Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 90 of 226
Found at i:31669870 original size:123 final size:123
Alignment explanation
Indices: 31669652--31669928 Score: 459
Period size: 123 Copynumber: 2.3 Consensus size: 123
31669642 TCACGAGGGC
*
31669652 GCGATTTTATA-TATTTGCTCAGAAACGTCAAAAAAATTATTGCTTACATGACCAACTGTAGCGA
1 GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATATTGCTTACATGACCAACTGTAGCGA
* *
31669716 AATCGCATCCACGAGGGCACGATTTCACAATTCCTTCTCAAATAGCATCCTGGTATAA
66 AATCGCATCCACGAGGGCACGATTTCACAATTCCTTCTCAAATAGCATCCTAGTAGAA
* *
31669774 GCGATTTTATACTATTTGCTCAGAAATGTCAAAAAAAATATTTCTTACATGACCAACTGTAGCGA
1 GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATATTGCTTACATGACCAACTGTAGCGA
*
31669839 AATCGCATCCACGAGGGCACGATTTCACAATTTCTTCTCAAATAGCATCCTAGTAGAA
66 AATCGCATCCACGAGGGCACGATTTCACAATTCCTTCTCAAATAGCATCCTAGTAGAA
* *
31669897 GCTATTTTATACTATTTGAC-CAGAACCGTCAA
1 GCGATTTTATACTATTTG-CTCAGAAACGTCAA
31669929 CTCGAAATAA
Statistics
Matches: 144, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
122 11 0.08
123 132 0.92
124 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.30
Consensus pattern (123 bp):
GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATATTGCTTACATGACCAACTGTAGCGA
AATCGCATCCACGAGGGCACGATTTCACAATTCCTTCTCAAATAGCATCCTAGTAGAA
Found at i:31671397 original size:43 final size:43
Alignment explanation
Indices: 31671257--31671400 Score: 180
Period size: 43 Copynumber: 3.3 Consensus size: 43
31671247 TTTATGTGAA
* * *
31671257 AAAAATGCCGCTATAGAACATGACCTTTAGCGGCGCTTTTATA
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATC
* * * * *
31671300 AAAAATGCCGCTAAAGAACATGTCTTTTAGCGGCGCTTTAACC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATC
* *
31671343 ACAAACGCCGCTAAAGAACATGACCTTTAGCAGCGCTTTTATC
1 AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATC
* *
31671386 ATAAACACCGCTAAA
1 AAAAACGCCGCTAAA
31671401 CAAACTCCGT
Statistics
Matches: 86, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 86 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATC
Found at i:31671416 original size:57 final size:57
Alignment explanation
Indices: 31671343--31671457 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 57
31671333 CGCTTTAACC
* *
31671343 ACAAACGCCGCTAAAGAACATGACCTTTAGCAGCGCTTTTATCATAAACACCGCTAA
1 ACAAACGCCGCTAAAGAACATAACCTTTAGCAGCGCTTTTATCACAAACACCGCTAA
* * * * *
31671400 ACAAACTCCGTTAAAGAATATAACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAA
1 ACAAACGCCGCTAAAGAACATAACCTTTAGCAGCGCTTTTATCACAAACACCGCTAA
31671457 A
1 A
31671458 GAGCATGACC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.23
Consensus pattern (57 bp):
ACAAACGCCGCTAAAGAACATAACCTTTAGCAGCGCTTTTATCACAAACACCGCTAA
Found at i:31671469 original size:43 final size:43
Alignment explanation
Indices: 31671422--31671586 Score: 188
Period size: 43 Copynumber: 3.8 Consensus size: 43
31671412 AAAGAATATA
31671422 ACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAGCATG
1 ACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAGCATG
* * *
31671465 ACCTTTTGCGGCGCTTTTATCACAAACGCTGCTATAA-AGAATG
1 ACCTTTAGCGGCGCTTTTATCACAAACGCCGCTA-AAGAGCATG
* * ** * ** *
31671508 ACTTTTAGTGGCTTTTTTTTCACAAATTCCGCTAAAGAACATG
1 ACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAGCATG
* * *
31671551 ATCTTTAGCGGCGCTTTTATCACAAATGCCGTTAAA
1 ACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAA
31671587 AGTACCGTTC
Statistics
Matches: 98, Mismatches: 22, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
42 2 0.02
43 94 0.96
44 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (43 bp):
ACCTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAGAGCATG
Found at i:31674666 original size:42 final size:43
Alignment explanation
Indices: 31674612--31674722 Score: 136
Period size: 42 Copynumber: 2.6 Consensus size: 43
31674602 TATTTGAGAT
31674612 TTACGTGTAAGACCATGTCTGGGAC-GTTGACATCG-TATATGA
1 TTACGTGTAAGACCATGTCTGGGACAG-TGACATCGTTATATGA
* * * *
31674654 TTACGTGTAAGACCCTGTCTAGGACAGTGGCATCGTTATTTGA
1 TTACGTGTAAGACCATGTCTGGGACAGTGACATCGTTATATGA
* * *
31674697 TTGCATGTAAGACCATGTTTGGGACA
1 TTACGTGTAAGACCATGTCTGGGACA
31674723 TTGGCATTGT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
42 30 0.52
43 28 0.48
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
TTACGTGTAAGACCATGTCTGGGACAGTGACATCGTTATATGA
Found at i:31674709 original size:43 final size:42
Alignment explanation
Indices: 31674612--31674729 Score: 130
Period size: 43 Copynumber: 2.8 Consensus size: 42
31674602 TATTTGAGAT
* *
31674612 TTACGTGTAAGACCATGTCTGGGAC-GTTGACATCGTATATGA
1 TTACATGTAAGACCATGTCTGGGACAG-TGGCATCGTATATGA
* * * *
31674654 TTACGTGTAAGACCCTGTCTAGGACAGTGGCATCGTTATTTGA
1 TTACATGTAAGACCATGTCTGGGACAGTGGCATCG-TATATGA
* * *
31674697 TTGCATGTAAGACCATGTTTGGGACATTGGCAT
1 TTACATGTAAGACCATGTCTGGGACAGTGGCAT
31674730 TGTACGAGCT
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
42 30 0.47
43 34 0.53
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (42 bp):
TTACATGTAAGACCATGTCTGGGACAGTGGCATCGTATATGA
Found at i:31675198 original size:2 final size:2
Alignment explanation
Indices: 31675191--31675219 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31675181 TTTGAAATTG
31675191 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31675220 GTAAAGCCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31677985 original size:7 final size:7
Alignment explanation
Indices: 31677955--31678117 Score: 90
Period size: 7 Copynumber: 23.6 Consensus size: 7
31677945 CTTAGGCCCC
31677955 TAAACCT
1 TAAACCT
31677962 TAAA-CT
1 TAAACCT
*
31677968 CTAAACTT
1 -TAAACCT
31677976 TAAACCT
1 TAAACCT
*
31677983 TAAACCC
1 TAAACCT
* *
31677990 TAAGCCCC
1 TAA-ACCT
31677998 T-AACACT
1 TAAAC-CT
31678005 TAAACCT
1 TAAACCT
31678012 TAAACCT
1 TAAACCT
31678019 TAAACAC-
1 TAAAC-CT
*
31678026 TAAACCA
1 TAAACCT
31678033 TAAACC-
1 TAAACCT
* *
31678039 TACACCC
1 TAAACCT
*
31678046 TAAA-TT
1 TAAACCT
31678052 GTAAACAC-
1 -TAAAC-CT
* *
31678060 TAAATCA
1 TAAACCT
*
31678067 TAAACCC
1 TAAACCT
31678074 TAAACCT
1 TAAACCT
31678081 TAAA-CT
1 TAAACCT
* *
31678087 CAAACCA
1 TAAACCT
31678094 TAAACC-
1 TAAACCT
*
31678100 TACACCT
1 TAAACCT
31678107 TAAACCT
1 TAAACCT
31678114 TAAA
1 TAAA
31678118 TATATATTAC
Statistics
Matches: 122, Mismatches: 20, Indels: 28
0.72 0.12 0.16
Matches are distributed among these distances:
6 20 0.16
7 93 0.76
8 9 0.07
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.23
Consensus pattern (7 bp):
TAAACCT
Found at i:31678007 original size:43 final size:43
Alignment explanation
Indices: 31677939--31678031 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 43
31677929 AAATTAGACC
* * *
31677939 CTAAACCTTAGGCCCCTAAACCTTAAA-CTCTAAACTTTAAAC-
1 CTAAACCCTAAGCCCCTAAACCTTAAACCT-TAAACCTTAAACA
31677981 CTTAAACCCTAAGCCCCT-AACACTTAAACCTTAAACCTTAAACA
1 C-TAAACCCTAAGCCCCTAAAC-CTTAAACCTTAAACCTTAAACA
31678025 CTAAACC
1 CTAAACC
31678032 ATAAACCTAC
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
42 4 0.09
43 37 0.84
44 3 0.07
ACGTcount: A:0.40, C:0.33, G:0.03, T:0.24
Consensus pattern (43 bp):
CTAAACCCTAAGCCCCTAAACCTTAAACCTTAAACCTTAAACA
Found at i:31678292 original size:7 final size:7
Alignment explanation
Indices: 31678280--31678326 Score: 67
Period size: 7 Copynumber: 6.7 Consensus size: 7
31678270 TATAAAATAG
31678280 TAAACCC
1 TAAACCC
31678287 TAAACCC
1 TAAACCC
*
31678294 TAAACTC
1 TAAACCC
*
31678301 TAAACCA
1 TAAACCC
*
31678308 TAAACCA
1 TAAACCC
31678315 TAAACCC
1 TAAACCC
31678322 TAAAC
1 TAAAC
31678327 TCAAAACTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAACCC
Found at i:31678303 original size:14 final size:14
Alignment explanation
Indices: 31678280--31678338 Score: 66
Period size: 14 Copynumber: 4.2 Consensus size: 14
31678270 TATAAAATAG
*
31678280 TAAACCCTAAACCC
1 TAAACTCTAAACCC
*
31678294 TAAACTCTAAACCA
1 TAAACTCTAAACCC
31678308 TAAAC-CATAAACCC
1 TAAACTC-TAAACCC
* *
31678322 TAAACTCAAAACTC
1 TAAACTCTAAACCC
31678336 TAA
1 TAA
31678339 TCCTAAAATG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
13 1 0.03
14 36 0.95
15 1 0.03
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.19
Consensus pattern (14 bp):
TAAACTCTAAACCC
Found at i:31678397 original size:14 final size:14
Alignment explanation
Indices: 31678363--31678423 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
31678353 ATATATATCA
* *
31678363 TAAACCCTAAAAAGC
1 TAAACCATAAACA-C
*
31678378 TAAACCATAAACAT
1 TAAACCATAAACAC
* *
31678392 TAAACCTTAAATAC
1 TAAACCATAAACAC
* *
31678406 TAAACCCTAAACCC
1 TAAACCATAAACAC
31678420 TAAA
1 TAAA
31678424 ATAAAATGAT
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
14 26 0.70
15 11 0.30
ACGTcount: A:0.52, C:0.26, G:0.02, T:0.20
Consensus pattern (14 bp):
TAAACCATAAACAC
Found at i:31678416 original size:28 final size:29
Alignment explanation
Indices: 31678363--31678417 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
31678353 ATATATATCA
31678363 TAAACCCTAAAAAGCTAAACCATAAACAT
1 TAAACCCTAAAAAGCTAAACCATAAACAT
* * *
31678392 TAAACCTTAAATA-CTAAACCCTAAAC
1 TAAACCCTAAAAAGCTAAACCATAAAC
31678418 CCTAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.53, C:0.25, G:0.02, T:0.20
Consensus pattern (29 bp):
TAAACCCTAAAAAGCTAAACCATAAACAT
Found at i:31678842 original size:72 final size:71
Alignment explanation
Indices: 31678716--31678874 Score: 273
Period size: 72 Copynumber: 2.2 Consensus size: 71
31678706 ATTTTTTGAC
* *
31678716 AAAGCACCGCTAATGCCACTAAAGCTCAACAAACTACGTCGTTTTGCTCAACTTTTTTGTGACGT
1 AAAGCGCCCCTAATGCCACTAAAGCTCAACAAACTACGTCGTTTTGCTCAAC-TTTTTGTGACGT
31678781 TTTCCAA
65 TTTCCAA
* *
31678788 ATAGCTCCCCTAATGCCACTAAAGCTCAACAAACTACGTCGTTTTGCTCAACTTTTTGTGACGTT
1 AAAGCGCCCCTAATGCCACTAAAGCTCAACAAACTACGTCGTTTTGCTCAACTTTTTGTGACGTT
31678853 TTCCAA
66 TTCCAA
31678859 AAAGCGCCCCTAATGC
1 AAAGCGCCCCTAATGC
31678875 TAGATCTATA
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 33 0.40
72 49 0.60
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (71 bp):
AAAGCGCCCCTAATGCCACTAAAGCTCAACAAACTACGTCGTTTTGCTCAACTTTTTGTGACGTT
TTCCAA
Found at i:31678986 original size:81 final size:80
Alignment explanation
Indices: 31678850--31678999 Score: 228
Period size: 81 Copynumber: 1.9 Consensus size: 80
31678840 TTTTTGTGAC
* * *
31678850 GTTTTCCAAAAAGCGCCCCTAATGCTAGATCTATATCGGCGTTTTTCCAATAGCACCGCTAATGC
1 GTTTTCCAAAAAGCGCCCCTAATGCTAGATCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATGC
31678915 TTGATTTATAACGGT
66 TTGATTTATAACGGT
* * * *
31678930 GTTTTTCAAAAAGTGCCCACTAATGCTCGATCTATAGCGGCGTTTTTTAAAAAGCACCGCTAATG
1 GTTTTCCAAAAAGCGCCC-CTAATGCTAGATCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATG
31678995 CTTGA
65 CTTGA
31679000 CCTATAGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
80 16 0.26
81 46 0.74
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (80 bp):
GTTTTCCAAAAAGCGCCCCTAATGCTAGATCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATGC
TTGATTTATAACGGT
Found at i:31679006 original size:40 final size:40
Alignment explanation
Indices: 31678849--31679008 Score: 169
Period size: 40 Copynumber: 4.0 Consensus size: 40
31678839 CTTTTTGTGA
* * * * *
31678849 CGTTTTCCAAAAAGCGCCCCTAATGCTAGATCTATATCGG
1 CGTTTTTCAAAAAGCACCGCTAATGCTTGATCTATAGCGG
* * * *
31678889 CGTTTTTCCAATAGCACCGCTAATGCTTGATTTATAACGG
1 CGTTTTTCAAAAAGCACCGCTAATGCTTGATCTATAGCGG
* * *
31678929 TGTTTTTCAAAAAGTGC-CCACTAATGCTCGATCTATAGCGG
1 CGTTTTTCAAAAA--GCACCGCTAATGCTTGATCTATAGCGG
* *
31678970 CGTTTTTTAAAAAGCACCGCTAATGCTTGACCTATAGCG
1 CGTTTTTCAAAAAGCACCGCTAATGCTTGATCTATAGCG
31679009 ACATTTGTTT
Statistics
Matches: 97, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
39 2 0.02
40 62 0.64
41 31 0.32
42 2 0.02
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (40 bp):
CGTTTTTCAAAAAGCACCGCTAATGCTTGATCTATAGCGG
Found at i:31681845 original size:46 final size:45
Alignment explanation
Indices: 31681680--31681845 Score: 133
Period size: 46 Copynumber: 3.6 Consensus size: 45
31681670 GCTATTTTTT
* *
31681680 GTGTAGGTTTAACCCTTACGAGTGA-TCAGACACTATTATCCGATTC
1 GTGTAGGTTCAACCCTTACGAGTGACT-AGACA-TATTATTCGATTC
* * *
31681726 GTGTAAGTTCAACCCTTACG-GTTGACCAAGGACTATGATTTATT--ATTT
1 GTGTAGGTTCAACCCTTACGAG-TGA-CTA-GAC-AT-A-TTATTCGATTC
* * * *
31681774 GTGTAGGTTTAATCCTTATGGGTGACTAGACAGTATTATTCGATTC
1 GTGTAGGTTCAACCCTTACGAGTGACTAGACA-TATTATTCGATTC
*
31681820 ATGTAGGTTCAACCCTTACGAGTGAC
1 GTGTAGGTTCAACCCTTACGAGTGAC
31681846 CAAGAATTAT
Statistics
Matches: 93, Mismatches: 16, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
44 5 0.05
45 3 0.03
46 49 0.53
47 3 0.03
48 26 0.28
49 3 0.03
50 4 0.04
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (45 bp):
GTGTAGGTTCAACCCTTACGAGTGACTAGACATATTATTCGATTC
Found at i:31681882 original size:48 final size:48
Alignment explanation
Indices: 31681681--31681882 Score: 125
Period size: 46 Copynumber: 4.3 Consensus size: 48
31681671 CTATTTTTTG
* * * *
31681681 TGTAGGTTTAACCCTTACGAGTGATC-AGACACTATTATCCGAT-TCG-
1 TGTAGGTTTAACCCTTACGAGTGACCAAGACACTATGATTC-ATATTGT
* * * *
31681727 TGTAAGTTCAACCCTTACG-GTTGACCAAG-GACTATGATTTATTATT-T
1 TGTAGGTTTAACCCTTACGAG-TGACCAAGACACTATGATTCA-TATTGT
* * * * * * * **
31681774 GTGTAGGTTTAATCCTTATGGGTGA-CTAGACAGTATTATTC-GATTCA
1 -TGTAGGTTTAACCCTTACGAGTGACCAAGACACTATGATTCATATTGT
* *
31681821 TGTAGGTTCAACCCTTACGAGTGACCAAGA-ATTATGATTCATTATTGT
1 TGTAGGTTTAACCCTTACGAGTGACCAAGACACTATGATTCA-TATTGT
31681869 TGTAGGTTTAACCC
1 TGTAGGTTTAACCC
31681883 AAATGGGTAA
Statistics
Matches: 114, Mismatches: 30, Indels: 22
0.69 0.18 0.13
Matches are distributed among these distances:
45 2 0.02
46 60 0.53
47 10 0.09
48 41 0.36
49 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (48 bp):
TGTAGGTTTAACCCTTACGAGTGACCAAGACACTATGATTCATATTGT
Found at i:31681889 original size:94 final size:94
Alignment explanation
Indices: 31681677--31681905 Score: 284
Period size: 94 Copynumber: 2.4 Consensus size: 94
31681667 CATGCTATTT
* * *
31681677 TTTGTGTAGGTTTAACCCTTACGAGTGA-TCAGACACTATTATCCGATTCGTGTAAGTTCAACCC
1 TTTGTGTAGGTTTAACCCTTATGGGTGACT-AGACACTATTATCCGATTCATGTAAGTTCAACCC
* *
31681741 TTACGGTTGACCAAGGACTATGATTTATTA
65 TTACGGTTGACCAAGAACTATGATTCATTA
* * * *
31681771 TTTGTGTAGGTTTAATCCTTATGGGTGACTAGACAGTATTATTCGATTCATGTAGGTTCAACCCT
1 TTTGTGTAGGTTTAACCCTTATGGGTGACTAGACACTATTATCCGATTCATGTAAGTTCAACCCT
*
31681836 TACGAG-TGACCAAGAATTATGATTCATTA
66 TACG-GTTGACCAAGAACTATGATTCATTA
** * *
31681865 -TTGTTGTAGGTTTAACCCAAATGGGTAACCAGACACTATTA
1 TTTG-TGTAGGTTTAACCCTTATGGGTGACTAGACACTATTA
31681906 CTTTTACCTG
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
93 3 0.03
94 111 0.96
95 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (94 bp):
TTTGTGTAGGTTTAACCCTTATGGGTGACTAGACACTATTATCCGATTCATGTAAGTTCAACCCT
TACGGTTGACCAAGAACTATGATTCATTA
Found at i:31684515 original size:24 final size:24
Alignment explanation
Indices: 31684488--31684537 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
31684478 CGATGTACTA
31684488 TCAGTCTAATCACTCACATCTATG
1 TCAGTCTAATCACTCACATCTATG
*
31684512 TCAGTCTAATCAGTCACATCTATG
1 TCAGTCTAATCACTCACATCTATG
31684536 TC
1 TC
31684538 TTTATCTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.10, T:0.34
Consensus pattern (24 bp):
TCAGTCTAATCACTCACATCTATG
Found at i:31696698 original size:25 final size:25
Alignment explanation
Indices: 31696670--31696742 Score: 69
Period size: 27 Copynumber: 2.8 Consensus size: 25
31696660 CCTGATATAT
31696670 GGCTCTTCGAAGCTTCTCGATTAAA
1 GGCTCTTCGAAGCTTCTCGATTAAA
*
31696695 GGCTCTTTC-ATGAGCTTC-CTGATTAAT
1 GGCTC-TTCGA--AGCTTCTC-GATTAAA
* *
31696722 GGCTCTGCGGAGCTTCTCGAT
1 GGCTCTTCGAAGCTTCTCGAT
31696743 ATTGGCTCGC
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
25 15 0.38
26 7 0.18
27 17 0.44
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (25 bp):
GGCTCTTCGAAGCTTCTCGATTAAA
Found at i:31696785 original size:24 final size:24
Alignment explanation
Indices: 31696731--31696785 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
31696721 TGGCTCTGCG
31696731 GAGCTTCTCGATATTGGCTCGCTT
1 GAGCTTCTCGATATTGGCTCGCTT
*
31696755 GAACTTCTCGATATTGGCTCG-TAT
1 GAGCTTCTCGATATTGGCTCGCT-T
31696779 GAGCTTC
1 GAGCTTC
31696786 CTGTAAATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 1 0.04
24 27 0.96
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (24 bp):
GAGCTTCTCGATATTGGCTCGCTT
Found at i:31696866 original size:24 final size:24
Alignment explanation
Indices: 31696817--31696872 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
31696807 TTTTTGTTAC
* *
31696817 ATGGCTC-ACATATCTTCCCTTAT
1 ATGGCTCGAAATAGCTTCCCTTAT
31696840 ATGGCTCGAAATAGCTTCCCGTT-T
1 ATGGCTCGAAATAGCTTCCC-TTAT
31696864 ATGTGCTCG
1 ATG-GCTCG
31696873 TATAAGCATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 7 0.25
24 14 0.50
25 7 0.25
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.36
Consensus pattern (24 bp):
ATGGCTCGAAATAGCTTCCCTTAT
Found at i:31697360 original size:107 final size:107
Alignment explanation
Indices: 31697174--31697390 Score: 407
Period size: 107 Copynumber: 2.0 Consensus size: 107
31697164 ATGATATGTG
31697174 TTAGGGTTTTTGGCCAAATTGGTTTGAATGTGCTTTACATGTTATTCTTTATATGAATGAATGGC
1 TTAGGGTTTTTGGCCAAATTGGTTTGAATGTGCTTTACATGTTATTCTTTATATGAATGAATGGC
**
31697239 AAGTTAATTACCATGTTATATGAACTTACTAAGCTTTAAAGC
66 AAGTTAATTACCATGTTATACAAACTTACTAAGCTTTAAAGC
*
31697281 TTAGGGTTTTTGGCCAAATTGGTTTGAATGTGCTTTACATGTTATTCTTTATATGAATGAATGGT
1 TTAGGGTTTTTGGCCAAATTGGTTTGAATGTGCTTTACATGTTATTCTTTATATGAATGAATGGC
31697346 AAGTTAATTACCATGTTATACAAACTTACTAAGCTTTAAAGC
66 AAGTTAATTACCATGTTATACAAACTTACTAAGCTTTAAAGC
31697388 TTA
1 TTA
31697391 CTCTATTTTA
Statistics
Matches: 107, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 107 1.00
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.41
Consensus pattern (107 bp):
TTAGGGTTTTTGGCCAAATTGGTTTGAATGTGCTTTACATGTTATTCTTTATATGAATGAATGGC
AAGTTAATTACCATGTTATACAAACTTACTAAGCTTTAAAGC
Found at i:31700319 original size:20 final size:22
Alignment explanation
Indices: 31700294--31700335 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
31700284 GATATTTATG
*
31700294 TATATTTGTTT-T-TTATTTTA
1 TATATTTATTTATCTTATTTTA
31700314 TATATTTATTTATCTTATTTTA
1 TATATTTATTTATCTTATTTTA
31700336 GTTAGTGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (22 bp):
TATATTTATTTATCTTATTTTA
Found at i:31701109 original size:21 final size:20
Alignment explanation
Indices: 31701063--31701118 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
31701053 CATGGGCTGC
31701063 TCACACGGGCGTGTGCCCCT
1 TCACACGGGCGTGTGCCCCT
*
31701083 TCCACACGGGCATGTGTG-GCCT
1 T-CACACGGGC--GTGTGCCCCT
*
31701105 TCACATGGGCGTGT
1 TCACACGGGCGTGT
31701119 AGACCCCCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
19 4 0.13
20 1 0.03
21 17 0.55
22 4 0.13
23 5 0.16
ACGTcount: A:0.12, C:0.32, G:0.32, T:0.23
Consensus pattern (20 bp):
TCACACGGGCGTGTGCCCCT
Found at i:31705448 original size:3 final size:3
Alignment explanation
Indices: 31705442--31705475 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
31705432 TGATGATGAT
*
31705442 GAG GAG GAG GAG GAG GAG GAG GAG AAG GATG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GA-G GAG
31705476 ATGGAGAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.00, G:0.62, T:0.03
Consensus pattern (3 bp):
GAG
Found at i:31708072 original size:16 final size:16
Alignment explanation
Indices: 31708053--31708093 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
31708043 AAACTTAAGG
31708053 TGATTTGAACTAGAAA
1 TGATTTGAACTAGAAA
* * *
31708069 TGATTAGGACTCGAAA
1 TGATTTGAACTAGAAA
31708085 TGATTTGAA
1 TGATTTGAA
31708094 TAAATAATTT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (16 bp):
TGATTTGAACTAGAAA
Found at i:31711357 original size:45 final size:44
Alignment explanation
Indices: 31711306--31711398 Score: 116
Period size: 44 Copynumber: 2.1 Consensus size: 44
31711296 AGGTGGCTGT
** *
31711306 AATGGAATAGAGGCGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAAACGTAACAGT-ATTC-ATGTGTTTGGTTGAATGG
* *
31711351 AATGGAATAGAAATGTAACAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAAACGTAACAGTATTCATGTGTTTGGTTGAATGG
31711395 AATG
1 AATG
31711399 ATGTTGCAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.55
45 18 0.43
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.34
Consensus pattern (44 bp):
AATGGAATAGAAACGTAACAGTATTCATGTGTTTGGTTGAATGG
Found at i:31711622 original size:56 final size:55
Alignment explanation
Indices: 31711511--31711748 Score: 194
Period size: 56 Copynumber: 4.1 Consensus size: 55
31711501 GATTATTAAT
* * * * *
31711511 ATAAATAATAAATAATTTAATCATATT-TTAACA-TAATTATTATTAAATATAATTTA
1 ATAAA-AATATATAATTTAATAAAATTCTTAATATTAAATATTATT--ATATAATTTA
*
31711567 ATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTA
1 ATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTATTATAT-AATTTA
* ** * * *
31711623 CTAAAATCATAATATAAAATAATTTAAAATATAATTTAA-AATAATTATTATTAAATATAATTTA
1 ATAAAA--AT-ATATAATTTAA--TAAAAT-T--CTTAATATTAAATATTATT--ATATAATTTA
*
31711687 ATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTTTTATATGAATTTA
1 ATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTATTATAT-AATTTA
*
31711743 CTAAAA
1 ATAAAA
31711749 TCATAATATA
Statistics
Matches: 146, Mismatches: 21, Indels: 30
0.74 0.11 0.15
Matches are distributed among these distances:
55 26 0.18
56 36 0.25
57 19 0.13
58 3 0.02
59 15 0.10
61 15 0.10
62 3 0.02
63 10 0.07
64 15 0.10
65 4 0.03
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (55 bp):
ATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTATTATATAATTTA
Found at i:31711656 original size:22 final size:23
Alignment explanation
Indices: 31711624--31711668 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
31711614 ATGAATTTAC
31711624 TAAAATCATAATATAAAATAATT
1 TAAAATCATAATATAAAATAATT
*
31711647 TAAAAT-ATAATTTAAAATAATT
1 TAAAATCATAATATAAAATAATT
31711669 ATTATTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAAATCATAATATAAAATAATT
Found at i:31711658 original size:12 final size:12
Alignment explanation
Indices: 31711624--31711687 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
31711614 ATGAATTTAC
*
31711624 TAAAATCATAATA
1 TAAAAT-ATAATT
31711637 T-AAA-ATAATT
1 TAAAATATAATT
31711647 TAAAATATAATT
1 TAAAATATAATT
*
31711659 TAAAATAATTATT
1 TAAAAT-ATAATT
*
31711672 ATTAAATATAATT
1 -TAAAATATAATT
31711685 TAA
1 TAA
31711688 TAAAAATATA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
10 6 0.14
11 3 0.07
12 17 0.40
13 11 0.26
14 5 0.12
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:31711672 original size:120 final size:120
Alignment explanation
Indices: 31711518--31711768 Score: 436
Period size: 120 Copynumber: 2.1 Consensus size: 120
31711508 AATATAAATA
* *
31711518 ATAAATAATTT--AATCATATTTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAA
1 ATAAATAATTTAAAATCATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAA
31711581 TTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAAT
66 TTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAAT
31711636 ATAAAATAATTTAAAAT-ATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATA
1 AT-AAATAATTTAAAATCATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATA
*
31711700 ATTTAATAAAATTCTTAATATTAAATATTTTTATATGAATTTACTAAAATCATAAT
65 ATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAAT
*
31711756 ATATATAATTTAA
1 ATAAATAATTTAA
31711769 TTTTTGAATG
Statistics
Matches: 126, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
118 2 0.02
119 19 0.15
120 102 0.81
121 3 0.02
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.44
Consensus pattern (120 bp):
ATAAATAATTTAAAATCATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAA
TTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAAT
Found at i:31713785 original size:34 final size:34
Alignment explanation
Indices: 31713746--31713814 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
31713736 ATCACAAACT
31713746 TTAGACAGTAATCAAAATACCATGATCAAATATA
1 TTAGACAGTAATCAAAATACCATGATCAAATATA
*
31713780 TTAGACAGTAATTAAAATACCATGATCAAATATA
1 TTAGACAGTAATCAAAATACCATGATCAAATATA
31713814 T
1 T
31713815 CTTTATAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.29
Consensus pattern (34 bp):
TTAGACAGTAATCAAAATACCATGATCAAATATA
Found at i:31717378 original size:67 final size:67
Alignment explanation
Indices: 31717248--31717378 Score: 156
Period size: 67 Copynumber: 2.0 Consensus size: 67
31717238 AGAGGTTTAA
* * * * *
31717248 AGGTGTAAAACCATAGCTCGGCTATGGCAACCACTAGAGTCTACCAGGACATTGAACATGGGGTT
1 AGGTGTAAAACCATAGCTCGACTATGGCAACCAATAGAGTCTACCAGGACAATAAACACGGGGTT
31717313 AT
66 AT
* * * * *
31717315 AGGTGTAAGATCATAGCTCGACTATGGTAACCAAT-GAAGTCTACCGGGACAATAAATACGGGGT
1 AGGTGTAAAACCATAGCTCGACTATGGCAACCAATAG-AGTCTACCAGGACAATAAACACGGGGT
31717379 AGTTCATCAG
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
66 1 0.02
67 52 0.98
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (67 bp):
AGGTGTAAAACCATAGCTCGACTATGGCAACCAATAGAGTCTACCAGGACAATAAACACGGGGTT
AT
Found at i:31719910 original size:16 final size:16
Alignment explanation
Indices: 31719889--31719923 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
31719879 ACAAAAAGAA
31719889 TTTTTTGCAGTTTACT
1 TTTTTTGCAGTTTACT
31719905 TTTTTTGCAGTTTACT
1 TTTTTTGCAGTTTACT
31719921 TTT
1 TTT
31719924 CTTAGCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.66
Consensus pattern (16 bp):
TTTTTTGCAGTTTACT
Found at i:31727577 original size:27 final size:27
Alignment explanation
Indices: 31727547--31727823 Score: 267
Period size: 27 Copynumber: 10.3 Consensus size: 27
31727537 CAAGATACGA
* *
31727547 CACAAATGCATTCCTTTCAGAGCAAGC
1 CACAAAGGCATTCCTTTCAGAGTAAGC
* *
31727574 CAC-AA-GCATTTCTTTCAGAGTATGC
1 CACAAAGGCATTCCTTTCAGAGTAAGC
31727599 CACAAAGGCATTCCTTTCAGAGTACA-C
1 CACAAAGGCATTCCTTTCAGAGTA-AGC
*
31727626 TACAAAGGCATTCCTTTCAGAGTACA-C
1 CACAAAGGCATTCCTTTCAGAGTA-AGC
* *
31727653 TACAAAGGCATTCCTTTCAGAGTATGC
1 CACAAAGGCATTCCTTTCAGAGTAAGC
* * *
31727680 CACAAAGGCATTCTTTTCAGAATATGC
1 CACAAAGGCATTCCTTTCAGAGTAAGC
* * * *
31727707 CATAAATGCATTCCTGTCAGAGTACGC
1 CACAAAGGCATTCCTTTCAGAGTAAGC
* ** *
31727734 CATAAAGTTATTCCTTTTAGAGTACA-C
1 CACAAAGGCATTCCTTTCAGAGTA-AGC
* * *
31727761 CAAAAAGGCATTTCTTTCAGAGTACGC
1 CACAAAGGCATTCCTTTCAGAGTAAGC
** * *
31727788 CACAAAGGCATTTATTTCAAAGTATGC
1 CACAAAGGCATTCCTTTCAGAGTAAGC
31727815 CACAAAGGC
1 CACAAAGGC
31727824 TAACACGATG
Statistics
Matches: 212, Mismatches: 32, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
25 20 0.09
26 4 0.02
27 188 0.89
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (27 bp):
CACAAAGGCATTCCTTTCAGAGTAAGC
Found at i:31727683 original size:81 final size:81
Alignment explanation
Indices: 31727516--31727823 Score: 291
Period size: 81 Copynumber: 3.8 Consensus size: 81
31727506 CATACAGAAC
* * ** * * *
31727516 ATGCCACAAAAGCAATCCACTCA-AGATACGACACAAATGCATTCCTTTCAGAGCA-AGCCAC-A
1 ATGCCACAAAGGCATTCCTTTCAGAG-TACGCCACAAAGGCATTCCTTTCAGAGTACA-CCACAA
*
31727578 A-GCATTTCTTTCAGAGT
64 AGGCATTCCTTTCAGAGT
* * *
31727595 ATGCCACAAAGGCATTCCTTTCAGAGTACACTACAAAGGCATTCCTTTCAGAGTACACTACAAAG
1 ATGCCACAAAGGCATTCCTTTCAGAGTACGCCACAAAGGCATTCCTTTCAGAGTACACCACAAAG
31727660 GCATTCCTTTCAGAGT
66 GCATTCCTTTCAGAGT
* * * * * * * *
31727676 ATGCCACAAAGGCATTCTTTTCAGAATATGCCATAAATGCATTCCTGTCAGAGTACGCCATAAAG
1 ATGCCACAAAGGCATTCCTTTCAGAGTACGCCACAAAGGCATTCCTTTCAGAGTACACCACAAAG
** *
31727741 TTATTCCTTTTAGAGT
66 GCATTCCTTTCAGAGT
** * * ** * **
31727757 ACACCAAAAAGGCATTTCTTTCAGAGTACGCCACAAAGGCATTTATTTCAAAGTATGCCACAAAG
1 ATGCCACAAAGGCATTCCTTTCAGAGTACGCCACAAAGGCATTCCTTTCAGAGTACACCACAAAG
31727822 GC
66 GC
31727824 TAACACGATG
Statistics
Matches: 183, Mismatches: 42, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
79 46 0.25
80 5 0.03
81 132 0.72
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.26
Consensus pattern (81 bp):
ATGCCACAAAGGCATTCCTTTCAGAGTACGCCACAAAGGCATTCCTTTCAGAGTACACCACAAAG
GCATTCCTTTCAGAGT
Found at i:31731561 original size:36 final size:36
Alignment explanation
Indices: 31731521--31731597 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
31731511 GGTTCTATGA
*
31731521 ATATATTTTTTAAACACTATTTCTATGAATCAATCC
1 ATATATTTTTTAAACACTATTTCCATGAATCAATCC
31731557 ATATATTTTTTAAACACTATTTCCATGAATCAATCC
1 ATATATTTTTTAAACACTATTTCCATGAATCAATCC
31731593 ATATA
1 ATATA
31731598 ATTTAGTACT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.38, C:0.17, G:0.03, T:0.43
Consensus pattern (36 bp):
ATATATTTTTTAAACACTATTTCCATGAATCAATCC
Found at i:31731729 original size:19 final size:18
Alignment explanation
Indices: 31731683--31731730 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
31731673 GTTAAATTCT
*
31731683 TGTTGAAAAAAATTAAATA
1 TGTT-AAAATAATTAAATA
31731702 T-TATAAAATAATTAAATTA
1 TGT-TAAAATAATTAAA-TA
31731721 TGTTAAAATA
1 TGTTAAAATA
31731731 TGAACATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 12 0.48
19 12 0.48
20 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
TGTTAAAATAATTAAATA
Found at i:31738430 original size:27 final size:27
Alignment explanation
Indices: 31738411--31738636 Score: 310
Period size: 27 Copynumber: 8.4 Consensus size: 27
31738401 GGGTATAAAA
31738411 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
31738438 ATCATTTTACCTTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
31738465 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
31738492 GTCATTTTACCTTATGAGGGCATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
31738519 CTCATTTTACCCTATGGGGGTGTTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
31738546 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
31738573 ATCATTTTACCCTAT-GGGATATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
31738599 ATCATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
31738626 GTCATTTTACC
1 GTCATTTTACC
31738637 TATTTTAGGG
Statistics
Matches: 173, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
26 24 0.14
27 149 0.86
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:31739461 original size:23 final size:23
Alignment explanation
Indices: 31739427--31739486 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 23
31739417 TTCACACCAA
31739427 AATTT-GGACAGCATATATACAAC
1 AATTTAGG-CAGCATATATACAAC
31739450 AATTTAGGCAGCATATATACAAC
1 AATTTAGGCAGCATATATACAAC
*
31739473 ATATTGA-GCAGCAT
1 A-ATTTAGGCAGCAT
31739487 TTTTGCACCA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
23 28 0.82
24 6 0.18
ACGTcount: A:0.42, C:0.17, G:0.15, T:0.27
Consensus pattern (23 bp):
AATTTAGGCAGCATATATACAAC
Found at i:31739532 original size:70 final size:70
Alignment explanation
Indices: 31739410--31739815 Score: 616
Period size: 70 Copynumber: 5.7 Consensus size: 70
31739400 CCAAACTAAA
* * * * * * *
31739410 CAGCAATTTCACACCAAAATTTGGACAGCATATATACAACAATTTAGGCAGCATATATACAACAT
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATT-GGCAGCAAATATACAACAA
31739475 ATTGAG
65 ATTGAG
* * * *
31739481 CAGCATTTTTGCACC-AAAATTGGACAGCTTATACACAACAAATTGGACAGCAATTACACAACAA
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGG-CAGCAAATATACAACAA
31739545 ATTGAG
65 ATTGAG
* *
31739551 CAGCATTTTTTTACACCAAAAATTGGACAGCTTATATAAAACAAATTGGCAGCAAATATACAATA
1 CAGCA--TTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAATATACAACA
31739616 AATTGAG
64 AATTGAG
* * *
31739623 CAGCATTTTTACACCAAAAATTAGACAGCTTATATAAAACAAATTGGCAGCAAATATACAATAAA
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAATATACAACAAA
31739688 TTGAG
66 TTGAG
31739693 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAATATACAACAAA
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAATATACAACAAA
31739758 TTGAG
66 TTGAG
31739763 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGAGCAGCA
1 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTG-GCAGCA
31739816 TTTTTACACC
Statistics
Matches: 309, Mismatches: 21, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
69 2 0.01
70 226 0.73
71 18 0.06
72 34 0.11
73 29 0.09
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (70 bp):
CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAATATACAACAAA
TTGAG
Found at i:31739799 original size:118 final size:117
Alignment explanation
Indices: 31739663--31739925 Score: 456
Period size: 118 Copynumber: 2.2 Consensus size: 117
31739653 TATATAAAAC
** *
31739663 AAATTGG-CAGCAAATATACAATAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCTTATA
1 AAATTGGACAGCTTATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCTTATA
31739727 TACAACAAATTGGCAGCAAATATACAACAAATTGAGCAGCATTTTTACACCAA
66 TACAACAAATTGGCAGCAAATATACAACAAATTGAGCAGCATTTTTACACC-A
31739780 AAATTGGACAGCTTATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCTTATA
1 AAATTGGACAGCTTATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCTTATA
* *
31739845 TACAACAAATTGGCAGCAAATATACAACGAATTGAGCAGCATTTTTGCACCA
66 TACAACAAATTGGCAGCAAATATACAACAAATTGAGCAGCATTTTTACACCA
*
31739897 AAATTGGACAGCTTATACACAACAAATTG
1 AAATTGGACAGCTTATATACAACAAATTG
31739926 GACAGCAATT
Statistics
Matches: 139, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
117 36 0.26
118 103 0.74
ACGTcount: A:0.43, C:0.18, G:0.14, T:0.25
Consensus pattern (117 bp):
AAATTGGACAGCTTATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCTTATA
TACAACAAATTGGCAGCAAATATACAACAAATTGAGCAGCATTTTTACACCA
Found at i:31739817 original size:48 final size:46
Alignment explanation
Indices: 31739458--31739862 Score: 287
Period size: 48 Copynumber: 8.6 Consensus size: 46
31739448 ACAATTTAGG
* * * *
31739458 CAGCATATATACAACATATTGAGCAGCATTTTTGCACCAAAATTGGA
1 CAGCTTATATACAACAAATTG-GCAGCATTTTTACACAAAAATTGGA
* *
31739505 CAGCTTATACACAACAAATTGGACAGCA--ATTACACAACAAATT-GA
1 CAGCTTATATACAACAAATTGG-CAGCATTTTTACACAA-AAATTGGA
* * * *
31739550 GCAGCATTTTTTTACACCAAAAATTGGACAGC-TTATATA-A-AACAAATTGG-
1 -CAGC--TTATATACA--ACAAATTGG-CAGCATT-TTTACACAA-AAATTGGA
** * *
31739600 CAGCAAATATACAATAAATTGAGCAGCATTTTTACACCAAAAATTAGA
1 CAGCTTATATACAACAAATTG-GCAGCATTTTTACA-CAAAAATTGGA
* ** * *
31739648 CAGCTTATATAAAACAAATTGGCAGCAAATATACA-ATAAATT-GA
1 CAGCTTATATACAACAAATTGGCAGCATTTTTACACAAAAATTGGA
* * * *
31739692 GCAGCATT-TTTACACCAAAAATTGGACAGC-TTATATACA-ACAAATTGG-
1 -CAGC-TTATATACA--ACAAATTGG-CAGCATT-TTTACACAAAAATTGGA
**
31739740 CAGCAAATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGA
1 CAGCTTATATACAACAAATTG-GCAGCATTTTTACA-CAAAAATTGGA
31739788 CAGCTTATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGA
1 CAGCTTATATACAACAAATTG-GCAGCATTTTTACA-CAAAAATTGGA
31739836 CAGCTTATATACAACAAATTGGCAGCA
1 CAGCTTATATACAACAAATTGGCAGCA
31739863 AATATACAAC
Statistics
Matches: 287, Mismatches: 41, Indels: 60
0.74 0.11 0.15
Matches are distributed among these distances:
44 2 0.01
45 52 0.18
46 19 0.07
47 76 0.26
48 108 0.38
49 5 0.02
50 21 0.07
51 2 0.01
52 2 0.01
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.25
Consensus pattern (46 bp):
CAGCTTATATACAACAAATTGGCAGCATTTTTACACAAAAATTGGA
Found at i:31739840 original size:188 final size:187
Alignment explanation
Indices: 31739593--31739958 Score: 608
Period size: 188 Copynumber: 2.0 Consensus size: 187
31739583 TATATAAAAC
*
31739593 AAATTGGCAGCAAATATACAATAAATTGAGCAGCATTTTTACACCAAAAATTAGACAGCTTATAT
1 AAATTGGCAGCAAATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTAGACAGCTTATAT
*
31739658 AAAACAAATTGGCAGCAAATATACAATAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCT
66 AAAACAAATTGGCAGCAAATATACAACAAATTGAGCAGCATTTTTACACC-AAAATTGGACAGCT
* *
31739723 TATATACAACAAATTGG-CAGCAAATATACAACAAATTGAGCAGCATTTTTACACCAA
130 TATACACAACAAATTGGACAGCAAATACACAACAAATTGAGCAGCATTTTTACACCAA
** *
31739780 AAATTGGACAGCTTATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGACAGCTTATA
1 AAATTGG-CAGCAAATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTAGACAGCTTATA
* * *
31739845 TACAACAAATTGGCAGCAAATATACAACGAATTGAGCAGCATTTTTGCACCAAAATTGGACAGCT
65 TAAAACAAATTGGCAGCAAATATACAACAAATTGAGCAGCATTTTTACACCAAAATTGGACAGCT
*
31739910 TATACACAACAAATTGGACAGCAATTACACAACAAATTGAGCAGCATTT
130 TATACACAACAAATTGGACAGCAAATACACAACAAATTGAGCAGCATTT
31739959 AAGCATAAAA
Statistics
Matches: 166, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
187 37 0.22
188 129 0.78
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (187 bp):
AAATTGGCAGCAAATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTAGACAGCTTATAT
AAAACAAATTGGCAGCAAATATACAACAAATTGAGCAGCATTTTTACACCAAAATTGGACAGCTT
ATACACAACAAATTGGACAGCAAATACACAACAAATTGAGCAGCATTTTTACACCAA
Found at i:31739868 original size:70 final size:70
Alignment explanation
Indices: 31739702--31739958 Score: 292
Period size: 70 Copynumber: 3.7 Consensus size: 70
31739692 GCAGCATTTT
** ** * *
31739702 TACACCAA-AAATTGGACAGCTTATATACAACAAATTG-GCAGCAAATATACAAC-AAATT-GAG
1 TACA-CAACAAATTGGACAGCAAATATACAACAAATTGAGCAGCATTTTTACACCAAAATTGGA-
*
31739763 CAGCATTTT
64 CAGC--TTA
**
31739772 TACACCAA-AAATTGGACAGCTTATATACAACAAATTGAGCAGCATTTTTACACCAAAAATTGGA
1 TACA-CAACAAATTGGACAGCAAATATACAACAAATTGAGCAGCATTTTTACACC-AAAATTGGA
31739836 CAGCTTA
64 CAGCTTA
* * *
31739843 TATACAACAAATTGG-CAGCAAATATACAACGAATTGAGCAGCATTTTTGCACCAAAATTGGACA
1 TACACAACAAATTGGACAGCAAATATACAACAAATTGAGCAGCATTTTTACACCAAAATTGGACA
31739907 GCTTA
66 GCTTA
* *
31739912 TACACAACAAATTGGACAGCAATTACACAACAAATTGAGCAGCATTT
1 TACACAACAAATTGGACAGCAAATATACAACAAATTGAGCAGCATTT
31739959 AAGCATAAAA
Statistics
Matches: 167, Mismatches: 14, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
69 30 0.18
70 102 0.61
71 24 0.14
73 9 0.05
74 2 0.01
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (70 bp):
TACACAACAAATTGGACAGCAAATATACAACAAATTGAGCAGCATTTTTACACCAAAATTGGACA
GCTTA
Found at i:31739868 original size:140 final size:140
Alignment explanation
Indices: 31739410--31739958 Score: 566
Period size: 140 Copynumber: 3.9 Consensus size: 140
31739400 CCAAACTAAA
* * * * * *
31739410 CAGCAATTTCACACCAAAATTTGGACAGCATATATACAACAATTTAGGCAGCATATATACAACAT
1 CAGCATTTTTACA-CAAAAATTGGACAGCATATATACAACAAATT-GGCAGCAAATATACAACAA
* *
31739475 ATTGAGCAGCATTTTTGCACC-AAAATTGGACAGCTTATACACAACAAATTGGACAGCA--ATTA
64 ATTGAGCAGCATTTTTACACCAAAAATTGGACAGCTTATACACAACAAATTGG-CAGCATTTTTA
31739537 CACAACAAATTGAG
128 CACAA-AAATTGAG
* * *
31739551 CAGCATTTTTTTACACCAAAAATTGGACAGCTTATATAAAACAAATTGGCAGCAAATATACAATA
1 CAGCA--TTTTTACA-CAAAAATTGGACAGCATATATACAACAAATTGGCAGCAAATATACAACA
* * * ** *
31739616 AATTGAGCAGCATTTTTACACCAAAAATTAGACAGCTTATATAAAACAAATTGGCAGCAAATATA
63 AATTGAGCAGCATTTTTACACCAAAAATTGGACAGCTTATACACAACAAATTGGCAGCATTTTTA
*
31739681 CA-ATAAATTGAG
128 CACAAAAATTGAG
*
31739693 CAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGGCAGCAAATATACAACAAA
1 CAGCATTTTTACA-CAAAAATTGGACAGCATATATACAACAAATTGGCAGCAAATATACAACAAA
*
31739758 TTGAGCAGCATTTTTACACCAAAAATTGGACAGCTTATATACAACAAATTGAGCAGCATTTTTAC
65 TTGAGCAGCATTTTTACACCAAAAATTGGACAGCTTATACACAACAAATTG-GCAGCATTTTTAC
31739823 ACCAAAAATTG-G
129 A-CAAAAATTGAG
* * * * ** * * *
31739835 ACAGC-TTATATACA-ACAAATTGG-CAGCAAATATACAACGAATTGAGCAGCATTTTTGCACCA
1 -CAGCATT-TTTACACAAAAATTGGACAGCATATATACAACAAATTG-GCAGCAAATATACAAC-
* *
31739897 AAATTG-GACAGC--TTATACA-CAACAAATTGGACAGC-AATTACACAACAAATTGAGCAGCAT
62 AAATTGAG-CAGCATTTTTACACCAA-AAATTGGACAGCTTA-TACACAACAAATTG-GCAGCAT
31739957 TT
123 TT
31739959 AAGCATAAAA
Statistics
Matches: 356, Mismatches: 37, Indels: 31
0.84 0.09 0.07
Matches are distributed among these distances:
139 4 0.01
140 166 0.47
141 36 0.10
142 67 0.19
143 79 0.22
144 4 0.01
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.25
Consensus pattern (140 bp):
CAGCATTTTTACACAAAAATTGGACAGCATATATACAACAAATTGGCAGCAAATATACAACAAAT
TGAGCAGCATTTTTACACCAAAAATTGGACAGCTTATACACAACAAATTGGCAGCATTTTTACAC
AAAAATTGAG
Found at i:31740723 original size:28 final size:28
Alignment explanation
Indices: 31740691--31740816 Score: 173
Period size: 28 Copynumber: 4.5 Consensus size: 28
31740681 TTTAATAAGT
* * *
31740691 TCGCACACTTAGTGCTCAATAATCAAAC
1 TCGCACACTTAGTGCTCTACAATTAAAC
*
31740719 TCGCACACTTAGTGCTTCT-CCATTAAAC
1 TCGCACACTTAGTGC-TCTACAATTAAAC
*
31740747 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTCTACAATTAAAC
* *
31740775 TCGCACACTTAGTGCTTTCCAATTAAAC
1 TCGCACACTTAGTGCTCTACAATTAAAC
31740803 TCGCACACTTAGTG
1 TCGCACACTTAGTG
31740817 TCGAAAGTCA
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
27 2 0.02
28 85 0.96
29 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.30
Consensus pattern (28 bp):
TCGCACACTTAGTGCTCTACAATTAAAC
Found at i:31740757 original size:56 final size:56
Alignment explanation
Indices: 31740691--31740816 Score: 200
Period size: 56 Copynumber: 2.2 Consensus size: 56
31740681 TTTAATAAGT
*
31740691 TCGCACACTTAGTGCTCAATAATCAAACTCGCACACTTAGTGCTTCTCC-ATTAAAC
1 TCGCACACTTAGTGCTCAACAATCAAACTCGCACACTTAGTGCTT-TCCAATTAAAC
** *
31740747 TCGCACACTTAGTGCTTTACAATTAAACTCGCACACTTAGTGCTTTCCAATTAAAC
1 TCGCACACTTAGTGCTCAACAATCAAACTCGCACACTTAGTGCTTTCCAATTAAAC
31740803 TCGCACACTTAGTG
1 TCGCACACTTAGTG
31740817 TCGAAAGTCA
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
55 3 0.05
56 62 0.95
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.30
Consensus pattern (56 bp):
TCGCACACTTAGTGCTCAACAATCAAACTCGCACACTTAGTGCTTTCCAATTAAAC
Found at i:31748709 original size:25 final size:24
Alignment explanation
Indices: 31748681--31748736 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 24
31748671 TATTATAAAA
*
31748681 ATAATTTATATGTTATAAAAATATT
1 ATAATTTATATATTATAAAAA-ATT
* * * *
31748706 ATAATATATTTATTTTAAAAAGTT
1 ATAATTTATATATTATAAAAAATT
31748730 ATAATTT
1 ATAATTT
31748737 TTTTTATAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 8 0.32
25 17 0.68
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
ATAATTTATATATTATAAAAAATT
Found at i:31748761 original size:16 final size:16
Alignment explanation
Indices: 31748740--31748778 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
31748730 ATAATTTTTT
* *
31748740 TTATAAATGCTGTATA
1 TTATAAATGATATATA
*
31748756 TTATAAATTATATATA
1 TTATAAATGATATATA
31748772 TTATAAA
1 TTATAAA
31748779 ATTATTTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (16 bp):
TTATAAATGATATATA
Found at i:31749567 original size:44 final size:44
Alignment explanation
Indices: 31749499--31749585 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
31749489 TGTAAGTGTT
*
31749499 TAATTACAATTTGTACTACCAAACATG-ACATAAGAAATTACAATG
1 TAATTACAATTTGTACAACCAAACATGTACA-AAG-AATTACAATG
* *
31749544 TAATTACAGTTTG-ACAACCAAACATGTCCAAAGAATTACAAT
1 TAATTACAATTTGTACAACCAAACATGTACAAAGAATTACAAT
31749586 TCTTTGTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
43 9 0.24
44 15 0.39
45 14 0.37
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (44 bp):
TAATTACAATTTGTACAACCAAACATGTACAAAGAATTACAATG
Found at i:31754245 original size:40 final size:41
Alignment explanation
Indices: 31754200--31754288 Score: 99
Period size: 41 Copynumber: 2.2 Consensus size: 41
31754190 GCTATGTTTA
*
31754200 GCACTTA-ATATGAAATTCGGGATAGCTTCAGCTATTTATG
1 GCACTTAGATATGAAATTCGGAATAGCTTCAGCTATTTATG
* * ** * *
31754240 GCACTTAGTTGTGCGATTTGGAATAGCTTCGGCTATTTATG
1 GCACTTAGATATGAAATTCGGAATAGCTTCAGCTATTTATG
*
31754281 ACACTTAG
1 GCACTTAG
31754289 TGTGCGAGAC
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
40 7 0.17
41 33 0.82
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (41 bp):
GCACTTAGATATGAAATTCGGAATAGCTTCAGCTATTTATG
Found at i:31754275 original size:41 final size:41
Alignment explanation
Indices: 31754220--31754357 Score: 156
Period size: 41 Copynumber: 3.4 Consensus size: 41
31754210 TGAAATTCGG
* **
31754220 GATAGCTTCAGCTATTTATGGCACTTAGTTGTGCGA-TTTG-
1 GATAGCTTCGGCTATTTATGGCACTTAG-TGTGCGAGACTGA
*
31754260 GAATAGCTTCGGCTATTTATGACACTTAGTGTGCGAGACTGA
1 G-ATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGACTGA
* * *
31754302 GATAGCTTCGGCTATGTAAGGCACTTAGTGTGCGAGA-TTA
1 GATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGACTGA
*
31754342 TGATAGCTTCAGCTAT
1 -GATAGCTTCGGCTAT
31754358 ACGATGGCAA
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
40 10 0.12
41 74 0.87
42 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (41 bp):
GATAGCTTCGGCTATTTATGGCACTTAGTGTGCGAGACTGA
Found at i:31754672 original size:42 final size:42
Alignment explanation
Indices: 31754611--31754710 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 42
31754601 CTATATGAAC
* *
31754611 GGCACTAAGTGTGCAAAATTAAAATAATGATGTTGGATAATG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAACG
* *
31754653 GGCACTAAGTGTGCGAAATTAAAATGATGATGTTGTATAACG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAACG
31754695 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
31754711 TACCGAGAGC
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.36, C:0.10, G:0.27, T:0.27
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGGATAACG
Found at i:31757336 original size:44 final size:44
Alignment explanation
Indices: 31757271--31757357 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
31757261 TATGTTTTTA
* * *
31757271 GTTTCTCACTTAAACTCTGATTAGTATAAGTTGTTTTAATATTG
1 GTTTCCCACTTAAACTATGATTAGTATAAGTTATTTTAATATTG
* *
31757315 GTTTCCCACTTAAACTATGATTAGTGTAGGTTATTTTAATATT
1 GTTTCCCACTTAAACTATGATTAGTATAAGTTATTTTAATATT
31757358 ATTTGACCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (44 bp):
GTTTCCCACTTAAACTATGATTAGTATAAGTTATTTTAATATTG
Found at i:31758980 original size:56 final size:57
Alignment explanation
Indices: 31758906--31759014 Score: 134
Period size: 56 Copynumber: 1.9 Consensus size: 57
31758896 AATTGAATAG
* *
31758906 TTGGCTGACCATTTTGTAAATTGAT-ATAATTAGG-TGACC-AAAAAAGAAATTTTCTA
1 TTGGATGACCATTTTGTAAATTG-TCATAATT-GGTTAACCAAAAAAAGAAATTTTCTA
* * *
31758962 TTGGATGATCATTTTGTAACTTGTCATAGTTGGTTAACCAAAAAAAGAAATTT
1 TTGGATGACCATTTTGTAAATTGTCATAATTGGTTAACCAAAAAAAGAAATTT
31759015 ACTAATAGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
55 3 0.07
56 29 0.64
57 13 0.29
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (57 bp):
TTGGATGACCATTTTGTAAATTGTCATAATTGGTTAACCAAAAAAAGAAATTTTCTA
Found at i:31766850 original size:104 final size:104
Alignment explanation
Indices: 31766666--31767036 Score: 579
Period size: 105 Copynumber: 3.6 Consensus size: 104
31766656 TGTATATAAA
** * *
31766666 AGGGGTTGCTGTGTGCTGATTCCCCGATTT-ATGGGTGGTGCTATGTGCG-TGATCCACCATATC
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATC
*
31766729 TTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
31766770 AGGGGTTGCTAAGTGATGATTCCCCGATTTCATTGGTGGTGCTAAGTGTGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
31766835 TTGAAATGAAAAGGGGGGTTGCTATGTGCTGATTCCCCCG
66 TTGAAATGAAAA-GGGGGTTGCTATGTGCTGATTCCCCCG
*
31766875 AGGGGTTGCTAAGTGCTGATTCCCC-AATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
*
31766939 TTGAAATAAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* **
31766978 AGGGGTTGCTAAGTGCTGATTCCCCGA-TTCAGTGGTGGTGCTAAGTGCGGGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCA
31767037 ATAACGGCTA
Statistics
Matches: 249, Mismatches: 14, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
103 81 0.33
104 79 0.32
105 88 0.35
106 1 0.00
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCT
TTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:31768491 original size:15 final size:16
Alignment explanation
Indices: 31768462--31768491 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31768452 GTAATTTAAT
31768462 TAACTAAATTAATTTC
1 TAACTAAATTAATTTC
31768478 TAACTAAA-TAATTT
1 TAACTAAATTAATTT
31768492 TTTCAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (16 bp):
TAACTAAATTAATTTC
Found at i:31781757 original size:21 final size:21
Alignment explanation
Indices: 31781716--31781758 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
31781706 AATAAAGTAG
*
31781716 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
31781737 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
31781758 A
1 A
31781759 AATTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:31781901 original size:58 final size:57
Alignment explanation
Indices: 31781737--31781903 Score: 178
Period size: 58 Copynumber: 2.9 Consensus size: 57
31781727 TTTTTATAGT
* * * **
31781737 ATTATATATTATGATTTTAGTAAATTCATA--TAATAATAAATATATTAAGAATTTTATTAA
1 ATTATATATT-T--TTTTATTAAATT-ATATTTAATAATAATTATATTAA-AATATGGTTAA
*
31781797 ATTATATATTTTTTTATTAAATTATATTTAATAATAATTATGTTAAAATATGGTTAA
1 ATTATATATTTTTTTATTAAATTATATTTAATAATAATTATATTAAAATATGGTTAA
* *
31781854 ATTATTTATTATTTTTATTAAATTATTTTTAATAATAATCT-TATTAAAAT
1 ATTATATATT-TTTTTATTAAATTATATTTAATAATAAT-TATATTAAAAT
31781904 TTAATAACAA
Statistics
Matches: 94, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
56 3 0.03
57 28 0.30
58 51 0.54
59 2 0.02
60 10 0.11
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (57 bp):
ATTATATATTTTTTTATTAAATTATATTTAATAATAATTATATTAAAATATGGTTAA
Found at i:31782087 original size:45 final size:44
Alignment explanation
Indices: 31781996--31782088 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
31781986 ATTACAATAT
31781996 CATTCCATTCAACCAAACACAAGAATACTATTACACTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACACTTCTATTC
* * *
31782040 CATTTCATTCAACCAAACA-ATTGATTACTGATTACAGCTT-TATTC
1 CATTCCATTCAACCAAACACA-AGAATACT-ATTACA-CTTCTATTC
31782085 CATT
1 CATT
31782089 ACAGCTCTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
43 1 0.02
44 24 0.56
45 15 0.35
46 3 0.07
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.34
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACACTTCTATTC
Found at i:31782125 original size:16 final size:16
Alignment explanation
Indices: 31782070--31782125 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
31782060 TTGATTACTG
31782070 ATTACAGCTT-TATTCC
1 ATTACAG-TTCTATTCC
* *
31782086 ATTACAGCTCTATTCA
1 ATTACAGTTCTATTCC
31782102 ATTACAGTTCTATTCC
1 ATTACAGTTCTATTCC
31782118 ATTACAGT
1 ATTACAGT
31782126 GAACCAAACG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 1 0.03
16 34 0.97
ACGTcount: A:0.29, C:0.23, G:0.07, T:0.41
Consensus pattern (16 bp):
ATTACAGTTCTATTCC
Found at i:31791502 original size:23 final size:22
Alignment explanation
Indices: 31791474--31791531 Score: 98
Period size: 23 Copynumber: 2.6 Consensus size: 22
31791464 TAATTTGAAA
*
31791474 TATTTTTAAAATACTTTTTTAT
1 TATTTTTAAAATAATTTTTTAT
31791496 TATTTTTAAAATAAATTTTTTAT
1 TATTTTTAAAAT-AATTTTTTAT
31791519 TATTTTTAAAATA
1 TATTTTTAAAATA
31791532 TTTCGGGCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTTTTAAAATAATTTTTTAT
Found at i:31791782 original size:17 final size:17
Alignment explanation
Indices: 31791762--31791797 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
31791752 ATACTTTTAT
31791762 TTTTAAAAAAAATTGAA
1 TTTTAAAAAAAATTGAA
*
31791779 TTTTACAAAAAATTGAA
1 TTTTAAAAAAAATTGAA
31791796 TT
1 TT
31791798 ATTCAGTTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (17 bp):
TTTTAAAAAAAATTGAA
Found at i:31794840 original size:36 final size:35
Alignment explanation
Indices: 31794791--31794858 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 35
31794781 AAAAGTTGAG
*
31794791 ACAAACCAAGTATATGAT-AAAATAGGGTTTTAAGAT
1 ACAAACCAAGTATA-AATAAAAATA-GGTTTTAAGAT
* *
31794827 ACAAATCATGTATAAATAAAAATAGGTTTTAA
1 ACAAACCAAGTATAAATAAAAATAGGTTTTAA
31794859 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
35 10 0.36
36 18 0.64
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.29
Consensus pattern (35 bp):
ACAAACCAAGTATAAATAAAAATAGGTTTTAAGAT
Found at i:31794866 original size:2 final size:2
Alignment explanation
Indices: 31794859--31794920 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
31794849 TAGGTTTTAA
31794859 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31794901 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
31794921 CAAAGCGTGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31795526 original size:22 final size:24
Alignment explanation
Indices: 31795473--31795529 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 24
31795463 ATATGATCTA
31795473 AAAAGAAGAAATAAAAAAATTAGT
1 AAAAGAAGAAATAAAAAAATTAGT
* *
31795497 AATA-AAGAAAT-CAAAAA-TAGT
1 AAAAGAAGAAATAAAAAAATTAGT
31795518 AAAAGAAGAAAT
1 AAAAGAAGAAAT
31795530 TTGAAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 7 0.24
22 12 0.41
23 7 0.24
24 3 0.10
ACGTcount: A:0.70, C:0.02, G:0.12, T:0.16
Consensus pattern (24 bp):
AAAAGAAGAAATAAAAAAATTAGT
Found at i:31798432 original size:50 final size:53
Alignment explanation
Indices: 31798319--31798435 Score: 136
Period size: 56 Copynumber: 2.2 Consensus size: 53
31798309 ACATTTGGGT
* *
31798319 GATGAGA--TCCCATGTAAGACCATGTTTGGAACATGGCATTGGCATCATTGAG
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGAACATGGCATTGGCATCA-CGAG
* *
31798371 GTTATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C-CGA-
1 G--ATGAGAGGTCCCATGTAAGACCATGTCTGGAACATGGCATTGGCATCACGAG
31798423 GATGAGAGGTCCC
1 GATGAGAGGTCCC
31798436 CNNNNNNNNN
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
50 12 0.21
52 2 0.04
53 2 0.04
54 6 0.11
55 1 0.02
56 34 0.60
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.24
Consensus pattern (53 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGAACATGGCATTGGCATCACGAG
Found at i:31802002 original size:21 final size:22
Alignment explanation
Indices: 31801963--31802025 Score: 85
Period size: 23 Copynumber: 2.9 Consensus size: 22
31801953 CTTGATCAAT
31801963 ATACGACACATAAGTGCCTG-A
1 ATACGACACATAAGTGCCTGAA
*
31801984 A-ACGACACACAAGGTGCCTGAA
1 ATACGACACATAA-GTGCCTGAA
31802006 ATACGACACATAAAGTGCCT
1 ATACGACACAT-AAGTGCCT
31802026 AATCGGTAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
20 10 0.28
21 8 0.22
22 2 0.06
23 14 0.39
24 2 0.06
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.16
Consensus pattern (22 bp):
ATACGACACATAAGTGCCTGAA
Found at i:31803516 original size:25 final size:24
Alignment explanation
Indices: 31803449--31803516 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 24
31803439 ATGAAAATGT
*
31803449 TATTGTATAAATAAAATTA-CAAA
1 TATTGTAAAAATAAAATTATCAAA
* * * *
31803472 TA-TATAAAAATGGAATTTATGAATA
1 TATTGTAAAAAT-AAAATTATCAA-A
31803497 TATTGTAAAAATAAAATTAT
1 TATTGTAAAAATAAAATTAT
31803517 AAAAATGTGT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
22 7 0.21
23 7 0.21
24 2 0.06
25 9 0.27
26 8 0.24
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.37
Consensus pattern (24 bp):
TATTGTAAAAATAAAATTATCAAA
Found at i:31803680 original size:12 final size:12
Alignment explanation
Indices: 31803664--31803699 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
31803654 AATAACATCT
31803664 ATAATAATAGTA
1 ATAATAATAGTA
*
31803676 GTAATAATAGTA
1 ATAATAATAGTA
31803688 ATAATAATAGTA
1 ATAATAATAGTA
31803700 TTATAACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (12 bp):
ATAATAATAGTA
Found at i:31803714 original size:24 final size:24
Alignment explanation
Indices: 31803664--31803720 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
31803654 AATAACATCT
**
31803664 ATAATAATAGTAGTAATAATAGTA
1 ATAATAATAGTAGTAATAATAAAA
*
31803688 ATAATAATAGTA-TTATAACTAAAA
1 ATAATAATAGTAGTAATAA-TAAAA
*
31803712 ATAAGAATA
1 ATAATAATA
31803721 AAAAAAAGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.32
Consensus pattern (24 bp):
ATAATAATAGTAGTAATAATAAAA
Found at i:31804908 original size:22 final size:22
Alignment explanation
Indices: 31804878--31804926 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
31804868 GTTGGGCTGA
* *
31804878 TTTGGGCTAAGTGTAAT-TGGG
1 TTTGGGCTAAATGTAATCTAGG
31804899 TTTGAGGCTAAATGTAATCTAGG
1 TTTG-GGCTAAATGTAATCTAGG
31804922 TTTGG
1 TTTGG
31804927 ATGTAATACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 13 0.54
23 7 0.29
ACGTcount: A:0.22, C:0.06, G:0.33, T:0.39
Consensus pattern (22 bp):
TTTGGGCTAAATGTAATCTAGG
Found at i:31805352 original size:44 final size:44
Alignment explanation
Indices: 31805256--31805523 Score: 141
Period size: 44 Copynumber: 6.2 Consensus size: 44
31805246 ACTTGATGTG
* * ** *
31805256 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATTACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTACAACTTCA
* * *
31805300 ATCCGCTCCACTACAACTTCAGGGAGATAGGAT-TACCAACTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTA-CAACTTCA
* * * * * **
31805344 ATCTGCTCCACTGCAACCTCAAGGAGATGAGATTTGCTTCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTACAACTTCA
* * ** * * * * *
31805388 GTCTGCCCCACTGTGACTTCAGGGGGATAAGACCT--GA-TGCG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTACAACTTCA
** * * * ** *
31805429 ATCCACTCTACTGCAACGTCAGAGAGATAAGATCTATTACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTACAACTTCA
* * * * * *
31805473 ATCCGCTCCACTACAACTTCAGGGAAATAGGAT-TATAGGCTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTACA-ACTTCA
31805517 ATCTGCT
1 ATCTGCT
31805524 TCCTTACACT
Statistics
Matches: 161, Mismatches: 57, Indels: 12
0.70 0.25 0.05
Matches are distributed among these distances:
41 26 0.16
43 6 0.04
44 128 0.80
45 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTACAACTTCA
Found at i:31805631 original size:128 final size:128
Alignment explanation
Indices: 31805491--31806149 Score: 1061
Period size: 128 Copynumber: 5.2 Consensus size: 128
31805481 CACTACAACT
* * *
31805491 TCAGGGAAATAGGA-TTATAGGCTTCAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCT
1 TCAGGGACATAGGACTTGT-GGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCT
* * *
31805555 GCAATCTACTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
65 TCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
* *
31805619 TCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCTTTACACTTGAAGATAAGATTCGCCGTCTT
1 TCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTT
*
31805684 CGATCTGCCCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
66 CGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
* *
31805747 TCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTT
1 TCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTT
* * *
31805812 CGATCTGGTCCGCTACTGCTTAAGGAGACAAGATCTACAATTTCCAACCTATTCCACTGCTGG
66 CGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
* *
31805875 TCAGGGGCATAGGACCTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTT
1 TCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTT
*
31805940 CGATCTGCTCCGCTACTGC-TAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTACTGG
66 CGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
* * * **
31806002 TCAGGGACATAGGAATTGTGGCTTAAATCTACTTCTTTACACTTGAAGATAAGATTTTCCGTCTT
1 TCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTT
* *
31806067 CGATCTTCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTAG
66 CGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
* *
31806130 CCAGGGATATAGGACTTGTG
1 TCAGGGACATAGGACTTGTG
31806150 ATTTCACCGA
Statistics
Matches: 493, Mismatches: 36, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
127 116 0.24
128 374 0.76
129 3 0.01
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (128 bp):
TCAGGGACATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCGTCTT
CGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAATTTCCAACCTATTCCACTGCTGG
Found at i:31807328 original size:6 final size:7
Alignment explanation
Indices: 31807312--31807352 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
31807302 CCGTCATTAC
31807312 TTTTCAT
1 TTTTCAT
31807319 TTTTCAT
1 TTTTCAT
31807326 TTTTCA-
1 TTTTCAT
31807332 TTTTCAT
1 TTTTCAT
*
31807339 TTTTAAT
1 TTTTCAT
31807346 TTTTCAT
1 TTTTCAT
31807353 CCCCCCCCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 6 0.19
7 25 0.81
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTCAT
Found at i:31807335 original size:13 final size:13
Alignment explanation
Indices: 31807312--31807348 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
31807302 CCGTCATTAC
31807312 TTTTCATTTTTCAT
1 TTTTCA-TTTTCAT
31807326 TTTTCATTTTCAT
1 TTTTCATTTTCAT
*
31807339 TTTTAATTTT
1 TTTTCATTTT
31807349 TCATCCCCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTCATTTTCAT
Found at i:31807337 original size:20 final size:20
Alignment explanation
Indices: 31807312--31807352 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
31807302 CCGTCATTAC
*
31807312 TTTTCATTTTTCATTTTTCA
1 TTTTCATTTTTAATTTTTCA
31807332 TTTTCATTTTTAATTTTTCA
1 TTTTCATTTTTAATTTTTCA
31807352 T
1 T
31807353 CCCCCCCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.12, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTCATTTTTAATTTTTCA
Found at i:31808266 original size:30 final size:28
Alignment explanation
Indices: 31808217--31808295 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 28
31808207 CTTTTTTCTC
* *
31808217 TTTTTCATATTTTTATTTTGACTTTAAT
1 TTTTTCTTTTTTTTATTTTGACTTTAAT
* *
31808245 TTATTTCTCTTTTTTTCTTTTGACTTTGAT
1 TT-TTTCT-TTTTTTTATTTTGACTTTAAT
*
31808275 TTTTTCTTTTTTCTTTTTTTG
1 TTTTTCTTTTTT-TTATTTTG
31808296 TTTTTGATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
28 7 0.16
29 16 0.37
30 20 0.47
ACGTcount: A:0.11, C:0.10, G:0.05, T:0.73
Consensus pattern (28 bp):
TTTTTCTTTTTTTTATTTTGACTTTAAT
Found at i:31808286 original size:29 final size:28
Alignment explanation
Indices: 31808226--31808306 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 28
31808216 CTTTTTCATA
* *
31808226 TTTTTATTTTGACTTTAATTTATTTCTCT
1 TTTTTTTTTTGACTTTGATTT-TTTCTCT
*
31808255 TTTTTTCTTTTGACTTTGATTTTTTCTTT
1 TTTTTT-TTTTGACTTTGATTTTTTCTCT
**
31808284 TTTCTTTTTTTGTTTTTGATTTT
1 TTT-TTTTTTTGACTTTGATTTT
31808307 GATTTGATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
29 28 0.62
30 17 0.38
ACGTcount: A:0.10, C:0.09, G:0.06, T:0.75
Consensus pattern (28 bp):
TTTTTTTTTTGACTTTGATTTTTTCTCT
Found at i:31813234 original size:25 final size:24
Alignment explanation
Indices: 31813167--31813234 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 24
31813157 ATGAAAATGT
*
31813167 TATTGTATAAATAAAATTA-CAAA
1 TATTGTAAAAATAAAATTATCAAA
* * * *
31813190 TA-TATAAAAATGGAATTTATGAATA
1 TATTGTAAAAAT-AAAATTATCAA-A
31813215 TATTGTAAAAATAAAATTAT
1 TATTGTAAAAATAAAATTAT
31813235 AAAAATGTGT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
22 7 0.21
23 7 0.21
24 2 0.06
25 9 0.27
26 8 0.24
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.37
Consensus pattern (24 bp):
TATTGTAAAAATAAAATTATCAAA
Found at i:31813692 original size:16 final size:16
Alignment explanation
Indices: 31813671--31813706 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
31813661 GAAGAAAACT
31813671 GAATCAAAACGACACC
1 GAATCAAAACGACACC
31813687 GAATCAAAACGACACC
1 GAATCAAAACGACACC
31813703 GAAT
1 GAAT
31813707 GCACAGTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.28, G:0.14, T:0.08
Consensus pattern (16 bp):
GAATCAAAACGACACC
Found at i:31818810 original size:17 final size:18
Alignment explanation
Indices: 31818788--31818837 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 18
31818778 ACCCACATAA
31818788 TATTTTT-TATTTTTCTT
1 TATTTTTGTATTTTTCTT
31818805 TATTTTTCGTA-TTTTCTT
1 TATTTTT-GTATTTTTCTT
31818823 T-TTTTTGTATTTTTC
1 TATTTTTGTATTTTTC
31818838 GATCAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
16 3 0.10
17 17 0.57
18 8 0.27
19 2 0.07
ACGTcount: A:0.10, C:0.08, G:0.04, T:0.78
Consensus pattern (18 bp):
TATTTTTGTATTTTTCTT
Found at i:31818819 original size:18 final size:16
Alignment explanation
Indices: 31818798--31818835 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 16
31818788 TATTTTTTAT
31818798 TTTTCTTTATTTTTCGTA
1 TTTTCTTT-TTTTT-GTA
31818816 TTTTCTTTTTTTTGTA
1 TTTTCTTTTTTTTGTA
31818832 TTTT
1 TTTT
31818836 TCGATCAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 7 0.35
17 5 0.25
18 8 0.40
ACGTcount: A:0.08, C:0.08, G:0.05, T:0.79
Consensus pattern (16 bp):
TTTTCTTTTTTTTGTA
Found at i:31818825 original size:25 final size:26
Alignment explanation
Indices: 31818788--31818838 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
31818778 ACCCACATAA
*
31818788 TATTTTTTATTTTTCTT-TATTTTTCG
1 TATTTTCTATTTTT-TTGTATTTTTCG
31818814 TATTTTCT-TTTTTTTGTATTTTTCG
1 TATTTTCTATTTTTTTGTATTTTTCG
31818839 ATCAATTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 2 0.09
25 14 0.61
26 7 0.30
ACGTcount: A:0.10, C:0.08, G:0.06, T:0.76
Consensus pattern (26 bp):
TATTTTCTATTTTTTTGTATTTTTCG
Found at i:31819715 original size:8 final size:8
Alignment explanation
Indices: 31819704--31819729 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
31819694 AAAGAAATTT
31819704 AATAATAA
1 AATAATAA
31819712 AATAATAA
1 AATAATAA
31819720 AATAATAA
1 AATAATAA
31819728 AA
1 AA
31819730 GTTGATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AATAATAA
Found at i:31821935 original size:15 final size:15
Alignment explanation
Indices: 31821899--31821931 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
31821889 TATAAAGGTT
31821899 ATAATAATAAAAGTA
1 ATAATAATAAAAGTA
31821914 ATAATAATAAAA-TA
1 ATAATAATAAAAGTA
31821928 ATAA
1 ATAA
31821932 ATAAAGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
ATAATAATAAAAGTA
Found at i:31827351 original size:24 final size:24
Alignment explanation
Indices: 31827307--31827353 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
31827297 ATTGAAATGG
* *
31827307 ATTGATTTTGTATGTGATGAATTT
1 ATTGAATTTATATGTGATGAATTT
31827331 ATTGAATTTATAT-TGATTGAATT
1 ATTGAATTTATATGTGA-TGAATT
31827354 GGATAGGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (24 bp):
ATTGAATTTATATGTGATGAATTT
Found at i:31828308 original size:2 final size:2
Alignment explanation
Indices: 31828301--31828330 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31828291 TTAGTTTGGC
31828301 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31828331 GTAAACATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31836629 original size:27 final size:27
Alignment explanation
Indices: 31836582--31836653 Score: 74
Period size: 27 Copynumber: 2.5 Consensus size: 27
31836572 AATTAATTTC
*
31836582 AATTTGAATATTTTTTGTAATT-TTAAATA
1 AATTT-AAT-TTTTTTATAATTCTT-AATA
31836611 AATTTAATTTTTTTATAATTCTTAATA
1 AATTTAATTTTTTTATAATTCTTAATA
*
31836638 ATTGTTAATTATTTTT
1 AAT-TTAATT-TTTTT
31836654 TCATAATTAC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 17 0.45
28 11 0.29
29 10 0.26
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (27 bp):
AATTTAATTTTTTTATAATTCTTAATA
Found at i:31839366 original size:19 final size:19
Alignment explanation
Indices: 31839342--31839381 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
31839332 TTAATACTAG
31839342 TTGCATTGCTATTAAGGCA
1 TTGCATTGCTATTAAGGCA
31839361 TTGCATTGCTATTAAGGCA
1 TTGCATTGCTATTAAGGCA
31839380 TT
1 TT
31839382 AGCTTGATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (19 bp):
TTGCATTGCTATTAAGGCA
Found at i:31845852 original size:10 final size:10
Alignment explanation
Indices: 31845837--31845871 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
31845827 AAAGTTGCCA
31845837 TATGTATGTG
1 TATGTATGTG
31845847 TATGTATGTG
1 TATGTATGTG
31845857 TATGTATGTG
1 TATGTATGTG
31845867 TATGT
1 TATGT
31845872 GTGTATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (10 bp):
TATGTATGTG
Found at i:31845860 original size:16 final size:16
Alignment explanation
Indices: 31845839--31845873 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
31845829 AGTTGCCATA
*
31845839 TGTATGTGTATGTATG
1 TGTATGTATATGTATG
*
31845855 TGTATGTATGTGTATG
1 TGTATGTATATGTATG
31845871 TGT
1 TGT
31845874 GTATAAATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.51
Consensus pattern (16 bp):
TGTATGTATATGTATG
Found at i:31848203 original size:24 final size:24
Alignment explanation
Indices: 31848165--31848464 Score: 171
Period size: 24 Copynumber: 12.8 Consensus size: 24
31848155 TGAATTGGAT
* *
31848165 AATTTACAATAAATAATATATAATA
1 AATTTAAAAT-AATAATATATGATA
* *
31848190 AATTTGAAATAATAATACAT-ATAA
1 AATTTAAAATAATAATATATGAT-A
*
31848214 AATTT-AAA-AAT--TTTGATGAT-
1 AATTTAAAATAATAATAT-ATGATA
* **
31848234 AATTCTAGAATAATAATACGTGATA
1 AATT-TAAAATAATAATATATGATA
** *
31848259 AATCCAAAATAATAATATATAATA
1 AATTTAAAATAATAATATATGATA
*
31848283 AATTT-AAA-AATATTA-ATGATA
1 AATTTAAAATAATAATATATGATA
* *
31848304 AATTTGAAATAA-ATATACATGATA
1 AATTTAAAATAATA-ATATATGATA
** * *
31848328 AATTTAAAATAATGTTA-ACGATG
1 AATTTAAAATAATAATATATGATA
31848351 AATTTAAAATAATAATAT-TGATA
1 AATTTAAAATAATAATATATGATA
* *
31848374 AA-TTACAAATAATAAAACATGATA
1 AATTTA-AAATAATAATATATGATA
* **
31848398 AATCTAAAATAATAATATACAATA
1 AATTTAAAATAATAATATATGATA
* * * *
31848422 AACTT-AGATAATATTA-ATGATT
1 AATTTAAAATAATAATATATGATA
*
31848444 AATTTAATGATAATAAGTATA
1 AATTTAA-AATAATAA-TATA
31848465 AACATTCAAA
Statistics
Matches: 208, Mismatches: 45, Indels: 43
0.70 0.15 0.15
Matches are distributed among these distances:
20 5 0.02
21 13 0.06
22 27 0.13
23 59 0.28
24 87 0.42
25 16 0.08
26 1 0.00
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (24 bp):
AATTTAAAATAATAATATATGATA
Found at i:31848237 original size:69 final size:68
Alignment explanation
Indices: 31848162--31848450 Score: 228
Period size: 69 Copynumber: 4.1 Consensus size: 68
31848152 AAATGAATTG
* * * *
31848162 GATAATTTACAATAAATAATATATAATAAATTTGAAATAATAATACAT-ATAAAATTTAAAAATT
1 GATAATTTA-AATAAATAATACATGATAAATTTAAAATAATAATACATAAT-AAATTTAAAAATA
*
31848226 TTGAT
64 TTAAT
* ** *
31848231 GATAATTCTAGAAT-AATAATACGTGATAAATCCAAAATAATAATATATAATAAATTTAAAAATA
1 GATAATT-TA-AATAAATAATACATGATAAATTTAAAATAATAATACATAATAAATTTAAAAATA
31848295 TTAAT
64 TTAAT
** ** *
31848300 GATAAATTTGAAATAAAT-ATACATGATAAATTTAAAATAATGTTA-ACGATGAATTTAAAATAA
1 GAT-AATTT-AAATAAATAATACATGATAAATTTAAAATAATAATACATAATAAATTT-AAA-AA
* *
31848363 TAATATT
62 TATTAAT
* * * * * * *
31848370 GATAAATTACAA-ATAATAAAACATGATAAATCTAAAATAATAATATACAATAAACTTAGATAAT
1 GATAATTTA-AATA-AATAATACATGATAAATTTAAAATAATAATACATAATAAATTTA-AAAAT
31848434 ATTAAT
63 ATTAAT
31848440 GATTAATTTAA
1 GA-TAATTTAA
31848451 TGATAATAAG
Statistics
Matches: 175, Mismatches: 32, Indels: 25
0.75 0.14 0.11
Matches are distributed among these distances:
68 10 0.06
69 91 0.52
70 59 0.34
71 15 0.09
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (68 bp):
GATAATTTAAATAAATAATACATGATAAATTTAAAATAATAATACATAATAAATTTAAAAATATT
AAT
Found at i:31848384 original size:46 final size:45
Alignment explanation
Indices: 31848255--31848459 Score: 139
Period size: 47 Copynumber: 4.4 Consensus size: 45
31848245 AATAATACGT
** * * *
31848255 GATAAATCCAAAATAATAATATATAATAAATTTAAA-AATATTAAT
1 GATAAATTTAAAATAATAATAT-TGATAAATTAAAATAATATTAAC
* * *
31848300 GATAAATTTGAAATAA-ATATACATGATAAATTTAAAATAATGTTAAC
1 GATAAATTTAAAATAATA-ATA-TTGATAAA-TTAAAATAATATTAAC
* *
31848347 GATGAATTTAAAATAATAATATTGATAAATTACAAATAATA-AAAC
1 GATAAATTTAAAATAATAATATTGATAAATTA-AAATAATATTAAC
* ** * *
31848392 ATGATAAATCTAAAATAATAATATACAATAAACTT-AGATAATATTAAT
1 --GATAAATTTAAAATAATAATAT-TGATAAA-TTAAAATAATATTAAC
* *
31848440 GATTAATTTAATGATAATAA
1 GATAAATTTAA-AATAATAA
31848460 GTATAAACAT
Statistics
Matches: 125, Mismatches: 23, Indels: 22
0.74 0.14 0.13
Matches are distributed among these distances:
44 1 0.01
45 28 0.22
46 28 0.22
47 58 0.46
48 8 0.06
49 2 0.02
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (45 bp):
GATAAATTTAAAATAATAATATTGATAAATTAAAATAATATTAAC
Found at i:31848433 original size:70 final size:69
Alignment explanation
Indices: 31848242--31848447 Score: 209
Period size: 70 Copynumber: 3.0 Consensus size: 69
31848232 ATAATTCTAG
* * * * *
31848242 AATAATAATACGTGATAAATCCAAAATAATAATATATAATAAATTTAAAAATATTAATGATAAAT
1 AATAATAATACATGATAAATCTAAAATAATAATATACAATAAATTTAATAATAATAATGATAAAT
**
31848307 TTGA
66 TACA
* ** * * *
31848311 AATAA-ATATACATGATAAATTTAAAATAATGTTA-ACGATGAATTTAAAATAATAATATTGATA
1 AATAATA-ATACATGATAAATCTAAAATAATAATATACAATAAATTT--AATAATAATAATGATA
31848374 AATTACA
63 AATTACA
* * * *
31848381 AATAATAAAACATGATAAATCTAAAATAATAATATACAATAAACTTAGATAATATTAATGATTAA
1 AATAATAATACATGATAAATCTAAAATAATAATATACAATAAATTTA-ATAATAATAATGATAAA
31848446 TT
65 TT
31848448 TAATGATAAT
Statistics
Matches: 108, Mismatches: 23, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
68 9 0.08
69 28 0.26
70 62 0.57
71 9 0.08
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (69 bp):
AATAATAATACATGATAAATCTAAAATAATAATATACAATAAATTTAATAATAATAATGATAAAT
TACA
Found at i:31849280 original size:18 final size:20
Alignment explanation
Indices: 31849219--31849288 Score: 92
Period size: 19 Copynumber: 3.6 Consensus size: 20
31849209 TTTATTTCTT
*
31849219 TTTTCCTCCCTTTACACTAA
1 TTTTCCTCCCTTTACACTGA
* *
31849239 TTTT-TTCTCTTTACACTGA
1 TTTTCCTCCCTTTACACTGA
31849258 TTTTCC-CCCTTTACACTGA
1 TTTTCCTCCCTTTACACTGA
31849277 -TTTCCTCCCTTT
1 TTTTCCTCCCTTT
31849289 TTTATGAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
18 5 0.12
19 34 0.79
20 4 0.09
ACGTcount: A:0.14, C:0.33, G:0.03, T:0.50
Consensus pattern (20 bp):
TTTTCCTCCCTTTACACTGA
Found at i:31856926 original size:18 final size:18
Alignment explanation
Indices: 31856868--31856927 Score: 52
Period size: 20 Copynumber: 3.3 Consensus size: 18
31856858 AAATATAAAG
31856868 TATTCTATTTATATTT-TA
1 TATT-TATTTATATTTATA
* **
31856886 T-TTTATATATATAAATAA
1 TATTTATTTATATTTAT-A
31856904 TTATTTATTTATATTTATA
1 -TATTTATTTATATTTATA
31856923 TATTT
1 TATTT
31856928 TCTTCACTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 8 0.25
17 3 0.09
18 7 0.22
19 2 0.06
20 12 0.38
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTTATTTATATTTATA
Found at i:31857542 original size:30 final size:30
Alignment explanation
Indices: 31857506--31857567 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
31857496 ACCCACAAGA
31857506 TTATGATTGTCTTGTGACTGAAGATAATGT
1 TTATGATTGTCTTGTGACTGAAGATAATGT
31857536 TTATGATTGTCTTGTGACTGAAGATAATGT
1 TTATGATTGTCTTGTGACTGAAGATAATGT
31857566 TT
1 TT
31857568 TTTTACTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (30 bp):
TTATGATTGTCTTGTGACTGAAGATAATGT
Found at i:31860932 original size:2 final size:2
Alignment explanation
Indices: 31860925--31860959 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31860915 CATAAACTAA
31860925 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31860960 CGCAATACCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31864192 original size:9 final size:9
Alignment explanation
Indices: 31864180--31864217 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
31864170 ATAACTTTTG
31864180 TTTATAATT
1 TTTATAATT
*
31864189 TTTATGATT
1 TTTATAATT
31864198 TTTAATAATT
1 TTT-ATAATT
31864208 TTTA-AATT
1 TTTATAATT
31864216 TT
1 TT
31864218 AAAAGTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 6 0.23
9 12 0.46
10 8 0.31
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTATAATT
Found at i:31866322 original size:9 final size:9
Alignment explanation
Indices: 31866308--31866339 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
31866298 AAACAAAAAG
31866308 ATAATAACA
1 ATAATAACA
31866317 ATAATAACA
1 ATAATAACA
*
31866326 ATAATAATA
1 ATAATAACA
31866335 ATAAT
1 ATAAT
31866340 TTATTAGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (9 bp):
ATAATAACA
Found at i:31867845 original size:44 final size:44
Alignment explanation
Indices: 31867767--31868109 Score: 190
Period size: 44 Copynumber: 7.8 Consensus size: 44
31867757 TTGTGGTAGA
* * * *
31867767 TTTAATCCGAC-CTACTGCAACTTCAGAGG-TATAGGATCCATCAT
1 TTTAATCCG-CTCCACTGCAACTTCAG-GGAGATAGGATCTATGAT
*
31867811 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGAT-TA-GTAGC
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATCTATG-A-T
* * *
31867855 TTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGG-T-T-TGAT
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGAT-AGGATCTATGAT
* * * * * * *
31867897 ATCTTCAGTCTGCTCCACTACAACTTCAGAGAGATAAGATCTGTGGT
1 -T-TT-AATCCGCTCCACTGCAACTTCAGGGAGATAGGATCTATGAT
* *
31867944 TTTAATCCGCTCCGCTGCAACTTTAGGGAGATAGGA--T-TGACT
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATCTATGA-T
** * * * *
31867986 TCTTCTGTCTGCTCCACTGCAACTTCAGAGAGATAAGA-CT-GGA-
1 T-TT-AATCCGCTCCACTGCAACTTCAGGGAGATAGGATCTATGAT
** * * * * * *
31868029 TGCAATCTGCTCTACTGCAACTTCAGAGACATAAGATCTATGGT
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATCTATGAT
* * *
31868073 TTTAATCCGTTCCACTGCAACTCCAGGGAGATTGGAT
1 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGAT
31868110 TGACTTCTTC
Statistics
Matches: 230, Mismatches: 50, Indels: 38
0.72 0.16 0.12
Matches are distributed among these distances:
41 31 0.13
42 5 0.02
43 11 0.05
44 144 0.63
45 34 0.15
46 2 0.01
47 3 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATCTATGAT
Found at i:31868049 original size:41 final size:41
Alignment explanation
Indices: 31867993--31868193 Score: 127
Period size: 41 Copynumber: 4.8 Consensus size: 41
31867983 ACTTCTTCTG
*
31867993 TCTGCTCCACTGCAACTTCAGAGAGATAAGACTGGATGCAA
1 TCTGCTCTACTGCAACTTCAGAGAGATAAGACTGGATGCAA
* * **
31868034 TCTGCTCTACTGCAACTTCAGAGACATAAGATCTATGGTTTTAA
1 TCTGCTCTACTGCAACTTCAGAGAGATAAGA-C--TGGATGCAA
* * * * * ** * * *
31868078 TCCGTTCCACTGCAACTCCAGGGAGATTGGA-TTGACTTC-T
1 TCTGCTCTACTGCAACTTCAGAGAGATAAGACTGGA-TGCAA
* * * **
31868118 TCTGTCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGATGCGG
1 TCTG-CT-CT--ACTGCAACTTCAGAGAGATAAGACTGGATGCAA
*
31868163 TCTACTCTACTGCAACTTCAGAGAGATAAGA
1 TCTGCTCTACTGCAACTTCAGAGAGATAAGA
31868194 TCTGTGGTTT
Statistics
Matches: 120, Mismatches: 30, Indels: 20
0.71 0.18 0.12
Matches are distributed among these distances:
40 5 0.04
41 53 0.44
42 2 0.02
43 2 0.02
44 52 0.43
45 6 0.05
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (41 bp):
TCTGCTCTACTGCAACTTCAGAGAGATAAGACTGGATGCAA
Found at i:31868101 original size:129 final size:129
Alignment explanation
Indices: 31867778--31868206 Score: 547
Period size: 129 Copynumber: 3.3 Consensus size: 129
31867768 TTAATCCGAC
* * **
31867778 CTACTGCAACTTCAGAG-GTATAGGATCCATCATTTTAATCCGCTCCACTGCAACTTCAGGGAGA
1 CTACTGCAACTTCAGAGAG-ATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGA
* * ** * * *
31867842 TAGGATT-AGTAGCTTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGGTTTGATATCTTCAGT
65 TAGGATTGACT-TCTTCTGTCTGCTCCACTGTAACTTCAGGGAGATAA-GATTG-GA--TGCAGT
31867906 CTGCT
125 CTGCT
* * * * *
31867911 CCACTACAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCGCTGCAACTTTAGGGAGAT
1 CTACTGCAACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGAT
* * * *
31867976 AGGATTGACTTCTTCTGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTGGATGCAATCTGCT
66 AGGATTGACTTCTTCTGTCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGATGCAGTCTGCT
* * *
31868040 CTACTGCAACTTCAGAGACATAAGATCTATGGTTTTAATCCGTTCCACTGCAACTCCAGGGAGAT
1 CTACTGCAACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGAT
* * *
31868105 TGGATTGACTTCTTCTGTCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGATGCGGTCTACT
66 AGGATTGACTTCTTCTGTCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGATGCAGTCTGCT
*
31868169 CTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTAA
1 CTACTGCAACTTCAGAGAGATAAGATCTATGGTTTTAA
31868207 ATCCACTCAC
Statistics
Matches: 257, Mismatches: 37, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
129 159 0.62
131 1 0.00
132 3 0.01
133 91 0.35
134 3 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (129 bp):
CTACTGCAACTTCAGAGAGATAAGATCTATGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGAT
AGGATTGACTTCTTCTGTCTGCTCCACTGTAACTTCAGGGAGATAAGATTGGATGCAGTCTGCT
Found at i:31868155 original size:44 final size:43
Alignment explanation
Indices: 31867819--31868194 Score: 223
Period size: 44 Copynumber: 8.7 Consensus size: 43
31867809 ATTTTAATCC
* * **
31867819 GCTCCACTGCAACTTCAGGGAGATAGGATT-AGTAGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGA-T-TCTTCTGTCT
* * *
31867863 GCTCCACTGTAACTTCAGGGAGATAAGGTTTGATATCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAA-GATTGAT-TCTTCTGTCT
* * ** * * *
31867908 GCTCCACTACAACTTCAGAGAGATAAGATCTG-TGGTTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGAT-TGATTCTTCT-GTCT
* * *
31867952 GCTCCGCTGCAACTTTAGGGAGATAGGATTGACTTCTTCTGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGA-TTCTTCTGTCT
* * * *
31867996 GCTCCACTGCAACTTCAGAGAGATAAGACTGGATGCAATCTG-CT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTGATTC-TTCTGTCT
* * ** * * *
31868040 -CT--ACTGCAACTTCAGAGACATAAGATCT-ATGGTTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGAT-TGATTCTTCT-GTCT
* * **
31868081 GTTCCACTGCAACTCCAGGGAGATTGGATTGACTTCTTCTGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGA-TTCTTCTGTCT
* * *
31868125 GCTCCACTGTAACTTCAGGGAGATAAGATTGGA---TGCGGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATT-GATTCTTCTGTCT
* * *
31868166 ACTCTACTGCAACTTCAGAGAGATAAGAT
1 GCTCCACTGCAACTTCAGGGAGATAAGAT
31868195 CTGTGGTTTT
Statistics
Matches: 254, Mismatches: 61, Indels: 37
0.72 0.17 0.11
Matches are distributed among these distances:
39 2 0.01
40 4 0.02
41 54 0.21
42 1 0.00
43 7 0.03
44 130 0.51
45 55 0.22
46 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (43 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTGATTCTTCTGTCT
Found at i:31868292 original size:50 final size:50
Alignment explanation
Indices: 31868217--31869001 Score: 600
Period size: 50 Copynumber: 15.7 Consensus size: 50
31868207 ATCCACTCAC
* **
31868217 CAGGGAAGTAAGATTAGCTGTTGTAGCTTCAATCTACTTAACTGCAATGT
1 CAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTTTAACTGCAATGT
** * * *
31868267 CAGGGAAACAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAACGC
1 CAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * * * *
31868317 CTGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGT
1 CAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * * ** * ** *
31868367 CGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGTACCGC
1 CAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * *
31868417 CAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGT
1 CAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * * ** * ** ****
31868467 CGGGGAAGCAAGATTCACCATTGTAGCTTCAATCTGTTCCACTGCACCAC
1 CAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * *
31868517 CAGGAAAGTAAGATTCG-TCGTTGTGGCTTCAATCTTTTTAATTGCAATGT
1 CAGGGAAGTAAGATTCGCT-GTTGTAGCTTCAATCTTTTTAACTGCAATGT
* ** * * ** * **
31868567 CGGGGAAACAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTACACCG-
1 CAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * *
31868616 CAAGGGAAGTAAGATTCG-TCGTTGTGGCTTCAATCTTTTTAATTGCGATGT
1 C-AGGGAAGTAAGATTCGCT-GTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * * * ** *
31868667 -TGGGAAAATAAGATTCG-TCGTTGTAGCTTCAATATGTTCCACTGCACTG-
1 CAGGG-AAGTAAGATTCGCT-GTTGTAGCTTCAATCTTTTTAACTGCAATGT
** * * *
31868716 CAAGGGAAGTAAGATTCGCCATTGTGGCTTCAATCTTTTTAATTGCGATGT
1 C-AGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* ** * * *
31868767 CGGGGAAACAAGATTCGCCGTTGTAGCTTCAATCTGTTCT-ACTGCACTGT
1 CAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCT-TTTTAACTGCAATGT
* * * * *
31868817 AAGGGAAGTAAGATTCG-TCGTTATGGCTTCAATCTTTTTAATTGTAATGT
1 CAGGGAAGTAAGATTCGCT-GTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * * * ** **
31868867 CGGGGAAGTAAGATTCGCCGCTGTAGCTTCAATCTATTCCACTGCACCG-
1 CAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTTTAACTGCAATGT
* * * * *
31868916 CTTGGGAAGTAAGATTCGCTGTTGTGGCTTCAATTTTTTTAATTGCGATGT
1 C-AGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTTTAACTGCAATGT
*
31868967 C-GAGGAAGCAAGATTCGCTGTTGTAGCTTCAATCT
1 CAG-GGAAGTAAGATTCGCTGTTGTAGCTTCAATCT
31869002 GTTCCACTAC
Statistics
Matches: 553, Mismatches: 165, Indels: 34
0.74 0.22 0.05
Matches are distributed among these distances:
49 9 0.02
50 536 0.97
51 8 0.01
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (50 bp):
CAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTTTTTAACTGCAATGT
Found at i:31868392 original size:100 final size:100
Alignment explanation
Indices: 31868216--31869032 Score: 1121
Period size: 100 Copynumber: 8.2 Consensus size: 100
31868206 AATCCACTCA
* * * ** * *
31868216 CCAGGGAAGTAAGATTAGCTGTTGTAGCTTCAATCTACTTAACTGCAATGTCAGGGAAACAAGAT
1 CCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGAT
* * ** *
31868281 TCGCTGTTGTAGCTTCAATCTATTTAACTGCAACG
66 TCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
* * *
31868316 CCTGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGAT
1 CCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGAT
* *
31868381 TCGCTGTTGTAGCTTCAATCTGTTCCACTGTACCG
66 TCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
*
31868416 CCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGAT
1 CCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGAT
* * *
31868481 TCACCATTGTAGCTTCAATCTGTTCCACTGCACCA
66 TCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
* *
31868516 CCAGGAAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGAT
1 CCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGAT
*
31868581 TCGCCGTTGTAGCTTCAATCTGTTCCACTACACCG
66 TCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
* * * * * *
31868616 CAAGGGAAGTAAGATTCGTCGTTGTGGCTTCAATCTTTTTAATTGCGATGTTGGGAAAATAAGAT
1 CCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGAT
* * *
31868681 TCGTCGTTGTAGCTTCAATATGTTCCACTGCACTG
66 TCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
* * *
31868716 CAAGGGAAGTAAGATTCGCCATTGTGGCTTCAATCTTTTTAATTGCGATGTCGGGGAAACAAGAT
1 CCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGAT
* *
31868781 TCGCCGTTGTAGCTTCAATCTGTTCTACTGCACTG
66 TCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
** * * * **
31868816 TAAGGGAAGTAAGATTCGTCGTTATGGCTTCAATCTTTTTAATTGTAATGTCGGGGAAGTAAGAT
1 CCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGAT
* *
31868881 TCGCCGCTGTAGCTTCAATCTATTCCACTGCACCG
66 TCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
** * * * * *
31868916 CTTGGGAAGTAAGATTCGCTGTTGTGGCTTCAATTTTTTTAATTGCGATGTCGAGGAAGCAAGAT
1 CCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGAT
* *
31868981 TCGCTGTTGTAGCTTCAATCTGTTCCACTACACCG
66 TCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
*
31869016 CCTGGGAAGTAAGATTC
1 CCAGGGAAGTAAGATTC
31869033 ACTGTCTTTG
Statistics
Matches: 642, Mismatches: 75, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
100 642 1.00
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (100 bp):
CCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAAACAAGAT
TCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG
Found at i:31869222 original size:44 final size:43
Alignment explanation
Indices: 31869174--31869373 Score: 144
Period size: 44 Copynumber: 4.6 Consensus size: 43
31869164 CATATTCGAT
31869174 ATGCTCCACTACTGCTTAGGGAGACAAGATCTGCAATCTTCAAC
1 ATGCTCCACTACTGCTTAGGGAGACAAGATCT-CAATCTTCAAC
* * *
31869218 ATGCTCCACTACTGCTTAGGGAGATAGGA-CT-AATGGCTTAAATC
1 ATGCTCCACTACTGCTTAGGGAGACAAGATCTCAAT--CTTCAA-C
* * ** *
31869262 TACTTCTCCACTA-T-CTT-GGGAAGATAAGAT-TCACTATCTTTGAT
1 -A-TGCTCCACTACTGCTTAGGG-AGACAAGATCTCA--ATCTTCAAC
*
31869306 TTGCTCCACTACTGCTTAGGGAGAC-AGAATCTGCAATCTTCAAC
1 ATGCTCCACTACTGCTTAGGGAGACAAG-ATCT-CAATCTTCAAC
* * *
31869350 CTACTCCACTACGGCTTAGGGAGA
1 ATGCTCCACTACTGCTTAGGGAGA
31869374 TAGGACTAAT
Statistics
Matches: 123, Mismatches: 17, Indels: 32
0.72 0.10 0.19
Matches are distributed among these distances:
41 3 0.02
42 9 0.07
43 13 0.11
44 74 0.60
45 11 0.09
46 11 0.09
47 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (43 bp):
ATGCTCCACTACTGCTTAGGGAGACAAGATCTCAATCTTCAAC
Found at i:31869328 original size:132 final size:132
Alignment explanation
Indices: 31869018--31869652 Score: 967
Period size: 132 Copynumber: 4.8 Consensus size: 132
31869008 CTACACCGCC
**
31869018 TGGGAAG-TAAGATTCACTGTCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGCAAT
1 TGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGCAAT
* * * *
31869082 CTTCGACCTACTCCATTACTGCTTAGGGAGATAGG---AGTGGTTTAAATCTGCTTCTCCACTAT
66 CTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTAT
31869144 CT
131 CT
* * *
31869146 TGGGAAGATAAGATTCACCATATTCGATATGCTCCACTACTGCTTAGGGAGACA-AGATCTGCAA
1 TGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGA-ATCTGCAA
* * *
31869210 TCTTCAACATGCTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTACTTCTCCACTA
65 TCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTA
31869275 TCT
130 TCT
* *
31869278 TGGGAAGATAAGATTCACTATCTTTGATTTGCTCCACTACTGCTTAGGGAGACAGAATCTGCAAT
1 TGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGCAAT
* *
31869343 CTTCAACCTACTCCACTACGGCTTAGGGAGATAGGACTAATGACTTAAATCTGCTTCTCCACTAT
66 CTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTAT
31869408 CT
131 CT
* * * * *
31869410 TGGAAAGATAATATTCACCATCTTCGATCTACTCCACTACTGCTTAGGGAGACAGAATATGCAAT
1 TGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGCAAT
*
31869475 CTTCAGCCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTAT
66 CTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTAT
31869540 CT
131 CT
* * * *
31869542 TGGGAAGATAAGATTCACCGTCTTTGATCTGCTCTACTACTGCTTAGAGAGACA-ATATCTGTAA
1 TGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGA-ATCTGCAA
*
31869606 TCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAGTGGCTT
65 TCTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTT
31869653 CATCGATCTA
Statistics
Matches: 458, Mismatches: 42, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
128 8 0.02
129 81 0.18
131 1 0.00
132 367 0.80
133 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (132 bp):
TGGGAAGATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAGAATCTGCAAT
CTTCAACCTACTCCACTACTGCTTAGGGAGATAGGACTAATGGCTTAAATCTGCTTCTCCACTAT
CT
Found at i:31869486 original size:44 final size:43
Alignment explanation
Indices: 31869309--31869505 Score: 147
Period size: 44 Copynumber: 4.5 Consensus size: 43
31869299 CTTTGATTTG
* *
31869309 CTCCACTACTGCTTAGGGAGACAGAATCTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGACAGAATATGCAATCTTC-GCCTA
* * * *
31869353 CTCCACTACGGCTTAGGGAGATAGGACTAATGACTTAAATC-T-G-CTT
1 CTCCACTACTGCTTAGGGAGACA-GAAT-ATG-C---AATCTTCGCCTA
* * * * *
31869399 CTCCACTA-T-CTT--GGAAAGATAATATTCACCATCTTCGATCTA
1 CTCCACTACTGCTTAGGGAGACAGAATATGCA--ATCTTCG-CCTA
31869441 CTCCACTACTGCTTAGGGAGACAGAATATGCAATCTTCAGCCTA
1 CTCCACTACTGCTTAGGGAGACAGAATATGCAATCTTC-GCCTA
31869485 CTCCACTACTGCTTAGGGAGA
1 CTCCACTACTGCTTAGGGAGA
31869506 TAGGACTAAT
Statistics
Matches: 118, Mismatches: 18, Indels: 34
0.69 0.11 0.20
Matches are distributed among these distances:
36 1 0.01
38 3 0.03
39 2 0.02
40 3 0.03
41 2 0.02
42 15 0.13
43 1 0.01
44 57 0.48
45 4 0.03
46 24 0.20
47 1 0.01
49 1 0.01
50 4 0.03
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.27
Consensus pattern (43 bp):
CTCCACTACTGCTTAGGGAGACAGAATATGCAATCTTCGCCTA
Found at i:31870895 original size:6 final size:6
Alignment explanation
Indices: 31870884--31870946 Score: 56
Period size: 6 Copynumber: 10.3 Consensus size: 6
31870874 CATTGGCCTC
* ** *
31870884 TTCTTT TTCTTT TTCTTT TTCTTA TGGTCT TTCTTT CTTCTTT TT-TTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT -TTCTTT TTCTTT
*
31870932 CTTTTTT TTCTTT TT
1 -TTCTTT TTCTTT TT
31870947 TAAATATTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
5 3 0.07
6 33 0.73
7 9 0.20
ACGTcount: A:0.02, C:0.16, G:0.03, T:0.79
Consensus pattern (6 bp):
TTCTTT
Found at i:31870936 original size:8 final size:9
Alignment explanation
Indices: 31870911--31870947 Score: 56
Period size: 9 Copynumber: 3.9 Consensus size: 9
31870901 TTTCTTATGG
31870911 TCTTTCTTTCT
1 TCTTT-TTT-T
31870922 TCTTTTTTT
1 TCTTTTTTT
31870931 TCTTTTTTT
1 TCTTTTTTT
31870940 TCTTTTTT
1 TCTTTTTT
31870948 AAATATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 18 0.69
10 3 0.12
11 5 0.19
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:31873246 original size:12 final size:12
Alignment explanation
Indices: 31873215--31873248 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
31873205 ATTTTCTAGT
31873215 TGTTCTTGCATC
1 TGTTCTTGCATC
**
31873227 TGGGCTTGCATC
1 TGTTCTTGCATC
31873239 TGTTCTTGCA
1 TGTTCTTGCA
31873249 ATTGCTCTAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.09, C:0.24, G:0.24, T:0.44
Consensus pattern (12 bp):
TGTTCTTGCATC
Found at i:31875705 original size:14 final size:14
Alignment explanation
Indices: 31875686--31875725 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
31875676 TTTTTTAAAA
* *
31875686 ATATATATATGTGT
1 ATATATATATATCT
*
31875700 ATATATCTATATCT
1 ATATATATATATCT
31875714 ATATATATATAT
1 ATATATATATAT
31875726 AAGTAATTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (14 bp):
ATATATATATATCT
Found at i:31875830 original size:3 final size:3
Alignment explanation
Indices: 31875824--31875894 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
31875814 TAACACTAAT
31875824 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
31875872 AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AA
31875895 TAATAATAAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:31875947 original size:3 final size:3
Alignment explanation
Indices: 31875893--31875928 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
31875883 CAACAACAAC
31875893 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
31875929 TTATTAGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Done.