Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 82 of 141
Found at i:23534441 original size:18 final size:19
Alignment explanation
Indices: 23534414--23534562 Score: 112
Period size: 20 Copynumber: 7.6 Consensus size: 19
23534404 AGAAGAGAAA
23534414 AAAGGA-AAGAAAGAAAGG
1 AAAGGAGAAGAAAGAAAGG
*
23534432 AGAGGGAAGAAAGAAAGAAAGG
1 A-AAGG-AG-AAGAAAGAAAGG
*
23534454 AGAGGA-AAGAAAGAAAAGG
1 AAAGGAGAAGAAAG-AAAGG
*
23534473 AAAGGAGAAGAGAAAAAAGG
1 AAAGGAGAAGA-AAGAAAGG
*
23534493 AAAGAAAGAAG-AAGAAAAGG
1 AAAG-GAGAAGAAAG-AAAGG
23534513 AGAA-GAGAAGAAA-AAA-G
1 A-AAGGAGAAGAAAGAAAGG
*
23534530 AAAGAAAGAAGGAAAGAAAGGG
1 AAAG-GAGAA-GAAAGAAA-GG
23534552 AAAGGAGAAGA
1 AAAGGAGAAGA
23534563 GAAAAAAAAA
Statistics
Matches: 104, Mismatches: 10, Indels: 32
0.71 0.07 0.22
Matches are distributed among these distances:
16 2 0.02
17 2 0.02
18 15 0.14
19 24 0.23
20 28 0.27
21 15 0.14
22 18 0.17
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (19 bp):
AAAGGAGAAGAAAGAAAGG
Found at i:23534443 original size:22 final size:22
Alignment explanation
Indices: 23534418--23534500 Score: 103
Period size: 22 Copynumber: 3.6 Consensus size: 22
23534408 GAGAAAAAAG
23534418 GAAAGAAAGAAAGGAGAGGGAA
1 GAAAGAAAGAAAGGAGAGGGAA
*
23534440 GAAAGAAAGAAAGGAGAGGAAA
1 GAAAGAAAGAAAGGAGAGGGAA
*
23534462 GAAAGAAAAGGAAAGGAGAAGAGAA
1 GAAAG-AAA-GAAAGGAG-AGGGAA
*
23534487 AAAAGGAAAGAAAG
1 GAAA-GAAAGAAAG
23534501 AAGAAGAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
22 26 0.49
23 3 0.06
24 13 0.25
25 10 0.19
26 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (22 bp):
GAAAGAAAGAAAGGAGAGGGAA
Found at i:23534461 original size:14 final size:14
Alignment explanation
Indices: 23534413--23534549 Score: 85
Period size: 12 Copynumber: 10.0 Consensus size: 14
23534403 CAGAAGAGAA
23534413 AAAAGGAAAGAAAG
1 AAAAGGAAAGAAAG
* *
23534427 -AAAGGAGAGGGAAG
1 AAAAGGA-AAGAAAG
23534441 -AAA-GAAAGAAAG
1 AAAAGGAAAGAAAG
* *
23534453 GAGAGGAAAGAAAG
1 AAAAGGAAAGAAAG
*
23534467 AAAAGGAAAG-GAG
1 AAAAGGAAAGAAAG
*
23534480 AAGA-GAAA-AAAG
1 AAAAGGAAAGAAAG
*
23534492 GAAA-GAAAGAAGAAG
1 AAAAGGAAAG-A-AAG
23534507 AAAAGGAGAAGAGAAG
1 AAAAGGA-AAGA-AAG
*
23534523 AAAAAAGAAAGAAAG
1 -AAAAGGAAAGAAAG
23534538 --AAGGAAAGAAAG
1 AAAAGGAAAGAAAG
23534550 GGAAAGGAGA
Statistics
Matches: 98, Mismatches: 15, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
12 28 0.29
13 15 0.15
14 26 0.27
15 9 0.09
16 11 0.11
17 9 0.09
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (14 bp):
AAAAGGAAAGAAAG
Found at i:23534525 original size:74 final size:78
Alignment explanation
Indices: 23534438--23534584 Score: 185
Period size: 79 Copynumber: 1.9 Consensus size: 78
23534428 AAGGAGAGGG
*
23534438 AAGAAAG-AAAGAAAGGAGAGGAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAGGAAAGAAAGA
1 AAGAAAGAAAAGAAA-GA-AAGAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAGGAAAGAAAGA
23534502 AGAAGAAAAGG-AGA
64 AGAAGAAAAGGAAGA
* * * *
23534516 AGAGAAGAAAAAAGAAAGAAAGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAA-AAAAG-AAGA
1 A-AGAA-AGAAAAGAAAGAAAGAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAGGAAAGAAAGA
23534579 AGAAGA
64 AGAAGA
23534585 GGGAAGAAAG
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
77 10 0.16
78 5 0.08
79 36 0.59
80 3 0.05
81 7 0.11
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (78 bp):
AAGAAAGAAAAGAAAGAAAGAAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAGGAAAGAAAGAAG
AAGAAAAGGAAGA
Found at i:23534540 original size:58 final size:58
Alignment explanation
Indices: 23534462--23534598 Score: 62
Period size: 61 Copynumber: 2.2 Consensus size: 58
23534452 GGAGAGGAAA
* * * * *
23534462 GAAAGAAAAGGAAAGGAGAAGAGAAAAAAGGAAAGAAAGAAGAAGAAAAGGAGAAGAGAAGAA
1 GAAAG-AAAGGAAAGAAG-A-AGAAAAAA--AAAGAGAGAAGAAGAAAAGAAAAAGAGAAGAG
* *** * *
23534525 AAAAGAAA-GAAAGAAGGAAAGAAAGGGAAAG-GAGAAGAGAAAAAAAAAAGAAGAAGAAGAG
1 GAAAGAAAGGAAAGAA-G-AAGAAAAAAAAAGAGAGAAGA-AGAAAAGAAA-AAG-AGAAGAG
*
23534586 GGAAGAAAGGAAA
1 GAAAGAAAGGAAA
23534599 AAAAAGGTTA
Statistics
Matches: 56, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
58 6 0.11
59 10 0.18
60 3 0.05
61 23 0.41
62 10 0.18
63 4 0.07
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (58 bp):
GAAAGAAAGGAAAGAAGAAGAAAAAAAAAGAGAGAAGAAGAAAAGAAAAAGAGAAGAG
Found at i:23534543 original size:49 final size:45
Alignment explanation
Indices: 23534478--23534595 Score: 123
Period size: 45 Copynumber: 2.5 Consensus size: 45
23534468 AAAGGAAAGG
*
23534478 AGAAGAGAAAAAAGGAAAGAAAGAAGAAGAAAAGGAGAAGAGAAGAAAAA
1 AGAAGAGAAAAAAGGAAAGAAAG--G--G-AAAGGAGAAGAGAAAAAAAA
*
23534528 AGAA-AGAAAGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAAAAA
1 AGAAGAGAAAAAAGGAAAGAAAGGGAAAGGAGAAGAG-AAAAAAAA
* * *
23534573 AGAAGA-AGAAGAGGGAAGAAAGG
1 AGAAGAGAAAAAAGGAAAGAAAGG
23534596 AAAAAAAAGG
Statistics
Matches: 60, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
44 12 0.20
45 25 0.42
46 1 0.02
47 1 0.02
49 17 0.28
50 4 0.07
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (45 bp):
AGAAGAGAAAAAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAAAA
Found at i:23534579 original size:44 final size:42
Alignment explanation
Indices: 23534406--23534583 Score: 158
Period size: 40 Copynumber: 4.3 Consensus size: 42
23534396 GGTGGGGCAG
* * * *
23534406 AAGAGAAAAAAGGAAAGAAAG-AAAGGAG-AGGGAAGAAAGA
1 AAGAGAAAGAAGGAAAGAAAGAAAAGGAGAAGAGAAAAAAAA
* *
23534446 AAGA-AAGGAGAGGAAAGAAAGAAAAGGA-AAGGAGAAGAGAAAA
1 AAGAGAAAGA-AGGAAAGAAAGAAAAGGAGAA-GAGAA-AAAAAA
*
23534489 AAG-GAAAGAAAG-AAG-AAGAAAAGGAGAAGAGAAGAAAAAA
1 AAGAGAAAGAAGGAAAGAAAGAAAAGGAGAAGAGAA-AAAAAA
*
23534529 GAA-AGAAAGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAAAA
1 -AAGAGAAAGAAGGAAAGAAA-GAAAAGGAGAAGAGAAAAAAAA
23534572 AAGA-AGAAGAAG
1 AAGAGA-AAGAAG
23534584 AGGGAAGAAA
Statistics
Matches: 113, Mismatches: 11, Indels: 25
0.76 0.07 0.17
Matches are distributed among these distances:
39 3 0.03
40 36 0.32
41 22 0.19
42 12 0.11
43 25 0.22
44 15 0.13
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (42 bp):
AAGAGAAAGAAGGAAAGAAAGAAAAGGAGAAGAGAAAAAAAA
Found at i:23539206 original size:18 final size:18
Alignment explanation
Indices: 23539183--23539227 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
23539173 ATCCCAATGA
23539183 TCGCCACCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
23539201 TCGCCAGCACCTTCTTCT
1 TCGCCACCACCTTCTTCT
*
23539219 TCACCACCA
1 TCGCCACCA
23539228 ACCATGTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.16, C:0.49, G:0.07, T:0.29
Consensus pattern (18 bp):
TCGCCACCACCTTCTTCT
Found at i:23539796 original size:12 final size:12
Alignment explanation
Indices: 23539770--23539832 Score: 63
Period size: 12 Copynumber: 5.1 Consensus size: 12
23539760 TTACTTAAAA
* *
23539770 AAAATTATACTC
1 AAAATAATACAC
*
23539782 AAAATATTACAC
1 AAAATAATACAC
23539794 AAAATAATACAC
1 AAAATAATACAC
* *
23539806 ACTAAATTATACTC
1 A--AAATAATACAC
23539820 AAAATAATACAC
1 AAAATAATACAC
23539832 A
1 A
23539833 CTAAAATTAT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
12 31 0.76
14 10 0.24
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.25
Consensus pattern (12 bp):
AAAATAATACAC
Found at i:23539807 original size:14 final size:14
Alignment explanation
Indices: 23539790--23539839 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
23539780 TCAAAATATT
23539790 ACACAAAATAATAC
1 ACACAAAATAATAC
* *
23539804 ACACTAAAT--TAT
1 ACACAAAATAATAC
*
23539816 ACTCAAAATAATAC
1 ACACAAAATAATAC
23539830 ACACTAAAAT
1 ACAC-AAAAT
23539840 TATTAATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
12 9 0.33
14 13 0.48
15 5 0.19
ACGTcount: A:0.58, C:0.20, G:0.00, T:0.22
Consensus pattern (14 bp):
ACACAAAATAATAC
Found at i:23539812 original size:26 final size:26
Alignment explanation
Indices: 23539783--23539841 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
23539773 ATTATACTCA
23539783 AAATATTACACAAAATAATACACACT
1 AAATATTACACAAAATAATACACACT
*
23539809 AAAT-TATACTCAAAATAATACACACT
1 AAATAT-TACACAAAATAATACACACT
23539835 AAA-ATTA
1 AAATATTA
23539842 TTAATTTTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 3 0.10
26 27 0.90
ACGTcount: A:0.58, C:0.17, G:0.00, T:0.25
Consensus pattern (26 bp):
AAATATTACACAAAATAATACACACT
Found at i:23540022 original size:3 final size:3
Alignment explanation
Indices: 23540014--23540039 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
23540004 TCTTCATACT
23540014 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
23540040 TAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:23540142 original size:12 final size:12
Alignment explanation
Indices: 23540101--23540128 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
23540091 AACTACAACA
23540101 AAAAAATATTAC
1 AAAAAATATTAC
23540113 AAAAAATATTAC
1 AAAAAATATTAC
23540125 AAAA
1 AAAA
23540129 TATACAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (12 bp):
AAAAAATATTAC
Found at i:23540151 original size:21 final size:20
Alignment explanation
Indices: 23540103--23540153 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 20
23540093 CTACAACAAA
23540103 AAAATATTACAAAAAATATTAC
1 AAAATA-TACAAAAAATA-TAC
23540125 AAAATATACAAAATAATA-AC
1 AAAATATACAAAA-AATATAC
23540145 AATAATATA
1 AA-AATATA
23540154 ATCAATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 4 0.15
21 13 0.48
22 10 0.37
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAATATACAAAAAATATAC
Found at i:23540442 original size:28 final size:28
Alignment explanation
Indices: 23540383--23540481 Score: 155
Period size: 28 Copynumber: 3.5 Consensus size: 28
23540373 TTTTTTTTAT
*
23540383 ATATTTTGGTAAATAATAAAAAAATT-TAA
1 ATATTTTGGTAAATAA-AAAAAAGTTGT-A
23540412 ATATTTTGGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
23540440 ATATTTTGGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTGTA
*
23540468 ATATTTTAGTAAAT
1 ATATTTTGGTAAAT
23540482 TTTTATTTTT
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
28 50 0.75
29 17 0.25
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTGTA
Found at i:23540682 original size:6 final size:6
Alignment explanation
Indices: 23540673--23540697 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
23540663 GTCATGTGCA
23540673 TGGTGT TGGTGT TGGTGT TGGTGT T
1 TGGTGT TGGTGT TGGTGT TGGTGT T
23540698 CACATTACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (6 bp):
TGGTGT
Found at i:23542029 original size:14 final size:14
Alignment explanation
Indices: 23541999--23542040 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
23541989 CATCTTTAAA
*
23541999 AATATATAT-ACAT
1 AATATATATAATAT
*
23542012 AATATCTATAATAT
1 AATATATATAATAT
*
23542026 AATATATATTATAT
1 AATATATATAATAT
23542040 A
1 A
23542041 TTGGGGGAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATATAATAT
Found at i:23554037 original size:14 final size:14
Alignment explanation
Indices: 23554012--23554053 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
23554002 ATTTTAATTA
23554012 TTTATACAATAATAT
1 TTTATA-AATAATAT
* *
23554027 TTTATATATAAAAT
1 TTTATAAATAATAT
23554041 TTTATAAATAATA
1 TTTATAAATAATA
23554054 CGTTTTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 17 0.74
15 6 0.26
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
TTTATAAATAATAT
Found at i:23556875 original size:10 final size:11
Alignment explanation
Indices: 23556857--23556881 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
23556847 TTTGTTTTCC
23556857 TTTCTTTTTTT
1 TTTCTTTTTTT
23556868 TTTCTTTTTTT
1 TTTCTTTTTTT
23556879 TTT
1 TTT
23556882 GGTTGATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:23558985 original size:125 final size:124
Alignment explanation
Indices: 23558764--23559015 Score: 450
Period size: 125 Copynumber: 2.0 Consensus size: 124
23558754 AAAATATAAT
23558764 AATAATTAATAATAAAACAGGGGTGGGAAGGGTGACACCTTCACCAATAAAACATTGATATTATT
1 AATAATTAATAATAAAACAGGGGTGGGAAGGGTGACACCTTCACCAATAAAACATTGATATTATT
* *
23558829 GTCTTGAATTAACTGGTAACTCAACTGTTTATAGTTTAAGTGGGAAACCAGGAATCGCA
66 GTCTTGAATTAAATGGTAACTCAACTGTTTATAGTTTAAGTGGGAAACAAGGAATCGCA
** *
23558888 AATAATTAATAATAAAATGGGGGTGGAGAGGGGTGACACCTTCACCAATAAAACATTGATATTAT
1 AATAATTAATAATAAAACAGGGGTGG-GAAGGGTGACACCTTCACCAATAAAACATTGATATTAT
23558953 TGTCTTGAATTAAATGGTAACTCAACTGTTTATAGTTTAAGTGGGAAACAAGGAATCGCA
65 TGTCTTGAATTAAATGGTAACTCAACTGTTTATAGTTTAAGTGGGAAACAAGGAATCGCA
23559013 AAT
1 AAT
23559016 TCACTTTATG
Statistics
Matches: 122, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
124 24 0.20
125 98 0.80
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (124 bp):
AATAATTAATAATAAAACAGGGGTGGGAAGGGTGACACCTTCACCAATAAAACATTGATATTATT
GTCTTGAATTAAATGGTAACTCAACTGTTTATAGTTTAAGTGGGAAACAAGGAATCGCA
Found at i:23560768 original size:4 final size:4
Alignment explanation
Indices: 23560761--23560786 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
23560751 CAAACAATAA
23560761 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
23560787 TGTTTAGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:23560908 original size:4 final size:4
Alignment explanation
Indices: 23560901--23560934 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
23560891 AAACAAACAA
23560901 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
23560935 TGTTTAGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:23572028 original size:49 final size:50
Alignment explanation
Indices: 23571935--23572030 Score: 142
Period size: 49 Copynumber: 1.9 Consensus size: 50
23571925 ATCTATTTAT
* * *
23571935 AGGTTGAAAAAACCTTATTCTAATCAATGTCAATTAGATAAAGTATAGTA
1 AGGTTGAAAAAACCTTATTCTAATCAATGTAAAATAGAAAAAGTATAGTA
23571985 AGGTTG-AAAAACCTTATTCTAATCAATGTAAAATA-AAAGAAGTATA
1 AGGTTGAAAAAACCTTATTCTAATCAATGTAAAATAGAAA-AAGTATA
23572031 ATTCTATATG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
48 2 0.05
49 34 0.81
50 6 0.14
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (50 bp):
AGGTTGAAAAAACCTTATTCTAATCAATGTAAAATAGAAAAAGTATAGTA
Found at i:23577954 original size:14 final size:16
Alignment explanation
Indices: 23577935--23577971 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
23577925 AATTAAGTAC
23577935 TAAATTTT-TAAT-AT
1 TAAATTTTATAATCAT
23577949 TAAATTTTATAATCAT
1 TAAATTTTATAATCAT
*
23577965 TGAATTT
1 TAAATTT
23577972 ATATTATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 8 0.40
15 4 0.20
16 8 0.40
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (16 bp):
TAAATTTTATAATCAT
Found at i:23584850 original size:11 final size:13
Alignment explanation
Indices: 23584826--23584857 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
23584816 TAGTTTATTA
23584826 ATATTTTAATATG
1 ATATTTTAATATG
23584839 AT-TTTTAA-ATG
1 ATATTTTAATATG
23584850 ATATTTTA
1 ATATTTTA
23584858 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:23586822 original size:11 final size:11
Alignment explanation
Indices: 23586798--23586849 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
23586788 GGGGTGTTAC
23586798 AATAATAAAT-A
1 AATAA-AAATCA
23586809 AATAAAAATCA
1 AATAAAAATCA
* *
23586820 AATCAAAATAAA
1 AATAAAAAT-CA
*
23586832 AATAAAAACCA
1 AATAAAAATCA
23586843 AATAAAA
1 AATAAAA
23586850 TAACAGTCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
10 4 0.12
11 22 0.65
12 8 0.24
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.17
Consensus pattern (11 bp):
AATAAAAATCA
Found at i:23586830 original size:17 final size:17
Alignment explanation
Indices: 23586808--23586849 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
23586798 AATAATAAAT
* *
23586808 AAATAAAAATCAAATCA
1 AAATAAAAATAAAAACA
*
23586825 AAATAAAAATAAAAACC
1 AAATAAAAATAAAAACA
23586842 AAATAAAA
1 AAATAAAA
23586850 TAACAGTCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (17 bp):
AAATAAAAATAAAAACA
Found at i:23587052 original size:18 final size:18
Alignment explanation
Indices: 23587029--23587067 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
23587019 GCACACAGAC
23587029 AAAGAAAC-AACATAAAAG
1 AAAGAAACGAA-ATAAAAG
*
23587047 AAAGAAACGAAATAACAG
1 AAAGAAACGAAATAAAAG
23587065 AAA
1 AAA
23587068 AGAGGACTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.72, C:0.10, G:0.13, T:0.05
Consensus pattern (18 bp):
AAAGAAACGAAATAAAAG
Found at i:23589458 original size:11 final size:11
Alignment explanation
Indices: 23589434--23589485 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
23589424 GGGGTGTTAC
23589434 AATAATAAAT-A
1 AATAA-AAATCA
23589445 AATAAAAATCA
1 AATAAAAATCA
* *
23589456 AATCAAAATAAA
1 AATAAAAAT-CA
*
23589468 AATAAAAACCA
1 AATAAAAATCA
23589479 AATAAAA
1 AATAAAA
23589486 TAACAGTCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
10 4 0.12
11 22 0.65
12 8 0.24
ACGTcount: A:0.75, C:0.08, G:0.00, T:0.17
Consensus pattern (11 bp):
AATAAAAATCA
Found at i:23589466 original size:17 final size:17
Alignment explanation
Indices: 23589444--23589485 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
23589434 AATAATAAAT
* *
23589444 AAATAAAAATCAAATCA
1 AAATAAAAATAAAAACA
*
23589461 AAATAAAAATAAAAACC
1 AAATAAAAATAAAAACA
23589478 AAATAAAA
1 AAATAAAA
23589486 TAACAGTCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (17 bp):
AAATAAAAATAAAAACA
Found at i:23589688 original size:18 final size:18
Alignment explanation
Indices: 23589665--23589703 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
23589655 GCACACAGAC
23589665 AAAGAAAC-AACATAAAAG
1 AAAGAAACGAA-ATAAAAG
*
23589683 AAAGAAACGAAATAACAG
1 AAAGAAACGAAATAAAAG
23589701 AAA
1 AAA
23589704 AGAGGACTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.72, C:0.10, G:0.13, T:0.05
Consensus pattern (18 bp):
AAAGAAACGAAATAAAAG
Found at i:23608703 original size:45 final size:46
Alignment explanation
Indices: 23608636--23608759 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
23608626 CATATGACCT
*
23608636 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
23608679 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
23608725 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
23608760 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:23608742 original size:46 final size:45
Alignment explanation
Indices: 23608636--23608870 Score: 207
Period size: 37 Copynumber: 5.8 Consensus size: 45
23608626 CATATGACCT
*
23608636 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
23608679 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
23608725 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
23608762 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
23608799 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
23608836 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
23608871 CACTTATCAC
Statistics
Matches: 177, Mismatches: 7, Indels: 18
0.88 0.03 0.09
Matches are distributed among these distances:
37 101 0.57
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.05
44 6 0.03
45 21 0.12
46 34 0.19
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:23608763 original size:37 final size:37
Alignment explanation
Indices: 23608721--23608897 Score: 300
Period size: 37 Copynumber: 4.8 Consensus size: 37
23608711 AGCTGAAGCT
* **
23608721 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
* *
23608758 GCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
23608795 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
23608832 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
23608869 GCCACTTATCACTTTGTTTCTTGATCAGA
1 ACCACTTATCACTTTGTTTCTTGATCAGA
23608898 AGTACTCAAA
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:23616401 original size:45 final size:46
Alignment explanation
Indices: 23616334--23616457 Score: 200
Period size: 46 Copynumber: 2.8 Consensus size: 46
23616324 CATATGACCT
*
23616334 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
23616377 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
*
23616423 CTTATCACTTTATCACTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
23616458 CACTTATCAC
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 8 0.11
44 4 0.05
45 21 0.28
46 41 0.55
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
Found at i:23616440 original size:46 final size:45
Alignment explanation
Indices: 23616334--23616568 Score: 207
Period size: 37 Copynumber: 5.8 Consensus size: 45
23616324 CATATGACCT
*
23616334 CTTATCAC-TTGTC-CTTGATCAGATAAGTGTAGCTAGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
23616377 CTTATCACTTTGCCACTTGATCAGATAAGTGTAGCTGAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGCTACCA
*
23616423 CTTATCACTTTATCACTTGATCAGATAA--GT-G-T-AG---CCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
*
23616460 CTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
23616497 CTTATCACTTTGTTTCTTGATCAGATAA--GT-G-T-A---ACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
**
23616534 CTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGC
23616569 CACTTATCAC
Statistics
Matches: 177, Mismatches: 7, Indels: 18
0.88 0.03 0.09
Matches are distributed among these distances:
37 101 0.57
39 2 0.01
40 3 0.02
42 1 0.01
43 9 0.05
44 6 0.03
45 21 0.12
46 34 0.19
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (45 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGCTACCA
Found at i:23616461 original size:37 final size:37
Alignment explanation
Indices: 23616419--23616595 Score: 300
Period size: 37 Copynumber: 4.8 Consensus size: 37
23616409 AGCTGAAGCT
* **
23616419 ACCACTTATCACTTTATCACTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
* *
23616456 GCCACTTATCACTTTGTCTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
23616493 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
23616530 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
1 ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
*
23616567 GCCACTTATCACTTTGTTTCTTGATCAGA
1 ACCACTTATCACTTTGTTTCTTGATCAGA
23616596 AGTACTCAAA
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 134 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.39
Consensus pattern (37 bp):
ACCACTTATCACTTTGTTTCTTGATCAGATAAGTGTA
Found at i:23619155 original size:54 final size:54
Alignment explanation
Indices: 23619068--23619175 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
23619058 GGGGCAACTC
* ** *
23619068 AGAGAGTTACACGGTTTAGCACAAGGCCGAGCACTCCCCCATGTGACCCAAAAT
1 AGAGAGTTACACGGTCTAGCACAAGGCAAAGCACACCCCCATGTGACCCAAAAT
* ** * *
23619122 AGAGAGTTACACGGTCTAGCACACGTTAAAGCACACGCCCGTGTGACCCAAAAT
1 AGAGAGTTACACGGTCTAGCACAAGGCAAAGCACACCCCCATGTGACCCAAAAT
23619176 GAAAGTCTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.32, C:0.29, G:0.22, T:0.17
Consensus pattern (54 bp):
AGAGAGTTACACGGTCTAGCACAAGGCAAAGCACACCCCCATGTGACCCAAAAT
Found at i:23619611 original size:21 final size:22
Alignment explanation
Indices: 23619587--23619628 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
23619577 AGAAGACAAA
*
23619587 TCAAAC-ACTTAAACAGAAAAT
1 TCAAACAAATTAAACAGAAAAT
*
23619608 TCAAGCAAATTAAACAGAAAA
1 TCAAACAAATTAAACAGAAAA
23619629 CCAATTTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.60, C:0.17, G:0.07, T:0.17
Consensus pattern (22 bp):
TCAAACAAATTAAACAGAAAAT
Found at i:23621652 original size:94 final size:94
Alignment explanation
Indices: 23621491--23621677 Score: 347
Period size: 94 Copynumber: 2.0 Consensus size: 94
23621481 AGGTAGATCA
23621491 ACATCCCTCTTAGCTTTCACCACATAAGCTCTTGCTAATACTCCAGAACTTGGCTTACTAAGATT
1 ACATCCCTCTTAGCTTTCACCACATAAGCTCTTGCTAATACTCCAGAACTTGGCTTACTAAGATT
*
23621556 TCTCATCTGTTCTCCCAGTACCAAACCAG
66 TCTCATCTGTCCTCCCAGTACCAAACCAG
*
23621585 ACATCCCTCTTAGCTTTCATCACATAAGCTCTTGCTAATACTCCAGAACTTGGCTTACTAAGATT
1 ACATCCCTCTTAGCTTTCACCACATAAGCTCTTGCTAATACTCCAGAACTTGGCTTACTAAGATT
*
23621650 TCTCCTCTGTCCTCCCAGTACCAAACCA
66 TCTCATCTGTCCTCCCAGTACCAAACCA
23621678 AATTTAGCTG
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
94 90 1.00
ACGTcount: A:0.26, C:0.33, G:0.10, T:0.31
Consensus pattern (94 bp):
ACATCCCTCTTAGCTTTCACCACATAAGCTCTTGCTAATACTCCAGAACTTGGCTTACTAAGATT
TCTCATCTGTCCTCCCAGTACCAAACCAG
Found at i:23631836 original size:20 final size:21
Alignment explanation
Indices: 23631808--23631855 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
23631798 TTTAGTAAAA
* *
23631808 ATATGTTTTT-AAGTGATATG
1 ATATTTTTTTAAAGTAATATG
*
23631828 ATATTTTTTTAAAGTAATATT
1 ATATTTTTTTAAAGTAATATG
23631849 ATATTTT
1 ATATTTT
23631856 GTCAATCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (21 bp):
ATATTTTTTTAAAGTAATATG
Found at i:23632222 original size:21 final size:21
Alignment explanation
Indices: 23632160--23632223 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
23632150 ATCCTAATTC
*
23632160 TAAAAAAATATATGAAAATAAAA
1 TAAAAAAATATAT-ATAA-AAAA
** *
23632183 TAAAAATTTAT-TTTAAAAAAA
1 TAAAAAAATATATAT-AAAAAA
23632204 TAAAAAAATATATATAAAAA
1 TAAAAAAATATATATAAAAA
23632224 TAATTTAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
21 18 0.56
22 5 0.16
23 9 0.28
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (21 bp):
TAAAAAAATATATATAAAAAA
Found at i:23632233 original size:23 final size:23
Alignment explanation
Indices: 23632160--23632233 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
23632150 ATCCTAATTC
* * *
23632160 TAAAAAAATATATGAAAATAAAA
1 TAAAAATATATATAAAAATAATA
* *
23632183 TAAAAATTTATTTTAAAAA-AATA
1 TAAAAATATA-TATAAAAATAATA
* *
23632206 AAAAAATATATATAAAAATAATT
1 TAAAAATATATATAAAAATAATA
23632229 TAAAA
1 TAAAA
23632234 TTCAAACAAT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
22 7 0.18
23 26 0.67
24 6 0.15
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (23 bp):
TAAAAATATATATAAAAATAATA
Found at i:23635571 original size:5 final size:5
Alignment explanation
Indices: 23635561--23635590 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
23635551 ATGGAAAGAA
23635561 AGGTG AGGTG AGGTG AGGTG AGGTG AGGTG
1 AGGTG AGGTG AGGTG AGGTG AGGTG AGGTG
23635591 GGAGAGCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.60, T:0.20
Consensus pattern (5 bp):
AGGTG
Found at i:23638103 original size:5 final size:5
Alignment explanation
Indices: 23638093--23638200 Score: 92
Period size: 5 Copynumber: 21.4 Consensus size: 5
23638083 TCTTAATATT
* * * *
23638093 TCATA TCATA TCATA TTTCATA -CAGA TGATA TCCTA TCATA TCATA TCAAA
1 TCATA TCATA TCATA --TCATA TCATA TCATA TCATA TCATA TCATA TCATA
* * * * * * *
23638144 TCAAA TCAAA TCAAA TCATA GCTTA TCATA TCATA TCATA TCAAA TCAAA
1 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
23638194 TCATA TC
1 TCATA TC
23638201 CTACCCCCAT
Statistics
Matches: 86, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
4 3 0.03
5 78 0.91
7 5 0.06
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.34
Consensus pattern (5 bp):
TCATA
Found at i:23638717 original size:29 final size:29
Alignment explanation
Indices: 23638684--23638741 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
23638674 TCCACACTGT
*
23638684 CGTGTGCCTTACACGACCTACCACACGAC
1 CGTGTGCCATACACGACCTACCACACGAC
*
23638713 CGTGTGCCATACACGGCCTACCACACGAC
1 CGTGTGCCATACACGACCTACCACACGAC
23638742 TGTATGGCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.24, C:0.41, G:0.19, T:0.16
Consensus pattern (29 bp):
CGTGTGCCATACACGACCTACCACACGAC
Found at i:23641538 original size:14 final size:15
Alignment explanation
Indices: 23641511--23641539 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
23641501 TATTGTGTTA
23641511 AAAAAAATATATGAT
1 AAAAAAATATATGAT
23641526 AAAAAAATA-ATGAT
1 AAAAAAATATATGAT
23641540 TTTATTAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (15 bp):
AAAAAAATATATGAT
Found at i:23645855 original size:2 final size:2
Alignment explanation
Indices: 23645848--23645875 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
23645838 GTAAAAGAAA
23645848 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
23645876 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:23648067 original size:17 final size:17
Alignment explanation
Indices: 23648034--23648066 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
23648024 AATATTAGAA
*
23648034 AATATTTTTATAATTTT
1 AATAATTTTATAATTTT
23648051 AATAATTTTA-AATTTT
1 AATAATTTTATAATTTT
23648067 TTTATAGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AATAATTTTATAATTTT
Found at i:23648089 original size:27 final size:27
Alignment explanation
Indices: 23648033--23648085 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
23648023 AAATATTAGA
23648033 AAATATTTTTATAATTTTAATAATTTT
1 AAATATTTTTATAATTTTAATAATTTT
* * *
23648060 AAATTTTTTTATAGTTTT-TTAATTTT
1 AAATATTTTTATAATTTTAATAATTTT
23648086 TAAAATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (27 bp):
AAATATTTTTATAATTTTAATAATTTT
Found at i:23654089 original size:29 final size:29
Alignment explanation
Indices: 23654004--23654090 Score: 147
Period size: 29 Copynumber: 3.0 Consensus size: 29
23653994 AAAAGCACTT
*
23654004 TCTAAATAACTTATAGCATTGCACATGAG
1 TCTAAATAACTTATAGCATTGCACATGGG
**
23654033 TCTAAATAACTTATAGCATCACACATGGG
1 TCTAAATAACTTATAGCATTGCACATGGG
23654062 TCTAAATAACTTATAGCATTGCACATGGG
1 TCTAAATAACTTATAGCATTGCACATGGG
23654091 GGGCTCTGAG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (29 bp):
TCTAAATAACTTATAGCATTGCACATGGG
Found at i:23658129 original size:30 final size:30
Alignment explanation
Indices: 23658093--23658161 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
23658083 AAACTACACC
* *
23658093 AACAGTCACTCAACTTTGAGAAAATAACAA
1 AACAGTCACTAAACTTTAAGAAAATAACAA
23658123 AACAGTCACTAAACTTTAAGAAAATAACAA
1 AACAGTCACTAAACTTTAAGAAAATAACAA
23658153 AACAGTCAC
1 AACAGTCAC
23658162 CCGCTAACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.52, C:0.20, G:0.09, T:0.19
Consensus pattern (30 bp):
AACAGTCACTAAACTTTAAGAAAATAACAA
Found at i:23659098 original size:12 final size:12
Alignment explanation
Indices: 23659081--23659105 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23659071 GTATCTCTAT
23659081 TTTTTCTTCTTC
1 TTTTTCTTCTTC
23659093 TTTTTCTTCTTC
1 TTTTTCTTCTTC
23659105 T
1 T
23659106 ACTGCCTGGC
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:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTCTTCTTC
Found at i:23665534 original size:23 final size:23
Alignment explanation
Indices: 23665508--23665570 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 23
23665498 GGATACTCCG
23665508 AAGAGCTATAACGGGAAGCTCAC
1 AAGAGCTATAACGGGAAGCTCAC
* * *
23665531 AAGAACTATATAACGAGAAGCTCAT
1 AAGAGC--TATAACGGGAAGCTCAC
*
23665556 GAGAGCTAATAACGG
1 AAGAGCT-ATAACGG
23665571 AACGCTCTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
23 6 0.19
24 6 0.19
25 19 0.61
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.16
Consensus pattern (23 bp):
AAGAGCTATAACGGGAAGCTCAC
Found at i:23668303 original size:15 final size:15
Alignment explanation
Indices: 23668266--23668319 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
23668256 TTAGGGATCG
*
23668266 CACCTAGGGGTTTGCA
1 CACCTA-GGGTTTACA
*
23668282 CA-TTAGGGTTTACA
1 CACCTAGGGTTTACA
*
23668296 CACCTAGGGTTCACA
1 CACCTAGGGTTTACA
23668311 CACCTAGGG
1 CACCTAGGG
23668320 GTTCATACGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 10 0.30
15 21 0.64
16 2 0.06
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (15 bp):
CACCTAGGGTTTACA
Found at i:23669738 original size:43 final size:42
Alignment explanation
Indices: 23669583--23669747 Score: 170
Period size: 43 Copynumber: 3.9 Consensus size: 42
23669573 TTAGGGTTAC
* *
23669583 CGAGATTATGTGTAAGACCATATCTGGGATATGGCATTGATA
1 CGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATA
* * * *
23669625 TGAGACTT-CGTGTAAGACCATGTCTAGGACATTGGCATCGATA
1 CGAGA-TTACGTGTAAGACCATATCTGGGATA-TGGCATCGATA
* * ** ** *
23669668 TGTGATTTTGTGTAAGACCATGGCTGGGCTATTGGCATCGATA
1 CGAGATTACGTGTAAGACCATATCTGGGATA-TGGCATCGATA
*
23669711 CGAGATTACATGTAAGACCATATCTGGGATATGGCAT
1 CGAGATTACGTGTAAGACCATATCTGGGATATGGCAT
23669748 TGTTACGGTA
Statistics
Matches: 100, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
42 31 0.31
43 69 0.69
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (42 bp):
CGAGATTACGTGTAAGACCATATCTGGGATATGGCATCGATA
Found at i:23669765 original size:85 final size:85
Alignment explanation
Indices: 23669589--23669766 Score: 182
Period size: 85 Copynumber: 2.1 Consensus size: 85
23669579 TTACCGAGAT
* * * * *
23669589 TATGTGTAAGACCATATCTGGGATATGGCATTGATATGAGACTTCGTGTAAGACCATGTCTAGGA
1 TATGTGTAAGACCATAGCTGGGATATGGCATCGATACGAGACTTCATGTAAGACCATATCTAGGA
* *
23669654 CATTGGCATCGATATGTGAT
66 CATTGGCATCGATAGGTGAC
* * * *
23669674 TTTGTGTAAGACCATGGCTGGGCTATTGGCATCGATACGAGA-TTACATGTAAGACCATATCTGG
1 TATGTGTAAGACCATAGCTGGGATA-TGGCATCGATACGAGACTT-CATGTAAGACCATATCTAG
* * *
23669738 GATA-TGGCATTGTTACGGT-AC
64 GACATTGGCATCGATA-GGTGAC
23669759 TATGTGTA
1 TATGTGTA
23669767 CGAGATCCCC
Statistics
Matches: 75, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
85 40 0.53
86 35 0.47
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (85 bp):
TATGTGTAAGACCATAGCTGGGATATGGCATCGATACGAGACTTCATGTAAGACCATATCTAGGA
CATTGGCATCGATAGGTGAC
Found at i:23671930 original size:13 final size:14
Alignment explanation
Indices: 23671904--23671938 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
23671894 GGGTTCACAT
23671904 ATAGGTTCATATAC
1 ATAGGTTCATATAC
*
23671918 ATGGGTT-ATATAC
1 ATAGGTTCATATAC
23671931 ATAGGTTC
1 ATAGGTTC
23671939 TCCTAGCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.37
Consensus pattern (14 bp):
ATAGGTTCATATAC
Found at i:23674860 original size:7 final size:7
Alignment explanation
Indices: 23674848--23674875 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
23674838 TATTTTAAAA
23674848 AAAATTT
1 AAAATTT
23674855 AAAATTT
1 AAAATTT
23674862 AAAATTT
1 AAAATTT
23674869 AAAATTT
1 AAAATTT
23674876 TTTTATTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AAAATTT
Found at i:23675323 original size:78 final size:78
Alignment explanation
Indices: 23675235--23675492 Score: 332
Period size: 78 Copynumber: 3.4 Consensus size: 78
23675225 TTTGACCAAA
23675235 CTCAAAAGTGCTCCATTTAACATTGTTGATTAAGATTCTCAATCAAATTTTAAAGATTTTCAACC
1 CTCAAAAGTGCTCCATTTAACATTGTTGATTAAGATTCTCAATCAAATTTTAAAGATTTTCAACC
*
23675300 AAATCCCTAAATC
66 AAATCCCTAAATT
* * *
23675313 CTCAAAAGTGCTCCATTTAACATTGTTGATTAAAATT-TGCAATCAAATCTTACAGATTTTCAA-
1 CTCAAAAGTGCTCCATTTAACATTGTTGATTAAGATTCT-CAATCAAATTTTAAAGATTTTCAAC
23675376 C----CCCTAAATT
65 CAAATCCCTAAATT
* * * *
23675386 CTTAAAAATGATCCATTTAACATTATTGATTAAGATTCTCAATC-AATTCTTAAAGATTTTCAAC
1 CTCAAAAGTGCTCCATTTAACATTGTTGATTAAGATTCTCAATCAAATT-TTAAAGATTTTCAAC
* *
23675450 CAAATTCTTAAATT
65 CAAATCCCTAAATT
* * *
23675464 CTCATAACTGTTCCATTTAACATTGTTGA
1 CTCAAAAGTGCTCCATTTAACATTGTTGA
23675493 CTAAAATCAA
Statistics
Matches: 154, Mismatches: 18, Indels: 16
0.82 0.10 0.09
Matches are distributed among these distances:
72 3 0.02
73 58 0.38
74 2 0.01
77 2 0.01
78 89 0.58
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.37
Consensus pattern (78 bp):
CTCAAAAGTGCTCCATTTAACATTGTTGATTAAGATTCTCAATCAAATTTTAAAGATTTTCAACC
AAATCCCTAAATT
Found at i:23675429 original size:73 final size:73
Alignment explanation
Indices: 23675246--23675461 Score: 269
Period size: 73 Copynumber: 2.9 Consensus size: 73
23675236 TCAAAAGTGC
*
23675246 TCCATTTAACATTGTTGATTAAGATTCTCAATCAAATTTTAAAGATTTTCAACCAAATCCCTAAA
1 TCCATTTAACATTGTTGATTAAGATTCTCAATCAAATCTTAAAGATTTTCAA-C----CCCTAAA
* * * *
23675311 TCCTCAAAAGTGC
61 TTCTTAAAAATGA
* *
23675324 TCCATTTAACATTGTTGATTAAAATT-TGCAATCAAATCTTACAGATTTTCAACCCCTAAATTCT
1 TCCATTTAACATTGTTGATTAAGATTCT-CAATCAAATCTTAAAGATTTTCAACCCCTAAATTCT
23675388 TAAAAATGA
65 TAAAAATGA
* *
23675397 TCCATTTAACATTATTGATTAAGATTCTCAATCAATTCTTAAAGATTTTCAA--CC-AAATTCTT
1 TCCATTTAACATTGTTGATTAAGATTCTCAATCAAATCTTAAAGATTTTCAACCCCTAAATTCTT
23675459 AAA
66 AAA
23675462 TTCTCATAAC
Statistics
Matches: 125, Mismatches: 11, Indels: 12
0.84 0.07 0.08
Matches are distributed among these distances:
70 11 0.09
71 2 0.02
73 62 0.50
74 1 0.01
77 2 0.02
78 47 0.38
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (73 bp):
TCCATTTAACATTGTTGATTAAGATTCTCAATCAAATCTTAAAGATTTTCAACCCCTAAATTCTT
AAAAATGA
Found at i:23675430 original size:151 final size:145
Alignment explanation
Indices: 23675163--23675499 Score: 426
Period size: 151 Copynumber: 2.3 Consensus size: 145
23675153 TTAAAGATTT
* * * * *
23675163 TAAATTCTAAAAAGTGCTCCA-TTAACATTGTTCATAAAAATTTTCAATTAAATCTGAAAGATTT
1 TAAATTCTCAAAAGTGCTCCATTTAACATTGTTGATTAAAATTTGCAATCAAATCTGAAAGATTT
* * * *
23675227 TGACCAAACTCAAAAGTGCTCCATTTAACATTGTTGATTAAGATTCTCAATCAAATT-TTAAAGA
66 TAACCAAACTCAAAAATGATCCATTTAACATTATTGATTAAGATTCTCAATC-AATTCTTAAAGA
23675291 TTTTCAACCAAATCCC
130 TTTTCAACCAAATCCC
* * *
23675307 TAAATCCTCAAAAGTGCTCCATTTAACATTGTTGATTAAAATTTGCAATCAAATCTTACAGATTT
1 TAAATTCTCAAAAGTGCTCCATTTAACATTGTTGATTAAAATTTGCAATCAAATCTGAAAGATTT
*
23675372 TCAACCCCTAAATTCTTAAAAATGATCCATTTAACATTATTGATTAAGATTCTCAATCAATTCTT
66 T-AA--CC-AAA--CTCAAAAATGATCCATTTAACATTATTGATTAAGATTCTCAATCAATTCTT
* *
23675437 AAAGATTTTCAACCAAATTCT
125 AAAGATTTTCAACCAAATCCC
* * * *
23675458 TAAATTCTCATAACTGTTCCATTTAACATTGTTGACTAAAAT
1 TAAATTCTCAAAAGTGCTCCATTTAACATTGTTGATTAAAAT
23675500 CAAATCTATA
Statistics
Matches: 165, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
144 19 0.12
145 38 0.23
146 1 0.01
148 2 0.01
149 3 0.02
150 4 0.02
151 98 0.59
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.36
Consensus pattern (145 bp):
TAAATTCTCAAAAGTGCTCCATTTAACATTGTTGATTAAAATTTGCAATCAAATCTGAAAGATTT
TAACCAAACTCAAAAATGATCCATTTAACATTATTGATTAAGATTCTCAATCAATTCTTAAAGAT
TTTCAACCAAATCCC
Found at i:23675441 original size:21 final size:22
Alignment explanation
Indices: 23675417--23675461 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
23675407 ATTATTGATT
*
23675417 AAGATTCTCAATC-AATTCTTA
1 AAGATTCTCAACCAAATTCTTA
*
23675438 AAGATTTTCAACCAAATTCTTA
1 AAGATTCTCAACCAAATTCTTA
23675460 AA
1 AA
23675462 TTCTCATAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.42, C:0.18, G:0.04, T:0.36
Consensus pattern (22 bp):
AAGATTCTCAACCAAATTCTTA
Found at i:23687799 original size:20 final size:20
Alignment explanation
Indices: 23687776--23687828 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
23687766 AATAAAGTGA
*
23687776 AAATGATTTTAACCAAGTCC
1 AAATAATTTTAACCAAGTCC
** **
23687796 AAATAATTCCAACCAAGTTT
1 AAATAATTTTAACCAAGTCC
*
23687816 AAATCATTTTAAC
1 AAATAATTTTAAC
23687829 ACATCAAAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (20 bp):
AAATAATTTTAACCAAGTCC
Found at i:23690682 original size:155 final size:155
Alignment explanation
Indices: 23690400--23690710 Score: 622
Period size: 155 Copynumber: 2.0 Consensus size: 155
23690390 AAAAACTTGA
23690400 TTTCAAAATGGATACCTAAAGGGACTAAAATTATAGGAACTAATGCTTATAGACCTAAAAGAATT
1 TTTCAAAATGGATACCTAAAGGGACTAAAATTATAGGAACTAATGCTTATAGACCTAAAAGAATT
23690465 TAGGTACCAAAAATCAAACTTTAATTCTATGTTTGTAGGAAAAGGAGCATTACTTTGAGGTGGAT
66 TAGGTACCAAAAATCAAACTTTAATTCTATGTTTGTAGGAAAAGGAGCATTACTTTGAGGTGGAT
23690530 TATTCAAGGAAAAACTTATGGTACG
131 TATTCAAGGAAAAACTTATGGTACG
23690555 TTTCAAAATGGATACCTAAAGGGACTAAAATTATAGGAACTAATGCTTATAGACCTAAAAGAATT
1 TTTCAAAATGGATACCTAAAGGGACTAAAATTATAGGAACTAATGCTTATAGACCTAAAAGAATT
23690620 TAGGTACCAAAAATCAAACTTTAATTCTATGTTTGTAGGAAAAGGAGCATTACTTTGAGGTGGAT
66 TAGGTACCAAAAATCAAACTTTAATTCTATGTTTGTAGGAAAAGGAGCATTACTTTGAGGTGGAT
23690685 TATTCAAGGAAAAACTTATGGTACG
131 TATTCAAGGAAAAACTTATGGTACG
23690710 T
1 T
23690711 CGATAGTGGA
Statistics
Matches: 156, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
155 156 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.30
Consensus pattern (155 bp):
TTTCAAAATGGATACCTAAAGGGACTAAAATTATAGGAACTAATGCTTATAGACCTAAAAGAATT
TAGGTACCAAAAATCAAACTTTAATTCTATGTTTGTAGGAAAAGGAGCATTACTTTGAGGTGGAT
TATTCAAGGAAAAACTTATGGTACG
Found at i:23692151 original size:3 final size:3
Alignment explanation
Indices: 23692145--23692192 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
23692135 AAGAAAGATA
* * * * *
23692145 AAT AAT AAT GAT AAT AAT AAT AAT ATT AAT AAC AGT AAC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
23692193 CATAGAGGCA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:23692357 original size:30 final size:28
Alignment explanation
Indices: 23692302--23692358 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
23692292 ATAAAAGGTT
23692302 GAATTCAAATAAATAAAAGACTAAATTA
1 GAATTCAAATAAATAAAAGACTAAATTA
*
23692330 GAATTTAAATGAAATTAAAAG-CATAAATT
1 GAATTCAAAT-AAA-TAAAAGAC-TAAATT
23692359 GTGACAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 9 0.36
29 4 0.16
30 12 0.48
ACGTcount: A:0.58, C:0.05, G:0.09, T:0.28
Consensus pattern (28 bp):
GAATTCAAATAAATAAAAGACTAAATTA
Found at i:23694171 original size:132 final size:132
Alignment explanation
Indices: 23693985--23694448 Score: 492
Period size: 132 Copynumber: 3.5 Consensus size: 132
23693975 CTTGCCCCAT
* * * *
23693985 TGCAACTTCAGAGAAATAAGATTTGTTA-CTTCAATCTACTCCACTACAACTTCAGGGAGATAAG
1 TGCAACTTCAGGGAGATAAGATTTG-TAGCTTTAATCTGCTCCACTACAACTTCAGGGAGATAAG
* *
23694049 ATTTGTAGCTTTAATCTGCTCCACTACAACTTTAGAGAGATAAGATTGGTAGCTTCAATCTGCTC
65 ATTGGTAGCTTTAATCTGCTCCATTACAACTTTAGAGAGATAAGATTGGTAGCTTCAATCTGCTC
23694114 CAC
130 CAC
* * *
23694117 TGTAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCTACTGCAACTTCAGGGAGATAAGA
1 TGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGA
* * * * *
23694182 TTGGTAGCTTTAATTTGCTCCATTGA-AACTTCA-AGGAGATAAGA-CGTGTAGCTTTAATATGC
66 TTGGTAGCTTTAATCTGCTCCATT-ACAACTTTAGA-GAGATAAGATTG-GTAGCTTCAATCTGC
*
23694244 TCTAC
128 TCCAC
* * *
23694249 TGCAACTTCAGGGAGATAAGATTAGTAGCTTTAATCTGCTCCAATACAACTTCAGGGGGATAAGA
1 TGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGA
* * * **
23694314 TTGGTAGCTTTCATCTGCTCCATTGCAAATTTATGA-AGATAAGATTCCTATGGTATATTCAATC
66 TTGGTAGCTTTAATCTGCTCCATTACAACTTTA-GAGAGATAAGA----T-TGGTAGCTTCAATC
*
23694378 AGAC-CCAC
125 TG-CTCCAC
* * * * * * *
23694386 TGCAACTTCAGAGG-TATAGGATTTTTAGCTTTAATCTGCTCCATTGCAACTTTAGGGATATAA
1 TGCAACTTCAG-GGAGATAAGATTTGTAGCTTTAATCTGCTCCACTACAACTTCAGGGAGATAA
23694449 TATTTACTAT
Statistics
Matches: 275, Mismatches: 42, Indels: 25
0.80 0.12 0.07
Matches are distributed among these distances:
131 4 0.01
132 202 0.73
133 1 0.00
134 1 0.00
137 63 0.23
138 4 0.01
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (132 bp):
TGCAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGA
TTGGTAGCTTTAATCTGCTCCATTACAACTTTAGAGAGATAAGATTGGTAGCTTCAATCTGCTCC
AC
Found at i:23694355 original size:44 final size:44
Alignment explanation
Indices: 23693985--23694448 Score: 441
Period size: 44 Copynumber: 10.4 Consensus size: 44
23693975 CTTGCCCCAT
* * * * *
23693985 TGCAACTTCAGAGAAATAAGATTTGTTA-CTTCAATCTACTCCAC
1 TGCAACTTCAGGGAGATAAGA-TTGGTAGCTTTAATCTGCTCCAC
* *
23694029 TACAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTGGTAGCTTTAATCTGCTCCAC
* * * *
23694073 TACAACTTTAGAGAGATAAGATTGGTAGCTTCAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTGGTAGCTTTAATCTGCTCCAC
* * *
23694117 TGTAACTTCAGGGAGATAAGATTTGTAGCTTTAATCTGCTCTAC
1 TGCAACTTCAGGGAGATAAGATTGGTAGCTTTAATCTGCTCCAC
* *
23694161 TGCAACTTCAGGGAGATAAGATTGGTAGCTTTAATTTGCTCCAT
1 TGCAACTTCAGGGAGATAAGATTGGTAGCTTTAATCTGCTCCAC
* * * * *
23694205 TGAAACTTCAAGGAGATAAGA-CGTGTAGCTTTAATATGCTCTAC
1 TGCAACTTCAGGGAGATAAGATTG-GTAGCTTTAATCTGCTCCAC
* *
23694249 TGCAACTTCAGGGAGATAAGATTAGTAGCTTTAATCTGCTCCAA
1 TGCAACTTCAGGGAGATAAGATTGGTAGCTTTAATCTGCTCCAC
* * * *
23694293 TACAACTTCAGGGGGATAAGATTGGTAGCTTTCATCTGCTCCAT
1 TGCAACTTCAGGGAGATAAGATTGGTAGCTTTAATCTGCTCCAC
* * * * ** * *
23694337 TGCAAATTTATGAAGATAAGATTCCTATGGTATATTCAATCAGAC-CCAC
1 TGCAACTTCAGGGAGATAAGA----T-TGGTAGCTTTAATCTG-CTCCAC
* * ** *
23694386 TGCAACTTCAGAGG-TATAGGATTTTTAGCTTTAATCTGCTCCAT
1 TGCAACTTCAG-GGAGATAAGATTGGTAGCTTTAATCTGCTCCAC
* *
23694430 TGCAACTTTAGGGATATAA
1 TGCAACTTCAGGGAGATAA
23694449 TATTTACTAT
Statistics
Matches: 340, Mismatches: 68, Indels: 24
0.79 0.16 0.06
Matches are distributed among these distances:
43 8 0.02
44 301 0.89
45 1 0.00
48 1 0.00
49 27 0.08
50 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (44 bp):
TGCAACTTCAGGGAGATAAGATTGGTAGCTTTAATCTGCTCCAC
Found at i:23696037 original size:37 final size:37
Alignment explanation
Indices: 23695987--23696097 Score: 179
Period size: 37 Copynumber: 3.0 Consensus size: 37
23695977 GCATTGTTAG
*
23695987 ATATGATCCTTTCTGGCATTCCATACCGACATATGAT
1 ATATGATCTTTTCTGGCATTCCATACCGACATATGAT
* *
23696024 ATATGATCTTTTCTGGCATTCAATACTGACATATGAT
1 ATATGATCTTTTCTGGCATTCCATACCGACATATGAT
23696061 ATAT-AGTCTTTTCTGGCATTCCATACCGACATATGAT
1 ATATGA-TCTTTTCTGGCATTCCATACCGACATATGAT
23696098 CTCTTTCTTC
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
36 1 0.01
37 67 0.99
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.38
Consensus pattern (37 bp):
ATATGATCTTTTCTGGCATTCCATACCGACATATGAT
Found at i:23700319 original size:17 final size:17
Alignment explanation
Indices: 23700297--23700330 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
23700287 GTTCAGCGTG
23700297 TATCCATTGTCAATTAA
1 TATCCATTGTCAATTAA
*
23700314 TATCCATTGTCGATTAA
1 TATCCATTGTCAATTAA
23700331 CACTCCTGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.09, T:0.41
Consensus pattern (17 bp):
TATCCATTGTCAATTAA
Found at i:23706630 original size:3 final size:3
Alignment explanation
Indices: 23706624--23706669 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
23706614 AAGAAAGATA
* *
23706624 AAT AAT AAT GAT AAT AAT AAT -AT AAAT AAT AAT GAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
23706669 A
1 A
23706670 GCGGCAACAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.89
4 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:23706641 original size:12 final size:12
Alignment explanation
Indices: 23706624--23706668 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
23706614 AAGAAAGATA
23706624 AATAATAATGAT
1 AATAATAATGAT
23706636 AATAATAAT-AT
1 AATAATAATGAT
23706647 AAATAATAATGAT
1 -AATAATAATGAT
23706660 AATAATAAT
1 AATAATAAT
23706669 AGCGGCAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 2 0.06
12 27 0.87
13 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (12 bp):
AATAATAATGAT
Found at i:23706665 original size:24 final size:24
Alignment explanation
Indices: 23706621--23706669 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
23706611 TAAAAGAAAG
23706621 ATAAATAATAATGATAATAATAAT
1 ATAAATAATAATGATAATAATAAT
23706645 ATAAATAATAATGATAATAATAAT
1 ATAAATAATAATGATAATAATAAT
23706669 A
1 A
23706670 GCGGCAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (24 bp):
ATAAATAATAATGATAATAATAAT
Found at i:23713042 original size:20 final size:20
Alignment explanation
Indices: 23713014--23713072 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
23713004 TTTTAAAATT
*
23713014 AAGTGAAAATGATTTTAACC
1 AAGTTAAAATGATTTTAACC
** *
23713034 AAGTTAAAATGATTCCAATC
1 AAGTTAAAATGATTTTAACC
*
23713054 AAGTTAAAATCATTTTAAC
1 AAGTTAAAATGATTTTAAC
23713073 ACATCAAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (20 bp):
AAGTTAAAATGATTTTAACC
Found at i:23713268 original size:20 final size:21
Alignment explanation
Indices: 23713245--23713283 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
23713235 TTTTTTTGGT
*
23713245 ATCGATA-CTTTTTTAAAATA
1 ATCGATACCTTTCTTAAAATA
23713265 ATCGATACCTTTCTTAAAA
1 ATCGATACCTTTCTTAAAA
23713284 ACAATATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.15, G:0.05, T:0.41
Consensus pattern (21 bp):
ATCGATACCTTTCTTAAAATA
Found at i:23714543 original size:25 final size:24
Alignment explanation
Indices: 23714461--23714554 Score: 84
Period size: 25 Copynumber: 3.8 Consensus size: 24
23714451 GTTAAACTCG
*
23714461 AACTTAAGTACCAAATTGGGACCAAACA
1 AACTCAAGTACCAAATT-GGA--AAA-A
* *
23714489 AACCTCAAGTATCAAGTT-G-AAAA
1 AA-CTCAAGTACCAAATTGGAAAAA
*
23714512 AATTCAAGTACCAAATTAGGAAAAA
1 AACTCAAGTACCAAATT-GGAAAAA
23714537 AACTCAAGTACCAAATTG
1 AACTCAAGTACCAAATTG
23714555 AACATTGAAG
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
22 12 0.22
23 3 0.05
24 5 0.09
25 20 0.36
27 1 0.02
28 2 0.04
29 12 0.22
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.20
Consensus pattern (24 bp):
AACTCAAGTACCAAATTGGAAAAA
Found at i:23722889 original size:31 final size:31
Alignment explanation
Indices: 23722840--23722900 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
23722830 ATGAAAAAAA
* *
23722840 AATTTAACTCAAACACCCAGTTTTTGTTTTG
1 AATTAAACTCAAACACCCAGATTTTGTTTTG
* *
23722871 AATTAAACTCGAAGACCCAGATTTTGTTTT
1 AATTAAACTCAAACACCCAGATTTTGTTTT
23722901 TGTGTTTTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.39
Consensus pattern (31 bp):
AATTAAACTCAAACACCCAGATTTTGTTTTG
Found at i:23731039 original size:89 final size:89
Alignment explanation
Indices: 23730913--23731138 Score: 267
Period size: 89 Copynumber: 2.5 Consensus size: 89
23730903 AATTAAGTCC
* * * * * *
23730913 TTTTTTTGCACTCAATTAGGCATTTGAACTTTCAAAATGCATCAAAAAA-GCCCTCAAACTTTTT
1 TTTTTTTGCACTCAATTGGGTACTTAAACTTTCAAAATGCATCAAAAAATGACATCAAACTTTTT
* *
23730977 CGAAAAAAATAGTTAAGCCCCTACT
66 C-AAAAAAACAATTAAGCCCCTACT
* *
23731002 TTTTTTTGCACTCAATTGGGTACTTAAACTTTTAAAATACAT-AAAAAATGACATCAAACTTTTT
1 TTTTTTTGCACTCAATTGGGTACTTAAACTTTCAAAATGCATCAAAAAATGACATCAAACTTTTT
* *
23731066 CAAAAAAGCAATTAAGCCCCTGCT
66 CAAAAAAACAATTAAGCCCCTACT
* * * * *
23731090 TTTATTTTACGCTTAATTGGGTACTTAAACTGTCAAAATGAATCAAAAA
1 TTT-TTTTGCACTCAATTGGGTACTTAAACTTTCAAAATGCATCAAAAA
23731139 GCTCATTTGA
Statistics
Matches: 115, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
88 28 0.24
89 82 0.71
90 5 0.04
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.34
Consensus pattern (89 bp):
TTTTTTTGCACTCAATTGGGTACTTAAACTTTCAAAATGCATCAAAAAATGACATCAAACTTTTT
CAAAAAAACAATTAAGCCCCTACT
Found at i:23731293 original size:9 final size:9
Alignment explanation
Indices: 23731243--23731296 Score: 56
Period size: 9 Copynumber: 6.0 Consensus size: 9
23731233 GACATGTGGC
*
23731243 AAAAAATAT
1 AAAAATTAT
*
23731252 AAAAA-AAT
1 AAAAATTAT
*
23731260 AAAAATCAAT
1 AAAAAT-TAT
*
23731270 AAAAGTTAT
1 AAAAATTAT
23731279 AAAAATTAT
1 AAAAATTAT
23731288 AAAAATTAT
1 AAAAATTAT
23731297 TAAGTTTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
8 7 0.18
9 24 0.62
10 8 0.21
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (9 bp):
AAAAATTAT
Found at i:23731569 original size:20 final size:20
Alignment explanation
Indices: 23731546--23731619 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 20
23731536 TGGTATGATA
23731546 AATTTTATAATTTTTTTACG
1 AATTTTATAATTTTTTTACG
*
23731566 AATTTTAT-ATTTCTTTAC-
1 AATTTTATAATTTTTTTACG
* * *
23731584 ATTTTTTATAATCTTCTTACG
1 A-ATTTTATAATTTTTTTACG
* *
23731605 ACTTTATAAAATTTT
1 AATTT-TATAATTTT
23731620 ATATATTTCT
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
18 1 0.02
19 15 0.36
20 18 0.43
21 8 0.19
ACGTcount: A:0.30, C:0.09, G:0.03, T:0.58
Consensus pattern (20 bp):
AATTTTATAATTTTTTTACG
Found at i:23731582 original size:19 final size:20
Alignment explanation
Indices: 23731546--23731605 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 20
23731536 TGGTATGATA
*
23731546 AATTTTATAATTTTTTTACG
1 AATTTTATAATTTCTTTACG
23731566 AATTTTAT-ATTTCTTTAC-
1 AATTTTATAATTTCTTTACG
*
23731584 ATTTTTTATAATCTTC-TTACG
1 A-ATTTTATAAT-TTCTTTACG
23731605 A
1 A
23731606 CTTTATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 1 0.03
19 15 0.44
20 14 0.41
21 4 0.12
ACGTcount: A:0.28, C:0.10, G:0.03, T:0.58
Consensus pattern (20 bp):
AATTTTATAATTTCTTTACG
Found at i:23731648 original size:10 final size:10
Alignment explanation
Indices: 23731635--23731688 Score: 74
Period size: 10 Copynumber: 5.3 Consensus size: 10
23731625 TTTCTATTTA
23731635 TTTTATAATT
1 TTTTATAATT
23731645 TTTT-TACATTT
1 TTTTATA-A-TT
23731656 TTTTATAATT
1 TTTTATAATT
*
23731666 TTTTACAATT
1 TTTTATAATT
23731676 TTTTATAATT
1 TTTTATAATT
23731686 TTT
1 TTT
23731689 ATTAAAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
9 2 0.05
10 28 0.72
11 7 0.18
12 2 0.05
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTATAATT
Found at i:23731648 original size:29 final size:28
Alignment explanation
Indices: 23731607--23731691 Score: 73
Period size: 30 Copynumber: 2.9 Consensus size: 28
23731597 TTCTTACGAC
** *
23731607 TTTATAAAATTTTATATATTTCTATTTAT
1 TTTATAATTTTTTATATATTTTTATTT-T
* *
23731636 TTTATAATTTTTTTACATTTTTTTATAATTT
1 TTTATAA-TTTTTTATATATTTTTAT--TTT
*
23731667 TTTACAATTTTTTATA-ATTTTTATT
1 TTTATAATTTTTTATATATTTTTATT
23731692 AAAATTTAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
27 1 0.02
29 14 0.31
30 21 0.47
31 7 0.16
32 2 0.04
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTATAATTTTTTATATATTTTTATTTT
Found at i:23731657 original size:11 final size:11
Alignment explanation
Indices: 23731630--23731698 Score: 72
Period size: 10 Copynumber: 6.4 Consensus size: 11
23731620 ATATATTTCT
23731630 ATTTATTTTATA
1 ATTT-TTTTATA
*
23731642 ATTTTTTTA-C
1 ATTTTTTTATA
23731652 ATTTTTTTATA
1 ATTTTTTTATA
*
23731663 A-TTTTTTACA
1 ATTTTTTTATA
23731673 A-TTTTTTATA
1 ATTTTTTTATA
*
23731683 ATTTTTATTAAA
1 ATTTTT-TTATA
23731695 ATTT
1 ATTT
23731699 AATAATTCTT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
10 27 0.55
11 10 0.20
12 12 0.24
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (11 bp):
ATTTTTTTATA
Found at i:23731661 original size:21 final size:21
Alignment explanation
Indices: 23731630--23731688 Score: 93
Period size: 20 Copynumber: 2.8 Consensus size: 21
23731620 ATATATTTCT
23731630 ATTTATTTTATAATTTTTTTAC
1 ATTT-TTTTATAATTTTTTTAC
23731652 ATTTTTTTATAA-TTTTTTAC
1 ATTTTTTTATAATTTTTTTAC
*
23731672 AATTTTTTATAATTTTT
1 ATTTTTTTATAATTTTT
23731689 ATTAAAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 19 0.54
21 12 0.34
22 4 0.11
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTTTTTTATAATTTTTTTAC
Found at i:23731727 original size:10 final size:10
Alignment explanation
Indices: 23731635--23731738 Score: 56
Period size: 10 Copynumber: 10.4 Consensus size: 10
23731625 TTTCTATTTA
23731635 TTTTA-TAAT
1 TTTTATTAAT
23731644 TTTT-TTACAT
1 TTTTATTA-AT
*
23731654 TTTTTTATAAT
1 TTTTAT-TAAT
*
23731665 TTTT-TACAAT
1 TTTTAT-TAAT
23731675 TTTT-TATAAT
1 TTTTAT-TAAT
*
23731685 TTTTATTAAA
1 TTTTATTAAT
* *
23731695 ATTTAATAAT
1 TTTTATTAAT
* *
23731705 TCTTA-TAAA
1 TTTTATTAAT
23731714 TTTTATTAAT
1 TTTTATTAAT
*
23731724 TTTTTTTATAT
1 TTTTATTA-AT
23731735 TTTT
1 TTTT
23731739 TGCTATATGT
Statistics
Matches: 76, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
9 13 0.17
10 47 0.62
11 14 0.18
12 2 0.03
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (10 bp):
TTTTATTAAT
Found at i:23732016 original size:99 final size:87
Alignment explanation
Indices: 23731823--23732080 Score: 288
Period size: 99 Copynumber: 2.9 Consensus size: 87
23731813 TCAAATGGTC
* * * *
23731823 TTTTTGATGCATTTTGACAATTCAAGTATCCAATTTAGTG---AAAAAAAAAGTAGGGACTTAAT
1 TTTTTGATGCATTTTGAAAATTCAAGTACCCAATTAAGTGCAAAAAAAAAAAGTAGGGGCTTAAT
23731885 TGTTTTTTTTTAATTTGAGGCA
66 TGTTTTTTTTTAATTTGAGGCA
* * *
23731907 TTTTTTATGCATTTTGAAAATTCAAGTACCCAATTGAGTGCAAAAAAAAAAAGCAGGGGCTTAAT
1 TTTTTGATGCATTTTGAAAATTCAAGTACCCAATTAAGTGCAAAAAAAAAAAGTAGGGGCTTAAT
23731972 TGCTTCTCTTTTTTTTTGAAAAAGTTTGAGGGCA
66 TG------TTTTTTTTT----AA-TTTGA-GGCA
* *
23732006 TTTTTGATGCATTTTGAAAATCCAAGTACCCAATTAAGTGCAAAAAAAAAGAGTAGGGGCTTAAT
1 TTTTTGATGCATTTTGAAAATTCAAGTACCCAATTAAGTGCAAAAAAAAAAAGTAGGGGCTTAAT
**
23732071 TACTTTTTTT
66 TGTTTTTTTT
23732081 GAAAAAGTTG
Statistics
Matches: 146, Mismatches: 13, Indels: 21
0.81 0.07 0.12
Matches are distributed among these distances:
84 36 0.25
87 22 0.15
93 16 0.11
97 2 0.01
98 5 0.03
99 65 0.45
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (87 bp):
TTTTTGATGCATTTTGAAAATTCAAGTACCCAATTAAGTGCAAAAAAAAAAAGTAGGGGCTTAAT
TGTTTTTTTTTAATTTGAGGCA
Found at i:23734206 original size:34 final size:34
Alignment explanation
Indices: 23734139--23734223 Score: 100
Period size: 34 Copynumber: 2.5 Consensus size: 34
23734129 TGATTCTAGG
*
23734139 AAGTTTGTTAACTTGTTAATGAAAGTAGAAAGCT
1 AAGTTTGTTAGCTTGTTAATGAAAGTAGAAAGCT
* **
23734173 AAGTTTGTTAGCTTGTTAGTGGGAGTA-AGAAGCT
1 AAGTTTGTTAGCTTGTTAATGAAAGTAGA-AAGCT
* *
23734207 AAATTTATTAGCTTGTT
1 AAGTTTGTTAGCTTGTT
23734224 TTTGAGTCAT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
33 1 0.02
34 43 0.98
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.39
Consensus pattern (34 bp):
AAGTTTGTTAGCTTGTTAATGAAAGTAGAAAGCT
Found at i:23738130 original size:50 final size:52
Alignment explanation
Indices: 23738072--23738187 Score: 173
Period size: 50 Copynumber: 2.3 Consensus size: 52
23738062 TTAATAAAGT
* *
23738072 CATGCATTATGTAACTCTCATGTT-AGTTAAGTTTGCATCA-TAAATTATGA
1 CATGCATTATGTAACTCTCATGTTAAGTTAAGTCTGCATCATTAAATTAAGA
* *
23738122 CATGCATTATGTAACTCTCATGTTAATTTAAGTCTGCATCATTAAATTAAGT
1 CATGCATTATGTAACTCTCATGTTAAGTTAAGTCTGCATCATTAAATTAAGA
*
23738174 CATGCATTAAGTAA
1 CATGCATTATGTAA
23738188 ACTCATTTTT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
50 24 0.41
51 14 0.24
52 21 0.36
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.39
Consensus pattern (52 bp):
CATGCATTATGTAACTCTCATGTTAAGTTAAGTCTGCATCATTAAATTAAGA
Found at i:23738213 original size:52 final size:52
Alignment explanation
Indices: 23738059--23738187 Score: 172
Period size: 50 Copynumber: 2.5 Consensus size: 52
23738049 ATGTGTTCTG
* * * *
23738059 CATTTAATAAAGTCATGCATTATGTAACTCTCATGTT-AGTTAAGTTTGCAT
1 CATTAAATTAAGTCATGCATTAAGTAACTCTCATGTTAATTTAAGTTTGCAT
* * * *
23738110 CA-TAAATTATGACATGCATTATGTAACTCTCATGTTAATTTAAGTCTGCAT
1 CATTAAATTAAGTCATGCATTAAGTAACTCTCATGTTAATTTAAGTTTGCAT
23738161 CATTAAATTAAGTCATGCATTAAGTAA
1 CATTAAATTAAGTCATGCATTAAGTAA
23738188 ACTCATTTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
50 30 0.45
51 16 0.24
52 21 0.31
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (52 bp):
CATTAAATTAAGTCATGCATTAAGTAACTCTCATGTTAATTTAAGTTTGCAT
Found at i:23743452 original size:28 final size:28
Alignment explanation
Indices: 23743395--23743454 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
23743385 TACATGGACC
* *
23743395 GATTATTTAACTAATAGACGAAGTACAT
1 GATTATTTAACTAATAAACGAAGTAAAT
23743423 GATTATTTAACTACATAAAC-AA-TATAAT
1 GATTATTTAACTA-ATAAACGAAGTA-AAT
23743451 GATT
1 GATT
23743455 TTGTCTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 2 0.07
28 21 0.75
29 5 0.18
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (28 bp):
GATTATTTAACTAATAAACGAAGTAAAT
Found at i:23773635 original size:31 final size:30
Alignment explanation
Indices: 23773576--23773635 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
23773566 AGCCCAAATC
*
23773576 TAAAACATCTAAGAATCGTGTACGGGTCTG
1 TAAAACATCTAAGAATCGTGTACAGGTCTG
*
23773606 TAAAACGTCTAAGAAATCGTG-ATCAGGTCT
1 TAAAACATCTAAG-AATCGTGTA-CAGGTCT
23773636 ACATACGAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.27
Consensus pattern (30 bp):
TAAAACATCTAAGAATCGTGTACAGGTCTG
Found at i:23781410 original size:23 final size:25
Alignment explanation
Indices: 23781375--23781428 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
23781365 TTTCTAAACT
* **
23781375 TATATACGCA-TT-TTTATATAGTA
1 TATATACACATTTATTTATATAAAA
*
23781398 TATATACATATTTATTTATATAAAA
1 TATATACACATTTATTTATATAAAA
23781423 TATATA
1 TATATA
23781429 TGTTCATAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 8 0.32
24 2 0.08
25 15 0.60
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.48
Consensus pattern (25 bp):
TATATACACATTTATTTATATAAAA
Found at i:23783798 original size:15 final size:15
Alignment explanation
Indices: 23783774--23783803 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
23783764 ACCCTGCCTA
*
23783774 TCCCCTAAAATTTAT
1 TCCCCCAAAATTTAT
23783789 TCCCCCAAAATTTAT
1 TCCCCCAAAATTTAT
23783804 CCCAATAAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.37
Consensus pattern (15 bp):
TCCCCCAAAATTTAT
Found at i:23785706 original size:7 final size:7
Alignment explanation
Indices: 23785688--23785729 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
23785678 GTGATGTGAA
23785688 AAAAATG
1 AAAAATG
23785695 AAAAAATG
1 -AAAAATG
23785703 -AAAATG
1 AAAAATG
23785709 AAAAATG
1 AAAAATG
23785716 AAAAA-G
1 AAAAATG
23785722 TAAAAATG
1 -AAAAATG
23785730 GAGAGGCTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 7 0.23
7 16 0.52
8 8 0.26
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:23785714 original size:21 final size:21
Alignment explanation
Indices: 23785688--23785729 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
23785678 GTGATGTGAA
*
23785688 AAAAATGAAAAAATGAAAATG
1 AAAAATGAAAAAATAAAAATG
*
23785709 AAAAATGAAAAAGTAAAAATG
1 AAAAATGAAAAAATAAAAATG
23785730 GAGAGGCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (21 bp):
AAAAATGAAAAAATAAAAATG
Found at i:23787061 original size:45 final size:43
Alignment explanation
Indices: 23786996--23787091 Score: 111
Period size: 45 Copynumber: 2.2 Consensus size: 43
23786986 TGACTACAAA
* ** *
23786996 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAAATCCAAGAAAAC
1 AGATCTTGTCTTCACATACTGG-CATGAAGTAAATCAAAG-AAAC
** *
23787041 AGATCTTGTCTTCATGTACTGGCATGAAGTAGATCAAAGAAAC
1 AGATCTTGTCTTCACATACTGGCATGAAGTAAATCAAAGAAAC
23787084 AGATCTTG
1 AGATCTTG
23787092 CCTCCCTAAG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 12 0.27
44 13 0.30
45 19 0.43
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (43 bp):
AGATCTTGTCTTCACATACTGGCATGAAGTAAATCAAAGAAAC
Found at i:23787306 original size:50 final size:50
Alignment explanation
Indices: 23787249--23787905 Score: 367
Period size: 50 Copynumber: 13.3 Consensus size: 50
23787239 ATTGCAATTA
* * *
23787249 AAAAGATTGAAGTCACAACGGCGGATCTTACTTCTTTAGCAGTGCAGTGG
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAATGG
* * * * *** * * *
23787299 AACAGATTGAAGCTACGACGGCGAATCTGGTTTCCCT-G-A-T--ATTGC
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAATGG
* * **
23787344 AATAG-TTGAAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAGCGG
1 AAAAGATTG-AAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAATGG
* ** * * * * * * * *
23787394 AATAGATTGAAGTTACGACGGCAGATC-TAGTTTCCCT-GATATTGAAAT-T
1 AAAAGATTGAAGCCACAACGGCGGATCTTA-CTTCCTTAG-CAGTGCAATGG
*
23787443 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGG
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAATGG
* * *** * * * **
23787493 AACAGATTGAAGCTACGAA-GGCGGATCTGGTTTCCCT-GATATTGCAATAA
1 AAAAGATTGAAGCCAC-AACGGCGGATCTTACTTCCTTAG-CAGTGCAATGG
* * * * * *
23787543 AAAAGATTAAAGCCATAACGGTGGATCTTGCTTCCTTAACAGTGCAGTGG
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAATGG
* * * *** * * * **
23787593 AACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCT-GATATTGCAATCA
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAG-CAGTGCAATGG
*
23787643 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAATGG
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAATGG
* * * * * * * * * **
23787693 GATAGATTGAAGCTACGACGGCGAATC-TAGTTTCCCT-GATATTGCAATCA
1 AAAAGATTGAAGCCACAACGGCGGATCTTA-CTTCCTTAG-CAGTGCAATGG
*
23787743 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTACAATGG
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAATGG
* * * * * * * * * **
23787793 GATAGATTGAAGCTACGACGGCGAATC-TAGTTTCCCT-GATATTGCAATCA
1 AAAAGATTGAAGCCACAACGGCGGATCTTA-CTTCCTTAG-CAGTGCAATGG
*
23787843 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAGTGG
1 AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAATGG
23787893 AACAA-ATTGAAGC
1 AA-AAGATTGAAGC
23787906 TACAGGTCTT
Statistics
Matches: 432, Mismatches: 148, Indels: 54
0.68 0.23 0.09
Matches are distributed among these distances:
44 3 0.01
45 28 0.06
46 1 0.00
47 2 0.00
48 2 0.00
49 45 0.10
50 337 0.78
51 14 0.03
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.25
Consensus pattern (50 bp):
AAAAGATTGAAGCCACAACGGCGGATCTTACTTCCTTAGCAGTGCAATGG
Found at i:23787309 original size:100 final size:100
Alignment explanation
Indices: 23787192--23787908 Score: 1088
Period size: 100 Copynumber: 7.2 Consensus size: 100
23787182 TCTCTGGGCA
*
23787192 GCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATTAAAAAGATT
1 GCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATCAAAAAGATT
* *
23787257 GAAGTCACAACGGCGGATCTTACTTCTTTAGCAGT
66 GAAGCCACAACGGCGGATCTTACTTCCTTAGCAGT
*
23787292 GCAGTGGAACAGATTGAAGCTACGACGGCGAATCTGGTTTCCCTGATATTGCAAT-----AG-TT
1 GCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATCAAAAAGATT
23787351 GAAAGCCACAACGGCGGATCTTACTTCCTTAGCAGT
66 G-AAGCCACAACGGCGGATCTTACTTCCTTAGCAGT
* * * * * * * *
23787387 ACAGCGGAATAGATTGAAGTTACGACGGCAGATCTAGTTTCCCTGATATTGAAAT-TAAAAGATT
1 GCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATCAAAAAGATT
23787451 GAAGCCACAACGGCGGATCTTACTTCCTTAGCAGT
66 GAAGCCACAACGGCGGATCTTACTTCCTTAGCAGT
* *
23787486 GCAGTGGAACAGATTGAAGCTACGAAGGCGGATCTGGTTTCCCTGATATTGCAATAAAAAAGATT
1 GCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATCAAAAAGATT
* * * * *
23787551 AAAGCCATAACGGTGGATCTTGCTTCCTTAACAGT
66 GAAGCCACAACGGCGGATCTTACTTCCTTAGCAGT
23787586 GCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATCAAAAAGATT
1 GCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATCAAAAAGATT
23787651 GAAGCCACAACGGCGGATCTTACTTCCTTAGCAGT
66 GAAGCCACAACGGCGGATCTTACTTCCTTAGCAGT
* * * * * *
23787686 ACAATGGGATAGATTGAAGCTACGACGGCGAATCTAGTTTCCCTGATATTGCAATCAAAAAGATT
1 GCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATCAAAAAGATT
23787751 GAAGCCACAACGGCGGATCTTACTTCCTTAGCAGT
66 GAAGCCACAACGGCGGATCTTACTTCCTTAGCAGT
* * * * * *
23787786 ACAATGGGATAGATTGAAGCTACGACGGCGAATCTAGTTTCCCTGATATTGCAATCAAAAAGATT
1 GCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATCAAAAAGATT
23787851 GAAGCCACAACGGCGGATCTTACTTCCTTAGCAGT
66 GAAGCCACAACGGCGGATCTTACTTCCTTAGCAGT
*
23787886 GCAGTGGAACAAATTGAAGCTAC
1 GCAGTGGAACAGATTGAAGCTAC
23787909 AGGTCTTATC
Statistics
Matches: 567, Mismatches: 43, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
94 3 0.01
95 81 0.14
99 83 0.15
100 400 0.71
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (100 bp):
GCAGTGGAACAGATTGAAGCTACGACGGCGGATCTGGTTTCCCTGATATTGCAATCAAAAAGATT
GAAGCCACAACGGCGGATCTTACTTCCTTAGCAGT
Found at i:23789393 original size:23 final size:25
Alignment explanation
Indices: 23789358--23789411 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
23789348 TTTCTAAACT
* **
23789358 TATATACGCA-TT-TTTATATAGTA
1 TATATACACATTTATTTATATAAAA
*
23789381 TATATACATATTTATTTATATAAAA
1 TATATACACATTTATTTATATAAAA
23789406 TATATA
1 TATATA
23789412 TGTTCATAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 8 0.32
24 2 0.08
25 15 0.60
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.48
Consensus pattern (25 bp):
TATATACACATTTATTTATATAAAA
Found at i:23791927 original size:22 final size:22
Alignment explanation
Indices: 23791879--23791928 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
23791869 TTTTCACATA
* *
23791879 CTATTTATTTGTTTTTTATCAC
1 CTATTTAATTGTTTTCTATCAC
*
23791901 TTATTTAAATTGTTTTCTAT-AC
1 CTATTT-AATTGTTTTCTATCAC
23791923 CTATTT
1 CTATTT
23791929 TTAAACTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.22, C:0.12, G:0.04, T:0.62
Consensus pattern (22 bp):
CTATTTAATTGTTTTCTATCAC
Found at i:23795589 original size:42 final size:42
Alignment explanation
Indices: 23795530--23795649 Score: 152
Period size: 42 Copynumber: 2.9 Consensus size: 42
23795520 GCGTTTACAG
*
23795530 AAAAAA-ACGCCGTTAAAGATCATGTTCTTTAGCGGCATTTA
1 AAAAAAGACGCCGTTAAAGATCATGTTCTTTAGCGGCACTTA
* * * * * *
23795571 AAAAGAGATGCCGCTAAAGATCATATTCTTTAGCAGCGCTTA
1 AAAAAAGACGCCGTTAAAGATCATGTTCTTTAGCGGCACTTA
* *
23795613 AAAAAAGACGCCGTTAAAGATCATGATCTTTAACGGC
1 AAAAAAGACGCCGTTAAAGATCATGTTCTTTAGCGGC
23795650 GTTTTTTTCT
Statistics
Matches: 64, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
41 5 0.08
42 59 0.92
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (42 bp):
AAAAAAGACGCCGTTAAAGATCATGTTCTTTAGCGGCACTTA
Found at i:23796117 original size:21 final size:21
Alignment explanation
Indices: 23796091--23796155 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
23796081 GCTTCTCTCG
*
23796091 CTGCTTCTCGCGTTGTAGCCT
1 CTGCTTCTCTCGTTGTAGCCT
* *
23796112 CTGCTTCTCTCGCTGCAGCCT
1 CTGCTTCTCTCGTTGTAGCCT
23796133 CTGCTTCTCTCGTTGCT-GCCT
1 CTGCTTCTCTCGTTG-TAGCCT
23796154 CT
1 CT
23796156 ATTTTAAGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.03, C:0.38, G:0.20, T:0.38
Consensus pattern (21 bp):
CTGCTTCTCTCGTTGTAGCCT
Found at i:23801105 original size:13 final size:13
Alignment explanation
Indices: 23801087--23801145 Score: 82
Period size: 13 Copynumber: 4.5 Consensus size: 13
23801077 CAAATTTTAG
*
23801087 TAAGTAATGTATT
1 TAAGTAATATATT
*
23801100 TAAGTAATTTATT
1 TAAGTAATATATT
23801113 TAAGTAATATATT
1 TAAGTAATATATT
*
23801126 CAAGTAATATATT
1 TAAGTAATATATT
*
23801139 AAAGTAA
1 TAAGTAA
23801146 ATTTTAGTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (13 bp):
TAAGTAATATATT
Found at i:23802132 original size:15 final size:15
Alignment explanation
Indices: 23802112--23802143 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
23802102 GAAATAACAG
23802112 TAAATTAGTACCAAA
1 TAAATTAGTACCAAA
23802127 TAAATTAGTACCAAA
1 TAAATTAGTACCAAA
23802142 TA
1 TA
23802144 CTTCAACCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.12, G:0.06, T:0.28
Consensus pattern (15 bp):
TAAATTAGTACCAAA
Found at i:23802182 original size:7 final size:7
Alignment explanation
Indices: 23802170--23802199 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
23802160 AATTTTTGAT
23802170 TACCAAA
1 TACCAAA
23802177 TACCAAA
1 TACCAAA
23802184 TACCAAA
1 TACCAAA
23802191 TACCAAA
1 TACCAAA
23802198 TA
1 TA
23802200 AACAGTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.17
Consensus pattern (7 bp):
TACCAAA
Found at i:23803499 original size:147 final size:144
Alignment explanation
Indices: 23803072--23803500 Score: 384
Period size: 147 Copynumber: 2.9 Consensus size: 144
23803062 AAATCATCCA
* *
23803072 TTTGCGGCGTTTATAA--ATAAGCGCCACTAACTAAAAGTCAAAACGAAGCCGTTTCATCAACAA
1 TTTGCGGCGTTT-TAACCA-AAGCGCCACTAACTATAAGTCAAAACGAAGTCGTTTCATCAACAA
* * * * *
23803135 ATAGCTCACACCTGTGGCGTTTT-TGAATAAACGCCACTAATA-ATACAACAAAACGGCCTCGTA
64 TTAACTCA-ACCTGTGGCGTTTTCT-AA-AAACGCCACTAATACATA-AACAAAACGACCACGTT
* *
23803198 TCAATAAATGTTAAAACATT
125 TCAATAAACGTTAAAACAAT
* * * * * *
23803218 TTTGCGGCGTTTTAACCGAAGCGCCACAAACTATAAATCAAAACGCAGTCGCTTCATCAACACTT
1 TTTGCGGCGTTTTAACCAAAGCGCCACTAACTATAAGTCAAAACGAAGTCGTTTCATCAACAATT
* * * * * **
23803283 ACCTCAAACCCGTGGCGTTTTCGCAAAAATGCCACTGATAACATTTACAAAACGA-CAGCGTTTC
66 AACTC-AACCTGTGGCGTTTTC-TAAAAACGCCACTAAT-ACATAAACAAAACGACCA-CGTTTC
* *
23803347 TATAAACGTTAGAACAAT
127 AATAAACGTTAAAACAAT
* * ** ** *
23803365 TTTGCGGTGTTTTGAGTAAAGCGCCACTAACTATAAGCTC-AAACGAAGTCGTTTCCCCAACAGT
1 TTTGCGGCGTTTTAACCAAAGCGCCACTAACTATAAG-TCAAAACGAAGTCGTTTCATCAACAAT
* * *
23803429 TAACTCAAGCTTGTGGCGTTTTCATAAAAACGCCACTAATACCATAGACAAAACGACCACATTTC
65 TAACTCAA-CCTGTGGCGTTTTC-TAAAAACGCCACTAATA-CATAAACAAAACGACCACGTTTC
23803494 AATAAAC
127 AATAAAC
23803501 AAAATTATAA
Statistics
Matches: 225, Mismatches: 46, Indels: 23
0.77 0.16 0.08
Matches are distributed among these distances:
145 3 0.01
146 83 0.37
147 133 0.59
148 6 0.03
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (144 bp):
TTTGCGGCGTTTTAACCAAAGCGCCACTAACTATAAGTCAAAACGAAGTCGTTTCATCAACAATT
AACTCAACCTGTGGCGTTTTCTAAAAACGCCACTAATACATAAACAAAACGACCACGTTTCAATA
AACGTTAAAACAAT
Found at i:23804454 original size:13 final size:14
Alignment explanation
Indices: 23804429--23804468 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
23804419 CATAAATTCT
23804429 AAACCTTAAACCCCA
1 AAACC-TAAACCCCA
23804444 AAACC-AAACCCCA
1 AAACCTAAACCCCA
*
23804457 AACCCTAAACCC
1 AAACCTAAACCC
23804469 TAAATCCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 12 0.52
14 6 0.26
15 5 0.22
ACGTcount: A:0.47, C:0.45, G:0.00, T:0.07
Consensus pattern (14 bp):
AAACCTAAACCCCA
Found at i:23804480 original size:14 final size:13
Alignment explanation
Indices: 23804436--23804480 Score: 54
Period size: 14 Copynumber: 3.3 Consensus size: 13
23804426 TCTAAACCTT
*
23804436 AAACCCCAAAACC
1 AAACCCCAAACCC
23804449 AAACCCCAAACCC
1 AAACCCCAAACCC
*
23804462 TAAACCCTAAATCCC
1 -AAACCCCAAA-CCC
23804477 AAAC
1 AAAC
23804481 TGTAATATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 12 0.43
14 13 0.46
15 3 0.11
ACGTcount: A:0.49, C:0.44, G:0.00, T:0.07
Consensus pattern (13 bp):
AAACCCCAAACCC
Found at i:23804838 original size:28 final size:28
Alignment explanation
Indices: 23804802--23804863 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
23804792 CGAATCTCTA
*
23804802 AACCTTAAATCACCAACTCTTAACTTCT
1 AACCCTAAATCACCAACTCTTAACTTCT
*
23804830 AACCCTAAATCACCAACTCTTAACTTTT
1 AACCCTAAATCACCAACTCTTAACTTCT
23804858 AACCCT
1 AACCCT
23804864 TAACCCCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.35, C:0.34, G:0.00, T:0.31
Consensus pattern (28 bp):
AACCCTAAATCACCAACTCTTAACTTCT
Found at i:23804875 original size:14 final size:14
Alignment explanation
Indices: 23804864--23804902 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
23804854 TTTTAACCCT
23804864 TAACCCCAAACCAC
1 TAACCCCAAACCAC
* *
23804878 TAACCCCTAACTAC
1 TAACCCCAAACCAC
*
23804892 TAACCCTAAAC
1 TAACCCCAAAC
23804903 TTTATTTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (14 bp):
TAACCCCAAACCAC
Found at i:23805757 original size:114 final size:112
Alignment explanation
Indices: 23805479--23805781 Score: 283
Period size: 114 Copynumber: 2.7 Consensus size: 112
23805469 GCTGCGCTTT
* * * * * *
23805479 TTAAAAGCGCCGCTAAAGCCCTAAAAGTTTAGAAAACGACGCCGTTGGGCTTAGGTTTTTTGCGA
1 TTAAAAACGCCGCTAAA-CCCCAAAAG-TCAGAAAACGACGTCGTTGGGCTTAGTTTTTTTGCGG
*
23805544 CGC-TTCAACAAAAATGCCGCTAAAGCCCTAAGCATTAGCGGCGCATTC
64 CGCTTTCAACAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCATTC
* * * ** * *
23805592 -TAAAAACGTCGCTAAAGCCCATGAATTGTCAGAAAACGGTGTAGTTCGGCTTAGTTTTTGTTGC
1 TTAAAAACGCCGCTAAACCCCA--AA-AGTCAGAAAACGACGTCGTTGGGCTTAGTTTTT-TTGC
* *
23805656 GGCGCTTTC-TCAAAAACGCCGCTAAAGGCCTGAA-CATTAGCGGCGC-TTAC
62 GGCGCTTTCAACAAAAACGCCGCTAAAGCCCT-AAGCATTAGCGGCGCATT-C
* * * * *
23805706 TTAAAAACGCCACTAAATCCCCAAAAGCTCAAAAAATGACGTCGTTGGGCTTTGGTTTTTTTGTG
1 TTAAAAACGCCGCTAAA-CCCCAAAAG-TCAGAAAACGACGTCGTTGGGC-TTAGTTTTTTTGCG
23805771 GCGCTTTCAAC
63 GCGCTTTCAAC
23805782 TTTATGGGTA
Statistics
Matches: 149, Mismatches: 29, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
111 3 0.02
112 14 0.09
113 29 0.19
114 71 0.48
115 28 0.19
116 4 0.03
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (112 bp):
TTAAAAACGCCGCTAAACCCCAAAAGTCAGAAAACGACGTCGTTGGGCTTAGTTTTTTTGCGGCG
CTTTCAACAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCGCATTC
Found at i:23806584 original size:18 final size:18
Alignment explanation
Indices: 23806545--23806585 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
23806535 CGTTCGTTTC
23806545 CAAAACATTATTCATTTA
1 CAAAACATTATTCATTTA
*
23806563 CAAATCATTATTCAATTT-
1 CAAAACATTATTC-ATTTA
23806581 CAAAA
1 CAAAA
23806586 TGCTTTCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (18 bp):
CAAAACATTATTCATTTA
Found at i:23807419 original size:103 final size:103
Alignment explanation
Indices: 23807285--23807490 Score: 376
Period size: 103 Copynumber: 2.0 Consensus size: 103
23807275 CATTATAATC
23807285 CCCAACCCAATGCAATGCAACATACAAATATGACATACTATAACATAATATCATGCATGTAAACA
1 CCCAACCCAATGCAATGCAACATACAAATATGACATACTATAACATAATATCATGCATGTAAACA
23807350 GGGCATACAGTATCAAATCAGTGGGACATCATCAGGTT
66 GGGCATACAGTATCAAATCAGTGGGACATCATCAGGTT
* * * *
23807388 CCCAACCCAATGCAATGCAATATATAGATATGACATACTGTAACATAATATCATGCATGTAAACA
1 CCCAACCCAATGCAATGCAACATACAAATATGACATACTATAACATAATATCATGCATGTAAACA
23807453 GGGCATACAGTATCAAATCAGTGGGACATCATCAGGTT
66 GGGCATACAGTATCAAATCAGTGGGACATCATCAGGTT
23807491 TAATCATATC
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 99 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (103 bp):
CCCAACCCAATGCAATGCAACATACAAATATGACATACTATAACATAATATCATGCATGTAAACA
GGGCATACAGTATCAAATCAGTGGGACATCATCAGGTT
Found at i:23808964 original size:43 final size:43
Alignment explanation
Indices: 23808814--23809091 Score: 276
Period size: 43 Copynumber: 6.5 Consensus size: 43
23808804 GCGTCGCTAA
* * * *
23808814 CTTTAGCGGCGTTTTTTGAAATAAACGCCGCTATAGATCAAAAC
1 CTTTAGCGGCGCTTTTTCACA-AAACGCCGCTATAGATCAAGAC
* * *
23808858 CTTTAGCGGCGCTTTTCCA-AAAACGCCGCTATAGATTAGGAC
1 CTTTAGCGGCGCTTTTTCACAAAACGCCGCTATAGATCAAGAC
* ***** *
23808900 CTTTAGCGGTGCAACCACACAAAACGCCGCTATAGATCAGGAC
1 CTTTAGCGGCGCTTTTTCACAAAACGCCGCTATAGATCAAGAC
**
23808943 CTTTAGCAACGCTTTTTCACAAAACGCCGCTATAGATCAAGAC
1 CTTTAGCGGCGCTTTTTCACAAAACGCCGCTATAGATCAAGAC
* * * * *
23808986 TTTTAGCGGCGCTTGTTC-CACAAACGCTGCTATATATAAAGAC
1 CTTTAGCGGCGCTTTTTCACA-AAACGCCGCTATAGATCAAGAC
* * *
23809029 CTTTAGCGGCGCTTTTTCCCACAAACGCTGCTATAGAAC-AGAC
1 CTTTAGCGGCGCTTTTTCACA-AAACGCCGCTATAGATCAAGAC
*
23809072 CTTTAGTGGCGC-TTTTCACA
1 CTTTAGCGGCGCTTTTTCACA
23809092 CAAGCGCTGC
Statistics
Matches: 195, Mismatches: 36, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
42 41 0.21
43 121 0.62
44 33 0.17
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTTCACAAAACGCCGCTATAGATCAAGAC
Found at i:23809258 original size:27 final size:27
Alignment explanation
Indices: 23809226--23809281 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
23809216 AAATTTTAAC
23809226 TTTAAAACTA-AATATAAAATTAATAAA
1 TTTAAAACTAGAATATAAAA-TAATAAA
** *
23809253 TTTAAATTTAGAATTTAAAATAATAAA
1 TTTAAAACTAGAATATAAAATAATAAA
23809280 TT
1 TT
23809282 AATAACACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (27 bp):
TTTAAAACTAGAATATAAAATAATAAA
Found at i:23809359 original size:104 final size:104
Alignment explanation
Indices: 23809235--23809441 Score: 389
Period size: 104 Copynumber: 2.0 Consensus size: 104
23809225 CTTTAAAACT
23809235 AAATATAAAATTAATAAATTTAAATTTAGAATTTAAAATAATAAATTAATAACACAATTAAAATC
1 AAATATAAAATTAATAAATTTAAATTTAGAATTTAAAATAATAAATTAATAACACAATTAAAATC
23809300 CAAAAGTTAGAACTCTTAAGTAAAAA-AAAAATTTAGAC
66 CAAAAGTTAGAACTCTTAAGTAAAAATAAAAATTTAGAC
*
23809338 AAATATAAAAATTAATGAATTTAAATTTAGAATTTAAAATAATAAATTAATAACACAATTAAAAT
1 AAATAT-AAAATTAATAAATTTAAATTTAGAATTTAAAATAATAAATTAATAACACAATTAAAAT
23809403 CCAAAAGTTAGAACTCTTAAGTAAAAATAAAAATTTAGA
65 CCAAAAGTTAGAACTCTTAAGTAAAAATAAAAATTTAGA
23809442 ATCAAAACTA
Statistics
Matches: 101, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
103 6 0.06
104 84 0.83
105 11 0.11
ACGTcount: A:0.58, C:0.06, G:0.05, T:0.30
Consensus pattern (104 bp):
AAATATAAAATTAATAAATTTAAATTTAGAATTTAAAATAATAAATTAATAACACAATTAAAATC
CAAAAGTTAGAACTCTTAAGTAAAAATAAAAATTTAGAC
Found at i:23809454 original size:53 final size:51
Alignment explanation
Indices: 23809269--23809455 Score: 134
Period size: 53 Copynumber: 3.5 Consensus size: 51
23809259 TTTAGAATTT
* * *
23809269 AAAATAATAAATTAATAACACAATTAAAATCCAAAAGTTAGAACTCTTAAGTA
1 AAAATAA-AAATTTAGAACA-AAATAAAATCCAAAAGTTAGAACTCTTAAGTA
* * * *
23809322 AAAA-AAAAATTTAG-ACAAATATAAAAAT-TAATGAATTTA-AA-T-TTAGAATTT
1 AAAATAAAAATTTAGAACAAA-AT-AAAATCCAA--AAGTTAGAACTCTT--AAGTA
* * *
23809373 AAAATAATAAATTAATAACACAATTAAAATCCAAAAGTTAGAACTCTTAAGTA
1 AAAATAA-AAATTTAGAACA-AAATAAAATCCAAAAGTTAGAACTCTTAAGTA
23809426 AAAATAAAAATTTAGAATCAAAACTAAAAT
1 AAAATAAAAATTTAGAA-CAAAA-TAAAAT
23809456 AAATAATACA
Statistics
Matches: 101, Mismatches: 17, Indels: 32
0.67 0.11 0.21
Matches are distributed among these distances:
49 4 0.04
50 7 0.07
51 20 0.20
52 24 0.24
53 35 0.35
54 7 0.07
55 4 0.04
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.28
Consensus pattern (51 bp):
AAAATAAAAATTTAGAACAAAATAAAATCCAAAAGTTAGAACTCTTAAGTA
Found at i:23814434 original size:7 final size:7
Alignment explanation
Indices: 23814422--23814464 Score: 59
Period size: 7 Copynumber: 6.1 Consensus size: 7
23814412 TACCTATCCA
23814422 TAACCCC
1 TAACCCC
23814429 TAACCCC
1 TAACCCC
* *
23814436 TAATCCT
1 TAACCCC
*
23814443 TAACCTC
1 TAACCCC
23814450 TAACCCC
1 TAACCCC
23814457 TAACCCC
1 TAACCCC
23814464 T
1 T
23814465 CTTTTACAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.28, C:0.49, G:0.00, T:0.23
Consensus pattern (7 bp):
TAACCCC
Done.