Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 32 of 206
Found at i:9401120 original size:34 final size:32
Alignment explanation
Indices: 9401066--9401134 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 32
9401056 TTTAAAATAC
9401066 TTTTTTAATTTTTTTAATTTTAAAAATAT-AT
1 TTTTTTAATTTTTTTAATTTTAAAAATATAAT
*
9401097 TTTTTTAATTTTTGTTTTAATTTTTAAAATA-AAT
1 TTTTTTAA--TTT-TTTTAATTTTAAAAATATAAT
9401131 TTTT
1 TTTT
9401135 GGTATTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
31 8 0.24
33 3 0.09
34 22 0.67
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (32 bp):
TTTTTTAATTTTTTTAATTTTAAAAATATAAT
Found at i:9401542 original size:26 final size:26
Alignment explanation
Indices: 9401513--9401578 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
9401503 AGTTTTTCAT
9401513 TACTTTTAAAAAATAATTTTGAAAAG
1 TACTTTTAAAAAATAATTTTGAAAAG
* * * * *
9401539 TACTGTGAAAAAATACTTTTGAGAGG
1 TACTTTTAAAAAATAATTTTGAAAAG
* *
9401565 TGCTTTTGAAAAAT
1 TACTTTTAAAAAAT
9401579 TTGGTTTAAA
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.36
Consensus pattern (26 bp):
TACTTTTAAAAAATAATTTTGAAAAG
Found at i:9407174 original size:13 final size:12
Alignment explanation
Indices: 9407154--9407191 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
9407144 CACTTTTGAT
9407154 AAAAAAAGAAAA
1 AAAAAAAGAAAA
9407166 AACAAAAAGAAAA
1 AA-AAAAAGAAAA
*
9407179 AAGAAAAGAAAA
1 AAAAAAAGAAAA
9407191 A
1 A
9407192 TGAGAGGCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.87, C:0.03, G:0.11, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:9408248 original size:21 final size:21
Alignment explanation
Indices: 9408222--9408265 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
9408212 CTGGCGTTGC
*
9408222 AGTGGAATAGATTAAAGCTGA
1 AGTGGAACAGATTAAAGCTGA
* *
9408243 AGTGGAGCGGATTAAAGCTGA
1 AGTGGAACAGATTAAAGCTGA
9408264 AG
1 AG
9408266 GCGACGAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.07, G:0.34, T:0.20
Consensus pattern (21 bp):
AGTGGAACAGATTAAAGCTGA
Found at i:9408441 original size:100 final size:100
Alignment explanation
Indices: 9408287--9408989 Score: 971
Period size: 100 Copynumber: 7.0 Consensus size: 100
9408277 TATCTCCTTA
* * * * *
9408287 GCGGTGTAGTAGAACAGATTGAAGCTACAATAGTGAATCTTGCTTCTCCGACATTACAATTAAAA
1 GCGGTGCAGTGGAACAGATTGAAGCTACAACAGTGAATCTTGCTTCCCCGACATTGCAATTAAAA
*
9408352 AGATTGAAGCCACCACGACGAATCTTACTTCCCTG
66 AGATTGAAGCCACAACGACGAATCTTACTTCCCTG
* * * * * *
9408387 GTGGTGCAGCGGAACAGATTGAAGCTACAACGGTGAATCTTACTTCCCCAACATTACAATTAAAA
1 GCGGTGCAGTGGAACAGATTGAAGCTACAACAGTGAATCTTGCTTCCCCGACATTGCAATTAAAA
9408452 AGATTGAAGCCACAACGACGAATCTTACTTCCCTG
66 AGATTGAAGCCACAACGACGAATCTTACTTCCCTG
* * * *
9408487 GCGGTGCAGTGGAACATATTAAAGCTACAACAATGAATCTTGCTTCCCCAACATTGCAATTAAAA
1 GCGGTGCAGTGGAACAGATTGAAGCTACAACAGTGAATCTTGCTTCCCCGACATTGCAATTAAAA
*
9408552 AGATTGAAGCCACAACGACGAATCTTATTTCCCTG
66 AGATTGAAGCCACAACGACGAATCTTACTTCCCTG
* * *
9408587 GCGGTGTAGTGGAACAGATTGAAGCTACAACAGCGAATCTTGTTTCCCCGACATTGCAATTAAAA
1 GCGGTGCAGTGGAACAGATTGAAGCTACAACAGTGAATCTTGCTTCCCCGACATTGCAATTAAAA
9408652 AGATTGAAGCCACAACGACGAATCTTACTTCCCTG
66 AGATTGAAGCCACAACGACGAATCTTACTTCCCTG
* * * * *
9408687 ACAGTGTAGTGGAACAGATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAA
1 GCGGTGCAGTGGAACAGATTGAAGCTACAACAGTGAATCTTGCTTCCCCGACATTGCAATTAAAA
* * *
9408752 AGATTGAAGCTACAAC-AGTGAATCTTACTTCTCTG
66 AGATTGAAGCCACAACGA-CGAATCTTACTTCCCTG
* * ** *
9408787 GTGGTGCAGTGGAACAGATTAAAGCTACAATGGTGAATTTTGCTTCCCCGACATTGCAATTAAAA
1 GCGGTGCAGTGGAACAGATTGAAGCTACAACAGTGAATCTTGCTTCCCCGACATTGCAATTAAAA
* *
9408852 AGATTGAAGCTACAAC-AGCGAATCTTACTTCCCTA
66 AGATTGAAGCCACAACGA-CGAATCTTACTTCCCTG
* ** * * *
9408887 GCGGTGCAGTGGAATAGATTGAAGCTACAACAACGAATCTTGCTTCCCTGACATTGCAGTTAAAT
1 GCGGTGCAGTGGAACAGATTGAAGCTACAACAGTGAATCTTGCTTCCCCGACATTGCAATTAAAA
* *
9408952 AGATTGAAGCTACAAC-AGCAAATCTTACTTCCCTG
66 AGATTGAAGCCACAACGA-CGAATCTTACTTCCCTG
9408987 GCG
1 GCG
9408990 AACAGATCGA
Statistics
Matches: 544, Mismatches: 58, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
99 1 0.00
100 543 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (100 bp):
GCGGTGCAGTGGAACAGATTGAAGCTACAACAGTGAATCTTGCTTCCCCGACATTGCAATTAAAA
AGATTGAAGCCACAACGACGAATCTTACTTCCCTG
Found at i:9408985 original size:50 final size:50
Alignment explanation
Indices: 9408302--9408986 Score: 509
Period size: 50 Copynumber: 13.7 Consensus size: 50
9408292 GTAGTAGAAC
* * * * *
9408302 AGATTGAAGCTACAATAGTGAATCTTGCTTCTCC-GACATTACAATTAAAA
1 AGATTGAAGCTACAACAGCGAATCTTACTTC-CCTGACATTGCAGTTAAAA
* * **** *** *
9408352 AGATTGAAGCCACCAC-GACGAATCTTACTTCCCTGGTGGTGCAGCGGAAC
1 AGATTGAAGCTACAACAG-CGAATCTTACTTCCCTGACATTGCAGTTAAAA
* * ** * *
9408402 AGATTGAAGCTACAACGGTGAATCTTACTTCCCCAACATTACAATTAAAA
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTTAAAA
* * ** ** *
9408452 AGATTGAAGCCACAAC-GACGAATCTTACTTCCCTGGCGGTGCAGTGGAAC
1 AGATTGAAGCTACAACAG-CGAATCTTACTTCCCTGACATTGCAGTTAAAA
* * ** * ** *
9408502 ATATTAAAGCTACAACAATGAATCTTGCTTCCCCAACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTTAAAA
* * * ** * ** *
9408552 AGATTGAAGCCACAAC-GACGAATCTTATTTCCCTGGCGGTGTAGTGGAAC
1 AGATTGAAGCTACAACAG-CGAATCTTACTTCCCTGACATTGCAGTTAAAA
** * *
9408602 AGATTGAAGCTACAACAGCGAATCTTGTTTCCCCGACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTTAAAA
* * * ** *
9408652 AGATTGAAGCCACAAC-GACGAATCTTACTTCCCTGACAGTGTAGTGGAAC
1 AGATTGAAGCTACAACAG-CGAATCTTACTTCCCTGACATTGCAGTTAAAA
* * * *
9408702 AGATTGAAGCTACAACGGCGAATCTTGCTTCCCCGACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTTAAAA
* * **** ** *
9408752 AGATTGAAGCTACAACAGTGAATCTTACTTCTCTGGTGGTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTTAAAA
* ** * * * * *
9408802 AGATTAAAGCTACAATGGTGAATTTTGCTTCCCCGACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTTAAAA
** ** *
9408852 AGATTGAAGCTACAACAGCGAATCTTACTTCCCT-AGCGGTGCAGTGGAAT
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTGA-CATTGCAGTTAAAA
* * *
9408902 AGATTGAAGCTACAACAACGAATCTTGCTTCCCTGACATTGCAGTTAAAT
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTTAAAA
*
9408952 AGATTGAAGCTACAACAGCAAATCTTACTTCCCTG
1 AGATTGAAGCTACAACAGCGAATCTTACTTCCCTG
9408987 GCGAACAGAT
Statistics
Matches: 470, Mismatches: 154, Indels: 22
0.73 0.24 0.03
Matches are distributed among these distances:
49 6 0.01
50 460 0.98
51 4 0.01
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (50 bp):
AGATTGAAGCTACAACAGCGAATCTTACTTCCCTGACATTGCAGTTAAAA
Found at i:9409091 original size:45 final size:50
Alignment explanation
Indices: 9409014--9409136 Score: 130
Period size: 45 Copynumber: 2.5 Consensus size: 50
9409004 GGCAAGTCTC
* * *
9409014 ATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG-AT-AAC-A-A-ATCTT
1 ATCTCTCTGAAGTTGCAGTAGAACAGACTAAAGCATAAACTATAGATCTT
* *
9409059 ATCTCTCTGAAGTTGCAGTAGAATAGATTAAAGCTATAAACTATAGATCTT
1 ATCTCTCTGAAGTTGCAGTAGAACAGACTAAAGC-ATAAACTATAGATCTT
* * *
9409110 ATCTCTCTAAAGTTACAGTAGAGCAGA
1 ATCTCTCTGAAGTTGCAGTAGAACAGA
9409137 TCACATCAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
45 28 0.44
47 2 0.03
48 3 0.05
49 1 0.02
50 1 0.02
51 28 0.44
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (50 bp):
ATCTCTCTGAAGTTGCAGTAGAACAGACTAAAGCATAAACTATAGATCTT
Found at i:9409256 original size:44 final size:44
Alignment explanation
Indices: 9409140--9409302 Score: 139
Period size: 44 Copynumber: 3.7 Consensus size: 44
9409130 GAGCAGATCA
* * * *
9409140 CATCAAACCTTATCTCCCTGAAGTTACAATGGAGCAGGTTGAAAAC
1 CATCAATCC-TATCTCCCTGAAGTTGCAGTGGAGCAGATTG-AAAC
* * * * *
9409186 CACCAATCTTATCTCCTTGAGGTTGCAGTGGAGCAGATTGAAGC
1 CATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAC
* * ** *
9409230 TATTAATCCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAAC
1 CATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAC
* * *
9409274 GATGAATCCTATAC-CTCTGAAGTTGCAGT
1 CATCAATCCTAT-CTCCCTGAAGTTGCAGT
9409303 AGGTCGGATT
Statistics
Matches: 94, Mismatches: 22, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
44 61 0.65
45 27 0.29
46 6 0.06
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (44 bp):
CATCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAAC
Found at i:9409392 original size:45 final size:45
Alignment explanation
Indices: 9409322--9409414 Score: 123
Period size: 45 Copynumber: 2.1 Consensus size: 45
9409312 TAGGTCTACC
* * *
9409322 ATAACAAGTCTTATCTCCATGAAGTTGCAGTGGAGAAGGCTGAAG
1 ATAACAAGCCTTATCTCCATAAAGTTACAGTGGAGAAGGCTGAAG
* * * *
9409367 ATAACCAGCCTTATCTCCCTAAAGTTACAGTGGAGCAGGTTGAAG
1 ATAACAAGCCTTATCTCCATAAAGTTACAGTGGAGAAGGCTGAAG
9409412 ATA
1 ATA
9409415 CCAATCTCGT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (45 bp):
ATAACAAGCCTTATCTCCATAAAGTTACAGTGGAGAAGGCTGAAG
Found at i:9412332 original size:41 final size:41
Alignment explanation
Indices: 9412287--9412388 Score: 143
Period size: 41 Copynumber: 2.5 Consensus size: 41
9412277 GCTTAGCGCT
*
9412287 TAGCAGGCTTATTGCCGGTGAAACACTTCAGACTAAATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTAAATGTC
* * * *
9412328 TAGCAGGCTTAATGTCGGTGAAATATTTCAGACTATATGTC
1 TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTAAATGTC
9412369 TAGCAGGC-TAAGTGCCGGTG
1 TAGCAGGCTTAA-TGCCGGTG
9412389 TACTGAATCA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 3 0.06
41 51 0.94
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGAAACACTTCAGACTAAATGTC
Found at i:9441157 original size:16 final size:16
Alignment explanation
Indices: 9441136--9441175 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
9441126 ACCCAAATCC
9441136 GAAAAAATTTGAGTTG
1 GAAAAAATTTGAGTTG
** *
9441152 GAAAAAGCTTGAGTTT
1 GAAAAAATTTGAGTTG
9441168 GAAAAAAT
1 GAAAAAAT
9441176 CCGAACCCAT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.23, T:0.28
Consensus pattern (16 bp):
GAAAAAATTTGAGTTG
Found at i:9442804 original size:23 final size:24
Alignment explanation
Indices: 9442774--9442824 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
9442764 TGACTACCAA
9442774 AAAATTG-ATTTT-ATATATTTTTT
1 AAAATTGAATTTTAAT-TATTTTTT
*
9442797 AAAATTGAATTTTAATTTTTTTTT
1 AAAATTGAATTTTAATTATTTTTT
9442821 AAAA
1 AAAA
9442825 ATATTGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 7 0.28
24 16 0.64
25 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
AAAATTGAATTTTAATTATTTTTT
Found at i:9442895 original size:23 final size:23
Alignment explanation
Indices: 9442865--9442913 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
9442855 CCTTAAGTTT
9442865 TTTTTTTTAAAATTGGA-TTTTTA
1 TTTTTTTTAAAATT-GATTTTTTA
*
9442888 TTTTTTTTCAAATTGATTTTTTA
1 TTTTTTTTAAAATTGATTTTTTA
9442911 TTT
1 TTT
9442914 GGCGGTGCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.69
Consensus pattern (23 bp):
TTTTTTTTAAAATTGATTTTTTA
Found at i:9443004 original size:16 final size:16
Alignment explanation
Indices: 9442983--9443015 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
9442973 TTTTGAAAAA
9442983 TAATTATATAAATAAT
1 TAATTATATAAATAAT
*
9442999 TAATTATATACATAAT
1 TAATTATATAAATAAT
9443015 T
1 T
9443016 TGGTATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATTATATAAATAAT
Found at i:9454341 original size:7 final size:7
Alignment explanation
Indices: 9454323--9454398 Score: 50
Period size: 7 Copynumber: 11.0 Consensus size: 7
9454313 TTCAACAAAT
9454323 ATTTTATA
1 ATTTT-TA
9454331 ATTTTTA
1 ATTTTTA
9454338 ATTTTTA
1 ATTTTTA
*
9454345 AATTTTA
1 ATTTTTA
**
9454352 A--AATA
1 ATTTTTA
9454357 ATTTTCTA
1 ATTTT-TA
*
9454365 ATATTTA
1 ATTTTTA
*
9454372 CTTTTTA
1 ATTTTTA
* *
9454379 A-TATAA
1 ATTTTTA
9454385 ATTTTTA
1 ATTTTTA
9454392 ATTTTTA
1 ATTTTTA
9454399 GGATAAAAAA
Statistics
Matches: 51, Mismatches: 13, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
5 3 0.06
6 4 0.08
7 33 0.65
8 11 0.22
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (7 bp):
ATTTTTA
Found at i:9454371 original size:27 final size:26
Alignment explanation
Indices: 9454328--9454398 Score: 88
Period size: 27 Copynumber: 2.7 Consensus size: 26
9454318 CAAATATTTT
9454328 ATAATTTTTAATTTTTAAATTTTAAA
1 ATAATTTTTAATTTTTAAATTTTAAA
* ** *
9454354 ATAATTTTCTAATATTTACTTTTTAAT
1 ATAATTTT-TAATTTTTAAATTTTAAA
9454381 ATAAATTTTTAATTTTTA
1 AT-AATTTTTAATTTTTA
9454399 GGATAAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
26 8 0.21
27 24 0.63
28 6 0.16
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (26 bp):
ATAATTTTTAATTTTTAAATTTTAAA
Found at i:9460278 original size:25 final size:25
Alignment explanation
Indices: 9460238--9460318 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
9460228 ATGCTCATAC
*
9460238 GAGCACATA-AAT-GGAAGCTCTTTT
1 GAGC-CATATAATGGGAAGCTCTTGT
*
9460262 GAGCCATATAATGGGAAGCTCATGT
1 GAGCCATATAATGGGAAGCTCTTGT
* * * * *
9460287 GAGCCATGTAACGGAAAGCTCTAGA
1 GAGCCATATAATGGGAAGCTCTTGT
9460312 GAGCCAT
1 GAGCCAT
9460319 TAACAGGAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
23 4 0.09
24 7 0.15
25 36 0.77
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (25 bp):
GAGCCATATAATGGGAAGCTCTTGT
Found at i:9460339 original size:24 final size:24
Alignment explanation
Indices: 9460261--9460339 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 24
9460251 GAAGCTCTTT
* * *
9460261 TGAGCCATATAATGGGAAGCTCATG
1 TGAGCCATATAA-CGGAAGCTTATA
* *
9460286 TGAGCCATGTAACGGAAAGCTCTAGA
1 TGAGCCATATAACGG-AAGCT-TATA
9460312 -GAGCCAT-TAACAGGAAGCTTATA
1 TGAGCCATATAAC-GGAAGCTTATA
9460335 TGAGC
1 TGAGC
9460340 TAATATCGAG
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
23 3 0.07
24 15 0.34
25 25 0.57
26 1 0.02
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.22
Consensus pattern (24 bp):
TGAGCCATATAACGGAAGCTTATA
Found at i:9460362 original size:24 final size:24
Alignment explanation
Indices: 9460335--9460400 Score: 96
Period size: 24 Copynumber: 2.8 Consensus size: 24
9460325 GAAGCTTATA
*
9460335 TGAGCTAATATCGAGAAGTTCAAG
1 TGAGCCAATATCGAGAAGTTCAAG
*
9460359 TGAGCCAATATCAAGAAGTTCAAG
1 TGAGCCAATATCGAGAAGTTCAAG
* *
9460383 CGAGCCAATATCGGGAAG
1 TGAGCCAATATCGAGAAG
9460401 CTCCGAAGAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.20
Consensus pattern (24 bp):
TGAGCCAATATCGAGAAGTTCAAG
Found at i:9460434 original size:25 final size:24
Alignment explanation
Indices: 9460384--9460435 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
9460374 AAGTTCAAGC
*
9460384 GAGCCAATATCGGGAAGCTCCGAA
1 GAGCCAATATCGGGAAGCTCAGAA
*
9460408 GAGCCATATATC-GGAATGCTCATAA
1 GAGCCA-ATATCGGGAA-GCTCAGAA
9460433 GAG
1 GAG
9460436 TTGCGGTGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.35, C:0.21, G:0.27, T:0.17
Consensus pattern (24 bp):
GAGCCAATATCGGGAAGCTCAGAA
Found at i:9460524 original size:25 final size:25
Alignment explanation
Indices: 9460496--9460558 Score: 117
Period size: 25 Copynumber: 2.5 Consensus size: 25
9460486 GAAGAGCTAT
*
9460496 TAACGGGAAGCTCGCAAGAATCATA
1 TAACGGGAAGCTCGCAAGAACCATA
9460521 TAACGGGAAGCTCGCAAGAACCATA
1 TAACGGGAAGCTCGCAAGAACCATA
9460546 TAACGGGAAGCTC
1 TAACGGGAAGCTC
9460559 ATGAGAGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.14
Consensus pattern (25 bp):
TAACGGGAAGCTCGCAAGAACCATA
Found at i:9465003 original size:22 final size:21
Alignment explanation
Indices: 9464972--9465013 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
9464962 TAAATTGTGT
* *
9464972 ATATTTATATGTTTGAATTGG
1 ATATTTATATATGTGAATTGG
9464993 ATATTGTATATATGTGAATTG
1 ATATT-TATATATGTGAATTG
9465014 TATAAATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (21 bp):
ATATTTATATATGTGAATTGG
Found at i:9465503 original size:24 final size:23
Alignment explanation
Indices: 9465476--9465521 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
9465466 CCCGTTATTA
9465476 GCTCGCATGAGCTTCCTGATTATG
1 GCTCGCATGAGCTTCCTG-TTATG
** *
9465500 GCTCTTATGAGCTTTCTGTTAT
1 GCTCGCATGAGCTTCCTGTTAT
9465522 ACTGCTTGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (23 bp):
GCTCGCATGAGCTTCCTGTTATG
Found at i:9470867 original size:31 final size:31
Alignment explanation
Indices: 9470832--9470937 Score: 131
Period size: 31 Copynumber: 3.4 Consensus size: 31
9470822 GTATATGTTT
* * * **
9470832 TATACATTGCCAAATTTGATTTGTATATATA
1 TATACATTGCCGAATTTGAATTGTTTATGGA
**
9470863 TATACATTATCGAATTTGAATTGTTTATGGA
1 TATACATTGCCGAATTTGAATTGTTTATGGA
*
9470894 TATATATTGCCGAATTTGAATTGTTTATGGA
1 TATACATTGCCGAATTTGAATTGTTTATGGA
*
9470925 TATATATTGCCGA
1 TATACATTGCCGA
9470938 GTTGATTTGA
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 65 1.00
ACGTcount: A:0.32, C:0.08, G:0.15, T:0.44
Consensus pattern (31 bp):
TATACATTGCCGAATTTGAATTGTTTATGGA
Found at i:9470956 original size:31 final size:31
Alignment explanation
Indices: 9470889--9470956 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
9470879 TGAATTGTTT
* ***
9470889 ATGGATATATATTGCCGAATTTGAATTGTTT
1 ATGGATATATATTGCCGAAGTTGAATTGAGC
*
9470920 ATGGATATATATTGCCG-AGTTGATTTGAGC
1 ATGGATATATATTGCCGAAGTTGAATTGAGC
9470950 ATTGGAT
1 A-TGGAT
9470957 GACTAGTTTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 9 0.29
31 22 0.71
ACGTcount: A:0.28, C:0.07, G:0.24, T:0.41
Consensus pattern (31 bp):
ATGGATATATATTGCCGAAGTTGAATTGAGC
Found at i:9471196 original size:43 final size:43
Alignment explanation
Indices: 9471061--9471188 Score: 204
Period size: 43 Copynumber: 3.0 Consensus size: 43
9471051 ACTTCCGAGG
* *
9471061 TGAGATTTTGTGTAAGACCATAGCT-AGGCTATTGGCATCAATT
1 TGAGATTTCGTGTAAGACCATAGCTGA-GCTATTGGCATCGATT
* *
9471104 TGAGATTTCGTGTAAGACTATAGCTGGGCTATTGGCATCGATT
1 TGAGATTTCGTGTAAGACCATAGCTGAGCTATTGGCATCGATT
9471147 TGAGATTTCGTGTAAGACCATAGCTGAGCTATTGGCATCGAT
1 TGAGATTTCGTGTAAGACCATAGCTGAGCTATTGGCATCGAT
9471189 ACGAGATTCT
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
43 78 1.00
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.34
Consensus pattern (43 bp):
TGAGATTTCGTGTAAGACCATAGCTGAGCTATTGGCATCGATT
Found at i:9472671 original size:2 final size:2
Alignment explanation
Indices: 9472664--9472689 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9472654 GGTTGTAAGC
9472664 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
9472690 GTCAAAGTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9496250 original size:3 final size:3
Alignment explanation
Indices: 9496242--9496279 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
9496232 ATACATGAGA
9496242 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
9496280 AGATGATAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:9496380 original size:17 final size:18
Alignment explanation
Indices: 9496350--9496383 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
9496340 ATAGGGTTTT
9496350 TAAAAGTATATTAAAAAA
1 TAAAAGTATATTAAAAAA
9496368 TAAAAGT-TATTAAAAA
1 TAAAAGTATATTAAAAA
9496384 TATATTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
TAAAAGTATATTAAAAAA
Found at i:9498847 original size:14 final size:14
Alignment explanation
Indices: 9498816--9498856 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
9498806 AAATGTACAC
9498816 TATAATTAAA-TAA
1 TATAATTAAATTAA
9498829 TATAAATTAAATTAA
1 TAT-AATTAAATTAA
*
9498844 -ATAATTTAATTAA
1 TATAATTAAATTAA
9498857 CTGTTTACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 13 0.52
14 9 0.36
15 3 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TATAATTAAATTAA
Found at i:9503793 original size:23 final size:22
Alignment explanation
Indices: 9503743--9503793 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
9503733 CTCGGGATCA
9503743 AAAT-AAGATTTCTAGCAAAAG
1 AAATGAAGATTTCTAGCAAAAG
* *
9503764 AAGATGAAGATTTTTAGGAAAAGG
1 AA-ATGAAGATTTCTAGCAAAA-G
9503788 AAATGA
1 AAATGA
9503794 GGAAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 2 0.08
22 2 0.08
23 18 0.72
24 3 0.12
ACGTcount: A:0.51, C:0.04, G:0.22, T:0.24
Consensus pattern (22 bp):
AAATGAAGATTTCTAGCAAAAG
Found at i:9518196 original size:3 final size:3
Alignment explanation
Indices: 9518188--9518217 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
9518178 CATAAGAGGA
*
9518188 TTG TTG TTG TTG TTG TTG TTG TTG TGG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
9518218 ATTTTCTGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.37, T:0.63
Consensus pattern (3 bp):
TTG
Found at i:9518727 original size:3 final size:3
Alignment explanation
Indices: 9518719--9518754 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
9518709 TCACTAGGTG
*
9518719 GAT GAT GAT GGT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
9518755 CAGGTCCGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:9519338 original size:2 final size:2
Alignment explanation
Indices: 9519331--9519365 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
9519321 ATTAATTTTA
9519331 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9519366 GATGCATAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9522421 original size:1 final size:1
Alignment explanation
Indices: 9522415--9522440 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
9522405 CTACTCTTGA
9522415 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
9522441 GGTATCTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:9530100 original size:19 final size:19
Alignment explanation
Indices: 9530076--9530121 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
9530066 ACTGTTTTCT
*
9530076 CTTTTGATTCGTAGCCTCC
1 CTTTTGATTCGCAGCCTCC
*
9530095 CTTTTGATTCGCAGGCTCC
1 CTTTTGATTCGCAGCCTCC
9530114 CTTTTGAT
1 CTTTTGAT
9530122 CTTGTTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.11, C:0.28, G:0.17, T:0.43
Consensus pattern (19 bp):
CTTTTGATTCGCAGCCTCC
Found at i:9537866 original size:16 final size:16
Alignment explanation
Indices: 9537845--9537875 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9537835 CTTCCATCCG
*
9537845 TTTTATTATTTAAATA
1 TTTTATTAATTAAATA
9537861 TTTTATTAATTAAAT
1 TTTTATTAATTAAAT
9537876 TAAATAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTATTAATTAAATA
Found at i:9539852 original size:30 final size:30
Alignment explanation
Indices: 9539816--9539872 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
9539806 GAGAATCTGA
*
9539816 GATAAAGTTTCTAAAACCCCAAAATCCTAT
1 GATAAAGTTTCTAAAACCCAAAAATCCTAT
*
9539846 GATAAAGTTTCTGAAACCCAAAAATCC
1 GATAAAGTTTCTAAAACCCAAAAATCC
9539873 CGCGATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.44, C:0.23, G:0.09, T:0.25
Consensus pattern (30 bp):
GATAAAGTTTCTAAAACCCAAAAATCCTAT
Found at i:9539880 original size:30 final size:30
Alignment explanation
Indices: 9539816--9539881 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
9539806 GAGAATCTGA
* * *
9539816 GATAAAGTTTCTAAAACCCCAAAATCCTAT
1 GATAAAGTTTCTAAAACCCAAAAATCCCAC
* *
9539846 GATAAAGTTTCTGAAACCCAAAAATCCCGC
1 GATAAAGTTTCTAAAACCCAAAAATCCCAC
9539876 GATAAA
1 GATAAA
9539882 ATTTACATCC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.44, C:0.23, G:0.11, T:0.23
Consensus pattern (30 bp):
GATAAAGTTTCTAAAACCCAAAAATCCCAC
Found at i:9543312 original size:21 final size:21
Alignment explanation
Indices: 9543288--9543359 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
9543278 ACAGAATTGC
*
9543288 TAAATAGAAACCCATAAGGGT
1 TAAACAGAAACCCATAAGGGT
* * * *
9543309 TAAACGGAAGCTCATAAGAGCT
1 TAAACAGAAACCCATAAG-GGT
*
9543331 T-AACAGAAACCCATAAAGGT
1 TAAACAGAAACCCATAAGGGT
9543351 TAAACAGAA
1 TAAACAGAA
9543360 GCTCAAAAGA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
20 3 0.08
21 33 0.85
22 3 0.08
ACGTcount: A:0.49, C:0.17, G:0.18, T:0.17
Consensus pattern (21 bp):
TAAACAGAAACCCATAAGGGT
Found at i:9543340 original size:42 final size:42
Alignment explanation
Indices: 9543286--9543423 Score: 141
Period size: 42 Copynumber: 3.3 Consensus size: 42
9543276 GCACAGAATT
* *
9543286 GCTAAATAGAAACCCATAAGGGTTAAACGGAAGCTCATAAGA
1 GCTAAACAGAAACCCATAAGGGTTAAACAGAAGCTCATAAGA
* * *
9543328 GCTTAACAGAAACCCATAAAGGTTAAACAGAAGCTCAAAAGA
1 GCTAAACAGAAACCCATAAGGGTTAAACAGAAGCTCATAAGA
* * * ** * * * * *
9543370 TCTGAACGGAAACTTATATGAGTTAAATAGAAGCTCGTGAGA
1 GCTAAACAGAAACCCATAAGGGTTAAACAGAAGCTCATAAGA
9543412 GCTAAACAGAAA
1 GCTAAACAGAAA
9543424 GTAAACACGG
Statistics
Matches: 76, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 76 1.00
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.18
Consensus pattern (42 bp):
GCTAAACAGAAACCCATAAGGGTTAAACAGAAGCTCATAAGA
Found at i:9545979 original size:20 final size:20
Alignment explanation
Indices: 9545954--9546000 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
9545944 AACTACAATC
*
9545954 AAAGAAA-ACAAATAATAAAG
1 AAAGAAATA-AAATAAAAAAG
9545974 AAAGAAATAAAATAAAAAAG
1 AAAGAAATAAAATAAAAAAG
*
9545994 GAAGAAA
1 AAAGAAA
9546001 GTCTCTTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.77, C:0.02, G:0.13, T:0.09
Consensus pattern (20 bp):
AAAGAAATAAAATAAAAAAG
Found at i:9548775 original size:6 final size:6
Alignment explanation
Indices: 9548757--9548830 Score: 130
Period size: 6 Copynumber: 12.3 Consensus size: 6
9548747 TTAAGTCCTT
*
9548757 TACAGA TATAGA TACAGA TACAGA TACAGA TACAGA TACAGA TACAGA
1 TACAGA TACAGA TACAGA TACAGA TACAGA TACAGA TACAGA TACAGA
*
9548805 TACAGA TACAGA TATAGA TACAGA TA
1 TACAGA TACAGA TACAGA TACAGA TA
9548831 TGCAGAACAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 64 1.00
ACGTcount: A:0.50, C:0.14, G:0.16, T:0.20
Consensus pattern (6 bp):
TACAGA
Found at i:9556151 original size:43 final size:43
Alignment explanation
Indices: 9556067--9556172 Score: 108
Period size: 43 Copynumber: 2.5 Consensus size: 43
9556057 AGTGTTATTG
* * **
9556067 TGTAAGACCCTGTGTGGGACAGTGGCATCAATTTATAATTACGA
1 TGTAAGACCCTGTGTGGGACAGCGACATCAATACATAATTAC-A
** * *
9556111 -GTAAGACCCTGTGTGGGACAGCGACATCGCTACGTGATTACA
1 TGTAAGACCCTGTGTGGGACAGCGACATCAATACATAATTACA
9556153 TGTAAGACCAC-GTGTGGGAC
1 TGTAAGACC-CTGTGTGGGAC
9556173 GTTGGCATTG
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
42 1 0.02
43 50 0.96
44 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (43 bp):
TGTAAGACCCTGTGTGGGACAGCGACATCAATACATAATTACA
Found at i:9556885 original size:2 final size:2
Alignment explanation
Indices: 9556880--9556939 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
9556870 TATATATATA
9556880 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
9556922 TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG
9556940 ACGTGTTTGG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:9560678 original size:12 final size:12
Alignment explanation
Indices: 9560661--9560685 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9560651 TATTAAAATT
9560661 TTATATATTATA
1 TTATATATTATA
9560673 TTATATATTATA
1 TTATATATTATA
9560685 T
1 T
9560686 GAATATTGAA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATATATTATA
Found at i:9561263 original size:7 final size:7
Alignment explanation
Indices: 9561251--9561283 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
9561241 CTTATAAAGT
9561251 TTTATTC
1 TTTATTC
9561258 TTTATTC
1 TTTATTC
9561265 TTTATTC
1 TTTATTC
9561272 TTTATTC
1 TTTATTC
9561279 TTTAT
1 TTTAT
9561284 ATAAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTATTC
Found at i:9570726 original size:108 final size:108
Alignment explanation
Indices: 9570594--9570799 Score: 315
Period size: 108 Copynumber: 1.9 Consensus size: 108
9570584 CTTGGACTGA
* * *
9570594 CAGATCACGACATGAGAATGTGTAAGTTCATGTGGCT-AAGACCCATGACAATATATGATTGTAT
1 CAGATCACGACATGAGAATATGTAAGTCCATGTGGCTGAA-ACCCATGACAATATATGACTGTAT
*
9570658 GAATGTTCATAGTGAAGCCGGCGATAATGTGTAGATTGACTTGG
65 GAATATTCATAGTGAAGCCGGCGATAATGTGTAGATTGACTTGG
* *
9570702 CAGATCACGACATGAGAATATGTAAGTCCATGTGGTTGAAACCCATGGCAATATATGACTGTATG
1 CAGATCACGACATGAGAATATGTAAGTCCATGTGGCTGAAACCCATGACAATATATGACTGTATG
* **
9570767 AATATTCATGGTGAAGCCTTCGATAATGTGTAG
66 AATATTCATAGTGAAGCCGGCGATAATGTGTAG
9570800 GTCAAACTAG
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
108 86 0.98
109 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.29
Consensus pattern (108 bp):
CAGATCACGACATGAGAATATGTAAGTCCATGTGGCTGAAACCCATGACAATATATGACTGTATG
AATATTCATAGTGAAGCCGGCGATAATGTGTAGATTGACTTGG
Found at i:9570815 original size:108 final size:108
Alignment explanation
Indices: 9570595--9570833 Score: 295
Period size: 108 Copynumber: 2.2 Consensus size: 108
9570585 TTGGACTGAC
* * *
9570595 AGATCACGACATGAGAATGTGTAAGTTCATGTGGCTAAGACCCATGACAATATATGATTGTATGA
1 AGATCACGACATGAGAATATGTAAGTCCATGTGGCTAAGACCCATGACAATATATGACTGTATGA
* ** * *
9570660 ATGTTCATAGTGAAGCCGGCGATAATGTGTAGATTGACTTGGC
66 ATATTCATAGTGAAGCCGGCGATAATGTGTAGATAAACTTAGA
* *
9570703 AGATCACGACATGAGAATATGTAAGTCCATGTGGTTGAA-ACCCATGGCAATATATGACTGTATG
1 AGATCACGACATGAGAATATGTAAGTCCATGTGGCT-AAGACCCATGACAATATATGACTGTATG
* ** *
9570767 AATATTCATGGTGAAGCCTTCGATAATGTGTAGGTCAAAC-TAGA
65 AATATTCATAGTGAAGCCGGCGATAATGTGTAGAT-AAACTTAGA
*
9570811 AGATCAAGACATGA-AATTATGTA
1 AGATCACGACATGAGAA-TATGTA
9570834 TGAGTACATG
Statistics
Matches: 113, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
107 2 0.02
108 107 0.95
109 4 0.04
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (108 bp):
AGATCACGACATGAGAATATGTAAGTCCATGTGGCTAAGACCCATGACAATATATGACTGTATGA
ATATTCATAGTGAAGCCGGCGATAATGTGTAGATAAACTTAGA
Found at i:9570963 original size:22 final size:23
Alignment explanation
Indices: 9570916--9570963 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
9570906 TGTTTGCTTG
* *
9570916 TGTGGCATGATTTGCTAAGATTT
1 TGTGGCAAGATTTGCTAACATTT
*
9570939 TGTGGCAAGTTTTG-TAACATTT
1 TGTGGCAAGATTTGCTAACATTT
9570961 TGT
1 TGT
9570964 TGGCGTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.21, C:0.08, G:0.25, T:0.46
Consensus pattern (23 bp):
TGTGGCAAGATTTGCTAACATTT
Found at i:9576064 original size:21 final size:20
Alignment explanation
Indices: 9576042--9576086 Score: 67
Period size: 18 Copynumber: 2.3 Consensus size: 20
9576032 TCCTCATTGC
9576042 CTCCTCCGGTTCCCATGTCG
1 CTCCTCCGGTTCCCATGTCG
9576062 --CCTCCGGTTCCCATGTCG
1 CTCCTCCGGTTCCCATGTCG
9576080 CTTCCTC
1 C-TCCTC
9576087 TATCCCGTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 18 0.82
21 4 0.18
ACGTcount: A:0.04, C:0.47, G:0.18, T:0.31
Consensus pattern (20 bp):
CTCCTCCGGTTCCCATGTCG
Found at i:9576067 original size:18 final size:18
Alignment explanation
Indices: 9576044--9576080 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
9576034 CTCATTGCCT
9576044 CCTCCGGTTCCCATGTCG
1 CCTCCGGTTCCCATGTCG
9576062 CCTCCGGTTCCCATGTCG
1 CCTCCGGTTCCCATGTCG
9576080 C
1 C
9576081 TTCCTCTATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.46, G:0.22, T:0.27
Consensus pattern (18 bp):
CCTCCGGTTCCCATGTCG
Found at i:9584203 original size:21 final size:21
Alignment explanation
Indices: 9584179--9584224 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
9584169 CCAAACTAGA
*
9584179 AAAATAAGCAAATGCTGAATT
1 AAAAGAAGCAAATGCTGAATT
*
9584200 AAAAGCAGCAAATGCTGAATT
1 AAAAGAAGCAAATGCTGAATT
9584221 AAAA
1 AAAA
9584225 ACAATCACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.54, C:0.11, G:0.15, T:0.20
Consensus pattern (21 bp):
AAAAGAAGCAAATGCTGAATT
Found at i:9585335 original size:12 final size:12
Alignment explanation
Indices: 9585318--9585351 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
9585308 TAAGTCTAAG
*
9585318 AACATAACAATA
1 AACATAAAAATA
9585330 AACATAAAAATA
1 AACATAAAAATA
*
9585342 AAAATAAAAA
1 AACATAAAAA
9585352 AAATAAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (12 bp):
AACATAAAAATA
Found at i:9586646 original size:22 final size:22
Alignment explanation
Indices: 9586594--9586636 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
9586584 TTTATTGTTC
9586594 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
9586616 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
9586637 TAGCCATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:9587904 original size:21 final size:21
Alignment explanation
Indices: 9587879--9587922 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
9587869 AGCCGTGTAA
9587879 TAGTCGATTTTTGTGAAAAAT
1 TAGTCGATTTTTGTGAAAAAT
*
9587900 TAGTCGATTTTTTTGAAAAAT
1 TAGTCGATTTTTGTGAAAAAT
9587921 TA
1 TA
9587923 TGTCCCAGGA
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:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (21 bp):
TAGTCGATTTTTGTGAAAAAT
Found at i:9593727 original size:2 final size:2
Alignment explanation
Indices: 9593720--9593749 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9593710 CCTTTCCCTT
9593720 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
9593750 AATGAATAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9596021 original size:17 final size:17
Alignment explanation
Indices: 9595995--9596029 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
9595985 TGTTAATATT
*
9595995 AAAAACAAAAGGAAAAA
1 AAAAACAAAAAGAAAAA
*
9596012 AAAAAGAAAAAGAAAAA
1 AAAAACAAAAAGAAAAA
9596029 A
1 A
9596030 GGCAAGTCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.86, C:0.03, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAACAAAAAGAAAAA
Found at i:9597284 original size:32 final size:31
Alignment explanation
Indices: 9597221--9597286 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
9597211 AGGAATTAAA
* * **
9597221 TTAATTTTTTTAGAGAGGTTATAATTGAATT
1 TTAATTTTTTTAGAAAGGTTAAAATACAATT
*
9597252 TTAATTTTTTTTGAAAGGATTAAAATACAATT
1 TTAATTTTTTTAGAAAGG-TTAAAATACAATT
9597284 TTA
1 TTA
9597287 CAATCGAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 16 0.55
32 13 0.45
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (31 bp):
TTAATTTTTTTAGAAAGGTTAAAATACAATT
Found at i:9600912 original size:5 final size:5
Alignment explanation
Indices: 9600902--9600936 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
9600892 TAAATATATA
*
9600902 ATAAT ATAAT ATAAT ATATT AATAAT ATAAT ATAA
1 ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAA
9600937 AAACATACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:9610886 original size:14 final size:14
Alignment explanation
Indices: 9610867--9610905 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
9610857 ATAATATAAT
*
9610867 ATTAAAATAAATTA
1 ATTAAAATAAAATA
9610881 ATTAAAATAAAAATA
1 ATTAAAAT-AAAATA
9610896 ATTGAAAATA
1 ATT-AAAATA
9610906 TTTTCTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 8 0.36
15 9 0.41
16 5 0.23
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
ATTAAAATAAAATA
Found at i:9621227 original size:30 final size:30
Alignment explanation
Indices: 9621193--9621253 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
9621183 TATTTTTGGC
9621193 GAAAGTTTAGTTTTGATTAGAACTAGTAAG
1 GAAAGTTTAGTTTTGATTAGAACTAGTAAG
9621223 GAAAGTTTAGTTTTGATTAGAACTAGTAAG
1 GAAAGTTTAGTTTTGATTAGAACTAGTAAG
9621253 G
1 G
9621254 TATATGGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (30 bp):
GAAAGTTTAGTTTTGATTAGAACTAGTAAG
Found at i:9640217 original size:27 final size:27
Alignment explanation
Indices: 9640177--9640482 Score: 409
Period size: 27 Copynumber: 11.4 Consensus size: 27
9640167 TTGCGATTCG
*
9640177 TGGGT-AAATAACCGAAATACCCTCGA
1 TGGGTAAAATGACCGAAATACCCTCGA
*
9640203 TGGGTAAAATGACCGAAATACGCTCGA
1 TGGGTAAAATGACCGAAATACCCTCGA
* * *
9640230 AGGGTAAAATGACCGAAATACTCTAGA
1 TGGGTAAAATGACCGAAATACCCTCGA
* *
9640257 TGGGTAAAATGACTGAAATACCTTCGA
1 TGGGTAAAATGACCGAAATACCCTCGA
*
9640284 TGGGTAAAATGACCAAAATACCCTCGA
1 TGGGTAAAATGACCGAAATACCCTCGA
* *
9640311 TGGGTAAAATGATCAAAATACCCTCGA
1 TGGGTAAAATGACCGAAATACCCTCGA
9640338 TGGGTAAAATGACCGAAATACCCTCGA
1 TGGGTAAAATGACCGAAATACCCTCGA
**
9640365 TGGGTAAAATGACCGAAATACCCTTTA
1 TGGGTAAAATGACCGAAATACCCTCGA
* *
9640392 TGGGTAAAATAACCGAAATATCCTCGA
1 TGGGTAAAATGACCGAAATACCCTCGA
* * *
9640419 TGGGTAAAATAACCAAAATACCCCCGA
1 TGGGTAAAATGACCGAAATACCCTCGA
* * *
9640446 AGGGTAAAATGACCAAAATACCC-CCA
1 TGGGTAAAATGACCGAAATACCCTCGA
9640472 TAGGGTAAAAT
1 T-GGGTAAAAT
9640483 AACTGTTATA
Statistics
Matches: 249, Mismatches: 29, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
26 7 0.03
27 242 0.97
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (27 bp):
TGGGTAAAATGACCGAAATACCCTCGA
Found at i:9640896 original size:33 final size:34
Alignment explanation
Indices: 9640841--9640904 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
9640831 ATTACTGTAT
* *
9640841 TGTATTGATTACTGTATTGGGCT-AAGGCCCACAC
1 TGTACTGATTACTGTATAGGGCTCAA-GCCCACAC
9640875 TGTACTGA-TACTGTATAGGGCTCAAGCCCA
1 TGTACTGATTACTGTATAGGGCTCAAGCCCA
9640905 AATTGATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 18 0.67
34 9 0.33
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (34 bp):
TGTACTGATTACTGTATAGGGCTCAAGCCCACAC
Found at i:9645417 original size:20 final size:18
Alignment explanation
Indices: 9645392--9645435 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
9645382 TTAGGCTATT
9645392 TGGGCCACGATGGGCCGAAA
1 TGGGCCA-GATGGGCC-AAA
* *
9645412 TGGGCCATATGGGGCAAA
1 TGGGCCAGATGGGCCAAA
9645430 TGGGCC
1 TGGGCC
9645436 CGTGGGCTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.41
19 6 0.27
20 7 0.32
ACGTcount: A:0.23, C:0.23, G:0.41, T:0.14
Consensus pattern (18 bp):
TGGGCCAGATGGGCCAAA
Found at i:9645631 original size:27 final size:27
Alignment explanation
Indices: 9645599--9645736 Score: 133
Period size: 27 Copynumber: 5.1 Consensus size: 27
9645589 TAATACTTTG
9645599 GTTTACAAAATTACTGAAATACCCTT-
1 GTTTACAAAATTACTGAAATACCCTTA
*
9645625 GATTTACAAAATTATTGAAATACCCTTA
1 G-TTTACAAAATTACTGAAATACCCTTA
*
9645653 GTTTACAAAATTACTGAAATACCCTCGA
1 GTTTACAAAATTACTGAAATACCCT-TA
* * **
9645681 CTTGT--AAAATTAC-CAAAGTACCCCCA
1 GTT-TACAAAATTACTGAAA-TACCCTTA
* *
9645707 GTTTACAAAATTACCG-AATACCCTCA
1 GTTTACAAAATTACTGAAATACCCTTA
9645733 GTTT
1 GTTT
9645737 GTGAAATTGC
Statistics
Matches: 94, Mismatches: 10, Indels: 16
0.78 0.08 0.13
Matches are distributed among these distances:
25 1 0.01
26 18 0.19
27 70 0.74
28 4 0.04
29 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (27 bp):
GTTTACAAAATTACTGAAATACCCTTA
Found at i:9645750 original size:53 final size:54
Alignment explanation
Indices: 9645599--9645812 Score: 168
Period size: 54 Copynumber: 3.9 Consensus size: 54
9645589 TAATACTTTG
* * * ** ** **
9645599 GTTTACAAAATTACTGAAATACCCTTGATTTACAAAATTATTGAAA-TACCCTTA
1 GTTTACAAAATTACCGAAATACCCTCGACTTGTAAAATTA-CCAAAGTACCCCCA
*
9645653 GTTTACAAAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCCCA
1 GTTTACAAAATTACCGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCCCA
* * * *
9645707 GTTTACAAAATTACCG-AATACCCTC-AGTTTGTGAAATTGCCAAAGTA-CCCCT
1 GTTTACAAAATTACCGAAATACCCTCGA-CTTGTAAAATTACCAAAGTACCCCCA
* * * * *
9645759 GATTTACAAAAAAGTACCAAAATACCCTC-ATTTTGGAAAATTACCAAAATACCC
1 G-TTTAC--AAAATTACCGAAATACCCTCGA-CTTGTAAAATTACCAAAGTACCC
9645813 TTATAGGGTA
Statistics
Matches: 133, Mismatches: 20, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
52 6 0.05
53 34 0.26
54 57 0.43
55 8 0.06
56 26 0.20
57 2 0.02
ACGTcount: A:0.40, C:0.22, G:0.09, T:0.29
Consensus pattern (54 bp):
GTTTACAAAATTACCGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCCCA
Found at i:9645806 original size:27 final size:27
Alignment explanation
Indices: 9645642--9645813 Score: 100
Period size: 27 Copynumber: 6.3 Consensus size: 27
9645632 AAAATTATTG
* ** **
9645642 AAATACCCTTAGTTTACAAAATTACTG
1 AAATACCCTCAGTTTGGAAAATTACCA
* *
9645669 AAATACCCTC-GACTTGTAAAATTACCA
1 AAATACCCTCAG-TTTGGAAAATTACCA
* * **
9645696 AAGTACCCCCAGTTTACAAAATTACC-
1 AAATACCCTCAGTTTGGAAAATTACCA
* *
9645722 GAATACCCTCAGTTTGTG-AAATTGCCA
1 AAATACCCTCAGTTTG-GAAAATTACCA
* * ** *
9645749 AAGTACCC-CTGATTTACAAAAAAGTACCA
1 AAATACCCTCAG-TTT--GGAAAATTACCA
*
9645778 AAATACCCTCATTTTGGAAAATTACCA
1 AAATACCCTCAGTTTGGAAAATTACCA
9645805 AAATACCCT
1 AAATACCCT
9645814 TATAGGGTAA
Statistics
Matches: 106, Mismatches: 30, Indels: 18
0.69 0.19 0.12
Matches are distributed among these distances:
26 22 0.21
27 65 0.61
28 1 0.01
29 17 0.16
30 1 0.01
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.27
Consensus pattern (27 bp):
AAATACCCTCAGTTTGGAAAATTACCA
Found at i:9645825 original size:27 final size:27
Alignment explanation
Indices: 9645768--9645826 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
9645758 TGATTTACAA
* **
9645768 AAAAGTACCAAAATACCCTCATTTTGG
1 AAAATTACCAAAATACCCTCATTAGGG
*
9645795 AAAATTACCAAAATACCCTTA-TAGGG
1 AAAATTACCAAAATACCCTCATTAGGG
9645821 TAAAAT
1 -AAAAT
9645827 GACTATTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 3 0.11
27 24 0.89
ACGTcount: A:0.46, C:0.19, G:0.10, T:0.25
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTCATTAGGG
Found at i:9646317 original size:27 final size:27
Alignment explanation
Indices: 9646279--9646334 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
9646269 TACTGATATG
* *
9646279 GTATTAGGCTAAGGCCCACCTTGTTCT
1 GTATTAGGCTAAAGCCCACATTGTTCT
*
9646306 GTATTGGGCTAAAGCCCACATTGTTCT
1 GTATTAGGCTAAAGCCCACATTGTTCT
9646333 GT
1 GT
9646335 TCTGTTACTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (27 bp):
GTATTAGGCTAAAGCCCACATTGTTCT
Found at i:9649628 original size:15 final size:13
Alignment explanation
Indices: 9649594--9649618 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9649584 ATATATTTAT
9649594 TTTTAAAATTCTC
1 TTTTAAAATTCTC
9649607 TTTTAAAATTCT
1 TTTTAAAATTCT
9649619 ATGTTTTAAA
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:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTAAAATTCTC
Found at i:9656063 original size:19 final size:19
Alignment explanation
Indices: 9656039--9656079 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
9656029 AAGAGACCCT
9656039 CAACGACGATTGAACCCAC
1 CAACGACGATTGAACCCAC
9656058 CAACGACGATTGAACCCAC
1 CAACGACGATTGAACCCAC
9656077 CAA
1 CAA
9656080 AGTGGTTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.37, G:0.15, T:0.10
Consensus pattern (19 bp):
CAACGACGATTGAACCCAC
Found at i:9669554 original size:17 final size:15
Alignment explanation
Indices: 9669527--9669580 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
9669517 GTAGAGGATA
*
9669527 AAAAAAGAAAAAATAC
1 AAAAAACAAAAAA-AC
*
9669543 AAAAATACAAAAAAAT
1 AAAAA-ACAAAAAAAC
9669559 AAAAAACAAAAAGAAAC
1 AAAAAAC-AAAA-AAAC
9669576 AAAAA
1 AAAAA
9669581 CTTTTACCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 2 0.06
16 15 0.47
17 15 0.47
ACGTcount: A:0.83, C:0.07, G:0.04, T:0.06
Consensus pattern (15 bp):
AAAAAACAAAAAAAC
Found at i:9670138 original size:53 final size:55
Alignment explanation
Indices: 9670005--9670140 Score: 170
Period size: 55 Copynumber: 2.5 Consensus size: 55
9669995 AAAGAAGGAG
* *
9670005 AAGAGACCAAGGTGAAAACTCGCAAAGGGCGATTTGAGTCCTAAATACAAAAACA
1 AAGAGACCAAGGTGAAAACCCGCAAAGGACGATTTGAGTCCTAAATACAAAAACA
* * * *
9670060 AAAAGACCAAGGTGAAAACCCGCAAAGGACGCTTTGAGTTCTAAA-A-AAGAAA-G
1 AAGAGACCAAGGTGAAAACCCGCAAAGGACGATTTGAGTCCTAAATACAA-AAACA
* *
9670113 GAGAGGCCAAGGTGAAAACCCGCAAAGG
1 AAGAGACCAAGGTGAAAACCCGCAAAGG
9670141 GTTCCTTGAG
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
53 27 0.38
54 4 0.06
55 40 0.56
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (55 bp):
AAGAGACCAAGGTGAAAACCCGCAAAGGACGATTTGAGTCCTAAATACAAAAACA
Found at i:9671400 original size:51 final size:51
Alignment explanation
Indices: 9671338--9672097 Score: 913
Period size: 51 Copynumber: 15.4 Consensus size: 51
9671328 TATTATGGCA
* *
9671338 AATCTTTTTTCCCTGGTGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCG
1 AATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCG
* *
9671389 AATCTTATTTCCTTAGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCG
1 AATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCG
* ** * *
9671440 ACTCTTATTTCCCTGGAATTGTAGTGGAACAGATTAAAGTTGAAGGCAGCG
1 AATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCG
* *
9671491 AATCTTATTTCCCTTGGCATTGCAGTGGAACAGATTAAAGCTGAAGGCAGTG
1 AATCTTATTTCCC-TGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCG
* * *
9671543 AATCTTTTTTCCCTGGCGTTGCAGTGGAACAAATTAAAGCTGAAGGCAGTG
1 AATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCG
* * * * *
9671594 AATCTTATTTCTCTGGCGTTACAGTGGAACAAATTAAAGCTGAAAGTAGCG
1 AATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCG
*
9671645 AATCTTATTTCCCTAGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCG
1 AATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCG
* * *
9671696 AATCTTATTTCCCTGGCATTGCAGTGGAATAGATTAAAGCTGAAGGCAGTG
1 AATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCG
* * * *
9671747 AATCTTTTTTCCCTGGTGTTGTAGTGGAACAGATTAAAGTTGAAGGCAGCG
1 AATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCG
* * * *
9671798 AATCTTTTTTCCCTAGCGTTGC-----AATAGATTAAAGCTAAAGGCAGCG
1 AATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCG
* * * * *
9671844 AATCTTATTTCCCTGGCATTGTAGTGGAACTGATTAAAGCTGAAGGCAACA
1 AATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCG
* *
9671895 AATCTTTTTTCCCTGGTGTTGCAGTGGAAC-------A---GAAGGCAGCG
1 AATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCG
* *
9671936 AATCTTATTTCCCTGGCGTTGCAATGGAACAGATTAAAGCTGAAAGCAGCG
1 AATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCG
* * * *
9671987 AATCTTTTTTCCCTAGTGTTGCAGTGG----GA-T--A---GAATGCAGCG
1 AATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCG
* *
9672028 AATATTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTGAAGGCAGCG
1 AATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCG
*
9672079 AATCTTTTTTCCCTGGCGT
1 AATCTTATTTCCCTGGCGT
9672098 GAATTAAAAC
Statistics
Matches: 602, Mismatches: 81, Indels: 52
0.82 0.11 0.07
Matches are distributed among these distances:
41 66 0.11
44 2 0.00
45 2 0.00
46 41 0.07
47 2 0.00
48 2 0.00
51 441 0.73
52 46 0.08
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (51 bp):
AATCTTATTTCCCTGGCGTTGCAGTGGAACAGATTAAAGCTGAAGGCAGCG
Found at i:9671947 original size:41 final size:41
Alignment explanation
Indices: 9671885--9672060 Score: 145
Period size: 41 Copynumber: 4.0 Consensus size: 41
9671875 GATTAAAGCT
* * * *
9671885 GAAGGCAACAAATCTTTTTTCCCTGGTGTTGCAGTGGAACA
1 GAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACA
*
9671926 GAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAATGGAACA
1 GAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACA
* * * * *
9671967 GATTAAAGCTGAAAGCAGCGAATCTTTTTTCCCTAGTGTTGCAGTGGGATA
1 G----AA---G---GCAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACA
* * *
9672018 GAATGCAGCGAATATTATTTCCCTGGCATTGCAGTGGAACA
1 GAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACA
9672059 GA
1 GA
9672061 TTAAAGCTGA
Statistics
Matches: 106, Mismatches: 19, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
41 69 0.65
45 2 0.02
47 2 0.02
48 1 0.01
51 32 0.30
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (41 bp):
GAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAGTGGAACA
Found at i:9671971 original size:92 final size:92
Alignment explanation
Indices: 9671737--9672092 Score: 469
Period size: 92 Copynumber: 3.8 Consensus size: 92
9671727 GATTAAAGCT
* * ** * *
9671737 GAAGGCAGTGAATCTTTTTTCCCTGGTGTTGTAGTGGAACAGATTAAAGTTGAAGGCAGCGAATC
1 GAAGGCAGCGAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATC
* * *
9671802 TTTTTTCCCTAGCGTTGCAATAGATTAAA
66 TTTTTTCCCTAGTGTTGCAGTGGA--AAA
* * * *
9671831 GCTAAAGGCAGCGAATCTTATTTCCCTGGCATTGTAGTGGAACTGATTAAAGCTGAAGGCAACAA
1 G---AAGGCAGCGAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGA
* *
9671896 ATCTTTTTTCCCTGGTGTTGCAGTGGAACA
63 ATCTTTTTTCCCTAGTGTTGCAGTGGAAAA
* * *
9671926 GAAGGCAGCGAATCTTATTTCCCTGGCGTTGCAATGGAACAGATTAAAGCTGAAAGCAGCGAATC
1 GAAGGCAGCGAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATC
* *
9671991 TTTTTTCCCTAGTGTTGCAGTGGGATA
66 TTTTTTCCCTAGTGTTGCAGTGGAAAA
* *
9672018 GAATGCAGCGAATATTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATC
1 GAAGGCAGCGAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATC
9672083 TTTTTTCCCT
66 TTTTTTCCCT
9672093 GGCGTGAATT
Statistics
Matches: 231, Mismatches: 28, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
92 151 0.65
94 1 0.00
95 3 0.01
97 76 0.33
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (92 bp):
GAAGGCAGCGAATCTTATTTCCCTGGCATTGCAGTGGAACAGATTAAAGCTGAAGGCAGCGAATC
TTTTTTCCCTAGTGTTGCAGTGGAAAA
Found at i:9674315 original size:17 final size:18
Alignment explanation
Indices: 9674283--9674316 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
9674273 GCTCTTGTGT
9674283 GTATTGTATTGCTTATTG
1 GTATTGTATTGCTTATTG
*
9674301 GTATT-TATTGGTTATT
1 GTATTGTATTGCTTATT
9674317 TGTAGTTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.18, C:0.03, G:0.21, T:0.59
Consensus pattern (18 bp):
GTATTGTATTGCTTATTG
Found at i:9675739 original size:21 final size:21
Alignment explanation
Indices: 9675709--9675757 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
9675699 TGTTTTTTTT
*
9675709 TTTTGATGAT-GATAAATAAA
1 TTTTGTTGATAGATAAATAAA
* *
9675729 TATTTGTTGATAGATTATTAAA
1 T-TTTGTTGATAGATAAATAAA
9675751 TTTTGTT
1 TTTTGTT
9675758 AAGTAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 14 0.58
22 9 0.38
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (21 bp):
TTTTGTTGATAGATAAATAAA
Found at i:9678259 original size:42 final size:42
Alignment explanation
Indices: 9678176--9678465 Score: 384
Period size: 42 Copynumber: 6.8 Consensus size: 42
9678166 ACGTCGTAAA
* *
9678176 CTTTTGCGGCGCTTACAGAGAA-AAACGCCACTAAAGTTCATGTT
1 CTTTAGCGGCGCTT--AGA-AATAAACGCCACTAAAGATCATGTT
* *
9678220 CTTTAGCGGCGCTTAGAAAGAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAATAAACGCCACTAAAGATCATGTT
* *
9678262 CTTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCT-TAGAAATAAACGCCACTAAAGATCATGTT
* * *
9678305 CTTTAGCGGCGCTAAAAAATAAACGCCACTAAAGACCATGTT
1 CTTTAGCGGCGCTTAGAAATAAACGCCACTAAAGATCATGTT
9678347 CTTTAGCGGCGCTTAGAAATAAACGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGAAATAAACGCCACTAAAGATCATGTT
* *
9678389 CTTTAGCGGCGCTAAGGAAATAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-GAAATAAACGCCACTAAAGATCATGTT
* * * *
9678432 CTTTAGCGGCACTTTGAAAGAAAACGCCTCTAAA
1 CTTTAGCGGCGCTTAGAAA-TAAACGCCACTAAA
9678466 AGTAATATTC
Statistics
Matches: 224, Mismatches: 18, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
41 2 0.01
42 121 0.54
43 88 0.39
44 13 0.06
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGAAATAAACGCCACTAAAGATCATGTT
Found at i:9678302 original size:85 final size:84
Alignment explanation
Indices: 9678198--9678441 Score: 398
Period size: 85 Copynumber: 2.9 Consensus size: 84
9678188 TTACAGAGAA
* * *
9678198 AAACGCCACTAAAGTTCATGTTCTTTAGCGGCGCTTAGAAAGAAACGCCGCTAAAGATCATGTTC
1 AAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTAAGAAATAAACGCCGCTAAAGATCATGTTC
9678263 TTTAGCGGCGCTAAAAAAAT
66 TTTAGCGGCGCT-AAAAAAT
* * *
9678283 AAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTAAAAAATAAACGCCACTAAAGACCATGTTC
1 AAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTAAGAAATAAACGCCGCTAAAGATCATGTTC
* *
9678348 TTTAGCGGCGCTTAGAAAT
66 TTTAGCGGCGCTAAAAAAT
9678367 AAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTAAGGAAATAAACGCCGCTAAAGATCATGTT
1 AAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTAA-GAAATAAACGCCGCTAAAGATCATGTT
9678432 CTTTAGCGGC
65 CTTTAGCGGC
9678442 ACTTTGAAAG
Statistics
Matches: 147, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
84 42 0.29
85 105 0.71
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (84 bp):
AAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTAAGAAATAAACGCCGCTAAAGATCATGTTC
TTTAGCGGCGCTAAAAAAT
Found at i:9678338 original size:127 final size:127
Alignment explanation
Indices: 9678198--9678441 Score: 425
Period size: 127 Copynumber: 1.9 Consensus size: 127
9678188 TTACAGAGAA
** *
9678198 AAACGCCACTAAAGTTCATGTTCTTTAGCGGCGCTTAGAAAGAAACGCCGCTAAAGATCATGTTC
1 AAACGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAGAAACGCCACTAAAGATCATGTTC
9678263 TTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTAAAAAAT
66 TTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTAAAAAAT
*
9678325 AAACGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGAAATAAACGCCACTAAAGATCATGTTC
1 AAACGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAGAAACGCCACTAAAGATCATGTTC
** *
9678390 TTTAGCGGCGCTAAGGAAATAAACGCCGCTAAAGATCATGTTCTTTAGCGGC
66 TTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGATCATGTTCTTTAGCGGC
9678442 ACTTTGAAAG
Statistics
Matches: 110, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
127 110 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (127 bp):
AAACGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAGAAACGCCACTAAAGATCATGTTC
TTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTAAAAAAT
Found at i:9678507 original size:85 final size:84
Alignment explanation
Indices: 9678176--9678465 Score: 375
Period size: 85 Copynumber: 3.4 Consensus size: 84
9678166 ACGTCGTAAA
* * * *
9678176 CTTTTGCGGCGCTTACAGAGAAAAACGCCACTAAAGTTCATGTTCTTTAGCGGCGCTT-AGAAAG
1 CTTTAGCGGCGCTT--AGAAAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTGA-AAAT
9678240 AAACGCCGCTAAAGATCATGTT
63 AAACGCCGCTAAAGATCATGTT
* * **
9678262 CTTTAGCGGCGCTAAAAAAATAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTAAAAAATAA
1 CTTTAGCGGCGCTTAGAAAA-AAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTGAAAATAA
* *
9678327 ACGCCACTAAAGACCATGTT
65 ACGCCGCTAAAGATCATGTT
* * *
9678347 CTTTAGCGGCGCTTAGAAATAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTAAGGAAATAA
1 CTTTAGCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCT-TGAAAATAA
9678412 ACGCCGCTAAAGATCATGTT
65 ACGCCGCTAAAGATCATGTT
* * *
9678432 CTTTAGCGGCACTTTGAAAGAAAACGCCTCTAAA
1 CTTTAGCGGCGCTTAGAAA-AAAACGCCACTAAA
9678466 AGTAATATTC
Statistics
Matches: 180, Mismatches: 20, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
84 39 0.22
85 116 0.64
86 25 0.14
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (84 bp):
CTTTAGCGGCGCTTAGAAAAAAACGCCACTAAAGATCATGTTCTTTAGCGGCGCTTGAAAATAAA
CGCCGCTAAAGATCATGTT
Found at i:9678987 original size:21 final size:21
Alignment explanation
Indices: 9678963--9679031 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
9678953 GCTTCTATCG
9678963 CTGCTTCTCTCGCTGCAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
9678984 CTGCTTCTCTCACTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
9679005 CTGCTTCTCTCGTTGCTGCCT
1 CTGCTTCTCTCGCTGCAGCCT
9679026 CTGCTT
1 CTGCTT
9679032 TAAGTTGTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.03, C:0.41, G:0.19, T:0.38
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:9685094 original size:41 final size:41
Alignment explanation
Indices: 9685049--9685186 Score: 100
Period size: 41 Copynumber: 3.1 Consensus size: 41
9685039 ATTTAAGTTA
9685049 TAAATTTATTATTAATAAAATTTAAATATAGCTTACATACG
1 TAAATTTATTATTAATAAAATTTAAATATAGCTTACATACG
** * * * *
9685090 TAAATGAATATATGT-ATAATATTAAAAAAATAG-TAATACTTATTTAAG
1 TAAATTTAT-TAT-TAATAAAATT-TAAATATAGCT--TAC--A--TACG
9685138 TTATAAATTTATTATTAATAAAATTTAAATATAGCTTACATACG
1 ---TAAATTTATTATTAATAAAATTTAAATATAGCTTACATACG
9685182 TAAAT
1 TAAAT
9685187 GAATATATGC
Statistics
Matches: 71, Mismatches: 12, Indels: 28
0.64 0.11 0.25
Matches are distributed among these distances:
41 12 0.17
42 11 0.15
43 8 0.11
44 6 0.08
46 2 0.03
48 6 0.08
49 8 0.11
50 11 0.15
51 7 0.10
ACGTcount: A:0.49, C:0.05, G:0.06, T:0.41
Consensus pattern (41 bp):
TAAATTTATTATTAATAAAATTTAAATATAGCTTACATACG
Found at i:9685113 original size:51 final size:49
Alignment explanation
Indices: 9685055--9685195 Score: 138
Period size: 44 Copynumber: 3.0 Consensus size: 49
9685045 GTTATAAATT
9685055 TATTATTAATAAAATTTAAATATAGCTTACATACGTAAATGAATATATG
1 TATTATTAATAAAATTTAAATATAGCTTACATACGTAAATGAATATATG
* * ** * *
9685104 TATAATATTAA-AAAA-AT-AGTAATA-CTTATTTAAGT-TAT-AA-AT-T-
1 TAT--TATTAATAAAATTTAAAT-ATAGCTTACATACGTAAATGAATATATG
9685147 TATTATTAATAAAATTTAAATATAGCTTACATACGTAAATGAATATATG
1 TATTATTAATAAAATTTAAATATAGCTTACATACGTAAATGAATATATG
9685196 CAAGTTATGT
Statistics
Matches: 68, Mismatches: 12, Indels: 24
0.65 0.12 0.23
Matches are distributed among these distances:
41 6 0.09
42 4 0.06
43 7 0.10
44 11 0.16
45 4 0.06
46 4 0.06
47 4 0.06
48 11 0.16
49 7 0.10
50 4 0.06
51 6 0.09
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (49 bp):
TATTATTAATAAAATTTAAATATAGCTTACATACGTAAATGAATATATG
Found at i:9685175 original size:92 final size:92
Alignment explanation
Indices: 9685018--9685195 Score: 356
Period size: 92 Copynumber: 1.9 Consensus size: 92
9685008 NNNNNNNNNN
9685018 ATTAAAAAAATAGTAATACTTATTTAAGTTATAAATTTATTATTAATAAAATTTAAATATAGCTT
1 ATTAAAAAAATAGTAATACTTATTTAAGTTATAAATTTATTATTAATAAAATTTAAATATAGCTT
9685083 ACATACGTAAATGAATATATGTATAAT
66 ACATACGTAAATGAATATATGTATAAT
9685110 ATTAAAAAAATAGTAATACTTATTTAAGTTATAAATTTATTATTAATAAAATTTAAATATAGCTT
1 ATTAAAAAAATAGTAATACTTATTTAAGTTATAAATTTATTATTAATAAAATTTAAATATAGCTT
9685175 ACATACGTAAATGAATATATG
66 ACATACGTAAATGAATATATG
9685196 CAAGTTATGT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 86 1.00
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (92 bp):
ATTAAAAAAATAGTAATACTTATTTAAGTTATAAATTTATTATTAATAAAATTTAAATATAGCTT
ACATACGTAAATGAATATATGTATAAT
Found at i:9685217 original size:12 final size:12
Alignment explanation
Indices: 9685200--9685224 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9685190 TATATGCAAG
9685200 TTATGTAAGTTA
1 TTATGTAAGTTA
9685212 TTATGTAAGTTA
1 TTATGTAAGTTA
9685224 T
1 T
9685225 ACAAGATTAT
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:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TTATGTAAGTTA
Found at i:9685261 original size:8 final size:7
Alignment explanation
Indices: 9685243--9685280 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
9685233 ATAATATAAG
9685243 TTATGTA
1 TTATGTA
9685250 TTATGTTA
1 TTATG-TA
9685258 TTATGTA
1 TTATGTA
9685265 TTATGTA
1 TTATGTA
9685272 --ATGTA
1 TTATGTA
9685277 TTAT
1 TTAT
9685281 CAGATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
5 5 0.18
7 16 0.57
8 7 0.25
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (7 bp):
TTATGTA
Found at i:9685337 original size:21 final size:19
Alignment explanation
Indices: 9685285--9685341 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 19
9685275 TATTATCAGA
*
9685285 TTATATATAAGTTACGAAAG
1 TTATATATAAGTTA-TAAAG
*
9685305 TTATTATGTAAGTTATACAAG
1 TTA-TATATAAGTTATA-AAG
9685326 CTTATATATAAGTTAT
1 -TTATATATAAGTTAT
9685342 GTATTATGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 4 0.13
21 24 0.77
22 3 0.10
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.42
Consensus pattern (19 bp):
TTATATATAAGTTATAAAG
Found at i:9685384 original size:52 final size:52
Alignment explanation
Indices: 9685306--9685414 Score: 166
Period size: 52 Copynumber: 2.1 Consensus size: 52
9685296 TTACGAAAGT
* *
9685306 TATTATGTAAGTTATACAAGCTTATATA-TAAGTTATGTATTATGTTATTATG
1 TATTATGTAAGTTATACAAACTTATATACCAA-TTATGTATTATGTTATTATG
* *
9685358 TATTATGTAAGTTATGCAAACTTATATACCAATTATGTATTGTGTTATTATG
1 TATTATGTAAGTTATACAAACTTATATACCAATTATGTATTATGTTATTATG
9685410 TATTA
1 TATTA
9685415 AGTTATATAC
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
52 50 0.96
53 2 0.04
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.48
Consensus pattern (52 bp):
TATTATGTAAGTTATACAAACTTATATACCAATTATGTATTATGTTATTATG
Found at i:9693659 original size:8 final size:8
Alignment explanation
Indices: 9693646--9693677 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
9693636 GTTAAAATAT
9693646 ATATTATA
1 ATATTATA
9693654 ATATTATA
1 ATATTATA
9693662 ATATTATA
1 ATATTATA
9693670 ATATTATA
1 ATATTATA
9693678 TCTTAATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATATTATA
Found at i:9715472 original size:44 final size:44
Alignment explanation
Indices: 9715410--9715770 Score: 490
Period size: 44 Copynumber: 8.2 Consensus size: 44
9715400 ACTATTGCTT
* * *
9715410 AGGGAGACAGGA-TCTACAATCTTCAACCTATTCCACTGCTGTTC
1 AGGGAGATAGGACT-TACAATCTTCAACCTATTCCACTACTGGTC
* * * ** * *
9715454 AGGGAGATAGGACATACAATCTTCCACCTATTTCACTGTTGTTT
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTACTGGTC
* * *
9715498 AGGGAGCTAGGACTTACAATCTTCCACCTATTCCACTACTGTTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTACTGGTC
* * *
9715542 AGGGAGATAGGACTTACAATCTTCCACCTATTCCACTGCTGTTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTACTGGTC
* *
9715586 AGGGAGATAGGACTTCCAATCTTCAACCTATTTCACTACTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTACTGGTC
* * *
9715630 AGGGAGATAGGACTTAGAATCTTCAACCTATTTCACTGCTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTACTGGTC
9715674 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTACTGGTC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTACTGGTC
* * *
9715718 AAGGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGGCC
1 AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTACTGGTC
9715762 AGGGAGATA
1 AGGGAGATA
9715771 AGGCTTTGTG
Statistics
Matches: 287, Mismatches: 29, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
44 287 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
AGGGAGATAGGACTTACAATCTTCAACCTATTCCACTACTGGTC
Found at i:9720211 original size:2 final size:2
Alignment explanation
Indices: 9720204--9720238 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
9720194 TCTTAGGTGC
9720204 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 T
9720239 TATCTTATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:9730121 original size:41 final size:41
Alignment explanation
Indices: 9730064--9730209 Score: 136
Period size: 41 Copynumber: 3.6 Consensus size: 41
9730054 TTGTATAAAA
* *
9730064 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCGATACATTC
1 CACCGGCACAAAGCCTGCTAGACACAAAGCCCGATACATTC
* * * * *
9730105 CACCGGCACAAAGCCTGCTAGACATAAGGTCTGATACATTT
1 CACCGGCACAAAGCCTGCTAGACACAAAGCCCGATACATTC
* * * * *
9730146 CACTGGCACTAAGCCTGCTAGACATAAAGTCTGAAGTA-ATT-
1 CACCGGCACAAAGCCTGCTAGACACAAAGCCCG-A-TACATTC
9730187 CACCGGCATC-AAGCCTGCTAGAC
1 CACCGGCA-CAAAGCCTGCTAGAC
9730210 GTAAAGTCTG
Statistics
Matches: 91, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
41 84 0.92
42 5 0.05
43 2 0.02
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.19
Consensus pattern (41 bp):
CACCGGCACAAAGCCTGCTAGACACAAAGCCCGATACATTC
Found at i:9730215 original size:41 final size:41
Alignment explanation
Indices: 9730105--9730304 Score: 278
Period size: 41 Copynumber: 4.9 Consensus size: 41
9730095 CGATACATTC
* * * * *
9730105 CACCGGCA-CAAAGCCTGCTAGACATAAGGTCTGATACATTT
1 CACCGGCATC-AAGCCTGCTAGACGTAAAGTCTGAAATAATT
* * *
9730146 CACTGGCA-CTAAGCCTGCTAGACATAAAGTCTGAAGTAATT
1 CACCGGCATC-AAGCCTGCTAGACGTAAAGTCTGAAATAATT
9730187 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAATAATT
1 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAATAATT
*
9730228 CACCGGCATCAAGCCTACTAGACGTAAAGTCTGAAATAATT
1 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAATAATT
*
9730269 CACTGGCATCAAGCCTGCTAGACGTAAAGTCTGAAA
1 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAA
9730305 CATCTTATTT
Statistics
Matches: 145, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
41 144 0.99
42 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (41 bp):
CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAATAATT
Found at i:9730970 original size:16 final size:17
Alignment explanation
Indices: 9730949--9730983 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
9730939 ATCTAATAAT
9730949 TTATACAT-GTATATAC
1 TTATACATCGTATATAC
*
9730965 TTATACATCGTTTATAC
1 TTATACATCGTATATAC
9730982 TT
1 TT
9730984 CGACTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (17 bp):
TTATACATCGTATATAC
Found at i:9740936 original size:16 final size:16
Alignment explanation
Indices: 9740915--9740951 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
9740905 AGACAGGTCA
9740915 CCACTCCCTCAACTCG
1 CCACTCCCTCAACTCG
*
9740931 CCACTCTCTCAACTCG
1 CCACTCCCTCAACTCG
9740947 CCACT
1 CCACT
9740952 GCCAATTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.19, C:0.54, G:0.05, T:0.22
Consensus pattern (16 bp):
CCACTCCCTCAACTCG
Found at i:9744103 original size:66 final size:66
Alignment explanation
Indices: 9744016--9744149 Score: 259
Period size: 66 Copynumber: 2.0 Consensus size: 66
9744006 GTTCTTGCCT
*
9744016 ACCCGTTATTCTAGTGGAAGATCGGAAGATCCTACTAGGATATTGACTACTTGATTGAACAAGAA
1 ACCCATTATTCTAGTGGAAGATCGGAAGATCCTACTAGGATATTGACTACTTGATTGAACAAGAA
9744081 A
66 A
9744082 ACCCATTATTCTAGTGGAAGATCGGAAGATCCTACTAGGATATTGACTACTTGATTGAACAAGAA
1 ACCCATTATTCTAGTGGAAGATCGGAAGATCCTACTAGGATATTGACTACTTGATTGAACAAGAA
9744147 A
66 A
9744148 AC
1 AC
9744150 TCAAAGCGAT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (66 bp):
ACCCATTATTCTAGTGGAAGATCGGAAGATCCTACTAGGATATTGACTACTTGATTGAACAAGAA
A
Found at i:9746443 original size:5 final size:5
Alignment explanation
Indices: 9746433--9746471 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
9746423 AAATGTTAAG
9746433 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATA
9746472 ATAAAACAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:9746539 original size:17 final size:15
Alignment explanation
Indices: 9746504--9746558 Score: 67
Period size: 16 Copynumber: 3.6 Consensus size: 15
9746494 AAGAATTAAA
9746504 AAAAAGAAACAAAGC
1 AAAAAGAAACAAAGC
*
9746519 AAAAACGAAACAGAAGG
1 AAAAA-GAAACA-AAGC
*
9746536 AAAAAGAAAGAAAG-
1 AAAAAGAAACAAAGC
9746550 AAAAAGAAA
1 AAAAAGAAA
9746559 AGGGAGAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
14 9 0.25
15 8 0.22
16 11 0.31
17 8 0.22
ACGTcount: A:0.75, C:0.07, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAAGAAACAAAGC
Found at i:9746567 original size:15 final size:14
Alignment explanation
Indices: 9746504--9746558 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
9746494 AAGAATTAAA
*
9746504 AAAAAGAAACAAAG
1 AAAAAGAAAGAAAG
*
9746518 CAAAAACGAAACAGAAGG
1 -AAAAA-G-AA-AGAAAG
9746536 AAAAAGAAAGAAAG
1 AAAAAGAAAGAAAG
9746550 AAAAAGAAA
1 AAAAAGAAA
9746559 AGGGAGAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 14 0.41
15 7 0.21
16 2 0.06
17 7 0.21
18 4 0.12
ACGTcount: A:0.75, C:0.07, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAGAAAG
Found at i:9747609 original size:23 final size:23
Alignment explanation
Indices: 9747582--9747631 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
9747572 GCTTTCTGAA
* *
9747582 ATATGGCTCTCTAGAGCTTCCCG
1 ATATGGCTCGCTAGAACTTCCCG
* *
9747605 ATATGGCTCGCTTGAACTTCTCG
1 ATATGGCTCGCTAGAACTTCCCG
9747628 ATAT
1 ATAT
9747632 ATGGCTCTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (23 bp):
ATATGGCTCGCTAGAACTTCCCG
Found at i:9747761 original size:25 final size:25
Alignment explanation
Indices: 9747695--9747774 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
9747685 TCTTATGAGT
* *
9747695 TTCCCGTTATACAGCCTGGATA-AGC
1 TTCCCGTTATACAG-CTCGAAAGAGC
* *
9747720 TTCTCGTTATACAGCTC-ACACGAGC
1 TTCCCGTTATACAGCTCGA-AAGAGC
**
9747745 TTCCCGTTATATGGCTCGAAAGAGC
1 TTCCCGTTATACAGCTCGAAAGAGC
9747770 TTCCC
1 TTCCC
9747775 ATTTATGTGC
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
23 1 0.02
24 2 0.05
25 40 0.91
26 1 0.02
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.29
Consensus pattern (25 bp):
TTCCCGTTATACAGCTCGAAAGAGC
Found at i:9755689 original size:50 final size:50
Alignment explanation
Indices: 9755614--9755715 Score: 143
Period size: 50 Copynumber: 2.0 Consensus size: 50
9755604 CATGGTTTGA
* *
9755614 ATTTTGTCATTGTTTAAGTAATGAAAGCGTA-AAAATTTATACCTTAGAT
1 ATTTTATCATTGTTTAAGTAATGAAAGCGTATAAAATTTATACATTAGAT
* * *
9755663 ATTTTATCATTGTTTTAAGTAATGAAAGTGTATAAATTTTATAGATTAGAT
1 ATTTTATCATTG-TTTAAGTAATGAAAGCGTATAAAATTTATACATTAGAT
9755714 AT
1 AT
9755716 AAAGTATTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
49 11 0.24
50 18 0.39
51 17 0.37
ACGTcount: A:0.37, C:0.05, G:0.14, T:0.44
Consensus pattern (50 bp):
ATTTTATCATTGTTTAAGTAATGAAAGCGTATAAAATTTATACATTAGAT
Found at i:9769942 original size:10 final size:10
Alignment explanation
Indices: 9769923--9769969 Score: 62
Period size: 10 Copynumber: 4.9 Consensus size: 10
9769913 ATGTATATAC
9769923 TTTTTA-AAT
1 TTTTTATAAT
9769932 TTTTTATAAT
1 TTTTTATAAT
9769942 TTTTTA-AAT
1 TTTTTATAAT
* *
9769951 TTTTTTTAAA
1 TTTTTATAAT
9769961 TTTTTATAA
1 TTTTTATAA
9769970 ACCACGCATT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.42
10 19 0.58
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:9769947 original size:19 final size:19
Alignment explanation
Indices: 9769923--9769966 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
9769913 ATGTATATAC
*
9769923 TTTTTAAATTTTTTATAAT
1 TTTTTAAATTTTTTATAAA
*
9769942 TTTTTAAATTTTTTTTAAA
1 TTTTTAAATTTTTTATAAA
9769961 TTTTTA
1 TTTTTA
9769967 TAAACCACGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTTAAATTTTTTATAAA
Found at i:9769955 original size:11 final size:11
Alignment explanation
Indices: 9769923--9769965 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
9769913 ATGTATATAC
9769923 TTTTTAAATTT
1 TTTTTAAATTT
*
9769934 TTTAT-AA--T
1 TTTTTAAATTT
9769942 TTTTTAAATTT
1 TTTTTAAATTT
9769953 TTTTTAAATTT
1 TTTTTAAATTT
9769964 TT
1 TT
9769966 ATAAACCACG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
8 5 0.19
9 2 0.07
10 2 0.07
11 18 0.67
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTTTTAAATTT
Found at i:9769970 original size:10 final size:9
Alignment explanation
Indices: 9769923--9769970 Score: 60
Period size: 9 Copynumber: 4.9 Consensus size: 9
9769913 ATGTATATAC
9769923 TTTTTAAAT
1 TTTTTAAAT
9769932 TTTTTATAAT
1 TTTTTA-AAT
9769942 TTTTTAAATTT
1 TTTTTAAA--T
9769953 TTTTTAAAT
1 TTTTTAAAT
9769962 TTTTATAAA
1 TTTT-TAAA
9769971 CCACGCATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
9 13 0.37
10 13 0.37
11 9 0.26
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:9770601 original size:31 final size:31
Alignment explanation
Indices: 9770566--9770634 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
9770556 CTTAACAACC
*
9770566 CAATGATTTAAATAAAAACTTTTGAATAGTT
1 CAATGATTTAAATAAAAACTTTTCAATAGTT
* *
9770597 CAATGACTTAAATGAAAACTTTTCAATAGTT
1 CAATGATTTAAATAAAAACTTTTCAATAGTT
*
9770628 CAGTGAT
1 CAATGAT
9770635 CAAATTGTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (31 bp):
CAATGATTTAAATAAAAACTTTTCAATAGTT
Found at i:9774427 original size:2 final size:2
Alignment explanation
Indices: 9774420--9774453 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9774410 AAACACCCTC
9774420 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
9774454 TGGCTCTTAA
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:9779556 original size:21 final size:21
Alignment explanation
Indices: 9779530--9779569 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
9779520 CAATCTATTA
9779530 TGTTTGTAGGTTTATAAAAAT
1 TGTTTGTAGGTTTATAAAAAT
*
9779551 TGTTTGTGGGTTTATAAAA
1 TGTTTGTAGGTTTATAAAA
9779570 TATGTATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (21 bp):
TGTTTGTAGGTTTATAAAAAT
Found at i:9779906 original size:29 final size:28
Alignment explanation
Indices: 9779873--9779933 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
9779863 AAAAAGCCCT
9779873 TTTTTTCAAAATTTACCGAAATGGGCCAA
1 TTTTTTCAAAATTTACCGAAATGGGCC-A
* ** *
9779902 TTTTTTGATTATTTACCGGAATGGGCCA
1 TTTTTTCAAAATTTACCGAAATGGGCCA
9779930 TTTT
1 TTTT
9779934 CCGGGAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.26, C:0.15, G:0.16, T:0.43
Consensus pattern (28 bp):
TTTTTTCAAAATTTACCGAAATGGGCCA
Found at i:9780926 original size:29 final size:29
Alignment explanation
Indices: 9780860--9780926 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
9780850 CAATTTCGCG
*
9780860 AAAAATGGCCCATTTCAGTAAATAATCAA
1 AAAAACGGCCCATTTCAGTAAATAATCAA
* * ** *
9780889 AAAATCGGCCCATTTCGGTAAATTTTGAA
1 AAAAACGGCCCATTTCAGTAAATAATCAA
9780918 AAAAACGGC
1 AAAAACGGC
9780927 TTTTTTTGGT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (29 bp):
AAAAACGGCCCATTTCAGTAAATAATCAA
Found at i:9787962 original size:16 final size:16
Alignment explanation
Indices: 9787941--9787987 Score: 94
Period size: 16 Copynumber: 2.9 Consensus size: 16
9787931 ATTTTTGTTC
9787941 TAATTTTTCAATTCTG
1 TAATTTTTCAATTCTG
9787957 TAATTTTTCAATTCTG
1 TAATTTTTCAATTCTG
9787973 TAATTTTTCAATTCT
1 TAATTTTTCAATTCT
9787988 AAGCTATTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.26, C:0.13, G:0.04, T:0.57
Consensus pattern (16 bp):
TAATTTTTCAATTCTG
Found at i:9794126 original size:18 final size:19
Alignment explanation
Indices: 9794103--9794138 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
9794093 ACACATGCCA
9794103 AAGTGAAA-AATGATTTTT
1 AAGTGAAAGAATGATTTTT
*
9794121 AAGTGAAAGATTGATTTT
1 AAGTGAAAGAATGATTTT
9794139 GTGGCCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (19 bp):
AAGTGAAAGAATGATTTTT
Found at i:9794237 original size:48 final size:46
Alignment explanation
Indices: 9794185--9794290 Score: 151
Period size: 48 Copynumber: 2.2 Consensus size: 46
9794175 AGGTGGAAGA
*
9794185 ATGTGGCAGCTTATCTGCAAAAGTGGTGGCTTGTCCACAAATTTTG-TT
1 ATGTGGCAG-TTATCTGCAAAAGTGGAGGCTTGTCCAC-AA-TTTGATT
9794233 ATGTGGCAGTATATCTGCAAAAGTGGAGGCTTGTCCACAATTTGATT
1 ATGTGGCAGT-TATCTGCAAAAGTGGAGGCTTGTCCACAATTTGATT
*
9794280 ATGTGACAGTT
1 ATGTGGCAGTT
9794291 TATTTGCATT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
46 5 0.09
47 14 0.26
48 35 0.65
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (46 bp):
ATGTGGCAGTTATCTGCAAAAGTGGAGGCTTGTCCACAATTTGATT
Found at i:9797409 original size:11 final size:11
Alignment explanation
Indices: 9797393--9797417 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9797383 ATCTTTATTA
9797393 TTTAGAACTTG
1 TTTAGAACTTG
9797404 TTTAGAACTTG
1 TTTAGAACTTG
9797415 TTT
1 TTT
9797418 TCAAAGTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (11 bp):
TTTAGAACTTG
Found at i:9808978 original size:29 final size:29
Alignment explanation
Indices: 9808944--9809043 Score: 137
Period size: 29 Copynumber: 3.3 Consensus size: 29
9808934 TATATACAAT
*
9808944 ATATATATGCGCGGGTTTTGTTATATATA
1 ATATATATGCGTGGGTTTTGTTATATATA
* *
9808973 ATATATATGCGTGGGTTTAGATATATATA
1 ATATATATGCGTGGGTTTTGTTATATATA
*
9809002 ATATATATGCGTGGGTCTTGATTATATATA
1 ATATATATGCGTGGGTTTTG-TTATATATA
9809032 TGATATATATGC
1 --ATATATATGC
9809044 ATATATGGGT
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
29 44 0.71
30 8 0.13
32 10 0.16
ACGTcount: A:0.31, C:0.06, G:0.20, T:0.43
Consensus pattern (29 bp):
ATATATATGCGTGGGTTTTGTTATATATA
Found at i:9809064 original size:37 final size:37
Alignment explanation
Indices: 9809013--9809096 Score: 102
Period size: 37 Copynumber: 2.3 Consensus size: 37
9809003 TATATATGCG
9809013 TGGGTCTTG-ATTATAT-ATAT-GATATATATGCATATA
1 TGGGTCTTGTATTATATAATATAGATATATATG--TATA
* *
9809049 TGGGTCTTGTTTTATATAATATATATATATATGTATA
1 TGGGTCTTGTATTATATAATATAGATATATATGTATA
*
9809086 TGGGTTTTGTA
1 TGGGTCTTGTA
9809097 ATGCTTGCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
36 9 0.22
37 19 0.46
38 4 0.10
39 9 0.22
ACGTcount: A:0.30, C:0.04, G:0.18, T:0.49
Consensus pattern (37 bp):
TGGGTCTTGTATTATATAATATAGATATATATGTATA
Done.