Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008985.1 Hibiscus syriacus cultivar Beakdansim tig00112349_pilon, 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: 1528252
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 1 of 9
Found at i:450 original size:16 final size:16
Alignment explanation
Indices: 429--466 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
419 AATTATATTT
429 TAATTTT-ATGTTTTTA
1 TAATTTTAAT-TTTTTA
*
445 TAATTTTAATTTTTTT
1 TAATTTTAATTTTTTA
461 TAATTT
1 TAATTT
467 AATGATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TAATTTTAATTTTTTA
Found at i:10067 original size:17 final size:18
Alignment explanation
Indices: 10045--10079 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
10035 TTTACCCTAT
10045 AAAAAATTAAATA-GAAA
1 AAAAAATTAAATATGAAA
10062 AAAAAATTAAATATGAAA
1 AAAAAATTAAATATGAAA
10080 GATTAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (18 bp):
AAAAAATTAAATATGAAA
Found at i:23887 original size:11 final size:13
Alignment explanation
Indices: 23855--23884 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
23845 TGGCCAAAGA
23855 TGAAAAGGTATGT
1 TGAAAAGGTATGT
23868 TGAAAAGGTATG-
1 TGAAAAGGTATGT
23880 TGAAA
1 TGAAA
23885 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:31422 original size:30 final size:30
Alignment explanation
Indices: 31386--31451 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
31376 TCAAAGAAGT
31386 ATTATTCTGTATTAAACTACATACTTAAAA
1 ATTATTCTGTATTAAACTACATACTTAAAA
31416 ATTATTCTGTATTAAACTACATACTTAAAA
1 ATTATTCTGTATTAAACTACATACTTAAAA
31446 ATTATT
1 ATTATT
31452 TCGTTTGTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.42
Consensus pattern (30 bp):
ATTATTCTGTATTAAACTACATACTTAAAA
Found at i:31850 original size:2 final size:2
Alignment explanation
Indices: 31843--31873 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
31833 AAATAAATAA
31843 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31874 AATCACAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35823 original size:13 final size:13
Alignment explanation
Indices: 35805--35846 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
35795 TGCGTCATAA
*
35805 ATTTATGACGCGC
1 ATTTATGACGCAC
*
35818 ATTTATGACACAC
1 ATTTATGACGCAC
*
35831 ATTTATGACGCTC
1 ATTTATGACGCAC
35844 ATT
1 ATT
35847 GCGCGTCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (13 bp):
ATTTATGACGCAC
Found at i:36010 original size:2 final size:2
Alignment explanation
Indices: 36003--36051 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
35993 TGTCGTAAAT
36003 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
36045 TA TA TA T
1 TA TA TA T
36052 TGTAGATTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43878 original size:21 final size:21
Alignment explanation
Indices: 43849--43888 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
43839 ACATGTTTAG
*
43849 TACCTAAATTATTAGTTTTGA
1 TACCAAAATTATTAGTTTTGA
* *
43870 TACCAAAATTTTTATTTTT
1 TACCAAAATTATTAGTTTT
43889 TTAAAAATCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.53
Consensus pattern (21 bp):
TACCAAAATTATTAGTTTTGA
Found at i:45108 original size:30 final size:31
Alignment explanation
Indices: 45032--45113 Score: 103
Period size: 36 Copynumber: 2.5 Consensus size: 31
45022 AAGATAATGA
*
45032 TTTCTTTAAATATCGATCATTCTCAATTCTTT
1 TTTCTTTTAATATCGATCATTCTCAATTC-TT
45064 TCTTCATGTATTAATATCGATCATTCTCAATTC-T
1 T-TTC-T-T-TTAATATCGATCATTCTCAATTCTT
45098 TTTCTTTTAATATCGA
1 TTTCTTTTAATATCGA
45114 CAAATAGGTG
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
30 10 0.22
31 1 0.02
32 2 0.04
33 6 0.13
34 3 0.07
35 1 0.02
36 22 0.49
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.51
Consensus pattern (31 bp):
TTTCTTTTAATATCGATCATTCTCAATTCTT
Found at i:48848 original size:41 final size:40
Alignment explanation
Indices: 48773--48863 Score: 112
Period size: 41 Copynumber: 2.2 Consensus size: 40
48763 TAGAAGGATA
* * *
48773 ACATGGCAGTCATATGTGTTGATGTGAATCGATTTTTGTTG
1 ACATGGCA-TCATATGTGCTGATATGAATCGATTTCTGTTG
*
48814 ACATGGCATCCATGTGTGCTGATATGGAAT-GATTTCTGTTG
1 ACATGGCAT-CATATGTGCTGATAT-GAATCGATTTCTGTTG
48855 ACATGGCAT
1 ACATGGCAT
48864 TCACATCATT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
40 1 0.02
41 39 0.89
42 4 0.09
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.37
Consensus pattern (40 bp):
ACATGGCATCATATGTGCTGATATGAATCGATTTCTGTTG
Found at i:50583 original size:26 final size:26
Alignment explanation
Indices: 50546--50608 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
50536 AAATTACAAT
* *
50546 TAATATAATTATGTTATTTAAATTTA
1 TAATATAATTATGATAATTAAATTTA
50572 TAATA-AATTTATGATAATTAAA-TTA
1 TAATATAA-TTATGATAATTAAATTTA
*
50597 TTATGATAATTA
1 TAAT-ATAATTA
50609 AATTAATATG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
25 8 0.26
26 21 0.68
27 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (26 bp):
TAATATAATTATGATAATTAAATTTA
Found at i:50588 original size:14 final size:15
Alignment explanation
Indices: 50571--50612 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 15
50561 ATTTAAATTT
50571 ATAA-TAAATTTATG
1 ATAATTAAATTTATG
50585 ATAATTAAATTATTATG
1 ATAATTAAA-T-TTATG
50602 ATAATTAAATT
1 ATAATTAAATT
50613 AATATGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.16
15 5 0.20
16 2 0.08
17 14 0.56
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (15 bp):
ATAATTAAATTTATG
Found at i:50600 original size:17 final size:17
Alignment explanation
Indices: 50580--50670 Score: 75
Period size: 17 Copynumber: 5.4 Consensus size: 17
50570 TATAATAAAT
50580 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
50597 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
* *
50614 ATATGATTATTTTTGAAA-T-
1 TTATGA-TA--ATT-AAATTA
*
50633 TT-T-ATCA-TAAATTA
1 TTATGATAATTAAATTA
50647 TTATGATAATTAAATTA
1 TTATGATAATTAAATTA
*
50664 ATATGAT
1 TTATGAT
50671 TACTTTTTTG
Statistics
Matches: 58, Mismatches: 7, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
12 3 0.05
13 2 0.03
14 2 0.03
15 1 0.02
16 4 0.07
17 36 0.62
18 3 0.05
19 1 0.02
20 3 0.05
21 3 0.05
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (17 bp):
TTATGATAATTAAATTA
Found at i:50646 original size:50 final size:51
Alignment explanation
Indices: 50590--50686 Score: 178
Period size: 50 Copynumber: 1.9 Consensus size: 51
50580 TTATGATAAT
50590 TAAATTATTATGATAATTAAATTAATATGATTA-TTTTTGAAATTTTATCA
1 TAAATTATTATGATAATTAAATTAATATGATTACTTTTTGAAATTTTATCA
50640 TAAATTATTATGATAATTAAATTAATATGATTACTTTTTTGAAATTT
1 TAAATTATTATGATAATTAAATTAATATGATTAC-TTTTTGAAATTT
50687 AGTTTTATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
50 33 0.73
52 12 0.27
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (51 bp):
TAAATTATTATGATAATTAAATTAATATGATTACTTTTTGAAATTTTATCA
Found at i:50660 original size:67 final size:67
Alignment explanation
Indices: 50531--50670 Score: 189
Period size: 67 Copynumber: 2.1 Consensus size: 67
50521 ATCCTGACTT
*
50531 ATATGA-AATTACAATTAATATAATTATGTTATTTAAATTTATAATAAATTTATGATAATTAAAT
1 ATATGATAATTACAATTAATATAATTATGTTATTGAAATTTATAATAAATTTATGATAATTAAAT
50595 TA
66 TA
* * *
50597 TTATGATAATTA-AATTAATATGATTAT-TT-TTGAAATTTTATCATAAATTATTATGATAATTA
1 ATATGATAATTACAATTAATATAATTATGTTATTGAAA-TTTATAATAAA-T-TTATGATAATTA
50659 AATTA
63 AATTA
50664 ATATGAT
1 ATATGAT
50671 TACTTTTTTG
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
64 5 0.08
65 12 0.18
66 20 0.31
67 28 0.43
ACGTcount: A:0.46, C:0.01, G:0.06, T:0.47
Consensus pattern (67 bp):
ATATGATAATTACAATTAATATAATTATGTTATTGAAATTTATAATAAATTTATGATAATTAAAT
TA
Found at i:51545 original size:20 final size:20
Alignment explanation
Indices: 51512--51572 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
51502 AACCCTTACA
**
51512 AATATCAAGTAGAAGAAAGC
1 AATATCAAACAGAAGAAAGC
*
51532 AATATCAAACAGAAGCAAA-T
1 AATATCAAACAGAAG-AAAGC
* *
51552 AATATAAAACAGAATAAAGC
1 AATATCAAACAGAAGAAAGC
51572 A
1 A
51573 GAATCAATCA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 3 0.09
20 27 0.82
21 3 0.09
ACGTcount: A:0.61, C:0.11, G:0.13, T:0.15
Consensus pattern (20 bp):
AATATCAAACAGAAGAAAGC
Found at i:54283 original size:31 final size:31
Alignment explanation
Indices: 53883--54280 Score: 618
Period size: 31 Copynumber: 12.8 Consensus size: 31
53873 CCTTGATTAG
* * *
53883 TTTACATTAACAACAATAAACCAATATATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
* *
53914 TTTACATCAACAGCAATAAACCAGTATATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
53945 TTTACATCAA-AAGCAATAAACCAGTACATCA
1 TTTACATCAACAA-CAATAAACCAGTACATCA
*
53976 TTTACATCAACAGCAATAAACCAGTACATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
* * *
54007 TTTACATCAACATCAATAAACCAATATATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
*
54038 TTTACATCAACAACAATAAACCAATACATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
*
54069 TTTACATCAACAACAATAAACCAGTACATTA
1 TTTACATCAACAACAATAAACCAGTACATCA
*
54100 TTTACATCAACAACAATAAACCACTACATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
* *
54131 TTTACATCAACAGCAATAAACCAATACATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
*
54162 TTTACATCAACATCAATAAACCAGTACATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
*
54193 TTTACATCAACAACAATAAACCAGTATATCA
1 TTTACATCAACAACAATAAACCAGTACATCA
* *
54224 TTTACATCAACAACAATAAACCAGTATATTA
1 TTTACATCAACAACAATAAACCAGTACATCA
54255 TTTACATCAACAACAATAAACCAGTA
1 TTTACATCAACAACAATAAACCAGTA
54281 TATATATATC
Statistics
Matches: 343, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
30 1 0.00
31 341 0.99
32 1 0.00
ACGTcount: A:0.48, C:0.24, G:0.03, T:0.25
Consensus pattern (31 bp):
TTTACATCAACAACAATAAACCAGTACATCA
Found at i:54552 original size:6 final size:6
Alignment explanation
Indices: 54509--54734 Score: 201
Period size: 6 Copynumber: 38.5 Consensus size: 6
54499 GTTTTGAATA
* * * *
54509 GTTTGG GTTCGG GTTTAG GTTCGG GTGTGG GTTT-G GTTTGG GTTT-G
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* * * **
54555 GTTTGG GTTTGG ATTTGG GTTTAG GTTTGG GTTCGG G-TTCA GTTTGG
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* * * * *
54602 GTTTGG GTTTAG GTTTAG GTTTGG GTTTGG TTTTGG GTCTGG GTTAGG
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* * * * * *
54650 GTCTAG GTTTGG GATTGG GTTTGG GTTCGG GTTCGG GTTCGG GTTTGG
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG
* * * *
54698 GTTTGG GTCTAG GTTAGG GTTT-- ATTTGG GTTTGG GTT
1 GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTTTGG GTT
54735 AAGGTTAGGG
Statistics
Matches: 173, Mismatches: 42, Indels: 10
0.77 0.19 0.04
Matches are distributed among these distances:
4 3 0.02
5 12 0.07
6 158 0.91
ACGTcount: A:0.05, C:0.04, G:0.45, T:0.46
Consensus pattern (6 bp):
GTTTGG
Found at i:54733 original size:28 final size:28
Alignment explanation
Indices: 54693--54748 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
54683 CGGGTTCGGG
54693 TTTGGGTTTGGGTCT-AGGTTAGGGTTTA
1 TTTGGGTTTGGGT-TAAGGTTAGGGTTTA
54721 TTTGGGTTTGGGTTAAGGTTAGGGTTTA
1 TTTGGGTTTGGGTTAAGGTTAGGGTTTA
54749 GGCTAGGGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 1 0.04
28 26 0.96
ACGTcount: A:0.12, C:0.02, G:0.39, T:0.46
Consensus pattern (28 bp):
TTTGGGTTTGGGTTAAGGTTAGGGTTTA
Found at i:54734 original size:22 final size:22
Alignment explanation
Indices: 54699--54740 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
54689 CGGGTTTGGG
*
54699 TTTGGGTCTAGGTTAGGGTTTA
1 TTTGGGTCTAGGTTAAGGTTTA
* *
54721 TTTGGGTTTGGGTTAAGGTT
1 TTTGGGTCTAGGTTAAGGTT
54741 AGGGTTTAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.12, C:0.02, G:0.38, T:0.48
Consensus pattern (22 bp):
TTTGGGTCTAGGTTAAGGTTTA
Found at i:55174 original size:114 final size:114
Alignment explanation
Indices: 55048--55258 Score: 361
Period size: 114 Copynumber: 1.9 Consensus size: 114
55038 AATTTGGGTG
55048 TTTGATCGAAAAAAACACG-AAATGATTTGTGTTTAGGTGTTTTTGAAGATCAAATGAGGGTTTT
1 TTTGATCGAAAAAAACACGAAAATGATTTG-GTTTAGGTGTTTTTGAAGATCAAATGAGGGTTTT
55112 GGGGAAGAACTGGGATGAACAAATGAAGAACACGGAAGAATATTTAGGCC
65 GGGGAAGAACTGGGATGAACAAATGAAGAACACGGAAGAATATTTAGGCC
* * *
55162 TTTGATCGAAAAACACACGAAAATGTTTTGGTTTTGGTGTTTTTGAAGATCAAATGAGGGTTTTG
1 TTTGATCGAAAAAAACACGAAAATGATTTGGTTTAGGTGTTTTTGAAGATCAAATGAGGGTTTTG
* *
55227 GGGATGAATTGGGATGAACAAATGAAGAACAC
66 GGGAAGAACTGGGATGAACAAATGAAGAACAC
55259 AATTGATTTT
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
114 82 0.90
115 9 0.10
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.29
Consensus pattern (114 bp):
TTTGATCGAAAAAAACACGAAAATGATTTGGTTTAGGTGTTTTTGAAGATCAAATGAGGGTTTTG
GGGAAGAACTGGGATGAACAAATGAAGAACACGGAAGAATATTTAGGCC
Found at i:55716 original size:18 final size:18
Alignment explanation
Indices: 55693--55937 Score: 219
Period size: 18 Copynumber: 14.1 Consensus size: 18
55683 AACTTTTCAA
55693 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
55711 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
55729 TA-AT-G--AACTATATAA
1 TATATAGTTTA-TATATAC
*
55744 TATATAGTTTACATATAC
1 TATATAGTTTATATATAC
55762 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
55780 TA-AT-G--AACTATATAA
1 TATATAGTTTA-TATATAC
55795 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
** *
55813 TA-AT-GAAATATATATAA
1 TATATAG-TTTATATATAC
*
55830 TGTATAGTTTATATATAC
1 TATATAGTTTATATATAC
* *
55848 CATATAGTTTATATATAT
1 TATATAGTTTATATATAC
55866 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
** *
55884 TA-ATAAATTATAT-GA-
1 TATATAGTTTATATATAC
*
55899 TGTATAGTTTTATATATAC
1 TATATAG-TTTATATATAC
*
55918 CATATAGTTTATATATAC
1 TATATAGTTTATATATAC
55936 TA
1 TA
55938 ATGAACTATA
Statistics
Matches: 178, Mismatches: 32, Indels: 34
0.73 0.13 0.14
Matches are distributed among these distances:
14 2 0.01
15 17 0.10
16 11 0.06
17 32 0.18
18 108 0.61
19 8 0.04
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.46
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:55734 original size:51 final size:51
Alignment explanation
Indices: 55659--55959 Score: 369
Period size: 51 Copynumber: 5.8 Consensus size: 51
55649 AATAAATTAA
* *
55659 TATATAGGTTATAATATACTAATGAACT-TTTCAATATATAGTTTATATATAC
1 TATATAGTTTAT-ATATACTAATGAACTATAT-AATATATAGTTTATATATAC
*
55711 TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTACATATAC
1 TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATAC
55762 TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATAC
1 TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATAC
** * * *
55813 TA-AT-G-AAATATATA-TAATGTATAGTTTATATATACCATATAGTTTATATATAT
1 TATATAGTTTATATATACTAATG-A-A--CTATATA-A-TATATAGTTTATATATAC
* * * *
55866 TATATAGTTTATATATACTAATAAATTATATGATGTATAGTTTTATATATAC
1 TATATAGTTTATATATACTAATGAACTATATAATATATAG-TTTATATATAC
*
55918 CATATAGTTTATATATACTAATGAACTATATAATATATAGTT
1 TATATAGTTTATATATACTAATGAACTATATAATATATAGTT
55960 CATTTAGTAT
Statistics
Matches: 216, Mismatches: 21, Indels: 25
0.82 0.08 0.10
Matches are distributed among these distances:
47 5 0.02
48 8 0.04
49 2 0.01
50 2 0.01
51 99 0.46
52 60 0.28
53 24 0.11
54 2 0.01
55 2 0.01
56 8 0.04
57 4 0.02
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (51 bp):
TATATAGTTTATATATACTAATGAACTATATAATATATAGTTTATATATAC
Found at i:55793 original size:17 final size:17
Alignment explanation
Indices: 55771--55828 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
55761 CTATATAGTT
*
55771 TATATATACTAATGAAC
1 TATATATACTAATGAAA
**
55788 TATATA-A-TATAT-AGT
1 TATATATACTA-ATGAAA
55803 TTATATATACTAATGAAA
1 T-ATATATACTAATGAAA
55821 TATATATA
1 TATATATA
55829 ATGTATAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 4 0.12
16 8 0.25
17 16 0.50
18 4 0.12
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.41
Consensus pattern (17 bp):
TATATATACTAATGAAA
Found at i:55793 original size:33 final size:31
Alignment explanation
Indices: 55756--55917 Score: 153
Period size: 33 Copynumber: 4.7 Consensus size: 31
55746 TATAGTTTAC
55756 ATATACTATATAGTTTATATATACTAATGAACT
1 ATATA-TATATAGTTTATATATACTAATGAA-T
55789 ATATAATATATAGTTTATATATACTAATGAAAT
1 ATAT-ATATATAGTTTATATATACTAATG-AAT
**
55822 ATATATAATGTATAGTTTATATATACCATATAGTTTAT
1 ATATAT-A--TATAGTTTATATATA-C-TA-A-TGAAT
*
55860 ATATATTATATAGTTTATATATACTAATAAATT
1 ATATA-TATATAGTTTATATATACTAATGAA-T
*
55893 ATATGATGTATAGTTTTATATATAC
1 ATAT-ATATATAG-TTTATATATAC
55918 CATATAGTTT
Statistics
Matches: 111, Mismatches: 5, Indels: 25
0.79 0.04 0.18
Matches are distributed among these distances:
32 4 0.04
33 45 0.41
34 17 0.15
35 16 0.14
36 16 0.14
37 2 0.02
38 9 0.08
39 2 0.02
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.46
Consensus pattern (31 bp):
ATATATATATAGTTTATATATACTAATGAAT
Found at i:56003 original size:18 final size:18
Alignment explanation
Indices: 55988--56024 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
55978 AAACTATAGT
*
55988 TTATATATATAGTATATA
1 TTATATAAATAGTATATA
*
56006 TTATATAAATAGTTTATA
1 TTATATAAATAGTATATA
56024 T
1 T
56025 AGTTCACTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.51
Consensus pattern (18 bp):
TTATATAAATAGTATATA
Found at i:56134 original size:18 final size:18
Alignment explanation
Indices: 56102--56229 Score: 68
Period size: 18 Copynumber: 6.8 Consensus size: 18
56092 TGTAAATATC
*
56102 AACTATAGTTTATATGTA
1 AACTATAGTTCATATGTA
* *
56120 AACTATAATTCATATATA
1 AACTATAGTTCATATGTA
**
56138 AA-TATCAACT-ATA-GTA
1 AACTAT-AGTTCATATGTA
*
56154 TATA-TATAGTACATATGTA
1 -A-ACTATAGTTCATATGTA
*
56173 AACTATATAGTTTATATAGTTTA
1 AAC--TATAGTTCATAT-G--TA
56196 TATA-TATAGTTCATATGTA
1 -A-ACTATAGTTCATATGTA
56215 AACTATAGTTCATAT
1 AACTATAGTTCATAT
56230 ATAGTATATA
Statistics
Matches: 85, Mismatches: 11, Indels: 28
0.69 0.09 0.23
Matches are distributed among these distances:
16 2 0.02
17 10 0.12
18 41 0.48
19 5 0.06
20 10 0.12
21 2 0.02
22 11 0.13
23 2 0.02
24 1 0.01
25 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (18 bp):
AACTATAGTTCATATGTA
Found at i:56179 original size:22 final size:22
Alignment explanation
Indices: 56154--56221 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
56144 AACTATAGTA
*
56154 TATATATAGTACATATGTAAAC
1 TATATATAGTTCATATGTAAAC
* **
56176 --TATATAGTTTATATAGTTTA-
1 TATATATAGTTCATAT-GTAAAC
56196 TATATATAGTTCATATGTAAAC
1 TATATATAGTTCATATGTAAAC
56218 TATA
1 TATA
56222 GTTCATATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
20 12 0.34
21 6 0.17
22 17 0.49
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (22 bp):
TATATATAGTTCATATGTAAAC
Found at i:56231 original size:42 final size:41
Alignment explanation
Indices: 56152--56245 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 41
56142 TCAACTATAG
*
56152 TATATATATAGTACATATGTAAACTATATAGTTTATATAGTT
1 TATATATATAGTACATATGTAAAC-ATATAGTTTATATAGTA
*
56194 TATATATATAGTTCATATGTAAAC-TATAGTTCATATATAGTA
1 TATATATATAGTACATATGTAAACATATAGTT--TATATAGTA
*
56236 TATAAATATA
1 TATATATATA
56246 AATTATAGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
40 7 0.15
42 40 0.85
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.44
Consensus pattern (41 bp):
TATATATATAGTACATATGTAAACATATAGTTTATATAGTA
Found at i:56239 original size:18 final size:17
Alignment explanation
Indices: 56194--56239 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
56184 TTATATAGTT
56194 TATATATATAGTTCATA
1 TATATATATAGTTCATA
* *
56211 TGTAAACTATAGTTCATA
1 TATATA-TATAGTTCATA
56229 TATAGTATATA
1 TATA-TATATA
56240 AATATAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 4 0.17
18 18 0.78
19 1 0.04
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (17 bp):
TATATATATAGTTCATA
Found at i:56278 original size:7 final size:7
Alignment explanation
Indices: 56268--56299 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
56258 TAGTTTATAT
56268 AACCCTA
1 AACCCTA
56275 AACCCTA
1 AACCCTA
56282 AACCCTA
1 AACCCTA
56289 AACCCTA
1 AACCCTA
56296 AACC
1 AACC
56300 ATATATACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.44, G:0.00, T:0.12
Consensus pattern (7 bp):
AACCCTA
Found at i:56389 original size:23 final size:23
Alignment explanation
Indices: 56345--56390 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
56335 AAACTATATT
* *
56345 TTATACAATATATATGATTATAA
1 TTATACAATATATATAAATATAA
56368 TTATAC-ATAATATATAAATATAA
1 TTATACAAT-ATATATAAATATAA
56391 ATTGTATAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (23 bp):
TTATACAATATATATAAATATAA
Found at i:56439 original size:38 final size:40
Alignment explanation
Indices: 56308--56483 Score: 108
Period size: 39 Copynumber: 4.6 Consensus size: 40
56298 CCATATATAC
56308 TATATATAAAC--TATAGTTTATAT-TA-ATAAACTATATT
1 TATATATAAACTATATAGTTTATATATACATAAA-TATATT
* *
56345 T-TATA-CAA-TATATATGATTATAATTATACAT-AATATA--
1 TATATATAAACTATATA-GTTTAT-A-TATACATAAATATATT
* * *
56382 TAAATATAAATTGTATAGTTTATATATA-AT-AATATATT
1 TATATATAAACTATATAGTTTATATATACATAAATATATT
* * ** * *
56420 TATATATAAACTATGTAGTTTCTATATAGTTCAATA-GTT
1 TATATATAAACTATATAGTTTATATATACATAAATATATT
*
56459 CATATATAAACTATATAGTATTATA
1 TATATATAAACTATATAGT-TTATA
56484 GTTTATACAT
Statistics
Matches: 108, Mismatches: 16, Indels: 27
0.72 0.11 0.18
Matches are distributed among these distances:
35 2 0.02
36 16 0.15
37 11 0.10
38 28 0.26
39 32 0.30
40 17 0.16
41 2 0.02
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (40 bp):
TATATATAAACTATATAGTTTATATATACATAAATATATT
Found at i:56517 original size:18 final size:18
Alignment explanation
Indices: 56480--56519 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
56470 TATATAGTAT
**
56480 TATAGTTTATACATGGTA
1 TATAGTTTATACATAATA
56498 TATAGTTTATACATAATA
1 TATAGTTTATACATAATA
56516 TATA
1 TATA
56520 TATAAACTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (18 bp):
TATAGTTTATACATAATA
Found at i:56518 original size:2 final size:2
Alignment explanation
Indices: 56513--56626 Score: 110
Period size: 2 Copynumber: 57.0 Consensus size: 2
56503 TTTATACATA
* *
56513 AT AT AT AT AT AA ACT AT AT A- AT -T AT AT AT AT A- AT AC AT ACT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * * *
56554 TT AT AT AA ACT AT AT AGT TT AT AT GT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
56597 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
56627 TAGTTTTAAT
Statistics
Matches: 93, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
1 4 0.04
2 85 0.91
3 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:56653 original size:43 final size:44
Alignment explanation
Indices: 56605--56690 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 44
56595 ATATATATAT
56605 ATATATATATATATATATATATTAGTTTTAA-TTTTTTCTCAAA
1 ATATATATATATATATATATATTAGTTTTAATTTTTTTCTCAAA
56648 ATATATATATATATATATATATTAGTTTTAATTTTTTTCTCAA
1 ATATATATATATATATATATATTAGTTTTAATTTTTTTCTCAA
56691 CTTTTGAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 31 0.74
44 11 0.26
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (44 bp):
ATATATATATATATATATATATTAGTTTTAATTTTTTTCTCAAA
Found at i:57234 original size:216 final size:215
Alignment explanation
Indices: 56748--57238 Score: 876
Period size: 216 Copynumber: 2.3 Consensus size: 215
56738 TTGATCCCTT
56748 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
*
56813 TTTTATTTGCATCTAAAATTGACTCATACTTATTACTTATTTCTATTTTTTAATTGGTCCATAAC
66 TTTTATTTGCATCTAAAATTGACTCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAAC
*
56878 TTTTTAAATGGGTATAATTTAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTC
131 TTTTTAAATGGGTATAATTCAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTC
56943 AATTTGACCCCTCATCAATG
196 AATTTGACCCCTCATCAATG
56963 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
*
57028 TTTTATTTGCATCTGAAATTGAC-CATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAAC
66 TTTTATTTGCATCTAAAATTGACTCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAAC
* *
57092 TTTTTTAAATGGGTATAATTCATTATTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATT
131 -TTTTTAAATGGGTATAATTCAGTA-CTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATT
* *
57157 TCGATTTGATCCCTCATCAATG
194 TCAATTTGACCCCTCATCAATG
* *
57179 TGTGTTATTTAATTTATTTAAATTTTTATTTATAATTTCATATTTGTTCAATTTAGTCCT
1 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCT
57239 TAAATTTGTA
Statistics
Matches: 265, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
214 40 0.15
215 109 0.41
216 116 0.44
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (215 bp):
TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAA
TTTTATTTGCATCTAAAATTGACTCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAAC
TTTTTAAATGGGTATAATTCAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTC
AATTTGACCCCTCATCAATG
Found at i:58022 original size:26 final size:25
Alignment explanation
Indices: 57971--58043 Score: 67
Period size: 26 Copynumber: 2.8 Consensus size: 25
57961 AAATTAGATT
* *
57971 TTTATATTTTTAAGCTATATTTATTT-
1 TTTATATTTTTAA--TATAATCATTTA
*
57997 TTATATGTTTTTATATATAATCATTTAA
1 TT-TATATTTTTA-ATATAATCATTT-A
58025 TTTATATTTTTAATATAAT
1 TTTATATTTTTAATATAAT
58044 TAATAATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
26 18 0.46
27 18 0.46
28 3 0.08
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (25 bp):
TTTATATTTTTAATATAATCATTTA
Found at i:58054 original size:26 final size:25
Alignment explanation
Indices: 57970--58054 Score: 59
Period size: 26 Copynumber: 3.2 Consensus size: 25
57960 AAAATTAGAT
*
57970 TTTTATATTTTTAAGCTAT-ATT-TAT
1 TTTTATATTTTTAA--TATAATTATAA
*
57995 TTTTATATGTTTTTATATATAATCATTTAA
1 TTTTATA--TTTTTA-ATATAAT--TATAA
58025 -TTTATATTTTTAATATAATTAATAA
1 TTTTATATTTTTAATATAATT-ATAA
58050 TTTTA
1 TTTTA
58055 GTTTTATTTA
Statistics
Matches: 49, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
24 1 0.02
25 10 0.20
26 14 0.29
27 14 0.29
28 1 0.02
29 7 0.14
30 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (25 bp):
TTTTATATTTTTAATATAATTATAA
Found at i:58059 original size:25 final size:28
Alignment explanation
Indices: 57996--58059 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 28
57986 TATATTTATT
*
57996 TTTATATGTTTTTATATATAATCATTTAA
1 TTTATA-GTTTTTATATATAATCATATAA
*
58025 TTTATA-TTTTTA-ATATAATTA-ATAA
1 TTTATAGTTTTTATATATAATCATATAA
58050 TTT-TAGTTTT
1 TTTATAGTTTT
58060 ATTTAATGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 2 0.06
25 10 0.31
26 8 0.25
27 6 0.19
29 6 0.19
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (28 bp):
TTTATAGTTTTTATATATAATCATATAA
Found at i:58238 original size:21 final size:19
Alignment explanation
Indices: 58202--58259 Score: 53
Period size: 21 Copynumber: 2.9 Consensus size: 19
58192 TAAATTTTAA
58202 ATTTTTTTTAAAATATTGG
1 ATTTTTTTTAAAATATTGG
* **
58221 ATTTATTTTTATACATATTAA
1 ATTT-TTTTTA-AAATATTGG
*
58242 ATTTAATTTTAAAATATT
1 ATTT-TTTTTAAAATATT
58260 AAATTCATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
19 4 0.12
20 12 0.38
21 16 0.50
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (19 bp):
ATTTTTTTTAAAATATTGG
Found at i:58260 original size:20 final size:20
Alignment explanation
Indices: 58185--58264 Score: 83
Period size: 20 Copynumber: 4.0 Consensus size: 20
58175 TCAGGTGAAA
*
58185 TTAATTTT-AAATTTTAAAT
1 TTAATTTTAAAATATTAAAT
* **
58204 TT-TTTTTAAAATATTGGAT
1 TTAATTTTAAAATATTAAAT
* *
58223 TTATTTTTATACATATTAAAT
1 TTAATTTTA-AAATATTAAAT
58244 TTAATTTTAAAATATTAAAT
1 TTAATTTTAAAATATTAAAT
58264 T
1 T
58265 CATTACTATT
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
18 4 0.08
19 12 0.24
20 17 0.35
21 16 0.33
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (20 bp):
TTAATTTTAAAATATTAAAT
Found at i:60377 original size:157 final size:155
Alignment explanation
Indices: 60204--60554 Score: 465
Period size: 154 Copynumber: 2.3 Consensus size: 155
60194 GTGGTACATT
* *
60204 AGCATGTGGTTTAAATTTGGTAAAAAATGAACTTAAAATAAATCACAAAATGAATGAATAAGGAG
1 AGCATGTGGTTCAAATTTGGTAAAAAATGAACTTAAAATAAATCACAAAATGAA--AATAA-GAA
* *
60269 ATTATGAAAAATTGAAGGACTAAATTAAAAAATAAAGAAA-ATGTTATAAAAAATAAGAATTGAA
63 ATTATGAAAAATTGAAGGACTAAATTAAAAAATAAA-AAATATATTATAAAAAAGAAGAATTGAA
*
60333 AGTAGACATGTATTCTACTATG-GTTAGG
127 AGTACACATGTATTCTACTATGAGTTAGG
* * * * *
60361 AGCATGTGGTTCAAATTTGATAAAAAA-CATACTTAAAATAAATGACGAATTGAAAATAAGAAAT
1 AGCATGTGGTTCAAATTTGGTAAAAAATGA-ACTTAAAATAAATCACAAAATGAAAATAAGAAAT
* * * * *
60425 TATGAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTTATTTTCAAAAAGAGGAATTGAAAGT
65 TATGAAAAATTGAAGGACTAAATTAAAAAATAAAAAATATATTATAAAAAAGAAGAATTGAAAGT
*
60490 ACACATGTATTCTACTATGATTTAGG
130 ACACATGTATTCTACTATGAGTTAGG
* * *
60516 AGCATGTGATACAAATTTGGTAAAAAATGGACTTAAAAT
1 AGCATGTGGTTCAAATTTGGTAAAAAATGAACTTAAAAT
60555 GAAGGAGAAA
Statistics
Matches: 169, Mismatches: 21, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
153 3 0.02
154 76 0.45
155 43 0.25
156 1 0.01
157 46 0.27
ACGTcount: A:0.49, C:0.06, G:0.16, T:0.28
Consensus pattern (155 bp):
AGCATGTGGTTCAAATTTGGTAAAAAATGAACTTAAAATAAATCACAAAATGAAAATAAGAAATT
ATGAAAAATTGAAGGACTAAATTAAAAAATAAAAAATATATTATAAAAAAGAAGAATTGAAAGTA
CACATGTATTCTACTATGAGTTAGG
Found at i:66435 original size:16 final size:16
Alignment explanation
Indices: 66414--66444 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
66404 TTGTTAGGTC
66414 AAAGTTTAAACTTGGA
1 AAAGTTTAAACTTGGA
66430 AAAGTTTAAACTTGG
1 AAAGTTTAAACTTGG
66445 GTTAATAGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (16 bp):
AAAGTTTAAACTTGGA
Found at i:72315 original size:12 final size:12
Alignment explanation
Indices: 72298--72322 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
72288 TTTATTTAAA
72298 AAAATTATATTT
1 AAAATTATATTT
72310 AAAATTATATTT
1 AAAATTATATTT
72322 A
1 A
72323 CTTTTCTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAAATTATATTT
Found at i:77301 original size:198 final size:197
Alignment explanation
Indices: 77036--77421 Score: 539
Period size: 198 Copynumber: 1.9 Consensus size: 197
77026 GTAAAGGTAG
* * *
77036 TAAAGCATGTAGTAGATGATGTAGGTATGTAAGAAAATACTAAAGCAAATAGTAGAATTTTTTTG
1 TAAAGCA-GTAGTAGATGATGTAGGTATGTAAGAAAATAATAAAGCAAAAAGTAGAATTTGTTTG
* *** *
77101 GAAGTGTTAAAAATAATTGA-AAAAATTGAATTTAAAAAATC-AAATATTAAAAAAATTTGTAAT
65 GAAGTGTTAAAAATAATTGAGAAAAAATGAATTT--AAAATCAAAATATTAAAAAAA-TCACAAC
*
77164 CAAAGTAAGAAGTAAAGAAGGCAAC-AGAGGAAGTATG-GAAACTCTAGTTTCAAAGTGTAAGTG
127 CAAAGTAAGAAGTAAAGAAGGCAACGAGAGGAAG-AGGAGAAACTCTAGTTTCAAAGTGTAAGTG
77227 AAAGTAT
191 AAAGTAT
* * *
77234 TAAAGCA-TAGTAGATGATGTAGGTGTGTAAGAAAGTAATAAATCAAAAAGTAGAGAATTTGTTT
1 TAAAGCAGTAGTAGATGATGTAGGTATGTAAGAAAATAATAAAGCAAAAAGT--AGAATTTGTTT
77298 GGAAGTGTTAAAAATAATTGAGAAAAAATGAATTTAAAATCAAAATATTAAAAAAATCACAACCA
64 GGAAGTGTTAAAAATAATTGAGAAAAAATGAATTTAAAATCAAAATATTAAAAAAATCACAACCA
* * *
77363 AAGTAAGAAGTAAAGAAGGCAACGGGAGGAAGCGGAGAAACTTTAGTTTCAAAGTGTAA
129 AAGTAAGAAGTAAAGAAGGCAACGAGAGGAAGAGGAGAAACTCTAGTTTCAAAGTGTAA
77422 ACCTTTCATC
Statistics
Matches: 167, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
196 39 0.23
197 35 0.21
198 81 0.49
199 12 0.07
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (197 bp):
TAAAGCAGTAGTAGATGATGTAGGTATGTAAGAAAATAATAAAGCAAAAAGTAGAATTTGTTTGG
AAGTGTTAAAAATAATTGAGAAAAAATGAATTTAAAATCAAAATATTAAAAAAATCACAACCAAA
GTAAGAAGTAAAGAAGGCAACGAGAGGAAGAGGAGAAACTCTAGTTTCAAAGTGTAAGTGAAAGT
AT
Found at i:80208 original size:15 final size:15
Alignment explanation
Indices: 80184--80217 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
80174 CGTCAAGTGT
* *
80184 TGGTGGTGGTGATGA
1 TGGTGATGGTGATCA
80199 TGGTGATGGTGATCA
1 TGGTGATGGTGATCA
80214 TGGT
1 TGGT
80218 AGTGATAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.03, G:0.47, T:0.35
Consensus pattern (15 bp):
TGGTGATGGTGATCA
Found at i:83694 original size:31 final size:31
Alignment explanation
Indices: 83632--83830 Score: 255
Period size: 31 Copynumber: 6.5 Consensus size: 31
83622 TACCAAAATA
* *
83632 TTAAAATAATATATATATAT-TATTTTATTT
1 TTAAAATAATATATATATATATATATTATAT
*
83662 TTAAAATAATATATATATATATATATTATTT
1 TTAAAATAATATATATATATATATATTATAT
*
83693 TTAAAATAATATATATATATATATATTATTT
1 TTAAAATAATATATATATATATATATTATAT
* *
83724 TTAAAATATTA-AAATAATATATATATATATAT
1 TTAAAATAATATATAT-ATATATATAT-TATAT
*
83756 ATAATAATAATATATATATATATATA-TATAT
1 TTAA-AATAATATATATATATATATATTATAT
* *
83787 AT-ATATAATATATATATATATATA-TATAT
1 TTAAAATAATATATATATATATATATTATAT
83816 TTAAAATAATATATA
1 TTAAAATAATATATA
83831 GTTTTAATCA
Statistics
Matches: 153, Mismatches: 10, Indels: 12
0.87 0.06 0.07
Matches are distributed among these distances:
29 26 0.17
30 35 0.23
31 67 0.44
32 7 0.05
33 15 0.10
34 3 0.02
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TTAAAATAATATATATATATATATATTATAT
Found at i:83830 original size:2 final size:2
Alignment explanation
Indices: 83670--83815 Score: 145
Period size: 2 Copynumber: 79.0 Consensus size: 2
83660 TTTTAAAATA
* * *
83670 AT AT AT AT AT AT AT AT AT -T AT TT TT A- AA AT A- 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
* * * *
83709 AT AT AT AT AT -T AT TT TT A- AA AT AT -T A- AA AT A- 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
83746 AT AT AT AT AT AT A- AT A- AT A- 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
83785 AT AT AT AT A- 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
83816 TTAAAATAAT
Statistics
Matches: 125, Mismatches: 7, Indels: 24
0.80 0.04 0.15
Matches are distributed among these distances:
1 12 0.10
2 113 0.90
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:85722 original size:10 final size:10
Alignment explanation
Indices: 85702--85756 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
85692 ACGGGTCGTG
85702 ACCGGTC-AA
1 ACCGGTCAAA
85711 ACCGGTCAAA
1 ACCGGTCAAA
85721 ACCGGTTCAAA
1 ACCGG-TCAAA
*
85732 ACCGGT-TAA
1 ACCGGTCAAA
85741 ACCGGTCAAA
1 ACCGGTCAAA
85751 ACCGGT
1 ACCGGT
85757 TTCCAGCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:85757 original size:19 final size:19
Alignment explanation
Indices: 85702--85757 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
85692 ACGGGTCGTG
*
85702 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
85721 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
85741 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
85758 TCCAGCGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 9 0.26
21 8 0.24
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:92944 original size:13 final size:13
Alignment explanation
Indices: 92928--92958 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
92918 GTCAACGGGT
*
92928 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
92941 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
92954 CGGGT
1 CGGGT
92959 AAACGGGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:92991 original size:10 final size:10
Alignment explanation
Indices: 92971--93025 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
92961 ACGGGTCGTG
92971 ACCGGTC-AA
1 ACCGGTCAAA
92980 ACCGGTCAAA
1 ACCGGTCAAA
92990 ACCGGTTCAAA
1 ACCGG-TCAAA
*
93001 ACCGGT-TAA
1 ACCGGTCAAA
93010 ACCGGTCAAA
1 ACCGGTCAAA
93020 ACCGGT
1 ACCGGT
93026 TTCCAGCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:93026 original size:19 final size:19
Alignment explanation
Indices: 92971--93026 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
92961 ACGGGTCGTG
*
92971 ACCGGTC-AAACCGGTCAAA
1 ACCGGTCAAAACCGGT-TAA
92990 ACCGGTTCAAAACCGGTTAA
1 ACCGG-TCAAAACCGGTTAA
93010 ACCGGTCAAAACCGGTT
1 ACCGGTCAAAACCGGTT
93027 TCCAGCGTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.50
20 9 0.26
21 8 0.24
ACGTcount: A:0.34, C:0.29, G:0.21, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAAACCGGTTAA
Found at i:93741 original size:28 final size:31
Alignment explanation
Indices: 93678--93735 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
93668 AAAAACTTCC
* *
93678 AATTAAATCCTCAAATTTCACCAATTAACTT
1 AATTAAAACCTCAAATTTCACCAATTAAATT
93709 AATTAAAACCTC-AA-TTC-CCAATTAAAT
1 AATTAAAACCTCAAATTTCACCAATTAAAT
93736 ATATTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.36
29 3 0.12
30 2 0.08
31 11 0.44
ACGTcount: A:0.45, C:0.22, G:0.00, T:0.33
Consensus pattern (31 bp):
AATTAAAACCTCAAATTTCACCAATTAAATT
Found at i:95814 original size:9 final size:10
Alignment explanation
Indices: 95786--95831 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
95776 TTTAAAATAT
95786 ATATATTTGTA
1 ATATATTT-TA
* *
95797 TTATATTTTT
1 ATATATTTTA
95807 AT-TATTTTA
1 ATATATTTTA
95816 ATATATTTT-
1 ATATATTTTA
95825 ATATATT
1 ATATATT
95832 CGTATTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
9 15 0.50
10 8 0.27
11 7 0.23
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (10 bp):
ATATATTTTA
Found at i:95819 original size:28 final size:28
Alignment explanation
Indices: 95786--95848 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
95776 TTTAAAATAT
**
95786 ATATATTTGTATTATATTTTTATTATTTTA
1 ATATA-TTGTA-TATATTCGTATTATTTTA
* *
95816 ATATATTTTATATATTCGTATTTTTTTA
1 ATATATTGTATATATTCGTATTATTTTA
95844 ATATA
1 ATATA
95849 ACAAATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 20 0.69
29 4 0.14
30 5 0.17
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (28 bp):
ATATATTGTATATATTCGTATTATTTTA
Found at i:95830 original size:11 final size:11
Alignment explanation
Indices: 95783--95830 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
95773 TATTTTAAAA
95783 TATATATATTT
1 TATATATATTT
95794 GTAT-TATATTT
1 -TATATATATTT
95805 T-TAT-TATTT
1 TATATATATTT
95814 TA-ATATATTT
1 TATATATATTT
95824 TATATAT
1 TATATAT
95831 TCGTATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
9 9 0.28
10 9 0.28
11 11 0.34
12 3 0.09
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (11 bp):
TATATATATTT
Found at i:95831 original size:19 final size:20
Alignment explanation
Indices: 95785--95831 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
95775 TTTTAAAATA
*
95785 TATATATTTGTATTATATTT
1 TATATATTTGTAATATATTT
95805 T-TATTATTT-TAATATATTT
1 TATA-TATTTGTAATATATTT
95824 TATATATT
1 TATATATT
95832 CGTATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TATATATTTGTAATATATTT
Found at i:96250 original size:17 final size:17
Alignment explanation
Indices: 96228--96272 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
96218 GCAAATAATT
96228 TAATTAAATTATTTAAA
1 TAATTAAATTATTTAAA
** **
96245 TAATTAAATGGTTTATT
1 TAATTAAATTATTTAAA
96262 TAATTAAATTA
1 TAATTAAATTA
96273 AAACATAAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (17 bp):
TAATTAAATTATTTAAA
Found at i:99700 original size:23 final size:23
Alignment explanation
Indices: 99654--99700 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
99644 AAAAAATTAG
*
99654 TATATTTATTTATCTAATTTCAA
1 TATATTTATTTATCTAATTACAA
*
99677 TATATTT-TTTATCTAGCTTACAA
1 TATATTTATTTATCTA-ATTACAA
99700 T
1 T
99701 TTAATCTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.32, C:0.11, G:0.02, T:0.55
Consensus pattern (23 bp):
TATATTTATTTATCTAATTACAA
Found at i:105008 original size:12 final size:14
Alignment explanation
Indices: 104991--105025 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
104981 TCTCATTCTC
104991 TTTTTTCTTT-AGT
1 TTTTTTCTTTCAGT
105004 TTTTTTCTTTCA-T
1 TTTTTTCTTTCAGT
105017 TTTTTTCTT
1 TTTTTTCTT
105026 CTGTTCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 20 0.95
14 1 0.05
ACGTcount: A:0.06, C:0.11, G:0.03, T:0.80
Consensus pattern (14 bp):
TTTTTTCTTTCAGT
Found at i:105489 original size:16 final size:16
Alignment explanation
Indices: 105459--105489 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
105449 TTAAAACTCA
*
105459 ACTCAAACTCGAAAAT
1 ACTCAAACTCAAAAAT
105475 ACTCAAACTCAAAAA
1 ACTCAAACTCAAAAA
105490 AAATTTCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.26, G:0.03, T:0.16
Consensus pattern (16 bp):
ACTCAAACTCAAAAAT
Found at i:107157 original size:21 final size:20
Alignment explanation
Indices: 107102--107158 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
107092 AGAGTTTAGG
*
107102 GTTT-AGGTTTAGGGTTTGT
1 GTTTAAGGTTTAGGGTTTAT
** *
107121 GATTTAATATTAAGGGTTTAT
1 G-TTTAAGGTTTAGGGTTTAT
107142 AGTTTAAGGTTTAGGGT
1 -GTTTAAGGTTTAGGGT
107159 GTAATCTAAC
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
19 1 0.04
20 3 0.11
21 23 0.82
22 1 0.04
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (20 bp):
GTTTAAGGTTTAGGGTTTAT
Found at i:115159 original size:16 final size:16
Alignment explanation
Indices: 115134--115182 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 16
115124 ATTATTATAA
*
115134 AAATATTATAAAAAAT
1 AAATAATATAAAAAAT
*
115150 AAATAATAT-AAAATT
1 AAATAATATAAAAAAT
115165 AAA-AAT-TAAAAAA-
1 AAATAATATAAAAAAT
115178 AAATA
1 AAATA
115183 GAAGTTATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
13 4 0.14
14 8 0.29
15 8 0.29
16 8 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATAATATAAAAAAT
Found at i:115248 original size:22 final size:23
Alignment explanation
Indices: 115205--115248 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
115195 TGATAAATTT
* **
115205 AAAATTTAATAATTTTTTATATA
1 AAAAATTAATAATTTTAAATATA
115228 AAAAATTAA-AATTTTAAATAT
1 AAAAATTAATAATTTTAAATAT
115249 TTTTATCAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AAAAATTAATAATTTTAAATATA
Found at i:115262 original size:31 final size:30
Alignment explanation
Indices: 115203--115262 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
115193 AATGATAAAT
*
115203 TTAAAATTTAATAATTTTTTATATAAAAAA
1 TTAAAATTTAATAATTTTTTATAGAAAAAA
*
115233 TTAAAATTTTA-AATATTTTTATCAGAAAAA
1 TTAAAATTTAATAAT-TTTTTAT-AGAAAAA
115263 TTTGATTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 17 0.65
31 6 0.23
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (30 bp):
TTAAAATTTAATAATTTTTTATAGAAAAAA
Found at i:116277 original size:17 final size:16
Alignment explanation
Indices: 116257--116290 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
116247 TTAAATTATA
116257 AAAATCCCCAAATACTT
1 AAAATCCCCAAAT-CTT
*
116274 AAAATCCTCAAATCTT
1 AAAATCCCCAAATCTT
116290 A
1 A
116291 TCCTTAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATCCCCAAATCTT
Found at i:116960 original size:3 final size:3
Alignment explanation
Indices: 116952--116980 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
116942 TAAACTTTTA
116952 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
116981 CACTTAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:121494 original size:11 final size:11
Alignment explanation
Indices: 121478--121534 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
121468 AAAATTACAT
121478 TATTAAAAATA
1 TATTAAAAATA
121489 TATTAAAAATA
1 TATTAAAAATA
* **
121500 CATTATTAATA
1 TATTAAAAATA
*
121511 -ATTATAAAT-
1 TATTAAAAATA
*
121520 TTTTAAAAATA
1 TATTAAAAATA
121531 TATT
1 TATT
121535 TTTAAATGTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
10 15 0.41
11 22 0.59
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:121537 original size:14 final size:14
Alignment explanation
Indices: 121463--121540 Score: 54
Period size: 14 Copynumber: 5.6 Consensus size: 14
121453 AATTTTAGAT
*
121463 TTTTTAAAATTACA
1 TTTTTAAAAATACA
*
121477 TTATTAAAAAT--A
1 TTTTTAAAAATACA
*
121489 -TATTAAAAATACA
1 TTTTTAAAAATACA
* *
121502 TTATTAATAATTATAAA
1 TTTTTAA-AA--ATACA
*
121519 TTTTTAAAAATATA
1 TTTTTAAAAATACA
121533 TTTTTAAA
1 TTTTTAAA
121541 TGTAATATAA
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
11 10 0.19
12 1 0.02
13 1 0.02
14 27 0.51
15 2 0.04
16 2 0.04
17 10 0.19
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (14 bp):
TTTTTAAAAATACA
Found at i:125854 original size:26 final size:26
Alignment explanation
Indices: 125812--125875 Score: 110
Period size: 26 Copynumber: 2.4 Consensus size: 26
125802 CGAGACCTAA
125812 AGTTGGGCCCAAAGGACTTTATAAATT
1 AGTTGGG-CCAAAGGACTTTATAAATT
125839 AGTTGGGCCAAAGGACTTTATAAATT
1 AGTTGGGCCAAAGGACTTTATAAATT
*
125865 AGTTGGACCAA
1 AGTTGGGCCAA
125876 GTCTAGTGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 29 0.81
27 7 0.19
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (26 bp):
AGTTGGGCCAAAGGACTTTATAAATT
Found at i:137550 original size:7 final size:7
Alignment explanation
Indices: 137528--137572 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
137518 CATAATTCTT
*
137528 TTCTTTC
1 TTCTTCC
*
137535 TTATTCC
1 TTCTTCC
137542 TTCTTCC
1 TTCTTCC
137549 TTCTTCC
1 TTCTTCC
137556 TTCTTCC
1 TTCTTCC
137563 TTCTTCC
1 TTCTTCC
137570 TTC
1 TTC
137573 CAAGTTGAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.02, C:0.38, G:0.00, T:0.60
Consensus pattern (7 bp):
TTCTTCC
Found at i:143492 original size:12 final size:12
Alignment explanation
Indices: 143475--143500 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
143465 AAATAAGTAA
143475 TTAATATTTTAT
1 TTAATATTTTAT
143487 TTAATATTTTAT
1 TTAATATTTTAT
143499 TT
1 TT
143501 TAAAAAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTAATATTTTAT
Found at i:149755 original size:18 final size:18
Alignment explanation
Indices: 149732--149766 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
149722 AAGATATTAC
149732 TAAGAGTCCTAGCTAAGG
1 TAAGAGTCCTAGCTAAGG
*
149750 TAAGAGTTCTAGCTAAG
1 TAAGAGTCCTAGCTAAG
149767 TTAGAAATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (18 bp):
TAAGAGTCCTAGCTAAGG
Found at i:151327 original size:2 final size:2
Alignment explanation
Indices: 151320--151365 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
151310 CAATCTTAGC
151320 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
151362 TA TA
1 TA TA
151366 AAAAATAGGT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:152560 original size:21 final size:21
Alignment explanation
Indices: 152536--152588 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
152526 CAGGCAGTAA
152536 TACCGATACTCTGGATGGGAG
1 TACCGATACTCTGGATGGGAG
*
152557 TACCGATACTTTGGATGGGAG
1 TACCGATACTCTGGATGGGAG
152578 TACCGATACTC
1 TACCGATACTC
152589 CCTTTATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (21 bp):
TACCGATACTCTGGATGGGAG
Found at i:153436 original size:27 final size:27
Alignment explanation
Indices: 153396--153474 Score: 140
Period size: 27 Copynumber: 2.9 Consensus size: 27
153386 AACTGATAGT
* *
153396 TATGTATTGTGAATGTGTTTGGAAAGA
1 TATGTACTGCGAATGTGTTTGGAAAGA
153423 TATGTACTGCGAATGTGTTTGGAAAGA
1 TATGTACTGCGAATGTGTTTGGAAAGA
153450 TATGTACTGCGAATGTGTTTGGAAA
1 TATGTACTGCGAATGTGTTTGGAAA
153475 CACTTAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.37
Consensus pattern (27 bp):
TATGTACTGCGAATGTGTTTGGAAAGA
Found at i:154691 original size:18 final size:18
Alignment explanation
Indices: 154668--154702 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
154658 AAGATATTAC
*
154668 TAAGAGTCCTGACTAAGG
1 TAAGAGTCCTAACTAAGG
154686 TAAGAGTCCTAACTAAG
1 TAAGAGTCCTAACTAAG
154703 TTAGAAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (18 bp):
TAAGAGTCCTAACTAAGG
Found at i:156223 original size:23 final size:23
Alignment explanation
Indices: 156186--156249 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
156176 TAGCTCATAT
*
156186 AAATACACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * *
156209 AATTGCACCGTAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
156232 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
156250 TATAATATTG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:157459 original size:18 final size:18
Alignment explanation
Indices: 157412--157452 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
157402 AATTTCTTAT
157412 CATATCATCATAACATAG
1 CATATCATCATAACATAG
157430 CATATCATCATAACATAG
1 CATATCATCATAACATAG
157448 CATAT
1 CATAT
157453 ATTCATATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.44, C:0.22, G:0.05, T:0.29
Consensus pattern (18 bp):
CATATCATCATAACATAG
Found at i:157886 original size:24 final size:20
Alignment explanation
Indices: 157829--157891 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 20
157819 TTTCCCTTGA
*
157829 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
157849 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
157872 ATGTGCATCGATGCACTCCT
1 A-GTGCATCGATGCA-TCCT
157892 TATGCATTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
20 14 0.40
21 1 0.03
22 1 0.03
23 4 0.11
24 14 0.40
25 1 0.03
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:157892 original size:24 final size:22
Alignment explanation
Indices: 157829--157893 Score: 71
Period size: 24 Copynumber: 2.9 Consensus size: 22
157819 TTTCCCTTGA
*
157829 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATCCTTAAC
*
157849 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CCTTAAC
157872 ATGTGCATCGATGCACTCCTTA
1 A-GTGCATCGATGCA-TCCTTA
157894 TGCATTGATG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
20 14 0.38
21 1 0.03
22 1 0.03
23 3 0.08
24 17 0.46
25 1 0.03
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATCCTTAAC
Found at i:158030 original size:83 final size:83
Alignment explanation
Indices: 157937--158116 Score: 324
Period size: 83 Copynumber: 2.2 Consensus size: 83
157927 ATTTTTAAGG
*
157937 GTGCATCGATGCACTTCCTGTGCATCGATACACACTGAACAATTTCTGGAAATTTACCCTTGATG
1 GTGCATCGATGCACTTCCTGTGCATCGATACACACTGAACAATTTCTAGAAATTTACCCTTGATG
*
158002 CACCGGTGCACATTGAAT
66 CACCGGTGCACATTGAAC
*
158020 GTGCATCGATGCACTTCCTGTGCATCGATACATACTGAACAATTTCTAGAAATTTACCCTTGATG
1 GTGCATCGATGCACTTCCTGTGCATCGATACACACTGAACAATTTCTAGAAATTTACCCTTGATG
*
158085 CATCGGTGCACATTGAAC
66 CACCGGTGCACATTGAAC
158103 GTGCATCGATGCAC
1 GTGCATCGATGCAC
158117 ATATCCCAGA
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 93 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (83 bp):
GTGCATCGATGCACTTCCTGTGCATCGATACACACTGAACAATTTCTAGAAATTTACCCTTGATG
CACCGGTGCACATTGAAC
Found at i:166846 original size:3 final size:3
Alignment explanation
Indices: 166838--166880 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
166828 TGTTTTGCTT
*
166838 AAG AAG AAG AAG AAAG AAT AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG -AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
166881 GGGAGAGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:167056 original size:6 final size:6
Alignment explanation
Indices: 167045--167085 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
167035 AAATGACTTT
*
167045 CTATAA CTATAA CTATAA CTATAA ATATAA CTATAA CTATA
1 CTATAA CTATAA CTATAA CTATAA CTATAA CTATAA CTATA
167086 TATATATATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (6 bp):
CTATAA
Found at i:167068 original size:18 final size:18
Alignment explanation
Indices: 167045--167091 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
167035 AAATGACTTT
*
167045 CTATAACTATAACTATAA
1 CTATAAATATAACTATAA
167063 CTATAAATATAACTATAA
1 CTATAAATATAACTATAA
*
167081 CTATATATATA
1 CTATAAATATA
167092 TATCTCTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (18 bp):
CTATAAATATAACTATAA
Found at i:175752 original size:2 final size:2
Alignment explanation
Indices: 175745--175774 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
175735 TAGTTTCTGA
175745 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
175775 TACTTCTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:176673 original size:70 final size:70
Alignment explanation
Indices: 176587--176738 Score: 184
Period size: 71 Copynumber: 2.2 Consensus size: 70
176577 AAGTACATAG
* *
176587 CATCACTAAGAACCCT-AAAATTCATGTTTAAGGACCTT-TTTGGAAAGT-ATTACCAAGTTTAA
1 CATCA-TAAGACCCCTAAAAATTCATG-TTAAGGAACTTATTTGGAAAGTGATT-CCAAGTTTAA
176649 GGACTCAA
63 GGACTCAA
* * * *
176657 CATCATTAAGACCCCTAAAAATTCATGTTCAGGAACTTATTTGGAAAGTGCTTCCACGTTTGAGG
1 CATCA-TAAGACCCCTAAAAATTCATGTTAAGGAACTTATTTGGAAAGTGATTCCAAGTTTAAGG
*
176722 AGTCAA
65 ACTCAA
176728 CATCATAAGAC
1 CATCATAAGAC
176739 AAACCTAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
70 29 0.41
71 40 0.56
72 2 0.03
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (70 bp):
CATCATAAGACCCCTAAAAATTCATGTTAAGGAACTTATTTGGAAAGTGATTCCAAGTTTAAGGA
CTCAA
Found at i:177141 original size:2 final size:2
Alignment explanation
Indices: 177134--177288 Score: 135
Period size: 2 Copynumber: 83.0 Consensus size: 2
177124 TAGTAGCGTG
177134 AT AT AT AT -T AT AGT AT A- AT AT A- AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
177173 AT AT AT AT AT A- AT AT AT AT GT AT AT AT AT -T AT AGT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
*
177214 -T AT AGT -T AT GT AT -T AT AT AT -T AT -T AT AT -T AT AT AGT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
177252 AT AT -T AT AT A- AT A- AT AT AT -T AT AT AT AGT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
177289 TTTTAGGTCC
Statistics
Matches: 128, Mismatches: 4, Indels: 42
0.74 0.02 0.24
Matches are distributed among these distances:
1 16 0.12
2 103 0.80
3 9 0.07
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:177155 original size:10 final size:9
Alignment explanation
Indices: 177134--177287 Score: 96
Period size: 9 Copynumber: 17.8 Consensus size: 9
177124 TAGTAGCGTG
*
177134 ATATATATT
1 ATATATAAT
177143 ATAGTATAAT
1 ATA-TATAAT
177153 ATA-AT-AT
1 ATATATAAT
177160 A-ATAT-AT
1 ATATATAAT
177167 ATATATATAT
1 ATATATA-AT
177177 ATATATAAT
1 ATATATAAT
*
177186 ATATAT-GT
1 ATATATAAT
*
177194 ATATATATT
1 ATATATAAT
177203 ATAGTAT-AT
1 ATA-TATAAT
*
177212 AT-TATAGT
1 ATATATAAT
* *
177220 -TATGTATT
1 ATATATAAT
*
177228 ATATATTAT
1 ATATATAAT
*
177237 -TATATTAT
1 ATATATAAT
177245 ATAGTAT-AT
1 ATA-TATAAT
177254 ATTATATAAT
1 A-TATATAAT
*
177264 A-ATATATT
1 ATATATAAT
*
177272 ATATATAGT
1 ATATATAAT
177281 ATATATA
1 ATATATA
177288 TTTTTAGGTC
Statistics
Matches: 118, Mismatches: 12, Indels: 30
0.74 0.08 0.19
Matches are distributed among these distances:
6 1 0.01
7 12 0.10
8 33 0.28
9 44 0.37
10 28 0.24
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (9 bp):
ATATATAAT
Found at i:177172 original size:31 final size:28
Alignment explanation
Indices: 177134--177288 Score: 130
Period size: 29 Copynumber: 5.6 Consensus size: 28
177124 TAGTAGCGTG
*
177134 ATATATATTATA-GTATA-ATATAATAT
1 ATATATATTATATATATATATATAATAT
177160 A-ATATATATATATATATATATATAATAT
1 ATATATAT-TATATATATATATATAATAT
* *
177188 ATATGTA-TATATATTATAGTATATATTAT
1 ATATATATTATATA-TATA-TATATAATAT
* *
177217 AGTTATGTATTATATAT-TATTATATTATAT
1 A--TATATATTATATATATA-TATATAATAT
177247 AGTATATATTATATA-ATA-ATAT-AT-T
1 A-TATATATTATATATATATATATAATAT
*
177272 ATATATAGTATATATAT
1 ATATATATTATATATAT
177289 TTTTAGGTCC
Statistics
Matches: 109, Mismatches: 9, Indels: 23
0.77 0.06 0.16
Matches are distributed among these distances:
24 12 0.11
25 10 0.09
26 7 0.06
27 14 0.13
28 14 0.13
29 28 0.26
30 11 0.10
31 7 0.06
32 6 0.06
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.50
Consensus pattern (28 bp):
ATATATATTATATATATATATATAATAT
Found at i:177179 original size:29 final size:29
Alignment explanation
Indices: 177134--177288 Score: 132
Period size: 27 Copynumber: 5.6 Consensus size: 29
177124 TAGTAGCGTG
177134 ATATATAT-TATAGTATAATATAATATAAT
1 ATATATATATATA-TATAATATAATATAAT
177163 ATATATATATATATAT-ATATAATAT-AT
1 ATATATATATATATATAATATAATATAAT
* * *
177190 ATGTATATATAT-TATAGTAT-ATATTAT
1 ATATATATATATATATAATATAATATAAT
* * * *
177217 AGT-TATGTAT-TATATATTATTATATTAT
1 A-TATATATATATATATAATATAATATAAT
*
177245 ATAGTATATAT-TATAT-A-ATAATATATT
1 ATA-TATATATATATATAATATAATATAAT
177272 ATATATAGTATATATAT
1 ATATATA-TATATATAT
177289 TTTTAGGTCC
Statistics
Matches: 107, Mismatches: 9, Indels: 21
0.78 0.07 0.15
Matches are distributed among these distances:
26 12 0.11
27 46 0.43
28 23 0.21
29 22 0.21
30 4 0.04
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.50
Consensus pattern (29 bp):
ATATATATATATATATAATATAATATAAT
Found at i:177217 original size:5 final size:5
Alignment explanation
Indices: 177137--177289 Score: 88
Period size: 5 Copynumber: 30.2 Consensus size: 5
177127 TAGCGTGATA
* * * * *
177137 TATAT TATAG TATAA TATAA TATAA TATA- TATAT ATATAT ATATAT AATA-
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT -TATAT -TATAT TATAT
177187 TATAT GTATA- TATAT TATAGT ATATAT TATAGT TATGTAT TATA- TATTAT
1 TATAT -TATAT TATAT TATA-T -TATAT TATA-T TA--TAT TATAT TA-TAT
* * *
177237 TATAT TATA- TAGTA- TATAT TATAT AATAA TATAT TATA- TATAG TATA-
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
177284 TATAT T
1 TATAT T
177290 TTTAGGTCCA
Statistics
Matches: 124, Mismatches: 8, Indels: 32
0.76 0.05 0.20
Matches are distributed among these distances:
4 25 0.20
5 68 0.55
6 22 0.18
7 7 0.06
8 2 0.02
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (5 bp):
TATAT
Found at i:186980 original size:19 final size:18
Alignment explanation
Indices: 186956--187007 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
186946 TTTTTTGTAA
186956 TTTTTAAAAAAATAGGATTT
1 TTTTTAAAAAAATA--ATTT
*
186976 TTTTATAAATATAATAATTT
1 TTTT-TAAA-AAAATAATTT
186996 TTTTTAAAAAAA
1 TTTTTAAAAAAA
187008 CAAGAATTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 3 0.11
19 4 0.14
20 12 0.43
21 4 0.14
22 5 0.18
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (18 bp):
TTTTTAAAAAAATAATTT
Found at i:187015 original size:21 final size:20
Alignment explanation
Indices: 186956--187015 Score: 50
Period size: 21 Copynumber: 3.0 Consensus size: 20
186946 TTTTTTGTAA
* *
186956 TTTTTAAAAAAATAGGA-TT
1 TTTTTAAAAAAAAAGAATTT
* * *
186975 TTTTTATAAATATAATAATTT
1 TTTTTA-AAAAAAAAGAATTT
186996 TTTTTAAAAAAACAAGAATT
1 TTTTTAAAAAAA-AAGAATT
187016 ACCAAAGCGT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
19 6 0.20
20 10 0.33
21 14 0.47
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (20 bp):
TTTTTAAAAAAAAAGAATTT
Found at i:188721 original size:35 final size:35
Alignment explanation
Indices: 188675--188746 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
188665 CCAAAAAAGA
*
188675 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACAAGTCTAAAAT
188710 AGAGTTGGATTAGGACTCAAATACAAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACAAGTCTAAAAT
188745 AG
1 AG
188747 GGTTTTTAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACAAGTCTAAAAT
Found at i:189132 original size:17 final size:18
Alignment explanation
Indices: 189106--189145 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
189096 ATTATATGGA
189106 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
189122 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
189140 TATTAT
1 TATTAT
189146 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:189156 original size:2 final size:2
Alignment explanation
Indices: 189149--189173 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
189139 TTATTATACG
189149 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 T
189174 TTTAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:189207 original size:2 final size:2
Alignment explanation
Indices: 189202--189230 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
189192 GATTTTTTAT
189202 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
189231 TTCTTTAATA
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:189590 original size:41 final size:39
Alignment explanation
Indices: 189545--189621 Score: 118
Period size: 41 Copynumber: 1.9 Consensus size: 39
189535 AGGGCCCATT
* *
189545 TTTTTGTTTTATTTCTAACTAAAGTCTCTCCCACTTTCATC
1 TTTTTGTCTTATTTCTAACTAAAG-C-CCCCCACTTTCATC
189586 TTTTTGTCTTATTTCTAACTAAAGCCCCCCACTTTC
1 TTTTTGTCTTATTTCTAACTAAAGCCCCCCACTTTC
189622 GGTGAAGTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 10 0.29
40 1 0.03
41 23 0.68
ACGTcount: A:0.19, C:0.27, G:0.05, T:0.48
Consensus pattern (39 bp):
TTTTTGTCTTATTTCTAACTAAAGCCCCCCACTTTCATC
Found at i:189795 original size:9 final size:9
Alignment explanation
Indices: 189783--189825 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
189773 CCTTATCTTA
189783 TTTATTTAT
1 TTTATTTAT
189792 TTTATTTAT
1 TTTATTTAT
189801 TTTATTT-T
1 TTTATTTAT
*
189809 TTTCCTTTTAT
1 TTT--ATTTAT
189820 TTTATT
1 TTTATT
189826 CTGTTTATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
8 4 0.14
9 18 0.62
10 3 0.10
11 4 0.14
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTATTTAT
Found at i:189832 original size:14 final size:13
Alignment explanation
Indices: 189775--189844 Score: 52
Period size: 14 Copynumber: 5.2 Consensus size: 13
189765 ATTTTTTTCC
* *
189775 TTATCTTATTTAT
1 TTATTTTATTTGT
*
189788 TTATTTTATTTATT
1 TTATTTTATTT-GT
*
189802 TTATTTT-TTTCCTT
1 TTATTTTATTT--GT
189816 TTATTTTATTCTGT
1 TTATTTTATT-TGT
*
189830 TTATCTTATTTGT
1 TTATTTTATTTGT
189843 TT
1 TT
189845 TCTTTACCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
13 18 0.38
14 27 0.56
15 2 0.04
16 1 0.02
ACGTcount: A:0.16, C:0.07, G:0.03, T:0.74
Consensus pattern (13 bp):
TTATTTTATTTGT
Found at i:200897 original size:14 final size:14
Alignment explanation
Indices: 200878--200904 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
200868 GATCGAAACT
200878 TCAAGATTCCAGAG
1 TCAAGATTCCAGAG
200892 TCAAGATTCCAGA
1 TCAAGATTCCAGA
200905 CAGATTTTAG
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:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (14 bp):
TCAAGATTCCAGAG
Found at i:201048 original size:95 final size:95
Alignment explanation
Indices: 200939--201442 Score: 400
Period size: 106 Copynumber: 5.0 Consensus size: 95
200929 AACTTCACAA
* * *
200939 CGAATGATATTGGACTCAAGACAACACAAGTTCAACTTCCCAACGAAGGGACGACTGGTTGTCAA
1 CGAAGGATATTGGACTCGAGAC-ACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAA
*
201004 CAAACAATCTCCCAATTTCAGAGCCAAT-AG
65 CAAACAATTTCCCAATTTCAGAGCCAATCAG
201034 CGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAA
1 CGAAGGATATTGGACTCGAGAC-ACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAA
* * *
201099 CAAACAATTTCCTAATTTCAGGGTCAATTTCAACTTCACAT
65 CAAACAATTTCCCAATTTCAGAG-C-----CAA--T--CAG
*
201140 CGAAGGATATTGGACTCGAGAC-CACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC
1 CGAAGGATATTGGACTCGAGACACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAAC
* * *
201204 AAATAATTTCCCAATTTTAGAGCCAATTTCAACTTCACAT
66 AAACAATTTCCCAATTTCAGAG-C-----CAA--T--CAG
* * * * * *
201244 CGAAGGATATTGGACTCGAGAAGACACAAGTTCAACTTCATAATGAAGGGGCGGCTGATTGTCAA
1 CGAAGGATATTGGACTCGAG-ACACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAA
* * *
201309 CAAATAATTTCCCAATTTCAGGGTCAATTTCAACTTCACAT
65 CAAACAATTTCCCAATTTCAGAG-C-----CAA--T--CAG
* ** * * * ** *
201350 CGAAGGATATTAGACTTAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGTTGGCTGTCAA
1 CGAAGGATATTGGACTCGAGACA-CACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAA
* * *
201415 CAAACAATTTTCCAGTTCCAGAGCCAAT
65 CAAACAATTTCCCAATTTCAGAGCCAAT
201443 TTCAACTTCA
Statistics
Matches: 357, Mismatches: 38, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
95 81 0.23
96 1 0.00
98 1 0.00
100 3 0.01
101 3 0.01
103 1 0.00
104 96 0.27
105 4 0.01
106 167 0.47
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.23
Consensus pattern (95 bp):
CGAAGGATATTGGACTCGAGACACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAAC
AAACAATTTCCCAATTTCAGAGCCAATCAG
Found at i:201220 original size:104 final size:105
Alignment explanation
Indices: 201034--201473 Score: 587
Period size: 106 Copynumber: 4.2 Consensus size: 105
201024 GAGCCAATAG
*
201034 CGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAA
1 CGAAGGATATTGGACTCGAGAC-ACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA
* * *
201099 CAAACAATTTCCTAATTTCAGGGTCAATTTCAACTTCACAT
65 CAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAT
201140 CGAAGGATATTGGACTCGAGAC-CACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC
1 CGAAGGATATTGGACTCGAGACACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC
* *
201204 AAATAATTTCCCAATTTTAGAGCCAATTTCAACTTCACAT
66 AAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAT
* * * * *
201244 CGAAGGATATTGGACTCGAGAAGACACAAGTTCAACTTCATAATGAAGGGGCGGCTGATTGTCAA
1 CGAAGGATATTGGACTCGAG-ACACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA
* * *
201309 CAAATAATTTCCCAATTTCAGGGTCAATTTCAACTTCACAT
65 CAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAT
* ** * * * * *
201350 CGAAGGATATTAGACTTAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGTTGGCTGTCAA
1 CGAAGGATATTGGACTCGAGACA-CACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA
* * * **
201415 CAAACAATTTTCCAGTTCCAGAGCCAATTTCAACTTCACGG
65 CAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAT
201456 C-AGAGGATATTGGACTCG
1 CGA-AGGATATTGGACTCG
201474 GAACAATACA
Statistics
Matches: 294, Mismatches: 36, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
104 96 0.33
105 4 0.01
106 194 0.66
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.24
Consensus pattern (105 bp):
CGAAGGATATTGGACTCGAGACACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC
AAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAT
Found at i:201274 original size:210 final size:211
Alignment explanation
Indices: 201032--201473 Score: 645
Period size: 210 Copynumber: 2.1 Consensus size: 211
201022 CAGAGCCAAT
* *
201032 AGCGAAGGATATTGGACTCGAGACGACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTC
1 AGCGAAGGATATTGGACTCGAGAAGACACAAGTTCAACTTCACAACGAAGGGACGACTGATTGTC
* * *
201097 AACAAACAATTTCCTAATTTCAGGGTCAATTTCAACTTCACATCGAAGGATATTGGACTCGAGAC
66 AACAAACAATTTCCCAATTTCAGGGTCAATTTCAACTTCACATCGAAGGATATTAGACTCAAGAC
* * * **
201162 -CACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTTCCCAATTTTAGAG
131 ACACAAGCTCAACTTCACAACGAAGGGACGGCTGGCTGTCAACAAACAATTTCCCAATTCCAGAG
201226 CCAATTTCAACTTCAC
196 CCAATTTCAACTTCAC
* * * * *
201242 ATCGAAGGATATTGGACTCGAGAAGACACAAGTTCAACTTCATAATGAAGGGGCGGCTGATTGTC
1 AGCGAAGGATATTGGACTCGAGAAGACACAAGTTCAACTTCACAACGAAGGGACGACTGATTGTC
* *
201307 AACAAATAATTTCCCAATTTCAGGGTCAATTTCAACTTCACATCGAAGGATATTAGACTTAAGAC
66 AACAAACAATTTCCCAATTTCAGGGTCAATTTCAACTTCACATCGAAGGATATTAGACTCAAGAC
* * * * *
201372 AGCACAAGCTCAACTTCACAGCGAAGGGGCGGTTGGCTGTCAACAAACAATTTTCCAGTTCCAGA
131 A-CACAAGCTCAACTTCACAACGAAGGGACGGCTGGCTGTCAACAAACAATTTCCCAATTCCAGA
201437 GCCAATTTCAACTTCAC
195 GCCAATTTCAACTTCAC
*
201454 GGC-AGAGGATATTGGACTCG
1 AGCGA-AGGATATTGGACTCG
201474 GAACAATACA
Statistics
Matches: 205, Mismatches: 24, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
210 118 0.58
211 1 0.00
212 86 0.42
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.24
Consensus pattern (211 bp):
AGCGAAGGATATTGGACTCGAGAAGACACAAGTTCAACTTCACAACGAAGGGACGACTGATTGTC
AACAAACAATTTCCCAATTTCAGGGTCAATTTCAACTTCACATCGAAGGATATTAGACTCAAGAC
ACACAAGCTCAACTTCACAACGAAGGGACGGCTGGCTGTCAACAAACAATTTCCCAATTCCAGAG
CCAATTTCAACTTCAC
Found at i:202048 original size:35 final size:35
Alignment explanation
Indices: 201956--202027 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
201946 ACCAAAAAGA
201956 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
201991 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
202026 AG
1 AG
202028 GGTTTTTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.28
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
Found at i:202428 original size:17 final size:18
Alignment explanation
Indices: 202402--202441 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
202392 ATTATATGGA
202402 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
202418 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
202436 TATTAT
1 TATTAT
202442 ACATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:202635 original size:17 final size:17
Alignment explanation
Indices: 202613--202647 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
202603 ATAGTTTATT
202613 TATATACATATTATTAA
1 TATATACATATTATTAA
* *
202630 TATATATATATTCTTAA
1 TATATACATATTATTAA
202647 T
1 T
202648 TATTTTTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (17 bp):
TATATACATATTATTAA
Found at i:202690 original size:26 final size:28
Alignment explanation
Indices: 202660--202729 Score: 83
Period size: 28 Copynumber: 2.6 Consensus size: 28
202650 TTTTTATTTG
202660 ATTATTTCTTTATT-TATATA-ATATAT
1 ATTATTTCTTTATTATATATACATATAT
* **
202686 CTTATAACTTTATATATATATACATATAT
1 ATTATTTCTTTAT-TATATATACATATAT
202715 ATTATTT-TTTATTAT
1 ATTATTTCTTTATTAT
202730 TTTCATTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
26 10 0.29
27 4 0.11
28 11 0.31
29 10 0.29
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTATTTCTTTATTATATATACATATAT
Found at i:202713 original size:22 final size:22
Alignment explanation
Indices: 202672--202713 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
202662 TATTTCTTTA
*
202672 TTTATATAATATATCTTATAAC
1 TTTATATAATATATCATATAAC
202694 TTTATAT-ATATATACATATA
1 TTTATATAATATAT-CATATA
202714 TATTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTATATAATATATCATATAAC
Found at i:202979 original size:38 final size:40
Alignment explanation
Indices: 202928--203007 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
202918 AGTGAGAGGG
*
202928 TAGCTTTTCTATTTT-TAAATA-TTTGTTGTATATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
202966 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATATA
203006 TA
1 TA
203008 TATATTTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 7 0.19
40 18 0.49
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.56
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:211089 original size:22 final size:22
Alignment explanation
Indices: 211058--211111 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
211048 TGGCTGGAAA
*
211058 GCTTAGCAGCACGGAAAGACAG
1 GCTTAACAGCACGGAAAGACAG
211080 GCTTAACAGCACGGAAAGACAG
1 GCTTAACAGCACGGAAAGACAG
211102 GCTTAACAGC
1 GCTTAACAGC
211112 TCTTGACAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.37, C:0.24, G:0.28, T:0.11
Consensus pattern (22 bp):
GCTTAACAGCACGGAAAGACAG
Found at i:211527 original size:20 final size:21
Alignment explanation
Indices: 211502--211553 Score: 79
Period size: 23 Copynumber: 2.4 Consensus size: 21
211492 ACTAAACTTG
211502 ATAGTTTA-GATACTAAATGC
1 ATAGTTTACGATACTAAATGC
211522 ATAGTTTACCCGATACTAAATGC
1 ATAGTTTA--CGATACTAAATGC
211545 ATAGTTTAC
1 ATAGTTTAC
211554 CCGATAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.28
21 1 0.03
23 20 0.69
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (21 bp):
ATAGTTTACGATACTAAATGC
Found at i:211540 original size:23 final size:23
Alignment explanation
Indices: 211510--211559 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
211500 TGATAGTTTA
211510 GATACTAAATGCATAGTTTACCC
1 GATACTAAATGCATAGTTTACCC
211533 GATACTAAATGCATAGTTTACCC
1 GATACTAAATGCATAGTTTACCC
211556 GATA
1 GATA
211560 AAAAACCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (23 bp):
GATACTAAATGCATAGTTTACCC
Found at i:212511 original size:8 final size:8
Alignment explanation
Indices: 212500--212542 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
212490 ATATTTGCAT
*
212500 ATACATAC
1 ATACATGC
*
212508 ATACTTGC
1 ATACATGC
212516 ATACATGC
1 ATACATGC
*
212524 ATGCATGC
1 ATACATGC
*
212532 ATACATAC
1 ATACATGC
212540 ATA
1 ATA
212543 TGTATGTATG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (8 bp):
ATACATGC
Found at i:212521 original size:16 final size:16
Alignment explanation
Indices: 212500--212542 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
212490 ATATTTGCAT
*
212500 ATACATACATACTTGC
1 ATACATACATACATGC
* *
212516 ATACATGCATGCATGC
1 ATACATACATACATGC
212532 ATACATACATA
1 ATACATACATA
212543 TGTATGTATG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (16 bp):
ATACATACATACATGC
Found at i:214999 original size:60 final size:58
Alignment explanation
Indices: 214896--215086 Score: 179
Period size: 60 Copynumber: 3.2 Consensus size: 58
214886 TGTATCACAT
* * * *
214896 ATCCTTAAACTATG-TTCCTCATTTTAAATTGGTCCTCAAACTTTTAAATGTTTCAATTCC
1 ATCCCTAAACTATGATT--TCATTCTAAATTAGTCCTCAAACTTTTAAA-GTTTCAATTTC
* * * *
214956 ATCCCTAAACTATGATTATCATTCTAAATTAGTCTTCAGACTTTTTACGTTTCAATTTC
1 ATCCCTAAACTATGATT-TCATTCTAAATTAGTCCTCAAACTTTTAAAGTTTCAATTTC
** * * * * *
215015 ATCCCCCAATTATGACTCCATTCTAAATCAATCCTCAAACTTTTTCAAAGTTTCAATTTC
1 ATCCCTAAACTATGATTTCATTCTAAATTAGTCCTCAAAC-TTTT-AAAGTTTCAATTTC
215075 ATCCC-AAACTAT
1 ATCCCTAAACTAT
215087 ACGTATATAC
Statistics
Matches: 106, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
58 18 0.17
59 32 0.30
60 54 0.51
61 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.40
Consensus pattern (58 bp):
ATCCCTAAACTATGATTTCATTCTAAATTAGTCCTCAAACTTTTAAAGTTTCAATTTC
Found at i:215029 original size:59 final size:59
Alignment explanation
Indices: 214928--215086 Score: 171
Period size: 59 Copynumber: 2.7 Consensus size: 59
214918 TTTAAATTGG
* * * * * *
214928 TCCTCAAAC-TTTTAAATGTTTCAATTCCATCCCTAAACTATGATTATCATTCTAAATTAG
1 TCCTCAAACTTTTTAAA-GTTTCAATTTCATCCCCAAACTATGACT-CCATTCTAAATCAA
* * * * *
214988 TCTTCAGACTTTTT-ACGTTTCAATTTCATCCCCCAATTATGACTCCATTCTAAATCAA
1 TCCTCAAACTTTTTAAAGTTTCAATTTCATCCCCAAACTATGACTCCATTCTAAATCAA
215046 TCCTCAAACTTTTTCAAAGTTTCAATTTCAT-CCCAAACTAT
1 TCCTCAAACTTTTT-AAAGTTTCAATTTCATCCCCAAACTAT
215087 ACGTATATAC
Statistics
Matches: 80, Mismatches: 16, Indels: 7
0.78 0.16 0.07
Matches are distributed among these distances:
58 23 0.29
59 31 0.39
60 22 0.28
61 4 0.05
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.40
Consensus pattern (59 bp):
TCCTCAAACTTTTTAAAGTTTCAATTTCATCCCCAAACTATGACTCCATTCTAAATCAA
Done.