Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 45 of 378
Found at i:11199192 original size:22 final size:20
Alignment explanation
Indices: 11199164--11199223 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 20
11199154 GTGTGTGTAG
11199164 GAAAAAACTTAAATTTTTACAT
1 GAAAAAACTT--ATTTTTACAT
*
11199186 GAAAAAACTTGTTTTTACAT
1 GAAAAAACTTATTTTTACAT
*
11199206 GGAAAATAATTTATTTTT
1 -GAAAA-AACTTATTTTT
11199224 TAATTTCCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 9 0.27
21 5 0.15
22 19 0.58
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (20 bp):
GAAAAAACTTATTTTTACAT
Found at i:11199484 original size:22 final size:22
Alignment explanation
Indices: 11199404--11199485 Score: 59
Period size: 22 Copynumber: 4.0 Consensus size: 22
11199394 AAAAGAAAAA
* *
11199404 ACTTGAGGTTTTACAAGGAATT
1 ACTTGAGTTTTTACAATGAATT
*
11199426 ACATGAGTTTTTAC-ATGAA--
1 ACTTGAGTTTTTACAATGAATT
* * **
11199445 AATT-A--TTTTCCAGCGAATT
1 ACTTGAGTTTTTACAATGAATT
11199464 ACTTGAGTTTTTACAATGAATT
1 ACTTGAGTTTTTACAATGAATT
11199486 GAGTTGAAAG
Statistics
Matches: 42, Mismatches: 12, Indels: 12
0.64 0.18 0.18
Matches are distributed among these distances:
16 5 0.12
17 3 0.07
18 1 0.02
19 5 0.12
20 1 0.02
21 4 0.10
22 23 0.55
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (22 bp):
ACTTGAGTTTTTACAATGAATT
Found at i:11202087 original size:12 final size:12
Alignment explanation
Indices: 11202070--11202095 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11202060 TACTTATTAT
11202070 TGATAATCAGTA
1 TGATAATCAGTA
11202082 TGATAATCAGTA
1 TGATAATCAGTA
11202094 TG
1 TG
11202096 TCATTAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (12 bp):
TGATAATCAGTA
Found at i:11206646 original size:17 final size:17
Alignment explanation
Indices: 11206624--11206682 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 17
11206614 AAAATAAAAT
11206624 ATTATTTTTATTACTTA
1 ATTATTTTTATTACTTA
*
11206641 ATTATTTTTAAGTACTATA
1 ATTATTTTT-ATTACT-TA
11206660 TATTATTATTTATCT-CTTA
1 -ATTATT-TTTAT-TACTTA
11206679 ATTA
1 ATTA
11206683 ATTTAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 9 0.26
18 9 0.26
19 4 0.11
20 9 0.26
21 4 0.11
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (17 bp):
ATTATTTTTATTACTTA
Found at i:11207634 original size:15 final size:16
Alignment explanation
Indices: 11207594--11207635 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
11207584 CTCCCCTCTC
**
11207594 TTTAAAATTTTTAAAA
1 TTTAAAATTACTAAAA
*
11207610 TTTTAAATTACTAAAA
1 TTTAAAATTACTAAAA
11207626 -TTAAAATTAC
1 TTTAAAATTAC
11207636 ACTTCGATCC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTAAAATTACTAAAA
Found at i:11213681 original size:7 final size:7
Alignment explanation
Indices: 11213671--11213707 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
11213661 TTCTCTTTTC
11213671 TTTTCTT
1 TTTTCTT
11213678 TTTTCTT
1 TTTTCTT
11213685 TTTTCTT
1 TTTTCTT
11213692 TTTTCTT
1 TTTTCTT
*
11213699 TTTTATT
1 TTTTCTT
11213706 TT
1 TT
11213708 CGTCTCTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTCTT
Found at i:11213717 original size:26 final size:26
Alignment explanation
Indices: 11213666--11213719 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
11213656 TTTCCTTCTC
* * *
11213666 TTTTCTTTTCTTTTTTCTTTTTTCTT
1 TTTTCTTTTCTTTTTTCGTCTCTCTT
11213692 TTTTCTTTT-TTATTTTCGTCTCTCTT
1 TTTTCTTTTCTT-TTTTCGTCTCTCTT
11213718 TT
1 TT
11213720 CCCAATCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (26 bp):
TTTTCTTTTCTTTTTTCGTCTCTCTT
Found at i:11220513 original size:18 final size:18
Alignment explanation
Indices: 11220475--11220526 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
11220465 TGGTTCAAGC
* *
11220475 TTTCAATCTCATATCTCAA
1 TTTCAAT-TCACATTTCAA
11220494 TTTCAATTCACATTTCAA
1 TTTCAATTCACATTTCAA
*
11220512 TTCTTAATTC-CATTT
1 TT-TCAATTCACATTT
11220527 TTTTTTTCAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 16 0.55
19 13 0.45
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.48
Consensus pattern (18 bp):
TTTCAATTCACATTTCAA
Found at i:11221434 original size:5 final size:5
Alignment explanation
Indices: 11221421--11221456 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
11221411 TCATAATTAC
*
11221421 ATTCC ATTCA ATTCA ATTCA ATTCA ATTCAA ATTCA
1 ATTCA ATTCA ATTCA ATTCA ATTCA ATTC-A ATTCA
11221457 CTTTTCCACT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (5 bp):
ATTCA
Found at i:11226810 original size:8 final size:8
Alignment explanation
Indices: 11226797--11226824 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
11226787 AATATATATG
11226797 AAAAAGTA
1 AAAAAGTA
11226805 AAAAAGTA
1 AAAAAGTA
11226813 AAAAAGTA
1 AAAAAGTA
11226821 AAAA
1 AAAA
11226825 TAAATATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAAAGTA
Found at i:11227228 original size:11 final size:11
Alignment explanation
Indices: 11227214--11227254 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
11227204 TATTTTCTCC
11227214 CTATTTTGCTA
1 CTATTTTGCTA
*
11227225 CTATTTTACTA
1 CTATTTTGCTA
* *
11227236 TTATGTTGCTA
1 CTATTTTGCTA
11227247 CTATTTTG
1 CTATTTTG
11227255 TTGTTATTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:11227497 original size:12 final size:12
Alignment explanation
Indices: 11227476--11227509 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
11227466 TATATATTTT
*
11227476 AAAATTATATAA
1 AAAATAATATAA
11227488 AAAATAATATAA
1 AAAATAATATAA
*
11227500 AAATTAATAT
1 AAAATAATAT
11227510 GAGCGGGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:11235709 original size:32 final size:32
Alignment explanation
Indices: 11235668--11235729 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
11235658 ATTAGAGTGG
11235668 CTAAATTGAGAAAAAAATTAGAGTAACAAAGA
1 CTAAATTGAGAAAAAAATTAGAGTAACAAAGA
11235700 CTAAATTGAGAAAAAAATTAGAGTAACAAA
1 CTAAATTGAGAAAAAAATTAGAGTAACAAA
11235730 AATAGGACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.60, C:0.06, G:0.15, T:0.19
Consensus pattern (32 bp):
CTAAATTGAGAAAAAAATTAGAGTAACAAAGA
Found at i:11240130 original size:7 final size:7
Alignment explanation
Indices: 11240118--11240235 Score: 87
Period size: 7 Copynumber: 16.9 Consensus size: 7
11240108 AGGGTGTAAG
11240118 GGTTTAA
1 GGTTTAA
11240125 GGTTTAA
1 GGTTTAA
*
11240132 GGTTTCA
1 GGTTTAA
*
11240139 GGTTTTA
1 GGTTTAA
*
11240146 GGTTTAG
1 GGTTTAA
*
11240153 GGTTTAG
1 GGTTTAA
11240160 GGTTTAA
1 GGTTTAA
**
11240167 AATTTAA
1 GGTTTAA
*
11240174 GGTTTGA
1 GGTTTAA
* *
11240181 GTTTTGA
1 GGTTTAA
* *
11240188 TGTTTGA
1 GGTTTAA
11240195 GGTTTAA
1 GGTTTAA
11240202 GGTTT-A
1 GGTTTAA
*
11240208 GGCTTCAA
1 GG-TTTAA
11240216 GGTTT-A
1 GGTTTAA
*
11240222 GCCTTTAA
1 G-GTTTAA
11240230 GGTTTA
1 GGTTTA
11240236 GGGTATAAGA
Statistics
Matches: 88, Mismatches: 19, Indels: 8
0.77 0.17 0.07
Matches are distributed among these distances:
6 5 0.06
7 78 0.89
8 5 0.06
ACGTcount: A:0.22, C:0.04, G:0.29, T:0.45
Consensus pattern (7 bp):
GGTTTAA
Found at i:11240398 original size:7 final size:7
Alignment explanation
Indices: 11240368--11240429 Score: 52
Period size: 7 Copynumber: 8.9 Consensus size: 7
11240358 GTGCATAGAA
*
11240368 TTAGGGA
1 TTAGGGT
*
11240375 TTATGGT
1 TTAGGGT
**
11240382 TTAGAAT
1 TTAGGGT
11240389 TTAGGGT
1 TTAGGGT
*
11240396 TTAAGGT
1 TTAGGGT
11240403 TTAGGGT
1 TTAGGGT
**
11240410 TTAGTCT
1 TTAGGGT
*
11240417 ATAGGGT
1 TTAGGGT
11240424 TTAGGG
1 TTAGGG
11240430 GTAAAATTTG
Statistics
Matches: 40, Mismatches: 15, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.23, C:0.02, G:0.34, T:0.42
Consensus pattern (7 bp):
TTAGGGT
Found at i:11240413 original size:21 final size:21
Alignment explanation
Indices: 11240363--11240406 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
11240353 TTAGGGTGCA
*
11240363 TAGAA-TTAGGGATTATGGTT
1 TAGAATTTAGGGATTAAGGTT
*
11240383 TAGAATTTAGGGTTTAAGGTT
1 TAGAATTTAGGGATTAAGGTT
11240404 TAG
1 TAG
11240407 GGTTTAGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.41
Consensus pattern (21 bp):
TAGAATTTAGGGATTAAGGTT
Found at i:11240867 original size:83 final size:83
Alignment explanation
Indices: 11240763--11240919 Score: 210
Period size: 83 Copynumber: 1.9 Consensus size: 83
11240753 CGACGCAATG
* * * *
11240763 TAAAAAATACCACTAAAAATATGGGAAATTGAATTAAAAC-ATCGTCATTTTAAGTGGCGCGGTA
1 TAAAAAACACCACTAAAAATATGAGAAATTGAATCAAAACGA-CATCATTTTAAGTGGCG-GGTA
*
11240827 GTGGACTTAGCGGTGCATAT
64 GTGGAATTAGCGGTGCATAT
* * *
11240847 TAAAAAACACCGC-AAAAATATGAGAAATTGAATCAAAACGACATCGTTTTAAGTGTCGGGTAGT
1 TAAAAAACACCACTAAAAATATGAGAAATTGAATCAAAACGACATCATTTTAAGTGGCGGGTAGT
11240911 GGAATTAGC
66 GGAATTAGC
11240920 AGCGCTAGGT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
82 14 0.22
83 38 0.59
84 12 0.19
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.25
Consensus pattern (83 bp):
TAAAAAACACCACTAAAAATATGAGAAATTGAATCAAAACGACATCATTTTAAGTGGCGGGTAGT
GGAATTAGCGGTGCATAT
Found at i:11241058 original size:83 final size:83
Alignment explanation
Indices: 11240960--11241125 Score: 244
Period size: 84 Copynumber: 2.0 Consensus size: 83
11240950 AGCATTAACA
* *
11240960 GCGCTTATCAAAAAACCTGC-TAAAAATACGAGAAATTGAATGAAAATGACGTCGTTTTAAGTGG
1 GCGCTTATCAAAAAA-CTCCATAAAAATACGAGAAATTGAATGAAAACGACGTCGTTTTAAGTGG
**
11241024 CGGGGTAGTGGAATTAGCG
65 AAGGGTAGTGGAATTAGCG
* * *
11241043 GCGCTTATTAAAAAACTCCATTAAAAATATGAGAAATTGAATGAAAACGACGTCGTTTTATGTGG
1 GCGCTTATCAAAAAACTCCA-TAAAAATACGAGAAATTGAATGAAAACGACGTCGTTTTAAGTGG
11241108 AAGGGTAGTGGAATTAGC
65 AAGGGTAGTGGAATTAGC
11241126 TGTGCTAGGT
Statistics
Matches: 74, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
82 3 0.04
83 14 0.19
84 57 0.77
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (83 bp):
GCGCTTATCAAAAAACTCCATAAAAATACGAGAAATTGAATGAAAACGACGTCGTTTTAAGTGGA
AGGGTAGTGGAATTAGCG
Found at i:11241646 original size:16 final size:16
Alignment explanation
Indices: 11241625--11241659 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11241615 GGAACGCAGA
* *
11241625 TTTCTGTTGTTAAGGC
1 TTTCTGTTGCTAAGCC
11241641 TTTCTGTTGCTAAGCC
1 TTTCTGTTGCTAAGCC
11241657 TTT
1 TTT
11241660 GATTTGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.11, C:0.17, G:0.20, T:0.51
Consensus pattern (16 bp):
TTTCTGTTGCTAAGCC
Found at i:11243318 original size:24 final size:24
Alignment explanation
Indices: 11243288--11243340 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
11243278 CTATGTTATA
11243288 ATATTTGTAACTAAAATTAATATT
1 ATATTTGTAACTAAAATTAATATT
**
11243312 ATATTTGTGTCTAAAATTAATATT
1 ATATTTGTAACTAAAATTAATATT
11243336 ATATT
1 ATATT
11243341 ATAAAACACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.49
Consensus pattern (24 bp):
ATATTTGTAACTAAAATTAATATT
Found at i:11244324 original size:23 final size:23
Alignment explanation
Indices: 11244298--11244369 Score: 59
Period size: 23 Copynumber: 3.4 Consensus size: 23
11244288 AATATTAAAA
11244298 TAAAAGAAGTGTTATTATTTTTG
1 TAAAAGAAGTGTTATTATTTTTG
* * **
11244321 TAAAATAA-----A-TATTATAA
1 TAAAAGAAGTGTTATTATTTTTG
11244338 TAAAAGAAGTGTTATTATTTTTG
1 TAAAAGAAGTGTTATTATTTTTG
11244361 TAAAA-AAGT
1 TAAAAGAAGT
11244370 AAATTTAATT
Statistics
Matches: 35, Mismatches: 8, Indels: 13
0.62 0.14 0.23
Matches are distributed among these distances:
17 12 0.34
18 1 0.03
22 5 0.14
23 17 0.49
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (23 bp):
TAAAAGAAGTGTTATTATTTTTG
Found at i:11244340 original size:40 final size:40
Alignment explanation
Indices: 11244281--11244365 Score: 161
Period size: 40 Copynumber: 2.1 Consensus size: 40
11244271 AAATTAAAAT
11244281 TAAAATAAATATTAAAATAAAAGAAGTGTTATTATTTTTG
1 TAAAATAAATATTAAAATAAAAGAAGTGTTATTATTTTTG
*
11244321 TAAAATAAATATTATAATAAAAGAAGTGTTATTATTTTTG
1 TAAAATAAATATTAAAATAAAAGAAGTGTTATTATTTTTG
11244361 TAAAA
1 TAAAA
11244366 AAGTAAATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (40 bp):
TAAAATAAATATTAAAATAAAAGAAGTGTTATTATTTTTG
Found at i:11244413 original size:18 final size:20
Alignment explanation
Indices: 11244376--11244414 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
11244366 AAGTAAATTT
11244376 AATTCATAAAAATATATATA
1 AATTCATAAAAATATATATA
*
11244396 AATTCA-AAACATAT-TATA
1 AATTCATAAAAATATATATA
11244414 A
1 A
11244415 CCAAAACACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
AATTCATAAAAATATATATA
Found at i:11244546 original size:9 final size:9
Alignment explanation
Indices: 11244528--11244604 Score: 100
Period size: 9 Copynumber: 8.6 Consensus size: 9
11244518 GTTTAAATTT
11244528 CATAACTTA
1 CATAACTTA
*
11244537 CATAATTTA
1 CATAACTTA
* *
11244546 CATACCTCA
1 CATAACTTA
* *
11244555 CATACCTCA
1 CATAACTTA
11244564 CATAACTTA
1 CATAACTTA
*
11244573 CATAACTCA
1 CATAACTTA
11244582 CATAACTTA
1 CATAACTTA
11244591 CATAACTTA
1 CATAACTTA
11244600 CATAA
1 CATAA
11244605 TACATAAATA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 60 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (9 bp):
CATAACTTA
Found at i:11246376 original size:12 final size:12
Alignment explanation
Indices: 11246359--11246396 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
11246349 AAGATCGAGG
*
11246359 GATGAATCTGAT
1 GATGAATTTGAT
11246371 GATGAATTTGAT
1 GATGAATTTGAT
11246383 GATGAATTTGAT
1 GATGAATTTGAT
11246395 GA
1 GA
11246397 AGAGGATCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (12 bp):
GATGAATTTGAT
Found at i:11249729 original size:13 final size:14
Alignment explanation
Indices: 11249713--11249741 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11249703 TTTTAAATAT
11249713 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
11249726 TTATAATGGTTTAA
1 TTATAATGGTTTAA
11249740 TT
1 TT
11249742 CGTTGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:11250667 original size:12 final size:12
Alignment explanation
Indices: 11250633--11250669 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
11250623 TGGCATTGTC
* *
11250633 TTTAGTGGCAAT
1 TTTAGCGGCACT
11250645 TTTAGCGGCACT
1 TTTAGCGGCACT
11250657 TTTAGCGGCACT
1 TTTAGCGGCACT
11250669 T
1 T
11250670 ATAAGGCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (12 bp):
TTTAGCGGCACT
Found at i:11253136 original size:18 final size:18
Alignment explanation
Indices: 11253109--11253159 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
11253099 TATATATATA
11253109 TTTT-TAAATTTTA-AAT
1 TTTTATAAATTTTATAAT
11253125 TTCTTATAAATTTCTATAAT
1 TT-TTATAAATTT-TATAAT
*
11253145 TTTTATAATTTTTAT
1 TTTTATAAATTTTAT
11253160 TTAGTTTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.07
17 2 0.07
18 10 0.33
19 11 0.37
20 5 0.17
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTATAAATTTTATAAT
Found at i:11253151 original size:9 final size:9
Alignment explanation
Indices: 11253103--11253159 Score: 57
Period size: 9 Copynumber: 6.3 Consensus size: 9
11253093 ATTGTTTATA
11253103 TATATATTTT
1 TATA-ATTTT
11253113 TA-AA-TTT
1 TATAATTTT
11253120 TA-AATTTCT
1 TATAATTT-T
*
11253129 TATAAATTTC
1 TAT-AATTTT
11253139 TATAATTTT
1 TATAATTTT
11253148 TATAATTTT
1 TATAATTTT
11253157 TAT
1 TAT
11253160 TTAGTTTTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
7 7 0.17
8 3 0.07
9 21 0.51
10 5 0.12
11 5 0.12
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (9 bp):
TATAATTTT
Found at i:11253211 original size:17 final size:16
Alignment explanation
Indices: 11253172--11253222 Score: 50
Period size: 17 Copynumber: 3.2 Consensus size: 16
11253162 AGTTTTTCTG
*
11253172 TATTT-TAAAAATTTT
1 TATTTATAATAATTTT
* * *
11253187 AATATATATTAGATTTT
1 TATTTATAATA-ATTTT
11253204 TATTTATAATAATTTT
1 TATTTATAATAATTTT
11253220 TAT
1 TAT
11253223 AACTTTTTAC
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
15 3 0.11
16 11 0.41
17 13 0.48
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
TATTTATAATAATTTT
Found at i:11255570 original size:22 final size:22
Alignment explanation
Indices: 11255544--11255600 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
11255534 AAAAAATGCA
*
11255544 TAAAATTATTAAATGT-TAATTT
1 TAAAATTATTAAATATAT-ATTT
*
11255566 TAAAATAATATAAATATATATTT
1 TAAAATTAT-TAAATATATATTT
11255589 TAAAA-TATTAAA
1 TAAAATTATTAAA
11255601 AAATAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 4 0.13
22 10 0.33
23 15 0.50
24 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TAAAATTATTAAATATATATTT
Found at i:11263676 original size:46 final size:46
Alignment explanation
Indices: 11263626--11263801 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
11263616 TGGTTGAGCA
11263626 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
11263672 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
11263717 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
11263765 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
11263802 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:11263782 original size:93 final size:93
Alignment explanation
Indices: 11263623--11263794 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
11263613 GGATGGTTGA
* *
11263623 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
11263688 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
11263716 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
11263781 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
11263795 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:11269770 original size:46 final size:46
Alignment explanation
Indices: 11269720--11269895 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
11269710 TGGTTGAGCA
11269720 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
11269766 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
11269811 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
11269859 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
11269896 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:11269876 original size:93 final size:93
Alignment explanation
Indices: 11269717--11269888 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
11269707 GGATGGTTGA
* *
11269717 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
11269782 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
11269810 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
11269875 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
11269889 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:11275146 original size:15 final size:16
Alignment explanation
Indices: 11275116--11275162 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
11275106 TAGATACTTT
11275116 TTTTAAAAATTAATAA
1 TTTTAAAAATTAATAA
*
11275132 TTTTAGAAA-TAATAA
1 TTTTAAAAATTAATAA
*
11275147 ATTTAACAAATGTAAT
1 TTTTAA-AAAT-TAAT
11275163 TCTTCTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 10 0.40
16 11 0.44
18 4 0.16
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (16 bp):
TTTTAAAAATTAATAA
Found at i:11276498 original size:2 final size:2
Alignment explanation
Indices: 11276491--11276521 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
11276481 TCTTATGCAT
11276491 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
11276522 CTAATTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11277566 original size:48 final size:48
Alignment explanation
Indices: 11277511--11277608 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
11277501 TCTATCCAAC
11277511 TAAACACACTTTAAATCTTTGACCATCTACTTTTTATAATGATATTAG
1 TAAACACACTTTAAATCTTTGACCATCTACTTTTTATAATGATATTAG
11277559 TAAACACACTTTAAATCTTTGACCATCTACTTTTTATAATGATATTAG
1 TAAACACACTTTAAATCTTTGACCATCTACTTTTTATAATGATATTAG
11277607 TA
1 TA
11277609 GATTCAAACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.42
Consensus pattern (48 bp):
TAAACACACTTTAAATCTTTGACCATCTACTTTTTATAATGATATTAG
Found at i:11279967 original size:18 final size:19
Alignment explanation
Indices: 11279944--11279979 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
11279934 TTATTTTACC
11279944 TAATT-ACTATAAAAATAA
1 TAATTAACTATAAAAATAA
*
11279962 TAATTAATTATAAAAATA
1 TAATTAACTATAAAAATA
11279980 GTATGGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (19 bp):
TAATTAACTATAAAAATAA
Found at i:11281477 original size:26 final size:26
Alignment explanation
Indices: 11281439--11281514 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 26
11281429 ATATGTATAA
* **
11281439 GAAATTTTAAAATAGGTAATATA-GG
1 GAAAGTTTAAAATAAATAATATACGG
*
11281464 CGAAAGTTTGAAATAAATAATATACGG
1 -GAAAGTTTAAAATAAATAATATACGG
*
11281491 GAAAGAGTTTAAAATGAATAATAT
1 G-AA-AGTTTAAAATAAATAATAT
11281515 GTAAAATAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 20 0.49
27 4 0.10
28 17 0.41
ACGTcount: A:0.50, C:0.03, G:0.18, T:0.29
Consensus pattern (26 bp):
GAAAGTTTAAAATAAATAATATACGG
Found at i:11281536 original size:26 final size:27
Alignment explanation
Indices: 11281498--11281588 Score: 85
Period size: 28 Copynumber: 3.3 Consensus size: 27
11281488 CGGGAAAGAG
*
11281498 TTTAAAATGAATAATATGTAAAAT-AA
1 TTTAAAATAAATAATATGTAAAATGAA
* * *
11281524 TTTAAGATAAATAATATATATAAATGAG
1 TTTAAAATAAATAATATGTA-AAATGAA
* * *
11281552 TTTAAAATAAGTATTATGTAAAAAGAAA
1 TTTAAAATAAATAATATGTAAAATG-AA
*
11281580 CTTAAAATA
1 TTTAAAATA
11281589 GGTAATATAC
Statistics
Matches: 51, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
26 17 0.33
27 8 0.16
28 26 0.51
ACGTcount: A:0.56, C:0.01, G:0.09, T:0.34
Consensus pattern (27 bp):
TTTAAAATAAATAATATGTAAAATGAA
Found at i:11281555 original size:28 final size:27
Alignment explanation
Indices: 11281468--11281561 Score: 84
Period size: 28 Copynumber: 3.4 Consensus size: 27
11281458 TATAGGCGAA
* **
11281468 AGTTTGAAATAAATAATATACGGGAAA-G
1 AGTTTAAAATAAATAATATA--TAAAATG
* *
11281496 AGTTTAAAATGAATAATATGTAAAAT-
1 AGTTTAAAATAAATAATATATAAAATG
* *
11281522 AATTTAAGATAAATAATATATATAAATG
1 AGTTTAAAATAAATAATATATA-AAATG
11281550 AGTTTAAAATAA
1 AGTTTAAAATAA
11281562 GTATTATGTA
Statistics
Matches: 52, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
26 21 0.40
27 4 0.08
28 27 0.52
ACGTcount: A:0.54, C:0.01, G:0.13, T:0.32
Consensus pattern (27 bp):
AGTTTAAAATAAATAATATATAAAATG
Found at i:11281982 original size:2 final size:2
Alignment explanation
Indices: 11281975--11282034 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
11281965 AAGTTTAGAA
11281975 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
11282017 AT AT AA AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT A
11282035 CGAAATAATT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11285973 original size:46 final size:46
Alignment explanation
Indices: 11285927--11286185 Score: 358
Period size: 46 Copynumber: 5.6 Consensus size: 46
11285917 GCTCTCTGAT
** * *
11285927 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * *
11285973 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
11286019 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * *
11286065 GGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGCGTGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
11286111 ATGAAATGAATAAGACCACGGTTGAAAGATACCATGGCAAAATGAC
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
11286157 A-GAAAATGAGTAAGACCATAGTTGAAAGA
1 ATG-AAATGAATAAGACCATGGTTGAAAGA
11286186 CACTATGGTA
Statistics
Matches: 194, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 1 0.01
46 193 0.99
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (46 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:11286080 original size:92 final size:92
Alignment explanation
Indices: 11285923--11286185 Score: 400
Period size: 92 Copynumber: 2.9 Consensus size: 92
11285913 GTGTGCTCTC
** * * * *
11285923 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAGTAAGA
11285988 CCATGGTTGAAAGATACCATGGCAACG
66 CCATGGTTGAAAGATACCATGGCAACG
* *
11286015 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACGGGAAATGAATAAGA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAGTAAGA
*
11286080 CCATGGTTGAAAGATACCATGGCAGCG
66 CCATGGTTGAAAGATACCATGGCAACG
* * * *
11286107 TGACATGAAATGAATAAGACCACGGTTGAAAGATACCATGGCAAAATGACAGAAAATGAGTAAGA
1 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAGTAAGA
*
11286172 CCATAGTTGAAAGA
66 CCATGGTTGAAAGA
11286186 CACTATGGTA
Statistics
Matches: 155, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
92 155 1.00
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.21
Consensus pattern (92 bp):
TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAGGAAATGAGTAAGA
CCATGGTTGAAAGATACCATGGCAACG
Found at i:11297425 original size:4 final size:4
Alignment explanation
Indices: 11297410--11297444 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
11297400 GAGCAAACGT
11297410 GAAA GAAA -AAA GAAA GAAA GAAA GAAA GAAA -AAA G
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G
11297445 GGAAATTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.21
4 23 0.79
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:11302916 original size:25 final size:26
Alignment explanation
Indices: 11302888--11302954 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 26
11302878 CCAATTTTTA
11302888 TTATTCTTTATTA-TTATTTTATTAT
1 TTATTCTTTATTATTTATTTTATTAT
11302913 TTATT-TATTACTTTATTTTATTTTATTAT
1 TTATTCT-TTA--TTA-TTTATTTTATTAT
11302942 TTATTACTTTATT
1 TTATT-CTTTATT
11302955 TTGTTTGGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
24 1 0.03
25 8 0.23
27 3 0.09
28 2 0.06
29 17 0.49
30 3 0.09
31 1 0.03
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (26 bp):
TTATTCTTTATTATTTATTTTATTAT
Found at i:11302933 original size:29 final size:29
Alignment explanation
Indices: 11302884--11302946 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
11302874 CAACCCAATT
11302884 TTTA-TTATTCTTTATTATTATTTTATTA
1 TTTATTTATTCTTTATTATTATTTTATTA
11302912 TTTATTTATTACTTTATT-TTATTTTATTA
1 TTTATTTATT-CTTTATTATTATTTTATTA
11302941 TTTATT
1 TTTATT
11302947 ACTTTATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
28 4 0.12
29 22 0.67
30 7 0.21
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (29 bp):
TTTATTTATTCTTTATTATTATTTTATTA
Found at i:11302955 original size:25 final size:25
Alignment explanation
Indices: 11302888--11302956 Score: 99
Period size: 25 Copynumber: 2.9 Consensus size: 25
11302878 CCAATTTTTA
*
11302888 TTATTCTTTATTA--TTATTTTATT
1 TTATTATTTATTACTTTATTTTATT
*
11302911 AT-TTATTTATTACTTTATTTTATT
1 TTATTATTTATTACTTTATTTTATT
11302935 TTATTATTTATTACTTTATTTT
1 TTATTATTTATTACTTTATTTT
11302957 GTTTGGGTGA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
22 9 0.22
23 1 0.03
24 11 0.28
25 19 0.47
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.72
Consensus pattern (25 bp):
TTATTATTTATTACTTTATTTTATT
Found at i:11306426 original size:21 final size:21
Alignment explanation
Indices: 11306385--11306426 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
11306375 ATATTGCCAT
* *
11306385 GTATCGATACTAGATACCAAA
1 GTATCGATACTAGAAAACAAA
11306406 GTATCGATACTTA-AAAACAAA
1 GTATCGATAC-TAGAAAACAAA
11306427 TATGGTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.24
Consensus pattern (21 bp):
GTATCGATACTAGAAAACAAA
Found at i:11312920 original size:16 final size:16
Alignment explanation
Indices: 11312899--11312939 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
11312889 TAATAATAAA
11312899 ATATTATAGGCCCAAT
1 ATATTATAGGCCCAAT
*
11312915 ATATTAGATAGGTCCAAT
1 ATATT--ATAGGCCCAAT
11312933 ATATTAT
1 ATATTAT
11312940 GTAAGTCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 7 0.32
18 15 0.68
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (16 bp):
ATATTATAGGCCCAAT
Found at i:11312931 original size:18 final size:18
Alignment explanation
Indices: 11312904--11312938 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
11312894 ATAAAATATT
11312904 ATAGGCCCAATATATTAG
1 ATAGGCCCAATATATTAG
*
11312922 ATAGGTCCAATATATTA
1 ATAGGCCCAATATATTA
11312939 TGTAAGTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (18 bp):
ATAGGCCCAATATATTAG
Found at i:11312947 original size:18 final size:18
Alignment explanation
Indices: 11312910--11312954 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
11312900 TATTATAGGC
*
11312910 CCAATATATTAGATAGGT
1 CCAATATATTAGATAAGT
11312928 CCAATATATTATG-TAAGT
1 CCAATATATTA-GATAAGT
*
11312946 CCAAAATAT
1 CCAATATAT
11312955 AAAAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.33
Consensus pattern (18 bp):
CCAATATATTAGATAAGT
Found at i:11313482 original size:15 final size:15
Alignment explanation
Indices: 11313452--11313494 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
11313442 GTTGTTAATG
11313452 TATTATTTGTTATTTGT
1 TATT-TTTGTT-TTTGT
11313469 TATTTTTGTTTTTGT
1 TATTTTTGTTTTTGT
*
11313484 TTTTTTTGTTT
1 TATTTTTGTTT
11313495 AAAAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 15 0.60
16 6 0.24
17 4 0.16
ACGTcount: A:0.09, C:0.00, G:0.12, T:0.79
Consensus pattern (15 bp):
TATTTTTGTTTTTGT
Found at i:11315163 original size:90 final size:90
Alignment explanation
Indices: 11314996--11315218 Score: 283
Period size: 90 Copynumber: 2.5 Consensus size: 90
11314986 TTAAGTGTGT
* * * **
11314996 AAAAAG-CCCTCAAACTTTTTCAAAAAAATAATAATTAAGCCCCTCATTTTCTTTTGCACTCAAT
1 AAAAAGACCCTCAAACTTTTTC-AAAAAA-AGTAATTAAGCCCTTCATTTTCTCTCCCACTCAAT
*
11315060 TGAGTACTTGAACTTTCAAAATGCATC
64 TGAGTACTTGAACTTTCAAAATGCATA
*
11315087 AAAAAGACCCTCAAACTTCTTCAAAAAAAGTAATTAAGCCCTTGC-TTTT-TCTCCCACTCAATT
1 AAAAAGACCCTCAAACTTTTTCAAAAAAAGTAATTAAGCCCTT-CATTTTCTCTCCCACTCAATT
*
11315150 GGGTACTTGGAACTTTCAAAATGCATA
65 GAGTACTT-GAACTTTCAAAATGCATA
* *
11315177 AAAAAGACCTTCAAAATTTTTC-AAAAAAGTAATTAAGTCCCT
1 AAAAAGACCCTCAAACTTTTTCAAAAAAAGTAATTAAG-CCCT
11315219 GCTCATATTA
Statistics
Matches: 117, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
89 33 0.28
90 57 0.49
91 13 0.11
92 14 0.12
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.31
Consensus pattern (90 bp):
AAAAAGACCCTCAAACTTTTTCAAAAAAAGTAATTAAGCCCTTCATTTTCTCTCCCACTCAATTG
AGTACTTGAACTTTCAAAATGCATA
Found at i:11315521 original size:10 final size:10
Alignment explanation
Indices: 11315508--11315587 Score: 64
Period size: 10 Copynumber: 8.5 Consensus size: 10
11315498 CTTTATAAAA
11315508 TTTTATAATT
1 TTTTATAATT
11315518 TTTTAT-A-T
1 TTTTATAATT
* *
11315526 TTCTAT-ATA
1 TTTTATAATT
11315535 TTTTATAATT
1 TTTTATAATT
*
11315545 TTTTACAA-T
1 TTTTATAATT
11315554 TTTTAT-ATAT
1 TTTTATAAT-T
11315564 TTTT-TAATT
1 TTTTATAATT
* *
11315573 TTTAATAAAT
1 TTTTATAATT
11315583 TTTTA
1 TTTTA
11315588 ATATATGAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
8 8 0.15
9 17 0.31
10 30 0.55
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTTATAATT
Found at i:11315532 original size:28 final size:28
Alignment explanation
Indices: 11315507--11315575 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
11315497 CCTTTATAAA
*
11315507 ATTTTATAATTTTTTA-TATTTCTATAT
1 ATTTTATAATTTTTTACAATTTCTATAT
*
11315534 ATTTTATAATTTTTTACAATTTTTATAT
1 ATTTTATAATTTTTTACAATTTCTATAT
*
11315562 ATTTTTTAATTTTT
1 ATTTTATAATTTTT
11315576 AATAAATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 16 0.42
28 22 0.58
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (28 bp):
ATTTTATAATTTTTTACAATTTCTATAT
Found at i:11315557 original size:19 final size:18
Alignment explanation
Indices: 11315535--11315588 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
11315525 TTTCTATATA
11315535 TTTTATAATTTTTTACAAT
1 TTTTATAATTTTTTA-AAT
11315554 TTTTATATATTTTTT-AAT
1 TTTTATA-ATTTTTTAAAT
*
11315572 TTTTAATAAATTTTTAA
1 TTTT-ATAATTTTTTAA
11315589 TATATGAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
18 13 0.42
19 11 0.35
20 7 0.23
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTATAATTTTTTAAAT
Found at i:11315576 original size:18 final size:18
Alignment explanation
Indices: 11315507--11315586 Score: 67
Period size: 19 Copynumber: 4.3 Consensus size: 18
11315497 CCTTTATAAA
*
11315507 ATTTTATAATTTTT-TAT
1 ATTTTTTAATTTTTATAT
*
11315524 A-TTTCTATATATTTTATA-
1 ATTTTTTA-AT-TTTTATAT
11315542 ATTTTTTACAATTTTTATAT
1 ATTTTTT--AATTTTTATAT
*
11315562 ATTTTTTAATTTTTAATAA
1 ATTTTTTAATTTTT-ATAT
11315581 ATTTTT
1 ATTTTT
11315587 AATATATGAA
Statistics
Matches: 52, Mismatches: 3, Indels: 14
0.75 0.04 0.20
Matches are distributed among these distances:
16 5 0.10
17 3 0.06
18 12 0.23
19 22 0.42
20 9 0.17
21 1 0.02
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTTTAATTTTTATAT
Found at i:11315585 original size:28 final size:27
Alignment explanation
Indices: 11315507--11315585 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 27
11315497 CCTTTATAAA
*
11315507 ATTTTATAATTTTT-TATATTTCTATAT
1 ATTTTATAATTTTTATAAATTT-TATAT
11315534 ATTTTATAATTTTT-TACAATTTTTATAT
1 ATTTTATAATTTTTATA-AA-TTTTATAT
*
11315562 ATTTTTTAATTTTTAATAAATTTT
1 ATTTTATAATTTTT-ATAAATTTT
11315586 TAATATATGA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
27 16 0.35
28 23 0.50
29 5 0.11
30 2 0.04
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (27 bp):
ATTTTATAATTTTTATAAATTTTATAT
Found at i:11315587 original size:18 final size:18
Alignment explanation
Indices: 11315499--11315589 Score: 64
Period size: 18 Copynumber: 4.9 Consensus size: 18
11315489 TTCTTATGCC
*
11315499 TTTATAAAATTTTATAATT
1 TTTATATAATTTT-TAATT
*
11315518 TTT-TAT-ATTTCTATATAT
1 TTTATATAATTTTTA-AT-T
*
11315536 TTTATA-ATTTTTTACAATT
1 TTTATATAATTTTT--AATT
*
11315555 TTTATATATTTTTTAATT
1 TTTATATAATTTTTAATT
11315573 TTTA-ATAAATTTTTAAT
1 TTTATAT-AATTTTTAAT
11315590 ATATGAATTT
Statistics
Matches: 59, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
16 2 0.03
17 8 0.14
18 23 0.39
19 16 0.27
20 9 0.15
21 1 0.02
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTATATAATTTTTAATT
Found at i:11324895 original size:42 final size:42
Alignment explanation
Indices: 11324778--11324932 Score: 195
Period size: 42 Copynumber: 3.7 Consensus size: 42
11324768 TAACATACCA
* * *
11324778 ATGCCATATCCCAGATATGGTCTTACATGGGAG-CTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACA-CGAAGTCTCATATCG
* * * *
11324820 ATGCCAATAGCTCAGCTATGGTCTTACATGAAGTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
* * *
11324863 ATGACATATCCTAGATATGGTCTTACACGAAGTCTCATATAG
1 ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
11324905 ATGCCATATCCCAGATATGGTCTTACAC
1 ATGCCATATCCCAGATATGGTCTTACAC
11324933 ATAGTCTTAG
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
42 65 0.68
43 31 0.32
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATATCG
Found at i:11329236 original size:91 final size:91
Alignment explanation
Indices: 11329076--11329252 Score: 291
Period size: 91 Copynumber: 1.9 Consensus size: 91
11329066 TCAAAATATC
* * *
11329076 AAAAATGTAACTTTACAGCAATTAAATAATATGAAAACACTTTCTAAAATCTCCATTTAAGATTA
1 AAAAATGTAACTTTACACCAAATAAATAATATGAAAACACTTTCCAAAATCTCCATTTAAGATTA
* *
11329141 CATCAATCAAACACATCCAAACAGTA
66 CATCAACCAAAAACATCCAAACAGTA
* *
11329167 AAAAATGTAACTTTACACCAAATAAATAATGTGAAAACACTTTCCAAAATCTCCATTTAAGATTG
1 AAAAATGTAACTTTACACCAAATAAATAATATGAAAACACTTTCCAAAATCTCCATTTAAGATTA
11329232 CATCAACCAAAAACATCCAAA
66 CATCAACCAAAAACATCCAAA
11329253 TAACAGAAGG
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 79 1.00
ACGTcount: A:0.49, C:0.20, G:0.06, T:0.26
Consensus pattern (91 bp):
AAAAATGTAACTTTACACCAAATAAATAATATGAAAACACTTTCCAAAATCTCCATTTAAGATTA
CATCAACCAAAAACATCCAAACAGTA
Found at i:11341783 original size:25 final size:25
Alignment explanation
Indices: 11341750--11341797 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
11341740 AAAAAGACCT
11341750 AAAAAATTCTACTTTATTTAATTCA
1 AAAAAATTCTACTTTATTTAATTCA
11341775 AAAAAATTCTACTTTATTTAATT
1 AAAAAATTCTACTTTATTTAATT
11341798 TAGGTTACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (25 bp):
AAAAAATTCTACTTTATTTAATTCA
Found at i:11343201 original size:20 final size:20
Alignment explanation
Indices: 11343176--11343215 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
11343166 AGAAAAAGAT
11343176 GACAAATTTTGTCCATCTTC
1 GACAAATTTTGTCCATCTTC
11343196 GACAAATTTTGTCCATCTTC
1 GACAAATTTTGTCCATCTTC
11343216 CACTTTTAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (20 bp):
GACAAATTTTGTCCATCTTC
Found at i:11349519 original size:19 final size:20
Alignment explanation
Indices: 11349485--11349522 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
11349475 AGTTATGGGT
*
11349485 TGAATTATATTTTAATTAGG
1 TGAATTATAGTTTAATTAGG
11349505 TGAATT-TAGTTTAATTAG
1 TGAATTATAGTTTAATTAG
11349523 AAGTAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (20 bp):
TGAATTATAGTTTAATTAGG
Found at i:11349736 original size:3 final size:3
Alignment explanation
Indices: 11349728--11349777 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
11349718 AGATATTTAC
11349728 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TT- TTA TCTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
11349775 TTA
1 TTA
11349778 AATGAGATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 37 0.84
4 3 0.07
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:11350243 original size:18 final size:18
Alignment explanation
Indices: 11350212--11350247 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
11350202 CGGTGATGAA
11350212 ATTTGTATTTTTTATTTT
1 ATTTGTATTTTTTATTTT
11350230 ATTT-TATTTATTTATTTT
1 ATTTGTATTT-TTTATTTT
11350248 TGTTTTTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (18 bp):
ATTTGTATTTTTTATTTT
Found at i:11351360 original size:25 final size:26
Alignment explanation
Indices: 11351332--11351387 Score: 64
Period size: 23 Copynumber: 2.3 Consensus size: 26
11351322 TTTTGAAATT
* *
11351332 TATTTTTATATCATATTAT-TTTAAC
1 TATTTTTATATAATATTATGTTTAAA
*
11351357 TA--TTTATATAATATTTTGTTTAAA
1 TATTTTTATATAATATTATGTTTAAA
11351381 TATTTTT
1 TATTTTT
11351388 TGTGTATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 13 0.52
24 7 0.28
25 2 0.08
26 3 0.12
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (26 bp):
TATTTTTATATAATATTATGTTTAAA
Found at i:11351370 original size:23 final size:24
Alignment explanation
Indices: 11351336--11351385 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
11351326 GAAATTTATT
* *
11351336 TTTATATCATATTAT-TTTAACTA
1 TTTATATAATATTATGTTTAAATA
*
11351359 TTTATATAATATTTTGTTTAAATA
1 TTTATATAATATTATGTTTAAATA
11351383 TTT
1 TTT
11351386 TTTGTGTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTATATAATATTATGTTTAAATA
Found at i:11353184 original size:19 final size:18
Alignment explanation
Indices: 11353148--11353195 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
11353138 AGAAAGTTAC
*
11353148 AGAGAAAGAAACGTGAAA
1 AGAGAAAGAAACGAGAAA
11353166 GAGAGAAAGAAA-GAAGAAA
1 -AGAGAAAGAAACG-AGAAA
*
11353185 AGAAAAAGAAA
1 AGAGAAAGAAA
11353196 AAGGGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.69, C:0.02, G:0.27, T:0.02
Consensus pattern (18 bp):
AGAGAAAGAAACGAGAAA
Found at i:11355064 original size:20 final size:20
Alignment explanation
Indices: 11355039--11355093 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
11355029 CCACGGGCAG
*
11355039 GCCACACGGGCATGTTCCAA
1 GCCACACGGGCATGTCCCAA
* *
11355059 GCCACACGGGCGTGTCCCAG
1 GCCACACGGGCATGTCCCAA
*
11355079 GCCATACGGGCATGT
1 GCCACACGGGCATGT
11355094 GCCCTATCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.35, G:0.31, T:0.15
Consensus pattern (20 bp):
GCCACACGGGCATGTCCCAA
Found at i:11356002 original size:7 final size:7
Alignment explanation
Indices: 11355983--11356012 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
11355973 TAGCCAAAGC
11355983 TATCTCA
1 TATCTCA
11355990 -ATCTCA
1 TATCTCA
11355996 TATCTCA
1 TATCTCA
11356003 TATCTCA
1 TATCTCA
11356010 TAT
1 TAT
11356013 AATGCTCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.43
Consensus pattern (7 bp):
TATCTCA
Found at i:11358115 original size:16 final size:16
Alignment explanation
Indices: 11358094--11358125 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
11358084 AGCTAAAGAC
11358094 ATTAATACTAATAGAT
1 ATTAATACTAATAGAT
11358110 ATTAATACTAATAGAT
1 ATTAATACTAATAGAT
11358126 GAAGAGCAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTAATACTAATAGAT
Found at i:11359521 original size:23 final size:23
Alignment explanation
Indices: 11359495--11359539 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
11359485 TCCATACTTA
*
11359495 ATTTTAAAAAATATATTAAATAG
1 ATTTTAAAAAATAAATTAAATAG
* *
11359518 ATTTTATAAATTAAATTAAATA
1 ATTTTAAAAAATAAATTAAATA
11359540 CTTAATTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
ATTTTAAAAAATAAATTAAATAG
Found at i:11379302 original size:16 final size:16
Alignment explanation
Indices: 11379218--11379307 Score: 54
Period size: 17 Copynumber: 5.0 Consensus size: 16
11379208 ATCCAAAAAC
11379218 AAATATATAAAAAATTCA
1 AAAT-TATAAAAAATT-A
* *
11379236 AAATTTTAAAAATTTAGA
1 AAATTATAAAAAATT--A
*
11379254 AAATTATAAGAAAAGAAATA
1 AAATTAT---AAAA-AATTA
*
11379274 TAAATTCTAAAAAAATTA
1 -AAATTAT-AAAAAATTA
11379292 AAATTATAAAAAATTA
1 AAATTATAAAAAATTA
11379308 GTTAAAATTT
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
16 9 0.16
17 15 0.27
18 15 0.27
19 4 0.07
20 1 0.02
21 10 0.18
22 2 0.04
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.30
Consensus pattern (16 bp):
AAATTATAAAAAATTA
Found at i:11380624 original size:15 final size:15
Alignment explanation
Indices: 11380592--11380637 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
11380582 ATTTATCTAT
*
11380592 TTATAATTCTACTATTA
1 TTATATTTCTA-T-TTA
11380609 TTATATTTCTATTTA
1 TTATATTTCTATTTA
*
11380624 TTATATTTTTATTT
1 TTATATTTCTATTT
11380638 CTATTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 16 0.59
16 1 0.04
17 10 0.37
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATATTTCTATTTA
Found at i:11388094 original size:133 final size:133
Alignment explanation
Indices: 11387788--11388217 Score: 603
Period size: 133 Copynumber: 3.2 Consensus size: 133
11387778 AAATGGCGAG
* * *
11387788 TCTTATCTCCATTTATCAGCTATGGAGCAGATTTTAGCCACCGGCCTTATCTCTCTAAGGTAGTA
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCGGCCTTATCTCTCTAAGGTAGCA
* * * ** * * * * *
11387853 AGAGAGTAGGTTGAAGATACGAGCCTTAACCCCCTAA-GCAGTAGGGTAA-CAGGCTAAAAATTA
66 AGAGAGTAGGTTGAAGATACAAGTCTTATCTTCCTAAGGTAGCAAGG-AAGCAGACTGAAAATTA
11387916 CAGA
130 CAGA
* * * *
11387920 TCTTATCTCTATGTATCGGCTATGGAGCAGATTTTAACCACCGGTCTTATCTCTCTAAGGTAACA
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCGGCCTTATCTCTCTAAGGTAGCA
* *
11387985 AGAGAGTAGGTTGAGGATACAAGTCTTATCTTCCTAAGGTAGCAAGGAAGCAGACTGAAAATTAT
66 AGAGAGTAGGTTGAAGATACAAGTCTTATCTTCCTAAGGTAGCAAGGAAGCAGACTGAAAATTAC
11388050 AGA
131 AGA
* * ** *
11388053 TCTTATCTCTATGTATCGGCAATGGAGCAGATTTTAGCCACCAACCTTATCTCTCTGAGGTAGCA
1 TCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCGGCCTTATCTCTCTAAGGTAGCA
* *
11388118 AGAGAGCAGGTTAAAGATACAAGTCTTATCTTCCTAAGGTAGCAAGGAAGCAGACTGAAAATTAC
66 AGAGAGTAGGTTGAAGATACAAGTCTTATCTTCCTAAGGTAGCAAGGAAGCAGACTGAAAATTAC
11388183 AGA
131 AGA
11388186 TCTTATCTCCATGTATCGGCTATGGAGCAGAT
1 TCTTATCTCCATGTATCGGCTATGGAGCAGAT
11388218 CGATAATGGC
Statistics
Matches: 264, Mismatches: 32, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
132 91 0.34
133 173 0.66
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (133 bp):
TCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCGGCCTTATCTCTCTAAGGTAGCA
AGAGAGTAGGTTGAAGATACAAGTCTTATCTTCCTAAGGTAGCAAGGAAGCAGACTGAAAATTAC
AGA
Found at i:11388215 original size:45 final size:44
Alignment explanation
Indices: 11388166--11388441 Score: 195
Period size: 45 Copynumber: 6.2 Consensus size: 44
11388156 GTAGCAAGGA
*
11388166 AGCAGACTGAAAATTACAGATCTTATCTCCATGTATCGGCTATGG
1 AGCAGA-TGAAAATTACAGATCTTATCTCCATGTATCAGCTATGG
* ** *
11388211 AGCAGATCGATAATGGCA-AGTCTTATCTCCATGTATCGGCTATGG
1 AGCAGAT-GAAAATTACAGA-TCTTATCTCCATGTATCAGCTATGG
*** *** * *
11388256 AGCAGATTTTAGCCACCAG-TCTTATCTCTC-TGAAGT-AG-TAAGAG
1 AGCAGATGAAAATTA-CAGATCTTATCTC-CATGTA-TCAGCTATG-G
* * * * * *
11388300 AGCAGGTTGAAAAATGCAGGTCTTATTTCCATGTATCAGCTATAG
1 AGCA-GATGAAAATTACAGATCTTATCTCCATGTATCAGCTATGG
*
11388345 AGCAGACTGAGAATTACAGATCTTATCTCCATGTATCAGCTATGG
1 AGCAGA-TGAAAATTACAGATCTTATCTCCATGTATCAGCTATGG
* ** *
11388390 AGTAGATCGAAAATGGC-GAGTCCTATCTCCATGTATCAGCTATGG
1 AGCAGAT-GAAAATTACAGA-TCTTATCTCCATGTATCAGCTATGG
11388435 AGCAGAT
1 AGCAGAT
11388442 TTTAGCCACC
Statistics
Matches: 179, Mismatches: 37, Indels: 30
0.73 0.15 0.12
Matches are distributed among these distances:
43 3 0.02
44 31 0.17
45 143 0.80
46 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (44 bp):
AGCAGATGAAAATTACAGATCTTATCTCCATGTATCAGCTATGG
Found at i:11388419 original size:179 final size:179
Alignment explanation
Indices: 11388056--11388546 Score: 670
Period size: 179 Copynumber: 2.7 Consensus size: 179
11388046 TTATAGATCT
* *
11388056 TATCTCTATGTATCGGCAATGGAGCAGATTTTAGCCACCAACCTTATCTCTCTGAGGTAGCAAGA
1 TATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAACCTTATCTCTCTGAGGTAGCAAGA
* * * * *
11388121 GAGCAGGTTAAAGATACAAGTCTTATCTTCCTAAG-GT-AGC-A-AGGAAGCAGACTGAAAATTA
66 GAGCAGGTTAAAAATGCAGGTCTTATCTTCC-ATGTATCAGCTATA-G-AGCAGACTGAAAATTA
* * *
11388182 CAGATCTTATCTCCATGTATCGGCTATGGAGCAGATCGATAATGGCAAGTCT
128 CAGATCTTATCTCCATGTATCAGCTATGGAGCAGATCGAAAATGGCAAGTCC
** * *
11388234 TATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGTCTTATCTCTCTGAAGTAGTAAGA
1 TATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAACCTTATCTCTCTGAGGTAGCAAGA
*
11388299 GAGCAGGTTGAAAAATGCAGGTCTTAT-TTCCATGTATCAGCTATAGAGCAGACTGAGAATTACA
66 GAGCAGGTT-AAAAATGCAGGTCTTATCTTCCATGTATCAGCTATAGAGCAGACTGAAAATTACA
* *
11388363 GATCTTATCTCCATGTATCAGCTATGGAGTAGATCGAAAATGGCGAGTCC
130 GATCTTATCTCCATGTATCAGCTATGGAGCAGATCGAAAATGGCAAGTCC
* *
11388413 TATCTCCATGTATCAGCTATGGAGCAGATTTTAGCCACCAACCTTATCTCTCTGAGGTAGCAGGA
1 TATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAACCTTATCTCTCTGAGGTAGCAAGA
* * * * * *
11388478 GAGCAGGTTCAAAATTGCAGGTCTTATCTT-CATATATCGGCTATGGAGTAGACTGAAAAATACA
66 GAGCAGGTT-AAAAATGCAGGTCTTATCTTCCATGTATCAGCTATAGAGCAGACTGAAAATTACA
11388542 GATCT
130 GATCT
11388547 CCCCTAAACA
Statistics
Matches: 276, Mismatches: 31, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
177 2 0.01
178 73 0.26
179 196 0.71
180 4 0.01
181 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (179 bp):
TATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAACCTTATCTCTCTGAGGTAGCAAGA
GAGCAGGTTAAAAATGCAGGTCTTATCTTCCATGTATCAGCTATAGAGCAGACTGAAAATTACAG
ATCTTATCTCCATGTATCAGCTATGGAGCAGATCGAAAATGGCAAGTCC
Found at i:11388521 original size:89 final size:88
Alignment explanation
Indices: 11388230--11388525 Score: 255
Period size: 89 Copynumber: 3.3 Consensus size: 88
11388220 ATAATGGCAA
* * *
11388230 GTCTTATCTCCATGTATCGGCTATGGAGCAGATTTTAGCCACCAGTCTTATCTCTCTGAAGTAGT
1 GTCTTATCTCCATGTATCAGCTATGGAGCAGATTTTAGCCACCAATCTTATCTCTCTG-AGTAGC
* *
11388295 AAGAGAGCAGGTTGAAAAATGCAG
65 AAGAGAGCAGGTTCAAAATTGCAG
* * * * * *
11388319 GTCTTATTTCCATGTATCAGCTATAGAGCAGA-CTGAG-AATTACAGATCTTATCTC-CATGTA-
1 GTCTTATCTCCATGTATCAGCTATGGAGCAGATTTTAGCCA--CCA-ATCTTATCTCTC-TG-AG
* * * *
11388380 TCAGCTATG-GAGTA-GATCGAAAATGGC-G
61 T-AGC-AAGAGAGCAGGTTC-AAAATTGCAG
* *
11388408 AGTCCTATCTCCATGTATCAGCTATGGAGCAGATTTTAGCCACCAACCTTATCTCTCTGAGGTAG
1 -GTCTTATCTCCATGTATCAGCTATGGAGCAGATTTTAGCCACCAATCTTATCTCTCTGA-GTAG
*
11388473 CAGGAGAGCAGGTTCAAAATTGCAG
64 CAAGAGAGCAGGTTCAAAATTGCAG
* * *
11388498 GTCTTATCTTCATATATCGGCTATGGAG
1 GTCTTATCTCCATGTATCAGCTATGGAG
11388526 TAGACTGAAA
Statistics
Matches: 159, Mismatches: 32, Indels: 32
0.71 0.14 0.14
Matches are distributed among these distances:
87 1 0.01
88 6 0.04
89 85 0.53
90 61 0.38
91 5 0.03
92 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (88 bp):
GTCTTATCTCCATGTATCAGCTATGGAGCAGATTTTAGCCACCAATCTTATCTCTCTGAGTAGCA
AGAGAGCAGGTTCAAAATTGCAG
Found at i:11388766 original size:88 final size:88
Alignment explanation
Indices: 11388543--11389076 Score: 690
Period size: 88 Copynumber: 6.1 Consensus size: 88
11388533 AAAAATACAG
* * * ** *
11388543 ATCTCCCCTAAACAATAGTGGAGCAGATCGAAGACAGCAAACCTTAACCCCCTAAGCAGTAGGGT
1 ATCT-CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACCCCCTAAGCAGTAGGGT
11388608 AACAGGCTGGAAAA-TA-A-A---T
65 AACAGGCT-GAAAATTACAGATCTT
* * *
11388627 ATCTCCCCTAAACAGTAGTGGAGCAGATCGAAGACAGCGAG-CTTCAACCCCCTAAGCAGTAGGG
1 ATCT-CCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAGCCTT-AACCCCCTAAGCAGTAGGG
11388691 TAACAGGCTGAAAATTACAGATCTT
64 TAACAGGCTGAAAATTACAGATCTT
* * * *
11388716 ATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATGGTGAGCCTTAACCCCCTAAGCAGTAAGGTA
1 ATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACCCCCTAAGCAGTAGGGTA
*
11388781 ACAGGCTGAAAATTACAGACCTT
66 ACAGGCTGAAAATTACAGATCTT
* * * *
11388804 ATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTGAGCCTTAACTCTCTAAGCAATAGGGTA
1 ATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACCCCCTAAGCAGTAGGGTA
*
11388869 ACAGGCTAAAAATTACAGATCTT
66 ACAGGCTGAAAATTACAGATCTT
* * * * *
11388892 ATCTCCCTAAGTAGTAGTGGAGTAGATCGAAGACAGTGAGCTTTAACCACCTAAGCAGTAGGGTA
1 ATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACCCCCTAAGCAGTAGGGTA
11388957 ACAGGCTGAAAATTACAGATCTT
66 ACAGGCTGAAAATTACAGATCTT
* * * * *
11388980 ATCTCCCTAAGCAGTAGTGGAGCAGATCTAGGACGGTGAGCCTTATCTCCCTAAGCAGT-GGGAA
1 ATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACCCCCTAAGCAGTAGGGTA
* *
11389044 ACAGACTG-AAATTACAAATCTT
66 ACAGGCTGAAAATTACAGATCTT
11389066 ATCTCCCTAAG
1 ATCTCCCTAAG
11389077 TAATAGGGAA
Statistics
Matches: 401, Mismatches: 41, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
83 8 0.02
84 68 0.17
85 1 0.00
86 25 0.06
87 11 0.03
88 280 0.70
89 8 0.02
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (88 bp):
ATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGTGAGCCTTAACCCCCTAAGCAGTAGGGTA
ACAGGCTGAAAATTACAGATCTT
Found at i:11389109 original size:130 final size:132
Alignment explanation
Indices: 11388963--11389208 Score: 336
Period size: 130 Copynumber: 1.9 Consensus size: 132
11388953 GGTAACAGGC
* * * ** *
11388963 TGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCTAGGACGGTGAGCCTTATCT
1 TGAAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAAATCGAAAACGGTAAGCCTTATCT
*
11389028 CCCTAAGCAGT-G-GGAAACAGACT-GAAATTACAAATCTTATCTCCCTAAGTAATAGGGAAACA
66 CCCTAAGCAGTAGTGG-AACAGACTAAAAATTACAAATCTTATCTCCCTAAGTAATAGGGAAACA
11389090 AGT
130 AGT
* *
11389093 TGAAAATTACAGATCTTATCTCCCTAAGTAGTAGCGGAGCAAATCGAAAATGGTAAGCCTTATCT
1 TGAAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAAATCGAAAACGGTAAGCCTTATCT
* * * * *
11389158 CCCTGAGTAGTAGTGGAGCAGGCTAAAAATTACAGATCTTATCTCCCTAAG
66 CCCTAAGCAGTAGTGGAACAGACTAAAAATTACAAATCTTATCTCCCTAAG
11389209 CAGTAGTGGA
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
130 66 0.67
131 7 0.07
132 26 0.26
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (132 bp):
TGAAAATTACAGATCTTATCTCCCTAAGCAGTAGCGGAGCAAATCGAAAACGGTAAGCCTTATCT
CCCTAAGCAGTAGTGGAACAGACTAAAAATTACAAATCTTATCTCCCTAAGTAATAGGGAAACAA
GT
Found at i:11389234 original size:44 final size:44
Alignment explanation
Indices: 11388676--11389234 Score: 294
Period size: 44 Copynumber: 12.8 Consensus size: 44
11388666 AGCTTCAACC
* **
11388676 CCCTAAGCAGTAG-GGTAACAGGCTGAAAATTACAGATCTTATCT
1 CCCTAAGCAGTAGTGG-AGCAGATTGAAAATTACAGATCTTATCT
* * * * * *
11388720 CCCTAAGCAGTAGTGGAGTAGATTGAAGATGGT-GAG-CCTTAACC
1 CCCTAAGCAGTAGTGGAGCAGATTGAAAAT--TACAGATCTTATCT
* * ** *
11388764 CCCTAAGCAGTAAG-GTAACAGGCTGAAAATTACAGACCTTATCT
1 CCCTAAGCAGT-AGTGGAGCAGATTGAAAATTACAGATCTTATCT
* * * * *
11388808 CCCTAAGCAGTAGTGGAGCAGATCGAAGATGGT-GAG-CCTTAACT
1 CCCTAAGCAGTAGTGGAGCAGATTGAAAAT--TACAGATCTTATCT
* * * ** *
11388852 CTCTAAGCAATAG-GGTAACAGGCTAAAAATTACAGATCTTATCT
1 CCCTAAGCAGTAGTGG-AGCAGATTGAAAATTACAGATCTTATCT
* * * * * * *
11388896 CCCTAAGTAGTAGTGGAGTAGATCGAAGACAGT-GAGCT-TTAAC-
1 CCCTAAGCAGTAGTGGAGCAGATTGAA-A-ATTACAGATCTTATCT
* **
11388939 CACCTAAGCAGTAG-GGTAACAGGCTGAAAATTACAGATCTTATCT
1 C-CCTAAGCAGTAGTGG-AGCAGATTGAAAATTACAGATCTTATCT
* *** * *
11388984 CCCTAAGCAGTAGTGGAGCAGATCTAGGACGGT-GAG-CCTTATCT
1 CCCTAAGCAGTAGTGGAGCAGAT-T-GAAAATTACAGATCTTATCT
* * *
11389028 CCCTAAGCAGT-G-GGAAACAGACTG-AAATTACAAATCTTATCT
1 CCCTAAGCAGTAGTGG-AGCAGATTGAAAATTACAGATCTTATCT
* * *
11389070 CCCTAAGTAATAG-GGAAACA-AGTTGAAAATTACAGATCTTATCT
1 CCCTAAGCAGTAGTGG-AGCAGA-TTGAAAATTACAGATCTTATCT
* * * * *
11389114 CCCTAAGTAGTAGCGGAGCAAATCGAAAATGGTA-AG-CCTTATCT
1 CCCTAAGCAGTAGTGGAGCAGATTGAAAAT--TACAGATCTTATCT
* * ** *
11389158 CCCTGAGTAGTAGTGGAGCAGGCTAAAAATTACAGATCTTATCT
1 CCCTAAGCAGTAGTGGAGCAGATTGAAAATTACAGATCTTATCT
*
11389202 CCCTAAGCAGTAGTGGAGCAGATTGAAGATTAC
1 CCCTAAGCAGTAGTGGAGCAGATTGAAAATTAC
11389235 CAAATTTTAT
Statistics
Matches: 381, Mismatches: 99, Indels: 70
0.69 0.18 0.13
Matches are distributed among these distances:
40 2 0.01
41 2 0.01
42 26 0.07
43 33 0.09
44 284 0.75
45 25 0.07
46 9 0.02
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (44 bp):
CCCTAAGCAGTAGTGGAGCAGATTGAAAATTACAGATCTTATCT
Found at i:11389817 original size:36 final size:33
Alignment explanation
Indices: 11389777--11389848 Score: 81
Period size: 35 Copynumber: 2.1 Consensus size: 33
11389767 ACTTTTGGTA
* *
11389777 TTCCTACTTCAATTTGAAATTGGATTATTCTCTCTT
1 TTCCTACTTCAA-TTAAAATTGAATTATT-T-TCTT
* *
11389813 TTCCTATTTCCATTAAAATTGAATTATTTTCTT
1 TTCCTACTTCAATTAAAATTGAATTATTTTCTT
11389846 TTC
1 TTC
11389849 TCTCTCAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 7 0.22
34 1 0.03
35 14 0.44
36 10 0.31
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (33 bp):
TTCCTACTTCAATTAAAATTGAATTATTTTCTT
Found at i:11390268 original size:15 final size:15
Alignment explanation
Indices: 11390248--11390314 Score: 68
Period size: 15 Copynumber: 4.5 Consensus size: 15
11390238 TTCTAATACT
11390248 ATTATTATTTATCTA
1 ATTATTATTTATCTA
11390263 ATTATTATTTATCTA
1 ATTATTATTTATCTA
* *
11390278 TTTA-TATTTCTACT-
1 ATTATTATTTAT-CTA
11390292 ATTATTATATT-TCTA
1 ATTATTAT-TTATCTA
*
11390307 TTTATTAT
1 ATTATTAT
11390315 ATTTTTATTT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
14 11 0.25
15 31 0.70
16 2 0.05
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATTTATCTA
Found at i:11390278 original size:29 final size:29
Alignment explanation
Indices: 11390246--11390314 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 29
11390236 TATTCTAATA
11390246 CTATTATTATTTAT-CTAATTATTAT-TTAT
1 CTATTATTATTTATACT-ATTATTATATT-T
*
11390275 CTATT-TATATTTCTACTATTATTATATTT
1 CTATTAT-TATTTATACTATTATTATATTT
11390304 CTATTTATTAT
1 CTA-TTATTAT
11390315 ATTTTTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
28 1 0.03
29 23 0.68
30 9 0.26
31 1 0.03
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.62
Consensus pattern (29 bp):
CTATTATTATTTATACTATTATTATATTT
Found at i:11390315 original size:15 final size:15
Alignment explanation
Indices: 11390279--11390324 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
11390269 ATTTATCTAT
11390279 TTATATTTCTACTATTA
1 TTATATTTCTA-T-TTA
11390296 TTATATTTCTATTTA
1 TTATATTTCTATTTA
*
11390311 TTATATTTTTATTT
1 TTATATTTCTATTT
11390325 CTATTTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 16 0.57
16 1 0.04
17 11 0.39
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATATTTCTATTTA
Found at i:11392550 original size:15 final size:16
Alignment explanation
Indices: 11392525--11392559 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
11392515 TACAGATAGA
11392525 TTTATATTTTTATAAT
1 TTTATATTTTTATAAT
*
11392541 TTTATA-TTTTATTAT
1 TTTATATTTTTATAAT
11392556 TTTA
1 TTTA
11392560 CAAATTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTATATTTTTATAAT
Found at i:11402235 original size:17 final size:16
Alignment explanation
Indices: 11402194--11402236 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
11402184 GGATTTTGGT
*
11402194 AAATTATAT-TTAGTC
1 AAATTATATATGAGTC
*
11402209 AAATTTTATATGAGTC
1 AAATTATATATGAGTC
11402225 AAATTCATATAT
1 AAATT-ATATAT
11402237 ATTAATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
15 8 0.35
16 10 0.43
17 5 0.22
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (16 bp):
AAATTATATATGAGTC
Found at i:11404613 original size:20 final size:21
Alignment explanation
Indices: 11404580--11404620 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
11404570 TTGACACAAC
11404580 TTTTAGGGCATTTT-ATTTTA
1 TTTTAGGGCATTTTCATTTTA
**
11404600 TTTTAGGGTGTTTTCATTTTA
1 TTTTAGGGCATTTTCATTTTA
11404621 GTCAGCCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.17, C:0.05, G:0.17, T:0.61
Consensus pattern (21 bp):
TTTTAGGGCATTTTCATTTTA
Found at i:11406098 original size:38 final size:40
Alignment explanation
Indices: 11406025--11406112 Score: 135
Period size: 38 Copynumber: 2.2 Consensus size: 40
11406015 TAAAAAATAT
*
11406025 TTATATTAAAAACACTACCATAAATATAATAAATATTTTA
1 TTATATTAAAAACACTACAATAAATATAATAAATATTTTA
*
11406065 TTATATTAAAAACAC-A-AATAAATATAATGAATATTTTA
1 TTATATTAAAAACACTACAATAAATATAATAAATATTTTA
*
11406103 TTGTATTAAA
1 TTATATTAAA
11406113 TGTAATTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 29 0.64
39 1 0.02
40 15 0.33
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (40 bp):
TTATATTAAAAACACTACAATAAATATAATAAATATTTTA
Found at i:11408196 original size:23 final size:23
Alignment explanation
Indices: 11408153--11408196 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
11408143 TAATACGTTG
* *
11408153 TTTTATTTATTATCTATTTTAGA
1 TTTTATATATTATCTAATTTAGA
*
11408176 TTTTATATATTATTTAATTTA
1 TTTTATATATTATCTAATTTA
11408197 AATTATATCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (23 bp):
TTTTATATATTATCTAATTTAGA
Found at i:11408682 original size:13 final size:13
Alignment explanation
Indices: 11408664--11408706 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
11408654 TCTTTTTACC
*
11408664 ATTTACTATTATT
1 ATTTACTATTTTT
11408677 ATTTACATATTTTT
1 ATTTAC-TATTTTT
11408691 ATTGTA-TATTTTT
1 ATT-TACTATTTTT
11408704 ATT
1 ATT
11408707 ATTATTAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 16 0.59
14 9 0.33
15 2 0.07
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (13 bp):
ATTTACTATTTTT
Found at i:11410112 original size:21 final size:20
Alignment explanation
Indices: 11410086--11410128 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
11410076 ATCCTATAAG
*
11410086 AAATTATTAATAATAATACTT
1 AAATTATAAATAATAATA-TT
*
11410107 AAATTATAAATTATAATATT
1 AAATTATAAATAATAATATT
11410127 AA
1 AA
11410129 TATTCAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATTATAAATAATAATATT
Found at i:11410137 original size:27 final size:28
Alignment explanation
Indices: 11410086--11410142 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
11410076 ATCCTATAAG
*
11410086 AAATTATTAATAATAATACTTAAATTAT
1 AAATTATTAATAATAATACTTAAATCAT
*
11410114 AAATTA-TAATATTAATA-TTCAAATCAT
1 AAATTATTAATAATAATACTT-AAATCAT
11410141 AA
1 AA
11410143 TGAATTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 2 0.08
27 18 0.69
28 6 0.23
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.40
Consensus pattern (28 bp):
AAATTATTAATAATAATACTTAAATCAT
Found at i:11410179 original size:15 final size:15
Alignment explanation
Indices: 11410159--11410188 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11410149 TTTATATATT
*
11410159 TTTTAATATTAAATA
1 TTTTAAAATTAAATA
11410174 TTTTAAAATTAAATA
1 TTTTAAAATTAAATA
11410189 AAATTGATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTTAAAATTAAATA
Found at i:11410359 original size:21 final size:21
Alignment explanation
Indices: 11410335--11410398 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
11410325 ATACAAGTAG
11410335 TAAATATAATTATTTTTTTAA
1 TAAATATAATTATTTTTTTAA
* *
11410356 TAAA-ACTAAATATTTATTTTTA
1 TAAATA-TAATTATTT-TTTTAA
* *
11410378 -AAATATTATTAATTTTTTAA
1 TAAATATAATTATTTTTTTAA
11410398 T
1 T
11410399 TTTAAACTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
20 6 0.18
21 21 0.64
22 6 0.18
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (21 bp):
TAAATATAATTATTTTTTTAA
Found at i:11411167 original size:10 final size:10
Alignment explanation
Indices: 11411129--11411188 Score: 50
Period size: 10 Copynumber: 5.6 Consensus size: 10
11411119 TGGTGCTATT
11411129 AAAATTTAGAA
1 AAAATTTAG-A
*
11411140 AAAATAATA-A
1 AAAAT-TTAGA
11411150 ACAAATTTAGA
1 A-AAATTTAGA
*
11411161 AAAATTTAATAA
1 AAAATTT-A-GA
11411173 AAAATTTAGA
1 AAAATTTAGA
11411183 AAAATT
1 AAAATT
11411189 ATTAAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
10 17 0.43
11 13 0.32
12 10 0.25
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (10 bp):
AAAATTTAGA
Found at i:11411188 original size:22 final size:22
Alignment explanation
Indices: 11411129--11411188 Score: 95
Period size: 22 Copynumber: 2.7 Consensus size: 22
11411119 TGGTGCTATT
*
11411129 AAAATTTAGAAAAA-ATAATAA
1 AAAATTTAGAAAAATTTAATAA
11411150 ACAAATTTAGAAAAATTTAATAA
1 A-AAATTTAGAAAAATTTAATAA
11411173 AAAATTTAGAAAAATT
1 AAAATTTAGAAAAATT
11411189 ATTAAATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
21 1 0.03
22 28 0.78
23 7 0.19
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.28
Consensus pattern (22 bp):
AAAATTTAGAAAAATTTAATAA
Found at i:11413076 original size:24 final size:22
Alignment explanation
Indices: 11413049--11413095 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
11413039 CTCGTACTAC
11413049 TTATTCTAAAACTTGCTTTATATG
1 TTATT-TAAAACTTG-TTTATATG
* *
11413073 TTATTTTAAACTTGTTTTTATG
1 TTATTTAAAACTTGTTTATATG
11413095 T
1 T
11413096 ACTATTGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.38
23 8 0.38
24 5 0.24
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.57
Consensus pattern (22 bp):
TTATTTAAAACTTGTTTATATG
Found at i:11413168 original size:19 final size:20
Alignment explanation
Indices: 11413129--11413175 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
11413119 AAATTGTTAC
*
11413129 TTTATTTTAAACATCTTTTA
1 TTTATTTTAAACAGCTTTTA
*
11413149 TTTATTTTAAA-AGGTTTTA
1 TTTATTTTAAACAGCTTTTA
11413168 -TTATTTTA
1 TTTATTTTA
11413176 TTCTAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.32
19 6 0.24
20 11 0.44
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (20 bp):
TTTATTTTAAACAGCTTTTA
Found at i:11413409 original size:62 final size:62
Alignment explanation
Indices: 11413342--11413466 Score: 223
Period size: 62 Copynumber: 2.0 Consensus size: 62
11413332 TTTATCATCC
* * *
11413342 TAAAATTTTTTTACATCTTATTTATCTTGATTTGCTTTATATCTTTTTATCATTTAATTCAT
1 TAAAATTTGTTTACATCTTATTTATCTTGATTTGCATTATACCTTTTTATCATTTAATTCAT
11413404 TAAAATTTGTTTACATCTTATTTATCTTGATTTGCATTATACCTTTTTATCATTTAATTCAT
1 TAAAATTTGTTTACATCTTATTTATCTTGATTTGCATTATACCTTTTTATCATTTAATTCAT
11413466 T
1 T
11413467 CTCTTATTTG
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.26, C:0.12, G:0.04, T:0.58
Consensus pattern (62 bp):
TAAAATTTGTTTACATCTTATTTATCTTGATTTGCATTATACCTTTTTATCATTTAATTCAT
Found at i:11413442 original size:37 final size:37
Alignment explanation
Indices: 11413371--11413442 Score: 85
Period size: 37 Copynumber: 1.9 Consensus size: 37
11413361 ATTTATCTTG
* *
11413371 ATTTGCTTTATATCTTTTTATCATTTAATTCATTAAA
1 ATTTGCTTTACATCTTTTTATCATTGAATTCATTAAA
*
11413408 ATTTG-TTTACATCTTATTTATC-TTGATTTGCATTA
1 ATTTGCTTTACATCTT-TTTATCATTGAATT-CATTA
11413443 TACCTTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
36 14 0.47
37 16 0.53
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (37 bp):
ATTTGCTTTACATCTTTTTATCATTGAATTCATTAAA
Found at i:11425524 original size:137 final size:137
Alignment explanation
Indices: 11425377--11426012 Score: 932
Period size: 137 Copynumber: 4.6 Consensus size: 137
11425367 GAATAGATCA
11425377 AAAATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACTACAGATCC
1 AAAATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACTACAGATCC
* * *
11425442 TATCTCTCTGAAGTTGCAGTAGAGCAGGTCAAAACAAGCCTTATCT-TCCTGAAGTTGCAGTGGA
66 TATCTCTCTGAAGTTGCAGTAGAGCAGGTCAAAACAAGCCTCATCTCT-CTGAAGTTACAGTAGA
11425506 GCAGACTG
130 GCAGACTG
* *
11425514 AAAATAGCAAATCTTATTTCCCTGAAGTTGAAGTGGAACAAATTGAAGCTATAAACTACAGATCC
1 AAAATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACTACAGATCC
* ** *
11425579 TATCTCTCTGAAGTTGTAGTAGAGCAGGTCAAAATGAGTCTCATCTCTCTGAAGTTACAGTAGAG
66 TATCTCTCTGAAGTTGCAGTAGAGCAGGTCAAAACAAGCCTCATCTCTCTGAAGTTACAGTAGAG
11425644 CAGACTG
131 CAGACTG
* * * *
11425651 AAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTAGAACAGATTGAAGCTATAAATTACAGATCT
1 AAAATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACTACAGATCC
* ** * * * * * ** *
11425716 TATTTCTCTGAAGTTGCAGTAGAATAGATTAAAACAAGCCTTATCTCCCTGAAATTGTAGTGGAG
66 TATCTCTCTGAAGTTGCAGTAGAGCAGGTCAAAACAAGCCTCATCTCTCTGAAGTTACAGTAGAG
11425781 CAGACTG
131 CAGACTG
* *
11425788 AAAATAGCAAATTTTATTTCCTTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACTACAGATCC
1 AAAATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACTACAGATCC
* * *
11425853 TATCTCTCTGAAGTTGTAGTAGAGCAGGTCAAAACGAGTCTCATCTCTCTGAAGTTACAGTAGAG
66 TATCTCTCTGAAGTTGCAGTAGAGCAGGTCAAAACAAGCCTCATCTCTCTGAAGTTACAGTAGAG
*
11425918 CAGGCTG
131 CAGACTG
* * * *
11425925 AAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGGTATAAATTACAGATCT
1 AAAATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACTACAGATCC
* *
11425990 TATTTCTTTGAAGTTGCAGTAGA
66 TATCTCTCTGAAGTTGCAGTAGA
11426013 ATAGATCATG
Statistics
Matches: 438, Mismatches: 60, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
137 437 1.00
138 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (137 bp):
AAAATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACTACAGATCC
TATCTCTCTGAAGTTGCAGTAGAGCAGGTCAAAACAAGCCTCATCTCTCTGAAGTTACAGTAGAG
CAGACTG
Found at i:11425869 original size:274 final size:274
Alignment explanation
Indices: 11425380--11426020 Score: 1111
Period size: 274 Copynumber: 2.3 Consensus size: 274
11425370 TAGATCAAAA
* *
11425380 ATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACTACAGATCCTAT
1 ATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTACAGATCTTAT
* ** * * *
11425445 CTCTCTGAAGTTGCAGTAGAGCAGGTCAAAACAAGCCTTATCTTCCTGAAGTTGCAGTGGAGCAG
66 TTCTCTGAAGTTGCAGTAGAATAGATCAAAACAAGCCTTATCTCCCTGAAATTGCAGTGGAGCAG
11425510 ACTGAAAATAGCAAATCTTATTTCCCTGAAGTTGAAGTGGAACAAATTGAAGCTATAAACTACAG
131 ACTGAAAATAGCAAATCTTATTTCCCTGAAGTTGAAGTGGAACAAATTGAAGCTATAAACTACAG
*
11425575 ATCCTATCTCTCTGAAGTTGTAGTAGAGCAGGTCAAAATGAGTCTCATCTCTCTGAAGTTACAGT
196 ATCCTATCTCTCTGAAGTTGTAGTAGAGCAGGTCAAAACGAGTCTCATCTCTCTGAAGTTACAGT
11425640 AGAGCAGACTGAAG
261 AGAGCAGACTGAAG
*
11425654 ATAGCAAATCTTATTTCCCTGAAGTTGCAGTAGAACAGATTGAAGCTATAAATTACAGATCTTAT
1 ATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTACAGATCTTAT
* *
11425719 TTCTCTGAAGTTGCAGTAGAATAGATTAAAACAAGCCTTATCTCCCTGAAATTGTAGTGGAGCAG
66 TTCTCTGAAGTTGCAGTAGAATAGATCAAAACAAGCCTTATCTCCCTGAAATTGCAGTGGAGCAG
* * * *
11425784 ACTGAAAATAGCAAATTTTATTTCCTTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACTACAG
131 ACTGAAAATAGCAAATCTTATTTCCCTGAAGTTGAAGTGGAACAAATTGAAGCTATAAACTACAG
11425849 ATCCTATCTCTCTGAAGTTGTAGTAGAGCAGGTCAAAACGAGTCTCATCTCTCTGAAGTTACAGT
196 ATCCTATCTCTCTGAAGTTGTAGTAGAGCAGGTCAAAACGAGTCTCATCTCTCTGAAGTTACAGT
*
11425914 AGAGCAGGCTGAAG
261 AGAGCAGACTGAAG
*
11425928 ATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGGTATAAATTACAGATCTTAT
1 ATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTACAGATCTTAT
*
11425993 TTCTTTGAAGTTGCAGTAGAATAGATCA
66 TTCTCTGAAGTTGCAGTAGAATAGATCA
11426021 TGTAACGCCC
Statistics
Matches: 346, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
274 346 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (274 bp):
ATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTACAGATCTTAT
TTCTCTGAAGTTGCAGTAGAATAGATCAAAACAAGCCTTATCTCCCTGAAATTGCAGTGGAGCAG
ACTGAAAATAGCAAATCTTATTTCCCTGAAGTTGAAGTGGAACAAATTGAAGCTATAAACTACAG
ATCCTATCTCTCTGAAGTTGTAGTAGAGCAGGTCAAAACGAGTCTCATCTCTCTGAAGTTACAGT
AGAGCAGACTGAAG
Found at i:11426328 original size:26 final size:26
Alignment explanation
Indices: 11426291--11426426 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
11426281 TGATACAAAT
* *
11426291 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11426317 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
11426343 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
*
11426369 TGATAATGGATTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11426395 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
11426421 TGATAA
1 TGATAA
11426427 GAATATCATG
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 102 1.00
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:11427930 original size:26 final size:26
Alignment explanation
Indices: 11427900--11427952 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
11427890 TTTATAGTTT
11427900 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
11427926 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
11427952 T
1 T
11427953 GCATGTTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:11428459 original size:135 final size:135
Alignment explanation
Indices: 11428201--11428483 Score: 496
Period size: 134 Copynumber: 2.1 Consensus size: 135
11428191 AGTAGTCTCC
11428201 CCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
1 CCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
* *
11428266 GTTATCTGAATAAGGGGCTAAGGCCAGTTTATTGTAATCTGAAAAGGGCTTTGGCCCAGCATCAC
66 GTTATCTGAATAAGGGGCTAAGGCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGCACCAC
11428331 TGTTA
131 TGTTA
*
11428336 CCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
1 CCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
*
11428400 GTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCA
66 GTTATCTGAATAAGGGGCTAAGG-CCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGCACCA
11428465 CTGTTA
130 CTGTTA
*
11428471 CCTGAATGGGCTT
1 CC-AAATGGGCTT
11428484 AGGCCCAATG
Statistics
Matches: 141, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
134 67 0.48
135 65 0.46
136 9 0.06
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (135 bp):
CCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACT
GTTATCTGAATAAGGGGCTAAGGCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGCACCAC
TGTTA
Found at i:11432204 original size:26 final size:26
Alignment explanation
Indices: 11432167--11432301 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
11432157 TGATACAAAT
*
11432167 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
11432193 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
11432219 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
11432245 TGATAAT-GGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
11432270 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
11432296 TGATAA
1 TGATAA
11432302 GAATATCATG
Statistics
Matches: 103, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
25 24 0.23
26 79 0.77
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:11432282 original size:51 final size:52
Alignment explanation
Indices: 11432167--11432301 Score: 245
Period size: 51 Copynumber: 2.6 Consensus size: 52
11432157 TGATACAAAT
11432167 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
11432219 TGATAATAGGTTAGGTAAATGTTCCATGATAAT-GGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
* *
11432270 TGATAATGGGTTAGGTAAATGTTTCATGATAA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAA
11432302 GAATATCATG
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
51 48 0.59
52 33 0.41
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.37
Consensus pattern (52 bp):
TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
Found at i:11433809 original size:25 final size:25
Alignment explanation
Indices: 11433780--11433828 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
11433770 ATAGTTTTAC
11433780 CCCTAGGAGATAAATT-ACCGAAATA
1 CCCTAGG-GATAAATTGACCGAAATA
* *
11433805 CCCTAGGGTTAAATTGACCTAAAT
1 CCCTAGGGATAAATTGACCGAAAT
11433829 GCATGTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (25 bp):
CCCTAGGGATAAATTGACCGAAATA
Found at i:11434349 original size:135 final size:138
Alignment explanation
Indices: 11434079--11434360 Score: 509
Period size: 135 Copynumber: 2.1 Consensus size: 138
11434069 TAGTCTCCCC
11434079 AAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGT
1 AAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGT
* *
11434144 TATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTTTGGCCCAGTATCACT
66 TATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACT
11434209 GTTACC-G
131 GTTACCTG
*
11434216 AAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGT
1 AAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGT
11434280 TATCTGAATAA-GGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACT
66 TATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACT
11434344 GTTACCTG
131 GTTACCTG
11434352 -AATGGGCTT
1 AAATGGGCTT
11434361 AGGCCCAATG
Statistics
Matches: 141, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
135 66 0.47
136 58 0.41
137 17 0.12
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.33
Consensus pattern (138 bp):
AAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATACTGT
TATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACCACT
GTTACCTG
Found at i:11435389 original size:140 final size:136
Alignment explanation
Indices: 11435081--11435354 Score: 334
Period size: 136 Copynumber: 2.0 Consensus size: 136
11435071 TACAGATCAA
* * * * * *
11435081 AACAAGTCTTATCTCCCTAAAGTTGTAATGGAGTAGACTGAAGATAGTGAATCTTGTCTCCTTGA
1 AACAAGCCTAATCTCCCTAAAGTTGCAATGGAGTAGACTGAAGATAGCGAATCTTATCTCCATGA
* * * **
11435146 AGTTGCAGTGGAGCAGATTGAAGAAACCATAAACCTTATCTCCTTGAAGTTGCAGTGGAGCAGGT
66 AGTTGCAGTGGAGCAAATTGAAGAAACCACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC
11435211 TGAAAT
131 TGAAAT
* * * * *
11435217 TACAAGTCTAATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATAGCGAATTTTATCTCCATGA
1 AACAAGCCTAATCTCCCTAAAGTTGCAATGGAGTAGACTGAAGATAGCGAATCTTATCTCCATGA
* *
11435282 AGTTGTAGTAGG-GCAAATTGAAGCTACAAATCACAAACCTTATCTCCCTGAAGTTGCAGTGGAG
66 AGTTGCAGT-GGAGCAAATTGAAG----AAACCACAAACCTTATCTCCCTGAAGTTGCAGTGGAG
11435346 CAGACTGAA
126 CAGACTGAA
11435355 GAAAGTAGAC
Statistics
Matches: 117, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
136 74 0.63
137 2 0.02
140 41 0.35
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (136 bp):
AACAAGCCTAATCTCCCTAAAGTTGCAATGGAGTAGACTGAAGATAGCGAATCTTATCTCCATGA
AGTTGCAGTGGAGCAAATTGAAGAAACCACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC
TGAAAT
Found at i:11437323 original size:24 final size:22
Alignment explanation
Indices: 11437296--11437342 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
11437286 CTCGTACTAC
11437296 TTATTCTAAAACTTGCTTTATATG
1 TTATT-TAAAACTTG-TTTATATG
* *
11437320 TTATTTTAAACTTGTTTTTATG
1 TTATTTAAAACTTGTTTATATG
11437342 T
1 T
11437343 ACTATTGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.38
23 8 0.38
24 5 0.24
ACGTcount: A:0.26, C:0.09, G:0.09, T:0.57
Consensus pattern (22 bp):
TTATTTAAAACTTGTTTATATG
Found at i:11437721 original size:62 final size:62
Alignment explanation
Indices: 11437588--11437712 Score: 214
Period size: 62 Copynumber: 2.0 Consensus size: 62
11437578 TTTATCATCC
* * * *
11437588 TAAAATTTTTTTACATCTTATTTATCTTGATTTGCTTTATATCTTTTTATCATTTAATTCAT
1 TAAAATTTGTTTACATCTTACTCATCTTGATTTGCTTTATACCTTTTTATCATTTAATTCAT
11437650 TAAAATTTGTTTACATCTTACTCATCTTGATTTGCTTTATACCTTTTTATCATTTAATTCAT
1 TAAAATTTGTTTACATCTTACTCATCTTGATTTGCTTTATACCTTTTTATCATTTAATTCAT
11437712 T
1 T
11437713 CTTATTTGTC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.26, C:0.14, G:0.04, T:0.57
Consensus pattern (62 bp):
TAAAATTTGTTTACATCTTACTCATCTTGATTTGCTTTATACCTTTTTATCATTTAATTCAT
Found at i:11438673 original size:28 final size:27
Alignment explanation
Indices: 11438601--11438695 Score: 84
Period size: 29 Copynumber: 3.3 Consensus size: 27
11438591 ACATTTTGTG
*
11438601 TAATTTTCTTACGACTTTATAAAATTTTA
1 TAATTTT-TTACGATTTTAT-AAATTTTA
* *
11438630 TAATTTTTTTA-TATTTCTATATATTTTA
1 TAA-TTTTTTACGATTT-TATAAATTTTA
*
11438658 TAATTTTTTACGATTTTTATAAAATTTCA
1 TAATTTTTTACGA-TTTTAT-AAATTTTA
*
11438687 CAATTTTTT
1 TAATTTTTT
11438696 TTATATATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
27 7 0.13
28 17 0.31
29 26 0.48
30 4 0.07
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (27 bp):
TAATTTTTTACGATTTTATAAATTTTA
Found at i:11438675 original size:19 final size:19
Alignment explanation
Indices: 11438653--11438726 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 19
11438643 TTTCTATATA
11438653 TTTTATAATTTTTTACGAT
1 TTTTATAATTTTTTACGAT
** * *
11438672 TTTTATAAAATTTCACAATT
1 TTTTATAATTTTTTACGA-T
* *
11438692 TTTTTTATATATTTTTACGGT
1 TTTTATA-AT-TTTTTACGAT
11438713 TTTTATAATTTTTT
1 TTTTATAATTTTTT
11438727 TTTCTAATTT
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
19 19 0.46
20 9 0.22
21 8 0.20
22 5 0.12
ACGTcount: A:0.27, C:0.05, G:0.04, T:0.64
Consensus pattern (19 bp):
TTTTATAATTTTTTACGAT
Found at i:11438677 original size:57 final size:60
Alignment explanation
Indices: 11438578--11438701 Score: 157
Period size: 57 Copynumber: 2.1 Consensus size: 60
11438568 TTTTATGAAA
* * * *
11438578 TTTATATTTCTTTACATTTTGTGTAATTTTCTTACGACTTTATAAAATTTTATAA-TTTT
1 TTTATATTTCTATACATTTTGTATAATTTTCTTACGACTTTATAAAATTTCACAATTTTT
* *
11438637 TTTATATTTCTATATA-TTT-TATAATTTT-TTACGATTTTTATAAAATTTCACAATTTTT
1 TTTATATTTCTATACATTTTGTATAATTTTCTTACGA-CTTTATAAAATTTCACAATTTTT
11438695 TTTATAT
1 TTTATAT
11438702 ATTTTTACGG
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
56 6 0.11
57 23 0.40
58 14 0.25
59 14 0.25
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.60
Consensus pattern (60 bp):
TTTATATTTCTATACATTTTGTATAATTTTCTTACGACTTTATAAAATTTCACAATTTTT
Found at i:11439274 original size:22 final size:22
Alignment explanation
Indices: 11439249--11439300 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
11439239 TTTCACGGTA
11439249 ATAAAAACGTTTTTTTACAGAT
1 ATAAAAACGTTTTTTTACAGAT
11439271 ATAAAAACGTTTTTTTACAGAT
1 ATAAAAACGTTTTTTTACAGAT
11439293 ATAAAAAC
1 ATAAAAAC
11439301 AGATACACGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.37
Consensus pattern (22 bp):
ATAAAAACGTTTTTTTACAGAT
Done.