Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, 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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 36 of 121
Found at i:6416449 original size:22 final size:22
Alignment explanation
Indices: 6416424--6416511 Score: 81
Period size: 22 Copynumber: 3.9 Consensus size: 22
6416414 CCATAAAGCT
*
6416424 AAAACCTTAAAACCCTATAATC
1 AAAACCTTAAAACCCTAAAATC
6416446 AAAACCTCT-AAACCCTCAAAACCTC
1 AAAACCT-TAAAACCCT-AAAA--TC
** *
6416471 AAAAATTTGAAACCCTAAAATCC
1 AAAACCTTAAAACCCTAAAAT-C
6416494 AAAACC-TAAAACCCTAAA
1 AAAACCTTAAAACCCTAAA
6416512 TTTTAAAATT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
22 26 0.48
23 9 0.17
24 5 0.09
25 14 0.26
ACGTcount: A:0.51, C:0.30, G:0.01, T:0.18
Consensus pattern (22 bp):
AAAACCTTAAAACCCTAAAATC
Found at i:6416518 original size:29 final size:29
Alignment explanation
Indices: 6416486--6416543 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
6416476 TTTGAAACCC
*
6416486 TAAAATCCAAAACCTAAAACCCTAAATTT
1 TAAAATCCAAAACCTAAAACCCCAAATTT
** *
6416515 TAAAATTTAAAACTTAAAACCCCAAATTT
1 TAAAATCCAAAACCTAAAACCCCAAATTT
6416544 GGCACATAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (29 bp):
TAAAATCCAAAACCTAAAACCCCAAATTT
Found at i:6416525 original size:22 final size:22
Alignment explanation
Indices: 6416472--6416527 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
6416462 CAAAACCTCA
*
6416472 AAAATTTGAAACCCTAAAATCC
1 AAAATTTAAAACCCTAAAATCC
** * **
6416494 AAAACCTAAAACCCTAAATTTT
1 AAAATTTAAAACCCTAAAATCC
6416516 AAAATTTAAAAC
1 AAAATTTAAAAC
6416528 TTAAAACCCC
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.54, C:0.20, G:0.02, T:0.25
Consensus pattern (22 bp):
AAAATTTAAAACCCTAAAATCC
Found at i:6418256 original size:28 final size:30
Alignment explanation
Indices: 6418196--6418256 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
6418186 TTTTACTATT
*
6418196 TATGGACACAAATTAAAACCTAACTATATA
1 TATGGACACAAATTAAAACCTAACTATAAA
*
6418226 TATGGACA-AAATTAAAACCTAA-TTTAAA
1 TATGGACACAAATTAAAACCTAACTATAAA
6418254 TAT
1 TAT
6418257 TGTGACCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 7 0.24
29 14 0.48
30 8 0.28
ACGTcount: A:0.51, C:0.13, G:0.07, T:0.30
Consensus pattern (30 bp):
TATGGACACAAATTAAAACCTAACTATAAA
Found at i:6422836 original size:7 final size:7
Alignment explanation
Indices: 6422824--6422871 Score: 60
Period size: 7 Copynumber: 6.4 Consensus size: 7
6422814 AGATTTTGTT
6422824 AATAAAA
1 AATAAAA
6422831 AATAAAA
1 AATAAAA
6422838 AATAAAAA
1 AAT-AAAA
*
6422846 AGAAAAAA
1 A-ATAAAA
6422854 AATGAAAA
1 AAT-AAAA
6422862 AATAAAA
1 AATAAAA
6422869 AAT
1 AAT
6422872 TAGAAAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
7 18 0.50
8 17 0.47
9 1 0.03
ACGTcount: A:0.83, C:0.00, G:0.04, T:0.12
Consensus pattern (7 bp):
AATAAAA
Found at i:6422845 original size:8 final size:8
Alignment explanation
Indices: 6422827--6422880 Score: 58
Period size: 8 Copynumber: 6.9 Consensus size: 8
6422817 TTTTGTTAAT
6422827 AAAAAAT-
1 AAAAAATA
6422834 AAAAAATA
1 AAAAAATA
6422842 AAAAAGA-A
1 AAAAA-ATA
*
6422850 AAAAAATG
1 AAAAAATA
6422858 AAAAAATA
1 AAAAAATA
*
6422866 AAAAATTA
1 AAAAAATA
*
6422874 GAAAAAT
1 AAAAAAT
6422881 TTTAGGGTGG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
7 8 0.21
8 30 0.77
9 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (8 bp):
AAAAAATA
Found at i:6422853 original size:16 final size:17
Alignment explanation
Indices: 6422834--6422870 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
6422824 AATAAAAAAT
6422834 AAAAAAT-AAAAAAGAA
1 AAAAAATGAAAAAAGAA
*
6422850 AAAAAATGAAAAAATAA
1 AAAAAATGAAAAAAGAA
6422867 AAAA
1 AAAA
6422871 TTAGAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.08
Consensus pattern (17 bp):
AAAAAATGAAAAAAGAA
Found at i:6423206 original size:20 final size:20
Alignment explanation
Indices: 6423155--6423198 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
6423145 TTTGGAAAAA
6423155 TCTGA-AAAA-TTTCTAGAT
1 TCTGATAAAATTTTCTAGAT
6423173 TCTGATAAAATTTTCTAGAT
1 TCTGATAAAATTTTCTAGAT
*
6423193 TTTGAT
1 TCTGAT
6423199 GAATTTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.22
19 4 0.17
20 14 0.61
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.45
Consensus pattern (20 bp):
TCTGATAAAATTTTCTAGAT
Found at i:6423657 original size:13 final size:14
Alignment explanation
Indices: 6423639--6423667 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6423629 ATTTTGGTAT
6423639 TTTTATTATTT-TA
1 TTTTATTATTTCTA
6423652 TTTTATTATTTCTA
1 TTTTATTATTTCTA
6423666 TT
1 TT
6423668 GATTTATTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTATTATTTCTA
Found at i:6423661 original size:22 final size:23
Alignment explanation
Indices: 6423627--6423672 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
6423617 GAGCCGTGCC
* *
6423627 TTATTTTGGTATTTTTATT-ATT
1 TTATTTTAGTATTTCTATTGATT
*
6423649 TTATTTTATTATTTCTATTGATT
1 TTATTTTAGTATTTCTATTGATT
6423672 T
1 T
6423673 ATTCCATTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.20, C:0.02, G:0.07, T:0.72
Consensus pattern (23 bp):
TTATTTTAGTATTTCTATTGATT
Found at i:6423813 original size:25 final size:25
Alignment explanation
Indices: 6423780--6423832 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
6423770 AAATATTAAT
6423780 TTTTCAATGATGAAA-TTTTTAAAAA
1 TTTTCAATGAT-AAATTTTTTAAAAA
* *
6423805 TTTTGAATGGTAAATTTTTTTAAAAA
1 TTTTCAATGATAAA-TTTTTTAAAAA
6423831 TT
1 TT
6423833 CTGAGGTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.12
25 9 0.38
26 12 0.50
ACGTcount: A:0.40, C:0.02, G:0.09, T:0.49
Consensus pattern (25 bp):
TTTTCAATGATAAATTTTTTAAAAA
Found at i:6423935 original size:6 final size:6
Alignment explanation
Indices: 6423926--6423953 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
6423916 TTTTAATTTA
6423926 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA
6423954 TATTAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:6423941 original size:11 final size:11
Alignment explanation
Indices: 6423927--6423966 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
6423917 TTTAATTTAA
6423927 AAAATAAAAAT
1 AAAATAAAAAT
6423938 AAAAATAAAAAT
1 -AAAATAAAAAT
**
6423950 AAAATATTAAT
1 AAAATAAAAAT
6423961 AAAATA
1 AAAATA
6423967 TTGAAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:6428087 original size:8 final size:8
Alignment explanation
Indices: 6428064--6428175 Score: 76
Period size: 8 Copynumber: 13.9 Consensus size: 8
6428054 CTAATGGATG
6428064 GAAAAAAT
1 GAAAAAAT
6428072 GAGAAAAATAT
1 --GAAAAA-AT
6428083 GAAAAATAT
1 GAAAAA-AT
6428092 GAAAAAAT
1 GAAAAAAT
6428100 GAAAAAAT
1 GAAAAAAT
6428108 G-AAAAA-
1 GAAAAAAT
6428114 GAAAAAAAT
1 G-AAAAAAT
6428123 GAAAAAA-
1 GAAAAAAT
*
6428130 -AAAAGA-
1 GAAAAAAT
*
6428136 GAAAAAAG
1 GAAAAAAT
6428144 GAAAAAGA-
1 GAAAAA-AT
*
6428152 GAAACAAAA
1 GAAA-AAAT
6428161 GAGAAAAAT
1 GA-AAAAAT
6428170 -AAAAAA
1 GAAAAAA
6428176 AGAGAGAAAA
Statistics
Matches: 89, Mismatches: 3, Indels: 23
0.77 0.03 0.20
Matches are distributed among these distances:
6 6 0.07
7 15 0.17
8 34 0.38
9 24 0.27
10 8 0.09
11 2 0.02
ACGTcount: A:0.76, C:0.01, G:0.15, T:0.08
Consensus pattern (8 bp):
GAAAAAAT
Found at i:6428089 original size:18 final size:17
Alignment explanation
Indices: 6428064--6428128 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 17
6428054 CTAATGGATG
6428064 GAAAAAATGAGAAAAATAT
1 GAAAAAAT--GAAAAATAT
6428083 GAAAAATATGAAAAA-AT
1 GAAAAA-ATGAAAAATAT
*
6428100 GAAAAAATGAAAAAGA-
1 GAAAAAATGAAAAATAT
6428116 -AAAAAATGAAAAA
1 GAAAAAATGAAAAA
6428129 AAAAAGAGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
15 13 0.30
16 8 0.18
17 9 0.20
18 6 0.14
19 6 0.14
20 2 0.05
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (17 bp):
GAAAAAATGAAAAATAT
Found at i:6428119 original size:15 final size:14
Alignment explanation
Indices: 6428084--6428142 Score: 66
Period size: 15 Copynumber: 4.1 Consensus size: 14
6428074 GAAAAATATG
*
6428084 AAAAATATGAAAAA
1 AAAAAAATGAAAAA
6428098 ATGAAAAAATGAAAAA
1 A--AAAAAATGAAAAA
6428114 GAAAAAAATGAAAAA
1 -AAAAAAATGAAAAA
*
6428129 AAAAAGA-GAAAAA
1 AAAAAAATGAAAAA
6428142 A
1 A
6428143 GGAAAAAGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
13 7 0.17
14 7 0.17
15 13 0.32
16 12 0.30
17 1 0.03
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (14 bp):
AAAAAAATGAAAAA
Found at i:6428148 original size:18 final size:19
Alignment explanation
Indices: 6428109--6428185 Score: 56
Period size: 18 Copynumber: 4.1 Consensus size: 19
6428099 TGAAAAAATG
*
6428109 AAAAAGAAA-AAAATGAAAAA
1 AAAAAGAAACAAAA-G-AGAA
6428129 AAAAAGAGAA-AAAAG-GAA
1 AAAAAGA-AACAAAAGAGAA
*
6428147 AAAGAGAAACAAAAGAGAA
1 AAAAAGAAACAAAAGAGAA
*
6428166 AAATAA-AAA-AAGAGAGAA
1 AAA-AAGAAACAAAAGAGAA
6428184 AA
1 AA
6428186 GGAAAACTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
17 2 0.04
18 23 0.47
19 9 0.18
20 9 0.18
21 6 0.12
ACGTcount: A:0.79, C:0.01, G:0.17, T:0.03
Consensus pattern (19 bp):
AAAAAGAAACAAAAGAGAA
Found at i:6428149 original size:43 final size:43
Alignment explanation
Indices: 6428067--6428191 Score: 112
Period size: 43 Copynumber: 2.8 Consensus size: 43
6428057 ATGGATGGAA
* * * *
6428067 AAAATGAGAAAAATATGAAAAATATGAAAAAATGAAAAAATGAAAAAG
1 AAAA-GAGAAAAATA-AAAAAAGA-GAAAAAA-GGAAAAA-GAAAAAC
*
6428115 AAAA-A-AATGAAA-AAAAAAAGAGAAAAAAGGAAAAAGAGAAAC
1 AAAAGAGAA--AAATAAAAAAAGAGAAAAAAGGAAAAAGAAAAAC
*
6428157 AAAAGAGAAAAATAAAAAAAGAGAGAAAAGGAAAA
1 AAAAGAGAAAAATAAAAAAAGAGAAAAAAGGAAAA
6428192 CTCAAATTGA
Statistics
Matches: 66, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
42 12 0.18
43 28 0.42
44 9 0.14
45 8 0.12
46 2 0.03
47 3 0.05
48 4 0.06
ACGTcount: A:0.75, C:0.01, G:0.17, T:0.07
Consensus pattern (43 bp):
AAAAGAGAAAAATAAAAAAAGAGAAAAAAGGAAAAAGAAAAAC
Found at i:6428179 original size:27 final size:26
Alignment explanation
Indices: 6428108--6428185 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 26
6428098 ATGAAAAAAT
*
6428108 GAAAAAGAAAAAAATGAAAAAAAAAAGA
1 GAAAAA-AAAAAAA-GAGAAAAAAAAGA
* *
6428136 GAAAAAAGGAAAAAGAGAAACAAAAGA
1 GAAAAAA-AAAAAAGAGAAAAAAAAGA
*
6428163 GAAAAATAAAAAAAGAGAGAAAA
1 GAAAAA-AAAAAAAGAGAAAAAA
6428186 GGAAAACTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
27 30 0.71
28 12 0.29
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (26 bp):
GAAAAAAAAAAAAGAGAAAAAAAAGA
Found at i:6428191 original size:18 final size:17
Alignment explanation
Indices: 6428137--6428191 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
6428127 AAAAAAAGAG
6428137 AAAAAAG-GAAAAAGAGA
1 AAAAAAGAGAAAAAG-GA
*
6428154 AACAAAAGAGAAAAA-TA
1 AA-AAAAGAGAAAAAGGA
6428171 AAAAAAGAGAGAAAAGGA
1 AAAAAAGAGA-AAAAGGA
6428189 AAA
1 AAA
6428192 CTCAAATTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
16 8 0.25
17 9 0.28
18 9 0.28
19 6 0.19
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (17 bp):
AAAAAAGAGAAAAAGGA
Found at i:6429351 original size:21 final size:22
Alignment explanation
Indices: 6429327--6429605 Score: 238
Period size: 21 Copynumber: 13.1 Consensus size: 22
6429317 TTTTTAAGAT
*
6429327 AAAAT-TTTGAGTTTTCAAGTG
1 AAAATCTTTGAGTTTTCAAATG
*
6429348 AAAATCTTTGAGTTTTCAAGTG
1 AAAATCTTTGAGTTTTCAAATG
6429370 AAAATCTTTGAGTTTTCAAATG
1 AAAATCTTTGAGTTTTCAAATG
* * *
6429392 AAGATTTTTAAG-TTTCAAATG
1 AAAATCTTTGAGTTTTCAAATG
* **
6429413 AGAATCTTTGAG-TTT-ATTTG
1 AAAATCTTTGAGTTTTCAAATG
* *
6429433 AATATCTTTAAGTTTT-AAATG
1 AAAATCTTTGAGTTTTCAAATG
* * *
6429454 AGAATATTTAAG-TTTCAAATG
1 AAAATCTTTGAGTTTTCAAATG
* * * *
6429475 AGACTCTTTAAGTTTTCGAATG
1 AAAATCTTTGAGTTTTCAAATG
* *
6429497 AGAATATTTGAG-TTTCAAATG
1 AAAATCTTTGAGTTTTCAAATG
* * *
6429518 AGAATATTTGAG-TTTCAAATT
1 AAAATCTTTGAGTTTTCAAATG
*
6429539 AGAATCTTTGAG-TTTCAAAT-
1 AAAATCTTTGAGTTTTCAAATG
* * *
6429559 ACGAATGTTTGAGTTTTAAAATG
1 A-AAATCTTTGAGTTTTCAAATG
6429582 AAAATCTTTGAG-TTTCAAATG
1 AAAATCTTTGAGTTTTCAAATG
6429603 AAA
1 AAA
6429606 TGTGAAACCC
Statistics
Matches: 219, Mismatches: 32, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
20 16 0.07
21 123 0.56
22 79 0.36
23 1 0.00
ACGTcount: A:0.36, C:0.07, G:0.16, T:0.41
Consensus pattern (22 bp):
AAAATCTTTGAGTTTTCAAATG
Found at i:6429409 original size:43 final size:43
Alignment explanation
Indices: 6429332--6429604 Score: 263
Period size: 43 Copynumber: 6.4 Consensus size: 43
6429322 AAGATAAAAT
* * * * *
6429332 TTTGAGTTTTCAAGTGAAAATCTTTGAGTTTTCAAGTGAAAATC
1 TTTGAG-TTTCAAATGAAGATCTTTAAGTTTTCAAATGAGAATC
*
6429376 TTTGAGTTTTCAAATGAAGATTTTTAAG-TTTCAAATGAGAATC
1 TTTGAG-TTTCAAATGAAGATCTTTAAGTTTTCAAATGAGAATC
** * *
6429419 TTTGAGTTT-ATTTGAATATCTTTAAGTTTT-AAATGAGAATA
1 TTTGAGTTTCAAATGAAGATCTTTAAGTTTTCAAATGAGAATC
* * *
6429460 TTTAAGTTTCAAATG-AGACTCTTTAAGTTTTCGAATGAGAATA
1 TTTGAGTTTCAAATGAAGA-TCTTTAAGTTTTCAAATGAGAATC
* * *
6429503 TTTGAGTTTCAAATG-AGAATATTTGAG-TTTCAAATTAGAATC
1 TTTGAGTTTCAAATGAAG-ATCTTTAAGTTTTCAAATGAGAATC
* * * * *
6429545 TTTGAGTTTCAAAT-ACGAATGTTTGAGTTTTAAAATGAAAATC
1 TTTGAGTTTCAAATGAAG-ATCTTTAAGTTTTCAAATGAGAATC
6429588 TTTGAGTTTCAAATGAA
1 TTTGAGTTTCAAATGAA
6429605 ATGTGAAACC
Statistics
Matches: 193, Mismatches: 28, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
41 33 0.17
42 57 0.30
43 77 0.40
44 26 0.13
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.42
Consensus pattern (43 bp):
TTTGAGTTTCAAATGAAGATCTTTAAGTTTTCAAATGAGAATC
Found at i:6429879 original size:21 final size:21
Alignment explanation
Indices: 6429855--6429898 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
6429845 TAACTTTTGT
6429855 ATGTGAATCACTAGAATTCGA
1 ATGTGAATCACTAGAATTCGA
*
6429876 ATGTGAATCTCTAGAATTCGA
1 ATGTGAATCACTAGAATTCGA
6429897 AT
1 AT
6429899 CTTTAAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (21 bp):
ATGTGAATCACTAGAATTCGA
Found at i:6429948 original size:20 final size:20
Alignment explanation
Indices: 6429895--6429948 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
6429885 TCTAGAATTC
6429895 GAATCTTTAAATGTTGTATGT
1 GAATCTTTAAAT-TTGTATGT
* *
6429916 G-AGCCTTACAATTTGTATGT
1 GAATCTTTA-AATTTGTATGT
6429936 GAATCTTTAAATT
1 GAATCTTTAAATT
6429949 AAAATTTTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.44
Consensus pattern (20 bp):
GAATCTTTAAATTTGTATGT
Found at i:6430009 original size:18 final size:19
Alignment explanation
Indices: 6429986--6430022 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
6429976 GCGAATTTTG
6429986 AAATCTTGCAAAT-TAAAA
1 AAATCTTGCAAATCTAAAA
*
6430004 AAATCTTGCCAATCTAAAA
1 AAATCTTGCAAATCTAAAA
6430023 TTTTGTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.51, C:0.16, G:0.05, T:0.27
Consensus pattern (19 bp):
AAATCTTGCAAATCTAAAA
Found at i:6430082 original size:151 final size:148
Alignment explanation
Indices: 6429877--6430173 Score: 495
Period size: 151 Copynumber: 2.0 Consensus size: 148
6429867 AGAATTCGAA
* * * *
6429877 TGTGAATCTCTAGAATTCGAATCTTTAAATGTTGTATGTGAGCCTTACAATTTGTATGTGAATCT
1 TGTGAATCTCTAGAATTCGAATATTTAAATGTTGGATGTGAGCCTTACAATTTGTATATGAACCT
* *
6429942 TTAAATTAAAATTTTGGATGTGAATATCACAAATGCGAATTTTGAAATCTTGCAAATTAAAAAAA
66 CTAAATTAAAATTTTGGATGTG-ATATCACAAATGCGAATTTTGAAATCTTGCAAATCAAAAAAA
6430007 TCTTGCCAATCTAAAATTT
130 TCTTGCCAATCTAAAATTT
*
6430026 TGTGAATCTTGCTAGAATTTGAATATTTAAATGTTGGATGTGAGCCTTACAATTTGTATATGAAC
1 TGTGAATC-T-CTAGAATTCGAATATTTAAATGTTGGATGTGAGCCTTACAATTTGTATATGAAC
*
6430091 CTCTAAATTAAAATTTTGGATGTGATATCACAAATGCGAATTTTGAAATCTTGTAAATCAAAAAA
64 CTCTAAATTAAAATTTTGGATGTGATATCACAAATGCGAATTTTGAAATCTTGCAAATCAAAAAA
6430156 ATCTTGCCAATCTAAAAT
129 ATCTTGCCAATCTAAAAT
6430174 ATGAATCAAA
Statistics
Matches: 138, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
149 8 0.06
150 58 0.42
151 72 0.52
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.37
Consensus pattern (148 bp):
TGTGAATCTCTAGAATTCGAATATTTAAATGTTGGATGTGAGCCTTACAATTTGTATATGAACCT
CTAAATTAAAATTTTGGATGTGATATCACAAATGCGAATTTTGAAATCTTGCAAATCAAAAAAAT
CTTGCCAATCTAAAATTT
Found at i:6430449 original size:44 final size:44
Alignment explanation
Indices: 6430382--6430707 Score: 360
Period size: 44 Copynumber: 7.5 Consensus size: 44
6430372 GATTGTCGAT
* *
6430382 GAGCTTTATTTATTTTTTCAAAGTCGTTGAGCCTTTAATTA-AA
1 GAGCTTTATTTATTTTTTCAAAGTTGTTGAGCCTTTGATTAGAA
* * ** * *
6430425 TGTGCTTTATTTATTTTTTGAAAGTCATTGAGCCTCTGATTAAAA
1 -GAGCTTTATTTATTTTTTCAAAGTTGTTGAGCCTTTGATTAGAA
* * * *
6430470 TAGTTTTATTTATTTTTTCAAAGTTGTGGAGCCTTTGCTTAGATA
1 GAGCTTTATTTATTTTTTCAAAGTTGTTGAGCCTTTGATTAGA-A
* *
6430515 -AGCTTTATTTAATTTTTCAAAGTTTTTGAGCCTTTGATTAGAA
1 GAGCTTTATTTATTTTTTCAAAGTTGTTGAGCCTTTGATTAGAA
* *
6430558 GAGTTTTATTTATTTTTT-AAAGTTTTTGAGCCTTTGATTAGAA
1 GAGCTTTATTTATTTTTTCAAAGTTGTTGAGCCTTTGATTAGAA
*
6430601 GAGCTTTATTTA-TTTTTCAAAGTTGTTGAGCCTCTGATTAGAA
1 GAGCTTTATTTATTTTTTCAAAGTTGTTGAGCCTTTGATTAGAA
* ** * * *
6430644 AAGCTTTATTT-TTTTTT-AAAGTCATTAAGCCTCTGTTTAGAA
1 GAGCTTTATTTATTTTTTCAAAGTTGTTGAGCCTTTGATTAGAA
*
6430686 GAG-TTATATTTATTTTTCCAAA
1 GAGCTT-TATTTATTTTTTCAAA
6430708 AATTGTAAGC
Statistics
Matches: 242, Mismatches: 32, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
41 2 0.01
42 33 0.14
43 80 0.33
44 124 0.51
45 3 0.01
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.48
Consensus pattern (44 bp):
GAGCTTTATTTATTTTTTCAAAGTTGTTGAGCCTTTGATTAGAA
Found at i:6430949 original size:7 final size:7
Alignment explanation
Indices: 6430903--6430932 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
6430893 AGATTTTGTT
6430903 AATAAAA
1 AATAAAA
6430910 AATAAAA
1 AATAAAA
6430917 AATAAAA
1 AATAAAA
6430924 AATAAAA
1 AATAAAA
6430931 AA
1 AA
6430933 AATGAAAAAA
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:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AATAAAA
Found at i:6430959 original size:24 final size:23
Alignment explanation
Indices: 6430906--6430950 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
6430896 TTTTGTTAAT
*
6430906 AAAAAATAAAAAATAAAAAATAA
1 AAAAAATAAAAAACAAAAAATAA
6430929 AAAAAATGAAAAAACAAAAAAT
1 AAAAAAT-AAAAAACAAAAAAT
6430951 TAGGAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.11
Consensus pattern (23 bp):
AAAAAATAAAAAACAAAAAATAA
Found at i:6431277 original size:19 final size:20
Alignment explanation
Indices: 6431245--6431283 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
6431235 AAATTCCTAG
6431245 ATTTCGATAAAATTTTTCAA
1 ATTTCGATAAAATTTTTCAA
*
6431265 ATTTCGAT-GAATTTTTCAA
1 ATTTCGATAAAATTTTTCAA
6431284 CGTCGGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (20 bp):
ATTTCGATAAAATTTTTCAA
Found at i:6431803 original size:26 final size:24
Alignment explanation
Indices: 6431750--6431813 Score: 60
Period size: 26 Copynumber: 2.6 Consensus size: 24
6431740 ATATTTTGGT
**
6431750 ATTTTAATTA-TTTTTTATTATTTT
1 ATTTT-ATTATTTTTTTATTATTCC
6431774 ATTTTATTATTTCTTTTATTTATTCC
1 ATTTTATTATTT-TTTTA-TTATTCC
6431800 ATTTGT-TTATTTTT
1 ATTT-TATTATTTTT
6431814 CTTTTTCTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
23 4 0.12
24 7 0.21
25 7 0.21
26 15 0.44
27 1 0.03
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (24 bp):
ATTTTATTATTTTTTTATTATTCC
Found at i:6431925 original size:26 final size:25
Alignment explanation
Indices: 6431896--6431948 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
6431886 AATAAATATT
*
6431896 AATTATCAGATAATAGAATTTTTAAA
1 AATTATCAAATAATA-AATTTTTAAA
* * *
6431922 AATTTTGAAATAGTAAATTTTTAAA
1 AATTATCAAATAATAAATTTTTAAA
6431947 AA
1 AA
6431949 ATTCTTAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.51, C:0.02, G:0.08, T:0.40
Consensus pattern (25 bp):
AATTATCAAATAATAAATTTTTAAA
Found at i:6445433 original size:16 final size:16
Alignment explanation
Indices: 6445396--6445435 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
6445386 ATTGGATATG
* *
6445396 AATTATATTAAATTTG
1 AATTATTTTAAATTTA
*
6445412 AGTTATTTTAAATTTA
1 AATTATTTTAAATTTA
6445428 AATTATTT
1 AATTATTT
6445436 GCGATTAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (16 bp):
AATTATTTTAAATTTA
Found at i:6445609 original size:18 final size:18
Alignment explanation
Indices: 6445588--6445627 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
6445578 CAAATGATTT
6445588 TTTTAATT-AATATTTGTA
1 TTTTAATTGAATATTT-TA
*
6445606 TTTTTATTGAATATTTTA
1 TTTTAATTGAATATTTTA
6445624 TTTT
1 TTTT
6445628 TTAATTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTAATTGAATATTTTA
Found at i:6445611 original size:19 final size:19
Alignment explanation
Indices: 6445586--6445636 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
6445576 TTCAAATGAT
6445586 TTTTTTAATTAATATTTGTA
1 TTTTTTAATTAATATTT-TA
6445606 -TTTTT-ATTGAATATTTTA
1 TTTTTTAATT-AATATTTTA
6445624 TTTTTTAATTAAT
1 TTTTTTAATTAAT
6445637 TCAAATTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
18 5 0.18
19 20 0.71
20 3 0.11
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (19 bp):
TTTTTTAATTAATATTTTA
Found at i:6447508 original size:34 final size:34
Alignment explanation
Indices: 6447435--6447516 Score: 85
Period size: 34 Copynumber: 2.4 Consensus size: 34
6447425 ATTATGTTTG
* ** * *
6447435 AAAATGTATTTTCGGATAATTGTAATGCTTTTCT
1 AAAATGCATTTTCGGATAATTACAATACTTTTCA
*
6447469 GAAATGCATATTT-GGATAATTACAATACTTTTCA
1 AAAATGCAT-TTTCGGATAATTACAATACTTTTCA
*
6447503 AAAATGAATTTTCG
1 AAAATGCATTTTCG
6447517 ATATAGTTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
33 3 0.08
34 32 0.84
35 3 0.08
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.41
Consensus pattern (34 bp):
AAAATGCATTTTCGGATAATTACAATACTTTTCA
Found at i:6448354 original size:2 final size:2
Alignment explanation
Indices: 6448347--6448374 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6448337 TTCACACTTT
6448347 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
6448375 ATGTTAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6459647 original size:20 final size:20
Alignment explanation
Indices: 6459619--6459656 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6459609 ATGAAAATGT
6459619 ATGTAAAAGATCAAATGAAA
1 ATGTAAAAGATCAAATGAAA
* *
6459639 ATGTGAAAGATGAAATGA
1 ATGTAAAAGATCAAATGA
6459657 CATTCAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (20 bp):
ATGTAAAAGATCAAATGAAA
Found at i:6467691 original size:14 final size:14
Alignment explanation
Indices: 6467672--6467712 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
6467662 TTTTTTAATT
6467672 TTTTTTGTTCTTTA
1 TTTTTTGTTCTTTA
* *
6467686 TTTTTTATTTTTTA
1 TTTTTTGTTCTTTA
*
6467700 TTTTCTGTTCTTT
1 TTTTTTGTTCTTT
6467713 GCTTCTTTTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.07, C:0.07, G:0.05, T:0.80
Consensus pattern (14 bp):
TTTTTTGTTCTTTA
Found at i:6467806 original size:5 final size:5
Alignment explanation
Indices: 6467791--6467851 Score: 50
Period size: 5 Copynumber: 11.0 Consensus size: 5
6467781 ATACAACCAG
* *
6467791 TAAAA TTAAA TAAAA TTGAAAA TAAAA TAAAAA CTCAAAA TAAATA AAAAA
1 TAAAA TAAAA TAAAA -T-AAAA TAAAA T-AAAA -T-AAAA TAAA-A TAAAA
6467842 TAAAA TAAAA
1 TAAAA TAAAA
6467852 ATGGAAAAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
5 26 0.57
6 11 0.24
7 9 0.20
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:6467835 original size:17 final size:16
Alignment explanation
Indices: 6467791--6467850 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
6467781 ATACAACCAG
*
6467791 TAAAATTAAAT-AAAAT
1 TAAAA-TAAATAAAAAA
*
6467807 TGAAAATAAAATAAAAAC
1 T-AAAAT-AAATAAAAAA
6467825 TCAAAATAAATAAAAAA
1 T-AAAATAAATAAAAAA
6467842 TAAAATAAA
1 TAAAATAAA
6467851 AATGGAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
16 10 0.26
17 18 0.47
18 10 0.26
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.22
Consensus pattern (16 bp):
TAAAATAAATAAAAAA
Found at i:6468750 original size:3 final size:3
Alignment explanation
Indices: 6468744--6468929 Score: 116
Period size: 3 Copynumber: 63.0 Consensus size: 3
6468734 GAAGAAAGAA
* *
6468744 AAT AAT AAAT GAT AAT GAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
6468790 AAT AAT AAT -AT AAC ACT -AT ACCAT AA- ACT ATAT TAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT A--AT AAT AAT A-AT AAT AAT AAT AAT
* * * * * * * * * * * *
6468834 AGT -AT ACT -AT ACT -AT AGT AGT AGT AAT AGT AGT AGT AGT AGT ACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
6468879 AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6468927 AAT
1 AAT
6468930 TATTATTGTT
Statistics
Matches: 147, Mismatches: 25, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
2 9 0.06
3 131 0.89
4 4 0.03
5 3 0.02
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6469857 original size:86 final size:86
Alignment explanation
Indices: 6469765--6470046 Score: 280
Period size: 86 Copynumber: 3.3 Consensus size: 86
6469755 GAATATTCGC
* *
6469765 AAGATTCCAAGTTTCACAAAAGTTCTAGATTCACAAAGATCTT-AGGTTTGCAAAAACTTTCAAA
1 AAGATTCCAAGTTTCACAAAAGTTCTAGATTCGCAAAGAT-TTCAGGTTTGCAAGAACTTTCAAA
* * *
6469829 TTTGTAGGAAAGAAAGATTTGT
65 TTTGCAAGAAAGAAAGATTTAT
* * ** * * * * * *
6469851 AGGATTCTAAGTTTTGCTAAGGTTCTAGATTCGCACAGATTTCAGATTCGCAAGAACTTTCAGAT
1 AAGATTCCAAGTTTCACAAAAGTTCTAGATTCGCAAAGATTTCAGGTTTGCAAGAACTTTCAAAT
* * *
6469916 TCGCAAGAAAGAAAAATTTCT
66 TTGCAAGAAAGAAAGATTTAT
* * * * *
6469937 AAGATTCTAAGTTTCAC-AAAGATTGTAGATTCGGAAAGATTTCAGGTTTGTAAGGACTTTCAAA
1 AAGATTCCAAGTTTCACAAAAG-TTCTAGATTCGCAAAGATTTCAGGTTTGCAAGAACTTTCAAA
* *
6470001 TTTACAAGAAAGAAGGATTTAT
65 TTTGCAAGAAAGAAAGATTTAT
* **
6470023 AAGATTTCAAGTTTTGCAAAAGTT
1 AAGATTCCAAGTTTCACAAAAGTT
6470047 AAAAAAATGA
Statistics
Matches: 155, Mismatches: 38, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
85 5 0.03
86 146 0.94
87 4 0.03
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.32
Consensus pattern (86 bp):
AAGATTCCAAGTTTCACAAAAGTTCTAGATTCGCAAAGATTTCAGGTTTGCAAGAACTTTCAAAT
TTGCAAGAAAGAAAGATTTAT
Found at i:6469899 original size:17 final size:18
Alignment explanation
Indices: 6469877--6469924 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
6469867 CTAAGGTTCT
6469877 AGATTCGCACAG-A-TTTC
1 AGATTCGCA-AGAACTTTC
6469894 AGATTCGCAAGAACTTTC
1 AGATTCGCAAGAACTTTC
6469912 AGATTCGCAAGAA
1 AGATTCGCAAGAA
6469925 AGAAAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 2 0.07
17 10 0.34
18 17 0.59
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (18 bp):
AGATTCGCAAGAACTTTC
Found at i:6471140 original size:23 final size:23
Alignment explanation
Indices: 6471114--6471167 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
6471104 TCATGATTCT
*
6471114 TCAAATTGAGTATTCACATTTGA
1 TCAAAATGAGTATTCACATTTGA
6471137 TCAAAATGAGTATTCACATTTGA
1 TCAAAATGAGTATTCACATTTGA
6471160 TCAAAATG
1 TCAAAATG
6471168 GACTTTTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (23 bp):
TCAAAATGAGTATTCACATTTGA
Found at i:6471331 original size:10 final size:10
Alignment explanation
Indices: 6471307--6471339 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
6471297 TCCCAACAAA
6471307 TTTTCTTCA-
1 TTTTCTTCAT
*
6471316 TTTTCTTTAT
1 TTTTCTTCAT
6471326 TTTTCTTCAT
1 TTTTCTTCAT
6471336 TTTT
1 TTTT
6471340 TTATCCATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTCTTCAT
Found at i:6471331 original size:19 final size:18
Alignment explanation
Indices: 6471307--6471343 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
6471297 TCCCAACAAA
6471307 TTTTCTTCATTTTCTTTAT
1 TTTTCTTCATTTT-TTTAT
6471326 TTTTCTTCATTTTTTTAT
1 TTTTCTTCATTTTTTTAT
6471344 CCATCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTCTTCATTTTTTTAT
Found at i:6477428 original size:23 final size:25
Alignment explanation
Indices: 6477381--6477483 Score: 79
Period size: 27 Copynumber: 4.0 Consensus size: 25
6477371 TGAATACAAA
6477381 TAAAT-AAATAAATAAAATTAGTAAAAT
1 TAAATCAAATAAATAAAA-T--TAAAAT
6477408 TAAAT-AAA-AAATAAAATTAAAAT
1 TAAATCAAATAAATAAAATTAAAAT
* *
6477431 AAAAACTCAAAATAAATAAAAAATAAAAT
1 -TAAA-TC-AAATAAAT-AAAATTAAAAT
* *
6477460 GAAATCAAA-AAATAAAATAAAAAT
1 TAAATCAAATAAATAAAATTAAAAT
6477484 GGGAAAAAGA
Statistics
Matches: 65, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
23 6 0.09
24 12 0.18
25 6 0.09
26 11 0.17
27 13 0.20
28 7 0.11
29 10 0.15
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.22
Consensus pattern (25 bp):
TAAATCAAATAAATAAAATTAAAAT
Found at i:6477432 original size:18 final size:17
Alignment explanation
Indices: 6477402--6477477 Score: 100
Period size: 18 Copynumber: 4.4 Consensus size: 17
6477392 ATAAAATTAG
6477402 TAAAATTAAATAAAAAA
1 TAAAATTAAATAAAAAA
*
6477419 TAAAATTAAAATAAAAAC
1 TAAAATT-AAATAAAAAA
6477437 TCAAAA-TAAATAAAAAA
1 T-AAAATTAAATAAAAAA
*
6477454 TAAAATGAAATCAAAAAA
1 TAAAATTAAAT-AAAAAA
6477472 TAAAAT
1 TAAAAT
6477478 AAAAATGGGA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
16 4 0.08
17 21 0.40
18 23 0.44
19 4 0.08
ACGTcount: A:0.74, C:0.04, G:0.01, T:0.21
Consensus pattern (17 bp):
TAAAATTAAATAAAAAA
Found at i:6477450 original size:35 final size:34
Alignment explanation
Indices: 6477402--6477480 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 34
6477392 ATAAAATTAG
*
6477402 TAAAATTAAATAAAAAATAAAATTAAAAT-AAAAAC
1 TAAAA-TAAATAAAAAATAAAA-TAAAATCAAAAAA
*
6477437 TCAAAATAAATAAAAAATAAAATGAAATCAAAAAA
1 T-AAAATAAATAAAAAATAAAATAAAATCAAAAAA
6477472 TAAAATAAA
1 TAAAATAAA
6477481 AATGGGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
34 13 0.32
35 23 0.57
36 4 0.10
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.20
Consensus pattern (34 bp):
TAAAATAAATAAAAAATAAAATAAAATCAAAAAA
Found at i:6478049 original size:18 final size:19
Alignment explanation
Indices: 6478008--6478050 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
6477998 AATCCTTCCA
*
6478008 AAAATCAACTATTTCCCTC
1 AAAATCAACTATGTCCCTC
*
6478027 AAAATCAACTATGTCTC-C
1 AAAATCAACTATGTCCCTC
6478045 AAAATC
1 AAAATC
6478051 CATTGTTATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.42, C:0.28, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATCAACTATGTCCCTC
Found at i:6478335 original size:13 final size:14
Alignment explanation
Indices: 6478317--6478403 Score: 59
Period size: 15 Copynumber: 6.1 Consensus size: 14
6478307 GAAGAAAGAA
6478317 AATAATA-AATGAT
1 AATAATATAATGAT
6478330 AATAATATAATGAT
1 AATAATATAATGAT
* * *
6478344 GATGATGATGATGAT
1 AATAAT-ATAATGAT
* * * *
6478359 GATGATGATGATAAT
1 AATAAT-ATAATGAT
*
6478374 AATAATAATAATAAT
1 AATAAT-ATAATGAT
*
6478389 AATAATAAAATGAT
1 AATAATATAATGAT
6478403 A
1 A
6478404 TAACACTATA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
13 7 0.11
14 17 0.27
15 38 0.61
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.32
Consensus pattern (14 bp):
AATAATATAATGAT
Found at i:6478345 original size:3 final size:3
Alignment explanation
Indices: 6478339--6478370 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
6478329 TAATAATATA
6478339 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
6478371 AATAATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:6478375 original size:3 final size:3
Alignment explanation
Indices: 6478369--6478396 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6478359 GATGATGATG
6478369 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
6478397 AATGATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:6478445 original size:18 final size:18
Alignment explanation
Indices: 6478422--6478461 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
6478412 TACCATAAAC
6478422 TATACTATAATAAAATAG
1 TATACTATAATAAAATAG
* *
6478440 TATACTATAATATAGTAG
1 TATACTATAATAAAATAG
6478458 TATA
1 TATA
6478462 GTAGTAGTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (18 bp):
TATACTATAATAAAATAG
Found at i:6478484 original size:3 final size:3
Alignment explanation
Indices: 6478478--6478517 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
6478468 GTAGTAGTAG
6478478 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
6478518 CGACTCCGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:6479204 original size:24 final size:24
Alignment explanation
Indices: 6479172--6479219 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
6479162 CAACTATTAT
6479172 TTTTATTAGGTTGACCTTTTAATC
1 TTTTATTAGGTTGACCTTTTAATC
6479196 TTTTATTAGGTTGACCTTTTAATC
1 TTTTATTAGGTTGACCTTTTAATC
6479220 CTTACTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.54
Consensus pattern (24 bp):
TTTTATTAGGTTGACCTTTTAATC
Found at i:6479424 original size:2 final size:2
Alignment explanation
Indices: 6479417--6479449 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6479407 TTAATAATTA
6479417 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6479450 GTATTTGATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6481080 original size:13 final size:13
Alignment explanation
Indices: 6481064--6481089 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6481054 CATAATAATT
6481064 AGAAATAAAATAA
1 AGAAATAAAATAA
6481077 AGAAATAAAATAA
1 AGAAATAAAATAA
6481090 TTGCATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (13 bp):
AGAAATAAAATAA
Found at i:6481311 original size:12 final size:12
Alignment explanation
Indices: 6481294--6481320 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6481284 ATGATAGAAA
6481294 AAAATTAAAAAG
1 AAAATTAAAAAG
6481306 AAAATTAAAAAG
1 AAAATTAAAAAG
6481318 AAA
1 AAA
6481321 CTAAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (12 bp):
AAAATTAAAAAG
Found at i:6481658 original size:23 final size:23
Alignment explanation
Indices: 6481631--6481674 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
6481621 TCTCTCTCTT
6481631 TCTCTAAAAC-CAAACCAATTCTC
1 TCTCT-AAACTCAAACCAATTCTC
6481654 TCTCTAAACTCAAACCAATTC
1 TCTCTAAACTCAAACCAATTC
6481675 ACAAACATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.39, C:0.34, G:0.00, T:0.27
Consensus pattern (23 bp):
TCTCTAAACTCAAACCAATTCTC
Found at i:6484587 original size:66 final size:66
Alignment explanation
Indices: 6484480--6484603 Score: 169
Period size: 66 Copynumber: 1.9 Consensus size: 66
6484470 GCTAATCTCT
* * * *
6484480 ACTAGTCCTATAGGGTGTTTATCCCATAAAATCCTACAACTCTTTTACATCTTTTTCTCATGTTT
1 ACTAGTCCTATAGGATGTCTATCCCATAAAATCCTACAACTCTCTTACACCTTTTTCTCATGTTT
6484545 A
66 A
* * *
6484546 ACTAGTCCTAT-GTGATGTCTATCTCATAAAATCTTATAACTCTCTTACACCTTTTTCT
1 ACTAGTCCTATAG-GATGTCTATCCCATAAAATCCTACAACTCTCTTACACCTTTTTCT
6484604 TATACTTAAC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 1 0.02
66 49 0.98
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.43
Consensus pattern (66 bp):
ACTAGTCCTATAGGATGTCTATCCCATAAAATCCTACAACTCTCTTACACCTTTTTCTCATGTTT
A
Found at i:6484712 original size:89 final size:89
Alignment explanation
Indices: 6484561--6484737 Score: 291
Period size: 89 Copynumber: 2.0 Consensus size: 89
6484551 TCCTATGTGA
* *
6484561 TGTCTATCTCATAAAATCTTATAACTCTCTTACACCTTTTTCTTATACTTAACCCTATAGAGACT
1 TGTCTATCCCATAAAATCTTATAACTCTCTTACACATTTTTCTTATACTTAACCCTATAGAGACT
*
6484626 TCGCCTATTTATTAGTATACAAAG
66 TCACCTATTTATTAGTATACAAAG
* * *
6484650 TGTCTATCCCATAAAATCTTATAATTCTCTTACATATTTTTCTTATACTTAACCTTATAGAGACT
1 TGTCTATCCCATAAAATCTTATAACTCTCTTACACATTTTTCTTATACTTAACCCTATAGAGACT
*
6484715 TCACCTATTTGTTAGTATACAAA
66 TCACCTATTTATTAGTATACAAA
6484738 CTTACCTATT
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
89 81 1.00
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (89 bp):
TGTCTATCCCATAAAATCTTATAACTCTCTTACACATTTTTCTTATACTTAACCCTATAGAGACT
TCACCTATTTATTAGTATACAAAG
Found at i:6488412 original size:63 final size:62
Alignment explanation
Indices: 6488204--6488477 Score: 199
Period size: 63 Copynumber: 4.3 Consensus size: 62
6488194 AAATTGAATA
* * * * * * *
6488204 GGATTATTAAATGCATTTATGGCTAAAAACATCTTCAATAATCTATTCAAAAAATTTGGAGAG
1 GGATTATTAAAGGCATTTTTGACCAAAAACACCTTCAATAATCTATACAAAAAATTTTGA-AG
** * * * * ** * * * *
6488267 AAAATATTGAAGGCATTTTTGATCGAAAATGCTTTAAATAATCCTCTA-AAAAAATTTTTAAG
1 GGATTATTAAAGGCATTTTTGACCAAAAACACCTTCAATAAT-CTATACAAAAAATTTTGAAG
* * * *
6488329 GGATTATTGAAGGCGTTTTTGACCAAAAATACCTTCAATAATCTATACAAAAAGTTTTGAAG
1 GGATTATTAAAGGCATTTTTGACCAAAAACACCTTCAATAATCTATACAAAAAATTTTGAAG
* * * * * * *
6488391 TGGATTATTAAAGGTATTTTTGTCTATAAACGCCTTCAATAATCCATACAAAAAATTTTGTTGAG
1 -GGATTATTAAAGGCATTTTTGACCAAAAACACCTTCAATAATCTATACAAAAAA--TT-TTGAA
6488456 G
62 G
* *
6488457 GGATTATAAAAGGCAATTTTG
1 GGATTATTAAAGGCATTTTTG
6488478 GCAAAAAATA
Statistics
Matches: 160, Mismatches: 45, Indels: 10
0.74 0.21 0.05
Matches are distributed among these distances:
61 4 0.03
62 47 0.29
63 81 0.51
64 3 0.02
65 20 0.12
66 5 0.03
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (62 bp):
GGATTATTAAAGGCATTTTTGACCAAAAACACCTTCAATAATCTATACAAAAAATTTTGAAG
Found at i:6495612 original size:24 final size:25
Alignment explanation
Indices: 6495580--6495627 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
6495570 TTATCAATAA
*
6495580 TTATCA-TTTACAAAGAATGTTATT
1 TTATCATTTTAAAAAGAATGTTATT
*
6495604 TTATTATTTTAAAAAGAATGTTAT
1 TTATCATTTTAAAAAGAATGTTAT
6495628 GATAAATCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (25 bp):
TTATCATTTTAAAAAGAATGTTATT
Found at i:6496242 original size:58 final size:60
Alignment explanation
Indices: 6496168--6496308 Score: 153
Period size: 62 Copynumber: 2.4 Consensus size: 60
6496158 TTTTCAAGGC
* * * *
6496168 AAAAATGCCTTTAATAATCCAAAAAAAAATT-CA-TGGATTATTGGAGGCATTTTT-GAT
1 AAAAATGCCTTCAATAATCCAAAAAAAAATTGAAGGGGATTATTGAAGGCATTTTTAGAT
** *
6496225 AGAAAATGCCTTCAATAATCCCCACTAAAAAATTGAAGGGGATTATTGAAGGCATTTTTAGCT
1 A-AAAATGCCTTCAATAAT--CCAAAAAAAAATTGAAGGGGATTATTGAAGGCATTTTTAGAT
* *
6496288 AAAAAAGCCTTCAACAATCCA
1 AAAAATGCCTTCAATAATCCA
6496309 TGAATTATTG
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
57 1 0.01
58 16 0.23
60 14 0.20
61 1 0.01
62 34 0.49
63 3 0.04
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (60 bp):
AAAAATGCCTTCAATAATCCAAAAAAAAATTGAAGGGGATTATTGAAGGCATTTTTAGAT
Found at i:6496942 original size:63 final size:62
Alignment explanation
Indices: 6496843--6497248 Score: 221
Period size: 63 Copynumber: 6.5 Consensus size: 62
6496833 TAATCCATGA
* * *
6496843 ATTATTCATGGCATTTT-TAGCCAAAAAATGCCTTCAATAATCCCATTCAATATTTTGTAAAGG
1 ATTATTCAAGGCATTTTCTAG-CTAAAAATGCCTTCAATAATCCCA-TCAATATATTGTAAAGG
* *
6496906 ATTATTCAAGGCATTTTCTAGCTAAAAATGCCTTCAATAATCCCATCTAGA-AAATTGAAAAGG
1 ATTATTCAAGGCATTTTCTAGCTAAAAATGCCTTCAATAATCCCATC-A-ATATATTGTAAAGG
* * ** * * * * * * *
6496969 ATTATTGAAGGCGTTTTCTAGCCCAAAATGCCTT-GATTAT-TCA-AAAAAAAATGCT-AA-G
1 ATTATTCAAGGCATTTTCTAGCTAAAAATGCCTTCAATAATCCCATCAATATATTG-TAAAGG
* * * * * *
6497027 ATTATTGAAGGCATTTTTTTA-CGAAAAACGCCTTCATTAATCTCCAATGAATGAATAATT-T-A
1 ATTATTCAAGGCA-TTTTCTAGCTAAAAATGCCTTCAATAATC-CC-ATCAAT--AT-ATTGTAA
6497089 AGG
60 AGG
* * * * * * *
6497092 GTTATAT-AAGGCATTTT-T-GATCAAAAATACCTTTAATAACCCCATTCAATATTTTGTAAGGG
1 ATTAT-TCAAGGCATTTTCTAGCT-AAAAATGCCTTCAATAATCCCA-TCAATATATTGTAAAGG
* ** * *
6497154 ATTATTCAAGGTATTTTCTAGCTAAAAATGCCTTCAATAATCCTTTCTAAAAAATTG-AAAGGG
1 ATTATTCAAGGCATTTTCTAGCTAAAAATGCCTTCAATAATCCCATC-AATATATTGTAAA-GG
* * *
6497217 ATTATTAAAGGCGTTTTCT-GACCAAAAATGCC
1 ATTATTCAAGGCATTTTCTAG-CTAAAAATGCC
6497249 ATGATTATTC
Statistics
Matches: 261, Mismatches: 55, Indels: 54
0.71 0.15 0.15
Matches are distributed among these distances:
58 24 0.09
59 17 0.07
60 2 0.01
61 7 0.03
62 29 0.11
63 140 0.54
64 27 0.10
65 12 0.05
66 3 0.01
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (62 bp):
ATTATTCAAGGCATTTTCTAGCTAAAAATGCCTTCAATAATCCCATCAATATATTGTAAAGG
Found at i:6497545 original size:62 final size:63
Alignment explanation
Indices: 6497439--6497608 Score: 166
Period size: 63 Copynumber: 2.7 Consensus size: 63
6497429 AATATTTTGT
* * * * * * *
6497439 AAGGGATTATTCAAGGTATTTTCT-AGCTAAAAACACCTTTAATAATC-CCATCTAAAAAA-ATG
1 AAGGGATTATTAAAGGTATTTT-TGA-CCAAAAATACCTTCAATAATCTACATATAAAAAATATA
* * * * *
6497501 GAGGGAATTATTGAAGGTGTTTTTGACCAAAAATACCTTCAATAATCTACTTATAAAAAATCTA
1 AAGGG-ATTATTAAAGGTATTTTTGACCAAAAATACCTTCAATAATCTACATATAAAAAATATA
* *
6497565 AAGGGATTATTAAAGGTATTTTTGACCAAAAATGCTTTCAATAA
1 AAGGGATTATTAAAGGTATTTTTGACCAAAAATACCTTCAATAA
6497609 CCCTATTCAA
Statistics
Matches: 88, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
62 23 0.26
63 60 0.68
64 5 0.06
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (63 bp):
AAGGGATTATTAAAGGTATTTTTGACCAAAAATACCTTCAATAATCTACATATAAAAAATATA
Found at i:6497746 original size:188 final size:188
Alignment explanation
Indices: 6497394--6497749 Score: 416
Period size: 188 Copynumber: 1.9 Consensus size: 188
6497384 TACTCAAGAC
* *
6497394 ATTTTTAACCAGAAATGCCTTCAATAACCCCATTCAATATTTTGTAAGGGATTATTCAAGGTATT
1 ATTTTTAACCAAAAATGCCTTCAATAACCCCATTCAATATTTTATAAGGGATTATTCAAGGTATT
* * ***
6497459 TTCTAGCTAAAAACACCTTTAATAATCCCATCTAAAAAAATGGAGGGAATTATTGAAGGTGTTTT
66 TTCTAGCTAAAAACACCTTGAATAATCCCATCTAAAAAAATAGAGGGAATTATTGAAGGCACTTT
* * *
6497524 TGACCAAAAATACCTTCAATAATCTACTTATAAAAAATCTAAAGGGATTATTAAAGGT
131 TGACCAAAAATACCCTCAATAATATACCTATAAAAAATCTAAAGGGATTATTAAAGGT
* * * * * *
6497582 ATTTTTGACCAAAAATGCTTTCAATAACCCTATTCAATTTTTTATAAGGGATTATTTAAGGTGTT
1 ATTTTTAACCAAAAATGCCTTCAATAACCCCATTCAATATTTTATAAGGGATTATTCAAGGTATT
* ** * * * *
6497647 TTTTAGGCT-AAAATGCCTTGATTAATCCCTGTCT-AAAAAATAGAGGGGATTGTTGAAGGCACT
66 TTCTA-GCTAAAAACACCTTGAATAATCCC-ATCTAAAAAAATAGAGGGAATTATTGAAGGCACT
*
6497710 TTTG-GCAGAAAA-ACGCCTCGAATAATAT-CCTATAAAAAAT
129 TTTGACCA-AAAATAC-CCTC-AATAATATACCTATAAAAAAT
6497750 TAGAAGGAAT
Statistics
Matches: 139, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
187 4 0.03
188 122 0.88
189 13 0.09
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (188 bp):
ATTTTTAACCAAAAATGCCTTCAATAACCCCATTCAATATTTTATAAGGGATTATTCAAGGTATT
TTCTAGCTAAAAACACCTTGAATAATCCCATCTAAAAAAATAGAGGGAATTATTGAAGGCACTTT
TGACCAAAAATACCCTCAATAATATACCTATAAAAAATCTAAAGGGATTATTAAAGGT
Found at i:6505626 original size:55 final size:55
Alignment explanation
Indices: 6505508--6505652 Score: 155
Period size: 55 Copynumber: 2.6 Consensus size: 55
6505498 CAAAATATAA
* * *
6505508 TAACAAAATTAAAACATATAAGTTTATACTGACAATCTCTAACCATCAGTAAAAG
1 TAACAAAATTAAAACATACAAGTTTATACTAACAATATCTAACCATCAGTAAAAG
* * * * * * * *
6505563 TAAGAAAATTAAAGCATACAATTTTATATTAACAGTATCTAACCGTCAGTATAGG
1 TAACAAAATTAAAACATACAAGTTTATACTAACAATATCTAACCATCAGTAAAAG
* * *
6505618 TAACAAAATAAAAAAAATACAAGTCTATACTAACA
1 TAACAAAAT-TAAAACATACAAGTTTATACTAACA
6505653 GATGCTAAGC
Statistics
Matches: 71, Mismatches: 18, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
55 52 0.73
56 19 0.27
ACGTcount: A:0.50, C:0.14, G:0.08, T:0.27
Consensus pattern (55 bp):
TAACAAAATTAAAACATACAAGTTTATACTAACAATATCTAACCATCAGTAAAAG
Found at i:6506422 original size:18 final size:18
Alignment explanation
Indices: 6506395--6506434 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
6506385 TACATAATCA
6506395 TATATGTGTATGTATATG
1 TATATGTGTATGTATATG
* *
6506413 TATATTTGTATGTATTTG
1 TATATGTGTATGTATATG
6506431 TATA
1 TATA
6506435 CATACATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (18 bp):
TATATGTGTATGTATATG
Found at i:6506565 original size:3 final size:3
Alignment explanation
Indices: 6506559--6506591 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
6506549 AATGATGATG
6506559 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6506592 TTATTATCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:6506769 original size:44 final size:39
Alignment explanation
Indices: 6506679--6506759 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 39
6506669 TTTATGTATT
*
6506679 TTTAAATATATAATTTAATATATTGTTATCAACAAAATC
1 TTTAAATATATAATATAATATATTGTTATCAACAAAATC
* *
6506718 TGTAAATA-ATAATAATAATTAGTATTGTTGTCAACAAAATC
1 TTTAAATATATAAT-ATAA-TA-TATTGTTATCAACAAAATC
6506759 T
1 T
6506760 AATTTAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 5 0.14
39 10 0.28
40 2 0.06
41 19 0.53
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (39 bp):
TTTAAATATATAATATAATATATTGTTATCAACAAAATC
Found at i:6507257 original size:26 final size:26
Alignment explanation
Indices: 6507208--6507258 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
6507198 AATTATTTTT
* * *
6507208 AAAATTGATTTCTTGATTACTTAAAG
1 AAAATAGATTTATTGATAACTTAAAG
*
6507234 AAAATAGATTTATTGATAATTTAAA
1 AAAATAGATTTATTGATAACTTAAA
6507259 TGTATATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (26 bp):
AAAATAGATTTATTGATAACTTAAAG
Found at i:6510445 original size:18 final size:18
Alignment explanation
Indices: 6510422--6510461 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
6510412 AAATGCCTTC
6510422 ATTAATCCAATCTAAAAA
1 ATTAATCCAATCTAAAAA
*
6510440 ATTAATCCCATCTAAAAA
1 ATTAATCCAATCTAAAAA
6510458 ATTA
1 ATTA
6510462 GAAAGGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (18 bp):
ATTAATCCAATCTAAAAA
Found at i:6510818 original size:61 final size:61
Alignment explanation
Indices: 6510701--6510818 Score: 136
Period size: 61 Copynumber: 1.9 Consensus size: 61
6510691 TTTTTTGTAA
* *
6510701 AGGATTATTAAAGGCATTTTCTAGGCTAAAATGCCTTGAATAATCCTTTCATAAAAAATGG
1 AGGATTATTAAAGGCATTTTCTAGGCTAAAACGCCTTGAATAATCCTTTCAAAAAAAATGG
* *
6510762 AGGATTATTAAAGGTATTTT-T-GG-TAGAAAACGCCTTTAATAATCTCTTAT-AAAAAAA
1 AGGATTATTAAAGGCATTTTCTAGGCT--AAAACGCCTTGAATAATC-CTT-TCAAAAAAA
6510819 TTTTAAGGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
58 1 0.02
59 2 0.04
60 17 0.35
61 28 0.57
62 1 0.02
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (61 bp):
AGGATTATTAAAGGCATTTTCTAGGCTAAAACGCCTTGAATAATCCTTTCAAAAAAAATGG
Found at i:6515395 original size:68 final size:68
Alignment explanation
Indices: 6515248--6515374 Score: 200
Period size: 68 Copynumber: 1.9 Consensus size: 68
6515238 GCATTACACT
* * * *
6515248 AATGAATATGATGTTTATAAAATTATTTTTACTGCTATATAAATGGATGATTATCTTTTGTATAT
1 AATGAATAAGATGTTTATAAAATTATTTCTACTGCTATATAAATGGATGATTAACTTCTGTATAT
6515313 ATG
66 ATG
* *
6515316 AATGAATAAGATGTTTATAAAATTATTTCTACTGGTATATGAATGGATGATTAACTTCT
1 AATGAATAAGATGTTTATAAAATTATTTCTACTGCTATATAAATGGATGATTAACTTCT
6515375 TACTTTTTGT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 53 1.00
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (68 bp):
AATGAATAAGATGTTTATAAAATTATTTCTACTGCTATATAAATGGATGATTAACTTCTGTATAT
ATG
Found at i:6516283 original size:55 final size:55
Alignment explanation
Indices: 6516196--6516341 Score: 161
Period size: 55 Copynumber: 2.7 Consensus size: 55
6516186 TTGTCAATAA
* * * *
6516196 AATATAA-T-AAAAAATTAAAACATATAAGTCTATACTGATAATTTCTAACTGTT
1 AATATAAGTAAAAAAATCAAAACATATAAGTCTATACTGACAATCTCTAACTGTC
* * *
6516249 AATATAAGTAAAAAAATCAAAGCATATAATTCTATACTGACACTCTCTAACTGTC
1 AATATAAGTAAAAAAATCAAAACATATAAGTCTATACTGACAATCTCTAACTGTC
* * * * * *
6516304 AGTATAGGTAAGAAAATTAAAAAATACAAGTCTATACT
1 AATATAAGTAAAAAAATCAAAACATATAAGTCTATACT
6516342 AATGGATGTT
Statistics
Matches: 76, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
53 7 0.09
54 1 0.01
55 68 0.89
ACGTcount: A:0.49, C:0.12, G:0.08, T:0.31
Consensus pattern (55 bp):
AATATAAGTAAAAAAATCAAAACATATAAGTCTATACTGACAATCTCTAACTGTC
Found at i:6517247 original size:12 final size:12
Alignment explanation
Indices: 6517230--6517254 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6517220 ACATTTTTAC
6517230 TAATGACATTTT
1 TAATGACATTTT
6517242 TAATGACATTTT
1 TAATGACATTTT
6517254 T
1 T
6517255 GTAATTTGAT
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:0.32, C:0.08, G:0.08, T:0.52
Consensus pattern (12 bp):
TAATGACATTTT
Found at i:6517354 original size:7 final size:7
Alignment explanation
Indices: 6517298--6517397 Score: 51
Period size: 7 Copynumber: 14.3 Consensus size: 7
6517288 CTCAAATTTA
*
6517298 AAACCTT
1 AAACCCT
*
6517305 AAATCCT
1 AAACCCT
*
6517312 AAATCCT
1 AAACCCT
6517319 AAACCAC-
1 AAACC-CT
*
6517326 AAACCCC
1 AAACCCT
* *
6517333 AAACTCA
1 AAACCCT
*
6517340 AAATCCT
1 AAACCCT
6517347 AAACCCT
1 AAACCCT
*
6517354 AAACCTT
1 AAACCCT
*
6517361 AAA-TCT
1 AAACCCT
**
6517367 CAAACTTT
1 -AAACCCT
**
6517375 AAACTTT
1 AAACCCT
6517382 AAACCCT
1 AAACCCT
6517389 AAACCCT
1 AAACCCT
6517396 AA
1 AA
6517398 CTTAGACCTA
Statistics
Matches: 74, Mismatches: 15, Indels: 8
0.76 0.15 0.08
Matches are distributed among these distances:
6 2 0.03
7 69 0.93
8 3 0.04
ACGTcount: A:0.46, C:0.32, G:0.00, T:0.22
Consensus pattern (7 bp):
AAACCCT
Found at i:6517364 original size:21 final size:21
Alignment explanation
Indices: 6517340--6517397 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
6517330 CCCAAACTCA
6517340 AAATCCTAAACCCTAAACCTT
1 AAATCCTAAACCCTAAACCTT
** *
6517361 AAAT-CTCAAACTTTAAACTTT
1 AAATCCT-AAACCCTAAACCTT
*
6517382 AAACCCTAAACCCTAA
1 AAATCCTAAACCCTAA
6517398 CTTAGACCTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (21 bp):
AAATCCTAAACCCTAAACCTT
Found at i:6519501 original size:16 final size:18
Alignment explanation
Indices: 6519482--6519518 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6519472 ATTATCCTTC
6519482 TTTAAAGT-TT-ATATAA
1 TTTAAAGTATTGATATAA
*
6519498 TTTAAATTATTGATATAA
1 TTTAAAGTATTGATATAA
6519516 TTT
1 TTT
6519519 TTAAATGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
TTTAAAGTATTGATATAA
Found at i:6522106 original size:14 final size:14
Alignment explanation
Indices: 6522072--6522123 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
6522062 ATAAAATTTT
*
6522072 ATAAAATCTA-AAA
1 ATAAAATTTATAAA
* **
6522085 ATATAATTTATGCA
1 ATAAAATTTATAAA
6522099 ATAAAATTTATAAA
1 ATAAAATTTATAAA
6522113 ATAAAAATTTA
1 AT-AAAATTTA
6522124 AAAGCAATAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
13 8 0.27
14 14 0.47
15 8 0.27
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.35
Consensus pattern (14 bp):
ATAAAATTTATAAA
Found at i:6527139 original size:17 final size:16
Alignment explanation
Indices: 6527117--6527148 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6527107 TCGACATCCC
*
6527117 AAAAAAATTCCCAAAA
1 AAAAAAAATCCCAAAA
6527133 AAAAAAAATCCCAAAA
1 AAAAAAAATCCCAAAA
6527149 CACTTATCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.19, G:0.00, T:0.09
Consensus pattern (16 bp):
AAAAAAAATCCCAAAA
Found at i:6527608 original size:12 final size:12
Alignment explanation
Indices: 6527581--6527621 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
6527571 GGGAAAACGG
6527581 AAGAAGAAAAAGAA
1 AAGAA-AAAAA-AA
6527595 AAGAAAAAAAAA
1 AAGAAAAAAAAA
*
6527607 AAGAAAGAAAAA
1 AAGAAAAAAAAA
6527619 AAG
1 AAG
6527622 GGAATATCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 16 0.62
13 5 0.19
14 5 0.19
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAGAAAAAAAAA
Found at i:6527613 original size:16 final size:17
Alignment explanation
Indices: 6527587--6527620 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
6527577 ACGGAAGAAG
6527587 AAAAAGAAAAGAAAAAA
1 AAAAAGAAAAGAAAAAA
6527604 AAAAAG-AAAGAAAAAA
1 AAAAAGAAAAGAAAAAA
6527620 A
1 A
6527621 GGGAATATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (17 bp):
AAAAAGAAAAGAAAAAA
Found at i:6528172 original size:33 final size:34
Alignment explanation
Indices: 6528131--6528251 Score: 113
Period size: 34 Copynumber: 3.6 Consensus size: 34
6528121 AAAGCTCATT
**
6528131 TAACTAGAGGCTATGGCACTTTAAAA-AC-TCTTA
1 TAACTAGAGGCTATGAAACTTTAAAACACTTC-TA
*
6528164 TAACTAGAGG-TGATAAAACTTTAAAACACTTCTA
1 TAACTAGAGGCT-ATGAAACTTTAAAACACTTCTA
* * *
6528198 TAACTAGAGGCCATGAAACTTTAAAAGAACTTCTC
1 TAACTAGAGGCTATGAAACTTTAAAA-CACTTCTA
* * *
6528233 CAATTAAAGGCTATGAAAC
1 TAACTAGAGGCTATGAAAC
6528252 CTCTTTTTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
32 1 0.01
33 21 0.29
34 27 0.38
35 23 0.32
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.27
Consensus pattern (34 bp):
TAACTAGAGGCTATGAAACTTTAAAACACTTCTA
Found at i:6528249 original size:35 final size:34
Alignment explanation
Indices: 6528179--6528251 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 34
6528169 AGAGGTGATA
* * *
6528179 AAACTTTAAAACACTTCTATAACTAGAGGCCATG
1 AAACTTTAAAAAACTTCTACAACTAAAGGCCATG
* * *
6528213 AAACTTTAAAAGAACTTCTCCAATTAAAGGCTATG
1 AAACTTTAAAA-AACTTCTACAACTAAAGGCCATG
6528248 AAAC
1 AAAC
6528252 CTCTTTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 11 0.34
35 21 0.66
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.26
Consensus pattern (34 bp):
AAACTTTAAAAAACTTCTACAACTAAAGGCCATG
Found at i:6528535 original size:34 final size:34
Alignment explanation
Indices: 6528416--6528562 Score: 118
Period size: 34 Copynumber: 4.3 Consensus size: 34
6528406 CCCAGATGCT
*
6528416 ATGATACTTGAAAAAAACTTCTCTAACTAGAGGCA
1 ATGATACTT-AAAAAAACTTCTCTAACTAAAGGCA
* ** * * *
6528451 ATGGAT-TTTAAAGGAACTTCTTTAACCAAAAGGCT
1 AT-GATACTTAAAAAAACTTCTCTAA-CTAAAGGCA
* ** * *
6528486 ATGACACTTTGAAAAACTCCTCTAACTAAAGGTA
1 ATGATACTTAAAAAAACTTCTCTAACTAAAGGCA
* *
6528520 ATGATACTTAAAAAAACTAT-TCTAATTAGAGGCA
1 ATGATACTTAAAAAAACT-TCTCTAACTAAAGGCA
6528554 ATGATACTT
1 ATGATACTT
6528563 GAAATTAAAT
Statistics
Matches: 83, Mismatches: 25, Indels: 9
0.71 0.21 0.08
Matches are distributed among these distances:
34 56 0.67
35 24 0.29
36 3 0.04
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (34 bp):
ATGATACTTAAAAAAACTTCTCTAACTAAAGGCA
Found at i:6528696 original size:33 final size:33
Alignment explanation
Indices: 6528659--6528810 Score: 139
Period size: 33 Copynumber: 4.6 Consensus size: 33
6528649 GGCTCTTAAA
* * *
6528659 TTTAAAAACTCCTATAACCAGAGGTTATGATAC
1 TTTAAAAACTCCTCTAACCAGAAGCTATGATAC
* * * *
6528692 TTTAAAACCTCCTCTAACTAGAAGCAATGAT-T
1 TTTAAAAACTCCTCTAACCAGAAGCTATGATAC
**
6528724 TTTAAAAACTTATCTAACCAGAAGCTATGATAC
1 TTTAAAAACTCCTCTAACCAGAAGCTATGATAC
* * *
6528757 TTTAAAGACTCCTCTAACCA-ACGATTATAGA-AC
1 TTTAAAAACTCCTCTAACCAGAAG-CTAT-GATAC
*
6528790 TTTAAAAGATTCCTCTAACCA
1 TTTAAAA-ACTCCTCTAACCA
6528811 TAAACAATGG
Statistics
Matches: 95, Mismatches: 20, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
32 28 0.29
33 53 0.56
34 14 0.15
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.30
Consensus pattern (33 bp):
TTTAAAAACTCCTCTAACCAGAAGCTATGATAC
Found at i:6528804 original size:34 final size:32
Alignment explanation
Indices: 6528755--6528845 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 32
6528745 AAGCTATGAT
* * **
6528755 ACTTTAAAGACTCCTCTAACCAACGATTATAGA
1 ACTTTAAAGATTCCTCTAACCAA-AACAATAGA
*
6528788 ACTTTAAAAGATTCCTCTAACCATAAACAATGGA
1 ACTTT-AAAGATTCCTCTAACCA-AAACAATAGA
6528822 A-TTTGAAAGATTCCTCTAACCAAA
1 ACTTT-AAAGATTCCTCTAACCAAA
6528846 TGCATTATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
32 2 0.04
33 25 0.50
34 22 0.44
35 1 0.02
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.27
Consensus pattern (32 bp):
ACTTTAAAGATTCCTCTAACCAAAACAATAGA
Found at i:6531247 original size:3 final size:3
Alignment explanation
Indices: 6531239--6531264 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6531229 ATTAAATATA
6531239 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
6531265 AATCACAAAA
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:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:6533376 original size:34 final size:34
Alignment explanation
Indices: 6533298--6533377 Score: 83
Period size: 34 Copynumber: 2.4 Consensus size: 34
6533288 TGTTTGCGTA
*
6533298 TAATTTGAA-TTTTATGCATATTTAATTTTCTTAT
1 TAATTT-AATTTTTATGCATATTTAAGTTTCTTAT
** * *
6533332 TAATGAAATTTTTATGCTTATTTTAGTTT-TTAT
1 TAATTTAATTTTTATGCATATTTAAGTTTCTTAT
6533365 GTAATTTAATTTT
1 -TAATTTAATTTT
6533378 CATGTTGTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
33 6 0.16
34 31 0.84
ACGTcount: A:0.29, C:0.04, G:0.07, T:0.60
Consensus pattern (34 bp):
TAATTTAATTTTTATGCATATTTAAGTTTCTTAT
Found at i:6533614 original size:14 final size:17
Alignment explanation
Indices: 6533594--6533634 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 17
6533584 GGAGAATTAT
6533594 TAAATAATAAA-ATA-A
1 TAAATAATAAAGATAGA
6533609 -AAATAATGAAAGATAGA
1 TAAATAAT-AAAGATAGA
6533626 TAAATAATA
1 TAAATAATA
6533635 TTAATAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 7 0.32
15 3 0.14
16 3 0.14
17 2 0.09
18 7 0.32
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.24
Consensus pattern (17 bp):
TAAATAATAAAGATAGA
Found at i:6533781 original size:13 final size:13
Alignment explanation
Indices: 6533763--6533807 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
6533753 TTTGTGAAAT
6533763 CCTAAAATAGAAC
1 CCTAAAATAGAAC
* *
6533776 CCTAAAATAAAAA
1 CCTAAAATAGAAC
6533789 CCTAAAAT-GAAAC
1 CCTAAAATAG-AAC
6533802 CCTAAA
1 CCTAAA
6533808 CTTTAGGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.58, C:0.22, G:0.04, T:0.16
Consensus pattern (13 bp):
CCTAAAATAGAAC
Found at i:6533851 original size:20 final size:20
Alignment explanation
Indices: 6533823--6533861 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
6533813 GGTAAAATAC
6533823 AAAACCCTAAATGAAACCTT
1 AAAACCCTAAATGAAACCTT
* *
6533843 AAAATCCTAAGTGAAACCT
1 AAAACCCTAAATGAAACCT
6533862 GAAACCTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.23, G:0.08, T:0.21
Consensus pattern (20 bp):
AAAACCCTAAATGAAACCTT
Found at i:6533882 original size:26 final size:27
Alignment explanation
Indices: 6533834--6533886 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
6533824 AAACCCTAAA
6533834 TGAAACCTTAAAATCCTAAGTGAAACC
1 TGAAACCTTAAAATCCTAAGTGAAACC
* *
6533861 TGAAACCTT-AAATTCTAGGTGAAACC
1 TGAAACCTTAAAATCCTAAGTGAAACC
6533887 CAAAACCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.25
Consensus pattern (27 bp):
TGAAACCTTAAAATCCTAAGTGAAACC
Found at i:6533892 original size:26 final size:27
Alignment explanation
Indices: 6533836--6533893 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 27
6533826 ACCCTAAATG
**
6533836 AAACCTTAAAATCCTAAGTGAAACCTG
1 AAACCTTAAAATCCTAAGTGAAACCCA
* *
6533863 AAACCTT-AAATTCTAGGTGAAACCCA
1 AAACCTTAAAATCCTAAGTGAAACCCA
6533889 AAACC
1 AAACC
6533894 CTAGGCCTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
26 20 0.74
27 7 0.26
ACGTcount: A:0.45, C:0.24, G:0.10, T:0.21
Consensus pattern (27 bp):
AAACCTTAAAATCCTAAGTGAAACCCA
Found at i:6534992 original size:12 final size:13
Alignment explanation
Indices: 6534975--6535003 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
6534965 TAATTTTCCA
6534975 AAATAAAT-AAAT
1 AAATAAATAAAAT
6534987 AAATAAATAAAAT
1 AAATAAATAAAAT
6535000 AAAT
1 AAAT
6535004 TGCATGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:6539615 original size:17 final size:17
Alignment explanation
Indices: 6539585--6539618 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
6539575 AGGAGGCATG
* *
6539585 TAAAAGAAATAAAAAAA
1 TAAAACAAAGAAAAAAA
6539602 TAAAACAAAGAAAAAAA
1 TAAAACAAAGAAAAAAA
6539619 AGACAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.03, G:0.06, T:0.09
Consensus pattern (17 bp):
TAAAACAAAGAAAAAAA
Found at i:6541078 original size:32 final size:32
Alignment explanation
Indices: 6541041--6541114 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 32
6541031 GCACCCAGGT
*
6541041 TTTAAGCCCACATTATCTAGCA-CTAATGAA-A
1 TTTAAGCCCACATTAGCTAGCATC-AATGAAGA
* **
6541072 TCTTAAGCCTATTTTAGCTAGCATCAATGAAGA
1 T-TTAAGCCCACATTAGCTAGCATCAATGAAGA
6541105 TTTAAGCCCA
1 TTTAAGCCCA
6541115 GCTTAGTTGG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
31 1 0.03
32 31 0.89
33 3 0.09
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (32 bp):
TTTAAGCCCACATTAGCTAGCATCAATGAAGA
Found at i:6541482 original size:32 final size:32
Alignment explanation
Indices: 6541419--6541492 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
6541409 TCAAGAAAAG
**
6541419 ATTTAAACCTAGCTTAGTTGGTACCCAATGAA
1 ATTTAAACCTAGCTTAGTTGACACCCAATGAA
* * * *
6541451 ATTTAAGCCTAGTTTAGTTGACACTCGATGAA
1 ATTTAAACCTAGCTTAGTTGACACCCAATGAA
6541483 AGTTTAAACC
1 A-TTTAAACC
6541493 CAGATTATCT
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 27 0.79
33 7 0.21
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (32 bp):
ATTTAAACCTAGCTTAGTTGACACCCAATGAA
Found at i:6541866 original size:33 final size:32
Alignment explanation
Indices: 6541821--6541905 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 32
6541811 TAGTTGGTAC
* *
6541821 CCAATG-AAATTTAAGCCTAATTTAACTAGCA
1 CCAATGAAAATTTAAGCCCAAATTAACTAGCA
** *
6541852 CCTAATGAAAATTTAAGCCCAAATTATTTGGCA
1 CC-AATGAAAATTTAAGCCCAAATTAACTAGCA
*
6541885 CCAATAAAAATTTAAGCCCAA
1 CCAATGAAAATTTAAGCCCAA
6541906 TATAGCTTGC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
31 2 0.04
32 22 0.48
33 22 0.48
ACGTcount: A:0.44, C:0.20, G:0.09, T:0.27
Consensus pattern (32 bp):
CCAATGAAAATTTAAGCCCAAATTAACTAGCA
Found at i:6542010 original size:23 final size:23
Alignment explanation
Indices: 6541951--6542016 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
6541941 TATGAAAATT
6541951 TAAGCCC-AATTTAGTTGGCACA
1 TAAGCCCAAATTTAGTTGGCACA
* * *
6541973 TAAGCCTAGAA-TTAGTTGGTACG
1 TAAGCCCA-AATTTAGTTGGCACA
*
6541996 TAAGCCCAAATTTAGCTGGCA
1 TAAGCCCAAATTTAGTTGGCA
6542017 TGAAAGCTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
22 8 0.23
23 25 0.71
24 2 0.06
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (23 bp):
TAAGCCCAAATTTAGTTGGCACA
Found at i:6546893 original size:244 final size:244
Alignment explanation
Indices: 6546464--6546948 Score: 727
Period size: 244 Copynumber: 2.0 Consensus size: 244
6546454 TAGTATTTTA
* ** * *
6546464 GATTCTAGAATCTTGTTGTGACCTTCAGCATTTGATTGTTAGGTTTCACCATTACCTACAAAGTA
1 GATTCTAGAATCTTATTACGACCTTCAGCATTTGATTGTTAGGTTTCACCATTACCAACAAAGCA
* * * *
6546529 ATATCTCTGTACTTAACTGTGAAAGCTACTTTTATTTTTGGGTCCTATTGACTCTAAACACTCTC
66 ATATCTCTGTACTTAACTATGAAAGCTACCTTCATTTTTGGGTCCTATTGACTCCAAACACTCTC
* * * **
6546594 CAAATTTGTTGTAACATTCTGTCTTAAGTTTATATACACCATTTTCGGAAGGCTTGCAACATATG
131 CAAATTTGCTATAACATTCTGTCTTAAGTTTATATACACCATCTTCGGAAGGCTTGCAACATACC
* **
6546659 CATCCATCAAACAGTTTTTTTCTATTTGTTGCCTATTTTCTAACTATTG
196 CATCCATCAAACAGTCTGATTCTATTTGTTGCCTATTTTCTAACTATTG
* *
6546708 GATTCTAGAATCTTATTACGACCTTCAGCATTTGATTGTTAGGTTTCACCATTGCCAACAAGGCA
1 GATTCTAGAATCTTATTACGACCTTCAGCATTTGATTGTTAGGTTTCACCATTACCAACAAAGCA
* * * *
6546773 ATATCTCTGTACTTAACTATGAAAGTTGCCTTCATTTTTGGGTCTTATTGACTCCAAATACTCTC
66 ATATCTCTGTACTTAACTATGAAAGCTACCTTCATTTTTGGGTCCTATTGACTCCAAACACTCTC
* *
6546838 TAAATTTGCTATAACATTCTGTCTTAAGTTTATATGCACCATCTTCGGAAGGCTTGCAACATACC
131 CAAATTTGCTATAACATTCTGTCTTAAGTTTATATACACCATCTTCGGAAGGCTTGCAACATACC
* *
6546903 CATCTATTAAACAGTCTGATTCTATTTGTTGCCTATTTTCTAACTA
196 CATCCATCAAACAGTCTGATTCTATTTGTTGCCTATTTTCTAACTA
6546949 ATCTTTAACC
Statistics
Matches: 214, Mismatches: 27, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
244 214 1.00
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.40
Consensus pattern (244 bp):
GATTCTAGAATCTTATTACGACCTTCAGCATTTGATTGTTAGGTTTCACCATTACCAACAAAGCA
ATATCTCTGTACTTAACTATGAAAGCTACCTTCATTTTTGGGTCCTATTGACTCCAAACACTCTC
CAAATTTGCTATAACATTCTGTCTTAAGTTTATATACACCATCTTCGGAAGGCTTGCAACATACC
CATCCATCAAACAGTCTGATTCTATTTGTTGCCTATTTTCTAACTATTG
Found at i:6548629 original size:541 final size:541
Alignment explanation
Indices: 6547581--6549199 Score: 3163
Period size: 541 Copynumber: 3.0 Consensus size: 541
6547571 AATTAAGTTT
6547581 TAAAAATTTAAAAACATGTACCACCA---TTTTTTTTATTTTGAAATTCATGCTGTTAGGCTTGA
1 TAAAAATTTAAAAACATGTACCACCATTTTTTTTTTTATTTTGAAATTCATGCTGTTAGGCTTGA
6547643 ATTGATCCTTATTTTGAAATGACAAAACATTAAGCTAAATAAGGTCGATAAAGATTTTGAAAAAG
66 ATTGATCCTTATTTTGAAATGACAAAACATTAAGCTAAATAAGGTCGATAAAGATTTTGAAAAAG
6547708 ATTTATTTAGTACATGTTCTTAAGTTTTATATTTTGGTACTAAATAAATAGTATGATTTTCAAAG
131 ATTTATTTAGTACATGTTCTTAAGTTTTATATTTTGGTACTAAATAAATAGTATGATTTTCAAAG
6547773 CTTAAACAAACCTTTCTTTATTTTCATATTTCTCAAACCAAATCTACCTTTAAAGATTATTTAGT
196 CTTAAACAAACCTTTCTTTATTTTCATATTTCTCAAACCAAATCTACCTTTAAAGATTATTTAGT
6547838 TGAGCTTAAATGAAAGTCCAATTGTTGTTTTTAAAGTGAACTTATTCATTTTGGACTTAATACAA
261 TGAGCTTAAATGAAAGTCCAATTGTTGTTTTTAAAGTGAACTTATTCATTTTGGACTTAATACAA
6547903 TTTTTGATAATATTGGTTTTGAGAAAAAGATTAACTTAAGAAAGTTGTTTTACAAGAATAAAGTT
326 TTTTTGATAATATTGGTTTTGAGAAAAAGATTAACTTAAGAAAGTTGTTTTACAAGAATAAAGTT
6547968 TTCCAACATTGAACTTATTTTATTTTTTTGTATTAATTCACAAAGTTTTAATATTTGAATTTTAT
391 TTCCAACATTGAACTTATTTTATTTTTTTGTATTAATTCACAAAGTTTTAATATTTGAATTTTAT
6548033 ATGGTTGGAAAGCTCTTTGAGTCTACTTTCTAATGGATCAAACAAAAGTCAAATTCAAATTTTCT
456 ATGGTTGGAAAGCTCTTTGAGTCTACTTTCTAATGGATCAAACAAAAGTCAAATTCAAATTTTCT
*
6548098 AAGAAAAGACTTTAACTTTTC
521 AAGAAAAGACTTTAAATTTTC
6548119 TAAAAATTTAAAAACATGTACCACCATTTTTTTTTTTATTTTGAAATTCATGCTGTTAGGCTTGA
1 TAAAAATTTAAAAACATGTACCACCATTTTTTTTTTTATTTTGAAATTCATGCTGTTAGGCTTGA
6548184 ATTGATCCTTATTTTGAAATGACAAAACATTAAGCTAAATAAGGTCGATAAAGATTTTGAAAAAG
66 ATTGATCCTTATTTTGAAATGACAAAACATTAAGCTAAATAAGGTCGATAAAGATTTTGAAAAAG
*
6548249 ATTTATTTAGTACATGTTCTTAAGTTTTATATTTTGGTACTAAATGAATAGTATGATTTTCAAAG
131 ATTTATTTAGTACATGTTCTTAAGTTTTATATTTTGGTACTAAATAAATAGTATGATTTTCAAAG
6548314 CTTAAACAAACCTTTCTTTATTTTCATATTTCTCAAACCAAATCTACCTTTAAAGATTATTTAGT
196 CTTAAACAAACCTTTCTTTATTTTCATATTTCTCAAACCAAATCTACCTTTAAAGATTATTTAGT
6548379 TGAGCTTAAATGAAAGTCCAATTGTTGTTTTTAAAGTGAACTTATTCATTTTGGACTTAATACAA
261 TGAGCTTAAATGAAAGTCCAATTGTTGTTTTTAAAGTGAACTTATTCATTTTGGACTTAATACAA
6548444 TTTTTGATAATATTGGTTTTGAGAAAAAGATTAACTTAAGAAAGTTGTTTTACAAGAATAAAGTT
326 TTTTTGATAATATTGGTTTTGAGAAAAAGATTAACTTAAGAAAGTTGTTTTACAAGAATAAAGTT
6548509 TTCCAACATTGAACTTATTTTATTTTTTTGTATTAATTCACAAAGTTTTAATATTTGAATTTTAT
391 TTCCAACATTGAACTTATTTTATTTTTTTGTATTAATTCACAAAGTTTTAATATTTGAATTTTAT
6548574 ATGGTTGGAAAGCTCTTTGAGTCTACTTTCTAATGGATCAAACAAAAGTCAAATTCAAATTTTCT
456 ATGGTTGGAAAGCTCTTTGAGTCTACTTTCTAATGGATCAAACAAAAGTCAAATTCAAATTTTCT
6548639 AAGAAAAGACTTTAAATTTTC
521 AAGAAAAGACTTTAAATTTTC
6548660 TAAAAATTTAAAAACATGTACCACCATTTTTTTTTTTATTTTGAAATTCATGCTGTTAGGCTTGA
1 TAAAAATTTAAAAACATGTACCACCATTTTTTTTTTTATTTTGAAATTCATGCTGTTAGGCTTGA
6548725 ATTGATCCTTATTTTGAAATGACAAAACATTAAGCTAAATAAGGTCGATAAAGATTTTGAAAAAG
66 ATTGATCCTTATTTTGAAATGACAAAACATTAAGCTAAATAAGGTCGATAAAGATTTTGAAAAAG
*
6548790 ATTTATTTAGTACATGTTCTTAAGTTTTATATCTTGGTACTAAATAAATAGTATGATTTTCAAAG
131 ATTTATTTAGTACATGTTCTTAAGTTTTATATTTTGGTACTAAATAAATAGTATGATTTTCAAAG
6548855 CTTAAACAAACCTTTCTTTATTTTCATATTTCTCAAACCAAATCTACCTTTAAAGATTATTTAGT
196 CTTAAACAAACCTTTCTTTATTTTCATATTTCTCAAACCAAATCTACCTTTAAAGATTATTTAGT
6548920 TGAGCTTAAATGAAAGTCCAATTGTTGTTTTTAAAGTGAACTTATTCATTTTGGACTTAATACAA
261 TGAGCTTAAATGAAAGTCCAATTGTTGTTTTTAAAGTGAACTTATTCATTTTGGACTTAATACAA
*
6548985 TTTTTGATAATATTGGTTTTGAGAAAAAGATTAACTTAAGAAAGTTGTTTTACAAGAACAAAGTT
326 TTTTTGATAATATTGGTTTTGAGAAAAAGATTAACTTAAGAAAGTTGTTTTACAAGAATAAAGTT
*
6549050 TTCCAACATTGAGCTTATTTTATTTTTTTGTATTAATTCACAAAGTTTTAATATTTGAATTTTAT
391 TTCCAACATTGAACTTATTTTATTTTTTTGTATTAATTCACAAAGTTTTAATATTTGAATTTTAT
*
6549115 ATGGTTGGAAAGCTCTTTGAGTCTACTTTCTAATGGATCAAATAAAAGTCAAATTCAAATTTTCT
456 ATGGTTGGAAAGCTCTTTGAGTCTACTTTCTAATGGATCAAACAAAAGTCAAATTCAAATTTTCT
6549180 AAGAAAAGACTTTAAATTTT
521 AAGAAAAGACTTTAAATTTT
6549200 TACTAGACAT
Statistics
Matches: 1071, Mismatches: 7, Indels: 3
0.99 0.01 0.00
Matches are distributed among these distances:
538 26 0.02
541 1045 0.98
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (541 bp):
TAAAAATTTAAAAACATGTACCACCATTTTTTTTTTTATTTTGAAATTCATGCTGTTAGGCTTGA
ATTGATCCTTATTTTGAAATGACAAAACATTAAGCTAAATAAGGTCGATAAAGATTTTGAAAAAG
ATTTATTTAGTACATGTTCTTAAGTTTTATATTTTGGTACTAAATAAATAGTATGATTTTCAAAG
CTTAAACAAACCTTTCTTTATTTTCATATTTCTCAAACCAAATCTACCTTTAAAGATTATTTAGT
TGAGCTTAAATGAAAGTCCAATTGTTGTTTTTAAAGTGAACTTATTCATTTTGGACTTAATACAA
TTTTTGATAATATTGGTTTTGAGAAAAAGATTAACTTAAGAAAGTTGTTTTACAAGAATAAAGTT
TTCCAACATTGAACTTATTTTATTTTTTTGTATTAATTCACAAAGTTTTAATATTTGAATTTTAT
ATGGTTGGAAAGCTCTTTGAGTCTACTTTCTAATGGATCAAACAAAAGTCAAATTCAAATTTTCT
AAGAAAAGACTTTAAATTTTC
Found at i:6556883 original size:18 final size:18
Alignment explanation
Indices: 6556851--6556899 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
6556841 GATAAAACAG
*
6556851 TAAAATTAAAT-AAAA-T
1 TAAAATAAAATAAAAACT
6556867 TGAAAATAAAATAAAAACT
1 T-AAAATAAAATAAAAACT
6556886 TAAAATAAAA-AAAA
1 TAAAATAAAATAAAA
6556900 TGAAATAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 1 0.03
17 13 0.45
18 13 0.45
19 2 0.07
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (18 bp):
TAAAATAAAATAAAAACT
Found at i:6556925 original size:27 final size:27
Alignment explanation
Indices: 6556869--6556927 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
6556859 AATAAAATTG
* *
6556869 AAAATAAAATAAAAACTTAAAATAAAA
1 AAAATAAAATAAAAAATGAAAATAAAA
* *
6556896 AAAATGAAATAATAAAATGAAAA-AAGA
1 AAAATAAAATAA-AAAATGAAAATAAAA
6556923 AAAAT
1 AAAAT
6556928 CTACGATTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (27 bp):
AAAATAAAATAAAAAATGAAAATAAAA
Found at i:6557305 original size:20 final size:21
Alignment explanation
Indices: 6557282--6557325 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
6557272 AAAATTCATG
*
6557282 TTTTTCC-TAAAAA-TTTAGA
1 TTTTTCCAAAAAAATTTTAGA
6557301 TTTTTCCAAAAAAATTTTAGA
1 TTTTTCCAAAAAAATTTTAGA
6557322 TTTT
1 TTTT
6557326 CCAGATTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.32
20 5 0.23
21 10 0.45
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (21 bp):
TTTTTCCAAAAAAATTTTAGA
Found at i:6557791 original size:3 final size:3
Alignment explanation
Indices: 6557785--6557853 Score: 68
Period size: 3 Copynumber: 23.0 Consensus size: 3
6557775 GAAGAAAGAA
* * * * * *
6557785 AAT AAT AAAT GAT AAT GAT AAT AAC AAC AAC AAC AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6557831 AAT AAT -AT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
6557854 TATTTATTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 2 0.03
3 53 0.91
4 3 0.05
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:6557842 original size:14 final size:14
Alignment explanation
Indices: 6557823--6557851 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6557813 AACAACAATA
6557823 ATAATAATAATAAT
1 ATAATAATAATAAT
6557837 ATAATAATAATAAT
1 ATAATAATAATAAT
6557851 A
1 A
6557852 ATTATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
ATAATAATAATAAT
Found at i:6557842 original size:17 final size:17
Alignment explanation
Indices: 6557820--6557853 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
6557810 AACAACAACA
6557820 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
6557837 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
6557854 TATTTATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:6557863 original size:3 final size:3
Alignment explanation
Indices: 6557852--6557955 Score: 94
Period size: 3 Copynumber: 35.7 Consensus size: 3
6557842 AATAATAATA
* *
6557852 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT AAT A-T AGT -TT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
6557896 ATGT A-T AGT GTT A-T ATT ATT -TT -TT GTT ATT ATTT ATT ATT ATT
1 AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT
6557939 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
6557956 GAAAATTGAC
Statistics
Matches: 87, Mismatches: 6, Indels: 16
0.80 0.06 0.15
Matches are distributed among these distances:
2 11 0.13
3 68 0.78
4 8 0.09
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:6558819 original size:86 final size:85
Alignment explanation
Indices: 6558727--6558998 Score: 300
Period size: 86 Copynumber: 3.2 Consensus size: 85
6558717 GAATATTCAC
6558727 AAGATTCTAAGTTTCACAGAAGTTCTAGATTCGCAAAGATCTT-AGGTTTGCAAAGACTTTCAAA
1 AAGATTCTAAGTTTCACA-AAGTTCTAGATTCGCAAAGAT-TTCAGGTTTGCAAAGACTTTCAAA
* * * *
6558791 TTTGTAGGAAAAAAAGATTTGT
64 TTTGCAAGAAAGAAAGATTTCT
* ** * * * *
6558813 AGGATTCTAAGTTTTGCTAAGGTTCTAGATTCGCACAGATTTCA-GATT-CACAAGAACTTTCAG
1 AAGATTCTAAGTTTCAC-AAAGTTCTAGATTCGCAAAGATTTCAGGTTTGCA-AAG-ACTTTCAA
*
6558876 ATTCGCAAGAAAGAAAGATTTCT
63 ATTTGCAAGAAAGAAAGATTTCT
* * * *
6558899 AAGATTCTAAGTTTCACAAAGATTGTAGATTCGGAAAGATTTCAGGTTTGTAAGGACTTTCAAAT
1 AAGATTCTAAGTTTCACAAAG-TTCTAGATTCGCAAAGATTTCAGGTTTGCAAAGACTTTCAAAT
*
6558964 TTGCAAGAAAGAAAGATTTAT
65 TTGCAAGAAAGAAAGATTTCT
6558985 AAGATT-TCAAGTTT
1 AAGATTCT-AAGTTT
6558999 TGCAAAAGTT
Statistics
Matches: 153, Mismatches: 25, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
84 2 0.01
85 12 0.08
86 132 0.86
87 6 0.04
88 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.19, T:0.33
Consensus pattern (85 bp):
AAGATTCTAAGTTTCACAAAGTTCTAGATTCGCAAAGATTTCAGGTTTGCAAAGACTTTCAAATT
TGCAAGAAAGAAAGATTTCT
Found at i:6558861 original size:17 final size:18
Alignment explanation
Indices: 6558839--6558886 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
6558829 CTAAGGTTCT
6558839 AGATTCGCACAG-A-TTTC
1 AGATTCGCA-AGAACTTTC
*
6558856 AGATTCACAAGAACTTTC
1 AGATTCGCAAGAACTTTC
6558874 AGATTCGCAAGAA
1 AGATTCGCAAGAA
6558887 AGAAAGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 2 0.07
17 9 0.33
18 16 0.59
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.25
Consensus pattern (18 bp):
AGATTCGCAAGAACTTTC
Found at i:6559909 original size:11 final size:10
Alignment explanation
Indices: 6559889--6559914 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
6559879 TAAGTCTCCC
6559889 TTTTTCTTTT
1 TTTTTCTTTT
6559899 TTTTTCTTTT
1 TTTTTCTTTT
6559909 TTTTTC
1 TTTTTC
6559915 ATTTCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:6566352 original size:17 final size:16
Alignment explanation
Indices: 6566303--6566365 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 16
6566293 GAATACAAAT
6566303 AAAT-AAATAAATAAA
1 AAATAAAATAAATAAA
*
6566318 ATTAGTAAAATAAAATAAA
1 A--AATAAAAT-AAATAAA
*
6566337 AACTCAAAATAAATAAA
1 AAAT-AAAATAAATAAA
6566354 AAATAAAATAAA
1 AAATAAAATAAA
6566366 AATGGGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
15 1 0.03
16 8 0.20
17 14 0.35
18 9 0.22
19 8 0.20
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.21
Consensus pattern (16 bp):
AAATAAAATAAATAAA
Found at i:6566794 original size:20 final size:19
Alignment explanation
Indices: 6566771--6566809 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
6566761 CTCTAGAATT
*
6566771 CTAATTCAAACCCTAGAAAC
1 CTAAATCAAA-CCTAGAAAC
*
6566791 CTAAATCTAACCTAGAAAC
1 CTAAATCAAACCTAGAAAC
6566810 TTCTAATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.46, C:0.28, G:0.05, T:0.21
Consensus pattern (19 bp):
CTAAATCAAACCTAGAAAC
Found at i:6567233 original size:3 final size:3
Alignment explanation
Indices: 6567227--6567258 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
6567217 TAATAATATA
6567227 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
6567259 AATAATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:6567327 original size:18 final size:18
Alignment explanation
Indices: 6567304--6567343 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
6567294 TACCATAAAC
6567304 TATACTATAATAAAATAG
1 TATACTATAATAAAATAG
* *
6567322 TATACTATAATATAGTAG
1 TATACTATAATAAAATAG
6567340 TATA
1 TATA
6567344 GTAGTAGTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (18 bp):
TATACTATAATAAAATAG
Done.