Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 97 of 410
Found at i:28478826 original size:80 final size:81
Alignment explanation
Indices: 28478686--28478891 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 81
28478676 CGGAATACAA
* * *
28478686 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGA-TAGAACGACTTGCACAAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
*
28478750 GCCTTCGGGTATTAGC
66 GCCTTCGGGTATTAAC
* * *
28478766 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAG-TC-ACTAGCACAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-TAGAACGACTAGCACAAA
*
28478829 TGCCTTCGGGTCTTAAC
65 TGCCTTCGGGTATTAAC
** * ** * *
28478846 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT
28478892 ATCATTCAAT
Statistics
Matches: 108, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
80 104 0.96
81 1 0.01
82 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (81 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
GCCTTCGGGTATTAAC
Found at i:28484054 original size:28 final size:29
Alignment explanation
Indices: 28484023--28484081 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
28484013 AAAGTGATTT
*
28484023 TTGACAAAAATGTCAATT-AGGGATTAAA
1 TTGACAAAAATGTAAATTGAGGGATTAAA
* * *
28484051 TTGAGAAAAGTGTAAATTGAGGGGTTAAA
1 TTGACAAAAATGTAAATTGAGGGATTAAA
28484080 TT
1 TT
28484082 ATGAAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 15 0.58
29 11 0.42
ACGTcount: A:0.42, C:0.03, G:0.24, T:0.31
Consensus pattern (29 bp):
TTGACAAAAATGTAAATTGAGGGATTAAA
Found at i:28485394 original size:19 final size:20
Alignment explanation
Indices: 28485370--28485410 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
28485360 TGGAATAGAG
28485370 TAGATGAAATGAT-TGTGTA
1 TAGATGAAATGATATGTGTA
**
28485389 TAGATGGCATGATATGTGTA
1 TAGATGAAATGATATGTGTA
28485409 TA
1 TA
28485411 AATTGGCTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.37
Consensus pattern (20 bp):
TAGATGAAATGATATGTGTA
Found at i:28489692 original size:40 final size:40
Alignment explanation
Indices: 28489556--28489709 Score: 157
Period size: 40 Copynumber: 3.9 Consensus size: 40
28489546 GTGTGCATGA
* *
28489556 GCAAATTGTGATATCCGGGCTAAGTCCCG-AGGACATTTAT
1 GCAAATTGTGATATCCGGGCTAAGACCCGAAGG-CATTTGT
* * ** * *
28489596 GCTAGTAATTATATCCGGGCTAAGACCCGAAGGCATTCGT
1 GCAAATTGTGATATCCGGGCTAAGACCCGAAGGCATTTGT
* * *
28489636 GCAAGTTGTTAAATCCGGGCTAAGACCCGAAGGCATTTGT
1 GCAAATTGTGATATCCGGGCTAAGACCCGAAGGCATTTGT
* * * *
28489676 GCAAATCGTGATATCCGGGTTAAGTCCCGTAGGC
1 GCAAATTGTGATATCCGGGCTAAGACCCGAAGGC
28489710 CTTGGTGCGG
Statistics
Matches: 93, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 90 0.97
41 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (40 bp):
GCAAATTGTGATATCCGGGCTAAGACCCGAAGGCATTTGT
Found at i:28497854 original size:40 final size:40
Alignment explanation
Indices: 28497718--28497871 Score: 157
Period size: 40 Copynumber: 3.9 Consensus size: 40
28497708 GTGTGCATGA
* *
28497718 GCAAATTGTGATATCCGGGCTAAGTCCCG-AGGACATTTAT
1 GCAAATTGTGATATCCGGGCTAAGACCCGAAGG-CATTTGT
* * ** * *
28497758 GCTAGTAATTATATCCGGGCTAAGACCCGAAGGCATTCGT
1 GCAAATTGTGATATCCGGGCTAAGACCCGAAGGCATTTGT
* * *
28497798 GCAAGTTGTTAAATCCGGGCTAAGACCCGAAGGCATTTGT
1 GCAAATTGTGATATCCGGGCTAAGACCCGAAGGCATTTGT
* * * *
28497838 GCAAATCGTGATATCCGGGTTAAGTCCCGTAGGC
1 GCAAATTGTGATATCCGGGCTAAGACCCGAAGGC
28497872 CTTGGTGCGG
Statistics
Matches: 93, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 90 0.97
41 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (40 bp):
GCAAATTGTGATATCCGGGCTAAGACCCGAAGGCATTTGT
Found at i:28514215 original size:13 final size:13
Alignment explanation
Indices: 28514197--28514223 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28514187 ATTAATTATT
28514197 CTTTCACTAATTA
1 CTTTCACTAATTA
28514210 CTTTCACTAATTA
1 CTTTCACTAATTA
28514223 C
1 C
28514224 ATAAATACTC
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:0.30, C:0.26, G:0.00, T:0.44
Consensus pattern (13 bp):
CTTTCACTAATTA
Found at i:28516621 original size:47 final size:47
Alignment explanation
Indices: 28516549--28517182 Score: 989
Period size: 47 Copynumber: 13.3 Consensus size: 47
28516539 CCCTTCGGGA
* * * * * * *
28516549 CTTATCACATTTATACACTTCCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
28516596 CCTATCACATATATACACTTTCACATTCATTACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28516643 CTTATCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28516690 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28516739 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATAT--ACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
28516788 CTTGTCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28516835 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28516882 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28516931 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATAT--ACACTTTCACATTCATCACATCGGCCATTAGGC
* *
28516980 CTTATCACATATATATACTTTCGCATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
28517027 CTTGTCACATATATATACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28517074 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
28517121 CTTATCACATATATGCACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
28517168 CTTATCACATATATA
1 CTTATCACATATATA
28517183 TATCTCATAC
Statistics
Matches: 548, Mismatches: 31, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
47 362 0.66
49 186 0.34
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28516896 original size:192 final size:192
Alignment explanation
Indices: 28516549--28517182 Score: 1037
Period size: 192 Copynumber: 3.3 Consensus size: 192
28516539 CCCTTCGGGA
* * * * * * * *
28516549 CTTATCACAT-T-TATACACTTCCACATCCATCACGTTGGCCACTCGGCCCTATCACATATATAC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
* *
28516612 ACTTTCACATTCATTACATTGGCCATTCGGCCTTATCACATATATACACCTTCACATTCATCACA
66 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
28516677 TCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 TCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28516739 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTGTCACATATATAC
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
28516804 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
28516869 TCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 TCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
28516931 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
* * * * *
28516996 ACTTTCGCATTCATCACATCGGCCATTAGGCCTTGTCACATATATATACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
*
28517061 TCGGCCATTCGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
131 TCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
28517121 CTTATCACATATAT--GCACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATA
1 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
28517183 TATCTCATAC
Statistics
Matches: 420, Mismatches: 22, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
188 45 0.11
190 63 0.15
191 1 0.00
192 311 0.74
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (192 bp):
CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:28517009 original size:239 final size:238
Alignment explanation
Indices: 28516553--28517182 Score: 1064
Period size: 239 Copynumber: 2.6 Consensus size: 238
28516543 TCGGGACTTA
* * * * * *
28516553 TCACATTTATACACTTCCACATCCATCACGTTGGCCACTCGGCCCTATCACATATATACACTTTC
1 TCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTC
* * * *
28516618 ACATTCATTACATTGGCCATTCGGCCTTATCACATATATACACCTTCACATTCATCACATCGGCC
66 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCC
*
28516683 ATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
131 ATTAGGCCTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
28516748 TATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTG
196 TATATA-ACACTTTCACATTCATCACATCGGCCATTAGGCCTTG
28516792 TCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTC
1 TCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTC
28516857 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACATCGG
66 ACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACATCGG
28516922 CCATTAGGCCTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
129 CCATTAGGCCTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCA
* *
28516987 CATATAT-ATACTTTCGCATTCATCACATCGGCCATTAGGCCTTG
194 CATATATAACACTTTCACATTCATCACATCGGCCATTAGGCCTTG
* *
28517031 TCACATATATATACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACATATATACACTTTC
1 TCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTC
* *
28517096 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATGCACTTTCACATTCATCACATTGGCC
66 ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCC
*
28517161 ATTCGGCCTTATCACATATATA
131 ATTAGGCCTTATCACATATATA
28517183 TATCTCATAC
Statistics
Matches: 371, Mismatches: 18, Indels: 6
0.94 0.05 0.02
Matches are distributed among these distances:
237 51 0.14
239 220 0.59
241 100 0.27
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (238 bp):
TCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTC
ACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCC
ATTAGGCCTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA
TATATAACACTTTCACATTCATCACATCGGCCATTAGGCCTTG
Found at i:28521071 original size:40 final size:40
Alignment explanation
Indices: 28521022--28521292 Score: 427
Period size: 40 Copynumber: 6.8 Consensus size: 40
28521012 CCAGCATGAT
* * *
28521022 TGCTCTTCGGGACCTAGCCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* * * *
28521062 TGCTCTTCGGGACTTAGTCCGGTTGCATTACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
28521102 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
28521142 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
28521182 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
*
28521222 TGCTCTT-GAAACTTAGTCCGGATACATCACTAGCACGAA
1 TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
* * * *
28521261 TGCTCTTCGGGATTTAGCCCGGATATATCACT
1 TGCTCTTCGGAACTTAGTCCGGATACATCACT
28521293 CTCAATTCTC
Statistics
Matches: 215, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
39 38 0.18
40 177 0.82
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (40 bp):
TGCTCTTCGGAACTTAGTCCGGATACATCACTAGCACGAA
Found at i:28523496 original size:47 final size:47
Alignment explanation
Indices: 28523420--28523512 Score: 132
Period size: 47 Copynumber: 2.0 Consensus size: 47
28523410 CTTCGGGACT
* *
28523420 TATCACATTTATACACTTCCACATCCATCACGTTGGCCACTCGGCCC
1 TATCACATATATACACTTCCACATCCATCACATTGGCCACTCGGCCC
* * * *
28523467 TATCACATATATACACTTTCATATTCATCACATTGGCCATTCGGCC
1 TATCACATATATACACTTCCACATCCATCACATTGGCCACTCGGCC
28523513 TAATTTACTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
47 40 1.00
ACGTcount: A:0.26, C:0.33, G:0.10, T:0.31
Consensus pattern (47 bp):
TATCACATATATACACTTCCACATCCATCACATTGGCCACTCGGCCC
Found at i:28523573 original size:50 final size:50
Alignment explanation
Indices: 28523514--28523612 Score: 198
Period size: 50 Copynumber: 2.0 Consensus size: 50
28523504 CATTCGGCCT
28523514 AATTTACTCAACGTTTAATCACTTAAAACTTATCTCGGATATTTTGAATG
1 AATTTACTCAACGTTTAATCACTTAAAACTTATCTCGGATATTTTGAATG
28523564 AATTTACTCAACGTTTAATCACTTAAAACTTATCTCGGATATTTTGAAT
1 AATTTACTCAACGTTTAATCACTTAAAACTTATCTCGGATATTTTGAAT
28523613 AGTTGCGGAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.40
Consensus pattern (50 bp):
AATTTACTCAACGTTTAATCACTTAAAACTTATCTCGGATATTTTGAATG
Found at i:28525409 original size:15 final size:15
Alignment explanation
Indices: 28525389--28525418 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28525379 ACATACTATA
28525389 ATTTATATCACCTTC
1 ATTTATATCACCTTC
28525404 ATTTATATCACCTTC
1 ATTTATATCACCTTC
28525419 TCTTCCTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTATATCACCTTC
Found at i:28536199 original size:40 final size:40
Alignment explanation
Indices: 28535980--28536177 Score: 278
Period size: 40 Copynumber: 5.0 Consensus size: 40
28535970 TCGAATGATG
* *
28535980 TCCGGGCTAAG-TCCTGAAGGC-TTTGTGCTAAGTTACTAAA
1 TCCGGACTAAGATCC-GAAGGCATTTGTGC-GAGTTACTAAA
*
28536020 TCCGGACTAAGATCCGAAGGCAATTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
28536060 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
28536100 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
* * *
28536140 TTCGAGA-TAAG-TCCCGAAGGCATTTGTGTGAGCTACTA
1 TCCG-GACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA
28536178 TAACCGGGCT
Statistics
Matches: 147, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
39 1 0.01
40 135 0.92
41 11 0.07
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (40 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:28536212 original size:80 final size:80
Alignment explanation
Indices: 28535980--28536212 Score: 244
Period size: 80 Copynumber: 2.9 Consensus size: 80
28535970 TCGAATGATG
* * * *
28535980 TCCGGGCTAAG-TCCTGAAGGC-TTTGTGCTAAGTTACTAAATCCGGACTAAGATCCGAAGGCAA
1 TCCGGACTAAGATCC-GAAGGCATTTGTGC-GAGCTACTAAATCCGGACTAAGATCCGAAGGCAT
**
28536043 TTGTGCGAGTTACTAAA
64 TTGAACGAGTTACTAAA
*
28536060 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGCTACTAAATCCGGACTAAGATCCGAAGGCATTT
**
28536125 GTGCGAGTTACTAAA
66 GAACGAGTTACTAAA
* * * * *
28536140 TTCGAGA-TAAG-TCCCGAAGGCATTTGTGTGAGCTACTATAA-CCGGGCTATG-TCCCGAAGGT
1 TCCG-GACTAAGAT-CCGAAGGCATTTGTGCGAGCTACTA-AATCCGGACTAAGAT-CCGAAGGC
28536201 ATTTGAACGAGT
62 ATTTGAACGAGT
28536213 AGCTATATCC
Statistics
Matches: 136, Mismatches: 11, Indels: 12
0.86 0.07 0.08
Matches are distributed among these distances:
79 2 0.01
80 120 0.88
81 14 0.10
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (80 bp):
TCCGGACTAAGATCCGAAGGCATTTGTGCGAGCTACTAAATCCGGACTAAGATCCGAAGGCATTT
GAACGAGTTACTAAA
Found at i:28536224 original size:120 final size:120
Alignment explanation
Indices: 28535980--28536212 Score: 271
Period size: 120 Copynumber: 1.9 Consensus size: 120
28535970 TCGAATGATG
*
28535980 TCCGGGCTAAGTCCTGAAGGCTTTGTGCTAAGTTACTAAATCCGGACTAAGATCCGAAGGCAATT
1 TCCGGACTAAGTCCTGAAGGCTTTGTGCTAAGTTACTAAATCCGGACTAAGATCCGAAGGCAATT
* **
28536045 GTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
66 GTGCGAGCTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTTACTAAA
* *
28536100 TCCGGACTAAGATCC-GAAGGCATTTGTGC-GAGTTACTAAATTCGAGA-TAAG-TCCCGAAGGC
1 TCCGGACTAAG-TCCTGAAGGC-TTTGTGCTAAGTTACTAAATCCG-GACTAAGAT-CCGAAGGC
* * * * *
28536161 ATTTGTGTGAGCTACTATAA-CCGGGCTATG-TCCCGAAGGTATTTGAACGAGT
62 AATTGTGCGAGCTACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGT
28536213 AGCTATATCC
Statistics
Matches: 96, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
119 2 0.02
120 80 0.83
121 14 0.15
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (120 bp):
TCCGGACTAAGTCCTGAAGGCTTTGTGCTAAGTTACTAAATCCGGACTAAGATCCGAAGGCAATT
GTGCGAGCTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTTACTAAA
Found at i:28543828 original size:40 final size:40
Alignment explanation
Indices: 28543784--28544009 Score: 237
Period size: 40 Copynumber: 5.7 Consensus size: 40
28543774 GCTACTCGTT
* * *
28543784 CAAATACCTTTGGGACATAGCCCGG-TTATAGTAGCTCGCA
1 CAAATGCCTTTGGGACTTAGCCCGGATT-TAGTAACTCGCA
* * *
28543824 CAAATGCCTTCGGGACTTATCCCGGATTTAGTAACTTGCA
1 CAAATGCCTTTGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
28543864 CAAATGCC-TTCGGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTTGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* *
28543904 CAAATGCC-TTCGGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTTGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * *
28543944 CAATTGCC-TTCGGATCTTAGTCCGGATTTAGTAACTTAGCA
1 CAAATGCCTTTGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
*
28543985 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTTGGGACTTAGCCCGGA
28544010 CATCATTCGA
Statistics
Matches: 165, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
39 4 0.02
40 148 0.90
41 13 0.08
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.28
Consensus pattern (40 bp):
CAAATGCCTTTGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:28543903 original size:80 final size:80
Alignment explanation
Indices: 28543812--28544009 Score: 303
Period size: 80 Copynumber: 2.5 Consensus size: 80
28543802 AGCCCGGTTA
* *
28543812 TAGTAGCTCGCACAAATGCCTTCGGGACTTATCCCGGATTTAGTAACTTGCACAAATGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGGGACTTATCCCGGATTTAGTAACTCGCACAAATGCCTTCGG
28543877 ATCTTAGTCCGGATT
66 ATCTTAGTCCGGATT
*
28543892 TAGTAACTCGCACAAATGCCTTC-GGATCTTAGT-CCGGATTTAGTAACTCGCACAATTGCCTTC
1 TAGTAACTCGCACAAATGCCTTCGGGA-CTTA-TCCCGGATTTAGTAACTCGCACAAATGCCTTC
28543955 GGATCTTAGTCCGGATT
64 GGATCTTAGTCCGGATT
* *
28543972 TAGTAACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 TAGTAAC-TCGCACAAATGCCTTCGGGACTTATCCCGGA
28544010 CATCATTCGA
Statistics
Matches: 108, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
79 3 0.03
80 93 0.86
81 12 0.11
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (80 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTATCCCGGATTTAGTAACTCGCACAAATGCCTTCGG
ATCTTAGTCCGGATT
Found at i:28548771 original size:124 final size:124
Alignment explanation
Indices: 28548549--28548773 Score: 317
Period size: 124 Copynumber: 1.8 Consensus size: 124
28548539 GAATTATGTG
* * * * * * *
28548549 AAATGAAATATGGATGTGTATTGATTATTGATTTATGTGTGTATGAGTATTTGAATGATACCCGG
1 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG
* **
28548614 GCTAAGTCCCGAAGGCGATTATGCTAGTGATTATATTTGTGTTTGAGCCTTAGTAACGA
66 GCTAAGTCCCGAAGACGATTATGCTAGAAATTATATTTGTGTTTGAGCCTTAGTAACGA
* *
28548673 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATATCTGG
1 AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG
*
28548738 GCTAAGTCCCGAAGACG-TTATTGCTGGAAATTATAT
66 GCTAAGTCCCGAAGACGATTA-TGCTAGAAATTATAT
28548774 CCGGGTTAAG
Statistics
Matches: 87, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
123 3 0.03
124 84 0.97
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.36
Consensus pattern (124 bp):
AAATGAAATATGAATGTCTAATGATTATTGATGTATGTGTGCATGAGCAATTGAATGATACCCGG
GCTAAGTCCCGAAGACGATTATGCTAGAAATTATATTTGTGTTTGAGCCTTAGTAACGA
Found at i:28548895 original size:40 final size:40
Alignment explanation
Indices: 28548768--28548897 Score: 165
Period size: 40 Copynumber: 3.2 Consensus size: 40
28548758 TTGCTGGAAA
* * *
28548768 TTATATCCGGGTTAAGACCCGAAGGCAATT-GTGCTAGCGG
1 TTATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTGG
* * *
28548808 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
*
28548848 TTCTATCCGGGCTAAGACCCGAAGGCATTCGTGC-ACGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGA-GTGG
28548888 TTATATCCGG
1 TTATATCCGG
28548898 TTGTATTCCG
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 4 0.05
40 73 0.95
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.23
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTGG
Found at i:28553732 original size:2 final size:2
Alignment explanation
Indices: 28553725--28553751 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28553715 CACATATAAC
28553725 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
28553752 TTTTTCATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28559819 original size:2 final size:2
Alignment explanation
Indices: 28559812--28559842 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28559802 TCATGACGTG
28559812 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28559843 GACTAGTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28578678 original size:27 final size:26
Alignment explanation
Indices: 28578622--28578722 Score: 107
Period size: 27 Copynumber: 3.8 Consensus size: 26
28578612 TCTCATCCCT
*
28578622 ATTTTACCACTAATAAAA-TTTTGAAA
1 ATTTTACC-CTAGTAAAATTTTTGAAA
*
28578648 ATTTTACCCTCAGTAAAATTTTTGACA
1 ATTTTACCCT-AGTAAAATTTTTGAAA
* **
28578675 ATTTTACCCTCGGTAAAAATTTTT-ATG
1 ATTTTACCCT-AGT-AAAATTTTTGAAA
28578702 ATTTTACCCTAGTAAAATTTT
1 ATTTTACCCTAGTAAAATTTT
28578723 GAGAAAATAT
Statistics
Matches: 66, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
25 10 0.15
26 16 0.24
27 31 0.47
28 9 0.14
ACGTcount: A:0.36, C:0.15, G:0.07, T:0.43
Consensus pattern (26 bp):
ATTTTACCCTAGTAAAATTTTTGAAA
Found at i:28581826 original size:21 final size:21
Alignment explanation
Indices: 28581800--28581839 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28581790 AATGGTCATG
*
28581800 GATGATTTAAGAGTGACTTAA
1 GATGATTTAAGAGTCACTTAA
*
28581821 GATGATTTACGAGTCACTT
1 GATGATTTAAGAGTCACTT
28581840 GTGTTTAGTT
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:0.33, C:0.10, G:0.23, T:0.35
Consensus pattern (21 bp):
GATGATTTAAGAGTCACTTAA
Found at i:28582378 original size:28 final size:28
Alignment explanation
Indices: 28582344--28582435 Score: 139
Period size: 28 Copynumber: 3.2 Consensus size: 28
28582334 ATTGCATGAC
28582344 TATGAATGTGATTGGGCTAGATGGGCCA
1 TATGAATGTGATTGGGCTAGATGGGCCA
*
28582372 TATGAATGTGATTGGGCCAGATGGGCCA
1 TATGAATGTGATTGGGCTAGATGGGCCA
* *
28582400 TATGAATGAGATTGGGCCTAAATGGGCCA
1 TATGAATGTGATTGGG-CTAGATGGGCCA
*
28582429 AATGAAT
1 TATGAAT
28582436 AAGTATGGAT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
28 42 0.72
29 16 0.28
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.26
Consensus pattern (28 bp):
TATGAATGTGATTGGGCTAGATGGGCCA
Found at i:28583703 original size:17 final size:19
Alignment explanation
Indices: 28583667--28583703 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
28583657 TATTTTAAAG
28583667 AAGGATTTTCAATGAAAAC
1 AAGGATTTTCAATGAAAAC
28583686 AAGG-TTTTCAAT-AAAAC
1 AAGGATTTTCAATGAAAAC
28583703 A
1 A
28583704 CTTCAATGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 8 0.44
19 4 0.22
ACGTcount: A:0.49, C:0.11, G:0.14, T:0.27
Consensus pattern (19 bp):
AAGGATTTTCAATGAAAAC
Found at i:28585316 original size:15 final size:15
Alignment explanation
Indices: 28585296--28585343 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
28585286 GTAGATTACA
28585296 ACTCCACCAGCTCTT
1 ACTCCACCAGCTCTT
*
28585311 ACTCCACCAACTCTT
1 ACTCCACCAGCTCTT
* *
28585326 GCTCCACCAGCTCCT
1 ACTCCACCAGCTCTT
28585341 ACT
1 ACT
28585344 GAAACAACTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.21, C:0.48, G:0.06, T:0.25
Consensus pattern (15 bp):
ACTCCACCAGCTCTT
Found at i:28599806 original size:22 final size:21
Alignment explanation
Indices: 28599772--28599812 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
28599762 CAAAAATAAT
28599772 TTAAAAATATTTTCTACAACCG
1 TTAAAAATATTTT-TACAACCG
28599794 TTAAAAGAT-TTTTTACAAC
1 TTAAAA-ATATTTTTACAAC
28599813 TGAAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.33
22 10 0.56
23 2 0.11
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (21 bp):
TTAAAAATATTTTTACAACCG
Found at i:28600396 original size:22 final size:21
Alignment explanation
Indices: 28600371--28600412 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
28600361 TTTAAAATAT
28600371 TTTAAAA-ATATTTTCTACAACC
1 TTTAAAAGAT-TTTT-TACAACC
28600393 TTTAAAAGATTTTTTACAAC
1 TTTAAAAGATTTTTTACAAC
28600413 TGAAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 11 0.58
23 2 0.11
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.43
Consensus pattern (21 bp):
TTTAAAAGATTTTTTACAACC
Found at i:28604479 original size:2 final size:2
Alignment explanation
Indices: 28604472--28604498 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28604462 TTTTATGATT
28604472 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
28604499 GTATCAATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28614532 original size:43 final size:42
Alignment explanation
Indices: 28614398--28614536 Score: 140
Period size: 43 Copynumber: 3.3 Consensus size: 42
28614388 TTATTTAAAA
* * **
28614398 AAACACCGCTAAAAGCCATGG-TTTTAGCGGCGCTTTTT-TTC
1 AAACGCCGCTAAAAGTCATGGCTTTTAGCGGCG-TTTTTCCAC
** * *
28614439 AAACGCCGCTAAAAGTCATGGCTTTTAGCAACGTTTATGCGA-
1 AAACGCCGCTAAAAGTCATGGCTTTTAGCGGCGTTT-TTCCAC
*
28614481 AAAGCGCCGCTAAAAGTAATGGCTTTTAGCGGCGTTTTTCCCAC
1 AAA-CGCCGCTAAAAGTCATGGCTTTTAGCGGCGTTTTT-CCAC
28614525 AAACGCCGCTAA
1 AAACGCCGCTAA
28614537 TTTTGGCAGA
Statistics
Matches: 80, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
41 22 0.28
42 14 0.17
43 41 0.51
44 3 0.04
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (42 bp):
AAACGCCGCTAAAAGTCATGGCTTTTAGCGGCGTTTTTCCAC
Found at i:28614625 original size:31 final size:31
Alignment explanation
Indices: 28614590--28614656 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
28614580 CTTCCTGCAT
*
28614590 TAAAATCCTA-CCAAATACAACAAATATAGCA
1 TAAAATCC-AGCCAAAAACAACAAATATAGCA
* * *
28614621 TAAAATGCAGCCAAAAACAGCAAATTTAGCA
1 TAAAATCCAGCCAAAAACAACAAATATAGCA
28614652 TAAAA
1 TAAAA
28614657 AATACAAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 1 0.03
31 30 0.97
ACGTcount: A:0.55, C:0.19, G:0.07, T:0.18
Consensus pattern (31 bp):
TAAAATCCAGCCAAAAACAACAAATATAGCA
Found at i:28615377 original size:13 final size:14
Alignment explanation
Indices: 28615352--28615380 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28615342 TGATGAATTG
28615352 AATTAAACAATTAT
1 AATTAAACAATTAT
28615366 AATTAAAC-ATTAT
1 AATTAAACAATTAT
28615379 AA
1 AA
28615381 ATATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACAATTAT
Found at i:28618676 original size:45 final size:46
Alignment explanation
Indices: 28618579--28618687 Score: 150
Period size: 45 Copynumber: 2.3 Consensus size: 46
28618569 AGCTTAAGAT
*
28618579 CGAATGGCCAATGTGATGAATGTGAAAGTGTGTATATGTGATAAGGC
1 CGAATGGCCAATGTGATGAATGTGAAAG-GTGAATATGTGATAAGGC
*
28618626 CGAATGGCCAATGTGAT-ATATGTGTAA-GTGAATATGTGATAAGGC
1 CGAATGGCCAATGTGATGA-ATGTGAAAGGTGAATATGTGATAAGGC
*
28618671 CGAATGACCAATTGTGA
1 CGAATGGCCAA-TGTGA
28618688 AAAGTGTGCA
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
45 27 0.47
46 6 0.11
47 24 0.42
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.28
Consensus pattern (46 bp):
CGAATGGCCAATGTGATGAATGTGAAAGGTGAATATGTGATAAGGC
Found at i:28619346 original size:2 final size:2
Alignment explanation
Indices: 28619339--28619365 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
28619329 AATTAAGTTT
28619339 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
28619366 TCATGTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28626439 original size:46 final size:45
Alignment explanation
Indices: 28626372--28626541 Score: 198
Period size: 46 Copynumber: 3.7 Consensus size: 45
28626362 TGTAACCCGC
*
28626372 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTC-GGCATTCGCAT
* *
28626418 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-ATGCCCAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCA--T
* *** * * *
28626464 ACATCTCTCGAACTCAGACTCAACTCAACGAGTTCGGACATTTGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGG-CATTCGCAT
28626511 CCATAAGTGAACTCGGACTCAACTCAACGAG
1 CCATAAGTGAACTCGGACTCAACTCAACGAG
28626542 TTCGAATGCC
Statistics
Matches: 102, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
44 4 0.04
45 2 0.02
46 61 0.60
47 31 0.30
49 4 0.04
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCATTCGCAT
Found at i:28626488 original size:93 final size:93
Alignment explanation
Indices: 28626380--28626553 Score: 278
Period size: 93 Copynumber: 1.9 Consensus size: 93
28626370 GCCCATAAGT
* *
28626380 GAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCAGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
28626444 ACGAGCTCGGATGCCCAGTTACATCTCTC
65 ACGAGCTCGAATGCCCAGTTACATCTCTC
* *
28626473 GAACTCAGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
28626538 CGAGTTCGAATGCCCA
66 CGAGCTCGAATGCCCA
28626554 AACATCCTAG
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
92 2 0.03
93 72 0.97
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGAATGCCCAGTTACATCTCTC
Found at i:28626566 original size:46 final size:46
Alignment explanation
Indices: 28626423--28626566 Score: 125
Period size: 46 Copynumber: 3.1 Consensus size: 46
28626413 CGCATCCATA
* *
28626423 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCCAGTTACATCTCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGAATGCCCA--TACATC-CT
* * *** * *
28626472 --CGAACTCAGACTCAACTCAACGAGTTCGGACATTTGCATCCAT--A
1 AGTGAACTCGGACTCAACTCAACGAGTTC-GA-ATGCCCATACATCCT
*
28626516 AGTGAACTCGGACTCAACTCAACGAGTTCGAATGCCCAAACATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGAATGCCCATACATCCT
28626562 AGTGA
1 AGTGA
28626567 CATGTCACTT
Statistics
Matches: 72, Mismatches: 17, Indels: 15
0.69 0.16 0.14
Matches are distributed among these distances:
44 7 0.10
45 2 0.03
46 30 0.42
47 28 0.39
48 1 0.01
49 4 0.06
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGAATGCCCATACATCCT
Found at i:28628096 original size:9 final size:9
Alignment explanation
Indices: 28628082--28628411 Score: 183
Period size: 9 Copynumber: 36.6 Consensus size: 9
28628072 TATTTAAGTA
28628082 TTATGTAAG
1 TTATGTAAG
28628091 TTATGTAAG
1 TTATGTAAG
*
28628100 TTATGATATG
1 TTATG-TAAG
* * *
28628110 ATATAT-AT
1 TTATGTAAG
*
28628118 TTATGTAAA
1 TTATGTAAG
* *
28628127 TTATAT-AT
1 TTATGTAAG
*
28628135 TTATCTAAG
1 TTATGTAAG
*
28628144 TTATATAAG
1 TTATGTAAG
28628153 TTATGTAAG
1 TTATGTAAG
*
28628162 TTTTGTAAG
1 TTATGTAAG
*
28628171 TTATGTAAA
1 TTATGTAAG
*
28628180 TTATGATATAAAA
1 TTATG---T-AAG
*
28628193 TATATTTAAG
1 T-TATGTAAG
28628203 TATTATGTAAG
1 --TTATGTAAG
28628214 TTATGTAAG
1 TTATGTAAG
*
28628223 TTATGGTATG
1 TTAT-GTAAG
* *
28628233 ATATAT-A-
1 TTATGTAAG
28628240 TTGATGTAAG
1 TT-ATGTAAG
*
28628250 TTATAT-A-
1 TTATGTAAG
*
28628257 -TATATAAG
1 TTATGTAAG
*
28628265 TTATTTAAG
1 TTATGTAAG
28628274 TTATGTAAG
1 TTATGTAAG
* *
28628283 TTATAT-AT
1 TTATGTAAG
*
28628291 TTATCTAAG
1 TTATGTAAG
*
28628300 TTATATAAG
1 TTATGTAAG
*
28628309 TTATATAAG
1 TTATGTAAG
*
28628318 TTATGTATG
1 TTATGTAAG
*
28628327 TTATATAAG
1 TTATGTAAG
28628336 TTATGTAAG
1 TTATGTAAG
* *
28628345 TTATATAAA
1 TTATGTAAG
* *
28628354 TTATAT-AT
1 TTATGTAAG
*
28628362 TTATCTAAG
1 TTATGTAAG
*
28628371 TTATATAAG
1 TTATGTAAG
*
28628380 TTATGTACG
1 TTATGTAAG
*
28628389 TTTTGTAAG
1 TTATGTAAG
* *
28628398 TTATATAAA
1 TTATGTAAG
28628407 TTATG
1 TTATG
28628412 ATATCAAATA
Statistics
Matches: 249, Mismatches: 53, Indels: 38
0.73 0.16 0.11
Matches are distributed among these distances:
6 5 0.02
7 2 0.01
8 26 0.10
9 182 0.73
10 17 0.07
11 8 0.03
12 2 0.01
13 4 0.02
14 3 0.01
ACGTcount: A:0.38, C:0.01, G:0.14, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:28628098 original size:43 final size:43
Alignment explanation
Indices: 28628046--28628241 Score: 187
Period size: 43 Copynumber: 4.7 Consensus size: 43
28628036 TTCACAAGCT
*
28628046 AGTTATGTAAGATATGTTATGATATATATTTAAGTATTATGTA
1 AGTTATGTAAGATATGATATGATATATATTTAAGTATTATGTA
* * *
28628089 AGTTATGTAAGTTATGATATGATATATATTTATGTAAATTATAT-
1 AGTTATGTAAGATATGATATGATATATATTTAAGT--ATTATGTA
* * *
28628133 ATTTATCTAAG-T-T-ATAT-A-AGT-TATGTAAGT-TT-TGTA
1 AGTTATGTAAGATATGATATGATA-TATATTTAAGTATTATGTA
* *
28628169 AGTTATGTAA-ATTATGATATAAAATATATTTAAGTATTATGTA
1 AGTTATGTAAGA-TATGATATGATATATATTTAAGTATTATGTA
* *
28628212 AGTTATGTAAGTTATGGTATGATATATATT
1 AGTTATGTAAGATATGATATGATATATATT
28628242 GATGTAAGTT
Statistics
Matches: 123, Mismatches: 16, Indels: 28
0.74 0.10 0.17
Matches are distributed among these distances:
35 2 0.02
36 10 0.08
37 1 0.01
38 1 0.01
39 12 0.10
40 4 0.03
41 13 0.11
42 3 0.02
43 62 0.50
44 9 0.07
45 6 0.05
ACGTcount: A:0.38, C:0.01, G:0.15, T:0.47
Consensus pattern (43 bp):
AGTTATGTAAGATATGATATGATATATATTTAAGTATTATGTA
Found at i:28628237 original size:123 final size:121
Alignment explanation
Indices: 28628046--28628442 Score: 414
Period size: 123 Copynumber: 3.4 Consensus size: 121
28628036 TTCACAAGCT
* * *
28628046 AGTTATGTAAGATATGTTATGATATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGA
1 AGTTATGTAAGATATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGA
* *
28628111 TATATATTTATGTAAATTATATATTTATCTAAGTTATATAAGTTATGTAAGTTTTGTA
66 TATATATTGATGTAAATTATATA--TATATAAGTTATATAAGTTATGTAAGTTTTGTA
*
28628169 AGTTATGTAA-ATTATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGGTATG
1 AGTTATGTAAGA-TATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATG
* * * *
28628233 ATATATATTGATGTAAGTTATATATATATAAGTTATTTAAGTTATGTAAGTTATAT-
65 ATATATATTGATGTAAATTATATATATATAAGTTATATAAGTTATGTAAGTTTTGTA
* * * * * * *
28628289 ATTTATCTAAG-T-T-ATAT-AAGT-TATATAAG--TTATGTATGTTATATAAGTTATG-TAAG-
1 AGTTATGTAAGATATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGA
** * * *
28628345 T-TATATAAAT-T--A-TATATTTATCTAAGTTATATAAGTTATGTACGTTTTGTA
66 TATATATTGATGTAAATTATATATATATAAGTTATATAAGTTATGTAAGTTTTGTA
* * *
28628396 AGTTATATAA-ATTATGATATCAAATATATTTATGTATTATGTAAGTT
1 AGTTATGTAAGA-TATGATATAAAATATATTTAAGTATTATGTAAGTT
28628443 TTTTATTTGA
Statistics
Matches: 231, Mismatches: 32, Indels: 31
0.79 0.11 0.11
Matches are distributed among these distances:
106 32 0.14
107 8 0.03
108 1 0.00
109 2 0.01
110 11 0.05
111 4 0.02
112 9 0.04
113 21 0.09
114 10 0.04
115 7 0.03
116 3 0.01
117 4 0.02
118 1 0.00
119 1 0.00
120 8 0.03
121 28 0.12
122 1 0.00
123 80 0.35
ACGTcount: A:0.38, C:0.01, G:0.14, T:0.47
Consensus pattern (121 bp):
AGTTATGTAAGATATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATGATATGA
TATATATTGATGTAAATTATATATATATAAGTTATATAAGTTATGTAAGTTTTGTA
Found at i:28628336 original size:71 final size:71
Alignment explanation
Indices: 28628257--28628411 Score: 238
Period size: 71 Copynumber: 2.2 Consensus size: 71
28628247 AAGTTATATA
* * *
28628257 TATATAAGTTATTTAAGTTATGTAAGTTATATATTTATCTAAGTTATATAAGTTATATAAGTTAT
1 TATATAAGTTATGTAAGTTATATAAATTATATATTTATCTAAGTTATATAAGTTATATAAGTTAT
*
28628322 GTATGT
66 GTAAGT
* * *
28628328 TATATAAGTTATGTAAGTTATATAAATTATATATTTATCTAAGTTATATAAGTTATGTACGTTTT
1 TATATAAGTTATGTAAGTTATATAAATTATATATTTATCTAAGTTATATAAGTTATATAAGTTAT
28628393 GTAAGT
66 GTAAGT
*
28628399 TATATAAATTATG
1 TATATAAGTTATG
28628412 ATATCAAATA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 76 1.00
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.48
Consensus pattern (71 bp):
TATATAAGTTATGTAAGTTATATAAATTATATATTTATCTAAGTTATATAAGTTATATAAGTTAT
GTAAGT
Found at i:28628411 original size:27 final size:26
Alignment explanation
Indices: 28628336--28628411 Score: 100
Period size: 26 Copynumber: 2.9 Consensus size: 26
28628326 GTTATATAAG
*
28628336 TTATGTAAGTTATATAAATTATATAT
1 TTATGTAAGTTATATAAATTATGTAT
* *
28628362 TTATCTAAGTTATATAAGTTATGTACGT
1 TTATGTAAGTTATATAAATTATGTA--T
28628390 TT-TGTAAGTTATATAAATTATG
1 TTATGTAAGTTATATAAATTATG
28628412 ATATCAAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 22 0.51
27 18 0.42
28 3 0.07
ACGTcount: A:0.37, C:0.03, G:0.12, T:0.49
Consensus pattern (26 bp):
TTATGTAAGTTATATAAATTATGTAT
Found at i:28628564 original size:29 final size:29
Alignment explanation
Indices: 28628516--28628585 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
28628506 AAGTTGCGGG
* *
28628516 ATTAAATAATATTTATAAAAATTATTTTA
1 ATTAAATAATATTGAAAAAAATTATTTTA
*
28628545 ATTAAATAATATTGAAAAAATTTATTTTA
1 ATTAAATAATATTGAAAAAAATTATTTTA
28628574 ATTAAATAATAT
1 ATTAAATAATAT
28628586 ACATGTCGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (29 bp):
ATTAAATAATATTGAAAAAAATTATTTTA
Found at i:28628800 original size:24 final size:24
Alignment explanation
Indices: 28628759--28628829 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
28628749 TTAACTTAAA
*
28628759 TGATAAAACGGGCGATAATATTTG
1 TGATAAAACGGACGATAATATTTG
* *
28628783 TGATAAAATGGACAATAATATTTG
1 TGATAAAACGGACGATAATATTTG
28628807 TGATAAAACGGACGATAATATTT
1 TGATAAAACGGACGATAATATTT
28628830 CAATAATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.42, C:0.07, G:0.20, T:0.31
Consensus pattern (24 bp):
TGATAAAACGGACGATAATATTTG
Found at i:28628946 original size:64 final size:64
Alignment explanation
Indices: 28628877--28629010 Score: 259
Period size: 64 Copynumber: 2.1 Consensus size: 64
28628867 ATATTTTATT
*
28628877 AAATATTTGTATATTAGATGGGACATATTATATTAATAAATAAATTTATTAAAAATCGTGATAG
1 AAATATTTGTATATTAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCGTGATAG
28628941 AAATATTTGTATATTAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCGTGATAG
1 AAATATTTGTATATTAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCGTGATAG
28629005 AAATAT
1 AAATAT
28629011 AGAAATATTA
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 69 1.00
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.38
Consensus pattern (64 bp):
AAATATTTGTATATTAGATGGGACATATTATATCAATAAATAAATTTATTAAAAATCGTGATAG
Found at i:28629580 original size:11 final size:11
Alignment explanation
Indices: 28629566--28629591 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28629556 AATCTAAGGA
28629566 TAAACAAGAAT
1 TAAACAAGAAT
28629577 TAAACAAGAAT
1 TAAACAAGAAT
28629588 TAAA
1 TAAA
28629592 AACATAATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.19
Consensus pattern (11 bp):
TAAACAAGAAT
Found at i:28631780 original size:16 final size:17
Alignment explanation
Indices: 28631761--28631797 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
28631751 ATTATTTAAT
28631761 ATATAAA-TAAAAAACA
1 ATATAAATTAAAAAACA
28631777 ATATAAATTAAAAAACA
1 ATATAAATTAAAAAACA
28631794 ATAT
1 ATAT
28631798 GTTATATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.24
Consensus pattern (17 bp):
ATATAAATTAAAAAACA
Found at i:28631926 original size:16 final size:16
Alignment explanation
Indices: 28631905--28631958 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
28631895 AGAACTACAT
28631905 AAAATTTGAAATCTTG
1 AAAATTTGAAATCTTG
28631921 AAAA-TT---A--TTG
1 AAAATTTGAAATCTTG
28631931 AAAATTTGAAATCATT-
1 AAAATTTGAAATC-TTG
28631947 AAAATTTGAAAT
1 AAAATTTGAAAT
28631959 TATTTAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 14
0.69 0.00 0.31
Matches are distributed among these distances:
10 7 0.23
11 2 0.06
12 1 0.03
14 1 0.03
15 2 0.06
16 16 0.52
17 2 0.06
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (16 bp):
AAAATTTGAAATCTTG
Found at i:28632212 original size:80 final size:79
Alignment explanation
Indices: 28632074--28632267 Score: 264
Period size: 80 Copynumber: 2.4 Consensus size: 79
28632064 ACTAATTATC
* * *
28632074 CTAAACCCTTAACCTATGTCCCCTTAACCCCTAAACCCTCAAACCTAAACCATTAACCCTTAATC
1 CTAAACCCTAAACC-ATGTCCCCTTAACCCTTAAACCCTCAAACCTAAACCATAAACCCTTAATC
28632139 CCTAAAATTTAAACA
65 CCTAAAATTTAAACA
* *
28632154 CTAAACCCTAAACCATGTCCCATTAACCCTTAAACCCCTC-AGCCTTAAACCATAAACCCTTAAT
1 CTAAACCCTAAACCATGTCCCCTTAACCCTTAAA-CCCTCAAACC-TAAACCATAAACCCTTAAT
* * *
28632218 CTCTAAACTTTAAACT
64 CCCTAAAATTTAAACA
*
28632234 CTAAACCCTAAACCATATCCCCTTAACCCCTTAA
1 CTAAACCCTAAACCATGTCCCCTTAA-CCCTTAA
28632268 CTCTTAACCT
Statistics
Matches: 101, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
79 21 0.21
80 73 0.72
81 7 0.07
ACGTcount: A:0.37, C:0.37, G:0.02, T:0.25
Consensus pattern (79 bp):
CTAAACCCTAAACCATGTCCCCTTAACCCTTAAACCCTCAAACCTAAACCATAAACCCTTAATCC
CTAAAATTTAAACA
Found at i:28632281 original size:22 final size:22
Alignment explanation
Indices: 28632256--28632303 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
28632246 CCATATCCCC
* *
28632256 TTAACCCCTTA-ACTCTTAACCT
1 TTAACCCC-TAGACCCTCAACCT
28632278 TTAACCCCTAGACCCTCAACCT
1 TTAACCCCTAGACCCTCAACCT
28632300 TTAA
1 TTAA
28632304 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 2 0.09
22 21 0.91
ACGTcount: A:0.29, C:0.38, G:0.02, T:0.31
Consensus pattern (22 bp):
TTAACCCCTAGACCCTCAACCT
Found at i:28632293 original size:80 final size:78
Alignment explanation
Indices: 28632074--28632293 Score: 228
Period size: 80 Copynumber: 2.7 Consensus size: 78
28632064 ACTAATTATC
* * *
28632074 CTAAACCCTTAACCTATGTCCCCTTAACCCCTAAACCCTCAAACC-TAAACCATTAACCCTTAAT
1 CTAAACCCTAAACC-ATGTCCCCTTAACCCCTTAACCCT-AAACCTTAACCCA-TAACCCTTAAT
28632138 CCCTAAAATTTAAACA
63 CCCTAAAATTTAAACA
* * * *
28632154 CTAAACCCTAAACCATGTCCCATTAA-CCCTTAAACCCCTCAGCCTTAAACCATAAACCCTTAAT
1 CTAAACCCTAAACCATGTCCCCTTAACCCCTT-AA-CCCTAAACCTTAACCCAT-AACCCTTAAT
* * *
28632218 CTCTAAACTTTAAACT
63 CCCTAAAATTTAAACA
* * * *
28632234 CTAAACCCTAAACCATATCCCCTTAACCCCTTAACTCTTAACCTTTAACCCCTAGACCCT
1 CTAAACCCTAAACCATGTCCCCTTAACCCCTTAACCCTAAACC-TTAACCCATA-ACCCT
28632294 CAACCTTTAA
Statistics
Matches: 118, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
78 4 0.03
79 24 0.20
80 85 0.72
81 5 0.04
ACGTcount: A:0.35, C:0.37, G:0.02, T:0.26
Consensus pattern (78 bp):
CTAAACCCTAAACCATGTCCCCTTAACCCCTTAACCCTAAACCTTAACCCATAACCCTTAATCCC
TAAAATTTAAACA
Found at i:28632778 original size:14 final size:14
Alignment explanation
Indices: 28632759--28632804 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
28632749 GTGTCATTAA
28632759 TTTAGGGTTTATAG
1 TTTAGGGTTTATAG
*
28632773 TTTAGGGTTTCA-AA
1 TTTAGGGTTT-ATAG
*
28632787 TTTAAGGTTTATAG
1 TTTAGGGTTTATAG
28632801 TTTA
1 TTTA
28632805 TGGATTTAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.22, T:0.50
Consensus pattern (14 bp):
TTTAGGGTTTATAG
Found at i:28633391 original size:42 final size:41
Alignment explanation
Indices: 28633335--28633475 Score: 151
Period size: 41 Copynumber: 3.4 Consensus size: 41
28633325 AATAGTTTAG
* *
28633335 ATCTATAGCGGCGTTTTTCCAAAAAGCGCCGCTAAAACTCAA
1 ATCTATAGCAGCGTTTTT-CAAAAAGCGCCACTAAAACTCAA
*
28633377 ATCTATTGCAGCGTTTTTCAAAAAGCGCCACTAAAACTCAA
1 ATCTATAGCAGCGTTTTTCAAAAAGCGCCACTAAAACTCAA
* * * ** * *
28633418 ATCCATAGC-GACGTTTTTTAAAAAGCACCGTTAATATTC-A
1 ATCTATAGCAG-CGTTTTTCAAAAAGCGCCACTAAAACTCAA
*
28633458 ATCTATAGCGGCGTTTTT
1 ATCTATAGCAGCGTTTTT
28633476 GAGGAAGCAC
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
40 17 0.20
41 52 0.61
42 16 0.19
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (41 bp):
ATCTATAGCAGCGTTTTTCAAAAAGCGCCACTAAAACTCAA
Found at i:28641728 original size:40 final size:40
Alignment explanation
Indices: 28641684--28641908 Score: 414
Period size: 40 Copynumber: 5.6 Consensus size: 40
28641674 GCTACTAGCT
28641684 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
28641724 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
28641764 CAAATGCCTTCGGGACTTAGCCCAGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
28641804 CAAATGCCTTCAGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
28641844 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
28641884 CAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
28641909 GTATCAAGCC
Statistics
Matches: 180, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 180 1.00
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:28647661 original size:28 final size:28
Alignment explanation
Indices: 28647596--28647696 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
28647586 ATAGTGAATC
*
28647596 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
28647625 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
28647653 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
28647683 CGCACACTTAGTGC
1 CGCACACTTAGTGC
28647697 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:28655614 original size:28 final size:28
Alignment explanation
Indices: 28655549--28655649 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
28655539 ATAGTGAATC
*
28655549 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
28655578 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
28655606 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
28655636 CGCACACTTAGTGC
1 CGCACACTTAGTGC
28655650 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:28660095 original size:24 final size:24
Alignment explanation
Indices: 28660068--28660250 Score: 312
Period size: 24 Copynumber: 7.6 Consensus size: 24
28660058 CTTATTATGT
* * *
28660068 TCGCACACATAGAGCTATAGCAAA
1 TCGCACACATAGTGCCATAGTAAA
*
28660092 TCGCACACATAGTGCTATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
28660116 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
28660140 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
28660164 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
28660188 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
*
28660212 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
28660236 TCGCACACATAGTGC
1 TCGCACACATAGTGC
28660251 ATTTGAGATA
Statistics
Matches: 155, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 155 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:28660102 original size:48 final size:47
Alignment explanation
Indices: 28660046--28660250 Score: 284
Period size: 48 Copynumber: 4.3 Consensus size: 47
28660036 ACCGAATGTG
* ** * * *
28660046 GCACACATAGTGCTTATTATGTTCGCACACATAGAGCTATAGCAAATC
1 GCACACATAGTGCTTAGTA-AATCGCACACATAGTGCCATAGTAAATC
28660094 GCACACATAGTGCTATAGTAAATCGCACACATAGTGCCATAGTAAATC
1 GCACACATAGTGCT-TAGTAAATCGCACACATAGTGCCATAGTAAATC
*
28660142 GCACACATAGTGCCATAGTAAATCGCACACATAGTGCCATAGTAAATC
1 GCACACATAGTG-CTTAGTAAATCGCACACATAGTGCCATAGTAAATC
* * *
28660190 GCACACATAGTGCCATAGTGAATCGCACACATAGTGCCATAGTGAATC
1 GCACACATAGTG-CTTAGTAAATCGCACACATAGTGCCATAGTAAATC
28660238 GCACACATAGTGC
1 GCACACATAGTGC
28660251 ATTTGAGATA
Statistics
Matches: 146, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
47 1 0.01
48 140 0.96
49 5 0.03
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (47 bp):
GCACACATAGTGCTTAGTAAATCGCACACATAGTGCCATAGTAAATC
Found at i:28664810 original size:24 final size:24
Alignment explanation
Indices: 28664783--28664965 Score: 312
Period size: 24 Copynumber: 7.6 Consensus size: 24
28664773 CTTATTATGT
* * *
28664783 TCGCACACATAGAGCTATAGCAAA
1 TCGCACACATAGTGCCATAGTAAA
*
28664807 TCGCACACATAGTGCTATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
28664831 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
28664855 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
28664879 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
*
28664903 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
*
28664927 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
28664951 TCGCACACATAGTGC
1 TCGCACACATAGTGC
28664966 ATTTGAGATA
Statistics
Matches: 155, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 155 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:28664817 original size:48 final size:47
Alignment explanation
Indices: 28664761--28664965 Score: 284
Period size: 48 Copynumber: 4.3 Consensus size: 47
28664751 ACCGAATGTG
* ** * * *
28664761 GCACACATAGTGCTTATTATGTTCGCACACATAGAGCTATAGCAAATC
1 GCACACATAGTGCTTAGTA-AATCGCACACATAGTGCCATAGTAAATC
28664809 GCACACATAGTGCTATAGTAAATCGCACACATAGTGCCATAGTAAATC
1 GCACACATAGTGCT-TAGTAAATCGCACACATAGTGCCATAGTAAATC
*
28664857 GCACACATAGTGCCATAGTAAATCGCACACATAGTGCCATAGTAAATC
1 GCACACATAGTG-CTTAGTAAATCGCACACATAGTGCCATAGTAAATC
* * *
28664905 GCACACATAGTGCCATAGTGAATCGCACACATAGTGCCATAGTGAATC
1 GCACACATAGTG-CTTAGTAAATCGCACACATAGTGCCATAGTAAATC
28664953 GCACACATAGTGC
1 GCACACATAGTGC
28664966 ATTTGAGATA
Statistics
Matches: 146, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
47 1 0.01
48 140 0.96
49 5 0.03
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (47 bp):
GCACACATAGTGCTTAGTAAATCGCACACATAGTGCCATAGTAAATC
Found at i:28672622 original size:24 final size:22
Alignment explanation
Indices: 28672595--28672794 Score: 131
Period size: 24 Copynumber: 8.6 Consensus size: 22
28672585 ACCGAATGTG
*
28672595 GCACACATAGTGCTTATTATGTTC
1 GCACACATAGTGCTTA-TA-GATC
*
28672619 GCACACATAGAGC-TATAGCAATC
1 GCACACATAGTGCTTATAG--ATC
*
28672642 GCACACATAGTGCTATAGTAAATC
1 GCACACATAGTGCT-TA-TAGATC
* *
28672666 GCACACATAGTGCCATAGTAAATC
1 GCACACATAGTG-CTTA-TAGATC
* *
28672690 GCACACATAGTGCCATAGTAAATC
1 GCACACATAGTG-CTTA-TAGATC
*
28672714 GCACACATAGTGC-CATAGTAATC
1 GCACACATAGTGCTTATAG--ATC
*
28672737 GCACACATAGTGC-CATAGTGATC
1 GCACACATAGTGCTTATA--GATC
*
28672760 GCAC-CATAGTGCATAGT-GAATC
1 GCACACATAGTGCTTA-TAG-ATC
28672782 GCACACATAGTGC
1 GCACACATAGTGC
28672795 ATTTGAGATA
Statistics
Matches: 154, Mismatches: 8, Indels: 29
0.81 0.04 0.15
Matches are distributed among these distances:
21 4 0.03
22 18 0.12
23 53 0.34
24 73 0.47
25 4 0.03
26 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (22 bp):
GCACACATAGTGCTTATAGATC
Found at i:28672796 original size:23 final size:24
Alignment explanation
Indices: 28672617--28672794 Score: 267
Period size: 24 Copynumber: 7.6 Consensus size: 24
28672607 CTTATTATGT
* * *
28672617 TCGCACACATAGAGCTATAG-CAA
1 TCGCACACATAGTGCCATAGTAAA
*
28672640 TCGCACACATAGTGCTATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
28672664 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
28672688 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
28672712 TCGCACACATAGTGCCATAGT-AA
1 TCGCACACATAGTGCCATAGTAAA
*
28672735 TCGCACACATAGTGCCATAGT-GA
1 TCGCACACATAGTGCCATAGTAAA
*
28672758 TCGCAC-CATAGTG-CATAGTGAA
1 TCGCACACATAGTGCCATAGTAAA
28672780 TCGCACACATAGTGC
1 TCGCACACATAGTGC
28672795 ATTTGAGATA
Statistics
Matches: 146, Mismatches: 5, Indels: 7
0.92 0.03 0.04
Matches are distributed among these distances:
21 6 0.04
22 14 0.10
23 56 0.38
24 70 0.48
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:28674995 original size:40 final size:40
Alignment explanation
Indices: 28674950--28675117 Score: 167
Period size: 40 Copynumber: 4.2 Consensus size: 40
28674940 CGGAATATAA
*
28674950 CCGGATATAACCA-TGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACT-AGCACAAATGCCTTCGGGTCTTAGC
* ** * *
28674990 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
28675030 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * * *
28675070 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
28675110 CCGGATAT
1 CCGGATAT
28675118 CATTCAATTT
Statistics
Matches: 105, Mismatches: 22, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
40 104 0.99
41 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:28675100 original size:80 final size:80
Alignment explanation
Indices: 28674966--28675117 Score: 200
Period size: 80 Copynumber: 1.9 Consensus size: 80
28674956 ATAACCATGT
* *
28674966 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
28675031 CGGATATAGCCACTA
66 CGGATATAGCCACTA
* * ** * *
28675046 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGGCTTAG
28675109 CCCGGATAT
64 CCCGGATAT
28675118 CATTCAATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
79 3 0.05
80 59 0.95
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
CGGATATAGCCACTA
Found at i:28682983 original size:40 final size:40
Alignment explanation
Indices: 28682938--28683067 Score: 142
Period size: 40 Copynumber: 3.2 Consensus size: 40
28682928 CGGAATATAA
28682938 CCGGATATAAGCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAAGCATGTGCACAAATGCCTTCGGGTCTTAGC
* * *
28682978 CCGGATAGAATG-ACT-CGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA-GCA-TGTGCACAAATGCCTTCGGGTCTTAGC
* * *
28683018 CCGGATAT-AGC-CGCTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAAGCATG-T-GCACAAATGCCTTCGGGTCTTAGC
28683058 CCGGATATAA
1 CCGGATATAA
28683068 TTTCCAGCAT
Statistics
Matches: 74, Mismatches: 9, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
38 1 0.01
39 1 0.01
40 69 0.93
41 3 0.04
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.24
Consensus pattern (40 bp):
CCGGATATAAGCATGTGCACAAATGCCTTCGGGTCTTAGC
Found at i:28683082 original size:40 final size:40
Alignment explanation
Indices: 28682954--28683104 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
28682944 ATAAGCATGT
* * *
28682954 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCAC-CA
** * *
28682994 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAGCCGCTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCACCA
* **
28683034 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCACCA
* *
28683074 GCATAATTGTCTTCGGG-CTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
28683105 CATTCAATTT
Statistics
Matches: 93, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
39 15 0.16
40 76 0.82
41 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCACCA
Found at i:28683088 original size:80 final size:79
Alignment explanation
Indices: 28682954--28683104 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
28682944 ATAAGCATGT
*
28682954 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGG-CTTAGCC
28683019 CGGATATAGCCGCTA
65 CGGATATAGCCGCTA
* * ** * *
28683034 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGCTTAGC
28683097 CCGGATAT
64 CCGGATAT
28683105 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCGCTA
Found at i:28685418 original size:60 final size:60
Alignment explanation
Indices: 28685336--28685449 Score: 219
Period size: 60 Copynumber: 1.9 Consensus size: 60
28685326 TCACACTTTC
28685336 ATATAGCCAAATGAACACATTATGGGAAATAACACATTTAATTATATATCTTTCACAATT
1 ATATAGCCAAATGAACACATTATGGGAAATAACACATTTAATTATATATCTTTCACAATT
*
28685396 ATATAGCCAAATGAACATATTATGGGAAATAACACATTTAATTATATATCTTTC
1 ATATAGCCAAATGAACACATTATGGGAAATAACACATTTAATTATATATCTTTC
28685450 TCATATGAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (60 bp):
ATATAGCCAAATGAACACATTATGGGAAATAACACATTTAATTATATATCTTTCACAATT
Found at i:28686040 original size:34 final size:34
Alignment explanation
Indices: 28685999--28686068 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
28685989 TAATTTCCCT
28685999 TTGAATCATTCGATATTTCACACACTAAGTGTCA
1 TTGAATCATTCGATATTTCACACACTAAGTGTCA
**
28686033 TTGAATCATTCGATATTTTGCACACTAAGTGTCA
1 TTGAATCATTCGATATTTCACACACTAAGTGTCA
28686067 TT
1 TT
28686069 CTCAATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (34 bp):
TTGAATCATTCGATATTTCACACACTAAGTGTCA
Found at i:28689471 original size:20 final size:20
Alignment explanation
Indices: 28689446--28689483 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28689436 GTTTATTCGC
*
28689446 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
28689466 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
28689484 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:28690036 original size:14 final size:12
Alignment explanation
Indices: 28690001--28690036 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
28689991 CTTAGGGTTG
28690001 TTTTTCCTCTCT
1 TTTTTCCTCTCT
28690013 TTTTTCCTCTCT
1 TTTTTCCTCTCT
28690025 TTTTTCCTCTCT
1 TTTTTCCTCTCT
28690037 AGCCGAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTTTCCTCTCT
Found at i:28691154 original size:28 final size:28
Alignment explanation
Indices: 28691122--28691190 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
28691112 GCGTAGATCA
28691122 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
28691150 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
28691178 CGATA-TACCCCTA
1 CGAAATTACCCCTA
28691191 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:28700872 original size:40 final size:40
Alignment explanation
Indices: 28700828--28700936 Score: 182
Period size: 40 Copynumber: 2.7 Consensus size: 40
28700818 TTAAGGGAAT
*
28700828 CAAAGTACAAATAGGGTCACGTATGTGCATTCAGGGGTAC
1 CAAAGTACAAATAGGGGCACGTATGTGCATTCAGGGGTAC
28700868 CAAAGTACAAATAGGGGCACGTATGTGCATTCAGGGGTAC
1 CAAAGTACAAATAGGGGCACGTATGTGCATTCAGGGGTAC
* * *
28700908 CGAAGTACAAACAGGGGCAAGTATGTGCA
1 CAAAGTACAAATAGGGGCACGTATGTGCA
28700937 ATCATCAATA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.19
Consensus pattern (40 bp):
CAAAGTACAAATAGGGGCACGTATGTGCATTCAGGGGTAC
Found at i:28700903 original size:20 final size:20
Alignment explanation
Indices: 28700840--28700904 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
28700830 AAGTACAAAT
*
28700840 AGGGTCACGTATGTGCATTC
1 AGGGGCACGTATGTGCATTC
* ** * * *
28700860 AGGGGTACCAAAGTACAAAT-
1 AGGGGCACGTATGTGC-ATTC
28700880 AGGGGCACGTATGTGCATTC
1 AGGGGCACGTATGTGCATTC
28700900 AGGGG
1 AGGGG
28700905 TACCGAAGTA
Statistics
Matches: 30, Mismatches: 13, Indels: 4
0.64 0.28 0.09
Matches are distributed among these distances:
19 2 0.07
20 26 0.87
21 2 0.07
ACGTcount: A:0.28, C:0.17, G:0.34, T:0.22
Consensus pattern (20 bp):
AGGGGCACGTATGTGCATTC
Found at i:28700922 original size:20 final size:20
Alignment explanation
Indices: 28700859--28700924 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
28700849 TATGTGCATT
*
28700859 CAGGGGTACCAAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
* * * * **
28700879 TAGGGGCA-CGTATGTGCATT
1 CAGGGGTACCG-AAGTACAAA
28700899 CAGGGGTACCGAAGTACAAA
1 CAGGGGTACCGAAGTACAAA
28700919 CAGGGG
1 CAGGGG
28700925 CAAGTATGTG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
19 1 0.03
20 28 0.90
21 2 0.06
ACGTcount: A:0.33, C:0.18, G:0.33, T:0.15
Consensus pattern (20 bp):
CAGGGGTACCGAAGTACAAA
Found at i:28701857 original size:21 final size:21
Alignment explanation
Indices: 28701831--28701874 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
28701821 CATATGAGTC
28701831 CTCTCTCATATAATAATTAAA
1 CTCTCTCATATAATAATTAAA
28701852 CTCTCTCATATAATAATTAAA
1 CTCTCTCATATAATAATTAAA
28701873 CT
1 CT
28701875 AGTTGATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.20, G:0.00, T:0.39
Consensus pattern (21 bp):
CTCTCTCATATAATAATTAAA
Found at i:28705325 original size:2 final size:2
Alignment explanation
Indices: 28705318--28705353 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
28705308 GATTGAATCA
28705318 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
28705354 GTTATTATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28709920 original size:50 final size:50
Alignment explanation
Indices: 28709845--28709966 Score: 217
Period size: 50 Copynumber: 2.4 Consensus size: 50
28709835 GTCGATGCCA
28709845 TGTCCCAGACATGGTCTTACACAAGCTCTAGCATATCTATGCCGATACTG
1 TGTCCCAGACATGGTCTTACACAAGCTCTAGCATATCTATGCCGATACTG
* * *
28709895 TGTCCCAGGCATGGTCTTACACAAGCTCTAGCATATCTGTGCCGATGCTG
1 TGTCCCAGACATGGTCTTACACAAGCTCTAGCATATCTATGCCGATACTG
28709945 TGTCCCAGACATGGTCTTACAC
1 TGTCCCAGACATGGTCTTACAC
28709967 TAACACATCT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 68 1.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (50 bp):
TGTCCCAGACATGGTCTTACACAAGCTCTAGCATATCTATGCCGATACTG
Found at i:28710044 original size:46 final size:47
Alignment explanation
Indices: 28709837--28710105 Score: 173
Period size: 50 Copynumber: 5.7 Consensus size: 47
28709827 GGTAAAGTGT
* *
28709837 CGATGCCATGTCCCAGACATGGTCTTACAC-AAGCTCTAGCA-TATCTATGC
1 CGATG-CATGTCCCAGACATGGTCTTACACTAA-CT-TA-CATTAT-GAGGC
* * * * *
28709887 CGATACTGTGTCCCAGGCATGGTCTTACAC-AAGCTCTAGCATATCTG-TGC
1 CGATGC-ATGTCCCAGACATGGTCTTACACTAA-CT-TA-CAT-TATGAGGC
* *
28709937 CGATGCTGTGTCCCAGACATGGTCTTACACTAAC--ACATCTCCT-A-GC
1 CGATGC-ATGTCCCAGACATGGTCTTACACTAACTTACAT-T-ATGAGGC
* *
28709983 CGGTGCATGTCCCAGACAT-GTCTTACACTAACTTACATTTTGAGGC
1 CGATGCATGTCCCAGACATGGTCTTACACTAACTTACATTATGAGGC
* ** * *
28710029 CAATGCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAATGTGGC
1 CGATGCATGTCCCAGACATGGTCTTACACTAACT-TACATTATGAGGC
* *
28710076 CGATGCATGTCCCAAACAT-GTCTTATACTA
1 CGATGCATGTCCCAGACATGGTCTTACACTA
28710106 GCTCACAATA
Statistics
Matches: 185, Mismatches: 22, Indels: 28
0.79 0.09 0.12
Matches are distributed among these distances:
44 14 0.08
45 14 0.08
46 43 0.23
47 40 0.22
48 1 0.01
49 1 0.01
50 68 0.37
51 2 0.01
52 2 0.01
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.28
Consensus pattern (47 bp):
CGATGCATGTCCCAGACATGGTCTTACACTAACTTACATTATGAGGC
Found at i:28710478 original size:30 final size:30
Alignment explanation
Indices: 28710444--28710502 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
28710434 AAATTCATAT
* *
28710444 CTTTGGCAAAATGACCATTTTGCCCCTAGA
1 CTTTGACAAAATGACCATTTTACCCCTAGA
*
28710474 CTTTGATAAAATGACCATTTTACCCCTAG
1 CTTTGACAAAATGACCATTTTACCCCTAG
28710503 GCTCGAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (30 bp):
CTTTGACAAAATGACCATTTTACCCCTAGA
Found at i:28712475 original size:39 final size:39
Alignment explanation
Indices: 28712430--28712550 Score: 215
Period size: 39 Copynumber: 3.1 Consensus size: 39
28712420 AAGCAAGACA
*
28712430 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
28712469 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
* *
28712508 CTGGAAATGTATCCGAGCTAAAGTCCCGCAGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
28712547 CTGG
1 CTGG
28712551 TAATATAATT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 79 1.00
ACGTcount: A:0.21, C:0.25, G:0.31, T:0.23
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
Found at i:28715278 original size:22 final size:23
Alignment explanation
Indices: 28715253--28715298 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
28715243 CAACCAAATC
28715253 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
28715275 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
28715298 A
1 A
28715299 GATAACGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:28721102 original size:39 final size:39
Alignment explanation
Indices: 28721057--28721371 Score: 515
Period size: 39 Copynumber: 8.1 Consensus size: 39
28721047 AAGCAAGACA
28721057 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
*
28721096 CTGGAAATGTATCCGGGCTAAAGACCCACAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
*
28721135 CTGGAAATGTATCCGGGCTAAAGACCCACAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
* *
28721174 CTGGAAATGTATTCGGGCTAAAGTCCCGTC-GGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCG-CAGGCTTCGTG
*
28721213 CTGGAAATGTATCCGGGCTAAAGACCAGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
28721252 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
* *
28721291 CTGGAAATGTATCCAGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
* * * *
28721330 CTGGAAATGTATCCGAGCTAAAGTCCCACAGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
28721369 CTG
1 CTG
28721372 ATAATATAAT
Statistics
Matches: 260, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
38 1 0.00
39 258 0.99
40 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
Found at i:28725100 original size:40 final size:38
Alignment explanation
Indices: 28725024--28725284 Score: 281
Period size: 40 Copynumber: 6.6 Consensus size: 38
28725014 ATACTATCTA
* * * * * *
28725024 ATTCGAGGTTACCAAAGTATAAATAGGGCACATATGTGT
1 ATTC-AGGGTACCGAAGTACAAACAGGGCACGTATGTGC
*
28725063 ATTCAGGGATACCTAAGTACAAACAGGGACACGTATGTGC
1 ATTCAGGG-TACCGAAGTACAAACAGGG-CACGTATGTGC
*
28725103 ATTCAAGGATACCGAAGTACAAACAAGGGCACGTATGTGC
1 ATTC-AGGGTACCGAAGTACAAAC-AGGGCACGTATGTGC
* ** *
28725143 AATCAGGGGTACTAAAGTACAAATAAGGGCACGTATGTGC
1 ATTCA-GGGTACCGAAGTACAAA-CAGGGCACGTATGTGC
28725183 ATTCAAGGGTACCGAAGTACACAA-AGGGGCACGTATGTGC
1 ATTC-AGGGTACCGAAGTACA-AACA-GGGCACGTATGTGC
*
28725223 ATTCATGGGTACCGAAGTATAAACAGGGGCACGTATGTGC
1 ATTCA-GGGTACCGAAGTACAAACA-GGGCACGTATGTGC
28725263 ATTCAGGGGTACCGAAGTACAA
1 ATTCA-GGGTACCGAAGTACAA
28725285 TCATCACTAA
Statistics
Matches: 192, Mismatches: 19, Indels: 21
0.83 0.08 0.09
Matches are distributed among these distances:
38 3 0.02
39 25 0.13
40 154 0.80
41 10 0.05
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.21
Consensus pattern (38 bp):
ATTCAGGGTACCGAAGTACAAACAGGGCACGTATGTGC
Found at i:28725261 original size:120 final size:119
Alignment explanation
Indices: 28725033--28725284 Score: 355
Period size: 120 Copynumber: 2.1 Consensus size: 119
28725023 AATTCGAGGT
* * *
28725033 TACCAAAGTATAAATAGGGCACATATGTGTATTCAGGGATACCTAAGTACAAACAGGGACACGTA
1 TACCAAAGTACAAATAGGGCACATATGTGCATTCAGGGATACCGAAGTACAAACAGGGACACGTA
28725098 TGTGCATTCAAGGATACCGAAGTACAAACAAGGGCACGTATGTGCAATCAGGGG
66 TGTGCATTCAAGGATACCGAAGTACAAACAAGGGCACGTATGTGCAATCAGGGG
* * *
28725152 TACTAAAGTACAAATAAGGGCACGTATGTGCATTCAAGGG-TACCGAAGTACACAA-AGGGGCAC
1 TACCAAAGTACAAAT-AGGGCACATATGTGCATTC-AGGGATACCGAAGTACA-AACAGGGACAC
* * * * *
28725215 GTATGTGCATTCATGGGTACCGAAGTATAAACAGGGGCACGTATGTGCATTCAGGGG
63 GTATGTGCATTCAAGGATACCGAAGTACAAACAAGGGCACGTATGTGCAATCAGGGG
*
28725272 TACCGAAGTACAA
1 TACCAAAGTACAA
28725285 TCATCACTAA
Statistics
Matches: 117, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
119 13 0.11
120 98 0.84
121 6 0.05
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (119 bp):
TACCAAAGTACAAATAGGGCACATATGTGCATTCAGGGATACCGAAGTACAAACAGGGACACGTA
TGTGCATTCAAGGATACCGAAGTACAAACAAGGGCACGTATGTGCAATCAGGGG
Found at i:28725363 original size:25 final size:29
Alignment explanation
Indices: 28725344--28725402 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
28725334 ATATTACATG
*
28725344 TAAAAAATTATTTACGTATTGAAATGCTA
1 TAAAAGATTATTTACGTATTGAAATGCTA
* *
28725373 TAAAAGTTTATTTACGTATTGAAATACTA
1 TAAAAGATTATTTACGTATTGAAATGCTA
28725402 T
1 T
28725403 GGACTTACCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.41
Consensus pattern (29 bp):
TAAAAGATTATTTACGTATTGAAATGCTA
Found at i:28727111 original size:42 final size:42
Alignment explanation
Indices: 28727015--28727169 Score: 116
Period size: 42 Copynumber: 3.7 Consensus size: 42
28727005 GAATCGAAGT
* * * * **
28727015 AATTATACTAGCACGTATAGTGCATCATCGAATAGGCCAAAGA-
1 AATTATATTGGCACATA-AGTGCATCATCGGATATACCAAA-AC
* * *** *
28727058 AATCATGTTGGCACATAAGTGCATCATCGGATGA-ATTGAAGC
1 AATTATATTGGCACATAAGTGCATCATCGGAT-ATACCAAAAC
** *
28727100 AATTATATTGGCATGTAAGTGCATCATTGGATATACCAAAAC
1 AATTATATTGGCACATAAGTGCATCATCGGATATACCAAAAC
* *
28727142 AATTATACTAGCACATAAGTGCATCATC
1 AATTATATTGGCACATAAGTGCATCATC
28727170 AAATAAGCCA
Statistics
Matches: 84, Mismatches: 25, Indels: 7
0.72 0.22 0.06
Matches are distributed among these distances:
41 1 0.01
42 70 0.83
43 13 0.15
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.27
Consensus pattern (42 bp):
AATTATATTGGCACATAAGTGCATCATCGGATATACCAAAAC
Found at i:28727181 original size:42 final size:40
Alignment explanation
Indices: 28726965--28727181 Score: 101
Period size: 42 Copynumber: 5.1 Consensus size: 40
28726955 ACTGGGCAAG
* * * *
28726965 CCAAAGAAATTATAGTAACACATAACGTGCATCATCAAACGAA
1 CCAAA-AAATTATACTAGCACATAA-GTGCATCATCGAA-TAA
* ** * *
28727008 TCGAAGTAATTATACTAGCACGTATAGTGCATCATCGAATAGG
1 -CCAAAAAATTATACTAGCACATA-AGTGCATCATCGAATA-A
* ** * *
28727051 CCAAAGAAATCATGTTGGCACATAAGTGCATCATCGGATGAA
1 CCAAA-AAATTATACTAGCACATAAGTGCATCATCGAAT-AA
** ** * * ** * *
28727093 TTGAAGCAATTATATTGGCATGTAAGTGCATCATTGGATATA
1 -CCAAAAAATTATACTAGCACATAAGTGCATCATCGAATA-A
*
28727135 CCAAAACAATTATACTAGCACATAAGTGCATCATCAAATAA
1 CCAAAA-AATTATACTAGCACATAAGTGCATCATCGAATAA
28727176 GCCAAA
1 -CCAAA
28727182 GCAAACATAC
Statistics
Matches: 126, Mismatches: 39, Indels: 18
0.69 0.21 0.10
Matches are distributed among these distances:
41 4 0.03
42 77 0.61
43 41 0.33
44 4 0.03
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (40 bp):
CCAAAAAATTATACTAGCACATAAGTGCATCATCGAATAA
Found at i:28736186 original size:43 final size:43
Alignment explanation
Indices: 28736125--28736211 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
28736115 ATGGCACAGG
28736125 TATGTACTAAAACCCTATGAGGACTTAGTATATGATGATATTA
1 TATGTACTAAAACCCTATGAGGACTTAGTATATGATGATATTA
28736168 TATGTACTAAAACCCTATGAGGACTTAGTATATGATGATATTA
1 TATGTACTAAAACCCTATGAGGACTTAGTATATGATGATATTA
28736211 T
1 T
28736212 GAATGATATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (43 bp):
TATGTACTAAAACCCTATGAGGACTTAGTATATGATGATATTA
Found at i:28740612 original size:25 final size:24
Alignment explanation
Indices: 28740560--28740616 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
28740550 ATAGCTCAGA
*
28740560 CGAGCATCTTGTTAAAAGTTTTCT
1 CGAGCATCTTGTTAAAAGTTTTCG
*
28740584 CGAGCATTTTGTTAAATAGTTCTT-G
1 CGAGCATCTTGTTAAA-AGTT-TTCG
28740609 CGAGCATC
1 CGAGCATC
28740617 CTGATCGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 15 0.54
25 11 0.39
26 2 0.07
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.39
Consensus pattern (24 bp):
CGAGCATCTTGTTAAAAGTTTTCG
Found at i:28743350 original size:27 final size:27
Alignment explanation
Indices: 28743193--28743350 Score: 217
Period size: 27 Copynumber: 5.9 Consensus size: 27
28743183 ATTACCAAAG
* *
28743193 TACCCCCGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * * * *
28743220 TACCCCCAATTTATATAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
28743247 TACCCTCGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
28743274 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
28743301 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
28743328 TACCCTCGATTTACAAAATTACT
1 TACCCTCGATTTACAGAATTACT
28743351 AAAATACCCT
Statistics
Matches: 114, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 114 1.00
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:28743358 original size:27 final size:27
Alignment explanation
Indices: 28743093--28743549 Score: 195
Period size: 27 Copynumber: 16.8 Consensus size: 27
28743083 AATACTTTAG
** *
28743093 TTTACTAAAATTACCGAAATACCCT-TA
1 TTTA-TAAAATTACTAAAATACCCTCGA
* * *
28743120 GTTTGTAAAAATACTGAAATACCCTCGA
1 -TTTATAAAATTACTAAAATACCCTCGA
* *
28743148 TTTGTAAAATTACTAAAATACCTTCGA
1 TTTATAAAATTACTAAAATACCCTCGA
* * * * *
28743175 CTTGTAAAATTACCAAAGTACCCCCGA
1 TTTATAAAATTACTAAAATACCCTCGA
* * *** * *
28743202 TTTACAGAATTACTATTTTACCCCCAA
1 TTTATAAAATTACTAAAATACCCTCGA
* *****
28743229 TTTATATAATTACCGTTTTACCCTCGA
1 TTTATAAAATTACTAAAATACCCTCGA
* * ***
28743256 TTTACAGAATTACTATTTTACCCTCGA
1 TTTATAAAATTACTAAAATACCCTCGA
* **** *
28743283 TTTATAGAATTACTGTTTTACCCTTGA
1 TTTATAAAATTACTAAAATACCCTCGA
* * ****
28743310 TTTACAGAATTACTGTTTTACCCTCGA
1 TTTATAAAATTACTAAAATACCCTCGA
* * *
28743337 TTTACAAAATTACTAAAATACCCTTGG
1 TTTATAAAATTACTAAAATACCCTCGA
* * *
28743364 TTTGTAAAATTACCAAAATACCC-CTA
1 TTTATAAAATTACTAAAATACCCTCGA
* * * *
28743390 GTTTGTAAAATTACCAAAATACCCTTGG
1 -TTTATAAAATTACTAAAATACCCTCGA
* ** *
28743418 TTTATGAAATTACCGAAATACCCTCAA
1 TTTATAAAATTACTAAAATACCCTCGA
* * *
28743445 TTTGTAAAATTACCAAAATACCC-CTAA
1 TTTATAAAATTACTAAAATACCCTC-GA
* * *
28743472 TTTACAAAGTTAC-AGAAATACCCTTGA
1 TTTATAAAATTACTA-AAATACCCTCGA
* * *
28743499 CTTTATAAAAATTA-TAGAAATACCATTGG
1 -TTTAT-AAAATTACTA-AAATACCCTCGA
* *
28743528 TTTACAAAATTACTGAAATACC
1 TTTATAAAATTACTAAAATACC
28743550 TTTGGTTTGT
Statistics
Matches: 347, Mismatches: 72, Indels: 21
0.79 0.16 0.05
Matches are distributed among these distances:
26 2 0.01
27 314 0.90
28 13 0.04
29 18 0.05
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.34
Consensus pattern (27 bp):
TTTATAAAATTACTAAAATACCCTCGA
Found at i:28743360 original size:81 final size:81
Alignment explanation
Indices: 28743180--28743360 Score: 227
Period size: 81 Copynumber: 2.2 Consensus size: 81
28743170 TTCGACTTGT
* * * * *
28743180 AAAATTACCAAAGTACCCCCGATTTACAGAATTACTATTTTACCCCCAATTTATATAATTACCGT
1 AAAATTACTAAAATACCCTCGATTTACAGAATTACTATTTTACCCCCAATTTACAGAATTACCGT
28743245 TTTACCCTCGATTTAC
66 TTTACCCTCGATTTAC
* *** * * *** *
28743261 AGAATTACTATTTTACCCTCGATTTATAGAATTACTGTTTTACCCTTGATTTACAGAATTACTGT
1 AAAATTACTAAAATACCCTCGATTTACAGAATTACTATTTTACCCCCAATTTACAGAATTACCGT
28743326 TTTACCCTCGATTTAC
66 TTTACCCTCGATTTAC
28743342 AAAATTACTAAAATACCCT
1 AAAATTACTAAAATACCCT
28743361 TGGTTTGTAA
Statistics
Matches: 82, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.38
Consensus pattern (81 bp):
AAAATTACTAAAATACCCTCGATTTACAGAATTACTATTTTACCCCCAATTTACAGAATTACCGT
TTTACCCTCGATTTAC
Found at i:28743554 original size:27 final size:27
Alignment explanation
Indices: 28743328--28743580 Score: 186
Period size: 27 Copynumber: 9.3 Consensus size: 27
28743318 ATTACTGTTT
* * * *
28743328 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTTGGTTTATAAAATTACCAAAA
*
28743355 TACCCTTGGTTTGTAAAATTACCAAAA
1 TACCCTTGGTTTATAAAATTACCAAAA
* * *
28743382 TACCCCTAGTTTGTAAAATTACCAAAA
1 TACCCTTGGTTTATAAAATTACCAAAA
* *
28743409 TACCCTTGGTTTATGAAATTACCGAAA
1 TACCCTTGGTTTATAAAATTACCAAAA
*** *
28743436 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTTGGTTTATAAAATTACCAAAA
* ** * *
28743463 TACCCCTAATTTACAAAGTTA-CAGAAA
1 TACCCTTGGTTTATAAAATTACCA-AAA
* *
28743490 TACCCTTGACTTTATAAAAATTA-TAGAAA
1 TACCCTTG-GTTTAT-AAAATTACCA-AAA
* * **
28743519 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGGTTTATAAAATTACCAAAA
* * * *
28743546 TACCTTTGGTTTGTAGATTTACCAAAA
1 TACCCTTGGTTTATAAAATTACCAAAA
*
28743573 CACCCTTG
1 TACCCTTG
28743581 TAGGATGAAA
Statistics
Matches: 180, Mismatches: 42, Indels: 8
0.78 0.18 0.03
Matches are distributed among these distances:
26 2 0.01
27 151 0.84
28 9 0.05
29 18 0.10
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (27 bp):
TACCCTTGGTTTATAAAATTACCAAAA
Found at i:28743675 original size:27 final size:27
Alignment explanation
Indices: 28743611--28743675 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
28743601 ACCCCTATTA
* * *
28743611 GGTAAAAAGACCGTAAAGCCTCTGTAG
1 GGTAAAATGACCGTAAACCCTCTGTAC
*
28743638 GGTAAAGTGACCGTAATACCCT-TGTAC
1 GGTAAAATGACCGTAA-ACCCTCTGTAC
28743665 GGTAAAATGAC
1 GGTAAAATGAC
28743676 GAATATGCCG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 28 0.88
28 4 0.12
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (27 bp):
GGTAAAATGACCGTAAACCCTCTGTAC
Found at i:28744407 original size:20 final size:20
Alignment explanation
Indices: 28744374--28744448 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
28744364 ATACGTGGGA
28744374 TATGATAT--ACATGAT-TG
1 TATGATATGCACATGATATG
28744391 ATATGATATGCACATGATATG
1 -TATGATATGCACATGATATG
*
28744412 TATGATATACACATGATATG
1 TATGATATGCACATGATATG
*
28744432 TATGAGATGCACATGAT
1 TATGATATGCACATGAT
28744449 GAATTCATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
18 8 0.16
20 41 0.80
21 2 0.04
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (20 bp):
TATGATATGCACATGATATG
Found at i:28744527 original size:26 final size:26
Alignment explanation
Indices: 28744498--28744672 Score: 273
Period size: 26 Copynumber: 6.8 Consensus size: 26
28744488 GAGGAAGTGC
*
28744498 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
28744524 AAAAGGGCTTATGCCCCAGTTTACTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
*
28744550 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
* *
28744576 AAAAGGACTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACTG
* *
28744602 AAAAGGGCTTATGCCTCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACTG
*
28744628 AAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACTG
28744653 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
28744673 ATTAAAGAGG
Statistics
Matches: 137, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
25 32 0.23
26 105 0.77
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACTG
Found at i:28744576 original size:52 final size:52
Alignment explanation
Indices: 28744498--28744672 Score: 309
Period size: 52 Copynumber: 3.4 Consensus size: 52
28744488 GAGGAAGTGC
*
28744498 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACTG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
*
28744550 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGACTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
*
28744602 AAAAGGGCTTATGCCTCAGTTTATTGAAAAGGGCTT-TGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
28744653 AAAAGGGCTT-TGCCCCAGTT
1 AAAAGGGCTTATGCCCCAGTT
28744673 ATTAAAGAGG
Statistics
Matches: 118, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
50 9 0.08
51 25 0.21
52 84 0.71
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (52 bp):
AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
Found at i:28744876 original size:42 final size:42
Alignment explanation
Indices: 28744817--28744908 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
28744807 TAGTCTCCCC
*
28744817 AAATGGGCTTGCATACATTCATTGGTATTTCATGTGATATTG
1 AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
*
28744859 AAATGGGCTTGCATACATTCATTGATATTTCATGTGTTATTG
1 AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
28744901 AAATGGGC
1 AAATGGGC
28744909 CTATGGGCCA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (42 bp):
AAATGGGCTTGCATACATTCATTGATATTTCATGTGATATTG
Found at i:28744967 original size:31 final size:31
Alignment explanation
Indices: 28744932--28745010 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
28744922 CGTTTATAAT
28744932 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
28744963 AAAGGCTTCGGCCCAGTGATTTGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
28744994 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
28745011 AACCGTTAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:28746611 original size:23 final size:23
Alignment explanation
Indices: 28746553--28746612 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
28746543 AATTTAAAAA
*
28746553 AAAAGCATACCTAAT-ATAAGTT
1 AAAAGCATGCCTAATAATAAGTT
* * * *
28746575 AAAA-TATGCATAATAATTATTT
1 AAAAGCATGCCTAATAATAAGTT
28746597 AAAAGCATGCCTAATA
1 AAAAGCATGCCTAATA
28746613 TAATATTATT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
21 7 0.24
22 13 0.45
23 9 0.31
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.30
Consensus pattern (23 bp):
AAAAGCATGCCTAATAATAAGTT
Found at i:28747716 original size:112 final size:114
Alignment explanation
Indices: 28747505--28747718 Score: 276
Period size: 112 Copynumber: 1.9 Consensus size: 114
28747495 TTTAAAGTTG
* *
28747505 GAATAAGCAATCATTTATATAAATTGATTACGAGTGTTTCTTTTAAAATTAATATTATATTAGGC
1 GAATAAGCAATCATATATATAAATTGATTACGAGTGTTTCTTTT-AAATTAATATTATACTAGGC
* * *
28747570 ATGGTTTTATTAACAAGAAATTAGAATAAAAATTATTACTTCCTTGATTA
65 ATGATTTTAATAACAAGAAATCAGAATAAAAATTATTACTTCCTTGATTA
* *
28747620 GAATAAGTCAA-CATATATATGAAA-TGATTATGGGTGTTT-TTTT-AATTAATATTATACTAGG
1 GAATAAG-CAATCATATATAT-AAATTGATTACGAGTGTTTCTTTTAAATTAATATTATACTAGG
* *
28747681 CATGATTTTAATAACAATAAATCATAA-AAATAATTATT
64 CATGATTTTAATAACAAGAAATCAGAATAAA-AATTATT
28747719 CTTTATTAAT
Statistics
Matches: 87, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
111 3 0.03
112 46 0.53
114 4 0.05
115 28 0.32
116 6 0.07
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (114 bp):
GAATAAGCAATCATATATATAAATTGATTACGAGTGTTTCTTTTAAATTAATATTATACTAGGCA
TGATTTTAATAACAAGAAATCAGAATAAAAATTATTACTTCCTTGATTA
Found at i:28751783 original size:39 final size:39
Alignment explanation
Indices: 28751699--28751867 Score: 268
Period size: 39 Copynumber: 4.3 Consensus size: 39
28751689 CAAGACTTTA
* * * *
28751699 AGCCCGAATATAATACCAGCAC-AAAGCCTACGGGACTTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGAC-TT
* *
28751738 ATCCCGGATATAACACCAGCACGAATGCCTTCGGGGCTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
28751777 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
28751816 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
1 AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
28751855 AGCCCGGATATAA
1 AGCCCGGATATAA
28751868 TTCTCCATTA
Statistics
Matches: 121, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
39 110 0.91
40 11 0.09
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (39 bp):
AGCCCGGATATAACACCAGCACGAATGCCTTCGGGACTT
Found at i:28751893 original size:2 final size:2
Alignment explanation
Indices: 28751886--28751919 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28751876 TATCATGCAC
28751886 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
28751920 CATAACACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28752892 original size:2 final size:2
Alignment explanation
Indices: 28752887--28752915 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
28752877 ATAATCACAC
28752887 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 A
28752916 CCTAAATCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28756962 original size:26 final size:27
Alignment explanation
Indices: 28756933--28756986 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
28756923 TCACACAAGT
*
28756933 TAGTCATTT-ACGCACGAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
* *
28756959 TAGTCATTTAACACCCTAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
28756986 T
1 T
28756987 GGTAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (27 bp):
TAGTCATTTAACACACGAGGGGCAAAA
Found at i:28757017 original size:27 final size:27
Alignment explanation
Indices: 28756987--28757186 Score: 256
Period size: 27 Copynumber: 7.4 Consensus size: 27
28756977 GGGGCAAAAT
* * *
28756987 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
28757014 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
28757041 GGTAATTCTACCTTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
28757068 GGTAATTCTATCCTACAGGGGTCTTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
28757095 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
** * * * *
28757122 AATAATTCTATCCTATAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
28757149 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
28757176 AGTAATTCTAC
1 GGTAATTCTAC
28757187 AACTTATCCA
Statistics
Matches: 149, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 149 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:28762970 original size:27 final size:26
Alignment explanation
Indices: 28762922--28762981 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
28762912 GCGAGGCTGC
*
28762922 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
28762949 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
28762975 TAGATAT
1 CAGATAT
28762982 ATATATGTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:28763067 original size:27 final size:26
Alignment explanation
Indices: 28763019--28763070 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
28763009 AACGAGCTGC
*
28763019 CAGATATTGTGACGAAGTCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
* *
28763045 CAGATATATGTGGCGAGGCCACCAGA
1 CAGATAT-TGTGACGAAGCCACCAGA
28763071 TTGTAGCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:28763753 original size:27 final size:27
Alignment explanation
Indices: 28763723--28763922 Score: 220
Period size: 27 Copynumber: 7.4 Consensus size: 27
28763713 AGGGCAAAAT
* * *
28763723 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
28763750 GGTAATTCTACCCTACATGGGTGTTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
28763777 GGTAATTCTACCTTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * * *
28763804 GATAATTCTATCGTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
28763831 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
** * * * *
28763858 AATAATTCTATCCTATAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
28763885 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
28763912 AGTAATTCTAC
1 GGTAATTCTAC
28763923 AACTTATCCA
Statistics
Matches: 146, Mismatches: 27, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 146 1.00
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:28768123 original size:10 final size:10
Alignment explanation
Indices: 28768108--28768132 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28768098 TGTTGCACAC
28768108 ACACTAAGAT
1 ACACTAAGAT
28768118 ACACTAAGAT
1 ACACTAAGAT
28768128 ACACT
1 ACACT
28768133 TCATGTTACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.24, G:0.08, T:0.20
Consensus pattern (10 bp):
ACACTAAGAT
Found at i:28769846 original size:15 final size:15
Alignment explanation
Indices: 28769815--28769852 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
28769805 CATAGATTAA
**
28769815 AATTTAATTAAGTTT
1 AATTTAATTAAAATT
28769830 AATTTAATTAAAATT
1 AATTTAATTAAAATT
28769845 AA-TTAATT
1 AATTTAATT
28769853 TAATCTAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
AATTTAATTAAAATT
Found at i:28771492 original size:2 final size:2
Alignment explanation
Indices: 28771449--28771478 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28771439 TATATATATA
28771449 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
28771479 GCACTTAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:28771508 original size:28 final size:26
Alignment explanation
Indices: 28771477--28771543 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 26
28771467 TGTGTGTGTG
*
28771477 TGGCACTTAGTGTGTGAAATATTGAGAA
1 TGGCACTTAGTGTGCGAAATATT-A-AA
* *
28771505 TGGCACTTGGTGTGCGAGATATTAAA
1 TGGCACTTAGTGTGCGAAATATTAAA
28771531 TAAGGCACTTAGT
1 T--GGCACTTAGT
28771544 TTACGAGACA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 3 0.09
27 1 0.03
28 29 0.88
ACGTcount: A:0.30, C:0.10, G:0.28, T:0.31
Consensus pattern (26 bp):
TGGCACTTAGTGTGCGAAATATTAAA
Found at i:28773402 original size:23 final size:23
Alignment explanation
Indices: 28773372--28773419 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
28773362 TTAAGGGACG
28773372 TTATACATATGTATGAATATTTT
1 TTATACATATGTATGAATATTTT
28773395 TTATACATATGTATGAATATTTT
1 TTATACATATGTATGAATATTTT
28773418 TT
1 TT
28773420 TATTTGAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.54
Consensus pattern (23 bp):
TTATACATATGTATGAATATTTT
Found at i:28774298 original size:36 final size:37
Alignment explanation
Indices: 28774198--28774307 Score: 129
Period size: 37 Copynumber: 3.0 Consensus size: 37
28774188 TGGCAATACA
28774198 TGTGAGTACGTGTAAGACCATAGT-TGGGCTATGGCAT
1 TGTGA-TACGTGTAAGACCATAGTCTGGGCTATGGCAT
** *
28774235 CATGATGACATGTAAGACCATAG-CTGGGCTATGGCAT
1 TGTGAT-ACGTGTAAGACCATAGTCTGGGCTATGGCAT
*
28774272 TGTGATATGTGTAAGACCAT-GTCTGGGAC-ATGGCAT
1 TGTGATACGTGTAAGACCATAGTCTGGG-CTATGGCAT
28774308 CGATATGAGA
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
35 1 0.02
36 25 0.40
37 36 0.58
ACGTcount: A:0.26, C:0.15, G:0.30, T:0.28
Consensus pattern (37 bp):
TGTGATACGTGTAAGACCATAGTCTGGGCTATGGCAT
Found at i:28778208 original size:16 final size:16
Alignment explanation
Indices: 28778187--28778225 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
28778177 AATAGGGGTA
28778187 AAAATGTAATTTTTCT
1 AAAATGTAATTTTTCT
28778203 AAAATGTAATTTTTCT
1 AAAATGTAATTTTTCT
28778219 AAAATGT
1 AAAATGT
28778226 GTAAATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (16 bp):
AAAATGTAATTTTTCT
Found at i:28780699 original size:14 final size:15
Alignment explanation
Indices: 28780680--28780712 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
28780670 TAATTTTTTA
28780680 TTTTAAATA-TATTT
1 TTTTAAATATTATTT
28780694 TTTT-AATATTATTT
1 TTTTAAATATTATTT
28780708 TTTTA
1 TTTTA
28780713 CATCAATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTAAATATTATTT
Found at i:28788261 original size:21 final size:20
Alignment explanation
Indices: 28788237--28788276 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
28788227 ACTTGTTTAA
28788237 CTATCAACAACCATTCAAAAT
1 CTATCAACAACCA-TCAAAAT
* *
28788258 CTATCATCAATCATCAAAA
1 CTATCAACAACCATCAAAA
28788277 CTCATACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (20 bp):
CTATCAACAACCATCAAAAT
Done.