Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 74 of 438
Found at i:19789979 original size:164 final size:148
Alignment explanation
Indices: 19789909--19790200 Score: 458
Period size: 149 Copynumber: 2.0 Consensus size: 148
19789899 ATTAAAAAAC
19789909 AGAAACTAAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
1 AGAAACTAAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-T
*
19789974 TTTTTTGCAAAACAGAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT
65 TTTTTTACAAAACAGAAATT-AAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT
19790039 ATGAGTTGATTTTGACGAAT
129 ATGAGTTGATTTTGACGAAT
* * *
19790059 AGAAACTGAAAATACCTCAGCATGTGAGCTGAGGCTCAACTCACCTTTCGCAATATGAGTTGATT
1 AGAAACTAAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
* ** * * *
19790124 TTTTGATGAAACAGAAATTAAAATTACCTCAGCGTGTCCTAAGGCTTAACTCACCTCTCCCAATA
66 TTTTTACAAAACAGAAATTAAAA-TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATA
*
19790189 TAAGTTGATTTT
130 TGAGTTGATTTT
19790201 TGAAACAGAA
Statistics
Matches: 130, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
148 4 0.03
149 66 0.51
150 60 0.46
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (148 bp):
AGAAACTAAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
TTTTTACAAAACAGAAATTAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
GAGTTGATTTTGACGAAT
Found at i:19790039 original size:76 final size:76
Alignment explanation
Indices: 19789904--19790201 Score: 351
Period size: 75 Copynumber: 3.9 Consensus size: 76
19789894 CAAAAATTAA
*
19789904 AAAACAGAAACTAAAAATACCTCAGCATGTGAGCC-GAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAACAGAAACTAAAAATACCTCAGCA-GTG-TCCTGAGGCTCAACTCACCTCTCGCAATATGAG
19789968 TTGATTTTTTTTG
64 TTGATTTTTTTTG
*
19789981 CAAAACAGAAATTAAAAATACCTCAGC-GTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 -AAAACAGAAACTAAAAATACCTCAGCAGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
19790045 TGA----TTTTG
65 TGATTTTTTTTG
* * * ** *
19790053 ACGAATAGAAACTGAAAATACCTCAGCATGTGAGCTGAGGCTCAACTCACCTTTCGCAATATGAG
1 A-AAACAGAAACTAAAAATACCTCAGCA-GTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
*
19790118 TTGATTTTTTGATG
64 TTGATTTTTT-TTG
* * * * * *
19790132 -AAACAGAAATTAAAATTACCTCAGC-GTGTCCTAAGGCTTAACTCACCTCTCCCAATATAAGTT
1 AAAACAGAAACTAAAAATACCTCAGCAGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
19790195 GATTTTT
66 GATTTTT
19790202 GAAACAGAAA
Statistics
Matches: 189, Mismatches: 22, Indels: 21
0.81 0.09 0.09
Matches are distributed among these distances:
71 1 0.01
72 26 0.14
74 37 0.20
75 40 0.21
76 36 0.19
77 20 0.11
78 27 0.14
79 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (76 bp):
AAAACAGAAACTAAAAATACCTCAGCAGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTTTTG
Found at i:19790203 original size:150 final size:149
Alignment explanation
Indices: 19789909--19790200 Score: 478
Period size: 150 Copynumber: 2.0 Consensus size: 149
19789899 ATTAAAAAAC
19789909 AGAAACTAAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
1 AGAAACTAAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
* * *
19789974 TTTTTTGCAAAACAGAAATTAAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAAT
66 TTTTATG-AAAACAGAAATTAAAAATACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCCCAAT
*
19790039 ATGAGTTGATTTTGACGAAT
130 ATAAGTTGATTTTGACGAAT
* * *
19790059 AGAAACTGAAAATACCTCAGCATGTGAGCTGAGGCTCAACTCACCTTTCGCAATATGAGTTGATT
1 AGAAACTAAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
* *
19790124 TTTTGATG-AAACAGAAATTAAAATTACCTCAGCGTGTCCTAAGGCTTAACTCACCTCTCCCAAT
66 TTTT-ATGAAAACAGAAATTAAAAATACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCCCAAT
19790188 ATAAGTTGATTTT
130 ATAAGTTGATTTT
19790201 TGAAACAGAA
Statistics
Matches: 132, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
149 64 0.48
150 66 0.50
151 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (149 bp):
AGAAACTAAAAATACCTCAGCATGTGAGCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT
TTTTATGAAAACAGAAATTAAAAATACCTCAGCGTGTCCTAAGGCTCAACTCACCTCTCCCAATA
TAAGTTGATTTTGACGAAT
Found at i:19801327 original size:15 final size:16
Alignment explanation
Indices: 19801307--19801341 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
19801297 CGTTTTATTT
*
19801307 AAAAACT-AAACTATA
1 AAAAACTAAAACCATA
19801322 AAAAACTAAAACCATA
1 AAAAACTAAAACCATA
19801338 AAAA
1 AAAA
19801342 CTTAGAGCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAAACTAAAACCATA
Found at i:19802836 original size:25 final size:26
Alignment explanation
Indices: 19802808--19802872 Score: 87
Period size: 25 Copynumber: 2.5 Consensus size: 26
19802798 AATAATGTGA
*
19802808 TATTAAAAATATATACAATATATA-G
1 TATTAAAAATATACACAATATATAGG
* *
19802833 TATTAAGAATATACGCAATATATATGG
1 TATTAAAAATATACACAATATATA-GG
19802860 TATTAAAAATATA
1 TATTAAAAATATA
19802873 GTATTAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 21 0.62
27 13 0.38
ACGTcount: A:0.52, C:0.05, G:0.08, T:0.35
Consensus pattern (26 bp):
TATTAAAAATATACACAATATATAGG
Found at i:19803232 original size:2 final size:2
Alignment explanation
Indices: 19803170--19803213 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
19803160 GTATATTGTA
*
19803170 AT AT A- AT AT -T AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19803210 AT AT
1 AT AT
19803214 GGTAATATGA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19807708 original size:46 final size:45
Alignment explanation
Indices: 19807610--19807825 Score: 179
Period size: 46 Copynumber: 4.6 Consensus size: 45
19807600 ATCTCAATTC
* *
19807610 GATGCCATGTCCCAGAAATGGTCTTACACTGACTATCATCTCGTAGTC-
1 GATG-CATGTCCCAGACAT-GTCTTACACTGACT-TCATCTCG-AGGCT
* * *
19807658 GATGCATGTCCCAGACATGTTTTACACTGACTTACGTCTTGAGGCT
1 GATGCATGTCCCAGACATGTCTTACACTGACTT-CATCTCGAGGCT
* * * *
19807704 GATGCACGTCCCAGACATGGT-TTACACTAGCAGTT-GTCTCGATGCT
1 GATGCATGTCCCAGACAT-GTCTTACACT-G-ACTTCATCTCGAGGCT
* * * *
19807750 GATGCAATGTCCCAGACATGGTCTTACACTGGCTCTCATAAT-GTGGCC
1 GATGC-ATGTCCCAGACAT-GTCTTACACTGACT-TCAT-CTCGAGGCT
19807798 GATGCATGTCCCAGACATGTCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
19807826 AGCTCACAAT
Statistics
Matches: 141, Mismatches: 17, Indels: 22
0.78 0.09 0.12
Matches are distributed among these distances:
45 4 0.03
46 67 0.48
47 46 0.33
48 23 0.16
49 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.29
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTGACTTCATCTCGAGGCT
Found at i:19814979 original size:23 final size:22
Alignment explanation
Indices: 19814949--19814995 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
19814939 GAAAATTAGT
19814949 AAATTAGAATTG-AATCAAAAATA
1 AAATTAG-ATTGCAA-CAAAAATA
*
19814972 AAATTAGATTGCAAGAAAAATA
1 AAATTAGATTGCAACAAAAATA
19814994 AA
1 AA
19814996 TGGCTAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.62, C:0.04, G:0.11, T:0.23
Consensus pattern (22 bp):
AAATTAGATTGCAACAAAAATA
Found at i:19820826 original size:267 final size:267
Alignment explanation
Indices: 19820341--19820864 Score: 976
Period size: 267 Copynumber: 2.0 Consensus size: 267
19820331 CATTCATCAA
*
19820341 CAAGTATCATAATACACAAGTGGGCATAAGCAAAACTTACTCATCAATATTCAATACACATCATA
1 CAAGTATCATAATACACAAGTGGGCATAAGAAAAACTTACTCATCAATATTCAATACACATCATA
*
19820406 TAGCATATAATGTGGCTCACATTTTATACATACCAAATAGGTACCTGTATCACTCACAACACGGT
66 GAGCATATAATGTGGCTCACATTTTATACATACCAAATAGGTACCTGTATCACTCACAACACGGT
*
19820471 TATAGTTTCTCATTAACTAGAAATCAAAACTTTCACCGTTGAACCATTCGGAATGCTATCGAATA
131 TATAGTTTCTCATTAACTAGAAATCAAAACTTTCACCGTTGAACCATTCAGAATGCTATCGAATA
* * *
19820536 TTCCATAGCATTAAACGTGGGTTAAGGTGCTGATGCCATGTCCCAGACATGGTCTTACACTAGCT
196 TTCCATAGCATCAAACATGGGTTAAGGTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCT
19820601 CATATCT
261 CATATCT
*
19820608 CAAGTATCATAATACACAAGTGGGCATAAGAAAAACTTACTTATCAATATTCAATACACATCATA
1 CAAGTATCATAATACACAAGTGGGCATAAGAAAAACTTACTCATCAATATTCAATACACATCATA
19820673 GAGCATATAATGTGGCTCACATTTTATACATACCAAATAGGTACCTGTATCACTCACAACACGGT
66 GAGCATATAATGTGGCTCACATTTTATACATACCAAATAGGTACCTGTATCACTCACAACACGGT
*
19820738 TATAGTTTCTCATTAACTAGAAATCAAAACTTTCGCCGTTGAACCATTCAGAATGCTATCGAATA
131 TATAGTTTCTCATTAACTAGAAATCAAAACTTTCACCGTTGAACCATTCAGAATGCTATCGAATA
19820803 TTCCATAGCATCAAACATGGGTTAAGGTGCCGATGCCATGTCCCAGACATGGTCTTACACTA
196 TTCCATAGCATCAAACATGGGTTAAGGTGCCGATGCCATGTCCCAGACATGGTCTTACACTA
19820865 ACTATCATCT
Statistics
Matches: 249, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
267 249 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (267 bp):
CAAGTATCATAATACACAAGTGGGCATAAGAAAAACTTACTCATCAATATTCAATACACATCATA
GAGCATATAATGTGGCTCACATTTTATACATACCAAATAGGTACCTGTATCACTCACAACACGGT
TATAGTTTCTCATTAACTAGAAATCAAAACTTTCACCGTTGAACCATTCAGAATGCTATCGAATA
TTCCATAGCATCAAACATGGGTTAAGGTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCT
CATATCT
Found at i:19820922 original size:46 final size:46
Alignment explanation
Indices: 19820831--19821057 Score: 185
Period size: 46 Copynumber: 4.8 Consensus size: 46
19820821 GGGTTAAGGT
*
19820831 GCCGATGCCATGTCCCAGACATGGTCTTACACTAAC-TATCATCTCGTA-
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTTA-CATCTCG-AG
* *
19820879 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTTACGTCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTACATCTCGAG
* * * *
19820925 GCCAATGCATGTCCCAGACATGTCTTACACTAGCACT-CGTCTCGAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC-TTACATCTCGAG
* * * * * * * *
19820971 GCCGATGCAATGTTCTAGACGTGGTCTTAGAATGGCTCT-CATAAT-GTG
1 GCCGATGC-ATGTCCCAGACAT-GTCTTACACTAGCT-TACAT-CTCGAG
* *
19821019 GCCGATGCATGTCCTAGAAATGTCTTACACTAGCTTACA
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTACA
19821058 ATAACCCCTA
Statistics
Matches: 146, Mismatches: 25, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
45 2 0.01
46 77 0.53
47 37 0.25
48 29 0.20
49 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.28
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTACATCTCGAG
Found at i:19823738 original size:76 final size:76
Alignment explanation
Indices: 19823644--19823797 Score: 236
Period size: 76 Copynumber: 2.0 Consensus size: 76
19823634 TAATCTTGTA
** * *
19823644 TGCTGCAATGCAGTATAGGTATTGTATCGAACTGTTAACTTCGTGGAATGGTACTAGATGAAGGG
1 TGCTGCAATGCAACATAGGTATTGTATCAAACTATTAACTTCGTGGAATGGTACTAGATGAAGGG
* *
19823709 GCTCTTGGTGT
66 ACTCTCGGTGT
* *
19823720 TGCTGCAATGCAACATAGGTATTGTATCAAACTATTAACTTTGTGGAATGGTGCTAGATGAAGGG
1 TGCTGCAATGCAACATAGGTATTGTATCAAACTATTAACTTCGTGGAATGGTACTAGATGAAGGG
19823785 ACTCTCGGTGT
66 ACTCTCGGTGT
19823796 TG
1 TG
19823798 AACTTAGAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
76 70 1.00
ACGTcount: A:0.25, C:0.14, G:0.29, T:0.32
Consensus pattern (76 bp):
TGCTGCAATGCAACATAGGTATTGTATCAAACTATTAACTTCGTGGAATGGTACTAGATGAAGGG
ACTCTCGGTGT
Found at i:19827400 original size:13 final size:13
Alignment explanation
Indices: 19827382--19827422 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
19827372 CTTTTTCAAT
*
19827382 AGGGAAATTGACA
1 AGGGAAATCGACA
*
19827395 AGGGAAATCGATA
1 AGGGAAATCGACA
*
19827408 AGGGAAATGGACA
1 AGGGAAATCGACA
19827421 AG
1 AG
19827423 AAAAAGGGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.46, C:0.07, G:0.34, T:0.12
Consensus pattern (13 bp):
AGGGAAATCGACA
Found at i:19834891 original size:44 final size:44
Alignment explanation
Indices: 19834837--19834924 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
19834827 CCAAAGAGTA
19834837 AAAAAGAGTGGAATGAAGAAGATAAAAGGAAGATTCAACTCAAT
1 AAAAAGAGTGGAATGAAGAAGATAAAAGGAAGATTCAACTCAAT
*
19834881 AAAAAGAGTGGAATGAAGAAGATAGAAGGAAGATTCAACTCAAT
1 AAAAAGAGTGGAATGAAGAAGATAAAAGGAAGATTCAACTCAAT
19834925 GCACACTTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.53, C:0.07, G:0.24, T:0.16
Consensus pattern (44 bp):
AAAAAGAGTGGAATGAAGAAGATAAAAGGAAGATTCAACTCAAT
Found at i:19838123 original size:57 final size:57
Alignment explanation
Indices: 19838055--19838228 Score: 192
Period size: 57 Copynumber: 3.1 Consensus size: 57
19838045 TAAAGGCATC
* * * *
19838055 CTTTAAGAGGTTCACTATAAAGGCTTA-CTCTTCTAGAGTTTTGCCACAAAGGTTGTT
1 CTTTAATAGGTTCACCAAAAAGGCTTACCT-TTCTAGAGTTTTTCCACAAAGGTTGTT
* * * * * * * *
19838112 CTTTAATAGGTTCGCCACAAAGGTTTGCCTTTCTAGAATTTTTCCACAAAGGCTATC
1 CTTTAATAGGTTCACCAAAAAGGCTTACCTTTCTAGAGTTTTTCCACAAAGGTTGTT
*
19838169 CTTTCATTA-GTTCACCAAAAAGGCTTACCTTTCTAGAGTTTTTCCACAAAGGTTG-T
1 CTTT-AATAGGTTCACCAAAAAGGCTTACCTTTCTAGAGTTTTTCCACAAAGGTTGTT
19838225 CTTT
1 CTTT
19838229 TAGCAGGTTT
Statistics
Matches: 95, Mismatches: 20, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
56 4 0.04
57 86 0.91
58 5 0.05
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (57 bp):
CTTTAATAGGTTCACCAAAAAGGCTTACCTTTCTAGAGTTTTTCCACAAAGGTTGTT
Found at i:19838170 original size:114 final size:113
Alignment explanation
Indices: 19838046--19838287 Score: 276
Period size: 114 Copynumber: 2.1 Consensus size: 113
19838036 GTCTCGCCAT
* *
19838046 AAAGGC-ATCCTTTAAGAGGTTCACTATAAAGGCTTA-CTCTTCTAGAGTTTTGCCACAAAGGTT
1 AAAGGCTATCCTTTAAGA-GTTCACCAAAAAGGCTTACCT-TTCTAGAGTTTTGCCACAAAGGTT
* * *
19838109 GT-TCTTTAATAGGTTCGCCACAAAGGTTTGCCTTTCTAGAATTTT-TCCAC
64 GTCT-TTTAACAGGTTCGCCACAAAGGCTTGCCTTTCCAGAATTTTGT-CAC
** *
19838159 AAAGGCTATCCTTTCATTAGTTCACCAAAAAGGCTTACCTTTCTAGAGTTTTTCCACAAAGGTTG
1 AAAGGCTATCCTTT-AAGAGTTCACCAAAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGTTG
* ** * * *
19838224 TCTTTTAGCAGGTTTTCCACATAGGCTTGCCTTTCCAGAGTTTTGTCAT
65 TCTTTTAACAGGTTCGCCACAAAGGCTTGCCTTTCCAGAATTTTGTCAC
*
19838273 AAAGGCTATCTTTTA
1 AAAGGCTATCCTTTA
19838288 GCAGGTTTGC
Statistics
Matches: 109, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
113 7 0.06
114 96 0.88
115 6 0.06
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.37
Consensus pattern (113 bp):
AAAGGCTATCCTTTAAGAGTTCACCAAAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGTTGT
CTTTTAACAGGTTCGCCACAAAGGCTTGCCTTTCCAGAATTTTGTCAC
Found at i:19838228 original size:28 final size:29
Alignment explanation
Indices: 19838126--19838267 Score: 123
Period size: 28 Copynumber: 5.0 Consensus size: 29
19838116 AATAGGTTCG
* *
19838126 CCACAAAGGTTTGCCTTTCTAGAATTTTT
1 CCACAAAGGCTTGCCTTTCTAGAGTTTTT
* **
19838155 CCACAAAGGCTAT-CCTTTC-ATTAG-TTCA
1 CCACAAAGGCT-TGCCTTTCTA-GAGTTTTT
* *
19838183 CCAAAAAGGCTTACCTTTCTAGAGTTTTT
1 CCACAAAGGCTTGCCTTTCTAGAGTTTTT
* *
19838212 CCACAAAGG-TTGTCTTT-TAGCAGGTTTT
1 CCACAAAGGCTTGCCTTTCTAG-AGTTTTT
* *
19838240 CCACATAGGCTTGCCTTTCCAGAGTTTT
1 CCACAAAGGCTTGCCTTTCTAGAGTTTT
19838268 GTCATAAAGG
Statistics
Matches: 88, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
27 4 0.05
28 41 0.47
29 40 0.45
30 3 0.03
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.37
Consensus pattern (29 bp):
CCACAAAGGCTTGCCTTTCTAGAGTTTTT
Found at i:19838250 original size:57 final size:57
Alignment explanation
Indices: 19838073--19838316 Score: 208
Period size: 57 Copynumber: 4.3 Consensus size: 57
19838063 GGTTCACTAT
* * * **
19838073 AAAGGCTTA-CTCTTCTAGAGTTTTGCCACAAAGGTTGT-TCTTTAATAGGTTCGCCAC
1 AAAGGCTTACCT-TTCTAGAGTTTTTCCACAAAGGCTATCT-TTTAGCAGGTTCGCCAC
* * * * ** * *
19838130 AAAGGTTTGCCTTTCTAGAATTTTTCCACAAAGGCTATCCTTTCATTA-GTTCACCAA
1 AAAGGCTTACCTTTCTAGAGTTTTTCCACAAAGGCTAT-CTTTTAGCAGGTTCGCCAC
* * **
19838187 AAAGGCTTACCTTTCTAGAGTTTTTCCACAAAGGTTGTCTTTTAGCAGGTTTTCCAC
1 AAAGGCTTACCTTTCTAGAGTTTTTCCACAAAGGCTATCTTTTAGCAGGTTCGCCAC
* * * * * *
19838244 ATAGGCTTGCCTTTCCAGAGTTTTGT-CATAAAGGCTATCTTTTAGCAGGTTTGCCAG
1 AAAGGCTTACCTTTCTAGAGTTTT-TCCACAAAGGCTATCTTTTAGCAGGTTCGCCAC
*
19838301 AAAGGTTTACCTTTCT
1 AAAGGCTTACCTTTCT
19838317 TGGTGATTTA
Statistics
Matches: 149, Mismatches: 33, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
56 6 0.04
57 134 0.90
58 8 0.05
59 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (57 bp):
AAAGGCTTACCTTTCTAGAGTTTTTCCACAAAGGCTATCTTTTAGCAGGTTCGCCAC
Found at i:19838305 original size:114 final size:114
Alignment explanation
Indices: 19838046--19838316 Score: 275
Period size: 114 Copynumber: 2.4 Consensus size: 114
19838036 GTCTCGCCAT
* * *
19838046 AAAGGC-ATCCTTTAAG-AGGTTCACTATAAAGGCTTA-CTCTTCTAGAGTTTTGCCACAAAGGT
1 AAAGGCTATCCTTTCAGCA-GTTCACCAAAAAGGCTTACCT-TTCTAGAGTTTTGCCACAAAGGT
* * *
19838108 TGTTCTTTAATAGGTTCGCCACAAAGGTTTGCCTTTCTAGAATTTTTCCAC
64 TGTTCTTTAACAGGTTCGCCACAAAGGCTTGCCTTTCCAGAATTTTTCCAC
** *
19838159 AAAGGCTATCCTTTCATTAGTTCACCAAAAAGGCTTACCTTTCTAGAGTTTTTCCACAAAGGTTG
1 AAAGGCTATCCTTTCAGCAGTTCACCAAAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGTTG
* ** * * *
19838224 -TCTTTTAGCAGGTTTTCCACATAGGCTTGCCTTTCCAGAGTTTTGT-CAT
66 TTC-TTTAACAGGTTCGCCACAAAGGCTTGCCTTTCCAGAATTTT-TCCAC
* ** * *
19838273 AAAGGCTAT-CTTTTAGCAGGTTTGCCAGAAAGGTTTACCTTTCT
1 AAAGGCTATCCTTTCAGCA-GTTCACCAAAAAGGCTTACCTTTCT
19838317 TGGTGATTTA
Statistics
Matches: 131, Mismatches: 21, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
113 14 0.11
114 113 0.86
115 4 0.03
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.37
Consensus pattern (114 bp):
AAAGGCTATCCTTTCAGCAGTTCACCAAAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGTTG
TTCTTTAACAGGTTCGCCACAAAGGCTTGCCTTTCCAGAATTTTTCCAC
Found at i:19844157 original size:21 final size:21
Alignment explanation
Indices: 19844123--19844162 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
19844113 AATGGTCATG
*
19844123 GATGATTTAAGAGTGACTTAA
1 GATGATTTAAGAGTCACTTAA
**
19844144 GATGATTTGTGAGTCACTT
1 GATGATTTAAGAGTCACTT
19844163 GTTGTTTAGT
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:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (21 bp):
GATGATTTAAGAGTCACTTAA
Found at i:19844707 original size:28 final size:29
Alignment explanation
Indices: 19844670--19844739 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 29
19844660 TCATGACTAT
*
19844670 GAATGTGATTGGTC-CTGACGGGCCATATG
1 GAATGTGATTGGGCGC-GACGGGCCATATG
*
19844699 GAAT-TGATTGGGCGCGATGGGCCATAT-
1 GAATGTGATTGGGCGCGACGGGCCATATG
*
19844726 GAATGAGATTGGGC
1 GAATGTGATTGGGC
19844740 CTAAAGGGGC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 4 0.11
28 27 0.75
29 5 0.14
ACGTcount: A:0.23, C:0.14, G:0.37, T:0.26
Consensus pattern (29 bp):
GAATGTGATTGGGCGCGACGGGCCATATG
Found at i:19857486 original size:36 final size:33
Alignment explanation
Indices: 19857439--19857507 Score: 84
Period size: 36 Copynumber: 2.0 Consensus size: 33
19857429 CCGTTAGCTC
*
19857439 CAGTTAGGGCCTCAGCCTCTTTTTCAGTAACAGTAT
1 CAGTTAGGGCCTCAGCC-C-ATTTCAGT-ACAGTAT
* *
19857475 CAGTTTGGGCCTGAGCCCATTTCAGTACAGTAT
1 CAGTTAGGGCCTCAGCCCATTTCAGTACAGTAT
19857508 ACAAACAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 7 0.23
34 7 0.23
35 1 0.03
36 15 0.50
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (33 bp):
CAGTTAGGGCCTCAGCCCATTTCAGTACAGTAT
Found at i:19861623 original size:40 final size:40
Alignment explanation
Indices: 19861515--19861724 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
19861505 CGGGATTTAA
* * * * *
19861515 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
19861555 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
19861595 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
19861635 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
19861675 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
19861715 CCGGATATAT
1 CCGGATATAT
19861725 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:19869761 original size:40 final size:40
Alignment explanation
Indices: 19869653--19869862 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
19869643 CGGGATTTAA
* * * * *
19869653 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
19869693 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
19869733 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
19869773 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
19869813 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
19869853 CCGGATATAT
1 CCGGATATAT
19869863 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:19877909 original size:28 final size:28
Alignment explanation
Indices: 19877863--19877931 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
19877853 TTTAAAACCC
*
19877863 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
19877890 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
19877918 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
19877932 TGATCTACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:19879561 original size:20 final size:20
Alignment explanation
Indices: 19879538--19879575 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
19879528 CACATCCAAA
*
19879538 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
19879558 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
19879576 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:19886320 original size:40 final size:39
Alignment explanation
Indices: 19886276--19886463 Score: 173
Period size: 40 Copynumber: 4.7 Consensus size: 39
19886266 ATAACCACAA
* *** *
19886276 GCACAATTGCCTTCGGGTCTTAACCCGGATTTGGTAACTT
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATTTAACAACTC
*
19886316 GCACAAATGCCTTCGGGTCTTAGCCCGGATATAACAACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATTTAACAACTC
*
19886356 GCACGAATGCCTTCGGGTCTTAGCCCGGATTTAATC-ACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATTTAA-CAACTC
* * * * *
19886396 GCATAAATGCCTTCGAGACTTAGCCCGGATATAATC-ACTA
1 GCA-CAATGCCTTCGGGTCTTAGCCCGGATTTAA-CAACTC
* *
19886436 GCATAAATGCCTTCGGGACTTAGCCCGG
1 GCA-CAATGCCTTCGGGTCTTAGCCCGG
19886464 GTATCATTCA
Statistics
Matches: 131, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
40 128 0.98
41 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATTTAACAACTC
Found at i:19886383 original size:80 final size:80
Alignment explanation
Indices: 19886263--19886463 Score: 251
Period size: 80 Copynumber: 2.5 Consensus size: 80
19886253 AATTTAGCCA
* * * * ** *
19886263 GATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGATTTGGTAACTTGCACAAATGCCT
1 GATATAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAATAACTAGCACAAATGCCT
* *
19886328 TCGGGTCTTAGCCCG
66 TCGAGACTTAGCCCG
* * * *
19886343 GATATAA-CAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATTTAATCACTAGCATAAATGCC
1 GATATAATC-ACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAATAACTAGCACAAATGCC
19886407 TTCGAGACTTAGCCCG
65 TTCGAGACTTAGCCCG
* *
19886423 GATATAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGG
1 GATATAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGG
19886464 GTATCATTCA
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
79 1 0.01
80 101 0.98
81 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (80 bp):
GATATAATCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAATAACTAGCACAAATGCCT
TCGAGACTTAGCCCG
Found at i:19894368 original size:40 final size:40
Alignment explanation
Indices: 19894319--19894525 Score: 249
Period size: 40 Copynumber: 5.2 Consensus size: 40
19894309 TCTTCGGAAT
* * *
19894319 TTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
* * ** * *
19894358 TTAACCCGGATTTGGTAACTTGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
* *
19894398 TTAGCCCGGATATAA-CAACTCGCACGAATGCCTTCGGGTC
1 TTAGCCCGGATATAATC-ACTAGCACAAATGCCTTCGGGTC
* *
19894438 TTAGCCCGGAT-TAATCACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
* *
19894477 TTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
19894517 TTAGCCCGG
1 TTAGCCCGG
19894526 GTATCATTCA
Statistics
Matches: 144, Mismatches: 20, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
39 36 0.25
40 108 0.75
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTAGCCCGGATATAATCACTAGCACAAATGCCTTCGGGTC
Found at i:19894507 original size:79 final size:79
Alignment explanation
Indices: 19894310--19894525 Score: 256
Period size: 79 Copynumber: 2.7 Consensus size: 79
19894300 AACCGAGCTT
* * * * * **
19894310 CTTCGGAATTTAG-CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGATTTGGT
1 CTTCGGGACTTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAAT
*
19894374 AACTTGCACAAATGC
65 AACTAGCACAAATGC
* * *
19894389 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGA-TTAAT
1 CTTCGGGACTTAGCCCGGATATAAC-ACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAAT
* *
19894453 CACTAGCATAAATGC
65 AACTAGCACAAATGC
* *
19894468 CTTCGGGACTTAGCCCGGATATAATCACTAGCATAAATGCCTTCGGGACTTAGCCCGG
1 CTTCGGGACTTAGCCCGGATATAA-CACTAGCACAAATGCCTTCGGGTCTTAGCCCGG
19894526 GTATCATTCA
Statistics
Matches: 116, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
79 77 0.66
80 39 0.34
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (79 bp):
CTTCGGGACTTAGCCCGGATATAACACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAATA
ACTAGCACAAATGC
Found at i:19896755 original size:40 final size:40
Alignment explanation
Indices: 19896697--19896993 Score: 334
Period size: 40 Copynumber: 7.5 Consensus size: 40
19896687 CGGATGATAA
* * * * *
19896697 CCGGGCTAAGTCCAGAAGGCATTGGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
* * * *
19896737 TCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
19896777 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
19896817 CCGGGTTAAGTCCCAAAGGCATTTGTGAGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
19896857 CCGGGTTAAGTCCCGAAGGCATTTGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
19896897 CCGGGCTAAGTTCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
19896937 CCGGGCTATGT-CCGAAGGCATTCGAGCAAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
19896976 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
19896994 TACTTGGCTT
Statistics
Matches: 231, Mismatches: 23, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
38 7 0.03
39 32 0.14
40 192 0.83
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:19898702 original size:47 final size:47
Alignment explanation
Indices: 19898633--19898803 Score: 165
Period size: 47 Copynumber: 3.7 Consensus size: 47
19898623 TGGATGCGAA
*
19898633 CATCCGAA-CTCGTTGAGTTGAGTCTAAGTTCGTGAGATGTAACTAGG
1 CATCC-AAGCTCGTTGAGTTGAGTCCAAGTTCGTGAGATGTAACTAGG
* * * * * *
19898680 CATCCAAGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC--GT
1 CATCCAAGCTCGTTGAGTTGAGTCCAAGTTC-GTGA--GATG-TAACTAGG
*
19898729 C-T-GAA-CTCGTTGAGTTGAGTCCAAGTTCGTGAGATGTAACTAGG
1 CATCCAAGCTCGTTGAGTTGAGTCCAAGTTCGTGAGATGTAACTAGG
* *
19898773 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTC
1 CATCCAAGCTCGTTGAGTTGAGTCCAAGTTC
19898804 ACTTATGGAT
Statistics
Matches: 97, Mismatches: 17, Indels: 20
0.72 0.13 0.15
Matches are distributed among these distances:
42 3 0.03
43 4 0.04
44 2 0.02
45 3 0.03
46 24 0.25
47 49 0.51
48 3 0.03
49 2 0.02
50 4 0.04
51 3 0.03
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.29
Consensus pattern (47 bp):
CATCCAAGCTCGTTGAGTTGAGTCCAAGTTCGTGAGATGTAACTAGG
Found at i:19898745 original size:93 final size:93
Alignment explanation
Indices: 19898586--19898850 Score: 451
Period size: 93 Copynumber: 2.8 Consensus size: 93
19898576 GGATATTTGA
*
19898586 GCATCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACATCCGAACTCGTTGAG
1 GCATCC-AAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAG
19898650 TTGAGTCTAAGTTCGTGAGATGTAACTAG
65 TTGAGTCTAAGTTCGTGAGATGTAACTAG
* *
19898679 GCATCCAAGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCTGAACTCGTTGAGT
1 GCATCCAAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
*
19898744 TGAGTCCAAGTTCGTGAGATGTAACTAG
66 TGAGTCTAAGTTCGTGAGATGTAACTAG
* *
19898772 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAGCTCGTTGAGT
1 GCATCCAAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
*
19898837 TGAGTCTGAGTTCG
66 TGAGTCTAAGTTCG
19898851 CCTATGGGCG
Statistics
Matches: 161, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
92 2 0.01
93 159 0.99
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCAAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCTAAGTTCGTGAGATGTAACTAG
Found at i:19898857 original size:46 final size:46
Alignment explanation
Indices: 19898587--19898849 Score: 234
Period size: 46 Copynumber: 5.7 Consensus size: 46
19898577 GATATTTGAG
19898587 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
** * * * *
19898633 CATCCGAACTCGTTGAGTTGAGTCTAAGTTC-GTGA--GATGTAACTAGG
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-A
*
19898680 CATCC-AAGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* * * * * * *
19898726 CGTCTGAACTCGTTGAGTTGAGTCCAAGTTC-GTGA--GATGTAACTAGG
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-A
*
19898773 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* * *
19898819 CGTCCGAGCTCGTTGAGTTGAGTCTGAGTTC
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTC
19898850 GCCTATGGGC
Statistics
Matches: 170, Mismatches: 31, Indels: 32
0.73 0.13 0.14
Matches are distributed among these distances:
43 8 0.05
45 4 0.02
46 88 0.52
47 58 0.34
48 4 0.02
50 8 0.05
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
Found at i:19911309 original size:17 final size:17
Alignment explanation
Indices: 19911283--19911317 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
19911273 GGGCCAAAAT
19911283 TGGCCATGTGGGCCCCA
1 TGGCCATGTGGGCCCCA
*
19911300 TGGCCTTGTGGGCCCCA
1 TGGCCATGTGGGCCCCA
19911317 T
1 T
19911318 AGGGGTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.09, C:0.34, G:0.34, T:0.23
Consensus pattern (17 bp):
TGGCCATGTGGGCCCCA
Found at i:19914391 original size:14 final size:14
Alignment explanation
Indices: 19914357--19914396 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
19914347 GTACATATAC
19914357 ATATAAAAAAGATAA
1 ATATAAAAAA-ATAA
* *
19914372 AAATAAAAAAATAT
1 ATATAAAAAAATAA
19914386 ATATAAAAAAA
1 ATATAAAAAAA
19914397 GGAAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (14 bp):
ATATAAAAAAATAA
Found at i:19915738 original size:3 final size:3
Alignment explanation
Indices: 19915730--19915758 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19915720 TTTGTCACTT
19915730 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19915759 GGCGTTATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19916015 original size:23 final size:23
Alignment explanation
Indices: 19916004--19916062 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
19915994 CTTTAATACT
*
19916004 TTATGTATATATTCTTATATATA
1 TTATGTATATATACTTATATATA
* * *
19916027 TTATGTATATACATTTTTATATA
1 TTATGTATATATACTTATATATA
*
19916050 TTACGTATATATA
1 TTATGTATATATA
19916063 TACCTTTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (23 bp):
TTATGTATATATACTTATATATA
Found at i:19918255 original size:24 final size:24
Alignment explanation
Indices: 19918173--19918262 Score: 81
Period size: 24 Copynumber: 3.7 Consensus size: 24
19918163 AAGAAATTTC
* **
19918173 AGCACTATGTGTGCGAGGTTATGC
1 AGCACTATGTGTGCGAGATTATAT
* * * * *
19918197 GGCACTATGTGTGCAAAAACTACAT
1 AGCACTATGTGTGC-GAGATTATAT
*
19918222 GGCACTATGTGTGCGAGATTATAT
1 AGCACTATGTGTGCGAGATTATAT
*
19918246 AGCACTATGTGTACGAG
1 AGCACTATGTGTGCGAG
19918263 GAAGCACGAC
Statistics
Matches: 51, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
24 34 0.67
25 17 0.33
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (24 bp):
AGCACTATGTGTGCGAGATTATAT
Found at i:19923826 original size:30 final size:31
Alignment explanation
Indices: 19923735--19923828 Score: 95
Period size: 30 Copynumber: 3.1 Consensus size: 31
19923725 ACTAAAATGG
*
19923735 GCTAAGCTTTAGCTCGTGAGCT-AAAGTTGA
1 GCTAAGGTTTAGCTCGTGAGCTGAAAGTTGA
* * * * * *
19923765 GCTGAGGCTAAACTCTTAAGCTG-AAGTTGA
1 GCTAAGGTTTAGCTCGTGAGCTGAAAGTTGA
*
19923795 GCTAAGGTTTAGCTCGTGAGTTGAAAG-TGA
1 GCTAAGGTTTAGCTCGTGAGCTGAAAGTTGA
19923825 GCTA
1 GCTA
19923829 GGAATGAGCT
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
30 45 0.94
31 3 0.06
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.29
Consensus pattern (31 bp):
GCTAAGGTTTAGCTCGTGAGCTGAAAGTTGA
Found at i:19928660 original size:14 final size:14
Alignment explanation
Indices: 19928643--19928675 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
19928633 TCAAAAATCA
19928643 CTTAACAAAATACT
1 CTTAACAAAATACT
19928657 CTTAACAAAATACT
1 CTTAACAAAATACT
*
19928671 TTTAA
1 CTTAA
19928676 ATAACAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (14 bp):
CTTAACAAAATACT
Found at i:19932930 original size:46 final size:46
Alignment explanation
Indices: 19932791--19932911 Score: 215
Period size: 46 Copynumber: 2.6 Consensus size: 46
19932781 GCCCATGAGC
* *
19932791 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGT
*
19932837 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGT
19932883 GAACTCGGACTCAACTCAACGAGTTCGGA
1 GAACTCGGACTCAACTCAACGAGTTCGGA
19932912 TGGTCAACCA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGT
Found at i:19940433 original size:93 final size:93
Alignment explanation
Indices: 19940274--19940445 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
19940264 CGCCCATAAG
* *
19940274 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
19940339 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
19940367 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
19940432 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
19940446 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:19940442 original size:46 final size:46
Alignment explanation
Indices: 19940267--19940442 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
19940257 TGTAACCCGC
* * *
19940267 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
19940313 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
19940363 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
19940406 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
19940443 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:19941789 original size:24 final size:24
Alignment explanation
Indices: 19941762--19941810 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
19941752 ATTATGAACT
19941762 TTTATTCATACCCTCATGAGTTTC
1 TTTATTCATACCCTCATGAGTTTC
19941786 TTTATTCATACCCTCATGAGTTTC
1 TTTATTCATACCCTCATGAGTTTC
19941810 T
1 T
19941811 ACTCGTCCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.24, G:0.08, T:0.47
Consensus pattern (24 bp):
TTTATTCATACCCTCATGAGTTTC
Found at i:19944873 original size:27 final size:28
Alignment explanation
Indices: 19944816--19944885 Score: 115
Period size: 27 Copynumber: 2.5 Consensus size: 28
19944806 AAACTTGTAC
*
19944816 AGCACTAAGTGTGCGAGTTTGATCATGT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
*
19944844 AGCACTAAGTGTGCGAG-TTGATTATAT
1 AGCACTAAGTGTGCGAGTTTGATCATAT
19944871 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
19944886 GACTCACTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.27, C:0.14, G:0.29, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTGATCATAT
Found at i:19944896 original size:27 final size:27
Alignment explanation
Indices: 19944816--19944897 Score: 69
Period size: 27 Copynumber: 3.0 Consensus size: 27
19944806 AAACTTGTAC
* * *
19944816 AGCACTAAGTGTGCGAGTTTGA-TCATGT
1 AGCACTAAGTGTGCGAG-CTCACT-ATAT
* * *
19944844 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGCTCACTATAT
19944871 AGCACTAAGTGTGCG-GACTCACTATAT
1 AGCACTAAGTGTGCGAG-CTCACTATAT
19944898 GCTTTTGAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 1 0.02
27 29 0.60
28 18 0.38
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGCTCACTATAT
Found at i:19948115 original size:24 final size:24
Alignment explanation
Indices: 19948088--19948134 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
19948078 TTATTGCCAA
19948088 TTCATATCAGTCAAATATTCATTT
1 TTCATATCAGTCAAATATTCATTT
**
19948112 TTCATATCAGTTGAATATTCATT
1 TTCATATCAGTCAAATATTCATT
19948135 GTACCCATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.32, C:0.15, G:0.06, T:0.47
Consensus pattern (24 bp):
TTCATATCAGTCAAATATTCATTT
Found at i:19949842 original size:48 final size:50
Alignment explanation
Indices: 19949763--19949955 Score: 189
Period size: 50 Copynumber: 3.9 Consensus size: 50
19949753 GGACATGTAT
* * *
19949763 CGAATTTGAGATGTGTCAGTGTAAGACCATGTCTAGGACATGGCATCAGCA
1 CGAATATGAGA-GTGTTAGTGTAAGACCATGTCTGGGACATGGCATCAGCA
* *
19949814 CGTATA-GAG-GTGTTAGTGTAAGACCATGTCTGGGACATGGCATCGGCA
1 CGAATATGAGAGTGTTAGTGTAAGACCATGTCTGGGACATGGCATCAGCA
* * * * *
19949862 CGAATATGTGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGC-
1 CGAATATGAGAGTGTTAGTGTAAGACCATGTCTGGGACATGGCATCAGCA
* * * * *
19949911 CTCAATTTCA-A-TAGTCAGTGTAAGACCATGTCTAGGACATGGCAT
1 C-GAATATGAGAGT-GTTAGTGTAAGACCATGTCTGGGACATGGCAT
19949956 TGGCATTATA
Statistics
Matches: 119, Mismatches: 19, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
48 41 0.34
49 32 0.27
50 42 0.35
51 4 0.03
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.25
Consensus pattern (50 bp):
CGAATATGAGAGTGTTAGTGTAAGACCATGTCTGGGACATGGCATCAGCA
Found at i:19949893 original size:50 final size:49
Alignment explanation
Indices: 19949780--19949960 Score: 183
Period size: 48 Copynumber: 3.7 Consensus size: 49
19949770 GAGATGTGTC
* * * *
19949780 AGTGTAAGACCATGTCTAGGACATGGCATCAGCACGTATA-GAG-GTGTT
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCACGAATATGTGAGAG-T
*
19949828 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGAATATGTGAGAGCT
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCACGAATATGTGAGAG-T
* * * * *
19949878 AGTGTAAGACCATGTCTGGGACATGGCGTCGGC-CTCAAT-T-TCAATAGT
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCAC-GAATATGT-GAGAGT
*
19949926 CAGTGTAAGACCATGTCTAGGACATGGCATTGGCA
1 -AGTGTAAGACCATGTCTAGGACATGGCATCGGCA
19949961 TTATACCCAA
Statistics
Matches: 114, Mismatches: 13, Indels: 10
0.83 0.09 0.07
Matches are distributed among these distances:
48 39 0.34
49 37 0.32
50 38 0.33
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (49 bp):
AGTGTAAGACCATGTCTAGGACATGGCATCGGCACGAATATGTGAGAGT
Found at i:19951916 original size:24 final size:24
Alignment explanation
Indices: 19951866--19951916 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
19951856 GTAGATCGGC
*
19951866 AAAAGCCGAAAATCCAAAATGCCA
1 AAAAGCCGAAAATCCAAAAAGCCA
*
19951890 AAAAGCCG-AAATGCCAAAAAGCTA
1 AAAAGCCGAAAAT-CCAAAAAGCCA
19951914 AAA
1 AAA
19951917 GTTTGGCTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 20 0.83
ACGTcount: A:0.57, C:0.22, G:0.14, T:0.08
Consensus pattern (24 bp):
AAAAGCCGAAAATCCAAAAAGCCA
Found at i:19952180 original size:29 final size:29
Alignment explanation
Indices: 19952140--19952246 Score: 151
Period size: 29 Copynumber: 3.7 Consensus size: 29
19952130 ATGAATGTGA
19952140 TTGGGCCTAACGGGCCATATAAATGTTAT
1 TTGGGCCTAACGGGCCATATAAATGTTAT
* *
19952169 TTAGGCCTAACGGGCCATATAAATGTGAT
1 TTGGGCCTAACGGGCCATATAAATGTTAT
* * *
19952198 TTGGGCCTAATGGGCCATATATAGGTTAT
1 TTGGGCCTAACGGGCCATATAAATGTTAT
**
19952227 TTGGGCCTAATAGGCCATAT
1 TTGGGCCTAACGGGCCATAT
19952247 GAATATGATT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 70 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (29 bp):
TTGGGCCTAACGGGCCATATAAATGTTAT
Found at i:19952226 original size:58 final size:57
Alignment explanation
Indices: 19952128--19952271 Score: 189
Period size: 58 Copynumber: 2.5 Consensus size: 57
19952118 TTGAGCATGA
* * *
19952128 ATATGAATGTGATTGGGCCTAACGGGCCATATAAATGTTATTTAGGCCTAACGGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCCATATAAAGGTTATTTAGGCCTAACAGGCC
* * * *
19952185 ATATAAATGTGATTTGGGCCTAATGGGCCATATATAGGTTATTTGGGCCTAATAGGCC
1 ATATGAATGTGA-TTGGGCCTAATGGGCCATATAAAGGTTATTTAGGCCTAACAGGCC
* * *
19952243 ATATGAATATGATTGGGCTTAATTGGCCA
1 ATATGAATGTGATTGGGCCTAATGGGCCA
19952272 GATACAAGTA
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
57 26 0.35
58 49 0.65
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (57 bp):
ATATGAATGTGATTGGGCCTAATGGGCCATATAAAGGTTATTTAGGCCTAACAGGCC
Found at i:19957229 original size:20 final size:20
Alignment explanation
Indices: 19957165--19957231 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
19957155 GGTGTACGTG
19957165 CAAAC-AGGAGTACTGAAGTA
1 CAAACAAGG-GTACTGAAGTA
* * * *
19957185 GAAACAGGGGCA-TGTATGTA
1 CAAACAAGGGTACTG-AAGTA
19957205 CAAACAAGGGTACTGAAGTA
1 CAAACAAGGGTACTGAAGTA
*
19957225 TAAACAA
1 CAAACAA
19957232 TGGCACCTAT
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
19 2 0.06
20 29 0.83
21 4 0.11
ACGTcount: A:0.45, C:0.13, G:0.25, T:0.16
Consensus pattern (20 bp):
CAAACAAGGGTACTGAAGTA
Found at i:19957256 original size:40 final size:40
Alignment explanation
Indices: 19957162--19957257 Score: 120
Period size: 40 Copynumber: 2.4 Consensus size: 40
19957152 GGGGGTGTAC
* * **
19957162 GTGCAAACAGGAGTACTGAAGTAGAAACAGGGGCATGTAT
1 GTGCAAACAGGGGTACTGAAGTAGAAACAAGGGCACCTAT
* * * *
19957202 GTACAAACAAGGGTACTGAAGTATAAACAATGGCACCTAT
1 GTGCAAACAGGGGTACTGAAGTAGAAACAAGGGCACCTAT
19957242 GTGCAAACAGGGGTAC
1 GTGCAAACAGGGGTAC
19957258 CAAAGTACAA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.39, C:0.16, G:0.28, T:0.18
Consensus pattern (40 bp):
GTGCAAACAGGGGTACTGAAGTAGAAACAAGGGCACCTAT
Found at i:19957264 original size:40 final size:40
Alignment explanation
Indices: 19957162--19957269 Score: 117
Period size: 40 Copynumber: 2.7 Consensus size: 40
19957152 GGGGGTGTAC
* * * **
19957162 GTGCAAACAGGAGTACTGAAGTAGAAACAGGGGCATGTAT
1 GTGCAAACAGGGGTACTGAAGTACAAACAAGGGCACCTAT
* * * *
19957202 GTACAAACAAGGGTACTGAAGTATAAACAATGGCACCTAT
1 GTGCAAACAGGGGTACTGAAGTACAAACAAGGGCACCTAT
**
19957242 GTGCAAACAGGGGTACCAAAGTACAAAC
1 GTGCAAACAGGGGTACTGAAGTACAAAC
19957270 TAAGAAACCA
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.41, C:0.17, G:0.26, T:0.17
Consensus pattern (40 bp):
GTGCAAACAGGGGTACTGAAGTACAAACAAGGGCACCTAT
Found at i:19960962 original size:93 final size:93
Alignment explanation
Indices: 19960850--19961021 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
19960840 CGCCCATAAG
* *
19960850 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
19960915 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
19960943 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
19961008 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
19961022 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:19961018 original size:46 final size:46
Alignment explanation
Indices: 19960843--19961018 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
19960833 TGTAACCCGC
* * *
19960843 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
19960889 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
19960939 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
19960982 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
19961019 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:19964715 original size:2 final size:2
Alignment explanation
Indices: 19964708--19964734 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19964698 ACATCTCATT
19964708 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
19964735 CAAATTAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19965128 original size:27 final size:27
Alignment explanation
Indices: 19965098--19965151 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
19965088 ATAAATGAGA
19965098 TCAACAGATTACCCTTCTGGGATAAAT
1 TCAACAGATTACCCTTCTGGGATAAAT
*
19965125 TCAACAGATTACCCTTCTGGGCTAAAT
1 TCAACAGATTACCCTTCTGGGATAAAT
19965152 CCTTACTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (27 bp):
TCAACAGATTACCCTTCTGGGATAAAT
Found at i:19966029 original size:27 final size:27
Alignment explanation
Indices: 19965991--19966044 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
19965981 GGAGAAGAAG
19965991 AATGGCTGATTTTTGGTACATTTTTCC
1 AATGGCTGATTTTTGGTACATTTTTCC
19966018 AATGGCTGATTTTTGGTACATTTTTCC
1 AATGGCTGATTTTTGGTACATTTTTCC
19966045 CATTTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.19, T:0.48
Consensus pattern (27 bp):
AATGGCTGATTTTTGGTACATTTTTCC
Found at i:19975353 original size:21 final size:21
Alignment explanation
Indices: 19975312--19975353 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
19975302 TAAATCGGGT
* *
19975312 CACGTATGTGCAATTCGGGGG
1 CACGCATGTGCAATTCAGGGG
*
19975333 CACGCATGTGCAATTTAGGGG
1 CACGCATGTGCAATTCAGGGG
19975354 TACCGAAGTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.24
Consensus pattern (21 bp):
CACGCATGTGCAATTCAGGGG
Found at i:19975389 original size:41 final size:41
Alignment explanation
Indices: 19975329--19975434 Score: 149
Period size: 41 Copynumber: 2.6 Consensus size: 41
19975319 GTGCAATTCG
** * *
19975329 GGGGCACGCATGTGCAATTTAGGGGTACCGAAGTACAAACA
1 GGGGCACATATGTGTAATTTAGGGGTACCAAAGTACAAACA
* *
19975370 GGGGCATATATGTGTAATTTAGGGGTACTAAAGTACAAACA
1 GGGGCACATATGTGTAATTTAGGGGTACCAAAGTACAAACA
*
19975411 GGGGCACATATGTGTAATTCAGGG
1 GGGGCACATATGTGTAATTTAGGG
19975435 AATAATTAAC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.32, C:0.14, G:0.31, T:0.23
Consensus pattern (41 bp):
GGGGCACATATGTGTAATTTAGGGGTACCAAAGTACAAACA
Found at i:19977099 original size:48 final size:48
Alignment explanation
Indices: 19977047--19977159 Score: 190
Period size: 48 Copynumber: 2.4 Consensus size: 48
19977037 TAAAACCACA
* * *
19977047 TCTGGGACATGGCGTCGGCATTGTTATGTGAGCAAGTGTAAGACCATG
1 TCTGGGACATGGCATCGGCATCGTTATGTAAGCAAGTGTAAGACCATG
*
19977095 TCTGGGACATGGCATCGGCATCGTTATGTAAGCCAGTGTAAGACCATG
1 TCTGGGACATGGCATCGGCATCGTTATGTAAGCAAGTGTAAGACCATG
19977143 TCTGGGACATGGCATCG
1 TCTGGGACATGGCATCG
19977160 ACATGAGGCA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 61 1.00
ACGTcount: A:0.23, C:0.19, G:0.32, T:0.26
Consensus pattern (48 bp):
TCTGGGACATGGCATCGGCATCGTTATGTAAGCAAGTGTAAGACCATG
Found at i:19978498 original size:48 final size:48
Alignment explanation
Indices: 19978446--19978575 Score: 199
Period size: 48 Copynumber: 2.7 Consensus size: 48
19978436 ATGTGTAACC
19978446 GTGTAAGACCATGTCTGGGACATGGCATCGGCAT-TGTTATGTGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCATCT-TTATGTGAGCCA
* * *
19978494 GTGTAAGACCATGTTTGGGACATGGCATCAGAATCTTTATGTGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCATCTTTATGTGAGCCA
* *
19978542 GTGTAAGACCATTTCTAGGACATGGCATCGGCAT
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCAT
19978576 GGGGCATCGT
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
48 72 0.99
49 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.28
Consensus pattern (48 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGGCATCTTTATGTGAGCCA
Found at i:19979421 original size:14 final size:14
Alignment explanation
Indices: 19979402--19979431 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
19979392 AAGCTATGAT
19979402 TTATATTTTTTAAA
1 TTATATTTTTTAAA
19979416 TTATATTTTTTAAA
1 TTATATTTTTTAAA
19979430 TT
1 TT
19979432 CTTAGTGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATATTTTTTAAA
Found at i:19979760 original size:9 final size:10
Alignment explanation
Indices: 19979737--19979762 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
19979727 TGAATAGTAA
19979737 AAAAATCATT
1 AAAAATCATT
19979747 AAAAATCATT
1 AAAAATCATT
19979757 AAAAAT
1 AAAAAT
19979763 AGTCAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAAATCATT
Found at i:19982131 original size:39 final size:39
Alignment explanation
Indices: 19982077--19982155 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
19982067 CTTATTATGA
19982077 TCTATATGTGTGAAAGTCGAATAATGACTAGTTTAAAAT
1 TCTATATGTGTGAAAGTCGAATAATGACTAGTTTAAAAT
19982116 TCTATATGTGTGAAAGTCGAATAATGACTAGTTTAAAAT
1 TCTATATGTGTGAAAGTCGAATAATGACTAGTTTAAAAT
19982155 T
1 T
19982156 TTTGAATCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.37
Consensus pattern (39 bp):
TCTATATGTGTGAAAGTCGAATAATGACTAGTTTAAAAT
Found at i:19982638 original size:38 final size:39
Alignment explanation
Indices: 19982577--19982678 Score: 127
Period size: 38 Copynumber: 2.6 Consensus size: 39
19982567 ATTTGATGTG
*
19982577 TATCCGGGCTTAAAGACCCGCAGGCTATA-TGCTGGAATTA
1 TATCCGGG-TTAAAGTCCCGCAGGC-ATAGTGCTGGAATTA
*
19982617 TATCCGGGTTAAA-TCCCGCAGGCATAGTGCTGGTATTA
1 TATCCGGGTTAAAGTCCCGCAGGCATAGTGCTGGAATTA
* *
19982655 TATCCGAGCTTAAAGTCCCACAGG
1 TATCCG-GGTTAAAGTCCCGCAGG
19982679 TTTTGTGTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
37 3 0.05
38 25 0.45
39 11 0.20
40 16 0.29
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (39 bp):
TATCCGGGTTAAAGTCCCGCAGGCATAGTGCTGGAATTA
Found at i:19982978 original size:19 final size:19
Alignment explanation
Indices: 19982927--19982978 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
19982917 TCATTATATG
*
19982927 AAAGTATGTGACT-TAAATT
1 AAAGTATGTG-CTATAAAGT
* *
19982946 AATTGTATGAGCTATAAAGT
1 AA-AGTATGTGCTATAAAGT
19982966 AAAGTATGTGCTA
1 AAAGTATGTGCTA
19982979 AAATTTCTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (19 bp):
AAAGTATGTGCTATAAAGT
Found at i:19983277 original size:16 final size:18
Alignment explanation
Indices: 19983246--19983278 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
19983236 AGTTCATCAC
19983246 ACTATTTATCATTTTGGT
1 ACTATTTATCATTTTGGT
19983264 ACTA-TTAT-ATTTTGG
1 ACTATTTATCATTTTGG
19983279 AGTTGATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (18 bp):
ACTATTTATCATTTTGGT
Found at i:19984357 original size:375 final size:374
Alignment explanation
Indices: 19983856--19984554 Score: 1254
Period size: 375 Copynumber: 1.9 Consensus size: 374
19983846 TTGACTTTGG
19983856 AAAATCATTAAAAATAGTAAAAAAAATAATTACAAACTATGATTTATATTTTTTAAATTCTTAAT
1 AAAATCATTAAAAATAGTAAAAAAAATAATTACAAACTATGATTTATATTTTTTAAATTCTTAAT
*
19983921 GAATATATTTTGAAGAGAATCAAACCAGAACATCATCCGAGTCTCGTACGAGGAGATAATAAATT
66 GAATATATTTTGAAGAGAATCAAACCAGAACATCATCCGAGTCTCGTACGAGGACATAATAAATT
*
19983986 TTTAGTGAAGAAGGGTTGAAACTGTCAGACAGCAGAACAGGGACGATTTTAAAAAATAAACTGTA
131 TTTAGTGAAGAAGGGTTGAAACTGTCAGACAGCAGAACAGGGAC-AATTTAAAAAATAAACTGTA
*
19984051 CTTATTGGCTAAACAAAAAATTTTGAAAATTTTATTGTAAGGAGATAGCTGAGTTTAGTTCCAGG
195 CTTATTAGCTAAACAAAAAATTTTGAAAATTTTATTGTAAGGAGATAGCTGAGTTTAGTTCCAGG
* *
19984116 GAAAATTAGCAAAACTAAATTTGGAGTTCCGTAGCTCAAGATATAAATAATTTAGTGACTATAAC
260 AAAAATTAGCAAAAATAAATTTGGAGTTCCGTAGCTCAAGATATAAATAATTTAGTGACTATAAC
19984181 TTGCGTAGACAACTTGGTATGAACATAAGTGATTAGTAAAAAAAACATTA
325 TTGCGTAGACAACTTGGTATGAACATAAGTGATTAGTAAAAAAAACATTA
* *
19984231 AAAATCATTAAAAATAGTAAAAAAAATAATTACAAGCTATGATTTATATTTTTTAAATTCTTAGT
1 AAAATCATTAAAAATAGTAAAAAAAATAATTACAAACTATGATTTATATTTTTTAAATTCTTAAT
*
19984296 GAATATATTTTGAAGAGAATCAAACCAGAACATCATCCGAGTCTCGTACGAGGACATAATAATTT
66 GAATATATTTTGAAGAGAATCAAACCAGAACATCATCCGAGTCTCGTACGAGGACATAATAAATT
* *
19984361 TTTAGTGAAGAAGGGTTGAAACTGTTAGACAGCAGAATAGGGACAATTTAAAAAATAAACTGTAC
131 TTTAGTGAAGAAGGGTTGAAACTGTCAGACAGCAGAACAGGGACAATTTAAAAAATAAACTGTAC
* ** *
19984426 TTATTAGCTAAACCAAAAATTTTGAAAATTTTATTGTAAGGAGATATTTGAGTTTAGTTTCAGGA
196 TTATTAGCTAAACAAAAAATTTTGAAAATTTTATTGTAAGGAGATAGCTGAGTTTAGTTCCAGGA
*
19984491 AAAATTAGCAAAAATTAATTTGGAGTTCCGTAGCTCAAGATATAAATAATTTAGTGACTATAAC
261 AAAATTAGCAAAAATAAATTTGGAGTTCCGTAGCTCAAGATATAAATAATTTAGTGACTATAAC
19984555 GAGTTTTCCT
Statistics
Matches: 309, Mismatches: 15, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
374 141 0.46
375 168 0.54
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (374 bp):
AAAATCATTAAAAATAGTAAAAAAAATAATTACAAACTATGATTTATATTTTTTAAATTCTTAAT
GAATATATTTTGAAGAGAATCAAACCAGAACATCATCCGAGTCTCGTACGAGGACATAATAAATT
TTTAGTGAAGAAGGGTTGAAACTGTCAGACAGCAGAACAGGGACAATTTAAAAAATAAACTGTAC
TTATTAGCTAAACAAAAAATTTTGAAAATTTTATTGTAAGGAGATAGCTGAGTTTAGTTCCAGGA
AAAATTAGCAAAAATAAATTTGGAGTTCCGTAGCTCAAGATATAAATAATTTAGTGACTATAACT
TGCGTAGACAACTTGGTATGAACATAAGTGATTAGTAAAAAAAACATTA
Found at i:19985818 original size:48 final size:48
Alignment explanation
Indices: 19985762--19985886 Score: 187
Period size: 48 Copynumber: 2.6 Consensus size: 48
19985752 GTGTAACCGC
* *
19985762 GTAAGACCATGTCTAGGACATGGCATCGGCATTGTTATGTGAGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCATCGTTATGTGAGCCAGT
*** *
19985810 GTAAGACCATGTCTGGGACATGTTTTCAGCATCGTTATGTGAGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGCATCGTTATGTGAGCCAGT
*
19985858 GTAAGACCATGTTTGGGACATGGCATCGG
1 GTAAGACCATGTCTGGGACATGGCATCGG
19985887 TACGAGGCAT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 66 1.00
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (48 bp):
GTAAGACCATGTCTGGGACATGGCATCGGCATCGTTATGTGAGCCAGT
Found at i:19987062 original size:9 final size:10
Alignment explanation
Indices: 19987039--19987064 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
19987029 TGAATAGTAA
19987039 AAAAATCATT
1 AAAAATCATT
19987049 AAAAATCATT
1 AAAAATCATT
19987059 AAAAAT
1 AAAAAT
19987065 AGTAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAAATCATT
Found at i:19989829 original size:9 final size:10
Alignment explanation
Indices: 19989806--19989831 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
19989796 TGAATAGTAA
19989806 AAAAATCATT
1 AAAAATCATT
19989816 AAAAATCATT
1 AAAAATCATT
19989826 AAAAAT
1 AAAAAT
19989832 AGTAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAAATCATT
Found at i:19991408 original size:48 final size:48
Alignment explanation
Indices: 19991350--19991474 Score: 169
Period size: 48 Copynumber: 2.6 Consensus size: 48
19991340 GTGTAACCGC
* * *
19991350 GTAAGACCATGTCTAGGACATGGCATCGGCATTGTTATGTGAGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGAATCGTTATGTGAGCCAGT
*** *
19991398 GTAAGACCATGTCTGGGACATGTTTTCAGAATCGTTATGTGAGCCAGT
1 GTAAGACCATGTCTGGGACATGGCATCGGAATCGTTATGTGAGCCAGT
* *
19991446 GTAAGACCATGTTTGGGACTTGGCATCGG
1 GTAAGACCATGTCTGGGACATGGCATCGG
19991475 TACGAGGCAT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 64 1.00
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.29
Consensus pattern (48 bp):
GTAAGACCATGTCTGGGACATGGCATCGGAATCGTTATGTGAGCCAGT
Found at i:19992837 original size:48 final size:48
Alignment explanation
Indices: 19992785--19992909 Score: 169
Period size: 48 Copynumber: 2.6 Consensus size: 48
19992775 ATGTGTAACC
* * **
19992785 GTGTAAGACCATGTCTGGGACGTGGCATCGGCATTTTTATGTGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGAATCGTTATGTGAGCCA
* * *
19992833 GTGTAGGACCATGCCTGGGACATGGCATTGGAATCGTTATGTGAGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGAATCGTTATGTGAGCCA
* *
19992881 GTGTAAGACCATGTCTAGGACATAGCATC
1 GTGTAAGACCATGTCTGGGACATGGCATC
19992910 AGCATGAGGC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 65 1.00
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.26
Consensus pattern (48 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGGAATCGTTATGTGAGCCA
Found at i:19994580 original size:37 final size:37
Alignment explanation
Indices: 19994530--19994601 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
19994520 TTTAGCTCGA
* *
19994530 ATAATCCCCACACGTAGTCATCGGGTCTTACCCGGGC
1 ATAATCCCCACACGTAGCCATCGGGTCTTAACCGGGC
*
19994567 ATAATCTCCACACGTAGCCATCGGGTCTTAACCGG
1 ATAATCCCCACACGTAGCCATCGGGTCTTAACCGG
19994602 AATATATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.22
Consensus pattern (37 bp):
ATAATCCCCACACGTAGCCATCGGGTCTTAACCGGGC
Found at i:19994799 original size:48 final size:47
Alignment explanation
Indices: 19994743--19994839 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 47
19994733 ATATATCCAC
* *
19994743 ATCTCATACATATTTCACATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATT-GGCTTTACCACACATACAT
*
19994791 ATCTCATACATATTTCACACTAGCCATTGGCTTTACCACACATATAT
1 ATCTCATACATATTTCACACTAGCCATTGGCTTTACCACACATACAT
19994838 AT
1 AT
19994840 ATTTATCTTG
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
47 19 0.41
48 27 0.59
ACGTcount: A:0.32, C:0.27, G:0.06, T:0.35
Consensus pattern (47 bp):
ATCTCATACATATTTCACACTAGCCATTGGCTTTACCACACATACAT
Found at i:19998557 original size:40 final size:40
Alignment explanation
Indices: 19998512--19998641 Score: 163
Period size: 40 Copynumber: 3.2 Consensus size: 40
19998502 CGGAATATAA
19998512 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
19998552 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
19998592 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
19998632 CCGGATATAA
1 CCGGATATAA
19998642 TTTCCAGCAT
Statistics
Matches: 74, Mismatches: 15, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
39 1 0.01
40 73 0.99
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:19998656 original size:40 final size:40
Alignment explanation
Indices: 19998512--19998678 Score: 151
Period size: 40 Copynumber: 4.2 Consensus size: 40
19998502 CGGAATATAA
* ** *
19998512 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC
* *
19998552 CCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-CAGCAC-AATTGCCTTCGGGTCTTAGC
* ** * *
19998592 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC
** * * *
19998632 CCGGATATAATTTCCAGCATAATTGTCTT-GGGGCTTAGC
1 CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC
19998671 CCGGATAT
1 CCGGATAT
19998679 CATTCAATTT
Statistics
Matches: 102, Mismatches: 21, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
39 18 0.18
40 82 0.80
41 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACCAGCACAATTGCCTTCGGGTCTTAGC
Found at i:20004785 original size:25 final size:27
Alignment explanation
Indices: 20004748--20004801 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
20004738 TCAAACATGC
20004748 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
* **
20004774 ATTTCGGT-AATTTTGCACCTAGGGGT
1 ATTTAGGTCAATTTAACACCTAGGGGT
20004800 AT
1 AT
20004802 AACAGTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACACCTAGGGGT
Found at i:20006319 original size:26 final size:26
Alignment explanation
Indices: 20006283--20006392 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
20006273 CATGAATTTC
*
20006283 TTATCATGAAACATTTACCTAAACCA
1 TTATCATGAAACATTTACCTAACCCA
20006309 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* * *
20006335 TTATCATGGAATATTTACCTAATCCA
1 TTATCATGAAACATTTACCTAACCCA
*
20006361 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
20006387 TTATCA
1 TTATCA
20006393 ATTTGTATCA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:20007261 original size:40 final size:39
Alignment explanation
Indices: 20007199--20007445 Score: 250
Period size: 40 Copynumber: 6.2 Consensus size: 39
20007189 CGAATGATAA
* *
20007199 CCGGGCTAAGTCCCG-AGAGCATTTGAGCTAGTGGCTA-ATT
1 CCGGGCTAAGTCCCGAAG-GCATTTGTGCTAGT-ACTATA-T
* *
20007239 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TACTATAT
* * * *
20007279 CCGGGCTAAGTCCCGAAGGCGTTTGTACGAGCTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TACTATAT
* *
20007319 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA-
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TACTATAT
** * *
20007358 CTTGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TACTATAT
* *
20007398 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGTCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGT-ACTATAT
20007438 CC-GGCTAA
1 CCGGGCTAA
20007446 ACTCCGAAGG
Statistics
Matches: 181, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
39 42 0.23
40 135 0.75
41 4 0.02
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTACTATAT
Found at i:20007406 original size:79 final size:80
Alignment explanation
Indices: 20007239--20007422 Score: 262
Period size: 79 Copynumber: 2.3 Consensus size: 80
20007229 GTGGCTAATT
* *
20007239 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCGTTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
* * *
20007304 TACGAGCTATTATAT
66 TACAAGCTACTATAA
* * **
20007319 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTATTATA-CTTGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
* *
20007383 TGCAAGTTACTATAA
66 TACAAGCTACTATAA
20007398 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
20007423 AGCTAGTGTC
Statistics
Matches: 93, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
79 57 0.61
80 36 0.39
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
TACAAGCTACTATAA
Found at i:20007455 original size:79 final size:78
Alignment explanation
Indices: 20007239--20007445 Score: 254
Period size: 79 Copynumber: 2.6 Consensus size: 78
20007229 GTGGCTAATT
* * *
20007239 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGCTACTATATCCGGGCTAAGTCCCGAAGGCGTTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TTCTATATCC-GGCTAAGTCCCGAAGGCATTTG
* * *
20007304 TACGAGCTATTATAT
64 TACAAGCTACTATAA
* *
20007319 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTAT-TATACTTGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTCTATAT-C-CGGCTAAGTCCCGAAGGCATTTG
* *
20007383 TGCAAGTTACTATAA
64 TACAAGCTACTATAA
* *
20007398 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAGTGTCTATATCCGGCTAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT-TCTATATCCGGCTAA
20007446 ACTCCGAAGG
Statistics
Matches: 109, Mismatches: 14, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
78 3 0.03
79 70 0.64
80 33 0.30
81 3 0.03
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.27
Consensus pattern (78 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTCTATATCCGGCTAAGTCCCGAAGGCATTTGTA
CAAGCTACTATAA
Found at i:20008882 original size:21 final size:19
Alignment explanation
Indices: 20008856--20008900 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
20008846 ATTTTATAAC
20008856 AAAAAATAATTTTTTCCCTAT
1 AAAAAAT-ATTTTTT-CCTAT
*
20008877 AAAAAATATTTTTTTCTAT
1 AAAAAATATTTTTTCCTAT
20008896 AAAAA
1 AAAAA
20008901 TTCATGTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.39
20 7 0.30
21 7 0.30
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAAAATATTTTTTCCTAT
Found at i:20009078 original size:26 final size:26
Alignment explanation
Indices: 20009030--20009080 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
20009020 TCCTTCATTA
** **
20009030 GAAAAACTAAATTAAATCTAAAAAAG
1 GAAAAACTAAAGGAAATAAAAAAAAG
20009056 GAAAAACTAAAGGAAATAAAAAAAA
1 GAAAAACTAAAGGAAATAAAAAAAA
20009081 TATTTTTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.71, C:0.06, G:0.10, T:0.14
Consensus pattern (26 bp):
GAAAAACTAAAGGAAATAAAAAAAAG
Found at i:20013078 original size:67 final size:67
Alignment explanation
Indices: 20012995--20013136 Score: 250
Period size: 67 Copynumber: 2.1 Consensus size: 67
20012985 TTGAATTGTA
*
20012995 TATTGCTTTAAGGACTTCTGTATTTACTTGTTTGTAACTCAAAA-ATTTTGATTGTACTTATCCA
1 TATTGCTTTAAGGACTTCTGTATTTACTTGTTTGTAACT-AAAACATTTTGATTGAACTTATCCA
20013059 TAG
65 TAG
*
20013062 TATTGCTTTAAGGACTTCTGTATTTACTTGTTTGTAACTAAAACATTTTGATTGAACTTATCTAT
1 TATTGCTTTAAGGACTTCTGTATTTACTTGTTTGTAACTAAAACATTTTGATTGAACTTATCCAT
20013127 AG
66 AG
20013129 TATTGCTT
1 TATTGCTT
20013137 GGATAGTTGT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
66 4 0.06
67 68 0.94
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (67 bp):
TATTGCTTTAAGGACTTCTGTATTTACTTGTTTGTAACTAAAACATTTTGATTGAACTTATCCAT
AG
Found at i:20019531 original size:26 final size:26
Alignment explanation
Indices: 20019498--20019551 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
20019488 AAAAATTGGG
20019498 TATTAACTAAATACTTTAAGACAAGA
1 TATTAACTAAATACTTTAAGACAAGA
20019524 TATTAACTAAATACTTTAAGACAAGA
1 TATTAACTAAATACTTTAAGACAAGA
20019550 TA
1 TA
20019552 GGGGCAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.31
Consensus pattern (26 bp):
TATTAACTAAATACTTTAAGACAAGA
Found at i:20024354 original size:30 final size:30
Alignment explanation
Indices: 20024318--20024380 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
20024308 ACTTATTTTA
20024318 TTGTTAATTTTCTTATTATTTTAAAGGCAT
1 TTGTTAATTTTCTTATTATTTTAAAGGCAT
* *
20024348 TTGTTAATTTTTTTATTATTTTAGAGGCAT
1 TTGTTAATTTTCTTATTATTTTAAAGGCAT
20024378 TTG
1 TTG
20024381 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.24, C:0.05, G:0.13, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTCTTATTATTTTAAAGGCAT
Found at i:20030168 original size:13 final size:13
Alignment explanation
Indices: 20030150--20030199 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 13
20030140 AGGGGCACAG
20030150 GCCCGTGTGGCCA
1 GCCCGTGTGGCCA
20030163 GCCCGTGTGGCTCCCA
1 GCCCGTGTGG---CCA
*
20030179 TGGCCGTGTGGCCA
1 -GCCCGTGTGGCCA
20030193 GCCCGTG
1 GCCCGTG
20030200 GGCAGATCTG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 16 0.52
14 3 0.10
16 3 0.10
17 9 0.29
ACGTcount: A:0.06, C:0.38, G:0.38, T:0.18
Consensus pattern (13 bp):
GCCCGTGTGGCCA
Found at i:20031261 original size:24 final size:25
Alignment explanation
Indices: 20031234--20031311 Score: 88
Period size: 25 Copynumber: 3.2 Consensus size: 25
20031224 GCCTAGCCTC
20031234 TTTTAAT-AACTGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
* *
20031258 TTTTGATAAACCGGGGCAAAGCCCT
1 TTTTAATAAACTGGGGCAAAGCCCT
*** *
20031283 TTTCGGTAAACTGGGGCATAG-CCT
1 TTTTAATAAACTGGGGCAAAGCCCT
20031307 TTTTA
1 TTTTA
20031312 GCACTTCCTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
24 12 0.27
25 33 0.73
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (25 bp):
TTTTAATAAACTGGGGCAAAGCCCT
Found at i:20031279 original size:25 final size:25
Alignment explanation
Indices: 20031245--20031310 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 25
20031235 TTTAATAACT
20031245 GGGGCAAAGCCCTTTTTGATAAACC
1 GGGGCAAAGCCCTTTTTGATAAACC
* * *
20031270 GGGGCAAAGCCCTTTTCGGTAAACT
1 GGGGCAAAGCCCTTTTTGATAAACC
*
20031295 GGGGCATAG-CCTTTTT
1 GGGGCAAAGCCCTTTTT
20031311 AGCACTTCCT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
24 6 0.17
25 30 0.83
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.27
Consensus pattern (25 bp):
GGGGCAAAGCCCTTTTTGATAAACC
Found at i:20032243 original size:27 final size:27
Alignment explanation
Indices: 20032213--20032310 Score: 101
Period size: 27 Copynumber: 3.6 Consensus size: 27
20032203 GTAAATCTAC
*
20032213 AAACCAAGGGTATTTCAGTAATTTTGT
1 AAACCAAAGGTATTTCAGTAATTTTGT
20032240 AAACCAAAGGTATTTCTA-TAATTTT-T
1 AAACCAAAGGTATTTC-AGTAATTTTGT
* *
20032266 AGAAAGTCAAAGGTATTTCTGTAATTTTGT
1 --AAA-CCAAAGGTATTTCAGTAATTTTGT
* *
20032296 AAATCAGAGGTATTT
1 AAACCAAAGGTATTT
20032311 TGATAATTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
26 1 0.02
27 33 0.54
28 7 0.11
29 19 0.31
30 1 0.02
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (27 bp):
AAACCAAAGGTATTTCAGTAATTTTGT
Found at i:20032317 original size:27 final size:27
Alignment explanation
Indices: 20032231--20032399 Score: 103
Period size: 27 Copynumber: 6.2 Consensus size: 27
20032221 GGTATTTCAG
* * *
20032231 TAATTTTGTAAACCAAAGGTATTTCT-A
1 TAATTTTATAAATCAGAGGTATTT-TGA
* *
20032258 TAATTTTTAGAAAGTCAAAGGTATTTCTG-
1 TAA-TTTTATAAA-TCAGAGGTATTT-TGA
*
20032287 TAATTTTGTAAATCAGAGGTATTTTGA
1 TAATTTTATAAATCAGAGGTATTTTGA
* * * *
20032314 TAATTTTACAAAT-TGAGGGTATTTCGG
1 TAATTTTATAAATCAGA-GGTATTTTGA
* * * *
20032341 TAATTTCACAAATCAGTGGTATTTTGG
1 TAATTTTATAAATCAGAGGTATTTTGA
* * *
20032368 TAATTTTACAAA-CTAGGGGTATTTTGG
1 TAATTTTATAAATC-AGAGGTATTTTGA
20032395 TAATT
1 TAATT
20032400 CTATCCTACA
Statistics
Matches: 118, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
26 5 0.04
27 82 0.69
28 15 0.13
29 16 0.14
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.42
Consensus pattern (27 bp):
TAATTTTATAAATCAGAGGTATTTTGA
Found at i:20032354 original size:54 final size:54
Alignment explanation
Indices: 20032277--20032399 Score: 158
Period size: 54 Copynumber: 2.3 Consensus size: 54
20032267 GAAAGTCAAA
* *** *
20032277 GGTATTTCTGTAATTTTGTAAATCAGAGGTATTTTGATAATTTTACAAA-TTGAG
1 GGTATTTCGGTAATTTCACAAATCAGAGGTATTTTGATAATTTTACAAACTAG-G
* *
20032331 GGTATTTCGGTAATTTCACAAATCAGTGGTATTTTGGTAATTTTACAAACTAGG
1 GGTATTTCGGTAATTTCACAAATCAGAGGTATTTTGATAATTTTACAAACTAGG
*
20032385 GGTATTTTGGTAATT
1 GGTATTTCGGTAATT
20032400 CTATCCTACA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
54 58 0.97
55 2 0.03
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.43
Consensus pattern (54 bp):
GGTATTTCGGTAATTTCACAAATCAGAGGTATTTTGATAATTTTACAAACTAGG
Found at i:20032416 original size:54 final size:54
Alignment explanation
Indices: 20032277--20032441 Score: 149
Period size: 54 Copynumber: 3.1 Consensus size: 54
20032267 GAAAGTCAAA
* *** * * *
20032277 GGTATTTCTGTAATTTTGTAAATCAGAGGTATTTTGATAATTTTACAAATTGAG
1 GGTATTTCGGTAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAATAGAG
*
20032331 GGTATTTCGGTAATTTCACAAATCAGTGGTATTTTGGTAATTTTACAAACTAG-G
1 GGTATTTCGGTAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAA-TAGAG
* ** * * *
20032385 GGTATTTTGGTAA-TTCTATCCTA-CAGGGGTATTTTAGTAATTTCAC-AATCGAG
1 GGTATTTCGGTAATTTC-A-CAAATCAGGGGTATTTTGGTAATTTTACAAATAGAG
20032438 GGTA
1 GGTA
20032442 AAACGGTAAT
Statistics
Matches: 93, Mismatches: 14, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
52 2 0.02
53 10 0.11
54 77 0.83
55 4 0.04
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.41
Consensus pattern (54 bp):
GGTATTTCGGTAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAATAGAG
Found at i:20032439 original size:27 final size:26
Alignment explanation
Indices: 20032297--20032439 Score: 103
Period size: 27 Copynumber: 5.3 Consensus size: 26
20032287 TAATTTTGTA
* * *
20032297 AATCAGAGGTATTTTGATAATTTTAC
1 AATCAGGGGTATTTTGGTAATTTCAC
* *
20032323 AAAT-TGAGGGTATTTCGGTAATTTCAC
1 -AATCAG-GGGTATTTTGGTAATTTCAC
* *
20032350 AAATCAGTGGTATTTTGGTAATTTTAC
1 -AATCAGGGGTATTTTGGTAATTTCAC
*
20032377 AAACTAGGGGTATTTTGGTAA-TTCTATC
1 AATC-AGGGGTATTTTGGTAATTTC-A-C
* *
20032405 -CTACAGGGGTATTTTAGTAATTTCAC
1 AAT-CAGGGGTATTTTGGTAATTTCAC
20032431 AATCGAGGG
1 AATC-AGGG
20032440 TAAAACGGTA
Statistics
Matches: 91, Mismatches: 16, Indels: 18
0.73 0.13 0.14
Matches are distributed among these distances:
26 8 0.09
27 77 0.85
28 6 0.07
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.38
Consensus pattern (26 bp):
AATCAGGGGTATTTTGGTAATTTCAC
Found at i:20032461 original size:27 final size:27
Alignment explanation
Indices: 20032431--20032522 Score: 139
Period size: 27 Copynumber: 3.4 Consensus size: 27
20032421 GTAATTTCAC
* * *
20032431 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCAAGGGTAAAACGGTAATTCTATA
*
20032458 AATCAAGGGTAAAATGGTAATTCTATA
1 AATCAAGGGTAAAACGGTAATTCTATA
20032485 AATCAAGGGTAAAACGGTAATTCTATA
1 AATCAAGGGTAAAACGGTAATTCTATA
*
20032512 AATCGAGGGTA
1 AATCAAGGGTA
20032523 CTTTGGTAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 59 1.00
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (27 bp):
AATCAAGGGTAAAACGGTAATTCTATA
Found at i:20035470 original size:16 final size:17
Alignment explanation
Indices: 20035417--20035470 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 17
20035407 ATTAATATAT
* *
20035417 TATAATTATATAATTTA
1 TATAATTATTTACTTTA
* *
20035434 -AT-ATAATTTACTTTT
1 TATAATTATTTACTTTA
20035449 TATAATTATTTAC-TTA
1 TATAATTATTTACTTTA
20035465 TATAAT
1 TATAAT
20035471 AAGTAAATTC
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
15 9 0.31
16 12 0.41
17 8 0.28
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (17 bp):
TATAATTATTTACTTTA
Found at i:20036620 original size:31 final size:31
Alignment explanation
Indices: 20036584--20036668 Score: 152
Period size: 31 Copynumber: 2.7 Consensus size: 31
20036574 AGGCCCTGTG
*
20036584 GGCCACACAGGCGTGTGGGCCCACACGGTTA
1 GGCCACATAGGCGTGTGGGCCCACACGGTTA
20036615 GGCCACATAGGCGTGTGGGCCCACACGGTTA
1 GGCCACATAGGCGTGTGGGCCCACACGGTTA
*
20036646 GGCCACATAGGCGTGTGAGCCCA
1 GGCCACATAGGCGTGTGGGCCCA
20036669 TTATTTCTGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.20, C:0.31, G:0.35, T:0.14
Consensus pattern (31 bp):
GGCCACATAGGCGTGTGGGCCCACACGGTTA
Found at i:20043792 original size:9 final size:9
Alignment explanation
Indices: 20043769--20043831 Score: 54
Period size: 9 Copynumber: 6.7 Consensus size: 9
20043759 AAATAATTTA
*
20043769 AAAAATCAT
1 AAAAATTAT
*
20043778 ATAAATTAT
1 AAAAATTAT
* *
20043787 AGAAATCAT
1 AAAAATTAT
*
20043796 AGAAACTTAT
1 A-AAAATTAT
20043806 ATAAAATATAT
1 A-AAAAT-TAT
20043817 AAAAATTAT
1 AAAAATTAT
20043826 AAAAAT
1 AAAAAT
20043832 ATTTTTAAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
9 24 0.56
10 15 0.35
11 4 0.09
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:20047389 original size:26 final size:26
Alignment explanation
Indices: 20047358--20047465 Score: 153
Period size: 26 Copynumber: 4.2 Consensus size: 26
20047348 TGAAATGCCC
*
20047358 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
20047384 ATCATGGAATATTTATCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
20047410 ATCATGAAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
20047436 ATCATGGAACATTTACCTAGCCCATT
1 ATCATGGAACATTTACCTAACCCATT
20047462 ATCA
1 ATCA
20047466 ATTTGTACCA
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.34
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:20047989 original size:21 final size:20
Alignment explanation
Indices: 20047952--20047999 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
20047942 TTTTTATACT
* *
20047952 TTTTAATGATTTTTATAAAA
1 TTTTAATAATTTATATAAAA
*
20047972 TTTTAATAATTATATATATAA
1 TTTTAATAATT-TATATAAAA
20047993 TTTTAAT
1 TTTTAAT
20048000 TTAATTGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TTTTAATAATTTATATAAAA
Found at i:20048495 original size:21 final size:21
Alignment explanation
Indices: 20048469--20048510 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
20048459 TCACATATTT
20048469 TATATAATTTATATTTTGTACAC
1 TATAT-ATTTATA-TTTGTACAC
*
20048492 TATATGTTTATATTTGTAC
1 TATATATTTATATTTGTAC
20048511 TAATTATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TATATATTTATATTTGTACAC
Found at i:20050027 original size:39 final size:38
Alignment explanation
Indices: 20049953--20050055 Score: 136
Period size: 39 Copynumber: 2.7 Consensus size: 38
20049943 TCGTAGGAGC
*
20049953 GCCTTT-GTCACAGCAGGCAGTGGGTCTTTCACAAGAGT
1 GCCTTTGGTCACAGTAGGCAGTGGG-CTTTCACAAGAGT
* *
20049991 GCCTTTGGTCAGAGTAGGCAGTGGGCATTTCGCAAGAGT
1 GCCTTTGGTCACAGTAGGCAGTGGGC-TTTCACAAGAGT
* *
20050030 GCCTTGGGTCATAGTAGGCAGTGGGC
1 GCCTTTGGTCACAGTAGGCAGTGGGC
20050056 CAAAACAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
38 7 0.12
39 51 0.88
ACGTcount: A:0.19, C:0.20, G:0.35, T:0.25
Consensus pattern (38 bp):
GCCTTTGGTCACAGTAGGCAGTGGGCTTTCACAAGAGT
Found at i:20073669 original size:6 final size:6
Alignment explanation
Indices: 20073658--20073693 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
20073648 CATTTAATTA
* *
20073658 TTTTAT TTTTAT TTTTAT TTTTCT TTTTAA TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
20073694 CTTTCTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:20073684 original size:18 final size:18
Alignment explanation
Indices: 20073658--20073706 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
20073648 CATTTAATTA
* *
20073658 TTTTATTTTTATTTTTAT
1 TTTTCTTTTTAATTTTAT
20073676 TTTTCTTTTTAATTTTAT
1 TTTTCTTTTTAATTTTAT
*
20073694 CTTTC-TTTTAATT
1 TTTTCTTTTTAATT
20073707 ATTTTTGAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 8 0.29
18 20 0.71
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCTTTTTAATTTTAT
Found at i:20085698 original size:23 final size:24
Alignment explanation
Indices: 20085646--20085798 Score: 89
Period size: 24 Copynumber: 6.4 Consensus size: 24
20085636 GCCTTGTAAA
* *
20085646 GGGAAGCTCACACAGAGCCATTTC
1 GGGAAGCTCACAAAGAGCCATATC
*
20085670 GGGAAGCTCATAAAGAGCC-TATC
1 GGGAAGCTCACAAAGAGCCATATC
* * *
20085693 GGGAAGCTTATC--TGAGCTATATAAC
1 GGGAAGCTCA-CAAAGAGCCATAT--C
* *
20085718 GGGAAGCTCA-TAGGAGCCATAATC
1 GGGAAGCTCACAAAGAGCCAT-ATC
* * * * *
20085742 GGGAAGTTCACAAAGAACCTTGTT
1 GGGAAGCTCACAAAGAGCCATATC
* * * *
20085766 GAGAAGTTCACAAAGAACAATATC
1 GGGAAGCTCACAAAGAGCCATATC
20085790 GGGAAGCTC
1 GGGAAGCTC
20085799 TAAATAGCCA
Statistics
Matches: 97, Mismatches: 24, Indels: 16
0.71 0.18 0.12
Matches are distributed among these distances:
22 4 0.04
23 15 0.15
24 54 0.56
25 22 0.23
26 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (24 bp):
GGGAAGCTCACAAAGAGCCATATC
Found at i:20085734 original size:25 final size:24
Alignment explanation
Indices: 20085669--20085747 Score: 63
Period size: 25 Copynumber: 3.3 Consensus size: 24
20085659 AGAGCCATTT
* *
20085669 CGGGAAGCTCATAAAGAGCC-T-AT
1 CGGGAAGCTCAT-AGGAGCCATAAA
* ** *
20085692 CGGGAAGCTTATCTGAGCTATATAA
1 CGGGAAGCTCATAGGAGCCATA-AA
*
20085717 CGGGAAGCTCATAGGAGCCATAAT
1 CGGGAAGCTCATAGGAGCCATAAA
20085741 CGGGAAG
1 CGGGAAG
20085748 TTCACAAAGA
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
22 4 0.09
23 12 0.28
24 8 0.19
25 19 0.44
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.19
Consensus pattern (24 bp):
CGGGAAGCTCATAGGAGCCATAAA
Found at i:20086374 original size:21 final size:21
Alignment explanation
Indices: 20086336--20086376 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
20086326 AAATTTAACA
* *
20086336 TCAATTTCATCCATTTCATAG
1 TCAATTTAATCCAATTCATAG
*
20086357 TCAATTTAATTCAATTCATA
1 TCAATTTAATCCAATTCATA
20086377 TCCAAGGTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.20, G:0.02, T:0.44
Consensus pattern (21 bp):
TCAATTTAATCCAATTCATAG
Found at i:20093136 original size:29 final size:28
Alignment explanation
Indices: 20093102--20093204 Score: 100
Period size: 29 Copynumber: 3.6 Consensus size: 28
20093092 TAATCGATCA
*
20093102 CGCACACTTAGTGCCATGTGATTTAAGCT
1 CGCACACTTAGTGCCATAT-ATTTAAGCT
* * **
20093131 CGCACACATAGTGCCGTATAATTTAAATT
1 CGCACACTTAGTGCCATAT-ATTTAAGCT
*
20093160 TGCACACTTAGTGCCATACT-TTTCAAGCT
1 CGCACACTTAGTGCCATA-TATTT-AAGCT
*
20093189 TGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
20093205 ATCTTGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 3 0.05
29 57 0.93
30 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTTAAGCT
Found at i:20097991 original size:2 final size:2
Alignment explanation
Indices: 20097984--20098010 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20097974 GGCCCATCTT
20097984 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
20098011 GGTAAATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20099673 original size:18 final size:17
Alignment explanation
Indices: 20099652--20099696 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
20099642 TTTTTGAAAA
20099652 ATATAAAATTTGAAATTT
1 ATATAAAATTTG-AATTT
20099670 ATATAAACATTTGAATTT
1 ATATAAA-ATTTGAATTT
*
20099688 TTA-AAAATT
1 ATATAAAATT
20099697 ATTTTGAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 3 0.12
17 3 0.12
18 14 0.56
19 5 0.20
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (17 bp):
ATATAAAATTTGAATTT
Found at i:20102042 original size:54 final size:54
Alignment explanation
Indices: 20101852--20102106 Score: 309
Period size: 54 Copynumber: 4.7 Consensus size: 54
20101842 TTTCCTTTTT
* * * * * * *
20101852 GAACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-
1 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATTTCCTTGCCTTATA
* ***
20101905 GAACTCA-CTAATGCCATGCCTTGGCATGGTCTTACATG-GGACCTTTGCCTTATA
1 GAACTTATC-AATGCCATGCCTTGGCATGGTCTTACATGATTTCC-TTGCCTTATA
* * * * * *
20101959 GTAACTCATCAATGCCATGTCTTGACATGGTCTTATATAATTTCCTTGACTTATA
1 G-AACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATTTCCTTGCCTTATA
20102014 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATTTCCTTGCCTTATA
1 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATTTCCTTGCCTTATA
20102068 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGA
1 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGA
20102107 CTTATCAATG
Statistics
Matches: 174, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
52 3 0.02
53 40 0.23
54 87 0.50
55 41 0.24
56 3 0.02
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.36
Consensus pattern (54 bp):
GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATTTCCTTGCCTTATA
Found at i:20114410 original size:13 final size:13
Alignment explanation
Indices: 20114392--20114416 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20114382 TCAAGGCAAA
20114392 TAATGCTATCAAC
1 TAATGCTATCAAC
20114405 TAATGCTATCAA
1 TAATGCTATCAA
20114417 TACTTGATGT
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:0.40, C:0.20, G:0.08, T:0.32
Consensus pattern (13 bp):
TAATGCTATCAAC
Found at i:20116763 original size:6 final size:6
Alignment explanation
Indices: 20116749--20116802 Score: 81
Period size: 6 Copynumber: 9.0 Consensus size: 6
20116739 AACGGAAGAG
* * *
20116749 AGTGGA AGTGAA AGTGAA AGTGAA AGTGAA AGTGAA GGTGAA ACTGAA
1 AGTGAA AGTGAA AGTGAA AGTGAA AGTGAA AGTGAA AGTGAA AGTGAA
20116797 AGTGAA
1 AGTGAA
20116803 GAGGCAACTG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.46, C:0.02, G:0.35, T:0.17
Consensus pattern (6 bp):
AGTGAA
Found at i:20118563 original size:27 final size:27
Alignment explanation
Indices: 20118525--20118579 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
20118515 TTCAGGAGTT
20118525 ATGTTAGGCTATGTATCTGAAACAGTA
1 ATGTTAGGCTATGTATCTGAAACAGTA
20118552 ATGTTAGGCTATGTATCTGAAACAGTA
1 ATGTTAGGCTATGTATCTGAAACAGTA
20118579 A
1 A
20118580 AGAAGCTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.33
Consensus pattern (27 bp):
ATGTTAGGCTATGTATCTGAAACAGTA
Found at i:20120957 original size:57 final size:57
Alignment explanation
Indices: 20120894--20121077 Score: 147
Period size: 57 Copynumber: 3.2 Consensus size: 57
20120884 TATAGATAGA
**
20120894 ATTAATATATGAACTTGATTCATACAAAATATTAATTTTATATATTTTACCGAATTT
1 ATTAATATATGAACTTGATTCATACAAAATATTAATTTTATATATTTTAAAGAATTT
* * * * * * * * * *
20120951 ATTAATATA-AATAGTTAATT-ATAAAAAACATGAAAATTAATATTCTTTTGGAAAGAATATA
1 ATTAATATATGA-ACTTGATTCATACAAAATAT-TAATTTTATA-TATTTT--AAAGAAT-TT
* * * **
20121012 ATTGATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTATTGAATTT
1 ATTAATATATGAACTTGATTCATACAAAATATTAATTTTATATATTTTAAAGAATTT
20121069 ATTAATATA
1 ATTAATATA
20121078 AATAGTTATA
Statistics
Matches: 92, Mismatches: 27, Indels: 16
0.68 0.20 0.12
Matches are distributed among these distances:
56 10 0.11
57 31 0.34
58 10 0.11
60 10 0.11
61 21 0.23
62 10 0.11
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (57 bp):
ATTAATATATGAACTTGATTCATACAAAATATTAATTTTATATATTTTAAAGAATTT
Found at i:20124751 original size:20 final size:21
Alignment explanation
Indices: 20124724--20124766 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
20124714 TTGGAAAGTT
*
20124724 GAAAAAAAATTCATAAATCTG
1 GAAAAAAATTTCATAAATCTG
20124745 GAAAAAAATTTCATAAATCTG
1 GAAAAAAATTTCATAAATCTG
20124766 G
1 G
20124767 TATTTAGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.53, C:0.09, G:0.12, T:0.26
Consensus pattern (21 bp):
GAAAAAAATTTCATAAATCTG
Done.