Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000851.1 Hibiscus syriacus cultivar Beakdansim tig00001644_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 7304151
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 29 of 31
Found at i:6772519 original size:155 final size:157
Alignment explanation
Indices: 6772237--6772548 Score: 610
Period size: 155 Copynumber: 2.0 Consensus size: 157
6772227 TGCAAGAAAA
6772237 TGAAAATTTGACACAAGCAATTTTAGAGCGGTTCAACTTCTTCAATGAAGTTTATATTCACTACC
1 TGAAAATTTGACACAAGCAATTTTAGAGCGGTTCAACTTCTTCAATGAAGTTTATATTCACTACC
6772302 TTAGCTTCCACACTAAGGATTTCAACAAATCTACTAATTTGTTCTAACCTTTTAGGACAATGTGT
66 TTAGCTTCCACACTAAGGATTTCAACAAATCTACTAATTTGTTCTAACCTTTTAGGACAATGTGT
6772367 AACTTTAC-A-ACACTTAGACTTATAC
131 AACTTTACAACACACTTAGACTTATAC
6772392 TGAAAATTTGACACAAGCAATTTTAGAGCGGTTCAACTTCTTCAATGAAGTTTATATTCACTACC
1 TGAAAATTTGACACAAGCAATTTTAGAGCGGTTCAACTTCTTCAATGAAGTTTATATTCACTACC
6772457 TTAGCTTCCACACTAAGGATTTCAACAAATCTACTAATTTGTTCTAACCTTTTAGGACAATGTGT
66 TTAGCTTCCACACTAAGGATTTCAACAAATCTACTAATTTGTTCTAACCTTTTAGGACAATGTGT
6772522 AACTTTACAACACACTTAGACTTATAC
131 AACTTTACAACACACTTAGACTTATAC
6772549 CCCAAAGTCT
Statistics
Matches: 155, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
155 138 0.89
156 1 0.01
157 16 0.10
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.35
Consensus pattern (157 bp):
TGAAAATTTGACACAAGCAATTTTAGAGCGGTTCAACTTCTTCAATGAAGTTTATATTCACTACC
TTAGCTTCCACACTAAGGATTTCAACAAATCTACTAATTTGTTCTAACCTTTTAGGACAATGTGT
AACTTTACAACACACTTAGACTTATAC
Found at i:6773633 original size:29 final size:27
Alignment explanation
Indices: 6773575--6773642 Score: 82
Period size: 29 Copynumber: 2.4 Consensus size: 27
6773565 TACGTTTTAA
* *
6773575 AAAAATTAATAAGTCCTCAAACTTTCT
1 AAAAATTAATTAGTCCTCAAACTTACT
*
6773602 AAAATATTAATTAGATCCTCAAACTTAGT
1 AAAA-ATTAATTAG-TCCTCAAACTTACT
*
6773631 AAAAATCAATTA
1 AAAAATTAATTA
6773643 AACTCATTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 4 0.11
28 15 0.43
29 16 0.46
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (27 bp):
AAAAATTAATTAGTCCTCAAACTTACT
Found at i:6775919 original size:20 final size:19
Alignment explanation
Indices: 6775894--6775942 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
6775884 ATATTTTTAT
*
6775894 TAAAATGATACTAAAAATAA
1 TAAAATAATACTAAAAAT-A
* *
6775914 TAAAATAATATTAAATATA
1 TAAAATAATACTAAAAATA
6775933 TAAAATAATA
1 TAAAATAATA
6775943 ACATTTTGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (19 bp):
TAAAATAATACTAAAAATA
Found at i:6779466 original size:24 final size:24
Alignment explanation
Indices: 6779434--6779482 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
6779424 ATACTCAACC
6779434 AGACGTATCATTT-ATTGTTAATTT
1 AGACGTATCATTTGA-TGTTAATTT
6779458 AGACGTATCATTTGATGTTAATTT
1 AGACGTATCATTTGATGTTAATTT
6779482 A
1 A
6779483 TTAGTCAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (24 bp):
AGACGTATCATTTGATGTTAATTT
Found at i:6781977 original size:51 final size:51
Alignment explanation
Indices: 6781901--6781998 Score: 178
Period size: 51 Copynumber: 1.9 Consensus size: 51
6781891 CTTTCAGATT
*
6781901 GAATATTCACCTTGTCTTTCAACTTCACTTCCCTTTTCCCTTTTGTTTATA
1 GAATATTCACCTTGTCTTTAAACTTCACTTCCCTTTTCCCTTTTGTTTATA
*
6781952 GAATATTCACCTTGTCTTTAAACTTCACTTCCCTTTTTCCTTTTGTT
1 GAATATTCACCTTGTCTTTAAACTTCACTTCCCTTTTCCCTTTTGTT
6781999 GTTTTAAAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.17, C:0.27, G:0.06, T:0.50
Consensus pattern (51 bp):
GAATATTCACCTTGTCTTTAAACTTCACTTCCCTTTTCCCTTTTGTTTATA
Found at i:6783298 original size:12 final size:12
Alignment explanation
Indices: 6783281--6783308 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
6783271 TATCAGCAAT
6783281 GCTACAACTCTA
1 GCTACAACTCTA
6783293 GCTACAACTCTA
1 GCTACAACTCTA
6783305 GCTA
1 GCTA
6783309 ACCACTGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.11, T:0.25
Consensus pattern (12 bp):
GCTACAACTCTA
Found at i:6788211 original size:203 final size:205
Alignment explanation
Indices: 6787859--6788270 Score: 767
Period size: 203 Copynumber: 2.0 Consensus size: 205
6787849 TTGAGCCTGT
6787859 TAATGGATTTCGAGTATGCTCAAAACAAAAATATACTTTGTTCTCGAACTATCACACTCCAATAC
1 TAATGGATTTCGAGTATGCTCAAAACAAAAATATACTTTGTTCTCGAACTATCACACTCCAATAC
6787924 TACTAAACCATTGTTTCAGCTAATTGAAGGAGCACCAACCTAGACAGCACTCAGGTGCAGTGAAA
66 TACTAAACCATTGTTTCAGCTAATTGAAGGAGCACCAACCTAGACAGCACTCAGGTGCAGTGAAA
6787989 AACAGGAGTCCCCGAGAACGACGAAGCTCGTCAGTTGTCA-TATAAAACAAACTGATTTTGTTGA
131 AACAGGAGTCCCCGAGAACGACGAAGCTCGTCAGTTGTCACTATAAAACAAACTGATTTTGTTGA
6788053 AAACA-TACA
196 AAACAGTACA
6788062 TAATGGATTTCGAGTATGCTCAAAACAAAAATATACTTTGTTCTCGAACTATCACACTCCAATAC
1 TAATGGATTTCGAGTATGCTCAAAACAAAAATATACTTTGTTCTCGAACTATCACACTCCAATAC
6788127 TACTAAACCATTGTTTCAGCTAATTGAAGGAGCACCAACCTAGACAGCACTCAGGTGCAGTG-AA
66 TACTAAACCATTGTTTCAGCTAATTGAAGGAGCACCAACCTAGACAGCACTCAGGTGCAGTGAAA
*
6788191 AACAGGAGTCCCCGGAGAACGACGAAGCTCGTCATTTGTCATCCTATAAAACAAACTGATTTTGT
131 AACAGGAGTCCCC-GAGAACGACGAAGCTCGTCAGTTGTCA--CTATAAAACAAACTGATTTTGT
6788256 TGAAAACAGTACA
193 TGAAAACAGTACA
6788269 TA
1 TA
6788271 TAACCGCAAG
Statistics
Matches: 203, Mismatches: 1, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
202 15 0.07
203 153 0.75
206 29 0.14
207 6 0.03
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (205 bp):
TAATGGATTTCGAGTATGCTCAAAACAAAAATATACTTTGTTCTCGAACTATCACACTCCAATAC
TACTAAACCATTGTTTCAGCTAATTGAAGGAGCACCAACCTAGACAGCACTCAGGTGCAGTGAAA
AACAGGAGTCCCCGAGAACGACGAAGCTCGTCAGTTGTCACTATAAAACAAACTGATTTTGTTGA
AAACAGTACA
Found at i:6788901 original size:18 final size:18
Alignment explanation
Indices: 6788851--6788901 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
6788841 AATCTAATTA
*
6788851 CTAATTTCTAGAGACAAG
1 CTAATTTCTAGAGATAAG
6788869 CTAATTTCTAGAGATAAG
1 CTAATTTCTAGAGATAAG
6788887 CTAATTTCTAGAGAT
1 CTAATTTCTAGAGAT
6788902 TATTTCATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (18 bp):
CTAATTTCTAGAGATAAG
Found at i:6800079 original size:21 final size:21
Alignment explanation
Indices: 6800055--6800094 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
6800045 AAGACTATTT
6800055 TCATTTTTCA-ATTTTGAAACA
1 TCATTTTT-ATATTTTGAAACA
6800076 TCATTTTTATATTTTGAAA
1 TCATTTTTATATTTTGAAA
6800095 ATAGAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.53
Consensus pattern (21 bp):
TCATTTTTATATTTTGAAACA
Found at i:6802164 original size:45 final size:46
Alignment explanation
Indices: 6802076--6802166 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
6802066 TTGAAAAAGC
* *
6802076 CTGAGTGCATCGATGCATGATATTGTGCATCGATGCATCAAATGCA
1 CTGAGGGCATCGATGCATGATATTGTGCATCGATGCATAAAATGCA
* *
6802122 CTGAGGGCATCGTTGCATGGTA-TGTGCATCGATGCATAAAATGCA
1 CTGAGGGCATCGATGCATGATATTGTGCATCGATGCATAAAATGCA
6802167 TTCAATGTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 22 0.54
46 19 0.46
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.27
Consensus pattern (46 bp):
CTGAGGGCATCGATGCATGATATTGTGCATCGATGCATAAAATGCA
Found at i:6806623 original size:15 final size:15
Alignment explanation
Indices: 6806603--6806637 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
6806593 ACTTATGTTT
6806603 TTTTTAAATAAA-ATA
1 TTTTTAAA-AAATATA
6806618 TTTTTAAAAAATATA
1 TTTTTAAAAAATATA
6806633 TTTTT
1 TTTTT
6806638 TTAAAATCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.16
15 16 0.84
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTTTAAAAAATATA
Found at i:6817872 original size:20 final size:20
Alignment explanation
Indices: 6817847--6817909 Score: 72
Period size: 20 Copynumber: 3.0 Consensus size: 20
6817837 TTTTGGTGTA
*
6817847 GAGGGAATCGATCCCCCCTT
1 GAGGGAACCGATCCCCCCTT
*
6817867 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGA-TCCCCCCTT
*
6817888 GAAGGGGAACCGATTCCCCCTT
1 G-A-GGGAACCGATCCCCCCTT
6817910 TGAAGGGGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 8 0.22
23 9 0.25
ACGTcount: A:0.21, C:0.33, G:0.25, T:0.21
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCTT
Found at i:6817899 original size:23 final size:23
Alignment explanation
Indices: 6817849--6817930 Score: 116
Period size: 23 Copynumber: 3.7 Consensus size: 23
6817839 TTGGTGTAGA
* *
6817849 GGGAATCGA-TCCCCCCTTG-A-
1 GGGAACCGATTCCCCCTTTGAAG
6817869 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
6817892 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
*
6817915 GGGAACTGATTCCCCC
1 GGGAACCGATTCCCCC
6817931 CACAGGGGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.14
21 9 0.16
22 1 0.02
23 38 0.68
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.21
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:6821457 original size:29 final size:29
Alignment explanation
Indices: 6821406--6821461 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
6821396 TTTAATTAAC
* *
6821406 TTAAGTAATTATTTTTATTTTTTATTAGT
1 TTAAATAATTATTTTTATATTTTATTAGT
6821435 TTAAATAATTATTTTT-TGATTTTATTA
1 TTAAATAATTATTTTTAT-ATTTTATTA
6821462 ATATGAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.64
Consensus pattern (29 bp):
TTAAATAATTATTTTTATATTTTATTAGT
Found at i:6825864 original size:59 final size:60
Alignment explanation
Indices: 6825772--6825907 Score: 220
Period size: 59 Copynumber: 2.3 Consensus size: 60
6825762 ATTATTTCCC
* *
6825772 ATATGGAAATTCATACACTTGGTATGAATTCCTTCTCATGTT-AGCACACGAAGTGTCCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAAGCACACGAAGTGCCCT
* *
6825831 ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAAGCAGATGAAGTGCCCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAAGCACACGAAGTGCCCT
*
6825891 ATATGAAAATTCATACA
1 ATATGGAAATTCATACA
6825908 TCAATATTTC
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
59 41 0.58
60 30 0.42
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (60 bp):
ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAAGCACACGAAGTGCCCT
Found at i:6827617 original size:22 final size:23
Alignment explanation
Indices: 6827590--6827638 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
6827580 TATTATTTAG
* *
6827590 AAAAAAATATA-AAAATCAATTC
1 AAAAAAATACATAAAATAAATTC
*
6827612 AAAAAAATACATAAAATAAATTT
1 AAAAAAATACATAAAATAAATTC
6827635 AAAA
1 AAAA
6827639 TATTAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 10 0.43
23 13 0.57
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.22
Consensus pattern (23 bp):
AAAAAAATACATAAAATAAATTC
Found at i:6828090 original size:21 final size:21
Alignment explanation
Indices: 6828064--6828111 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
6828054 TACATATTTA
6828064 CATTGCGATAGTCCAAGTTCG
1 CATTGCGATAGTCCAAGTTCG
*
6828085 CATTGCGATAGTCGAAGTTCG
1 CATTGCGATAGTCCAAGTTCG
*
6828106 CGTTGC
1 CATTGC
6828112 AATTTTCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.23, G:0.27, T:0.29
Consensus pattern (21 bp):
CATTGCGATAGTCCAAGTTCG
Found at i:6828149 original size:21 final size:21
Alignment explanation
Indices: 6828125--6828196 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
6828115 TTTCCAAATC
6828125 CGACTATCGCAACGCGAACTT
1 CGACTATCGCAACGCGAACTT
**
6828146 CGACTATCGCATTGCGAA-TAT
1 CGACTATCGCAACGCGAACT-T
6828167 --ACTATCGCAACGCGAACTT
1 CGACTATCGCAACGCGAACTT
*
6828186 TGACTATCGCA
1 CGACTATCGCA
6828197 TTGCGATTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
19 15 0.35
20 2 0.05
21 26 0.60
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (21 bp):
CGACTATCGCAACGCGAACTT
Found at i:6828172 original size:19 final size:19
Alignment explanation
Indices: 6828148--6828222 Score: 80
Period size: 19 Copynumber: 3.8 Consensus size: 19
6828138 GCGAACTTCG
*
6828148 ACTATCGCATTGCGAATAT
1 ACTATCGCATTGCGAATTT
**
6828167 ACTATCGCAACGCGAACTTT
1 ACTATCGCATTGCGAA-TTT
6828187 GACTATCGCATTGCG-ATTT
1 -ACTATCGCATTGCGAATTT
6828206 ACATATTCGCATTGCGA
1 AC-TA-TCGCATTGCGA
6828223 TAGTCCAAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
18 2 0.04
19 19 0.41
20 13 0.28
21 12 0.26
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (19 bp):
ACTATCGCATTGCGAATTT
Found at i:6828182 original size:40 final size:40
Alignment explanation
Indices: 6828127--6828202 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
6828117 TCCAAATCCG
6828127 ACTATCGCAACGCGAACTTCGACTATCGCATTGCGAATAT
1 ACTATCGCAACGCGAACTTCGACTATCGCATTGCGAATAT
*
6828167 ACTATCGCAACGCGAACTTTGACTATCGCATTGCGA
1 ACTATCGCAACGCGAACTTCGACTATCGCATTGCGA
6828203 TTTACATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (40 bp):
ACTATCGCAACGCGAACTTCGACTATCGCATTGCGAATAT
Found at i:6828202 original size:21 final size:20
Alignment explanation
Indices: 6828126--6828222 Score: 83
Period size: 21 Copynumber: 4.8 Consensus size: 20
6828116 TTCCAAATCC
** *
6828126 GACTATCGCAACGCGAACTTC
1 GACTATCGCATTGCGAA-TTT
*
6828147 GACTATCGCATTGCGAATAT
1 GACTATCGCATTGCGAATTT
**
6828167 -ACTATCGCAACGCGAACTTT
1 GACTATCGCATTGCGAA-TTT
6828187 GACTATCGCATTGCG-ATTT
1 GACTATCGCATTGCGAATTT
6828206 -ACATATTCGCATTGCGA
1 GAC-TA-TCGCATTGCGA
6828223 TAGTCCAAGT
Statistics
Matches: 62, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
18 2 0.03
19 19 0.31
20 14 0.23
21 27 0.44
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (20 bp):
GACTATCGCATTGCGAATTT
Found at i:6828241 original size:21 final size:22
Alignment explanation
Indices: 6828211--6828258 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
6828201 GATTTACATA
6828211 TTCGCATTGCGA-TAGTCCAAG
1 TTCGCATTGCGATTAGTCCAAG
* *
6828232 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCATTGCGA-TTAGTCCAAG
6828255 TTCG
1 TTCG
6828259 TTGATAGTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
23 12 0.52
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (22 bp):
TTCGCATTGCGATTAGTCCAAG
Found at i:6828888 original size:6 final size:6
Alignment explanation
Indices: 6828877--6828902 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
6828867 GTCTCGTCTC
6828877 GTCGTG GTCGTG GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GT
6828903 AATACGTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.15, G:0.50, T:0.35
Consensus pattern (6 bp):
GTCGTG
Found at i:6829024 original size:21 final size:21
Alignment explanation
Indices: 6828995--6829140 Score: 197
Period size: 21 Copynumber: 6.9 Consensus size: 21
6828985 ATTTTGGACT
* *
6828995 ATCGTAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
6829016 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
6829037 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
6829058 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
6829079 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
6829100 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
6829121 ATCGCAATGCGAACTTGGAA
1 ATCGCAA--CGAACTTGGAA
6829141 CGAATTTGGA
Statistics
Matches: 113, Mismatches: 6, Indels: 10
0.88 0.05 0.08
Matches are distributed among these distances:
19 10 0.09
21 81 0.72
23 22 0.19
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:6829067 original size:63 final size:61
Alignment explanation
Indices: 6828988--6829116 Score: 222
Period size: 63 Copynumber: 2.1 Consensus size: 61
6828978 CGTTGCGATT
*
6828988 TTGGACTATCGTAACGAATTTGGAATAAATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGAACTTGGAATAAATCGCAA--CGAAC
*
6829051 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGAACTTGGAATAAATCGCAACGAAC
6829112 TTGGA
1 TTGGA
6829117 ATAAATCGCA
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
61 10 0.16
63 54 0.84
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (61 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGAACTTGGAATAAATCGCAACGAAC
Found at i:6829150 original size:34 final size:35
Alignment explanation
Indices: 6829105--6829175 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 35
6829095 AATAAATCGC
*
6829105 AACGAACTTGGAATAAATCGCAATGCGAAC-TTGG
1 AACGAACTTGGAATAAATCGCAACGCGAACTTTGG
*
6829139 AACGAATTTGGAATAAATCGCAACGCGAACTTTGG
1 AACGAACTTGGAATAAATCGCAACGCGAACTTTGG
6829174 AA
1 AA
6829176 TAAATATCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 28 0.82
35 6 0.18
ACGTcount: A:0.39, C:0.17, G:0.23, T:0.21
Consensus pattern (35 bp):
AACGAACTTGGAATAAATCGCAACGCGAACTTTGG
Found at i:6831866 original size:21 final size:21
Alignment explanation
Indices: 6831836--6831875 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
6831826 AATTGCACCT
*
6831836 ATTTTACTCACTGTACTTTTA
1 ATTTTACTCACTGAACTTTTA
*
6831857 ATTTTTCTCACTGAACTTT
1 ATTTTACTCACTGAACTTT
6831876 CGAATTGCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.20, G:0.05, T:0.53
Consensus pattern (21 bp):
ATTTTACTCACTGAACTTTTA
Found at i:6831881 original size:22 final size:21
Alignment explanation
Indices: 6831836--6831881 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
6831826 AATTGCACCT
* *
6831836 ATTTTACTCACTGTACTTTTA
1 ATTTTACTCACTGAACTTTGA
*
6831857 ATTTTTCTCACTGAACTTTCGA
1 ATTTTACTCACTGAACTTT-GA
6831879 ATT
1 ATT
6831882 GCTCCTGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.50
Consensus pattern (21 bp):
ATTTTACTCACTGAACTTTGA
Found at i:6837460 original size:3 final size:3
Alignment explanation
Indices: 6837452--6837600 Score: 210
Period size: 3 Copynumber: 47.7 Consensus size: 3
6837442 GGTGTGGCAG
*
6837452 CTT CTT CTT CTT CATC CTT -TT CTT CTT CTT CTT CTT CTT CCTT CTT
1 CTT CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT -CTT CTT
*
6837498 CATT CTT CTT CCTT CTT CCTT CTT CCTT CTT CATT CTT CCT CTT CTT
1 C-TT CTT CTT -CTT CTT -CTT CTT -CTT CTT C-TT CTT CTT CTT CTT
6837545 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
6837593 CTT CTT CT
1 CTT CTT CT
6837601 CACACACTTT
Statistics
Matches: 134, Mismatches: 4, Indels: 16
0.87 0.03 0.10
Matches are distributed among these distances:
2 2 0.01
3 112 0.84
4 20 0.15
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:6838975 original size:3 final size:3
Alignment explanation
Indices: 6838967--6839089 Score: 189
Period size: 3 Copynumber: 40.7 Consensus size: 3
6838957 AGAGTGTGAG
6838967 AGA AGA AG- AGA AGAA AGAA AGAA AGA AGA AG- AGA AGA AGA AG- AGA
1 AGA AGA AGA AGA AG-A AG-A AG-A AGA AGA AGA AGA AGA AGA AGA AGA
6839012 AGGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
6839058 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
6839090 TTGTCAAATC
Statistics
Matches: 115, Mismatches: 0, Indels: 10
0.92 0.00 0.08
Matches are distributed among these distances:
2 6 0.05
3 95 0.83
4 14 0.12
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:6839350 original size:3 final size:3
Alignment explanation
Indices: 6839342--6839367 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6839332 TTTGTCTGAG
6839342 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
6839368 TATTTGCTCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6842291 original size:22 final size:22
Alignment explanation
Indices: 6842263--6842902 Score: 610
Period size: 22 Copynumber: 29.5 Consensus size: 22
6842253 ATTTTAAAAT
6842263 TTTATTTTAAAATATGAATTGA
1 TTTATTTTAAAATATGAATTGA
6842285 TTTATTTTAAAATAT-AGATTGA
1 TTTATTTTAAAATATGA-ATTGA
6842307 TTTA-TTT-AAATATGAATTGA
1 TTTATTTTAAAATATGAATTGA
6842327 TTTATTTTAAAATATGAATTGA
1 TTTATTTTAAAATATGAATTGA
*
6842349 TTTATTTTAAAATATGGAA--AA
1 TTTATTTTAAAATAT-GAATTGA
*
6842370 TTTTATTTTAAAATATGGATTGA
1 -TTTATTTTAAAATATGAATTGA
*
6842393 TTTATTTTAAAAATATGGATTGA
1 TTTATTTT-AAAATATGAATTGA
*
6842416 TTTATTTTAAAAATATGCATTGA
1 TTTATTTT-AAAATATGAATTGA
**
6842439 TTTATTTTAAAATATGAA-AAA
1 TTTATTTTAAAATATGAATTGA
** * *
6842460 AATATTTTAAAATATGGATTAA
1 TTTATTTTAAAATATGAATTGA
*
6842482 TTTA-TTTAAAATATGGAA--AA
1 TTTATTTTAAAATAT-GAATTGA
*
6842502 TTTTATTTTAAAATATGGATTGA
1 -TTTATTTTAAAATATGAATTGA
6842525 TTTATTTTAAAATATTG-ATTGA
1 TTTATTTTAAAATA-TGAATTGA
* *
6842547 CTTATTTT-AAATATGGATTGA
1 TTTATTTTAAAATATGAATTGA
* ***
6842568 TTTATTTAAAAATATGAAAAAA
1 TTTATTTTAAAATATGAATTGA
*
6842590 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGAATTGA
* *
6842612 TTTATTTTAAAGTATAGAA--AA
1 TTTATTTTAAAATAT-GAATTGA
*
6842633 TTTTATTTTAAAATATGGATTGA
1 -TTTATTTTAAAATATGAATTGA
**
6842656 TTTATTTTAAAATATGGAA-AAA
1 TTTATTTTAAAATAT-GAATTGA
* *
6842678 ATTATTTTAAAATA-GGATTGA
1 TTTATTTTAAAATATGAATTGA
* **
6842699 TTTATTTTAAAAT-GGAA-AAA
1 TTTATTTTAAAATATGAATTGA
*
6842719 TTTATTTTAAAATATGGA-TGA
1 TTTATTTTAAAATATGAATTGA
* *
6842740 TTTATTTTAAAATATGGATAGA
1 TTTATTTTAAAATATGAATTGA
*
6842762 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGAATTGA
*
6842784 TTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGAATTGA
***
6842806 -TTATTTTAAAATATGGAAAAAA
1 TTTATTTTAAAATAT-GAATTGA
*
6842828 TTTTATTTTAAAATATGGAA--AA
1 -TTTATTTTAAAATAT-GAATTGA
*
6842850 TTT-TATTTAAAATATGTA-TGA
1 TTTAT-TTTAAAATATGAATTGA
*
6842871 TTTATTTT-AAATATGGATTGA
1 TTTATTTTAAAATATGAATTGA
6842892 -TTATTTTAAAA
1 TTTATTTTAAAA
6842903 AATTTATTAT
Statistics
Matches: 525, Mismatches: 58, Indels: 71
0.80 0.09 0.11
Matches are distributed among these distances:
20 53 0.10
21 138 0.26
22 260 0.50
23 56 0.11
24 18 0.03
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (22 bp):
TTTATTTTAAAATATGAATTGA
Found at i:6842358 original size:43 final size:43
Alignment explanation
Indices: 6842263--6842902 Score: 709
Period size: 44 Copynumber: 14.8 Consensus size: 43
6842253 ATTTTAAAAT
* *
6842263 TTTATTTTAAAATATGAATTGATTTATTTTAAAATATAGATTGA
1 TTTATTTTAAAATATGAA-TAATTTATTTTAAAATATGGATTGA
* *
6842307 TTTA-TTT-AAATATGAATTGATTTATTTTAAAATATGAATTGA
1 TTTATTTTAAAATATGAA-TAATTTATTTTAAAATATGGATTGA
6842349 TTTATTTTAAAATATGGAA-AATTTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATAT-GAATAA-TTTATTTTAAAATATGGATTGA
* * *
6842393 TTTATTTTAAAAATATGGATTGATTTATTTTAAAAATATGCATTGA
1 TTTATTTT-AAAATAT-GAATAATTTATTTT-AAAATATGGATTGA
* ** *
6842439 TTTATTTTAAAATATGAAAAAAATATTTTAAAATATGGATTAA
1 TTTATTTTAAAATATGAATAATTTATTTTAAAATATGGATTGA
6842482 TTTA-TTTAAAATATGGAA-AATTTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATAT-GAATAA-TTTATTTTAAAATATGGATTGA
* * *
6842525 TTTATTTTAAAATATTGATTGACTTATTTT-AAATATGGATTGA
1 TTTATTTTAAAATA-TGAATAATTTATTTTAAAATATGGATTGA
* *
6842568 TTTATTTAAAAATATGAAAAAATTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATG-AATAATTTATTTTAAAATATGGATTGA
*
6842612 TTTATTTTAAAGTATAGAA-AATTTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATAT-GAATAA-TTTATTTTAAAATATGGATTGA
* *
6842656 TTTATTTTAAAATATGGAAAAAATTATTTTAAAATA-GGATTGA
1 TTTATTTTAAAATAT-GAATAATTTATTTTAAAATATGGATTGA
* *
6842699 TTTATTTTAAAAT-GGAAAAATTTATTTTAAAATATGGA-TGA
1 TTTATTTTAAAATATGAATAATTTATTTTAAAATATGGATTGA
*
6842740 TTTATTTTAAAATATGGATAGATTTATTTTAAAATATGGATTGA
1 TTTATTTTAAAATATGAATA-ATTTATTTTAAAATATGGATTGA
* * ***
6842784 TTTATTTTAAAATATGGATTGA-TTATTTTAAAATATGGAAAAAA
1 TTTATTTTAAAATAT-GAATAATTTATTTTAAAATATGG-ATTGA
*
6842828 TTTTATTTTAAAATATGGAA-AATTT-TATTTAAAATATGTA-TGA
1 -TTTATTTTAAAATAT-GAATAATTTAT-TTTAAAATATGGATTGA
* *
6842871 TTTATTTT-AAATATGGATTGA-TTATTTTAAAA
1 TTTATTTTAAAATAT-GAATAATTTATTTTAAAA
6842903 AATTTATTAT
Statistics
Matches: 520, Mismatches: 48, Indels: 59
0.83 0.08 0.09
Matches are distributed among these distances:
41 53 0.10
42 67 0.13
43 142 0.27
44 170 0.33
45 66 0.13
46 22 0.04
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (43 bp):
TTTATTTTAAAATATGAATAATTTATTTTAAAATATGGATTGA
Found at i:6842983 original size:31 final size:31
Alignment explanation
Indices: 6842925--6842984 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
6842915 TAGTTGTATG
*
6842925 AATTATTTAAATTTCAGTATTATAAAACTAA
1 AATTATTTAAATTTCAGTATTACAAAACTAA
*
6842956 AATTATTTAAATTTCAGTATTGCAAAACT
1 AATTATTTAAATTTCAGTATTACAAAACT
6842985 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATTTCAGTATTACAAAACTAA
Found at i:6844286 original size:20 final size:20
Alignment explanation
Indices: 6844261--6844298 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
6844251 CACATGTTAA
6844261 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
6844281 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
6844299 TCAAGGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:6845819 original size:23 final size:23
Alignment explanation
Indices: 6845788--6845847 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
6845778 CTTATATGGT
6845788 ACTTCGGTGCATTTCTACGCGGC
1 ACTTCGGTGCATTTCTACGCGGC
* * * *
6845811 ACTTAGGTGTAATTCTACGTGGC
1 ACTTCGGTGCATTTCTACGCGGC
6845834 ACTTCGGTGCATTT
1 ACTTCGGTGCATTT
6845848 ATACAAGCTG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (23 bp):
ACTTCGGTGCATTTCTACGCGGC
Found at i:6846745 original size:20 final size:20
Alignment explanation
Indices: 6846716--6846772 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
6846706 CCGATACGAC
*
6846716 CCTTTAGTATCGATACTAAA
1 CCTTTGGTATCGATACTAAA
**
6846736 CCTTTGGTATCGATAC-CCA
1 CCTTTGGTATCGATACTAAA
6846755 CCTGTTGGTATCGATACT
1 CCT-TTGGTATCGATACT
6846773 CCATGGCTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.12
20 28 0.88
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (20 bp):
CCTTTGGTATCGATACTAAA
Found at i:6846947 original size:19 final size:20
Alignment explanation
Indices: 6846923--6846974 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
6846913 ACCTAGGGGA
*
6846923 GTATCGATACTCCTG-CCTG
1 GTATCGATACTCATGCCCTG
6846942 GTATCGATACTCATGCCCTG
1 GTATCGATACTCATGCCCTG
6846962 GTATCGATACTCA
1 GTATCGATACTCA
6846975 ATGAATGATT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.21, C:0.29, G:0.19, T:0.31
Consensus pattern (20 bp):
GTATCGATACTCATGCCCTG
Found at i:6848900 original size:21 final size:21
Alignment explanation
Indices: 6848874--6848922 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
6848864 TGGTAACAAG
6848874 TCATCATAAAGAAATACCACA
1 TCATCATAAAGAAATACCACA
6848895 TCATCATAAAGAAATACCACA
1 TCATCATAAAGAAATACCACA
6848916 TCATCAT
1 TCATCAT
6848923 TGAAAAAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.49, C:0.24, G:0.04, T:0.22
Consensus pattern (21 bp):
TCATCATAAAGAAATACCACA
Found at i:6857978 original size:3 final size:3
Alignment explanation
Indices: 6857970--6858035 Score: 105
Period size: 3 Copynumber: 22.0 Consensus size: 3
6857960 ATTGATTTAT
* * *
6857970 TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TAA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6858018 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
6858036 AATATATTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:6870823 original size:7 final size:7
Alignment explanation
Indices: 6870797--6870879 Score: 75
Period size: 7 Copynumber: 11.9 Consensus size: 7
6870787 TATTATGCTT
6870797 GAAAAAA
1 GAAAAAA
*
6870804 AAAGAAAA
1 GAA-AAAA
6870812 GAAAAGAA
1 GAAAA-AA
6870820 -AAAAGAA
1 GAAAA-AA
6870827 GAAAAAGA
1 GAAAAA-A
6870835 GAAAAAA
1 GAAAAAA
*
6870842 G-AAAGA
1 GAAAAAA
6870848 -AAAAAA
1 GAAAAAA
*
6870854 GAGAAAA
1 GAAAAAA
6870861 GAAAAAA
1 GAAAAAA
6870868 G-AAAAA
1 GAAAAAA
6870874 GAAAAA
1 GAAAAA
6870880 GGGGTCAAGA
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
6 14 0.22
7 30 0.48
8 19 0.30
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:6870839 original size:28 final size:27
Alignment explanation
Indices: 6870800--6870879 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 27
6870790 TATGCTTGAA
*
6870800 AAAAAAAGAAAAGAAAAGAAAAAAGAAG
1 AAAAAGAGAAAAGAAAAGAAAAAA-AAG
*
6870828 AAAAAGAGAAAAAAGAAAG-AAAAAAAG
1 AAAAAGAGAAAAGA-AAAGAAAAAAAAG
*
6870855 AGAAAAGAAAAAAGAAAAAGAAAAA
1 A-AAAAGAGAAAAG-AAAAGAAAAA
6870880 GGGGTCAAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
27 4 0.09
28 31 0.70
29 9 0.20
ACGTcount: A:0.82, C:0.00, G:0.17, T:0.00
Consensus pattern (27 bp):
AAAAAGAGAAAAGAAAAGAAAAAAAAG
Found at i:6870847 original size:39 final size:40
Alignment explanation
Indices: 6870797--6870879 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 40
6870787 TATTATGCTT
*
6870797 GAAAAAAAAAGAAAAGAAA-AG-AAA-AAAGAAGAAAAAGA
1 GAAAAAAAAAGAAAA-AAAGAGAAAAGAAAAAAGAAAAAGA
6870835 GAAAAAAGAAAGAAAAAAAGAGAAAAGAAAAAAGAAAAAGA
1 GAAAAAA-AAAGAAAAAAAGAGAAAAGAAAAAAGAAAAAGA
6870876 -AAAA
1 GAAAA
6870880 GGGGTCAAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
38 10 0.25
39 10 0.25
40 7 0.17
41 13 0.32
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (40 bp):
GAAAAAAAAAGAAAAAAAGAGAAAAGAAAAAAGAAAAAGA
Found at i:6870870 original size:26 final size:26
Alignment explanation
Indices: 6870801--6870880 Score: 92
Period size: 26 Copynumber: 3.0 Consensus size: 26
6870791 ATGCTTGAAA
*
6870801 AAAAAAGAAAAGA-AAAGAAAAAAGAAG
1 AAAAAAGAAAAAAGAAAG-AAAAA-AAG
6870828 AAAAAGAGAAAAAAGAAAGAAAAAAAG
1 AAAAA-AGAAAAAAGAAAGAAAAAAAG
*
6870855 AGAAAAGAAAAAAGAAA-AAGAAAAAG
1 AAAAAAGAAAAAAGAAAGAA-AAAAAG
6870881 GGGTCAAGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
25 2 0.04
26 18 0.38
27 12 0.25
28 12 0.25
29 4 0.08
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (26 bp):
AAAAAAGAAAAAAGAAAGAAAAAAAG
Found at i:6870880 original size:19 final size:18
Alignment explanation
Indices: 6870801--6870879 Score: 88
Period size: 18 Copynumber: 4.3 Consensus size: 18
6870791 ATGCTTGAAA
*
6870801 AAAAAAG-AAAAGAAAAG
1 AAAAAAGAAAAAAAAAAG
* *
6870818 AAAAAAGAAGAAAAAGAG
1 AAAAAAGAAAAAAAAAAG
6870836 AAAAAAGAAAGAAAAAAAG
1 AAAAAAGAAA-AAAAAAAG
*
6870855 AGAAAAGAAAAAAGAAAAAG
1 AAAAAAG-AAAAA-AAAAAG
6870875 AAAAA
1 AAAAA
6870880 GGGGTCAAGA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
17 7 0.14
18 16 0.31
19 15 0.29
20 13 0.25
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAAAAAAAAG
Found at i:6872163 original size:83 final size:83
Alignment explanation
Indices: 6872024--6872335 Score: 453
Period size: 83 Copynumber: 3.7 Consensus size: 83
6872014 GAACAAATGC
*
6872024 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
6872089 AATTGAATTTGAAAGATG
66 AATTGAATTTGAAAGATG
6872107 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
*
6872172 CATTGAATTTGAAAGATG
66 AATTGAATTTGAAAGATG
6872190 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG--T-----A-
* * * *
6872255 AGAACCAGTTATTGAATTTGGAAGAGG
58 A-AACCAATAATTGAATTTGAAAGATG
* * * *
6872282 AATGTGCTAATAGTATCTTCTGGAAGTGTTCTTTGAGTTCTCTGATTTGGTTTG
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
6872336 ATATAAAACC
Statistics
Matches: 210, Mismatches: 10, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
83 136 0.65
85 1 0.00
90 1 0.00
91 1 0.00
92 71 0.34
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (83 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
AATTGAATTTGAAAGATG
Found at i:6872335 original size:175 final size:166
Alignment explanation
Indices: 6872024--6872335 Score: 462
Period size: 175 Copynumber: 1.8 Consensus size: 166
6872014 GAACAAATGC
6872024 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
1 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
* *
6872089 AATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
66 AATTGAATTTGAAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
6872154 TGGTTTGGTAAAACCAATCATTGAATTTGAAAGATG
131 TGGTTTGGTAAAACCAATCATTGAATTTGAAAGATG
*
6872190 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCAC
1 AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG--T-----A-
* * * *
6872255 AGAACCAGTTATTGAATTTGGAAGAGGAATGTGCTAATAGTATCTTCTGGAAGTGTTCTTTGAGT
58 A-AACCAATAATTGAATTTGAAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGT
* *
6872320 TCTCTGATTTGGTTTG
122 TATCTGATCTGGTTTG
6872336 ATATAAAACC
Statistics
Matches: 128, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
166 54 0.42
168 1 0.01
173 1 0.01
174 1 0.01
175 71 0.55
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (166 bp):
AATGTACTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACCAAT
AATTGAATTTGAAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTTGGTAAAACCAATCATTGAATTTGAAAGATG
Found at i:6872372 original size:92 final size:92
Alignment explanation
Indices: 6872165--6872376 Score: 293
Period size: 92 Copynumber: 2.3 Consensus size: 92
6872155 GGTTTGGTAA
* *
6872165 AACCAATCATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
1 AACCAATCATTGAATTTGAAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
* *
6872230 TCTGATCTGGTTTGGTATGAACCACAG
66 TCTGATCTGGTTTGATATAAACCACAG
* * * * *
6872257 AACCAGTTATTGAATTTGGAAGAGGAATGTGCTAATAGTATCTTCTGGAAGTGTTCTTTGAGTTC
1 AACCAATCATTGAATTTGAAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
*
6872322 TCTGATTTGGTTTGATATAAAACC-CAG
66 TCTGATCTGGTTTGATAT-AAACCACAG
*
6872349 AACCAATCATTGGAA-TTAAAAGAGGAAT
1 AACCAATCATT-GAATTTGAAAGAGGAAT
6872377 TGCATGATCG
Statistics
Matches: 104, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
92 97 0.93
93 7 0.07
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.34
Consensus pattern (92 bp):
AACCAATCATTGAATTTGAAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
TCTGATCTGGTTTGATATAAACCACAG
Found at i:6873262 original size:113 final size:113
Alignment explanation
Indices: 6873099--6873844 Score: 979
Period size: 113 Copynumber: 6.7 Consensus size: 113
6873089 GTGCCAGTTC
*
6873099 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * ***
6873164 CAACCTTTTGCTCAAATCCATCACTTGATGGATCAACTTTTCCAGTTC
66 TAACCTTTTGCTCAAATTCATCATTTGATGGATCAACTTTTCCAGAGA
* *
6873212 GAGTTCATAATGAGAAAAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * *
6873277 CAACCTTTTGCTCAAATTCATCATTTGATGGATTAGCTTTTCCAGAAA
66 TAACCTTTTGCTCAAATTCATCATTTGATGGATCAACTTTTCCAGAGA
*
6873325 GAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* ** * * *
6873390 TAACCCTTTGCTTGAATTCATCATTTGATAGATCAGCTTTGCCAGAGA
66 TAACCTTTTGCTCAAATTCATCATTTGATGGATCAACTTTTCCAGAGA
*
6873438 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* ** *
6873503 TAACCCTTTGCTTGAATTCATCATTTGATGGATC-AGTTTTGCCAGAGA
66 TAACCTTTTGCTCAAATTCATCATTTGATGGATCAACTTTT-CCAGAGA
*
6873551 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* ** * **** *
6873616 TAACCCTTTGCTTGAATTCATCATTTGATGGATCAGCAGCGCCAAAGA
66 TAACCTTTTGCTCAAATTCATCATTTGATGGATCAACTTTTCCAGAGA
6873664 GAGTTCATAATGAGAAGAACTCATCTGAAGAA--AAG-A-AAGTTCATAATGAGAAGAACTTGTT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* * * * * *
6873725 TAACCCTTTTGTTCAAATTCATCACTTAATGGATTAACCTTTACAGAGA
66 TAA-CCTTTTGCTCAAATTCATCATTTGATGGATCAACTTTTCCAGAGA
* * * * * *
6873774 AAGTTCATAATGAGAAGAACCCATTTGAAGAA--AAG-A-AAGTTCATAATAAGAAGAGCTTATT
1 GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
6873835 CAACCTTTTG
66 TAACCTTTTG
6873845 GATAACTCTA
Statistics
Matches: 576, Mismatches: 54, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
109 35 0.06
110 89 0.15
111 3 0.01
112 3 0.01
113 446 0.77
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
GAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
TAACCTTTTGCTCAAATTCATCATTTGATGGATCAACTTTTCCAGAGA
Found at i:6873380 original size:24 final size:23
Alignment explanation
Indices: 6873337--6873381 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
6873327 GTTCATAATG
*
6873337 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
6873360 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
6873382 AACTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:6874088 original size:3 final size:3
Alignment explanation
Indices: 6874080--6874154 Score: 114
Period size: 3 Copynumber: 25.0 Consensus size: 3
6874070 ATTGATTTAT
* * * *
6874080 TTA TTA TTA TTA TTA TTA TAA TAA TTA TTA TTA TTA TAA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6874128 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
6874155 AATATATTAA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:6874162 original size:15 final size:15
Alignment explanation
Indices: 6874087--6874163 Score: 69
Period size: 12 Copynumber: 5.3 Consensus size: 15
6874077 TATTTATTAT
6874087 TATTATTATTATAATAA
1 TATTATTATTA-AAT-A
6874104 TTATTATTATTATAA-A
1 -TATTATTATTA-AATA
6874120 TATTATTATT--AT-
1 TATTATTATTAAATA
6874132 TATTATTATT--AT-
1 TATTATTATTAAATA
6874144 TATTATTATTAAATA
1 TATTATTATTAAATA
6874159 TATTA
1 TATTA
6874164 AATATATATG
Statistics
Matches: 55, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
12 23 0.42
14 2 0.04
15 15 0.27
16 1 0.02
18 14 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATTATTATTAAATA
Found at i:6874162 original size:18 final size:19
Alignment explanation
Indices: 6874084--6874163 Score: 112
Period size: 18 Copynumber: 4.3 Consensus size: 19
6874074 ATTTATTTAT
6874084 TATTATTATTATTATAATA
1 TATTATTATTATTATAATA
6874103 -ATTATTATTATTATAA-A
1 TATTATTATTATTATAATA
*
6874120 TATTATTATTATTATTAT-
1 TATTATTATTATTATAATA
6874138 TATTATTATTATTATTAAATA
1 TATTATTATTATTA-T-AATA
6874159 TATTA
1 TATTA
6874164 AATATATATG
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
17 1 0.02
18 45 0.83
19 1 0.02
20 2 0.04
21 5 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTATTATTATTATAATA
Found at i:6875495 original size:13 final size:13
Alignment explanation
Indices: 6875474--6875524 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
6875464 GTCATAAATA
*
6875474 TATTATAAATATT
1 TATTTTAAATATT
*
6875487 TATTTTAAATAAAT
1 TATTTTAAAT-ATT
*
6875501 TATTTT-AACATT
1 TATTTTAAATATT
*
6875513 TATTTTCAATAT
1 TATTTTAAATAT
6875525 CGAAGAAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 8 0.26
13 15 0.48
14 8 0.26
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (13 bp):
TATTTTAAATATT
Found at i:6882443 original size:24 final size:24
Alignment explanation
Indices: 6882415--6882471 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
6882405 GTGGGTTTAC
6882415 TTTATGAAGGAAAATTTAGAGACT
1 TTTATGAAGGAAAATTTAGAGACT
*
6882439 TTTATGAAGGAAAATTTATAGACT
1 TTTATGAAGGAAAATTTAGAGACT
6882463 TTTATGAAG
1 TTTATGAAG
6882472 TTCAAAGAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.40, C:0.04, G:0.19, T:0.37
Consensus pattern (24 bp):
TTTATGAAGGAAAATTTAGAGACT
Found at i:6891861 original size:20 final size:20
Alignment explanation
Indices: 6891836--6891890 Score: 58
Period size: 23 Copynumber: 2.6 Consensus size: 20
6891826 TATTTTATAA
6891836 ATATTAACTT-AAAATATTTT
1 ATATTAACTTAAAAATA-TTT
*
6891856 ATATTATCTTATTAAAATATTT
1 ATATTAACTTA--AAAATATTT
6891878 ATGATTAACTTAA
1 AT-ATTAACTTAA
6891891 TTTAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
20 9 0.31
21 1 0.03
22 5 0.17
23 14 0.48
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (20 bp):
ATATTAACTTAAAAATATTT
Found at i:6891884 original size:23 final size:23
Alignment explanation
Indices: 6891844--6891907 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 23
6891834 AAATATTAAC
*
6891844 TTAAAATATTTTATATTATCTTA
1 TTAAAATATTTTATATTAACTTA
6891867 TTAAAATA-TTTATGATTAACTTAA
1 TTAAAATATTTTAT-ATTAACTT-A
6891891 TTTAAAAATTATTTTAT
1 -TT-AAAA-TATTTTAT
6891908 TTTCATTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
22 5 0.15
23 15 0.44
24 1 0.03
25 2 0.06
26 4 0.12
27 2 0.06
28 5 0.15
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (23 bp):
TTAAAATATTTTATATTAACTTA
Found at i:6891946 original size:17 final size:16
Alignment explanation
Indices: 6891903--6891947 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 16
6891893 TAAAAATTAT
6891903 TTTATTTTCATTTAAAA
1 TTTATTTT-ATTTAAAA
6891920 TATATATTTTATGTTAAAA
1 T-T-TATTTTAT-TTAAAA
6891939 TTTATTTTA
1 TTTATTTTA
6891948 AAATATGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 8 0.32
18 4 0.16
19 13 0.52
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTATTTTATTTAAAA
Found at i:6892452 original size:21 final size:21
Alignment explanation
Indices: 6892422--6892470 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
6892412 ATATATATAT
* *
6892422 ATATATATAATAAATTTTTAA
1 ATATAAATAATAAATTTTAAA
*
6892443 TTATAAATAATAAATTTTAAA
1 ATATAAATAATAAATTTTAAA
6892464 ATATAAA
1 ATATAAA
6892471 ATCTGTATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATAAATAATAAATTTTAAA
Found at i:6897404 original size:50 final size:49
Alignment explanation
Indices: 6897330--6897427 Score: 187
Period size: 50 Copynumber: 2.0 Consensus size: 49
6897320 TGTTTAACCA
6897330 AAACTAATTCAGTCATGTCGTAGATCGACCAAGTCCCATTAAACAAAGC
1 AAACTAATTCAGTCATGTCGTAGATCGACCAAGTCCCATTAAACAAAGC
6897379 AAACTAATTCAGTTCATGTCGTAGATCGACCAAGTCCCATTAAACAAAG
1 AAACTAATTCAG-TCATGTCGTAGATCGACCAAGTCCCATTAAACAAAG
6897428 AGCACAACAA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 12 0.25
50 36 0.75
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.23
Consensus pattern (49 bp):
AAACTAATTCAGTCATGTCGTAGATCGACCAAGTCCCATTAAACAAAGC
Found at i:6903076 original size:15 final size:16
Alignment explanation
Indices: 6903056--6903100 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
6903046 GAATATTATT
6903056 AATTTAATTTATAAA-
1 AATTTAATTTATAAAG
*
6903071 AATTTAAATTATAAAG
1 AATTTAATTTATAAAG
* *
6903087 AATTCAATGTATAA
1 AATTTAATTTATAA
6903101 TTAATATTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (16 bp):
AATTTAATTTATAAAG
Found at i:6904308 original size:49 final size:49
Alignment explanation
Indices: 6904249--6904342 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 49
6904239 AGCACCTCTA
* **
6904249 AGGGGCGGACCTCCATGGAGTCCGGGGTATCCCGGGCAACCCCTCATCC
1 AGGGGCGGACCTCCATGGAGCCCGGGGTATCCCAAGCAACCCCTCATCC
* *
6904298 AGGGGTGGACCTCCATGGTGCCCGGGGTATCCCAAGCAACCCCTC
1 AGGGGCGGACCTCCATGGAGCCCGGGGTATCCCAAGCAACCCCTC
6904343 CATAAGTGCC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.17, C:0.36, G:0.32, T:0.15
Consensus pattern (49 bp):
AGGGGCGGACCTCCATGGAGCCCGGGGTATCCCAAGCAACCCCTCATCC
Found at i:6905587 original size:2 final size:2
Alignment explanation
Indices: 6905580--6905615 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
6905570 AGCTTTGTCA
*
6905580 AT AT AT AT AT AT A- AT AT AT AT AG AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6905616 ATCCTTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:6908111 original size:2 final size:2
Alignment explanation
Indices: 6908104--6908138 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
6908094 TAGGTCATTA
6908104 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6908139 AAAATGTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6911696 original size:15 final size:15
Alignment explanation
Indices: 6911676--6911706 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6911666 CAACAGATAG
6911676 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
6911691 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
6911706 A
1 A
6911707 TTTAGAGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:6915387 original size:20 final size:19
Alignment explanation
Indices: 6915362--6915428 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
6915352 ATACAGGTTC
*
6915362 GAAACTTTGAAGAAAGTTTT
1 GAAACTTTG-AGAAAGTTTA
*
6915382 GAAACTTTTGAGAAAGATTA
1 GAAAC-TTTGAGAAAGTTTA
* *
6915402 GAAACTTTGTA-AAAGTATC
1 GAAACTTTG-AGAAAGTTTA
6915421 GAAACTTT
1 GAAACTTT
6915429 TAAACGTACT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 17 0.43
20 19 0.47
21 4 0.10
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (19 bp):
GAAACTTTGAGAAAGTTTA
Found at i:6915651 original size:20 final size:20
Alignment explanation
Indices: 6915628--6915665 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6915618 TATTTAAAAA
6915628 ACTTTAAACACATTTTAAAC
1 ACTTTAAACACATTTTAAAC
*
6915648 ACTTTAAACATATTTTAA
1 ACTTTAAACACATTTTAA
6915666 TTAACTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (20 bp):
ACTTTAAACACATTTTAAAC
Found at i:6917080 original size:19 final size:21
Alignment explanation
Indices: 6917037--6917085 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
6917027 TTTAAATTCT
* *
6917037 TTTTCAAAATTTCATTTTTGA
1 TTTTCAAAATTCCATTTTAGA
6917058 TTTTCAAAA-TCCATTTTAG-
1 TTTTCAAAATTCCATTTTAGA
6917077 TTTTCAAAA
1 TTTTCAAAA
6917086 GAAAATCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 8 0.31
21 9 0.35
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.51
Consensus pattern (21 bp):
TTTTCAAAATTCCATTTTAGA
Found at i:6917975 original size:27 final size:21
Alignment explanation
Indices: 6917922--6917973 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
6917912 ACTAATTTGT
6917922 TCTTACCTTTCAAGGATAAGG
1 TCTTACCTTTCAAGGATAAGG
6917943 TCTTACCTTTCAAGGATAAGG
1 TCTTACCTTTCAAGGATAAGG
* *
6917964 TGTAACCTTT
1 TCTTACCTTT
6917974 ACAACTCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (21 bp):
TCTTACCTTTCAAGGATAAGG
Found at i:6918313 original size:20 final size:20
Alignment explanation
Indices: 6918290--6918327 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6918280 TGCAGTTTAG
6918290 AAACTTTGAAGAAAGTTTCA
1 AAACTTTGAAGAAAGTTTCA
*
6918310 AAACTTTTAAGAAAGTTT
1 AAACTTTGAAGAAAGTTT
6918328 GTGAAAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (20 bp):
AAACTTTGAAGAAAGTTTCA
Found at i:6918606 original size:20 final size:20
Alignment explanation
Indices: 6918579--6918624 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
6918569 TTGTTTCATA
6918579 TTTAAAAAGCTTTAAACACAT
1 TTTAAAAA-CTTTAAACACAT
*
6918600 TTTAAAAACTTTAAACATAT
1 TTTAAAAACTTTAAACACAT
6918620 TTTAA
1 TTTAA
6918625 GTAACTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.48, C:0.11, G:0.02, T:0.39
Consensus pattern (20 bp):
TTTAAAAACTTTAAACACAT
Found at i:6922569 original size:31 final size:30
Alignment explanation
Indices: 6922534--6922608 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
6922524 ATTCAGGGGT
* * * * *
6922534 TAATATGAGAAAAGTAGCTAAATTTAATGAC
1 TAATATGAGAAAA-AAACGAAATTCAATAAC
6922565 TAATATG-GAACAAAAACGAAATTCAATAAC
1 TAATATGAGAA-AAAAACGAAATTCAATAAC
6922595 TAATATGAGAAAAA
1 TAATATGAGAAAAA
6922609 TAAACAATGT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
30 25 0.68
31 12 0.32
ACGTcount: A:0.55, C:0.08, G:0.13, T:0.24
Consensus pattern (30 bp):
TAATATGAGAAAAAAACGAAATTCAATAAC
Found at i:6929307 original size:30 final size:30
Alignment explanation
Indices: 6929271--6929333 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
6929261 TATTTCTGTT
6929271 GGTCCAGTGAGTCCTGGTCCTGGTAGTGGG
1 GGTCCAGTGAGTCCTGGTCCTGGTAGTGGG
*
6929301 GGTCCAGTGTGTCCTGGTCCTGGTAGTGGG
1 GGTCCAGTGAGTCCTGGTCCTGGTAGTGGG
6929331 GGT
1 GGT
6929334 TTGATCCGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.08, C:0.19, G:0.44, T:0.29
Consensus pattern (30 bp):
GGTCCAGTGAGTCCTGGTCCTGGTAGTGGG
Found at i:6932740 original size:41 final size:41
Alignment explanation
Indices: 6932695--6932896 Score: 377
Period size: 41 Copynumber: 4.9 Consensus size: 41
6932685 ACGCGATAGT
*
6932695 CGAAGTTCGCGTTGCGATTCATTCCAAATCGTTGCGACAGG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
6932736 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
6932777 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
6932818 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
1 CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
*
6932859 CGAAGTTCGCGTTGCGATTCATTCCAAATTCGTCGCGA
1 CGAAGTTCGCGTTGCGATTCATTCC-AATTCGTTGCGA
6932897 TAGTCCAAAT
Statistics
Matches: 158, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
41 147 0.93
42 11 0.07
ACGTcount: A:0.20, C:0.25, G:0.26, T:0.29
Consensus pattern (41 bp):
CGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCGACAGG
Found at i:6933022 original size:3 final size:3
Alignment explanation
Indices: 6933014--6933039 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6933004 CGAGACTGGA
6933014 CGG CGG CGG CGG CGG CGG CGG CGG CG
1 CGG CGG CGG CGG CGG CGG CGG CGG CG
6933040 CGCGAGAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.65, T:0.00
Consensus pattern (3 bp):
CGG
Found at i:6934484 original size:13 final size:15
Alignment explanation
Indices: 6934452--6934486 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
6934442 ATTTTTAATG
6934452 AATATTAAATAAAAT
1 AATATTAAATAAAAT
6934467 AATATTAAA-AAAAT
1 AATATTAAATAAAAT
6934481 -ATATTA
1 AATATTA
6934487 TTAGTGGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 6 0.30
14 5 0.25
15 9 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AATATTAAATAAAAT
Found at i:6945298 original size:2 final size:2
Alignment explanation
Indices: 6945291--6945318 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6945281 GGATCCTGTC
6945291 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
6945319 GTGTGTCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6955201 original size:43 final size:43
Alignment explanation
Indices: 6955133--6955227 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 43
6955123 CTAAAGTTCA
6955133 CGGCGTTTGTTAACGAAAACGCCGCAATAGGTGACGATATATAG
1 CGGCGTTTGTTAAC-AAAACGCCGCAATAGGTGACGATATATAG
** * *
6955177 CGGCGTTTGTTGAA-AAAACGCCGCAATAGGTGTTGCTATTTAG
1 CGGCGTTTGTT-AACAAAACGCCGCAATAGGTGACGATATATAG
6955220 CGGCGTTT
1 CGGCGTTT
6955228 ATCTTAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
43 33 0.72
44 11 0.24
45 2 0.04
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.27
Consensus pattern (43 bp):
CGGCGTTTGTTAACAAAACGCCGCAATAGGTGACGATATATAG
Found at i:6955237 original size:43 final size:43
Alignment explanation
Indices: 6955148--6955261 Score: 140
Period size: 43 Copynumber: 2.7 Consensus size: 43
6955138 TTTGTTAACG
** * * *
6955148 AAAACGCCGCAATAGGTGACGATATATAGCGGCGTTTGTTGAA
1 AAAACGCCGCAATAGGTGTTGCTATTTAGCGGCGTTTATTGAA
*
6955191 AAAACGCCGCAATAGGTGTTGCTATTTAGCGGCGTTTATCT-TA
1 AAAACGCCGCAATAGGTGTTGCTATTTAGCGGCGTTTAT-TGAA
* *
6955234 AAAATGACGCAATAGGTGTTGCTATTTA
1 AAAACGCCGCAATAGGTGTTGCTATTTA
6955262 ACTATGATAA
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
43 61 0.98
44 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.29
Consensus pattern (43 bp):
AAAACGCCGCAATAGGTGTTGCTATTTAGCGGCGTTTATTGAA
Found at i:6955800 original size:17 final size:18
Alignment explanation
Indices: 6955780--6955821 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
6955770 AAAATTTTAA
6955780 TTTTTTTAAAAATAGT-T
1 TTTTTTTAAAAATAGTAT
* *
6955797 TTTTTTCAAAAATTGTAT
1 TTTTTTTAAAAATAGTAT
6955815 TTTTTTT
1 TTTTTTT
6955822 CTTTTTTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (18 bp):
TTTTTTTAAAAATAGTAT
Found at i:6958201 original size:29 final size:29
Alignment explanation
Indices: 6958168--6958238 Score: 142
Period size: 29 Copynumber: 2.4 Consensus size: 29
6958158 TTAGTTCGTG
6958168 AGTTTGAGTCGAGTTGAGCTTACTTTTAA
1 AGTTTGAGTCGAGTTGAGCTTACTTTTAA
6958197 AGTTTGAGTCGAGTTGAGCTTACTTTTAA
1 AGTTTGAGTCGAGTTGAGCTTACTTTTAA
6958226 AGTTTGAGTCGAG
1 AGTTTGAGTCGAG
6958239 CTCAGCAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (29 bp):
AGTTTGAGTCGAGTTGAGCTTACTTTTAA
Found at i:6959607 original size:162 final size:165
Alignment explanation
Indices: 6959340--6959666 Score: 633
Period size: 162 Copynumber: 2.0 Consensus size: 165
6959330 TGAGAATAAG
6959340 TATGTTCAATTATTTAAAGACATCGAAATCAGGCCGTAGATCCAATTTAACAGTTTTTTAGGTGA
1 TATGTTCAATTATTTAAAGACATCGAAATCAGGCCGTAGATCCAATTTAACAGTTTTTTAGGTGA
6959405 ATTTAATTAAAAAACATAGTCTTTTTCTTATTCCCAAATTTTAT-TGAAATCAA-TTTAGGATTA
66 ATTTAATTAAAAAACATAGTCTTTTTCTTATTCCCAAATTTTATATGAAATCAATTTTAGGATTA
6959468 CACTTAATAGGATACCC-TTTATTTTAAGATTATC
131 CACTTAATAGGATACCCTTTTATTTTAAGATTATC
6959502 TATGTTCAATTATTTAAAGACATCGAAATCAGGCCGTAGATCCAATTTAACAGTTTTTTAGGTGA
1 TATGTTCAATTATTTAAAGACATCGAAATCAGGCCGTAGATCCAATTTAACAGTTTTTTAGGTGA
6959567 ATTTAATTAAAAAACATAGTCTTTTTCTTATTCCCAAATTTTATATGAAATCAATTTTAGGATTA
66 ATTTAATTAAAAAACATAGTCTTTTTCTTATTCCCAAATTTTATATGAAATCAATTTTAGGATTA
6959632 CACTTAATAGGATACCCTTTTATTTTAAGATTATC
131 CACTTAATAGGATACCCTTTTATTTTAAGATTATC
6959667 GGAAGTGACA
Statistics
Matches: 162, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
162 109 0.67
163 9 0.06
164 27 0.17
165 17 0.10
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.40
Consensus pattern (165 bp):
TATGTTCAATTATTTAAAGACATCGAAATCAGGCCGTAGATCCAATTTAACAGTTTTTTAGGTGA
ATTTAATTAAAAAACATAGTCTTTTTCTTATTCCCAAATTTTATATGAAATCAATTTTAGGATTA
CACTTAATAGGATACCCTTTTATTTTAAGATTATC
Found at i:6960329 original size:49 final size:49
Alignment explanation
Indices: 6960258--6960563 Score: 260
Period size: 49 Copynumber: 6.2 Consensus size: 49
6960248 AGATTTTTCA
* ** * **
6960258 CTGCTCTACAGGGTAGGTCAGATTAGGAAAAGAAGGGTGATCTGCTCTA
1 CTGCTCTTCAGGGTAGGTCAGATTAGGAAAAGAAATGAGATCTGCTCCG
* * *
6960307 CTGCTATTCAGGGTAGGTCAGATGAGGAAAAGAAATGAGATTTGCTCCG
1 CTGCTCTTCAGGGTAGGTCAGATTAGGAAAAGAAATGAGATCTGCTCCG
* * * * * * *
6960356 TTTCTCTTCACGGTAGGTTAGA-TCGAAAAGAGAAATGAGATATGCTCCG
1 CTGCTCTTCAGGGTAGGTCAGATTAGGAAA-AGAAATGAGATCTGCTCCG
* * * **
6960405 CTGCTTTTCAAGGTAGGTTAGATCGGGAAAAG-AATGAGGATCTGCTCCG
1 CTGCTCTTCAGGGTAGGTCAGATTAGGAAAAGAAATGA-GATCTGCTCCG
* * * * **
6960454 CTGCTCTTAAGGGTAGGTCAGA-TCGAGAAAAGAATTGAGATTTGCTATG
1 CTGCTCTTCAGGGTAGGTCAGATTAG-GAAAAGAAATGAGATCTGCTCCG
* * * *
6960503 CTTCTCTTCAGGGTAGGTCAGATCAGGAAAAG-AATGGTGATCTGCTCCA
1 CTGCTCTTCAGGGTAGGTCAGATTAGGAAAAGAAAT-GAGATCTGCTCCG
*
6960552 TTGCTCTTCAGG
1 CTGCTCTTCAGG
6960564 AAAAGAAGTG
Statistics
Matches: 202, Mismatches: 48, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
48 12 0.06
49 181 0.90
50 9 0.04
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27
Consensus pattern (49 bp):
CTGCTCTTCAGGGTAGGTCAGATTAGGAAAAGAAATGAGATCTGCTCCG
Found at i:6960526 original size:147 final size:148
Alignment explanation
Indices: 6960269--6960535 Score: 360
Period size: 147 Copynumber: 1.8 Consensus size: 148
6960259 TGCTCTACAG
* * * *
6960269 GGTAGGTCAGATTAGGAAAAGAAGGGTGATCTGCTCTACTGCTATTCAGGGTAGGTCAGATGAGG
1 GGTAGGTCAGATCAGGAAAAGAAGAGTGATCTGCTCCACTGCTATTAAGGGTAGGTCAGATGAGG
* * *
6960334 AAAAGAAATGAGATTTGCTCCGTTTCTCTTCACGGTAGGTTAGATC-GAAAAGAGAAATGAGATA
66 AAAAGAAATGAGATTTGCTACGCTTCTCTTCACGGTAGGTCAGATCAGAAAAGAGAAATGAGATA
6960398 TGCTCCGCTGCTTTTCAA
131 TGCTCCGCTGCTTTTCAA
* * * *
6960416 GGTAGGTTAGATCGGGAAAAGAATGAG-GATCTGCTCCGCTGCTCTTAAGGGTAGGTCAGATCGA
1 GGTAGGTCAGATCAGGAAAAGAA-GAGTGATCTGCTCCACTGCTATTAAGGGTAGGTCAGAT-GA
* * *
6960480 -GAAAAGAATTGAGATTTGCTATGCTTCTCTTCAGGGTAGGTCAGATCAGGAAAAGA
64 GGAAAAGAAATGAGATTTGCTACGCTTCTCTTCACGGTAGGTCAGATCA-GAAAAGA
6960536 ATGGTGATCT
Statistics
Matches: 102, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
147 91 0.89
148 4 0.04
149 7 0.07
ACGTcount: A:0.30, C:0.15, G:0.29, T:0.26
Consensus pattern (148 bp):
GGTAGGTCAGATCAGGAAAAGAAGAGTGATCTGCTCCACTGCTATTAAGGGTAGGTCAGATGAGG
AAAAGAAATGAGATTTGCTACGCTTCTCTTCACGGTAGGTCAGATCAGAAAAGAGAAATGAGATA
TGCTCCGCTGCTTTTCAA
Found at i:6968707 original size:6 final size:6
Alignment explanation
Indices: 6968696--6968738 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
6968686 AATAAACTTT
* **
6968696 AGGGCA ATGGCA TTGGCA AGGGCA AGGGCA AGGGCA AGGGCA A
1 AGGGCA AGGGCA AGGGCA AGGGCA AGGGCA AGGGCA AGGGCA A
6968739 TGAAGGTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.16, G:0.44, T:0.07
Consensus pattern (6 bp):
AGGGCA
Found at i:6975575 original size:24 final size:24
Alignment explanation
Indices: 6975540--6975604 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
6975530 TTGCCTGAGC
*
6975540 CCACTA-ACATGATCCTGGATG-ACA
1 CCACTAGA-ATGATCAT-GATGCACA
* *
6975564 CCACTAGAATGATCATGTTGCCCA
1 CCACTAGAATGATCATGATGCACA
6975588 CCACTAGAATGATCATG
1 CCACTAGAATGATCATG
6975605 TTGCCATTAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 3 0.08
24 32 0.89
25 1 0.03
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (24 bp):
CCACTAGAATGATCATGATGCACA
Found at i:6975605 original size:24 final size:24
Alignment explanation
Indices: 6975562--6975609 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
6975552 TCCTGGATGA
6975562 CACCACTAGAATGATCATGTTGCC
1 CACCACTAGAATGATCATGTTGCC
6975586 CACCACTAGAATGATCATGTTGCC
1 CACCACTAGAATGATCATGTTGCC
6975610 ATTAGCATAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.25
Consensus pattern (24 bp):
CACCACTAGAATGATCATGTTGCC
Found at i:6978299 original size:21 final size:21
Alignment explanation
Indices: 6978256--6978300 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
6978246 CGGTAAAAAA
* *
6978256 TTACCTAAAACATTATTATTT
1 TTACCTAAAACATAATTAGTT
6978277 TTACCTAAAACATCAATT-GTT
1 TTACCTAAAACAT-AATTAGTT
6978298 TTA
1 TTA
6978301 ACATTTTCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.44
Consensus pattern (21 bp):
TTACCTAAAACATAATTAGTT
Found at i:6981608 original size:29 final size:25
Alignment explanation
Indices: 6981548--6981617 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 25
6981538 CTAAATATGT
6981548 TTTTATTTATTTTAATTTGGCCATG
1 TTTTATTTATTTTAATTTGGCCATG
6981573 CAATTTTAATTTATTTTAATTTAGTGTCCATG
1 ---TTTT-ATTTATTTTAATTT-G-G-CCATG
6981605 TTTTATTTATTTT
1 TTTTATTTATTTT
6981618 TATTATTAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
28 13 0.34
29 18 0.47
30 1 0.03
31 1 0.03
32 5 0.13
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.61
Consensus pattern (25 bp):
TTTTATTTATTTTAATTTGGCCATG
Found at i:6982417 original size:131 final size:131
Alignment explanation
Indices: 6982243--6982574 Score: 432
Period size: 131 Copynumber: 2.5 Consensus size: 131
6982233 CATTTTGGTC
*
6982243 GGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTTGATA
1 GGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATA
* ** * * * * * * *
6982308 TTGTTGTTTTCTCTAGAATTAATATCT-ATTTTTAAGATGGAATAATGATAACTCTTTATTTCGA
66 TTATCATTTTCACTAGAATCAATAT-TGAATTTTAAGACGAAATAATAATAACTCTTTATTTCAA
6982372 TT
130 TT
* * *
6982374 GGAGCAATAAATGACTGCTTTAAGGTATGAGAGGTCATTTATTCTCGATTGAAAATAATTAGATA
1 GGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATA
* * *
6982439 TTATCATTTTCACTTGAATCAATATTGAATTTTAAGACGAAATAGTAATATCTCTTTATTTCAAT
66 TTATCATTTTCACTAGAATCAATATTGAATTTTAAGACGAAATAATAATAACTCTTTATTTCAAT
6982504 T
131 T
* * * ** * *
6982505 GGGGTAATAAATGATTGTTTTATTGCACGAAAGGTCATTTATTCTCGATTGGAAATAATTAGATA
1 GGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATA
6982570 TTATC
66 TTATC
6982575 GTTCACTCTT
Statistics
Matches: 173, Mismatches: 27, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
130 1 0.01
131 172 0.99
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (131 bp):
GGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATA
TTATCATTTTCACTAGAATCAATATTGAATTTTAAGACGAAATAATAATAACTCTTTATTTCAAT
T
Found at i:6984489 original size:29 final size:30
Alignment explanation
Indices: 6984432--6984503 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
6984422 GAGGGCTGGA
* * *
6984432 AACCGGTTTGACCGGTTTTCAATCGGTTCTG
1 AACCGATTTGACCAGTTTTCAATCAGTTC-G
*
6984463 -ACCGATTTGACCAG-TTTCGATCAGTTCG
1 AACCGATTTGACCAGTTTTCAATCAGTTCG
6984491 AACCGATTTGACC
1 AACCGATTTGACC
6984504 GGTCTGACCC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 23 0.64
30 12 0.33
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (30 bp):
AACCGATTTGACCAGTTTTCAATCAGTTCG
Found at i:6984524 original size:14 final size:14
Alignment explanation
Indices: 6984507--6984535 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6984497 TTTGACCGGT
6984507 CTGACCCGACCCGA
1 CTGACCCGACCCGA
6984521 CTGACCCGACCCGA
1 CTGACCCGACCCGA
6984535 C
1 C
6984536 CGTTGACTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.52, G:0.21, T:0.07
Consensus pattern (14 bp):
CTGACCCGACCCGA
Found at i:6993222 original size:287 final size:286
Alignment explanation
Indices: 6992849--6993423 Score: 1093
Period size: 288 Copynumber: 2.0 Consensus size: 286
6992839 AAATCCGTTT
6992849 AATTTCCTCATTAAACTTAACATAATTAGCATTTTATCCTCAACAGTTAAATATTTAACGGCGTT
1 AATTTCCTCATTAAACTTAACATAATTAGCATTTTATCCTCAACAGTTAAATATTTAACGGCGTT
6992914 AAAACGATGCTATTTTAGAAAAAC-AAATTTTCACTAAAATGACGTCGTTTTTGCATCTATATAA
66 AAAACGATGCTATTTTAGAAAAACAAAATTTTCACTAAAATGACGTCG-TTTTGCATCTATATAA
6992978 CAGATCATTTATAAGGTCG-TTATTGAGAAAACGACAGAATGACCAAAAAAGCTAATTATATTAA
130 CAGATCATTTATAAGGTCGTTTATTGAGAAAACGACAGAATGACCAAAAAAGCTAATTATATTAA
6993042 GTTCAGTGAGGAAATTGAATGGATTTAAATTACA-TGAGTGAAATAGCAAAGAGAATAAAGTTAT
195 GTTCAGTGAGGAAATTGAATGGATTTAAATTACAGTGAGTGAAATAGCAAAGAGAATAAAGTTAT
6993106 GTCATGATTGATGTAATTTACCCAAAA
260 GTCATGATTGATGTAATTTACCCAAAA
6993133 AATTTCCTCATTAAACTTAACATAATTAGCATTTTTAATCACTCAACAGTTAAATATTTAACGGC
1 AATTTCCTCATTAAACTTAACATAATTAGCA-TTTT-ATC-CTCAACAGTTAAATATTTAACGGC
6993198 GTTAAAACGATGCTATTTTAGAAAAACAAAATTTTCACTAAAATGACGTCGTTTTGCATCTATAT
63 GTTAAAACGATGCTATTTTAGAAAAACAAAATTTTCACTAAAATGACGTCGTTTTGCATCTATAT
6993263 AACAGATCATTTATAAGGTCGTTTATTGAGAAAACGACAGAATGACCAAAAAAGCTAATTATATT
128 AACAGATCATTTATAAGGTCGTTTATTGAGAAAACGACAGAATGACCAAAAAAGCTAATTATATT
6993328 AAGTTCAGTGAGGAAATTGAATGGATTTAAATTACAGTGAGTGAAATAGCAAAGAGAATAAAGTT
193 AAGTTCAGTGAGGAAATTGAATGGATTTAAATTACAGTGAGTGAAATAGCAAAGAGAATAAAGTT
6993393 ATGTCATGATTGATGTAATTTACCCAAAA
258 ATGTCATGATTGATGTAATTTACCCAAAA
6993422 AA
1 AA
6993424 ATTAATGATC
Statistics
Matches: 285, Mismatches: 0, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
284 31 0.11
285 4 0.01
286 3 0.01
287 86 0.30
288 102 0.36
289 59 0.21
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (286 bp):
AATTTCCTCATTAAACTTAACATAATTAGCATTTTATCCTCAACAGTTAAATATTTAACGGCGTT
AAAACGATGCTATTTTAGAAAAACAAAATTTTCACTAAAATGACGTCGTTTTGCATCTATATAAC
AGATCATTTATAAGGTCGTTTATTGAGAAAACGACAGAATGACCAAAAAAGCTAATTATATTAAG
TTCAGTGAGGAAATTGAATGGATTTAAATTACAGTGAGTGAAATAGCAAAGAGAATAAAGTTATG
TCATGATTGATGTAATTTACCCAAAA
Found at i:6993481 original size:18 final size:19
Alignment explanation
Indices: 6993455--6993491 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
6993445 ACGTTAACAT
6993455 GTTGATTGAGA-TATGATA
1 GTTGATTGAGATTATGATA
*
6993473 GTTGCTTGAGATTATGATA
1 GTTGATTGAGATTATGATA
6993492 TTATATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.30, C:0.03, G:0.27, T:0.41
Consensus pattern (19 bp):
GTTGATTGAGATTATGATA
Found at i:7005165 original size:23 final size:23
Alignment explanation
Indices: 7005139--7005184 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
7005129 AAACTTACCA
7005139 AAAAACATAAAAAAATGTGTCAT
1 AAAAACATAAAAAAATGTGTCAT
** **
7005162 AAAAGTATATGAAAATGTGTCAT
1 AAAAACATAAAAAAATGTGTCAT
7005185 TCAGGCAAAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.54, C:0.07, G:0.13, T:0.26
Consensus pattern (23 bp):
AAAAACATAAAAAAATGTGTCAT
Found at i:7010063 original size:16 final size:18
Alignment explanation
Indices: 7010042--7010077 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
7010032 TCTCTAAATA
7010042 ATTTT-AATATAATT-AT
1 ATTTTAAATATAATTCAT
7010058 ATTTTAAATATAATTCAT
1 ATTTTAAATATAATTCAT
7010076 AT
1 AT
7010078 ATAAATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 9 0.50
18 4 0.22
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTAAATATAATTCAT
Found at i:7010082 original size:17 final size:17
Alignment explanation
Indices: 7010047--7010085 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
7010037 AAATAATTTT
*
7010047 AATATAATTATATTTTA
1 AATATAATTATATTATA
7010064 AATATAATTCATA-TATA
1 AATATAATT-ATATTATA
7010081 AATAT
1 AATAT
7010086 TTGAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
AATATAATTATATTATA
Found at i:7010187 original size:2 final size:2
Alignment explanation
Indices: 7010180--7010273 Score: 181
Period size: 2 Copynumber: 47.5 Consensus size: 2
7010170 TTACCTAAAT
7010180 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7010222 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7010263 TA TA TA TA TA T
1 TA TA TA TA TA T
7010274 GTTTGTTTTA
Statistics
Matches: 91, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 90 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7013542 original size:35 final size:35
Alignment explanation
Indices: 7013503--7013585 Score: 130
Period size: 35 Copynumber: 2.4 Consensus size: 35
7013493 CAAAACAATC
*
7013503 ATCAATTTCATTCTAAACCCCAATTTCCAAAATAA
1 ATCAATTTCATTCTAAACCCCAAATTCCAAAATAA
*
7013538 ATCAATTTCATTCTAAACCCTAAATTCCAAAATAA
1 ATCAATTTCATTCTAAACCCCAAATTCCAAAATAA
* *
7013573 TTCAATTTAATTC
1 ATCAATTTCATTC
7013586 AATTATGTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (35 bp):
ATCAATTTCATTCTAAACCCCAAATTCCAAAATAA
Found at i:7014119 original size:129 final size:130
Alignment explanation
Indices: 7013975--7014221 Score: 406
Period size: 129 Copynumber: 1.9 Consensus size: 130
7013965 TATTTATATA
* **
7013975 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
7014040 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCA-CACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
7014104 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * * *
7014169 TTAACACATGATCATGATATATGTTATTGGTGACACGTGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
7014222 GAAGAAAATT
Statistics
Matches: 108, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
129 98 0.91
130 10 0.09
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:7014581 original size:29 final size:28
Alignment explanation
Indices: 7014548--7014606 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
7014538 AGTTGATACA
*
7014548 ATATTTTAAAAGATAAATTTAAGATTTAT
1 ATATTTTAAAA-ATAAATTTAAGAATTAT
* * *
7014577 ATATTTTTAAACTAAATTTAATAATTAT
1 ATATTTTAAAAATAAATTTAAGAATTAT
7014605 AT
1 AT
7014607 TTTCATATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (28 bp):
ATATTTTAAAAATAAATTTAAGAATTAT
Found at i:7014705 original size:16 final size:18
Alignment explanation
Indices: 7014684--7014717 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
7014674 ATTTCTTATT
7014684 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
7014700 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
7014718 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:7016872 original size:15 final size:16
Alignment explanation
Indices: 7016838--7016870 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
7016828 AATAATATTT
7016838 AAATATAAAACAAGTA
1 AAATATAAAACAAGTA
7016854 AAAT-TAAAACAA-TA
1 AAATATAAAACAAGTA
7016868 AAA
1 AAA
7016871 ATACAATTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 8 0.47
16 4 0.24
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.18
Consensus pattern (16 bp):
AAATATAAAACAAGTA
Found at i:7018202 original size:3 final size:3
Alignment explanation
Indices: 7018194--7018281 Score: 103
Period size: 3 Copynumber: 30.3 Consensus size: 3
7018184 AATTATTTTT
* *
7018194 TAA TAA TAA TAA TAA T-A TATA TAA TAA TAA TAA TAA T-A TTA TTA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
* *
7018238 TTA TAA TAA TAA T-A TTA TAA TAA TAA T-A TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
7018282 GGGTAAAAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
2 8 0.10
3 67 0.86
4 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:7018243 original size:17 final size:17
Alignment explanation
Indices: 7018202--7018281 Score: 97
Period size: 17 Copynumber: 4.6 Consensus size: 17
7018192 TTTAATAATA
* *
7018202 ATAATAATATATATAATA
1 ATAATAATA-ATATTATT
7018220 ATAATAATAATATTATT
1 ATAATAATAATATTATT
* *
7018237 ATTATAATAATAATATT
1 ATAATAATAATATTATT
* *
7018254 ATAATAATAATATAATA
1 ATAATAATAATATTATT
7018271 ATAATAATAAT
1 ATAATAATAAT
7018282 GGGTAAAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
17 45 0.83
18 9 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATAATAATATTATT
Found at i:7018245 original size:14 final size:14
Alignment explanation
Indices: 7018199--7018279 Score: 112
Period size: 14 Copynumber: 5.9 Consensus size: 14
7018189 TTTTTTAATA
7018199 ATAATAATAATATAT
1 ATAATAATAATAT-T
7018214 ATAATAATAATA--
1 ATAATAATAATATT
* *
7018226 ATAATATTATTATT
1 ATAATAATAATATT
7018240 ATAATAATAATATT
1 ATAATAATAATATT
*
7018254 ATAATAATAATATA
1 ATAATAATAATATT
7018268 ATAATAATAATA
1 ATAATAATAATA
7018280 ATGGGTAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
12 10 0.17
14 37 0.63
15 12 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAATAATATT
Found at i:7018564 original size:122 final size:119
Alignment explanation
Indices: 7018427--7018698 Score: 343
Period size: 124 Copynumber: 2.3 Consensus size: 119
7018417 TCTTCTCTTT
* * * *
7018427 CTTCAAATGAGTTCTTCTCATTATGAACTTTCCGCTGAGGAA-GATG-T-TGACCTATTTCCTTC
1 CTTCAGATGAGTTCTTCTCATTATGAACTTT-CGCTG-GAAAGGATGCTCTAACCTATCTCCTTC
* *
7018489 TGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTCTTCTTTCTC
64 TGTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAA---CTT-TTTCTC
* * * *
7018549 CTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGCTGCTAATCTATCTGCTTCT
1 CTTCAGATGAGTTCTTCTCATTATGAACTTTCGCTGGAAAGGATGCT-CTAACCTATCTCCTTCT
* * *
7018614 GTGATAGAATTATGCAAAAGGTTGAATAAGCTCTTCTCATTGTGAACTTTTTCTT
65 GTGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTTTTCTC
7018669 CTTCAGATGAGTTCTTCTCATTATGAACTT
1 CTTCAGATGAGTTCTTCTCATTATGAACTT
7018699 CTTCTTTTTC
Statistics
Matches: 133, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
120 38 0.29
121 10 0.08
122 31 0.23
124 54 0.41
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.40
Consensus pattern (119 bp):
CTTCAGATGAGTTCTTCTCATTATGAACTTTCGCTGGAAAGGATGCTCTAACCTATCTCCTTCTG
TGATAGAATCATGCAAAAGGTTGAATAAGCTCTTCTCATTATGAACTTTTTCTC
Found at i:7018685 original size:36 final size:36
Alignment explanation
Indices: 7018645--7018736 Score: 157
Period size: 36 Copynumber: 2.6 Consensus size: 36
7018635 TTGAATAAGC
* *
7018645 TCTTCTCATTGTGAACTTTTTCTTCTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
*
7018681 TCTTCTCATTATGAACTTCTTCTTTTTCAGATGAGT
1 TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
7018717 TCTTCTCATTATGAACTTCT
1 TCTTCTCATTATGAACTTCT
7018737 CTGGAAAAGC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.18, C:0.21, G:0.11, T:0.50
Consensus pattern (36 bp):
TCTTCTCATTATGAACTTCTTCTTCTTCAGATGAGT
Found at i:7018702 original size:17 final size:17
Alignment explanation
Indices: 7018680--7018736 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
7018670 TTCAGATGAG
7018680 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
** *
7018697 TTCTTCTTTTTCA-GATGAG
1 TTCTTCTCATT-ATGA--AC
7018716 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
7018733 TTCT
1 TTCT
7018737 CTGGAAAAGC
Statistics
Matches: 30, Mismatches: 6, Indels: 8
0.68 0.14 0.18
Matches are distributed among these distances:
17 16 0.53
18 2 0.07
19 12 0.40
ACGTcount: A:0.19, C:0.21, G:0.09, T:0.51
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:7018982 original size:113 final size:108
Alignment explanation
Indices: 7018680--7019109 Score: 463
Period size: 113 Copynumber: 3.9 Consensus size: 108
7018670 TTCAGATGAG
* *
7018680 TTCTTCTCATTATGAAC-TTCTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTC-TCTGGAA
1 TTCTTCTCATTATGAACTTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TCAACTGGAA
* * * *
7018743 AAGCTGATCTATCAAGTGATGGTTTGAGCAAAA-GTTGAACAAA
65 AAGCTGATCCATCAAATGATGATTTGAACAAAAGGTTGAACAAA
* *
7018786 TTCTTCTTATTATGAA-TTTCTTCTTCTTCAGATGACAAGTTCTTCTCATTATGAACTCTACCTG
1 TTCTTCTCATTATGAACTTTCTTCTTCTTCAGATG---AGTTCTTCTCATTATGAACTC-AACTG
* * * * *
7018850 GCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAA
62 GAAAAGCTGATCCATCAAATGATG-ATTTGAACAAAAGGTTGAACAAA
*
7018898 TTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTCGAACTG
1 TTCTTCTCATTATGAAC-T-TTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAACTC-AACTG
* *
7018963 GTAAAGCTGATCCATCAAATGATGGATTTGATCAAAAGGTTGAACAAA
62 GAAAAGCTGATCCATCAAATGAT-GATTTGAACAAAAGGTTGAACAAA
* * * ***
7019011 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTTATTATGAACTTTTTTTC
1 TTCTTCTCATTATGAA-CT-TTCTT-CTTCTTCAGATGAGTTCTTCTCATTATGAAC---TCAAC
*
7019076 TGGAAAAGTTGATCCATCAAATGATGGATTTGAA
60 TGGAAAAGCTGATCCATCAAATGAT-GATTTGAA
7019110 TCTTTGCTAA
Statistics
Matches: 276, Mismatches: 31, Indels: 25
0.83 0.09 0.08
Matches are distributed among these distances:
106 31 0.11
108 2 0.01
109 19 0.07
110 21 0.08
111 9 0.03
112 25 0.09
113 117 0.42
114 2 0.01
115 37 0.13
116 13 0.05
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (108 bp):
TTCTTCTCATTATGAACTTTCTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTCAACTGGAAA
AGCTGATCCATCAAATGATGATTTGAACAAAAGGTTGAACAAA
Found at i:7020082 original size:114 final size:115
Alignment explanation
Indices: 7019828--7020152 Score: 534
Period size: 114 Copynumber: 2.9 Consensus size: 115
7019818 TTTTAGTTCT
* * * * *
7019828 AATGATTGG-TTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGAACACTTCTAGAAGAT
1 AATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
7019892 GCTA-TGGGTCTTCTTA-TT-TACTATGAGCACATTCATCTTTCAAATCC
66 GCTATTGGGTCTTCTTATTTCTACTATGAGCACATTCATCTTTCAAATCC
* * *
7019939 AATAATTGGTTTTTGGGGTTCATATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGACGAT
1 AATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
*
7020004 GTTATTGGGTCTTCTTATTTCTACTATGAGCACATTCATCTTTC-AATCC
66 GCTATTGGGTCTTCTTATTTCTACTATGAGCACATTCATCTTTCAAATCC
7020053 AATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
1 AATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
7020118 GCTATTGGGTCTTCTTATTTCTACTATGAGCACAT
66 GCTATTGGGTCTTCTTATTTCTACTATGAGCACAT
7020153 GGCACTTGCT
Statistics
Matches: 197, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
111 8 0.04
112 51 0.26
113 12 0.06
114 103 0.52
115 23 0.12
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Consensus pattern (115 bp):
AATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
GCTATTGGGTCTTCTTATTTCTACTATGAGCACATTCATCTTTCAAATCC
Found at i:7021415 original size:1 final size:1
Alignment explanation
Indices: 7021409--7021472 Score: 65
Period size: 1 Copynumber: 64.0 Consensus size: 1
7021399 TCTTGACCCC
* * * * * * *
7021409 TTTTTTTTCTTTTTCTTTTTCTTTTTTCTTTTTTCTTTTTTTTTTCTTTTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
7021473 CTTTAAGCGT
Statistics
Matches: 49, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (1 bp):
T
Found at i:7021423 original size:6 final size:6
Alignment explanation
Indices: 7021412--7021476 Score: 78
Period size: 6 Copynumber: 10.5 Consensus size: 6
7021402 TGACCCCTTT
*
7021412 TTTTTC TTTTTC TTTTTC TTTTTTC TTTTTTC TTTTT- TTTTTC TTTTTT
1 TTTTTC TTTTTC TTTTTC -TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC
*
7021461 TTTCTTT TTTTTC TTT
1 TTT-TTC TTTTTC TTT
7021477 AAGCGTAATA
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
5 5 0.09
6 30 0.56
7 19 0.35
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTTTC
Found at i:7021428 original size:7 final size:7
Alignment explanation
Indices: 7021411--7021470 Score: 81
Period size: 7 Copynumber: 8.9 Consensus size: 7
7021401 TTGACCCCTT
7021411 TTTTTTC
1 TTTTTTC
7021418 -TTTTTC
1 TTTTTTC
7021424 -TTTTTC
1 TTTTTTC
7021430 TTTTTTC
1 TTTTTTC
7021437 TTTTTTC
1 TTTTTTC
7021444 TTTTTT-
1 TTTTTTC
*
7021450 TTTTCTTT
1 TTTT-TTC
7021458 TTTTTTC
1 TTTTTTC
7021465 TTTTTT
1 TTTTTT
7021471 TTCTTTAAGC
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
6 16 0.33
7 29 0.59
8 4 0.08
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:7021433 original size:19 final size:17
Alignment explanation
Indices: 7021409--7021476 Score: 91
Period size: 19 Copynumber: 3.7 Consensus size: 17
7021399 TCTTGACCCC
7021409 TTTTTTTTCTTTTTCTTT
1 TTTTTTTTCTTTTT-TTT
7021427 TTCTTTTTTCTTTTTTCTT
1 TT-TTTTTTCTTTTTT-TT
7021446 TTTTTTTTCTTTTTTTTT
1 TTTTTTTTC-TTTTTTTT
7021464 CTTTTTTTTCTTT
1 -TTTTTTTTCTTT
7021477 AAGCGTAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
18 15 0.33
19 31 0.67
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTTTTCTTTTTTTT
Found at i:7034289 original size:3 final size:3
Alignment explanation
Indices: 7034281--7034332 Score: 95
Period size: 3 Copynumber: 17.0 Consensus size: 3
7034271 AATTATTTTT
7034281 TAA TAA TAA TAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
7034327 TAA TAA
1 TAA TAA
7034333 AAATGGGTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:7035813 original size:187 final size:182
Alignment explanation
Indices: 7035500--7035873 Score: 466
Period size: 187 Copynumber: 2.0 Consensus size: 182
7035490 TTAGAGGAGC
* * * *
7035500 ATCTCCGGGGATATAGGATCTTTACAGCTTTATATTTTCCAAAAATTACAATTATCTGACATGAT
1 ATCTCCGGAGATATAGGATATGTACAGCTTTACATTTTCCAAAAATTACAATTATCTGACATGAT
* * * *
7035565 TTTTAATAAGACCAAAATCAATTAACCGTGAATCACATCAATGAAGCCTATCTGTCCTATCAATC
66 TTCTAATAAGACCAAAATCAACTAACAGTGAATCACATCAATGAAGCCTATCTATCCTATCAATC
* **
7035630 TATCGATAATCATCATAATTCTACGCCTAATGATAACAAGAAGAATTATTATAAA
131 TATCGATAATCATCATAATTATACGCCTAACAATAACAAG-AG--TTATTATAAA
* * *
7035685 ATCTCCGGAGATATAGGATATGTAGAGTTTTACATTTTCCAAAAAAATTAGAATTATCTGACATG
1 ATCTCCGGAGATATAGGATATGTACAGCTTTACATTTTCC--AAAAATTACAATTATCTGACATG
* * * * *
7035750 GTTTCTGATAAGATCAAAATCAACTGACAGTTG-ATCACATCAATCTAA-CCTA-CTTATCCTAT
64 ATTTCTAATAAGACCAAAATCAACTAACAG-TGAATCACATCAAT-GAAGCCTATC-TATCCTAT
* *
7035812 CAATCTATCGATAATCATCATAATTATATGTCTAACAATAACAAGAGTTATTATAAA
126 CAATCTATCGATAATCATCATAATTATACGCCTAACAATAACAAGAGTTATTATAAA
7035869 ATCTC
1 ATCTC
7035874 GGGAATCAAA
Statistics
Matches: 163, Mismatches: 21, Indels: 11
0.84 0.11 0.06
Matches are distributed among these distances:
184 15 0.09
185 34 0.21
186 3 0.02
187 107 0.66
188 4 0.02
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.33
Consensus pattern (182 bp):
ATCTCCGGAGATATAGGATATGTACAGCTTTACATTTTCCAAAAATTACAATTATCTGACATGAT
TTCTAATAAGACCAAAATCAACTAACAGTGAATCACATCAATGAAGCCTATCTATCCTATCAATC
TATCGATAATCATCATAATTATACGCCTAACAATAACAAGAGTTATTATAAA
Found at i:7037355 original size:21 final size:21
Alignment explanation
Indices: 7037331--7037397 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
7037321 GATTCGCAAC
7037331 GCGATAGTCAAAGTTCGCGTT
1 GCGATAGTCAAAGTTCGCGTT
*
7037352 GCGATTCATTCCAAA--T--CGTT
1 GCGA-T-AGT-CAAAGTTCGCGTT
*
7037372 GCGATAGTCGAAGTTCGCGTT
1 GCGATAGTCAAAGTTCGCGTT
7037393 GCGAT
1 GCGAT
7037398 TCATTCCAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 14
0.68 0.06 0.26
Matches are distributed among these distances:
17 3 0.08
18 2 0.06
19 2 0.06
20 8 0.22
21 13 0.36
22 2 0.06
23 2 0.06
24 4 0.11
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (21 bp):
GCGATAGTCAAAGTTCGCGTT
Found at i:7037373 original size:20 final size:20
Alignment explanation
Indices: 7037348--7037457 Score: 84
Period size: 20 Copynumber: 5.4 Consensus size: 20
7037338 TCAAAGTTCG
*
7037348 CGTTGCGATTCATTCCAAAT
1 CGTTGCGATTCATTCCAATT
* *
7037368 CGTTGCGA-T-AGTCGAAGTT
1 CGTTGCGATTCATTCCAA-TT
7037387 CGCGTTGCGATTCATTCCAATT
1 --CGTTGCGATTCATTCCAATT
** *
7037409 CGTTGCGA-T-AGGCGAAGTT
1 CGTTGCGATTCATTCCAA-TT
7037428 CGCATTGCGATTCATTCCAATT
1 CG--TTGCGATTCATTCCAATT
7037450 CGTTGCGA
1 CGTTGCGA
7037458 CAAACAAAAT
Statistics
Matches: 69, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
18 9 0.13
19 7 0.10
20 22 0.32
21 14 0.20
22 8 0.12
23 9 0.13
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.33
Consensus pattern (20 bp):
CGTTGCGATTCATTCCAATT
Found at i:7037510 original size:41 final size:41
Alignment explanation
Indices: 7037331--7037518 Score: 238
Period size: 41 Copynumber: 4.6 Consensus size: 41
7037321 GATTCGCAAC
* * *
7037331 GCGATAGTCAAAGTTCGCGTTGCGATTCATTCCAAATCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAATTCGTT
*
7037372 GCGATAGTCGAAGTTCGCGTTGCGATTCATTCCAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAATTCGTT
*
7037413 GCGATAGGCGAAGTTCGCATTGCGATTCATTCCAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAATTCGTT
* ** * * * *
7037454 GCGACAAACAAAATTCGCGTTGCGGTTCATTCCAAATTTGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCC-AATTCGTT
7037496 GCGATAGGCGAA-TT--CGTTGCGAT
1 GCGATAGGCGAAGTTCGCGTTGCGAT
7037519 AGTCCAAATA
Statistics
Matches: 129, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
39 8 0.06
41 106 0.82
42 15 0.12
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.31
Consensus pattern (41 bp):
GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAATTCGTT
Done.