTTACACTGAC
*
40889303 TTTTC-CCCTTTACACTGA-
1 TTTCCTCCCTTTACACTGAC
40889321 TTTCCTCCCTTT
1 TTTCCTCCCTTT
40889333 TTATGAATAT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 4 0.09
19 18 0.42
20 21 0.49
ACGTcount: A:0.13, C:0.31, G:0.04, T:0.51
Consensus pattern (20 bp):
TTTCCTCCCTTTACACTGAC
Found at i:40898179 original size:9 final size:9
Alignment explanation
Indices: 40898165--40898210 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
40898155 TATAGTTTGA
40898165 TATTCGAAT
1 TATTCGAAT
40898174 TATTCGAAT
1 TATTCGAAT
*
40898183 TATTTGAAT
1 TATTCGAAT
*
40898192 TATTCGAGT
1 TATTCGAAT
40898201 TATTCGAAT
1 TATTCGAAT
40898210 T
1 T
40898211 CTAAAACTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (9 bp):
TATTCGAAT
Found at i:40898281 original size:9 final size:9
Alignment explanation
Indices: 40898264--40898294 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
40898254 TCGAGTTGAT
40898264 TCGAATAAC
1 TCGAATAAC
*
40898273 TCGATTAAC
1 TCGAATAAC
40898282 TCGAATAAC
1 TCGAATAAC
40898291 TCGA
1 TCGA
40898295 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:40911477 original size:6 final size:6
Alignment explanation
Indices: 40911466--40911497 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
40911456 GGTCGAAACC
40911466 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TT
1 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TT
40911498 ACATCGATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTCCT
Found at i:40915531 original size:16 final size:17
Alignment explanation
Indices: 40915498--40915532 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
40915488 ACATTGAAGG
40915498 GGCAAAATAATAATTTT
1 GGCAAAATAATAATTTT
*
40915515 GGCAAAAT-ATGATTTT
1 GGCAAAATAATAATTTT
40915531 GG
1 GG
40915533 GTTAAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.40, C:0.06, G:0.20, T:0.34
Consensus pattern (17 bp):
GGCAAAATAATAATTTT
Found at i:40915950 original size:25 final size:25
Alignment explanation
Indices: 40915914--40915991 Score: 84
Period size: 25 Copynumber: 3.1 Consensus size: 25
40915904 ACGTTCTGAC
*
40915914 CTACAGTGCGTGAGAGCATACCGAT
1 CTACAGTTCGTGAGAGCATACCGAT
* *
40915939 CTACAGTTCGTGTGAGCATACCAAT
1 CTACAGTTCGTGAGAGCATACCGAT
* * ** *
40915964 TTATAACTCATGAGAGCATACCGAT
1 CTACAGTTCGTGAGAGCATACCGAT
40915989 CTA
1 CTA
40915992 TAGCTCGAGT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (25 bp):
CTACAGTTCGTGAGAGCATACCGAT
Found at i:40916111 original size:25 final size:25
Alignment explanation
Indices: 40916077--40916189 Score: 111
Period size: 25 Copynumber: 4.5 Consensus size: 25
40916067 AGTTAGAGTG
*
40916077 CGTGAGAGCATACCGATCTACAGCT
1 CGTGTGAGCATACCGATCTACAGCT
** *
40916102 CGTGTGAGCATACTAATTTACAGCT
1 CGTGTGAGCATACCGATCTACAGCT
* * *
40916127 CGTGAGAGCATATCGATCTATAGCT
1 CGTGTGAGCATACCGATCTACAGCT
* * *
40916152 CGAGTGAGAAAACCGAT-TCACAGCT
1 CGTGTGAGCATACCGATCT-ACAGCT
*
40916177 CGTATGAGCATAC
1 CGTGTGAGCATAC
40916190 ATGTACAGGA
Statistics
Matches: 67, Mismatches: 20, Indels: 2
0.75 0.22 0.02
Matches are distributed among these distances:
24 1 0.01
25 66 0.99
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (25 bp):
CGTGTGAGCATACCGATCTACAGCT
Found at i:40916175 original size:50 final size:50
Alignment explanation
Indices: 40916077--40916189 Score: 138
Period size: 50 Copynumber: 2.3 Consensus size: 50
40916067 AGTTAGAGTG
* * * * *
40916077 CGTGAGAGCATACCGATCTACAGCTCGTGTGAGCATACTAATTTACAGCT
1 CGTGAGAGCATACCGATCTACAGCTCGAGTGAGAAAACCAATTCACAGCT
* * *
40916127 CGTGAGAGCATATCGATCTATAGCTCGAGTGAGAAAACCGATTCACAGCT
1 CGTGAGAGCATACCGATCTACAGCTCGAGTGAGAAAACCAATTCACAGCT
40916177 CGT-ATGAGCATAC
1 CGTGA-GAGCATAC
40916190 ATGTACAGGA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
49 1 0.02
50 52 0.98
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (50 bp):
CGTGAGAGCATACCGATCTACAGCTCGAGTGAGAAAACCAATTCACAGCT
Found at i:40916200 original size:155 final size:155
Alignment explanation
Indices: 40915918--40916227 Score: 566
Period size: 155 Copynumber: 2.0 Consensus size: 155
40915908 TCTGACCTAC
* *
40915918 AGTGCGTGAGAGCATACCGATCTACAGTTCGTGTGAGCATACCAATTTATAACTCATGAGAGCAT
1 AGTGCGTGAGAGCATACCGATCTACAGCTCGTGTGAGCATACCAATTTACAACTCATGAGAGCAT
40915983 ACCGATCTATAGCTCGAGTGAGAAAACCGATTCACAGCTCGTATGAGCATACATGTACAGGATTT
66 ACCGATCTATAGCTCGAGTGAGAAAACCGATTCACAGCTCGTATGAGCATACATGTACAGGATTT
40916048 GATAGATTACAGTTATATGAGTTAG
131 GATAGATTACAGTTATATGAGTTAG
* * *
40916073 AGTGCGTGAGAGCATACCGATCTACAGCTCGTGTGAGCATACTAATTTACAGCTCGTGAGAGCAT
1 AGTGCGTGAGAGCATACCGATCTACAGCTCGTGTGAGCATACCAATTTACAACTCATGAGAGCAT
*
40916138 ATCGATCTATAGCTCGAGTGAGAAAACCGATTCACAGCTCGTATGAGCATACATGTACAGGATTT
66 ACCGATCTATAGCTCGAGTGAGAAAACCGATTCACAGCTCGTATGAGCATACATGTACAGGATTT
40916203 GATAGATTACAGTTATATGAGTTAG
131 GATAGATTACAGTTATATGAGTTAG
40916228 CACACAATGT
Statistics
Matches: 149, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
155 149 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (155 bp):
AGTGCGTGAGAGCATACCGATCTACAGCTCGTGTGAGCATACCAATTTACAACTCATGAGAGCAT
ACCGATCTATAGCTCGAGTGAGAAAACCGATTCACAGCTCGTATGAGCATACATGTACAGGATTT
GATAGATTACAGTTATATGAGTTAG
Found at i:40919233 original size:6 final size:6
Alignment explanation
Indices: 40919222--40919249 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
40919212 AGGCCACTAT
40919222 GTGAAA GTGAAA GTGAAA GTGAAA GTGA
1 GTGAAA GTGAAA GTGAAA GTGAAA GTGA
40919250 CGGTCACATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.36, T:0.18
Consensus pattern (6 bp):
GTGAAA
Found at i:40919372 original size:51 final size:50
Alignment explanation
Indices: 40919253--40919437 Score: 178
Period size: 51 Copynumber: 3.7 Consensus size: 50
40919243 AAAGTGACGG
* * *** * *
40919253 TCACATGTGTAGTACTAAGTGTAGGCTACTACATGTACCAGA-A-TGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-AT-GA
*
40919303 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCT-TCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAG-TAT-GA
* * * * * *
40919354 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGATAGTGATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-ATGA
40919405 TCACATGTGTAGTACTATGTGCAGGCTACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
40919438 TGAACCGGTA
Statistics
Matches: 111, Mismatches: 19, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
50 36 0.32
51 73 0.66
52 1 0.01
53 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTATGA
Found at i:40919382 original size:101 final size:102
Alignment explanation
Indices: 40919253--40919437 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
40919243 AAAGTGACGG
*
40919253 TCACATGTGTAGTACTAAGTGTAGGCTACTACATGTACCAGA-A-TGATAGGTCGCATGTGTAGT
1 TCACATGTGTAGTACTAAGTGTAGGCTACTACATGTACCAGATAGTGAT-GGTCACATGTGTAGT
40919316 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
* * * * *
40919354 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGATAGTGATGGTCACATGTGTAGTA
1 TCACATGTGTAGTACTAAGTGTAGGCTACTACATGTACCAGATAGTGATGGTCACATGTGTAGTA
40919419 CTATGTGCAGGCTACTATG
66 CTATGTGCAGGCTACTATG
40919438 TGAACCGGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 37 0.49
102 35 0.46
103 4 0.05
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (102 bp):
TCACATGTGTAGTACTAAGTGTAGGCTACTACATGTACCAGATAGTGATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:40919445 original size:102 final size:101
Alignment explanation
Indices: 40919253--40919445 Score: 289
Period size: 102 Copynumber: 1.9 Consensus size: 101
40919243 AAAGTGACGG
*
40919253 TCACATGTGTAGTACTAAGTGTAGGCTACTACATGTACCAGAATGATAGGTCGCATGTGTAGTAC
1 TCACATGTGTAGTACTAAGTGTAGGCTACTACATGTACCAGAATGATAGGTCACATGTGTAGTAC
*
40919318 TATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
66 TATGTGCAGGCTACTATGCGAACCGGATAGCTTCGA
* * * * *
40919354 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATCGGATAGTGAT-GGTCACATGTGTAGT
1 TCACATGTGTAGTACTAAGTGTAGGCTACTACATGTACCAGA-A-TGATAGGTCACATGTGTAGT
*
40919418 ACTATGTGCAGGCTACTATGTGAACCGG
64 ACTATGTGCAGGCTACTATGCGAACCGG
40919446 TATCATTAAT
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
101 37 0.45
102 41 0.50
103 4 0.05
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (101 bp):
TCACATGTGTAGTACTAAGTGTAGGCTACTACATGTACCAGAATGATAGGTCACATGTGTAGTAC
TATGTGCAGGCTACTATGCGAACCGGATAGCTTCGA
Found at i:40919514 original size:46 final size:43
Alignment explanation
Indices: 40919441--40919539 Score: 110
Period size: 46 Copynumber: 2.2 Consensus size: 43
40919431 TACTATGTGA
*
40919441 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTG-ATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAAT-CC
* * *
40919484 ACCGGATATCATTGATTACAAAGGGTGGTTGTTGTGTGCTGAATCC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCTGAATCC
40919530 ACCGTGTATC
1 ACCG-GTATC
40919540 TGTTATTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
43 5 0.11
44 11 0.23
45 2 0.04
46 26 0.55
47 3 0.06
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTGAATCC
Found at i:40919684 original size:16 final size:16
Alignment explanation
Indices: 40919663--40919694 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40919653 TGATTGAAAG
*
40919663 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
40919679 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
40919695 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:40927451 original size:17 final size:17
Alignment explanation
Indices: 40927429--40927461 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40927419 TGGTTGTCGC
40927429 TAGAATTAAATTAATTA
1 TAGAATTAAATTAATTA
*
40927446 TAGAATTAATTTAATT
1 TAGAATTAAATTAATT
40927462 GGGTTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
TAGAATTAAATTAATTA
Found at i:40928651 original size:25 final size:24
Alignment explanation
Indices: 40928623--40928748 Score: 92
Period size: 25 Copynumber: 5.0 Consensus size: 24
40928613 GAGCTACGTT
*
40928623 CTGACTCACAGCTCGTGTGAGGATA
1 CTGA-TCACAGCTCGTGTGAGCATA
*
40928648 CTGATCTACAGCTCATGTGAGCATA
1 CTGATC-ACAGCTCGTGTGAGCATA
** * *
40928673 CCAATTTACAGCTCGTGAGAGCATA
1 CTGA-TCACAGCTCGTGTGAGCATA
* *
40928698 CCT-ATCTACAGCTCGAGTGGGCATA
1 -CTGATC-ACAGCTCGTGTGAGCATA
* **
40928723 TTGATTCACAGCTCGTACGAGCATA
1 CTGA-TCACAGCTCGTGTGAGCATA
40928748 C
1 C
40928749 ATGTACAGGA
Statistics
Matches: 77, Mismatches: 18, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
24 4 0.05
25 69 0.90
26 4 0.05
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.25
Consensus pattern (24 bp):
CTGATCACAGCTCGTGTGAGCATA
Found at i:40928722 original size:50 final size:51
Alignment explanation
Indices: 40928628--40928748 Score: 133
Period size: 50 Copynumber: 2.4 Consensus size: 51
40928618 ACGTTCTGAC
* *
40928628 TCACAGCTCGTGTGAGGATA-CTGATCTACAGCTCATGTGAGCATACCAAT
1 TCACAGCTCGTGAGAGCATACCTGATCTACAGCTCATGTGAGCATACCAAT
* * ***
40928678 TTACAGCTCGTGAGAGCATACCT-ATCTACAGCTCGA-GTGGGCATATTGAT
1 TCACAGCTCGTGAGAGCATACCTGATCTACAGCTC-ATGTGAGCATACCAAT
40928728 TCACAGCTCGT-ACGAGCATAC
1 TCACAGCTCGTGA-GAGCATAC
40928749 ATGTACAGGA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
49 1 0.02
50 56 0.93
51 3 0.05
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (51 bp):
TCACAGCTCGTGAGAGCATACCTGATCTACAGCTCATGTGAGCATACCAAT
Found at i:40931715 original size:50 final size:50
Alignment explanation
Indices: 40931655--40931802 Score: 161
Period size: 50 Copynumber: 3.0 Consensus size: 50
40931645 GTGATGTCGA
* * *
40931655 GGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTACACCGCCCG
1 GGAAGCAAGATTCGCTGTTGTAGCTTTAATCTGTTCCACTGCAACGCCCG
* * * ** * * *
40931705 GGAAGTAAGATTGGCTGTTGTAGCTTTAATCTTTTTAACTGCAATGTCGG
1 GGAAGCAAGATTCGCTGTTGTAGCTTTAATCTGTTCCACTGCAACGCCCG
* * * *
40931755 GGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCACTGCATCGCC
1 GGAAGCAAGATTCGCTGTTGTAGCTTTAATCTGTTCCACTGCAACGCC
40931803 TGGGGAGTAA
Statistics
Matches: 76, Mismatches: 22, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
50 76 1.00
ACGTcount: A:0.22, C:0.23, G:0.24, T:0.31
Consensus pattern (50 bp):
GGAAGCAAGATTCGCTGTTGTAGCTTTAATCTGTTCCACTGCAACGCCCG
Found at i:40931762 original size:100 final size:100
Alignment explanation
Indices: 40931628--40931814 Score: 266
Period size: 100 Copynumber: 1.9 Consensus size: 100
40931618 TAACTCGTAA
** * *
40931628 CTTTAATCTGTTTAACTGTGATGTCGAGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCA
1 CTTTAATCTGTTTAACTGCAATGTCGAGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCA
40931693 CTACACCGCCCGGGAAGTAAGATTGGCTGTTGTAG
66 CTACACCGCCCGGGAAGTAAGATTGGCTGTTGTAG
* * * *
40931728 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCCA
1 CTTTAATCTGTTTAACTGCAATGTCGAGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCA
* * * *
40931793 CTGCATCGCCTGGGGAGTAAGA
66 CTACACCGCCCGGGAAGTAAGA
40931815 ATTGCTATTC
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
100 75 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (100 bp):
CTTTAATCTGTTTAACTGCAATGTCGAGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCA
CTACACCGCCCGGGAAGTAAGATTGGCTGTTGTAG
Found at i:40931876 original size:44 final size:44
Alignment explanation
Indices: 40931804--40931949 Score: 159
Period size: 44 Copynumber: 3.2 Consensus size: 44
40931794 TGCATCGCCT
* * * *
40931804 GGGGAGTAAGAATTGCTATTCTCAGTCTGCCCCACTGGAACTTCAG
1 GGGGA-TAAGACTTG-TCTTCTCAGTCTGCCCCACTGCAACCTCAG
*
40931850 GGGGATAAGACTTGTCTTCTCAGTCTGCTCCACTGCAACCTCAG
1 GGGGATAAGACTTGTCTTCTCAGTCTGCCCCACTGCAACCTCAG
* * * * *
40931894 GGAGATAAGATTTATCATCTTC-GATCTACCCCACTGCAACCTCAG
1 GGGGATAAGACTTGTCTTC-TCAG-TCTGCCCCACTGCAACCTCAG
40931939 GGGGATAAGAC
1 GGGGATAAGAC
40931950 CTGCTATTTT
Statistics
Matches: 85, Mismatches: 13, Indels: 5
0.83 0.13 0.05
Matches are distributed among these distances:
44 42 0.49
45 38 0.45
46 5 0.06
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.25
Consensus pattern (44 bp):
GGGGATAAGACTTGTCTTCTCAGTCTGCCCCACTGCAACCTCAG
Found at i:40931973 original size:45 final size:44
Alignment explanation
Indices: 40931835--40931975 Score: 138
Period size: 45 Copynumber: 3.2 Consensus size: 44
40931825 TCAGTCTGCC
* * * * * *
40931835 CCACTGGAACTTCAGGGGGATAAGACTTGTCTTCTCAGTCTGCT
1 CCACTGCAACCTCAGGGGGATAAGACTTGTATTTTCAATCTACT
* * * * * *
40931879 CCACTGCAACCTCAGGGAGATAAGATTTATCATCTTCGATCTACC
1 CCACTGCAACCTCAGGGGGATAAGACTTGT-ATTTTCAATCTACT
* *
40931924 CCACTGCAACCTCAGGGGGATAAGACCTGCTATTTTCAACCTACT
1 CCACTGCAACCTCAGGGGGATAAGACTTG-TATTTTCAATCTACT
40931969 CCACTGC
1 CCACTGC
40931976 TGCTCAGGGA
Statistics
Matches: 75, Mismatches: 20, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
44 25 0.33
45 49 0.65
46 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (44 bp):
CCACTGCAACCTCAGGGGGATAAGACTTGTATTTTCAATCTACT
Found at i:40932077 original size:44 final size:44
Alignment explanation
Indices: 40932029--40932213 Score: 137
Period size: 44 Copynumber: 4.2 Consensus size: 44
40932019 TATCTTGGAA
*
40932029 AGATAAGATTTATCGTCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTATCGTCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * * *
40932073 AGATAAGATCTA-CAATCTTCAACCTACTCCGCTACTGCTCAGGG
1 AGATAAGATTTATC-GTCTTTAATCTGCTCCACTACTGCTTAGGG
* * * * * *
40932117 AGACAAGGTTTGGT-GGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTT-ATCGTCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* * *
40932161 AGATAAGATTTGTCGTCTTTGATCTGCTCCACTACTGTTTAGGG
1 AGATAAGATTTATCGTCTTTAATCTGCTCCACTACTGCTTAGGG
40932205 AGATAAGAT
1 AGATAAGAT
40932214 CTACAATCTT
Statistics
Matches: 104, Mismatches: 27, Indels: 20
0.69 0.18 0.13
Matches are distributed among these distances:
42 6 0.06
43 7 0.07
44 82 0.79
45 4 0.04
46 5 0.05
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (44 bp):
AGATAAGATTTATCGTCTTTAATCTGCTCCACTACTGCTTAGGG
Found at i:40932116 original size:132 final size:131
Alignment explanation
Indices: 40931958--40932357 Score: 665
Period size: 132 Copynumber: 3.0 Consensus size: 131
40931948 ACCTGCTATT
*
40931958 TTCAACCTACTCCACTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATC
1 TTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGG-TTGGTGGCTTAAATCTGCTTCCCACTATC
*
40932023 TTGGAAAGATAAGATTTATCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
65 TTGGAAAGATAAGATTTGTCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
40932088 TC
130 TC
*
40932090 TTCAACCTACTCCGCTACTGCTCAGGGAGACAAGGTTTGGTGGCTTAAATCTGCTTCCCACTATC
1 TTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGG-TTGGTGGCTTAAATCTGCTTCCCACTATC
*
40932155 TTGGAAAGATAAGATTTGTCGTCTTTGATCTGCTCCACTACTGTTTAGGGAGATAAGATCTACAA
65 TTGGAAAGATAAGATTTGTCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
40932220 TC
130 TC
*
40932222 TTCAACCTACTCCGCTGCTGCTTAGGGAGACAAGGTTCGGTGGCTTAAATCTGCTTCCCACTATC
1 TTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGTT-GGTGGCTTAAATCTGCTTCCCACTATC
* * * * * * *
40932287 TTGGAAAGATAAGATTTGCCGTCTTCGATATGCTCCACTACTACTTTGGGAGATAAGATCTGCTA
65 TTGGAAAGATAAGATTTGTCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAA
40932352 TC
130 TC
40932354 TTCA
1 TTCA
40932358 CTGATCTGTT
Statistics
Matches: 252, Mismatches: 15, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
131 2 0.01
132 250 0.99
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (131 bp):
TTCAACCTACTCCGCTGCTGCTCAGGGAGACAAGGTTGGTGGCTTAAATCTGCTTCCCACTATCT
TGGAAAGATAAGATTTGTCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAAT
C
Found at i:40958178 original size:20 final size:20
Alignment explanation
Indices: 40958153--40958191 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
40958143 TTCTTATTTG
40958153 GGGTTTTTGATGTATCTTCA
1 GGGTTTTTGATGTATCTTCA
40958173 GGGTTTTTGATGTATCTTC
1 GGGTTTTTGATGTATCTTC
40958192 TAGACGATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.13, C:0.10, G:0.26, T:0.51
Consensus pattern (20 bp):
GGGTTTTTGATGTATCTTCA
Found at i:40961511 original size:40 final size:40
Alignment explanation
Indices: 40961480--40961691 Score: 275
Period size: 40 Copynumber: 5.3 Consensus size: 40
40961470 GGACTAAGAT
40961480 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACTAAA-TCCGGGTTAAGCC
*
40961520 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGCC
* *
40961560 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGCC
* * * * *
40961600 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGCC
* * * * * *
40961640 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGCC
40961679 CCGAAGGCATTTG
1 CCGAAGGCATTTG
40961692 AACGAGGAGC
Statistics
Matches: 158, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 34 0.22
40 121 0.77
41 3 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGCC
Found at i:40961709 original size:79 final size:80
Alignment explanation
Indices: 40961428--40961724 Score: 212
Period size: 80 Copynumber: 3.7 Consensus size: 80
40961418 TGAATGCTGT
* ** * * * ** **
40961428 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCCAT
*
40961491 TGTGCGAGATAC-AAATT
64 TGTGCGAGATACTAAA-A
* * * * ** * *
40961508 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGCCCCGAAGGCCTTT
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCCATT
*
40961572 GTGCGAGATACTAAAT
65 GTGCGAGATACTAAAA
* ** * * *
40961588 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGG-CATTG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCCATTG
* *
40961652 TGTGAGTTACTAAAA
66 TGCGAGATACTAAAA
* * * *
40961667 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
40961725 TACGTGATTT
Statistics
Matches: 182, Mismatches: 29, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
78 15 0.08
79 49 0.27
80 107 0.59
81 11 0.06
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCCATTG
TGCGAGATACTAAAA
Found at i:40973912 original size:27 final size:27
Alignment explanation
Indices: 40973882--40974058 Score: 167
Period size: 27 Copynumber: 6.5 Consensus size: 27
40973872 AAATTGTACA
* *
40973882 GCACTAAGGGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGTG
* ** *
40973909 GCACTCAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGATTTGACTATG-TG
* * *
40973936 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGACTATGTG
* *
40973963 GCACTAAGTGTGCGAGTCTGACTATGTA
1 GCACTAAGTGTGCGA-TTTGACTATGTG
* *
40973991 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGATTTGACTATGTG
* * * *
40974018 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGATTTGACTATGTG
*
40974045 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
40974059 GGCTCAATAT
Statistics
Matches: 123, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGACTATGTG
Found at i:40973995 original size:82 final size:81
Alignment explanation
Indices: 40973882--40974037 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 81
40973872 AAATTGTACA
* * * *
40973882 GCACTAAGGGTGCGATTTGACTATGTTGCACTCAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGGGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
40973946 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
40973963 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGGGTGCGA-TCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
40974028 TGCGAGTTGA
65 TGCGAATTGA
40974038 TTATATAGCA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
81 15 0.23
82 49 0.77
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGGGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:40974049 original size:82 final size:81
Alignment explanation
Indices: 40973878--40974058 Score: 202
Period size: 82 Copynumber: 2.2 Consensus size: 81
40973868 GATTAAATTG
* * * * *
40973878 TACAGCACTAAGGGTGCGATTTGACTATGTTGCACTCAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
40973943 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
40973959 TGCGGCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGA-TCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
40974023 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
40974041 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
40974059 GGCTCAATAT
Statistics
Matches: 81, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
81 17 0.21
82 64 0.79
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:40980960 original size:40 final size:40
Alignment explanation
Indices: 40980916--40981262 Score: 624
Period size: 40 Copynumber: 8.7 Consensus size: 40
40980906 GCAAACACAT
* *
40980916 TTGCCTTCGGGTCTTAGCCCGAACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
40980956 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
40980996 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
40981036 TTGCCTTC-GGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
40981075 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
40981115 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
40981155 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
40981195 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
40981235 TTGCCTTCGGGTCATAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
40981263 TCCAATGCTC
Statistics
Matches: 299, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
39 38 0.13
40 261 0.87
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:40981170 original size:159 final size:160
Alignment explanation
Indices: 40980916--40981262 Score: 651
Period size: 159 Copynumber: 2.2 Consensus size: 160
40980906 GCAAACACAT
* *
40980916 TTGCCTTCGGGTCTTAGCCCGAACATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
40980981 TATCAACTCGCATAATTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAATTGCCTTC-G
66 TATCAACTCGCATAATTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAATTGCCTTCGG
40981045 GTCATAGCCCGGATATATCAACTCGCATAA
131 GTCATAGCCCGGATATATCAACTCGCATAA
40981075 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
40981140 TATCAACTCGCATAATTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAATTGCCTTCGG
66 TATCAACTCGCATAATTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAATTGCCTTCGG
*
40981205 GTCCTAGCCCGGATATATCAACTCGCATAA
131 GTCATAGCCCGGATATATCAACTCGCATAA
*
40981235 TTGCCTTCGGGTCATAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
40981263 TCCAATGCTC
Statistics
Matches: 183, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
159 126 0.69
160 57 0.31
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (160 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAATTGCCTTCGGGTCTTAGCCCGGATA
TATCAACTCGCATAATTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAATTGCCTTCGG
GTCATAGCCCGGATATATCAACTCGCATAA
Found at i:40989570 original size:40 final size:40
Alignment explanation
Indices: 40989526--40989872 Score: 633
Period size: 40 Copynumber: 8.7 Consensus size: 40
40989516 GCAAACACAT
* *
40989526 TTGCCTTCGGGTCTTAGCCCGAACATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
40989566 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
40989606 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
40989646 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
40989686 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
40989726 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
40989766 TTGCCTTCGGGTCCTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
40989806 TTGCCTTCGGGTC-TAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
40989845 TTGCCTTCGGGTCATAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
40989873 TCCAATGCTC
Statistics
Matches: 300, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
39 39 0.13
40 261 0.87
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:40994406 original size:27 final size:27
Alignment explanation
Indices: 40994376--40994552 Score: 167
Period size: 27 Copynumber: 6.5 Consensus size: 27
40994366 AAATTGTACA
* *
40994376 GCACTAAGGGTGCGATTTGACTATGTT
1 GCACTAAGTGTGCGATTTGACTATGTG
* ** *
40994403 GCACTCAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGATTTGACTATG-TG
* * *
40994430 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGATTTGACTATGTG
* *
40994457 GCACTAAGTGTGCGAGTCTGACTATGTA
1 GCACTAAGTGTGCGA-TTTGACTATGTG
* *
40994485 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGATTTGACTATGTG
* * * *
40994512 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGATTTGACTATGTG
*
40994539 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
40994553 GGCTCAATAT
Statistics
Matches: 123, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTGACTATGTG
Found at i:40994489 original size:82 final size:81
Alignment explanation
Indices: 40994376--40994531 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 81
40994366 AAATTGTACA
* * * *
40994376 GCACTAAGGGTGCGATTTGACTATGTTGCACTCAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGGGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
40994440 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
40994457 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGGGTGCGA-TCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
40994522 TGCGAGTTGA
65 TGCGAATTGA
40994532 TTATATAGCA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
81 15 0.23
82 49 0.77
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGGGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:40994543 original size:82 final size:81
Alignment explanation
Indices: 40994372--40994552 Score: 202
Period size: 82 Copynumber: 2.2 Consensus size: 81
40994362 GATTAAATTG
* * * * *
40994372 TACAGCACTAAGGGTGCGATTTGACTATGTTGCACTCAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
40994437 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
40994453 TGCGGCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGA-TCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
40994517 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
40994535 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
40994553 GGCTCAATAT
Statistics
Matches: 81, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
81 17 0.21
82 64 0.79
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATCTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:41000841 original size:17 final size:17
Alignment explanation
Indices: 41000801--41000844 Score: 58
Period size: 15 Copynumber: 2.7 Consensus size: 17
41000791 AAAACTGATA
41000801 ATAATTAA-TATACATT
1 ATAATTAATTATACATT
41000817 ATAA-TAATTATA-ATT
1 ATAATTAATTATACATT
41000832 ATATATTAATTAT
1 ATA-ATTAATTAT
41000845 TATCACCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 9 0.36
16 9 0.36
17 7 0.28
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
ATAATTAATTATACATT
Found at i:41001741 original size:25 final size:25
Alignment explanation
Indices: 41001712--41001764 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
41001702 GTAGGCCCAT
* *
41001712 AATGCATCGTCTAGTCTTTTGGACC
1 AATGCATCATCCAGTCTTTTGGACC
41001737 AATGCATCATCCAGTCTTTTGGACC
1 AATGCATCATCCAGTCTTTTGGACC
41001762 AAT
1 AAT
41001765 CTCGTCAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.34
Consensus pattern (25 bp):
AATGCATCATCCAGTCTTTTGGACC
Found at i:41005833 original size:16 final size:18
Alignment explanation
Indices: 41005795--41005836 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
41005785 TTCCAACACT
*
41005795 TTTTTTTGAAGTTTCATTG
1 TTTTTTTGAAG-TTCATTA
41005814 TTTTTTTGAA-TT-ATTA
1 TTTTTTTGAAGTTCATTA
41005830 TTTTTTT
1 TTTTTTT
41005837 TCAATACTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 10 0.45
17 2 0.09
19 10 0.45
ACGTcount: A:0.17, C:0.02, G:0.10, T:0.71
Consensus pattern (18 bp):
TTTTTTTGAAGTTCATTA
Found at i:41005836 original size:19 final size:19
Alignment explanation
Indices: 41005794--41005837 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
41005784 TTTCCAACAC
41005794 TTTTTTTTGAAGTTTCATT
1 TTTTTTTTGAAGTTTCATT
* *
41005813 GTTTTTTTGAA-TTATTATT
1 TTTTTTTTGAAGTT-TCATT
41005832 TTTTTT
1 TTTTTT
41005838 CAATACTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.16, C:0.02, G:0.09, T:0.73
Consensus pattern (19 bp):
TTTTTTTTGAAGTTTCATT
Found at i:41006445 original size:21 final size:22
Alignment explanation
Indices: 41006419--41006465 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
41006409 AATTCTCACC
*
41006419 AAATGAACAAAATTTCATT-CA
1 AAATGAACAAAAGTTCATTACA
*
41006440 AAATGATCAAAAGTTCATTACA
1 AAATGAACAAAAGTTCATTACA
41006462 AAAT
1 AAAT
41006466 CTGATTTCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.53, C:0.13, G:0.06, T:0.28
Consensus pattern (22 bp):
AAATGAACAAAAGTTCATTACA
Found at i:41009066 original size:22 final size:25
Alignment explanation
Indices: 41009020--41009066 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
41009010 TCATTTATTA
41009020 AAGCATACTTACGAAAGAAATAATTG
1 AAGCATACTTA-GAAAGAAATAATTG
41009046 AAGCATACTT-GAAA-AAA-AATT
1 AAGCATACTTAGAAAGAAATAATT
41009067 AAAAGTTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 4 0.19
23 3 0.14
24 4 0.19
26 10 0.48
ACGTcount: A:0.53, C:0.11, G:0.13, T:0.23
Consensus pattern (25 bp):
AAGCATACTTAGAAAGAAATAATTG
Found at i:41009352 original size:23 final size:24
Alignment explanation
Indices: 41009324--41009382 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
41009314 TTTATTCTTC
*
41009324 AAAAATTAAATCCTAATTA-CGAA
1 AAAAATTAAATCCTAAATACCGAA
*
41009347 AAAAA-TAAATTCCTAAATACCTAA
1 AAAAATTAAA-TCCTAAATACCGAA
41009371 AAATAATTAAAT
1 AAA-AATTAAAT
41009383 AAATAATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 4 0.13
23 13 0.43
24 6 0.20
25 3 0.10
26 4 0.13
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (24 bp):
AAAAATTAAATCCTAAATACCGAA
Found at i:41011517 original size:20 final size:21
Alignment explanation
Indices: 41011484--41011525 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
41011474 AAGTTTGTTG
41011484 AGCTCAATTGAGCTCATTTCC
1 AGCTCAATTGAGCTCATTTCC
41011505 AGCTCAA-TGAGCTCATTTCC
1 AGCTCAATTGAGCTCATTTCC
41011525 A
1 A
41011526 TCTTTCTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (21 bp):
AGCTCAATTGAGCTCATTTCC
Found at i:41011597 original size:13 final size:14
Alignment explanation
Indices: 41011574--41011602 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
41011564 AATAAATTAT
41011574 TTAATTTTAGTTAG
1 TTAATTTTAGTTAG
41011588 TTAA-TTTAGTTAG
1 TTAATTTTAGTTAG
41011601 TT
1 TT
41011603 CAGTTCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (14 bp):
TTAATTTTAGTTAG
Found at i:41012896 original size:18 final size:17
Alignment explanation
Indices: 41012874--41012908 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
41012864 AAAAGAAAAA
41012874 GAAAAAATTTTCAAGGT
1 GAAAAAATTTTCAAGGT
41012891 GAAAAAATTTTCAAGGT
1 GAAAAAATTTTCAAGGT
41012908 G
1 G
41012909 TAATTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.29
Consensus pattern (17 bp):
GAAAAAATTTTCAAGGT
Found at i:41013009 original size:20 final size:18
Alignment explanation
Indices: 41012966--41013019 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 18
41012956 AAAATTTGAA
41012966 AAAATTCAAAAAAAAATC
1 AAAATTCAAAAAAAAATC
*
41012984 AGAAATTCGAAAAAAAAGTTC
1 A-AAATTC-AAAAAAAA-ATC
41013005 AAAATT-ATAAAAAAA
1 AAAATTCA-AAAAAAA
41013020 GGAAATTTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
18 2 0.06
19 13 0.42
20 13 0.42
21 3 0.10
ACGTcount: A:0.69, C:0.07, G:0.06, T:0.19
Consensus pattern (18 bp):
AAAATTCAAAAAAAAATC
Found at i:41020687 original size:8 final size:8
Alignment explanation
Indices: 41020674--41020702 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
41020664 TTTTAAATGA
41020674 TATTTTAT
1 TATTTTAT
41020682 TATTTTAT
1 TATTTTAT
41020690 TATTTTAT
1 TATTTTAT
41020698 TATTT
1 TATTT
41020703 AAGTATATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:41023812 original size:21 final size:23
Alignment explanation
Indices: 41023767--41023813 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
41023757 TCACCTGCAA
* *
41023767 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
41023790 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
41023811 TAA
1 TAA
41023814 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:41029158 original size:15 final size:15
Alignment explanation
Indices: 41029138--41029192 Score: 85
Period size: 16 Copynumber: 3.7 Consensus size: 15
41029128 TAGCTTCTTC
41029138 TTTTTTTTCACGAAA
1 TTTTTTTTCACGAAA
*
41029153 TTTTTTTTTCACGAAT
1 -TTTTTTTTCACGAAA
41029169 TTTTTTTTCACG-AA
1 TTTTTTTTCACGAAA
41029183 TTTTTTTTCA
1 TTTTTTTTCA
41029193 ACTTGATATC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.30
15 12 0.32
16 14 0.38
ACGTcount: A:0.20, C:0.13, G:0.05, T:0.62
Consensus pattern (15 bp):
TTTTTTTTCACGAAA
Found at i:41029159 original size:16 final size:15
Alignment explanation
Indices: 41029138--41029190 Score: 97
Period size: 15 Copynumber: 3.5 Consensus size: 15
41029128 TAGCTTCTTC
41029138 TTTTTTTTCACGAAAT
1 TTTTTTTTCACG-AAT
41029154 TTTTTTTTCACGAAT
1 TTTTTTTTCACGAAT
41029169 TTTTTTTTCACGAAT
1 TTTTTTTTCACGAAT
41029184 TTTTTTT
1 TTTTTTT
41029191 CAACTTGATA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 25 0.68
16 12 0.32
ACGTcount: A:0.19, C:0.11, G:0.06, T:0.64
Consensus pattern (15 bp):
TTTTTTTTCACGAAT
Found at i:41029247 original size:11 final size:11
Alignment explanation
Indices: 41029231--41029264 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
41029221 TGGAAACCAA
41029231 ATTTTTTTTTG
1 ATTTTTTTTTG
41029242 ATTTTTTTTTG
1 ATTTTTTTTTG
**
41029253 AAATTTTTTTG
1 ATTTTTTTTTG
41029264 A
1 A
41029265 AGAAACTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (11 bp):
ATTTTTTTTTG
Found at i:41032630 original size:50 final size:50
Alignment explanation
Indices: 41032519--41032765 Score: 212
Period size: 50 Copynumber: 4.8 Consensus size: 50
41032509 ATTTGGGTAA
* * * *
41032519 AGAGATCCCATGTAAGACCATGTCTTGGACATGAAATTGGCATCATTGAGGTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGACATTGGCACCA---A-G--ATG
* *
41032575 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGACATTGGCACCAAGATG
** * * * *
41032625 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGACATTGGCACCAAGATG
** * * * *
41032675 AGAACTCCCATGTAAGACCATATCTGGGATATGACATTGGAAGTACAAGA--
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGACATTGGCA--CCAAGATG
** *
41032725 A-ACATCCCATGTAAGACCATGTCTGGGACATGACTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGACATTGGCA
41032766 TGTTATTATC
Statistics
Matches: 159, Mismatches: 30, Indels: 11
0.80 0.15 0.05
Matches are distributed among these distances:
49 34 0.21
50 81 0.51
52 4 0.03
53 1 0.01
56 39 0.25
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGACATTGGCACCAAGATG
Found at i:41035649 original size:40 final size:40
Alignment explanation
Indices: 41035605--41035829 Score: 260
Period size: 40 Copynumber: 5.7 Consensus size: 40
41035595 GCTCCTCGTT
* * *
41035605 CAAATGCCTTTGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
41035645 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
41035685 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
41035725 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* ** * * * *
41035764 CAAATACCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
41035805 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
41035830 CATCATTCAA
Statistics
Matches: 162, Mismatches: 18, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
38 2 0.01
39 31 0.19
40 116 0.72
41 13 0.08
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:41035789 original size:119 final size:120
Alignment explanation
Indices: 41035607--41035829 Score: 283
Period size: 119 Copynumber: 1.9 Consensus size: 120
41035597 TCCTCGTTCA
* * *
41035607 AATGCCTTTGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGGAT
* *
41035672 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
41035727 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATACCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATACCTTCGGGA-CTTAACCCGG
* * *
41035789 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
41035830 CATCATTCAA
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
118 4 0.05
119 65 0.74
120 19 0.22
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:41042917 original size:40 final size:40
Alignment explanation
Indices: 41042873--41043097 Score: 278
Period size: 40 Copynumber: 5.7 Consensus size: 40
41042863 GCTCCTCATT
* *
41042873 CAAATGCCTTCGGGACATAGCCC-GATTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
41042913 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
41042953 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
41042993 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
41043032 CAAATACCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
41043073 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41043098 CATCATTCAA
Statistics
Matches: 162, Mismatches: 18, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
38 2 0.01
39 31 0.19
40 114 0.70
41 15 0.09
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:41043057 original size:119 final size:120
Alignment explanation
Indices: 41042875--41043097 Score: 283
Period size: 119 Copynumber: 1.9 Consensus size: 120
41042865 TCCTCATTCA
* * *
41042875 AATGCCTTCGGGACATAGCCCGATTATAGTAACTTGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGGAT
* *
41042940 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
* * **
41042995 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATACCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCC-GAATATAGTAACTCGCACAAATACCTTCGGGA-CTTAACCCGG
* * *
41043057 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
41043098 CATCATTCAA
Statistics
Matches: 88, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
118 3 0.03
119 62 0.70
120 23 0.26
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACC
Found at i:41058359 original size:691 final size:691
Alignment explanation
Indices: 41057038--41058418 Score: 2420
Period size: 691 Copynumber: 2.0 Consensus size: 691
41057028 AAAGTATTTA
*
41057038 GTCTAAGATCAGCCGAATATACATTGAATTTAAGTTGCTCATGTCTTTTGTAGGTACAGCCGAAT
1 GTCTAAGATCAGCCGAATATACATTGAATTTAAGTTGCTCATGTCTTTTGTAGGTACAACCGAAT
* * *
41057103 GTGGAAAACACAATCAATGATGGTTCATGAACGGGCTGGTTCAATGTATGTGCGGGTGCATGAAT
66 ATGGAAAACACAATCAATGATGGTTCATGAACGGGCTAGTTCAATGTACGTGCGGGTGCATGAAT
* * * * *
41057168 GACTGCCTTCAACATATGAATGCATTAAGGATGGTGCATGAACGGTTCATTAGAATGGATGGAAG
131 GACTACCTTCAACATATGAATGCATTAAGGATGGTGCATAAACAGTCCATTAGAATGAATGGAAG
* * *
41057233 AGTGCATGAATACTCACCTACATGTATCGTTTGCTGGCTATTGATCTCCTATGTGTTTATTGGGC
196 AGTGCATGAATACTCACCTACATGCATCGTTTACTAGCTATTGATCTCCTATGTGTTTATTGGGC
41057298 CAAAAGGCATCTATTAGAGGGACCATTCACCCTTTGGCCGAACCTAGACATGGCCGATGGTCTCC
261 CAAAAGGCATCTATTAGAGGGACCATTCACCCTTTGGCCGAACCTAGACATGGCCGATGGTCTCC
** * * * * *
41057363 TATGCATTCACCAACTATGACATTCATTTCTTTAGGTTTGAAGTTGAACATTGCACCTTACATCT
326 TATGCATTCACCAACTACCACATTCATTTCCTTAGCTTTGAAGCTGAACATTGAACCTTACATCC
*
41057428 AGCCGAATCTAGACATAGCTAATAGGAAATACATTTCTAGATTAATCCATACAATTAAAGTCGAA
391 AGCCGAATCTAGACATAGCTAATAGGAAATACATTTCTAGATTAATCCATACAATTAAAGCCGAA
* *
41057493 TTACTTAGTCTTTAAGTTTGTTTATTCTGTCTATTCAACTATCATATAGAGGCTATAAATAGTTT
456 TTACTTAGTCTCTAAGTTTGTTTATTCTGTCCATTCAACTATCATATAGAGGCTATAAATAGTTT
41057558 GTTATTTCATGTTGTAAAGAACTTTTTGCCAAATTATTGAATGAACATATTGTTCTTGTGAGGTT
521 GTTATTTCATGTTGTAAAGAACTTTTTGCCAAATTATTGAATGAACATATTGTTCTTGTGAGGTT
*
41057623 TCCTTCCTCTCCATTTCGTTCGAGTCTCGAATTGACTTACCTAGTTCGCTAGCGGTGTCAACTTG
586 TCCTTCCTCTCCATTTCGTTCGAGTCTCGAATTGACTTACCTAGTTCGCTAGCGGTGTCAACTCG
41057688 AACTCTTGTTTCCTTCCATCTTTTATACCTTTGAATCTTTT
651 AACTCTTGTTTCCTTCCATCTTTTATACCTTTGAATCTTTT
41057729 GTCTAAGATCAGCCGAATATACATTGAATTTAAGTTGCTCATGTCTTTTGTAGGTACAACCGAAT
1 GTCTAAGATCAGCCGAATATACATTGAATTTAAGTTGCTCATGTCTTTTGTAGGTACAACCGAAT
41057794 ATGGAAAACACAATCAATGATGGTTCATGAACGGGCTAGTTCAATGTACGTGCGGGTGCATGAAT
66 ATGGAAAACACAATCAATGATGGTTCATGAACGGGCTAGTTCAATGTACGTGCGGGTGCATGAAT
* * * * *
41057859 TACTACGTTCTACGTATGAATTCATTAAGGATGGTGCATAAACAGTCCATTAGAATGAATGGAAG
131 GACTACCTTCAACATATGAATGCATTAAGGATGGTGCATAAACAGTCCATTAGAATGAATGGAAG
41057924 AGTGCATGAATACTCACCTACATGCATCGTTTACTAGCTATTGATCTCCTATGTGTTTATTGGGC
196 AGTGCATGAATACTCACCTACATGCATCGTTTACTAGCTATTGATCTCCTATGTGTTTATTGGGC
* * *
41057989 CAAGAGGCATCTATTAGAGGGACCATTTACCCTTTGGTCGAACCTAGACATGGCCGATGGTCTCC
261 CAAAAGGCATCTATTAGAGGGACCATTCACCCTTTGGCCGAACCTAGACATGGCCGATGGTCTCC
* * *
41058054 TATGCATTCACCAGCTGCCACATTCTTTTCCTTAGCTTTGAAGCTGAACATTGAACCTTACATCC
326 TATGCATTCACCAACTACCACATTCATTTCCTTAGCTTTGAAGCTGAACATTGAACCTTACATCC
*
41058119 AGCCGAATCTAGACATAGCTAATAGGAAATACATTTCTAGATTAATTCATACAATTAAAGCCGAA
391 AGCCGAATCTAGACATAGCTAATAGGAAATACATTTCTAGATTAATCCATACAATTAAAGCCGAA
* *
41058184 TTACTTAGTCTCTAAGTTTGTTTATTTTGTCCATTCGACTATCATATAGAGGCTATAAATAGTTT
456 TTACTTAGTCTCTAAGTTTGTTTATTCTGTCCATTCAACTATCATATAGAGGCTATAAATAGTTT
41058249 GTTATTTCATGTTGTAAAGAACTTTTTGCCAAATTATTGAATGAACATATTGTTCTTGTGAGGTT
521 GTTATTTCATGTTGTAAAGAACTTTTTGCCAAATTATTGAATGAACATATTGTTCTTGTGAGGTT
*
41058314 TCCTTCCTCTCCGTTTCGTTCGAGTCTCGAATTGACTTACCTAGTTCGCTAGCGGTGTCAACTCG
586 TCCTTCCTCTCCATTTCGTTCGAGTCTCGAATTGACTTACCTAGTTCGCTAGCGGTGTCAACTCG
41058379 AACTCTTGTTTCCTTCCATCTTTTATACCTTTGAATCTTT
651 AACTCTTGTTTCCTTCCATCTTTTATACCTTTGAATCTTT
41058419 CTTCTTATAA
Statistics
Matches: 652, Mismatches: 38, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
691 652 1.00
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (691 bp):
GTCTAAGATCAGCCGAATATACATTGAATTTAAGTTGCTCATGTCTTTTGTAGGTACAACCGAAT
ATGGAAAACACAATCAATGATGGTTCATGAACGGGCTAGTTCAATGTACGTGCGGGTGCATGAAT
GACTACCTTCAACATATGAATGCATTAAGGATGGTGCATAAACAGTCCATTAGAATGAATGGAAG
AGTGCATGAATACTCACCTACATGCATCGTTTACTAGCTATTGATCTCCTATGTGTTTATTGGGC
CAAAAGGCATCTATTAGAGGGACCATTCACCCTTTGGCCGAACCTAGACATGGCCGATGGTCTCC
TATGCATTCACCAACTACCACATTCATTTCCTTAGCTTTGAAGCTGAACATTGAACCTTACATCC
AGCCGAATCTAGACATAGCTAATAGGAAATACATTTCTAGATTAATCCATACAATTAAAGCCGAA
TTACTTAGTCTCTAAGTTTGTTTATTCTGTCCATTCAACTATCATATAGAGGCTATAAATAGTTT
GTTATTTCATGTTGTAAAGAACTTTTTGCCAAATTATTGAATGAACATATTGTTCTTGTGAGGTT
TCCTTCCTCTCCATTTCGTTCGAGTCTCGAATTGACTTACCTAGTTCGCTAGCGGTGTCAACTCG
AACTCTTGTTTCCTTCCATCTTTTATACCTTTGAATCTTTT
Found at i:41066830 original size:18 final size:18
Alignment explanation
Indices: 41066803--41066844 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
41066793 TGTTGGAATA
*
41066803 AATTAATTAAGTT-AGTTT
1 AATTAATTAA-TTGAGCTT
*
41066821 AATTAGTTAATTGAGCTT
1 AATTAATTAATTGAGCTT
41066839 AATTAA
1 AATTAA
41066845 ATGTTGAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.45
Consensus pattern (18 bp):
AATTAATTAATTGAGCTT
Found at i:41071550 original size:18 final size:18
Alignment explanation
Indices: 41071523--41071564 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
41071513 AGTTGGAATA
*
41071523 AATTAATTAAGTT-AGTTT
1 AATTAATTAA-TTCAGCTT
*
41071541 AATTAGTTAATTCAGCTT
1 AATTAATTAATTCAGCTT
41071559 AATTAA
1 AATTAA
41071565 ATGTTGAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (18 bp):
AATTAATTAATTCAGCTT
Found at i:41080458 original size:80 final size:79
Alignment explanation
Indices: 41080374--41080545 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
41080364 GGACTAAGAT
*
41080374 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
41080438 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
41080454 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
41080519 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
41080533 CCGAAGGCATTTG
1 CCGAAGGCATTTG
41080546 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:41080525 original size:39 final size:39
Alignment explanation
Indices: 41080321--41080543 Score: 209
Period size: 40 Copynumber: 5.6 Consensus size: 39
41080311 TTGAATGCTG
* * * * *
41080321 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
41080361 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
41080400 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* *
41080441 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
41080481 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
41080520 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
41080544 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
39 40 0.25
40 103 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:41080563 original size:79 final size:80
Alignment explanation
Indices: 41080401--41080578 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
41080391 AGATACAAAT
* * * *
41080401 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
41080466 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
41080481 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
41080545 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
41080560 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
41080579 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:41096271 original size:40 final size:40
Alignment explanation
Indices: 41096227--41096397 Score: 213
Period size: 39 Copynumber: 4.3 Consensus size: 40
41096217 AGACTAAGAT
*
41096227 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
1 CCGAAGGCATTTGTGCGAGATACTAAA-TCCGGGTTAAGTC
*
41096267 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGT-
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
* * * *
41096306 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
* * * * *
41096346 CCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
41096385 CCGAAGGCATTTG
1 CCGAAGGCATTTG
41096398 AACGAGGAGC
Statistics
Matches: 116, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
39 68 0.59
40 45 0.39
41 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:41096322 original size:79 final size:78
Alignment explanation
Indices: 41096220--41096395 Score: 210
Period size: 79 Copynumber: 2.2 Consensus size: 78
41096210 TATATCCAGA
* *
41096220 CTAAGATCCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCG
1 CTAAG-TCCGAAGGCATTCGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCG
*
41096284 AGATACTAAATCCGGG
63 AGATACTAAAACCGGG
* * * * * * *
41096300 TTAAGTCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGT
1 CTAAGTCCGAAGGCATTCGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGA
41096365 TACTAAAACCGGG
66 TACTAAAACCGGG
*
41096378 CTATGTCCCGAAGGCATT
1 CTAAGT-CCGAAGGCATT
41096396 TGAACGAGGA
Statistics
Matches: 82, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
78 25 0.30
79 50 0.61
80 7 0.09
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (78 bp):
CTAAGTCCGAAGGCATTCGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGA
TACTAAAACCGGG
Found at i:41099373 original size:28 final size:27
Alignment explanation
Indices: 41099316--41099465 Score: 237
Period size: 27 Copynumber: 5.5 Consensus size: 27
41099306 TAAATTGTGC
*
41099316 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
41099343 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
41099371 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
41099398 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
41099426 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
41099453 AGCACTGAGTGTG
1 AGCACTAAGTGTG
41099466 TGGACTTAAT
Statistics
Matches: 117, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 64 0.55
28 53 0.45
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:41099380 original size:55 final size:55
Alignment explanation
Indices: 41099316--41099465 Score: 255
Period size: 55 Copynumber: 2.7 Consensus size: 55
41099306 TAAATTGTGC
*
41099316 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
41099371 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
41099426 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTG
41099466 TGGACTTAAT
Statistics
Matches: 90, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 90 1.00
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:41106486 original size:28 final size:27
Alignment explanation
Indices: 41106429--41106580 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
41106419 TAAATTGTGC
*
41106429 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
41106456 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
41106484 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
41106511 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
41106539 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
41106566 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41106581 GACTTAATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:41106493 original size:55 final size:55
Alignment explanation
Indices: 41106429--41106580 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
41106419 TAAATTGTGC
*
41106429 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
41106484 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
41106539 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
41106581 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:41111443 original size:70 final size:70
Alignment explanation
Indices: 41111329--41111469 Score: 237
Period size: 70 Copynumber: 2.0 Consensus size: 70
41111319 GTCATTTGCA
* * *
41111329 ATCTTTTGCAAGTTTAACTTTAATTTGATTAAACTCATCATAGTTAATGATTGAGTTGCTGGACT
1 ATCTTTTGCAAGCTGAACTTTAATTTGATTAAACTCATCATAGTTAATAATTGAGTTGCTGGACT
41111394 TTATT
66 TTATT
* *
41111399 ATCTTTTGCAAGCTGAACTTTAATTTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGGACT
1 ATCTTTTGCAAGCTGAACTTTAATTTGATTAAACTCATCATAGTTAATAATTGAGTTGCTGGACT
41111464 TTATT
66 TTATT
41111469 A
1 A
41111470 AACTCATCTT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.45
Consensus pattern (70 bp):
ATCTTTTGCAAGCTGAACTTTAATTTGATTAAACTCATCATAGTTAATAATTGAGTTGCTGGACT
TTATT
Found at i:41111467 original size:40 final size:40
Alignment explanation
Indices: 41111423--41111501 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
41111413 GAACTTTAAT
41111423 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGGAC
1 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGGAC
*
41111463 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGTTGGA
1 TTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGGA
41111502 TTCTATTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.30, C:0.10, G:0.15, T:0.44
Consensus pattern (40 bp):
TTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGGAC
Found at i:41113340 original size:17 final size:17
Alignment explanation
Indices: 41113318--41113359 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
41113308 AAATTGAGAG
41113318 AAGAAAAATGAAA-GAAA
1 AAGAAAAA-GAAACGAAA
41113335 AAGAAAAAGAAATCGAAA
1 AAGAAAAAGAAA-CGAAA
41113353 AAGAAAA
1 AAGAAAA
41113360 TGAGAGTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.17
17 8 0.35
18 11 0.48
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.05
Consensus pattern (17 bp):
AAGAAAAAGAAACGAAA
Found at i:41115744 original size:40 final size:40
Alignment explanation
Indices: 41115700--41115784 Score: 134
Period size: 40 Copynumber: 2.1 Consensus size: 40
41115690 AACTTTAATT
* * *
41115700 TTATTAAATTCATCTTATTTAATAATTGAGTTGTTGGACC
1 TTATTAAACTCATCTTAGTTAATAATTGAGTTGTTGAACC
*
41115740 TTATTAAACTCATCTTAGTTAATAATTGAGTTGTTGAACT
1 TTATTAAACTCATCTTAGTTAATAATTGAGTTGTTGAACC
41115780 TTATT
1 TTATT
41115785 TTTATTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (40 bp):
TTATTAAACTCATCTTAGTTAATAATTGAGTTGTTGAACC
Found at i:41115744 original size:70 final size:70
Alignment explanation
Indices: 41115605--41115745 Score: 228
Period size: 70 Copynumber: 2.0 Consensus size: 70
41115595 GTCATTTGCA
* *
41115605 ATCTTTTGCAAGCTAAACTTTAATTTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGGGCT
1 ATCTTTTGCAAGCTAAACTTTAATTTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGGACC
41115670 TTATT
66 TTATT
* * * *
41115675 ATCTTTTGCAAGCTGAACTTTAATTTTATTAAATTCATCTTATTTAATAATTGAGTTGTTGGACC
1 ATCTTTTGCAAGCTAAACTTTAATTTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGGACC
41115740 TTATT
66 TTATT
41115745 A
1 A
41115746 AACTCATCTT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (70 bp):
ATCTTTTGCAAGCTAAACTTTAATTTTATTAAACTCATCTTAGTTAATAATTGAGTTGCTGGACC
TTATT
Found at i:41115888 original size:9 final size:9
Alignment explanation
Indices: 41115867--41115922 Score: 67
Period size: 11 Copynumber: 5.7 Consensus size: 9
41115857 AACTTAATAA
41115867 GTGTTTAAAT
1 GTGTTT-AAT
41115877 GTGTTTAAT
1 GTGTTTAAT
41115886 GTGTTTAAT
1 GTGTTTAAT
41115895 GTGTTTTTAAT
1 GTG--TTTAAT
41115906 GTGTTTTTAAT
1 GTG--TTTAAT
41115917 GTGTTT
1 GTGTTT
41115923 GATTGTAAGT
Statistics
Matches: 44, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
9 18 0.41
10 6 0.14
11 20 0.45
ACGTcount: A:0.20, C:0.00, G:0.21, T:0.59
Consensus pattern (9 bp):
GTGTTTAAT
Found at i:41115905 original size:11 final size:11
Alignment explanation
Indices: 41115880--41115922 Score: 72
Period size: 11 Copynumber: 4.1 Consensus size: 11
41115870 TTTAAATGTG
41115880 TTTAATGTG--
1 TTTAATGTGTT
41115889 TTTAATGTGTT
1 TTTAATGTGTT
41115900 TTTAATGTGTT
1 TTTAATGTGTT
41115911 TTTAATGTGTT
1 TTTAATGTGTT
41115922 T
1 T
41115923 GATTGTAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
9 9 0.28
11 23 0.72
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.63
Consensus pattern (11 bp):
TTTAATGTGTT
Found at i:41128316 original size:18 final size:18
Alignment explanation
Indices: 41128295--41128333 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
41128285 AAAGAAAGAC
41128295 AGAAAAAGA-AATCGAAAA
1 AGAAAAAGAGAAT-GAAAA
41128313 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
41128331 AGA
1 AGA
41128334 GCAAAAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.72, C:0.03, G:0.21, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:41132317 original size:33 final size:34
Alignment explanation
Indices: 41132271--41132334 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
41132261 TTTCTTAATT
*
41132271 TCTTTCTTCACTCG-TTTCTTTTGCAGACTCTTTC
1 TCTTTCTTCACTCGATTTCTTTT-CAAACTCTTTC
41132305 TCTTTC-TCACTCGATTTCTTTTCAAACTCT
1 TCTTTCTTCACTCGATTTCTTTTCAAACTCT
41132335 CCTTCATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 14 0.50
34 14 0.50
ACGTcount: A:0.12, C:0.30, G:0.06, T:0.52
Consensus pattern (34 bp):
TCTTTCTTCACTCGATTTCTTTTCAAACTCTTTC
Found at i:41133468 original size:10 final size:10
Alignment explanation
Indices: 41133453--41133477 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41133443 ACAATGATGC
41133453 AATTTATTTG
1 AATTTATTTG
41133463 AATTTATTTG
1 AATTTATTTG
41133473 AATTT
1 AATTT
41133478 TTTTTAAACA
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:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (10 bp):
AATTTATTTG
Found at i:41142792 original size:39 final size:38
Alignment explanation
Indices: 41142695--41142798 Score: 127
Period size: 39 Copynumber: 2.7 Consensus size: 38
41142685 TGTCCTAAAC
* * * *
41142695 TATGACATAATTAAAACCCTTATTAATGCTGTTCAAAT
1 TATGACATAATTAAAACTCATACTAATGATGTTCAAAT
* *
41142733 TATGACACAATTAAAAACTCATACTAATGATGTTCGAAT
1 TATGACATAATT-AAAACTCATACTAATGATGTTCAAAT
*
41142772 TATGACATAATTAAAGACTCAAACTAA
1 TATGACATAATTAAA-ACTCATACTAA
41142799 ATTAACTAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
38 14 0.25
39 42 0.75
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (38 bp):
TATGACATAATTAAAACTCATACTAATGATGTTCAAAT
Found at i:41146885 original size:92 final size:91
Alignment explanation
Indices: 41146775--41146978 Score: 275
Period size: 92 Copynumber: 2.2 Consensus size: 91
41146765 TAATATGGAG
* * * * *
41146775 CATGCACCTGATTATGCATGAATA-TCGGGAGTTGTTTTTTAGCTGGACATTCATGTATCTTCCA
1 CATGCACCTGATTGTGCATGAA-AGTC-GGAGCTATTTTTTAGCTGAACATACATGTATCTTCCA
* *
41146839 AATTCAATGAAGCTACTTTAATGAAGAA
64 AATTCAACGAAGCTACTTTAAAGAAGAA
* * *
41146867 CATGCACCTGATTGTGCATGAAAGTTCGGAGCTATTTTTTAGCTGAATATACATGTATCTTCTAG
1 CATGCACCTGATTGTGCATGAAAG-TCGGAGCTATTTTTTAGCTGAACATACATGTATCTTCCAA
41146932 ATTCAACGAAGCTACTTTAAAGAAGAA
65 ATTCAACGAAGCTACTTTAAAGAAGAA
*
41146959 CATGCACCCGATTGTGCATG
1 CATGCACCTGATTGTGCATG
41146979 TATTTTGAAA
Statistics
Matches: 99, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
91 1 0.01
92 96 0.97
93 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Consensus pattern (91 bp):
CATGCACCTGATTGTGCATGAAAGTCGGAGCTATTTTTTAGCTGAACATACATGTATCTTCCAAA
TTCAACGAAGCTACTTTAAAGAAGAA
Found at i:41148503 original size:16 final size:16
Alignment explanation
Indices: 41148464--41148505 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
41148454 AATGAGCCAT
*
41148464 ATCCATGAATCCAGCC
1 ATCCATGTATCCAGCC
41148480 ATCCATGTATCCAGCC
1 ATCCATGTATCCAGCC
*
41148496 ATTCATGTAT
1 ATCCATGTAT
41148506 GCTCCCATAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.29, C:0.31, G:0.12, T:0.29
Consensus pattern (16 bp):
ATCCATGTATCCAGCC
Found at i:41150091 original size:44 final size:44
Alignment explanation
Indices: 41150042--41150133 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
41150032 ATATAAGTCT
41150042 TTAATATGCTTTGTCTTTGCTGAATTAAATATGTCCGGATTTAA
1 TTAATATGCTTTGTCTTTGCTGAATTAAATATGTCCGGATTTAA
*
41150086 TTAATATGCTTTGTCTTTGCTGAATTAAATATGTCCTGATTTAA
1 TTAATATGCTTTGTCTTTGCTGAATTAAATATGTCCGGATTTAA
41150130 TTAA
1 TTAA
41150134 GTTTGTCTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (44 bp):
TTAATATGCTTTGTCTTTGCTGAATTAAATATGTCCGGATTTAA
Found at i:41151476 original size:21 final size:22
Alignment explanation
Indices: 41151432--41151473 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
41151422 TACGAAAAAA
*
41151432 TTCGTATTTAAAAAAAAAGAAG
1 TTCGAATTTAAAAAAAAAGAAG
41151454 TTCGAATTTAAAAAAAAAGA
1 TTCGAATTTAAAAAAAAAGA
41151474 GTTGCAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.12, T:0.26
Consensus pattern (22 bp):
TTCGAATTTAAAAAAAAAGAAG
Found at i:41151483 original size:22 final size:22
Alignment explanation
Indices: 41151437--41151484 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
41151427 AAAAATTCGT
*
41151437 ATTTAAAAAAAAAGAAGTTCGA
1 ATTTAAAAAAAAAGAAGTTCAA
41151459 ATTTAAAAAAAAAG-AGTTGCAA
1 ATTTAAAAAAAAAGAAGTT-CAA
41151481 ATTT
1 ATTT
41151485 GTGAATTGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.56, C:0.04, G:0.12, T:0.27
Consensus pattern (22 bp):
ATTTAAAAAAAAAGAAGTTCAA
Found at i:41158141 original size:11 final size:10
Alignment explanation
Indices: 41158115--41158140 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
41158105 AGAAAATATC
41158115 AAAAAATTGA
1 AAAAAATTGA
41158125 AAAAAATTGA
1 AAAAAATTGA
41158135 AAAAAA
1 AAAAAA
41158141 AGTTCATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (10 bp):
AAAAAATTGA
Found at i:41159361 original size:39 final size:39
Alignment explanation
Indices: 41159318--41159424 Score: 126
Period size: 39 Copynumber: 2.7 Consensus size: 39
41159308 AAATGAAAAA
* * *
41159318 GAAAAAGAAATTGAATTAAAAGAAAAAGAAAAATAGATT
1 GAAAAAGAAATTGAATGAAAAGAAAAAGAAAAAGACATT
* *
41159357 GAAAAATAAATTGAAAGAAAAGAAAAAGAAAAAGACATT
1 GAAAAAGAAATTGAATGAAAAGAAAAAGAAAAAGACATT
* * *
41159396 G-TAAAGAAAATGAGTGAAAAGGAAAAAGA
1 GAAAAAGAAATTGAATGAAAA-GAAAAAGA
41159425 GCTTGAACAT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
38 14 0.25
39 43 0.75
ACGTcount: A:0.66, C:0.01, G:0.19, T:0.14
Consensus pattern (39 bp):
GAAAAAGAAATTGAATGAAAAGAAAAAGAAAAAGACATT
Found at i:41159415 original size:33 final size:33
Alignment explanation
Indices: 41159378--41159453 Score: 86
Period size: 33 Copynumber: 2.3 Consensus size: 33
41159368 TGAAAGAAAA
41159378 GAAAAAGAAAAAGA-CATTGTAA-AGAAAAT-GAGT
1 GAAAAAGAAAAAGAGC-TTG-AACA-AAAATCGAGT
* *
41159411 GAAAAGGAAAAAGAGCTTGAACATAAATCGAGT
1 GAAAAAGAAAAAGAGCTTGAACAAAAATCGAGT
41159444 GAAAAAGAAA
1 GAAAAAGAAA
41159454 GAAAGTTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
32 6 0.16
33 30 0.81
34 1 0.03
ACGTcount: A:0.59, C:0.05, G:0.22, T:0.13
Consensus pattern (33 bp):
GAAAAAGAAAAAGAGCTTGAACAAAAATCGAGT
Found at i:41167854 original size:12 final size:13
Alignment explanation
Indices: 41167837--41167880 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 13
41167827 TTATATTCTT
41167837 TTTTTTTAC-AAA
1 TTTTTTTACGAAA
41167849 TTTTTTTACGAAA
1 TTTTTTTACGAAA
* *
41167862 -TTTTTTATGAAG
1 TTTTTTTACGAAA
41167874 TTTTTTT
1 TTTTTTT
41167881 CAGCTAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.64
Consensus pattern (13 bp):
TTTTTTTACGAAA
Found at i:41173947 original size:11 final size:11
Alignment explanation
Indices: 41173933--41173975 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
41173923 TTTTCTTCTT
41173933 TTTCTTTTCCA
1 TTTCTTTTCCA
41173944 TTTC-TTTCCA
1 TTTCTTTTCCA
*
41173954 TTTCTTTTTCAA
1 TTTC-TTTTCCA
41173966 TGTTCTTTTC
1 T-TTCTTTTC
41173976 TCGCTCACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 10 0.36
11 4 0.14
12 11 0.39
13 3 0.11
ACGTcount: A:0.09, C:0.23, G:0.02, T:0.65
Consensus pattern (11 bp):
TTTCTTTTCCA
Found at i:41175042 original size:15 final size:13
Alignment explanation
Indices: 41175021--41175054 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
41175011 AAATAAACTC
41175021 TTTTTTTTCGAATT
1 TTTTTTTTCG-ATT
41175035 TCTTTTTTTCGATT
1 T-TTTTTTTCGATT
41175049 TTTTTT
1 TTTTTT
41175055 CAATTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 5 0.26
15 9 0.47
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.76
Consensus pattern (13 bp):
TTTTTTTTCGATT
Found at i:41175070 original size:12 final size:11
Alignment explanation
Indices: 41175037--41175070 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
41175027 TTCGAATTTC
*
41175037 TTTTTTTCGAT
1 TTTTTTTCAAT
41175048 TTTTTTTCAAT
1 TTTTTTTCAAT
41175059 TTTTTTTACAAT
1 TTTTTTT-CAAT
41175071 CTCGTAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.18, C:0.09, G:0.03, T:0.71
Consensus pattern (11 bp):
TTTTTTTCAAT
Found at i:41176397 original size:22 final size:21
Alignment explanation
Indices: 41176372--41176414 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
41176362 TTTAACACTT
* *
41176372 AACTAAATTAATTAAATATTTA
1 AACTAAACTAACTAAA-ATTTA
41176394 AACTAAACTAACTAAAATTTA
1 AACTAAACTAACTAAAATTTA
41176415 TTTAAGCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (21 bp):
AACTAAACTAACTAAAATTTA
Found at i:41176427 original size:19 final size:20
Alignment explanation
Indices: 41176403--41176449 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
41176393 AAACTAAACT
41176403 AACTAAAATT-TATT-TAAGC
1 AACTAAAATTGTATTCT-AGC
41176422 AACT-AAATTGTATTCTAGC
1 AACTAAAATTGTATTCTAGC
41176441 AACTAAAAT
1 AACTAAAAT
41176450 GCATGAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 5 0.20
19 15 0.60
20 5 0.20
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (20 bp):
AACTAAAATTGTATTCTAGC
Found at i:41177176 original size:91 final size:92
Alignment explanation
Indices: 41177012--41177181 Score: 198
Period size: 91 Copynumber: 1.9 Consensus size: 92
41177002 GCATGAATCT
* * ** * * **
41177012 TTCATTAACTAGCTTCAATATATCGGCAAGATACATGAACATTCAGCTGAATAATAGCTCCCTTC
1 TTCATTAAATAGCTTCAATATATCAGCAAGATACATGAACATTCAAATGAAAAACAGCTCCCAAC
* *
41177077 ATTCATGCAGAATTAGGTACGTTACTC
66 ATTAATGCACAATTAGGTACGTTACTC
* * * **
41177104 TTCATTAAATAGCTT-AATGTATCAGCTAGGTACATGAATGTTCAAATGAAAAACAGCTCCCAAC
1 TTCATTAAATAGCTTCAATATATCAGCAAGATACATGAACATTCAAATGAAAAACAGCTCCCAAC
41177168 ATTAATGCACAATT
66 ATTAATGCACAATT
41177182 CGGGTGCACG
Statistics
Matches: 63, Mismatches: 15, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
91 49 0.78
92 14 0.22
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.31
Consensus pattern (92 bp):
TTCATTAAATAGCTTCAATATATCAGCAAGATACATGAACATTCAAATGAAAAACAGCTCCCAAC
ATTAATGCACAATTAGGTACGTTACTC
Found at i:41179328 original size:19 final size:19
Alignment explanation
Indices: 41179282--41179321 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
41179272 TCTTCACTCG
41179282 TTTC-TTTTTCAAGCTCTC
1 TTTCTTTTTTCAAGCTCTC
41179300 TTTCTTTTTTCACA-CTCTC
1 TTTCTTTTTTCA-AGCTCTC
41179319 TTT
1 TTT
41179322 TGTTTTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 4 0.20
19 15 0.75
20 1 0.05
ACGTcount: A:0.10, C:0.28, G:0.03, T:0.60
Consensus pattern (19 bp):
TTTCTTTTTTCAAGCTCTC
Found at i:41179479 original size:7 final size:6
Alignment explanation
Indices: 41179458--41179501 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
41179448 TCTTTCATTT
* *
41179458 TTTTCA TTTTCA TTTTCA ATTTCC TTTTC- TTATTCA TTTTCA TT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TT-TTCA TTTTCA TT
41179502 CTTTTTCTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 2 0.06
6 29 0.88
7 2 0.06
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTTCA
Found at i:41179512 original size:24 final size:22
Alignment explanation
Indices: 41179434--41179522 Score: 78
Period size: 24 Copynumber: 4.0 Consensus size: 22
41179424 CTCGCACTCT
41179434 TTTTCTTTCTCTTTTC--TTTCA
1 TTTT-TTTCTCTTTTCATTTTCA
*
41179455 TTTTTTTC-ATTTTCATTTTCAA
1 TTTTTTTCTCTTTTCATTTTC-A
*
41179477 TTTCCTTTTCT-TATTCATTTTCA
1 TTT--TTTTCTCTTTTCATTTTCA
41179500 TTCTTTTTCTCTTATTCATTTTC
1 TT-TTTTTCTCTT-TTCATTTTC
41179523 TCTCAACTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
19 5 0.09
20 4 0.07
21 8 0.14
22 10 0.18
23 4 0.07
24 25 0.45
ACGTcount: A:0.11, C:0.20, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTTTTCTCTTTTCATTTTCA
Found at i:41181075 original size:47 final size:49
Alignment explanation
Indices: 41181018--41181113 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 49
41181008 TGTCGAAATT
* *
41181018 ATTTAAGCAACTAAA-ATAAA-AAAAA-AACTTAATTCATTAAACTAATG
1 ATTTAAGCAACTAAAGA-AAATAAAAACAAATTAATTAATTAAACTAATG
41181065 ATTTAAGCAACTAAAGAAAATTAAAAACAAATTAATTAATTAAACTAAT
1 ATTTAAGCAACTAAAGAAAA-TAAAAACAAATTAATTAATTAAACTAAT
41181114 TTAACTAAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
47 18 0.42
48 1 0.02
49 5 0.12
50 19 0.44
ACGTcount: A:0.58, C:0.09, G:0.04, T:0.28
Consensus pattern (49 bp):
ATTTAAGCAACTAAAGAAAATAAAAACAAATTAATTAATTAAACTAATG
Found at i:41181117 original size:47 final size:46
Alignment explanation
Indices: 41181018--41181112 Score: 120
Period size: 47 Copynumber: 2.0 Consensus size: 46
41181008 TGTCGAAATT
* *
41181018 ATTTAAGCAACTAAAATAAAAAAAAAACTTAATTCATTAAACTAATG
1 ATTTAAGCAACTAAAATAAAAAAAAAAATTAATTAATTAAACTAA-G
41181065 ATTTAAGCAACTAAAGA-AAATTAAAAACAAATTAATTAATTAAACTAA
1 ATTTAAGCAACTAAA-ATAAA--AAAAA-AAATTAATTAATTAAACTAA
41181113 TTTAACTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
47 18 0.43
48 1 0.02
49 5 0.12
50 18 0.43
ACGTcount: A:0.59, C:0.09, G:0.04, T:0.27
Consensus pattern (46 bp):
ATTTAAGCAACTAAAATAAAAAAAAAAATTAATTAATTAAACTAAG
Found at i:41201366 original size:116 final size:114
Alignment explanation
Indices: 41201221--41201781 Score: 612
Period size: 116 Copynumber: 4.9 Consensus size: 114
41201211 GGTGATTTCC
* *
41201221 AGAAAGCGCCGC--AAAAAACCTAAGCCCAACGACGTCGTTTACCGAGCTTTCAGGGATTTAGCG
1 AGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACGCCGTTT-CTGAGCTTTCAGGGATTTAGCG
* * * *
41201284 GCATTTTCAAGAAAGCGTCGCTAATGCTCAGGGCTTTTGCGACGTTTTTG
65 GCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
* * * * *
41201334 AGAAAGCGCCACAAAAAAAAACCGAAGCCCAACGACGCCATTTTTTGAGCTTTCTGGGATTTAGC
1 AGAAAGCGCCGC-AAAAAAAACCTAAGCCCAACGACGCC-GTTTCTGAGCTTTCAGGGATTTAGC
* * **
41201399 GGCATTTTTAATAAAGCGCCGCTAATGCTCAGGGATAAAGCGGCGTTTTTG
64 GGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
* * * *
41201450 AAAAAGCGTCGC-AAAAAAACCTAAGCCCAACGACGCCAATTTCTGAGCTTTCCA-GGATTTAGT
1 AGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACGCC-GTTTCTGAGCTTT-CAGGGATTTAGC
* * * * *
41201513 GACTTTTTTAATAAAGCGCAGCTAATGCTCAGGGCTTTTAGCGGTGTTTTTG
64 GGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGC-TTTAGCGGCGTTTTTG
* * * *
41201565 AGAAAGCGCCGCAAAAAAAACCTAGGCCCAACAACGCCGTTTCCTGAGTTTTCGGGGATTTAGCG
1 AGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACGCCGTTT-CTGAGCTTTCAGGGATTTAGCG
*** * *
41201630 TTGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCATTTTT-
65 GCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
* * * ** * *
41201679 AGGAAAGCCCCGGAAGAAAAA-CTAAGCCCAACGGTGCCGTTTACTGTGCTTTCGGGGATTTAGC
1 A-GAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACGCCGTTT-CTGAGCTTTCAGGGATTTAGC
* * *
41201743 GGCGTTTTTAAGAAAGCGTCGCTAATGCTCAGGGATTTA
64 GGCATTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTA
41201782 AAATAATTTA
Statistics
Matches: 377, Mismatches: 61, Indels: 19
0.82 0.13 0.04
Matches are distributed among these distances:
113 11 0.03
114 146 0.39
115 57 0.15
116 160 0.42
117 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (114 bp):
AGAAAGCGCCGCAAAAAAAACCTAAGCCCAACGACGCCGTTTCTGAGCTTTCAGGGATTTAGCGG
CATTTTTAAGAAAGCGCCGCTAATGCTCAGGGCTTTAGCGGCGTTTTTG
Found at i:41201639 original size:230 final size:230
Alignment explanation
Indices: 41201223--41201776 Score: 663
Period size: 230 Copynumber: 2.4 Consensus size: 230
41201213 TGATTTCCAG
* *
41201223 AAAGCGCCGC-AAAAAACCTAAGCCCAACGACGTCGTTTACCGAGCTTT-CAGGGATTTAGCGGC
1 AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTACTGAGCTTTCCA-GGATTTAGCGGC
*
41201286 ATTTTCAAGAAAGCGTCGCTAATGCTCAGGGCTTTTGCGACGTTTTTGAGAAAGCGCCACAAAAA
65 ATTTTTAAGAAAGCGTCGCTAATGCTCAGGGCTTTTGCGACGTTTTTGAGAAAGCGCCACAAAAA
* ** * *
41201351 AAAACCGAAGCCCAACGACGCCATTTTTTGAGCTTTCTGGGATTTAGCGGCATTTTTAATAAAGC
130 AAAACCGAAGCCCAACAACGCCATTTCCTGAGCTTTCGGGGATTTAGCGGCATTTTTAAGAAAGC
*
41201416 GCCGCTAATGCTCAGGGATAAAGCGGCGTTTTT-GAA
195 GCCGCTAATGCTCAGGGATAAAGCGGCATTTTTAG-A
* * * *
41201452 AAAGCGTCGCAAAAAAACCTAAGCCCAACGACGCCAATTT-CTGAGCTTTCCAGGATTTAGTGAC
1 AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCC-GTTTACTGAGCTTTCCAGGATTTAGCGGC
* * ** *
41201516 TTTTTTAATAAAGCG-CAGCTAATGCTCAGGGCTTTTAGCGGTGTTTTTGAGAAAGCGCCGC-AA
65 ATTTTTAAGAAAGCGTC-GCTAATGCTCAGGGCTTTT-GCGACGTTTTTGAGAAAGCGCCACAAA
* * * * *** *
41201579 AAAAAACCTAGGCCCAACAACGCCGTTTCCTGAGTTTTCGGGGATTTAGCGTTGTTTTTAAGGAA
128 AAAAAACCGAAGCCCAACAACGCCATTTCCTGAGCTTTCGGGGATTTAGCGGCATTTTTAAGAAA
* ** *
41201644 GCGCCGCTAATGCTCAGGGCTTTAGCGGCATTTTTAGG
193 GCGCCGCTAATGCTCAGGGATAAAGCGGCATTTTTAGA
* * ** * **
41201682 AAAGCCCCGGAAGAAAAA-CTAAGCCCAACGGTGCCGTTTACTGTGCTTTCGGGGATTTAGCGGC
1 AAAGCGCCGCAA-AAAAACCTAAGCCCAACGACGCCGTTTACTGAGCTTTCCAGGATTTAGCGGC
*
41201746 GTTTTTAAGAAAGCGTCGCTAATGCTCAGGG
65 ATTTTTAAGAAAGCGTCGCTAATGCTCAGGG
41201777 ATTTAAAATA
Statistics
Matches: 273, Mismatches: 43, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
229 13 0.05
230 227 0.83
231 33 0.12
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (230 bp):
AAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTACTGAGCTTTCCAGGATTTAGCGGCA
TTTTTAAGAAAGCGTCGCTAATGCTCAGGGCTTTTGCGACGTTTTTGAGAAAGCGCCACAAAAAA
AAACCGAAGCCCAACAACGCCATTTCCTGAGCTTTCGGGGATTTAGCGGCATTTTTAAGAAAGCG
CCGCTAATGCTCAGGGATAAAGCGGCATTTTTAGA
Found at i:41202061 original size:45 final size:43
Alignment explanation
Indices: 41202006--41202144 Score: 142
Period size: 38 Copynumber: 3.5 Consensus size: 43
41201996 TTTAGGGTTT
* *
41202006 GGGATTTAAGGTTTAGGGGTTAGGTGTTATGCTTTATGGGTTAAG
1 GGGATTTAAGGGTTA-GGGTTAGG-GTTATGCTTTAGGGGTTAAG
41202051 GGGATTTAAGGGTTA----T-GGGTTATGCTTTAGGGGTTAAG
1 GGGATTTAAGGGTTAGGGTTAGGGTTATGCTTTAGGGGTTAAG
41202089 GGGATTTAAGGGTTA----T-GGGTTATGCTTTAGGGGTTAA-
1 GGGATTTAAGGGTTAGGGTTAGGGTTATGCTTTAGGGGTTAAG
41202126 -GGATTT-AGGGTTTAGGGTT
1 GGGATTTAAGGG-TTAGGGTT
41202145 TCAATGGTTA
Statistics
Matches: 87, Mismatches: 2, Indels: 15
0.84 0.02 0.14
Matches are distributed among these distances:
35 4 0.05
36 9 0.10
38 56 0.64
39 2 0.02
40 2 0.02
45 14 0.16
ACGTcount: A:0.20, C:0.02, G:0.39, T:0.39
Consensus pattern (43 bp):
GGGATTTAAGGGTTAGGGTTAGGGTTATGCTTTAGGGGTTAAG
Found at i:41202063 original size:17 final size:17
Alignment explanation
Indices: 41202038--41202103 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
41202028 GGTGTTATGC
*
41202038 TTTATGGGTTAAGGGGA
1 TTTAAGGGTTAAGGGGA
* *
41202055 TTTAAGGGTTATGGGTTATGC
1 TTTAAGGGTTAAGGG----GA
*
41202076 TTTAGGGGTTAAGGGGA
1 TTTAAGGGTTAAGGGGA
41202093 TTTAAGGGTTA
1 TTTAAGGGTTA
41202104 TGGGTTATGC
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
17 24 0.63
21 14 0.37
ACGTcount: A:0.23, C:0.02, G:0.38, T:0.38
Consensus pattern (17 bp):
TTTAAGGGTTAAGGGGA
Found at i:41202065 original size:38 final size:38
Alignment explanation
Indices: 41202017--41202127 Score: 188
Period size: 38 Copynumber: 2.9 Consensus size: 38
41202007 GGATTTAAGG
* *
41202017 TTTAGGGGTTA-GGTGTTATGCTTTATGGGTTAAGGGGA
1 TTTAAGGGTTATGG-GTTATGCTTTAGGGGTTAAGGGGA
41202055 TTTAAGGGTTATGGGTTATGCTTTAGGGGTTAAGGGGA
1 TTTAAGGGTTATGGGTTATGCTTTAGGGGTTAAGGGGA
41202093 TTTAAGGGTTATGGGTTATGCTTTAGGGGTTAAGG
1 TTTAAGGGTTATGGGTTATGCTTTAGGGGTTAAGG
41202128 ATTTAGGGTT
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
38 68 0.97
39 2 0.03
ACGTcount: A:0.20, C:0.03, G:0.39, T:0.39
Consensus pattern (38 bp):
TTTAAGGGTTATGGGTTATGCTTTAGGGGTTAAGGGGA
Found at i:41202084 original size:21 final size:21
Alignment explanation
Indices: 41202055--41202124 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
41202045 GTTAAGGGGA
41202055 TTTAAGGGTTATGGGTTATGC
1 TTTAAGGGTTATGGGTTATGC
* * *
41202076 TTTAGGGGTTAAGGG----GA
1 TTTAAGGGTTATGGGTTATGC
41202093 TTTAAGGGTTATGGGTTATGC
1 TTTAAGGGTTATGGGTTATGC
*
41202114 TTTAGGGGTTA
1 TTTAAGGGTTA
41202125 AGGATTTAGG
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
17 14 0.37
21 24 0.63
ACGTcount: A:0.20, C:0.03, G:0.37, T:0.40
Consensus pattern (21 bp):
TTTAAGGGTTATGGGTTATGC
Found at i:41203211 original size:17 final size:17
Alignment explanation
Indices: 41203186--41203230 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
41203176 GGGGTTATGC
41203186 TTTAAGGGTTAGGGGGA
1 TTTAAGGGTTAGGGGGA
*
41203203 TTTAGGGGTTAGGGGGA
1 TTTAAGGGTTAGGGGGA
41203220 TTTAAGGGTTA
1 TTTAAGGGTTA
41203231 TGGGTTAGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.33
Consensus pattern (17 bp):
TTTAAGGGTTAGGGGGA
Found at i:41205760 original size:9 final size:9
Alignment explanation
Indices: 41205748--41205847 Score: 66
Period size: 9 Copynumber: 11.4 Consensus size: 9
41205738 AATTCACATA
41205748 ATAACTTAC
1 ATAACTTAC
41205757 ATAACTTA-
1 ATAACTTAC
*
41205765 ACAACTTA-
1 ATAACTTAC
* *
41205773 ACAACTCAC
1 ATAACTTAC
*
41205782 ATAATTTAC
1 ATAACTTAC
*
41205791 ATAATTTAC
1 ATAACTTAC
*
41205800 ATAATACATA-
1 AT-A-ACTTAC
41205810 ATAACTTA-
1 ATAACTTAC
* *
41205818 ACAACTCAC
1 ATAACTTAC
*
41205827 ATAATTTAC
1 ATAACTTAC
41205836 ATAACTTA-
1 ATAACTTAC
41205844 ATAA
1 ATAA
41205848 TTTTAAAATA
Statistics
Matches: 73, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
8 28 0.38
9 39 0.53
10 3 0.04
11 3 0.04
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (9 bp):
ATAACTTAC
Found at i:41205965 original size:17 final size:17
Alignment explanation
Indices: 41205943--41206014 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
41205933 ATAACTCACA
41205943 TAATAACTTACATAACT
1 TAATAACTTACATAACT
*
41205960 TAATAACTTATATATA-T
1 TAATAACTTACATA-ACT
**
41205977 GCATAACTTA-ATAACT
1 TAATAACTTACATAACT
* * *
41205993 CATATTATTTACATAACT
1 TA-ATAACTTACATAACT
41206011 TAAT
1 TAAT
41206015 CATTGTAAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
15 1 0.02
16 4 0.09
17 30 0.70
18 8 0.19
ACGTcount: A:0.44, C:0.14, G:0.01, T:0.40
Consensus pattern (17 bp):
TAATAACTTACATAACT
Found at i:41205987 original size:25 final size:26
Alignment explanation
Indices: 41205951--41206014 Score: 94
Period size: 25 Copynumber: 2.5 Consensus size: 26
41205941 CATAATAACT
*
41205951 TACATAACTTAATAACTTATA-TATA
1 TACATAACTTAATAACTCATATTATA
* *
41205976 TGCATAACTTAATAACTCATATTATT
1 TACATAACTTAATAACTCATATTATA
41206002 TACATAACTTAAT
1 TACATAACTTAAT
41206015 CATTGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 19 0.56
26 15 0.44
ACGTcount: A:0.44, C:0.14, G:0.02, T:0.41
Consensus pattern (26 bp):
TACATAACTTAATAACTCATATTATA
Found at i:41207778 original size:21 final size:21
Alignment explanation
Indices: 41207752--41207821 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
41207742 CTACAACTTA
*
41207752 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
41207773 AAGCAGAGGCTGCAGCAAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
41207794 AAGCAGAGGTTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
41207815 -AGCAGAG
1 AAGCAGAG
41207822 CAGAGCAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 7 0.16
21 38 0.84
ACGTcount: A:0.31, C:0.17, G:0.47, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:41208210 original size:43 final size:43
Alignment explanation
Indices: 41208163--41208343 Score: 249
Period size: 43 Copynumber: 4.2 Consensus size: 43
41208153 CAAAACAATT
** *
41208163 GCGGCGTTTGTGAGA-AAAGGGCTGCTAAAGAACATGACCTTTA
1 GCGGCGTTTGTGA-ATAAAGCACCGCTAAAGAACATGACCTTTA
* * *
41208206 GCGGCGTTTGTGAA-AAATGCGCTGCTAAAGAACATTACCTTTA
1 GCGGCGTTTGTGAATAAA-GCACCGCTAAAGAACATGACCTTTA
* *
41208249 GCGGCGTTTATGAATAAAGCACCGCTAAAGAACATTACCTTTA
1 GCGGCGTTTGTGAATAAAGCACCGCTAAAGAACATGACCTTTA
*
41208292 GCGGCGTTTGTGGATAAAGCACCGCTAAAGAACATGACCTTTA
1 GCGGCGTTTGTGAATAAAGCACCGCTAAAGAACATGACCTTTA
41208335 GCGGCGTTT
1 GCGGCGTTT
41208344 ATAGAAATAA
Statistics
Matches: 128, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
42 4 0.03
43 121 0.95
44 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (43 bp):
GCGGCGTTTGTGAATAAAGCACCGCTAAAGAACATGACCTTTA
Found at i:41208666 original size:41 final size:43
Alignment explanation
Indices: 41208565--41208681 Score: 141
Period size: 41 Copynumber: 2.8 Consensus size: 43
41208555 GGCTCGTACA
* *
41208565 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCACATATCG
1 ATGCCAATGTCCCAGACAG-GGTCTTACATGTAATCAAATATCG
* * * *
41208608 TTGCCACTGTCCCAGACAGGGTCTTACCTG-AATTAAATA-CG
1 ATGCCAATGTCCCAGACAGGGTCTTACATGTAATCAAATATCG
*
41208649 ATGCCAATGTCCCAGACATGGTCTTACATGTAA
1 ATGCCAATGTCCCAGACAGGGTCTTACATGTAA
41208682 AGACAAATCG
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
41 28 0.45
42 9 0.15
43 24 0.39
44 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACATGTAATCAAATATCG
Found at i:41211130 original size:28 final size:30
Alignment explanation
Indices: 41211068--41211140 Score: 100
Period size: 28 Copynumber: 2.5 Consensus size: 30
41211058 GTCATGAGAT
*
41211068 TGGCACTAAGTGTGCGGGTTTAAATTGTACA
1 TGGCACTAAGTGTGCGAGTTTAAA-TGTACA
41211099 --GCACTAAGTGTGCGAG-TTAAA-GTACA
1 TGGCACTAAGTGTGCGAGTTTAAATGTACA
41211125 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
41211141 CGGTTGATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 5 0.13
28 19 0.49
29 15 0.38
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (30 bp):
TGGCACTAAGTGTGCGAGTTTAAATGTACA
Found at i:41211363 original size:174 final size:174
Alignment explanation
Indices: 41211099--41211662 Score: 1067
Period size: 174 Copynumber: 3.2 Consensus size: 174
41211089 AAATTGTACA
*
41211099 GCACTAAGTGTGCGAG-TTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
41211163 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
*
41211228 TTTTAGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
*
41211272 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
41211337 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
41211402 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* *
41211446 GCACTAAGTGTGTGAGTTTAAAGTGCATGGCACTAAGTGTGCGCGGTTGATTATTGAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
*
41211511 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
41211576 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
41211620 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCG
41211663 AACTCAATAT
Statistics
Matches: 384, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
173 15 0.04
174 369 0.96
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (174 bp):
GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Done.