Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 154 of 318
Found at i:47316217 original size:20 final size:20
Alignment explanation
Indices: 47316192--47316240 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
47316182 AATTGAGATT
47316192 GATACTGAACTGAATTATGG
1 GATACTGAACTGAATTATGG
47316212 GATACTGAACTGAATTATGG
1 GATACTGAACTGAATTATGG
47316232 GATACTGAA
1 GATACTGAA
47316241 AACTGTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (20 bp):
GATACTGAACTGAATTATGG
Found at i:47316580 original size:45 final size:45
Alignment explanation
Indices: 47316530--47316633 Score: 172
Period size: 45 Copynumber: 2.3 Consensus size: 45
47316520 CTACTGTTAT
* *
47316530 TGTTACTGTTACTGTTACCGATTCGACACTTTGTGTGTCGAATAC
1 TGTTACTGTTACTGTTACAGATTCAACACTTTGTGTGTCGAATAC
* *
47316575 TGTTACCGTTACTGTTACAGATTCAACACTTTGTGTGTTGAATAC
1 TGTTACTGTTACTGTTACAGATTCAACACTTTGTGTGTCGAATAC
47316620 TGTTACTGTTACTG
1 TGTTACTGTTACTG
47316634 CTACTGCTAC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.41
Consensus pattern (45 bp):
TGTTACTGTTACTGTTACAGATTCAACACTTTGTGTGTCGAATAC
Found at i:47316628 original size:6 final size:6
Alignment explanation
Indices: 47316617--47316658 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
47316607 GTGTGTTGAA
* *
47316617 TACTGT TACTGT TACTGC TACTGC TACTGT TACTGAT TACTG
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTG
47316659 ATCAGGTACT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.43
Consensus pattern (6 bp):
TACTGT
Found at i:47316668 original size:24 final size:24
Alignment explanation
Indices: 47316617--47316679 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
47316607 GTGTGTTGAA
* *
47316617 TACTGTTACTGTTACTGCTACTGC
1 TACTGTTACTGTTACTGATACAGC
*
47316641 TACTGTTACTGATTACTGAT-CAGG
1 TACTGTTACTG-TTACTGATACAGC
*
47316665 TACTGTATACCGTTA
1 TACTGT-TACTGTTA
47316680 AGGCACATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 22 0.67
25 11 0.33
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (24 bp):
TACTGTTACTGTTACTGATACAGC
Found at i:47321093 original size:26 final size:26
Alignment explanation
Indices: 47321063--47321144 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
47321053 TGAAATGCCC
47321063 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
47321089 ATCATGGAAAATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
47321115 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
47321141 ATCA
1 ATCA
47321145 ATTTGTACCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.37, C:0.26, G:0.07, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:47325527 original size:13 final size:13
Alignment explanation
Indices: 47325509--47325535 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
47325499 AAATAAATTC
47325509 AAAAATATTTATG
1 AAAAATATTTATG
47325522 AAAAATATTTATG
1 AAAAATATTTATG
47325535 A
1 A
47325536 GCCTATTGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (13 bp):
AAAAATATTTATG
Found at i:47325763 original size:21 final size:20
Alignment explanation
Indices: 47325749--47325818 Score: 56
Period size: 20 Copynumber: 3.5 Consensus size: 20
47325739 ATTATATATA
47325749 TATTATATTATATTATTGAT
1 TATTATATTATATTATTGAT
*
47325769 TATTATAATTAT-TAATTG-T
1 TATTAT-ATTATATTATTGAT
** *
47325788 TATGGTTTTATATTATT-AT
1 TATTATATTATATTATTGAT
*
47325807 TAGTACTATTAT
1 TATTA-TATTAT
47325819 TAAATAAATT
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
18 4 0.11
19 12 0.32
20 16 0.43
21 5 0.14
ACGTcount: A:0.33, C:0.01, G:0.07, T:0.59
Consensus pattern (20 bp):
TATTATATTATATTATTGAT
Found at i:47327426 original size:45 final size:45
Alignment explanation
Indices: 47327376--47327482 Score: 171
Period size: 45 Copynumber: 2.4 Consensus size: 45
47327366 TGACTACTGT
**
47327376 TACTGTTACCGTTACTGTTACTGATTC-GACACTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACAAATTCAG-CACTTTGTGTGTTGAA
47327421 TACTGTTACCGTTACTGTTACAAATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACAAATTCAGCACTTTGTGTGTTGAA
*
47327466 TACTGTTACTGTTACTG
1 TACTGTTACCGTTACTG
47327483 CTATTGCTAC
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
45 57 0.98
46 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACAAATTCAGCACTTTGTGTGTTGAA
Found at i:47327435 original size:51 final size:51
Alignment explanation
Indices: 47327361--47327480 Score: 146
Period size: 45 Copynumber: 2.5 Consensus size: 51
47327351 CAGGCACTTA
* * **
47327361 TGTGCTGACTACTGTTACTGTTACCGTTACTGTTACTGATTC-GACACTTTG
1 TGTGTTGAATACTGTTACTGTTACCGTTACTGTTACAAATTCAG-CACTTTG
47327412 TGTGTTG-A-A----TACTGTTACCGTTACTGTTACAAATTCAGCACTTTG
1 TGTGTTGAATACTGTTACTGTTACCGTTACTGTTACAAATTCAGCACTTTG
47327457 TGTGTTGAATACTGTTACTGTTAC
1 TGTGTTGAATACTGTTACTGTTAC
47327481 TGCTATTGCT
Statistics
Matches: 58, Mismatches: 4, Indels: 14
0.76 0.05 0.18
Matches are distributed among these distances:
45 39 0.67
46 2 0.03
47 1 0.02
49 1 0.02
51 15 0.26
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (51 bp):
TGTGTTGAATACTGTTACTGTTACCGTTACTGTTACAAATTCAGCACTTTG
Found at i:47334143 original size:21 final size:21
Alignment explanation
Indices: 47334101--47334185 Score: 64
Period size: 21 Copynumber: 4.1 Consensus size: 21
47334091 CAGAAGTCCG
* **
47334101 AAGA-CTAAACAGAAGCATAT
1 AAGAGCTAAACAGAAACCCAT
*
47334121 AAGTGCTAAACAGAAACCCAT
1 AAGAGCTAAACAGAAACCCAT
* * * * * *
47334142 AAGGGTTGAACGGAAGCTCAT
1 AAGAGCTAAACAGAAACCCAT
*
47334163 AAGAGCTAAACGGAAACCCAT
1 AAGAGCTAAACAGAAACCCAT
47334184 AA
1 AA
47334186 AGGTTAAACA
Statistics
Matches: 49, Mismatches: 15, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
20 3 0.06
21 46 0.94
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (21 bp):
AAGAGCTAAACAGAAACCCAT
Found at i:47334165 original size:42 final size:41
Alignment explanation
Indices: 47334108--47334247 Score: 147
Period size: 42 Copynumber: 3.3 Consensus size: 41
47334098 CCGAAGACTA
*
47334108 AACAGAAGCAT-ATAAGTGCTAAACAGAAACCCATAAGGGTTG
1 AACAGAAGC-TCATAAGAGCTAAAC-GAAACCCATAAGGGTTG
* * *
47334150 AACGGAAGCTCATAAGAGCTAAACGGAAACCCATAAAGGTTA
1 AACAGAAGCTCATAAGAGCTAAAC-GAAACCCATAAGGGTTG
* * * *
47334192 AACAAAAGCTCAAAAGAGCTGAACGAAAACCCATTAGGGTTG
1 AACAGAAGCTCATAAGAGCTAAACG-AAACCCATAAGGGTTG
* *
47334234 AACTGAAACTCATA
1 AACAGAAGCTCATA
47334248 TAAGTTAAGC
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
41 2 0.03
42 78 0.98
ACGTcount: A:0.46, C:0.19, G:0.20, T:0.16
Consensus pattern (41 bp):
AACAGAAGCTCATAAGAGCTAAACGAAACCCATAAGGGTTG
Found at i:47334193 original size:21 final size:21
Alignment explanation
Indices: 47334127--47334194 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
47334117 ATATAAGTGC
* *
47334127 TAAACAGAAACCCATAAGGGT
1 TAAACGGAAACCCATAAAGGT
* * * *
47334148 TGAACGGAAGCTCAT-AAGAGC
1 TAAACGGAAACCCATAAAG-GT
47334169 TAAACGGAAACCCATAAAGGT
1 TAAACGGAAACCCATAAAGGT
47334190 TAAAC
1 TAAAC
47334195 AAAAGCTCAA
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
20 2 0.06
21 30 0.86
22 3 0.09
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.15
Consensus pattern (21 bp):
TAAACGGAAACCCATAAAGGT
Found at i:47336025 original size:36 final size:35
Alignment explanation
Indices: 47335961--47336044 Score: 98
Period size: 36 Copynumber: 2.4 Consensus size: 35
47335951 TTTAACATAG
* * *
47335961 TGGCATGCTTAACATGTGAACTAGAATCAGAAATAA
1 TGGCATGCTTAACATGTCAACTAAAATCAG-AAGAA
*
47335997 TGGCATGCTTAACATG-CAAGTCAAAATCAGAAGAA
1 TGGCATGCTTAACATGTCAACT-AAAATCAGAAGAA
*
47336032 TAGCATGCTTAAC
1 TGGCATGCTTAAC
47336045 TTGCGAATCA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
35 19 0.45
36 23 0.55
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (35 bp):
TGGCATGCTTAACATGTCAACTAAAATCAGAAGAA
Found at i:47336706 original size:25 final size:25
Alignment explanation
Indices: 47336672--47336721 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
47336662 TACGAAAGAG
*
47336672 AGAGTTATGAACAAAGGATTTTCCA
1 AGAGTAATGAACAAAGGATTTTCCA
**
47336697 AGAGTAATGAAGGAAGGATTTTCCA
1 AGAGTAATGAACAAAGGATTTTCCA
47336722 TACTTACGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.10, G:0.24, T:0.26
Consensus pattern (25 bp):
AGAGTAATGAACAAAGGATTTTCCA
Found at i:47359766 original size:20 final size:20
Alignment explanation
Indices: 47359741--47359784 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
47359731 AATAGTTGAA
47359741 AAAAATCAAAACTTTACTTT
1 AAAAATCAAAACTTTACTTT
** *
47359761 AAAAATTTAAACTTTCCTTT
1 AAAAATCAAAACTTTACTTT
47359781 AAAA
1 AAAA
47359785 TGACTAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAATCAAAACTTTACTTT
Found at i:47359939 original size:160 final size:159
Alignment explanation
Indices: 47359512--47359982 Score: 522
Period size: 160 Copynumber: 2.9 Consensus size: 159
47359502 AAAATCAAAG
* * *
47359512 TTTTC-TTTAAAAAAATTTACTACTTTTCTTAAAAATTAAA-ACTTTATTTTGAAATAGTTGAAA
1 TTTTCTTTTAAAAAAA--TACTACTTTTCTTAAAGATCAAAGATTTTATTTTGAAATAGTTGAAA
* ** *
47359575 AATATCAAAACTTTGTTTTAAAAATTTAAATTTTTTCCTTTAAAATGACTAAAAAAACAAATTTT
64 AAAATCAAAACTTTGTTTTAAAAA-TTAAA-AATTTCCTTTAAAATGACTAAAAAAACATATTTT
* *
47359640 TATTTTTAAAAATCTAAACTTTCTCACTCTCTTTTT
127 TATTTTAAAAAATATAAAC--TCT-ACTCTCTTTTT
* * * **
47359676 TTTTCTTTT-AAAAAATCACTATTTTTTTTATTAAAGATCAAAGTTTTTATTTCAAAATAGTTGA
1 TTTTCTTTTAAAAAAAT-ACTA---CTTTTCTTAAAGATCAAAGATTTTATTTTGAAATAGTTGA
** * * * *
47359740 AAAAAATCAAAACTTTACTTTAAAAATTTAAACTTTCCTTTAAAATGACTAAAATAATATATTTT
62 AAAAAATCAAAACTTTGTTTTAAAAATTAAAAATTTCCTTTAAAATGACTAAAAAAACATATTTT
*
47359805 TATTTTAAAAAA-ATATAAC-CT-TTCTCTTTTT
127 TATTTTAAAAAATATA-AACTCTACTCTCTTTTT
*
47359836 TTTTCTTTTAAAAAAATACTACTTTTCTTAAAGATCAAAGGTTTTATTTTGAAATAGTTGAAAAC
1 TTTTCTTTTAAAAAAATACTACTTTTCTTAAAGATCAAAGATTTTATTTTGAAATAGTTG-AAA-
* * *
47359901 AAAATCAAAAAATTTGTTTTAAAAATTAAAAATTTCCTTTAGAATGACTAAAAAAACATATTTTC
64 AAAATC-AAAACTTTGTTTTAAAAATTAAAAATTTCCTTTAAAATGACTAAAAAAACATATTTTT
* *
47359966 ATTTTTAAAAATCTAAA
128 ATTTTAAAAAATATAAA
47359983 AGATCAAGCC
Statistics
Matches: 259, Mismatches: 36, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
157 34 0.13
158 3 0.01
159 6 0.02
160 83 0.32
161 9 0.03
162 3 0.01
163 4 0.02
164 13 0.05
165 46 0.18
166 18 0.07
167 40 0.15
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (159 bp):
TTTTCTTTTAAAAAAATACTACTTTTCTTAAAGATCAAAGATTTTATTTTGAAATAGTTGAAAAA
AATCAAAACTTTGTTTTAAAAATTAAAAATTTCCTTTAAAATGACTAAAAAAACATATTTTTATT
TTAAAAAATATAAACTCTACTCTCTTTTT
Found at i:47360303 original size:3 final size:3
Alignment explanation
Indices: 47360297--47360347 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
47360287 GTAAAAAAAG
* * * *
47360297 ATA ATA ATA ATA TTTA ATA ATA ATA ATA GTA GTA ATA ATG ATA ATA
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
47360343 ATA AT
1 ATA AT
47360348 TTGAGCCCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 39 0.95
4 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:47363037 original size:33 final size:33
Alignment explanation
Indices: 47362996--47363061 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
47362986 GATGATGTTC
47362996 GTTCTCACTCATTATTGTGAAAACTATCCCTTT
1 GTTCTCACTCATTATTGTGAAAACTATCCCTTT
47363029 GTTCTCACTCATTATTGTGAAAACTATCCCTTT
1 GTTCTCACTCATTATTGTGAAAACTATCCCTTT
47363062 ATAGAATCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.24, G:0.09, T:0.42
Consensus pattern (33 bp):
GTTCTCACTCATTATTGTGAAAACTATCCCTTT
Found at i:47367553 original size:42 final size:44
Alignment explanation
Indices: 47367494--47367578 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
47367484 CTTTTATTAC
47367494 ATTGATAATGA-TTTTTTTT-AAAAAAAATTATAAACTAGTTAT
1 ATTGATAATGATTTTTTTTTAAAAAAAAATTATAAACTAGTTAT
* *
47367536 ATTGATAATGCTTTTTTTTTAAAAAAAAATTATAAACTGGTTA
1 ATTGATAATGATTTTTTTTTAAAAAAAAATTATAAACTAGTTA
47367579 AGAGATTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 10 0.26
43 8 0.21
44 21 0.54
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.45
Consensus pattern (44 bp):
ATTGATAATGATTTTTTTTTAAAAAAAAATTATAAACTAGTTAT
Found at i:47367770 original size:17 final size:18
Alignment explanation
Indices: 47367748--47367783 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
47367738 CAAATATTAA
47367748 ATTATTTA-TATAATTTT
1 ATTATTTATTATAATTTT
*
47367765 ATTATTTATTATATTTTT
1 ATTATTTATTATAATTTT
47367783 A
1 A
47367784 AATTTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTATTTATTATAATTTT
Found at i:47370786 original size:24 final size:24
Alignment explanation
Indices: 47370771--47370837 Score: 125
Period size: 24 Copynumber: 2.8 Consensus size: 24
47370761 CGGATTTAAG
47370771 TGGCACTATGTGTGCGTATTTGTA
1 TGGCACTATGTGTGCGTATTTGTA
*
47370795 TGGCACTATGTGAGCGTATTTGTA
1 TGGCACTATGTGTGCGTATTTGTA
47370819 TGGCACTATGTGTGCGTAT
1 TGGCACTATGTGTGCGTAT
47370838 ATAATGGCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.18, C:0.13, G:0.30, T:0.39
Consensus pattern (24 bp):
TGGCACTATGTGTGCGTATTTGTA
Found at i:47374629 original size:13 final size:13
Alignment explanation
Indices: 47374611--47374644 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
47374601 TATTTTATTA
47374611 ATATTTTAATAAG
1 ATATTTTAATAAG
47374624 ATATTTTAATAAG
1 ATATTTTAATAAG
47374637 ATATTTTA
1 ATATTTTA
47374645 TTATTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (13 bp):
ATATTTTAATAAG
Found at i:47377195 original size:79 final size:80
Alignment explanation
Indices: 47377027--47377207 Score: 208
Period size: 79 Copynumber: 2.3 Consensus size: 80
47377017 ACTACTTGCT
* * *
47377027 CAAACGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCAGGACTTAACCCGG
1 CAAA-GCCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATGCCTTCAGGACTTAACCCGG
* * *
47377092 ATTTAGTGACTCGCAC
65 ATATAGTCACTAGCAC
* ** *
47377108 CAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCACACAAATGCCTTC-GGATCTTAGTCTG
1 CAAAGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCACACAAATGCCTTCAGGA-CTTAACCCG
47377170 GATATAGTCACTTAGCA-
64 GATATAGTCAC-TAGCAC
47377187 CAAAGCCTTCGGGACTTAGCC
1 CAAAGCCTTCGGGACTTAGCC
47377208 TGGACATCAT
Statistics
Matches: 85, Mismatches: 11, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
78 4 0.05
79 58 0.68
80 20 0.24
81 3 0.04
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
CAAAGCCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATGCCTTCAGGACTTAACCCGGA
TATAGTCACTAGCAC
Found at i:47377211 original size:40 final size:40
Alignment explanation
Indices: 47377027--47377207 Score: 174
Period size: 40 Copynumber: 4.5 Consensus size: 40
47377017 ACTACTTGCT
* * * *
47377027 CAAACGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
* * * * *
47377067 CAAATGCCTTCAGGACTTAACCCGGATTTAGTGACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
*
47377107 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCA-CA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACT-AGCA
* * *
47377146 CAAATGCCTTC-GGATCTTAGTCTGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TAGCA
47377187 CAAA-GCCTTCGGGACTTAGCC
1 CAAATGCCTTCGGGACTTAGCC
47377208 TGGACATCAT
Statistics
Matches: 115, Mismatches: 18, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
38 2 0.02
39 29 0.25
40 73 0.63
41 11 0.10
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTAGCA
Found at i:47383574 original size:29 final size:28
Alignment explanation
Indices: 47383542--47383644 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
47383532 GTGACGAGAT
* *
47383542 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AATATA
* *
47383571 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAATATA
* * *
47383600 TGGCACTATGTGTGCGGGCTTGAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAT-ATA
47383629 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
47383645 TGATTGAGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.05
29 58 0.94
30 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGAATATA
Found at i:47391374 original size:29 final size:28
Alignment explanation
Indices: 47391342--47391444 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
47391332 GTGACGAGAT
* *
47391342 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AATATA
* *
47391371 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAATATA
* * *
47391400 TGGCACTATGTGTGCGGGCTTGAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAT-ATA
47391429 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
47391445 TGATTGAGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.05
29 58 0.94
30 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGAATATA
Found at i:47393996 original size:29 final size:28
Alignment explanation
Indices: 47393964--47394066 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
47393954 GTGACGAGAT
* *
47393964 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AATATA
* *
47393993 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAATATA
* * *
47394022 TGGCACTATGTGTGCGGGCTTGAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAT-ATA
47394051 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
47394067 TGATTGAGTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 3 0.05
29 58 0.94
30 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (28 bp):
TGGCACTAAGTGTGCGAGCTTGAATATA
Found at i:47398683 original size:40 final size:40
Alignment explanation
Indices: 47398627--47398777 Score: 189
Period size: 40 Copynumber: 3.8 Consensus size: 40
47398617 GGATATAACT
* * *
47398627 ACTCGCTCAAACGCCTTCGGGACATAGCCTGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACATAGCCCGGTTATAGTA
*
47398667 ACTCGCACAAATGCCTTCGGGACATAGCCCGATTATAGTA
1 ACTCGCACAAATGCCTTCGGGACATAGCCCGGTTATAGTA
* * * *
47398707 ACTCGCACAAATGCCTTCTGGACTTAACCCGGATT-TAGTG
1 ACTCGCACAAATGCCTTCGGGACATAGCCCGG-TTATAGTA
* *
47398747 ACTCGCACCAATGCCTTCGGG-CTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACATAGCCCGG
47398778 AATTAGTAAC
Statistics
Matches: 98, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
39 9 0.09
40 87 0.89
41 2 0.02
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACATAGCCCGGTTATAGTA
Found at i:47405362 original size:20 final size:20
Alignment explanation
Indices: 47405353--47405423 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
47405343 TTGATATAAT
*
47405353 ATGCACATGATATGTATAAA
1 ATGCACATGATATGTATGAA
*
47405373 ATGCACATAATATGTATGAA
1 ATGCACATGATATGTATGAA
47405393 ATGCACATGATATGTATGAA
1 ATGCACATGATATGTATGAA
47405413 ATGCACATGAT
1 ATGCACATGAT
47405424 GTATTCATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (20 bp):
ATGCACATGATATGTATGAA
Found at i:47405556 original size:52 final size:50
Alignment explanation
Indices: 47405486--47405605 Score: 190
Period size: 52 Copynumber: 2.4 Consensus size: 50
47405476 CACTATTATG
47405486 CAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCGAAAAGGGCTTATGCCC
1 CAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCGAAAA-GGCTTATGCCC
*
47405538 CAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCGAAAAGGCTTTTGCCC
1 CAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCGAAAAGGCTTATGCCC
47405588 CAG-TTATT-AAAAGAGGCT
1 CAGTTTATTGAAAAG-GGCT
47405606 AGGCCTCCAA
Statistics
Matches: 66, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
48 5 0.08
49 9 0.14
50 13 0.20
51 19 0.29
52 20 0.30
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (50 bp):
CAGTTTATTGAAAAGGGCTTTGCCCCAGTTTACCGAAAAGGCTTATGCCC
Found at i:47405567 original size:25 final size:26
Alignment explanation
Indices: 47405486--47405605 Score: 158
Period size: 26 Copynumber: 4.7 Consensus size: 26
47405476 CACTATTATG
47405486 CAGTTTATTGAAAAGGGCTTATGCCC
1 CAGTTTATTGAAAAGGGCTTATGCCC
**
47405512 CAGTTTACCGAAAAGGGCTTATGCCC
1 CAGTTTATTGAAAAGGGCTTATGCCC
47405538 CAGTTTATTGAAAAGGGCTT-TGCCC
1 CAGTTTATTGAAAAGGGCTTATGCCC
** *
47405563 CAGTTTACCGAAAA-GGCTTTTGCCC
1 CAGTTTATTGAAAAGGGCTTATGCCC
47405588 CAG-TTATT-AAAAGAGGCT
1 CAGTTTATTGAAAAG-GGCT
47405606 AGGCCTCCAA
Statistics
Matches: 83, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
23 4 0.05
24 8 0.10
25 29 0.35
26 42 0.51
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.28
Consensus pattern (26 bp):
CAGTTTATTGAAAAGGGCTTATGCCC
Found at i:47405845 original size:30 final size:31
Alignment explanation
Indices: 47405811--47405893 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
47405801 CGCTTACAGT
47405811 AAAGGCTTCGG-CCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
47405841 AAAGGCTTCGGTCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
47405872 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
47405894 TCGAGACTGA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
30 16 0.31
31 35 0.69
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:47408183 original size:42 final size:42
Alignment explanation
Indices: 47408087--47408183 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
47408077 TGAGTTTCCT
* * * * *
47408087 TTCAACCCTAATGGATTTTCGTTTAGCTCTTTTGAGCTTCTG
1 TTCAACCCTTATGGATTTCCATTCAGCTCTTCTGAGCTTCTG
* * * *
47408129 TTTAACCTTTATGGGTTTCCATTCAGCTCTTCTGAGCTTTTG
1 TTCAACCCTTATGGATTTCCATTCAGCTCTTCTGAGCTTCTG
47408171 TTCAACCCTTATG
1 TTCAACCCTTATG
47408184 AGCTCTCGTT
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.16, C:0.23, G:0.15, T:0.45
Consensus pattern (42 bp):
TTCAACCCTTATGGATTTCCATTCAGCTCTTCTGAGCTTCTG
Found at i:47408185 original size:21 final size:21
Alignment explanation
Indices: 47408161--47408204 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
47408151 TCAGCTCTTC
* *
47408161 TGAGCTTTTGTTCAACCCTTA
1 TGAGCTCTCGTTCAACCCTTA
47408182 TGAGCTCTCGTTCAACCCTTA
1 TGAGCTCTCGTTCAACCCTTA
47408203 TG
1 TG
47408205 GGTTTCTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.27, G:0.16, T:0.39
Consensus pattern (21 bp):
TGAGCTCTCGTTCAACCCTTA
Found at i:47409900 original size:20 final size:21
Alignment explanation
Indices: 47409862--47409909 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
47409852 TGGACTTCAA
*
47409862 TTTT-GGACTTTGGTTTTTGG
1 TTTTGGGACTTTGGTATTTGG
47409882 TTTTGGGACTTTGG-ATTTGG
1 TTTTGGGACTTTGGTATTTGG
*
47409902 ATTTGGGA
1 TTTTGGGA
47409910 ATTATTCTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.10, C:0.04, G:0.33, T:0.52
Consensus pattern (21 bp):
TTTTGGGACTTTGGTATTTGG
Found at i:47414293 original size:42 final size:42
Alignment explanation
Indices: 47414246--47414345 Score: 191
Period size: 42 Copynumber: 2.4 Consensus size: 42
47414236 TATTGGTCTC
47414246 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
47414288 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
*
47414330 GGCACTACGTGTGCGG
1 GGCACTAAGTGTGCGG
47414346 TTTAAAATTG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 57 1.00
ACGTcount: A:0.28, C:0.16, G:0.35, T:0.21
Consensus pattern (42 bp):
GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
Found at i:47414416 original size:27 final size:28
Alignment explanation
Indices: 47414359--47414428 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
47414349 AAAATTGTAC
**
47414359 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
* *
47414387 AGCACTATGTGTGCG-AGCTGATTTTAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
47414414 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
47414429 GATTCACTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:47421512 original size:42 final size:42
Alignment explanation
Indices: 47421465--47421571 Score: 196
Period size: 42 Copynumber: 2.5 Consensus size: 42
47421455 TATTGGTCTC
47421465 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
47421507 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
* *
47421549 GGCACTACGTGTGCGGGTTTAAA
1 GGCACTAAGTGTGCGGGTATAAA
47421572 ATTGTACAGC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.29, C:0.15, G:0.34, T:0.22
Consensus pattern (42 bp):
GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
Found at i:47421636 original size:27 final size:28
Alignment explanation
Indices: 47421579--47421648 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
47421569 AAAATTGTAC
**
47421579 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
* *
47421607 AGCACTATGTGTGCG-AGCTGATTTTAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
47421634 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
47421649 GATTCACTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:47425733 original size:53 final size:53
Alignment explanation
Indices: 47425653--47425764 Score: 215
Period size: 53 Copynumber: 2.1 Consensus size: 53
47425643 TTAATTTTTT
47425653 TCTAAAATTTCTCATTCTCCTTATTTTGTGCCACCCAAGCCTTGAACCCTAGG
1 TCTAAAATTTCTCATTCTCCTTATTTTGTGCCACCCAAGCCTTGAACCCTAGG
47425706 TCTAAAATTTCTCATTCTCCTTATTTTGTGCCACCCAAGCCTTGAACCCTAGG
1 TCTAAAATTTCTCATTCTCCTTATTTTGTGCCACCCAAGCCTTGAACCCTAGG
*
47425759 TATAAA
1 TCTAAA
47425765 TACAAATTTT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.25, C:0.29, G:0.11, T:0.36
Consensus pattern (53 bp):
TCTAAAATTTCTCATTCTCCTTATTTTGTGCCACCCAAGCCTTGAACCCTAGG
Found at i:47429491 original size:15 final size:14
Alignment explanation
Indices: 47429473--47429528 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
47429463 GTTAATCATG
47429473 TTTTATATTTAATTA
1 TTTTA-ATTTAATTA
*
47429488 TTTTAAATTAATTA
1 TTTTAATTTAATTA
*
47429502 GTTTAATTATAATTA
1 TTTTAATT-TAATTA
*
47429517 TTTTAACTTAAT
1 TTTTAATTTAAT
47429529 GTCCAACCTC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 18 0.51
15 17 0.49
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (14 bp):
TTTTAATTTAATTA
Found at i:47429720 original size:138 final size:138
Alignment explanation
Indices: 47429472--47429749 Score: 504
Period size: 138 Copynumber: 2.0 Consensus size: 138
47429462 AGTTAATCAT
**
47429472 GTTTTATATTTAATTATTTTAAATTAATTAGTTTAATTATAATTATTTTAACTTAATGTCCAACC
1 GTTTTATATTTAATTAACTTAAATTAATTAGTTTAATTATAATTATTTTAACTTAATGTCCAACC
*
47429537 TCATCACCATCCACTATCTACTAACTAAAATTGATTTTTAACCATTTTAGTCTTTGGAATAATTA
66 TCATCACCATCCACTATCTACTAACTAAAATTGATTTTTAACCATTTTAGTCTTTGGAAAAATTA
47429602 CTATCTAA
131 CTATCTAA
*
47429610 GTTTTATATTTAATTACACTT-AATTAATTATTTTAATTATAATTATTTTAACTTAATGTCCAAC
1 GTTTTATATTTAATTA-ACTTAAATTAATTAGTTTAATTATAATTATTTTAACTTAATGTCCAAC
47429674 CTCATCACCATCCACTATCTACTAACTAAAATTGATTTTTAACCATTTTAGTCTTTGGAAAAATT
65 CTCATCACCATCCACTATCTACTAACTAAAATTGATTTTTAACCATTTTAGTCTTTGGAAAAATT
47429739 ACTATCTAA
130 ACTATCTAA
47429748 GT
1 GT
47429750 CCCCAGACTT
Statistics
Matches: 135, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
138 133 0.99
139 2 0.01
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (138 bp):
GTTTTATATTTAATTAACTTAAATTAATTAGTTTAATTATAATTATTTTAACTTAATGTCCAACC
TCATCACCATCCACTATCTACTAACTAAAATTGATTTTTAACCATTTTAGTCTTTGGAAAAATTA
CTATCTAA
Found at i:47432624 original size:79 final size:80
Alignment explanation
Indices: 47432513--47432674 Score: 263
Period size: 79 Copynumber: 2.0 Consensus size: 80
47432503 TAAATTGACA
*
47432513 AAAAATAAAATTTTAAGTGACCAAAATAGAAAGACACTATTTTAAAGTGACCTAAGATATAATTT
1 AAAAATAAAATTTTAAGTGACCAAAATAGAAAGACACTATTTTAAAGTCACCTAAGATATAATTT
47432578 ACACTATTTTTAAAT
66 ACACTATTTTTAAAT
* * *
47432593 AAAAA-AAAATTTTAAGTGATCAAAATAGAAAGATACTATTTTAAAGTCACCTACGATATAATTT
1 AAAAATAAAATTTTAAGTGACCAAAATAGAAAGACACTATTTTAAAGTCACCTAAGATATAATTT
**
47432657 ATGCTATTTTTAAAT
66 ACACTATTTTTAAAT
47432672 AAA
1 AAA
47432675 TTCAATTTTA
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
79 71 0.93
80 5 0.07
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (80 bp):
AAAAATAAAATTTTAAGTGACCAAAATAGAAAGACACTATTTTAAAGTCACCTAAGATATAATTT
ACACTATTTTTAAAT
Found at i:47433145 original size:20 final size:18
Alignment explanation
Indices: 47433108--47433155 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 18
47433098 CAATTTTTTT
47433108 ATTTTTTTATTTTGAAGA
1 ATTTTTTTATTTTGAAGA
*
47433126 ATTTTTTATATGTTTTAAGA
1 ATTTTTT-TAT-TTTGAAGA
47433146 TTATTTTTTT
1 --ATTTTTTT
47433156 CCTCTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.28
19 3 0.12
20 7 0.28
21 1 0.04
22 7 0.28
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (18 bp):
ATTTTTTTATTTTGAAGA
Found at i:47433677 original size:24 final size:23
Alignment explanation
Indices: 47433650--47433694 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
47433640 TTCTCTCTCC
*
47433650 TAGGGTTATGGTTTTTAATATTTT
1 TAGGGTTA-GGGTTTTAATATTTT
*
47433674 TAGGTTTAGGGTTTTAATATT
1 TAGGGTTAGGGTTTTAATATT
47433695 CTTACAGTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (23 bp):
TAGGGTTAGGGTTTTAATATTTT
Found at i:47433736 original size:16 final size:16
Alignment explanation
Indices: 47433715--47433769 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
47433705 GTTTGGTTCA
47433715 CTGTAATGGAATACG-G
1 CTGTAATGGAATA-GAG
*
47433731 CTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
* *
47433747 CTGTGATGGAATAGAC
1 CTGTAATGGAATAGAG
47433763 CTGTAAT
1 CTGTAAT
47433770 CAGTAATTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
15 1 0.03
16 32 0.97
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:47433814 original size:46 final size:44
Alignment explanation
Indices: 47433752--47433844 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 44
47433742 TAGAGCTGTG
**
47433752 ATGGAATAGACCTGTAATCAGTAATTCAACTG-TTTGCTTGAATGGA
1 ATGGAATAGAAATGTAAT-AGT-ATTCAACTGTTTTG-TTGAATGGA
***
47433798 ATGGAATAGAAATGTAATAGTATTCTTGTGTTTTGTTGAATGGA
1 ATGGAATAGAAATGTAATAGTATTCAACTGTTTTGTTGAATGGA
47433842 ATG
1 ATG
47433845 ATGTTGTAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
44 18 0.44
45 7 0.17
46 16 0.39
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.37
Consensus pattern (44 bp):
ATGGAATAGAAATGTAATAGTATTCAACTGTTTTGTTGAATGGA
Found at i:47436632 original size:15 final size:15
Alignment explanation
Indices: 47436612--47436643 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
47436602 CCTAACTTGA
47436612 GAGGGCGAAGGCGTC
1 GAGGGCGAAGGCGTC
47436627 GAGGGCGAAGGCGTC
1 GAGGGCGAAGGCGTC
47436642 GA
1 GA
47436644 TGGAGCTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.19, G:0.53, T:0.06
Consensus pattern (15 bp):
GAGGGCGAAGGCGTC
Found at i:47439849 original size:48 final size:48
Alignment explanation
Indices: 47439753--47439939 Score: 304
Period size: 48 Copynumber: 3.9 Consensus size: 48
47439743 TAGGGTTATG
* *
47439753 TGTGATCCTATGTAAGACCATGTC-GGGACATGGCATTGGCATCAATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
*
47439800 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
*
47439848 TGTGATCCTATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
* * *
47439896 TGTGATCCCATGTAAGACCATATCTGGGATATGGCATTTGCATC
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
47439940 TTACTATGTG
Statistics
Matches: 130, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
47 23 0.18
48 107 0.82
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (48 bp):
TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
Found at i:47443907 original size:28 final size:28
Alignment explanation
Indices: 47443876--47443946 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
47443866 TATATATATG
* *
47443876 TGGCACTTAGTGTGTGAAATATTGAGAA
1 TGGCACTTAGTGTGCGAAATATTAAGAA
* * **
47443904 TGGCACTTGGTGTGCGAGATATTAAGTC
1 TGGCACTTAGTGTGCGAAATATTAAGAA
*
47443932 TGGCTCTTAGTGTGC
1 TGGCACTTAGTGTGC
47443947 AGACATCGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.34
Consensus pattern (28 bp):
TGGCACTTAGTGTGCGAAATATTAAGAA
Found at i:47448018 original size:46 final size:45
Alignment explanation
Indices: 47447965--47448140 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 45
47447955 TGGTTGAGCA
47447965 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
* *** * *
47448010 GTCTGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 -TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAT
*
47448058 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACT
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T
* *
47448104 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
47448141 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 68 0.62
47 31 0.28
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
Found at i:47448121 original size:93 final size:93
Alignment explanation
Indices: 47447962--47448132 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
47447952 GGATGGTTGA
* *
47447962 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
47448027 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
47448055 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACT-CCCGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-TGCCCGAACTCGTTGAG
47448119 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
47448133 ACTTATGGGC
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
93 72 0.99
94 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:47451856 original size:30 final size:30
Alignment explanation
Indices: 47451822--47451881 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
47451812 TGATAAAAAG
47451822 GACCAAATTGTAAAAGTTGTAAAAAAACTA
1 GACCAAATTGTAAAAGTTGTAAAAAAACTA
47451852 GACCAAATTGTAAAAGTTGTAAAAAAACTA
1 GACCAAATTGTAAAAGTTGTAAAAAAACTA
47451882 TGTGTAAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.53, C:0.10, G:0.13, T:0.23
Consensus pattern (30 bp):
GACCAAATTGTAAAAGTTGTAAAAAAACTA
Found at i:47452508 original size:48 final size:49
Alignment explanation
Indices: 47452397--47452527 Score: 165
Period size: 48 Copynumber: 2.7 Consensus size: 49
47452387 ATGAGATCTT
*
47452397 GTGTAAGACCATGTCTAGGACATGGCGTCAGCATTCGAGACGAGAGCCA
1 GTGTAAGACCATGTCTAGGACATGGCATCAGCATTCGAGACGAGAGCCA
* * * * * * * * *
47452446 GTGTAAGACTATGTCTGGGACATGGCATCGGCGTT-GATATGTGTGCTA
1 GTGTAAGACCATGTCTAGGACATGGCATCAGCATTCGAGACGAGAGCCA
47452494 GTGTAAGACCATGTCTAGGACATGGCATCAGCAT
1 GTGTAAGACCATGTCTAGGACATGGCATCAGCAT
47452528 CAATGTATGA
Statistics
Matches: 68, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
48 38 0.56
49 30 0.44
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (49 bp):
GTGTAAGACCATGTCTAGGACATGGCATCAGCATTCGAGACGAGAGCCA
Found at i:47452549 original size:48 final size:48
Alignment explanation
Indices: 47452387--47452707 Score: 154
Period size: 48 Copynumber: 6.8 Consensus size: 48
47452377 ACCATGGTTG
* * *
47452387 ATGA-GATCTTGTGTAAGACCATGTCTAGGACATGGCGTCAGCATTCGAG
1 ATGATGATCTTGTATAAGACCATGTCTAGGACATGGCATCAGCA-TC-AT
* * ** * * * * * *
47452436 ACGA-GAGCCAGTGTAAGACTATGTCTGGGACATGGCATCGGCGTTGAT
1 ATGATGATCTTGTATAAGACCATGTCTAGGACATGGCATCAGC-ATCAT
* *
47452484 ATG-TG-TGCTAGTGTAAGACCATGTCTAGGACATGGCATCAGCATCA-
1 ATGATGAT-CTTGTATAAGACCATGTCTAGGACATGGCATCAGCATCAT
* * * *
47452530 ATGTATGATCTTGTATAAGACCATATC-AGGGATATGGCTTC-GACATCGT
1 ATG-ATGATCTTGTATAAGACCATGTCTA-GGACATGGCATCAG-CATCAT
* * * * *
47452579 -TAAGTGAT-TTCATATAAGACCATGTCTGGGTCATGGCAT-----TGAT
1 ATGA-TGATCTT-GTATAAGACCATGTCTAGGACATGGCATCAGCATCAT
** * *
47452622 ATGATG-TCCCGTATAAGACCATGTCTGGGACATGGCATCGGCATCGAT
1 ATGATGATCTTGTATAAGACCATGTCTAGGACATGGCATCAGCATC-AT
* *
47452670 ATGA-GA-CTTCGTATAAGACCATATCTAGGATATGGCAT
1 ATGATGATCTT-GTATAAGACCATGTCTAGGACATGGCAT
47452708 TGATACGTGA
Statistics
Matches: 205, Mismatches: 45, Indels: 45
0.69 0.15 0.15
Matches are distributed among these distances:
42 27 0.13
43 4 0.02
44 2 0.01
46 3 0.01
47 10 0.05
48 123 0.60
49 36 0.18
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (48 bp):
ATGATGATCTTGTATAAGACCATGTCTAGGACATGGCATCAGCATCAT
Found at i:47452667 original size:90 final size:90
Alignment explanation
Indices: 47452542--47452746 Score: 234
Period size: 90 Copynumber: 2.3 Consensus size: 90
47452532 GTATGATCTT
* * * * * * * *
47452542 GTATAAGACCATATCAGGGATATGGCTTCGACATCGTTAAGTGATTTCATATAAGACCATGTCT-
1 GTATAAGACCATGTCTGGGACATGGCATCGACATCGATAAGAGACTTCATATAAGACCATATCTA
* *
47452606 GGGTCATGGCATTGATATGATG-TCCC
66 GGAT-ATGGCATTGATACG-TGATCCC
* * *
47452632 GTATAAGACCATGTCTGGGACATGGCATCGGCATCGATATGAGACTTCGTATAAGACCATATCTA
1 GTATAAGACCATGTCTGGGACATGGCATCGACATCGATAAGAGACTTCATATAAGACCATATCTA
47452697 GGATATGGCATTGATACGTGATCCC
66 GGATATGGCATTGATACGTGATCCC
* * *
47452722 ATGTAAGACCATGTCTAGGACATGG
1 GTATAAGACCATGTCTGGGACATGG
47452747 TTTTGGCACT
Statistics
Matches: 97, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
89 2 0.02
90 92 0.95
91 3 0.03
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (90 bp):
GTATAAGACCATGTCTGGGACATGGCATCGACATCGATAAGAGACTTCATATAAGACCATATCTA
GGATATGGCATTGATACGTGATCCC
Found at i:47464591 original size:29 final size:29
Alignment explanation
Indices: 47464556--47464691 Score: 134
Period size: 29 Copynumber: 4.7 Consensus size: 29
47464546 CTACTCGATT
* *
47464556 TCGCACACTTAGTGCCACGTAATTT-AAGC
1 TCGCACACTTAGTGCCA-ATAATTTCCAGC
** **
47464585 TCGCACACACAGTGCCATATTTTTTCCAGC
1 TCGCACACTTAGTGCCA-ATAATTTCCAGC
*
47464615 TTGCACACTTAGTGCCAA-ATATTTCCAGC
1 TCGCACACTTAGTGCCAATA-ATTTCCAGC
*
47464644 ACGCACACTTAGTGCC-ATATATTTCCAGC
1 TCGCACACTTAGTGCCAATA-ATTTCCAGC
*
47464673 ACGCACACTTAGTGCCAAT
1 TCGCACACTTAGTGCCAAT
47464692 CTCGACACCA
Statistics
Matches: 89, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
28 1 0.01
29 69 0.78
30 19 0.21
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.28
Consensus pattern (29 bp):
TCGCACACTTAGTGCCAATAATTTCCAGC
Found at i:47464625 original size:59 final size:58
Alignment explanation
Indices: 47464557--47464690 Score: 162
Period size: 59 Copynumber: 2.3 Consensus size: 58
47464547 TACTCGATTT
** * * *
47464557 CGCACACTTAGTGCCACGTAATTT-AAGCTCGCACACACAGTGCCATATTTTTTCCAGCT
1 CGCACACTTAGTGCCAAAT-ATTTCAAGCACGCACACACAGTGCCATA-TATTTCCAGCA
* * **
47464616 TGCACACTTAGTGCCAAATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCAAATATTTCAAGCACGCACACACAGTGCCATATATTTCCAGCA
47464674 CGCACACTTAGTGCCAA
1 CGCACACTTAGTGCCAA
47464691 TCTCGACACC
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
58 29 0.45
59 35 0.55
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.27
Consensus pattern (58 bp):
CGCACACTTAGTGCCAAATATTTCAAGCACGCACACACAGTGCCATATATTTCCAGCA
Found at i:47476593 original size:40 final size:40
Alignment explanation
Indices: 47476485--47476654 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
47476475 CGGGATTTAA
* * * * *
47476485 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
47476525 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
47476565 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
47476605 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
47476645 CCGGATATAT
1 CCGGATATAT
47476655 TTCCAATGTT
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.01
40 112 0.99
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:47484688 original size:40 final size:40
Alignment explanation
Indices: 47484580--47484749 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
47484570 CGGGATTTAA
* * * * *
47484580 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
47484620 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
47484660 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
47484700 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
47484740 CCGGATATAT
1 CCGGATATAT
47484750 TTCCAATGTT
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.01
40 112 0.99
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:47493879 original size:40 final size:40
Alignment explanation
Indices: 47493832--47493934 Score: 107
Period size: 40 Copynumber: 2.4 Consensus size: 40
47493822 CGGCTAAGAA
*
47493832 TGGCACTTAGTGTGCGGTTTGAAATAACTTCAGCTAAATG
1 TGGCACTTAGTGTGCGATTTGAAATAACTTCAGCTAAATG
* * * *
47493872 TGGCACTTGGTGTTCGATTTGAGATAGCTTCAGCTATATATATATG
1 TGGCACTTAGTGTGCGATTTGAAATAACTTCAGC----TA-A-ATG
47493918 TGGCACTTAGTGTGCGA
1 TGGCACTTAGTGTGCGA
47493935 AATATTGAGA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
40 29 0.58
44 2 0.04
45 1 0.02
46 18 0.36
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (40 bp):
TGGCACTTAGTGTGCGATTTGAAATAACTTCAGCTAAATG
Found at i:47493949 original size:28 final size:28
Alignment explanation
Indices: 47493918--47493985 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
47493908 TATATATATG
47493918 TGGCACTTAGTGTGCGAAATATTGAGAA
1 TGGCACTTAGTGTGCGAAATATTGAGAA
* * * *
47493946 TGGCACTTGGTGTGTGAGATATTGAGTA
1 TGGCACTTAGTGTGCGAAATATTGAGAA
*
47493974 TGACACTTAGTG
1 TGGCACTTAGTG
47493986 CGATAGACAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.26, C:0.10, G:0.31, T:0.32
Consensus pattern (28 bp):
TGGCACTTAGTGTGCGAAATATTGAGAA
Found at i:47500941 original size:39 final size:40
Alignment explanation
Indices: 47500887--47501103 Score: 332
Period size: 40 Copynumber: 5.5 Consensus size: 40
47500877 AAACCAAGTA
* * * *
47500887 CCTTCGGAATTTAG-CCGGATATAGCT-ACTTGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
47500926 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
47500966 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
47501006 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
47501046 CCTTCGGGACTTAGCCCGGA-ATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
47501085 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
47501104 TTATCATCCG
Statistics
Matches: 166, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
39 49 0.30
40 117 0.70
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:47500964 original size:40 final size:40
Alignment explanation
Indices: 47500920--47501107 Score: 333
Period size: 40 Copynumber: 4.7 Consensus size: 40
47500910 GCTACTTGCT
47500920 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
47500960 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
47501000 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
47501040 CAAATGCCTTCGGGACTTAGCCCGG-AATAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
47501079 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
47501108 CATCCGAATA
Statistics
Matches: 141, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
39 36 0.26
40 105 0.74
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:47506303 original size:29 final size:29
Alignment explanation
Indices: 47506213--47506400 Score: 229
Period size: 29 Copynumber: 6.5 Consensus size: 29
47506203 ACTCGATTTC
* * **
47506213 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
47506242 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
47506270 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
47506300 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
47506329 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
47506358 GCACACTTAGTG-CATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
47506386 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
47506401 ATCTCGTCAC
Statistics
Matches: 138, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
28 30 0.22
29 107 0.78
30 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.27
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:47512388 original size:39 final size:40
Alignment explanation
Indices: 47512330--47512430 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 40
47512320 AAATTGAATG
* *
47512330 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * * *
47512369 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
47512409 ATATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
47512431 GCATTCGTGC
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 29 0.55
40 24 0.45
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.22
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:47512423 original size:40 final size:40
Alignment explanation
Indices: 47512330--47512480 Score: 180
Period size: 40 Copynumber: 3.8 Consensus size: 40
47512320 AAATTGAATG
* * * * *
47512330 ATATCCGGGCTAAGCCCCGAAGACAATTATGCT-GAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
47512369 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
47512409 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* *
47512449 AAATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
47512481 AAATCGTGAT
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
39 32 0.33
40 62 0.65
41 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:47512495 original size:40 final size:38
Alignment explanation
Indices: 47512326--47512497 Score: 161
Period size: 40 Copynumber: 4.4 Consensus size: 38
47512316 TGAGAAATTG
* *
47512326 AATG-ATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-A
1 AATGTATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCA
* * *
47512365 AAT-TATATCCGGGTTAAGACCCGAAGGCAATTGTGCT
1 AATGTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
* *
47512402 AGTAGCTATATCCGGGCTAAGACCCGAAGGCATTCGTGCA
1 AAT-G-TATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
* *
47512442 AGTTGTTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCA
1 A-ATG-TATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
47512482 AATCGTGATATCCGGG
1 AAT-GT-ATATCCGGG
47512498 TAAAGTCCCG
Statistics
Matches: 109, Mismatches: 16, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
36 2 0.02
37 4 0.04
38 2 0.02
39 26 0.24
40 74 0.68
41 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (38 bp):
AATGTATATCCGGGCTAAGACCCGAAGGCATTTGTGCA
Found at i:47515166 original size:40 final size:38
Alignment explanation
Indices: 47515122--47515271 Score: 153
Period size: 38 Copynumber: 3.9 Consensus size: 38
47515112 ATATCACGAT
*
47515122 TTGCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAAC
1 TTGCACAAATGCCTTCGGGTCTTAGCCCGGATAT-A-AAC
* *
47515162 TTGCACGAATGCCTTCGGGTCTTAGCCCGGATATAGAC
1 TTGCACAAATGCCTTCGGGTCTTAGCCCGGATATAAAC
* * *
47515200 TAGCACAATTGCCTTCGGGTCTTAACCCGG--ATAAA-
1 TTGCACAAATGCCTTCGGGTCTTAGCCCGGATATAAAC
* * *
47515235 TTTCAGCATAATTGTCTTCGGGGCTTAGCCCGGATAT
1 TTGCA-CA-AA-TGCCTTCGGGTCTTAGCCCGGATAT
47515272 CATTCAATTT
Statistics
Matches: 91, Mismatches: 14, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
35 3 0.03
36 6 0.07
37 1 0.01
38 46 0.51
39 1 0.01
40 34 0.37
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (38 bp):
TTGCACAAATGCCTTCGGGTCTTAGCCCGGATATAAAC
Found at i:47523173 original size:40 final size:40
Alignment explanation
Indices: 47523114--47523282 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 40
47523104 CGGGACTTTA
* * *
47523114 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
47523154 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
47523194 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * *
47523234 CCCGGATAT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG
1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG
47523274 CCCGGATAT
1 CCCGGATAT
47523283 CATTCAATTT
Statistics
Matches: 106, Mismatches: 20, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
37 3 0.03
38 3 0.03
39 1 0.01
40 99 0.93
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:47530732 original size:40 final size:40
Alignment explanation
Indices: 47530535--47530718 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
47530525 CGAATGATGT
* * *
47530535 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
47530575 CCGGACTAAGAT-CCGAAGGCATTCGTGCGAGTTACTA-AA
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
*
47530614 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-AA
1 -CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
47530654 TCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
47530694 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
47530719 AACGAGTAGC
Statistics
Matches: 127, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
38 1 0.01
39 33 0.26
40 86 0.68
41 7 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:47530740 original size:79 final size:79
Alignment explanation
Indices: 47530534--47530741 Score: 230
Period size: 79 Copynumber: 2.6 Consensus size: 79
47530524 TCGAATGATG
* *
47530534 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGT-GACTATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTAG-CTATATCCGG-TTAAGATCCGAAGGCAT
47530597 TCGTGCGAGTTACTAAA
63 TCGTGCGAGTTACTAAA
* * *
47530614 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTA-CTAAATCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TAGCTATATCCGGTTAAGAT-CCGAAGGCAT
*
47530676 TTGTGCGAGTTACTATAA
63 TCGTGCGAGTTACTA-AA
* **
47530694 -CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATATCCGGTTAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAA
47530742 ACTTGAAGGT
Statistics
Matches: 108, Mismatches: 12, Indels: 17
0.79 0.09 0.12
Matches are distributed among these distances:
78 4 0.04
79 65 0.60
80 30 0.28
81 9 0.08
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGCTATATCCGGTTAAGATCCGAAGGCATTCG
TGCGAGTTACTAAA
Found at i:47537554 original size:44 final size:43
Alignment explanation
Indices: 47537484--47537650 Score: 178
Period size: 43 Copynumber: 3.9 Consensus size: 43
47537474 GGAACTTTGA
* *
47537484 CATCGATCTGAGATATCGTGTAAGACCGTGTCTGGGACACAGG
1 CATCGATCTGAGATTTCGTGTAAGACCATGTCTGGGACACAGG
* * *
47537527 CCTCGATTTGAGATTTACGTGTAAGACCATGTCTGGGACATAGG
1 CATCGATCTGAGATTT-CGTGTAAGACCATGTCTGGGACACAGG
* * *
47537571 CATCGTAACT--GATTTCGTGTAAGACCCTGTCTGGGACAGAGG
1 CATCG-ATCTGAGATTTCGTGTAAGACCATGTCTGGGACACAGG
* * * *
47537613 CATCGATACTGA-ATTACATGCAAAACCATGTCTGGGAC
1 CATCGAT-CTGAGATTTCGTGTAAGACCATGTCTGGGAC
47537651 GTTGGTATTG
Statistics
Matches: 103, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
41 1 0.01
42 32 0.31
43 39 0.38
44 29 0.28
45 2 0.02
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (43 bp):
CATCGATCTGAGATTTCGTGTAAGACCATGTCTGGGACACAGG
Found at i:47538990 original size:18 final size:17
Alignment explanation
Indices: 47538969--47539027 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
47538959 TAGAAAAATC
* *
47538969 AAAAGAAAAAGAACAAG
1 AAAAAAAAAAGAAAAAG
*
47538986 AAAAAAAGAATGAAAAAG
1 AAAAAAA-AAAGAAAAAG
*
47539004 -AAAAAAAAAGAAAGTAG
1 AAAAAAAAAAGAAA-AAG
47539021 AAAAAAA
1 AAAAAAA
47539028 GAGAGGAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
16 6 0.18
17 14 0.41
18 14 0.41
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.03
Consensus pattern (17 bp):
AAAAAAAAAAGAAAAAG
Found at i:47538994 original size:20 final size:18
Alignment explanation
Indices: 47538969--47539016 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
47538959 TAGAAAAATC
47538969 AAAAGAAAAAGAACAAGAAA
1 AAAAGAAAAA-AACAA-AAA
*
47538989 AAAAGAATGAAAAAGAAAAA
1 AAAAGAA--AAAAACAAAAA
47539009 AAAAGAAA
1 AAAAGAAA
47539017 GTAGAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 1 0.04
20 17 0.68
21 4 0.16
22 3 0.12
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAAAACAAAAA
Found at i:47539017 original size:24 final size:23
Alignment explanation
Indices: 47538971--47539025 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
47538961 GAAAAATCAA
*
47538971 AAGAAAAAGAACAAGAAAAAAAG
1 AAGAAAAAGAACAAAAAAAAAAG
47538994 AATGAAAAAGAA-AAAAAAAGAAAG
1 AA-GAAAAAGAACAAAAAAA-AAAG
*
47539018 TAGAAAAA
1 AAGAAAAA
47539026 AAGAGAGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (23 bp):
AAGAAAAAGAACAAAAAAAAAAG
Found at i:47539022 original size:17 final size:18
Alignment explanation
Indices: 47538983--47539039 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 18
47538973 GAAAAAGAAC
47538983 AAGAAAAAAAGAATGAAA
1 AAGAAAAAAAGAATGAAA
47539001 AAGAAAAAAA-AA-GAAA
1 AAGAAAAAAAGAATGAAA
* *
47539017 GTAGAAAAAAAGAGAGGAAA
1 -AAGAAAAAAAGA-ATGAAA
47539037 AAG
1 AAG
47539040 TGAGAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
16 4 0.12
17 11 0.33
18 11 0.33
19 3 0.09
20 4 0.12
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (18 bp):
AAGAAAAAAAGAATGAAA
Found at i:47539036 original size:20 final size:17
Alignment explanation
Indices: 47538977--47539039 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 17
47538967 TCAAAAGAAA
*
47538977 AAGAACAAGAAAAAAAG
1 AAGAAAAAGAAAAAAAG
47538994 AATGAAAAAGAAAAAAA-
1 AA-GAAAAAGAAAAAAAG
*
47539011 AAGAAAGTAGAAAAAAAG
1 AAGAAA-AAGAAAAAAAG
47539029 AGAGGAAAAAG
1 A-A-GAAAAAG
47539040 TGAGAAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
16 4 0.11
17 13 0.34
18 14 0.37
19 3 0.08
20 4 0.11
ACGTcount: A:0.75, C:0.02, G:0.21, T:0.03
Consensus pattern (17 bp):
AAGAAAAAGAAAAAAAG
Found at i:47541538 original size:22 final size:22
Alignment explanation
Indices: 47541510--47541553 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
47541500 GCGAAAGGTT
47541510 GAATTTGTGAAACAACTTCATC
1 GAATTTGTGAAACAACTTCATC
47541532 GAATTTGTGAAACAACTTCATC
1 GAATTTGTGAAACAACTTCATC
47541554 AAAGAGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (22 bp):
GAATTTGTGAAACAACTTCATC
Found at i:47545360 original size:94 final size:93
Alignment explanation
Indices: 47545262--47545519 Score: 220
Period size: 94 Copynumber: 2.8 Consensus size: 93
47545252 GACGAGGGCT
** *
47545262 AGTGTAAGATGTGTCTAGGACATGCATCAGCCAC-ATCATGATAGCCCGTGTAAGACCACGTCTG
1 AGTGTAAGACATGTCTAGGACATGCATCAGCCACAATCATGATAGCCAGTGTAAGA-CACGTCTG
47545326 GGACATGGCATCGATGTAGAGGTGAATGCC
65 GGACAT-GCATCGATGTAGAGGTGAATGCC
* * * * * * **
47545356 AGTGTAATACATGTCTGGGACATGCATCGGCCTCAATGATGTTAGCCAGTGTAAGACGTGTCTGG
1 AGTGTAAGACATGTCTAGGACATGCATCAGCCACAATCATGATAGCCAGTGTAAGACACGTCTGG
* *** *
47545421 GACATGCATCG--GCTA-AGTTTCGTGCT
66 GACATGCATCGATG-TAGAGGTGAATGCC
* * * * ** *
47545447 AGTGTAAGACATGTTTGGGACATGCATCAG-CACATATACACGAGAGATAGTGTAAGATCATGTC
1 AGTGTAAGACATGTCTAGGACATGCATCAGCCACA-AT-CATGATAGCCAGTGTAAGA-CACGTC
47545511 TGGGACATG
63 TGGGACATG
47545520 ACAGCGGCAA
Statistics
Matches: 132, Mismatches: 27, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
90 3 0.02
91 36 0.27
92 15 0.11
93 20 0.15
94 40 0.30
95 18 0.14
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (93 bp):
AGTGTAAGACATGTCTAGGACATGCATCAGCCACAATCATGATAGCCAGTGTAAGACACGTCTGG
GACATGCATCGATGTAGAGGTGAATGCC
Found at i:47552802 original size:47 final size:46
Alignment explanation
Indices: 47552728--47553086 Score: 243
Period size: 47 Copynumber: 7.7 Consensus size: 46
47552718 TGGGGTTATG
*
47552728 TGAGAGCCAGTATAAGACCATGTCTGGGACATGACATCGGCATTGAGA
1 TGAGAGCCAGTGTAAGA-CATGTCTGGGACATG-CATCGGCATTGAGA
* * * * *
47552776 TGAGGGCTAGTGTAAGACGTGTCTGGGACATGCATCAGC--TGCATCA
1 TGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTG-A-GA
* * * *
47552822 TGATAGCCCGTGT-AGACCACGTCTGGGACATGGCATCGGCATAGA-A
1 TGAGAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGAGA
* * *
47552868 GTGAGTGCCAGTGTAAGACATGT-TGGGACATGCATCGGCCTCGATGA
1 -TGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGA-GA
** * * *
47552915 TGTTAGCCAGTGTAAGACATGTCTGGGACATGCATC-G-ACTAAGT
1 TGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGA
** * * * *
47552959 TTTGTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCACGTAT-ACA
1 TGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCA--T-TGAGA
* * * *
47553007 CG-GAGCTAGTGTAAGACATGTCTGGGACATGGCATCGGCCTCGATGGA
1 TGAGAGCCAGTGTAAGACATGTCTGGGACAT-GCATCGGCATTGA--GA
* *
47553055 -GATAGCCAGCGTAAGACCATGTCTGGGACATG
1 TGAGAGCCAGTGTAAGA-CATGTCTGGGACATG
47553087 GAAGTGGTAA
Statistics
Matches: 244, Mismatches: 45, Indels: 44
0.73 0.14 0.13
Matches are distributed among these distances:
44 35 0.14
45 17 0.07
46 60 0.25
47 77 0.32
48 39 0.16
49 16 0.07
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (46 bp):
TGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGA
Found at i:47552881 original size:93 final size:94
Alignment explanation
Indices: 47552732--47553045 Score: 335
Period size: 93 Copynumber: 3.4 Consensus size: 94
47552722 GTTATGTGAG
* * * *
47552732 AGCCAGTATAAGACCATGTCTGGGACATGACATCGGCATTG-AGATGAGGGCTAGTGTAAGACGT
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA-TGAAGATGAGTGCTAGTGTAAGACAT
47552796 GTCTGGGACATGCATCAGCT-GCATCATGAT
65 GTCTGGGACATGCATCAGCTCG-ATCATGAT
* * *
47552826 AGCCCGTGT-AGACCACGTCTGGGACATGGCATCGGCATAGAAG-TGAGTGCCAGTGTAAGACAT
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCAT-GAAGATGAGTGCTAGTGTAAGACAT
* * *
47552889 GT-TGGGACATGCATCGGCCTCGATGATGTT
65 GTCTGGGACATGCATCAG-CTCGATCATGAT
* * **
47552919 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGAC-T-AAGTTTTGTGCTAGTGTAAGACATG
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATGAAGATGAGTGCTAGTGTAAGACATG
* * *
47552980 TCTGGGACATGCATCAGCACGTATACACG-G
66 TCTGGGACATGCATCAGCTCG-AT-CATGAT
*
47553010 AGCTAGTGTAAGA-CATGTCTGGGACATGGCATCGGC
1 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
47553046 CTCGATGGAG
Statistics
Matches: 187, Mismatches: 23, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
89 3 0.02
90 22 0.12
91 43 0.23
92 31 0.17
93 75 0.40
94 13 0.07
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (94 bp):
AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCATGAAGATGAGTGCTAGTGTAAGACATG
TCTGGGACATGCATCAGCTCGATCATGAT
Found at i:47553969 original size:55 final size:54
Alignment explanation
Indices: 47553854--47553972 Score: 150
Period size: 55 Copynumber: 2.2 Consensus size: 54
47553844 CTTAATCTTT
* * * *
47553854 TAAA-TCAGTATTGTCCACGGTTAGGCCACACGGGCGCGTGCCATAGCGGTGTC
1 TAAAGTCAGTATTGCCCACGGGTAGGCCACACGGGCGCGTGCCATAGCCGTGCC
* * *
47553907 TATAAGTCAGTATTGCCCACGGGTAGGCCACACGGGCGTGTGTCATGGCCGTGCCC
1 TA-AAGTCAGTATTGCCCACGGGTAGGCCACACGGGCGCGTGCCATAGCCGTG-CC
47553963 TAAAGTCAGT
1 TAAAGTCAGT
47553973 GTCACACACG
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
53 2 0.04
54 2 0.04
55 49 0.88
56 3 0.05
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.23
Consensus pattern (54 bp):
TAAAGTCAGTATTGCCCACGGGTAGGCCACACGGGCGCGTGCCATAGCCGTGCC
Found at i:47553983 original size:55 final size:55
Alignment explanation
Indices: 47553869--47553984 Score: 126
Period size: 55 Copynumber: 2.1 Consensus size: 55
47553859 CAGTATTGTC
* * * ** *
47553869 CACGGTTAGGCCACACGGGCGCGTGCCATAGCGGTGTCTATAAGTCAGTATTGCC
1 CACGGGTAGGCCACACGGGCGCGTGCCATAGCCGTGCCTATAAGTCAGTATCACA
* * * *
47553924 CACGGGTAGGCCACACGGGCGTGTGTCATGGCCGTGCCCTA-AAGTCAGTGTCACA
1 CACGGGTAGGCCACACGGGCGCGTGCCATAGCCGTG-CCTATAAGTCAGTATCACA
47553979 CACGGG
1 CACGGG
47553985 CTGAGGACGT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
55 47 0.94
56 3 0.06
ACGTcount: A:0.20, C:0.28, G:0.33, T:0.19
Consensus pattern (55 bp):
CACGGGTAGGCCACACGGGCGCGTGCCATAGCCGTGCCTATAAGTCAGTATCACA
Found at i:47556240 original size:78 final size:77
Alignment explanation
Indices: 47556129--47556294 Score: 251
Period size: 77 Copynumber: 2.1 Consensus size: 77
47556119 GGTCTTTAAC
* * *
47556129 CCGGATATTTTTCCAGCACGTAGCCTGCGGACCTCAAGTCCGGATATATTTCTAGCATATAGCCT
1 CCGGATATTTTTCCAGCACATAGCCTGCGGACCTCAAGTCC-GATATATTTCCAACATATAGCCT
47556194 GCGGACCTCATGT
65 GCGGACCTCATGT
* * *
47556207 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCCGATATTTTTCCAACATATAGCCTG
1 CCGGATATTTTTCCAGCACATAGCCTGCGGACCTCAAGTCCGATATATTTCCAACATATAGCCTG
47556272 CGGACCTCATGT
66 CGGACCTCATGT
**
47556284 CTAGATATTTT
1 CCGGATATTTT
47556295 CAATCTCATA
Statistics
Matches: 80, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
77 42 0.52
78 38 0.47
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.31
Consensus pattern (77 bp):
CCGGATATTTTTCCAGCACATAGCCTGCGGACCTCAAGTCCGATATATTTCCAACATATAGCCTG
CGGACCTCATGT
Found at i:47556295 original size:38 final size:39
Alignment explanation
Indices: 47556129--47556294 Score: 253
Period size: 39 Copynumber: 4.3 Consensus size: 39
47556119 GGTCTTTAAC
** *
47556129 CCGGATATTTTTCCAGCACGTAGCCTGCGGACCTCAAGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* *
47556168 CCGGATATATTTCTAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
47556207 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
*
47556246 CC-GATATTTTTCCAACATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
**
47556284 CTAGATATTTT
1 CCGGATATTTT
47556295 CAATCTCATA
Statistics
Matches: 117, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
38 36 0.31
39 81 0.69
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.31
Consensus pattern (39 bp):
CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
Found at i:47558204 original size:17 final size:17
Alignment explanation
Indices: 47558173--47558205 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
47558163 TATAACACCA
47558173 ACAACATATATTATAAT
1 ACAACATATATTATAAT
47558190 ACAA-ATATATGTATAA
1 ACAACATATAT-TATAA
47558206 ATTACATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (17 bp):
ACAACATATATTATAAT
Found at i:47564192 original size:39 final size:39
Alignment explanation
Indices: 47564149--47564315 Score: 262
Period size: 39 Copynumber: 4.3 Consensus size: 39
47564139 GGTCTTTAAC
** *
47564149 CCGGATATTTTTCCAGCACGTAGCCTGCGGACCTCAAGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* * *
47564188 CCGGATATATTTCTAGCATATAGCCTGCGAACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* *
47564227 CCGGATATTTTCCCAGCATATAGCCTGTGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
47564266 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
47564305 CCGGATATTTT
1 CCGGATATTTT
47564316 CAATCTCATA
Statistics
Matches: 115, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 115 1.00
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.31
Consensus pattern (39 bp):
CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
Found at i:47566223 original size:17 final size:17
Alignment explanation
Indices: 47566192--47566224 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
47566182 TATAACACCA
47566192 ACAACATATATTATAAT
1 ACAACATATATTATAAT
47566209 ACAA-ATATATGTATAA
1 ACAACATATAT-TATAA
47566225 ATTACATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (17 bp):
ACAACATATATTATAAT
Found at i:47566876 original size:14 final size:14
Alignment explanation
Indices: 47566853--47566882 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
47566843 TTGGAAATAT
47566853 GTTGAATTGGATTG
1 GTTGAATTGGATTG
*
47566867 GTTGATTTGGATTG
1 GTTGAATTGGATTG
47566881 GT
1 GT
47566883 CTAGGTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.37, T:0.47
Consensus pattern (14 bp):
GTTGAATTGGATTG
Found at i:47568797 original size:29 final size:29
Alignment explanation
Indices: 47568763--47568865 Score: 154
Period size: 29 Copynumber: 3.6 Consensus size: 29
47568753 TAATCAGCCG
** *
47568763 CGCACACTTAGTGCCATATACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAGCT
47568792 CGCACACTTAGTGCCATGCATTTCAAGCT
1 CGCACACTTAGTGCCATGCATTTCAAGCT
47568821 CGCACACTTAGTGCCATGCATTTCAAGCT
1 CGCACACTTAGTGCCATGCATTTCAAGCT
*
47568850 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
47568866 ATCTCTCAAC
Statistics
Matches: 69, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
28 3 0.04
29 66 0.96
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAGCT
Found at i:47576875 original size:29 final size:29
Alignment explanation
Indices: 47576841--47576914 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
47576831 TAATCAGCCG
*
47576841 CGCACACTTAGTGCCATATACTTT-AAACT
1 CGCACACTTAGTGCCATACA-TTTCAAACT
* *
47576870 CGCACACTTAGTGCCATGCATTTCAAGCT
1 CGCACACTTAGTGCCATACATTTCAAACT
*
47576899 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
47576915 ATCTCTCAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATACATTTCAAACT
Found at i:47578800 original size:20 final size:20
Alignment explanation
Indices: 47578763--47578801 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
47578753 GAACACAAGC
*
47578763 TGTCCAATCAGCTCACTTAG
1 TGTCCAATCAGCTAACTTAG
* *
47578783 TGTCCATTCGGCTAACTTA
1 TGTCCAATCAGCTAACTTA
47578802 TGTAGTGAAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.33
Consensus pattern (20 bp):
TGTCCAATCAGCTAACTTAG
Found at i:47584989 original size:31 final size:32
Alignment explanation
Indices: 47584951--47585017 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
47584941 GAAATAGGGT
* *
47584951 CACACGCCCGTGTAGG-TAGGCCGTGTGGTCA
1 CACACGCCCATGTAGGTTAGGCCGTATGGTCA
*
47584982 CACACGCCCATGTGGGTTAGGCCGTATGGTCA
1 CACACGCCCATGTAGGTTAGGCCGTATGGTCA
47585014 CACA
1 CACA
47585018 TGCTCGTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 14 0.44
32 18 0.56
ACGTcount: A:0.19, C:0.30, G:0.31, T:0.19
Consensus pattern (32 bp):
CACACGCCCATGTAGGTTAGGCCGTATGGTCA
Found at i:47586770 original size:28 final size:28
Alignment explanation
Indices: 47586728--47586804 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
47586718 ATCTTCGATG
*
47586728 TCTCGCGCACTAAGTGCCATACCCAATA
1 TCTCGCACACTAAGTGCCATACCCAATA
* ** * *
47586756 TCTCGCACACCAAGTGTTATTCTCAATA
1 TCTCGCACACTAAGTGCCATACCCAATA
*
47586784 TTTCGCACACTAAGTGCCATA
1 TCTCGCACACTAAGTGCCATA
47586805 TATATATATA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.27
Consensus pattern (28 bp):
TCTCGCACACTAAGTGCCATACCCAATA
Found at i:47586809 original size:2 final size:2
Alignment explanation
Indices: 47586802--47586848 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
47586792 ACTAAGTGCC
47586802 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47586844 AT AT A
1 AT AT A
47586849 GCCGAAGCTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:47586905 original size:40 final size:40
Alignment explanation
Indices: 47586847--47586922 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
47586837 TATATATATA
47586847 TAGCCGAAGCTATCTCAAATC-GCACATC-AAGTGCCACATT
1 TAGCCGAAGCTATCTCAAA-CAGCACA-CGAAGTGCCACATT
*
47586887 TAGCCGAAGCTATTTCAAACAGCACACGAAGTGCCA
1 TAGCCGAAGCTATCTCAAACAGCACACGAAGTGCCA
47586923 TTCTTAACCG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
39 2 0.06
40 31 0.94
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (40 bp):
TAGCCGAAGCTATCTCAAACAGCACACGAAGTGCCACATT
Found at i:47588147 original size:15 final size:15
Alignment explanation
Indices: 47588127--47588157 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
47588117 TTAACATCAC
47588127 TTAATTTCCATATTA
1 TTAATTTCCATATTA
47588142 TTAATTTCCATATTA
1 TTAATTTCCATATTA
47588157 T
1 T
47588158 ATCATAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (15 bp):
TTAATTTCCATATTA
Found at i:47590186 original size:20 final size:20
Alignment explanation
Indices: 47590157--47590197 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
47590147 TGCTTGCTCT
*
47590157 GTTTCTTTCCTATAAAAATA
1 GTTTCCTTCCTATAAAAATA
47590177 GTTTCCTTCCTATAAAAATA
1 GTTTCCTTCCTATAAAAATA
47590197 G
1 G
47590198 ACTCAATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (20 bp):
GTTTCCTTCCTATAAAAATA
Found at i:47592166 original size:46 final size:46
Alignment explanation
Indices: 47592116--47592288 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
47592106 TGGTTGAGCA
*
47592116 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
47592162 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
47592209 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCAAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
47592255 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
47592289 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 60 0.56
47 29 0.27
48 3 0.03
50 6 0.06
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:47592272 original size:93 final size:93
Alignment explanation
Indices: 47592113--47592283 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
47592103 GGATGGTTGA
* * *
47592113 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCATTGAGT
47592178 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
47592206 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCAAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCATTGAGT
47592271 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
47592284 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:47592550 original size:19 final size:20
Alignment explanation
Indices: 47592513--47592550 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
47592503 ATAAGGTGGT
47592513 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
47592533 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
47592551 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:47599173 original size:46 final size:46
Alignment explanation
Indices: 47599123--47599294 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
47599113 TGGTTGAGCA
*
47599123 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
47599169 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
47599216 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
47599262 CCCGAGCTCGTTGAGTTGAGT-CGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
47599295 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 13, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
43 6 0.06
45 14 0.13
46 49 0.46
47 29 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:47599279 original size:93 final size:92
Alignment explanation
Indices: 47599120--47599289 Score: 286
Period size: 93 Copynumber: 1.8 Consensus size: 92
47599110 GGATGGTTGA
* *
47599120 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
47599185 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGT-CGAGTTCGTGAGATGTAACTAG
* * *
47599213 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
47599278 TGAGTCGAGTTC
66 TGAGTCGAGTTC
47599290 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
92 7 0.10
93 65 0.90
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCGAGTTCGTGAGATGTAACTAG
Found at i:47599556 original size:19 final size:20
Alignment explanation
Indices: 47599519--47599556 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
47599509 ATAAGGTGGT
47599519 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
47599539 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
47599557 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:47600777 original size:54 final size:54
Alignment explanation
Indices: 47600613--47600785 Score: 204
Period size: 55 Copynumber: 3.2 Consensus size: 54
47600603 GGGCGTTACA
* * *
47600613 TACATGGTATCCTTGCCTTAT-GAACTCACCATTGCCATGCCTTGGCATGGTCT
1 TACATGGTATCCTTGCCTTATAAAACTTACCAATGCCATGCCTTGGCATGGTCT
* * ** * * *
47600666 TACATGGGATCTTTGCCTTATAGAAGTTTATCAATGCCATGTCTTGACATGGTCT
1 TACATGGTATCCTTGCCTTATA-AAACTTACCAATGCCATGCCTTGGCATGGTCT
* * *
47600721 TACATGATTTCCTTGCCTTGTAAAACTTACCAATGCCATGCCTTGGCATGGTCT
1 TACATGGTATCCTTGCCTTATAAAACTTACCAATGCCATGCCTTGGCATGGTCT
*
47600775 TACTTGGTATC
1 TACATGGTATC
47600786 TTTAAACCCT
Statistics
Matches: 95, Mismatches: 23, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
53 19 0.20
54 35 0.37
55 41 0.43
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.36
Consensus pattern (54 bp):
TACATGGTATCCTTGCCTTATAAAACTTACCAATGCCATGCCTTGGCATGGTCT
Found at i:47611990 original size:33 final size:36
Alignment explanation
Indices: 47611948--47612022 Score: 120
Period size: 33 Copynumber: 2.2 Consensus size: 36
47611938 AAATTGCATA
*
47611948 AATTTTATTTTTTCGAG-CTAGGGAC-AAAATTGG-
1 AATTTTATTTTTTCGAGCCTAGGGACGAAAAATGGT
47611981 AATTTTATTTTTTCGAGCCTAGGGACGAAAAATGGT
1 AATTTTATTTTTTCGAGCCTAGGGACGAAAAATGGT
47612017 AATTTT
1 AATTTT
47612023 TCCTAGGATG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
33 17 0.45
34 8 0.21
35 7 0.18
36 6 0.16
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (36 bp):
AATTTTATTTTTTCGAGCCTAGGGACGAAAAATGGT
Found at i:47612704 original size:57 final size:58
Alignment explanation
Indices: 47612581--47612721 Score: 158
Period size: 57 Copynumber: 2.4 Consensus size: 58
47612571 CTCATTCCTA
* ** * * *
47612581 AAAGGATTTAGCCCAGACGAGTAATCTTGATATAAGCCCTCTCGAGCATATGTTATAG
1 AAAGGATTTAGCCTAGACGAGTAATCCAGATACAAGCCCTCTAGAGCATATGTCATAG
** * * *
47612639 ATTGGATTTAGCCTAGACGGGTAATCCAGAT-CAAGCTCTTTAGAGCATATGTCATAG
1 AAAGGATTTAGCCTAGACGAGTAATCCAGATACAAGCCCTCTAGAGCATATGTCATAG
* *
47612696 AAAGGATTTAGCCTGGACTAGTAATC
1 AAAGGATTTAGCCTAGACGAGTAATC
47612722 TTGTTGTATA
Statistics
Matches: 67, Mismatches: 16, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
57 42 0.63
58 25 0.37
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (58 bp):
AAAGGATTTAGCCTAGACGAGTAATCCAGATACAAGCCCTCTAGAGCATATGTCATAG
Found at i:47614386 original size:93 final size:93
Alignment explanation
Indices: 47614274--47614444 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
47614264 CCCATAAGTG
* * * *
47614274 AACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAAATCGGACTCAACTCAAT
1 AACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAAATCGGACTCAACTCAAC
47614339 GAGCTCGGATGCCTAGTTACATCTCTTT
66 GAGCTCGGATGCCTAGTTACATCTCTTT
* * *
47614367 AACTCGAACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAAGTCAAC
1 AACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAAATCGGACTCAACTCAAC
*
47614432 GAGTTCGGATGCC
66 GAGCTCGGATGCC
47614445 CAAATATTCT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (93 bp):
AACTCGAACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAAATCGGACTCAACTCAAC
GAGCTCGGATGCCTAGTTACATCTCTTT
Found at i:47614440 original size:46 final size:46
Alignment explanation
Indices: 47614265--47614440 Score: 173
Period size: 46 Copynumber: 3.8 Consensus size: 46
47614255 TGTAACCCGC
* *
47614265 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* * *
47614311 CCATAAGTGAAATCGGACTCAACTCAATGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTCGCAT
* * *
47614361 CTC-T---TTAACTCGAACTCAACTCAACGAGTTCGGACATTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
47614404 CCATAAGTGAACTCGGACTCAAGTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
47614441 TGCCCAAATA
Statistics
Matches: 105, Mismatches: 14, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
42 3 0.03
43 6 0.06
44 1 0.01
46 61 0.58
47 25 0.24
49 1 0.01
50 5 0.05
51 3 0.03
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:47616507 original size:16 final size:16
Alignment explanation
Indices: 47616482--47616519 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
47616472 TGCATGAATG
47616482 CATG-TATCAATATAT
1 CATGTTATCAATATAT
47616497 CATGTTATCAATATAT
1 CATGTTATCAATATAT
47616513 CATGTTA
1 CATGTTA
47616520 GATGTTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (16 bp):
CATGTTATCAATATAT
Found at i:47616999 original size:22 final size:22
Alignment explanation
Indices: 47616967--47617023 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
47616957 GTTTGAGGGT
*
47616967 CACACGGGCGTGTCCCTTGGAC
1 CACACGAGCGTGTCCCTTGGAC
47616989 CACACGAGCGTGTCCCTTGGAC
1 CACACGAGCGTGTCCCTTGGAC
47617011 CACACGAGCGTGT
1 CACACGAGCGTGT
47617024 GAGCCCTGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.18, C:0.35, G:0.30, T:0.18
Consensus pattern (22 bp):
CACACGAGCGTGTCCCTTGGAC
Found at i:47619705 original size:27 final size:26
Alignment explanation
Indices: 47619663--47619714 Score: 86
Period size: 27 Copynumber: 2.0 Consensus size: 26
47619653 GCGAGGCTGC
47619663 CAGATATTGTGACAAGGCCACCAGAA
1 CAGATATTGTGACAAGGCCACCAGAA
*
47619689 CAGATATATGTGGCAAGGCCACCAGA
1 CAGATAT-TGTGACAAGGCCACCAGA
47619715 TTGCAACGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.37, C:0.23, G:0.25, T:0.15
Consensus pattern (26 bp):
CAGATATTGTGACAAGGCCACCAGAA
Found at i:47630798 original size:42 final size:43
Alignment explanation
Indices: 47630696--47630852 Score: 178
Period size: 43 Copynumber: 3.7 Consensus size: 43
47630686 TGTGTTATCT
* * * **
47630696 TGTAAGACCACGTCTGGGACGTTGGCTTTGA-ATTATGATTTATG
1 TGTAAGACCACTTCTGGGACGTTGGCATCGATATT-TGA-TTACA
* *
47630740 TGTAAGACCACTTCTGGAACGTTGGCATCG-TATTTGATTTCA
1 TGTAAGACCACTTCTGGGACGTTGGCATCGATATTTGATTACA
47630782 TGTAAGACC-CTATCTGGGACAG-TGGCATCGATATTTGATTACA
1 TGTAAGACCACT-TCTGGGAC-GTTGGCATCGATATTTGATTACA
*
47630825 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACTTCTGGGACGTTGGCAT
47630853 TGTACGAGCT
Statistics
Matches: 97, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
41 2 0.02
42 27 0.28
43 38 0.39
44 30 0.31
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (43 bp):
TGTAAGACCACTTCTGGGACGTTGGCATCGATATTTGATTACA
Found at i:47634976 original size:40 final size:40
Alignment explanation
Indices: 47634874--47635057 Score: 172
Period size: 40 Copynumber: 4.6 Consensus size: 40
47634864 AAATTGAATG
* * * * * *
47634874 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
47634914 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* *
47634954 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTAGTAGTT
* * * * * *
47634994 AAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
* * *
47635034 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
47635058 CTTGGTGCGG
Statistics
Matches: 119, Mismatches: 23, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
39 3 0.03
40 114 0.96
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTAGTAGTT
Found at i:47635082 original size:80 final size:80
Alignment explanation
Indices: 47634914--47635102 Score: 184
Period size: 80 Copynumber: 2.4 Consensus size: 80
47634904 GCTGGAAATT
* * *
47634914 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCTATATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATAGCTATATCCGGGCTAAGACCCGAAGGCA
***
47634979 TTCGTGCAAGTTGTT
66 TTCGTGCAAGTTACC
* * * * *
47634994 A-AATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGG
1 ATAA-CCGGGCTAAGACCCGAAGGCAATTGTGCAAATAGCT-ATATCCGGGCTAAGACCCGAAGG
* * **
47635057 CCTTGGTGCGGGTTACC
64 CATTCGTGCAAGTTACC
* * *
47635074 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
47635103 AACGAGTAGC
Statistics
Matches: 87, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
79 3 0.03
80 82 0.94
81 2 0.02
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (80 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATAGCTATATCCGGGCTAAGACCCGAAGGCA
TTCGTGCAAGTTACC
Found at i:47643021 original size:40 final size:39
Alignment explanation
Indices: 47642927--47643107 Score: 168
Period size: 39 Copynumber: 4.6 Consensus size: 39
47642917 AAATTGAATG
* * * * *
47642927 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGC-ATTGTGCTAGTAGTT
* *
47642966 ATA-CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAGCT
1 ATATCCGGGCTAAGACCCGAAGGC-ATTGTGCTAGTAGTT
* *
47643005 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATT-GTGCTAGTAGTT
* * * * *
47643045 AAATCCGGGCTAAGACCCGAAGGCATTGTGCAAATCGTG
1 ATATCCGGGCTAAGACCCGAAGGCATTGTGCTAGTAGTT
* * *
47643084 ATATCCGGGTTAAGTCCCGTAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
47643108 CTTGGTGCGG
Statistics
Matches: 120, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
38 9 0.08
39 57 0.47
40 54 0.45
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTGTGCTAGTAGTT
Found at i:47643090 original size:39 final size:38
Alignment explanation
Indices: 47642965--47643107 Score: 153
Period size: 40 Copynumber: 3.7 Consensus size: 38
47642955 TGCTGGAAAT
* *
47642965 TATA-CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCAAGTAG
*
47643003 CTATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TATATCCGGGCTAAGACCCGAAGGCATT-GTGCAAGTAG
* * *
47643043 TTAAATCCGGGCTAAGACCCGAAGGCATTGTGCAAATCG
1 -TATATCCGGGCTAAGACCCGAAGGCATTGTGCAAGTAG
* * *
47643082 TGATATCCGGGTTAAGTCCCGTAGGC
1 T-ATATCCGGGCTAAGACCCGAAGGC
47643108 CTTGGTGCGG
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
38 1 0.01
39 35 0.39
40 54 0.60
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (38 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCAAGTAG
Found at i:47647053 original size:25 final size:26
Alignment explanation
Indices: 47647001--47647053 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
47646991 CCCTTATAAT
* *
47647001 GTGAAAATGACCTTTTTTTACCCCTAG
1 GTGAAAATGACC-TATTATACCCCTAG
47647028 GTGAAAATGACC-ATTATACCCCTAG
1 GTGAAAATGACCTATTATACCCCTAG
47647053 G
1 G
47647054 GTTATGTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 12 0.50
27 12 0.50
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (26 bp):
GTGAAAATGACCTATTATACCCCTAG
Found at i:47647109 original size:10 final size:10
Alignment explanation
Indices: 47647094--47647132 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
47647084 TGCTTCTGTA
47647094 CATGATATGC
1 CATGATATGC
47647104 CATGATATGC
1 CATGATATGC
47647114 ACATGATATGC
1 -CATGATATGC
47647125 CATGATAT
1 CATGATAT
47647133 ATTCACATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (10 bp):
CATGATATGC
Done.