Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015167.1 Kokia drynarioides strain JFW-HI SEQ_130211, whole genome shotgun sequence
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: 274785
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 395 characters in sequence are not A, C, G, or T
Found at i:13512 original size:12 final size:13
Alignment explanation
Indices: 13492--13520 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
13482 ACTTAAATAC
13492 AAGTAAAAATTGT
1 AAGTAAAAATTGT
13505 AAGT-AAAATTGT
1 AAGTAAAAATTGT
13517 AAGT
1 AAGT
13521 TAAGAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.31
Consensus pattern (13 bp):
AAGTAAAAATTGT
Found at i:21742 original size:21 final size:21
Alignment explanation
Indices: 21716--21772 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
21706 CTACTTAAGG
21716 CTCGAGACAAGTGGCATTTGT
1 CTCGAGACAAGTGGCATTTGT
21737 CTCGAGACAAGTGGCATTTGT
1 CTCGAGACAAGTGGCATTTGT
21758 CTCGAGACAAG-GGCA
1 CTCGAGACAAGTGGCA
21773 CATCGAAGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.11
21 32 0.89
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (21 bp):
CTCGAGACAAGTGGCATTTGT
Found at i:26852 original size:16 final size:17
Alignment explanation
Indices: 26826--26874 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
26816 AGAATCAAAG
*
26826 TTGAGAAAATTATTTAA
1 TTGAGAAAATTAATTAA
26843 TTGA-AAAATTAATTAA
1 TTGAGAAAATTAATTAA
* *
26859 TTAATTAAAATTAATT
1 TTGA-GAAAATTAATT
26875 TATGATGTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 14 0.50
17 4 0.14
18 10 0.36
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (17 bp):
TTGAGAAAATTAATTAA
Found at i:26862 original size:20 final size:18
Alignment explanation
Indices: 26833--26874 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
26823 AAGTTGAGAA
*
26833 AATTATTTAATTGAAAAATT
1 AATTAATTAATT--AAAATT
26853 AATTAATTAATTAAAATT
1 AATTAATTAATTAAAATT
26871 AATT
1 AATT
26875 TATGATGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
20 11 0.52
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
AATTAATTAATTAAAATT
Found at i:42662 original size:37 final size:37
Alignment explanation
Indices: 42621--42694 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
42611 CTCAGGCTCG
* *
42621 CCAATAGATACCTATGGGAAGTATACTCGATATATTC
1 CCAATAGAAACCTATGGGAAGTATACTCAATATATTC
*
42658 CCAATAGAAACCTATGGGAAGTATGCTCAATATATTC
1 CCAATAGAAACCTATGGGAAGTATACTCAATATATTC
42695 TCACTACAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (37 bp):
CCAATAGAAACCTATGGGAAGTATACTCAATATATTC
Found at i:45796 original size:26 final size:26
Alignment explanation
Indices: 45767--45820 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
45757 TCTTTCGGCC
45767 TTAAGGATTATTATTTCGGGTATAAT
1 TTAAGGATTATTATTTCGGGTATAAT
*
45793 TTAAGGGTTATTATTTCGGGTATAAT
1 TTAAGGATTATTATTTCGGGTATAAT
45819 TT
1 TT
45821 GATATATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.48
Consensus pattern (26 bp):
TTAAGGATTATTATTTCGGGTATAAT
Found at i:47218 original size:103 final size:101
Alignment explanation
Indices: 47034--47219 Score: 223
Period size: 103 Copynumber: 1.8 Consensus size: 101
47024 CACTTGTTGA
* * * ** * *
47034 TTTTAAAATAGGATATTCAATTACTTAGGTTCAAAAAAATCATACCCAGTATGTTTGAGCACAAT
1 TTTTAAAATAGAATATTCAATTACTTAAGTTCAAAAAAATCATACACAACACGTTAGAGCACAAT
* *
47099 TTTTTGAGTTTCCTAAAAAAAGAAACATTGCCTCGT
66 TTTTCGAATTTCCTAAAAAAAGAAACATTGCCTCGT
* *
47135 TTTTTAAATAGAATATTCAATTTCTTAAGTTCAAGGAAAAATCATACACAACACGTTA-AGACAC
1 TTTTAAAATAGAATATTCAATTACTTAAGTTCAA--AAAAATCATACACAACACGTTAGAG-CAC
47199 AATTTTTCGAA-TTCTCTAAAA
63 AATTTTTCGAATTTC-CTAAAA
47220 TAAAATAATA
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
101 30 0.43
102 5 0.07
103 35 0.50
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (101 bp):
TTTTAAAATAGAATATTCAATTACTTAAGTTCAAAAAAATCATACACAACACGTTAGAGCACAAT
TTTTCGAATTTCCTAAAAAAAGAAACATTGCCTCGT
Found at i:47776 original size:35 final size:35
Alignment explanation
Indices: 47727--47796 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
47717 TTTAGAAAAA
47727 AAAAAAAAAGAAAAGAAACATTTGGAGGTCAAATT
1 AAAAAAAAAGAAAAGAAACATTTGGAGGTCAAATT
47762 NAAAAAAAAA-AAAAGAAACATTTGGAGGTCAAATT
1 -AAAAAAAAAGAAAAGAAACATTTGGAGGTCAAATT
47797 GAAGTTCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 25 0.74
36 9 0.26
ACGTcount: A:0.60, C:0.06, G:0.16, T:0.17
Consensus pattern (35 bp):
AAAAAAAAAGAAAAGAAACATTTGGAGGTCAAATT
Found at i:49532 original size:30 final size:30
Alignment explanation
Indices: 49477--49589 Score: 160
Period size: 29 Copynumber: 3.9 Consensus size: 30
49467 AAATTGTTCG
**
49477 AAAATTCCATTTTT-ACCTCCGAACTTCCA
1 AAAATTCCATTTTTAACCTCAAAACTTCCA
49506 AAAATTCCATTTTTAACCTCAAAACTT-CA
1 AAAATTCCATTTTTAACCTCAAAACTTCCA
*
49535 AAAATTCCATTTTTACCCT-AAAACTTCCA
1 AAAATTCCATTTTTAACCTCAAAACTTCCA
* *
49564 AAAATTCCATTTTTGACCTCGAAACT
1 AAAATTCCATTTTTAACCTCAAAACT
49590 CTCAAAATTA
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
28 7 0.09
29 53 0.71
30 15 0.20
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTCCATTTTTAACCTCAAAACTTCCA
Found at i:49567 original size:58 final size:59
Alignment explanation
Indices: 49477--49596 Score: 181
Period size: 58 Copynumber: 2.1 Consensus size: 59
49467 AAATTGTTCG
**
49477 AAAATTCCATTTTTACCTCCGAACTTCCAAAAATTCCATTTTTAACCTCAAAACT-TCA
1 AAAATTCCATTTTTACCTCAAAACTTCCAAAAATTCCATTTTTAACCTCAAAACTCTCA
* *
49535 AAAATTCCATTTTTACC-CTAAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTCTCA
1 AAAATTCCATTTTTACCTC-AAAACTTCCAAAAATTCCATTTTTAACCTCAAAACTCTCA
49594 AAA
1 AAA
49597 TTAGCCGTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
57 1 0.02
58 49 0.88
59 6 0.11
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.33
Consensus pattern (59 bp):
AAAATTCCATTTTTACCTCAAAACTTCCAAAAATTCCATTTTTAACCTCAAAACTCTCA
Found at i:53523 original size:49 final size:49
Alignment explanation
Indices: 53466--53561 Score: 183
Period size: 49 Copynumber: 2.0 Consensus size: 49
53456 ACTAGATGAA
*
53466 TTTGAATGAATTGTTAGGTTTGGCAGTGTGGAATTCATTTATAATTGAG
1 TTTGAATGAATTGTTAGGTTTGGCAGTGTGGAATTCAATTATAATTGAG
53515 TTTGAATGAATTGTTAGGTTTGGCAGTGTGGAATTCAATTATAATTG
1 TTTGAATGAATTGTTAGGTTTGGCAGTGTGGAATTCAATTATAATTG
53562 TGCGTAGCTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.27, C:0.04, G:0.26, T:0.43
Consensus pattern (49 bp):
TTTGAATGAATTGTTAGGTTTGGCAGTGTGGAATTCAATTATAATTGAG
Found at i:55038 original size:17 final size:17
Alignment explanation
Indices: 55016--55049 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
55006 AAAAAAATCC
*
55016 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
55033 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
55050 TCATGTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:55411 original size:2 final size:2
Alignment explanation
Indices: 55406--55433 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
55396 TTATTAAAAC
55406 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55434 ATTCAATTTA
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):
TA
Found at i:58921 original size:26 final size:25
Alignment explanation
Indices: 58892--58961 Score: 95
Period size: 26 Copynumber: 2.7 Consensus size: 25
58882 GCTAACTTTC
58892 TGTTTCCTTTCTTTCTTCAAAAATTT
1 TGTTTCCTTTCTTTCTTCAAAAA-TT
*
58918 TGTTTCCTTTCATTCTTCAAAAATT
1 TGTTTCCTTTCTTTCTTCAAAAATT
* *
58943 TGCTTCTCTTTTTTTCTTC
1 TGTTTC-CTTTCTTTCTTC
58962 TTTTACTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 7 0.18
26 32 0.82
ACGTcount: A:0.16, C:0.21, G:0.04, T:0.59
Consensus pattern (25 bp):
TGTTTCCTTTCTTTCTTCAAAAATT
Found at i:59516 original size:27 final size:27
Alignment explanation
Indices: 59486--59546 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
59476 CCAAGTAGGC
* * *
59486 AGGCACCTTTGGTGCCGCCTGTCAGGT
1 AGGCACCTCTAGTGCCGCCTGTCAGAT
59513 AGGCACCTCTAGTGCCGCCTGTCAGAT
1 AGGCACCTCTAGTGCCGCCTGTCAGAT
59540 AGGCACC
1 AGGCACC
59547 ACCCCACTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.16, C:0.33, G:0.30, T:0.21
Consensus pattern (27 bp):
AGGCACCTCTAGTGCCGCCTGTCAGAT
Found at i:62792 original size:19 final size:19
Alignment explanation
Indices: 62758--62795 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
62748 AATGGTTTTT
*
62758 GTTAATTAAATATAATTAA
1 GTTAATTAAACATAATTAA
*
62777 GTTAATTAAACCTAATTAA
1 GTTAATTAAACATAATTAA
62796 CTAATCCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (19 bp):
GTTAATTAAACATAATTAA
Found at i:77800 original size:7 final size:6
Alignment explanation
Indices: 77769--77798 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
77759 TAAAAAAGTA
77769 AAAATAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAA-AG AAAAAG AAAAAG AAAAAG AAAAA
77799 AGGAAGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:79817 original size:17 final size:17
Alignment explanation
Indices: 79789--79848 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
79779 GGCCTATTAG
*
79789 AAATTGAATTTATTTTA
1 AAATTAAATTTATTTTA
*
79806 AAATTAAGTTTA-TTTA
1 AAATTAAATTTATTTTA
*
79822 AAATTTAAATTTATTATA
1 AAA-TTAAATTTATTTTA
*
79840 AATTTAAAT
1 AAATTAAAT
79849 ATAAAATGTC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 7 0.19
17 24 0.67
18 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
AAATTAAATTTATTTTA
Found at i:79913 original size:15 final size:15
Alignment explanation
Indices: 79889--79944 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
79879 GTACAGATCT
79889 AAATGGCCCAATTAC
1 AAATGGCCCAATTAC
*
79904 AAATGACCCAATT-C
1 AAATGGCCCAATTAC
79918 TAAATGGCCCAATTAC
1 -AAATGGCCCAATTAC
79934 AAATGGCCCAA
1 AAATGGCCCAA
79945 GATTCCAAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
14 1 0.03
15 35 0.95
16 1 0.03
ACGTcount: A:0.41, C:0.27, G:0.12, T:0.20
Consensus pattern (15 bp):
AAATGGCCCAATTAC
Found at i:79920 original size:30 final size:30
Alignment explanation
Indices: 79886--79944 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
79876 CAAGTACAGA
79886 TCTAAATGGCCCAATTACAAATGACCCAAT
1 TCTAAATGGCCCAATTACAAATGACCCAAT
*
79916 TCTAAATGGCCCAATTACAAATGGCCCAA
1 TCTAAATGGCCCAATTACAAATGACCCAA
79945 GATTCCAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.27, G:0.12, T:0.22
Consensus pattern (30 bp):
TCTAAATGGCCCAATTACAAATGACCCAAT
Found at i:81747 original size:29 final size:28
Alignment explanation
Indices: 81706--81992 Score: 247
Period size: 29 Copynumber: 9.9 Consensus size: 28
81696 GGAGGTCCCT
*
81706 AAACTTCCAAAAATTCCATTTTTACCCT
1 AAACTTCCAAAAATTCCATTTTTACCCC
* *
81734 AGAACTTCAAAAAATTCTATTTTTACCCCC
1 A-AACTTCCAAAAATTCCATTTTTA-CCCC
*
81764 AAAACTTCCAAAAATTCCATTTTTAGCCTC
1 -AAACTTCCAAAAATTCCATTTTTA-CCCC
* * *
81794 GATCTTCCAAAAATTCCATTTTAACCCC
1 AAACTTCCAAAAATTCCATTTTTACCCC
*
81822 AAAACCTCCAAAAATTACCA-TTTTACCCCC
1 -AAACTTCCAAAAATT-CCATTTTTA-CCCC
*
81852 AAACTTCCAAAAATCCCATTTTTGACCCC
1 AAACTTCCAAAAATTCCATTTTT-ACCCC
* *
81881 TAAACTTCAAAAAATTCTA-TTTTACCCCC
1 -AAACTTCCAAAAATTCCATTTTTA-CCCC
* * * *
81910 GAACTTCCAAGAATGCCATTTTTGATCCCG
1 AAACTTCCAAAAATTCCATTTTT-A-CCCC
* * *
81940 AAATTTTCAAAAATTCCATTTTCACCCCC
1 AAACTTCCAAAAATTCCATTTTTA-CCCC
* *
81969 GAA-TGTCTAAAAATTCCATTTTTA
1 AAACT-TCCAAAAATTCCATTTTTA
81993 AACCCTAAAT
Statistics
Matches: 207, Mismatches: 39, Indels: 25
0.76 0.14 0.09
Matches are distributed among these distances:
28 22 0.11
29 113 0.55
30 71 0.34
31 1 0.00
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (28 bp):
AAACTTCCAAAAATTCCATTTTTACCCC
Found at i:82003 original size:59 final size:58
Alignment explanation
Indices: 81702--82028 Score: 325
Period size: 58 Copynumber: 5.6 Consensus size: 58
81692 CCTTGGAGGT
** * * *
81702 CCCTAAACTTCCAAAAATTCCATTTTTACCCTAGAACTTCAAAAAATTCTATTTTTACC
1 CCCTAAACTTCCAAAAATTCCA-TTTTACCCCCGAACTTCCAAAAATTCCATTTTTAAC
* * * *
81761 CCCAAAACTTCCAAAAATTCCATTTTTAGCCTCGATCTTCCAAAAATTCCA-TTTTAAC
1 CCCTAAACTTCCAAAAATTCCA-TTTTACCCCCGAACTTCCAAAAATTCCATTTTTAAC
* * * * *
81819 CCCAAAACCTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGAC
1 CCCTAAACTTCCAAAAATT-CCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAAC
* * * * * *
81878 CCCTAAACTTCAAAAAATTCTATTTTACCCCCGAACTTCCAAGAATGCCATTTTTGAT
1 CCCTAAACTTCCAAAAATTCCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAAC
* * * * *
81936 CCCGAAATTTTCAAAAATTCCATTTTCACCCCCGAA-TGTCTAAAAATTCCATTTTTAAA
1 CCCTAAACTTCCAAAAATTCCATTTT-ACCCCCGAACT-TCCAAAAATTCCATTTTTAAC
* * *
81995 CCCTAAATTTTCCCAAAATTACCATTTTCCCCCC
1 CCCTAAA-CTTCCAAAAATT-CCATTTTACCCCC
82029 CGGGTATCCG
Statistics
Matches: 226, Mismatches: 36, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
58 103 0.46
59 101 0.45
60 15 0.07
61 7 0.03
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.32
Consensus pattern (58 bp):
CCCTAAACTTCCAAAAATTCCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTAAC
Found at i:93223 original size:27 final size:27
Alignment explanation
Indices: 93171--93223 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
93161 TGCTTGTTTT
**
93171 CTTTGATCCTCTTTTCAATATTATTTC
1 CTTTGATCCTCTTTTCAATAGAATTTC
*
93198 CTTTGATCCTCTTTTTAATAGAATTT
1 CTTTGATCCTCTTTTCAATAGAATTT
93224 TTGAAATACG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.21, C:0.19, G:0.06, T:0.55
Consensus pattern (27 bp):
CTTTGATCCTCTTTTCAATAGAATTTC
Found at i:94056 original size:48 final size:48
Alignment explanation
Indices: 93985--94147 Score: 290
Period size: 48 Copynumber: 3.4 Consensus size: 48
93975 TTCGAACCCC
*
93985 AGCTTCCTGATAAGATACTGAGAAGCAGGTCGAAGTAATAAAACGGAT
1 AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAACGGAT
*
94033 AGCTTCCTGATGAGATACTGAGAAGTAGGTCGAAGTAATAAAACGGAT
1 AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAACGGAT
* *
94081 AGCTTCCTGTTGAGATACTGAGAAGCAGGTCGAAGTAATAAAATGGAT
1 AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAACGGAT
94129 AGCTTCCTGATGAGATACT
1 AGCTTCCTGATGAGATACT
94148 AGGGAGTGAA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 109 1.00
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (48 bp):
AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGTAATAAAACGGAT
Found at i:94869 original size:17 final size:17
Alignment explanation
Indices: 94845--94901 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
94835 TTGGAATTTG
94845 AATTTATTTTAAAATTA
1 AATTTATTTTAAAATTA
*
94862 AGTTTA-TTTAAAATTTA
1 AATTTATTTTAAAA-TTA
* *
94879 AATTTATTATAAATTTA
1 AATTTATTTTAAAATTA
94896 AATTTA
1 AATTTA
94902 AAATGTCCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
16 7 0.21
17 22 0.65
18 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAAATTA
Found at i:96754 original size:29 final size:29
Alignment explanation
Indices: 96713--97171 Score: 365
Period size: 30 Copynumber: 15.6 Consensus size: 29
96703 TAAATTGTCA
96713 AAAAATTCCATTTTTACCCCCGAACTTCC
1 AAAAATTCCATTTTTACCCCCGAACTTCC
** ** *
96742 AAAAA-TCTCATTTTTGACTTCAAAACATCC
1 AAAAATTC-CATTTTT-ACCCCCGAACTTCC
*
96772 AAAAACTCCATTTTTACCCCCGAACTTCC
1 AAAAATTCCATTTTTACCCCCGAACTTCC
* **
96801 AAAAA-TCTCATTTTTAACCACAAAACTTCC
1 AAAAATTC-CATTTTT-ACCCCCGAACTTCC
***
96831 AAAAA-TCTCATTTTTGACCCTAAAACTTCC
1 AAAAATTC-CATTTTT-ACCCCCGAACTTCC
* *
96861 AAAAATTCCATTTTTACCCTCGAAACTTCA
1 AAAAATTCCATTTTTACCCCCG-AACTTCC
**
96891 AAAAATTCCATTTTTAGTCCCGTAACTTCC
1 AAAAATTCCATTTTTACCCCCG-AACTTCC
* * *
96921 AAAAATTCCATTTTTAACCCCGAGACATCT
1 AAAAATTCCATTTTTACCCCCGA-ACTTCC
96951 AAAAATTACCA-TTTTACCCCCGAACTTCC
1 AAAAATT-CCATTTTTACCCCCGAACTTCC
* * **
96980 -AAAATCCCATTTTTTATCCCTAAACTTCC
1 AAAAATTCCA-TTTTTACCCCCGAACTTCC
* * * * *
97009 AAAAATTCCATTTCTACCCTCAAACCTCT
1 AAAAATTCCATTTTTACCCCCGAACTTCC
* * * *
97038 AAAAATCCCATTTTTAGCCTCGAAACTTCT
1 AAAAATTCCATTTTTACCCCCG-AACTTCC
*
97068 AAAAATTCCATTTTTACCCCTGAACTTCC
1 AAAAATTCCATTTTTACCCCCGAACTTCC
* * * * *
97097 AAGAATGCCATTTTTTA-TCCCGAAATTTCT
1 AAAAATTCCA-TTTTTACCCCCG-AACTTCC
* * *
97127 AAAAATTCTATTTTTCCCCCCGAA-TATCT
1 AAAAATTCCATTTTTACCCCCGAACT-TCC
97156 AAAAATTCCATTTTTA
1 AAAAATTCCATTTTTA
97172 AACCTCAAAT
Statistics
Matches: 348, Mismatches: 65, Indels: 34
0.78 0.15 0.08
Matches are distributed among these distances:
27 3 0.01
28 10 0.03
29 130 0.37
30 198 0.57
31 7 0.02
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCCCGAACTTCC
Found at i:96804 original size:59 final size:58
Alignment explanation
Indices: 96713--97171 Score: 398
Period size: 59 Copynumber: 7.8 Consensus size: 58
96703 TAAATTGTCA
* * *
96713 AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACTTCAAAACATCC
1 AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCTCATTTTT-ACCTCGAAACTTCC
* * *
96772 AAAAACTCCATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTAACCACAAAACTTCC
1 AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCTCATTTTT-ACCTCGAAACTTCC
*** *
96831 AAAAA-TCTCATTTTTGACCCTAAAACTTCCAAAAAT-TCCATTTTTACCCTCGAAACTTCA
1 AAAAATTC-CATTTTT-ACCCCCGAACTTCCAAAAATCT-CATTTTTA-CCTCGAAACTTCC
** * * * *
96891 AAAAATTCCATTTTTAGTCCCGTAACTTCCAAAAAT-TCCATTTTTAACCCCGAGACATCT
1 AAAAATTCCATTTTTACCCCCG-AACTTCCAAAAATCT-CATTTTT-ACCTCGAAACTTCC
* *
96951 AAAAATTACCA-TTTTACCCCCGAACTTCC-AAAATCCCATTTTTTATCC-CTAAACTTCC
1 AAAAATT-CCATTTTTACCCCCGAACTTCCAAAAATCTCA-TTTTTA-CCTCGAAACTTCC
* * * * * * *
97009 AAAAATTCCATTTCTACCCTCAAACCTCTAAAAATCCCATTTTTAGCCTCGAAACTTCT
1 AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTA-CCTCGAAACTTCC
* * * *
97068 AAAAATTCCATTTTTACCCCTGAACTTCCAAGAATGC-CATTTTTTATCC-CGAAATTTCT
1 AAAAATTCCATTTTTACCCCCGAACTTCCAAAAAT-CTCA-TTTTTA-CCTCGAAACTTCC
* * *
97127 AAAAATTCTATTTTTCCCCCCGAA-TATCTAAAAAT-TCCATTTTTA
1 AAAAATTCCATTTTTACCCCCGAACT-TCCAAAAATCT-CATTTTTA
97172 AACCTCAAAT
Statistics
Matches: 332, Mismatches: 49, Indels: 39
0.79 0.12 0.09
Matches are distributed among these distances:
57 3 0.01
58 51 0.15
59 170 0.51
60 102 0.31
61 6 0.02
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (58 bp):
AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTACCTCGAAACTTCC
Found at i:100585 original size:17 final size:17
Alignment explanation
Indices: 100561--100617 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
100551 TTGGAATTTG
100561 AATTTATTTTAAAATTA
1 AATTTATTTTAAAATTA
*
100578 AGTTTA-TTTAAAATTTA
1 AATTTATTTTAAAA-TTA
* *
100595 AATTTATTATAAATTTA
1 AATTTATTTTAAAATTA
100612 AATTTA
1 AATTTA
100618 AAATGTCCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
16 7 0.21
17 22 0.65
18 5 0.15
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAAATTA
Found at i:102470 original size:29 final size:29
Alignment explanation
Indices: 102429--102887 Score: 365
Period size: 30 Copynumber: 15.6 Consensus size: 29
102419 TAAATTGTCA
102429 AAAAATTCCATTTTTACCCCCGAACTTCC
1 AAAAATTCCATTTTTACCCCCGAACTTCC
** ** *
102458 AAAAA-TCTCATTTTTGACTTCAAAACATCC
1 AAAAATTC-CATTTTT-ACCCCCGAACTTCC
*
102488 AAAAACTCCATTTTTACCCCCGAACTTCC
1 AAAAATTCCATTTTTACCCCCGAACTTCC
* **
102517 AAAAA-TCTCATTTTTAACCACAAAACTTCC
1 AAAAATTC-CATTTTT-ACCCCCGAACTTCC
***
102547 AAAAA-TCTCATTTTTGACCCTAAAACTTCC
1 AAAAATTC-CATTTTT-ACCCCCGAACTTCC
* *
102577 AAAAATTCCATTTTTACCCTCGAAACTTCA
1 AAAAATTCCATTTTTACCCCCG-AACTTCC
**
102607 AAAAATTCCATTTTTAGTCCCGTAACTTCC
1 AAAAATTCCATTTTTACCCCCG-AACTTCC
* * *
102637 AAAAATTCCATTTTTAACCCCGAGACATCT
1 AAAAATTCCATTTTTACCCCCGA-ACTTCC
102667 AAAAATTACCA-TTTTACCCCCGAACTTCC
1 AAAAATT-CCATTTTTACCCCCGAACTTCC
* * **
102696 -AAAATCCCATTTTTTATCCCTAAACTTCC
1 AAAAATTCCA-TTTTTACCCCCGAACTTCC
* * * * *
102725 AAAAATTCCATTTCTACCCTCAAACCTCT
1 AAAAATTCCATTTTTACCCCCGAACTTCC
* * * *
102754 AAAAATCCCATTTTTAGCCTCGAAACTTCT
1 AAAAATTCCATTTTTACCCCCG-AACTTCC
*
102784 AAAAATTCCATTTTTACCCCTGAACTTCC
1 AAAAATTCCATTTTTACCCCCGAACTTCC
* * * * *
102813 AAGAATGCCATTTTTTA-TCCCGAAATTTCT
1 AAAAATTCCA-TTTTTACCCCCG-AACTTCC
* * *
102843 AAAAATTCTATTTTTCCCCCCGAA-TATCT
1 AAAAATTCCATTTTTACCCCCGAACT-TCC
102872 AAAAATTCCATTTTTA
1 AAAAATTCCATTTTTA
102888 AACCTCAAAT
Statistics
Matches: 348, Mismatches: 65, Indels: 34
0.78 0.15 0.08
Matches are distributed among these distances:
27 3 0.01
28 10 0.03
29 130 0.37
30 198 0.57
31 7 0.02
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCCCGAACTTCC
Found at i:102520 original size:59 final size:58
Alignment explanation
Indices: 102429--102887 Score: 398
Period size: 59 Copynumber: 7.8 Consensus size: 58
102419 TAAATTGTCA
* * *
102429 AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTGACTTCAAAACATCC
1 AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCTCATTTTT-ACCTCGAAACTTCC
* * *
102488 AAAAACTCCATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTAACCACAAAACTTCC
1 AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCTCATTTTT-ACCTCGAAACTTCC
*** *
102547 AAAAA-TCTCATTTTTGACCCTAAAACTTCCAAAAAT-TCCATTTTTACCCTCGAAACTTCA
1 AAAAATTC-CATTTTT-ACCCCCGAACTTCCAAAAATCT-CATTTTTA-CCTCGAAACTTCC
** * * * *
102607 AAAAATTCCATTTTTAGTCCCGTAACTTCCAAAAAT-TCCATTTTTAACCCCGAGACATCT
1 AAAAATTCCATTTTTACCCCCG-AACTTCCAAAAATCT-CATTTTT-ACCTCGAAACTTCC
* *
102667 AAAAATTACCA-TTTTACCCCCGAACTTCC-AAAATCCCATTTTTTATCC-CTAAACTTCC
1 AAAAATT-CCATTTTTACCCCCGAACTTCCAAAAATCTCA-TTTTTA-CCTCGAAACTTCC
* * * * * * *
102725 AAAAATTCCATTTCTACCCTCAAACCTCTAAAAATCCCATTTTTAGCCTCGAAACTTCT
1 AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTA-CCTCGAAACTTCC
* * * *
102784 AAAAATTCCATTTTTACCCCTGAACTTCCAAGAATGC-CATTTTTTATCC-CGAAATTTCT
1 AAAAATTCCATTTTTACCCCCGAACTTCCAAAAAT-CTCA-TTTTTA-CCTCGAAACTTCC
* * *
102843 AAAAATTCTATTTTTCCCCCCGAA-TATCTAAAAAT-TCCATTTTTA
1 AAAAATTCCATTTTTACCCCCGAACT-TCCAAAAATCT-CATTTTTA
102888 AACCTCAAAT
Statistics
Matches: 332, Mismatches: 49, Indels: 39
0.79 0.12 0.09
Matches are distributed among these distances:
57 3 0.01
58 51 0.15
59 170 0.51
60 102 0.31
61 6 0.02
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (58 bp):
AAAAATTCCATTTTTACCCCCGAACTTCCAAAAATCTCATTTTTACCTCGAAACTTCC
Found at i:106798 original size:21 final size:20
Alignment explanation
Indices: 106770--106808 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
106760 ATTTAATATT
106770 CATTAATTTTAATACAATAA
1 CATTAATTTTAATACAATAA
*
106790 CATTAAATTTTAATTCAAT
1 CATT-AATTTTAATACAAT
106809 TTAATACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (20 bp):
CATTAATTTTAATACAATAA
Found at i:107084 original size:2 final size:2
Alignment explanation
Indices: 107079--107110 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
107069 GAAAAAAAAA
*
107079 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
107111 TTTCGTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:107302 original size:20 final size:21
Alignment explanation
Indices: 107249--107301 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
107239 AAAAATTCAG
* * *
107249 AAAAATATAAAAATTATTTTT
1 AAAAATATAAAAATCATATTA
107270 AAAAAT-TAAAAATCATATTA
1 AAAAATATAAAAATCATATTA
107290 AAAAATATAAAA
1 AAAAATATAAAA
107302 TTTTAAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAAATATAAAAATCATATTA
Found at i:113007 original size:31 final size:30
Alignment explanation
Indices: 112931--113008 Score: 77
Period size: 31 Copynumber: 2.6 Consensus size: 30
112921 TGTGCAATTG
*
112931 TATACATG-AATTTTAATTTGATACAATTA
1 TATACATGAAATTTTAATTTGATACAAATA
* * * * *
112960 TACACGTGAAACTTTAATTGTGTTTCAAATA
1 TATACATGAAATTTTAATT-TGATACAAATA
*
112991 TATACTTGAAATTTTAAT
1 TATACATGAAATTTTAAT
113009 ATTTGATTTA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 6 0.16
30 9 0.24
31 23 0.61
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (30 bp):
TATACATGAAATTTTAATTTGATACAAATA
Found at i:115840 original size:27 final size:28
Alignment explanation
Indices: 115797--115863 Score: 93
Period size: 27 Copynumber: 2.5 Consensus size: 28
115787 GAGATTGACA
115797 AGCAGACTAT-TTGGTGAACAGGTGATT
1 AGCAGACTATCTTGGTGAACAGGTGATT
* *
115824 GGCAGACTATCTT-GTGAATAGGTGATT
1 AGCAGACTATCTTGGTGAACAGGTGATT
*
115851 AGCGGACTATCTT
1 AGCAGACTATCTT
115864 ACCAACGAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 33 0.94
28 2 0.06
ACGTcount: A:0.27, C:0.13, G:0.28, T:0.31
Consensus pattern (28 bp):
AGCAGACTATCTTGGTGAACAGGTGATT
Found at i:128817 original size:21 final size:22
Alignment explanation
Indices: 128772--128831 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
128762 GATCTAAGTA
*
128772 AAAATAAATG-AAATAGAATCG
1 AAAATAAAAGAAAATAGAATCG
*
128793 AAAATAAAAGAAAATAGAAT-T
1 AAAATAAAAGAAAATAGAATCG
*
128814 AAAAGAAATAGAAAATAG
1 AAAATAAA-AGAAAATAG
128832 GGAAGTCGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.47
22 18 0.53
ACGTcount: A:0.68, C:0.02, G:0.13, T:0.17
Consensus pattern (22 bp):
AAAATAAAAGAAAATAGAATCG
Found at i:128822 original size:15 final size:16
Alignment explanation
Indices: 128797--128826 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
128787 GAATCGAAAA
128797 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
128813 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
128827 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:131861 original size:24 final size:24
Alignment explanation
Indices: 131834--131892 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
131824 TTTAGTTTAC
131834 ACGAGCCCAAAATGATTAGCTCTT
1 ACGAGCCCAAAATGATTAGCTCTT
* * *
131858 ACGAGCTCAGAATGGTTAGCTCTT
1 ACGAGCCCAAAATGATTAGCTCTT
131882 ACGAGCCCAAA
1 ACGAGCCCAAA
131893 CAGAGTTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.22
Consensus pattern (24 bp):
ACGAGCCCAAAATGATTAGCTCTT
Found at i:136911 original size:43 final size:43
Alignment explanation
Indices: 136853--137008 Score: 195
Period size: 43 Copynumber: 3.6 Consensus size: 43
136843 TTTATGGGGG
*
136853 AAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTATGGTAA
1 AAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGTAA
* * * * * * *
136896 AAGTGTCGCTGAAGACCATGGTCTTTAGCGTCATTTGTTGTAA
1 AAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGTAA
* * * **
136939 AAGCACCGCTAAAGACCATATTCTTTAACGGCGTTTGTGGGGA
1 AAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGTAA
136982 AAGCGCCGCTAAAGACCATGTTCTTTA
1 AAGCGCCGCTAAAGACCATGTTCTTTA
137009 AATATTAAAG
Statistics
Matches: 91, Mismatches: 22, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 91 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (43 bp):
AAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTGGTAA
Found at i:140067 original size:22 final size:23
Alignment explanation
Indices: 140030--140072 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
140020 TAGAGTTATT
140030 ATTTTAGAAATTAATTAGATTTG
1 ATTTTAGAAATTAATTAGATTTG
*
140053 ATTTTA-AATTTAATTAGATT
1 ATTTTAGAAATTAATTAGATT
140073 CTAATAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (23 bp):
ATTTTAGAAATTAATTAGATTTG
Found at i:145167 original size:2 final size:2
Alignment explanation
Indices: 145160--145191 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
145150 AAGACACCCT
145160 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
145192 GGACATAAAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:148185 original size:18 final size:18
Alignment explanation
Indices: 148162--148200 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
148152 TTAGTAATGC
148162 TTTTGTCTCAAAAGTGAT
1 TTTTGTCTCAAAAGTGAT
* *
148180 TTTTGTCTCAAGAGTGCT
1 TTTTGTCTCAAAAGTGAT
148198 TTT
1 TTT
148201 GAGAAGCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.49
Consensus pattern (18 bp):
TTTTGTCTCAAAAGTGAT
Found at i:175155 original size:20 final size:19
Alignment explanation
Indices: 175089--175180 Score: 80
Period size: 20 Copynumber: 4.5 Consensus size: 19
175079 AAAAAATTAT
*
175089 ATTTTTTAGAATT-TTTATA
1 ATTTTTTAAAATTATTT-TA
175108 ATTTTTTAAAAATATAAATTTTA
1 ATTTTTT-AAAAT-T--ATTTTA
175131 ATTTTTTATAAA-TATTTTGA
1 ATTTTTTA-AAATTATTTT-A
*
175151 ATTTTTGAAAATTATTTTCA
1 ATTTTTTAAAATTATTTT-A
175171 ATTTTTTAAA
1 ATTTTTTAAA
175181 TTTTTTTTGA
Statistics
Matches: 61, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
19 15 0.25
20 28 0.46
21 2 0.03
22 1 0.02
23 12 0.20
24 3 0.05
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (19 bp):
ATTTTTTAAAATTATTTTA
Found at i:175173 original size:10 final size:9
Alignment explanation
Indices: 175126--175186 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
175116 AAAATATAAA
*
175126 TTTTAATTT
1 TTTTAAATT
*
175135 TTTATAAATA
1 TTT-TAAATT
*
175145 TTTTGAATT
1 TTTTAAATT
*
175154 TTTGAAAATT
1 TTT-TAAATT
*
175164 ATTTTCAATT
1 -TTTTAAATT
175174 TTTTAAATT
1 TTTTAAATT
175183 TTTT
1 TTTT
175187 TTGAGGGAGA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
9 22 0.55
10 15 0.38
11 3 0.08
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (9 bp):
TTTTAAATT
Found at i:185382 original size:59 final size:59
Alignment explanation
Indices: 185309--185471 Score: 240
Period size: 59 Copynumber: 2.8 Consensus size: 59
185299 TCTTGGGGTC
*
185309 AAAAATGAAATTTTTAGAAGTTTGGGGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTT
1 AAAAATGGAATTTTTAGAAGTTTGGGGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTT
* *
185368 AAAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGTGATTTTTGGAAGTTTCGAGGTT
1 AAAAATGGAATTTTTAGAAGTTTGGGGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTT
* * *
185427 -AAAATGGAA-TTTTAGATAAGTTTAGGGGTCAAAATATAATTTTTG
1 AAAAATGGAATTTTTAG--AAGTTTGGGGGTAAAAATGTAATTTTTG
185472 AATAGTTTAG
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
57 5 0.05
58 9 0.10
59 80 0.85
ACGTcount: A:0.35, C:0.02, G:0.26, T:0.37
Consensus pattern (59 bp):
AAAAATGGAATTTTTAGAAGTTTGGGGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTT
Found at i:185461 original size:30 final size:29
Alignment explanation
Indices: 185303--185483 Score: 166
Period size: 29 Copynumber: 6.1 Consensus size: 29
185293 GGAAAATCTT
* * *
185303 GGGGTCAAAAATGAAATTTTTAGAAGTTTG
1 GGGGT-AAAAATGGAATTTTTGGAAGTTTA
* *
185333 GGGGTAAAAATGTAATTTTTGGAAGTTTC
1 GGGGTAAAAATGGAATTTTTGGAAGTTTA
* *
185362 GAGGTTAAAAATGGAATTTTTGGAAGTTTG
1 G-GGGTAAAAATGGAATTTTTGGAAGTTTA
*
185392 GGGGTAAAAATGTG-ATTTTTGGAAGTTTC
1 GGGGTAAAAATG-GAATTTTTGGAAGTTTA
* * * *
185421 GAGGTTAAAATGGAATTTTAGATAAGTTTA
1 GGGGTAAAAATGGAATTTTTG-GAAGTTTA
* ** *
185451 GGGGTCAAAATATAATTTTTGAATAGTTTA
1 GGGGTAAAAATGGAATTTTTGGA-AGTTTA
185481 GGG
1 GGG
185484 ACCTTCAAGG
Statistics
Matches: 127, Mismatches: 19, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
28 1 0.01
29 63 0.50
30 63 0.50
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTTA
Found at i:187401 original size:6 final size:6
Alignment explanation
Indices: 187390--187461 Score: 53
Period size: 6 Copynumber: 12.7 Consensus size: 6
187380 TATAATAAGT
* * * *
187390 TTTAAA TTTAAA TATGAA TCTAAA TTTATA -TTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
187437 --AAAA ATTAAA TTTAAA -ATAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA
187462 TATTCAAAAT
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
4 3 0.06
5 8 0.16
6 39 0.78
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (6 bp):
TTTAAA
Found at i:187426 original size:11 final size:11
Alignment explanation
Indices: 187390--187461 Score: 56
Period size: 11 Copynumber: 6.4 Consensus size: 11
187380 TATAATAAGT
187390 TTTAAATTTAAA
1 TTTAAA-TTAAA
* *
187402 TATGAATCTAAA
1 TTTAAAT-TAAA
*
187414 TTTATATTAAA
1 TTTAAATTAAA
187425 TTTAAATTTAAA
1 TTTAAA-TTAAA
**
187437 -AAAAATTAAA
1 TTTAAATTAAA
*
187447 TTTAAAATAAA
1 TTTAAATTAAA
187458 TTTA
1 TTTA
187462 TATTCAAAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
10 5 0.11
11 24 0.52
12 17 0.37
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:187432 original size:17 final size:17
Alignment explanation
Indices: 187390--187494 Score: 104
Period size: 17 Copynumber: 6.2 Consensus size: 17
187380 TATAATAAGT
*
187390 TTTAAATTTAAATATGAA
1 TTTAAATTTAAA-ATAAA
* * *
187408 TCTAAATTTATATTAAA
1 TTTAAATTTAAAATAAA
187425 TTTAAATTTAAAA-AAA
1 TTTAAATTTAAAATAAA
*
187441 ATTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
187458 TTTATATTCAAAATAAA
1 TTTAAATTTAAAATAAA
***
187475 TTTAGCCTTAAAATAAA
1 TTTAAATTTAAAATAAA
187492 TTT
1 TTT
187495 TAGAATGAGT
Statistics
Matches: 71, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
16 15 0.21
17 46 0.65
18 10 0.14
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:187447 original size:16 final size:16
Alignment explanation
Indices: 187426--187459 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
187416 TATATTAAAT
187426 TTAAATTTAAAAAAAA
1 TTAAATTTAAAAAAAA
*
187442 TTAAATTTAAAATAAA
1 TTAAATTTAAAAAAAA
187458 TT
1 TT
187460 TATATTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAATTTAAAAAAAA
Found at i:188296 original size:207 final size:200
Alignment explanation
Indices: 187894--188431 Score: 682
Period size: 207 Copynumber: 2.6 Consensus size: 200
187884 CCGCTTCTTT
* * * *
187894 GTATCTCATTAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAAGAAGT
1 GTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGC
* * * * *
187959 TGGGATTCGAAGATTTACTCACATCGAGCCCTGAGTTGGTATACTTCTCTGTATCTCATCAGGAA
66 TGGGGTTCGAAGATTTGCTCACTTTGAG-CCTGAGTTGGTATACTTCTCAGTATCTCATCAGGAA
* * * * * * **
188024 GATGACGACCTCACTTGTTTCAATCTGCTTTTCTGTATTTCATCAGGAAGATGAATTTAGTCCAC
130 GATGACGACATCACTTGCTTCAATCCGCTTCTCTGTATCTCATCAAGAAGACAAATTTAGTCCAC
188089 TTCTCA
195 TTCTCA
* * * * * *
188095 GTGTCTTATCAGGAAGCTAACCTTTTTATCGCTTCGTCTTGCTTCTCAGTATCTCATCAGGAAGC
1 GTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGC
* * *
188160 TGGGGTTCGAAGATTTGCTCGCTTTGAGCCTGGATTTGATTTTGGTCTTCTTCTCAGTATCTCAT
66 TGGGGTTCGAAGATTTGCTCACTTTGAGCCT-GA---G---TTGGTATACTTCTCAGTATCTCAT
*
188225 CAGGAAGATGACTG-CATCGCTTGCTTCAATCCGCTTCTCTGTATCTCATCAAGAAGACAAATTT
124 CAGGAAGATGAC-GACATCACTTGCTTCAATCCGCTTCTCTGTATCTCATCAAGAAGACAAATTT
*
188289 GGTCCACTTCTCA
188 AGTCCACTTCTCA
*
188302 GTATCTCATCAGGAAGCTGACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGC
1 GTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGC
* * **
188367 TGAGGTTTGAAGATTTGCTCACTTTGAGCCTTGAGTTGGTATACTTCTTTGTATCTCATCAGGAA
66 TGGGGTTCGAAGATTTGCTCACTTTGAGCC-TGAGTTGGTATACTTCTCAGTATCTCATCAGGAA
188432 AACAAATTTG
Statistics
Matches: 286, Mismatches: 42, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
200 3 0.01
201 106 0.37
204 2 0.01
207 173 0.60
208 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (200 bp):
GTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGC
TGGGGTTCGAAGATTTGCTCACTTTGAGCCTGAGTTGGTATACTTCTCAGTATCTCATCAGGAAG
ATGACGACATCACTTGCTTCAATCCGCTTCTCTGTATCTCATCAAGAAGACAAATTTAGTCCACT
TCTCA
Found at i:188549 original size:151 final size:152
Alignment explanation
Indices: 188258--188579 Score: 529
Period size: 151 Copynumber: 2.1 Consensus size: 152
188248 CTTCAATCCG
* * *
188258 CTTCTCTGTATCTCATCAAGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTGAC
1 CTTCTCTGTATCTCATCAGGAAAACAAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTGAC
* * *
188323 CATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTTGAAGATTTGCTCA
66 CATTTTATTGCTTCGACCTACTTCTCAGTATATCATCAGGAAGCTGAGGTTCGAAGATTTGCTCA
*
188388 CTTTGAGCCTTGAGTTGGTATA
131 CTTTGAGCCTTGAGTTGATATA
*
188410 CTTCTTTGTATCTCATCAGGAAAACAAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTGAC
1 CTTCTCTGTATCTCATCAGGAAAACAAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTGAC
* * *
188475 C-TTTTTTTGCTTCGACCTACTTCTCAGTATATTATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
66 CATTTTATTGCTTCGACCTACTTCTCAGTATATCATCAGGAAGCTGAGGTTCGAAGATTTGCTCA
188539 CTTTGAGCCTTGAGTTGATATA
131 CTTTGAGCCTTGAGTTGATATA
*
188561 CTTCTCCGTATCTCATCAG
1 CTTCTCTGTATCTCATCAG
188580 AAAGATAACC
Statistics
Matches: 157, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
151 95 0.61
152 62 0.39
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.36
Consensus pattern (152 bp):
CTTCTCTGTATCTCATCAGGAAAACAAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTGAC
CATTTTATTGCTTCGACCTACTTCTCAGTATATCATCAGGAAGCTGAGGTTCGAAGATTTGCTCA
CTTTGAGCCTTGAGTTGATATA
Found at i:193780 original size:6 final size:6
Alignment explanation
Indices: 193769--193812 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
193759 TATAATAAGT
* * *
193769 TTTAAA TTTAAA TATAAA TCTAAA TTT-AT TTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
193813 TATATTCAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:193814 original size:18 final size:18
Alignment explanation
Indices: 193769--193815 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
193759 TATAATAAGT
* *
193769 TTTAAATTTAAATATAAA
1 TTTAAATTTTATTATAAA
* *
193787 TCTAAA-TTTATTTTAAA
1 TTTAAATTTTATTATAAA
193804 TTTAAATTTTAT
1 TTTAAATTTTAT
193816 ATTCAAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAAATTTTATTATAAA
Found at i:193827 original size:18 final size:17
Alignment explanation
Indices: 193806--193849 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
193796 ATTTTAAATT
*
193806 TAAATTTTATATTCAAAA
1 TAAATTTTACATT-AAAA
* *
193824 TAAATTTAACCTTAAAA
1 TAAATTTTACATTAAAA
193841 TAAATTTTA
1 TAAATTTTA
193850 GAATGAGTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTTACATTAAAA
Found at i:197806 original size:78 final size:79
Alignment explanation
Indices: 197719--197884 Score: 266
Period size: 77 Copynumber: 2.1 Consensus size: 79
197709 AAGTGAAAAG
*
197719 ATATATATATGGGGAAAAATAATACTTTTTGCATTTTTTTA-CAACATGACAATTTTTAGTTGAT
1 ATATATATAT-AGGAAAAATAATACTTTTTGCATTTTTTTATC-ACATGACAATTTTTAGTTGAT
*
197783 T-ATTTTTTATTATA-
64 TAATTTTTTATAATAT
*
197797 ATATATATATATGAAAAATAATACTTTTTGCATTTTTTTATCACATGACAATTTTTAGTTGATTA
1 ATATATATATAGGAAAAATAATACTTTTTGCATTTTTTTATCACATGACAATTTTTAGTTGATTA
197862 ATTTTTTATAATAT
66 ATTTTTTATAATAT
197876 ATATATATA
1 ATATATATA
197885 GACTTAAAAA
Statistics
Matches: 82, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
77 50 0.61
78 23 0.28
79 9 0.11
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.49
Consensus pattern (79 bp):
ATATATATATAGGAAAAATAATACTTTTTGCATTTTTTTATCACATGACAATTTTTAGTTGATTA
ATTTTTTATAATAT
Found at i:198678 original size:12 final size:12
Alignment explanation
Indices: 198663--198704 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
198653 ATTCAATTAT
*
198663 ATGTTCATGAAC
1 ATGTTCGTGAAC
**
198675 ATGTTCGTTTA-
1 ATGTTCGTGAAC
198686 ATGTTCGTGAAC
1 ATGTTCGTGAAC
198698 ATGTTCG
1 ATGTTCG
198705 ATTAACTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.40
Consensus pattern (12 bp):
ATGTTCGTGAAC
Found at i:198696 original size:23 final size:23
Alignment explanation
Indices: 198640--198709 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
198630 TCATTAACAT
* *
198640 TGTTCGTGAACATATTCAATTATA
1 TGTTCGTGAACATGTTCGATTA-A
* *
198664 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCGATTAA
198687 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCGATTAA
198710 CTTAAATGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 22 0.55
24 18 0.45
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCGATTAA
Found at i:198737 original size:23 final size:23
Alignment explanation
Indices: 198693--198738 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
198683 TTAATGTTCG
* *
198693 TGAACATGTTCGATTAACTTAAA
1 TGAACATGCTCGATGAACTTAAA
198716 TGAACATGCTCG-TGAACATTAAA
1 TGAACATGCTCGATGAAC-TTAAA
198739 CAAACAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (23 bp):
TGAACATGCTCGATGAACTTAAA
Found at i:201730 original size:31 final size:30
Alignment explanation
Indices: 201657--201728 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
201647 TTTAGAAAAT
* *
201657 TTTTAAAATATT-AATTATTTTATATATAT
1 TTTTAAAATTTTAAATTATTTTATATATAA
*
201686 TTTTAGAAATTTTAAATTTTTTTA-ATATAAA
1 TTTTA-AAATTTTAAATTATTTTATATAT-AA
201717 TTTTAAAATTTT
1 TTTTAAAATTTT
201729 TATAAATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 5 0.14
30 17 0.46
31 15 0.41
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (30 bp):
TTTTAAAATTTTAAATTATTTTATATATAA
Found at i:201739 original size:20 final size:20
Alignment explanation
Indices: 201694--201767 Score: 64
Period size: 23 Copynumber: 3.6 Consensus size: 20
201684 ATTTTTAGAA
*
201694 ATTTT-AAATTTTTTTAATAT
1 ATTTTAAAATTTTTATAA-AT
201714 AAATTTTAAAATTTTTATAAAT
1 --ATTTTAAAATTTTTATAAAT
* *
201736 ATTTTGAAA--TTTAAAAATT
1 ATTTTAAAATTTTTATAAA-T
201755 ATTTTAAAATTTT
1 ATTTTAAAATTTT
201768 GAAATTTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
18 7 0.16
19 9 0.20
20 8 0.18
21 2 0.05
22 7 0.16
23 11 0.25
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (20 bp):
ATTTTAAAATTTTTATAAAT
Found at i:201748 original size:18 final size:19
Alignment explanation
Indices: 201716--201766 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
201706 TTTAATATAA
*
201716 ATTTTAAAATTTTTATAAA-T
1 ATTTTAAAA--TTTAAAAATT
*
201736 ATTTTGAAATTTAAAAATT
1 ATTTTAAAATTTAAAAATT
201755 ATTTTAAAATTT
1 ATTTTAAAATTT
201767 TGAAATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 7 0.26
19 12 0.44
20 8 0.30
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
ATTTTAAAATTTAAAAATT
Found at i:201766 original size:27 final size:28
Alignment explanation
Indices: 201714--201775 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
201704 TTTTTAATAT
*
201714 AAATTTTAAAATTTTTATAAATATTTTG
1 AAATTTAAAAATTTTTATAAATATTTTG
201742 AAATTTAAAAATTATTT-TAAA-ATTTTG
1 AAATTTAAAAATT-TTTATAAATATTTTG
201769 AAATTTA
1 AAATTTA
201776 TTTTGCGCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 13 0.41
28 16 0.50
29 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (28 bp):
AAATTTAAAAATTTTTATAAATATTTTG
Found at i:201778 original size:20 final size:19
Alignment explanation
Indices: 201716--201779 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
201706 TTTAATATAA
201716 ATTTTAAAATTTTTATAAA-T
1 ATTTTAAAA-TTTTA-AAATT
* *
201736 ATTTTGAAATTTAAAAATT
1 ATTTTAAAATTTTAAAATT
*
201755 ATTTTAAAATTTTGAAATTT
1 ATTTTAAAATTTT-AAAATT
201775 ATTTT
1 ATTTT
201780 GCGCTCATGT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
18 3 0.08
19 16 0.43
20 18 0.49
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
ATTTTAAAATTTTAAAATT
Found at i:206740 original size:2 final size:2
Alignment explanation
Indices: 206733--206758 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
206723 AAAATTTTAA
206733 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
206759 TTTTATGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:209138 original size:2 final size:2
Alignment explanation
Indices: 209131--209159 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
209121 ATTAAAACAC
209131 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 T
209160 TGAAAATGTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:224844 original size:24 final size:22
Alignment explanation
Indices: 224801--224844 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 22
224791 ATAAATTTTA
224801 AAATTTTAAAAGTAAAATAACC
1 AAATTTTAAAAGTAAAATAACC
224823 AAATTCTTGAAAA-TAAAGATAA
1 AAATT-TT-AAAAGTAAA-ATAA
224845 AGAAACTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.26
23 6 0.32
24 8 0.42
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (22 bp):
AAATTTTAAAAGTAAAATAACC
Found at i:255112 original size:29 final size:27
Alignment explanation
Indices: 255064--255117 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
255054 TTTTAACATA
*
255064 ATAAAAATTTTCAAAATTATATAAATT
1 ATAAAAATTTTAAAAATTATATAAATT
*
255091 ATAAAAATATTGTAAAAATTATGTAAA
1 ATAAAAAT-TT-TAAAAATTATATAAA
255118 ATGTTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.35
28 2 0.09
29 13 0.57
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (27 bp):
ATAAAAATTTTAAAAATTATATAAATT
Found at i:255170 original size:2 final size:2
Alignment explanation
Indices: 255165--255191 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
255155 ACTTATTATC
255165 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 A
255192 CTATTATTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:259807 original size:22 final size:21
Alignment explanation
Indices: 259779--259821 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
259769 TCAAGCATAG
*
259779 CTGTCAAATATGTTGTAGATAT
1 CTGTCAAATA-GCTGTAGATAT
*
259801 CTGTCAAGTAGCTGTAGATAT
1 CTGTCAAATAGCTGTAGATAT
259822 ATATTTTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (21 bp):
CTGTCAAATAGCTGTAGATAT
Found at i:260882 original size:15 final size:14
Alignment explanation
Indices: 260858--260899 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
260848 CCCATTCATT
260858 AGGGTTAGGGTTTA
1 AGGGTTAGGGTTTA
*
260872 GAGGGTGAGGGTTTA
1 -AGGGTTAGGGTTTA
*
260887 AGAGTTAGGGTTT
1 AGGGTTAGGGTTT
260900 GATTTAGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.21, C:0.00, G:0.45, T:0.33
Consensus pattern (14 bp):
AGGGTTAGGGTTTA
Found at i:261423 original size:15 final size:17
Alignment explanation
Indices: 261396--261428 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
261386 TCCAAATTTT
261396 AAATTTAATTTTA-CAA
1 AAATTTAATTTTATCAA
261412 AAATTT-ATTTTATCAA
1 AAATTTAATTTTATCAA
261428 A
1 A
261429 TGTTTGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATTTAATTTTATCAA
Found at i:267285 original size:26 final size:27
Alignment explanation
Indices: 267265--267430 Score: 77
Period size: 30 Copynumber: 5.6 Consensus size: 27
267255 ATTTTTTCCT
*
267265 AATTTGGTACTTAAATTTTTTTGACTC
1 AATTTGGTACCTAAATTTTTTTGACTC
267292 AATTTGGTACCTAAACTTGACACTTTTT--C-C
1 AATTTGGTACCTAAA-TT-----TTTTTGACTC
* *
267322 TATTTGGTACCTAAACTTTTTTTGGACCC
1 AATTTGGTACCTAAA-TTTTTTT-GACTC
* ** *
267351 AATTTGGTATCTAAACTTGGCATTTTTTCCCC
1 AATTTGGTACCTAAA-TT----TTTTTGACTC
* *
267383 TAATTTAGTACCTAAACTTTTTTTTAGATTC
1 -AATTTGGTACCTAAA--TTTTTTT-GACTC
267414 AATTTGGTACCTAAATT
1 AATTTGGTACCTAAATT
267431 GTGTAGAATT
Statistics
Matches: 108, Mismatches: 14, Indels: 33
0.70 0.09 0.21
Matches are distributed among these distances:
25 5 0.05
27 14 0.13
28 5 0.05
29 17 0.16
30 37 0.34
31 2 0.02
32 3 0.03
33 23 0.21
34 2 0.02
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (27 bp):
AATTTGGTACCTAAATTTTTTTGACTC
Found at i:267357 original size:59 final size:59
Alignment explanation
Indices: 267257--267428 Score: 222
Period size: 59 Copynumber: 2.9 Consensus size: 59
267247 AGCTTGATAT
*
267257 TTTTTCCTAATTTGGTACTTAAA-TTTTTTTGACTCAATTTGGTACCTAAACTTGACAC
1 TTTTTCCTAATTTGGTACCTAAACTTTTTTTGACTCAATTTGGTACCTAAACTTGACAC
* * * *
267315 TTTTTCCT-ATTTGGTACCTAAACTTTTTTTGGACCCAATTTGGTATCTAAACTTGGCAT
1 TTTTTCCTAATTTGGTACCTAAACTTTTTTT-GACTCAATTTGGTACCTAAACTTGACAC
* *
267374 TTTTTCCCCTAATTTAGTACCTAAACTTTTTTTTAGATTCAATTTGGTACCTAAA
1 TTTTT--CCTAATTTGGTACCTAAAC-TTTTTTT-GACTCAATTTGGTACCTAAA
267429 TTGTGTAGAA
Statistics
Matches: 98, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
57 13 0.13
58 15 0.15
59 29 0.30
61 3 0.03
62 14 0.14
63 24 0.24
ACGTcount: A:0.25, C:0.18, G:0.10, T:0.47
Consensus pattern (59 bp):
TTTTTCCTAATTTGGTACCTAAACTTTTTTTGACTCAATTTGGTACCTAAACTTGACAC
Found at i:268672 original size:12 final size:13
Alignment explanation
Indices: 268641--268678 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
268631 TACCTGCAAA
268641 AAAGAGCAAAGAAC
1 AAAG-GCAAAGAAC
*
268655 ATAGGCAAA-AAC
1 AAAGGCAAAGAAC
268667 AAAGGCAAAGAA
1 AAAGGCAAAGAA
268679 ACAGAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 11 0.52
13 7 0.33
14 3 0.14
ACGTcount: A:0.63, C:0.13, G:0.21, T:0.03
Consensus pattern (13 bp):
AAAGGCAAAGAAC
Found at i:269943 original size:30 final size:30
Alignment explanation
Indices: 269817--269947 Score: 142
Period size: 30 Copynumber: 4.4 Consensus size: 30
269807 AAGAGGTCCC
* *
269817 AAAC-TTTCCAAAATTACA-TTTGACCCTT
1 AAACTTTTCCAAAATTACATTTTAACCCCT
* * *
269845 AAACTTTT-AAAAATATATATTTTAACCACT
1 AAACTTTTCCAAAAT-TACATTTTAACCCCT
* * *
269875 AAACTTCTCTAAAATTACATTTTAACCCTT
1 AAACTTTTCCAAAATTACATTTTAACCCCT
* *
269905 AAAATTTTCCAAAATTACATTTTGACCCCT
1 AAACTTTTCCAAAATTACATTTTAACCCCT
269935 AAACTTTTCCAAA
1 AAACTTTTCCAAA
269948 CTTTTCCAAA
Statistics
Matches: 83, Mismatches: 16, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
28 9 0.11
29 6 0.07
30 63 0.76
31 5 0.06
ACGTcount: A:0.40, C:0.21, G:0.02, T:0.37
Consensus pattern (30 bp):
AAACTTTTCCAAAATTACATTTTAACCCCT
Found at i:269985 original size:39 final size:40
Alignment explanation
Indices: 269909--269986 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
269899 ACCCTTAAAA
* *
269909 TTTTCCAAAATTACATTTTGACCCCTAAACTTTTCCAAAC
1 TTTTCCAAAATTACATTTTGAACCCTAAAATTTTCCAAAC
269949 TTTTCCAAAATTACATTTT-AACCCTAAAATTTTCCAAA
1 TTTTCCAAAATTACATTTTGAACCCTAAAATTTTCCAAA
269987 ATCACATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 17 0.47
40 19 0.53
ACGTcount: A:0.36, C:0.24, G:0.01, T:0.38
Consensus pattern (40 bp):
TTTTCCAAAATTACATTTTGAACCCTAAAATTTTCCAAAC
Found at i:270018 original size:99 final size:100
Alignment explanation
Indices: 269845--270026 Score: 233
Period size: 99 Copynumber: 1.8 Consensus size: 100
269835 TTTGACCCTT
* * * * *
269845 AAACTTTTAAAAATATATATTTTAACCACTAAACTTCTCTAAAATTACATTTTAACCCTTAAAAT
1 AAACTTTTAAAAATATACATTTTAACCACTAAAATTCTCCAAAATCACATTTTAACCCTCAAAAT
269910 TTTCCAAAATTACATTTTGACCCCTAAACTTTTCC
66 TTTCCAAAATTACATTTTGACCCCTAAACTTTTCC
* * * **
269945 AAACTTTTCCAAAAT-TACATTTTAACC-CTAAAATTTTCCAAAATCACATTTTAACCCTCGAGC
1 AAACTTTT-AAAAATATACATTTTAACCACTAAAATTCTCCAAAATCACATTTTAACCCTCAAAA
* *
270008 TTTTCTAAAATTTCATTTT
65 TTTTCCAAAATTACATTTT
270027 CATCCCGAGT
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
99 45 0.65
100 19 0.28
101 5 0.07
ACGTcount: A:0.37, C:0.21, G:0.02, T:0.40
Consensus pattern (100 bp):
AAACTTTTAAAAATATACATTTTAACCACTAAAATTCTCCAAAATCACATTTTAACCCTCAAAAT
TTTCCAAAATTACATTTTGACCCCTAAACTTTTCC
Found at i:270025 original size:30 final size:29
Alignment explanation
Indices: 269945--270026 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
269935 AAACTTTTCC
269945 AAACTTTTCCAAAATTACATTTTAACCCT
1 AAACTTTTCCAAAATTACATTTTAACCCT
* *
269974 AAAATTTTCCAAAATCACATTTTAACCCT
1 AAACTTTTCCAAAATTACATTTTAACCCT
* * * *
270003 CGAGCTTTTCTAAAATTTCATTTT
1 -AAACTTTTCCAAAATTACATTTT
270027 CATCCCGAGT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 27 0.61
30 17 0.39
ACGTcount: A:0.35, C:0.22, G:0.02, T:0.40
Consensus pattern (29 bp):
AAACTTTTCCAAAATTACATTTTAACCCT
Found at i:274660 original size:11 final size:11
Alignment explanation
Indices: 274644--274701 Score: 66
Period size: 11 Copynumber: 5.3 Consensus size: 11
274634 GGAGACCAAT
* *
274644 GAAAAATGAAG
1 GAAAAAAGAAA
274655 GAAAAAAGAAA
1 GAAAAAAGAAA
274666 GAAAAAAG--A
1 GAAAAAAGAAA
274675 GAAAGAAAGAAA
1 GAAA-AAAGAAA
274687 GAAAGAAAGAAA
1 GAAA-AAAGAAA
274699 GAA
1 GAA
274702 GGAAGAAGGA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
9 5 0.12
10 4 0.10
11 17 0.40
12 16 0.38
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:274668 original size:4 final size:4
Alignment explanation
Indices: 274655--274701 Score: 69
Period size: 4 Copynumber: 11.8 Consensus size: 4
274645 AAAAATGAAG
*
274655 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAA
274702 GGAAGAAGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 3 0.08
4 33 0.85
5 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:274670 original size:21 final size:21
Alignment explanation
Indices: 274655--274701 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
274645 AAAAATGAAG
274655 GAAA-AAAGAAAGAAAAAAGA
1 GAAAGAAAGAAAGAAAAAAGA
*
274675 GAAAGAAAGAAAGAAAGAA-A
1 GAAAGAAAGAAAGAAAAAAGA
274695 GAAAGAA
1 GAAAGAA
274702 GGAAGAAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAGAAAAAAGA
Done.