Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167827.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_10, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 24162007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 47000 characters in sequence are not A, C, G, or T
File 26 of 131
Found at i:6251652 original size:18 final size:18
Alignment explanation
Indices: 6251583--6251669 Score: 55
Period size: 18 Copynumber: 5.1 Consensus size: 18
6251573 TATTAAATGC
*
6251583 AAAT-AAATAAAAACTAAA
1 AAATAAAATGAAAA-TAAA
* *
6251601 AAATAAAATAAAAACT-TA
1 AAATAAAATGAAAA-TAAA
6251619 AAAT--AATG-AAAT--A
1 AAATAAAATGAAAATAAA
*
6251632 AAATAAACT-AAAATTAAA
1 AAATAAAATGAAAA-TAAA
6251650 AAATAAAATGAAAATAAA
1 AAATAAAATGAAAATAAA
6251668 AA
1 AA
6251670 TGAAAAAGAA
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
13 5 0.09
14 1 0.02
15 8 0.14
16 4 0.07
18 24 0.42
19 15 0.26
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (18 bp):
AAATAAAATGAAAATAAA
Found at i:6251675 original size:18 final size:17
Alignment explanation
Indices: 6251648--6251681 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6251638 ACTAAAATTA
*
6251648 AAAAATAAAATGAAAAT
1 AAAAATAAAAAGAAAAT
6251665 AAAAATGAAAAAGAAAA
1 AAAAAT-AAAAAGAAAA
6251682 ACCTGCAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (17 bp):
AAAAATAAAAAGAAAAT
Found at i:6252530 original size:3 final size:3
Alignment explanation
Indices: 6252522--6252607 Score: 80
Period size: 3 Copynumber: 31.3 Consensus size: 3
6252512 ACTATAGTAC
*
6252522 TAA TAA TAA TAA TAA TAA T-A TAC T-A TAA TAA -AA T-A TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
6252565 T-A TAA AAA TAA TAA TAA -AA AAA TAA T-A TAA TAA TAC TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
6252608 GAAAATTGGT
Statistics
Matches: 68, Mismatches: 7, Indels: 16
0.75 0.08 0.18
Matches are distributed among these distances:
2 15 0.22
3 53 0.78
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:6252551 original size:10 final size:10
Alignment explanation
Indices: 6252524--6252596 Score: 60
Period size: 10 Copynumber: 7.1 Consensus size: 10
6252514 TATAGTACTA
6252524 ATAATAATAAT
1 ATAAT-ATAAT
*
6252535 AATAATATACT
1 -ATAATATAAT
*
6252546 ATAATAAAAT
1 ATAATATAAT
6252556 ATAATATAAT
1 ATAATATAAT
6252566 ATAA-A-AAT
1 ATAATATAAT
* *
6252574 AATAATAAAAAA
1 -ATAAT-ATAAT
6252586 ATAATATAAT
1 ATAATATAAT
6252596 A
1 A
6252597 ATACTAATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
8 3 0.06
9 5 0.10
10 25 0.50
11 10 0.20
12 7 0.14
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (10 bp):
ATAATATAAT
Found at i:6252564 original size:25 final size:27
Alignment explanation
Indices: 6252530--6252613 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 27
6252520 ACTAATAATA
6252530 ATAATAATAATATACT-ATAAT-AAAAT
1 ATAAT-ATAATATACTAATAATAAAAAT
* *
6252556 ATAATATAATATAAAAATAATAATAAAAAA
1 ATAATATAATAT---ACTAATAATAAAAAT
*
6252586 ATAATATAATAATACTAATAATGAAAAT
1 ATAATATAAT-ATACTAATAATAAAAAT
6252614 TGGTTTGATT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
25 7 0.15
26 5 0.11
28 14 0.30
29 5 0.11
30 14 0.30
31 2 0.04
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.31
Consensus pattern (27 bp):
ATAATATAATATACTAATAATAAAAAT
Found at i:6252971 original size:15 final size:14
Alignment explanation
Indices: 6252953--6252988 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
6252943 TAAATAATTT
6252953 AAAAAAAATAAAATG
1 AAAAAAAA-AAAATG
6252968 AAAATAAAAAAAATG
1 AAAA-AAAAAAAATG
6252983 AAAAAA
1 AAAAAA
6252989 TGTGAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.10
15 14 0.70
16 4 0.20
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (14 bp):
AAAAAAAAAAAATG
Found at i:6253736 original size:3 final size:3
Alignment explanation
Indices: 6253728--6253763 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
6253718 TGGATTAATC
6253728 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6253764 AAAAAAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:6257401 original size:7 final size:7
Alignment explanation
Indices: 6257391--6257431 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
6257381 AATTAATTTC
6257391 TAAAAAA
1 TAAAAAA
*
6257398 TAAAAAT
1 TAAAAAA
6257405 TAAAAAA
1 TAAAAAA
6257412 TAAAAAGA
1 TAAAAA-A
6257420 -AAAAAA
1 TAAAAAA
6257426 TAAAAA
1 TAAAAA
6257432 TAATATGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 1 0.03
7 28 0.93
8 1 0.03
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:6257410 original size:14 final size:14
Alignment explanation
Indices: 6257391--6257432 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
6257381 AATTAATTTC
6257391 TAAAAAATAAAAAT
1 TAAAAAATAAAAAT
*
6257405 TAAAAAATAAAAAG
1 TAAAAAATAAAAAT
*
6257419 AAAAAAATAAAAAT
1 TAAAAAATAAAAAT
6257433 AATATGTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (14 bp):
TAAAAAATAAAAAT
Found at i:6264759 original size:47 final size:45
Alignment explanation
Indices: 6264705--6264887 Score: 125
Period size: 46 Copynumber: 4.0 Consensus size: 45
6264695 AGATAAGCCT
*
6264705 TTCAATTTAATTTTTAAAAGTTGTTAAG-CTTTTGGTGAGAGGAACCC
1 TTCAATTTAA-TTTTAAAA-TTGTTAAGTC-TTTGATGAGAGGAACCC
* * **
6264752 TTCAATTTAACTTTTAAAATCGTTGAGTCTTTGATGAGAGGAGTCC
1 TTCAATTTAA-TTTTAAAATTGTTAAGTCTTTGATGAGAGGAACCC
* * * * * * * *
6264798 TTTAGTTTAATTTTAAAAATTGTTCAGCCTCTGATGAGAAGAGCAC
1 TTCAATTTAATTTT-AAAATTGTTAAGTCTTTGATGAGAGGAACCC
* * * * * * *
6264844 TTTAGTTTAATTTTTAAATTGGTTTAGCCTCTAATGAGAGGAAC
1 TTCAATTTAATTTTAAAATT-GTTAAGTCTTTGATGAGAGGAAC
6264888 TTATGGATTT
Statistics
Matches: 113, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
45 9 0.08
46 85 0.75
47 19 0.17
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (45 bp):
TTCAATTTAATTTTAAAATTGTTAAGTCTTTGATGAGAGGAACCC
Found at i:6264807 original size:46 final size:45
Alignment explanation
Indices: 6264757--6264882 Score: 128
Period size: 46 Copynumber: 2.7 Consensus size: 45
6264747 AACCCTTCAA
* * * *
6264757 TTTAACTTTTAAAATCGTTGAGTCTTTGATGAGAGGAGTC-CTTTAG
1 TTTAA-TTTTAAAATCGTTCAGCCTCTGATGAGAAGAG-CACTTTAG
*
6264803 TTTAATTTTAAAAATTGTTCAGCCTCTGATGAGAAGAGCACTTTAG
1 TTTAATTTT-AAAATCGTTCAGCCTCTGATGAGAAGAGCACTTTAG
* * * *
6264849 TTTAATTTTTAAATTGGTTTAGCCTCTAATGAGA
1 TTTAA-TTTTAAAATCGTTCAGCCTCTGATGAGA
6264883 GGAACTTATG
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
45 5 0.07
46 59 0.87
47 4 0.06
ACGTcount: A:0.29, C:0.11, G:0.18, T:0.41
Consensus pattern (45 bp):
TTTAATTTTAAAATCGTTCAGCCTCTGATGAGAAGAGCACTTTAG
Found at i:6265819 original size:13 final size:13
Alignment explanation
Indices: 6265801--6265830 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6265791 AACCTGTTAA
6265801 CAAAAAAAAAAAC
1 CAAAAAAAAAAAC
*
6265814 CAAAAAAAAAAAT
1 CAAAAAAAAAAAC
6265827 CAAA
1 CAAA
6265831 TCCCCTAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.83, C:0.13, G:0.00, T:0.03
Consensus pattern (13 bp):
CAAAAAAAAAAAC
Found at i:6266820 original size:22 final size:22
Alignment explanation
Indices: 6266779--6266820 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
6266769 AGTGTATTAA
* *
6266779 AGTATTTATAAAATTTTTTTAT
1 AGTATTTATAAAAATATTTTAT
6266801 AGTATTTATAAAAATATTTT
1 AGTATTTATAAAAATATTTT
6266821 CAATAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
AGTATTTATAAAAATATTTTAT
Found at i:6267950 original size:22 final size:21
Alignment explanation
Indices: 6267925--6267971 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
6267915 ATTTAAATTA
6267925 TTTAAAAAATAAAAAATATAAT
1 TTTAAAAAATAAAAAA-ATAAT
** *
6267947 TTTAATTAATAAATAAATAAT
1 TTTAAAAAATAAAAAAATAAT
6267968 TTTA
1 TTTA
6267972 TTTTAATTCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTAAAAAATAAAAAAATAAT
Found at i:6267955 original size:26 final size:26
Alignment explanation
Indices: 6267926--6267979 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
6267916 TTTAAATTAT
6267926 TTAAAAAATAAAAAATATAATTTTAA
1 TTAAAAAATAAAAAATATAATTTTAA
* * * *
6267952 TTAATAAATAAATAATTTTATTTTAA
1 TTAAAAAATAAAAAATATAATTTTAA
6267978 TT
1 TT
6267980 CTTGTATACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
TTAAAAAATAAAAAATATAATTTTAA
Found at i:6269035 original size:20 final size:20
Alignment explanation
Indices: 6269010--6269058 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
6269000 ATTAATTTAA
*
6269010 ATAAACAATCTTAAAAAAAT
1 ATAAACAATCTCAAAAAAAT
* *
6269030 ATAAACAAACTCAAATAAAT
1 ATAAACAATCTCAAAAAAAT
6269050 ATAAACAAT
1 ATAAACAAT
6269059 TTTTAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.65, C:0.12, G:0.00, T:0.22
Consensus pattern (20 bp):
ATAAACAATCTCAAAAAAAT
Found at i:6269139 original size:11 final size:11
Alignment explanation
Indices: 6269125--6269156 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
6269115 AATGAACAAC
6269125 AAATAAATAAT
1 AAATAAATAAT
6269136 AAATAAATAAT
1 AAATAAATAAT
6269147 AAATAAATAA
1 AAATAAATAA
6269157 ATTTTAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:6269143 original size:15 final size:15
Alignment explanation
Indices: 6269133--6269169 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
6269123 ACAAATAAAT
6269133 AATAAATAAATAATA
1 AATAAATAAATAATA
**
6269148 AATAAATAAATTTTA
1 AATAAATAAATAATA
6269163 AATAAAT
1 AATAAAT
6269170 TTTAAACGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAAATAAATAATA
Found at i:6269164 original size:11 final size:11
Alignment explanation
Indices: 6269150--6269175 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6269140 AAATAATAAA
6269150 TAAATAAATTT
1 TAAATAAATTT
6269161 TAAATAAATTT
1 TAAATAAATTT
6269172 TAAA
1 TAAA
6269176 CGAATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAATAAATTT
Found at i:6269169 original size:4 final size:4
Alignment explanation
Indices: 6269125--6269158 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
6269115 AATGAACAAC
6269125 AAAT AAAT -AAT AAAT AAAT -AAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
6269159 TTTAAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 6 0.21
4 22 0.79
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:6270356 original size:23 final size:24
Alignment explanation
Indices: 6270298--6270358 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 24
6270288 ATAAATTACT
6270298 CATATAAATTATAATAAAATATTTAA
1 CATATAAA-T-TAATAAAATATTTAA
*
6270324 CATA-ATATTAAT-AAATATTTAA
1 CATATAAATTAATAAAATATTTAA
6270346 -ATTATAAATTAAT
1 CA-TATAAATTAAT
6270359 TAATTAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
21 1 0.03
22 12 0.39
23 11 0.35
24 1 0.03
25 2 0.06
26 4 0.13
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (24 bp):
CATATAAATTAATAAAATATTTAA
Found at i:6270384 original size:41 final size:41
Alignment explanation
Indices: 6270302--6270385 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 41
6270292 ATTACTCATA
* *
6270302 TAAATTATAATAAAATATTTAACATAATATTAATAAATATT
1 TAAATTATAATAAAATAATTAACATAATATGAATAAATATT
* * * *
6270343 TAAATTATAAATTAATTAATTAATATAATATGAA-AATTATT
1 TAAATTAT-AATAAAATAATTAACATAATATGAATAAATATT
6270384 TA
1 TA
6270386 TTTATTATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
41 16 0.44
42 20 0.56
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (41 bp):
TAAATTATAATAAAATAATTAACATAATATGAATAAATATT
Found at i:6270438 original size:18 final size:17
Alignment explanation
Indices: 6270415--6270462 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
6270405 TATAATTAAT
6270415 TATATTAAAAATAAATGC
1 TATATTAAAAATAAAT-C
** *
6270433 TATATTATTAATAAATT
1 TATATTAAAAATAAATC
*
6270450 TATATTGAAAATA
1 TATATTAAAAATA
6270463 TCATATAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (17 bp):
TATATTAAAAATAAATC
Found at i:6271211 original size:12 final size:12
Alignment explanation
Indices: 6271186--6271221 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
6271176 TAATTAATTA
*
6271186 AATAAAATAGAT
1 AATAAAATAAAT
*
6271198 AATTAAATAAAT
1 AATAAAATAAAT
6271210 AATAAAATAAAT
1 AATAAAATAAAT
6271222 TAGTATTACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (12 bp):
AATAAAATAAAT
Found at i:6273989 original size:21 final size:21
Alignment explanation
Indices: 6273963--6274004 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
6273953 AAAAAACTTG
*
6273963 ATTTGAATTCTTTTGAGAGAT
1 ATTTGAATTCTTTTGACAGAT
6273984 ATTTGAATTCTTTTGACAGAT
1 ATTTGAATTCTTTTGACAGAT
6274005 GTTTTATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.48
Consensus pattern (21 bp):
ATTTGAATTCTTTTGACAGAT
Found at i:6274497 original size:2 final size:2
Alignment explanation
Indices: 6274490--6274518 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6274480 GGCCCAAATT
6274490 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 T
6274519 TAGATTCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6274594 original size:27 final size:28
Alignment explanation
Indices: 6274555--6274607 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
6274545 TAAATTAGAA
6274555 CAAAAAATAAAAAA-ACAAAAAAAAAGG
1 CAAAAAATAAAAAACACAAAAAAAAAGG
* *
6274582 CAAAATATCAAAAACACAAAAAAAAA
1 CAAAAAATAAAAAACACAAAAAAAAA
6274608 AAAAAATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 12 0.52
28 11 0.48
ACGTcount: A:0.79, C:0.11, G:0.04, T:0.06
Consensus pattern (28 bp):
CAAAAAATAAAAAACACAAAAAAAAAGG
Found at i:6274603 original size:28 final size:27
Alignment explanation
Indices: 6274555--6274607 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
6274545 TAAATTAGAA
6274555 CAAAAAATAAAAAAACAAAAAAAAAGG
1 CAAAAAATAAAAAAACAAAAAAAAAGG
* *
6274582 CAAAATATCAAAAACACAAAAAAAAA
1 CAAAAAAT-AAAAAAACAAAAAAAAA
6274608 AAAAAATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 7 0.30
28 16 0.70
ACGTcount: A:0.79, C:0.11, G:0.04, T:0.06
Consensus pattern (27 bp):
CAAAAAATAAAAAAACAAAAAAAAAGG
Found at i:6276787 original size:59 final size:58
Alignment explanation
Indices: 6276506--6276887 Score: 425
Period size: 58 Copynumber: 6.4 Consensus size: 58
6276496 GCTTTTGTAC
* *
6276506 AAGGAAAAATTGATACTTTCAAC-TTTTCTCCAAAATA-TTTTTTTGAAAACTTTAATTTT
1 AAGG-AAAATTGATACTTTCAACTTTTTCT-CAAAAAACCTTTTTTGAAAA-TTTAATTTT
* * * *
6276565 GAGAAAAATTGATACTTTTAA-TTTTTCCTCAAAAAAACCTTTTTTTGAAAATTTATTTTT
1 AAGGAAAATTGATACTTTCAACTTTTT-CTC-AAAAAACC-TTTTTTGAAAATTTAATTTT
* * *
6276625 AAGGAAAAGTGATACTTTCAACTTTTCCTAAAAAAAAAAACCTTTTTT-AGAAATTT-ATCTTT
1 AAGGAAAATTGATACTTTCAACTTTTTCT----CAAAAAACCTTTTTTGA-AAATTTAAT-TTT
* * ** *
6276687 AAGAAAAATTGATACTTTCAACTTTTT-TCCAAAAATATTTTTTGAAAACTTTAATTTC
1 AAGGAAAATTGATACTTTCAACTTTTTCTCAAAAAACCTTTTTTGAAAA-TTTAATTTT
* *
6276745 AAGGAAAATTGATACTTTTAACTTTTTCTCAAAAAACCTTTTTTGAAAATTTATTTTT
1 AAGGAAAATTGATACTTTCAACTTTTTCTCAAAAAACCTTTTTTGAAAATTTAATTTT
* * *
6276803 AAAGAAAATTGATACTTTCAACTTTTTCTCAAAAAAATCTTTTTTGAAAATTTATTTTT
1 AAGGAAAATTGATACTTTCAACTTTTTCTC-AAAAAACCTTTTTTGAAAATTTAATTTT
6276862 AAGGAAAATTGATACTTTCAACTTTT
1 AAGGAAAATTGATACTTTCAACTTTT
6276888 CCCTAAAAAT
Statistics
Matches: 274, Mismatches: 32, Indels: 34
0.81 0.09 0.10
Matches are distributed among these distances:
57 14 0.05
58 87 0.32
59 81 0.30
60 27 0.10
61 18 0.07
62 39 0.14
63 8 0.03
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.43
Consensus pattern (58 bp):
AAGGAAAATTGATACTTTCAACTTTTTCTCAAAAAACCTTTTTTGAAAATTTAATTTT
Found at i:6276896 original size:59 final size:58
Alignment explanation
Indices: 6276506--6276896 Score: 425
Period size: 59 Copynumber: 6.6 Consensus size: 58
6276496 GCTTTTGTAC
* * * *
6276506 AAGGAAAAATTGATACTTTCAACTTTT-CTCCAAAATA-TTTTTTTGAAAACTTTAATTTT
1 AAGG-AAAATTGATACTTTCAACTTTTCCT-AAAAAAACCTTTTTTGAAAA-TTTATTTTT
* * * *
6276565 GAGAAAAATTGATACTTTTAATTTTTCCTCAAAAAAACCTTTTTTTGAAAATTTATTTTT
1 AAGGAAAATTGATACTTTCAACTTTTCCT-AAAAAAACC-TTTTTTGAAAATTTATTTTT
* *
6276625 AAGGAAAAGTGATACTTTCAACTTTTCCTAAAAAAAAAAACCTTTTTT-AGAAATTTATCTTT
1 AAGGAAAATTGATACTTTCAACTTTTCCT----AAAAAAACCTTTTTTGA-AAATTTATTTTT
* * * *
6276687 AAGAAAAATTGATACTTTCAACTTTTTTCC-AAAAATA--TTTTTTGAAAACTTTAATTTC
1 AAGGAAAATTGATACTTTCAAC--TTTTCCTAAAAAAACCTTTTTTGAAAA-TTTATTTTT
* * *
6276745 AAGGAAAATTGATACTTTTAACTTTTTCTCAAAAAACCTTTTTTGAAAATTTATTTTT
1 AAGGAAAATTGATACTTTCAACTTTTCCTAAAAAAACCTTTTTTGAAAATTTATTTTT
* * *
6276803 AAAGAAAATTGATACTTTCAACTTTTTCTCAAAAAAATCTTTTTTGAAAATTTATTTTT
1 AAGGAAAATTGATACTTTCAACTTTTCCT-AAAAAAACCTTTTTTGAAAATTTATTTTT
6276862 AAGGAAAATTGATACTTTCAACTTTTCCCTAAAAA
1 AAGGAAAATTGATACTTTCAACTTTT-CCTAAAAA
6276897 TATATATTTT
Statistics
Matches: 282, Mismatches: 34, Indels: 32
0.81 0.10 0.09
Matches are distributed among these distances:
56 5 0.02
57 14 0.05
58 81 0.29
59 84 0.30
60 34 0.12
61 12 0.04
62 37 0.13
63 9 0.03
64 6 0.02
ACGTcount: A:0.39, C:0.12, G:0.07, T:0.43
Consensus pattern (58 bp):
AAGGAAAATTGATACTTTCAACTTTTCCTAAAAAAACCTTTTTTGAAAATTTATTTTT
Found at i:6276951 original size:6 final size:6
Alignment explanation
Indices: 6276923--6276989 Score: 61
Period size: 6 Copynumber: 11.5 Consensus size: 6
6276913 TTATTTAAAG
* *
6276923 AAAAT- AAAATAA TAAAATA AAAATG AAAATA AAAAT- AAAA-A AAAGT-
1 AAAATA AAAAT-A -AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
*
6276969 AAAATA AAGATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAA
6276990 GAATATTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
5 16 0.32
6 28 0.56
7 1 0.02
8 5 0.10
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:6276972 original size:21 final size:21
Alignment explanation
Indices: 6276919--6276984 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 21
6276909 AATTTTATTT
6276919 AAAG-AAAATAAAATAATAAAATA
1 AAAGTAAAAT-AAA-AATAAAA-A
*
6276942 AAAATGAAAATAAAAATAAAAA
1 AAAGT-AAAATAAAAATAAAAA
*
6276964 AAAGTAAAATAAAGATAAAAA
1 AAAGTAAAATAAAAATAAAAA
6276985 TAAAAGAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
21 15 0.39
22 5 0.13
23 10 0.26
24 3 0.08
25 5 0.13
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (21 bp):
AAAGTAAAATAAAAATAAAAA
Found at i:6276976 original size:33 final size:31
Alignment explanation
Indices: 6276923--6276989 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 31
6276913 TTATTTAAAG
* *
6276923 AAAATAAAATAATAAAATAAAAATGAAAATA
1 AAAATAAAAAAATAAAATAAAAATAAAAATA
*
6276954 AAAATAAAAAAAAGTAAAATAAAGATAAAAATA
1 AAAAT-AAAAAAA-TAAAATAAAAATAAAAATA
6276987 AAA
1 AAA
6276990 GAATATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 5 0.16
32 6 0.19
33 20 0.65
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.16
Consensus pattern (31 bp):
AAAATAAAAAAATAAAATAAAAATAAAAATA
Found at i:6277018 original size:3 final size:3
Alignment explanation
Indices: 6277006--6277046 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
6276996 TAAACAATTC
*
6277006 TAA T-A TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6277047 ATAAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:6277051 original size:4 final size:4
Alignment explanation
Indices: 6277042--6277066 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
6277032 TAATAATAAT
6277042 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
6277067 CAAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:6277445 original size:27 final size:27
Alignment explanation
Indices: 6277409--6277473 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
6277399 ATAACAAAAA
*
6277409 AATAGATAAATAA-AAGAAATAGATAAAT
1 AATA-ATAAATAATAA-AAACAGATAAAT
*
6277437 AATAATAAATAATAAAAGCAGATAAAT
1 AATAATAAATAATAAAAACAGATAAAT
6277464 AATAA-AAATA
1 AATAATAAATA
6277474 TTAATAGATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 5 0.15
27 23 0.68
28 6 0.18
ACGTcount: A:0.69, C:0.02, G:0.08, T:0.22
Consensus pattern (27 bp):
AATAATAAATAATAAAAACAGATAAAT
Found at i:6277487 original size:17 final size:17
Alignment explanation
Indices: 6277372--6277507 Score: 80
Period size: 17 Copynumber: 8.5 Consensus size: 17
6277362 AAAATTAATC
6277372 AAAATA-AAA-AGAT-A
1 AAAATATAAATAGATAA
* *
6277386 AATATATTAATAGATAA
1 AAAATATAAATAGATAA
*
6277403 CAAA-A-AAATAGATAA
1 AAAATATAAATAGATAA
*
6277418 ATAAA-AGAAATAGATAA
1 A-AAATATAAATAGATAA
*
6277435 ATAATAATAAATA-ATAA
1 AAAAT-ATAAATAGATAA
* *
6277452 AAGCAGATAAATA-AT-A
1 AA-AATATAAATAGATAA
*
6277468 AAAATATTAATAGATAA
1 AAAATATAAATAGATAA
6277485 AAAA-ATAAA-A-ATAA
1 AAAATATAAATAGATAA
6277499 AAATATATA
1 AAA-ATATA
6277508 TTAAATAATG
Statistics
Matches: 95, Mismatches: 15, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
14 12 0.13
15 20 0.21
16 23 0.24
17 33 0.35
18 7 0.07
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.23
Consensus pattern (17 bp):
AAAATATAAATAGATAA
Found at i:6277500 original size:5 final size:6
Alignment explanation
Indices: 6277458--6277532 Score: 53
Period size: 6 Copynumber: 12.0 Consensus size: 6
6277448 ATAAAAGCAG
** * *
6277458 ATAAATA ATAAAA ATATTA ATAGATA A-AAAA ATAAAA ATAAAA ATATATA
1 ATAAA-A ATAAAA ATAAAA ATA-AAA ATAAAA ATAAAA ATAAAA ATA-AAA
* *
6277508 TTAAATA ATGAAA ATAAAA ATAAAA
1 ATAAA-A ATAAAA ATAAAA ATAAAA
6277533 GCCCATTGGG
Statistics
Matches: 54, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
5 3 0.06
6 35 0.65
7 16 0.30
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (6 bp):
ATAAAA
Found at i:6277503 original size:24 final size:24
Alignment explanation
Indices: 6277425--6277529 Score: 86
Period size: 24 Copynumber: 4.2 Consensus size: 24
6277415 TAAATAAAAG
6277425 AAATAGATAAATAATAATAAATAATAA
1 AAATAGATAAA-AA-AATAAA-AATAA
** * *
6277452 AAGCAGAT-AAATAATAAAAATAT
1 AAATAGATAAAAAAATAAAAATAA
*
6277475 TAATAGATAAAAAAATAAAAATAA
1 AAATAGATAAAAAAATAAAAATAA
* * *
6277499 AAATATATATTAAATAATGAAAATAA
1 AAATAGATA--AAAAAATAAAAATAA
6277525 AAATA
1 AAATA
6277530 AAAGCCCATT
Statistics
Matches: 62, Mismatches: 13, Indels: 7
0.76 0.16 0.09
Matches are distributed among these distances:
23 9 0.15
24 26 0.42
25 1 0.02
26 20 0.32
27 6 0.10
ACGTcount: A:0.70, C:0.01, G:0.05, T:0.25
Consensus pattern (24 bp):
AAATAGATAAAAAAATAAAAATAA
Found at i:6277527 original size:32 final size:30
Alignment explanation
Indices: 6277414--6277532 Score: 100
Period size: 30 Copynumber: 3.8 Consensus size: 30
6277404 AAAAAAATAG
*
6277414 ATAAATAAAAGAAATAGATAAATAATAATA--A
1 ATAAATAAAA-AAATA-A-AAATAAAAATATTA
*
6277445 AT-AATAAAAGCAGATAAATAATAAAAATATTA
1 ATAAATAAAA--AAATAAA-AATAAAAATATTA
*
6277477 ATAGATAAAAAAATAAAAATAAAAATATATA
1 ATAAATAAAAAAATAAAAATAAAAATAT-TA
* *
6277508 TTAAATAATGAAAATAAAAATAAAA
1 ATAAATAA-AAAAATAAAAATAAAA
6277533 GCCCATTGGG
Statistics
Matches: 73, Mismatches: 8, Indels: 13
0.78 0.09 0.14
Matches are distributed among these distances:
29 1 0.01
30 28 0.38
31 20 0.27
32 18 0.25
33 6 0.08
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.24
Consensus pattern (30 bp):
ATAAATAAAAAAATAAAAATAAAAATATTA
Found at i:6277801 original size:25 final size:25
Alignment explanation
Indices: 6277773--6277820 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
6277763 ATAATTATCC
6277773 AATGATAGAATCTTTA-AAAATTTCA
1 AATGATA-AATCTTTATAAAATTTCA
*
6277798 AATGATAAATTTTTATAAAATTT
1 AATGATAAATCTTTATAAAATTT
6277821 TTAGGTGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (25 bp):
AATGATAAATCTTTATAAAATTTCA
Found at i:6278185 original size:24 final size:26
Alignment explanation
Indices: 6278158--6278208 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
6278148 AGGATGAGAA
*
6278158 TCTTAA-AAATTTC-AAGTGACAAAT
1 TCTTAAGAAATCTCTAAGTGACAAAT
*
6278182 TCTTAAGAAATCTCTAAGTGAGAAAT
1 TCTTAAGAAATCTCTAAGTGACAAAT
6278208 T
1 T
6278209 TCTTTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 6 0.26
25 6 0.26
26 11 0.48
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (26 bp):
TCTTAAGAAATCTCTAAGTGACAAAT
Found at i:6279130 original size:3 final size:3
Alignment explanation
Indices: 6279124--6279241 Score: 111
Period size: 3 Copynumber: 40.7 Consensus size: 3
6279114 TTTTATAAAG
* * *
6279124 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC T-T TCT T-T T-T TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
6279169 TAT T-T TTT TGT GTTT TTT TTT TCT T-T TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6279213 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
6279242 CTACTACTAT
Statistics
Matches: 103, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
2 9 0.09
3 92 0.89
4 2 0.02
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.72
Consensus pattern (3 bp):
TAT
Found at i:6279285 original size:14 final size:14
Alignment explanation
Indices: 6279262--6279311 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
6279252 TATATTTCTA
*
6279262 TTTTCATTTTTTTC
1 TTTTCTTTTTTTTC
*
6279276 TTTTCTTTTTCTTC
1 TTTTCTTTTTTTTC
*
6279290 TTTGTTTTTTTTTTC
1 TTT-TCTTTTTTTTC
*
6279305 CTTTCTT
1 TTTTCTT
6279312 GTCCAAATCT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
14 18 0.62
15 11 0.38
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (14 bp):
TTTTCTTTTTTTTC
Found at i:6280155 original size:19 final size:18
Alignment explanation
Indices: 6280128--6280173 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
6280118 GAACACAGGC
*
6280128 TTTTCTTTTTTCATTTTAT
1 TTTTATTTTTTCATTTT-T
*
6280147 TTTTATTTTTTGATTTTT
1 TTTTATTTTTTCATTTTT
*
6280165 ATTTATTTT
1 TTTTATTTT
6280174 ATTTTTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.13, C:0.04, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTATTTTTTCATTTTT
Found at i:6280162 original size:14 final size:13
Alignment explanation
Indices: 6280141--6280179 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
6280131 TCTTTTTTCA
6280141 TTTTATTTTTATT
1 TTTTATTTTTATT
6280154 TTTTGATTTTTATTT
1 TTTT-ATTTTTA-TT
6280169 ATTTTATTTTT
1 -TTTTATTTTT
6280180 TTAACCTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 4 0.17
14 7 0.30
15 8 0.35
16 4 0.17
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:6280182 original size:13 final size:13
Alignment explanation
Indices: 6280128--6280213 Score: 50
Period size: 13 Copynumber: 6.3 Consensus size: 13
6280118 GAACACAGGC
* *
6280128 TTTTCTTTTTTCA
1 TTTTATTTTTTTA
6280141 TTTTATTTTTATT-
1 TTTTATTTTT-TTA
6280154 TTTTGATTTTTATTTA
1 TTTT-A-TTTT-TTTA
6280170 TTTTATTTTTTTA
1 TTTTATTTTTTTA
***
6280183 ACCTATTTTTATTA
1 TTTTATTTTT-TTA
*
6280197 TTTT-TTGGTTTTA
1 TTTTATT-TTTTTA
6280210 TTTT
1 TTTT
6280214 TTTCTTAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
13 33 0.58
14 12 0.21
15 7 0.12
16 5 0.09
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:6290576 original size:10 final size:9
Alignment explanation
Indices: 6290561--6290586 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
6290551 TGATTTGAAC
6290561 AAAAAAAAT
1 AAAAAAAAT
6290570 AAAAAAAAT
1 AAAAAAAAT
6290579 AAAAAAAA
1 AAAAAAAA
6290587 GAACAAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:6291630 original size:117 final size:117
Alignment explanation
Indices: 6291388--6291601 Score: 270
Period size: 117 Copynumber: 1.8 Consensus size: 117
6291378 TGGTTCCATC
** * *
6291388 CCAATCATTCATTTTTGACCTTGACTCGATCTTGATTACTTAATTTTGACTCGTGACATTATCCT
1 CCAATCATTCATTTTCAACCTCGACTCGATCTTGATTACTTAATTTTGACTCGCGACATTATCCT
* * *
6291453 AGTCATTTGATCTCGACTCAGGTCAGATCATTGTTAGACTTGTGACATCAAT
66 AGTAATTCGATCTCGACTCAGGTCAGATCATTGTTAGACATGTGACATCAAT
* * * * *
6291505 CCAGTCATTCATTTTCAACCTCGACTC-AGTCTT-AGTTACTTTATTTTGACTTGCGATATTATT
1 CCAATCATTCATTTTCAACCTCGACTCGA-TCTTGA-TTACTTAATTTTGACTCGCGACATTATC
* *
6291568 CTAGTAATTCGATCTCGACTTAGGTTAGATCATT
64 CTAGTAATTCGATCTCGACTCAGGTCAGATCATT
6291602 TTCAAATTGA
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
116 2 0.02
117 80 0.98
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (117 bp):
CCAATCATTCATTTTCAACCTCGACTCGATCTTGATTACTTAATTTTGACTCGCGACATTATCCT
AGTAATTCGATCTCGACTCAGGTCAGATCATTGTTAGACATGTGACATCAAT
Found at i:6292040 original size:114 final size:114
Alignment explanation
Indices: 6291812--6292030 Score: 267
Period size: 114 Copynumber: 1.9 Consensus size: 114
6291802 GTCATTCATT
* * ** * *
6291812 TCGACTTAAGTCAGATCATCTTTAGACTAATGATACCAGTCCAATCATTTATTAATTACCTCGAC
1 TCGACTTAAGTCAGATCATCTTCAAACTAACAACACCAGTCCAATCATTTATTAATGACCTCGAC
* ** * *
6291877 TCGATCTTGGTCACCTTGAGACTCGTGATATCGTCCTAGTCATCCGATC
66 TCGATCTTGGTCACCTTCAGACTCGCAACATCATCCTAGTCATCCGATC
* * * * * * *
6291926 TCGACTTAGGTCAGATCATCTTCAAACTCACAACATCAGTCCAGTCATTTATTTATGATCTTGAC
1 TCGACTTAAGTCAGATCATCTTCAAACTAACAACACCAGTCCAATCATTTATTAATGACCTCGAC
*
6291991 TCGATCTTGGTCACCTTCAGGCTCGCAACATCATCCTAGT
66 TCGATCTTGGTCACCTTCAGACTCGCAACATCATCCTAGT
6292031 TATTTGATCT
Statistics
Matches: 86, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
114 86 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (114 bp):
TCGACTTAAGTCAGATCATCTTCAAACTAACAACACCAGTCCAATCATTTATTAATGACCTCGAC
TCGATCTTGGTCACCTTCAGACTCGCAACATCATCCTAGTCATCCGATC
Found at i:6292070 original size:54 final size:54
Alignment explanation
Indices: 6292012--6292122 Score: 143
Period size: 54 Copynumber: 2.1 Consensus size: 54
6292002 CACCTTCAGG
* * *
6292012 CTCGCAACATCATCCTAGTTATTTGATCTT-AGCTCTGATCAAATCGTCTTCTGA
1 CTCGCAACATCATCCCAGTCATTTGATCTTGA-CTCTGATCAAATCATCTTCTGA
* ** *
6292066 CTCGCGACATTGTCCCAGTCATTTGATCTTGACTTTGATCAAATCATCTTCTGA
1 CTCGCAACATCATCCCAGTCATTTGATCTTGACTCTGATCAAATCATCTTCTGA
6292120 CTC
1 CTC
6292123 ATGGCATTGT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
54 48 0.98
55 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.14, T:0.37
Consensus pattern (54 bp):
CTCGCAACATCATCCCAGTCATTTGATCTTGACTCTGATCAAATCATCTTCTGA
Found at i:6292131 original size:54 final size:54
Alignment explanation
Indices: 6292032--6292142 Score: 152
Period size: 54 Copynumber: 2.1 Consensus size: 54
6292022 CATCCTAGTT
* *
6292032 ATTTGATCTTAGCTCTGATCAAATCGTCTTCTGACTCGCGACATTGTCCCAGTC
1 ATTTGATCTTAGCTCTGATCAAATCATCTTCTGACTCACGACATTGTCCCAGTC
* * * *
6292086 ATTTGATCTT-GACTTTGATCAAATCATCTTCTGACTCATGGCATTGTCCCGGTC
1 ATTTGATCTTAG-CTCTGATCAAATCATCTTCTGACTCACGACATTGTCCCAGTC
6292140 ATT
1 ATT
6292143 CAACCTCAGC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
53 1 0.02
54 49 0.98
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (54 bp):
ATTTGATCTTAGCTCTGATCAAATCATCTTCTGACTCACGACATTGTCCCAGTC
Found at i:6292398 original size:26 final size:25
Alignment explanation
Indices: 6292315--6292404 Score: 92
Period size: 26 Copynumber: 3.5 Consensus size: 25
6292305 TCCAAGTCCT
* *
6292315 ATTAGGCTCGTTGATGTCTAGACCCG
1 ATTAGGCCCATTGATGTC-AGACCCG
*
6292341 ATTA-GCCTCATTGATGTCCAGACCTG
1 ATTAGGCC-CATTGATGT-CAGACCCG
*
6292367 ATTAGGCCCATTGATGTCAGGGCCCG
1 ATTAGGCCCATTGATGTCA-GACCCG
*
6292393 ATTAGGTCCATT
1 ATTAGGCCCATT
6292405 AATTTTTAGG
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
25 4 0.07
26 46 0.85
27 4 0.07
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.30
Consensus pattern (25 bp):
ATTAGGCCCATTGATGTCAGACCCG
Found at i:6292599 original size:3 final size:3
Alignment explanation
Indices: 6292593--6292640 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
6292583 TTTTCATTTA
* * *
6292593 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TA- TAT TTT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6292640 T
1 T
6292641 TTTTTTTCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:6297033 original size:8 final size:8
Alignment explanation
Indices: 6297022--6297114 Score: 55
Period size: 8 Copynumber: 11.8 Consensus size: 8
6297012 AAAAAAATTC
6297022 TAAAACCT
1 TAAAACCT
*
6297030 TAAATCCT
1 TAAAACCT
** *
6297038 CGAAACCC
1 TAAAACCT
*
6297046 TAAAA-TT
1 TAAAACCT
*
6297053 TAAAAACCC
1 T-AAAACCT
6297062 T-AAACCT
1 TAAAACCT
*
6297069 TAAAACCC
1 TAAAACCT
*
6297077 TAAAATCT
1 TAAAACCT
* * *
6297085 CAAAGCCC
1 TAAAACCT
6297093 TAAAACCT
1 TAAAACCT
*
6297101 TAAAACCC
1 TAAAACCT
6297109 TAAAAC
1 TAAAAC
6297115 GAGATTTTAA
Statistics
Matches: 59, Mismatches: 23, Indels: 6
0.67 0.26 0.07
Matches are distributed among these distances:
7 7 0.12
8 51 0.86
9 1 0.02
ACGTcount: A:0.48, C:0.29, G:0.02, T:0.20
Consensus pattern (8 bp):
TAAAACCT
Found at i:6297051 original size:32 final size:32
Alignment explanation
Indices: 6297015--6297113 Score: 114
Period size: 32 Copynumber: 3.1 Consensus size: 32
6297005 TATAAGAAAA
* **
6297015 AAAATTCT-AAAACCTTAAATCCTCGAAACCCT
1 AAAATTCTAAAAACCCTAAA-CCTTAAAACCCT
6297047 AAAATT-TAAAAACCCTAAACCTTAAAACCCT
1 AAAATTCTAAAAACCCTAAACCTTAAAACCCT
* *
6297078 AAAA-TCTCAAAGCCCTAAAACCTTAAAACCCT
1 AAAATTCTAAAAACCCT-AAACCTTAAAACCCT
6297110 AAAA
1 AAAA
6297114 CGAGATTTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
30 1 0.02
31 23 0.39
32 35 0.59
ACGTcount: A:0.49, C:0.27, G:0.02, T:0.21
Consensus pattern (32 bp):
AAAATTCTAAAAACCCTAAACCTTAAAACCCT
Found at i:6297059 original size:16 final size:15
Alignment explanation
Indices: 6297040--6297114 Score: 87
Period size: 16 Copynumber: 4.8 Consensus size: 15
6297030 TAAATCCTCG
*
6297040 AAACCCTAAAATTTAA
1 AAACCCTAAAACTT-A
*
6297056 AAACCCTAAACCTTA
1 AAACCCTAAAACTTA
*
6297071 AAACCCTAAAATCTCA
1 AAACCCTAAAA-CTTA
*
6297087 AAGCCCTAAAACCTTA
1 AAACCCTAAAA-CTTA
6297103 AAACCCTAAAAC
1 AAACCCTAAAAC
6297115 GAGATTTTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
15 12 0.24
16 38 0.76
ACGTcount: A:0.51, C:0.29, G:0.01, T:0.19
Consensus pattern (15 bp):
AAACCCTAAAACTTA
Found at i:6301774 original size:25 final size:27
Alignment explanation
Indices: 6301720--6301775 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
6301710 TTTTTAAAAA
* *
6301720 TTTTAATAAATATTCTTAGATAGACAT
1 TTTTAATAAATAATATTAGATAGACAT
6301747 TTTTAATAAA-AATATTA-ATAGA-AT
1 TTTTAATAAATAATATTAGATAGACAT
6301771 TTTTA
1 TTTTA
6301776 CTGTTGAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 7 0.26
25 5 0.19
26 5 0.19
27 10 0.37
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (27 bp):
TTTTAATAAATAATATTAGATAGACAT
Found at i:6317971 original size:190 final size:187
Alignment explanation
Indices: 6317635--6318013 Score: 616
Period size: 190 Copynumber: 2.0 Consensus size: 187
6317625 TTTTCTGAAC
*
6317635 AGTCGTTCCAAATCAGACTGACGTGCATCATACTCAAAGTTTCCACAGAAAATGGGCCTCATATT
1 AGTCGTTCCAAATCAGACTGACATGCATCATACTCAAAGTTTCCACAGAAAATGGGCCTCATATT
* * *
6317700 GCCTGAGCAGATGTGACAATTTTTCCATGATTATTTATGTAAAAAATATTTGCATACAATAATAC
66 GCCTGAGAAGATGTGACAACTTTTCCATGATTATTTATATAAAAAATATTTGCATACAATAATAC
*
6317765 AAAAGAACATGCCAAAAATAGTGAGTTAAACATCCAGTGACAATGCAAGTTCAAAAG
131 AAAAGAACATGCCAAAAATAGTGAGTTAAACATCCAGTGACAACGCAAGTTCAAAAG
* *
6317822 AGTCGTTCCAAATCAGACTGATATGCATCATACTCAATGTTTCCACAGAAAATGGGCCTCATATT
1 AGTCGTTCCAAATCAGACTGACATGCATCATACTCAAAGTTTCCACAGAAAATGGGCCTCATATT
* *
6317887 GTCTGAGTAGAAGATGTGACAACTTTTCCCTGATTATTTATATAAAAAATATTTGCATACAA-AC
66 GCCT--G-AGAAGATGTGACAACTTTTCCATGATTATTTATATAAAAAATATTTGCATACAATA-
* *
6317951 ATACAAAAGAACATGCCAAAAATAGTGAGTTAAACATCCGGTGTCAACGCAAGTTCAAAAG
127 ATACAAAAGAACATGCCAAAAATAGTGAGTTAAACATCCAGTGACAACGCAAGTTCAAAAG
6318012 AG
1 AG
6318014 AATGATCAAA
Statistics
Matches: 177, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
187 65 0.37
189 2 0.01
190 110 0.62
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (187 bp):
AGTCGTTCCAAATCAGACTGACATGCATCATACTCAAAGTTTCCACAGAAAATGGGCCTCATATT
GCCTGAGAAGATGTGACAACTTTTCCATGATTATTTATATAAAAAATATTTGCATACAATAATAC
AAAAGAACATGCCAAAAATAGTGAGTTAAACATCCAGTGACAACGCAAGTTCAAAAG
Found at i:6322890 original size:15 final size:16
Alignment explanation
Indices: 6322870--6322902 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
6322860 AAGTATGAAG
6322870 ATATAAAAACA-AAAA
1 ATATAAAAACACAAAA
6322885 ATATAAAAACACAAAA
1 ATATAAAAACACAAAA
6322901 AT
1 AT
6322903 CCTTAACAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (16 bp):
ATATAAAAACACAAAA
Found at i:6334873 original size:7 final size:8
Alignment explanation
Indices: 6334861--6334933 Score: 100
Period size: 8 Copynumber: 9.6 Consensus size: 8
6334851 AAAGGATGTA
*
6334861 AAAAAATA
1 AAAAAATG
6334869 AAAAAATG
1 AAAAAATG
*
6334877 -AAAACT-
1 AAAAAATG
6334883 -AAAAATG
1 AAAAAATG
6334890 AAAAAATG
1 AAAAAATG
6334898 AAAAAATG
1 AAAAAATG
6334906 AAAAAATG
1 AAAAAATG
6334914 AAAAAATG
1 AAAAAATG
6334922 -AAAAATG
1 AAAAAATG
6334929 AAAAA
1 AAAAA
6334934 GAACAAGAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
6 5 0.08
7 12 0.20
8 42 0.71
ACGTcount: A:0.77, C:0.01, G:0.10, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:6334886 original size:21 final size:21
Alignment explanation
Indices: 6334862--6334901 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6334852 AAGGATGTAA
6334862 AAAAATAAAAAAATGAAAACT
1 AAAAATAAAAAAATGAAAACT
*
6334883 AAAAATGAAAAAATGAAAA
1 AAAAATAAAAAAATGAAAA
6334902 AATGAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.78, C:0.03, G:0.07, T:0.12
Consensus pattern (21 bp):
AAAAATAAAAAAATGAAAACT
Found at i:6334947 original size:23 final size:22
Alignment explanation
Indices: 6334862--6334957 Score: 81
Period size: 24 Copynumber: 4.2 Consensus size: 22
6334852 AAGGATGTAA
*
6334862 AAAAAT-AAAAAAATGAAAACT-
1 AAAAATGAAAAAAA-GAAAAATG
*
6334883 AAAAATGAAAAAATGAAAAAATG
1 AAAAATGAAAAAAAG-AAAAATG
*
6334906 AAAAAATGAAAAAATGAAAAATG
1 -AAAAATGAAAAAAAGAAAAATG
*
6334929 AAAAA-GAACAAGAAAGAAAGAAAG
1 AAAAATGAA-AA-AAAGAAA-AATG
6334953 AAAAA
1 AAAAA
6334958 AAGGAAAACT
Statistics
Matches: 64, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
21 10 0.16
22 18 0.28
23 13 0.20
24 23 0.36
ACGTcount: A:0.76, C:0.02, G:0.12, T:0.09
Consensus pattern (22 bp):
AAAAATGAAAAAAAGAAAAATG
Found at i:6334956 original size:31 final size:31
Alignment explanation
Indices: 6334883--6334957 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 31
6334873 AATGAAAACT
*
6334883 AAAAATGAAAAAATGAAAAAATGAAAAAATGA
1 AAAAATG-AAAAATGAAAAAATGAAAAAAAGA
6334915 AAAAATGAAAAATG-AAAAA-GAACAAGAAAGA
1 AAAAATGAAAAATGAAAAAATGAA-AA-AAAGA
6334946 AAGAAA-GAAAAA
1 AA-AAATGAAAAA
6334958 AAGGAAAACT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
29 3 0.08
30 7 0.18
31 19 0.49
32 10 0.26
ACGTcount: A:0.76, C:0.01, G:0.15, T:0.08
Consensus pattern (31 bp):
AAAAATGAAAAATGAAAAAATGAAAAAAAGA
Found at i:6336177 original size:24 final size:23
Alignment explanation
Indices: 6336112--6336177 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 23
6336102 ATTCTTGATA
* *
6336112 CTTTGAAATCTTGG-ATGTGAAT
1 CTTTGAAATTTTGGAATGAGAAT
* * *
6336134 CCTTGAAGTTTTTTGAATGAGAAT
1 CTTTGAA-ATTTTGGAATGAGAAT
6336158 CTTTGAAATTTTGGATATGA
1 CTTTGAAATTTTGGA-ATGA
6336178 ATCTCTAAGA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
22 6 0.18
23 10 0.30
24 17 0.52
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (23 bp):
CTTTGAAATTTTGGAATGAGAAT
Found at i:6336179 original size:22 final size:22
Alignment explanation
Indices: 6336112--6336181 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
6336102 ATTCTTGATA
* *
6336112 CTTTGAAATCTTGGATGTGAAT
1 CTTTGAAATTTTGGATATGAAT
* * *
6336134 CCTTGAAGTTTTTTGA-ATGAGAAT
1 CTTTGAA-ATTTTGGATAT--GAAT
6336158 CTTTGAAATTTTGGATATGAAT
1 CTTTGAAATTTTGGATATGAAT
6336180 CT
1 CT
6336182 CTAAGACTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 8
0.69 0.15 0.15
Matches are distributed among these distances:
22 13 0.36
23 11 0.31
24 12 0.33
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.43
Consensus pattern (22 bp):
CTTTGAAATTTTGGATATGAAT
Found at i:6336193 original size:46 final size:46
Alignment explanation
Indices: 6336112--6336209 Score: 110
Period size: 46 Copynumber: 2.1 Consensus size: 46
6336102 ATTCTTGATA
* * * * *
6336112 CTTTGAAATCTTGGATGTGAATCCTTGAAGTTTTTTGAATGAGAAT
1 CTTTGAAATCTTGGATATGAATCCTTGAAGCTTTTTAAATAAAAAT
*
6336158 CTTTGAAATTTTGGATATGAAT-CTCT-AAGACTTTTTAAATAAAAAT
1 CTTTGAAATCTTGGATATGAATCCT-TGAAG-CTTTTTAAATAAAAAT
6336204 CTTTGA
1 CTTTGA
6336210 GTTTCACATG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
45 5 0.11
46 39 0.89
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (46 bp):
CTTTGAAATCTTGGATATGAATCCTTGAAGCTTTTTAAATAAAAAT
Found at i:6336276 original size:41 final size:42
Alignment explanation
Indices: 6336218--6336306 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 42
6336208 GAGTTTCACA
* * * *
6336218 TGCAAATATTTAGGATTTTAGTTATGAATCTC-CAAATTTTT
1 TGCAAATATTTAAGATTTTAGATATAAATCTCTAAAATTTTT
*
6336259 TGCAAATCTTTAAGATTTTAGATATAAATCTCTAAAATTTTT
1 TGCAAATATTTAAGATTTTAGATATAAATCTCTAAAATTTTT
6336301 T-CAAAT
1 TGCAAAT
6336307 GTGAATCATT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 33 0.79
42 9 0.21
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (42 bp):
TGCAAATATTTAAGATTTTAGATATAAATCTCTAAAATTTTT
Found at i:6336677 original size:34 final size:34
Alignment explanation
Indices: 6336591--6336700 Score: 89
Period size: 34 Copynumber: 3.2 Consensus size: 34
6336581 TTTCTTACAT
* * * **
6336591 ATCTAAAAATCTTAGGAATCTTAAAATCTTACAA
1 ATCTGAAAATTTTATGAATCTTAAAATCTTATGA
* * * * *
6336625 AT-TTAAATTTTTTGTGAAT-TTGGAAATCTTCTGA
1 ATCTGAAA-ATTTTATGAATCTT-AAAATCTTATGA
6336659 ATCTGAAAATTTTATGAATCTTAAAATCTTATGA
1 ATCTGAAAATTTTATGAATCTTAAAATCTTATGA
*
6336693 ATTTGAAA
1 ATCTGAAA
6336701 TTCTTCAAAA
Statistics
Matches: 57, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
33 6 0.11
34 45 0.79
35 6 0.11
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (34 bp):
ATCTGAAAATTTTATGAATCTTAAAATCTTATGA
Found at i:6336694 original size:51 final size:51
Alignment explanation
Indices: 6336639--6336739 Score: 143
Period size: 51 Copynumber: 2.0 Consensus size: 51
6336629 AAATTTTTTG
**
6336639 TGAATTTGGAAA-TCTTCTGAATCTGAAAATTTTATGAATCTT-AAAATCTTA
1 TGAATTT-GAAATTCTTCAAAATCTGAAAATTTTATGAAT-TTGAAAATCTTA
*
6336690 TGAATTTGAAATTCTTCAAAATCTGAAAATTTTGTGAATTTGAAAATCTT
1 TGAATTTGAAATTCTTCAAAATCTGAAAATTTTATGAATTTGAAAATCTT
6336740 TTCAAGATGA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
50 6 0.13
51 39 0.87
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.42
Consensus pattern (51 bp):
TGAATTTGAAATTCTTCAAAATCTGAAAATTTTATGAATTTGAAAATCTTA
Found at i:6336764 original size:51 final size:51
Alignment explanation
Indices: 6336658--6336756 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
6336648 AAATCTTCTG
* * ** *
6336658 AATCTGAAAATTTTATGAATCTT-AAAATCTTATGAATTTGAAATTCTTCAA
1 AATCTGAAAATTTTGTGAAT-TTGAAAATCTTATCAAGATGAAAGTCTTCAA
*
6336709 AATCTGAAAATTTTGTGAATTTGAAAATCTTTTCAAGATGAAAGTCTT
1 AATCTGAAAATTTTGTGAATTTGAAAATCTTATCAAGATGAAAGTCTT
6336757 GTTAATCTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 2 0.05
51 39 0.95
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.40
Consensus pattern (51 bp):
AATCTGAAAATTTTGTGAATTTGAAAATCTTATCAAGATGAAAGTCTTCAA
Found at i:6336790 original size:17 final size:17
Alignment explanation
Indices: 6336636--6336791 Score: 105
Period size: 17 Copynumber: 9.2 Consensus size: 17
6336626 TTTAAATTTT
* *
6336636 TTGTGAATTTGGAAATC
1 TTGTGAATCTGAAAATC
* *
6336653 TTCTGAATCTGAAAATT
1 TTGTGAATCTGAAAATC
* *
6336670 TTATGAATCTTAAAATC
1 TTGTGAATCTGAAAATC
* * *
6336687 TTATGAATTTGAAATTC
1 TTGTGAATCTGAAAATC
*** *
6336704 TTCAAAATCTGAAAATT
1 TTGTGAATCTGAAAATC
*
6336721 TTGTGAATTTGAAAATC
1 TTGTGAATCTGAAAATC
* * ** *
6336738 TTTTCAAGATGAAAGTC
1 TTGTGAATCTGAAAATC
* ** *
6336755 TTGTTAATCTTCAATTC
1 TTGTGAATCTGAAAATC
6336772 TTGTGAATCTGAAAATC
1 TTGTGAATCTGAAAATC
6336789 TTG
1 TTG
6336792 CAAATCTAAA
Statistics
Matches: 102, Mismatches: 37, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 102 1.00
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (17 bp):
TTGTGAATCTGAAAATC
Found at i:6336871 original size:18 final size:18
Alignment explanation
Indices: 6336814--6336888 Score: 89
Period size: 18 Copynumber: 4.2 Consensus size: 18
6336804 CCTTATGAAC
*
6336814 ATTTGAGTTCTTGCAAAT
1 ATTTGAATTCTTGCAAAT
* *
6336832 -TTTGAATCCTTGCAAAC
1 ATTTGAATTCTTGCAAAT
*
6336849 CTTTGAATTCTTGCAAAT
1 ATTTGAATTCTTGCAAAT
* *
6336867 ATTTGAAATCTTACAAAT
1 ATTTGAATTCTTGCAAAT
6336885 ATTT
1 ATTT
6336889 CAAATGTTGT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
17 14 0.29
18 34 0.71
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (18 bp):
ATTTGAATTCTTGCAAAT
Found at i:6336893 original size:18 final size:18
Alignment explanation
Indices: 6336857--6336893 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
6336847 ACCTTTGAAT
* *
6336857 TCTTGCAAATATTTGAAA
1 TCTTACAAATATTTCAAA
6336875 TCTTACAAATATTTCAAA
1 TCTTACAAATATTTCAAA
6336893 T
1 T
6336894 GTTGTGAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (18 bp):
TCTTACAAATATTTCAAA
Found at i:6338153 original size:25 final size:26
Alignment explanation
Indices: 6338122--6338181 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
6338112 ACACAAAGCC
* *
6338122 AAGGAAAAAGCAAAGC-GAAATCAAA
1 AAGGAAAAAGAAAAGCAGAAATAAAA
* *
6338147 AATGAAAAAGAAAAGCATAAATAAAA
1 AAGGAAAAAGAAAAGCAGAAATAAAA
6338173 AAGGAAAAA
1 AAGGAAAAA
6338182 TTTTTTGGGG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 14 0.48
26 15 0.52
ACGTcount: A:0.70, C:0.07, G:0.17, T:0.07
Consensus pattern (26 bp):
AAGGAAAAAGAAAAGCAGAAATAAAA
Found at i:6339007 original size:17 final size:16
Alignment explanation
Indices: 6338987--6339040 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 16
6338977 TGAAAGGGTT
6338987 TAAAATTTTAAAGAAAA
1 TAAAATTTT-AAGAAAA
*
6339004 T-AAATTTTTA-AAAA
1 TAAAATTTTAAGAAAA
*
6339018 TAAAATTTGAAGAAAAA
1 TAAAATTTTAAG-AAAA
6339035 TAAAAT
1 TAAAAT
6339041 AAAATCTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 5 0.16
15 8 0.26
16 7 0.23
17 11 0.35
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (16 bp):
TAAAATTTTAAGAAAA
Found at i:6342343 original size:14 final size:13
Alignment explanation
Indices: 6342320--6342353 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
6342310 CGATCACAAG
6342320 TTTTTTTTTTCTA
1 TTTTTTTTTTCTA
*
6342333 TTTTATTTTTTTTA
1 TTTT-TTTTTTCTA
6342347 TTTTTTT
1 TTTTTTT
6342354 CTTTATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTTCTA
Found at i:6344947 original size:15 final size:16
Alignment explanation
Indices: 6344895--6344940 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 16
6344885 ATGCAAAATT
*
6344895 AAAAAAAATGAAAAAAA
1 AAAAAAAATG-AAAAAG
6344912 AAGGAAAAAATGAAAAAG
1 AA--AAAAAATGAAAAAG
6344930 AAAAAAAATGA
1 AAAAAAAATGA
6344941 GAAGAAATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 9 0.35
17 2 0.08
18 7 0.27
19 8 0.31
ACGTcount: A:0.80, C:0.00, G:0.13, T:0.07
Consensus pattern (16 bp):
AAAAAAAATGAAAAAG
Found at i:6346416 original size:46 final size:46
Alignment explanation
Indices: 6346359--6346551 Score: 162
Period size: 46 Copynumber: 4.2 Consensus size: 46
6346349 GCATAATCTT
*
6346359 TAAAATTTTTCAAAT-AAGAATCTTTGAAATTTTGGATGTGAAACCC
1 TAAAGTTTTTCAAATGAA-AATCTTTGAAATTTTGGATGTGAAACCC
* * * *
6346405 TAACA-TTTTTCAAATGAAAATTTTTAAAATTTTAGG-TGTGAAGCCA
1 TAA-AGTTTTTCAAATGAAAATCTTTGAAATTTT-GGATGTGAAACCC
** * * * *
6346451 TAAAGTTTTTTGAATGAAAA-CTTTTAAATTTTTTGATGTAAAACAC
1 TAAAGTTTTTCAAATGAAAATCTTTGAAA-TTTTGGATGTGAAACCC
** ** * *
6346497 TAAAGTTTTTTGAATGTGAATATTTGAAATTTTGGATGTGAATCCC
1 TAAAGTTTTTCAAATGAAAATCTTTGAAATTTTGGATGTGAAACCC
6346543 T-AAGTTTTT
1 TAAAGTTTTT
6346552 AATTTTTGGG
Statistics
Matches: 119, Mismatches: 21, Indels: 15
0.77 0.14 0.10
Matches are distributed among these distances:
45 16 0.13
46 92 0.77
47 11 0.09
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (46 bp):
TAAAGTTTTTCAAATGAAAATCTTTGAAATTTTGGATGTGAAACCC
Found at i:6346482 original size:23 final size:24
Alignment explanation
Indices: 6346451--6346513 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 24
6346441 TGTGAAGCCA
**
6346451 TAAAGTTTTTTGAATG-AAAACTTT
1 TAAAGTTTTTTGAATGTAAAAC-AC
6346475 TAAA-TTTTTTG-ATGTAAAACAC
1 TAAAGTTTTTTGAATGTAAAACAC
6346497 TAAAGTTTTTTGAATGT
1 TAAAGTTTTTTGAATGT
6346514 GAATATTTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 7 0.21
23 19 0.56
24 8 0.24
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.46
Consensus pattern (24 bp):
TAAAGTTTTTTGAATGTAAAACAC
Found at i:6346869 original size:17 final size:18
Alignment explanation
Indices: 6346842--6346880 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
6346832 TCTTACGATT
*
6346842 TGAAAATTCTTGCAAATC
1 TGAAAATTCTTGCAAATA
6346860 TGAAAA-TCTTGCAAATA
1 TGAAAATTCTTGCAAATA
6346877 TGAA
1 TGAA
6346881 TTCCTACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (18 bp):
TGAAAATTCTTGCAAATA
Found at i:6346939 original size:16 final size:16
Alignment explanation
Indices: 6346904--6346956 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
6346894 GAATTACTAC
* *
6346904 GAATCTGAAATTCTTAT
1 GAATCTG-AGTTCTTGT
6346921 GAATCTGAGTTCTTGT
1 GAATCTGAGTTCTTGT
* *
6346937 GAATCTAAGTTTTTGT
1 GAATCTGAGTTCTTGT
6346953 GAAT
1 GAAT
6346957 ACAAAATTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 25 0.78
17 7 0.22
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.43
Consensus pattern (16 bp):
GAATCTGAGTTCTTGT
Found at i:6346974 original size:33 final size:33
Alignment explanation
Indices: 6346937--6347034 Score: 94
Period size: 33 Copynumber: 3.0 Consensus size: 33
6346927 GAGTTCTTGT
6346937 GAATCT-AAGTTTTTGTGAATACAAAATT-TCTAC
1 GAATCTGAA-TTTTTGTGAATACAAAATTCT-TAC
* * *
6346970 GAATCTGAATTTTTATGAAAATAAAATTCTTAC
1 GAATCTGAATTTTTGTGAATACAAAATTCTTAC
* * *
6347003 AAATATGAAATTTTTGTGAAT-CTAAATTCTTA
1 GAATCTG-AATTTTTGTGAATACAAAATTCTTA
6347035 TCAATTTGAA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
33 39 0.74
34 14 0.26
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (33 bp):
GAATCTGAATTTTTGTGAATACAAAATTCTTAC
Found at i:6347016 original size:34 final size:33
Alignment explanation
Indices: 6346977--6347047 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 33
6346967 TACGAATCTG
6346977 AATTTTTATGAAAATAAAATTCTTA-CAAATATGA
1 AATTTTTATGAAAAT-AAATTCTTATC-AATATGA
* ** *
6347011 AATTTTTGTGAATCTAAATTCTTATCAATTTGA
1 AATTTTTATGAAAATAAATTCTTATCAATATGA
6347044 AATT
1 AATT
6347048 CTTGCAAATC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
33 19 0.59
34 13 0.41
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.44
Consensus pattern (33 bp):
AATTTTTATGAAAATAAATTCTTATCAATATGA
Found at i:6347047 original size:50 final size:50
Alignment explanation
Indices: 6346993--6347100 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
6346983 TATGAAAATA
* **
6346993 AAATTCTTACAAATATGAAATTTTTGTGAATCT-AAATTCTTATC-AATTTG
1 AAATTCTTACAAATATG-AATTCTTACGAATCTAAAATTCTTA-CAAATTTG
* * *
6347043 AAATTCTTGCAAATCTGAGTTCTTACGAATCTAAAATTCTTACAAATTTG
1 AAATTCTTACAAATATGAATTCTTACGAATCTAAAATTCTTACAAATTTG
6347093 AAATTCTT
1 AAATTCTT
6347101 GTGAATCTGA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
49 12 0.24
50 38 0.76
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (50 bp):
AAATTCTTACAAATATGAATTCTTACGAATCTAAAATTCTTACAAATTTG
Found at i:6347058 original size:33 final size:34
Alignment explanation
Indices: 6346993--6347150 Score: 146
Period size: 33 Copynumber: 4.8 Consensus size: 34
6346983 TATGAAAATA
* * * **
6346993 AAATTCTTACAAATATGAAATTTTTGTGAATCT-
1 AAATTCTTACGAATCTGAAATTCTTGCAAATCTG
*
6347026 AAATTCTTATC-AATTTGAAATTCTTGCAAATCTG
1 AAATTCTTA-CGAATCTGAAATTCTTGCAAATCTG
* * * *
6347060 -AGTTCTTACGAATCTAAAATTCTTACAAATTTG
1 AAATTCTTACGAATCTGAAATTCTTGCAAATCTG
** *
6347093 AAATTCTTGTGAATCTG-AA-TCTTGCAAACCTG
1 AAATTCTTACGAATCTGAAATTCTTGCAAATCTG
*
6347125 AAATTCTTACGAATCTAAAATTCTTG
1 AAATTCTTACGAATCTGAAATTCTTG
6347151 TGAATATGAA
Statistics
Matches: 100, Mismatches: 19, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
32 25 0.25
33 57 0.57
34 18 0.18
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (34 bp):
AAATTCTTACGAATCTGAAATTCTTGCAAATCTG
Found at i:6347080 original size:66 final size:66
Alignment explanation
Indices: 6346993--6347160 Score: 178
Period size: 66 Copynumber: 2.5 Consensus size: 66
6346983 TATGAAAATA
* * * * * *
6346993 AAATTCTTACAAATATGAAATTTTTGTGAATCT-AAATTCTTATCAATTTGAAATTCTTGCAAAT
1 AAATTCTTACGAATCTAAAATTCTTGTGAATCTGAAATTCTTATCAATCTG-AA-TCTTGCAAAC
6347057 CTG
64 CTG
* *** * * *
6347060 -AGTTCTTACGAATCTAAAATTCTTACAAATTTGAAATTCTTGTGAATCTGAATCTTGCAAACCT
1 AAATTCTTACGAATCTAAAATTCTTGTGAATCTGAAATTCTTATCAATCTGAATCTTGCAAACCT
6347124 G
66 G
*
6347125 AAATTCTTACGAATCTAAAATTCTTGTGAATATGAA
1 AAATTCTTACGAATCTAAAATTCTTGTGAATCTGAA
6347161 CTCTAGTGAA
Statistics
Matches: 81, Mismatches: 18, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
65 12 0.15
66 55 0.68
67 14 0.17
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.39
Consensus pattern (66 bp):
AAATTCTTACGAATCTAAAATTCTTGTGAATCTGAAATTCTTATCAATCTGAATCTTGCAAACCT
G
Found at i:6347101 original size:50 final size:47
Alignment explanation
Indices: 6347020--6347150 Score: 136
Period size: 49 Copynumber: 2.7 Consensus size: 47
6347010 AAATTTTTGT
*
6347020 GAATCTAAATTCTTATCAATTTGAAATTCTTGCAAATCTGAGTTCTTAC
1 GAATCTAAATTCTTA-CAATTTGAAATTCTTGCAAATCTGA-ATCTTAC
** *
6347069 GAATCTAAAATTCTTACAAATTTGAAATTCTTGTGAATCTGAATCTTGC
1 GAATCT-AAATTCTTAC-AATTTGAAATTCTTGCAAATCTGAATCTTAC
* * * *
6347118 AAACCTGAAATTCTTACGAATCTAAAATTCTTG
1 GAATCT-AAATTCTTAC-AATTTGAAATTCTTG
6347151 TGAATATGAA
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
49 39 0.56
50 31 0.44
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (47 bp):
GAATCTAAATTCTTACAATTTGAAATTCTTGCAAATCTGAATCTTAC
Found at i:6347148 original size:49 final size:50
Alignment explanation
Indices: 6347073--6347193 Score: 154
Period size: 49 Copynumber: 2.4 Consensus size: 50
6347063 TCTTACGAAT
* * * * *
6347073 CTAAAATTCTTACAAATTTGAAATTCTTGTGAATCTGAA-TCTTGCAAAC
1 CTAAAATTCTTACGAATCTAAAATTCTTGTGAATATGAACTCTAGCAAAC
* **
6347122 CTGAAATTCTTACGAATCTAAAATTCTTGTGAATATGAACTCTAGTGAAC
1 CTAAAATTCTTACGAATCTAAAATTCTTGTGAATATGAACTCTAGCAAAC
*
6347172 CTAAAAATCTTACGAATCTAAA
1 CTAAAATTCTTACGAATCTAAA
6347194 TTTTTACAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
49 34 0.56
50 27 0.44
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.34
Consensus pattern (50 bp):
CTAAAATTCTTACGAATCTAAAATTCTTGTGAATATGAACTCTAGCAAAC
Found at i:6347344 original size:17 final size:18
Alignment explanation
Indices: 6347315--6347368 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 18
6347305 ATTTGAATTC
*
6347315 TTGTAAATA-TGGAGTTT
1 TTGTGAATATTGGAGTTT
* *
6347332 TTGTGAAT-TTGGAATCT
1 TTGTGAATATTGGAGTTT
6347349 TTGTGAATATTGGAGTTT
1 TTGTGAATATTGGAGTTT
6347367 TT
1 TT
6347369 ACGAATCTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 21 0.70
18 9 0.30
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.50
Consensus pattern (18 bp):
TTGTGAATATTGGAGTTT
Found at i:6347387 original size:36 final size:34
Alignment explanation
Indices: 6347315--6347392 Score: 93
Period size: 36 Copynumber: 2.2 Consensus size: 34
6347305 ATTTGAATTC
* ** *
6347315 TTGTAAATATGGAGTTTTTGTGAATTTGGAATCT
1 TTGTGAATATGGAGTTTTTACGAATTTGGAACCT
6347349 TTGTGAATATTGGAGTTTTTACGAATCTTGGAACCT
1 TTGTGAATA-TGGAGTTTTTACGAAT-TTGGAACCT
*
6347385 TTGAGAAT
1 TTGTGAAT
6347393 CTTAAATCAT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 8 0.22
35 14 0.38
36 15 0.41
ACGTcount: A:0.27, C:0.06, G:0.23, T:0.44
Consensus pattern (34 bp):
TTGTGAATATGGAGTTTTTACGAATTTGGAACCT
Found at i:6347795 original size:6 final size:6
Alignment explanation
Indices: 6347784--6347810 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6347774 TTTAACCTTG
6347784 ATTTTA ATTTTA ATTTTA ATTTTA ATT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATT
6347811 CTATTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
ATTTTA
Found at i:6347795 original size:18 final size:18
Alignment explanation
Indices: 6347772--6347810 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6347762 GTCTTAGTTG
*
6347772 ATTTTAACCTTGATTTTA
1 ATTTTAACCTTAATTTTA
**
6347790 ATTTTAATTTTAATTTTA
1 ATTTTAACCTTAATTTTA
6347808 ATT
1 ATT
6347811 CTATTATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.62
Consensus pattern (18 bp):
ATTTTAACCTTAATTTTA
Found at i:6351279 original size:21 final size:21
Alignment explanation
Indices: 6351229--6351284 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
6351219 ATCACTTGTG
* *
6351229 ATTTTATTTCTATTT-ATTAT
1 ATTTTATTTATTTTTCATTAT
6351249 ATTTTATTTATTTTTCATTATT
1 ATTTTATTTATTTTTCATTA-T
6351271 ATTTT-TTTATTTTT
1 ATTTTATTTATTTTT
6351285 TTATTCTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 13 0.41
21 13 0.41
22 6 0.19
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (21 bp):
ATTTTATTTATTTTTCATTAT
Found at i:6352557 original size:3 final size:3
Alignment explanation
Indices: 6352549--6352582 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
6352539 AAGGAAAAAT
6352549 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
6352583 CTGGATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:6352806 original size:44 final size:43
Alignment explanation
Indices: 6352757--6352842 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 43
6352747 TTAAAAAATT
*
6352757 AAAAGGCTTCTCTAAGTAGAAGCTTGAA-AACTTTTGAAAATTTA
1 AAAAGGCTCCTCTAAGTAGAAGCTT-AATAACTTTT-AAAATTTA
* * *
6352801 AAAAGGCTCCTTTAAGTATAAGCTTAATGACTTTTAAAATTT
1 AAAAGGCTCCTCTAAGTAGAAGCTTAATAACTTTTAAAATTT
6352843 TATCTTGGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 9 0.24
44 28 0.76
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (43 bp):
AAAAGGCTCCTCTAAGTAGAAGCTTAATAACTTTTAAAATTTA
Found at i:6353032 original size:47 final size:48
Alignment explanation
Indices: 6352979--6353471 Score: 311
Period size: 47 Copynumber: 10.2 Consensus size: 48
6352969 AAAAAATTCA
6352979 ACAACTTTAAAA-TTCATCTTGAAAAAGCTTCTCTAAGCAGAAGCTCT
1 ACAACTTTAAAATTTCATCTTGAAAAAGCTTCTCTAAGCAGAAGCTCT
* * * * *
6353026 ATAACTTTAAACTTT-ATCTTAAAAAAGCTTCTCTAAGTA-AAGGCTCA
1 ACAACTTTAAAATTTCATCTTGAAAAAGCTTCTCTAAGCAGAA-GCTCT
* * * *
6353073 ACAACTTTAAAAATTTCATCTTGGAAAAGCTCCTATAAGCA-AAGGCTTT
1 ACAACTTT-AAAATTTCATCTTGAAAAAGCTTCTCTAAGCAGAA-GCTCT
* * * * * *
6353122 ACAA-TTTTAAACTTCATCTAGGAAAAGCTTCTTTAAGCAGAGGCTCT
1 ACAACTTTAAAATTTCATCTTGAAAAAGCTTCTCTAAGCAGAAGCTCT
* * *
6353169 ACAAC-TTAAAATTTCATCTTGGAAAAGC-TCTTCTAAGAAGAGGCT-T
1 ACAACTTTAAAATTTCATCTTGAAAAAGCTTC-TCTAAGCAGAAGCTCT
* * * * * *
6353215 AACAA-TTTTAAACTTCATCTTGGAAGAA-CTCCTCTAAGCAAAAACTCT
1 -ACAACTTTAAAATTTCATCTT-GAAAAAGCTTCTCTAAGCAGAAGCTCT
* *
6353263 ACAAC-TTAAAACTTCATCTTAAAAAAGCTAT-TCTAAGCA-AAGGCT-T
1 ACAACTTTAAAATTTCATCTTGAAAAAGCT-TCTCTAAGCAGAA-GCTCT
** * * * *
6353309 AACAACTTTAAAATTTAAAATTTTCATCTCAAAAAAGC-TCTTTTACGTAGAGGCT-T
1 -ACAAC-------TTTAAAA-TTTCATCTTGAAAAAGCTTC-TCTAAGCAGAAGCTCT
* * * *
6353365 AATAACTTTAAAAATTTTATCTTGAAAAAGCTCCTCTAAACAGAAGCTCT
1 -ACAACTTT-AAAATTTCATCTTGAAAAAGCTTCTCTAAGCAGAAGCTCT
* * * *
6353415 ATAACTTT-AAACTTCATCTTG-AAAAGCTTCTTTAAGTAGAAGCTCT
1 ACAACTTTAAAATTTCATCTTGAAAAAGCTTCTCTAAGCAGAAGCTCT
*
6353461 ACAACTATAAA
1 ACAACTTTAAA
6353472 CTTTAAAAAT
Statistics
Matches: 349, Mismatches: 64, Indels: 66
0.73 0.13 0.14
Matches are distributed among these distances:
46 39 0.11
47 186 0.53
48 18 0.05
49 63 0.18
50 6 0.02
54 1 0.00
55 6 0.02
56 29 0.08
57 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (48 bp):
ACAACTTTAAAATTTCATCTTGAAAAAGCTTCTCTAAGCAGAAGCTCT
Found at i:6353074 original size:94 final size:94
Alignment explanation
Indices: 6352976--6353471 Score: 350
Period size: 94 Copynumber: 5.1 Consensus size: 94
6352966 TATAAAAAAT
*
6352976 TCAACAACTTTAAAA-TTCATCTTGAAAAAGCTTCTCTAAGCAGAAGCTCTATAACTTTAAACTT
1 TCAACAACTTTAAAATTTCATCTTGAAAAAGCTTCTCTAAGCAGAAGCT-TACAACTTTAAACTT
* *
6353040 TATCTTAAAAAAGCTTCTCTAAGTAAAGGC
65 CATCTTAAAAAAGCTTCTTTAAGTAAAGGC
* * * *
6353070 TCAACAACTTTAAAAATTTCATCTTGGAAAAGCTCCTATAAGCA-AAGGCTTTACAATTTTAAAC
1 TCAACAACTTT-AAAATTTCATCTTGAAAAAGCTTCTCTAAGCAGAA-GC-TTACAACTTTAAAC
* * *
6353134 TTCATC-TAGGAAAAGCTTCTTTAAGCAGAGGC
63 TTCATCTTA-AAAAAGCTTCTTTAAGTAAAGGC
* * * * *
6353166 TCTACAAC-TTAAAATTTCATCTTGGAAAAGC-TCTTCTAAGAAGAGGCTTAACAATTTTAAACT
1 TCAACAACTTTAAAATTTCATCTTGAAAAAGCTTC-TCTAAGCAGAAGCTT-ACAACTTTAAACT
* * * * * **
6353229 TCATCTTGGAAGAA-CTCCTCTAAGCAAAAAC
64 TCATCTT-AAAAAAGCTTCTTTAAGTAAAGGC
* * *
6353260 TCTACAAC-TTAAAACTTCATCTTAAAAAAGCTAT-TCTAAGCA-AAGGCTTAACAACTTTAAAA
1 TCAACAACTTTAAAATTTCATCTTGAAAAAGCT-TCTCTAAGCAGAA-GCTT-ACAAC-------
* * * *
6353322 TTTAAAATTTTCATCTCAAAAAAGC-TCTTTTACGTAGAGGC
56 TTT-AAA-CTTCATCTTAAAAAAGCTTC-TTTAAGTAAAGGC
* * * * * *
6353363 TTAATAACTTTAAAAATTTTATCTTGAAAAAGCTCCTCTAAACAGAAGCTCTATAACTTTAAACT
1 TCAACAACTTT-AAAATTTCATCTTGAAAAAGCTTCTCTAAGCAGAAGCT-TACAACTTTAAACT
*
6353428 TCATCTT-GAAAAGCTTCTTTAAGTAGAA-GC
64 TCATCTTAAAAAAGCTTCTTTAAGTA-AAGGC
* *
6353458 TCTACAACTATAAA
1 TCAACAACTTTAAA
6353472 CTTTAAAAAT
Statistics
Matches: 313, Mismatches: 58, Indels: 62
0.72 0.13 0.14
Matches are distributed among these distances:
93 4 0.01
94 117 0.37
95 37 0.12
96 79 0.25
97 4 0.01
98 3 0.01
101 3 0.01
102 8 0.03
103 20 0.06
104 2 0.01
105 33 0.11
106 3 0.01
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (94 bp):
TCAACAACTTTAAAATTTCATCTTGAAAAAGCTTCTCTAAGCAGAAGCTTACAACTTTAAACTTC
ATCTTAAAAAAGCTTCTTTAAGTAAAGGC
Found at i:6353149 original size:143 final size:143
Alignment explanation
Indices: 6352979--6353477 Score: 473
Period size: 143 Copynumber: 3.4 Consensus size: 143
6352969 AAAAAATTCA
* * * *
6352979 ACAACTTTAAAATTCATCTTGAAAAAGCTTCTCTAAGCAGAAGCTCTATAACTTTAAACTTT-AT
1 ACAACTTTAAACTTCATCTAGAAAAAGCTTCTCTAAGCAGAAGCTCTACAACTTTAAAATTTAAT
*
6353043 CTTAAAAAAGCT-TCTCTAAGTAAAGGCTCAACAACTTTAAAAATTTCATCTTGGAAAAGCTCCT
66 CTTAAAAAAGCTCT-TCTAAGTAAAGGCTTAACAACTTTAAAAATTTCATCTTGGAAAAGCTCCT
* *
6353107 ATAAGCAAAGGCTTT
130 CTAAGCAAA-GCTCT
* * * * *
6353122 ACAATTTTAAACTTCATCTAGGAAAAGCTTCTTTAAGCAGAGGCTCTACAAC-TTAAAATTTCAT
1 ACAACTTTAAACTTCATCTAGAAAAAGCTTCTCTAAGCAGAAGCTCTACAACTTTAAAATTTAAT
** * *
6353186 CTTGGAAAAGCTCTTCTAAG-AAGAGGCTTAACAA-TTT-TAAACTTCATCTTGGAAGAA-CTCC
66 CTTAAAAAAGCTCTTCTAAGTAA-AGGCTTAACAACTTTAAAAATTTCATCTTGGAA-AAGCTCC
*
6353247 TCTAAGCAAAAACTCT
129 TCTAAGC-AAAGCTCT
*
6353263 ACAACTTAAAACTTCATCTTA-AAAAAGCTAT-TCTAAGCA-AAGGCT-TAACAACTTTAAAATT
1 ACAACTTTAAACTTCATC-TAGAAAAAGCT-TCTCTAAGCAGAA-GCTCT-ACAACTTTAAAATT
* * * * *
6353324 TAAAATTTTCATCTCAAAAAAGCTCTTTTACGTAGAGGCTTAATAACTTTAAAAATTTTATCTTG
62 T--AA---TC-T-T-AAAAAAGCTCTTCTAAGTAAAGGCTTAACAACTTTAAAAATTTCATCTTG
* *
6353389 AAAAAGCTCCTCTAAACAGAAGCTCT
119 GAAAAGCTCCTCTAAGCA-AAGCTCT
* * * * * *
6353415 ATAACTTTAAACTTCATCTTG-AAAAGCTTCTTTAAGTAGAAGCTCTACAACTATAAACTTTAA
1 ACAACTTTAAACTTCATCTAGAAAAAGCTTCTCTAAGCAGAAGCTCTACAACTTTAAAATTTAA
6353478 AAATTTTATT
Statistics
Matches: 288, Mismatches: 41, Indels: 48
0.76 0.11 0.13
Matches are distributed among these distances:
140 2 0.01
141 66 0.23
142 30 0.10
143 73 0.25
144 2 0.01
147 2 0.01
148 1 0.00
149 3 0.01
150 24 0.08
151 37 0.13
152 48 0.17
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (143 bp):
ACAACTTTAAACTTCATCTAGAAAAAGCTTCTCTAAGCAGAAGCTCTACAACTTTAAAATTTAAT
CTTAAAAAAGCTCTTCTAAGTAAAGGCTTAACAACTTTAAAAATTTCATCTTGGAAAAGCTCCTC
TAAGCAAAGCTCT
Found at i:6353456 original size:46 final size:47
Alignment explanation
Indices: 6353383--6353474 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 47
6353373 TAAAAATTTT
* *
6353383 ATCTTGAAAAAGCTCCTCTAAACAGAAGCTCTATAACTTTAAACTTC
1 ATCTTGAAAAAGCTCCTCTAAACAGAAGCTCTACAACTATAAACTTC
* * **
6353430 ATCTTG-AAAAGCTTCTTTAAGTAGAAGCTCTACAACTATAAACTT
1 ATCTTGAAAAAGCTCCTCTAAACAGAAGCTCTACAACTATAAACTT
6353475 TAAAAATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
46 33 0.85
47 6 0.15
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.32
Consensus pattern (47 bp):
ATCTTGAAAAAGCTCCTCTAAACAGAAGCTCTACAACTATAAACTTC
Found at i:6353481 original size:152 final size:151
Alignment explanation
Indices: 6352981--6353635 Score: 412
Period size: 143 Copynumber: 4.4 Consensus size: 151
6352971 AAAATTCAAC
* * * *
6352981 AACTTTAAAATTCATCTTGAAAAAGCTTCTCTAAGCAGAAGCTCT---A---T-AACTTT-AAAC
1 AACTTTAAACTTCATCTTAAAAAAGCTTCTCTAAGTAGAAGCTCTACAACTTTAAACTTTAAAAT
* * * * * *
6353038 TTTATCTTAAAAAAGCTTCTCTA-A-GTAAAGGCTCAACAACTTTAAAAATTTCATCTTGGAAAA
66 TTTATCTCAAAAAAGC-TCT-TATACGTAGAGGCTTAAAAACTTTAAAAATTTTATCTTGAAAAA
* * * *
6353101 GCTCCTATAAGCA-AAGGCTTTAC
129 GCTCCTCTAAACAGAA-GCTCTAT
* * * * *
6353124 AATTTTAAACTTCATC-TAGGAAAAGCTTCTTTAAGCAGAGGCTCT---AC----AAC-TTAAAA
1 AACTTTAAACTTCATCTTA-AAAAAGCTTCTCTAAGTAGAAGCTCTACAACTTTAAACTTTAAAA
* *** * * * * * * * *
6353180 TTTCATCTTGGAAAAGCTCTTCTAAGAAGAGGCTTAACAA-TTT-TAAACTTCATCTTGGAAGAA
65 TTTTATCTCAAAAAAGCTCTTATACGTAGAGGCTTAAAAACTTTAAAAATTTTATCTT-GAAAAA
* * * *
6353243 -CTCCTCTAAGCAAAAACTCTAC
129 GCTCCTCTAAACAGAAGCTCTAT
* * *
6353265 AACTTAAAACTTCATCTTAAAAAAGCTAT-TCTAAGCA-AAGGCT-TAACAACTTTAAAATTTAA
1 AACTTTAAACTTCATCTTAAAAAAGCT-TCTCTAAGTAGAA-GCTCT-ACAACTTTAAACTTTAA
* *
6353327 AATTTTCATCTCAAAAAAGCTCTTTTACGTAGAGGCTTAATAACTTTAAAAATTTTATCTTGAAA
63 AATTTT-ATCTCAAAAAAGCTCTTATACGTAGAGGCTTAAAAACTTTAAAAATTTTATCTTGAAA
6353392 AAGCTCCTCTAAACAGAAGCTCTAT
127 AAGCTCCTCTAAACAGAAGCTCTAT
* * *
6353417 AACTTTAAACTTCATCTT-GAAAAGCTTCTTTAAGTAGAAGCTCTACAACTATAAACTTTAAAAA
1 AACTTTAAACTTCATCTTAAAAAAGCTTCTCTAAGTAGAAGCTCTACAACTTTAAACTTT-AAAA
* * * * * *
6353481 TTTTATTTCAGAAAAGCTCCTCTAAACATAAGCTCAACGACTTTAAAAAC-TTAAAAATTCTATC
65 TTTTATCTCAAAAAAGCT-CT-TATACGT-AG----A-GGC-TTAAAAACTTTAAAAATTTTATC
* * * *
6353545 TTGGAAAAGCTCATCTAAAAAGAAGCTCAAT
121 TTGAAAAAGCTCCTCTAAACAGAAGCTCTAT
* * * * *
6353576 GACTTTAAAAATTCATCTTAAAAAAGTTTCTCTAAATAGAGGCTCTACAACTTTAAACTT
1 AACTTT-AAACTTCATCTTAAAAAAGCTTCTCTAAGTAGAAGCTCTACAACTTTAAACTT
6353636 CATTTTTTTT
Statistics
Matches: 405, Mismatches: 69, Indels: 58
0.76 0.13 0.11
Matches are distributed among these distances:
140 2 0.00
141 59 0.15
142 19 0.05
143 69 0.17
144 2 0.00
148 2 0.00
149 9 0.02
150 30 0.07
151 49 0.12
152 58 0.14
153 4 0.01
154 2 0.00
158 1 0.00
159 47 0.12
160 18 0.04
161 34 0.08
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (151 bp):
AACTTTAAACTTCATCTTAAAAAAGCTTCTCTAAGTAGAAGCTCTACAACTTTAAACTTTAAAAT
TTTATCTCAAAAAAGCTCTTATACGTAGAGGCTTAAAAACTTTAAAAATTTTATCTTGAAAAAGC
TCCTCTAAACAGAAGCTCTAT
Found at i:6353514 original size:56 final size:56
Alignment explanation
Indices: 6353452--6353574 Score: 133
Period size: 57 Copynumber: 2.2 Consensus size: 56
6353442 TTCTTTAAGT
* * * * *
6353452 AGAAGCTCTACAAC-TATAAACTTTAAAAATTTTAT-TTCAGAAAAGCTCCTCTAAAC
1 AGAAGCTCAACAACTTAAAAAC-TTAAAAATTCTATCTT-AGAAAAGCTCATCTAAAA
* * *
6353508 ATAAGCTCAACGACTTTAAAAACTTAAAAATTCTATCTTGGAAAAGCTCATCTAAAA
1 AGAAGCTCAACAAC-TTAAAAACTTAAAAATTCTATCTTAGAAAAGCTCATCTAAAA
6353565 AGAAGCTCAA
1 AGAAGCTCAA
6353575 TGACTTTAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
56 11 0.20
57 36 0.65
58 8 0.15
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.28
Consensus pattern (56 bp):
AGAAGCTCAACAACTTAAAAACTTAAAAATTCTATCTTAGAAAAGCTCATCTAAAA
Found at i:6353552 original size:57 final size:58
Alignment explanation
Indices: 6353469--6353586 Score: 159
Period size: 57 Copynumber: 2.1 Consensus size: 58
6353459 CTACAACTAT
* * * *
6353469 AAACTTTAAAAATTTTATTTCAGAAAAGCTCCTCTAAACATAAGCTCAACGACTTTAA
1 AAACTTTAAAAATTCTATTTCAGAAAAGCTCATCTAAAAAGAAGCTCAACGACTTTAA
* *
6353527 AAAC-TTAAAAATTCTATCTT-GGAAAAGCTCATCTAAAAAGAAGCTCAATGACTTTAA
1 AAACTTTAAAAATTCTAT-TTCAGAAAAGCTCATCTAAAAAGAAGCTCAACGACTTTAA
6353584 AAA
1 AAA
6353587 TTCATCTTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
57 47 0.89
58 6 0.11
ACGTcount: A:0.46, C:0.17, G:0.08, T:0.29
Consensus pattern (58 bp):
AAACTTTAAAAATTCTATTTCAGAAAAGCTCATCTAAAAAGAAGCTCAACGACTTTAA
Found at i:6365783 original size:20 final size:21
Alignment explanation
Indices: 6365758--6365807 Score: 66
Period size: 22 Copynumber: 2.4 Consensus size: 21
6365748 ATCAAAATTT
6365758 TATAAAAAAATAACA-AAAAA
1 TATAAAAAAATAACAGAAAAA
* *
6365778 TATAAAATAAATAATAGAAATA
1 TATAAAA-AAATAACAGAAAAA
6365800 TATAAAAA
1 TATAAAAA
6365808 TTTTAAGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 7 0.27
21 8 0.31
22 11 0.42
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (21 bp):
TATAAAAAAATAACAGAAAAA
Found at i:6366787 original size:5 final size:5
Alignment explanation
Indices: 6366779--6366824 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
6366769 CAAATAGATT
*
6366779 AGAAA AGAAA AGAAGA CGAAA AGAAGA A-AAA AGAAA AGAAA A-AAA A
1 AGAAA AGAAA AGAA-A AGAAA AGAA-A AGAAA AGAAA AGAAA AGAAA A
6366825 AATTATTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
4 6 0.17
5 24 0.67
6 6 0.17
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:6366816 original size:15 final size:14
Alignment explanation
Indices: 6366779--6366824 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 14
6366769 CAAATAGATT
6366779 AGAAAAGAAAAGAAGA
1 AGAAAAGAAAA-AA-A
*
6366795 CGAAAAGAAGAAAAA
1 AGAAAAGAA-AAAAA
6366810 AGAAAAGAAAAAAA
1 AGAAAAGAAAAAAA
6366824 A
1 A
6366825 AATTATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.22
15 9 0.33
16 10 0.37
17 2 0.07
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (14 bp):
AGAAAAGAAAAAAA
Found at i:6368956 original size:1 final size:1
Alignment explanation
Indices: 6368950--6368980 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
6368940 GGCTAAAATG
6368950 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
6368981 CTAAAGAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:6380476 original size:2 final size:2
Alignment explanation
Indices: 6380429--6380457 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6380419 AAGGAAACTT
6380429 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 T
6380458 GTCATGCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6382772 original size:2 final size:2
Alignment explanation
Indices: 6382765--6382792 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6382755 TATGAGCAAG
6382765 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
6382793 TATTCCCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6383305 original size:12 final size:12
Alignment explanation
Indices: 6383288--6383312 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6383278 AAATGAATTT
6383288 AAAAGAAGAAGA
1 AAAAGAAGAAGA
6383300 AAAAGAAGAAGA
1 AAAAGAAGAAGA
6383312 A
1 A
6383313 GAGGAAACTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAAGAAGAAGA
Found at i:6384254 original size:2 final size:2
Alignment explanation
Indices: 6384247--6384275 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6384237 AACCATAAAA
6384247 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6384276 TAAAGAATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6385236 original size:2 final size:2
Alignment explanation
Indices: 6385229--6385262 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
6385219 AAATAAATAA
*
6385229 AT AT AT AT AT CT 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
6385263 TCTTGAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6394788 original size:57 final size:57
Alignment explanation
Indices: 6394727--6395049 Score: 391
Period size: 57 Copynumber: 5.6 Consensus size: 57
6394717 AAAAAAAAGC
* *
6394727 ATTTTAAGGAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAATTTTTAAAAAAT
1 ATTTTAAGAAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAAT
* * * **
6394784 ATTTTAAGAAAGAGTTAAAAGTATTAATTTTT-TT-AAAATAAAAATTTTTTAAAAAGC
1 ATTTTAAGAAAAAGTTAAAAGTATCAATTTTTCTTAAAAAT-AAAA-TTTTCAAAAAAT
* * *
6394841 ATTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAATTAAAATTTTCAAAAAAC
1 ATTTTAAGAAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAAT
* * * *
6394898 ATTTTAAGGAAGAGTTAAAAGTATCAA-TTTTCTTTAAAAATAAAAATTTCAAAAGAT
1 ATTTTAAGAAAAAGTTAAAAGTATCAATTTTTC-TTAAAAATAAAATTTTCAAAAAAT
* * * * *
6394955 ATTTTTAAGAAAAAATTGAGAGTATCAATTTTCCTTAGAAATAAAATTTTCAAAAAAT
1 A-TTTTAAGAAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAAT
*
6395013 ATTGTTTGAGAAAAAGTTAAAAGTATCAATTTTTCTT
1 A-T-TTTAAGAAAAAGTTAAAAGTATCAATTTTTCTT
6395050 GCATGAAGAC
Statistics
Matches: 226, Mismatches: 32, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
55 5 0.02
56 11 0.05
57 123 0.54
58 51 0.23
59 36 0.16
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.38
Consensus pattern (57 bp):
ATTTTAAGAAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAAT
Found at i:6394848 original size:114 final size:112
Alignment explanation
Indices: 6394720--6395046 Score: 440
Period size: 114 Copynumber: 2.9 Consensus size: 112
6394710 AATTTAAAAA
* * *
6394720 AAAAAGCATTTTAAGGAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAATTTTTAAAAAATA
1 AAAAAGCATTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAATA
*
6394785 TTTTAAGAAAGAGTTAAAAGTATTAATTTTTTT-AAAATAAAAATTTTTT
66 TTTTAAGAAAGAGTTAAAAGTATCAATTTTTTTAAAAATAAAAA---TTT
* *
6394834 AAAAAGCATTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAATTAAAATTTTCAAAAAACA
1 AAAAAGCATTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAATA
*
6394899 TTTTAAGGAAGAGTTAAAAGTATCAATTTTCTTTAAAAATAAAAATTT
66 TTTTAAGAAAGAGTTAAAAGTATCAATTTT-TTTAAAAATAAAAATTT
* * * * * *
6394947 CAAAAGATATTTTTAAGAAAAAATTGAGAGTATCAATTTTCCTTAGAAATAAAATTTTCAAAAAA
1 AAAAAG-CA-TTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAA
* *
6395012 TATTGTTTGAGAAAAAGTTAAAAGTATCAATTTTT
64 TA-T-TTTAAGAAAGAGTTAAAAGTATCAATTTTT
6395047 CTTGCATGAA
Statistics
Matches: 189, Mismatches: 18, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
113 8 0.04
114 89 0.47
115 54 0.29
116 12 0.06
117 26 0.14
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (112 bp):
AAAAAGCATTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTCAAAAAATA
TTTTAAGAAAGAGTTAAAAGTATCAATTTTTTTAAAAATAAAAATTT
Found at i:6398981 original size:18 final size:19
Alignment explanation
Indices: 6398965--6399011 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
6398955 AATAATGGAT
6398965 AAAGTAAAAAAAATGGAAA
1 AAAGTAAAAAAAATGGAAA
*
6398984 AAAGTAAAAAAGAT--AAA
1 AAAGTAAAAAAAATGGAAA
6399001 AAA-TAAAAAAA
1 AAAGTAAAAAAA
6399012 TGTGAAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 7 0.27
17 6 0.23
19 13 0.50
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (19 bp):
AAAGTAAAAAAAATGGAAA
Found at i:6400330 original size:45 final size:44
Alignment explanation
Indices: 6400221--6400330 Score: 114
Period size: 45 Copynumber: 2.5 Consensus size: 44
6400211 CTTGAAAATG
* ** *
6400221 TTTTGGTGTGAATTCCTAAAGTTTTTGAATGATAACCTTTTAAA
1 TTTTGGTGTGAATCCCTAAAGTTTTAAAATGAGAACCTTTTAAA
* * * *
6400265 TATTGGATGTGAAACGCTAAAGTTTTAAAATGAGAA-TTTTTGAAA
1 TTTTGG-TGTGAATCCCTAAAGTTTTAAAATGAGAACCTTTT-AAA
6400310 TTTTGGTTGTGAATCCCTAAA
1 TTTTGG-TGTGAATCCCTAAA
6400331 AATTTTTCAA
Statistics
Matches: 52, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
44 9 0.17
45 43 0.83
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (44 bp):
TTTTGGTGTGAATCCCTAAAGTTTTAAAATGAGAACCTTTTAAA
Found at i:6400364 original size:17 final size:17
Alignment explanation
Indices: 6400342--6400384 Score: 70
Period size: 17 Copynumber: 2.5 Consensus size: 17
6400332 ATTTTTCAAA
6400342 TGTGAATCTTTGAATT-T
1 TGTGAATCTTT-AATTCT
6400359 TGTGAATCTTTAATTCT
1 TGTGAATCTTTAATTCT
6400376 TGTGAATCT
1 TGTGAATCT
6400385 AAAAATCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.23, C:0.09, G:0.16, T:0.51
Consensus pattern (17 bp):
TGTGAATCTTTAATTCT
Found at i:6400519 original size:65 final size:64
Alignment explanation
Indices: 6400354--6400539 Score: 178
Period size: 65 Copynumber: 2.8 Consensus size: 64
6400344 TGAATCTTTG
* ** * * *
6400354 AATTTTGTGAATCTTTAATTCTTGTGAATCTAAAAATCTTACGAATTTTCAATTCTTGCGAATCT
1 AATTTTGCGAATCTTT-ATTCTTGTGAAT-TTGAAATCTTACGAAATTTCAATTTTTACGAATCT
6400419 A
64 A
*** * * * *
6400420 AATTTT-CATGAATCTCCGTTCCTGCGAATCTGAAATCTTACGAACTTTCAATTTTTACGAATCT
1 AATTTTGC--GAATCTTTATTCTTGTGAATTTGAAATCTTACGAAATTTCAATTTTTACGAATCT
6400484 A
64 A
6400485 AATTTATGCGAATCTTTATTCTTGTGAATTTGAAAATCTTAC-AAATCTTCAATTT
1 AATTT-TGCGAATCTTTATTCTTGTGAATTTG-AAATCTTACGAAAT-TTCAATTT
6400540 ATGTGAATCT
Statistics
Matches: 95, Mismatches: 19, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
65 55 0.58
66 33 0.35
67 7 0.07
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.42
Consensus pattern (64 bp):
AATTTTGCGAATCTTTATTCTTGTGAATTTGAAATCTTACGAAATTTCAATTTTTACGAATCTA
Found at i:6400559 original size:34 final size:34
Alignment explanation
Indices: 6400535--6400609 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
6400525 ACAAATCTTC
**
6400535 AATTTATGTGAATCTCCAATTCTTATGAATATGAA
1 AATTT-TGTGAATCTCCAATTCTTACAAATATGAA
* *
6400570 AATTTTGTGAATCTCCAATTCTTGCGAATATGAA
1 AATTTTGTGAATCTCCAATTCTTACAAATATGAA
*
6400604 GATTTT
1 AATTTT
6400610 ACAAATCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
34 32 0.86
35 5 0.14
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.41
Consensus pattern (34 bp):
AATTTTGTGAATCTCCAATTCTTACAAATATGAA
Found at i:6400633 original size:34 final size:34
Alignment explanation
Indices: 6400586--6400650 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
6400576 GTGAATCTCC
6400586 AATTCTTGCGAATATGAAGATT-TTACAAATCATT
1 AATTCTTGCGAATATGAA-ATTCTTACAAATCATT
* *
6400620 AATTTTTGTGAATATGAAATTCTTACAAATC
1 AATTCTTGCGAATATGAAATTCTTACAAATC
6400651 TTTGAACCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 3 0.11
34 25 0.89
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (34 bp):
AATTCTTGCGAATATGAAATTCTTACAAATCATT
Done.