Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 165 of 352
Found at i:54065354 original size:43 final size:43
Alignment explanation
Indices: 54065307--54065405 Score: 153
Period size: 43 Copynumber: 2.3 Consensus size: 43
54065297 CAGATATGGT
* *
54065307 CTTACATGAAATCGATTATCGATGCCACTGTCCCAGACAGGGC
1 CTTACATGAAATCGATTAACGATGCCAATGTCCCAGACAGGGC
* *
54065350 CTTACATGAAATCGATTAACGATGCCAATGTCCCAGACATGGT
1 CTTACATGAAATCGATTAACGATGCCAATGTCCCAGACAGGGC
*
54065393 CTTACATGTAATC
1 CTTACATGAAATC
54065406 ACATCTCGAT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (43 bp):
CTTACATGAAATCGATTAACGATGCCAATGTCCCAGACAGGGC
Found at i:54071032 original size:46 final size:45
Alignment explanation
Indices: 54070866--54071038 Score: 154
Period size: 46 Copynumber: 3.8 Consensus size: 45
54070856 AACCCGCCCC
* * * *
54070866 TAAGTGAACTCGGACTCAACTAAACGAGCTCGGGCGTTCACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTC-CATCCA
* *
54070912 TAAGTGAACTCGGACTCAACTCAACGAGTTC--AGATTCCTAGTTACA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCC-A--TCCA
* * * *
54070958 TTTCA-CGAACTTGAACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 --TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTC-CATCCA
* *
54071005 TAAGTGAACTCGGACTCAACTCCACGAGTCCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54071039 TGCTCAACCA
Statistics
Matches: 100, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
43 1 0.01
44 4 0.04
45 2 0.02
46 57 0.57
47 27 0.27
48 2 0.02
49 6 0.06
50 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.23
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCCATCCA
Found at i:54078078 original size:93 final size:93
Alignment explanation
Indices: 54077966--54078136 Score: 263
Period size: 93 Copynumber: 1.8 Consensus size: 93
54077956 GCCCCTAAGT
* * * *
54077966 GAACTCGGACTCAACTCAACGAGCTCGGGA-GTTCGCATTCATAAGTGAACTTGGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-AGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
54078030 ACGAGTTCAGATGCCTAGTTACATTTCAC
65 ACGAGTTCAGATGCCTAGTTACATTTCAC
* *
54078059 GAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCCA
1 GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
54078124 CGAGTTCGGATGC
66 CGAGTTCAGATGC
54078137 TCAACCATCC
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
92 2 0.03
93 68 0.97
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATTTCAC
Found at i:54078127 original size:46 final size:45
Alignment explanation
Indices: 54077961--54078130 Score: 159
Period size: 46 Copynumber: 3.7 Consensus size: 45
54077951 AACCCGCCCC
* * *
54077961 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGA-GTTCGCATTCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-AGACATTCGCA-TCA
* * *
54078007 TAAGTGAACTTGGACTCAACTCAACGAGTTCAGATGCCTAGTT-ACAT-T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGA---C-A-TTCGCATCA
* *
54078055 TCA-CGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCAT-CA
*
54078100 TAAGTGAACTCGGACTCAACTCCACGAGTTC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC
54078131 GGATGCTCAA
Statistics
Matches: 100, Mismatches: 14, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 4 0.04
46 54 0.54
47 28 0.28
48 2 0.02
49 1 0.01
50 2 0.02
51 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCAGACATTCGCATCA
Found at i:54085770 original size:51 final size:51
Alignment explanation
Indices: 54085713--54085817 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
54085703 ATTGCTTAGC
*
54085713 TATGTTTTATTATTTTTTGTAATTTGACTTTTTATTAAAAAAATGTATACA
1 TATGTTTCATTATTTTTTGTAATTTGACTTTTTATTAAAAAAATGTATACA
54085764 TATGTTTCATTATTTTTTGTAATTTGACTTTTTATTAAAAAAATGTATACA
1 TATGTTTCATTATTTTTTGTAATTTGACTTTTTATTAAAAAAATGTATACA
54085815 TAT
1 TAT
54085818 TAGTAGTAGT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.54
Consensus pattern (51 bp):
TATGTTTCATTATTTTTTGTAATTTGACTTTTTATTAAAAAAATGTATACA
Found at i:54088017 original size:21 final size:21
Alignment explanation
Indices: 54087978--54088017 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
54087968 ATTGTTGGAA
*
54087978 GTAACAATGAAATGGTAAAAC
1 GTAACAAAGAAATGGTAAAAC
* *
54087999 GTAACAAAGACATGTTAAA
1 GTAACAAAGAAATGGTAAA
54088018 TTCAAGATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.10, G:0.17, T:0.20
Consensus pattern (21 bp):
GTAACAAAGAAATGGTAAAAC
Found at i:54090775 original size:13 final size:13
Alignment explanation
Indices: 54090757--54090781 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54090747 ATATTCTGAA
54090757 ACACAAAAATAAC
1 ACACAAAAATAAC
54090770 ACACAAAAATAA
1 ACACAAAAATAA
54090782 TATTATAGTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.20, G:0.00, T:0.08
Consensus pattern (13 bp):
ACACAAAAATAAC
Found at i:54093470 original size:6 final size:6
Alignment explanation
Indices: 54093459--54093493 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
54093449 CATATCATAT
54093459 CATTGA CATTGA CATTGA CATTGA CATTGA CATTG
1 CATTGA CATTGA CATTGA CATTGA CATTGA CATTG
54093494 TCACATCAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (6 bp):
CATTGA
Found at i:54097197 original size:32 final size:32
Alignment explanation
Indices: 54097160--54097254 Score: 109
Period size: 32 Copynumber: 2.9 Consensus size: 32
54097150 GTGGTACAAC
* *
54097160 TTGGAAAGGTTATGTACACTTTGTGTGTACAT
1 TTGGAAAGGTTAGGTATACTTTGTGTGTACAT
* *
54097192 TTGGAAAGGTTAGGTATATTTTGTGTATACCAT
1 TTGGAAAGGTTAGGTATACTTTGTGTGTA-CAT
* * **
54097225 ATGAAAAGGAAAGGTATACTTTGTGTGTAC
1 TTGGAAAGGTTAGGTATACTTTGTGTGTAC
54097255 CACTTGAAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
32 26 0.50
33 26 0.50
ACGTcount: A:0.29, C:0.07, G:0.25, T:0.38
Consensus pattern (32 bp):
TTGGAAAGGTTAGGTATACTTTGTGTGTACAT
Found at i:54104809 original size:33 final size:33
Alignment explanation
Indices: 54104723--54104810 Score: 90
Period size: 33 Copynumber: 2.7 Consensus size: 33
54104713 GTTTATGTAC
* * **
54104723 ACTTTGTGTGTA-CACTCGGAAAAGTTAGGTAT
1 ACTTTGTGTGTACCACTTGAAAAAGAAAGGTAT
* *
54104755 ACTTTGTGTATACC-GTATGAAAAAGAAAGGTAT
1 ACTTTGTGTGTACCACT-TGAAAAAGAAAGGTAT
*
54104788 ACTTTGTATGTACCACTTGAAAA
1 ACTTTGTGTGTACCACTTGAAAA
54104811 TGAATGTACA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
32 12 0.27
33 31 0.70
34 1 0.02
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.33
Consensus pattern (33 bp):
ACTTTGTGTGTACCACTTGAAAAAGAAAGGTAT
Found at i:54110777 original size:47 final size:48
Alignment explanation
Indices: 54110669--54110895 Score: 179
Period size: 47 Copynumber: 4.8 Consensus size: 48
54110659 CGTGGGTAAG
* * * *
54110669 GTGCCGATGCCATGTCCCAGAAATGGTCTTACATTGGATCAT-ATCTCAA
1 GTGCCGATGCCATGTCCCAGACAGGGTCTTACACTGGCTC-TCATCTC-A
* * *
54110718 GT--CTATGCCATGTCCCAGACAGGGTCTTACACTGGCTATCATCT-T
1 GTGCCGATGCCATGTCCCAGACAGGGTCTTACACTGGCTCTCATCTCA
** * * *
54110763 GTAGTTGATG-CATGTCCCAGACA-TGTCTTACACTAGCTCTCGTCTCA
1 GT-GCCGATGCCATGTCCCAGACAGGGTCTTACACTGGCTCTCATCTCA
*
54110810 GTGCCGATGCCATGTCCCAGAC-GTGGTCTTACACTGGCTCTCATAATGC-
1 GTGCCGATGCCATGTCCCAGACAG-GGTCTTACACTGGCTCTCAT-CT-CA
* * *
54110859 G-GCCGATG-CATGTCCCAAACA-TGTCTTACACTAGCTC
1 GTGCCGATGCCATGTCCCAGACAGGGTCTTACACTGGCTC
54110896 ACACACAAAT
Statistics
Matches: 144, Mismatches: 23, Indels: 25
0.75 0.12 0.13
Matches are distributed among these distances:
45 2 0.01
46 38 0.26
47 72 0.50
48 27 0.19
49 4 0.03
50 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.29
Consensus pattern (48 bp):
GTGCCGATGCCATGTCCCAGACAGGGTCTTACACTGGCTCTCATCTCA
Found at i:54110840 original size:94 final size:94
Alignment explanation
Indices: 54110722--54110895 Score: 260
Period size: 94 Copynumber: 1.9 Consensus size: 94
54110712 TCTCAAGTCT
** * ** *
54110722 ATGCCATGTCCCAGACAGGGTCTTACACTGGCTATCATCTTGTAGTTGATGCATGTCCCAGACAT
1 ATGCCATGTCCCAGACAGGGTCTTACACTGGCTATCATAATGCAGCCGATGCATGTCCCAAACAT
54110787 GTCTTACACTAGCTCTCGTCTCAGTGCCG
66 GTCTTACACTAGCTCTCGTCTCAGTGCCG
* *
54110816 ATGCCATGTCCCAGAC-GTGGTCTTACACTGGCTCTCATAATGCGGCCGATGCATGTCCCAAACA
1 ATGCCATGTCCCAGACAG-GGTCTTACACTGGCTATCATAATGCAGCCGATGCATGTCCCAAACA
54110880 TGTCTTACACTAGCTC
65 TGTCTTACACTAGCTC
54110896 ACACACAAAT
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
93 1 0.01
94 70 0.99
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.28
Consensus pattern (94 bp):
ATGCCATGTCCCAGACAGGGTCTTACACTGGCTATCATAATGCAGCCGATGCATGTCCCAAACAT
GTCTTACACTAGCTCTCGTCTCAGTGCCG
Found at i:54120019 original size:40 final size:40
Alignment explanation
Indices: 54119936--54120198 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
54119926 TTGAATGCTG
* * * * * *
54119936 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
54119976 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
54120016 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
54120056 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
54120096 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
54120136 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
54120175 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
54120199 TGAACGAGGA
Statistics
Matches: 199, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.18
40 156 0.78
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:54120218 original size:79 final size:80
Alignment explanation
Indices: 54119975--54120233 Score: 238
Period size: 80 Copynumber: 3.3 Consensus size: 80
54119965 AAGTGAATAT
* * * * * * *
54119975 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAG
** * *
54120039 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
54120055 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
** ** *
54120120 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * * *
54120135 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
* *
54120199 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
54120214 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
54120234 TACGTGATTT
Statistics
Matches: 154, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 14 0.09
79 47 0.31
80 93 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
CGAACGAGGAGCTAA
Found at i:54127956 original size:40 final size:40
Alignment explanation
Indices: 54127873--54128135 Score: 316
Period size: 40 Copynumber: 6.6 Consensus size: 40
54127863 TTGAATGCTG
* * * * * *
54127873 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
54127913 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
54127953 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
54127993 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* *
54128033 TCCGGGTTAAGTCCCGAAGGCAGTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
54128073 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
54128112 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
54128136 TGAACGAGGA
Statistics
Matches: 199, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
39 35 0.18
40 156 0.78
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:54128155 original size:79 final size:80
Alignment explanation
Indices: 54127912--54128170 Score: 238
Period size: 80 Copynumber: 3.3 Consensus size: 80
54127902 AAGTGAATAT
* * * * * * *
54127912 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAG
** * *
54127976 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
54127992 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCAGT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
** ** *
54128057 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * * *
54128072 ATCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
* *
54128136 TGAACGAGGAGCTAT
66 CGAACGAGGAGCTAA
*
54128151 ATCC-GGTTAAATCCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
54128171 TACGTGATTT
Statistics
Matches: 154, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
78 14 0.09
79 47 0.31
80 93 0.60
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAGT
CGAACGAGGAGCTAA
Found at i:54130691 original size:46 final size:46
Alignment explanation
Indices: 54130595--54130816 Score: 180
Period size: 46 Copynumber: 4.7 Consensus size: 46
54130585 TATCTCAAGT
* * ** * * * *
54130595 CGATGTCATGTCCCAGACAGGGTCTTACATTAACTATCATCTTGTAGC
1 CGATG-CATGTCCCAGACA-TGTCTTACACTGGCTCTCGTCTCGTGGC
*
54130643 CGATGCATGTTCCAGACATGTCTTACACTGGCT-TACGTCTCGTGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTCT-CGTCTCGTGGC
* * * **
54130689 CGATGCATGTCCCAAACATGTCTTACACTAGCTCTCGTCTCAAT-AT
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTCTCGTCTC-GTGGC
* * * *
54130735 CGATGCCATGTCCTAGACATGGTCTTACACGGGCTCTCATAAT-GTGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCGT-CTCGTGGC
* *
54130783 TGATGCATGTCCCAGACATGTCTTACACTAGCTC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTC
54130817 ACACACAAAT
Statistics
Matches: 140, Mismatches: 27, Indels: 16
0.77 0.15 0.09
Matches are distributed among these distances:
45 1 0.01
46 73 0.52
47 40 0.29
48 25 0.18
49 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.30
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCTCTCGTCTCGTGGC
Found at i:54133026 original size:15 final size:15
Alignment explanation
Indices: 54133001--54133036 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
54132991 ATCACACTAT
54133001 CATAGTTCATTTATGG
1 CATA-TTCATTTATGG
*
54133017 CATATTCATTTGTGG
1 CATATTCATTTATGG
54133032 CATAT
1 CATAT
54133037 ATAGCTAGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.44
Consensus pattern (15 bp):
CATATTCATTTATGG
Found at i:54134626 original size:42 final size:42
Alignment explanation
Indices: 54134578--54134690 Score: 127
Period size: 43 Copynumber: 2.7 Consensus size: 42
54134568 AGTACAATAC
** **
54134578 CAATGCCATATCCCAGATATGGTCTTACATGGGATCTTAAAT
1 CAATGCCATATCCCAGATATGGTCTTACATGAAATCCCAAAT
* * *
54134620 CAATGCCAATAGCCCAGCTATGGTCTTACATGAAATCCCATAT
1 CAATGCC-ATATCCCAGATATGGTCTTACATGAAATCCCAAAT
** *
54134663 TGATGCCATATCCCAGATATAGTCTTAC
1 CAATGCCATATCCCAGATATGGTCTTAC
54134691 TCCTAAACTC
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
42 25 0.43
43 33 0.57
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (42 bp):
CAATGCCATATCCCAGATATGGTCTTACATGAAATCCCAAAT
Found at i:54152165 original size:42 final size:44
Alignment explanation
Indices: 54152065--54152178 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 44
54152055 CAATGCCAAC
* * *
54152065 ATCCCAGAC-GTGGTCTTACATGT-AACCAAATATCGATGACACT
1 ATCCCAGACAG-GGTCTTACACGTAAATCAAATATCGATGACAAT
* *
54152108 ATCCCAGACAGGGTCTTCCAC-TAAATCAAATAT-GATGTCAAT
1 ATCCCAGACAGGGTCTTACACGTAAATCAAATATCGATGACAAT
* *
54152150 GTCCCAGACATGGTCTTACACGTAAATCA
1 ATCCCAGACAGGGTCTTACACGTAAATCA
54152179 TAAGTCGATG
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
42 26 0.43
43 33 0.55
44 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (44 bp):
ATCCCAGACAGGGTCTTACACGTAAATCAAATATCGATGACAAT
Found at i:54164364 original size:13 final size:13
Alignment explanation
Indices: 54164346--54164371 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54164336 CACACTTAGT
54164346 GCCTCAAATTCAA
1 GCCTCAAATTCAA
54164359 GCCTCAAATTCAA
1 GCCTCAAATTCAA
54164372 TTCACATTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (13 bp):
GCCTCAAATTCAA
Found at i:54167960 original size:39 final size:40
Alignment explanation
Indices: 54167883--54167989 Score: 119
Period size: 40 Copynumber: 2.7 Consensus size: 40
54167873 TAGCTCCTCG
* * *
54167883 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
54167923 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
**
54167962 CACGAATGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
54167990 ATTAATAACT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 25 0.43
40 33 0.57
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:54167978 original size:40 final size:40
Alignment explanation
Indices: 54167926--54168069 Score: 143
Period size: 40 Copynumber: 3.6 Consensus size: 40
54167916 TAACTCATTC
* *
54167926 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
54167966 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
54168006 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
54168047 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
54168070 CAGCATTCAA
Statistics
Matches: 88, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
39 9 0.10
40 68 0.77
41 11 0.12
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:54175804 original size:39 final size:40
Alignment explanation
Indices: 54175727--54175873 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
54175717 TAGCTCCTCG
* * *
54175727 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
54175767 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
54175806 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
54175846 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
54175874 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:54175884 original size:80 final size:80
Alignment explanation
Indices: 54175773--54175953 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
54175763 CTCATTCAAT
* * *
54175773 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
54175836 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
54175852 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
54175916 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
54175933 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
54175954 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:54175913 original size:40 final size:40
Alignment explanation
Indices: 54175770--54175953 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
54175760 TAACTCATTC
* *
54175770 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
54175810 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
54175850 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
54175890 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
54175931 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
54175954 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:54182569 original size:11 final size:11
Alignment explanation
Indices: 54182536--54182569 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
54182526 GTACATATGC
*
54182536 TCTTTTTTTGT
1 TCTTTTTTTTT
*
54182547 TCTTTTTCTTT
1 TCTTTTTTTTT
54182558 TCTTTTTTTTT
1 TCTTTTTTTTT
54182569 T
1 T
54182570 TCATGAGCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (11 bp):
TCTTTTTTTTT
Found at i:54183847 original size:3 final size:3
Alignment explanation
Indices: 54183839--54183876 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
54183829 CTCTATGGGA
54183839 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
54183877 AGGATCCTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:54187206 original size:27 final size:27
Alignment explanation
Indices: 54187152--54187564 Score: 233
Period size: 27 Copynumber: 15.7 Consensus size: 27
54187142 TTAGTTTACC
* * *
54187152 AAATTA-CTAAATACCCTCGACTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* *
54187178 AAATTACCAAAGTACCCCCGATTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* * *
54187205 AAATTACCTAAATATCCTCGATTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
** *
54187232 AAATTACTGAAATA------A--GATA
1 AAATTACCAAAATACCCTCGATTTATA
* *** *
54187251 GAATTACCATTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* *** *
54187278 GAATTACCATTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
** * * *
54187305 AAATTACTGAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGATTTATA
** **
54187332 AAATTACCCTAATACCCTCGATCAATA
1 AAATTACCAAAATACCCTCGATTTATA
* *
54187359 AAATTACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTATA
* * *
54187386 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* *
54187413 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTATA
* * *
54187440 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* * *
54187467 AAATCACCAAAATACCC-CTAGTTTCTA
1 AAATTACCAAAATACCCTCGA-TTTATA
* *
54187494 AAATTACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTATA
* * * *
54187521 AAATTATCGAAATACCCT-GATTTGTG
1 AAATTACCAAAATACCCTCGATTTATA
* *
54187547 AAATTATCGAAATACCCT
1 AAATTACCAAAATACCCT
54187565 TGTAGGGTAG
Statistics
Matches: 305, Mismatches: 67, Indels: 30
0.76 0.17 0.07
Matches are distributed among these distances:
19 10 0.03
21 1 0.00
25 1 0.00
26 31 0.10
27 262 0.86
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTATA
Found at i:54187523 original size:54 final size:54
Alignment explanation
Indices: 54187356--54187566 Score: 282
Period size: 54 Copynumber: 3.9 Consensus size: 54
54187346 CCCTCGATCA
54187356 ATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTT
1 ATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTT
* * *
54187410 ACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTGGTTT
1 ATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTT
* * * *
54187464 ATAAAATCACCAAAATACCCCTAGTTTCTAAAATTACCAAAATACCCCTAGTTT
1 ATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTT
* * * * * *
54187518 GTAAAATTATCGAAATA-CCCT-GATTTGTGAAATTATCGAAATACCCTTG
1 ATAAAATTACCAAAATACCCCTAG-TTTGTAAAATTACCAAAATACCCTTG
54187567 TAGGGTAGAA
Statistics
Matches: 136, Mismatches: 20, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
52 1 0.01
53 24 0.18
54 111 0.82
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.31
Consensus pattern (54 bp):
ATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTT
Found at i:54187586 original size:27 final size:27
Alignment explanation
Indices: 54187548--54187877 Score: 439
Period size: 27 Copynumber: 12.3 Consensus size: 27
54187538 TGATTTGTGA
* *
54187548 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54187575 AATTATCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
54187602 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54187629 AATTACCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
54187656 AATTATC-ACAATACCCCTGTACGGTAA
1 AATTACCGA-AATACCCCTGTAGGGTAG
54187683 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* **
54187710 AATTACCAAAATACCCCTACAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54187737 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
54187764 AATTATCGCAATACCCTTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
**
54187791 AATTACTAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54187818 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
54187845 AATTACCGAGATA-CCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
54187871 AATTACC
1 AATTACC
54187878 ATTTTTCCCC
Statistics
Matches: 269, Mismatches: 32, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
26 18 0.07
27 250 0.93
28 1 0.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:54188356 original size:22 final size:22
Alignment explanation
Indices: 54188304--54188368 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
54188294 TTAAAGCCTT
* *
54188304 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
54188326 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
* *
54188348 CTGATTATGGTTGTGTGCCAA
1 CTGATTATGGCTCTGTGCCAA
54188369 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:54188557 original size:27 final size:27
Alignment explanation
Indices: 54188527--54188628 Score: 116
Period size: 27 Copynumber: 3.8 Consensus size: 27
54188517 ATTCTATTAT
* *
54188527 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTATGCCACAATATCTGTTTCTG
54188554 GTGGCTATGCCACAAATATCTG-TTCTG
1 GTGGCTATGCCAC-AATATCTGTTTCTG
* *
54188581 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTATGCCACAATATCTGTTTCTG
* * * *
54188608 GTGACTCTGTCATAATATCTG
1 GTGGCTATGCCACAATATCTG
54188629 ATAACTGAGC
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 8 0.12
27 51 0.77
28 7 0.11
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.37
Consensus pattern (27 bp):
GTGGCTATGCCACAATATCTGTTTCTG
Found at i:54188809 original size:31 final size:31
Alignment explanation
Indices: 54188765--54188845 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
54188755 TTGCATTCAC
54188765 ATTCTGATTTTTGATTCTGTTACCTCATACTA
1 ATTCTGA-TTTTGATTCTGTTACCTCATACTA
* * *
54188797 ATTCTGGTTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTCATACTA
* *
54188828 ATTTTGATTCTGATTCTG
1 ATTCTGATTTTGATTCTG
54188846 ATTCTAGTTC
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 37 0.86
32 6 0.14
ACGTcount: A:0.19, C:0.16, G:0.15, T:0.51
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTCATACTA
Found at i:54190835 original size:27 final size:27
Alignment explanation
Indices: 54190805--54191193 Score: 131
Period size: 27 Copynumber: 14.7 Consensus size: 27
54190795 TTAGTTTACC
* *
54190805 AAATTACTGAAATACCCTCGACTTGTA
1 AAATTACTCAAATACCCTCGATTTGTA
*
54190832 AAATTAC-CAAAGTACCC-CTGATTTATA
1 AAATTACTCAAA-TACCCTC-GATTTGTA
* *
54190859 AAATTACCCAAATATCCTCGATTTGTA
1 AAATTACTCAAATACCCTCGATTTGTA
* *
54190886 AAATTACTGAAATA----AGA----TA
1 AAATTACTCAAATACCCTCGATTTGTA
* ** * **
54190905 GAATTAC-CATTTTACCCTTGATTTACA
1 AAATTACTCA-AATACCCTCGATTTGTA
* * * **
54190932 AAATTACTGAAATACCCTTGGTTTACA
1 AAATTACTCAAATACCCTCGATTTGTA
* * ***
54190959 AAATTACCCAAATACCCTCAATCAATA
1 AAATTACTCAAATACCCTCGATTTGTA
*
54190986 AAATTAC-CAAAATACCC-CTGGTTTGTA
1 AAATTACTC-AAATACCCTC-GATTTGTA
* * * **
54191013 AGATTAC-CAAAATACCCTTGGTTTACA
1 AAATTACTC-AAATACCCTCGATTTGTA
* *
54191040 AAATTAC-CAAAATACCC-CTGGTTTATA
1 AAATTACTC-AAATACCCTC-GATTTGTA
* * * *
54191067 AAATTACTAAAATACCCTTTGGTTTATA
1 AAATTACTCAAATACCC-TCGATTTGTA
*
54191095 AAATTAC-CAAAATACCC-CTAGTTTGTA
1 AAATTACTC-AAATACCCTCGA-TTTGTA
*
54191122 AAATTAC-CAAAATATCCCTAG-TTTGTA
1 AAATTACTC-AAATA-CCCTCGATTTGTA
*
54191149 AAATTA-TCGAAATACCC-CTGATTTGTG
1 AAATTACTC-AAATACCCTC-GATTTGTA
54191176 AAATTA-TCGAAATACCCT
1 AAATTACTC-AAATACCCT
54191194 GTAGGGTAGA
Statistics
Matches: 282, Mismatches: 51, Indels: 57
0.72 0.13 0.15
Matches are distributed among these distances:
18 1 0.00
19 10 0.04
23 4 0.01
26 10 0.04
27 225 0.80
28 32 0.11
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATTACTCAAATACCCTCGATTTGTA
Found at i:54190887 original size:54 final size:53
Alignment explanation
Indices: 54190805--54191193 Score: 249
Period size: 54 Copynumber: 7.3 Consensus size: 53
54190795 TTAGTTTACC
** * *
54190805 AAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCCTGATTTATA
1 AAATTACCAAAATACCCTCGATTTATAAAATTACCAAA-TACCCCTGATTTATA
* * * * *
54190859 AAATTACCCAAATATCCTCGATTTGTAAAATTACTGAAATA------A--GATA
1 AAATTACCAAAATACCCTCGATTTATAAAATTAC-CAAATACCCCTGATTTATA
* *** * * * * * *
54190905 GAATTACCATTTTACCCTTGATTTACAAAATTACTGAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGATTTATAAAATTAC-CAAATACCCCTGATTTATA
* * ** * *
54190959 AAATTACCCAAATACCCTCAATCAATAAAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCTCGATTTATAAAATTACC-AAATACCCCTGATTTATA
* * * * *
54191013 AGATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTGGTTTATA
1 AAATTACCAAAATACCCTCGATTTATAAAATTACC-AAATACCCCTGATTTATA
* * * *
54191067 AAATTACTAAAATACCCTTTGGTTTATAAAATTACCAAAATACCCCT-AGTTTGTA
1 AAATTACCAAAATACCC-TCGATTTATAAAATTACC-AAATACCCCTGA-TTTATA
* * * * *
54191122 AAATTACCAAAATATCCCTAG-TTTGTAAAATTATCGAAATACCCCTGATTTGTG
1 AAATTACCAAAATA-CCCTCGATTTATAAAATTA-CCAAATACCCCTGATTTATA
* *
54191176 AAATTATCGAAATACCCT
1 AAATTACCAAAATACCCT
54191194 GTAGGGTAGA
Statistics
Matches: 267, Mismatches: 53, Indels: 31
0.76 0.15 0.09
Matches are distributed among these distances:
46 35 0.13
48 1 0.00
53 4 0.01
54 171 0.64
55 53 0.20
56 3 0.01
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (53 bp):
AAATTACCAAAATACCCTCGATTTATAAAATTACCAAATACCCCTGATTTATA
Found at i:54191128 original size:82 final size:81
Alignment explanation
Indices: 54190917--54191192 Score: 266
Period size: 81 Copynumber: 3.4 Consensus size: 81
54190907 ATTACCATTT
* * * ** * * * *
54190917 TACCCTTGATTTACAAAATTACTGAAATACCCTTGGTTTACAAAATTACCCAAATA-CCCTCAAT
1 TACCCCTGGTTTATAAAATTACCAAAATACCCCTAGTTTACAAAATTACCAAAATACCCCT-AGT
**
54190981 CAATAAAATTACCAAAA
65 TTATAAAATTACCAAAA
* * * * *
54190998 TACCCCTGGTTTGTAAGATTACCAAAATACCCTTGGTTTACAAAATTACCAAAATACCCCTGGTT
1 TACCCCTGGTTTATAAAATTACCAAAATACCCCTAGTTTACAAAATTACCAAAATACCCCTAGTT
*
54191063 TATAAAATTACTAAAA
66 TATAAAATTACCAAAA
* ** *
54191079 TACCCTTTGGTTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAATATCCCTAGT
1 TACCC-CTGGTTTATAAAATTACCAAAATACCCCTAGTTTACAAAATTACCAAAATACCCCTAGT
* * *
54191144 TTGTAAAATTATCGAAA
65 TTATAAAATTACCAAAA
* * * * *
54191161 TACCCCTGATTTGTGAAATTATCGAAATACCC
1 TACCCCTGGTTTATAAAATTACCAAAATACCC
54191193 TGTAGGGTAG
Statistics
Matches: 161, Mismatches: 32, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
81 89 0.55
82 72 0.45
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.31
Consensus pattern (81 bp):
TACCCCTGGTTTATAAAATTACCAAAATACCCCTAGTTTACAAAATTACCAAAATACCCCTAGTT
TATAAAATTACCAAAA
Found at i:54191193 original size:109 final size:109
Alignment explanation
Indices: 54190917--54191181 Score: 293
Period size: 109 Copynumber: 2.4 Consensus size: 109
54190907 ATTACCATTT
** * * * ** ***
54190917 TACCCTT-GATTTACAAAATTACTGAAATACCCTTGGTTTACAAAATTACCCAAATACCC-TCAA
1 TACCCTTAG-TTTACAAAATTACCAAAATACCCCTGATTTATAAAATTACTAAAATACCCTTTGG
** * *
54190980 TCAATAAAATTACCAAAATACCCCTGGTTTGTAAGATTACCAAAA
65 TTTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAA
* *
54191025 TACCCTTGGTTTACAAAATTACCAAAATACCCCTGGTTTATAAAATTACTAAAATACCCTTTGGT
1 TACCCTTAGTTTACAAAATTACCAAAATACCCCTGATTTATAAAATTACTAAAATACCCTTTGGT
54191090 TTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAA
66 TTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAA
** * * * *
54191134 TATCCC-TAGTTTGTAAAATTATCGAAATACCCCTGATTTGTGAAATTA
1 TA-CCCTTAGTTTACAAAATTACCAAAATACCCCTGATTTATAAAATTA
54191182 TCGAAATACC
Statistics
Matches: 133, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
108 51 0.38
109 79 0.59
110 3 0.02
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (109 bp):
TACCCTTAGTTTACAAAATTACCAAAATACCCCTGATTTATAAAATTACTAAAATACCCTTTGGT
TTATAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAAA
Found at i:54191231 original size:27 final size:27
Alignment explanation
Indices: 54191177--54191622 Score: 644
Period size: 27 Copynumber: 16.6 Consensus size: 27
54191167 TGATTTGTGA
*
54191177 AATTATCGAAATA-CCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54191203 AATTACCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
54191230 AATTACCGGAATACCCTTGT-GTGGTAG
1 AATTACCGAAATACCCCTGTAG-GGTAG
* *
54191257 AATTACCGGAATACCCCTGTAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
54191284 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
54191311 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
54191338 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54191365 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** * *
54191392 AATTATTGCAATACCCCTGTAAGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
54191419 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
54191446 AATTATCGCAATACCCCTGTAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54191473 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
54191500 AATTACTGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * *
54191527 AATTATCGCAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
54191554 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*** *
54191581 AATTAGTAAAATACCCCTGTAGGGTGG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
54191608 AATTACCGAGATACC
1 AATTACCGAAATACC
54191623 TTGTGGGCTA
Statistics
Matches: 380, Mismatches: 37, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
26 13 0.03
27 366 0.96
28 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:54192092 original size:22 final size:22
Alignment explanation
Indices: 54192040--54192104 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
54192030 TTAAAGCCTT
* *
54192040 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
54192062 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
* * *
54192084 TTGATTATGGCTGTATGCCAA
1 CTGATTATGGCTCTGTGCCAA
54192105 ACGTATTTGC
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
21 1 0.03
22 32 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:54192293 original size:27 final size:27
Alignment explanation
Indices: 54192263--54192364 Score: 116
Period size: 27 Copynumber: 3.8 Consensus size: 27
54192253 ATTCTGTTAT
* *
54192263 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTATGCCACAATATCTGTTTCTG
54192290 GTGGCTATGCCACAAATATCTG-TTCTG
1 GTGGCTATGCCAC-AATATCTGTTTCTG
* * *
54192317 GTGGCTCTGCCACAATATCTGTATCTA
1 GTGGCTATGCCACAATATCTGTTTCTG
* * *
54192344 GTGACTCTGTCACAATATCTG
1 GTGGCTATGCCACAATATCTG
54192365 ATAACTGAGC
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 8 0.12
27 51 0.77
28 7 0.11
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.36
Consensus pattern (27 bp):
GTGGCTATGCCACAATATCTGTTTCTG
Found at i:54192321 original size:54 final size:52
Alignment explanation
Indices: 54192255--54192364 Score: 130
Period size: 54 Copynumber: 2.1 Consensus size: 52
54192245 TGCCACGTAT
* * * * *
54192255 TCTGTTATGTGGCTTTGCCACATTATCTGTTTCTGGTGGCTATGCCACAAATA
1 TCTGTTATGTGGCTCTGCCACAATATCTGTATCTAGTGACTATGCCAC-AATA
* * *
54192308 TCTGTTCTGGTGGCTCTGCCACAATATCTGTATCTAGTGACTCTGTCACAATA
1 TCTGTTAT-GTGGCTCTGCCACAATATCTGTATCTAGTGACTATGCCACAATA
54192361 TCTG
1 TCTG
54192365 ATAACTGAGC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 15 0.31
54 33 0.69
ACGTcount: A:0.19, C:0.23, G:0.20, T:0.38
Consensus pattern (52 bp):
TCTGTTATGTGGCTCTGCCACAATATCTGTATCTAGTGACTATGCCACAATA
Found at i:54192539 original size:6 final size:6
Alignment explanation
Indices: 54192501--54192578 Score: 52
Period size: 6 Copynumber: 12.5 Consensus size: 6
54192491 TTGCATTCAC
* * *
54192501 ATTCTG AGTTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTTTG ATTCTG
1 ATTCTG A-TTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* *
54192551 -TTACCTG ATACTG ATTTTG ATTCTG ATT
1 ATT--CTG ATTCTG ATTCTG ATTCTG ATT
54192579 TTGTCACCTA
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
5 4 0.07
6 38 0.69
7 11 0.20
8 2 0.04
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (6 bp):
ATTCTG
Found at i:54192546 original size:12 final size:12
Alignment explanation
Indices: 54192531--54192581 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
54192521 TACCTGATAC
54192531 TGATTCTGATTT
1 TGATTCTGATTT
*
54192543 TGATTCTG-TTACC
1 TGATTCTGATT--T
*
54192556 TGATACTGATTT
1 TGATTCTGATTT
54192568 TGATTCTGATTT
1 TGATTCTGATTT
54192580 TG
1 TG
54192582 TCACCTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
11 2 0.06
12 21 0.66
13 7 0.22
14 2 0.06
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.53
Consensus pattern (12 bp):
TGATTCTGATTT
Found at i:54192546 original size:31 final size:31
Alignment explanation
Indices: 54192501--54192587 Score: 129
Period size: 31 Copynumber: 2.8 Consensus size: 31
54192491 TTGCATTCAC
54192501 ATTCTGAGTTTTGATTCTGTTACCTGATACTG
1 ATTCTGA-TTTTGATTCTGTTACCTGATACTG
54192533 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTTTGATTCTGTTACCTGATACTG
* * * *
54192564 ATTTTGATTCTGATTTTGTCACCT
1 ATTCTGATTTTGATTCTGTTACCT
54192588 AATTTTCATT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 44 0.86
32 7 0.14
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.49
Consensus pattern (31 bp):
ATTCTGATTTTGATTCTGTTACCTGATACTG
Found at i:54197080 original size:29 final size:27
Alignment explanation
Indices: 54197062--54197131 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
54197052 ATATTAAGTC
54197062 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
54197089 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
54197117 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
54197132 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:54197125 original size:28 final size:28
Alignment explanation
Indices: 54197062--54197159 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
54197052 ATATTAAGTC
*
54197062 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
54197089 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
54197117 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
54197146 CGCACACTTAGTGC
1 CGCACACTTAGTGC
54197160 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:54206007 original size:27 final size:27
Alignment explanation
Indices: 54205955--54206010 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
54205945 ATAATTTAAG
*
54205955 TACAATTTAATTATTTTATAATAATTA
1 TACAATTTAATTATTTTATAAGAATTA
54205982 TACAATTTAATTATTTTATAAGAATTA
1 TACAATTTAATTATTTTATAAGAATTA
54206009 TA
1 TA
54206011 TATTTTTGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.50
Consensus pattern (27 bp):
TACAATTTAATTATTTTATAAGAATTA
Found at i:54213915 original size:19 final size:19
Alignment explanation
Indices: 54213867--54213905 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
54213857 GTGATCCTTG
54213867 TTTCTAAAATTTTCATATT
1 TTTCTAAAATTTTCATATT
54213886 TTTCTAAAATTTTC-TATT
1 TTTCTAAAATTTTCATATT
54213904 TT
1 TT
54213906 GTTTCAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTCTAAAATTTTCATATT
Found at i:54216350 original size:28 final size:28
Alignment explanation
Indices: 54216335--54216397 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
54216325 GTCTTTGGTG
*
54216335 GACATTCCACATAAGATAGCCCATGGCA
1 GACATTCCACATAAGATAGTCCATGGCA
* *
54216363 GACATTCCACGTAAGATAGTCCATGGCG
1 GACATTCCACATAAGATAGTCCATGGCA
54216391 GAC-TTCC
1 GACATTCC
54216398 TTTTTTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 4 0.12
28 28 0.88
ACGTcount: A:0.30, C:0.29, G:0.21, T:0.21
Consensus pattern (28 bp):
GACATTCCACATAAGATAGTCCATGGCA
Found at i:54222744 original size:27 final size:27
Alignment explanation
Indices: 54222713--54222771 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
54222703 ACATCATACT
54222713 TAGTCCGATGAGACATTAAACAC-GGG
1 TAGTCCGATGAGACATTAAACACAGGG
* * *
54222739 ATAGTCCTATGGGACGTTAAACACAGGG
1 -TAGTCCGATGAGACATTAAACACAGGG
54222767 TAGTC
1 TAGTC
54222772 TACTGGGCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 25 0.89
28 3 0.11
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (27 bp):
TAGTCCGATGAGACATTAAACACAGGG
Found at i:54237785 original size:31 final size:31
Alignment explanation
Indices: 54237734--54237847 Score: 92
Period size: 31 Copynumber: 3.5 Consensus size: 31
54237724 TATAAAATTA
54237734 ATAATACATAAGATATTTTAAA-AACTTAAAT
1 ATAATACATAAGATATTTTAAATAA-TTAAAT
*
54237765 ATAATA-ATAA-ATTATATTTAAATAATTTAAT
1 ATAATACATAAGA-TAT-TTTAAATAATTAAAT
*
54237796 ATAATGTTACATAAAATA-TTTAAATAATTTAACAT
1 ATAA---TACATAAGATATTTTAAATAA-TTAA-AT
*
54237831 AATAATACATAAAATAT
1 -ATAATACATAAGATAT
54237848 AAATTGATCT
Statistics
Matches: 69, Mismatches: 2, Indels: 21
0.75 0.02 0.23
Matches are distributed among these distances:
29 1 0.01
30 7 0.10
31 21 0.30
32 2 0.03
33 20 0.29
34 5 0.07
35 8 0.12
36 5 0.07
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (31 bp):
ATAATACATAAGATATTTTAAATAATTAAAT
Found at i:54237818 original size:33 final size:33
Alignment explanation
Indices: 54237732--54237847 Score: 132
Period size: 33 Copynumber: 3.5 Consensus size: 33
54237722 TATATAAAAT
* *
54237732 TAATAATACATAAGATATTTTAAA-AACTTAA-A
1 TAATAATACATAAAATA-TTTAAATAATTTAACA
*
54237764 T-ATAATA-ATAAATTATATTTAAATAATTTAATA
1 TAATAATACATAAA--ATATTTAAATAATTTAACA
**
54237797 TAATGTTACATAAAATATTTAAATAATTTAACA
1 TAATAATACATAAAATATTTAAATAATTTAACA
54237830 TAATAATACATAAAATAT
1 TAATAATACATAAAATAT
54237848 AAATTGATCT
Statistics
Matches: 71, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
30 4 0.06
31 12 0.17
32 10 0.14
33 36 0.51
34 4 0.06
35 5 0.07
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (33 bp):
TAATAATACATAAAATATTTAAATAATTTAACA
Found at i:54237830 original size:23 final size:24
Alignment explanation
Indices: 54237784--54237837 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 24
54237774 AATTATATTT
54237784 AAATAATTTAATATAATGTTACATA
1 AAAT-ATTTAATATAATGTTACATA
54237809 AAATATTTAA-ATAAT-TTAACATA
1 AAATATTTAATATAATGTT-ACATA
54237832 ATAATA
1 A-AATA
54237838 CATAAAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 2 0.07
23 11 0.41
24 10 0.37
25 4 0.15
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (24 bp):
AAATATTTAATATAATGTTACATA
Found at i:54242904 original size:19 final size:19
Alignment explanation
Indices: 54242854--54242904 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
54242844 TAAAAATAAA
*
54242854 ATACATGTGTATTGAATATT
1 ATACATGTAT-TTGAATATT
**
54242874 ATACATACATTTGTAATA-T
1 ATACATGTATTTG-AATATT
54242893 ATACATGTATTT
1 ATACATGTATTT
54242905 ACTTATAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (19 bp):
ATACATGTATTTGAATATT
Found at i:54242945 original size:5 final size:5
Alignment explanation
Indices: 54242937--54242968 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
54242927 ATTATTAAGT
54242937 TAATA TAATA TAATA TAATA TAATA TAATA TA
1 TAATA TAATA TAATA TAATA TAATA TAATA TA
54242969 GCATAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
TAATA
Found at i:54242974 original size:15 final size:15
Alignment explanation
Indices: 54242941--54242983 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
54242931 TTAAGTTAAT
*
54242941 ATAATATAATATAAT
1 ATAATATAATATAAC
*
54242956 ATAATATAATATAGC
1 ATAATATAATATAAC
*
54242971 ATAA-ATTATATAA
1 ATAATATAATATAA
54242984 TAGAAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 7 0.29
15 17 0.71
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (15 bp):
ATAATATAATATAAC
Found at i:54244065 original size:41 final size:43
Alignment explanation
Indices: 54243994--54244087 Score: 120
Period size: 41 Copynumber: 2.2 Consensus size: 43
54243984 CGACCTCAAG
* * *
54243994 TCGATGAGGCACTATATGTGTCGTAATATTGCTTCGGA-TAATT
1 TCGATGAGGCAC-ATATGTGTCATAATATTGCTTCAGATTAAAT
*
54244037 TCGATGAGGCAC-TATGTGTCATATTATTGCTTCAGATTAAAT
1 TCGATGAGGCACATATGTGTCATAATATTGCTTCAGATTAAAT
*
54244079 CCGATGAGG
1 TCGATGAGG
54244088 TATTGAGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 21 0.47
42 12 0.27
43 12 0.27
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (43 bp):
TCGATGAGGCACATATGTGTCATAATATTGCTTCAGATTAAAT
Found at i:54248912 original size:42 final size:43
Alignment explanation
Indices: 54248804--54248916 Score: 131
Period size: 43 Copynumber: 2.7 Consensus size: 43
54248794 AACATATACA
* *
54248804 ATGCCACCGTCCCAGACATGGTCTTACATGTAATAAAACATCG
1 ATGCCACTGTCCCAGACATGGTCTTACATGAAATAAAACATCG
* * * * *
54248847 ATGCCACTGTCCCAGATAGGGTCTTACATGAAATCAGATAT-G
1 ATGCCACTGTCCCAGACATGGTCTTACATGAAATAAAACATCG
*
54248889 ATGTCGA-TGTCCCAGACATGGTCTTACA
1 ATG-CCACTGTCCCAGACATGGTCTTACA
54248917 CGTAAAATAG
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
42 23 0.39
43 36 0.61
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (43 bp):
ATGCCACTGTCCCAGACATGGTCTTACATGAAATAAAACATCG
Found at i:54254580 original size:58 final size:58
Alignment explanation
Indices: 54254463--54254585 Score: 158
Period size: 58 Copynumber: 2.1 Consensus size: 58
54254453 AATCACCAAC
* * * * * *
54254463 TATACTTGAAAAAATTTTGAAAGATAACCAACTGGGGATGTGAATCTATGAGTTTTTT
1 TATACTTGAAAAAATTCTGAAAGATAACCAACTAGGGATGTGAATCCACGAGCTGTTT
* *
54254521 TATACTT-AAGAAAATTCTGAGAGATAACCAACTAGGGATGTGAATCCGCGAGCTGTTT
1 TATACTTGAA-AAAATTCTGAAAGATAACCAACTAGGGATGTGAATCCACGAGCTGTTT
54254579 TATACTT
1 TATACTT
54254586 CCTTAAAATT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
57 2 0.04
58 54 0.96
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (58 bp):
TATACTTGAAAAAATTCTGAAAGATAACCAACTAGGGATGTGAATCCACGAGCTGTTT
Found at i:54254845 original size:70 final size:70
Alignment explanation
Indices: 54254654--54255102 Score: 342
Period size: 70 Copynumber: 6.4 Consensus size: 70
54254644 GAGGCAGTAG
* * * * * **
54254654 TTTTTATCCTATGAGCCTTAATATGACAACTT-GGAGCTTTGCT-TTCACTAACTATGTTAAAGG
1 TTTTTATCTTACGAGCCTTAGTATGACAA-TTGGGAGCTTTGCTCTT-GCTAACTGTGTTGGAGG
* *
54254717 CTATGGTT
64 CT-TCGAT
* ** *
54254725 TTTTTATTCTATA--AGTCTTAGTATGACAGCTGGGAGCTTTACT-TTCGCTAACTGTGTTGGAG
1 TTTTTA-TCT-TACGAGCCTTAGTATGACAATTGGGAGCTTTGCTCTT-GCTAACTGTGTTGGAG
54254787 GCTTCGAT
63 GCTTCGAT
* * ** * * *
54254795 TTTTTATCTTACGATCCTTAGTATGATAGCTGGGAGTTTTGCTCTTGCTAACTGTATTTGAGGCT
1 TTTTTATCTTACGAGCCTTAGTATGACAATTGGGAGCTTTGCTCTTGCTAACTGTGTTGGAGGCT
*
54254860 GT-GGT
66 -TCGAT
* * * *
54254865 TTTTTATAC-TGCGAGCCTTAGAATGACAATTGGGAGCTTTTCT-TTCGCTAACTATGTTGGAGG
1 TTTTTAT-CTTACGAGCCTTAGTATGACAATTGGGAGCTTTGCTCTT-GCTAACTGTGTTGGAGG
*
54254928 -TTACGAG
64 CTT-CGAT
* * ** * * *
54254935 TTTTTATCTTGCGAGCCTTAGTATGACAATTGGGAGCTTTGTTCTCACCAATTGTGTTGAAGGCT
1 TTTTTATCTTACGAGCCTTAGTATGACAATTGGGAGCTTTGCTCTTGCTAACTGTGTTGGAGGCT
*
54255000 ATAG-T
66 -TCGAT
* * * * * * *
54255005 TTTTTATCCTACGAGCCTTAATATGATAATTAGGAGCTTTGCTCTCGCTAACCGTGATGGAGGCT
1 TTTTTATCTTACGAGCCTTAGTATGACAATTGGGAGCTTTGCTCTTGCTAACTGTGTTGGAGGCT
*
54255070 GCGAT
66 TCGAT
*
54255075 TTTTTATCTTATGAGCCTTAGTATGACA
1 TTTTTATCTTACGAGCCTTAGTATGACA
54255103 TAAATGTTGT
Statistics
Matches: 300, Mismatches: 62, Indels: 33
0.76 0.16 0.08
Matches are distributed among these distances:
68 3 0.01
69 8 0.03
70 230 0.77
71 54 0.18
72 3 0.01
73 2 0.01
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (70 bp):
TTTTTATCTTACGAGCCTTAGTATGACAATTGGGAGCTTTGCTCTTGCTAACTGTGTTGGAGGCT
TCGAT
Found at i:54254891 original size:140 final size:140
Alignment explanation
Indices: 54254625--54255102 Score: 462
Period size: 140 Copynumber: 3.4 Consensus size: 140
54254615 GGAGTTTTTA
* * * * * * *
54254625 ACTTTCGCTAACTATGTTGGAGGC--AGTAGTTTTTATCCTATGAGCCTTAATATGACAACTTGG
1 ACTTTCGCTAACTGTGTTGGAGGCTTCG-ATTTTTTATCTTACGAGCCTTAGTATGACAACTGGG
* * * * * * ** * *
54254688 AGCTTTGCTTTCACTAACTATGTTAAAGGCTATGGTTTTTTTATTCTATAAGTCTTAGTATGACA
65 AGCTTTGCTCTCACCAACTGTGTTGAAGGCTATAG-TTTTTTATACTACGAGCCTTAGAATGACA
**
54254753 GCTGGGAGCTTT
129 ATTGGGAGCTTT
* * *
54254765 ACTTTCGCTAACTGTGTTGGAGGCTTCGATTTTTTATCTTACGATCCTTAGTATGATAGCTGGGA
1 ACTTTCGCTAACTGTGTTGGAGGCTTCGATTTTTTATCTTACGAGCCTTAGTATGACAACTGGGA
* ** * * * * *
54254830 GTTTTGCTCTTGCTAACTGTATTTG-AGGCTGTGGTTTTTTATACTGCGAGCCTTAGAATGACAA
66 GCTTTGCTCTCACCAACTGT-GTTGAAGGCTATAGTTTTTTATACTACGAGCCTTAGAATGACAA
54254894 TTGGGAGCTTT
130 TTGGGAGCTTT
* * * * *
54254905 TCTTTCGCTAACTATGTTGGAGG-TTACGAGTTTTTATCTTGCGAGCCTTAGTATGACAATTGGG
1 ACTTTCGCTAACTGTGTTGGAGGCTT-CGATTTTTTATCTTACGAGCCTTAGTATGACAACTGGG
* * * *
54254969 AGCTTTGTTCTCACCAATTGTGTTGAAGGCTATAGTTTTTTATCCTACGAGCCTTA-ATATGATA
65 AGCTTTGCTCTCACCAACTGTGTTGAAGGCTATAGTTTTTTATACTACGAGCCTTAGA-ATGACA
*
54255033 ATTAGGAGCTTT
129 ATTGGGAGCTTT
* * * * * *
54255045 GCTCTCGCTAACCGTGATGGAGGCTGCGATTTTTTATCTTATGAGCCTTAGTATGACA
1 ACTTTCGCTAACTGTGTTGGAGGCTTCGATTTTTTATCTTACGAGCCTTAGTATGACA
54255103 TAAATGTTGT
Statistics
Matches: 275, Mismatches: 56, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
139 6 0.02
140 213 0.77
141 53 0.19
142 3 0.01
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (140 bp):
ACTTTCGCTAACTGTGTTGGAGGCTTCGATTTTTTATCTTACGAGCCTTAGTATGACAACTGGGA
GCTTTGCTCTCACCAACTGTGTTGAAGGCTATAGTTTTTTATACTACGAGCCTTAGAATGACAAT
TGGGAGCTTT
Found at i:54255093 original size:210 final size:209
Alignment explanation
Indices: 54254654--54255102 Score: 455
Period size: 210 Copynumber: 2.1 Consensus size: 209
54254644 GAGGCAGTAG
54254654 TTTTTATCCTATGAGCCTTA-ATATGACAACTTGGAGCTTTGCTTTCACTAACTATGTTAAAGGC
1 TTTTTAT-CTATGAGCCTTAGA-ATGACAACTTGGAGCTTTGCTTTCACTAACTATGTTAAAGGC
* * * * *
54254718 TATGGTTTTTTTATTCTATAAGTCTTAGTATGACAGCTGGGAGCTTTACTTTCGCTAACTGTGTT
64 TACGG-TTTTTTATTCTATAAGCCTTAGTATGACAACTGGGAGCTTTACTTTCACCAACTGTGTT
* * * * * * * * * *
54254783 GGAGGCTTCGATTTTTTATCTTACGATCCTTAGTATGATAGCTGGGAGTTTTGCTCTTGCTAACT
128 GAAGGCTTAGATTTTTTATCCTACGAGCCTTAATATGATAACTAGGAGCTTTGCTCTCGCTAACC
* * *
54254848 GTATTTGAGGCTGTGGT
193 GTATTGGAGGCTGCGAT
** * * ** *
54254865 TTTTTATACTGCGAGCCTTAGAATGACAA-TTGGGAGCTTTTCTTTCGCTAACTATGTTGGAGGT
1 TTTTTAT-CTATGAGCCTTAGAATGACAACTT-GGAGCTTTGCTTTCACTAACTATGTTAAAGGC
* * * *
54254929 TACGAG-TTTTTA-TCT-TGCGAGCCTTAGTATGACAATTGGGAGCTTT-GTTCTCACCAATTGT
64 TACG-GTTTTTTATTCTAT--AAGCCTTAGTATGACAACTGGGAGCTTTACTT-TCACCAACTGT
*
54254990 GTTGAAGGCTATAG-TTTTTTATCCTACGAGCCTTAATATGATAATTAGGAGCTTTGCTCTCGCT
125 GTTGAAGGCT-TAGATTTTTTATCCTACGAGCCTTAATATGATAACTAGGAGCTTTGCTCTCGCT
54255054 AACCGTGA-TGGAGGCTGCGAT
189 AACCGT-ATTGGAGGCTGCGAT
*
54255075 TTTTTATCTTATGAGCCTTAGTATGACA
1 TTTTTATC-TATGAGCCTTAGAATGACA
54255103 TAAATGTTGT
Statistics
Matches: 195, Mismatches: 34, Indels: 19
0.79 0.14 0.08
Matches are distributed among these distances:
208 1 0.01
209 6 0.03
210 129 0.66
211 57 0.29
212 2 0.01
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (209 bp):
TTTTTATCTATGAGCCTTAGAATGACAACTTGGAGCTTTGCTTTCACTAACTATGTTAAAGGCTA
CGGTTTTTTATTCTATAAGCCTTAGTATGACAACTGGGAGCTTTACTTTCACCAACTGTGTTGAA
GGCTTAGATTTTTTATCCTACGAGCCTTAATATGATAACTAGGAGCTTTGCTCTCGCTAACCGTA
TTGGAGGCTGCGAT
Found at i:54255493 original size:24 final size:24
Alignment explanation
Indices: 54255455--54255500 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
54255445 CAAGACTTAA
54255455 CCTGTTGACCACCTAATTAGCTAG
1 CCTGTTGACCACCTAATTAGCTAG
* *
54255479 CCTGTTGGCCTCCTAATTAGCT
1 CCTGTTGACCACCTAATTAGCT
54255501 TTCTCATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.33
Consensus pattern (24 bp):
CCTGTTGACCACCTAATTAGCTAG
Found at i:54261355 original size:41 final size:40
Alignment explanation
Indices: 54261279--54261447 Score: 187
Period size: 41 Copynumber: 4.1 Consensus size: 40
54261269 GCAAAAATTG
* *
54261279 TAAAACACAGAGCAATAGCGGCGTTTTTGGTAAAACGCCGC
1 TAAAA-ACAAAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
*
54261320 TAAAAACAAAGCAATAGCGGCG-TTTTAGTAAAAAACGCCGC
1 TAAAAACAAAGCAATAGCGGCGCTTTTGGT--AAAACGCCGC
* * * * *
54261361 TAAAGACAAGAGCACTAGCAGTGCTTTTGATAAAACGCCGC
1 TAAAAACAA-AGCAATAGCGGCGCTTTTGGTAAAACGCCGC
* * *
54261402 TAAAGATCAGAGCATTAGCGGCGCTTTTGGTAAAACGCCGC
1 TAAA-AACAAAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
54261443 TAAAA
1 TAAAA
54261448 GTCATATAAC
Statistics
Matches: 108, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
39 6 0.06
40 17 0.16
41 68 0.63
42 12 0.11
43 5 0.05
ACGTcount: A:0.37, C:0.21, G:0.22, T:0.20
Consensus pattern (40 bp):
TAAAAACAAAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
Found at i:54261627 original size:14 final size:14
Alignment explanation
Indices: 54261605--54261699 Score: 63
Period size: 14 Copynumber: 6.9 Consensus size: 14
54261595 TTAATTATCA
* *
54261605 TTATAGTTTAAGGT
1 TTATGGTTTAAGAT
54261619 TTATGGTTTAAGAT
1 TTATGGTTTAAGAT
* *
54261633 ATATGGGTTTAAGCT
1 TTAT-GGTTTAAGAT
54261648 TTATGAG-TT-A-A-
1 TTATG-GTTTAAGAT
*
54261659 CTATGGTTTAAGAT
1 TTATGGTTTAAGAT
* * *
54261673 ATATGGTTTAGGGT
1 TTATGGTTTAAGAT
*
54261687 TTAAGGTTTAAGA
1 TTATGGTTTAAGA
54261700 GTTAACTAGT
Statistics
Matches: 61, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
10 1 0.02
11 6 0.10
12 1 0.02
13 2 0.03
14 38 0.62
15 13 0.21
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.44
Consensus pattern (14 bp):
TTATGGTTTAAGAT
Found at i:54263282 original size:7 final size:7
Alignment explanation
Indices: 54263272--54263337 Score: 66
Period size: 7 Copynumber: 9.7 Consensus size: 7
54263262 TAGTTTATGA
54263272 TTTAGGG
1 TTTAGGG
*
54263279 TTTATGG
1 TTTAGGG
*
54263286 TTTAAGG
1 TTTAGGG
*
54263293 -AT-GGG
1 TTTAGGG
54263298 TTTAGGG
1 TTTAGGG
*
54263305 CTTAGGG
1 TTTAGGG
54263312 -TTAGGG
1 TTTAGGG
54263318 TTTAGGG
1 TTTAGGG
54263325 TTTTAGGG
1 -TTTAGGG
54263333 TTTAG
1 TTTAG
54263338 AGTATAATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
5 2 0.04
6 8 0.16
7 32 0.65
8 7 0.14
ACGTcount: A:0.17, C:0.02, G:0.39, T:0.42
Consensus pattern (7 bp):
TTTAGGG
Found at i:54264313 original size:44 final size:44
Alignment explanation
Indices: 54264211--54264305 Score: 122
Period size: 43 Copynumber: 2.2 Consensus size: 44
54264201 CTCGAAATCT
* * *
54264211 CTAATATTTTCCCCAAATCCCCTATTTTCCCCATAGTCATTTCC
1 CTAACATTTTCCCCAAATCCCCCATTTTCCCCATACTCATTTCC
* **
54264255 CTAACATTTTCCCCAAA-CCCCCCTTTTCCCCATACTTTTTTCC
1 CTAACATTTTCCCCAAATCCCCCATTTTCCCCATACTCATTTCC
54264298 CTAA-ATTT
1 CTAACATTT
54264306 GTTCCCCATC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
42 4 0.09
43 25 0.56
44 16 0.36
ACGTcount: A:0.22, C:0.38, G:0.01, T:0.39
Consensus pattern (44 bp):
CTAACATTTTCCCCAAATCCCCCATTTTCCCCATACTCATTTCC
Found at i:54267972 original size:23 final size:23
Alignment explanation
Indices: 54267938--54267987 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
54267928 AACATTAATC
54267938 AAATGTAAGAATTGCAGCCCTTT
1 AAATGTAAGAATTGCAGCCCTTT
*
54267961 AAATGTATGAATTGCAGCCCTTT
1 AAATGTAAGAATTGCAGCCCTTT
54267984 AAAT
1 AAAT
54267988 AAACTTGAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (23 bp):
AAATGTAAGAATTGCAGCCCTTT
Found at i:54268533 original size:241 final size:241
Alignment explanation
Indices: 54268110--54268596 Score: 911
Period size: 241 Copynumber: 2.0 Consensus size: 241
54268100 ATGAATTAAT
*
54268110 TTTATTACCATGTAGCTTGCTTGTCCGTTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
*
54268175 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGTTGGAAACCTGACAGGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACAGGTTGCCTTATATCGAG
* *
54268240 CTGTAAGATATAATGGATCCTCTCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
131 CTGTAAGATATAATGGATCCTCCCTAGGTCTAACAACGCCACGTATGATGAATCTTAAAAAATTC
54268305 AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
196 AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
54268351 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
1 TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
*
54268416 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACAGGTTGCCTTATATCGAG
*
54268481 CTGTAAGATATAATGGATCCTCCCTAGGTCTAACAATGCCACGTATGATGAATCTTAAAAAATTC
131 CTGTAAGATATAATGGATCCTCCCTAGGTCTAACAACGCCACGTATGATGAATCTTAAAAAATTC
*
54268546 AAAAAGACTTGAAAGAAGTTCTATCGAGCTCATTTACTATTGAATA
196 AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
54268592 TTTAT
1 TTTAT
54268597 ATAACCTTAA
Statistics
Matches: 239, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
241 239 1.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (241 bp):
TTTATTACCATGTAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTT
ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACAGGTTGCCTTATATCGAG
CTGTAAGATATAATGGATCCTCCCTAGGTCTAACAACGCCACGTATGATGAATCTTAAAAAATTC
AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
Found at i:54269058 original size:9 final size:9
Alignment explanation
Indices: 54269035--54269162 Score: 112
Period size: 9 Copynumber: 13.6 Consensus size: 9
54269025 AGTGATCATT
*
54269035 ACTTAAATA
1 ACTTACATA
*
54269044 AATTACATA
1 ACTTACATA
54269053 ACTTACATA
1 ACTTACATA
* *
54269062 ACTCATATA
1 ACTTACATA
54269071 ACTTACATA
1 ACTTACATA
* *
54269080 ATTTACAAA
1 ACTTACATA
54269089 ACAAGTTACATA
1 AC---TTACATA
*
54269101 ACTCACATA
1 ACTTACATA
54269110 ACTTACATA
1 ACTTACATA
*
54269119 ATTTACATA
1 ACTTACATA
*
54269128 ACTCACATA
1 ACTTACATA
*
54269137 ACGTACATAACA
1 ACTTACAT---A
54269149 ACTTACATA
1 ACTTACATA
54269158 ACTTA
1 ACTTA
54269163 ACTAATACAT
Statistics
Matches: 94, Mismatches: 19, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
9 78 0.83
12 16 0.17
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.30
Consensus pattern (9 bp):
ACTTACATA
Found at i:54269136 original size:57 final size:57
Alignment explanation
Indices: 54269048--54269160 Score: 154
Period size: 57 Copynumber: 2.0 Consensus size: 57
54269038 TAAATAAATT
* * ** *
54269048 ACATAACTTACATAACTCATATAACTTACATAATTTACAAAACAAGTTACATAACTC
1 ACATAACTTACATAACTCACATAACTCACATAACGTACAAAACAACTTACATAACTC
* * *
54269105 ACATAACTTACATAATTTACATAACTCACATAACGTACATAACAACTTACATAACT
1 ACATAACTTACATAACTCACATAACTCACATAACGTACAAAACAACTTACATAACT
54269161 TAACTAATAC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
57 48 1.00
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.29
Consensus pattern (57 bp):
ACATAACTTACATAACTCACATAACTCACATAACGTACAAAACAACTTACATAACTC
Found at i:54275103 original size:43 final size:42
Alignment explanation
Indices: 54275003--54275102 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 42
54274993 ACTGGGCAAA
* *
54275003 TTAGCGGTGTTTTTTATAAAAGCGCCACTAAAGGTTCCGATCT
1 TTAGCGGCGTTTTTTA-AAAAGCGCCACTAAAAGTTCCGATCT
* * *
54275046 TTAGCGGCGGTTTTTAAAAAGCGCCGCTAAAAG-TCATGATCT
1 TTAGCGGCGTTTTTTAAAAAGCGCCACTAAAAGTTC-CGATCT
* *
54275088 TTAGTGGCATTTTTT
1 TTAGCGGCGTTTTTT
54275103 TAAACAAACA
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 2 0.04
42 32 0.67
43 14 0.29
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (42 bp):
TTAGCGGCGTTTTTTAAAAAGCGCCACTAAAAGTTCCGATCT
Found at i:54276393 original size:234 final size:234
Alignment explanation
Indices: 54275980--54276406 Score: 728
Period size: 234 Copynumber: 1.8 Consensus size: 234
54275970 AAGTGTACCA
*
54275980 ATCCCTCTAATTCATCCTTCTTCTGATGAAGAGTACCGGGGGTGGCTTGGGTAAGATCCCAAGGC
1 ATCCCTCTAATTCATCCTTCTTCTAATGAAGAGTACCGGGGGTGGCTTGGGTAAGATCCCAAGGC
* * * *
54276045 TCTTGACTTGAGTGAGAATGTAGGCTCGGGTAGTGTTTAAGGGGGTGTAAGCTTCAAATCTTCCC
66 TCTTGACTTGAATGAGAATATAGGCTCGGGTAGCGTTTAAGGGGGTGTAAGCTTCAAATATTCCC
* *
54276110 TGAGGAGCATATCTTCTGGTGTGGTCTTACTAAAGTCTTAAGGGAGCCCTGAGTGTGTCACCTTG
131 TGAGGAACATATCTTCTGGTGTGGTCTTACTAAAGTCTTAAGAGAGCCCTGAGTGTGTCACCTTG
54276175 GGCCTGAATCTTCTGTAGCCTATCGAGTAAACTGCACCG
196 GGCCTGAATCTTCTGTAGCCTATCGAGTAAACTGCACCG
*
54276214 ATCCCTCTAATTCATCCTTCTTCTAATGAAGAGTATCGGGGGTGGCTTGGGTAAGATCCCAAGGC
1 ATCCCTCTAATTCATCCTTCTTCTAATGAAGAGTACCGGGGGTGGCTTGGGTAAGATCCCAAGGC
* * * *
54276279 TCTTGACTTGAATGAGAATATAGGTTTGGGTAGCGTTTAAGGGTGTGTAAGCTTCAAATATTCCT
66 TCTTGACTTGAATGAGAATATAGGCTCGGGTAGCGTTTAAGGGGGTGTAAGCTTCAAATATTCCC
* *
54276344 TGAGGAACATATCTTCTGGTGTGTTCTTACTAAAGTCTTAAGAGAGCCCTGAGTGTGTTACCT
131 TGAGGAACATATCTTCTGGTGTGGTCTTACTAAAGTCTTAAGAGAGCCCTGAGTGTGTCACCT
54276407 GACTCTTCTA
Statistics
Matches: 179, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
234 179 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (234 bp):
ATCCCTCTAATTCATCCTTCTTCTAATGAAGAGTACCGGGGGTGGCTTGGGTAAGATCCCAAGGC
TCTTGACTTGAATGAGAATATAGGCTCGGGTAGCGTTTAAGGGGGTGTAAGCTTCAAATATTCCC
TGAGGAACATATCTTCTGGTGTGGTCTTACTAAAGTCTTAAGAGAGCCCTGAGTGTGTCACCTTG
GGCCTGAATCTTCTGTAGCCTATCGAGTAAACTGCACCG
Found at i:54278015 original size:26 final size:26
Alignment explanation
Indices: 54277954--54278016 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
54277944 ACCTTGACTT
*
54277954 GCGAGCTAGGTCATTGGCTTTGCCTC
1 GCGAGCTGGGTCATTGGCTTTGCCTC
* *
54277980 GCGAGTTGGGTCTTTGGCTTTGCCTC
1 GCGAGCTGGGTCATTGGCTTTGCCTC
54278006 GCGAGCTGGGT
1 GCGAGCTGGGT
54278017 TCATGAGCTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.08, C:0.24, G:0.37, T:0.32
Consensus pattern (26 bp):
GCGAGCTGGGTCATTGGCTTTGCCTC
Found at i:54283849 original size:30 final size:30
Alignment explanation
Indices: 54283792--54283849 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
54283782 TTTTCGAGTA
* **
54283792 TAGGGGTAAAATGGTCATTTTGTCAAAGTT
1 TAGGGGCAAAATGGTCATTTTACCAAAGTT
54283822 TAGGGGCAAAATGGTCATTTTACCAAAG
1 TAGGGGCAAAATGGTCATTTTACCAAAG
54283850 ATGTGAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (30 bp):
TAGGGGCAAAATGGTCATTTTACCAAAGTT
Found at i:54284259 original size:47 final size:46
Alignment explanation
Indices: 54284190--54284360 Score: 170
Period size: 47 Copynumber: 3.7 Consensus size: 46
54284180 TACTTGTGTG
*
54284190 CCAGTGTAAGACATGTCTGGGACATGGCATCAGCTAGAGAATGAGCA
1 CCAGTGTAAGACATGTCTGGGACAT-GCATCAGCTAGAGAATGAGTA
* * *
54284237 CCAGTGTAAGACATGTCTGGGACATACATCGGCCTCGACG-ATGA-TA
1 CCAGTGTAAGACATGTCTGGGACATGCATCAG-CTAGA-GAATGAGTA
** * * *
54284283 GCCAGTGTAAGATGTGTCTGGGACATGCATCAGCTA-AGAGT-TGTT
1 -CCAGTGTAAGACATGTCTGGGACATGCATCAGCTAGAGAATGAGTA
* * *
54284328 CTAGTGTAAGACATGTCTGGTACATGTATCAGC
1 CCAGTGTAAGACATGTCTGGGACATGCATCAGC
54284361 ACACATAGAC
Statistics
Matches: 102, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
44 29 0.28
45 3 0.03
46 8 0.08
47 61 0.60
48 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (46 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCAGCTAGAGAATGAGTA
Found at i:54290481 original size:30 final size:30
Alignment explanation
Indices: 54290445--54290501 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
54290435 TTTGATTTTC
* * *
54290445 AAGTCTAGGGGTAAAATGGTCATTTTGTGA
1 AAGTCTAAGGGCAAAATAGTCATTTTGTGA
54290475 AAGTCTAAGGGCAAAATAGTCATTTTG
1 AAGTCTAAGGGCAAAATAGTCATTTTG
54290502 CCCAATAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.32
Consensus pattern (30 bp):
AAGTCTAAGGGCAAAATAGTCATTTTGTGA
Found at i:54290937 original size:48 final size:46
Alignment explanation
Indices: 54290839--54291109 Score: 200
Period size: 48 Copynumber: 5.8 Consensus size: 46
54290829 TTTATGTACC
* *
54290839 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATTA-TGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG---CATTAGAGAGAGCT
**
54290885 AGTGTAAGACCATGTCTGGGACATGAAATCGGCATTGAGACGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATT-AGA-GAGAGCT
* * * * * *
54290933 AGTGTAAGA-CATGTTTGGGATA-AGTATCGG--TTACA-AGATGTGT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTAGAGAGA-G-CT
* *
54290976 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAG-GTGCC
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGGCA--T-TAGAGAGAGCT
* * * *
54291025 AGTGTAAGACCATGTCTAGGACATGGCATCAGCATAGATATGTGAGAGAT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAT---TA-GAGAGAGCT
54291075 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAT
54291110 CATACCATAT
Statistics
Matches: 178, Mismatches: 27, Indels: 36
0.74 0.11 0.15
Matches are distributed among these distances:
41 3 0.02
42 1 0.01
43 3 0.02
44 11 0.06
45 15 0.08
46 22 0.12
47 25 0.14
48 55 0.31
49 2 0.01
50 37 0.21
51 4 0.02
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCATTAGAGAGAGCT
Found at i:54293064 original size:31 final size:31
Alignment explanation
Indices: 54293028--54293090 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
54293018 AAGAGTTTGT
*
54293028 TTCTTCATTTGGACTGCTCTAAAATAAAGAC
1 TTCTTCATTTGAACTGCTCTAAAATAAAGAC
54293059 TTCTTCATTTGAACTGCTCTAAAATAAAGAC
1 TTCTTCATTTGAACTGCTCTAAAATAAAGAC
54293090 T
1 T
54293091 CATTACAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.37
Consensus pattern (31 bp):
TTCTTCATTTGAACTGCTCTAAAATAAAGAC
Found at i:54295168 original size:42 final size:44
Alignment explanation
Indices: 54295097--54295187 Score: 107
Period size: 42 Copynumber: 2.1 Consensus size: 44
54295087 TCTTGCATGT
*
54295097 AATCAAATATCGATGCCACTGTCCTAGACAGGGTCTTACACG-A
1 AATCAAATATCGATGCCACTGTCCTAGACAGAGTCTTACACGTA
* * * *
54295140 AATCAAATA-CGATGCCGATTTTCC-AGACATAGTCTTACATGTA
1 AATCAAATATCGATGCC-ACTGTCCTAGACAGAGTCTTACACGTA
54295183 AATCA
1 AATCA
54295188 TAAGTCGATG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
42 21 0.51
43 20 0.49
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.26
Consensus pattern (44 bp):
AATCAAATATCGATGCCACTGTCCTAGACAGAGTCTTACACGTA
Found at i:54295186 original size:43 final size:44
Alignment explanation
Indices: 54295086--54295187 Score: 113
Period size: 43 Copynumber: 2.4 Consensus size: 44
54295076 CCTAGACGTG
* *
54295086 GTCTTGCATGT-AATCAAATATCGATGCCACTGTCCTAGACAGG
1 GTCTTACATGTAAATCAAATATCGATGCCACTGTCCTAGACAGA
* * * *
54295129 GTCTTACACG-AAATCAAATA-CGATGCCGATTTTCC-AGACATA
1 GTCTTACATGTAAATCAAATATCGATGCC-ACTGTCCTAGACAGA
54295171 GTCTTACATGTAAATCA
1 GTCTTACATGTAAATCA
54295188 TAAGTCGATG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
42 21 0.43
43 28 0.57
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (44 bp):
GTCTTACATGTAAATCAAATATCGATGCCACTGTCCTAGACAGA
Found at i:54300928 original size:25 final size:25
Alignment explanation
Indices: 54300899--54300949 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
54300889 AAGAATAATT
*
54300899 TGAATATTTGATATTGCCTAATAAA
1 TGAATATCTGATATTGCCTAATAAA
* *
54300924 TGAATATCTGATATTGCTTAGTAAA
1 TGAATATCTGATATTGCCTAATAAA
54300949 T
1 T
54300950 CTCAAGCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (25 bp):
TGAATATCTGATATTGCCTAATAAA
Found at i:54304942 original size:31 final size:31
Alignment explanation
Indices: 54304907--54304997 Score: 112
Period size: 31 Copynumber: 2.9 Consensus size: 31
54304897 AAAAAAACTT
*
54304907 AACAACTTAGTGACTTAAATAAAAACTTTTG
1 AACAACTTAGTGACATAAATAAAAACTTTTG
* * *
54304938 AACAATTTAGTGACATAAACAAAAATTTTTG
1 AACAACTTAGTGACATAAATAAAAACTTTTG
* *
54304969 AAC-AGTTCAGTGACATAAATGAAAACTTT
1 AACAACTT-AGTGACATAAATAAAAACTTT
54304998 CAAATAATTC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
30 3 0.06
31 48 0.94
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.31
Consensus pattern (31 bp):
AACAACTTAGTGACATAAATAAAAACTTTTG
Found at i:54310265 original size:49 final size:49
Alignment explanation
Indices: 54310196--54310633 Score: 683
Period size: 49 Copynumber: 9.1 Consensus size: 49
54310186 GAAATGATAG
54310196 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
54310245 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
54310294 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
54310343 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
54310392 T-AGGCCTAATGGCCGGTGTGATGAATGTGAAAGTG--TATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
54310438 TAAGGCCTAATGGCCGATGTGATGAATGTGGAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
* * * * * *
54310487 CAGGGCCGAGTGGCCAACGTGATGAATGTGAAAGTG--TATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
*
54310534 TAAGGCCTAATGGCCGATGTGATGAATGTGGAAGTGTATATATATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
* * * * * * *
54310583 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGA
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
54310630 TAAG
1 TAAG
54310634 TCCCGAAGGG
Statistics
Matches: 357, Mismatches: 27, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
46 12 0.03
47 80 0.22
48 34 0.10
49 231 0.65
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (49 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGA
Found at i:54310365 original size:98 final size:98
Alignment explanation
Indices: 54310196--54310633 Score: 683
Period size: 96 Copynumber: 4.5 Consensus size: 98
54310186 GAAATGATAG
54310196 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
54310261 ATGTGATGAATGTGAAAGTGTATATATATGTGA
66 ATGTGATGAATGTGAAAGTGTATATATATGTGA
54310294 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
54310359 ATGTGATGAATGTGAAAGTGTATATATATGTGA
66 ATGTGATGAATGTGAAAGTGTATATATATGTGA
*
54310392 T-AGGCCTAATGGCCGGTGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
*
54310454 ATGTGATGAATGTGGAAGTGTATATATATGTGA
66 ATGTGATGAATGTGAAAGTGTATATATATGTGA
* * * * * *
54310487 CAGGGCCGAGTGGCCAACGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
*
54310550 ATGTGATGAATGTGGAAGTGTATATATATGTGA
66 ATGTGATGAATGTGAAAGTGTATATATATGTGA
* * * * * * *
54310583 CAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA-A-ATGTGATAAG
1 TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAG
54310634 TCCCGAAGGG
Statistics
Matches: 327, Mismatches: 10, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
95 59 0.18
96 133 0.41
97 34 0.10
98 101 0.31
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (98 bp):
TAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
ATGTGATGAATGTGAAAGTGTATATATATGTGA
Found at i:54316512 original size:46 final size:45
Alignment explanation
Indices: 54316442--54316690 Score: 363
Period size: 46 Copynumber: 5.4 Consensus size: 45
54316432 TACCATAATG
* *
54316442 TCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTATTCA-TTTCTGTCATGTTGCCATGGTA
* *
54316488 TCTTTCAACCATGGTCTTATTCATTTCTTGTCACGTTGCCATAGTA
1 TCTTTCAACCATGGTCTTATTCATTTC-TGTCATGTTGCCATGGTA
* *
54316534 TCTTTCAACCATAGTCTTATTCATTTCCTTTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTATTCATTT-CTGTCATGTTGCCATGGTA
54316580 TCTTTCAACCATGGTCTTATTCATTTCTTGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTATTCATTTC-TGTCATGTTGCCATGGTA
* * *
54316626 TCTTTCAAGCATGGTCTTATTCATTTCTCGTCATATTGCCATAGTA
1 TCTTTCAACCATGGTCTTATTCATTTCT-GTCATGTTGCCATGGTA
*
54316672 TCTTTCAACTATGGTCTTA
1 TCTTTCAACCATGGTCTTA
54316691 CACATTTCAA
Statistics
Matches: 184, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
45 6 0.03
46 177 0.96
47 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.13, T:0.45
Consensus pattern (45 bp):
TCTTTCAACCATGGTCTTATTCATTTCTGTCATGTTGCCATGGTA
Found at i:54316690 original size:138 final size:138
Alignment explanation
Indices: 54316442--54316690 Score: 410
Period size: 138 Copynumber: 1.8 Consensus size: 138
54316432 TACCATAATG
*
54316442 TCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
1 TCTTTCAACCATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
* *
54316507 TTCATTTCTTGTCACGTTGCCATAGTATCTTTCAACCATAGTCTTATTCATTTCCTTTCATGTTG
66 TTCATTTCTCGTCACATTGCCATAGTATCTTTCAACCATAGTCTTATTCATTTCCTTTCATGTTG
54316572 CCATGGTA
131 CCATGGTA
* *
54316580 TCTTTCAACCATGGTCTTATTCA-TTTCTTGTCATGTTGCCATGGTATCTTTCAAGCATGGTCTT
1 TCTTTCAACCATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATCTTTCAACCATGGTCTT
* * *
54316644 ATTCATTTCTCGTCATATTGCCATAGTATCTTTCAACTATGGTCTTA
65 ATTCATTTCTCGTCACATTGCCATAGTATCTTTCAACCATAGTCTTA
54316691 CACATTTCAA
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
137 4 0.04
138 98 0.96
ACGTcount: A:0.19, C:0.22, G:0.13, T:0.45
Consensus pattern (138 bp):
TCTTTCAACCATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAACCATGGTCTTA
TTCATTTCTCGTCACATTGCCATAGTATCTTTCAACCATAGTCTTATTCATTTCCTTTCATGTTG
CCATGGTA
Found at i:54316730 original size:45 final size:45
Alignment explanation
Indices: 54316662--54316788 Score: 155
Period size: 45 Copynumber: 2.8 Consensus size: 45
54316652 CTCGTCATAT
* * *
54316662 TGCCATAGTATCTTTCAACTATGGTCTTACACATTTCAATCGCGA
1 TGCCATAGCATCTTTCAGCTATGGTCTTACTCATTTCAATCGCGA
* * ** * * *
54316707 TGCCATAGCACCTTTCAGTTATGGTCTTACTTGTCTGAATCGTGA
1 TGCCATAGCATCTTTCAGCTATGGTCTTACTCATTTCAATCGCGA
*
54316752 TGCCATAGCGTCTTTCAGCTATGGTCTTACTCATTTC
1 TGCCATAGCATCTTTCAGCTATGGTCTTACTCATTTC
54316789 TGGTATGATG
Statistics
Matches: 65, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
45 65 1.00
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (45 bp):
TGCCATAGCATCTTTCAGCTATGGTCTTACTCATTTCAATCGCGA
Found at i:54316854 original size:33 final size:33
Alignment explanation
Indices: 54316812--54316952 Score: 92
Period size: 33 Copynumber: 4.3 Consensus size: 33
54316802 TAGTCCAACT
*
54316812 ATGGTCTTACACGTGTATTGCCATGGCCCAGCC
1 ATGGTCTTACACGTGTATTGCCATAGCCCAGCC
** * * **
54316845 ATGGTCTTACAC-TCGTGGTGTCATATCCCAGAT
1 ATGGTCTTACACGT-GTATTGCCATAGCCCAGCC
* *
54316878 ATGGTCTTATCATCAG-G-A-TGCCATAGCCTAGCT
1 ATGGTCTTA-CA-C-GTGTATTGCCATAGCCCAGCC
* * * * *
54316911 ATGGTCTTAAACATATATTGTCATGGCCCAGCC
1 ATGGTCTTACACGTGTATTGCCATAGCCCAGCC
54316944 ATGGTCTTA
1 ATGGTCTTA
54316953 TCCGTCAATT
Statistics
Matches: 81, Mismatches: 19, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
31 1 0.01
32 3 0.04
33 73 0.90
34 2 0.02
35 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (33 bp):
ATGGTCTTACACGTGTATTGCCATAGCCCAGCC
Found at i:54318529 original size:8 final size:8
Alignment explanation
Indices: 54318516--54318540 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
54318506 ATATATATTG
54318516 AATAAAAT
1 AATAAAAT
54318524 AATAAAAT
1 AATAAAAT
54318532 AATAAAAT
1 AATAAAAT
54318540 A
1 A
54318541 TCATTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:54319998 original size:23 final size:23
Alignment explanation
Indices: 54319968--54320013 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
54319958 TATAATTCCT
*
54319968 TTGTGAACAAACTCTGGACAAAA
1 TTGTGAACAAACTCTGAACAAAA
54319991 TTGTGAACAAACTCTGAACAAAA
1 TTGTGAACAAACTCTGAACAAAA
54320014 GAAGTTGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.17, G:0.15, T:0.22
Consensus pattern (23 bp):
TTGTGAACAAACTCTGAACAAAA
Found at i:54323781 original size:28 final size:28
Alignment explanation
Indices: 54323749--54323810 Score: 124
Period size: 28 Copynumber: 2.2 Consensus size: 28
54323739 GATGAAGAAC
54323749 TTAGTAGAATGGACAAGTTACTGGATTT
1 TTAGTAGAATGGACAAGTTACTGGATTT
54323777 TTAGTAGAATGGACAAGTTACTGGATTT
1 TTAGTAGAATGGACAAGTTACTGGATTT
54323805 TTAGTA
1 TTAGTA
54323811 CCTAGAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (28 bp):
TTAGTAGAATGGACAAGTTACTGGATTT
Found at i:54326187 original size:13 final size:12
Alignment explanation
Indices: 54326164--54326226 Score: 55
Period size: 12 Copynumber: 5.4 Consensus size: 12
54326154 AATAATTTTA
54326164 TATTAAAATTAT
1 TATTAAAATTAT
54326176 TATT-AAA-TAT
1 TATTAAAATTAT
54326186 TATTAATAATTA-
1 TATTAA-AATTAT
*
54326198 TATTAAGAA-TGT
1 TATTAA-AATTAT
54326210 TATT-AAATTAT
1 TATTAAAATTAT
54326221 ATATTA
1 -TATTA
54326227 TTTTATAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 13
0.72 0.05 0.23
Matches are distributed among these distances:
10 9 0.22
11 8 0.20
12 22 0.54
13 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (12 bp):
TATTAAAATTAT
Found at i:54326191 original size:22 final size:23
Alignment explanation
Indices: 54326164--54326226 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 23
54326154 AATAATTTTA
54326164 TATTAAAATTATTATTA-AATAT
1 TATTAAAATTATTATTAGAATAT
*
54326186 TATTAATAATTA-TATTAAGAATGT
1 TATTAA-AATTATTATT-AGAATAT
54326210 TATT-AAATTATATATTA
1 TATTAAAATTAT-TATTA
54326227 TTTTATAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
22 15 0.43
23 8 0.23
24 12 0.34
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (23 bp):
TATTAAAATTATTATTAGAATAT
Found at i:54326219 original size:29 final size:28
Alignment explanation
Indices: 54326187--54326275 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 28
54326177 ATTAAATATT
54326187 ATTAATAATTATATTAAGAATGTTATTAA
1 ATTAATAATTATATTAA-AATGTTATTAA
* *
54326216 ATT-ATATATTATTTTATAAAT-TGTATTTA
1 ATTAATA-ATTATATTA-AAATGT-TATTAA
* *
54326245 A-TAATAATTATGTTAAAATGTGATTAA
1 ATTAATAATTATATTAAAATGTTATTAA
54326272 ATTA
1 ATTA
54326276 TTTATTTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
27 9 0.18
28 16 0.33
29 23 0.47
30 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (28 bp):
ATTAATAATTATATTAAAATGTTATTAA
Found at i:54326233 original size:34 final size:33
Alignment explanation
Indices: 54326156--54326233 Score: 88
Period size: 34 Copynumber: 2.3 Consensus size: 33
54326146 TTCTTAATAA
54326156 TAATTTTATATTAAAATTATTATTAAATATTAT
1 TAATTTTATATTAAAATTATTATTAAATATTAT
* *
54326189 TAATAATTATATTAAGAA-TGTTATTAAATTATATAT
1 TAAT-TTTATATTAA-AATTATTATTAAA-TAT-TAT
54326225 T-ATTTTATA
1 TAATTTTATA
54326234 AATTGTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
33 4 0.11
34 23 0.61
35 7 0.18
36 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (33 bp):
TAATTTTATATTAAAATTATTATTAAATATTAT
Found at i:54326339 original size:25 final size:26
Alignment explanation
Indices: 54326290--54326340 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
54326280 TTTTTTATTT
*
54326290 TTATTAAAATATATTTAACAATAATC
1 TTATTAAAATATATATAACAATAATC
*
54326316 TTATTAAAATTTA-ATAACAATAATC
1 TTATTAAAATATATATAACAATAATC
54326341 ATCTACCTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (26 bp):
TTATTAAAATATATATAACAATAATC
Found at i:54326470 original size:44 final size:46
Alignment explanation
Indices: 54326410--54326501 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 46
54326400 TATTACAACA
54326410 TCTATTCCATTCAACCAAACACAAGAATT-CT-ATTACAGCTCTAT
1 TCTATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTAT
* * *** *
54326454 TCTATTTCATTTAACCAAACAGTTGAATTATTGATTACAGCTCTAT
1 TCTATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTAT
54326500 TC
1 TC
54326502 CATTACATCT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
44 24 0.60
45 1 0.03
46 15 0.38
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.37
Consensus pattern (46 bp):
TCTATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTAT
Found at i:54326508 original size:16 final size:16
Alignment explanation
Indices: 54326487--54326541 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
54326477 TGAATTATTG
54326487 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
* *
54326503 ATTACATCTCTATTCA
1 ATTACAGCTCTATTCC
* *
54326519 ATTACAACCCTATTCC
1 ATTACAGCTCTATTCC
54326535 ATTACAG
1 ATTACAG
54326542 TGAACCAAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:54328959 original size:59 final size:60
Alignment explanation
Indices: 54328870--54328987 Score: 152
Period size: 59 Copynumber: 2.0 Consensus size: 60
54328860 TTAAAAATAT
* *
54328870 AAAAAATTTAAAATTTACTAAAAATTAGTAAAAAAATTAT-AAAATATATAGAAATATTG
1 AAAAAATTTAAAATTTACTAAAAATCAGTAAAAAAATTATAAAAATATAAAGAAATATTG
* *
54328929 AAAAAATTATAAAATTT--TATAAAGTCAGTAAGAAAATTATGAAAAATATAAAGAAATAT
1 AAAAAATT-TAAAATTTACTA-AAAATCAGTAAAAAAATTAT-AAAAATATAAAGAAATAT
54328988 AAAATTAGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
58 2 0.04
59 25 0.49
60 8 0.16
61 16 0.31
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.31
Consensus pattern (60 bp):
AAAAAATTTAAAATTTACTAAAAATCAGTAAAAAAATTATAAAAATATAAAGAAATATTG
Found at i:54329111 original size:31 final size:29
Alignment explanation
Indices: 54329076--54329133 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 29
54329066 TGTAAAAAAA
54329076 TTATAAAATA-TATAGAAAAAATTATAAAATT
1 TTATAAAATAGTA-AG--AAAATTATAAAATT
*
54329107 TTATAAAGTAGTAAGAAAATTATAAAA
1 TTATAAAATAGTAAGAAAATTATAAAA
54329134 AAAGTAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 12 0.48
31 11 0.44
32 2 0.08
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (29 bp):
TTATAAAATAGTAAGAAAATTATAAAATT
Found at i:54329185 original size:162 final size:162
Alignment explanation
Indices: 54328910--54329204 Score: 456
Period size: 162 Copynumber: 1.8 Consensus size: 162
54328900 AAAAAATTAT
54328910 AAAATATATAGAAATATTGAAAAAATTATAAAATTTTATAAAGTCAGTAAGAAAATTATGAAAAA
1 AAAATATATAGAAATATTGAAAAAATTATAAAATTTTATAAAGTCAGTAAGAAAATTATGAAAAA
*
54328975 TATAAAGAAATATAAAATTAGTAAAATAAAATAAAATTAATAGTACCAAAAGAAACATTTTATAA
66 AATAAAGAAATATAAAATTAGTAAAATAAAATAAAATTAATAGTACCAAAAGAAACATTTTATAA
54329040 TTTAAATTAATAAAAAATATAAAAATTGTAAA
131 TTTAAATTAATAAAAAATATAAAAATTGTAAA
54329072 AAAAT-TATA-AAATATATAGAAAAAATTATAAAATTTTATAAAGT-AGTAAGAAAATTAT-AAA
1 AAAATATATAGAAATAT-T-GAAAAAATTATAAAATTTTATAAAGTCAGTAAGAAAATTATGAAA
* * * *
54329133 AAAAGTAAAGAAATATAAAATTCGTAAAA-AATATGTAAAATTTATCGTACCAAAAGAAACATTT
64 AAAA-TAAAGAAATATAAAATTAGTAAAATAA-A-ATAAAATTAATAGTACCAAAAGAAACATTT
*
54329197 TATGATTT
126 TATAATTT
54329205 TTCTATAAAT
Statistics
Matches: 122, Mismatches: 6, Indels: 10
0.88 0.04 0.07
Matches are distributed among these distances:
160 14 0.11
161 43 0.35
162 65 0.53
ACGTcount: A:0.59, C:0.03, G:0.07, T:0.30
Consensus pattern (162 bp):
AAAATATATAGAAATATTGAAAAAATTATAAAATTTTATAAAGTCAGTAAGAAAATTATGAAAAA
AATAAAGAAATATAAAATTAGTAAAATAAAATAAAATTAATAGTACCAAAAGAAACATTTTATAA
TTTAAATTAATAAAAAATATAAAAATTGTAAA
Found at i:54329421 original size:11 final size:10
Alignment explanation
Indices: 54329359--54329502 Score: 73
Period size: 10 Copynumber: 15.5 Consensus size: 10
54329349 GTTTGATATA
54329359 TTTTATAATT
1 TTTTATAATT
*
54329369 TTTTATGA-T
1 TTTTATAATT
**
54329378 TTTTATAAAA
1 TTTTATAATT
* * *
54329388 TATTACAAAT
1 TTTTATAATT
54329398 TTTTAT-ATT
1 TTTTATAATT
54329407 TTTTATAACTT
1 TTTTATAA-TT
54329418 TTTTATAA--
1 TTTTATAATT
54329426 TTTTA-AA-T
1 TTTTATAATT
54329434 TTTTA-AATAT
1 TTTTATAAT-T
*
54329444 TTTTATTAA-A
1 TTTTA-TAATT
*
54329454 TTTAATAA-T
1 TTTTATAATT
54329463 TTTTATAATT
1 TTTTATAATT
* *
54329473 TTAT-TGA--
1 TTTTATAATT
54329480 TTTT-T-ATT
1 TTTTATAATT
54329488 TTTTATAATT
1 TTTTATAATT
54329498 TTTTA
1 TTTTA
54329503 CCACATGTTA
Statistics
Matches: 105, Mismatches: 16, Indels: 26
0.71 0.11 0.18
Matches are distributed among these distances:
6 1 0.01
7 6 0.06
8 16 0.15
9 29 0.28
10 41 0.39
11 10 0.10
12 2 0.02
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:54329501 original size:18 final size:18
Alignment explanation
Indices: 54329395--54329502 Score: 66
Period size: 18 Copynumber: 5.9 Consensus size: 18
54329385 AAATATTACA
54329395 AATTTTTATATTTTTTAT
1 AATTTTTATATTTTTTAT
*
54329413 AACTTTTT-TATAATTTTA-
1 AA-TTTTTATAT-TTTTTAT
*
54329431 AATTTTTAAATATTTTTATT
1 AATTTTTATAT-TTTTTA-T
* * *
54329451 AAATTTAATAATTTTTAT
1 AATTTTTATATTTTTTAT
54329469 AA-TTTTAT-TGATTTTTAT
1 AATTTTTATAT--TTTTTAT
54329487 --TTTTTATAATTTTTTA
1 AATTTTTAT-ATTTTTTA
54329503 CCACATGTTA
Statistics
Matches: 71, Mismatches: 9, Indels: 21
0.70 0.09 0.21
Matches are distributed among these distances:
17 22 0.31
18 25 0.35
19 17 0.24
20 7 0.10
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (18 bp):
AATTTTTATATTTTTTAT
Found at i:54329501 original size:27 final size:27
Alignment explanation
Indices: 54329395--54329502 Score: 98
Period size: 27 Copynumber: 3.9 Consensus size: 27
54329385 AAATATTACA
54329395 AATTTTTATATTTTTTATAACTTTTTTA-T
1 AATTTTTA-A-TTTTTATAA-TTTTTTATT
*
54329424 AATTTTAAATTTTTA-AATATTTTTATT
1 AATTTTTAATTTTTATAAT-TTTTTATT
*
54329451 AAATTTAATAATTTTTATAA--TTTTATT
1 -AATTT-TTAATTTTTATAATTTTTTATT
* *
54329478 GATTTTTATTTTTTATAATTTTTTA
1 AATTTTTAATTTTTATAATTTTTTA
54329503 CCACATGTTA
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
25 12 0.18
26 12 0.18
27 19 0.29
28 6 0.09
29 15 0.23
30 2 0.03
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (27 bp):
AATTTTTAATTTTTATAATTTTTTATT
Found at i:54329894 original size:86 final size:87
Alignment explanation
Indices: 54329650--54330145 Score: 378
Period size: 86 Copynumber: 5.5 Consensus size: 87
54329640 GAGTGCAAAA
* * * * * * *
54329650 AAGGGCTTAATTTCAATTTTTTGAAAAAAATTGAGGGTCTTTTTTATGCATTTTGACAGTTCAAG
1 AAGGGCTTAATTGC-TTTTTTTG-AAAAAATTGAGAGCCTTTTTTATACATTTT-AAAATTCAAG
*
54329715 TACCCAATTAAGTGCAAAAAGAAAAAGC
63 TACCCAATTGAGT--AAAAA-AAAAAGC
* * * * *
54329743 ATGGGCTTAATTGCTTTATTTTGAAAAAAATTGACG-GTCTTTTTTATGCATTTGAAAGTTCAAG
1 AAGGGCTTAATTGCTTT-TTTTG-AAAAAATTGA-GAGCCTTTTTTATACATTTTAAAATTCAAG
* * *
54329807 TACTCGATTGAGTAAAAAAGAAAGC
63 TACCCAATTGAGTAAAAAAAAAAGC
* * * *
54329832 AGGGGCTTAATTGC-TTTTTTGAAAAATTTGAAAGCCTTTTTTATACATTTTAAAATTTAAGTAC
1 AAGGGCTTAATTGCTTTTTTTGAAAAAATTGAGAGCCTTTTTTATACATTTTAAAATTCAAGTAC
*
54329896 CCAATTGAGTGCAAAAAAAAA-C
66 CCAATTGAGT-AAAAAAAAAAGC
* * * * *
54329918 AATGGCTTAATTGCTTTATTTTGAAAAAAAATTGAGGGCATTTTTTATGCATTTTGAAAGTTCAA
1 AAGGGCTTAATTGCTTT-TTTTG--AAAAAATTGAGAGCCTTTTTTATACATTTT-AAAATTCAA
*
54329983 GTATCCAATTGAGTACAAAAAAAAAAATAAAGC
62 GTACCCAATTGAGT------AAAAAAA-AAAGC
* ** * *
54330016 AGGGGCTTAATTGCTTTTCTTTGAAAATTTTGAGAG-CATTTTTA-AGCATTTTAAAAGTTTAAG
1 AAGGGCTTAATTGCTTTT-TTTGAAAAAATTGAGAGCCTTTTTTATA-CATTTTAAAA-TTCAAG
*
54330079 TACCCAATTGAGTGGAAAAAAAAA-C
63 TACCCAATTGAGT-AAAAAAAAAAGC
*
54330104 AAAGGG-TTAATTGTTTTTTTTGAAAAAAATTGA-AGACCTTTT
1 -AAGGGCTTAATTGCTTTTTTTG-AAAAAATTGAGAG-CCTTTT
54330146 ACACTCTTAA
Statistics
Matches: 329, Mismatches: 51, Indels: 50
0.77 0.12 0.12
Matches are distributed among these distances:
86 56 0.17
87 21 0.06
88 27 0.08
89 30 0.09
90 36 0.11
91 20 0.06
92 21 0.06
93 45 0.14
94 4 0.01
95 29 0.09
96 16 0.05
97 4 0.01
98 20 0.06
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (87 bp):
AAGGGCTTAATTGCTTTTTTTGAAAAAATTGAGAGCCTTTTTTATACATTTTAAAATTCAAGTAC
CCAATTGAGTAAAAAAAAAAGC
Found at i:54330100 original size:186 final size:176
Alignment explanation
Indices: 54329690--54330136 Score: 548
Period size: 186 Copynumber: 2.5 Consensus size: 176
54329680 TTGAGGGTCT
* * * * *
54329690 TTTTTATGCATTTTGACAGTTCAAGTACCCAATTAAGTGCAAAAAGAAAA-AGCATGGGCTTAAT
1 TTTTTAAGCATTTTAAAAGTTTAAGTACCCAATTGAGTGCAAAAA-AAAACA--AT-GGCTTAAT
* *
54329754 TGCTTTATTTTGAAAAAAATTGACGGTCTTTTTTATGCATTTGAAAGTTCAAGTACTCGATTGAG
62 TGCTTTATTTTGAAAAAAATTGACGGGCTTTTTTATGCATTTGAAAGTTCAAGTACTCAATTGAG
*
54329819 TAAAAAAGAAAGCAGGGGCTTAATTGCTTTTTTGAAAAATTTGAAAGCCT
127 TAAAAAAGAAAGCAGGGGCTTAATTGCTTTTTTGAAAAATTTGAAAGCCA
54329869 TTTTTATA-CATTTTAAAA-TTTAAGTACCCAATTGAGTGCAAAAAAAAACAATGGCTTAATTGC
1 TTTTTA-AGCATTTTAAAAGTTTAAGTACCCAATTGAGTGCAAAAAAAAACAATGGCTTAATTGC
54329932 TTTATTTTGAAAAAAAATTGA-GGGCATTTTTTATGCATTTTGAAAGTTCAAGTA-TCCAATTGA
65 TTTATTTTG-AAAAAAATTGACGGGC-TTTTTTATGCA-TTTGAAAGTTCAAGTACT-CAATTGA
* * *
54329995 GTACAAAAAAAAAAATAAAGCAGGGGCTTAATTGCTTTTCTTTGAAAATTTTGAGAG-CA
126 GT-------AAAAAAGAAAGCAGGGGCTTAATTGC-TTT-TTTGAAAAATTTGAAAGCCA
* * *
54330054 TTTTTAAGCATTTTAAAAGTTTAAGTACCCAATTGAGTGGAAAAAAAAACAAAGGGTTAATTG-T
1 TTTTTAAGCATTTTAAAAGTTTAAGTACCCAATTGAGTGCAAAAAAAAACAATGGCTTAATTGCT
*
54330118 TTTTTTTGAAAAAAATTGA
66 TTATTTTGAAAAAAATTGA
54330137 AGACCTTTTA
Statistics
Matches: 236, Mismatches: 15, Indels: 29
0.84 0.05 0.10
Matches are distributed among these distances:
175 23 0.10
176 25 0.11
177 28 0.12
178 25 0.11
179 14 0.06
184 37 0.16
185 28 0.12
186 56 0.24
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (176 bp):
TTTTTAAGCATTTTAAAAGTTTAAGTACCCAATTGAGTGCAAAAAAAAACAATGGCTTAATTGCT
TTATTTTGAAAAAAATTGACGGGCTTTTTTATGCATTTGAAAGTTCAAGTACTCAATTGAGTAAA
AAAGAAAGCAGGGGCTTAATTGCTTTTTTGAAAAATTTGAAAGCCA
Found at i:54334309 original size:21 final size:21
Alignment explanation
Indices: 54334285--54334329 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
54334275 AAACCAACTC
*
54334285 ATATTTTTTCTA-GCCCAACAA
1 ATATTTTTCCTATGCCCAA-AA
54334306 ATA-TTTTCCTATGCCCAAAA
1 ATATTTTTCCTATGCCCAAAA
54334326 ATAT
1 ATAT
54334330 GATTTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.38
Consensus pattern (21 bp):
ATATTTTTCCTATGCCCAAAA
Found at i:54338031 original size:14 final size:14
Alignment explanation
Indices: 54338012--54338038 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54338002 ACTCTTATGT
54338012 AATAAAAATAAAAA
1 AATAAAAATAAAAA
54338026 AATAAAAATAAAA
1 AATAAAAATAAAA
54338039 TTTAGTTGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (14 bp):
AATAAAAATAAAAA
Found at i:54339320 original size:15 final size:17
Alignment explanation
Indices: 54339295--54339326 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
54339285 TAGGTTATTG
54339295 GATCAAAATGAA-AATT
1 GATCAAAATGAACAATT
54339311 GATC-AAATGAACAATT
1 GATCAAAATGAACAATT
54339327 AAAATGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.25
Consensus pattern (17 bp):
GATCAAAATGAACAATT
Found at i:54341862 original size:26 final size:26
Alignment explanation
Indices: 54341833--54341914 Score: 164
Period size: 26 Copynumber: 3.2 Consensus size: 26
54341823 TGATACAAAT
54341833 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54341859 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54341885 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54341911 TGAT
1 TGAT
54341915 GGAAATTTCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:54342794 original size:26 final size:26
Alignment explanation
Indices: 54342765--54342872 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
54342755 TGATACAAAT
*
54342765 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
54342791 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
54342817 TGATAATGGATTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54342843 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54342869 TGAT
1 TGAT
54342873 GGAAATTTCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:54344369 original size:54 final size:53
Alignment explanation
Indices: 54344287--54344395 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 53
54344277 TGGAGGAAGC
* * *
54344287 GTCCTAGTGGCTATGCCACAATTATCTGATTTAGTGGCTCTGCCACATATATCT
1 GTCCTAGTGGCTATGCCACAATAATCTGATCTAGTAGCTCTGCCACA-ATATCT
*
54344341 GTCCTAGTGGCTATGCCACAATAATCTGATCTGGTAGCTCTGCCACAATATCT
1 GTCCTAGTGGCTATGCCACAATAATCTGATCTAGTAGCTCTGCCACAATATCT
54344394 GT
1 GT
54344396 ATCTGGTGAC
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
53 8 0.16
54 43 0.84
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (53 bp):
GTCCTAGTGGCTATGCCACAATAATCTGATCTAGTAGCTCTGCCACAATATCT
Found at i:54344400 original size:27 final size:26
Alignment explanation
Indices: 54344290--54344421 Score: 124
Period size: 27 Copynumber: 4.9 Consensus size: 26
54344280 AGGAAGCGTC
*
54344290 CTAGTGGCTATGCCACAATTATCTGAT
1 CTAGTGGCTCTGCCACAA-TATCTGAT
*
54344317 TTAGTGGCTCTGCCACATATATCTG-T
1 CTAGTGGCTCTGCCACA-ATATCTGAT
*
54344343 CCTAGTGGCTATGCCACAATAATCTGAT
1 -CTAGTGGCTCTGCCACAAT-ATCTGAT
* *
54344371 CTGGTAGCTCTGCCACAATATCTGTAT
1 CTAGTGGCTCTGCCACAATATCTG-AT
* * *
54344398 CTGGTGACT-TCGTCACAATATCTG
1 CTAGTGGCTCT-GCCACAATATCTG
54344422 GCAGTCTAGC
Statistics
Matches: 89, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
26 9 0.10
27 78 0.88
28 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.33
Consensus pattern (26 bp):
CTAGTGGCTCTGCCACAATATCTGAT
Found at i:54344415 original size:54 final size:53
Alignment explanation
Indices: 54344287--54344421 Score: 148
Period size: 54 Copynumber: 2.5 Consensus size: 53
54344277 TGGAGGAAGC
* * *
54344287 GTCCTAGTGGCTATGCCACAATTATCTGATTTAGTGGCTCTGCCACATATATCT
1 GTCCTAGTGACTATGCCACAA-TATCTGATCTAGTAGCTCTGCCACATATATCT
* *
54344341 GTCCTAGTGGCTATGCCACAATAATCTGATCTGGTAGCTCTGCCACA-ATATCT
1 GTCCTAGTGACTATGCCACAAT-ATCTGATCTAGTAGCTCTGCCACATATATCT
* * *
54344394 GTATCTGGTGACT-TCGTCACAATATCTG
1 GT-CCTAGTGACTAT-GCCACAATATCTG
54344422 GCAGTCTAGC
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
53 15 0.21
54 56 0.79
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.33
Consensus pattern (53 bp):
GTCCTAGTGACTATGCCACAATATCTGATCTAGTAGCTCTGCCACATATATCT
Found at i:54349718 original size:25 final size:26
Alignment explanation
Indices: 54349677--54349781 Score: 189
Period size: 25 Copynumber: 4.2 Consensus size: 26
54349667 TGATACAAAT
54349677 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54349703 TGATAAT-GGTTAGGTAAATGTT-CA
1 TGATAATGGGTTAGGTAAATGTTCCA
54349727 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54349753 TGATAAT-GGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54349778 TGAT
1 TGAT
54349782 GGAATTTCAT
Statistics
Matches: 77, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
24 9 0.12
25 52 0.68
26 16 0.21
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:54351412 original size:27 final size:27
Alignment explanation
Indices: 54351372--54351511 Score: 182
Period size: 27 Copynumber: 5.2 Consensus size: 27
54351362 AGGAAGCGTC
54351372 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTATGCCACAATTATCTGAT
*
54351399 CTGGTGGCTCTGCCAC-ATATATCTG-T
1 CTGGTGGCTATGCCACAAT-TATCTGAT
54351425 CCTGGTGGCTATGCCACAATTATCTGAT
1 -CTGGTGGCTATGCCACAATTATCTGAT
*
54351453 CTGGTGGCT-TGCCAC-ATATATCTGTT
1 CTGGTGGCTATGCCACAAT-TATCTGAT
*
54351479 CTGGTGGCTCTGCCACAA-TATCTGTAT
1 CTGGTGGCTATGCCACAATTATCTG-AT
54351506 CTGGTG
1 CTGGTG
54351512 ACTTCGTCAC
Statistics
Matches: 101, Mismatches: 4, Indels: 16
0.83 0.03 0.13
Matches are distributed among these distances:
25 2 0.02
26 31 0.31
27 64 0.63
28 4 0.04
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTATGCCACAATTATCTGAT
Found at i:54351493 original size:53 final size:53
Alignment explanation
Indices: 54351369--54351529 Score: 245
Period size: 53 Copynumber: 3.0 Consensus size: 53
54351359 TGGAGGAAGC
54351369 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCT-TGCCACATATATCT
54351423 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTTGCCACATATATCT
* * * *
54351476 GTTCTGGTGGCTCTGCCACAA-TATCTGTATCTGGTGACTTCGTCACA-ATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTGGCTT-GCCACATATATCT
54351529 G
1 G
54351530 GCAGCCTCGC
Statistics
Matches: 101, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
52 6 0.06
53 51 0.50
54 44 0.44
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (53 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTTGCCACATATATCT
Found at i:54351522 original size:27 final size:27
Alignment explanation
Indices: 54351372--54351529 Score: 154
Period size: 27 Copynumber: 5.9 Consensus size: 27
54351362 AGGAAGCGTC
54351372 CTGGTGGCTAT-GCCACAATTATCTG-AT
1 CTGGTGGCT-TCGCCACAA-TATCTGTAT
*
54351399 CTGGTGGC-TCTGCCACATATATCTGT-C
1 CTGGTGGCTTC-GCCACA-ATATCTGTAT
54351426 CTGGTGGCTAT-GCCACAATTATCTG-AT
1 CTGGTGGCT-TCGCCACAA-TATCTGTAT
54351453 CTGGTGGCTT-GCCACATATATCTGT-T
1 CTGGTGGCTTCGCCACA-ATATCTGTAT
54351479 CTGGTGGC-TCTGCCACAATATCTGTAT
1 CTGGTGGCTTC-GCCACAATATCTGTAT
* *
54351506 CTGGTGACTTCGTCACAATATCTG
1 CTGGTGGCTTCGCCACAATATCTG
54351530 GCAGCCTCGC
Statistics
Matches: 113, Mismatches: 4, Indels: 28
0.78 0.03 0.19
Matches are distributed among these distances:
25 2 0.02
26 31 0.27
27 76 0.67
28 3 0.03
29 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTTCGCCACAATATCTGTAT
Done.