Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, 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: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 17 of 138
Found at i:4802790 original size:21 final size:21
Alignment explanation
Indices: 4802730--4802795 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
4802720 TTTGAAACTT
* *
4802730 AAAAATCAAAGATTTTTC-TTT
1 AAAATTCAAAGA-TTTTCATTC
* * *
4802751 GAAATTCAAAGACTCTCATTC
1 AAAATTCAAAGATTTTCATTC
4802772 AAAATTCAAAGATTTTCA-TC
1 AAAATTCAAAGATTTTCATTC
4802792 AAAA
1 AAAA
4802796 AGTTCACAAT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
20 9 0.25
21 27 0.75
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.33
Consensus pattern (21 bp):
AAAATTCAAAGATTTTCATTC
Found at i:4814415 original size:174 final size:174
Alignment explanation
Indices: 4814189--4814502 Score: 483
Period size: 174 Copynumber: 1.8 Consensus size: 174
4814179 TCTTGGAAAG
* * *
4814189 AAAATAATGACAATTATTTTTATTGAAATTTCATCTAAATTATTGCACCATTTG-GGTCAAATTT
1 AAAAGAATGACAATTACTTTTATTGAAATTTCATCTAAATTATTGCACCATTTGAGAT-AAATTT
* *
4814253 TGAGAAAATTTCTTACCTAGAGATTTATT-AGAAATTTACCATTTGAAATTTCTAAGAATCTCAT
65 AGAGAAAATTTCTCACCTAGAGATTTATTAAG-AATTTACCATTTGAAATTTCTAAGAATCTCAT
*
4814317 CCTTGGATAATTATCATATATTTTCAACCAAAATTTTTTGTTTGGA
129 CATTGGATAATTATCATATATTTTCAACCAAAATTTTTTGTTTGGA
4814363 AAAAGAAT-ACAATTACTTTTATTGAAACTTTCATCTAAATTATT-CTACCATTTGAGATAAATT
1 AAAAGAATGACAATTACTTTTATTGAAA-TTTCATCTAAATTATTGC-ACCATTTGAGATAAATT
* * *
4814426 TAGAGAAAATTTCTCACTTTGAGATTTCTTAAGAATTTACCATTTGAAATTTCTAAGAATCTCAT
64 TAGAGAAAATTTCTCACCTAGAGATTTATTAAGAATTTACCATTTGAAATTTCTAAGAATCTCAT
4814491 CATTGGATAATT
129 CATTGGATAATT
4814503 TGTATTTAAT
Statistics
Matches: 127, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
173 19 0.15
174 104 0.82
175 4 0.03
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (174 bp):
AAAAGAATGACAATTACTTTTATTGAAATTTCATCTAAATTATTGCACCATTTGAGATAAATTTA
GAGAAAATTTCTCACCTAGAGATTTATTAAGAATTTACCATTTGAAATTTCTAAGAATCTCATCA
TTGGATAATTATCATATATTTTCAACCAAAATTTTTTGTTTGGA
Found at i:4814494 original size:25 final size:25
Alignment explanation
Indices: 4814443--4814503 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
4814433 AATTTCTCAC
* *
4814443 TTTGAGATTTCTTAAGAATTTACCA
1 TTTGAAATTTCTTAAGAATTCACCA
*
4814468 TTTGAAATTTC-TAAGAATCTCATCA
1 TTTGAAATTTCTTAAGAAT-TCACCA
*
4814493 TTGGATAATTT
1 TTTGA-AATTT
4814504 GTATTTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 7 0.23
25 18 0.60
26 5 0.17
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (25 bp):
TTTGAAATTTCTTAAGAATTCACCA
Found at i:4814669 original size:25 final size:25
Alignment explanation
Indices: 4814641--4814689 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
4814631 TTCTCACCAA
4814641 AAAATTT-TATAAAAATTTATCATTT
1 AAAATTTCTAT-AAAATTTATCATTT
*
4814666 AAAATTTCTATAAATTTTATCATT
1 AAAATTTCTATAAAATTTATCATT
4814690 GGATAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.49
Consensus pattern (25 bp):
AAAATTTCTATAAAATTTATCATTT
Found at i:4814690 original size:195 final size:195
Alignment explanation
Indices: 4814350--4814718 Score: 478
Period size: 195 Copynumber: 1.9 Consensus size: 195
4814340 TCAACCAAAA
* * *
4814350 TTTTTTGTTTGGAAAAAGAATACAATTACTTTTATTGAAACTTTCATCTAAATTATTCTACCATT
1 TTTTTTGTTTGAAAAAAAAATACAATTACTTTTATTGAAACTTTCATCTAAATTATTCCACCATT
**** * * *
4814415 TGAGATAAATTTAGAGAAAATTTCTCACTTTGAGATTTCTTAAGAATTTACCATTTGAAATTTCT
66 TGAGATAAATTTAGAGAAAATTTCTCACCAAAAAATTTCTTAAAAATTTACCATTTAAAATTTCT
* ** *
4814480 AAGAATCTCATCATTGGATAATTTGTATTTAATTCTCACAATTTTTATATTTTCTTCATTTTTTA
131 AAGAATCTCATCATTGGATAAATAATATTT-ATTCTCAAAATTTTTATATTTTCTTCATTTTTTA
4814545 T
195 T
*
4814546 TTTTTTGTTTGAAAATAAAAAT-TAATTA-TTGTTATTGAAACTTT-ATCTAAATTATTCCACCA
1 TTTTTTGTTTGAAAA-AAAAATACAATTACTT-TTATTGAAACTTTCATCTAAATTATTCCACCA
* * *
4814608 TTTGAGCTAAATTTAGATAAAATTTCTCACCAAAAAATTT-TATAAAAATTTATCATTTAAAATT
64 TTTGAGATAAATTTAGAGAAAATTTCTCACCAAAAAATTTCT-TAAAAATTTACCATTTAAAATT
* *
4814672 TCTATA-AATTTTATCATTGGATAAATAATATTTATTCTCAAAATTTT
128 TCTA-AGAATCTCATCATTGGATAAATAATATTTATTCTCAAAATTTT
4814719 ATTTTAATTA
Statistics
Matches: 149, Mismatches: 20, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
194 14 0.09
195 97 0.65
196 33 0.22
197 5 0.03
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.46
Consensus pattern (195 bp):
TTTTTTGTTTGAAAAAAAAATACAATTACTTTTATTGAAACTTTCATCTAAATTATTCCACCATT
TGAGATAAATTTAGAGAAAATTTCTCACCAAAAAATTTCTTAAAAATTTACCATTTAAAATTTCT
AAGAATCTCATCATTGGATAAATAATATTTATTCTCAAAATTTTTATATTTTCTTCATTTTTTAT
Found at i:4815696 original size:12 final size:13
Alignment explanation
Indices: 4815678--4815715 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
4815668 AAAAATTTGA
*
4815678 AAATAAAAGAAAT
1 AAATAAAAAAAAT
4815691 -AATAAAAAAAAT
1 AAATAAAAAAAAT
*
4815703 AAATAAATAAAAT
1 AAATAAAAAAAAT
4815716 TAAAACTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (13 bp):
AAATAAAAAAAAT
Found at i:4819022 original size:2 final size:2
Alignment explanation
Indices: 4819015--4819050 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4819005 TGATTTGTTT
4819015 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4819051 AATAGATGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4819749 original size:18 final size:17
Alignment explanation
Indices: 4819717--4819750 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4819707 ATGGCAACTC
*
4819717 ATTTTAAAGGAAAATTA
1 ATTTTAAACGAAAATTA
4819734 ATTTTAAACCGAAAATT
1 ATTTTAAA-CGAAAATT
4819751 TGAATGGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (17 bp):
ATTTTAAACGAAAATTA
Found at i:4820210 original size:21 final size:19
Alignment explanation
Indices: 4820172--4820210 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
4820162 TTATGGACTA
4820172 ATAATTTACCATTATGTGC
1 ATAATTTACCATTATGTGC
*
4820191 ATAATATTACTATTGATGTG
1 ATAAT-TTACCATT-ATGTG
4820211 ATTTTTGGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 7 0.41
21 5 0.29
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (19 bp):
ATAATTTACCATTATGTGC
Found at i:4822026 original size:19 final size:20
Alignment explanation
Indices: 4821983--4822033 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
4821973 ACCTCTCCAG
4821983 TTAAAAA-AAT-TTAAGAAA
1 TTAAAAATAATATTAAGAAA
*
4822001 -TACAAATAATATTAA-AAA
1 TTAAAAATAATATTAAGAAA
4822019 TTAAAAATACATATT
1 TTAAAAATA-ATATT
4822034 TAATGCATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 5 0.19
18 6 0.22
19 11 0.41
20 5 0.19
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (20 bp):
TTAAAAATAATATTAAGAAA
Found at i:4830994 original size:16 final size:17
Alignment explanation
Indices: 4830973--4831004 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
4830963 ATGAATCTAT
4830973 AAAATTTATA-ATTTTG
1 AAAATTTATATATTTTG
4830989 AAAATTTATATATTTT
1 AAAATTTATATATTTT
4831005 ATTAGTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
AAAATTTATATATTTTG
Found at i:4831741 original size:26 final size:26
Alignment explanation
Indices: 4831668--4831763 Score: 76
Period size: 26 Copynumber: 3.7 Consensus size: 26
4831658 GTAAATAAAT
*
4831668 TTTTTATTAAATAACATA-AATTATTA
1 TTTTTATTAAATAAAATATAA-TATTA
* *
4831694 TTTTAAATTAATTAAAAT-TAATA-TA
1 TTTT-TATTAAATAAAATATAATATTA
4831719 TTTTTATTGAAATAAAATATAATAATATA
1 TTTTTATT-AAATAAAATATAAT-AT-TA
*
4831748 TATTTA-TAAA-AAAATA
1 TTTTTATTAAATAAAATA
4831764 ATCTAAATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
24 3 0.05
25 14 0.25
26 16 0.28
27 16 0.28
28 1 0.02
29 7 0.12
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (26 bp):
TTTTTATTAAATAAAATATAATATTA
Found at i:4832785 original size:33 final size:29
Alignment explanation
Indices: 4832728--4832819 Score: 112
Period size: 30 Copynumber: 3.0 Consensus size: 29
4832718 AAGTCTTTGT
4832728 ATTTTTATTTTATCTAAATAAATTTTTAA
1 ATTTTTATTTTATCTAAATAAATTTTTAA
4832757 CATTTATTATTTTATACTCAAATAAATTTTTAA
1 -ATTT-TTATTTTAT-CT-AAATAAATTTTTAA
* * *
4832790 ATTTTAATTTGTATTTAAATAAATTCTTAA
1 ATTTTTATTT-TATCTAAATAAATTTTTAA
4832820 TATAAAATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
30 17 0.31
31 15 0.27
32 9 0.16
33 14 0.25
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.54
Consensus pattern (29 bp):
ATTTTTATTTTATCTAAATAAATTTTTAA
Found at i:4832831 original size:17 final size:18
Alignment explanation
Indices: 4832806--4832844 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
4832796 ATTTGTATTT
4832806 AAATAAATTCTTAATATA
1 AAATAAATTCTTAATATA
* *
4832824 AAAT-AATTTTTAATTTA
1 AAATAAATTCTTAATATA
4832841 AAAT
1 AAAT
4832845 GCAGATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATAAATTCTTAATATA
Found at i:4832916 original size:24 final size:23
Alignment explanation
Indices: 4832889--4832935 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
4832879 AAAAATTTAT
4832889 TTTAATATAATAAAAATATAAAAA
1 TTTAATATAAT-AAAATATAAAAA
* * *
4832913 TTTATTTTAATAAAATTTAAAAA
1 TTTAATATAATAAAATATAAAAA
4832936 CTCTTTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TTTAATATAATAAAATATAAAAA
Found at i:4833504 original size:7 final size:7
Alignment explanation
Indices: 4833492--4833525 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
4833482 ATTGATATTG
4833492 AAATTTA
1 AAATTTA
4833499 AAATTTA
1 AAATTTA
4833506 AAATTTA
1 AAATTTA
4833513 AAA-TT-
1 AAATTTA
4833518 AAATTTA
1 AAATTTA
4833525 A
1 A
4833526 TTGTTACCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 3 0.12
6 4 0.16
7 18 0.72
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AAATTTA
Found at i:4850606 original size:21 final size:21
Alignment explanation
Indices: 4850577--4850616 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4850567 TTTGATATAA
*
4850577 ATTTGAATTGAATTTTATTTG
1 ATTTGAATTAAATTTTATTTG
*
4850598 ATTTTAATTAAATTTTATT
1 ATTTGAATTAAATTTTATT
4850617 AATTTAGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (21 bp):
ATTTGAATTAAATTTTATTTG
Found at i:4852139 original size:23 final size:23
Alignment explanation
Indices: 4852087--4852141 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
4852077 TCTCTTTCTG
* *
4852087 TTTTTTTT-TTTTTTTCAAATTC
1 TTTTTTTTATTTATTTCAAATTA
4852109 TTTATTTTTATTTATTT-AAATTGA
1 TTT-TTTTTATTTATTTCAAATT-A
4852133 TTTTTTTTA
1 TTTTTTTTA
4852142 CTTTTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 3 0.11
23 16 0.57
24 9 0.32
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTTTTTTATTTATTTCAAATTA
Found at i:4855298 original size:10 final size:9
Alignment explanation
Indices: 4855286--4855321 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
4855276 AAATTTTCAA
4855286 AAAAAAATT
1 AAAAAAATT
*
4855295 AAAAAAATC
1 AAAAAAATT
4855304 AAAAAAATT
1 AAAAAAATT
4855313 GAAAAAAAT
1 -AAAAAAAT
4855322 GAAACAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (9 bp):
AAAAAAATT
Found at i:4855307 original size:18 final size:19
Alignment explanation
Indices: 4855286--4855321 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
4855276 AAATTTTCAA
4855286 AAAAAAATT-AAAAAAATC
1 AAAAAAATTGAAAAAAATC
4855304 AAAAAAATTGAAAAAAAT
1 AAAAAAATTGAAAAAAAT
4855322 GAAACAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (19 bp):
AAAAAAATTGAAAAAAATC
Found at i:4855442 original size:25 final size:25
Alignment explanation
Indices: 4855408--4855482 Score: 123
Period size: 25 Copynumber: 3.0 Consensus size: 25
4855398 ACGTGTTTTA
4855408 CATTTCATGCATATGTTAATTATGT
1 CATTTCATGCATATGTTAATTATGT
*
4855433 CATTTCATGCATATGTTAATTATGA
1 CATTTCATGCATATGTTAATTATGT
* *
4855458 CATTTCTTGCATATTTTAATTATGT
1 CATTTCATGCATATGTTAATTATGT
4855483 TTTTTATTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.28, C:0.12, G:0.11, T:0.49
Consensus pattern (25 bp):
CATTTCATGCATATGTTAATTATGT
Found at i:4860669 original size:21 final size:21
Alignment explanation
Indices: 4860622--4860670 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
4860612 TCAAAGTCAT
* *
4860622 AAAAAAAAAGAAAAAAATGCC
1 AAAAAAAAAGAAAAAAAGGCA
** *
4860643 TTAAAAAAAGAAAAAAAGGGA
1 AAAAAAAAAGAAAAAAAGGCA
4860664 AAAAAAA
1 AAAAAAA
4860671 GGTTTTCCTT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.78, C:0.04, G:0.12, T:0.06
Consensus pattern (21 bp):
AAAAAAAAAGAAAAAAAGGCA
Found at i:4861307 original size:20 final size:19
Alignment explanation
Indices: 4861282--4861335 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
4861272 GGAGGCATGC
*
4861282 AAAAAAAAAAACAAAAGAG
1 AAAAAAAAAAAAAAAAGAG
4861301 AAAAAAAAAAGAAAAAAGAG
1 AAAAAAAAAA-AAAAAAGAG
4861321 AAAAGAAAGAAAAAA
1 AAAA-AAA-AAAAAA
4861336 TTTTGATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 10 0.32
20 12 0.39
21 6 0.19
22 3 0.10
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAAAAAAAGAG
Found at i:4861324 original size:18 final size:18
Alignment explanation
Indices: 4861283--4861335 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
4861273 GAGGCATGCA
* *
4861283 AAAAAAAAAACAAAAGAG
1 AAAAAAAAAAGAAAAAAG
4861301 AAAAAAAAAAGAAAAAAG
1 AAAAAAAAAAGAAAAAAG
* *
4861319 AGAAAAGAAAGAAAAAA
1 AAAAAAAAAAGAAAAAA
4861336 TTTTGATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAGAAAAAAG
Found at i:4861850 original size:16 final size:16
Alignment explanation
Indices: 4861824--4861874 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 16
4861814 AATGATGGGT
4861824 AGAAGAAAAAAATAAAA
1 AGAA-AAAAAAATAAAA
4861841 AGAAAAAAAAAATAAAA
1 AG-AAAAAAAAATAAAA
4861858 A-AAATAAAAAATAAAA
1 AGAAA-AAAAAATAAAA
4861874 A
1 A
4861875 AAATGAGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.09
16 12 0.38
17 15 0.47
18 2 0.06
ACGTcount: A:0.86, C:0.00, G:0.06, T:0.08
Consensus pattern (16 bp):
AGAAAAAAAAATAAAA
Found at i:4861858 original size:26 final size:25
Alignment explanation
Indices: 4861829--4861887 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
4861819 TGGGTAGAAG
4861829 AAAAAAATAAAAAGAAAAAAAAAATA
1 AAAAAAATAAAAA-AAAAAAAAAATA
* *
4861855 AAAAAAATAAAAAATAAAAAAAATG
1 AAAAAAATAAAAAAAAAAAAAAATA
*
4861880 AGAAAAAT
1 AAAAAAAT
4861888 GAATAATTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 17 0.57
26 13 0.43
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (25 bp):
AAAAAAATAAAAAAAAAAAAAAATA
Found at i:4861875 original size:16 final size:16
Alignment explanation
Indices: 4861830--4861878 Score: 80
Period size: 16 Copynumber: 3.0 Consensus size: 16
4861820 GGGTAGAAGA
*
4861830 AAAAAATAAAAAGAAAA
1 AAAAAATAAAAA-AAAT
4861847 AAAAAATAAAAAAAAT
1 AAAAAATAAAAAAAAT
4861863 AAAAAATAAAAAAAAT
1 AAAAAATAAAAAAAAT
4861879 GAGAAAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 19 0.61
17 12 0.39
ACGTcount: A:0.88, C:0.00, G:0.02, T:0.10
Consensus pattern (16 bp):
AAAAAATAAAAAAAAT
Found at i:4861886 original size:1 final size:1
Alignment explanation
Indices: 4861829--4861877 Score: 53
Period size: 1 Copynumber: 49.0 Consensus size: 1
4861819 TGGGTAGAAG
* * * * *
4861829 AAAAAAATAAAAAGAAAAAAAAAATAAAAAAAATAAAAAATAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4861878 TGAGAAAAAT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.90, C:0.00, G:0.02, T:0.08
Consensus pattern (1 bp):
A
Found at i:4861886 original size:10 final size:9
Alignment explanation
Indices: 4861829--4861878 Score: 70
Period size: 9 Copynumber: 5.9 Consensus size: 9
4861819 TGGGTAGAAG
4861829 AAAAAAATA
1 AAAAAAATA
*
4861838 AAAAGAA-A
1 AAAAAAATA
4861846 AAAAAAATA
1 AAAAAAATA
4861855 AAAAAAAT-
1 AAAAAAATA
4861863 -AAAAAATA
1 AAAAAAATA
4861871 AAAAAAAT
1 AAAAAAAT
4861879 GAGAAAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
7 7 0.19
8 7 0.19
9 22 0.61
ACGTcount: A:0.88, C:0.00, G:0.02, T:0.10
Consensus pattern (9 bp):
AAAAAAATA
Found at i:4863510 original size:42 final size:41
Alignment explanation
Indices: 4863361--4863596 Score: 197
Period size: 42 Copynumber: 5.7 Consensus size: 41
4863351 TGCTCCACTC
* ** *
4863361 TGAATCCAAAATTTTCAAACTATGAATCA-TTACTCTGTTA
1 TGAATCCAAAGTCATCAAACTATGAATCATTTACTCTGCTA
* * *
4863401 TGAATCCAGAGTCTTCAAACTATGAAT-AGTTTACTCTTCTA
1 TGAATCCAAAGTCATCAAACTATGAATCA-TTTACTCTGCTA
* * * * * *
4863442 TGACTCCAGAGTCTTCAAACTTTGAATCATTTACTCTACTG
1 TGAATCCAAAGTCATCAAACTATGAATCATTTACTCTGCTA
* *
4863483 TGAATGCAAAGTCATCTAAACTATGAATTATTTACTCTGCTA
1 TGAATCCAAAGTCATC-AAACTATGAATCATTTACTCTGCTA
* * * * * **
4863525 TGAATCCAAAGTTATCTAAATTGTGAATCATTTTCTTTATTA
1 TGAATCCAAAGTCATC-AAACTATGAATCATTTACTCTGCTA
* *
4863567 TGAATCCAATAGTCTTTCCAACTATGAATC
1 TGAATCCAA-AGTC-ATCAAACTATGAATC
4863597 GTTCTCTGTT
Statistics
Matches: 159, Mismatches: 31, Indels: 9
0.80 0.16 0.05
Matches are distributed among these distances:
39 1 0.01
40 24 0.15
41 56 0.35
42 64 0.40
43 12 0.08
44 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (41 bp):
TGAATCCAAAGTCATCAAACTATGAATCATTTACTCTGCTA
Found at i:4863518 original size:83 final size:81
Alignment explanation
Indices: 4863361--4863595 Score: 224
Period size: 83 Copynumber: 2.8 Consensus size: 81
4863351 TGCTCCACTC
* * ** * *
4863361 TGAATCCAAAATTTTCAAACTATGAATCA-TTACTCTGTTATGAATCCAGAGTCTTCAAACTATG
1 TGAATCC-AAAGTTTCAAACTTTGAATCATTTACTCTACTATGAATCCAAAGTCATCAAACTATG
*
4863425 AATAGTTTACTCTTCTA
65 AATAGTTTACTCTGCTA
* * * *
4863442 TGACTCCAGAGTCTTCAAACTTTGAATCATTTACTCTACTGTGAATGCAAAGTCATCTAAACTAT
1 TGAATCCAAAGT-TTCAAACTTTGAATCATTTACTCTACTATGAATCCAAAGTCATC-AAACTAT
4863507 GAATTA-TTTACTCTGCTA
64 GAA-TAGTTTACTCTGCTA
* * * * *
4863525 TGAATCCAAAGTTATCTAAA-TTGTGAATCATTTTCTTTATTATGAATCCAATAGTCTTTCCAAC
1 TGAATCCAAAGTT-TC-AAACTT-TGAATCATTTACTCTACTATGAATCCAA-AGTC-ATCAAAC
4863589 TATGAAT
61 TATGAAT
4863596 CGTTCTCTGT
Statistics
Matches: 125, Mismatches: 20, Indels: 15
0.78 0.12 0.09
Matches are distributed among these distances:
80 3 0.02
81 21 0.17
82 22 0.18
83 35 0.28
84 29 0.23
85 13 0.10
86 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (81 bp):
TGAATCCAAAGTTTCAAACTTTGAATCATTTACTCTACTATGAATCCAAAGTCATCAAACTATGA
ATAGTTTACTCTGCTA
Found at i:4863715 original size:30 final size:33
Alignment explanation
Indices: 4863646--4863727 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 33
4863636 TTTACTTTTG
4863646 GTGTGAATCCCAAATCTTTTGAAAAAGCCTTTCA
1 GTGTGAATCCCAAA-CTTTTGAAAAAGCCTTTCA
* *
4863680 ATGTGAATCCCAAACTTTT-AAAGAA-TC-TT-A
1 GTGTGAATCCCAAACTTTTGAAA-AAGCCTTTCA
*
4863710 GTGTGAATCCCAACCTTT
1 GTGTGAATCCCAAACTTT
4863728 CAATGTGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
30 17 0.40
31 2 0.05
32 4 0.09
33 7 0.16
34 13 0.30
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (33 bp):
GTGTGAATCCCAAACTTTTGAAAAAGCCTTTCA
Found at i:4863770 original size:51 final size:51
Alignment explanation
Indices: 4863673--4863779 Score: 128
Period size: 50 Copynumber: 2.1 Consensus size: 51
4863663 TTTGAAAAAG
* * *
4863673 CCTTTCAATGTGAATCCCAAACTTTTAAAGAATCTTAGTGTGAATCC-CAA
1 CCTTTCAATGTGAATCCCAAACTTTTAAAGAACCTTAGTGCGAATCCTAAA
* * *
4863723 CCTTTCAATGTGAATCCCTAACCTTTTTAAGAAACCTT-TTGCGAATCCTAAA
1 CCTTTCAATGTGAATCCC-AAACTTTTAAAG-AACCTTAGTGCGAATCCTAAA
4863775 CCTTT
1 CCTTT
4863780 TGAAAAACCT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
50 18 0.38
51 18 0.38
52 12 0.25
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.35
Consensus pattern (51 bp):
CCTTTCAATGTGAATCCCAAACTTTTAAAGAACCTTAGTGCGAATCCTAAA
Found at i:4863830 original size:30 final size:31
Alignment explanation
Indices: 4863773--4863844 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 31
4863763 GCGAATCCTA
* * *
4863773 AACCTTTTGAAAAACCTTCTGGTGTGAATCTC
1 AACCTTTTGAAAAA-CTCCTAGTGTGAACCTC
4863805 GAA-CTTTTGAAAAA-TCCTAGTGTGAACCTC
1 -AACCTTTTGAAAAACTCCTAGTGTGAACCTC
4863835 AACCTTTTGA
1 AACCTTTTGA
4863845 TGTGAATCCT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 2 0.06
30 20 0.57
32 11 0.31
33 2 0.06
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (31 bp):
AACCTTTTGAAAAACTCCTAGTGTGAACCTC
Found at i:4864069 original size:18 final size:19
Alignment explanation
Indices: 4864046--4864083 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
4864036 CCACTTGAAA
*
4864046 AAACCTTTTG-TGAATCCT
1 AAACCTTTTGAAGAATCCT
4864064 AAACCTTTTGAAGAATCCT
1 AAACCTTTTGAAGAATCCT
4864083 A
1 A
4864084 GTGTGAATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (19 bp):
AAACCTTTTGAAGAATCCT
Found at i:4864075 original size:31 final size:31
Alignment explanation
Indices: 4863994--4864107 Score: 113
Period size: 31 Copynumber: 3.7 Consensus size: 31
4863984 ATCTTGGTAG
* *
4863994 GAATCCTAAACCTTTTGAAAAAAACATTTTAT
1 GAATCCTAAACCTTTTG-AAAAAACCTTTTGT
* **
4864026 GAATCTTAAACCACTTGAAAAAACCTTTTGT
1 GAATCCTAAACCTTTTGAAAAAACCTTTTGT
* * **
4864057 GAATCCTAAACCTTTTGAAGAATCCTAGTGT
1 GAATCCTAAACCTTTTGAAAAAACCTTTTGT
**
4864088 GAATCCCGAA-CTTTTGAAAA
1 GAATCCTAAACCTTTTGAAAA
4864108 TTCTTAATGT
Statistics
Matches: 67, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
30 9 0.13
31 44 0.66
32 14 0.21
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (31 bp):
GAATCCTAAACCTTTTGAAAAAACCTTTTGT
Found at i:4864119 original size:30 final size:31
Alignment explanation
Indices: 4864054--4864120 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
4864044 AAAAACCTTT
* *
4864054 TGTGAATCCTAAACCTTTTGAAGAATCCTAG
1 TGTGAATCCCAAACCTTTTGAAGAATCCTAA
* *
4864085 TGTGAATCCCGAA-CTTTTGAA-AATTCTTAA
1 TGTGAATCCCAAACCTTTTGAAGAA-TCCTAA
4864115 TGTGAA
1 TGTGAA
4864121 CCCTAGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 2 0.06
30 18 0.58
31 11 0.35
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (31 bp):
TGTGAATCCCAAACCTTTTGAAGAATCCTAA
Found at i:4867875 original size:19 final size:20
Alignment explanation
Indices: 4867838--4867887 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
4867828 AAATTTTGTG
*
4867838 TAATTTTTACTTTATTTGAC
1 TAATTTTGACTTTATTTGAC
4867858 TAATTTTGACTTTA-TTGAC
1 TAATTTTGACTTTATTTGAC
*
4867877 TAAATTTGACT
1 TAATTTTGACT
4867888 AGAGTTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.28, C:0.10, G:0.08, T:0.54
Consensus pattern (20 bp):
TAATTTTGACTTTATTTGAC
Found at i:4869369 original size:44 final size:43
Alignment explanation
Indices: 4869297--4869406 Score: 166
Period size: 44 Copynumber: 2.5 Consensus size: 43
4869287 TGCTGAAAAT
* *
4869297 ATTAAGAAGAGCAACGAAAAGCTTGCTTAGTTGGGCTGCATCA
1 ATTAAGAAGAGCAATGAAAAGCTAGCTTAGTTGGGCTGCATCA
* * *
4869340 ATTAAGAATAGCAAATGAAAAGCTAGCTTAGTTGTGTTGCATCA
1 ATTAAGAAGAGC-AATGAAAAGCTAGCTTAGTTGGGCTGCATCA
4869384 ATTAAGAAGAGCAATGAAAAGCT
1 ATTAAGAAGAGCAATGAAAAGCT
4869407 GTCTGCACAC
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
43 22 0.37
44 38 0.63
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.25
Consensus pattern (43 bp):
ATTAAGAAGAGCAATGAAAAGCTAGCTTAGTTGGGCTGCATCA
Found at i:4873670 original size:21 final size:20
Alignment explanation
Indices: 4873646--4873685 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
4873636 TTTATACTAA
*
4873646 TAATTTTTTACATTAATAATT
1 TAATTATTTACATT-ATAATT
4873667 TAATTATTTACATTATAAT
1 TAATTATTTACATTATAAT
4873686 AATATGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TAATTATTTACATTATAATT
Found at i:4874340 original size:18 final size:19
Alignment explanation
Indices: 4874304--4874349 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
4874294 AATTTTCAAC
* *
4874304 TTTTTTCTTTAACACTTAT
1 TTTTTTATTTAACAATTAT
4874323 TTTTTTATTTAA-AATTAT
1 TTTTTTATTTAACAATTAT
4874341 TTTTATTAT
1 TTTT-TTAT
4874350 AATACTAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTTTATTTAACAATTAT
Found at i:4874574 original size:21 final size:19
Alignment explanation
Indices: 4874530--4874576 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
4874520 TACTTAACTC
*
4874530 TTTTTT-TTTGTTTAAAAA
1 TTTTTTATTTGTATAAAAA
4874548 TATTTTTATTTGTGATAATAAA
1 T-TTTTTATTTGT-ATAA-AAA
4874570 TTTTTTA
1 TTTTTTA
4874577 CATTAACAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 1 0.04
19 5 0.21
20 5 0.21
21 9 0.38
22 4 0.17
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (19 bp):
TTTTTTATTTGTATAAAAA
Found at i:4876820 original size:37 final size:37
Alignment explanation
Indices: 4876774--4876846 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
4876764 ATTCTCACAT
4876774 TATTATATTAATTAATT-TTTAATTAAAAAATTTTAAA
1 TATTATATTAATTAATTATTT-ATTAAAAAATTTTAAA
* * * *
4876811 TATTATATTATTTTATTATTTTTTAAAGAATTTTAA
1 TATTATATTAATTAATTATTTATTAAAAAATTTTAA
4876847 GTAAATTGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (37 bp):
TATTATATTAATTAATTATTTATTAAAAAATTTTAAA
Found at i:4877364 original size:1 final size:1
Alignment explanation
Indices: 4877360--4877384 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
4877350 GCTTAAACCC
4877360 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
4877385 TCCTAACGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4879641 original size:232 final size:232
Alignment explanation
Indices: 4879235--4879703 Score: 861
Period size: 232 Copynumber: 2.0 Consensus size: 232
4879225 TTTGATTTTC
4879235 AATTTTAATTTTTATTTATTCATTTTTAATAAAAAAACTTCACGAATCCTACTTACAAAATTTTA
1 AATTTTAATTTTTATTTATTCATTTTTAATAAAAAAACTTCACGAATCCTACTTACAAAATTTTA
*
4879300 TGTAAATTTTTCTGAGATAAGACAAGTTTTGAGGTCAATCTATAAGGGCAACCTGGTATTCCAAT
66 TGTAAATTTTTCTGAGATAAGACAAGTTTTGAGGTCAATCTATAAGGGCAACCTGGTATTCAAAT
4879365 TTAACATAGATCATTGCAAAAACCATAATTTCAAGGTGGGACACCTTTGATCAGATATATTCCAA
131 TTAACATAGATCATTGCAAAAACCATAATTTCAAGGTGGGACACCTTTGATCAGATATATTCCAA
4879430 ATTTAAATACCAAGTTTAAAGAGTCTTATTACTTCTT
196 ATTTAAATACCAAGTTTAAAGAGTCTTATTACTTCTT
* **
4879467 AATTTTAATTTTTATTTATTCATTTTTAAT-AAGAAACTTCACGAATTTTACTTACAAAATTTTA
1 AATTTTAATTTTTATTTATTCATTTTTAATAAAAAAACTTCACGAATCCTACTTACAAAATTTTA
*
4879531 TGTAAATTTTT-TGGAGATAAGACAAGTTTTGAGGTCAGTTCTATAAGGGCAACCTGGTATTCAA
66 TGTAAATTTTTCT-GAGATAAGACAAGTTTTGAGGTCA-ATCTATAAGGGCAACCTGGTATTCAA
4879595 ATTTAACATAGATCATTGCAAAAACCATAATTTCAAGGTGGGACACCTTTGATCAGATATATTCC
129 ATTTAACATAGATCATTGCAAAAACCATAATTTCAAGGTGGGACACCTTTGATCAGATATATTCC
4879660 AAATTTAAATACCAAGTTTAAAGAGTCTTATTACTTCTT
194 AAATTTAAATACCAAGTTTAAAGAGTCTTATTACTTCTT
4879699 AATTT
1 AATTT
4879704 AGACACCAAC
Statistics
Matches: 230, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
230 1 0.00
231 66 0.29
232 163 0.71
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (232 bp):
AATTTTAATTTTTATTTATTCATTTTTAATAAAAAAACTTCACGAATCCTACTTACAAAATTTTA
TGTAAATTTTTCTGAGATAAGACAAGTTTTGAGGTCAATCTATAAGGGCAACCTGGTATTCAAAT
TTAACATAGATCATTGCAAAAACCATAATTTCAAGGTGGGACACCTTTGATCAGATATATTCCAA
ATTTAAATACCAAGTTTAAAGAGTCTTATTACTTCTT
Found at i:4880886 original size:27 final size:26
Alignment explanation
Indices: 4880826--4880888 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 26
4880816 TTTAATTTGT
**
4880826 ATATTTTACGATTTTATTTTATAAAA
1 ATATTTTATAATTTTATTTTATAAAA
*
4880852 GTGA--TTATAATTTTATTTTATAAAAA
1 AT-ATTTTATAATTTTATTTTAT-AAAA
4880878 ATATTTTATAA
1 ATATTTTATAA
4880889 ATTTGAGTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
25 16 0.55
26 6 0.21
27 7 0.24
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (26 bp):
ATATTTTATAATTTTATTTTATAAAA
Found at i:4881005 original size:18 final size:18
Alignment explanation
Indices: 4880982--4881023 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
4880972 TGAACTCAAC
4880982 ATAAAACATACA-TAAATA
1 ATAAAA-ATACATTAAATA
*
4881000 ATAAAATTACATTAAATA
1 ATAAAAATACATTAAATA
*
4881018 TTAAAA
1 ATAAAA
4881024 TTTTAATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAAAAATACATTAAATA
Found at i:4881024 original size:18 final size:17
Alignment explanation
Indices: 4880990--4881025 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
4880980 ACATAAAACA
4880990 TACATAAATAATAAAAT
1 TACATAAATAATAAAAT
*
4881007 TACATTAAATATTAAAAT
1 TACA-TAAATAATAAAAT
4881025 T
1 T
4881026 TTAATGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
TACATAAATAATAAAAT
Found at i:4881182 original size:23 final size:24
Alignment explanation
Indices: 4881121--4881182 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
4881111 ATCGATAATC
* *
4881121 ATTTAAATTTATAAAATATTATTT
1 ATTTTAATTTATAAAATATTATTG
*
4881145 ATTTTAATTTA-AAAATTTTA-TG
1 ATTTTAATTTATAAAATATTATTG
4881167 ATTTT-ATCTTATAAAA
1 ATTTTAAT-TTATAAAA
4881183 AATATTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 2 0.06
22 9 0.27
23 12 0.36
24 10 0.30
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
ATTTTAATTTATAAAATATTATTG
Found at i:4888994 original size:30 final size:29
Alignment explanation
Indices: 4888960--4889022 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 29
4888950 TGAATAAGTA
*
4888960 AAATTATATTTAATAATTTTAAATATATAT
1 AAATTATATTTAATAATTTTAAATAAAT-T
*
4888990 AAATTATATTTAATGATTTTAAATAAATT
1 AAATTATATTTAATAATTTTAAATAAATT
4889019 AAAT
1 AAAT
4889023 ATTAATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 5 0.16
30 26 0.84
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
AAATTATATTTAATAATTTTAAATAAATT
Found at i:4889037 original size:30 final size:30
Alignment explanation
Indices: 4888952--4889039 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
4888942 AGTTTACTTG
* * *
4888952 AATAAGTA-AAATTATATTTAATAATTTTA
1 AATAAATATAAATTATAATTAATGATTTTA
* *
4888981 AATATATATAAATTATATTTAATGATTTTA
1 AATAAATATAAATTATAATTAATGATTTTA
4889011 AATAAAT-TAAA-TATTAATTAATTGATTTT
1 AATAAATATAAATTA-TAATTAA-TGATTTT
4889040 GAAGTGATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
28 2 0.04
29 16 0.31
30 33 0.65
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
AATAAATATAAATTATAATTAATGATTTTA
Found at i:4896014 original size:6 final size:6
Alignment explanation
Indices: 4896003--4896031 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
4895993 TCTGATGAAA
4896003 AATCTC AATCTC AATCTC AATCTC AATCT
1 AATCTC AATCTC AATCTC AATCTC AATCT
4896032 TGCATTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (6 bp):
AATCTC
Found at i:4900305 original size:32 final size:31
Alignment explanation
Indices: 4900268--4900334 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 31
4900258 ATATAATTAA
* ** *
4900268 AAAATTTAAGATGTAAATTATATATTTTTTT
1 AAAATTCAAGATACAAATTATATATTATTTT
4900299 GAAAATTCAAGATACAAATTATATATTATTTT
1 -AAAATTCAAGATACAAATTATATATTATTTT
4900331 AAAA
1 AAAA
4900335 CTTAGATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 4 0.13
32 27 0.87
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (31 bp):
AAAATTCAAGATACAAATTATATATTATTTT
Found at i:4900342 original size:30 final size:31
Alignment explanation
Indices: 4900268--4900342 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
4900258 ATATAATTAA
** *
4900268 AAAATTTAAGATGTAAATTATATATTTTTTTG
1 AAAA-TTAAGATACAAATTATATATTATTTTG
4900300 AAAATTCAAGATACAAATTATATATTATTTT-
1 AAAATT-AAGATACAAATTATATATTATTTTG
4900331 AAAACTT-AGATA
1 AAAA-TTAAGATA
4900343 ATACATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
30 5 0.13
31 6 0.16
32 27 0.71
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.43
Consensus pattern (31 bp):
AAAATTAAGATACAAATTATATATTATTTTG
Found at i:4900601 original size:20 final size:21
Alignment explanation
Indices: 4900576--4900633 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
4900566 TATTTTTGTA
4900576 TTATATAAAATTTTA-ATAAT
1 TTATATAAAATTTTATATAAT
*
4900596 TTATAT--AATTTTATTATATT
1 TTATATAAAATTTTA-TATAAT
*
4900616 TTATATAAAA-ATTATATA
1 TTATATAAAATTTTATATA
4900634 CTACAAATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 7 0.22
20 20 0.62
21 3 0.09
22 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTATATAAAATTTTATATAAT
Found at i:4901786 original size:30 final size:31
Alignment explanation
Indices: 4901752--4901812 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
4901742 AATGGATGAA
4901752 ATAATGGATCA-TAACTGCTAATTCATTGAC
1 ATAATGGATCATTAACTGCTAATTCATTGAC
*
4901782 ATAATGGATCATTAACTGTTAATTCATTGAC
1 ATAATGGATCATTAACTGCTAATTCATTGAC
4901813 TTTCTGACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 11 0.38
31 18 0.62
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (31 bp):
ATAATGGATCATTAACTGCTAATTCATTGAC
Found at i:4902074 original size:23 final size:22
Alignment explanation
Indices: 4902049--4902093 Score: 72
Period size: 24 Copynumber: 2.0 Consensus size: 22
4902039 TATTATTTAT
4902049 AAAATAAAAATATATAAAAAGTTA
1 AAAATAAAAA-ATA-AAAAAGTTA
4902073 AAAATAAAAAATAAAAAAGTT
1 AAAATAAAAAATAAAAAAGTT
4902094 TTCATCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.38
23 3 0.14
24 10 0.48
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.22
Consensus pattern (22 bp):
AAAATAAAAAATAAAAAAGTTA
Found at i:4905818 original size:18 final size:18
Alignment explanation
Indices: 4905781--4905817 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
4905771 TTTTTTCATA
4905781 TTGTGGGTATTATAATTT
1 TTGTGGGTATTATAATTT
*
4905799 TTGTGGGT-TTATGATTT
1 TTGTGGGTATTATAATTT
4905816 TT
1 TT
4905818 TTAAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.16, C:0.00, G:0.24, T:0.59
Consensus pattern (18 bp):
TTGTGGGTATTATAATTT
Found at i:4907230 original size:42 final size:41
Alignment explanation
Indices: 4907143--4907346 Score: 184
Period size: 42 Copynumber: 5.0 Consensus size: 41
4907133 TTGATTTATA
* * * * *
4907143 GTTTTCTGTTATTATTTTTAA-TGCTCAAATTTATAGTTAAA
1 GTTTTTTGTTATTGTTCTTAATTGCTCAAAATTATAGTT-AG
* * *
4907184 GTTTTTTATTATTGTTCTTAATTGCTCAAATTTATATTTGAG
1 GTTTTTTGTTATTGTTCTTAATTGCTCAAAATTATAGTT-AG
* * * *
4907226 GTTTTCTGTTAGTGTTTTTAATTGCTCAAAATAATAGTTAG
1 GTTTTTTGTTATTGTTCTTAATTGCTCAAAATTATAGTTAG
* * *
4907267 G--GTTT-TT-TTGTTCTTAATTGGTTAAAATTATAGTTAG
1 GTTTTTTGTTATTGTTCTTAATTGCTCAAAATTATAGTTAG
* * *
4907304 GATTTTTTGTTGTTATTCTTAATTGTTCAAAATTATAGTTAG
1 G-TTTTTTGTTATTGTTCTTAATTGCTCAAAATTATAGTTAG
4907346 G
1 G
4907347 ACTTTCTAAT
Statistics
Matches: 132, Mismatches: 25, Indels: 11
0.79 0.15 0.07
Matches are distributed among these distances:
37 26 0.20
38 2 0.02
39 2 0.02
40 3 0.02
41 22 0.17
42 77 0.58
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.53
Consensus pattern (41 bp):
GTTTTTTGTTATTGTTCTTAATTGCTCAAAATTATAGTTAG
Found at i:4907294 original size:37 final size:39
Alignment explanation
Indices: 4907238--4907347 Score: 118
Period size: 37 Copynumber: 2.8 Consensus size: 39
4907228 TTTCTGTTAG
* * * *
4907238 TGTTTTTAATTGCTCAAAATAATAGTTAGG-GTTTTT-T
1 TGTTCTTAATTGGTTAAAATTATAGTTAGGAGTTTTTGT
*
4907275 TGTTCTTAATTGGTTAAAATTATAGTTAGGATTTTTTGT
1 TGTTCTTAATTGGTTAAAATTATAGTTAGGAGTTTTTGT
4907314 TGTTATTCTTAATT-GTTCAAAATTATAGTTAGGA
1 TG---TTCTTAATTGGTT-AAAATTATAGTTAGGA
4907348 CTTTCTAATA
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
37 26 0.42
38 5 0.08
39 3 0.05
41 3 0.05
42 25 0.40
ACGTcount: A:0.28, C:0.05, G:0.16, T:0.51
Consensus pattern (39 bp):
TGTTCTTAATTGGTTAAAATTATAGTTAGGAGTTTTTGT
Found at i:4907326 original size:79 final size:79
Alignment explanation
Indices: 4907195--4907346 Score: 193
Period size: 79 Copynumber: 1.9 Consensus size: 79
4907185 TTTTTTATTA
* *
4907195 TTGTTCTTAATTGCTCAAATTTATATTTGAGGTTTTCTGTTAGTGTTTTTAATTGCTCAAAATAA
1 TTGTTCTTAATTGCTCAAAATTATAGTTGAGGTTTTCTGTTAGTGTTTTTAATTGCTCAAAATAA
4907260 TAGTTAGGGTTTTT
66 TAGTTAGGGTTTTT
* * * *
4907274 TTGTTCTTAATTGGTTAAAATTATAGTT-AGGATTTTTTGTT-GT-TATTCTTAATTGTTCAAAA
1 TTGTTCTTAATTGCTCAAAATTATAGTTGAGG-TTTTCTGTTAGTGT-TT-TTAATTGCTCAAAA
*
4907336 TTATAGTTAGG
63 TAATAGTTAGG
4907347 ACTTTCTAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
77 1 0.02
78 7 0.11
79 55 0.87
ACGTcount: A:0.26, C:0.06, G:0.16, T:0.52
Consensus pattern (79 bp):
TTGTTCTTAATTGCTCAAAATTATAGTTGAGGTTTTCTGTTAGTGTTTTTAATTGCTCAAAATAA
TAGTTAGGGTTTTT
Found at i:4908081 original size:18 final size:18
Alignment explanation
Indices: 4908058--4908117 Score: 56
Period size: 18 Copynumber: 3.6 Consensus size: 18
4908048 TATAACATGG
4908058 TTATAACAAAGTAAAAGC
1 TTATAACAAAGTAAAAGC
**
4908076 TTAT-A-AAAG-AAATTC
1 TTATAACAAAGTAAAAGC
* *
4908091 -TATAATAAAGTAAAAGA
1 TTATAACAAAGTAAAAGC
4908108 TTATAACAAA
1 TTATAACAAA
4908118 AATTAGATAA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
14 3 0.09
15 5 0.16
16 8 0.25
17 4 0.12
18 12 0.38
ACGTcount: A:0.58, C:0.07, G:0.08, T:0.27
Consensus pattern (18 bp):
TTATAACAAAGTAAAAGC
Found at i:4908101 original size:32 final size:32
Alignment explanation
Indices: 4908059--4908130 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
4908049 ATAACATGGT
*
4908059 TATAACAAAGTAAAAGCTTATAA-AAGAAATTC
1 TATAACAAAGTAAAAGATTATAACAA-AAATTC
* *
4908091 TATAATAAAGTAAAAGATTATAACAAAAATTA
1 TATAACAAAGTAAAAGATTATAACAAAAATTC
*
4908123 GATAACAA
1 TATAACAA
4908131 TGTATGGGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 32 0.94
33 2 0.06
ACGTcount: A:0.60, C:0.07, G:0.08, T:0.25
Consensus pattern (32 bp):
TATAACAAAGTAAAAGATTATAACAAAAATTC
Found at i:4908771 original size:42 final size:42
Alignment explanation
Indices: 4908683--4908777 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
4908673 GAGGTGGTAG
* * * *
4908683 AGAATAGAAGGGTAAAAAATCAACACGTAGCAGATGCAATAG
1 AGAATAAAAGGGTAAAAAATCAACACGTAGCAAAGGCAATAA
* *
4908725 AGAATAAAAGGGTAAAAAATCAACATGTAG-ATAAGGCAGTAA
1 AGAATAAAAGGGTAAAAAATCAACACGTAGCA-AAGGCAATAA
*
4908767 AGAATGAAAGG
1 AGAATAAAAGG
4908778 ATAGAAACTA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 1 0.02
42 44 0.98
ACGTcount: A:0.53, C:0.08, G:0.24, T:0.15
Consensus pattern (42 bp):
AGAATAAAAGGGTAAAAAATCAACACGTAGCAAAGGCAATAA
Found at i:4908952 original size:33 final size:33
Alignment explanation
Indices: 4908836--4908954 Score: 82
Period size: 33 Copynumber: 3.6 Consensus size: 33
4908826 GTAGTTAAAA
*
4908836 CAGCAAAGGTAA-AAATTGAAGATGATG-TCAAGG
1 CAGCAAAGGTAAGAAA-TGAAGATGATGTTGAA-G
* * * *** *
4908869 TAGCAATGGT-AGAAAATAAAGATGCCATTGAGG
1 CAGCAAAGGTAAG-AAATGAAGATGATGTTGAAG
* * * *
4908902 TAGCAGAGATAAAAAATGAAGATGATGTTGAAG
1 CAGCAAAGGTAAGAAATGAAGATGATGTTGAAG
4908935 CAGCAAAGGTAAGAAATGAA
1 CAGCAAAGGTAAGAAATGAA
4908955 AATGTGATTG
Statistics
Matches: 61, Mismatches: 21, Indels: 8
0.68 0.23 0.09
Matches are distributed among these distances:
32 1 0.02
33 54 0.89
34 6 0.10
ACGTcount: A:0.47, C:0.08, G:0.27, T:0.18
Consensus pattern (33 bp):
CAGCAAAGGTAAGAAATGAAGATGATGTTGAAG
Found at i:4910365 original size:10 final size:11
Alignment explanation
Indices: 4910340--4910369 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4910330 AGATAATTTA
4910340 AAAAAAATAAG
1 AAAAAAATAAG
*
4910351 AAAAATATAAG
1 AAAAAAATAAG
4910362 AAAAAAAT
1 AAAAAAAT
4910370 GATACTACAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (11 bp):
AAAAAAATAAG
Found at i:4912706 original size:23 final size:23
Alignment explanation
Indices: 4912679--4912733 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
4912669 ATCAAGAAAT
4912679 AAATACCAACAAAAACACCAAAG
1 AAATACCAACAAAAACACCAAAG
* *
4912702 AAATACTAGCAAAAACACCAAAG
1 AAATACCAACAAAAACACCAAAG
4912725 AAATACCAA
1 AAATACCAA
4912734 TAAACTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.64, C:0.24, G:0.05, T:0.07
Consensus pattern (23 bp):
AAATACCAACAAAAACACCAAAG
Found at i:4917640 original size:14 final size:12
Alignment explanation
Indices: 4917611--4917649 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
4917601 TAATATGGTA
*
4917611 TCTCTCTCTTTG
1 TCTCTCTCTTTC
*
4917623 TCTCTCTCTTAC
1 TCTCTCTCTTTC
*
4917635 TCTCTCTCTCTC
1 TCTCTCTCTTTC
4917647 TCT
1 TCT
4917650 GTCGCACACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.03, C:0.41, G:0.03, T:0.54
Consensus pattern (12 bp):
TCTCTCTCTTTC
Found at i:4921285 original size:25 final size:25
Alignment explanation
Indices: 4921257--4921315 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
4921247 GAATTCGAGT
4921257 TCGAGTATAAATAATCGAACTCTTG
1 TCGAGTATAAATAATCGAACTCTTG
*
4921282 TCGAGTATGAATAATCGAACTCTTG
1 TCGAGTATAAATAATCGAACTCTTG
4921307 TCGAGTATA
1 TCGAGTATA
4921316 CGAATCGAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (25 bp):
TCGAGTATAAATAATCGAACTCTTG
Found at i:4927276 original size:2 final size:2
Alignment explanation
Indices: 4927269--4927294 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4927259 AAATTCATCA
4927269 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
4927295 CAATACACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4927684 original size:18 final size:19
Alignment explanation
Indices: 4927650--4927691 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
4927640 GTGTATATAT
*
4927650 AAATTAGTATTTTATTT-A
1 AAATTAGTATTTAATTTCA
4927668 AAATTA-TATTTAAATTTCA
1 AAATTAGTATTT-AATTTCA
4927687 AAATT
1 AAATT
4927692 TATAATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 5 0.24
18 10 0.48
19 6 0.29
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (19 bp):
AAATTAGTATTTAATTTCA
Found at i:4928872 original size:16 final size:16
Alignment explanation
Indices: 4928851--4928881 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
4928841 TATTTTTTAC
4928851 AAAAAATTTTAAAACT
1 AAAAAATTTTAAAACT
4928867 AAAAAATTTTAAAAC
1 AAAAAATTTTAAAAC
4928882 ATAAGATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAAATTTTAAAACT
Found at i:4929371 original size:32 final size:32
Alignment explanation
Indices: 4929324--4929390 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
4929314 ATCCTTAATT
* *
4929324 TTTTTCTTCCCTTTTATAAAGCAAAGCCTATA
1 TTTTTCATCCCTTTTATAAAGCAAAGCCTAAA
* * * *
4929356 TTTTTCATCCTTTTTATCATGCGAAGCCTAAA
1 TTTTTCATCCCTTTTATAAAGCAAAGCCTAAA
4929388 TTT
1 TTT
4929391 GTGTCCCGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.25, C:0.21, G:0.07, T:0.46
Consensus pattern (32 bp):
TTTTTCATCCCTTTTATAAAGCAAAGCCTAAA
Found at i:4932802 original size:9 final size:9
Alignment explanation
Indices: 4932773--4932866 Score: 62
Period size: 9 Copynumber: 10.1 Consensus size: 9
4932763 AATGTCACAT
*
4932773 AAATATAAA
1 AAATTTAAA
* *
4932782 AAATTCATA
1 AAATTTAAA
4932791 AAATTTAAAA
1 AAATTT-AAA
*
4932801 AAATCTAAA
1 AAATTTAAA
*
4932810 AAATTATTTAA
1 AAA-T-TTAAA
*
4932821 AATTTTAAA
1 AAATTTAAA
* *
4932830 ATATTTGAA
1 AAATTTAAA
*
4932839 ATATTTAAA
1 AAATTTAAA
*
4932848 AAATTCAAA
1 AAATTTAAA
*
4932857 AAAATTAAA
1 AAATTTAAA
4932866 A
1 A
4932867 CAAAGCTCAA
Statistics
Matches: 64, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
9 50 0.78
10 9 0.14
11 5 0.08
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (9 bp):
AAATTTAAA
Found at i:4937562 original size:183 final size:184
Alignment explanation
Indices: 4937241--4937581 Score: 431
Period size: 183 Copynumber: 1.9 Consensus size: 184
4937231 GAAGAAAATG
* * *
4937241 AAAATTTTATTATATTGAAGATTTTCTATAAATACTCCAATACACTAGTAATATTTTAAAAATCT
1 AAAAATTTATTATATTGAAAATTTTCTATAAATACTCCAATACACTAGTAATATTTAAAAAATCT
* * * * * * *
4937306 TCTCACCTAAGAATTTTTAAAGCATCTCTACTTGAAATACTTTTAGAATCCCATCATTGGACAAA
66 TCTCACATAAGAATTTATAAAGCATCACTACTCGAAATACTCTTAGAATCCCATCATCGGAAAAA
* *
4937371 ATTTTTTTTCTT-ATTTTTTCTTAATTATTTTTTAATTTTTATTATTAAAGAAA
131 AATTTTTTTCTTAATTTTTTATTAATTATTTTTTAATTTTTATTATTAAAGAAA
* *
4937424 AAAAATTTATTATATTGAAAAATTTT-TATAAATACTCCAATACATTAGTAATATTTAAAAAATT
1 AAAAATTTATTATATTG-AAAATTTTCTATAAATACTCCAATACACTAGTAATATTTAAAAAATC
* * * *
4937488 TTCTCACAT-AGAGATTTCAT-AAGCATCACTACTCGGAGTAC-CTTAGAATCTCATCGTCGGAT
65 TTCTCACATAAGA-ATTT-ATAAAGCATCACTACTCGAAATACTCTTAGAATCCCATCATCGGA-
*
4937550 AAAAAATTTTTTTTTTACATTTTTTATTAATT
127 AAAAAATTTTTTTCTTA-ATTTTTTATTAATT
4937582 TATATTATTA
Statistics
Matches: 133, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
182 19 0.14
183 93 0.70
184 8 0.06
185 13 0.10
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (184 bp):
AAAAATTTATTATATTGAAAATTTTCTATAAATACTCCAATACACTAGTAATATTTAAAAAATCT
TCTCACATAAGAATTTATAAAGCATCACTACTCGAAATACTCTTAGAATCCCATCATCGGAAAAA
AATTTTTTTCTTAATTTTTTATTAATTATTTTTTAATTTTTATTATTAAAGAAA
Found at i:4938741 original size:13 final size:12
Alignment explanation
Indices: 4938715--4938780 Score: 53
Period size: 13 Copynumber: 5.3 Consensus size: 12
4938705 GTGTCTTAGC
4938715 TTTTGTTTTTTT
1 TTTTGTTTTTTT
**
4938727 TTTT-TTTTTGG
1 TTTTGTTTTTTT
*
4938738 TTTTGTATTTTCT
1 TTTTGT-TTTTTT
*
4938751 GTTTGTTTTTTT
1 TTTTGTTTTTTT
*
4938763 TCTTTCTTTTTATT
1 T-TTTGTTTTT-TT
4938777 TTTT
1 TTTT
4938781 ATTATTATAT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
11 9 0.21
12 10 0.24
13 20 0.48
14 3 0.07
ACGTcount: A:0.03, C:0.05, G:0.09, T:0.83
Consensus pattern (12 bp):
TTTTGTTTTTTT
Found at i:4938742 original size:37 final size:36
Alignment explanation
Indices: 4938692--4938783 Score: 89
Period size: 36 Copynumber: 2.5 Consensus size: 36
4938682 CGGCCATTTG
*
4938692 TTTTTTTTCTTTTGTGTCTTAGCT-TTTGTTTTTTTT-
1 TTTTTTTTCTTTTGTAT-TT-GCTGTTTGTTTTTTTTC
* *
4938728 TTTTTTTTGGTTTTGTATTTTCTGTTTGTTTTTTTTC
1 TTTTTTTT-CTTTTGTATTTGCTGTTTGTTTTTTTTC
* *
4938765 TTTCTTTTTATTTTTTATT
1 TTT-TTTTTCTTTTGTATT
4938784 ATTATATTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
35 2 0.04
36 22 0.47
37 18 0.38
38 5 0.11
ACGTcount: A:0.04, C:0.07, G:0.10, T:0.79
Consensus pattern (36 bp):
TTTTTTTTCTTTTGTATTTGCTGTTTGTTTTTTTTC
Found at i:4939376 original size:9 final size:9
Alignment explanation
Indices: 4939353--4939432 Score: 54
Period size: 9 Copynumber: 8.7 Consensus size: 9
4939343 CATAAATATA
*
4939353 AAAAAATTC
1 AAAAAATTT
*
4939362 ATAAAATTT
1 AAAAAATTT
*
4939371 AAAAAAATCT
1 -AAAAAATTT
4939381 AAAAAATTATT
1 AAAAAA-T-TT
* *
4939392 TAAAATTTT
1 AAAAAATTT
*
4939401 AAAATATTT
1 AAAAAATTT
* *
4939410 GAAATATTT
1 AAAAAATTT
4939419 -AAAAATTT
1 AAAAAATTT
4939427 AAAAAA
1 AAAAAA
4939433 AATTAAAAAT
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
8 7 0.13
9 34 0.62
10 9 0.16
11 5 0.09
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (9 bp):
AAAAAATTT
Found at i:4939386 original size:19 final size:19
Alignment explanation
Indices: 4939346--4939388 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
4939336 AATGTCACAT
* *
4939346 AAATATAAAAAAATTCATA
1 AAATTTAAAAAAATTCAAA
4939365 AAATTTAAAAAAA-TCTAAA
1 AAATTTAAAAAAATTC-AAA
4939384 AAATT
1 AAATT
4939389 ATTTAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (19 bp):
AAATTTAAAAAAATTCAAA
Found at i:4939401 original size:8 final size:9
Alignment explanation
Indices: 4939383--4939430 Score: 64
Period size: 8 Copynumber: 5.4 Consensus size: 9
4939373 AAAAATCTAA
4939383 AAAATTATTT
1 AAAA-TATTT
4939393 AAAAT-TTT
1 AAAATATTT
4939401 AAAATATTT
1 AAAATATTT
*
4939410 GAAATATTT
1 AAAATATTT
4939419 AAAA-ATTT
1 AAAATATTT
4939427 AAAA
1 AAAA
4939431 AAAATTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 16 0.46
9 15 0.43
10 4 0.11
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (9 bp):
AAAATATTT
Found at i:4939414 original size:17 final size:18
Alignment explanation
Indices: 4939383--4939430 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
4939373 AAAAATCTAA
4939383 AAAATTATTTAAAAT-TTT
1 AAAA-TATTTAAAATATTT
*
4939401 AAAATATTTGAAATATTT
1 AAAATATTTAAAATATTT
4939419 AAAA-ATTTAAAA
1 AAAATATTTAAAA
4939431 AAAATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
AAAATATTTAAAATATTT
Found at i:4939449 original size:27 final size:28
Alignment explanation
Indices: 4939419--4939478 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
4939409 TGAAATATTT
*
4939419 AAAAATTTAA-AAAAAAT-TAAAAATCTC
1 AAAAATTTAATAAAAAATAAAAAAAT-TC
*
4939446 AAAATTTTAATAAAAAATAAAAAAATTC
1 AAAAATTTAATAAAAAATAAAAAAATTC
4939474 AAAAA
1 AAAAA
4939479 AATTGTGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 9 0.32
28 13 0.46
29 6 0.21
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (28 bp):
AAAAATTTAATAAAAAATAAAAAAATTC
Found at i:4939461 original size:28 final size:27
Alignment explanation
Indices: 4939350--4939478 Score: 91
Period size: 29 Copynumber: 4.6 Consensus size: 27
4939340 TCACATAAAT
4939350 ATAAAAAAATTCATAAAATTTAAAAAAA
1 ATAAAAAAATTCA-AAAATTTAAAAAAA
* * * *
4939378 TCTAAAAAATTATT-TAAAATTTTAAAATA
1 -ATAAAAAA--ATTCAAAAATTTAAAAAAA
* ** * *
4939407 TTTGAAATATTTAAAAATTTAAAAAAA
1 ATAAAAAAATTCAAAAATTTAAAAAAA
* *
4939434 AT-TAAAAATCTCAAAATTTTAATAAAAA
1 ATAAAAAAAT-TCAAAAATTTAA-AAAAA
4939462 ATAAAAAAATTCAAAAA
1 ATAAAAAAATTCAAAAA
4939479 AATTGTGAAA
Statistics
Matches: 76, Mismatches: 18, Indels: 13
0.71 0.17 0.12
Matches are distributed among these distances:
26 8 0.11
27 23 0.30
28 17 0.22
29 25 0.33
31 3 0.04
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.32
Consensus pattern (27 bp):
ATAAAAAAATTCAAAAATTTAAAAAAA
Found at i:4940490 original size:6 final size:6
Alignment explanation
Indices: 4940479--4940505 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
4940469 CTAATTGTGG
4940479 TTCATT TTCATT TTCATT TTCATT TTC
1 TTCATT TTCATT TTCATT TTCATT TTC
4940506 TAAAAAGCAT
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:0.15, C:0.19, G:0.00, T:0.67
Consensus pattern (6 bp):
TTCATT
Found at i:4940650 original size:20 final size:21
Alignment explanation
Indices: 4940627--4940685 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
4940617 ATTTTCTTTT
4940627 TAAATCT-AAAATTTTTTTAA
1 TAAATCTAAAAATTTTTTTAA
* *
4940647 TAAATTGTAAAAATATTTTTAA
1 TAAA-TCTAAAAATTTTTTTAA
*
4940669 AAAATCTTAAAAATTTT
1 TAAATC-TAAAAATTTT
4940686 CACTTTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 4 0.13
21 3 0.10
22 24 0.77
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (21 bp):
TAAATCTAAAAATTTTTTTAA
Found at i:4940659 original size:22 final size:22
Alignment explanation
Indices: 4940634--4940685 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
4940624 TTTTAAATCT
*
4940634 AAAATTTTTTTAATAAAT-TGTA
1 AAAATTTTTTTAAAAAATCT-TA
*
4940656 AAAATATTTTTAAAAAATCTTA
1 AAAATTTTTTTAAAAAATCTTA
4940678 AAAATTTT
1 AAAATTTT
4940686 CACTTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (22 bp):
AAAATTTTTTTAAAAAATCTTA
Found at i:4940790 original size:15 final size:16
Alignment explanation
Indices: 4940751--4940790 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
4940741 TAGGCTTTTA
4940751 TTAAAATTTTAAGTTT
1 TTAAAATTTTAAGTTT
*
4940767 TT-AATTTTTAA-TTT
1 TTAAAATTTTAAGTTT
4940781 TTAAAATTTT
1 TTAAAATTTT
4940791 TTTAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 5 0.24
15 14 0.67
16 2 0.10
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TTAAAATTTTAAGTTT
Found at i:4940804 original size:10 final size:11
Alignment explanation
Indices: 4940778--4940803 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4940768 TAATTTTTAA
4940778 TTTTTAAAATT
1 TTTTTAAAATT
4940789 TTTTTAAAATT
1 TTTTTAAAATT
4940800 TTTT
1 TTTT
4940804 ATTTTTAATT
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTAAAATT
Found at i:4940872 original size:19 final size:20
Alignment explanation
Indices: 4940848--4940910 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
4940838 AAAATTAAAA
4940848 TTTT-AAAAAATTTTAGACT
1 TTTTAAAAAAATTTTAGACT
4940867 TTTTAAAAAAATTTTAGACT
1 TTTTAAAAAAATTTTAGACT
* *
4940887 TTTTCAAAAAATTTTAGAAT
1 TTTTAAAAAAATTTTAGACT
4940907 TTTT
1 TTTT
4940911 TAATTTTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 4 0.10
20 37 0.90
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (20 bp):
TTTTAAAAAAATTTTAGACT
Found at i:4940946 original size:19 final size:19
Alignment explanation
Indices: 4940842--4940947 Score: 76
Period size: 20 Copynumber: 5.6 Consensus size: 19
4940832 TTTTTTAAAA
4940842 TTAAAATTTT-AAAAAATT
1 TTAAAATTTTCAAAAAATT
** *
4940860 TTAGACTTTTTAAAAAAATT
1 TTA-AAATTTTCAAAAAATT
**
4940880 TTAGACTTTTTCAAAAAATT
1 TTA-AAATTTTCAAAAAATT
* **
4940900 TTAGAATTTT---TTAATT
1 TTAAAATTTTCAAAAAATT
4940916 TTAAAGAATTTTCAAAAAATT
1 TT-AA-AATTTTCAAAAAATT
4940937 TTAAAATTTTC
1 TTAAAATTTTC
4940948 TATATTTTTA
Statistics
Matches: 70, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
16 6 0.09
17 1 0.01
18 9 0.13
19 16 0.23
20 32 0.46
21 6 0.09
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (19 bp):
TTAAAATTTTCAAAAAATT
Found at i:4946835 original size:14 final size:15
Alignment explanation
Indices: 4946816--4946844 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4946806 AGAATGTATC
4946816 AAATTTAATA-TTAA
1 AAATTTAATACTTAA
4946830 AAATTTAATACTTAA
1 AAATTTAATACTTAA
4946845 TTTTTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTTAATACTTAA
Found at i:4950348 original size:10 final size:11
Alignment explanation
Indices: 4950315--4950363 Score: 52
Period size: 10 Copynumber: 4.8 Consensus size: 11
4950305 CAATAAATTT
4950315 TATATA-ATAA
1 TATATATATAA
* *
4950325 T-TATGTATAC
1 TATATATATAA
4950335 TATA-ATATAA
1 TATATATATAA
4950345 TATATATAT-A
1 TATATATATAA
4950355 TATATATAT
1 TATATATAT
4950364 GTGGCTGTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
9 3 0.09
10 23 0.72
11 6 0.19
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (11 bp):
TATATATATAA
Found at i:4950356 original size:23 final size:22
Alignment explanation
Indices: 4950316--4950362 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
4950306 AATAAATTTT
*
4950316 ATATAATAATTATGTATACTATA
1 ATATAATAATTATATATA-TATA
4950339 ATATAATATATATATATATATATA
1 ATATAATA-AT-TATATATATATA
4950363 TGTGGCTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 6 0.29
25 7 0.33
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
ATATAATAATTATATATATATA
Found at i:4950441 original size:2 final size:2
Alignment explanation
Indices: 4950434--4950466 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4950424 TGTTGTGTAA
4950434 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4950467 TTATATTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4954197 original size:17 final size:18
Alignment explanation
Indices: 4954155--4954197 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
4954145 ATGATATAAT
4954155 TTTATTAATAAAAATTAA
1 TTTATTAATAAAAATTAA
*
4954173 TATT-TTAA-AAAAATTTA
1 T-TTATTAATAAAAATTAA
4954190 TTTATTAA
1 TTTATTAA
4954198 CTAGATAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 2 0.09
17 13 0.59
18 5 0.23
19 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTATTAATAAAAATTAA
Found at i:4954291 original size:24 final size:24
Alignment explanation
Indices: 4954244--4954291 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
4954234 TTGTATTATC
* * *
4954244 TTATTTACTGATAATATATAAAAT
1 TTATATACTAATAATACATAAAAT
*
4954268 TTATATACTAATAATACATTAAAT
1 TTATATACTAATAATACATAAAAT
4954292 ATAAATTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (24 bp):
TTATATACTAATAATACATAAAAT
Found at i:4955294 original size:20 final size:21
Alignment explanation
Indices: 4955248--4955303 Score: 87
Period size: 20 Copynumber: 2.6 Consensus size: 21
4955238 TTTGATTTAA
4955248 TTTAAAATTAATAAAATATTATT
1 TTTAAAA-T-ATAAAATATTATT
4955271 TTTAAAATATAAAATATT-TT
1 TTTAAAATATAAAATATTATT
4955291 TTTAAAATATAAA
1 TTTAAAATATAAA
4955304 TATAAAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
20 15 0.45
21 10 0.30
22 1 0.03
23 7 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTAAAATATAAAATATTATT
Found at i:4959724 original size:11 final size:11
Alignment explanation
Indices: 4959701--4959748 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
4959691 GTAATTATCG
*
4959701 ATAACTTAATA
1 ATAAATTAATA
*
4959712 ATAAATTAGTA
1 ATAAATTAATA
*
4959723 ATAACTTAATA
1 ATAAATTAATA
* *
4959734 GTAAATTAATT
1 ATAAATTAATA
4959745 ATAA
1 ATAA
4959749 TTTGATAGTT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (11 bp):
ATAAATTAATA
Found at i:4959726 original size:22 final size:22
Alignment explanation
Indices: 4959701--4959826 Score: 78
Period size: 22 Copynumber: 5.7 Consensus size: 22
4959691 GTAATTATCG
4959701 ATAACTTAATAATAAATTAGTA
1 ATAACTTAATAATAAATTAGTA
* * *
4959723 ATAACTTAATAGTAAATTAATT
1 ATAACTTAATAATAAATTAGTA
* * * *
4959745 ATAATTTGATAGTTAA-TAGTTA
1 ATAACTTAATAATAAATTAG-TA
** * *
4959767 ATAACTTTTTTATAAATCAGTA
1 ATAACTTAATAATAAATTAGTA
* *
4959789 CTAA-TATAATAATAAATGCA-TA
1 ATAACT-TAATAATAAAT-TAGTA
*
4959811 ATACCTTAATAATAAA
1 ATAACTTAATAATAAA
4959827 ATAATTATAA
Statistics
Matches: 78, Mismatches: 21, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
21 3 0.04
22 70 0.90
23 5 0.06
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (22 bp):
ATAACTTAATAATAAATTAGTA
Found at i:4960055 original size:22 final size:22
Alignment explanation
Indices: 4960021--4960257 Score: 98
Period size: 22 Copynumber: 11.0 Consensus size: 22
4960011 TAATTCGTTA
* * *
4960021 ATAACTTAATAGTAAATCAATT
1 ATAATTTAGTAGTAAATCAATC
*
4960043 ATAATTTAGTAGTTAATC-ATC
1 ATAATTTAGTAGTAAATCAATC
* * **
4960064 AAAATTAAAAAGTAAATCAA-C
1 ATAATTTAGTAGTAAATCAATC
* *
4960085 ATAATTTAGTAGTAAATCATTG
1 ATAATTTAGTAGTAAATCAATC
* * **
4960107 ATAACTT-GATAGTTAAT-AAGAG
1 ATAATTTAG-TAGTAAATCAA-TC
*
4960129 ATAATTTAATAGTAAA-C-ATGC
1 ATAATTTAGTAGTAAATCAAT-C
* * * *
4960150 ATAATTTAAT-TTAAATCAGTA
1 ATAATTTAGTAGTAAATCAATC
* * * *
4960171 ATAATTTGGTAATGAATC-ATAA
1 ATAATTTAGTAGTAAATCAAT-C
*
4960193 ATAATTTAGTAAGT-AATCAATG
1 ATAATTTAGT-AGTAAATCAATC
* *
4960215 ATAATTTTGTAGTAAAT-AATTG
1 ATAATTTAGTAGTAAATCAA-TC
* *
4960237 AAAATTAAGTAGTAAATCAAT
1 ATAATTTAGTAGTAAATCAAT
4960258 AATGTTAGCC
Statistics
Matches: 160, Mismatches: 39, Indels: 32
0.69 0.17 0.14
Matches are distributed among these distances:
20 4 0.03
21 59 0.37
22 91 0.57
23 6 0.04
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.36
Consensus pattern (22 bp):
ATAATTTAGTAGTAAATCAATC
Found at i:4961894 original size:22 final size:22
Alignment explanation
Indices: 4961869--4961992 Score: 67
Period size: 22 Copynumber: 5.8 Consensus size: 22
4961859 AACAAATGAT
4961869 AATATAGTAGTAAAT-ATATAAA
1 AATATAGTAGTAAATCAT-TAAA
* * *
4961891 AATATAATAGTAAATCATTGAT
1 AATATAGTAGTAAATCATTAAA
* *
4961913 AATTTAGTAGT-AA--ATTAAT
1 AATATAGTAGTAAATCATTAAA
** * *
4961932 AACGTAGTAGTAAATCACTAAT
1 AATATAGTAGTAAATCATTAAA
* * * *
4961954 GATATAATAGTAAATTATTAAT
1 AATATAGTAGTAAATCATTAAA
* * *
4961976 AATTTAATTGTAAATCA
1 AATATAGTAGTAAATCA
4961993 ATGATAATTT
Statistics
Matches: 79, Mismatches: 19, Indels: 8
0.75 0.18 0.08
Matches are distributed among these distances:
19 14 0.18
20 2 0.03
21 2 0.03
22 59 0.75
23 2 0.03
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.36
Consensus pattern (22 bp):
AATATAGTAGTAAATCATTAAA
Found at i:4961943 original size:41 final size:41
Alignment explanation
Indices: 4961895--4962014 Score: 123
Period size: 44 Copynumber: 2.9 Consensus size: 41
4961885 TATAAAAATA
* *
4961895 TAATAGTAAATCATTGATAATTTAGTAGTAAATTAATAACG
1 TAATAGTAAATCAATGATAATTTAATAGTAAATTAATAACG
* * * * * **
4961936 TAGTAGTAAATCACTAATGATATAATAGTAAATTATTAATAATT
1 TAATAGTAAATCAATGATAATTTAATAGT-AA--ATTAATAACG
*
4961980 TAATTGTAAATCAATGATAATTTAATAGTAAATTA
1 TAATAGTAAATCAATGATAATTTAATAGTAAATTA
4962015 CTTAAATTAT
Statistics
Matches: 62, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
41 27 0.44
42 2 0.03
43 2 0.03
44 31 0.50
ACGTcount: A:0.47, C:0.04, G:0.10, T:0.38
Consensus pattern (41 bp):
TAATAGTAAATCAATGATAATTTAATAGTAAATTAATAACG
Found at i:4961974 original size:44 final size:44
Alignment explanation
Indices: 4961867--4962019 Score: 116
Period size: 44 Copynumber: 3.5 Consensus size: 44
4961857 CTAACAAATG
* * ** * *
4961867 ATAATATAGTAGTAAA-TATATAAAAATATAATAGTAAATCATTG
1 ATAATATAATAGTAAATTAT-TAATAACGTAATAGTAAATCAATA
* * * *
4961911 ATAATTTAGTAGT-AA--ATTAATAACGTAGTAGTAAATCACTA
1 ATAATATAATAGTAAATTATTAATAACGTAATAGTAAATCAATA
* ** * *
4961952 ATGATATAATAGTAAATTATTAATAATTTAATTGTAAATCAATG
1 ATAATATAATAGTAAATTATTAATAACGTAATAGTAAATCAATA
*
4961996 ATAATTTAATAGTAAATTACTTAA
1 ATAATATAATAGTAAATTA-TTAA
4962020 ATTATTGATA
Statistics
Matches: 87, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
41 28 0.32
42 4 0.05
43 2 0.02
44 49 0.56
45 4 0.05
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (44 bp):
ATAATATAATAGTAAATTATTAATAACGTAATAGTAAATCAATA
Found at i:4962182 original size:22 final size:22
Alignment explanation
Indices: 4962170--4962250 Score: 101
Period size: 22 Copynumber: 3.7 Consensus size: 22
4962160 AATTAATAAC
*
4962170 AAATCTTTGATAATTTAATAGT
1 AAATCATTGATAATTTAATAGT
*
4962192 AAATCATTGATAACTT-ATAGT
1 AAATCATTGATAATTTAATAGT
*
4962213 AAATCATTGATAATTTAATTGT
1 AAATCATTGATAATTTAATAGT
* * *
4962235 CAATTATTGATGATTT
1 AAATCATTGATAATTT
4962251 TTTTTATACT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
21 20 0.39
22 31 0.61
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (22 bp):
AAATCATTGATAATTTAATAGT
Found at i:4962587 original size:22 final size:22
Alignment explanation
Indices: 4962518--4962729 Score: 93
Period size: 22 Copynumber: 9.7 Consensus size: 22
4962508 GAAACAAGTG
* * *
4962518 ATAATTTAATAGTTAA-TCATTT
1 ATAATTTAATAGTAAATTGA-TA
* *
4962540 ATAATTTAATAATAAATTGATG
1 ATAATTTAATAGTAAATTGATA
4962562 ATAATTTAATAGTAAATTAGA-A
1 ATAATTTAATAGTAAATT-GATA
* *
4962584 ATAACTTAATCGTAAATATG-T-
1 ATAATTTAATAGTAAAT-TGATA
* * *
4962605 TTCAGTTTAATAGT-AATTAATTA
1 AT-AATTTAATAGTAAATTGA-TA
* *
4962628 ATAAATTTAGTAATAAATT-ATGA
1 AT-AATTTAATAGTAAATTGAT-A
* *
4962651 ATAACTTAATAGT-AATTAATA
1 ATAATTTAATAGTAAATTGATA
* *
4962672 ATAATTTATTAGTTAATT-ATTGA
1 ATAATTTAATAGTAAATTGA-T-A
* *
4962695 A-AATTTAAAAGTAAATTAAT-
1 ATAATTTAATAGTAAATTGATA
* *
4962715 ATAACTTAGTAGTAA
1 ATAATTTAATAGTAA
4962730 TAAATTATTG
Statistics
Matches: 145, Mismatches: 29, Indels: 33
0.70 0.14 0.16
Matches are distributed among these distances:
20 2 0.01
21 31 0.21
22 87 0.60
23 21 0.14
24 4 0.03
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.42
Consensus pattern (22 bp):
ATAATTTAATAGTAAATTGATA
Found at i:4962744 original size:21 final size:21
Alignment explanation
Indices: 4962720--4962762 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
4962710 TTAATATAAC
*
4962720 TTAGTAGTAATAAATTATTGA
1 TTAGTAATAATAAATTATTGA
*
4962741 TTAGTAATAGTAAATTATTGA
1 TTAGTAATAATAAATTATTGA
4962762 T
1 T
4962763 AATTTAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (21 bp):
TTAGTAATAATAAATTATTGA
Found at i:4962907 original size:22 final size:22
Alignment explanation
Indices: 4962881--4962939 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
4962871 AAATTAAGTC
*
4962881 GTAAATAAATGATAACATAGTA
1 GTAAATAAATGATAACATAATA
* *
4962903 GTAAATGAATAATAACATAATA
1 GTAAATAAATGATAACATAATA
* * *
4962925 CTAAATCATTGATAA
1 GTAAATAAATGATAA
4962940 TTTAGATGTA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.29
Consensus pattern (22 bp):
GTAAATAAATGATAACATAATA
Found at i:4963299 original size:22 final size:22
Alignment explanation
Indices: 4963159--4963303 Score: 78
Period size: 22 Copynumber: 6.6 Consensus size: 22
4963149 AACTTAATTA
** *
4963159 TAAATAATCAATAATTTATTAG
1 TAAATAATTGATAATTTAGTAG
* * * *
4963181 TAAATCATTCATAACTTAGTAT
1 TAAATAATTGATAATTTAGTAG
* * * *
4963203 TAAATTATTCATAAATTAGTAA
1 TAAATAATTGATAATTTAGTAG
** * *
4963225 TACTTCAA-TGCTAATTTAGTAA
1 TAAAT-AATTGATAATTTAGTAG
* *
4963247 TAAATTACTGATAATTT-GTAG
1 TAAATAATTGATAATTTAGTAG
** *
4963268 TTTATAATTGATAGTTTAGTAG
1 TAAATAATTGATAATTTAGTAG
*
4963290 TAAATCATTGATAA
1 TAAATAATTGATAA
4963304 AATAATACTA
Statistics
Matches: 91, Mismatches: 29, Indels: 6
0.72 0.23 0.05
Matches are distributed among these distances:
21 16 0.18
22 74 0.81
23 1 0.01
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (22 bp):
TAAATAATTGATAATTTAGTAG
Found at i:4963782 original size:17 final size:17
Alignment explanation
Indices: 4963760--4963792 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4963750 CAAATGTTAC
*
4963760 CAAAATTTTATCAAAAT
1 CAAAATTATATCAAAAT
4963777 CAAAATTATATCAAAA
1 CAAAATTATATCAAAA
4963793 GTTATCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (17 bp):
CAAAATTATATCAAAAT
Found at i:4963801 original size:21 final size:21
Alignment explanation
Indices: 4963656--4963801 Score: 104
Period size: 21 Copynumber: 7.2 Consensus size: 21
4963646 AAGAGATTAC
* * *
4963656 CAAAATTTTATAAAAAATTAT
1 CAAAATTATATCAAAAGTTAT
** *
4963677 CAAAATT-TATCAATGGTTAC
1 CAAAATTATATCAAAAGTTAT
*
4963697 CAAAATTATATCAAAAGTTAC
1 CAAAATTATATCAAAAGTTAT
* * * *
4963718 CAAACTAATATTAAAGGTTAT
1 CAAAATTATATCAAAAGTTAT
* * * * *
4963739 TAAAAGTGTATCAAATGTTAC
1 CAAAATTATATCAAAAGTTAT
*
4963760 CAAAATTTTATC-AAA---AT
1 CAAAATTATATCAAAAGTTAT
4963777 CAAAATTATATCAAAAGTTAT
1 CAAAATTATATCAAAAGTTAT
4963798 CAAA
1 CAAA
4963802 TTTTATTTAT
Statistics
Matches: 94, Mismatches: 26, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
17 12 0.13
18 3 0.03
20 17 0.18
21 62 0.66
ACGTcount: A:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (21 bp):
CAAAATTATATCAAAAGTTAT
Found at i:4963938 original size:82 final size:80
Alignment explanation
Indices: 4963778--4963939 Score: 220
Period size: 80 Copynumber: 2.0 Consensus size: 80
4963768 TATCAAAATC
* * * *
4963778 AAAATTATATCAAAAGTTATCAAATTTTATTTATAGTATAATAATACAAATTAAATTGTTAATAT
1 AAAAATATATCAAAAGTTATCAAATTTTACTTATAGTATAAAAATACAAATTAAATGGTTAATAT
4963843 TTTTCATTATTATCA
66 TTTTCATTATTATCA
* *
4963858 AAAAATATATCGAAAGTTATCAAATTTTACTTATATTATATCAAAAT-CAAAATTAAATGGTTAA
1 AAAAATATATCAAAAGTTATCAAATTTTACTTATAGTATA--AAAATAC-AAATTAAATGGTTAA
4963922 TATTTATT-ATTATTATCA
63 TATTT-TTCATTATTATCA
4963940 TAATATCAAA
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
80 36 0.50
81 1 0.01
82 33 0.46
83 2 0.03
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (80 bp):
AAAAATATATCAAAAGTTATCAAATTTTACTTATAGTATAAAAATACAAATTAAATGGTTAATAT
TTTTCATTATTATCA
Found at i:4968067 original size:22 final size:22
Alignment explanation
Indices: 4968037--4968080 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
4968027 AATTTCCATA
4968037 AAATAAAATAAAATAATATTAT
1 AAATAAAATAAAATAATATTAT
* *
4968059 AAATTAAATTAAATAATATTAT
1 AAATAAAATAAAATAATATTAT
4968081 TTTATTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATAAAATAAAATAATATTAT
Found at i:4970798 original size:21 final size:21
Alignment explanation
Indices: 4970765--4970804 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4970755 AATCAATGAA
*
4970765 TTAACATATAATTGAATAATT
1 TTAACATAAAATTGAATAATT
*
4970786 TTAATATAAAATTGAATAA
1 TTAACATAAAATTGAATAA
4970805 AATCCAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (21 bp):
TTAACATAAAATTGAATAATT
Found at i:4973059 original size:17 final size:18
Alignment explanation
Indices: 4973037--4973076 Score: 64
Period size: 17 Copynumber: 2.3 Consensus size: 18
4973027 TTTCATCAAT
*
4973037 TAAAAATAATT-AATATA
1 TAAAAATAATTAAATAAA
4973054 TAAAAATAATTAAATAAA
1 TAAAAATAATTAAATAAA
4973072 TAAAA
1 TAAAA
4973077 TAAAAACTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
TAAAAATAATTAAATAAA
Found at i:4973769 original size:5 final size:5
Alignment explanation
Indices: 4973761--4973785 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4973751 TATTAATAAA
4973761 TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT
4973786 CAAATTACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:4973966 original size:23 final size:23
Alignment explanation
Indices: 4973925--4973968 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
4973915 TATAAAATTT
* *
4973925 TTATTTTTTTTCATATTTTAAAA
1 TTATTTTTTATAATATTTTAAAA
*
4973948 TTATTTTTTATAATTTTTTAA
1 TTATTTTTTATAATATTTTAA
4973969 CTATTTGACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (23 bp):
TTATTTTTTATAATATTTTAAAA
Found at i:4975894 original size:21 final size:21
Alignment explanation
Indices: 4975869--4975924 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 21
4975859 TCTCAATTGC
4975869 TTATTTGATTTTTTT-TAATTA
1 TTATTTGATTTTTTTCT-ATTA
*
4975890 TTATTTGAATTGTTTTTCTTTTA
1 TTATTTG-ATT-TTTTTCTATTA
*
4975913 TTATCTGATTTT
1 TTATTTGATTTT
4975925 ACTCAAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 9 0.30
22 6 0.20
23 14 0.47
24 1 0.03
ACGTcount: A:0.20, C:0.04, G:0.07, T:0.70
Consensus pattern (21 bp):
TTATTTGATTTTTTTCTATTA
Found at i:4976437 original size:2 final size:2
Alignment explanation
Indices: 4976430--4976461 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
4976420 GGATACACTT
4976430 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4976462 AAACTAGTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4979908 original size:66 final size:66
Alignment explanation
Indices: 4979779--4979909 Score: 199
Period size: 66 Copynumber: 2.0 Consensus size: 66
4979769 TCAGGTTTTG
* * * * * *
4979779 AACTTATCTCTATTTTTCAAGCCAGTTTAGGAATATAATTGTGTTTGTGTGTGTGTGTGTATATA
1 AACTTATCTCTATTTCTCAAGCCAGTTTAGGAATATAATTGTGTGTGTGGGTGTATATATATATA
4979844 A
66 A
*
4979845 AACTTGTCTCTATTTCTCAAGCCAGTTTAGGAATATAATTGTGTGTGTGGGTGTATATATATATA
1 AACTTATCTCTATTTCTCAAGCCAGTTTAGGAATATAATTGTGTGTGTGGGTGTATATATATATA
4979910 TATATTTTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.44
Consensus pattern (66 bp):
AACTTATCTCTATTTCTCAAGCCAGTTTAGGAATATAATTGTGTGTGTGGGTGTATATATATATA
A
Found at i:4982770 original size:23 final size:23
Alignment explanation
Indices: 4982740--4982783 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
4982730 TATTTATGTT
*
4982740 AAAAATAAGAACTTTTTATAACA
1 AAAAATAAGAACTTTTAATAACA
*
4982763 AAAAATAAGAGCTTTTAATAA
1 AAAAATAAGAACTTTTAATAA
4982784 AGTAATCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (23 bp):
AAAAATAAGAACTTTTAATAACA
Done.