Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 130 of 185
Found at i:40491313 original size:89 final size:84
Alignment explanation
Indices: 40491215--40491424 Score: 244
Period size: 89 Copynumber: 2.4 Consensus size: 84
40491205 GTACTGGCGT
* * * * * *
40491215 GAAGTAGATCATAGATACCAGATCTTGTC-TCCCGTACAGGTGGTGGAGTAGATCGAAGAAAGCA
1 GAAGCAGATCA-AGAAAGCAGATCTTGTCTTCACGTACAGG-CGTGAAGTAGATC-AAGAAA-CA
40491279 GATCTTGCCTTCCCATACTGGTGGC
62 GATCTTG-CTT-CCATACTGGTGGC
* ** *
40491304 GAAGCAGATCAAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAGATACAGAT
1 GAAGCAGATC-AAGAAAGCAGATCTTGTCTTCACGTACAGGCGTGAAGTAGATCAAGAAACAGAT
40491369 CTTGCTTCCATACTGGTGGC
65 CTTGCTTCCATACTGGTGGC
*
40491389 GAAGCAGATCAAGAAAGCAGATCTTGT-TTCATGTAC
1 GAAGCAGATCAAGAAAGCAGATCTTGTCTTCACGTAC
40491425 CGCGAAACAG
Statistics
Matches: 108, Mismatches: 11, Indels: 10
0.84 0.09 0.08
Matches are distributed among these distances:
83 8 0.07
84 17 0.16
85 23 0.21
86 3 0.03
87 9 0.08
88 5 0.05
89 35 0.32
90 8 0.07
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (84 bp):
GAAGCAGATCAAGAAAGCAGATCTTGTCTTCACGTACAGGCGTGAAGTAGATCAAGAAACAGATC
TTGCTTCCATACTGGTGGC
Found at i:40492615 original size:1 final size:1
Alignment explanation
Indices: 40492609--40492634 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
40492599 ACCTGTTGAG
40492609 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
40492635 CTCATTCGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:40493171 original size:19 final size:19
Alignment explanation
Indices: 40493139--40493199 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
40493129 CGCATTTTAC
* *
40493139 ATATATTTACTTTATTTATT
1 ATATATTT-TTTTATATATT
40493159 -TCATATTTTTTTATATATT
1 AT-ATATTTTTTTATATATT
*
40493178 ATATATTTTTTTATATTTT
1 ATATATTTTTTTATATATT
40493197 ATA
1 ATA
40493200 AATACATCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 29 0.81
20 7 0.19
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
ATATATTTTTTTATATATT
Found at i:40493186 original size:17 final size:17
Alignment explanation
Indices: 40493161--40493199 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
40493151 TATTTATTTC
*
40493161 ATATTTTTTTATATATT
1 ATATATTTTTATATATT
*
40493178 ATATATTTTTTTATATT
1 ATATATTTTTATATATT
*
40493195 TTATA
1 ATATA
40493200 AATACATCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
ATATATTTTTATATATT
Found at i:40493289 original size:27 final size:26
Alignment explanation
Indices: 40493232--40493291 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 26
40493222 ATTTTCTCAT
*
40493232 ATTTTATAATGTATAATATACATATC
1 ATTTTATAATGTATAATATACATAAC
* *
40493258 GTTTTCATAATTTATAATATACATAAC
1 ATTTT-ATAATGTATAATATACATAAC
40493285 ATTTTAT
1 ATTTTAT
40493292 TTTAAATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 6 0.21
27 23 0.79
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.48
Consensus pattern (26 bp):
ATTTTATAATGTATAATATACATAAC
Found at i:40496654 original size:22 final size:22
Alignment explanation
Indices: 40496620--40496675 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
40496610 CCATTTGATA
*
40496620 AATATAAATTTTAAAAATAAAT
1 AATATAAATTTTAAAAACAAAT
*
40496642 AATATATAA-TTTAATAACAAAT
1 AATATA-AATTTTAAAAACAAAT
40496664 AATA-AATATTTT
1 AATATAA-ATTTT
40496676 TGTGAGATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
20 1 0.03
21 2 0.07
22 24 0.83
23 2 0.07
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AATATAAATTTTAAAAACAAAT
Found at i:40501119 original size:18 final size:18
Alignment explanation
Indices: 40501079--40501122 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
40501069 AATTTTTATG
**
40501079 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
40501097 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
40501115 CTTGGGTT
1 ATTGGGTT
40501123 TTGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:40507264 original size:38 final size:38
Alignment explanation
Indices: 40507222--40507300 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
40507212 TTAATTAAAT
40507222 TTTAAACACCTTTGTTTCTATTGTATAAGTAATTTATA
1 TTTAAACACCTTTGTTTCTATTGTATAAGTAATTTATA
*
40507260 TTTAAACACCTTTGTTTGTATTGTATAAGTAATTTATA
1 TTTAAACACCTTTGTTTCTATTGTATAAGTAATTTATA
40507298 TTT
1 TTT
40507301 GATGTGTGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (38 bp):
TTTAAACACCTTTGTTTCTATTGTATAAGTAATTTATA
Found at i:40524293 original size:45 final size:45
Alignment explanation
Indices: 40524244--40524342 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 45
40524234 TAGATACCAT
* * * **
40524244 ATCTTGTCTCCCCGTACAGGCGGTGGAGTAGATCGAAGAAAGCAG
1 ATCTTGTCTCCCCATACAGGCGGCGGAGCAGATAAAAGAAAGCAG
* * * *
40524289 ATCTTGTATTCCCATACTGGTGGCGGAGCAGATAAAAGAAAGCAG
1 ATCTTGTCTCCCCATACAGGCGGCGGAGCAGATAAAAGAAAGCAG
40524334 ATCTTGTCT
1 ATCTTGTCT
40524343 TCATGTATTG
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.24
Consensus pattern (45 bp):
ATCTTGTCTCCCCATACAGGCGGCGGAGCAGATAAAAGAAAGCAG
Found at i:40524747 original size:44 final size:45
Alignment explanation
Indices: 40524684--40524781 Score: 144
Period size: 44 Copynumber: 2.2 Consensus size: 45
40524674 CAGTAGAATC
** *
40524684 GATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTA
1 GATCGAAGAAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTA
* *
40524728 GATCGAAGAAAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTA
1 GATCGAAGAAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTA
40524773 GATCGAAGA
1 GATCGAAGA
40524782 TACAAGTCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 31 0.65
45 17 0.35
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.27
Consensus pattern (45 bp):
GATCGAAGAAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTA
Found at i:40525309 original size:44 final size:44
Alignment explanation
Indices: 40525242--40525329 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
40525232 AAGGCCCAAT
* *
40525242 CGGCCCAAAACAGTTCCTAGTCCAACATTACAAAATTAAACAGA
1 CGGCCCAAAACAGTCCCTAGTCCAACACTACAAAATTAAACAGA
* * * *
40525286 CGGCCCAAAACGGTCCCTGGTCCAACACTACAAAGTTAAGCAGA
1 CGGCCCAAAACAGTCCCTAGTCCAACACTACAAAATTAAACAGA
40525330 AAAACCCTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.39, C:0.30, G:0.16, T:0.16
Consensus pattern (44 bp):
CGGCCCAAAACAGTCCCTAGTCCAACACTACAAAATTAAACAGA
Found at i:40525884 original size:8 final size:8
Alignment explanation
Indices: 40525871--40525900 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
40525861 CTGTTGAGTT
40525871 TTTTTTTA
1 TTTTTTTA
40525879 TTTTTTTA
1 TTTTTTTA
40525887 -TTTTTTA
1 TTTTTTTA
40525894 TTTTTTT
1 TTTTTTT
40525901 CTCATTCGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTA
Found at i:40525892 original size:15 final size:15
Alignment explanation
Indices: 40525872--40525900 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40525862 TGTTGAGTTT
40525872 TTTTTTATTTTTTTA
1 TTTTTTATTTTTTTA
40525887 TTTTTTATTTTTTT
1 TTTTTTATTTTTTT
40525901 CTCATTCGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (15 bp):
TTTTTTATTTTTTTA
Found at i:40526498 original size:22 final size:22
Alignment explanation
Indices: 40526473--40526514 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
40526463 TTTATTTTCA
40526473 TATTTT-TTTAATATATTATACT
1 TATTTTATTT-ATATATTATACT
*
40526495 TATTTTATTTATATTTTATA
1 TATTTTATTTATATATTATA
40526515 AAGTACATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TATTTTATTTATATATTATACT
Found at i:40526509 original size:33 final size:33
Alignment explanation
Indices: 40526445--40526511 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 33
40526435 TACATGCGCA
40526445 TTTTACATATATATATTATTTATTTTCATATTT
1 TTTTACATATATATATTATTTATTTTCATATTT
40526478 TTTTA-ATATATTATACTTATTT-TATTT-ATATTT
1 TTTTACATATA-TATA-TTATTTAT-TTTCATATTT
40526511 T
1 T
40526512 ATAAAGTACA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
32 5 0.16
33 17 0.55
34 9 0.29
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (33 bp):
TTTTACATATATATATTATTTATTTTCATATTT
Found at i:40526512 original size:30 final size:34
Alignment explanation
Indices: 40526444--40526512 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 34
40526434 ATACATGCGC
*
40526444 ATTTTACATATATATATTATTTATTTTCATATTT
1 ATTTTACATATATATATTACTTATTTTCATATTT
40526478 -TTTTA-ATATAT-TA-TACTTATTTT-AT-TTAT
1 ATTTTACATATATATATTACTTATTTTCATATT-T
40526507 ATTTTA
1 ATTTTA
40526513 TAAAGTACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
28 2 0.06
29 3 0.09
30 14 0.44
31 2 0.06
32 6 0.19
33 5 0.16
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (34 bp):
ATTTTACATATATATATTACTTATTTTCATATTT
Found at i:40527761 original size:75 final size:75
Alignment explanation
Indices: 40527622--40527762 Score: 169
Period size: 75 Copynumber: 1.9 Consensus size: 75
40527612 GCTTACATAT
* * * * * * *
40527622 ATGTATATGTTCTTTTATTGAATTTAGGAATGACATTTATATAAGTTTTTATGAGATACTATTAT
1 ATGTATATGTTCTTGTAATGAATTTAAGAATGAAATTTATATAAGTGTATATGAGATACGATTAT
40527687 GCCGGTATAC
66 GCCGGTATAC
* *
40527697 ATGTATATGTTCTTGTAATGAATTTAAGTATGAAATTTATAT-A-TGTATATGGAAGATTCGATT
1 ATGTATATGTTCTTGTAATGAATTTAAGAATGAAATTTATATAAGTGTATAT-G-AGATACGATT
40527760 ATG
64 ATG
40527763 TATATATATT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
73 5 0.09
74 2 0.04
75 48 0.87
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.45
Consensus pattern (75 bp):
ATGTATATGTTCTTGTAATGAATTTAAGAATGAAATTTATATAAGTGTATATGAGATACGATTAT
GCCGGTATAC
Found at i:40527943 original size:41 final size:41
Alignment explanation
Indices: 40527857--40527950 Score: 98
Period size: 41 Copynumber: 2.3 Consensus size: 41
40527847 TAGACTTTAT
** * * * * *
40527857 GTCTAGCAGATTTGATGCCGGTGAAATATTTCAAACTTTAT
1 GTCTAGCAGGCTTAATGCCGGTGAAACAATTCAAACTATAA
* **
40527898 GTCTAGTAGGCTTAATGCCGGTGAAACAATTCGGACTATAA
1 GTCTAGCAGGCTTAATGCCGGTGAAACAATTCAAACTATAA
40527939 GTCTAGCAGGCT
1 GTCTAGCAGGCT
40527951 GAAAGTCGGT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (41 bp):
GTCTAGCAGGCTTAATGCCGGTGAAACAATTCAAACTATAA
Found at i:40528164 original size:69 final size:71
Alignment explanation
Indices: 40528075--40528229 Score: 190
Period size: 69 Copynumber: 2.2 Consensus size: 71
40528065 TTGAAGAACA
* * * **
40528075 TGTATATACATTTGGTGATAATACTTGTTAGGC-ATATGTATATATGCATTC-AGCTATTCATG-
1 TGTATATACATTCGATGATAATACTTGTTAAGCAATATGTATATACACATTCGA-CTATTCATGT
40528137 TTTAAAG
65 TTTAAAG
* *
40528144 TGTATATACATTCGATGATAATATTTTTTAAGCATATATGTATATACACATTCGACTATTCATGT
1 TGTATATACATTCGATGATAATACTTGTTAAGCA-ATATGTATATACACATTCGACTATTCATGT
*
40528209 TTTAAAT
65 TTTAAAG
*
40528216 TGTATATGCATTCG
1 TGTATATACATTCG
40528230 GTTTTAAGTG
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
69 28 0.38
71 25 0.34
72 20 0.27
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (71 bp):
TGTATATACATTCGATGATAATACTTGTTAAGCAATATGTATATACACATTCGACTATTCATGTT
TTAAAG
Found at i:40529237 original size:21 final size:21
Alignment explanation
Indices: 40529208--40529261 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
40529198 TTTCTAGTGA
*
40529208 TATCACGATACCAAGGATGGG
1 TATCGCGATACCAAGGATGGG
40529229 TATCGCGATACCAAGGATGGG
1 TATCGCGATACCAAGGATGGG
40529250 TATCGCGATACC
1 TATCGCGATACC
40529262 GAGACCCTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.22, G:0.28, T:0.20
Consensus pattern (21 bp):
TATCGCGATACCAAGGATGGG
Found at i:40529903 original size:9 final size:9
Alignment explanation
Indices: 40529889--40529965 Score: 84
Period size: 9 Copynumber: 8.4 Consensus size: 9
40529879 TTTGGTTAAA
40529889 AATTACCCG
1 AATTACCCG
*
40529898 AATTACCTG
1 AATTACCCG
40529907 AATTACCCG
1 AATTACCCG
*
40529916 AATTAACCG
1 AATTACCCG
*
40529925 AATTAACCG
1 AATTACCCG
40529934 AATTA-CCG
1 AATTACCCG
*
40529942 AAAAATACCCG
1 --AATTACCCG
*
40529953 AATTACCCA
1 AATTACCCG
40529962 AATT
1 AATT
40529966 TTTTTTTTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
8 3 0.05
9 49 0.83
10 4 0.07
11 3 0.05
ACGTcount: A:0.42, C:0.26, G:0.09, T:0.23
Consensus pattern (9 bp):
AATTACCCG
Found at i:40538382 original size:18 final size:18
Alignment explanation
Indices: 40538353--40538434 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 18
40538343 TTTAGAATTT
40538353 TTTTTTGAAATTTTTATAA
1 TTTTTTG-AATTTTTATAA
40538372 TTTTTTGAATTTTTATAAA
1 TTTTTTGAATTTTTAT-AA
* *
40538391 TATTTTG-ATTTTTAAAAA
1 TTTTTTGAATTTTT-ATAA
*
40538409 TTATTTTGAACTATTTTGTAA
1 TT-TTTTGAA-T-TTTTATAA
40538430 TTTTT
1 TTTTT
40538435 GTTAGGAGAA
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
18 18 0.35
19 21 0.40
20 4 0.08
21 5 0.10
22 4 0.08
ACGTcount: A:0.30, C:0.01, G:0.06, T:0.62
Consensus pattern (18 bp):
TTTTTTGAATTTTTATAA
Found at i:40542055 original size:19 final size:19
Alignment explanation
Indices: 40542005--40542053 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
40541995 TTTCTCAATT
* * *
40542005 TAAGTATGTTAAAGTAAAA
1 TAAGTTTGTTTAATTAAAA
*
40542024 TAATTTTGTTTAATTAAAA
1 TAAGTTTGTTTAATTAAAA
40542043 TATAGTTTGTT
1 TA-AGTTTGTT
40542054 AACCTATAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (19 bp):
TAAGTTTGTTTAATTAAAA
Found at i:40552476 original size:18 final size:18
Alignment explanation
Indices: 40552455--40552498 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
40552445 GTAAAAAATA
*
40552455 ATAAAAATATTAAAATCG
1 ATAAAAATATAAAAATCG
**
40552473 ATAAAAATATAAAAATTT
1 ATAAAAATATAAAAATCG
40552491 ATAAAAAT
1 ATAAAAAT
40552499 TATAGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (18 bp):
ATAAAAATATAAAAATCG
Found at i:40552501 original size:9 final size:9
Alignment explanation
Indices: 40552448--40552507 Score: 52
Period size: 10 Copynumber: 6.6 Consensus size: 9
40552438 ACACATGGTA
*
40552448 AAAAATAAT
1 AAAAATTAT
40552457 AAAAA-TAT
1 AAAAATTAT
* *
40552465 TAAAATCGAT
1 AAAAAT-TAT
40552475 AAAAA-TAT
1 AAAAATTAT
40552483 AAAAATTTAT
1 AAAAA-TTAT
40552493 AAAAATTAT
1 AAAAATTAT
40552502 AGAAAA
1 A-AAAA
40552508 ATATTTAAAG
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
8 13 0.32
9 10 0.24
10 18 0.44
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (9 bp):
AAAAATTAT
Found at i:40552574 original size:20 final size:20
Alignment explanation
Indices: 40552549--40552592 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
40552539 AAATTGTATT
*
40552549 AAAATTTATT-TAAAATATA
1 AAAATTTATTAGAAAATATA
40552568 GAAAA-TTATTAGAAAATATA
1 -AAAATTTATTAGAAAATATA
40552588 AAAAT
1 AAAAT
40552593 ATAAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (20 bp):
AAAATTTATTAGAAAATATA
Found at i:40552693 original size:10 final size:10
Alignment explanation
Indices: 40552680--40552731 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 10
40552670 TAAAATCAAT
40552680 AAAAATATAA
1 AAAAATATAA
40552690 AAAAATATAA
1 AAAAATATAA
** *
40552700 AATTAT-TAC
1 AAAAATATAA
**
40552709 AAATTTATAA
1 AAAAATATAA
40552719 AAAAATATAA
1 AAAAATATAA
40552729 AAA
1 AAA
40552732 TAGAGAAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
9 6 0.18
10 27 0.82
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAAATATAA
Found at i:40552703 original size:37 final size:37
Alignment explanation
Indices: 40552661--40552733 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
40552651 GATAAAGATA
*
40552661 AAAATTGATTA-AAATCAATAAAAATATAAAAAAATAT
1 AAAATT-ATTACAAATCAATAAAAAAATAAAAAAATAT
** *
40552698 AAAATTATTACAAATTTATAAAAAAATATAAAAATA
1 AAAATTATTACAAATCAATAAAAAAATAAAAAAATA
40552734 GAGAAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 4 0.13
37 27 0.87
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (37 bp):
AAAATTATTACAAATCAATAAAAAAATAAAAAAATAT
Found at i:40552720 original size:46 final size:45
Alignment explanation
Indices: 40552659--40552778 Score: 116
Period size: 47 Copynumber: 2.6 Consensus size: 45
40552649 CGGATAAAGA
* *
40552659 TAAAAATTGATTAAAATCAATAAAAATATA-AAAAAATATAAAATTAT
1 TAAAAATTCA-TAAAATCAATAAAAATAGAGAAAAAATA-AAAA-TAT
* * **
40552706 TACAAATTTATAAAAAAATATAAAAATAGAGAAAAAATAAAAATAT
1 TAAAAATTCATAAAATCA-ATAAAAATAGAGAAAAAATAAAAATAT
*
40552752 TAAAAATTCATGAAAATCTATAGAAAA
1 TAAAAATTCAT-AAAATCAATA-AAAA
40552779 ATTAGTTACT
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
46 21 0.36
47 30 0.51
48 8 0.14
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.27
Consensus pattern (45 bp):
TAAAAATTCATAAAATCAATAAAAATAGAGAAAAAATAAAAATAT
Found at i:40552757 original size:17 final size:17
Alignment explanation
Indices: 40552718--40552750 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40552708 CAAATTTATA
40552718 AAAAAATATAAAAATAG
1 AAAAAATATAAAAATAG
40552735 AGAAAAA-ATAAAAATA
1 A-AAAAATATAAAAATA
40552751 TTAAAAATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (17 bp):
AAAAAATATAAAAATAG
Found at i:40555728 original size:43 final size:43
Alignment explanation
Indices: 40555638--40555741 Score: 113
Period size: 43 Copynumber: 2.4 Consensus size: 43
40555628 TACAGCATGT
* * *
40555638 TATGCGAACCATGTTATAATTTCATGCGAACCTTGCAGTGTGT
1 TATGCGAACCATGTTATATTTTCATGCGAACCTTGCAGTATGA
* * *
40555681 TATGCGAACCATGTTATATTTTCATGTG-AGCTCTGTAGTATGA
1 TATGCGAACCATGTTATATTTTCATGCGAACCT-TGCAGTATGA
* *
40555724 TATGCAAACC-TGCTATAT
1 TATGCGAACCATGTTATAT
40555742 GACATGCAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
42 10 0.19
43 42 0.81
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (43 bp):
TATGCGAACCATGTTATATTTTCATGCGAACCTTGCAGTATGA
Found at i:40555929 original size:25 final size:25
Alignment explanation
Indices: 40555901--40555958 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
40555891 AATATGCTAG
* * **
40555901 GTTGAGTGATGTGCGATCATGTTAT
1 GTTGAATGATGTGCGAACATACTAT
*
40555926 GTTGAATGCTGTGCGAACATACTAT
1 GTTGAATGATGTGCGAACATACTAT
40555951 GTTGAATG
1 GTTGAATG
40555959 GTATCTAAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.24, C:0.10, G:0.29, T:0.36
Consensus pattern (25 bp):
GTTGAATGATGTGCGAACATACTAT
Found at i:40555994 original size:25 final size:25
Alignment explanation
Indices: 40555940--40556013 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 25
40555930 AATGCTGTGC
* * *
40555940 GAACATACTATGTTGAATGGTATCTA
1 GAACATGCTATGTTGAATGATAT-AA
*
40555966 -AACATGTTATGTTGAATGATATAA
1 GAACATGCTATGTTGAATGATATAA
*
40555990 GAACATGCTATGATTGAGTGATAT
1 GAACATGCTATG-TTGAATGATAT
40556014 GCGAACCCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
24 1 0.03
25 29 0.73
26 10 0.25
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.35
Consensus pattern (25 bp):
GAACATGCTATGTTGAATGATATAA
Found at i:40557683 original size:40 final size:41
Alignment explanation
Indices: 40557604--40557689 Score: 147
Period size: 40 Copynumber: 2.1 Consensus size: 41
40557594 TGTGGATTCT
*
40557604 CCACAGCTCGTGTGAGCAGTATCGTGTAGCTTACATTTCGAC
1 CCACAGCTCGTGTGAGCAGCATC-TGTAGCTTACATTTCGAC
40557646 CCACAGCTCGTGTGAGCAGCAT-TGTAGCTTACATTTCGAC
1 CCACAGCTCGTGTGAGCAGCATCTGTAGCTTACATTTCGAC
40557686 CCAC
1 CCAC
40557690 TTTGTGTGAG
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
40 22 0.51
42 21 0.49
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (41 bp):
CCACAGCTCGTGTGAGCAGCATCTGTAGCTTACATTTCGAC
Found at i:40560618 original size:22 final size:22
Alignment explanation
Indices: 40560593--40560723 Score: 136
Period size: 22 Copynumber: 5.9 Consensus size: 22
40560583 GCAAACCCAT
40560593 GCTATGTGATATGCGAACTTAA
1 GCTATGTGATATGCGAACTTAA
* *
40560615 GCTATATGATATGCGAACTTAT
1 GCTATGTGATATGCGAACTTAA
* * * *
40560637 GCTAAAGTGACATGCCAACCTAA
1 GCT-ATGTGATATGCGAACTTAA
* * * *
40560660 GCTATATAATATGTGAACTTAT
1 GCTATGTGATATGCGAACTTAA
* *
40560682 GCTAAAGTGATATGCGAACCTAA
1 GCT-ATGTGATATGCGAACTTAA
40560705 GCTATGTGATATGCGAACT
1 GCTATGTGATATGCGAACT
40560724 ATGACTTATG
Statistics
Matches: 83, Mismatches: 24, Indels: 4
0.75 0.22 0.04
Matches are distributed among these distances:
22 51 0.61
23 32 0.39
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (22 bp):
GCTATGTGATATGCGAACTTAA
Found at i:40560631 original size:67 final size:68
Alignment explanation
Indices: 40560553--40560700 Score: 172
Period size: 67 Copynumber: 2.2 Consensus size: 68
40560543 TTATTGCAAT
* * * *
40560553 GTGATATGCGAACTTAAATTAAAATAACATGCAAACCCATGCTATGTGATATGCGAACTTAAGCT
1 GTGATATGCGAACTTAAACTAAAATAACATGCAAACCCAAGCTATATAATATGCGAACTTAAGCT
*
40560618 ATA
66 AAA
** * * * * * *
40560621 -TGATATGCGAACTTATGCTAAAGTGACATGCCAACCTAAGCTATATAATATGTGAACTTATGCT
1 GTGATATGCGAACTTAAACTAAAATAACATGCAAACCCAAGCTATATAATATGCGAACTTAAGCT
40560685 AAA
66 AAA
40560688 GTGATATGCGAAC
1 GTGATATGCGAAC
40560701 CTAAGCTATG
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
67 54 0.82
68 12 0.18
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.28
Consensus pattern (68 bp):
GTGATATGCGAACTTAAACTAAAATAACATGCAAACCCAAGCTATATAATATGCGAACTTAAGCT
AAA
Found at i:40560662 original size:45 final size:45
Alignment explanation
Indices: 40560598--40560723 Score: 198
Period size: 45 Copynumber: 2.8 Consensus size: 45
40560588 CCCATGCTAT
*
40560598 GTGATATGCGAACTTAAGCTATATGATATGCGAACTTATGCTAAA
1 GTGATATGCGAACCTAAGCTATATGATATGCGAACTTATGCTAAA
* * * *
40560643 GTGACATGCCAACCTAAGCTATATAATATGTGAACTTATGCTAAA
1 GTGATATGCGAACCTAAGCTATATGATATGCGAACTTATGCTAAA
*
40560688 GTGATATGCGAACCTAAGCTATGTGATATGCGAACT
1 GTGATATGCGAACCTAAGCTATATGATATGCGAACT
40560724 ATGACTTATG
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (45 bp):
GTGATATGCGAACCTAAGCTATATGATATGCGAACTTATGCTAAA
Found at i:40561322 original size:17 final size:17
Alignment explanation
Indices: 40561302--40561365 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 17
40561292 AGAACTTTTA
* *
40561302 TTTGGTATGAATTGTTG
1 TTTGATATGAACTGTTG
40561319 TTTGATATGAACTGTTG
1 TTTGATATGAACTGTTG
* *
40561336 TTT-ATTGTGAACTGATG
1 TTTGA-TATGAACTGTTG
* *
40561353 TTTTATGTGAACT
1 TTTGATATGAACT
40561366 ACCTATTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
16 1 0.02
17 39 0.95
18 1 0.02
ACGTcount: A:0.22, C:0.05, G:0.23, T:0.50
Consensus pattern (17 bp):
TTTGATATGAACTGTTG
Found at i:40561374 original size:18 final size:18
Alignment explanation
Indices: 40561353--40561419 Score: 71
Period size: 18 Copynumber: 3.7 Consensus size: 18
40561343 TGAACTGATG
*
40561353 TTTTATGTGAACTACCTA
1 TTTTATGTGAACTACTTA
* *
40561371 TTTTATGTGAATTGCTTA
1 TTTTATGTGAACTACTTA
* * *
40561389 CTCTATGTGAACTATTTA
1 TTTTATGTGAACTACTTA
*
40561407 TTTTATGGGAACT
1 TTTTATGTGAACT
40561420 GTAAGTCGTG
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.48
Consensus pattern (18 bp):
TTTTATGTGAACTACTTA
Found at i:40565826 original size:20 final size:20
Alignment explanation
Indices: 40565803--40565905 Score: 68
Period size: 20 Copynumber: 5.2 Consensus size: 20
40565793 AAAATACAAA
40565803 CAGGGGCACGTATGTGCATT
1 CAGGGGCACGTATGTGCATT
* * * *
40565823 CAGGGGTACCG-AAGTACAAAT
1 CAGGGGCA-CGTATGTGC-ATT
*
40565844 -AGGGGCACATATGTGCATT
1 CAGGGGCACGTATGTGCATT
* * * **
40565863 CAGGGGTACCG-AAGTACAAA
1 CAGGGGCA-CGTATGTGCATT
40565883 CAGGGGCACGTATGTGCATT
1 CAGGGGCACGTATGTGCATT
40565903 CAG
1 CAG
40565906 TAATATTTTA
Statistics
Matches: 57, Mismatches: 20, Indels: 12
0.64 0.22 0.13
Matches are distributed among these distances:
19 5 0.09
20 47 0.82
21 5 0.09
ACGTcount: A:0.29, C:0.19, G:0.32, T:0.19
Consensus pattern (20 bp):
CAGGGGCACGTATGTGCATT
Found at i:40565829 original size:40 final size:40
Alignment explanation
Indices: 40565774--40565905 Score: 219
Period size: 40 Copynumber: 3.3 Consensus size: 40
40565764 CAGAGCATGA
* * *
40565774 ATGTGCATTCAGGGGTATCAAAATACAAACAGGGGCACGT
1 ATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCACGT
* *
40565814 ATGTGCATTCAGGGGTACCGAAGTACAAATAGGGGCACAT
1 ATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCACGT
40565854 ATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCACGT
1 ATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCACGT
40565894 ATGTGCATTCAG
1 ATGTGCATTCAG
40565906 TAATATTTTA
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 85 1.00
ACGTcount: A:0.32, C:0.18, G:0.30, T:0.20
Consensus pattern (40 bp):
ATGTGCATTCAGGGGTACCGAAGTACAAACAGGGGCACGT
Found at i:40569950 original size:21 final size:21
Alignment explanation
Indices: 40569924--40569967 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
40569914 TTACTAATTC
40569924 TAAAAAT-TCTAAAATATA-TTT
1 TAAAAATCT-TAAAA-ATACTTT
40569945 TAAAAATCTTAAAAATACTTT
1 TAAAAATCTTAAAAATACTTT
40569966 TA
1 TA
40569968 TGTTAACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 3 0.14
21 17 0.81
22 1 0.05
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAAATCTTAAAAATACTTT
Found at i:40570820 original size:5 final size:5
Alignment explanation
Indices: 40570805--40570835 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
40570795 ATATTTATCT
40570805 TTTAA -TTAA TTTAA TTTAA TTTAA TTTAA TT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TT
40570836 AGAGAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTAA
Found at i:40571503 original size:13 final size:11
Alignment explanation
Indices: 40571475--40571506 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
40571465 TCTTTCAATA
40571475 TTCTCTCAAAT
1 TTCTCTCAAAT
40571486 TTCTCTCAAAT
1 TTCTCTCAAAT
*
40571497 TCCTCTCAAA
1 TTCTCTCAAA
40571507 GCTCTCTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.28, C:0.31, G:0.00, T:0.41
Consensus pattern (11 bp):
TTCTCTCAAAT
Found at i:40571512 original size:22 final size:22
Alignment explanation
Indices: 40571469--40571513 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
40571459 CTTCAATCTT
**
40571469 TCAATATTCTCTCAAATTTCTC
1 TCAATATTCTCTCAAAGCTCTC
40571491 TCAA-ATTCCTCTCAAAGCTCTC
1 TCAATATT-CTCTCAAAGCTCTC
40571513 T
1 T
40571514 TTAATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.27, C:0.31, G:0.02, T:0.40
Consensus pattern (22 bp):
TCAATATTCTCTCAAAGCTCTC
Found at i:40573600 original size:21 final size:21
Alignment explanation
Indices: 40573576--40573616 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40573566 ATTCCCTACT
* * *
40573576 GGAGGAACCAGAATCCCGGCC
1 GGAGCAACCACAACCCCGGCC
40573597 GGAGCAACCACAACCCCGGC
1 GGAGCAACCACAACCCCGGC
40573617 TGAAAGCTGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.39, G:0.29, T:0.02
Consensus pattern (21 bp):
GGAGCAACCACAACCCCGGCC
Found at i:40574574 original size:31 final size:32
Alignment explanation
Indices: 40574513--40574574 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
40574503 AAATTACAAG
40574513 AGTAATTGAATCCTAATAAAAACTCTTTAAAT
1 AGTAATTGAATCCTAATAAAAACTCTTTAAAT
40574545 AGTAATTGAATCCTAATAAAAA-TCTTTAAA
1 AGTAATTGAATCCTAATAAAAACTCTTTAAA
40574575 ATTATCTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 8 0.27
32 22 0.73
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.34
Consensus pattern (32 bp):
AGTAATTGAATCCTAATAAAAACTCTTTAAAT
Found at i:40579604 original size:23 final size:24
Alignment explanation
Indices: 40579574--40579625 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 24
40579564 AGTAGGCAAC
*
40579574 TTTTTTTTTTACGTTTTTT-TTCT
1 TTTTTTTTTTACGTTTTTTGCTCT
*
40579597 TTTTTTTTTTGCGTTTTTTGCTCT
1 TTTTTTTTTTACGTTTTTTGCTCT
40579621 TTTTT
1 TTTTT
40579626 CTGTTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.02, C:0.10, G:0.08, T:0.81
Consensus pattern (24 bp):
TTTTTTTTTTACGTTTTTTGCTCT
Found at i:40581803 original size:126 final size:125
Alignment explanation
Indices: 40581578--40581861 Score: 406
Period size: 126 Copynumber: 2.3 Consensus size: 125
40581568 GCCAAATAGG
* * * * *
40581578 AACTACTGTAACAAAAGAGCGTCCACGTGGGAGATTCTTTTAGTACTTTTGCTGATATTGAATCC
1 AACTACTGTAGCAAAAGAGCATCCACGTGGGAGATTCTTTCAGTACTTTTGCTGACAATGAATCC
* * *
40581643 TGCTTGAAGCGTTTTTGACACTATTTGCTCAGAAACATCTTTTCAAAATTATTTTTTCAGA
66 TGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTT-AGA
* * *
40581704 AACTACTGTAGCAAAAGAGCATTCACGTGGGAGTTTCTTTCAGTACTTTTGCTGACAATGCATCC
1 AACTACTGTAGCAAAAGAGCATCCACGTGGGAGATTCTTTCAGTACTTTTGCTGACAATGAATCC
** *
40581769 TGCTTAAAGCATTTTTGACACTATTTGCTCAGAAATGTCTTCTCAAAATTATTTTTTAGG
66 TGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTAGA
* * *
40581829 AACTACTATAGCAAAAGAGCGTCCACGTAGGAG
1 AACTACTGTAGCAAAAGAGCATCCACGTGGGAG
40581862 CTTTTTTAAA
Statistics
Matches: 140, Mismatches: 18, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
125 31 0.22
126 109 0.78
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (125 bp):
AACTACTGTAGCAAAAGAGCATCCACGTGGGAGATTCTTTCAGTACTTTTGCTGACAATGAATCC
TGCTTAAAGCATTTTTGACACTATTTGCTCAGAAACATCTTCTCAAAATTATTTTTTAGA
Found at i:40582195 original size:97 final size:96
Alignment explanation
Indices: 40581907--40582370 Score: 556
Period size: 97 Copynumber: 4.9 Consensus size: 96
40581897 CTTAAACCCC
* * * * *
40581907 AAACCCTAATTTGTTTGA-TTTTTCCTTAAAAACCTTAAACCCTAAACCCTAATCT-A-TTTAAA
1 AAACCCTAATTTATTTGATTTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTAA
* * *
40581969 AAAATTATAATTAATTTACTCAAGTAATCAT
66 AAATTTATAATTAATTTACTCAAGTAACCTT
40582000 AAACCCTAATTTATTTGA-TTTTTTCTTAAAAA--C----C-CTAAACCCTAATCTAATTTTTAA
1 AAACCCTAATTTATTTGATTTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTT--
* *
40582057 AAAAAATTATAATTAATTTACTCAAGTAATCTT
64 AAAAATTTATAATTAATTTACTCAAGTAACCTT
* *
40582090 AAACCCTAATTTATTTGATTTTTTTTCTTAAAAACCCTAAACACTAAACCATAATCTAATTTTTT
1 AAACCCTAATTTATTTGA-TTTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTA
*
40582155 TAAATTTATAATTAATTTACTCAAGTAACCTT
65 AAAATTTATAATTAATTTACTCAAGTAACCTT
* * *
40582187 GAATCCTAATTTATTTGATTTTTTTCCTTAAAAA-CCAAAACCACTAAACCCTAATCTAATTTTT
1 AAACCCTAATTTATTTGATTTTTTT-CTTAAAAACCCTAAA-CACTAAACCCTAATCTAA----T
** * *
40582251 TTTTTTAAATTTATAACTAATTTACTCAAGTAACCCT
60 TTTTAAAAATTTATAATTAATTTACTCAAGTAACCTT
* * *
40582288 AAACCGTAATTTATTTGATTTTTTTCTTAAAAACCATAAACACCAAACCCTAATCTAATTTTTAA
1 AAACCCTAATTTATTTGATTTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTAA
40582353 AAATTTATAATTAATTTA
66 AAATTTATAATTAATTTA
40582371 ATTAAGAAAC
Statistics
Matches: 326, Mismatches: 25, Indels: 37
0.84 0.06 0.10
Matches are distributed among these distances:
86 14 0.04
87 2 0.01
88 3 0.01
90 50 0.15
92 14 0.04
93 30 0.09
94 1 0.00
96 34 0.10
97 70 0.21
98 1 0.00
99 20 0.06
100 25 0.08
101 62 0.19
ACGTcount: A:0.39, C:0.17, G:0.03, T:0.41
Consensus pattern (96 bp):
AAACCCTAATTTATTTGATTTTTTTCTTAAAAACCCTAAACACTAAACCCTAATCTAATTTTTAA
AAATTTATAATTAATTTACTCAAGTAACCTT
Found at i:40591054 original size:23 final size:22
Alignment explanation
Indices: 40591011--40591054 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
40591001 TTCTAAGTTG
40591011 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
40591034 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
40591055 TTAGTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:40591165 original size:45 final size:45
Alignment explanation
Indices: 40591101--40591187 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
40591091 CAGATACTCG
* *
40591101 GTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCCA
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCA
40591146 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
40591188 TCGGTTCACA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (45 bp):
GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCA
Found at i:40591260 original size:51 final size:51
Alignment explanation
Indices: 40591208--40591384 Score: 196
Period size: 51 Copynumber: 3.5 Consensus size: 51
40591198 TAGTAAGCTG
* * *
40591208 CACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTG
1 CACATAGTACTACACACGTGACCATTACCATCCGGTACACGTAGTAGCCTA
* * ** * * * *
40591259 CACATAGAACTACACACGTGATCAAAACTATCTGGTACGCATAGTAGCCTA
1 CACATAGTACTACACACGTGACCATTACCATCCGGTACACGTAGTAGCCTA
* * *
40591310 CACATAGTACTACACATGCGACC--TATCATTCCGGTACACGTAGTAGCCTA
1 CACATAGTACTACACACGTGACCATTACCA-TCCGGTACACGTAGTAGCCTA
*
40591360 CACATAGTACTATACACGTGACCAT
1 CACATAGTACTACACACGTGACCAT
40591385 CACTTTCACT
Statistics
Matches: 99, Mismatches: 24, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
49 2 0.02
50 38 0.38
51 59 0.60
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.23
Consensus pattern (51 bp):
CACATAGTACTACACACGTGACCATTACCATCCGGTACACGTAGTAGCCTA
Found at i:40597432 original size:138 final size:138
Alignment explanation
Indices: 40597184--40597606 Score: 675
Period size: 138 Copynumber: 3.1 Consensus size: 138
40597174 TAGAAAAATG
* *
40597184 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTTTTTTATATTTTGACCAAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTAA
* * * *
40597249 TATAATTGTTCATAATAATAAATTTGGTAAAATATATACAATTAATATTTTTTATGAATCAAATT
66 TATAAATGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
40597314 CATATATT
131 CATATATT
* *
40597322 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTACATTTTGACTAAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTAA
* * * *
40597387 TATAAATGTTTATATTAATAAATTCGATAAAATATATACAATTAATATTTTGTACGAATGAAATT
66 TATAAATGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
40597452 CATATATT
131 CATATATT
* * *
40597460 ACTTATATTTTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTAA
* * *
40597525 TATAACTATTTCTATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAAATGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
40597590 CATATATT
131 CATATATT
*
40597598 AATTTTATT
1 AATTATATT
40597607 TATGTTCTCC
Statistics
Matches: 259, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
138 259 1.00
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCAAAATTAATTAA
TATAAATGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:40599827 original size:44 final size:43
Alignment explanation
Indices: 40599739--40599827 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 43
40599729 CCATCACAGA
**
40599739 ATCAGTTTGGGCCTTAGCCCATTCAGATACAGTCTCAGAAATAC
1 ATCAGTTTGGGCCTTAGCCCATTCAGATACAGAATCAG-AATAC
*
40599783 ATCAGTTTGGGCCTTGGCCCATATCAGATACAGAATACAG-ATAC
1 ATCAGTTTGGGCCTTAGCCCAT-TCAGATACAGAAT-CAGAATAC
40599827 A
1 A
40599828 GTAAATCAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
44 26 0.65
45 11 0.28
46 3 0.08
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (43 bp):
ATCAGTTTGGGCCTTAGCCCATTCAGATACAGAATCAGAATAC
Found at i:40604411 original size:40 final size:40
Alignment explanation
Indices: 40604340--40604485 Score: 177
Period size: 40 Copynumber: 3.6 Consensus size: 40
40604330 TGCTCAGACA
* * * *
40604340 AGCCTTACCTACTGAATCTACTAAAACGTATGCACTTTCG
1 AGCCATACCTATTGAATCTACTGAAATGTATGCACTTTCG
* * *
40604380 AGCCATACTTATTGAATCTATTGGAAA-GTATGCACTTTTG
1 AGCCATACCTATTGAATCTACT-GAAATGTATGCACTTTCG
* * *
40604420 AGCCACACCTACTGAATCTACTGAAATGTATGCACTTTCA
1 AGCCATACCTATTGAATCTACTGAAATGTATGCACTTTCG
*
40604460 AGCCATACCTATTAAATCTACTGAAA
1 AGCCATACCTATTGAATCTACTGAAA
40604486 AGAATGCTCT
Statistics
Matches: 89, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
39 4 0.04
40 82 0.92
41 3 0.03
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (40 bp):
AGCCATACCTATTGAATCTACTGAAATGTATGCACTTTCG
Found at i:40604958 original size:18 final size:19
Alignment explanation
Indices: 40604929--40604964 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
40604919 ACTTGTTTGC
*
40604929 TTAAGTTGAAATGAATGAT
1 TTAAGTTGAAATCAATGAT
40604948 TTAAG-TGAAATCAATGA
1 TTAAGTTGAAATCAATGA
40604965 CCCTATATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.33
Consensus pattern (19 bp):
TTAAGTTGAAATCAATGAT
Found at i:40606810 original size:12 final size:12
Alignment explanation
Indices: 40606793--40606820 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
40606783 ACCTTTCGTC
40606793 ATTAACTTAAGT
1 ATTAACTTAAGT
40606805 ATTAACTTAAGT
1 ATTAACTTAAGT
40606817 ATTA
1 ATTA
40606821 GAGAATGTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (12 bp):
ATTAACTTAAGT
Found at i:40607592 original size:17 final size:16
Alignment explanation
Indices: 40607568--40607600 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
40607558 TATAATATGT
40607568 TATTATTTATATTATA
1 TATTATTTATATTATA
40607584 TATTGATTTATATTATA
1 TATT-ATTTATATTATA
40607601 AAAAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
TATTATTTATATTATA
Found at i:40611678 original size:40 final size:40
Alignment explanation
Indices: 40611633--40611768 Score: 150
Period size: 40 Copynumber: 3.4 Consensus size: 40
40611623 GTTTGCATAA
40611633 AAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTTATAT
1 AAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTTATAT
* * *
40611673 AAAACGCCGCTAAAGATCGAGCATTAGCGGCGCTTTA-AGG
1 AAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTTATA-T
* * * * * *
40611713 AAAATGCCGCTAATAA-TGAGTATTAGCGGCGTTTTTTGT
1 AAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTTATAT
*
40611752 AAAAACGCCGCAAAAAA
1 -AAAACGCCGCTAAAAA
40611769 CCTAAACCCA
Statistics
Matches: 78, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 17 0.22
40 61 0.78
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATTGAGCATTAGCGGCGCTTTATAT
Found at i:40611906 original size:42 final size:41
Alignment explanation
Indices: 40611802--40611958 Score: 233
Period size: 41 Copynumber: 3.8 Consensus size: 41
40611792 CTTACCTTTT
*
40611802 AGGGCTTTAGCGGCGTTTTTGTAGAAGCGCCGCTAATGCTC
1 AGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTC
*
40611843 AGGCCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTC
1 AGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTC
* * * *
40611884 AAGGGCTTTAACGGCGTTTTTGGAGAAACGCCGCTAATACTG
1 -AGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTC
* *
40611926 AGGGCTTTAGCGGCGTTTTTGTAAAAGCGCCGC
1 AGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGC
40611959 AAAAACATTT
Statistics
Matches: 104, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
41 68 0.65
42 36 0.35
ACGTcount: A:0.20, C:0.22, G:0.31, T:0.27
Consensus pattern (41 bp):
AGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTC
Found at i:40611941 original size:83 final size:83
Alignment explanation
Indices: 40611802--40611958 Score: 242
Period size: 83 Copynumber: 1.9 Consensus size: 83
40611792 CTTACCTTTT
* * * * *
40611802 AGGGCTTTAGCGGCGTTTTTGTAGAAGCGCCGCTAATGCTCAGGCCTTTAGCGGCGTTTTTGGAG
1 AGGGCTTTAACGGCGTTTTTGGAGAAACGCCGCTAATACTCAGGCCTTTAGCGGCGTTTTTGGAA
40611867 AAGCGCCGCTAATGCTCA
66 AAGCGCCGCTAATGCTCA
* * *
40611885 AGGGCTTTAACGGCGTTTTTGGAGAAACGCCGCTAATACTGAGGGCTTTAGCGGCGTTTTTGTAA
1 AGGGCTTTAACGGCGTTTTTGGAGAAACGCCGCTAATACTCAGGCCTTTAGCGGCGTTTTTGGAA
40611950 AAGCGCCGC
66 AAGCGCCGC
40611959 AAAAACATTT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
83 66 1.00
ACGTcount: A:0.20, C:0.22, G:0.31, T:0.27
Consensus pattern (83 bp):
AGGGCTTTAACGGCGTTTTTGGAGAAACGCCGCTAATACTCAGGCCTTTAGCGGCGTTTTTGGAA
AAGCGCCGCTAATGCTCA
Found at i:40612360 original size:14 final size:14
Alignment explanation
Indices: 40612265--40612382 Score: 62
Period size: 14 Copynumber: 8.4 Consensus size: 14
40612255 TATCTCTATA
*
40612265 GTTTAAGGTTTTTG
1 GTTTAAGGTTTATG
*
40612279 GTTT-AGGCTATATG
1 GTTTAAGG-TTTATG
* *
40612293 GTAT-AGAGTTTAAG
1 GTTTAAG-GTTTATG
* *
40612307 GTTTATGGATTATGG
1 GTTTAAGGTTTAT-G
* *
40612322 GTTTAGGGGTTATG
1 GTTTAAGGTTTATG
*
40612336 ATTTATA-GTTTATG
1 GTTTA-AGGTTTATG
*
40612350 GTTTAAGGTTTAGG
1 GTTTAAGGTTTATG
* * *
40612364 GTTTAGGGGTTACG
1 GTTTAAGGTTTATG
40612378 GTTTA
1 GTTTA
40612383 TGATTTAAGG
Statistics
Matches: 79, Mismatches: 19, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
13 4 0.05
14 61 0.77
15 14 0.18
ACGTcount: A:0.21, C:0.02, G:0.31, T:0.46
Consensus pattern (14 bp):
GTTTAAGGTTTATG
Found at i:40612407 original size:42 final size:42
Alignment explanation
Indices: 40612299--40612408 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 42
40612289 TATGGTATAG
* * *
40612299 AGTTTAAGGTTTATGGATTATGGGTTTAGGGGTTATGATTTAT
1 AGTTTAAGG-TTATAGATTAAGGGTTTAGGGGTTACGATTTAT
* * * *
40612342 AGTTTATGGTT-TAAGGTTTAGGGTTTAGGGGTTACGGTTTAT
1 AGTTTAAGGTTAT-AGATTAAGGGTTTAGGGGTTACGATTTAT
40612384 -GATTTAAGGTTATAGATTAAGGGTT
1 AG-TTTAAGGTTATAGATTAAGGGTT
40612409 GGGGTTTAAG
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
41 2 0.04
42 43 0.80
43 9 0.17
ACGTcount: A:0.24, C:0.01, G:0.31, T:0.45
Consensus pattern (42 bp):
AGTTTAAGGTTATAGATTAAGGGTTTAGGGGTTACGATTTAT
Found at i:40612473 original size:7 final size:7
Alignment explanation
Indices: 40612300--40612474 Score: 70
Period size: 7 Copynumber: 24.9 Consensus size: 7
40612290 ATGGTATAGA
*
40612300 GTTTAAG
1 GTTTAGG
*
40612307 GTTTATG
1 GTTTAGG
*
40612314 GATTATGG
1 GTTTA-GG
40612322 GTTTAGG
1 GTTTAGG
* *
40612329 GGTTATG
1 GTTTAGG
* **
40612336 ATTTATA
1 GTTTAGG
*
40612343 GTTTATG
1 GTTTAGG
*
40612350 GTTTAAG
1 GTTTAGG
40612357 GTTTAGG
1 GTTTAGG
40612364 GTTTAGG
1 GTTTAGG
* *
40612371 GGTTACG
1 GTTTAGG
*
40612378 GTTTATG
1 GTTTAGG
* *
40612385 ATTTAAG
1 GTTTAGG
40612392 GTTATA-G
1 GTT-TAGG
* *
40612399 ATTAAGG
1 GTTTAGG
*
40612406 G-TTGGG
1 GTTTAGG
*
40612412 GTTTAAG
1 GTTTAGG
40612419 GTTTAGG
1 GTTTAGG
40612426 AG-TTAGGG
1 -GTTTA-GG
*
40612434 GTTGAGG
1 GTTTAGG
* *
40612441 GTTAAGA
1 GTTTAGG
40612448 G-TTAGGG
1 GTTTA-GG
40612455 GTTTAGG
1 GTTTAGG
*
40612462 ATTTAGG
1 GTTTAGG
40612469 GTTTAG
1 GTTTAG
40612475 ATTAATTAGT
Statistics
Matches: 124, Mismatches: 35, Indels: 18
0.70 0.20 0.10
Matches are distributed among these distances:
6 7 0.06
7 102 0.82
8 15 0.12
ACGTcount: A:0.22, C:0.01, G:0.36, T:0.41
Consensus pattern (7 bp):
GTTTAGG
Found at i:40612600 original size:16 final size:17
Alignment explanation
Indices: 40612581--40612622 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
40612571 AAATTATTTA
40612581 TAAATAATTT-ATATAT
1 TAAATAATTTAATATAT
40612597 TAAATAATTTAATATAT
1 TAAATAATTTAATATAT
40612614 TAAAATAAT
1 T-AAATAAT
40612623 GATTATAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 10 0.42
17 7 0.29
18 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TAAATAATTTAATATAT
Found at i:40618443 original size:43 final size:42
Alignment explanation
Indices: 40618396--40618619 Score: 286
Period size: 43 Copynumber: 5.2 Consensus size: 42
40618386 ACTGTACTTT
* *
40618396 TAGCGGCGTTTGTAACCAAAGCGTCGCTAAAGGTCTTGAGCTA
1 TAGCGGCGTTTGTAA-AAAAGCGTCGCTAAAGGTCTTGATCTA
* * *
40618439 TAGCGGCGTTTTTGAAAAAAGCGTCGCTAAAGATCATGATCTA
1 TAGCGGCGTTTGT-AAAAAAGCGTCGCTAAAGGTCTTGATCTA
* *
40618482 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGT-AAAAAAGCGTCGCTAAAGGTCTTGATCTA
*
40618525 TAGCGGCGTTTGTGAAAAAAGCGTCGCTAAAGGTCTTGTTCTA
1 TAGCGGCGTTTGT-AAAAAAGCGTCGCTAAAGGTCTTGATCTA
* * * * *
40618568 TAGCGGCGTTTGTAAAAAAGTGCCACTAAAGATCATGATCTA
1 TAGCGGCGTTTGTAAAAAAGCGTCGCTAAAGGTCTTGATCTA
*
40618610 TAGTGGCGTT
1 TAGCGGCGTT
40618620 CGTGGAAAAA
Statistics
Matches: 160, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
42 32 0.20
43 126 0.79
44 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (42 bp):
TAGCGGCGTTTGTAAAAAAGCGTCGCTAAAGGTCTTGATCTA
Found at i:40618519 original size:86 final size:85
Alignment explanation
Indices: 40618396--40618632 Score: 321
Period size: 86 Copynumber: 2.8 Consensus size: 85
40618386 ACTGTACTTT
* * * *
40618396 TAGCGGCGTTTGTAACCAAAGCGTCGCTAAAGGTCTTGAGCTATAGCGGCGTTTTTGAAAAAAGC
1 TAGCGGCGTTTGTAA-AAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAAAAAAGC
40618461 GTCGCTAAAGATCATGATCTA
65 GTCGCTAAAGATCATGATCTA
*
40618482 TAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAAAAAAGC
1 TAGCGGCGTTTGT-AAAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAAAAAAGC
* * *
40618547 GTCGCTAAAGGTCTTGTTCTA
65 GTCGCTAAAGATCATGATCTA
* * * * * * *
40618568 TAGCGGCGTTTGTAAAAAAGTGCCACTAAAGATCATGATCTATAGTGGCGTTCGTGGAAAAAGCG
1 TAGCGGCGTTTGTAAAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAAAAAAGCG
40618633 CCGCAAACGT
Statistics
Matches: 134, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
85 44 0.33
86 89 0.66
87 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (85 bp):
TAGCGGCGTTTGTAAAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGAAAAAAGCG
TCGCTAAAGATCATGATCTA
Found at i:40620185 original size:3 final size:3
Alignment explanation
Indices: 40620168--40620212 Score: 72
Period size: 3 Copynumber: 14.3 Consensus size: 3
40620158 CTTGGCAATT
40620168 TTA TTA TTTA GTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
40620213 CATCTACTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
3 34 0.85
4 6 0.15
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:40622575 original size:19 final size:19
Alignment explanation
Indices: 40622535--40622577 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
40622525 ATCTCTTTAG
* *
40622535 GCATTCATTTCATGCATGT
1 GCATTCATTGCATGCATAT
40622554 GCATTGCATTGCAT-CATAT
1 GCATT-CATTGCATGCATAT
40622573 GCATT
1 GCATT
40622578 AGATTTTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (19 bp):
GCATTCATTGCATGCATAT
Found at i:40624688 original size:144 final size:144
Alignment explanation
Indices: 40624443--40624707 Score: 368
Period size: 144 Copynumber: 1.8 Consensus size: 144
40624433 AAACTGCTAC
* * * *
40624443 CGGGGCAACATATTGGCTTATCGCAGTTTTGCTCATCAAGGTTAAGATTCCTTCTCTCTGAGTGT
1 CGGGGCAACATATTGGCTTATCACAGTTTTCCTCATCAAGGTCAAGATTCCTTCTCTCCGAGTGT
* * * * *
40624508 TGGATCAAATCTCGATTGAAGAGAAATGTTAAAAGTTATCTGTCTTGGTCAAATGCGAAAAAAGA
66 TGGATCAAATCCCAATTAAAGAGAAATGTTAAAAGTTATCCGTCTGGGTCAAATGCGAAAAAAGA
40624573 AAAAAAACTATTGT
131 AAAAAAACTATTGT
* * *** *
40624587 CGGGGTAACATATTGGCTTATCATAGTTTTCCTCATTGGGGTCAAGATTCTTTCTCTCCGAGTGT
1 CGGGGCAACATATTGGCTTATCACAGTTTTCCTCATCAAGGTCAAGATTCCTTCTCTCCGAGTGT
* * *
40624652 TGGATCAGATCCCAATTAAAGAGAAATGTTTAAAGTTATCCGTCTGGGTCGAATGC
66 TGGATCAAATCCCAATTAAAGAGAAATGTTAAAAGTTATCCGTCTGGGTCAAATGC
40624708 TCCAAAAACA
Statistics
Matches: 103, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
144 103 1.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (144 bp):
CGGGGCAACATATTGGCTTATCACAGTTTTCCTCATCAAGGTCAAGATTCCTTCTCTCCGAGTGT
TGGATCAAATCCCAATTAAAGAGAAATGTTAAAAGTTATCCGTCTGGGTCAAATGCGAAAAAAGA
AAAAAAACTATTGT
Found at i:40624984 original size:17 final size:18
Alignment explanation
Indices: 40624945--40624990 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
40624935 AAGAATTTTC
40624945 AAAAGAAAAAAAGGTAAAA
1 AAAAGAAAAAAA-GTAAAA
* *
40624964 AAAAGAAAAAAA-TGAAG
1 AAAAGAAAAAAAGTAAAA
40624981 AAAAGAAAAA
1 AAAAGAAAAA
40624991 GAAAAAGGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 13 0.52
19 12 0.48
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.04
Consensus pattern (18 bp):
AAAAGAAAAAAAGTAAAA
Found at i:40625440 original size:92 final size:95
Alignment explanation
Indices: 40625323--40625507 Score: 279
Period size: 97 Copynumber: 2.0 Consensus size: 95
40625313 TCTCATTTCG
* *
40625323 TATCTTAGCAAATTTGCTATCTTGATT-ATTTA-T-T-TCGAGCTTTGTTCTCAATAAAATTTCA
1 TATCTTAGCAAATTTGCTATCTTGATTAATTTATTATCTCCAGCTTTGTTCTCAATAAAATTACA
*
40625384 TCTTATCCATTGTGATAATCTTTTTCATCT
66 TCTTATCCATTGTAATAATCTTTTTCATCT
*
40625414 TATCTTAGCAAAATTTTCTATCTTGATTAATTTATTCATCTCCAGCTTTGTTCTCAATAAAATTA
1 TATCTTAGC-AAATTTGCTATCTTGATTAATTTATT-ATCTCCAGCTTTGTTCTCAATAAAATTA
*
40625479 CATCTTGTCCATTGTAATAATCTTTTTCA
64 CATCTTATCCATTGTAATAATCTTTTTCA
40625508 AGCATTTTTT
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
91 9 0.11
92 17 0.20
93 5 0.06
94 1 0.01
96 1 0.01
97 50 0.60
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (95 bp):
TATCTTAGCAAATTTGCTATCTTGATTAATTTATTATCTCCAGCTTTGTTCTCAATAAAATTACA
TCTTATCCATTGTAATAATCTTTTTCATCT
Found at i:40626492 original size:46 final size:46
Alignment explanation
Indices: 40626406--40627246 Score: 1037
Period size: 46 Copynumber: 18.3 Consensus size: 46
40626396 AAAAAAACAA
* * ** * * * *
40626406 ATCTTATCTTCTTGTATCAGGCAG-GGAAGTAAATCAAAGATAGTAG
1 ATCTTGTCTTCCTGTATTTGGCAGCGG-AGTAGATCGAAGAAAGCAG
* *
40626452 ATCCTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGATAGCAG
1 ATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAAAGCAG
* * * * **
40626498 ATCTTATCTTCCTATATTAGACAGCAAAGTAGATCGAAGAAAGCAG
1 ATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAAAGCAG
* * *
40626544 ATCTTGTCTTCCTGTATTAGGCAGCGGGGTAGATTGAAGAAAGCAG
1 ATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAAAGCAG
* *
40626590 ATCTTGTCTTCCTGTATTTGGCAGCAGAGTAGATCGAAGATAGCAG
1 ATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAAAGCAG
* * * * *
40626636 ATCTTGTCTTCCTGTATTAGGCAGCGAAGTAGATCAAAGATAGTAG
1 ATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAAAGCAG
* * *
40626682 ATCTTGTCTTCCTGTATTAGACAGCGGATTAGATCGAAGAAAGCAG
1 ATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAAAGCAG
* * *
40626728 ATCTTGTCTTCCTGTATTTGACAGCGGAGTAGATCGAAGATAGTAG
1 ATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAAAGCAG
* *
40626774 ATCTTGTCTTCCTGTATTAGGCAGCGGAGTATATCGAAGAAAGCAG
1 ATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAAAGCAG
* *
40626820 ATCTTGTCTTCCTGTATTTGGCAGCGAAGTAGATCGAAGATAGCAG
1 ATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAAAGCAG
*
40626866 ATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGATAGCAG
1 ATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAAAGCAG
* * * *
40626912 ATCTTGTCTTCCTATATTTTGCAGCGGAGTAAATCGAAGATAGCAG
1 ATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAAAGCAG
** * *
40626958 ATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATAAAAAAAAGTAG
1 ATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAAAGCAG
* * *
40627004 ATCTTGTCTTCCTATATTAGGCAGCGGAGTAGATCGAAGAAAGTAG
1 ATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAAAGCAG
* * **
40627050 ATCTTGTCTTCCTGTTTTTGGCAGCGGAGTAGATCGAAAAAAATAG
1 ATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAAAGCAG
*
40627096 ATCTTGTCTTCCCT-TATTAGGCAGCGGAGTAGATCGAAGAAAGCAG
1 ATCTTGTCTT-CCTGTATTTGGCAGCGGAGTAGATCGAAGAAAGCAG
* **
40627142 ATCTTGTCTTCTTGTATTTGGCAGCGGAGTAGATCGAAG-TTGCAG
1 ATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAAAGCAG
* * * * * * *
40627187 ATCTTGCCTTCTTGTA-CTGACGGCGAAGCAGATCGAAGAAA-CTAG
1 ATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAAAGC-AG
*
40627232 -TCTTGCCTTCCTGTA
1 ATCTTGTCTTCCTGTA
40627247 CTGACAGTGG
Statistics
Matches: 698, Mismatches: 92, Indels: 12
0.87 0.11 0.01
Matches are distributed among these distances:
44 32 0.05
45 23 0.03
46 638 0.91
47 5 0.01
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (46 bp):
ATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAAAGCAG
Found at i:40628867 original size:3 final size:3
Alignment explanation
Indices: 40628859--40628883 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40628849 CTTGGCAATT
40628859 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
40628884 CTACTTATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:40633331 original size:107 final size:110
Alignment explanation
Indices: 40633125--40633432 Score: 441
Period size: 107 Copynumber: 2.8 Consensus size: 110
40633115 TCAAAAAACA
*
40633125 AAAAATTTTATAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGCGCT
1 AAAAA-TTTATAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
* *
40633190 GGGTGTCGATTTTTCTCGTTCAACGAAATGGCTTAATAT-CTTTTT
65 GGGTGTCGATTTTTCTCGTTCAACCAAATAGCTTAATATCCTTTTT
* * *
40633235 AAAAATTT-TAAAT-AGGTAATGTTTTGCGTTTGGAAATTTGAGAAAACATGCCGTAAGGTGCTG
1 AAAAATTTATAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
*
40633298 GGTGTCGATTTTTCTTGTTCAACCAAATAGCTTAATATCCTTTTT
66 GGTGTCGATTTTTCTCGTTCAACCAAATAGCTTAATATCCTTTTT
** *
40633343 AAAAATTTCA-AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GGACGTGCCCTAAGGTGCT
1 AAAAATTT-ATAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
* *
40633406 GGGTTTCGA--TTTCTCGTTTAACCAAAT
65 GGGTGTCGATTTTTCTCGTTCAACCAAAT
40633433 TGCCAAATAT
Statistics
Matches: 178, Mismatches: 16, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
107 97 0.54
108 19 0.11
109 30 0.17
110 32 0.18
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.36
Consensus pattern (110 bp):
AAAAATTTATAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
GGTGTCGATTTTTCTCGTTCAACCAAATAGCTTAATATCCTTTTT
Found at i:40634612 original size:22 final size:23
Alignment explanation
Indices: 40634579--40634621 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
40634569 TTTTTATTGG
*
40634579 ATTAGTAATTTAATATATATATA
1 ATTAGTAATTTAACATATATATA
40634602 ATTA-TAATTTAACATATATA
1 ATTAGTAATTTAACATATATA
40634622 ATTAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTAGTAATTTAACATATATATA
Found at i:40638376 original size:25 final size:25
Alignment explanation
Indices: 40638339--40638650 Score: 104
Period size: 25 Copynumber: 12.5 Consensus size: 25
40638329 AAACCAAACC
** *
40638339 AAGCCTTCATGGTGATTTATTTGGG
1 AAGCCTTTGTGGTGATTTACTTGGG
* * * ***
40638364 AAGCCTTTGTGGTGAGTCACCTATA
1 AAGCCTTTGTGGTGATTTACTTGGG
* *
40638389 AAGCCTTTGTGGAGATTTATTTGGG
1 AAGCCTTTGTGGTGATTTACTTGGG
*** * * * *
40638414 AAGCCTTTACAGTAAGTCACTTGTG
1 AAGCCTTTGTGGTGATTTACTTGGG
*
40638439 AAGCTTTTGTGGTGATTTACTTGGG
1 AAGCCTTTGTGGTGATTTACTTGGG
* * * * **
40638464 AAGCCTTTGTGGCGAGTCACCTGTA
1 AAGCCTTTGTGGTGATTTACTTGGG
* ** * *
40638489 AAG-CTCTTGTAGCAATTTATTTAGG
1 AAGCCT-TTGTGGTGATTTACTTGGG
** * * * **
40638514 AAGCCTTTGTGGCAAGTCACCTGTA
1 AAGCCTTTGTGGTGATTTACTTGGG
* ** *
40638539 AAGCCCTTGTGGAAATTTATTTGGG
1 AAGCCTTTGTGGTGATTTACTTGGG
* * * * * **
40638564 AAGCCTTTCTGGCGAGTCACCTGTA
1 AAGCCTTTGTGGTGATTTACTTGGG
*
40638589 AAGCCTTTGTGGTGATTTATTTGGG
1 AAGCCTTTGTGGTGATTTACTTGGG
* * * * **
40638614 GAGCCCTTGTGGTAAGTTACTTGTA
1 AAGCCTTTGTGGTGATTTACTTGGG
*
40638639 AAGCCTATGTGG
1 AAGCCTTTGTGG
40638651 CGTAATGTCT
Statistics
Matches: 191, Mismatches: 94, Indels: 4
0.66 0.33 0.01
Matches are distributed among these distances:
24 2 0.01
25 187 0.98
26 2 0.01
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (25 bp):
AAGCCTTTGTGGTGATTTACTTGGG
Found at i:40638393 original size:50 final size:50
Alignment explanation
Indices: 40638339--40638650 Score: 338
Period size: 50 Copynumber: 6.2 Consensus size: 50
40638329 AAACCAAACC
** ** *
40638339 AAGCCTTCATGGTGATTTATTTGGGAAGCCTTTGTGGTGAGTCACCTATA
1 AAGCCTTTGTGGTGATTTATTTGGGAAGCCTTTGTGGCAAGTCACCTGTA
* *** * * *
40638389 AAGCCTTTGTGGAGATTTATTTGGGAAGCCTTTACAGTAAGTCACTTGTG
1 AAGCCTTTGTGGTGATTTATTTGGGAAGCCTTTGTGGCAAGTCACCTGTA
* * *
40638439 AAGCTTTTGTGGTGATTTACTTGGGAAGCCTTTGTGGCGAGTCACCTGTA
1 AAGCCTTTGTGGTGATTTATTTGGGAAGCCTTTGTGGCAAGTCACCTGTA
* ** *
40638489 AAG-CTCTTGTAGCAATTTATTTAGGAAGCCTTTGTGGCAAGTCACCTGTA
1 AAGCCT-TTGTGGTGATTTATTTGGGAAGCCTTTGTGGCAAGTCACCTGTA
* ** * *
40638539 AAGCCCTTGTGGAAATTTATTTGGGAAGCCTTTCTGGCGAGTCACCTGTA
1 AAGCCTTTGTGGTGATTTATTTGGGAAGCCTTTGTGGCAAGTCACCTGTA
* * * * *
40638589 AAGCCTTTGTGGTGATTTATTTGGGGAGCCCTTGTGGTAAGTTACTTGTA
1 AAGCCTTTGTGGTGATTTATTTGGGAAGCCTTTGTGGCAAGTCACCTGTA
*
40638639 AAGCCTATGTGG
1 AAGCCTTTGTGG
40638651 CGTAATGTCT
Statistics
Matches: 216, Mismatches: 44, Indels: 4
0.82 0.17 0.02
Matches are distributed among these distances:
49 1 0.00
50 214 0.99
51 1 0.00
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (50 bp):
AAGCCTTTGTGGTGATTTATTTGGGAAGCCTTTGTGGCAAGTCACCTGTA
Found at i:40638624 original size:150 final size:150
Alignment explanation
Indices: 40638353--40638625 Score: 395
Period size: 150 Copynumber: 1.8 Consensus size: 150
40638343 CTTCATGGTG
* ** * *
40638353 ATTTATTTGGGAAGCCTTTGTGGTGAGTCACCTATAAAGCCTTTGTGGAGATTTATTTGGGAAGC
1 ATTTATTTAGGAAGCCTTTGTGGCAAGTCACCTATAAAGCCCTTGTGGAAATTTATTTGGGAAGC
* * * * *
40638418 CTTTACAGTAAGTCACTTGTGAAGCTTTTGTGGTGATTTACTTGGGAAGCCTTTGTGGCGAGTCA
66 CTTTACAGCAAGTCACCTGTAAAGCCTTTGTGGTGATTTACTTGGGAAGCCCTTGTGGCGAGTCA
40638483 CCTGTAAAGCTCTTGTAGCA
131 CCTGTAAAGCTCTTGTAGCA
*
40638503 ATTTATTTAGGAAGCCTTTGTGGCAAGTCACCTGTAAAGCCCTTGTGGAAATTTATTTGGGAAGC
1 ATTTATTTAGGAAGCCTTTGTGGCAAGTCACCTATAAAGCCCTTGTGGAAATTTATTTGGGAAGC
* * * *
40638568 CTTT-CTGGCGAGTCACCTGTAAAGCCTTTGTGGTGATTTATTTGGGGAGCCCTTGTGG
66 CTTTAC-AGCAAGTCACCTGTAAAGCCTTTGTGGTGATTTACTTGGGAAGCCCTTGTGG
40638626 TAAGTTACTT
Statistics
Matches: 107, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
149 1 0.01
150 106 0.99
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (150 bp):
ATTTATTTAGGAAGCCTTTGTGGCAAGTCACCTATAAAGCCCTTGTGGAAATTTATTTGGGAAGC
CTTTACAGCAAGTCACCTGTAAAGCCTTTGTGGTGATTTACTTGGGAAGCCCTTGTGGCGAGTCA
CCTGTAAAGCTCTTGTAGCA
Found at i:40641882 original size:20 final size:21
Alignment explanation
Indices: 40641846--40641890 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
40641836 AATGTTACTA
*
40641846 AAAGAAATGTTTTCAAAATGC
1 AAAGAAATGTTTCCAAAATGC
*
40641867 AAAGAAA-GTTTCCAAAATTC
1 AAAGAAATGTTTCCAAAATGC
40641887 AAAG
1 AAAG
40641891 TGACCAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.24
Consensus pattern (21 bp):
AAAGAAATGTTTCCAAAATGC
Found at i:40650397 original size:10 final size:10
Alignment explanation
Indices: 40650382--40650411 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
40650372 TGTGTGATGA
40650382 TATAATATGT
1 TATAATATGT
40650392 TATAATATGT
1 TATAATATGT
40650402 TATAAT-TGT
1 TATAATATGT
40650411 T
1 T
40650412 TTATCATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.20
10 16 0.80
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (10 bp):
TATAATATGT
Found at i:40650692 original size:37 final size:37
Alignment explanation
Indices: 40650615--40650692 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
40650605 TTTTTTTACT
* * *
40650615 TGTTTTCGGTTGGACTAGCTCTTATAAGCATCTTGTG
1 TGTTTTCGGTTGGACTAGCTCTTAGAAGCATCTGGCG
* * *
40650652 TGTTTTTGGTTGGACTAGCTGTTAGGAGCATCTGGCG
1 TGTTTTCGGTTGGACTAGCTCTTAGAAGCATCTGGCG
40650689 TGTT
1 TGTT
40650693 ATCAGGTGGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.14, C:0.14, G:0.29, T:0.42
Consensus pattern (37 bp):
TGTTTTCGGTTGGACTAGCTCTTAGAAGCATCTGGCG
Found at i:40664244 original size:57 final size:57
Alignment explanation
Indices: 40664145--40664267 Score: 158
Period size: 57 Copynumber: 2.1 Consensus size: 57
40664135 ATAGAAATAG
* *
40664145 TGAAAATGGAGAAAAGGGAAACATTTGGAAATGATTATGGTTTTCTCCAAAATGAAAA
1 TGAAAATGGAGAAAA-GGAAACATTTGGAAATGAATACGGTTTTCTCCAAAATGAAAA
* * * * *
40664203 TGAAAATGGAGAAATA-GAATCATTTGGAAATGAATGCGGTTTTCTTCAAATTTAAAA
1 TGAAAATGGAGAAA-AGGAAACATTTGGAAATGAATACGGTTTTCTCCAAAATGAAAA
40664260 TGAAAATG
1 TGAAAATG
40664268 ACTTGGAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
57 42 0.74
58 14 0.25
59 1 0.02
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.28
Consensus pattern (57 bp):
TGAAAATGGAGAAAAGGAAACATTTGGAAATGAATACGGTTTTCTCCAAAATGAAAA
Found at i:40664757 original size:17 final size:17
Alignment explanation
Indices: 40664731--40664764 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
40664721 TCCACTCATC
40664731 TTTTCTATTTCTTCTCCT
1 TTTTCTATTTCTT-TCCT
40664749 TTTTC-ATTTCTTTCCT
1 TTTTCTATTTCTTTCCT
40664765 CTTCTTTGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTCTATTTCTTTCCT
Found at i:40665566 original size:38 final size:38
Alignment explanation
Indices: 40665524--40665614 Score: 112
Period size: 38 Copynumber: 2.4 Consensus size: 38
40665514 TTGCATGTTT
* * *
40665524 AGCATGCCTACTATTACTGTTGAATTGAATTCAAGTTA
1 AGCATGTCTACTATTACTGTTGAACTGAATACAAGTTA
* **
40665562 AGCATGTCTA-TAGATACTGTTGAACTGAATACGTGTTA
1 AGCATGTCTACTA-TTACTGTTGAACTGAATACAAGTTA
40665600 AGCATGTCTACTATT
1 AGCATGTCTACTATT
40665615 TCTATATGAT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 2 0.05
38 40 0.91
39 2 0.05
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (38 bp):
AGCATGTCTACTATTACTGTTGAACTGAATACAAGTTA
Found at i:40667349 original size:19 final size:19
Alignment explanation
Indices: 40667322--40667359 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40667312 TGATCTTTAT
* *
40667322 GAATTATAATACTTTAAAA
1 GAATAATAATACCTTAAAA
40667341 GAATAATAATACCTTAAAA
1 GAATAATAATACCTTAAAA
40667360 TCTAATAGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (19 bp):
GAATAATAATACCTTAAAA
Found at i:40667681 original size:23 final size:21
Alignment explanation
Indices: 40667639--40667682 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
40667629 TTTTATTTTT
* *
40667639 TTAAAAAATAAGTAATTAGAA
1 TTAAAAAATAAATAAATAGAA
40667660 TTAAAAAATCAAATAACATAGAA
1 TTAAAAAAT-AAATAA-ATAGAA
40667683 ATTTTAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 5 0.26
23 5 0.26
ACGTcount: A:0.64, C:0.05, G:0.07, T:0.25
Consensus pattern (21 bp):
TTAAAAAATAAATAAATAGAA
Found at i:40667864 original size:24 final size:25
Alignment explanation
Indices: 40667836--40667890 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
40667826 AAAAGAAAAG
*
40667836 AAATTGGT-TGGACAAAAATAA-TAT
1 AAATT-GTCTGGAAAAAAATAATTAT
*
40667860 TAATT-TCTGGAAAAAAATAATTAT
1 AAATTGTCTGGAAAAAAATAATTAT
40667884 AAATTGT
1 AAATTGT
40667891 AAGAGAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
22 1 0.04
23 12 0.48
24 11 0.44
25 1 0.04
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.35
Consensus pattern (25 bp):
AAATTGTCTGGAAAAAAATAATTAT
Found at i:40668194 original size:24 final size:25
Alignment explanation
Indices: 40668166--40668213 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
40668156 AATAAGATAG
*
40668166 TTATTTTAACTTTT-TATTTTTCTT
1 TTATTTTAAATTTTGTATTTTTCTT
*
40668190 TTATTTTAAATTTTGTTTTTTTCT
1 TTATTTTAAATTTTGTATTTTTCT
40668214 CTCTCCCTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (25 bp):
TTATTTTAAATTTTGTATTTTTCTT
Found at i:40697914 original size:17 final size:17
Alignment explanation
Indices: 40697892--40697927 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
40697882 GAAAAAAAAC
40697892 AACAAGAAAATAAG-AAA
1 AACAAGAAAA-AAGTAAA
40697909 AACAAGAAAAAAGTAAA
1 AACAAGAAAAAAGTAAA
40697926 AA
1 AA
40697928 AAAAAAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.78, C:0.06, G:0.11, T:0.06
Consensus pattern (17 bp):
AACAAGAAAAAAGTAAA
Found at i:40697929 original size:20 final size:20
Alignment explanation
Indices: 40697883--40697935 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
40697873 CAAAATAGTG
*
40697883 AAAAAAAACAACAAGAAAAT
1 AAAAAAAACAAGAAGAAAAT
*
40697903 AAGAAAAACAAGAA-AAAAGT
1 AAAAAAAACAAGAAGAAAA-T
*
40697923 AAAAAAAAAAAGA
1 AAAAAAAACAAGA
40697936 CAACAATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.81, C:0.06, G:0.09, T:0.04
Consensus pattern (20 bp):
AAAAAAAACAAGAAGAAAAT
Found at i:40698112 original size:57 final size:56
Alignment explanation
Indices: 40698024--40698137 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 56
40698014 TTACCCAAAC
40698024 CCATTTTTCAGACCTATATTTTTACCCAAACCCTCCCATGGACAAGTTTAAGTGGGA
1 CCATTTTTCAGACCTATATTTTTACCCAAA-CCTCCCATGGACAAGTTTAAGTGGGA
40698081 CCATTTTTCAGACCTATATTTTTACCCAAACCTCCCATGGACAAGTTTAAGTGGGA
1 CCATTTTTCAGACCTATATTTTTACCCAAACCTCCCATGGACAAGTTTAAGTGGGA
40698137 C
1 C
40698138 AGAGATGGGG
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 27 0.47
57 30 0.53
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (56 bp):
CCATTTTTCAGACCTATATTTTTACCCAAACCTCCCATGGACAAGTTTAAGTGGGA
Found at i:40698530 original size:31 final size:31
Alignment explanation
Indices: 40698492--40698556 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
40698482 AAAAAATAAA
40698492 AACATATAAATATTGGTTAATTCAATTAACC
1 AACATATAAATATTGGTTAATTCAATTAACC
*
40698523 AACATATAAATGTTGGTTAATTCAATTAACC
1 AACATATAAATATTGGTTAATTCAATTAACC
40698554 AAC
1 AAC
40698557 CAAATTAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.34
Consensus pattern (31 bp):
AACATATAAATATTGGTTAATTCAATTAACC
Found at i:40701802 original size:13 final size:13
Alignment explanation
Indices: 40701780--40701818 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
40701770 GTAAATCCAG
40701780 CTACATATTTTAA
1 CTACATATTTTAA
*
40701793 CTACA-AATTTAA
1 CTACATATTTTAA
*
40701805 CTATATATTTTAA
1 CTACATATTTTAA
40701818 C
1 C
40701819 CTGACTTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.41, C:0.15, G:0.00, T:0.44
Consensus pattern (13 bp):
CTACATATTTTAA
Found at i:40711031 original size:30 final size:30
Alignment explanation
Indices: 40710995--40711056 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
40710985 CTTATAAAAG
40710995 TTAGTTTTCTTAATAATGTTAATGTAACTC
1 TTAGTTTTCTTAATAATGTTAATGTAACTC
40711025 TTAGTTTTCTTAATAATGTTAATGTAACTC
1 TTAGTTTTCTTAATAATGTTAATGTAACTC
40711055 TT
1 TT
40711057 CAGACTTGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (30 bp):
TTAGTTTTCTTAATAATGTTAATGTAACTC
Found at i:40714905 original size:34 final size:34
Alignment explanation
Indices: 40714831--40714896 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
40714821 ATATGTATAT
* *
40714831 AAATATATATACTTATGTATAATAATACGAAATA
1 AAATATATATACGTATGTATAATAATACAAAATA
40714865 AAATATAT-TACGTATGTATAA-AATA-AAAATA
1 AAATATATATACGTATGTATAATAATACAAAATA
40714896 A
1 A
40714897 TTTAATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 6 0.20
32 4 0.13
33 12 0.40
34 8 0.27
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (34 bp):
AAATATATATACGTATGTATAATAATACAAAATA
Found at i:40716930 original size:100 final size:100
Alignment explanation
Indices: 40716826--40717037 Score: 282
Period size: 100 Copynumber: 2.1 Consensus size: 100
40716816 ACACTGCTAG
* * * * *
40716826 GGAAGTGAGATTCGCCGTTGTGGTTTTAATCTTTTTAACTACAATGTCAGGGAAGCGAGATTCAC
1 GGAAGTAAGATTCGCCGTTGTAGCTTTAATCATTTTAACTACAATGTCAGGGAAGCAAGATTCAC
40716891 CGATGTGGCTTTAATCTGTTCCACCGCACCGCCAA
66 CGATGTGGCTTTAATCTGTTCCACCGCACCGCCAA
* * * *
40716926 GGAAGTAAGATTCGCTGTTGTAGCTTTAATCATTTTAACTGCAATGTCGGGGAAGCAAGATTCAT
1 GGAAGTAAGATTCGCCGTTGTAGCTTTAATCATTTTAACTACAATGTCAGGGAAGCAAGATTCAC
* * * * *
40716991 TGTTGTGGCTTTAATCTGTTCCACTGCATCG-CATG
66 CGATGTGGCTTTAATCTGTTCCACCGCACCGCCA-A
40717026 GGAAGTAAGATT
1 GGAAGTAAGATT
40717038 TGAAATTCTT
Statistics
Matches: 97, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
99 2 0.02
100 95 0.98
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (100 bp):
GGAAGTAAGATTCGCCGTTGTAGCTTTAATCATTTTAACTACAATGTCAGGGAAGCAAGATTCAC
CGATGTGGCTTTAATCTGTTCCACCGCACCGCCAA
Found at i:40717017 original size:50 final size:50
Alignment explanation
Indices: 40716824--40717018 Score: 158
Period size: 50 Copynumber: 3.9 Consensus size: 50
40716814 CTACACTGCT
** * * * * * *
40716824 AGGGAAGTGAGATTCGCCGTTGTGGTTTTAATCTTTTTAACTACAATGTC
1 AGGGAAGCAAGATTCACTGTTGTGGCTTTAATCTGTTCAACTGCAATGTC
* * * * * ** *
40716874 AGGGAAGCGAGATTCACCGATGTGGCTTTAATCTGTTCCACCGCACCGCC
1 AGGGAAGCAAGATTCACTGTTGTGGCTTTAATCTGTTCAACTGCAATGTC
* * * * *
40716924 AAGGAAGTAAGATTCGCTGTTGTAGCTTTAATCAT-TTTAACTGCAATGTC
1 AGGGAAGCAAGATTCACTGTTGTGGCTTTAATC-TGTTCAACTGCAATGTC
* * *
40716974 GGGGAAGCAAGATTCATTGTTGTGGCTTTAATCTGTTCCACTGCA
1 AGGGAAGCAAGATTCACTGTTGTGGCTTTAATCTGTTCAACTGCA
40717019 TCGCATGGGA
Statistics
Matches: 110, Mismatches: 33, Indels: 4
0.75 0.22 0.03
Matches are distributed among these distances:
49 1 0.01
50 108 0.98
51 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (50 bp):
AGGGAAGCAAGATTCACTGTTGTGGCTTTAATCTGTTCAACTGCAATGTC
Found at i:40717029 original size:50 final size:50
Alignment explanation
Indices: 40716873--40717037 Score: 147
Period size: 50 Copynumber: 3.3 Consensus size: 50
40716863 ACTACAATGT
* * * * *
40716873 CAGGGAAGCGAGATTCACCGATGTGGCTTTAATCTGTTCCACCGCACCGC
1 CAGGGAAGCAAGATTCACTGTTGTGGCTTTAATCTGTTCCACTGCATCGC
* * * * ** *
40716923 CAAGGAAGTAAGATTCGCTGTTGTAGCTTTAATCAT-TTTAACTGCAAT-GT
1 CAGGGAAGCAAGATTCACTGTTGTGGCTTTAATC-TGTTCCACTGC-ATCGC
* *
40716973 CGGGGAAGCAAGATTCATTGTTGTGGCTTTAATCTGTTCCACTGCATCG-
1 CAGGGAAGCAAGATTCACTGTTGTGGCTTTAATCTGTTCCACTGCATCGC
*
40717022 CATGGGAAGTAAGATT
1 CA-GGGAAGCAAGATT
40717038 TGAAATTCTT
Statistics
Matches: 88, Mismatches: 22, Indels: 10
0.73 0.18 0.08
Matches are distributed among these distances:
49 4 0.05
50 82 0.93
51 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (50 bp):
CAGGGAAGCAAGATTCACTGTTGTGGCTTTAATCTGTTCCACTGCATCGC
Found at i:40717219 original size:44 final size:44
Alignment explanation
Indices: 40717140--40717257 Score: 146
Period size: 44 Copynumber: 2.7 Consensus size: 44
40717130 TTTTAATCCA
* * * *
40717140 CTCCACTGTCATCTCAAGGAAATAGGATTACTGGCTTCAATCTG
1 CTCCACTGTAATCTCAAGGAGATAAGATTTCTGGCTTCAATCTG
* * *
40717184 CTCCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATTTG
1 CTCCACTGTAATCTCAAGGAGATAAGATTTCTGGCTTCAATCTG
* * *
40717228 CTCCACTGTAACCTCATGGAGATGAGATTT
1 CTCCACTGTAATCTCAAGGAGATAAGATTT
40717258 GAAATTCTTC
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 63 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.31
Consensus pattern (44 bp):
CTCCACTGTAATCTCAAGGAGATAAGATTTCTGGCTTCAATCTG
Found at i:40717278 original size:19 final size:19
Alignment explanation
Indices: 40717254--40717294 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
40717244 TGGAGATGAG
40717254 ATTTGAAATTCTTCGGTCT
1 ATTTGAAATTCTTCGGTCT
40717273 ATTTGAAATTCTTCGGTCT
1 ATTTGAAATTCTTCGGTCT
40717292 ATT
1 ATT
40717295 CCCCTGTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.22, C:0.15, G:0.15, T:0.49
Consensus pattern (19 bp):
ATTTGAAATTCTTCGGTCT
Found at i:40717425 original size:44 final size:43
Alignment explanation
Indices: 40717378--40717773 Score: 253
Period size: 44 Copynumber: 9.0 Consensus size: 43
40717368 TTTTAATCCG
* * *
40717378 CTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTACT-GCTTCAATCTA
* * * ** *
40717422 CTCCGCTGTAATCTCAGGGGGATAAGATTTGAAATTTTTCAGTCTA
1 CTCCACTGTAATCTCAGGGAGATAAGA-TT--ACTGCTTCAATCTA
* * * * * *
40717468 TTCCCCTGTAATCTCAGGGAGATAAGA--CCTGATGCGATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTACTGCTTCAATCTA
* * * * ** * **
40717509 CTCTACTGTAATTTCAGAGAGATAAGATCCT-TTATTTTAATCCG
1 CTCCACTGTAATCTCAGGGAGATAAGAT--TACTGCTTCAATCTA
* *
40717553 CTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGATTACT-GCTTCAATCTA
* ** * * *
40717597 CTCCGCTGTAATCTCAGGGAGATAAGATT-CTTTATTTTACTCTG
1 CTCCACTGTAATCTCAGGGAGATAAGATTAC--TGCTTCAATCTA
*
40717641 CTCCACTGTAATCTC-GGAGAGATAGGATTACTAGCTTCAATCTA
1 CTCCACTGTAATCTCAGG-GAGATAAGATTACT-GCTTCAATCTA
* * *
40717685 CTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGATCTA
1 CTCCACTGTAATCTCAGGGAGATAAGAT-T--ACTGCTTCAATCTA
* * * * *
40717731 TTCCAGTGTAATCTCAGGGTGATAGGATTATCAGCTTCAATCT
1 CTCCACTGTAATCTCAGGGAGATAAGATTA-CTGCTTCAATCT
40717774 GCTTTCTTAC
Statistics
Matches: 263, Mismatches: 70, Indels: 38
0.71 0.19 0.10
Matches are distributed among these distances:
41 29 0.11
42 1 0.00
43 6 0.02
44 151 0.57
45 8 0.03
46 64 0.24
47 4 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (43 bp):
CTCCACTGTAATCTCAGGGAGATAAGATTACTGCTTCAATCTA
Found at i:40717564 original size:175 final size:175
Alignment explanation
Indices: 40717273--40717625 Score: 643
Period size: 175 Copynumber: 2.0 Consensus size: 175
40717263 TCTTCGGTCT
* *
40717273 ATTTGAAATTCTTCGGTCTATTCCCCTGTAATCTCAAGGAGATAAGGCCTGATGCGATCTACTCT
1 ATTTGAAATTCTTCAGTCTATTCCCCTGTAATCTCAAGGAGATAAGACCTGATGCGATCTACTCT
*
40717338 ACTGTAATTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAG
66 ACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAG
* *
40717403 GATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGGGATAAG
131 GATTACTGGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAG
* *
40717448 ATTTGAAATTTTTCAGTCTATTCCCCTGTAATCTCAGGGAGATAAGACCTGATGCGATCTACTCT
1 ATTTGAAATTCTTCAGTCTATTCCCCTGTAATCTCAAGGAGATAAGACCTGATGCGATCTACTCT
40717513 ACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAG
66 ACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAG
40717578 GATTACTGGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAG
131 GATTACTGGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAG
40717623 ATT
1 ATT
40717626 CTTTATTTTA
Statistics
Matches: 171, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
175 171 1.00
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (175 bp):
ATTTGAAATTCTTCAGTCTATTCCCCTGTAATCTCAAGGAGATAAGACCTGATGCGATCTACTCT
ACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAAATAG
GATTACTGGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAG
Found at i:40717608 original size:88 final size:88
Alignment explanation
Indices: 40717329--40717713 Score: 431
Period size: 88 Copynumber: 4.4 Consensus size: 88
40717319 GCCTGATGCG
* * * *
40717329 ATCTACTCTACTGTAATTTTAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCA
1 ATCTACTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCA
40717394 GGGAAATAGGATTACTGGCTTCA
66 GGGAAATAGGATTACTGGCTTCA
* * * * * *** *
40717417 ATCTGCTCCGCTGTAATCTCAGGGGGATAAGAT--TTGAAATTTTTCAGTCTATTCCCCTGTAAT
1 ATCTACTCCACTGTAATCTCAGGGAGATAAGATCCTT--TA-TTTT-AATCCGCTCCACTGTAAT
* * * * * *
40717480 CTCAGGGAGATAAGA--CCT-GATGCG
62 CTCAGGGAAATAGGATTACTGGCTTCA
* * *
40717504 ATCTACTCTACTGTAATTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCA
1 ATCTACTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCA
40717569 GGGAAATAGGATTACTGGCTTCA
66 GGGAAATAGGATTACTGGCTTCA
* * * *
40717592 ATCTACTCCGCTGTAATCTCAGGGAGATAAGATTCTTTATTTTACTCTGCTCCACTGTAATCTC-
1 ATCTACTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCA
* *
40717656 GGAGAGATAGGATTACTAGCTTCA
66 GG-GAAATAGGATTACTGGCTTCA
40717680 ATCTACTCCACTGTAATCTCAGGGAGATAAGATC
1 ATCTACTCCACTGTAATCTCAGGGAGATAAGATC
40717714 TGAAATTCTT
Statistics
Matches: 239, Mismatches: 48, Indels: 20
0.78 0.16 0.07
Matches are distributed among these distances:
85 26 0.11
86 6 0.03
87 35 0.15
88 140 0.59
89 6 0.03
90 26 0.11
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (88 bp):
ATCTACTCCACTGTAATCTCAGGGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCA
GGGAAATAGGATTACTGGCTTCA
Found at i:40718008 original size:129 final size:129
Alignment explanation
Indices: 40717764--40718000 Score: 375
Period size: 129 Copynumber: 1.8 Consensus size: 129
40717754 AGGATTATCA
* * * *
40717764 GCTTCAATCTGCTTTCTTACACTTGAAGATAAGATTCACCGTTTTCGATCTGTTCCGCTACTGCT
1 GCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCT
*
40717829 TAGGGAGACAAGATTTCTAATTTCCCAACCTAATCCACTGCTGACCAGGGATATAGGACTTGTG
66 TAGGGAGACAAGATCTCTAATTTCCCAACCTAATCCACTGCTGACCAGGGATATAGGACTTGTG
* **
40717893 GCTTAAATCTGCTTCCTTACACTTGAAGATAATATTTGCCGTCTTCGATCTGCTCCGCTACTGCT
1 GCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCT
* * *
40717958 TAGGGAGACATGATCTGTAATTTCCCAACCTATTCCACTGCTG
66 TAGGGAGACAAGATCTCTAATTTCCCAACCTAATCCACTGCTG
40718001 GTCAGGGAGC
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
129 97 1.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (129 bp):
GCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCT
TAGGGAGACAAGATCTCTAATTTCCCAACCTAATCCACTGCTGACCAGGGATATAGGACTTGTG
Found at i:40720237 original size:6 final size:6
Alignment explanation
Indices: 40720178--40720279 Score: 105
Period size: 6 Copynumber: 16.7 Consensus size: 6
40720168 TTCTCTCTTT
* * * * * ** *
40720178 TTTTCA TTTTCA TTTTGA CTTTGA TTATGA TTATGA TTTTTC TTTTGCTT
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTG--A
*
40720228 TTTTTA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA
1 TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA TTTTGA
40720276 TTTT
1 TTTT
40720280 TTTTTTAATT
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
6 78 0.95
8 4 0.05
ACGTcount: A:0.16, C:0.05, G:0.12, T:0.68
Consensus pattern (6 bp):
TTTTGA
Found at i:40720243 original size:50 final size:51
Alignment explanation
Indices: 40720174--40720282 Score: 148
Period size: 50 Copynumber: 2.2 Consensus size: 51
40720164 TTCCTTCTCT
**
40720174 CTTTTTTTCATTTTCATTTTGACTTTGATTATGATTATGATTTTTCTTTTG
1 CTTTTTTTCATTTTCATTTTGACTTTGATTATGATTATGATTTTGATTTTG
* * * *
40720225 CTTTTTTT-ATTTTGATTTTGATTTTGATTTTGATTTTGATTTTGATTTTG
1 CTTTTTTTCATTTTCATTTTGACTTTGATTATGATTATGATTTTGATTTTG
*
40720275 ATTTTTTT
1 CTTTTTTT
40720283 TTTAATTGCA
Statistics
Matches: 51, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
50 43 0.84
51 8 0.16
ACGTcount: A:0.15, C:0.06, G:0.11, T:0.69
Consensus pattern (51 bp):
CTTTTTTTCATTTTCATTTTGACTTTGATTATGATTATGATTTTGATTTTG
Found at i:40720268 original size:44 final size:44
Alignment explanation
Indices: 40720184--40720273 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
40720174 CTTTTTTTCA
** *
40720184 TTTTCATTTTGACTTTGATTATGATTATGATTTTTCTTTTGCTT
1 TTTTCATTTTGACTTTGATTATGATTATGATTTTGATTTTGATT
* * * *
40720228 TTTTTATTTTGATTTTGATTTTGATTTTGATTTTGATTTTGATT
1 TTTTCATTTTGACTTTGATTATGATTATGATTTTGATTTTGATT
40720272 TT
1 TT
40720274 GATTTTTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.16, C:0.04, G:0.12, T:0.68
Consensus pattern (44 bp):
TTTTCATTTTGACTTTGATTATGATTATGATTTTGATTTTGATT
Found at i:40720971 original size:25 final size:27
Alignment explanation
Indices: 40720942--40720998 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 27
40720932 GAAGAAAATA
*
40720942 AAAGAATAGTTA-TTCAAAAA-GAATG-
1 AAAGAATA-TTAGCTCAAAAATGAATGC
40720967 AAAGAATATTAGCTCAAAAATGAATGC
1 AAAGAATATTAGCTCAAAAATGAATGC
40720994 AAAGA
1 AAAGA
40720999 TGTATTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 3 0.11
25 15 0.54
26 5 0.18
27 5 0.18
ACGTcount: A:0.56, C:0.07, G:0.16, T:0.21
Consensus pattern (27 bp):
AAAGAATATTAGCTCAAAAATGAATGC
Found at i:40728636 original size:50 final size:51
Alignment explanation
Indices: 40728511--40728636 Score: 123
Period size: 50 Copynumber: 2.5 Consensus size: 51
40728501 TTAATCCATT
* * * * *
40728511 TAACTGCAATGCCGGGGAAGCAAAATTCATTGTTGTAGCTTCAATCTGTTC
1 TAACTGCAATGCTGGGGAAGCAAGATTCACTATTGCAGCTTCAATCTGTTC
* ** * *
40728562 -CACTGCACCGACT-GGGCAGTAAGATTCACTATTGCAGCTTCAATCT-TTC
1 TAACTGCAATG-CTGGGGAAGCAAGATTCACTATTGCAGCTTCAATCTGTTC
*
40728611 TAACTGCAATGTTGGGGAAGCAAGAT
1 TAACTGCAATGCTGGGGAAGCAAGAT
40728637 CCGTTGTTGT
Statistics
Matches: 56, Mismatches: 16, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
49 4 0.07
50 51 0.91
51 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (51 bp):
TAACTGCAATGCTGGGGAAGCAAGATTCACTATTGCAGCTTCAATCTGTTC
Found at i:40728932 original size:129 final size:130
Alignment explanation
Indices: 40728767--40729004 Score: 381
Period size: 129 Copynumber: 1.8 Consensus size: 130
40728757 GTCTATTCCA
** * * *
40728767 CTGTAACCTCAGGGAGATAAGACCTGGTGCGATCTACTCTACTGTAATTTCAGAGAGATAAGATC
1 CTGTAACCTCAGGGAGATAAGACCTAATGCGATCTACTCTACTGCAACTTCAAAGAGATAAGATC
*
40728832 ATTTATTTTAATCCGCTCCAC-TGTAA-TCTCTGGGAAATAGGATTACTGGCTTCGATCTGCTCT
66 ATTTATTTTAATCCGCTCCACTTGTAACT-TCAGGGAAATAGGATTACTGGCTTCGATCTGCTCT
40728895 G
130 G
40728896 CTGTAACCTCAGGGAGATAAGACCTAATGCGATCTACTCTACTGCAACTTCAAAGAGATAAGATC
1 CTGTAACCTCAGGGAGATAAGACCTAATGCGATCTACTCTACTGCAACTTCAAAGAGATAAGATC
* *
40728961 TTTTATTTTAATCCGCTCCACTTGTAACTTCAGGGAGATAGGAT
66 ATTTATTTTAATCCGCTCCACTTGTAACTTCAGGGAAATAGGAT
40729005 CTGTAATTTC
Statistics
Matches: 99, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
129 80 0.81
130 18 0.18
131 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.31
Consensus pattern (130 bp):
CTGTAACCTCAGGGAGATAAGACCTAATGCGATCTACTCTACTGCAACTTCAAAGAGATAAGATC
ATTTATTTTAATCCGCTCCACTTGTAACTTCAGGGAAATAGGATTACTGGCTTCGATCTGCTCTG
Found at i:40729159 original size:127 final size:128
Alignment explanation
Indices: 40728992--40730057 Score: 1636
Period size: 127 Copynumber: 8.3 Consensus size: 128
40728982 TTGTAACTTC
* * * *
40728992 AGGGAGATAGGATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAAGACTTGTAGC
1 AGGGAGACAAGATCTGTAATTT-CCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGC
* * * *
40729057 TTAAATCTGCTTCCTTACACTTGAAGGTAAGATTCACCGTCTCCGATCTGCTCCGCTACTGCTT
65 TTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTT
*
40729121 AGGGAGACAAGATCTATAA-TTCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCT
1 AGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCT
* * *
40729185 TAAATCTGCTTCCTTACACTTGAAGATAAGATTTGTCGTCTTCGATCTACTCCGCTATTGCTT
66 TAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTT
* * * *
40729248 AAGGAGACAAGATCTGTAA-TTCCAACCTATTCCACTACTGACCATGGATATAGGATTTGTGGCT
1 AGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCT
* * * *
40729312 TAAATCTGCTTCCTTACACTTGAAGATAAGATTTGCCATCTTCGATCTGCTCCACTATTGCCT
66 TAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTT
* **
40729375 AGAGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTGGTCAGGGATATAGGACTTGTGGC
1 AGGGAGACAAGATCTGTAATTT-CCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGC
* * * *
40729440 TTAAATATGCTTCCTTACACTTGAAGATAAGATTTGTCGTCTTCGATCTGCTCTGCTATTGCTT
65 TTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTT
*
40729504 AGAGAGACAAGATCTGTAATTTCCAAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGC
1 AGGGAGACAAGATCTGTAATTTCC-AACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGC
*
40729569 TTAAATATGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTT
65 TTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTT
40729633 AGGGAGACAAGATCTGTAA-TTCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCT
1 AGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCT
* * * *
40729697 TAAATCTGATTCCTTACACTTGAAGATAAGATTCGCCATCTTTGATCTGCTCCGCTACTGCTT
66 TAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTT
* * * *
40729760 AGGGAGGCAAGATCTATAATTTCCCAACCTATTCCACTACTGACCGGGGATATAGGACTTGTGGC
1 AGGGAGACAAGATCTGTAATTT-CCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGC
* * *
40729825 TTAAATCTGCTTCCTTACACTTGAAGATAAGATTTGTCGTCTTCGATCTGCTCCGCTACTGCTT
65 TTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTT
* * * *
40729889 AGGGAGACAAGATCTGTAA-TTCTAACCTATTCCACTGCTAACCATGGATATAAGACTTGTGGCT
1 AGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCT
* *
40729953 TAAATCTGCTTCCTTACACTTGAAGATAAGATTCGTCGTCTTTGATCTGCTCCGCTATTGCTT
66 TAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTT
*
40730016 AGGGAGACAAGATCTGTAATTTCCCAACCTATTCAACTGCTG
1 AGGGAGACAAGATCTGTAATTT-CCAACCTATTCCACTGCTG
40730058 GTCAGGTAGC
Statistics
Matches: 861, Mismatches: 69, Indels: 14
0.91 0.07 0.01
Matches are distributed among these distances:
127 463 0.54
128 16 0.02
129 382 0.44
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (128 bp):
AGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCT
TAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTT
Found at i:40729468 original size:256 final size:256
Alignment explanation
Indices: 40729002--40730049 Score: 1661
Period size: 256 Copynumber: 4.1 Consensus size: 256
40728992 AGGGAGATAG
* * *
40729002 GATCTGTAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAAGACTTGTAGCTTAAATCTGC
1 GATCTGTAATTTCCCAACCTATTCCACTACTGACCAGGGATATAGGACTTGTGGCTTAAATCTGC
* * *
40729067 TTCCTTACACTTGAAGGTAAGATTCACCGTCTCCGATCTGCTCCGCTACTGCTTAGGGAGACAAG
66 TTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAG
*
40729132 ATCTATAATTCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTC
131 ATCTGTAATTCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTC
* *
40729197 CTTACACTTGAAGATAAGATTTGTCGTCTTCGATCTACTCCGCTATTGCTTAAGGAGACAA
196 CTTACACTTGAAGATAAGATTCGTCGTCTTCGATCTGCTCCGCTATTGCTTAAGGAGACAA
* *
40729258 GATCTGTAA-TT-CCAACCTATTCCACTACTGACCATGGATATAGGATTTGTGGCTTAAATCTGC
1 GATCTGTAATTTCCCAACCTATTCCACTACTGACCAGGGATATAGGACTTGTGGCTTAAATCTGC
* * * * * *
40729321 TTCCTTACACTTGAAGATAAGATTTGCCATCTTCGATCTGCTCCACTATTGCCTAGAGAGACAAG
66 TTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAG
** *
40729386 ATCTGTAATTTCCCAACCTATTCCACTGCTGGTCAGGGATATAGGACTTGTGGCTTAAATATGCT
131 ATCTGTAA-TT-CCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCT
* *
40729451 TCCTTACACTTGAAGATAAGATTTGTCGTCTTCGATCTGCTCTGCTATTGCTT-AGAGAGACAA
194 TCCTTACACTTGAAGATAAGATTCGTCGTCTTCGATCTGCTCCGCTATTGCTTAAG-GAGACAA
* * *
40729514 GATCTGTAATTTCCAAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATATGC
1 GATCTGTAATTTCCCAACCTATTCCACTACTGACCAGGGATATAGGACTTGTGGCTTAAATCTGC
*
40729579 TTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTATTGCTTAGGGAGACAAG
66 TTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAG
*
40729644 ATCTGTAATTCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGATTC
131 ATCTGTAATTCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTC
* * * * * *
40729709 CTTACACTTGAAGATAAGATTCGCCATCTTTGATCTGCTCCGCTACTGCTTAGGGAGGCAA
196 CTTACACTTGAAGATAAGATTCGTCGTCTTCGATCTGCTCCGCTATTGCTTAAGGAGACAA
* *
40729770 GATCTATAATTTCCCAACCTATTCCACTACTGACCGGGGATATAGGACTTGTGGCTTAAATCTGC
1 GATCTGTAATTTCCCAACCTATTCCACTACTGACCAGGGATATAGGACTTGTGGCTTAAATCTGC
* *
40729835 TTCCTTACACTTGAAGATAAGATTTGTCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAG
66 TTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAG
* * * *
40729900 ATCTGTAATTCTAACCTATTCCACTGCTAACCATGGATATAAGACTTGTGGCTTAAATCTGCTTC
131 ATCTGTAATTCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTC
* *
40729965 CTTACACTTGAAGATAAGATTCGTCGTCTTTGATCTGCTCCGCTATTGCTTAGGGAGACAA
196 CTTACACTTGAAGATAAGATTCGTCGTCTTCGATCTGCTCCGCTATTGCTTAAGGAGACAA
40730026 GATCTGTAATTTCCCAACCTATTC
1 GATCTGTAATTTCCCAACCTATTC
40730050 AACTGCTGGT
Statistics
Matches: 726, Mismatches: 60, Indels: 12
0.91 0.08 0.02
Matches are distributed among these distances:
254 110 0.15
255 6 0.01
256 490 0.67
257 5 0.01
258 115 0.16
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (256 bp):
GATCTGTAATTTCCCAACCTATTCCACTACTGACCAGGGATATAGGACTTGTGGCTTAAATCTGC
TTCCTTACACTTGAAGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAG
ATCTGTAATTCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTC
CTTACACTTGAAGATAAGATTCGTCGTCTTCGATCTGCTCCGCTATTGCTTAAGGAGACAA
Found at i:40731060 original size:17 final size:17
Alignment explanation
Indices: 40731038--40731070 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40731028 CATTTTTGAT
40731038 TTTCATTTTTTCATTCA
1 TTTCATTTTTTCATTCA
*
40731055 TTTCATTTTTTTATTC
1 TTTCATTTTTTCATTC
40731071 CAAAATCACC
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:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTCATTTTTTCATTCA
Found at i:40741670 original size:42 final size:43
Alignment explanation
Indices: 40741596--40741677 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 43
40741586 TACATCTCGT
* * *
40741596 TGTGGACAAGCCACCAGTATTTGCAGGTAAACTGCCAGAAATA
1 TGTGGACAAACCACCAGTAATTGCAGATAAACTGCCAGAAATA
*
40741639 TGTGGATAAACCACCA-TAATTGCAGATAAACTGCCAGAA
1 TGTGGACAAACCACCAGTAATTGCAGATAAACTGCCAGAA
40741678 GTTCCTCCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
42 21 0.60
43 14 0.40
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (43 bp):
TGTGGACAAACCACCAGTAATTGCAGATAAACTGCCAGAAATA
Found at i:40743929 original size:19 final size:19
Alignment explanation
Indices: 40743876--40743930 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
40743866 TTGTCTTAAA
40743876 AATATATAATATAT-AAATT
1 AATATA-AATATATAAAATT
* *
40743895 AATAAAAAAACT-TAAAATT
1 AATATAAATA-TATAAAATT
*
40743914 TATATAAATATATAAAA
1 AATATAAATATATAAAA
40743931 GAATTAAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
18 5 0.18
19 23 0.82
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
AATATAAATATATAAAATT
Found at i:40743940 original size:29 final size:29
Alignment explanation
Indices: 40743885--40743939 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
40743875 AAATATATAA
40743885 TATATAAATTAATAAAAAAACTTAAAATT
1 TATATAAATTAATAAAAAAACTTAAAATT
*
40743914 TATATAAA-TATATAAAAGAA-TTAAAA
1 TATATAAATTA-ATAAAAAAACTTAAAA
40743940 ACTTGCCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (29 bp):
TATATAAATTAATAAAAAAACTTAAAATT
Found at i:40748684 original size:24 final size:24
Alignment explanation
Indices: 40748633--40748684 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
40748623 CAAAGCCACT
* **
40748633 AAAAACATTAAAATAAATGTTTCT
1 AAAAAAATTAAAATAAATGTTTAA
40748657 AAAAAAATTAAAAATAAAT-TTTAA
1 AAAAAAATT-AAAATAAATGTTTAA
40748681 AAAA
1 AAAA
40748685 GTCTTTATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (24 bp):
AAAAAAATTAAAATAAATGTTTAA
Found at i:40751646 original size:29 final size:28
Alignment explanation
Indices: 40751609--40751691 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 28
40751599 ACTCAATGTA
40751609 CAATATTATACATGAAGTTTGATTTTGTG
1 CAATATTATACATGAAGTTTGATTTT-TG
* * * **
40751638 CAATGTTATATACGAAGTTCAATTTTTG
1 CAATATTATACATGAAGTTTGATTTTTG
* *
40751666 CAATTTTATACATGAAATTTTGATTT
1 CAATATTATACATG-AAGTTTGATTT
40751692 GATTCAATTT
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
28 13 0.31
29 29 0.69
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (28 bp):
CAATATTATACATGAAGTTTGATTTTTG
Done.