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 67 of 206
Found at i:18895135 original size:22 final size:22
Alignment explanation
Indices: 18895083--18895137 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
18895073 CATTTGTTTT
* * *
18895083 TGATCTGTTTTGCATTTGTATA
1 TGATCTGTTCTGCATCTGCATA
*
18895105 TGAAT-TGTTCTGCATCTGCATC
1 TG-ATCTGTTCTGCATCTGCATA
18895127 TGATCTGTTCT
1 TGATCTGTTCT
18895138 TTGTCTTACC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 2 0.07
22 23 0.85
23 2 0.07
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.49
Consensus pattern (22 bp):
TGATCTGTTCTGCATCTGCATA
Found at i:18895495 original size:25 final size:25
Alignment explanation
Indices: 18895467--18895523 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
18895457 AGCATTTTGC
**
18895467 TTAAATTTGAATTAACATATCTCTT
1 TTAAATTTGAATTAACATATCTCCG
18895492 TTAAATTTGAATTAACATATCTCCG
1 TTAAATTTGAATTAACATATCTCCG
18895517 TTAAATT
1 TTAAATT
18895524 ACTTTAATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (25 bp):
TTAAATTTGAATTAACATATCTCCG
Found at i:18899971 original size:25 final size:25
Alignment explanation
Indices: 18899939--18900022 Score: 87
Period size: 25 Copynumber: 3.4 Consensus size: 25
18899929 AAATATAAAT
*
18899939 GGGAAGCTCTTCCGAGCCATATAAC
1 GGGAAGCTCTTACGAGCCATATAAC
* * ** **
18899964 GAGAAGCTCATGTGAGCTGTATAAC
1 GGGAAGCTCTTACGAGCCATATAAC
* *
18899989 GGGAAGCTCTTACGAGCCAAATATC
1 GGGAAGCTCTTACGAGCCATATAAC
18900014 GGGAAGCTC
1 GGGAAGCTC
18900023 AAGAGAGCCA
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (25 bp):
GGGAAGCTCTTACGAGCCATATAAC
Found at i:18900030 original size:25 final size:25
Alignment explanation
Indices: 18899952--18900098 Score: 91
Period size: 25 Copynumber: 5.9 Consensus size: 25
18899942 AAGCTCTTCC
* * * *
18899952 GAGCCATATAACGAGAAGCTCATGT
1 GAGCCAAATATCGGGAAGCTCATGA
*** * *
18899977 GAGCTGTATAACGGGAAGCTC-TTA
1 GAGCCAAATATCGGGAAGCTCATGA
*
18900001 CGAGCCAAATATCGGGAAGCTCAAGA
1 -GAGCCAAATATCGGGAAGCTCATGA
* * *
18900027 GAGCC-ATTAATCGAGAAGCTCATGG
1 GAGCCAAAT-ATCGGGAAGCTCATGA
* * *
18900052 GAGCTAAATATCAGGAAGCTCGTGA
1 GAGCCAAATATCGGGAAGCTCATGA
* * *
18900077 GAGCCAAGTATTGGGACGCTCA
1 GAGCCAAATATCGGGAAGCTCA
18900099 CAAGAATTGT
Statistics
Matches: 91, Mismatches: 27, Indels: 8
0.72 0.21 0.06
Matches are distributed among these distances:
24 3 0.03
25 85 0.93
26 3 0.03
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.19
Consensus pattern (25 bp):
GAGCCAAATATCGGGAAGCTCATGA
Found at i:18900045 original size:50 final size:50
Alignment explanation
Indices: 18899941--18900082 Score: 133
Period size: 50 Copynumber: 2.8 Consensus size: 50
18899931 ATATAAATGG
* * * * * ** *
18899941 GAAGCTCTTCCGAGCCATATAACGAGAAGCTCATGTGAGCTGTATAACGG
1 GAAGCTCTTACGAGCCAAATATCGGGAAGCTCATGAGAGCCATATAACGA
*
18899991 GAAGCTCTTACGAGCCAAATATCGGGAAGCTCAAGAGAGCCAT-TAATCGA
1 GAAGCTCTTACGAGCCAAATATCGGGAAGCTCATGAGAGCCATATAA-CGA
* ** * * *
18900041 GAAGCTCATGGGAGCTAAATATCAGGAAGCTCGTGAGAGCCA
1 GAAGCTCTTACGAGCCAAATATCGGGAAGCTCATGAGAGCCA
18900083 AGTATTGGGA
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
49 3 0.04
50 72 0.96
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.19
Consensus pattern (50 bp):
GAAGCTCTTACGAGCCAAATATCGGGAAGCTCATGAGAGCCATATAACGA
Found at i:18900069 original size:75 final size:75
Alignment explanation
Indices: 18899952--18900098 Score: 181
Period size: 75 Copynumber: 2.0 Consensus size: 75
18899942 AAGCTCTTCC
* ** * *
18899952 GAGCCATATAACGAGAAGCTCATGTGAGCTGTATAACGGGAAGCTC-TTACGAGCCAAATATCGG
1 GAGCCATATAACGAGAAGCTCATGGGAGCTAAATAACAGGAAGCTCGTGA-GAGCCAAATATCGG
18900016 GAAGCTCAAGA
65 GAAGCTCAAGA
* * *
18900027 GAGCCAT-TAATCGAGAAGCTCATGGGAGCTAAATATCAGGAAGCTCGTGAGAGCCAAGTATTGG
1 GAGCCATATAA-CGAGAAGCTCATGGGAGCTAAATAACAGGAAGCTCGTGAGAGCCAAATATCGG
*
18900091 GACGCTCA
65 GAAGCTCA
18900099 CAAGAATTGT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
74 3 0.05
75 56 0.92
76 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.19
Consensus pattern (75 bp):
GAGCCATATAACGAGAAGCTCATGGGAGCTAAATAACAGGAAGCTCGTGAGAGCCAAATATCGGG
AAGCTCAAGA
Found at i:18906992 original size:25 final size:25
Alignment explanation
Indices: 18906933--18907052 Score: 82
Period size: 25 Copynumber: 4.8 Consensus size: 25
18906923 AAGCTTTTCC
* * *
18906933 GAGCCATATAACGGGAAACTCAT-A
1 GAGCCAAATAATGGGAAGCTCATGA
** * *
18906957 TGAGCTGAATAATGGGAAGCTCTTGC
1 -GAGCCAAATAATGGGAAGCTCATGA
* * *
18906983 GAGCCAAATATTGAGAAGCTCAAGA
1 GAGCCAAATAATGGGAAGCTCATGA
*
18907008 GAGCC-ATTAATCGGGAAGCTCATGA
1 GAGCCAAATAAT-GGGAAGCTCATGA
* * *
18907033 GATCTAAATAATGAGAAGCT
1 GAGCCAAATAATGGGAAGCT
18907053 TGTGATTGCC
Statistics
Matches: 70, Mismatches: 22, Indels: 6
0.71 0.22 0.06
Matches are distributed among these distances:
24 4 0.06
25 61 0.87
26 5 0.07
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.21
Consensus pattern (25 bp):
GAGCCAAATAATGGGAAGCTCATGA
Found at i:18920848 original size:49 final size:50
Alignment explanation
Indices: 18920709--18920848 Score: 132
Period size: 49 Copynumber: 2.8 Consensus size: 50
18920699 AGGTTCAATG
18920709 GTTAAGTTATTATAATTTTATTAAAAAATTAAGACTAAAAAATAAATTTA
1 GTTAAGTTATTATAATTTTATTAAAAAATTAAGACTAAAAAATAAATTTA
** * * * *
18920759 GTCTAA---AAAATCCATTTGATAAAATAAATGT--GTAAT-AAAAATAAATTTA
1 GT-TAAGTTATTAT-AATTTTATTAAA-AAAT-TAAG-ACTAAAAAATAAATTTA
18920808 -TTAAGTTATTATAATTTTATTAAAAAATTAAGACTAAAAAA
1 GTTAAGTTATTATAATTTTATTAAAAAATTAAGACTAAAAAA
18920849 ATGCTAAACT
Statistics
Matches: 67, Mismatches: 12, Indels: 23
0.66 0.12 0.23
Matches are distributed among these distances:
47 4 0.06
48 10 0.15
49 38 0.57
50 11 0.16
51 4 0.06
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (50 bp):
GTTAAGTTATTATAATTTTATTAAAAAATTAAGACTAAAAAATAAATTTA
Found at i:18920979 original size:26 final size:27
Alignment explanation
Indices: 18920909--18920981 Score: 69
Period size: 26 Copynumber: 2.7 Consensus size: 27
18920899 GTTTACTTTT
*
18920909 AGGTAATCTTATATTTTGTCAACCAAACAC
1 AGGTAATCTTATA--TT-CCAACCAAACAC
* * *
18920939 ATG-AATTTTACATTCCAACCAAACA-
1 AGGTAATCTTATATTCCAACCAAACAC
18920964 AGGTAATCTTATATTCCA
1 AGGTAATCTTATATTCCA
18920982 CTTGTAATCG
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
25 2 0.06
26 22 0.63
27 2 0.06
29 7 0.20
30 2 0.06
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (27 bp):
AGGTAATCTTATATTCCAACCAAACAC
Found at i:18926584 original size:39 final size:39
Alignment explanation
Indices: 18926541--18926734 Score: 246
Period size: 39 Copynumber: 5.0 Consensus size: 39
18926531 CAGAAATACG
**
18926541 GTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTATCA
1 GTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGCCA
*
18926580 GTGATTATTCAGGCTAAGTGCCTAGCAGGCTTTGTGCCA
1 GTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGCCA
* * * * *
18926619 GTGAATGTTCAGGCTAAGTGCCTAGCAAG-TATTGTGCCG
1 GTGATTATTCGGGCTAAGTGCCTAGCAGGCT-TTGTGCCA
* * *
18926658 GTGATTATTCGGGCTAAGTACCTAACAGGCTTTGTGCCG
1 GTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGCCA
* * *
18926697 GTGATTATTCGGGCTAAATGCTTAGTAGGCTTTGTGCC
1 GTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGCC
18926735 TAACAGGCTG
Statistics
Matches: 135, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
38 1 0.01
39 133 0.99
40 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.32
Consensus pattern (39 bp):
GTGATTATTCGGGCTAAGTGCCTAGCAGGCTTTGTGCCA
Found at i:18935030 original size:45 final size:45
Alignment explanation
Indices: 18934979--18935065 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
18934969 TGTGAACCAA
* *
18934979 ACATCATTGATTAGTAAAGTGGTTGCTATGTGTTGATTCCACTGG
1 ACATCATTGATTAATAAAGTGGTTGCTATGTGTTGACTCCACTGG
*
18935024 ACATCATTGATTAATAAGGTGGTTGCTATGTGTTGACTCCAC
1 ACATCATTGATTAATAAAGTGGTTGCTATGTGTTGACTCCAC
18935066 CGAGTATCTG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (45 bp):
ACATCATTGATTAATAAAGTGGTTGCTATGTGTTGACTCCACTGG
Found at i:18952476 original size:12 final size:12
Alignment explanation
Indices: 18952459--18952483 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18952449 TAGATGTGAC
18952459 TGATTATACTGA
1 TGATTATACTGA
18952471 TGATTATACTGA
1 TGATTATACTGA
18952483 T
1 T
18952484 AGTATATCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TGATTATACTGA
Found at i:18953522 original size:26 final size:26
Alignment explanation
Indices: 18953435--18953522 Score: 113
Period size: 26 Copynumber: 3.4 Consensus size: 26
18953425 GAAATTTCTC
** *
18953435 AAAATTTTATTAGGGGTAAAATCGTT
1 AAAATTTTACCAGGGGTAAAATCATT
* *
18953461 AAAATTTTAACAAGGGTAAAATCATT
1 AAAATTTTACCAGGGGTAAAATCATT
* *
18953487 AAAATTTTACCTGGGGTAAAATTATT
1 AAAATTTTACCAGGGGTAAAATCATT
18953513 AAAATTTTAC
1 AAAATTTTAC
18953523 TAGAGTAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (26 bp):
AAAATTTTACCAGGGGTAAAATCATT
Found at i:18958079 original size:16 final size:18
Alignment explanation
Indices: 18958053--18958085 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
18958043 TTAATTTAAA
18958053 TAAATTAATTTT-TCAAT
1 TAAATTAATTTTCTCAAT
18958070 TAAA-TAATTTTCTCAA
1 TAAATTAATTTTCTCAA
18958086 CCAAATTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:18973321 original size:39 final size:39
Alignment explanation
Indices: 18973271--18973378 Score: 123
Period size: 39 Copynumber: 2.8 Consensus size: 39
18973261 TGATCTATAA
* *
18973271 AGGTG-TT-TTTGAGTATTGGGATATATGCTTGAATGTT
1 AGGTGATTATTTGAGTATTGAGATATATGCTTGAATATT
* *
18973308 ATGTGATTATTTGAGTATTGAGATATATGCTTGTATATT
1 AGGTGATTATTTGAGTATTGAGATATATGCTTGAATATT
* * *
18973347 AGGTGATTATATGTGTAAT-ATGATATATGCTT
1 AGGTGATTATTTGAGTATTGA-GATATATGCTT
18973379 AAAAGTGAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
37 4 0.07
38 3 0.05
39 53 0.88
ACGTcount: A:0.27, C:0.03, G:0.24, T:0.46
Consensus pattern (39 bp):
AGGTGATTATTTGAGTATTGAGATATATGCTTGAATATT
Found at i:18976843 original size:61 final size:57
Alignment explanation
Indices: 18976737--18976851 Score: 158
Period size: 61 Copynumber: 1.9 Consensus size: 57
18976727 ATCACTTTAA
* *
18976737 TATTAAATTATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAATC
1 TATTAAATTATAGAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATC
* *
18976794 TATTAAATTAATAGAATATTTATCTATAAGATAAATATTAAATTTAATTTAATATTAA
1 TATTAAATT-ATAGAATACTTATC---AAGATAAATATTAAATTAAATTTAATATTAA
18976852 GATAATCACT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
57 9 0.18
58 12 0.24
61 29 0.58
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.43
Consensus pattern (57 bp):
TATTAAATTATAGAATACTTATCAAGATAAATATTAAATTAAATTTAATATTAAATC
Found at i:18978628 original size:18 final size:18
Alignment explanation
Indices: 18978605--18978640 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
18978595 GGAAGTATAT
18978605 CTGTATTTTGGAATTTCA
1 CTGTATTTTGGAATTTCA
18978623 CTGTATTTTGGAATTTCA
1 CTGTATTTTGGAATTTCA
18978641 TGGAGTACCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (18 bp):
CTGTATTTTGGAATTTCA
Found at i:18991689 original size:13 final size:14
Alignment explanation
Indices: 18991673--18991702 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
18991663 GCCAAAAAAT
18991673 ATTTTTA-AAATTA
1 ATTTTTAGAAATTA
18991686 ATTTTTAGAAATTA
1 ATTTTTAGAAATTA
18991700 ATT
1 ATT
18991703 ATTTTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
ATTTTTAGAAATTA
Found at i:18992158 original size:18 final size:18
Alignment explanation
Indices: 18992132--18992167 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
18992122 TCACCGTATA
18992132 GCCACTTTCAATTTTCCT
1 GCCACTTTCAATTTTCCT
*
18992150 GCCATTTTCAATTTTCCT
1 GCCACTTTCAATTTTCCT
18992168 TAACGTCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.31, G:0.06, T:0.47
Consensus pattern (18 bp):
GCCACTTTCAATTTTCCT
Found at i:19000522 original size:17 final size:18
Alignment explanation
Indices: 19000492--19000536 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
19000482 ATTTAAATTG
19000492 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCGTTTT
19000510 CGGTCGC-GTCGCG-TTT
1 CGGTCGCGGTCGCGTTTT
19000526 --GTCGCGGTCGC
1 CGGTCGCGGTCGC
19000537 AGACATAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 5 0.19
16 3 0.12
17 6 0.23
18 7 0.27
ACGTcount: A:0.00, C:0.31, G:0.40, T:0.29
Consensus pattern (18 bp):
CGGTCGCGGTCGCGTTTT
Found at i:19009042 original size:3 final size:3
Alignment explanation
Indices: 19009034--19009063 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
19009024 GATCAAGAAC
19009034 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19009064 GAAAAGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19009285 original size:23 final size:22
Alignment explanation
Indices: 19009245--19009288 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
19009235 AAAATTATAA
*
19009245 ATATAAAAATATATATATGTAC
1 ATATAAAAAAATATATATGTAC
19009267 ATATAAGAAAAATATATATGTA
1 ATATAA-AAAAATATATATGTA
19009289 TGTGAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (22 bp):
ATATAAAAAAATATATATGTAC
Found at i:19009304 original size:27 final size:26
Alignment explanation
Indices: 19009237--19009304 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 26
19009227 AATAGATAAA
19009237 AATTATAAATATAAAAATATATATATGT
1 AATTATAAA-A-AAAAATATATATATGT
* *
19009265 ACA-TATAAGAAAAATATATATGTATGT
1 A-ATTATAA-AAAAAAATATATATATGT
19009292 GAATTATAAAAAA
1 -AATTATAAAAAA
19009305 TAAAAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
27 19 0.56
28 13 0.38
29 2 0.06
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.34
Consensus pattern (26 bp):
AATTATAAAAAAAAATATATATATGT
Found at i:19010036 original size:23 final size:22
Alignment explanation
Indices: 19009993--19010050 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
19009983 AAAGGGTATC
* *
19009993 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
19010014 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
19010037 TGCATATCATATCT
1 TACAAATCATATCT
19010051 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:19010601 original size:44 final size:45
Alignment explanation
Indices: 19010502--19010604 Score: 113
Period size: 44 Copynumber: 2.3 Consensus size: 45
19010492 ACTACACCGC
* *
19010502 CAGGGA-AGTAAGATTTGCTATTCTCAGTCTGCCTCACTACAACTT
1 CAGGGAGA-TAAGACTTGCTATTCTCAGTCTGCCTCACTACAACCT
* * * *
19010547 TAGGGGGATAAGACTTGCT-TTCTCAGTCTG-CTCCGCTGCAACCT
1 CAGGGAGATAAGACTTGCTATTCTCAGTCTGCCT-CACTACAACCT
19010591 CAGGGAGATAAGAC
1 CAGGGAGATAAGAC
19010605 CTGATACGAT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
43 2 0.04
44 31 0.65
45 14 0.29
46 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.27
Consensus pattern (45 bp):
CAGGGAGATAAGACTTGCTATTCTCAGTCTGCCTCACTACAACCT
Found at i:19010886 original size:44 final size:43
Alignment explanation
Indices: 19010838--19010937 Score: 110
Period size: 44 Copynumber: 2.3 Consensus size: 43
19010828 CTTTGATCTG
* ** *
19010838 CTCCACTACTGCTTACGAAGATAAGATCTGTAATTTTCAACCT
1 CTCCACTGCTGCTTACGAAGATAAGATCTACAATCTTCAACCT
* * * * *
19010881 ACTCCATTGCTGATTAGGGAGATAAGGTCTACAATCTTCAACCT
1 -CTCCACTGCTGCTTACGAAGATAAGATCTACAATCTTCAACCT
19010925 CTCCACTGCTGCT
1 CTCCACTGCTGCT
19010938 CAGGGAGATA
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
43 11 0.24
44 34 0.76
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (43 bp):
CTCCACTGCTGCTTACGAAGATAAGATCTACAATCTTCAACCT
Found at i:19010963 original size:175 final size:176
Alignment explanation
Indices: 19010718--19011111 Score: 542
Period size: 175 Copynumber: 2.2 Consensus size: 176
19010708 CCACTACAAC
** ** * *
19010718 TTAGGGAGATAAAATCTGTAATTTTCAGCCTACTCCACTGCTGCTCAGAGAGATAAGACTAGTAG
1 TTAGGGAGATAAGGTCTACAATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAAGACTAGTAG
* *
19010783 CTTAAATATGCTTCCCTACTACCTTGGGAAGATAAGAATCACCGTCTTTGATCTGCTCCACTACT
66 CTTAAATATGCTTCCCTACTACCTTGGAAAGATAAGAATCACCGTCTTCGATCTGCTCCACTACT
*
19010848 GCTTACGAAGATAAGATCTGTAATTTTCAACCTACTCCATTGCTGA
131 GCTTACGAAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGA
* * *
19010894 TTAGGGAGATAAGGTCTACAATCTTCAACCT-CTCCACTGCTGCTCAGGGAGATAAGGCTAGTGG
1 TTAGGGAGATAAGGTCTACAATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAAGACTAGTAG
* * * *
19010958 CTTAAATCTGCTTCCCTACTACCTTGGAAAGATGAGATTCGCCGTCTTCGATCTGCTCCACTACT
66 CTTAAATATGCTTCCCTACTACCTTGGAAAGATAAGAATCACCGTCTTCGATCTGCTCCACTACT
* * * * *
19011023 GGTTAGGGAGATAAGATCTGTAATTTTCAACCTATTCCACTGCTGC
131 GCTTACGAAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGA
* *
19011069 TCAGGGAGAT-AGGAT-TCACAATCTTCAACCTATTCCACTGCTG
1 TTAGGGAGATAAGG-TCT-ACAATCTTCAACCTACTCCACTGCTG
19011112 ACCAGGAAGA
Statistics
Matches: 192, Mismatches: 23, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
174 4 0.02
175 153 0.80
176 35 0.18
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (176 bp):
TTAGGGAGATAAGGTCTACAATCTTCAACCTACTCCACTGCTGCTCAGAGAGATAAGACTAGTAG
CTTAAATATGCTTCCCTACTACCTTGGAAAGATAAGAATCACCGTCTTCGATCTGCTCCACTACT
GCTTACGAAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTGA
Found at i:19011062 original size:44 final size:44
Alignment explanation
Indices: 19011014--19011350 Score: 260
Period size: 44 Copynumber: 7.9 Consensus size: 44
19011004 TTCGATCTGC
* * ** *
19011014 TCCACTACTGGTTAGGGAGATAAGA-TCTGTAATTTTCAACCTAT
1 TCCACTACTGCTCAGGGAGATAAGATTC-ACAATCTTCAACCTAT
* *
19011058 TCCACTGCTGCTCAGGGAGATAGGATTCACAATCTTCAACCTAT
1 TCCACTACTGCTCAGGGAGATAAGATTCACAATCTTCAACCTAT
* * *
19011102 TCCACTGCTGAC-CAGGAAGATAGGATTCACAATCTTCAACCTAT
1 TCCACTACTG-CTCAGGGAGATAAGATTCACAATCTTCAACCTAT
** * * *
19011146 TCCACTGTTGAC-CTGGGAGATAGGACTCACAATCTTCAACCTAT
1 TCCACTACTG-CTCAGGGAGATAAGATTCACAATCTTCAACCTAT
* *
19011190 TCCACTACTGACT-AAGGAGAT-AG------GA--TTC-ACCTAT
1 TCCACTACTG-CTCAGGGAGATAAGATTCACAATCTTCAACCTAT
* *
19011224 TCCACTGCTGAC-CAGGGAGATAGGACTT-ACAATCTTCAACCTAT
1 TCCACTACTG-CTCAGGGAGATAAGA-TTCACAATCTTCAACCTAT
*
19011268 TCCACTACTGAC-CAGGGAGATAGGATTCACAATCTTCAACCTAT
1 TCCACTACTG-CTCAGGGAGATAAGATTCACAATCTTCAACCTAT
* * * *
19011312 TCCATTGCTGAC-CAGGGAGATATGACTCACAATCTTCAA
1 TCCACTACTG-CTCAGGGAGATAAGATTCACAATCTTCAA
19011351 GGGAGATAGG
Statistics
Matches: 251, Mismatches: 27, Indels: 30
0.81 0.09 0.10
Matches are distributed among these distances:
34 24 0.10
35 4 0.02
37 1 0.00
41 1 0.00
43 6 0.02
44 212 0.84
45 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (44 bp):
TCCACTACTGCTCAGGGAGATAAGATTCACAATCTTCAACCTAT
Found at i:19011094 original size:88 final size:88
Alignment explanation
Indices: 19011048--19011350 Score: 403
Period size: 88 Copynumber: 3.6 Consensus size: 88
19011038 ATCTGTAATT
* *
19011048 TTCAACCTATTCCACTGCTG-CTCAGGGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTG
1 TTCAACCTATTCCACTGCTGAC-CAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTACTG
* *
19011112 ACCAGGAAGATAGGATTCACAATC
65 ACCAGGGAGATAAGATTCACAATC
* *
19011136 TTCAACCTATTCCACTGTTGACCTGGGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGA
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGA
* * *
19011201 CTAAGGAGAT-AG------GA--
66 CCAGGGAGATAAGATTCACAATC
*
19011215 TTC-ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTACTGA
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGA
*
19011279 CCAGGGAGATAGGATTCACAATC
66 CCAGGGAGATAAGATTCACAATC
* *
19011302 TTCAACCTATTCCATTGCTGACCAGGGAGATATGACTCACAATCTTCAA
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAA
19011351 GGGAGATAGG
Statistics
Matches: 185, Mismatches: 19, Indels: 22
0.82 0.08 0.10
Matches are distributed among these distances:
78 66 0.36
79 4 0.02
81 1 0.01
85 1 0.01
87 4 0.02
88 108 0.58
89 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (88 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGA
CCAGGGAGATAAGATTCACAATC
Found at i:19011227 original size:34 final size:34
Alignment explanation
Indices: 19011184--19011248 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
19011174 ACAATCTTCA
*
19011184 ACCTATTCCACTACTGACTAAGGAGATAGGATTC
1 ACCTATTCCACTACTGACCAAGGAGATAGGATTC
* *
19011218 ACCTATTCCACTGCTGACCAGGGAGATAGGA
1 ACCTATTCCACTACTGACCAAGGAGATAGGA
19011249 CTTACAATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.23
Consensus pattern (34 bp):
ACCTATTCCACTACTGACCAAGGAGATAGGATTC
Found at i:19011269 original size:78 final size:78
Alignment explanation
Indices: 19011140--19011453 Score: 274
Period size: 78 Copynumber: 4.0 Consensus size: 78
19011130 ACAATCTTCA
* * *
19011140 ACCTATTCCACTGTTGACCTGGGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGACTAA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGACCAA
19011205 GGAGATAGGATTC
66 GGAGATAGGATTC
* *
19011218 ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTACTGACCAG
1 ACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGACCAA
19011283 GGAGATAGGATTCACAATCTTC
66 GGAGATAGG-------A--TTC
* * *** * *
19011305 AACCTATTCCATTGCTGACCAGGGAGATATGACTCACAATCTTCAAGGGA---GA-TA-GGA-CA
1 -ACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGACCA
* *
19011364 TA-CA-AT---CTTC
65 -AGGAGATAGGATTC
* * *
19011374 AACCTATTTCACTGCTGACCAGGGAGATAGGACTCAGAATCTTCAACCTATTCCACTGCTGACC-
1 -ACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGACCA
19011438 AGAGAGATAGGATTC
65 AG-GAGATAGGATTC
19011453 A
1 A
19011454 TAATCTTCAA
Statistics
Matches: 185, Mismatches: 28, Indels: 46
0.71 0.11 0.18
Matches are distributed among these distances:
69 46 0.25
72 1 0.01
73 2 0.01
74 2 0.01
75 2 0.01
76 2 0.01
78 70 0.38
79 3 0.02
81 2 0.01
82 3 0.02
83 2 0.01
84 2 0.01
85 2 0.01
87 3 0.02
88 43 0.23
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (78 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGACCAA
GGAGATAGGATTC
Found at i:19011313 original size:122 final size:121
Alignment explanation
Indices: 19011096--19011453 Score: 466
Period size: 122 Copynumber: 3.0 Consensus size: 121
19011086 ACAATCTTCA
* * *
19011096 ACCTATTCCACTGCTGACCAGGAAGATAGGA-TTCACAATCTTCAACCTATTCCACTGTTGACCT
1 ACCTATTCCACTGCTGACCAGGGAGATAGGACTT-ACAATCTTCAACCTATTCCACTGCTGACCA
*
19011160 GGGAGATAGGACTCACAATCTTCAACCTATTCCACTACTGACTAAGGAGATAGGATTC
65 GGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGAC-AAGGAGATAGGATTC
*
19011218 ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTACTGACCAG
1 ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGACCAG
* * * * *
19011283 GGAGATAGGATTCACAATCTTCAACCTATTCCATTGCTGACCAGGGAGATATGACTC
66 GGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGA-CAAGGAGATAGGATTC
* * * *
19011340 A-C-A----A-T-CT-TCAAGGGAGATAGGACATACAATCTTCAACCTATTTCACTGCTGACCAG
1 ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGACCAG
* *
19011396 GGAGATAGGACTCAGAATCTTCAACCTATTCCACTGCTGACCAGAGAGATAGGATTC
66 GGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACAAG-GAGATAGGATTC
19011453 A
1 A
19011454 TAATCTTCAA
Statistics
Matches: 211, Mismatches: 22, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
112 2 0.01
113 92 0.44
114 2 0.01
115 1 0.00
116 1 0.00
120 1 0.00
121 1 0.00
122 108 0.51
123 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (121 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGACCAG
GGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACAAGGAGATAGGATTC
Found at i:19011368 original size:25 final size:25
Alignment explanation
Indices: 19011325--19011375 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
19011315 ATTGCTGACC
*
19011325 AGGGAGATATGACTCACAATCTTCA
1 AGGGAGATAGGACTCACAATCTTCA
19011350 AGGGAGATAGGACAT-ACAATCTTCA
1 AGGGAGATAGGAC-TCACAATCTTCA
19011375 A
1 A
19011376 CCTATTTCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.22
Consensus pattern (25 bp):
AGGGAGATAGGACTCACAATCTTCA
Found at i:19011392 original size:69 final size:69
Alignment explanation
Indices: 19011281--19011419 Score: 217
Period size: 69 Copynumber: 2.0 Consensus size: 69
19011271 ACTACTGACC
* * *
19011281 AGGGAGATAGGATTCACAATCTTCAACCTATTCCATTGCTGACCAGGGAGATATGACTCACAATC
1 AGGGAGATAGGAATCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATC
19011346 TTCA
66 TTCA
* *
19011350 AGGGAGATAGGACAT-ACAATCTTCAACCTATTTCACTGCTGACCAGGGAGATAGGACTCAGAAT
1 AGGGAGATAGGA-ATCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAAT
19011414 CTTCA
65 CTTCA
19011419 A
1 A
19011420 CCTATTCCAC
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
69 63 0.98
70 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.24
Consensus pattern (69 bp):
AGGGAGATAGGAATCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGACTCACAATC
TTCA
Found at i:19011415 original size:44 final size:44
Alignment explanation
Indices: 19011350--19011490 Score: 212
Period size: 44 Copynumber: 3.2 Consensus size: 44
19011340 ACAATCTTCA
*
19011350 AGGGAGATAGGACAT-ACAATCTTCAACCTATTTCACTGCTGACC
1 AGGGAGATAGGAC-TCACAATCTTCAACCTATTCCACTGCTGACC
*
19011394 AGGGAGATAGGACTCAGAATCTTCAACCTATTCCACTGCTGACC
1 AGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACC
* * * *
19011438 AGAGAGATAGGATTCATAATCTTCAACCTATTCCATTGCTGACC
1 AGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACC
19011482 AGGGAGATA
1 AGGGAGATA
19011491 AAGCTTTGTG
Statistics
Matches: 89, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
43 1 0.01
44 88 0.99
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (44 bp):
AGGGAGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACC
Found at i:19011435 original size:113 final size:113
Alignment explanation
Indices: 19011130--19011463 Score: 409
Period size: 113 Copynumber: 2.9 Consensus size: 113
19011120 GATAGGATTC
** *
19011130 ACAATCTTCAACCTATTCCACTGTTGACCTGGGAGATAGGACTCACAATCTTCAACCTATTCCAC
1 ACAATCTTCAACCTATTCCACTACTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCAC
* * * * * *
19011195 TACTGACTA-AGGAGATAGGATTCACCTATTCCACTGCTGACCAGGGAGATAGGACTT
66 TGCTGACCAGA-GAGATAGGACTCA-C-A----A-T-CT-TCAAGGGAGATAGGACAT
* *
19011252 ACAATCTTCAACCTATTCCACTACTGACCAGGGAGATAGGATTCACAATCTTCAACCTATTCCAT
1 ACAATCTTCAACCTATTCCACTACTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCAC
* *
19011317 TGCTGACCAGGGAGATATGACTCACAATCTTCAAGGGAGATAGGACAT
66 TGCTGACCAGAGAGATAGGACTCACAATCTTCAAGGGAGATAGGACAT
* * *
19011365 ACAATCTTCAACCTATTTCACTGCTGACCAGGGAGATAGGACTCAGAATCTTCAACCTATTCCAC
1 ACAATCTTCAACCTATTCCACTACTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCAC
* *
19011430 TGCTGACCAGAGAGATAGGATTCATAATCTTCAA
66 TGCTGACCAGAGAGATAGGACTCACAATCTTCAA
19011464 CCTATTCCAT
Statistics
Matches: 189, Mismatches: 22, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
113 105 0.56
114 2 0.01
115 1 0.01
116 1 0.01
120 1 0.01
121 1 0.01
122 78 0.41
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (113 bp):
ACAATCTTCAACCTATTCCACTACTGACCAGGGAGATAGGACTCACAATCTTCAACCTATTCCAC
TGCTGACCAGAGAGATAGGACTCACAATCTTCAAGGGAGATAGGACAT
Found at i:19012802 original size:23 final size:22
Alignment explanation
Indices: 19012762--19012810 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
19012752 TCCTTTTTCC
*
19012762 TTTTCTTTTTGTCATTTTTATTT
1 TTTTCTTTTT-ACATTTTTATTT
** *
19012785 TTTTCTTTTTATTTTTTTCTTT
1 TTTTCTTTTTACATTTTTATTT
19012807 TTTT
1 TTTT
19012811 GGTTTTTTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.06, C:0.08, G:0.02, T:0.84
Consensus pattern (22 bp):
TTTTCTTTTTACATTTTTATTT
Found at i:19012809 original size:15 final size:14
Alignment explanation
Indices: 19012755--19012808 Score: 72
Period size: 14 Copynumber: 3.8 Consensus size: 14
19012745 TGGCCTCTCC
* *
19012755 TTTTTCCTTTTCTT
1 TTTTTCTTTTTATT
*
19012769 TTTGTCATTTTTATT
1 TTTTTC-TTTTTATT
19012784 TTTTTCTTTTTATT
1 TTTTTCTTTTTATT
19012798 TTTTTCTTTTT
1 TTTTTCTTTTT
19012809 TTGGTTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 24 0.69
15 11 0.31
ACGTcount: A:0.06, C:0.11, G:0.02, T:0.81
Consensus pattern (14 bp):
TTTTTCTTTTTATT
Found at i:19017814 original size:3 final size:3
Alignment explanation
Indices: 19017806--19017856 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
19017796 TCAATAACAA
19017806 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19017854 AAT
1 AAT
19017857 GAAAAGATAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19018575 original size:23 final size:22
Alignment explanation
Indices: 19018532--19018589 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
19018522 AAAGGGTATC
* *
19018532 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
19018553 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
19018576 TGCATATCATATCT
1 TACAAATCATATCT
19018590 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:19018605 original size:21 final size:21
Alignment explanation
Indices: 19018568--19018622 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
19018558 AATCATATCT
19018568 TCTAAGATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
19018587 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
19018608 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
19018623 CCTTGAAGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 11 0.32
21 23 0.68
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:19025109 original size:23 final size:24
Alignment explanation
Indices: 19025082--19025129 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
19025072 GTGGACACTT
19025082 AGAA-GTTAGGTAGAACTCTTAGG
1 AGAATGTTAGGTAGAACTCTTAGG
*
19025105 AGAAGTTGTTAGGTAGGACTCTTAG
1 AGAA--TGTTAGGTAGAACTCTTAG
19025130 AATAAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
26 17 0.81
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.29
Consensus pattern (24 bp):
AGAATGTTAGGTAGAACTCTTAGG
Found at i:19028809 original size:4 final size:4
Alignment explanation
Indices: 19028802--19028828 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
19028792 GATTAAAAAA
19028802 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
19028829 AATAAAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:19035336 original size:18 final size:19
Alignment explanation
Indices: 19035291--19035339 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
19035281 GAATATTTAC
*
19035291 ATAAAAATTAAACTAAGTAA
1 ATAAAAA-TAAACTAAATAA
19035311 A-AATAAATAAA-TAAATAA
1 ATAA-AAATAAACTAAATAA
19035329 ATAAAAATAAA
1 ATAAAAATAAA
19035340 ACTTTACAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 8 0.31
20 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAATAAACTAAATAA
Found at i:19038756 original size:28 final size:28
Alignment explanation
Indices: 19038724--19038779 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
19038714 ATTTTGAGTA
19038724 AGATTAAGATAAGGATGATAAATTTTAT
1 AGATTAAGATAAGGATGATAAATTTTAT
*
19038752 AGATTAAGATAATGATGATAAATTTTAT
1 AGATTAAGATAAGGATGATAAATTTTAT
19038780 TGTAGGACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.16, T:0.38
Consensus pattern (28 bp):
AGATTAAGATAAGGATGATAAATTTTAT
Found at i:19039963 original size:16 final size:16
Alignment explanation
Indices: 19039942--19040006 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
19039932 TTCGCTGTAT
19039942 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
19039958 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
19039974 TGGAATAGAGGTGTAA
1 TGGAATAGAGGCGTAA
19039990 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
19040006 T
1 T
19040007 AGCAAATCAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.37, C:0.05, G:0.37, T:0.22
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:19040101 original size:55 final size:56
Alignment explanation
Indices: 19039972--19040101 Score: 174
Period size: 56 Copynumber: 2.3 Consensus size: 56
19039962 ATAGAGGCGT
*
19039972 AATGGAATAGAGGTGTAATGGAATAGAGGCGTAATAGCAAATCAATTGTTTGGTTG
1 AATGGAATAGAGGTGTAATGGAATAGAGACGTAATAGCAAATCAATTGTTTGGTTG
* * * * *
19040028 AATGGAATAGAGGCGTAATGGAATAGAGACGTGATAG-TATTC-TTGTGTTTGGTTG
1 AATGGAATAGAGGTGTAATGGAATAGAGACGTAATAGCAAATCAAT-TGTTTGGTTG
*
19040083 AATGGAATAGATGTGTAAT
1 AATGGAATAGAGGTGTAAT
19040102 AGCATAATGG
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
54 1 0.02
55 30 0.46
56 34 0.52
ACGTcount: A:0.34, C:0.05, G:0.31, T:0.31
Consensus pattern (56 bp):
AATGGAATAGAGGTGTAATGGAATAGAGACGTAATAGCAAATCAATTGTTTGGTTG
Found at i:19040268 original size:16 final size:16
Alignment explanation
Indices: 19040231--19040271 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
19040221 TTCATCATAT
*
19040231 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
19040247 TT-AAATATATTATAA
1 TTAAAATATATTATAA
19040262 TTAAAATATA
1 TTAAAATATA
19040272 GAATTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 3 0.14
15 10 0.45
16 9 0.41
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:19040372 original size:120 final size:119
Alignment explanation
Indices: 19040234--19040882 Score: 1128
Period size: 120 Copynumber: 5.4 Consensus size: 119
19040224 ATCATATTTA
19040234 AACATAATTATTATTAAATATATTATAATTAAAATATAGAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATT-TAATTAAAATATAGAATTTAATAAAATTCTTAATAATTAA
*
19040299 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTT
65 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
*
19040354 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATT-TAATTAAAATATAGAATTTAATAAAATTCTTAATAATTAA
*
19040419 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTT
65 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
*
19040474 AACATAATTATTATTAAATATATTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAAT
1 AACATAATTATTATTAAATATATTTAATTAAAATATAGAATTTAATAAAATTCTTAATAATTAAT
*
19040539 ATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 ATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
*
19040593 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATA-TTTAATTAAAATATAGAATTTAATAAAATTCTTAATAATTAA
19040658 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAAGATAAATT
65 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
19040712 AACATAATTATTA-T-AATATATTTAAATTAAAATATATG-ATTTAATAAAATTCTTAATAATTA
1 AACATAATTATTATTAAATATATTT-AATTAAAATATA-GAATTTAATAAAATTCTTAATAATTA
* *
19040774 ATATTCCTATATGAATTTATTCAAATCATAATATATGATACTATAAAAGATAAATT
64 ATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
19040830 AACATAATTATTATTAAATATATTTTAATTAAAATATATG-ATTTAATAAAATT
1 AACATAATTATTATTAAATATA-TTTAATTAAAATATA-GAATTTAATAAAATT
19040883 TAAAATAATT
Statistics
Matches: 515, Mismatches: 7, Indels: 14
0.96 0.01 0.03
Matches are distributed among these distances:
116 3 0.01
117 84 0.16
118 25 0.05
119 139 0.27
120 261 0.51
121 3 0.01
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (119 bp):
AACATAATTATTATTAAATATATTTAATTAAAATATAGAATTTAATAAAATTCTTAATAATTAAT
ATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATT
Found at i:19040390 original size:16 final size:16
Alignment explanation
Indices: 19040347--19040392 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
19040337 ACTATAAAAG
*
19040347 ATAATTTAACATA-ATT
1 ATAA-TTAAAATATATT
*
19040363 ATTATT-AAATATATT
1 ATAATTAAAATATATT
19040378 ATAATTAAAATATAT
1 ATAATTAAAATATAT
19040393 AATTTAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATTAAAATATATT
Found at i:19040399 original size:14 final size:15
Alignment explanation
Indices: 19040347--19040401 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
19040337 ACTATAAAAG
19040347 ATAATTTAACATA-ATT
1 ATAA-TTAA-ATATATT
*
19040363 ATTATTAAATATATT
1 ATAATTAAATATATT
19040378 ATAATTAAA-ATA-T
1 ATAATTAAATATATT
*
19040391 ATAATTTAATA
1 ATAATTAAATA
19040402 AAATTCTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.26
14 7 0.21
15 15 0.44
16 3 0.09
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAATTAAATATATT
Found at i:19040511 original size:17 final size:17
Alignment explanation
Indices: 19040491--19040524 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
19040481 TTATTATTAA
19040491 ATAT-ATTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
19040508 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
19040525 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:19040631 original size:18 final size:17
Alignment explanation
Indices: 19040610--19040644 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
19040600 TTATTATTAA
*
19040610 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
19040628 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
19040645 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:19040678 original size:239 final size:238
Alignment explanation
Indices: 19040229--19040882 Score: 1177
Period size: 239 Copynumber: 2.7 Consensus size: 238
19040219 ATTTCATCAT
*
19040229 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAGAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATT-TAATTAAAATATATAATTTAATAAAATTCTTAATA
*
19040294 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAATTTAACAT
64 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTAACAT
*
19040359 AATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTC
129 AATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTC
19040424 TTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATA
194 TTATATGAATTTACTCAAATCATAATATATGATACTAT-AAAGATA
19040470 ATTTAACATAATTATTATTAAATATATTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 ATTTAACATAATTATTATTAAATATATTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
*
19040535 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATTAACATAA
66 TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTAACATAA
19040600 TTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTT
131 TTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTT
19040665 ATATGAATTTACTCAAATCATAATATATGATACTATAAAGATA
196 ATATGAATTTACTCAAATCATAATATATGATACTATAAAGATA
* *
19040708 AATTAACATAATTATTA-T-AATATATTTAAATTAAAATATATGATTTAATAAAATTCTTAATAA
1 ATTTAACATAATTATTATTAAATATATTT-AATTAAAATATATAATTTAATAAAATTCTTAATAA
* *
19040771 TTAATATTCCTATATGAATTTATTCAAATCATAATATATGATACTATAAAAGATAAATTAACATA
65 TTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTAACATA
*
19040836 ATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
130 ATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
19040883 TAAAATAATT
Statistics
Matches: 402, Mismatches: 10, Indels: 6
0.96 0.02 0.01
Matches are distributed among these distances:
236 9 0.02
237 143 0.36
238 23 0.06
239 199 0.50
240 24 0.06
241 4 0.01
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (238 bp):
ATTTAACATAATTATTATTAAATATATTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
TAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGATAAATTAACATAA
TTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAATATTCTT
ATATGAATTTACTCAAATCATAATATATGATACTATAAAGATA
Found at i:19040868 original size:18 final size:17
Alignment explanation
Indices: 19040845--19040881 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
19040835 AATTATTATT
19040845 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
19040861 AAATATATGATTTAATA
1 AAATATATGATTTAATA
19040878 AAAT
1 AAAT
19040882 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:19040930 original size:47 final size:46
Alignment explanation
Indices: 19040864--19041122 Score: 175
Period size: 47 Copynumber: 5.7 Consensus size: 46
19040854 TTAATTAAAA
*
19040864 TATATG-ATTTAATAAAATTTAAAATAATTATAACTAATAAATTTTCT
1 TATATGAATTT-ATATAATTTAAAATAATTATAA-TAATAAATTTTCT
* * **
19040911 TATATGAATTTGTATAATTTAAAATAATTATTATTACATATAA-TTTAA
1 TATATGAATTTATATAATTTAAAATAATTA-TAATA-ATA-AATTTTCT
* * *
19040959 TA-AT-AA--TATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAATTTATATAATTT-AAAATAATT-ATAATAATAAATTTTCT
* * *
19041002 TATATGAATTTATACAATTTAAAATAA-T-TAATATTAAATATAAT-T
1 TATATGAATTTATATAATTTAAAATAATTATAATAATAAAT-T-TTCT
* * * *
19041047 TA-AT-AATGATATATAATTTCATAA-AATTCTTGATAATAAATTTTCT
1 TATATGAAT-TTATATAATTT-AAAATAATT-ATAATAATAAATTTTCT
*
19041093 TATATGAATTTATACAATTTAAAATAATTA
1 TATATGAATTTATATAATTTAAAATAATTA
19041123 ATATTAAATA
Statistics
Matches: 162, Mismatches: 27, Indels: 47
0.69 0.11 0.20
Matches are distributed among these distances:
42 2 0.01
43 11 0.07
44 40 0.25
45 14 0.09
46 14 0.09
47 62 0.38
48 17 0.10
49 2 0.01
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (46 bp):
TATATGAATTTATATAATTTAAAATAATTATAATAATAAATTTTCT
Found at i:19040953 original size:26 final size:28
Alignment explanation
Indices: 19040923--19040983 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
19040913 TATGAATTTG
*
19040923 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
19040949 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
19040977 TAAAATT
1 TATAATT
19040984 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:19040993 original size:91 final size:91
Alignment explanation
Indices: 19040898--19041196 Score: 526
Period size: 91 Copynumber: 3.3 Consensus size: 91
19040888 TAATTATAAC
* * * *
19040898 TAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
19040963 AATATATAATTTCATAAAATTCTTGA
66 GATATATAATTTCATAAAATTCTTGA
19040989 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
19041054 GATATATAATTTCATAAAATTCTTGA
66 GATATATAATTTCATAAAATTCTTGA
19041080 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
19041145 GATATATAATTTCATAAAATTCTTAA
66 GATATATAATTTCATAAAATTCTTGA
*
19041171 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAATTTTCTTATATGAATTTA
19041197 CTAAAATCAA
Statistics
Matches: 200, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
91 180 0.90
92 20 0.10
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
GATATATAATTTCATAAAATTCTTGA
Found at i:19048409 original size:21 final size:21
Alignment explanation
Indices: 19048383--19048430 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
19048373 AATTGGGTCG
*
19048383 GGTAAGGGGTGTTACAATGTT
1 GGTAAGGGGTGCTACAATGTT
19048404 GGTAAGGGGTGCTACAATGTT
1 GGTAAGGGGTGCTACAATGTT
19048425 GTGTAA
1 G-GTAA
19048431 CAAGCTCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.25, C:0.06, G:0.38, T:0.31
Consensus pattern (21 bp):
GGTAAGGGGTGCTACAATGTT
Found at i:19049548 original size:22 final size:21
Alignment explanation
Indices: 19049519--19049589 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
19049509 AGATTAAAGA
19049519 ATTGATTAATGGTGTTATTGG
1 ATTGATTAATGGTGTTATTGG
*
19049540 ATTGCATTAA--GTAGTTA--GA
1 ATTG-ATTAATGGT-GTTATTGG
*
19049559 ATTGATTAATGTTGTTATTGG
1 ATTGATTAATGGTGTTATTGG
19049580 ATTGCATTAA
1 ATTG-ATTAA
19049590 GTAGTTAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 13
0.71 0.05 0.23
Matches are distributed among these distances:
18 5 0.12
19 9 0.22
20 3 0.08
21 13 0.32
22 10 0.25
ACGTcount: A:0.30, C:0.03, G:0.23, T:0.45
Consensus pattern (21 bp):
ATTGATTAATGGTGTTATTGG
Found at i:19049556 original size:21 final size:21
Alignment explanation
Indices: 19049532--19049596 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
19049522 GATTAATGGT
19049532 GTTATTGGATTGCATTAAGTA
1 GTTATTGGATTGCATTAAGTA
* *
19049553 GTTA--GAATTG-ATTAATGTT
1 GTTATTGGATTGCATTAA-GTA
19049572 GTTATTGGATTGCATTAAGTA
1 GTTATTGGATTGCATTAAGTA
19049593 GTTA
1 GTTA
19049597 GAATTTCAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
18 5 0.14
19 11 0.31
21 15 0.42
22 5 0.14
ACGTcount: A:0.29, C:0.03, G:0.23, T:0.45
Consensus pattern (21 bp):
GTTATTGGATTGCATTAAGTA
Found at i:19049561 original size:40 final size:40
Alignment explanation
Indices: 19049516--19049601 Score: 163
Period size: 40 Copynumber: 2.1 Consensus size: 40
19049506 TACAGATTAA
19049516 AGAATTGATTAATGGTGTTATTGGATTGCATTAAGTAGTT
1 AGAATTGATTAATGGTGTTATTGGATTGCATTAAGTAGTT
*
19049556 AGAATTGATTAATGTTGTTATTGGATTGCATTAAGTAGTT
1 AGAATTGATTAATGGTGTTATTGGATTGCATTAAGTAGTT
19049596 AGAATT
1 AGAATT
19049602 TCAACTTAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.31, C:0.02, G:0.23, T:0.43
Consensus pattern (40 bp):
AGAATTGATTAATGGTGTTATTGGATTGCATTAAGTAGTT
Found at i:19053996 original size:55 final size:55
Alignment explanation
Indices: 19053893--19054000 Score: 130
Period size: 55 Copynumber: 2.0 Consensus size: 55
19053883 TCAATATGTA
* *
19053893 ACATGGTCTAGCACACGGCCTACGACACGACTGTGTGTCCATAATTCGAATATAC
1 ACATGGTCTAGCACACGGCCTACGACACGACCGTGTGGCCATAATTCGAATATAC
* * * *
19053948 ACATGGTTTGGCACACGGCCTGCGACAC-AGCCGTGTGGCTC-TATTTCGAATAT
1 ACATGGTCTAGCACACGGCCTACGACACGA-CCGTGTGGC-CATAATTCGAATAT
19054001 CTACACGGGC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
54 1 0.02
55 43 0.96
56 1 0.02
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (55 bp):
ACATGGTCTAGCACACGGCCTACGACACGACCGTGTGGCCATAATTCGAATATAC
Found at i:19062538 original size:132 final size:132
Alignment explanation
Indices: 19062409--19063133 Score: 1114
Period size: 132 Copynumber: 5.5 Consensus size: 132
19062399 GGGAGATAGG
* * * *
19062409 ATTAGTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCTTCAATCTGCT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTACT
* * * * *
19062474 CCACTACTGCTTAGGGAGATAAGATCT-ATAATCTTCAATCTATTCCACTACTGTCCAGAG-AGA
66 CCACTACTACTTAGGGAGGTAAGATCTGA-AATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-
19062537 TAGA
129 TAGA
*
19062541 ATTACTGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCCGCCATCTTCGATCTACT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTACT
*** *
19062606 CCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGAG-AGAT
66 CCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-T
19062670 AGA
130 AGA
* *
19062673 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATTCACCATCTTCGATCTACT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTACT
* *
19062738 CCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATATATTCCACTGCTGCTCAGGGAAGTA
66 CCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTA
19062803 GA
131 GA
* * **
19062805 ATTACCGGCTTTAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTTCCATCTTCGATCTACT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTACT
* *
19062870 CCACTACTACTTAGAGAGGTAAGATCTAAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTA
66 CCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTA
19062935 GA
131 GA
* *
19062937 ATTACTGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATCTGCCATCTTCGATCTACT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTACT
*
19063002 CCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGCA
66 CCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTA
19063067 GA
131 GA
** * * *
19063069 ATTACTATCTTCAATTTACTCCACTATAACCACAGGGAGGTAAAATCCACCATCTTCGATCTACT
1 ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTACT
19063134 TCGCTGTCAA
Statistics
Matches: 548, Mismatches: 43, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
132 545 0.99
133 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (132 bp):
ATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTACT
CCACTACTACTTAGGGAGGTAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTA
GA
Found at i:19063062 original size:44 final size:44
Alignment explanation
Indices: 19062417--19063062 Score: 274
Period size: 44 Copynumber: 14.7 Consensus size: 44
19062407 GGATTAGTGG
* * * *
19062417 CTTCAATGTACTCCACTG-TAACCTCAGGGAGGTAAAATCCGCCAT
1 CTTCAATCTACTCCACTGCT-ACC-CAGGGAGGTAAGATCTGACAT
* * * ** * *
19062462 CTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-ATAAT
1 CTTCAATCTACTCCACTGCTACCCAGGGAGGTAAGATCTGA-CAT
* * ** * *
19062506 CTTCAATCTATTCCACTACTGTCCAGAGAGAT-AGAAT-T-AC-T
1 CTTCAATCTACTCCACTGCTACCCAGGGAGGTAAG-ATCTGACAT
* * * * *
19062547 GGCTTCAATGTACTCCACTG-TAATCACAGGGAGGTAAAATCCGCCAT
1 --CTTCAATCTACTCCACTGCT-A-CCCAGGGAGGTAAGATCTGACAT
* * ** *
19062594 CTTCGATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAAT
1 CTTCAATCTACTCCACTGCTACCCAGGGAGGTAAGATCTGACAT
* * * * *
19062638 CTTCAATCTATTCCACTGCCAACCAGAGAGAT-AGAAT-T-AC-T
1 CTTCAATCTACTCCACTGCTACCCAGGGAGGTAAG-ATCTGACAT
* * *
19062679 GGCTTCAATGTACTCCACTG-TAACCACAGGGAGGTAAAAT-TCACCAT
1 --CTTCAATCTACTCCACTGCT-ACC-CAGGGAGGTAAGATCTGA-CAT
* * ** *
19062726 CTTCGATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAAT
1 CTTCAATCTACTCCACTGCTACCCAGGGAGGTAAGATCTGACAT
* * * * * **
19062770 CTTCAATATATTCCACTGCTGCTCAGGGAAGT-AGAAT-T-ACCGG
1 CTTCAATCTACTCCACTGCTACCCAGGGAGGTAAG-ATCTGA-CAT
* * * **
19062813 CTTTAATGTACTCCACTG-TAACCACAGGGAGGTAAAATCTTCCAT
1 CTTCAATCTACTCCACTGCT-ACC-CAGGGAGGTAAGATCTGACAT
* * ** * * *
19062858 CTTCGATCTACTCCACTACTACTTAGAGAGGTAAGATCTAAAAT
1 CTTCAATCTACTCCACTGCTACCCAGGGAGGTAAGATCTGACAT
* * *
19062902 CTTCAATCTATTCCACTGCTGCCCAGGGAAGT-AGAAT-T-AC-T
1 CTTCAATCTACTCCACTGCTACCCAGGGAGGTAAG-ATCTGACAT
* * * *
19062943 GGCTTCAATGTACTCCACTG-TAATCACAGGGAGGTAAAATCTGCCAT
1 --CTTCAATCTACTCCACTGCT-A-CCCAGGGAGGTAAGATCTGACAT
* * ** *
19062990 CTTCGATCTACTCCACTACTACTTAGGGAGGTAAGATCTGAAAT
1 CTTCAATCTACTCCACTGCTACCCAGGGAGGTAAGATCTGACAT
* *
19063034 CTTCAATCTATTCCACTGCTGCCCAGGGA
1 CTTCAATCTACTCCACTGCTACCCAGGGA
19063063 AGCAGAATTA
Statistics
Matches: 436, Mismatches: 124, Indels: 83
0.68 0.19 0.13
Matches are distributed among these distances:
41 3 0.01
42 6 0.01
43 78 0.18
44 247 0.57
45 91 0.21
46 8 0.02
47 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (44 bp):
CTTCAATCTACTCCACTGCTACCCAGGGAGGTAAGATCTGACAT
Found at i:19064468 original size:7 final size:7
Alignment explanation
Indices: 19064449--19064506 Score: 57
Period size: 7 Copynumber: 8.0 Consensus size: 7
19064439 TTAGCCTCTC
19064449 CATTTTT
1 CATTTTT
19064456 -ACTTTTT
1 CA-TTTTT
19064463 CATTTTTT
1 CA-TTTTT
19064471 CATTTTT
1 CATTTTT
19064478 CA-TTTT
1 CATTTTT
19064484 CATTTTTT
1 CA-TTTTT
*
19064492 CCTTTTT
1 CATTTTT
19064499 CATATTTT
1 CAT-TTTT
19064507 TTCTGACTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
6 7 0.16
7 19 0.44
8 17 0.40
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.71
Consensus pattern (7 bp):
CATTTTT
Found at i:19064476 original size:15 final size:15
Alignment explanation
Indices: 19064449--19064507 Score: 61
Period size: 15 Copynumber: 4.0 Consensus size: 15
19064439 TTAGCCTCTC
*
19064449 CATTTTT-ACTTTTT
1 CATTTTTCATTTTTT
19064463 CATTTTTTCA-TTTTT
1 CA-TTTTTCATTTTTT
19064478 CA-TTTTCATTTTTT
1 CATTTTTCATTTTTT
*
19064492 CCTTTTTCATATTTTT
1 CATTTTTCAT-TTTTT
19064508 TCTGACTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
13 6 0.15
14 8 0.21
15 19 0.49
16 6 0.15
ACGTcount: A:0.14, C:0.15, G:0.00, T:0.71
Consensus pattern (15 bp):
CATTTTTCATTTTTT
Found at i:19064483 original size:21 final size:21
Alignment explanation
Indices: 19064449--19064501 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
19064439 TTAGCCTCTC
*
19064449 CATTTTTACTTTTTCATTTTTT
1 CATTTTT-CATTTTCATTTTTT
19064471 CATTTTTCATTTTCATTTTTT
1 CATTTTTCATTTTCATTTTTT
*
19064492 CCTTTTTCAT
1 CATTTTTCAT
19064502 ATTTTTTCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 22 0.76
22 7 0.24
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (21 bp):
CATTTTTCATTTTCATTTTTT
Found at i:19065374 original size:7 final size:7
Alignment explanation
Indices: 19065358--19065386 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
19065348 TAGCCTCTCC
19065358 TTTTTC-
1 TTTTTCT
19065364 TTTTTCT
1 TTTTTCT
19065371 TTTTTCT
1 TTTTTCT
19065378 TTTTTCT
1 TTTTTCT
19065385 TT
1 TT
19065387 ATTTTTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTCT
Found at i:19065400 original size:13 final size:13
Alignment explanation
Indices: 19065358--19065412 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 13
19065348 TAGCCTCTCC
* *
19065358 TTTTTCTTTTTCT
1 TTTTTATTTTTAT
*
19065371 TTTTT-CTTTT-T
1 TTTTTATTTTTAT
*
19065382 TCTTTATTTTTAT
1 TTTTTATTTTTAT
*
19065395 TTTTTATTTTGAT
1 TTTTTATTTTTAT
19065408 TTTTT
1 TTTTT
19065413 TTATTTTTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
11 5 0.14
12 8 0.23
13 22 0.63
ACGTcount: A:0.07, C:0.07, G:0.02, T:0.84
Consensus pattern (13 bp):
TTTTTATTTTTAT
Found at i:19065421 original size:29 final size:29
Alignment explanation
Indices: 19065378--19065482 Score: 88
Period size: 29 Copynumber: 3.5 Consensus size: 29
19065368 TCTTTTTTCT
19065378 TTTTTCTTTA-TTTTTATTTTTTATTTTGA
1 TTTTT-TTTATTTTTTATTTTTTATTTTGA
** * *
19065407 TTTTTTTTATTTTTTGCTTTTGACTTTGA
1 TTTTTTTTATTTTTTATTTTTTATTTTGA
* * *
19065436 TTTTTCTT-TTTCTTCTTTTTTGATTTTGA
1 TTTTTTTTATTTTTTATTTTTT-ATTTTGA
19065465 TTTTGATTTTGATTTTTT
1 TTTT--TTTT-ATTTTTT
19065483 TGATTGAATC
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
28 13 0.22
29 37 0.64
31 3 0.05
33 5 0.09
ACGTcount: A:0.10, C:0.06, G:0.08, T:0.76
Consensus pattern (29 bp):
TTTTTTTTATTTTTTATTTTTTATTTTGA
Found at i:19065446 original size:35 final size:35
Alignment explanation
Indices: 19065400--19065483 Score: 114
Period size: 35 Copynumber: 2.4 Consensus size: 35
19065390 TTTATTTTTT
*
19065400 ATTTTGATTTTTTTTATTTTTTGCTTTTGACTTTG
1 ATTTTGATTTTTTTTATTTTTTGATTTTGACTTTG
** * * *
19065435 ATTTTTCTTTTTCTTCTTTTTTGATTTTGATTTTG
1 ATTTTGATTTTTTTTATTTTTTGATTTTGACTTTG
19065470 ATTTTGATTTTTTT
1 ATTTTGATTTTTTT
19065484 GATTGAATCT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.11, C:0.06, G:0.10, T:0.74
Consensus pattern (35 bp):
ATTTTGATTTTTTTTATTTTTTGATTTTGACTTTG
Found at i:19071585 original size:11 final size:11
Alignment explanation
Indices: 19071569--19071593 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19071559 TTGTATTTGG
19071569 TTTTTTATTTA
1 TTTTTTATTTA
19071580 TTTTTTATTTA
1 TTTTTTATTTA
19071591 TTT
1 TTT
19071594 GGATTTGGGT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTATTTA
Found at i:19074744 original size:26 final size:26
Alignment explanation
Indices: 19074715--19074768 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
19074705 TTATGAGATT
19074715 GAATTAATTGTTTGAATTGGCATAGA
1 GAATTAATTGTTTGAATTGGCATAGA
19074741 GAATTAATTGTTTGAATTGGCATAGA
1 GAATTAATTGTTTGAATTGGCATAGA
19074767 GA
1 GA
19074769 TATGTACAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (26 bp):
GAATTAATTGTTTGAATTGGCATAGA
Found at i:19076499 original size:14 final size:14
Alignment explanation
Indices: 19076480--19076519 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
19076470 TTGATTGGCA
19076480 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
19076494 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
19076508 GGAAAATGTTTT
1 GTAAAATGTTTT
19076520 ACTTCTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:19080634 original size:13 final size:13
Alignment explanation
Indices: 19080616--19080640 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19080606 CGGAAACTGG
19080616 TTTGCAGAAAACA
1 TTTGCAGAAAACA
19080629 TTTGCAGAAAAC
1 TTTGCAGAAAAC
19080641 TACCCATTTG
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:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (13 bp):
TTTGCAGAAAACA
Found at i:19092374 original size:17 final size:16
Alignment explanation
Indices: 19092346--19092398 Score: 88
Period size: 16 Copynumber: 3.2 Consensus size: 16
19092336 TTTGGTTCGC
19092346 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
19092362 TGTATTGGGATTAGAGT
1 TGTATT-GGATTAGAGG
19092379 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
19092395 TGTA
1 TGTA
19092399 ATAGCTAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
16 19 0.56
17 15 0.44
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.40
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:19092463 original size:44 final size:45
Alignment explanation
Indices: 19092379--19092469 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
19092369 GGATTAGAGT
* * *
19092379 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
19092424 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
19092468 TG
1 TG
19092470 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:19098461 original size:62 final size:62
Alignment explanation
Indices: 19098388--19098535 Score: 287
Period size: 62 Copynumber: 2.4 Consensus size: 62
19098378 CTTCTGGGTC
*
19098388 TGTTACCGAAAACAAAGAAAGAAAGGAGAAGAATTTGGGGCTTCTGGGTTAAAACTTCGGTA
1 TGTTACAGAAAACAAAGAAAGAAAGGAGAAGAATTTGGGGCTTCTGGGTTAAAACTTCGGTA
19098450 TGTTACAGAAAACAAAGAAAGAAAGGAGAAGAATTTGGGGCTTCTGGGTTAAAACTTCGGTA
1 TGTTACAGAAAACAAAGAAAGAAAGGAGAAGAATTTGGGGCTTCTGGGTTAAAACTTCGGTA
19098512 TGTTACAGAAAACAAAGAAAGAAA
1 TGTTACAGAAAACAAAGAAAGAAA
19098536 AACAGAAGCA
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 85 1.00
ACGTcount: A:0.43, C:0.10, G:0.26, T:0.21
Consensus pattern (62 bp):
TGTTACAGAAAACAAAGAAAGAAAGGAGAAGAATTTGGGGCTTCTGGGTTAAAACTTCGGTA
Found at i:19099521 original size:18 final size:18
Alignment explanation
Indices: 19099498--19099532 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
19099488 TATAAACTTT
19099498 AAAATTATATA-TTTTTTA
1 AAAATTA-ATACTTTTTTA
19099516 AAAATTAATACTTTTTT
1 AAAATTAATACTTTTTT
19099533 TCTTTTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
AAAATTAATACTTTTTTA
Found at i:19099868 original size:18 final size:17
Alignment explanation
Indices: 19099826--19099859 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
19099816 TACTTGAACG
19099826 ATTTTTTTTATTTTTAA
1 ATTTTTTTTATTTTTAA
19099843 ATATTTTTTTATTTTTA
1 AT-TTTTTTTATTTTTA
19099860 TGGTTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTTTTTTATTTTTAA
Found at i:19103932 original size:26 final size:26
Alignment explanation
Indices: 19103868--19103934 Score: 84
Period size: 25 Copynumber: 2.6 Consensus size: 26
19103858 TGTGGATTCT
19103868 CTGAAGCTAGTGTTAGCAACATCGAA
1 CTGAAGCTAGTGTTAGCAACATCGAA
* *
19103894 CT-AAGCTAGTGTTAGCAAC-CCTGAT
1 CTGAAGCTAGTGTTAGCAACATC-GAA
*
19103919 TTGAAGCTAGTGTTAG
1 CTGAAGCTAGTGTTAG
19103935 TAGCTCGGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 1 0.03
25 20 0.56
26 15 0.42
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (26 bp):
CTGAAGCTAGTGTTAGCAACATCGAA
Found at i:19110197 original size:15 final size:16
Alignment explanation
Indices: 19110177--19110211 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
19110167 AATTTTTTTC
19110177 AAATGA-AATCGAGTG
1 AAATGAGAATCGAGTG
*
19110192 AAATGAGATTCGAGTG
1 AAATGAGAATCGAGTG
19110208 AAAT
1 AAAT
19110212 TATTTGAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.46, C:0.06, G:0.26, T:0.23
Consensus pattern (16 bp):
AAATGAGAATCGAGTG
Found at i:19110494 original size:19 final size:19
Alignment explanation
Indices: 19110464--19110511 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
19110454 AATATATTTT
19110464 TTTTGAAATTTTTATAAA-TA
1 TTTTG-AATTTTTA-AAATTA
19110484 TTTTGAA-TTTTAAAATTTA
1 TTTTGAATTTTTAAAA-TTA
19110503 TTTTGAATT
1 TTTTGAATT
19110512 ATTTTGTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.12
18 5 0.20
19 11 0.44
20 6 0.24
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
TTTTGAATTTTTAAAATTA
Found at i:19117522 original size:2 final size:2
Alignment explanation
Indices: 19117515--19117540 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19117505 ATGAAAGATA
19117515 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
19117541 GTTTCTTGCA
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:19126281 original size:20 final size:20
Alignment explanation
Indices: 19126240--19126282 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
19126230 TAGATTTTTA
* *
19126240 ATATCAATATTTATATAAAT
1 ATATCAATATTTAAAGAAAT
19126260 ATAT-AATATTTAAAGAAGAT
1 ATATCAATATTTAAAGAA-AT
19126280 ATA
1 ATA
19126283 GTATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (20 bp):
ATATCAATATTTAAAGAAAT
Found at i:19127322 original size:5 final size:5
Alignment explanation
Indices: 19127312--19127339 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
19127302 TTATTTATTA
19127312 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
19127340 AAAACGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:19128077 original size:12 final size:12
Alignment explanation
Indices: 19128062--19128103 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
19128052 AAAGTTTTTT
*
19128062 TTATTATCATTG
1 TTATTATCATTA
* *
19128074 TTATTATTAATA
1 TTATTATCATTA
19128086 TTATTATCATTA
1 TTATTATCATTA
19128098 TTATTA
1 TTATTA
19128104 CTTTTTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (12 bp):
TTATTATCATTA
Found at i:19129718 original size:13 final size:12
Alignment explanation
Indices: 19129689--19129716 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
19129679 CAAAACGGGC
19129689 TTTTAGCGGCGT
1 TTTTAGCGGCGT
19129701 TTTTAGCGGCGT
1 TTTTAGCGGCGT
19129713 TTTT
1 TTTT
19129717 TATTCAAACG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.14, G:0.29, T:0.50
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:19129986 original size:113 final size:113
Alignment explanation
Indices: 19129788--19130136 Score: 536
Period size: 113 Copynumber: 3.0 Consensus size: 113
19129778 AAGCAATAGT
* *
19129788 GGCGTTTTTTAAAAAGCGCCGCAAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTTTGTGG
1 GGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTTTGTGG
19129853 ATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGC
66 ATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGC
19129901 GGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTTTGTGG
1 GGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTTTGTGG
*
19129966 ATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCACGGCTTTAGC
66 ATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGC
** * * * *
19130014 GGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATGTAAAACGACGCAATTTTTATGAGCTTTCGG
1 GGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGATGC-AGTTTTGTGAGCTTT-GT
* *
19130079 GGGTTTAGCGGCGTTTTTAAGAAAGCGCCGCTAAATAGCTACAAGGGCTTTTAGC
64 GGATTTAGCGGCGTTTTTAAGGAAGCGCCGCT-AAT-GCT-C-AGGGC-TTTAGC
19130134 GGC
1 GGC
19130137 AATAAAGCGC
Statistics
Matches: 217, Mismatches: 12, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
113 153 0.71
114 13 0.06
115 31 0.14
116 3 0.01
117 3 0.01
118 1 0.00
119 4 0.02
120 9 0.04
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.27
Consensus pattern (113 bp):
GGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCAAAACGATGCAGTTTTGTGAGCTTTGTGG
ATTTAGCGGCGTTTTTAAGGAAGCGCCGCTAATGCTCAGGGCTTTAGC
Found at i:19130172 original size:155 final size:153
Alignment explanation
Indices: 19129986--19130265 Score: 452
Period size: 155 Copynumber: 1.8 Consensus size: 153
19129976 GTTTTTAAGG
* **
19129986 AAGCGCCGCTAATGCTCACGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATGTA
1 AAGCGCCGCTAATGCTCACGGCTTTAACGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCA
* *
19130051 AAACGACGCAATTTTTATGAGCTTTCGGGGGTTTAGCGGCGTTTTTAAGAAAGCGCCGCTAAATA
66 AAACGACGC-AGTTTTATGAGCTTT-GGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAAATA
19130116 GCTACAAGGGCTTTTAGCGGCAATA
129 GCTACAAGGGCTTTTAGCGGCAATA
*
19130141 AAGCGCCGCTAATGCTCAGGGCTTTAACGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCA
1 AAGCGCCGCTAATGCTCACGGCTTTAACGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCA
* * **
19130206 AAACGACGCAGTTTTGTGAGCTTTGTGGATTTAGCGGCGTTTTTAAGGTAGCGCCGCTAA
66 AAACGACGCAGTTTTATGAGCTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAA
19130266 TGCTCAGGGC
Statistics
Matches: 115, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
153 32 0.28
154 13 0.11
155 70 0.61
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (153 bp):
AAGCGCCGCTAATGCTCACGGCTTTAACGGCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCA
AAACGACGCAGTTTTATGAGCTTTGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAAATAGC
TACAAGGGCTTTTAGCGGCAATA
Found at i:19130767 original size:15 final size:15
Alignment explanation
Indices: 19130727--19130788 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 15
19130717 TAGGGAGTAT
19130727 TTATGGATTTAAGTAGTA
1 TTATGGATTTAAG--G-A
*
19130745 TATATGGATTTAGGGA
1 T-TATGGATTTAAGGA
19130761 TTATGGATTAATAAGGA
1 TTATGGATT--TAAGGA
19130778 TTATGG-TTTAA
1 TTATGGATTTAA
19130789 TTAAGGGTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 3 0.08
15 8 0.21
16 4 0.10
17 12 0.31
18 1 0.03
19 11 0.28
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.42
Consensus pattern (15 bp):
TTATGGATTTAAGGA
Found at i:19130780 original size:17 final size:18
Alignment explanation
Indices: 19130758--19130794 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
19130748 ATGGATTTAG
19130758 GGATTATGGATTAA-TAA
1 GGATTATGGATTAATTAA
*
19130775 GGATTATGGTTTAATTAA
1 GGATTATGGATTAATTAA
19130793 GG
1 GG
19130795 GTTGGGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.35, C:0.00, G:0.27, T:0.38
Consensus pattern (18 bp):
GGATTATGGATTAATTAA
Found at i:19130828 original size:22 final size:22
Alignment explanation
Indices: 19130793--19130872 Score: 78
Period size: 22 Copynumber: 3.7 Consensus size: 22
19130783 GTTTAATTAA
*
19130793 GGGTT-GGGATTTAAG-GCTTAG
1 GGGTTAGGGGTTTAAGAG-TTAG
19130814 GGGTTAGGGGTTTAAGAGTTAG
1 GGGTTAGGGGTTTAAGAGTTAG
**
19130836 ATGTTAGGGG-TTAAGAGTTAG
1 GGGTTAGGGGTTTAAGAGTTAG
*
19130857 GGATTTA-GGGTTTAAG
1 GG-GTTAGGGGTTTAAG
19130873 GTTTCAGGGG
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
21 19 0.39
22 29 0.59
23 1 0.02
ACGTcount: A:0.24, C:0.01, G:0.41, T:0.34
Consensus pattern (22 bp):
GGGTTAGGGGTTTAAGAGTTAG
Found at i:19131087 original size:14 final size:15
Alignment explanation
Indices: 19131061--19131098 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
19131051 GTACTATATA
19131061 TATGGATTTAGGGAT
1 TATGGATTTAGGGAT
19131076 TATGGA-TTAGGGAT
1 TATGGATTTAGGGAT
19131090 TATGG-TTTA
1 TATGGATTTA
19131099 ATTTAAGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (15 bp):
TATGGATTTAGGGAT
Found at i:19131595 original size:19 final size:18
Alignment explanation
Indices: 19131557--19131600 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
19131547 GGGCCAATTT
* *
19131557 ATAAGAAATAAAATTAAA
1 ATAAAAAATAAAAATAAA
*
19131575 ATACAAAAATAAAAATGAA
1 ATA-AAAAATAAAAATAAA
19131594 ATAAAAA
1 ATAAAAA
19131601 CACTAAACTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (18 bp):
ATAAAAAATAAAAATAAA
Found at i:19131660 original size:47 final size:46
Alignment explanation
Indices: 19131595--19131695 Score: 166
Period size: 47 Copynumber: 2.2 Consensus size: 46
19131585 AAAAATGAAA
*
19131595 TAAAAACACTAAACTTTTAATTTTATCTAATTTTTATAAATATTACT
1 TAAAAA-ACTAAACTTTTAATTTTATCTAATTTTTATAAATATAACT
*
19131642 TAAAAAACTAAAATTTTTAATTTTATCTAATTTTTATAAATATAACT
1 TAAAAAACT-AAACTTTTAATTTTATCTAATTTTTATAAATATAACT
19131689 TAAAAAA
1 TAAAAAA
19131696 ACCTATGTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
46 3 0.06
47 48 0.94
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.45
Consensus pattern (46 bp):
TAAAAAACTAAACTTTTAATTTTATCTAATTTTTATAAATATAACT
Found at i:19143341 original size:31 final size:31
Alignment explanation
Indices: 19143303--19143440 Score: 197
Period size: 31 Copynumber: 4.5 Consensus size: 31
19143293 NNNNNNNNNN
19143303 ATGTAATTTATGTATAATATTAATGTAAGTT
1 ATGTAATTTATGTATAATATTAATGTAAGTT
*** **
19143334 ATGTAATTCCGGTATTTTAATTAAT-TAAGTT
1 ATGTAATTTATGTATAAT-ATTAATGTAAGTT
19143365 ATGTAATTTATGTATAATATTAATGTAAGTT
1 ATGTAATTTATGTATAATATTAATGTAAGTT
*
19143396 ATGTAATTTATGTTTAATATTAATGTAAGTT
1 ATGTAATTTATGTATAATATTAATGTAAGTT
*
19143427 ATGTAAGTTATGTA
1 ATGTAATTTATGTA
19143441 ACTTATATAT
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
30 6 0.07
31 80 0.87
32 6 0.07
ACGTcount: A:0.36, C:0.01, G:0.14, T:0.49
Consensus pattern (31 bp):
ATGTAATTTATGTATAATATTAATGTAAGTT
Found at i:19143377 original size:9 final size:9
Alignment explanation
Indices: 19143363--19143446 Score: 60
Period size: 9 Copynumber: 8.4 Consensus size: 9
19143353 ATTAATTAAG
19143363 TTATGTAAT
1 TTATGTAAT
19143372 TTATGTATAAT
1 TTATG--TAAT
*
19143383 ATTAATGTAAG
1 -TT-ATGTAAT
19143394 TTATGTAAT
1 TTATGTAAT
19143403 TTATGTTTAAT
1 TTATG--TAAT
*
19143414 ATTAATGTAAG
1 -TT-ATGTAAT
*
19143425 TTATGTAAG
1 TTATGTAAT
*
19143434 TTATGTAAC
1 TTATGTAAT
19143443 TTAT
1 TTAT
19143447 ATATAATATT
Statistics
Matches: 63, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
9 35 0.56
10 4 0.06
11 14 0.22
12 4 0.06
13 6 0.10
ACGTcount: A:0.36, C:0.01, G:0.13, T:0.50
Consensus pattern (9 bp):
TTATGTAAT
Found at i:19143431 original size:40 final size:42
Alignment explanation
Indices: 19143387--19143479 Score: 127
Period size: 40 Copynumber: 2.2 Consensus size: 42
19143377 TATAATATTA
* * *
19143387 ATGTAAGTTATGTAATTTATGTTTAATATTAA-T-GTAAGTT
1 ATGTAAGTTATGTAACTTATATATAATATTAATTAGTAAGTT
*
19143427 ATGTAAGTTATGTAACTTATATATAATATTAATTAATTAAGTT
1 ATGTAAGTTATGTAACTTATATATAATATTAATT-AGTAAGTT
19143470 ATGTAAGTTA
1 ATGTAAGTTA
19143480 ACTATTTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
40 29 0.63
41 1 0.02
43 16 0.35
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (42 bp):
ATGTAAGTTATGTAACTTATATATAATATTAATTAGTAAGTT
Found at i:19144494 original size:33 final size:33
Alignment explanation
Indices: 19144457--19144519 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
19144447 GAAAAATAAT
**
19144457 AATTAAACTATACAACTAAAATATAACCAAAAA
1 AATTAAACTATACAAAAAAAATATAACCAAAAA
19144490 AATTAAACTATACAAAAAAAATATAACCAA
1 AATTAAACTATACAAAAAAAATATAACCAA
19144520 CTTAAAGTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.65, C:0.14, G:0.00, T:0.21
Consensus pattern (33 bp):
AATTAAACTATACAAAAAAAATATAACCAAAAA
Found at i:19144501 original size:20 final size:19
Alignment explanation
Indices: 19144473--19144511 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
19144463 ACTATACAAC
*
19144473 TAAAATATAACCAAAAAAAT
1 TAAAATAT-ACAAAAAAAAT
*
19144493 TAAACTATACAAAAAAAAT
1 TAAAATATACAAAAAAAAT
19144512 ATAACCAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (19 bp):
TAAAATATACAAAAAAAAT
Found at i:19146003 original size:22 final size:22
Alignment explanation
Indices: 19145962--19146015 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
19145952 TTGTATTTTC
* *
19145962 ATTAAAATTTTTAGTAAATAATT
1 ATTAAAGTTTTAAGTAAAT-ATT
19145985 ATTAAAGTTTTAAGT-AATATT
1 ATTAAAGTTTTAAGTAAATATT
*
19146006 -TAAAAGTTTT
1 ATTAAAGTTTT
19146016 TGATAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.32
21 3 0.11
22 3 0.11
23 13 0.46
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
ATTAAAGTTTTAAGTAAATATT
Found at i:19146030 original size:21 final size:21
Alignment explanation
Indices: 19145964--19146030 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 21
19145954 GTATTTTCAT
*
19145964 TAAAA-TTTTTAGTAAATAATTA
1 TAAAAGTTTTAAGT-AA-AATTA
* *
19145986 TTAAAGTTTTAAGTAATATT-
1 TAAAAGTTTTAAGTAAAATTA
*
19146006 TAAAAGTTTT-TGATAAAATTA
1 TAAAAGTTTTAAG-TAAAATTA
19146027 TAAA
1 TAAA
19146031 TTTTAGTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
19 1 0.03
20 15 0.42
21 7 0.19
22 6 0.17
23 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (21 bp):
TAAAAGTTTTAAGTAAAATTA
Found at i:19146271 original size:4 final size:4
Alignment explanation
Indices: 19146262--19146287 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
19146252 GCATAAAGTG
19146262 ATCT ATCT ATCT ATCT ATCT ATCT AT
1 ATCT ATCT ATCT ATCT ATCT ATCT AT
19146288 ATATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (4 bp):
ATCT
Found at i:19146890 original size:20 final size:21
Alignment explanation
Indices: 19146865--19146903 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19146855 ACTAATTAAT
19146865 CTAAAT-CCTAAACCCTAACC
1 CTAAATCCCTAAACCCTAACC
*
19146885 CTAAATCCCTAACCCCTAA
1 CTAAATCCCTAAACCCTAA
19146904 ACATTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (21 bp):
CTAAATCCCTAAACCCTAACC
Found at i:19146955 original size:80 final size:77
Alignment explanation
Indices: 19146725--19146964 Score: 264
Period size: 89 Copynumber: 2.9 Consensus size: 77
19146715 AAACCCCTAC
* *
19146725 CCCTAAACCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACC
1 CCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACC
*
19146790 CTAACTCGACCCCGAATCACTAAC
66 CT-A----A-CCC---T-A--AAT
*
19146814 CCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACC
1 CCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACC
19146879 CTAACCCTAAAT
66 CTAACCCTAAAT
* * * *
19146891 CCCTAACCCCTAAACATTATTTAATATTATATAATTTAAAATATATTAATTACTCTAAACCCTAA
1 CCCTAACCCCTAAACATTATTTAATA-TATA-AA-TTAAAAAACACTAATTAATCTAAACCCTAA
*
19146956 ACTCTAACC
63 ACCCTAACC
19146965 TAACACCGAA
Statistics
Matches: 140, Mismatches: 8, Indels: 15
0.86 0.05 0.09
Matches are distributed among these distances:
77 28 0.20
78 4 0.03
79 3 0.02
80 34 0.24
83 3 0.02
84 1 0.01
88 1 0.01
89 66 0.47
ACGTcount: A:0.45, C:0.25, G:0.01, T:0.30
Consensus pattern (77 bp):
CCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCCTAAACC
CTAACCCTAAAT
Found at i:19147529 original size:41 final size:41
Alignment explanation
Indices: 19147504--19147830 Score: 485
Period size: 41 Copynumber: 8.0 Consensus size: 41
19147494 CTAAAGGTAC
19147504 GAGCATTAGCGGCGCTTATTAAAAAACGCCGCTAAAGACCT
1 GAGCATTAGCGGCGCTTATTAAAAAACGCCGCTAAAGACCT
* * * *
19147545 GAGCATTCGCGGTGCTTATTAATAAATGCCGCTAAAGACCT
1 GAGCATTAGCGGCGCTTATTAAAAAACGCCGCTAAAGACCT
* * * *
19147586 GAGAATTAGTGGCGCTTATTAGAAAACGCCGCTGAAGACCT
1 GAGCATTAGCGGCGCTTATTAAAAAACGCCGCTAAAGACCT
* *
19147627 GAGCATTAGCGGTGCTTATTCAAAAACGCCGCTAAAGACCT
1 GAGCATTAGCGGCGCTTATTAAAAAACGCCGCTAAAGACCT
19147668 GAGCATTAGCGGCGCTTATTAAAAAACGCCGCTAAAGACCT
1 GAGCATTAGCGGCGCTTATTAAAAAACGCCGCTAAAGACCT
* * *
19147709 GCGAATTAGCGGCGATTATTAAAAAACGCCGCTAAAGACCT
1 GAGCATTAGCGGCGCTTATTAAAAAACGCCGCTAAAGACCT
*
19147750 GAGCATTAGCGGCGCTTATTAAAAAACACCGCTAAAGACCT
1 GAGCATTAGCGGCGCTTATTAAAAAACGCCGCTAAAGACCT
* * *
19147791 GAGCTTTAGCGGCGCTT-TTCAGAAAATGCCGCTAAAGACC
1 GAGCATTAGCGGCGCTTATT-AAAAAACGCCGCTAAAGACC
19147831 CCAAAAACTC
Statistics
Matches: 254, Mismatches: 31, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
40 2 0.01
41 252 0.99
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (41 bp):
GAGCATTAGCGGCGCTTATTAAAAAACGCCGCTAAAGACCT
Found at i:19147973 original size:40 final size:39
Alignment explanation
Indices: 19147879--19148001 Score: 122
Period size: 40 Copynumber: 3.1 Consensus size: 39
19147869 TTTGCGGTGC
* * *
19147879 TTTCCAAAAAACGCCGCTAATGCTTATTTTTAGCAGCGTT
1 TTTCC-AAAAACGCCGCTAATGATGATTTTTAGCGGCGTT
* *
19147919 TTT-TAAAAATCGCCGCTAATGATCGATCTTTAGCGGCGTT
1 TTTCCAAAAA-CGCCGCTAATGAT-GATTTTTAGCGGCGTT
* * * *
19147959 TTTCCAAAAGCGCCGCTACTGTTTGATTTTTAGTGGCGTT
1 TTTCCAAAAACGCCGCTAATG-ATGATTTTTAGCGGCGTT
19147999 TTT
1 TTT
19148002 TGTCCAAACG
Statistics
Matches: 68, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
38 5 0.07
39 12 0.18
40 46 0.68
41 5 0.07
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (39 bp):
TTTCCAAAAACGCCGCTAATGATGATTTTTAGCGGCGTT
Found at i:19152604 original size:19 final size:20
Alignment explanation
Indices: 19152576--19152614 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
19152566 GTTTATTTTC
19152576 TTTAAATTAA-GAATTATTT
1 TTTAAATTAATGAATTATTT
* *
19152595 TTTAATTTAATGTATTATTT
1 TTTAAATTAATGAATTATTT
19152615 ATTCTATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTAAATTAATGAATTATTT
Found at i:19153799 original size:12 final size:12
Alignment explanation
Indices: 19153776--19153811 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 12
19153766 ACTGTAATAT
19153776 TATTAGTATTAAA
1 TATTA-TATTAAA
19153789 TATTATATTAAA
1 TATTATATTAAA
19153801 TATTAATATTA
1 TATT-ATATTA
19153812 TTATACCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (12 bp):
TATTATATTAAA
Found at i:19161494 original size:24 final size:24
Alignment explanation
Indices: 19161436--19161510 Score: 73
Period size: 26 Copynumber: 3.1 Consensus size: 24
19161426 TTGAGCCAGT
* *
19161436 ATTCTTTCATTCTTTTTCGAGTAATT
1 ATTCTTTTATTCTTTTTC--GTAATC
19161462 ATTCTTTTATTCTTTTTC-TACATC
1 ATTCTTTTATTCTTTTTCGTA-ATC
* *
19161486 ATTCTTTTATTC-ATTTCATAATC
1 ATTCTTTTATTCTTTTTCGTAATC
19161509 AT
1 AT
19161511 ATTTTGTTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
23 11 0.25
24 16 0.36
26 17 0.39
ACGTcount: A:0.21, C:0.17, G:0.03, T:0.59
Consensus pattern (24 bp):
ATTCTTTTATTCTTTTTCGTAATC
Found at i:19161509 original size:23 final size:23
Alignment explanation
Indices: 19161457--19161510 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
19161447 CTTTTTCGAG
* *
19161457 TAATTATTCTTTTATTCTTTTTC
1 TAATCATTCTTTTATTCTATTTC
19161480 TACATCATTCTTTTATTC-ATTTC
1 TA-ATCATTCTTTTATTCTATTTC
19161503 ATAATCAT
1 -TAATCAT
19161511 ATTTTGTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 11 0.41
24 16 0.59
ACGTcount: A:0.24, C:0.17, G:0.00, T:0.59
Consensus pattern (23 bp):
TAATCATTCTTTTATTCTATTTC
Found at i:19166437 original size:126 final size:126
Alignment explanation
Indices: 19166212--19166514 Score: 491
Period size: 126 Copynumber: 2.4 Consensus size: 126
19166202 AGAACAGATC
*
19166212 GAAGAAAGTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATTAGATCTCACCTCTCT
1 GAAGAAAGTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTCACCTCTCT
* * *
19166277 GAAGTTGCAGAGAGCATGTCGCATCCAGTCTTATCTCCCTGAAGATGCAGCGGAGTAGACA
66 GAAGTTGCAGAGAGCATATCGCATCCAGTCTTATCTCCCTGAAGATGCAGCAGAGCAGACA
* * * *
19166338 GAAGAAAGTAATCTTATCCCCCTAAAGTTGTAGTGGAGCGGATTAAAATCAGATCTCACCTCTCT
1 GAAGAAAGTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTCACCTCTCT
* *
19166403 GAAGTTGCAGAGAGCATATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTAGAGCAGACA
66 GAAGTTGCAGAGAGCATATCGCATCCAGTCTTATCTCCCTGAAGATGCAGCAGAGCAGACA
*
19166464 GGAGAAA-TCAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCA
1 GAAGAAAGT-AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCA
19166515 CAGATCTTGT
Statistics
Matches: 161, Mismatches: 15, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
125 1 0.01
126 160 0.99
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (126 bp):
GAAGAAAGTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTCACCTCTCT
GAAGTTGCAGAGAGCATATCGCATCCAGTCTTATCTCCCTGAAGATGCAGCAGAGCAGACA
Found at i:19167829 original size:20 final size:20
Alignment explanation
Indices: 19167804--19167845 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
19167794 TTTTTATAAA
* *
19167804 TACTGTTAGATTGTTAGTAT
1 TACTGTAAGATTATTAGTAT
*
19167824 TACTGTAATATTATTAGTAT
1 TACTGTAAGATTATTAGTAT
19167844 TA
1 TA
19167846 TTTAATAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.14, T:0.50
Consensus pattern (20 bp):
TACTGTAAGATTATTAGTAT
Found at i:19171342 original size:23 final size:21
Alignment explanation
Indices: 19171316--19171360 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
19171306 ATTAATAAAA
19171316 ATAAAATTATTTATATTTATTAT
1 ATAAAA-TATTTATATTT-TTAT
*
19171339 ATAAAATATTTTTATTTTTAT
1 ATAAAATATTTATATTTTTAT
19171360 A
1 A
19171361 CATCCTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 10 0.48
23 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATAAAATATTTATATTTTTAT
Found at i:19171557 original size:21 final size:21
Alignment explanation
Indices: 19171527--19171600 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
19171517 GTTTTTTTTA
*
19171527 TTTT-TAAATTTAT-TTATTAT
1 TTTTATAAATTTATAATATT-T
19171547 TTTTATAAATTT-TAATATTT
1 TTTTATAAATTTATAATATTT
* *
19171567 TTTTACAAATTTATAACATTT
1 TTTTATAAATTTATAATATTT
* *
19171588 TTATAAAAATTTA
1 TTTTATAAATTTA
19171601 AAAATTTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
20 17 0.37
21 29 0.63
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTATAAATTTATAATATTT
Found at i:19171568 original size:19 final size:20
Alignment explanation
Indices: 19171546--19171600 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
19171536 TTATTTATTA
*
19171546 TTTTTATAAATTT-TAATATT
1 TTTTTATAAATTTATAACA-T
*
19171566 TTTTTACAAATTTATAACAT
1 TTTTTATAAATTTATAACAT
*
19171586 TTTTATAAAAATTTA
1 TTTT-TATAAATTTA
19171601 AAAATTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTTATAAATTTATAACAT
Found at i:19171604 original size:8 final size:8
Alignment explanation
Indices: 19171591--19171618 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
19171581 AACATTTTTA
19171591 TAAAAATT
1 TAAAAATT
19171599 TAAAAATT
1 TAAAAATT
19171607 TAAAAATT
1 TAAAAATT
19171615 TAAA
1 TAAA
19171619 TTTTTAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
TAAAAATT
Found at i:19171607 original size:20 final size:19
Alignment explanation
Indices: 19171545--19171618 Score: 57
Period size: 21 Copynumber: 3.9 Consensus size: 19
19171535 TTTATTTATT
* *
19171545 ATTTTTAT-AAATTTTAAT
1 ATTTTTATAAAATTTAAAA
* *
19171563 ATTTTTTTACAAATTTATAAC
1 ATTTTTATA-AAATTTA-AAA
19171584 ATTTTTATAAAAATTTAAAA
1 ATTTTTAT-AAAATTTAAAA
19171604 A--TTTA-AAAATTTAAA
1 ATTTTTATAAAATTTAAA
19171619 TTTTTAAAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
16 10 0.21
18 11 0.23
20 9 0.19
21 16 0.34
22 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTTTATAAAATTTAAAA
Done.