Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr5
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: 55438857
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1812582 characters in sequence are not A, C, G, or T
File 38 of 167
Found at i:11641621 original size:8 final size:8
Alignment explanation
Indices: 11641565--11641625 Score: 50
Period size: 8 Copynumber: 6.9 Consensus size: 8
11641555 GATATCATCT
11641565 AAAATTTA
1 AAAATTTA
11641573 TGAAACATTTA
1 --AAA-ATTTA
11641584 AAAATTTTA
1 AAAA-TTTA
*
11641593 AAATTTTA
1 AAAATTTA
*
11641601 AAAATAATAA
1 AAAAT--TTA
11641611 AAAATTTA
1 AAAATTTA
11641619 AAAATTT
1 AAAATTT
11641626 CACAAAAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
8 18 0.42
9 10 0.23
10 10 0.23
11 5 0.12
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (8 bp):
AAAATTTA
Found at i:11642226 original size:29 final size:30
Alignment explanation
Indices: 11642188--11642260 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 30
11642178 TTTTTAGTCT
* * *
11642188 AAATTTTAAAATATTAATATCAATA-TTAC
1 AAATTATAAAATATTAAGATCAAGATTTAC
*
11642217 AAATTAT-AAATACTAAGATCAAGATTTAC
1 AAATTATAAAATATTAAGATCAAGATTTAC
11642246 AAA-TATTAAAATATT
1 AAATTA-TAAAATATT
11642261 CCAATCCTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 16 0.44
29 14 0.39
30 6 0.17
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (30 bp):
AAATTATAAAATATTAAGATCAAGATTTAC
Found at i:11644763 original size:43 final size:43
Alignment explanation
Indices: 11644670--11644801 Score: 176
Period size: 43 Copynumber: 3.1 Consensus size: 43
11644660 AAAAGACGCA
*
11644670 AAAGACCAGGACTTTTAGCGGCGCTTTT-TAAAAAACGCCGTT
1 AAAGACCAGGACTTTTAGCGGCGCTTTTCTAAAAAACGCCGCT
* * *
11644712 AAAAACCAGGGCTTTTAGCGGCGCTTTTCTAAAAAACGCCACT
1 AAAGACCAGGACTTTTAGCGGCGCTTTTCTAAAAAACGCCGCT
* * ** *
11644755 AAAGACCAGGACTTTTCGCTGCGCTTTTCCCACAAACGCCGCT
1 AAAGACCAGGACTTTTAGCGGCGCTTTTCTAAAAAACGCCGCT
11644798 AAAG
1 AAAG
11644802 GTCATAAATT
Statistics
Matches: 77, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
42 26 0.34
43 51 0.66
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (43 bp):
AAAGACCAGGACTTTTAGCGGCGCTTTTCTAAAAAACGCCGCT
Found at i:11644928 original size:12 final size:12
Alignment explanation
Indices: 11644911--11644940 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
11644901 ATAAATATAA
11644911 AAAATTCCTATT
1 AAAATTCCTATT
11644923 AAAATT-CTATT
1 AAAATTCCTATT
11644934 AAAATTC
1 AAAATTC
11644941 ATTATCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATTCCTATT
Found at i:11644934 original size:11 final size:11
Alignment explanation
Indices: 11644911--11644944 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
11644901 ATAAATATAA
11644911 AAAATTCCTATT
1 AAAATT-CTATT
11644923 AAAATTCTATT
1 AAAATTCTATT
11644934 AAAATTC-ATT
1 AAAATTCTATT
11644944 A
1 A
11644945 TCAAATTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 4 0.18
11 12 0.55
12 6 0.27
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (11 bp):
AAAATTCTATT
Found at i:11645071 original size:15 final size:15
Alignment explanation
Indices: 11645051--11645085 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
11645041 AGTTTTAAAG
*
11645051 TTAAAATTTTAAATA
1 TTAAAATTTAAAATA
11645066 TTAAAATTTAAAATA
1 TTAAAATTTAAAATA
*
11645081 ATAAA
1 TTAAA
11645086 TTAATAACAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAAAATTTAAAATA
Found at i:11648502 original size:24 final size:24
Alignment explanation
Indices: 11648475--11648526 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
11648465 TTAGTAAGTC
*
11648475 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
11648499 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
11648523 AAAT
1 AAAT
11648527 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:11650472 original size:24 final size:24
Alignment explanation
Indices: 11650445--11650496 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
11650435 TTAGTAAGTC
*
11650445 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
11650469 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
11650493 AAAT
1 AAAT
11650497 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:11651116 original size:16 final size:16
Alignment explanation
Indices: 11651084--11651127 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
11651074 AACTAAAATA
*
11651084 TTAAATTTTTAAGTTTT
1 TTAAATTTTTTA-TTTT
11651101 TT--ATTTTTTATTTT
1 TTAAATTTTTTATTTT
11651115 TTAAATTTTTTAT
1 TTAAATTTTTTAT
11651128 GAAGATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 6 0.25
15 7 0.29
16 9 0.38
17 2 0.08
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (16 bp):
TTAAATTTTTTATTTT
Found at i:11651781 original size:14 final size:15
Alignment explanation
Indices: 11651762--11651797 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
11651752 AACTCCTAAT
11651762 CCCTAAACAT-TAAA
1 CCCTAAACATATAAA
11651776 CCCTAAA-ATATAAA
1 CCCTAAACATATAAA
11651790 CCCTAAAC
1 CCCTAAAC
11651798 CCTGAACCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 18 0.90
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (15 bp):
CCCTAAACATATAAA
Found at i:11651813 original size:21 final size:21
Alignment explanation
Indices: 11651789--11651829 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11651779 TAAAATATAA
11651789 ACCC-TAAACCCTGAACCCCTT
1 ACCCTTAAACCCT-AACCCCTT
*
11651810 ACCCTTAACCCCTAACCCCT
1 ACCCTTAAACCCTAACCCCT
11651830 AACACATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.27, C:0.51, G:0.02, T:0.20
Consensus pattern (21 bp):
ACCCTTAAACCCTAACCCCTT
Found at i:11651830 original size:7 final size:7
Alignment explanation
Indices: 11651790--11651832 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
11651780 AAAATATAAA
*
11651790 CCCTAAA
1 CCCTAAC
11651797 CCCTGAAC
1 CCCT-AAC
*
11651805 CCCTTAC
1 CCCTAAC
*
11651812 CCTTAAC
1 CCCTAAC
11651819 CCCTAAC
1 CCCTAAC
11651826 CCCTAAC
1 CCCTAAC
11651833 ACATAAATCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.28, C:0.51, G:0.02, T:0.19
Consensus pattern (7 bp):
CCCTAAC
Found at i:11652001 original size:41 final size:40
Alignment explanation
Indices: 11651940--11652035 Score: 147
Period size: 41 Copynumber: 2.4 Consensus size: 40
11651930 CTAGTTGGTA
* *
11651940 TCTTTAGCGGCGTTTTACCAAAAGCGGCGCTAATGCTCTGG
1 TCTTTAGCGGCGTTTCACCAAAAGCGCCGCTAATGCTCT-G
*
11651981 TCTTTCGCGGCGTTTCACCAAAAGCGCCGCTAATGCTCTG
1 TCTTTAGCGGCGTTTCACCAAAAGCGCCGCTAATGCTCTG
*
11652021 TTTTTAGCGGCGTTT
1 TCTTTAGCGGCGTTT
11652036 TTGTCAAAAC
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 14 0.28
41 36 0.72
ACGTcount: A:0.17, C:0.26, G:0.25, T:0.32
Consensus pattern (40 bp):
TCTTTAGCGGCGTTTCACCAAAAGCGCCGCTAATGCTCTG
Found at i:11654731 original size:87 final size:87
Alignment explanation
Indices: 11654640--11654884 Score: 303
Period size: 87 Copynumber: 2.8 Consensus size: 87
11654630 TCAACTTGGG
* *
11654640 CCACTGCAACTTCAGGGGGATAAGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATA
1 CCACTGTAACTTCAGGGAGATAAGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATA
* * * *
11654705 AGATCTCTTATTTTAATCCGTT
66 AGATCTCTGACTTCAATCCGCT
* *
11654727 CCACTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATG
1 CCACTGTAACTTCAGGGAGATAAGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATA
* *
11654792 AGATCTCTGGCTTCAATCTGCT
66 AGATCTCTGACTTCAATCCGCT
* * * * * *
11654814 CCACTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTTTGGTCTGTTCCACTGTAATCTCAGGGA
1 CCACTGTAACTTCAGGGAGATAAGATAGTG----TCTTCGATCTGCTCCGCTGTAATCTCAGGGA
11654878 GATAAGA
62 GATAAGA
11654885 CCTGATGTGA
Statistics
Matches: 136, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
86 2 0.01
87 101 0.74
90 33 0.24
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (87 bp):
CCACTGTAACTTCAGGGAGATAAGATAGTGTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATA
AGATCTCTGACTTCAATCCGCT
Found at i:11654876 original size:46 final size:45
Alignment explanation
Indices: 11654670--11655054 Score: 245
Period size: 44 Copynumber: 8.8 Consensus size: 45
11654660 TAAGATAGTG
* * *
11654670 TCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT--CT
1 TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
* * * * * *
11654713 TATTTTAATCCGTTCCACTGTAA-CTTCAGGGAGATAGGA--T-AGT
1 T-CTTTGATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTGAAT
* * * *
11654756 GTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATGAGATCT--CT
1 -TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
* ** *
11654800 GGCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
1 -TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AAT
* * *
11654847 TCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTG-A-
1 TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
* * * *
11654890 --TGTGATCTTCTCTACTGTAA-CTTCAGAGAGAT---A-C-G-AT
1 TCTTTGATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTGAAT
* * * * * * *
11654927 CCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGAT-T-ACT
1 TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
*
11654970 ATCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
1 -TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AAT
* *
11655017 TCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAAGA
1 TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGA
11655055 CCTGTATTAT
Statistics
Matches: 261, Mismatches: 56, Indels: 47
0.72 0.15 0.13
Matches are distributed among these distances:
36 2 0.01
37 1 0.00
38 1 0.00
39 22 0.08
40 2 0.01
41 24 0.09
42 2 0.01
43 31 0.12
44 101 0.39
45 2 0.01
46 70 0.27
47 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.32
Consensus pattern (45 bp):
TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
Found at i:11656349 original size:59 final size:54
Alignment explanation
Indices: 11656254--11656363 Score: 157
Period size: 54 Copynumber: 1.9 Consensus size: 54
11656244 GCCTCTCCAA
* *
11656254 AGTTTTTTTTTTTTTTTTTTTTTTTTGGAAGTGCCCTTTACGGGTTTTCACCTT
1 AGTTTTTTTTTTTTTTTTTTTTTTTGGGAAGCGCCCTTTACGGGTTTTCACCTT
11656308 AGTTTTTTTTTTTTTTTTTTTTTTTAGGAAGCAAAGCGCCCTTTACGGGTTTTCAC
1 AGTTTTTTTTTTTTTTTTTTTTTTT-GG--G--AAGCGCCCTTTACGGGTTTTCAC
11656364 TTTGGTTCCC
Statistics
Matches: 49, Mismatches: 2, Indels: 5
0.88 0.04 0.09
Matches are distributed among these distances:
54 25 0.51
55 1 0.02
57 1 0.02
59 22 0.45
ACGTcount: A:0.13, C:0.14, G:0.15, T:0.58
Consensus pattern (54 bp):
AGTTTTTTTTTTTTTTTTTTTTTTTGGGAAGCGCCCTTTACGGGTTTTCACCTT
Found at i:11667540 original size:3 final size:3
Alignment explanation
Indices: 11667494--11667528 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
11667484 AACATAAACA
11667494 AAT AAGT AAT AAT AAT AAT AAT AAT AAT AA- AAT AA
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
11667529 ACAAAATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.83
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:11674329 original size:31 final size:29
Alignment explanation
Indices: 11674262--11674338 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 29
11674252 AAGCTATGGA
*
11674262 TTTAGTCCCTATATTTTAATTCGATTAAG
1 TTTAGTCCCTATATTTTAATTCGATCAAG
*
11674291 TTTAGTCCCTATACTTTTCGAATTCG-TCAAT
1 TTTAGTCCCTATA-TTTT--AATTCGATCAAG
11674322 TTTAGT-CCTAGTATTTT
1 TTTAGTCCCTA-TATTTT
11674339 TTAAAAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
29 13 0.31
30 12 0.29
31 11 0.26
32 6 0.14
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.49
Consensus pattern (29 bp):
TTTAGTCCCTATATTTTAATTCGATCAAG
Found at i:11703219 original size:23 final size:24
Alignment explanation
Indices: 11703193--11703245 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
11703183 GAAATTGGTG
11703193 GAATTCATGT-TTAA-TCTTGGATT
1 GAATT-ATGTGTTAAGTCTTGGATT
*
11703216 GAATATATGTGTTAAGTTTTGGATT
1 GAAT-TATGTGTTAAGTCTTGGATT
*
11703241 AAATT
1 GAATT
11703246 TGAATTGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 8 0.32
24 6 0.24
25 11 0.44
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.47
Consensus pattern (24 bp):
GAATTATGTGTTAAGTCTTGGATT
Found at i:11704176 original size:12 final size:12
Alignment explanation
Indices: 11704140--11704168 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
11704130 AGTTTGGCAT
11704140 GGCCTAGCACAC
1 GGCCTAGCACAC
11704152 GGCCTAGCACAC
1 GGCCTAGCACAC
11704164 GGCCT
1 GGCCT
11704169 GACACACGAG
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:0.21, C:0.41, G:0.28, T:0.10
Consensus pattern (12 bp):
GGCCTAGCACAC
Found at i:11705149 original size:12 final size:12
Alignment explanation
Indices: 11705132--11705168 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
11705122 CATATCAGTG
11705132 GTGGAATACTTT
1 GTGGAATACTTT
11705144 GTGGAATACTTT
1 GTGGAATACTTT
11705156 GTGGAATACTTT
1 GTGGAATACTTT
11705168 G
1 G
11705169 ATATCAGTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.27, T:0.41
Consensus pattern (12 bp):
GTGGAATACTTT
Found at i:11705184 original size:22 final size:22
Alignment explanation
Indices: 11705156--11705202 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
11705146 GGAATACTTT
11705156 GTGGAATACTTTGATATCAGTG
1 GTGGAATACTTTGATATCAGTG
11705178 GTGGAATACTTTGATATCAGTG
1 GTGGAATACTTTGATATCAGTG
11705200 GTG
1 GTG
11705203 CTAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.26, C:0.09, G:0.30, T:0.36
Consensus pattern (22 bp):
GTGGAATACTTTGATATCAGTG
Found at i:11705501 original size:21 final size:21
Alignment explanation
Indices: 11705475--11705516 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11705465 AATTTGTTGT
* * *
11705475 GTTAGTCGACAGATCTTGCAA
1 GTTAGTCAACAAAGCTTGCAA
11705496 GTTAGTCAACAAAGCTTGCAA
1 GTTAGTCAACAAAGCTTGCAA
11705517 AGCCGAGGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (21 bp):
GTTAGTCAACAAAGCTTGCAA
Found at i:11706660 original size:52 final size:51
Alignment explanation
Indices: 11706564--11706664 Score: 130
Period size: 52 Copynumber: 2.0 Consensus size: 51
11706554 CTAGACTTCC
* *
11706564 TCACACGGTCAGAACACACAGTCGTGTCAATTTGGCAGAATCGAAACACGAT
1 TCACACGGGCAGAACACACAGTCGTGTCAAATTGGCAGAATCG-AACACGAT
* * * **
11706616 TCACACGGGCAGACCACACGGTCGTGTCAAATTGGTAGGCTCGAACACG
1 TCACACGGGCAGAACACACAGTCGTGTCAAATTGGCAGAATCGAACACG
11706665 GCCTGAAGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
51 6 0.14
52 36 0.86
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.18
Consensus pattern (51 bp):
TCACACGGGCAGAACACACAGTCGTGTCAAATTGGCAGAATCGAACACGAT
Found at i:11713707 original size:104 final size:104
Alignment explanation
Indices: 11713527--11713750 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
11713517 TTGTATATAA
** * *
11713527 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
11713592 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
11713631 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
11713695 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
11713735 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
11713751 GATATCCATT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:11713803 original size:71 final size:71
Alignment explanation
Indices: 11713669--11713892 Score: 385
Period size: 71 Copynumber: 3.1 Consensus size: 71
11713659 TCATTGGTGG
*** * *
11713669 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
11713734 GAGGGGT
65 GAGGGGT
*
11713741 TGCTAAGTGCGATATCCATTGTATATTTGAAATGAAAAGGGGGTTGTTATGTGCTGATTCCCCCG
1 TGCTAAGTGCGATATCCATTGTATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
11713806 AGGGGT
66 AGGGGT
11713812 TGCTAAGTGCGATATCCATTGTATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
1 TGCTAAGTGCGATATCCATTGTATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
11713877 AGGGGT
66 AGGGGT
11713883 TGCTAAGTGC
1 TGCTAAGTGC
11713893 TGATTCCCCG
Statistics
Matches: 145, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
71 115 0.79
72 30 0.21
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (71 bp):
TGCTAAGTGCGATATCCATTGTATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
AGGGGT
Found at i:11721336 original size:104 final size:104
Alignment explanation
Indices: 11721156--11721379 Score: 378
Period size: 104 Copynumber: 2.2 Consensus size: 104
11721146 TGTATATAAA
** * *
11721156 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
11721221 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
11721260 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCATATCT
11721324 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
11721364 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
11721380 GATATCCATT
Statistics
Matches: 113, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
104 112 0.99
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.32, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:11721431 original size:71 final size:72
Alignment explanation
Indices: 11721298--11721449 Score: 252
Period size: 71 Copynumber: 2.1 Consensus size: 72
11721288 TCATTGGTGG
* *
11721298 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
11721363 GAGGGGT
66 GAGGGGT
***
11721370 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
11721434 GAGGGGT
66 GAGGGGT
11721441 TGCTAAGTG
1 TGCTAAGTG
11721450 ATGATTCCCC
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 45 0.60
72 30 0.40
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGGT
Found at i:11733064 original size:153 final size:152
Alignment explanation
Indices: 11732773--11733064 Score: 435
Period size: 153 Copynumber: 1.9 Consensus size: 152
11732763 GATTGGACGC
* *
11732773 TGATAAACCGTAATTTATACATATTTTTATCCCATGCTTAGCACATTTATGGATGATTTCTCCTT
1 TGATAAACCGTAATTTATACATATTTTTACCCCATGCTTAACACATTTATGGATGATTTCTCCTT
* * * * *
11732838 AGATTTGGTGAATTCAATGCTCCTAATTCTTTAATTTTATGTTTTATACTTAGGTAAGCATAGGA
66 AAAATTGGTGAATTCAATGCTCCTAATACTTTAATTTCATGTTTTATACTTAGGTAAGCAAAGGA
**
11732903 GGGCAAAAAGAGCTAGAAACGG
131 ACGCAAAAAGAGCTAGAAACGG
*
11732925 TGATAAACCGTAATTTATACATATTTTTACCCCATGCTTAACACATTTTATGGATGATTTTTCCT
1 TGATAAACCGTAATTTATACATATTTTTACCCCATGCTTAACACA-TTTATGGATGATTTCTCCT
* *
11732990 TAAAATTGGTGAATTCGATGCTCCTAATACTTTAATTTCATGTTTTATGCTTAGG-AGAGCGAAA
65 TAAAATTGGTGAATTCAATGCTCCTAATACTTTAATTTCATGTTTTATACTTAGGTA-AGC-AAA
11733054 GGAACG-AAAAA
128 GGAACGCAAAAA
11733065 CGGGCCAAAA
Statistics
Matches: 125, Mismatches: 12, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
152 44 0.35
153 75 0.60
154 6 0.05
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (152 bp):
TGATAAACCGTAATTTATACATATTTTTACCCCATGCTTAACACATTTATGGATGATTTCTCCTT
AAAATTGGTGAATTCAATGCTCCTAATACTTTAATTTCATGTTTTATACTTAGGTAAGCAAAGGA
ACGCAAAAAGAGCTAGAAACGG
Found at i:11739549 original size:19 final size:19
Alignment explanation
Indices: 11739505--11739556 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
11739495 AATTATAAAA
*
11739505 AATAAAAATAATAAATTTT
1 AATAAAAATAATAAATTCT
* *
11739524 AGA-AAAATTATTAAATTCT
1 A-ATAAAAATAATAAATTCT
11739543 AATAAAAAT-ATAAA
1 AATAAAAATAATAAA
11739557 AATTAGAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
18 5 0.19
19 20 0.77
20 1 0.04
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
AATAAAAATAATAAATTCT
Found at i:11739864 original size:28 final size:28
Alignment explanation
Indices: 11739782--11739901 Score: 91
Period size: 29 Copynumber: 4.1 Consensus size: 28
11739772 ATTTATGAAA
* *
11739782 TTTATATTTCTTTACATTTTGTATAATTTT
1 TTTATATTTCTATA-AATTT-TATAATTTT
* *
11739812 CTTACGACTTTCTA-AAATTTTATAATTTT
1 TTTA-TA-TTTCTATAAATTTTATAATTTT
*
11739841 TTTATATTTCTATATATTTTATAA-TTT
1 TTTATATTTCTATAAATTTTATAATTTT
* * * *
11739868 TTTAGGATTTTTATAAAATTTTACACTTTT
1 TTTA-TATTTCTAT-AAATTTTATAATTTT
11739898 TTTA
1 TTTA
11739902 AAAATTTTTA
Statistics
Matches: 72, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
27 13 0.18
28 18 0.25
29 20 0.28
30 14 0.19
31 2 0.03
32 5 0.07
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.61
Consensus pattern (28 bp):
TTTATATTTCTATAAATTTTATAATTTT
Found at i:11739885 original size:57 final size:59
Alignment explanation
Indices: 11739782--11739901 Score: 147
Period size: 57 Copynumber: 2.1 Consensus size: 59
11739772 ATTTATGAAA
* * *
11739782 TTTATATTTCTTTACATTTTGTATAATTTTCTTACGACTTTCTAAAATTTTATAATTTT
1 TTTATATTTCTATACATTTTGTATAATTTTCTTACGACTTTATAAAATTTTACAATTTT
* * * *
11739841 TTTATATTTCTATATA-TTT-TATAATTTT-TTAGGATTTTTATAAAATTTTACACTTTT
1 TTTATATTTCTATACATTTTGTATAATTTTCTTACGA-CTTTATAAAATTTTACAATTTT
11739898 TTTA
1 TTTA
11739902 AAAATTTTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
56 5 0.09
57 31 0.58
58 3 0.06
59 14 0.26
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.61
Consensus pattern (59 bp):
TTTATATTTCTATACATTTTGTATAATTTTCTTACGACTTTATAAAATTTTACAATTTT
Found at i:11739889 original size:21 final size:19
Alignment explanation
Indices: 11739857--11739922 Score: 55
Period size: 19 Copynumber: 3.4 Consensus size: 19
11739847 TTTCTATATA
*
11739857 TTTTAT-AATTTTTTAGGAT
1 TTTTATAAAATTTTTA-GAT
*
11739876 TTTTATAAAA-TTTTACACT
1 TTTTATAAAATTTTTAGA-T
*
11739895 TTTTTTAAAAATTTTTACGAT
1 TTTTAT-AAAATTTTTA-GAT
11739916 TTTTATA
1 TTTTATA
11739923 TTTTTTTCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
18 1 0.03
19 17 0.46
20 7 0.19
21 11 0.30
22 1 0.03
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTATAAAATTTTTAGAT
Found at i:11739976 original size:21 final size:21
Alignment explanation
Indices: 11739936--11739976 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11739926 TTTTCTAATT
*
11739936 TTAAATATTTGAAATTTTTAA
1 TTAAATATTTGAAATATTTAA
11739957 TTAAA-ATTTGATAATATTTA
1 TTAAATATTTGA-AATATTTA
11739977 TAGCTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (21 bp):
TTAAATATTTGAAATATTTAA
Found at i:11740184 original size:93 final size:92
Alignment explanation
Indices: 11740038--11740230 Score: 246
Period size: 93 Copynumber: 2.1 Consensus size: 92
11740028 AAAGCAGGGG
* * * * *
11740038 CTTAATTACTTTTTTTGAAAAAAGTTTGTGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACTC
1 CTTAATTTCTTTTTTTAAAAAAAGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCC
* * *
11740103 AATTGAGTGCAAAAAA-AAAGTAGGAA
66 AAATGAGTGAAAAAAATAAAATAGGAA
*
11740129 CTTAATTTCTGTTTTTTAAAAAAAGGTTTGAGGGCCTTTTTGATTG-ATTTTGAAAGTTTAAGTA
1 CTTAATTTCT-TTTTTTAAAAAAA-GTTTGAGGGCCTTTTTGA-TGCATTTTGAAAGTTCAAGTA
**
11740193 CCCAAATGAGTGAAAAAAATAAAATAGGGG
63 CCCAAATGAGTGAAAAAAATAAAATAGGAA
11740223 CTTAATTT
1 CTTAATTT
11740231 ATTGGTACAT
Statistics
Matches: 87, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
91 9 0.10
92 12 0.14
93 49 0.56
94 17 0.20
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (92 bp):
CTTAATTTCTTTTTTTAAAAAAAGTTTGAGGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACCC
AAATGAGTGAAAAAAATAAAATAGGAA
Found at i:11741026 original size:21 final size:22
Alignment explanation
Indices: 11740977--11741026 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 22
11740967 ACCAAAACGT
*
11740977 AAACTT-ACTAATAGTTAAATA
1 AAACTTAACTAATACTTAAATA
*
11740998 AAATTTAACTAATACTTAAA-A
1 AAACTTAACTAATACTTAAATA
11741019 AAACTTAA
1 AAACTTAA
11741027 TAGTTCAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.32
Consensus pattern (22 bp):
AAACTTAACTAATACTTAAATA
Found at i:11741040 original size:26 final size:30
Alignment explanation
Indices: 11741011--11741066 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
11741001 TTTAACTAAT
11741011 ACTTAAA-AAAA-C-TT-AATAGTTCAATG
1 ACTTAAATAAAAGCTTTGAATAGTTCAATG
11741037 ACTTAAATAAAAGCTTTTGAATAGTTCAAT
1 ACTTAAATAAAAGC-TTTGAATAGTTCAAT
11741067 AGCTTAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 7 0.28
27 4 0.16
28 1 0.04
30 2 0.08
31 11 0.44
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (30 bp):
ACTTAAATAAAAGCTTTGAATAGTTCAATG
Found at i:11744734 original size:14 final size:14
Alignment explanation
Indices: 11744715--11744753 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
11744705 AAATCAATAA
11744715 AATTTTCTTATCAG
1 AATTTTCTTATCAG
11744729 AATTTTCTTATCAG
1 AATTTTCTTATCAG
11744743 AATTTTCTTAT
1 AATTTTCTTAT
11744754 GACATTCCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.28, C:0.13, G:0.05, T:0.54
Consensus pattern (14 bp):
AATTTTCTTATCAG
Found at i:11746807 original size:26 final size:26
Alignment explanation
Indices: 11746778--11746885 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
11746768 TGGTACAAAT
11746778 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
11746804 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
11746830 TGATAATGGGTTGGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
11746856 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
11746882 TGAT
1 TGAT
11746886 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.31, C:0.07, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:11748361 original size:28 final size:28
Alignment explanation
Indices: 11748330--11748392 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
11748320 AAAAGCAGTT
11748330 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTATAATACCCCTATGTATGGA
* *
11748358 AAATTACTGTTATACCCCTATGTATGGA
1 AAATTACTATAATACCCCTATGTATGGA
11748386 AAATTAC
1 AAATTAC
11748393 CGTTATACCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.33
Consensus pattern (28 bp):
AAATTACTATAATACCCCTATGTATGGA
Found at i:11748397 original size:28 final size:28
Alignment explanation
Indices: 11748341--11748405 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
11748331 AATTACTATA
*
11748341 ATACCCCTATGTATGGAAAATTACTGTT
1 ATACCCCTATGTATGGAAAATTACCGTT
11748369 ATACCCCTATGTATGGAAAATTACCGTT
1 ATACCCCTATGTATGGAAAATTACCGTT
11748397 ATACCCCTA
1 ATACCCCTA
11748406 GGGTTAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.32, C:0.23, G:0.12, T:0.32
Consensus pattern (28 bp):
ATACCCCTATGTATGGAAAATTACCGTT
Found at i:11748593 original size:54 final size:53
Alignment explanation
Indices: 11748511--11748651 Score: 237
Period size: 54 Copynumber: 2.6 Consensus size: 53
11748501 AGGAAGCGTC
11748511 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
11748565 CTGGTGGCTATGCCACGATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCAC-ATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
* *
11748619 CTGGTGGCTCTGCCACAATATCTGTATCTGGTG
1 CTGGTGGCTATGCCACATTATCTG-ATCTGGTG
11748652 ACTTCGTCAC
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
53 7 0.08
54 76 0.92
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (53 bp):
CTGGTGGCTATGCCACATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
Found at i:11748662 original size:27 final size:27
Alignment explanation
Indices: 11748511--11748669 Score: 193
Period size: 27 Copynumber: 5.9 Consensus size: 27
11748501 AGGAAGCGTC
*
11748511 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
11748538 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
* *
11748565 CTGGTGGCTATGCCACGATTATCTG-AT
1 CTGGTGGCTCTGCCAC-AATATCTGTAT
11748592 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
11748619 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
11748646 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
11748670 GCAGCCTCGC
Statistics
Matches: 117, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
26 10 0.09
27 105 0.90
28 2 0.02
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.35
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:11750029 original size:23 final size:24
Alignment explanation
Indices: 11749999--11750045 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
11749989 TATAATATAT
11749999 ATAATTTTTAAAAAAATT-TAAAA
1 ATAATTTTTAAAAAAATTCTAAAA
* *
11750022 ATAATTTTTTATAAAATTCTAAAA
1 ATAATTTTTAAAAAAATTCTAAAA
11750046 TATATAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
ATAATTTTTAAAAAAATTCTAAAA
Found at i:11750095 original size:20 final size:19
Alignment explanation
Indices: 11750063--11750112 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
11750053 TTATAAATTT
*
11750063 TAAAAAGTG-AAAATAATA
1 TAAAAATTGAAAAATAATA
**
11750081 TATAAAATTGAAAAATGTTA
1 TA-AAAATTGAAAAATAATA
11750101 TAAAAATTGAAA
1 TAAAAATTGAAA
11750113 TTTTGAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 2 0.07
19 16 0.59
20 9 0.33
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (19 bp):
TAAAAATTGAAAAATAATA
Found at i:11750201 original size:29 final size:30
Alignment explanation
Indices: 11750169--11750225 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
11750159 TTTTAGAATT
11750169 TTATAAAAAATTATT-TTTAT-TTTTTAAAA
1 TTATAAAAAATT-TTATTTATATTTTTAAAA
*
11750198 TTATAAATAATTTTATTTATATTTTTAA
1 TTATAAAAAATTTTATTTATATTTTTAA
11750226 TCAATATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 2 0.08
29 16 0.64
30 7 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
TTATAAAAAATTTTATTTATATTTTTAAAA
Found at i:11750385 original size:20 final size:19
Alignment explanation
Indices: 11750345--11750400 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 19
11750335 TAATTAAATA
11750345 TTAAATTTTATAATTTT--T
1 TTAAATTTT-TAATTTTAAT
11750363 TTATAATTTTTAATTTTAAT
1 TTA-AATTTTTAATTTTAAT
11750383 TTAATATTTTT-ATTTTAA
1 TTAA-ATTTTTAATTTTAA
11750401 ATAAATTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 14 0.41
20 10 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTAAATTTTTAATTTTAAT
Found at i:11754056 original size:25 final size:25
Alignment explanation
Indices: 11754028--11754105 Score: 102
Period size: 25 Copynumber: 3.1 Consensus size: 25
11754018 ACAAAGCGGG
**
11754028 AGTCCTAATCTAATTCCTAATTTGA
1 AGTCCTAATAGAATTCCTAATTTGA
* * *
11754053 AGTCCTGATAGAATTCTTAATTTAA
1 AGTCCTAATAGAATTCCTAATTTGA
*
11754078 AGTTCTAATAGAATTCCTAATTTGA
1 AGTCCTAATAGAATTCCTAATTTGA
11754103 AGT
1 AGT
11754106 TTATAAAAAC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 44 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (25 bp):
AGTCCTAATAGAATTCCTAATTTGA
Found at i:11758746 original size:25 final size:25
Alignment explanation
Indices: 11758718--11758795 Score: 102
Period size: 25 Copynumber: 3.1 Consensus size: 25
11758708 ACAAAGGGAG
** * *
11758718 AGTCCTAATCTAATTCCTAATTTGA
1 AGTCCTAATAGAATTCTTAATTTAA
*
11758743 AGTCCTGATAGAATTCTTAATTTAA
1 AGTCCTAATAGAATTCTTAATTTAA
*
11758768 AGTTCTAATAGAATTCTTAATTTAA
1 AGTCCTAATAGAATTCTTAATTTAA
11758793 AGT
1 AGT
11758796 TTATAAAAAC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 46 1.00
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (25 bp):
AGTCCTAATAGAATTCTTAATTTAA
Found at i:11762406 original size:17 final size:17
Alignment explanation
Indices: 11762384--11762416 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
11762374 AAGGATGGTT
11762384 TTTACAAAGAGAGAATG
1 TTTACAAAGAGAGAATG
11762401 TTTACAAAGAGAGAAT
1 TTTACAAAGAGAGAAT
11762417 TCTAAAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.21, T:0.24
Consensus pattern (17 bp):
TTTACAAAGAGAGAATG
Found at i:11762424 original size:15 final size:17
Alignment explanation
Indices: 11762386--11762424 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
11762376 GGATGGTTTT
*
11762386 TACAAAGAGAGAATGTT
1 TACAAAGAGAGAATGTC
11762403 TACAAAGAGAGAAT-TC
1 TACAAAGAGAGAATGTC
11762419 TA-AAAG
1 TACAAAG
11762425 TAAGATAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 3 0.14
17 14 0.67
ACGTcount: A:0.51, C:0.08, G:0.21, T:0.21
Consensus pattern (17 bp):
TACAAAGAGAGAATGTC
Found at i:11776701 original size:22 final size:22
Alignment explanation
Indices: 11776676--11776721 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
11776666 CAAATCGTAA
*
11776676 AAATGCAACTATTAAGTTTTTT
1 AAATGCAACAATTAAGTTTTTT
11776698 AAATGCAACAATTAAGTTTTTT
1 AAATGCAACAATTAAGTTTTTT
11776720 AA
1 AA
11776722 CTAACATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (22 bp):
AAATGCAACAATTAAGTTTTTT
Found at i:11778993 original size:14 final size:14
Alignment explanation
Indices: 11778974--11779003 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11778964 TGCTTGATTG
11778974 TTAGTCCATCATTT
1 TTAGTCCATCATTT
*
11778988 TTAGTCCATTATTT
1 TTAGTCCATCATTT
11779002 TT
1 TT
11779004 GTGTCATGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.17, G:0.07, T:0.57
Consensus pattern (14 bp):
TTAGTCCATCATTT
Found at i:11779590 original size:129 final size:132
Alignment explanation
Indices: 11779365--11779604 Score: 296
Period size: 129 Copynumber: 1.8 Consensus size: 132
11779355 GATATTTAGT
* * *
11779365 AATTCTTGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTTGCATTTGCTCAAAATAATCGAATA
1 AATTCGTGGAATCGTGCCCTAACGTGTTGGGTAGCAATTTTGCATTTGCTCAAAATAATCAAATA
* * *
11779430 TCGCTTTAAAATTTCGCTCGTGTCTT-TTAAAATCC-CTAAAACGAAGGCGATATCTGGTATTTG
66 TCCCTTTAAAATTTCACTCGTGTCTTCTAAAAATCCTCTAAAACGAAGGCGATATCTGGTATTTG
11779493 GC
131 GC
* * * *
11779495 AATTCGTGGGATCGTGCCCTAACGT-TTGGGTAGCAATTTCT-CGA-TTGTTTAAACTAATCAAA
1 AATTCGTGGAATCGTGCCCTAACGTGTTGGGTAGCAATTT-TGC-ATTTGCTCAAAATAATCAAA
*
11779557 TATCCCTTCT-AAATTTCACTCG-GCTCTTCTAAAAATCCTTTAAAACGA
64 TATCCCTT-TAAAATTTCACTCGTG-TCTTCTAAAAATCCTCTAAAACGA
11779605 GGGCAATACT
Statistics
Matches: 93, Mismatches: 11, Indels: 11
0.81 0.10 0.10
Matches are distributed among these distances:
128 1 0.01
129 50 0.54
130 34 0.37
131 8 0.09
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (132 bp):
AATTCGTGGAATCGTGCCCTAACGTGTTGGGTAGCAATTTTGCATTTGCTCAAAATAATCAAATA
TCCCTTTAAAATTTCACTCGTGTCTTCTAAAAATCCTCTAAAACGAAGGCGATATCTGGTATTTG
GC
Found at i:11780547 original size:34 final size:33
Alignment explanation
Indices: 11780483--11780565 Score: 87
Period size: 32 Copynumber: 2.5 Consensus size: 33
11780473 ATTAATAATT
*
11780483 ATATATATAATATTTATTTTTAAAAATTATT-A
1 ATATATATAATATTAATTTTTAAAAATTATTGA
* *
11780515 ATATATATAATATTAAGTTTTGTATAATTTATTGA
1 ATATATATAATATTAA-TTTT-TAAAAATTATTGA
* *
11780550 GTATATACCAATATTA
1 ATATATA-TAATATTA
11780566 TATGATATGC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
32 15 0.36
33 4 0.10
34 9 0.21
35 7 0.17
36 7 0.17
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (33 bp):
ATATATATAATATTAATTTTTAAAAATTATTGA
Found at i:11780803 original size:25 final size:25
Alignment explanation
Indices: 11780769--11780820 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
11780759 TAGTTAGATG
11780769 AGAACACCCAACCATATGATATTAA
1 AGAACACCCAACCATATGATATTAA
11780794 AGAACACCCAACCATATGATATTAA
1 AGAACACCCAACCATATGATATTAA
11780819 AG
1 AG
11780821 GTAGAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.48, C:0.23, G:0.10, T:0.19
Consensus pattern (25 bp):
AGAACACCCAACCATATGATATTAA
Found at i:11783655 original size:19 final size:19
Alignment explanation
Indices: 11783631--11783668 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11783621 GCCACTGCCA
*
11783631 CCCACCATAATTAAATTTG
1 CCCACCATAATCAAATTTG
*
11783650 CCCACCGTAATCAAATTTG
1 CCCACCATAATCAAATTTG
11783669 TTCTTAACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.08, T:0.29
Consensus pattern (19 bp):
CCCACCATAATCAAATTTG
Found at i:11788057 original size:17 final size:17
Alignment explanation
Indices: 11787990--11788057 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 17
11787980 GCTCTCAAGC
** *
11787990 TTGGTGAGCTCGTGGTC
1 TTGGTGAGCTCGCAGTT
* * *
11788007 TTAGTAAGCTCGCAATT
1 TTGGTGAGCTCGCAGTT
*
11788024 TTGGTGAGCTCGTAGTT
1 TTGGTGAGCTCGCAGTT
*
11788041 TTGGTGAGCTTGCAGTT
1 TTGGTGAGCTCGCAGTT
11788058 CACAGTTTGC
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.15, C:0.15, G:0.32, T:0.38
Consensus pattern (17 bp):
TTGGTGAGCTCGCAGTT
Found at i:11795353 original size:41 final size:41
Alignment explanation
Indices: 11795280--11795415 Score: 159
Period size: 41 Copynumber: 3.3 Consensus size: 41
11795270 AGAGCAATAG
* * *
11795280 AAACGCCGCTAAAAGCCAGAGCATTTGTGGCGCTTTTGGTA
1 AAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTA
* * *
11795321 AAACGCCACTAAAAACCAAAGAATTAGCGGCGCTTTAT-GTA
1 AAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTT-TGGTA
* * *
11795362 AAACGCCGCTAGAAACCAGAGCATTAGCGGC-ATTTCGGTA
1 AAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTA
*
11795402 AAGCGCCGCTAAAA
1 AAACGCCGCTAAAA
11795416 GTCATATAAC
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
40 18 0.23
41 60 0.76
42 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.19
Consensus pattern (41 bp):
AAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTTGGTA
Found at i:11795486 original size:45 final size:45
Alignment explanation
Indices: 11795420--11795547 Score: 141
Period size: 45 Copynumber: 2.8 Consensus size: 45
11795410 CTAAAAGTCA
*
11795420 TATAACCCCTAAAACCTTAAACCCCAAAAAACATAAACACTAATC
1 TATAACCCCTAAAACCTTAAACCCCAAAAAACATAAACACTAAAC
** * *
11795465 TATAACCCCTAAAACAC-TAAACCCCCTAAACCCTAAACACTAAAC
1 TATAACCCCTAAAAC-CTTAAACCCCAAAAAACATAAACACTAAAC
**
11795510 TATAACCTTTAAAACCTTAATTAAACCCCAAAAAACAT
1 TATAACCCCTAAAACC----TTAAACCCCAAAAAACAT
11795548 CATATGGATG
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
44 1 0.02
45 51 0.77
46 1 0.02
49 13 0.20
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (45 bp):
TATAACCCCTAAAACCTTAAACCCCAAAAAACATAAACACTAAAC
Found at i:11797765 original size:114 final size:115
Alignment explanation
Indices: 11797553--11798149 Score: 534
Period size: 114 Copynumber: 5.2 Consensus size: 115
11797543 AAAAAATTGG
* * * * ***
11797553 ATTTAGCGGCGCTAGGGAATAAACGCCGCTAAAGGGTT-TTCT-ATTATA-CAAGACGACACCGT
1 ATTTAGCGGCGCAAGGGAATAAACGCCACTAAA-GGTTATTCTGTTTATATCAAAACGATGTCGT
* * *
11797615 TTTCTTTGGATTTTTAGTGGCGTTTTAGGTTAAAACGCCACAATAGGGTTG-
65 TTT-TATGGATTTTTAGTGGCGTTTTAGGGTAAAACGCCACAATAGGTTTGC
* * * * * *
11797666 ATTTAGCGGTGCAAGGGAATAAACGCCACTAAGGGTTATTTTGTTTAGATCAAAACGGTGTAGTT
1 ATTTAGCGGCGCAAGGGAATAAACGCCACTAAAGGTTATTCTGTTTATATCAAAACGATGTCGTT
* * *
11797731 TTTATGGATTTTTAGTGGCGTTTTTGGTTTAAACGCCACAATAGGTTTG-
66 TTTATGGATTTTTAGTGGCGTTTTAGGGTAAAACGCCACAATAGGTTTGC
* * * * * * *
11797780 ATTTAGCGGTGCTAGGGTATAAACGCCACTAATGGTTATTTTGTTTATATCAAAACAATGTTGTT
1 ATTTAGCGGCGCAAGGGAATAAACGCCACTAAAGGTTATTCTGTTTATATCAAAACGATGTCGTT
* * * * *
11797845 TTGATCGATTCTTAGTGGCGTTTTAGGGTAAAATGCCGCAATA-GTTTCGC
66 TTTATGGATTTTTAGTGGCGTTTTAGGGTAAAACGCCACAATAGGTTT-GC
* ** * * * *
11797895 CTTTAGCGGCGC-TTGGAGATAAAACGCCACTAAATGTTATTCTGTTCATATGAAAACGACGTCG
1 ATTTAGCGGCGCAAGGGA-AT-AAACGCCACTAAAGGTTATTCTGTTTATATCAAAACGATGTCG
* * * * *
11797959 TTTTTTTGGATTTTTAGTGGCGTTTTAGGGTGAAACGCCGCAATTGATTTGC
64 TTTTTATGGATTTTTAGTGGCGTTTTAGGGTAAAACGCCACAATAGGTTTGC
* * * *
11798011 ATTTAGCGGCGCTATGGG-A-AAACGCCACTAAAGTTTATTCTATTTATATCAAAACGGTGTCGT
1 ATTTAGCGGCGC-AAGGGAATAAACGCCACTAAAGGTTATTCTGTTTATATCAAAACGATGTCGT
* * * * * * *
11798074 TTTGT-TTGTTTTTTAGTGGCG-TTTATGTTAAAACGTCGCAATTGGTTTGC
65 TTT-TATGGATTTTTAGTGGCGTTTTAGGGTAAAACGCCACAATAGGTTTGC
* * *
11798124 CTTTAGCGGCGCTAGGGGA-AAACGCC
1 ATTTAGCGGCGCAAGGGAATAAACGCC
11798150 GCAAATGTTA
Statistics
Matches: 400, Mismatches: 72, Indels: 24
0.81 0.15 0.05
Matches are distributed among these distances:
112 7 0.02
113 79 0.20
114 197 0.49
115 24 0.06
116 87 0.22
117 3 0.01
118 3 0.01
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.35
Consensus pattern (115 bp):
ATTTAGCGGCGCAAGGGAATAAACGCCACTAAAGGTTATTCTGTTTATATCAAAACGATGTCGTT
TTTATGGATTTTTAGTGGCGTTTTAGGGTAAAACGCCACAATAGGTTTGC
Found at i:11797978 original size:230 final size:229
Alignment explanation
Indices: 11797686--11798136 Score: 548
Period size: 230 Copynumber: 2.0 Consensus size: 229
11797676 GCAAGGGAAT
* * * **
11797686 AAACGCCACTAAGGGTTATTTTGTTTAGATCAAAACGGTGTAGTTTTTATGGATTTTTAGTGGCG
1 AAACGCCACTAAAGGTTATTCTGTTCAGATCAAAACGACGTAGTTTTTATGGATTTTTAGTGGCG
* * * * * *
11797751 TTTTTGGTTTAAACGCCACAATAGGTTTG-ATTTAGCGGTGCTA-GGGTATAAACGCCACTAATG
66 TTTTAGGGTGAAACGCCACAATAGATTTGCATTTAGCGGCGCTATGGG-A-AAACGCCACTAAAG
* * * *
11797814 GTTATTTTGTTTATATCAAAACAATGTTGTTTTGATCGATTCTTAGTGGCGTTTTAGGGTAAAAT
129 GTTATTCTATTTATATCAAAACAATGTCGTTTTGATCGATTCTTAGTGGCG-TTTAGGGTAAAAC
11797879 GCCGCAA-TAGTTTCGCCTTTAGCGGCGCTTGGAGATA
193 GCCGCAATTAGTTT-GCCTTTAGCGGCGCTTGGAGATA
* * * * *
11797916 AAACGCCACTAAATGTTATTCTGTTCATATGAAAACGACGTCGTTTTTTTGGATTTTTAGTGGCG
1 AAACGCCACTAAAGGTTATTCTGTTCAGATCAAAACGACGTAGTTTTTATGGATTTTTAGTGGCG
* * *
11797981 TTTTAGGGTGAAACGCCGCAATTGATTTGCATTTAGCGGCGCTATGGGAAAACGCCACTAAAGTT
66 TTTTAGGGTGAAACGCCACAATAGATTTGCATTTAGCGGCGCTATGGGAAAACGCCACTAAAGGT
** * * * * * * *
11798046 TATTCTATTTATATCAAAACGGTGTCGTTTTGTTTGTTTTTTAGTGGCGTTTATGTTAAAACGTC
131 TATTCTATTTATATCAAAACAATGTCGTTTTGATCGATTCTTAGTGGCGTTTAGGGTAAAACGCC
*
11798111 GCAATTGGTTTGCCTTTAGCGGCGCT
196 GCAATTAGTTTGCCTTTAGCGGCGCT
11798137 AGGGGAAAAC
Statistics
Matches: 185, Mismatches: 33, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
229 31 0.17
230 137 0.74
231 14 0.08
232 3 0.02
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.38
Consensus pattern (229 bp):
AAACGCCACTAAAGGTTATTCTGTTCAGATCAAAACGACGTAGTTTTTATGGATTTTTAGTGGCG
TTTTAGGGTGAAACGCCACAATAGATTTGCATTTAGCGGCGCTATGGGAAAACGCCACTAAAGGT
TATTCTATTTATATCAAAACAATGTCGTTTTGATCGATTCTTAGTGGCGTTTAGGGTAAAACGCC
GCAATTAGTTTGCCTTTAGCGGCGCTTGGAGATA
Found at i:11798349 original size:60 final size:59
Alignment explanation
Indices: 11798227--11798357 Score: 181
Period size: 60 Copynumber: 2.2 Consensus size: 59
11798217 TATTCATTTT
* * ** * *
11798227 CCCCCTTCTCCCTGGTTTATTTCCCCTATTTTCCCTTCTTCGAATCCCTAAAATAATCA
1 CCCCCTTCTCCCTAGTTTATTTCCCCCATTTTCCCTAATTCAAAACCCTAAAATAATCA
*
11798286 CCCCCTTCTCCCTAGTTTATTTCCCCCCATTTTCCCTAATTCAAAACCCTAAAATAATTA
1 CCCCCTTCTCCCTAGTTTATTT-CCCCCATTTTCCCTAATTCAAAACCCTAAAATAATCA
*
11798346 CCCCCTTTTCCC
1 CCCCCTTCTCCC
11798358 CAATTCGAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
59 21 0.33
60 42 0.67
ACGTcount: A:0.21, C:0.40, G:0.03, T:0.37
Consensus pattern (59 bp):
CCCCCTTCTCCCTAGTTTATTTCCCCCATTTTCCCTAATTCAAAACCCTAAAATAATCA
Found at i:11799822 original size:19 final size:18
Alignment explanation
Indices: 11799790--11799839 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
11799780 AATCAATTAA
11799790 AATTTATAAT-AATAAAAAT
1 AATTT-TAATAAAT-AAAAT
11799809 AATTTTAATAAATAAAAT
1 AATTTTAATAAATAAAAT
*
11799827 ATTTTTAAATAAA
1 AATTTT-AATAAA
11799840 CTGAAGAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTTTAATAAATAAAAT
Found at i:11801286 original size:26 final size:26
Alignment explanation
Indices: 11801257--11801364 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
11801247 TGGTACAAAT
11801257 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
11801283 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
11801309 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
11801335 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
11801361 TGAT
1 TGAT
11801365 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:11805379 original size:25 final size:24
Alignment explanation
Indices: 11805351--11805424 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 24
11805341 TTTATTTTGG
11805351 ATTAATCAGGACACAATTTTTTTAA
1 ATTAATCA-GACACAATTTTTTTAA
**
11805376 ATT-A-C-GACAC-ATATTTTGCAA
1 ATTAATCAGACACAAT-TTTTTTAA
*
11805397 TTTAATCACGACACAA-TTTTTTAA
1 ATTAATCA-GACACAATTTTTTTAA
11805421 ATTA
1 ATTA
11805425 CATATTTTGG
Statistics
Matches: 37, Mismatches: 6, Indels: 13
0.66 0.11 0.23
Matches are distributed among these distances:
20 2 0.05
21 13 0.35
22 1 0.03
23 2 0.05
24 10 0.27
25 8 0.22
26 1 0.03
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (24 bp):
ATTAATCAGACACAATTTTTTTAA
Found at i:11805512 original size:9 final size:9
Alignment explanation
Indices: 11805500--11805530 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
11805490 ATATCATATA
11805500 ATAACTTAC
1 ATAACTTAC
11805509 ATAACTTAC
1 ATAACTTAC
*
11805518 AAAACTTAC
1 ATAACTTAC
11805527 ATAA
1 ATAA
11805531 TACATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.52, C:0.19, G:0.00, T:0.29
Consensus pattern (9 bp):
ATAACTTAC
Found at i:11805551 original size:13 final size:13
Alignment explanation
Indices: 11805533--11805562 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
11805523 TTACATAATA
11805533 CATAAATATATAT
1 CATAAATATATAT
11805546 CATAAATATATAT
1 CATAAATATATAT
11805559 CATA
1 CATA
11805563 TCATAACTTA
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:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (13 bp):
CATAAATATATAT
Found at i:11805569 original size:56 final size:56
Alignment explanation
Indices: 11805508--11805662 Score: 249
Period size: 56 Copynumber: 2.8 Consensus size: 56
11805498 TAATAACTTA
*
11805508 CATAACTTACAAAACTTACATAATACATAAATATATATCATAAATATATATCATAT
1 CATAACTTACACAACTTACATAATACATAAATATATATCATAAATATATATCATAT
* * *
11805564 CATAACTTACACAACTAACATAATACATAAATATATTTCATAAATATGTATCATAT
1 CATAACTTACACAACTTACATAATACATAAATATATATCATAAATATATATCATAT
11805620 CATAACTTACACAACTTACATAATAC-TCCAAATATATATCATA
1 CATAACTTACACAACTTACATAATACAT--AAATATATATCATA
11805663 CAAATGAAGA
Statistics
Matches: 91, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
55 1 0.01
56 77 0.85
57 13 0.14
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.33
Consensus pattern (56 bp):
CATAACTTACACAACTTACATAATACATAAATATATATCATAAATATATATCATAT
Found at i:11810727 original size:21 final size:21
Alignment explanation
Indices: 11810620--11810716 Score: 135
Period size: 21 Copynumber: 4.6 Consensus size: 21
11810610 ACTTAGAGCG
*
11810620 GAGGCAGCAGAGAGGGAGGCA
1 GAGGCAGCAGCGAGGGAGGCA
11810641 GTA-GCAGCAGCGAGGGAGGCA
1 G-AGGCAGCAGCGAGGGAGGCA
* *
11810662 GTGGCAGTAGCGAGGGAGGCA
1 GAGGCAGCAGCGAGGGAGGCA
11810683 GAGGCA-CGAGCGAGGGAGGCA
1 GAGGCAGC-AGCGAGGGAGGCA
11810704 GAGGCAGCAGCGA
1 GAGGCAGCAGCGA
11810717 TGGCAGCAGA
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
21 65 0.97
22 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.51, T:0.03
Consensus pattern (21 bp):
GAGGCAGCAGCGAGGGAGGCA
Found at i:11813343 original size:20 final size:20
Alignment explanation
Indices: 11813318--11813382 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
11813308 CACGCTTATT
11813318 CTGTTTGCACTTTGGTGCCC
1 CTGTTTGCACTTTGGTGCCC
*
11813338 CTGTTTGCACTATGGTGCCC
1 CTGTTTGCACTTTGGTGCCC
* *
11813358 TTGTATGCACATTT-GTGCCC
1 CTGTTTGCAC-TTTGGTGCCC
*
11813378 TTGTT
1 CTGTT
11813383 CAAACATTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
20 37 0.95
21 2 0.05
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (20 bp):
CTGTTTGCACTTTGGTGCCC
Found at i:11813429 original size:12 final size:13
Alignment explanation
Indices: 11813398--11813429 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
11813388 ATTATAATAA
11813398 TTAAAAATCTATC
1 TTAAAAATCTATC
11813411 TTAAAAATCTATC
1 TTAAAAATCTATC
11813424 TTAAAA
1 TTAAAA
11813430 GTTTTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (13 bp):
TTAAAAATCTATC
Found at i:11816288 original size:47 final size:44
Alignment explanation
Indices: 11816219--11816571 Score: 232
Period size: 47 Copynumber: 7.6 Consensus size: 44
11816209 GATTTGTACT
* *
11816219 CCAGTGTAAGACATGTCTGGGACATCCTTCGGCCATATTATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATC-GCCATA-TATGAGAG
* * *
11816265 CCAGTGTAAGACCATGTCTGGGACATGGCATCTG-CATCCAGACGAGGG
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATC-GCCAT--ATATGAGAG
* * *
11816313 CTAGTGTAAGACATGTCTGGGACATGCATCGCCATACTATAATAG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGCCATA-TATGAGAG
* * * *
11816358 CCAGTGTAAAACCATGTCTGGGACATGGCATCGACACAGAGATGAGTG
1 CCAGTGTAAGA-CATGTCTGGGACAT-GCATCG-C-CATATATGAGAG
* * *
11816406 CCAGTGTAAGACATGTTTGGGACATGCGTCGGCC-TCGACA-GAGATAG
1 CCAGTGTAAGACATGTCTGGGACATGCATC-GCCAT--ATATGAG--AG
* * * * *
11816453 CCAGTGTAAGACGTGTTTGGGACACGCATTGCC-TA-A-GAGTTGTG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGCCATATATGA---GAG
* *
11816497 CAAGTGTAAGACATGTCTGGGACATGCATCAGCACGCGTATATGAGAG
1 CCAGTGTAAGACATGTCTGGGACATGCATC-G--C-CATATATGAGAG
*
11816545 CCCGTGTAAGACCATGTCTGGGACATG
1 CCAGTGTAAGA-CATGTCTGGGACATG
11816572 GAATCGACAA
Statistics
Matches: 243, Mismatches: 38, Indels: 49
0.74 0.12 0.15
Matches are distributed among these distances:
43 3 0.01
44 28 0.12
45 18 0.07
46 45 0.19
47 79 0.33
48 46 0.19
49 21 0.09
50 1 0.00
51 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (44 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCGCCATATATGAGAG
Found at i:11816381 original size:93 final size:94
Alignment explanation
Indices: 11816219--11816580 Score: 298
Period size: 93 Copynumber: 3.9 Consensus size: 94
11816209 GATTTGTACT
* * * * *
11816219 CCAGTGTAAGACATGTCTGGGACATCCTTCGGCCATATTATGAGAGCCAGTGTAAGACCATGTCT
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCCATACTATAAGAGCCAGTGTAAAACCATGTCT
11816284 GGGACATGGCATCTG-CATC-CAGACGAGGG
66 GGGACATGGCATC-GACA-CACAGACGAGGG
* *
11816313 CTAGTGTAAGACATGTCTGGGACATGCATC-GCCATACTATAATAGCCAGTGTAAAACCATGTCT
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCCATACTATAAGAGCCAGTGTAAAACCATGTCT
* * *
11816377 GGGACATGGCATCGACACAGAGATGAGTG
66 GGGACATGGCATCGACACACAGACGAGGG
* * * * * *
11816406 CCAGTGTAAGACATGTTTGGGACATGCGTCGGCC-TCGAC-AGAGATAGCCAGTGTAAGA-CGTG
1 CCAGTGTAAGACATGTCTGGGACATGCATCGGCCAT--ACTATA-AGAGCCAGTGTAAAACCATG
* * * * *
11816468 TTTGGGACA-CGCATTG-C-CTA-AGA-GTTGTG
63 TCTGGGACATGGCATCGACAC-ACAGACG-AGGG
* * * * * *
11816497 CAAGTGTAAGACATGTCTGGGACATGCATCAGCACGCGTA-TATGAGAGCCCGTGTAAGACCATG
1 CCAGTGTAAGACATGTCTGGGACATGCATC-G-GC-CATACTATAAGAGCCAGTGTAAAACCATG
*
11816561 TCTGGGACATGGAATCGACA
63 TCTGGGACATGGCATCGACA
11816581 ATATATCTCA
Statistics
Matches: 218, Mismatches: 33, Indels: 32
0.77 0.12 0.11
Matches are distributed among these distances:
90 1 0.00
91 34 0.16
92 18 0.08
93 99 0.45
94 48 0.22
95 18 0.08
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (94 bp):
CCAGTGTAAGACATGTCTGGGACATGCATCGGCCATACTATAAGAGCCAGTGTAAAACCATGTCT
GGGACATGGCATCGACACACAGACGAGGG
Found at i:11816561 original size:140 final size:138
Alignment explanation
Indices: 11816221--11816571 Score: 345
Period size: 140 Copynumber: 2.5 Consensus size: 138
11816211 TTTGTACTCC
* * * *
11816221 AGTGTAAGACATGTCTGGGACATCCTTCG-GCCATATTATGAGAGCCAGTGTAAGACCATGTCTG
1 AGTGTAAGACATGTCTGGGACATGCATCGCACCGTA-TATGAGAGCCAGTGTAAGACCATGTCTG
* * * * *
11816285 GGACATGGCATCTGCATCCAGACGAGGGCTAGTGTAAGACATGTCTGGGACATGCATCGCCATAC
65 GGACAT-GCATCGGCATCCAGACGAGAGCCAGTGTAAGACATGTCTGGGACACGCATCGCCATAA
* *
11816350 TATAATAGCC
129 GATAATAGCA
* * * * *
11816360 AGTGTAAAACCATGTCTGGGACATGGCATCGACACAG-AGATGAGTGCCAGTGTAAGA-CATGTT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCG-CACCGTATATGAGAGCCAGTGTAAGACCATGTC
* * * * * *
11816423 TGGGACATGCGTCGGCCTCGACAGA-GATAGCCAGTGTAAGACGTGTTTGGGACACGCATTGCC-
63 TGGGACATGCATCGGCATC--CAGACGAGAGCCAGTGTAAGACATGTCTGGGACACGCATCGCCA
**
11816486 TAAGAGTTGT-GCA
126 TAAGA-TAATAGCA
*
11816499 AGTGTAAGACATGTCTGGGACATGCATCAGCACGCGTATATGAGAGCCCGTGTAAGACCATGTCT
1 AGTGTAAGACATGTCTGGGACATGCATC-GCAC-CGTATATGAGAGCCAGTGTAAGACCATGTCT
11816564 GGGACATG
64 GGGACATG
11816572 GAATCGACAA
Statistics
Matches: 171, Mismatches: 30, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
137 8 0.05
138 16 0.09
139 46 0.27
140 74 0.43
141 25 0.15
142 1 0.01
143 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (138 bp):
AGTGTAAGACATGTCTGGGACATGCATCGCACCGTATATGAGAGCCAGTGTAAGACCATGTCTGG
GACATGCATCGGCATCCAGACGAGAGCCAGTGTAAGACATGTCTGGGACACGCATCGCCATAAGA
TAATAGCA
Found at i:11829191 original size:3 final size:3
Alignment explanation
Indices: 11829183--11829212 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
11829173 AAAATGAGAA
11829183 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11829213 TTAAAGCCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:11832648 original size:13 final size:13
Alignment explanation
Indices: 11832630--11832658 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
11832620 GGTTGTTTAT
11832630 TAAACTAATTAAC
1 TAAACTAATTAAC
11832643 TAAACTAATTAAC
1 TAAACTAATTAAC
11832656 TAA
1 TAA
11832659 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:11835360 original size:18 final size:17
Alignment explanation
Indices: 11835327--11835365 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
11835317 TTGTATAAAT
11835327 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
11835345 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
11835362 TGTG
1 TGTG
11835366 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:11835618 original size:23 final size:23
Alignment explanation
Indices: 11835592--11835665 Score: 114
Period size: 23 Copynumber: 3.3 Consensus size: 23
11835582 GTGTTATTGA
11835592 TCAGTGGTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
*
11835615 TCAGTGGTAGCTTTGGCTACA-T
1 TCAGTGGTAGCTTCGGCTACATT
* *
11835637 CCAGTGGTAGCTTCGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
11835660 TCAGTG
1 TCAGTG
11835666 TGGCACTTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
22 20 0.44
23 25 0.56
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.32
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:11835644 original size:22 final size:22
Alignment explanation
Indices: 11835593--11835658 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
11835583 TGTTATTGAT
*
11835593 CAGTGGTAGCTTCGGCTACATTT
1 CAGTGGTAGCTTCGGCTACA-TC
*
11835616 CAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATC
11835638 CAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACAT
11835659 ATCAGTGTGG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 21 0.52
23 19 0.47
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (22 bp):
CAGTGGTAGCTTCGGCTACATC
Found at i:11842700 original size:18 final size:17
Alignment explanation
Indices: 11842667--11842705 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
11842657 TTGTATAAAT
11842667 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
11842685 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
11842702 TGTG
1 TGTG
11842706 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:11842958 original size:23 final size:23
Alignment explanation
Indices: 11842931--11843028 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
11842921 AGTGTTATTG
11842931 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
11842954 TTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
11842977 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
11842999 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
11843022 ATCAGTG
1 ATCAGTG
11843029 TGGCACTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
22 20 0.29
23 49 0.71
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:11842997 original size:45 final size:45
Alignment explanation
Indices: 11842933--11843021 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
11842923 TGTTATTGAT
* *
11842933 CAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
11842978 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
11843022 ATCAGTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.27, T:0.31
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:11845569 original size:6 final size:6
Alignment explanation
Indices: 11845555--11845587 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
11845545 AATACAATTG
*
11845555 AAATGA AAATAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAA
11845588 GATAGAAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:11850946 original size:13 final size:13
Alignment explanation
Indices: 11850928--11850956 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
11850918 GGTTGTTTAT
11850928 TAAACTAATTAAC
1 TAAACTAATTAAC
11850941 TAAACTAATTAAC
1 TAAACTAATTAAC
11850954 TAA
1 TAA
11850957 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:11852652 original size:17 final size:17
Alignment explanation
Indices: 11852613--11852656 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
11852603 AATTAGGAAT
*
11852613 GTAATTTTTCAGTTTTA
1 GTAATTTTTCAGTTTAA
11852630 GT-ATTTTTCTAG-TTAA
1 GTAATTTTTC-AGTTTAA
11852646 GTAATTTTTCA
1 GTAATTTTTCA
11852657 ATTCAATCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 13 0.54
17 11 0.46
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.57
Consensus pattern (17 bp):
GTAATTTTTCAGTTTAA
Found at i:11854905 original size:22 final size:22
Alignment explanation
Indices: 11854879--11854927 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
11854869 CAATGTTGTT
*
11854879 GTTATCATGTGGTGTAATATTA
1 GTTATCATATGGTGTAATATTA
11854901 GTTATCATATGGTGTAATATTA
1 GTTATCATATGGTGTAATATTA
11854923 GTTAT
1 GTTAT
11854928 GCACTTGGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (22 bp):
GTTATCATATGGTGTAATATTA
Found at i:11854987 original size:68 final size:68
Alignment explanation
Indices: 11854842--11854990 Score: 237
Period size: 68 Copynumber: 2.2 Consensus size: 68
11854832 ACTTTTAATG
* *
11854842 TGGTATAATATTAGTTATGCACTTGGACAATGTTGTTGTTATCATGTGGTGTAATATTAGTTATC
1 TGGTATAATATTAGTTATGCACTTGGACAATGTTGTTGTTATCATGTGGTGTAATACTAATTATC
11854907 ATA
66 ATA
* *
11854910 TGGTGTAATATTAGTTATGCACTTGGACAATGTTGTTGTTATCATGTGGTGTACTACTAATTATG
1 TGGTATAATATTAGTTATGCACTTGGACAATGTTGTTGTTATCATGTGGTGTAATACTAATTAT-
*
11854975 CATT
65 CATA
11854979 TGG-ATAATATTA
1 TGGTATAATATTA
11854991 TTAATTTCTA
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
68 68 0.92
69 6 0.08
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.44
Consensus pattern (68 bp):
TGGTATAATATTAGTTATGCACTTGGACAATGTTGTTGTTATCATGTGGTGTAATACTAATTATC
ATA
Found at i:11857478 original size:15 final size:15
Alignment explanation
Indices: 11857455--11857560 Score: 56
Period size: 15 Copynumber: 7.1 Consensus size: 15
11857445 TTCTTTGAAT
*
11857455 TTAATATATATTATA
1 TTAAAATATATTATA
* *
11857470 TTAAAATATCTTTTA
1 TTAAAATATATTATA
*
11857485 CTTAACATATA--AGTA
1 -TTAAAATATATTA-TA
* *
11857500 -TAAATATGTATTATG
1 TTAAA-ATATATTATA
* *
11857515 TTATATTATATTATA
1 TTAAAATATATTATA
* *
11857530 TTATATTATATTATA
1 TTAAAATATATTATA
* *
11857545 TTATATTATATTATA
1 TTAAAATATATTATA
11857560 T
1 T
11857561 ATAATAAAAA
Statistics
Matches: 72, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
13 3 0.04
14 4 0.06
15 53 0.74
16 12 0.17
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (15 bp):
TTAAAATATATTATA
Found at i:11857523 original size:5 final size:5
Alignment explanation
Indices: 11857508--11857560 Score: 97
Period size: 5 Copynumber: 10.6 Consensus size: 5
11857498 TATAAATATG
*
11857508 TATTA TGTTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
11857558 TAT
1 TAT
11857561 ATAATAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:11857645 original size:4 final size:4
Alignment explanation
Indices: 11857631--11857669 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
11857621 AACGAAACAG
* *
11857631 AGAA GGAA AGAA AGAAA AGAA AAAA AGAA AGAA AGAA AG
1 AGAA AGAA AGAA AG-AA AGAA AGAA AGAA AGAA AGAA AG
11857670 GAGAAAAAGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
4 26 0.87
5 4 0.13
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:11857651 original size:17 final size:17
Alignment explanation
Indices: 11857637--11857668 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11857627 ACAGAGAAGG
11857637 AAAGAAAGAAAAGAAAA
1 AAAGAAAGAAAAGAAAA
11857654 AAAGAAAG-AAAGAAA
1 AAAGAAAGAAAAGAAA
11857669 GGAGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAAAGAAAA
Found at i:11857660 original size:21 final size:21
Alignment explanation
Indices: 11857636--11857678 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
11857626 AACAGAGAAG
11857636 GAAAGAAAGAAAAGAAAAAAA
1 GAAAGAAAGAAAAGAAAAAAA
* *
11857657 GAAAGAAAGAAAGGAGAAAAA
1 GAAAGAAAGAAAAGAAAAAAA
11857678 G
1 G
11857679 CTAGGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAAGAAAAAAA
Found at i:11859288 original size:9 final size:9
Alignment explanation
Indices: 11859274--11859333 Score: 77
Period size: 9 Copynumber: 6.7 Consensus size: 9
11859264 ATAAGTATAA
11859274 AATTAACCG
1 AATTAACCG
11859283 AATTAACCG
1 AATTAACCG
*
11859292 AATTACCCG
1 AATTAACCG
*
11859301 AATT-ACCTA
1 AATTAACC-G
11859310 AATTAACCG
1 AATTAACCG
*
11859319 AATTAACCA
1 AATTAACCG
11859328 AATTAA
1 AATTAA
11859334 TCAAATTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
8 2 0.05
9 39 0.89
10 3 0.07
ACGTcount: A:0.47, C:0.22, G:0.07, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:11859338 original size:9 final size:9
Alignment explanation
Indices: 11859273--11859341 Score: 68
Period size: 9 Copynumber: 7.7 Consensus size: 9
11859263 AATAAGTATA
11859273 AAATTAACC
1 AAATTAACC
*
11859282 GAATTAACC
1 AAATTAACC
* *
11859291 GAATTACCC
1 AAATTAACC
*
11859300 GAATT-ACC
1 AAATTAACC
11859308 TAAATTAACC
1 -AAATTAACC
*
11859318 GAATTAACC
1 AAATTAACC
*
11859327 AAATTAATC
1 AAATTAACC
11859336 AAATTA
1 AAATTA
11859342 TTTGTATAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
8 2 0.04
9 46 0.90
10 3 0.06
ACGTcount: A:0.48, C:0.20, G:0.06, T:0.26
Consensus pattern (9 bp):
AAATTAACC
Found at i:11859341 original size:18 final size:18
Alignment explanation
Indices: 11859273--11859333 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
11859263 AATAAGTATA
11859273 AAATTAACCGAATTAACC
1 AAATTAACCGAATTAACC
* *
11859291 GAATTACCCGAATT-ACC
1 AAATTAACCGAATTAACC
11859308 TAAATTAACCGAATTAACC
1 -AAATTAACCGAATTAACC
11859327 AAATTAA
1 AAATTAA
11859334 TCAAATTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
17 3 0.08
18 31 0.84
19 3 0.08
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.25
Consensus pattern (18 bp):
AAATTAACCGAATTAACC
Found at i:11859450 original size:18 final size:18
Alignment explanation
Indices: 11859427--11859474 Score: 96
Period size: 18 Copynumber: 2.7 Consensus size: 18
11859417 ATTTTTATGA
11859427 TTGGGTTGGGTAATTGGG
1 TTGGGTTGGGTAATTGGG
11859445 TTGGGTTGGGTAATTGGG
1 TTGGGTTGGGTAATTGGG
11859463 TTGGGTTGGGTA
1 TTGGGTTGGGTA
11859475 CTTGAGTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.10, C:0.00, G:0.50, T:0.40
Consensus pattern (18 bp):
TTGGGTTGGGTAATTGGG
Found at i:11859468 original size:13 final size:13
Alignment explanation
Indices: 11859426--11859450 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11859416 AATTTTTATG
11859426 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
11859439 ATTGGGTTGGGT
1 ATTGGGTTGGGT
11859451 TGGGTAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:11864316 original size:17 final size:17
Alignment explanation
Indices: 11864287--11864328 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
11864277 AAGCAGAAAC
11864287 AAAACAGAGAAGAAA-AG
1 AAAA-AGAGAAGAAAGAG
11864304 AAAAAGAGAAAGAAAGGAG
1 AAAAAGAG-AAGAAA-GAG
11864323 AAAAAG
1 AAAAAG
11864329 CTAGGACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.18
17 10 0.45
19 8 0.36
ACGTcount: A:0.71, C:0.02, G:0.26, T:0.00
Consensus pattern (17 bp):
AAAAAGAGAAGAAAGAG
Found at i:11883061 original size:33 final size:33
Alignment explanation
Indices: 11883024--11883088 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
11883014 TATATCAATG
*
11883024 TGCGAGTCGTAATGATGTGTGAGCTGTGTAATT
1 TGCGAGTCATAATGATGTGTGAGCTGTGTAATT
*
11883057 TGCGAGTCATAGTGATGTGTGAGCTGTGTAAT
1 TGCGAGTCATAATGATGTGTGAGCTGTGTAAT
11883089 CTGTAAGCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.22, C:0.09, G:0.34, T:0.35
Consensus pattern (33 bp):
TGCGAGTCATAATGATGTGTGAGCTGTGTAATT
Found at i:11883106 original size:33 final size:31
Alignment explanation
Indices: 11883034--11883108 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 31
11883024 TGCGAGTCGT
* *
11883034 AATGATGTGTGAGCTGTGTAATTTGCGAGTC
1 AATGATGTGTGAGCTGTGTAATCTGCAAGTC
*
11883065 ATAGTGATGTGTGAGCTGTGTAATCTGTAAGCTAC
1 A-A-TGATGTGTGAGCTGTGTAATCTGCAAG-T-C
11883100 AATGATGTG
1 AATGATGTG
11883109 CGAATTGTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
31 1 0.03
32 1 0.03
33 31 0.84
34 2 0.05
35 2 0.05
ACGTcount: A:0.25, C:0.09, G:0.31, T:0.35
Consensus pattern (31 bp):
AATGATGTGTGAGCTGTGTAATCTGCAAGTC
Found at i:11883127 original size:27 final size:27
Alignment explanation
Indices: 11883096--11883148 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
11883086 AATCTGTAAG
11883096 CTACAATGATGTGCGAATTGTGTAATA
1 CTACAATGATGTGCGAATTGTGTAATA
*
11883123 CTACAATGATGTGCGAGTTGTGTAAT
1 CTACAATGATGTGCGAATTGTGTAAT
11883149 GAGCGAGCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (27 bp):
CTACAATGATGTGCGAATTGTGTAATA
Found at i:11886308 original size:22 final size:20
Alignment explanation
Indices: 11886265--11886303 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
11886255 TAATTTAAAA
11886265 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
11886285 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
11886304 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:11886365 original size:32 final size:32
Alignment explanation
Indices: 11886324--11886401 Score: 88
Period size: 33 Copynumber: 2.4 Consensus size: 32
11886314 AACTTTTACG
11886324 GAAAATATTTTCA-AGAAATC-TACCAAACAACA
1 GAAAATATTTTCACAG-AATCAT-CCAAACAACA
** *
11886356 GAAAATATTTTACACAGCTTCATCCAAACACCA
1 GAAAATATTTT-CACAGAATCATCCAAACAACA
11886389 GAAAATATTTTCA
1 GAAAATATTTTCA
11886402 GTAAATCATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 13 0.32
33 24 0.60
34 3 0.08
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (32 bp):
GAAAATATTTTCACAGAATCATCCAAACAACA
Found at i:11889361 original size:63 final size:63
Alignment explanation
Indices: 11889252--11889376 Score: 214
Period size: 63 Copynumber: 2.0 Consensus size: 63
11889242 CCAAACCCTC
* * *
11889252 CCACTTTTCTAATGGACATTCAAATCTGGACAGATAACCCGACTCATGATGAGGCCTAAATTT
1 CCACATTTCGAATGGACATTCAAATCTGGACAGATAACCCGACTCATAATGAGGCCTAAATTT
*
11889315 CCACATTTCGAATGGACATTCAAATCTGGACAGATAACCTGACTCATAATGAGGCCTAAATT
1 CCACATTTCGAATGGACATTCAAATCTGGACAGATAACCCGACTCATAATGAGGCCTAAATT
11889377 GTGGGAGAGA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (63 bp):
CCACATTTCGAATGGACATTCAAATCTGGACAGATAACCCGACTCATAATGAGGCCTAAATTT
Found at i:11891125 original size:3 final size:3
Alignment explanation
Indices: 11891117--11891298 Score: 101
Period size: 3 Copynumber: 60.3 Consensus size: 3
11891107 TAGTATCATG
* * * *
11891117 ATA ATA ATA AGA ATA ATA ATA ATA A-A ATA ATA AAA ATA ACA AT- ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
11891163 TTA CTA ATA ATA ATAA ATAA ATAA ATA ATG GTA ATA A-A TATA TATA
1 ATA ATA ATA ATA AT-A AT-A AT-A ATA ATA ATA ATA ATA -ATA -ATA
* * *
11891209 A-A ATA ATA GTA ACA GTA ATA A-A ATA A-A TATA AT- ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
* * *
11891250 TATA ATA ATA ATA AGTA ATA ATA TATA ATA ATA ACA ATA TTA AAA ATA
1 -ATA ATA ATA ATA A-TA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
11891298 A
1 A
11891299 CACTCTCCCC
Statistics
Matches: 139, Mismatches: 26, Indels: 28
0.72 0.13 0.15
Matches are distributed among these distances:
2 13 0.09
3 102 0.73
4 24 0.17
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:11891210 original size:31 final size:29
Alignment explanation
Indices: 11891172--11891260 Score: 79
Period size: 35 Copynumber: 2.8 Consensus size: 29
11891162 GTTACTAATA
**
11891172 ATAATAAATAAATAAATAATGGTAATAAAT
1 ATAATAAATAAATAAATAAT-AAAATAAAT
11891202 ATATATAAAATAATAGTAACAGTAATAAAATAAAT
1 ATA-AT-AAATAA-A-TAA-A-TAATAAAATAAAT
11891237 ATAATATAATAAATATAATAATAA
1 ATAATA-AATAAATA-AATAATAA
11891261 TAAGTAATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
30 3 0.06
31 8 0.16
32 9 0.18
33 4 0.08
34 10 0.20
35 11 0.22
36 4 0.08
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (29 bp):
ATAATAAATAAATAAATAATAAAATAAAT
Found at i:11891281 original size:23 final size:22
Alignment explanation
Indices: 11891117--11891288 Score: 113
Period size: 23 Copynumber: 7.7 Consensus size: 22
11891107 TAGTATCATG
*
11891117 ATAATAATAAGAATAATAATAAT
1 ATAATAATAATAATAATAAT-AT
* * *
11891140 AAAATAATAAAAATAACAATAT
1 ATAATAATAATAATAATAATAT
* *
11891162 GTTACTAATAATAATAAATAA-AT
1 -ATAATAATAATAAT-AATAATAT
**
11891185 A-AATAATGGTAATAAATATATAT
1 ATAATAATAATAAT-AATA-ATAT
* * *
11891208 AAAATAATAGTAACAGTAATAAAAT
1 ATAATAATAAT-A-A-TAATAATAT
11891233 A-AAT-ATAAT-ATAATAA-AT
1 ATAATAATAATAATAATAATAT
11891251 ATAATAATAATAAGTAATAATAT
1 ATAATAATAATAA-TAATAATAT
*
11891274 ATAATAATAACAATA
1 ATAATAATAATAATA
11891289 TTAAAAATAA
Statistics
Matches: 120, Mismatches: 16, Indels: 27
0.74 0.10 0.17
Matches are distributed among these distances:
18 3 0.03
19 9 0.08
20 6 0.05
21 15 0.12
22 11 0.09
23 50 0.42
24 15 0.12
25 5 0.04
26 5 0.04
27 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (22 bp):
ATAATAATAATAATAATAATAT
Found at i:11891775 original size:25 final size:25
Alignment explanation
Indices: 11891746--11891799 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
11891736 GGAGTGTTAA
11891746 TTGGACTGTTAATTCATTTGGTGTT
1 TTGGACTGTTAATTCATTTGGTGTT
* *
11891771 TTGGATTGTTAATTTATTTGGTGTT
1 TTGGACTGTTAATTCATTTGGTGTT
11891796 TTGG
1 TTGG
11891800 GCTCTACTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.15, C:0.04, G:0.26, T:0.56
Consensus pattern (25 bp):
TTGGACTGTTAATTCATTTGGTGTT
Found at i:11892280 original size:132 final size:131
Alignment explanation
Indices: 11892043--11892606 Score: 759
Period size: 132 Copynumber: 4.3 Consensus size: 131
11892033 TTGTAGCTTA
* * * ** *
11892043 GATCTACTCCGCTACTGCTTAAGGAGATAAGATCTACATTCTTCAGCCTGCTCACTGCTGCTCAG
1 GATCTGCTCCACTACTACTTAAGGAGATAAGATCTGTAATCTTCAGCCTGCTCACTGCTGCTCAG
* * *
11892108 AGAGATAAGGCTAGTGGTTTAAGTCTGCTTCCTTACTACCTCGGGAAGATAAGATTCGTCGTCTT
66 AGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGATTCGTCGTCTT
11892173 C
131 C
*
11892174 GATCTGCTCCATTAC-AGCTTAAGGAGATAAGATCTGTAATCTTCAGCCTGCTCTACTGCTGCTC
1 GATCTGCTCCACTACTA-CTTAAGGAGATAAGATCTGTAATCTTCAGCCTGCTC-ACTGCTGCTC
* * * *
11892238 AGGGAGATAAGGTTGGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGATTCGCCGTC
64 AGAGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGATTCGTCGTC
11892303 TTC
129 TTC
* * ** *
11892306 GATCTACTCCACTACTACTTAGGGAGATAAGATCTACAATCTTCAACCTGCTCACTGCTGCTCAG
1 GATCTGCTCCACTACTACTTAAGGAGATAAGATCTGTAATCTTCAGCCTGCTCACTGCTGCTCAG
* *
11892371 AAAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATGAGATTCG-CTGTCT
66 AGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGATTCGTC-GTCT
11892435 TC
130 TC
* * *
11892437 AATCTGCTCCATTACTACTTACA-AAGATAAGATCTGTAATCTTCAGCCTGCTCCACTGCTGCTC
1 GATCTGCTCCACTACTACTTA-AGGAGATAAGATCTGTAATCTTCAGCCTGCT-CACTGCTGCTC
* * **
11892501 AGTGAGATAAGGCTAGTGGCTTAAATCAGCTTCCCTACTACCTCAAGAAGATAAGA-T--TC-T-
64 AGAGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGATTCGTCGTC
11892561 TT-
129 TTC
*
11892563 GATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATCTTC
1 GATCTGCTCCACTACTACTTAAGGAGATAAGATCTGTAATCTTC
11892607 TTCAATCCAT
Statistics
Matches: 382, Mismatches: 43, Indels: 21
0.86 0.10 0.05
Matches are distributed among these distances:
126 39 0.10
127 2 0.01
128 1 0.00
130 2 0.01
131 160 0.42
132 177 0.46
133 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (131 bp):
GATCTGCTCCACTACTACTTAAGGAGATAAGATCTGTAATCTTCAGCCTGCTCACTGCTGCTCAG
AGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGATTCGTCGTCTT
C
Found at i:11892443 original size:45 final size:45
Alignment explanation
Indices: 11892261--11892444 Score: 128
Period size: 44 Copynumber: 4.2 Consensus size: 45
11892251 TGGTGGCTTA
*
11892261 AATCTGCTTCCCTACTACCTCGGGAAGATAAGATTCGCCGTCTTC
1 AATCTGCTTCCCTACTACCTCGGGAAGATAAGATTCGCTGTCTTC
* * * * * **
11892306 GATCTAC-TCCACTACTACTTAGGG-AGATAAGA-TCTACAATCTTC
1 AATCTGCTTCC-CTACTACCTCGGGAAGATAAGATTC-GCTGTCTTC
* * * * * * ** * * *
11892350 AACCTGC-TCACTGCT-GCTCAGAAAGATAAGGCTAG-TGGCTTA
1 AATCTGCTTCCCTACTACCTCGGGAAGATAAGATTCGCTGTCTTC
*
11892392 AATCTGCTTCCCTACTACCTCGGGAAGATGAGATTCGCTGTCTTC
1 AATCTGCTTCCCTACTACCTCGGGAAGATAAGATTCGCTGTCTTC
11892437 AATCTGCT
1 AATCTGCT
11892445 CCATTACTAC
Statistics
Matches: 96, Mismatches: 36, Indels: 14
0.66 0.25 0.10
Matches are distributed among these distances:
42 11 0.11
43 19 0.20
44 37 0.39
45 29 0.30
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (45 bp):
AATCTGCTTCCCTACTACCTCGGGAAGATAAGATTCGCTGTCTTC
Found at i:11892510 original size:263 final size:257
Alignment explanation
Indices: 11892043--11892606 Score: 828
Period size: 263 Copynumber: 2.2 Consensus size: 257
11892033 TTGTAGCTTA
* * * * *
11892043 GATCTACTCCGCTACTGCTTAAGGAGATAAGATCTACATTCTTCAGCCTGCTCACTGCTGCTCAG
1 GATCTACTCCACTACTACTTAGGGAGATAAGATCTACAATCTTCAACCTGCTCACTGCTGCTCAG
* * * *
11892108 AGAGATAAGGCTAGTGGTTTAAGTCTGCTTCCTTACTACCTCGGGAAGATAAGATTCGTCGTCTT
66 AAAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGATTCGTCGTCTT
* * *
11892173 CGATCTGCTCCATTACAGCTTAAGGAGATAAGATCTGTAATCTTCAGCCTGCTCTACTGCTGCTC
131 CAATCTGCTCCATTACAGCTTAAGAAGATAAGATCTGTAATCTTCAGCCTGCTCCACTGCTGCTC
* * * **
11892238 AGGGAGATAAGGTTGGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGATTCGCCGTC
196 AGGGAGATAAGGCTAGTGGCTTAAATCAGCTTCCCTACTACCTCAAGAAGATAAGATT---C-T-
11892303 TT
256 TT
11892305 CGATCTACTCCACTACTACTTAGGGAGATAAGATCTACAATCTTCAACCTGCTCACTGCTGCTCA
1 -GATCTACTCCACTACTACTTAGGGAGATAAGATCTACAATCTTCAACCTGCTCACTGCTGCTCA
*
11892370 GAAAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATGAGATTCG-CTGTC
65 GAAAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGATTCGTC-GTC
11892434 TTCAATCTGCTCCATTACTA-CTTACA-AAGATAAGATCTGTAATCTTCAGCCTGCTCCACTGCT
129 TTCAATCTGCTCCATTAC-AGCTTA-AGAAGATAAGATCTGTAATCTTCAGCCTGCTCCACTGCT
*
11892497 GCTCAGTGAGATAAGGCTAGTGGCTTAAATCAGCTTCCCTACTACCTCAAGAAGATAAGATTCTT
192 GCTCAGGGAGATAAGGCTAGTGGCTTAAATCAGCTTCCCTACTACCTCAAGAAGATAAGATTCTT
11892562 T
257 T
* **
11892563 GATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAATCTTC
1 GATCTACTCCACTACTACTTAGGGAGATAAGATCTACAATCTTC
11892607 TTCAATCCAT
Statistics
Matches: 276, Mismatches: 22, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
257 41 0.15
258 2 0.01
259 1 0.00
260 1 0.00
262 1 0.00
263 228 0.83
264 2 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (257 bp):
GATCTACTCCACTACTACTTAGGGAGATAAGATCTACAATCTTCAACCTGCTCACTGCTGCTCAG
AAAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTACCTCGGGAAGATAAGATTCGTCGTCTT
CAATCTGCTCCATTACAGCTTAAGAAGATAAGATCTGTAATCTTCAGCCTGCTCCACTGCTGCTC
AGGGAGATAAGGCTAGTGGCTTAAATCAGCTTCCCTACTACCTCAAGAAGATAAGATTCTTT
Found at i:11892660 original size:46 final size:46
Alignment explanation
Indices: 11892604--11892829 Score: 308
Period size: 46 Copynumber: 4.9 Consensus size: 46
11892594 ATCTGTAATC
* *
11892604 TTCTTCAATCCATTCCACTGCGTCTCAAGGGTATAGGATCTACATT
1 TTCTTCAATCCATCCCACTGCGTCTCAAGGGTATAGGATCTGCATT
* ** *
11892650 TTCTTCAATCCATCTCACCACGTCTCAAGGGTATAGGATCTGTATT
1 TTCTTCAATCCATCCCACTGCGTCTCAAGGGTATAGGATCTGCATT
* * * *
11892696 CTCTTCAATCCATCCCATTGCGTCTCAAGGATATAGGATTTGCATT
1 TTCTTCAATCCATCCCACTGCGTCTCAAGGGTATAGGATCTGCATT
* * * *
11892742 TTCTTTAATCCATCCCACTGCGTCTCAGGGGTATAAGTTCTGCATT
1 TTCTTCAATCCATCCCACTGCGTCTCAAGGGTATAGGATCTGCATT
* *
11892788 TTCTTCAATCCATCCCACTACGTCTCAGGGGTATAGGATCTG
1 TTCTTCAATCCATCCCACTGCGTCTCAAGGGTATAGGATCTG
11892830 TAATTTCATG
Statistics
Matches: 154, Mismatches: 26, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 154 1.00
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.35
Consensus pattern (46 bp):
TTCTTCAATCCATCCCACTGCGTCTCAAGGGTATAGGATCTGCATT
Found at i:11892918 original size:12 final size:12
Alignment explanation
Indices: 11892901--11892925 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
11892891 TTATGCCGAA
11892901 TGATTAGGATGC
1 TGATTAGGATGC
11892913 TGATTAGGATGC
1 TGATTAGGATGC
11892925 T
1 T
11892926 ATGAACAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.32, T:0.36
Consensus pattern (12 bp):
TGATTAGGATGC
Found at i:11899945 original size:3 final size:3
Alignment explanation
Indices: 11899937--11900148 Score: 161
Period size: 3 Copynumber: 70.3 Consensus size: 3
11899927 TAGTACCATG
* * * *
11899937 ATA ATA ATA AGA ATA ATA ATA ATA A-A ATA ATA AAA ATA ACA AT- ATG
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
11899983 TTA CTA ATA ATA ATA ATA ATA ATA AGTAA ATA ATG GTA ATA A-A TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-T-A ATA ATA ATA ATA ATA -ATA
* * *
11900030 TATA ATA ATA GTA ACA GTA ATA A-A A-A AT- ATA AT- ATA ATA A-A
1 -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
11900071 TATA ATA ATA ATA ATA AGTA ATA ATA TATA ATA ATA ATA ATA AGTA ATA
1 -ATA ATA ATA ATA ATA A-TA ATA ATA -ATA ATA ATA ATA ATA A-TA ATA
* * *
11900120 ATA TATA ATA ATA ACA ATA TTA AAA ATA A
1 ATA -ATA ATA ATA ATA ATA ATA ATA ATA A
11900149 CACACTCTCC
Statistics
Matches: 168, Mismatches: 26, Indels: 30
0.75 0.12 0.13
Matches are distributed among these distances:
2 14 0.08
3 132 0.79
4 20 0.12
5 2 0.01
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:11899980 original size:26 final size:26
Alignment explanation
Indices: 11899937--11900148 Score: 139
Period size: 26 Copynumber: 8.0 Consensus size: 26
11899927 TAGTACCATG
*
11899937 ATAATAATAAGAATAATAATAATAAA
1 ATAATAATAATAATAATAATAATAAA
* * ** *
11899963 ATAATAAAAATAACAAT-ATGTTACTA
1 ATAATAATAATAATAATAATAATA-AA
*
11899989 ATAATAATAATAATAATAAGTAAATAATG
1 ATAATAATAATAATAATAA-T-AATAA-A
* *
11900018 GTAATAA-ATATATATAATAATAGTAACA
1 ATAATAATA-ATA-ATAATAATAATAA-A
* *
11900046 GTAATAA-AAAATATAAT-ATAATAAA
1 ATAATAATAATA-ATAATAATAATAAA
*
11900071 TATAATAATAATAATAAGTAATAAT-AT
1 -ATAATAATAATAATAA-TAATAATAAA
*
11900098 ATAATAATAATAATAAGTAATAAT-AT
1 ATAATAATAATAATAA-TAATAATAAA
* * *
11900124 ATAATAATAACAATATTAAAAATAA
1 ATAATAATAATAATAATAATAATAA
11900149 CACACTCTCC
Statistics
Matches: 150, Mismatches: 24, Indels: 24
0.76 0.12 0.12
Matches are distributed among these distances:
25 11 0.07
26 87 0.58
27 14 0.09
28 19 0.13
29 12 0.08
30 7 0.05
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (26 bp):
ATAATAATAATAATAATAATAATAAA
Found at i:11900131 original size:23 final size:23
Alignment explanation
Indices: 11899937--11900133 Score: 126
Period size: 23 Copynumber: 8.4 Consensus size: 23
11899927 TAGTACCATG
*
11899937 ATAATAATAAGAA-TAATAATAAT
1 ATAATAATAATAAGTAATAAT-AT
* * *
11899960 AAAATAATAA-AAATAACAATAT
1 ATAATAATAATAAGTAATAATAT
* *
11899982 GTTACTAATAATAA-TAATAATA-
1 -ATAATAATAATAAGTAATAATAT
*
11900004 ATAAGTAAATAAT-GGTAATAA-AT
1 ATAA-T-AATAATAAGTAATAATAT
*
11900027 ATATATAATAAT-AGTAACAGTAATAA
1 ATA-ATAATAATAAGT-A-A-TAATAT
*
11900053 AAAAT-ATAAT-A-TAATAAATAT
1 ATAATAATAATAAGTAAT-AATAT
11900074 AATAATAATAATAAGTAATAATATAT
1 -ATAATAATAATAAGTAAT-A-ATAT
11900100 AATAATAATAATAAGTAATAATAT
1 -ATAATAATAATAAGTAATAATAT
11900124 ATAATAATAA
1 ATAATAATAA
11900134 CAATATTAAA
Statistics
Matches: 142, Mismatches: 14, Indels: 36
0.74 0.07 0.19
Matches are distributed among these distances:
20 1 0.01
21 7 0.05
22 19 0.13
23 62 0.44
24 15 0.11
25 12 0.08
26 26 0.18
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (23 bp):
ATAATAATAATAAGTAATAATAT
Found at i:11900875 original size:13 final size:13
Alignment explanation
Indices: 11900857--11900882 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11900847 ATAAGTAAAA
11900857 TTTAAAAATATTT
1 TTTAAAAATATTT
11900870 TTTAAAAATATTT
1 TTTAAAAATATTT
11900883 AGAATTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTAAAAATATTT
Found at i:11901667 original size:26 final size:26
Alignment explanation
Indices: 11901638--11901691 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
11901628 TTTAATAATA
11901638 TATAGATAATTTTAAATTAAGAAATT
1 TATAGATAATTTTAAATTAAGAAATT
11901664 TATAGATAATTTTAAATTAAGAAATT
1 TATAGATAATTTTAAATTAAGAAATT
11901690 TA
1 TA
11901692 CTTGTTCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (26 bp):
TATAGATAATTTTAAATTAAGAAATT
Found at i:11905438 original size:22 final size:21
Alignment explanation
Indices: 11905408--11905449 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
11905398 ATAGACAATA
*
11905408 AAAAAAACGATAGAAAAAAAAG
1 AAAAAAACG-CAGAAAAAAAAG
*
11905430 AAAAGAACGCAGAAAAAAAA
1 AAAAAAACGCAGAAAAAAAA
11905450 TGAAGTACCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.76, C:0.07, G:0.14, T:0.02
Consensus pattern (21 bp):
AAAAAAACGCAGAAAAAAAAG
Done.