Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 75 of 106
Found at i:28550455 original size:42 final size:41
Alignment explanation
Indices: 28550406--28550505 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 41
28550396 ATAATAATAT
*
28550406 TTAAATTATAAATAAAATATTAATACTTTATAATG-TTAATGA
1 TTAAATTATAAATAAAATATTAATA-TTTA-AATGATCAATGA
* *
28550448 TTAAATTAGAAATAAAATATTAATATTTAAATGATCAATTA
1 TTAAATTATAAATAAAATATTAATATTTAAATGATCAATGA
*
28550489 TTAATATTTTAAATAAA
1 TTAA-ATTATAAATAAA
28550506 TTATAAATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
40 4 0.08
41 13 0.25
42 34 0.67
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (41 bp):
TTAAATTATAAATAAAATATTAATATTTAAATGATCAATGA
Found at i:28550514 original size:27 final size:26
Alignment explanation
Indices: 28550475--28550531 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
28550465 TATTAATATT
* *
28550475 TAAATGATCAATTATTAATATTTTAAA
1 TAAATGATAAATTATAAATA-TTTAAA
*
28550502 TAAATTATAAATTATAAATATTTAAA
1 TAAATGATAAATTATAAATATTTAAA
28550528 -AAAT
1 TAAAT
28550532 AAAAAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 4 0.15
26 6 0.22
27 17 0.63
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (26 bp):
TAAATGATAAATTATAAATATTTAAA
Found at i:28550533 original size:22 final size:22
Alignment explanation
Indices: 28550365--28550534 Score: 69
Period size: 22 Copynumber: 7.2 Consensus size: 22
28550355 TGATTAAATT
28550365 ATAAATTATTAATATTT-AAAA
1 ATAAATTATTAATATTTAAAAA
28550386 ATAAATAATCATAATAATATTTAAATTATAA
1 ATAAAT--T-AT--TAATATTT-AA--A-AA
* * *
28550417 ATAAAATATTAATACTTTATAAT
1 ATAAATTATTAATA-TTTAAAAA
* * * *
28550440 GTTAATGATTAA-A-TT-AGAA
1 ATAAATTATTAATATTTAAAAA
* **
28550459 ATAAAATATTAATATTTAAATG
1 ATAAATTATTAATATTTAAAAA
*
28550481 ATCAATTATTAATATTTTAAATAAA
1 ATAAATTATTAATA-TTT-AA-AAA
*
28550506 TTATAAATTATAAATATTTAAAAA
1 --ATAAATTATTAATATTTAAAAA
28550530 ATAAA
1 ATAAA
28550535 AAAAAATCAT
Statistics
Matches: 107, Mismatches: 23, Indels: 37
0.64 0.14 0.22
Matches are distributed among these distances:
19 9 0.08
20 3 0.03
21 8 0.07
22 19 0.18
23 13 0.12
24 8 0.07
25 3 0.03
26 17 0.16
27 15 0.14
28 3 0.03
29 1 0.01
30 1 0.01
31 7 0.07
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
ATAAATTATTAATATTTAAAAA
Found at i:28550609 original size:144 final size:142
Alignment explanation
Indices: 28550192--28550787 Score: 654
Period size: 143 Copynumber: 4.1 Consensus size: 142
28550182 AATATTAATG
* * *
28550192 ATTATCAAATATTAATATTTTATATAAATTATAAATTATTAATATTTAAAAATAAATAATCATAA
1 ATTATCAATTATTAATATTTTAAATAAATTATAAATTATTAATATTTAAAAATAAAAAATCATAA
** * * * * *
28550257 TTGTATTTAAATTATAAATAAATTATTAAGATTTTTTAAGAATTAATGATTAAATTAT-AATAAA
66 TAATATTT-AATTATAAATAAAATATTAATACTTTATAA-TATTAATGATTAAATTATAAATAAA
*
28550321 ATAGTAATATTTAA
129 ATATTAATATTTAA
* * * * *
28550335 ATTATCAATTAGTAATATATTGATTAAATTATAAATTATTAATATTTAAAAATAAATAATCATAA
1 ATTATCAATTATTAATATTTTAAATAAATTATAAATTATTAATATTTAAAAATAAAAAATCATAA
* *
28550400 TAATATTTAAATTATAAATAAAATATTAATACTTTATAATGTTAATGATTAAATTAGAAATAAAA
66 TAATATTT-AATTATAAATAAAATATTAATACTTTATAATATTAATGATTAAATTATAAATAAAA
28550465 TATTAATATTTAA
130 TATTAATATTTAA
* *
28550478 ATGATCAATTATTAATATTTTAAATAAATTATAAATTATAAATATTTAAAAAATAAAAAAAAATC
1 ATTATCAATTATTAATATTTTAAATAAATTATAAATTATTAATATTT-AAAAAT---AAAAAATC
* *
28550543 ATAATAACATTT-ATTAT-AATAAAATATTAATACTTTATAATATTAATAATTAAATTATAAATA
62 ATAATAATATTTAATTATAAATAAAATATTAATACTTTATAATATTAATGATTAAATTATAAATA
** * *
28550606 AAATAACATTATTTTA
127 AAATATTAATATTTAA
*
28550622 ATTATCAATTATTAATATTTGT-AATAAATTATTAAATTATTAA-ATTAAAAAATATAAATTTAA
1 ATTATCAATTATTAATATTT-TAAATAAATTA-TAAATTATTAATATT------TA-AAA-ATAA
* **
28550685 AATAATCATAATAATATTTAAATTAT-AATAAAATATTAATA-TTATGTAATGCTAATGATTAAA
56 AA-AATCATAATAATATTT-AATTATAAATAAAATATTAATACTT-TATAATATTAATGATTAAA
28550748 TTATAAAT-AAATATT-A-ATTTAA
118 TTATAAATAAAATATTAATATTTAA
*
28550770 ATTATAAATTATTTAATA
1 ATTATCAATTA-TTAATA
28550788 ATTAAAAATA
Statistics
Matches: 389, Mismatches: 44, Indels: 34
0.83 0.09 0.07
Matches are distributed among these distances:
142 15 0.04
143 152 0.39
144 92 0.24
145 16 0.04
147 18 0.05
148 19 0.05
149 22 0.06
150 11 0.03
151 44 0.11
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (142 bp):
ATTATCAATTATTAATATTTTAAATAAATTATAAATTATTAATATTTAAAAATAAAAAATCATAA
TAATATTTAATTATAAATAAAATATTAATACTTTATAATATTAATGATTAAATTATAAATAAAAT
ATTAATATTTAA
Found at i:28550707 original size:20 final size:21
Alignment explanation
Indices: 28550675--28550721 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
28550665 ATTAAAAAAT
*
28550675 ATAA-ATTTAAAATAATCATA
1 ATAATATTTAAAATAATAATA
*
28550695 ATAATATTT-AAATTATAATA
1 ATAATATTTAAAATAATAATA
28550715 A-AATATT
1 ATAATATT
28550722 AATATTATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.25
20 14 0.58
21 4 0.17
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAATATTTAAAATAATAATA
Found at i:28550712 original size:17 final size:19
Alignment explanation
Indices: 28550692--28550729 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
28550682 TAAAATAATC
*
28550692 ATAATAATAT-TTAA-ATT
1 ATAATAAAATATTAATATT
28550709 ATAATAAAATATTAATATT
1 ATAATAAAATATTAATATT
28550728 AT
1 AT
28550730 GTAATGCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 9 0.50
18 4 0.22
19 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATAATAAAATATTAATATT
Found at i:28554359 original size:12 final size:11
Alignment explanation
Indices: 28554342--28554382 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
28554332 AATAGAATAG
28554342 AAATAAATAACT
1 AAATAAATAA-T
28554354 AAATAAATAAT
1 AAATAAATAAT
28554365 -AAT-AATAAT
1 AAATAAATAAT
28554374 AATATAAAT
1 AA-ATAAAT
28554383 TGAAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 6 0.23
10 4 0.15
11 3 0.12
12 13 0.50
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:28556843 original size:14 final size:14
Alignment explanation
Indices: 28556824--28556869 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
28556814 TAGACCGTTT
28556824 AAACAACCAGCATC
1 AAACAACCAGCATC
28556838 AAACAACCA-CATC
1 AAACAACCAGCATC
* *
28556851 -AACAACTAGCATT
1 AAACAACCAGCATC
28556864 AAACAA
1 AAACAA
28556870 ATAATCAGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 7 0.25
13 7 0.25
14 14 0.50
ACGTcount: A:0.54, C:0.30, G:0.04, T:0.11
Consensus pattern (14 bp):
AAACAACCAGCATC
Found at i:28558329 original size:34 final size:33
Alignment explanation
Indices: 28558273--28558403 Score: 97
Period size: 34 Copynumber: 3.9 Consensus size: 33
28558263 CCTTTAAAAT
**
28558273 AATGCCTTTTTC-CAAGCTCAAGCACAACCTATAC
1 AATGCC-TTTTCACAAGAACAAGCACAACCT-TAC
* **
28558307 AATGCCTTTTCACAAGAACAAGCATAATCCTTGT
1 AATGCCTTTTCACAAGAACAAGCACAA-CCTTAC
** * * *
28558341 AATGTTTTTTCATAGGAGCAAGCACAACCTTTAC
1 AATGCCTTTTCACAAGAACAAGCACAACC-TTAC
*
28558375 AATGCCTTTTCA-AGGAGA-AAGCACAACCT
1 AATGCCTTTTCACAAGA-ACAAGCACAACCT
28558404 CTTTACCTTT
Statistics
Matches: 77, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
32 1 0.01
33 21 0.27
34 52 0.68
35 3 0.04
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.27
Consensus pattern (33 bp):
AATGCCTTTTCACAAGAACAAGCACAACCTTAC
Found at i:28558397 original size:33 final size:34
Alignment explanation
Indices: 28558292--28558403 Score: 106
Period size: 34 Copynumber: 3.3 Consensus size: 34
28558282 TTCCAAGCTC
* *
28558292 AAGCACAACCTATACAATGCCTTTTCACAAGA-A
1 AAGCACAACCTTTACAATGCCTTTTCACAGGAGA
* ** * *
28558325 CAAGCATAATCCTTGT--AATGTTTTTTCATAGGAGC
1 -AAGCACAA-CCTT-TACAATGCCTTTTCACAGGAGA
28558360 AAGCACAACCTTTACAATGCCTTTTCA-AGGAGA
1 AAGCACAACCTTTACAATGCCTTTTCACAGGAGA
28558393 AAGCACAACCT
1 AAGCACAACCT
28558404 CTTTACCTTT
Statistics
Matches: 62, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
32 1 0.02
33 20 0.32
34 37 0.60
35 3 0.05
36 1 0.02
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (34 bp):
AAGCACAACCTTTACAATGCCTTTTCACAGGAGA
Found at i:28565571 original size:2 final size:2
Alignment explanation
Indices: 28565564--28565595 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28565554 GTTATGTATG
28565564 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28565596 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28578947 original size:42 final size:42
Alignment explanation
Indices: 28578888--28578982 Score: 145
Period size: 42 Copynumber: 2.3 Consensus size: 42
28578878 TTATGCGCAT
28578888 ATAGCCGGGTCAGCAACGGCTTATGTGCACTCCCACTCACAC
1 ATAGCCGGGTCAGCAACGGCTTATGTGCACTCCCACTCACAC
* * * *
28578930 ATAGCCGGGTTAGCAACGGTTTATGTGCACTCCTACTCGCAC
1 ATAGCCGGGTCAGCAACGGCTTATGTGCACTCCCACTCACAC
*
28578972 ATAGCTGGGTC
1 ATAGCCGGGTC
28578983 CAAATCAACA
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.22, C:0.31, G:0.24, T:0.23
Consensus pattern (42 bp):
ATAGCCGGGTCAGCAACGGCTTATGTGCACTCCCACTCACAC
Found at i:28584598 original size:18 final size:18
Alignment explanation
Indices: 28584517--28584601 Score: 66
Period size: 18 Copynumber: 4.7 Consensus size: 18
28584507 ACATTGAGAC
*
28584517 TATTCTTGATGCTGGGGT
1 TATTCTTGATGCTGAGGT
* * *
28584535 TGTTCTTGATGCTAAAGT
1 TATTCTTGATGCTGAGGT
* * *
28584553 TATTCTTGTTGTTG-GAGC
1 TATTCTTGATGCTGAG-GT
*
28584571 TATT-TCTGATGTTGAGGT
1 TATTCT-TGATGCTGAGGT
28584589 TATTCTTGATGCT
1 TATTCTTGATGCT
28584602 AATCCTAATC
Statistics
Matches: 50, Mismatches: 13, Indels: 8
0.70 0.18 0.11
Matches are distributed among these distances:
17 1 0.02
18 47 0.94
19 2 0.04
ACGTcount: A:0.15, C:0.11, G:0.26, T:0.48
Consensus pattern (18 bp):
TATTCTTGATGCTGAGGT
Found at i:28589532 original size:20 final size:20
Alignment explanation
Indices: 28589491--28589534 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
28589481 TCTAAACTTG
* *
28589491 AAATCATACTTCAATTACTC
1 AAATCATACTCCAATAACTC
*
28589511 AAATCATACTCCAATAAGTC
1 AAATCATACTCCAATAACTC
28589531 AAAT
1 AAAT
28589535 GGGGCTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.45, C:0.23, G:0.02, T:0.30
Consensus pattern (20 bp):
AAATCATACTCCAATAACTC
Found at i:28590041 original size:11 final size:11
Alignment explanation
Indices: 28590025--28590050 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28590015 AAAGGTGAAT
28590025 AAAAAAATTAG
1 AAAAAAATTAG
28590036 AAAAAAATTAG
1 AAAAAAATTAG
28590047 AAAA
1 AAAA
28590051 GGTGCAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (11 bp):
AAAAAAATTAG
Found at i:28594076 original size:35 final size:35
Alignment explanation
Indices: 28594048--28594296 Score: 265
Period size: 35 Copynumber: 7.2 Consensus size: 35
28594038 CTTAATTGTT
* *
28594048 TAATTTAATCAATTAGGCCCAATAACTTAATTAAA
1 TAATTTAATTAATTAGGCCCAATGACTTAATTAAA
* * * * *
28594083 CAATTTAGTTAATTAAGCCCAA-CAATTAATTAAA
1 TAATTTAATTAATTAGGCCCAATGACTTAATTAAA
*
28594117 CAATTTTAATTAATTAGGCCCAATGACTTAATTAAA
1 TAA-TTTAATTAATTAGGCCCAATGACTTAATTAAA
* * * ** ***
28594153 CAAATTTAATCAATTAGACTGAATGACTTAATTGTT
1 -TAATTTAATTAATTAGGCCCAATGACTTAATTAAA
28594189 TAATTTAATTAATTAGGCCCAATGACTTAATTAAA
1 TAATTTAATTAATTAGGCCCAATGACTTAATTAAA
*
28594224 TAATTTAATTAATTAGGCCCAATGATTTAATTAAGA
1 TAATTTAATTAATTAGGCCCAATGACTTAATTAA-A
*
28594260 -AATTTAATTAATTAGGCAC-A--ACTTAATTAAA
1 TAATTTAATTAATTAGGCCCAATGACTTAATTAAA
*
28594291 CAATTT
1 TAATTT
28594297 TAATCAAGTG
Statistics
Matches: 180, Mismatches: 29, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
31 1 0.01
32 14 0.08
34 14 0.08
35 113 0.63
36 36 0.20
37 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (35 bp):
TAATTTAATTAATTAGGCCCAATGACTTAATTAAA
Found at i:28594162 original size:106 final size:104
Alignment explanation
Indices: 28594049--28594296 Score: 295
Period size: 106 Copynumber: 2.4 Consensus size: 104
28594039 TTAATTGTTT
*
28594049 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAGTTAATTAAGCCCAA-CAATTAAT
1 AATTTAATCAATTAGG-CCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAATCAATTAAT
28594113 TAAACAATTTTAATTAATTAGGCCCAATGACTTAATTAAACA
65 TAAACAA-TTTAATTAATTAGGCCCAATGACTTAATT-AACA
* * * **** * * *
28594155 AATTTAATCAATTAGACTGAATGACTTAATTGTTTAATTTAATTAATTAGGCCCAATGACTTAAT
1 AATTTAATCAATTAGGC-CAATAACTTAATTAAACAATTTAATTAATTAAGCCCAATCAATTAAT
* * *
28594220 TAAATAATTTAATTAATTAGGCCCAATGATTTAATTAAGA
65 TAAACAATTTAATTAATTAGGCCCAATGACTTAATTAACA
* *
28594260 AATTTAATTAATTAGG-C-ACAACTTAATTAAACAATTT
1 AATTTAATCAATTAGGCCAATAACTTAATTAAACAATTT
28594297 TAATCAAGTG
Statistics
Matches: 117, Mismatches: 23, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
102 14 0.12
105 18 0.15
106 73 0.62
107 12 0.10
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (104 bp):
AATTTAATCAATTAGGCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAATCAATTAATT
AAACAATTTAATTAATTAGGCCCAATGACTTAATTAACA
Found at i:28594197 original size:141 final size:138
Alignment explanation
Indices: 28594037--28594303 Score: 394
Period size: 141 Copynumber: 1.9 Consensus size: 138
28594027 AGCCCAGTTA
*
28594037 ACTTAATTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAGTTAATTAAGCC
1 ACTTAATTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCC
*
28594102 CAA-CAATTAATTAA-ACAATTTTAATTAATTAGGCCCAATGACTTAATTAAACAAATTTAATCA
66 CAATCAATTAATTAAGA-AA-TTTAATTAATTAGGCAC-A--ACTTAATTAAACAAATTTAATCA
28594165 ATTAGACTGAATG
126 ATTAGACTGAATG
* * * *
28594178 ACTTAATTGTTTAATTTAATTAATTAGGCCCAATGACTTAATTAAATAATTTAATTAATTAGGCC
1 ACTTAATTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCC
* * *
28594243 CAATGATTTAATTAAGAAATTTAATTAATTAGGCACAACTTAATTAAACAATTTTAATCAA
66 CAATCAATTAATTAAGAAATTTAATTAATTAGGCACAACTTAATTAAACAAATTTAATCAA
28594304 GTGCTTGAGA
Statistics
Matches: 115, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
138 23 0.20
140 1 0.01
141 79 0.69
142 11 0.10
143 1 0.01
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (138 bp):
ACTTAATTGTTTAATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCC
CAATCAATTAATTAAGAAATTTAATTAATTAGGCACAACTTAATTAAACAAATTTAATCAATTAG
ACTGAATG
Found at i:28601355 original size:29 final size:29
Alignment explanation
Indices: 28601322--28601389 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
28601312 ATAAAAATTC
*
28601322 ACAATATCCACAGTAGCTAAACAAGATAT
1 ACAATATCCACAGTAACTAAACAAGATAT
* *
28601351 ACAATATCCATAGTAACTAAGCAAGATAT
1 ACAATATCCACAGTAACTAAACAAGATAT
28601380 ATTCAATATC
1 A--CAATATC
28601390 TATAATAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 27 0.79
31 7 0.21
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (29 bp):
ACAATATCCACAGTAACTAAACAAGATAT
Found at i:28606031 original size:25 final size:25
Alignment explanation
Indices: 28605976--28606032 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
28605966 ATTGCAACCG
* *
28605976 CGTATATCAACTTATGGCCTAGCCA
1 CGTATAACAACTTATGCCCTAGCCA
* * * *
28606001 CATATAACAACTTGTGCCCTTGTCA
1 CGTATAACAACTTATGCCCTAGCCA
28606026 CGTATAA
1 CGTATAA
28606033 TCACAAACCG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (25 bp):
CGTATAACAACTTATGCCCTAGCCA
Found at i:28608066 original size:19 final size:19
Alignment explanation
Indices: 28608042--28608081 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
28608032 GCTCAAATTA
28608042 TCAACTGGAC-GAGGGTTTC
1 TCAACTGG-CTGAGGGTTTC
28608061 TCAACTGGCTGAGGGTTTC
1 TCAACTGGCTGAGGGTTTC
28608080 TC
1 TC
28608082 TCTAAAACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (19 bp):
TCAACTGGCTGAGGGTTTC
Found at i:28608542 original size:2 final size:2
Alignment explanation
Indices: 28608537--28608570 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28608527 CATATTTATC
28608537 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28608571 CACACACACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28608695 original size:42 final size:41
Alignment explanation
Indices: 28608602--28608734 Score: 167
Period size: 42 Copynumber: 3.1 Consensus size: 41
28608592 ACCATCCCAC
* * *
28608602 CATCATCAGCTCATGTGCACTCCCCATTCACACATAACTGGGT
1 CATCATCAGCTCATGTGCACT-CCCA-CCGCACATAGCTGGGT
28608645 CATCATCAGCTCATGTGCACTCCACACCGCACATAGCTGGGT
1 CATCATCAGCTCATGTGCACTCC-CACCGCACATAGCTGGGT
* * * *
28608687 CATTATCAGCTCATGTGCATTCCCACACGCATATAGCTAGGT
1 CATCATCAGCTCATGTGCACTCCCAC-CGCACATAGCTGGGT
28608729 CATCAT
1 CATCAT
28608735 TATCACATAA
Statistics
Matches: 80, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
41 3 0.04
42 54 0.68
43 23 0.29
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.26
Consensus pattern (41 bp):
CATCATCAGCTCATGTGCACTCCCACCGCACATAGCTGGGT
Found at i:28614133 original size:2 final size:2
Alignment explanation
Indices: 28614126--28614167 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
28614116 TATTCGTGTT
28614126 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28614168 AATGCATAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28626286 original size:40 final size:38
Alignment explanation
Indices: 28626228--28626333 Score: 115
Period size: 38 Copynumber: 2.7 Consensus size: 38
28626218 CACACCCGGC
* *
28626228 TCATGTGCATTCCCCCACATCGTGCACATAGCTGGAGCCA
1 TCATGTGCATCCCCCCACATCGTGCACA-AGC-AGAGCCA
* * *
28626268 TCGTGTGCATCCCCCCACATC-TGGCACAATCAGTGCCA
1 TCATGTGCATCCCCCCACATCGT-GCACAAGCAGAGCCA
* *
28626306 TCATGTACATCCCCCAACATCGTGCACA
1 TCATGTGCATCCCCCCACATCGTGCACA
28626334 CGGGCACTAT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
38 28 0.50
39 4 0.07
40 24 0.43
ACGTcount: A:0.24, C:0.38, G:0.17, T:0.22
Consensus pattern (38 bp):
TCATGTGCATCCCCCCACATCGTGCACAAGCAGAGCCA
Found at i:28633543 original size:39 final size:38
Alignment explanation
Indices: 28633489--28633630 Score: 142
Period size: 40 Copynumber: 3.7 Consensus size: 38
28633479 ACCCGGCTCA
* * *
28633489 TGTGCATCCCCCCACATTGTGCACATAGCTGGTGCC-TTG
1 TGTGCATCCCCCCACATCGTGCACA-AGC-AGTGCCATCG
* *
28633528 TGTGCATCCCCCCACATCATGCACAATCAGTGCCATCG
1 TGTGCATCCCCCCACATCGTGCACAAGCAGTGCCATCG
* * * **
28633566 TGTACATCCCCCCACATCGTGCACACGGGCATTATCATCG
1 TGTGCATCCCCCCACATCGTGCACA--AGCAGTGCCATCG
*
28633606 TGTACATCCCCCCACATCGTGCACA
1 TGTGCATCCCCCCACATCGTGCACA
28633631 TGGGCACTAT
Statistics
Matches: 88, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
37 5 0.06
38 27 0.31
39 23 0.26
40 33 0.38
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.23
Consensus pattern (38 bp):
TGTGCATCCCCCCACATCGTGCACAAGCAGTGCCATCG
Found at i:28633583 original size:19 final size:19
Alignment explanation
Indices: 28633561--28633631 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
28633551 CAATCAGTGC
*
28633561 CATCGTGTACATCCCCCCA
1 CATCGTGCACATCCCCCCA
* ***
28633580 CATCGTGCACA-CGGGCATTA
1 CATCGTGCACATC--CCCCCA
*
28633600 TCATCGTGTACATCCCCCCA
1 -CATCGTGCACATCCCCCCA
28633620 CATCGTGCACAT
1 CATCGTGCACAT
28633632 GGGCACTATC
Statistics
Matches: 37, Mismatches: 11, Indels: 8
0.66 0.20 0.14
Matches are distributed among these distances:
18 1 0.03
19 21 0.57
20 4 0.11
21 10 0.27
22 1 0.03
ACGTcount: A:0.23, C:0.39, G:0.15, T:0.23
Consensus pattern (19 bp):
CATCGTGCACATCCCCCCA
Found at i:28633616 original size:40 final size:40
Alignment explanation
Indices: 28633561--28633644 Score: 150
Period size: 40 Copynumber: 2.1 Consensus size: 40
28633551 CAATCAGTGC
*
28633561 CATCGTGTACATCCCCCCACATCGTGCACACGGGCATTAT
1 CATCGTGTACATCCCCCCACATCGTGCACACGGGCACTAT
*
28633601 CATCGTGTACATCCCCCCACATCGTGCACATGGGCACTAT
1 CATCGTGTACATCCCCCCACATCGTGCACACGGGCACTAT
28633641 CATC
1 CATC
28633645 ATCCATCTCG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.23
Consensus pattern (40 bp):
CATCGTGTACATCCCCCCACATCGTGCACACGGGCACTAT
Found at i:28638886 original size:7 final size:7
Alignment explanation
Indices: 28638874--28638907 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
28638864 CTCTTGGAGC
28638874 TTTTTTA
1 TTTTTTA
*
28638881 TTTTTTT
1 TTTTTTA
28638888 TTTTGTTA
1 TTTT-TTA
28638896 TTTTTTA
1 TTTTTTA
28638903 TTTTT
1 TTTTT
28638908 CTTGGTTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
7 18 0.75
8 6 0.25
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:28638898 original size:15 final size:15
Alignment explanation
Indices: 28638874--28638907 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
28638864 CTCTTGGAGC
28638874 TTTTTTATTTTTT-T
1 TTTTTTATTTTTTAT
28638888 TTTTGTTATTTTTTAT
1 TTTT-TTATTTTTTAT
28638904 TTTT
1 TTTT
28638908 CTTGGTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 9 0.50
16 5 0.28
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (15 bp):
TTTTTTATTTTTTAT
Found at i:28639552 original size:22 final size:23
Alignment explanation
Indices: 28639527--28639572 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
28639517 AGTTTGTTAG
*
28639527 ATTTAATTTTACTT-TTTGAATA
1 ATTTAAATTTACTTGTTTGAATA
**
28639549 ATTTAAATTTGGTTGTTTGAATA
1 ATTTAAATTTACTTGTTTGAATA
28639572 A
1 A
28639573 GATTATGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.33, C:0.02, G:0.11, T:0.54
Consensus pattern (23 bp):
ATTTAAATTTACTTGTTTGAATA
Found at i:28642452 original size:22 final size:22
Alignment explanation
Indices: 28642427--28642472 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
28642417 TCACTGCAGC
28642427 GAGAATGAATTTTTGCTACAGT
1 GAGAATGAATTTTTGCTACAGT
*
28642449 GAGAATGAATTTTTGCTGCAGT
1 GAGAATGAATTTTTGCTACAGT
28642471 GA
1 GA
28642473 CACTTGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35
Consensus pattern (22 bp):
GAGAATGAATTTTTGCTACAGT
Found at i:28643030 original size:42 final size:42
Alignment explanation
Indices: 28642941--28643059 Score: 139
Period size: 42 Copynumber: 2.8 Consensus size: 42
28642931 TCTCCCATCG
* * * * * * *
28642941 TCATCAGCTCATGTGCACCCCCACTAGCACATGGTTGGGTCA
1 TCATCGGCTTATGTGCACTCCCACTCGCACATAGCTAGGTCA
28642983 TCATCGGCTTATGTGCACTCCCACTCGCACATAGCTAGGTCA
1 TCATCGGCTTATGTGCACTCCCACTCGCACATAGCTAGGTCA
* * * *
28643025 TCATCGACTTATGTACACTTCTACTCGCACATAGC
1 TCATCGGCTTATGTGCACTCCCACTCGCACATAGC
28643060 AGGGTCAACA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.27
Consensus pattern (42 bp):
TCATCGGCTTATGTGCACTCCCACTCGCACATAGCTAGGTCA
Found at i:28644914 original size:36 final size:36
Alignment explanation
Indices: 28644827--28644955 Score: 179
Period size: 36 Copynumber: 3.6 Consensus size: 36
28644817 ATATGCCATG
* * * * *
28644827 TGCGGTGTGGGAGTGCATATGATGATATT-GCCATG
1 TGCGGTGTGGGAGTGCACATGACGGTATTAGCTATA
28644862 TGCGGTGTGGGAGTGCACATGACGGTATTAGCTATA
1 TGCGGTGTGGGAGTGCACATGACGGTATTAGCTATA
* *
28644898 TGCGATGTGGGAGTGCACATGACGGTATTACCTATA
1 TGCGGTGTGGGAGTGCACATGACGGTATTAGCTATA
*
28644934 TGCGGTGTGGGAGTGCGCATGA
1 TGCGGTGTGGGAGTGCACATGA
28644956 GCTGGTGAGC
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 26 0.31
36 58 0.69
ACGTcount: A:0.21, C:0.14, G:0.37, T:0.28
Consensus pattern (36 bp):
TGCGGTGTGGGAGTGCACATGACGGTATTAGCTATA
Found at i:28644990 original size:2 final size:2
Alignment explanation
Indices: 28644983--28645027 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
28644973 GGTATACATG
28644983 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28645025 TA T
1 TA T
28645028 NNNNNNNNNN
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28657848 original size:28 final size:27
Alignment explanation
Indices: 28657795--28657848 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
28657785 ATGTCCTGGT
* * *
28657795 GGTGGAAAATTACTATTTTGCCCCTAG
1 GGTGGAAAATTACCATTTTACACCTAG
28657822 GGTGGCAAAATTACCATTTTACACCTA
1 GGTGG-AAAATTACCATTTTACACCTA
28657849 TGCTTTGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (27 bp):
GGTGGAAAATTACCATTTTACACCTAG
Found at i:28658422 original size:489 final size:487
Alignment explanation
Indices: 28657497--28658476 Score: 1768
Period size: 489 Copynumber: 2.0 Consensus size: 487
28657487 AAAAATCTCA
28657497 CCTTTTTCACTTAATTTCCTTGAAAATTCACACTTTTTCTTTGATTTTCTCTCTCTAGGGTTTTG
1 CCTTTTTCACTTAATTTCCTTGAAAATTCACACTTTTTCTTTGATTTTCTCTCTCTAGGGTTTTG
28657562 TTTTTGTTTTCTCTCTCTTCTTGCTGGTTTGGCCGGCCATGGGGTGGAAGATGGGCTGATTTTTG
66 TTTTTGTTTTCTCTCTCTTCTTGCTGGTTTGGCCGGCCATGGGGTGGAAGATGGGCTGATTTTTG
28657627 TGCCTTTTAAAAAGAAAATAATAAATTAATAAAGGATGACACGTGGCATCATGTCAATGGCTCGT
131 TGCCTTTTAAAAAGAAAATAATAAATTAATAAAGGATGACACGTGGCATCATGTCAATGGCTCGT
28657692 TTTTAAAACTTAAAAATTTTAATCCTTTTATTCTCCACCACACAATTAGTCAATGGTCAAAATGA
196 TTTTAAAACTTAAAAATTTTAATCCTTTTATTCTCCACCACACAATTAGTCAATGGTCAAAATGA
* * *
28657757 GAATAAATGAAGACCATGTGCTGGACAAATGTCCTGGTGGTGGAAAATTACTATTTTGCCCCTAG
261 GAATAAAGGAAAACCATGTGCTGGACAAATATCCTGGTGGTGGAAAATTACTATTTTGCCCCTAG
*
28657822 GGTGGCAAAATTACCATTTTACACCTATGCTTTGAAAAATACCAAGAATAAATTTTTTTTTTACT
326 GGTGGCAAAATTACCATTTTACACCTATGCTTTGAAAAATACCAAGAATAAA-TTTTTTTTCACT
* * *
28657887 TCTTAATCCTCAAATCATACTCCAATAAGTCAAATGGGGCCAAAAATCTTTTCTAAAAATTTCCA
390 TCTTAATCCTCAAATCATACTCCAATAAGTCAAATGGGGACAAAAATCGTTTCTAAAAATCTCCA
* *
28657952 TTTTGTCCTCAAGTGGTAAATGACCATTTTGCC
455 TTTTGTCCTCAAGTAGCAAATGACCATTTTGCC
28657985 NCCTTTTTCACTTAATTTCCTTGAAAATTCACACTTTTTCTTTGATTTTCTCTCTCTAGGGTTTT
1 -CCTTTTTCACTTAATTTCCTTGAAAATTCACACTTTTTCTTTGATTTTCTCTCTCTAGGGTTTT
28658050 GTTTTTGTTTTCTCTCTCTTCTTGCTGGTTTGGCCGGCCATGGGGTGGAAGATGGGCTGATTTTT
65 GTTTTTGTTTTCTCTCTCTTCTTGCTGGTTTGGCCGGCCATGGGGTGGAAGATGGGCTGATTTTT
28658115 GTGCCTTTTAAAAAGAAAAATAATAAATTAATAAAGGATGACACGTGGCATCATGTCAATGGCTC
130 GTGCCTTTTAAAAAG-AAAATAATAAATTAATAAAGGATGACACGTGGCATCATGTCAATGGCTC
28658180 GTTTTTAAAACTTTAAAAATTTTAATCCTTTT-TATCTCCACCACACAATTAGTCAATGGTCAAA
194 GTTTTTAAAAC-TTAAAAATTTTAATCCTTTTAT-TCTCCACCACACAATTAGTCAATGGTCAAA
* *
28658244 ATGAGAATAAGGGAAAACCATGTGCTGGACAAATATCCTGGTGGTGGAAAATTACTGTTTTGCCC
257 ATGAGAATAAAGGAAAACCATGTGCTGGACAAATATCCTGGTGGTGGAAAATTACTATTTTGCCC
*
28658309 CTAGGGTGGCAAAATTACCATTTTGC-CCATATGCTTTGAAAAATACCAAGAATAAA-TTTTTTT
322 CTAGGGTGGCAAAATTACCATTTTACACC-TATGCTTTGAAAAATACCAAGAATAAATTTTTTTT
28658372 CACTTCTTAATCCTCAAATCATACTCCAATAAGTCAAATGGGGACAAAAATCGTTTCTAAAAATC
386 CACTTCTTAATCCTCAAATCATACTCCAATAAGTCAAATGGGGACAAAAATCGTTTCTAAAAATC
*
28658437 TCCATTTTGTCCTCAAGTAGCAAATGACCATTTTACC
451 TCCATTTTGTCCTCAAGTAGCAAATGACCATTTTGCC
28658474 CCT
1 CCT
28658477 AGATAGTGAA
Statistics
Matches: 474, Mismatches: 13, Indels: 9
0.96 0.03 0.02
Matches are distributed among these distances:
488 3 0.01
489 246 0.52
490 63 0.13
491 162 0.34
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (487 bp):
CCTTTTTCACTTAATTTCCTTGAAAATTCACACTTTTTCTTTGATTTTCTCTCTCTAGGGTTTTG
TTTTTGTTTTCTCTCTCTTCTTGCTGGTTTGGCCGGCCATGGGGTGGAAGATGGGCTGATTTTTG
TGCCTTTTAAAAAGAAAATAATAAATTAATAAAGGATGACACGTGGCATCATGTCAATGGCTCGT
TTTTAAAACTTAAAAATTTTAATCCTTTTATTCTCCACCACACAATTAGTCAATGGTCAAAATGA
GAATAAAGGAAAACCATGTGCTGGACAAATATCCTGGTGGTGGAAAATTACTATTTTGCCCCTAG
GGTGGCAAAATTACCATTTTACACCTATGCTTTGAAAAATACCAAGAATAAATTTTTTTTCACTT
CTTAATCCTCAAATCATACTCCAATAAGTCAAATGGGGACAAAAATCGTTTCTAAAAATCTCCAT
TTTGTCCTCAAGTAGCAAATGACCATTTTGCC
Found at i:28660618 original size:59 final size:56
Alignment explanation
Indices: 28660520--28660683 Score: 175
Period size: 59 Copynumber: 2.8 Consensus size: 56
28660510 NNNNNNNNNN
* *
28660520 AATTAAGACAAAAATATTTTATCTTGTCTAAATTGAGACAAATATGTTTTCCTGTCTA
1 AATTAAGACAAAAATATTTT-T-TTGTCTAAATTAAGACAAACATGTTTTCCTGTCTA
* * * *
28660578 GATTAAGACAAAAAATATTGTTTTTGTCTTAAATTAAGACAAACATATTTTCTTTTCTA
1 AATTAAGAC-AAAAATATT-TTTTTGTC-TAAATTAAGACAAACATGTTTTCCTGTCTA
* * * * *
28660637 AATTGAGACCAAACATGTTTTCTTATCTAAATTAAGACAAACATGTT
1 AATTAAGA-CAAAAATATTTTTTTGTCTAAATTAAGACAAACATGTT
28660684 AAAGCTGCCA
Statistics
Matches: 89, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
57 19 0.21
58 19 0.21
59 48 0.54
60 3 0.03
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (56 bp):
AATTAAGACAAAAATATTTTTTTGTCTAAATTAAGACAAACATGTTTTCCTGTCTA
Found at i:28660657 original size:29 final size:28
Alignment explanation
Indices: 28660520--28660683 Score: 157
Period size: 29 Copynumber: 5.6 Consensus size: 28
28660510 NNNNNNNNNN
* *
28660520 AATTAAGACAAAAATATTTTATCTTGTCTA
1 AATTAAGACAAACAT-GTTT-TCTTGTCTA
* * *
28660550 AATTGAGACAAATATGTTTTCCTGTCTA
1 AATTAAGACAAACATGTTTTCTTGTCTA
* * * *
28660578 GATTAAGACAAAAAATATTGTTTTTGTCTTA
1 AATTAAGAC-AAACATGTT-TTCTTGTC-TA
* *
28660609 AATTAAGACAAACATATTTTCTTTTCTA
1 AATTAAGACAAACATGTTTTCTTGTCTA
* *
28660637 AATTGAGACCAAACATGTTTTCTTATCTA
1 AATTAAGA-CAAACATGTTTTCTTGTCTA
28660666 AATTAAGACAAACATGTT
1 AATTAAGACAAACATGTT
28660684 AAAGCTGCCA
Statistics
Matches: 112, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
28 34 0.30
29 41 0.37
30 27 0.24
31 10 0.09
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (28 bp):
AATTAAGACAAACATGTTTTCTTGTCTA
Found at i:28669276 original size:43 final size:43
Alignment explanation
Indices: 28669228--28669346 Score: 132
Period size: 43 Copynumber: 2.8 Consensus size: 43
28669218 TCACCAACTC
** **** *
28669228 ATGCGCACTCCCTACTCGTACATGGTTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCACACATAACCGGGTCATC-CTCGGCTT
28669271 ATGCGCACTCCCTACTCACACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCACACATAACCGGGTCATCCTCGGCTT
** *
28669314 ATGCGCACTCCCTACTTGCACATAACCGAGTCA
1 ATGCGCACTCCCTACTCACACATAACCGGGTCA
28669347 ATATAATTAC
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 1 0.02
43 64 0.98
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.24
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCACACATAACCGGGTCATCCTCGGCTT
Found at i:28677097 original size:43 final size:43
Alignment explanation
Indices: 28677050--28677162 Score: 122
Period size: 43 Copynumber: 2.6 Consensus size: 43
28677040 GCTCATGCGT
** *
28677050 ACTCCCTACTCGCACATGGCTGGGTCATCAC-CGAG-TTATGCAC
1 ACTCCCTACTCGCACATAACCGGGTCATC-CTCG-GCTTATGCAC
*
28677093 ACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTTATGCGC
1 ACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTTATGCAC
* * * *
28677136 ACTTCCTACTTGCACATAGCCGAGTCA
1 ACTCCCTACTCGCACATAACCGGGTCA
28677163 ATATAATTAC
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 2 0.03
43 58 0.97
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (43 bp):
ACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTTATGCAC
Found at i:28684650 original size:42 final size:42
Alignment explanation
Indices: 28684553--28684681 Score: 134
Period size: 42 Copynumber: 3.1 Consensus size: 42
28684543 GTAATGATAT
* * * * **
28684553 TGACCCGGCTATGTGCGAATAAGAGTGTGCATAAGTTGATGC
1 TGACCCGACTATGTACGAGTAGGAGTGTGCATAAGCCGATGC
* *
28684595 TGACCCGACTATGTGCGAGTGGGAGTGTGCATAAGCCGATGC
1 TGACCCGACTATGTACGAGTAGGAGTGTGCATAAGCCGATGC
* * * *
28684637 TGACCC-AGTTATGTACTAGTAGGAGTGCGCAGAAGCCGATGC
1 TGACCCGA-CTATGTACGAGTAGGAGTGTGCATAAGCCGATGC
28684679 TGA
1 TGA
28684682 TTCGACCATA
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
41 1 0.01
42 73 0.99
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.23
Consensus pattern (42 bp):
TGACCCGACTATGTACGAGTAGGAGTGTGCATAAGCCGATGC
Found at i:28684750 original size:2 final size:2
Alignment explanation
Indices: 28684743--28684774 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
28684733 GTGCATGATG
*
28684743 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28684775 GGATATGTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:28691092 original size:42 final size:42
Alignment explanation
Indices: 28691028--28691122 Score: 154
Period size: 42 Copynumber: 2.3 Consensus size: 42
28691018 GTTATGTAAT
* * *
28691028 GATATTGACCCGGCTATGTGCGAGTAGGAGTGTGCATAAGCC
1 GATACTGACCCAGCTATGTGCGAGTAGGAGTGCGCATAAGCC
*
28691070 GATGCTGACCCAGCTATGTGCGAGTAGGAGTGCGCATAAGCC
1 GATACTGACCCAGCTATGTGCGAGTAGGAGTGCGCATAAGCC
28691112 GATACTGACCC
1 GATACTGACCC
28691123 GACCATATAC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.24, C:0.23, G:0.32, T:0.21
Consensus pattern (42 bp):
GATACTGACCCAGCTATGTGCGAGTAGGAGTGCGCATAAGCC
Found at i:28691142 original size:42 final size:42
Alignment explanation
Indices: 28691048--28691144 Score: 115
Period size: 42 Copynumber: 2.3 Consensus size: 42
28691038 CGGCTATGTG
* * * * *
28691048 CGAGTAGGAGTGTGCATAAGCCGATGCTGACCCAGCTATGTG
1 CGAGTAGGAGTGCGCATAAGCCGATACTGACCCAGCCATATA
28691090 CGAGTAGGAGTGCGCATAAGCCGATACTGACCC-GACCATATA
1 CGAGTAGGAGTGCGCATAAGCCGATACTGACCCAG-CCATATA
* *
28691132 CTAGTGGGAGTGC
1 CGAGTAGGAGTGC
28691145 ATATGAGCTG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.02
42 46 0.98
ACGTcount: A:0.26, C:0.23, G:0.32, T:0.20
Consensus pattern (42 bp):
CGAGTAGGAGTGCGCATAAGCCGATACTGACCCAGCCATATA
Found at i:28691285 original size:37 final size:37
Alignment explanation
Indices: 28691242--28691346 Score: 124
Period size: 37 Copynumber: 2.8 Consensus size: 37
28691232 ATAGTGCCCG
* *
28691242 TGTGCACGATGTGAGGGGATGTACACATGACACTGAC-
1 TGTGCACGATGTGGGGGGATG-ACACATGACACAGACA
* *
28691279 TGTGCACGATGTGGGGGGATGCACACGATGACTCAGGCTA
1 TGTGCACGATGTGGGGGGATG-ACAC-ATGACACAGAC-A
28691319 TGTGCACGATGTGGGGGGATG-CACATGA
1 TGTGCACGATGTGGGGGGATGACACATGA
28691347 TCTGGGTGAG
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
37 28 0.47
38 11 0.18
40 21 0.35
ACGTcount: A:0.24, C:0.18, G:0.37, T:0.21
Consensus pattern (37 bp):
TGTGCACGATGTGGGGGGATGACACATGACACAGACA
Found at i:28691328 original size:40 final size:37
Alignment explanation
Indices: 28691242--28691343 Score: 132
Period size: 40 Copynumber: 2.7 Consensus size: 37
28691232 ATAGTGCCCG
* * *
28691242 TGTGCACGATGTGAGGGGATGTACACATGACACTGAC
1 TGTGCACGATGTGGGGGGATGCACACATGACACAGAC
* *
28691279 TGTGCACGATGTGGGGGGATGCACACGATGACTCAGGC
1 TGTGCACGATGTGGGGGGATGCACAC-ATGACACAGAC
28691317 TATGTGCACGATGTGGGGGGATGCACA
1 --TGTGCACGATGTGGGGGGATGCACA
28691344 TGATCTGGGT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
37 24 0.42
38 8 0.14
40 25 0.44
ACGTcount: A:0.24, C:0.19, G:0.37, T:0.21
Consensus pattern (37 bp):
TGTGCACGATGTGGGGGGATGCACACATGACACAGAC
Found at i:28709756 original size:19 final size:22
Alignment explanation
Indices: 28709709--28709762 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
28709699 GGCCTAAGGA
28709709 ATAAATGAATGATGTATATAATG
1 ATAAAT-AATGATGTATATAATG
28709732 ATAAATAAATGATG-A-A-AAT-
1 ATAAAT-AATGATGTATATAATG
28709751 ATAAATAATGAT
1 ATAAATAATGAT
28709763 CATTTCCATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.20
19 6 0.20
20 3 0.10
21 1 0.03
22 1 0.03
23 13 0.43
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (22 bp):
ATAAATAATGATGTATATAATG
Found at i:28710683 original size:27 final size:28
Alignment explanation
Indices: 28710661--28710717 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
28710651 ATTTTTGGAG
*
28710661 CATAGGGGTAAAATAGTAATTTTGCCAC
1 CATAGGGGCAAAATAGTAATTTTGCCAC
* *
28710689 CCTATGGGCAAAATAGTAATTTT-CCAC
1 CATAGGGGCAAAATAGTAATTTTGCCAC
28710716 CA
1 CA
28710718 CCAGGACACT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (28 bp):
CATAGGGGCAAAATAGTAATTTTGCCAC
Found at i:28730071 original size:54 final size:54
Alignment explanation
Indices: 28729989--28730093 Score: 192
Period size: 54 Copynumber: 1.9 Consensus size: 54
28729979 TCATCATGTG
*
28729989 CATCTCACCCAGCTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
1 CATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
*
28730043 CATCTCACCCAACTTATGTGCATCCCACCACATCGTGCACATAGCCGGACA
1 CATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGGACA
28730094 GTATCACCAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.26, C:0.41, G:0.14, T:0.19
Consensus pattern (54 bp):
CATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCCGGACATCC
Found at i:28735336 original size:19 final size:20
Alignment explanation
Indices: 28735309--28735348 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
28735299 GCCTCAAACT
*
28735309 AGATCAAATAGAG-ATTTTA
1 AGATAAAATAGAGAATTTTA
*
28735328 AGATAAAATTGAGAATTTTA
1 AGATAAAATAGAGAATTTTA
28735348 A
1 A
28735349 AACCCCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.50, C:0.03, G:0.15, T:0.33
Consensus pattern (20 bp):
AGATAAAATAGAGAATTTTA
Found at i:28749900 original size:42 final size:42
Alignment explanation
Indices: 28749836--28749966 Score: 145
Period size: 42 Copynumber: 3.1 Consensus size: 42
28749826 TGTTGTGTAA
* * * *
28749836 TGATATTGACCCAGTTATGTGCGAGTAGAAGTGTGCATAAGC
1 TGATGTTGACCCGGCTATGTGCGAGTAGAAGTGCGCATAAGC
* *
28749878 TGATGTTGACCCGGCTATGTGCGAGTGGGAGTGCGCATAAGC
1 TGATGTTGACCCGGCTATGTGCGAGTAGAAGTGCGCATAAGC
* * * * * *
28749920 CGATGCTGACCAGGCTATGTGCGAGTGGGAGTGCACATAAGC
1 TGATGTTGACCCGGCTATGTGCGAGTAGAAGTGCGCATAAGC
*
28749962 CGATG
1 TGATG
28749967 CATATGAGCT
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 79 1.00
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.24
Consensus pattern (42 bp):
TGATGTTGACCCGGCTATGTGCGAGTAGAAGTGCGCATAAGC
Found at i:28749967 original size:42 final size:42
Alignment explanation
Indices: 28749851--28749967 Score: 171
Period size: 42 Copynumber: 2.8 Consensus size: 42
28749841 TTGACCCAGT
* * * * * *
28749851 TATGTGCGAGTAGAAGTGTGCATAAGCTGATGTTGACCCGGC
1 TATGTGCGAGTGGGAGTGCGCATAAGCCGATGCTGACCAGGC
28749893 TATGTGCGAGTGGGAGTGCGCATAAGCCGATGCTGACCAGGC
1 TATGTGCGAGTGGGAGTGCGCATAAGCCGATGCTGACCAGGC
*
28749935 TATGTGCGAGTGGGAGTGCACATAAGCCGATGC
1 TATGTGCGAGTGGGAGTGCGCATAAGCCGATGC
28749968 ATATGAGCTG
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.22
Consensus pattern (42 bp):
TATGTGCGAGTGGGAGTGCGCATAAGCCGATGCTGACCAGGC
Found at i:28750013 original size:2 final size:2
Alignment explanation
Indices: 28750008--28750057 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
28749998 ATGATGATTG
*
28750008 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
28750050 AC AT AT AT
1 AT AT AT AT
28750058 GGTATATGGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28751576 original size:42 final size:41
Alignment explanation
Indices: 28751517--28751644 Score: 177
Period size: 42 Copynumber: 3.0 Consensus size: 41
28751507 TTTTATGTGA
*
28751517 TAATGATGACCCAGCTATGTGAGTGGGGGAGTGCACATGAGC
1 TAATGATGACCCAGCTATGTGAGT-GAGGAGTGCACATGAGC
*
28751559 TAATGATGACCCAGCTATGTGCGATGTA-GAGTGCACATGAGC
1 TAATGATGACCCAGCTATGTGAG-TG-AGGAGTGCACATGAGC
*
28751601 TGATGATGACCCAGCTATGTTTGAGTGAGGAGTGCACATGAGC
1 TAATGATGACCCAGCTATG--TGAGTGAGGAGTGCACATGAGC
28751644 T
1 T
28751645 GATAATGGTG
Statistics
Matches: 77, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
42 56 0.73
43 18 0.23
44 3 0.04
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (41 bp):
TAATGATGACCCAGCTATGTGAGTGAGGAGTGCACATGAGC
Found at i:28753280 original size:12 final size:13
Alignment explanation
Indices: 28753263--28753292 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
28753253 TCTTCTTTTG
28753263 AATTTTCAACCA-
1 AATTTTCAACCAT
28753275 AATTTTCAACCAT
1 AATTTTCAACCAT
28753288 AATTT
1 AATTT
28753293 CCTTTTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTTTCAACCAT
Found at i:28753557 original size:21 final size:21
Alignment explanation
Indices: 28753533--28753579 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
28753523 AATCTTAGCT
* *
28753533 ATGAAGGTATCATTCTTTGTC
1 ATGAAGGCATCAGTCTTTGTC
28753554 ATGAAGGCATCAGTCTTTGTC
1 ATGAAGGCATCAGTCTTTGTC
28753575 ATGAA
1 ATGAA
28753580 TTGCACAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (21 bp):
ATGAAGGCATCAGTCTTTGTC
Found at i:28760776 original size:13 final size:13
Alignment explanation
Indices: 28760758--28760782 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28760748 GGCAGAGAGT
28760758 ACTTAGTTGACTG
1 ACTTAGTTGACTG
28760771 ACTTAGTTGACT
1 ACTTAGTTGACT
28760783 AAATTGATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (13 bp):
ACTTAGTTGACTG
Found at i:28785234 original size:23 final size:23
Alignment explanation
Indices: 28785204--28785257 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
28785194 TACATATACT
28785204 CATCATCATCATGCACACCATCC
1 CATCATCATCATGCACACCATCC
* *
28785227 CATCATCATCATGCACACCGTCT
1 CATCATCATCATGCACACCATCC
28785250 CATCATCA
1 CATCATCA
28785258 CCAGCTCATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.30, C:0.41, G:0.06, T:0.24
Consensus pattern (23 bp):
CATCATCATCATGCACACCATCC
Found at i:28785299 original size:43 final size:43
Alignment explanation
Indices: 28785252--28785383 Score: 124
Period size: 43 Copynumber: 3.1 Consensus size: 43
28785242 CACCGTCTCA
****
28785252 TCATCACCAGCTCATGCGCACTCCCTACTCGCACATGGTTGGG
1 TCATCACCAGCTCATGCGCACTCCCTACTCGCACATAACCGGG
* * *
28785295 TCATCACCAAG-TTATGCACACTCCCTACTCGTACATAACCGGG
1 TCATCACC-AGCTCATGCGCACTCCCTACTCGCACATAACCGGG
* * * * *
28785338 TCATCATCGGC-CTATACGCACTCCCTACTCGCACATAGCCGAG
1 TCATCACCAGCTC-ATGCGCACTCCCTACTCGCACATAACCGGG
28785381 TCA
1 TCA
28785384 ATATAATTAC
Statistics
Matches: 71, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
42 1 0.01
43 68 0.96
44 2 0.03
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.23
Consensus pattern (43 bp):
TCATCACCAGCTCATGCGCACTCCCTACTCGCACATAACCGGG
Found at i:28787684 original size:54 final size:54
Alignment explanation
Indices: 28787601--28787809 Score: 303
Period size: 54 Copynumber: 3.9 Consensus size: 54
28787591 TCATCATGTG
* *
28787601 CATCTCACCCAGCCCATGTGCATCCCACCACATCATGCACATAGCCAAACATCC
1 CATCTCACCCAACTCATGTGCATCCCACCACATCATGCACATAGCCAAACATCC
* * **
28787655 TATCTCACCCAACTCATGTGCATCCCACCACAT-AGTGCACATAACCGGACATCC
1 CATCTCACCCAACTCATGTGCATCCCACCACATCA-TGCACATAGCCAAACATCC
* **
28787709 CATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCTGAACATCC
1 CATCTCACCCAACTCATGTGCATCCCACCACATCATGCACATAGCCAAACATCC
* *
28787763 CATCTCACCCAACTCATGCGCATCCCACCACATCGTGCACATAGCCA
1 CATCTCACCCAACTCATGTGCATCCCACCACATCATGCACATAGCCA
28787810 GACAATATCA
Statistics
Matches: 139, Mismatches: 14, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
53 1 0.01
54 138 0.99
ACGTcount: A:0.29, C:0.42, G:0.11, T:0.19
Consensus pattern (54 bp):
CATCTCACCCAACTCATGTGCATCCCACCACATCATGCACATAGCCAAACATCC
Found at i:28787786 original size:25 final size:25
Alignment explanation
Indices: 28787704--28787789 Score: 64
Period size: 25 Copynumber: 3.3 Consensus size: 25
28787694 CATAACCGGA
*
28787704 CATCCCATCTCACCCAACTCATGTG
1 CATCCCATCTCACCCAACTCATGCG
* * * *** *
28787729 CATCCCACCACATCGTGCACATAGCTG
1 CATCCCATCTCACCCAACTCAT-GC-G
28787756 AACATCCCATCTCACCCAACTCATGCG
1 --CATCCCATCTCACCCAACTCATGCG
28787783 CATCCCA
1 CATCCCA
28787790 CCACATCGTG
Statistics
Matches: 42, Mismatches: 15, Indels: 8
0.65 0.23 0.12
Matches are distributed among these distances:
25 22 0.52
26 1 0.02
27 2 0.05
28 2 0.05
29 15 0.36
ACGTcount: A:0.27, C:0.44, G:0.09, T:0.20
Consensus pattern (25 bp):
CATCCCATCTCACCCAACTCATGCG
Found at i:28787790 original size:108 final size:108
Alignment explanation
Indices: 28787601--28787805 Score: 338
Period size: 108 Copynumber: 1.9 Consensus size: 108
28787591 TCATCATGTG
* *
28787601 CATCTCACCCAGCCCATGTGCATCCCACCACATCATGCACATAGCCAAACATCCTATCTCACCCA
1 CATCTCACCCAACCCATGTGCATCCCACCACATCATGCACATAGCCAAACATCCCATCTCACCCA
*
28787666 ACTCATGTGCATCCCACCACATAGTGCACATAACCGGACATCC
66 ACTCATGCGCATCCCACCACATAGTGCACATAACCGGACATCC
* * **
28787709 CATCTCACCCAACTCATGTGCATCCCACCACATCGTGCACATAGCTGAACATCCCATCTCACCCA
1 CATCTCACCCAACCCATGTGCATCCCACCACATCATGCACATAGCCAAACATCCCATCTCACCCA
*
28787774 ACTCATGCGCATCCCACCACATCGTGCACATA
66 ACTCATGCGCATCCCACCACATAGTGCACATA
28787806 GCCAGACAAT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
108 89 1.00
ACGTcount: A:0.29, C:0.42, G:0.10, T:0.19
Consensus pattern (108 bp):
CATCTCACCCAACCCATGTGCATCCCACCACATCATGCACATAGCCAAACATCCCATCTCACCCA
ACTCATGCGCATCCCACCACATAGTGCACATAACCGGACATCC
Found at i:28792049 original size:41 final size:42
Alignment explanation
Indices: 28791974--28792149 Score: 230
Period size: 42 Copynumber: 4.2 Consensus size: 42
28791964 GAAAACTACA
* * * *
28791974 CAATCCACTTTA-AATCAAAAACATGGGAAATGGAGACCTACT
1 CAATCCACTTGACAAT-AAAATCATGGGAAGTGGAGACATACT
* * * *
28792016 CAATCCAGTTTACCA-CAAATCATGGGAAGTGGAGACATACT
1 CAATCCACTTGACAATAAAATCATGGGAAGTGGAGACATACT
28792057 CAATCCACTTGACAATAAAATCATGGGAAGTGGAGACATACT
1 CAATCCACTTGACAATAAAATCATGGGAAGTGGAGACATACT
* *
28792099 CAATCCACTTGACAATAAAATCATGGGAATGTGGAGACTTTCT
1 CAATCCACTTGACAATAAAATCATGGGAA-GTGGAGACATACT
28792142 CAATCCAC
1 CAATCCAC
28792150 ATCACAACAC
Statistics
Matches: 119, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
41 34 0.29
42 65 0.55
43 20 0.17
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.23
Consensus pattern (42 bp):
CAATCCACTTGACAATAAAATCATGGGAAGTGGAGACATACT
Found at i:28795529 original size:20 final size:20
Alignment explanation
Indices: 28795484--28795521 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
28795474 TTTTGGCCCC
28795484 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
*
28795504 ATTTGACTTATTTGAGTA
1 ATTTGACTTATTGGAGTA
28795522 AGATTTGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.05, G:0.18, T:0.47
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:28799760 original size:21 final size:21
Alignment explanation
Indices: 28799734--28799775 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
28799724 AAAGAGAAGG
28799734 TTTCTCACTGCAACGAAATTC
1 TTTCTCACTGCAACGAAATTC
* *
28799755 TTTCTCGCTGCAGCGAAATTC
1 TTTCTCACTGCAACGAAATTC
28799776 AGCTGATGAA
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:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (21 bp):
TTTCTCACTGCAACGAAATTC
Found at i:28800259 original size:38 final size:39
Alignment explanation
Indices: 28800170--28800275 Score: 135
Period size: 38 Copynumber: 2.7 Consensus size: 39
28800160 CACACCCGGC
* *
28800170 TCATGTACATCCCCTCACATCGTGCACATAGCCGGCACCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAGG-ACCA
* * *
28800210 TCGTGTGCATCCCCCCACATCGTGCACA-ATCAGTG-CCA
1 TCATGTACATCCCCCCACATCGTGCACATAGCAG-GACCA
28800248 TCATGTACATCCCCCCACATCGTGCACA
1 TCATGTACATCCCCCCACATCGTGCACA
28800276 CAGGCACTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
38 29 0.50
39 3 0.05
40 26 0.45
ACGTcount: A:0.24, C:0.41, G:0.15, T:0.21
Consensus pattern (39 bp):
TCATGTACATCCCCCCACATCGTGCACATAGCAGGACCA
Found at i:28806638 original size:22 final size:24
Alignment explanation
Indices: 28806612--28806657 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 24
28806602 TTACAAATAA
28806612 GAGATAATAAT-AA-AAAAATATT
1 GAGATAATAATAAATAAAAATATT
28806634 GAGATAATAATAAATAAAAATATT
1 GAGATAATAATAAATAAAAATATT
28806658 AATTGAAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 11 0.50
23 2 0.09
24 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (24 bp):
GAGATAATAATAAATAAAAATATT
Found at i:28809027 original size:11 final size:11
Alignment explanation
Indices: 28809000--28809043 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
28808990 CCTAGGGTTC
28809000 TTGTTCTT-C-
1 TTGTTCTTCCT
28809009 TT-TTCTTCCT
1 TTGTTCTTCCT
28809019 TTGTTCTTCCTT
1 TTGTTCTTCC-T
28809031 TTGTT-TTCCT
1 TTGTTCTTCCT
28809041 TTG
1 TTG
28809044 GCAGGCCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 5 0.16
9 3 0.10
10 6 0.19
11 11 0.35
12 6 0.19
ACGTcount: A:0.00, C:0.23, G:0.09, T:0.68
Consensus pattern (11 bp):
TTGTTCTTCCT
Found at i:28814882 original size:11 final size:11
Alignment explanation
Indices: 28814855--28814898 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
28814845 TCTAGGGTTC
28814855 TTGTTCTT-C-
1 TTGTTCTTCCT
28814864 TT-TTCTTCCT
1 TTGTTCTTCCT
28814874 TTGTTCTTCCTT
1 TTGTTCTTCC-T
28814886 TTGTT-TTCCT
1 TTGTTCTTCCT
28814896 TTG
1 TTG
28814899 GCTGGCCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
8 5 0.16
9 3 0.10
10 6 0.19
11 11 0.35
12 6 0.19
ACGTcount: A:0.00, C:0.23, G:0.09, T:0.68
Consensus pattern (11 bp):
TTGTTCTTCCT
Found at i:28816254 original size:23 final size:23
Alignment explanation
Indices: 28816224--28816274 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
28816214 AGAAACATTG
28816224 AAGCTGCCATTGGCCTTGTTTAA
1 AAGCTGCCATTGGCCTTGTTTAA
28816247 AAGCTGCCATTGGCCTTGTTTAA
1 AAGCTGCCATTGGCCTTGTTTAA
28816270 AAGCT
1 AAGCT
28816275 TACTTTCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (23 bp):
AAGCTGCCATTGGCCTTGTTTAA
Found at i:28836738 original size:24 final size:24
Alignment explanation
Indices: 28836710--28836759 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
28836700 ATCATGTTTT
28836710 TGATGATATACCTTATGATAATTA
1 TGATGATATACCTTATGATAATTA
28836734 TGATGATATACCTTATGATAATTA
1 TGATGATATACCTTATGATAATTA
28836758 TG
1 TG
28836760 CTCAATTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (24 bp):
TGATGATATACCTTATGATAATTA
Found at i:28839535 original size:27 final size:29
Alignment explanation
Indices: 28839489--28839543 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
28839479 GACAAGTGCT
*
28839489 GGGGTGAAAAATTTACCGA-TTTGCCCCC
1 GGGGTGAAAAAATTACCGATTTTGCCCCC
28839517 GGGGTGAAAAAATTA-CGATTTTGCCCC
1 GGGGTGAAAAAATTACCGATTTTGCCCC
28839544 TATACTCCGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 3 0.12
28 22 0.88
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (29 bp):
GGGGTGAAAAAATTACCGATTTTGCCCCC
Found at i:28844239 original size:4 final size:4
Alignment explanation
Indices: 28844230--28844297 Score: 61
Period size: 4 Copynumber: 17.2 Consensus size: 4
28844220 CAAGCCTAAC
* * * *
28844230 CTTT CTTT CTCT CTTT CTCT C-TT CTTT CTTC CTTT CCTTT CGTTT CTCT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT -CTTT C-TTT CTTT
28844279 -TTT C-TT CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT C
28844298 CCTTTCTCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
3 7 0.14
4 36 0.71
5 8 0.16
ACGTcount: A:0.00, C:0.32, G:0.01, T:0.66
Consensus pattern (4 bp):
CTTT
Found at i:28845763 original size:2 final size:2
Alignment explanation
Indices: 28845756--28845792 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
28845746 ACAATGGTTG
28845756 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28845793 GTANAGCTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28845901 original size:161 final size:160
Alignment explanation
Indices: 28845634--28845953 Score: 631
Period size: 161 Copynumber: 2.0 Consensus size: 160
28845624 ACTTAGTCTT
28845634 TAAGCTATGTTTTCTTTTTTGATGTGTTTTATGATTGAACAATGTTTTATGCTGTGTTATGAACA
1 TAAGCTATGTTTTCTTTTTTGATGTGTTTTATGATTGAACAATGTTTTATGCTGTGTTATGAACA
28845699 ATGGTTAAAGTTTATGTCTTTATGATGGAATTGTGTTGAATAGCTAAACAATGGTTGTATATATA
66 ATGGTTAAAGTTTATGTCTTTATGATGGAATTGTGTTGAATAGCTAAACAATGGTTGTATATATA
28845764 TATATATATATATATATATATATATATATG
131 TATATATATATATATATATATATATATATG
28845794 TANAGCTATGTTTTCTTTTTTGATGTGTTTTATGATTGAACAATGTTTTATGCTGTGTTATGAAC
1 TA-AGCTATGTTTTCTTTTTTGATGTGTTTTATGATTGAACAATGTTTTATGCTGTGTTATGAAC
28845859 AATGGTTAAAGTTTATGTCTTTATGATGGAATTGTGTTGAATAGCTAAACAATGGTTGTATATAT
65 AATGGTTAAAGTTTATGTCTTTATGATGGAATTGTGTTGAATAGCTAAACAATGGTTGTATATAT
28845924 ATATATATATATATATATATATATATATAT
130 ATATATATATATATATATATATATATATAT
28845954 TGGTATATGC
Statistics
Matches: 159, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
160 2 0.01
161 157 0.99
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.47
Consensus pattern (160 bp):
TAAGCTATGTTTTCTTTTTTGATGTGTTTTATGATTGAACAATGTTTTATGCTGTGTTATGAACA
ATGGTTAAAGTTTATGTCTTTATGATGGAATTGTGTTGAATAGCTAAACAATGGTTGTATATATA
TATATATATATATATATATATATATATATG
Found at i:28845924 original size:2 final size:2
Alignment explanation
Indices: 28845917--28845953 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
28845907 ACAATGGTTG
28845917 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28845954 TGGTATATGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:28851521 original size:69 final size:68
Alignment explanation
Indices: 28851439--28851610 Score: 256
Period size: 69 Copynumber: 2.5 Consensus size: 68
28851429 TAAATAATAG
* * * *
28851439 GAAATTGTTTCCTACTTTAAAAGTAATTCCTAAAATTAAGGATAGAATTTTAATTTGGGAAATTC
1 GAAATAGTTTCCTACTTTAAAAGAAATTCCTAAAATTAAAGATAGAATTTTAATTTGAGAAATTC
28851504 ATAA
66 AT-A
*
28851508 GAAATAGTTTCCTACTTTAAGAA-AAATTCCTAAAATTAAAGATAGCATTTTAATTTGAGAAATT
1 GAAATAGTTTCCTACTTTAA-AAGAAATTCCTAAAATTAAAGATAGAATTTTAATTTGAGAAATT
28851572 CATA
65 CATA
*
28851576 GAAAATAGTTTACTACTTTAAAAGAAATTCCTAAA
1 G-AAATAGTTTCCTACTTTAAAAGAAATTCCTAAA
28851611 TTTATGTGAT
Statistics
Matches: 94, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
68 4 0.04
69 88 0.94
70 2 0.02
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.35
Consensus pattern (68 bp):
GAAATAGTTTCCTACTTTAAAAGAAATTCCTAAAATTAAAGATAGAATTTTAATTTGAGAAATTC
ATA
Found at i:28854983 original size:43 final size:43
Alignment explanation
Indices: 28854935--28855066 Score: 176
Period size: 43 Copynumber: 3.1 Consensus size: 43
28854925 CACCCTCCAA
* * * *
28854935 TCATCATCAGCTTATAGGCACTCCTTACTCGCACATAGCTGGG
1 TCATCATCGGCTTATAGGCACTCCCTACTCGCACATAGCCGAG
* * *
28854978 TCATCATCGGTTTATACGCACTCCCTACTCGCACATAACCGAG
1 TCATCATCGGCTTATAGGCACTCCCTACTCGCACATAGCCGAG
*
28855021 TCATCATCGGCTTAT-GCTCACTCCCTACTCGCACATAGCCGAG
1 TCATCATCGGCTTATAG-GCACTCCCTACTCGCACATAGCCGAG
28855064 TCA
1 TCA
28855067 ATATCATTAC
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
43 77 1.00
ACGTcount: A:0.23, C:0.34, G:0.16, T:0.27
Consensus pattern (43 bp):
TCATCATCGGCTTATAGGCACTCCCTACTCGCACATAGCCGAG
Found at i:28861873 original size:43 final size:43
Alignment explanation
Indices: 28861823--28861904 Score: 146
Period size: 43 Copynumber: 1.9 Consensus size: 43
28861813 CACATGGCTG
*
28861823 GGTCATTATCGGTTTATGCGCACTCCTTACTCGCACATAACCA
1 GGTCATTATCGGCTTATGCGCACTCCTTACTCGCACATAACCA
*
28861866 GGTCATTATCGGCTTATGCGCACTCCTTACTCGTACATA
1 GGTCATTATCGGCTTATGCGCACTCCTTACTCGCACATA
28861905 GCCGAGTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (43 bp):
GGTCATTATCGGCTTATGCGCACTCCTTACTCGCACATAACCA
Found at i:28864509 original size:38 final size:38
Alignment explanation
Indices: 28864459--28864555 Score: 167
Period size: 38 Copynumber: 2.6 Consensus size: 38
28864449 TCATTATGTG
**
28864459 CATCCCCCCACATCGTGCACGGTCAGTGCCATCGTGTA
1 CATCCCCCCACATCGTGCACAATCAGTGCCATCGTGTA
*
28864497 CATCCCCTCACATCGTGCACAATCAGTGCCATCGTGTA
1 CATCCCCCCACATCGTGCACAATCAGTGCCATCGTGTA
28864535 CATCCCCCCACATCGTGCACA
1 CATCCCCCCACATCGTGCACA
28864556 CGGGCACTAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 55 1.00
ACGTcount: A:0.22, C:0.41, G:0.16, T:0.21
Consensus pattern (38 bp):
CATCCCCCCACATCGTGCACAATCAGTGCCATCGTGTA
Found at i:28864510 original size:19 final size:19
Alignment explanation
Indices: 28864488--28864551 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
28864478 CGGTCAGTGC
28864488 CATCGTGTACATCCCCTCA
1 CATCGTGTACATCCCCTCA
* **
28864507 CATCGTGCACAAT-CAGTGC-
1 CATCGTGTAC-ATCCCCT-CA
*
28864526 CATCGTGTACATCCCCCCA
1 CATCGTGTACATCCCCTCA
28864545 CATCGTG
1 CATCGTG
28864552 CACACGGGCA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
18 3 0.09
19 28 0.82
20 3 0.09
ACGTcount: A:0.22, C:0.39, G:0.16, T:0.23
Consensus pattern (19 bp):
CATCGTGTACATCCCCTCA
Found at i:28864679 original size:2 final size:2
Alignment explanation
Indices: 28864672--28864719 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
28864662 AATGCACATC
28864672 AT AT AT AT 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 AT AT AT AT AT
28864713 AT AT AT A
1 AT AT AT A
28864720 NNNNNNNNNN
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28876558 original size:17 final size:17
Alignment explanation
Indices: 28876538--28876574 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
28876528 TTTTATTAAG
*
28876538 GCACATATTTAGGGGGA
1 GCACATATTCAGGGGGA
28876555 GCACATATTCAGGGGGA
1 GCACATATTCAGGGGGA
28876572 GCA
1 GCA
28876575 ATCCCTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.16, G:0.35, T:0.19
Consensus pattern (17 bp):
GCACATATTCAGGGGGA
Found at i:28885475 original size:19 final size:19
Alignment explanation
Indices: 28885451--28885488 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28885441 ACTTCTAAAC
28885451 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
28885470 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
28885489 AGTCAAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:28887440 original size:55 final size:55
Alignment explanation
Indices: 28887356--28887493 Score: 186
Period size: 55 Copynumber: 2.5 Consensus size: 55
28887346 GGGTGTTACA
* * * *
28887356 ACTCCCACACCGTACATAGCTAGAATCATCGCCCACCGGTCATCAGATCATGTGC
1 ACTCCCAAACCGCACATAGCTGGAATCATCACCCACCGGTCATCAGATCATGTGC
* * ** *
28887411 ACTCCCAAATCGCACATAGCTGGAATCATCATCCATTGGTCATCAGCTCATGTGC
1 ACTCCCAAACCGCACATAGCTGGAATCATCACCCACCGGTCATCAGATCATGTGC
*
28887466 ACTCCCACACCGCACATAGCTGGAATCA
1 ACTCCCAAACCGCACATAGCTGGAATCA
28887494 CTCGTCATCA
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 72 1.00
ACGTcount: A:0.28, C:0.35, G:0.16, T:0.21
Consensus pattern (55 bp):
ACTCCCAAACCGCACATAGCTGGAATCATCACCCACCGGTCATCAGATCATGTGC
Found at i:28888137 original size:11 final size:11
Alignment explanation
Indices: 28888123--28888152 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
28888113 AATAATATTT
28888123 TATTAATAAAA
1 TATTAATAAAA
*
28888134 TATTATTAAAA
1 TATTAATAAAA
28888145 TATTAATA
1 TATTAATA
28888153 TTTTATTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAATAAAA
Found at i:28889903 original size:54 final size:54
Alignment explanation
Indices: 28889838--28889942 Score: 174
Period size: 54 Copynumber: 1.9 Consensus size: 54
28889828 ATGGTGATAC
* * *
28889838 TGTCCGGCTATGTGCATGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGA
1 TGTCCAGCTATGTGCACGATGTGGTGGGATGCACATGAGCTAGGTGAGATGGGA
*
28889892 TGTCCAGCTATGTGCACGATGTTGTGGGATGCACATGAGCTAGGTGAGATG
1 TGTCCAGCTATGTGCACGATGTGGTGGGATGCACATGAGCTAGGTGAGATG
28889943 CACATGATGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.20, C:0.14, G:0.39, T:0.27
Consensus pattern (54 bp):
TGTCCAGCTATGTGCACGATGTGGTGGGATGCACATGAGCTAGGTGAGATGGGA
Found at i:28894160 original size:20 final size:19
Alignment explanation
Indices: 28894137--28894183 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
28894127 AGGAAGAAGT
* *
28894137 AAGAAAAGATAGGAAAGGAA
1 AAGAAAACA-AGGAAAAGAA
28894157 AAGAAAACAAGGAAAAGAA
1 AAGAAAACAAGGAAAAGAA
28894176 AATGAAAA
1 AA-GAAAA
28894184 AACTTGATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.70, C:0.02, G:0.23, T:0.04
Consensus pattern (19 bp):
AAGAAAACAAGGAAAAGAA
Found at i:28894170 original size:14 final size:14
Alignment explanation
Indices: 28894151--28894177 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
28894141 AAAGATAGGA
28894151 AAGGAAAAGAAAAC
1 AAGGAAAAGAAAAC
28894165 AAGGAAAAGAAAA
1 AAGGAAAAGAAAA
28894178 TGAAAAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.04, G:0.22, T:0.00
Consensus pattern (14 bp):
AAGGAAAAGAAAAC
Found at i:28901319 original size:20 final size:20
Alignment explanation
Indices: 28901296--28901334 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
28901286 TAAGAAAAGA
28901296 AAGGAAAAAAAAAAGAAAAC
1 AAGGAAAAAAAAAAGAAAAC
* *
28901316 AAGGAAAAGAAAATGAAAA
1 AAGGAAAAAAAAAAGAAAA
28901335 AACTTGATCT
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:0.77, C:0.03, G:0.18, T:0.03
Consensus pattern (20 bp):
AAGGAAAAAAAAAAGAAAAC
Found at i:28909736 original size:43 final size:43
Alignment explanation
Indices: 28909684--28909849 Score: 187
Period size: 43 Copynumber: 3.9 Consensus size: 43
28909674 ATTCATCGTC
* *
28909684 ATGTGCACTCCCTAC-TCGCACAT-GGTCGGGTCATCATCGGCTT
1 ATGTGCACTCCC-ACATCGCACATAGCT-GGGTCATCATCAGCTT
* * * *
28909727 ATGCGCACTCCCTAC-CCGTACATAGCTGGGTCATCATCAGCTC
1 ATGTGCACTCCC-ACATCGCACATAGCTGGGTCATCATCAGCTT
* *
28909770 ATGTGCACTCCCACATCGCACGTAGTTGGGTCATCATCAGCTCT
1 ATGTGCACTCCCACATCGCACATAGCTGGGTCATCATCAGCT-T
*
28909814 -TGTGCACTCTCACATCGCACATAGCTGGGTCATCAT
1 ATGTGCACTCCCACATCGCACATAGCTGGGTCATCAT
28909850 TATCACACAA
Statistics
Matches: 105, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
42 2 0.02
43 101 0.96
44 2 0.02
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.27
Consensus pattern (43 bp):
ATGTGCACTCCCACATCGCACATAGCTGGGTCATCATCAGCTT
Found at i:28909836 original size:86 final size:86
Alignment explanation
Indices: 28909682--28909849 Score: 216
Period size: 86 Copynumber: 2.0 Consensus size: 86
28909672 TCATTCATCG
* * *
28909682 TCATGTGCACTCCCTACTCGCACATGGTCGGGTCATCATCGGCTTATGCGCACTCCCTACCCGTA
1 TCATGTGCACTCCCTACTCGCACATAGTCGGGTCATCATCAGCTTATGCGCACTCCCTACCCGCA
28909747 CATAGCTGGGTCATCATCAGC
66 CATAGCTGGGTCATCATCAGC
* * * * *
28909768 TCATGTGCACTCCC-ACATCGCACGTAGTTGGGTCATCATCAGCTCT-TGTGCACTCTC-ACATC
1 TCATGTGCACTCCCTAC-TCGCACATAGTCGGGTCATCATCAGCT-TATGCGCACTCCCTAC-CC
28909830 GCACATAGCTGGGTCATCAT
63 GCACATAGCTGGGTCATCAT
28909850 TATCACACAA
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
85 4 0.06
86 66 0.93
87 1 0.01
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.27
Consensus pattern (86 bp):
TCATGTGCACTCCCTACTCGCACATAGTCGGGTCATCATCAGCTTATGCGCACTCCCTACCCGCA
CATAGCTGGGTCATCATCAGC
Found at i:28915079 original size:19 final size:19
Alignment explanation
Indices: 28915039--28915080 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
28915029 AGGCCTAAGG
* *
28915039 AATAAATGAATGAGGGTAA
1 AATAAATGAATGAAGATAA
28915058 AATAAATGAA-GAAGATATA
1 AATAAATGAATGAAGATA-A
28915077 AATA
1 AATA
28915081 CTGATAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.60, C:0.00, G:0.19, T:0.21
Consensus pattern (19 bp):
AATAAATGAATGAAGATAA
Found at i:28924641 original size:42 final size:42
Alignment explanation
Indices: 28924586--28924668 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
28924576 TGTTGATGTG
*
28924586 GACCCGACTATGTGCGACTAAGAGTGTACATAAGCCGATGAT
1 GACCCGACTATGTGCGACTAAGAGTGCACATAAGCCGATGAT
* **
28924628 GACCCGACTATGTGCGAGTGGGAGTGCACATAAGCCGATGA
1 GACCCGACTATGTGCGACTAAGAGTGCACATAAGCCGATGA
28924669 NNNNNNNNNN
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.29, C:0.22, G:0.30, T:0.19
Consensus pattern (42 bp):
GACCCGACTATGTGCGACTAAGAGTGCACATAAGCCGATGAT
Found at i:28925288 original size:19 final size:19
Alignment explanation
Indices: 28925264--28925300 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28925254 AGGTTTGGTG
*
28925264 AGAAACCCTCTGTTAGTTA
1 AGAAACCCTCGGTTAGTTA
28925283 AGAAACCCTCGGTTAGTT
1 AGAAACCCTCGGTTAGTT
28925301 GATAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.30
Consensus pattern (19 bp):
AGAAACCCTCGGTTAGTTA
Found at i:28929197 original size:20 final size:20
Alignment explanation
Indices: 28929151--28929208 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
28929141 GTTTAAATTT
* * *
28929151 TTATTTTACGTTAATGAT-G
1 TTATTTTACGTTATTTATAA
28929170 TTAGTTTTACGTTATTTATAA
1 TTA-TTTTACGTTATTTATAA
*
28929191 TTATTTTATGTT-TTTATA
1 TTATTTTACGTTATTTATA
28929209 GGAGTAGGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 9 0.27
20 21 0.64
21 3 0.09
ACGTcount: A:0.26, C:0.03, G:0.10, T:0.60
Consensus pattern (20 bp):
TTATTTTACGTTATTTATAA
Found at i:28930345 original size:55 final size:55
Alignment explanation
Indices: 28930276--28930484 Score: 276
Period size: 55 Copynumber: 3.8 Consensus size: 55
28930266 TGATGACAGG
* ** *
28930276 TGATTCCAGTTATGTGCAATGTGGGAAAGCACATGAGCTGATGACCGGTGAATGA
1 TGATTCCAGCTATGTGCAATGTGGGAGTGCACATGAGCTGATGACCGGTGGATGA
* * *
28930331 TGATTCCAGCTATGTGCGATGTGGGAGTGCACATGAGCTGATGACCGATGGGTGA
1 TGATTCCAGCTATGTGCAATGTGGGAGTGCACATGAGCTGATGACCGGTGGATGA
* * * * *
28930386 TGATAT-TAGCTATGTGCAGTGTGGGAGTGCACATAAGCTGATGATCAGTGGATGA
1 TGAT-TCCAGCTATGTGCAATGTGGGAGTGCACATGAGCTGATGACCGGTGGATGA
**
28930441 TGATTCCAGCTATGTGCGGTGTGGGAGTGCACATGAGCTGATGA
1 TGATTCCAGCTATGTGCAATGTGGGAGTGCACATGAGCTGATGA
28930485 GCCGATGGTT
Statistics
Matches: 134, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
54 1 0.01
55 132 0.99
56 1 0.01
ACGTcount: A:0.25, C:0.14, G:0.34, T:0.27
Consensus pattern (55 bp):
TGATTCCAGCTATGTGCAATGTGGGAGTGCACATGAGCTGATGACCGGTGGATGA
Found at i:28930426 original size:110 final size:111
Alignment explanation
Indices: 28930286--28930492 Score: 335
Period size: 110 Copynumber: 1.9 Consensus size: 111
28930276 TGATTCCAGT
* *
28930286 TATGTGCAATGTGGGAAAGCACATGAGCTGATGACCGGTGAATGATGATTCCAGCTATGTGCGAT
1 TATGTGCAATGTGGGAAAGCACATAAGCTGATGACCAGTGAATGATGATTCCAGCTATGTGCGAT
28930351 GTGGGAGTGCACATGAGCTGATGA-CCGATGGGTGATGATATTAGC
66 GTGGGAGTGCACATGAGCTGATGAGCCGATGGGTGATGATATTAGC
* ** * * *
28930396 TATGTGCAGTGTGGGAGTGCACATAAGCTGATGATCAGTGGATGATGATTCCAGCTATGTGCGGT
1 TATGTGCAATGTGGGAAAGCACATAAGCTGATGACCAGTGAATGATGATTCCAGCTATGTGCGAT
28930461 GTGGGAGTGCACATGAGCTGATGAGCCGATGG
66 GTGGGAGTGCACATGAGCTGATGAGCCGATGG
28930493 TTGTATACAC
Statistics
Matches: 88, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
110 81 0.92
111 7 0.08
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.26
Consensus pattern (111 bp):
TATGTGCAATGTGGGAAAGCACATAAGCTGATGACCAGTGAATGATGATTCCAGCTATGTGCGAT
GTGGGAGTGCACATGAGCTGATGAGCCGATGGGTGATGATATTAGC
Found at i:28932519 original size:70 final size:69
Alignment explanation
Indices: 28932437--28932575 Score: 260
Period size: 70 Copynumber: 2.0 Consensus size: 69
28932427 ATTTGATTTA
28932437 AGTCTAACTTAAATCATCACACTCTCAATTTAATCCAAATTGCAACCTTTGTGGGTGACCCATTA
1 AGTCTAACTTAAATCATCACACTCTCAATTTAATCCAAATTGCAACCTTTGTGGGTGACCCATTA
28932502 GGTT
66 GGTT
*
28932506 NAGTCTAACTTAAATCATCACACTCTCAATTTAATCCAAATTGCAACCTTTGTGTGTGACCCATT
1 -AGTCTAACTTAAATCATCACACTCTCAATTTAATCCAAATTGCAACCTTTGTGGGTGACCCATT
28932571 AGGTT
65 AGGTT
28932576 CTTAACATGT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.34
Consensus pattern (69 bp):
AGTCTAACTTAAATCATCACACTCTCAATTTAATCCAAATTGCAACCTTTGTGGGTGACCCATTA
GGTT
Found at i:28933901 original size:29 final size:31
Alignment explanation
Indices: 28933864--28933921 Score: 77
Period size: 29 Copynumber: 1.9 Consensus size: 31
28933854 TGAGTTTTAC
28933864 GGATCGAAA-ATTGATCA-CTTAA-GTTATGT
1 GGATCGAAAGA-TGATCACCTTAATGTTATGT
*
28933893 GGATGGAAAGATGATCACCTTAATGTTAT
1 GGATCGAAAGATGATCACCTTAATGTTAT
28933922 ATGATTGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 14 0.56
30 6 0.24
31 5 0.20
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.33
Consensus pattern (31 bp):
GGATCGAAAGATGATCACCTTAATGTTATGT
Found at i:28935647 original size:34 final size:31
Alignment explanation
Indices: 28935586--28935647 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 31
28935576 TCTTCATCCC
*
28935586 ATCACTTATCTTTTTATTTTTTCCTCTTGCA
1 ATCACTTATCTTTTCATTTTTTCCTCTTGCA
28935617 ATCACTTATCTTTTCATGATTTTTCTCTCTT
1 ATCACTTATCTTTTCAT--TTTTTC-CTCTT
28935648 CTTAAAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 16 0.59
33 6 0.22
34 5 0.19
ACGTcount: A:0.16, C:0.23, G:0.03, T:0.58
Consensus pattern (31 bp):
ATCACTTATCTTTTCATTTTTTCCTCTTGCA
Found at i:28946326 original size:2 final size:2
Alignment explanation
Indices: 28946314--28946342 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
28946304 ATAAAAGGGA
28946314 GT GT GT G- GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
28946343 AACGATAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:28949886 original size:22 final size:21
Alignment explanation
Indices: 28949847--28949887 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28949837 CACTCGCTAG
* *
28949847 CCTTTTTTTTCCCTTACATGT
1 CCTTTTTTTCCCCATACATGT
28949868 CCTTTTTTTCCCCCATACAT
1 CCTTTTTTT-CCCCATACAT
28949888 ATGTCATGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.12, C:0.34, G:0.02, T:0.51
Consensus pattern (21 bp):
CCTTTTTTTCCCCATACATGT
Found at i:28952712 original size:2 final size:2
Alignment explanation
Indices: 28952695--28952729 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
28952685 ACATACGTAT
* *
28952695 AC AC AT AC AT AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
28952730 TATACATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.43, G:0.00, T:0.06
Consensus pattern (2 bp):
AC
Found at i:28953554 original size:71 final size:70
Alignment explanation
Indices: 28953387--28953556 Score: 193
Period size: 72 Copynumber: 2.4 Consensus size: 70
28953377 TGGGCAACCT
* *
28953387 AAGATTGACTATGGAGGGTTTATGGTCGATCTTGGACTGGAAAGTTTTATGACTCACCCATTTCC
1 AAGATTGACTATGGAGGGTTTATAGTCGATCTTGGACTAGAAAGTTTTATGACTCA--CATTTCC
28953452 CCTTCAC
64 CCTTCAC
* * * * *
28953459 AAGTTTGATTATGGAGAGTCTATAGTCGATCTTGGACTAGAATGTTAGTTTT-TTACTCA-ATTT
1 AAGATTGACTATGGAGGGTTTATAGTCGATCTTGGACTAGAA----AGTTTTATGACTCACATTT
*
28953522 -TCCTTCAC
62 CCCCTTCAC
28953530 AAGATTGACTATGGAGGGTTTATAGTC
1 AAGATTGACTATGGAGGGTTTATAGTC
28953557 AATCCTAAAC
Statistics
Matches: 82, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
71 30 0.37
72 40 0.49
75 6 0.07
76 6 0.07
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (70 bp):
AAGATTGACTATGGAGGGTTTATAGTCGATCTTGGACTAGAAAGTTTTATGACTCACATTTCCCC
TTCAC
Found at i:28955897 original size:11 final size:11
Alignment explanation
Indices: 28955853--28955898 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
28955843 ATGGCCGGCC
*
28955853 AAAGGAAGAAC
1 AAAGGAAGAAA
*
28955864 AAAGCAAGAAA
1 AAAGGAAGAAA
28955875 AAAGGAAG-AA
1 AAAGGAAGAAA
*
28955885 AAAGAAAGAAA
1 AAAGGAAGAAA
28955896 AAA
1 AAA
28955899 ACCCTAGGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
10 9 0.30
11 21 0.70
ACGTcount: A:0.74, C:0.04, G:0.22, T:0.00
Consensus pattern (11 bp):
AAAGGAAGAAA
Found at i:28955899 original size:22 final size:22
Alignment explanation
Indices: 28955853--28955898 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
28955843 ATGGCCGGCC
*
28955853 AAAGGAAGAACAAAGCAAGAAA
1 AAAGGAAGAACAAAGAAAGAAA
28955875 AAAGGAAGAA-AAAGAAAGAAA
1 AAAGGAAGAACAAAGAAAGAAA
28955896 AAA
1 AAA
28955899 ACCCTAGGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.74, C:0.04, G:0.22, T:0.00
Consensus pattern (22 bp):
AAAGGAAGAACAAAGAAAGAAA
Found at i:28955937 original size:22 final size:23
Alignment explanation
Indices: 28955909--28955952 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
28955899 ACCCTAGGTG
*
28955909 GAAAAATTCAAGGGAA-AAGTGT
1 GAAAAATTCAAGGAAACAAGTGT
28955931 GAAAAATTCAAGGAAACAAGTG
1 GAAAAATTCAAGGAAACAAGTG
28955953 ACAAAAGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.52, C:0.07, G:0.25, T:0.16
Consensus pattern (23 bp):
GAAAAATTCAAGGAAACAAGTGT
Found at i:28955958 original size:23 final size:22
Alignment explanation
Indices: 28955910--28955958 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
28955900 CCCTAGGTGG
* **
28955910 AAAAATTCAAGGGAAAAGTGTG
1 AAAAATTCAAGGAAAAAGTGAC
28955932 AAAAATTCAAGGAAACAAGTGAC
1 AAAAATTCAAGGAAA-AAGTGAC
28955955 AAAA
1 AAAA
28955959 GGTAAGATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.57, C:0.08, G:0.20, T:0.14
Consensus pattern (22 bp):
AAAAATTCAAGGAAAAAGTGAC
Found at i:28960199 original size:38 final size:39
Alignment explanation
Indices: 28960143--28960222 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 39
28960133 TAATTTTTTC
* * *
28960143 TTTATTATTTATTGTTTATATTTGC-CTTAGGAAAATAGT
1 TTTATTATTGATTGTTTAT-TTTACACTTAGAAAAATAGT
* *
28960182 TTTA-TATTGATTTTTTATTTTACACTTAGAAAAATATT
1 TTTATTATTGATTGTTTATTTTACACTTAGAAAAATAGT
28960220 TTT
1 TTT
28960223 CCTTTTACTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
37 4 0.11
38 27 0.77
39 4 0.11
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.56
Consensus pattern (39 bp):
TTTATTATTGATTGTTTATTTTACACTTAGAAAAATAGT
Found at i:28965895 original size:1 final size:1
Alignment explanation
Indices: 28965891--28965923 Score: 57
Period size: 1 Copynumber: 33.0 Consensus size: 1
28965881 GAGCTTGGCC
*
28965891 TTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
28965924 GGAGATAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:28967485 original size:3 final size:3
Alignment explanation
Indices: 28967479--28967515 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
28967469 CGAATAATTT
28967479 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
28967516 GACACGATCC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:28967765 original size:28 final size:27
Alignment explanation
Indices: 28967725--28967798 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 27
28967715 TAATAAAAAA
*
28967725 ATTCAAATAAATTTTTTTCTTTTATTTC
1 ATTCAAATAAATTTTTAT-TTTTATTTC
* *
28967753 ATTCAATTAAATTTTTATTTTTATTTTA
1 ATTCAAATAAATTTTTATTTTTA-TTTC
* *
28967781 AATGAAATAAATTTTTAT
1 ATTCAAATAAATTTTTAT
28967799 AATTAATAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 5 0.13
28 34 0.87
ACGTcount: A:0.35, C:0.05, G:0.01, T:0.58
Consensus pattern (27 bp):
ATTCAAATAAATTTTTATTTTTATTTC
Found at i:28968061 original size:30 final size:29
Alignment explanation
Indices: 28968027--28968102 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 29
28968017 AATTATTAGT
*
28968027 TATAAAAATTTATTTAATTTATAATAAAAA
1 TATAAAAATTTATTTAA-ATATAATAAAAA
28968057 TATAAAAATTT-TATTAAATATAATAAAAA
1 TATAAAAATTTAT-TTAAATATAATAAAAA
*
28968086 -ATAATAATTTATTTAAA
1 TATAAAAATTTATTTAAA
28968103 ATTTTTTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
28 14 0.33
29 13 0.31
30 15 0.36
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
TATAAAAATTTATTTAAATATAATAAAAA
Found at i:28968066 original size:21 final size:21
Alignment explanation
Indices: 28968042--28968085 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
28968032 AAATTTATTT
28968042 AATTTATAATAAAAAT-ATAAA
1 AATTT-TAATAAAAATAATAAA
* *
28968063 AATTTTATTAAATATAATAAA
1 AATTTTAATAAAAATAATAAA
28968084 AA
1 AA
28968086 ATAATAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
AATTTTAATAAAAATAATAAA
Found at i:28977213 original size:16 final size:18
Alignment explanation
Indices: 28977194--28977229 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28977184 TCTAATCTTA
28977194 ATCC-AATCTA-ATATAC
1 ATCCAAATCTAGATATAC
28977210 ATCCAAATCTAGATATAC
1 ATCCAAATCTAGATATAC
28977228 AT
1 AT
28977230 AGCATAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 6 0.33
18 8 0.44
ACGTcount: A:0.44, C:0.22, G:0.03, T:0.31
Consensus pattern (18 bp):
ATCCAAATCTAGATATAC
Found at i:28982591 original size:3 final size:3
Alignment explanation
Indices: 28982583--28982619 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
28982573 ATCAAAACTA
*
28982583 AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
28982620 CATTCCAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:28991175 original size:13 final size:13
Alignment explanation
Indices: 28991157--28991193 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
28991147 AAATCAGATT
28991157 TTTCCAACGAAAA
1 TTTCCAACGAAAA
*
28991170 TTTCCAAC--AGA
1 TTTCCAACGAAAA
28991181 TTTCCAACGAAAA
1 TTTCCAACGAAAA
28991194 AGTATTACCG
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
11 10 0.50
13 10 0.50
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.24
Consensus pattern (13 bp):
TTTCCAACGAAAA
Found at i:28995858 original size:71 final size:70
Alignment explanation
Indices: 28995707--28995889 Score: 170
Period size: 71 Copynumber: 2.6 Consensus size: 70
28995697 AGCTTCATAG
* * * * * * * **
28995707 AGAGATTTTAATCGATTAATATACAGTTTAATCGATTAAAATAACATTGGAATGGACTTTGAGAA
1 AGAGATTTTAATCAATTAACACAAAATTTAATCGATTAAAACAACATTGGAATGCACACTGAGAA
*
28995772 GGAGAG
66 -GAGAA
* * * * *
28995778 AGAGGTTTTAATCAATTAGCACATATTTTAATCGATTAAAACAACATTGTAATGCACACTGAGAC
1 AGAGATTTTAATCAATTAACACAAAATTTAATCGATTAAAACAACATTGGAATGCACACTGAGA-
28995843 A-AGTAA
65 AGAG-AA
* **
28995849 AGAGATTTTAATCGATTAACACAAAATTTAATAAATTAAAA
1 AGAGATTTTAATCAATTAACACAAAATTTAATCGATTAAAA
28995890 TAGTACTGGA
Statistics
Matches: 90, Mismatches: 20, Indels: 4
0.79 0.18 0.04
Matches are distributed among these distances:
70 2 0.02
71 87 0.97
72 1 0.01
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (70 bp):
AGAGATTTTAATCAATTAACACAAAATTTAATCGATTAAAACAACATTGGAATGCACACTGAGAA
GAGAA
Done.