Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 162 of 297
Found at i:54741722 original size:79 final size:81
Alignment explanation
Indices: 54741613--54741795 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
54741603 TACTCGTTCA
* *
54741613 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGAGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCG-GATCTTAACCCGG
* *
54741676 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
54741693 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
54741756 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
54741772 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
54741796 CATCATTCAA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 2 0.02
79 60 0.67
80 28 0.31
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:54741795 original size:40 final size:40
Alignment explanation
Indices: 54741611--54741795 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
54741601 GCTACTCGTT
* *
54741611 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
54741651 CAAATGCCTTCGAGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
54741691 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
54741730 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
54741771 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
54741796 CATCATTCAA
Statistics
Matches: 124, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 78 0.63
41 12 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:54742418 original size:17 final size:18
Alignment explanation
Indices: 54742385--54742419 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
54742375 ATCATATATA
54742385 AAAAATTTTGAACATTTAG
1 AAAAATTTT-AACATTTAG
54742404 AAAAATTTT-ACATTTA
1 AAAAATTTTAACATTTA
54742420 TGCCCGTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (18 bp):
AAAAATTTTAACATTTAG
Found at i:54750187 original size:49 final size:48
Alignment explanation
Indices: 54750081--54750222 Score: 182
Period size: 49 Copynumber: 3.0 Consensus size: 48
54750071 CAACCGATAG
* * *
54750081 GTACCTATACCAAGGCCTGTAGCCAAATCAAGGTAACTTA-TC-C-CGGA
1 GTACCTATACCATGGCCCGTAGCCAAATCAAGGT-A-TTACTCTCACAGA
* *
54750128 GTACCTATACCATGGCCCGTAGTCAAATCAAGGTATTACTCCTCACATA
1 GTACCTATACCATGGCCCGTAGCCAAATCAAGGTATTACT-CTCACAGA
*
54750177 GTACCTATACCATGGGCCGTAGCCAAATCAAGGTATTACTCTCACA
1 GTACCTATACCATGGCCCGTAGCCAAATCAAGGTATTACTCTCACA
54750223 CAAAGTGCCG
Statistics
Matches: 84, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
45 3 0.04
46 2 0.02
47 32 0.38
48 7 0.08
49 40 0.48
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (48 bp):
GTACCTATACCATGGCCCGTAGCCAAATCAAGGTATTACTCTCACAGA
Found at i:54761979 original size:31 final size:31
Alignment explanation
Indices: 54761944--54762039 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 31
54761934 ATCGGCATTG
54761944 AGTAATGAAAATAATTTACGTTTGATGATAA
1 AGTAATGAAAATAATTTACGTTTGATGATAA
* * * *
54761975 AGTAATG--AATGAGTT-C---T-AAGCATTA
1 AGTAATGAAAATAATTTACGTTTGATG-ATAA
*
54762000 AGTAATGAAAAGAATTTACGTTTGATGATAA
1 AGTAATGAAAATAATTTACGTTTGATGATAA
54762031 AGTAATGAA
1 AGTAATGAA
54762040 TGAGTTCTAG
Statistics
Matches: 48, Mismatches: 9, Indels: 16
0.66 0.12 0.22
Matches are distributed among these distances:
24 2 0.04
25 11 0.23
27 5 0.10
28 2 0.04
29 6 0.12
31 20 0.42
32 2 0.04
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.32
Consensus pattern (31 bp):
AGTAATGAAAATAATTTACGTTTGATGATAA
Found at i:54762004 original size:56 final size:56
Alignment explanation
Indices: 54761938--54762048 Score: 204
Period size: 56 Copynumber: 2.0 Consensus size: 56
54761928 TTATGAATCG
* *
54761938 GCATTGAGTAATGAAAATAATTTACGTTTGATGATAAAGTAATGAATGAGTTCTAA
1 GCATTAAGTAATGAAAAGAATTTACGTTTGATGATAAAGTAATGAATGAGTTCTAA
54761994 GCATTAAGTAATGAAAAGAATTTACGTTTGATGATAAAGTAATGAATGAGTTCTA
1 GCATTAAGTAATGAAAAGAATTTACGTTTGATGATAAAGTAATGAATGAGTTCTA
54762049 GTATTGAAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.33
Consensus pattern (56 bp):
GCATTAAGTAATGAAAAGAATTTACGTTTGATGATAAAGTAATGAATGAGTTCTAA
Found at i:54762442 original size:45 final size:45
Alignment explanation
Indices: 54762292--54762469 Score: 207
Period size: 45 Copynumber: 3.9 Consensus size: 45
54762282 ATGTATATGA
* * *
54762292 GGCATCGACATGTGAATTCCAATATGTGATGTGCGAGTAAGACCAT
1 GGCATCGATATGTG-ATTCCGATATATGATGTGCGAGTAAGACCAT
* * * *
54762338 GGCATCGATGTGTGATTCCTATACATG-TGTGCAAGTAAGACCATGTTT
1 GGCATCGATATGTGATTCCGATATATGATGTGCGAGTAAGACCA----T
* *
54762386 GGCATCGATATGTGATTGCGATATATGATATGCGAGTAAGACCAT
1 GGCATCGATATGTGATTCCGATATATGATGTGCGAGTAAGACCAT
*
54762431 GGCATCGATATGTGATTCCGATATATG-TGTGTGAGTAAG
1 GGCATCGATATGTGATTCCGATATATGATGTGCGAGTAAG
54762470 TCCACGTTTT
Statistics
Matches: 112, Mismatches: 15, Indels: 12
0.81 0.11 0.09
Matches are distributed among these distances:
44 25 0.22
45 37 0.33
46 12 0.11
48 24 0.21
49 14 0.12
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (45 bp):
GGCATCGATATGTGATTCCGATATATGATGTGCGAGTAAGACCAT
Found at i:54762459 original size:93 final size:94
Alignment explanation
Indices: 54762292--54762461 Score: 261
Period size: 93 Copynumber: 1.8 Consensus size: 94
54762282 ATGTATATGA
* * *
54762292 GGCATCGACATGTGAATTCCAATATGTGATGTGCGAGTAAGACCATGGCATCGATGTGTGATTCC
1 GGCATCGACATGTGAATTCCAATATATGATATGCGAGTAAGACCATGGCATCGATATGTGATTCC
*
54762357 TATACATGTGTGCAAGTAAGACCATGTTT
66 GATACATGTGTGCAAGTAAGACCATGTTT
* * *
54762386 GGCATCGATATGTG-ATTGCGATATATGATATGCGAGTAAGACCATGGCATCGATATGTGATTCC
1 GGCATCGACATGTGAATTCCAATATATGATATGCGAGTAAGACCATGGCATCGATATGTGATTCC
*
54762450 GATATATGTGTG
66 GATACATGTGTG
54762462 TGAGTAAGTC
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
93 55 0.81
94 13 0.19
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (94 bp):
GGCATCGACATGTGAATTCCAATATATGATATGCGAGTAAGACCATGGCATCGATATGTGATTCC
GATACATGTGTGCAAGTAAGACCATGTTT
Found at i:54767639 original size:40 final size:41
Alignment explanation
Indices: 54767591--54767756 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 41
54767581 AGACTAAGAT
*
54767591 CCGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGCTGACTATATCCGGGCTAAGTC
* *
54767631 CCGAAGGCATTCGTGCGAG-TTACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGCTGACTATATCCGGGCTAAGTC
* *
54767671 CTGAAGGCAATTGTGCGAGCT-ACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCGAGCTGACTATATCCGGGCTAAGTC
* *
54767711 CCGAAGGCATTTGTGCGAGTTG-CTATATCC-GGCTAAATC
1 CCGAAGGCATTTGTGCGAGCTGACTATATCCGGGCTAAGTC
*
54767750 CCAAAGG
1 CCGAAGG
54767757 TACTTGGGTT
Statistics
Matches: 113, Mismatches: 11, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
39 14 0.12
40 98 0.87
41 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.25
Consensus pattern (41 bp):
CCGAAGGCATTTGTGCGAGCTGACTATATCCGGGCTAAGTC
Found at i:54767717 original size:80 final size:79
Alignment explanation
Indices: 54767584--54767750 Score: 250
Period size: 80 Copynumber: 2.1 Consensus size: 79
54767574 GATAACCAGA
* *
54767584 CTAAGATCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCGA
1 CTAAGATCCGAAGGCAATTGTGCGAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCGA
54767649 GTTACTATATCCGGG
66 GTTACTATATCC-GG
*
54767664 CTAAG-TCCTGAAGGCAATTGTGCGAGCT-ACTATATCCGGGCTAAGTCCCGAAGGCATTTGTGC
1 CTAAGATCC-GAAGGCAATTGTGCGAG-TGACTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
*
54767727 GAGTTGCTATATCCGG
64 GAGTTACTATATCCGG
54767743 CTAA-ATCC
1 CTAAGATCC
54767751 CAAAGGTACT
Statistics
Matches: 80, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
79 12 0.15
80 67 0.84
81 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.26
Consensus pattern (79 bp):
CTAAGATCCGAAGGCAATTGTGCGAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCGA
GTTACTATATCCGG
Found at i:54787060 original size:41 final size:41
Alignment explanation
Indices: 54787015--54787097 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
54787005 TTTAAAAGAG
* * *
54787015 AAAAACTTCTATATGTTTTTATTGCGCCATTGTCATGGTCA
1 AAAAACTTCTAAATGTCTTTACTGCGCCATTGTCATGGTCA
54787056 AAAAACTTCTAAATGTCTTTACTGCGCCATTGTCATGGTCA
1 AAAAACTTCTAAATGTCTTTACTGCGCCATTGTCATGGTCA
54787097 A
1 A
54787098 TGTGATCTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.37
Consensus pattern (41 bp):
AAAAACTTCTAAATGTCTTTACTGCGCCATTGTCATGGTCA
Found at i:54788982 original size:27 final size:27
Alignment explanation
Indices: 54788951--54789297 Score: 299
Period size: 27 Copynumber: 12.9 Consensus size: 27
54788941 TTAGTTTACC
*
54788951 AAATTAACAAAATACCCCTGATTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
* * * * *
54788978 AAATTACTAGAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGATTTGTA
* * *
54789005 AAATCACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
* * **
54789032 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCCTGATTTGTA
* *
54789059 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
* * *
54789086 AAATTACTAAAATACCCTTTG-TTTATA
1 AAATTACCAAAATACCC-CTGATTTGTA
* *
54789113 AAATCACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
*
54789140 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGATTTGTA
**
54789167 AAATTTTC-AAATACCCCT-AGTTTGTA
1 AAATTACCAAAATACCCCTGA-TTTGTA
* *
54789193 AAATTACCAAAATATCCCTGATTTGTG
1 AAATTACCAAAATACCCCTGATTTGTA
*** **
54789220 AAATTATTGAAATA-CCCTCGACCTGTA
1 AAATTACCAAAATACCCCT-GATTTGTA
*** *
54789247 AAATTATTGAAATA-CCCTCGACTTGTA
1 AAATTACCAAAATACCCCT-GATTTGTA
* *
54789274 AAATTACCAAAGTACCCTTGATTT
1 AAATTACCAAAATACCCCTGATTT
54789298 ACAGAATTAC
Statistics
Matches: 271, Mismatches: 42, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
26 28 0.10
27 236 0.87
28 7 0.03
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGATTTGTA
Found at i:54789016 original size:54 final size:54
Alignment explanation
Indices: 54788958--54789211 Score: 357
Period size: 54 Copynumber: 4.7 Consensus size: 54
54788948 ACCAAATTAA
* * *
54788958 CAAAATACCCCTGATTTGTAAAATTACTAGAATACCCTTGGTTTATAAAATCAC
1 CAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTATAAAATCAC
* * *
54789012 CAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTAC
1 CAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTATAAAATCAC
* * *
54789066 CAAAATACCCTTGGTTTGTAAAATTACTAAAATACCCTTTGTTTATAAAATCAC
1 CAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTATAAAATCAC
* * ***
54789120 CAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTTT
1 CAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTATAAAATCAC
*
54789174 C-AAATACCCCTAGTTTGTAAAATTACCAAAATATCCCT
1 CAAAATACCCCTGGTTTGTAAAATTACCAAAATA-CCCT
54789212 GATTTGTGAA
Statistics
Matches: 179, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
53 31 0.17
54 148 0.83
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (54 bp):
CAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTATAAAATCAC
Found at i:54789088 original size:81 final size:81
Alignment explanation
Indices: 54788951--54789225 Score: 354
Period size: 81 Copynumber: 3.4 Consensus size: 81
54788941 TTAGTTTACC
* * * * * *
54788951 AAATTAACAAAATACCCCTGATTTGTAAAATTACTAGAATACCCTTGGTTTATAAAATCACCAAA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAA
*
54789016 ATACCCTTGGTTTGTA
66 ATACCCTTAGTTTGTA
* ** *
54789032 AAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCTTGGTTTGTAAAATTACTAAA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAA
* *
54789097 ATACCCTTTGTTTATA
66 ATACCCTTAGTTTGTA
* * **
54789113 AAATCACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGGTTTGTAAAATTTTC-AA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAA
*
54789177 ATACCCCTAGTTTGTA
66 ATACCCTTAGTTTGTA
* * *
54789193 AAATTACCAAAATATCCCTGATTTGTGAAATTA
1 AAATTACCAAAATACCCCTGGTTTGTAAAATTA
54789226 TTGAAATACC
Statistics
Matches: 167, Mismatches: 27, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
80 44 0.26
81 123 0.74
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (81 bp):
AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAA
ATACCCTTAGTTTGTA
Found at i:54789305 original size:27 final size:26
Alignment explanation
Indices: 54789273--54789347 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 26
54789263 CTCGACTTGT
54789273 AAAATTACCAAAGTACCCTTGATTTAC
1 AAAATTACCAAA-TACCCTTGATTTAC
* * *
54789300 AGAATTA-CAATTTTACCCTCGATTTAC
1 AAAATTACCAA--ATACCCTTGATTTAC
54789327 AAAATTACCGAAATACCCTTG
1 AAAATTACC-AAATACCCTTG
54789348 TAGGGTAGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
26 3 0.08
27 32 0.84
28 1 0.03
29 2 0.05
ACGTcount: A:0.39, C:0.23, G:0.08, T:0.31
Consensus pattern (26 bp):
AAAATTACCAAATACCCTTGATTTAC
Found at i:54789639 original size:27 final size:27
Alignment explanation
Indices: 54789329--54789658 Score: 428
Period size: 27 Copynumber: 12.3 Consensus size: 27
54789319 CGATTTACAA
*
54789329 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
54789356 AAATACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54789383 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54789410 AATTACCGCAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
54789437 AATTATCGCAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
54789464 AATTACCGGAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
54789491 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
54789518 AATTACTGAAATAACCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
54789545 AAGTATCGCAACACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54789572 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
54789599 AATTACTAAAATACCCATGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * * *
54789626 AATTATCGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
54789652 AATTACC
1 AATTACC
54789659 AATTTGCCCC
Statistics
Matches: 264, Mismatches: 39, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
26 15 0.06
27 249 0.94
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:54790145 original size:22 final size:21
Alignment explanation
Indices: 54790085--54790149 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
54790075 TTAAATCCTG
*
54790085 CTGATTATGGCTTCGTGTCAAC
1 CTGATTATGGCTT-GTGCCAAC
* *
54790107 CT-ACATATAGCTCTGTGCCAAC
1 CTGA-TTATGGCT-TGTGCCAAC
54790129 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCT-TGTGCCAA
54790150 ACGTATTTGC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 1 0.03
22 31 0.91
23 2 0.06
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (21 bp):
CTGATTATGGCTTGTGCCAAC
Found at i:54790338 original size:27 final size:27
Alignment explanation
Indices: 54790308--54790409 Score: 107
Period size: 27 Copynumber: 3.8 Consensus size: 27
54790298 ATTCTGTTAA
* * *
54790308 GTGGCTTTGCTACATTATCTGTTTCTG
1 GTGGCTATGCCACAATATCTGTTTCTG
54790335 GTGGCTATGCCACAAATATCTG-TTCTG
1 GTGGCTATGCCAC-AATATCTGTTTCTG
* * *
54790362 GTGGCTCTGCCACAATATCTATATCTG
1 GTGGCTATGCCACAATATCTGTTTCTG
* * *
54790389 GTGACTCTGTCACAATATCTG
1 GTGGCTATGCCACAATATCTG
54790410 ATAACTGAGC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
26 7 0.11
27 50 0.78
28 7 0.11
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.37
Consensus pattern (27 bp):
GTGGCTATGCCACAATATCTGTTTCTG
Found at i:54790381 original size:54 final size:53
Alignment explanation
Indices: 54790308--54790409 Score: 123
Period size: 54 Copynumber: 1.9 Consensus size: 53
54790298 ATTCTGTTAA
* * * * * *
54790308 GTGGCTTTGCTACATTATCTGTTTCTGGTGGCTATGCCACAAATATCTGTTCTG
1 GTGGCTCTGCCACAATATCTATATCTGGTGACTATGCCAC-AATATCTGTTCTG
* *
54790362 GTGGCTCTGCCACAATATCTATATCTGGTGACTCTGTCACAATATCTG
1 GTGGCTCTGCCACAATATCTATATCTGGTGACTATGCCACAATATCTG
54790410 ATAACTGAGC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
53 8 0.20
54 32 0.80
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.37
Consensus pattern (53 bp):
GTGGCTCTGCCACAATATCTATATCTGGTGACTATGCCACAATATCTGTTCTG
Found at i:54790585 original size:6 final size:6
Alignment explanation
Indices: 54790546--54790665 Score: 72
Period size: 6 Copynumber: 19.3 Consensus size: 6
54790536 TTGCATTCAC
*
54790546 ATTCTG ATTTTAG ATTCTG -TTACTTG ATAT-TG ATTCTG ATT-TGG ATTCTG
1 ATTCTG ATTCT-G ATTCTG ATT-C-TG AT-TCTG ATTCTG ATTCT-G ATTCTG
* * *
54790596 -TTACCTG ATTCTG ATTCTG ATTCTG -TCACCTA ATTCTA ATTCTG ATTCTG
1 ATT--CTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG
54790646 ATTCTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG A-TTCTG AT
54790666 AATGTTTCTT
Statistics
Matches: 92, Mismatches: 6, Indels: 32
0.71 0.05 0.25
Matches are distributed among these distances:
5 8 0.09
6 65 0.71
7 14 0.15
8 4 0.04
9 1 0.01
ACGTcount: A:0.20, C:0.16, G:0.15, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:54790596 original size:31 final size:31
Alignment explanation
Indices: 54790546--54790617 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
54790536 TTGCATTCAC
*
54790546 ATTCTGATTTTAGATTCTGTTACTTGATAT-TG
1 ATTCTGA-TTTAGATTCTGTTACCTGAT-TCTG
*
54790578 ATTCTGATTTGGATTCTGTTACCTGATTCTG
1 ATTCTGATTTAGATTCTGTTACCTGATTCTG
54790609 ATTCTGATT
1 ATTCTGATT
54790618 CTGTCACCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 1 0.03
31 29 0.78
32 7 0.19
ACGTcount: A:0.19, C:0.12, G:0.17, T:0.51
Consensus pattern (31 bp):
ATTCTGATTTAGATTCTGTTACCTGATTCTG
Found at i:54790604 original size:25 final size:25
Alignment explanation
Indices: 54790576--54790645 Score: 97
Period size: 25 Copynumber: 2.8 Consensus size: 25
54790566 TACTTGATAT
*
54790576 TGATTCTGATT-TGGATTCTGTTACC
1 TGATTCTGATTCT-GATTCTGTCACC
54790601 TGATTCTGATTCTGATTCTGTCACC
1 TGATTCTGATTCTGATTCTGTCACC
* *
54790626 TAATTCTAATTCTGATTCTG
1 TGATTCTGATTCTGATTCTG
54790646 ATTCTGATTC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
25 40 0.98
26 1 0.02
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.47
Consensus pattern (25 bp):
TGATTCTGATTCTGATTCTGTCACC
Found at i:54792985 original size:46 final size:46
Alignment explanation
Indices: 54792932--54793050 Score: 211
Period size: 46 Copynumber: 2.6 Consensus size: 46
54792922 ACATCTCTCA
* *
54792932 CATTAGCCATTTGGCTTTACCACATATCCATCTCATACACGTTTCG
1 CATTAGCCATTCGGCTTTACCACATATCCATCTCATACACATTTCG
*
54792978 CATTAGCCATTCGGCTTTACCTCATATCCATCTCATACACATTTCG
1 CATTAGCCATTCGGCTTTACCACATATCCATCTCATACACATTTCG
54793024 CATTAGCCATTCGGCTTTACCACATAT
1 CATTAGCCATTCGGCTTTACCACATAT
54793051 ATACACTTCC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.24, C:0.31, G:0.10, T:0.34
Consensus pattern (46 bp):
CATTAGCCATTCGGCTTTACCACATATCCATCTCATACACATTTCG
Found at i:54793188 original size:37 final size:37
Alignment explanation
Indices: 54793086--54793196 Score: 104
Period size: 37 Copynumber: 3.0 Consensus size: 37
54793076 GCCTTTTTGC
54793086 CTTATCACATATATGCATGTTCACATTCATCACATTGG
1 CTTATCACATATATGCATGTTCACATTCATCACATT-G
* * * * * *
54793124 C-CATTCGGCCT-TATCACAT-AT-ATATTCATCACATTG
1 CTTA-TC-ACATATAT-GCATGTTCACATTCATCACATTG
54793160 CTTATCACATATATGCATGTTCACATTCATCACATTG
1 CTTATCACATATATGCATGTTCACATTCATCACATTG
54793197 GCCATTCGGC
Statistics
Matches: 54, Mismatches: 12, Indels: 15
0.67 0.15 0.19
Matches are distributed among these distances:
35 5 0.09
36 8 0.15
37 29 0.54
38 7 0.13
39 5 0.09
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.37
Consensus pattern (37 bp):
CTTATCACATATATGCATGTTCACATTCATCACATTG
Found at i:54793218 original size:47 final size:47
Alignment explanation
Indices: 54793160--54793335 Score: 316
Period size: 47 Copynumber: 3.7 Consensus size: 47
54793150 CATCACATTG
54793160 CTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
*
54793207 CTTATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
54793254 CTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
* **
54793301 CTTATCTCATATATGCACATTCACATTCATCACAT
1 CTTATCACATATATGCATGTTCACATTCATCACAT
54793336 AAAATCCTAA
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 124 1.00
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (47 bp):
CTTATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGC
Found at i:54793263 original size:22 final size:22
Alignment explanation
Indices: 54793235--54793306 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
54793225 GTTCACATTC
54793235 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
* * *
54793257 ATCACATATATG-CATGTTC-ACATT
1 ATCACAT-T-GGCCA--TTCGGCCTT
54793281 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
54793304 ATC
1 ATC
54793307 TCATATATGC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 13 0.35
23 7 0.19
24 7 0.19
25 10 0.27
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:54793367 original size:94 final size:91
Alignment explanation
Indices: 54793163--54793356 Score: 250
Period size: 94 Copynumber: 2.1 Consensus size: 91
54793153 CACATTGCTT
* **
54793163 ATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTT
1 ATCAAATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCACATT
** * *
54793228 CACATTCATCACATTGGCCATTCGGCCTT
66 CACATTCATCACATT-GAAAAT--GCCTA
*
54793257 ATCACATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCACATT
1 ATCAAATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCACATT
54793322 CACATTCATCACA-T-AAAAT-CCTAA
66 CACATTCATCACATTGAAAATGCCT-A
54793346 ATCAAAATATA
1 ATC-AAATATA
54793357 AATTTTCATG
Statistics
Matches: 91, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
88 3 0.03
89 3 0.03
90 6 0.07
91 2 0.02
93 1 0.01
94 76 0.84
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.34
Consensus pattern (91 bp):
ATCAAATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCACATT
CACATTCATCACATTGAAAATGCCTA
Found at i:54796098 original size:35 final size:35
Alignment explanation
Indices: 54796052--54796121 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
54796042 ACAAAAATAG
54796052 GCCATTTTACCAAGCCTTTTTGCCACCCATTTTGC
1 GCCATTTTACCAAGCCTTTTTGCCACCCATTTTGC
*
54796087 GCCATTTTACCAAGTCTTTTTGCCACCCATTTTGC
1 GCCATTTTACCAAGCCTTTTTGCCACCCATTTTGC
54796122 ACATACTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.17, C:0.33, G:0.11, T:0.39
Consensus pattern (35 bp):
GCCATTTTACCAAGCCTTTTTGCCACCCATTTTGC
Found at i:54796978 original size:40 final size:40
Alignment explanation
Indices: 54796923--54797016 Score: 125
Period size: 40 Copynumber: 2.4 Consensus size: 40
54796913 CGATATCTCA
54796923 CACACTAAGTGCCATACATAGCCGAAGATATCTTAAATCG
1 CACACTAAGTGCCATACATAGCCGAAGATATCTTAAATCG
** * * ** *
54796963 CACACTAAGTGCCATATTTAGCCGAAGCTATGTTGGATTG
1 CACACTAAGTGCCATACATAGCCGAAGATATCTTAAATCG
54797003 CACACTAAGTGCCA
1 CACACTAAGTGCCA
54797017 CAAATAGTTG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (40 bp):
CACACTAAGTGCCATACATAGCCGAAGATATCTTAAATCG
Found at i:54803818 original size:40 final size:40
Alignment explanation
Indices: 54803708--54804091 Score: 598
Period size: 40 Copynumber: 9.7 Consensus size: 40
54803698 CTTGAGTAAT
*
54803708 AATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 AATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
* *
54803748 ATTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA
1 AATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
*
54803787 AATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 AATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
* *
54803827 ATTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA
1 AATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
*
54803866 AATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 AATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
* *
54803906 ATTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA
1 AATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
*
54803945 AATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 AATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
* *
54803985 ATTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA
1 AATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
*
54804024 AATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
1 AATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
*
54804064 TAA-CCGGGCTATGTCCCGAAGGCATTTG
1 -AATCCGGGCTAAGTCCCGAAGGCATTTG
54804092 AACAAGTAGC
Statistics
Matches: 313, Mismatches: 26, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
39 144 0.46
40 167 0.53
41 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.26
Consensus pattern (40 bp):
AATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
Found at i:54804124 original size:79 final size:79
Alignment explanation
Indices: 54803708--54804089 Score: 721
Period size: 79 Copynumber: 4.8 Consensus size: 79
54803698 CTTGAGTAAT
54803708 AATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATT
1 AATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATT
54803773 GGTGCGAGTTACTA
66 GGTGCGAGTTACTA
54803787 AATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATT
1 AATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATT
54803852 GGTGCGAGTTACTA
66 GGTGCGAGTTACTA
54803866 AATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATT
1 AATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATT
54803931 GGTGCGAGTTACTA
66 GGTGCGAGTTACTA
54803945 AATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATT
1 AATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATT
54804010 GGTGCGAGTTACTA
66 GGTGCGAGTTACTA
* *
54804024 AATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCA
1 AATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGCTAAG-CCCGAAGGCA
54804088 TT
64 TT
54804090 TGAACAAGTA
Statistics
Matches: 299, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
78 2 0.01
79 285 0.95
80 12 0.04
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (79 bp):
AATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATT
GGTGCGAGTTACTA
Found at i:54807736 original size:240 final size:240
Alignment explanation
Indices: 54807313--54807801 Score: 944
Period size: 240 Copynumber: 2.0 Consensus size: 240
54807303 GGCCCAGAAA
54807313 TATGTAAGAAAAGGGTGCGAAGCATACCTTGCGTATGTACTTGATGACAAAGAATTAGAAAAGAA
1 TATGTAAGAAAAGGGTGCGAAGCATACCTTGCGTATGTACTTGATGACAAAGAATTAGAAAAGAA
54807378 ACCCGAATCTGTGCCGGTGGTTTGTGAATACCCAGATGTTTTTCCTGAAGAATTACCGGGTTTAC
66 ACCCGAATCTGTGCCGGTGGTTTGTGAATACCCAGATGTTTTTCCTGAAGAATTACCGGGTTTAC
54807443 CACCTGTTCGGGAGGTAGAGTTTGGTATTGAGCTTGTACCTGGAACTACGCCAATTTCGATAGCT
131 CACCTGTTCGGGAGGTAGAGTTTGGTATTGAGCTTGTACCTGGAACTACGCCAATTTCGATAGCT
*
54807508 CCGTATCGTATGGCACCAACTGAGTTAAAAGAATTGAAAGCTCAG
196 CCGTATCGTATGGCACCAACCGAGTTAAAAGAATTGAAAGCTCAG
54807553 TATGTAAGAAAAGGGTGCGAAGCATACCTTGCGTATGTACTTGATGACAAAGAATTAGAAAAGAA
1 TATGTAAGAAAAGGGTGCGAAGCATACCTTGCGTATGTACTTGATGACAAAGAATTAGAAAAGAA
54807618 ACCCGAATCTGTGCCGGTGGTTTGTGAATACCCAGATGTTTTTCCTGAAGAATTACCGGGTTTAC
66 ACCCGAATCTGTGCCGGTGGTTTGTGAATACCCAGATGTTTTTCCTGAAGAATTACCGGGTTTAC
54807683 CACCTGTTCGGGAGGTAGAGTTTGGTATTGAGCTTGTACCTGGAACTACGCCAATTTCGATAGCT
131 CACCTGTTCGGGAGGTAGAGTTTGGTATTGAGCTTGTACCTGGAACTACGCCAATTTCGATAGCT
*
54807748 CCGTATCGTATGGCACCAACCGAGTTAAAAGAGTTGAAAGCTCAG
196 CCGTATCGTATGGCACCAACCGAGTTAAAAGAATTGAAAGCTCAG
*
54807793 T-TGCAAGAA
1 TATGTAAGAA
54807802 TTGACGGATA
Statistics
Matches: 246, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
239 7 0.03
240 239 0.97
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (240 bp):
TATGTAAGAAAAGGGTGCGAAGCATACCTTGCGTATGTACTTGATGACAAAGAATTAGAAAAGAA
ACCCGAATCTGTGCCGGTGGTTTGTGAATACCCAGATGTTTTTCCTGAAGAATTACCGGGTTTAC
CACCTGTTCGGGAGGTAGAGTTTGGTATTGAGCTTGTACCTGGAACTACGCCAATTTCGATAGCT
CCGTATCGTATGGCACCAACCGAGTTAAAAGAATTGAAAGCTCAG
Found at i:54813368 original size:39 final size:40
Alignment explanation
Indices: 54813244--54813396 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
54813234 GGATATAGCT
* *
54813244 ACTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTATAGTA
1 ACTCGTACAAATGCCTTCGGGACTTAGCCCGGATT-TAGTA
* *
54813284 ACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTA
1 ACTCGTACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* *
54813324 ACTCGTGCAAATGCCTTCGGG-CTTAGCCCGGAATTAGTA
1 ACTCGTACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
* * *
54813363 TCTCGTACAAATGCC-TCCGGATCTTAGTCCGGAT
1 ACTCGTACAAATGCCTTCGGGA-CTTAGCCCGGAT
54813397 ATGGTCACTT
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
38 4 0.04
39 29 0.30
40 62 0.64
41 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (40 bp):
ACTCGTACAAATGCCTTCGGGACTTAGCCCGGATTTAGTA
Found at i:54813373 original size:79 final size:79
Alignment explanation
Indices: 54813228--54813378 Score: 200
Period size: 79 Copynumber: 1.9 Consensus size: 79
54813218 CCTTCAGAAT
* *
54813228 TTAACCGGATATAGCTACTCGTTCAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACA
1 TTAACCGGATATAGCTACTCGTGCAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACA
54813293 AATGCCTTCGGGAC
66 AATGCCTTCGGGAC
* * * *
54813307 TTAACCCGGATTTAG-TAACTCGTGCAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGT
1 TTAA-CCGGATATAGCT-ACTCGTGCAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGC
54813369 ACAAATGCCT
63 ACAAATGCCT
54813379 CCGGATCTTA
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
78 1 0.02
79 33 0.52
80 29 0.46
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (79 bp):
TTAACCGGATATAGCTACTCGTGCAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACA
AATGCCTTCGGGAC
Found at i:54813458 original size:39 final size:40
Alignment explanation
Indices: 54813409--54813499 Score: 121
Period size: 39 Copynumber: 2.3 Consensus size: 40
54813399 GGTCACTTAT
* *
54813409 CTTAGTCCGGATTTAGTAACTCGTGCAAATGCCTTCGG-G
1 CTTAGTCCGGATTTAGTAACTCGTACAAATGCCTCCGGAG
* * * *
54813448 CTTAGCCCGGAATTAGTATCTCGTACAAATGCCTCCGGAT
1 CTTAGTCCGGATTTAGTAACTCGTACAAATGCCTCCGGAG
54813488 CTTAGTCCGGAT
1 CTTAGTCCGGAT
54813500 ATGGTCACTT
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
39 33 0.77
40 10 0.23
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (40 bp):
CTTAGTCCGGATTTAGTAACTCGTACAAATGCCTCCGGAG
Found at i:54813491 original size:103 final size:103
Alignment explanation
Indices: 54813312--54813510 Score: 398
Period size: 103 Copynumber: 1.9 Consensus size: 103
54813302 GGGACTTAAC
54813312 CCGGATTTAGTAACTCGTGCAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGTACAAATGC
1 CCGGATTTAGTAACTCGTGCAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGTACAAATGC
54813377 CTCCGGATCTTAGTCCGGATATGGTCACTTATCTTAGT
66 CTCCGGATCTTAGTCCGGATATGGTCACTTATCTTAGT
54813415 CCGGATTTAGTAACTCGTGCAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGTACAAATGC
1 CCGGATTTAGTAACTCGTGCAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGTACAAATGC
54813480 CTCCGGATCTTAGTCCGGATATGGTCACTTA
66 CTCCGGATCTTAGTCCGGATATGGTCACTTA
54813511 GCACAAAGCC
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
103 96 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (103 bp):
CCGGATTTAGTAACTCGTGCAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGTACAAATGC
CTCCGGATCTTAGTCCGGATATGGTCACTTATCTTAGT
Found at i:54821546 original size:79 final size:81
Alignment explanation
Indices: 54821410--54821593 Score: 216
Period size: 79 Copynumber: 2.3 Consensus size: 81
54821400 TGAATGATGT
* *
54821410 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
*
54821474 GTGCGAGATACTA-ATT
66 GTGCGAGATACTATA-A
* * * * **
54821490 TCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCTCGAAGGCAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATC-CGAAGGCAAT
*
54821552 TGTGCGAGTTACTATAA
65 TGTGCGAGATACTATAA
*
54821569 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
54821594 AACGAGTAGC
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
78 2 0.02
79 55 0.62
80 31 0.35
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAATT
GTGCGAGATACTATAA
Found at i:54821600 original size:40 final size:40
Alignment explanation
Indices: 54821409--54821593 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
54821399 TTGAATGATG
* * * *
54821409 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
54821449 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
54821489 TTCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
54821528 TCCGGGTTAAGTCTCGAAGGCAATTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
54821569 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
54821594 AACGAGTAGC
Statistics
Matches: 121, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
39 34 0.28
40 77 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:54821615 original size:79 final size:78
Alignment explanation
Indices: 54821410--54821616 Score: 188
Period size: 79 Copynumber: 2.6 Consensus size: 78
54821400 TGAATGATGT
** * * * * *
54821410 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAG-CCCGAAGGCATTTGAAC-GAGTTACTATATCCGG-TTAAGATCCGAAGGCAATT
*
54821474 GTGCGAGATACTAATT
63 GTGCGAGATACTAATA
* ** *
54821490 TCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAG-TCTCGAAGGCAATTG
1 CCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTATATCC-GGTTAAGATC-CGAAGGCAATTG
*
54821554 TGCGAGTTACT-ATAA
64 TGCGAGATACTAAT-A
*
54821569 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGCTATATCCGGTTAA
1 CCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-CTATATCCGGTTAA
54821617 ATTTTGAAGG
Statistics
Matches: 107, Mismatches: 14, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
78 4 0.04
79 60 0.56
80 43 0.40
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (78 bp):
CCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTATATCCGGTTAAGATCCGAAGGCAATTGTG
CGAGATACTAATA
Found at i:54823840 original size:38 final size:38
Alignment explanation
Indices: 54823797--54824055 Score: 365
Period size: 38 Copynumber: 6.8 Consensus size: 38
54823787 ATGAAGATAT
* *
54823797 ATCCCGCAGGCTTCGTGCTGGTAATACATCTGGGTTAA
1 ATCCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAA
*
54823835 ATCCCGTAGGCTTCGTGCTGGTAATATATCCGGGCTTAA
1 ATCCCGCAGGCTTCGTGCTGGTAATATATCCGGG-TTAA
* * * *
54823874 AGACCCGCAGGCTTTGTGCTGGTATTATATCCGAGTTAA
1 A-TCCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAA
54823913 ATCCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAA
1 ATCCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAA
* *
54823951 ATCCTGCAGGCTTCGTGCTGGTAATATATCCAGGTTAA
1 ATCCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAA
* *
54823989 ATCCCGTAGGCTTCGTGCTGGTATTATATCCGGGTTAA
1 ATCCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAA
* * * *
54824027 ATCCCGCAGGCCTAGTACTGGTATTATAT
1 ATCCCGCAGGCTTCGTGCTGGTAATATAT
54824056 TCAGGCCTTT
Statistics
Matches: 197, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
38 159 0.81
39 10 0.05
40 28 0.14
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (38 bp):
ATCCCGCAGGCTTCGTGCTGGTAATATATCCGGGTTAA
Found at i:54832030 original size:46 final size:45
Alignment explanation
Indices: 54831977--54832152 Score: 176
Period size: 46 Copynumber: 3.8 Consensus size: 45
54831967 TATTTGGGCA
54831977 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *** * *
54832023 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAAATGTAACTAG-GCA-
1 TCCGAACTCATTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* * * *
54832070 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAGCG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGA-AG
* *
54832116 CCCGATCTCATTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGG
54832153 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
44 2 0.02
45 1 0.01
46 66 0.62
47 32 0.30
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (45 bp):
TCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:54832132 original size:93 final size:93
Alignment explanation
Indices: 54831973--54832144 Score: 272
Period size: 93 Copynumber: 1.8 Consensus size: 93
54831963 AGGATATTTG
* * * *
54831973 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCATTGAG
54832038 TTGAGTCCGAGTTCGAGAAATGTAACTA
66 TTGAGTCCGAGTTCGAGAAATGTAACTA
* * * *
54832066 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACGAGCGCCCGATCTCATTGAG
1 GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCATTGAG
54832131 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
54832145 ACTTATGGGC
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCATTGAGTTGAGTCCGAGTTCACTTATGGATACGAACGCCCGAACTCATTGAG
TTGAGTCCGAGTTCGAGAAATGTAACTA
Found at i:54835354 original size:26 final size:27
Alignment explanation
Indices: 54835325--54835375 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
54835315 TAACGCCCCA
* *
54835325 ATTTTTAGGTTTTCTGTGT-TTCTGTG
1 ATTTTTAAGATTTCTGTGTGTTCTGTG
*
54835351 ATTTTTAAGATTTGTGTGTGTTCTG
1 ATTTTTAAGATTTCTGTGTGTTCTG
54835376 GTTGGTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.12, C:0.06, G:0.24, T:0.59
Consensus pattern (27 bp):
ATTTTTAAGATTTCTGTGTGTTCTGTG
Found at i:54836173 original size:27 final size:27
Alignment explanation
Indices: 54836139--54836311 Score: 190
Period size: 27 Copynumber: 6.4 Consensus size: 27
54836129 TGGATAAGTT
*
54836139 GTAGAATTATCGAAATACCCTTGTAAG
1 GTAGAATTACCGAAATACCCTTGTAAG
* *
54836166 GTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCTTGTAAG
*
54836193 GTAGAATTACCGAAATACCCCTGT-AG
1 GTAGAATTACCGAAATACCCTTGTAAG
* *
54836219 GATAGAATTACCGAAATACCCTTTTAGG
1 G-TAGAATTACCGAAATACCCTTGTAAG
* *
54836247 GTAGAAATACCAAAATAGCCC-TGT-AG
1 GTAGAATTACCGAAATA-CCCTTGTAAG
* **
54836273 AGTAGAATTACCGAGATACCCTTGTGGG
1 -GTAGAATTACCGAAATACCCTTGTAAG
*
54836301 GTAAAATTACC
1 GTAGAATTACC
54836312 ATTTTGCCCC
Statistics
Matches: 124, Mismatches: 16, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
26 6 0.05
27 112 0.90
28 6 0.05
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCTTGTAAG
Found at i:54836225 original size:54 final size:54
Alignment explanation
Indices: 54836139--54836311 Score: 224
Period size: 54 Copynumber: 3.2 Consensus size: 54
54836129 TGGATAAGTT
* * *
54836139 GTAGAATTATCGAAATACCCTTGTAAGG-TAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGT-AGGATAGAATTACCGAAATACCCTTGTAGG
*
54836193 GTAGAATTACCGAAATACCCCTGTAGGATAGAATTACCGAAATACCCTTTTAGG
1 GTAGAATTACCGAAATACCCCTGTAGGATAGAATTACCGAAATACCCTTGTAGG
* * * * *
54836247 GTAGAAATACCAAAATAGCCCTGTA-GAGTAGAATTACCGAGATACCCTTGTGGG
1 GTAGAATTACCGAAATACCCCTGTAGGA-TAGAATTACCGAAATACCCTTGTAGG
*
54836301 GTAAAATTACC
1 GTAGAATTACC
54836312 ATTTTGCCCC
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
53 5 0.05
54 100 0.95
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (54 bp):
GTAGAATTACCGAAATACCCCTGTAGGATAGAATTACCGAAATACCCTTGTAGG
Found at i:54836278 original size:81 final size:81
Alignment explanation
Indices: 54836140--54836311 Score: 236
Period size: 81 Copynumber: 2.1 Consensus size: 81
54836130 GGATAAGTTG
* * * *
54836140 TAGAATTATCGAAATACCCTTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACCG
1 TAGAATTACCGAAATACCCTTGTAAGGTAGAAATACCAAAATACCCCTGTAGAGTAGAATTACCG
54836205 AAATACCCCTGTAGGA
66 AAATACCCCTGTAGGA
* * *
54836221 TAGAATTACCGAAATACCCTTTTAGGGTAGAAATACCAAAATAGCCCTGTAGAGTAGAATTACCG
1 TAGAATTACCGAAATACCCTTGTAAGGTAGAAATACCAAAATACCCCTGTAGAGTAGAATTACCG
* * * *
54836286 AGATACCCTTGTGGGG
66 AAATACCCCTGTAGGA
*
54836302 TAAAATTACC
1 TAGAATTACC
54836312 ATTTTGCCCC
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (81 bp):
TAGAATTACCGAAATACCCTTGTAAGGTAGAAATACCAAAATACCCCTGTAGAGTAGAATTACCG
AAATACCCCTGTAGGA
Found at i:54843751 original size:27 final size:27
Alignment explanation
Indices: 54843718--54843889 Score: 209
Period size: 27 Copynumber: 6.4 Consensus size: 27
54843708 GGATAAGTTA
** *
54843718 TAGAATTACAAAAATACCCTTGTAAGG
1 TAGAATTACCGAAATACCCTTGTAGGG
* * *
54843745 TTGAATTACCGAAATACCCCTCTAGGG
1 TAGAATTACCGAAATACCCTTGTAGGG
* * *
54843772 TAGAATTACCGAAATACCCATATAGGA
1 TAGAATTACCGAAATACCCTTGTAGGG
*
54843799 TAGAATTACTGAAATACCCTTGTAGGG
1 TAGAATTACCGAAATACCCTTGTAGGG
* *
54843826 TAGAAATACCGAAATACCCCTGTAGGG
1 TAGAATTACCGAAATACCCTTGTAGGG
* *
54843853 TAGAATTACCGAGATACCCTTGTGGGG
1 TAGAATTACCGAAATACCCTTGTAGGG
*
54843880 TAAAATTACC
1 TAGAATTACC
54843890 ATTTTGCCTC
Statistics
Matches: 123, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 123 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (27 bp):
TAGAATTACCGAAATACCCTTGTAGGG
Found at i:54843852 original size:81 final size:81
Alignment explanation
Indices: 54843717--54843871 Score: 247
Period size: 81 Copynumber: 1.9 Consensus size: 81
54843707 TGGATAAGTT
* *
54843717 ATAGAATTACAAAAATACCCTTGTAAGGTTGAATTACCGAAATACCCCTCTAGGGTAGAATTACC
1 ATAGAATTACAAAAATACCCTTGTAAGGTAGAAATACCGAAATACCCCTCTAGGGTAGAATTACC
54843782 GAAATACCCATATAGG
66 GAAATACCCATATAGG
** * *
54843798 ATAGAATTACTGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTGTAGGGTAGAATTACC
1 ATAGAATTACAAAAATACCCTTGTAAGGTAGAAATACCGAAATACCCCTCTAGGGTAGAATTACC
*
54843863 GAGATACCC
66 GAAATACCC
54843872 TTGTGGGGTA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 67 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (81 bp):
ATAGAATTACAAAAATACCCTTGTAAGGTAGAAATACCGAAATACCCCTCTAGGGTAGAATTACC
GAAATACCCATATAGG
Found at i:54844585 original size:27 final size:26
Alignment explanation
Indices: 54844541--54844591 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
54844531 CTCGCTGCAA
*
54844541 TCTGGTGGCCTCGCCACATATATCTAT
1 TCTGGTGACCTCGCCACA-ATATCTAT
* *
54844568 TCTGGTGACTTCGTCACAATATCT
1 TCTGGTGACCTCGCCACAATATCT
54844592 GGCAGCCTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTAT
Found at i:54844714 original size:100 final size:100
Alignment explanation
Indices: 54844541--54844908 Score: 684
Period size: 100 Copynumber: 3.7 Consensus size: 100
54844531 CTCGCTGCAA
* * * *
54844541 TCTGGTGGCCTCGCCACA-TATATCTATTCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTG
1 TCTGGTGGCCTAGACACACTATCTGTA-TCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTG
54844605 CAATCTGGTGGCTTCGCCACATATATATATATCTGT
65 CAATCTGGTGGCTTCGCCACATATATATATATCTGT
54844641 TCTGGTGGCCTAGACACACTATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTGC
1 TCTGGTGGCCTAGACACACTATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTGC
54844706 AATCTGGTGGCTTCGCCACATATATATATATCTGT
66 AATCTGGTGGCTTCGCCACATATATATATATCTGT
54844741 TCTGGTGGCCTAGACACACTATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTGC
1 TCTGGTGGCCTAGACACACTATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTGC
54844806 AATCTGGTGGCTTCGCCACATATATATATATCTGT
66 AATCTGGTGGCTTCGCCACATATATATATATCTGT
54844841 TCTGGTGGCCTAGACACACTATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTGC
1 TCTGGTGGCCTAGACACACTATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTGC
54844906 AAT
66 AAT
54844909 TTCTATGGTG
Statistics
Matches: 263, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
100 257 0.98
101 6 0.02
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.32
Consensus pattern (100 bp):
TCTGGTGGCCTAGACACACTATCTGTATCTGGTGACTTCGTCACAATATCTGGCAGCCTCGCTGC
AATCTGGTGGCTTCGCCACATATATATATATCTGT
Found at i:54852970 original size:101 final size:101
Alignment explanation
Indices: 54852844--54853078 Score: 285
Period size: 101 Copynumber: 2.3 Consensus size: 101
54852834 GGTTTTACTA
* * * * *
54852844 GCACA-CATATATCGGAATCACATATCGATGTCAATGTATAAAACGTGGACTTACTCACACAGAT
1 GCACATCACATATCAGAATCACATATCGATGCCAATGTATAAAACATGGACTTACTCACACACAT
* *
54852908 CTAT-CGAAGTCACATATCGATGCCATGGTCTTACAC
66 ATATACGAA-TCACACATCGATGCCATGGTCTTACAC
* * * *
54852944 GCACATCACATATCAGAATCACATATCGATGCCAATGTATTAAACATGGTCTTACTCGCGCACAT
1 GCACATCACATATCAGAATCACATATCGATGCCAATGTATAAAACATGGACTTACTCACACACAT
* * *
54853009 ATATAGGAATCGCACATCGATGCCATGGTCTTACTC
66 ATATACGAATCACACATCGATGCCATGGTCTTACAC
* * *
54853045 ACACATCACATATCAGAATTCACATGTCAATGCC
1 GCACATCACATATCAGAA-TCACATATCGATGCC
54853079 TTATATACAT
Statistics
Matches: 115, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
100 5 0.04
101 94 0.82
102 16 0.14
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.26
Consensus pattern (101 bp):
GCACATCACATATCAGAATCACATATCGATGCCAATGTATAAAACATGGACTTACTCACACACAT
ATATACGAATCACACATCGATGCCATGGTCTTACAC
Found at i:54856013 original size:31 final size:28
Alignment explanation
Indices: 54855975--54856049 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
54855965 AGCCCAAAAC
54855975 TTACATTTATT-TCATAATTAACCCCCTCAAT
1 TTACATTT-TTCTCA-AATTAA-CCCCT-AAT
*
54856006 TTACATTTTTCTCAAATTAATCCCTAAT
1 TTACATTTTTCTCAAATTAACCCCTAAT
* *
54856034 TAACATTTTTGTCAAA
1 TTACATTTTTCTCAAA
54856050 AATCTCTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
28 17 0.43
29 4 0.10
30 8 0.20
31 11 0.28
ACGTcount: A:0.33, C:0.21, G:0.01, T:0.44
Consensus pattern (28 bp):
TTACATTTTTCTCAAATTAACCCCTAAT
Found at i:54860575 original size:11 final size:11
Alignment explanation
Indices: 54860559--54860584 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
54860549 CACAATCAAA
54860559 CATACATTTTT
1 CATACATTTTT
54860570 CATACATTTTT
1 CATACATTTTT
54860581 CATA
1 CATA
54860585 TCTAAATAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (11 bp):
CATACATTTTT
Found at i:54865307 original size:27 final size:27
Alignment explanation
Indices: 54865277--54865794 Score: 580
Period size: 27 Copynumber: 19.2 Consensus size: 27
54865267 AAAGTATTCC
54865277 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
54865304 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
54865331 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** * *
54865358 CGATTTGTAAAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
54865385 CGATTTACAGAATTACCGTTTTACATT
1 CGATTTACAGAATTACCGTTTTACCCT
**
54865412 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
54865439 CGATTTACAGAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* ** *
54865466 CAATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* * * *
54865493 TGATTTACAGAATTACTGGTTTACTCT
1 CGATTTACAGAATTACCGTTTTACCCT
* * *
54865520 C-ACTTTACAAAATTATCATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
54865547 CGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
**
54865574 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
54865601 CGATTTACAGAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
54865628 C-AGTTTATAGAATTACTGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
*
54865655 CGATTTAGAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
** *
54865682 CGATTTGTAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
* *
54865709 TGATTTACAGAATTACTAG-TTTACCCT
1 CGATTTACAGAATTAC-CGTTTTACCCT
* *
54865736 C-AGTTTACAAAATTATCGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCT
* *
54865763 CGATTTACAAAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCT
*
54865790 TGATT
1 CGATT
54865795 GTGAAATTAC
Statistics
Matches: 416, Mismatches: 63, Indels: 24
0.83 0.13 0.05
Matches are distributed among these distances:
26 6 0.01
27 404 0.97
28 6 0.01
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.40
Consensus pattern (27 bp):
CGATTTACAGAATTACCGTTTTACCCT
Found at i:54865829 original size:27 final size:27
Alignment explanation
Indices: 54865799--54865994 Score: 205
Period size: 27 Copynumber: 7.2 Consensus size: 27
54865789 TTGATTGTGA
54865799 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
54865826 AATTTCCGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * *
54865853 AATTACTGAAATACCCTTATAGGATAG
1 AATTACTGAAATACCCCTGTAGGGTAG
**
54865880 AATTACCAAAAATACCCCTGTAGGGTAG
1 AATTA-CTGAAATACCCCTGTAGGGTAG
* *
54865908 AATTA-TCGAGATACCCTTGTAGGGTAG
1 AATTACT-GAAATACCCCTGTAGGGTAG
* * *
54865935 AAATACCGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCCTGTAGGGTAG
* * * * *
54865962 AATTACTGAGATTCCCTTGTGGGGTAA
1 AATTACTGAAATACCCCTGTAGGGTAG
54865989 AATTAC
1 AATTAC
54865995 CATTTTGCCC
Statistics
Matches: 137, Mismatches: 29, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
27 115 0.84
28 22 0.16
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (27 bp):
AATTACTGAAATACCCCTGTAGGGTAG
Found at i:54865906 original size:82 final size:82
Alignment explanation
Indices: 54865807--54865967 Score: 243
Period size: 82 Copynumber: 2.0 Consensus size: 82
54865797 GAAATTACTG
* * *
54865807 AAATACCCCTGTAGGGTAGAATT-TCCGAAATACCCCTATAGGGTAGAATTACTGAAATACCCTT
1 AAATACCCCTGTAGGGTAGAATTAT-CGAAATACCCCTATAGGGTAGAAATACCGAAATACCCCT
54865871 ATAGGATAGAATTACCAA
65 ATAGGATAGAATTACCAA
* * *
54865889 AAATACCCCTGTAGGGTAGAATTATCGAGATACCCTTGTAGGGTAGAAATACCGAAATACCCCTA
1 AAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTATAGGGTAGAAATACCGAAATACCCCTA
*
54865954 TAGGGTAGAATTAC
66 TAGGATAGAATTAC
54865968 TGAGATTCCC
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
82 70 0.99
83 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (82 bp):
AAATACCCCTGTAGGGTAGAATTATCGAAATACCCCTATAGGGTAGAAATACCGAAATACCCCTA
TAGGATAGAATTACCAA
Found at i:54865973 original size:54 final size:54
Alignment explanation
Indices: 54865799--54865991 Score: 246
Period size: 54 Copynumber: 3.6 Consensus size: 54
54865789 TTGATTGTGA
* * *
54865799 AATTACTGAAATACCCCTGTAGGGTAGAATTTCCGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTATAGGGTAG
* * * * *
54865853 AATTACTGAAATACCCTTATAGGATAGAATTACCAAAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAGAAATACC-GAAATACCCCTATAGGGTAG
*
54865908 AATTA-TCGAGATACCCTTGTAGGGTAGAAATACCGAAATACCCCTATAGGGTAG
1 AATTACT-GAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTATAGGGTAG
* * *
54865962 AATTACTGAGATTCCCTTGTGGGGTA-AAAT
1 AATTACTGAAATACCCTTGTAGGGTAGAAAT
54865992 TACCATTTTG
Statistics
Matches: 122, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
53 4 0.03
54 71 0.58
55 47 0.39
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.26
Consensus pattern (54 bp):
AATTACTGAAATACCCTTGTAGGGTAGAAATACCGAAATACCCCTATAGGGTAG
Found at i:54866232 original size:27 final size:26
Alignment explanation
Indices: 54866194--54866276 Score: 112
Period size: 27 Copynumber: 3.1 Consensus size: 26
54866184 CGGAGGAAGC
*
54866194 GTTCTGGTGGCTATGCCACAAATATCT
1 GTTCTGGTGGCTCTGCCAC-AATATCT
54866221 GTTCTGGTGGCTCTGCCACAATATCT
1 GTTCTGGTGGCTCTGCCACAATATCT
* * *
54866247 GTATTTGGTGACTCTGTCACAATATCT
1 GT-TCTGGTGGCTCTGCCACAATATCT
54866274 GTT
1 GTT
54866277 GACCGATCGA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
26 10 0.20
27 41 0.80
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (26 bp):
GTTCTGGTGGCTCTGCCACAATATCT
Found at i:54866396 original size:22 final size:22
Alignment explanation
Indices: 54866364--54866422 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
54866354 CCCGTTATTA
*
54866364 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * ***
54866386 ATGGCTTTGTGCCATCTTGTCT
1 ATGGCTTTGTGCCAACCTAAAT
54866408 ATGGCTTTGTGCCAA
1 ATGGCTTTGTGCCAA
54866423 ACGTATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.36
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:54866651 original size:27 final size:27
Alignment explanation
Indices: 54866588--54866660 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
54866578 AGGTGGGTTT
* *
54866588 GCCACATTATCTG-ATTCTGGTGGCTCA
1 GCCACAATATCTGTA-TCTGGTGACTCA
*
54866615 GCCACAATATCTGTATCTGGTGACTCT
1 GCCACAATATCTGTATCTGGTGACTCA
* *
54866642 GTCACGATATCTGT-TCTGG
1 GCCACAATATCTGTATCTGG
54866661 CAGCCATGCT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
26 5 0.12
27 34 0.85
28 1 0.03
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
GCCACAATATCTGTATCTGGTGACTCA
Found at i:54866787 original size:6 final size:6
Alignment explanation
Indices: 54866778--54866916 Score: 117
Period size: 6 Copynumber: 22.8 Consensus size: 6
54866768 TTGCATTCAC
* *
54866778 ATTCTG ATTCTG ATTCTG -TCACGTA ATTCTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG AT-TC-TG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
54866827 -TTACTG ATTCTG ATTCTG ATTCTG -TCACCTA ATTCTT ATTCTA ATTCTG
1 ATT-CTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG
*
54866876 ATTCTG -TTACTA ATAT-TG ATTCTG ATTCTG ATTCTG ATTCT
1 ATTCTG ATT-CTG AT-TCTG ATTCTG ATTCTG ATTCTG ATTCT
54866917 CATTTTGGTT
Statistics
Matches: 109, Mismatches: 12, Indels: 24
0.75 0.08 0.17
Matches are distributed among these distances:
5 7 0.06
6 92 0.84
7 7 0.06
8 3 0.03
ACGTcount: A:0.20, C:0.18, G:0.13, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:54866862 original size:55 final size:55
Alignment explanation
Indices: 54866778--54866905 Score: 204
Period size: 55 Copynumber: 2.3 Consensus size: 55
54866768 TTGCATTCAC
* * *
54866778 ATTCTGATTCTGATTCTGTCACGTAATTCTGATTCTGATTCTGATTCTGTTACTG
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTAATTCTGATTCTGTTACTA
*
54866833 ATTCTGATTCTGATTCTGTCACCTAATTCTTATTCTAATTCTGATTCTGTTACTA
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTAATTCTGATTCTGTTACTA
54866888 ATAT-TGATTCTGATTCTG
1 AT-TCTGATTCTGATTCTG
54866906 ATTCTGATTC
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
55 67 0.99
56 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.13, T:0.48
Consensus pattern (55 bp):
ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTAATTCTGATTCTGTTACTA
Found at i:54878004 original size:43 final size:43
Alignment explanation
Indices: 54877953--54878180 Score: 294
Period size: 43 Copynumber: 5.3 Consensus size: 43
54877943 CATAGGATTT
* * * *
54877953 TCAATATGTGATTATGTGTACGACTACGTTTGGGACATTGGCA
1 TCAATATGTGATTACGTGTAAGACCACGTTTGGGACGTTGGCA
* *
54877996 TCAATATGTGATTATGTGTAAGACAACGTTTGGGACGTTGGCA
1 TCAATATGTGATTACGTGTAAGACCACGTTTGGGACGTTGGCA
*
54878039 TCAATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
1 TCAATATGTGATTACGTGTAAGACCACGTTTGGGACGTTGGCA
* * *
54878082 TCGATATGTGATTACGTGTAAAACCACGTTTGGGATGTTGGCA
1 TCAATATGTGATTACGTGTAAGACCACGTTTGGGACGTTGGCA
* * * *** *
54878125 TCGATATGTGATTAAGAGTAAGACCACGTTTAATATGTTGGCA
1 TCAATATGTGATTACGTGTAAGACCACGTTTGGGACGTTGGCA
*
54878168 TCGATATGTGATT
1 TCAATATGTGATT
54878181 TCGATATGTG
Statistics
Matches: 169, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 169 1.00
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (43 bp):
TCAATATGTGATTACGTGTAAGACCACGTTTGGGACGTTGGCA
Found at i:54878186 original size:13 final size:13
Alignment explanation
Indices: 54878168--54878197 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
54878158 TATGTTGGCA
54878168 TCGATATGTGATT
1 TCGATATGTGATT
*
54878181 TCGATATGTGTTT
1 TCGATATGTGATT
54878194 TCGA
1 TCGA
54878198 GTAAGACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.10, G:0.23, T:0.47
Consensus pattern (13 bp):
TCGATATGTGATT
Found at i:54883954 original size:55 final size:53
Alignment explanation
Indices: 54883768--54884022 Score: 229
Period size: 55 Copynumber: 4.8 Consensus size: 53
54883758 ACATAGGTAC
* * * * *
54883768 CTTACCATTTCCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-TGAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTCCCTTATG-AA
* * *
54883817 CTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATGAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTCCCTTATGAA
* * * *
54883870 CTCACCAATGCCATGCCTTGGCATGGTCTTACATAGG-A-CCTTTCCCTTATATTAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACAT-GGTATCC-TTCCC-T-TATGAA
* *
54883925 CTTATCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTA-GAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTCCCTTATG-AA
* * *
54883978 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACACGGTATCCTT
1 -CTTACCAA-TGCCATGTCTTGACATGGTCTTACATGGTATCCTT
54884023 AAACCCTAAT
Statistics
Matches: 170, Mismatches: 22, Indels: 22
0.79 0.10 0.10
Matches are distributed among these distances:
49 36 0.21
50 1 0.01
52 2 0.01
53 42 0.25
54 15 0.09
55 72 0.42
56 2 0.01
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (53 bp):
CTTACCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTCCCTTATGAA
Found at i:54883961 original size:108 final size:110
Alignment explanation
Indices: 54883815--54884012 Score: 330
Period size: 108 Copynumber: 1.8 Consensus size: 110
54883805 ATCCTTTTGA
*
54883815 AACTTACCATTGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTA-GAAACCTCACCAA
54883878 -TGCCATGCCTTGGCATGGTCTTACATAGGACCTTTCCCTTATATT
65 TTGCCATGCCTTGGCATGGTCTTACATAGGACCTTTCCCTTATATT
* * *
54883923 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTAGAAACCTCACCAAT
54883988 TGCCATGCCTTGGCATGGTCTTACA
66 TGCCATGCCTTGGCATGGTCTTACA
54884013 CGGTATCCTT
Statistics
Matches: 83, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
107 1 0.01
108 50 0.60
109 7 0.08
110 25 0.30
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTCGACATGGTCTTACATGGTATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATAGGACCTTTCCCTTATATT
Found at i:54888192 original size:27 final size:27
Alignment explanation
Indices: 54888162--54888339 Score: 164
Period size: 27 Copynumber: 6.6 Consensus size: 27
54888152 ATATTGAGTC
* *
54888162 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
54888189 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
54888216 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
54888244 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
**
54888271 CGCACACTTAGTGC-ATCAT-ATCCATTT
1 CGCACACTTAGTGCTA-CATAAT-CAACT
* * *
54888298 CGCACACTTAGTG-TAACGTAGTCAAAT
1 CGCACACTTAGTGCT-ACATAATCAACT
54888325 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54888340 GTACAATTTA
Statistics
Matches: 126, Mismatches: 18, Indels: 13
0.80 0.11 0.08
Matches are distributed among these distances:
26 1 0.01
27 99 0.79
28 26 0.21
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:54897004 original size:19 final size:19
Alignment explanation
Indices: 54896975--54897074 Score: 132
Period size: 19 Copynumber: 5.3 Consensus size: 19
54896965 AATCTTTAAG
*
54896975 GATAAGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* *
54896994 GATATGAAATCTTAAATAT
1 GATATGCAATCTTAGATAT
*
54897013 GATA--CTATCTTAGATAT
1 GATATGCAATCTTAGATAT
54897030 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
54897049 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
54897070 GATAT
1 GATAT
54897075 TGTAATCTTG
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
17 14 0.20
19 45 0.64
21 11 0.16
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:54897005 original size:36 final size:36
Alignment explanation
Indices: 54896965--54897083 Score: 91
Period size: 36 Copynumber: 3.2 Consensus size: 36
54896955 ATGGAAATAT
*
54896965 AATCTTTAAGGATAAGCAATCTTAGATATGATATGA
1 AATCTTTAAAGATAAGCAATCTTAGATATGATATGA
* * *
54897001 AATC-TTAAATATGATA-CTATCTTAGATATGATATGC
1 AATCTTTAAAGAT-A-AGCAATCTTAGATATGATATGA
* *
54897037 AATC-TTAGATATGATATGCAATCTTGAAGATATGATATTGT
1 AATCTTTA-A-A-GATAAGCAATCTT--AGATATGATA-TGA
54897078 AATCTT
1 AATCTT
54897084 GGAGATTTAA
Statistics
Matches: 65, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
35 6 0.09
36 30 0.46
37 2 0.03
38 8 0.12
39 2 0.03
40 10 0.15
41 6 0.09
42 1 0.02
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (36 bp):
AATCTTTAAAGATAAGCAATCTTAGATATGATATGA
Found at i:54899926 original size:33 final size:34
Alignment explanation
Indices: 54899864--54899962 Score: 94
Period size: 33 Copynumber: 2.9 Consensus size: 34
54899854 TTACACATTA
** * * *
54899864 CCAGAAACATATGTCAAATTAGAACGTCATATTT
1 CCAGAAACATATACCAGATCAGAAAGTCATATTT
*
54899898 CCA-TAACATATACCAGATCAGAAAGTCATATTT
1 CCAGAAACATATACCAGATCAGAAAGTCATATTT
* * *
54899931 TCAGAAACATATATCATATCA-AAATGTCATAT
1 CCAGAAACATATACCAGATCAGAAA-GTCATAT
54899963 CATATCAGAA
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
33 29 0.55
34 24 0.45
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.29
Consensus pattern (34 bp):
CCAGAAACATATACCAGATCAGAAAGTCATATTT
Found at i:54902033 original size:29 final size:28
Alignment explanation
Indices: 54901993--54902076 Score: 91
Period size: 29 Copynumber: 3.0 Consensus size: 28
54901983 AAGCATGTAA
54901993 AAAGAA-AAGAAAAGAAAAATGAAAGAAG
1 AAAGAAGAAGAAAAGAAAAATGAAA-AAG
* * *
54902021 AAAGAAGAAGAAAAGGAAAAGGAAAAAT
1 AAAGAAGAAGAAAAGAAAAATGAAAAAG
*
54902049 AAAGTAAGAA-AAAAAAAGAAATGAAAAA
1 AAAG-AAGAAGAAAAGAA-AAATGAAAAA
54902077 ATGTTAAAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
28 17 0.36
29 30 0.64
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (28 bp):
AAAGAAGAAGAAAAGAAAAATGAAAAAG
Found at i:54902058 original size:36 final size:34
Alignment explanation
Indices: 54901991--54902075 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 34
54901981 GAAAGCATGT
*
54901991 AAAAAGAAAAGAAAAGAAAAATGAAAGAAGAAAG
1 AAAAAGAAAAGAAAAGAAAAATGAAAGAAGAAAA
*
54902025 AAGAAGAAAAGGAAAAGGAAAAAT-AAAGTAAGAAAA
1 AAAAAGAAAA-GAAAA-GAAAAATGAAAG-AAGAAAA
*
54902061 AAAAAGAAATGAAAA
1 AAAAAGAAAAGAAAA
54902076 AATGTTAAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
34 9 0.20
35 14 0.32
36 21 0.48
ACGTcount: A:0.75, C:0.00, G:0.20, T:0.05
Consensus pattern (34 bp):
AAAAAGAAAAGAAAAGAAAAATGAAAGAAGAAAA
Found at i:54902076 original size:15 final size:14
Alignment explanation
Indices: 54901991--54902077 Score: 56
Period size: 14 Copynumber: 6.1 Consensus size: 14
54901981 GAAAGCATGT
54901991 AAAAAGAAAAGAAAA
1 AAAAAG-AAAGAAAA
*
54902006 GAAAAATGAAAGAAGA
1 -AAAAA-GAAAGAAAA
*
54902022 AAGAAG-AAGAAAA
1 AAAAAGAAAGAAAA
*
54902035 GGAAAAG---GAAAA
1 -AAAAAGAAAGAAAA
* *
54902047 ATAAAGTAAGAAAA
1 AAAAAGAAAGAAAA
54902061 AAAAAGAAATGAAAA
1 AAAAAGAAA-GAAAA
54902076 AA
1 AA
54902078 TGTTAAAGAA
Statistics
Matches: 56, Mismatches: 9, Indels: 13
0.72 0.12 0.17
Matches are distributed among these distances:
11 4 0.07
12 5 0.09
13 6 0.11
14 17 0.30
15 11 0.20
16 12 0.21
17 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.20, T:0.05
Consensus pattern (14 bp):
AAAAAGAAAGAAAA
Found at i:54907038 original size:17 final size:19
Alignment explanation
Indices: 54907016--54907050 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
54907006 TATGTGTATA
54907016 GTAAGTA-AAAT-TTTAAG
1 GTAAGTATAAATATTTAAG
54907033 GTAAGTATAAATATTTAA
1 GTAAGTATAAATATTTAA
54907051 TTTAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (19 bp):
GTAAGTATAAATATTTAAG
Found at i:54907710 original size:23 final size:22
Alignment explanation
Indices: 54907671--54907780 Score: 95
Period size: 23 Copynumber: 5.0 Consensus size: 22
54907661 GGGTTTACCA
54907671 ATCAGGCACTTATGTGTCGTAT
1 ATCAGGCACTTATGTGTCGTAT
54907693 ATCAGGCACTTTATGTGTCGTAT
1 ATCAGGCAC-TTATGTGTCGTAT
* *
54907716 TTCAGGTACCTCT-TGTGTC--AT
1 ATCAGGCA-CT-TATGTGTCGTAT
* * *
54907737 ATCAGGCACCT-GGTAT-GTCAT
1 ATCAGGCACTTATGTGTCGT-AT
*
54907758 TTCAGGCACTTATGTGTCGTAT
1 ATCAGGCACTTATGTGTCGTAT
54907780 A
1 A
54907781 CTGATCAGGT
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
19 4 0.06
20 1 0.01
21 19 0.28
22 14 0.21
23 28 0.41
24 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (22 bp):
ATCAGGCACTTATGTGTCGTAT
Found at i:54907747 original size:21 final size:21
Alignment explanation
Indices: 54907691--54907766 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 21
54907681 TATGTGTCGT
*
54907691 ATATCAGGCA-CTTTATGTGTC
1 ATATCAGGCACCTCT-TGTGTC
* *
54907712 GTATTTCAGGTACCTCTTGTGTC
1 --ATATCAGGCACCTCTTGTGTC
** *
54907735 ATATCAGGCACCTGGTATGTC
1 ATATCAGGCACCTCTTGTGTC
*
54907756 ATTTCAGGCAC
1 ATATCAGGCAC
54907767 TTATGTGTCG
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
21 26 0.60
23 14 0.33
24 3 0.07
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (21 bp):
ATATCAGGCACCTCTTGTGTC
Found at i:54912802 original size:16 final size:16
Alignment explanation
Indices: 54912763--54912803 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
54912753 TAACCCAAAT
54912763 TAAATTAGATTAAATTA
1 TAAATTA-ATTAAATTA
*
54912780 -AAATTAATTATATTA
1 TAAATTAATTAAATTA
54912795 TAAATTAAT
1 TAAATTAAT
54912804 ACACATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
TAAATTAATTAAATTA
Found at i:54915841 original size:25 final size:26
Alignment explanation
Indices: 54915812--54915867 Score: 73
Period size: 25 Copynumber: 2.2 Consensus size: 26
54915802 TTAATCAGTA
*
54915812 TAAAATATTAA-TAATTCAAT-AAAT
1 TAAAATATTAATTAATTAAATAAAAT
54915836 TGAAAA-ATTAATTAATTAAATAAAAT
1 T-AAAATATTAATTAATTAAATAAAAT
54915862 TAAAAT
1 TAAAAT
54915868 TTAGGAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 6 0.22
25 16 0.59
26 5 0.19
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (26 bp):
TAAAATATTAATTAATTAAATAAAAT
Found at i:54934834 original size:49 final size:49
Alignment explanation
Indices: 54934765--54934897 Score: 153
Period size: 49 Copynumber: 2.7 Consensus size: 49
54934755 GCACATTAAA
** * *
54934765 GTCAATGCTGTGTCCTAGACAGGTCTTACACTGACTTTCATATATCGAG-
1 GTCAATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCG-GT
* ** *
54934814 G-CTAATGCCATGTCCCAGACAGGTCTTACATTGGGTCTCATCTATCGGT
1 GTC-AATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCGGT
*
54934863 GTCGATGCCATGTCCCAGACAGGTCTTACACTGAC
1 GTCAATGCCATGTCCCAGACAGGTCTTACACTGAC
54934898 ACACAACAAG
Statistics
Matches: 69, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
48 2 0.03
49 66 0.96
50 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (49 bp):
GTCAATGCCATGTCCCAGACAGGTCTTACACTGACTCTCATATATCGGT
Found at i:54947353 original size:95 final size:95
Alignment explanation
Indices: 54947190--54947480 Score: 573
Period size: 95 Copynumber: 3.1 Consensus size: 95
54947180 ACAATACATC
54947190 AGACTGGATTCAAAAAGAATACATCCTGAATTCATTTATAGATTTATTCACTTGTGATGTTCATA
1 AGACTGGATTCAAAAAGAATACATCCTGAATTCATTTATAGATTTATTCACTTGTGATGTTCATA
54947255 GTGTGGCCTACCAAATCCTGAGTGGATGAT
66 GTGTGGCCTACCAAATCCTGAGTGGATGAT
54947285 AGACTGGATTCAAAAAGAATACATCCTGAATTCATTTATAGATTTATTCACTTGTGATGTTCATA
1 AGACTGGATTCAAAAAGAATACATCCTGAATTCATTTATAGATTTATTCACTTGTGATGTTCATA
54947350 GTGTGGCCTACCAAATCCTGAGTGGATGAT
66 GTGTGGCCTACCAAATCCTGAGTGGATGAT
54947380 AGACTGGATTCAAAAAGAATACATCCTGAATTCATTTATAGATTTATTCACTTGTGATGTTCATA
1 AGACTGGATTCAAAAAGAATACATCCTGAATTCATTTATAGATTTATTCACTTGTGATGTTCATA
54947445 GTGTGGCCTACCTAAATCCTGAGTGGATGAT
66 GTGTGGCCTACC-AAATCCTGAGTGGATGAT
54947476 AGACT
1 AGACT
54947481 ATGTATGCAT
Statistics
Matches: 195, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
95 172 0.88
96 23 0.12
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.34
Consensus pattern (95 bp):
AGACTGGATTCAAAAAGAATACATCCTGAATTCATTTATAGATTTATTCACTTGTGATGTTCATA
GTGTGGCCTACCAAATCCTGAGTGGATGAT
Found at i:54954837 original size:21 final size:22
Alignment explanation
Indices: 54954786--54954837 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
54954776 AATAAAGTCT
*
54954786 ATGTA-CAAATATCATCATCTC
1 ATGTATCATATATCATCATCTC
* *
54954807 ATGTTTTCATATATCAT-ATGTC
1 ATG-TATCATATATCATCATCTC
54954829 ATGTATCAT
1 ATGTATCAT
54954838 CATTTACTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 8 0.32
22 8 0.32
23 9 0.36
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (22 bp):
ATGTATCATATATCATCATCTC
Found at i:54955993 original size:19 final size:20
Alignment explanation
Indices: 54955969--54956006 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54955959 TATCAACAAC
54955969 ATTTCAT-TTTCTACCATAA
1 ATTTCATATTTCTACCATAA
*
54955988 ATTTCATATTTCTAGCATA
1 ATTTCATATTTCTACCATA
54956007 TTCATCCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.32, C:0.18, G:0.03, T:0.47
Consensus pattern (20 bp):
ATTTCATATTTCTACCATAA
Found at i:54964459 original size:25 final size:25
Alignment explanation
Indices: 54964419--54964490 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 25
54964409 TAAGGCTCCC
54964419 CAAATAATTCGCCACATA-GGCTTTT
1 CAAATAATTCGCCACA-AGGGCTTTT
* * *
54964444 CAAATAATTTGGCACAAGGGCTTTA
1 CAAATAATTCGCCACAAGGGCTTTT
* * * *
54964469 CAGACAACTCGCCACAAAGGCT
1 CAAATAATTCGCCACAAGGGCT
54964491 CTGTTTGGTT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
24 1 0.03
25 36 0.97
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.24
Consensus pattern (25 bp):
CAAATAATTCGCCACAAGGGCTTTT
Found at i:54973340 original size:107 final size:106
Alignment explanation
Indices: 54973137--54973373 Score: 272
Period size: 107 Copynumber: 2.2 Consensus size: 106
54973127 ACCTAAAATA
* ** * * *
54973137 ATAATAATATTAAGAATGCTAATAAATTATATAATATTTTATTAAATTGTATTAATAATTGTGTT
1 ATAATTATATTAAGAATATTATTAAATTATATAATATTTTATTAAATTATATTAATAATTATGTT
* *
54973202 AAAATATGATTAAATTATTTATTATGATTTTTATT-AATTCAT
66 AAAATATGATGAAATTATTTA-TATTATTTTTATTAAATT-AT
*
54973244 ATAATTATATTAAGAATATTATTAAATTATATATTATTTTATTAAATTATATTTAATAATAATTA
1 ATAATTATATTAAGAATATTATTAAATTATATAATATTTTATTAAATTATA--T--TAATAATTA
*
54973309 TGTTAAAATATGATGAAATTATTTA-CTT-TTTTTATTAAATTAT
62 TGTTAAAATATGATGAAATTATTTATATTATTTTTATTAAATTAT
*
54973352 AT--TTA-A-TAATAATATTATTAAA
1 ATAATTATATTAAGAATATTATTAAA
54973374 ATTTAATAAC
Statistics
Matches: 114, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
104 15 0.13
105 1 0.01
106 3 0.03
107 45 0.39
108 12 0.11
109 6 0.05
111 32 0.28
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (106 bp):
ATAATTATATTAAGAATATTATTAAATTATATAATATTTTATTAAATTATATTAATAATTATGTT
AAAATATGATGAAATTATTTATATTATTTTTATTAAATTAT
Found at i:54973373 original size:58 final size:57
Alignment explanation
Indices: 54973244--54973375 Score: 185
Period size: 58 Copynumber: 2.3 Consensus size: 57
54973234 ATTAATTCAT
* *
54973244 ATAATTATATTAAGAATATTATTAAATTATATATTATTTTATTAAATTATATTTAATA
1 ATAATTATATTAA-AATATGATGAAATTATATATTATTTTATTAAATTATATTTAATA
* * *
54973302 ATAATTATGTTAAAATATGATGAAATTATTTACTTTTTTTATTAAATTATATTTAATA
1 ATAATTATATTAAAATATGATGAAATTATATA-TTATTTTATTAAATTATATTTAATA
54973360 ATAA-TATTATTAAAAT
1 ATAATTA-TATTAAAAT
54973376 TTAATAACAA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
57 18 0.27
58 48 0.73
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (57 bp):
ATAATTATATTAAAATATGATGAAATTATATATTATTTTATTAAATTATATTTAATA
Found at i:54973563 original size:16 final size:16
Alignment explanation
Indices: 54973542--54973577 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
54973532 TTAATTACTG
54973542 ATTACATCTCTATTCC
1 ATTACATCTCTATTCC
* *
54973558 ATTACATTTCTATTTC
1 ATTACATCTCTATTCC
54973574 ATTA
1 ATTA
54973578 TAGTCTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTACATCTCTATTCC
Found at i:54980410 original size:93 final size:93
Alignment explanation
Indices: 54980242--54980414 Score: 240
Period size: 93 Copynumber: 1.9 Consensus size: 93
54980232 CGCCCATAAG
* * *
54980242 CGAACTCGGACTCAAATCAATGAGCTCAGGCGTTCACATCCACAAGTGAACTCAGACTCAACTCA
1 CGAACTCGAACTCAAATCAACGAGCTCAGGCATTCACATCCACAAGTGAACTCAGACTCAACTCA
*
54980307 GCGAGCTCGGATGCCTAGTTACATCTCT
66 ACGAGCTCGGATGCCTAGTTACATCTCT
* * * * *
54980335 CGAACTCGAACTCAACTCAACGAGTTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGAACTCAAATCAACGAGCTCAGG-CATTCACATCCACAAGTGAACTCAGACTCAACTC
*
54980399 AACGAGTTCGGATGCC
65 AACGAGCTCGGATGCC
54980415 CAAATATCCT
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
92 2 0.03
93 67 0.97
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGAACTCAAATCAACGAGCTCAGGCATTCACATCCACAAGTGAACTCAGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCT
Found at i:54982300 original size:26 final size:26
Alignment explanation
Indices: 54982269--54982350 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
54982259 TGAAATTTCC
54982269 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
54982295 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
54982321 ATCATGGAACATTTATCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
54982347 ATCA
1 ATCA
54982351 ATTTGTATCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:54982814 original size:45 final size:45
Alignment explanation
Indices: 54982742--54982873 Score: 167
Period size: 45 Copynumber: 2.9 Consensus size: 45
54982732 ACGCTTTCAT
*
54982742 ATGATGTCATAGCATCTTTTAGGTATGGTCTTACTAATTCTT-ATA
1 ATGATGTCATAGCATCTTTTAGCTATGGTCTTACTAATT-TTAATA
* * * * *
54982787 ATGATGCCATAGCATCTTTCAACTATGGTCTTACTCATTTTAATC
1 ATGATGTCATAGCATCTTTTAGCTATGGTCTTACTAATTTTAATA
** *
54982832 ATGATGTCATAATATCTTTTAGCTATGGTCTTACTCATTTTA
1 ATGATGTCATAGCATCTTTTAGCTATGGTCTTACTAATTTTA
54982874 GGAATATAGC
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
44 2 0.03
45 73 0.97
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.44
Consensus pattern (45 bp):
ATGATGTCATAGCATCTTTTAGCTATGGTCTTACTAATTTTAATA
Found at i:54989337 original size:25 final size:25
Alignment explanation
Indices: 54989304--54989357 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
54989294 AAGTGTATAC
* **
54989304 ATAGTGTTAAAAATATGTACATAAT
1 ATAGCGTTAAAAATACATACATAAT
54989329 ATAGCGTTAAAAATACATACATAAT
1 ATAGCGTTAAAAATACATACATAAT
54989354 ATAG
1 ATAG
54989358 TTATTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.31
Consensus pattern (25 bp):
ATAGCGTTAAAAATACATACATAAT
Found at i:54989422 original size:29 final size:30
Alignment explanation
Indices: 54989363--54989422 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 30
54989353 TATAGTTATT
* *
54989363 AAAAAATATATACATAAGATAATATGCAAG
1 AAAAAATATATAAATAAGATAATATGAAAG
* * *
54989393 AAAAAA-ATATAAATAATATAGTATTAAAG
1 AAAAAATATATAAATAAGATAATATGAAAG
54989422 A
1 A
54989423 TATATACATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.25
Consensus pattern (30 bp):
AAAAAATATATAAATAAGATAATATGAAAG
Found at i:54989433 original size:29 final size:29
Alignment explanation
Indices: 54989341--54989443 Score: 65
Period size: 31 Copynumber: 3.6 Consensus size: 29
54989331 AGCGTTAAAA
*
54989341 ATACAT-ACATAATATAGTTATTAAAAAATAT
1 ATACATAAGATAATATAG-TATT--AAAATAT
* **
54989372 ATACATAAGATAATAT-GCAAGAAAA-A-
1 ATACATAAGATAATATAGTATTAAAATAT
*
54989398 A-ATATAA-ATAATATAGTATTAAAGATAT
1 ATACATAAGATAATATAGTATTAAA-ATAT
*
54989426 ATACATAATATATATATA
1 ATACATAAGATA-ATATA
54989444 AAAAAATCAT
Statistics
Matches: 55, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
24 7 0.13
25 10 0.18
26 2 0.04
27 2 0.04
28 5 0.09
29 5 0.09
30 4 0.07
31 12 0.22
32 8 0.15
ACGTcount: A:0.57, C:0.05, G:0.06, T:0.32
Consensus pattern (29 bp):
ATACATAAGATAATATAGTATTAAAATAT
Found at i:54989442 original size:15 final size:15
Alignment explanation
Indices: 54989422--54989472 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
54989412 AGTATTAAAG
54989422 ATATATACATAATAT
1 ATATATACATAATAT
* *
54989437 ATATATA-AAAAAAT
1 ATATATACATAATAT
54989451 CATATATACATGACATAT
1 -ATATATACAT-A-ATAT
54989469 ATAT
1 ATAT
54989473 TAGCAACAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 5 0.18
15 14 0.50
16 1 0.04
17 5 0.18
18 3 0.11
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (15 bp):
ATATATACATAATAT
Found at i:54989562 original size:24 final size:25
Alignment explanation
Indices: 54989533--54989662 Score: 109
Period size: 24 Copynumber: 5.4 Consensus size: 25
54989523 ACGTACATAT
*
54989533 ATATATAAATAATAATGGTATTAGAA
1 ATATAT-AATAATAATAGTATTAGAA
*
54989559 ATATACAAT-AT-ATAGTATTAGAA
1 ATATATAATAATAATAGTATTAGAA
*
54989582 ATATATACATAA-AATAGTA-TAAAA
1 ATATATA-ATAATAATAGTATTAGAA
54989606 ATATAT-ATAACTAAT-GATATTA-AA
1 ATATATAATAA-TAATAG-TATTAGAA
54989630 ATATATACATAATAATA-TA-TA-AA
1 ATATATA-ATAATAATAGTATTAGAA
*
54989653 AAATATAATA
1 ATATATAATA
54989663 TTAAAAAAAT
Statistics
Matches: 89, Mismatches: 5, Indels: 24
0.75 0.04 0.20
Matches are distributed among these distances:
22 7 0.08
23 28 0.31
24 29 0.33
25 16 0.18
26 9 0.10
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (25 bp):
ATATATAATAATAATAGTATTAGAA
Found at i:54989615 original size:22 final size:25
Alignment explanation
Indices: 54989533--54989816 Score: 137
Period size: 23 Copynumber: 11.7 Consensus size: 25
54989523 ACGTACATAT
* * *
54989533 ATATATAAATAATAATGGTATTAGA
1 ATATATACATAATAATAGTATTAAA
54989558 A-ATATAC--AATATATAGTATTAGAA
1 ATATATACATAATA-ATAGTATTA-AA
54989582 ATATATACATAA-AATAGTA-TAAA
1 ATATATACATAATAATAGTATTAAA
*
54989605 A-ATATATATAACTAAT-GATATTAAA
1 ATATATACATAA-TAATAG-TATTAAA
54989630 ATATATACATAATAATA-TA-TAAA
1 ATATATACATAATAATAGTATTAAA
* *
54989653 AAATATA-ATATTAA-A--A--AAA
1 ATATATACATAATAATAGTATTAAA
* * *
54989672 TATATGTACATAA-CATA-TA-AAAA
1 -ATATATACATAATAATAGTATTAAA
54989695 ATATATACATAAT-ATAGTATTAAA
1 ATATATACATAATAATAGTATTAAA
* *
54989719 ATATTTACATAATATATACATATTAGAA
1 ATATATACATAATA-ATA-GTATTA-AA
* * * *
54989747 ATAAAAAACGACTATTAATAATATTACATAA
1 AT-ATATAC-A-TAATAATAGTATT--A-AA
54989778 ATATATACAT-AT-ATA-TATTAAA
1 ATATATACATAATAATAGTATTAAA
54989800 GATATATACAT-ATAATA
1 -ATATATACATAATAATA
54989817 AAACATATAC
Statistics
Matches: 206, Mismatches: 23, Indels: 61
0.71 0.08 0.21
Matches are distributed among these distances:
19 3 0.01
20 7 0.03
21 5 0.02
22 36 0.17
23 40 0.19
24 34 0.17
25 26 0.13
26 16 0.08
27 8 0.04
28 5 0.02
29 9 0.04
30 8 0.04
31 9 0.04
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (25 bp):
ATATATACATAATAATAGTATTAAA
Found at i:54989660 original size:16 final size:16
Alignment explanation
Indices: 54989641--54989675 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
54989631 TATATACATA
54989641 ATAATA-TATAAAAAAT
1 ATAATATTA-AAAAAAT
54989657 ATAATATTAAAAAAAT
1 ATAATATTAAAAAAAT
54989673 ATA
1 ATA
54989676 TGTACATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATAATATTAAAAAAAT
Found at i:54989708 original size:11 final size:11
Alignment explanation
Indices: 54989629--54989740 Score: 57
Period size: 11 Copynumber: 10.1 Consensus size: 11
54989619 ATGATATTAA
54989629 AATATATACAT
1 AATATATACAT
* *
54989640 AATAATATATAA
1 AAT-ATATACAT
*
54989652 AAAATATA-AT
1 AATATATACAT
* * * *
54989662 ATTAAAAAAAT
1 AATATATACAT
*
54989673 -ATATGTACAT
1 AATATATACAT
* * *
54989683 AACATATAAAA
1 AATATATACAT
54989694 AATATATACAT
1 AATATATACAT
* *
54989705 AATATAGTATTAA
1 AATATA-TA-CAT
*
54989718 AATATTTACAT
1 AATATATACAT
54989729 AATATATACAT
1 AATATATACAT
54989740 A
1 A
54989741 TTAGAAATAA
Statistics
Matches: 70, Mismatches: 26, Indels: 10
0.66 0.25 0.09
Matches are distributed among these distances:
10 10 0.14
11 42 0.60
12 12 0.17
13 6 0.09
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (11 bp):
AATATATACAT
Found at i:54989956 original size:25 final size:23
Alignment explanation
Indices: 54989853--54989978 Score: 93
Period size: 23 Copynumber: 5.4 Consensus size: 23
54989843 AATAAGGATA
*
54989853 ATATAAAAATATATACATGAA-AT
1 ATATAAAAACATATACAT-AATAT
* *
54989876 AGTAAAAAAAAATATA-ACTAATA-
1 A-TATAAAAACATATACA-TAATAT
*
54989899 ATACTAAAAATATATACATAATAT
1 ATA-TAAAAACATATACATAATAT
54989923 ATATAAAAACATATACGATATATAT
1 ATATAAAAACATATAC-ATA-ATAT
*
54989948 ATATTAAAA-ATGATA-ATAATAT
1 ATATAAAAACAT-ATACATAATAT
*
54989970 A-AAAAAAAC
1 ATATAAAAAC
54989979 TATTAATACA
Statistics
Matches: 85, Mismatches: 8, Indels: 21
0.75 0.07 0.18
Matches are distributed among these distances:
21 5 0.06
22 7 0.08
23 35 0.41
24 23 0.27
25 15 0.18
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.29
Consensus pattern (23 bp):
ATATAAAAACATATACATAATAT
Found at i:54990076 original size:18 final size:18
Alignment explanation
Indices: 54990051--54990094 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
54990041 ATACTAGTAC
54990051 TAATAATATTAATAATGAATA
1 TAATAATA-T-AT-ATGAATA
*
54990072 TAATAATATATATGCATA
1 TAATAATATATATGAATA
54990090 TAATA
1 TAATA
54990095 GTAAAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 11 0.50
19 2 0.09
20 1 0.05
21 8 0.36
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (18 bp):
TAATAATATATATGAATA
Found at i:54990941 original size:21 final size:20
Alignment explanation
Indices: 54990903--54990945 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
54990893 AAAAATCACC
*
54990903 TTTGTTTCTGATTTTGATCTT
1 TTTGTTTCTGATTCTGAT-TT
54990924 TTTGTTTTCTGA-TCTGATTT
1 TTTG-TTTCTGATTCTGATTT
54990944 TT
1 TT
54990946 GTGGTGTTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 9 0.45
22 7 0.35
ACGTcount: A:0.09, C:0.09, G:0.14, T:0.67
Consensus pattern (20 bp):
TTTGTTTCTGATTCTGATTT
Found at i:54992023 original size:87 final size:88
Alignment explanation
Indices: 54991729--54992047 Score: 375
Period size: 87 Copynumber: 3.6 Consensus size: 88
54991719 CAATCTTTAT
* * * *
54991729 CCTCGGCGTGTGACCTGAGGCTCAACTCACCTATCT-CAATATGAGTTGACTTTTTTTGAAAAAC
1 CCTCGGCATGTGACCCGAGGCTCAACTCACCTCT-TGAAATATGAGTTGA---TTTTTGAAAAAC
54991793 A-AATATTAAAAACA-AATTTTGAAAATA
62 AGAA-ATTAAAAACAGAA-TTTGAAAATA
* * * *
54991820 CCTCAGCATATGGCCCGAGGCTCAACTCACCT-TTCGCAATATGAGTTGATTTTTG-AAAACAGA
1 CCTCGGCATGTGACCCGAGGCTCAACTCACCTCTT-GAAATATGAGTTGATTTTTGAAAAACAGA
* *
54991883 CATTAAAAACAGAAATTG-AAATA
65 AATTAAAAACAGAATTTGAAAATA
** * *
54991906 CCTCGGTGTGTGACCCAAGGCTCAACTCACCTCTTGAAATATGAGTTGATTTTTGAAAAATAGAA
1 CCTCGGCATGTGACCCGAGGCTCAACTCACCTCTTGAAATATGAGTTGATTTTTGAAAAACAGAA
54991971 ATT-AAAACAGAATTTGAAAATA
66 ATTAAAAACAGAATTTGAAAATA
*
54991993 CCTCGGCATGTGACCCGAGGCTCAACTCACCTC-TCACAATATGAGTTGATTTTTG
1 CCTCGGCATGTGACCCGAGGCTCAACTCACCTCTTGA-AATATGAGTTGATTTTTG
54992048 GAATAACTGA
Statistics
Matches: 199, Mismatches: 21, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
86 64 0.32
87 84 0.42
88 9 0.05
89 1 0.01
90 1 0.01
91 40 0.20
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (88 bp):
CCTCGGCATGTGACCCGAGGCTCAACTCACCTCTTGAAATATGAGTTGATTTTTGAAAAACAGAA
ATTAAAAACAGAATTTGAAAATA
Found at i:54992035 original size:173 final size:175
Alignment explanation
Indices: 54991729--54992047 Score: 459
Period size: 173 Copynumber: 1.8 Consensus size: 175
54991719 CAATCTTTAT
** *
54991729 CCTCGGCGTGTGACCTGAGGCTCAACTCACCTATCTCAATATGAGTTGACTTTTTTTGAAAAACA
1 CCTCGGCGTGTGACCCAAGGCTCAACTCACCTATCTAAATATGAGTTGA--TTTTTTGAAAAACA
* * *
54991794 AATATTAAAAACAAATTTTGAAAATACCTCAGCATATGGCCCGAGGCTCAACTCACCTTTCGCAA
64 AATATTAAAAACAAATTTTGAAAATACCTCAGCATATGACCCGAGGCTCAACTCACCTCTCACAA
54991859 TATGAGTTGATTTTTGAAAACAGACATTAAAAACAGAAATTGAAATA
129 TATGAGTTGATTTTTGAAAACAGACATTAAAAACAGAAATTGAAATA
* * *
54991906 CCTCGGTGTGTGACCCAAGGCTCAACTCACCTCT-TGAAATATGAGTTGA-TTTTTGAAAAATAG
1 CCTCGGCGTGTGACCCAAGGCTCAACTCACCTATCT-AAATATGAGTTGATTTTTTGAAAAACA-
* *
54991969 AA-ATT-AAAACAGAA-TTTGAAAATACCTCGGCATGTGACCCGAGGCTCAACTCACCTCTCACA
64 AATATTAAAAACA-AATTTTGAAAATACCTCAGCATATGACCCGAGGCTCAACTCACCTCTCACA
54992031 ATATGAGTTGATTTTTG
128 ATATGAGTTGATTTTTG
54992048 GAATAACTGA
Statistics
Matches: 128, Mismatches: 11, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
173 66 0.52
174 17 0.13
175 2 0.02
176 1 0.01
177 42 0.33
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (175 bp):
CCTCGGCGTGTGACCCAAGGCTCAACTCACCTATCTAAATATGAGTTGATTTTTTGAAAAACAAA
TATTAAAAACAAATTTTGAAAATACCTCAGCATATGACCCGAGGCTCAACTCACCTCTCACAATA
TGAGTTGATTTTTGAAAACAGACATTAAAAACAGAAATTGAAATA
Found at i:55003721 original size:25 final size:25
Alignment explanation
Indices: 55003693--55003740 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
55003683 ATACATAGTA
**
55003693 TTAAAAATATGTACATAATATAGCG
1 TTAAAAATACATACATAATATAGCG
55003718 TTAAAAATACATACATAATATAG
1 TTAAAAATACATACATAATATAG
55003741 TTATTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.31
Consensus pattern (25 bp):
TTAAAAATACATACATAATATAGCG
Found at i:55003749 original size:25 final size:25
Alignment explanation
Indices: 55003687--55003749 Score: 60
Period size: 25 Copynumber: 2.5 Consensus size: 25
55003677 AAGTGTATAC
**
55003687 ATAG-TATTAAAAATATGTACATAAT
1 ATAGTTATT-AAAATACATACATAAT
55003712 ATAGCGTTA--AAAATACATACATAAT
1 ATA--GTTATTAAAATACATACATAAT
55003737 ATAGTTATTAAAA
1 ATAGTTATTAAAA
55003750 AATATATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
23 4 0.13
25 24 0.77
27 1 0.03
28 2 0.06
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.33
Consensus pattern (25 bp):
ATAGTTATTAAAATACATACATAAT
Found at i:55003818 original size:25 final size:25
Alignment explanation
Indices: 55003632--55004111 Score: 154
Period size: 24 Copynumber: 19.6 Consensus size: 25
55003622 CGATATATAA
55003632 ATATACAT-ATAT-GTATT-AAAAT
1 ATATACATAATATAGTATTAAAAAT
**
55003654 ATATACATAATAATAAAATTAAAAAGT
1 ATATACATAAT-ATAGTATTAAAAA-T
*
55003681 GTATAC-----ATAGTATTAAAAAT
1 ATATACATAATATAGTATTAAAAAT
* **
55003701 ATGTACATAATATAGCGTTAAAAAT
1 ATATACATAATATAGTATTAAAAAT
*
55003726 ACATACATAATATAGTTATTAAAAAAT
1 ATATACATAATATAG-TATT-AAAAAT
* **
55003753 ATATACATAAGATAATATGCAAGAAAAAAAT
1 ATATACAT-A-AT-ATA-G-TA-TTAAAAAT
* *
55003784 ATATAAATAATATAGTATTAAAGAT
1 ATATACATAATATAGTATTAAAAAT
*
55003809 ATATACATAATATA-TATAAAAAAATCAT
1 ATATACATAATATAGTAT--TAAAA--AT
** *
55003837 ATATACATGATATATA-TATTAGCAAC
1 ATATACAT-A-ATATAGTATTAAAAAT
* * ** **
55003863 A-ATA-ATGATACAAAAAGAAACAACT
1 ATATACATAATATAGTATTAAA-AA-T
* *
55003888 ATAATACAATAA-ATACG---TACATAT
1 AT-ATAC-ATAATATA-GTATTAAAAAT
* *
55003912 ATATAAATAATA-ACGGTATTAGAAAT
1 ATATACATAATATA--GTATTAAAAAT
* *
55003938 ATACA-AT-ATATAGTATTAGAAAT
1 ATATACATAATATAGTATTAAAAAT
*
55003961 ATATACATAAAATAGTA-TAAAAAT
1 ATATACATAATATAGTATTAAAAAT
55003985 ATAT--ATAACTA-ATGATATT-AAAAT
1 ATATACATAA-TATA-G-TATTAAAAAT
55004009 ATATACATAATA-A-TATATAAAAAT
1 ATATACATAATATAGTAT-TAAAAAT
55004033 -TATA-AT-AT-TA--A--AAAAAT
1 ATATACATAATATAGTATTAAAAAT
*
55004050 ATATGTACATAACATA-TA--AAAAAT
1 ATA--TACATAATATAGTATTAAAAAT
55004074 ATATACATAATATAGTATT-AAAAT
1 ATATACATAATATAGTATTAAAAAT
*
55004098 ATTTACATAATATA
1 ATATACATAATATA
55004112 TACATATTAT
Statistics
Matches: 344, Mismatches: 56, Indels: 114
0.67 0.11 0.22
Matches are distributed among these distances:
17 6 0.02
18 2 0.01
20 8 0.02
21 16 0.05
22 38 0.11
23 35 0.10
24 71 0.21
25 65 0.19
26 27 0.08
27 23 0.07
28 18 0.05
29 8 0.02
30 12 0.03
31 15 0.04
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (25 bp):
ATATACATAATATAGTATTAAAAAT
Found at i:55003825 original size:13 final size:13
Alignment explanation
Indices: 55003807--55003854 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
55003797 AGTATTAAAG
55003807 ATATATACATAAT
1 ATATATACATAAT
* *
55003820 ATATATAAAAAAAT
1 ATATAT-ACATAAT
*
55003834 CATATATACATGAT
1 -ATATATACATAAT
55003848 ATATATA
1 ATATATA
55003855 TTAGCAACAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
13 13 0.46
14 9 0.32
15 6 0.21
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.35
Consensus pattern (13 bp):
ATATATACATAAT
Found at i:55004085 original size:11 final size:11
Alignment explanation
Indices: 55004050--55004117 Score: 55
Period size: 11 Copynumber: 6.0 Consensus size: 11
55004040 TTAAAAAAAT
*
55004050 ATATGTACATA
1 ATATATACATA
* * *
55004061 ACATATAAAAA
1 ATATATACATA
55004072 ATATATACATA
1 ATATATACATA
* *
55004083 ATATAGTATTAAA
1 ATATA-TA-CATA
*
55004096 ATATTTACATA
1 ATATATACATA
55004107 ATATATACATA
1 ATATATACATA
55004118 TTATGTAATA
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
11 32 0.76
12 4 0.10
13 6 0.14
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.35
Consensus pattern (11 bp):
ATATATACATA
Found at i:55005205 original size:19 final size:19
Alignment explanation
Indices: 55005183--55005240 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
55005173 AATTTAAGTA
55005183 ATATAATGTTATTTATATG
1 ATATAATGTTATTTATATG
* *
55005202 ATATGATG--A-TTATTATC
1 ATATAATGTTATTTA-TATG
55005219 AT-TAATGTTATTTATATG
1 ATATAATGTTATTTATATG
55005237 ATAT
1 ATAT
55005241 GAAGATTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
16 7 0.23
17 6 0.20
18 6 0.20
19 11 0.37
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (19 bp):
ATATAATGTTATTTATATG
Found at i:55005225 original size:35 final size:35
Alignment explanation
Indices: 55005186--55005252 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
55005176 TTAAGTAATA
*
55005186 TAATGTTATTTATATGATATGATGATTATTATCAT
1 TAATGTTATTTATATGATATGAAGATTATTATCAT
55005221 TAATGTTATTTATATGATATGAAGATTATTAT
1 TAATGTTATTTATATGATATGAAGATTATTAT
55005253 TATGAAATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.51
Consensus pattern (35 bp):
TAATGTTATTTATATGATATGAAGATTATTATCAT
Found at i:55007013 original size:40 final size:40
Alignment explanation
Indices: 55006969--55007352 Score: 574
Period size: 40 Copynumber: 9.6 Consensus size: 40
55006959 AAGTGAATAT
* * * * **
55006969 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAA
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTGTTAA
55007009 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* *
55007049 ATCCGAGTTAAGTCCCGAAGGAATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
55007089 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* *
55007129 ATCCGAGTTAAGTCCCGAAGGAATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
55007169 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* *
55007209 ATCCGAGTTAAGTCCCGAAGGAATTCGTGCGAGTTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
*
55007249 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAATTGTTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* * **
55007289 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAA
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
* *
55007328 ATCCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATT
55007353 TGAACGAGGA
Statistics
Matches: 318, Mismatches: 25, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
39 35 0.11
40 283 0.89
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAA
Found at i:55015407 original size:19 final size:19
Alignment explanation
Indices: 55015385--55015442 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
55015375 AATTTAAGTA
55015385 ATATAATGTTATTTATATG
1 ATATAATGTTATTTATATG
* *
55015404 ATATGATG--A-TTATTATC
1 ATATAATGTTATTTA-TATG
*
55015421 AT-TAATTTTATTTATATG
1 ATATAATGTTATTTATATG
55015439 ATAT
1 ATAT
55015443 GAAGACTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 10
0.66 0.11 0.23
Matches are distributed among these distances:
16 6 0.21
17 6 0.21
18 6 0.21
19 11 0.38
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (19 bp):
ATATAATGTTATTTATATG
Found at i:55015432 original size:35 final size:35
Alignment explanation
Indices: 55015388--55015454 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
55015378 TTAAGTAATA
* *
55015388 TAATGTTATTTATATGATATGATGATTATTATCAT
1 TAATGTTATTTATATGATATGAAGACTATTATCAT
*
55015423 TAATTTTATTTATATGATATGAAGACTATTAT
1 TAATGTTATTTATATGATATGAAGACTATTAT
55015455 TATGAAATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (35 bp):
TAATGTTATTTATATGATATGAAGACTATTATCAT
Found at i:55017300 original size:23 final size:23
Alignment explanation
Indices: 55017265--55017336 Score: 78
Period size: 23 Copynumber: 3.1 Consensus size: 23
55017255 AAAAAAATAT
55017265 ATATATA-ACTAATAATATTAAAA
1 ATATATACA-TAATAATATTAAAA
55017288 ATATATACATAAT-ATATATAAAA
1 ATATATACATAATAATAT-TAAAA
*
55017311 ACATATACGAT-ATATATATTAAAA
1 ATATATAC-ATAATA-ATATTAAAA
55017335 AT
1 AT
55017337 GATAATAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
22 4 0.10
23 25 0.60
24 9 0.21
25 4 0.10
ACGTcount: A:0.58, C:0.06, G:0.01, T:0.35
Consensus pattern (23 bp):
ATATATACATAATAATATTAAAA
Found at i:55017327 original size:25 final size:22
Alignment explanation
Indices: 55017274--55017335 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 22
55017264 TATATATAAC
*
55017274 TAATAATATTAAAAATATATACA
1 TAAT-ATATTAAAAACATATACA
55017297 TAATATATATAAAAACATATACGA
1 TAATATAT-TAAAAACATATAC-A
55017321 TATATATATTAAAAA
1 TA-ATATATTAAAAA
55017336 TGATAATAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
22 4 0.11
23 16 0.46
24 9 0.26
25 6 0.17
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.34
Consensus pattern (22 bp):
TAATATATTAAAAACATATACA
Found at i:55017446 original size:3 final size:3
Alignment explanation
Indices: 55017431--55017472 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
55017421 ATACTAGTAC
* *
55017431 TAA TAA TAT TAA TAA TGAA T-A TAA TAA TAG TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
55017473 ATATATATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:55020574 original size:24 final size:25
Alignment explanation
Indices: 55020530--55020577 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
55020520 AAAAAAAATT
*
55020530 ATATTTGTTAAAGAATGTTAAAAAC
1 ATATTTGTTAAAGAATATTAAAAAC
55020555 ATATTTG-TAAA-AATTATTAAAAA
1 ATATTTGTTAAAGAA-TATTAAAAA
55020578 AATGATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 12 0.57
25 7 0.33
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (25 bp):
ATATTTGTTAAAGAATATTAAAAAC
Found at i:55025486 original size:28 final size:28
Alignment explanation
Indices: 55025448--55025501 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
55025438 AAATTACAGC
55025448 ATTATTGTTGTATTATTATCATACCATT
1 ATTATTGTTGTATTATTATCATACCATT
55025476 ATTATTGTTGTATTATTATCATACCA
1 ATTATTGTTGTATTATTATCATACCA
55025502 ACTTACATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (28 bp):
ATTATTGTTGTATTATTATCATACCATT
Found at i:55025774 original size:30 final size:30
Alignment explanation
Indices: 55025740--55025800 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
55025730 TCCTTAACTC
55025740 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
55025770 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
55025800 A
1 A
55025801 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:55028465 original size:36 final size:35
Alignment explanation
Indices: 55028416--55028487 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 35
55028406 GACATTTTCT
*
55028416 CGGCATTCTTTTACCTAGATTTGTTCATATTTGGA
1 CGGCATTCATTTACCTAGATTTGTTCATATTTGGA
55028451 NCGGCATTCATTTACCTAGATTTGTTCATATTTGGA
1 -CGGCATTCATTTACCTAGATTTGTTCATATTTGGA
55028487 C
1 C
55028488 TGGTTCGTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 1 0.03
36 34 0.97
ACGTcount: A:0.21, C:0.18, G:0.17, T:0.43
Consensus pattern (35 bp):
CGGCATTCATTTACCTAGATTTGTTCATATTTGGA
Found at i:55036321 original size:40 final size:40
Alignment explanation
Indices: 55036244--55036421 Score: 279
Period size: 40 Copynumber: 4.5 Consensus size: 40
55036234 AAACCAAGTA
* *
55036244 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCACTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCACACAAATG
* *
55036283 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
55036323 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
*
55036363 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
*
55036403 CCTCCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
55036422 TTATCATCCG
Statistics
Matches: 129, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 14 0.11
40 115 0.89
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
Done.