Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 66 of 276
Found at i:20424922 original size:3 final size:3
Alignment explanation
Indices: 20424914--20424944 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
20424904 AGACTTCGAA
20424914 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
20424945 TGCTCTACAG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:20427150 original size:32 final size:32
Alignment explanation
Indices: 20427109--20427174 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
20427099 TACCCAATAC
20427109 CAATTATATGCAACAACTAAGAATTTCTTTAT
1 CAATTATATGCAACAACTAAGAATTTCTTTAT
* *
20427141 CAATTATATGCACCAATTAAGAATTTCTTTAT
1 CAATTATATGCAACAACTAAGAATTTCTTTAT
20427173 CA
1 CA
20427175 TACTACTGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (32 bp):
CAATTATATGCAACAACTAAGAATTTCTTTAT
Found at i:20429772 original size:20 final size:20
Alignment explanation
Indices: 20429744--20429782 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
20429734 CTCTTACATT
*
20429744 ATTATATAATTGAAACTTTC
1 ATTACATAATTGAAACTTTC
20429764 ATTACATAATTGAAACTTT
1 ATTACATAATTGAAACTTT
20429783 TCTGAGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (20 bp):
ATTACATAATTGAAACTTTC
Found at i:20429886 original size:23 final size:23
Alignment explanation
Indices: 20429857--20429908 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
20429847 ATATTTCTAT
*
20429857 TGTTCACTCTAGAGAATATTTCC
1 TGTTCACTCTAAAGAATATTTCC
20429880 TGTTCACTCTAAAGAATATTTCC
1 TGTTCACTCTAAAGAATATTTCC
20429903 TGTTCA
1 TGTTCA
20429909 TCTTCATTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (23 bp):
TGTTCACTCTAAAGAATATTTCC
Found at i:20430749 original size:22 final size:23
Alignment explanation
Indices: 20430724--20430769 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
20430714 CAACCAAACC
20430724 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
20430746 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
20430769 A
1 A
20430770 CGTCATCACA
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:20430775 original size:23 final size:23
Alignment explanation
Indices: 20430731--20430775 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
20430721 ACCAATTCAA
*
20430731 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
20430754 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
20430776 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:20431505 original size:59 final size:59
Alignment explanation
Indices: 20431359--20431550 Score: 290
Period size: 59 Copynumber: 3.3 Consensus size: 59
20431349 TTGCAGCGGG
* * *
20431359 ATTACCAGTCCAGGCTAAATCCCCTGCAA-TACAA--ACTC--ATAGAGTATT-G-TCGGG
1 ATTACCAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTAAT-GAGT-TTGGATCTGA
20431413 ATTACCAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTAATGAGTTTGGATCTGA
1 ATTACCAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTAATGAGTTTGGATCTGA
20431472 ATTACCAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTAATGAGTTTGGATCTGA
1 ATTACCAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTAATGAGTTTGGATCTGA
20431531 ATTACCAGTCCAGGCTAAAT
1 ATTACCAGTCCAGGCTAAAT
20431551 TCAGACCCTA
Statistics
Matches: 128, Mismatches: 3, Indels: 9
0.91 0.02 0.06
Matches are distributed among these distances:
54 29 0.23
55 4 0.03
57 6 0.05
58 5 0.04
59 84 0.66
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (59 bp):
ATTACCAGTCCAGGCTAAATCCCCTGCAACGACAATTACTCTAATGAGTTTGGATCTGA
Found at i:20433825 original size:283 final size:283
Alignment explanation
Indices: 20433313--20434163 Score: 1612
Period size: 283 Copynumber: 3.0 Consensus size: 283
20433303 TAAAATTTCC
*
20433313 TAACGAAATTTTAATACCACATTACTAACATTTCATAAATATTTATAAAATTATTTTTGACTCGG
1 TAACAAAATTTTAATACCACATTACTAACATTTCATAAATATTTATAAAATTATTTTTGACTCGG
*
20433378 TTTTACAAGATAAAGGTCTCGATACTTTATTTTTACCCAATTTCTTCAATAATTTCTTTTTCTAA
66 TTTTACGAGATAAAGGTCTCGATACTTTATTTTTACCCAATTTCTTCAATAATTTCTTTTTCTAA
* * * *
20433443 CTAACTACTAAATCGGTAAAATTTTTCTATCAATATTTTCATACGATTTTCCTATCATATCAATT
131 CTAACCACTAAATCGATACAATTTTTCTATCAATATTTTCATACGATTTTCCTATCATTTCAATT
20433508 TTCATGCAAAAATATTGAAATAAATTTCTCTTTAAATCGGATTTGTGGTTATGAAACCACTATTC
196 TTCATGCAAAAATATTGAAATAAATTTCTCTTTAAATCGGATTTGTGGTTATGAAACCACTATTC
20433573 CGATAACCTTGAATTTAGGCCAT
261 CGATAACCTTGAATTTAGGCCAT
20433596 TAACAAAATTTTAATACCACATTACTAACATTTCATAAATATTTATAAAATTATTTTTGACTCGG
1 TAACAAAATTTTAATACCACATTACTAACATTTCATAAATATTTATAAAATTATTTTTGACTCGG
20433661 TTTTACGAGATAAAGGTCTCGATACTTTATTTTTACCCAATTTCTTCAATAATTTCTTTTTCTAA
66 TTTTACGAGATAAAGGTCTCGATACTTTATTTTTACCCAATTTCTTCAATAATTTCTTTTTCTAA
20433726 CTAACCACTAAATCGATACAATTTTTCTATCAATATTTTCATACGATTTTCCTATCATTTCAATT
131 CTAACCACTAAATCGATACAATTTTTCTATCAATATTTTCATACGATTTTCCTATCATTTCAATT
20433791 TTCATGCAAAAATATTGAAATAAATTTCTCTTTAAATCGGATTTGTGGTTATGAAACCACTATTC
196 TTCATGCAAAAATATTGAAATAAATTTCTCTTTAAATCGGATTTGTGGTTATGAAACCACTATTC
20433856 CGATAACCTTGAATTTAGGCCAT
261 CGATAACCTTGAATTTAGGCCAT
20433879 TAACAAAATTTTAATACCACATTACTAACATTTCATAAATATTTATAAAATTATTTTTGACTCGG
1 TAACAAAATTTTAATACCACATTACTAACATTTCATAAATATTTATAAAATTATTTTTGACTCGG
20433944 TTTTACGAGATAAAGGTCTCGATACTTTATTTTTACCCAATTTCTTCAATAATTTCTTTTTCTAA
66 TTTTACGAGATAAAGGTCTCGATACTTTATTTTTACCCAATTTCTTCAATAATTTCTTTTTCTAA
20434009 CTAACCACTAAATCGATACAATTTTTCTATCAATATTTTCATACGATTTTCCTATCATTTCAATT
131 CTAACCACTAAATCGATACAATTTTTCTATCAATATTTTCATACGATTTTCCTATCATTTCAATT
** *
20434074 TTCATGCAAAAATATTGAAATAAATTTCTCTTTAAATTAGATTTGTGGTTACGAAACCACTATTC
196 TTCATGCAAAAATATTGAAATAAATTTCTCTTTAAATCGGATTTGTGGTTATGAAACCACTATTC
*
20434139 CGATAACCTTGAATTTAGACCAT
261 CGATAACCTTGAATTTAGGCCAT
20434162 TA
1 TA
20434164 CACGTTCATT
Statistics
Matches: 558, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
283 558 1.00
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (283 bp):
TAACAAAATTTTAATACCACATTACTAACATTTCATAAATATTTATAAAATTATTTTTGACTCGG
TTTTACGAGATAAAGGTCTCGATACTTTATTTTTACCCAATTTCTTCAATAATTTCTTTTTCTAA
CTAACCACTAAATCGATACAATTTTTCTATCAATATTTTCATACGATTTTCCTATCATTTCAATT
TTCATGCAAAAATATTGAAATAAATTTCTCTTTAAATCGGATTTGTGGTTATGAAACCACTATTC
CGATAACCTTGAATTTAGGCCAT
Found at i:20437702 original size:14 final size:14
Alignment explanation
Indices: 20437683--20437712 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
20437673 AAATTGGTAA
20437683 TAATTATGAATTTC
1 TAATTATGAATTTC
20437697 TAATTATGAATTTC
1 TAATTATGAATTTC
20437711 TA
1 TA
20437713 TCTTTAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (14 bp):
TAATTATGAATTTC
Found at i:20440311 original size:55 final size:55
Alignment explanation
Indices: 20440199--20440311 Score: 190
Period size: 55 Copynumber: 2.1 Consensus size: 55
20440189 ATTTCGAAAC
* *
20440199 CTAAAAAAACCTGCTCCTCCTTGACTCTGATAATAATAAATTATTTTCTGTTAAT
1 CTAAAAAAACCTGCTCCTCCTTGACTCTGATAATAATAAATTATTTTCCGCTAAT
* *
20440254 CTAAAAATACCTGCTCCTCCTTGACTCTGATAATAATAAATTATTTTCCGCTGAT
1 CTAAAAAAACCTGCTCCTCCTTGACTCTGATAATAATAAATTATTTTCCGCTAAT
20440309 CTA
1 CTA
20440312 TTTTTTTTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (55 bp):
CTAAAAAAACCTGCTCCTCCTTGACTCTGATAATAATAAATTATTTTCCGCTAAT
Found at i:20445977 original size:50 final size:49
Alignment explanation
Indices: 20445901--20446001 Score: 184
Period size: 50 Copynumber: 2.0 Consensus size: 49
20445891 TTTGCCACAC
*
20445901 ACTCTTTCTCTACATTGAAATTCAATGACTCATTTCCATAACTATTCCA
1 ACTCTTTCTCTAAATTGAAATTCAATGACTCATTTCCATAACTATTCCA
20445950 ANCTCTTTCTCTAAATTGAAATTCAATGACTCATTTCCATAACTATTCCA
1 A-CTCTTTCTCTAAATTGAAATTCAATGACTCATTTCCATAACTATTCCA
20446000 AC
1 AC
20446002 GAATTTTACC
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
49 2 0.04
50 48 0.96
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (49 bp):
ACTCTTTCTCTAAATTGAAATTCAATGACTCATTTCCATAACTATTCCA
Found at i:20451340 original size:55 final size:55
Alignment explanation
Indices: 20451256--20451366 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
20451246 ATGACCGTGC
*
20451256 CTCTGCACCACATGGGCGTGTGCCTTTGCCACACGGCTGTGTGCTACTCCCTACA
1 CTCTGCACCACATGGGCGTGTGCCTTTGCCACACGGCTGTGTGCTACTCCCAACA
20451311 CTCTGCACCACATGGGCGTGTGCCTTTGCCACACGGCTGTGTGCTACTCCCAACA
1 CTCTGCACCACATGGGCGTGTGCCTTTGCCACACGGCTGTGTGCTACTCCCAACA
20451366 C
1 C
20451367 GGGCGTTTGG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.15, C:0.37, G:0.23, T:0.24
Consensus pattern (55 bp):
CTCTGCACCACATGGGCGTGTGCCTTTGCCACACGGCTGTGTGCTACTCCCAACA
Found at i:20452975 original size:8 final size:8
Alignment explanation
Indices: 20452957--20452991 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
20452947 TTTATTTTAT
20452957 AAAAAAT-
1 AAAAAATA
20452964 AAAAAATA
1 AAAAAATA
20452972 AAAAAATA
1 AAAAAATA
20452980 AAAAAATA
1 AAAAAATA
20452988 AAAA
1 AAAA
20452992 CAATGTCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAAATA
Found at i:20454560 original size:19 final size:21
Alignment explanation
Indices: 20454527--20454566 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
20454517 GTCCCCTGTA
20454527 GTTTAAAAAATTTTCT-AAGT
1 GTTTAAAAAATTTTCTGAAGT
*
20454547 GTTTCAAAAA-TTTCTGAAGT
1 GTTTAAAAAATTTTCTGAAGT
20454567 TATCGGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.42
Consensus pattern (21 bp):
GTTTAAAAAATTTTCTGAAGT
Found at i:20454790 original size:23 final size:24
Alignment explanation
Indices: 20454764--20454814 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
20454754 GGTGTTACAA
20454764 TTTAATATAA-AAATAAAAAATAT
1 TTTAATATAATAAATAAAAAATAT
* *
20454787 TTTAATATAATTCAATATAAAATAT
1 TTTAATATAA-TAAATAAAAAATAT
20454812 TTT
1 TTT
20454815 TCTAAATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.42
25 14 0.58
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTAATATAATAAATAAAAAATAT
Found at i:20456434 original size:24 final size:22
Alignment explanation
Indices: 20456394--20456442 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 22
20456384 CTATTTTATG
20456394 TATAATTTATTTAAAATTGCTT
1 TATAATTTATTTAAAATTGCTT
* *
20456416 TATAATATTCATTTTAAATTGTTT
1 TATAAT-TT-ATTTAAAATTGCTT
20456440 TAT
1 TAT
20456443 TGTGCATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 6 0.26
23 2 0.09
24 15 0.65
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (22 bp):
TATAATTTATTTAAAATTGCTT
Found at i:20456552 original size:26 final size:25
Alignment explanation
Indices: 20456501--20456607 Score: 79
Period size: 26 Copynumber: 4.0 Consensus size: 25
20456491 TTTGCATTAG
* *
20456501 TTATTTTAAACTGTTTTACATATTAT
1 TTATTTTAAA-TTTTTTACATGTTAT
*
20456527 TTATTTTAAATATTTTTATATGTTAT
1 TTATTTTAAAT-TTTTTACATGTTAT
* * * *
20456553 TTACTTTAAGCTATTTTATATGTATAT
1 TTATTTTAA-ATTTTTTACATGT-TAT
20456580 GATCTATTTTAAATTTTTATACATGTTA
1 --T-TATTTTAAATTTTT-TACATGTTA
20456608 ACTTTCAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
25 1 0.02
26 39 0.61
27 4 0.06
29 7 0.11
30 13 0.20
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.58
Consensus pattern (25 bp):
TTATTTTAAATTTTTTACATGTTAT
Found at i:20456837 original size:24 final size:24
Alignment explanation
Indices: 20456800--20456861 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
20456790 ATATTATTTT
*
20456800 ATTGTTTTGAATATTAATGATTTTAA
1 ATTGTTTT--ATATTAATGACTTTAA
* *
20456826 ATTGTTTTATATTATTTACTTTAA
1 ATTGTTTTATATTAATGACTTTAA
20456850 ATTGCTTTTATA
1 ATTG-TTTTATA
20456862 GTATCTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 17 0.53
25 7 0.22
26 8 0.25
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.58
Consensus pattern (24 bp):
ATTGTTTTATATTAATGACTTTAA
Found at i:20456873 original size:25 final size:24
Alignment explanation
Indices: 20456819--20456875 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
20456809 AATATTAATG
* *
20456819 ATTTTAAATTGTTTTATATTATTT
1 ATTTTAAATTGTTTTATAGTATCT
*
20456843 ACTTTAAATTGCTTTTATAGTATCT
1 ATTTTAAATTG-TTTTATAGTATCT
20456868 ATTTTAAA
1 ATTTTAAA
20456876 CCTTTATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (24 bp):
ATTTTAAATTGTTTTATAGTATCT
Found at i:20460801 original size:57 final size:57
Alignment explanation
Indices: 20460708--20460821 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
20460698 TCAACTCAAA
20460708 TGCTACCCTTTAAAACTAAAACCAAACGCAGAAGCCGGTCAACTCCGGCGTCGAGTC
1 TGCTACCCTTTAAAACTAAAACCAAACGCAGAAGCCGGTCAACTCCGGCGTCGAGTC
*
20460765 TGCTCCCCTTTAAAACTAAAACCAAACGCAGAAGCCGGTCAACTCCGGCGTCGAGTC
1 TGCTACCCTTTAAAACTAAAACCAAACGCAGAAGCCGGTCAACTCCGGCGTCGAGTC
20460822 GCTGCACCTG
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (57 bp):
TGCTACCCTTTAAAACTAAAACCAAACGCAGAAGCCGGTCAACTCCGGCGTCGAGTC
Found at i:20462524 original size:24 final size:24
Alignment explanation
Indices: 20462474--20462525 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
20462464 TTAGTAAGTC
* **
20462474 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATAAT
*
20462498 AAATATATTATACTAATAAATAAT
1 AAATAAATTATACTAATAAATAAT
20462522 AAAT
1 AAAT
20462526 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATAAT
Found at i:20467175 original size:25 final size:25
Alignment explanation
Indices: 20467147--20467208 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
20467137 TTTCTAACTA
* *
20467147 ATCACTAAATTGATAAAATTTTCCT
1 ATCAATAAATTCATAAAATTTTCCT
** *
20467172 ATCAATATTTTCATACAATTTTCCT
1 ATCAATAAATTCATAAAATTTTCCT
20467197 ATCATATAAATT
1 ATCA-ATAAATT
20467209 TTCAAGCAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
25 24 0.83
26 5 0.17
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.44
Consensus pattern (25 bp):
ATCAATAAATTCATAAAATTTTCCT
Found at i:20469915 original size:13 final size:13
Alignment explanation
Indices: 20469877--20469919 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
20469867 GCTCAATGCA
*
20469877 AAATTGTAATTTT
1 AAATTCTAATTTT
* * *
20469890 GAATTTTATTTTT
1 AAATTCTAATTTT
20469903 AAATTCTAATTTT
1 AAATTCTAATTTT
20469916 AAAT
1 AAAT
20469920 CAAAATAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (13 bp):
AAATTCTAATTTT
Found at i:20471883 original size:79 final size:75
Alignment explanation
Indices: 20471740--20471893 Score: 209
Period size: 79 Copynumber: 2.0 Consensus size: 75
20471730 AGAATTCAAG
* * *
20471740 TAATCAAAGAAAGGGACTCTGACTCTGCCGTTATGCTTCAGAGGAACCGCATCAAACTCAGAGGG
1 TAATAAAAGAAAGGGACTCTGACTCTGCCGTTATGCTTCAAAGGAACCACATCAAACTCAGAGGG
*
20471805 TAAAGTGTAA
66 TAAAGCGTAA
* * *
20471815 TAATAAAAGAAAGGGACTCTGACTCTGCGCGCGGTTATGTTTCAAAGGAATCACATCAAACTCGG
1 TAATAAAAGAAAGGGACTCTGACTCT--GC-C-GTTATGCTTCAAAGGAACCACATCAAACTCAG
20471880 AGGGTAAAGCGTAA
62 AGGGTAAAGCGTAA
20471894 ATCCATTTGA
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
75 25 0.37
77 2 0.03
78 1 0.01
79 40 0.59
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (75 bp):
TAATAAAAGAAAGGGACTCTGACTCTGCCGTTATGCTTCAAAGGAACCACATCAAACTCAGAGGG
TAAAGCGTAA
Found at i:20472141 original size:27 final size:27
Alignment explanation
Indices: 20472108--20472170 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
20472098 TAGGTTTTAG
20472108 TTAAGATAATTAAGAATTTAAATCAAA
1 TTAAGATAATTAAGAATTTAAATCAAA
* *
20472135 TTAAGATAATTAAGAGTTTAAATTAAA
1 TTAAGATAATTAAGAATTTAAATCAAA
*
20472162 TTAGGATAA
1 TTAAGATAA
20472171 CTAGAGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.35
Consensus pattern (27 bp):
TTAAGATAATTAAGAATTTAAATCAAA
Found at i:20472184 original size:26 final size:27
Alignment explanation
Indices: 20472108--20472184 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
20472098 TAGGTTTTAG
* * *
20472108 TTAAGATAATTAAGAATTTAAATCAAA
1 TTAAGATAACTAAGAGTTTAAATTAAA
*
20472135 TTAAGATAATTAAGAGTTTAAATTAAA
1 TTAAGATAACTAAGAGTTTAAATTAAA
* *
20472162 TTAGGATAACT-AGAGTTTTAATT
1 TTAAGATAACTAAGAGTTTAAATT
20472185 TATTTAAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 11 0.24
27 34 0.76
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.38
Consensus pattern (27 bp):
TTAAGATAACTAAGAGTTTAAATTAAA
Found at i:20475506 original size:2 final size:2
Alignment explanation
Indices: 20475485--20475561 Score: 127
Period size: 2 Copynumber: 38.5 Consensus size: 2
20475475 ATTGGCTTAT
* * *
20475485 AC AC AC AA AT AC AC AT 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 AC AC AC AC AC AC AC
20475527 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
20475562 TAAATACATA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.52, C:0.45, G:0.00, T:0.03
Consensus pattern (2 bp):
AC
Found at i:20478258 original size:16 final size:16
Alignment explanation
Indices: 20478234--20478277 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
20478224 TGCAATTAGG
20478234 TTAGGGTTTTGAAAATT
1 TTAGGGTTTT-AAAATT
*
20478251 TT-GGGTTTTTAAATT
1 TTAGGGTTTTAAAATT
20478266 TTAGGGTTTTAA
1 TTAGGGTTTTAA
20478278 GGAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 15 0.62
17 2 0.08
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (16 bp):
TTAGGGTTTTAAAATT
Found at i:20478276 original size:15 final size:15
Alignment explanation
Indices: 20478234--20478277 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 15
20478224 TGCAATTAGG
20478234 TTAGGGTTTTGAAAATT
1 TTAGGGTTTT--AAATT
20478251 TT-GGGTTTTTAAATT
1 TTAGGG-TTTTAAATT
20478266 TTAGGGTTTTAA
1 TTAGGGTTTTAA
20478278 GGAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 13 0.52
16 6 0.24
17 6 0.24
ACGTcount: A:0.25, C:0.00, G:0.23, T:0.52
Consensus pattern (15 bp):
TTAGGGTTTTAAATT
Found at i:20478419 original size:97 final size:99
Alignment explanation
Indices: 20478272--20478451 Score: 240
Period size: 97 Copynumber: 1.8 Consensus size: 99
20478262 AATTTTAGGG
* ** *
20478272 TTTTAAGGAAAAAAATAAAATAAATTAAGGTTTAGTGTTTGTTAATTAAATTAATTACT-AA-TT
1 TTTTAAGGAAAAAAATAAAATAAATTAAGGTTTAGGGTTACTTAAGTAAATTAATTA-TAAATTT
*
20478335 TTAAAAAAATTAGATTATGGTTTAGTGTTTATGAT
65 TTAAAAAAATCAGATTATGGTTTAGTGTTTATGAT
* * *
20478370 TTTTAAGG-AAAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTATAAATTTT
1 TTTTAAGGAAAAAAATAAAATAAATTAAGGTTTAGGGTTACTTAAGTAAATTAATTATAAA--TT
20478434 TTTAAAAAAATCAGATTA
64 TTTAAAAAAATCAGATTA
20478452 GGATTTTAGG
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
96 1 0.01
97 43 0.61
98 8 0.11
100 18 0.26
ACGTcount: A:0.44, C:0.02, G:0.13, T:0.41
Consensus pattern (99 bp):
TTTTAAGGAAAAAAATAAAATAAATTAAGGTTTAGGGTTACTTAAGTAAATTAATTATAAATTTT
TAAAAAAATCAGATTATGGTTTAGTGTTTATGAT
Found at i:20478942 original size:125 final size:125
Alignment explanation
Indices: 20478562--20479098 Score: 790
Period size: 126 Copynumber: 4.3 Consensus size: 125
20478552 AAAAGCTTCT
* * * * * *
20478562 ACGTGGACGCTCTTTTCCTACAATAGTCTATGAAAAAATAAATTTGAGAAGACATGTCTGCGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTAAGAAGACGTGTCTGCGCAA
* *
20478627 ATAGTGTCAAAACGCTTCAAGCAGAATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
66 ATAGTGTAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* *
20478687 ACGTGGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTTAAGAAGACGTGTCTGTGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTAAGAAGACGTGTCTGCGCAA
*
20478752 ATAGTGTAAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTTCC
66 ATAGTGT-AAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
*
20478813 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTAAGAAGACGTGTCTGCGCAA
* * * * *
20478878 ATAGTGGT-AAAACGCTTTAAGCAGGATGTATTTTCAGCAAAATTACTGGAAGAAGCTCCC
66 ATAGT-GTAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* * * *
20478938 ACGTGGATGCTCTTTTGCTACAGTGGTCTCTGAAAAAATAATTTTAAGAAGACGTATTTGC-CTA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTAAGAAGACGTGTCTGCGC-A
* *
20479002 AATAGTGTCAAAAACTCTTCAAGCAGGATGCATTTTCAGCAAAAGTACTGAAAGAAGCTCCC
65 AATAGTGT-AAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
* * *
20479064 ACGTGGACACTCTTTTGCTACAGTGGTTTCTGAAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAA
20479099 TAACTTGGGC
Statistics
Matches: 374, Mismatches: 33, Indels: 9
0.90 0.08 0.02
Matches are distributed among these distances:
124 3 0.01
125 173 0.46
126 196 0.52
127 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (125 bp):
ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTAAGAAGACGTGTCTGCGCAA
ATAGTGTAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAGAAGCTCCC
Found at i:20479007 original size:251 final size:251
Alignment explanation
Indices: 20478554--20479098 Score: 835
Period size: 251 Copynumber: 2.2 Consensus size: 251
20478544 TAATCTAAAA
* * * *
20478554 AAGCTTCTACGTGGACGCTCTTTTCCTACAATAGTCTATGAAAAAATAAATTTGAGAAGACATGT
1 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACATGT
20478619 CTGCGCAAATAGTGTCAAAACGCTTCAAGCAGAATGCATTGTCAGCAAAAGTACTGAAAGAAGCT
66 CTGCGCAAATAGTGTCAAAACGCTTCAAGCAGAATGCATTGTCAGCAAAAGTACTGAAAGAAGCT
*
20478684 CCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTTAAGAAGACGTGTCTGTG
131 CCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTTAAGAAGACGTATCTGTG
20478749 CAAATAGTGTAAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
196 CAAATAGTGTAAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
* *
20478805 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGT
1 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACATGT
* * * * * *
20478870 CTGCGCAAATAGTGGT-AAAACGCTTTAAGCAGGATGTATTTTCAGCAAAATTACTGGAAGAAGC
66 CTGCGCAAATAGT-GTCAAAACGCTTCAAGCAGAATGCATTGTCAGCAAAAGTACTGAAAGAAGC
* * *
20478934 TCCCACGTGGATGCTCTTTTGCTACAGTGGTCTCTGAAAAAATAATTTTAAGAAGACGTAT-T-T
130 TCCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTTAAGAAGACGTATCTGT
* * *
20478997 GCCTAAATAGTGTCAAAAACTCTTCAAGCAGGATGCATTTTCAGCAAAAGTACTGAAAG
195 G-C-AAATAGTGTAAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
* * * *
20479056 AAGCTCCCACGTGGACACTCTTTTGCTACAGTGGTTTCTGAAA
1 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAA
20479099 TAACTTGGGC
Statistics
Matches: 268, Mismatches: 23, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
249 2 0.01
250 2 0.01
251 262 0.98
252 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (251 bp):
AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACATGT
CTGCGCAAATAGTGTCAAAACGCTTCAAGCAGAATGCATTGTCAGCAAAAGTACTGAAAGAAGCT
CCCACGTGGACGCTCTTTTGCTACAGTAGTATCTGAAAAAATAATTTTAAGAAGACGTATCTGTG
CAAATAGTGTAAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTGAAAG
Found at i:20482247 original size:100 final size:101
Alignment explanation
Indices: 20482124--20482326 Score: 354
Period size: 100 Copynumber: 2.0 Consensus size: 101
20482114 AATATTCAAA
* * *
20482124 ATGTTGCTTTATTTAAAATAATTTGCATTTTAATAAAAATATAAAAGTAAATTATAATTACTTTA
1 ATGTTGCCTTATTTAAAATAATTTCCATTTTAATAAAAATATAAAAGTAAATTACAATTACTTTA
20482189 TTTAAAACAACCTTTTATCTAATT-CATGAAATAAT
66 TTTAAAACAACCTTTTATCTAATTACATGAAATAAT
*
20482224 ATGTTGCCTTATTTAAAATAATTTCCATTTTATTAAAAATATAAAAGTAAATTACAATTACTTTA
1 ATGTTGCCTTATTTAAAATAATTTCCATTTTAATAAAAATATAAAAGTAAATTACAATTACTTTA
*
20482289 TTTGAAACAACCTTTTATCTAATTACATGAAATAAT
66 TTTAAAACAACCTTTTATCTAATTACATGAAATAAT
20482325 AT
1 AT
20482327 AAAAAGATTC
Statistics
Matches: 97, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
100 84 0.87
101 13 0.13
ACGTcount: A:0.43, C:0.09, G:0.05, T:0.42
Consensus pattern (101 bp):
ATGTTGCCTTATTTAAAATAATTTCCATTTTAATAAAAATATAAAAGTAAATTACAATTACTTTA
TTTAAAACAACCTTTTATCTAATTACATGAAATAAT
Found at i:20482305 original size:50 final size:49
Alignment explanation
Indices: 20482151--20482306 Score: 124
Period size: 50 Copynumber: 3.1 Consensus size: 49
20482141 ATAATTTGCA
*
20482151 TTTTAATAAAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACC
1 TTTTATTAAAAATATAAAAGTAAATTA-AATTACTTTATTTAAAACAACC
* * ** * * *
20482201 TTTTATCT--AATTCATGAAA-T-AA-TATGTTGCCTTATTTAAAATAATTTCC
1 TTTTAT-TAAAAAT-ATAAAAGTAAATTAAATTACTTTATTTAAAACAA---CC
*
20482250 ATTTTATTAAAAATATAAAAGTAAATTACAATTACTTTATTTGAAACAACC
1 -TTTTATTAAAAATATAAAAGTAAATTA-AATTACTTTATTTAAAACAACC
20482301 TTTTAT
1 TTTTAT
20482307 CTAATTACAT
Statistics
Matches: 78, Mismatches: 16, Indels: 24
0.66 0.14 0.20
Matches are distributed among these distances:
46 15 0.19
47 2 0.03
48 2 0.03
49 7 0.09
50 27 0.35
51 7 0.09
52 2 0.03
53 2 0.03
54 14 0.18
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (49 bp):
TTTTATTAAAAATATAAAAGTAAATTAAATTACTTTATTTAAAACAACC
Found at i:20482363 original size:100 final size:99
Alignment explanation
Indices: 20482157--20482373 Score: 244
Period size: 100 Copynumber: 2.2 Consensus size: 99
20482147 TGCATTTTAA
*
20482157 TAAAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACCTTTTATCTAATTCATGAAATA
1 TAAAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTAATTCATGAAATA
****** * * * *
20482222 ATATGTTGCCTTATTTAAAATAATTTCCATTTTAT
66 ATA-GTAAAAAGATTCAAAATAATTTCAAATATAT
*
20482257 TAAAAATATAAAAGTAAATTACAATTACTTTATTTGAAACAACCTTTTATCTAATTACATGAAAT
1 TAAAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTAATT-CATGAAAT
**
20482322 AATA-TAAAAAGATTCAAAATGTTTGTACAAATATAT
65 AATAGTAAAAAGATTCAAAATAATT-T-CAAATATAT
20482358 T-AAAATA-AAAA-TAAAT
1 TAAAAATATAAAAGTAAAT
20482374 GTCCGTGCCG
Statistics
Matches: 100, Mismatches: 14, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
98 5 0.05
99 15 0.15
100 61 0.61
101 19 0.19
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (99 bp):
TAAAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTAATTCATGAAATA
ATAGTAAAAAGATTCAAAATAATTTCAAATATAT
Found at i:20482866 original size:30 final size:30
Alignment explanation
Indices: 20482825--20482890 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
20482815 GTTGAACTGT
*
20482825 TGGGCCCGGTGACTGTGTAGGTCCTGTTGC
1 TGGGCCCGGTGACTGTGTAGGTCCTGTTGA
* * * **
20482855 TGGGCCGGGTGATTGTGTGGGTGTTGTTGA
1 TGGGCCCGGTGACTGTGTAGGTCCTGTTGA
20482885 TGGGCC
1 TGGGCC
20482891 TACGTCGTCG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.06, C:0.17, G:0.45, T:0.32
Consensus pattern (30 bp):
TGGGCCCGGTGACTGTGTAGGTCCTGTTGA
Found at i:20484570 original size:22 final size:22
Alignment explanation
Indices: 20484558--20484607 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
20484548 TAACGAGAGT
20484558 TTTGAGAGGAATTTAAGAGAAA
1 TTTGAGAGGAATTTAAGAGAAA
*
20484580 TTTGAGA-G-ATTTGAGA-AGAA
1 TTTGAGAGGAATTTAAGAGA-AA
20484600 TTTGAGAG
1 TTTGAGAG
20484608 AATATTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.04
20 16 0.64
21 1 0.04
22 7 0.28
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (22 bp):
TTTGAGAGGAATTTAAGAGAAA
Found at i:20484602 original size:11 final size:10
Alignment explanation
Indices: 20484558--20484615 Score: 64
Period size: 11 Copynumber: 5.5 Consensus size: 10
20484548 TAACGAGAGT
20484558 TTTGAGAGGAA
1 TTTGAGA-GAA
*
20484569 TTTAAGAGAAA
1 TTTGAGAG-AA
20484580 TTTGAGAG-A
1 TTTGAGAGAA
20484589 TTTGAGAAGAA
1 TTTGAG-AGAA
20484600 TTTGAGAGAA
1 TTTGAGAGAA
20484610 TATTGA
1 T-TTGA
20484616 AAGATTGAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 7 0.17
10 8 0.20
11 26 0.63
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (10 bp):
TTTGAGAGAA
Found at i:20484621 original size:31 final size:31
Alignment explanation
Indices: 20484558--20484621 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
20484548 TAACGAGAGT
* *
20484558 TTTGAGAGGAATTTAAGAGAAATTTGAGAGA
1 TTTGAGAAGAATTTAAGAGAAATTTGAAAGA
*
20484589 TTTGAGAAGAATTTGAGAG-AATATTGAAAGA
1 TTTGAGAAGAATTTAAGAGAAAT-TTGAAAGA
20484620 TT
1 TT
20484622 GAAGATTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 3 0.10
31 26 0.90
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (31 bp):
TTTGAGAAGAATTTAAGAGAAATTTGAAAGA
Found at i:20484812 original size:75 final size:75
Alignment explanation
Indices: 20484684--20484836 Score: 261
Period size: 75 Copynumber: 2.0 Consensus size: 75
20484674 TAGTTTTTTT
* * *
20484684 TTGGACCGTTGGGGGGGTTACCAACGGTCAAAAAAGTAGTCTTTGCTACTGTTCAAACACGGGGA
1 TTGGACCGTTGGGGGGGTTACCAACGGTAAAAAAAGTAGCCGTTGCTACTGTTCAAACACGGGGA
*
20484749 AATCGCTTCC
66 AAACGCTTCC
*
20484759 TTGGCCCGTTGGGGGGGTTACCAACGGTAAAAAAAGTAGCCGTTGCTACTGTTCAAACACGGGGA
1 TTGGACCGTTGGGGGGGTTACCAACGGTAAAAAAAGTAGCCGTTGCTACTGTTCAAACACGGGGA
20484824 AAACGCTTCC
66 AAACGCTTCC
20484834 TTG
1 TTG
20484837 AGGAAGAGTT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (75 bp):
TTGGACCGTTGGGGGGGTTACCAACGGTAAAAAAAGTAGCCGTTGCTACTGTTCAAACACGGGGA
AAACGCTTCC
Found at i:20494071 original size:46 final size:46
Alignment explanation
Indices: 20494021--20494197 Score: 182
Period size: 46 Copynumber: 3.8 Consensus size: 46
20494011 ATGGTTGAGC
* *
20494021 ATCCGAACTCGCTGAGTTGAGTCCAAGTTCACTTATGGATGCGAAT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
* * *
20494067 ATCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACT
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T
*
20494110 AGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
1 ----ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
** * * *
20494160 GCCCGAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
20494198 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 2 0.02
46 61 0.56
47 30 0.28
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (46 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT
Found at i:20494178 original size:93 final size:93
Alignment explanation
Indices: 20494019--20494190 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
20494009 GGATGGTTGA
* * *
20494019 GCATCCGAACTCGCTGAGTTGAGTCCAAGTTCACTTATGGATGCGAATATCCGAACTCGTTGAGT
1 GCATCCGAACTCGCTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACACCCGAACTCATTGAGT
20494084 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
20494112 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGT
1 GCATCCGAACTCGCTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACACCCGAACTCATTGAGT
20494177 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
20494191 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGCTGAGTTGAGTCCAAGTTCACTTATGGATGCGAACACCCGAACTCATTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:20495755 original size:25 final size:25
Alignment explanation
Indices: 20495727--20495779 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
20495717 CCTATTATTC
* * * *
20495727 AGCTTGCATGAGCTTCTCGTTATAT
1 AGCTCGCAAGAGCTTCCCATTATAT
*
20495752 AGCTCGGAAGAGCTTCCCATTATAT
1 AGCTCGCAAGAGCTTCCCATTATAT
20495777 AGC
1 AGC
20495780 GAAGAGCTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.32
Consensus pattern (25 bp):
AGCTCGCAAGAGCTTCCCATTATAT
Found at i:20496001 original size:30 final size:30
Alignment explanation
Indices: 20495962--20496023 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
20495952 TATAGGTAAT
20495962 ACATGGAAAT-GAT-ATTACATGATATATTGAA
1 ACATGGAAATGGATGA-TACATG-TATA-TGAA
20495993 ACAT-GAAATGGATGATACATGTATATGAA
1 ACATGGAAATGGATGATACATGTATATGAA
20496022 AC
1 AC
20496024 TTGCTTAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
29 6 0.21
30 9 0.31
31 13 0.45
32 1 0.03
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (30 bp):
ACATGGAAATGGATGATACATGTATATGAA
Found at i:20497746 original size:22 final size:22
Alignment explanation
Indices: 20497717--20497763 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
20497707 AAAAGCTATC
20497717 TACAAATCAAATCTT-TAAGAT
1 TACAAATCAAATCTTCTAAGAT
* *
20497738 TACAGAATCATATCTTCTAATAT
1 TACA-AATCAAATCTTCTAAGAT
20497761 TAC
1 TAC
20497764 GTTTCATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 4 0.18
22 10 0.45
23 8 0.36
ACGTcount: A:0.43, C:0.17, G:0.04, T:0.36
Consensus pattern (22 bp):
TACAAATCAAATCTTCTAAGAT
Found at i:20498586 original size:32 final size:34
Alignment explanation
Indices: 20498549--20498611 Score: 103
Period size: 32 Copynumber: 1.9 Consensus size: 34
20498539 TAAAATGGGG
*
20498549 TTTTAGGTTCCTTAAAAG-TTGG-AAAAAAATGT
1 TTTTAGGTCCCTTAAAAGTTTGGTAAAAAAATGT
20498581 TTTTAGGTCCCTTAAAAGTTTGGTAAAAAAA
1 TTTTAGGTCCCTTAAAAGTTTGGTAAAAAAA
20498612 ATTTTGGGCC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 17 0.61
33 4 0.14
34 7 0.25
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (34 bp):
TTTTAGGTCCCTTAAAAGTTTGGTAAAAAAATGT
Found at i:20498627 original size:31 final size:31
Alignment explanation
Indices: 20498549--20498628 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 31
20498539 TAAAATGGGG
** *
20498549 TTTTAGGTTCCTTAAAAGTTGGAAAAAAATGT
1 TTTTAGGGCCCTTAAAAGTTGGAAAAAAA-GA
*
20498581 TTTTAGGTCCCTTAAAAGTTTGGTAAAAAAA-A
1 TTTTAGGGCCCTTAAAAG-TTGG-AAAAAAAGA
20498613 TTTT-GGGCCCTTAAAA
1 TTTTAGGGCCCTTAAAA
20498629 ACTAAAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
31 11 0.26
32 21 0.49
33 4 0.09
34 7 0.16
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (31 bp):
TTTTAGGGCCCTTAAAAGTTGGAAAAAAAGA
Found at i:20505979 original size:101 final size:101
Alignment explanation
Indices: 20505804--20505985 Score: 247
Period size: 101 Copynumber: 1.8 Consensus size: 101
20505794 CCACACGGGT
* * * * ** *
20505804 GTGTGATAATTGGGTCAGGCCGTGTGATCTACACGGTCTAGGCCAATCTAGACGTATGGGCTACA
1 GTGTGATAACTGGGCCAGGCCGTGTGATCCACACGGGCTAGGCCAATCTAGACGTATGACCCACA
*
20505869 TGAGCGTGTGGACCCACACGGGCATGCCATACTGGC
66 GGAGCGTGTGGACCCACACGGGCATGCCATACTGGC
* * *
20505905 GTGTGATAACTGGGCCAGGCCGTGTGTTCCACACGGGCTAGGCCAATCTGGACGTGTGACCCACA
1 GTGTGATAACTGGGCCAGGCCGTGTGATCCACACGGGCTAGGCCAATCTAGACGTATGACCCACA
* *
20505970 GGAGTGTGTGGGCCCA
66 GGAGCGTGTGGACCCA
20505986 TAGGGTATGC
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
101 68 1.00
ACGTcount: A:0.20, C:0.25, G:0.34, T:0.21
Consensus pattern (101 bp):
GTGTGATAACTGGGCCAGGCCGTGTGATCCACACGGGCTAGGCCAATCTAGACGTATGACCCACA
GGAGCGTGTGGACCCACACGGGCATGCCATACTGGC
Found at i:20508875 original size:6 final size:7
Alignment explanation
Indices: 20508859--20508884 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
20508849 ATATAATCTT
20508859 AAAAAGA
1 AAAAAGA
20508866 AAAAAGA
1 AAAAAGA
20508873 AAAAAGA
1 AAAAAGA
20508880 AAAAA
1 AAAAA
20508885 AAGAGTGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:20510705 original size:19 final size:19
Alignment explanation
Indices: 20510667--20510706 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20510657 AAAATATCAT
* *
20510667 ATTAATTTTAATTGATTTG
1 ATTAATTTAAATTGACTTG
*
20510686 ATTAATTTAAATTTACTTG
1 ATTAATTTAAATTGACTTG
20510705 AT
1 AT
20510707 CAAAATTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (19 bp):
ATTAATTTAAATTGACTTG
Found at i:20516300 original size:16 final size:17
Alignment explanation
Indices: 20516281--20516318 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
20516271 GGATAACGAA
20516281 AAAAAAT-TATAAAT-AT
1 AAAAAATCTA-AAATAAT
20516297 AAAAAATCTAAAATAAT
1 AAAAAATCTAAAATAAT
20516314 AAAAA
1 AAAAA
20516319 TAAATAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAAAAATCTAAAATAAT
Found at i:20516315 original size:23 final size:24
Alignment explanation
Indices: 20516283--20516327 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
20516273 ATAACGAAAA
* *
20516283 AAAATTATAAATATAAA-AAATCT
1 AAAATAATAAAAATAAATAAATCT
20516306 AAAATAATAAAAATAAATAAAT
1 AAAATAATAAAAATAAATAAAT
20516328 TAAGTTCCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (24 bp):
AAAATAATAAAAATAAATAAATCT
Found at i:20517694 original size:14 final size:14
Alignment explanation
Indices: 20517675--20517705 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
20517665 CATAGTACAG
20517675 TTTGTATTAAGAAA
1 TTTGTATTAAGAAA
20517689 TTTGTATTAAGAAA
1 TTTGTATTAAGAAA
20517703 TTT
1 TTT
20517706 ATTTGGTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTTGTATTAAGAAA
Found at i:20525409 original size:6 final size:6
Alignment explanation
Indices: 20525398--20525423 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
20525388 AAATATTTTT
20525398 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
20525424 CTAATATCGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:20525681 original size:18 final size:17
Alignment explanation
Indices: 20525638--20525685 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
20525628 AAATATATAT
20525638 ATAC-AATATATATTAAAA
1 ATACTAATA-ATA-TAAAA
*
20525656 ATAGTAATAATATAAAA
1 ATACTAATAATATAAAA
20525673 ATAACTAATAATA
1 AT-ACTAATAATA
20525686 ACGATATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 7 0.27
18 15 0.58
19 4 0.15
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (17 bp):
ATACTAATAATATAAAA
Found at i:20525904 original size:25 final size:24
Alignment explanation
Indices: 20525834--20526055 Score: 192
Period size: 23 Copynumber: 9.2 Consensus size: 24
20525824 TAAATATGTA
*
20525834 AATATATATTAAAAATAAATACAT
1 AATATATATTAAAAATATATACAT
* * *
20525858 AATA-CTATTAAAAGTATGTACAT
1 AATATATATTAAAAATATATACAT
* *
20525881 AATATAGTGTTAAAAATACATACAT
1 AATATA-TATTAAAAATATATACAT
20525906 AATATAGTTATTAAAAAATATATACAT
1 AATATA--TATT-AAAAATATATACAT
* *
20525933 AAGATA-ATATAAAAATATACACAT
1 AATATATAT-TAAAAATATATACAT
*
20525957 GAA-ATAGTATAAAAAATATATA-ACT
1 -AATATA-TATTAAAAATATATACA-T
20525982 AATA-ATATTAAAAATATATACAT
1 AATATATATTAAAAATATATACAT
*
20526005 AATATATA-TAAAAACATATACA-
1 AATATATATTAAAAATATATACAT
* *
20526027 ATATATATATTAGAAAT-GATA-AT
1 A-ATATATATTAAAAATATATACAT
20526050 AATATA
1 AATATA
20526056 AAAAAAATTA
Statistics
Matches: 162, Mismatches: 21, Indels: 32
0.75 0.10 0.15
Matches are distributed among these distances:
22 7 0.04
23 62 0.38
24 35 0.22
25 35 0.22
26 5 0.03
27 18 0.11
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (24 bp):
AATATATATTAAAAATATATACAT
Found at i:20526084 original size:12 final size:12
Alignment explanation
Indices: 20526045--20526157 Score: 55
Period size: 12 Copynumber: 9.6 Consensus size: 12
20526035 ATTAGAAATG
20526045 ATAAT-AATATA
1 ATAATAAATATA
*
20526056 A-AAAAAATTATTA
1 ATAATAAA-TA-TA
20526069 ATAATAAATATA
1 ATAATAAATATA
*
20526081 ATAATAAATCTA
1 ATAATAAATATA
*
20526093 GTATATAAATAT-
1 ATA-ATAAATATA
20526105 -TAAGTGAAA-ATCA
1 ATAA-T-AAATAT-A
* *
20526118 ATACT-AGTACTA
1 ATAATAAATA-TA
20526130 ATAAT--AT-TA
1 ATAATAAATATA
20526139 ATAATAAATATA
1 ATAATAAATATA
20526151 ATAATAA
1 ATAATAA
20526158 TAAATATATA
Statistics
Matches: 78, Mismatches: 9, Indels: 29
0.67 0.08 0.25
Matches are distributed among these distances:
9 7 0.09
10 3 0.04
11 12 0.15
12 35 0.45
13 14 0.18
14 7 0.09
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.34
Consensus pattern (12 bp):
ATAATAAATATA
Found at i:20526178 original size:19 final size:15
Alignment explanation
Indices: 20526137--20526165 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20526127 CTAATAATAT
20526137 TAATAATAAATATAA
1 TAATAATAAATATAA
20526152 TAATAATAAATATA
1 TAATAATAAATATA
20526166 TATGCATATA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAATAATAAATATAA
Found at i:20527921 original size:75 final size:75
Alignment explanation
Indices: 20527784--20527932 Score: 181
Period size: 75 Copynumber: 2.0 Consensus size: 75
20527774 TCAGCGTATG
* * * * * *
20527784 ACCTCAGCGTCTGATCTGAGGCTTAACTCACCTCTCGCAATACGAGTTGACTTTTAAAAAACAGG
1 ACCTCAACGTCTGACCTGAGGATCAACTCACCTCTCACAATACGAGTTGACTTTTAAAAAACAGA
20527849 AATTGAAAAT
66 AATTGAAAAT
* * * *** *
20527859 ACCTCAACGTGTGACCTGAGGATCAACTCACCTCTCACAATATGAGTTGATTTTTTTGAAACATA
1 ACCTCAACGTCTGACCTGAGGATCAACTCACCTCTCACAATACGAGTTGACTTTTAAAAAACAGA
20527924 AATTGAAAA
66 AATTGAAAA
20527933 ACAGAAATTG
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (75 bp):
ACCTCAACGTCTGACCTGAGGATCAACTCACCTCTCACAATACGAGTTGACTTTTAAAAAACAGA
AATTGAAAAT
Found at i:20527940 original size:14 final size:14
Alignment explanation
Indices: 20527917--20527946 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20527907 GATTTTTTTG
*
20527917 AAACATAAATTGAA
1 AAACAGAAATTGAA
20527931 AAACAGAAATTGAA
1 AAACAGAAATTGAA
20527945 AA
1 AA
20527947 TACCTCGGCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.10, T:0.17
Consensus pattern (14 bp):
AAACAGAAATTGAA
Found at i:20528042 original size:72 final size:72
Alignment explanation
Indices: 20527925--20528071 Score: 276
Period size: 72 Copynumber: 2.0 Consensus size: 72
20527915 TGAAACATAA
* *
20527925 ATTGAAAAACAGAAATTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATA
1 ATTGAAAAAAAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATA
20527990 TGAGTTG
66 TGAGTTG
20527997 ATTGAAAAAAAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATA
1 ATTGAAAAAAAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATA
20528062 TGAGTTG
66 TGAGTTG
20528069 ATT
1 ATT
20528072 TTTTTCGAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.25
Consensus pattern (72 bp):
ATTGAAAAAAAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATA
TGAGTTG
Found at i:20528101 original size:90 final size:91
Alignment explanation
Indices: 20527997--20528167 Score: 245
Period size: 90 Copynumber: 1.9 Consensus size: 91
20527987 ATATGAGTTG
* * * * **
20527997 ATTGAAAAAAAGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATA
1 ATTGAAAAAAAGAAATTGAAAATACCTCGACATATAACCCAAGGCTCAACTCACCTCTCGCAATA
**
20528062 TGAGTTGA-TTTTTTTCGAAACATGA
66 CAAGTTGACTTTTTTTCGAAACATGA
* *
20528087 ATTGAAAAATAGAAATTGAAAATACCTCGACATATAACCCAAGGCTCAACTCGCCTCTCGCAATA
1 ATTGAAAAAAAGAAATTGAAAATACCTCGACATATAACCCAAGGCTCAACTCACCTCTCGCAATA
20528152 CAAGTTGACTTTTTTT
66 CAAGTTGACTTTTTTT
20528168 AAAAAATAAG
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
90 63 0.90
91 7 0.10
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (91 bp):
ATTGAAAAAAAGAAATTGAAAATACCTCGACATATAACCCAAGGCTCAACTCACCTCTCGCAATA
CAAGTTGACTTTTTTTCGAAACATGA
Found at i:20528238 original size:168 final size:163
Alignment explanation
Indices: 20527801--20528352 Score: 743
Period size: 167 Copynumber: 3.3 Consensus size: 163
20527791 CGTCTGATCT
* * * *
20527801 GAGGCTTAACTCACCTCTCGCAATACGAGTTGACTTTTAAAAAACAGGAATTGAAAATACCTCAA
1 GAGGCTCAACTCACCTCTCGCAATACAAGTTGACTTTTAAAAAA-AAGAATTGAAAATACCTCAG
* * *
20527866 CGTGTGACCTGAGGATCAACTCACCTCTCACAATATGAGTTGATTTTTTTGAAACATAAATTGAA
65 CGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAACATGAATTGAA
* * * * *
20527931 AAACAGAAATTGAAAATACCTCGGCGTGTGATCT
130 AAACAGAAATTGAAAATACCTCGACATGTAACCC
** * *
20527965 GAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTGAAAAAAAGAAATTGAAAATACCTCGG
1 GAGGCTCAACTCACCTCTCGCAATACAAGTTGACTTTTAAAAAAAAG-AATTGAAAATACCTCAG
20528027 CGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTCGAAACATGAATTGA
65 CGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT-GAAACATGAATTGA
* *
20528092 AAAATAGAAATTGAAAATACCTCGACATATAACCC
129 AAAACAGAAATTGAAAATACCTCGACATGTAACCC
* *
20528127 AAGGCTCAACTCGCCTCTCGCAATACAAGTTGACTTTTTTTAAAAAATAAGAATTGAAAATACCT
1 GAGGCTCAACTCACCTCTCGCAATACAAGTTGAC---TTTTAAAAAA-AAGAATTGAAAATACCT
* *
20528192 CAGCGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGACACA-GAAAT
62 CAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAACATG-AAT
20528256 TGAAAAACAGAAATTGAAAATACCTCGACATGTAACCC
126 TGAAAAACAGAAATTGAAAATACCTCGACATGTAACCC
* * * *
20528294 GAGGCTCAACTCACCTCTCGCAATATAAGTTAATTTTTATGAAAAACAGAATTTGAAAA
1 GAGGCTCAACTCACCTCTCGCAATACAAGTTGACTTTTA--AAAAAAAGAA-TTGAAAA
20528353 ACAGAATTGA
Statistics
Matches: 343, Mismatches: 32, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
160 2 0.01
161 70 0.20
162 70 0.20
164 36 0.10
165 4 0.01
166 13 0.04
167 73 0.21
168 72 0.21
169 3 0.01
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (163 bp):
GAGGCTCAACTCACCTCTCGCAATACAAGTTGACTTTTAAAAAAAAGAATTGAAAATACCTCAGC
GTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAACATGAATTGAAA
AACAGAAATTGAAAATACCTCGACATGTAACCC
Found at i:20528267 original size:14 final size:14
Alignment explanation
Indices: 20528248--20528275 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20528238 TTTTTTTGAC
20528248 ACAGAAATTGAAAA
1 ACAGAAATTGAAAA
20528262 ACAGAAATTGAAAA
1 ACAGAAATTGAAAA
20528276 TACCTCGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.14, T:0.14
Consensus pattern (14 bp):
ACAGAAATTGAAAA
Found at i:20528271 original size:89 final size:89
Alignment explanation
Indices: 20528176--20528395 Score: 277
Period size: 89 Copynumber: 2.5 Consensus size: 89
20528166 TTAAAAAATA
* * *
20528176 AGAATTGAAAATACCTCAGCGTGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 AGAATTGAAAATACCTCAGCGTGTATCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTAATTT
* *
20528241 TTTTG-ACACAGAAATTGAAAAAC
66 TTATGAAAACAGAAATTGAAAAAC
* * *
20528264 AGAAATTGAAAATACCTC-GACATGTAACCCGAGGCTCAACTCACCTCTCGCAATATAAGTTAAT
1 AG-AATTGAAAATACCTCAG-CGTGTATCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTAAT
*
20528328 TTTTATGAAAAACAGAATTTGAAAAAC
64 TTTTATG-AAAACAGAAATTGAAAAAC
* **
20528355 AGAATTGAAAATACCTCA--GTGTCTTTTGAGGCTCAACTCAC
1 AGAATTGAAAATACCTCAGCGTGTATCCTGAGGCTCAACTCAC
20528396 TTTTCGTGTT
Statistics
Matches: 112, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
88 20 0.18
89 59 0.53
90 15 0.13
91 18 0.16
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (89 bp):
AGAATTGAAAATACCTCAGCGTGTATCCTGAGGCTCAACTCACCTCTCGCAATATAAGTTAATTT
TTATGAAAACAGAAATTGAAAAAC
Found at i:20528362 original size:13 final size:14
Alignment explanation
Indices: 20528333--20528365 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
20528323 TTAATTTTTA
20528333 TGAAAAACAGAATT
1 TGAAAAACAGAATT
20528347 TGAAAAACAGAA-T
1 TGAAAAACAGAATT
20528360 TGAAAA
1 TGAAAA
20528366 TACCTCAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.61, C:0.06, G:0.15, T:0.18
Consensus pattern (14 bp):
TGAAAAACAGAATT
Found at i:20529647 original size:19 final size:20
Alignment explanation
Indices: 20529610--20529663 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
20529600 GATTTAAGTT
*
20529610 TATTTTCATATTATCTTTAC
1 TATTTTCATATTATCTTTAA
* *
20529630 TATTTT-ATTTTATTTTTAA
1 TATTTTCATATTATCTTTAA
*
20529649 TATTATTTATATTAT
1 TATT-TTCATATTAT
20529664 TCTCGTGATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 14 0.50
20 8 0.29
21 6 0.21
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTTCATATTATCTTTAA
Found at i:20529802 original size:11 final size:13
Alignment explanation
Indices: 20529777--20529801 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20529767 GTGCATTTTT
20529777 TTTATATAATATA
1 TTTATATAATATA
20529790 TTTATATAATAT
1 TTTATATAATAT
20529802 TATTAATAAG
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTATATAATATA
Found at i:20529978 original size:21 final size:21
Alignment explanation
Indices: 20529952--20529995 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
20529942 TATATTCTTA
20529952 TATTATGTGTATTAAATGTAT
1 TATTATGTGTATTAAATGTAT
* * *
20529973 TATTATTTTTATTATATGTAT
1 TATTATGTGTATTAAATGTAT
20529994 TA
1 TA
20529996 CGTATATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (21 bp):
TATTATGTGTATTAAATGTAT
Found at i:20532907 original size:20 final size:20
Alignment explanation
Indices: 20532875--20532912 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
20532865 ATACATATAT
*
20532875 TAAAAACATATAA-AAAACA
1 TAAAAAAATATAATAAAACA
20532894 TAAAAAAATAATAATAAAA
1 TAAAAAAAT-ATAATAAAA
20532913 GGGTACCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 8 0.50
20 4 0.25
21 4 0.25
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (20 bp):
TAAAAAAATATAATAAAACA
Found at i:20533637 original size:15 final size:15
Alignment explanation
Indices: 20533619--20533647 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20533609 TATATGCATA
20533619 TATATTTATTATTAT
1 TATATTTATTATTAT
20533634 TATATTTATTATTA
1 TATATTTATTATTA
20533648 ATATTATAGT
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:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TATATTTATTATTAT
Found at i:20533796 original size:25 final size:25
Alignment explanation
Indices: 20533768--20533958 Score: 157
Period size: 25 Copynumber: 7.8 Consensus size: 25
20533758 ATATATATTG
20533768 TATATGTTTTTAT-TTATATTATGTA
1 TATAT-TTTTTATATTATATTATGTA
*
20533793 TATATTTTTAATA-T-TATTA-GTTA
1 TATATTTTTTATATTATATTATG-TA
*
20533816 TATATTTTTTATACTAT-TTCATGTA
1 TATATTTTTTATATTATATT-ATGTA
*
20533841 TATA-TTTTTATATTATCTTATGTA
1 TATATTTTTTATATTATATTATGTA
*
20533865 TATATTTTTTAATAACTATATTATGTA
1 TATATTTTTT-AT-ATTATATTATGTA
* * * *
20533892 TGTATTTTTAACACTATATTATGTA
1 TATATTTTTTATATTATATTATGTA
* * *
20533917 CATACTTTTAATA-T-TATTATGTA
1 TATATTTTTTATATTATATTATGTA
* *
20533940 TTTATTTTTAATA-TATATT
1 TATATTTTTTATATTATATT
20533959 TACATATTTA
Statistics
Matches: 140, Mismatches: 15, Indels: 23
0.79 0.08 0.13
Matches are distributed among these distances:
22 1 0.01
23 39 0.28
24 35 0.25
25 42 0.30
26 4 0.03
27 19 0.14
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.59
Consensus pattern (25 bp):
TATATTTTTTATATTATATTATGTA
Found at i:20533824 original size:24 final size:23
Alignment explanation
Indices: 20533749--20533958 Score: 167
Period size: 23 Copynumber: 8.7 Consensus size: 23
20533739 TATTATTATC
*
20533749 ATTTCTAATA-TATATATTGTATAT
1 ATTTTTAATATTAT-TA-TGTATAT
* *
20533773 GTTTTT-ATTTATATTATGTATAT
1 ATTTTTAATAT-TATTATGTATAT
20533796 ATTTTTAATATTATTA-GTTATAT
1 ATTTTTAATATTATTATG-TATAT
* *
20533819 ATTTTTTATACTATTTCATGTATAT
1 ATTTTTAATATTA-TT-ATGTATAT
20533844 ATTTTT-ATATTATCTTATGTATAT
1 ATTTTTAATATTA--TTATGTATAT
*
20533868 ATTTTTTAATAACTATATTATGTATGT
1 A-TTTTTAAT-A-T-TATTATGTATAT
* *
20533895 ATTTTTAACACTATATTATGTACAT
1 ATTTTTAATA-T-TATTATGTATAT
* *
20533920 ACTTTTAATATTATTATGTATTT
1 ATTTTTAATATTATTATGTATAT
20533943 ATTTTTAATATATATT
1 ATTTTTAATAT-TATT
20533959 TACATATTTA
Statistics
Matches: 154, Mismatches: 18, Indels: 28
0.77 0.09 0.14
Matches are distributed among these distances:
22 1 0.01
23 55 0.36
24 30 0.19
25 44 0.29
26 10 0.06
27 11 0.07
28 1 0.01
29 2 0.01
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.59
Consensus pattern (23 bp):
ATTTTTAATATTATTATGTATAT
Found at i:20533966 original size:25 final size:23
Alignment explanation
Indices: 20533922--20533969 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
20533912 ATGTACATAC
**
20533922 TTTTAATATTATTATGTATTTAT
1 TTTTAATATTATTACATATTTAT
20533945 TTTTAATATATATTTACATATTTAT
1 TTTTAATAT-TA-TTACATATTTAT
20533970 GTAGTATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 2 0.10
25 10 0.48
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
TTTTAATATTATTACATATTTAT
Found at i:20534145 original size:18 final size:18
Alignment explanation
Indices: 20534107--20534141 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
20534097 TGTATGTCGT
*
20534107 TATTATTAGTTATTTTTA
1 TATTATTAGCTATTTTTA
20534125 TATTATTA-CTATTTTTA
1 TATTATTAGCTATTTTTA
20534142 ATATATATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (18 bp):
TATTATTAGCTATTTTTA
Found at i:20534375 original size:6 final size:6
Alignment explanation
Indices: 20534364--20534389 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
20534354 TCGATATTAG
20534364 TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TT
20534390 AAAAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:20535487 original size:33 final size:33
Alignment explanation
Indices: 20535445--20535531 Score: 147
Period size: 33 Copynumber: 2.6 Consensus size: 33
20535435 GGGCCCACAC
*
20535445 GCCCGTGTGGCTCACACGGCCCAACTTGGCCTT
1 GCCCGTGTGGATCACACGGCCCAACTTGGCCTT
20535478 GCCCGTGTGGATCACACGGCCCAACTTGGCCTT
1 GCCCGTGTGGATCACACGGCCCAACTTGGCCTT
* *
20535511 GCTCGTGTGGATTACACGGCC
1 GCCCGTGTGGATCACACGGCC
20535532 TGGCCTAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.14, C:0.36, G:0.29, T:0.22
Consensus pattern (33 bp):
GCCCGTGTGGATCACACGGCCCAACTTGGCCTT
Found at i:20538488 original size:85 final size:85
Alignment explanation
Indices: 20538338--20538643 Score: 337
Period size: 85 Copynumber: 3.6 Consensus size: 85
20538328 AGATAAAAAC
* * **
20538338 ATTTGCAGTTACTGCCACTTGTTGTGAGTGCACAACATGGTT-GCAGATTAAACAAACTGTAATT
1 ATTTGCAGTTACTGCCACTTGTTGTAAGTGCACAACAT-ATTCGCAGATTAAACAAACTGCCATT
* * *
20538402 GGG-GTTGTGGACGATCCATAT
65 GGGTTTTGTGGA-GAGCCACAT
** * * *
20538423 ATTTTTAGTTACTACTACTTGTTGTAAGTGCACAACATATTCGCAGATTAAACAATCTGCCATTG
1 ATTTGCAGTTACTGCCACTTGTTGTAAGTGCACAACATATTCGCAGATTAAACAAACTGCCATTG
20538488 GGTTTTGTGGAGAGCCACAT
66 GGTTTTGTGGAGAGCCACAT
* * * * * * * *
20538508 ATTTGCGGTTATTGCCACTTGTTATGAGTGCACAACATGTTCGCAAATTAAACAAACTCCCACTG
1 ATTTGCAGTTACTGCCACTTGTTGTAAGTGCACAACATATTCGCAGATTAAACAAACTGCCATTG
20538573 GGTTTTGTGGATGAGCCACAT
66 GGTTTTGTGGA-GAGCCACAT
* * * *
20538594 ATTTGCAGTTATTGCCACTTGTTGTGAGTGTGTACAACATATTTGCAGAT
1 ATTTGCAGTTACTGCCACTTGTTGT-A-AGTGCACAACATATTCGCAGAT
20538644 CATGAAAATA
Statistics
Matches: 183, Mismatches: 33, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
84 2 0.01
85 125 0.68
86 39 0.21
88 17 0.09
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (85 bp):
ATTTGCAGTTACTGCCACTTGTTGTAAGTGCACAACATATTCGCAGATTAAACAAACTGCCATTG
GGTTTTGTGGAGAGCCACAT
Found at i:20539826 original size:43 final size:43
Alignment explanation
Indices: 20539765--20539854 Score: 180
Period size: 43 Copynumber: 2.1 Consensus size: 43
20539755 CCTTAAACTT
20539765 TAAGGACGAATATCGTCCCAATATTCATAAATACATACCAAAA
1 TAAGGACGAATATCGTCCCAATATTCATAAATACATACCAAAA
20539808 TAAGGACGAATATCGTCCCAATATTCATAAATACATACCAAAA
1 TAAGGACGAATATCGTCCCAATATTCATAAATACATACCAAAA
20539851 TAAG
1 TAAG
20539855 TATGGATGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.47, C:0.20, G:0.10, T:0.23
Consensus pattern (43 bp):
TAAGGACGAATATCGTCCCAATATTCATAAATACATACCAAAA
Found at i:20541767 original size:30 final size:30
Alignment explanation
Indices: 20541731--20541803 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
20541721 TTCTATATTT
* *
20541731 TTTTTATAGATTT-GGAATTTAGTTCTTCTA
1 TTTTTATA-ATTTAGGAATTTAGTTCCTCCA
*
20541761 TTTTTAT-TTTTAGGAATTTAGTTCCTCCA
1 TTTTTATAATTTAGGAATTTAGTTCCTCCA
*
20541790 TGTTTTATATTTTA
1 T-TTTTATAATTTA
20541804 AAATTATGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 3 0.08
29 16 0.43
30 13 0.35
31 5 0.14
ACGTcount: A:0.22, C:0.08, G:0.11, T:0.59
Consensus pattern (30 bp):
TTTTTATAATTTAGGAATTTAGTTCCTCCA
Found at i:20541776 original size:29 final size:31
Alignment explanation
Indices: 20541744--20541803 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
20541734 TTATAGATTT
* *
20541744 GGAATTTAGTTCTTCTAT-TTTTAT-TTTTA
1 GGAATTTAGTTCCTCCATGTTTTATATTTTA
20541773 GGAATTTAGTTCCTCCATGTTTTATATTTTA
1 GGAATTTAGTTCCTCCATGTTTTATATTTTA
20541804 AAATTATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 16 0.59
30 6 0.22
31 5 0.19
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.57
Consensus pattern (31 bp):
GGAATTTAGTTCCTCCATGTTTTATATTTTA
Found at i:20557445 original size:69 final size:70
Alignment explanation
Indices: 20557270--20557446 Score: 212
Period size: 71 Copynumber: 2.5 Consensus size: 70
20557260 CTTTCTAAGG
* * ** *
20557270 AAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAAGACACGCCGAGGTATTTTTAATTTAT
*
20557335 TTTTT
66 GTTTT
* ** * *
20557340 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGGGGCACGCCGAGGTATTTTTAGTTTA
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAAGACACGCCGAGGTATTTTTAATTTA
20557405 TGTTTT
65 TGTTTT
** *
20557411 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTT
20557447 TTAATTTTTG
Statistics
Matches: 91, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
69 32 0.35
71 59 0.65
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (70 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTAAGACACGCCGAGGTATTTTTAATTTAT
GTTTT
Found at i:20557577 original size:75 final size:75
Alignment explanation
Indices: 20557463--20557801 Score: 427
Period size: 75 Copynumber: 4.5 Consensus size: 75
20557453 TTTGTTTTTC
* *
20557463 AAAATCAACTCATATTGCTAGAGGTCAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTCT
20557528 GTTGTT-AAAA
66 GTT-TTAAAAA
** *
20557538 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTCT
*
20557603 GTTTT---CA
66 GTTTTAAAAA
* * ** * ** *
20557610 AAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTCT
*
20557675 GTTTTCAAAA
66 GTTTTAAAAA
* * *
20557685 AAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-ACACA--CTGAGGTAATTTCAATT
20557749 TCTGTTTTTAAAAA
63 TCTG-TTTTAAAAA
*
20557763 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
20557802 ATTACACACT
Statistics
Matches: 234, Mismatches: 22, Indels: 12
0.87 0.08 0.04
Matches are distributed among these distances:
72 66 0.28
74 3 0.01
75 101 0.43
77 20 0.09
78 43 0.18
79 1 0.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (75 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTAATTTCAATTTCT
GTTTTAAAAA
Found at i:20557716 original size:147 final size:146
Alignment explanation
Indices: 20557449--20557784 Score: 415
Period size: 147 Copynumber: 2.2 Consensus size: 146
20557439 TAAGCCTTTT
* * ** *
20557449 AATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTCAGTTGAGCCTCAGGACACACTGAGG
1 AATTTCTG-TTTTCAAAATCAACTCATATTGCGAGAAATCAGTTGAGCCTCAAGACACACTGAGG
20557514 TAATTTCAATTTCTGTTGTTAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGG-
65 TAATTTCAATTTCTGTTGTTAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC-GGT
20557578 ACACGCTGAGGTAATTTC
129 ACACGCTGAGGTAATTTC
* * **
20557596 AATTTCTGTTTTCAAAATTCAACTTATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGG
1 AATTTCTGTTTTCAAAA-TCAACTCATATTGCGAGAAATCAGTTGAGCCTCAAGACACACTGAGG
* * **
20557661 TATTTTCAATTTCTGTT-TTCAAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGT
65 TAATTTCAATTTCTGTTGTT-AAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGG-
* *
20557725 TCACATGCTGAGGTATTTTC
128 T-ACACGCTGAGGTAATTTC
*
20557745 AATTTCTGTTTTTAAAAAAAAATCAACTCATATTGCGAGA
1 AATTTCTG-TTTT----CAAAATCAACTCATATTGCGAGA
20557785 GGTGAGTTGA
Statistics
Matches: 162, Mismatches: 17, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
146 13 0.08
147 100 0.62
149 24 0.15
150 4 0.02
153 17 0.10
154 4 0.02
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (146 bp):
AATTTCTGTTTTCAAAATCAACTCATATTGCGAGAAATCAGTTGAGCCTCAAGACACACTGAGGT
AATTTCAATTTCTGTTGTTAAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGTAC
ACGCTGAGGTAATTTC
Found at i:20558316 original size:72 final size:72
Alignment explanation
Indices: 20558199--20558812 Score: 1077
Period size: 72 Copynumber: 8.5 Consensus size: 72
20558189 TTTGAAAGAA
20558199 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
20558264 TCAAAAT
66 TCAAAAT
20558271 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
20558336 TCAAAAT
66 TCAAAAT
20558343 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
20558408 TCAAAAT
66 TCAAAAT
20558415 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
20558480 TCAAAAT
66 TCAAAAT
20558487 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
20558552 TCAAAAT
66 TCAAAAT
* *
20558559 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTG-TT
20558624 TTCAAAAT
65 TTCAAAAT
* *
20558632 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGCTT
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTG-TT
20558697 TTCAAAAT
65 TTCAAAAT
* **
20558705 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTG
1 TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTT-
** *
20558770 TAAAAAAAA
65 T-TCAAAAT
*
20558779 TCAACTCATATTGC-AAAAAGTGAGTTGAGCCTCA
1 TCAACTCATATTGCGAGAAA-TGAGTTGAGCCTCA
20558813 GTTCACATGT
Statistics
Matches: 529, Mismatches: 9, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
72 350 0.66
73 147 0.28
74 32 0.06
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (72 bp):
TCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACATTGAGGTAATTTCAATTTCTGTTT
TCAAAAT
Found at i:20559551 original size:16 final size:16
Alignment explanation
Indices: 20559530--20559561 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
20559520 GCCCAATAAC
*
20559530 CTAAACTACCAGCCCA
1 CTAAACTAACAGCCCA
20559546 CTAAACTAACAGCCCA
1 CTAAACTAACAGCCCA
20559562 TTACACAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.41, G:0.06, T:0.12
Consensus pattern (16 bp):
CTAAACTAACAGCCCA
Found at i:20563986 original size:27 final size:27
Alignment explanation
Indices: 20563956--20564044 Score: 81
Period size: 27 Copynumber: 3.2 Consensus size: 27
20563946 TTGTTTATAT
20563956 ATAATCTTAATTTATGTTCATATTTTG
1 ATAATCTTAATTTATGTTCATATTTTG
* ** * *
20563983 ATAAT-TCAACAGAATATAGTTGATAATTTG
1 ATAATCT-TA-A-TTTAT-GTTCATATTTTG
*
20564013 TTAATCTTAATTTATGTTCATATTTTG
1 ATAATCTTAATTTATGTTCATATTTTG
20564040 ATAAT
1 ATAAT
20564045 TCAACAGAAT
Statistics
Matches: 45, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
26 1 0.02
27 20 0.44
28 4 0.09
29 4 0.09
30 15 0.33
31 1 0.02
ACGTcount: A:0.35, C:0.07, G:0.09, T:0.49
Consensus pattern (27 bp):
ATAATCTTAATTTATGTTCATATTTTG
Found at i:20564026 original size:57 final size:57
Alignment explanation
Indices: 20563957--20564071 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
20563947 TGTTTATATA
20563957 TAATCTTAATTTATGTTCATATTTTGATAATTCAACAGAATATAGTTGATAATTTGT
1 TAATCTTAATTTATGTTCATATTTTGATAATTCAACAGAATATAGTTGATAATTTGT
20564014 TAATCTTAATTTATGTTCATATTTTGATAATTCAACAGAATATAGTTGATAATTTGT
1 TAATCTTAATTTATGTTCATATTTTGATAATTCAACAGAATATAGTTGATAATTTGT
20564071 T
1 T
20564072 GAATTATTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.48
Consensus pattern (57 bp):
TAATCTTAATTTATGTTCATATTTTGATAATTCAACAGAATATAGTTGATAATTTGT
Found at i:20573674 original size:23 final size:24
Alignment explanation
Indices: 20573642--20573693 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
20573632 TCCATGGTAT
**
20573642 AAAATAAATAAAGTGAT-AAAAATA
1 AAAATAAAT-AAGAAATGAAAAATA
20573666 AAAAT-AATAAGAAATGAAAAATA
1 AAAATAAATAAGAAATGAAAAATA
20573689 AAAAT
1 AAAAT
20573694 GCTATATGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.20
23 15 0.60
24 5 0.20
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (24 bp):
AAAATAAATAAGAAATGAAAAATA
Found at i:20573872 original size:19 final size:18
Alignment explanation
Indices: 20573844--20573882 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
20573834 TTATTTTTTA
*
20573844 AAATATATAAAAAATAGAT
1 AAATAAATAAAAAATA-AT
*
20573863 AAATAAATAAATAATAAT
1 AAATAAATAAAAAATAAT
20573881 AA
1 AA
20573883 TTGTAATGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
AAATAAATAAAAAATAAT
Found at i:20574095 original size:3 final size:3
Alignment explanation
Indices: 20574087--20574154 Score: 55
Period size: 3 Copynumber: 22.0 Consensus size: 3
20574077 ATGAATGGAC
* * * * * *
20574087 AAT AAT AAT GAT GAT AAT AAT ACT AAT AAT AAC AAC AAT AAT AAA ACAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
*
20574136 AGT AAT AAT AAT AAAT AAT
1 AAT AAT AAT AAT -AAT AAT
20574155 CTAATTTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
3 48 0.91
4 5 0.09
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:20574250 original size:5 final size:5
Alignment explanation
Indices: 20574233--20574269 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
20574223 AAACGTAAAG
*
20574233 AATAA AATGA AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AA
20574270 ATGCACAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:20578812 original size:21 final size:21
Alignment explanation
Indices: 20578771--20578814 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
20578761 ATCAAAGAAA
*
20578771 AAAACAAATAAAATAACTAAT
1 AAAACAAATAAAACAACTAAT
*
20578792 AAAACGAATAACAACAA-TAAT
1 AAAACAAATAA-AACAACTAAT
20578813 AA
1 AA
20578815 TAATAACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.70, C:0.11, G:0.02, T:0.16
Consensus pattern (21 bp):
AAAACAAATAAAACAACTAAT
Found at i:20578905 original size:19 final size:19
Alignment explanation
Indices: 20578881--20578918 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
20578871 TTTTAAATAT
20578881 GAAAAGAATAAAAA-GAAAA
1 GAAAAGAA-AAAAAGGAAAA
20578900 GAAAAGAAAAAAAGGAAAA
1 GAAAAGAAAAAAAGGAAAA
20578919 TATATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (19 bp):
GAAAAGAAAAAAAGGAAAA
Found at i:20580442 original size:68 final size:68
Alignment explanation
Indices: 20580271--20580453 Score: 222
Period size: 68 Copynumber: 2.7 Consensus size: 68
20580261 GAGTATTATC
* * * *
20580271 ATTTAATATCGCAGCCTTCAAACAGCTCGTTGATTTAACATCACAGCTGATATCACTAGGGCTCG
1 ATTTAAGATCGCAGCCTTCAAACAGCTCGCTGATTTAACATCACAGCTGATATCACTAAGACTCG
20580336 TTG
66 TTG
* * * * * * * *
20580339 ATTTAAGATCACAGCCTCCAAACAACTCTCAGATTTAATATCGCAGTTGATATCACTAAGACTCG
1 ATTTAAGATCGCAGCCTTCAAACAGCTCGCTGATTTAACATCACAGCTGATATCACTAAGACTCG
20580404 TTG
66 TTG
* * * *
20580407 ATTTAAGATCGTAGCCTTCAAATAGCTCGCTGATTTAAGACCACAGC
1 ATTTAAGATCGCAGCCTTCAAACAGCTCGCTGATTTAACATCACAGC
20580454 ATCTAAACAG
Statistics
Matches: 92, Mismatches: 23, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
68 92 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (68 bp):
ATTTAAGATCGCAGCCTTCAAACAGCTCGCTGATTTAACATCACAGCTGATATCACTAAGACTCG
TTG
Found at i:20580444 original size:100 final size:100
Alignment explanation
Indices: 20580331--20580543 Score: 228
Period size: 100 Copynumber: 2.1 Consensus size: 100
20580321 TATCACTAGG
* * * * * * *
20580331 GCTCGTTGATTTAAGATCACAGCCTCCAAACAACTCTCAGATTTAATATCGCAGTTGATATCACT
1 GCTCGCTGATTTAAGACCACAGCATCCAAACAACTCGCAGATTTAACATCGCAGCTAATATCACT
* *
20580396 AAGACTCGTTGATTTAAGATCGTAGCCTTCAAATA
66 AAGACTCGTTGATTTAAGATCGTAACCTCCAAATA
* ** * **
20580431 GCTCGCTGATTTAAGACCACAGCATCTAAACAGGTCGCTGATTTAACATCGCAGCTAATATCGTT
1 GCTCGCTGATTTAAGACCACAGCATCCAAACAACTCGCAGATTTAACATCGCAGCTAATATCACT
* * * * *
20580496 AGGGCTGGTTGATTTAATATTGTAACCTCCAAATA
66 AAGACTCGTTGATTTAAGATCGTAACCTCCAAATA
* *
20580531 GCTCTCTAATTTA
1 GCTCGCTGATTTA
20580544 TTATTGCAAC
Statistics
Matches: 91, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
100 91 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (100 bp):
GCTCGCTGATTTAAGACCACAGCATCCAAACAACTCGCAGATTTAACATCGCAGCTAATATCACT
AAGACTCGTTGATTTAAGATCGTAACCTCCAAATA
Found at i:20580581 original size:168 final size:168
Alignment explanation
Indices: 20580290--20580614 Score: 400
Period size: 168 Copynumber: 1.9 Consensus size: 168
20580280 CGCAGCCTTC
* * *
20580290 AAACAGCTCGTTGATTTAACATCACAGCTGATATCACTAGGGCTCGTTGATTTAAGATCACAGCC
1 AAACAGCTCGCTGATTTAACATCACAGCTAATATCACTAGGGCTCGTTGATTTAAGATCACAACC
** * * *
20580355 TCCAAACAACTCTCAGATTTAATATCGCAGTTGATATCACTAAGACTCGTTGATTTAAGATCGTA
66 TCCAAACAACTCTCAGATTTAATATCGCAACTGATATCACTAAGACTCGCTAATTTAAGATCGCA
20580420 GCCTTCAAATAGCTCGCTGATTTAAGACCACAGCATCT
131 GCCTTCAAATAGCTCGCTGATTTAAGACCACAGCATCT
* * ** * * ***
20580458 AAACAGGTCGCTGATTTAACATCGCAGCTAATATCGTTAGGGCTGGTTGATTTAATATTGTAACC
1 AAACAGCTCGCTGATTTAACATCACAGCTAATATCACTAGGGCTCGTTGATTTAAGATCACAACC
* * * * * * * *
20580523 TCCAAATAGCTCTCTA-ATTTATTATTGCAACTGATATCATTAAGGCTCGCTAATTTAAGGTTGC
66 TCCAAACAACTCTC-AGATTTAATATCGCAACTGATATCACTAAGACTCGCTAATTTAAGATCGC
*
20580587 AGCCTTCAAATAGCTCGTTGATTTAAGA
130 AGCCTTCAAATAGCTCGCTGATTTAAGA
20580615 TCGCGACCTT
Statistics
Matches: 130, Mismatches: 26, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
168 129 0.99
169 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (168 bp):
AAACAGCTCGCTGATTTAACATCACAGCTAATATCACTAGGGCTCGTTGATTTAAGATCACAACC
TCCAAACAACTCTCAGATTTAATATCGCAACTGATATCACTAAGACTCGCTAATTTAAGATCGCA
GCCTTCAAATAGCTCGCTGATTTAAGACCACAGCATCT
Found at i:20586054 original size:49 final size:48
Alignment explanation
Indices: 20585995--20586117 Score: 140
Period size: 49 Copynumber: 2.5 Consensus size: 48
20585985 TAACGTACCT
*
20585995 TACTAGTGGCCCATCATTCATGCCAATCTAGTTAGCAACTAACATGCCC
1 TACTAGTGGCCCATCATTC-TGCCAACCTAGTTAGCAACTAACATGCCC
* * *
20586044 TACTAGTGGCCCATCTTATTCT-CCCACCTGGTTAGCAACTAGCATGCCC
1 TACTAGTGGCCCATC--ATTCTGCCAACCTAGTTAGCAACTAACATGCCC
* * *
20586093 TACCAATGGTCCATCATATCTGCCA
1 TACTAGTGGCCCATCAT-TCTGCCA
20586118 TTTTGTGTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
47 2 0.03
48 3 0.05
49 52 0.84
50 1 0.02
51 4 0.06
ACGTcount: A:0.25, C:0.33, G:0.15, T:0.28
Consensus pattern (48 bp):
TACTAGTGGCCCATCATTCTGCCAACCTAGTTAGCAACTAACATGCCC
Found at i:20592276 original size:28 final size:28
Alignment explanation
Indices: 20592245--20592309 Score: 87
Period size: 28 Copynumber: 2.3 Consensus size: 28
20592235 TAGTAAAAAC
* *
20592245 ACAAATATATTAATATATCAAAATTTAT
1 ACAAATATATAAATATACCAAAATTTAT
20592273 ACAAATCAT-TAAATATACCAAAATTTAT
1 ACAAAT-ATATAAATATACCAAAATTTAT
*
20592301 ATAAATATA
1 ACAAATATA
20592310 AAGTATCGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 2 0.06
28 28 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.35
Consensus pattern (28 bp):
ACAAATATATAAATATACCAAAATTTAT
Found at i:20614533 original size:13 final size:13
Alignment explanation
Indices: 20614515--20614558 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
20614505 ACATTAACGT
*
20614515 TTAATTAAAATAA
1 TTAATTAAATTAA
*
20614528 TTAATTATATTAA
1 TTAATTAAATTAA
* *
20614541 TTATTTGAATTAA
1 TTAATTAAATTAA
20614554 TTAAT
1 TTAAT
20614559 AATTTTATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (13 bp):
TTAATTAAATTAA
Found at i:20614558 original size:17 final size:18
Alignment explanation
Indices: 20614530--20614563 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
20614520 TAAAATAATT
*
20614530 AATTATATTAATTATTTG
1 AATTATATTAATAATTTG
20614548 AATTA-ATTAATAATTT
1 AATTATATTAATAATTT
20614564 TATAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
AATTATATTAATAATTTG
Found at i:20614636 original size:22 final size:22
Alignment explanation
Indices: 20614590--20614637 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
20614580 CAAATTATAC
*
20614590 TAAGTATGAAAAGAAATAAATT
1 TAAGTATGAAAAGAAATAAAAT
20614612 TAAGTAT-AACAA-AAATCAAAAT
1 TAAGTATGAA-AAGAAAT-AAAAT
20614634 TAAG
1 TAAG
20614638 GTAAAAAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.60, C:0.04, G:0.10, T:0.25
Consensus pattern (22 bp):
TAAGTATGAAAAGAAATAAAAT
Found at i:20619099 original size:43 final size:43
Alignment explanation
Indices: 20619051--20619198 Score: 140
Period size: 43 Copynumber: 3.4 Consensus size: 43
20619041 TACCGAGATG
* * *
20619051 TGATTACATGTAAGACCATGTCAGGGACATCGGTATTGTAT-TT
1 TGATTACATGTAAGACCATGTCA-GGACATCGGCATCGTATATA
** * *
20619094 TGATTATGTGTAAGACCATGTCTCGGACATTGGCATCGT-TATA
1 TGATTACATGTAAGACCATGTC-AGGACATCGGCATCGTATATA
*** *
20619137 TGATTTTGTGTAAGACCATGTCTAGGACATCGGCATCG-ATATG
1 TGATTACATGTAAGACCATGTC-AGGACATCGGCATCGTATATA
*
20619180 TGATAACATGTAAGACCAT
1 TGATTACATGTAAGACCAT
20619199 ATCTGGGATA
Statistics
Matches: 87, Mismatches: 15, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
42 1 0.01
43 86 0.99
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (43 bp):
TGATTACATGTAAGACCATGTCAGGACATCGGCATCGTATATA
Found at i:20622844 original size:40 final size:39
Alignment explanation
Indices: 20622699--20622879 Score: 175
Period size: 39 Copynumber: 4.6 Consensus size: 39
20622689 ACTAGCTCGA
* ** * * ***
20622699 AGCCTGCGGGATTTTTGCCCGGACATATTTCCAGCGCGT
1 AGCCTGCGGGCTTTAAGCCCGGATATAATTCCAGCATAT
* * * * *
20622738 AGCCTGCGGACCTTAAGTCCGGTTATAATTCCAGCACAT
1 AGCCTGCGGGCTTTAAGCCCGGATATAATTCCAGCATAT
* * * * *
20622777 AGCCTGCGGACCTTAAGTCCGGGTATAATTCCAGTATAT
1 AGCCTGCGGGCTTTAAGCCCGGATATAATTCCAGCATAT
*
20622816 AGCCAGCGGGTCTTTAAGCCCGGATATAATTCCAGCATAT
1 AGCCTGCGGG-CTTTAAGCCCGGATATAATTCCAGCATAT
20622856 AGCCTGCGGG-TTTAAGCCCGGATA
1 AGCCTGCGGGCTTTAAGCCCGGATA
20622880 CACATAAAAT
Statistics
Matches: 120, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
38 14 0.12
39 72 0.60
40 34 0.28
ACGTcount: A:0.23, C:0.26, G:0.25, T:0.26
Consensus pattern (39 bp):
AGCCTGCGGGCTTTAAGCCCGGATATAATTCCAGCATAT
Found at i:20630720 original size:40 final size:39
Alignment explanation
Indices: 20630636--20630764 Score: 168
Period size: 40 Copynumber: 3.3 Consensus size: 39
20630626 TTCCAGCGCG
* * *
20630636 TAGCCTGCGAACCTTAAGTCCGGTTATAATTCCAGCACA
1 TAGCCTGCGGACCTTAAGTCCGGATATAATTCCAGCATA
* *
20630675 TAGCCTGCGGACCTTAAGTCCGGGTATAATTTCCAGTATA
1 TAGCCTGCGGACCTTAAGTCCGGATATAA-TTCCAGCATA
* * *
20630715 TAGCCTGCGGGTCTTTAAGCCCGGATATAATTCCAGCATA
1 TAGCCTGC-GGACCTTAAGTCCGGATATAATTCCAGCATA
20630755 TAGCCTGCGG
1 TAGCCTGCGG
20630765 GTCTTTAAGC
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
39 29 0.37
40 33 0.42
41 17 0.22
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (39 bp):
TAGCCTGCGGACCTTAAGTCCGGATATAATTCCAGCATA
Found at i:20630765 original size:40 final size:40
Alignment explanation
Indices: 20630546--20630781 Score: 214
Period size: 39 Copynumber: 6.0 Consensus size: 40
20630536 ACTTGAAACC
* *
20630546 AATTACCAGCACA-AGCCTGCGGGAATTTAAACCCGGA-AT
1 AATT-CCAGCACATAGCCTGCGGGACTTTAAGCCCGGATAT
* * * *
20630585 AATACCAGCTCGA-AGCCTGCGGGACTTT-TGCCCGGACAT
1 AATTCCAGCAC-ATAGCCTGCGGGACTTTAAGCCCGGATAT
* * * * * * *
20630624 ATTTCCAGCGCGTAGCCTGC-GAACCTTAAGTCCGGTTAT
1 AATTCCAGCACATAGCCTGCGGGACTTTAAGCCCGGATAT
* * *
20630663 AATTCCAGCACATAGCCTGC-GGACCTTAAGTCCGGGTAT
1 AATTCCAGCACATAGCCTGCGGGACTTTAAGCCCGGATAT
* * *
20630702 AATTTCCAGTATATAGCCTGCGGGTCTTTAAGCCCGGATAT
1 AA-TTCCAGCACATAGCCTGCGGGACTTTAAGCCCGGATAT
* *
20630743 AATTCCAGCATATAGCCTGCGGGTCTTTAAGCCCGGATA
1 AATTCCAGCACATAGCCTGCGGGACTTTAAGCCCGGATA
20630782 CACATCAAAT
Statistics
Matches: 164, Mismatches: 27, Indels: 11
0.81 0.13 0.05
Matches are distributed among these distances:
38 17 0.10
39 78 0.48
40 52 0.32
41 17 0.10
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
AATTCCAGCACATAGCCTGCGGGACTTTAAGCCCGGATAT
Found at i:20633474 original size:27 final size:27
Alignment explanation
Indices: 20633444--20633534 Score: 130
Period size: 27 Copynumber: 3.4 Consensus size: 27
20633434 TAGTCCAACA
*
20633444 AGATAAGAAACATGAGATAGTCCGTTG
1 AGATAAGAAACATGAGATAGTCCGTCG
* * *
20633471 AGATAGGAAATACGAGATAGTCCGTCG
1 AGATAAGAAACATGAGATAGTCCGTCG
20633498 AGATAAGAAACATGAGATAGTCCGTC-
1 AGATAAGAAACATGAGATAGTCCGTCG
20633524 AGGATAAGAAA
1 A-GATAAGAAA
20633535 TACATGATAG
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
26 1 0.02
27 55 0.98
ACGTcount: A:0.43, C:0.12, G:0.26, T:0.19
Consensus pattern (27 bp):
AGATAAGAAACATGAGATAGTCCGTCG
Found at i:20633535 original size:54 final size:54
Alignment explanation
Indices: 20633444--20633547 Score: 158
Period size: 54 Copynumber: 1.9 Consensus size: 54
20633434 TAGTCCAACA
* *
20633444 AGATAAGAAACATGAGATAGTCCGTTGAGATAGGAAATACGA-GATAGTCCGTCG
1 AGATAAGAAACATGAGATAGTCCGTAGAGATAAGAAATAC-ATGATAGTCCGTCG
20633498 AGATAAGAAACATGAGATAGTCCGTCAG-GATAAGAAATACATGATAGTCC
1 AGATAAGAAACATGAGATAGTCCGT-AGAGATAAGAAATACATGATAGTCC
20633548 ATCAGAATAG
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
53 1 0.02
54 44 0.96
55 1 0.02
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.20
Consensus pattern (54 bp):
AGATAAGAAACATGAGATAGTCCGTAGAGATAAGAAATACATGATAGTCCGTCG
Found at i:20633570 original size:27 final size:27
Alignment explanation
Indices: 20633446--20633570 Score: 112
Period size: 27 Copynumber: 4.6 Consensus size: 27
20633436 GTCCAACAAG
* * *
20633446 ATAAGAAACATGAGATAGTCCGT-TGA
1 ATAAGAAATACGAGATAGTCCGTCAGA
*
20633472 GATAGGAAATACGAGATAGTCCGTC-GA
1 -ATAAGAAATACGAGATAGTCCGTCAGA
* * *
20633499 GATAAGAAACATGAGATAGTCCGTCAGG
1 -ATAAGAAATACGAGATAGTCCGTCAGA
*
20633527 ATAAGAAATAC-ATGATAGTCCATCAGA
1 ATAAGAAATACGA-GATAGTCCGTCAGA
* *
20633554 ATAGGAAATACGGGATA
1 ATAAGAAATACGAGATA
20633571 ATACGTTGGG
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
26 1 0.01
27 79 0.98
28 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.25, T:0.20
Consensus pattern (27 bp):
ATAAGAAATACGAGATAGTCCGTCAGA
Found at i:20633610 original size:27 final size:27
Alignment explanation
Indices: 20633580--20633681 Score: 80
Period size: 27 Copynumber: 3.8 Consensus size: 27
20633570 AATACGTTGG
*
20633580 GACAAAAAACATGGGATAGTCCATCAA
1 GACAAAAAACATGGGATAGTCCATCGA
** * * *
20633607 GACAAGCAATATGGGATAAAT-CGTCGA
1 GACAAAAAACATGGGAT-AGTCCATCGA
* * * *
20633634 GACAGAAAACACGAGATAGTCCACCGA
1 GACAAAAAACATGGGATAGTCCATCGA
* *
20633661 GATAGAAAACATGGGATAGTC
1 GACAAAAAACATGGGATAGTC
20633682 TGTCAGGATA
Statistics
Matches: 55, Mismatches: 18, Indels: 4
0.71 0.23 0.05
Matches are distributed among these distances:
26 2 0.04
27 51 0.93
28 2 0.04
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (27 bp):
GACAAAAAACATGGGATAGTCCATCGA
Found at i:20640269 original size:27 final size:27
Alignment explanation
Indices: 20640239--20640379 Score: 173
Period size: 27 Copynumber: 5.2 Consensus size: 27
20640229 ATGACGAAGT
*
20640239 CACCAGATATAGATATTGTGGCAGAGC
1 CACCAGATACAGATATTGTGGCAGAGC
*
20640266 CACCAGA-ATAGATATATGTGGCAGAGC
1 CACCAGATACAGATAT-TGTGGCAGAGC
*
20640293 CACCAGAT-CAGATAATTGTGGCATAGC
1 CACCAGATACAGAT-ATTGTGGCAGAGC
*
20640320 CACCA-AGACAGATATATGTGGCAGAGC
1 CACCAGATACAGATAT-TGTGGCAGAGC
*
20640347 CACCAGAT-CAGATAATTGTGGCATAGC
1 CACCAGATACAGAT-ATTGTGGCAGAGC
20640374 CACCAG
1 CACCAG
20640380 GACGCTTCCT
Statistics
Matches: 101, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
26 11 0.11
27 85 0.84
28 5 0.05
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (27 bp):
CACCAGATACAGATATTGTGGCAGAGC
Found at i:20640311 original size:54 final size:55
Alignment explanation
Indices: 20640239--20640379 Score: 225
Period size: 54 Copynumber: 2.6 Consensus size: 55
20640229 ATGACGAAGT
* * *
20640239 CACCAGATATAGAT-ATTGTGGCAGAGCCACCAGA-ATAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAGACAGATATATGTGGCAGAGC
20640293 CACCAGATCAGATAATTGTGGCATAGCCACCA-AGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAGACAGATATATGTGGCAGAGC
20640347 CACCAGATCAGATAATTGTGGCATAGCCACCAG
1 CACCAGATCAGATAATTGTGGCATAGCCACCAG
20640380 GACGCTTCCT
Statistics
Matches: 81, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
53 5 0.06
54 76 0.94
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (55 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAGACAGATATATGTGGCAGAGC
Found at i:20642008 original size:26 final size:26
Alignment explanation
Indices: 20641978--20642059 Score: 128
Period size: 26 Copynumber: 3.2 Consensus size: 26
20641968 TGAAATGCCC
20641978 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
20642004 ATCATGGAATATTTACATAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
20642030 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
20642056 ATCA
1 ATCA
20642060 ATTTGTACCA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:20645718 original size:12 final size:12
Alignment explanation
Indices: 20645701--20645730 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
20645691 ACATGTCTCA
20645701 CACACGGCCTAC
1 CACACGGCCTAC
*
20645713 CACACGGGCTAC
1 CACACGGCCTAC
20645725 CACACG
1 CACACG
20645731 CCCGTGTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.47, G:0.20, T:0.07
Consensus pattern (12 bp):
CACACGGCCTAC
Found at i:20655961 original size:29 final size:29
Alignment explanation
Indices: 20655928--20655987 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
20655918 CCCCTACCAA
20655928 GAAAGATTCGATTTAGGTTGTCATTGATT
1 GAAAGATTCGATTTAGGTTGTCATTGATT
* *
20655957 GAAAGATTTGATTTGGGTTGTCATTGATT
1 GAAAGATTCGATTTAGGTTGTCATTGATT
20655986 GA
1 GA
20655988 TTGACCAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.27, C:0.05, G:0.27, T:0.42
Consensus pattern (29 bp):
GAAAGATTCGATTTAGGTTGTCATTGATT
Found at i:20659291 original size:27 final size:27
Alignment explanation
Indices: 20659253--20659310 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
20659243 ATTTATTTTA
20659253 AAGCCTATGAACTTACTAAGCTTTCAT
1 AAGCCTATGAACTTACTAAGCTTTCAT
20659280 AAGCCTATGAACTTACTAAGCTTTCAT
1 AAGCCTATGAACTTACTAAGCTTTCAT
20659307 AAGC
1 AAGC
20659311 TTACTTTTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.31
Consensus pattern (27 bp):
AAGCCTATGAACTTACTAAGCTTTCAT
Found at i:20661648 original size:35 final size:37
Alignment explanation
Indices: 20661567--20661659 Score: 118
Period size: 40 Copynumber: 2.5 Consensus size: 37
20661557 ATGGGAAATG
**
20661567 CCATACCTACGTTTCTTAACTCAGTATGGATTTGATAATA
1 CCATACCTACGTTTCACAACTCAGTATGGA-TTG--AATA
*
20661607 CCATACCTACGTTTCACAACTCATTATGGA-TG-ATA
1 CCATACCTACGTTTCACAACTCAGTATGGATTGAATA
20661642 CCATACCTACGTTTCACA
1 CCATACCTACGTTTCACA
20661660 CTTTGCCATG
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
35 21 0.42
38 2 0.04
40 27 0.54
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (37 bp):
CCATACCTACGTTTCACAACTCAGTATGGATTGAATA
Found at i:20666856 original size:6 final size:6
Alignment explanation
Indices: 20666845--20666879 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
20666835 GTCAATATCC
* *
20666845 ATCATA ATCATA ACCATA ATCATA ATCATT ATCAT
1 ATCATA ATCATA ATCATA ATCATA ATCATA ATCAT
20666880 CGTAATCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (6 bp):
ATCATA
Found at i:20671649 original size:2 final size:2
Alignment explanation
Indices: 20671642--20671671 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
20671632 CCAACAACTT
*
20671642 GA GA GA GA GA GA GA GA GA GA GA GA CA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
20671672 AGGGTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:20674342 original size:164 final size:164
Alignment explanation
Indices: 20674071--20674394 Score: 630
Period size: 164 Copynumber: 2.0 Consensus size: 164
20674061 AAAACTAAGG
*
20674071 AATATACGTAAGTTCCTATCTGAGACAATAAGTTATGTGTGAAATCTTATTTTTGCAGGTGCCCG
1 AATATACGTAAGTTCCTATCTGAGACAATAAGTTATGTGTGAAATCTTATTTTTGAAGGTGCCCG
20674136 TGCATGTAATCAGGCAACAAACCATGTTCAAGTTCAGGCAACAATATTTCCATATAACCACATTA
66 TGCATGTAATCAGGCAACAAACCATGTTCAAGTTCAGGCAACAATATTTCCATATAACCACATTA
20674201 CAGATTTAAGAAAGAAGAAATTCCTCACCGCAAC
131 CAGATTTAAGAAAGAAGAAATTCCTCACCGCAAC
20674235 AATATACGTAAGTTCCTATCTGAGACAATAAGTTATGTGTGAAATCTTATTTTTGAAGGTGCCCG
1 AATATACGTAAGTTCCTATCTGAGACAATAAGTTATGTGTGAAATCTTATTTTTGAAGGTGCCCG
*
20674300 TGCATGTAATCAGGCAACAAACCATGTTCAAGTTCAGGCAACAATATTTCCATGTAACCACATTA
66 TGCATGTAATCAGGCAACAAACCATGTTCAAGTTCAGGCAACAATATTTCCATATAACCACATTA
20674365 CAGATTTAAGAAAGAAGAAATTCCTCACCG
131 CAGATTTAAGAAAGAAGAAATTCCTCACCG
20674395 ACATGCAAGA
Statistics
Matches: 158, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
164 158 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (164 bp):
AATATACGTAAGTTCCTATCTGAGACAATAAGTTATGTGTGAAATCTTATTTTTGAAGGTGCCCG
TGCATGTAATCAGGCAACAAACCATGTTCAAGTTCAGGCAACAATATTTCCATATAACCACATTA
CAGATTTAAGAAAGAAGAAATTCCTCACCGCAAC
Done.