Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397257.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_95.0, whole genome shotgun sequence
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: 12062019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 103452 characters in sequence are not A, C, G, or T
File 3 of 26
Found at i:825546 original size:14 final size:15
Alignment explanation
Indices: 825522--825551 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
825512 ACATATAGGG
825522 ACAACATCTTAATCA
1 ACAACATCTTAATCA
825537 ACAA-ATCTTAATCA
1 ACAACATCTTAATCA
825551 A
1 A
825552 ATTTCACATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (15 bp):
ACAACATCTTAATCA
Found at i:826096 original size:7 final size:7
Alignment explanation
Indices: 826084--826151 Score: 50
Period size: 7 Copynumber: 9.1 Consensus size: 7
826074 TCCTCTAGCT
826084 TTTCTTC
1 TTTCTTC
826091 TTTCTTC
1 TTTCTTC
826098 TTTCTTTC
1 TTTC-TTC
826106 TTT-TCTC
1 TTTCT-TC
*
826113 TTTTTTTC
1 -TTTCTTC
*
826121 TTTCTTT
1 TTTCTTC
826128 TTTCCTTCC
1 TTT-CTT-C
826137 TTTC-TC
1 TTTCTTC
826143 TTTTCTTC
1 -TTTCTTC
826151 T
1 T
826152 CTCAAAGGTG
Statistics
Matches: 50, Mismatches: 3, Indels: 16
0.72 0.04 0.23
Matches are distributed among these distances:
6 2 0.04
7 27 0.54
8 17 0.34
9 4 0.08
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTCTTC
Found at i:826100 original size:15 final size:15
Alignment explanation
Indices: 826082--826151 Score: 67
Period size: 15 Copynumber: 4.7 Consensus size: 15
826072 CTTCCTCTAG
826082 CTTTTCTTCTTTCTT
1 CTTTTCTTCTTTCTT
826097 C-TTTCTTTCTTT-TCT
1 CTTTTC-TTCTTTCT-T
*
826112 CTTTTTTTCTTTCTT
1 CTTTTCTTCTTTCTT
826127 -TTTTCCTTCCTTTC-T
1 CTTTT-CTT-CTTTCTT
826142 CTTTTCTTCT
1 CTTTTCTTCT
826152 CTCAAAGGTG
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
14 11 0.24
15 22 0.48
16 13 0.28
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (15 bp):
CTTTTCTTCTTTCTT
Found at i:826102 original size:4 final size:4
Alignment explanation
Indices: 826084--826141 Score: 52
Period size: 4 Copynumber: 15.2 Consensus size: 4
826074 TCCTCTAGCT
* *
826084 TTTC -TTC TTTC -TTC TTTC TTTC TTT- TCTC TTTT TTTC TTTC TTT-
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
826128 TTTCC TTCC TTTC T
1 TTT-C TTTC TTTC T
826142 CTTTTCTTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
3 11 0.26
4 30 0.70
5 2 0.05
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTC
Found at i:826122 original size:30 final size:30
Alignment explanation
Indices: 826082--826151 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
826072 CTTCCTCTAG
* *
826082 CTTTTCTTCTTTCTTCTTTCTTTCTTTTCT
1 CTTTTCTTCTTTCTTCTTTCCTTCCTTTCT
* *
826112 CTTTTTTTCTTTCTTTTTTCCTTCCTTTCT
1 CTTTTCTTCTTTCTTCTTTCCTTCCTTTCT
826142 CTTTTCTTCT
1 CTTTTCTTCT
826152 CTCAAAGGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (30 bp):
CTTTTCTTCTTTCTTCTTTCCTTCCTTTCT
Found at i:837982 original size:10 final size:10
Alignment explanation
Indices: 837967--837997 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
837957 TTCCTTGCTT
837967 TTTCTCTCTC
1 TTTCTCTCTC
837977 TTTCTCTCTC
1 TTTCTCTCTC
837987 TTTCTCTCTC
1 TTTCTCTCTC
837997 T
1 T
837998 CTCTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (10 bp):
TTTCTCTCTC
Found at i:838782 original size:35 final size:35
Alignment explanation
Indices: 838742--838820 Score: 113
Period size: 35 Copynumber: 2.3 Consensus size: 35
838732 GGGTCACATG
*
838742 TAACCTCTACAACATACCTTTTGCAAGATCAGGCA
1 TAACCTCTACAACATACCTTTTGCAAGATCAAGCA
* * * *
838777 TAACCTTTACAACATGCCTTTTGTAGGATCAAGCA
1 TAACCTCTACAACATACCTTTTGCAAGATCAAGCA
838812 TAACCTCTA
1 TAACCTCTA
838821 TCAAGACACT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.29
Consensus pattern (35 bp):
TAACCTCTACAACATACCTTTTGCAAGATCAAGCA
Found at i:844893 original size:26 final size:27
Alignment explanation
Indices: 844855--844906 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
844845 CATACAAATA
844855 AATCTTGAAAA-TTA-TTCAAAGGAATC
1 AATCTTGAAAATTTACTT-AAAGGAATC
* *
844881 AATCTTTATAATTTACTTAAAGGAAT
1 AATCTTGAAAATTTACTTAAAGGAAT
844907 TAACTAGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 9 0.41
27 11 0.50
28 2 0.09
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (27 bp):
AATCTTGAAAATTTACTTAAAGGAATC
Found at i:845745 original size:63 final size:62
Alignment explanation
Indices: 845676--845832 Score: 161
Period size: 62 Copynumber: 2.5 Consensus size: 62
845666 ATTATATGGT
* * * *
845676 AAAATTATAAAATTTTTAAAAAATAAAAATATGTTAGAAAAATTTTAAAATTTTTGTAAGGGC
1 AAAATTATAAAATTTTTAAAAAATAAAAATAAG-TAGAAAAATTTAAAAATTATTGGAAGGGC
* * ** *** * *
845739 AAAATTAAAAAATTTCTAAAAAGCAAAGGCAAGTATAAAAATTTAAAAATTATTGGAAGGGT
1 AAAATTATAAAATTTTTAAAAAATAAAAATAAGTAGAAAAATTTAAAAATTATTGGAAGGGC
* * *
845801 GAAATTATAAACTTTTTAAAAAATACAAATAA
1 AAAATTATAAAATTTTTAAAAAATAAAAATAA
845833 ATTTTAAAAA
Statistics
Matches: 71, Mismatches: 23, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
62 46 0.65
63 25 0.35
ACGTcount: A:0.55, C:0.04, G:0.10, T:0.31
Consensus pattern (62 bp):
AAAATTATAAAATTTTTAAAAAATAAAAATAAGTAGAAAAATTTAAAAATTATTGGAAGGGC
Found at i:846952 original size:23 final size:23
Alignment explanation
Indices: 846888--846942 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
846878 CTATGGTGAA
*
846888 AATATGTGAGACA-CCATGGAAGG
1 AATATGTGACA-AGCCATGGAAGG
846911 AATATGTGACAAGCCATGG-AGTG
1 AATATGTGACAAGCCATGGAAG-G
846934 AATATGTGA
1 AATATGTGA
846943 TGTGCCATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 3 0.10
23 26 0.90
ACGTcount: A:0.38, C:0.11, G:0.29, T:0.22
Consensus pattern (23 bp):
AATATGTGACAAGCCATGGAAGG
Found at i:847086 original size:69 final size:68
Alignment explanation
Indices: 846999--847176 Score: 169
Period size: 69 Copynumber: 2.6 Consensus size: 68
846989 CACAACATAG
** * * * *
846999 AGGAAATAAATGAGATGCCATGAATGGAATATGTGACACGTCATGAAAGGAATATGTGACACGTC
1 AGGAAATATGTGACATGCCATG-ATGGAATATGTGACACGACATGAAAGAAATATGTGACACGCC
847064 ATGAA
65 ATG-A
* * * * * * *
847069 AGG-AATATGTGACATGCCATGGTGAGAATAAGTAACAAGACATGGAATAAATATGTGACATGCC
1 AGGAAATATGTGACATGCCATGATG-GAATATGTGACACGACATGAAAGAAATATGTGACACGCC
*
847133 ATGG
65 ATGA
**
847137 AGGAAATATGTGACACACCATGGATGGAATATGTGACACG
1 AGGAAATATGTGACATGCCAT-GATGGAATATGTGACACG
847177 GCTTGGAGGG
Statistics
Matches: 85, Mismatches: 20, Indels: 7
0.76 0.18 0.06
Matches are distributed among these distances:
68 5 0.06
69 74 0.87
70 6 0.07
ACGTcount: A:0.40, C:0.12, G:0.26, T:0.21
Consensus pattern (68 bp):
AGGAAATATGTGACATGCCATGATGGAATATGTGACACGACATGAAAGAAATATGTGACACGCCA
TGA
Found at i:847183 original size:23 final size:23
Alignment explanation
Indices: 847015--847338 Score: 146
Period size: 23 Copynumber: 14.2 Consensus size: 23
847005 TAAATGAGAT
*
847015 GCCATGAATGGAATATGTGACAC
1 GCCATGGATGGAATATGTGACAC
* * *
847038 GTCATGAAAGGAATATGTGACAC
1 GCCATGGATGGAATATGTGACAC
* * * *
847061 GTCATGAAAGGAATATGTGACAT
1 GCCATGGATGGAATATGTGACAC
* * *
847084 GCCATGG-TGAGAATAAGTAACAA
1 GCCATGGATG-GAATATGTGACAC
* * *
847107 GACATGGAAT-AAATATGTGACAT
1 GCCATGG-ATGGAATATGTGACAC
847130 GCCATGGA-GGAAATATGTGACAC
1 GCCATGGATGG-AATATGTGACAC
*
847153 ACCATGGATGGAATATGTGACAC
1 GCCATGGATGGAATATGTGACAC
* * * * *
847176 GGCTTGGAGGGAA-A-ATGCCAC
1 GCCATGGATGGAATATGTGACAC
** *
847197 TTCATGG-TGAGAATATTTGACAC
1 GCCATGGATG-GAATATGTGACAC
* ** * *
847220 ACCATGGGGGGAATATATGACAT
1 GCCATGGATGGAATATGTGACAC
* * * *
847243 GCCATAG-TGAGAATCTTTGAGAC
1 GCCATGGATG-GAATATGTGACAC
** * * * *
847266 ATCACGG-TGGGAATATATAACAT
1 GCCATGGAT-GGAATATGTGACAC
*
847289 GCCATGGAGGGAATATGTGACA-
1 GCCATGGATGGAATATGTGACAC
* *
847311 GCCATGG-TAAGAATATGTGACAT
1 GCCATGGAT-GGAATATGTGACAC
847334 GCCAT
1 GCCAT
847339 AAATTTAAAT
Statistics
Matches: 227, Mismatches: 59, Indels: 30
0.72 0.19 0.09
Matches are distributed among these distances:
20 1 0.00
21 12 0.05
22 24 0.11
23 185 0.81
24 4 0.02
25 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.27, T:0.23
Consensus pattern (23 bp):
GCCATGGATGGAATATGTGACAC
Found at i:856583 original size:70 final size:71
Alignment explanation
Indices: 856505--856672 Score: 175
Period size: 71 Copynumber: 2.4 Consensus size: 71
856495 AAGACTAGTG
* *
856505 TGTAACAATATAAGACTTTAACAAAATGACATGTCA-CAAGAA-ATGTCAACAACATCTAACAAG
1 TGTAACAATATAAGACTTTAACAAAATGACATATAACCAA-AAGATGTCAACAACATCTAACAA-
856568 AA-TGGCA
64 AAGTGGCA
* ** * * * *
856575 TGTAACAATATACGA-TTTGAATGAAATGGCGTATAACCAAAAGATGTCAACGACATCTATCAAA
1 TGTAACAATATAAGACTTT-AACAAAATGACATATAACCAAAAGATGTCAACAACATCTAACAAA
*
856639 AGTGGCG
65 AGTGGCA
*
856646 TGTAACAATATAAGAC-TTCACAAAATG
1 TGTAACAATATAAGACTTTAACAAAATG
856673 GCGTGCAACC
Statistics
Matches: 79, Mismatches: 14, Indels: 10
0.77 0.14 0.10
Matches are distributed among these distances:
69 3 0.04
70 35 0.44
71 41 0.52
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.23
Consensus pattern (71 bp):
TGTAACAATATAAGACTTTAACAAAATGACATATAACCAAAAGATGTCAACAACATCTAACAAAA
GTGGCA
Found at i:856675 original size:30 final size:30
Alignment explanation
Indices: 856635--856774 Score: 138
Period size: 30 Copynumber: 4.6 Consensus size: 30
856625 CGACATCTAT
856635 CAAAAGTGGCGTGTAACAATATAAGACTTCA
1 CAAAA-TGGCGTGTAACAATATAAGACTTCA
* ** *
856666 CAAAATGGCGTGCAACCCTATAAGAGTTCA
1 CAAAATGGCGTGTAACAATATAAGACTTCA
*
856696 CAAAATGGTGTGTAACAATATAAGACTTCAA
1 CAAAATGGCGTGTAACAATATAAGACTTC-A
*** * *
856727 CAAAATTATGTGTAATAATGTAAGACTTCA
1 CAAAATGGCGTGTAACAATATAAGACTTCA
* *
856757 -ACGAATGGCGTGTCACAA
1 CA-AAATGGCGTGTAACAA
856775 GAAGATGTCA
Statistics
Matches: 88, Mismatches: 19, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
29 1 0.01
30 56 0.64
31 31 0.35
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (30 bp):
CAAAATGGCGTGTAACAATATAAGACTTCA
Found at i:856849 original size:69 final size:69
Alignment explanation
Indices: 856751--856948 Score: 227
Period size: 69 Copynumber: 2.8 Consensus size: 69
856741 ATAATGTAAG
** *
856751 ACTTCAACGAATGGCGTGTCACAAGAAGATGTCAATGACATCTAGCAAGAATGGCATGTAACAAA
1 ACTTCAA-GAATGATGTGTCACAAGAAGATGTCAATGACATCTAACAAGAATGGCATGTAACAAA
856816 ATAAA
65 ATAAA
* * ** * *
856821 ACTTCAAGAATGATGTGTGACAAGAAGATGTCAATTACATCTAACAAGAATGGTGTGTGACAATA
1 ACTTCAAGAATGATGTGTCACAAGAAGATGTCAATGACATCTAACAAGAATGGCATGTAACAAAA
*
856886 TAAG
66 TAAA
* * * *
856890 ACTTCAACAA-AATGGCTTGTCACAAGAAGATGTAAATGACATCTAACAAAAATGGCATG
1 ACTTCAAGAATGAT-G--TGTCACAAGAAGATGTCAATGACATCTAACAAGAATGGCATG
856949 CAATAACATA
Statistics
Matches: 107, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
68 2 0.02
69 62 0.58
70 7 0.07
71 36 0.34
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (69 bp):
ACTTCAAGAATGATGTGTCACAAGAAGATGTCAATGACATCTAACAAGAATGGCATGTAACAAAA
TAAA
Found at i:856932 original size:71 final size:71
Alignment explanation
Indices: 856737--857044 Score: 293
Period size: 71 Copynumber: 4.4 Consensus size: 71
856727 CAAAATTATG
* * * * *
856737 TGTAATAATGTAAGACTTCAAC-GAATGGCGTGTCACAAGAAGATGTCAATGACATCTAGCAAGA
1 TGTAACAATATAAGACTTCAACAAAATGGCGTGTCACAAGAAGATGTAAATGACATCTAACAAGA
856801 ATGGCA
66 ATGGCA
* * * ** * * *
856807 TGTAACAAAATAAAACTTC-A-AGAATGATGTGTGACAAGAAGATGTCAATTACATCTAACAAGA
1 TGTAACAATATAAGACTTCAACAAAATGGCGTGTCACAAGAAGATGTAAATGACATCTAACAAGA
**
856870 ATGGTG
66 ATGGCA
* * *
856876 TGTGACAATATAAGACTTCAACAAAATGGCTTGTCACAAGAAGATGTAAATGACATCTAACAAAA
1 TGTAACAATATAAGACTTCAACAAAATGGCGTGTCACAAGAAGATGTAAATGACATCTAACAAGA
856941 ATGGCA
66 ATGGCA
* * * * * * * * * * *
856947 TGCAATAACATAAGATTTCAGCGAAATGGCGTGTAACTAGAAAATG-ATAATGACATCCATCAAG
1 TGTAACAATATAAGACTTCAACAAAATGGCGTGTCACAAGAAGATGTA-AATGACATCTAACAAG
*
857011 CATGGCA
65 AATGGCA
*
857018 TGCAACAATATAAGACTTC-ACAAAATG
1 TGTAACAATATAAGACTTCAACAAAATG
857045 CTATGTAACC
Statistics
Matches: 190, Mismatches: 44, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
69 58 0.31
70 23 0.12
71 109 0.57
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.23
Consensus pattern (71 bp):
TGTAACAATATAAGACTTCAACAAAATGGCGTGTCACAAGAAGATGTAAATGACATCTAACAAGA
ATGGCA
Found at i:857163 original size:71 final size:69
Alignment explanation
Indices: 857078--857371 Score: 229
Period size: 67 Copynumber: 4.3 Consensus size: 69
857068 ACGAAATGTG
** * * * *
857078 TGTAACAAGGTAAGACTTCGACAAAATGGCATGTCACAAGAAGATGTAAACAGCATTTAACAAGA
1 TGTAACAATATAAGACTTC-ATAAAATGGCATGTCAC-AGAAGATGTCAACAGCATTTATCAAGC
*
857143 ATAGCA
64 ATGGCA
* * * * * *
857149 TGTAACAATATAAGACTTCAATGAAATGGCGTGTAACTAGAAGATCTCAA-TGACATCTATCAAG
1 TGTAACAATATAAGACTTC-ATAAAATGGCATGTCAC-AGAAGATGTCAACAG-CATTTATCAAG
**
857213 CATGGTG
63 CATGGCA
* ** *
857220 TGTAACAATATAAGACTTCATTAAATGATATGTCAC--AAGATGTCAACAACATTTATCAAGCAT
1 TGTAACAATATAAGACTTCATAAAATGGCATGTCACAGAAGATGTCAACAGCATTTATCAAGCAT
857283 GGCA
66 GGCA
* * * * * * * * *
857287 TGTAACAATATAAAACTTCATGATATGGCGTGTCAC--AAGATATCAACAACATCTAACAAGCTT
1 TGTAACAATATAAGACTTCATAAAATGGCATGTCACAGAAGATGTCAACAGCATTTATCAAGCAT
**
857350 GGTG
66 GGCA
*
857354 TGTAACAATATAATACTT
1 TGTAACAATATAAGACTT
857372 TTTCAAATGA
Statistics
Matches: 180, Mismatches: 41, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
67 96 0.53
70 13 0.07
71 71 0.39
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (69 bp):
TGTAACAATATAAGACTTCATAAAATGGCATGTCACAGAAGATGTCAACAGCATTTATCAAGCAT
GGCA
Found at i:857291 original size:67 final size:67
Alignment explanation
Indices: 857118--857371 Score: 247
Period size: 67 Copynumber: 3.7 Consensus size: 67
857108 ATGTCACAAG
* * * * *
857118 AAGATGTAAACAGCATTTAACAAGAATAGCATGTAACAATATAAGACTTCAATGAAATGGCGTGT
1 AAGATGTCAACAACATCTAACAAGCATGGCATGTAACAATATAAGACTTC-ATGAAATGGCGTGT
*
857183 AACTAG
65 --C-AC
* ** * ** * ***
857189 AAGATCTCAATGACATCTATCAAGCATGGTGTGTAACAATATAAGACTTCATTAAATGATATGTC
1 AAGATGTCAACAACATCTAACAAGCATGGCATGTAACAATATAAGACTTCATGAAATGGCGTGTC
857254 AC
66 AC
* * * *
857256 AAGATGTCAACAACATTTATCAAGCATGGCATGTAACAATATAAAACTTCATGATATGGCGTGTC
1 AAGATGTCAACAACATCTAACAAGCATGGCATGTAACAATATAAGACTTCATGAAATGGCGTGTC
857321 AC
66 AC
* * ** *
857323 AAGATATCAACAACATCTAACAAGCTTGGTGTGTAACAATATAATACTT
1 AAGATGTCAACAACATCTAACAAGCATGGCATGTAACAATATAAGACTT
857372 TTTCAAATGA
Statistics
Matches: 148, Mismatches: 35, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
67 98 0.66
68 1 0.01
70 10 0.07
71 39 0.26
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (67 bp):
AAGATGTCAACAACATCTAACAAGCATGGCATGTAACAATATAAGACTTCATGAAATGGCGTGTC
AC
Found at i:857381 original size:134 final size:137
Alignment explanation
Indices: 857118--857371 Score: 352
Period size: 134 Copynumber: 1.9 Consensus size: 137
857108 ATGTCACAAG
* *
857118 AAGATGTAAACAGCATTTAACAAGAATAGCATGTAACAATATAAGACTTCAATGAAATGGCGTGT
1 AAGATGTAAACAACATTTAACAAGAATAGCATGTAACAATATAAAACTTCAATGAAATGGCGTGT
* * ** *
857183 AACTAGAAGATCTCAATGACATCTATCAAGCATGGTGTGTAACAATATAAGACTTCATTAAATGA
66 -ACTACAAGATATCAACAACATCTAACAAGCATGGTGTGTAACAATATAAGACTTCATTAAATGA
857248 TATGTCAC
130 TATGTCAC
* * * * *
857256 AAGATGTCAACAACATTTATCAAGCATGGCATGTAACAATATAAAACTTC-ATGATATGGCGTGT
1 AAGATGTAAACAACATTTAACAAGAATAGCATGTAACAATATAAAACTTCAATGAAATGGCGTGT
* *
857320 -C-ACAAGATATCAACAACATCTAACAAGCTTGGTGTGTAACAATATAATACTT
66 ACTACAAGATATCAACAACATCTAACAAGCATGGTGTGTAACAATATAAGACTT
857372 TTTCAAATGA
Statistics
Matches: 102, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
134 44 0.43
135 1 0.01
137 13 0.13
138 44 0.43
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (137 bp):
AAGATGTAAACAACATTTAACAAGAATAGCATGTAACAATATAAAACTTCAATGAAATGGCGTGT
ACTACAAGATATCAACAACATCTAACAAGCATGGTGTGTAACAATATAAGACTTCATTAAATGAT
ATGTCAC
Found at i:857386 original size:67 final size:66
Alignment explanation
Indices: 857201--857393 Score: 224
Period size: 67 Copynumber: 2.9 Consensus size: 66
857191 GATCTCAATG
* ** *
857201 ACATCTATCAAGCATGGTGTGTAACAATATAAGACTTCATTAAATGATATGTCACAAGATGTCAA
1 ACATCTATCAAGCATGGTGTGTAACAATATAAAACTT-ATTAAATGACGTGTCACAAGATATCAA
857266 CA
65 CA
* ** * * *
857268 ACATTTATCAAGCATGGCATGTAACAATATAAAACTTCATGATATGGCGTGTCACAAGATATCAA
1 ACATCTATCAAGCATGGTGTGTAACAATATAAAACTT-ATTAAATGACGTGTCACAAGATATCAA
857333 CA
65 CA
* * * * *
857335 ACATCTAACAAGCTTGGTGTGTAACAATATAATACTTTTTCAAATGACGTGTAACAAGA
1 ACATCTATCAAGCATGGTGTGTAACAATATAAAACTTATT-AAATGACGTGTCACAAGA
857394 CGATGTTACC
Statistics
Matches: 104, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
66 1 0.01
67 103 0.99
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.28
Consensus pattern (66 bp):
ACATCTATCAAGCATGGTGTGTAACAATATAAAACTTATTAAATGACGTGTCACAAGATATCAAC
A
Found at i:857392 original size:134 final size:137
Alignment explanation
Indices: 857118--857431 Score: 348
Period size: 138 Copynumber: 2.3 Consensus size: 137
857108 ATGTCACAAG
* *
857118 AAGATGTAAACAGCATTTAACAAGAATAGCATGTAACAATATAAGACTTCAATGAAATGGCGTGT
1 AAGATGTAAACAACATTTAACAAGAATAGCATGTAACAATATAAAACTTCAATGAAATGGCGTGT
* * ** *
857183 AACTAGAAGATCTCAATGACATCTATCAAGCATGGTGTGTAACAATATAAGACTTCATTAAATGA
66 -ACTACAAGATATCAACAACATCTAACAAGCATGGTGTGTAACAATATAAGACTTCATTAAATGA
* *
857248 TATGTCAC
130 CATGTAAC
* * * * *
857256 AAGATGTCAACAACATTTATCAAGCATGGCATGTAACAATATAAAACTTC-ATGATATGGCGTGT
1 AAGATGTAAACAACATTTAACAAGAATAGCATGTAACAATATAAAACTTCAATGAAATGGCGTGT
* * *
857320 -C-ACAAGATATCAACAACATCTAACAAGCTTGGTGTGTAACAATATAATACTT-TTTCAAATGA
66 ACTACAAGATATCAACAACATCTAACAAGCATGGTGTGTAACAATATAAGACTTCATT-AAATGA
*
857382 CGTGTAAC
130 CATGTAAC
* * * *
857390 AAGACGATGTTACCAACATTTAACAAGCCATAACATGTAACA
1 -A-A-GATGTAAACAACATTTAACAAG-AATAGCATGTAACA
857432 CTGTATGAGT
Statistics
Matches: 148, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
133 2 0.01
134 55 0.37
135 2 0.01
136 1 0.01
137 32 0.22
138 56 0.38
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (137 bp):
AAGATGTAAACAACATTTAACAAGAATAGCATGTAACAATATAAAACTTCAATGAAATGGCGTGT
ACTACAAGATATCAACAACATCTAACAAGCATGGTGTGTAACAATATAAGACTTCATTAAATGAC
ATGTAAC
Found at i:859120 original size:20 final size:18
Alignment explanation
Indices: 859088--859142 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 18
859078 TTTGTAATGT
859088 TATAATAAAAATAAAATA
1 TATAATAAAAATAAAATA
*
859106 TATAATATAAGAATAAAAAA
1 TATAATA-AA-AATAAAATA
*
859126 TAAAATAAAATATAAAA
1 TATAATAAAA-ATAAAA
859143 AATTAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 8 0.25
19 10 0.31
20 14 0.44
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (18 bp):
TATAATAAAAATAAAATA
Found at i:859143 original size:20 final size:19
Alignment explanation
Indices: 859091--859151 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 19
859081 GTAATGTTAT
*
859091 AATAAAAATAAAATATATAA
1 AATAAAAATAAAA-AAATAA
* *
859111 TATAAGAAT-AAAAAATAA
1 AATAAAAATAAAAAAATAA
*
859129 AATAAAATATAAAAAATTAA
1 AATAAAA-ATAAAAAAATAA
859149 AAT
1 AAT
859152 TTATATAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 10 0.30
19 5 0.15
20 18 0.55
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.25
Consensus pattern (19 bp):
AATAAAAATAAAAAAATAA
Found at i:859150 original size:27 final size:27
Alignment explanation
Indices: 859094--859143 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
859084 ATGTTATAAT
*
859094 AAAAATAAAATATATAATATAAGAATA
1 AAAAATAAAATATATAATATAAAAATA
859121 AAAAATAAAATA-A-AATATAAAAA
1 AAAAATAAAATATATAATATAAAAA
859144 ATTAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.41
26 1 0.05
27 12 0.55
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (27 bp):
AAAAATAAAATATATAATATAAAAATA
Found at i:859252 original size:33 final size:34
Alignment explanation
Indices: 859201--859264 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 34
859191 AATATCAAAA
*
859201 ATTATATTAAAGAAATGAAAATAAAATATATAAG
1 ATTATAATAAAGAAATGAAAATAAAATATATAAG
859235 ATTATAAT-AAGAAATGAAAATAAAATATAT
1 ATTATAATAAAGAAATGAAAATAAAATATAT
859265 GCAATTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 22 0.76
34 7 0.24
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.30
Consensus pattern (34 bp):
ATTATAATAAAGAAATGAAAATAAAATATATAAG
Found at i:863155 original size:26 final size:26
Alignment explanation
Indices: 863126--863176 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
863116 GACAAAGACC
*
863126 GATGCCGTCATGATAAAGACAGATGA
1 GATGCCGTCATGACAAAGACAGATGA
* *
863152 GATGCCTTCATGACGAAGACAGATG
1 GATGCCGTCATGACAAAGACAGATG
863177 CCTTCATAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (26 bp):
GATGCCGTCATGACAAAGACAGATGA
Found at i:863177 original size:21 final size:21
Alignment explanation
Indices: 863151--863197 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
863141 AAGACAGATG
* *
863151 AGATGCCTTCATGACGAAGAC
1 AGATGCCTTCATAACAAAGAC
863172 AGATGCCTTCATAACAAAGAC
1 AGATGCCTTCATAACAAAGAC
*
863193 TGATG
1 AGATG
863198 GCATCATTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (21 bp):
AGATGCCTTCATAACAAAGAC
Found at i:865091 original size:21 final size:21
Alignment explanation
Indices: 865067--865109 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
865057 TATATTTTTC
*
865067 CTTAAGTTCATGATTGATAGA
1 CTTAAGTTAATGATTGATAGA
865088 CTTAAGTTAATGATTGATAGA
1 CTTAAGTTAATGATTGATAGA
865109 C
1 C
865110 ATGCTTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.37
Consensus pattern (21 bp):
CTTAAGTTAATGATTGATAGA
Found at i:867161 original size:23 final size:23
Alignment explanation
Indices: 867133--867208 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
867123 ATTCAAATAA
* *
867133 ATGTTACACGTCATGTTGACAAC
1 ATGTTACATGCCATGTTGACAAC
* *
867156 ATGTTACATGCCATGTTCA-AAA
1 ATGTTACATGCCATGTTGACAAC
*
867178 ATTGTTACATGCCATTTTGACAAC
1 A-TGTTACATGCCATGTTGACAAC
*
867202 ATTTTAC
1 ATGTTAC
867209 TACCCACCAT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
22 3 0.07
23 37 0.86
24 3 0.07
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.36
Consensus pattern (23 bp):
ATGTTACATGCCATGTTGACAAC
Found at i:867198 original size:46 final size:47
Alignment explanation
Indices: 867119--867208 Score: 119
Period size: 46 Copynumber: 1.9 Consensus size: 47
867109 TTATTACACA
*
867119 CCATATTCAAATAAATGTTACACGTCATGTTGACAACATGTTACATG
1 CCATATTCAAATAAATGTTACACGCCATGTTGACAACATGTTACATG
* * * * *
867166 CCATGTTCAAA-AATTGTTACATGCCATTTTGACAACATTTTAC
1 CCATATTCAAATAAATGTTACACGCCATGTTGACAACATGTTAC
867209 TACCCACCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
46 27 0.73
47 10 0.27
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (47 bp):
CCATATTCAAATAAATGTTACACGCCATGTTGACAACATGTTACATG
Found at i:868272 original size:19 final size:19
Alignment explanation
Indices: 868248--868285 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
868238 AAAATATTTT
868248 TGAATAAAATAATATTAAA
1 TGAATAAAATAATATTAAA
868267 TGAATAAAATAATATTAAA
1 TGAATAAAATAATATTAAA
868286 ATATTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
TGAATAAAATAATATTAAA
Found at i:874350 original size:18 final size:18
Alignment explanation
Indices: 874327--874365 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
874317 ATTTTTTATT
* *
874327 TTTATTATAAATATAAAA
1 TTTATTAGAAATAAAAAA
*
874345 TTTATTAGCAATAAAAAA
1 TTTATTAGAAATAAAAAA
874363 TTT
1 TTT
874366 GGAAGAAAGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (18 bp):
TTTATTAGAAATAAAAAA
Found at i:874806 original size:17 final size:18
Alignment explanation
Indices: 874778--874811 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
874768 AGTGAAAAAG
*
874778 AAATTCAAATCATTTTCA
1 AAATTCAAATCAGTTTCA
874796 AAATT-AAATCAGTTTC
1 AAATTCAAATCAGTTTC
874812 GTTTGAGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (18 bp):
AAATTCAAATCAGTTTCA
Found at i:875527 original size:3 final size:3
Alignment explanation
Indices: 875519--875557 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
875509 AACTAAACTA
875519 AAT 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 AAT
875558 TCATATCTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:911370 original size:6 final size:6
Alignment explanation
Indices: 911354--911398 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
911344 AGTTTCTTTG
* * *
911354 TCTTTA TCTTCA TCTTCA ACTTCA TCTTCA TCTTCA TTTTCA TCT
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCT
911399 CCTTCCATGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.18, C:0.29, G:0.00, T:0.53
Consensus pattern (6 bp):
TCTTCA
Found at i:911418 original size:30 final size:30
Alignment explanation
Indices: 911384--911451 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
911374 TTCATCTTCA
* * *
911384 TCTTCATTTTCATCTCCTTCCATGCCATCT
1 TCTTCATCTTCATATCCCTCCATGCCATCT
* * *
911414 TCTTCATCTTCGTATCCCTGCATGTCATCT
1 TCTTCATCTTCATATCCCTCCATGCCATCT
911444 TCTTCATC
1 TCTTCATC
911452 CTGAATCAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.13, C:0.35, G:0.06, T:0.46
Consensus pattern (30 bp):
TCTTCATCTTCATATCCCTCCATGCCATCT
Found at i:923410 original size:79 final size:77
Alignment explanation
Indices: 923317--923471 Score: 274
Period size: 79 Copynumber: 2.0 Consensus size: 77
923307 ACTCAGTTGT
* *
923317 AAAATTTAATACTCATACCTTAACCAAACCCAATTAACAATATCTATTAAAATCCAATTAAACCA
1 AAAATTTAAAACTCATACCTTAACCAAACCCAATTAACAATATCTATTAAAACCCAATT-AACCA
923382 AACACATTTATTA
65 AACACATTTATTA
923395 AAAATTTTAAAACTCATACCTTAACCAAACCCAATTAACAATATCTATTAAAACCCAATTAACCA
1 AAAA-TTTAAAACTCATACCTTAACCAAACCCAATTAACAATATCTATTAAAACCCAATTAACCA
923460 AACACATTTATT
65 AACACATTTATT
923472 TAGTTAAAAA
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
78 21 0.28
79 53 0.72
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (77 bp):
AAAATTTAAAACTCATACCTTAACCAAACCCAATTAACAATATCTATTAAAACCCAATTAACCAA
ACACATTTATTA
Found at i:923460 original size:38 final size:38
Alignment explanation
Indices: 923336--923462 Score: 136
Period size: 38 Copynumber: 3.3 Consensus size: 38
923326 TACTCATACC
*
923336 TTAACCAAACCCAATTAACAATATCTATTAAAATCCAA
1 TTAACCAAACCCAATTAACAATATCTATTAAAACCCAA
* *
923374 TTAAACCAAACACATTTATTAA-AA-AT-T-TTAAAACTCATA
1 TT-AACCAAACCCA---ATTAACAATATCTATTAAAACCCA-A
923413 CCTTAACCAAACCCAATTAACAATATCTATTAAAACCCAA
1 --TTAACCAAACCCAATTAACAATATCTATTAAAACCCAA
923453 TTAACCAAAC
1 TTAACCAAAC
923463 ACATTTATTT
Statistics
Matches: 73, Mismatches: 5, Indels: 22
0.73 0.05 0.22
Matches are distributed among these distances:
37 5 0.07
38 22 0.30
39 14 0.19
40 14 0.19
41 13 0.18
42 5 0.07
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.27
Consensus pattern (38 bp):
TTAACCAAACCCAATTAACAATATCTATTAAAACCCAA
Found at i:924799 original size:23 final size:23
Alignment explanation
Indices: 924750--924868 Score: 132
Period size: 23 Copynumber: 5.2 Consensus size: 23
924740 ACAAAATTTT
* *
924750 GAATCACGTGACTAGT-TATATG
1 GAATCGCGTGACTAGTAAATATG
* * *
924772 CAATCGCGTAACTAGTTAATATG
1 GAATCGCGTGACTAGTAAATATG
* * *
924795 GAATCGTGTGAGTAGCAAATATG
1 GAATCGCGTGACTAGTAAATATG
*
924818 GAATCGCGTGAGTAGTAAATATG
1 GAATCGCGTGACTAGTAAATATG
* *
924841 GAATCGCATGATTAGTAAATATG
1 GAATCGCGTGACTAGTAAATATG
924864 GAATC
1 GAATC
924869 ATACGAGTAT
Statistics
Matches: 82, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
22 13 0.16
23 69 0.84
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (23 bp):
GAATCGCGTGACTAGTAAATATG
Found at i:924877 original size:46 final size:46
Alignment explanation
Indices: 924784--924906 Score: 120
Period size: 46 Copynumber: 2.7 Consensus size: 46
924774 ATCGCGTAAC
** * * * **
924784 TAGTTAATATGGAATCGTGTGAGTAGCAAATATGGAATCGCGTGAG
1 TAGTTAATATGGAATCGCATGACTAGTAAATATGGAATCACACGAG
* * *
924830 TAGTAAATATGGAATCGCATGATTAGTAAATATGGAATCATACGAG
1 TAGTTAATATGGAATCGCATGACTAGTAAATATGGAATCACACGAG
* * * *
924876 TATTTGATATGGAATCACATGACTACTAAAT
1 TAGTTAATATGGAATCGCATGACTAGTAAAT
924907 TTTGAAGGAT
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (46 bp):
TAGTTAATATGGAATCGCATGACTAGTAAATATGGAATCACACGAG
Found at i:924877 original size:69 final size:68
Alignment explanation
Indices: 924722--924900 Score: 162
Period size: 69 Copynumber: 2.6 Consensus size: 68
924712 CGAGTATTTG
* * * * *
924722 ATATGGAATCACGCGAGTACAAAATTTTGAATCACGTGACTAGTTATATGCAATCGCGTAACTAG
1 ATATGGAATCATGCGAGTACAAAATATGGAATCACGTGACTAGTAATATGCAATCGCATAACTAG
*
924787 TTA
66 TAA
* * * * * * *
924790 ATATGGAATCGTGTGAGTAGC-AAATATGGAATCGCGTGAGTAGTAAATATGGAATCGCATGATT
1 ATATGGAATCATGCGAGTA-CAAAATATGGAATCACGTGACTAGT-AATATGCAATCGCATAACT
924854 AGTAA
64 AGTAA
* **** *
924859 ATATGGAATCATACGAGTATTTGATATGGAATCACATGACTA
1 ATATGGAATCATGCGAGTACAAAATATGGAATCACGTGACTA
924901 CTAAATTTTG
Statistics
Matches: 86, Mismatches: 22, Indels: 5
0.76 0.19 0.04
Matches are distributed among these distances:
68 35 0.41
69 51 0.59
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.29
Consensus pattern (68 bp):
ATATGGAATCATGCGAGTACAAAATATGGAATCACGTGACTAGTAATATGCAATCGCATAACTAG
TAA
Found at i:929376 original size:202 final size:204
Alignment explanation
Indices: 928880--929388 Score: 671
Period size: 205 Copynumber: 2.5 Consensus size: 204
928870 AGGCCTCCCC
* * * * * * *
928880 ATATTATGCATTGTGTGAGTTATTATTAGGTATTGCGATAGTGGAGGTGCGTGACTTGTGTAATT
1 ATATTATGCATTGAGTGACTTATTATTAAGTATTGCGAGAATGGCGGTGCGTGACTTGTGCAATT
* * * *
928945 CATCCCTTGTTTTGAGGCTTTTTTTCACTAGTTTGTAGACTTTACGTGACTAGTTTTTATGTATT
66 CATCACTTGTTTTGAGGCTTTTGTTCACTAGTTTTTAGACGTTACGTGACTAGTTTTTATGTATT
** * * ** * ** *
929010 GTGTGACCTGTTGTTATTTTTTGTGTGGCATTGGGCTGTTATGTGACTGGTTCTGTTGGCATAAT
131 GCATAACCTGTTGTTATGTTTTGTGTGGCATTGGGCCATTACGTGACTGGTTAAGTTAGCATAA-
929075 GTGTGAGTGG
195 GTGTGAGTGG
* * * * * *
929085 ATGTTACGCATTGAGTGACTTGTTATTATGTATTGCGAGACTGACGGTGCGTGACTTGTGCAATT
1 ATATTATGCATTGAGTGACTTATTATTAAGTATTGCGAGAATGGCGGTGCGTGACTTGTGCAATT
* *
929150 CATCACTTGTTTTGAGGCTTTTGTTAACTAGTTTTTAGACGTTACTTGAC-AGTTTTTATGTATT
66 CATCACTTGTTTTGAGGCTTTTGTTCACTAGTTTTTAGACGTTACGTGACTAGTTTTTATGTATT
929214 GCATAACCTGTTGTTATGTTTTGTGTGGCATTGGGCCATTACGTGACTGGTTAAGTTAGCATAA-
131 GCATAACCTGTTGTTATGTTTTGTGTGGCATTGGGCCATTACGTGACTGGTTAAGTTAGCATAAG
929278 TGTGAGTGG
196 TGTGAGTGG
* ** *
929287 ATATTATGCATTGAGTGACTTATTATTAAGTATTGCAAGAATGGCGGTGTATGGCTTGTGCAATT
1 ATATTATGCATTGAGTGACTTATTATTAAGTATTGCGAGAATGGCGGTGCGTGACTTGTGCAATT
** *
929352 CATCTTTTGTTTTTAGGCTTTTGTTCACTAGTTTTTA
66 CATCACTTGTTTTGAGGCTTTTGTTCACTAGTTTTTA
929389 AGGTCTGCAT
Statistics
Matches: 263, Mismatches: 41, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
202 97 0.37
204 68 0.26
205 98 0.37
ACGTcount: A:0.20, C:0.11, G:0.25, T:0.44
Consensus pattern (204 bp):
ATATTATGCATTGAGTGACTTATTATTAAGTATTGCGAGAATGGCGGTGCGTGACTTGTGCAATT
CATCACTTGTTTTGAGGCTTTTGTTCACTAGTTTTTAGACGTTACGTGACTAGTTTTTATGTATT
GCATAACCTGTTGTTATGTTTTGTGTGGCATTGGGCCATTACGTGACTGGTTAAGTTAGCATAAG
TGTGAGTGG
Found at i:930525 original size:28 final size:28
Alignment explanation
Indices: 930494--930578 Score: 118
Period size: 28 Copynumber: 3.0 Consensus size: 28
930484 AATGTCGATA
* *
930494 TAAGTGTAATTAAGGGGGCCGAATTGGT
1 TAAGTGCAATTAAGGGGGCTGAATTGGT
930522 TAAGTGCAATTAAGGGGGCTGAATTGGT
1 TAAGTGCAATTAAGGGGGCTGAATTGGT
* *
930550 TCAA-TGCAATTAAAGGGGTTGAATTGGT
1 T-AAGTGCAATTAAGGGGGCTGAATTGGT
930578 T
1 T
930579 GAATCAGTAG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
28 50 0.96
29 2 0.04
ACGTcount: A:0.29, C:0.07, G:0.33, T:0.31
Consensus pattern (28 bp):
TAAGTGCAATTAAGGGGGCTGAATTGGT
Found at i:930998 original size:38 final size:38
Alignment explanation
Indices: 930945--931017 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
930935 GTTGGATGGC
* *
930945 GATATAGACCTCGATGGTGTTGGAGAGCTAGACGGTGA
1 GATATAGACCCCGATGGTGTTAGAGAGCTAGACGGTGA
* *
930983 GATATATACCCCGATGGTGTTAGAGATCTAGACGG
1 GATATAGACCCCGATGGTGTTAGAGAGCTAGACGG
931018 AGGGATAGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.25
Consensus pattern (38 bp):
GATATAGACCCCGATGGTGTTAGAGAGCTAGACGGTGA
Found at i:931717 original size:2 final size:2
Alignment explanation
Indices: 931710--931735 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
931700 TCTCATATGC
931710 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
931736 TAACTTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:931835 original size:2 final size:2
Alignment explanation
Indices: 931830--931876 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
931820 AATACAGGTT
931830 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
931872 TA TA T
1 TA TA T
931877 TCTATAGCTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:932654 original size:12 final size:13
Alignment explanation
Indices: 932638--932692 Score: 51
Period size: 15 Copynumber: 4.2 Consensus size: 13
932628 AAATTCACAA
*
932638 AAATTTCTATTGG
1 AAATTTCCATTGG
932651 -AA-TTCCATTGG
1 AAATTTCCATTGG
*
932662 AAATTTCCAATGG
1 AAATTTCCATTGG
*
932675 TATATTTTCCATTGG
1 -A-AATTTCCATTGG
932690 AAA
1 AAA
932693 AAATCTATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
11 8 0.24
12 4 0.12
13 9 0.27
14 2 0.06
15 10 0.30
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.40
Consensus pattern (13 bp):
AAATTTCCATTGG
Found at i:933201 original size:20 final size:20
Alignment explanation
Indices: 933178--933220 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
933168 TAAATTTCAT
* *
933178 AATCTATTGATACATTACCA
1 AATCTATTGATAAATGACCA
933198 AATCTATTGATAAATGACCA
1 AATCTATTGATAAATGACCA
933218 AAT
1 AAT
933221 TTATCGCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (20 bp):
AATCTATTGATAAATGACCA
Found at i:934357 original size:12 final size:12
Alignment explanation
Indices: 934340--934372 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
934330 CAAGTATGTA
934340 AATGGTTAATAG
1 AATGGTTAATAG
934352 AATGGTTAATAG
1 AATGGTTAATAG
*
934364 AATGATTAA
1 AATGGTTAA
934373 ATGATTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.33
Consensus pattern (12 bp):
AATGGTTAATAG
Found at i:944807 original size:22 final size:22
Alignment explanation
Indices: 944759--944807 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
944749 GGTATGACAT
* * *
944759 TGAAAAAAAAAAAGAGAAAATG
1 TGAAGAAAAAAAAGAAAAAATA
* *
944781 GGAAGAAAAAGAAGAAAAAATA
1 TGAAGAAAAAAAAGAAAAAATA
944803 TGAAG
1 TGAAG
944808 TGTTGAAGAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.08
Consensus pattern (22 bp):
TGAAGAAAAAAAAGAAAAAATA
Found at i:947758 original size:24 final size:25
Alignment explanation
Indices: 947723--947775 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
947713 AAAGTAGAAA
947723 AAATCTAAAAAGAATAATAAA-AAG
1 AAATCTAAAAAGAATAATAAATAAG
*
947747 AAAT-TAATAAAGAATTATAAATAAG
1 AAATCTAA-AAAGAATAATAAATAAG
947772 AAAT
1 AAAT
947776 AAAATAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 3 0.12
24 16 0.62
25 7 0.27
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.23
Consensus pattern (25 bp):
AAATCTAAAAAGAATAATAAATAAG
Found at i:947793 original size:26 final size:24
Alignment explanation
Indices: 947730--947786 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
947720 AAAAAATCTA
* *
947730 AAAAGAATAATAAAAAGAAATTAAT
1 AAAA-AATTATAAAAAGAAATAAAT
*
947755 AAAGAATTATAAATAAGAAATAAAAT
1 AAAAAATTATAAA-AAGAAAT-AAAT
947781 AAAAAA
1 AAAAAA
947787 CTTTAAAGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 8 0.31
25 10 0.38
26 8 0.31
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (24 bp):
AAAAAATTATAAAAAGAAATAAAT
Found at i:948898 original size:18 final size:18
Alignment explanation
Indices: 948875--948909 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
948865 TTCACCAGAA
948875 TTTTCAACTAG-AATTTCT
1 TTTTCAA-TAGTAATTTCT
948893 TTTTCAATAGTAATTTC
1 TTTTCAATAGTAATTTC
948910 AACTTCTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.29, C:0.14, G:0.06, T:0.51
Consensus pattern (18 bp):
TTTTCAATAGTAATTTCT
Found at i:951014 original size:77 final size:75
Alignment explanation
Indices: 950884--951101 Score: 242
Period size: 77 Copynumber: 2.8 Consensus size: 75
950874 CATCTACTTT
* * *
950884 AATTTTGAGTGATTCATAAA-AAGTCAGAAATTGTTTCGTACTTTAAAGTAAATTTC-TAAAATT
1 AATTTTGGGTGATTCATAAAGAA-T-AGAAATTGTTTCCTACTTTAAA--AAAATTCATAAAATT
950947 AAGAATAAAATTTC
62 AAGAATAAAATTTC
* * *
950961 AATTTTGGGTGATTCATAAAGAATAGGAAATTGTTTCTTACTTTTAAAAAAATTCTTAAAATTTA
1 AATTTTGGGTGATTCATAAAGAATA-GAAATTGTTTCCTAC-TTTAAAAAAATTCATAAAATTAA
* * *
951026 GGATAGAATTTT
64 GAATAAAATTTC
* * *
951038 AATTTTGGGTGATTTATAAAGAATATAAAATGGTTTCCTACTTTAAAAGAAATTCATAAAATTA
1 AATTTTGGGTGATTCATAAAGAATA-GAAATTGTTTCCTACTTTAAAA-AAATTCATAAAATTA
951102 TGTGATAGCA
Statistics
Matches: 122, Mismatches: 14, Indels: 10
0.84 0.10 0.07
Matches are distributed among these distances:
76 14 0.11
77 100 0.82
78 8 0.07
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (75 bp):
AATTTTGGGTGATTCATAAAGAATAGAAATTGTTTCCTACTTTAAAAAAATTCATAAAATTAAGA
ATAAAATTTC
Found at i:951288 original size:28 final size:28
Alignment explanation
Indices: 951248--951311 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
951238 AGGTTTCCAA
951248 AATTAAAAGGAGTTTTAATTATGGAAAG
1 AATTAAAAGGAGTTTTAATTATGGAAAG
951276 AATTAAAAGGAGTTTTAATTATGGAAAG
1 AATTAAAAGGAGTTTTAATTATGGAAAG
951304 AATTAAAA
1 AATTAAAA
951312 TGAAAAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (28 bp):
AATTAAAAGGAGTTTTAATTATGGAAAG
Found at i:953236 original size:24 final size:26
Alignment explanation
Indices: 953209--953262 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
953199 TTCCTTTATT
*
953209 ATGAATC-A-AAAGTAAATTAATAAG
1 ATGAATCAATAAAATAAATTAATAAG
*
953233 ATGACTCAGATAAAATAAATTAATAAG
1 ATGAATCA-ATAAAATAAATTAATAAG
953260 ATG
1 ATG
953263 GCTTAGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.24
26 1 0.04
27 18 0.72
ACGTcount: A:0.56, C:0.06, G:0.13, T:0.26
Consensus pattern (26 bp):
ATGAATCAATAAAATAAATTAATAAG
Found at i:953251 original size:27 final size:27
Alignment explanation
Indices: 953216--953275 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
953206 ATTATGAATC
953216 AAAAGTAAATTAATAAGATGACTCAGAT
1 AAAA-TAAATTAATAAGATGACTCAGAT
* *
953244 AAAATAAATTAATAAGATGGCTTAGAT
1 AAAATAAATTAATAAGATGACTCAGAT
953271 AAAAT
1 AAAAT
953276 TAGGTCTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 26 0.87
28 4 0.13
ACGTcount: A:0.55, C:0.05, G:0.13, T:0.27
Consensus pattern (27 bp):
AAAATAAATTAATAAGATGACTCAGAT
Found at i:957902 original size:228 final size:229
Alignment explanation
Indices: 957463--957920 Score: 837
Period size: 228 Copynumber: 2.0 Consensus size: 229
957453 CTAACTTATA
957463 AATATACCACATTTTTTGAGGATTGGCAACCTTCAGTTGCATTTGCAAGGTAAAACCTTAATTCT
1 AATATACCACATTTTTTGAGGATTGGCAACCTTCAGTTGCATTTGCAAGGTAAAACCTTAATTCT
*
957528 TAAGCTCTTCCAACTCATTTTTAACTCAAAACTCCATTTTTATGATTTTAAAACATAGTTTTGGG
66 TAAGCTCTTCCAACTCATTTTTAACTCAAAACTCCATTTTTATGATTTTAAAACATAGTTTTAGG
957593 TTTTTATAGATAAAGATAACATTTTTAGCTTTTAAATCTTTTGGTCTTGGATTTTCTAAACTTAA
131 TTTTTATAGATAAAGATAACATTTTTAGCTTTTAAATCTTTTGGTCTTGGATTTTCTAAACTTAA
957658 ATAGTTTCTTTATTACCAAAATTTTCTATTGGTG
196 ATAGTTTCTTTATTACCAAAATTTTCTATTGGTG
* * * *
957692 AATATACCACATTTTTTTAGGATTGGCAACTTTTAGTTGCATTTGCAAGGTAAAACCTTAATTTT
1 AATATACCACATTTTTTGAGGATTGGCAACCTTCAGTTGCATTTGCAAGGTAAAACCTTAATTCT
*
957757 TAAGCTCTTCCAACTCATTTTTAACTCAAAACTCCATTTTT-TTATTTTAAAACATAGTTTTAGG
66 TAAGCTCTTCCAACTCATTTTTAACTCAAAACTCCATTTTTATGATTTTAAAACATAGTTTTAGG
* *
957821 TTTTTATGGATAAAGATAACATTTTTAGCTTTTAAATCTTTTGGTCTTGGATTTTCTGAACTTAA
131 TTTTTATAGATAAAGATAACATTTTTAGCTTTTAAATCTTTTGGTCTTGGATTTTCTAAACTTAA
957886 ATAGTTTCTTTATTACCAAAATTTTCTATTGGTG
196 ATAGTTTCTTTATTACCAAAATTTTCTATTGGTG
957920 A
1 A
957921 TTGATGTTTA
Statistics
Matches: 221, Mismatches: 8, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
228 119 0.54
229 102 0.46
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (229 bp):
AATATACCACATTTTTTGAGGATTGGCAACCTTCAGTTGCATTTGCAAGGTAAAACCTTAATTCT
TAAGCTCTTCCAACTCATTTTTAACTCAAAACTCCATTTTTATGATTTTAAAACATAGTTTTAGG
TTTTTATAGATAAAGATAACATTTTTAGCTTTTAAATCTTTTGGTCTTGGATTTTCTAAACTTAA
ATAGTTTCTTTATTACCAAAATTTTCTATTGGTG
Found at i:959333 original size:32 final size:33
Alignment explanation
Indices: 959297--959361 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 33
959287 TTAAAATTAG
* *
959297 TTAATTAAG-TTATGCCTAATTCATTAAATTGT
1 TTAATTAAGATTAGGCCTAATTAATTAAATTGT
959329 TTAATTAAGTCATTAGGCCTAATTAATTAAATT
1 TTAATTAAG--ATTAGGCCTAATTAATTAAATT
959362 AAAGAAGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 9 0.32
35 19 0.68
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (33 bp):
TTAATTAAGATTAGGCCTAATTAATTAAATTGT
Found at i:959358 original size:35 final size:35
Alignment explanation
Indices: 959297--959519 Score: 145
Period size: 36 Copynumber: 6.5 Consensus size: 35
959287 TTAAAATTAG
*
959297 TTAATTAAGTTA-T--GCCTAATTCATTAAATTGT
1 TTAATTAAGTTATTGGGCCTAATTAATTAAATTGT
* *
959329 TTAATTAAGTCATTAGGCCTAATTAATTAAA----
1 TTAATTAAGTTATTGGGCCTAATTAATTAAATTGT
** * *
959360 TTAAAGAAGTCATTGGGCCTAATTAATTAAATTTGN
1 TTAATTAAGTTATTGGGCCTAATTAATTAAA-TTGT
********* * *
959396 NNNNNNNNNTTATTGGGCCTAATTGATTAAATTAT
1 TTAATTAAGTTATTGGGCCTAATTAATTAAATTGT
* * *
959431 TTAATCAAGTTATTGTGCCTAATTGATTAAATTTGT
1 TTAATTAAGTTATTGGGCCTAATTAATTAAA-TTGT
* **
959467 TTAATTAAGTTATTGGGTCTAATTAATTAAATTAA
1 TTAATTAAGTTATTGGGCCTAATTAATTAAATTGT
*
959502 ATAATTAAGTTAATTGGG
1 TTAATTAAGTT-ATTGGG
959520 NNNNNNNNNN
Statistics
Matches: 145, Mismatches: 36, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
31 28 0.19
32 11 0.08
33 1 0.01
35 49 0.34
36 56 0.39
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.41
Consensus pattern (35 bp):
TTAATTAAGTTATTGGGCCTAATTAATTAAATTGT
Found at i:959518 original size:36 final size:35
Alignment explanation
Indices: 959405--959519 Score: 149
Period size: 36 Copynumber: 3.2 Consensus size: 35
959395 NNNNNNNNNN
*
959405 TTATTGGGCCTAATTGATTAAATTATTTAATCAAG
1 TTATTGGGCCTAATTGATTAAATTATTTAATTAAG
* *
959440 TTATTGTGCCTAATTGATTAAATTTGTTTAATTAAG
1 TTATTGGGCCTAATTGATTAAA-TTATTTAATTAAG
* * **
959476 TTATTGGGTCTAATTAATTAAATTAAATAATTAAG
1 TTATTGGGCCTAATTGATTAAATTATTTAATTAAG
959511 TTAATTGGG
1 TT-ATTGGG
959520 NNNNNNNNNN
Statistics
Matches: 69, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
35 33 0.48
36 36 0.52
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (35 bp):
TTATTGGGCCTAATTGATTAAATTATTTAATTAAG
Found at i:968562 original size:80 final size:79
Alignment explanation
Indices: 968450--968676 Score: 328
Period size: 80 Copynumber: 2.8 Consensus size: 79
968440 TGTAACATGT
* * *
968450 ATGCCATGAGATGTATGTGCTGAGATAGTCATATACACTATGGGCTAAGTATGTGAGTGATTTAT
1 ATGCCATGAGATGTATGTGTTGAGTTAGTCATATACACTATGGGCTAAGCATGTGA-TGATTTAT
968515 GAGGTTATGAAACGC
65 GAGGTTATGAAACGC
* *
968530 ATGCCATGAGATGTATGTGTTGAGTTAGTCATATACACAATGGGCTAAGCATATGAATGATTTAT
1 ATGCCATGAGATGTATGTGTTGAGTTAGTCATATACACTATGGGCTAAGCATGTG-ATGATTTAT
*
968595 GAGGTTATGAAATGC
65 GAGGTTATGAAACGC
* * * * *
968610 ATACCATGAGATGTATATGTTGAGTTAATTATACACACTATGGGCTAAGCATGATGATGATTTAT
1 ATGCCATGAGATGTATGTGTTGAGTTAGTCATATACACTATGGGCTAAGCATG-TGATGATTTAT
968675 GA
65 GA
968677 AATGTTATAT
Statistics
Matches: 132, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
80 129 0.98
81 3 0.02
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.33
Consensus pattern (79 bp):
ATGCCATGAGATGTATGTGTTGAGTTAGTCATATACACTATGGGCTAAGCATGTGATGATTTATG
AGGTTATGAAACGC
Found at i:969560 original size:72 final size:73
Alignment explanation
Indices: 969407--969563 Score: 183
Period size: 72 Copynumber: 2.2 Consensus size: 73
969397 ATATTGTTAC
* *
969407 TCGACAAAGAGCTTACTGCCAAAAACTGAGTTCAGAGACAAAAATGACTTAATTGACTAAAAAGT
1 TCGACTAAGAGCTTACTGCCAAAAACTGAGTTCAGAGACAAAAATGACTTAATTGACTAAAAAGC
* *
969472 AGTGTTAG
66 AATGATAG
* * * * * * *
969480 TCGCCTAAGAGCTTACTGGCAGAAATTGGGTTCAGAGAC-ATAATGACTTAATTGACTAAGTAA-
1 TCGACTAAGAGCTTACTGCCAAAAACTGAGTTCAGAGACAAAAATGACTTAATTGACTAA-AAAG
969543 CAATGATAG
65 CAATGATAG
*
969552 TTGACTAAGAGC
1 TCGACTAAGAGC
969564 ATTCTGTCTG
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
72 35 0.50
73 35 0.50
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (73 bp):
TCGACTAAGAGCTTACTGCCAAAAACTGAGTTCAGAGACAAAAATGACTTAATTGACTAAAAAGC
AATGATAG
Found at i:997890 original size:11 final size:11
Alignment explanation
Indices: 997876--997912 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
997866 AATAATATTT
*
997876 TATTAATAAAA
1 TATTATTAAAA
997887 TATTATTAAAA
1 TATTATTAAAA
*
997898 TAATATTAAAA
1 TATTATTAAAA
997909 TATT
1 TATT
997913 TCTATCATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTATTAAAA
Found at i:1003337 original size:29 final size:31
Alignment explanation
Indices: 1003289--1003355 Score: 111
Period size: 29 Copynumber: 2.2 Consensus size: 31
1003279 GTTTTCAATC
*
1003289 ATACAAATAATATCTTATATTATTCATATAG
1 ATACAAATAATATCATATATTATTCATATAG
1003320 ATACAAATAA-AT-ATATATTATTCATATAG
1 ATACAAATAATATCATATATTATTCATATAG
1003349 ATACAAA
1 ATACAAA
1003356 CCACATTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 23 0.66
30 2 0.06
31 10 0.29
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (31 bp):
ATACAAATAATATCATATATTATTCATATAG
Found at i:1003662 original size:19 final size:21
Alignment explanation
Indices: 1003626--1003673 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
1003616 ATTTTGAAGA
1003626 AAAATAAAATATTAATTT-TGT
1 AAAA-AAAATATTAATTTATGT
*
1003647 AAAAAAAATATT-ATTTATTT
1 AAAAAAAATATTAATTTATGT
1003667 AAAAAAA
1 AAAAAAA
1003674 GGGACAACAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 4 0.16
20 17 0.68
21 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAAAAAATATTAATTTATGT
Found at i:1009968 original size:19 final size:19
Alignment explanation
Indices: 1009940--1009984 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
1009930 CGATTAAGTT
* *
1009940 GTTTCAGTCTCTGAACCCA
1 GTTTCTGTCTCTAAACCCA
*
1009959 GTTTCTGTCTCTAAACTCA
1 GTTTCTGTCTCTAAACCCA
1009978 GTTTCTG
1 GTTTCTG
1009985 GCAGTAATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.18, C:0.27, G:0.16, T:0.40
Consensus pattern (19 bp):
GTTTCTGTCTCTAAACCCA
Found at i:1023704 original size:16 final size:16
Alignment explanation
Indices: 1023683--1023723 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1023673 TCTCTCAACC
1023683 TTTTCTTTTCTTTAT-T
1 TTTTCTTTTC-TTATGT
1023699 TTTTC-TTTCTTATGT
1 TTTTCTTTTCTTATGT
1023714 TTTTGCTTTT
1 TTTT-CTTTT
1023724 TCATCTCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.18
15 9 0.41
16 6 0.27
17 3 0.14
ACGTcount: A:0.05, C:0.12, G:0.05, T:0.78
Consensus pattern (16 bp):
TTTTCTTTTCTTATGT
Found at i:1026727 original size:17 final size:17
Alignment explanation
Indices: 1026701--1026771 Score: 51
Period size: 17 Copynumber: 4.4 Consensus size: 17
1026691 TTTATTTTTA
1026701 TTTA-TTATTATAATCT
1 TTTATTTATTATAATCT
** *
1026717 TTTATTTATTATTTTCA
1 TTTATTTATTATAATCT
* *
1026734 TTTCTTTAATATAAT-T
1 TTTATTTATTATAATCT
* *
1026750 TTT-TATATTAT-ATAT
1 TTTATTTATTATAATCT
1026765 TTTATTT
1 TTTATTT
1026772 TAATTACATT
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
14 2 0.05
15 10 0.24
16 9 0.22
17 20 0.49
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATTTATTATAATCT
Found at i:1026870 original size:15 final size:15
Alignment explanation
Indices: 1026847--1026878 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1026837 TTCTTATATT
1026847 ATATATTTTATTTTA
1 ATATATTTTATTTTA
*
1026862 ATATTTTTTATTTTA
1 ATATATTTTATTTTA
1026877 AT
1 AT
1026879 TATAATATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATATATTTTATTTTA
Found at i:1030889 original size:15 final size:15
Alignment explanation
Indices: 1030871--1030925 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 15
1030861 AAATTTTTAA
*
1030871 AAAATTAATTAAAAC
1 AAAATTAAATAAAAC
1030886 AAAATTAAAATAAACAC
1 AAAATT-AAATAAA-AC
* *
1030903 TAAATTAAATAACA-
1 AAAATTAAATAAAAC
1030917 AAAATTAAA
1 AAAATTAAA
1030926 ATTACTTGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
14 8 0.24
15 7 0.21
16 12 0.35
17 7 0.21
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAATTAAATAAAAC
Found at i:1043421 original size:14 final size:13
Alignment explanation
Indices: 1043372--1043423 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
1043362 TACCTTAGGC
1043372 CATTTCATCAATTA
1 CATTTCAT-AATTA
* *
1043386 CATCTCAT-ATTT
1 CATTTCATAATTA
*
1043398 CATATCATAACTTA
1 CATTTCATAA-TTA
1043412 CATTTCATAATT
1 CATTTCATAATT
1043424 TTAAACTGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
12 10 0.32
13 3 0.10
14 18 0.58
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (13 bp):
CATTTCATAATTA
Found at i:1047430 original size:2 final size:2
Alignment explanation
Indices: 1047423--1047481 Score: 61
Period size: 2 Copynumber: 30.5 Consensus size: 2
1047413 AATGTTATGA
* *
1047423 AT AT AT AT AT AT AT AT AT AT AT AT A- AT GGT AT AA AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
*
1047464 AT AT AT A- AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1047482 AGCATTACTT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
1 3 0.06
2 43 0.91
3 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1047460 original size:34 final size:34
Alignment explanation
Indices: 1047407--1047482 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 34
1047397 ATGGTTCGTA
* * *
1047407 ATATAAAATGTTATGAATA-TATATATATATATAT
1 ATATATAATGGTATAAATATTATATATATA-ATAT
*
1047441 ATATATAATGGTATAAATATTATATATATAATTT
1 ATATATAATGGTATAAATATTATATATATAATAT
1047475 ATATATAA
1 ATATATAA
1047483 GCATTACTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
34 27 0.73
35 10 0.27
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (34 bp):
ATATATAATGGTATAAATATTATATATATAATAT
Found at i:1047691 original size:216 final size:216
Alignment explanation
Indices: 1047462--1047913 Score: 608
Period size: 216 Copynumber: 2.1 Consensus size: 216
1047452 TATAAATATT
* *
1047462 ATATATATAATTTATATATAAGCATTACTT-TAACTTATAATAAACTTTATTTATATGATTACAC
1 ATATATTTAATTTATATATAAGCATTA-TTGTAACTTATAATAAACTTTATTTATATAATTACAC
* *
1047526 TTAATAACCTTATTAATTATCACCTTAGTTTTTATAAAATATTGTTTATAATTAGTTATTATTTA
65 TTAATAACCTTATTAATTATCACCTTAATTTTTATAAAATATTGATTATAATTAGTTATTATTTA
** * *
1047591 TATGAACTTTGATGTAAAACATT-ATA-AT-ATATAAGTTGTATCATTAATTTCATATATACATA
130 TACAAACTTTGATATAAAA-ATTAATACATAATATAAGTTGTATCATTAATTTCACATAT--ATA
*
1047653 ATAAAGTAATATATTATACT-TATAC
192 ATAAAGTAATATATTA-AATATATAC
* *
1047678 ATATATTTAATTTATATATAAGCATTATTGTAACTTGTAATAGACTTTATTTATATAATTACACT
1 ATATATTTAATTTATATATAAGCATTATTGTAACTTATAATAAACTTTATTTATATAATTACACT
** * * ** *
1047743 TAATAATTTTATTAGTTGTCGTCTTAATTTTTATAACATATTGATTATAATTAGTTATTATTTAT
66 TAATAACCTTATTAATTATCACCTTAATTTTTATAAAATATTGATTATAATTAGTTATTATTTAT
*
1047808 ACAAACTTTGATATAAAAATTAAAATACTATAACATATAAGTTGTGTCATTAATTTCACATATAT
131 ACAAACTTTGATATAAAAATT--AATAC-AT-A-ATATAAGTTGTATCATTAATTTCACATATAT
1047873 AATAAAGTAATATATTAAATATATAC
191 AATAAAGTAATATATTAAATATATAC
1047899 ATATATTTAATTTAT
1 ATATATTTAATTTAT
1047914 TCAAAATTTG
Statistics
Matches: 207, Mismatches: 19, Indels: 15
0.86 0.08 0.06
Matches are distributed among these distances:
215 5 0.02
216 129 0.62
218 3 0.01
220 4 0.02
221 39 0.19
223 27 0.13
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.46
Consensus pattern (216 bp):
ATATATTTAATTTATATATAAGCATTATTGTAACTTATAATAAACTTTATTTATATAATTACACT
TAATAACCTTATTAATTATCACCTTAATTTTTATAAAATATTGATTATAATTAGTTATTATTTAT
ACAAACTTTGATATAAAAATTAATACATAATATAAGTTGTATCATTAATTTCACATATATAATAA
AGTAATATATTAAATATATAC
Found at i:1048273 original size:2 final size:2
Alignment explanation
Indices: 1048266--1048337 Score: 135
Period size: 2 Copynumber: 36.0 Consensus size: 2
1048256 GGTTGATCAA
1048266 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
1048308 AG AG AG AG AG AG AG AG AG AG AG AT AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1048338 GGGAGGGGGC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.49, T:0.01
Consensus pattern (2 bp):
AG
Found at i:1048715 original size:23 final size:21
Alignment explanation
Indices: 1048677--1048718 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1048667 CATATTTTAA
*
1048677 AAGTTTTTTTTAATTTAAAAG
1 AAGTTTTTTTAAATTTAAAAG
1048698 AAGTGTTTTTTAATATTTAAA
1 AAGT-TTTTTTAA-ATTTAAA
1048719 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 7 0.39
23 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (21 bp):
AAGTTTTTTTAAATTTAAAAG
Found at i:1050578 original size:16 final size:17
Alignment explanation
Indices: 1050554--1050597 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
1050544 ATATTTACCA
1050554 AATAT-AATAAAAT-TC
1 AATATCAATAAAATCTC
1050569 AATATCAAT-AAATCTC
1 AATATCAATAAAATCTC
1050585 AATCATC-ATAAAA
1 AAT-ATCAATAAAA
1050598 ATATCAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 9 0.36
16 10 0.40
17 6 0.24
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.30
Consensus pattern (17 bp):
AATATCAATAAAATCTC
Found at i:1055077 original size:14 final size:14
Alignment explanation
Indices: 1055038--1055135 Score: 101
Period size: 14 Copynumber: 6.9 Consensus size: 14
1055028 TTAACCAGGT
*
1055038 ATCACATTAACATAC
1 ATCA-ATTAACATTC
* *
1055053 ATC-ATGAAACATTT
1 ATCAAT-TAACATTC
1055067 ATCAATTAACATTC
1 ATCAATTAACATTC
*
1055081 ATCAACTAACATTC
1 ATCAATTAACATTC
*
1055095 ATCAACTAACATTC
1 ATCAATTAACATTC
1055109 ATC-ATCTAACATTC
1 ATCAAT-TAACATTC
*
1055123 ATCATTTAACATT
1 ATCAATTAACATT
1055136 TGTGACGAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
13 3 0.04
14 62 0.87
15 6 0.08
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (14 bp):
ATCAATTAACATTC
Found at i:1055078 original size:28 final size:28
Alignment explanation
Indices: 1055038--1055135 Score: 124
Period size: 28 Copynumber: 3.5 Consensus size: 28
1055028 TTAACCAGGT
* ** *
1055038 ATCACATTAACATACATCATGAAACATTT
1 ATCA-ATTAACATTCATCATCTAACATTC
*
1055067 ATCAATTAACATTCATCAACTAACATTC
1 ATCAATTAACATTCATCATCTAACATTC
*
1055095 ATCAACTAACATTCATCATCTAACATTC
1 ATCAATTAACATTCATCATCTAACATTC
*
1055123 ATCATTTAACATT
1 ATCAATTAACATT
1055136 TGTGACGAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
28 56 0.93
29 4 0.07
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (28 bp):
ATCAATTAACATTCATCATCTAACATTC
Found at i:1056238 original size:17 final size:17
Alignment explanation
Indices: 1056216--1056249 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1056206 ATCTATTTTT
1056216 CTTTAAT-TTGTTAAAAG
1 CTTTAATATT-TTAAAAG
1056233 CTTTAATATTTTAAAAG
1 CTTTAATATTTTAAAAG
1056250 GGCTGATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (17 bp):
CTTTAATATTTTAAAAG
Found at i:1057360 original size:20 final size:21
Alignment explanation
Indices: 1057323--1057367 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
1057313 CCTATTCCTT
**
1057323 AATGAAGAAACCTGAAAGA-A
1 AATGAAGAAACCAAAAAGAGA
1057343 AATGAAGAAACCAAAAAGAGA
1 AATGAAGAAACCAAAAAGAGA
1057364 AATG
1 AATG
1057368 GTGACAGCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.62, C:0.09, G:0.20, T:0.09
Consensus pattern (21 bp):
AATGAAGAAACCAAAAAGAGA
Found at i:1062891 original size:45 final size:45
Alignment explanation
Indices: 1062828--1062979 Score: 144
Period size: 45 Copynumber: 3.4 Consensus size: 45
1062818 AGAAGAATAG
* * *
1062828 GAAAAGGAAAAGACACCAACCACAAAAGAAAATAAGGAAAAAAGA
1 GAAATGGAAAAAAAACCAACCACAAAAGAAAATAAGGAAAAAAGA
* * * * *
1062873 GGAATGGAAAAAAAACCAACCATAAAAGAGAATGAGGAAGAAAGA
1 GAAATGGAAAAAAAACCAACCACAAAAGAAAATAAGGAAAAAAGA
* * * ** *
1062918 GAAATGGAGAAAAAACCTACCACAGAAGGGAATGAGGAAGAAAA-A
1 GAAATGGAAAAAAAACCAACCACAAAAGAAAATAAGGAA-AAAAGA
* *
1062963 GAAATGGAGAAAGAACC
1 GAAATGGAAAAAAAACC
1062980 TAAGGGGAAA
Statistics
Matches: 90, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
45 87 0.97
46 3 0.03
ACGTcount: A:0.60, C:0.11, G:0.24, T:0.05
Consensus pattern (45 bp):
GAAATGGAAAAAAAACCAACCACAAAAGAAAATAAGGAAAAAAGA
Found at i:1062980 original size:45 final size:45
Alignment explanation
Indices: 1062846--1062981 Score: 166
Period size: 45 Copynumber: 3.0 Consensus size: 45
1062836 AAAGACACCA
* * * * *
1062846 ACCACAAAAGAAAATAAGGAA-AAAAGAGGAATGGAAAAAAAACCA
1 ACCACAAAAGAGAATGAGGAAGAAAA-AGAAATGGAGAAAAAACCT
* *
1062891 ACCATAAAAGAGAATGAGGAAGAAAGAGAAATGGAGAAAAAACCT
1 ACCACAAAAGAGAATGAGGAAGAAAAAGAAATGGAGAAAAAACCT
* * *
1062936 ACCACAGAAGGGAATGAGGAAGAAAAAGAAATGGAGAAAGAACCT
1 ACCACAAAAGAGAATGAGGAAGAAAAAGAAATGGAGAAAAAACCT
1062981 A
1 A
1062982 AGGGGAAAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
45 75 0.96
46 3 0.04
ACGTcount: A:0.60, C:0.10, G:0.24, T:0.07
Consensus pattern (45 bp):
ACCACAAAAGAGAATGAGGAAGAAAAAGAAATGGAGAAAAAACCT
Found at i:1064477 original size:16 final size:16
Alignment explanation
Indices: 1064452--1064484 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1064442 AAGTTTGATG
1064452 AAGAAGAGAAG-CTTA
1 AAGAAGAGAAGTCTTA
1064467 AAGATAGAGAAGTCTTA
1 AAGA-AGAGAAGTCTTA
1064484 A
1 A
1064485 TCAGTTAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 7 0.44
17 5 0.31
ACGTcount: A:0.52, C:0.06, G:0.24, T:0.18
Consensus pattern (16 bp):
AAGAAGAGAAGTCTTA
Found at i:1071014 original size:37 final size:37
Alignment explanation
Indices: 1070941--1071064 Score: 122
Period size: 37 Copynumber: 3.4 Consensus size: 37
1070931 AACCTAACCA
* * *** * *
1070941 AGGACAATGGTACAATCCCCACTGTGTCGGATAATCG
1 AGGATAATGGTACAATCCCCATTAACTAGGACAATCG
* * *
1070978 AGGATAATGGTACAATTCCTATTATCTAGGACAATCG
1 AGGATAATGGTACAATCCCCATTAACTAGGACAATCG
* * * *
1071015 AGCATAATGATACAGTCCCCATTAACTAGGACAATGG
1 AGGATAATGGTACAATCCCCATTAACTAGGACAATCG
1071052 AGGATAATGGTAC
1 AGGATAATGGTAC
1071065 GATCTTCACT
Statistics
Matches: 70, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (37 bp):
AGGATAATGGTACAATCCCCATTAACTAGGACAATCG
Found at i:1072689 original size:15 final size:15
Alignment explanation
Indices: 1072652--1072690 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
1072642 TCATGCTAAT
*
1072652 AGCTCATAAAGACAA
1 AGCTCATTAAGACAA
1072667 AGCTCATTAAGACAA
1 AGCTCATTAAGACAA
1072682 AGCTCATTA
1 AGCTCATTA
1072691 TATTTTTAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.21
Consensus pattern (15 bp):
AGCTCATTAAGACAA
Found at i:1078769 original size:20 final size:20
Alignment explanation
Indices: 1078744--1078791 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1078734 ATTAGTTATT
1078744 GCCATGACCCAAACTTTAGG
1 GCCATGACCCAAACTTTAGG
1078764 GCCATGACCCAAACTTTAGG
1 GCCATGACCCAAACTTTAGG
*
1078784 GTCATGAC
1 GCCATGAC
1078792 TAGCGCATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (20 bp):
GCCATGACCCAAACTTTAGG
Found at i:1079739 original size:67 final size:67
Alignment explanation
Indices: 1079666--1079821 Score: 208
Period size: 67 Copynumber: 2.3 Consensus size: 67
1079656 TCTCTCCACG
* * *
1079666 GATGGCACCACAATCCTCATCTAAGGAAATATCCCAACA-A-ATGGCATCACCCAGAGTATTCTC
1 GATGGCATCACAATCATCATCCAAGGAAATATCCCAACAGACAT--CATCACCCAGAGTATTCTC
1079729 CATA
64 CATA
* * * *
1079733 GATGGCATCATAATCATCATCCAAGGCAATATCCCAGCAGACATCATCACCTAGAGTATTCTCCA
1 GATGGCATCACAATCATCATCCAAGGAAATATCCCAACAGACATCATCACCCAGAGTATTCTCCA
1079798 TA
66 TA
*
1079800 AATGGCATCACAATCATCATCC
1 GATGGCATCACAATCATCATCC
1079822 GGAGTAATCT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
67 75 0.96
68 1 0.01
69 2 0.03
ACGTcount: A:0.35, C:0.29, G:0.13, T:0.22
Consensus pattern (67 bp):
GATGGCATCACAATCATCATCCAAGGAAATATCCCAACAGACATCATCACCCAGAGTATTCTCCA
TA
Found at i:1081356 original size:30 final size:30
Alignment explanation
Indices: 1081322--1081378 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
1081312 AGGCAGTGCT
*
1081322 ATTATTTACCCCTAAATTTATACTTCACAA
1 ATTATTAACCCCTAAATTTATACTTCACAA
*
1081352 ATTATTAACCCCTAAATTTCTACTTCA
1 ATTATTAACCCCTAAATTTATACTTCA
1081379 TAAGATCGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.35, C:0.25, G:0.00, T:0.40
Consensus pattern (30 bp):
ATTATTAACCCCTAAATTTATACTTCACAA
Found at i:1081742 original size:22 final size:22
Alignment explanation
Indices: 1081717--1081779 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
1081707 GTGATCAGCT
*
1081717 TATTTGGCATTATGTGACTAAA
1 TATTAGGCATTATGTGACTAAA
* * *
1081739 TATTAGGTA-TGTGTGACTAGA
1 TATTAGGCATTATGTGACTAAA
*
1081760 TATTAGGCATTATGAGACTA
1 TATTAGGCATTATGTGACTA
1081780 GCTTTTAGGA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (22 bp):
TATTAGGCATTATGTGACTAAA
Found at i:1081838 original size:22 final size:22
Alignment explanation
Indices: 1081806--1081869 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
1081796 TGAGTTGTGC
1081806 ATTACTTGACTAGGTTTTAGGA
1 ATTACTTGACTAGGTTTTAGGA
* *
1081828 ATTGCTTGACTA-GTTTGTAGGC
1 ATTACTTGACTAGGTTT-TAGGA
* *
1081850 ATTACATGACTAGTTTTTAG
1 ATTACTTGACTAGGTTTTAG
1081870 TTATTGTGTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 4 0.11
22 28 0.80
23 3 0.09
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (22 bp):
ATTACTTGACTAGGTTTTAGGA
Found at i:1093257 original size:25 final size:25
Alignment explanation
Indices: 1093227--1093434 Score: 186
Period size: 25 Copynumber: 8.3 Consensus size: 25
1093217 TGACCATCAT
*
1093227 GCAATGCCATACAGATAACAATCAC
1 GCAATGCCATACAGATAACAGTCAC
* * * * *
1093252 GTAATGCCATATAAATAATAGTCAT
1 GCAATGCCATACAGATAACAGTCAC
* **
1093277 GCATTGCCATACAGATAACAGTCGT
1 GCAATGCCATACAGATAACAGTCAC
* * *
1093302 GCATTGCCATACAGATAACAATCAT
1 GCAATGCCATACAGATAACAGTCAC
* *
1093327 GCAATGCCCTACAGATAACAGTCAT
1 GCAATGCCATACAGATAACAGTCAC
* * * *
1093352 GTAATGTCC-TATATATAA-TGATCAC
1 GCAATG-CCATACAGATAACAG-TCAC
*
1093377 GCAATGCCATATAGATAACAGTCAC
1 GCAATGCCATACAGATAACAGTCAC
* *
1093402 GCAATGCCATATAAATAACAGTCAC
1 GCAATGCCATACAGATAACAGTCAC
*
1093427 TCAATGCC
1 GCAATGCC
1093435 TTATCAAGCA
Statistics
Matches: 152, Mismatches: 27, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
24 3 0.02
25 146 0.96
26 3 0.02
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (25 bp):
GCAATGCCATACAGATAACAGTCAC
Found at i:1093310 original size:50 final size:50
Alignment explanation
Indices: 1093223--1093434 Score: 223
Period size: 50 Copynumber: 4.2 Consensus size: 50
1093213 GCAATGACCA
* * *
1093223 TCATGCAATGCCATACAGATAACAATCACGTAATGCCATATAAATAATAG
1 TCATGCAATGCCATACAGATAACAGTCACGCAATGCCATATAAATAACAG
* ** * * * *
1093273 TCATGCATTGCCATACAGATAACAGTCGTGCATTGCCATACAGATAACAA
1 TCATGCAATGCCATACAGATAACAGTCACGCAATGCCATATAAATAACAG
* * * * *
1093323 TCATGCAATGCCCTACAGATAACAGTCATGTAATGTCC-TATATATAA-TG
1 TCATGCAATGCCATACAGATAACAGTCACGCAATG-CCATATAAATAACAG
* *
1093372 ATCACGCAATGCCATATAGATAACAGTCACGCAATGCCATATAAATAACAG
1 -TCATGCAATGCCATACAGATAACAGTCACGCAATGCCATATAAATAACAG
1093423 TCACT-CAATGCC
1 TCA-TGCAATGCC
1093435 TTATCAAGCA
Statistics
Matches: 130, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
49 2 0.02
50 125 0.96
51 3 0.02
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.25
Consensus pattern (50 bp):
TCATGCAATGCCATACAGATAACAGTCACGCAATGCCATATAAATAACAG
Found at i:1093385 original size:75 final size:74
Alignment explanation
Indices: 1093221--1093434 Score: 234
Period size: 75 Copynumber: 2.9 Consensus size: 74
1093211 ATGCAATGAC
* * *
1093221 CATCATGCAATGCCATACAGATAACAATCACGTAATGCCATATAAATAATAGTCATGCATTGCCA
1 CATCATGCAATGCCATACAGATAACAATCACGCAATGCCATATAAATAACAGTCATGCAATGCCA
1093286 TACAGATAA
66 TACAGATAA
* * * * * * *
1093295 CAGTCGTGCATTGCCATACAGATAACAATCATGCAATGCCCTACAGATAACAGTCATGTAATGTC
1 CA-TCATGCAATGCCATACAGATAACAATCACGCAATGCCATATAAATAACAGTCATGCAATG-C
* *
1093360 C-TATATATAA
64 CATACAGATAA
* * * *
1093370 TGATCACGCAATGCCATATAGATAACAGTCACGCAATGCCATATAAATAACAGTCACT-CAATGC
1 -CATCATGCAATGCCATACAGATAACAATCACGCAATGCCATATAAATAACAGTCA-TGCAATGC
1093434 C
64 C
1093435 TTATCAAGCA
Statistics
Matches: 113, Mismatches: 23, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
74 4 0.04
75 105 0.93
76 4 0.04
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (74 bp):
CATCATGCAATGCCATACAGATAACAATCACGCAATGCCATATAAATAACAGTCATGCAATGCCA
TACAGATAA
Found at i:1103253 original size:14 final size:15
Alignment explanation
Indices: 1103227--1103255 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1103217 TAGATTAAGT
1103227 TTAGTTATTAGTTTA
1 TTAGTTATTAGTTTA
1103242 TTAGTT-TTAGTTTA
1 TTAGTTATTAGTTTA
1103256 ATTTTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (15 bp):
TTAGTTATTAGTTTA
Found at i:1109870 original size:35 final size:35
Alignment explanation
Indices: 1109830--1110019 Score: 229
Period size: 35 Copynumber: 5.4 Consensus size: 35
1109820 CACTTGATAA
* *
1109830 AAATTATTTAATTAAGTCATTGGGCCTAATTTATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTGATT
** *
1109865 AAATTA-ACAATTAAGTTATTGGGCCCAATTGATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTGATT
* * *
1109899 AAATTGTTTAATTAGGTTATTGGGCTTAATTGATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTGATT
* *
1109934 AAATTTGTTTAATCAAGTTATTGGGCCTAATTGATT
1 AAA-TTATTTAATTAAGTTATTGGGCCTAATTGATT
* * *
1109970 AAGTTATTTAATTAAGTTATTAGGTCTAATTGATT
1 AAATTATTTAATTAAGTTATTGGGCCTAATTGATT
**
1110005 AAATTAAATAATTAA
1 AAATTATTTAATTAA
1110020 ATTAATTGAG
Statistics
Matches: 131, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
34 28 0.21
35 72 0.55
36 31 0.24
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (35 bp):
AAATTATTTAATTAAGTTATTGGGCCTAATTGATT
Found at i:1109980 original size:71 final size:70
Alignment explanation
Indices: 1109830--1110009 Score: 220
Period size: 71 Copynumber: 2.6 Consensus size: 70
1109820 CACTTGATAA
* * * *
1109830 AAATTATTTAATTAAGTCATTGGGCCTAATTTATTAAA-TTAACAATTAAGTTATTGGGCCCAAT
1 AAATTATTTAATTAAGTTATTGGGCTTAATTGATTAAATTTAACAATCAAGTTATTGGGCCCAAT
1109894 TGATT
66 TGATT
* * *** *
1109899 AAATTGTTTAATTAGGTTATTGGGCTTAATTGATTAAATTTGTTTAATCAAGTTATTGGGCCTAA
1 AAATTATTTAATTAAGTTATTGGGCTTAATTGATTAAATTT-AACAATCAAGTTATTGGGCCCAA
1109964 TTGATT
65 TTGATT
* *
1109970 AAGTTATTTAATTAAGTTATTAGG-TCTAATTGATTAAATT
1 AAATTATTTAATTAAGTTATTGGGCT-TAATTGATTAAATT
1110010 AAATAATTAA
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
69 33 0.35
70 3 0.03
71 58 0.62
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (70 bp):
AAATTATTTAATTAAGTTATTGGGCTTAATTGATTAAATTTAACAATCAAGTTATTGGGCCCAAT
TGATT
Found at i:1114030 original size:20 final size:20
Alignment explanation
Indices: 1114005--1114049 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1113995 TTATTGCTTT
*
1114005 ATTTAATTTATTTAGGCATA
1 ATTTAATCTATTTAGGCATA
1114025 ATTTAATCTATTTAGGCATA
1 ATTTAATCTATTTAGGCATA
1114045 ATTTA
1 ATTTA
1114050 TACACATGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.49
Consensus pattern (20 bp):
ATTTAATCTATTTAGGCATA
Found at i:1114277 original size:23 final size:23
Alignment explanation
Indices: 1114250--1114304 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
1114240 CATCATAAGG
1114250 ATGATGCTGATCAGGTAGCATGC
1 ATGATGCTGATCAGGTAGCATGC
*
1114273 GTGATGCTGATCAGGTAGCATGC
1 ATGATGCTGATCAGGTAGCATGC
1114296 ATGATGCTG
1 ATGATGCTG
1114305 GCTAGTATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.27
Consensus pattern (23 bp):
ATGATGCTGATCAGGTAGCATGC
Found at i:1116805 original size:35 final size:35
Alignment explanation
Indices: 1116729--1116912 Score: 207
Period size: 35 Copynumber: 5.3 Consensus size: 35
1116719 TCTCAAGCAC
*
1116729 TTGATTAAAATTGTTTAATTAAG---TTGTGCCTAA
1 TTGATT-AAATTGTTTAATTAAGTTATTGGGCCTAA
* *
1116762 TTCATTAAATTGTTTAATTAAGTCATTGGGCCTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
**** *
1116797 TTTG-TTAAATTAAACAATTAAGTTATTGGGCCCAA
1 -TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
*
1116832 TTGATTAAATTTGTTTAATCAAGTTATTGGGCCTAA
1 TTGATTAAA-TTGTTTAATTAAGTTATTGGGCCTAA
* *
1116868 TTGATTAAATTTTTTAA-TAAGTTATTGGGCTTAA
1 TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
1116902 TTGATTAAATT
1 TTGATTAAATT
1116913 AAACAATTAA
Statistics
Matches: 127, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
32 16 0.13
33 5 0.04
34 29 0.23
35 46 0.36
36 31 0.24
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.45
Consensus pattern (35 bp):
TTGATTAAATTGTTTAATTAAGTTATTGGGCCTAA
Found at i:1118207 original size:19 final size:19
Alignment explanation
Indices: 1118183--1118221 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1118173 ACATGGTGGA
1118183 TTATAATATTATATCTTAT
1 TTATAATATTATATCTTAT
*
1118202 TTATAATATTATATTTTAT
1 TTATAATATTATATCTTAT
1118221 T
1 T
1118222 ATCTTAGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATAATATTATATCTTAT
Found at i:1124985 original size:143 final size:145
Alignment explanation
Indices: 1124741--1125013 Score: 367
Period size: 143 Copynumber: 1.9 Consensus size: 145
1124731 TCCTTGGCCA
*
1124741 AGGACTTTTAGTCAACAAAAGCCAGGACAAAATGAGATATTTCCCTTTTAAATCACTTGGAGTGA
1 AGGACTTTTAGTCAACAAAAGCCAGGACAAAATGAAATATTTCCCTTTTAAATCACTTGGAGTGA
** * * * *
1124806 TGAATCCTCTCTAGACTACTCATTCATCTTTGCATGCTTCATGTCATACCTAAAAGCACCTTGTT
66 TGAATCCTCTCTAGACTACTCATTCATCTTCACATGCTTCAAGCCACACCCAAAAGCACCTTGTT
1124871 GAGGCATTTAGGCTT
131 GAGGCATTTAGGCTT
* * *
1124886 AGGACTTTTAGTCAACATAAGCTAGGAGC-AAATGAAATATGTAT-CC-TTT-AATCAC-TGGGG
1 AGGACTTTTAGTCAACAAAAGCCAGGA-CAAAATGAAATAT-T-TCCCTTTTAAATCACTTGGAG
* * *
1124946 TGATGAATCCTTTCTAGACTACTTATTCATCTTCACATGCTTCAAGCCACACCCAAAAGCACTTT
63 TGATGAATCCTCTCTAGACTACTCATTCATCTTCACATGCTTCAAGCCACACCCAAAAGCACCTT
1125011 GTT
128 GTT
1125014 TAGGTAACTG
Statistics
Matches: 112, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
143 63 0.56
144 6 0.05
145 38 0.34
146 4 0.04
147 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (145 bp):
AGGACTTTTAGTCAACAAAAGCCAGGACAAAATGAAATATTTCCCTTTTAAATCACTTGGAGTGA
TGAATCCTCTCTAGACTACTCATTCATCTTCACATGCTTCAAGCCACACCCAAAAGCACCTTGTT
GAGGCATTTAGGCTT
Found at i:1126338 original size:17 final size:17
Alignment explanation
Indices: 1126316--1126354 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1126306 ACCAAAGTCC
1126316 ATAGTTGGTTTACATGA
1 ATAGTTGGTTTACATGA
1126333 ATAGTTGGTTTACATGA
1 ATAGTTGGTTTACATGA
1126350 ATAGT
1 ATAGT
1126355 ATCTATCTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.31, C:0.05, G:0.23, T:0.41
Consensus pattern (17 bp):
ATAGTTGGTTTACATGA
Found at i:1147834 original size:13 final size:13
Alignment explanation
Indices: 1147798--1147837 Score: 59
Period size: 12 Copynumber: 3.3 Consensus size: 13
1147788 TTAGGGTTTT
1147798 GAAAG-GTT-AGA
1 GAAAGAGTTGAGA
1147809 GAAAGAG-TGAGA
1 GAAAGAGTTGAGA
1147821 GAAAGAGTTGAGA
1 GAAAGAGTTGAGA
1147834 GAAA
1 GAAA
1147838 AGGGTAGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 6 0.23
12 11 0.42
13 9 0.35
ACGTcount: A:0.50, C:0.00, G:0.38, T:0.12
Consensus pattern (13 bp):
GAAAGAGTTGAGA
Found at i:1152747 original size:15 final size:15
Alignment explanation
Indices: 1152727--1152764 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1152717 AGGTCAATAT
1152727 TATAAATAGTTATAA
1 TATAAATAGTTATAA
*
1152742 TATAAACAGTTATAA
1 TATAAATAGTTATAA
1152757 TATTAAAT
1 TA-TAAAT
1152765 CTTCAATTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (15 bp):
TATAAATAGTTATAA
Found at i:1156025 original size:68 final size:67
Alignment explanation
Indices: 1155790--1156024 Score: 233
Period size: 68 Copynumber: 3.5 Consensus size: 67
1155780 GTTTGGTACC
* * * *
1155790 ATGAATGCCATAAGATTATGTATATGATGTAAATTCTATACACCATATGAGATGATTAAGTATGC
1 ATGAATGCCATAAGATTATGTATATGATGTAAATTCCATATACCATATGAGATGATT-AGAAAGC
1155855 ATG
65 ATG
* ** * *
1155858 AT-ATATACTGTAAGATTGTGTATATGATGTAAATTCCATATACCATATGAGGTGATTA-AATAT
1 ATGA-ATGCCATAAGATTATGTATATGATGTAAATTCCATATACCATATGAGATGATTAGAA-A-
*
1155921 GAATG
63 GCATG
* ** * * *
1155926 ATAAATGCCATGGGA-TACTGTATATGATGTATATTCCATATACTACATGAGATGATTGAGAAAG
1 ATGAATGCCATAAGATTA-TGTATATGATGTAAATTCCATATACCATATGAGATGATT-AGAAAG
1155990 CATG
64 CATG
* *
1155994 ATGAATGCCATGAGATTATGTGTATGATGTA
1 ATGAATGCCATAAGATTATGTATATGATGTA
1156025 TTTTTCCATA
Statistics
Matches: 135, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
66 1 0.01
67 3 0.02
68 124 0.92
69 5 0.04
70 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.34
Consensus pattern (67 bp):
ATGAATGCCATAAGATTATGTATATGATGTAAATTCCATATACCATATGAGATGATTAGAAAGCA
TG
Found at i:1168884 original size:35 final size:35
Alignment explanation
Indices: 1168776--1168891 Score: 105
Period size: 35 Copynumber: 3.4 Consensus size: 35
1168766 CCAAGTTTTT
* * * *
1168776 ACAATGGCTTTTCATAGGCTCATCAACAACCTTTA
1 ACAATGGTTTTTCAAAGGCTCAACCACAACCTTTA
* * * * *
1168811 ACAATGGTTTGTC-ACGAGATCAACCAAAAGC--TA
1 ACAATGGTTTTTCAAAG-GCTCAACCACAACCTTTA
*
1168844 A-AATGGTTTTTCAAAGGCTCAGCCACAACCTTTA
1 ACAATGGTTTTTCAAAGGCTCAACCACAACCTTTA
1168878 ACAATGGTTTTTCA
1 ACAATGGTTTTTCA
1168892 CGCGGTTAAC
Statistics
Matches: 61, Mismatches: 15, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
32 20 0.33
33 5 0.08
34 4 0.07
35 32 0.52
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (35 bp):
ACAATGGTTTTTCAAAGGCTCAACCACAACCTTTA
Found at i:1169428 original size:73 final size:74
Alignment explanation
Indices: 1169342--1169499 Score: 212
Period size: 73 Copynumber: 2.1 Consensus size: 74
1169332 ACTTAGATAT
* * * * *
1169342 TTCTTAATCGATTAAG-TCTTCTTTGTCTTGTAATTGAATTCTCTGGTAGTAAGCTCTTAGTTGA
1 TTCTTAGTTGATTAAGTTCTT-TTTGTCTTGTAATTGAAGTCTATGGCAGTAAGCTCTTAGTTGA
1169406 CTA-CCATGC
65 CTACCCATGC
* * * *
1169415 TTTTTAGTTGATTACGTTCTTTTTGTTTTGTAATTGAAGTCTATGGCAGTGAGCTCTTAGTTGAC
1 TTCTTAGTTGATTAAGTTCTTTTTGTCTTGTAATTGAAGTCTATGGCAGTAAGCTCTTAGTTGAC
1169480 TACCCATGC
66 TACCCATGC
1169489 TTCTTAGTTGA
1 TTCTTAGTTGA
1169500 CTACCCATGC
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
73 53 0.73
74 20 0.27
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.46
Consensus pattern (74 bp):
TTCTTAGTTGATTAAGTTCTTTTTGTCTTGTAATTGAAGTCTATGGCAGTAAGCTCTTAGTTGAC
TACCCATGC
Found at i:1169495 original size:21 final size:21
Alignment explanation
Indices: 1169469--1169523 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
1169459 GGCAGTGAGC
1169469 TCTTAGTTGACTACCCATGCT
1 TCTTAGTTGACTACCCATGCT
1169490 TCTTAGTTGACTACCCATGCT
1 TCTTAGTTGACTACCCATGCT
*
1169511 TCTTAGTCGACTA
1 TCTTAGTTGACTA
1169524 AGTCTTCTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.20, C:0.27, G:0.15, T:0.38
Consensus pattern (21 bp):
TCTTAGTTGACTACCCATGCT
Found at i:1170311 original size:23 final size:23
Alignment explanation
Indices: 1170269--1170313 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1170259 TTCCTAAATT
* **
1170269 TCCCTTAAATTACTTTTACTTTA
1 TCCCCTAAATTACTACTACTTTA
1170292 TCCCCTAAATTACTACTACTTT
1 TCCCCTAAATTACTACTACTTT
1170314 TTTCCTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (23 bp):
TCCCCTAAATTACTACTACTTTA
Found at i:1177115 original size:35 final size:35
Alignment explanation
Indices: 1177052--1177189 Score: 93
Period size: 35 Copynumber: 4.0 Consensus size: 35
1177042 TTCCACCAAG
* * * *
1177052 CTTTTACAATGGTTTTTTACAAGCTCAACCATAAC
1 CTTTAACAATGGTTTTTCACAAGATCAACCAAAAC
**
1177087 CTTTAACAATGGTTTTTCATTAGATCAACCAAAAC
1 CTTTAACAATGGTTTTTCACAAGATCAACCAAAAC
* * * * * * *
1177122 C--CAA-ACTGGCTTTTCAAAAGCTCAACCACAAG
1 CTTTAACAATGGTTTTTCACAAGATCAACCAAAAC
* * * **
1177154 CATTAACAACGGCTTTTCACGGGATCAACCAAAAC
1 CTTTAACAATGGTTTTTCACAAGATCAACCAAAAC
1177189 C
1 C
1177190 CAAAATCTAA
Statistics
Matches: 77, Mismatches: 23, Indels: 6
0.73 0.22 0.06
Matches are distributed among these distances:
32 22 0.29
33 2 0.03
34 2 0.03
35 51 0.66
ACGTcount: A:0.36, C:0.26, G:0.11, T:0.28
Consensus pattern (35 bp):
CTTTAACAATGGTTTTTCACAAGATCAACCAAAAC
Found at i:1180964 original size:85 final size:87
Alignment explanation
Indices: 1180812--1180984 Score: 269
Period size: 85 Copynumber: 2.0 Consensus size: 87
1180802 TTTTGTGACA
* * *
1180812 GTTTAGGTTAGTTTATTTTCATTAAATTTTTTTTTATGTATATGCATTTGTATTTTAGCTAGATT
1 GTTTAGGTTAGTTTATTTTCATTAAA-TTTTTTTTATGCATATGCATTTGCATTTTAACTAGATT
1180877 TAATTATGCCAGTTTCATTTAAT
65 TAATTATGCCAGTTTCATTTAAT
*
1180900 GTTTAGGTTAGTTTATTTTCATT-AA-TTTTTTTATGCGTATGCATTTGCATTTTAACTAGATTT
1 GTTTAGGTTAGTTTATTTTCATTAAATTTTTTTTATGCATATGCATTTGCATTTTAACTAGATTT
* *
1180963 AATTGTGCTAGTTTCATTTAAT
66 AATTATGCCAGTTTCATTTAAT
1180985 TTGCCTATCC
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
85 54 0.68
87 2 0.03
88 23 0.29
ACGTcount: A:0.24, C:0.08, G:0.13, T:0.55
Consensus pattern (87 bp):
GTTTAGGTTAGTTTATTTTCATTAAATTTTTTTTATGCATATGCATTTGCATTTTAACTAGATTT
AATTATGCCAGTTTCATTTAAT
Found at i:1182301 original size:21 final size:21
Alignment explanation
Indices: 1182265--1182314 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
1182255 ATATTTTGAA
1182265 TAGTT-AA-TTTAAGTTATTT
1 TAGTTAAATTTTAAGTTATTT
*
1182284 TAGTTAAATTTTATGTTATTT
1 TAGTTAAATTTTAAGTTATTT
**
1182305 TTTTTAAATT
1 TAGTTAAATT
1182315 ACTTTAAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 5 0.19
20 2 0.08
21 19 0.73
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (21 bp):
TAGTTAAATTTTAAGTTATTT
Found at i:1191722 original size:8 final size:8
Alignment explanation
Indices: 1191695--1191765 Score: 76
Period size: 8 Copynumber: 9.1 Consensus size: 8
1191685 GACTTTCTCT
1191695 TTTCTT-C
1 TTTCTTCC
1191702 TTTC-TCC
1 TTTCTTCC
*
1191709 TCTCTTCC
1 TTTCTTCC
*
1191717 CTTCTTCC
1 TTTCTTCC
*
1191725 TTTCATCC
1 TTTCTTCC
1191733 TTTC-TCC
1 TTTCTTCC
*
1191740 TTTCTTTC
1 TTTCTTCC
1191748 TTTCTTCC
1 TTTCTTCC
1191756 TTTGCTTCC
1 TTT-CTTCC
1191765 T
1 T
1191766 AGCCAAATCT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
6 1 0.02
7 15 0.28
8 31 0.58
9 6 0.11
ACGTcount: A:0.01, C:0.38, G:0.01, T:0.59
Consensus pattern (8 bp):
TTTCTTCC
Found at i:1213135 original size:21 final size:22
Alignment explanation
Indices: 1213109--1213152 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1213099 CTAGAAAAAT
*
1213109 ACCTAAAA-CGCTAAAATCTAA
1 ACCTAAAATCGCAAAAATCTAA
*
1213130 ACCTAAAATCTCAAAAATCTAA
1 ACCTAAAATCGCAAAAATCTAA
1213152 A
1 A
1213153 GTTATAGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.55, C:0.23, G:0.02, T:0.20
Consensus pattern (22 bp):
ACCTAAAATCGCAAAAATCTAA
Found at i:1218963 original size:79 final size:79
Alignment explanation
Indices: 1218820--1218966 Score: 204
Period size: 79 Copynumber: 1.9 Consensus size: 79
1218810 TTAGCCCATA
* * * *
1218820 GTGTATATGACTATCTCAGCACATACATCTCATGGCATACATTTCATAACCTCATAAATCATTCA
1 GTGTATATGACTATCTCAACACATACATATCATGGCATACATTTCATAACCTCAGAAATAATTCA
1218885 CATTCTTCGCCTAC
66 CATTCTTCGCCTAC
* * * ** *
1218899 GTGTATATGACTATCTCAACATATACTTATCATGGCATGCATTTCATAAGTTTAGAAATAATTCA
1 GTGTATATGACTATCTCAACACATACATATCATGGCATACATTTCATAACCTCAGAAATAATTCA
1218964 CAT
66 CAT
1218967 CCTTAGTGTG
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
79 58 1.00
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (79 bp):
GTGTATATGACTATCTCAACACATACATATCATGGCATACATTTCATAACCTCAGAAATAATTCA
CATTCTTCGCCTAC
Found at i:1220609 original size:42 final size:42
Alignment explanation
Indices: 1220549--1220730 Score: 188
Period size: 42 Copynumber: 4.4 Consensus size: 42
1220539 AGTGTCCATA
* *
1220549 TTCCTATGATTTTGTTGTAAAGTGGATTAAGTATGTCTCCAC
1 TTCCCATGATTTTATTGTAAAGTGGATTAAGTATGTCTCCAC
* * * * * *
1220591 TTCTCATGATCTTATTGTAAATTAGATTGAGTATTTCTCCAC
1 TTCCCATGATTTTATTGTAAAGTGGATTAAGTATGTCTCCAC
* *
1220633 TTCCCATGATTTTATGGTAAAGTGGATTGAA-TA-GTCTCCAT
1 TTCCCATGATTTTATTGTAAAGTGGATT-AAGTATGTCTCCAC
* * * * * * *
1220674 TTCCCATGAGTTTGTTGTAAAATGGATTGAGTAGGTCTCAAA
1 TTCCCATGATTTTATTGTAAAGTGGATTAAGTATGTCTCCAC
1220716 TTCCCATGATTTTAT
1 TTCCCATGATTTTAT
1220731 ATATTGGCTC
Statistics
Matches: 112, Mismatches: 25, Indels: 6
0.78 0.17 0.04
Matches are distributed among these distances:
40 1 0.01
41 32 0.29
42 78 0.70
43 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.42
Consensus pattern (42 bp):
TTCCCATGATTTTATTGTAAAGTGGATTAAGTATGTCTCCAC
Found at i:1220702 original size:83 final size:84
Alignment explanation
Indices: 1220548--1220730 Score: 219
Period size: 83 Copynumber: 2.2 Consensus size: 84
1220538 AAGTGTCCAT
* * * * *
1220548 ATTCCTATGATTTTGTTGTAAAGTGGATTAAGTATGTCTCCACTTCTCATGATCTTATTGTAAAT
1 ATTCCCATGATTTTATGGTAAAGTGGATTAAGTATGTCTCCACTTCCCATGATCTTATTGTAAAA
** *
1220613 TAGATTGAGTATTTCTCCA
66 TAGATTGAGTAGGTCTCAA
* * *
1220632 CTTCCCATGATTTTATGGTAAAGTGGATTGAA-TA-GTCTCCATTTCCCATGAGT-TTGTTGTAA
1 ATTCCCATGATTTTATGGTAAAGTGGATT-AAGTATGTCTCCACTTCCCATGA-TCTTATTGTAA
*
1220694 AATGGATTGAGTAGGTCTCAA
64 AATAGATTGAGTAGGTCTCAA
1220715 ATTCCCATGATTTTAT
1 ATTCCCATGATTTTAT
1220731 ATATTGGCTC
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
83 54 0.64
84 28 0.33
85 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (84 bp):
ATTCCCATGATTTTATGGTAAAGTGGATTAAGTATGTCTCCACTTCCCATGATCTTATTGTAAAA
TAGATTGAGTAGGTCTCAA
Found at i:1227344 original size:14 final size:14
Alignment explanation
Indices: 1227325--1227352 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1227315 CCTCAAAATT
1227325 GTAAAAATACATCA
1 GTAAAAATACATCA
1227339 GTAAAAATACATCA
1 GTAAAAATACATCA
1227353 AGGTTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.21
Consensus pattern (14 bp):
GTAAAAATACATCA
Done.