Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 49 of 433
Found at i:13447916 original size:20 final size:20
Alignment explanation
Indices: 13447891--13447953 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
13447881 ATTTTGATAA
13447891 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
13447911 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
13447931 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
13447951 ACA
1 ACA
13447954 CGAGATGTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:13448064 original size:24 final size:24
Alignment explanation
Indices: 13448007--13448197 Score: 262
Period size: 24 Copynumber: 8.0 Consensus size: 24
13447997 GGAGGAAGTG
13448007 AAAATGGGCTTATGCCCCAGTTAT-
1 AAAA-GGGCTTATGCCCCAGTTATC
* *
13448031 TAAAGAGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
*
13448055 AAAAGAGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
13448079 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
*
13448103 AAAAGGGCTTACGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
*
13448127 -AAAGGGCTTATGCCCCAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATC
* *
13448150 AAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
13448174 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
13448198 ATGATAAAGC
Statistics
Matches: 152, Mismatches: 11, Indels: 7
0.89 0.06 0.04
Matches are distributed among these distances:
23 39 0.26
24 102 0.67
25 11 0.07
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:13448136 original size:71 final size:71
Alignment explanation
Indices: 13448007--13448197 Score: 260
Period size: 71 Copynumber: 2.7 Consensus size: 71
13447997 GGAGGAAGTG
* * * *
13448007 AAAATGGGCTTATGCCCCAGTTATTAAAGAGCTTATGCCCCAGTTATCAAAAGAGCTTATGCCCC
1 AAAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTACGCCCCAGTTATCAAAAGAGCTTATGCCCC
13448072 AGTTAT
66 AGTTAT
* *
13448078 CAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTACGCCCCAGTTATC-AAAGGGCTTATGCCC
1 AAAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTACGCCCCAGTTATCAAAAGAGCTTATGCCC
13448142 CAGTTAT
65 CAGTTAT
* *
13448149 AAAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTA-TAAAAG-GGCTTACGCC-CCAGTTAT
13448198 ATGATAAAGC
Statistics
Matches: 107, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
71 74 0.69
72 33 0.31
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (71 bp):
AAAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTACGCCCCAGTTATCAAAAGAGCTTATGCCCC
AGTTAT
Found at i:13448154 original size:47 final size:47
Alignment explanation
Indices: 13448007--13448198 Score: 251
Period size: 47 Copynumber: 4.0 Consensus size: 47
13447997 GGAGGAAGTG
* * *
13448007 AAAATGGGCTTATGCCCCAGTTATTAAAGAGCTTATGCCCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTATCAAAGGGCTTATGCCCCAGTTAT
* *
13448054 CAAAAGAGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTATC-AAAGGGCTTATGCCCCAGTTAT
* *
13448102 CAAAAGGGCTTACGCCCCAGTTATCAAAGGGCTTATGCCCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTATCAAAGGGCTTATGCCCCAGTTAT
* * *
13448149 AAAAAGGGCTTTTGCCCCAGTTATTAAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAAGGGCTTATGCCCCAGTTA-TCAAAG-GGCTTATGCC-CCAGTTAT
13448198 A
1 A
13448199 TGATAAAGCA
Statistics
Matches: 129, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
47 63 0.49
48 54 0.42
49 12 0.09
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.26
Consensus pattern (47 bp):
AAAAAGGGCTTATGCCCCAGTTATCAAAGGGCTTATGCCCCAGTTAT
Found at i:13448434 original size:31 final size:31
Alignment explanation
Indices: 13448391--13448454 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
13448381 CGTTTACCGT
*
13448391 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
* **
13448422 AAAGTCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
13448453 AA
1 AA
13448455 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:13451980 original size:21 final size:21
Alignment explanation
Indices: 13451927--13451984 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
13451917 ACAACTTAGA
* *
13451927 GCAGATGCAACAGCGAGGGAG
1 GCAGAAGCAGCAGCGAGGGAG
*
13451948 GCA-ACAGTAGCAGCGAGGGAG
1 GCAGA-AGCAGCAGCGAGGGAG
*
13451969 GCAGAGGCAGCAGCGA
1 GCAGAAGCAGCAGCGA
13451985 TGGCAGCAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.33, C:0.21, G:0.43, T:0.03
Consensus pattern (21 bp):
GCAGAAGCAGCAGCGAGGGAG
Found at i:13451993 original size:21 final size:21
Alignment explanation
Indices: 13451956--13451995 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13451946 AGGCAACAGT
*
13451956 AGCAGCGAGGGAGGCAGAGGC
1 AGCAGCGAGGCAGGCAGAGGC
13451977 AGCAGCGATGGCA-GCAGAG
1 AGCAGCGA-GGCAGGCAGAG
13451996 CAGAGTAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.30, C:0.20, G:0.47, T:0.03
Consensus pattern (21 bp):
AGCAGCGAGGCAGGCAGAGGC
Found at i:13452404 original size:42 final size:43
Alignment explanation
Indices: 13452355--13452446 Score: 123
Period size: 43 Copynumber: 2.1 Consensus size: 43
13452345 AACAAAAGCA
*
13452355 ACTTTTAGCGGCTC-TTCCCCAAAAACGCCGCTAAAAGCCATG
1 ACTTTTAGCGGCGCTTTCCCCAAAAACGCCGCTAAAAGCCATG
* * * *
13452397 ACTTTTAGCGGCGCTTTCCCCACAAATGCTGCTAAAAGTCATG
1 ACTTTTAGCGGCGCTTTCCCCAAAAACGCCGCTAAAAGCCATG
13452440 ATCTTTT
1 A-CTTTT
13452447 GTGGGGCATT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 13 0.30
43 25 0.58
44 5 0.12
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.28
Consensus pattern (43 bp):
ACTTTTAGCGGCGCTTTCCCCAAAAACGCCGCTAAAAGCCATG
Found at i:13454809 original size:23 final size:25
Alignment explanation
Indices: 13454783--13454831 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
13454773 TTTGTTTTCT
13454783 ATTTA-GTTTTATTTTT-ACTTGTA
1 ATTTAGGTTTTATTTTTCACTTGTA
* *
13454806 ATTTAGGTTTTTTTTTTCAGTTGTA
1 ATTTAGGTTTTATTTTTCACTTGTA
13454831 A
1 A
13454832 GCGTAGGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 5 0.23
24 10 0.45
25 7 0.32
ACGTcount: A:0.20, C:0.04, G:0.12, T:0.63
Consensus pattern (25 bp):
ATTTAGGTTTTATTTTTCACTTGTA
Found at i:13454863 original size:22 final size:23
Alignment explanation
Indices: 13454816--13454860 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
13454806 ATTTAGGTTT
*
13454816 TTTTTTTCAGTTGTAAGCGTAGG
1 TTTTTTTCAATTGTAAGCGTAGG
13454839 TTTTTTTCAATTGTAAGCGTAG
1 TTTTTTTCAATTGTAAGCGTAG
13454861 TTTAGTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.09, G:0.22, T:0.49
Consensus pattern (23 bp):
TTTTTTTCAATTGTAAGCGTAGG
Found at i:13456804 original size:19 final size:18
Alignment explanation
Indices: 13456782--13456899 Score: 64
Period size: 19 Copynumber: 6.3 Consensus size: 18
13456772 ATAAAATGAT
13456782 TAAAAAATAATAAAAACTA
1 TAAAAAATAATAAAAA-TA
* *
13456801 TAAAAAA-ACCCAGAATAAT-
1 TAAAAAATA---ATAAAAATA
* *
13456820 TAGAAAAATTATAAAAAAA
1 TA-AAAAATAATAAAAATA
13456839 TAAAAAAGT-ATCAAAAATA
1 TAAAAAA-TAAT-AAAAATA
* *
13456858 TAAAAATTATTAAAAACTA
1 TAAAAAATAATAAAAA-TA
* *
13456877 TAAAATATTAT-AAAATA
1 TAAAAAATAATAAAAATA
13456894 TAAAAA
1 TAAAAA
13456900 TTCTAATAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 22
0.68 0.13 0.20
Matches are distributed among these distances:
17 7 0.09
18 23 0.31
19 34 0.45
20 6 0.08
21 5 0.07
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.24
Consensus pattern (18 bp):
TAAAAAATAATAAAAATA
Found at i:13456863 original size:9 final size:9
Alignment explanation
Indices: 13456823--13457007 Score: 70
Period size: 10 Copynumber: 19.6 Consensus size: 9
13456813 GAATAATTAG
*
13456823 AAAAATTAT
1 AAAAAATAT
13456832 AAAAAA-AT
1 AAAAAATAT
13456840 AAAAAAGTAT
1 AAAAAA-TAT
*
13456850 CAAAAATAT
1 AAAAAATAT
*
13456859 AAAAATTATT
1 AAAAAATA-T
*
13456869 AAAAACTAT
1 AAAAAATAT
*
13456878 AAAATAT-T
1 AAAAAATAT
*
13456886 ATAAAATAT
1 AAAAAATAT
* *
13456895 AAAAATTCT
1 AAAAAATAT
*
13456904 AATAAATTAT
1 AA-AAAATAT
13456914 AAAATTAATA-
1 AAAA--AATAT
*
13456924 AAAACATATTT
1 AAAA-A-ATAT
* *
13456935 AAAATATTT
1 AAAAAATAT
**
13456944 AAAATTTTAT
1 AAAA-AATAT
13456954 AAAAACATAT
1 AAAAA-ATAT
* * *
13456964 TAAAATTCT
1 AAAAAATAT
13456973 ATAAAAATCAT
1 A-AAAAAT-AT
*
13456984 AAAAATTAT
1 AAAAAATAT
*
13456993 GGAAAAATAT
1 -AAAAAATAT
13457003 AAAAA
1 AAAAA
13457008 GTCTTAAAAG
Statistics
Matches: 131, Mismatches: 31, Indels: 28
0.69 0.16 0.15
Matches are distributed among these distances:
8 14 0.11
9 48 0.37
10 60 0.46
11 9 0.07
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAAAATAT
Found at i:13456908 original size:19 final size:18
Alignment explanation
Indices: 13456852--13456926 Score: 61
Period size: 19 Copynumber: 4.2 Consensus size: 18
13456842 AAAAGTATCA
*
13456852 AAAATATAAAAA-TTATT
1 AAAATATAAAAATTTAAT
13456869 AAAA-ACTATAAAATATT-AT
1 AAAATA-TA-AAAAT-TTAAT
13456888 AAAATATAAAAATTCTAAT
1 AAAATATAAAAATT-TAAT
*
13456907 AAATTAT-AAAA-TTAAT
1 AAAATATAAAAATTTAAT
13456923 AAAA
1 AAAA
13456927 ACATATTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
16 8 0.17
17 8 0.17
18 14 0.29
19 15 0.31
20 3 0.06
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AAAATATAAAAATTTAAT
Found at i:13456927 original size:10 final size:9
Alignment explanation
Indices: 13456817--13457007 Score: 99
Period size: 9 Copynumber: 20.2 Consensus size: 9
13456807 AACCCAGAAT
*
13456817 AATTAGAAA
1 AATTATAAA
13456826 AATTATAAA
1 AATTATAAA
*
13456835 AA-AATAAAA
1 AATTAT-AAA
*
13456844 AAGTATCAAA
1 AATTAT-AAA
13456854 AA-TATAAA
1 AATTATAAA
13456862 AATTATTAAA
1 AATTA-TAAA
*
13456872 AACTATAAA
1 AATTATAAA
13456881 ATATTAT-AA
1 A-ATTATAAA
13456890 AA-TATAAA
1 AATTATAAA
*
13456898 AATTCTAATA
1 AATTATAA-A
13456908 AATTAT-AA
1 AATTATAAA
13456916 AATTAATAAAA
1 AATT-AT-AAA
*
13456927 ACATATTTAAA
1 A-AT-TATAAA
13456938 ATATT-TAAA
1 A-ATTATAAA
*
13456947 ATTTTATAAA
1 A-ATTATAAA
*
13456957 AACATATTAAA
1 AA-TTA-TAAA
*
13456968 ATTCTATAAA
1 AAT-TATAAA
*
13456978 AATCATAAA
1 AATTATAAA
13456987 AATTATGGAAA
1 AATTAT--AAA
13456998 AA-TATAAA
1 AATTATAAA
13457006 AA
1 AA
13457008 GTCTTAAAAG
Statistics
Matches: 145, Mismatches: 18, Indels: 39
0.72 0.09 0.19
Matches are distributed among these distances:
7 3 0.02
8 22 0.15
9 53 0.37
10 42 0.29
11 21 0.14
12 3 0.02
13 1 0.01
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (9 bp):
AATTATAAA
Found at i:13456958 original size:31 final size:29
Alignment explanation
Indices: 13456852--13456969 Score: 92
Period size: 26 Copynumber: 4.2 Consensus size: 29
13456842 AAAAGTATCA
* *
13456852 AAAATA-TAAAAATTATTAAAAAC-TA-T
1 AAAATATTTAAAATTAATAAAAACATATT
13456878 AAAATATTATAAAA-T-AT-AAAA-AT-TCT
1 AAAATATT-TAAAATTAATAAAAACATAT-T
13456904 AATAA-ATTATAAAATTAATAAAAACATATTT
1 AA-AATATT-TAAAATTAATAAAAACATA-TT
*
13456935 AAAATATTTAAAATTTTATAAAAACATATT
1 AAAATATTTAAAA-TTAATAAAAACATATT
13456965 AAAAT
1 AAAAT
13456970 TCTATAAAAA
Statistics
Matches: 75, Mismatches: 3, Indels: 24
0.74 0.03 0.24
Matches are distributed among these distances:
25 5 0.07
26 19 0.25
27 5 0.07
28 6 0.08
29 4 0.05
30 16 0.21
31 19 0.25
32 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (29 bp):
AAAATATTTAAAATTAATAAAAACATATT
Found at i:13456966 original size:21 final size:22
Alignment explanation
Indices: 13456935--13456984 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
13456925 AAACATATTT
*
13456935 AAAAT-AT-TTAAAATTTTATA
1 AAAATCATATTAAAATTCTATA
13456955 AAAA-CATATTAAAATTCTATA
1 AAAATCATATTAAAATTCTATA
13456976 AAAATCATA
1 AAAATCATA
13456985 AAAATTATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 6 0.23
21 16 0.62
22 4 0.15
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAATCATATTAAAATTCTATA
Found at i:13456978 original size:31 final size:31
Alignment explanation
Indices: 13456823--13456988 Score: 105
Period size: 30 Copynumber: 5.8 Consensus size: 31
13456813 GAATAATTAG
* **
13456823 AAAA-ATTATAAAA-AAATAAAAA-AGTATCA
1 AAAATATTATAAAATTAATAAAAACA-TATTT
*
13456852 AAAATA-TA-AAAATTATTAAAAAC-TA--T
1 AAAATATTATAAAATTAATAAAAACATATTT
*
13456878 AAAATATTATAAAA-T-AT-AAAA-AT-TCT
1 AAAATATTATAAAATTAATAAAAACATATTT
13456904 AATAA-ATTATAAAATTAATAAAAACATATTT
1 AA-AATATTATAAAATTAATAAAAACATATTT
*
13456935 AAAATATT-TAAAATTTTATAAAAACATA-TT
1 AAAATATTATAAAA-TTAATAAAAACATATTT
* *
13456965 AAAAT-TCTATAAAAATCATAAAAA
1 AAAATAT-TATAAAATTAATAAAAA
13456989 TTATGGAAAA
Statistics
Matches: 111, Mismatches: 8, Indels: 35
0.72 0.05 0.23
Matches are distributed among these distances:
25 5 0.05
26 19 0.17
27 6 0.05
28 12 0.11
29 18 0.16
30 26 0.23
31 25 0.23
ACGTcount: A:0.64, C:0.04, G:0.01, T:0.31
Consensus pattern (31 bp):
AAAATATTATAAAATTAATAAAAACATATTT
Found at i:13456988 original size:20 final size:20
Alignment explanation
Indices: 13456944--13457016 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 20
13456934 TAAAATATTT
*
13456944 AAAATTTTATAAAAA-CATA
1 AAAATTCTATAAAAATCATA
13456963 TTAAAATTCTATAAAAATCATA
1 --AAAATTCTATAAAAATCATA
* **
13456985 AAAATTATGGAAAAAT-ATA
1 AAAATTCTATAAAAATCATA
*
13457004 AAAAGTCT-TAAAA
1 AAAATTCTATAAAA
13457017 GTATTAAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
18 4 0.09
19 9 0.20
20 13 0.30
21 14 0.32
22 4 0.09
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.30
Consensus pattern (20 bp):
AAAATTCTATAAAAATCATA
Found at i:13457522 original size:10 final size:10
Alignment explanation
Indices: 13457507--13457549 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
13457497 TTAATTTTAT
13457507 AAATTATTAG
1 AAATTATTAG
13457517 AAATTATTAG
1 AAATTATTAG
13457527 AAAATTATTAG
1 -AAATTATTAG
* *
13457538 AATTTGTTAG
1 AAATTATTAG
13457548 AA
1 AA
13457550 TTTTTATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 20 0.67
11 10 0.33
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.40
Consensus pattern (10 bp):
AAATTATTAG
Found at i:13457532 original size:21 final size:21
Alignment explanation
Indices: 13457507--13457549 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
13457497 TTAATTTTAT
13457507 AAATTATTAGAAATTATTAGA
1 AAATTATTAGAAATTATTAGA
* *
13457528 AAATTATTAGAATTTGTTAGA
1 AAATTATTAGAAATTATTAGA
13457549 A
1 A
13457550 TTTTTATATT
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:0.49, C:0.00, G:0.12, T:0.40
Consensus pattern (21 bp):
AAATTATTAGAAATTATTAGA
Found at i:13457533 original size:11 final size:11
Alignment explanation
Indices: 13457507--13457539 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
13457497 TTAATTTTAT
13457507 AAATTATTAG-
1 AAATTATTAGA
13457517 AAATTATTAGA
1 AAATTATTAGA
13457528 AAATTATTAGA
1 AAATTATTAGA
13457539 A
1 A
13457540 TTTGTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (11 bp):
AAATTATTAGA
Found at i:13457597 original size:15 final size:16
Alignment explanation
Indices: 13457568--13457608 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
13457558 TTTTAATAAT
13457568 ATTTATAATTATTTATA
1 ATTTATAA-TATTTATA
*
13457585 ATTT-TAATATTTATT
1 ATTTATAATATTTATA
13457600 ATTTATAAT
1 ATTTATAAT
13457609 TTTTCTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 11 0.50
16 7 0.32
17 4 0.18
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTATAATATTTATA
Found at i:13457608 original size:16 final size:16
Alignment explanation
Indices: 13457567--13457619 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
13457557 ATTTTAATAA
13457567 TATTTATAATTATTTAT
1 TATTTATAA-TATTTAT
*
13457584 AATTT-TAATATTTAT
1 TATTTATAATATTTAT
* *
13457599 TATTTATAATTTTTCT
1 TATTTATAATATTTAT
13457615 TATTT
1 TATTT
13457620 TTTAATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
15 11 0.35
16 16 0.52
17 4 0.13
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
TATTTATAATATTTAT
Found at i:13457632 original size:24 final size:23
Alignment explanation
Indices: 13457575--13457636 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
13457565 AATATTTATA
**
13457575 ATTATTTATAA-TTTTAATATTT
1 ATTATTTATAATTTTTCTTATTT
13457597 ATTATTTATAATTTTTCTTATTT
1 ATTATTTATAATTTTTCTTATTT
* *
13457620 TTTAATTTTTAATTTTT
1 ATT-ATTTATAATTTTT
13457637 ATGGAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 11 0.32
23 11 0.32
24 12 0.35
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (23 bp):
ATTATTTATAATTTTTCTTATTT
Found at i:13459339 original size:27 final size:27
Alignment explanation
Indices: 13459280--13459433 Score: 148
Period size: 28 Copynumber: 5.6 Consensus size: 27
13459270 GGCAAAACTT
* * *
13459280 TAAAATTTCAAAAATAGGGGTAAAATTG
1 TAAAATCTAAAAAATA-GGGAAAAATTG
* * * *
13459308 CAAAATCTAGAAAATAGTGCAAAATTG
1 TAAAATCTAAAAAATAGGGAAAAATTG
13459335 TAAAATCTAAAAAATAGGGAAAAATTG
1 TAAAATCTAAAAAATAGGGAAAAATTG
*
13459362 TAAAATCTAAAAAAATAGGGGAAAATTG
1 TAAAATCT-AAAAAATAGGGAAAAATTG
* * * * *
13459390 TAAATTTTGAAAAAA-AGGGGCAACACTG
1 TAAAATCT-AAAAAATA-GGGAAAAATTG
13459418 TAAAATCTAAAAAATA
1 TAAAATCTAAAAAATA
13459434 TAGGACACAC
Statistics
Matches: 104, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
27 47 0.45
28 57 0.55
ACGTcount: A:0.55, C:0.06, G:0.16, T:0.23
Consensus pattern (27 bp):
TAAAATCTAAAAAATAGGGAAAAATTG
Found at i:13459340 original size:55 final size:55
Alignment explanation
Indices: 13459269--13459433 Score: 183
Period size: 55 Copynumber: 3.0 Consensus size: 55
13459259 ATAAATTTTT
* * * *
13459269 GGGCAAAACTT-TAAAATTTCAAAAATAGGGGTAAAATTGCAAAATCTAGAAAATA
1 GGGCAAAA-TTGTAAAATTTAAAAAATAGGGGAAAAATTGTAAAATCTAAAAAATA
* *
13459324 GTGCAAAATTGTAAAATCTAAAAAATA-GGGAAAAATTGTAAAATCTAAAAAAATA
1 GGGCAAAATTGTAAAATTTAAAAAATAGGGGAAAAATTGTAAAATCT-AAAAAATA
* * * * *
13459379 GGGGAAAATTGTAAATTTTGAAAAAA-AGGGGCAACACTGTAAAATCTAAAAAATA
1 GGGCAAAATTGTAAAATTT-AAAAAATAGGGGAAAAATTGTAAAATCTAAAAAATA
13459434 TAGGACACAC
Statistics
Matches: 93, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
54 19 0.20
55 52 0.56
56 22 0.24
ACGTcount: A:0.53, C:0.07, G:0.16, T:0.23
Consensus pattern (55 bp):
GGGCAAAATTGTAAAATTTAAAAAATAGGGGAAAAATTGTAAAATCTAAAAAATA
Found at i:13461739 original size:37 final size:37
Alignment explanation
Indices: 13461689--13461763 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
13461679 CTTTTCGTGG
13461689 ACTCCATCCAATATTCTACCACTATGGAAGTCGTTCC
1 ACTCCATCCAATATTCTACCACTATGGAAGTCGTTCC
13461726 ACTCCATCCAATATTCTACCACTATGGAAGTCGTTCC
1 ACTCCATCCAATATTCTACCACTATGGAAGTCGTTCC
13461763 A
1 A
13461764 ACAATCCTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.28, C:0.32, G:0.11, T:0.29
Consensus pattern (37 bp):
ACTCCATCCAATATTCTACCACTATGGAAGTCGTTCC
Found at i:13463530 original size:19 final size:19
Alignment explanation
Indices: 13463494--13463532 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
13463484 TTTTCATCAT
* *
13463494 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
13463513 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
13463532 A
1 A
13463533 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:13464036 original size:55 final size:56
Alignment explanation
Indices: 13463971--13464085 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 56
13463961 AGCATGGCTG
* *
13463971 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
* * *
13464027 CCAGA-ACAGATAATTGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
13464082 CCAG
1 CCAG
13464086 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.56
56 22 0.42
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (56 bp):
CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
Found at i:13464081 original size:28 final size:27
Alignment explanation
Indices: 13463996--13464085 Score: 119
Period size: 27 Copynumber: 3.2 Consensus size: 27
13463986 GTGACAGAGT
*
13463996 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
*
13464025 CACCAGAACAGATAA-TTGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCA-TGC
13464052 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
13464080 CACCAG
1 CACCAG
13464086 GACGCTTCCT
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
27 26 0.46
28 23 0.41
29 7 0.12
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATAATTTGTGGCATGC
Found at i:13464237 original size:27 final size:27
Alignment explanation
Indices: 13464194--13464250 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
13464184 TTAACCCTAG
*
13464194 GGGTATAAAGGTCATTTTGCATACATA
1 GGGTATAAAGGTAATTTTGCATACATA
*
13464221 GGGTATAATGGTAATTTTGCATACATA
1 GGGTATAAAGGTAATTTTGCATACATA
13464248 GGG
1 GGG
13464251 GTATTCTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.33
Consensus pattern (27 bp):
GGGTATAAAGGTAATTTTGCATACATA
Found at i:13471379 original size:19 final size:19
Alignment explanation
Indices: 13471343--13471381 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
13471333 TTTTCATCAT
* *
13471343 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
13471362 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
13471381 A
1 A
13471382 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:13471891 original size:28 final size:28
Alignment explanation
Indices: 13471843--13471933 Score: 139
Period size: 28 Copynumber: 3.2 Consensus size: 28
13471833 GTGATAGAGT
*
13471843 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCAGTGC
*
13471872 CACCAGAACAGATAATTTGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCAGTGC
13471900 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGATAATTTGTGGCAGT-GC
13471928 CACCAG
1 CACCAG
13471934 GACGCTTCCT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
28 51 0.88
29 7 0.12
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCAGTGC
Found at i:13472086 original size:28 final size:28
Alignment explanation
Indices: 13472039--13472103 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
13472029 AAATTAACCC
*
13472039 TAGGGGTATAAAGGTCATTTTACATACA
1 TAGGGGTATAAAGGTAATTTTACATACA
* *
13472067 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTACATACA
13472095 TAGGGGTAT
1 TAGGGGTAT
13472104 TCTAGTAACT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.32, C:0.08, G:0.26, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTACATACA
Found at i:13475747 original size:28 final size:27
Alignment explanation
Indices: 13475680--13475756 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 27
13475670 AAGCAGTGAC
* * *
13475680 AAAACTGTAAAATATGAAAAATAGGGG
1 AAAAATGTAAAATCTGAAAAATAAGGG
*
13475707 AAAACA-GTAAAAATCTGGAAAATAAGGG
1 AAAA-ATGT-AAAATCTGAAAAATAAGGG
*
13475735 AAAAATTGTAAAATCTAAAAAA
1 AAAAA-TGTAAAATCTGAAAAA
13475757 AAGTAGAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
27 7 0.17
28 31 0.77
29 2 0.05
ACGTcount: A:0.60, C:0.05, G:0.17, T:0.18
Consensus pattern (27 bp):
AAAAATGTAAAATCTGAAAAATAAGGG
Found at i:13478332 original size:14 final size:14
Alignment explanation
Indices: 13478313--13478342 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
13478303 GATTAAGTGA
13478313 ATGTAAATATTAGT
1 ATGTAAATATTAGT
13478327 ATGTAAATATTAGT
1 ATGTAAATATTAGT
13478341 AT
1 AT
13478343 AATTAATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (14 bp):
ATGTAAATATTAGT
Found at i:13478796 original size:16 final size:17
Alignment explanation
Indices: 13478762--13478796 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13478752 TGTACTTATA
13478762 TATATAAAGCATAATTG
1 TATATAAAGCATAATTG
*
13478779 TATATAAATCAT-ATTG
1 TATATAAAGCATAATTG
13478795 TA
1 TA
13478797 ATGCTATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.40
Consensus pattern (17 bp):
TATATAAAGCATAATTG
Found at i:13479466 original size:24 final size:24
Alignment explanation
Indices: 13479445--13479496 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
13479435 TATCAATGTC
13479445 AAATATATTATGA-TAATAAATGCT
1 AAATATATTAT-ACTAATAAATGCT
* *
13479469 AAGTATATTATACTAATAAATTCT
1 AAATATATTATACTAATAAATGCT
13479493 AAAT
1 AAAT
13479497 CTTCTATAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:13479637 original size:29 final size:29
Alignment explanation
Indices: 13479579--13479637 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
13479569 TCCACCCTGA
* * * *
13479579 CACAAATTTTCAACGAACAGGTTCTTCAC
1 CACAAACTGTCAACGAACAAGTTCTCCAC
*
13479608 CACAAACTGTCAACGAACAAGTTGTCCAC
1 CACAAACTGTCAACGAACAAGTTCTCCAC
13479637 C
1 C
13479638 TCTTCCACGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.36, C:0.31, G:0.12, T:0.22
Consensus pattern (29 bp):
CACAAACTGTCAACGAACAAGTTCTCCAC
Found at i:13482646 original size:43 final size:42
Alignment explanation
Indices: 13482598--13482756 Score: 189
Period size: 43 Copynumber: 3.7 Consensus size: 42
13482588 AGCTTGTACA
* *
13482598 ATGCCAATGTCCTAGACGTGGTCTTACATGTAATCAAATATGG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCAAATAT-G
* * *
13482641 ATGCCACTGTCCCA-A-ATAGAGTCTTACACGAAATCAAATATG
1 ATGCCAATGTCCCAGACGT-G-GTCTTACACGTAATCAAATATG
13482683 ATGCCAATGTCCCAGACGTGGTCTTACACGTAAATCATAAGT-TG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGT-AATCA-AA-TATG
*
13482727 ATGCCAACGTCCCAGACGTGGTCTTACACG
1 ATGCCAATGTCCCAGACGTGGTCTTACACG
13482757 AAAACACATA
Statistics
Matches: 100, Mismatches: 9, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
41 1 0.01
42 26 0.26
43 38 0.38
44 34 0.34
45 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGTAATCAAATATG
Found at i:13490255 original size:43 final size:46
Alignment explanation
Indices: 13490150--13490291 Score: 133
Period size: 43 Copynumber: 3.3 Consensus size: 46
13490140 GACGTCCTAG
* *
13490150 ACGTGGTCTTACATGT-AATCAAATATCGGTGCCACTGTCCCAGAT
1 ACGTGGTCTTACATGTAAATCAAATATCGATGCCAATGTCCCAGAT
*
13490195 A-G-GGTCTTACACG-AAATCAAATAT-GATGCCAATGTCCCA-A-
1 ACGTGGTCTTACATGTAAATCAAATATCGATGCCAATGTCCCAGAT
* ** * *
13490235 ACGTGGTTTTACATGTAAATCATAA-GCCAATGCCAACGTCCC--AT
1 ACGTGGTCTTACATGTAAATCA-AATATCGATGCCAATGTCCCAGAT
13490279 ACGTGGTCTTACA
1 ACGTGGTCTTACA
13490292 CGAAAACACA
Statistics
Matches: 80, Mismatches: 10, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
40 1 0.01
41 2 0.03
42 22 0.28
43 27 0.34
44 27 0.34
45 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (46 bp):
ACGTGGTCTTACATGTAAATCAAATATCGATGCCAATGTCCCAGAT
Found at i:13493792 original size:24 final size:24
Alignment explanation
Indices: 13493777--13493828 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
13493767 AATCAAAGTC
13493777 AAATATATTATACTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
*
13493801 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATGCT
13493825 AAAT
1 AAAT
13493829 CTTCTAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:13498137 original size:26 final size:26
Alignment explanation
Indices: 13498099--13498155 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
13498089 GACTTTAGCC
* *
13498099 CGGACATATTTCCAGCACGTAGCCTG
1 CGGACATAATTCCAGCACATAGCCTG
*
13498125 CGGATATAATTCCAGCACATAGCCTG
1 CGGACATAATTCCAGCACATAGCCTG
13498151 CGGAC
1 CGGAC
13498156 CCTAAGTCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (26 bp):
CGGACATAATTCCAGCACATAGCCTG
Found at i:13498168 original size:39 final size:39
Alignment explanation
Indices: 13498125--13498247 Score: 237
Period size: 39 Copynumber: 3.2 Consensus size: 39
13498115 ACGTAGCCTG
13498125 CGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGTC
1 CGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGTC
*
13498164 CGGATATAATTCCAGCACATAGCCTGCGGACCCTAACTC
1 CGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGTC
13498203 CGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGTC
1 CGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGTC
13498242 CGGATA
1 CGGATA
13498248 CACATCAAAT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 82 1.00
ACGTcount: A:0.28, C:0.31, G:0.20, T:0.20
Consensus pattern (39 bp):
CGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGTC
Found at i:13505242 original size:39 final size:39
Alignment explanation
Indices: 13505159--13505255 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
13505149 TGAAACCAAT
*
13505159 TACCAGCAC-AAGCCTGCGGGAATTTAAACCCGATATAA
1 TACCAGCACGAAGCCTGCGGGAATTTAAACCCGACATAA
* * * *
13505197 TACCAGCTCGAAGCCTGCGGGACTTT-AGCCCGGACATAT
1 TACCAGCACGAAGCCTGCGGGAATTTAAACCC-GACATAA
* *
13505236 TTCCAGCACGTAGCCTGCGG
1 TACCAGCACGAAGCCTGCGG
13505256 ATATAATTCC
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
38 12 0.24
39 37 0.76
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.20
Consensus pattern (39 bp):
TACCAGCACGAAGCCTGCGGGAATTTAAACCCGACATAA
Found at i:13505265 original size:26 final size:26
Alignment explanation
Indices: 13505227--13505279 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
13505217 GACTTTAGCC
* *
13505227 CGGACATATTTCCAGCACGTAGCCTG
1 CGGACATAATTCCAGCACATAGCCTG
*
13505253 CGGATATAATTCCAGCACATAGCCTG
1 CGGACATAATTCCAGCACATAGCCTG
13505279 C
1 C
13505280 AGACCCTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (26 bp):
CGGACATAATTCCAGCACATAGCCTG
Found at i:13505296 original size:39 final size:39
Alignment explanation
Indices: 13505253--13505375 Score: 219
Period size: 39 Copynumber: 3.2 Consensus size: 39
13505243 ACGTAGCCTG
*
13505253 CGGATATAATTCCAGCACATAGCCTGCAGACCCTAAGTC
1 CGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGTC
*
13505292 CGGATATAATTCCAGCACATAGCCTGCGGACCTTAAGTC
1 CGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGTC
13505331 CGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGTC
1 CGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGTC
*
13505370 TGGATA
1 CGGATA
13505376 CACATCAAAT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 80 1.00
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (39 bp):
CGGATATAATTCCAGCACATAGCCTGCGGACCCTAAGTC
Found at i:13505852 original size:2 final size:2
Alignment explanation
Indices: 13505840--13505871 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
13505830 TTCTTTCAGA
13505840 AT AT A- 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
13505872 CGACTTTCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13510072 original size:11 final size:11
Alignment explanation
Indices: 13510056--13510084 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
13510046 ATATAACTCG
13510056 TTTTAAAATGT
1 TTTTAAAATGT
13510067 TTTTAAAATGT
1 TTTTAAAATGT
13510078 TTTTAAA
1 TTTTAAA
13510085 TGAATTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (11 bp):
TTTTAAAATGT
Found at i:13512150 original size:29 final size:30
Alignment explanation
Indices: 13512101--13512160 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
13512091 AGTATTCGTG
*
13512101 TTTGATACTTTTATTTTAATATGGTACTTA
1 TTTGATACATTTATTTTAATATGGTACTTA
13512131 TTTGATACATTT-TTTTAATATGGTACTTA
1 TTTGATACATTTATTTTAATATGGTACTTA
13512160 T
1 T
13512161 ATTTTTTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 18 0.62
30 11 0.38
ACGTcount: A:0.27, C:0.07, G:0.10, T:0.57
Consensus pattern (30 bp):
TTTGATACATTTATTTTAATATGGTACTTA
Found at i:13514495 original size:9 final size:9
Alignment explanation
Indices: 13514467--13514503 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
13514457 AGAAAATTAT
13514467 TTAATTT-A
1 TTAATTTAA
13514475 TTAATTTAAA
1 TTAATTT-AA
13514485 TTAATTTAA
1 TTAATTTAA
13514494 TTAATTTAA
1 TTAATTTAA
13514503 T
1 T
13514504 AAATAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 7 0.26
9 12 0.44
10 8 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TTAATTTAA
Found at i:13531844 original size:37 final size:36
Alignment explanation
Indices: 13531798--13531905 Score: 107
Period size: 37 Copynumber: 2.9 Consensus size: 36
13531788 ATTCCAGAAA
13531798 TAATATTATTTTAATAGT-TTAATATTAAATTTAAT-T
1 TAATATTATTTTAATAGTATT-ATATT-AATTTAATAT
*
13531834 TAATACTTATTTTAATAGTATTTTATTAATTTAATAT
1 TAATA-TTATTTTAATAGTATTATATTAATTTAATAT
* *
13531871 TAAAGTGATTATCTTAATATTA-TAT-TTAATTTAAT
1 T-AA-T-ATTATTTTAATAGTATTATATTAATTTAAT
13531906 GTTTATCTAC
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
36 13 0.21
37 29 0.47
38 6 0.10
39 13 0.21
40 1 0.02
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.55
Consensus pattern (36 bp):
TAATATTATTTTAATAGTATTATATTAATTTAATAT
Found at i:13531871 original size:11 final size:11
Alignment explanation
Indices: 13531798--13531873 Score: 52
Period size: 12 Copynumber: 6.8 Consensus size: 11
13531788 ATTCCAGAAA
*
13531798 TAATATTATTT
1 TAATATTAATT
13531809 TAATAGTTTAATAT
1 TAATA--TTAAT-T
13531823 TAA-ATTTAATT
1 TAATA-TTAATT
*
13531834 TAATACTTATTT
1 TAATA-TTAATT
*
13531846 TAATAGT-ATT
1 TAATATTAATT
13531856 T--TATTAATT
1 TAATATTAATT
13531865 TAATATTAA
1 TAATATTAA
13531874 AGTGATTATC
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 3 0.06
11 16 0.31
12 17 0.33
13 5 0.10
14 4 0.08
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (11 bp):
TAATATTAATT
Found at i:13537931 original size:15 final size:15
Alignment explanation
Indices: 13537911--13537942 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
13537901 CAATTCACTA
*
13537911 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
13537926 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
13537941 TT
1 TT
13537943 TGTATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:13539641 original size:20 final size:20
Alignment explanation
Indices: 13539593--13539646 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
13539583 AATGTAACAC
** *
13539593 TTATCTTAATATT-ATTTTA
1 TTATCTTAATATTAAAGTGA
13539612 TTAT-TTAATATTAAAGTGA
1 TTATCTTAATATTAAAGTGA
13539631 TTATCTTAATATTAAA
1 TTATCTTAATATTAAA
13539647 TTTATTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.27
19 11 0.37
20 11 0.37
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (20 bp):
TTATCTTAATATTAAAGTGA
Found at i:13549314 original size:7 final size:7
Alignment explanation
Indices: 13549302--13549335 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
13549292 ACTTTTAAAT
13549302 AATTTTG
1 AATTTTG
13549309 AATTTTG
1 AATTTTG
*
13549316 AATTTTA
1 AATTTTG
13549323 AATTTTG
1 AATTTTG
13549330 AATTTT
1 AATTTT
13549336 TAAGAATACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (7 bp):
AATTTTG
Found at i:13549757 original size:23 final size:23
Alignment explanation
Indices: 13549728--13549778 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
13549718 TTGTGTCAAG
13549728 CTCTCAATTTTCTAACTGAGATT
1 CTCTCAATTTTCTAACTGAGATT
*
13549751 CTCTCAATTTTCTAACTTAGATT
1 CTCTCAATTTTCTAACTGAGATT
13549774 CTCTC
1 CTCTC
13549779 TCTTGCATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.25, G:0.06, T:0.45
Consensus pattern (23 bp):
CTCTCAATTTTCTAACTGAGATT
Found at i:13550293 original size:25 final size:25
Alignment explanation
Indices: 13550259--13550308 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
13550249 CTGAATCCAC
13550259 CCAAGTATACCTTTCTTCATTCACT
1 CCAAGTATACCTTTCTTCATTCACT
13550284 CCAAGTATACCTTTCTTCATTCACT
1 CCAAGTATACCTTTCTTCATTCACT
13550309 TTCACTTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.32, G:0.04, T:0.40
Consensus pattern (25 bp):
CCAAGTATACCTTTCTTCATTCACT
Found at i:13551366 original size:2 final size:2
Alignment explanation
Indices: 13551359--13551396 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
13551349 AAGGTATACC
13551359 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
13551397 CGTCCTTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13552072 original size:142 final size:144
Alignment explanation
Indices: 13551892--13552162 Score: 361
Period size: 146 Copynumber: 1.9 Consensus size: 144
13551882 TTAACACCGG
* * * * * * *
13551892 TTTAATATTCAATTTAAATATGTGTTATTGAAGAAAAAAAT-A-CCTTA-ATTCAATAAAG-ACC
1 TTTAATAGTCAATCTAAATATATGTTATTCAAGAAAAAAATAAGCCTTACAATAAAT-AAGTA-A
* *
13551953 AGACCGAGAAGGTTCACTCAAGAATAATTTTATTTAATTTTAATTTTGATACTTAAATATTTTTA
64 AGACCAAGAAAGTTCACTCAAGAATAATTTTATTTAATTTTAATTTTGATACTTAAATATTTTTA
13552018 CCTCAATTTAATTTGC
129 CCTCAATTTAATTTGC
* *
13552034 TTTAATAGTCAATCTAAATATATGTTCTTCAAGAAAAAAATAAAAGCCTTACAATAAATCAGTAA
1 TTTAATAGTCAATCTAAATATATGTTATTCAAGAAAAAAAT--AAGCCTTACAATAAATAAGTAA
* *
13552099 AGACCAAGAAAGTTCACTCAAGAATAATTTTATTTAATTTTAATTTTGGTACTTGAATATTTTT
64 AGACCAAGAAAGTTCACTCAAGAATAATTTTATTTAATTTTAATTTTGATACTTAAATATTTTT
13552163 TTTATCTCAA
Statistics
Matches: 110, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
142 36 0.33
145 1 0.01
146 67 0.61
147 6 0.05
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (144 bp):
TTTAATAGTCAATCTAAATATATGTTATTCAAGAAAAAAATAAGCCTTACAATAAATAAGTAAAG
ACCAAGAAAGTTCACTCAAGAATAATTTTATTTAATTTTAATTTTGATACTTAAATATTTTTACC
TCAATTTAATTTGC
Found at i:13552867 original size:2 final size:2
Alignment explanation
Indices: 13552860--13552893 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
13552850 TTTCACAGTG
13552860 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
13552894 TATTGGACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13553311 original size:2 final size:2
Alignment explanation
Indices: 13553304--13553333 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13553294 ACAAAATTTC
13553304 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
13553334 TAGAGTAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13553936 original size:2 final size:2
Alignment explanation
Indices: 13553925--13553956 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
13553915 ATTCTTGCTT
13553925 TA TA -A 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 T
13553957 GAGGTTGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13554324 original size:31 final size:31
Alignment explanation
Indices: 13554289--13554354 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
13554279 AACCCTTCCT
13554289 GCATTAAATCCAAC-ACAAAACAGCAAATATA
1 GCATTAAATCCAACTA-AAAACAGCAAATATA
* *
13554320 GCATTGAATCCAACTAAAAACAGCAAATGTA
1 GCATTAAATCCAACTAAAAACAGCAAATATA
13554351 GCAT
1 GCAT
13554355 AAAAAATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.50, C:0.21, G:0.11, T:0.18
Consensus pattern (31 bp):
GCATTAAATCCAACTAAAAACAGCAAATATA
Found at i:13555068 original size:13 final size:14
Alignment explanation
Indices: 13555042--13555070 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
13555032 ACTAACGACG
13555042 AATTAAACCATTAT
1 AATTAAACCATTAT
13555056 AATTAAA-CATTAT
1 AATTAAACCATTAT
13555069 AA
1 AA
13555071 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:13560155 original size:9 final size:9
Alignment explanation
Indices: 13560141--13560259 Score: 118
Period size: 9 Copynumber: 13.4 Consensus size: 9
13560131 ATGTATTATA
13560141 TATGTAAGT
1 TATGTAAGT
13560150 TATGTAAGT
1 TATGTAAGT
*
13560159 TATGTTAGT
1 TATGTAAGT
*
13560168 TATGTAACT
1 TATGTAAGT
* *
13560177 TATATGAGT
1 TATGTAAGT
13560186 TATGTAAGT
1 TATGTAAGT
13560195 TATGTAAGT
1 TATGTAAGT
* *
13560204 TATGATATGA
1 TATG-TAAGT
* *
13560214 TATAT-ATT
1 TATGTAAGT
13560222 TATGT-A-T
1 TATGTAAGT
13560229 TATGTAAGT
1 TATGTAAGT
*
13560238 TATGTAAAT
1 TATGTAAGT
*
13560247 CATGTAAGT
1 TATGTAAGT
13560256 TATG
1 TATG
13560260 AAATTTAAAC
Statistics
Matches: 88, Mismatches: 19, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
7 6 0.07
8 6 0.07
9 70 0.80
10 6 0.07
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (9 bp):
TATGTAAGT
Found at i:13561345 original size:24 final size:24
Alignment explanation
Indices: 13561313--13561365 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
13561303 AGTGTTTTAT
13561313 AATATAATATTAATTTTAGATACA
1 AATATAATATTAATTTTAGATACA
*
13561337 AATATAATATTAATTTTAGTTACA
1 AATATAATATTAATTTTAGATACA
13561361 AATAT
1 AATAT
13561366 TATAACATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (24 bp):
AATATAATATTAATTTTAGATACA
Found at i:13564230 original size:17 final size:16
Alignment explanation
Indices: 13564197--13564231 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
13564187 TTTATTTAAT
*
13564197 ATATAAATTATAAACA
1 ATATAAATTAAAAACA
13564213 ATATAAATTAAAAAACA
1 ATATAAATT-AAAAACA
13564230 AT
1 AT
13564232 CAGTTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.29
Consensus pattern (16 bp):
ATATAAATTAAAAACA
Found at i:13564361 original size:16 final size:16
Alignment explanation
Indices: 13564342--13564395 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 16
13564332 AGAAATAGAT
13564342 AAAATTTGAAATCTTG
1 AAAATTTGAAATCTTG
13564358 AAAA-TT---A--TTG
1 AAAATTTGAAATCTTG
*
13564368 AAAATTTGAAATCTTT
1 AAAATTTGAAATCTTG
13564384 AAAATTTGAAAT
1 AAAATTTGAAAT
13564396 TATTTAATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 12
0.70 0.02 0.27
Matches are distributed among these distances:
10 7 0.23
11 2 0.06
12 1 0.03
14 1 0.03
15 2 0.06
16 18 0.58
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (16 bp):
AAAATTTGAAATCTTG
Found at i:13564523 original size:8 final size:7
Alignment explanation
Indices: 13564504--13564825 Score: 85
Period size: 7 Copynumber: 44.0 Consensus size: 7
13564494 CACTAATTAT
13564504 CCTAAAC
1 CCTAAAC
13564511 CCTAAATC
1 CCTAAA-C
*
13564519 CCTAACC
1 CCTAAAC
**
13564526 CCTATCC
1 CCTAAAC
**
13564533 CCTTAATG
1 CC-TAAAC
*
13564541 CCTTAAC
1 CCTAAAC
13564548 CCTTAAAC
1 CC-TAAAC
13564556 CCTAAA-
1 CCTAAAC
13564562 CCTAAAC
1 CCTAAAC
13564569 CCTTAAAC
1 CC-TAAAC
*
13564577 TACT-AAC
1 -CCTAAAC
13564584 CC-ATAAC
1 CCTA-AAC
13564591 CCTTAAAC
1 CC-TAAAC
*
13564599 CCTTAAC
1 CCTAAAC
*
13564606 CCTTAAC
1 CCTAAAC
* *
13564613 TCTTAAC
1 CCTAAAC
13564620 CCTAAAC
1 CCTAAAC
*
13564627 CATAAAC
1 CCTAAAC
*
13564634 CTTAAAAC
1 CCT-AAAC
*
13564642 CC-AAAA
1 CCTAAAC
* *
13564648 TCTCAAC
1 CCTAAAC
13564655 CCTTAAAC
1 CC-TAAAC
*
13564663 CTTAAAAC
1 CCT-AAAC
* *
13564671 CATAATC
1 CCTAAAC
*
13564678 CTTAAATC
1 CCTAAA-C
*
13564686 CATAAAC
1 CCTAAAC
* *
13564693 CTTAAAA
1 CCTAAAC
** *
13564700 TATTAAC
1 CCTAAAC
*
13564707 TCATAAAC
1 -CCTAAAC
*
13564715 CATAAACC
1 CCTAAA-C
13564723 CCTAAAC
1 CCTAAAC
*
13564730 CTTAAAC
1 CCTAAAC
13564737 CCTAAAC
1 CCTAAAC
*
13564744 CCATAATC
1 CC-TAAAC
*
13564752 CATAAAC
1 CCTAAAC
* *
13564759 CTTAAAA
1 CCTAAAC
** *
13564766 TATTAAC
1 CCTAAAC
13564773 TCATCATAAAC
1 -C--C-TAAAC
*
13564784 CATAAAC
1 CCTAAAC
13564791 CCTAAAC
1 CCTAAAC
* *
13564798 CATATAC
1 CCTAAAC
13564805 CCTAAAC
1 CCTAAAC
*
13564812 CATAAAC
1 CCTAAAC
*
13564819 CTTAAAC
1 CCTAAAC
13564826 TATAATGATA
Statistics
Matches: 232, Mismatches: 61, Indels: 44
0.69 0.18 0.13
Matches are distributed among these distances:
6 11 0.05
7 149 0.64
8 65 0.28
9 2 0.01
10 1 0.00
11 4 0.02
ACGTcount: A:0.43, C:0.34, G:0.00, T:0.24
Consensus pattern (7 bp):
CCTAAAC
Found at i:13564563 original size:15 final size:15
Alignment explanation
Indices: 13564541--13564764 Score: 71
Period size: 15 Copynumber: 15.5 Consensus size: 15
13564531 CCCCTTAATG
13564541 CCTT-AACCCTTAAAC
1 CCTTAAACCC-TAAAC
13564556 CC-TAAA-CCTAAAC
1 CCTTAAACCCTAAAC
*
13564569 CCTTAAACTACT-AAC
1 CCTTAAAC-CCTAAAC
*
13564584 CCAT-AACCCTTAAAC
1 CCTTAAACCC-TAAAC
*
13564599 CCTT-AACCCTTAAC
1 CCTTAAACCCTAAAC
*
13564613 TCTT-AACCCTAAA-
1 CCTTAAACCCTAAAC
* *
13564626 CCATAAACCTTAAAAC
1 CCTTAAACCCT-AAAC
** *
13564642 CC--AAAATCTCAAC
1 CCTTAAACCCTAAAC
* *
13564655 CCTTAAACCTTAAAA
1 CCTTAAACCCTAAAC
* * * *
13564670 CCATAATCCTTAAAT
1 CCTTAAACCCTAAAC
* * *
13564685 CCATAAACCTTAAAA
1 CCTTAAACCCTAAAC
** *
13564700 TATT-AACTCATAAA-
1 CCTTAAAC-CCTAAAC
*
13564714 CCATAAACCCCTAAA-
1 CCTTAAA-CCCTAAAC
13564729 CCTTAAACCCTAAAC
1 CCTTAAACCCTAAAC
* * *
13564744 CCATAATCCATAAA-
1 CCTTAAACCCTAAAC
13564758 CCTTAAA
1 CCTTAAA
13564765 ATATTAACTC
Statistics
Matches: 156, Mismatches: 38, Indels: 31
0.69 0.17 0.14
Matches are distributed among these distances:
13 15 0.10
14 51 0.33
15 85 0.54
16 5 0.03
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (15 bp):
CCTTAAACCCTAAAC
Found at i:13564591 original size:22 final size:20
Alignment explanation
Indices: 13564544--13564662 Score: 69
Period size: 22 Copynumber: 5.6 Consensus size: 20
13564534 CTTAATGCCT
*
13564544 TAACCCTTAAACCCTAAACC
1 TAACCCTTAAACACTAAACC
*
13564564 TAAACCCTTAAACTACTAACCC
1 T-AACCCTTAAAC-ACTAAACC
* *
13564586 ATAACCCTTAAACCCTTAACCC
1 -TAACCCTTAAACAC-TAAACC
* *
13564608 TTAACTCTT-AACCCTAAACC
1 -TAACCCTTAAACACTAAACC
* * * *
13564628 ATAAACCTTAAAACCCAAAATC
1 -TAACCCTT-AAACACTAAACC
13564650 TCAACCCTTAAAC
1 T-AACCCTTAAAC
13564663 CTTAAAACCA
Statistics
Matches: 80, Mismatches: 12, Indels: 13
0.76 0.11 0.12
Matches are distributed among these distances:
20 12 0.15
21 22 0.28
22 45 0.56
23 1 0.01
ACGTcount: A:0.41, C:0.36, G:0.00, T:0.23
Consensus pattern (20 bp):
TAACCCTTAAACACTAAACC
Found at i:13564619 original size:14 final size:15
Alignment explanation
Indices: 13564541--13564627 Score: 78
Period size: 15 Copynumber: 6.1 Consensus size: 15
13564531 CCCCTTAATG
13564541 CCTTAACCCTTAAAC
1 CCTTAACCCTTAAAC
*
13564556 CC-TAAACC-TAAAC
1 CCTTAACCCTTAAAC
*
13564569 CCTTAA-AC-TACTAAC
1 CCTTAACCCTTA--AAC
*
13564584 CCATAACCCTTAAAC
1 CCTTAACCCTTAAAC
13564599 CCTTAACCCTT-AAC
1 CCTTAACCCTTAAAC
*
13564613 TCTTAACCC-TAAAC
1 CCTTAACCCTTAAAC
13564627 C
1 C
13564628 ATAAACCTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
13 11 0.19
14 22 0.37
15 23 0.39
16 1 0.02
17 2 0.03
ACGTcount: A:0.37, C:0.39, G:0.00, T:0.24
Consensus pattern (15 bp):
CCTTAACCCTTAAAC
Found at i:13564634 original size:14 final size:14
Alignment explanation
Indices: 13564545--13564830 Score: 95
Period size: 14 Copynumber: 20.1 Consensus size: 14
13564535 TTAATGCCTT
*
13564545 AACCCTTAAACCCTA
1 AACCC-TAAACCATA
*
13564560 AA-CCTAAACCCTTA
1 AACCCTAAA-CCATA
* *
13564574 AACTACTAACCCAT-
1 AAC-CCTAAACCATA
* *
13564588 AACCCTTAAACCCTT
1 AACCC-TAAACCATA
* *
13564603 AACCCTTAACTC-TT
1 AACCCTAAAC-CATA
13564617 AACCCTAAACCATA
1 AACCCTAAACCATA
*
13564631 AACCTTAAAACCCA-A
1 AACCCT-AAA-CCATA
* * *
13564646 AA-TCTCAACCCTTA
1 AACCCT-AAACCATA
*
13564660 AACCTTAAAACCATA
1 AACCCT-AAACCATA
* *
13564675 ATCCTTAAATCCATA
1 AACCCTAAA-CCATA
* ** *
13564690 AACCTTAAAATATT
1 AACCCTAAACCATA
*
13564704 AACTCATAAACCATA
1 AAC-CCTAAACCATA
*
13564719 AACCCCTAAACCTTA
1 AA-CCCTAAACCATA
13564734 AACCCTAAACCCATA
1 AACCCTAAA-CCATA
* * *
13564749 ATCCATAAACCTTA
1 AACCCTAAACCATA
*** *
13564763 AAATATTAACTCAT-
1 AACCCTAAAC-CATA
*
13564777 ---CATAAACCATA
1 AACCCTAAACCATA
13564788 AACCCTAAACCATA
1 AACCCTAAACCATA
*
13564802 TACCCTAAACCATA
1 AACCCTAAACCATA
* *
13564816 AACCTTAAACTATA
1 AACCCTAAACCATA
13564830 A
1 A
13564831 TGATAATTAA
Statistics
Matches: 203, Mismatches: 48, Indels: 41
0.70 0.16 0.14
Matches are distributed among these distances:
10 3 0.01
11 5 0.02
13 8 0.04
14 104 0.51
15 75 0.37
16 8 0.04
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.23
Consensus pattern (14 bp):
AACCCTAAACCATA
Found at i:13564685 original size:36 final size:36
Alignment explanation
Indices: 13564545--13564685 Score: 114
Period size: 36 Copynumber: 3.9 Consensus size: 36
13564535 TTAATGCCTT
*
13564545 AACCCTTAAACCCTAAACC-TAAACCCTTAAA-CTAC
1 AACCCTTAAACCTTAAACCTTAAACCCTTAAATCT-C
* * * *
13564580 TAACCCATAACCCTTAAACCCTT-AACCCTTAACTCTT
1 -AACCCTTAAACCTTAAA-CCTTAAACCCTTAAATCTC
* *
13564617 AACCC-TAAACCATAAACCTTAAAACCC-AAAATCTC
1 AACCCTTAAACCTTAAACCTT-AAACCCTTAAATCTC
* *
13564652 AACCCTTAAACCTTAAAACCAT-AATCCTTAAATC
1 AACCCTTAAACCTT-AAACCTTAAACCCTTAAATC
13564686 CATAAACCTT
Statistics
Matches: 83, Mismatches: 14, Indels: 16
0.73 0.12 0.14
Matches are distributed among these distances:
34 4 0.05
35 23 0.28
36 36 0.43
37 17 0.20
38 3 0.04
ACGTcount: A:0.42, C:0.35, G:0.00, T:0.23
Consensus pattern (36 bp):
AACCCTTAAACCTTAAACCTTAAACCCTTAAATCTC
Found at i:13564735 original size:22 final size:22
Alignment explanation
Indices: 13564658--13564825 Score: 67
Period size: 22 Copynumber: 7.5 Consensus size: 22
13564648 TCTCAACCCT
* * * *
13564658 TAAACCTTAAAACCATAATCCT
1 TAAACCATAAACCCATAAACCA
* **
13564680 TAAATCCATAAA-CCTTAAAATA
1 TAAA-CCATAAACCCATAAACCA
* *
13564702 TTAACTCATAAA-CCATAAACCCC
1 TAAAC-CATAAACCCATAAA-CCA
*
13564725 TAAACCTTAAACCC-TAAACCCA
1 TAAACCATAAACCCATAAA-CCA
* * **
13564747 TAATCCATAAA-CCTTAAAATA
1 TAAACCATAAACCCATAAACCA
* * *
13564768 TTAACTCATCATAAACCATAAACCC
1 TAAAC-CAT-A-AACCCATAAACCA
*
13564793 TAAACCATATACCC-TAAACCA
1 TAAACCATAAACCCATAAACCA
*
13564814 TAAACCTTAAAC
1 TAAACCATAAAC
13564826 TATAATGATA
Statistics
Matches: 107, Mismatches: 30, Indels: 19
0.69 0.19 0.12
Matches are distributed among these distances:
21 23 0.21
22 55 0.51
23 14 0.13
24 5 0.05
25 10 0.09
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.24
Consensus pattern (22 bp):
TAAACCATAAACCCATAAACCA
Found at i:13568388 original size:102 final size:102
Alignment explanation
Indices: 13568212--13568405 Score: 379
Period size: 102 Copynumber: 1.9 Consensus size: 102
13568202 TTATACGTGA
13568212 GAAATTTACTTATGCTATGGATGAATTTACCAATGTCGTGAATAAACACACTAATTTGTGAATTG
1 GAAATTTACTTATGCTATGGATGAATTTACCAATGTCGTGAATAAACACACTAATTTGTGAATTG
13568277 ATAATGTTATTTAAGCTAATGCTAAGTAAATGGAACG
66 ATAATGTTATTTAAGCTAATGCTAAGTAAATGGAACG
*
13568314 GAAATTTACTTATGCTATGGATGAATTTACCTATGTCGTGAATAAACACACTAATTTGTGAATTG
1 GAAATTTACTTATGCTATGGATGAATTTACCAATGTCGTGAATAAACACACTAATTTGTGAATTG
13568379 ATAATGTTATTTAAGCTAATGCTAAGT
66 ATAATGTTATTTAAGCTAATGCTAAGT
13568406 GTTAGAATTA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 91 1.00
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (102 bp):
GAAATTTACTTATGCTATGGATGAATTTACCAATGTCGTGAATAAACACACTAATTTGTGAATTG
ATAATGTTATTTAAGCTAATGCTAAGTAAATGGAACG
Found at i:13573750 original size:25 final size:25
Alignment explanation
Indices: 13573716--13573810 Score: 95
Period size: 25 Copynumber: 3.8 Consensus size: 25
13573706 GAGAGATAAA
13573716 CAGTAAGCTCATTCGAGCTGAATAT
1 CAGTAAGCTCATTCGAGCTGAATAT
* * * *
13573741 CAGTAAGCTCCTCCGAGCTAAATAG
1 CAGTAAGCTCATTCGAGCTGAATAT
*
13573766 CGGTAAGCTC-TTACGAGCTGAGA-AT
1 CAGTAAGCTCATT-CGAGCTGA-ATAT
* *
13573791 CAATAAGCTCATACGAGCTG
1 CAGTAAGCTCATTCGAGCTG
13573811 TGGTGAGTCC
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
24 1 0.02
25 53 0.95
26 2 0.04
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (25 bp):
CAGTAAGCTCATTCGAGCTGAATAT
Found at i:13575542 original size:28 final size:27
Alignment explanation
Indices: 13575479--13575548 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
13575469 ATAGTGAGTC
13575479 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
13575506 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
13575534 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
13575549 GTACAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:13583376 original size:28 final size:27
Alignment explanation
Indices: 13583313--13583382 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
13583303 ATAGTGAGTC
13583313 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
*
13583340 CGCACACTTAGTGCTATATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
13583368 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
13583383 GTACAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:13594102 original size:14 final size:16
Alignment explanation
Indices: 13594071--13594107 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
13594061 AGGAAATATG
*
13594071 AAAGAAAGGAGAG-AA
1 AAAGAAAAGAGAGAAA
13594086 AAAGAAAAGAG-GAAA
1 AAAGAAAAGAGAGAAA
13594101 AAAGAAA
1 AAAGAAA
13594108 GAATGATAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 1 0.05
15 19 0.95
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (16 bp):
AAAGAAAAGAGAGAAA
Found at i:13597485 original size:30 final size:29
Alignment explanation
Indices: 13597427--13597487 Score: 77
Period size: 30 Copynumber: 2.1 Consensus size: 29
13597417 TTCAAATTTG
* *
13597427 AATATAAATAAAATTATTTAATACAATTA
1 AATATAAATAAAAGTAATTAATACAATTA
* *
13597456 AATATAATATCAAAGTAATTAATATAATTA
1 AATATAA-ATAAAAGTAATTAATACAATTA
13597486 AA
1 AA
13597488 AAAGCAAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 7 0.26
30 20 0.74
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (29 bp):
AATATAAATAAAAGTAATTAATACAATTA
Found at i:13601193 original size:28 final size:29
Alignment explanation
Indices: 13601161--13601352 Score: 192
Period size: 28 Copynumber: 6.7 Consensus size: 29
13601151 CAGTTTTTGT
* * *
13601161 AAGGAAGTCTTTGTGGCTATCTCTGTT-A
1 AAGGAAGCCTTTATGGCAATCTCTGTTAA
* **
13601189 AAGGAAGCCTTTGTGGTTATCTCTGTT-A
1 AAGGAAGCCTTTATGGCAATCTCTGTTAA
* * *
13601217 AAGGAAGCCTTTGTGGAAATCTCTATTTAA
1 AAGGAAGCCTTTATGGCAATCTCT-GTTAA
* * **
13601247 AATGAAGCCTTTTTGGGGATCTCTGTTAAA
1 AAGGAAGCCTTTATGGCAATCTCTGTT-AA
* *
13601277 AAGGAAGCCTTTATGGCGATCTCTATTAA
1 AAGGAAGCCTTTATGGCAATCTCTGTTAA
* *
13601306 AAGGAAGCCTTTATGGCAATCTTTG-TCA
1 AAGGAAGCCTTTATGGCAATCTCTGTTAA
13601334 AAGGAAGCCTTTATGGCAA
1 AAGGAAGCCTTTATGGCAA
13601353 GACTCTAAAA
Statistics
Matches: 143, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
28 69 0.48
29 28 0.20
30 46 0.32
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (29 bp):
AAGGAAGCCTTTATGGCAATCTCTGTTAA
Found at i:13601369 original size:28 final size:27
Alignment explanation
Indices: 13601275--13601371 Score: 88
Period size: 28 Copynumber: 3.4 Consensus size: 27
13601265 ATCTCTGTTA
* * *
13601275 AAAAGGAAGCCTTTATGGCGATCTCTATT
1 AAAAGGAAGCCTTTATGGCAAACT-T-CT
* *
13601304 AAAAGGAAGCCTTTATGGCAATCTTTGT
1 AAAAGGAAGCCTTTATGGCAAAC-TTCT
*
13601332 CAAAGGAAGCCTTTATGGCAAGAC-TCT
1 AAAAGGAAGCCTTTATGGCAA-ACTTCT
13601359 AAAAGGAAAGCCT
1 AAAAGG-AAGCCT
13601372 CTGTAGCTAT
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
27 7 0.12
28 27 0.46
29 24 0.41
30 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.26
Consensus pattern (27 bp):
AAAAGGAAGCCTTTATGGCAAACTTCT
Found at i:13611490 original size:35 final size:36
Alignment explanation
Indices: 13611451--13611525 Score: 116
Period size: 35 Copynumber: 2.1 Consensus size: 36
13611441 TTAAAATAAG
* * *
13611451 TTTAATTTTTCTTTTGGCACTCAATAAGTTAAATT-
1 TTTAATTTTCCTTTTCGCACTCAATAAATTAAATTC
13611486 TTTAATTTTCCTTTTCGCACTCAATAAATTAAATTC
1 TTTAATTTTCCTTTTCGCACTCAATAAATTAAATTC
13611522 TTTA
1 TTTA
13611526 GCAAATAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
35 32 0.89
36 4 0.11
ACGTcount: A:0.29, C:0.15, G:0.05, T:0.51
Consensus pattern (36 bp):
TTTAATTTTCCTTTTCGCACTCAATAAATTAAATTC
Found at i:13613484 original size:20 final size:20
Alignment explanation
Indices: 13613441--13613477 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
13613431 TTAGTGCTTT
*
13613441 ATTATGGATTAATTTAATAA
1 ATTATGGATTAAATTAATAA
13613461 ATTAT-GATTAAATTAAT
1 ATTATGGATTAAATTAAT
13613478 TTAATTAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (20 bp):
ATTATGGATTAAATTAATAA
Found at i:13613505 original size:24 final size:20
Alignment explanation
Indices: 13613441--13613505 Score: 53
Period size: 20 Copynumber: 3.0 Consensus size: 20
13613431 TTAGTGCTTT
*
13613441 ATTATGGATT-AATTTAATAA
1 ATTAT-GATTAAATTTAATTA
13613461 ATTATGATTAAA-TTAATTTA
1 ATTATGATTAAATTTAA-TTA
13613481 ATTAGGTGATTAAGAATTTAATTA
1 ATTA--TGATT-A-AATTTAATTA
13613505 A
1 A
13613506 AGTTTATATA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
19 8 0.22
20 13 0.35
22 5 0.14
23 1 0.03
24 6 0.16
25 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.45
Consensus pattern (20 bp):
ATTATGATTAAATTTAATTA
Found at i:13617723 original size:28 final size:28
Alignment explanation
Indices: 13617683--13617737 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
13617673 GAACCCTTCT
13617683 ATATACTTACTTTCCATTGCATTTACTC
1 ATATACTTACTTTCCATTGCATTTACTC
13617711 ATATACTTACTTTCCATTGCATTTACT
1 ATATACTTACTTTCCATTGCATTTACT
13617738 TACTTTAGCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.24, G:0.04, T:0.47
Consensus pattern (28 bp):
ATATACTTACTTTCCATTGCATTTACTC
Found at i:13620809 original size:48 final size:48
Alignment explanation
Indices: 13620726--13620856 Score: 156
Period size: 48 Copynumber: 2.7 Consensus size: 48
13620716 TTAAGGGATA
* *
13620726 CATTAATTTGGCTTCGAGCCATGATATCAGCACTTCGGCTGCGAGCTT
1 CATTGATTTGGCTTCGAGCCATAATATCAGCACTTCGGCTGCGAGCTT
* * * *
13620774 CATTGGTTTGGCTTC-AGACCATAATATTAGTACTTCGGGTGCGAGCTT
1 CATTGATTTGGCTTCGAG-CCATAATATCAGCACTTCGGCTGCGAGCTT
* * * *
13620822 CATTGATTTGGCTTTGGGCCATGATATTAGCACTT
1 CATTGATTTGGCTTCGAGCCATAATATCAGCACTT
13620857 AGTGTGTGAA
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
47 2 0.03
48 67 0.96
49 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.35
Consensus pattern (48 bp):
CATTGATTTGGCTTCGAGCCATAATATCAGCACTTCGGCTGCGAGCTT
Found at i:13622014 original size:23 final size:23
Alignment explanation
Indices: 13621984--13622030 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
13621974 TCCCCTTGTG
13621984 TTGAAATTAAAATCAAGTCAGTA
1 TTGAAATTAAAATCAAGTCAGTA
13622007 TTGAAATTAAAATCAAGTCAGTA
1 TTGAAATTAAAATCAAGTCAGTA
13622030 T
1 T
13622031 GCTCTACACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.32
Consensus pattern (23 bp):
TTGAAATTAAAATCAAGTCAGTA
Found at i:13627042 original size:182 final size:182
Alignment explanation
Indices: 13626729--13627083 Score: 593
Period size: 182 Copynumber: 2.0 Consensus size: 182
13626719 TCAGATCGGA
13626729 GATAAAGTATTTCTAAAAGTATCTCCGTGGAAGAAAATCCATCGATTTGGTCGTAAAGGTAAATT
1 GATAAAGTATTTCTAAAAGTATCTCCGTGGAAGAAAATCCATCGATTTGGTCGTAAAGGTAAATT
* * * *
13626794 GAGTACGCGTTTCATTGGGTCGTACAAGATCTTTGAAAGAACAGGGTCAGAGGCATATCGACTAG
66 GAGTACGCGTTTCATCGGGCCGTACAAGATCATTGAAAGAACAGGGTCAGAGGCATATCAACTAG
**
13626859 CTTTACTGGATAAGTTAGAGAAAATCCACAATGTGTTTCATGTTTTGATGGT
131 CTTTACTGGATAAGTTAGAGAAAATAAACAATGTGTTTCATGTTTTGATGGT
*
13626911 GATAAAGTATTTCTAAAAGTATCTCTGTGGAAGAAAATCCATCGATTTGGTCGTAAAGGTAAATT
1 GATAAAGTATTTCTAAAAGTATCTCCGTGGAAGAAAATCCATCGATTTGGTCGTAAAGGTAAATT
* ** * *
13626976 GAGTATGCGTTTCATCGGGCCGTATGAGATCATTGAAAGAATAGGGTCAGCGGCATATCAACTAG
66 GAGTACGCGTTTCATCGGGCCGTACAAGATCATTGAAAGAACAGGGTCAGAGGCATATCAACTAG
*
13627041 CTTTACTGGATGAGTTAGAGAAAATAAACAATGTGTTTCATGT
131 CTTTACTGGATAAGTTAGAGAAAATAAACAATGTGTTTCATGT
13627084 GTCGGTGTAG
Statistics
Matches: 160, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
182 160 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (182 bp):
GATAAAGTATTTCTAAAAGTATCTCCGTGGAAGAAAATCCATCGATTTGGTCGTAAAGGTAAATT
GAGTACGCGTTTCATCGGGCCGTACAAGATCATTGAAAGAACAGGGTCAGAGGCATATCAACTAG
CTTTACTGGATAAGTTAGAGAAAATAAACAATGTGTTTCATGTTTTGATGGT
Found at i:13629157 original size:15 final size:15
Alignment explanation
Indices: 13629125--13629153 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
13629115 ATTTTTTATG
13629125 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
13629140 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
13629154 ATTTTCATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:13630838 original size:45 final size:44
Alignment explanation
Indices: 13630764--13630911 Score: 148
Period size: 41 Copynumber: 3.4 Consensus size: 44
13630754 TGTGTTTTCG
* *
13630764 TGTAAGACCACGTCTGGGA-AGTTGGCATCGATATATGTGGTTACG
1 TGTAAGACCATGTCTGGGACAG-TGGCATCG-TATATGTGGTTACA
* *
13630809 TGTAAGACCATGTCTGGGACA-TCGACATCGTAT-T-TGATT-CA
1 TGTAAGACCATGTCTGGGACAGT-GGCATCGTATATGTGGTTACA
* * *
13630850 TGTAAGACCCTGTTTGGGACAGTGGCATCG-ATATGAGG-TAGCA
1 TGTAAGACCATGTCTGGGACAGTGGCATCGTATATGTGGTTA-CA
13630893 TGTAAGACCATGTCTGGGA
1 TGTAAGACCATGTCTGGGA
13630912 TGTTGGCATT
Statistics
Matches: 85, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
40 2 0.02
41 28 0.33
42 6 0.07
43 20 0.24
44 4 0.05
45 24 0.28
46 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (44 bp):
TGTAAGACCATGTCTGGGACAGTGGCATCGTATATGTGGTTACA
Found at i:13632120 original size:2 final size:2
Alignment explanation
Indices: 13632113--13632140 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13632103 TTGCACATAC
13632113 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
13632141 TGCACATGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13632973 original size:12 final size:12
Alignment explanation
Indices: 13632956--13632988 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
13632946 CGGCACGCCC
13632956 ATATTAATTTTT
1 ATATTAATTTTT
13632968 ATATT-ATTTTT
1 ATATTAATTTTT
13632979 ATA-TAATTTT
1 ATATTAATTTT
13632989 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:13633156 original size:30 final size:30
Alignment explanation
Indices: 13633113--13633170 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
13633103 CTTAACAAGA
*
13633113 AAATGCCTCTAAAATAATAACAAAATTAGC
1 AAATGCCTCTAAAATAATAAAAAAATTAGC
* *
13633143 AAATGTCTTTAAAATAATAAAAAAATTA
1 AAATGCCTCTAAAATAATAAAAAAATTA
13633171 ATAATAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAAAAAAATTAGC
Found at i:13633229 original size:22 final size:22
Alignment explanation
Indices: 13633204--13633246 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
13633194 TATTCAAACA
13633204 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
13633226 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
13633247 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:13633250 original size:11 final size:11
Alignment explanation
Indices: 13633211--13633251 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
13633201 ACAATAACAA
13633211 CAAAATAGTAG
1 CAAAATAGTAG
* *
13633222 CAACATAATAG
1 CAAAATAGTAG
*
13633233 TAAAATAGTAG
1 CAAAATAGTAG
13633244 CAAAATAG
1 CAAAATAG
13633252 GGAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:13635305 original size:45 final size:46
Alignment explanation
Indices: 13635241--13635356 Score: 180
Period size: 46 Copynumber: 2.5 Consensus size: 46
13635231 GTGTGTCATG
* *
13635241 GTGTCTTTCAACCATGGTCTTATTTATTCTT-GTCTTGATGCCCTA
1 GTGTCTTTCAACCATGGTCTTATTTATTCTTCGTCATGATGCCATA
* * *
13635286 GTGTCTTTCAACCATGGTCTTATTCATTTTTCGTCATGTTGCCATA
1 GTGTCTTTCAACCATGGTCTTATTTATTCTTCGTCATGATGCCATA
13635332 GTGTCTTTCAACCATGGTCTTATTT
1 GTGTCTTTCAACCATGGTCTTATTT
13635357 CTTTGATTCA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
45 29 0.45
46 35 0.55
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.47
Consensus pattern (46 bp):
GTGTCTTTCAACCATGGTCTTATTTATTCTTCGTCATGATGCCATA
Found at i:13635383 original size:45 final size:44
Alignment explanation
Indices: 13635241--13635384 Score: 159
Period size: 45 Copynumber: 3.2 Consensus size: 44
13635231 GTGTGTCATG
* * * *
13635241 GTGTCTTTCAACCATGGTCTTATTTATTCTTGTCTTGATGCCCTA
1 GTGTCTTTCAACCATGGTCTTATTTCTT-TTGTCATGATTCCATA
13635286 GTGTCTTTCAACCATGGTCTTA-TTCATTTTTCGTCATG-TTGCCATA
1 GTGTCTTTCAACCATGGTCTTATTTC--TTTT-GTCATGATT-CCATA
13635332 GTGTCTTTCAACCATGGTCTTATTTC-TTTGATTCATGATTCCATA
1 GTGTCTTTCAACCATGGTCTTATTTCTTTTG--TCATGATTCCATA
*
13635377 GCGTCTTT
1 GTGTCTTT
13635385 GAGCTATGGT
Statistics
Matches: 86, Mismatches: 5, Indels: 16
0.80 0.05 0.15
Matches are distributed among these distances:
43 1 0.01
44 5 0.06
45 42 0.49
46 35 0.41
47 3 0.03
ACGTcount: A:0.17, C:0.22, G:0.15, T:0.47
Consensus pattern (44 bp):
GTGTCTTTCAACCATGGTCTTATTTCTTTTGTCATGATTCCATA
Found at i:13635458 original size:90 final size:90
Alignment explanation
Indices: 13635364--13635534 Score: 229
Period size: 90 Copynumber: 1.9 Consensus size: 90
13635354 TTTCTTTGAT
* * * * *
13635364 TCATGATTCCATAGCGTCTTTGAG-CTATGGTTTTACTCGA-TAGAATCATGATGCCATAATGTC
1 TCATGATGCCATAACATCTTTCAGTC-ATGGTCTTACTC-ATTAGAATCATGATGCCATAATGTC
**
13635427 TTTCGGTCATGGTCTTACCCGATAGAA
64 TTTAAGTCATGGTCTTACCCGATAGAA
* *
13635454 TCATGATGCCATAACATCTTTCAGTCATGGTCTTGCTCATTAGAATCATGATGTCATAATGTCTT
1 TCATGATGCCATAACATCTTTCAGTCATGGTCTTACTCATTAGAATCATGATGCCATAATGTCTT
13635519 TAAGTCATGGTCTTAC
66 TAAGTCATGGTCTTAC
13635535 TCATTTCTGG
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
89 1 0.01
90 68 0.97
91 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (90 bp):
TCATGATGCCATAACATCTTTCAGTCATGGTCTTACTCATTAGAATCATGATGCCATAATGTCTT
TAAGTCATGGTCTTACCCGATAGAA
Found at i:13635539 original size:45 final size:45
Alignment explanation
Indices: 13635319--13635536 Score: 208
Period size: 45 Copynumber: 4.8 Consensus size: 45
13635309 TCATTTTTCG
* * ** * * * *
13635319 TCATGTTGCCATAGTGTCTTTCAACCATGGTCTTATTTC-TTTGAT
1 TCATGATGCCATAATGTCTTTCAGTCATGGTCTTA-CTCGATAGAA
* ** * *
13635364 TCATGATTCCATAGCGTCTTTGAG-CTATGGTTTTACTCGATAGAA
1 TCATGATGCCATAATGTCTTTCAGTC-ATGGTCTTACTCGATAGAA
* *
13635409 TCATGATGCCATAATGTCTTTCGGTCATGGTCTTACCCGATAGAA
1 TCATGATGCCATAATGTCTTTCAGTCATGGTCTTACTCGATAGAA
** *
13635454 TCATGATGCCATAACATCTTTCAGTCATGGTCTTGCTC-ATTAGAA
1 TCATGATGCCATAATGTCTTTCAGTCATGGTCTTACTCGA-TAGAA
* *
13635499 TCATGATGTCATAATGTCTTTAAGTCATGGTCTTACTC
1 TCATGATGCCATAATGTCTTTCAGTCATGGTCTTACTC
13635537 ATTTCTGGTA
Statistics
Matches: 142, Mismatches: 27, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
44 4 0.03
45 137 0.96
46 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.39
Consensus pattern (45 bp):
TCATGATGCCATAATGTCTTTCAGTCATGGTCTTACTCGATAGAA
Found at i:13637728 original size:37 final size:37
Alignment explanation
Indices: 13637678--13637753 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
13637668 AATACCGAGA
13637678 TAGCTCGTTGATAGAGTGAGGCGATCTCTGATGTCCT
1 TAGCTCGTTGATAGAGTGAGGCGATCTCTGATGTCCT
13637715 TAGCTCGTTGATAGAGTGAGGCGATCTCTGATGTCCT
1 TAGCTCGTTGATAGAGTGAGGCGATCTCTGATGTCCT
13637752 TA
1 TA
13637754 CGATTTTCCG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (37 bp):
TAGCTCGTTGATAGAGTGAGGCGATCTCTGATGTCCT
Found at i:13642262 original size:21 final size:21
Alignment explanation
Indices: 13642237--13642278 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
13642227 TGTTAACGCT
13642237 GTTGATATTTAAATTTATTTA
1 GTTGATATTTAAATTTATTTA
13642258 GTTGATATTTAAATTTATTTA
1 GTTGATATTTAAATTTATTTA
13642279 ATTTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (21 bp):
GTTGATATTTAAATTTATTTA
Found at i:13643321 original size:53 final size:53
Alignment explanation
Indices: 13643241--13643349 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
13643231 AATTACCGTT
13643241 ATATTCGATTTTTAATATAAAAATCACACTTACAAATTCATACAAAAGGAACG
1 ATATTCGATTTTTAATATAAAAATCACACTTACAAATTCATACAAAAGGAACG
13643294 ATATTCGATTTTTAATATAAAAATCACACTTACAAATTCATACAAAAGGAACG
1 ATATTCGATTTTTAATATAAAAATCACACTTACAAATTCATACAAAAGGAACG
13643347 ATA
1 ATA
13643350 GTAAAAAGTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (53 bp):
ATATTCGATTTTTAATATAAAAATCACACTTACAAATTCATACAAAAGGAACG
Found at i:13648578 original size:21 final size:21
Alignment explanation
Indices: 13648554--13648651 Score: 94
Period size: 21 Copynumber: 4.8 Consensus size: 21
13648544 CTTACTTCCT
13648554 TCGTCATCATCCTCATCCTCA
1 TCGTCATCATCCTCATCCTCA
* *
13648575 TCGTCAGCATCCTCATCCTCT
1 TCGTCATCATCCTCATCCTCA
* *
13648596 TCCTCATCATCCTCTTCCTC-
1 TCGTCATCATCCTCATCCTCA
* *
13648616 -C-TCATCATCATCATCGTCA
1 TCGTCATCATCCTCATCCTCA
* * *
13648635 TCTTCTTCATCGTCATC
1 TCGTCATCATCCTCATC
13648652 TATATCAAGC
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
18 14 0.22
19 1 0.02
20 1 0.02
21 48 0.75
ACGTcount: A:0.16, C:0.42, G:0.05, T:0.37
Consensus pattern (21 bp):
TCGTCATCATCCTCATCCTCA
Found at i:13648652 original size:15 final size:15
Alignment explanation
Indices: 13648557--13648651 Score: 73
Period size: 15 Copynumber: 6.3 Consensus size: 15
13648547 ACTTCCTTCG
*
13648557 TCATCATCCTCATCC
1 TCATCATCTTCATCC
* **
13648572 TCATCGTCAGCATCC
1 TCATCATCTTCATCC
* * *
13648587 TCATCCTCTTCCTCA
1 TCATCATCTTCATCC
* *
13648602 TCATCCTCTTCCTCC
1 TCATCATCTTCATCC
* *
13648617 TCATCATCATCATCG
1 TCATCATCTTCATCC
* *
13648632 TCATCTTCTTCATCG
1 TCATCATCTTCATCC
13648647 TCATC
1 TCATC
13648652 TATATCAAGC
Statistics
Matches: 65, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 65 1.00
ACGTcount: A:0.17, C:0.42, G:0.04, T:0.37
Consensus pattern (15 bp):
TCATCATCTTCATCC
Found at i:13654704 original size:36 final size:36
Alignment explanation
Indices: 13654648--13654719 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
13654638 TTAATAAAAA
13654648 TAAAATTATACTTTAATCCCTAAAATTATAAAATTT
1 TAAAATTATACTTTAATCCCTAAAATTATAAAATTT
* *
13654684 TAAAATTATATTTTAGTCCCTAAAATTATAAAATTT
1 TAAAATTATACTTTAATCCCTAAAATTATAAAATTT
13654720 GATTTAACCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (36 bp):
TAAAATTATACTTTAATCCCTAAAATTATAAAATTT
Found at i:13658954 original size:29 final size:29
Alignment explanation
Indices: 13658886--13658959 Score: 94
Period size: 29 Copynumber: 2.6 Consensus size: 29
13658876 AATAAAATCT
* *
13658886 ATCTCGTCAAAATAATTTTTTCAGAACAC
1 ATCTCGTCAAAATTATTTTTTCAAAACAC
* * * *
13658915 ATCACGCCAAATTTATTTTTTCAAAACCC
1 ATCTCGTCAAAATTATTTTTTCAAAACAC
13658944 ATCTCGTCAAAATTAT
1 ATCTCGTCAAAATTAT
13658960 ATTTCCCAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.35
Consensus pattern (29 bp):
ATCTCGTCAAAATTATTTTTTCAAAACAC
Found at i:13659140 original size:65 final size:64
Alignment explanation
Indices: 13659003--13659142 Score: 192
Period size: 65 Copynumber: 2.2 Consensus size: 64
13658993 ATTAAACCTT
* * * * *
13659003 AAAACCTTAAATAATTAAAAACCTAATACCCTATTTAATTTTCCCTGAACTCTAATCAAACACC
1 AAAACCCTAAAAAATTAAAAACATAATACCCTATTTAATTTTCCCTAAACCCTAATCAAACACC
*
13659067 AAAACCCTAAAAAATTAAAAACATAATACCCTAATTTAATTTTTCCTAAACCCTAATCAAAC-CA
1 AAAACCCTAAAAAATTAAAAACATAATACCCT-ATTTAATTTTCCCTAAACCCTAATCAAACAC-
13659131 C
64 C
*
13659132 AAATCCCTAAA
1 AAAACCCTAAA
13659143 CATAAGCCCT
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
64 30 0.45
65 37 0.55
ACGTcount: A:0.47, C:0.25, G:0.01, T:0.27
Consensus pattern (64 bp):
AAAACCCTAAAAAATTAAAAACATAATACCCTATTTAATTTTCCCTAAACCCTAATCAAACACC
Found at i:13660371 original size:23 final size:24
Alignment explanation
Indices: 13660326--13660371 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
13660316 ACTATTATAT
13660326 TAAAATAAAATTTTGATTTAATGG
1 TAAAATAAAATTTTGATTTAATGG
*
13660350 TAAAATTAATATTTT-A-TTAATG
1 TAAAA-TAAAATTTTGATTTAATG
13660372 CAAATCATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.46
Consensus pattern (24 bp):
TAAAATAAAATTTTGATTTAATGG
Found at i:13661571 original size:5 final size:5
Alignment explanation
Indices: 13661563--13661596 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
13661553 GGTTTGGTTG
*
13661563 GGTGA GGTGC GGTGC GGTGC GGTGC GGTGC GGTG
1 GGTGC GGTGC GGTGC GGTGC GGTGC GGTGC GGTG
13661597 TGTTTAGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.03, C:0.15, G:0.62, T:0.21
Consensus pattern (5 bp):
GGTGC
Found at i:13680813 original size:29 final size:29
Alignment explanation
Indices: 13680771--13680829 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
13680761 AAGAAAATGA
**
13680771 ATCATGGTTGTTGATAAACTGTAATTTAT
1 ATCATGGTTGTTGATAAACCATAATTTAT
13680800 ATCATGGTTGTTGATAAACCATAATTTAT
1 ATCATGGTTGTTGATAAACCATAATTTAT
13680829 A
1 A
13680830 CATATTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.08, G:0.15, T:0.42
Consensus pattern (29 bp):
ATCATGGTTGTTGATAAACCATAATTTAT
Found at i:13681150 original size:13 final size:13
Alignment explanation
Indices: 13681132--13681156 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13681122 GGAGTAATCG
13681132 CACACGGGCGTGA
1 CACACGGGCGTGA
13681145 CACACGGGCGTG
1 CACACGGGCGTG
13681157 TCCCTGCCGA
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:0.20, C:0.32, G:0.40, T:0.08
Consensus pattern (13 bp):
CACACGGGCGTGA
Found at i:13689209 original size:35 final size:35
Alignment explanation
Indices: 13689182--13689347 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
13689172 CATGGCAAAG
*
13689182 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
13689217 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
13689252 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * * *
13689292 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
13689327 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
13689348 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 79 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:13689301 original size:75 final size:75
Alignment explanation
Indices: 13689182--13689352 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
13689172 CATGGCAAAG
** *
13689182 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
13689241 CCATACTGAGC
65 CCATACCGAGC
13689252 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
13689317 CATACCGAGT
66 CATACCGAGC
**
13689327 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
13689353 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:13696704 original size:35 final size:35
Alignment explanation
Indices: 13696677--13696842 Score: 172
Period size: 35 Copynumber: 4.6 Consensus size: 35
13696667 CATGGCAAAG
*
13696677 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
13696712 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
*
13696747 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGC
** * * * *
13696787 TAAGAAATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATCAT-CCATACTGAGC
**
13696822 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
13696843 TTCAATGAGG
Statistics
Matches: 113, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 79 0.70
37 2 0.02
38 3 0.03
40 28 0.25
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATCATCCATACTGAGC
Found at i:13696796 original size:75 final size:75
Alignment explanation
Indices: 13696677--13696847 Score: 221
Period size: 75 Copynumber: 2.4 Consensus size: 75
13696667 CATGGCAAAG
** *
13696677 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATT-TC
*
13696736 CCATACTGAGC
65 CCATACCGAGC
13696747 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
*
13696812 CATACCGAGT
66 CATACCGAGC
**
13696822 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
13696848 TGAGGAAAAC
Statistics
Matches: 88, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
70 18 0.20
73 4 0.05
74 5 0.06
75 61 0.69
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAAGAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:13717630 original size:2 final size:2
Alignment explanation
Indices: 13717623--13717674 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
13717613 CAGAACCTTT
* *
13717623 CA CA CA CA CA CA TA CA CA CA CA CA CA CA CA CA CA CA CA TA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
*
13717665 CA CA TA CA CA
1 CA CA CA CA CA
13717675 TATTACATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.44, G:0.00, T:0.06
Consensus pattern (2 bp):
CA
Found at i:13717642 original size:14 final size:14
Alignment explanation
Indices: 13717623--13717676 Score: 85
Period size: 14 Copynumber: 4.0 Consensus size: 14
13717613 CAGAACCTTT
13717623 CACACACACACATA
1 CACACACACACATA
13717637 CACACACACAC--A
1 CACACACACACATA
13717649 CACACACACACATA
1 CACACACACACATA
*
13717663 CACACATACACATA
1 CACACACACACATA
13717677 TTACATATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
12 12 0.32
14 25 0.68
ACGTcount: A:0.50, C:0.43, G:0.00, T:0.07
Consensus pattern (14 bp):
CACACACACACATA
Done.