Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014779.1 Kokia drynarioides strain JFW-HI SEQ_129821, 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: 275255
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 455 characters in sequence are not A, C, G, or T
Found at i:3863 original size:72 final size:72
Alignment explanation
Indices: 3719--3854 Score: 200
Period size: 72 Copynumber: 1.9 Consensus size: 72
3709 GGATTTCATG
* * ***
3719 ATCGATGGCTTGAGATCTAGCATGTGTTGTGGATTCTCTAAAGCTTGTGTGAGAAACATCGAATT
1 ATCGATGGCTTGAGATCCAACATGTGTTACAGATTCTCTAAAGCTTGTGTGAGAAACATCGAATT
3784 AGTCTTT
66 AGTCTTT
* * *
3791 ATCGATGGCTTGAGATCCAACATGTGTTACAGATTCTCTGAAGCTTGTGTGAGCAGCATCGAAT
1 ATCGATGGCTTGAGATCCAACATGTGTTACAGATTCTCTAAAGCTTGTGTGAGAAACATCGAAT
3855 CGTTCTTTAG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
72 56 1.00
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (72 bp):
ATCGATGGCTTGAGATCCAACATGTGTTACAGATTCTCTAAAGCTTGTGTGAGAAACATCGAATT
AGTCTTT
Found at i:4658 original size:23 final size:23
Alignment explanation
Indices: 4609--4658 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
4599 TATAAAAATA
*
4609 AATTAAGTTGTACTTGTCCTGGT
1 AATTAAGTTGTACTTGTCCTGGC
4632 AATTAAGTTGTACTTGT-CTGTGC
1 AATTAAGTTGTACTTGTCCTG-GC
4655 AATT
1 AATT
4659 TTCTTTATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (23 bp):
AATTAAGTTGTACTTGTCCTGGC
Found at i:5038 original size:31 final size:32
Alignment explanation
Indices: 4994--5064 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 32
4984 GAATTAATTA
* * * *
4994 AATTGAATTATTTAACTTCTTAAG-TTAATTCG
1 AATTAAATAATTTAAATT-TTAAGTTTAAATCG
5026 AA-TAAATAATTTAAATTTTAAGTTTAAATCG
1 AATTAAATAATTTAAATTTTAAGTTTAAATCG
5057 AATTAAAT
1 AATTAAAT
5065 TTTATTATTC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 5 0.15
31 21 0.64
32 7 0.21
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.44
Consensus pattern (32 bp):
AATTAAATAATTTAAATTTTAAGTTTAAATCG
Found at i:6937 original size:28 final size:28
Alignment explanation
Indices: 6897--6984 Score: 176
Period size: 28 Copynumber: 3.1 Consensus size: 28
6887 ATGGGAATCC
6897 CTTTGTCTTGCCATACTGTTGCTTTTAT
1 CTTTGTCTTGCCATACTGTTGCTTTTAT
6925 CTTTGTCTTGCCATACTGTTGCTTTTAT
1 CTTTGTCTTGCCATACTGTTGCTTTTAT
6953 CTTTGTCTTGCCATACTGTTGCTTTTAT
1 CTTTGTCTTGCCATACTGTTGCTTTTAT
6981 CTTT
1 CTTT
6985 CTCAATAGAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 60 1.00
ACGTcount: A:0.10, C:0.22, G:0.14, T:0.55
Consensus pattern (28 bp):
CTTTGTCTTGCCATACTGTTGCTTTTAT
Found at i:13102 original size:36 final size:36
Alignment explanation
Indices: 13055--13126 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
13045 CCCAACTAAC
*
13055 CTTAGCCGAATTTTATAAGGTGTTTATCCCACTCCT
1 CTTAGCCGAATTCTATAAGGTGTTTATCCCACTCCT
* * * *
13091 CTTAGTCGAATTCTCTTAGGTGTTTATCCTACTCCT
1 CTTAGCCGAATTCTATAAGGTGTTTATCCCACTCCT
13127 TTACACATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.42
Consensus pattern (36 bp):
CTTAGCCGAATTCTATAAGGTGTTTATCCCACTCCT
Found at i:13581 original size:21 final size:22
Alignment explanation
Indices: 13557--13599 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
13547 ACTCTTATCA
13557 TTAAGCTTAATT-AACCCATTT
1 TTAAGCTTAATTAAACCCATTT
*
13578 TTAATCTTAATTAAACCCATTT
1 TTAAGCTTAATTAAACCCATTT
13600 ATACTTAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.35, C:0.19, G:0.02, T:0.44
Consensus pattern (22 bp):
TTAAGCTTAATTAAACCCATTT
Found at i:15817 original size:24 final size:24
Alignment explanation
Indices: 15769--15836 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 24
15759 ATGAAAAATA
15769 TAAAATATCAAGAATAATAGAAATTCATT
1 TAAAATAT-AA-AA-AATAGAAATT--TT
15798 TAAAA-ATAAAAAATA-AAATTTT
1 TAAAATATAAAAAATAGAAATTTT
15820 TAAAATTATAAAAAATA
1 TAAAA-TATAAAAAATA
15837 TTAAAAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
22 7 0.19
24 15 0.41
25 4 0.11
26 2 0.05
27 2 0.05
28 2 0.05
29 5 0.14
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (24 bp):
TAAAATATAAAAAATAGAAATTTT
Found at i:16753 original size:4 final size:4
Alignment explanation
Indices: 16744--16800 Score: 51
Period size: 4 Copynumber: 14.2 Consensus size: 4
16734 AGGTATAAAC
* * * * * *
16744 ATAT ATAT ATAC ATAC ATAT ACAT ATGT ATAT GTAT GTAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
16792 ATGT ATAT A
1 ATAT ATAT A
16801 AATTATTCCA
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (4 bp):
ATAT
Found at i:16794 original size:14 final size:14
Alignment explanation
Indices: 16771--16800 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
16761 TATACATATG
*
16771 TATATGTATGTATA
1 TATATATATGTATA
16785 TATATATATGTATA
1 TATATATATGTATA
16799 TA
1 TA
16801 AATTATTCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (14 bp):
TATATATATGTATA
Found at i:17338 original size:37 final size:39
Alignment explanation
Indices: 17254--17345 Score: 134
Period size: 40 Copynumber: 2.4 Consensus size: 39
17244 AATGCTAAAT
* *
17254 CGTAGCTTGAAATTAGACACCGGCTTAAAGCCTTCTAAGC
1 CGTAGCTTGAAATTAGACACCGACTCAAAGCC-TCTAAGC
*
17294 CTTAGCTTGAAATTAGACACCGACTCAAAG-C-CTAAGC
1 CGTAGCTTGAAATTAGACACCGACTCAAAGCCTCTAAGC
17331 CGTAGCTTGAAATTA
1 CGTAGCTTGAAATTA
17346 TTCTAACGTC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
37 20 0.42
39 1 0.02
40 27 0.56
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (39 bp):
CGTAGCTTGAAATTAGACACCGACTCAAAGCCTCTAAGC
Found at i:23548 original size:14 final size:14
Alignment explanation
Indices: 23529--23555 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23519 GTAAAATGCT
23529 GAAAAGCTTTTACA
1 GAAAAGCTTTTACA
23543 GAAAAGCTTTTAC
1 GAAAAGCTTTTAC
23556 TGGTAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (14 bp):
GAAAAGCTTTTACA
Found at i:27791 original size:14 final size:14
Alignment explanation
Indices: 27787--27827 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
27777 TTTATATATG
27787 TATATATATGTGTA
1 TATATATATGTGTA
*
27801 TATATATGTGTGTA
1 TATATATATGTGTA
27815 TATATATATGTGT
1 TATATATATGTGT
27828 GCATATACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (14 bp):
TATATATATGTGTA
Found at i:27794 original size:12 final size:12
Alignment explanation
Indices: 27779--27844 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
27769 TATACATATT
27779 TATATATGTATA
1 TATATATGTATA
*
27791 TATATGTGTATA
1 TATATATGTATA
*
27803 TATATGTGTGTATA
1 TATA--TATGTATA
*
27817 TATATATGTGTGCA
1 TATATATGTAT--A
*
27831 TATACATGTATA
1 TATATATGTATA
27843 TA
1 TA
27845 AATCATTCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
12 23 0.51
14 22 0.49
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.47
Consensus pattern (12 bp):
TATATATGTATA
Found at i:34259 original size:21 final size:21
Alignment explanation
Indices: 34234--34273 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
34224 CAAGTATCGG
34234 TACAAGTGACAATTCTACCGA
1 TACAAGTGACAATTCTACCGA
**
34255 TACAAGTGACTCTTCTACC
1 TACAAGTGACAATTCTACC
34274 AAAACAAGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.28
Consensus pattern (21 bp):
TACAAGTGACAATTCTACCGA
Found at i:34280 original size:21 final size:21
Alignment explanation
Indices: 34235--34281 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
34225 AAGTATCGGT
* *
34235 ACAAGTGACAATTCTACCGAT
1 ACAAGTGACAATTCTACCAAA
**
34256 ACAAGTGACTCTTCTACCAAA
1 ACAAGTGACAATTCTACCAAA
34277 ACAAG
1 ACAAG
34282 CCTTACTTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.26, G:0.13, T:0.21
Consensus pattern (21 bp):
ACAAGTGACAATTCTACCAAA
Found at i:36441 original size:90 final size:90
Alignment explanation
Indices: 36333--36513 Score: 317
Period size: 90 Copynumber: 2.0 Consensus size: 90
36323 GTTACACTTG
* *
36333 TTGACCTACGATAAATTGTCGCTGCAAAATAATTCTGTCATGCCATCGTTTGGTCTTTTCCTTGT
1 TTGACCTACAATAAATTGTCGCTGCAAAATAATTCTGTCATGCCATCATTTGGTCTTTTCCTTGT
*
36398 AAATTGCAGCATTTTCATAGGCATT
66 AAATTGCAGCAATTTCATAGGCATT
* *
36423 TTGACCTGCAATAAATTGTCGCTGCAAAATAATTTTGTCATGCCATCATTTGGTCTTTTCCTTGT
1 TTGACCTACAATAAATTGTCGCTGCAAAATAATTCTGTCATGCCATCATTTGGTCTTTTCCTTGT
36488 AAATTGCAGCAATTTCATAGGCATT
66 AAATTGCAGCAATTTCATAGGCATT
36513 T
1 T
36514 CGCCTAATTT
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.39
Consensus pattern (90 bp):
TTGACCTACAATAAATTGTCGCTGCAAAATAATTCTGTCATGCCATCATTTGGTCTTTTCCTTGT
AAATTGCAGCAATTTCATAGGCATT
Found at i:46486 original size:2 final size:2
Alignment explanation
Indices: 46481--46508 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
46471 TATATATATA
46481 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
46509 CGCATAAACT
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:46977 original size:30 final size:30
Alignment explanation
Indices: 46912--46978 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
46902 CGCAAAAACG
*
46912 AGAAAAAGGGAAAATGGAAAGAAAAGTAAA
1 AGAAAAGGGGAAAATGGAAAGAAAAGTAAA
* *
46942 GGAAAAGGGGAAAGATAGTAAA-AAAA-TAAA
1 AGAAAAGGGGAAA-AT-GGAAAGAAAAGTAAA
46972 AGAAAAG
1 AGAAAAG
46979 AGAAAAATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
30 21 0.68
31 6 0.19
32 4 0.13
ACGTcount: A:0.66, C:0.00, G:0.27, T:0.07
Consensus pattern (30 bp):
AGAAAAGGGGAAAATGGAAAGAAAAGTAAA
Found at i:47266 original size:34 final size:36
Alignment explanation
Indices: 47199--47287 Score: 105
Period size: 34 Copynumber: 2.6 Consensus size: 36
47189 TAGCATTTCT
*
47199 ATAA-TTTTTATAATATTTGAAAATTCTAATTTTTA
1 ATAATTTTTTATAATATTTGAAAATTATAATTTTTA
*
47234 ATAATTTTTTATAAT-TTT-AAAATTATATTTTTTA
1 ATAATTTTTTATAATATTTGAAAATTATAATTTTTA
* *
47268 AAAATATTTTA-AATGATTTG
1 ATAATTTTTTATAAT-ATTTG
47288 CTATTATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
33 3 0.07
34 23 0.50
35 10 0.22
36 10 0.22
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.55
Consensus pattern (36 bp):
ATAATTTTTTATAATATTTGAAAATTATAATTTTTA
Found at i:50641 original size:18 final size:16
Alignment explanation
Indices: 50609--50642 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
50599 TCGCATTTTA
50609 TATTGCAGGCATTGTC
1 TATTGCAGGCATTGTC
50625 TATTAGCAGGTCATTGTC
1 TATT-GCAGG-CATTGTC
50643 AAAGGCTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 5 0.31
18 7 0.44
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.38
Consensus pattern (16 bp):
TATTGCAGGCATTGTC
Found at i:60706 original size:29 final size:30
Alignment explanation
Indices: 60663--60719 Score: 107
Period size: 29 Copynumber: 1.9 Consensus size: 30
60653 ACACGGAACT
60663 ATTTGGCTCACACAAGCTGACATTTTATGA
1 ATTTGGCTCACACAAGCTGACATTTTATGA
60693 ATTT-GCTCACACAAGCTGACATTTTAT
1 ATTTGGCTCACACAAGCTGACATTTTAT
60720 CGGAGTTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (30 bp):
ATTTGGCTCACACAAGCTGACATTTTATGA
Found at i:63807 original size:10 final size:11
Alignment explanation
Indices: 63791--63837 Score: 57
Period size: 10 Copynumber: 4.6 Consensus size: 11
63781 TTATATACTT
63791 TAATTAAACTA
1 TAATTAAACTA
*
63802 -AATTAATC-A
1 TAATTAAACTA
63811 TAATT-AA-TA
1 TAATTAAACTA
63820 TAATTAAACTA
1 TAATTAAACTA
63831 TAATTAA
1 TAATTAA
63838 CAAATCCTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
9 8 0.27
10 13 0.43
11 9 0.30
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.38
Consensus pattern (11 bp):
TAATTAAACTA
Found at i:65899 original size:56 final size:55
Alignment explanation
Indices: 65758--65996 Score: 302
Period size: 56 Copynumber: 4.3 Consensus size: 55
65748 CGCTCCGATC
* * *
65758 TACTTACATCTCAGTTAAAGCGTAATGCTATTATAGCTCGGGTAGAGCTTT-G-A
1 TACTTACGTCTCGGTTAGAGCGTAATGCTATTATAGCTCGGGTAGAGCTTTGGTA
** *
65811 TACTTACGTCTCAATTAGAGCATAATGCTATTATAGCTCGGGTAGAGCTTTGGATA
1 TACTTACGTCTCGGTTAGAGCGTAATGCTATTATAGCTCGGGTAGAGCTTTGG-TA
* * * *
65867 TACTTACGTCTCGGTTAGAGCGTAATGTTATTATAGCTCAGGAAGAGCTTTGGACA
1 TACTTACGTCTCGGTTAGAGCGTAATGCTATTATAGCTCGGGTAGAGCTTTGG-TA
* * *
65923 TACTTACGTCTCGATTAGAGCGTAATGCTATTATAGCTCGAGTAGAGCTTTGGTT
1 TACTTACGTCTCGGTTAGAGCGTAATGCTATTATAGCTCGGGTAGAGCTTTGGTA
* * *
65978 TGCCTACATCTCGGTTAGA
1 TACTTACGTCTCGGTTAGA
65997 ATGTAAGGTT
Statistics
Matches: 161, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
53 47 0.29
54 1 0.01
55 15 0.09
56 98 0.61
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (55 bp):
TACTTACGTCTCGGTTAGAGCGTAATGCTATTATAGCTCGGGTAGAGCTTTGGTA
Found at i:69174 original size:23 final size:22
Alignment explanation
Indices: 69045--69206 Score: 123
Period size: 23 Copynumber: 7.0 Consensus size: 22
69035 AGTACTTAAT
69045 AGTAAGCACACAAGTGCTGGGGAAAC
1 AGTAAGCACACAAGTGC----GAAAC
* *
69071 AGTAAGCACACACAGCGC-AATCC
1 AGTAAGCACACA-AGTGCGAA-AC
*
69094 AGTAAGCACACACAGTGC-AATC
1 AGTAAGCACACA-AGTGCGAAAC
* * *
69116 AGTAGGCGCACATAGCGC-AAATC
1 AGTAAGCACACA-AGTGCGAAA-C
*
69139 AGTAGGCACACAAGGTGCGAAAC
1 AGTAAGCACACAA-GTGCGAAAC
69162 AGTAAGCACACAAAGTGCGAAAC
1 AGTAAGCACAC-AAGTGCGAAAC
*
69185 AGTAAGAACACGAAGTGCGAAA
1 AGTAAGCACAC-AAGTGCGAAA
69207 GAGTCAGCGC
Statistics
Matches: 116, Mismatches: 14, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
22 20 0.17
23 75 0.65
24 5 0.04
26 12 0.10
27 4 0.03
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.10
Consensus pattern (22 bp):
AGTAAGCACACAAGTGCGAAAC
Found at i:76071 original size:5 final size:5
Alignment explanation
Indices: 76061--76086 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
76051 TGAGCTCCAA
76061 GTGAT GTGAT GTGAT GTGAT GTGAT G
1 GTGAT GTGAT GTGAT GTGAT GTGAT G
76087 AGAGGTCTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.42, T:0.38
Consensus pattern (5 bp):
GTGAT
Found at i:76499 original size:23 final size:22
Alignment explanation
Indices: 76387--76511 Score: 110
Period size: 23 Copynumber: 5.5 Consensus size: 22
76377 AGTGCTGGGG
76387 AAACAGTAAGCACACACAGTGC
1 AAACAGTAAGCACACACAGTGC
* * *
76409 AATCCAGTAGGCACACACAATGC
1 AA-ACAGTAAGCACACACAGTGC
* * * *
76432 AATCAGTAGGCGCACATAGTGC
1 AAACAGTAAGCACACACAGTGC
*
76454 AAATCAGTAGGCACACA-AGGTGC
1 AAA-CAGTAAGCACACACA-GTGC
76477 GAAACAGTAAGCACACGA-AGTGC
1 -AAACAGTAAGCACAC-ACAGTGC
76500 GAAACAGTAAGC
1 -AAACAGTAAGC
76512 GCGCTAGCGT
Statistics
Matches: 88, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
22 21 0.24
23 62 0.70
24 5 0.06
ACGTcount: A:0.41, C:0.24, G:0.23, T:0.12
Consensus pattern (22 bp):
AAACAGTAAGCACACACAGTGC
Found at i:80113 original size:38 final size:38
Alignment explanation
Indices: 80062--80137 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
80052 AATGTGCAAG
*
80062 TGTACACATAAAGTGACAAGTAAATGTCGAGTTATCGT
1 TGTACAAATAAAGTGACAAGTAAATGTCGAGTTATCGT
80100 TGTACAAATAAAGTGACAAGTAAATGTCGAGTTATCGT
1 TGTACAAATAAAGTGACAAGTAAATGTCGAGTTATCGT
80138 ACCCACAGGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (38 bp):
TGTACAAATAAAGTGACAAGTAAATGTCGAGTTATCGT
Found at i:83697 original size:21 final size:21
Alignment explanation
Indices: 83685--83742 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
83675 GACTTATAGG
83685 CCAAGTATCGAGACTTAATGA
1 CCAAGTATCGAGACTTAATGA
83706 CCAAGTATCGAGACTTAATGA
1 CCAAGTATCGAGACTTAATGA
*
83727 CCAAGTACCGAGACTT
1 CCAAGTATCGAGACTT
83743 GCAACCCCTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (21 bp):
CCAAGTATCGAGACTTAATGA
Found at i:87046 original size:60 final size:60
Alignment explanation
Indices: 86971--87083 Score: 199
Period size: 60 Copynumber: 1.9 Consensus size: 60
86961 GTATAATAAC
86971 AAATTCAGCCTTCAATGTTTATATAGTTTGTCATTTTGGCCTTAATTCTAAAAAAATTAT
1 AAATTCAGCCTTCAATGTTTATATAGTTTGTCATTTTGGCCTTAATTCTAAAAAAATTAT
* **
87031 AAATTTAGCCTTCAATGTTTATATAGTTTGTCATTTTGGTGTTAATTCTAAAA
1 AAATTCAGCCTTCAATGTTTATATAGTTTGTCATTTTGGCCTTAATTCTAAAA
87084 TTTTTAACAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.45
Consensus pattern (60 bp):
AAATTCAGCCTTCAATGTTTATATAGTTTGTCATTTTGGCCTTAATTCTAAAAAAATTAT
Found at i:87118 original size:8 final size:8
Alignment explanation
Indices: 87105--87129 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
87095 TTCAGTCTCA
87105 ACATTTAC
1 ACATTTAC
87113 ACATTTAC
1 ACATTTAC
87121 ACATTTAC
1 ACATTTAC
87129 A
1 A
87130 TAAATATTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (8 bp):
ACATTTAC
Found at i:93061 original size:47 final size:47
Alignment explanation
Indices: 92992--93085 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
92982 ACACCCACAG
92992 TTATGGACTTCTTTATCTGCAAAAATAAGTTACACAAAGACATCGAT
1 TTATGGACTTCTTTATCTGCAAAAATAAGTTACACAAAGACATCGAT
93039 TTATGGACTTCTTTATCTGCAAAAATAAGTTACACAAAGACATCGAT
1 TTATGGACTTCTTTATCTGCAAAAATAAGTTACACAAAGACATCGAT
93086 ATTTGTATTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (47 bp):
TTATGGACTTCTTTATCTGCAAAAATAAGTTACACAAAGACATCGAT
Found at i:98106 original size:30 final size:30
Alignment explanation
Indices: 98060--98124 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
98050 AGAACACCGT
*
98060 CACACAACAAACATGTAGCACAAACAGAAA
1 CACACAACAAAAATGTAGCACAAACAGAAA
* * *
98090 CACATAACAAAAATGTAGCACAAATAGAGA
1 CACACAACAAAAATGTAGCACAAACAGAAA
98120 CACAC
1 CACAC
98125 CTCAAATGGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.55, C:0.25, G:0.11, T:0.09
Consensus pattern (30 bp):
CACACAACAAAAATGTAGCACAAACAGAAA
Found at i:98483 original size:12 final size:13
Alignment explanation
Indices: 98455--98487 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
98445 GTTGGTAAAA
*
98455 AAAGTCAACGATC
1 AAAGTCAAAGATC
98468 AAAGTCAAAG-TC
1 AAAGTCAAAGATC
98480 AAAGTCAA
1 AAAGTCAA
98488 TGGCCAGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.52, C:0.18, G:0.15, T:0.15
Consensus pattern (13 bp):
AAAGTCAAAGATC
Found at i:101991 original size:28 final size:28
Alignment explanation
Indices: 101933--101991 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
101923 GATACTCTGA
* * **
101933 TATAGCTCGGGTAAAGCTTTGACCTGTT
1 TATAGCTCGAGTAAAGCTTTGAACTACT
* *
101961 TATAGCTCGAGTAGAGCTTTTAACTACT
1 TATAGCTCGAGTAAAGCTTTGAACTACT
101989 TAT
1 TAT
101992 GTCTCTGTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.37
Consensus pattern (28 bp):
TATAGCTCGAGTAAAGCTTTGAACTACT
Found at i:102020 original size:55 final size:55
Alignment explanation
Indices: 101960--102124 Score: 226
Period size: 55 Copynumber: 3.0 Consensus size: 55
101950 TTTGACCTGT
** * *
101960 TTATAGCTCGAGTAGAGCTTTTAACTACTTATGTCTCTGTTAGAGCATAAAGCTA
1 TTATAGCTCGAGTAGAGCTTTGGACTACTTACGTCTCTGTTAGAGCGTAAAGCTA
* *
102015 TTATAGCTCG-GTTAGAGCTTTGGACTACTTACATCTCGGTTAGAGCGTAAAGCTA
1 TTATAGCTCGAG-TAGAGCTTTGGACTACTTACGTCTCTGTTAGAGCGTAAAGCTA
* *
102070 TTATAGCTCGAATAGAGCTTTGGACTGCTTACGTCT-TGCTTAGAGCGTAAAGCTA
1 TTATAGCTCGAGTAGAGCTTTGGACTACTTACGTCTCTG-TTAGAGCGTAAAGCTA
102125 ATTCAACTTA
Statistics
Matches: 97, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
54 2 0.02
55 95 0.98
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (55 bp):
TTATAGCTCGAGTAGAGCTTTGGACTACTTACGTCTCTGTTAGAGCGTAAAGCTA
Found at i:102028 original size:27 final size:26
Alignment explanation
Indices: 101998--102088 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 26
101988 TTATGTCTCT
101998 GTTAGAGCATAAAGCTATTATAGCTCG
1 GTTAGAGC-TAAAGCTATTATAGCTCG
*** * *
102025 GTTAGAGCTTTGGACTACTTACATCTCG
1 GTTAGAGCTAAAG-CTA-TTATAGCTCG
102053 GTTAGAGCGTAAAGCTATTATAGCTCG
1 GTTAGAGC-TAAAGCTATTATAGCTCG
**
102080 AATAGAGCT
1 GTTAGAGCT
102089 TTGGACTGCT
Statistics
Matches: 49, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
26 3 0.06
27 25 0.51
28 19 0.39
29 2 0.04
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (26 bp):
GTTAGAGCTAAAGCTATTATAGCTCG
Found at i:106844 original size:30 final size:30
Alignment explanation
Indices: 106793--106849 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
106783 ACAATCCTTA
*
106793 AAATCCCAATTTAACCACAAAATTTTAATT
1 AAATCCCAATTTAACCACAAAAATTTAATT
* *
106823 AAATCTCAATTTAGTCC-CAAAAATTTA
1 AAATCCCAATTTA-ACCACAAAAATTTA
106850 CTATATTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 21 0.91
31 2 0.09
ACGTcount: A:0.46, C:0.19, G:0.02, T:0.33
Consensus pattern (30 bp):
AAATCCCAATTTAACCACAAAAATTTAATT
Found at i:109455 original size:18 final size:18
Alignment explanation
Indices: 109426--109484 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
109416 TTGGTATAAA
*
109426 AATTATCCAAATTAACCG
1 AATTACCCAAATTAACCG
* *
109444 AGTTACCCAAATTAACTG
1 AATTACCCAAATTAACCG
* *
109462 AATTACCCGATTTAACCG
1 AATTACCCAAATTAACCG
109480 AATTA
1 AATTA
109485 AAGTATTGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (18 bp):
AATTACCCAAATTAACCG
Found at i:112765 original size:22 final size:22
Alignment explanation
Indices: 112737--112791 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
112727 GATTGGGATT
112737 TTTTAGTTTTA-CTCTTTTAGAC
1 TTTTAGTTTTAGC-CTTTTAGAC
*
112759 TTTTAGTTTTAGCCTTTTAGAT
1 TTTTAGTTTTAGCCTTTTAGAC
*
112781 TTTTATTTTTA
1 TTTTAGTTTTA
112792 TTTATTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.64
Consensus pattern (22 bp):
TTTTAGTTTTAGCCTTTTAGAC
Found at i:112768 original size:14 final size:15
Alignment explanation
Indices: 112751--112783 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
112741 AGTTTTACTC
112751 TTTTAGACTTTTAG-
1 TTTTAGACTTTTAGA
*
112765 TTTTAGCCTTTTAGA
1 TTTTAGACTTTTAGA
112780 TTTT
1 TTTT
112784 TATTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.18, C:0.09, G:0.12, T:0.61
Consensus pattern (15 bp):
TTTTAGACTTTTAGA
Found at i:112914 original size:15 final size:15
Alignment explanation
Indices: 112894--112923 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
112884 GGTAGTGGGC
112894 TAATATTATATATTA
1 TAATATTATATATTA
*
112909 TAATATTATTTATTA
1 TAATATTATATATTA
112924 ATTCGATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAATATTATATATTA
Found at i:114013 original size:27 final size:27
Alignment explanation
Indices: 113975--114028 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
113965 TTCTTTGTTT
113975 AGCTATATTCACATTAGGAGAGTTATC
1 AGCTATATTCACATTAGGAGAGTTATC
114002 AGCTATATTCACATTAGGAGAGTTATC
1 AGCTATATTCACATTAGGAGAGTTATC
114029 TCCATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (27 bp):
AGCTATATTCACATTAGGAGAGTTATC
Found at i:117519 original size:19 final size:19
Alignment explanation
Indices: 117495--117532 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
117485 CACTGTCACC
117495 CACCATAATCAAATTTGTT
1 CACCATAATCAAATTTGTT
117514 CACCATAATCAAATTTGTT
1 CACCATAATCAAATTTGTT
117533 ATTAACTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (19 bp):
CACCATAATCAAATTTGTT
Found at i:117722 original size:36 final size:37
Alignment explanation
Indices: 117646--117722 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
117636 ATTTTGAAAT
* **
117646 TAAAAAATATATTAAATATAAAAATATGAATTTTTAA
1 TAAAAAATATATTAAAGATAAAAATATGAATTGATAA
*
117683 TAAAAAATATTTTAAAGA-AAAAATATGAAATTGAT-A
1 TAAAAAATATATTAAAGATAAAAATATG-AATTGATAA
117719 TAAA
1 TAAA
117723 CATAAAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 14 0.40
37 21 0.60
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (37 bp):
TAAAAAATATATTAAAGATAAAAATATGAATTGATAA
Found at i:154404 original size:27 final size:27
Alignment explanation
Indices: 154374--154437 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
154364 GTTAGGGTTT
* *
154374 TGAAATTTTTTTGAGTTTAGTGTTCTA
1 TGAAATTTTTTTGAGCTTAATGTTCTA
* *
154401 TGAAAATTTTTTGAGCTTAATGTTTTA
1 TGAAATTTTTTTGAGCTTAATGTTCTA
154428 TGGAAATTTT
1 T-GAAATTTT
154438 GTTTTGGTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
27 24 0.77
28 7 0.23
ACGTcount: A:0.27, C:0.03, G:0.17, T:0.53
Consensus pattern (27 bp):
TGAAATTTTTTTGAGCTTAATGTTCTA
Found at i:154710 original size:16 final size:16
Alignment explanation
Indices: 154657--154701 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
154647 TTTGGTTGGT
154657 TGTAATGGAATAGAAC
1 TGTAATGGAATAGAAC
* *
154673 TGTAATGTAATAAAAC
1 TGTAATGGAATAGAAC
154689 TGTAATGGAATAG
1 TGTAATGGAATAG
154702 GGCTGTAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.29
Consensus pattern (16 bp):
TGTAATGGAATAGAAC
Found at i:154785 original size:44 final size:45
Alignment explanation
Indices: 154692--154785 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 45
154682 ATAAAACTGT
* *
154692 AATGGAATAGGGCTGTAATCAATATTTCAATTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATCAATATTT-AATTGTTTGATTGAATGG
* *
154738 AATGGAATAGAGCTGTAAT-AGTATTT-TTGTGTTTGATTGAATGG
1 AATGGAATAGAGCTGTAATCAATATTTAAT-TGTTTGATTGAATGG
154782 AATG
1 AATG
154786 ATATTGTAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 18 0.42
45 6 0.14
46 18 0.42
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.38
Consensus pattern (45 bp):
AATGGAATAGAGCTGTAATCAATATTTAATTGTTTGATTGAATGG
Found at i:159418 original size:29 final size:29
Alignment explanation
Indices: 159386--159541 Score: 86
Period size: 30 Copynumber: 5.3 Consensus size: 29
159376 GGATGCCCGA
159386 GGGTAAAACAATAATTTTTAGAAGGTTCG
1 GGGTAAAACAATAATTTTTAGAAGGTTCG
* * *
159415 GGGTCAAA-AATGGAATTTTTAGACA-TTTGG
1 GGGTAAAACAAT--AATTTTTAGA-AGGTTCG
**** *
159445 GGGTAAAATGGCAATTTTTGGAAGGTTCG
1 GGGTAAAACAATAATTTTTAGAAGGTTCG
* * *
159474 GGGTTAAAC-ATGGAATTTTTAGACA-TTTAG
1 GGGTAAAACAAT--AATTTTTAGA-AGGTTCG
* * * *
159504 GGGTAAAATAGTAATTTTTGGAAGGTTTG
1 GGGTAAAACAATAATTTTTAGAAGGTTCG
159533 GGGTTAAAA
1 GGG-TAAAA
159542 ATGGAATTTT
Statistics
Matches: 93, Mismatches: 23, Indels: 21
0.68 0.17 0.15
Matches are distributed among these distances:
28 5 0.05
29 41 0.44
30 44 0.47
31 3 0.03
ACGTcount: A:0.33, C:0.05, G:0.28, T:0.33
Consensus pattern (29 bp):
GGGTAAAACAATAATTTTTAGAAGGTTCG
Found at i:159434 original size:30 final size:29
Alignment explanation
Indices: 159398--159840 Score: 263
Period size: 29 Copynumber: 15.2 Consensus size: 29
159388 GTAAAACAAT
* *
159398 AATTTTTAGAAGGTTCGGGGTCAAAAATGG
1 AATTTTTAGAAAGTTTGGGGT-AAAAATGG
*
159428 AATTTTTAGACA-TTTGGGGGT-AAAATGG
1 AATTTTTAGAAAGTTT-GGGGTAAAAATGG
* * * *
159456 CAATTTTTGGAAGGTTCGGGGTTAAACATGG
1 -AATTTTTAGAAAGTTTGGGG-TAAAAATGG
* *
159487 AATTTTTAGACA-TTTAGGGGT-AAAATAGT
1 AATTTTTAGAAAGTTT-GGGGTAAAAAT-GG
* *
159516 AATTTTTGGAAGGTTTGGGGTTAAAAATGG
1 AATTTTTAGAAAGTTTGGGG-TAAAAATGG
*
159546 AA-TTTT-GACA-TTTAGGGGT--AAATGG
1 AATTTTTAGAAAGTTT-GGGGTAAAAATGG
* *
159571 TAA-TTTTGGAAAGTTTAGGGTTAAAAAATGG
1 -AATTTTTAGAAAGTTT-GGGGT-AAAAATGG
* *
159602 AA-TTTTACAAAGTTTAGGGGTAAAAATGT
1 AATTTTTAGAAAGTTT-GGGGTAAAAATGG
** * *
159631 AATTTACAAAAAGTTTGGGATCAAAAAT-G
1 AATTTTTAGAAAGTTTGGGGT-AAAAATGG
* *
159660 AAATTTTAGAAAGTTTGAGGGTAAAAATGT
1 AATTTTTAGAAAGTTTG-GGGTAAAAATGG
*
159690 AATTTTTAGAAAGTTTGTGGTCAAAAATGG
1 AATTTTTAGAAAGTTTGGGGT-AAAAATGG
* *
159720 AA-TTTTGGAAAGTTTGGGGCCAAAAAT-G
1 AATTTTTAGAAAGTTTGGGG-TAAAAATGG
* * * * *
159748 AAATTTTGGAAACTTCGGGGTAAAAATGT
1 AATTTTTAGAAAGTTTGGGGTAAAAATGG
*** *
159777 AATTTTT-GAAA-TGTCAAGGTCAAAATGG
1 AATTTTTAGAAAGT-TTGGGGTAAAAATGG
* * **
159805 AA-TTTTGGAAAGTTCAGGGGTAAAAATAT
1 AATTTTTAGAAAGTT-TGGGGTAAAAATGG
159834 AATTTTT
1 AATTTTT
159841 GGATAGTTCA
Statistics
Matches: 325, Mismatches: 58, Indels: 60
0.73 0.13 0.14
Matches are distributed among these distances:
25 6 0.02
26 6 0.02
27 12 0.04
28 56 0.17
29 124 0.38
30 104 0.32
31 17 0.05
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (29 bp):
AATTTTTAGAAAGTTTGGGGTAAAAATGG
Found at i:159461 original size:59 final size:58
Alignment explanation
Indices: 159397--159725 Score: 312
Period size: 59 Copynumber: 5.6 Consensus size: 58
159387 GGTAAAACAA
* *
159397 TAATTTTTAGAAGGTTCGGGGTCAAAAATGGAATTTTTAGACATTTGGGGGTAAAATGG
1 TAATTTTTAGAAGGTTTGGGGTCAAAAATGGAATTTTTAGACATTTAGGGGTAAAAT-G
* * * * *
159456 CAATTTTTGGAAGGTTCGGGGTTAAACATGGAATTTTTAGACATTTAGGGGTAAAATAG
1 TAATTTTTAGAAGGTTTGGGGTCAAAAATGGAATTTTTAGACATTTAGGGGTAAAAT-G
* *
159515 TAATTTTTGGAAGGTTTGGGGTTAAAAATGGAA-TTTT-GACATTTAGGGGT-AAATGG
1 TAATTTTTAGAAGGTTTGGGGTCAAAAATGGAATTTTTAGACATTTAGGGGTAAAAT-G
* * * * * *
159571 TAA-TTTTGGAAAGTTTAGGGTTAAAAAATGGAA-TTTTACAAAGTTTAGGGGTAAAAATG
1 TAATTTTTAGAAGGTTT-GGGGTCAAAAATGGAATTTTTAGACA-TTTAGGGGT-AAAATG
** * * * * *
159630 TAATTTACAAAAAGTTTGGGATCAAAAAT-GAAATTTTAGAAAGTTT-GAGGGTAAAAATG
1 TAATTTTTAGAAGGTTTGGGGTCAAAAATGGAATTTTTAGACA-TTTAG-GGGT-AAAATG
* *
159689 TAATTTTTAGAAAGTTTGTGGTCAAAAATGGAATTTT
1 TAATTTTTAGAAGGTTTGGGGTCAAAAATGGAATTTT
159726 GGAAAGTTTG
Statistics
Matches: 233, Mismatches: 28, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
55 12 0.05
56 26 0.11
57 15 0.06
58 17 0.07
59 144 0.62
60 19 0.08
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (58 bp):
TAATTTTTAGAAGGTTTGGGGTCAAAAATGGAATTTTTAGACATTTAGGGGTAAAATG
Found at i:159731 original size:59 final size:58
Alignment explanation
Indices: 159384--159831 Score: 287
Period size: 59 Copynumber: 7.7 Consensus size: 58
159374 TTGGATGCCC
* * * *
159384 GAGGGTAAAACA-ATAATTTTTAGAAGGTTCGGGGTCAAAAATGGAATTTTTAGACATTT
1 GAGGGTAAAA-ATGTAATTTTTAGAAAGTTTGGGGTCAAAAATGGAA-TTTTAGAAATTT
* * * * * * * *
159443 GGGGGT-AAAATGGCAATTTTTGGAAGGTTCGGGGTTAAACATGGAATTTTTAGACATTT
1 GAGGGTAAAAAT-GTAATTTTTAGAAAGTTTGGGGTCAAAAATGGAA-TTTTAGAAATTT
* * * *
159502 -AGGGGT-AAAATAGTAATTTTTGGAAGGTTTGGGGTTAAAAATGGAATTTT-GACATTT
1 GA-GGGTAAAAAT-GTAATTTTTAGAAAGTTTGGGGTCAAAAATGGAATTTTAGAAATTT
* * * *
159559 -AGGGGT--AAATGGTAA-TTTTGGAAAGTTTAGGGTTAAAAAATGGAATTTTACAAAGTTT
1 GA-GGGTAAAAAT-GTAATTTTTAGAAAGTTT-GGGGTCAAAAATGGAATTTTAGAAA-TTT
** * * *
159617 -AGGGGTAAAAATGTAATTTACAAAAAGTTTGGGATCAAAAATGAAATTTTAGAAAGTTT
1 GA-GGGTAAAAATGTAATTTTTAGAAAGTTTGGGGTCAAAAATGGAATTTTAGAAA-TTT
* *
159676 GAGGGTAAAAATGTAATTTTTAGAAAGTTTGTGGTCAAAAATGGAATTTTGGAAAGTTT
1 GAGGGTAAAAATGTAATTTTTAGAAAGTTTGGGGTCAAAAATGGAATTTTAGAAA-TTT
* * * * * * * *
159735 G-GGGCCAAAAATG-AAATTTTGGAAACTTCGGGGT-AAAAATGTAATTTTTGAAATGT
1 GAGGG-TAAAAATGTAATTTTTAGAAAGTTTGGGGTCAAAAATGGAATTTTAGAAATTT
* * * * * *
159791 CAAGGTCAAAATGGAA-TTTTGGAAAGTTCAGGGGT-AAAAAT
1 GAGGGTAAAAATGTAATTTTTAGAAAGTT-TGGGGTCAAAAAT
159832 ATAATTTTTG
Statistics
Matches: 328, Mismatches: 47, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
55 12 0.04
56 45 0.14
57 48 0.15
58 35 0.11
59 174 0.53
60 14 0.04
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (58 bp):
GAGGGTAAAAATGTAATTTTTAGAAAGTTTGGGGTCAAAAATGGAATTTTAGAAATTT
Found at i:160985 original size:2 final size:2
Alignment explanation
Indices: 160978--161037 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
160968 AAAATATTTA
160978 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
161020 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
161038 TTACACTTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:161751 original size:6 final size:6
Alignment explanation
Indices: 161742--161835 Score: 79
Period size: 6 Copynumber: 16.3 Consensus size: 6
161732 TAATTTTTTT
* * * * *
161742 AATTTA AA-TTA AATTCA AATTTA AA-GTA AATTTA AACTCA AA-ATA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
** * *
161787 AATTTA AATTTA AAAATA AATTTA AATTTA AA-ATA AATTCA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
161834 AA
1 AA
161836 AATTAAAAGT
Statistics
Matches: 67, Mismatches: 17, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
5 16 0.24
6 51 0.76
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (6 bp):
AATTTA
Found at i:161764 original size:17 final size:17
Alignment explanation
Indices: 161742--161836 Score: 127
Period size: 17 Copynumber: 5.5 Consensus size: 17
161732 TAATTTTTTT
* *
161742 AATTTAAATTAAATTCA
1 AATTTAAAATAAATTTA
*
161759 AATTTAAAGTAAATTTA
1 AATTTAAAATAAATTTA
* *
161776 AACTCAAAATAAATTTA
1 AATTTAAAATAAATTTA
161793 AATTTAAAAATAAATTTA
1 AATTT-AAAATAAATTTA
*
161811 AATTTAAAATAAATTCA
1 AATTTAAAATAAATTTA
161828 AATTTAAAA
1 AATTTAAAA
161837 ATTAAAAGTT
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
17 52 0.75
18 17 0.25
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:161820 original size:35 final size:35
Alignment explanation
Indices: 161742--161838 Score: 142
Period size: 35 Copynumber: 2.8 Consensus size: 35
161732 TAATTTTTTT
* *
161742 AATTTAAATTAAATTCAAATTT-AAAGTAAATTTA
1 AATTTAAAATAAATTCAAATTTAAAAATAAATTTA
* * *
161776 AACTCAAAATAAATTTAAATTTAAAAATAAATTTA
1 AATTTAAAATAAATTCAAATTTAAAAATAAATTTA
161811 AATTTAAAATAAATTCAAATTTAAAAAT
1 AATTTAAAATAAATTCAAATTTAAAAAT
161839 TAAAAGTTGG
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
34 18 0.33
35 36 0.67
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (35 bp):
AATTTAAAATAAATTCAAATTTAAAAATAAATTTA
Found at i:165925 original size:30 final size:30
Alignment explanation
Indices: 165891--165948 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
165881 ATAACATTGA
* *
165891 ATTAACGATGAGCAACTTAAATGAAAATTT
1 ATTAAAGATGAGCAACTAAAATGAAAATTT
* **
165921 ATTAAAGTTGAGTGACTAAAATGAAAAT
1 ATTAAAGATGAGCAACTAAAATGAAAAT
165949 GACTGTTAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.48, C:0.07, G:0.16, T:0.29
Consensus pattern (30 bp):
ATTAAAGATGAGCAACTAAAATGAAAATTT
Found at i:178456 original size:2 final size:2
Alignment explanation
Indices: 178444--178477 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
178434 TGCATTAAAT
*
178444 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
178478 GAATTAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 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:178647 original size:48 final size:48
Alignment explanation
Indices: 178571--178663 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
178561 AGACACATTG
* * * *
178571 ATTATTTTATTATTAAATTCAAATTTTGATAGATTTTTATCATAATCA
1 ATTAATTTATTATTAAATTCAAAATTTGATAAATCTTTATCATAATCA
*
178619 ATTAATTTATTATTAGATTCAAAATTTGATAAATCTTTATCATAA
1 ATTAATTTATTATTAAATTCAAAATTTGATAAATCTTTATCATAA
178664 CTGATTACTA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.49
Consensus pattern (48 bp):
ATTAATTTATTATTAAATTCAAAATTTGATAAATCTTTATCATAATCA
Found at i:198208 original size:3 final size:3
Alignment explanation
Indices: 198202--198231 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
198192 TCTTGGAGAG
198202 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
198232 GTACAAAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:202922 original size:10 final size:9
Alignment explanation
Indices: 202866--202926 Score: 50
Period size: 10 Copynumber: 6.0 Consensus size: 9
202856 AGGGAATGTG
*
202866 TAAAAAAAA
1 TAAATAAAA
202875 TAAATATAAA
1 TAAATA-AAA
202885 TAGACATGAAAA
1 TA-A-AT-AAAA
202897 TAAATAAAGA
1 TAAATAAA-A
202907 TGAAATAAGAA
1 T-AAATAA-AA
202918 TAAATAAAA
1 TAAATAAAA
202927 ATTATACAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 14
0.75 0.02 0.24
Matches are distributed among these distances:
9 10 0.23
10 15 0.34
11 10 0.23
12 8 0.18
13 1 0.02
ACGTcount: A:0.70, C:0.02, G:0.08, T:0.20
Consensus pattern (9 bp):
TAAATAAAA
Found at i:203639 original size:21 final size:20
Alignment explanation
Indices: 203571--203642 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 20
203561 CTAAAAACAT
*
203571 ATTTTTATTTTTAAAAAATCTAA
1 ATTTTTATTTTT--TAAATC-AA
*
203594 ACTTTT-TTTTTTAAATC--
1 ATTTTTATTTTTTAAATCAA
*
203611 ATTATTATTTTTTAAATCAAA
1 ATTTTTATTTTTTAAATC-AA
203632 ATTTTTATTTT
1 ATTTTTATTTT
203643 GAAATAATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
17 4 0.10
18 11 0.28
20 5 0.12
21 10 0.25
22 5 0.12
23 5 0.12
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTTTTATTTTTTAAATCAA
Found at i:203687 original size:138 final size:138
Alignment explanation
Indices: 203486--203747 Score: 386
Period size: 139 Copynumber: 1.9 Consensus size: 138
203476 CTTTTCTTAA
** * *
203486 AAATCAAAACTTTTATTTCGAAATGGTTAAAAATTCAAAACTTGTTTAAAATTTTAAATTTTTTC
1 AAATCAAAACTTTTATTTCGAAATAATTAAAAAATCAAAACTTGTTTAAAAATTTAAATTTTTTC
*
203551 TTTAAAATGACT-AAAAACATA-TTTTTATTTTTAAAAAATCTAAACTTTTTTTTT-TAAATCAT
66 TTTAAAATAACTAAAAAACA-AGTTTTTATTTTT-AAAAATCTAAA-TTTTTTTTTATAAATCAT
203613 TATTATTTTTT
128 TATTATTTTTT
* * *
203624 AAATCAAAATTTTTATTTTGAAATAATTAAAAAATCAAAAATTTGTTTAAAAATTTAAATTTTTT
1 AAATCAAAACTTTTATTTCGAAATAATTAAAAAATC-AAAACTTGTTTAAAAATTTAAATTTTTT
*
203689 CTTTAAAATAACTAAAAAACAAGTTTTTATTTTTAAAAATCTTAATTTTTTTTTATAAA
65 CTTTAAAATAACTAAAAAACAAGTTTTTATTTTTAAAAATCTAAATTTTTTTTTATAAA
203748 AAAATCAAAA
Statistics
Matches: 111, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
138 40 0.36
139 53 0.48
140 18 0.16
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.47
Consensus pattern (138 bp):
AAATCAAAACTTTTATTTCGAAATAATTAAAAAATCAAAACTTGTTTAAAAATTTAAATTTTTTC
TTTAAAATAACTAAAAAACAAGTTTTTATTTTTAAAAATCTAAATTTTTTTTTATAAATCATTAT
TATTTTTT
Found at i:205453 original size:2 final size:2
Alignment explanation
Indices: 205446--205472 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
205436 TTATAATTTA
205446 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
205473 ATTGTCTTAA
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:217247 original size:9 final size:9
Alignment explanation
Indices: 217233--217280 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
217223 GCAAATGATT
217233 TTAAAATTA
1 TTAAAATTA
217242 TTAAAATTA
1 TTAAAATTA
217251 TTTTTAAAA-TA
1 ---TTAAAATTA
217262 -TAAAATTA
1 TTAAAATTA
217270 TTAAAATTA
1 TTAAAATTA
217279 TT
1 TT
217281 TTTTTTGAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
7 5 0.15
8 2 0.06
9 19 0.56
11 2 0.06
12 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTAAAATTA
Found at i:217267 original size:19 final size:21
Alignment explanation
Indices: 217231--217271 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
217221 CAGCAAATGA
217231 TTTTAAAATTATTAAAATTAT
1 TTTTAAAATTATTAAAATTAT
217252 TTTTAAAA-TA-TAAAATTAT
1 TTTTAAAATTATTAAAATTAT
217271 T
1 T
217272 AAAATTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.50
20 2 0.10
21 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTTAAAATTATTAAAATTAT
Found at i:217274 original size:28 final size:29
Alignment explanation
Indices: 217234--217313 Score: 110
Period size: 28 Copynumber: 2.7 Consensus size: 29
217224 CAAATGATTT
217234 TAAAATTATTAAAATTATTTTTAAAAT-A
1 TAAAATTATTAAAATTATTTTTAAAATAA
*
217262 TAAAATTATTAAAATTATTTTTTTTGAAATAA
1 TAAAATTATTAAAATTA---TTTTTAAAATAA
217294 TAAAATTATT-AAATTATTTT
1 TAAAATTATTAAAATTATTTT
217314 AATTTTCAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
28 21 0.45
31 15 0.32
32 11 0.23
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTAAAATAA
Found at i:217292 original size:31 final size:32
Alignment explanation
Indices: 217234--217313 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 32
217224 CAAATGATTT
217234 TAAAATTATTAAAATTA---TTTTTAAAAT-A
1 TAAAATTATTAAAATTATTTTTTTTAAAATAA
*
217262 TAAAATTATTAAAATTATTTTTTTTGAAATAA
1 TAAAATTATTAAAATTATTTTTTTTAAAATAA
217294 TAAAATTATT-AAATTATTTT
1 TAAAATTATTAAAATTATTTT
217314 AATTTTCAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
28 17 0.36
31 19 0.40
32 11 0.23
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (32 bp):
TAAAATTATTAAAATTATTTTTTTTAAAATAA
Found at i:218837 original size:20 final size:20
Alignment explanation
Indices: 218804--218847 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
218794 ATAATTTTTC
*
218804 AAAAATTTATAAAAATATTAA
1 AAAAATTCATAAAAATA-TAA
218825 AAAAATTCA-AAAAATATAA
1 AAAAATTCATAAAAATATAA
218844 AAAA
1 AAAA
218848 TAATAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.32
20 7 0.32
21 8 0.36
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (20 bp):
AAAAATTCATAAAAATATAA
Found at i:219340 original size:20 final size:19
Alignment explanation
Indices: 219293--219341 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
219283 AGAAAAATTT
219293 ATAAAAATTATACTAAAAC
1 ATAAAAATTATACTAAAAC
* *
219312 ATTAAAATTA-ATTAAAAGCC
1 ATAAAAATTATACTAAAA--C
219332 ATAAAAATTA
1 ATAAAAATTA
219342 GAAAAAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 6 0.24
19 9 0.36
20 10 0.40
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.29
Consensus pattern (19 bp):
ATAAAAATTATACTAAAAC
Found at i:219599 original size:20 final size:20
Alignment explanation
Indices: 219574--219621 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
219564 TTAATAAAAT
*
219574 ATTTTTAAATAAATTTTATG
1 ATTTTTAAATAAATTTAATG
*
219594 ATTTTTAATTAAATTTAATG
1 ATTTTTAAATAAATTTAATG
219614 ACTTTTTA
1 A-TTTTTA
219622 TAATTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
ATTTTTAAATAAATTTAATG
Found at i:220028 original size:52 final size:52
Alignment explanation
Indices: 219960--220064 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
219950 TTAAATAATA
219960 TTAAAATAATCTACACCAATCAAAGCTTAAGTGTGAAACTAAAAATAGTGTT
1 TTAAAATAATCTACACCAATCAAAGCTTAAGTGTGAAACTAAAAATAGTGTT
220012 TTAAAATAATCTACACCAATCAAAGCTTAAGTGTGAAACTAAAAATAGTGTT
1 TTAAAATAATCTACACCAATCAAAGCTTAAGTGTGAAACTAAAAATAGTGTT
220064 T
1 T
220065 AACTGGGAGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (52 bp):
TTAAAATAATCTACACCAATCAAAGCTTAAGTGTGAAACTAAAAATAGTGTT
Found at i:223749 original size:22 final size:22
Alignment explanation
Indices: 223724--223769 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
223714 ATGGGGTAAA
*
223724 GAGCACAATAATTATATAACAT
1 GAGCACAATAATAATATAACAT
223746 GAGCACAATAATAATATAACAT
1 GAGCACAATAATAATATAACAT
223768 GA
1 GA
223770 TCTTCATCGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (22 bp):
GAGCACAATAATAATATAACAT
Found at i:242538 original size:113 final size:113
Alignment explanation
Indices: 242340--242570 Score: 417
Period size: 113 Copynumber: 2.0 Consensus size: 113
242330 TTAAATTGTC
* *
242340 ACAATATGAAATTATAACTGGTAATGTCACTCCAAAATCTCCTATCACATGTTTCATCCAAATGA
1 ACAATATGAAATTATAACTGGTAATGTCACTCCAAAATCTCCTATAACATGTTTCATCCAAAGGA
242405 GCTAAGCATAACAACTACCTACTACAATGTACTTTGCCTTAGTCGTTG
66 GCTAAGCATAACAACTACCTACTACAATGTACTTTGCCTTAGTCGTTG
* *
242453 ACAATATGAAATTATAACTGGTAGTGTCACTCCAAAATCTTCTATAACATGTTTCATCCAAAGGA
1 ACAATATGAAATTATAACTGGTAATGTCACTCCAAAATCTCCTATAACATGTTTCATCCAAAGGA
*
242518 GCTAAGCATAACAACTACCTACTACAATGTCCTTTGCCTTAGTCGTTG
66 GCTAAGCATAACAACTACCTACTACAATGTACTTTGCCTTAGTCGTTG
242566 ACAAT
1 ACAAT
242571 GTTATTGATT
Statistics
Matches: 113, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
113 113 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.31
Consensus pattern (113 bp):
ACAATATGAAATTATAACTGGTAATGTCACTCCAAAATCTCCTATAACATGTTTCATCCAAAGGA
GCTAAGCATAACAACTACCTACTACAATGTACTTTGCCTTAGTCGTTG
Found at i:250756 original size:19 final size:20
Alignment explanation
Indices: 250717--250758 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
250707 ATCATTATTC
*
250717 AATTG-AAATTAAAATTGAA
1 AATTGAAAATTAAAAATGAA
*
250736 AATTGAAAATTAAAAATAAA
1 AATTGAAAATTAAAAATGAA
250756 AAT
1 AAT
250759 GAATTTGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (20 bp):
AATTGAAAATTAAAAATGAA
Found at i:260490 original size:90 final size:86
Alignment explanation
Indices: 260395--260605 Score: 230
Period size: 90 Copynumber: 2.4 Consensus size: 86
260385 GCCTTTGACA
* * *
260395 TTAAAAAAAAAAAAATTAAATCCTTACTTTTTTTTTTTCA-TACACTT-AGAAACTTAAACTTTT
1 TTAAAAAAAAAACAATTAAACCCTTA-TTTTTTTTTTACACTA-A-TTGAG-AACTTAAACTTTT
* * *
260458 AAAATGTATTAAAAAGGT-CCTTAAAC
62 AAAATGCA-TAAAAA-ATCCCTCAAAC
* * * *
260484 TTTAAAAAAAAAAGCAATTAAGCCCTTATTTTTATTTTACACTTAATTGAGTACTTAAATTTTTA
1 -TTAAAAAAAAAA-CAATTAAACCCTTATTTTTTTTTTACAC-TAATTGAGAACTTAAACTTTTA
260549 AAATGCATAAAAAATCCCTCAAAC
63 AAATGCATAAAAAATCCCTCAAAC
260573 TTAAAAAAAAAACAATTAAACCCTTATTTTTTT
1 TTAAAAAAAAAACAATTAAACCCTTATTTTTTT
260606 ACACTCAATT
Statistics
Matches: 104, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
87 19 0.18
88 13 0.12
89 13 0.12
90 43 0.41
91 14 0.13
92 2 0.02
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.37
Consensus pattern (86 bp):
TTAAAAAAAAAACAATTAAACCCTTATTTTTTTTTTACACTAATTGAGAACTTAAACTTTTAAAA
TGCATAAAAAATCCCTCAAAC
Found at i:260645 original size:84 final size:88
Alignment explanation
Indices: 260480--260645 Score: 200
Period size: 84 Copynumber: 1.9 Consensus size: 88
260470 AAAGGTCCTT
* * *
260480 AAACTTTAAAAAAAAAAGCAATTAAGCCCTTATTTTTATTTTACACTTAATTGAGTACTTAAATT
1 AAACTTTAAAAAAAAAAGCAATTAAACCCTTA-TTTTATTTTACACTCAATTGAGTACTTAAATC
* *
260545 TTTAAAATGCATAAAAAATCCCTC
65 TGTAAAATACATAAAAAATCCCTC
*
260569 AAAC-TTAAAAAAAAAA-CAATTAAACCCTTA-TTT-TTTTACACTCAATT-AGGTACTTGAA-C
1 AAACTTTAAAAAAAAAAGCAATTAAACCCTTATTTTATTTTACACTCAATTGA-GTACTTAAATC
* *
260628 TGTCAAATACATTAAAAA
65 TGTAAAATACATAAAAAA
260646 GACCCTTTGA
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
83 15 0.22
84 21 0.31
85 3 0.04
87 13 0.19
88 12 0.18
89 4 0.06
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.34
Consensus pattern (88 bp):
AAACTTTAAAAAAAAAAGCAATTAAACCCTTATTTTATTTTACACTCAATTGAGTACTTAAATCT
GTAAAATACATAAAAAATCCCTC
Found at i:260782 original size:19 final size:19
Alignment explanation
Indices: 260749--260803 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
260739 GGCATGTGGC
* *
260749 AAAAAAATCAATAAAAATT
1 AAAAAAATTATTAAAAATT
**
260768 AAAAAAATTATTAAATTTT
1 AAAAAAATTATTAAAAATT
260787 AATAAAAA-TATTAAAAA
1 AA-AAAAATTATTAAAAA
260804 AATTAAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
19 24 0.83
20 5 0.17
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAAAATTATTAAAAATT
Found at i:270270 original size:40 final size:40
Alignment explanation
Indices: 270215--270301 Score: 120
Period size: 40 Copynumber: 2.2 Consensus size: 40
270205 TAAATTTACA
* * * *
270215 TTTTCGACCTTTTCATTTAGTATCCTTTCGGATGACATCC
1 TTTTCAACCTTTTCATTGAGTATCCTTCCGGATAACATCC
* *
270255 TTTTCAACCTTTTCATTGATTATCCTTCCGGATAATATCC
1 TTTTCAACCTTTTCATTGAGTATCCTTCCGGATAACATCC
270295 TTTTCAA
1 TTTTCAA
270302 TAATATCCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.21, C:0.24, G:0.09, T:0.46
Consensus pattern (40 bp):
TTTTCAACCTTTTCATTGAGTATCCTTCCGGATAACATCC
Found at i:270295 original size:15 final size:15
Alignment explanation
Indices: 270275--270342 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
270265 TTTCATTGAT
*
270275 TATCCTTCCGGATAA
1 TATCCTTTCGGATAA
*
270290 TATCCTTTTC-AATAA
1 TATCC-TTTCGGATAA
270305 TATCCTTTCGGAT-A
1 TATCCTTTCGGATAA
*
270319 TA-CCTCTTC-AATAA
1 TATCCT-TTCGGATAA
270333 TATCCTTTCG
1 TATCCTTTCG
270343 AATATACCCT
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
13 5 0.12
14 16 0.37
15 19 0.44
16 3 0.07
ACGTcount: A:0.26, C:0.25, G:0.07, T:0.41
Consensus pattern (15 bp):
TATCCTTTCGGATAA
Found at i:270347 original size:55 final size:54
Alignment explanation
Indices: 270303--270417 Score: 151
Period size: 55 Copynumber: 2.1 Consensus size: 54
270293 CCTTTTCAAT
270303 AATATCCTTTCGGATAT-ACCTCTTCAATAATATCCTTTCGAATATACCCTTTTCA
1 AATATCCTTTCGGATATAACCTCTTCAA-AATATCCTTTCGAATATA-CCTTTTCA
* * * * *
270358 AATATCTTTTCGGATATAACCTTTTCAAAATATTCTTTCGGATATAACTTTTTCA
1 AATATCCTTTCGGATATAACCTCTTCAAAATATCCTTTCGAATAT-ACCTTTTCA
270413 AATAT
1 AATAT
270418 TTTAAAGAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
55 43 0.81
56 10 0.19
ACGTcount: A:0.31, C:0.20, G:0.06, T:0.43
Consensus pattern (54 bp):
AATATCCTTTCGGATATAACCTCTTCAAAATATCCTTTCGAATATACCTTTTCA
Found at i:270356 original size:15 final size:13
Alignment explanation
Indices: 270288--270385 Score: 51
Period size: 14 Copynumber: 7.2 Consensus size: 13
270278 CCTTCCGGAT
270288 AATAT-CCTTTTC
1 AATATACCTTTTC
270300 AATAATATCC-TTTC
1 AAT-ATA-CCTTTTC
* *
270314 GGATATACCTCTTC
1 -AATATACCTTTTC
270328 AATAATATCC-TTTC
1 AAT-ATA-CCTTTTC
270342 GAATATACCCTTTTC
1 -AATATA-CCTTTTC
*
270357 AA-ATATCTTTTC
1 AATATACCTTTTC
*
270369 GGATATAACCTTTTC
1 -AATAT-ACCTTTTC
270384 AA
1 AA
270386 AATATTCTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 22
0.68 0.09 0.23
Matches are distributed among these distances:
12 9 0.14
13 10 0.15
14 26 0.40
15 20 0.31
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.42
Consensus pattern (13 bp):
AATATACCTTTTC
Found at i:270369 original size:27 final size:28
Alignment explanation
Indices: 270275--270414 Score: 167
Period size: 28 Copynumber: 5.0 Consensus size: 28
270265 TTTCATTGAT
* *
270275 TATCCTTCCGGATAATATCCTTTTCAATAA
1 TATCCTTTCGGAT-ATAACCTTTTCAA-AA
*
270305 TATCCTTTCGGATAT-ACCTCTTCAATAA
1 TATCCTTTCGGATATAACCTTTTCAA-AA
* *
270333 TATCCTTTCGAATATACCCTTTTC-AAA
1 TATCCTTTCGGATATAACCTTTTCAAAA
*
270360 TATCTTTTCGGATATAACCTTTTCAAAA
1 TATCCTTTCGGATATAACCTTTTCAAAA
* *
270388 TATTCTTTCGGATATAACTTTTTCAAA
1 TATCCTTTCGGATATAACCTTTTCAAA
270415 TATTTTAAAG
Statistics
Matches: 96, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
27 23 0.24
28 53 0.55
29 8 0.08
30 12 0.12
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.42
Consensus pattern (28 bp):
TATCCTTTCGGATATAACCTTTTCAAAA
Found at i:270948 original size:20 final size:21
Alignment explanation
Indices: 270923--270961 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
270913 TTTCATAACT
*
270923 TCAAAA-TCTAACAATTTCTA
1 TCAAAACTCAAACAATTTCTA
270943 TCAAAACTCAAACAATTTC
1 TCAAAACTCAAACAATTTC
270962 ACTCTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (21 bp):
TCAAAACTCAAACAATTTCTA
Found at i:274645 original size:6 final size:6
Alignment explanation
Indices: 274634--274678 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
274624 TGATCAAAAT
* * *
274634 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
274679 TATGAATTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:275095 original size:41 final size:41
Alignment explanation
Indices: 275050--275137 Score: 151
Period size: 41 Copynumber: 2.1 Consensus size: 41
275040 ACATGAAAGG
*
275050 TAAGTACAATATATGTATAAGAAA-TCAAAGAATGATAAAAC
1 TAAGTACAATATATGAATAA-AAAGTCAAAGAATGATAAAAC
275091 TAAGTACAATATATGAATAAAAAGTCAAAGAATGATAAAAC
1 TAAGTACAATATATGAATAAAAAGTCAAAGAATGATAAAAC
275132 TAAGTA
1 TAAGTA
275138 AGCTAAGAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 3 0.07
41 42 0.93
ACGTcount: A:0.57, C:0.07, G:0.12, T:0.24
Consensus pattern (41 bp):
TAAGTACAATATATGAATAAAAAGTCAAAGAATGATAAAAC
Done.