Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 34 of 343
Found at i:11425098 original size:3 final size:3
Alignment explanation
Indices: 11425090--11425121 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
11425080 AAAAGAAATC
11425090 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
11425122 GGCTATAGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:11425291 original size:6 final size:6
Alignment explanation
Indices: 11425280--11425307 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
11425270 ACAACTTTAG
11425280 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
11425308 TAATGCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:11426757 original size:24 final size:25
Alignment explanation
Indices: 11426719--11426769 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
11426709 AATTATTCAA
*
11426719 TTTATTTTATTTTTATATATATTTG
1 TTTATTTTATATTTATATATATTTG
*
11426744 TTTA-TTTATATTTATATATTTTTG
1 TTTATTTTATATTTATATATATTTG
11426768 TT
1 TT
11426770 CGGTAACGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.73
Consensus pattern (25 bp):
TTTATTTTATATTTATATATATTTG
Found at i:11429245 original size:13 final size:14
Alignment explanation
Indices: 11429219--11429245 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11429209 AAAATTTATT
11429219 AAATTTTAAAAAAA
1 AAATTTTAAAAAAA
11429233 AAATTTTAAAAAA
1 AAATTTTAAAAAA
11429246 GTAAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATTTTAAAAAAA
Found at i:11435152 original size:18 final size:18
Alignment explanation
Indices: 11435125--11435159 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
11435115 TTTATCATAC
11435125 TTATATTTTTTATAGTAAT
1 TTATATTTTTTAT-GTAAT
11435144 TTATA-TTTTTATGTAA
1 TTATATTTTTTATGTAA
11435160 CTATGGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 7 0.44
19 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
TTATATTTTTTATGTAAT
Found at i:11438091 original size:19 final size:19
Alignment explanation
Indices: 11438067--11438110 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
11438057 TTGGCATTTT
11438067 AATGAAATAAAATGGGAAA
1 AATGAAATAAAATGGGAAA
11438086 AATGAAATAAAATGGGAAA
1 AATGAAATAAAATGGGAAA
11438105 AATGAA
1 AATGAA
11438111 CCAAAAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.20, T:0.16
Consensus pattern (19 bp):
AATGAAATAAAATGGGAAA
Found at i:11438116 original size:19 final size:19
Alignment explanation
Indices: 11438067--11438116 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
11438057 TTGGCATTTT
*
11438067 AATGAAATAAAATGGGAAA
1 AATGAAACAAAATGGGAAA
*
11438086 AATGAAATAAAATGGGAAA
1 AATGAAACAAAATGGGAAA
*
11438105 AATGAACCAAAA
1 AATGAAACAAAA
11438117 ATCATCTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.64, C:0.04, G:0.18, T:0.14
Consensus pattern (19 bp):
AATGAAACAAAATGGGAAA
Found at i:11441235 original size:5 final size:5
Alignment explanation
Indices: 11441218--11441282 Score: 60
Period size: 5 Copynumber: 12.6 Consensus size: 5
11441208 TAGGAAAGTC
*
11441218 TTATT TTACT TTATT TTATT TTA-T TTATTT TTATT TTATTT TTGATT
1 TTATT TTATT TTATT TTATT TTATT TTA-TT TTATT TTA-TT TT-ATT
* **
11441265 TTATA TTAAA TTATT TTA
1 TTATT TTATT TTATT TTA
11441283 GGCTAAATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
4 4 0.08
5 33 0.66
6 12 0.24
7 1 0.02
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (5 bp):
TTATT
Found at i:11447922 original size:15 final size:15
Alignment explanation
Indices: 11447902--11447931 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
11447892 ATATGTAAGA
11447902 GTAGTGGATGCTGAT
1 GTAGTGGATGCTGAT
11447917 GTAGTGGATGCTGAT
1 GTAGTGGATGCTGAT
11447932 TTCAATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.40, T:0.33
Consensus pattern (15 bp):
GTAGTGGATGCTGAT
Found at i:11448719 original size:14 final size:14
Alignment explanation
Indices: 11448689--11448718 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
11448679 TACTGAATGG
11448689 TTTCTTTTTCTTTT
1 TTTCTTTTTCTTTT
11448703 TTTCTTTTT-TTTT
1 TTTCTTTTTCTTTT
11448716 TTT
1 TTT
11448719 TTGAATTCAA
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:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (14 bp):
TTTCTTTTTCTTTT
Found at i:11458595 original size:5 final size:5
Alignment explanation
Indices: 11458585--11458627 Score: 79
Period size: 5 Copynumber: 8.8 Consensus size: 5
11458575 TTTCAGTTAT
11458585 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT-A TATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA
11458628 CTTAACATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.11
5 33 0.89
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:11459247 original size:39 final size:39
Alignment explanation
Indices: 11459204--11459282 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
11459194 TGACTCTTTT
11459204 AAGATGTTTTGGTTTCTCATTTCCCTCATTTGAAATCAG
1 AAGATGTTTTGGTTTCTCATTTCCCTCATTTGAAATCAG
11459243 AAGATGTTTTGGTTTCTCATTTCCCTCATTTGAAATCAG
1 AAGATGTTTTGGTTTCTCATTTCCCTCATTTGAAATCAG
11459282 A
1 A
11459283 TCACAGTTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.43
Consensus pattern (39 bp):
AAGATGTTTTGGTTTCTCATTTCCCTCATTTGAAATCAG
Found at i:11460958 original size:17 final size:19
Alignment explanation
Indices: 11460931--11460970 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
11460921 AGGCCAAATT
11460931 GGGCTGTGTGAGC-CACAC
1 GGGCTGTGTGAGCTCACAC
11460949 GGGC-GTGTGAGCTCACAC
1 GGGCTGTGTGAGCTCACAC
11460967 GGGC
1 GGGC
11460971 AGGCTACATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.15, C:0.28, G:0.42, T:0.15
Consensus pattern (19 bp):
GGGCTGTGTGAGCTCACAC
Found at i:11461371 original size:40 final size:38
Alignment explanation
Indices: 11461327--11461416 Score: 90
Period size: 40 Copynumber: 2.3 Consensus size: 38
11461317 GTACCTCTTT
* * * *
11461327 GTGTGTAAGGTTGGATGGGTTGATTTTATCCCCATACTTG
1 GTGTGTAAGGTTGGATGGCTCGATCTTATCCCC--ACATG
* * *
11461367 GTGTGTAGGGCTGGGTGGCTCGATCTTATCCCCACATG
1 GTGTGTAAGGTTGGATGGCTCGATCTTATCCCCACATG
*
11461405 GTGTGTTAGGTT
1 GTGTGTAAGGTT
11461417 AGACAGAGAT
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
38 13 0.32
40 27 0.68
ACGTcount: A:0.14, C:0.16, G:0.33, T:0.37
Consensus pattern (38 bp):
GTGTGTAAGGTTGGATGGCTCGATCTTATCCCCACATG
Found at i:11464696 original size:24 final size:24
Alignment explanation
Indices: 11464667--11464748 Score: 73
Period size: 24 Copynumber: 3.5 Consensus size: 24
11464657 CAGTATATAA
*
11464667 ATTTTAAATTGACTTATATTACTT
1 ATTTTAAATTGACTTATATCACTT
*
11464691 ATTTTAAATT-ATTTCATATGC-CTT
1 ATTTTAAATTGACTT-ATAT-CACTT
* *
11464715 ATTTTAAACTGATCTT-T-TCATTT
1 ATTTTAAATTGA-CTTATATCACTT
11464738 ATTTTAAATTG
1 ATTTTAAATTG
11464749 TTTTACTTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
22 1 0.02
23 16 0.34
24 27 0.57
25 1 0.02
26 2 0.04
ACGTcount: A:0.30, C:0.10, G:0.05, T:0.55
Consensus pattern (24 bp):
ATTTTAAATTGACTTATATCACTT
Found at i:11464822 original size:32 final size:32
Alignment explanation
Indices: 11464767--11464836 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
11464757 TAATATTCTT
* * * * *
11464767 TATAATATTTATTTTACACTTTTATATTTATA
1 TATATTATCTATTTTAAAATTTTATATATATA
11464799 TATATTATCTATTTTAAAATTTTATATATATA
1 TATATTATCTATTTTAAAATTTTATATATATA
*
11464831 TCTATT
1 TATATT
11464837 TTTAAGTCGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.59
Consensus pattern (32 bp):
TATATTATCTATTTTAAAATTTTATATATATA
Found at i:11470421 original size:51 final size:51
Alignment explanation
Indices: 11470331--11470428 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
11470321 TCTACCATAG
* *
11470331 CAAATCTTATCCCTCTGAAATTGCAGTGGGGCAGATTGAAGCTACAAATCA
1 CAAACCTTATCCCTCTGAAATTGCAGTGGAGCAGATTGAAGCTACAAATCA
* * *
11470382 CAAACCTTATCTCC-CTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAA
1 CAAACCTTATC-CCTCTGAAATTGCAGTGGAGCAGATTGAAGCTACAA
11470429 GTCTTATCTC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
51 39 0.95
52 2 0.05
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (51 bp):
CAAACCTTATCCCTCTGAAATTGCAGTGGAGCAGATTGAAGCTACAAATCA
Found at i:11470450 original size:44 final size:44
Alignment explanation
Indices: 11470381--11471224 Score: 567
Period size: 44 Copynumber: 18.7 Consensus size: 44
11470371 GCTACAAATC
* *
11470381 ACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTT
* * * * **
11470425 ACAAGTCTTATCTCCCTGAAGTTGCAGCGGAGTAGACTGAAAAT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTT
* * * * * *
11470469 AGCGAATCTTATCTCTCTGAAGTTGCAGTAGAGCAAATTAAAGCT
1 A-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTT
* ** * * * *
11470514 ATAAAT-TCTATAC-CTGTGAAATTGCAGCAGGTTAGATCAAATCT-ACCA-TG
1 ACAAATCT-TAT-CTCCCTGAAGTTGCAG-TGG--AG--CAGAT-TGA--AGTT
* * * ***
11470564 GCAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACC
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTT
* *
11470608 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTT
* * * *
11470652 ACAAATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATCGAAAATT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTG-AAGTT
* * *
11470697 ACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-T-CA--T
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTT
* * *
11470737 AGCAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGTT
1 A-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTT
* * * * *
11470782 ACAAGTCTTATCTCCCTGAAATTGCAGTGGGGCAGACTGAAGAT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTT
* *
11470826 AGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTT
1 A-CAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT---G----AAGTT
* * * * * * *
11470878 ACAAGTCTTATATCTCTGAATTTGCAGTGG-GTCGGA-TCAAATCT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTGAAGT-T
* * *
11470922 ATCATGTTGAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTGAAGAT
1 A-CA-----AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTT
* *
11470972 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAA-TAT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGT-T
* * * ***
11471016 AACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAACC
1 -ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTT
** * *
11471061 ACAAATCTTATCTCCCTGAAGTTTTAGTGGAGTAGGTTGAAGTT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTT
* * * ***
11471105 ACAAGTCTTATCTCCCTGAAGTTGTAGTAGAGCAGATTGAAACC
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTT
* * * * * * *
11471149 ACAAACCTTATCCCCCTAAAATTGCAGTGGGGCAGGTTGGAGTT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTT
* * * *
11471193 ACGATTATTATCTCTCTGAAGTTGCAGTGGAG
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAG
11471225 TGGATCAAAG
Statistics
Matches: 614, Mismatches: 144, Indels: 84
0.73 0.17 0.10
Matches are distributed among these distances:
40 2 0.00
41 32 0.05
42 2 0.00
43 6 0.01
44 323 0.53
45 147 0.24
47 4 0.01
48 1 0.00
49 10 0.02
50 48 0.08
51 34 0.06
52 5 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (44 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGTT
Found at i:11470494 original size:89 final size:89
Alignment explanation
Indices: 11470382--11471145 Score: 582
Period size: 89 Copynumber: 8.4 Consensus size: 89
11470372 CTACAAATCA
* * *
11470382 CAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAGT
1 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGT
* *
11470447 TGCAGCGGAGTAGACTGAAAATAG
66 TGCAGTGGAGTAGACTGAAGATAG
* * * * * **
11470471 CGAATCTTATCTCTCTGAAGTTGCAGTAGAGCAAATTAAAGCTATA-AATTC-TATAC-CTGTGA
1 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAG-T-TACAAGTCTTAT-CTCCCTGA
* * * ** *
11470533 AATTGCAGCAGGTTAGATCAAATCT-ACCATGG
63 AGTTGCAG-TGG--AG-T-AGA-CTGAAGATAG
* ***
11470565 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCACAAGTCTTATCTCCCTGAAGT
1 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGT
* ** *
11470630 TGCAGTGGAGCAGGTTGAAGTTA-
66 TGCAGTGGAGTAGACTGAAGATAG
* * * * * * *
11470653 CAAATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATCGAAAATTACAAATCTTATCTCTCTGAAG
1 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTG-AAGTTACAAGTCTTATCTCCCTGAAG
* **
11470718 TTGCAGT--AG-AG-CAGATCATAG
65 TTGCAGTGGAGTAGACTGAAGATAG
* * *
11470739 CAAACCTTATCTCCCTGAAGTTGCAGTAGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAAAT
1 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGT
* *
11470804 TGCAGTGGGGCAGACTGAAGATAG
66 TGCAGTGGAGTAGACTGAAGATAG
* * * * *
11470828 CAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTACAAGTTACAAGTCTTATATCT
1 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATT---G----AAGTTACAAGTCTTATCTCC
* * * *
11470893 CTGAATTTGCAGTGG-GTCGGA-TCAA-ATCTAT
59 CTGAAGTTGCAGTGGAGT-AGACTGAAGA--TAG
* * * *
11470924 CATGTTGAATCTTATCTCTCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAGTCTTATCTCCCT
1 CA-----AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACAAGTCTTATCTCCCT
* * *
11470989 GAAGTTGCAGTGGAGCAGACTGAATATAA
61 GAAGTTGCAGTGGAGTAGACTGAAGATAG
* * *** *
11471018 CAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAACCACAAATCTTATCTCCCTGAAGT
1 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGT
** ** *
11471083 TTTAGTGGAGTAGGTTGAAGTTA-
66 TGCAGTGGAGTAGACTGAAGATAG
* *
11471106 CAAGTCTTATCTCCCTGAAGTTGTAGTAGAGCAGATTGAA
1 CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAA
11471146 ACCACAAACC
Statistics
Matches: 533, Mismatches: 105, Indels: 75
0.75 0.15 0.11
Matches are distributed among these distances:
85 33 0.06
86 34 0.06
87 3 0.01
88 72 0.14
89 191 0.36
90 8 0.02
91 4 0.01
92 4 0.01
93 8 0.02
94 95 0.18
95 10 0.02
96 39 0.07
98 1 0.00
101 31 0.06
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (89 bp):
CAAATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACAAGTCTTATCTCCCTGAAGT
TGCAGTGGAGTAGACTGAAGATAG
Found at i:11470706 original size:227 final size:230
Alignment explanation
Indices: 11470315--11470730 Score: 628
Period size: 227 Copynumber: 1.8 Consensus size: 230
11470305 AGTAGGCCAA
* * *
11470315 ATCAAATCTACCATAGCAAATCTTATCCCTCTGAAATTGCAGTGGGGCAGATTGAAGCTACAAAT
1 ATCAAATCTACCATAGCAAATCTTATCCCTCTGAAATTGCAGTAGAGCAGATT--A--TACAAAC
*
11470380 CACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAGTCTTATCTCCCTGAA
62 CACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAATCTTATCTCCCTGAA
*
11470445 GTTGCAGCGGAGTAGACTGAAAATAGCGAATCTTATCTCTCTGAAGTTGCAGTAGAGCAAATTAA
127 GTTGCAGCGGAGTAGACTGAAAATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAAATTAA
11470510 AGCTATAAATTCTATACCTGTGAAATTGCAGCAGGTTAG
192 AGCTATAAATTCTATACCTGTGAAATTGCAGCAGGTTAG
* *
11470549 ATCAAATCTACCATGGCAAATCTTATCTCC-CTGAAGTTGCAGTAGAGCAGA-T-TA-AAACCAC
1 ATCAAATCTACCATAGCAAATCTTATC-CCTCTGAAATTGCAGTAGAGCAGATTATACAAACCAC
** *
11470610 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAATCTTATCTCCTTGAAGTT
65 AAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAATCTTATCTCCCTGAAGTT
*
11470675 GCAGTGGAGTAGA-TCGAAAATTA-CAAATCTTATCTCTCTGAAGTTGCAGTAGAGCA
130 GCAGCGGAGTAGACT-GAAAA-TAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCA
11470731 GATCATAGCA
Statistics
Matches: 168, Mismatches: 11, Indels: 13
0.88 0.06 0.07
Matches are distributed among these distances:
226 1 0.01
227 116 0.69
228 4 0.02
233 1 0.01
234 44 0.26
235 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (230 bp):
ATCAAATCTACCATAGCAAATCTTATCCCTCTGAAATTGCAGTAGAGCAGATTATACAAACCACA
AACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGTTACAAATCTTATCTCCCTGAAGTTG
CAGCGGAGTAGACTGAAAATAGCAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAAATTAAAGCT
ATAAATTCTATACCTGTGAAATTGCAGCAGGTTAG
Found at i:11471858 original size:22 final size:22
Alignment explanation
Indices: 11471833--11471874 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
11471823 TTTTAAAAGG
*
11471833 TTTTGCTTT-GTTCTTTTTCTT
1 TTTTTCTTTCGTTCTTTTTCTT
*
11471854 TTTTTCTTTCTTTCTTTTTCT
1 TTTTTCTTTCGTTCTTTTTCT
11471875 GTAGATCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.79
Consensus pattern (22 bp):
TTTTTCTTTCGTTCTTTTTCTT
Found at i:11472964 original size:24 final size:24
Alignment explanation
Indices: 11472935--11473016 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
11472925 CAGTGTATAA
11472935 ATTTTAAATTGACTTATATCACTT
1 ATTTTAAATTGACTTATATCACTT
*
11472959 ATTTTAAATT-ATTTCATATGC-CTT
1 ATTTTAAATTGACTT-ATAT-CACTT
* *
11472983 ATTTTAAACTGATCTT-T-TCATTT
1 ATTTTAAATTGA-CTTATATCACTT
11473006 ATTTTAAATTG
1 ATTTTAAATTG
11473017 TTTTACTTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
22 1 0.02
23 16 0.33
24 27 0.56
25 2 0.04
26 2 0.04
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.54
Consensus pattern (24 bp):
ATTTTAAATTGACTTATATCACTT
Found at i:11473121 original size:27 final size:26
Alignment explanation
Indices: 11473063--11473112 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
11473053 CTTTTATATT
*
11473063 TATATATATTATCTATTTTAAAATTA
1 TATATATATAATCTATTTTAAAATTA
*
11473089 TATATATATAATCTATTTTTAAAT
1 TATATATATAATCTATTTTAAAAT
11473113 CGTTCTATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (26 bp):
TATATATATAATCTATTTTAAAATTA
Found at i:11475453 original size:18 final size:18
Alignment explanation
Indices: 11475420--11475464 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
11475410 TACCTATTGG
11475420 AATTTGT-GGAAAAAAGA
1 AATTTGTGGGAAAAAAGA
*
11475437 AATTTGTGGGAACAAAGA
1 AATTTGTGGGAAAAAAGA
11475455 AATTTGTGGG
1 AATTTGTGGG
11475465 TGTTTCAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 7 0.27
18 19 0.73
ACGTcount: A:0.42, C:0.02, G:0.29, T:0.27
Consensus pattern (18 bp):
AATTTGTGGGAAAAAAGA
Found at i:11478244 original size:33 final size:30
Alignment explanation
Indices: 11478207--11478312 Score: 97
Period size: 33 Copynumber: 3.2 Consensus size: 30
11478197 AATTAAATTT
11478207 ATATTTTATGTATCACTATGTTAAATTATTTAA
1 ATATTTTAT-TATCA-TAT-TTAAATTATTTAA
*
11478240 ATATTCTATATATCATTATATTAAAGTTATTTAA
1 ATATTTTAT-TATCA-TAT-TTAAA-TTATTTAA
*
11478274 ATATCATTTATTATCATATTTAAAATT-TTAAA
1 ATAT--TTTATTATCATATTT-AAATTATTTAA
11478306 ATATTTT
1 ATATTTT
11478313 GTAAATCATT
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
30 3 0.05
32 8 0.13
33 25 0.40
34 18 0.29
35 5 0.08
36 4 0.06
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.52
Consensus pattern (30 bp):
ATATTTTATTATCATATTTAAATTATTTAA
Found at i:11478261 original size:25 final size:24
Alignment explanation
Indices: 11478232--11478285 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
11478222 CTATGTTAAA
*
11478232 TTATTTAAA-TATTCTATATATCA-
1 TTATTTAAAGTATT-TAAATATCAT
11478255 TTATATTAAAGTTATTTAAATATCAT
1 TTAT-TTAAAG-TATTTAAATATCAT
11478281 TTATT
1 TTATT
11478286 ATCATATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 4 0.15
24 5 0.19
25 9 0.35
26 8 0.31
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.54
Consensus pattern (24 bp):
TTATTTAAAGTATTTAAATATCAT
Found at i:11484844 original size:14 final size:14
Alignment explanation
Indices: 11484825--11484853 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11484815 TTGTTTTCAA
11484825 TAAAAAAAATTATT
1 TAAAAAAAATTATT
11484839 TAAAAAAAATTATT
1 TAAAAAAAATTATT
11484853 T
1 T
11484854 TTATTCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAAAAAAATTATT
Found at i:11485368 original size:210 final size:209
Alignment explanation
Indices: 11484842--11485463 Score: 873
Period size: 210 Copynumber: 2.9 Consensus size: 209
11484832 AATTATTTAA
* * *
11484842 AAAAAATTATTTTTATTCTTTAATTTTAAAAATTATAAAATATTATGTTTGTTAAATGAAAATG-
1 AAAAAATAATTTTGATTCTTTAATTTTAAAAATTA-AAAA-ATCATGTTTGTTAAATGAAAATGA
*
11484906 AAA-ATG-AAA---ATATGATACTTATTTTTCACAATAAAAACATATAAAATAATTACTAAATAT
64 AAATATGAAAATGCATATGATACTTATTTTTCACAATAAAAACATGTAAAATAATTACTAAATAT
11484966 AATCAAATTAAAAATATGATTTTAGATAAATAAAAATGTTACTAATATAATAAAAATAAATTAAA
129 --T-AAATTAAAAATATGATTTTAGATAAATAAAAATGTTACTAATATAATAAAAATAAATTAAA
* *
11485031 TAAAATTATTTATTTTTGTTTTT
191 T--AA--AGTTATTTTTATTTTT
**
11485054 AAAAAATGTTTTTGATTCTTTAATTTTAAAAATTAAAAAAAATCATGTTTGTTAAATGAAAATGA
1 AAAAAATAATTTTGATTCTTTAATTTTAAAAATT--AAAAAATCATGTTTGTTAAATGAAAATGA
* ** *
11485119 AAATATCAAAATGCATATGATACTTATTTTTCACAATAAAAACATGTAAGCTAACTACTAAATAT
64 AAATATGAAAATGCATATGATACTTATTTTTCACAATAAAAACATGTAAAATAATTACTAAATAT
*
11485184 TAAATTAAAAAT-TTATTTTAGATAAATAAAAATGTTACTAATATAATAAAAATAAATTAAATAA
129 TAAATTAAAAATATGATTTTAGATAAATAAAAATGTTACTAATATAATAAAAATAAATTAAATAA
11485248 AGTTATTTTTATTTTT
194 AGTTATTTTTATTTTT
11485264 AAAAAATAATTTTGATTCTTTAATTTTAAAAATTGAAAAAATCATGTTTGTTAAATGAAAATGAA
1 AAAAAATAATTTTGATTCTTTAATTTTAAAAATT-AAAAAATCATGTTTGTTAAATGAAAATGAA
11485329 AATATGAAAATGCATATGATACTTATTTTTTCACAATAAAAACATGTAAAATAATTACTAAATAT
65 AATATGAAAATGCATATGATACTTA-TTTTTCACAATAAAAACATGTAAAATAATTACT-AA-AT
* * * *
11485394 AGTTAAATT-AAAATATGATTTTACATAAATAAAAATGTTATTAATATAGTAAAAAAATAAATAA
127 A-TTAAATTAAAAATATGATTTTAGATAAATAAAAATGTTACTAATATA--ATAAAAATAAATTA
11485458 AATAAA
189 AATAAA
11485464 CAAGAGGTAT
Statistics
Matches: 371, Mismatches: 24, Indels: 27
0.88 0.06 0.06
Matches are distributed among these distances:
209 54 0.15
210 76 0.20
211 2 0.01
212 63 0.17
213 44 0.12
214 52 0.14
215 32 0.09
216 1 0.00
218 47 0.13
ACGTcount: A:0.51, C:0.05, G:0.06, T:0.39
Consensus pattern (209 bp):
AAAAAATAATTTTGATTCTTTAATTTTAAAAATTAAAAAATCATGTTTGTTAAATGAAAATGAAA
ATATGAAAATGCATATGATACTTATTTTTCACAATAAAAACATGTAAAATAATTACTAAATATTA
AATTAAAAATATGATTTTAGATAAATAAAAATGTTACTAATATAATAAAAATAAATTAAATAAAG
TTATTTTTATTTTT
Found at i:11493860 original size:4 final size:4
Alignment explanation
Indices: 11493851--11493937 Score: 174
Period size: 4 Copynumber: 21.8 Consensus size: 4
11493841 TTTTGTTTTT
11493851 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
11493899 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
11493938 TTATATTTAT
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 83 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:11493968 original size:13 final size:13
Alignment explanation
Indices: 11493950--11493976 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
11493940 ATATTTATAG
11493950 TTAGGGTGAGTAT
1 TTAGGGTGAGTAT
11493963 TTAGGGTGAGTAT
1 TTAGGGTGAGTAT
11493976 T
1 T
11493977 CGATTCAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.37, T:0.41
Consensus pattern (13 bp):
TTAGGGTGAGTAT
Found at i:11494234 original size:15 final size:15
Alignment explanation
Indices: 11494211--11494240 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11494201 ATGACTAAAC
*
11494211 TTCACCAACAATGCA
1 TTCAACAACAATGCA
11494226 TTCAACAACAATGCA
1 TTCAACAACAATGCA
11494241 CACACAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.30, G:0.07, T:0.20
Consensus pattern (15 bp):
TTCAACAACAATGCA
Found at i:11501127 original size:11 final size:11
Alignment explanation
Indices: 11501099--11501159 Score: 61
Period size: 11 Copynumber: 5.4 Consensus size: 11
11501089 TATACATAAA
*
11501099 AATATAATAGAT
1 AATAT-ATATAT
11501111 ATATATATATAT
1 A-ATATATATAT
*
11501123 AATATATACAT
1 AATATATATAT
11501134 AATATAGTAT-T
1 AATATA-TATAT
*
11501145 AAAATATATAT
1 AATATATATAT
11501156 AATA
1 AATA
11501160 CATACACATT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
10 3 0.07
11 25 0.61
12 9 0.22
13 4 0.10
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (11 bp):
AATATATATAT
Found at i:11512600 original size:17 final size:16
Alignment explanation
Indices: 11512563--11512606 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
11512553 TCGATCCAAT
11512563 AATTTTAATAAATTAA
1 AATTTTAATAAATTAA
*
11512579 AATTTTTATAAATTAA
1 AATTTTAATAAATTAA
11512595 AGA-TTTAATAAA
1 A-ATTTTAATAAA
11512607 AACTTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 24 0.96
17 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
AATTTTAATAAATTAA
Found at i:11513349 original size:72 final size:72
Alignment explanation
Indices: 11513232--11513375 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
11513222 CAGATTCTAA
11513232 ATTAATGATATGTCCAATTAAGCATTTCCTTCCTTAAAAAACAATTGATATTTCACCTTATAAAT
1 ATTAATGATATGTCCAATTAAGCATTTCCTTCCTTAAAAAACAATTGATATTTCACCTTATAAAT
11513297 CATGCCT
66 CATGCCT
11513304 ATTAATGATATGTCCAATTAAGCATTTCCTTCCTTAAAAAACAATTGATATTTCACCTTATAAAT
1 ATTAATGATATGTCCAATTAAGCATTTCCTTCCTTAAAAAACAATTGATATTTCACCTTATAAAT
11513369 CATGCCT
66 CATGCCT
11513376 TTTGCCTTCT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.36, C:0.19, G:0.07, T:0.38
Consensus pattern (72 bp):
ATTAATGATATGTCCAATTAAGCATTTCCTTCCTTAAAAAACAATTGATATTTCACCTTATAAAT
CATGCCT
Found at i:11518322 original size:21 final size:21
Alignment explanation
Indices: 11518286--11518351 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
11518276 GGTATTTTTT
**
11518286 TTTTTTGAAAAATTTAAGGAA
1 TTTTTTGAAATTTTTAAGGAA
* * *
11518307 TTTTTTGCATTTTTTATGGAA
1 TTTTTTGAAATTTTTAAGGAA
* *
11518328 -ATTTTGAAATTTTAAAGGAA
1 TTTTTTGAAATTTTTAAGGAA
11518348 TTTT
1 TTTT
11518352 AAGTTTTTTT
Statistics
Matches: 33, Mismatches: 11, Indels: 2
0.72 0.24 0.04
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.52
Consensus pattern (21 bp):
TTTTTTGAAATTTTTAAGGAA
Found at i:11521412 original size:31 final size:31
Alignment explanation
Indices: 11521374--11521435 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
11521364 TGTTTGAAGT
11521374 TTGAATATTAGTATTTTTGTGTAAGACCACC
1 TTGAATATTAGTATTTTTGTGTAAGACCACC
11521405 TTGAATATTAGTATTTTTGTGTAAGACCACC
1 TTGAATATTAGTATTTTTGTGTAAGACCACC
11521436 CTCAAAGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (31 bp):
TTGAATATTAGTATTTTTGTGTAAGACCACC
Found at i:11532962 original size:27 final size:27
Alignment explanation
Indices: 11532932--11533011 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 27
11532922 TAAGTAAAGT
11532932 CTTAATCGATTTCACCAATAAGATCAA
1 CTTAATCGATTTCACCAATAAGATCAA
* *
11532959 CTTAAT-TATTTTAACC-A-AAG-T---
1 CTTAATCGA-TTTCACCAATAAGATCAA
*
11532980 CTTAATCGATTTCACCAATAAAATCAA
1 CTTAATCGATTTCACCAATAAGATCAA
11533007 CTTAA
1 CTTAA
11533012 CAAAGTAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 16
0.66 0.08 0.26
Matches are distributed among these distances:
21 12 0.30
22 2 0.05
23 2 0.05
24 2 0.05
25 3 0.08
26 2 0.05
27 17 0.43
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (27 bp):
CTTAATCGATTTCACCAATAAGATCAA
Found at i:11532965 original size:48 final size:48
Alignment explanation
Indices: 11532912--11533011 Score: 173
Period size: 48 Copynumber: 2.1 Consensus size: 48
11532902 CTGATCAATT
** *
11532912 TTAATTATTTTAAGTAAAGTCTTAATCGATTTCACCAATAAGATCAAC
1 TTAATTATTTTAACCAAAGTCTTAATCGATTTCACCAATAAAATCAAC
11532960 TTAATTATTTTAACCAAAGTCTTAATCGATTTCACCAATAAAATCAAC
1 TTAATTATTTTAACCAAAGTCTTAATCGATTTCACCAATAAAATCAAC
11533008 TTAA
1 TTAA
11533012 CAAAGTAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.41, C:0.16, G:0.06, T:0.37
Consensus pattern (48 bp):
TTAATTATTTTAACCAAAGTCTTAATCGATTTCACCAATAAAATCAAC
Found at i:11532996 original size:21 final size:21
Alignment explanation
Indices: 11532927--11532997 Score: 54
Period size: 21 Copynumber: 3.1 Consensus size: 21
11532917 TATTTTAAGT
11532927 AAAGTCTTAATCGATTTCACC
1 AAAGTCTTAATCGATTTCACC
* *
11532948 AATAAGATCAACTTAAT-TATTTTAACC
1 -A-AAG-T---CTTAATCGA-TTTCACC
11532975 AAAGTCTTAATCGATTTCACC
1 AAAGTCTTAATCGATTTCACC
11532996 AA
1 AA
11532998 TAAAATCAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 15
0.67 0.07 0.26
Matches are distributed among these distances:
21 14 0.37
22 2 0.05
23 3 0.08
24 2 0.05
25 3 0.08
26 2 0.05
27 12 0.32
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (21 bp):
AAAGTCTTAATCGATTTCACC
Found at i:11536590 original size:10 final size:10
Alignment explanation
Indices: 11536575--11536621 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
11536565 ATCAATCCTT
11536575 AATAAATATA
1 AATAAATATA
* *
11536585 AATAAATTTT
1 AATAAATATA
*
11536595 AATCAA-ATA
1 AATAAATATA
*
11536604 AATAAATAAA
1 AATAAATATA
11536614 AATAAATA
1 AATAAATA
11536622 AATTGAGATT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
9 6 0.21
10 23 0.79
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (10 bp):
AATAAATATA
Found at i:11540850 original size:11 final size:11
Alignment explanation
Indices: 11540834--11540858 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11540824 TATAATTAGG
11540834 TTAGTTGTAGA
1 TTAGTTGTAGA
11540845 TTAGTTGTAGA
1 TTAGTTGTAGA
11540856 TTA
1 TTA
11540859 TGACTTATAC
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:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (11 bp):
TTAGTTGTAGA
Found at i:11541168 original size:37 final size:37
Alignment explanation
Indices: 11541118--11541194 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
11541108 AAGCAATTCG
11541118 TTTTCAATCAAATGACCCTTGCCAAGGTACGAGCTAC
1 TTTTCAATCAAATGACCCTTGCCAAGGTACGAGCTAC
11541155 TTTTCAATCAAATGACCCTTGCCAAGGTACGAGCTAC
1 TTTTCAATCAAATGACCCTTGCCAAGGTACGAGCTAC
11541192 TTT
1 TTT
11541195 ATTAGCGTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (37 bp):
TTTTCAATCAAATGACCCTTGCCAAGGTACGAGCTAC
Found at i:11544190 original size:14 final size:15
Alignment explanation
Indices: 11544165--11544195 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
11544155 TATACCATGG
11544165 TTTAACTTAATTAAC
1 TTTAACTTAATTAAC
11544180 TTTAA-TTAATTAAC
1 TTTAACTTAATTAAC
11544194 TT
1 TT
11544196 AATCTTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.52
Consensus pattern (15 bp):
TTTAACTTAATTAAC
Found at i:11544220 original size:21 final size:20
Alignment explanation
Indices: 11544166--11544207 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
11544156 ATACCATGGT
11544166 TTAACTTAA-TTAA-CTTTAA
1 TTAA-TTAACTTAATCTTTAA
11544185 TTAATTAACTTAATCTTTAA
1 TTAATTAACTTAATCTTTAA
11544205 TTA
1 TTA
11544208 TTTTACCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.19
19 8 0.38
20 9 0.43
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAATTAACTTAATCTTTAA
Found at i:11546729 original size:73 final size:73
Alignment explanation
Indices: 11546610--11546756 Score: 294
Period size: 73 Copynumber: 2.0 Consensus size: 73
11546600 CCATGCGATC
11546610 CATAACAAAACTTAAAAACGACCAGTCAACTCTATCATAGGCCTTAGTAATATCAATTTTTAGCG
1 CATAACAAAACTTAAAAACGACCAGTCAACTCTATCATAGGCCTTAGTAATATCAATTTTTAGCG
11546675 TAACTTCA
66 TAACTTCA
11546683 CATAACAAAACTTAAAAACGACCAGTCAACTCTATCATAGGCCTTAGTAATATCAATTTTTAGCG
1 CATAACAAAACTTAAAAACGACCAGTCAACTCTATCATAGGCCTTAGTAATATCAATTTTTAGCG
11546748 TAACTTCA
66 TAACTTCA
11546756 C
1 C
11546757 CAATAGAGCC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (73 bp):
CATAACAAAACTTAAAAACGACCAGTCAACTCTATCATAGGCCTTAGTAATATCAATTTTTAGCG
TAACTTCA
Found at i:11547995 original size:15 final size:16
Alignment explanation
Indices: 11547970--11548000 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
11547960 ATGACATTTC
11547970 AATCTTTTAGTTTAAT
1 AATCTTTTAGTTTAAT
11547986 AATC-TTTAGTTTAAT
1 AATCTTTTAGTTTAAT
11548001 CTGTTAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (16 bp):
AATCTTTTAGTTTAAT
Found at i:11549739 original size:15 final size:14
Alignment explanation
Indices: 11549719--11549753 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
11549709 ACTAATTAAT
11549719 TGAAGTACTTTTCAA
1 TGAAGTA-TTTTCAA
11549734 TGAAGT-TTTTCAA
1 TGAAGTATTTTCAA
11549747 TGAAGTA
1 TGAAGTA
11549754 AGAATTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 13 0.68
15 6 0.32
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (14 bp):
TGAAGTATTTTCAA
Found at i:11549901 original size:13 final size:13
Alignment explanation
Indices: 11549883--11549908 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11549873 TTTAAAGTAC
11549883 TTTTCAATGAAGT
1 TTTTCAATGAAGT
11549896 TTTTCAATGAAGT
1 TTTTCAATGAAGT
11549909 AAGAATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
TTTTCAATGAAGT
Found at i:11550005 original size:156 final size:156
Alignment explanation
Indices: 11549721--11550036 Score: 632
Period size: 156 Copynumber: 2.0 Consensus size: 156
11549711 TAATTAATTG
11549721 AAGTACTTTTCAATGAAGTTTTTCAATGAAGTAAGAATTAAAAATTTGGAGACCAATTAATACAA
1 AAGTACTTTTCAATGAAGTTTTTCAATGAAGTAAGAATTAAAAATTTGGAGACCAATTAATACAA
11549786 GGGTTTTCGTTTCAACACAAAGGTATAAGGGTTTTTGTGGCAATTCAAACCGTGAAAGGTGTGGA
66 GGGTTTTCGTTTCAACACAAAGGTATAAGGGTTTTTGTGGCAATTCAAACCGTGAAAGGTGTGGA
11549851 AAGTCTCTAAAAAATTGTGGTTTTTA
131 AAGTCTCTAAAAAATTGTGGTTTTTA
11549877 AAGTACTTTTCAATGAAGTTTTTCAATGAAGTAAGAATTAAAAATTTGGAGACCAATTAATACAA
1 AAGTACTTTTCAATGAAGTTTTTCAATGAAGTAAGAATTAAAAATTTGGAGACCAATTAATACAA
11549942 GGGTTTTCGTTTCAACACAAAGGTATAAGGGTTTTTGTGGCAATTCAAACCGTGAAAGGTGTGGA
66 GGGTTTTCGTTTCAACACAAAGGTATAAGGGTTTTTGTGGCAATTCAAACCGTGAAAGGTGTGGA
11550007 AAGTCTCTAAAAAATTGTGGTTTTTA
131 AAGTCTCTAAAAAATTGTGGTTTTTA
11550033 AAGT
1 AAGT
11550037 TTTGGGCTTG
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
156 160 1.00
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (156 bp):
AAGTACTTTTCAATGAAGTTTTTCAATGAAGTAAGAATTAAAAATTTGGAGACCAATTAATACAA
GGGTTTTCGTTTCAACACAAAGGTATAAGGGTTTTTGTGGCAATTCAAACCGTGAAAGGTGTGGA
AAGTCTCTAAAAAATTGTGGTTTTTA
Found at i:11555925 original size:69 final size:69
Alignment explanation
Indices: 11555843--11555973 Score: 163
Period size: 69 Copynumber: 1.9 Consensus size: 69
11555833 TTGTCAATAT
* * * * *
11555843 TCAGGCTCAATTACACAATTAGAAATAAATCTTCAATCGAGTTCAATATCAATATCGAGCTTGAG
1 TCAGGCTCAATTACACAATTAAAAATAAATCTTCAATCGAGGTCAAGACCAATATCAAGCTTGAG
11555908 TTTG
66 TTTG
* * ** **
11555912 TCAGGCTCGATTACGCGTTTAAAAATCGATCTTCAATCGAGGTCAAGACCAATATCAAGCTT
1 TCAGGCTCAATTACACAATTAAAAATAAATCTTCAATCGAGGTCAAGACCAATATCAAGCTT
11555974 TGCTCAATAT
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
69 51 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (69 bp):
TCAGGCTCAATTACACAATTAAAAATAAATCTTCAATCGAGGTCAAGACCAATATCAAGCTTGAG
TTTG
Found at i:11559532 original size:13 final size:13
Alignment explanation
Indices: 11559514--11559539 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11559504 AATCAATCTC
11559514 AGAACATATTATA
1 AGAACATATTATA
11559527 AGAACATATTATA
1 AGAACATATTATA
11559540 GTAATATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
AGAACATATTATA
Found at i:11562045 original size:68 final size:68
Alignment explanation
Indices: 11561954--11562207 Score: 348
Period size: 68 Copynumber: 3.8 Consensus size: 68
11561944 TATCATCCTT
* * * * *
11561954 GCAGACTATATTGGTTGCTATAGCTGAGCTATGGTCTTACACCTTATAACCCCATGTTTAATGTC
1 GCAGACTCTATTGGTTGCCATAGCCGAGCTATGGTCTTACACATTATAACCCTATGTTTAATGTC
11562019 TTG
66 TTG
*
11562022 GCAGACTCTATTGGTTGCCATAGCCGAGCTATGGTCTTACACCTTATAACCCTATGTTTAATGTC
1 GCAGACTCTATTGGTTGCCATAGCCGAGCTATGGTCTTACACATTATAACCCTATGTTTAATGTC
11562087 TTG
66 TTG
* * * * * * *
11562090 GCGGACTCTATTGGTTGCCATAGTCGAGCTATGATCTTACACATTGTAACCCTATATTTATTATC
1 GCAGACTCTATTGGTTGCCATAGCCGAGCTATGGTCTTACACATTATAACCCTATGTTTAATGTC
*
11562155 CTG
66 TTG
* * *
11562158 GCAGATTCTATTGGTTGTCATAGCCGAGCTATAGTCTTACACATTA-AACC
1 GCAGACTCTATTGGTTGCCATAGCCGAGCTATGGTCTTACACATTATAACC
11562208 TCTTTTAAGG
Statistics
Matches: 166, Mismatches: 20, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
67 4 0.02
68 162 0.98
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (68 bp):
GCAGACTCTATTGGTTGCCATAGCCGAGCTATGGTCTTACACATTATAACCCTATGTTTAATGTC
TTG
Found at i:11567434 original size:13 final size:12
Alignment explanation
Indices: 11567406--11567431 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11567396 AAAAAATATA
11567406 TTATTTAATTTT
1 TTATTTAATTTT
11567418 TTATTTAATTTT
1 TTATTTAATTTT
11567430 TT
1 TT
11567432 TATCTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTATTTAATTTT
Found at i:11567634 original size:17 final size:18
Alignment explanation
Indices: 11567612--11567645 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
11567602 AAAATATGTT
*
11567612 TTAAAAATTA-AAAATTA
1 TTAAAAAGTATAAAATTA
11567629 TTAAAAAGTATAAAATT
1 TTAAAAAGTATAAAATT
11567646 TATAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
TTAAAAAGTATAAAATTA
Found at i:11567635 original size:39 final size:38
Alignment explanation
Indices: 11567571--11567644 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 38
11567561 TTAATTAATT
* *
11567571 TTTTAAAATTTAAAAACTTCAAAAAATTATGAAAATATG
1 TTTTAAAAATTAAAAACTTCAAAAAAGTAT-AAAATATG
11567610 TTTTAAAAATTAAAAA-TT-ATTAAAAAGTATAAAAT
1 TTTTAAAAATTAAAAACTTCA--AAAAAGTATAAAAT
11567645 TTATAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 1 0.03
38 7 0.23
39 23 0.74
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (38 bp):
TTTTAAAAATTAAAAACTTCAAAAAAGTATAAAATATG
Found at i:11574654 original size:24 final size:24
Alignment explanation
Indices: 11574626--11574678 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
11574616 CACCTTTGAA
*
11574626 ACCCTTTCCACAGCTCCTTTCTTC
1 ACCCTTTCCACAGCTCCTCTCTTC
11574650 ACCCTTTCCACAGCTCCTCTCTTC
1 ACCCTTTCCACAGCTCCTCTCTTC
11574674 ACCCT
1 ACCCT
11574679 ATCGATTGGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.13, C:0.49, G:0.04, T:0.34
Consensus pattern (24 bp):
ACCCTTTCCACAGCTCCTCTCTTC
Found at i:11577729 original size:49 final size:49
Alignment explanation
Indices: 11577675--11577774 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
11577665 AAAGATAGTT
11577675 AAAAATGTGATTACTAGGAATACTTATAATTATGGGAAAATGTTGCTAA
1 AAAAATGTGATTACTAGGAATACTTATAATTATGGGAAAATGTTGCTAA
11577724 AAAAATGTGATTACTAGGAATACTTATAATTATGGGAAAATGTTGCTAA
1 AAAAATGTGATTACTAGGAATACTTATAATTATGGGAAAATGTTGCTAA
11577773 AA
1 AA
11577775 TATTAAGAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (49 bp):
AAAAATGTGATTACTAGGAATACTTATAATTATGGGAAAATGTTGCTAA
Found at i:11578063 original size:20 final size:20
Alignment explanation
Indices: 11578038--11578077 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
11578028 AATATTTTTT
*
11578038 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
11578058 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
11578078 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:11578084 original size:14 final size:14
Alignment explanation
Indices: 11578061--11578100 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
11578051 ACAGAAAAGT
*
11578061 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
11578075 AAATCATTTTACGG
1 AAAACATTTTACAG
11578089 AAAACATTTTAC
1 AAAACATTTTAC
11578101 TGGCAATCAA
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:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:11582581 original size:22 final size:22
Alignment explanation
Indices: 11582535--11582584 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
11582525 AAGTTCATAG
*
11582535 ACCAAAATCGTTGTTTTAATAA
1 ACCAAAATCGTTGTTTTAAAAA
11582557 ACCAAAAT-GTT-TTATTAAAATA
1 ACCAAAATCGTTGTT-TTAAAA-A
11582579 ACCAAA
1 ACCAAA
11582585 TCCTTAGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 8 0.32
22 15 0.60
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (22 bp):
ACCAAAATCGTTGTTTTAAAAA
Found at i:11582828 original size:20 final size:20
Alignment explanation
Indices: 11582803--11582844 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
11582793 TAATACGATT
*
11582803 AATACAA-ATAAATAAACATG
1 AATACAATAAAAAT-AACATG
11582823 AATACAATAAAAATAACATG
1 AATACAATAAAAATAACATG
11582843 AA
1 AA
11582845 ATGAATCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.67, C:0.10, G:0.05, T:0.19
Consensus pattern (20 bp):
AATACAATAAAAATAACATG
Found at i:11585359 original size:40 final size:40
Alignment explanation
Indices: 11585285--11585495 Score: 257
Period size: 40 Copynumber: 5.3 Consensus size: 40
11585275 TCTTCGGAAT
** * *
11585285 TTAG-CCGGATATAACCACTCGCAC-AAGGCCTTCGGGTC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTC
* * *
11585323 TTAGCCCGGATATGGTCACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTC
*
11585363 TTAGCCCGGATATAGTCGCTAGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTC
* *
11585403 TTAGCCCGGATATAG-CAACTCGCACAAATGCCTTCGGATC
1 TTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGTC
* * * *
11585443 TTAGTCCGGATATAGTCACTAGCATAAAAGCCTTCGGGAC
1 TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTC
*
11585483 TTAGCCCGAATAT
1 TTAGCCCGGATAT
11585496 CATTCGAATA
Statistics
Matches: 147, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
38 4 0.03
39 16 0.11
40 126 0.86
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGTC
Found at i:11587696 original size:10 final size:9
Alignment explanation
Indices: 11587648--11587738 Score: 62
Period size: 9 Copynumber: 9.9 Consensus size: 9
11587638 TTTTTAAAAT
11587648 AATTATTAA
1 AATTATTAA
11587657 AATTATTAA
1 AATTATTAA
*
11587666 AA-TATAAAA
1 AATTAT-TAA
11587675 AATTATTTAA
1 AATTA-TTAA
11587685 GAATTATTAA
1 -AATTATTAA
* *
11587695 GAATTGCTAAA
1 -AATT-ATTAA
11587706 AATTA-TAA
1 AATTATTAA
* *
11587714 AATAATAAA
1 AATTATTAA
*
11587723 AATTAATAA
1 AATTATTAA
11587732 AA-TATTA
1 AATTATTA
11587739 GTGTCGAAAC
Statistics
Matches: 64, Mismatches: 12, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
8 13 0.20
9 25 0.39
10 17 0.27
11 9 0.14
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.36
Consensus pattern (9 bp):
AATTATTAA
Found at i:11587722 original size:17 final size:18
Alignment explanation
Indices: 11587702--11587735 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
11587692 TAAGAATTGC
11587702 TAAAAATT-ATAAAATAA
1 TAAAAATTAATAAAATAA
11587719 TAAAAATTAATAAAATA
1 TAAAAATTAATAAAATA
11587736 TTAGTGTCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAATTAATAAAATAA
Found at i:11589056 original size:31 final size:31
Alignment explanation
Indices: 11588985--11589064 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
11588975 TAATTTTATC
*
11588985 ATAAATTATA--TATGC-AATAGATTTTTAA
1 ATAAATTATATGTATACAAATAGATTTTTAA
* *
11589013 A-ACATAATTATGTATACAAATAGATTTTTAA
1 ATAAATTA-TATGTATACAAATAGATTTTTAA
11589044 ATAAATTATATGTATA-AAATA
1 ATAAATTATATGTATACAAATA
11589065 ACATAAGATT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
27 4 0.10
28 3 0.07
30 9 0.21
31 22 0.52
32 4 0.10
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (31 bp):
ATAAATTATATGTATACAAATAGATTTTTAA
Found at i:11591435 original size:24 final size:24
Alignment explanation
Indices: 11591376--11591435 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 24
11591366 AAACAAAAAA
*
11591376 AGAAACAAAGCAAGACAACAGAGC
1 AGAAACAAAGCAAGAAAACAGAGC
* *
11591400 --AAA-AAGGC--GAAAATAGAGC
1 AGAAACAAAGCAAGAAAACAGAGC
11591419 AGAAACAAAGCAAGAAA
1 AGAAACAAAGCAAGAAA
11591436 CAGCAAAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 10
0.66 0.10 0.24
Matches are distributed among these distances:
19 9 0.33
21 7 0.26
22 7 0.26
24 4 0.15
ACGTcount: A:0.62, C:0.15, G:0.22, T:0.02
Consensus pattern (24 bp):
AGAAACAAAGCAAGAAAACAGAGC
Found at i:11592478 original size:25 final size:24
Alignment explanation
Indices: 11592448--11592496 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
11592438 ATTAATTTAA
11592448 TATTTA-TCATTTACTTTGATTTTTT
1 TATTTATTCATTTA-TTT-ATTTTTT
11592473 TATTTATTCATTTATTTATTTTTT
1 TATTTATTCATTTATTTATTTTTT
11592497 CCTTCTCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 7 0.30
25 9 0.39
26 7 0.30
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.71
Consensus pattern (24 bp):
TATTTATTCATTTATTTATTTTTT
Found at i:11597938 original size:29 final size:30
Alignment explanation
Indices: 11597891--11597958 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
11597881 TGGCCCAAAA
* *
11597891 GTAAATACTCAAAATTTGAAGGATTAA-AGT
1 GTAAATA-TCAAAAGTTGAAGGACTAATAGT
*
11597921 GTAAATATGAAAAGTTGAAGGACTAATAGT
1 GTAAATATCAAAAGTTGAAGGACTAATAGT
*
11597951 GAAAATAT
1 GTAAATAT
11597959 TTTAAGGGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.49, C:0.04, G:0.19, T:0.28
Consensus pattern (30 bp):
GTAAATATCAAAAGTTGAAGGACTAATAGT
Found at i:11600411 original size:46 final size:46
Alignment explanation
Indices: 11600354--11600581 Score: 323
Period size: 46 Copynumber: 5.0 Consensus size: 46
11600344 GGTGTGCTCT
* *
11600354 CTGAAATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
11600400 CTGATATGAAATGTGTAAGACCATGGTTGAAAGACACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
11600446 CTGATATGTAATGTGTAAGACCATGGTTGAAAGATACCATGGTAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
11600492 CTGATATGAAATGTGTAAGACTATAGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
11600538 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
11600582 TCATGTCAAA
Statistics
Matches: 165, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 1 0.01
46 164 0.99
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:11604437 original size:128 final size:129
Alignment explanation
Indices: 11604201--11604437 Score: 377
Period size: 128 Copynumber: 1.8 Consensus size: 129
11604191 TGAAGATTCA
* * *
11604201 CTAAAACAAAGGCAATATTCGATGTTTGGAAATTCGGGGAATAGTGCCCTATCGTGCTGGGTTTC
1 CTAAAACAAAGGCAATATTCAATGTTTGGAAATTCGGGGAATAGTGCCCTATCATGCTGGATTTC
* * *
11604266 GATTTTCCGCTTGTTCAAAATAACCGAATATTCCTTTAGAATTTTATTTGTGTTTTTTCAAAAG
66 GATTTCCCGCTTGTTCAAAATAACCAAATATTCCTTCAGAATTTTATTTGTGTTTTTTCAAAAG
11604330 CTAAAAC-AAGGCAATATTCAATGTTTGGAAATTCGGGGAATAGTGCCCTATCATGCTGGATTTC
1 CTAAAACAAAGGCAATATTCAATGTTTGGAAATTCGGGGAATAGTGCCCTATCATGCTGGATTTC
* ** *
11604394 GATTTCCCGTTTGTTCAAAATAATTAAATATTCCTTCGGAATTT
66 GATTTCCCGCTTGTTCAAAATAACCAAATATTCCTTCAGAATTT
11604438 CACCCGTGTT
Statistics
Matches: 98, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
128 91 0.93
129 7 0.07
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (129 bp):
CTAAAACAAAGGCAATATTCAATGTTTGGAAATTCGGGGAATAGTGCCCTATCATGCTGGATTTC
GATTTCCCGCTTGTTCAAAATAACCAAATATTCCTTCAGAATTTTATTTGTGTTTTTTCAAAAG
Found at i:11606974 original size:43 final size:43
Alignment explanation
Indices: 11606890--11607036 Score: 118
Period size: 43 Copynumber: 3.4 Consensus size: 43
11606880 CAATCTGACA
* * * * *
11606890 CTGTAGTGCATCACCGGATAAATCAAAGGAAATTTATTGGCAC
1 CTGTAGTGCATCATCGGATAAGTCGAAGGAAATATACTGGCAC
* * *
11606933 CTGTAGTGCATCATTGGATAAGTCGAAGGAAACATACTGGCATA
1 CTGTAGTGCATCATCGGATAAGTCGAAGGAAATATACTGGCA-C
* * * * * *
11606977 C-ATAGAGCATCATCGAATAAGTCGAAGCAATTGTACTGGCAC
1 CTGTAGTGCATCATCGGATAAGTCGAAGGAAATATACTGGCAC
* * *
11607019 AT-AAGTGCATCATTGGAT
1 CTGTAGTGCATCATCGGAT
11607037 GAACCGAATC
Statistics
Matches: 80, Mismatches: 22, Indels: 5
0.75 0.21 0.05
Matches are distributed among these distances:
42 12 0.15
43 67 0.84
44 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (43 bp):
CTGTAGTGCATCATCGGATAAGTCGAAGGAAATATACTGGCAC
Found at i:11608282 original size:39 final size:39
Alignment explanation
Indices: 11608219--11608298 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
11608209 ATGGCCACAA
* *
11608219 CTCTATATATAATAACAATTTTCTTAGTCATTCATTGTC
1 CTCTAGATATAATAACAATCTTCTTAGTCATTCATTGTC
*
11608258 CTCTAGATATAATATCAATCTTCTTAGTCATTCATTGTC
1 CTCTAGATATAATAACAATCTTCTTAGTCATTCATTGTC
11608297 CT
1 CT
11608299 TGTTTATTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.45
Consensus pattern (39 bp):
CTCTAGATATAATAACAATCTTCTTAGTCATTCATTGTC
Found at i:11609281 original size:13 final size:13
Alignment explanation
Indices: 11609263--11609287 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11609253 ATTAATCGGT
11609263 TGATAAATAATAA
1 TGATAAATAATAA
11609276 TGATAAATAATA
1 TGATAAATAATA
11609288 TATAAGCCCA
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:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (13 bp):
TGATAAATAATAA
Found at i:11612776 original size:3 final size:3
Alignment explanation
Indices: 11612768--11612795 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
11612758 CCAACTCTTA
11612768 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
11612796 AATTTCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:11613338 original size:20 final size:20
Alignment explanation
Indices: 11613303--11613344 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
11613293 AAAATAAAAG
*
11613303 AATAAAAAATTCAAATTTTT
1 AATAAAAAATTCAAATCTTT
11613323 AATAAAAAATAT-AAATCTTT
1 AATAAAAAAT-TCAAATCTTT
11613343 AA
1 AA
11613345 GCAAACTGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
AATAAAAAATTCAAATCTTT
Found at i:11613721 original size:20 final size:20
Alignment explanation
Indices: 11613683--11613721 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11613673 AAAAAAGGAA
* * *
11613683 TTTTTTTTTTTGAAGAATTC
1 TTTTCTTTTTTCAAAAATTC
11613703 TTTTCTTTTTTCAAAAATT
1 TTTTCTTTTTTCAAAAATT
11613722 TGGAATTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.05, T:0.64
Consensus pattern (20 bp):
TTTTCTTTTTTCAAAAATTC
Found at i:11620961 original size:18 final size:19
Alignment explanation
Indices: 11620916--11620962 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
11620906 GAAATACTTA
*
11620916 ATATATAATATTTGAAATAT
1 ATATATAATA-TTAAAATAT
**
11620936 ATGCATAATA-TAAAATAT
1 ATATATAATATTAAAATAT
11620954 ATATATAAT
1 ATATATAAT
11620963 GTAGTATTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 14 0.64
20 8 0.36
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (19 bp):
ATATATAATATTAAAATAT
Found at i:11632527 original size:16 final size:16
Alignment explanation
Indices: 11632506--11632574 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
11632496 GATTAGCTAT
*
11632506 TACACCACTAATCCAA
1 TACACCTCTAATCCAA
11632522 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
11632539 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
11632555 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
11632571 TACA
1 TACA
11632575 GCGAACCAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
16 35 0.69
17 16 0.31
ACGTcount: A:0.39, C:0.38, G:0.00, T:0.23
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:11632550 original size:33 final size:32
Alignment explanation
Indices: 11632506--11632574 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
11632496 GATTAGCTAT
11632506 TACACCACTAATCCAATACACCTCTAATCCCAA
1 TACACCACTAATCCAATACACCTCTAAT-CCAA
*
11632539 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCACTAATCCAATACACCTCTAATCCAA
11632571 TACA
1 TACA
11632575 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.39, C:0.38, G:0.00, T:0.23
Consensus pattern (32 bp):
TACACCACTAATCCAATACACCTCTAATCCAA
Found at i:11634160 original size:17 final size:16
Alignment explanation
Indices: 11634133--11634172 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
11634123 TAAATAATTT
11634133 TTTTATATTTTTTAATAA
1 TTTT-TATTTTTTAAT-A
*
11634151 TTTTTATTTTTTGATA
1 TTTTTATTTTTTAATA
11634167 TTTTTA
1 TTTTTA
11634173 AATTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 10 0.48
18 4 0.19
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTTATTTTTTAATA
Found at i:11634628 original size:26 final size:25
Alignment explanation
Indices: 11634599--11634651 Score: 79
Period size: 26 Copynumber: 2.1 Consensus size: 25
11634589 ACTAATAAAC
*
11634599 TATTCTTTTATATTTTTAATAATTTT
1 TATTCTTTTACATTTTTAA-AATTTT
*
11634625 TATTTTTTTACATTTTTAAAATTTT
1 TATTCTTTTACATTTTTAAAATTTT
11634650 TA
1 TA
11634652 AAATTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 8 0.32
26 17 0.68
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (25 bp):
TATTCTTTTACATTTTTAAAATTTT
Found at i:11636490 original size:56 final size:59
Alignment explanation
Indices: 11636394--11636527 Score: 145
Period size: 56 Copynumber: 2.3 Consensus size: 59
11636384 ATGCTTAATT
* *
11636394 TTTTTTTCAAATTAATC-CTTAAATTTAGTAATTGTATTTATAATGAGGA-TT-AA-ATA
1 TTTTTTTCAAATTAATCTCTAAAATTTAGCAATTGTATTTAT-ATGAGGACTTGAACATA
* * *
11636450 TTTTTTTCAAATTAATCTC-AAAATTTAGCAACTT-TTTTTATATTAGGACTTGAACATT
1 TTTTTTTCAAATTAATCTCTAAAATTTAGCAA-TTGTATTTATATGAGGACTTGAACATA
11636508 TTTTTTGTCTAAATTAATCT
1 TTTTTT-TC-AAATTAATCT
11636528 ATGATATTTC
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
55 6 0.09
56 35 0.53
57 5 0.08
58 8 0.12
59 2 0.03
60 10 0.15
ACGTcount: A:0.34, C:0.09, G:0.07, T:0.50
Consensus pattern (59 bp):
TTTTTTTCAAATTAATCTCTAAAATTTAGCAATTGTATTTATATGAGGACTTGAACATA
Found at i:11637063 original size:19 final size:21
Alignment explanation
Indices: 11637035--11637076 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
11637025 TGAATGTGAT
11637035 TTTTTAAAAATAAT-AAAATA
1 TTTTTAAAAATAATAAAAATA
*
11637055 TTTTT-AAAATTATAAAAATA
1 TTTTTAAAAATAATAAAAATA
11637075 TT
1 TT
11637077 AAAAACTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTTTTAAAAATAATAAAAATA
Found at i:11639200 original size:24 final size:24
Alignment explanation
Indices: 11639176--11639256 Score: 87
Period size: 24 Copynumber: 3.4 Consensus size: 24
11639166 TTTTTATATT
*
11639176 ATTATTTATATAAATATATAAATTA
1 ATTATATATATAAATAT-TAAATTA
* *
11639201 ATTATAAAGTAT-ATTATTAAATTA
1 ATTATATA-TATAAATATTAAATTA
*
11639225 ATTATAT-TATAAATATTATATT-
1 ATTATATATATAAATATTAAATTA
11639247 ATTATATATA
1 ATTATATATA
11639257 AAAGAAACAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
22 10 0.21
23 11 0.23
24 13 0.28
25 10 0.21
26 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (24 bp):
ATTATATATATAAATATTAAATTA
Found at i:11639208 original size:11 final size:11
Alignment explanation
Indices: 11639192--11639230 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
11639182 TATATAAATA
11639192 TATAAATTAAT
1 TATAAATTAAT
*
11639203 TATAAAGTATAT
1 TATAAATTA-AT
11639215 TATTAAATTAAT
1 TA-TAAATTAAT
11639227 TATA
1 TATA
11639231 TTATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:11639232 original size:17 final size:15
Alignment explanation
Indices: 11639175--11639255 Score: 60
Period size: 15 Copynumber: 5.2 Consensus size: 15
11639165 ATTTTTATAT
11639175 TATTAT-TTATATAAA
1 TATTATATTAT-TAAA
*
11639190 TATATAAATTAATTATAA
1 TAT-TATATT-ATTA-AA
*
11639208 -AGTATATTATTAAA
1 TATTATATTATTAAA
11639222 TTAATTATATTA-TAAA
1 -T-ATTATATTATTAAA
*
11639238 TATTATATTATTATA
1 TATTATATTATTAAA
11639253 TAT
1 TAT
11639256 AAAAGAAACA
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
14 11 0.21
15 14 0.26
16 11 0.21
17 13 0.25
18 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
TATTATATTATTAAA
Found at i:11639242 original size:14 final size:16
Alignment explanation
Indices: 11639210--11639248 Score: 55
Period size: 14 Copynumber: 2.5 Consensus size: 16
11639200 AATTATAAAG
11639210 TATATTATTAAATTAAT
1 TATATTA-TAAATTAAT
11639227 TATATTATAAA-T-AT
1 TATATTATAAATTAAT
11639241 TATATTAT
1 TATATTAT
11639249 TATATATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.45
15 1 0.05
16 4 0.18
17 7 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATTATAAATTAAT
Found at i:11640581 original size:3 final size:3
Alignment explanation
Indices: 11640573--11640614 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
11640563 GTGAGGTAAG
11640573 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
11640615 GAGTGGGAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:11640796 original size:24 final size:27
Alignment explanation
Indices: 11640764--11640822 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
11640754 CGGATTAATT
11640764 ATTG-ATTGAAAG-GTG-GAAA-AATG
1 ATTGAATTGAAAGTGTGAGAAAGAATG
**
11640787 ATTGAATTGAAAGTGTGAGAAAGTGTG
1 ATTGAATTGAAAGTGTGAGAAAGAATG
11640814 ATTGAATTG
1 ATTGAATTG
11640823 GATATATGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 4 0.13
24 8 0.27
25 3 0.10
26 4 0.13
27 11 0.37
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (27 bp):
ATTGAATTGAAAGTGTGAGAAAGAATG
Found at i:11641024 original size:37 final size:39
Alignment explanation
Indices: 11640965--11641060 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
11640955 CGGATAGATT
* * * *
11640965 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
11641002 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
11641041 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
11641061 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:11651454 original size:21 final size:21
Alignment explanation
Indices: 11651412--11651454 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
11651402 TTCACTATAC
*
11651412 ATTCTTTCATCAGTATCATTT
1 ATTCTTTCATCAGCATCATTT
*
11651433 ATTCTTTCTTCAGACATC-TTT
1 ATTCTTTCATCAG-CATCATTT
11651454 A
1 A
11651455 ATCTATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTCTTTCATCAGCATCATTT
Found at i:11652560 original size:39 final size:37
Alignment explanation
Indices: 11652493--11652584 Score: 96
Period size: 39 Copynumber: 2.4 Consensus size: 37
11652483 ACCAGAATGG
* *
11652493 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
11652532 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
11652569 TACCCAGTACCTCATC
1 CACCCAGTGCCTCATC
11652585 CAATCTATCC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
37 18 0.40
38 2 0.04
39 22 0.49
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:11652938 original size:3 final size:3
Alignment explanation
Indices: 11652930--11652977 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
11652920 ATTCCCACTC
11652930 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11652978 CTTACCTCAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11654262 original size:15 final size:15
Alignment explanation
Indices: 11654242--11654277 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
11654232 TGTTTCTTTG
11654242 TTCTTTCTATTCTGT
1 TTCTTTCTATTCTGT
* *
11654257 TTCTTTCTGTTTTGT
1 TTCTTTCTATTCTGT
11654272 TTCTTT
1 TTCTTT
11654278 TATATAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.03, C:0.17, G:0.08, T:0.72
Consensus pattern (15 bp):
TTCTTTCTATTCTGT
Found at i:11654301 original size:20 final size:21
Alignment explanation
Indices: 11654277--11654356 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 21
11654267 TTTGTTTCTT
11654277 TTATATAAATAATATAATAT-
1 TTATATAAATAATATAATATA
11654297 TTATATATAATTAATTTAATAATATA
1 TTATATA-AA-TAA--T-ATAATATA
* *
11654323 CTT-TATAATTAAT-TTATATA
1 -TTATATAAATAATATAATATA
11654343 TTATATAAATAATA
1 TTATATAAATAATA
11654357 ATATAAATCT
Statistics
Matches: 48, Mismatches: 3, Indels: 17
0.71 0.04 0.25
Matches are distributed among these distances:
19 2 0.04
20 22 0.46
21 2 0.04
22 4 0.08
24 4 0.08
25 8 0.17
26 4 0.08
27 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (21 bp):
TTATATAAATAATATAATATA
Found at i:11654330 original size:12 final size:11
Alignment explanation
Indices: 11654302--11654345 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
11654292 AATATTTATA
11654302 TATAATTAATT
1 TATAATTAATT
*
11654313 TAATAATATACTT
1 T-ATAAT-TAATT
11654326 TATAATTAATT
1 TATAATTAATT
11654337 TATATATTA
1 TATA-ATTA
11654346 TATAAATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 9 0.32
12 14 0.50
13 5 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (11 bp):
TATAATTAATT
Found at i:11654354 original size:24 final size:23
Alignment explanation
Indices: 11654278--11654355 Score: 86
Period size: 24 Copynumber: 3.3 Consensus size: 23
11654268 TTGTTTCTTT
* *
11654278 TATATAAATAATATAATATT-TA
1 TATATAATTAATTTAATATTATA
*
11654300 TATATAATTAATTTAATAATATA
1 TATATAATTAATTTAATATTATA
*
11654323 CTTTATAATTAATTTATATATTATA
1 -TATATAATTAATTTA-ATATTATA
*
11654348 TAAATAAT
1 TATATAAT
11654356 AATATAAATC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
22 17 0.37
23 2 0.04
24 20 0.43
25 7 0.15
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (23 bp):
TATATAATTAATTTAATATTATA
Found at i:11658402 original size:18 final size:19
Alignment explanation
Indices: 11658357--11658403 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
11658347 GAAATACTTA
*
11658357 ATATATAATATTTGAAATAT
1 ATATATAATA-TTAAAATAT
**
11658377 ATGCATAATA-TAAAATAT
1 ATATATAATATTAAAATAT
11658395 ATATATAAT
1 ATATATAAT
11658404 GTAGTATTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
18 14 0.64
20 8 0.36
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (19 bp):
ATATATAATATTAAAATAT
Found at i:11669937 original size:44 final size:45
Alignment explanation
Indices: 11669872--11669962 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
11669862 ACCTCTATTC
* * *
11669872 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
11669916 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
11669961 CA
1 CA
11669963 CCTCTAATCC
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:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:11669964 original size:16 final size:16
Alignment explanation
Indices: 11669943--11670011 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
11669933 GATTAGCTAT
11669943 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
11669959 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
11669976 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
11669992 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
11670008 TACA
1 TACA
11670012 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:11669985 original size:33 final size:32
Alignment explanation
Indices: 11669943--11670011 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
11669933 GATTAGCTAT
11669943 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
11669976 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
11670008 TACA
1 TACA
11670012 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:11671775 original size:17 final size:17
Alignment explanation
Indices: 11671755--11671787 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11671745 AGTCCATAAT
11671755 AATCTTCAACTAACAAA
1 AATCTTCAACTAACAAA
*
11671772 AATCTTCATCTAACAA
1 AATCTTCAACTAACAA
11671788 GTCCACATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.27
Consensus pattern (17 bp):
AATCTTCAACTAACAAA
Found at i:11680755 original size:17 final size:19
Alignment explanation
Indices: 11680653--11680747 Score: 146
Period size: 17 Copynumber: 5.3 Consensus size: 19
11680643 CAAAATCATA
11680653 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
*
11680670 ATGATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
11680689 ATCATATCTAAGATTGCA-
1 ATCATATCTAAGATTGCAT
11680707 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
11680724 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
11680743 ATCAT
1 ATCAT
11680748 TAAAGATTAT
Statistics
Matches: 71, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
17 31 0.44
18 16 0.23
19 24 0.34
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.38
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:11680767 original size:54 final size:54
Alignment explanation
Indices: 11680652--11680756 Score: 169
Period size: 54 Copynumber: 2.0 Consensus size: 54
11680642 ACAAAATCAT
* * *
11680652 AATCATATCTAAGATTGTATGATATCTAAGATTGCATATCATATCTAAGATTGC
1 AATCATATCTAAGATTGTATCATATCTAAGATTGCATATCATATCAAAGATTAC
11680706 AATCATATCTAAGATTGTATCATATCTAAGATTGCATATCAT-T-AAAGATTA
1 AATCATATCTAAGATTGTATCATATCTAAGATTGCATATCATATCAAAGATTA
11680757 TATTTCCATA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
52 6 0.12
53 1 0.02
54 41 0.85
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.37
Consensus pattern (54 bp):
AATCATATCTAAGATTGTATCATATCTAAGATTGCATATCATATCAAAGATTAC
Found at i:11681129 original size:45 final size:45
Alignment explanation
Indices: 11681059--11681258 Score: 258
Period size: 45 Copynumber: 4.5 Consensus size: 45
11681049 GGAAGGCGAT
* * *
11681059 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATACAGAGACGACAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
*
11681104 ATCTATTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * ** * *
11681149 ATCTGCT-TCTTCAATCTGCTTTCCGTCTAATACAAAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* * *
11681193 ATCTGTTATCTCCGATTTGCTCCCCGTCTAATACAGAGATGCCAA
1 ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
* *
11681238 ATCTGTCATCTTGGATCTGCT
1 ATCTGTTATCTTCGATCTGCT
11681259 TCGATGTAAA
Statistics
Matches: 132, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
44 38 0.29
45 94 0.71
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.32
Consensus pattern (45 bp):
ATCTGTTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
Found at i:11681224 original size:89 final size:90
Alignment explanation
Indices: 11681059--11681242 Score: 262
Period size: 89 Copynumber: 2.1 Consensus size: 90
11681049 GGAAGGCGAT
** * *
11681059 ATCTGCTATCTTTGATCTGCTCCCCGTCTAATACAGAGACGACAAATCTATTATCTTCGATCTGC
1 ATCTGCTATCTTCAATCTGCTCCCCGTCTAATACAAAGACGACAAATCTATTATCTCCGATCTGC
11681124 TCCCCGTCTAATACAGAGACGCCAA
66 TCCCCGTCTAATACAGAGACGCCAA
** * * * *
11681149 ATCTGCT-TCTTCAATCTGCTTTCCGTCTAATACAAAGATGCCAAATCTGTTATCTCCGATTTGC
1 ATCTGCTATCTTCAATCTGCTCCCCGTCTAATACAAAGACGACAAATCTATTATCTCCGATCTGC
*
11681213 TCCCCGTCTAATACAGAGATGCCAA
66 TCCCCGTCTAATACAGAGACGCCAA
11681238 ATCTG
1 ATCTG
11681243 TCATCTTGGA
Statistics
Matches: 83, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
89 76 0.92
90 7 0.08
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (90 bp):
ATCTGCTATCTTCAATCTGCTCCCCGTCTAATACAAAGACGACAAATCTATTATCTCCGATCTGC
TCCCCGTCTAATACAGAGACGCCAA
Found at i:11681401 original size:78 final size:78
Alignment explanation
Indices: 11681272--11681654 Score: 518
Period size: 78 Copynumber: 4.8 Consensus size: 78
11681262 ATGTAAACAC
* * *
11681272 ATGAAGGTTAGATCTGCTATGTCTTTGATCTGCTTCCCGTCTAATACAGAGATGCCAAATCATCT
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
11681337 TGGATCTGCTTCA
66 TGGATCTGCTTCA
* *
11681350 ATGAAGGTCCA-ATCTGTTATGTCTTCGATCTGTTCCCCGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
11681414 TTGGATCTGCTTCAATGTAAACA
65 TTGGATCTG---C--T-T---CA
*
11681437 CATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCTGTCTAATACAGAGATGCCAAATCATC
1 -ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
11681502 TTGGATCTGCTTCA
65 TTGGATCTGCTTCA
* *
11681516 ATGAAGGTCCA-ATCTGTTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATC
1 ATGAAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATC
*
11681580 TTGGATCTGCCTCA
65 TTGGATCTGCTTCA
* ** * *
11681594 ATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCTTCGTCGAATATAGAGATGCCAAATC
1 ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
11681655 TATTTCTTCG
Statistics
Matches: 274, Mismatches: 17, Indels: 28
0.86 0.05 0.09
Matches are distributed among these distances:
77 2 0.01
78 190 0.69
79 5 0.02
81 1 0.00
82 1 0.00
83 2 0.01
84 1 0.00
85 1 0.00
87 4 0.01
88 67 0.24
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (78 bp):
ATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCT
TGGATCTGCTTCA
Found at i:11681491 original size:166 final size:165
Alignment explanation
Indices: 11681192--11681654 Score: 673
Period size: 166 Copynumber: 2.8 Consensus size: 165
11681182 AAAGATGCCA
* *
11681192 AATCTGTTA--TCTCCGATTTGCTCCCCGTCTAATACAGAGATGCCAAATCTGTCATCTTGGATC
1 AATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAA----TCATCTTGGATC
* *
11681255 TGCTTCGATGTAAACACATGAAGGTTAGATCTGCTATGTCTTTGATCTGCTTCCC-GTCTAATAC
62 TGCTTC-ATGTAAACACATGAAGGTCAGATCTGCTATGTCTTCGATCTGC-TCCCTGTCTAATAC
11681319 AGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCC
125 AGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCC
*
11681360 AATCTGTTATGTCTTCGATCTGTTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCT
1 AATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCT
11681425 TCAATGTAAACACATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCTGTCTAATACAGAGA
66 TC-ATGTAAACACATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCTGTCTAATACAGAGA
11681490 TGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCC
130 TGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCC
*
11681526 AATCTGTTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGC-
1 AATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCT
* * * *
11681590 -C---T---CA-ATGAAGGTCAGATCTGCTATGTCTTCGATCTACT-CTTCGTCGAATATAGAGA
66 TCATGTAAACACATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCT-GTCTAATACAGAGA
11681646 TGCCAAATC
130 TGCCAAATC
11681655 TATTTCTTCG
Statistics
Matches: 279, Mismatches: 12, Indels: 20
0.90 0.04 0.06
Matches are distributed among these distances:
155 2 0.01
156 54 0.19
157 2 0.01
160 1 0.00
164 1 0.00
165 4 0.01
166 171 0.61
168 9 0.03
170 35 0.13
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (165 bp):
AATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCT
TCATGTAAACACATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCTGTCTAATACAGAGAT
GCCAAATCATCTTGGATCTGCTTCAATGAAGGTCC
Found at i:11681871 original size:376 final size:375
Alignment explanation
Indices: 11681360--11682165 Score: 1235
Period size: 376 Copynumber: 2.1 Consensus size: 375
11681350 ATGAAGGTCC
* * *
11681360 AATCTGTTATGTCTTCGATCTGTTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCT
1 AATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATATTGGATCTACT
* *
11681425 TCAATGTAAACACATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCTGTCTAATACAGAGA
66 TCAATGTAAACACATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAAAGA
11681490 TGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCCAATCTGTTATGTCTTCGATCTACTCCCCG
131 TGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCCAATCTGTTATGTCTTCGATCTACTCCCCG
11681555 TCTAATACAGAGATGCCAAATCATCTTGGATCTGCCTCAATGAAGGTCAGATCTGCTATGTCTTC
196 TCTAATACAGAGATGCCAAATCATCTTGGATCTGCCTCAATGAAGGTCAGATCTGCTATGTCTTC
*
11681620 GATCTACTCTTCGTCGAATATAGAGATGCCAAATCTATTTCTTCGATTTGTTCTCTAACAGTACA
261 GATCTACTCTTCGTCGAATATAGAGATGCCAAATCTATTCCTTCGATTTGTTCTCTAACAGTACA
* ** * *
11681685 GAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGTGAAATCCA
326 GAGATGCCAAATCATCGTAGATCTGCAACAGCGTAAACACGTGAAAGCAA
**
11681735 AATCTGTTATGTCTTCGATCTGCTCCTTGTC-AACGTA-AG-GATGCCAAATCATATTGGATCTA
1 AATCTGTTATGTCTTCGATCTGCTCCCCGTCTAA--TACAGAGATGCCAAATCATATTGGATCTA
* * * *
11681797 CTTCGATGTGAAA-ACATCCTAAGGTTAGATCTGCTATGTCTTCGATCTGCTCCCCGTTTAATAC
64 CTTCAATGT-AAACACAT--GAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATAC
*
11681861 AAAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCCAATCTGTTATGTCTTCGATCTGCT
126 AAAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCCAATCTGTTATGTCTTCGATCTACT
* *
11681926 CCCCGTCTAATACAGAGATGCCAAATCATCTTGGATTTGCTTCAATGAAGGTCAGATCTGCTATG
191 CCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCCTCAATGAAGGTCAGATCTGCTATG
* * * *
11681991 TCTTCGATCTGCTCTTCGTCGAATATGGAGATGCCAAATCTGTTCCTTCGATTTGTTCTCTGACA
256 TCTTCGATCTACTCTTCGTCGAATATAGAGATGCCAAATCTATTCCTTCGATTTGTTCTCTAACA
* * *
11682056 GTACAGATATGTCAAATCATCGTAGATCTGCAACAGCGTAAACACGTGAAAGGAA
321 GTACAGAGATGCCAAATCATCGTAGATCTGCAACAGCGTAAACACGTGAAAGCAA
** * * **
11682111 AATCTACTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATC-TATT
1 AATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATATT
11682166 TATTCGATTT
Statistics
Matches: 390, Mismatches: 33, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
374 35 0.09
375 35 0.09
376 307 0.79
377 13 0.03
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (375 bp):
AATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATATTGGATCTACT
TCAATGTAAACACATGAAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAAAGA
TGCCAAATCATCTTGGATCTGCTTCAATGAAGGTCCAATCTGTTATGTCTTCGATCTACTCCCCG
TCTAATACAGAGATGCCAAATCATCTTGGATCTGCCTCAATGAAGGTCAGATCTGCTATGTCTTC
GATCTACTCTTCGTCGAATATAGAGATGCCAAATCTATTCCTTCGATTTGTTCTCTAACAGTACA
GAGATGCCAAATCATCGTAGATCTGCAACAGCGTAAACACGTGAAAGCAA
Found at i:11681919 original size:298 final size:287
Alignment explanation
Indices: 11681394--11681952 Score: 723
Period size: 298 Copynumber: 1.9 Consensus size: 287
11681384 CCCCGTCTAA
* * * *
11681394 TACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGTAAACACATGAAGGTCAGATCTGCTATG
1 TACAGAGATGCCAAATCATCTTAGATCTGCTTCAACGTAAACACATGAAGATCAAATCTGCTATG
* * **
11681459 TCTTCGATCTGCTCCCTGTCTAATACAGAGATGCCAAATCATCTTGGATCTGCTTCAATGAAGGT
66 TCTTCGATCTGCTCCCTGTCTAATACAGAGATGCCAAATCATATTGGATCTACTTCAATGAACAT
* *
11681524 CCAATCTGTTATGTCTTCGATCTACTCCCCGTCTAATACAGAGATGCCAAATCATCTTGGATCTG
131 CCAATCTGCTATGTCTTCGATCTACTCCCCGTCTAATACAAAGATGCCAAATCATCTTGGATCTG
** *
11681589 CCTCAATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCTTCGTCGAATATAGAGATGCCAAAT
196 CCTCAATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCCCCGTCGAATACAGAGATGCCAAAT
11681654 CTATTTCTTCGATTTGTTCTCTAACAG
261 CTATTTCTTCGATTTGTTCTCTAACAG
* * *
11681681 TACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGTGAA-ATCCAAATCTGTTAT
1 TACAGAGATGCCAAATCATCTTAGATCTGCTTCAACGTAAACACATGAAGAT-CAAATCTGCTAT
* *
11681745 GTCTTCGATCTGCTCCTTGTC-AACGTA-AG-GATGCCAAATCATATTGGATCTACTTCGATGTG
65 GTCTTCGATCTGCTCCCTGTCTAA--TACAGAGATGCCAAATCATATTGGATCTACTTC-A-ATG
* *
11681807 AAAACATCCTAAGGTTAGATCTGCTATGTCTTCGATCTGCTCCCCGTTTAATACAAAGATGCCAA
126 --AACATCC-------A-ATCTGCTATGTCTTCGATCTACTCCCCGTCTAATACAAAGATGCCAA
* * * *
11681872 ATCATCTTGGATCTGCTTCAATGAAGGTCCA-ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAA
181 ATCATCTTGGATCTGCCTCAATGAAGGT-CAGATCTGCTATGTCTTCGATCTACTCCCCGTCGAA
11681936 TACAGAGATGCCAAATC
245 TACAGAGATGCCAAATC
11681953 ATCTTGGATT
Statistics
Matches: 232, Mismatches: 24, Indels: 21
0.84 0.09 0.08
Matches are distributed among these distances:
286 28 0.12
287 78 0.34
288 4 0.02
290 5 0.02
297 1 0.00
298 114 0.49
299 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (287 bp):
TACAGAGATGCCAAATCATCTTAGATCTGCTTCAACGTAAACACATGAAGATCAAATCTGCTATG
TCTTCGATCTGCTCCCTGTCTAATACAGAGATGCCAAATCATATTGGATCTACTTCAATGAACAT
CCAATCTGCTATGTCTTCGATCTACTCCCCGTCTAATACAAAGATGCCAAATCATCTTGGATCTG
CCTCAATGAAGGTCAGATCTGCTATGTCTTCGATCTACTCCCCGTCGAATACAGAGATGCCAAAT
CTATTTCTTCGATTTGTTCTCTAACAG
Found at i:11681946 original size:78 final size:78
Alignment explanation
Indices: 11681817--11682030 Score: 322
Period size: 78 Copynumber: 2.7 Consensus size: 78
11681807 AAAACATCCT
* * *
11681817 AAGGTTAGATCTGCTATGTCTTCGATCTGCTCCCCGTTTAATACAAAGATGCCAAATCATCTTGG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
11681882 ATCTGCTTCAATG
66 ATCTGCTTCAATG
*
11681895 AAGGTCCA-ATCTGTTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTG
1 AAGGT-CAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTG
*
11681959 GATTTGCTTCAATG
65 GATCTGCTTCAATG
** * **
11681973 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCTTCGTCGAATATGGAGATGCCAAATC
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
11682031 TGTTCCTTCG
Statistics
Matches: 123, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
77 2 0.02
78 120 0.98
79 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (78 bp):
AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
ATCTGCTTCAATG
Found at i:11682224 original size:131 final size:131
Alignment explanation
Indices: 11681981--11682266 Score: 455
Period size: 131 Copynumber: 2.2 Consensus size: 131
11681971 TGAAGGTCAG
* * *
11681981 ATCTGCTATGTCTTCGATCTGCTCTTCGTCGAATATGGAGATGCCAAATCTGTTCCTTCGATTTG
1 ATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTATTCATTCGATTTG
* * * *
11682046 TTCTCTGACAGTACAGATATGTCAAATCATCGTAGATCTGCAACAGCGTAAACACGTGAAAGGAA
66 TTCTCTGAAAGTACAGAGATGCCAAATCATCGTAGATCTGCAACAGCGTAAACACGTGAAAGCAA
11682111 A
131 A
* *
11682112 ATCTACTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTATTTATTCGATTTG
1 ATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTATTCATTCGATTTG
* ** *
11682177 TTCTCTGAAAGTACAGAGATGCCAAATCATCTTAGATCTGCTTCAGCGTAAACACGTGAAAGCCA
66 TTCTCTGAAAGTACAGAGATGCCAAATCATCGTAGATCTGCAACAGCGTAAACACGTGAAAGCAA
11682242 A
131 A
11682243 ATCTGCTATGTCTTCGATCTGCTC
1 ATCTGCTATGTCTTCGATCTGCTC
11682267 CTTAACAACG
Statistics
Matches: 141, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
131 141 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (131 bp):
ATCTGCTATGTCTTCGATCTGCTCTCCGTCGAATATGGAGATGCCAAATCTATTCATTCGATTTG
TTCTCTGAAAGTACAGAGATGCCAAATCATCGTAGATCTGCAACAGCGTAAACACGTGAAAGCAA
A
Found at i:11690816 original size:19 final size:19
Alignment explanation
Indices: 11690772--11690831 Score: 97
Period size: 19 Copynumber: 3.3 Consensus size: 19
11690762 CAAAATCATA
11690772 ATCATATCTAAGATTG--T
1 ATCATATCTAAGATTGCAT
*
11690789 ATGATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
11690808 ATCATATCTAAGATTGCAT
1 ATCATATCTAAGATTGCAT
11690827 ATCAT
1 ATCAT
11690832 TGAAGATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
17 15 0.38
19 24 0.62
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (19 bp):
ATCATATCTAAGATTGCAT
Found at i:11690839 original size:17 final size:19
Alignment explanation
Indices: 11690772--11690839 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
11690762 CAAAATCATA
*
11690772 ATCATATCTAAGATTG--T
1 ATCATATCGAAGATTGCAT
* *
11690789 ATGATATCTAAGATTGCAT
1 ATCATATCGAAGATTGCAT
*
11690808 ATCATATCTAAGATTGCAT
1 ATCATATCGAAGATTGCAT
11690827 ATCAT-T-GAAGATT
1 ATCATATCGAAGATT
11690840 ATATTTCCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
17 21 0.46
18 1 0.02
19 24 0.52
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (19 bp):
ATCATATCGAAGATTGCAT
Found at i:11691504 original size:38 final size:38
Alignment explanation
Indices: 11691432--11691504 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
11691422 AAAATACGAT
* * * *
11691432 TTTTAGGGACTGAATCATAAAATTTTGTAAATTTGTGA
1 TTTTAGAGACTAAATCATAAAATATTGCAAATTTGTGA
11691470 TTTTAGAGACTAAATCATAAAA-ATTGCAATATTTG
1 TTTTAGAGACTAAATCATAAAATATTGCAA-ATTTG
11691505 AATTCCACGG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 5 0.17
38 25 0.83
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (38 bp):
TTTTAGAGACTAAATCATAAAATATTGCAAATTTGTGA
Found at i:11691790 original size:32 final size:32
Alignment explanation
Indices: 11691753--11691817 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
11691743 ATTTGTGATG
11691753 AATTAGTAAGAATGATTTTAAATTAAATTTTA
1 AATTAGTAAGAATGATTTTAAATTAAATTTTA
11691785 AATTAGTAAGAATGATTTTAAATTAAATTTTA
1 AATTAGTAAGAATGATTTTAAATTAAATTTTA
11691817 A
1 A
11691818 GGATATGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (32 bp):
AATTAGTAAGAATGATTTTAAATTAAATTTTA
Found at i:11697479 original size:25 final size:23
Alignment explanation
Indices: 11697404--11697520 Score: 78
Period size: 25 Copynumber: 4.9 Consensus size: 23
11697394 ATGTGATAAA
*
11697404 AATATAATA-AATAAATAATAAGT
1 AATATAATATAAAAAAT-ATAAGT
** *
11697427 AATGAT-ATATGTTAAAATATATATT
1 AAT-ATAATAT-AAAAAATATA-AGT
*
11697452 AATATGATAATAAAAAATATGAAGT
1 AATATAAT-ATAAAAAATAT-AAGT
*
11697477 AATATAATATAATAAGATATAAGT
1 AATATAATATAA-AAAATATAAGT
*
11697501 AA-ATAATTATAAAATATATA
1 AATATAA-TATAAAAAATATA
11697521 TAATATGTAT
Statistics
Matches: 75, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
23 17 0.23
24 22 0.29
25 33 0.44
26 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (23 bp):
AATATAATATAAAAAATATAAGT
Found at i:11699653 original size:206 final size:206
Alignment explanation
Indices: 11699156--11700057 Score: 1324
Period size: 206 Copynumber: 4.4 Consensus size: 206
11699146 GGTCAAATTT
* *
11699156 GCTACGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTG
1 GCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATGCCAAATCATCTTGGATCTGCTTCAGT-
* * * * *
11699221 A-AATCATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCCGTCAAATATGGAGACGCCAAACTT
65 ATAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCCATCGAATATGGAGATGCCAGACTT
* * *
11699285 CGATTTTTTCTCTGACAATACAGAAATGTCAAATCATCTT--A---G----A-CGTAAGCACGTG
130 CGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTCGCTTCAGCGTAAGCACGTG
11699340 AAAGCCAAATCA
195 AAAGCCAAATCA
* ** *
11699352 ACTATGTCTTCGATTTGTTCCTTGTGAA-CACAAGAATATCAAATCATCTTGGATCTACTTCAGT
1 GCTATGTCTTCGATTTGTTCCTTGT-AAGCACAAGAATGCCAAATCATCTTGGATCTGCTTCAGT
*
11699416 ATAAACATTTGAAGGTGAGATCTGCTATGTATCTGCTCTCCATCGAATATGGAGATGCCAGACTT
65 ATAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCCATCGAATATGGAGATGCCAGACTT
* *
11699481 CGATTTTTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTTGCTTCAGCGTAAGCACGTG
130 CGATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTCGCTTCAGCGTAAGCACGTG
*
11699546 AAAGCCAAATTA
195 AAAGCCAAATCA
* * * *
11699558 GCTATGTCTTCGATTCGCTCCTTGTAAGCACAAGGATGCCAAATCATCTTGGATCTTCTTCAGTA
1 GCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTA
* ***
11699623 TAAACATCTGAAGGTGGGATCCATTATGTATCTGCTCTCCATCGAATATGGAGATGCCAGACTTC
66 TAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCCATCGAATATGGAGATGCCAGACTTC
* * *
11699688 AATTTGTTCTCTGACAATACAGAGATACCAAATCATCTTAGATTCGCTTCAGCGTAAGCACGTTA
131 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTCGCTTCAGCGTAAGCACGTGA
11699753 AAGCCAAATCA
196 AAGCCAAATCA
* *
11699764 GCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATGTCAAACCATCTTGGATCTGCTTCAGTA
1 GCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTA
* * * *
11699829 TAATCATCTGAAGGTGAGATCTGCTATGTATCTGCTCTTCGTCGAATATGGAGATACCAGACTTC
66 TAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCCATCGAATATGGAGATGCCAGACTTC
*
11699894 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTCGCTTCAGCGTAAACACGTGA
131 GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTCGCTTCAGCGTAAGCACGTGA
11699959 AAGCCAAATCA
196 AAGCCAAATCA
* * * *
11699970 GTTATGTCTTCGATTTGTTCCTTGTAAGCACAAGGATACCAAACCATCTTGGATCTGCTTCAGTA
1 GCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTA
**
11700035 TAAACATCTGAAGGCCAGATCTG
66 TAAACATCTGAAGGTGAGATCTG
11700058 TTGTGTTGCT
Statistics
Matches: 636, Mismatches: 57, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
195 1 0.00
196 151 0.24
197 2 0.00
198 1 0.00
201 1 0.00
205 3 0.00
206 477 0.75
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (206 bp):
GCTATGTCTTCGATTTGTTCCTTGTAAGCACAAGAATGCCAAATCATCTTGGATCTGCTTCAGTA
TAAACATCTGAAGGTGAGATCTGCTATGTATCTGCTCTCCATCGAATATGGAGATGCCAGACTTC
GATTTGTTCTCTGACAATACAGAGATGCCAAATCATCTTAGATTCGCTTCAGCGTAAGCACGTGA
AAGCCAAATCA
Found at i:11711696 original size:16 final size:16
Alignment explanation
Indices: 11711643--11711696 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
11711633 TAACAATGTG
*
11711643 AATAATAATATACATGA
1 AATAATAATA-ATATGA
*
11711660 AAAAATATATAATA-G-
1 AATAATA-ATAATATGA
11711675 -ATAATAATAATATGA
1 AATAATAATAATATGA
11711690 AATAATA
1 AATAATA
11711697 TATTGTTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
13 6 0.20
14 6 0.20
16 7 0.23
17 8 0.27
18 3 0.10
ACGTcount: A:0.63, C:0.02, G:0.06, T:0.30
Consensus pattern (16 bp):
AATAATAATAATATGA
Found at i:11711822 original size:25 final size:23
Alignment explanation
Indices: 11711747--11711863 Score: 78
Period size: 25 Copynumber: 4.9 Consensus size: 23
11711737 ATGTGATAAA
*
11711747 AATATAATA-AATAAATAATAAGT
1 AATATAATATAAAAAAT-ATAAGT
** *
11711770 AATGAT-ATATGTTAAAATATATATT
1 AAT-ATAATAT-AAAAAATATA-AGT
*
11711795 AATATGATAATAAAAAATATGAAGT
1 AATATAAT-ATAAAAAATAT-AAGT
*
11711820 AATATAATATAATAAGATATAAGT
1 AATATAATATAA-AAAATATAAGT
*
11711844 AA-ATAATTATAAAATATATA
1 AATATAA-TATAAAAAATATA
11711864 TAATATGTAT
Statistics
Matches: 75, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
23 17 0.23
24 22 0.29
25 33 0.44
26 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (23 bp):
AATATAATATAAAAAATATAAGT
Done.