Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 87 of 167
Found at i:28746864 original size:31 final size:31
Alignment explanation
Indices: 28746828--28746889 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
28746818 ATTTGAATCA
* *
28746828 AATGCTTACTTTAATTCTTTTTCGAGATTAC
1 AATGCTCACTTTAATTCTTTTACGAGATTAC
*
28746859 AATGCTCACTTTAATTCTTTTACGGGATTAC
1 AATGCTCACTTTAATTCTTTTACGAGATTAC
28746890 TGACTCGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.45
Consensus pattern (31 bp):
AATGCTCACTTTAATTCTTTTACGAGATTAC
Found at i:28747088 original size:22 final size:22
Alignment explanation
Indices: 28747025--28747099 Score: 82
Period size: 22 Copynumber: 3.4 Consensus size: 22
28747015 GCTATGCATG
*
28747025 CAAAATATGAAAGACAGAAACA
1 CAAAATATGAAAGACAGAAATA
* * *
28747047 CAAAAGAT-ATA-ACAGTGAAATG
1 CAAAATATGAAAGACA--GAAATA
28747069 CAAAATATGAAAGACAGAAATA
1 CAAAATATGAAAGACAGAAATA
28747091 CAAAATATG
1 CAAAATATG
28747100 TCTTGTTACA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
20 3 0.07
21 2 0.05
22 32 0.76
23 2 0.05
24 3 0.07
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.15
Consensus pattern (22 bp):
CAAAATATGAAAGACAGAAATA
Found at i:28756129 original size:40 final size:40
Alignment explanation
Indices: 28756052--28756227 Score: 259
Period size: 40 Copynumber: 4.4 Consensus size: 40
28756042 AAACCAAGTA
* * * *
28756052 CCTTCGGAATTTAG-CCGGATATAGCT-ACTTGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
28756091 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
28756131 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
28756171 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
28756211 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
28756228 CGTTATCATC
Statistics
Matches: 128, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
39 14 0.11
40 114 0.89
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:28766044 original size:47 final size:48
Alignment explanation
Indices: 28765977--28766200 Score: 214
Period size: 47 Copynumber: 4.8 Consensus size: 48
28765967 CCACAATATA
* * **
28765977 AGAGCCAGTGTAAGACCATGTCCGGGACATGGCATCGGCATTGAGATG
1 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAACATTGAGATG
* * * * *
28766025 AGAGCTAGTGTAAGA-CATGTCTGAGACAT-GCATCGACCTCGAGACG
1 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAACATTGAGATG
* * *
28766071 TA-AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCTACTG-GATG
1 -AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAAC-ATTGAGATG
* *
28766117 ATAG-TCAGTGTAAGACCATGTCTGGGACATGGCATTAAC-TTGAGAT-
1 AGAGCT-AGTGTAAGACCATGTCTGGGACATGGCATCAACATTGAGATG
*
28766163 ATGAGCTAGTATAAGACCATGTCTGGGACATGGCATCA
1 A-GAGCTAGTGTAAGACCATGTCTGGGACATGGCATCA
28766201 GTACTTTACC
Statistics
Matches: 145, Mismatches: 22, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
45 1 0.01
46 61 0.42
47 62 0.43
48 21 0.14
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (48 bp):
AGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAACATTGAGATG
Found at i:28766082 original size:46 final size:46
Alignment explanation
Indices: 28765932--28766199 Score: 163
Period size: 46 Copynumber: 5.7 Consensus size: 46
28765922 ATTTGTGTGT
* * * * * * **
28765932 GAGCTAGTGTAAGACATGTTTGGGACATGCCTCAGCCA-CAATATAA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATC-GACATCGAGACGA
* * * *
28765978 GAGCCAGTGTAAGACCATGTCCGGGACATGGCATCGGCATTGAGATGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGACATCGAGACGA
* * *
28766026 GAGCTAGTGTAAGACATGTCTGAGACATGCATCGACCTCGAGACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGACATCGAGACG-A
*
28766073 -AGCCAGTGTAAGACATGTCTGGGACATGCATC-AGC-TACTG-GATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGA-CAT-C-GAGACGA
* * ** * *
28766118 TAGTCAGTGTAAGACCATGTCTGGGACATGGCATTAAC-TTGAGA-TA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGACATCGAGACGA
* *
28766164 TGAGCTAGTATAAGACCATGTCTGGGACATGGCATC
1 -GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATC
28766200 AGTACTTTAC
Statistics
Matches: 181, Mismatches: 28, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
45 3 0.02
46 75 0.41
47 75 0.41
48 27 0.15
49 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.23
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGACATCGAGACGA
Found at i:28766193 original size:140 final size:141
Alignment explanation
Indices: 28765937--28766199 Score: 352
Period size: 140 Copynumber: 1.9 Consensus size: 141
28765927 TGTGTGAGCT
* * *
28765937 AGTGTAAGACATGTTTGGGACATGCCTCAGCCACAATATAAGAGCCAGTGTAAGACCATGTCCGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGATAAGAGCCAGTGTAAGACCATGTCCGG
** *
28766002 GACATGGCATCGGCATTGAGATGAGAGCTAGTGTAAGACATGTCTGAGACAT-GCATCGACCTCG
66 GACATGGCATCAACATTGAGATGAGAGCTAGTATAAGACATGTCTGAGACATGGCATCGACCTCG
28766066 AGACGTAAGCC
131 AGACGTAAGCC
* ** * * * *
28766077 AGTGTAAGACATGTCTGGGACATGCATCAGCTACTGGATGATAGTCAGTGTAAGACCATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGATAAGAGCCAGTGTAAGACCATGTCCGG
* *
28766142 GACATGGCATTAAC-TTGAGAT-ATGAGCTAGTATAAGACCATGTCTGGGACATGGCATC
66 GACATGGCATCAACATTGAGATGA-GAGCTAGTATAAGA-CATGTCTGAGACATGGCATC
28766200 AGTACTTTAC
Statistics
Matches: 105, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
138 1 0.01
139 20 0.19
140 79 0.75
141 5 0.05
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (141 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGATAAGAGCCAGTGTAAGACCATGTCCGG
GACATGGCATCAACATTGAGATGAGAGCTAGTATAAGACATGTCTGAGACATGGCATCGACCTCG
AGACGTAAGCC
Found at i:28771051 original size:30 final size:30
Alignment explanation
Indices: 28770993--28771052 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
28770983 ATTTAATATG
*
28770993 AACTTTGGCAAAATCACATTTTTACCCCTA
1 AACTTTGGCAAAATCACACTTTTACCCCTA
* * * *
28771023 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATCACACTTTTACCCCTA
28771053 GGCTCGGGAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.37
Consensus pattern (30 bp):
AACTTTGGCAAAATCACACTTTTACCCCTA
Found at i:28778845 original size:38 final size:37
Alignment explanation
Indices: 28778802--28778879 Score: 131
Period size: 38 Copynumber: 2.1 Consensus size: 37
28778792 GTTAGTTAAA
28778802 ACAAAACCTCTTTATTCTTAGGT-TAGATAATAAAAAAG
1 ACAAAACCTCTTTATTCTTA-GTCTAGATAAT-AAAAAG
28778840 ACAAAACCTCTTTATTCTTAGTCTAGATAATAAAAAG
1 ACAAAACCTCTTTATTCTTAGTCTAGATAATAAAAAG
28778877 ACA
1 ACA
28778880 GTCATTACTA
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
37 11 0.28
38 28 0.72
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (37 bp):
ACAAAACCTCTTTATTCTTAGTCTAGATAATAAAAAG
Found at i:28781423 original size:39 final size:40
Alignment explanation
Indices: 28781264--28781439 Score: 218
Period size: 40 Copynumber: 4.5 Consensus size: 40
28781254 CAACCAAGTA
**
28781264 CCTTCGGGGTTTAG-CCGGATATAGCT-A-TCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
28781302 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
28781342 CCTTCGGGACTTAGCCCGGATATAATAACTCACACAATTG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
28781382 CCTTCGGG-CTTAGCCC-GAAATTAGTCACTTGCACAGATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
28781421 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
28781440 TTATCATCCG
Statistics
Matches: 120, Mismatches: 12, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
38 16 0.13
39 39 0.32
40 64 0.53
41 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:28782929 original size:56 final size:56
Alignment explanation
Indices: 28782862--28782981 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
28782852 TATTAGTTTA
28782862 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
28782918 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
28782974 TTGCCCAT
1 TTGCCCAT
28782982 CATCCCTTGT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:28789527 original size:40 final size:40
Alignment explanation
Indices: 28789481--28789705 Score: 290
Period size: 40 Copynumber: 5.6 Consensus size: 40
28789471 CTTGCGCAAG
* * *
28789481 GCCTTCGGGTCTTAGCCCGGATGTGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
28789521 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* * *
28789561 GCCTTCGGGTTTTAGCCCGGATATAATCGCTAGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
* *
28789601 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCACAAAT
* * * *
28789641 GCCTTCGGATCTTAGTCCGGTTATAGTCACCTAGCACAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCA-CTAGCACAAAT
*
28789682 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
28789706 CATTCGAATA
Statistics
Matches: 159, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 129 0.81
41 29 0.18
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAAT
Found at i:28789576 original size:80 final size:80
Alignment explanation
Indices: 28789445--28789705 Score: 303
Period size: 80 Copynumber: 3.3 Consensus size: 80
28789435 CTCAAGTAAT
* * * * * * * *
28789445 CTTCGGGATTTAG-CCGGATATAACTACTTGCGC-AAGGCCTTCGGGTCTTAGCCCGGATGTGGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
*
28789508 CACTAGCATAAATGC
66 CACTAGCACAAATGC
* * *
28789523 CTTCGGGACTTAGCCCGGATATAGTC-GCTAGCACAAATGCCTTCGGGTTTTAGCCCGGATATAA
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG
*
28789587 TCGCTAGCACAAATGC
65 TCACTAGCACAAATGC
* * * * * *
28789603 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACGAATGCCTTCGGATCTTAGTCCGGTTATAGT
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
*
28789668 CACCTAGCACAAAAGC
66 CA-CTAGCACAAATGC
28789684 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
28789706 CATTCGAATA
Statistics
Matches: 154, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
78 12 0.08
79 15 0.10
80 94 0.61
81 33 0.21
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:28793309 original size:20 final size:21
Alignment explanation
Indices: 28793276--28793314 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
28793266 GACTAAACCG
*
28793276 ACAACTTAGGAAACTTTTGGA
1 ACAACTTAGAAAACTTTTGGA
28793297 ACAA-TTAGAAAACTTTTG
1 ACAACTTAGAAAACTTTTG
28793315 CAAAATACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (21 bp):
ACAACTTAGAAAACTTTTGGA
Found at i:28805040 original size:28 final size:28
Alignment explanation
Indices: 28804977--28805102 Score: 173
Period size: 28 Copynumber: 4.5 Consensus size: 28
28804967 ATATTAAGTC
*
28804977 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
28805004 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* *
28805032 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
28805060 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
28805089 CGCACACTTAGTGC
1 CGCACACTTAGTGC
28805103 CAATCTCATG
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
27 22 0.25
28 48 0.55
29 18 0.20
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:28805047 original size:55 final size:57
Alignment explanation
Indices: 28804976--28805102 Score: 186
Period size: 55 Copynumber: 2.3 Consensus size: 57
28804966 TATATTAAGT
* * *
28804976 CCGCACACTCAGTGCTATATAATCAA-CTCGCACACTTAGTGCTATATAA-TCAAAC
1 CCGCACACTTAGTGCTACATAATCAAGCTCGCACACTTAGTGCTATACAATTCAAAC
* * *
28805031 TCGCACACTTAGTGCTACATAATCAAGCTCGCACACTTAGTGCTGTACAATTTAAAC
1 CCGCACACTTAGTGCTACATAATCAAGCTCGCACACTTAGTGCTATACAATTCAAAC
28805088 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
28805103 CAATCTCATG
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
55 23 0.37
56 21 0.33
57 19 0.30
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.26
Consensus pattern (57 bp):
CCGCACACTTAGTGCTACATAATCAAGCTCGCACACTTAGTGCTATACAATTCAAAC
Found at i:28828596 original size:54 final size:54
Alignment explanation
Indices: 28828511--28828642 Score: 246
Period size: 54 Copynumber: 2.4 Consensus size: 54
28828501 GTCATTACAA
28828511 GGGATTTAGCCTGGACTGGTAATCCCAACATCACCTTATGAGTTCATAAAATGG
1 GGGATTTAGCCTGGACTGGTAATCCCAACATCACCTTATGAGTTCATAAAATGG
*
28828565 GGGATTTAGCCTGGACTGGTAATCCCGACATCACCTTATGAGTTCATAAAATGG
1 GGGATTTAGCCTGGACTGGTAATCCCAACATCACCTTATGAGTTCATAAAATGG
*
28828619 GGGATTTAGCTTGGACTGGTAATC
1 GGGATTTAGCCTGGACTGGTAATC
28828643 TTGCCATAAG
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 76 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (54 bp):
GGGATTTAGCCTGGACTGGTAATCCCAACATCACCTTATGAGTTCATAAAATGG
Found at i:28830993 original size:25 final size:25
Alignment explanation
Indices: 28830965--28831012 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
28830955 TTTTAACCGT
*
28830965 TTATTTTTCTTAC-AATTTAATTTTA
1 TTATTTTTATTACTAA-TTAATTTTA
28830990 TTATTTTTATTACTAATTAATTT
1 TTATTTTTATTACTAATTAATTT
28831013 ACTTTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (25 bp):
TTATTTTTATTACTAATTAATTTTA
Found at i:28839262 original size:21 final size:21
Alignment explanation
Indices: 28839238--28839297 Score: 50
Period size: 25 Copynumber: 2.6 Consensus size: 21
28839228 TACTTTAGCC
28839238 ATTTATTTTTCTTAC-AATTTA
1 ATTTATTTTTCTTACTAA-TTA
*
28839259 ATTTTATTATTTTTATTACTAATTA
1 A---T-TTATTTTTCTTACTAATTA
28839284 ATTTACTTTTTCTT
1 ATTTA-TTTTTCTT
28839298 TCTCCTGGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
21 4 0.13
22 8 0.26
24 1 0.03
25 16 0.52
26 2 0.06
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTATTTTTCTTACTAATTA
Found at i:28839277 original size:25 final size:25
Alignment explanation
Indices: 28839240--28839287 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
28839230 CTTTAGCCAT
*
28839240 TTATTTTTCTTAC-AATTTAATTTTA
1 TTATTTTTATTACTAA-TTAATTTTA
28839265 TTATTTTTATTACTAATTAATTT
1 TTATTTTTATTACTAATTAATTT
28839288 ACTTTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (25 bp):
TTATTTTTATTACTAATTAATTTTA
Found at i:28842484 original size:145 final size:145
Alignment explanation
Indices: 28842221--28842512 Score: 584
Period size: 145 Copynumber: 2.0 Consensus size: 145
28842211 ATTTCAAAGT
28842221 ATAAGGCCAAGTGGCACCAATTCTAAAGGAAGACCTCAGAAGAATGTTGGAGTTGGGGCTGGTAG
1 ATAAGGCCAAGTGGCACCAATTCTAAAGGAAGACCTCAGAAGAATGTTGGAGTTGGGGCTGGTAG
28842286 CAAGAATGTGACGAGAGACACCACTGTAAGGTCTGAAGCTAGAGCTCCGGCTAGAACCTATGCCA
66 CAAGAATGTGACGAGAGACACCACTGTAAGGTCTGAAGCTAGAGCTCCGGCTAGAACCTATGCCA
28842351 TACGTGCATGTGAAG
131 TACGTGCATGTGAAG
28842366 ATAAGGCCAAGTGGCACCAATTCTAAAGGAAGACCTCAGAAGAATGTTGGAGTTGGGGCTGGTAG
1 ATAAGGCCAAGTGGCACCAATTCTAAAGGAAGACCTCAGAAGAATGTTGGAGTTGGGGCTGGTAG
28842431 CAAGAATGTGACGAGAGACACCACTGTAAGGTCTGAAGCTAGAGCTCCGGCTAGAACCTATGCCA
66 CAAGAATGTGACGAGAGACACCACTGTAAGGTCTGAAGCTAGAGCTCCGGCTAGAACCTATGCCA
28842496 TACGTGCATGTGAAG
131 TACGTGCATGTGAAG
28842511 AT
1 AT
28842513 GCATCCTCTC
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 147 1.00
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.20
Consensus pattern (145 bp):
ATAAGGCCAAGTGGCACCAATTCTAAAGGAAGACCTCAGAAGAATGTTGGAGTTGGGGCTGGTAG
CAAGAATGTGACGAGAGACACCACTGTAAGGTCTGAAGCTAGAGCTCCGGCTAGAACCTATGCCA
TACGTGCATGTGAAG
Found at i:28850286 original size:16 final size:16
Alignment explanation
Indices: 28850267--28850297 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28850257 CTTCTTCACT
28850267 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
28850283 TACTTACTTACTTAA
1 TACTCACTTACTTAA
28850298 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:28850303 original size:20 final size:20
Alignment explanation
Indices: 28850264--28850303 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28850254 AAACTTCTTC
* *
28850264 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
28850284 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
28850304 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:28850669 original size:55 final size:53
Alignment explanation
Indices: 28850541--28850685 Score: 166
Period size: 53 Copynumber: 2.7 Consensus size: 53
28850531 ATCCTTTTGA
* * * * * *
28850541 AACTTACCACTGCCATGTCTTGACATGGTCTTATATGGTATCATTGCCTTATG
1 AACTTACCAATGCCATGCCTTGGCATGGTCTTACATGGGACCATTGCCTTATG
* *
28850594 AA-TTCACCAATGCCATGCCTTGGCATGATCTTACATGGGACCTTTGCCTTATAG
1 AACTT-ACCAATGCCATGCCTTGGCATGGTCTTACATGGGACCATTGCCTTAT-G
* *
28850648 TAACTTATCAATGCCATGCCTTGGCATGGCCTTACATG
1 -AACTTACCAATGCCATGCCTTGGCATGGTCTTACATG
28850686 ATTTCCTTGC
Statistics
Matches: 77, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
52 2 0.03
53 41 0.53
54 1 0.01
55 31 0.40
56 2 0.03
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (53 bp):
AACTTACCAATGCCATGCCTTGGCATGGTCTTACATGGGACCATTGCCTTATG
Found at i:28850696 original size:55 final size:52
Alignment explanation
Indices: 28850541--28850713 Score: 154
Period size: 53 Copynumber: 3.2 Consensus size: 52
28850531 ATCCTTTTGA
* * * * *
28850541 AACTTACCACTGCCATGTCTTGACATGGTCTTATATGGTATCATTGCCTTATG
1 AACTTACCAATGCCATGCCTTGGCATGGTCTTACAT-GTATCCTTGCCTTATG
* *
28850594 AA-TTCACCAATGCCATGCCTTGGCATGATCTTACATGGGA-CCTTTGCCTTATAG
1 AACTT-ACCAATGCCATGCCTTGGCATGGTCTTACAT-GTATCC-TTGCCTTAT-G
* * *
28850648 TAACTTATCAATGCCATGCCTTGGCATGGCCTTACATGATTTCCTTGCCTTA-G
1 -AACTTACCAATGCCATGCCTTGGCATGGTCTTACATG-TATCCTTGCCTTATG
28850701 AAACCTTACCAAT
1 -AA-CTTACCAAT
28850714 TNNNNNNNNN
Statistics
Matches: 98, Mismatches: 14, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
52 3 0.03
53 43 0.44
54 10 0.10
55 38 0.39
56 4 0.04
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.34
Consensus pattern (52 bp):
AACTTACCAATGCCATGCCTTGGCATGGTCTTACATGTATCCTTGCCTTATG
Found at i:28857146 original size:16 final size:16
Alignment explanation
Indices: 28857127--28857157 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28857117 CTTCTTCACT
28857127 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
28857143 TACTTACTTACTTAA
1 TACTCACTTACTTAA
28857158 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:28857163 original size:20 final size:20
Alignment explanation
Indices: 28857124--28857163 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28857114 AAACTTCTTC
* *
28857124 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
28857144 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
28857164 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:28861712 original size:74 final size:73
Alignment explanation
Indices: 28861591--28861754 Score: 256
Period size: 74 Copynumber: 2.2 Consensus size: 73
28861581 CACGGCCTCA
* * *
28861591 GGACACGAGCGTGTGTCTTGGCCGTGTGACTTGAATTTGTTCTTGGGTGACAAATAGAGAGTTAC
1 GGACACG-GCGTGTGTCTTGGCCATGTGACTTAAATTTGTTCTTGGGTGAAAAATAGAGAGTTAC
28861656 ACAGGTTAG
65 ACAGGTTAG
28861665 GGACACAGGCGTGTGTCTTGGCCATGTGACTTAAATTTGTTCTTGGGTGAAAAATAGAGAGTTAC
1 GGACAC-GGCGTGTGTCTTGGCCATGTGACTTAAATTTGTTCTTGGGTGAAAAATAGAGAGTTAC
*
28861730 ACGGGTTAG
65 ACAGGTTAG
*
28861739 GGACATGGGCGTGTGT
1 GGACA-CGGCGTGTGT
28861755 GACCACACGG
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
74 82 0.99
75 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.34, T:0.29
Consensus pattern (73 bp):
GGACACGGCGTGTGTCTTGGCCATGTGACTTAAATTTGTTCTTGGGTGAAAAATAGAGAGTTACA
CAGGTTAG
Found at i:28867973 original size:418 final size:418
Alignment explanation
Indices: 28867196--28868031 Score: 1672
Period size: 418 Copynumber: 2.0 Consensus size: 418
28867186 ATAGAAGCCA
28867196 TCGAAGTCGGTAATAGAGATCCGAAGTTTTTTGGGGTTGGCAGGTTATTATCGGAGATTCGTGGA
1 TCGAAGTCGGTAATAGAGATCCGAAGTTTTTTGGGGTTGGCAGGTTATTATCGGAGATTCGTGGA
28867261 AGGATTTTCTGTGTTGGCAGCACCGTTAACGAAACTTATAAGGAAAGGAGCACCTTTTGTCTGGA
66 AGGATTTTCTGTGTTGGCAGCACCGTTAACGAAACTTATAAGGAAAGGAGCACCTTTTGTCTGGA
28867326 CGAATAAGCGGCAAGAGGCTTTTGAGAAACTGAAGAAGGTTTTGACAGAAGCGCCAGTGTTGATT
131 CGAATAAGCGGCAAGAGGCTTTTGAGAAACTGAAGAAGGTTTTGACAGAAGCGCCAGTGTTGATT
28867391 CAGCTAGAGTCTGGTAAGGATTTCACTGTGTTCAGTGATGCGTCACATGTAGGTTTGGGCTGCGT
196 CAGCTAGAGTCTGGTAAGGATTTCACTGTGTTCAGTGATGCGTCACATGTAGGTTTGGGCTGCGT
28867456 GTTGATGCAAGAGGGTAAAGTGGTCGCTTATGCTTCACGAAAGCTCAAGCCTCACGAGGTGAACT
261 GTTGATGCAAGAGGGTAAAGTGGTCGCTTATGCTTCACGAAAGCTCAAGCCTCACGAGGTGAACT
28867521 ATCCTATGCATGACTTGGAGTTGGCAGCGGTGATTTTCGTACTTAAGATATGGAGGCATTACTTG
326 ATCCTATGCATGACTTGGAGTTGGCAGCGGTGATTTTCGTACTTAAGATATGGAGGCATTACTTG
28867586 TATGGGGAGAAATGCATCATCTATACGG
391 TATGGGGAGAAATGCATCATCTATACGG
28867614 TCGAAGTCGGTAATAGAGATCCGAAGTTTTTTGGGGTTGGCAGGTTATTATCGGAGATTCGTGGA
1 TCGAAGTCGGTAATAGAGATCCGAAGTTTTTTGGGGTTGGCAGGTTATTATCGGAGATTCGTGGA
28867679 AGGATTTTCTGTGTTGGCAGCACCGTTAACGAAACTTATAAGGAAAGGAGCACCTTTTGTCTGGA
66 AGGATTTTCTGTGTTGGCAGCACCGTTAACGAAACTTATAAGGAAAGGAGCACCTTTTGTCTGGA
28867744 CGAATAAGCGGCAAGAGGCTTTTGAGAAACTGAAGAAGGTTTTGACAGAAGCGCCAGTGTTGATT
131 CGAATAAGCGGCAAGAGGCTTTTGAGAAACTGAAGAAGGTTTTGACAGAAGCGCCAGTGTTGATT
28867809 CAGCTAGAGTCTGGTAAGGATTTCACTGTGTTCAGTGATGCGTCACATGTAGGTTTGGGCTGCGT
196 CAGCTAGAGTCTGGTAAGGATTTCACTGTGTTCAGTGATGCGTCACATGTAGGTTTGGGCTGCGT
28867874 GTTGATGCAAGAGGGTAAAGTGGTCGCTTATGCTTCACGAAAGCTCAAGCCTCACGAGGTGAACT
261 GTTGATGCAAGAGGGTAAAGTGGTCGCTTATGCTTCACGAAAGCTCAAGCCTCACGAGGTGAACT
28867939 ATCCTATGCATGACTTGGAGTTGGCAGCGGTGATTTTCGTACTTAAGATATGGAGGCATTACTTG
326 ATCCTATGCATGACTTGGAGTTGGCAGCGGTGATTTTCGTACTTAAGATATGGAGGCATTACTTG
28868004 TATGGGGAGAAATGCATCATCTATACGG
391 TATGGGGAGAAATGCATCATCTATACGG
28868032 ATCACAAAAG
Statistics
Matches: 418, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
418 418 1.00
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.29
Consensus pattern (418 bp):
TCGAAGTCGGTAATAGAGATCCGAAGTTTTTTGGGGTTGGCAGGTTATTATCGGAGATTCGTGGA
AGGATTTTCTGTGTTGGCAGCACCGTTAACGAAACTTATAAGGAAAGGAGCACCTTTTGTCTGGA
CGAATAAGCGGCAAGAGGCTTTTGAGAAACTGAAGAAGGTTTTGACAGAAGCGCCAGTGTTGATT
CAGCTAGAGTCTGGTAAGGATTTCACTGTGTTCAGTGATGCGTCACATGTAGGTTTGGGCTGCGT
GTTGATGCAAGAGGGTAAAGTGGTCGCTTATGCTTCACGAAAGCTCAAGCCTCACGAGGTGAACT
ATCCTATGCATGACTTGGAGTTGGCAGCGGTGATTTTCGTACTTAAGATATGGAGGCATTACTTG
TATGGGGAGAAATGCATCATCTATACGG
Found at i:28868851 original size:587 final size:587
Alignment explanation
Indices: 28867739--28868912 Score: 2348
Period size: 587 Copynumber: 2.0 Consensus size: 587
28867729 CACCTTTTGT
28867739 CTGGACGAATAAGCGGCAAGAGGCTTTTGAGAAACTGAAGAAGGTTTTGACAGAAGCGCCAGTGT
1 CTGGACGAATAAGCGGCAAGAGGCTTTTGAGAAACTGAAGAAGGTTTTGACAGAAGCGCCAGTGT
28867804 TGATTCAGCTAGAGTCTGGTAAGGATTTCACTGTGTTCAGTGATGCGTCACATGTAGGTTTGGGC
66 TGATTCAGCTAGAGTCTGGTAAGGATTTCACTGTGTTCAGTGATGCGTCACATGTAGGTTTGGGC
28867869 TGCGTGTTGATGCAAGAGGGTAAAGTGGTCGCTTATGCTTCACGAAAGCTCAAGCCTCACGAGGT
131 TGCGTGTTGATGCAAGAGGGTAAAGTGGTCGCTTATGCTTCACGAAAGCTCAAGCCTCACGAGGT
28867934 GAACTATCCTATGCATGACTTGGAGTTGGCAGCGGTGATTTTCGTACTTAAGATATGGAGGCATT
196 GAACTATCCTATGCATGACTTGGAGTTGGCAGCGGTGATTTTCGTACTTAAGATATGGAGGCATT
28867999 ACTTGTATGGGGAGAAATGCATCATCTATACGGATCACAAAAGTCTTAAGTACTTGCTGACTCAA
261 ACTTGTATGGGGAGAAATGCATCATCTATACGGATCACAAAAGTCTTAAGTACTTGCTGACTCAA
28868064 AAAGAGCTGAATCTTAGACAGCGAAGGTGGATAGAGCTGCTAAAGGACTATGACTGTTCGATCGA
326 AAAGAGCTGAATCTTAGACAGCGAAGGTGGATAGAGCTGCTAAAGGACTATGACTGTTCGATCGA
28868129 GTACCATCCAGGAAAAGCAAATGTCGTGGCTGATGCGCTAAGTCGGAGGACTGTGGCGGAGTTGA
391 GTACCATCCAGGAAAAGCAAATGTCGTGGCTGATGCGCTAAGTCGGAGGACTGTGGCGGAGTTGA
28868194 AGGCAATGTTTGCTCGTCTAAGTTTGAATGATGATGGAAGCTTATTGGCGGAATTACAAGTGAGA
456 AGGCAATGTTTGCTCGTCTAAGTTTGAATGATGATGGAAGCTTATTGGCGGAATTACAAGTGAGA
28868259 CCAACTTGGGTAGAGCAGATTAAGAAGCAACAGTTGGAGGATGAGTCATTGGTTTCTCGGATTCA
521 CCAACTTGGGTAGAGCAGATTAAGAAGCAACAGTTGGAGGATGAGTCATTGGTTTCTCGGATTCA
28868324 AC
586 AC
28868326 CTGGACGAATAAGCGGCAAGAGGCTTTTGAGAAACTGAAGAAGGTTTTGACAGAAGCGCCAGTGT
1 CTGGACGAATAAGCGGCAAGAGGCTTTTGAGAAACTGAAGAAGGTTTTGACAGAAGCGCCAGTGT
28868391 TGATTCAGCTAGAGTCTGGTAAGGATTTCACTGTGTTCAGTGATGCGTCACATGTAGGTTTGGGC
66 TGATTCAGCTAGAGTCTGGTAAGGATTTCACTGTGTTCAGTGATGCGTCACATGTAGGTTTGGGC
28868456 TGCGTGTTGATGCAAGAGGGTAAAGTGGTCGCTTATGCTTCACGAAAGCTCAAGCCTCACGAGGT
131 TGCGTGTTGATGCAAGAGGGTAAAGTGGTCGCTTATGCTTCACGAAAGCTCAAGCCTCACGAGGT
28868521 GAACTATCCTATGCATGACTTGGAGTTGGCAGCGGTGATTTTCGTACTTAAGATATGGAGGCATT
196 GAACTATCCTATGCATGACTTGGAGTTGGCAGCGGTGATTTTCGTACTTAAGATATGGAGGCATT
28868586 ACTTGTATGGGGAGAAATGCATCATCTATACGGATCACAAAAGTCTTAAGTACTTGCTGACTCAA
261 ACTTGTATGGGGAGAAATGCATCATCTATACGGATCACAAAAGTCTTAAGTACTTGCTGACTCAA
28868651 AAAGAGCTGAATCTTAGACAGCGAAGGTGGATAGAGCTGCTAAAGGACTATGACTGTTCGATCGA
326 AAAGAGCTGAATCTTAGACAGCGAAGGTGGATAGAGCTGCTAAAGGACTATGACTGTTCGATCGA
28868716 GTACCATCCAGGAAAAGCAAATGTCGTGGCTGATGCGCTAAGTCGGAGGACTGTGGCGGAGTTGA
391 GTACCATCCAGGAAAAGCAAATGTCGTGGCTGATGCGCTAAGTCGGAGGACTGTGGCGGAGTTGA
28868781 AGGCAATGTTTGCTCGTCTAAGTTTGAATGATGATGGAAGCTTATTGGCGGAATTACAAGTGAGA
456 AGGCAATGTTTGCTCGTCTAAGTTTGAATGATGATGGAAGCTTATTGGCGGAATTACAAGTGAGA
28868846 CCAACTTGGGTAGAGCAGATTAAGAAGCAACAGTTGGAGGATGAGTCATTGGTTTCTCGGATTCA
521 CCAACTTGGGTAGAGCAGATTAAGAAGCAACAGTTGGAGGATGAGTCATTGGTTTCTCGGATTCA
28868911 AC
586 AC
28868913 AAGTTGAGAA
Statistics
Matches: 587, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
587 587 1.00
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.26
Consensus pattern (587 bp):
CTGGACGAATAAGCGGCAAGAGGCTTTTGAGAAACTGAAGAAGGTTTTGACAGAAGCGCCAGTGT
TGATTCAGCTAGAGTCTGGTAAGGATTTCACTGTGTTCAGTGATGCGTCACATGTAGGTTTGGGC
TGCGTGTTGATGCAAGAGGGTAAAGTGGTCGCTTATGCTTCACGAAAGCTCAAGCCTCACGAGGT
GAACTATCCTATGCATGACTTGGAGTTGGCAGCGGTGATTTTCGTACTTAAGATATGGAGGCATT
ACTTGTATGGGGAGAAATGCATCATCTATACGGATCACAAAAGTCTTAAGTACTTGCTGACTCAA
AAAGAGCTGAATCTTAGACAGCGAAGGTGGATAGAGCTGCTAAAGGACTATGACTGTTCGATCGA
GTACCATCCAGGAAAAGCAAATGTCGTGGCTGATGCGCTAAGTCGGAGGACTGTGGCGGAGTTGA
AGGCAATGTTTGCTCGTCTAAGTTTGAATGATGATGGAAGCTTATTGGCGGAATTACAAGTGAGA
CCAACTTGGGTAGAGCAGATTAAGAAGCAACAGTTGGAGGATGAGTCATTGGTTTCTCGGATTCA
AC
Found at i:28872449 original size:26 final size:26
Alignment explanation
Indices: 28872374--28872469 Score: 133
Period size: 27 Copynumber: 3.7 Consensus size: 26
28872364 GAGGAAGTGC
28872374 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
* *
28872400 AGAAAGGGCTTATGCCACAATTTATTG
1 A-AAAGGGCTTATGCCCCAGTTTATTG
**
28872427 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
28872453 -AAAGGGCTT-TGCCCCAG
1 AAAAGGGCTTATGCCCCAG
28872470 ATATTAAAGA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
24 8 0.13
25 9 0.14
26 22 0.35
27 24 0.38
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:28876708 original size:49 final size:50
Alignment explanation
Indices: 28876635--28876809 Score: 235
Period size: 52 Copynumber: 3.5 Consensus size: 50
28876625 ACCAGTGACT
*
28876635 CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAG-AGATAGCTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTGGTCA
* *
28876684 TAAGTGTCGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAGATAGC-TTGGTCA
* * * *
28876736 CAAGTGTGGTACTATGTGAAGGCCATTTTGTGAAGAAGGTAGCTTTGACTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTGGTC-A
* *
28876787 CAAGGGTGGTACTATGTGCAGGC
1 CAAGTGTGGTACTATGTGAAGGC
28876810 TACTGGCTAT
Statistics
Matches: 111, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
49 32 0.29
50 4 0.04
51 36 0.32
52 39 0.35
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (50 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTGGTCA
Found at i:28876755 original size:52 final size:51
Alignment explanation
Indices: 28876635--28876809 Score: 239
Period size: 51 Copynumber: 3.5 Consensus size: 51
28876625 ACCAGTGACT
*
28876635 CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAG-AGATAGC-TTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGGTCA
* *
28876684 TAAGTGTCGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAGATAGCTTTGGTCA
* * *
28876736 CAAGTGTGGTACTATGTGAAGGCCATTTTGTGAAGAAGGTAGCTTT-GACTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGGTC-A
* *
28876787 CAAGGGTGGTACTATGTGCAGGC
1 CAAGTGTGGTACTATGTGAAGGC
28876810 TACTGGCTAT
Statistics
Matches: 112, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
49 32 0.29
50 2 0.02
51 39 0.35
52 39 0.35
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (51 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGGTCA
Found at i:28882696 original size:13 final size:13
Alignment explanation
Indices: 28882678--28882702 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28882668 GAAGTAATTA
28882678 CACACGGGCATGT
1 CACACGGGCATGT
28882691 CACACGGGCATG
1 CACACGGGCATG
28882703 CCCCTGCCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.32, G:0.32, T:0.12
Consensus pattern (13 bp):
CACACGGGCATGT
Found at i:28894166 original size:28 final size:29
Alignment explanation
Indices: 28894133--28894233 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
28894123 TATAGTAAGT
* * *
28894133 CCGCACACTTAGTGTTATATAA-TCGAAC
1 CCGCACACTTAGTGCTATACAACTTGAAC
*
28894161 TCGCACACTTAGTGCTATACAACTTGAAC
1 CCGCACACTTAGTGCTATACAACTTGAAC
*
28894190 CCGCACACTTAGTGCTATACAATTTGAAC
1 CCGCACACTTAGTGCTATACAACTTGAAC
28894219 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
28894234 CAATTTCATG
Statistics
Matches: 66, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
28 19 0.29
29 47 0.71
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.27
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATACAACTTGAAC
Found at i:28905137 original size:28 final size:28
Alignment explanation
Indices: 28905090--28905154 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
28905080 GAATTAACCC
*
28905090 TAGGGGTATAAAGGTCATTTTGCACACA
1 TAGGGGTATAAAGGTAATTTTGCACACA
* * *
28905118 TAGGGGTATGATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCACACA
28905146 TAGGGGTAT
1 TAGGGGTAT
28905155 TCTAGTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.29, C:0.09, G:0.29, T:0.32
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCACACA
Found at i:28905454 original size:8 final size:8
Alignment explanation
Indices: 28905438--28905469 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
28905428 NNNNNNNTAC
28905438 CGGCTTTT
1 CGGCTTTT
*
28905446 CGGCATTT
1 CGGCTTTT
28905454 CGGCTTTT
1 CGGCTTTT
28905462 CGGCTTTT
1 CGGCTTTT
28905470 GCCGATCTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.03, C:0.25, G:0.25, T:0.47
Consensus pattern (8 bp):
CGGCTTTT
Found at i:28908813 original size:135 final size:135
Alignment explanation
Indices: 28908571--28908840 Score: 531
Period size: 135 Copynumber: 2.0 Consensus size: 135
28908561 CGCCGAAATC
*
28908571 GTTCGACCACATCCGAGGTAAGTTTTAAGTGATTAAACGTTGAGTAAATTCAGTCATAATAGGAC
1 GTTCGACCACATCCGAGGTAAGTTTTAAGTGATTAAACGTTGAGTAAATTCAGTCATAACAGGAC
28908636 ATAATGAGTTGATTTAATAAGATATGATGTGACCATGATATGTCTTAAACTCAAATGGTAAGTTC
66 ATAATGAGTTGATTTAATAAGATATGATGTGACCATGATATGTCTTAAACTCAAATGGTAAGTTC
28908701 ATAAG
131 ATAAG
28908706 GTTCGACCACATCCGAGGTAAGTTTTAAGTGATTAAACGTTGAGTAAATTCAGTCATAACAGGAC
1 GTTCGACCACATCCGAGGTAAGTTTTAAGTGATTAAACGTTGAGTAAATTCAGTCATAACAGGAC
28908771 ATAATGAGTTGATTTAATAAGATATGATGTGACCATGATATGTCTTAAACTCAAATGGTAAGTTC
66 ATAATGAGTTGATTTAATAAGATATGATGTGACCATGATATGTCTTAAACTCAAATGGTAAGTTC
28908836 ATAAG
131 ATAAG
28908841 TGTTTGGACT
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 134 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.31
Consensus pattern (135 bp):
GTTCGACCACATCCGAGGTAAGTTTTAAGTGATTAAACGTTGAGTAAATTCAGTCATAACAGGAC
ATAATGAGTTGATTTAATAAGATATGATGTGACCATGATATGTCTTAAACTCAAATGGTAAGTTC
ATAAG
Found at i:28909661 original size:47 final size:47
Alignment explanation
Indices: 28909604--28909860 Score: 331
Period size: 47 Copynumber: 5.4 Consensus size: 47
28909594 ATTGATGTAC
* *
28909604 AAGTATATATATGTGATAGGGCCGAGTGGCCAATGTGATGAATGTGA
1 AAGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
28909651 AAGTATATATATGCGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 AAGTATATATAT--GTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * *
28909700 ACA-TGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
1 A-AGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * *
28909747 ACATGCATATATA--AGATAAGGCCGAATGGCCAATGTGATGAATGAGA
1 A-A-GTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* * *
28909794 AAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGG
1 AAGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
* *
28909841 AAGTGTATAAATGTGATAAG
1 AAGTATATATATGTGATAAG
28909861 TCCCGAAGGG
Statistics
Matches: 185, Mismatches: 18, Indels: 14
0.85 0.08 0.06
Matches are distributed among these distances:
45 7 0.04
46 1 0.01
47 132 0.71
49 44 0.24
50 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.30, T:0.26
Consensus pattern (47 bp):
AAGTATATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGA
Found at i:28912352 original size:38 final size:38
Alignment explanation
Indices: 28912288--28912361 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
28912278 AATCCGAGTT
*
28912288 TAAAGACCCGCTGACTATATGAAGAGATTATGTCCGGG
1 TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
* *
28912326 TAAAGACCCGATGGCTATGT-ACAGAGATTATGTCCG
1 TAAAGACCCGATGACTATATGA-AGAGATTATGTCCG
28912362 AATTAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 31 0.97
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (38 bp):
TAAAGACCCGATGACTATATGAAGAGATTATGTCCGGG
Found at i:28912475 original size:40 final size:40
Alignment explanation
Indices: 28912420--28912816 Score: 632
Period size: 40 Copynumber: 9.9 Consensus size: 40
28912410 CTCGAAAATG
*
28912420 ATCCGGGCTAAGTCCCAAAGAGCATTCATGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
28912460 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
* *
28912500 ATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
28912540 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
*
28912580 ATCCGGGCTAAGTCCAGAAGAGCATTCATGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
*
28912620 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
*
28912660 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
* *
28912700 ATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
* ** ** * *
28912740 ATCCGTGCTAAACCCCGAAGAGCATTTGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
* * *
28912780 ATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGTGA
1 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
28912817 CGTGTATTCG
Statistics
Matches: 331, Mismatches: 26, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 331 1.00
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATAT
Found at i:28916418 original size:40 final size:40
Alignment explanation
Indices: 28916324--28916468 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
28916314 TACTCGAATG
*
28916324 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCT-AGCGACT
* *
28916365 ACATCCGGACTAAGAT-CCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCTAGCGACT
* * *
28916405 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
* * *
28916445 ATATCCGGGTTAAGACTCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGC
28916469 CTTGTGCGAG
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 1 0.01
40 61 0.67
41 28 0.31
42 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGCGACT
Found at i:28918409 original size:14 final size:14
Alignment explanation
Indices: 28918387--28918416 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28918377 GATAAATACT
*
28918387 TTATTTGTTCTTAA
1 TTATGTGTTCTTAA
28918401 TTATGTGTTCTTAA
1 TTATGTGTTCTTAA
28918415 TT
1 TT
28918417 CTTGCTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.10, T:0.63
Consensus pattern (14 bp):
TTATGTGTTCTTAA
Found at i:28919139 original size:16 final size:16
Alignment explanation
Indices: 28919120--28919155 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28919110 TACTTTAGCC
*
28919120 ATTTATTTTTATTGCA
1 ATTTAATTTTATTGCA
*
28919136 ATTTAATTTTATTTCA
1 ATTTAATTTTATTGCA
28919152 ATTT
1 ATTT
28919156 TGTTTATATT
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:0.06, G:0.03, T:0.64
Consensus pattern (16 bp):
ATTTAATTTTATTGCA
Found at i:28925179 original size:18 final size:18
Alignment explanation
Indices: 28925156--28925202 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
28925146 TCATCTTTTA
*
28925156 TTTATTTTTATTTTTATC
1 TTTATTTTTATTTTTAAC
* *
28925174 TTTATTTATCTTTTTAAC
1 TTTATTTTTATTTTTAAC
28925192 -TTACTTTTTAT
1 TTTA-TTTTTAT
28925203 CCTATTTCTC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTTTATTTTTAAC
Found at i:28927367 original size:18 final size:17
Alignment explanation
Indices: 28927341--28927378 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
28927331 ATTGTAAAAG
*
28927341 GGACGGATTTTTTTGAGA
1 GGACCGATTTTTTT-AGA
28927359 GGACCGATTTTTTTAGA
1 GGACCGATTTTTTTAGA
28927376 GGA
1 GGA
28927379 TAAAATACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.24, C:0.08, G:0.32, T:0.37
Consensus pattern (17 bp):
GGACCGATTTTTTTAGA
Found at i:28928180 original size:14 final size:14
Alignment explanation
Indices: 28928161--28928222 Score: 60
Period size: 14 Copynumber: 4.7 Consensus size: 14
28928151 TATTTAATAA
28928161 TATATTATTTTACT
1 TATATTATTTTACT
28928175 TATATTA-TTT-CT
1 TATATTATTTTACT
* ** *
28928187 AATATT-TAATA-A
1 TATATTATTTTACT
28928199 TATATTATTTTACT
1 TATATTATTTTACT
28928213 TATATTATTT
1 TATATTATTT
28928223 GTAATATTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
12 13 0.36
13 6 0.17
14 17 0.47
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (14 bp):
TATATTATTTTACT
Found at i:28928194 original size:38 final size:38
Alignment explanation
Indices: 28928150--28928230 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
28928140 TATATGTGTT
28928150 ATATTTAATAATATATTATTTTACTTATATTATTTCTA
1 ATATTTAATAATATATTATTTTACTTATATTATTTCTA
*
28928188 ATATTTAATAATATATTATTTTACTTATATTATTTGTA
1 ATATTTAATAATATATTATTTTACTTATATTATTTCTA
28928226 ATATT
1 ATATT
28928231 ATATATGTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (38 bp):
ATATTTAATAATATATTATTTTACTTATATTATTTCTA
Found at i:28932813 original size:46 final size:45
Alignment explanation
Indices: 28932746--28932920 Score: 181
Period size: 46 Copynumber: 3.8 Consensus size: 45
28932736 TGTAACCCGC
* *
28932746 CCATAAGTGAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTAGCAT
* * * *
28932792 CCATAAGTGAACTCAGACTCAACTCAACGAGCTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--GCTTAGCAT
* *** * * *
28932838 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTTGGACATTTGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGGC-TTAGCAT
28932885 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
28932921 ATGCCCAAAC
Statistics
Matches: 103, Mismatches: 21, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
45 1 0.01
46 68 0.66
47 32 0.31
48 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCTTAGCAT
Found at i:28932866 original size:93 final size:93
Alignment explanation
Indices: 28932754--28932925 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
28932744 GCCCATAAGT
* *
28932754 GAACTCGGACTCAACTCAACGAGATCGGGCGTTCGCATCCATAAGTGAACTCAGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGATCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
28932819 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
* * * *
28932847 GAACTCGGACTCAACTCAACGAGTTTGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGATCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
*
28932912 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
28932926 CAAACATCCT
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGATCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:28938452 original size:33 final size:33
Alignment explanation
Indices: 28938408--28938473 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
28938398 CTTGGGGAAG
* *
28938408 GGAAAGGGGTGAAAATTGGGACACTTATTGCCA
1 GGAAAGAGGTGAAAATTAGGACACTTATTGCCA
28938441 GGAAAGAGGTGAAAATTAGGACACTTATTGCCA
1 GGAAAGAGGTGAAAATTAGGACACTTATTGCCA
28938474 AGGACACAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.12, G:0.30, T:0.21
Consensus pattern (33 bp):
GGAAAGAGGTGAAAATTAGGACACTTATTGCCA
Found at i:28942921 original size:87 final size:87
Alignment explanation
Indices: 28942809--28943305 Score: 297
Period size: 87 Copynumber: 5.7 Consensus size: 87
28942799 GAGAGCAGAC
* * * *
28942809 ACATAACAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATTCTTGT
1 ACATAGCAGATCTGACTTTCAGATGTTTACACTGAAGCAGATCCAAGATGATTTGGCATTCTTGT
28942874 GTTTACAAGGAACAAATCGAAG
66 GTTTACAAGGAACAAATCGAAG
* ** ** * * *
28942896 ACATAGCAGATCTGATTTTTGGATGTTCTCACACCAAAACAGATTCAAGATAACAGATCTGGCA-
1 ACATAGCAGATCTGACTTTCAGATGTT-T-ACACTGAAGCAGATCCAAGAT----GATTTGGCAT
*** * *
28942960 TC-TCCATTT-CGACGGAGAGC--A--G-AC
60 TCTTGTGTTTAC-AAGGA-A-CAAATCGAAG
* * * * *
28942984 ACATAACAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTCGGCATTCTTGT
1 ACATAGCAGATCTGACTTTCAGATGTTTACACTGAAGCAGATCCAAGATGATTTGGCATTCTTGT
28943049 GTTTACAAGGAACAAATCGAAG
66 GTTTACAAGGAACAAATCGAAG
* * ** *
28943071 ACATAGCAGATTTGACTTTCGGATGTTCTCACACCAAAGCAGATCCAAGATAACAGATCTGGCA-
1 ACATAGCAGATCTGACTTTCAGATGTT-T-ACACTGAAGCAGATCCAAGAT----GATTTGGCAT
*** * * * * *
28943135 TC-TCCATTT-CGACGG-A-GAGTAG-AT
60 TCTTGTGTTTAC-AAGGAACAAATCGAAG
* * * *
28943159 ACATAGCAGATCTAACCTTCAGATGATTT-TACTGAAGCAGATCCAAGATGATTTGGCATCCTTG
1 ACATAGCAGATCTGACTTTCAGATG-TTTACACTGAAGCAGATCCAAGATGATTTGGCATTCTTG
* * *
28943223 TGTTCACAAGGAGCAAATCAAAG
65 TGTTTACAAGGAACAAATCGAAG
* * * * *
28943246 ACACAGCAGATTTGGCTTTCACG-TGTTTACGCTGAAGCAGATCTAAGATGATTTGGCATT
1 ACATAGCAGATCTGACTTTCA-GATGTTTACACTGAAGCAGATCCAAGATGATTTGGCATT
28943306 TCTATATTTG
Statistics
Matches: 295, Mismatches: 82, Indels: 66
0.67 0.19 0.15
Matches are distributed among these distances:
82 16 0.05
83 4 0.01
84 15 0.05
85 2 0.01
86 39 0.13
87 91 0.31
88 48 0.16
89 40 0.14
90 3 0.01
91 16 0.05
92 5 0.02
93 16 0.05
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (87 bp):
ACATAGCAGATCTGACTTTCAGATGTTTACACTGAAGCAGATCCAAGATGATTTGGCATTCTTGT
GTTTACAAGGAACAAATCGAAG
Found at i:28942931 original size:175 final size:175
Alignment explanation
Indices: 28942711--28943256 Score: 923
Period size: 175 Copynumber: 3.1 Consensus size: 175
28942701 CGACGAGGTG
*
28942711 CAAATCAAAGACATAGCAGATCTGACTTTTGGATGTTTTCACACCAAAGCAGATCCAAGATAACA
1 CAAATCAAAGACATAGCAGATCTGACTTTTGGATGTTCTCACACCAAAGCAGATCCAAGATAACA
*
28942776 GATCTGACATCTCCATTTCGACGGAGAGCAGACACATAACAGATCTAACCTTCAGATGTTTATAC
66 GATCTGGCATCTCCATTTCGACGGAGAGCAGACACATAACAGATCTAACCTTCAGATGTTTATAC
28942841 TGAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAA
131 TGAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAA
* * * *
28942886 CAAATCGAAGACATAGCAGATCTGATTTTTGGATGTTCTCACACCAAAACAGATTCAAGATAACA
1 CAAATCAAAGACATAGCAGATCTGACTTTTGGATGTTCTCACACCAAAGCAGATCCAAGATAACA
28942951 GATCTGGCATCTCCATTTCGACGGAGAGCAGACACATAACAGATCTAACCTTCAGATGTTTATAC
66 GATCTGGCATCTCCATTTCGACGGAGAGCAGACACATAACAGATCTAACCTTCAGATGTTTATAC
*
28943016 TGAAGCAGATCCAAGATGATTCGGCATTCTTGTGTTTACAAGGAA
131 TGAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAA
* * *
28943061 CAAATCGAAGACATAGCAGATTTGACTTTCGGATGTTCTCACACCAAAGCAGATCCAAGATAACA
1 CAAATCAAAGACATAGCAGATCTGACTTTTGGATGTTCTCACACCAAAGCAGATCCAAGATAACA
* * *
28943126 GATCTGGCATCTCCATTTCGACGGAGAGTAGATACATAGCAGATCTAACCTTCAGATGATTT-TA
66 GATCTGGCATCTCCATTTCGACGGAGAGCAGACACATAACAGATCTAACCTTCAGATG-TTTATA
* * *
28943190 CTGAAGCAGATCCAAGATGATTTGGCATCCTTGTGTTCACAAGGAG
130 CTGAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAA
*
28943236 CAAATCAAAGACACAGCAGAT
1 CAAATCAAAGACATAGCAGAT
28943257 TTGGCTTTCA
Statistics
Matches: 349, Mismatches: 21, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
175 346 0.99
176 3 0.01
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (175 bp):
CAAATCAAAGACATAGCAGATCTGACTTTTGGATGTTCTCACACCAAAGCAGATCCAAGATAACA
GATCTGGCATCTCCATTTCGACGGAGAGCAGACACATAACAGATCTAACCTTCAGATGTTTATAC
TGAAGCAGATCCAAGATGATTTGGCATTCTTGTGTTTACAAGGAA
Found at i:28944889 original size:14 final size:14
Alignment explanation
Indices: 28944870--28944931 Score: 60
Period size: 14 Copynumber: 4.7 Consensus size: 14
28944860 TATTTAATAA
28944870 TATATTATTTTACT
1 TATATTATTTTACT
28944884 TATATTA-TTT-CT
1 TATATTATTTTACT
* ** *
28944896 AATATT-TAATA-A
1 TATATTATTTTACT
28944908 TATATTATTTTACT
1 TATATTATTTTACT
28944922 TATATTATTT
1 TATATTATTT
28944932 GTAATATTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
12 13 0.36
13 6 0.17
14 17 0.47
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (14 bp):
TATATTATTTTACT
Found at i:28944903 original size:38 final size:38
Alignment explanation
Indices: 28944859--28944939 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
28944849 TATATGTGTT
28944859 ATATTTAATAATATATTATTTTACTTATATTATTTCTA
1 ATATTTAATAATATATTATTTTACTTATATTATTTCTA
*
28944897 ATATTTAATAATATATTATTTTACTTATATTATTTGTA
1 ATATTTAATAATATATTATTTTACTTATATTATTTCTA
28944935 ATATT
1 ATATT
28944940 ATATATGTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (38 bp):
ATATTTAATAATATATTATTTTACTTATATTATTTCTA
Found at i:28945160 original size:12 final size:12
Alignment explanation
Indices: 28945143--28945167 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28945133 ATATATATTT
28945143 TTTTATTATATA
1 TTTTATTATATA
28945155 TTTTATTATATA
1 TTTTATTATATA
28945167 T
1 T
28945168 ATATCTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTATTATATA
Found at i:28948732 original size:40 final size:40
Alignment explanation
Indices: 28948640--28948795 Score: 163
Period size: 40 Copynumber: 3.9 Consensus size: 40
28948630 CTTTTGGATA
* * *
28948640 AAAAACGCCGCTATAAATTGAGCATTAGCAGCGCTTTTTG
1 AAAAATGCCGCTATAGATCGAGCATTAGCAGCGCTTTTTG
* * * *
28948680 AAAAAAGTCGCTATAGATCGAGCATTAGTAGCCCTTTTTG
1 AAAAATGCCGCTATAGATCGAGCATTAGCAGCGCTTTTTG
* * * *
28948720 AAACATGCCGCTATAGATC-AACTATTAGCGGTGC-TTTTG
1 AAAAATGCCGCTATAGATCGAGC-ATTAGCAGCGCTTTTTG
* * *
28948759 AAAAATGCCGCTATAGGTCGACCATTAGCGGCGCTTT
1 AAAAATGCCGCTATAGATCGAGCATTAGCAGCGCTTT
28948796 CTACAAAACG
Statistics
Matches: 95, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
39 34 0.36
40 61 0.64
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (40 bp):
AAAAATGCCGCTATAGATCGAGCATTAGCAGCGCTTTTTG
Found at i:28948918 original size:101 final size:101
Alignment explanation
Indices: 28948743--28948997 Score: 363
Period size: 101 Copynumber: 2.5 Consensus size: 101
28948733 TAGATCAACT
* *
28948743 ATTAGCGGTGCTTTTGAAAAATGCCGCTATAGGTCGACCATTAGCGGCGCTTTCTACAAAACGCT
1 ATTAGCGGTGCTTTTGAAAAACG-CGCTATAGGTCGACCATTAGCGGCGCTTTCTACAAAACGCC
*
28948808 GCAAAAAAATTAAGCATAATGTTGAGC-TTTAGTGGC
65 GCAAAAAAATTAAGCACAATGTTGAGCTTTTAGTGGC
*
28948844 ATTAGCGGTGCTTTTTGAAAAACGTCGCTATAGGTCGACCA-TAGCGGCGCTTTCTTA-AAAATG
1 ATTAGCGGTGC-TTTTGAAAAACG-CGCTATAGGTCGACCATTAGCGGCGCTTTC-TACAAAACG
28948907 CCGCAAAAAAATTAAGCACAATGTTGAGCTTTTAGTGGC
63 CCGCAAAAAAATTAAGCACAATGTTGAGCTTTTAGTGGC
* ** * * *
28948946 ATTAGTGACGCTTTTGAAAAACGCGCTATAGATCGAGCATTAGCGACGCTTT
1 ATTAGCGGTGCTTTTGAAAAACGCGCTATAGGTCGACCATTAGCGGCGCTTT
28948998 TTGTAAATTG
Statistics
Matches: 139, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
100 14 0.10
101 79 0.57
102 46 0.33
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (101 bp):
ATTAGCGGTGCTTTTGAAAAACGCGCTATAGGTCGACCATTAGCGGCGCTTTCTACAAAACGCCG
CAAAAAAATTAAGCACAATGTTGAGCTTTTAGTGGC
Found at i:28949016 original size:140 final size:139
Alignment explanation
Indices: 28948842--28949102 Score: 337
Period size: 140 Copynumber: 1.8 Consensus size: 139
28948832 AGCTTTAGTG
** * * * *
28948842 GCATTAGCGGTGCTTTTTGAAAAACGTCGCTATAGGTCGACCA-TAGCGGCGCTTTCTTAAAAAT
1 GCATTAGCGACGCTTTTTGAAAAACGTAGCTATAGGTCAACCATTAGCGGCGC-TTCTGAAAAAC
*
28948906 GCCGCAAAAAAATTAAGCACA-ATGTTGAGCTTTTAGTGGCATTAGTGACGCTTTTGAAAAACGC
65 GCCGC-AAAAAATTAAGCACATATGTTGAGC-TTTAGTGGCATTAGCGACGCTTTTGAAAAACGC
28948970 GCTATAGATCGA
128 GCTATAGATCGA
* ** *
28948982 GCATTAGCGACGCTTTTTGTAAATTGTAGCTATAGGTCAACTATTAGCGGCGCTTCTGAAAAACG
1 GCATTAGCGACGCTTTTTGAAAAACGTAGCTATAGGTCAACCATTAGCGGCGCTTCTGAAAAACG
* *
28949047 TCGCAAAAAATTAAGCACACTTTATGTTGAGCTTTAGTGGCATTAGCGGCGCTTTT
66 CCGCAAAAAATTAAGCACA---TATGTTGAGCTTTAGTGGCATTAGCGACGCTTTT
28949103 TGAATAATTC
Statistics
Matches: 103, Mismatches: 13, Indels: 8
0.83 0.10 0.06
Matches are distributed among these distances:
139 15 0.15
140 48 0.47
141 9 0.09
142 22 0.21
143 9 0.09
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (139 bp):
GCATTAGCGACGCTTTTTGAAAAACGTAGCTATAGGTCAACCATTAGCGGCGCTTCTGAAAAACG
CCGCAAAAAATTAAGCACATATGTTGAGCTTTAGTGGCATTAGCGACGCTTTTGAAAAACGCGCT
ATAGATCGA
Found at i:28949942 original size:35 final size:35
Alignment explanation
Indices: 28949874--28949942 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
28949864 TAATTGTGTT
*
28949874 ATTAATTTATTATTTTAGATTGTAAATTTAAATTC
1 ATTAATTTATTATTTTAGATTGTAAATTAAAATTC
* * *
28949909 ATTAATTT-TTATATTTAGTTTTTAAGTTAAAATT
1 ATTAATTTATTAT-TTTAGATTGTAAATTAAAATT
28949943 TTAATATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 4 0.14
35 25 0.86
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (35 bp):
ATTAATTTATTATTTTAGATTGTAAATTAAAATTC
Found at i:28950195 original size:43 final size:43
Alignment explanation
Indices: 28950075--28950197 Score: 167
Period size: 42 Copynumber: 2.9 Consensus size: 43
28950065 AATATTTTTT
* * *
28950075 TAAAGGTCATGTTCTTTAGCAGTGTTTGTGGGAAAAGTGTCGC
1 TAAAGGTCATGTTCTTTAGCAGCGTTTGTGGGAAAAGCGCCGC
* * *
28950118 TAAAGGTC-TGTTCTATAACGGCGTTTGTGGGAAAAGCGCCGC
1 TAAAGGTCATGTTCTTTAGCAGCGTTTGTGGGAAAAGCGCCGC
* *
28950160 TAAAGGCCATGATCTTTAGCAGCGTTTGTGGGAAAAGC
1 TAAAGGTCATGTTCTTTAGCAGCGTTTGTGGGAAAAGC
28950198 AAATCCCCGA
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 35 0.51
43 33 0.49
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.29
Consensus pattern (43 bp):
TAAAGGTCATGTTCTTTAGCAGCGTTTGTGGGAAAAGCGCCGC
Found at i:28951349 original size:40 final size:39
Alignment explanation
Indices: 28951286--28951433 Score: 161
Period size: 40 Copynumber: 3.7 Consensus size: 39
28951276 CGTTTGGATA
* ** * * *
28951286 AAAAACGCCGCTATAAATTGAGCATTAGCGGCACATTTTG
1 AAAAACGCCACTATAGGTCGAGCATTAGCAGCGC-TTTTG
* * *
28951326 AAAAAGGCCATTATAGATCGAGCATTAGCAGCGCTTTTTG
1 AAAAACGCCACTATAGGTCGAGCATTAGCAGCGC-TTTTG
* *
28951366 AAAAACACCGCTATAGGTCGAGCATTAGCAGCGCTTCTTG
1 AAAAACGCCACTATAGGTCGAGCATTAGCAGCGCTT-TTG
*
28951406 AAAAACGCCACTATAGGTCGACCATTAG
1 AAAAACGCCACTATAGGTCGAGCATTAG
28951434 AAAGCGCCGC
Statistics
Matches: 91, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 2 0.02
40 89 0.98
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.24
Consensus pattern (39 bp):
AAAAACGCCACTATAGGTCGAGCATTAGCAGCGCTTTTG
Found at i:28951421 original size:80 final size:80
Alignment explanation
Indices: 28951286--28951433 Score: 190
Period size: 80 Copynumber: 1.9 Consensus size: 80
28951276 CGTTTGGATA
* * * * * *
28951286 AAAAACGCCGCTATAAATTGAGCATTAGCGGCACATTTTGAAAAAGGCCATTATAGATCGAGCAT
1 AAAAACACCGCTATAAATCGAGCATTAGCAGCACATTTTGAAAAACGCCACTATAGATCGACCAT
28951351 TAGCAGCGCTTTTTG
66 TAGCAGCGCTTTTTG
** * *
28951366 AAAAACACCGCTATAGGTCGAGCATTAGCAGCGC-TTCTTGAAAAACGCCACTATAGGTCGACCA
1 AAAAACACCGCTATAAATCGAGCATTAGCAGCACATT-TTGAAAAACGCCACTATAGATCGACCA
28951430 TTAG
65 TTAG
28951434 AAAGCGCCGC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
79 2 0.04
80 55 0.96
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.24
Consensus pattern (80 bp):
AAAAACACCGCTATAAATCGAGCATTAGCAGCACATTTTGAAAAACGCCACTATAGATCGACCAT
TAGCAGCGCTTTTTG
Found at i:28951702 original size:141 final size:141
Alignment explanation
Indices: 28951440--28951824 Score: 481
Period size: 141 Copynumber: 2.7 Consensus size: 141
28951430 TTAGAAAGCG
** * * *
28951440 CCGCAAAAAATTAAGCATTATGTTGAG-TTTTAGTGGCATTAGCAGCACTTTTTGAAAAACACCG
1 CCGCAAAAAATTAAGCACAATGTTGAGCTTTTAGTGGCATTAGCGGCGCTTTTTGAAAAAC-GCG
** * * * ***
28951504 CTATAGATCAAGCACTAGCAGTGCTTCTTGAAAAATGTCGCTATAGGACGAACATTAGCGGCGCT
65 CTATAGATTGAGCGCTAGCGGTGCTTTTTGAAAAACACCGCTATAGGACGAACATTAGCGGCGCT
*
28951569 TTCTAAAAACCT
130 TTCTAAAAACCA
28951581 CCGCAAAAAAATTAAGCACAATGTTGAGCTTTTAGTGGCATTAGCGGCGC-TTTTGAAAAACGCG
1 CCGC-AAAAAATTAAGCACAATGTTGAGCTTTTAGTGGCATTAGCGGCGCTTTTTGAAAAACGCG
* *
28951645 CTATAGATTGAGCGTTAGCGGTGCTTTTTGAAAAACACCGCTATAGGTCG-ACTATTAGCGGCGC
65 CTATAGATTGAGCGCTAGCGGTGCTTTTTGAAAAACACCGCTATAGGACGAAC-ATTAGCGGCGC
28951709 TTTCTAAAAACCA
129 TTTCTAAAAACCA
*
28951722 CCGCAAAAAATTAAGCACACTTTATGTTGAGC-GTTAGTGGCATTAGCGGCGCTTTTTGAAAAAC
1 CCGCAAAAAATTAAGCACA----ATGTTGAGCTTTTAGTGGCATTAGCGGCGCTTTTTGAAAAAC
* * * *
28951786 GCCACTATAGGTTGACCGCTAGCGGCGCTTTTTGAAAAA
62 G-CGCTATAGATTGAGCGCTAGCGGTGCTTTTTGAAAAA
28951825 TGCCGCAAAA
Statistics
Matches: 213, Mismatches: 22, Indels: 14
0.86 0.09 0.06
Matches are distributed among these distances:
140 17 0.08
141 73 0.34
142 32 0.15
143 38 0.18
144 21 0.10
145 32 0.15
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (141 bp):
CCGCAAAAAATTAAGCACAATGTTGAGCTTTTAGTGGCATTAGCGGCGCTTTTTGAAAAACGCGC
TATAGATTGAGCGCTAGCGGTGCTTTTTGAAAAACACCGCTATAGGACGAACATTAGCGGCGCTT
TCTAAAAACCA
Found at i:28951703 original size:40 final size:40
Alignment explanation
Indices: 28951618--28951725 Score: 116
Period size: 40 Copynumber: 2.8 Consensus size: 40
28951608 GCTTTTAGTG
* *
28951618 GCATTAGCGGCGC-TTTTGAAAAAC-GCGCTATAGATTGA
1 GCATTAGCGGCGCTTTTTGAAAAACACCGCTATAGATCGA
* * *
28951656 GCGTTAGCGGTGCTTTTTGAAAAACACCGCTATAGGTCGA
1 GCATTAGCGGCGCTTTTTGAAAAACACCGCTATAGATCGA
*
28951696 -CTATTAGCGGCGCTTTCT-AAAAACCACCGC
1 GC-ATTAGCGGCGCTTTTTGAAAAA-CACCGC
28951726 AAAAAATTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
38 11 0.19
39 17 0.29
40 30 0.52
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (40 bp):
GCATTAGCGGCGCTTTTTGAAAAACACCGCTATAGATCGA
Found at i:28952635 original size:74 final size:76
Alignment explanation
Indices: 28952497--28952643 Score: 262
Period size: 77 Copynumber: 1.9 Consensus size: 76
28952487 ATATTTAATC
*
28952497 TAATTTTTATTATTCATTTTAGTTTTGATTCTAAATTTTTATTTTTATTTTAATATTTAGGATAA
1 TAATTTTTATTATTCATTTTAGTTTTGATTCTAAA-TTTTATTTTTATTTTAATATTTAAGATAA
28952562 CTTGAGTTAAAA
65 CTTGAGTTAAAA
28952574 TAATTTTTATTATTCATTTTAGTTTTGATTCTAAA-TTT-TTTTTATTTTAATATTTAAGATAAC
1 TAATTTTTATTATTCATTTTAGTTTTGATTCTAAATTTTATTTTTATTTTAATATTTAAGATAAC
28952637 TTGAGTT
66 TTGAGTT
28952644 GTAACTTTTG
Statistics
Matches: 69, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
74 31 0.45
75 3 0.04
77 35 0.51
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (76 bp):
TAATTTTTATTATTCATTTTAGTTTTGATTCTAAATTTTATTTTTATTTTAATATTTAAGATAAC
TTGAGTTAAAA
Found at i:28952737 original size:35 final size:35
Alignment explanation
Indices: 28952669--28952737 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
28952659 TAATTGTGTT
*
28952669 ATTAATTTATTATTTTAGATTCTAAATTTAAATTC
1 ATTAATTTATTATTTTAGATTCTAAATTAAAATTC
* * *
28952704 ATTAATTT-TTATATTTAGTTTTTAAGTTAAAATT
1 ATTAATTTATTAT-TTTAGATTCTAAATTAAAATT
28952738 TTAATATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 4 0.14
35 25 0.86
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.57
Consensus pattern (35 bp):
ATTAATTTATTATTTTAGATTCTAAATTAAAATTC
Found at i:28953033 original size:44 final size:42
Alignment explanation
Indices: 28952870--28953030 Score: 189
Period size: 43 Copynumber: 3.7 Consensus size: 42
28952860 AATATTTTTT
*
28952870 TAAAGGTCATGTTCTTTAGCGGCATTTGTGGGAAAAGCGCCGC
1 TAAAGGT-ATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
* * * * *
28952913 TAAAAGTCTATTCTATAGCGGCGTTAGTGGGAAAAAGC-CTCGC
1 TAAAGGTATGTTCTTTAGCGGCGTTTGTGGG-AAAAGCGC-CGC
* * *
28952956 TAAAGGCCATGATCTTTAGCGGCGTTTGTGGGAAAAGCGCAGC
1 TAAAGG-TATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
28952999 TAAAGGATATGTTCTTTAGCGGCGTTTGTGGG
1 TAAAGG-TATGTTCTTTAGCGGCGTTTGTGGG
28953031 GAATGCGGCG
Statistics
Matches: 97, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
42 20 0.21
43 57 0.59
44 20 0.21
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (42 bp):
TAAAGGTATGTTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGC
Found at i:28953040 original size:18 final size:18
Alignment explanation
Indices: 28953017--28953055 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
28953007 ATGTTCTTTA
*
28953017 GCGGCGTTTGTGGGGAAT
1 GCGGCGATTGTGGGGAAT
28953035 GCGGCGATTGTGGGGAAT
1 GCGGCGATTGTGGGGAAT
28953053 GCG
1 GCG
28953056 CCGCTAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.13, C:0.13, G:0.51, T:0.23
Consensus pattern (18 bp):
GCGGCGATTGTGGGGAAT
Found at i:28954590 original size:38 final size:38
Alignment explanation
Indices: 28954539--28954614 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
28954529 AACCGTGAAG
28954539 TGAATCTCGGATCTCTATCTGACACAATAAACAATGAC
1 TGAATCTCGGATCTCTATCTGACACAATAAACAATGAC
*
28954577 TGAATCTCGGATCTCTATCTGACACAATAGACAATGAC
1 TGAATCTCGGATCTCTATCTGACACAATAAACAATGAC
28954615 ACCCCGTGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (38 bp):
TGAATCTCGGATCTCTATCTGACACAATAAACAATGAC
Found at i:28956910 original size:46 final size:46
Alignment explanation
Indices: 28956843--28957015 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
28956833 TGTAACCCGC
* *
28956843 CCATAAGCGAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
* *
28956889 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * *
28956939 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
28956982 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC
28957016 AGATGCTCAA
Statistics
Matches: 107, Mismatches: 11, Indels: 18
0.79 0.08 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 59 0.55
47 28 0.26
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:28956964 original size:93 final size:93
Alignment explanation
Indices: 28956850--28957021 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
28956840 CGCCCATAAG
* * *
28956850 CGAACTTGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
28956915 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCAGATGCCTAGTTACATCTCA
*
28956943 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28957008 ACGAGTTCAGATGC
66 ACGAGTTCAGATGC
28957022 TCAACCATCC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCAGATGCCTAGTTACATCTCA
Found at i:28958739 original size:518 final size:518
Alignment explanation
Indices: 28957756--28959826 Score: 4034
Period size: 518 Copynumber: 4.0 Consensus size: 518
28957746 ATATAAACCC
*
28957756 TAGGTTAAATTATTGCTAACATAAGCTTTATCGAGTTATCGGGATCTCAAAAACGTAAAAATCAT
1 TAGGTGAAATTATTGCTAACATAAGCTTTATCGAGTTATCGGGATCTCAAAAACGTAAAAATCAT
28957821 TAAAAACGGGGCTTAGAATCACTTACTATGGAGCTTGGAAGCTTGAAACAAACCCTAGCTATGGA
66 TAAAAACGGGGCTTAGAATCACTTACTATGGAGCTTGGAAGCTTGAAACAAACCCTAGCTATGGA
* *
28957886 GAATCCTTGAAATTTCGGCCTAATGAAGAAGATGGACAAAAATTGGCTTTTAATTTTGTTTTTAA
131 GAACCCTTGAAATTTCAGCCTAATGAAGAAGATGGACAAAAATTGGCTTTTAATTTTGTTTTTAA
28957951 TTCATTTTAATAACTAAATGACCAAAATACCCTTACTACTAAACTTTCCAAAATTTCCTTCCATG
196 TTCATTTTAATAACTAAATGACCAAAATACCCTTACTACTAAACTTTCCAAAATTTCCTTCCATG
28958016 TCCTAAATTTGTCCATGAACTCAAAATTGGTCAAATTGCTATTTAAGACCTCCTCATTAATATTC
261 TCCTAAATTTGTCCATGAACTCAAAATTGGTCAAATTGCTATTTAAGACCTCCTCATTAATATTC
28958081 CAAAACAATTTCATACTAAAAACTTCTAGAATGCAAGTTTTGCAACTTATTCGATTTAGTCCCTA
326 CAAAACAATTTCATACTAAAAACTTCTAGAATGCAAGTTTTGCAACTTATTCGATTTAGTCCCTA
28958146 CTTTCAATTTAAGCACTTTAGGCATAGAATTTCATCACGAAATTTTCACACAATCATGCAATCAT
391 CTTTCAATTTAAGCACTTTAGGCATAGAATTTCATCACGAAATTTTCACACAATCATGCAATCAT
28958211 ATCATAATCATCAAAATAATTATAAAATAATTATTTCTATCTCGGATTTGTGGTCACGAAACA
456 ATCATAATCATCAAAATAATTATAAAATAATTATTTCTATCTCGGATTTGTGGTCACGAAACA
28958274 TAGGTGAAATTATTGCTAACATAAGCTTTATCGAGTTATCGGGATCTCAAAAACGTAAAAATCAT
1 TAGGTGAAATTATTGCTAACATAAGCTTTATCGAGTTATCGGGATCTCAAAAACGTAAAAATCAT
* *
28958339 TAAAAACGGGGCTTTGAATCTCTTACTATGGAGCTTGGAAGCTTGAAACAAACCCTAGCTATGGA
66 TAAAAACGGGGCTTAGAATCACTTACTATGGAGCTTGGAAGCTTGAAACAAACCCTAGCTATGGA
*
28958404 GAACCCTTGCAATTTCAGCCTAATGAAGAAGATGGACAAAAATTGGCTTTTAATTTTGTTTTTAA
131 GAACCCTTGAAATTTCAGCCTAATGAAGAAGATGGACAAAAATTGGCTTTTAATTTTGTTTTTAA
28958469 TTCATTTTAATAACTAAATGACCAAAATACCCTTACTACTAAACTTTCCAAAATTTCCTTCCATG
196 TTCATTTTAATAACTAAATGACCAAAATACCCTTACTACTAAACTTTCCAAAATTTCCTTCCATG
28958534 TCCTAAATTTGTCCATGAACTCAAAATTGGTCAAATTGCTATTTAAGACCTCCTCATTAATATTC
261 TCCTAAATTTGTCCATGAACTCAAAATTGGTCAAATTGCTATTTAAGACCTCCTCATTAATATTC
28958599 CAAAACAATTTCATACTAAAAACTTCTAGAATGCAAGTTTTGCAACTTATTCGATTTAGTCCCTA
326 CAAAACAATTTCATACTAAAAACTTCTAGAATGCAAGTTTTGCAACTTATTCGATTTAGTCCCTA
28958664 CTTTCAATTTAAGCACTTTAGGCATAGAATTTCATCACGAAATTTTCACACAATCATGCAATCAT
391 CTTTCAATTTAAGCACTTTAGGCATAGAATTTCATCACGAAATTTTCACACAATCATGCAATCAT
28958729 ATCATAATCATCAAAATAATTATAAAATAATTATTTCTATCTCGGATTTGTGGTCACGAAACA
456 ATCATAATCATCAAAATAATTATAAAATAATTATTTCTATCTCGGATTTGTGGTCACGAAACA
28958792 TAGGTGAAATTATTGCTAACATAAGCTTTATCGAGTTATCGGGATCTCAAAAACGTAAAAATCAT
1 TAGGTGAAATTATTGCTAACATAAGCTTTATCGAGTTATCGGGATCTCAAAAACGTAAAAATCAT
28958857 TAAAAACGGGGCTTAGAATCACTTACTATGGAGCTTGGAAGCTTGAAACAAACCCTAGCTATGGA
66 TAAAAACGGGGCTTAGAATCACTTACTATGGAGCTTGGAAGCTTGAAACAAACCCTAGCTATGGA
* *
28958922 GAATCCTTGAAATTTCGGCCTAATGAAGAAGATGGACAAAAATTGGCTTTTAATTTTGTTTTTAA
131 GAACCCTTGAAATTTCAGCCTAATGAAGAAGATGGACAAAAATTGGCTTTTAATTTTGTTTTTAA
28958987 TTCATTTTAATAACTAAATGACCAAAATACCCTTACTACTAAACTTTCCAAAATTTCCTTCCATG
196 TTCATTTTAATAACTAAATGACCAAAATACCCTTACTACTAAACTTTCCAAAATTTCCTTCCATG
28959052 TCCTAAATTTGTCCATGAACTCAAAATTGGTCAAATTGCTATTTAAGACCTCCTCATTAATATTC
261 TCCTAAATTTGTCCATGAACTCAAAATTGGTCAAATTGCTATTTAAGACCTCCTCATTAATATTC
28959117 CAAAACAATTTCATACTAAAAACTTCTAGAATGCAAGTTTTGCAACTTATTCGATTTAGTCCCTA
326 CAAAACAATTTCATACTAAAAACTTCTAGAATGCAAGTTTTGCAACTTATTCGATTTAGTCCCTA
28959182 CTTTCAATTTAAGCACTTTAGGCATAGAATTTCATCACGAAATTTTCACACAATCATGCAATCAT
391 CTTTCAATTTAAGCACTTTAGGCATAGAATTTCATCACGAAATTTTCACACAATCATGCAATCAT
28959247 ATCATAATCATCAAAATAATTATAAAATAATTATTTCTATCTCGGATTTGTGGTCACGAAACA
456 ATCATAATCATCAAAATAATTATAAAATAATTATTTCTATCTCGGATTTGTGGTCACGAAACA
28959310 TAGGTGAAATTATTGCTAACATAAGCTTTATCGAGTTATCGGGATCTCAAAAACGTAAAAATCAT
1 TAGGTGAAATTATTGCTAACATAAGCTTTATCGAGTTATCGGGATCTCAAAAACGTAAAAATCAT
28959375 TAAAAACGGGGCTTAGAATCACTTACTATGGAGCTTGGAAGCTTGAAACAAACCCTAGCTATGGA
66 TAAAAACGGGGCTTAGAATCACTTACTATGGAGCTTGGAAGCTTGAAACAAACCCTAGCTATGGA
*
28959440 GAACCCTTGCAATTTCAGCCTAATGAAGAAGATGGACAAAAATTGGCTTTTAATTTTGTTTTTAA
131 GAACCCTTGAAATTTCAGCCTAATGAAGAAGATGGACAAAAATTGGCTTTTAATTTTGTTTTTAA
28959505 TTCATTTTAATAACTAAATGACCAAAATACCCTTACTACTAAACTTTCCAAAATTTCCTTCCATG
196 TTCATTTTAATAACTAAATGACCAAAATACCCTTACTACTAAACTTTCCAAAATTTCCTTCCATG
* *
28959570 TCCTAAATTTTTCCATGAACTTAAAATTGGTCAAATTGCTATTTAAGACCTCCTCATTAATATTC
261 TCCTAAATTTGTCCATGAACTCAAAATTGGTCAAATTGCTATTTAAGACCTCCTCATTAATATTC
28959635 CAAAACAATTTCATACTAAAAACTTCTAGAATGCAAGTTTTGCAACTTATTCGATTTAGTCCCTA
326 CAAAACAATTTCATACTAAAAACTTCTAGAATGCAAGTTTTGCAACTTATTCGATTTAGTCCCTA
28959700 CTTTCAATTTAAGCACTTTAGGCATAGAATTTCATCACGAAATTTTCACACAATCATGCAATCAT
391 CTTTCAATTTAAGCACTTTAGGCATAGAATTTCATCACGAAATTTTCACACAATCATGCAATCAT
*
28959765 ATCATAATCATCAAAATAATTATAAAATAATTATTTCTATATCGGATTTGTGGTCACGAAAC
456 ATCATAATCATCAAAATAATTATAAAATAATTATTTCTATCTCGGATTTGTGGTCACGAAAC
28959827 CACTATTCCG
Statistics
Matches: 1536, Mismatches: 17, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
518 1536 1.00
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (518 bp):
TAGGTGAAATTATTGCTAACATAAGCTTTATCGAGTTATCGGGATCTCAAAAACGTAAAAATCAT
TAAAAACGGGGCTTAGAATCACTTACTATGGAGCTTGGAAGCTTGAAACAAACCCTAGCTATGGA
GAACCCTTGAAATTTCAGCCTAATGAAGAAGATGGACAAAAATTGGCTTTTAATTTTGTTTTTAA
TTCATTTTAATAACTAAATGACCAAAATACCCTTACTACTAAACTTTCCAAAATTTCCTTCCATG
TCCTAAATTTGTCCATGAACTCAAAATTGGTCAAATTGCTATTTAAGACCTCCTCATTAATATTC
CAAAACAATTTCATACTAAAAACTTCTAGAATGCAAGTTTTGCAACTTATTCGATTTAGTCCCTA
CTTTCAATTTAAGCACTTTAGGCATAGAATTTCATCACGAAATTTTCACACAATCATGCAATCAT
ATCATAATCATCAAAATAATTATAAAATAATTATTTCTATCTCGGATTTGTGGTCACGAAACA
Found at i:28961076 original size:54 final size:54
Alignment explanation
Indices: 28961017--28961311 Score: 347
Period size: 54 Copynumber: 5.5 Consensus size: 54
28961007 TTAGTTTACC
* * **
28961017 AAATTACCAAAATACCATTGGTTTATAAAATCACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCATTGGTTTGTA
*
28961071 AAATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCATTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCATTGGTTTGTA
* *
28961125 AAATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCATTGGTTTGTA
* * * * *
28961179 AAATTATCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCATTGATTTGTG
1 AAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCATTGGTTTGTA
** * ** * *** * * **
28961233 AAATTACTGAAATACCCTCGACTTGTAAAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCATTGGTTTGTA
* *
28961287 AAATTACCAAAGTACCCTTGATTTA
1 AAATTACCAAAATACCCTTGGTTTA
28961312 CAGAATTATC
Statistics
Matches: 206, Mismatches: 35, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 206 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (54 bp):
AAATTACCAAAATACCCTTGGTTTATAAAATTACCAAAATACCATTGGTTTGTA
Found at i:28961259 original size:81 final size:81
Alignment explanation
Indices: 28961017--28961310 Score: 345
Period size: 81 Copynumber: 3.6 Consensus size: 81
28961007 TTAGTTTACC
* * * *
28961017 AAATTACCAAAATACCATTGGTTTATAAAATCACCAAAATACCCCTGGTTTGTAAAATTACCAAA
1 AAATTACCAAAATACCATTGGTTTGTAAAATTACCAAAATACCCTTGATTTGTAAAATTACCAAA
**
28961082 ATACCCTTGGTTTACA
66 ATACCCTTGGTTTGTA
* * *
28961098 AAATTACCAAAATACCATTGGTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATTACCAAA
1 AAATTACCAAAATACCATTGGTTTGTAAAATTACCAAAATACCCTTGATTTGTAAAATTACCAAA
28961163 ATACCCTTGGTTTGTA
66 ATACCCTTGGTTTGTA
* * * * * **
28961179 AAATTATCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCATTGATTTGTGAAATTACTGAA
1 AAATTACCAAAATACCATTGGTTTGTAAAATTACCAAAATACCCTTGATTTGTAAAATTACCAAA
* **
28961244 ATACCCTCGACTTGTA
66 ATACCCTTGGTTTGTA
*** * * ** *
28961260 AAATTATTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTTGATTT
1 AAATTACCAAAATACCATTGGTTTGTAAAATTACCAAAATACCCTTGATTT
28961311 ACAGAATTAT
Statistics
Matches: 185, Mismatches: 28, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 185 1.00
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (81 bp):
AAATTACCAAAATACCATTGGTTTGTAAAATTACCAAAATACCCTTGATTTGTAAAATTACCAAA
ATACCCTTGGTTTGTA
Found at i:28961319 original size:27 final size:27
Alignment explanation
Indices: 28961017--28961311 Score: 311
Period size: 27 Copynumber: 10.9 Consensus size: 27
28961007 TTAGTTTACC
*
28961017 AAATTACCAAAATACCATTGGTTTATA
1 AAATTACCAAAATACCCTTGGTTTATA
* * *
28961044 AAATCACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTATA
*
28961071 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTTGGTTTATA
* *
28961098 AAATTACCAAAATACCATTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTATA
*
28961125 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCTTGGTTTATA
*
28961152 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTATA
* * *
28961179 AAATTATCAAAATACCCTTAGTTTGTA
1 AAATTACCAAAATACCCTTGGTTTATA
* * * *
28961206 AAATTACCAAAATACCATTGATTTGTG
1 AAATTACCAAAATACCCTTGGTTTATA
** * ** *
28961233 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTTGGTTTATA
*** * ** *
28961260 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTTGGTTTATA
* *
28961287 AAATTACCAAAGTACCCTTGATTTA
1 AAATTACCAAAATACCCTTGGTTTA
28961312 CAGAATTATC
Statistics
Matches: 231, Mismatches: 37, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 231 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (27 bp):
AAATTACCAAAATACCCTTGGTTTATA
Found at i:28961372 original size:27 final size:27
Alignment explanation
Indices: 28961342--28961938 Score: 771
Period size: 27 Copynumber: 21.6 Consensus size: 27
28961332 CGATTTACAA
28961342 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28961369 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
28961396 AATTACCTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
1 AATTACC----G-A-AA-TA--------CCCCTGTAGGGTAG
*
28961438 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28961465 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28961492 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28961519 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28961546 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
28961573 AATTATCGAAATACCCCTATAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
28961600 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28961627 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28961654 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28961681 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28961708 AATTATCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28961735 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28961762 AATTACCGGAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
28961789 AATTACCGGAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
28961816 AATTACTAAAATACCCCTGTATGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
28961843 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28961870 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
28961897 AATTACTAAAATACCCCTGTAAGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
28961924 AATTATCGAGATACC
1 AATTACCGAAATACC
28961939 TTATTGGGTA
Statistics
Matches: 511, Mismatches: 44, Indels: 30
0.87 0.08 0.05
Matches are distributed among these distances:
27 480 0.94
32 1 0.00
33 2 0.00
34 2 0.00
35 2 0.00
36 2 0.00
37 1 0.00
42 21 0.04
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:28961408 original size:15 final size:15
Alignment explanation
Indices: 28961388--28961417 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28961378 AATACCCCTG
28961388 TAGGGTAGAATTACC
1 TAGGGTAGAATTACC
28961403 TAGGGTAGAATTACC
1 TAGGGTAGAATTACC
28961418 GAAATACCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (15 bp):
TAGGGTAGAATTACC
Found at i:28961408 original size:42 final size:42
Alignment explanation
Indices: 28961361--28961444 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
28961351 AATACCCCTG
28961361 TAGGGTAGAATTACCAAAATACCCCTGTAGGGTAGAATTACC
1 TAGGGTAGAATTACCAAAATACCCCTGTAGGGTAGAATTACC
*
28961403 TAGGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACC
1 TAGGGTAGAATTACCAAAATACCCCTGTAGGGTAGAATTACC
28961445 AAAATACCCC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.24
Consensus pattern (42 bp):
TAGGGTAGAATTACCAAAATACCCCTGTAGGGTAGAATTACC
Found at i:28962636 original size:27 final size:27
Alignment explanation
Indices: 28962606--28962707 Score: 127
Period size: 27 Copynumber: 3.8 Consensus size: 27
28962596 ATTCTGTTAA
* *
28962606 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTCTGCCACAATATCTGTTTCTG
*
28962633 GTGGCTATGCCACAAATATCTG-TTCTG
1 GTGGCTCTGCCAC-AATATCTGTTTCTG
28962660 GTGGCTCTGCCACAATATCTGTATT-TG
1 GTGGCTCTGCCACAATATCTGT-TTCTG
* *
28962687 GTGACTCTGTCACAATATCTG
1 GTGGCTCTGCCACAATATCTG
28962708 ATAACTGAGC
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
26 8 0.12
27 50 0.75
28 9 0.13
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.37
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTTTCTG
Found at i:28962882 original size:6 final size:6
Alignment explanation
Indices: 28962844--28962913 Score: 72
Period size: 6 Copynumber: 11.3 Consensus size: 6
28962834 TTGCATTCAC
* *
28962844 ATTCTG ATTTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTG ATTCTG
1 ATTCTG A-TTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
28962894 ATTCTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG A-TTCTG AT
28962914 AATGTTTCTT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
5 3 0.06
6 41 0.76
7 9 0.17
8 1 0.02
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:28965142 original size:18 final size:19
Alignment explanation
Indices: 28965119--28965155 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
28965109 CGAATGTACA
28965119 TTTCATATACA-CATATAT
1 TTTCATATACATCATATAT
*
28965137 TTTCATTTACATCATATAT
1 TTTCATATACATCATATAT
28965156 AATTTGCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTCATATACATCATATAT
Found at i:28969265 original size:46 final size:46
Alignment explanation
Indices: 28969179--28969388 Score: 147
Period size: 46 Copynumber: 4.7 Consensus size: 46
28969169 ACATATTTGT
* *
28969179 GCCGATGCCATGTCCTAGACATGGTCTTACACT-GA-CACATCTCATA
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGATTACATCTCATA
28969225 GCCGATGCATGTCCCAGACATGTCTTACACTGGATTACA--TC---
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGATTACATCTCATA
* * * *
28969266 -CCGATGCATGT-CCAGACATGTCTTACACTAGCTTTCATCTCAAA
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGATTACATCTCATA
* * * * * *
28969310 GTCAATGCCATGCCCCAGACATGGTTTTACACTGG-TT-C-TCATAATGTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGATTACATC-TCA--TA
* *
28969358 GACGATGTATGTCCCAGACATGTCTTACACT
1 GCCGATGCATGTCCCAGACATGTCTTACACT
28969389 AGCGCACAAA
Statistics
Matches: 132, Mismatches: 18, Indels: 28
0.74 0.10 0.16
Matches are distributed among these distances:
39 23 0.17
40 11 0.08
41 2 0.02
44 12 0.09
45 21 0.16
46 26 0.20
47 22 0.17
48 15 0.11
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGATTACATCTCATA
Found at i:28969305 original size:85 final size:88
Alignment explanation
Indices: 28969180--28969344 Score: 207
Period size: 85 Copynumber: 1.9 Consensus size: 88
28969170 CATATTTGTG
* * *
28969180 CCGATGCCATGTCCTAGACATGGTCTTACACTGACACATCTCATAGCCGATG-CATGTCCCAGAC
1 CCGATGCCATGTCCTAGACATGGTCTTACACTGACACATCTCAAAGCCAATGCCATGCCCCAGAC
28969244 AT-GTCTTACACTGGATTACATC
66 ATGGTCTTACACTGGATTACATC
* *
28969266 CCGATG-CATGTCC-AGACAT-GTCTTACACT-AGCTTTCATCTCAAAGTCAATGCCATGCCCCA
1 CCGATGCCATGTCCTAGACATGGTCTTACACTGA-C--ACATCTCAAAGCCAATGCCATGCCCCA
*
28969327 GACATGGTTTTACACTGG
63 GACATGGTCTTACACTGG
28969345 TTCTCATAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
82 1 0.01
83 11 0.16
84 6 0.09
85 20 0.29
86 19 0.28
87 11 0.16
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (88 bp):
CCGATGCCATGTCCTAGACATGGTCTTACACTGACACATCTCAAAGCCAATGCCATGCCCCAGAC
ATGGTCTTACACTGGATTACATC
Found at i:28973362 original size:68 final size:69
Alignment explanation
Indices: 28973297--28973448 Score: 188
Period size: 67 Copynumber: 2.2 Consensus size: 69
28973287 CATCATGTGT
* * *
28973297 ACAAGAGAGCTACGAGACATTATGATGTAGCTAGGTCACATGGGT-GATAC-TAT-AAGTACACC
1 ACAAGAGAGCTACGAGACA-TAT-ATGTAGCTAGGTCACATGCGTGGATACAGATGAAGGACACC
28973359 ATGTAG
64 ATGTAG
* * * *
28973365 ACAAGAGAGCTACG-G-GATATATGTAGCTAGGTCGCATGCGTGGTTCCAGATGAAGGACACCAT
1 ACAAGAGAGCTACGAGACATATATGTAGCTAGGTCACATGCGTGGATACAGATGAAGGACACCAT
28973428 GTAG
66 GTAG
28973432 ACAAGAGAGCTACGAGA
1 ACAAGAGAGCTACGAGA
28973449 TAAACTGGCT
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
64 19 0.26
65 6 0.08
66 3 0.04
67 29 0.40
68 15 0.21
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.20
Consensus pattern (69 bp):
ACAAGAGAGCTACGAGACATATATGTAGCTAGGTCACATGCGTGGATACAGATGAAGGACACCAT
GTAG
Found at i:28976704 original size:158 final size:158
Alignment explanation
Indices: 28976416--28976729 Score: 556
Period size: 158 Copynumber: 2.0 Consensus size: 158
28976406 TGTCTCTACT
* * *
28976416 CGTGTGGACAAAAATAGGCTACTTGCAAAGCCAAATTGCCACCCATTTTGGACCATCCCTACAAG
1 CGTGTAGACAAAAATAGGCTACTTACAAAGCCAAATTGCCACCCATTTTGGACAATCCCTACAAG
* *
28976481 CATGAAACAAAGCACATTTCATGACCCAAAGGCAGCCAAAATCATACTAAATCATGTACAAATTG
66 CATGAAACAAAGCACATTTCATGACCCAAAGGCAGCCAAAAACATACTAAATCATGCACAAATTG
28976546 ACCCATGATATCATCATTCATTCCCACC
131 ACCCATGATATCATCATTCATTCCCACC
*
28976574 CGTGTAGACAAAAATAGGCTATTTACAAAGCCAAATTGCCACCCATTTTGGACAATCCCTACAAG
1 CGTGTAGACAAAAATAGGCTACTTACAAAGCCAAATTGCCACCCATTTTGGACAATCCCTACAAG
**
28976639 CATGAAACAAAGCACATTTCATGATTCAAAGGCAGCCAAAAACATACTAAATCATGCACAAATTG
66 CATGAAACAAAGCACATTTCATGACCCAAAGGCAGCCAAAAACATACTAAATCATGCACAAATTG
28976704 ACCCATGATATCATCATTCATTCCCA
131 ACCCATGATATCATCATTCATTCCCA
28976730 TATAAAAATC
Statistics
Matches: 148, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
158 148 1.00
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (158 bp):
CGTGTAGACAAAAATAGGCTACTTACAAAGCCAAATTGCCACCCATTTTGGACAATCCCTACAAG
CATGAAACAAAGCACATTTCATGACCCAAAGGCAGCCAAAAACATACTAAATCATGCACAAATTG
ACCCATGATATCATCATTCATTCCCACC
Found at i:28977615 original size:42 final size:42
Alignment explanation
Indices: 28977510--28977634 Score: 119
Period size: 43 Copynumber: 2.9 Consensus size: 42
28977500 AGAAAGCTCG
* * * *
28977510 TACGATGCCAAAGTCCCAGAC-GTGGTCTTACACGTAATAAAAT
1 TACGATGCC-ATGTCCCAGACAG-GGTCTTACATGAAATCAAAT
**
28977553 TTTGATGCCACTGTCCCAGACAGGGTCTTACATGAAATCAAA-
1 TACGATGCCA-TGTCCCAGACAGGGTCTTACATGAAATCAAAT
**
28977595 TACGATGCCGATGTCCCAGACATTGTCTTACATGTAAATC
1 TACGATGCC-ATGTCCCAGACAGGGTCTTACATG-AAATC
28977635 TCAAATCGAC
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
42 29 0.43
43 38 0.56
44 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.26
Consensus pattern (42 bp):
TACGATGCCATGTCCCAGACAGGGTCTTACATGAAATCAAAT
Found at i:28977665 original size:44 final size:42
Alignment explanation
Indices: 28977559--28977678 Score: 116
Period size: 44 Copynumber: 2.8 Consensus size: 42
28977549 AAATTTTGAT
* * ** *
28977559 GCCACTGTCCCAGACAGGGTCTTACATGAAATCAAATACGAT
1 GCCAATGTCCCAAACATTGTCTTACATGAAATCAAATACGAC
* *
28977601 GCCGATGTCCCAGACATTGTCTTACATGTAAATCTCAAAT-CGAC
1 GCCAATGTCCCAAACATTGTCTTACATG-AAA--TCAAATACGAC
* * *
28977645 GCCAATGTCCTAAACGTTGTCTTACACGAAATCA
1 GCCAATGTCCCAAACATTGTCTTACATGAAATCA
28977679 CATATCGGAC
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
41 3 0.05
42 24 0.37
43 6 0.09
44 26 0.40
45 6 0.09
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.25
Consensus pattern (42 bp):
GCCAATGTCCCAAACATTGTCTTACATGAAATCAAATACGAC
Found at i:28980881 original size:48 final size:49
Alignment explanation
Indices: 28980763--28980889 Score: 177
Period size: 49 Copynumber: 2.6 Consensus size: 49
28980753 GTTGTGTGTA
* * *
28980763 AGTGTAAGACCTGTCTGGGACGTGGCATCAACACCGATAGATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAGAACC
*
28980812 AGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCGATATATGA-AACC
1 AGTGTAAGACCTGTCTGGGACATGGCATCGACAC-CGATAGATGAGAACC
* *
28980860 AGTGTAAGACCTATCTGGGACACGGCATCG
1 AGTGTAAGACCTGTCTGGGACATGGCATCG
28980890 GCTTTAATGT
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
48 32 0.45
49 39 0.55
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.20
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGACACCGATAGATGAGAACC
Found at i:28988037 original size:46 final size:46
Alignment explanation
Indices: 28987955--28988072 Score: 130
Period size: 46 Copynumber: 2.5 Consensus size: 46
28987945 CATGAATGCC
* * *
28987955 AGTGTAAGACATGTTTGGGACATGCATCGGCATTGAGACGAT-AGCT
1 AGTGTAAGACATGTCTAGGACATGCATAGGCATTGAGA-GATAAGCT
** *
28988001 AGTGTAAGACATGTCTAGGACATGCATAGGTTTTGAGATATACAAGCT
1 AGTGTAAGACATGTCTAGGACATGCATAGGCATTGAGAGAT--AAGCT
* *
28988049 AGTGTAAGACCTATCTAGGACATG
1 AGTGTAAGACATGTCTAGGACATG
28988073 GCGTCAGCTT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
45 2 0.03
46 33 0.54
48 26 0.43
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.27
Consensus pattern (46 bp):
AGTGTAAGACATGTCTAGGACATGCATAGGCATTGAGAGATAAGCT
Found at i:28988163 original size:49 final size:44
Alignment explanation
Indices: 28988049--28988163 Score: 122
Period size: 44 Copynumber: 2.5 Consensus size: 44
28988039 TATACAAGCT
* * * *
28988049 AGTGTAAGACCTATCTAGGACATGGCGTCAGCTTGTTGTGTGTC
1 AGTGTAAGACCTATCTAGGACATGGCATCAGCTCGTTATGAGTC
** *
28988093 AGTGTAAGACCTGCCTGGGACATGGCATCAGCCTCGATATATGAAAGTC
1 AGTGTAAGACCTATCTAGGACATGGCATCAG-CTCG-T-TATG--AGTC
28988142 AGTGTAAGACCTATCTAGGACA
1 AGTGTAAGACCTATCTAGGACA
28988164 CGACATTGAC
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
44 27 0.48
45 3 0.05
46 1 0.02
47 3 0.05
49 22 0.39
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (44 bp):
AGTGTAAGACCTATCTAGGACATGGCATCAGCTCGTTATGAGTC
Found at i:29014475 original size:27 final size:27
Alignment explanation
Indices: 29014422--29014484 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
29014412 ATAGGCGGTC
* * * * *
29014422 AACTATCCTGTGTTTATTTTTCTGACG
1 AACTACCCCGTGTTTATTGTCCCGACG
29014449 AACTACCCCGTGTTTATTGTCCCGACG
1 AACTACCCCGTGTTTATTGTCCCGACG
**
29014476 GGCTACCCC
1 AACTACCCC
29014485 TTATTTACTA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.17, C:0.30, G:0.17, T:0.35
Consensus pattern (27 bp):
AACTACCCCGTGTTTATTGTCCCGACG
Found at i:29016268 original size:46 final size:46
Alignment explanation
Indices: 29016203--29016426 Score: 215
Period size: 46 Copynumber: 4.8 Consensus size: 46
29016193 GGGCCATTTG
* * *
29016203 TGTGAGCTAATG-AAGGACATCTCTGGGACATGCATCGGCCAC-ATTA
1 TGTGAGCTAGTGTAA-GACATGTCTGGGACATGCATCGGCCACGA-GA
* *
29016249 TGTGAGCTAGTGTAAGACATATCTGGGACATGCATCGGCCTCGAGA
1 TGTGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGA
* * * *
29016295 TGTAAGCCAGTGTAAGACATGTCTGGGACATGCATTGGCTACGAGA
1 TGTGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGA
* * *
29016341 TGTG-TC-AGTGTAAGACCATGTCTGGGACATGGCATCGG-TACGGATA
1 TGTGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCAC-GAGA
*
29016387 TGCGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATC
1 T--GTGAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATC
29016427 AGCACCTTAC
Statistics
Matches: 153, Mismatches: 16, Indels: 14
0.84 0.09 0.08
Matches are distributed among these distances:
44 9 0.06
45 18 0.12
46 90 0.59
47 3 0.02
48 2 0.01
49 1 0.01
50 30 0.20
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.24
Consensus pattern (46 bp):
TGTGAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACGAGA
Found at i:29017310 original size:25 final size:25
Alignment explanation
Indices: 29017254--29017310 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
29017244 GTGTAGAGGA
* *
29017254 CACGGCCTGGTACACGGGCATGTAC
1 CACGGCCTAGTACACAGGCATGTAC
* * *
29017279 CATGGCCTAGTACACAGGCGTGTGC
1 CACGGCCTAGTACACAGGCATGTAC
29017304 CACGGCC
1 CACGGCC
29017311 GTGTGACATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.19, C:0.33, G:0.32, T:0.16
Consensus pattern (25 bp):
CACGGCCTAGTACACAGGCATGTAC
Found at i:29022453 original size:58 final size:55
Alignment explanation
Indices: 29022353--29022462 Score: 166
Period size: 58 Copynumber: 1.9 Consensus size: 55
29022343 TGGCAAAGCG
*
29022353 TTATCAGGTTGAAACAGTGATGTCGAAAATCGAGCCAACCGCCCCCCCTCCCGCA
1 TTATCAGGTTGAAACAGTGATGTCGAAAATCGAGCCAACCGCCACCCCTCCCGCA
**
29022408 TTATCAGGTTGAAACAGTGAAGATGTCGAAAATCGAGCCCCCCGCCACCCCTCCC
1 TTATCAGGTTGAAACAGT---GATGTCGAAAATCGAGCCAACCGCCACCCCTCCC
29022463 CCCCAAGTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
55 18 0.37
58 31 0.63
ACGTcount: A:0.27, C:0.35, G:0.20, T:0.18
Consensus pattern (55 bp):
TTATCAGGTTGAAACAGTGATGTCGAAAATCGAGCCAACCGCCACCCCTCCCGCA
Found at i:29024389 original size:20 final size:21
Alignment explanation
Indices: 29024366--29024407 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
29024356 GAAAAAAATC
29024366 AAATCCAA-ATTAA-AATACTG
1 AAATCCAAGA-TAAGAATACTG
*
29024386 AAATTCAAGATAAGAATACTG
1 AAATCCAAGATAAGAATACTG
29024407 A
1 A
29024408 TGTGGCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.24
Consensus pattern (21 bp):
AAATCCAAGATAAGAATACTG
Found at i:29026137 original size:27 final size:26
Alignment explanation
Indices: 29026107--29026193 Score: 93
Period size: 27 Copynumber: 3.3 Consensus size: 26
29026097 AAATAATAAC
* *
29026107 TTTAAAAAAATTTAATATACAAAACAA
1 TTTAAAAAAA-ATAATATATAAAACAA
29026134 TTTAAAATAAAATAATATATAAAACAA
1 TTTAAAA-AAAATAATATATAAAACAA
* ** * *
29026161 TCTAAAATGACTAATTTATAAAACAA
1 TTTAAAAAAAATAATATATAAAACAA
29026187 TTTAAAA
1 TTTAAAA
29026194 TGGCGTATAA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
26 21 0.41
27 27 0.53
28 3 0.06
ACGTcount: A:0.61, C:0.07, G:0.01, T:0.31
Consensus pattern (26 bp):
TTTAAAAAAAATAATATATAAAACAA
Found at i:29026182 original size:26 final size:26
Alignment explanation
Indices: 29026119--29026195 Score: 100
Period size: 26 Copynumber: 2.9 Consensus size: 26
29026109 TAAAAAAATT
* *
29026119 TAATATACAAAACAATTTAAAATAAAA
1 TAATATATAAAACAATTTAAAAT-GAA
* *
29026146 TAATATATAAAACAATCTAAAATGAC
1 TAATATATAAAACAATTTAAAATGAA
*
29026172 TAATTTATAAAACAATTTAAAATG
1 TAATATATAAAACAATTTAAAATG
29026196 GCGTATAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
26 23 0.52
27 21 0.48
ACGTcount: A:0.60, C:0.08, G:0.03, T:0.30
Consensus pattern (26 bp):
TAATATATAAAACAATTTAAAATGAA
Found at i:29026237 original size:26 final size:26
Alignment explanation
Indices: 29026202--29026258 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
29026192 AATGGCGTAT
* * *
29026202 AAAAGTTTAAACTAAATAATATGTAA
1 AAAATTTTAAAATAAATAATATATAA
*
29026228 AAAATTTTAAAATACATAATATATAA
1 AAAATTTTAAAATAAATAATATATAA
29026254 AAAAT
1 AAAAT
29026259 ATAAAACAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (26 bp):
AAAATTTTAAAATAAATAATATATAA
Found at i:29026421 original size:27 final size:28
Alignment explanation
Indices: 29026370--29026432 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
29026360 ATACACAAAG
*
29026370 ATTTAAAATAAATCACATATGAAAA-AA
1 ATTTAAAATAAATCACATATAAAAATAA
* * *
29026397 ATTTAAAATAAATGATATCTAAAAATAA
1 ATTTAAAATAAATCACATATAAAAATAA
29026425 A-TTAAAAT
1 ATTTAAAAT
29026433 GAATAATACA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 28 0.90
28 3 0.10
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (28 bp):
ATTTAAAATAAATCACATATAAAAATAA
Found at i:29026447 original size:27 final size:26
Alignment explanation
Indices: 29026346--29026440 Score: 68
Period size: 27 Copynumber: 3.6 Consensus size: 26
29026336 ATATAAAACT
* * * *
29026346 TTAAAATATATAATATAC-ACAAAGAT
1 TTAAAATAAATAATAT-CTAAAAAAAA
* *
29026372 TTAAAATAAATCACATAT-GAAAAAAAT
1 TTAAAATAAAT-A-ATATCTAAAAAAAA
*
29026399 TTAAAATAAATGATATCTAAAAATAAA
1 TTAAAATAAATAATATCTAAAAA-AAA
*
29026426 TTAAAATGAATAATA
1 TTAAAATAAATAATA
29026441 CATAAAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
25 4 0.07
26 15 0.27
27 33 0.59
28 4 0.07
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.29
Consensus pattern (26 bp):
TTAAAATAAATAATATCTAAAAAAAA
Found at i:29027596 original size:21 final size:21
Alignment explanation
Indices: 29027572--29027633 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
29027562 TCGTAAATTA
29027572 TAAACTATAAACCTTAAACCC
1 TAAACTATAAACCTTAAACCC
* * *
29027593 TAAA-TATTAAACATTGAATCC
1 TAAACTA-TAAACCTTAAACCC
* *
29027614 TAAACCATAAAACCCTAAAC
1 TAAACTAT-AAACCTTAAAC
29027634 TATAGACAGT
Statistics
Matches: 30, Mismatches: 8, Indels: 5
0.70 0.19 0.12
Matches are distributed among these distances:
20 2 0.07
21 20 0.67
22 8 0.27
ACGTcount: A:0.50, C:0.24, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAACTATAAACCTTAAACCC
Found at i:29027698 original size:21 final size:22
Alignment explanation
Indices: 29027674--29027767 Score: 68
Period size: 21 Copynumber: 4.4 Consensus size: 22
29027664 AATATAGATT
29027674 CCTAAATCATAAAACTATAAA-
1 CCTAAATCATAAAACTATAAAC
* * *
29027695 CCTAAATCACTAGACCT-TAAAT
1 CCTAAATCA-TAAAACTATAAAC
** * *
29027717 TATAAAACTTAAAACTATAAAC
1 CCTAAATCATAAAACTATAAAC
* * *
29027739 CTTAAATC-TTAAACCATAAAC
1 CCTAAATCATAAAACTATAAAC
29027760 CCTAAATC
1 CCTAAATC
29027768 CAAAACCATA
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
21 36 0.65
22 19 0.35
ACGTcount: A:0.50, C:0.22, G:0.01, T:0.27
Consensus pattern (22 bp):
CCTAAATCATAAAACTATAAAC
Found at i:29027751 original size:14 final size:15
Alignment explanation
Indices: 29027683--29027758 Score: 70
Period size: 14 Copynumber: 5.3 Consensus size: 15
29027673 TCCTAAATCA
*
29027683 TAAAACTATAAACC-
1 TAAATCTATAAACCT
*
29027697 TAAATC-ACTAGACCT
1 TAAATCTA-TAAACCT
*
29027712 TAAAT-TATAAAACT
1 TAAATCTATAAACCT
*
29027726 TAAAACTATAAACCT
1 TAAATCTATAAACCT
*
29027741 TAAATCT-TAAACCA
1 TAAATCTATAAACCT
29027755 TAAA
1 TAAA
29027759 CCCTAAATCC
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
13 1 0.02
14 29 0.58
15 20 0.40
ACGTcount: A:0.53, C:0.18, G:0.01, T:0.28
Consensus pattern (15 bp):
TAAATCTATAAACCT
Found at i:29027773 original size:21 final size:21
Alignment explanation
Indices: 29027727--29027779 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
29027717 TATAAAACTT
* * *
29027727 AAAACTATAAACCTTAAATCT
1 AAAACCATAAACCCTAAATCC
*
29027748 TAAACCATAAACCCTAAATCC
1 AAAACCATAAACCCTAAATCC
29027769 AAAACCATAAA
1 AAAACCATAAA
29027780 ACCTTAGTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.55, C:0.25, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAACCATAAACCCTAAATCC
Found at i:29028131 original size:3 final size:3
Alignment explanation
Indices: 29028123--29028154 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
29028113 ATTAATAGTA
29028123 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
29028155 AAGAGAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:29028526 original size:188 final size:187
Alignment explanation
Indices: 29028256--29028623 Score: 449
Period size: 188 Copynumber: 2.0 Consensus size: 187
29028246 TTGAAGCTAT
** *
29028256 GTTATTAGTGGCGCTTCTAAAAAACGTCACAAAACATCTATTAAGAGAATGTAAAACGGCGTCGT
1 GTTATTAGTGGCGCTTCTAAAAAACACCACAAAACATCTA-TAAGAGAATGTAAAACGGCATCGT
* * * ** *
29028321 TTACATCCCTCTTATTAGTGGCGCTTCTATAAACGCCGCAAAAGGTGTGATTTAC-TGACGTTTT
65 TTACATCCCTCTTATTAGTGGCGCTTCTATAAACACCACAAAAGATGTGAAATACAAG-CGTTTT
* * *
29028385 CACTAGAAAACGCCACAAACATCTATTAATAGATTG-TAAAACGGCGTCGTTAGTACCAA
129 CACTAG-AAACGCCACAAAAATCTATTAAAAGATTGCAAAAACGGCGTCGTTAGTACCAA
* *
29028444 GTTATTAGTGGCGCTTCTTAGAAAAACACCACAAAACATCTA-AAGAG-ATTTCAAAACGTCATC
1 GTTATTAGTGGCGCTTC-TA-AAAAACACCACAAAACATCTATAAGAGAATGT-AAAACGGCATC
* * * * *
29028507 GTTT-TATAGCCTTTTATTAGTGGCGCTTTTATAAACACCACAAAATATGTGAAATACAAGCGTT
63 GTTTACAT-CCCTCTTATTAGTGGCGCTTCTATAAACACCACAAAAGATGTGAAATACAAGCGTT
* *
29028571 TTCGCTAGAAACGCCACAAAAATCTATTAAAAGATTGCAAAAACTGCGTCGTT
127 TTCACTAGAAACGCCACAAAAATCTATTAAAAGATTGCAAAAACGGCGTCGTT
29028624 TGTAGCCTTT
Statistics
Matches: 153, Mismatches: 21, Indels: 12
0.82 0.11 0.06
Matches are distributed among these distances:
187 32 0.21
188 99 0.65
189 3 0.02
190 19 0.12
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29
Consensus pattern (187 bp):
GTTATTAGTGGCGCTTCTAAAAAACACCACAAAACATCTATAAGAGAATGTAAAACGGCATCGTT
TACATCCCTCTTATTAGTGGCGCTTCTATAAACACCACAAAAGATGTGAAATACAAGCGTTTTCA
CTAGAAACGCCACAAAAATCTATTAAAAGATTGCAAAAACGGCGTCGTTAGTACCAA
Found at i:29031476 original size:24 final size:24
Alignment explanation
Indices: 29031449--29031495 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
29031439 ATTATTATTG
*
29031449 AAATATGCTCGTCCGTTTTATCAC
1 AAATATGATCGTCCGTTTTATCAC
*
29031473 AAATATTATCGTCCGTTTTATCA
1 AAATATGATCGTCCGTTTTATCA
29031496 TTTAAGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (24 bp):
AAATATGATCGTCCGTTTTATCAC
Found at i:29031732 original size:15 final size:13
Alignment explanation
Indices: 29031714--29031816 Score: 52
Period size: 14 Copynumber: 7.8 Consensus size: 13
29031704 TCTTATTTTA
29031714 ATTAATATAATTTGG
1 ATTAAT-TAATTT-G
* *
29031729 ATTAATTTATTTA
1 ATTAATTAATTTG
*
29031742 ATT-ATT-ATTTA
1 ATTAATTAATTTG
29031753 ATTAATATAATTTGG
1 ATTAAT-TAATTT-G
* * *
29031768 ATTAATTTATGTA
1 ATTAATTAATTTG
* *
29031781 AAT-ATT-ATTTA
1 ATTAATTAATTTG
29031792 ATTAATATAATTTGG
1 ATTAAT-TAATTT-G
29031807 ATTAATTAAT
1 ATTAATTAAT
29031817 AATATAATTT
Statistics
Matches: 70, Mismatches: 10, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
11 14 0.20
12 10 0.14
13 7 0.10
14 21 0.30
15 18 0.26
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (13 bp):
ATTAATTAATTTG
Found at i:29031754 original size:39 final size:39
Alignment explanation
Indices: 29031710--29031813 Score: 190
Period size: 39 Copynumber: 2.7 Consensus size: 39
29031700 TCAATCTTAT
* *
29031710 TTTAATTAATATAATTTGGATTAATTTATTTAATTATTA
1 TTTAATTAATATAATTTGGATTAATTTATGTAAATATTA
29031749 TTTAATTAATATAATTTGGATTAATTTATGTAAATATTA
1 TTTAATTAATATAATTTGGATTAATTTATGTAAATATTA
29031788 TTTAATTAATATAATTTGGATTAATT
1 TTTAATTAATATAATTTGGATTAATT
29031814 AATAATATAA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 63 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (39 bp):
TTTAATTAATATAATTTGGATTAATTTATGTAAATATTA
Found at i:29031804 original size:29 final size:28
Alignment explanation
Indices: 29031770--29031891 Score: 102
Period size: 29 Copynumber: 4.1 Consensus size: 28
29031760 TAATTTGGAT
29031770 TAATTTATGTAAATATTATTTAATTAATA
1 TAATTTAT-TAAATATTATTTAATTAATA
* * * *
29031799 TAATTTGGATTAATTAATAATATAATTTGGAT-
1 TAATTT--ATTAAAT-ATTATTTAA-TT-AATA
*
29031831 TAATTTATTTAAATATTATTAAATTAATA
1 TAATTTA-TTAAATATTATTTAATTAATA
* *
29031860 TAATTTTTATAAATATTATTTAATTAAAA
1 TAATTTAT-TAAATATTATTTAATTAATA
29031889 TAA
1 TAA
29031892 ATTTTTTTCC
Statistics
Matches: 73, Mismatches: 12, Indels: 16
0.72 0.12 0.16
Matches are distributed among these distances:
28 3 0.04
29 35 0.48
30 11 0.15
31 14 0.19
32 8 0.11
33 2 0.03
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (28 bp):
TAATTTATTAAATATTATTTAATTAATA
Found at i:29031831 original size:61 final size:62
Alignment explanation
Indices: 29031745--29031865 Score: 208
Period size: 61 Copynumber: 2.0 Consensus size: 62
29031735 TTATTTAATT
* *
29031745 ATTATTTAATTAATATAATTTGGATTAATTTATGTAAATATTATTTAATTAATATAATTTGG
1 ATTAATTAATTAATATAATTTGGATTAATTTATGTAAATATTATTAAATTAATATAATTTGG
*
29031807 ATTAATTAA-TAATATAATTTGGATTAATTTATTTAAATATTATTAAATTAATATAATTT
1 ATTAATTAATTAATATAATTTGGATTAATTTATGTAAATATTATTAAATTAATATAATTT
29031866 TTATAAATAT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
61 48 0.86
62 8 0.14
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (62 bp):
ATTAATTAATTAATATAATTTGGATTAATTTATGTAAATATTATTAAATTAATATAATTTGG
Found at i:29032173 original size:9 final size:9
Alignment explanation
Indices: 29032156--29032276 Score: 122
Period size: 9 Copynumber: 13.7 Consensus size: 9
29032146 TATATACTTG
29032156 AACTTACAT
1 AACTTACAT
*
29032165 AACTCACAT
1 AACTTACAT
*
29032174 AACTCACAT
1 AACTTACAT
*
29032183 AACTCACAT
1 AACTTACAT
29032192 AACTTACAT
1 AACTTACAT
*
29032201 AACTTACAG
1 AACTTACAT
*
29032210 AAGTTACAT
1 AACTTACAT
*
29032219 AATTTACAT
1 AACTTACAT
29032228 AACTTACAT
1 AACTTACAT
29032237 AA--TACAT
1 AACTTACAT
* *
29032244 AA-ATATAT
1 AACTTACAT
* *
29032252 ATCATATCAT
1 AACTTA-CAT
29032262 AACTTACAT
1 AACTTACAT
29032271 AACTTA
1 AACTTA
29032277 ATTAGAGTTA
Statistics
Matches: 97, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
7 7 0.07
8 5 0.05
9 79 0.81
10 6 0.06
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (9 bp):
AACTTACAT
Found at i:29032174 original size:32 final size:31
Alignment explanation
Indices: 29032113--29032175 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 31
29032103 TTCTAAAAAT
* *
29032113 ATATATACTTGAATACATCACTAGTACATAAA
1 ATATATACTTGAATACATAACTA-CACATAAA
29032145 ATATATACTTGAACTTACATAACT-CACATAA
1 ATATATACTTGAA--TACATAACTACACATAA
29032176 CTCACATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 19 0.70
34 8 0.30
ACGTcount: A:0.46, C:0.17, G:0.05, T:0.32
Consensus pattern (31 bp):
ATATATACTTGAATACATAACTACACATAAA
Found at i:29036997 original size:49 final size:47
Alignment explanation
Indices: 29036776--29037134 Score: 540
Period size: 47 Copynumber: 7.6 Consensus size: 47
29036766 TCCTTCGGGA
* * * *
29036776 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCACTCA-GC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCA-TTAGGC
* *
29036823 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
29036870 CTCATCACATATAGACACTTTCACATTCATCACATCGGCTATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29036917 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29036964 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
29037013 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29037060 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
29037109 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
29037135 CACAATTATC
Statistics
Matches: 285, Mismatches: 22, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
46 2 0.01
47 191 0.67
49 92 0.32
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:29037015 original size:96 final size:96
Alignment explanation
Indices: 29036776--29037134 Score: 555
Period size: 96 Copynumber: 3.8 Consensus size: 96
29036766 TCCTTCGGGA
* * * * * *
29036776 CTTATCACAT-T-TATACACTTTCACATCCATCACATTGGCCACTCAGCCCTGTCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGCCTTATCACATATATAC
29036839 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* * *
29036870 CTCATCAC--ATATAGACACTTTCACATTCATCACATCGGCTATTAAGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGCCTTATCACATATATAC
29036933 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
**
29036964 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGCCTTATCACATATATAC
*
29037029 ACTTTCACATTCATCACATCGGCTATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* *
29037060 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGCCTTATCACATATATAC
*
29037125 ACATTCACAT
66 ACTTTCACAT
29037135 CACAATTATC
Statistics
Matches: 243, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
93 1 0.00
94 89 0.37
96 153 0.63
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.32
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:29040544 original size:29 final size:29
Alignment explanation
Indices: 29040511--29040580 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
29040501 CCAAATTAAA
29040511 CACCCCACTAAACCGA-CCACTAACTCCAT
1 CACCCCACTAAACC-ATCCACTAACTCCAT
* *
29040540 CACCCTACTAAACCATCCACTACCTCCAT
1 CACCCCACTAAACCATCCACTAACTCCAT
29040569 CACCCCCACTAA
1 CA-CCCCACTAA
29040581 CTCCATCACC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.03
29 27 0.75
30 8 0.22
ACGTcount: A:0.33, C:0.50, G:0.01, T:0.16
Consensus pattern (29 bp):
CACCCCACTAAACCATCCACTAACTCCAT
Found at i:29040579 original size:18 final size:18
Alignment explanation
Indices: 29040556--29040591 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29040546 ACTAAACCAT
*
29040556 CCACTACCTCCATCACCC
1 CCACTAACTCCATCACCC
29040574 CCACTAACTCCATCACCC
1 CCACTAACTCCATCACCC
29040592 TACTTGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.58, G:0.00, T:0.17
Consensus pattern (18 bp):
CCACTAACTCCATCACCC
Found at i:29041498 original size:126 final size:126
Alignment explanation
Indices: 29041273--29041516 Score: 452
Period size: 126 Copynumber: 1.9 Consensus size: 126
29041263 CATTGATCTT
* *
29041273 CTCTCAAAATTTTTCAAAATAAAGGCAATGTTCGGTATTTAAAGAATTCGAAGAATCGTGCCCTA
1 CTCTCAAAAATTTTCAAAATAAAGGCAATGTTCGGTATGTAAAGAATTCGAAGAATCGTGCCCTA
29041338 ACGTACTGGGTTTCGCTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAGTTCA
66 ACGTACTGGGTTTCGCTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAGTTCA
*
29041399 CTCTCAAAAATTTTCAAAATAAAGGCAATGTTCGGTATGTAAAGAATTTGAAGAATCGTGCCCTA
1 CTCTCAAAAATTTTCAAAATAAAGGCAATGTTCGGTATGTAAAGAATTCGAAGAATCGTGCCCTA
*
29041464 ACGTACTGGGTTTCGCTTTCTTTGTTTGTTTTGAATATTCGAATATCCTCTTA
66 ACGTACTGGGTTTCGCTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTA
29041517 AGGCAAAAAT
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
126 114 1.00
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (126 bp):
CTCTCAAAAATTTTCAAAATAAAGGCAATGTTCGGTATGTAAAGAATTCGAAGAATCGTGCCCTA
ACGTACTGGGTTTCGCTTTCTTTGTTTGTCTTGAATATTCGAATATCCTCTTACCAGTTCA
Found at i:29047406 original size:40 final size:40
Alignment explanation
Indices: 29047351--29047495 Score: 143
Period size: 39 Copynumber: 3.7 Consensus size: 40
29047341 ATTTGATGTG
*
29047351 TATCCGGGCTTAAAGACCCGCAGGTTATATGCTAGAATTA
1 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTAGAATTA
* *
29047391 TATCCGGGCTTAAAGACCTGCAGGCTATATGCTGGAATTA
1 TATCCGGGCTTAAAGACCCGCAGGCTATATGCTAGAATTA
* ** * * *
29047431 TA-CTCGGACTT-AAGGTCCGCAAGCTATGTGCTGGAATTA
1 TATC-CGGGCTTAAAGACCCGCAGGCTATATGCTAGAATTA
* * **
29047470 TAACCGGACTT-AAGGTCCGCAGGCTA
1 TATCCGGGCTTAAAGACCCGCAGGCTA
29047496 CGGCCTGGAA
Statistics
Matches: 93, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
39 47 0.51
40 46 0.49
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (40 bp):
TATCCGGGCTTAAAGACCCGCAGGCTATATGCTAGAATTA
Found at i:29047504 original size:39 final size:39
Alignment explanation
Indices: 29047420--29047505 Score: 122
Period size: 39 Copynumber: 2.2 Consensus size: 39
29047410 GCAGGCTATA
*
29047420 TGCTGGAATTATACTCGGACTTAAGGTCCGCAAGCTATG
1 TGCTGGAATTATACTCGGACTTAAGGTCCGCAAGCTACG
*
29047459 TGCTGGAATTATAAC-CGGACTTAAGGTCCGCAGGCTACG
1 TGCTGGAATTAT-ACTCGGACTTAAGGTCCGCAAGCTACG
29047498 -GCCTGGAA
1 TG-CTGGAA
29047506 ATATGTCCGG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
38 1 0.02
39 40 0.93
40 2 0.05
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
TGCTGGAATTATACTCGGACTTAAGGTCCGCAAGCTACG
Done.