Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 134 of 141
Found at i:40272218 original size:87 final size:87
Alignment explanation
Indices: 40272044--40272207 Score: 233
Period size: 87 Copynumber: 1.9 Consensus size: 87
40272034 AAATTTAAAT
*
40272044 TCGGTGAATTCATCAAGTCCGTCTCAATATGACCACCCAAACTCTGGGATATGAACTCATTAAGA
1 TCGGTGAATTCATCAAGTCCGTCTCAATAGGACCACCCAAACTCTGGGATATGAACTCATTAAGA
40272109 GTAATAAACTCAACCTCACATG
66 GTAATAAACTCAACCTCACATG
* * * * * **
40272131 TCGGTGAATTCGTCAAGTCTGTCTCAATAGGACCACCCAATC-CTGTGATATGAATTTGTTAAGA
1 TCGGTGAATTCATCAAGTCCGTCTCAATAGGACCACCCAAACTCTGGGATATGAACTCATTAAGA
*
40272195 GTGAT-AACTCAAC
66 GTAATAAACTCAAC
40272208 ATTATACATG
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
85 8 0.12
86 22 0.32
87 38 0.56
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.27
Consensus pattern (87 bp):
TCGGTGAATTCATCAAGTCCGTCTCAATAGGACCACCCAAACTCTGGGATATGAACTCATTAAGA
GTAATAAACTCAACCTCACATG
Found at i:40277211 original size:44 final size:43
Alignment explanation
Indices: 40277158--40277247 Score: 128
Period size: 44 Copynumber: 2.1 Consensus size: 43
40277148 TTGCTTTAAC
*
40277158 TTTCCCACTTAAACTCTT-TTAAGTATAAGTTATTTTAATATTTG
1 TTTCCCACTTAAAATCTTATT-AGTATAAGTTATTTTAATA-TTG
* *
40277202 TTTCTCACTTAAAATCTTATTAGTGTAAGTTATTTTAATATTG
1 TTTCCCACTTAAAATCTTATTAGTATAAGTTATTTTAATATTG
40277245 TTT
1 TTT
40277248 GACCTACAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 6 0.14
44 34 0.81
45 2 0.05
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (43 bp):
TTTCCCACTTAAAATCTTATTAGTATAAGTTATTTTAATATTG
Found at i:40281766 original size:24 final size:24
Alignment explanation
Indices: 40281739--40281788 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
40281729 CGGGCTTAAG
40281739 GACTAAGTTGTGAAAATGTTAAAA
1 GACTAAGTTGTGAAAATGTTAAAA
40281763 GACTAAGTTGTGAAAATGTTAAAA
1 GACTAAGTTGTGAAAATGTTAAAA
40281787 GA
1 GA
40281789 GATGTAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.04, G:0.22, T:0.28
Consensus pattern (24 bp):
GACTAAGTTGTGAAAATGTTAAAA
Found at i:40287112 original size:43 final size:42
Alignment explanation
Indices: 40287064--40287171 Score: 119
Period size: 42 Copynumber: 2.5 Consensus size: 42
40287054 CAATGCCATA
* ** *
40287064 TCCCAGATATGGTCTTACATGTTATAATATATCGATGT-CACTT
1 TCCCAGACATGGTCTTACATGAAATAATATA-CGAT-TCCAATT
* * *
40287107 TCCCAGACAGGGTCTTACAAGAAATCATATACGATTCCAATT
1 TCCCAGACATGGTCTTACATGAAATAATATACGATTCCAATT
*
40287149 TCCCAGACATGTTCTTACATGAA
1 TCCCAGACATGGTCTTACATGAA
40287172 TTCACACCTT
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
41 1 0.02
42 28 0.52
43 25 0.46
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.32
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACATGAAATAATATACGATTCCAATT
Found at i:40293521 original size:17 final size:17
Alignment explanation
Indices: 40293499--40293534 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
40293489 CGATTGCATG
40293499 TTTCTATTGCTGTTTAT
1 TTTCTATTGCTGTTTAT
40293516 TTTCTATTGCTGTTTAT
1 TTTCTATTGCTGTTTAT
40293533 TT
1 TT
40293535 CCCTTTGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTCTATTGCTGTTTAT
Found at i:40293999 original size:32 final size:34
Alignment explanation
Indices: 40293936--40293999 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
40293926 TCTAATAATT
* *
40293936 TCACTATTATAAAACTATTTTCCTTAAAAGAATG
1 TCACTATTATAAAACCATTCTCCTTAAAAGAATG
40293970 TCAC-ATTATAAAACCATTCT-CTTAAAAGAA
1 TCACTATTATAAAACCATTCTCCTTAAAAGAA
40294000 AATCGAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 10 0.36
33 14 0.50
34 4 0.14
ACGTcount: A:0.44, C:0.17, G:0.05, T:0.34
Consensus pattern (34 bp):
TCACTATTATAAAACCATTCTCCTTAAAAGAATG
Found at i:40294891 original size:22 final size:21
Alignment explanation
Indices: 40294864--40294955 Score: 80
Period size: 23 Copynumber: 4.1 Consensus size: 21
40294854 AAATTGTTGC
* *
40294864 ATTTGTTTTGATATTGTTCTTG
1 ATTTGTTCTGAAATTGTT-TTG
40294886 ATTTGTTCTGAAATTGTTTTG
1 ATTTGTTCTGAAATTGTTTTG
*
40294907 A-TTGTCTGCTGGAAATTGTTATG
1 ATTTGT-T-CT-GAAATTGTTTTG
40294930 A-TTGTCTGCTGGAAATTGTTTTG
1 ATTTGT-T-CT-GAAATTGTTTTG
40294953 ATT
1 ATT
40294956 GTCTGCTGGA
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
20 4 0.06
21 5 0.08
22 18 0.29
23 34 0.55
24 1 0.02
ACGTcount: A:0.18, C:0.07, G:0.22, T:0.53
Consensus pattern (21 bp):
ATTTGTTCTGAAATTGTTTTG
Found at i:40294923 original size:23 final size:23
Alignment explanation
Indices: 40294895--40294970 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
40294885 GATTTGTTCT
40294895 GAAATTGTTTTGATTGTCTGCTG
1 GAAATTGTTTTGATTGTCTGCTG
*
40294918 GAAATTGTTATGATTGTCTGCTG
1 GAAATTGTTTTGATTGTCTGCTG
40294941 GAAATTGTTTTGATTGTCTGCTG
1 GAAATTGTTTTGATTGTCTGCTG
40294964 GAAATTG
1 GAAATTG
40294971 AATTTGTTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.08, G:0.26, T:0.45
Consensus pattern (23 bp):
GAAATTGTTTTGATTGTCTGCTG
Found at i:40301325 original size:92 final size:91
Alignment explanation
Indices: 40301168--40301376 Score: 287
Period size: 92 Copynumber: 2.3 Consensus size: 91
40301158 TTGATTTTAG
* * *
40301168 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAATTATTAAATTAT
* *
40301233 ATTTAAT-ATTAATTATTTTAAATTGTA
65 ATGTAATAATT-ATTATTTTAAATTATA
40301260 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAATTATTAAATTA
40301324 TATGTAATAATTATTATTTTAAATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
40301352 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
40301377 GTTATAATTA
Statistics
Matches: 105, Mismatches: 9, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
90 1 0.01
91 29 0.28
92 72 0.69
93 3 0.03
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAATTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:40301339 original size:24 final size:25
Alignment explanation
Indices: 40301304--40301351 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
40301294 TTATGAAATT
40301304 TAATATTAATTA-TTAAATTATATG
1 TAATATTAATTATTTAAATTATATG
40301328 TAATAATT-ATTATTTTAAATTATA
1 TAAT-ATTAATTA-TTTAAATTATA
40301352 CAAATTCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 3 0.14
26 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TAATATTAATTATTTAAATTATATG
Found at i:40301471 original size:59 final size:57
Alignment explanation
Indices: 40301403--40301591 Score: 145
Period size: 59 Copynumber: 3.2 Consensus size: 57
40301393 ATTTTATTAA
40301403 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTTTCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTTT-TTTTATAGT
* * ** * *
40301462 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTA-TTAAGAATTTTATTA-A--
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTAA-ATTTTTTTTATAGT
* * *
40301523 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTT-T-TTTTATAGT
40301582 ATCATATATT
1 ATCATATATT
40301592 ATGATTTGAG
Statistics
Matches: 99, Mismatches: 16, Indels: 30
0.68 0.11 0.21
Matches are distributed among these distances:
54 13 0.13
55 6 0.06
56 7 0.07
57 3 0.03
59 20 0.20
60 8 0.08
61 10 0.10
63 4 0.04
64 7 0.07
65 10 0.10
66 11 0.11
ACGTcount: A:0.41, C:0.03, G:0.04, T:0.51
Consensus pattern (57 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTTTTTTTATAGT
Found at i:40301516 original size:66 final size:63
Alignment explanation
Indices: 40301430--40301637 Score: 184
Period size: 66 Copynumber: 3.3 Consensus size: 63
40301420 AAATATATTT
*
40301430 AATATTAATTATTTCAAATTTTCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTA-TT-AAAATTT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
40301495 G
63 G
* * * * **
40301496 AATATTAATTATTAAGAATTTTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTAA-AATTTTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* * *
40301550 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TAAAATT-T-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
40301615 G
63 G
40301616 AATATTAATTATTAAGAATTTT
1 AATATTAATTATTAA-AATTTT
40301638 ATTAAATTAT
Statistics
Matches: 108, Mismatches: 19, Indels: 32
0.68 0.12 0.20
Matches are distributed among these distances:
54 14 0.13
55 7 0.06
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.09
60 8 0.07
61 10 0.09
62 1 0.01
63 3 0.03
64 8 0.07
65 13 0.12
66 25 0.23
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (63 bp):
AATATTAATTATTAAAATTTTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:40301530 original size:120 final size:120
Alignment explanation
Indices: 40301392--40301684 Score: 518
Period size: 120 Copynumber: 2.4 Consensus size: 120
40301382 AATTATTTTA
* * * *
40301392 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTT-TCTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT--AATTTATATT
40301455 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
64 TTATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
40301512 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
40301577 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
40301632 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
1 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT
40301685 TAAATATGAT
Statistics
Matches: 167, Mismatches: 4, Indels: 4
0.95 0.02 0.02
Matches are distributed among these distances:
119 5 0.03
120 160 0.96
121 2 0.01
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:40301552 original size:15 final size:15
Alignment explanation
Indices: 40301517--40301568 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40301507 TTAAGAATTT
*
40301517 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40301531 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40301545 TATTTAATAATAAT-
1 TATTTAATTATAATA
40301559 TATGTTAATT
1 TAT-TTAATT
40301569 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40301650 original size:61 final size:61
Alignment explanation
Indices: 40301465--40301652 Score: 201
Period size: 61 Copynumber: 3.1 Consensus size: 61
40301455 TTATAGTATC
40301465 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * *
40301526 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAGTAT
1 ATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
40301584 C
61 T
40301585 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
40301646 ATATATT
1 ATATATT
40301653 TTAATTATAA
Statistics
Matches: 97, Mismatches: 18, Indels: 24
0.70 0.13 0.17
Matches are distributed among these distances:
57 11 0.11
58 8 0.08
59 18 0.19
60 16 0.16
61 25 0.26
62 8 0.08
63 11 0.11
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:40301667 original size:16 final size:16
Alignment explanation
Indices: 40301646--40301687 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
40301636 TTATTAAATT
*
40301646 ATATATTTTAATTATA
1 ATATATTTTAATAATA
40301662 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
40301677 AT-TATGTTTAA
1 ATATAT-TTTAA
40301688 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:40301672 original size:15 final size:15
Alignment explanation
Indices: 40301637--40301678 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40301627 TTAAGAATTT
*
40301637 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40301651 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40301665 TATTTAATAATAAT
1 TATTTAATTATAAT
40301679 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40301717 original size:76 final size:75
Alignment explanation
Indices: 40301637--40301873 Score: 180
Period size: 75 Copynumber: 3.1 Consensus size: 75
40301627 TTAAGAATTT
*
40301637 TATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
1 TATT-AATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
40301702 TTTATTATTGA
65 TTTATTATTGA
* * ** * * **** * * *
40301713 TATTAATAATCTTATTAAAATTACAATA-A--CAATAATAATT-TACCAAAACAAAT-TTCTGCT
1 TATTAATTAT-ATATTTTAATTAAAATATATTTAATAATAATTAT-GTTTAA-ATATGAT-T--A
* ** *
40301773 AATTATTAAGAATT-T
60 AATTATTTATTATTGA
*
40301788 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAAATA
1 TATT-AATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
40301853 TTTATTATTGA
65 TTTATTATTGA
*
40301864 TAATAATTAT
1 TATTAATTAT
40301874 CTTATTAAAA
Statistics
Matches: 112, Mismatches: 36, Indels: 27
0.64 0.21 0.15
Matches are distributed among these distances:
72 1 0.01
73 13 0.12
74 4 0.04
75 39 0.35
76 37 0.33
77 4 0.04
78 13 0.12
79 1 0.01
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (75 bp):
TATTAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTAT
TTATTATTGA
Found at i:40301776 original size:151 final size:154
Alignment explanation
Indices: 40301621--40301931 Score: 520
Period size: 151 Copynumber: 2.0 Consensus size: 154
40301611 ATAAGAATAT
*
40301621 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
* *
40301686 AAATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAA-T-T-ACAATAACAATAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTATAACAATAACAATAA
*
40301748 TAATTTACCAAAACAAATTTCTGC
131 TAATTTACCAAAACAAATTTATGC
40301772 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
*
40301837 AAATATGATTAAAATATTTATTATTGATAATAATTATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAA-TT--ATAACAATAACAA
*
40301902 TAATCATTTACCAAAACAAATTTATGC
128 TAATAATTTACCAAAACAAATTTATGC
40301929 TAA
1 TAA
40301932 GGGTATTCTA
Statistics
Matches: 148, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
151 108 0.73
153 1 0.01
156 1 0.01
157 38 0.26
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (154 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTATAACAATAACAATAA
TAATTTACCAAAACAAATTTATGC
Found at i:40301812 original size:18 final size:17
Alignment explanation
Indices: 40301784--40301818 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40301774 ATTATTAAGA
*
40301784 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
40301801 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
40301819 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:40302074 original size:45 final size:44
Alignment explanation
Indices: 40301983--40302074 Score: 112
Period size: 45 Copynumber: 2.1 Consensus size: 44
40301973 ACCTCTATTC
* * *
40301983 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCAATA
*** *
40302027 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTAATCCAATA
40302072 CAT
1 CAT
40302075 CTCTAATCCA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 16 0.40
45 24 0.60
ACGTcount: A:0.36, C:0.28, G:0.05, T:0.30
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTAATCCAATA
Found at i:40302078 original size:16 final size:16
Alignment explanation
Indices: 40302054--40302089 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
40302044 GATTTGCTAT
40302054 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
40302070 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
40302086 TACA
1 TACA
40302090 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.39, C:0.33, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:40304161 original size:18 final size:18
Alignment explanation
Indices: 40304138--40304199 Score: 83
Period size: 18 Copynumber: 3.4 Consensus size: 18
40304128 ATTACATTCT
40304138 ATATCATTTGTCCTTTCA
1 ATATCATTTGTCCTTTCA
*
40304156 ATATCATTTG-CTATTTCA
1 ATATCATTTGTC-CTTTCA
40304174 ATATCATTT-TCCATTTCA
1 ATATCATTTGTCC-TTTCA
40304192 ATATCATT
1 ATATCATT
40304200 GTAATACCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
17 1 0.03
18 38 0.97
ACGTcount: A:0.27, C:0.19, G:0.03, T:0.50
Consensus pattern (18 bp):
ATATCATTTGTCCTTTCA
Found at i:40311045 original size:60 final size:60
Alignment explanation
Indices: 40310952--40311066 Score: 212
Period size: 60 Copynumber: 1.9 Consensus size: 60
40310942 GGTATCAATT
*
40310952 CCAAATCTCTATTCTGATTTTTTACACATTTCAAAACACAGAGGAATTGATTTTATAATA
1 CCAAATCTCTATTCTGACTTTTTACACATTTCAAAACACAGAGGAATTGATTTTATAATA
*
40311012 CCAAATCTTTATTCTGACTTTTTACACATTTCAAAACACAGAGGAATTGATTTTA
1 CCAAATCTCTATTCTGACTTTTTACACATTTCAAAACACAGAGGAATTGATTTTA
40311067 AAACTTGATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (60 bp):
CCAAATCTCTATTCTGACTTTTTACACATTTCAAAACACAGAGGAATTGATTTTATAATA
Found at i:40314592 original size:101 final size:101
Alignment explanation
Indices: 40314410--40314611 Score: 269
Period size: 101 Copynumber: 2.0 Consensus size: 101
40314400 AATTAACTTA
* * * * * *
40314410 TCAAATGTAGCGGTATGGAGATCCTAATTGAATTCTCGATTATTCTTTGCATCGGGTGAGGGGTG
1 TCAAATGTAGCGGTAAGGAGATCCTAATTGAATTATCAATTATTCTTTGCATCAGGTAAAGGGTG
* * * *
40314475 TTACAATAGTGCATATTGTGTTCCCCTTATTTGAAC
66 TTACAACAGTGAATATTGTGCTCCACTTATTTGAAC
* * * *
40314511 TCAAATGTAGGGGTAAGGAGATCCTAATTGAATTATTAATTATTGTTTGCATCAGGTAAAGGTTG
1 TCAAATGTAGCGGTAAGGAGATCCTAATTGAATTATCAATTATTCTTTGCATCAGGTAAAGGGTG
*
40314576 TTACAACAGTGAATATTTTGCTCCACTTATTTGAAC
66 TTACAACAGTGAATATTGTGCTCCACTTATTTGAAC
40314612 ATCATTTTAT
Statistics
Matches: 86, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
101 86 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (101 bp):
TCAAATGTAGCGGTAAGGAGATCCTAATTGAATTATCAATTATTCTTTGCATCAGGTAAAGGGTG
TTACAACAGTGAATATTGTGCTCCACTTATTTGAAC
Found at i:40315411 original size:42 final size:43
Alignment explanation
Indices: 40315303--40315520 Score: 186
Period size: 42 Copynumber: 5.2 Consensus size: 43
40315293 GTGAAAAAAT
* *
40315303 GCCGCTAAAGATCATGATTTTTAGCGGCGCTTTTACCTA-AAAC
1 GCCGCTAAAGATCATGATCTTTAGCGGCGCTTTTATC-ACAAAC
40315346 GCCGCTAAAAGA-CATGA-CATTTAGCGGCGCTTTTA-CACAAAC
1 GCCGCT-AAAGATCATGATC-TTTAGCGGCGCTTTTATCACAAAC
* * * *
40315388 GCCGCTAAAGATCGTGGTCTTTAGCGGTGCTTTTATCAAAAAC
1 GCCGCTAAAGATCATGATCTTTAGCGGCGCTTTTATCACAAAC
* * * * * *
40315431 -ACGCTAAAAATCATGACCTTTAGCGGCACTTCTATTACAAAC
1 GCCGCTAAAGATCATGATCTTTAGCGGCGCTTTTATCACAAAC
* * * *
40315473 GCCG-T-TATAT-AGGA-CTTTTAGCGACGCTTTT-TCACAAAC
1 GCCGCTAAAGATCATGATC-TTTAGCGGCGCTTTTATCACAAAC
40315512 GCCGCTAAA
1 GCCGCTAAA
40315521 AACATACTTT
Statistics
Matches: 141, Mismatches: 24, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
39 12 0.09
40 16 0.11
41 10 0.07
42 62 0.44
43 36 0.26
44 5 0.04
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (43 bp):
GCCGCTAAAGATCATGATCTTTAGCGGCGCTTTTATCACAAAC
Found at i:40315471 original size:85 final size:85
Alignment explanation
Indices: 40315303--40315476 Score: 217
Period size: 85 Copynumber: 2.0 Consensus size: 85
40315293 GTGAAAAAAT
* * *
40315303 GCCGCTAAAGATCATGATTTTTAGCGGCGCTTTTACCTAAAACGCCGCTAAAAGACATGACATTT
1 GCCGCTAAAGATCATGATCTTTAGCGGCGCTTTTACCAAAAACGACGCTAAAAGACATGACATTT
* *
40315368 AGCGGCGCTTTTACACAAAC
66 AGCGGCACTTCTACACAAAC
* * * * *
40315388 GCCGCTAAAGATCGTGGTCTTTAGCGGTGCTTTTATCAAAAAC-ACGCTAAAA-ATCATGACCTT
1 GCCGCTAAAGATCATGATCTTTAGCGGCGCTTTTACCAAAAACGACGCTAAAAGA-CATGACATT
*
40315451 TAGCGGCACTTCTATTACAAAC
65 TAGCGGCACTTCTA-CACAAAC
40315473 GCCG
1 GCCG
40315477 TTATATAGGA
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
83 1 0.01
84 28 0.37
85 47 0.62
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (85 bp):
GCCGCTAAAGATCATGATCTTTAGCGGCGCTTTTACCAAAAACGACGCTAAAAGACATGACATTT
AGCGGCACTTCTACACAAAC
Found at i:40319659 original size:21 final size:21
Alignment explanation
Indices: 40319634--40319677 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
40319624 ATTGGGCTGT
* *
40319634 TACACTCCACCTGTTTTGGAG
1 TACACTCCACCTGCTGTGGAG
40319655 TACACTCCACCTGCTGTGGAG
1 TACACTCCACCTGCTGTGGAG
40319676 TA
1 TA
40319678 TTGCTCGTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (21 bp):
TACACTCCACCTGCTGTGGAG
Found at i:40323203 original size:185 final size:185
Alignment explanation
Indices: 40322891--40323260 Score: 713
Period size: 185 Copynumber: 2.0 Consensus size: 185
40322881 ACCATTTATG
40322891 GGCTGAATCAGTTTCCAAACAAGGTCTGCTAATTTTAGCTTTGGCTACTACAAGTTTCTAATATA
1 GGCTGAATCAGTTTCCAAACAAGGTCTGCTAATTTTAGCTTTGGCTACTACAAGTTTCTAATATA
*
40322956 TCATCACCTAATAAAACGGAGCCACTAAGAAAAACTTTAAATTGCAGAAAAGCATGATATAATAA
66 TCATCACCTAATAAAACGGAGCCACTAAGAAAAAATTTAAATTGCAGAAAAGCATGATATAATAA
*
40323021 TTGTCTGGTTAAAGCTCAAAATTTCTCTCTATTAACATATTAAGAGATGGATGTC
131 TTGTCAGGTTAAAGCTCAAAATTTCTCTCTATTAACATATTAAGAGATGGATGTC
*
40323076 GGCTGAATCAGTTTCCAAACGAGGTCTGCTAATTTTAGCTTTGGCTACTACAAGTTTCTAATATA
1 GGCTGAATCAGTTTCCAAACAAGGTCTGCTAATTTTAGCTTTGGCTACTACAAGTTTCTAATATA
40323141 TCATCACCTAATAAAACGGAGCCACTAAGAAAAAATTTAAATTGCAGAAAAGCATGATATAATAA
66 TCATCACCTAATAAAACGGAGCCACTAAGAAAAAATTTAAATTGCAGAAAAGCATGATATAATAA
40323206 TTGTCAGGTTAAAGCTCAAAATTTCTCTCTATTAACATATTAAGAGATGGATGTC
131 TTGTCAGGTTAAAGCTCAAAATTTCTCTCTATTAACATATTAAGAGATGGATGTC
40323261 AAATTAAGAA
Statistics
Matches: 182, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
185 182 1.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.31
Consensus pattern (185 bp):
GGCTGAATCAGTTTCCAAACAAGGTCTGCTAATTTTAGCTTTGGCTACTACAAGTTTCTAATATA
TCATCACCTAATAAAACGGAGCCACTAAGAAAAAATTTAAATTGCAGAAAAGCATGATATAATAA
TTGTCAGGTTAAAGCTCAAAATTTCTCTCTATTAACATATTAAGAGATGGATGTC
Found at i:40326945 original size:26 final size:25
Alignment explanation
Indices: 40326905--40326974 Score: 88
Period size: 26 Copynumber: 2.8 Consensus size: 25
40326895 ACTAATTAAT
*
40326905 CTAAAT-CTTAAACCCTAACCTGACC
1 CTAAATCCCTAAACCCTAACCTGA-C
40326930 CTAAATCCCTAAACCCTAACCTGAC
1 CTAAATCCCTAAACCCTAACCTGAC
* *
40326955 CTCGAATCCCTAACCCCTAA
1 CT-AAATCCCTAAACCCTAA
40326975 ACATTATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
25 9 0.22
26 31 0.77
ACGTcount: A:0.34, C:0.40, G:0.04, T:0.21
Consensus pattern (25 bp):
CTAAATCCCTAAACCCTAACCTGAC
Found at i:40326984 original size:108 final size:103
Alignment explanation
Indices: 40326859--40327051 Score: 296
Period size: 108 Copynumber: 1.8 Consensus size: 103
40326849 ACCACTAAGT
* *
40326859 ACCCCTAAACCTTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCTTAAACCCTAAC
1 ACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAA-CCTAAACCCTAAC
*
40326924 CTGACCCTAAATCCCTAAACCCTAACCTGACCTCGAATCCCTA
65 CT----CTAAATCCATAAACCCTAACCTGACCTCGAATCCCTA
* *
40326967 ACCCCTAAACATTATTTAATATATAAATTAAAACACACTAATTAATCTAAACCTAACCCCTAACC
1 ACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCTAAACCCTAACC
40327032 TCTAAATCCATAAACCCTAA
66 TCTAAATCCATAAACCCTAA
40327052 ATCCCTAACT
Statistics
Matches: 80, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
103 18 0.22
107 13 0.16
108 49 0.61
ACGTcount: A:0.43, C:0.28, G:0.02, T:0.27
Consensus pattern (103 bp):
ACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACCTAAACCCTAACC
TCTAAATCCATAAACCCTAACCTGACCTCGAATCCCTA
Found at i:40327049 original size:22 final size:20
Alignment explanation
Indices: 40327012--40327051 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
40327002 CACTAATTAA
*
40327012 TCTAAACCTAACCCCTAACC
1 TCTAAACCTAAACCCTAACC
40327032 TCTAAATCCATAAACCCTAA
1 TCTAAA-CC-TAAACCCTAA
40327052 ATCCCTAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 2 0.12
22 9 0.53
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.23
Consensus pattern (20 bp):
TCTAAACCTAAACCCTAACC
Found at i:40327159 original size:14 final size:15
Alignment explanation
Indices: 40327142--40327174 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
40327132 CTTAAATCAG
40327142 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
40327156 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
40327171 AATC
1 AATC
40327175 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:40327832 original size:41 final size:41
Alignment explanation
Indices: 40327787--40327974 Score: 227
Period size: 41 Copynumber: 4.5 Consensus size: 41
40327777 AATTTTTTTT
* **
40327787 ATTAGCAGCGCTTTTTCAAAAACGCCGCTAAAGGTTAGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGC
* **
40327828 ATTAGCGGCGC-TATTCAAAAACGCCCGCTAAAGGCTGGAGC
1 ATTAGCGGCGCTTTTTCAAAAACG-CCGCTAAAGGCCAGAGC
* *
40327869 ATTAGTGGCG-TTTCTTCAAAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTT-TTC--AAAAACGCCGCTAAAGGCCAGAGC
** *
40327912 ATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGGCCAGAGA
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGC
40327953 ATTAGCGGCGCTTTTTCAAAAA
1 ATTAGCGGCGCTTTTTCAAAAA
40327975 TCAGTTAAAG
Statistics
Matches: 126, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
40 11 0.09
41 77 0.61
42 3 0.02
43 25 0.20
44 10 0.08
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGC
Found at i:40327900 original size:84 final size:83
Alignment explanation
Indices: 40327787--40327974 Score: 240
Period size: 84 Copynumber: 2.3 Consensus size: 83
40327777 AATTTTTTTT
* **
40327787 ATTAGCAGCGCTTTTTC--AAAAACGCCGCTAAAGGTTAGAGCATTAGCGGCGCTATT-CAAAAA
1 ATTAGCGGCGCTTTTTCAAAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCT-TTCCAAAAA
** *
40327849 CGCCCGCTAAAGGCTGGAGC
65 CG-CCGCTAAAGGCCAGAGA
* *
40327869 ATTAGTGGCG-TTTCTTCAAAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCGCTTTCCCAAAA
1 ATTAGCGGCGCTTT-TTCAAAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTT-CCAAAA
40327933 ACGCCGCTAAAGGCCAGAGA
64 ACGCCGCTAAAGGCCAGAGA
40327953 ATTAGCGGCGCTTTTTCAAAAA
1 ATTAGCGGCGCTTTTTCAAAAA
40327975 TCAGTTAAAG
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
81 3 0.03
82 11 0.12
83 2 0.02
84 64 0.70
85 11 0.12
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.21
Consensus pattern (83 bp):
ATTAGCGGCGCTTTTTCAAAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTTCCAAAAAC
GCCGCTAAAGGCCAGAGA
Found at i:40328148 original size:40 final size:39
Alignment explanation
Indices: 40328042--40328175 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 39
40328032 GCGCTTTTCA
* *
40328042 AAAAACGCCGCTAATGCTT-ATTTTTAGCGCTGTTTTCCA-
1 AAAAGCGCCGCTAATGCTTGATTTTTAGCGC-GTTTT-TAT
* **
40328081 AAAAGCGCCGCTAATGCTCGACCTTTAGCGACGTTTTTAT
1 AAAAGCGCCGCTAATGCTTGATTTTTAGCG-CGTTTTTAT
*
40328121 AAAAGCGCCGCTAATGCTTGATTTTTAGTGGCGTTTTTTAT
1 AAAAGCGCCGCTAATGCTTGATTTTTAG-CGCG-TTTTTAT
*
40328162 CCAAA-CGCCGCTAA
1 -AAAAGCGCCGCTAA
40328176 AAGCCTGTTT
Statistics
Matches: 79, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
39 18 0.23
40 40 0.51
41 18 0.23
42 3 0.04
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (39 bp):
AAAAGCGCCGCTAATGCTTGATTTTTAGCGCGTTTTTAT
Found at i:40333314 original size:30 final size:29
Alignment explanation
Indices: 40333237--40333337 Score: 105
Period size: 30 Copynumber: 3.4 Consensus size: 29
40333227 AATCAGTTTG
* * * * *
40333237 GGCCTGAGCCCTATACAATAGCAGTGTGTG
1 GGCCTTAGCCCAATACAGTA-CAGAGTGTA
*
40333267 GGCCATAGCCCAATACAGTATCAGAGTGTA
1 GGCCTTAGCCCAATACAGTA-CAGAGTGTA
*
40333297 GGCCTTAGCCCAATACAGTA-ATAGTGTA
1 GGCCTTAGCCCAATACAGTACAGAGTGTA
*
40333325 GGCCTTATCCCAA
1 GGCCTTAGCCCAA
40333338 AATAGTAATC
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
28 19 0.31
30 42 0.69
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.23
Consensus pattern (29 bp):
GGCCTTAGCCCAATACAGTACAGAGTGTA
Found at i:40333331 original size:28 final size:28
Alignment explanation
Indices: 40333262--40333346 Score: 98
Period size: 28 Copynumber: 3.0 Consensus size: 28
40333252 CAATAGCAGT
* * *
40333262 GTGTGGGCCATAGCCCAATACAGTATCAGA
1 GTGTAGGCCTTAGCCCAATACAGTA--ATA
40333292 GTGTAGGCCTTAGCCCAATACAGTAATA
1 GTGTAGGCCTTAGCCCAATACAGTAATA
* * *
40333320 GTGTAGGCCTTATCCCAAAATAGTAAT
1 GTGTAGGCCTTAGCCCAATACAGTAAT
40333347 CAGTACAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
28 26 0.53
30 23 0.47
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (28 bp):
GTGTAGGCCTTAGCCCAATACAGTAATA
Found at i:40333491 original size:26 final size:26
Alignment explanation
Indices: 40333462--40333528 Score: 116
Period size: 26 Copynumber: 2.6 Consensus size: 26
40333452 AATATCGCAA
40333462 CAAAGCTGCCAGTATCAGTAATGCAG
1 CAAAGCTGCCAGTATCAGTAATGCAG
*
40333488 CAAAGCTGCCAGTAACAGTAATGCAG
1 CAAAGCTGCCAGTATCAGTAATGCAG
*
40333514 CAAAGCTGCAAGTAT
1 CAAAGCTGCCAGTAT
40333529 TAATATTGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.18
Consensus pattern (26 bp):
CAAAGCTGCCAGTATCAGTAATGCAG
Found at i:40333772 original size:27 final size:27
Alignment explanation
Indices: 40333742--40333801 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
40333732 CATCTCCTAG
* *
40333742 GGGTATAACGGTTATTTTACCCTTC-A
1 GGGTATAACAGTAATTTTACCCTTCGA
**
40333768 TGGGTATTTCAGTAATTTTACCCTTCGA
1 -GGGTATAACAGTAATTTTACCCTTCGA
40333796 GGGTAT
1 GGGTAT
40333802 TTCGATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 27 0.96
28 1 0.04
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (27 bp):
GGGTATAACAGTAATTTTACCCTTCGA
Found at i:40333802 original size:27 final size:27
Alignment explanation
Indices: 40333750--40333996 Score: 208
Period size: 27 Copynumber: 9.4 Consensus size: 27
40333740 AGGGGTATAA
*
40333750 CGGTTATTTTACCCTTC-ATGGGTATTT
1 CGGTAATTTTACCCTTCGA-GGGTATTT
*
40333777 CAGTAATTTTACCCTTCGAGGGTATTT
1 CGGTAATTTTACCCTTCGAGGGTATTT
* * * *
40333804 CGATAATTTTATTCATT-AAGGGTATTT
1 CGGTAATTTTA-CCCTTCGAGGGTATTT
* *
40333831 CGATAATTTTACCCTT-TAGAGGTATTT
1 CGGTAATTTTACCCTTCGAG-GGTATTT
**
40333858 CGGTAATTTTACCCTTTAAGGGTATTT
1 CGGTAATTTTACCCTTCGAGGGTATTT
*
40333885 TGGTAATTTTACCCATT-GAGGGTATTT
1 CGGTAATTTTACCC-TTCGAGGGTATTT
** * * *
40333912 CAATAATTTTATCCTTGGAGGATATTT
1 CGGTAATTTTACCCTTCGAGGGTATTT
*
40333939 TGGTAATTTTA-CC--C-A--GTATTT
1 CGGTAATTTTACCCTTCGAGGGTATTT
*
40333960 CGGTAATTTTACCCATCGAGGGTATTT
1 CGGTAATTTTACCCTTCGAGGGTATTT
**
40333987 TAGTAATTTT
1 CGGTAATTTT
40333997 CCCACGAATT
Statistics
Matches: 181, Mismatches: 27, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
21 15 0.08
22 2 0.01
23 1 0.01
24 1 0.01
25 1 0.01
26 9 0.05
27 144 0.80
28 8 0.04
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (27 bp):
CGGTAATTTTACCCTTCGAGGGTATTT
Found at i:40333880 original size:81 final size:81
Alignment explanation
Indices: 40333755--40333996 Score: 248
Period size: 81 Copynumber: 3.1 Consensus size: 81
40333745 TATAACGGTT
* * * **
40333755 ATTTTACCCTTCATG-GGTATTTCAGTAATTTTACCCTTCGAGGGTATTTCGATAATTTTATTCA
1 ATTTTACCCTTTA-GAGGTATTTCGGTAATTTTACCCTTCAAGGGTATTTCGATAATTTTACCCA
*
40333819 TTAAGGGTATTTCGATA
65 TTAAGGGTATTTCAATA
* * *
40333836 ATTTTACCCTTTAGAGGTATTTCGGTAATTTTACCCTTTAAGGGTATTTTGGTAATTTTACCCAT
1 ATTTTACCCTTTAGAGGTATTTCGGTAATTTTACCCTTCAAGGGTATTTCGATAATTTTACCCAT
*
40333901 TGAGGGTATTTCAATA
66 TAAGGGTATTTCAATA
* * * *
40333917 ATTTTATCC-TTGGAGGATATTTTGGTAATTTTA-CC--C-A--GTATTTCGGTAATTTTACCCA
1 ATTTTACCCTTTAGAGG-TATTTCGGTAATTTTACCCTTCAAGGGTATTTCGATAATTTTACCCA
** * *
40333975 TCGAGGGTATTTTAGTA
65 TTAAGGGTATTTCAATA
40333992 ATTTT
1 ATTTT
40333997 CCCACGAATT
Statistics
Matches: 141, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
75 39 0.28
77 1 0.01
80 9 0.06
81 92 0.65
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (81 bp):
ATTTTACCCTTTAGAGGTATTTCGGTAATTTTACCCTTCAAGGGTATTTCGATAATTTTACCCAT
TAAGGGTATTTCAATA
Found at i:40333964 original size:21 final size:21
Alignment explanation
Indices: 40333934--40333974 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
40333924 CCTTGGAGGA
*
40333934 TATTTTGGTAATTTTACCCAG
1 TATTTCGGTAATTTTACCCAG
40333955 TATTTCGGTAATTTTACCCA
1 TATTTCGGTAATTTTACCCA
40333975 TCGAGGGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.46
Consensus pattern (21 bp):
TATTTCGGTAATTTTACCCAG
Found at i:40337705 original size:50 final size:50
Alignment explanation
Indices: 40337578--40337874 Score: 307
Period size: 50 Copynumber: 5.8 Consensus size: 50
40337568 GATAGTAACA
* * *
40337578 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATG-TTTCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-GCTCTCATAT-CGG
* * *
40337627 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGG
* * *
40337677 TGCCCATGCCATGTCCCAGACATAGTCTTAC--GGGAGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAG--CTCTCATATCGG
* * * *
40337727 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGG
* * * *
40337777 TGCCAATTCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCAT-A--TC--GG
*
40337832 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCT
40337875 TTACCCAAAT
Statistics
Matches: 209, Mismatches: 26, Indels: 19
0.82 0.10 0.07
Matches are distributed among these distances:
48 7 0.03
49 40 0.19
50 116 0.56
52 4 0.02
53 2 0.01
55 2 0.01
56 38 0.18
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGG
Found at i:40346347 original size:13 final size:13
Alignment explanation
Indices: 40346331--40346360 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
40346321 ATTGTCATGT
40346331 AATTGTTTTTCTG
1 AATTGTTTTTCTG
40346344 AATTGTTTTTCTG
1 AATTGTTTTTCTG
40346357 AATT
1 AATT
40346361 TAGCTGATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.07, G:0.13, T:0.60
Consensus pattern (13 bp):
AATTGTTTTTCTG
Found at i:40347328 original size:82 final size:81
Alignment explanation
Indices: 40347237--40347486 Score: 186
Period size: 82 Copynumber: 3.1 Consensus size: 81
40347227 CATATAAGAA
*
40347237 TATTAATTATTAAGAATTTTATTAAATTATATATTTTAAGTATAATATATTTAATAATAATTATG
1 TATTTATTATTAAGAATTTTATTAAATTATATATTTTAA-TATAATATATTTAATAATAATTATG
40347302 TTTAAATATGATTAAAT
65 TTTAAATATGATTAAAT
* * * * * * * *
40347319 TATTTATTATT---CATATTAATAATCTTATCAAAATTTAA-ATAACA-A--TAACAATAA-TA-
1 TATTTATTATTAAGAATTTTATTAA-ATTAT-ATATTTTAATATAATATATTTAATAATAATTAT
* *
40347375 ATTTACCAA-A--A-CAAAT
64 GTTTA--AATATGATTAAAT
* *
40347391 T-TCTGGTAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATGTTTAATAATAAT
1 TAT-T--T-ATTATTAAGAATTTTATTAAATTATATATTTTAA-TATAATATATTTAATAATAAT
*
40347455 TATGTTTAAATATGATTAAAA
61 TATGTTTAAATATGATTAAAT
40347476 TATTTATTATT
1 TATTTATTATT
40347487 GATAATAATA
Statistics
Matches: 121, Mismatches: 24, Indels: 46
0.63 0.13 0.24
Matches are distributed among these distances:
71 1 0.01
72 6 0.05
73 1 0.01
74 5 0.04
75 9 0.07
76 17 0.14
77 4 0.03
78 13 0.11
79 13 0.11
80 4 0.03
81 17 0.14
82 19 0.16
83 5 0.04
84 1 0.01
85 5 0.04
86 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (81 bp):
TATTTATTATTAAGAATTTTATTAAATTATATATTTTAATATAATATATTTAATAATAATTATGT
TTAAATATGATTAAAT
Found at i:40347406 original size:157 final size:157
Alignment explanation
Indices: 40347240--40347549 Score: 539
Period size: 157 Copynumber: 2.0 Consensus size: 157
40347230 ATAAGAATAT
*
40347240 TAATTATTAAGAATTTTATTAAATTATATATTTTAAGTATAATATATTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAAGTAAAATATATTTAATAATAATTATGTTT
* *
40347305 AAATATGATTAAATTATTTATTATTCATATTAATAATCTTATCAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTCATAATAATAATCTTATCAAAATTTAAATAACAATAACAA
*
40347370 TAATAATTTACCAAAACAAATTTCTGG
131 CAATAATTTACCAAAACAAATTTCTGG
* *
40347397 TAATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATGTTTAATAATAATTATGTTT
1 TAATTATTAAGAATTTTATTAAATTATATATTTTAAGTAAAATATATTTAATAATAATTATGTTT
* *
40347462 AAATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAA
66 AAATATGATTAAAATATTTATTATTCATAATAATAATCTTATCAAAATTTAAATAACAATAACAA
*
40347527 CAATCATTTACCAAAACAAATTT
131 CAATAATTTACCAAAACAAATTT
40347550 ATGCTAAGGG
Statistics
Matches: 144, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
157 144 1.00
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (157 bp):
TAATTATTAAGAATTTTATTAAATTATATATTTTAAGTAAAATATATTTAATAATAATTATGTTT
AAATATGATTAAAATATTTATTATTCATAATAATAATCTTATCAAAATTTAAATAACAATAACAA
CAATAATTTACCAAAACAAATTTCTGG
Found at i:40347700 original size:16 final size:16
Alignment explanation
Indices: 40347679--40347746 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
40347669 GATTTGCTAT
* *
40347679 TACACCTTTAATCTAA
1 TACACCTCTAATCCAA
40347695 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
40347711 TACACTTCTAATCCAA
1 TACACCTCTAATCCAA
40347727 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
40347743 TACA
1 TACA
40347747 GCGAACCAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.38, C:0.32, G:0.00, T:0.29
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:40350870 original size:26 final size:25
Alignment explanation
Indices: 40350814--40350870 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
40350804 TTAATATTTC
* *
40350814 AAATATTATATATTTACAACAGTAA
1 AAATAATATAAATTTACAACAGTAA
40350839 ATAATAATATAAATTTA-AATCAGTACA
1 A-AATAATATAAATTTACAA-CAGTA-A
40350866 AAATA
1 AAATA
40350871 TAACGAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 3 0.11
26 22 0.81
27 2 0.07
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (25 bp):
AAATAATATAAATTTACAACAGTAA
Found at i:40357327 original size:11 final size:12
Alignment explanation
Indices: 40357297--40357330 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
40357287 CAGCTTGCCC
40357297 ATATTAATTTTT
1 ATATTAATTTTT
40357309 ATATTAATTTTT
1 ATATTAATTTTT
40357321 ATA-TAATTTT
1 ATATTAATTTT
40357331 AAAATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:40357478 original size:30 final size:30
Alignment explanation
Indices: 40357435--40357493 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
40357425 CTCAACAATA
40357435 AAATGCTTCTAAAATAATAA-AAGAATTAAT
1 AAATGCTTCTAAAATAATAACAA-AATTAAT
40357465 AAATGTCTT-TAAAATAATAACAAAATTAA
1 AAATG-CTTCTAAAATAATAACAAAATTAA
40357494 CAATAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.31
Consensus pattern (30 bp):
AAATGCTTCTAAAATAATAACAAAATTAAT
Found at i:40363518 original size:114 final size:113
Alignment explanation
Indices: 40363347--40363559 Score: 306
Period size: 114 Copynumber: 1.9 Consensus size: 113
40363337 AAAATAAGCA
** * *
40363347 TTAGCGGAGTTTTTCAGAAAGTGCCGCAAAAAACCTAAGCCCAATGACGCCGTTTTCTGAG-CTT
1 TTAGCGGAGTTTTTCAGAAAGTGCCGCAAAAAACCTAAGCCCAACAACCCCATTTTCTG-GCCTT
40363411 TCGGGGATTTAGCGGCGTTTTT-AGGAAAGCGCCGCTAATTGTCAGGGCT
65 TCGGGGATTTAGCGGCGTTTTTGAGG-AAGCGCCGCTAATTGTCAGGGCT
* * *
40363460 TTAGCGGCGTTTTTGATAAAGCT-CCGCAAAAAAACCTAAGCCCAACAACCCCATTTTCTGGCCT
1 TTAGCGGAGTTTTTCAGAAAG-TGCCGC-AAAAAACCTAAGCCCAACAACCCCATTTTCTGGCCT
40363524 TTCGGGGATTTAGCGGCGTTTTTGAGGAAGCGCCGC
64 TTCGGGGATTTAGCGGCGTTTTTGAGGAAGCGCCGC
40363560 AAAGAAACAT
Statistics
Matches: 89, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
113 23 0.26
114 63 0.71
115 3 0.03
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (113 bp):
TTAGCGGAGTTTTTCAGAAAGTGCCGCAAAAAACCTAAGCCCAACAACCCCATTTTCTGGCCTTT
CGGGGATTTAGCGGCGTTTTTGAGGAAGCGCCGCTAATTGTCAGGGCT
Found at i:40363590 original size:73 final size:73
Alignment explanation
Indices: 40363459--40363630 Score: 220
Period size: 73 Copynumber: 2.3 Consensus size: 73
40363449 TTGTCAGGGC
* * *
40363459 TTTAGCGGCGTTTTTGATAAAGCTCCGCAAAAAAACCTAAGCCCAACAACCCCATTTTCTG-GCC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACAACCCCATTTTCTGAG-C
40363523 TTTCGGGGA
65 TTTCGGGGA
* * ** * * *
40363532 TTTAGCGGCGTTTTTGAGGAAGCGCCGCAAAGAAACATAAGCCCAATGACGCCGTTTTCTGAGTT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACAACCCCATTTTCTGAGCT
40363597 TTCGGGGA
66 TTCGGGGA
*
40363605 TTTAGCGGCGTTTCTTAAGAAAGCGC
1 TTTAGCGGCGTTT-TTGAGAAAGCGC
40363631 TGCTAATGCT
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
73 74 0.87
74 11 0.13
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (73 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAAACATAAGCCCAACAACCCCATTTTCTGAGCT
TTCGGGGA
Found at i:40363723 original size:188 final size:186
Alignment explanation
Indices: 40363347--40363747 Score: 565
Period size: 188 Copynumber: 2.1 Consensus size: 186
40363337 AAAATAAGCA
* * * *
40363347 TTAGCGGAGTTTTTCAGAAAGTGCCGCAAAAAACCTAAGCCCAATGACGCCGTTTTCTGAGCTTT
1 TTAGCGGCGTTTTTCAGGAAGCGCCGCAAAAAACATAAGCCCAATGACGCCGTTTTCTGAGCTTT
* * *
40363412 CGGGGATTTAGCGGCGTTTTTAGGAAAGCGCCGCTAATTGTCAGGGCTTTAGCGGCGTTTTTGAT
66 CGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATTGTCAGGGATTTAGCGGCGTTTTTGAG
* * *
40363477 AAAGCTCCGCAAAAAAACCTAAGCCCAACAACCCCATTTTCTGGCCTTTCGGGGAT
131 AAAGCGCCGCAAAAAAACCTAAGCCCAACAACCCCATTTTCTAGCCTTTCGCGGAT
* *
40363533 TTAGCGGCGTTTTTGAGGAAGCGCCGCAAAGAAACATAAGCCCAATGACGCCGTTTTCTGAGTTT
1 TTAGCGGCGTTTTTCAGGAAGCGCCGCAAA-AAACATAAGCCCAATGACGCCGTTTTCTGAGCTT
* *
40363598 TCGGGGATTTAGCGGCGTTTCTTAAGAAAGCGCTGCTAA-TGCTGAGGGATTTAGCGGCGTTTTT
65 TCGGGGATTTAGCGGCGTTT-TTAAGAAAGCGCCGCTAATTG-TCAGGGATTTAGCGGCGTTTTT
* * *
40363662 GAGAAAGCGCCGCAAAATAAA-CTAAGCCCAACGACGCCGTTTTCTAAG-CTTTCGCGGAT
128 GAGAAAGCGCCGCAAAA-AAACCTAAGCCCAACAACCCCATTTTCT-AGCCTTTCGCGGAT
* *
40363721 TTAGTGGCGTTTTTTAGGAAGCGCCGC
1 TTAGCGGCGTTTTTCAGGAAGCGCCGC
40363748 TAATGCTCAG
Statistics
Matches: 191, Mismatches: 19, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
186 26 0.14
187 54 0.28
188 107 0.56
189 4 0.02
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (186 bp):
TTAGCGGCGTTTTTCAGGAAGCGCCGCAAAAAACATAAGCCCAATGACGCCGTTTTCTGAGCTTT
CGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATTGTCAGGGATTTAGCGGCGTTTTTGAG
AAAGCGCCGCAAAAAAACCTAAGCCCAACAACCCCATTTTCTAGCCTTTCGCGGAT
Found at i:40363802 original size:114 final size:115
Alignment explanation
Indices: 40363532--40364022 Score: 684
Period size: 115 Copynumber: 4.3 Consensus size: 115
40363522 CTTTCGGGGA
* * *
40363532 TTTAGCGGCGTTTTTGAGGAAGCGCCGCAAAGAA-ACATAAGCCCAATGACGCCGTTTTCTGAGT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAA-AAGACATAAGCCCAACGACGCCGTTTTCTGAGC
* * * * * *
40363596 TTTCGGGGATTTAGCGGCGTTTCTTAAGAAAGCGCTGCTAATGCTGAGGGA
65 TTTCGGGGATTTAACGGCGTTTTTTAGGAAAGCGCCGCTAATGCTCAGGGC
* *
40363647 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAATAAAC-TAAGCCCAACGACGCCGTTTTCTAAGC
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAA-AGACATAAGCCCAACGACGCCGTTTTCTGAGC
* **
40363711 TTTCGCGGATTTAGTGGCGTTTTTTAGG-AAGCGCCGCTAATGCTCAGGGC
65 TTTCGGGGATTTAACGGCGTTTTTTAGGAAAGCGCCGCTAATGCTCAGGGC
* *
40363761 TTTAGCGGCGTTTTTGAAAAAGTGCCGCAAAAAGACATAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAGACATAAGCCCAACGACGCCGTTTTCTGAGCT
* * ** *
40363826 TTCAGGGATTTAACGACGTTTTTTAGGAAAAAGCCGCTAATGCTCAGGTC
66 TTCGGGGATTTAACGGCGTTTTTTAGGAAAGCGCCGCTAATGCTCAGGGC
* *
40363876 TTTAGCGACGTTTTTGAGAAAGCACCGCAAAAAGACATAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAGACATAAGCCCAACGACGCCGTTTTCTGAGCT
* *
40363941 TTCGGGGATTTAACGGCG-TTTTTAGGAAAGCACCGCTAATGCTCAGGTC
66 TTCGGGGATTTAACGGCGTTTTTTAGGAAAGCGCCGCTAATGCTCAGGGC
* * *
40363990 TTTAGCGGTGTTTTTGGGAAAGCGCCGTAAAAA
1 TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAA
40364023 AATAGGGTTT
Statistics
Matches: 335, Mismatches: 37, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
113 3 0.01
114 155 0.46
115 175 0.52
116 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (115 bp):
TTTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAGACATAAGCCCAACGACGCCGTTTTCTGAGCT
TTCGGGGATTTAACGGCGTTTTTTAGGAAAGCGCCGCTAATGCTCAGGGC
Found at i:40363815 original size:229 final size:229
Alignment explanation
Indices: 40363532--40364016 Score: 670
Period size: 229 Copynumber: 2.1 Consensus size: 229
40363522 CTTTCGGGGA
** * *
40363532 TTTAGCGGCGTTTTTGAGGAAGCGCCGCAAAGAAACATAAGCCCAATGACGCCGTTTTCTGAGTT
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCAAAGAAACATAAGCCCAACGACGCCGTTTTCTGAGCT
* * * ** * * *
40363597 TTCGGGGATTTAGCGGCGTTTCTTAAGAAAGCGCTGCTAATGCTGAGGGATTTAGCGGCGTTTTT
66 TTCAGGGATTTAACGACGTTTCTTAAGAAAAAGCCGCTAATGCTCAGGGATTTAGCGACGTTTTT
* **
40363662 GAGAAAGCGCCGCAAAATAAAC-TAAGCCCAACGACGCCGTTTTCTAAGCTTTCGCGGATTTAGT
131 GAGAAAGCACCGCAAAA-AAACATAAGCCCAACGACGCCGTTTTCTAAGCTTTCGCGGATTTAAC
*
40363726 GGCGTTTTTTAGG-AAGCGCCGCTAATGCTCAGGGC
195 GGCG-TTTTTAGGAAAGCACCGCTAATGCTCAGGGC
*
40363761 TTTAGCGGCGTTTTTGAAAAAGTGCCGCAAA-AAGACATAAGCCCAACGACGCCGTTTTCTGAGC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCAAAGAA-ACATAAGCCCAACGACGCCGTTTTCTGAGC
* * **
40363825 TTTCAGGGATTTAACGACGTTTTTTAGGAAAAAGCCGCTAATGCTCAGGTCTTTAGCGACGTTTT
65 TTTCAGGGATTTAACGACGTTTCTTAAGAAAAAGCCGCTAATGCTCAGGGATTTAGCGACGTTTT
* * *
40363890 TGAGAAAGCACCGCAAAAAGACATAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAAC
130 TGAGAAAGCACCGCAAAAAAACATAAGCCCAACGACGCCGTTTTCTAAGCTTTCGCGGATTTAAC
*
40363955 GGCGTTTTTAGGAAAGCACCGCTAATGCTCAGGTC
195 GGCGTTTTTAGGAAAGCACCGCTAATGCTCAGGGC
* **
40363990 TTTAGCGGTGTTTTTGGGAAAGCGCCG
1 TTTAGCGGCGTTTTTGAAAAAGCGCCG
40364017 TAAAAAAATA
Statistics
Matches: 224, Mismatches: 29, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
228 13 0.06
229 211 0.94
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (229 bp):
TTTAGCGGCGTTTTTGAAAAAGCGCCGCAAAGAAACATAAGCCCAACGACGCCGTTTTCTGAGCT
TTCAGGGATTTAACGACGTTTCTTAAGAAAAAGCCGCTAATGCTCAGGGATTTAGCGACGTTTTT
GAGAAAGCACCGCAAAAAAACATAAGCCCAACGACGCCGTTTTCTAAGCTTTCGCGGATTTAACG
GCGTTTTTAGGAAAGCACCGCTAATGCTCAGGGC
Found at i:40364130 original size:14 final size:14
Alignment explanation
Indices: 40364111--40364137 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40364101 GAGTATGGGT
40364111 TTAGGGATTATGGA
1 TTAGGGATTATGGA
40364125 TTAGGGATTATGG
1 TTAGGGATTATGG
40364138 TTTAAGGGTT
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:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (14 bp):
TTAGGGATTATGGA
Found at i:40365156 original size:125 final size:125
Alignment explanation
Indices: 40364804--40365142 Score: 628
Period size: 125 Copynumber: 2.7 Consensus size: 125
40364794 AAAAATTAGC
40364804 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTCTATGAAAAACGC
1 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTCTATGAAAAACGC
40364869 CGCAAAAGATAACCAATAGCGGCGTACGCCGCAAAAAATAAATCAATTTATAGAAACAAA
66 CGCAAAAGATAACCAATAGCGGCGTACGCCGCAAAAAATAAATCAATTTATAGAAACAAA
40364929 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTCTATGAAAAACGC
1 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTCTATGAAAAACGC
40364994 CGCAAAAGATAACCAATAGCGGCGTACGCCGCAAAAAATAAATCAATTTATAGAAACAAA
66 CGCAAAAGATAACCAATAGCGGCGTACGCCGCAAAAAATAAATCAATTTATAGAAACAAA
* *
40365054 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGTGTTT-T-TCACAAAACG
1 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTCTATGA-AAAACG
*
40365117 CCGCAAAAGATAAGCAATAGCGGCGT
65 CCGCAAAAGATAACCAATAGCGGCGT
40365143 TTTCTATAAA
Statistics
Matches: 210, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
123 2 0.01
124 32 0.15
125 176 0.84
ACGTcount: A:0.41, C:0.17, G:0.18, T:0.24
Consensus pattern (125 bp):
ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTCTATGAAAAACGC
CGCAAAAGATAACCAATAGCGGCGTACGCCGCAAAAAATAAATCAATTTATAGAAACAAA
Found at i:40365196 original size:18 final size:19
Alignment explanation
Indices: 40365162--40365198 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
40365152 AAAAAACTGC
*
40365162 AAAATATAAATAAAATTAT
1 AAAAAATAAATAAAATTAT
40365181 AAAAAATAAA-AAAATTAT
1 AAAAAATAAATAAAATTAT
40365199 TTGCATAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAAATAAATAAAATTAT
Found at i:40365255 original size:103 final size:104
Alignment explanation
Indices: 40365132--40365343 Score: 270
Period size: 104 Copynumber: 2.0 Consensus size: 104
40365122 AAAGATAAGC
* * * * * *
40365132 AATAGCGGCGTTTTCTATAAAAAAAACTGCAAAATATAAATAAAATTATAAAA-AATA-AAAAAA
1 AATAACGGCGTTTTCCAT-AAAAAAACCGCAAAAAATAAATAAAATTAAAAAACAAAATAAAAAA
*
40365195 TTATT-TGCATAGCAAAACGGCGTCATTTTGA-TCAAAATGA
65 TT-TTGTGCATAGCAAAACGGAGTCATTTT-ATTCAAAATGA
** * *
40365235 AATAACGGCGTTTTCCATAAAAACGCCGCAAAAAATAAATCAATTTAAAAAACAAAATAAAAAAT
1 AATAACGGCGTTTTCCATAAAAAAACCGCAAAAAATAAATAAAATTAAAAAACAAAATAAAAAAT
40365300 TTTGTGCATAGCAAAACGGAGTCATTTTATTCAAAATGA
66 TTTGTGCATAGCAAAACGGAGTCATTTTATTCAAAATGA
40365339 AATAA
1 AATAA
40365344 TATTTTGCGG
Statistics
Matches: 94, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
102 27 0.29
103 22 0.23
104 45 0.48
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.26
Consensus pattern (104 bp):
AATAACGGCGTTTTCCATAAAAAAACCGCAAAAAATAAATAAAATTAAAAAACAAAATAAAAAAT
TTTGTGCATAGCAAAACGGAGTCATTTTATTCAAAATGA
Found at i:40365531 original size:255 final size:252
Alignment explanation
Indices: 40365054--40365565 Score: 771
Period size: 255 Copynumber: 2.0 Consensus size: 252
40365044 TAGAAACAAA
* * * *
40365054 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGTGTTTTTCACAAAACGCC
1 ATAGCAAAACGGAGTCATTTTATTCAAAATGAAATAATATTTTGCGGCGTTTTTCAAAAAACGCC
* *
40365119 GCAAAAGATAAGCAATAGCGGCGTTTTCTATAAAAAAAACTGCAAAATATAAATAAAATTATAAA
66 GCAAAAGATAAGCAATAGCGGCGTTTTCTATAAAAAAAACTCCAAAAAATAAATAAAATTATAAA
*
40365184 AAATAAAAAAATTATTTGCATAGCAAAACGGCGTCATTTTGATCAAAATGAAATAACGGCGTTTT
131 AAATAAAAAAAATATTTGCATAGCAAAACGGCGTCATTTTGATCAAAATGAAATAACGGCGTTTT
40365249 CCATAAAAACGCCGCAAAAAATAAATCAATTTAAAAAACAAAATAAAAAATTTTGT-GC
196 CCATAAAAACGCCGCAAAAAATAAATCAATTTAAAAAA-AAAATAAAAAATTTT-TAGC
*
40365307 ATAGCAAAACGGAGTCATTTTATTCAAAATGAAATAATATTTTGCGGCGATTTTGT-AAAAAATG
1 ATAGCAAAACGGAGTCATTTTATTCAAAATGAAATAATATTTTGCGGCG-TTTT-TCAAAAAACG
* * * *
40365371 CCGCAAAAGATAAGCAATAGTGGTGTTTTCTATAAAAACATC-CCAAAAAATAAATAAAATTATA
64 CCGCAAAAGATAAGCAATAGCGGCGTTTTCTATAAAAAAAACTCCAAAAAATAAATAAAATTAT-
* *
40365435 AAAAAATAGAAAAAAATATTTGCATAGCAAAACGGCG-CTATTTTGTTCAAAATGAAATAGCGGC
128 AAAAAATA-AAAAAAATATTTGCATAGCAAAACGGCGTC-ATTTTGATCAAAATGAAATAACGGC
* * * *
40365499 GTTTTTCATAAAAATGCCGCAAAAAGTAAATCAATTTATAAAAAAAATAAAAAATTTTTAGC
191 GTTTTCCATAAAAACGCCGCAAAAAATAAATCAATTTAAAAAAAAAATAAAAAATTTTTAGC
40365561 ATAGC
1 ATAGC
40365566 GGCGTTTTTT
Statistics
Matches: 235, Mismatches: 18, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
253 66 0.28
254 79 0.34
255 90 0.38
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (252 bp):
ATAGCAAAACGGAGTCATTTTATTCAAAATGAAATAATATTTTGCGGCGTTTTTCAAAAAACGCC
GCAAAAGATAAGCAATAGCGGCGTTTTCTATAAAAAAAACTCCAAAAAATAAATAAAATTATAAA
AAATAAAAAAAATATTTGCATAGCAAAACGGCGTCATTTTGATCAAAATGAAATAACGGCGTTTT
CCATAAAAACGCCGCAAAAAATAAATCAATTTAAAAAAAAAATAAAAAATTTTTAGC
Found at i:40366085 original size:22 final size:22
Alignment explanation
Indices: 40366059--40366106 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
40366049 TGTAAGTTTA
40366059 TTTTAGGGCAACTTTGAACCTT
1 TTTTAGGGCAACTTTGAACCTT
40366081 TTTTAGGGCAACTTTGAACCTT
1 TTTTAGGGCAACTTTGAACCTT
40366103 TTTT
1 TTTT
40366107 TTTGTCCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.46
Consensus pattern (22 bp):
TTTTAGGGCAACTTTGAACCTT
Found at i:40367498 original size:42 final size:42
Alignment explanation
Indices: 40367417--40367499 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
40367407 TTACATAACT
* *
40367417 TATATATTTTTAATATATAACTTAATAACTTATTAATATTTA
1 TATACATTTTTAATATATAACTTAAAAACTTATTAATATTTA
*
40367459 TATACATTTTTAATATATATA-TTAAAAATTTA-TATATATTT
1 TATACATTTTTAATATATA-ACTTAAAAACTTATTA-ATATTT
40367500 TTAATAACTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 2 0.06
42 33 0.92
43 1 0.03
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (42 bp):
TATACATTTTTAATATATAACTTAAAAACTTATTAATATTTA
Found at i:40367503 original size:20 final size:19
Alignment explanation
Indices: 40367471--40367516 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
40367461 TACATTTTTA
*
40367471 ATATATATATTAAAAATTT
1 ATATATATATTAAAAACTT
* *
40367490 ATATATATTTTTAATAACTT
1 ATATATA-TATTAAAAACTT
40367510 ATATATA
1 ATATATA
40367517 ACTTTCATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATATATATTAAAAACTT
Found at i:40367526 original size:20 final size:20
Alignment explanation
Indices: 40367488--40367550 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
40367478 TATTAAAAAT
**
40367488 TTATATATATTTTTAATAAC
1 TTATATATAACTTTAATAAC
*
40367508 TTATATATAACTTTCATAAC
1 TTATATATAACTTTAATAAC
* *
40367528 TTACATAATAAC-ATAATAAC
1 TTATAT-ATAACTTTAATAAC
40367548 TTA
1 TTA
40367551 CATAATACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
20 31 0.86
21 5 0.14
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATATATAACTTTAATAAC
Found at i:40367528 original size:9 final size:9
Alignment explanation
Indices: 40367514--40367816 Score: 149
Period size: 9 Copynumber: 34.9 Consensus size: 9
40367504 TAACTTATAT
*
40367514 ATAACTTTC
1 ATAACTTAC
40367523 ATAACTTAC
1 ATAACTTAC
*
40367532 ATAA-TAAC
1 ATAACTTAC
40367540 ATAATAACTTAC
1 ---ATAACTTAC
40367552 ATAA--TAC
1 ATAACTTAC
* *
40367559 ATAGCCTAC
1 ATAACTTAC
* *
40367568 ATGACTTGC
1 ATAACTTAC
40367577 ATAA--TAC
1 ATAACTTAC
*
40367584 ACAACTTAC
1 ATAACTTAC
*
40367593 ATAACTTAA
1 ATAACTTAC
*
40367602 ATAAATTAC
1 ATAACTTAC
40367611 ATAA--TAC
1 ATAACTTAC
*
40367618 ATAACTTTC
1 ATAACTTAC
40367627 ATAACTTAC
1 ATAACTTAC
*
40367636 ATAAAAACTTAA
1 AT---AACTTAC
*
40367648 ATAAATTAC
1 ATAACTTAC
40367657 ATAA--TAC
1 ATAACTTAC
**
40367664 AT-TTTTA-
1 ATAACTTAC
* *
40367671 ATCACTTAT
1 ATAACTTAC
*
40367680 ATAAAACTTTC
1 AT--AACTTAC
40367691 ATAACTTAC
1 ATAACTTAC
40367700 ATAA--TAC
1 ATAACTTAC
* *
40367707 ATAGCCTAC
1 ATAACTTAC
*
40367716 ATGACTTAC
1 ATAACTTAC
40367725 ATAA--TAC
1 ATAACTTAC
*
40367732 ACAACTTAC
1 ATAACTTAC
40367741 ATAACTTAC
1 ATAACTTAC
40367750 ATAA--TAC
1 ATAACTTAC
**
40367757 ATAACTTTG
1 ATAACTTAC
*
40367766 ATAGCTTAC
1 ATAACTTAC
*
40367775 ATTA--TAC
1 ATAACTTAC
* *
40367782 ACAACTTAT
1 ATAACTTAC
40367791 ATAACTTAC
1 ATAACTTAC
40367800 ATAACTTAC
1 ATAACTTAC
*
40367809 ATAGCTTA
1 ATAACTTA
40367817 ATTATACTTA
Statistics
Matches: 220, Mismatches: 47, Indels: 54
0.69 0.15 0.17
Matches are distributed among these distances:
7 49 0.22
8 8 0.04
9 142 0.65
11 10 0.05
12 11 0.05
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (9 bp):
ATAACTTAC
Found at i:40367551 original size:20 final size:20
Alignment explanation
Indices: 40367501--40367561 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
40367491 TATATATTTT
* *
40367501 TAATAACTTATAT-ATAACTT
1 TAATAACTTACATAATAAC-A
*
40367521 TCATAACTTACATAATAACA
1 TAATAACTTACATAATAACA
40367541 TAATAACTTACATAAT-ACA
1 TAATAACTTACATAATAACA
40367560 TA
1 TA
40367562 GCCTACATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (20 bp):
TAATAACTTACATAATAACA
Found at i:40367593 original size:25 final size:25
Alignment explanation
Indices: 40367522--40367803 Score: 124
Period size: 25 Copynumber: 11.6 Consensus size: 25
40367512 ATATAACTTT
40367522 CATAACTTACATAATA-AC-A--TA
1 CATAACTTACATAATACACAACCTA
* *
40367543 -ATAACTTACATAATACATAGCCTA
1 CATAACTTACATAATACACAACCTA
* * *
40367567 CATGACTTGCATAATACACAACTTA
1 CATAACTTACATAATACACAACCTA
* *
40367592 CATAACTTAAATAAATTACATAA--TA
1 CATAACTTACAT-AA-TACACAACCTA
* * *
40367617 CATAACTTTCATAACTTACATAAAAACTTA
1 CATAACTTACATAA--TAC---ACAACCTA
* * ****
40367647 AATAAATTACATAATACA-TTTTTA
1 CATAACTTACATAATACACAACCTA
* * *
40367671 -ATCACTT--AT-ATA-A-AACTTT
1 CATAACTTACATAATACACAACCTA
* *
40367690 CATAACTTACATAATACATAGCCTA
1 CATAACTTACATAATACACAACCTA
* *
40367715 CATGACTTACATAATACACAACTTA
1 CATAACTTACATAATACACAACCTA
* * *
40367740 CATAACTTACATAATACATAACTTT
1 CATAACTTACATAATACACAACCTA
* * * *
40367765 GATAGCTTACATTATACACAACTTA
1 CATAACTTACATAATACACAACCTA
*
40367790 TATAACTTACATAA
1 CATAACTTACATAA
40367804 CTTACATAGC
Statistics
Matches: 197, Mismatches: 45, Indels: 34
0.71 0.16 0.12
Matches are distributed among these distances:
19 3 0.02
20 24 0.12
21 3 0.02
22 2 0.01
23 8 0.04
24 8 0.04
25 122 0.62
26 2 0.01
27 6 0.03
28 6 0.03
30 13 0.07
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (25 bp):
CATAACTTACATAATACACAACCTA
Found at i:40367599 original size:50 final size:50
Alignment explanation
Indices: 40367543--40367813 Score: 211
Period size: 50 Copynumber: 5.4 Consensus size: 50
40367533 TAATAACATA
*
40367543 ATAACTTACATAATACATAGCCTACATGACTTGCATAATACACAACTTAC
1 ATAACTTACATAATACATAGCCTACATGACTTACATAATACACAACTTAC
* * * * * *
40367593 ATAACTTAAATAAATTACATA--ATACATAACTTTCATAACTTACATAAAAACTTAA
1 ATAACTTACAT-AA-TACATAGCCTACATGACTTACATAA--TAC---ACAACTTAC
* *** * *
40367648 ATAAATTACATAATACAT-TTTTA-ATCACTT--AT-ATA-A-AACTTTC
1 ATAACTTACATAATACATAGCCTACATGACTTACATAATACACAACTTAC
40367691 ATAACTTACATAATACATAGCCTACATGACTTACATAATACACAACTTAC
1 ATAACTTACATAATACATAGCCTACATGACTTACATAATACACAACTTAC
* * ** * *
40367741 ATAACTTACATAATACATAACTTTGAT-AGCTTACATTATACACAACTTAT
1 ATAACTTACATAATACATAGCCTACATGA-CTTACATAATACACAACTTAC
40367791 ATAACTTACATAACTTACATAGC
1 ATAACTTACATAA--TACATAGC
40367814 TTAATTATAC
Statistics
Matches: 177, Mismatches: 25, Indels: 36
0.74 0.11 0.15
Matches are distributed among these distances:
43 22 0.12
44 3 0.02
45 6 0.03
47 2 0.01
48 5 0.03
49 2 0.01
50 86 0.49
51 4 0.02
52 16 0.09
53 11 0.06
54 4 0.02
55 16 0.09
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (50 bp):
ATAACTTACATAATACATAGCCTACATGACTTACATAATACACAACTTAC
Found at i:40367614 original size:34 final size:34
Alignment explanation
Indices: 40367576--40367640 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
40367566 ACATGACTTG
40367576 CATAATACACAACTTACATAACTTAAATAAATTA
1 CATAATACACAACTTACATAACTTAAATAAATTA
* * *
40367610 CATAATACATAACTTTCATAACTTACATAAA
1 CATAATACACAACTTACATAACTTAAATAAA
40367641 AACTTAAATA
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:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (34 bp):
CATAATACACAACTTACATAACTTAAATAAATTA
Found at i:40367757 original size:16 final size:16
Alignment explanation
Indices: 40367690--40367763 Score: 62
Period size: 16 Copynumber: 4.5 Consensus size: 16
40367680 ATAAAACTTT
40367690 CATAACTTACATAATA
1 CATAACTTACATAATA
* * *
40367706 CATAGCCTACATGACTTA
1 CATAACTTACAT-A-ATA
*
40367724 CATAA--TACACAACTTA
1 CATAACTTACATAA--TA
40367740 CATAACTTACATAATA
1 CATAACTTACATAATA
40367756 CATAACTT
1 CATAACTT
40367764 TGATAGCTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
15 1 0.02
16 31 0.69
17 1 0.02
18 12 0.27
ACGTcount: A:0.45, C:0.23, G:0.03, T:0.30
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:40371204 original size:50 final size:49
Alignment explanation
Indices: 40371147--40371244 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 49
40371137 GTGTCTAGGC
* *
40371147 CGTGTAACACCCTGTTTTGGATTT-AGAATCAGACGGGCTAGGGACACGGT
1 CGTGTAACACACTGTTTTGGATTTAAG-ATCACACGGGCTAGGG-CACGGT
* *
40371197 CGTGTAACTCACTGTTTTGGATTTAAGGTCACACGGGCTAGGGCACGG
1 CGTGTAACACACTGTTTTGGATTTAAGATCACACGGGCTAGGGCACGG
40371245 ATGTGTGCCC
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
49 5 0.12
50 36 0.84
51 2 0.05
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (49 bp):
CGTGTAACACACTGTTTTGGATTTAAGATCACACGGGCTAGGGCACGGT
Found at i:40374929 original size:57 final size:57
Alignment explanation
Indices: 40374813--40374930 Score: 193
Period size: 57 Copynumber: 2.1 Consensus size: 57
40374803 ATAAAACATT
*
40374813 CTCTTCTTCATTCTAAACCCTAAAGAATCGGCCACCATTACAGTCTGTTGCGTCGAA
1 CTCTTCTTCATTCTAAACCCTAAAGAATCGGCCACCATTACAGTCTGTTGCGTCAAA
* *
40374870 CTCTTCTTCATTCTAAACCCTAAAGAA-CTGGCCACCATTACAGTCTGTTGTGTTAAA
1 CTCTTCTTCATTCTAAACCCTAAAGAATC-GGCCACCATTACAGTCTGTTGCGTCAAA
40374927 CTCT
1 CTCT
40374931 CTATTAATTG
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
56 1 0.02
57 56 0.98
ACGTcount: A:0.26, C:0.29, G:0.13, T:0.32
Consensus pattern (57 bp):
CTCTTCTTCATTCTAAACCCTAAAGAATCGGCCACCATTACAGTCTGTTGCGTCAAA
Found at i:40379087 original size:13 final size:13
Alignment explanation
Indices: 40379069--40379095 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40379059 TGAGAAACAC
40379069 TTTACACTAAGTT
1 TTTACACTAAGTT
40379082 TTTACACTAAGTT
1 TTTACACTAAGTT
40379095 T
1 T
40379096 AGCAAGTGTG
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:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (13 bp):
TTTACACTAAGTT
Found at i:40381366 original size:21 final size:20
Alignment explanation
Indices: 40381336--40381377 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
40381326 CATCAATAAC
*
40381336 TAAGTCTTTGTATCTGTGGT
1 TAAGTCTTTGTATATGTGGT
*
40381356 TAAGTGCTTTGTTTATGTGGT
1 TAAGT-CTTTGTATATGTGGT
40381377 T
1 T
40381378 GAGATTGGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.14, C:0.07, G:0.26, T:0.52
Consensus pattern (20 bp):
TAAGTCTTTGTATATGTGGT
Found at i:40381717 original size:23 final size:22
Alignment explanation
Indices: 40381674--40381717 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
40381664 ACCGTTTCTT
* *
40381674 TTTCTTTCCTTTTTTTTCCTCA
1 TTTCTTTCCTTTTTCTACCTCA
*
40381696 TTTCTTTTCTTTTTGCTACCTC
1 TTTCTTTCCTTTTT-CTACCTC
40381718 CTTGATTTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.05, C:0.27, G:0.02, T:0.66
Consensus pattern (22 bp):
TTTCTTTCCTTTTTCTACCTCA
Found at i:40392225 original size:31 final size:29
Alignment explanation
Indices: 40392171--40392256 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
40392161 TTTAGGGATA
40392171 AATTTTA-A-AATTATATAT-T-AATTTT
1 AATTTTATATAATTATATATATAAATTTT
* *
40392196 AATTTAATGTGTAATTATATATATAAATTTT
1 AATTT--TATATAATTATATATATAAATTTT
* *
40392227 GATTTTATATAATTTTATATATAAAATTTT
1 AATTTTATATAATTATATATAT-AAATTTT
40392257 GTTTTAATTC
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
25 5 0.10
27 1 0.02
29 24 0.50
30 8 0.17
31 10 0.21
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (29 bp):
AATTTTATATAATTATATATATAAATTTT
Found at i:40392237 original size:17 final size:17
Alignment explanation
Indices: 40392215--40392262 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 17
40392205 TGTAATTATA
40392215 TATATAAATTTTGATTT
1 TATATAAATTTTGATTT
*
40392232 TATAT-AATTTT-A-TA
1 TATATAAATTTTGATTT
40392246 TATA-AAATTTTG-TTT
1 TATATAAATTTTGATTT
40392261 TA
1 TA
40392263 ATTCAACTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
14 11 0.42
15 4 0.15
16 6 0.23
17 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (17 bp):
TATATAAATTTTGATTT
Found at i:40392239 original size:29 final size:29
Alignment explanation
Indices: 40392207--40392262 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
40392197 ATTTAATGTG
40392207 TAATTATATATAT-AAATTTTGATTTTATA
1 TAATTATATATATAAAATTTTG-TTTTATA
*
40392236 TAATTTTATATATAAAATTTTGTTTTA
1 TAATTATATATATAAAATTTTGTTTTA
40392263 ATTCAACTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (29 bp):
TAATTATATATATAAAATTTTGTTTTATA
Found at i:40398714 original size:23 final size:23
Alignment explanation
Indices: 40398688--40398742 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
40398678 TTAAATATTT
40398688 TTAAATTAAAAAATA-AAATTGCA
1 TTAAATTAAAAAATATAAATT-CA
* *
40398711 TTAAATATTAAAAATATACATTCA
1 TTAAAT-TAAAAAATATAAATTCA
40398735 -TAAATTAA
1 TTAAATTAA
40398743 TAATTAACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 2 0.07
23 11 0.41
24 10 0.37
25 4 0.15
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (23 bp):
TTAAATTAAAAAATATAAATTCA
Found at i:40404276 original size:45 final size:45
Alignment explanation
Indices: 40404200--40404315 Score: 133
Period size: 45 Copynumber: 2.6 Consensus size: 45
40404190 TACTACGTGT
* * * * *
40404200 ACCGGGTACCATTGATTATAAAGGTGGTTGCTGCGTGTTGATTCC
1 ACCGAGTACCATTGATTATAAAGGTGATTGCTACGTGCTAATTCC
* *
40404245 ACCGAGTACTATTGATTATGAAGGTGATTGCTACGTGCTAATTCC
1 ACCGAGTACCATTGATTATAAAGGTGATTGCTACGTGCTAATTCC
* * * *
40404290 ATCGAGTATCATTGACTATAAGGGTG
1 ACCGAGTACCATTGATTATAAAGGTG
40404316 GTGCTATGTG
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (45 bp):
ACCGAGTACCATTGATTATAAAGGTGATTGCTACGTGCTAATTCC
Found at i:40406646 original size:23 final size:23
Alignment explanation
Indices: 40406620--40406672 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
40406610 CTAAGGTATT
*
40406620 TTAAGTAAAAAAATTTTGATTTA
1 TTAAGCAAAAAAATTTTGATTTA
*
40406643 TTAAGCATAAAAATTTTGATTTA
1 TTAAGCAAAAAAATTTTGATTTA
40406666 TTAAGCA
1 TTAAGCA
40406673 TATTAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (23 bp):
TTAAGCAAAAAAATTTTGATTTA
Found at i:40406673 original size:23 final size:23
Alignment explanation
Indices: 40406628--40406674 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
40406618 TTTTAAGTAA
40406628 AAAAATTTTGATTTATTAAGCAT
1 AAAAATTTTGATTTATTAAGCAT
40406651 AAAAATTTTGATTTATTAAGCAT
1 AAAAATTTTGATTTATTAAGCAT
40406674 A
1 A
40406675 TTAAATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.43
Consensus pattern (23 bp):
AAAAATTTTGATTTATTAAGCAT
Found at i:40407512 original size:14 final size:14
Alignment explanation
Indices: 40407493--40407523 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
40407483 AATTTATATG
40407493 TTTATAAATCCATT
1 TTTATAAATCCATT
40407507 TTTATAAATCCATT
1 TTTATAAATCCATT
40407521 TTT
1 TTT
40407524 CCCCAAAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTATAAATCCATT
Found at i:40407872 original size:18 final size:18
Alignment explanation
Indices: 40407846--40407880 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40407836 GGTCGGGTCG
*
40407846 AGGAGGGCGATGCAACAT
1 AGGAAGGCGATGCAACAT
40407864 AGGAAGGCGATGCAACA
1 AGGAAGGCGATGCAACA
40407881 GATGGGTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.37, T:0.09
Consensus pattern (18 bp):
AGGAAGGCGATGCAACAT
Found at i:40408074 original size:40 final size:40
Alignment explanation
Indices: 40407999--40408076 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
40407989 AAAACAAAAT
* * *
40407999 GACCTTTTACGGCGTTTTTCTCCTAGAGCCTCTAATGCTC
1 GACCTTTTACGGCGTTTTTCACCTAGACCCGCTAATGCTC
* *
40408039 GACCTTTTGCGGCGTTTTTCACCTAGCCCCGCTAATGC
1 GACCTTTTACGGCGTTTTTCACCTAGACCCGCTAATGC
40408077 CACTAAAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.14, C:0.32, G:0.19, T:0.35
Consensus pattern (40 bp):
GACCTTTTACGGCGTTTTTCACCTAGACCCGCTAATGCTC
Found at i:40408449 original size:14 final size:14
Alignment explanation
Indices: 40408432--40408491 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
40408422 ACTCTTAATA
*
40408432 CTAAATCATAAACC
1 CTAAACCATAAACC
*
40408446 CTAAACCTTAAACC
1 CTAAACCATAAACC
*
40408460 CCAAACCATAAA-C
1 CTAAACCATAAACC
* * *
40408473 CTACACCCTAAATC
1 CTAAACCATAAACC
40408487 CTAAA
1 CTAAA
40408492 TATATTATAA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
13 10 0.27
14 27 0.73
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.18
Consensus pattern (14 bp):
CTAAACCATAAACC
Found at i:40408450 original size:7 final size:7
Alignment explanation
Indices: 40408440--40408491 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 7
40408430 TACTAAATCA
40408440 TAAACCC
1 TAAACCC
*
40408447 TAAACCT
1 TAAACCC
40408454 TAAACCC
1 TAAACCC
* *
40408461 CAAACCA
1 TAAACCC
40408468 TAAA-CC
1 TAAACCC
*
40408474 TACACCC
1 TAAACCC
*
40408481 TAAATCC
1 TAAACCC
40408488 TAAA
1 TAAA
40408492 TATATTATAA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
6 4 0.11
7 31 0.89
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAACCC
Found at i:40408465 original size:21 final size:20
Alignment explanation
Indices: 40408441--40408491 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
40408431 ACTAAATCAT
40408441 AAACCCTAAACCTTAAACCCC
1 AAACCCTAAACC-TAAACCCC
* * *
40408462 AAACCATAAACCTACACCCT
1 AAACCCTAAACCTAAACCCC
*
40408482 AAATCCTAAA
1 AAACCCTAAA
40408492 TATATTATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.16
Consensus pattern (20 bp):
AAACCCTAAACCTAAACCCC
Found at i:40408678 original size:21 final size:21
Alignment explanation
Indices: 40408654--40408700 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
40408644 TATAAAATAA
*
40408654 TAAACCCCAAACCCTAAACTC
1 TAAACCACAAACCCTAAACTC
*
40408675 TAAACCATAAACCCTAAACTC
1 TAAACCACAAACCCTAAACTC
*
40408696 AAAAC
1 TAAAC
40408701 TCTAATCCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.15
Consensus pattern (21 bp):
TAAACCACAAACCCTAAACTC
Found at i:40408679 original size:14 final size:14
Alignment explanation
Indices: 40408662--40408705 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
40408652 AATAAACCCC
40408662 AAACCCTAAACTCT
1 AAACCCTAAACTCT
* *
40408676 AAACCATAAACCCT
1 AAACCCTAAACTCT
* *
40408690 AAACTCAAAACTCT
1 AAACCCTAAACTCT
40408704 AA
1 AA
40408706 TCCCAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.50, C:0.32, G:0.00, T:0.18
Consensus pattern (14 bp):
AAACCCTAAACTCT
Found at i:40408784 original size:21 final size:21
Alignment explanation
Indices: 40408730--40408786 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
40408720 ACATTATATC
40408730 ATAAACCCTAAAACCTTGAACT
1 ATAAACCCT-AAACCTTGAACT
** *
40408752 ATAAACATTAAACCTT-AATT
1 ATAAACCCTAAACCTTGAACT
40408772 ACTAAACCCTAAACC
1 A-TAAACCCTAAACC
40408787 CAAAAATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 4 0.14
21 18 0.62
22 7 0.24
ACGTcount: A:0.47, C:0.26, G:0.02, T:0.25
Consensus pattern (21 bp):
ATAAACCCTAAACCTTGAACT
Found at i:40409037 original size:115 final size:115
Alignment explanation
Indices: 40408818--40409040 Score: 286
Period size: 116 Copynumber: 1.9 Consensus size: 115
40408808 CGACGTTTTT
* * * * * * * *
40408818 AAGCTCAATAACAAACGACGTTGTTTTCTTAACTTTTTTGCGGCGTTTTTCAACAAGCGCCGCTA
1 AAGCTCAAAAACAAACAACGTCGTTTTCTCAACTTTTTTGCGACGTTTCTAAAAAAGCGCCGCTA
* **
40408883 ATTCTCAATCTATTGCGACATTTTTTTAAAAAGCGCCGCTAATGCCACTA
66 ATGCTCAATCTATAACGACATTTTTTTAAAAAGCGCCGCTAATGCCACTA
*
40408933 AAGCTCAAAAACAAACAACGTCGTTTTGCTCAACTTTTTTGCGATGTTTCTAAAAAAGCGCCGCT
1 AAGCTCAAAAACAAACAACGTCGTTTT-CTCAACTTTTTTGCGACGTTTCTAAAAAAGCGCCGCT
* * * *
40408998 AATGCTCGATCTATAATGACA-TTTTTTGACAAGCGCCGCTAAT
65 AATGCTCAATCTATAACGACATTTTTTTAAAAAGCGCCGCTAAT
40409041 TCTCGATCTA
Statistics
Matches: 91, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
115 44 0.48
116 47 0.52
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (115 bp):
AAGCTCAAAAACAAACAACGTCGTTTTCTCAACTTTTTTGCGACGTTTCTAAAAAAGCGCCGCTA
ATGCTCAATCTATAACGACATTTTTTTAAAAAGCGCCGCTAATGCCACTA
Found at i:40409168 original size:40 final size:40
Alignment explanation
Indices: 40409124--40409233 Score: 116
Period size: 40 Copynumber: 2.8 Consensus size: 40
40409114 CAATTTTTTT
*
40409124 GCGGCCTTTTCCAAAAAGCACCGCTAATGCTCGATCTATA
1 GCGGCATTTTCCAAAAAGCACCGCTAATGCTCGATCTATA
* * *
40409164 GCGGCATTTTGCAAATAACGTA--GCTAATGCTCGATCTATT
1 GCGGCATTTTCCAAA-AA-GCACCGCTAATGCTCGATCTATA
* ** *
40409204 GCGGCGTTTTTTAAAAAGCGCCGCTAATGC
1 GCGGCATTTTCCAAAAAGCACCGCTAATGC
40409234 CACTAAAGCT
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
38 1 0.02
39 2 0.04
40 50 0.88
41 2 0.04
42 2 0.04
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (40 bp):
GCGGCATTTTCCAAAAAGCACCGCTAATGCTCGATCTATA
Found at i:40409326 original size:154 final size:154
Alignment explanation
Indices: 40408879--40409387 Score: 584
Period size: 151 Copynumber: 3.3 Consensus size: 154
40408869 AACAAGCGCC
* * * * *
40408879 GCTAATTCTCAATCTATTGCGACATTTTTTTAAAAAGCGCCGCTAATGCCACTAAAGCTCAAAAA
1 GCTAATGCTCGATCTATTGCGGCA-TTTTTTAAAAAGCACCGCTAATGCCACTAAAGCTCAACAA
* * *
40408944 CAAACAACGTCGTTTTGCTCAACTTTTTTGCGATG-TTTCTAAAAAAGCGCCGCTAATGCTCGAT
65 CGAACGACGTCGTTTTGCTCAACTTTTTTGCGATGTTTTCT-AAAAAGCACCGCTAATGCTCGAT
** * * * **
40409008 CTATAATGACATTTTTTG-ACAAGCGCC
129 CTATAGCGGCA--TTTTGCAAAAACGTA
* * * *
40409035 GCTAATTCTCGATCTATTGCGGCATTTTTTAAAAATCACCACTAATGCCACTAAAGCTTAACAAC
1 GCTAATGCTCGATCTATTGCGGCATTTTTTAAAAAGCACCGCTAATGCCACTAAAGCTCAACAAC
* * *** *
40409100 G---G-CATCGTTTTGCTCAATTTTTTTGCGGCCTTTTCCAAAAAGCACCGCTAATGCTCGATCT
66 GAACGACGTCGTTTTGCTCAACTTTTTTGCGATGTTTTCTAAAAAGCACCGCTAATGCTCGATCT
40409161 ATAGCGGCATTTTGCAAATAACGTA
131 ATAGCGGCATTTTGCAAA-AACGTA
* *
40409186 GCTAATGCTCGATCTATTGCGGCGTTTTTTAAAAAGCGCCGCTAATGCCACTAAAGCTCAACAAC
1 GCTAATGCTCGATCTATTGCGGCATTTTTTAAAAAGCACCGCTAATGCCACTAAAGCTCAACAAC
* * *
40409251 GAACGACGT-GTTTTGCTCAACTTTTTTACGATGTTTTCTGAAAAGCATCGCTAATGCTCGATCT
66 GAACGACGTCGTTTTGCTCAACTTTTTTGCGATGTTTTCTAAAAAGCACCGCTAATGCTCGATCT
*
40409315 ATAGCGGCATTTTTCAAAAAGCGCTA
131 ATAGCGGCATTTTGCAAAAA-CG-TA
* * * *
40409341 -CTAATGCTTGATCTATAGCGGCATTTTTCAGAAAGCACCGCTAATGC
1 GCTAATGCTCGATCTATTGCGGCATTTTTTAAAAAGCACCGCTAATGC
40409388 TCAACCTTTT
Statistics
Matches: 299, Mismatches: 45, Indels: 20
0.82 0.12 0.05
Matches are distributed among these distances:
149 5 0.02
150 2 0.01
151 116 0.39
152 4 0.01
153 2 0.01
154 108 0.36
155 40 0.13
156 22 0.07
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (154 bp):
GCTAATGCTCGATCTATTGCGGCATTTTTTAAAAAGCACCGCTAATGCCACTAAAGCTCAACAAC
GAACGACGTCGTTTTGCTCAACTTTTTTGCGATGTTTTCTAAAAAGCACCGCTAATGCTCGATCT
ATAGCGGCATTTTGCAAAAACGTA
Found at i:40409385 original size:40 final size:40
Alignment explanation
Indices: 40409291--40409389 Score: 144
Period size: 40 Copynumber: 2.5 Consensus size: 40
40409281 ATGTTTTCTG
*
40409291 AAAAGCATCGCTAATGCTCGATCTATAGCGGCATTTTTCA
1 AAAAGCACCGCTAATGCTCGATCTATAGCGGCATTTTTCA
* ** *
40409331 AAAAGCGCTACTAATGCTTGATCTATAGCGGCATTTTTCA
1 AAAAGCACCGCTAATGCTCGATCTATAGCGGCATTTTTCA
*
40409371 GAAAGCACCGCTAATGCTC
1 AAAAGCACCGCTAATGCTC
40409390 AACCTTTTAC
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.28
Consensus pattern (40 bp):
AAAAGCACCGCTAATGCTCGATCTATAGCGGCATTTTTCA
Found at i:40409737 original size:24 final size:24
Alignment explanation
Indices: 40409693--40409739 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
40409683 CCCAACAAAA
* *
40409693 ATCATTTATCCAAATCTAAACAAT
1 ATCATTTATCCAAACCCAAACAAT
*
40409717 ATCATTTATCTAAACCCAAACAA
1 ATCATTTATCCAAACCCAAACAA
40409740 AAATTAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (24 bp):
ATCATTTATCCAAACCCAAACAAT
Found at i:40413794 original size:20 final size:21
Alignment explanation
Indices: 40413750--40413797 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
40413740 GAACATGTTA
40413750 ATTTTTAGTCAATTTTACAATT
1 ATTTTTAGTCAATTTTA-AATT
* *
40413772 ATTTTTAGTGAATTTT-GATT
1 ATTTTTAGTCAATTTTAAATT
40413792 ATTTTT
1 ATTTTT
40413798 GATAGATTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.38
22 15 0.62
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.60
Consensus pattern (21 bp):
ATTTTTAGTCAATTTTAAATT
Found at i:40422997 original size:19 final size:18
Alignment explanation
Indices: 40422956--40422998 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
40422946 AATTTTTGCC
* *
40422956 ATAAAATAATTAATTTTT
1 ATAAAATAATTAAATTGT
40422974 ATAAAATAATTAAATTGT
1 ATAAAATAATTAAATTGT
40422992 ATTAAAA
1 A-TAAAA
40422999 ATTTGGACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (18 bp):
ATAAAATAATTAAATTGT
Found at i:40427361 original size:26 final size:26
Alignment explanation
Indices: 40427325--40427381 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
40427315 TCAATTTAAG
* *
40427325 TTGGTCAAAGGTCTCTTGAGTTTGAA
1 TTGGTCAAAGGACCCTTGAGTTTGAA
*
40427351 TTGGTCAAAGGACCCTTGAGTTTGAG
1 TTGGTCAAAGGACCCTTGAGTTTGAA
40427377 TTGGT
1 TTGGT
40427382 TAGAGAACCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.21, C:0.12, G:0.30, T:0.37
Consensus pattern (26 bp):
TTGGTCAAAGGACCCTTGAGTTTGAA
Found at i:40430381 original size:13 final size:14
Alignment explanation
Indices: 40430352--40430381 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
40430342 GCCTAAAACA
40430352 TTGAAAATTATTGT
1 TTGAAAATTATTGT
40430366 TTGAAAATTA-TGT
1 TTGAAAATTATTGT
40430379 TTG
1 TTG
40430382 GTCGGTTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (14 bp):
TTGAAAATTATTGT
Found at i:40436426 original size:12 final size:12
Alignment explanation
Indices: 40436409--40436437 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
40436399 CTCACACGCT
40436409 CGTGTGCTAGGC
1 CGTGTGCTAGGC
40436421 CGTGTGCTAGGC
1 CGTGTGCTAGGC
40436433 CGTGT
1 CGTGT
40436438 AACTGCCTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.24, G:0.41, T:0.28
Consensus pattern (12 bp):
CGTGTGCTAGGC
Found at i:40446306 original size:27 final size:27
Alignment explanation
Indices: 40446229--40446307 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 27
40446219 GCAACCACAT
* * *
40446229 AGAGTACGCCACCAAGGC-ATTCCTTTT
1 AGAGTTCGCCACAAAGGCTATT-CTTTC
* *
40446256 AGAGTTTGCCA-AACAAGCTATTCTTTC
1 AGAGTTCGCCACAA-AGGCTATTCTTTC
40446283 AGAGTTCGCCACAAAGGCTATTCTT
1 AGAGTTCGCCACAAAGGCTATTCTT
40446308 ACTTATCGTG
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
26 1 0.02
27 36 0.86
28 5 0.12
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (27 bp):
AGAGTTCGCCACAAAGGCTATTCTTTC
Found at i:40447122 original size:12 final size:12
Alignment explanation
Indices: 40447093--40447141 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
40447083 TAAGGAATAG
*
40447093 AAAGAGGAAGAA
1 AAAGAAGAAGAA
*
40447105 GAAGAAGAAGAA
1 AAAGAAGAAGAA
*
40447117 AAAGAAAAAGAAA
1 AAAGAAGAAG-AA
*
40447130 AAAAAAGAAGAA
1 AAAGAAGAAGAA
40447142 CCCTTTCATA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
12 20 0.67
13 10 0.33
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAGAAGAAGAA
Found at i:40449142 original size:9 final size:9
Alignment explanation
Indices: 40449122--40449152 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
40449112 AAAATATCAT
40449122 ATTAATTTTA
1 ATTAA-TTTA
40449132 ATTAATTTA
1 ATTAATTTA
40449141 ATTAATTTA
1 ATTAATTTA
40449150 ATT
1 ATT
40449153 TACTTGATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 16 0.76
10 5 0.24
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
ATTAATTTA
Found at i:40454587 original size:27 final size:27
Alignment explanation
Indices: 40454557--40454755 Score: 193
Period size: 27 Copynumber: 7.3 Consensus size: 27
40454547 TCATCTCCTA
**
40454557 GGGGTATAACAGTCATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * *
40454584 GGGGTATTTCGGTCATTTTATCTTATA
1 GGGGTATTTCAGTCATTTTACCCTATG
* * * *
40454611 GGGGTATTTCGGTCATTCTACCCAATA
1 GGGGTATTTCAGTCATTTTACCCTATG
**
40454638 GGGACATTTC-GATCATTTTACCCTATG
1 GGGGTATTTCAG-TCATTTTACCCTATG
*
40454665 GGGGTATTTCAGTTATTTTACCCTATG
1 GGGGTATTTCAGTCATTTTACCCTATG
* *
40454692 GGGGATATTTCAGTCATTTTACCTTATA
1 GGGG-TATTTCAGTCATTTTACCCTATG
** * *
40454720 AAGGTATTTCAGTCATTTTACTCTATT
1 GGGGTATTTCAGTCATTTTACCCTATG
*
40454747 AGGGTATTT
1 GGGGTATTT
40454756 TAGTTGTTTT
Statistics
Matches: 142, Mismatches: 27, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
26 1 0.01
27 118 0.83
28 23 0.16
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTATG
Found at i:40454617 original size:54 final size:54
Alignment explanation
Indices: 40454555--40454755 Score: 222
Period size: 54 Copynumber: 3.7 Consensus size: 54
40454545 ATTCATCTCC
** *
40454555 TAGGGGTATAACAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTATCTTA
1 TAGGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCTTA
* * * * ** * *
40454609 TAGGGGTATTTCGGTCATTCTACCCAATAGGGACATTTCGATCATTTTACCCTA
1 TAGGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCTTA
* * *
40454663 TGGGGGTATTTCAGTTATTTTACCCTATGGGGGATATTTCAGTCATTTTACCTTA
1 TAGGGGTATTTCAGTCATTTTACCCTATGGGGG-TATTTCGGTCATTTTACCTTA
** * **
40454718 TAAAGGTATTTCAGTCATTTTACTCTATTAGGGTATTT
1 TAGGGGTATTTCAGTCATTTTACCCTATGGGGGTATTT
40454756 TAGTTGTTTT
Statistics
Matches: 117, Mismatches: 29, Indels: 2
0.79 0.20 0.01
Matches are distributed among these distances:
54 74 0.63
55 43 0.37
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (54 bp):
TAGGGGTATTTCAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCTTA
Found at i:40454752 original size:82 final size:81
Alignment explanation
Indices: 40454566--40454768 Score: 221
Period size: 82 Copynumber: 2.5 Consensus size: 81
40454556 AGGGGTATAA
* * * * *
40454566 CAGTCATTTTACCCTATGGGGGTATTTCGGTCATTTTATCTTATAGGGGTATTTCGGTCATTCTA
1 CAGTCATTTTACCCTATGGGGGTATTTCAGTTATTTTACCCTATAGGGGTATTTCAGTCATTCTA
*
40454631 CCCAATAGGGACATTT
66 CCCAATAAGGACATTT
* *
40454647 C-GATCATTTTACCCTATGGGGGTATTTCAGTTATTTTACCCTATGGGGGATATTTCAGTCATTT
1 CAG-TCATTTTACCCTATGGGGGTATTTCAGTTATTTTACCCTATAGGGG-TATTTCAGTCATTC
** *
40454711 TACCTTATAAAGG-TATTT
64 TACCCAAT-AAGGACATTT
* ** * *
40454729 CAGTCATTTTACTCTATTAGGGTATTTTAGTTGTTTTACC
1 CAGTCATTTTACCCTATGGGGGTATTTCAGTTATTTTACC
40454769 TATTTTGGGG
Statistics
Matches: 102, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
80 1 0.01
81 42 0.41
82 55 0.54
83 4 0.04
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.43
Consensus pattern (81 bp):
CAGTCATTTTACCCTATGGGGGTATTTCAGTTATTTTACCCTATAGGGGTATTTCAGTCATTCTA
CCCAATAAGGACATTT
Found at i:40459654 original size:43 final size:42
Alignment explanation
Indices: 40459606--40459805 Score: 226
Period size: 43 Copynumber: 4.7 Consensus size: 42
40459596 TTTTAGAAAT
*
40459606 AAACGCCGCTATAGATCAGGACCTTTAGCGGCACCTCTTCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGC-CCTTTTCCAC
** * * *
40459649 AAACGCCGCTATAGATTGGGACCTTTAACGGCGCTTTTGCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCCCTTTTCCAC
**
40459691 AAACGCCGCTATAGATCAAGG-CCTTTAGCGGCGTTTTTGCCAC
1 AAACGCCGCTATAGATC-AGGACCTTTAGCGGCCCTTTT-CCAC
* *
40459734 AAACACCGCTATAGATCAAGG-CCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTATAGATC-AGGACCTTTAGCGGC-CCTTTTCCAC
* *
40459777 AAACGCCGCTATAGAACA-AACCTTTAGCG
1 AAACGCCGCTATAGATCAGGACCTTTAGCG
40459806 ACGCTTCTCG
Statistics
Matches: 137, Mismatches: 16, Indels: 9
0.85 0.10 0.06
Matches are distributed among these distances:
42 48 0.35
43 84 0.61
44 5 0.04
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.23
Consensus pattern (42 bp):
AAACGCCGCTATAGATCAGGACCTTTAGCGGCCCTTTTCCAC
Found at i:40459716 original size:85 final size:86
Alignment explanation
Indices: 40459606--40459805 Score: 248
Period size: 85 Copynumber: 2.3 Consensus size: 86
40459596 TTTTAGAAAT
* **
40459606 AAACGCCGCTATAGATC-AGGACCTTTAGCGGCACCTCTT-CCACAAACGCCGCTATAGAT-TGG
1 AAACGCCGCTATAGATCAAGG-CCTTTAGCGGC-CCTCTTGCCACAAACACCGCTATAGATCAAG
*
40459668 GACCTTTAACGGCGC-TTTTGCAC
64 G-CCTTTAACGGCGCTTTTTCCAC
** *
40459691 AAACGCCGCTATAGATCAAGGCCTTTAGCGGCGTTTTTGCCACAAACACCGCTATAGATCAAGGC
1 AAACGCCGCTATAGATCAAGGCCTTTAGCGGCCCTCTTGCCACAAACACCGCTATAGATCAAGGC
*
40459756 CTTTAGCGGCGCTTTTTCCAC
66 CTTTAACGGCGCTTTTTCCAC
* *
40459777 AAACGCCGCTATAGAACAA-ACCTTTAGCG
1 AAACGCCGCTATAGATCAAGGCCTTTAGCG
40459806 ACGCTTCTCG
Statistics
Matches: 101, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
84 3 0.03
85 68 0.67
86 30 0.30
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.23
Consensus pattern (86 bp):
AAACGCCGCTATAGATCAAGGCCTTTAGCGGCCCTCTTGCCACAAACACCGCTATAGATCAAGGC
CTTTAACGGCGCTTTTTCCAC
Found at i:40461690 original size:7 final size:8
Alignment explanation
Indices: 40461667--40461698 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
40461657 ATCTGACCCT
40461667 TAAATCCC
1 TAAATCCC
40461675 TAAAT-CC
1 TAAATCCC
40461682 T-AATCCC
1 TAAATCCC
40461689 TAAATCCC
1 TAAATCCC
40461697 TA
1 TA
40461699 GCTCTTAACC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 3 0.14
7 6 0.27
8 13 0.59
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.28
Consensus pattern (8 bp):
TAAATCCC
Found at i:40461711 original size:22 final size:22
Alignment explanation
Indices: 40461647--40461713 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 22
40461637 ACTAATTAAT
*
40461647 CTAAA-CCCT-AAT-CTGACCC
1 CTAAATCCCTAAATCCTAACCC
* *
40461666 TTAAATCCCTAAATCCTAATCC
1 CTAAATCCCTAAATCCTAACCC
** *
40461688 CTAAATCCCTAGCTCTTAACCC
1 CTAAATCCCTAAATCCTAACCC
40461710 CTAA
1 CTAA
40461714 CTCTTAATCC
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
19 4 0.11
20 4 0.11
21 3 0.08
22 26 0.70
ACGTcount: A:0.33, C:0.37, G:0.03, T:0.27
Consensus pattern (22 bp):
CTAAATCCCTAAATCCTAACCC
Found at i:40461732 original size:21 final size:21
Alignment explanation
Indices: 40461702--40461751 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
40461692 ATCCCTAGCT
* * * *
40461702 CTTAACCCCTAACTCTTAATC
1 CTTAAACCCTAAATCTCAACC
40461723 CTTAAACCCTAAATCTCAACC
1 CTTAAACCCTAAATCTCAACC
40461744 CTTAAACC
1 CTTAAACC
40461752 ATAATCCCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.38, G:0.00, T:0.28
Consensus pattern (21 bp):
CTTAAACCCTAAATCTCAACC
Found at i:40461779 original size:15 final size:15
Alignment explanation
Indices: 40461669--40461783 Score: 57
Period size: 14 Copynumber: 8.1 Consensus size: 15
40461659 CTGACCCTTA
40461669 AATCCCTAAATCC-T
1 AATCCCTAAATCCAT
*
40461683 AATCCCTAAATCCCT
1 AATCCCTAAATCCAT
* * * * *
40461698 -AGCTCTTAACCCCT
1 AATCCCTAAATCCAT
* * *
40461712 AA-CTCTTAATCCTT
1 AATCCCTAAATCCAT
*
40461726 AAACCCTAAAT-C-T
1 AATCCCTAAATCCAT
40461739 CAA-CCCTTAAA-CCAT
1 -AATCCC-TAAATCCAT
40461754 AATCCCT-AATCCAT
1 AATCCCTAAATCCAT
*
40461768 AATCTCTAAATCCAT
1 AATCCCTAAATCCAT
40461783 A
1 A
40461784 TATAATTATT
Statistics
Matches: 82, Mismatches: 9, Indels: 19
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.07
14 56 0.68
15 20 0.24
ACGTcount: A:0.36, C:0.35, G:0.01, T:0.29
Consensus pattern (15 bp):
AATCCCTAAATCCAT
Found at i:40461987 original size:7 final size:7
Alignment explanation
Indices: 40461958--40462036 Score: 54
Period size: 7 Copynumber: 11.1 Consensus size: 7
40461948 ACTAGTTAAT
40461958 CTAAACC
1 CTAAACC
* *
40461965 TTAAATC
1 CTAAACC
*
40461972 ATAAA-C
1 CTAAACC
40461978 CTAAACC
1 CTAAACC
40461985 CTAAAACC
1 CT-AAACC
*
40461993 ATAAACC
1 CTAAACC
* *
40462000 CTTAACA
1 CTAAACC
40462007 C-ATAACC
1 CTA-AACC
40462014 TCTAAACC
1 -CTAAACC
*
40462022 TTAAACC
1 CTAAACC
40462029 CTAAACC
1 CTAAACC
40462036 C
1 C
40462037 CAACCTTTTA
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
6 5 0.09
7 38 0.69
8 11 0.20
9 1 0.02
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:40462004 original size:36 final size:36
Alignment explanation
Indices: 40461959--40462036 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
40461949 CTAGTTAATC
40461959 TAAA-CCTTAA-ATCATAAAC-CTAAACCCTAAAACCA
1 TAAACCCTTAACA-CATAAACTCTAAA-CCTAAAACCA
* * *
40461994 TAAACCCTTAACACATAACCTCTAAACCTTAAACCC
1 TAAACCCTTAACACATAAACTCTAAACCTAAAACCA
40462030 TAAACCC
1 TAAACCC
40462037 CAACCTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
35 4 0.11
36 27 0.73
37 6 0.16
ACGTcount: A:0.46, C:0.33, G:0.00, T:0.21
Consensus pattern (36 bp):
TAAACCCTTAACACATAAACTCTAAACCTAAAACCA
Found at i:40462034 original size:14 final size:14
Alignment explanation
Indices: 40461958--40462084 Score: 71
Period size: 15 Copynumber: 8.9 Consensus size: 14
40461948 ACTAGTTAAT
* *
40461958 CTAAACCTTAAATC
1 CTAAACCATAAACC
*
40461972 ATAAACC-TAAACC
1 CTAAACCATAAACC
40461985 CTAAAACCATAAACC
1 CT-AAACCATAAACC
*
40462000 CTTAACACAT-AACC
1 CTAAAC-CATAAACC
*
40462014 TCTAAACCTTAAACC
1 -CTAAACCATAAACC
**
40462029 CTAAACC-CCAACC
1 CTAAACCATAAACC
* *
40462042 TTTTAAACCATAACCC
1 --CTAAACCATAAACC
*
40462058 CTAAACCCATAATCC
1 CTAAA-CCATAAACC
* *
40462073 ATAAACCTTAAA
1 CTAAACCATAAA
40462085 ATGGTAACAC
Statistics
Matches: 87, Mismatches: 17, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
13 10 0.11
14 36 0.41
15 38 0.44
16 3 0.03
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (14 bp):
CTAAACCATAAACC
Found at i:40462385 original size:41 final size:41
Alignment explanation
Indices: 40462322--40462689 Score: 569
Period size: 41 Copynumber: 9.0 Consensus size: 41
40462312 ATTTTAAATC
* *
40462322 CCTGAGCATTAGCGGCGTTTTCTAAAAAACGCCGCTAAAG-
1 CCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGA
**
40462362 CCTTGAGCATTAGCGGCGCTTTCTCAAAAAACGCCGCTAAATC
1 CC-TGAGCATTAGCGGCGCTTTCTC-AAAAACGCCGCTAAAGA
*
40462405 CCTGAGCATTAACGGCGCTTTCTCAAAAACGCCGCTAAAGA
1 CCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGA
* *
40462446 CCTTAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAAGA
1 CCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGA
* *
40462487 CCTGAGCATTAGCGGCGCTTTCTCAAAAACGTCGTTAAAGA
1 CCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGA
* * *
40462528 CCTGAGCATTAGCGACGCTTTATCAAAAACGCCGTTAAAGA
1 CCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGA
* *
40462569 CCAGAGCATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGA
1 CCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGA
*
40462610 CCAGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAG-
1 CCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGA
40462650 CCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAG
1 CCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAG
40462690 CCCCGAAAGC
Statistics
Matches: 304, Mismatches: 21, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
40 41 0.13
41 225 0.74
42 36 0.12
43 2 0.01
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.21
Consensus pattern (41 bp):
CCTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGA
Found at i:40463732 original size:18 final size:18
Alignment explanation
Indices: 40463694--40463729 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40463684 TTATTATTTT
*
40463694 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
40463712 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
40463730 TAATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:40463736 original size:16 final size:15
Alignment explanation
Indices: 40463715--40463763 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 15
40463705 ATTAAAATAA
40463715 AATTTAAATATTAAAT
1 AATTTAAA-ATTAAAT
40463731 AATTT--AATTAAA-
1 AATTTAAAATTAAAT
*
40463743 AATTAAAAATTAAAT
1 AATTTAAAATTAAAT
40463758 AATTTA
1 AATTTA
40463764 TTAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
12 4 0.14
13 6 0.21
14 8 0.29
15 5 0.18
16 5 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTTAAAATTAAAT
Done.