Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 201 of 210
Found at i:59204472 original size:86 final size:87
Alignment explanation
Indices: 59204298--59204472 Score: 217
Period size: 86 Copynumber: 2.0 Consensus size: 87
59204288 TCATCATTTC
* * * * * *
59204298 AACAATTTACATGCAAAAAATTAGCAAAAATTAACAATTCATGTATAATGTATTTACCAAAAACC
1 AACAATTTAAATGCAAAAAATTAACAAAAATTAACAATACAAGTATAATATATTCACCAAAAACC
* *
59204363 GGACCAACTTGTCAATTTTTAT
66 AGACCAAATTGTCAATTTTTAT
* * * *
59204385 AACATTTTAAATGCAACAAATTAACACAAATTAACAATACAAGT-TCATATATTCACCAAAAACC
1 AACAATTTAAATGCAAAAAATTAACAAAAATTAACAATACAAGTATAATATATTCACCAAAAACC
* *
59204449 AGACTAAATTTTCAATTTTTAT
66 AGACCAAATTGTCAATTTTTAT
59204471 AA
1 AA
59204473 AATAAGAGGA
Statistics
Matches: 74, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
86 37 0.50
87 37 0.50
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.31
Consensus pattern (87 bp):
AACAATTTAAATGCAAAAAATTAACAAAAATTAACAATACAAGTATAATATATTCACCAAAAACC
AGACCAAATTGTCAATTTTTAT
Found at i:59205336 original size:14 final size:14
Alignment explanation
Indices: 59205310--59205356 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
59205300 TTTCCCTATA
*
59205310 AACCCTAAATCTCT
1 AACCCTTAATCTCT
*
59205324 AACTCTTAATCTCT
1 AACCCTTAATCTCT
* *
59205338 AACCCTTAACCCCT
1 AACCCTTAATCTCT
59205352 AACCC
1 AACCC
59205357 CTAACCCATA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.32, C:0.40, G:0.00, T:0.28
Consensus pattern (14 bp):
AACCCTTAATCTCT
Found at i:59205388 original size:14 final size:14
Alignment explanation
Indices: 59205369--59205398 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
59205359 AACCCATAAA
59205369 CCTTAAATCACAAT
1 CCTTAAATCACAAT
*
59205383 CCTTAAATCAGAAT
1 CCTTAAATCACAAT
59205397 CC
1 CC
59205399 CTAATCCATA
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:0.40, C:0.30, G:0.03, T:0.27
Consensus pattern (14 bp):
CCTTAAATCACAAT
Found at i:59205411 original size:14 final size:15
Alignment explanation
Indices: 59205394--59205425 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
59205384 CTTAAATCAG
59205394 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
59205408 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
59205423 AAT
1 AAT
59205426 TTATAAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:59205513 original size:21 final size:20
Alignment explanation
Indices: 59205478--59205516 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
59205468 CTAAATTAAC
*
59205478 TATATATATACCCTAAACCA
1 TATATATAAACCCTAAACCA
59205498 TATATATTAAACCCTAAAC
1 TATATA-TAAACCCTAAAC
59205517 TATAATGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (20 bp):
TATATATAAACCCTAAACCA
Found at i:59205834 original size:41 final size:41
Alignment explanation
Indices: 59205776--59205975 Score: 337
Period size: 41 Copynumber: 4.9 Consensus size: 41
59205766 AAATGTTTTT
*
59205776 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTTAAAAACGCCGCTAAAGATCTGAGCATTA
*
59205817 GCGGCGCTTTTTTAAAAACGCCGTTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTTAAAAACGCCGCTAAAGATCTGAGCATTA
*
59205858 GCGGCGCTTTTTTAAAAACGCTGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTTTAAAAACGCCGCTAAAGATCTGAGCATTA
* *
59205899 GCGGCGCTTTTTTAAAAACGCAGCTAAAGATCTAAGCATTA
1 GCGGCGCTTTTTTAAAAACGCCGCTAAAGATCTGAGCATTA
*
59205940 GCGGCGCTTTTTTTAAAAACGCCACTAAAGATCTGA
1 GCGGCGC-TTTTTTAAAAACGCCGCTAAAGATCTGA
59205976 AAGGTACAAA
Statistics
Matches: 149, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
41 124 0.83
42 25 0.17
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (41 bp):
GCGGCGCTTTTTTAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:59206050 original size:40 final size:41
Alignment explanation
Indices: 59206006--59206141 Score: 118
Period size: 39 Copynumber: 3.4 Consensus size: 41
59205996 TCGGCTTAGG
* *
59206006 TTTTTTGCGGCGTTTTTCCAAAAAATGCCGCTAATGCT-AA
1 TTTTTAGCGGCGTTTTTCCAAAAAACGCCGCTAATGCTCAA
* *** *
59206046 TTTTTAGCGGCG-CTTTCCTGGAAACGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCCAAAAAACGCCGCTAATGCTCAA
* * ** * *
59206086 TCTTTAGCGGCG-TTTTACGTAAAGCGCC-CTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCCAAAAAACGCCGCTAATGCTCAA
*
59206125 TTTTTAGTGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
59206142 TGTCTAAACG
Statistics
Matches: 78, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
39 41 0.53
40 37 0.47
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.37
Consensus pattern (41 bp):
TTTTTAGCGGCGTTTTTCCAAAAAACGCCGCTAATGCTCAA
Found at i:59210101 original size:38 final size:38
Alignment explanation
Indices: 59210051--59210147 Score: 124
Period size: 38 Copynumber: 2.6 Consensus size: 38
59210041 TGTATTTGGC
*
59210051 TCAACAGCAACAGTAGACAT-TCTTATCATGTATTCAAT
1 TCAACAGTAACAGTAGACATGT-TTATCATGTATTCAAT
* ***
59210089 TCAATAGTAACAGTAGACATGTTTATCATGTATTTGGT
1 TCAACAGTAACAGTAGACATGTTTATCATGTATTCAAT
*
59210127 TCAACAGTAACAGTAGGCATG
1 TCAACAGTAACAGTAGACATG
59210148 CATCAGTAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 50 0.98
39 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (38 bp):
TCAACAGTAACAGTAGACATGTTTATCATGTATTCAAT
Found at i:59213901 original size:37 final size:35
Alignment explanation
Indices: 59213860--59213932 Score: 83
Period size: 37 Copynumber: 2.0 Consensus size: 35
59213850 GCCAAAAAAA
59213860 TTTTTTACCAACTTTTAAGGGGCCCTAAAATTTTTTT
1 TTTTTTACCAACTTTTAA-GGGCCC-AAAATTTTTTT
*** * *
59213897 TTTTTTTTTAGCTTTTAAGGGCCCAAAGTTTTTTT
1 TTTTTTACCAACTTTTAAGGGCCCAAAATTTTTTT
59213932 T
1 T
59213933 ACCAACTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 11 0.35
36 6 0.19
37 14 0.45
ACGTcount: A:0.21, C:0.14, G:0.12, T:0.53
Consensus pattern (35 bp):
TTTTTTACCAACTTTTAAGGGCCCAAAATTTTTTT
Found at i:59214674 original size:10 final size:10
Alignment explanation
Indices: 59214659--59214683 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
59214649 ATACTTATAG
59214659 AAATTTAAAA
1 AAATTTAAAA
59214669 AAATTTAAAA
1 AAATTTAAAA
59214679 AAATT
1 AAATT
59214684 AAAGATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
AAATTTAAAA
Found at i:59219830 original size:28 final size:29
Alignment explanation
Indices: 59219766--59219836 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 29
59219756 CACAAGATAA
*
59219766 TCCTATATAGATAG-TCACTGGCCGATTC
1 TCCTATATAGATAGTTCACTGGCCGAATC
* ** *
59219794 TTCGGTATAGATAGTTC-CTGGCGGAATC
1 TCCTATATAGATAGTTCACTGGCCGAATC
59219822 TCCTATATAGATAGT
1 TCCTATATAGATAGT
59219837 CTCTTTTGTT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
28 32 0.94
29 2 0.06
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (29 bp):
TCCTATATAGATAGTTCACTGGCCGAATC
Found at i:59224219 original size:22 final size:22
Alignment explanation
Indices: 59224182--59224228 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 22
59224172 AAGTTTGTAT
59224182 CAATCTATATGAAA-TTG-ATC
1 CAATCTATATGAAATTTGAATC
59224202 CAATCTAGTATTGAAATTTGAATC
1 CAATCTA-TA-TGAAATTTGAATC
59224226 CAA
1 CAA
59224229 CCACAGAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.30
21 2 0.09
22 5 0.22
23 3 0.13
24 6 0.26
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (22 bp):
CAATCTATATGAAATTTGAATC
Found at i:59226924 original size:101 final size:101
Alignment explanation
Indices: 59226799--59226985 Score: 275
Period size: 101 Copynumber: 1.9 Consensus size: 101
59226789 TGCATTGTGT
* **
59226799 CATAACTCAGTTATGGTCTTATCATCAAAATGCCTTAGCCCAGCTATGGTCATACATATAAACAC
1 CATAACCCAGTTATGGTCTTATCATCAAAATGCCACAGCCCAGCTATGGTCATACATATAAACAC
* * *
59226864 TGTCATAGTCCAACCATGGTCAGACGTCCATAGTGC
66 TGCCAAAGTCCAACCAAGGTCAGACGTCCATAGTGC
* * * * *
59226900 CATAACCCAGTTATGGTCTTATCATCAGAATGCCACAGCCTAGCTTTGGTCTTACATATATACAC
1 CATAACCCAGTTATGGTCTTATCATCAAAATGCCACAGCCCAGCTATGGTCATACATATAAACAC
59226965 TGCCAAAGTCCAACCAAGGTC
66 TGCCAAAGTCCAACCAAGGTC
59226986 TTAAATACTT
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
101 75 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (101 bp):
CATAACCCAGTTATGGTCTTATCATCAAAATGCCACAGCCCAGCTATGGTCATACATATAAACAC
TGCCAAAGTCCAACCAAGGTCAGACGTCCATAGTGC
Found at i:59232550 original size:28 final size:28
Alignment explanation
Indices: 59232486--59232556 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
59232476 CACAAGATAA
*
59232486 TCCTATATAGATAGTTACTGGCCGATTC
1 TCCTATATAGATAGTTACTGGCCGAATC
* ** *
59232514 TTCGGTATAGATAGTTACTGGCGGAATC
1 TCCTATATAGATAGTTACTGGCCGAATC
59232542 TCCTATATAGATAGT
1 TCCTATATAGATAGT
59232557 CTCTTTTGTT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (28 bp):
TCCTATATAGATAGTTACTGGCCGAATC
Found at i:59236848 original size:20 final size:21
Alignment explanation
Indices: 59236817--59236863 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
59236807 ATAGAGTTAT
*
59236817 AGAAAA-TAAAAATAATT-AA
1 AGAAAATTAAAAAAAATTGAA
59236836 AGAAAATTAAAAAAAATTGAA
1 AGAAAATTAAAAAAAATTGAA
*
59236857 ATAAAAT
1 AGAAAAT
59236864 ATCAAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 6 0.25
20 10 0.42
21 8 0.33
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.21
Consensus pattern (21 bp):
AGAAAATTAAAAAAAATTGAA
Found at i:59236913 original size:22 final size:22
Alignment explanation
Indices: 59236879--59236925 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 22
59236869 AATTTTGTAT
59236879 CAATCTATATGAAA-TTG-ATC
1 CAATCTATATGAAATTTGAATC
59236899 CAATCTAGTATTGAAATTTGAATC
1 CAATCTA-TA-TGAAATTTGAATC
59236923 CAA
1 CAA
59236926 CCACATAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.30
21 2 0.09
22 5 0.22
23 3 0.13
24 6 0.26
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (22 bp):
CAATCTATATGAAATTTGAATC
Found at i:59244064 original size:20 final size:20
Alignment explanation
Indices: 59244027--59244065 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
59244017 TTTTTTAAAA
*
59244027 AAAATCTACTTAATAATTTT
1 AAAATCTAATTAATAATTTT
59244047 AAAATCTAATATAA-AATTT
1 AAAATCTAAT-TAATAATTT
59244066 ACCTCGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATCTAATTAATAATTTT
Found at i:59245077 original size:22 final size:22
Alignment explanation
Indices: 59245052--59245122 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 22
59245042 TTAAATATGG
*
59245052 ATTTAAGAGAAATTTGGAAGGA
1 ATTTGAGAGAAATTTGGAAGGA
59245074 ATTTGAGAGCAAA-TT-GAGAGGA
1 ATTTGAGAG-AAATTTGGA-AGGA
*
59245096 AATTGAGAGGAAATTTGAGAAAGGA
1 ATTTGAGA-GAAATTTG-G-AAGGA
59245121 AT
1 AT
59245123 AGTTTGTGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
21 2 0.05
22 24 0.62
23 6 0.15
25 6 0.15
26 1 0.03
ACGTcount: A:0.45, C:0.01, G:0.30, T:0.24
Consensus pattern (22 bp):
ATTTGAGAGAAATTTGGAAGGA
Found at i:59245090 original size:11 final size:11
Alignment explanation
Indices: 59245070--59245115 Score: 65
Period size: 11 Copynumber: 4.1 Consensus size: 11
59245060 GAAATTTGGA
*
59245070 AGGAATTTGAG
1 AGGAAATTGAG
*
59245081 AGCAAATTGAG
1 AGGAAATTGAG
59245092 AGGAAATTGAG
1 AGGAAATTGAG
59245103 AGGAAATTTGAG
1 AGGAAA-TTGAG
59245115 A
1 A
59245116 AAGGAATAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
11 25 0.81
12 6 0.19
ACGTcount: A:0.43, C:0.02, G:0.33, T:0.22
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:59245782 original size:74 final size:72
Alignment explanation
Indices: 59245696--59245837 Score: 180
Period size: 72 Copynumber: 1.9 Consensus size: 72
59245686 AAAAAACACT
*
59245696 AAAATGTAACTCTCATA-AAGTTAAAAACAATTAATAT-ATATAAATAAAAATCATTTGCTTAAC
1 AAAATGTAACTCT-A-AGAA-TTAAAAACAA-TAATATGATATAAATAAAAATCATTTACTTAAC
59245759 AATAAAATAAA
62 AATAAAATAAA
* * * * *
59245770 AAAATGTAACTCTAAGAATTATAAATAATAATTTGATATAAATAAGAATCATTTATTTAACAATA
1 AAAATGTAACTCTAAGAATTAAAAACAATAATATGATATAAATAAAAATCATTTACTTAACAATA
59245835 AAA
66 AAA
59245838 CAATATTAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
71 5 0.08
72 39 0.65
73 3 0.05
74 13 0.22
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.32
Consensus pattern (72 bp):
AAAATGTAACTCTAAGAATTAAAAACAATAATATGATATAAATAAAAATCATTTACTTAACAATA
AAATAAA
Found at i:59249914 original size:12 final size:12
Alignment explanation
Indices: 59249897--59249923 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
59249887 AACTACGAGT
59249897 GCATCATAAAAG
1 GCATCATAAAAG
59249909 GCATCATAAAAG
1 GCATCATAAAAG
59249921 GCA
1 GCA
59249924 GTTTCAGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.15
Consensus pattern (12 bp):
GCATCATAAAAG
Found at i:59260149 original size:20 final size:20
Alignment explanation
Indices: 59260126--59260172 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
59260116 GATAACTAAC
* *
59260126 ATTTTTTTATTTATGGTAAT
1 ATTTTTTTATTAATAGTAAT
* *
59260146 ATTTTTATATTAATAGTAGT
1 ATTTTTTTATTAATAGTAAT
59260166 ATTTTTT
1 ATTTTTT
59260173 AATAATTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.64
Consensus pattern (20 bp):
ATTTTTTTATTAATAGTAAT
Found at i:59262515 original size:11 final size:11
Alignment explanation
Indices: 59262501--59262525 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
59262491 TTTCTAATTA
59262501 TTTAATAATAT
1 TTTAATAATAT
59262512 TTTAATAATAT
1 TTTAATAATAT
59262523 TTT
1 TTT
59262526 CTATATCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTAATAATAT
Found at i:59264230 original size:60 final size:63
Alignment explanation
Indices: 59264166--59264291 Score: 159
Period size: 70 Copynumber: 1.9 Consensus size: 63
59264156 CTCAATTATC
*
59264166 CCATAGAG-AT-A-GATAGAAAATACATAAATTATCTTAAGTGCAAGTAACACTTTTCTTCTT
1 CCATAGAGAATAAGGATAGAAAATACATAAATTATCTCAAGTGCAAGTAACACTTTTCTTCTT
59264226 CCATAGAGATAAATCACAAAGGATAGAAAATACATAAATTATCTCAAGTGCAAGTAACACTTTTC
1 CCATAGAG---AAT----AAGGATAGAAAATACATAAATTATCTCAAGTGCAAGTAACACTTTTC
59264291 T
59 T
59264292 CCTGAATCCC
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
60 8 0.15
64 2 0.04
69 1 0.02
70 44 0.80
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (63 bp):
CCATAGAGAATAAGGATAGAAAATACATAAATTATCTCAAGTGCAAGTAACACTTTTCTTCTT
Found at i:59276888 original size:6 final size:6
Alignment explanation
Indices: 59276879--59276907 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
59276869 CAATAAAATT
59276879 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
1 CTAAAA CTAAAA CTAAAA CTAAAA CTAAA
59276908 GTCTAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
CTAAAA
Found at i:59276967 original size:9 final size:9
Alignment explanation
Indices: 59276947--59277039 Score: 80
Period size: 9 Copynumber: 10.3 Consensus size: 9
59276937 GTAGTGATTC
*
59276947 AATTCGGTT
1 AATTCGGGT
*
59276956 AATTCCGGT
1 AATTCGGGT
59276965 AATAT-GGGT
1 AAT-TCGGGT
*
59276974 AATTCGGTT
1 AATTCGGGT
*
59276983 GATTCGGGT
1 AATTCGGGT
59276992 AATTCGGGT
1 AATTCGGGT
*
59277001 AATTCGGTT
1 AATTCGGGT
* *
59277010 GATTCGGTT
1 AATTCGGGT
* *
59277019 AATTCAGTT
1 AATTCGGGT
*
59277028 AATTCGGTT
1 AATTCGGGT
59277037 AAT
1 AAT
59277040 ATTTAACCAA
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
8 1 0.01
9 68 0.97
10 1 0.01
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.40
Consensus pattern (9 bp):
AATTCGGGT
Found at i:59276979 original size:27 final size:27
Alignment explanation
Indices: 59276947--59277039 Score: 109
Period size: 27 Copynumber: 3.4 Consensus size: 27
59276937 GTAGTGATTC
59276947 AATTCGGTTAATTCCGGTAATAT-GGGT
1 AATTCGGTTAATTCCGGTAAT-TCGGGT
* *
59276974 AATTCGGTTGATTCGGGTAATTCGGGT
1 AATTCGGTTAATTCCGGTAATTCGGGT
* * *
59277001 AATTCGGTTGATT-CGGTTAATTCAGTT
1 AATTCGGTTAATTCCGG-TAATTCGGGT
59277028 AATTCGGTTAAT
1 AATTCGGTTAAT
59277040 ATTTAACCAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
26 3 0.05
27 55 0.95
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.40
Consensus pattern (27 bp):
AATTCGGTTAATTCCGGTAATTCGGGT
Found at i:59276991 original size:18 final size:18
Alignment explanation
Indices: 59276947--59277039 Score: 91
Period size: 18 Copynumber: 5.2 Consensus size: 18
59276937 GTAGTGATTC
*
59276947 AATTCGGTTAATTCCGG-T
1 AATTCGGGTAATT-CGGTT
59276965 AATAT-GGGTAATTCGGTT
1 AAT-TCGGGTAATTCGGTT
* *
59276983 GATTCGGGTAATTCGGGT
1 AATTCGGGTAATTCGGTT
* *
59277001 AATTCGGTTGATTCGGTT
1 AATTCGGGTAATTCGGTT
* *
59277019 AATTCAGTTAATTCGGTT
1 AATTCGGGTAATTCGGTT
59277037 AAT
1 AAT
59277040 ATTTAACCAA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
17 4 0.06
18 58 0.92
19 1 0.02
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.40
Consensus pattern (18 bp):
AATTCGGGTAATTCGGTT
Found at i:59279832 original size:20 final size:20
Alignment explanation
Indices: 59279807--59279851 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
59279797 TTGATCTTCT
59279807 TCAACCCCTTAAGCTCTCAA
1 TCAACCCCTTAAGCTCTCAA
** *
59279827 TCAACCTTTTAAGCTCTTAA
1 TCAACCCCTTAAGCTCTCAA
59279847 TCAAC
1 TCAAC
59279852 ATTACTTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.31, C:0.33, G:0.04, T:0.31
Consensus pattern (20 bp):
TCAACCCCTTAAGCTCTCAA
Found at i:59280390 original size:46 final size:46
Alignment explanation
Indices: 59280312--59280496 Score: 307
Period size: 46 Copynumber: 4.0 Consensus size: 46
59280302 ACAATGCTAT
* ** *
59280312 AACTCAGTATGGTTTTCTTCATGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAACACCATACCTACTTTTCAC
*
59280358 AACTCAGTATGGTTTTCTTTACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAACACCATACCTACTTTTCAC
59280404 AACTCAGTATGGTTTTCTTTACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAACACCATACCTACTTTTCAC
* *
59280450 AACTCAATGTGGTTTTCTTTACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTTACCGAAACACCATACCTACTTTTCAC
59280496 A
1 A
59280497 CTTTGCCATG
Statistics
Matches: 132, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 132 1.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTTACCGAAACACCATACCTACTTTTCAC
Found at i:59290305 original size:16 final size:16
Alignment explanation
Indices: 59290286--59290316 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59290276 GTTTAAACCT
59290286 ATGTTCTTTTACATTC
1 ATGTTCTTTTACATTC
*
59290302 ATGTTCTTTTGCATT
1 ATGTTCTTTTACATT
59290317 GATAACAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.16, G:0.10, T:0.58
Consensus pattern (16 bp):
ATGTTCTTTTACATTC
Found at i:59292453 original size:31 final size:31
Alignment explanation
Indices: 59292382--59292462 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
59292372 AAAAGATTAT
* * *
59292382 ATACCAACTTAATAAAAAGTGTCAAGTTTAG
1 ATACCAAATTAAAAAAAAGTGTCAAATTTAG
* *
59292413 ATACCAAATTAAGAAAAAGTGTCAAATTTGG
1 ATACCAAATTAAAAAAAAGTGTCAAATTTAG
* *
59292444 GTACGAAATTAAAAAAAAG
1 ATACCAAATTAAAAAAAAG
59292463 GTTTAGGTAC
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.25
Consensus pattern (31 bp):
ATACCAAATTAAAAAAAAGTGTCAAATTTAG
Found at i:59293074 original size:6 final size:6
Alignment explanation
Indices: 59293063--59293151 Score: 97
Period size: 6 Copynumber: 13.8 Consensus size: 6
59293053 CTAGGGAGAA
*
59293063 GGAAAG GGAAAG GGAAAAG CGTGAAAG GGAAAG GGAAAG GGAAAG AGAAAGG
1 GGAAAG GGAAAG GG-AAAG -G-GAAAG GGAAAG GGAAAG GGAAAG GGAAA-G
* *
59293115 GAGAAGAG GGAAAG AGAAAG AGAAAG GGAAAG GGAAA
1 G-GAA-AG GGAAAG GGAAAG GGAAAG GGAAAG GGAAA
59293152 AAGAGAGGGA
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
6 52 0.71
7 9 0.12
8 10 0.14
9 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.45, T:0.01
Consensus pattern (6 bp):
GGAAAG
Found at i:59293098 original size:39 final size:39
Alignment explanation
Indices: 59293041--59293151 Score: 134
Period size: 39 Copynumber: 2.8 Consensus size: 39
59293031 AAGGAAAAGG
**
59293041 AGAGGGAAAGAGCTAGGGAGAA-GGAAAGGGAAAGGGAAA
1 AGAGGGAAAGAGAAAGGGA-AAGGGAAAGGGAAAGGGAAA
* * * * *
59293080 AGCGTGAAAGGGAAAGGGAAAGGGAAAGAGAAAGGGAGA
1 AGAGGGAAAGAGAAAGGGAAAGGGAAAGGGAAAGGGAAA
*
59293119 AGAGGGAAAGAGAAAGAGAAAGGGAAAGGGAAA
1 AGAGGGAAAGAGAAAGGGAAAGGGAAAGGGAAA
59293152 AAGAGAGGGA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
38 2 0.03
39 57 0.97
ACGTcount: A:0.51, C:0.02, G:0.45, T:0.02
Consensus pattern (39 bp):
AGAGGGAAAGAGAAAGGGAAAGGGAAAGGGAAAGGGAAA
Found at i:59293100 original size:33 final size:34
Alignment explanation
Indices: 59293055--59293145 Score: 107
Period size: 33 Copynumber: 2.7 Consensus size: 34
59293045 GGAAAGAGCT
*
59293055 AGGGAGAA-GGAAAGGGAAAGGGAAAAGCGTGAA-
1 AGGGA-AAGGGAAAGGGAAAGGGAAAAGCGAGAAG
* *
59293088 AGGGAAAGGGAAAGGGAAAGAG-AAAGGGAGAAG
1 AGGGAAAGGGAAAGGGAAAGGGAAAAGCGAGAAG
* *
59293121 AGGGAAAGAGAAAGAGAAAGGGAAA
1 AGGGAAAGGGAAAGGGAAAGGGAAA
59293146 GGGAAAAAGA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
32 10 0.20
33 37 0.76
34 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.45, T:0.01
Consensus pattern (34 bp):
AGGGAAAGGGAAAGGGAAAGGGAAAAGCGAGAAG
Found at i:59293124 original size:27 final size:27
Alignment explanation
Indices: 59293043--59293143 Score: 91
Period size: 27 Copynumber: 3.6 Consensus size: 27
59293033 GGAAAAGGAG
**
59293043 AGGGAAAGAGCTAGGGAGAAGGAAAGGGAA
1 AGGGAAAGAGAAAGGGAGAA-G--AGGGAA
*
59293073 AGGGAAAAGCGTGAAA-GG-GAA-AGGGAA
1 AGGG-AAA--GAGAAAGGGAGAAGAGGGAA
59293100 AGGGAAAGAGAAAGGGAGAAGAGGGAA
1 AGGGAAAGAGAAAGGGAGAAGAGGGAA
*
59293127 AGAGAAAGAGAAAGGGA
1 AGGGAAAGAGAAAGGGA
59293144 AAGGGAAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
24 5 0.08
25 2 0.03
26 6 0.10
27 32 0.53
30 4 0.07
31 6 0.10
32 2 0.03
33 3 0.05
ACGTcount: A:0.50, C:0.02, G:0.46, T:0.02
Consensus pattern (27 bp):
AGGGAAAGAGAAAGGGAGAAGAGGGAA
Found at i:59305947 original size:28 final size:27
Alignment explanation
Indices: 59305903--59305975 Score: 89
Period size: 28 Copynumber: 2.8 Consensus size: 27
59305893 ATATGCATAA
*
59305903 ATATA-ATAATAATAAAATAAAAAAAT
1 ATATATATATTAATAAAATAAAAAAAT
* *
59305929 GTATATATATTAATAAAAATAAAACAAT
1 ATATATATATTAAT-AAAATAAAAAAAT
59305957 ATATATATA-T-ATAAAATAA
1 ATATATATATTAATAAAATAA
59305976 GATACATATG
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 7 0.17
26 6 0.15
27 8 0.20
28 20 0.49
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (27 bp):
ATATATATATTAATAAAATAAAAAAAT
Found at i:59305984 original size:26 final size:26
Alignment explanation
Indices: 59305902--59305972 Score: 76
Period size: 26 Copynumber: 2.7 Consensus size: 26
59305892 TATATGCATA
* *
59305902 AATATA-ATAATAAT-AAAATAAAAA
1 AATATATATATTAATAAAAATAAAAC
59305926 AATGTATATATATTAATAAAAATAAAAC
1 AA--TATATATATTAATAAAAATAAAAC
59305954 AATATATATA-TATATAAAA
1 AATATATATATTA-ATAAAA
59305973 TAAGATACAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
24 2 0.05
25 2 0.05
26 18 0.45
27 7 0.17
28 11 0.28
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (26 bp):
AATATATATATTAATAAAAATAAAAC
Found at i:59306007 original size:3 final size:3
Alignment explanation
Indices: 59305999--59306059 Score: 67
Period size: 3 Copynumber: 21.3 Consensus size: 3
59305989 ATAAATATAT
* *
59305999 ATA ATA ATA ATA AAA ATA ATA ATA AGTA AT- ATA ATA ATA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA
59306044 A-A AT- ATA AT- ATA ATA A
1 ATA ATA ATA ATA ATA ATA A
59306060 CAAAGATAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
2 8 0.16
3 38 0.78
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:59306032 original size:24 final size:24
Alignment explanation
Indices: 59305997--59306059 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
59305987 GCATAAATAT
59305997 ATATAATAATAATAAAAATAATAATA
1 ATATAAT-ATAATAAAAATAATAA-A
* * *
59306023 A-GTAATATAATAATAATAGTAAA
1 ATATAATATAATAAAAATAATAAA
59306046 ATATAATATAATAA
1 ATATAATATAATAA
59306060 CAAAGATAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 25 0.78
25 4 0.12
26 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (24 bp):
ATATAATATAATAAAAATAATAAA
Found at i:59306038 original size:21 final size:20
Alignment explanation
Indices: 59305999--59306059 Score: 76
Period size: 18 Copynumber: 3.2 Consensus size: 20
59305989 ATAAATATAT
59305999 ATAATAATAATA-AA-AATA
1 ATAATAATAATATAATAATA
59306017 ATAATAAGTAATATAATAATA
1 ATAATAA-TAATATAATAATA
*
59306038 ATAGTAA-AATATAAT-ATA
1 ATAATAATAATATAATAATA
59306056 ATAA
1 ATAA
59306060 CAAAGATAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
18 13 0.34
19 13 0.34
20 2 0.05
21 10 0.26
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (20 bp):
ATAATAATAATATAATAATA
Found at i:59315660 original size:21 final size:21
Alignment explanation
Indices: 59315634--59315680 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
59315624 ATGGAGGCGA
*
59315634 TCTCCATGTAGATCA-TCAAGG
1 TCTCCAGGTAGAT-ATTCAAGG
59315655 TCTCCAGGTAGATATTCAAGG
1 TCTCCAGGTAGATATTCAAGG
59315676 TCTCC
1 TCTCC
59315681 TTCTGGGTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (21 bp):
TCTCCAGGTAGATATTCAAGG
Found at i:59317591 original size:22 final size:22
Alignment explanation
Indices: 59317563--59317605 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
59317553 AGTTAAAATT
*
59317563 AAATACGTTATATTTATTTATC
1 AAATACGCTATATTTATTTATC
*
59317585 AAATACGCTATATTTTTTTAT
1 AAATACGCTATATTTATTTAT
59317606 ATGTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.05, T:0.51
Consensus pattern (22 bp):
AAATACGCTATATTTATTTATC
Found at i:59317747 original size:13 final size:13
Alignment explanation
Indices: 59317731--59317757 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59317721 AAATAATTAA
59317731 AAATTTTAATTTT
1 AAATTTTAATTTT
59317744 AAATTTTAATTTT
1 AAATTTTAATTTT
59317757 A
1 A
59317758 TCATCTCTAC
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
AAATTTTAATTTT
Found at i:59321639 original size:36 final size:36
Alignment explanation
Indices: 59321592--59321664 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
59321582 TATGCCTGTA
59321592 AGTTCAAATTAAAATTTTAATTTGATGAATAAATTC
1 AGTTCAAATTAAAATTTTAATTTGATGAATAAATTC
59321628 AGTTCAAATTAAAATTTTAATTTGATGAATAAATTC
1 AGTTCAAATTAAAATTTTAATTTGATGAATAAATTC
59321664 A
1 A
59321665 TCTCAATTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.41
Consensus pattern (36 bp):
AGTTCAAATTAAAATTTTAATTTGATGAATAAATTC
Found at i:59328870 original size:33 final size:33
Alignment explanation
Indices: 59328731--59328874 Score: 98
Period size: 33 Copynumber: 4.3 Consensus size: 33
59328721 TGTATATATG
*
59328731 TAAGACCATAGCTGGGCTATGGCATTCTGATGA
1 TAAGACCATAGCTGGGCTATGGCATTCTAATGA
* * * *
59328764 TAAGGCCATAACTCGGTTATGGCA--CT-ATGGA
1 TAAGACCATAGCTGGGCTATGGCATTCTAAT-GA
* * * * * * *
59328795 CGTATGACCATGGTTGGACCATGACAGTGTTTATATG-
1 --TAAGACCATAGCTGGGCTATGGCA-T-TCTA-ATGA
59328832 TAAGACCATAGCTGGGCTATGGCATTCTAATGA
1 TAAGACCATAGCTGGGCTATGGCATTCTAATGA
59328865 TAAGACCATA
1 TAAGACCATA
59328875 ACTGAGTTAT
Statistics
Matches: 79, Mismatches: 22, Indels: 20
0.65 0.18 0.17
Matches are distributed among these distances:
30 2 0.03
31 4 0.05
32 3 0.04
33 47 0.59
34 1 0.01
35 18 0.23
37 1 0.01
38 1 0.01
39 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (33 bp):
TAAGACCATAGCTGGGCTATGGCATTCTAATGA
Found at i:59328875 original size:101 final size:101
Alignment explanation
Indices: 59328700--59328908 Score: 312
Period size: 101 Copynumber: 2.1 Consensus size: 101
59328690 AGTATTTAAT
** *
59328700 ACCATGGTTGGACCATGGTAGTGTATATATGTAAGACCATAGCTGGGCTATGGCATTCTGATGAT
1 ACCATGGTTGGACCATGACAGTGTATATATGTAAGACCATAGCTGGGCTATGGCATTCTAATGAT
* * * *
59328765 AAGGCCATAACTCG-GTTATGGCACTATGGACGTATG
66 AAGACCATAACT-GAGTTATGACACTATAGACGTAAG
*
59328801 ACCATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAGCTGGGCTATGGCATTCTAATGAT
1 ACCATGGTTGGACCATGACAGTGTATATATGTAAGACCATAGCTGGGCTATGGCATTCTAATGAT
* *
59328866 AAGACCATAACTGAGTTATGACCCTATATACGTAAG
66 AAGACCATAACTGAGTTATGACACTATAGACGTAAG
59328902 ACCATGG
1 ACCATGG
59328909 CAGGGCTGTG
Statistics
Matches: 97, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
100 1 0.01
101 96 0.99
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (101 bp):
ACCATGGTTGGACCATGACAGTGTATATATGTAAGACCATAGCTGGGCTATGGCATTCTAATGAT
AAGACCATAACTGAGTTATGACACTATAGACGTAAG
Found at i:59330616 original size:51 final size:49
Alignment explanation
Indices: 59330560--59330825 Score: 174
Period size: 51 Copynumber: 5.2 Consensus size: 49
59330550 TGTGGCACGG
* *
59330560 ACTGTGTGTAGGCCACTATATGAAAGTGA-AAGTGTTGGTCACGTGTGTAGT
1 ACTGTGTGAAGGCTACTATATG-AA-TGAGAAGT-TTGGTCACGTGTGTAGT
** * * * *
59330611 ACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGT
1 ACTGTGTGAAGGCTACTATATGAAT-GAGAAGT-TTGGTCACGTGTGTAGT
** * *
59330662 ACTAAGTGAAGGCTACAATATGTACTGAGAAGCTTTGGTCACGTGTGTAGT
1 ACTGTGTGAAGGCTACTATATG-AATGAGAAG-TTTGGTCACGTGTGTAGT
** * * * * *
59330713 ACTGTGTGAAGGCTACTACGTGAATTCATAAATGGTGGTCACATGTGTAGT
1 ACTGTGTGAAGGCTACTATATGAA-TGAGAAGT-TTGGTCACGTGTGTAGT
** * ** * * *
59330764 ACTAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTAGTCACGTATGTAGT
1 ACTGTGTGAAGGCTACTATATG-AATGAGAAG-TTTGGTCACGTGTGTAGT
*
59330815 ACTATGTGAAG
1 ACTGTGTGAAG
59330826 CCTATTACGT
Statistics
Matches: 165, Mismatches: 42, Indels: 16
0.74 0.19 0.07
Matches are distributed among these distances:
49 1 0.01
50 6 0.04
51 153 0.93
52 5 0.03
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (49 bp):
ACTGTGTGAAGGCTACTATATGAATGAGAAGTTTGGTCACGTGTGTAGT
Found at i:59330753 original size:102 final size:102
Alignment explanation
Indices: 59330594--59330880 Score: 391
Period size: 102 Copynumber: 2.8 Consensus size: 102
59330584 AGTGAAAGTG
59330594 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
* *
59330659 AGTACTAAGTGAAGGCTACAATATGTACTGAGAAGCT
66 AGTACTAAGTGAAGGCTACAATATGTACCGAAAAGCT
**
59330696 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATTC-ATAAATGGTGGTCACATGTG
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAA-TCGATAAATAATGGTCACATGTG
* *
59330760 TAGTACTAAGTGAAGGCTACTATGTGTACCGAAAAGCT
65 TAGTACTAAGTGAAGGCTACAATATGTACCGAAAAGCT
* * * * * * * *
59330798 TTAGTCACGTATGTAGTACTATGTGAAGCCTATTACGTGAACCG-TAAA-AATTGATCACGTGTG
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAA-TGGTCACATGTG
* *
59330861 TAATACTATGTGAAGGCTAC
65 TAGTACTAAGTGAAGGCTAC
59330881 TACGTGTATC
Statistics
Matches: 164, Mismatches: 18, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
101 33 0.20
102 129 0.79
103 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (102 bp):
TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
AGTACTAAGTGAAGGCTACAATATGTACCGAAAAGCT
Found at i:59331801 original size:5 final size:5
Alignment explanation
Indices: 59331791--59331848 Score: 80
Period size: 5 Copynumber: 11.6 Consensus size: 5
59331781 TGCTTGATGA
* * * *
59331791 AATGG AATGG AATGG AATGG TATGA AATGG AATGG TATGG AATGG TATGG
1 AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG
59331841 AATGG AAT
1 AATGG AAT
59331849 ATATATATAT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
5 45 1.00
ACGTcount: A:0.38, C:0.00, G:0.36, T:0.26
Consensus pattern (5 bp):
AATGG
Found at i:59336700 original size:19 final size:18
Alignment explanation
Indices: 59336678--59336715 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
59336668 TTTCAATTGG
*
59336678 AAAAAATGAAAGAGAAAA
1 AAAAAATGAAAAAGAAAA
59336696 AAAAAA-GAAAAAGAAAA
1 AAAAAATGAAAAAGAAAA
59336713 AAA
1 AAA
59336716 TAAAATATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (18 bp):
AAAAAATGAAAAAGAAAA
Found at i:59352275 original size:101 final size:101
Alignment explanation
Indices: 59352095--59352307 Score: 302
Period size: 101 Copynumber: 2.1 Consensus size: 101
59352085 CTGAAGTATT
* * * **
59352095 TAAGACCATGGTTGGACCATGGCAGTGTACATATGTAAGACTATAGCTGGGTTGTGGCATTCTGA
1 TAAGACCATGGTTGGACCATGACAGTGTACATATGTAAGACCATAGCTGGGCTACGGCATTCTGA
*
59352160 TGATAAGACCATAACTG-GTTTATGACACTATGGACG
66 TGATAAGACCATAACTGAG-TTATGACACTATGCACG
* ** *
59352196 TATGACCATGGTTGGACCATGACAGTGTTTATATGTAAGACCATAGCTGGGCTACGGTATTCTGA
1 TAAGACCATGGTTGGACCATGACAGTGTACATATGTAAGACCATAGCTGGGCTACGGCATTCTGA
* *
59352261 TGATAAGACTATAACTGAGTTATGGCACTATGCACG
66 TGATAAGACCATAACTGAGTTATGACACTATGCACG
59352297 TAAGACCATGG
1 TAAGACCATGG
59352308 CAGGGCTGCG
Statistics
Matches: 98, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
101 97 0.99
102 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (101 bp):
TAAGACCATGGTTGGACCATGACAGTGTACATATGTAAGACCATAGCTGGGCTACGGCATTCTGA
TGATAAGACCATAACTGAGTTATGACACTATGCACG
Found at i:59352330 original size:101 final size:101
Alignment explanation
Indices: 59352125--59352340 Score: 231
Period size: 101 Copynumber: 2.2 Consensus size: 101
59352115 GGCAGTGTAC
* * **
59352125 ATATGTAAGACTATAGCTGGGTTGTGGCATTCTGATGATAAGACCATAACTGGTTTATGACACTA
1 ATATGTAAGACCATAGCTGGGCTACGGCATTCTGATGATAAGACCATAACTGGTTTATGACACTA
* * ** * * **
59352190 TGGACGTATGACCATGGTTGGACCATGACAGTGTTT
66 TGCACGTAAGACCATGGCAGGACCACGACAATGCAT
* * *
59352226 ATATGTAAGACCATAGCTGGGCTACGGTATTCTGATGATAAGACTATAACTGAG-TTATGGCACT
1 ATATGTAAGACCATAGCTGGGCTACGGCATTCTGATGATAAGACCATAACTG-GTTTATGACACT
* ** *
59352290 ATGCACGTAAGACCATGGCAGGGCTGCGGCAATGCAT
65 ATGCACGTAAGACCATGGCAGGACCACGACAATGCAT
59352327 ATA--TAAGACCATAG
1 ATATGTAAGACCATAG
59352341 TTGGATTATG
Statistics
Matches: 95, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
99 11 0.12
101 83 0.87
102 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.28
Consensus pattern (101 bp):
ATATGTAAGACCATAGCTGGGCTACGGCATTCTGATGATAAGACCATAACTGGTTTATGACACTA
TGCACGTAAGACCATGGCAGGACCACGACAATGCAT
Found at i:59359087 original size:56 final size:56
Alignment explanation
Indices: 59359003--59359110 Score: 180
Period size: 56 Copynumber: 1.9 Consensus size: 56
59358993 AAATGGTATG
* *
59359003 TTTTTTTAATGGCGCCTATCTGATAGGCGCCAATGAATTTTTTATAATAAAAAATA
1 TTTTTTTAATGACGCCTATCTGACAGGCGCCAATGAATTTTTTATAATAAAAAATA
* *
59359059 TTTTTTTGATGACGCCTATCTGACAGGCGCCAATGAATTTTTTATATTAAAA
1 TTTTTTTAATGACGCCTATCTGACAGGCGCCAATGAATTTTTTATAATAAAA
59359111 TTTTTTCTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (56 bp):
TTTTTTTAATGACGCCTATCTGACAGGCGCCAATGAATTTTTTATAATAAAAAATA
Found at i:59359221 original size:27 final size:26
Alignment explanation
Indices: 59359191--59359265 Score: 78
Period size: 27 Copynumber: 2.8 Consensus size: 26
59359181 GCGAGTAGTT
* *
59359191 GCGCCTATCTCAGAGGCGCCAATGGTG
1 GCGCTTATCT-AGAGGCGCCAATGATG
*
59359218 GCGCTTATCTGGCAGGCGCCAATGATG
1 GCGCTTATCTAG-AGGCGCCAATGATG
* *
59359245 GAGCTTATCTGACAGGCGCCA
1 GCGCTTATCT-AGAGGCGCCA
59359266 CTGCTTCTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
26 1 0.03
27 39 0.98
ACGTcount: A:0.20, C:0.28, G:0.32, T:0.20
Consensus pattern (26 bp):
GCGCTTATCTAGAGGCGCCAATGATG
Found at i:59359473 original size:53 final size:54
Alignment explanation
Indices: 59359375--59359541 Score: 205
Period size: 53 Copynumber: 3.1 Consensus size: 54
59359365 TATTTAAACA
* *
59359375 AAAAAATATTTTTTAATATAAAAAATTGATTCGCGCCTGTGAGATAGGTGCGATT
1 AAAAAATA-TTTTTAATATAAAAAATTGATTCGCGCCTGTAAGATAGGCGCGATT
* * * *
59359430 AAAAAATAATTTTAATAT-AAAAATTGATTCGCGTCTGTCAGATAGGCGCTATT
1 AAAAAATATTTTTAATATAAAAAATTGATTCGCGCCTGTAAGATAGGCGCGATT
* * * *
59359483 --AAAATTTTTTTAATATAAAAAATTGATTGGCGCCTGTAAGATAGACACGATT
1 AAAAAATATTTTTAATATAAAAAATTGATTCGCGCCTGTAAGATAGGCGCGATT
59359535 ATAAAAA
1 A-AAAAA
59359542 AATATCATTT
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
51 14 0.15
52 29 0.31
53 31 0.33
54 9 0.09
55 12 0.13
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.34
Consensus pattern (54 bp):
AAAAAATATTTTTAATATAAAAAATTGATTCGCGCCTGTAAGATAGGCGCGATT
Found at i:59365023 original size:2 final size:2
Alignment explanation
Indices: 59365010--59365045 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
59365000 ATACTAATAG
*
59365010 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59365046 GCCCCATGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:59370751 original size:18 final size:18
Alignment explanation
Indices: 59370730--59370771 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 18
59370720 CTATTCCTTC
59370730 AAAAAAAGATAAT-TATT
1 AAAAAAAGATAATCTATT
*
59370747 AAAAAAAGATTATCTATT
1 AAAAAAAGATAATCTATT
59370765 AACAAAA
1 AA-AAAA
59370772 TTACTTTACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.55
18 6 0.27
19 4 0.18
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (18 bp):
AAAAAAAGATAATCTATT
Found at i:59376781 original size:25 final size:25
Alignment explanation
Indices: 59376753--59376806 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
59376743 TTTTAAAGTT
* * *
59376753 AAATACTAATGGACAAT-AAATAATA
1 AAATAATAATAGAAAATAAAATAA-A
59376778 AAATAATAATAGAAAATAAAATAAA
1 AAATAATAATAGAAAATAAAATAAA
59376803 AAAT
1 AAAT
59376807 TAATCTTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.22
Consensus pattern (25 bp):
AAATAATAATAGAAAATAAAATAAA
Found at i:59377257 original size:19 final size:19
Alignment explanation
Indices: 59377228--59377266 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
59377218 CAATTAATTA
59377228 ATTTTTAAAATATTTTATAT
1 ATTTTTAAAATATTTT-TAT
59377248 ATTTTT-AAATATTTTTAT
1 ATTTTTAAAATATTTTTAT
59377266 A
1 A
59377267 AAATTTTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 9 0.47
20 6 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTTAAAATATTTTTAT
Found at i:59377273 original size:20 final size:20
Alignment explanation
Indices: 59377230--59377280 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
59377220 ATTAATTAAT
*
59377230 TTTTAAAATATTTTAT-ATA
1 TTTTAAAATATTTTATAAAA
*
59377249 TTTTTAAATATTTTTATAAAA
1 TTTTAAAATA-TTTTATAAAA
59377270 TTTTCAAAATA
1 TTTT-AAAATA
59377281 AAATAAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 9 0.35
20 6 0.23
21 6 0.23
22 5 0.19
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTAAAATATTTTATAAAA
Found at i:59400929 original size:4 final size:4
Alignment explanation
Indices: 59400920--59400977 Score: 116
Period size: 4 Copynumber: 14.5 Consensus size: 4
59400910 TCATGTGTTT
59400920 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
59400968 TACA TACA TA
1 TACA TACA TA
59400978 GTTAATTGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:59404056 original size:23 final size:23
Alignment explanation
Indices: 59404027--59404148 Score: 181
Period size: 23 Copynumber: 5.3 Consensus size: 23
59404017 ATAAGTGCCG
59404027 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
59404050 CATTGATATGTAGCCGTAGCTAT
1 CACTGATATGTAGCCGAAGCTAC
*
59404073 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
59404096 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
59404119 CATTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
59404142 CACTGAT
1 CACTGAT
59404149 CAATAACACT
Statistics
Matches: 85, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 85 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:59404094 original size:46 final size:46
Alignment explanation
Indices: 59404027--59404148 Score: 208
Period size: 46 Copynumber: 2.7 Consensus size: 46
59404017 ATAAGTGCCG
* * *
59404027 CACTGATATGTAGCCGAAGCTACCATTGATATGTAGCCGTAGCTAT
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
59404073 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
*
59404119 CATTGAAATGTAGCCGAAGCTACCACTGAT
1 CACTGAAATGTAGCCGAAGCTACCACTGAT
59404149 CAATAACACT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 72 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
Found at i:59406552 original size:33 final size:33
Alignment explanation
Indices: 59406510--59406572 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
59406500 ATTTTTATTT
*
59406510 AGTTAAATTTGA-CTTTAAACCCTTTAAAAAATA
1 AGTTAAATTTGATCATT-AACCCTTTAAAAAATA
* *
59406543 AGTTGAATTTGATCATTAACCTTTTAAAAA
1 AGTTAAATTTGATCATTAACCCTTTAAAAA
59406573 GAGTCAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
33 23 0.88
34 3 0.12
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (33 bp):
AGTTAAATTTGATCATTAACCCTTTAAAAAATA
Found at i:59406671 original size:21 final size:18
Alignment explanation
Indices: 59406644--59406687 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
59406634 ATTTCATATT
*
59406644 ATTTTTTTAAAAATTTTATG
1 ATTTTTTTTAAAA-TTT-TG
*
59406664 ATTTTTTTTGAAATTTTG
1 ATTTTTTTTAAAATTTTG
59406682 ATTTTT
1 ATTTTT
59406688 GAATATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.36
19 3 0.14
20 11 0.50
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.66
Consensus pattern (18 bp):
ATTTTTTTTAAAATTTTG
Found at i:59407210 original size:2 final size:2
Alignment explanation
Indices: 59407203--59407231 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
59407193 TTAAATATTG
59407203 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
59407232 ATATATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:59407751 original size:51 final size:51
Alignment explanation
Indices: 59407624--59407752 Score: 116
Period size: 51 Copynumber: 2.5 Consensus size: 51
59407614 TATAATAAAA
** ** *
59407624 AAATATAACCTTCAA-AGTTTACACATTTTATCAATTTGATCTTGATATAAC
1 AAATATAACCCACAACA-TTTACACATTCCATCAATTTGATCCTGATATAAC
* * * * *
59407675 AAATATAACTCATAACATTTTCACATTCCATCAATTTGGTCCTGATTTAAC
1 AAATATAACCCACAACATTTACACATTCCATCAATTTGATCCTGATATAAC
* * * *
59407726 AAATTTATCCCGCAATATTTACACATT
1 AAATATAACCCACAACATTTACACATT
59407753 TTGTCAACAG
Statistics
Matches: 60, Mismatches: 17, Indels: 2
0.76 0.22 0.03
Matches are distributed among these distances:
51 59 0.98
52 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.38
Consensus pattern (51 bp):
AAATATAACCCACAACATTTACACATTCCATCAATTTGATCCTGATATAAC
Found at i:59409365 original size:24 final size:24
Alignment explanation
Indices: 59409338--59409388 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
59409328 ATCAAAGTCG
* *
59409338 AATATATTATGCTAATAAATACTA
1 AATATATTATACCAATAAATACTA
*
59409362 AATATATTATACCCATAAATACTA
1 AATATATTATACCAATAAATACTA
59409386 AAT
1 AAT
59409389 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.35
Consensus pattern (24 bp):
AATATATTATACCAATAAATACTA
Found at i:59420118 original size:17 final size:17
Alignment explanation
Indices: 59420078--59420125 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
59420068 CGTTTATCAA
59420078 TTTTTATAATCAAACTC
1 TTTTTATAATCAAACTC
* * *
59420095 -ATTTATAATTAAGCTC
1 TTTTTATAATCAAACTC
59420111 TTTTTATATATCAAA
1 TTTTTATA-ATCAAA
59420126 GATAAAAATG
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
16 13 0.57
17 6 0.26
18 4 0.17
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (17 bp):
TTTTTATAATCAAACTC
Found at i:59424253 original size:22 final size:22
Alignment explanation
Indices: 59424239--59424280 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
59424229 TAATAGTAGC
59424239 AAAATAACAACATAACAGCAAA
1 AAAATAACAACATAACAGCAAA
*
59424261 AAAATAACAACATAAAAGCA
1 AAAATAACAACATAACAGCA
59424281 GTAAACAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.69, C:0.17, G:0.05, T:0.10
Consensus pattern (22 bp):
AAAATAACAACATAACAGCAAA
Found at i:59426288 original size:3 final size:3
Alignment explanation
Indices: 59426280--59426319 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
59426270 TTTTAATCTC
59426280 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
59426320 GTTACTCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:59426514 original size:20 final size:19
Alignment explanation
Indices: 59426477--59426546 Score: 54
Period size: 20 Copynumber: 3.6 Consensus size: 19
59426467 TTCACATAGA
59426477 TATATATTTTTTTATATTT
1 TATATATTTTTTTATATTT
59426496 TATA-ATTTTTATCTATA-TT
1 TATATATTTTT-T-TATATTT
* * * *
59426515 CATTTATTTATTTATTTATT
1 TATATATTTTTTTATAT-TT
*
59426535 TATTTATTTTTT
1 TATATATTTTTT
59426547 GGATGAAAAC
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
18 9 0.22
19 10 0.25
20 21 0.52
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (19 bp):
TATATATTTTTTTATATTT
Found at i:59426525 original size:4 final size:4
Alignment explanation
Indices: 59426511--59426543 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
59426501 TTTTTATCTA
*
59426511 TATT CATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT T
59426544 TTTGGATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:59427970 original size:3 final size:3
Alignment explanation
Indices: 59427962--59428012 Score: 50
Period size: 3 Copynumber: 17.3 Consensus size: 3
59427952 CAAGACATAG
* * * * *
59427962 ATA ATA ATA ATA ATA TTA ATA ATA ATC ATA ATA GTT TTA ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
59428009 ATA A
1 ATA A
59428013 CCAAGATATA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:59429540 original size:3 final size:3
Alignment explanation
Indices: 59429532--59429587 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
59429522 CCAGACAAAG
* * * * *
59429532 ATA ATA ATA ATA ATA AT- ATA TTA ATA ATA ATC ATA ATA GTT TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
59429579 ATA A-A ATA A
1 ATA ATA ATA A
59429588 CCAAGATATA
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:59429558 original size:20 final size:21
Alignment explanation
Indices: 59429533--59429587 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
59429523 CAGACAAAGA
59429533 TAATAATAATAATAATA-TAT
1 TAATAATAATAATAATAGTAT
* *
59429553 TAATAATAATCATAATAGTTT
1 TAATAATAATAATAATAGTAT
59429574 TAATAATAA-AATAA
1 TAATAATAATAATAA
59429588 CCAAGATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
TAATAATAATAATAATAGTAT
Found at i:59434671 original size:16 final size:17
Alignment explanation
Indices: 59434650--59434682 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
59434640 ATAATTTTAC
*
59434650 TTTTATTAATT-TAAAA
1 TTTTATAAATTATAAAA
59434666 TTTTATAAATTATAAAA
1 TTTTATAAATTATAAAA
59434683 ATTATATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTTATAAATTATAAAA
Found at i:59460678 original size:7 final size:7
Alignment explanation
Indices: 59460666--59460699 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
59460656 ATTTGTCTGA
59460666 AATTTCC
1 AATTTCC
59460673 AATTTCC
1 AATTTCC
59460680 AATTTCC
1 AATTTCC
59460687 AATTTCC
1 AATTTCC
59460694 AATTTC
1 AATTTC
59460700 TCATATGAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.44
Consensus pattern (7 bp):
AATTTCC
Found at i:59464721 original size:24 final size:24
Alignment explanation
Indices: 59464694--59464745 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
59464684 TTAGTAAGTC
*
59464694 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
59464718 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
59464742 AAAT
1 AAAT
59464746 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:59466433 original size:15 final size:15
Alignment explanation
Indices: 59466413--59466442 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
59466403 AAGATGAACA
59466413 CACAAATTTAACGTG
1 CACAAATTTAACGTG
59466428 CACAAATTTAACGTG
1 CACAAATTTAACGTG
59466443 GAAAAACCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (15 bp):
CACAAATTTAACGTG
Found at i:59466705 original size:24 final size:24
Alignment explanation
Indices: 59466678--59466729 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
59466668 TTAGTAAGTC
*
59466678 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
59466702 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
59466726 AAAT
1 AAAT
59466730 CTTTTCTAGA
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:59473681 original size:25 final size:26
Alignment explanation
Indices: 59473653--59473711 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 26
59473643 TTTTAAAGTG
* * * *
59473653 AAATATTAATGGACAAT-AAATAATA
1 AAATAATAATAGAAAATAAAATAAGA
59473678 AAATAATAATAGAAAATAAAATAAGA
1 AAATAATAATAGAAAATAAAATAAGA
59473704 AAACTAAT
1 AAA-TAAT
59473712 CTTCATCTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 14 0.50
26 10 0.36
27 4 0.14
ACGTcount: A:0.66, C:0.03, G:0.07, T:0.24
Consensus pattern (26 bp):
AAATAATAATAGAAAATAAAATAAGA
Found at i:59473695 original size:13 final size:14
Alignment explanation
Indices: 59473671--59473711 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
59473661 ATGGACAATA
*
59473671 AATAATAAAATAAT
1 AATAAGAAAATAAT
59473685 AAT-AGAAAATAA-
1 AATAAGAAAATAAT
59473697 AATAAGAAAACTAAT
1 AATAAGAAAA-TAAT
59473712 CTTCATCTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
12 3 0.13
13 14 0.61
14 6 0.26
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (14 bp):
AATAAGAAAATAAT
Found at i:59481754 original size:23 final size:23
Alignment explanation
Indices: 59481724--59481788 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
59481714 GTTTAGTTCC
59481724 CATGCAAAGGTGGCCATGCACGA
1 CATGCAAAGGTGGCCATGCACGA
59481747 CATGCAAAGGTGGCCATGCACGA
1 CATGCAAAGGTGGCCATGCACGA
*
59481770 CATGCAAAGGTGGTCATGC
1 CATGCAAAGGTGGCCATGC
59481789 TCGAAGGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.29, C:0.25, G:0.31, T:0.15
Consensus pattern (23 bp):
CATGCAAAGGTGGCCATGCACGA
Found at i:59503956 original size:16 final size:15
Alignment explanation
Indices: 59503937--59503967 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
59503927 ATGGCCACCT
59503937 TTGCATGGGAAGCTAA
1 TTGCATGGGAA-CTAA
59503953 TTGCATGGGAACTAA
1 TTGCATGGGAACTAA
59503968 CTTTAACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.32, C:0.13, G:0.29, T:0.26
Consensus pattern (15 bp):
TTGCATGGGAACTAA
Found at i:59504048 original size:44 final size:44
Alignment explanation
Indices: 59503991--59504079 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
59503981 TTATTTCTTT
59503991 ACGGGTTCTCCTTTTAATTTATGTTGCTTCGATTGATCTTATTC
1 ACGGGTTCTCCTTTTAATTTATGTTGCTTCGATTGATCTTATTC
59504035 ACGGGTTCTCCTTTTAATTTATGTTGCTTCGATTGATCTTATTC
1 ACGGGTTCTCCTTTTAATTTATGTTGCTTCGATTGATCTTATTC
59504079 A
1 A
59504080 TTTGAAGTTC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.17, C:0.18, G:0.16, T:0.49
Consensus pattern (44 bp):
ACGGGTTCTCCTTTTAATTTATGTTGCTTCGATTGATCTTATTC
Found at i:59506944 original size:52 final size:50
Alignment explanation
Indices: 59506871--59507007 Score: 125
Period size: 52 Copynumber: 2.7 Consensus size: 50
59506861 GTATAATGAT
* * *
59506871 AAATTTAGCCCTCAAAGTTTACACATTCTATCAATTT-GTCATTGATTTAAAA
1 AAATTTAACCCACAAA-TTTACACATTCTATCAATTTAATCA-TGATTT-AAA
* *
59506923 AAATTTAACCCACAACATTTACACATT-TCGTCAATTTAATCATGATTTAAC
1 AAATTTAACCCACAA-ATTTACACATTCT-ATCAATTTAATCATGATTTAAA
* ** *
59506974 ATATTTAACCCGTAATAATTACACATTCTATCAA
1 AAATTTAACCCACAA-ATTTACACATTCTATCAA
59507008 CATTTACGCA
Statistics
Matches: 70, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
51 29 0.41
52 37 0.53
53 4 0.06
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (50 bp):
AAATTTAACCCACAAATTTACACATTCTATCAATTTAATCATGATTTAAA
Found at i:59509572 original size:22 final size:22
Alignment explanation
Indices: 59509526--59509572 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
59509516 TAAATTAATT
**
59509526 TAAAAGAAATTTAATTTCATGA
1 TAAAAGAAATTTAATTTCAAAA
59509548 TAAAA-AAATTTATATTTCAAAA
1 TAAAAGAAATTTA-ATTTCAAAA
59509570 TAA
1 TAA
59509573 TTAGAAAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.36
Consensus pattern (22 bp):
TAAAAGAAATTTAATTTCAAAA
Found at i:59509871 original size:13 final size:12
Alignment explanation
Indices: 59509848--59509875 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
59509838 TGCAAATGAG
59509848 TTTTCTTTTTTT
1 TTTTCTTTTTTT
59509860 TTTTCTTTTTTT
1 TTTTCTTTTTTT
59509872 TTTT
1 TTTT
59509876 AAATATAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:59512616 original size:29 final size:28
Alignment explanation
Indices: 59512549--59512619 Score: 70
Period size: 29 Copynumber: 2.5 Consensus size: 28
59512539 TCGGAGCTCA
59512549 AAAATAAATTTCAAATCCAAAACAAATG
1 AAAATAAATTTCAAATCCAAAACAAATG
* ** * * *
59512577 AAAATTTAATTTTTAATCCAAACCGATTG
1 AAAA-TAAATTTCAAATCCAAAACAAATG
*
59512606 AAAATAAAATTCAA
1 AAAATAAATTTCAA
59512620 TATACAACCA
Statistics
Matches: 32, Mismatches: 10, Indels: 2
0.73 0.23 0.05
Matches are distributed among these distances:
28 10 0.31
29 22 0.69
ACGTcount: A:0.55, C:0.13, G:0.04, T:0.28
Consensus pattern (28 bp):
AAAATAAATTTCAAATCCAAAACAAATG
Found at i:59517206 original size:2 final size:2
Alignment explanation
Indices: 59517199--59517234 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
59517189 NNNNNNNNNN
59517199 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59517235 GAATAGGTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59520645 original size:5 final size:5
Alignment explanation
Indices: 59520635--59520663 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
59520625 ATCATTCTCA
59520635 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
59520664 AAAAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:59523990 original size:51 final size:50
Alignment explanation
Indices: 59523914--59524054 Score: 135
Period size: 51 Copynumber: 2.8 Consensus size: 50
59523904 ATTGGTATAA
* *
59523914 TAATAAA-TTAAGCCCTCAAAGTTTACACATTCTATCAATTTG-TTATTGATT
1 TAATAAATTTAA-CCCACAAA-TTTACACATTCTATCAATTTGATCA-TGATT
* *
59523965 TAATAAATTTAACCCACAACATTTACACGTT-TCGTCAATTTGATCATGATT
1 TAATAAATTTAACCCACAA-ATTTACACATTCT-ATCAATTTGATCATGATT
* * * *
59524016 TAACATATTTAACCCATAATAATTACACATTCTATCAAT
1 TAATAAATTTAACCCACAA-ATTTACACATTCTATCAAT
59524055 ATTTAAGCGA
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
50 1 0.01
51 65 0.88
52 8 0.11
ACGTcount: A:0.38, C:0.18, G:0.06, T:0.38
Consensus pattern (50 bp):
TAATAAATTTAACCCACAAATTTACACATTCTATCAATTTGATCATGATT
Found at i:59530971 original size:2 final size:2
Alignment explanation
Indices: 59530958--59530994 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
59530948 GGGCATGGAT
*
59530958 TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
59530995 GAATAGGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:59531275 original size:17 final size:17
Alignment explanation
Indices: 59531253--59531288 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
59531243 GCAGCCTGTG
59531253 AGGTTTGAGTTTCCGCA
1 AGGTTTGAGTTTCCGCA
59531270 AGGTTTGAGTTTCCGCA
1 AGGTTTGAGTTTCCGCA
59531287 AG
1 AG
59531289 TGTCTTACCT
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:0.19, C:0.17, G:0.31, T:0.33
Consensus pattern (17 bp):
AGGTTTGAGTTTCCGCA
Found at i:59534606 original size:34 final size:34
Alignment explanation
Indices: 59534563--59534632 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
59534553 CCAGACACAA
59534563 TGGCGGCACCAACCTACCATCATCGACCACTGAT
1 TGGCGGCACCAACCTACCATCATCGACCACTGAT
*
59534597 TGGCGGCACCGACCTACCATCATCGACCACTGAT
1 TGGCGGCACCAACCTACCATCATCGACCACTGAT
59534631 TG
1 TG
59534633 TCTTTTATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.24, C:0.37, G:0.20, T:0.19
Consensus pattern (34 bp):
TGGCGGCACCAACCTACCATCATCGACCACTGAT
Found at i:59538569 original size:2 final size:2
Alignment explanation
Indices: 59538557--59538593 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
59538547 ATCTTTACAA
59538557 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59538594 TATTCCTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59540043 original size:51 final size:51
Alignment explanation
Indices: 59539988--59540103 Score: 146
Period size: 51 Copynumber: 2.3 Consensus size: 51
59539978 CTCAAAGTTG
* *
59539988 ACACATTCTATCAATTTG-TTATTGATTTAAC-TAATTTAACCCACAATATTT
1 ACACATTCTATCAATTTGATCA-TGATTTAACAT-ATTTAACCCACAATAATT
* * **
59540039 ACACATTTTGTCAATTTGATCATGATTTAACATATTTAACCCGTAATAATT
1 ACACATTCTATCAATTTGATCATGATTTAACATATTTAACCCACAATAATT
59540090 ACACATTCTATCAA
1 ACACATTCTATCAA
59540104 CATTTACACA
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
51 52 0.95
52 3 0.05
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (51 bp):
ACACATTCTATCAATTTGATCATGATTTAACATATTTAACCCACAATAATT
Found at i:59544509 original size:11 final size:11
Alignment explanation
Indices: 59544493--59544517 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
59544483 ATTGAAATAT
59544493 TATTTTTAAAA
1 TATTTTTAAAA
59544504 TATTTTTAAAA
1 TATTTTTAAAA
59544515 TAT
1 TAT
59544518 GGGAGGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTTTAAAA
Found at i:59544926 original size:16 final size:16
Alignment explanation
Indices: 59544907--59544947 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
59544897 AATTTGATAC
59544907 AATTTTAATAACAATT
1 AATTTTAATAACAATT
59544923 AATTTTAATAACAATT
1 AATTTTAATAACAATT
*
59544939 AGTTTTAAT
1 AATTTTAAT
59544948 TTTTATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (16 bp):
AATTTTAATAACAATT
Found at i:59544949 original size:22 final size:23
Alignment explanation
Indices: 59544921--59544982 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
59544911 TTAATAACAA
* *
59544921 TTAATTTTAATAACAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
*
59544943 TTAATTTTTATAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
59544966 TTAATTTTAATTAAAAA
1 TTAATTTTAA-TAAAAA
59544983 ACAGACCGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 15 0.44
23 13 0.38
24 6 0.18
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:59548278 original size:4 final size:4
Alignment explanation
Indices: 59548269--59548300 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
59548259 CAGCTTCAAC
59548269 CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA
59548301 TATATATATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:59557350 original size:16 final size:16
Alignment explanation
Indices: 59557305--59557351 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
59557295 TGATTTTCAG
*
59557305 TTTATATTTCTTTTTC
1 TTTATATTTATTTTTC
59557321 TTT-TATTTACTTTTATC
1 TTTATATTTA-TTTT-TC
59557338 TTTAT-TTTATTTTT
1 TTTATATTTATTTTT
59557352 TTTCCTCTCC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 6 0.22
16 11 0.41
17 9 0.33
18 1 0.04
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTATATTTATTTTTC
Found at i:59558673 original size:21 final size:21
Alignment explanation
Indices: 59558648--59558694 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
59558638 CGGCATTATT
59558648 ATTTAT-TAGTATCTTTATTTC
1 ATTTATGTAGTAT-TTTATTTC
* *
59558669 ATTTATGTATTATTTTATTTT
1 ATTTATGTAGTATTTTATTTC
59558690 ATTTA
1 ATTTA
59558695 AAAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.66
Consensus pattern (21 bp):
ATTTATGTAGTATTTTATTTC
Found at i:59558992 original size:64 final size:61
Alignment explanation
Indices: 59558916--59559053 Score: 188
Period size: 64 Copynumber: 2.2 Consensus size: 61
59558906 ATTTGTATAT
* * * *
59558916 ATATATATTATATTTTATACCTTATATTATTTATATATCTTTATATACGTATTTTTTTTAATTTT
1 ATATATA-TATATTTAATACCTTATATTA--CATATATCTTTATATAC--ATATTTTTAAATTTT
59558981 C
61 C
59558982 ATA-ATATATATTTAATACCTTATATTACATATATCTTTATATACATATTTTTAAATTTTC
1 ATATATATATATTTAATACCTTATATTACATATATCTTTATATACATATTTTTAAATTTTC
59559042 ATATATATATAT
1 ATATATATATAT
59559054 ACATACTTAT
Statistics
Matches: 67, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
60 17 0.25
61 8 0.12
62 16 0.24
64 20 0.30
65 3 0.04
66 3 0.04
ACGTcount: A:0.36, C:0.08, G:0.01, T:0.56
Consensus pattern (61 bp):
ATATATATATATTTAATACCTTATATTACATATATCTTTATATACATATTTTTAAATTTTC
Found at i:59559082 original size:62 final size:62
Alignment explanation
Indices: 59558932--59559084 Score: 177
Period size: 60 Copynumber: 2.5 Consensus size: 62
59558922 ATTATATTTT
* * *
59558932 ATACCTTATATTATTTATATATCTTTATATACGTATTTTTTTTAATTTTCATAATATATATTTA
1 ATACCTTATATTATTTATATA-CTTTATATACG-ATATTTTTAAATTTTCATAATATATATATA
**
59558996 ATACCTTATATTACATATAT-CTTTATATAC-ATATTTTTAAATTTTCAT-ATATATATATA
1 ATACCTTATATTATTTATATACTTTATATACGATATTTTTAAATTTTCATAATATATATATA
* * *
59559055 CATACTTATATATTTTTTTTATACTTTATA
1 -ATACCT-TATATTATTTATATACTTTATA
59559085 GTTTTAATAT
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
59 10 0.13
60 21 0.28
61 10 0.13
62 17 0.22
64 18 0.24
ACGTcount: A:0.35, C:0.09, G:0.01, T:0.56
Consensus pattern (62 bp):
ATACCTTATATTATTTATATACTTTATATACGATATTTTTAAATTTTCATAATATATATATA
Found at i:59561212 original size:18 final size:19
Alignment explanation
Indices: 59561181--59561221 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
59561171 GGGAAACAGT
*
59561181 AGCAAAATAACAACATAAC
1 AGCAAAATAACAACATAAA
59561200 AGCAAAA-AACAACATAAA
1 AGCAAAATAACAACATAAA
59561218 AGCA
1 AGCA
59561222 GTAAACAGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.66, C:0.20, G:0.07, T:0.07
Consensus pattern (19 bp):
AGCAAAATAACAACATAAA
Found at i:59565753 original size:2 final size:2
Alignment explanation
Indices: 59565746--59565777 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
59565736 GCCATGGATG
59565746 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59565778 GAATAGGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59566434 original size:2 final size:2
Alignment explanation
Indices: 59566429--59566461 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
59566419 TTATCATAAA
59566429 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59566462 ACAATGGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59571465 original size:4 final size:4
Alignment explanation
Indices: 59571456--59571601 Score: 247
Period size: 4 Copynumber: 36.5 Consensus size: 4
59571446 CATGTGTTTT
* * *
59571456 TACA TACA TACA TACG TACA TACA TACA TACA TACA TACA TACG TACG
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* *
59571504 TACA TACA TACA TACA TACA TACG TACA TACA TACA TACA TACA TACG
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
59571552 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
59571600 TA
1 TA
59571602 GTTAATTGAA
Statistics
Matches: 134, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 134 1.00
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:59574366 original size:2 final size:2
Alignment explanation
Indices: 59574359--59574385 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59574349 AAATGTAAAG
59574359 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
59574386 GTGTATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59575562 original size:8 final size:8
Alignment explanation
Indices: 59575549--59575574 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
59575539 AGGTGTGTAC
59575549 ATGCATAT
1 ATGCATAT
59575557 ATGCATAT
1 ATGCATAT
59575565 ATGCATAT
1 ATGCATAT
59575573 AT
1 AT
59575575 ATATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (8 bp):
ATGCATAT
Found at i:59575574 original size:2 final size:2
Alignment explanation
Indices: 59575569--59575640 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
59575559 GCATATATGC
59575569 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59575611 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
59575641 CAAGTTAAAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59576787 original size:20 final size:20
Alignment explanation
Indices: 59576751--59576806 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
59576741 TTTCGTTTAC
59576751 AAAATAAAAAA-ATAAGAAT-
1 AAAATAAAAAAGA-AAGAATG
*
59576770 AAAATAAAAATAGAAAGACTG
1 AAAATAAAAA-AGAAAGAATG
*
59576791 AAAAAAAAAAAGAAAG
1 AAAATAAAAAAGAAAG
59576807 CACCTTTAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 10 0.31
20 12 0.38
21 10 0.31
ACGTcount: A:0.77, C:0.02, G:0.11, T:0.11
Consensus pattern (20 bp):
AAAATAAAAAAGAAAGAATG
Found at i:59577443 original size:51 final size:50
Alignment explanation
Indices: 59577367--59577502 Score: 141
Period size: 51 Copynumber: 2.7 Consensus size: 50
59577357 GTATAATGAT
* * *
59577367 AAATTTAGCCCTCAAAGTTTACACATTCTATCAATTTG-TTATTGATTTAAC
1 AAATTTAACCCTCAAA-TTTACACATTCTATCAATATGATCA-TGATTTAAC
* *
59577418 AAATTTAACCCACAACATTTACACATT-TCGTCAATATGATCATGATTTAAC
1 AAATTTAACCCTCAA-ATTTACACATTCT-ATCAATATGATCATGATTTAAC
* * *
59577469 ATATTTAACCCTTAATAATTACACATTCTATCAA
1 AAATTTAACCCTCAA-ATTTACACATTCTATCAA
59577503 CATTTACGCA
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
50 1 0.01
51 65 0.93
52 4 0.06
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.38
Consensus pattern (50 bp):
AAATTTAACCCTCAAATTTACACATTCTATCAATATGATCATGATTTAAC
Found at i:59579430 original size:108 final size:109
Alignment explanation
Indices: 59579165--59579480 Score: 469
Period size: 108 Copynumber: 2.9 Consensus size: 109
59579155 GGCATGGATT
* * ** *
59579165 AAAATTCAAGAGGATATTTGGCCATTTGGTTAAACGAG--AAATCGATACCCAGCACCTTAGGGC
1 AAAATTTAAAAGGATATTAAGCCATTTGGTTAAACGAGAAAAATCGACACCCAGCACCTTAGGGC
* *
59579228 ATG-TTCCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGT
66 ATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGA
** * * *
59579271 AATTTTTGGAAAGGATATTAAGCCATTTGGTTGAACAAGAAAAATCGACACCCAGCACCTTAGGG
1 AAAATTT-AAAAGGATATTAAGCCATTTGGTTAAACGAGAAAAATCGACACCCAGCACCTTAGGG
59579336 CATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTT-A
65 CATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGA
*
59579380 AAAATTTAAAAGGATATTAAGCCATTTGGTTAAACGAGAAAAATCAACACCCAGCACCTTAGGGC
1 AAAATTTAAAAGGATATTAAGCCATTTGGTTAAACGAGAAAAATCGACACCCAGCACCTTAGGGC
*
59579445 ACGTTTTCTCGAATTTCCAAACGCAAAACATTGCCT
66 ATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCT
59579481 CAATTAGAAA
Statistics
Matches: 187, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
106 4 0.02
107 25 0.13
108 89 0.48
109 32 0.17
110 37 0.20
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (109 bp):
AAAATTTAAAAGGATATTAAGCCATTTGGTTAAACGAGAAAAATCGACACCCAGCACCTTAGGGC
ATGTTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATTTTGA
Found at i:59582323 original size:2 final size:2
Alignment explanation
Indices: 59582318--59582352 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
59582308 CCCTCTCTAC
59582318 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59582353 AAAGCATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59586444 original size:17 final size:18
Alignment explanation
Indices: 59586420--59586460 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
59586410 TTTAAGTTTA
59586420 TAATTTTT-GATATTATG
1 TAATTTTTAGATATTATG
* *
59586437 TTATTTTTATATATTATG
1 TAATTTTTAGATATTATG
59586455 TAATTT
1 TAATTT
59586461 AGAACACAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (18 bp):
TAATTTTTAGATATTATG
Found at i:59597436 original size:13 final size:14
Alignment explanation
Indices: 59597402--59597439 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
59597392 TACTTTTATA
59597402 TATATTCATTTCGTT
1 TATATT-ATTTCGTT
59597417 TAT-TTATTT-GTT
1 TATATTATTTCGTT
59597429 TATATTATTTC
1 TATATTATTTC
59597440 TATGCCATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 2 0.10
15 3 0.14
ACGTcount: A:0.21, C:0.08, G:0.05, T:0.66
Consensus pattern (14 bp):
TATATTATTTCGTT
Done.