Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397263.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_86.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 8461613
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 85630 characters in sequence are not A, C, G, or T
File 9 of 18
Found at i:4166063 original size:3 final size:3
Alignment explanation
Indices: 4166055--4166098 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
4166045 TGTAACCTCA
4166055 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4166099 GATGATGATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4166103 original size:3 final size:3
Alignment explanation
Indices: 4166097--4166127 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4166087 TATTATTATT
4166097 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
4166128 GAGAAATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:4166243 original size:3 final size:3
Alignment explanation
Indices: 4166235--4166263 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
4166225 GGTAACCTCA
4166235 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4166264 GAGAGAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4166397 original size:140 final size:137
Alignment explanation
Indices: 4166124--4166397 Score: 381
Period size: 140 Copynumber: 2.0 Consensus size: 137
4166114 GATGATGATG
4166124 ATGAGAGAAATATGTAACCTTGTTTAGAGACAACTTAGAGTTGATTTTTTTTTTTAATTTGCATC
1 ATGAGAGAAATATGTAACCTTGTTTAGAGACAACTTAGAGTTGATTTTTTTTTTTAATTTGCATC
* * * ** ** * *
4166189 ATGAACATGAAATAACTATTCTCTAAAATTATCTCAGGTAACCTCAATTATTATTATTATTATTA
66 ATGAACATGAAATAACTATTCTCTAAAATTATCTCAGGGAACATAAACCA-TAAGAGTATTATCA
4166254 TTATTATT
130 TTATTATT
*
4166262 ATGAGAGAAATATGTAACCTTGTTTAGAGATAACTTAGAGTTGATTTTTTTTTTTTTAATTTGCA
1 ATGAGAGAAATATGTAACCTTGTTTAGAGACAACTTAGAGTTGA--TTTTTTTTTTTAATTTGCA
*
4166327 TCATGAACATGAAATAACTATTCTCTAAAATTATCTCAGAGGGAATATAAACCA-AAGACGTATT
64 TCATGAACATGAAATAACTATTCTCTAAAATTATCTC--AGGGAACATAAACCATAAGA-GTATT
4166391 -TCATTAT
126 ATCATTAT
4166398 AAATAATTTG
Statistics
Matches: 120, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
138 43 0.36
140 64 0.53
141 4 0.03
142 9 0.08
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (137 bp):
ATGAGAGAAATATGTAACCTTGTTTAGAGACAACTTAGAGTTGATTTTTTTTTTTAATTTGCATC
ATGAACATGAAATAACTATTCTCTAAAATTATCTCAGGGAACATAAACCATAAGAGTATTATCAT
TATTATT
Found at i:4169365 original size:6 final size:6
Alignment explanation
Indices: 4169354--4169390 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
4169344 TAAGACAGGT
* *
4169354 AGAGAG AGAGAG AGAGAC AGAGAC AGAGAC AGAGAC A
1 AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC AGAGAC A
4169391 CAGAGAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.51, C:0.11, G:0.38, T:0.00
Consensus pattern (6 bp):
AGAGAC
Found at i:4173472 original size:30 final size:31
Alignment explanation
Indices: 4173438--4173505 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 31
4173428 ACTCTACTGG
**
4173438 AAAATAATTTT-CAGATGATCTAAATGATAA
1 AAAATAATTTTACAGATGATCTAAACAATAA
* * *
4173468 AAAATATTTTTAACAGTTTATCTAAACAATAA
1 AAAATAATTTT-ACAGATGATCTAAACAATAA
4173500 AAAATA
1 AAAATA
4173506 TTAATTTTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 10 0.32
32 21 0.68
ACGTcount: A:0.53, C:0.07, G:0.06, T:0.34
Consensus pattern (31 bp):
AAAATAATTTTACAGATGATCTAAACAATAA
Found at i:4174309 original size:9 final size:10
Alignment explanation
Indices: 4174282--4174311 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
4174272 ATAAAAAAAT
4174282 AATTAATTTA
1 AATTAATTTA
4174292 AATTAATTTA
1 AATTAATTTA
4174302 AA-TAATTTA
1 AATTAATTTA
4174311 A
1 A
4174312 TATTTTTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AATTAATTTA
Found at i:4175690 original size:21 final size:19
Alignment explanation
Indices: 4175643--4175692 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 19
4175633 GTTTTGTAGG
4175643 AAATATGATGAAAAAACCTT
1 AAATATGATG-AAAAACCTT
*
4175663 -AAT-TGATGAAAATCCATT
1 AAATATGATGAAAAACC-TT
4175681 CAAATATGATGA
1 -AAATATGATGA
4175693 TGGTTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
17 6 0.24
18 7 0.28
19 3 0.12
20 3 0.12
21 6 0.24
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (19 bp):
AAATATGATGAAAAACCTT
Found at i:4187634 original size:21 final size:22
Alignment explanation
Indices: 4187605--4187646 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
4187595 TGTCTTAATC
**
4187605 ATACTAAAAACAGGACAAAACA
1 ATACTAAAAACAAAACAAAACA
4187627 ATAC-AAAAACAAAACAAAAC
1 ATACTAAAAACAAAACAAAAC
4187647 TCCTCTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.69, C:0.19, G:0.05, T:0.07
Consensus pattern (22 bp):
ATACTAAAAACAAAACAAAACA
Found at i:4203071 original size:21 final size:23
Alignment explanation
Indices: 4203033--4203074 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
4203023 ATGAATAAAG
*
4203033 GGGTATTTCGGATGAAGTCCATA
1 GGGTATTTAGGATGAAGTCCATA
4203056 GGGT-TTTAGGAT-AAGTCCA
1 GGGTATTTAGGATGAAGTCCA
4203075 CCTTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 7 0.39
23 4 0.22
ACGTcount: A:0.26, C:0.12, G:0.31, T:0.31
Consensus pattern (23 bp):
GGGTATTTAGGATGAAGTCCATA
Found at i:4231177 original size:61 final size:61
Alignment explanation
Indices: 4231076--4231194 Score: 168
Period size: 61 Copynumber: 2.0 Consensus size: 61
4231066 TCTTTAAACA
*
4231076 TTTTGAGCATTTTAAAGTGATTTTTGATACACGAAAAAAAACCTTTAAGCATTTTGAGTAT
1 TTTTAAGCATTTTAAAGTGATTTTTGATACACGAAAAAAAACCTTTAAGCATTTTGAGTAT
* * * * *
4231137 TTTTAAGCATTTTAGAA-TGGTTTTTGATACATGAAGAAAAACCTTTGAGCGTTTTGAG
1 TTTTAAGCATTTTA-AAGTGATTTTTGATACACGAAAAAAAACCTTTAAGCATTTTGAG
4231195 CATTCTTCAT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
61 49 0.96
62 2 0.04
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (61 bp):
TTTTAAGCATTTTAAAGTGATTTTTGATACACGAAAAAAAACCTTTAAGCATTTTGAGTAT
Found at i:4231332 original size:22 final size:22
Alignment explanation
Indices: 4231284--4231342 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
4231274 GTAGTTTTGG
*
4231284 TAGTTTTTAGGCATTACACAAT
1 TAGTTTTTAGACATTACACAAT
* ***
4231306 CAGTTTTTAGACATTACGTGAT
1 TAGTTTTTAGACATTACACAAT
*
4231328 TAGTTTTTAAACATT
1 TAGTTTTTAGACATT
4231343 TTTTGACTGA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.44
Consensus pattern (22 bp):
TAGTTTTTAGACATTACACAAT
Found at i:4234180 original size:5 final size:5
Alignment explanation
Indices: 4234170--4234220 Score: 50
Period size: 5 Copynumber: 9.6 Consensus size: 5
4234160 TTTAAGGTAA
*
4234170 AAAAT AAAAT AAAAAT AAAAAT TAAAT AACAATT AAAAT AAAAT -AAAT
1 AAAAT AAAAT -AAAAT -AAAAT AAAAT AA-AA-T AAAAT AAAAT AAAAT
4234218 AAA
1 AAA
4234221 TTTAAAAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
4 4 0.10
5 18 0.45
6 15 0.38
7 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:4234185 original size:11 final size:11
Alignment explanation
Indices: 4234169--4234216 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
4234159 TTTTAAGGTA
4234169 AAAAATAAAAT
1 AAAAATAAAAT
4234180 AAAAATAAAA-
1 AAAAATAAAAT
*
4234190 ATTAAATAACAAT
1 A-AAAATAA-AAT
*
4234203 TAAAATAAAAT
1 AAAAATAAAAT
4234214 AAA
1 AAA
4234217 TAAATTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
10 1 0.03
11 21 0.70
12 8 0.27
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:4234191 original size:17 final size:17
Alignment explanation
Indices: 4234169--4234216 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
4234159 TTTTAAGGTA
4234169 AAAAATAAAATAAAAAT
1 AAAAATAAAATAAAAAT
* *
4234186 AAAAATTAAATAACAAT
1 AAAAATAAAATAAAAAT
*
4234203 TAAAATAAAATAAA
1 AAAAATAAAATAAA
4234217 TAAATTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAAATAAAATAAAAAT
Found at i:4234794 original size:23 final size:22
Alignment explanation
Indices: 4234753--4234828 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
4234743 AACTGATTTT
* * *
4234753 TAAGTATTGTATAATTAGTTAA
1 TAAGCATTGTATGACTAGTTAA
* *
4234775 TATGGCATTGTATGACTAGTTGA
1 TA-AGCATTGTATGACTAGTTAA
* *
4234798 TAAGCATTGCATGACTAGTTAG
1 TAAGCATTGTATGACTAGTTAA
4234820 TAAGACATT
1 TAAG-CATT
4234829 ACGTGACTAG
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
22 22 0.51
23 21 0.49
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (22 bp):
TAAGCATTGTATGACTAGTTAA
Found at i:4234811 original size:22 final size:22
Alignment explanation
Indices: 4234779--4234840 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
4234769 AGTTAATATG
*
4234779 GCATTGTATGACTAGTT-GATAA
1 GCATTGCATGACTAGTTAG-TAA
4234801 GCATTGCATGACTAGTTAGTAA
1 GCATTGCATGACTAGTTAGTAA
* *
4234823 GACATTACGTGACTAGTT
1 G-CATTGCATGACTAGTT
4234841 TTTAGGCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.34
Consensus pattern (22 bp):
GCATTGCATGACTAGTTAGTAA
Found at i:4234900 original size:22 final size:22
Alignment explanation
Indices: 4234848--4234900 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
4234838 GTTTTTAGGC
4234848 ATTATGT--TGTCTAAAAATCA
1 ATTATGTAATGTCTAAAAATCA
* * *
4234868 ATCACGCAATGTCTAAAAATCA
1 ATTATGTAATGTCTAAAAATCA
4234890 ATTATGTAATG
1 ATTATGTAATG
4234901 ATTAAATCAC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 4 0.16
22 21 0.84
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (22 bp):
ATTATGTAATGTCTAAAAATCA
Found at i:4236366 original size:23 final size:23
Alignment explanation
Indices: 4236340--4236387 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
4236330 CTATAAAACC
* *
4236340 TCACCTGTATGCTTAACTTCTTT
1 TCACCTGTATACTCAACTTCTTT
4236363 TCACCTGTATACTCAACTTCTTT
1 TCACCTGTATACTCAACTTCTTT
4236386 TC
1 TC
4236388 CCATTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.46
Consensus pattern (23 bp):
TCACCTGTATACTCAACTTCTTT
Found at i:4245312 original size:16 final size:17
Alignment explanation
Indices: 4245293--4245333 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
4245283 GAACAGAAAA
4245293 AAGGGTTTA-GCATTTT
1 AAGGGTTTAGGCATTTT
**
4245309 AAGGG-CCAGGCATTTT
1 AAGGGTTTAGGCATTTT
4245325 AAGGGTTTA
1 AAGGGTTTA
4245334 TCCGCTTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 3
0.73 0.15 0.12
Matches are distributed among these distances:
15 1 0.05
16 17 0.89
17 1 0.05
ACGTcount: A:0.27, C:0.10, G:0.29, T:0.34
Consensus pattern (17 bp):
AAGGGTTTAGGCATTTT
Found at i:4255206 original size:22 final size:22
Alignment explanation
Indices: 4255164--4255212 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
4255154 TTAAGCATAC
***
4255164 TATTTAAAAAAATCTTTTAAAT
1 TATTTAAAAAAATCAAATAAAT
4255186 TATTTAAAAAAATCAAATAAAT
1 TATTTAAAAAAATCAAATAAAT
4255208 T-TTTA
1 TATTTA
4255213 TTATTTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
TATTTAAAAAAATCAAATAAAT
Found at i:4255937 original size:3 final size:3
Alignment explanation
Indices: 4255929--4255967 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
4255919 AAAATGAGTT
*
4255929 TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4255968 GAATCTCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:4256361 original size:13 final size:13
Alignment explanation
Indices: 4256343--4256367 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4256333 TAAATAAGAT
4256343 ATGCACTTTTAAC
1 ATGCACTTTTAAC
4256356 ATGCACTTTTAA
1 ATGCACTTTTAA
4256368 ATATAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (13 bp):
ATGCACTTTTAAC
Found at i:4257735 original size:5 final size:5
Alignment explanation
Indices: 4257734--4257758 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4257724 ATCCTCTCCT
4257734 CTCTC CTCTC CTCTC CTCTC CTCTC
1 CTCTC CTCTC CTCTC CTCTC CTCTC
4257759 TTCGCCTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
CTCTC
Found at i:4257742 original size:12 final size:12
Alignment explanation
Indices: 4257725--4257759 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
4257715 GTAAATGTAA
4257725 TCCTCTCCTCTC
1 TCCTCTCCTCTC
4257737 TCCTCT-C-CTC
1 TCCTCTCCTCTC
4257747 TCCTCTCCTCTC
1 TCCTCTCCTCTC
4257759 T
1 T
4257760 TCGCCTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 9 0.43
11 2 0.10
12 10 0.48
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (12 bp):
TCCTCTCCTCTC
Found at i:4257766 original size:15 final size:15
Alignment explanation
Indices: 4257734--4257767 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4257724 ATCCTCTCCT
*
4257734 CTCTCCTCTCCTCTC
1 CTCTCCTCTCCTCGC
*
4257749 CTCTCCTCTCTTCGC
1 CTCTCCTCTCCTCGC
4257764 CTCT
1 CTCT
4257768 TTCAACAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.56, G:0.03, T:0.41
Consensus pattern (15 bp):
CTCTCCTCTCCTCGC
Found at i:4264771 original size:249 final size:245
Alignment explanation
Indices: 4264437--4264917 Score: 617
Period size: 249 Copynumber: 1.9 Consensus size: 245
4264427 AAAATAAATA
* * * * * *
4264437 TAAATACTTATTTTTTATTAAAATTAGACTTTTTTACTTAATTAACTTATTACGTTAACTCTAAT
1 TAAATACTTATTTTTCACTAAAATTAGAATTTTTTACTCAATTAACTTATTACGTCAACTCTAAC
* * *
4264502 ACATTTACGTTAAAATTTAAAATTTAATTA-TTCTACATTTATAAGTTTTTATATCAATTGTTAC
66 ACATTTACGTTAAAATTTAAAATTTAATTATTTC-ACATTTATAAATTTTTATATCAACTGCTAC
4264566 AGTTTTACGTCAAAATTTATCTATGA-TAATTTTGAACTATAATAATAATTATTATTATTATTTA
130 AGTTTTACGTCAAAATTTATCTAT-ACTAATTTTGAACTATAAT-ATAATTATTATTATTATTT-
*
4264630 TTTA-AAAATTAAAATTTATATATTGTTAAACACATTTAGTCAAAAAATATATATT
192 TTTATAAAA--AAAATTTATATATCGTTAAACACATTTAGTCAAAAAATATATATT
* * * * * *
4264685 TAAATATTTATTTTTCACTAAAATTAGAAATTTTTTACTCAATTGATTTGTTAGGTCAACTCTCA
1 TAAATACTTATTTTTCACTAAAATTAG-AATTTTTTACTCAATTAACTTATTACGTCAACTCTAA
* * *
4264750 CATATTTACGTTAAGATTTAAAATTTAATTATTTCACTTTTATAAATTTTTATATCAACTGCTAC
65 CACATTTACGTTAAAATTTAAAATTTAATTATTTCACATTTATAAATTTTTATATCAACTGCTAC
* * * * **
4264815 AGTTTTACGTCAATATTTGTCTATACTAATTTTGAATTATAATTTTTTTATTATTATTATTTTTT
130 AGTTTTACGTCAAAATTTATCTATACTAATTTTGAACTATAATATAATTATTATTATTATTTTTT
** *
4264880 ATTCCAAAAAATTTATATATCGTTAAACACTTTTAGTC
195 A-TAAAAAAAATTTATATATCGTTAAACACATTTAGTC
4264918 TGNNNNNNNN
Statistics
Matches: 200, Mismatches: 28, Indels: 11
0.84 0.12 0.05
Matches are distributed among these distances:
247 33 0.17
248 41 0.20
249 123 0.62
250 3 0.01
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.48
Consensus pattern (245 bp):
TAAATACTTATTTTTCACTAAAATTAGAATTTTTTACTCAATTAACTTATTACGTCAACTCTAAC
ACATTTACGTTAAAATTTAAAATTTAATTATTTCACATTTATAAATTTTTATATCAACTGCTACA
GTTTTACGTCAAAATTTATCTATACTAATTTTGAACTATAATATAATTATTATTATTATTTTTTA
TAAAAAAAATTTATATATCGTTAAACACATTTAGTCAAAAAATATATATT
Found at i:4289732 original size:2 final size:2
Alignment explanation
Indices: 4289719--4289755 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4289709 TGGCTGATGC
*
4289719 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4289756 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:4295570 original size:18 final size:17
Alignment explanation
Indices: 4295544--4295597 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 17
4295534 ACATATTTAA
* *
4295544 TTAATATTTATAAAAATT
1 TTAAAATTT-TAAAAAAT
4295562 TTAAAATTTTAAAATAAT
1 TTAAAATTTTAAAA-AAT
4295580 TTAAAATATTTTAAAAAA
1 TT-AAA-ATTTTAAAAAA
4295598 ATTATATCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 5 0.16
18 12 0.39
19 5 0.16
20 9 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAAATTTTAAAAAAT
Found at i:4295600 original size:20 final size:20
Alignment explanation
Indices: 4295546--4295600 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
4295536 ATATTTAATT
* *
4295546 AATA-TTTATAAAAATTTTA
1 AATATTTTAAAAAAATTTAA
*
4295565 AA-ATTTTAAAATAATTTAA
1 AATATTTTAAAAAAATTTAA
4295584 AATATTTTAAAAAAATT
1 AATATTTTAAAAAAATT
4295601 ATATCTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 1 0.03
19 16 0.53
20 13 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AATATTTTAAAAAAATTTAA
Found at i:4308470 original size:21 final size:20
Alignment explanation
Indices: 4308444--4308484 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
4308434 TGATATTTTA
*
4308444 ATTAATAATAATTAATTTATT
1 ATTAATAATAAAT-ATTTATT
*
4308465 ATTAATTATAAATATTTATT
1 ATTAATAATAAATATTTATT
4308485 TAATTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTAATAATAAATATTTATT
Found at i:4308478 original size:25 final size:23
Alignment explanation
Indices: 4308437--4308492 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
4308427 AGATAAATGA
4308437 TATTTTAATTAATAATAATTAATT
1 TATTTTAATTAATAAT-ATTAATT
*
4308461 TATTATTAATT-ATAAATATTTATT
1 TATT-TTAATTAAT-AATATTAATT
*
4308485 TAATTTAA
1 TATTTTAA
4308493 AATAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 4 0.14
24 15 0.54
25 9 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTTTAATTAATAATATTAATT
Found at i:4321822 original size:15 final size:15
Alignment explanation
Indices: 4321802--4321830 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4321792 ATTACAATGC
4321802 AATGTGATTGCAAGT
1 AATGTGATTGCAAGT
4321817 AATGTGATTGCAAG
1 AATGTGATTGCAAG
4321831 GAAAATAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.28, T:0.31
Consensus pattern (15 bp):
AATGTGATTGCAAGT
Found at i:4322065 original size:10 final size:10
Alignment explanation
Indices: 4322050--4322106 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
4322040 TATCATATAT
4322050 TTTATTTTTA
1 TTTATTTTTA
*
4322060 TTTATTATTA
1 TTTATTTTTA
*
4322070 TAATATTTTATA
1 T-TTATTTT-TA
4322082 TTTATTTTTA
1 TTTATTTTTA
* *
4322092 TATATTTATA
1 TTTATTTTTA
4322102 TTTAT
1 TTTAT
4322107 ATTATTAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
10 24 0.63
11 11 0.29
12 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:4322080 original size:20 final size:21
Alignment explanation
Indices: 4322052--4322221 Score: 93
Period size: 22 Copynumber: 7.9 Consensus size: 21
4322042 TCATATATTT
*
4322052 TATTTTTATTTATTATTATAA
1 TATTTATATTTATTATTATAA
*
4322073 TATTTTATATTTATTTTTAT-A
1 TA-TTTATATTTATTATTATAA
4322094 TATTTATATTTA-TATTATTAA
1 TATTTATATTTATTATTA-TAA
* * *
4322115 -ATTTTATATAATATCATTTCTTAA
1 TA-TTTATAT-TTATTA-TT-ATAA
* * **
4322139 -ATATATTTTTAATGTCATATATTT
1 TATTTATATTT-AT-T-AT-TATAA
4322163 TATTT-TATTTATTATTATAA
1 TATTTATATTTATTATTATAA
*
4322183 TATTTTATATTTATTTTTA-ATA
1 TA-TTTATATTTATTATTATA-A
4322205 TATTTATATTTA-TATTA
1 TATTTATATTTATTATTA
4322222 ATTTTTATAT
Statistics
Matches: 114, Mismatches: 19, Indels: 33
0.69 0.11 0.20
Matches are distributed among these distances:
19 4 0.04
20 21 0.18
21 29 0.25
22 33 0.29
23 10 0.09
24 12 0.11
25 5 0.04
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (21 bp):
TATTTATATTTATTATTATAA
Found at i:4322219 original size:111 final size:111
Alignment explanation
Indices: 4321974--4322309 Score: 540
Period size: 110 Copynumber: 3.0 Consensus size: 111
4321964 AAAATATAAG
4321974 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTTA
1 TTTAATATATTTATA--TTTTATTATTAATTTTTATATAATATCATTTCTTAAATATA-TTTTTA
*
4322039 ATATCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTATT
63 ATGTCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTATT
*
4322088 TTT-ATATATTTATATTTATATTATTAAATTTTATATAATATCATTTCTTAAATATATTTTTAAT
1 TTTAATATATTTATATTT-TATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
4322152 GTCATATATTTTA-TTTTATTTATTATTATAATATTTTATATTTATT
65 GTCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTATT
4322198 TTTAATATATTTATA-TTTA-TATTAATTTTTATATAATATTCATATT-TTAAATATATTTTTAA
1 TTTAATATATTTATATTTTATTATTAATTTTTATATAATA-TCAT-TTCTTAAATATATTTTTAA
4322260 TGTCATATATTTTATTTTTATTTATTATTATAAT-TTTATATATTTTATT
64 TGTCATATATTTTATTTTTATTTATTATTATAATATTT-TATA-TTTATT
4322309 T
1 T
4322310 CATTTCTTTA
Statistics
Matches: 212, Mismatches: 3, Indels: 17
0.91 0.01 0.07
Matches are distributed among these distances:
108 18 0.08
109 39 0.18
110 63 0.30
111 41 0.19
112 37 0.17
113 11 0.05
114 3 0.01
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (111 bp):
TTTAATATATTTATATTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATG
TCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTATT
Found at i:4322222 original size:20 final size:21
Alignment explanation
Indices: 4322163--4322231 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
4322153 TCATATATTT
4322163 TATTT-TATTTATTATT-ATAA
1 TATTTATATTTATTATTAAT-A
*
4322183 TATTTTATATTTATTTTTAATA
1 TA-TTTATATTTATTATTAATA
4322205 TATTTATATTTA-TATTAAT-
1 TATTTATATTTATTATTAATA
4322224 T-TTTATAT
1 TATTTATAT
4322232 AATATTCATA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
18 7 0.16
19 1 0.02
20 8 0.18
21 13 0.30
22 13 0.30
23 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTTATATTTATTATTAATA
Found at i:4322273 original size:27 final size:26
Alignment explanation
Indices: 4322135--4322273 Score: 95
Period size: 27 Copynumber: 5.1 Consensus size: 26
4322125 ATATCATTTC
*
4322135 TTAAATATATTTTTAATGTCATATATT
1 TTAAATATATTTTTAATAT-ATATATT
* * *
4322162 TT-ATTTTATTTATTATTATA-ATATT
1 TTAAATATATTT-TTAATATATATATT
* * *
4322187 TTATATTTATTTTTAATATATTTATAT
1 TTAAATATATTTTTAATATATATAT-T
*
4322214 TTATAT-TAATTTTTATATAATATTCATATT
1 TTAAATAT-ATTTTTA-AT-ATA-T-ATATT
*
4322244 TTAAATATATTTTTAATGTCATATATT
1 TTAAATATATTTTTAATAT-ATATATT
4322271 TTA
1 TTA
4322274 TTTTTATTTA
Statistics
Matches: 90, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
25 14 0.16
26 19 0.21
27 29 0.32
28 4 0.04
29 6 0.07
30 14 0.16
31 4 0.04
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.61
Consensus pattern (26 bp):
TTAAATATATTTTTAATATATATATT
Found at i:4322301 original size:10 final size:9
Alignment explanation
Indices: 4322044--4322345 Score: 59
Period size: 9 Copynumber: 33.2 Consensus size: 9
4322034 TTTTAATATC
4322044 ATATA-TTT
1 ATATATTTT
4322052 -TAT-TTTT
1 ATATATTTT
*
4322059 ATTTATTATT
1 ATATATT-TT
4322069 ATAATATTTT
1 AT-ATATTTT
4322079 ATATTTATTTTT
1 ATA--TA-TTTT
4322091 ATATATTTAT
1 ATATATTT-T
* *
4322101 ATTTATATT
1 ATATATTTT
*
4322110 ATTAAATTTT
1 A-TATATTTT
* *
4322120 ATATAATATC
1 ATAT-ATTTT
* * **
4322130 ATTTCTTAA
1 ATATATTTT
4322139 ATATATTTT
1 ATATATTTT
* *
4322148 -TA-ATGTC
1 ATATATTTT
4322155 ATATATTTT
1 ATATATTTT
*
4322164 AT-TTTATTT
1 ATATAT-TTT
*
4322173 AT-TATTAT
1 ATATATTTT
4322181 A-ATATTTT
1 ATATATTTT
4322189 ATATTTATTTTT
1 ATA--TA-TTTT
4322201 AATATATTTAT
1 -ATATATTT-T
* *
4322212 ATTTATATT
1 ATATATTTT
4322221 A-AT-TTTT
1 ATATATTTT
*
4322228 ATATAATATTC
1 ATAT-AT-TTT
*
4322239 ATAT-TTTAA
1 ATATATTT-T
4322248 ATATATTTT
1 ATATATTTT
* *
4322257 -TA-ATGTC
1 ATATATTTT
4322264 ATATA-TTT
1 ATATATTTT
4322272 -TAT-TTTT
1 ATATATTTT
*
4322279 ATTTATTATT
1 ATATATT-TT
4322289 ATA-ATTTT
1 ATATATTTT
4322297 ATATATTTT
1 ATATATTTT
*
4322306 ATTTCATTTCTTT
1 A--T-ATAT-TTT
4322319 AATATATTTT
1 -ATATATTTT
4322329 -TATA--TT
1 ATATATTTT
4322335 ATATATTTT
1 ATATATTTT
4322344 AT
1 AT
4322346 TTTAATTGTT
Statistics
Matches: 210, Mismatches: 42, Indels: 83
0.63 0.13 0.25
Matches are distributed among these distances:
6 2 0.01
7 26 0.12
8 38 0.18
9 52 0.25
10 49 0.23
11 21 0.10
12 15 0.07
13 6 0.03
14 1 0.00
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.64
Consensus pattern (9 bp):
ATATATTTT
Found at i:4322340 original size:109 final size:109
Alignment explanation
Indices: 4321974--4322340 Score: 460
Period size: 109 Copynumber: 3.3 Consensus size: 109
4321964 AAAATATAAG
*
4321974 TTTAATATATTTATAT-TTTTTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTT
1 TTTAATATATTTATATATATTT-TTA-T-A-TTTTATATAATATCATTTCTTAAATATA-TTTTT
*
4322038 AATATCATATATTTTATTTTTATTTATTATTATAATATTTTATA-TTTA
61 AATGTCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTA
* * *
4322086 TTTTTATATATTTATATTTATATTATTAAATTTTATATAATATCATTTCTTAAATATATTTTTAA
1 -TTTAATATATTTATA--TATATTTTTATATTTTATATAATATCATTTCTTAAATATATTTTTAA
*
4322151 TGTCATATATTTTA-TTTTATTTATTATTATAATATTTTATATTTATT
63 TGTCATATATTTTATTTTTATTTATTATTATAATATTTTATATTT-TA
* * *
4322198 TTTAATATATTTATATTTATATTAAT-TTTTATATAATATTCATATT-TTAAATATATTTTTAAT
1 TTTAATATATTTATATATATTTTTATATTTTATATAATA-TCAT-TTCTTAAATATATTTTTAAT
4322261 GTCATATATTTTATTTTTATTTATTATTATAAT-TTTATATATTTTA
64 GTCATATATTTTATTTTTATTTATTATTATAATATTT-TATATTTTA
* * * *
4322307 TTTCATTTCTTTA-ATATATTTTTATATTATATAT
1 TTTAATATATTTATATATATTTTTATATTTTATAT
4322341 TTTATTTTAA
Statistics
Matches: 224, Mismatches: 20, Indels: 24
0.84 0.07 0.09
Matches are distributed among these distances:
108 21 0.09
109 61 0.27
110 55 0.25
111 36 0.16
112 29 0.13
113 15 0.07
115 4 0.02
116 3 0.01
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (109 bp):
TTTAATATATTTATATATATTTTTATATTTTATATAATATCATTTCTTAAATATATTTTTAATGT
CATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTA
Found at i:4322416 original size:23 final size:24
Alignment explanation
Indices: 4322325--4322421 Score: 72
Period size: 23 Copynumber: 3.8 Consensus size: 24
4322315 CTTTAATATA
4322325 TTTTTATATTATATATTTTATTTTAAT
1 TTTTTATATT-TATA--TTATTTTAAT
* *
4322352 TGTTTTATCTATATTATATAAATATTAAT
1 T-TTTTA--TAT-TTATAT-TATTTTAAT
*
4322381 TTTTTATATTTATTTTATTTTAA-
1 TTTTTATATTTATATTATTTTAAT
4322404 TTTTTAT-TCTTATATTAT
1 TTTTTATAT-TTATATTAT
4322422 ATATTTATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 16
0.73 0.08 0.20
Matches are distributed among these distances:
22 1 0.02
23 15 0.26
24 6 0.10
25 5 0.09
26 3 0.05
27 1 0.02
28 11 0.19
29 8 0.14
30 7 0.12
31 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (24 bp):
TTTTTATATTTATATTATTTTAAT
Found at i:4328741 original size:41 final size:41
Alignment explanation
Indices: 4328681--4328760 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
4328671 AAAAGGCTCT
* *
4328681 AGGGTATTAACAATGTGCCATTGAGGATAAT-AGACCCTTTA
1 AGGGTATTAACAATATGCCATTGAGAATAATGAG-CCCTTTA
4328722 AGGGTATTAGA-AATATGCCATTGAGAATAATGAGCCCTT
1 AGGGTATTA-ACAATATGCCATTGAGAATAATGAGCCCTT
4328761 ATTGGAGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 32 0.91
42 3 0.09
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.29
Consensus pattern (41 bp):
AGGGTATTAACAATATGCCATTGAGAATAATGAGCCCTTTA
Found at i:4329714 original size:5 final size:5
Alignment explanation
Indices: 4329704--4329740 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
4329694 ATCGACAATA
4329704 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
4329741 GGGCCTTGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:4334989 original size:81 final size:79
Alignment explanation
Indices: 4334852--4334999 Score: 188
Period size: 81 Copynumber: 1.8 Consensus size: 79
4334842 TCTTGAAATC
* ** ** * *
4334852 ATTTAAAGATAATATTTAAATTAGACCAATTAAAATTTAATTATTTCTCATTTAATTTATCTCTA
1 ATTTAAAGATAATATTGAAATTAGACCAATTAAAATTTAACAATTGATCATCTAATTTATCTATA
4334917 AATAAATCAAGATA
66 AATAAATCAAGATA
* * *
4334931 ATTTAAAGATAATATTGAGATTTTTGACCAATTAAAATTTACCAATTGATCATCTAATTTATCTA
1 ATTTAAAGATAATATTGA-A-ATTAGACCAATTAAAATTTAACAATTGATCATCTAATTTATCTA
4334996 TAAA
64 TAAA
4335000 AACTTATGAT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
79 17 0.30
80 1 0.02
81 39 0.68
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.41
Consensus pattern (79 bp):
ATTTAAAGATAATATTGAAATTAGACCAATTAAAATTTAACAATTGATCATCTAATTTATCTATA
AATAAATCAAGATA
Found at i:4335348 original size:40 final size:38
Alignment explanation
Indices: 4335303--4335390 Score: 104
Period size: 40 Copynumber: 2.3 Consensus size: 38
4335293 TCAGATCGTG
* * * *
4335303 TTCAAGATTAAGTTTCCAAGACGCTTGAGAAGATGAAGTT
1 TTCAAGATCAAGTTGCCAAGACACTT--GAAGACGAAGTT
* *
4335343 TTCAAGATCAAGTTGCCACGACACTTGATGACGAAGTT
1 TTCAAGATCAAGTTGCCAAGACACTTGAAGACGAAGTT
4335381 TTCAAGATCA
1 TTCAAGATCA
4335391 GATCGTGTTC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
38 20 0.48
40 22 0.52
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (38 bp):
TTCAAGATCAAGTTGCCAAGACACTTGAAGACGAAGTT
Found at i:4336405 original size:57 final size:57
Alignment explanation
Indices: 4336319--4336431 Score: 208
Period size: 57 Copynumber: 2.0 Consensus size: 57
4336309 ACACATTTAA
4336319 TTAATTGCGTTAATCATGTTATCATGTTTAAATGTGTATATGTGACACGTTTATTAT
1 TTAATTGCGTTAATCATGTTATCATGTTTAAATGTGTATATGTGACACGTTTATTAT
* *
4336376 TTAATTGTGTTATTCATGTTATCATGTTTAAATGTGTATATGTGACACGTTTATTA
1 TTAATTGCGTTAATCATGTTATCATGTTTAAATGTGTATATGTGACACGTTTATTA
4336432 ACCTGTTAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.49
Consensus pattern (57 bp):
TTAATTGCGTTAATCATGTTATCATGTTTAAATGTGTATATGTGACACGTTTATTAT
Found at i:4336656 original size:25 final size:25
Alignment explanation
Indices: 4336626--4336689 Score: 110
Period size: 25 Copynumber: 2.6 Consensus size: 25
4336616 TTAGATGTTA
4336626 ATGATGGATTTTATCATATTATATG
1 ATGATGGATTTTATCATATTATATG
4336651 ATGATGGATTTTATCATATTATATG
1 ATGATGGATTTTATCATATTATATG
* *
4336676 ATAATGAATTTTAT
1 ATGATGGATTTTAT
4336690 GTATGTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.48
Consensus pattern (25 bp):
ATGATGGATTTTATCATATTATATG
Found at i:4336766 original size:31 final size:31
Alignment explanation
Indices: 4336708--4336767 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
4336698 TTTTTGTTCA
* * *
4336708 ATTTTATTATATTTGATGTTGTTATTATTTT
1 ATTTTATTATAATTGATGTTATAATTATTTT
* *
4336739 ATTTTATTATAATTGTTTTTATAATTATT
1 ATTTTATTATAATTGATGTTATAATTATT
4336768 GATTTTAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (31 bp):
ATTTTATTATAATTGATGTTATAATTATTTT
Found at i:4357587 original size:25 final size:25
Alignment explanation
Indices: 4357553--4357609 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
4357543 CTTTTGAAGC
* *
4357553 TAATGTTTATTTATTGTATAAAGAT
1 TAATATTTATTTATTATATAAAGAT
*
4357578 TAATATTTATTTATTATATAATGAT
1 TAATATTTATTTATTATATAAAGAT
4357603 TAATATT
1 TAATATT
4357610 ATTAGCTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (25 bp):
TAATATTTATTTATTATATAAAGAT
Found at i:4362099 original size:15 final size:15
Alignment explanation
Indices: 4362079--4362124 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
4362069 CCCTCATAAA
4362079 AATTCTTTTGGAAGG
1 AATTCTTTTGGAAGG
*
4362094 AATTCTTTTGGAGGG
1 AATTCTTTTGGAAGG
4362109 AATTCTTTTGG-AGG
1 AATTCTTTTGGAAGG
4362123 AA
1 AA
4362125 AATTGGCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 4 0.14
15 25 0.86
ACGTcount: A:0.26, C:0.07, G:0.28, T:0.39
Consensus pattern (15 bp):
AATTCTTTTGGAAGG
Found at i:4362346 original size:19 final size:22
Alignment explanation
Indices: 4362322--4362362 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
4362312 AGCAGTGTGC
4362322 TGCTTG-TGGG-T-GTGCTGAG
1 TGCTTGCTGGGCTAGTGCTGAG
4362341 TGCTTGCTGGGCTAGTGCTGAG
1 TGCTTGCTGGGCTAGTGCTGAG
4362363 CACCAAGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 4 0.21
21 1 0.05
22 8 0.42
ACGTcount: A:0.07, C:0.15, G:0.44, T:0.34
Consensus pattern (22 bp):
TGCTTGCTGGGCTAGTGCTGAG
Found at i:4367441 original size:45 final size:45
Alignment explanation
Indices: 4367344--4367441 Score: 106
Period size: 45 Copynumber: 2.2 Consensus size: 45
4367334 TCGCGATACG
* * * * *
4367344 CAAGCCCGGGGTGCGTTGGCCCGCATAGCAGGGGTGCACGGCACG
1 CAAGCCCGGGGCGCGTCGGCCAGCACAGCAGGGGTGCACGGCACC
** * **
4367389 CTGGCCCGGGGCGCGTCGGCCAGCACAGTAGGGGTGGGCGGCACC
1 CAAGCCCGGGGCGCGTCGGCCAGCACAGCAGGGGTGCACGGCACC
4367434 CAAGCCCG
1 CAAGCCCG
4367442 CACAGCGCCC
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.14, C:0.34, G:0.43, T:0.09
Consensus pattern (45 bp):
CAAGCCCGGGGCGCGTCGGCCAGCACAGCAGGGGTGCACGGCACC
Found at i:4368297 original size:12 final size:12
Alignment explanation
Indices: 4368267--4368303 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
4368257 AATGTTGAAA
4368267 TATTATTTT-TT
1 TATTATTTTATT
*
4368278 TA-TATTTTAAT
1 TATTATTTTATT
4368289 TATTATTTTATT
1 TATTATTTTATT
4368301 TAT
1 TAT
4368304 ATATCAAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
10 6 0.27
11 5 0.23
12 11 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TATTATTTTATT
Found at i:4392005 original size:106 final size:102
Alignment explanation
Indices: 4391845--4392152 Score: 439
Period size: 99 Copynumber: 3.0 Consensus size: 102
4391835 TCCAGATATA
* *
4391845 ATCCAATGCCACTTAAACTCATTAATCCTGGGCTTGCAATGAGCAAAAAAAAAAAAAAGAATTGA
1 ATCCAATGCAACTTAAACTCATTAATCCTAGGCTTGCAATGAGCAAAAAAAAAAAAAA-AA-T-A
*
4391910 TGACTCTAAAATTGCCCACAAGAGATCTGTCTAGT-AGCAGC
63 TGACTCTAAAATTGCCCAAAAGAGA-CTGTCTA-TAAGCAGC
* *
4391951 ATCCAACGCAACTCAAACTCATTAATCCTAGGCTTGCAATGAGC----AAAAAAAAAAAATATGA
1 ATCCAATGCAACTTAAACTCATTAATCCTAGGCTTGCAATGAGCAAAAAAAAAAAAAAAATATGA
4392012 CTCTAAAATTGCCCAAAAGAGAACTGTCTATAAGCAGC
66 CTCTAAAATTGCCCAAAAGAG-ACTGTCTATAAGCAGC
4392050 ATCCAATGCAACTTAAACTCATTAATCCTAGGCTTGCAATGAGCAAAAAATTTAAAAAAAAAA-A
1 ATCCAATGCAACTTAAACTCATTAATCCTAGGCTTGCAATGAGCAAAAAA---AAAAAAAAAATA
4392114 TGACTCTAAAATTGCCCAAAAGAGCACTGTCTATAAGCA
63 TGACTCTAAAATTGCCCAAAAGAG-ACTGTCTATAAGCA
4392153 ACATTCAAAT
Statistics
Matches: 185, Mismatches: 8, Indels: 19
0.87 0.04 0.09
Matches are distributed among these distances:
98 1 0.01
99 79 0.43
100 2 0.01
101 2 0.01
102 10 0.05
103 2 0.01
105 39 0.21
106 50 0.27
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.22
Consensus pattern (102 bp):
ATCCAATGCAACTTAAACTCATTAATCCTAGGCTTGCAATGAGCAAAAAAAAAAAAAAAATATGA
CTCTAAAATTGCCCAAAAGAGACTGTCTATAAGCAGC
Found at i:4393875 original size:15 final size:15
Alignment explanation
Indices: 4393857--4393915 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
4393847 TCAGCATTCT
4393857 CCTCCTCATCTTCCA
1 CCTCCTCATCTTCCA
* * *
4393872 CCTCCTCTTCTACCT
1 CCTCCTCATCTTCCA
* *
4393887 CTTCCTCAACTTCCA
1 CCTCCTCATCTTCCA
* *
4393902 CTTCCTCCTCTTCC
1 CCTCCTCATCTTCC
4393916 TCTACTTCTT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.10, C:0.53, G:0.00, T:0.37
Consensus pattern (15 bp):
CCTCCTCATCTTCCA
Found at i:4393893 original size:30 final size:30
Alignment explanation
Indices: 4393859--4393918 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
4393849 AGCATTCTCC
* *
4393859 TCCTCATCTTCCACCTCCTCTTCTACCTCT
1 TCCTCAACTTCCACCTCCTCCTCTACCTCT
* *
4393889 TCCTCAACTTCCACTTCCTCCTCTTCCTCT
1 TCCTCAACTTCCACCTCCTCCTCTACCTCT
4393919 ACTTCTTCGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.10, C:0.50, G:0.00, T:0.40
Consensus pattern (30 bp):
TCCTCAACTTCCACCTCCTCCTCTACCTCT
Found at i:4401327 original size:18 final size:18
Alignment explanation
Indices: 4401299--4401342 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
4401289 TCAATAACAA
*
4401299 ATTTA-TAATTTAATCATT
1 ATTTATTAATTT-ATCAAT
4401317 A-TTATTAATTTATCAAT
1 ATTTATTAATTTATCAAT
4401334 ATTTATTAA
1 ATTTATTAA
4401343 AATTATGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTTATTAATTTATCAAT
Found at i:4427675 original size:21 final size:20
Alignment explanation
Indices: 4427645--4427685 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
4427635 GCATTCAAAC
*
4427645 CTAATTTTATATGAATATTTT
1 CTAATCTTATATGAA-ATTTT
*
4427666 CTAATCTTATATTAAATTTT
1 CTAATCTTATATGAAATTTT
4427686 TCATGCTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (20 bp):
CTAATCTTATATGAAATTTT
Found at i:4430627 original size:31 final size:31
Alignment explanation
Indices: 4430590--4430653 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
4430580 ATTCATTTAC
*
4430590 AAAAATATTTACTTACTATATTACTTCTATA
1 AAAAATATTTACTTACTATATTACTTATATA
**
4430621 AAAAATATTTACTTGTTATATTACTTATATA
1 AAAAATATTTACTTACTATATTACTTATATA
4430652 AA
1 AA
4430654 GTTTTATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.45
Consensus pattern (31 bp):
AAAAATATTTACTTACTATATTACTTATATA
Found at i:4440045 original size:58 final size:59
Alignment explanation
Indices: 4439967--4440083 Score: 173
Period size: 58 Copynumber: 2.0 Consensus size: 59
4439957 GAGGATTTTG
* * *
4439967 GATACTATCTTTTTGTCCAAATCCATTTTATTCTAGTTTGACATTGAAT-ATTTTTCAA
1 GATAATATCCTTTTGCCCAAATCCATTTTATTCTAGTTTGACATTGAATAATTTTTCAA
* **
4440025 GATAATATCCTTTTGCCCAAATTCATTTTATTCTAGTTTGATGTTGAATAATTTTTCAA
1 GATAATATCCTTTTGCCCAAATCCATTTTATTCTAGTTTGACATTGAATAATTTTTCAA
4440084 TACATCTTCA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
58 43 0.83
59 9 0.17
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (59 bp):
GATAATATCCTTTTGCCCAAATCCATTTTATTCTAGTTTGACATTGAATAATTTTTCAA
Found at i:4440231 original size:27 final size:28
Alignment explanation
Indices: 4440196--4440255 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 28
4440186 TAGAAAATAA
*
4440196 GTTATACA-TTATATTT-AAAAAATGTT
1 GTTATACAGTTATATTTAAAAAAATATT
*
4440222 GTTATTACATGTTATGTTTAAAAAAATATT
1 GTTA-TACA-GTTATATTTAAAAAAATATT
4440252 GTTA
1 GTTA
4440256 CAATTGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 4 0.14
27 4 0.14
29 7 0.25
30 13 0.46
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (28 bp):
GTTATACAGTTATATTTAAAAAAATATT
Found at i:4440458 original size:34 final size:34
Alignment explanation
Indices: 4440404--4440486 Score: 112
Period size: 34 Copynumber: 2.4 Consensus size: 34
4440394 TGAACACCAT
4440404 ATGTTACACGCCAAGACCAAAGGTTTAGAACTAG
1 ATGTTACACGCCAAGACCAAAGGTTTAGAACTAG
* * * *
4440438 ATGTTACATGCTAAGGCCAAAGGTTTAGCACTAG
1 ATGTTACACGCCAAGACCAAAGGTTTAGAACTAG
* *
4440472 ACGTTACACGACAAG
1 ATGTTACACGCCAAG
4440487 GTCAAAACTG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (34 bp):
ATGTTACACGCCAAGACCAAAGGTTTAGAACTAG
Found at i:4464874 original size:30 final size:28
Alignment explanation
Indices: 4464800--4464879 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 28
4464790 TTAAAGAAAA
* * *
4464800 AAATTAAAAT-AAAATAAACAAAATA-AT
1 AAATTATAATAAAAATGAA-AATATATAT
*
4464827 AAATTATATTAAAAATGAAAATATATAT
1 AAATTATAATAAAAATGAAAATATATAT
4464855 AAGATTATAATAAGAAATGAAAATA
1 AA-ATTATAATAA-AAATGAAAATA
4464880 AAATATATCA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
27 13 0.30
28 11 0.25
29 9 0.20
30 11 0.25
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.28
Consensus pattern (28 bp):
AAATTATAATAAAAATGAAAATATATAT
Found at i:4467720 original size:47 final size:48
Alignment explanation
Indices: 4467627--4467725 Score: 128
Period size: 47 Copynumber: 2.1 Consensus size: 48
4467617 TGGGATTATT
* * *
4467627 AAAAAGAAAGTTTGTAAAAGATTTTGTTTTATATCTATGCACCCATCC
1 AAAAAGAAAGTTTGTAAAAGATTTTGCTTTATATCTATCCAACCATCC
* * * *
4467675 AAAAA-AAAGTTTTTAAAAGATTTTGCTTTATGTGTTTCCAACCATCC
1 AAAAAGAAAGTTTGTAAAAGATTTTGCTTTATATCTATCCAACCATCC
4467722 AAAA
1 AAAA
4467726 TCAAAATGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
47 39 0.89
48 5 0.11
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.35
Consensus pattern (48 bp):
AAAAAGAAAGTTTGTAAAAGATTTTGCTTTATATCTATCCAACCATCC
Found at i:4469122 original size:57 final size:57
Alignment explanation
Indices: 4469034--4469151 Score: 184
Period size: 57 Copynumber: 2.1 Consensus size: 57
4469024 GAATTGAACA
*
4469034 ATATACTTTCAATTTTAATTAAATATGATATAACAAATCAATCCACTTTACT-TTTTT
1 ATATACTTTCAATTTTAATTAAATATGATATAACAAATCAATCCACATTA-TATTTTT
* * *
4469091 ATATATTTTCAATTTTAATTAAATATGATATAACATATCAATTCACATTATATTTTT
1 ATATACTTTCAATTTTAATTAAATATGATATAACAAATCAATCCACATTATATTTTT
4469148 ATAT
1 ATAT
4469152 CATATCATAT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
56 1 0.02
57 55 0.98
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (57 bp):
ATATACTTTCAATTTTAATTAAATATGATATAACAAATCAATCCACATTATATTTTT
Found at i:4473939 original size:75 final size:72
Alignment explanation
Indices: 4473851--4473990 Score: 185
Period size: 72 Copynumber: 1.9 Consensus size: 72
4473841 TTTTATATAT
*
4473851 AGAAAATAAAATAGCTGTTGAAAATTATTAAATACATCTTACGATTAGTTGATT-GAAAATAAAA
1 AGAAAATAAAATA---GTTGAAAATTATTAAATACATATTACGATTAGTTGATTAG-AAATAAAA
4473915 AAAAATAGGTG
62 AAAAATAGGTG
* * *
4473926 AGAAAA-AACAATAGTTGAAGATTATTAAATACATATTACTATTAGTTGATTAGAAATAAGAAAA
1 AGAAAATAA-AATAGTTGAAAATTATTAAATACATATTACGATTAGTTGATTAGAAATAAAAAAA
4473990 A
65 A
4473991 TAATTGAGAA
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
72 46 0.78
73 1 0.02
74 2 0.03
75 10 0.17
ACGTcount: A:0.52, C:0.05, G:0.14, T:0.29
Consensus pattern (72 bp):
AGAAAATAAAATAGTTGAAAATTATTAAATACATATTACGATTAGTTGATTAGAAATAAAAAAAA
ATAGGTG
Found at i:4494324 original size:25 final size:20
Alignment explanation
Indices: 4494276--4494318 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
4494266 AGCTTTTTGT
4494276 ATGCAAAATTAAATTGTCAC
1 ATGCAAAATTAAATTGTCAC
4494296 ATGCAAAATTAAATTGTCAC
1 ATGCAAAATTAAATTGTCAC
4494316 ATG
1 ATG
4494319 TGATGCTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (20 bp):
ATGCAAAATTAAATTGTCAC
Found at i:4509251 original size:2 final size:2
Alignment explanation
Indices: 4509244--4509269 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4509234 GTCACAAGGC
4509244 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
4509270 TGCAATGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4510661 original size:2 final size:2
Alignment explanation
Indices: 4510654--4510680 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4510644 TCACATCAAC
4510654 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
4510681 CTCATTTTGA
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:4512062 original size:22 final size:22
Alignment explanation
Indices: 4512019--4512060 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
4512009 ATAAAAAACA
* *
4512019 TATTAATGTATTAATAATAAAT
1 TATTAATATATTAAAAATAAAT
4512041 TATTAATAT-TTAAAAATAAA
1 TATTAATATATTAAAAATAAA
4512061 ATACTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAATATATTAAAAATAAAT
Found at i:4513358 original size:27 final size:27
Alignment explanation
Indices: 4513322--4513438 Score: 108
Period size: 27 Copynumber: 4.2 Consensus size: 27
4513312 GATTGTAATA
**
4513322 TTTTTTCAATATGGCGTACAATAATTT
1 TTTTTTCAATATGGCGTGTAATAATTT
* **
4513349 TTTTTTCAATTTGGTATGTAATAATTT
1 TTTTTTCAATATGGCGTGTAATAATTT
4513376 TTTTTTCAATATATATGGCGTGTAATAATTT
1 TTTTTTC---A-ATATGGCGTGTAATAATTT
* *** *
4513407 TTTTTTCAACATAATGTGTAATAAATT
1 TTTTTTCAATATGGCGTGTAATAATTT
4513434 TTTTT
1 TTTTT
4513439 CAACATGACA
Statistics
Matches: 73, Mismatches: 13, Indels: 8
0.78 0.14 0.09
Matches are distributed among these distances:
27 48 0.66
28 1 0.01
30 1 0.01
31 23 0.32
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.54
Consensus pattern (27 bp):
TTTTTTCAATATGGCGTGTAATAATTT
Found at i:4513452 original size:26 final size:27
Alignment explanation
Indices: 4513396--4513626 Score: 104
Period size: 26 Copynumber: 8.6 Consensus size: 27
4513386 ATATATGGCG
* * **
4513396 TGTAATAATTTTTTTTTCAACATAATG
1 TGTAATAATATTTTTTTCAACATGACA
4513423 TGTAATAA-ATTTTTTTCAACATGACA
1 TGTAATAATATTTTTTTCAACATGACA
** *
4513449 TGTAA-AA-A-CATTTT-AGATATGACA
1 TGTAATAATATTTTTTTCA-ACATGACA
* * *
4513473 TGTAGTAACAATATTTCTTTTTAACATGACG
1 --T-GTAATAATATTT-TTTTCAACATGACA
* * * * *
4513504 TATAATAATTTTTTTTTTCAATAAGAGA
1 TGTAATAA-TATTTTTTTCAACATGACA
* * *
4513532 TGT-A-AA-CTTTCTTTCAACATGATA
1 TGTAATAATATTTTTTTCAACATGACA
* * *
4513556 AGTAATAATTTTTTTTTCATA-A-GACG
1 TGTAATAATATTTTTTTCA-ACATGACA
* * *
4513582 TGTAATAATATTTATTTCAACATAACG
1 TGTAATAATATTTTTTTCAACATGACA
4513609 TGTAATAATATGTTTTTT
1 TGTAATAATAT-TTTTTT
4513627 ATGTACATTT
Statistics
Matches: 152, Mismatches: 35, Indels: 33
0.69 0.16 0.15
Matches are distributed among these distances:
23 1 0.01
24 26 0.17
25 5 0.03
26 43 0.28
27 36 0.24
28 24 0.16
29 6 0.04
31 10 0.07
32 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (27 bp):
TGTAATAATATTTTTTTCAACATGACA
Found at i:4513859 original size:2 final size:2
Alignment explanation
Indices: 4513852--4513895 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
4513842 ATGCCTAACA
*
4513852 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4513894 AT
1 AT
4513896 TTTCTAAGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4514904 original size:8 final size:8
Alignment explanation
Indices: 4514891--4514917 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
4514881 ATTTAATAAT
4514891 TAATAAAA
1 TAATAAAA
4514899 TAATAAAA
1 TAATAAAA
4514907 TAATAAAA
1 TAATAAAA
4514915 TAA
1 TAA
4514918 CCCCATAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
TAATAAAA
Found at i:4515212 original size:8 final size:8
Alignment explanation
Indices: 4515199--4515225 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
4515189 TAAAAGAGAT
4515199 TTATGAGC
1 TTATGAGC
4515207 TTATGAGC
1 TTATGAGC
4515215 TTATGAGC
1 TTATGAGC
4515223 TTA
1 TTA
4515226 GACAAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.22, T:0.41
Consensus pattern (8 bp):
TTATGAGC
Found at i:4516445 original size:5 final size:5
Alignment explanation
Indices: 4516422--4516601 Score: 56
Period size: 5 Copynumber: 35.4 Consensus size: 5
4516412 ATGTTATAAT
* * * *
4516422 TAAAA TAAAA -AATAT TAAAA TAAAA T-ATA TAATA TAAGAA T-CAA -AAAA
1 TAAAA TAAAA TAA-AA TAAAA TAAAA TAAAA TAAAA TAA-AA TAAAA TAAAA
* ** * ** *
4516470 TAAAA TAAAA TATAAA -AAAT TAAAA T-TTA TATAA TATAGG TAAAA TAAAT
1 TAAAA TAAAA TA-AAA TAAAA TAAAA TAAAA TAAAA TA-AAA TAAAA TAAAA
*
4516520 TAAAA TAAAA TATATAA TAAAA -AAATA TATTAAA -GAAA TAAAA TAAAA
1 TAAAA TAAAA TA-A-AA TAAAA TAAA-A TA--AAA TAAAA TAAAA TAAAA
*
4516568 T-ATA TAAGATTA TAATAA T-AAA TAAAA TAAAA TA
1 TAAAA TAA-A--A TAA-AA TAAAA TAAAA TAAAA TA
4516602 TATGACATAA
Statistics
Matches: 130, Mismatches: 23, Indels: 44
0.66 0.12 0.22
Matches are distributed among these distances:
4 25 0.19
5 79 0.61
6 14 0.11
7 5 0.04
8 7 0.05
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (5 bp):
TAAAA
Found at i:4516474 original size:33 final size:33
Alignment explanation
Indices: 4516416--4516483 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
4516406 TTTATAATGT
4516416 TATAATTAAAATAAAAAATATTAAAATAAAATA
1 TATAATTAAAATAAAAAATATTAAAATAAAATA
*
4516449 TATAATATAAGAATCAAAAA-A-TAAAATAAAATA
1 TATAAT-TAA-AATAAAAAATATTAAAATAAAATA
4516482 TA
1 TA
4516484 AAAAATTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 20 0.62
34 4 0.12
35 8 0.25
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (33 bp):
TATAATTAAAATAAAAAATATTAAAATAAAATA
Found at i:4516474 original size:48 final size:47
Alignment explanation
Indices: 4516422--4516569 Score: 140
Period size: 48 Copynumber: 3.0 Consensus size: 47
4516412 ATGTTATAAT
*
4516422 TAAAATAAAAAATATTAAAATAAAATATATAATATAAG-AATCAA-AAAA
1 TAAAATAAAATATA-TAAAATAAAATATATAATATAAGTAA--AATAAAA
* * *
4516470 TAAAATAAAATATAAAAAATTAAAATTTATATAATATAGGTAAAATAAAT
1 TAAAATAAAATATATAAAA-TAAAA--TATATAATATAAGTAAAATAAAA
* * *
4516520 TAAAATAAAATATATAATAAAAAAATATATTAA-AGAAATAAAATAAAA
1 TAAAATAAAATATATAA-AATAAAATATA-TAATATAAGTAAAATAAAA
4516568 TA
1 TA
4516570 TATAAGATTA
Statistics
Matches: 83, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
47 4 0.05
48 35 0.42
49 5 0.06
50 35 0.42
51 4 0.05
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.28
Consensus pattern (47 bp):
TAAAATAAAATATATAAAATAAAATATATAATATAAGTAAAATAAAA
Found at i:4516477 original size:19 final size:19
Alignment explanation
Indices: 4516437--4516495 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
4516427 TAAAAAATAT
* *
4516437 TAAAATA-AAATATATAATA
1 TAAAATACAAA-AAATAAAA
4516456 TAAGAAT-CAAAAAATAAAA
1 TAA-AATACAAAAAATAAAA
*
4516475 TAAAATATAAAAAATTAAAA
1 TAAAATACAAAAAA-TAAAA
4516495 T
1 T
4516496 TTATATAATA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
18 3 0.09
19 18 0.55
20 12 0.36
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (19 bp):
TAAAATACAAAAAATAAAA
Found at i:4516587 original size:23 final size:24
Alignment explanation
Indices: 4516531--4516589 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
4516521 AAAATAAAAT
*
4516531 ATATAATAAAAAAATATATTAAAG
1 ATATAATAATAAAATATATTAAAG
*
4516555 AAATAA-AATAAAATATA-T-AAG
1 ATATAATAATAAAATATATTAAAG
4516576 ATTATAATAATAAA
1 A-TATAATAATAAA
4516590 TAAAATAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 4 0.13
22 5 0.17
23 16 0.53
24 5 0.17
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (24 bp):
ATATAATAATAAAATATATTAAAG
Found at i:4516663 original size:70 final size:70
Alignment explanation
Indices: 4516516--4516663 Score: 151
Period size: 70 Copynumber: 2.1 Consensus size: 70
4516506 TAGGTAAAAT
* *
4516516 AAAT-TAAAATAAAATATATAATAAAAAAATATATTAAAGAAATAAAATAAAATATATAAGATTA
1 AAATATAAAATAAAATATATAACAAAAAAATATATTAAAGAAAT-AAATAAAATATATAAAATTA
4516580 TAATAA
65 TAATAA
* * * * * * **
4516586 TAA-ATAAAATAAAATATATGACATAAAAATATATTTAAGAGAT-GATATTATATA-AAAATTAA
1 AAATATAAAATAAAATATATAACAAAAAAATATATTAAAGAAATAAATAAAATATATAAAATT-A
4516648 TAATAAA
65 TAAT-AA
4516655 AAATATAAA
1 AAATATAAA
4516664 TATATTAAAC
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
67 5 0.08
68 13 0.21
69 4 0.06
70 41 0.65
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.30
Consensus pattern (70 bp):
AAATATAAAATAAAATATATAACAAAAAAATATATTAAAGAAATAAATAAAATATATAAAATTAT
AATAA
Found at i:4516846 original size:15 final size:15
Alignment explanation
Indices: 4516826--4516884 Score: 75
Period size: 15 Copynumber: 3.9 Consensus size: 15
4516816 CCTTGTGATG
4516826 ACATTACTTGTAATC
1 ACATTACTTGTAATC
* *
4516841 ATATTAGC-TGCAATC
1 ACATTA-CTTGTAATC
4516856 ACATTACTTGTAATC
1 ACATTACTTGTAATC
4516871 ACATTACATTGTAA
1 ACATTAC-TTGTAA
4516885 AGTTTCAAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
14 1 0.03
15 29 0.78
16 7 0.19
ACGTcount: A:0.36, C:0.19, G:0.08, T:0.37
Consensus pattern (15 bp):
ACATTACTTGTAATC
Found at i:4518877 original size:14 final size:14
Alignment explanation
Indices: 4518842--4518878 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4518832 ATTAAACTTT
*
4518842 ACTAGTTCTTCTTA
1 ACTAGTTTTTCTTA
4518856 ACTAGTTTTTCTTA
1 ACTAGTTTTTCTTA
4518870 ACTAGTTTT
1 ACTAGTTTT
4518879 GAAGTATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.22, C:0.16, G:0.08, T:0.54
Consensus pattern (14 bp):
ACTAGTTTTTCTTA
Found at i:4523316 original size:39 final size:39
Alignment explanation
Indices: 4523273--4523349 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
4523263 ATTAAACTCT
* *
4523273 CTCAATTTCATAGTTTTATTTTTTATATAAAAAGCTTCC
1 CTCAATTTCATAGTTGTATTTTTTACATAAAAAGCTTCC
4523312 CTCAATTTCATAGTTGTATTTTTTACATAAAAAGCTTC
1 CTCAATTTCATAGTTGTATTTTTTACATAAAAAGCTTC
4523350 AAAATGATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (39 bp):
CTCAATTTCATAGTTGTATTTTTTACATAAAAAGCTTCC
Found at i:4524881 original size:2 final size:2
Alignment explanation
Indices: 4524874--4524898 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4524864 CTTATATTCA
4524874 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 A
4524899 AGACTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4527861 original size:30 final size:30
Alignment explanation
Indices: 4527827--4527884 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
4527817 AACAATCATC
4527827 AAAGAATGTATA-AGTTTTCTACAATTAGTT
1 AAAGAATGTA-AGAGTTTTCTACAATTAGTT
*
4527857 AAAGATTGTAAGAGTTTTCTACAATTAG
1 AAAGAATGTAAGAGTTTTCTACAATTAG
4527885 ATACAGTCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.38
Consensus pattern (30 bp):
AAAGAATGTAAGAGTTTTCTACAATTAGTT
Found at i:4537233 original size:28 final size:29
Alignment explanation
Indices: 4537187--4537248 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
4537177 ATGTTTTGTA
*
4537187 ATATAAAATGTTATGAATA-TATATATAC
1 ATATAAAATGTTATAAATATTATATATAC
*
4537215 ATATAAAAT-TGTATAAATATTGTATATAC
1 ATATAAAATGT-TATAAATATTATATATAC
4537244 ATATA
1 ATATA
4537249 TATTTAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 1 0.03
28 16 0.53
29 13 0.43
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.40
Consensus pattern (29 bp):
ATATAAAATGTTATAAATATTATATATAC
Found at i:4537723 original size:20 final size:19
Alignment explanation
Indices: 4537695--4537742 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
4537685 TACTAATACT
* *
4537695 TATTATAAATAAAAAATTAA
1 TATTTTAAA-AAAAAATAAA
*
4537715 TATTTTAAAAAATAATAAA
1 TATTTTAAAAAAAAATAAA
4537734 TATATTTAA
1 TAT-TTTAA
4537743 TAATTAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TATTTTAAAAAAAAATAAA
Found at i:4537740 original size:21 final size:22
Alignment explanation
Indices: 4537702--4537774 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 22
4537692 ACTTATTATA
4537702 AATAAAAAATTAATATTTTAAAA-
1 AATAAAAAA-T-ATATTTTAAAAT
*
4537725 AATAATAAATATA-TTTAATAATT
1 AATAAAAAATATATTTTAA-AA-T
*
4537748 AATAAAAAATATATTAT-AAAT
1 AATAAAAAATATATTTTAAAAT
4537769 AA-AAAA
1 AATAAAA
4537775 CAAAATAGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
20 9 0.21
21 8 0.19
22 3 0.07
23 21 0.49
24 2 0.05
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (22 bp):
AATAAAAAATATATTTTAAAAT
Found at i:4537750 original size:20 final size:19
Alignment explanation
Indices: 4537713--4537753 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
4537703 ATAAAAAATT
4537713 AATATTTTAAAAAATAATA
1 AATATTTTAAAAAATAATA
* *
4537732 AATATATTTAATAATTAATA
1 AATAT-TTTAAAAAATAATA
4537752 AA
1 AA
4537754 AAATATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATATTTTAAAAAATAATA
Found at i:4539339 original size:27 final size:26
Alignment explanation
Indices: 4539286--4539340 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
4539276 AAACCAATTC
***
4539286 TATATTTGGTCGGTTTGATCTTCTTT
1 TATATTTGGTCGGTTTGATCAGATTT
*
4539312 TATATTTGGTCGATTTTGATCAGATTT
1 TATATTTGGTCG-GTTTGATCAGATTT
4539339 TA
1 TA
4539341 AAAATGTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.18, C:0.09, G:0.18, T:0.55
Consensus pattern (26 bp):
TATATTTGGTCGGTTTGATCAGATTT
Found at i:4541735 original size:2 final size:2
Alignment explanation
Indices: 4541728--4541755 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4541718 CAATTCCAAA
4541728 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC
4541756 GTCATTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4542775 original size:42 final size:42
Alignment explanation
Indices: 4542723--4542804 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 42
4542713 TGTAATTTGC
* * *
4542723 TAATTTGTCCTTACACTAAATTGAACCATTCAATTAAGTTGT
1 TAATTAGTCCTTACACTAAATTAAACAATTCAATTAAGTTGT
* * * *
4542765 TAATTAGTCCTTATACTTAATTAAATAATTTAATTAAGTT
1 TAATTAGTCCTTACACTAAATTAAACAATTCAATTAAGTT
4542805 TAATTGAAGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
42 33 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (42 bp):
TAATTAGTCCTTACACTAAATTAAACAATTCAATTAAGTTGT
Found at i:4550615 original size:58 final size:57
Alignment explanation
Indices: 4550526--4550645 Score: 195
Period size: 58 Copynumber: 2.1 Consensus size: 57
4550516 AATGTCTCAT
* *
4550526 CTTTGCATGCATAGTATTTATTAAATCACATAAAATAAATCTATCACATGTAGACTA
1 CTTTGCATGCATAGCATTTATTAAATCACATAAAATAAATCTATCACATGTAAACTA
* *
4550583 CTTTGCATTGCATAGCATTTATTAGATCACATAAAATAAATCTATCATATGTAAACTA
1 CTTTGCA-TGCATAGCATTTATTAAATCACATAAAATAAATCTATCACATGTAAACTA
4550641 CTTTG
1 CTTTG
4550646 GATGATTATA
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
57 7 0.12
58 51 0.88
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (57 bp):
CTTTGCATGCATAGCATTTATTAAATCACATAAAATAAATCTATCACATGTAAACTA
Found at i:4557851 original size:14 final size:14
Alignment explanation
Indices: 4557834--4557879 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
4557824 AAATGTGAGA
4557834 TGATGAATGTTAAT
1 TGATGAATGTTAAT
* *
4557848 TGATTAATGTTACT
1 TGATGAATGTTAAT
*
4557862 TGATGCATGTTAA-
1 TGATGAATGTTAAT
4557875 TGATG
1 TGATG
4557880 TAGTTTATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 5 0.19
14 22 0.81
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.43
Consensus pattern (14 bp):
TGATGAATGTTAAT
Found at i:4560508 original size:32 final size:32
Alignment explanation
Indices: 4560463--4560523 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
4560453 TAATGAGAAC
* * *
4560463 AATTAGAATAAGTGAAGCACTACTTCACATAG
1 AATTAAAACAAGTGAAACACTACTTCACATAG
*
4560495 AATTAAAACAAGTGAAATACTACTTCACA
1 AATTAAAACAAGTGAAACACTACTTCACA
4560524 CAGATGACAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (32 bp):
AATTAAAACAAGTGAAACACTACTTCACATAG
Found at i:4563966 original size:17 final size:16
Alignment explanation
Indices: 4563939--4563972 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
4563929 AATGGTATGA
4563939 TATCTTTTAAAAAAAT
1 TATCTTTTAAAAAAAT
*
4563955 TATCTATTTAAAACAAT
1 TATCT-TTTAAAAAAAT
4563972 T
1 T
4563973 TAAATAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (16 bp):
TATCTTTTAAAAAAAT
Found at i:4564021 original size:30 final size:30
Alignment explanation
Indices: 4563969--4564044 Score: 111
Period size: 28 Copynumber: 2.6 Consensus size: 30
4563959 TATTTAAAAC
4563969 AATTTAAATAAATTTTTAT-TTTTTATTAT
1 AATTTAAATAAATTTTTATATTTTTATTAT
* *
4563998 -ATTTAATTAAATTTTTATATTTTTATTTT
1 AATTTAAATAAATTTTTATATTTTTATTAT
*
4564027 AAATTAAATAAATTTTTA
1 AATTTAAATAAATTTTTA
4564045 AAATTATTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
28 17 0.41
29 9 0.22
30 15 0.37
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
AATTTAAATAAATTTTTATATTTTTATTAT
Found at i:4564073 original size:14 final size:15
Alignment explanation
Indices: 4564046--4564076 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
4564036 AAATTTTTAA
4564046 AATTATTGATTAATT
1 AATTATTGATTAATT
4564061 AATTATT-ATTAATT
1 AATTATTGATTAATT
4564075 AA
1 AA
4564077 AATACAATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
AATTATTGATTAATT
Found at i:4565987 original size:40 final size:40
Alignment explanation
Indices: 4565942--4566144 Score: 264
Period size: 40 Copynumber: 5.0 Consensus size: 40
4565932 AAGGATCTTA
* *
4565942 AACATAAACTTAAATAACTAAAAACAAATATCCATACAAC
1 AACATAAACTTAAATAACTAAACACAAATATCCAAACAAC
* * * * *
4565982 GACATAAACTTAAATAACTATACATAAATATTCAAATAAC
1 AACATAAACTTAAATAACTAAACACAAATATCCAAACAAC
*
4566022 AACATAAACTTAAATAACTAAACACAAATATCCAAACAAAT
1 AACATAAACTTAAATAACTAAACACAAATATCCAAAC-AAC
* *
4566063 AACATAAACTTAAATAACCAAACACATATATCCAAACAACAAC
1 AACATAAACTTAAATAACTAAACACAAATATCC--A-AACAAC
*
4566106 AACATAAACTTAAATAACTAAA-ATAAATATCCAAACAAC
1 AACATAAACTTAAATAACTAAACACAAATATCCAAACAAC
4566145 TAGTTAAACA
Statistics
Matches: 140, Mismatches: 19, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
39 6 0.04
40 66 0.47
41 33 0.24
42 8 0.06
43 24 0.17
44 3 0.02
ACGTcount: A:0.59, C:0.20, G:0.00, T:0.21
Consensus pattern (40 bp):
AACATAAACTTAAATAACTAAACACAAATATCCAAACAAC
Found at i:4566077 original size:27 final size:26
Alignment explanation
Indices: 4566033--4566086 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
4566023 ACATAAACTT
*
4566033 AAATAACTAAACACAAATATCCAAAC
1 AAATAACTAAACACAAATAACCAAAC
**
4566059 AAATAACATAAACTTAAATAACCAAAC
1 AAATAAC-TAAACACAAATAACCAAAC
4566086 A
1 A
4566087 CATATATCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.63, C:0.20, G:0.00, T:0.17
Consensus pattern (26 bp):
AAATAACTAAACACAAATAACCAAAC
Found at i:4566079 original size:15 final size:14
Alignment explanation
Indices: 4566026--4566085 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
4566016 AATAACAACA
4566026 TAAACTTAAATAAC
1 TAAACTTAAATAAC
** *
4566040 TAAACACAAATATC
1 TAAACTTAAATAAC
*
4566054 CAAAC--AAATAAC
1 TAAACTTAAATAAC
4566066 ATAAACTTAAATAAC
1 -TAAACTTAAATAAC
*
4566081 CAAAC
1 TAAAC
4566086 ACATATATCC
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
12 6 0.17
13 4 0.11
14 19 0.53
15 7 0.19
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAACTTAAATAAC
Found at i:4569379 original size:15 final size:17
Alignment explanation
Indices: 4569359--4569393 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
4569349 TATATGAATT
4569359 TTATAA-TTTTATAA-A
1 TTATAATTTTTATAATA
4569374 TTATAATTTTTATAATA
1 TTATAATTTTTATAATA
4569391 TTA
1 TTA
4569394 ACATAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
16 8 0.44
17 4 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATAATTTTTATAATA
Found at i:4569544 original size:18 final size:19
Alignment explanation
Indices: 4569518--4569560 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
4569508 GTTAAAAGAC
*
4569518 ATTACAATTTAATTAA-TA
1 ATTATAATTTAATTAATTA
*
4569536 ATTATAATTTTATTAATTA
1 ATTATAATTTAATTAATTA
4569555 ATTATA
1 ATTATA
4569561 TGAATTTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTATAATTTAATTAATTA
Found at i:4577831 original size:17 final size:17
Alignment explanation
Indices: 4577809--4577842 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4577799 TTCCTATTTT
*
4577809 ATTTTTACTTGAGTTTA
1 ATTTTTACTTCAGTTTA
4577826 ATTTTTACTTCAGTTTA
1 ATTTTTACTTCAGTTTA
4577843 TCTAGCATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.59
Consensus pattern (17 bp):
ATTTTTACTTCAGTTTA
Found at i:4585668 original size:21 final size:21
Alignment explanation
Indices: 4585629--4585669 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4585619 ATACTCCTTG
*
4585629 AAAAAATTTTAAATTATTTTC
1 AAAAAATTTTAAATAATTTTC
4585650 AAAAAA-TTTAAATAAATTTT
1 AAAAAATTTTAAAT-AATTTT
4585670 TATTCTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAAAATTTTAAATAATTTTC
Found at i:4586861 original size:2 final size:2
Alignment explanation
Indices: 4586854--4586884 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4586844 TTGTTTACTG
4586854 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4586885 GAAGCATGAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4588923 original size:18 final size:18
Alignment explanation
Indices: 4588900--4588941 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
4588890 CTTTCTATCT
4588900 AGTCCATAAGCATTCAAA
1 AGTCCATAAGCATTCAAA
4588918 AGTCCATAAGCATTCAAA
1 AGTCCATAAGCATTCAAA
*
4588936 GGTCCA
1 AGTCCA
4588942 GCGCTTCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.21
Consensus pattern (18 bp):
AGTCCATAAGCATTCAAA
Found at i:4591159 original size:2 final size:2
Alignment explanation
Indices: 4591152--4591192 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
4591142 TTATCAAGTT
4591152 TA TA TA TA TA 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 TA TA TA TA TA T
4591193 TTGGGGAAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4593229 original size:47 final size:48
Alignment explanation
Indices: 4593171--4593261 Score: 157
Period size: 47 Copynumber: 1.9 Consensus size: 48
4593161 TTTGATTTGT
*
4593171 CAATTACTGGTAAAGCATTAACATGGACAAGC-TTTTTTAGAAAGAAC
1 CAATTACTGGTAAAGCATCAACATGGACAAGCATTTTTTAGAAAGAAC
*
4593218 CAATTACTGGTAAAGCATCAACATGTACAAGCATTTTTTAGAAA
1 CAATTACTGGTAAAGCATCAACATGGACAAGCATTTTTTAGAAA
4593262 TAACATAACA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
47 30 0.73
48 11 0.27
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (48 bp):
CAATTACTGGTAAAGCATCAACATGGACAAGCATTTTTTAGAAAGAAC
Found at i:4609881 original size:118 final size:118
Alignment explanation
Indices: 4609673--4609906 Score: 369
Period size: 118 Copynumber: 2.0 Consensus size: 118
4609663 GTGAAATCTA
**********
4609673 TGGATTAAGACTGAGATAGACCACTCTTTCTAAGATGCTTTNNNNNNNNNNTGTATCTTCATCAC
1 TGGATTAAGACTGAGATAGACCACTCTTTCTAAGATGCTTTGTCTTACTGGTGTATCTTCATCAC
*
4609738 AACAATACTCAAACTTTTCATTGTATGGCCTACAAATTACACCACTCTTTCAT
66 AACAATACTCAAACTTTTCATTGTATAGCCTACAAATTACACCACTCTTTCAT
4609791 TGGATTAAGACTGAGATAGACCACTCTTTCTAAGATGCTTTGTCTTACTGGTGTATCTTCATCAC
1 TGGATTAAGACTGAGATAGACCACTCTTTCTAAGATGCTTTGTCTTACTGGTGTATCTTCATCAC
4609856 AACAATACTCAAACTTTTCATTGTATAGCCTACAAATTACACCACTCTTTC
66 AACAATACTCAAACTTTTCATTGTATAGCCTACAAATTACACCACTCTTTC
4609907 TAAGATGCTT
Statistics
Matches: 105, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
118 105 1.00
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.34
Consensus pattern (118 bp):
TGGATTAAGACTGAGATAGACCACTCTTTCTAAGATGCTTTGTCTTACTGGTGTATCTTCATCAC
AACAATACTCAAACTTTTCATTGTATAGCCTACAAATTACACCACTCTTTCAT
Found at i:4609930 original size:86 final size:87
Alignment explanation
Indices: 4609810--4609981 Score: 328
Period size: 86 Copynumber: 2.0 Consensus size: 87
4609800 ACTGAGATAG
*
4609810 ACCACTCTTTCTAAGATGCTTTGTCTTACTGGTGTATCTTCATCACAACAATACTCAAACTTTTC
1 ACCACTCTTTCTAAGATGCTTTGTCCTACTGGTGTATCTTCATCACAACAATACTCAAACTTTTC
4609875 A-TTGTATAGCCTACAAATTAC
66 ATTTGTATAGCCTACAAATTAC
4609896 ACCACTCTTTCTAAGATGCTTTGTCCTACTGGTGTATCTTCATCACAACAATACTCAAACTTTTC
1 ACCACTCTTTCTAAGATGCTTTGTCCTACTGGTGTATCTTCATCACAACAATACTCAAACTTTTC
4609961 ATTTGTATAGCCTACAAATTA
66 ATTTGTATAGCCTACAAATTA
4609982 TATTTAACTA
Statistics
Matches: 84, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
86 65 0.77
87 19 0.23
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.37
Consensus pattern (87 bp):
ACCACTCTTTCTAAGATGCTTTGTCCTACTGGTGTATCTTCATCACAACAATACTCAAACTTTTC
ATTTGTATAGCCTACAAATTAC
Found at i:4618551 original size:45 final size:45
Alignment explanation
Indices: 4618492--4618621 Score: 233
Period size: 45 Copynumber: 2.9 Consensus size: 45
4618482 CGTTTTTCCT
* *
4618492 CTTGCTTTTATTGTTTGATCTTGCTATTAATAAAGTCATCCTCCA
1 CTTGCTTTTGTTGTTTGATCTTGCTGTTAATAAAGTCATCCTCCA
*
4618537 CTTGCTTTTGTTGTTTGATCTTGCTGTTAATAAAGTCATCCTCCT
1 CTTGCTTTTGTTGTTTGATCTTGCTGTTAATAAAGTCATCCTCCA
4618582 CTTGCTTTTGTTGTTTGATCTTGCTGTTAATAAAGTCATC
1 CTTGCTTTTGTTGTTTGATCTTGCTGTTAATAAAGTCATC
4618622 TAAAAGTTCT
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.48
Consensus pattern (45 bp):
CTTGCTTTTGTTGTTTGATCTTGCTGTTAATAAAGTCATCCTCCA
Found at i:4620220 original size:2 final size:2
Alignment explanation
Indices: 4620213--4620237 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4620203 GGATCTAGTC
4620213 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 A
4620238 ATAAACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4622451 original size:35 final size:36
Alignment explanation
Indices: 4622374--4622453 Score: 119
Period size: 36 Copynumber: 2.2 Consensus size: 36
4622364 TGGGCGAAGA
* *
4622374 AATAGATCATGCACTTGTCGAAGCAATAGGTTGGAG
1 AATAGATCATGCACATGTCGAAGCAATAGGGTGGAG
4622410 AATAGATCATGCACATGTCGAAG-AGAT-GGGTGGAG
1 AATAGATCATGCACATGTCGAAGCA-ATAGGGTGGAG
4622445 AATAGATCA
1 AATAGATCA
4622454 CGTAGAAAGC
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
35 17 0.41
36 24 0.59
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.23
Consensus pattern (36 bp):
AATAGATCATGCACATGTCGAAGCAATAGGGTGGAG
Found at i:4630495 original size:146 final size:146
Alignment explanation
Indices: 4630252--4630514 Score: 377
Period size: 146 Copynumber: 1.8 Consensus size: 146
4630242 CAAGAGACAG
* * *
4630252 TGTTAGTCGACTAAGAGCTTACTGCCAGAAACTAAGTTTAGAGACAAAAACGACTTAATTGACTT
1 TGTTAGTAGACTAAGAGCTTACTGCCAGAAACTAAGTTCAGAGACAAAAACGACTTAATTGACTA
4630317 AGAAGTTTAGTTAGTCGACTAAGAACTTACTGCCAGAAACT-GGCTTCAGAGATAGAAACAACTT
66 AGAAGTTTAGTTAGTCGACTAAGAACTTACTGCCAGAAACTAGG-TTCAGAGATAGAAACAACTT
4630381 AATCAACTGAGAAGTTT
130 AATCAACTGAGAAGTTT
* ** * ** * *
4630398 TGTTAGTAGATTAAGAGCTTACTGTTAGAAATTGGGTTCAGAGATAGAAACGACTTAATTGACTA
1 TGTTAGTAGACTAAGAGCTTACTGCCAGAAACTAAGTTCAGAGACAAAAACGACTTAATTGACTA
* *
4630463 AGAAGTTTTGTTAGTCGACTAAG-AGTCTACTGCCAGAAACTAGGTTCAGAGA
66 AGAAGTTTAGTTAGTCGACTAAGAACT-TACTGCCAGAAACTAGGTTCAGAGA
4630515 CAAAGACAAT
Statistics
Matches: 102, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
145 2 0.02
146 98 0.96
147 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.28
Consensus pattern (146 bp):
TGTTAGTAGACTAAGAGCTTACTGCCAGAAACTAAGTTCAGAGACAAAAACGACTTAATTGACTA
AGAAGTTTAGTTAGTCGACTAAGAACTTACTGCCAGAAACTAGGTTCAGAGATAGAAACAACTTA
ATCAACTGAGAAGTTT
Found at i:4630535 original size:73 final size:73
Alignment explanation
Indices: 4630252--4630561 Score: 331
Period size: 73 Copynumber: 4.2 Consensus size: 73
4630242 CAAGAGACAG
* * * * * *
4630252 TGTTAGTCGACTAAGAGCTTACTGCCAGAAACTAAGTTTAGAGACAAAAACGACTTAATTGACTT
1 TGTTAGTCGACTAAGAGCTTACTGCCAGAAACTAGGTTCAGAGACAGAAACAACTTAATCGACTA
4630317 AGAAGTTT
66 AGAAGTTT
* * * *
4630325 AGTTAGTCGACTAAGAACTTACTGCCAGAAACT-GGCTTCAGAGATAGAAACAACTTAATCAACT
1 TGTTAGTCGACTAAGAGCTTACTGCCAGAAACTAGG-TTCAGAGACAGAAACAACTTAATCGACT
*
4630389 GAGAAGTTT
65 AAGAAGTTT
* * ** * * * * *
4630398 TGTTAGTAGATTAAGAGCTTACTGTTAGAAATTGGGTTCAGAGATAGAAACGACTTAATTGACTA
1 TGTTAGTCGACTAAGAGCTTACTGCCAGAAACTAGGTTCAGAGACAGAAACAACTTAATCGACTA
4630463 AGAAGTTT
66 AGAAGTTT
* *
4630471 TGTTAGTCGACTAAGAG-TCTACTGCCAGAAACTAGGTTCAGAGACA-AAGACAATTTAGTCGAC
1 TGTTAGTCGACTAAGAGCT-TACTGCCAGAAACTAGGTTCAGAGACAGAA-ACAACTTAATCGAC
* **
4630534 TAAG-TGATAA
64 TAAGAAG-TTT
4630544 TGTTAGTCGACTAAGAGC
1 TGTTAGTCGACTAAGAGC
4630562 ATTCTATGTG
Statistics
Matches: 196, Mismatches: 35, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
72 5 0.03
73 189 0.96
74 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (73 bp):
TGTTAGTCGACTAAGAGCTTACTGCCAGAAACTAGGTTCAGAGACAGAAACAACTTAATCGACTA
AGAAGTTT
Found at i:4630548 original size:146 final size:146
Alignment explanation
Indices: 4630252--4630561 Score: 367
Period size: 146 Copynumber: 2.1 Consensus size: 146
4630242 CAAGAGACAG
* *
4630252 TGTTAGTCGACTAAGAGCTTACTGCCAGAAACTAAGTTTAGAGACAAAAACGACTTAATTGACTT
1 TGTTAGTCGACTAAGAGCTTACTGCCAGAAACTAAGTTCAGAGACAAAAACGACTTAATTGACTA
*
4630317 AGAAGTTTAGTTAGTCGACTAAGAACTTACTGCCAGAAACTGGCTTCAGAGATAGAAACAACTTA
66 AGAAGTTTAGTTAGTCGACTAAGAACTTACTGCCAGAAACTGGCTTCAGAGACAGAAACAACTTA
* **
4630382 ATCAACTGAGAAGTTT
131 ATCAACTAAGAAGTAA
* * ** * ** * *
4630398 TGTTAGTAGATTAAGAGCTTACTGTTAGAAATTGGGTTCAGAGATAGAAACGACTTAATTGACTA
1 TGTTAGTCGACTAAGAGCTTACTGCCAGAAACTAAGTTCAGAGACAAAAACGACTTAATTGACTA
* * *
4630463 AGAAGTTTTGTTAGTCGACTAAG-AGTCTACTGCCAGAAACTAGG-TTCAGAGACA-AAGACAAT
66 AGAAGTTTAGTTAGTCGACTAAGAACT-TACTGCCAGAAACT-GGCTTCAGAGACAGAA-ACAAC
* * *
4630525 TTAGTCGACTAAG-TGATAA
128 TTAATCAACTAAGAAG-TAA
4630544 TGTTAGTCGACTAAGAGC
1 TGTTAGTCGACTAAGAGC
4630562 ATTCTATGTG
Statistics
Matches: 137, Mismatches: 23, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
145 5 0.04
146 130 0.95
147 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (146 bp):
TGTTAGTCGACTAAGAGCTTACTGCCAGAAACTAAGTTCAGAGACAAAAACGACTTAATTGACTA
AGAAGTTTAGTTAGTCGACTAAGAACTTACTGCCAGAAACTGGCTTCAGAGACAGAAACAACTTA
ATCAACTAAGAAGTAA
Found at i:4632195 original size:18 final size:18
Alignment explanation
Indices: 4632172--4632208 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4632162 CTTACAGAAG
*
4632172 AAGAAGAAAAAGACAAGA
1 AAGAAGAAAAAGAAAAGA
*
4632190 AAGAAGCAAAAGAAAAGA
1 AAGAAGAAAAAGAAAAGA
4632208 A
1 A
4632209 GAAAAGCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.05, G:0.22, T:0.00
Consensus pattern (18 bp):
AAGAAGAAAAAGAAAAGA
Found at i:4650476 original size:20 final size:20
Alignment explanation
Indices: 4650410--4650482 Score: 58
Period size: 20 Copynumber: 3.6 Consensus size: 20
4650400 ATTAGTTTAT
* * *
4650410 TTTAATTTATGTTTA-AATG
1 TTTATTTTATGTTAATAATA
*
4650429 TTTATTTTAAGTTAATAATA
1 TTTATTTTATGTTAATAATA
** * *
4650449 TTCGTTTTATGTTATTTATA
1 TTTATTTTATGTTAATAATA
4650469 TTTATTTTTATGTT
1 TTTA-TTTTATGTT
4650483 TTTGTAGGAG
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 12 0.29
20 20 0.49
21 9 0.22
ACGTcount: A:0.27, C:0.01, G:0.08, T:0.63
Consensus pattern (20 bp):
TTTATTTTATGTTAATAATA
Done.