Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, 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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 31 of 125
Found at i:6198193 original size:8 final size:8
Alignment explanation
Indices: 6198177--6198237 Score: 72
Period size: 8 Copynumber: 7.9 Consensus size: 8
6198167 TATTTTTTAA
6198177 ATATAAAT
1 ATATAAAT
*
6198185 ATTTAAAT
1 ATATAAAT
*
6198193 ATATAATT
1 ATATAAAT
6198201 ATATAAAT
1 ATATAAAT
6198209 ATATAAAT
1 ATATAAAT
*
6198217 AGAT--AT
1 ATATAAAT
*
6198223 AAATAAAT
1 ATATAAAT
6198231 ATATAAA
1 ATATAAA
6198238 AAATAATTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
6 5 0.11
8 39 0.89
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (8 bp):
ATATAAAT
Found at i:6198222 original size:10 final size:9
Alignment explanation
Indices: 6198176--6198244 Score: 53
Period size: 8 Copynumber: 8.3 Consensus size: 9
6198166 TTATTTTTTA
6198176 AATATAAAT
1 AATATAAAT
*
6198185 -ATTTAAAT
1 AATATAAAT
6198193 -ATAT-AAT
1 AATATAAAT
*
6198200 TATATAAAT
1 AATATAAAT
6198209 -ATATAAAT
1 AATATAAAT
6198217 AGATATAAAT
1 A-ATATAAAT
*
6198227 AA-ATATAT
1 AATATAAAT
6198235 AA-A-AAAT
1 AATATAAAT
6198242 AAT
1 AAT
6198245 TTTTTATATA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
7 8 0.16
8 30 0.59
9 4 0.08
10 9 0.18
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (9 bp):
AATATAAAT
Found at i:6198228 original size:14 final size:13
Alignment explanation
Indices: 6198188--6198244 Score: 50
Period size: 12 Copynumber: 4.6 Consensus size: 13
6198178 TATAAATATT
*
6198188 TAAAT-ATATAAT
1 TAAATAATATAAA
* *
6198200 TATATAA-ATATA
1 TAAATAATATAAA
6198212 TAAATAGATATAAA
1 TAAATA-ATATAAA
6198226 TAAAT-ATATAAA
1 TAAATAATATAAA
6198238 -AAATAAT
1 TAAATAAT
6198245 TTTTTATATA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
11 4 0.11
12 21 0.58
13 2 0.06
14 9 0.25
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (13 bp):
TAAATAATATAAA
Found at i:6200191 original size:28 final size:28
Alignment explanation
Indices: 6200134--6200190 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 28
6200124 AGGGAGACAT
*
6200134 AACCGAACTCACTTTTTTAAGGCATAAA
1 AACCGAACCCACTTTTTTAAGGCATAAA
6200162 AACCGAACCCAC-TTTTTAAGGCATAAA
1 AACCGAACCCACTTTTTTAAGGCATAAA
6200189 AA
1 AA
6200191 AACTAAGACA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.25
Consensus pattern (28 bp):
AACCGAACCCACTTTTTTAAGGCATAAA
Found at i:6200287 original size:80 final size:80
Alignment explanation
Indices: 6200175--6200330 Score: 208
Period size: 80 Copynumber: 1.9 Consensus size: 80
6200165 CGAACCCACT
* *
6200175 TTTTAAGGCATAAAAAAACTAAGACATCCTATGAATGATGTCTTTAAGAGTTAAGT-ATGATCGA
1 TTTTAAGGCATAAAAAAACTAAGACATCCTATGAATGATGTCTCTAAGAG-CAA-TCATGATCGA
*
6200239 AAGTTAACAAACACACA
64 AAGATAACAAACACACA
* * * *
6200256 TTTTAAGGCAT-AAAATACTAAGAGATCCTATGGATGATGTGTCTAAGAGCAATCGATGATCGAA
1 TTTTAAGGCATAAAAAAACTAAGACATCCTATGAATGATGTCTCTAAGAGCAATC-ATGATCGAA
6200320 AGATAACAAAC
65 AGATAACAAAC
6200331 TCTTGATTAA
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
78 1 0.02
79 2 0.03
80 52 0.79
81 11 0.17
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (80 bp):
TTTTAAGGCATAAAAAAACTAAGACATCCTATGAATGATGTCTCTAAGAGCAATCATGATCGAAA
GATAACAAACACACA
Found at i:6202517 original size:1 final size:1
Alignment explanation
Indices: 6202511--6202544 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
6202501 TTCCCCATTC
6202511 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
6202545 CTGTTTGGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:6205009 original size:28 final size:28
Alignment explanation
Indices: 6204965--6205023 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
6204955 ATATAAGCTT
*
6204965 GGATGATTAGGTTGAGAGACTAAAAGTA
1 GGATGATTAGGTCGAGAGACTAAAAGTA
6204993 GGATGATTAGGTCGAGAGACTAAAAGTA
1 GGATGATTAGGTCGAGAGACTAAAAGTA
6205021 GGA
1 GGA
6205024 GAAGAAGAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.39, C:0.05, G:0.34, T:0.22
Consensus pattern (28 bp):
GGATGATTAGGTCGAGAGACTAAAAGTA
Found at i:6219981 original size:21 final size:22
Alignment explanation
Indices: 6219933--6219982 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
6219923 AACCACATCT
*
6219933 AAGAAAATATCATTTTAAAAAG
1 AAGAAAATATCATTTCAAAAAG
6219955 AA-AAAATAT-ATTTCAAAAA-
1 AAGAAAATATCATTTCAAAAAG
6219974 AATGAAAAT
1 AA-GAAAAT
6219983 CAGAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 9 0.36
21 12 0.48
22 2 0.08
ACGTcount: A:0.64, C:0.04, G:0.06, T:0.26
Consensus pattern (22 bp):
AAGAAAATATCATTTCAAAAAG
Found at i:6243170 original size:22 final size:20
Alignment explanation
Indices: 6243129--6243172 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
6243119 AAATCATTAT
* *
6243129 CTAAAAAATGTTTAGTAAAA
1 CTAAAAAATGTTGAGAAAAA
6243149 CTAAAAAATGTGATGAGAAAAA
1 CTAAAAAATGT--TGAGAAAAA
6243171 CT
1 CT
6243173 TATCATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
22 9 0.45
ACGTcount: A:0.55, C:0.07, G:0.14, T:0.25
Consensus pattern (20 bp):
CTAAAAAATGTTGAGAAAAA
Found at i:6249712 original size:76 final size:76
Alignment explanation
Indices: 6249623--6249782 Score: 189
Period size: 76 Copynumber: 2.1 Consensus size: 76
6249613 AAGAATTACA
* *
6249623 TTTTTTATCTTAAAAATATAGTTTTTGTTAAAATT-TCATAA-TTTCAAAAATATAATTTTAACA
1 TTTTTTATCTTAAAAATATAGTATTTGTTAAAATTCT-A-AATTTTCAAAAATAAAATTTTAACA
* **
6249686 TTTACTATGTTTT
64 TTCACTACATTTT
* * * * *
6249699 TTTTTTATTTTAAAAATGTGGTATTTGTTAAAATTCTAAATTTTTAAAAATAAAATTTTAATATT
1 TTTTTTATCTTAAAAATATAGTATTTGTTAAAATTCTAAATTTTCAAAAATAAAATTTTAACATT
6249764 CACTACATTTT
66 CACTACATTTT
6249775 TTATTTTA
1 TT-TTTTA
6249783 GAAACACAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
75 2 0.03
76 63 0.89
77 6 0.08
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (76 bp):
TTTTTTATCTTAAAAATATAGTATTTGTTAAAATTCTAAATTTTCAAAAATAAAATTTTAACATT
CACTACATTTT
Found at i:6252133 original size:29 final size:29
Alignment explanation
Indices: 6252022--6252165 Score: 105
Period size: 29 Copynumber: 4.9 Consensus size: 29
6252012 TCAGTTTTAC
* * *
6252022 AATTT-TATTTAAATAAATCTTTATTCTTT
1 AATTTATATCTAAATAAACCTTTA-ACTTT
* * *
6252051 TA-TTATATATAAATAAATCC-TTAATATTT
1 AATTTATATCTAAATAAA-CCTTTAA-CTTT
* * * *
6252080 AATTTACATCCAAATAATCCATTAACTTT
1 AATTTATATCTAAATAAACCTTTAACTTT
*
6252109 AATTTATATCTAAATAAACCTTTAAATTTTT
1 AATTTATATCTAAATAAACCTTT-AA-CTTT
* *
6252140 AATTTGTATCTAAATAAGCCTTTAAC
1 AATTTATATCTAAATAAACCTTTAAC
6252166 ATAAATCATT
Statistics
Matches: 89, Mismatches: 19, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
28 2 0.02
29 43 0.48
30 20 0.22
31 24 0.27
ACGTcount: A:0.40, C:0.12, G:0.01, T:0.47
Consensus pattern (29 bp):
AATTTATATCTAAATAAACCTTTAACTTT
Found at i:6252144 original size:31 final size:30
Alignment explanation
Indices: 6252106--6252164 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
6252096 ATCCATTAAC
*
6252106 TTTAATTTATATCTAAATAAACCTTTAAATT
1 TTTAATTTATATCTAAATAAACCTTT-AATA
* *
6252137 TTTAATTTGTATCTAAATAAGCCTTTAA
1 TTTAATTTATATCTAAATAAACCTTTAA
6252165 CATAAATCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.47
Consensus pattern (30 bp):
TTTAATTTATATCTAAATAAACCTTTAATA
Found at i:6252156 original size:60 final size:59
Alignment explanation
Indices: 6252053--6252165 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 59
6252043 TATTCTTTTA
*
6252053 TTATATATAAATAAATCCTTAATATTTAATTTACATCCAAATAATCCATTAACTTTAAT
1 TTATATATAAATAAATCCTTAATATTTAATTTACATCCAAATAAGCCATTAACTTTAAT
* * ** * *
6252112 TTATATCTAAATAAA-CCTTTAAATTTTTAATTTGTATCTAAATAAGCCTTTAAC
1 TTATATATAAATAAATCC-TT-AATATTTAATTTACATCCAAATAAGCCATTAAC
6252166 ATAAATCATT
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
58 2 0.04
59 16 0.36
60 27 0.60
ACGTcount: A:0.42, C:0.13, G:0.02, T:0.43
Consensus pattern (59 bp):
TTATATATAAATAAATCCTTAATATTTAATTTACATCCAAATAAGCCATTAACTTTAAT
Found at i:6254914 original size:20 final size:19
Alignment explanation
Indices: 6254893--6254943 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
6254883 CTATTTTGTA
6254893 AAATTAAAAATATATATAT
1 AAATTAAAAATATATATAT
* * *
6254912 AAA-TAAAATTTTATTTAT
1 AAATTAAAAATATATATAT
6254930 CAAATTAAAAATAT
1 -AAATTAAAAATAT
6254944 GAAACTTTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 12 0.48
19 6 0.24
20 7 0.28
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (19 bp):
AAATTAAAAATATATATAT
Found at i:6259553 original size:12 final size:12
Alignment explanation
Indices: 6259538--6259562 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6259528 TTTGTTCAAA
6259538 TCCATTCATCAT
1 TCCATTCATCAT
6259550 TCCATTCATCAT
1 TCCATTCATCAT
6259562 T
1 T
6259563 TTATATTAGG
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:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (12 bp):
TCCATTCATCAT
Found at i:6260102 original size:15 final size:15
Alignment explanation
Indices: 6260075--6260121 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
6260065 GAGATTAGAA
*
6260075 ATAATAATAATAATT
1 ATAATAATTATAATT
*
6260090 ATTATAATTATAATT
1 ATAATAATTATAATT
* *
6260105 AAAAAAATTATAATT
1 ATAATAATTATAATT
6260120 AT
1 AT
6260122 GATTAAAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAATAATTATAATT
Found at i:6260114 original size:21 final size:21
Alignment explanation
Indices: 6260090--6260129 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
6260080 AATAATAATT
6260090 ATTATAATTATAATTAAAAAA
1 ATTATAATTATAATTAAAAAA
*
6260111 ATTATAATTATGATTAAAA
1 ATTATAATTATAATTAAAA
6260130 TTTTAATAAA
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:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (21 bp):
ATTATAATTATAATTAAAAAA
Found at i:6264295 original size:22 final size:22
Alignment explanation
Indices: 6264267--6264315 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
6264257 TATAGTTGAT
6264267 AGCCTTGGAATGGACGTTACCA
1 AGCCTTGGAATGGACGTTACCA
6264289 AGCCTTGGAATGGACGTTACCA
1 AGCCTTGGAATGGACGTTACCA
6264311 AGCCT
1 AGCCT
6264316 AGGAGGCGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (22 bp):
AGCCTTGGAATGGACGTTACCA
Found at i:6265657 original size:8 final size:8
Alignment explanation
Indices: 6265648--6265678 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
6265638 AGAGAGAGAC
*
6265648 ACACACAC
1 ACACACAA
6265656 ACACACAA
1 ACACACAA
6265664 ACACACAA
1 ACACACAA
6265672 ACACACA
1 ACACACA
6265679 TAACCACGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.58, C:0.42, G:0.00, T:0.00
Consensus pattern (8 bp):
ACACACAA
Found at i:6266285 original size:21 final size:20
Alignment explanation
Indices: 6266259--6266327 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
6266249 GTCACTGATT
6266259 TTAATTTTATTATTATAATAA
1 TTAATTTTATT-TTATAATAA
6266280 TTAATTTTATTTT-T-AT-A
1 TTAATTTTATTTTATAATAA
*
6266297 TTATTTTTAATTTTATTAA-AA
1 TTAATTTT-ATTTTA-TAATAA
6266318 TTAATTTTAT
1 TTAATTTTAT
6266328 CATTCATCCA
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
17 8 0.20
18 7 0.17
19 1 0.02
20 5 0.12
21 20 0.49
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTAATTTTATTTTATAATAA
Found at i:6268644 original size:68 final size:67
Alignment explanation
Indices: 6268572--6268787 Score: 175
Period size: 68 Copynumber: 3.3 Consensus size: 67
6268562 TTTCATATAC
6268572 TTGAACATTAGTATTAAGGAAGATTGTTGGTAGATAGAAGGTTGGCTGTATCCATCAACTCAATG
1 TTGAACATTAGTATTAAGGAAGATTGTTGGTAGATAG-AGGTTGGCTGTATCCATCAACTCAATG
6268637 TGT
65 TGT
* ** * * *
6268640 TTGAATATTAGTATTAAAGGTTCGACTTGAAT-GTA-AT-GA-GTAT--ATGATAAT--AT-GA-
1 TTGAACATTAGTATT-AAGG-AAGA-TTG-TTGGTAGATAGAGGT-TGGCTG-T-ATCCATCAAC
* **
6268695 T-AATATAC
59 TCAATGTGT
*
6268703 TTGAACATTAGTATTAAGGAAGATTGTTGGCAGATAGGAGGTTGGCTGTATCCATCAACTCAATG
1 TTGAACATTAGTATTAAGGAAGATTGTTGGTAGATA-GAGGTTGGCTGTATCCATCAACTCAATG
6268768 TGT
65 TGT
*
6268771 TTGAATATTAGTATTAA
1 TTGAACATTAGTATTAA
6268788 AGGTTCAACT
Statistics
Matches: 109, Mismatches: 20, Indels: 38
0.65 0.12 0.23
Matches are distributed among these distances:
59 1 0.01
60 5 0.05
61 4 0.04
62 4 0.04
63 23 0.21
64 4 0.04
65 5 0.05
66 5 0.05
67 4 0.04
68 38 0.35
69 5 0.05
70 4 0.04
71 6 0.06
72 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.22, T:0.36
Consensus pattern (67 bp):
TTGAACATTAGTATTAAGGAAGATTGTTGGTAGATAGAGGTTGGCTGTATCCATCAACTCAATGT
GT
Found at i:6268800 original size:131 final size:131
Alignment explanation
Indices: 6268566--6268824 Score: 482
Period size: 131 Copynumber: 2.0 Consensus size: 131
6268556 CATCAATTTC
*
6268566 ATATACTTGAACATTAGTATTAAGGAAGATTGTTGGTAGATAGAAGGTTGGCTGTATCCATCAAC
1 ATATACTTGAACATTAGTATTAAGGAAGATTGTTGGCAGATAGAAGGTTGGCTGTATCCATCAAC
* *
6268631 TCAATGTGTTTGAATATTAGTATTAAAGGTTCGACTTGAATGTAATGAGTATATGATAATATGAT
66 TCAATGTGTTTGAATATTAGTATTAAAGGTTCAACTTGAATGTAACGAGTATATGATAATATGAT
6268696 A
131 A
*
6268697 ATATACTTGAACATTAGTATTAAGGAAGATTGTTGGCAGATAGGAGGTTGGCTGTATCCATCAAC
1 ATATACTTGAACATTAGTATTAAGGAAGATTGTTGGCAGATAGAAGGTTGGCTGTATCCATCAAC
6268762 TCAATGTGTTTGAATATTAGTATTAAAGGTTCAACTTGAATGTAACGAGTATATGATAATATG
66 TCAATGTGTTTGAATATTAGTATTAAAGGTTCAACTTGAATGTAACGAGTATATGATAATATG
6268825 TAGAAATGAA
Statistics
Matches: 124, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
131 124 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (131 bp):
ATATACTTGAACATTAGTATTAAGGAAGATTGTTGGCAGATAGAAGGTTGGCTGTATCCATCAAC
TCAATGTGTTTGAATATTAGTATTAAAGGTTCAACTTGAATGTAACGAGTATATGATAATATGAT
A
Found at i:6269878 original size:32 final size:33
Alignment explanation
Indices: 6269817--6269883 Score: 109
Period size: 32 Copynumber: 2.0 Consensus size: 33
6269807 TCAAACTCAT
6269817 ATGCTGAGGGAGCATTAAAAAAAAAAAAAACAAA
1 ATGCTGAGGGAGCATT-AAAAAAAAAAAAACAAA
*
6269851 ATGCTGAGGGAGCATT-AAAAAAGAAAAACAAA
1 ATGCTGAGGGAGCATTAAAAAAAAAAAAACAAA
6269883 A
1 A
6269884 CTATCTCCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 16 0.50
34 16 0.50
ACGTcount: A:0.60, C:0.09, G:0.19, T:0.12
Consensus pattern (33 bp):
ATGCTGAGGGAGCATTAAAAAAAAAAAAACAAA
Found at i:6270181 original size:21 final size:19
Alignment explanation
Indices: 6270147--6270185 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
6270137 ATTTTTATAA
6270147 TAAAATTATAAAAATAGATT
1 TAAAATTATAAAAA-AGATT
*
6270167 TAAAATTTATCAAAAAGAT
1 TAAAA-TTATAAAAAAGAT
6270186 AAATTTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (19 bp):
TAAAATTATAAAAAAGATT
Found at i:6271074 original size:25 final size:24
Alignment explanation
Indices: 6270963--6271076 Score: 81
Period size: 25 Copynumber: 4.7 Consensus size: 24
6270953 TTTAGATTTT
* *
6270963 AGGGTTTGAAAGATTTTAGGATTTTG
1 AGGGTTT-AGAGATTTTAGG-GTTTG
* * *
6270989 AGGGTCTAG-GATTTAAAGGTTT-
1 AGGGTTTAGAGATTTTAGGGTTTG
* * *
6271011 AGGGTTTAGAAATCTTAGGGTTTCA
1 AGGGTTTAGAGATTTTAGGGTTT-G
*
6271036 AGGATTTTAG-GATTTTAGGGTTTGG
1 AGG-GTTTAGAGATTTTAGGGTTT-G
6271061 AGGGTTTAGAGATTTT
1 AGGGTTTAGAGATTTT
6271077 GATTTTAGAT
Statistics
Matches: 67, Mismatches: 16, Indels: 11
0.71 0.17 0.12
Matches are distributed among these distances:
22 8 0.12
23 12 0.18
24 12 0.18
25 24 0.36
26 11 0.16
ACGTcount: A:0.25, C:0.03, G:0.32, T:0.40
Consensus pattern (24 bp):
AGGGTTTAGAGATTTTAGGGTTTG
Found at i:6271115 original size:14 final size:14
Alignment explanation
Indices: 6271096--6271146 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
6271086 TTTTAAAGGG
6271096 TTTAGGGTTTTGAT
1 TTTAGGGTTTTGAT
* **
6271110 TTTAGGGTTTAGGG
1 TTTAGGGTTTTGAT
*
6271124 TTTA-AGTTTTGAT
1 TTTAGGGTTTTGAT
6271137 TTTAGGGTTT
1 TTTAGGGTTT
6271147 AAAAAGTTTA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 9 0.32
14 19 0.68
ACGTcount: A:0.16, C:0.00, G:0.29, T:0.55
Consensus pattern (14 bp):
TTTAGGGTTTTGAT
Found at i:6271133 original size:21 final size:22
Alignment explanation
Indices: 6271083--6271214 Score: 85
Period size: 21 Copynumber: 6.0 Consensus size: 22
6271073 TTTTGATTTT
6271083 AGATTTTAAAGGGTTTAGGGTTT-
1 AGATTTT--AGGGTTTAGGGTTTA
*
6271106 TGATTTTAGGGTTTAGGGTTTA
1 AGATTTTAGGGTTTAGGGTTTA
**
6271128 AG-TTTT-GATTTTAGGGTTTAA
1 AGATTTTAGGGTTTAGGGTTT-A
* * *
6271149 AAAGTTTAGGGTTTTA-GTTTTA
1 AGATTTTAGGG-TTTAGGGTTTA
* *
6271171 AGATTTGGAGGGTTTAAGGTTT-
1 AGATTT-TAGGGTTTAGGGTTTA
* * *
6271193 CGATTTTAGAGTTTGGGGTTTA
1 AGATTTTAGGGTTTAGGGTTTA
6271215 GGGTTTTGAT
Statistics
Matches: 83, Mismatches: 18, Indels: 17
0.70 0.15 0.14
Matches are distributed among these distances:
20 11 0.13
21 31 0.37
22 18 0.22
23 19 0.23
24 4 0.05
ACGTcount: A:0.23, C:0.01, G:0.30, T:0.47
Consensus pattern (22 bp):
AGATTTTAGGGTTTAGGGTTTA
Found at i:6271138 original size:88 final size:88
Alignment explanation
Indices: 6271046--6271255 Score: 221
Period size: 87 Copynumber: 2.4 Consensus size: 88
6271036 AGGATTTTAG
** ** * *
6271046 GATTTTAGGGTTTGGAGGGTTTAGAGATTTT-GATTTT-AGATTTTAAAGGGTTTAGGGTTTTGA
1 GATTTTAGGGTTTAAAAAGTTTAG-GATTTTAG-TTTTAAGA-TTTAAAGGGTTTAAGGTTTCGA
*
6271109 TTTTAGGGTTTAGGGTTTA-AGTTTT
63 TTTTAGAGTTTAGGGTTTAGAGTTTT
* **
6271134 GATTTTAGGGTTTAAAAAGTTTAGGGTTTTAGTTTTAAGATTTGGAGGGTTTAAGGTTTCGATTT
1 GATTTTAGGGTTTAAAAAGTTTAGGATTTTAGTTTTAAGATTTAAAGGGTTTAAGGTTTCGATTT
* *
6271199 TAGAGTTTGGGGTTTAGGGTTTT
66 TAGAGTTTAGGGTTTAGAGTTTT
* * * *
6271222 GATTTTA-GGATTCAAAGGTTTAGGGTTTTAGTTT
1 GATTTTAGGGTTTAAAAAGTTTAGGATTTTAGTTT
6271256 AGGGTTTGAA
Statistics
Matches: 104, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
87 68 0.65
88 36 0.35
ACGTcount: A:0.21, C:0.01, G:0.30, T:0.48
Consensus pattern (88 bp):
GATTTTAGGGTTTAAAAAGTTTAGGATTTTAGTTTTAAGATTTAAAGGGTTTAAGGTTTCGATTT
TAGAGTTTAGGGTTTAGAGTTTT
Found at i:6271158 original size:36 final size:38
Alignment explanation
Indices: 6271116--6271187 Score: 103
Period size: 36 Copynumber: 1.9 Consensus size: 38
6271106 TGATTTTAGG
*
6271116 GTTTAGGGTTTAAGTTTT-GATTT-TAGGGTTTAAAAA
1 GTTTAGGGTTTAAGTTTTAGATTTGGAGGGTTTAAAAA
*
6271152 GTTTAGGGTTTTAGTTTTAAGATTTGGAGGGTTTAA
1 GTTTAGGGTTTAAGTTTT-AGATTTGGAGGGTTTAA
6271188 GGTTTCGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 17 0.55
38 5 0.16
39 9 0.29
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (38 bp):
GTTTAGGGTTTAAGTTTTAGATTTGGAGGGTTTAAAAA
Found at i:6271200 original size:87 final size:87
Alignment explanation
Indices: 6271092--6271255 Score: 240
Period size: 87 Copynumber: 1.9 Consensus size: 87
6271082 TAGATTTTAA
* * * *
6271092 AGGGTTTAGGGTTTTGATTTTAGGGTTTAGGGTTTA-AGTTTTGATTTTAGGGTTTAAAAAGTTT
1 AGGGTTTAAGGTTTCGATTTTAGAGTTTAGGGTTTAGAGTTTTGATTTTA-GGATTAAAAAGTTT
6271156 AGGGTTTTAGTTTTAAGATTTGG
65 AGGGTTTTAGTTTTAAGATTTGG
* * * *
6271179 AGGGTTTAAGGTTTCGATTTTAGAGTTTGGGGTTTAGGGTTTTGATTTTAGGATTCAAAGGTTTA
1 AGGGTTTAAGGTTTCGATTTTAGAGTTTAGGGTTTAGAGTTTTGATTTTAGGATTAAAAAGTTTA
6271244 GGGTTTTAGTTT
66 GGGTTTTAGTTT
6271256 AGGGTTTGAA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
87 56 0.82
88 12 0.18
ACGTcount: A:0.21, C:0.01, G:0.30, T:0.48
Consensus pattern (87 bp):
AGGGTTTAAGGTTTCGATTTTAGAGTTTAGGGTTTAGAGTTTTGATTTTAGGATTAAAAAGTTTA
GGGTTTTAGTTTTAAGATTTGG
Found at i:6271290 original size:14 final size:14
Alignment explanation
Indices: 6271267--6271314 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
6271257 GGGTTTGAAA
*
6271267 GTTTTGATTTTAGG
1 GTTTTAATTTTAGG
*
6271281 GTTTTAATTTTAGA
1 GTTTTAATTTTAGG
*
6271295 GTTTAAATGGTTTAGG
1 GTTTTAAT--TTTAGG
6271311 GTTT
1 GTTT
6271315 GATGGGTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 19 0.68
16 9 0.32
ACGTcount: A:0.21, C:0.00, G:0.25, T:0.54
Consensus pattern (14 bp):
GTTTTAATTTTAGG
Found at i:6271314 original size:16 final size:15
Alignment explanation
Indices: 6271275--6271330 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
6271265 AAGTTTTGAT
6271275 TTTAGGGTTTTAAT--
1 TTTAGGG-TTTAATGG
*
6271289 TTTAGAGTTTAAATGG
1 TTTAGGGTTT-AATGG
*
6271305 TTTAGGGTTTGATGGG
1 TTTAGGGTTTAAT-GG
6271321 TTTAGGGTTT
1 TTTAGGGTTT
6271331 CGCTTTTAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
13 3 0.09
14 9 0.26
15 2 0.06
16 21 0.60
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (15 bp):
TTTAGGGTTTAATGG
Found at i:6271322 original size:138 final size:142
Alignment explanation
Indices: 6271046--6271350 Score: 322
Period size: 138 Copynumber: 2.1 Consensus size: 142
6271036 AGGATTTTAG
* * *
6271046 GATTTTAGGGTTTGGAGGGTTTAGAGATTTTGATTTTAGATTTTAAAGGGTTTAGGGTTTTGATT
1 GATTTTAGAGTTT-G-GGGTTTAGAGATTTTGATTTTAGATTTCAAAGGGTTTAGGGTTTTGAGT
* * * *
6271111 TTAGGGTTTAGGGTTTAAGTTTTGATTTTAGGGTTTAAAAAGTTTAGGGTTTTAGTTTTAAGATT
64 TTAGGGTTT--GG-TAAAGTTTTGATTTTAGGGTTT-AAAAGTTTAGAGTTTAAGGTTTAAGATT
6271176 TGGAGGGTTTAAGGTTTC
125 TGGAGGGTTTAAGGTTTC
*
6271194 GATTTTAGAGTTTGGGGTTTAG-GGTTTTGATTTTAGGA-TTCAAA-GGTTTAGGGTTTT-AGTT
1 GATTTTAGAGTTTGGGGTTTAGAGATTTTGATTTTA-GATTTCAAAGGGTTTAGGGTTTTGAGTT
* * * *
6271255 TAGGGTTT-G-AAAGTTTTGATTTTAGGGTTT-TAATTTTAGAGTTTAAATGGTTTAGGGTTT-G
65 TAGGGTTTGGTAAAGTTTTGATTTTAGGGTTTAAAAGTTTAGAGTTT-AA-GGTTTAAGATTTGG
*
6271316 ATGGGTTTAGGGTTTC
128 A-GGGTTTAAGGTTTC
*
6271332 GCTTTTA-AGGTTTGGGGTT
1 GATTTTAGA-GTTTGGGGTT
6271351 AAAAATCCTA
Statistics
Matches: 138, Mismatches: 14, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
136 11 0.08
137 4 0.03
138 58 0.42
140 1 0.01
143 11 0.08
144 13 0.09
145 17 0.12
146 10 0.07
147 1 0.01
148 12 0.09
ACGTcount: A:0.21, C:0.01, G:0.30, T:0.48
Consensus pattern (142 bp):
GATTTTAGAGTTTGGGGTTTAGAGATTTTGATTTTAGATTTCAAAGGGTTTAGGGTTTTGAGTTT
AGGGTTTGGTAAAGTTTTGATTTTAGGGTTTAAAAGTTTAGAGTTTAAGGTTTAAGATTTGGAGG
GTTTAAGGTTTC
Found at i:6272622 original size:22 final size:22
Alignment explanation
Indices: 6272579--6272623 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
6272569 GAGGTGTGCA
*
6272579 GGGAGTTGGGTTGTTTAGGTAT
1 GGGAGTTGGGTTGTTGAGGTAT
*
6272601 GGGAGCTTGGG-TGTTGATGTAT
1 GGGAG-TTGGGTTGTTGAGGTAT
6272623 G
1 G
6272624 CCTCTGAGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.13, C:0.02, G:0.47, T:0.38
Consensus pattern (22 bp):
GGGAGTTGGGTTGTTGAGGTAT
Found at i:6273645 original size:13 final size:13
Alignment explanation
Indices: 6273615--6273647 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
6273605 TCTATTTTTT
6273615 CTTTTTTTTTAAA
1 CTTTTTTTTTAAA
*
6273628 CTTTTCTTTT-AA
1 CTTTTTTTTTAAA
6273640 CTTTTTTT
1 CTTTTTTT
6273648 AAGCAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (13 bp):
CTTTTTTTTTAAA
Found at i:6276688 original size:3 final size:3
Alignment explanation
Indices: 6276680--6276710 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
6276670 AGCATAATAT
6276680 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
6276711 GTTTTCACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6276839 original size:8 final size:8
Alignment explanation
Indices: 6276823--6276856 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
6276813 ATAGAATAAA
*
6276823 AAATAAAT
1 AAATCAAT
6276831 AAATCAAT
1 AAATCAAT
6276839 AAATCAAT
1 AAATCAAT
6276847 AAATC-AT
1 AAATCAAT
6276854 AAA
1 AAA
6276857 ATAATGAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
7 5 0.20
8 20 0.80
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.24
Consensus pattern (8 bp):
AAATCAAT
Found at i:6276858 original size:16 final size:15
Alignment explanation
Indices: 6276811--6276860 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
6276801 AAATCAACCA
*
6276811 AAATAGAATAAAAAAT
1 AAATA-AATCAAAAAT
6276827 AAATAAATCAATAAAT
1 AAATAAATCAA-AAAT
*
6276843 CAATAAATCATAAAAT
1 AAATAAATCA-AAAAT
6276859 AA
1 AA
6276861 TGAACGATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 5 0.17
16 23 0.79
17 1 0.03
ACGTcount: A:0.70, C:0.06, G:0.02, T:0.22
Consensus pattern (15 bp):
AAATAAATCAAAAAT
Found at i:6277137 original size:43 final size:40
Alignment explanation
Indices: 6277079--6277478 Score: 225
Period size: 43 Copynumber: 9.3 Consensus size: 40
6277069 AATATAAAAA
*
6277079 CTCCTCTAAGCAAAGGCTCACAACTTTTGAAAAATAACTAAGG
1 CTCCTCTAA-TAAAGGCTCACAAC-TTTGAAAAATAA-TAAGG
* * *
6277122 CTCTTCTACATAAAGGTTCA-ATGACTTTTGGAAAATAAATAAGG
1 CTCCTCTA-ATAAAGGCTCACA--AC-TTTGAAAAAT-AATAAGG
* * *
6277166 CTCCTCTAATCAGAGACTTAACAACTTTGAAAAAATGAATAAGG
1 CTCCTCTAAT-AAAGGC-TCACAACTTTG-AAAAAT-AATAAGG
* *
6277210 CTCATCTAATTAGAA-GCTCAACAACTTTGGAAAATAGATAAGG
1 CTCCTCTAA-TA-AAGGCTC-ACAACTTTGAAAAATA-ATAAGG
* *
6277253 CTCCTCTAATCAGAGGCTTAACAACTTTGAAAAATAAATAAGG
1 CTCCTCTAAT-AAAGGC-TCACAACTTTGAAAAAT-AATAAGG
* * *
6277296 CTCCTCTAATTAGAGGTTCAACAACTTTGGAAAAA-AGTTAAGG
1 CTCCTCTAA-TAAAGGCTC-ACAACTTT-GAAAAATA-ATAAGG
** * *
6277339 CTAATCTAATCAGAGGCTCAACAACTTT-AGAAAATAAATGAGG
1 CTCCTCTAAT-AAAGGCTC-ACAACTTTGA-AAAAT-AATAAGG
* * * * *
6277382 CCCCTTTAATCAGAGGCTAATAACTTTGAAAAAATAAATAAGG
1 CTCCTCTAAT-AAAGGCTCACAACTTTG-AAAAAT-AATAAGG
* * * *
6277425 CTCCTATAATCAGAGGCTCAACAACTTTGGAAAATAAATAAAG
1 CTCCTCTAAT-AAAGGCTC-ACAACTTTGAAAAAT-AATAAGG
6277468 CTCCTC-AATAA
1 CTCCTCTAATAA
6277479 TCATGTCTAG
Statistics
Matches: 287, Mismatches: 43, Indels: 56
0.74 0.11 0.15
Matches are distributed among these distances:
41 2 0.01
42 21 0.07
43 177 0.62
44 80 0.28
45 6 0.02
46 1 0.00
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (40 bp):
CTCCTCTAATAAAGGCTCACAACTTTGAAAAATAATAAGG
Found at i:6277338 original size:86 final size:86
Alignment explanation
Indices: 6277079--6277473 Score: 422
Period size: 86 Copynumber: 4.6 Consensus size: 86
6277069 AATATAAAAA
* * * * * * *
6277079 CTCCTCTAAGCAAAGGC-TCACAACTTTTGAAAAATAACTAAGGCTCTTCTACA-TAAAGGTTCA
1 CTCCTCTAATCAGAGGCTTAACAAC-TTTGAAAAATAAATAAGGCTCCTCTA-ATTAGAGGCTCA
**
6277142 ATGACTTTTGGAAAATAA-ATAAGG
64 ACAAC-TTTGGAAAA-AAGATAAGG
* * * *
6277166 CTCCTCTAATCAGAGACTTAACAACTTTGAAAAAATGAATAAGGCTCATCTAATTAGAAGCTCAA
1 CTCCTCTAATCAGAGGCTTAACAACTTTG-AAAAATAAATAAGGCTCCTCTAATTAGAGGCTCAA
*
6277231 CAACTTTGGAAAATAGATAAGG
65 CAACTTTGGAAAAAAGATAAGG
*
6277253 CTCCTCTAATCAGAGGCTTAACAACTTTGAAAAATAAATAAGGCTCCTCTAATTAGAGGTTCAAC
1 CTCCTCTAATCAGAGGCTTAACAACTTTGAAAAATAAATAAGGCTCCTCTAATTAGAGGCTCAAC
*
6277318 AACTTTGGAAAAAAGTTAAGG
66 AACTTTGGAAAAAAGATAAGG
** * * * * *
6277339 CTAATCTAATCAGAGGCTCAACAACTTT-AGAAAATAAATGAGGCCCCTTTAATCAGAGGCT-AA
1 CTCCTCTAATCAGAGGCTTAACAACTTTGA-AAAATAAATAAGGCTCCTCTAATTAGAGGCTCAA
* * *
6277402 TAACTTTGAAAAAATAAATAAGG
65 CAACTTTGGAAAAA-AGATAAGG
* * * *
6277425 CTCCTATAATCAGAGGCTCAACAACTTTGGAAAATAAATAAAGCTCCTC
1 CTCCTCTAATCAGAGGCTTAACAACTTTGAAAAATAAATAAGGCTCCTC
6277474 AATAATCATG
Statistics
Matches: 261, Mismatches: 40, Indels: 15
0.83 0.13 0.05
Matches are distributed among these distances:
85 15 0.06
86 149 0.57
87 62 0.24
88 35 0.13
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (86 bp):
CTCCTCTAATCAGAGGCTTAACAACTTTGAAAAATAAATAAGGCTCCTCTAATTAGAGGCTCAAC
AACTTTGGAAAAAAGATAAGG
Found at i:6277373 original size:129 final size:130
Alignment explanation
Indices: 6277148--6277458 Score: 432
Period size: 129 Copynumber: 2.4 Consensus size: 130
6277138 TTCAATGACT
* *
6277148 TTTGGAAAATAAATAAGGCTCCTCTAATCAGAGACTT-AACAACTTT-GAAAAAATGAATAAGGC
1 TTTGAAAAATAAATAAGGCTCCTCTAATCAGAG-GTTCAACAACTTTGGAAAAAATGAATAAGGC
* * * * *
6277211 TCATCTAATTAGAAGCTCAACAACTTTGGAAAATAGATAAGGCTCCTCTAATCAGAGGCTTAACA
65 TAATCTAATCAGAAGCTCAACAACTTTAGAAAATAAATAAGGCCCCTCTAATCAGAGGC-TAACA
6277276 AC
129 AC
* *
6277278 TTTGAAAAATAAATAAGGCTCCTCTAATTAGAGGTTCAACAACTTTGGAAAAAA-G-TTAAGGCT
1 TTTGAAAAATAAATAAGGCTCCTCTAATCAGAGGTTCAACAACTTTGGAAAAAATGAATAAGGCT
* * * *
6277341 AATCTAATCAGAGGCTCAACAACTTTAGAAAATAAATGAGGCCCCTTTAATCAGAGGCTAATAAC
66 AATCTAATCAGAAGCTCAACAACTTTAGAAAATAAATAAGGCCCCTCTAATCAGAGGCTAACAAC
* *
6277406 TTTGAAAAAATAAATAAGGCTCCTATAATCAGAGGCTCAACAACTTTGGAAAA
1 TTTG-AAAAATAAATAAGGCTCCTCTAATCAGAGGTTCAACAACTTTGGAAAA
6277459 TAAATAAAGC
Statistics
Matches: 162, Mismatches: 16, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
128 10 0.06
129 104 0.64
130 41 0.25
131 7 0.04
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (130 bp):
TTTGAAAAATAAATAAGGCTCCTCTAATCAGAGGTTCAACAACTTTGGAAAAAATGAATAAGGCT
AATCTAATCAGAAGCTCAACAACTTTAGAAAATAAATAAGGCCCCTCTAATCAGAGGCTAACAAC
Found at i:6278882 original size:8 final size:8
Alignment explanation
Indices: 6278869--6278986 Score: 60
Period size: 8 Copynumber: 15.8 Consensus size: 8
6278859 TTAAGTCTTT
6278869 ATTTTTTC
1 ATTTTTTC
*
6278877 ATTTTTTT
1 ATTTTTTC
6278885 ATTTTTT-
1 ATTTTTTC
6278892 -TTCATTTTC
1 ATT--TTTTC
6278901 A--TTTTC
1 ATTTTTTC
6278907 A--TTTTC
1 ATTTTTTC
6278913 ATTTTTTC
1 ATTTTTTC
6278921 ATTTTTTC
1 ATTTTTTC
*
6278929 -CTTTTTC
1 ATTTTTTC
6278936 -TTTCTTT-
1 ATTT-TTTC
6278943 -TTTTTTC
1 ATTTTTTC
*
6278950 CTTTTTTC
1 ATTTTTTC
* **
6278958 -CTTTCCC
1 ATTTTTTC
*
6278965 ATTTTTCC
1 ATTTTTTC
*
6278973 TTTTTTTC
1 ATTTTTTC
6278981 ATTTTT
1 ATTTTT
6278987 CTTCTTTTTT
Statistics
Matches: 89, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
6 17 0.19
7 15 0.17
8 57 0.64
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (8 bp):
ATTTTTTC
Found at i:6278891 original size:10 final size:10
Alignment explanation
Indices: 6278870--6278956 Score: 56
Period size: 10 Copynumber: 8.4 Consensus size: 10
6278860 TAAGTCTTTA
6278870 TTTTTTCA-T
1 TTTTTTCATT
6278879 TTTTTT-ATT
1 TTTTTTCATT
6278888 TTTTTTCATT
1 TTTTTTCATT
6278898 TTCATTTTCATT
1 TT--TTTTCATT
6278910 TTCATTTT--TT
1 TT--TTTTCATT
*
6278920 CATTTTTTCCTT
1 --TTTTTTCATT
*
6278932 TTTCTTTCTTT
1 TTT-TTTCATT
*
6278943 TTTTTTCCTT
1 TTTTTTCATT
6278953 TTTT
1 TTTT
6278957 CCTTTCCCAT
Statistics
Matches: 67, Mismatches: 2, Indels: 17
0.78 0.02 0.20
Matches are distributed among these distances:
8 1 0.01
9 13 0.19
10 24 0.36
11 9 0.13
12 20 0.30
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTTCATT
Found at i:6278925 original size:6 final size:6
Alignment explanation
Indices: 6278890--6278917 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
6278880 TTTTTATTTT
6278890 TTTTCA TTTTCA TTTTCA TTTTCA TTTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTT
6278918 TTCATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTCA
Found at i:6278956 original size:23 final size:22
Alignment explanation
Indices: 6278922--6278980 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
6278912 CATTTTTTCA
6278922 TTTTTTCCTTTTTCTTTCTTT---
1 TTTTTTCC-TTTT-TTTCTTTCCC
*
6278943 TTTTTTCCTTTTTTCCTTTCCC
1 TTTTTTCCTTTTTTTCTTTCCC
*
6278965 ATTTTTCCTTTTTTTC
1 TTTTTTCCTTTTTTTC
6278981 ATTTTTCTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
19 6 0.19
20 4 0.12
21 8 0.25
22 14 0.44
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTTTTCCTTTTTTTCTTTCCC
Found at i:6279336 original size:21 final size:21
Alignment explanation
Indices: 6279310--6279351 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
6279300 TCATCTTATT
6279310 TTCACAAAAAGATTCTCATTA
1 TTCACAAAAAGATTCTCATTA
6279331 TTCACAAAAAGATTCTCATTA
1 TTCACAAAAAGATTCTCATTA
6279352 CTTTGTCCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (21 bp):
TTCACAAAAAGATTCTCATTA
Found at i:6284659 original size:18 final size:18
Alignment explanation
Indices: 6284630--6284679 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
6284620 CAGAAAAGCT
6284630 AAAGATAAAATCAAATGAA
1 AAAGA-AAAATCAAATGAA
*
6284649 AAAGAAAAATCAAA-GAT
1 AAAGAAAAATCAAATGAA
*
6284666 AAATAAAAAT-AAAT
1 AAAGAAAAATCAAAT
6284680 AAATAATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 3 0.11
17 11 0.39
18 9 0.32
19 5 0.18
ACGTcount: A:0.72, C:0.04, G:0.08, T:0.16
Consensus pattern (18 bp):
AAAGAAAAATCAAATGAA
Found at i:6284702 original size:3 final size:3
Alignment explanation
Indices: 6284694--6284722 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6284684 AATCAACCAA
6284694 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6284723 ATCAATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6284751 original size:15 final size:16
Alignment explanation
Indices: 6284694--6284751 Score: 68
Period size: 15 Copynumber: 3.8 Consensus size: 16
6284684 AATCAACCAA
6284694 AATAATAATAAT-AAT
1 AATAATAATAATAAAT
6284709 AATAATAATAATAAAT
1 AATAATAATAATAAAT
*
6284725 CAATAA-ATTAATAAAT
1 -AATAATAATAATAAAT
*
6284741 TATAA-AATAAT
1 AATAATAATAAT
6284752 GAATGATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
15 21 0.55
16 12 0.32
17 5 0.13
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAATAATAATAAAT
Found at i:6289353 original size:17 final size:16
Alignment explanation
Indices: 6289317--6289390 Score: 59
Period size: 18 Copynumber: 4.8 Consensus size: 16
6289307 ATGAATTACT
6289317 AAATAAAT-AAAA--A
1 AAATAAATAAAAATTA
*
6289330 AAGTAAATAAAAATTGA
1 AAATAAATAAAAATT-A
*
6289347 AAATAAAATAAAATTTAA
1 AAAT-AAATAAAAATT-A
*
6289365 AAATAAATGAAAA-TA
1 AAATAAATAAAAATTA
6289380 AAA-AAATAAAA
1 AAATAAATAAAA
6289391 TGAAAATGGA
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
13 7 0.14
14 11 0.22
15 4 0.08
16 1 0.02
17 11 0.22
18 15 0.31
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (16 bp):
AAATAAATAAAAATTA
Found at i:6289355 original size:18 final size:18
Alignment explanation
Indices: 6289334--6289397 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
6289324 TAAAAAAAGT
*
6289334 AAATAAAAATTGAAAATA
1 AAATAAAAATTAAAAATA
*
6289352 AAATAAAATTTAAAAAT-
1 AAATAAAAATTAAAAATA
* *
6289369 AAATGAAAATAAAAAAATA
1 AAATAAAAAT-TAAAAATA
*
6289388 AAATGAAAAT
1 AAATAAAAAT
6289398 GGAAAAAAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
17 8 0.21
18 21 0.54
19 10 0.26
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (18 bp):
AAATAAAAATTAAAAATA
Found at i:6289403 original size:18 final size:18
Alignment explanation
Indices: 6289334--6289403 Score: 63
Period size: 17 Copynumber: 3.9 Consensus size: 18
6289324 TAAAAAAAGT
*
6289334 AAATAAAAATTGAAAATA
1 AAATGAAAATTGAAAATA
*
6289352 AAAT-AAAATTTAAAA-A
1 AAATGAAAATTGAAAATA
**
6289368 TAAATGAAAATAAAAAAATA
1 -AAATGAAAAT-TGAAAATA
*
6289388 AAATGAAAATGGAAAA
1 AAATGAAAATTGAAAA
6289404 AAGAAACCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
16 1 0.02
17 14 0.33
18 13 0.30
19 14 0.33
20 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (18 bp):
AAATGAAAATTGAAAATA
Found at i:6289404 original size:19 final size:19
Alignment explanation
Indices: 6289346--6289397 Score: 72
Period size: 18 Copynumber: 2.8 Consensus size: 19
6289336 ATAAAAATTG
**
6289346 AAAATAAAAT-AAAATTTA
1 AAAATAAAATGAAAATAAA
6289364 AAAAT-AAATGAAAATAAA
1 AAAATAAAATGAAAATAAA
6289382 AAAATAAAATGAAAAT
1 AAAATAAAATGAAAAT
6289398 GGAAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 4 0.13
18 16 0.53
19 10 0.33
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (19 bp):
AAAATAAAATGAAAATAAA
Found at i:6289698 original size:51 final size:51
Alignment explanation
Indices: 6289613--6289717 Score: 133
Period size: 51 Copynumber: 2.1 Consensus size: 51
6289603 AATGGCATCG
* * *
6289613 AAAAGTTCAATCGAAAACTAGAAAATCCACCGATTT-TTGGGAAACTTGCCA
1 AAAAGTTCAACCAAAAACTAGAAAATCCACCGATTTCTT-GAAAACTTGCCA
* *
6289664 AAAAGTTCAACCAAAAACTAG-AAATCTCATCGATTTCTTGAAAAGTTGCCA
1 AAAAGTTCAACCAAAAACTAGAAAATC-CACCGATTTCTTGAAAACTTGCCA
6289715 AAA
1 AAA
6289718 TCCCATCAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
50 5 0.11
51 40 0.85
52 2 0.04
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (51 bp):
AAAAGTTCAACCAAAAACTAGAAAATCCACCGATTTCTTGAAAACTTGCCA
Found at i:6290299 original size:3 final size:3
Alignment explanation
Indices: 6290241--6290279 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
6290231 AATAGTGATG
*
6290241 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6290280 GTAGTAGTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:6290703 original size:60 final size:60
Alignment explanation
Indices: 6290601--6291002 Score: 265
Period size: 60 Copynumber: 6.7 Consensus size: 60
6290591 AAATCGAGAT
** * ** * * *
6290601 TGAATGATTAGGATGATGCCACAAGTCTGAAAGCGACTAAGACTAAGTTGAGGTCGTAAA
1 TGAATGATCGGGATGATGCCGCAAGTCTGAAAATGACCAAGACTAAGTTAAGGTCATAAA
* * * * * * *
6290661 TGGATGATCGGGATGACGCCACGAGTCTGAAAATGACCAAGACCAAGTCAAGATCATAAA
1 TGAATGATCGGGATGATGCCGCAAGTCTGAAAATGACCAAGACTAAGTTAAGGTCATAAA
* * * * * *
6290721 TGAATGATCGAGACGATGTCGTAAGTCT-AAAAGTGACCAAGATTGAGTTAAGGTCATAAA
1 TGAATGATCGGGATGATGCCGCAAGTCTGAAAA-TGACCAAGACTAAGTTAAGGTCATAAA
* ** * * * ** * *
6290781 TTAATGA-CTGGGACAATGCCACGAGTCTGAAAATGACCAAAACCGAGTCAAGATCATAAA
1 TGAATGATC-GGGATGATGCCGCAAGTCTGAAAATGACCAAGACTAAGTTAAGGTCATAAA
* * * * * * * * * *
6290841 TGGATAACCAGGAAGATGTCGTAAGTCTGAAAATGACCAAGATCGAA-TTGAGGTCGTAAA
1 TGAATGATCGGGATGATGCCGCAAGTCTGAAAATGACCAAGA-CTAAGTTAAGGTCATAAA
* * * * *
6290901 TGAATAATCGGGATGATGCCGCAAGTTTGAAAGTGACCAAAACTGAGTTGAA-GTCATAAA
1 TGAATGATCGGGATGATGCCGCAAGTCTGAAAATGACCAAGACTAAGTT-AAGGTCATAAA
* * ** *
6290961 TTAATGA-CTGAGATGATGCCGTGAGTCTAAAAATGACCAAGA
1 TGAATGATC-GGGATGATGCCGCAAGTCTGAAAATGACCAAGA
6291003 TTGAGTCGAG
Statistics
Matches: 257, Mismatches: 77, Indels: 16
0.73 0.22 0.05
Matches are distributed among these distances:
59 8 0.03
60 241 0.94
61 8 0.03
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.22
Consensus pattern (60 bp):
TGAATGATCGGGATGATGCCGCAAGTCTGAAAATGACCAAGACTAAGTTAAGGTCATAAA
Found at i:6290814 original size:120 final size:118
Alignment explanation
Indices: 6290646--6291040 Score: 400
Period size: 120 Copynumber: 3.3 Consensus size: 118
6290636 ACTAAGACTA
* ** * * *
6290646 AGTTGAGGTCGTAAATGGATGA-TCGGGATGACGCCACGAGTCTGAAAATGACCAAGACCAAGTC
1 AGTTGAGGTCGTAAATGAATGACT-GGGACAATGCCACGAGTCTGAAAATGACCAAAACCGAGTC
*
6290710 AAGATCATAAATGAATGATCGAGACGATGTCGTAAGTCTAAAAGTGACCAAGATTG
65 AAGATCATAAATGAATGA-CGAGAAGATGTCGTAAGTCTAAAA-TGACCAAGATTG
* * *
6290766 AGTTAAGGTCATAAATTAATGACTGGGACAATGCCACGAGTCTGAAAATGACCAAAACCGAGTCA
1 AGTTGAGGTCGTAAATGAATGACTGGGACAATGCCACGAGTCTGAAAATGACCAAAACCGAGTCA
* * * *
6290831 AGATCATAAATGGATAACCAGGAAGATGTCGTAAGTCTGAAAATGACCAAGATCG
66 AGATCATAAATGAATGACGA-GAAGATGTCGTAAGTCT-AAAATGACCAAGATTG
* * ** * * * * *
6290886 AATTGAGGTCGTAAATGAAT-AATCGGGATGATGCCGCAAGTTTGAAAGTGACCAAAACTGAGTT
1 AGTTGAGGTCGTAAATGAATGACT-GGGACAATGCCACGAGTCTGAAAATGACCAAAACCGAG-T
* * * * *
6290950 GAAG-TCATAAATTAATGACTGAGATGATGCCGTGAGTCTAAAAATGACCAAGATTG
64 CAAGATCATAAATGAATGAC-GAGAAGATGTCGTAAGTCT-AAAATGACCAAGATTG
* * * *
6291006 AGTCGAGATCGTAGATGAATGACTGAGACAATGCC
1 AGTTGAGGTCGTAAATGAATGACTGGGACAATGCC
6291041 TCGAATTTGA
Statistics
Matches: 224, Mismatches: 44, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
119 4 0.02
120 208 0.93
121 12 0.05
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.22
Consensus pattern (118 bp):
AGTTGAGGTCGTAAATGAATGACTGGGACAATGCCACGAGTCTGAAAATGACCAAAACCGAGTCA
AGATCATAAATGAATGACGAGAAGATGTCGTAAGTCTAAAATGACCAAGATTG
Found at i:6291008 original size:60 final size:60
Alignment explanation
Indices: 6290684--6291040 Score: 226
Period size: 60 Copynumber: 6.0 Consensus size: 60
6290674 TGACGCCACG
* *
6290684 AGTCTGAAAATGACCAAGACCAAG-TCAAGATCATAAATGAATGA-TCGAGACGATGTCGTA
1 AGTCTGAAAATGACCAAGACCGAGTTCAAG-TCATAAATGAATGACT-GAGACGATGCCGTA
** * * * ***
6290744 AGTCT-AAAAGTGACCAAGATTGAGTT-AAGGTCATAAATTAATGACTGGGACAATGCCACG
1 AGTCTGAAAA-TGACCAAGACCGAGTTCAA-GTCATAAATGAATGACTGAGACGATGCCGTA
* * * * * *
6290804 AGTCTGAAAATGACCAAAACCGAG-TCAAGATCATAAATGGATAAC-CAGGAAGATGTCGTA
1 AGTCTGAAAATGACCAAGACCGAGTTCAAG-TCATAAATGAATGACTGA-GACGATGCCGTA
* * * * * * * * *
6290864 AGTCTGAAAATGACCAAGATCGAATTGAGGTCGTAAATGAAT-AATCGGGATGATGCCGCA
1 AGTCTGAAAATGACCAAGACCGAGTTCAAGTCATAAATGAATGACT-GAGACGATGCCGTA
* * * * * * * *
6290924 AGTTTGAAAGTGACCAAAACTGAGTTGAAGTCATAAATTAATGACTGAGATGATGCCGTG
1 AGTCTGAAAATGACCAAGACCGAGTTCAAGTCATAAATGAATGACTGAGACGATGCCGTA
* ** * * * *
6290984 AGTCTAAAAATGACCAAGATTGAG-TCGAGATCGTAGATGAATGACTGAGACAATGCC
1 AGTCTGAAAATGACCAAGACCGAGTTCAAG-TCATAAATGAATGACTGAGACGATGCC
6291041 TCGAATTTGA
Statistics
Matches: 222, Mismatches: 62, Indels: 26
0.72 0.20 0.08
Matches are distributed among these distances:
59 10 0.05
60 200 0.90
61 12 0.05
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (60 bp):
AGTCTGAAAATGACCAAGACCGAGTTCAAGTCATAAATGAATGACTGAGACGATGCCGTA
Found at i:6301789 original size:16 final size:16
Alignment explanation
Indices: 6301755--6301795 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
6301745 ATTCAAATCC
*
6301755 TTGTGAGTTATTTTTT
1 TTGTGAGTTATTTTGT
6301771 TTGTGAGTT-TTTCTGT
1 TTGTGAGTTATTT-TGT
6301787 TTGT-AGTTA
1 TTGTGAGTTA
6301796 ATCTCTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.32
16 15 0.68
ACGTcount: A:0.12, C:0.02, G:0.22, T:0.63
Consensus pattern (16 bp):
TTGTGAGTTATTTTGT
Found at i:6308792 original size:24 final size:24
Alignment explanation
Indices: 6308765--6308812 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
6308755 ATATCAAAGC
*
6308765 ATCATTAAATTTTCATACCAATAT
1 ATCATCAAATTTTCATACCAATAT
*
6308789 ATCATCAAATTTTCATACCGATAT
1 ATCATCAAATTTTCATACCAATAT
6308813 TTCTCTCCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.40
Consensus pattern (24 bp):
ATCATCAAATTTTCATACCAATAT
Found at i:6314519 original size:20 final size:20
Alignment explanation
Indices: 6314468--6314519 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
6314458 CCTTTAAGAG
*
6314468 GGGATCGATCCCTTACCTTA
1 GGGATCGATCCCTTACCTAA
* **
6314488 GGTGATCAATCCCTTATGTAA
1 GG-GATCGATCCCTTACCTAA
6314509 GGGATCGATCC
1 GGGATCGATCC
6314520 TTTTTCTGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (20 bp):
GGGATCGATCCCTTACCTAA
Found at i:6315896 original size:18 final size:18
Alignment explanation
Indices: 6315838--6315901 Score: 62
Period size: 18 Copynumber: 3.6 Consensus size: 18
6315828 ATAGACAATT
*
6315838 GAAAATAAAAT-AAAACTT
1 GAAAATAAAATGAAAA-TA
6315856 GAAAAT-AAATGAAAATCA
1 GAAAATAAAATGAAAAT-A
* *
6315874 AAAAATAAAATGAAAATG
1 GAAAATAAAATGAAAATA
6315892 GAAAA-AAAAT
1 GAAAATAAAAT
6315902 CTTATGAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 10 0.26
18 19 0.49
19 10 0.26
ACGTcount: A:0.70, C:0.03, G:0.09, T:0.17
Consensus pattern (18 bp):
GAAAATAAAATGAAAATA
Found at i:6315896 original size:19 final size:19
Alignment explanation
Indices: 6315839--6315897 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
6315829 TAGACAATTG
*
6315839 AAAATAAAAT-AAAACTTG-
1 AAAATAAAATGAAAA-TCGA
*
6315857 AAAAT-AAATGAAAATCAA
1 AAAATAAAATGAAAATCGA
*
6315875 AAAATAAAATGAAAATGGA
1 AAAATAAAATGAAAATCGA
6315894 AAAA
1 AAAA
6315898 AAATCTTATG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
17 5 0.15
18 14 0.41
19 15 0.44
ACGTcount: A:0.71, C:0.03, G:0.08, T:0.17
Consensus pattern (19 bp):
AAAATAAAATGAAAATCGA
Found at i:6316730 original size:3 final size:3
Alignment explanation
Indices: 6316724--6316871 Score: 181
Period size: 3 Copynumber: 49.3 Consensus size: 3
6316714 AAAAAATGGA
* *
6316724 AAT AAT AGT GAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
6316770 AAT -AC AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * *
6316817 AAC AAT AAT AAT AAT AAT AAC AAC AAC AAC AAC AAC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6316865 AAT AAT A
1 AAT AAT A
6316872 TGATATGGTA
Statistics
Matches: 131, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
2 1 0.01
3 127 0.97
4 3 0.02
ACGTcount: A:0.66, C:0.06, G:0.01, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:6322185 original size:31 final size:30
Alignment explanation
Indices: 6322150--6322239 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
6322140 TAAGATTTGG
6322150 AAGGTTTAAAGATTTTGATTTTAGGGTTTAA
1 AAGGTTTAAAG-TTTTGATTTTAGGGTTTAA
** **
6322181 AAGGTTTAGGGTTTT-AGTTTTAGGGTTTGG
1 AAGGTTTAAAGTTTTGA-TTTTAGGGTTTAA
** *
6322211 AAGGTTTATTGTTTCGATTTTAGGGTTTA
1 AAGGTTTAAAGTTTTGATTTTAGGGTTTA
6322240 GGGTTTTGAT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
29 1 0.02
30 38 0.78
31 10 0.20
ACGTcount: A:0.23, C:0.01, G:0.28, T:0.48
Consensus pattern (30 bp):
AAGGTTTAAAGTTTTGATTTTAGGGTTTAA
Found at i:6322204 original size:30 final size:29
Alignment explanation
Indices: 6322162--6322376 Score: 121
Period size: 30 Copynumber: 7.6 Consensus size: 29
6322152 GGTTTAAAGA
*
6322162 TTTTGATTTTAGGGTTTAAAAGGTTTAGGG
1 TTTTG-TTTTAGGGTTTAAAGGGTTTAGGG
*
6322192 TTTTAGTTTTAGGGTTTGGAA-GGTTTA---
1 TTTT-GTTTTAGGGTTT-AAAGGGTTTAGGG
* * *
6322219 --TTG-TTT-CGATTT-TAGGGTTTAGGG
1 TTTTGTTTTAGGGTTTAAAGGGTTTAGGG
** * *
6322243 TTTTGATTTTAGAATCTAGAGGGTTTAGGG
1 TTTTG-TTTTAGGGTTTAAAGGGTTTAGGG
* *
6322273 TTTTGATTTTAGGGTTT--GGGGTTTAAGG
1 TTTTG-TTTTAGGGTTTAAAGGGTTTAGGG
6322301 TTTTGATTTTA-GGTTTAAAGGGTTTAGGG
1 TTTTG-TTTTAGGGTTTAAAGGGTTTAGGG
* * * *
6322330 TTTTAGTTTTAGGATTTGAAGGGGTTAGTG
1 TTTT-GTTTTAGGGTTTAAAGGGTTTAGGG
**
6322360 TTTCAATTTTAGGGTTT
1 TTT-TGTTTTAGGGTTT
6322377 GGAGTTTAAA
Statistics
Matches: 146, Mismatches: 22, Indels: 34
0.72 0.11 0.17
Matches are distributed among these distances:
20 1 0.01
21 6 0.04
22 4 0.03
23 3 0.02
24 1 0.01
25 2 0.01
26 3 0.02
27 5 0.03
28 23 0.16
29 21 0.14
30 74 0.51
31 3 0.02
ACGTcount: A:0.19, C:0.01, G:0.31, T:0.49
Consensus pattern (29 bp):
TTTTGTTTTAGGGTTTAAAGGGTTTAGGG
Found at i:6322216 original size:61 final size:60
Alignment explanation
Indices: 6322123--6322239 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 60
6322113 TTTTAAAGAT
*
6322123 TTTAGGGTTTAGAATTTTAAGATTTGGAAGGTTTAAAGATTTTGATTTTAGGGTTTAAAAGG
1 TTTAGGGTTTAG-ATTTTAAGATTTGGAAGGTTTAAAG-TTTCGATTTTAGGGTTTAAAAGG
* * **
6322185 TTTAGGGTTTTAG-TTTTAGGGTTTGGAAGGTTTATTGTTTCGATTTTAGGGTTTA
1 TTTAGGG-TTTAGATTTTAAGATTTGGAAGGTTTAAAGTTTCGATTTTAGGGTTTA
6322240 GGGTTTTGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 17 0.35
61 20 0.41
62 7 0.14
63 5 0.10
ACGTcount: A:0.24, C:0.01, G:0.27, T:0.48
Consensus pattern (60 bp):
TTTAGGGTTTAGATTTTAAGATTTGGAAGGTTTAAAGTTTCGATTTTAGGGTTTAAAAGG
Found at i:6322244 original size:51 final size:51
Alignment explanation
Indices: 6322183--6322296 Score: 131
Period size: 51 Copynumber: 2.2 Consensus size: 51
6322173 GGGTTTAAAA
** * * **
6322183 GGTTTAGGGTTTT-AGTTTTAGGGTTTGGAAGGTTTATTGTTTCGATTTTAG
1 GGTTTAGGGTTTTGA-TTTTAGAATCTAGAAGGTTTAGGGTTTCGATTTTAG
* *
6322234 GGTTTAGGGTTTTGATTTTAGAATCTAGAGGGTTTAGGGTTTTGATTTTAG
1 GGTTTAGGGTTTTGATTTTAGAATCTAGAAGGTTTAGGGTTTCGATTTTAG
*
6322285 GGTTTGGGGTTT
1 GGTTTAGGGTTT
6322297 AAGGTTTTGA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 52 0.98
52 1 0.02
ACGTcount: A:0.16, C:0.02, G:0.33, T:0.49
Consensus pattern (51 bp):
GGTTTAGGGTTTTGATTTTAGAATCTAGAAGGTTTAGGGTTTCGATTTTAG
Found at i:6322285 original size:14 final size:14
Alignment explanation
Indices: 6322266--6322313 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
6322256 ATCTAGAGGG
6322266 TTTAGGGTTTTGAT
1 TTTAGGGTTTTGAT
* **
6322280 TTTAGGGTTTGGGG
1 TTTAGGGTTTTGAT
*
6322294 TTTAAGGTTTTGAT
1 TTTAGGGTTTTGAT
6322308 TTTAGG
1 TTTAGG
6322314 TTTAAAGGGT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.52
Consensus pattern (14 bp):
TTTAGGGTTTTGAT
Found at i:6322341 original size:57 final size:58
Alignment explanation
Indices: 6322233--6322347 Score: 162
Period size: 57 Copynumber: 2.0 Consensus size: 58
6322223 TTCGATTTTA
* * *
6322233 GGGTTTAGGGTTTTGATTTTAGAATCTAGAGGGTTTAGGGTTTTGATTTTAGGGTTTG
1 GGGTTTAAGGTTTTGATTTTAGAATCTAAAGGGTTTAGGGTTTTGATTTTAGGATTTG
* *
6322291 GGGTTTAAGGTTTTGATTTTAG-GTTTAAAGGGTTTAGGGTTTT-AGTTTTAGGATTTG
1 GGGTTTAAGGTTTTGATTTTAGAATCTAAAGGGTTTAGGGTTTTGA-TTTTAGGATTTG
6322348 AAGGGGTTAG
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
56 1 0.02
57 29 0.57
58 21 0.41
ACGTcount: A:0.18, C:0.01, G:0.33, T:0.48
Consensus pattern (58 bp):
GGGTTTAAGGTTTTGATTTTAGAATCTAAAGGGTTTAGGGTTTTGATTTTAGGATTTG
Found at i:6322738 original size:3 final size:3
Alignment explanation
Indices: 6322732--6322770 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
6322722 ATCAATTTTT
* * *
6322732 TTA TTA TTA TTG TTA TTG TCA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6322771 ATTAATTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:6328854 original size:14 final size:14
Alignment explanation
Indices: 6328835--6328873 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
6328825 GATCAATTTT
6328835 AAAAAAGAAAAATA
1 AAAAAAGAAAAATA
*
6328849 AAAAAATAAAAATA
1 AAAAAAGAAAAATA
*
6328863 AAAAGAGAAAA
1 AAAAAAGAAAA
6328874 GCTGGTTACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (14 bp):
AAAAAAGAAAAATA
Found at i:6330490 original size:22 final size:22
Alignment explanation
Indices: 6330462--6330513 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
6330452 AAAAAATATA
*
6330462 TATTTTTCATCTTTT-TACTTTT
1 TATTTTTCAT-TTTTCTAATTTT
*
6330484 TATTTTTTATTTTTCTAATTTT
1 TATTTTTCATTTTTCTAATTTT
6330506 TCATTTTT
1 T-ATTTTT
6330514 ATCCACCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 4 0.15
22 16 0.62
23 6 0.23
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (22 bp):
TATTTTTCATTTTTCTAATTTT
Found at i:6330635 original size:42 final size:42
Alignment explanation
Indices: 6330578--6330661 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
6330568 TATTAAAAAT
*
6330578 TTTACTAAAGATATTTTAATCGTTTATTATTATCATTTTTTA
1 TTTACTAAAGATATTTTAATCGTTTACTATTATCATTTTTTA
**
6330620 TTTACTAAA-ACTATTTTGGTCGTTTACTATTATCATTTTTTA
1 TTTACTAAAGA-TATTTTAATCGTTTACTATTATCATTTTTTA
6330662 AGTTCACATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 1 0.03
42 37 0.97
ACGTcount: A:0.29, C:0.10, G:0.06, T:0.56
Consensus pattern (42 bp):
TTTACTAAAGATATTTTAATCGTTTACTATTATCATTTTTTA
Found at i:6332703 original size:20 final size:20
Alignment explanation
Indices: 6332680--6332718 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6332670 TAATTATCTA
6332680 TTTAATTTTATATCTATATG
1 TTTAATTTTATATCTATATG
* *
6332700 TTTAATTTTTTATTTATAT
1 TTTAATTTTATATCTATAT
6332719 TAAAAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTAATTTTATATCTATATG
Found at i:6332736 original size:19 final size:21
Alignment explanation
Indices: 6332712--6332756 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
6332702 TAATTTTTTA
6332712 TTTATA-TT-AAAAATAATAT
1 TTTATATTTAAAAAATAATAT
6332731 TTTATATTTAAAAAATAATAT
1 TTTATATTTAAAAAATAATAT
6332752 TTTAT
1 TTTAT
6332757 TAATTTTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 16 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTATATTTAAAAAATAATAT
Found at i:6345503 original size:34 final size:34
Alignment explanation
Indices: 6345464--6345531 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
6345454 AAGTAAGAAT
*
6345464 GCTGGTTTTCTAAATTATGTTTATGTAGAATGTA
1 GCTGGTTTTCGAAATTATGTTTATGTAGAATGTA
6345498 GCTGGTTTTCGAAATTATGTTTATGTAGAATGTA
1 GCTGGTTTTCGAAATTATGTTTATGTAGAATGTA
6345532 TTTGTTGATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.26, C:0.06, G:0.22, T:0.46
Consensus pattern (34 bp):
GCTGGTTTTCGAAATTATGTTTATGTAGAATGTA
Found at i:6346441 original size:23 final size:25
Alignment explanation
Indices: 6346405--6346451 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
6346395 TCAAATTATA
*
6346405 ATGTCAAAACATTTC-TATATCATT
1 ATGTCAAAACATTTCGTAGATCATT
6346429 ATGTC-AAACATTTCGTAGATCAT
1 ATGTCAAAACATTTCGTAGATCAT
6346452 AAATCAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (25 bp):
ATGTCAAAACATTTCGTAGATCATT
Found at i:6349220 original size:3 final size:3
Alignment explanation
Indices: 6349214--6349244 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
6349204 TATAATTTTT
6349214 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
6349245 CTTAAAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6350135 original size:7 final size:6
Alignment explanation
Indices: 6350112--6350252 Score: 69
Period size: 6 Copynumber: 23.3 Consensus size: 6
6350102 TTTCTTTGTC
*
6350112 TTTTTA TTTTT- TGTTTTGA TTTTTA -TTTTA TTTTTA -TGTT- TTTTTA
1 TTTTTA TTTTTA T-TTTT-A TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* * * * *
6350158 TGTTT- TTTTTC TTTCTA TTGTTTA TTTATTTA TTTATT- TTCTTA TTATTA
1 TTTTTA TTTTTA TTTTTA TT-TTTA -TT-TTTA TTT-TTA TTTTTA TTTTTA
* * * * * *
6350208 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTTA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA TT
6350253 ATAGAAATAA
Statistics
Matches: 112, Mismatches: 11, Indels: 23
0.77 0.08 0.16
Matches are distributed among these distances:
5 18 0.16
6 71 0.63
7 16 0.14
8 7 0.06
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (6 bp):
TTTTTA
Found at i:6350163 original size:9 final size:10
Alignment explanation
Indices: 6350131--6350166 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
6350121 TTTGTTTTGA
*
6350131 TTTTTATTTT
1 TTTTTATGTT
6350141 ATTTTTATGTT
1 -TTTTTATGTT
6350152 TTTTTATGTT
1 TTTTTATGTT
6350162 TTTTT
1 TTTTT
6350167 TCTTTCTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.11, C:0.00, G:0.06, T:0.83
Consensus pattern (10 bp):
TTTTTATGTT
Found at i:6350207 original size:3 final size:3
Alignment explanation
Indices: 6350199--6350254 Score: 103
Period size: 3 Copynumber: 18.3 Consensus size: 3
6350189 ATTTATTTTC
6350199 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6350247 TTTA TTA T
1 -TTA TTA T
6350255 AGAAATAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6350885 original size:17 final size:17
Alignment explanation
Indices: 6350818--6350885 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 17
6350808 TAATTTTTTT
6350818 AAAATAATATAATAA-AA
1 AAAATAA-ATAATAATAA
* *
6350835 ACAAT-AA-AACAATAA
1 AAAATAAATAATAATAA
* *
6350850 ACAATAAATAATAACAA
1 AAAATAAATAATAATAA
* *
6350867 AAAATTAATCATAATAA
1 AAAATAAATAATAATAA
6350884 AA
1 AA
6350886 TTAATTAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.10
15 8 0.20
16 3 0.08
17 25 0.62
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAATAAATAATAATAA
Found at i:6351214 original size:3 final size:3
Alignment explanation
Indices: 6351206--6351232 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
6351196 TAGAATACAA
6351206 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
6351233 GTTAATTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6365278 original size:24 final size:24
Alignment explanation
Indices: 6365251--6365298 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
6365241 AGTTAGTTCG
6365251 TATGAATTTTGAACATGTCACTAT
1 TATGAATTTTGAACATGTCACTAT
6365275 TATGAATTTTGAACATGTCACTAT
1 TATGAATTTTGAACATGTCACTAT
6365299 CTTTTATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (24 bp):
TATGAATTTTGAACATGTCACTAT
Found at i:6367820 original size:67 final size:67
Alignment explanation
Indices: 6367737--6367871 Score: 252
Period size: 67 Copynumber: 2.0 Consensus size: 67
6367727 TGGATAATAC
6367737 AGCTAGGCACTTTCTGTTTTCATTCATGGATAGGTTTTCAAGCTACAATCAAATTAAGATAGCAC
1 AGCTAGGCACTTTCTGTTTTCATTCATGGATAGGTTTTCAAGCTACAATCAAATTAAGATAGCAC
6367802 AA
66 AA
* *
6367804 AGCTAGGCACTTTCTGTTTTCATTCATGGATGGGTTTTCAAGTTACAATCAAATTAAGATAGCAC
1 AGCTAGGCACTTTCTGTTTTCATTCATGGATAGGTTTTCAAGCTACAATCAAATTAAGATAGCAC
6367869 AA
66 AA
6367871 A
1 A
6367872 AAGATATGAA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (67 bp):
AGCTAGGCACTTTCTGTTTTCATTCATGGATAGGTTTTCAAGCTACAATCAAATTAAGATAGCAC
AA
Found at i:6369416 original size:18 final size:18
Alignment explanation
Indices: 6369389--6369430 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
6369379 TTAATGAAAA
*
6369389 ATTATGGTATTTTGACAT
1 ATTATAGTATTTTGACAT
6369407 ATTATAGTATTTTGACAT
1 ATTATAGTATTTTGACAT
6369425 ATTATA
1 ATTATA
6369431 ATATGTTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.50
Consensus pattern (18 bp):
ATTATAGTATTTTGACAT
Found at i:6371615 original size:40 final size:40
Alignment explanation
Indices: 6371571--6371796 Score: 188
Period size: 40 Copynumber: 5.7 Consensus size: 40
6371561 CAAATAAGTC
* ** * *
6371571 ATTTAAAGTTTTGTTGTTTTTAGTTAGAAGAACCTTTTGA
1 ATTTAAAGTTTTATTGCCTTTGGTCAGAAGAACCTTTTGA
* *
6371611 ATTTAAAGTTTTATTGCCTCTGGTCAGAA-AAGCCTTTTAA
1 ATTTAAAGTTTTATTGCCTTTGGTCAGAAGAA-CCTTTTGA
* ** *
6371651 ATTTAAAGTTTCATTGCCTTTTATCA-AAAAAGCCTTTTGA
1 ATTTAAAGTTTTATTGCCTTTGGTCAGAAGAA-CCTTTTGA
* * * * *
6371691 ATTTAAAGTTTCATTACCTCTGGTTA-AAGGAGCCTTTTGA
1 ATTTAAAGTTTTATTGCCTTTGGTCAGAA-GAACCTTTTGA
* * * * *
6371731 ATTTAAAGTTTTGTTGTCTTTGGACAGAAGAGCCTTTTAA
1 ATTTAAAGTTTTATTGCCTTTGGTCAGAAGAACCTTTTGA
* * *
6371771 ATTTAAAGTTTCACTACCTTTGGTCA
1 ATTTAAAGTTTTATTGCCTTTGGTCA
6371797 AATGAGCCAT
Statistics
Matches: 149, Mismatches: 33, Indels: 8
0.78 0.17 0.04
Matches are distributed among these distances:
39 4 0.03
40 142 0.95
41 3 0.02
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (40 bp):
ATTTAAAGTTTTATTGCCTTTGGTCAGAAGAACCTTTTGA
Found at i:6371695 original size:80 final size:80
Alignment explanation
Indices: 6371603--6371811 Score: 235
Period size: 80 Copynumber: 2.6 Consensus size: 80
6371593 GTTAGAAGAA
* *
6371603 CCTTTTGAATTTAAAGTTTTATTGCCTCTGGTCAGAA-AAGCCTTTTAAATTTAAAGTTTCATTG
1 CCTTTTGAATTTAAAGTTTCATTACCTCTGGTCA-AAGAAGCCTTTTAAATTTAAAGTTTCATTG
*
6371667 CCTTT-TATCAAAAAAG
65 CCTTTGGA-CAAAAAAG
* * * ** *
6371683 CCTTTTGAATTTAAAGTTTCATTACCTCTGGTTAAAGGAGCCTTTTGAATTTAAAGTTTTGTTGT
1 CCTTTTGAATTTAAAGTTTCATTACCTCTGGTCAAAGAAGCCTTTTAAATTTAAAGTTTCATTGC
* *
6371748 CTTTGGACAGAAGAG
66 CTTTGGACAAAAAAG
* * * *
6371763 CCTTTTAAATTTAAAGTTTCACTACCTTTGGTCAAATG-AGCCATTTAAA
1 CCTTTTGAATTTAAAGTTTCATTACCTCTGGTCAAA-GAAGCCTTTTAAA
6371812 GTTTCATAGT
Statistics
Matches: 109, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
79 2 0.02
80 105 0.96
81 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (80 bp):
CCTTTTGAATTTAAAGTTTCATTACCTCTGGTCAAAGAAGCCTTTTAAATTTAAAGTTTCATTGC
CTTTGGACAAAAAAG
Found at i:6371804 original size:40 final size:39
Alignment explanation
Indices: 6371598--6371811 Score: 203
Period size: 40 Copynumber: 5.4 Consensus size: 39
6371588 TTTTAGTTAG
* * * *
6371598 AAGAACCTTTTGAATTTAAAGTTTTATTGCCTCTGGTCA
1 AAGAGCCTTTTAAATTTAAAGTTTCATTGCCTTTGGTCA
* **
6371637 GAAAAGCCTTTTAAATTTAAAGTTTCATTGCCTTTTATCAA
1 -AAGAGCCTTTTAAATTTAAAGTTTCATTGCCTTTGGTC-A
* * * * *
6371678 AAAAGCCTTTTGAATTTAAAGTTTCATTACCTCTGGTTA
1 AAGAGCCTTTTAAATTTAAAGTTTCATTGCCTTTGGTCA
* ** * *
6371717 AAGGAGCCTTTTGAATTTAAAGTTTTGTTGTCTTTGGACA
1 AA-GAGCCTTTTAAATTTAAAGTTTCATTGCCTTTGGTCA
* *
6371757 GAAGAGCCTTTTAAATTTAAAGTTTCACTACCTTTGGTCA
1 -AAGAGCCTTTTAAATTTAAAGTTTCATTGCCTTTGGTCA
*
6371797 AATGAGCCATTTAAA
1 AA-GAGCCTTTTAAA
6371812 GTTTCATAGT
Statistics
Matches: 141, Mismatches: 29, Indels: 8
0.79 0.16 0.04
Matches are distributed among these distances:
39 5 0.04
40 133 0.94
41 3 0.02
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (39 bp):
AAGAGCCTTTTAAATTTAAAGTTTCATTGCCTTTGGTCA
Found at i:6372029 original size:40 final size:40
Alignment explanation
Indices: 6371985--6372265 Score: 209
Period size: 40 Copynumber: 7.1 Consensus size: 40
6371975 AGTTTCAACC
6371985 TTTTGAATTTAAAGTTTCATTACCTCTGGTTAAAAGAGCT
1 TTTTGAATTTAAAGTTTCATTACCTCTGGTTAAAAGAGCT
* * *
6372025 TTTTGAATTTAAAGTTT-GTTACCTCTGG-TCAGAGAAGC-
1 TTTTGAATTTAAAGTTTCATTACCTCTGGTTAAAAG-AGCT
* * * * * *
6372063 CTTTAACATTTAAAGTTTTATTGCCTCTGGTTAAAGGAGCC
1 TTTTGA-ATTTAAAGTTTCATTACCTCTGGTTAAAAGAGCT
* * *
6372104 TTTTGAATTTAAAGTTT-GTTACCTCTGGTCAGATA-AGC-
1 TTTTGAATTTAAAGTTTCATTACCTCTGGTTA-AAAGAGCT
* * * *
6372142 TTTTAACATTTAAAGTTTCATTGCCTCTGGTCAAATGAG-T
1 TTTTGA-ATTTAAAGTTTCATTACCTCTGGTTAAAAGAGCT
* * * ** * * *
6372182 CTTCTAAATTTAAAGTTTCATTGCCTCCAGTCAAAGGAGCC
1 -TTTTGAATTTAAAGTTTCATTACCTCTGGTTAAAAGAGCT
* * *
6372223 TTTTGAATTTAAAGTTTCA-TAGCCCCTGTTTAGAAGAGCT
1 TTTTGAATTTAAAGTTTCATTA-CCTCTGGTTAAAAGAGCT
6372263 TTT
1 TTT
6372266 CAAATTTTCT
Statistics
Matches: 190, Mismatches: 38, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
38 13 0.07
39 51 0.27
40 114 0.60
41 12 0.06
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (40 bp):
TTTTGAATTTAAAGTTTCATTACCTCTGGTTAAAAGAGCT
Found at i:6372077 original size:79 final size:79
Alignment explanation
Indices: 6371991--6372265 Score: 304
Period size: 79 Copynumber: 3.5 Consensus size: 79
6371981 AACCTTTTGA
6371991 ATTTAAAGTTTCATTACCTCTGGTTAAAAGAGCTTTTTGAATTTAAAGTTTGTTACCTCTGGTCA
1 ATTTAAAGTTTCATTACCTCTGGTTAAAAGAGCTTTTTGAATTTAAAGTTTGTTACCTCTGGTCA
6372056 GAGAAGCCTTTAAC
66 GAGAAGCCTTTAAC
* * * *
6372070 ATTTAAAGTTTTATTGCCTCTGGTTAAAGGAGCCTTTTGAATTTAAAGTTTGTTACCTCTGGTCA
1 ATTTAAAGTTTCATTACCTCTGGTTAAAAGAGCTTTTTGAATTTAAAGTTTGTTACCTCTGGTCA
* *
6372135 GATAAGCTTTTAAC
66 GAGAAGCCTTTAAC
* * * * * * * **
6372149 ATTTAAAGTTTCATTGCCTCTGGTCAAATGAG-TCTTCTAAATTTAAAGTTTCATTGCCTCCAGT
1 ATTTAAAGTTTCATTACCTCTGGTTAAAAGAGCT-TTTTGAATTTAAAGTTT-GTTACCTCTGGT
* * *
6372213 CAAAGGAGCCTTTTGA-
64 CAGAGAAGCC-TTTAAC
* * *
6372229 ATTTAAAGTTTCA-TAGCCCCTGTTTAGAAGAGCTTTT
1 ATTTAAAGTTTCATTA-CCTCTGGTTAAAAGAGCTTTT
6372266 CAAATTTTCT
Statistics
Matches: 163, Mismatches: 28, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
79 118 0.72
80 40 0.25
81 5 0.03
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.40
Consensus pattern (79 bp):
ATTTAAAGTTTCATTACCTCTGGTTAAAAGAGCTTTTTGAATTTAAAGTTTGTTACCTCTGGTCA
GAGAAGCCTTTAAC
Found at i:6372194 original size:119 final size:119
Alignment explanation
Indices: 6371983--6372242 Score: 332
Period size: 119 Copynumber: 2.2 Consensus size: 119
6371973 AAAGTTTCAA
* * *
6371983 CCTTTTGAATTTAAAGTTTCATTACCTCTGGTTAAAAGAGCTTTTTGAATTTAAAGTTTGTTACC
1 CCTTTTGAATTTAAAGTTTCATTACCTCTGGTCAAAAGAGCTTTTTAAATTTAAAGTTTATTACC
* * ** *
6372048 TCTGGTCAGAGAAGCCTTTAACATTTAAAGTTTTATTGCCTCTGGTTAAAGGAG
66 TCTGGTCAAAGAAGCCTTTAACATTTAAAGTTTCATTGCCTCCAGTCAAAGGAG
* *
6372102 CCTTTTGAATTTAAAGTTT-GTTACCTCTGGTCAGATA-AGC-TTTTAACATTTAAAGTTTCATT
1 CCTTTTGAATTTAAAGTTTCATTACCTCTGGTCA-AAAGAGCTTTTTAA-ATTTAAAGTTT-ATT
* *
6372164 GCCTCTGGTCAAATG-AGTCTTCTAA-ATTTAAAGTTTCATTGCCTCCAGTCAAAGGAG
63 ACCTCTGGTCAAA-GAAGCCTT-TAACATTTAAAGTTTCATTGCCTCCAGTCAAAGGAG
6372221 CCTTTTGAATTTAAAGTTTCAT
1 CCTTTTGAATTTAAAGTTTCAT
6372243 AGCCCCTGTT
Statistics
Matches: 122, Mismatches: 13, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
117 5 0.04
118 26 0.21
119 86 0.70
120 5 0.04
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (119 bp):
CCTTTTGAATTTAAAGTTTCATTACCTCTGGTCAAAAGAGCTTTTTAAATTTAAAGTTTATTACC
TCTGGTCAAAGAAGCCTTTAACATTTAAAGTTTCATTGCCTCCAGTCAAAGGAG
Found at i:6372448 original size:3 final size:3
Alignment explanation
Indices: 6372440--6372471 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
6372430 ATTTTGGTTA
*
6372440 TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
6372472 ATCTTTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:6373388 original size:5 final size:5
Alignment explanation
Indices: 6373380--6373422 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
6373370 TTTTTTTCTT
*
6373380 TTTTA TTTTCTA TTTTGA TTTTA TTTTA TTTTA TGTTA TTTTA
1 TTTTA -TTT-TA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA
6373423 GGGTTTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 20 0.61
6 11 0.33
7 2 0.06
ACGTcount: A:0.19, C:0.02, G:0.05, T:0.74
Consensus pattern (5 bp):
TTTTA
Found at i:6373471 original size:3 final size:3
Alignment explanation
Indices: 6373445--6373503 Score: 86
Period size: 3 Copynumber: 20.0 Consensus size: 3
6373435 GTTTATTTCT
*
6373445 TTA TT- TTA TTGA -TA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6373489 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
6373504 CTAATAAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
2 3 0.06
3 47 0.92
4 1 0.02
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:6377203 original size:24 final size:25
Alignment explanation
Indices: 6377131--6377206 Score: 79
Period size: 24 Copynumber: 3.2 Consensus size: 25
6377121 TATTATATAG
6377131 ATAAT-TCAAAATA-TTCATCAAATC
1 ATAATGTCAAAATATTTCAT-AAATC
* * *
6377155 ATAATGTCAAAACATTTC-CACATC
1 ATAATGTCAAAATATTTCATAAATC
*
6377179 ATTATGTC-AAATATTTCATAAATC
1 ATAATGTCAAAATATTTCATAAATC
6377203 ATAA
1 ATAA
6377207 ATCAATATCA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
23 8 0.20
24 23 0.56
25 7 0.17
26 3 0.07
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (25 bp):
ATAATGTCAAAATATTTCATAAATC
Found at i:6381610 original size:2 final size:2
Alignment explanation
Indices: 6381603--6381633 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6381593 ATCCTTGTTT
6381603 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
6381634 CCACCCAGTA
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:6383722 original size:30 final size:30
Alignment explanation
Indices: 6383672--6383768 Score: 108
Period size: 30 Copynumber: 3.3 Consensus size: 30
6383662 TGTTATAATT
*
6383672 AATTAAA-TCATAAATTTTTATTTTAAATC
1 AATTAAATTCTTAAATTTTTATTTTAAATC
* ***
6383701 AATTAAATTCTTAAATATTTATTTTTTCTC
1 AATTAAATTCTTAAATTTTTATTTTAAATC
* *
6383731 AATTAAATT-TTAAATTTTTATTTTCATTC
1 AATTAAATTCTTAAATTTTTATTTTAAATC
6383760 AAATTAAAT
1 -AATTAAAT
6383769 ACAAATGAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
29 23 0.40
30 34 0.60
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (30 bp):
AATTAAATTCTTAAATTTTTATTTTAAATC
Found at i:6384328 original size:21 final size:22
Alignment explanation
Indices: 6384304--6384348 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
6384294 ACTTTAATTC
* *
6384304 ATAAAATCTGTTTATATAT-TT
1 ATAAAATATGTTAATATATATT
*
6384325 ATAAATTATGTTAATATATATT
1 ATAAAATATGTTAATATATATT
6384347 AT
1 AT
6384349 CTTACCGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (22 bp):
ATAAAATATGTTAATATATATT
Found at i:6387587 original size:39 final size:40
Alignment explanation
Indices: 6387511--6387594 Score: 109
Period size: 39 Copynumber: 2.1 Consensus size: 40
6387501 GTATTAAAAG
* * *
6387511 AAAATTTCAAAAAAATTTATAGAAACATGAAATATTTTAA
1 AAAATTGCAAAAAAATTTATAGAAAAATGAAAAATTTTAA
*
6387551 AAAATTGCAAAAAAA-TTAT-GAAAAATTTAAAAATTTTAA
1 AAAATTGCAAAAAAATTTATAGAAAAA-TGAAAAATTTTAA
6387590 AAAAT
1 AAAAT
6387595 CTTCAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
38 5 0.13
39 20 0.51
40 14 0.36
ACGTcount: A:0.61, C:0.04, G:0.05, T:0.31
Consensus pattern (40 bp):
AAAATTGCAAAAAAATTTATAGAAAAATGAAAAATTTTAA
Found at i:6387797 original size:25 final size:27
Alignment explanation
Indices: 6387751--6387806 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 27
6387741 TTTTATTAAA
**
6387751 AAATTCTTAAAACTTATCAAAATTTTG
1 AAATTCTTAAAACTTATCAAAAAATTG
*
6387778 AAATT-TTAAAA-TTTTCAAAAAATTG
1 AAATTCTTAAAACTTATCAAAAAATTG
6387803 AAAT
1 AAAT
6387807 ATTCTCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 15 0.58
26 6 0.23
27 5 0.19
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (27 bp):
AAATTCTTAAAACTTATCAAAAAATTG
Found at i:6387860 original size:26 final size:27
Alignment explanation
Indices: 6387831--6387881 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
6387821 ATAAATTTTT
* *
6387831 TTAAATTTTTAA-AAAATTAAAAAAAC
1 TTAAAATTTTAATAAAAATAAAAAAAC
6387857 TTAAAATTTTAATAAAAATAAAAAA
1 TTAAAATTTTAATAAAAATAAAAAA
6387882 TTGAACAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (27 bp):
TTAAAATTTTAATAAAAATAAAAAAAC
Found at i:6388159 original size:17 final size:17
Alignment explanation
Indices: 6388119--6388161 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
6388109 AGATTTTTTG
* *
6388119 AATTTTTAAGTTTTCATA
1 AATTTTT-AGTTTTAAAA
*
6388137 ATTTTTTAGTTTTAAAA
1 AATTTTTAGTTTTAAAA
6388154 AATTTTTA
1 AATTTTTA
6388162 AATAAAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (17 bp):
AATTTTTAGTTTTAAAA
Found at i:6388214 original size:12 final size:11
Alignment explanation
Indices: 6388199--6388234 Score: 56
Period size: 10 Copynumber: 3.3 Consensus size: 11
6388189 TTTAAAAAAC
6388199 TTTTAAGAATTT
1 TTTTAA-AATTT
6388211 TTTTAAAATTT
1 TTTTAAAATTT
6388222 TTTT-AAATTT
1 TTTTAAAATTT
6388232 TTT
1 TTT
6388235 AATATTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.38
11 9 0.38
12 6 0.25
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (11 bp):
TTTTAAAATTT
Found at i:6388222 original size:10 final size:10
Alignment explanation
Indices: 6388185--6388236 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
6388175 AATATTTCAG
6388185 ATTTTTTAAAA
1 ATTTTTT-AAA
**
6388196 AACTTTTAAGA
1 ATTTTTTAA-A
6388207 ATTTTTTTAAA
1 A-TTTTTTAAA
*
6388218 ATTTTTTTAA
1 ATTTTTTAAA
6388228 ATTTTTTAA
1 ATTTTTTAA
6388237 TATTAATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
10 18 0.55
11 9 0.27
12 6 0.18
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:6391666 original size:8 final size:8
Alignment explanation
Indices: 6391655--6391680 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
6391645 TTTATAGGGT
6391655 TTTTCTTG
1 TTTTCTTG
6391663 TTTTCTTG
1 TTTTCTTG
6391671 TTTTCTTG
1 TTTTCTTG
6391679 TT
1 TT
6391681 CTTTTAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.77
Consensus pattern (8 bp):
TTTTCTTG
Found at i:6393092 original size:27 final size:27
Alignment explanation
Indices: 6393044--6393099 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
6393034 TAAAAAGTAT
* * *
6393044 ATATTATTTAATCTAATTATATTTATA
1 ATATTATTTAATATAATCATATTCATA
* *
6393071 ATATTATTTTATATTATCATATTCATA
1 ATATTATTTAATATAATCATATTCATA
6393098 AT
1 AT
6393100 CTTGTATATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (27 bp):
ATATTATTTAATATAATCATATTCATA
Found at i:6394113 original size:2 final size:2
Alignment explanation
Indices: 6394106--6394138 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
6394096 AAATAAACAA
*
6394106 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6394139 ACCATATCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6396847 original size:16 final size:17
Alignment explanation
Indices: 6396822--6396855 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
6396812 TTAAACTATT
*
6396822 TTTATGATAAACAATAA
1 TTTATGATAAAAAATAA
6396839 TTTAT-ATAAAAAATAA
1 TTTATGATAAAAAATAA
6396855 T
1 T
6396856 AAAATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (17 bp):
TTTATGATAAAAAATAA
Found at i:6402130 original size:25 final size:25
Alignment explanation
Indices: 6402102--6402153 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
6402092 TTCCTTTAGA
*
6402102 ATTTTTTTTGTCAACTGTGACCCAG
1 ATTTTGTTTGTCAACTGTGACCCAG
*
6402127 ATTTTGTTTGTCAACTGTGATCCAG
1 ATTTTGTTTGTCAACTGTGACCCAG
6402152 AT
1 AT
6402154 CTACTTAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.44
Consensus pattern (25 bp):
ATTTTGTTTGTCAACTGTGACCCAG
Found at i:6402820 original size:14 final size:14
Alignment explanation
Indices: 6402801--6402830 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6402791 CTAAAATTGA
6402801 TTTTAAAAAGATAT
1 TTTTAAAAAGATAT
*
6402815 TTTTAAAAATATAT
1 TTTTAAAAAGATAT
6402829 TT
1 TT
6402831 GTATTTTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
TTTTAAAAAGATAT
Found at i:6402959 original size:19 final size:17
Alignment explanation
Indices: 6402935--6402973 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
6402925 ATAATAATAT
6402935 TTAATATTAAAATATTATA
1 TTAATA-TAAAATATT-TA
6402954 TTAATATAAAATATTTA
1 TTAATATAAAATATTTA
6402971 TTA
1 TTA
6402974 TTCTTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAATATAAAATATTTA
Found at i:6403026 original size:20 final size:20
Alignment explanation
Indices: 6403003--6403072 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
6402993 AAAATATTTA
*
6403003 AAAATAGTATTATTATTCTT
1 AAAATAGTATTATTATTATT
* *
6403023 AAAATATTATTTTTATTAAAATT
1 AAAATAGTATTATTATT---ATT
*
6403046 AAAATAGTAATATATATTATT
1 AAAATAGTATTAT-TATTATT
6403067 AAAATA
1 AAAATA
6403073 TTTATACTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
20 15 0.38
21 9 0.22
23 12 0.30
24 4 0.10
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (20 bp):
AAAATAGTATTATTATTATT
Found at i:6403032 original size:17 final size:17
Alignment explanation
Indices: 6403010--6403044 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
6403000 TTAAAAATAG
*
6403010 TATTATTATTCTTAAAA
1 TATTATTATTATTAAAA
*
6403027 TATTATTTTTATTAAAA
1 TATTATTATTATTAAAA
6403044 T
1 T
6403045 TAAAATAGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
TATTATTATTATTAAAA
Found at i:6403037 original size:44 final size:44
Alignment explanation
Indices: 6402937--6403074 Score: 110
Period size: 44 Copynumber: 3.1 Consensus size: 44
6402927 AATAATATTT
* * *
6402937 AATATTAAAATATTATATTAATATAAAATA-T-TTATTATTCTT--
1 AATATTAATATTTTATA-AAAT-TAAAATAGTATTATTATTCTTAA
*
6402979 TATATTAATATTTTA-AAATATTTAAAAATAGTATTATTATTCTTAA
1 AATATTAATATTTTATAAA-A-TT-AAAATAGTATTATTATTCTTAA
* *
6403025 AATATT-AT-TTTTATTAAAATTAAAATAGTAATATATATTATTAA
1 AATATTAATATTTTA-TAAAATTAAAATAGTATTAT-TATTCTTAA
6403069 AATATT
1 AATATT
6403075 TATACTATTA
Statistics
Matches: 79, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
40 1 0.01
41 3 0.04
42 19 0.24
43 13 0.16
44 32 0.41
45 3 0.04
46 8 0.10
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (44 bp):
AATATTAATATTTTATAAAATTAAAATAGTATTATTATTCTTAA
Found at i:6403083 original size:17 final size:17
Alignment explanation
Indices: 6403058--6403094 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
6403048 AATAGTAATA
*
6403058 TATATTATTAAAATATT
1 TATACTATTAAAATATT
*
6403075 TATACTATTAAACTATT
1 TATACTATTAAAATATT
6403092 TAT
1 TAT
6403095 GTTTTATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (17 bp):
TATACTATTAAAATATT
Found at i:6403084 original size:44 final size:43
Alignment explanation
Indices: 6403003--6403086 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 43
6402993 AAAATATTTA
* * **
6403003 AAAATAGTATTATTATTCTTAAAATATTATTTTTATTAAAATT
1 AAAATAGTAATATTATTATTAAAATATTATTACTATTAAAATT
6403046 AAAATAGTAATATATATTATTAAAATATT-TATACTATTAAA
1 AAAATAGTAATAT-TATTATTAAAATATTAT-TACTATTAAA
6403087 CTATTTATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 13 0.37
44 22 0.63
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (43 bp):
AAAATAGTAATATTATTATTAAAATATTATTACTATTAAAATT
Found at i:6403274 original size:42 final size:41
Alignment explanation
Indices: 6403227--6403311 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 41
6403217 AATAAGATTT
6403227 TAAAAATATTATTATAT-TATTTA-ACATTAATTATTAAAATAA
1 TAAAAATATTATTATATAT-TTTAGA-ATT-ATTATTAAAATAA
6403269 TAAAAATATTATTATATATTTTAGTAATTATTATTAAAATAA
1 TAAAAATATTATTATATATTTTAG-AATTATTATTAAAATAA
6403311 T
1 T
6403312 GATATAATCC
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
42 35 0.88
43 4 0.10
44 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (41 bp):
TAAAAATATTATTATATATTTTAGAATTATTATTAAAATAA
Found at i:6403357 original size:15 final size:15
Alignment explanation
Indices: 6403338--6403393 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
6403328 TTATTGAAAT
*
6403338 ATTAAAATATTTATA
1 ATTAAAATATTTAAA
* **
6403353 TTTAATAATATACAAA
1 ATTAA-AATATTTAAA
6403369 ATTAAAATATTTAAA
1 ATTAAAATATTTAAA
6403384 ATTAAAATAT
1 ATTAAAATAT
6403394 CAAGAGACTT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
15 22 0.67
16 11 0.33
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTAAAATATTTAAA
Done.