Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006636.1 Hibiscus syriacus cultivar Beakdansim tig00016328_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: 160039
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:5560 original size:47 final size:45
Alignment explanation
Indices: 5491--5616 Score: 168
Period size: 47 Copynumber: 2.8 Consensus size: 45
5481 TATAAAATCT
*
5491 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAA-ATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTA-CAAATATA
* *
5536 TTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATAAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACAAATATA
*
5583 CTTGCCA-TTATT-CATAAGCTCGTAAGCTTATTTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTT
5617 CATACTTACC
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
43 22 0.30
44 3 0.04
45 9 0.12
46 5 0.07
47 34 0.47
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACAAATATA
Found at i:8742 original size:24 final size:24
Alignment explanation
Indices: 8715--8778 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
8705 CTACTTGACA
8715 TGGATTCTGTTATGATATCTAACT
1 TGGATTCTGTTATGATATCTAACT
* * *
8739 TGGATTCTGTTCTAATATCTGACT
1 TGGATTCTGTTATGATATCTAACT
* * *
8763 TGAATTATGTTTTGAT
1 TGGATTCTGTTATGAT
8779 TTTTGATATG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.48
Consensus pattern (24 bp):
TGGATTCTGTTATGATATCTAACT
Found at i:9100 original size:154 final size:155
Alignment explanation
Indices: 8805--9104 Score: 404
Period size: 154 Copynumber: 1.9 Consensus size: 155
8795 TACGGATGGA
* * *
8805 AAATGTTTTATTTGGGGGGTATTACTGGAGGAAGAATATTTGCAAGCTCCTCGACTTTATACTCA
1 AAATGTTTTATTT-GGGGGTATTACTGGAGAAAGAATACTTACAAGCTCCTCGACTTTATACTCA
* * * *
8870 GGGCCTTACACGAAGTGATAGTGTGTGTATGGTTTTGGGGAACCTACACATTATGATGTGTTCGG
65 GGGCCTTACACGAAGTGACAGTGGGTGTATGGTTATGAGGAACCTACACATTATGATGTGTTCGG
8935 TTGGAGGGATTACTATGATTTTTGAT
130 TTGGAGGGATTACTATGATTTTTGAT
** * * * * * *
8961 AAATGTTTTATTT-GGGGTATTGTTGGAGAAAGTATACTTACAGGCTTCTCGGCTTTGTGCTCAG
1 AAATGTTTTATTTGGGGGTATTACTGGAGAAAGAATACTTACAAGCTCCTCGACTTTATACTCAG
* * * * *
9025 GTCTTTACTCGATGTGACAGTGGGTGTATGGTTATGAGGAACCTACACATTATGATGTGTTGGGT
66 GGCCTTACACGAAGTGACAGTGGGTGTATGGTTATGAGGAACCTACACATTATGATGTGTTCGGT
9090 TGGAGGGATTACTAT
131 TGGAGGGATTACTAT
9105 AGTTTCTGCA
Statistics
Matches: 124, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
154 111 0.90
156 13 0.10
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.36
Consensus pattern (155 bp):
AAATGTTTTATTTGGGGGTATTACTGGAGAAAGAATACTTACAAGCTCCTCGACTTTATACTCAG
GGCCTTACACGAAGTGACAGTGGGTGTATGGTTATGAGGAACCTACACATTATGATGTGTTCGGT
TGGAGGGATTACTATGATTTTTGAT
Found at i:14910 original size:6 final size:6
Alignment explanation
Indices: 14899--14928 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
14889 CAAAGCAATG
14899 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
1 ATAAAT ATAAAT ATAAAT ATAAAT ATAAAT
14929 GAGTAATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
ATAAAT
Found at i:16879 original size:29 final size:29
Alignment explanation
Indices: 16821--16889 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 29
16811 ACACAACAAT
*
16821 CCATAACTTTCTAAAATTACTAATTTGATC
1 CCATAACTTTTTAAAATTACTAA-TTGATC
16851 CCATAACTTTTTAAAATTACATAA-TGATC
1 CCATAACTTTTTAAAATTAC-TAATTGATC
*
16880 CC-TAAATTTT
1 CCATAACTTTT
16890 CTAAGGCTTG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
28 7 0.19
29 7 0.19
30 19 0.53
31 3 0.08
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.41
Consensus pattern (29 bp):
CCATAACTTTTTAAAATTACTAATTGATC
Found at i:48808 original size:24 final size:24
Alignment explanation
Indices: 48776--48823 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
48766 GCATGATATG
48776 GTACATAGATGTTTTATACATCAT
1 GTACATAGATGTTTTATACATCAT
48800 GTACATAGATGTTTTATACATCAT
1 GTACATAGATGTTTTATACATCAT
48824 CTAGAAGACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (24 bp):
GTACATAGATGTTTTATACATCAT
Found at i:71412 original size:28 final size:28
Alignment explanation
Indices: 71372--71430 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
71362 CGAGTCACAG
71372 ATATCACGTGACTTTTGAAACATTCTCT
1 ATATCACGTGACTTTTGAAACATTCTCT
71400 ATATCACGTGACTTTTGAAACATTCTCT
1 ATATCACGTGACTTTTGAAACATTCTCT
71428 ATA
1 ATA
71431 CTTGAAATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (28 bp):
ATATCACGTGACTTTTGAAACATTCTCT
Found at i:72185 original size:54 final size:54
Alignment explanation
Indices: 72154--72263 Score: 204
Period size: 54 Copynumber: 2.1 Consensus size: 54
72144 TTGTACACTT
72154 AGTACCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
1 AGTACCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
*
72208 AGTGCCAATACGGAAATTCATAAACTTATTATGAATTTC-TAAGTTGCACACAC
1 AGTACCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
72261 AGT
1 AGT
72264 GCCCATTTGG
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 17 0.31
54 38 0.69
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (54 bp):
AGTACCAATACGGAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACAC
Found at i:76889 original size:5 final size:5
Alignment explanation
Indices: 76879--76903 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
76869 GTTTCGAATG
76879 AAAAC AAAAC AAAAC AAAAC AAAAC
1 AAAAC AAAAC AAAAC AAAAC AAAAC
76904 TTCACATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.20, G:0.00, T:0.00
Consensus pattern (5 bp):
AAAAC
Found at i:80420 original size:6 final size:6
Alignment explanation
Indices: 80404--80454 Score: 95
Period size: 6 Copynumber: 8.7 Consensus size: 6
80394 ACAACTCAAT
80404 TATTA- TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC
1 TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC TATTAC
80451 TATT
1 TATT
80455 TTAGATATGT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.11
6 40 0.89
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (6 bp):
TATTAC
Found at i:81871 original size:38 final size:38
Alignment explanation
Indices: 81829--81947 Score: 89
Period size: 38 Copynumber: 3.1 Consensus size: 38
81819 ATCATGGTTC
81829 ATTAAGAAATAGGTTGTGATATGTAATTTTAATATTTT
1 ATTAAGAAATAGGTTGTGATATGTAATTTTAATATTTT
* * * ** * * * *
81867 ATTAATAAAATAGATTGCGCCCAAG-AA-TGTCATAATTT
1 ATTAA-GAAATAGGTTGTG-ATATGTAATTTTAATATTTT
* * *
81905 ACTAAGAAATAGGTTGTGATCTGTAATGTTAATATTTTT
1 ATTAAGAAATAGGTTGTGATATGTAATTTTAATA-TTTT
81944 ATTA
1 ATTA
81948 GTAAAATAAG
Statistics
Matches: 54, Mismatches: 22, Indels: 9
0.64 0.26 0.11
Matches are distributed among these distances:
36 1 0.02
37 12 0.22
38 21 0.39
39 18 0.33
40 2 0.04
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.41
Consensus pattern (38 bp):
ATTAAGAAATAGGTTGTGATATGTAATTTTAATATTTT
Found at i:81892 original size:76 final size:77
Alignment explanation
Indices: 81812--81989 Score: 234
Period size: 76 Copynumber: 2.3 Consensus size: 77
81802 TGATTGTGTT
* * *
81812 CAAGAATATCATGGTTCATTAAGAAATAGGTTGTGATATGTAATTTTAATA-TTTTATTAATAAA
1 CAAGAATGTCATGGTTCACTAAGAAATAGGTTGTGATATGTAATGTTAATATTTTTATTAATAAA
*
81876 AT-AGATTGCGCC
66 ATAAG-TTGCACC
** * * *
81888 CAAGAATGTCATAATTTACTAAGAAATAGGTTGTGATCTGTAATGTTAATATTTTTATTAGTAAA
1 CAAGAATGTCATGGTTCACTAAGAAATAGGTTGTGATATGTAATGTTAATATTTTTATTAATAAA
81953 ATAAGTTGCACC
66 ATAAGTTGCACC
* *
81965 AAATAATGTCATGGTTCACTAAGAA
1 CAAGAATGTCATGGTTCACTAAGAA
81990 TATTAATATT
Statistics
Matches: 86, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
76 44 0.51
77 40 0.47
78 2 0.02
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.37
Consensus pattern (77 bp):
CAAGAATGTCATGGTTCACTAAGAAATAGGTTGTGATATGTAATGTTAATATTTTTATTAATAAA
ATAAGTTGCACC
Found at i:82777 original size:29 final size:29
Alignment explanation
Indices: 82745--82937 Score: 99
Period size: 29 Copynumber: 6.7 Consensus size: 29
82735 TAAATTACTT
*
82745 TTTTTATAAATTACATTTAA-GGACAAAGA
1 TTTTTATAAATTACA-ATAATGGACAAAGA
* * **
82774 TTTTTATAAACTATAATAATGGACAAATC
1 TTTTTATAAATTACAATAATGGACAAAGA
* * ** **
82803 TTTTTATAAATTATAATAGA-AGTTAAATC
1 TTTTTATAAATTACAATA-ATGGACAAAGA
* * **
82832 TTCTTATAAATTACAATAAAGGACAAATC
1 TTTTTATAAATTACAATAATGGACAAAGA
* * * * *
82861 TTTTTATAATTTAAAATAA-GAAAAAAATA
1 TTTTTATAAATTACAATAATG-GACAAAGA
*
82890 TTTTTATAAATTATAATAAT-GACATATA-A
1 TTTTTATAAATTACAATAATGGACA-A-AGA
**
82919 TTTTTGCAAATTACAATAA
1 TTTTTATAAATTACAATAA
82938 CAACTCATAA
Statistics
Matches: 130, Mismatches: 27, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
28 7 0.05
29 121 0.93
30 2 0.02
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (29 bp):
TTTTTATAAATTACAATAATGGACAAAGA
Found at i:82839 original size:58 final size:58
Alignment explanation
Indices: 82777--82910 Score: 171
Period size: 58 Copynumber: 2.3 Consensus size: 58
82767 ACAAAGATTT
* * ** *
82777 TTATAAACTATAATAATGGACAAATCTTTTTATAAATTATAAT-AGAAGTTAAATCTTC
1 TTATAAATTATAATAATGGACAAATCTTTTTATAAATTAAAATAAGAA-AAAAATATTC
* * * *
82835 TTATAAATTACAATAAAGGACAAATCTTTTTATAATTTAAAATAAGAAAAAAATATTT
1 TTATAAATTATAATAATGGACAAATCTTTTTATAAATTAAAATAAGAAAAAAATATTC
82893 TTATAAATTATAATAATG
1 TTATAAATTATAATAATG
82911 ACATATAATT
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 60 0.94
59 4 0.06
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (58 bp):
TTATAAATTATAATAATGGACAAATCTTTTTATAAATTAAAATAAGAAAAAAATATTC
Found at i:82843 original size:87 final size:87
Alignment explanation
Indices: 82748--82907 Score: 214
Period size: 87 Copynumber: 1.8 Consensus size: 87
82738 ATTACTTTTT
* * * * * *
82748 TTATAAATTACATTTAAGGACAAAGATTTTTATAAACTATAATAATG-GACAAATCTTTTTATAA
1 TTATAAATTACAATAAAGGACAAAGATTTTTATAAACTAAAATAA-GAAAAAAATATTTTTATAA
82812 ATTATAATAGAAGTTAAATCTTC
65 ATTATAATAGAAGTTAAATCTTC
** **
82835 TTATAAATTACAATAAAGGACAAATCTTTTTATAATTTAAAATAAGAAAAAAATATTTTTATAAA
1 TTATAAATTACAATAAAGGACAAAGATTTTTATAAACTAAAATAAGAAAAAAATATTTTTATAAA
82900 TTATAATA
66 TTATAATA
82908 ATGACATATA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
86 1 0.02
87 61 0.98
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.39
Consensus pattern (87 bp):
TTATAAATTACAATAAAGGACAAAGATTTTTATAAACTAAAATAAGAAAAAAATATTTTTATAAA
TTATAATAGAAGTTAAATCTTC
Found at i:82947 original size:29 final size:28
Alignment explanation
Indices: 82915--82983 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
82905 ATAATGACAT
82915 ATAATTTTTGCAAATTACAATAACAACTC
1 ATAATTTTTGCAAATTACAATAACAAC-C
* *
82944 ATAA-TTTTACATATTACAATAACAACC
1 ATAATTTTTGCAAATTACAATAACAACC
82971 -TATATTTTTGCAA
1 ATA-ATTTTTGCAA
82984 TCACTACATT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
26 2 0.06
27 2 0.06
28 26 0.76
29 4 0.12
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (28 bp):
ATAATTTTTGCAAATTACAATAACAACC
Found at i:82979 original size:28 final size:28
Alignment explanation
Indices: 82887--82979 Score: 82
Period size: 28 Copynumber: 3.3 Consensus size: 28
82877 TAAGAAAAAA
* * **
82887 ATATTTTTATAAATTATAATAATGACAT-
1 ATATTTTTACAAATTACAATAACAAC-TC
*
82915 ATAATTTTTGCAAATTACAATAACAACTC
1 AT-ATTTTTACAAATTACAATAACAACTC
* *
82944 ATAATTTTACATATTACAATAACAAC-C
1 ATATTTTTACAAATTACAATAACAACTC
82971 TATATTTTT
1 -ATATTTTT
82980 GCAATCACTA
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
27 1 0.02
28 31 0.58
29 21 0.40
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (28 bp):
ATATTTTTACAAATTACAATAACAACTC
Found at i:84830 original size:13 final size:13
Alignment explanation
Indices: 84812--84838 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
84802 TAAATTATGA
84812 CGAATCAAATTGT
1 CGAATCAAATTGT
84825 CGAATCAAATTGT
1 CGAATCAAATTGT
84838 C
1 C
84839 ACGAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (13 bp):
CGAATCAAATTGT
Found at i:85976 original size:17 final size:17
Alignment explanation
Indices: 85956--85994 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
85946 AAGAGAAAAC
85956 AAGAAAAC-AAAGAAGAA
1 AAGAAAACAAAAG-AGAA
*
85973 AAGAAAAGAAAAGAGAA
1 AAGAAAACAAAAGAGAA
85990 AAGAA
1 AAGAA
85995 GAAAAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.77, C:0.03, G:0.21, T:0.00
Consensus pattern (17 bp):
AAGAAAACAAAAGAGAA
Found at i:85978 original size:5 final size:5
Alignment explanation
Indices: 85968--86009 Score: 59
Period size: 5 Copynumber: 8.4 Consensus size: 5
85958 GAAAACAAAG
*
85968 AAGAA AAGAA AAGAA AAGAGA AA-AG AAGAA AAGAA AAGAA AA
1 AAGAA AAGAA AAGAA AAGA-A AAGAA AAGAA AAGAA AAGAA AA
86010 ATTAATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 2 0.06
5 28 0.85
6 3 0.09
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:86000 original size:20 final size:18
Alignment explanation
Indices: 85949--86010 Score: 72
Period size: 20 Copynumber: 3.4 Consensus size: 18
85939 AGATCATAAG
* *
85949 AGAAAACAAGAAAA-CAA
1 AGAAAAAAAGAAAAGAAA
*
85966 AGAAGAAAAGAAAAGAAA
1 AGAAAAAAAGAAAAGAAA
85984 AGAGAAAAGAAGAAAAGAAA
1 AGA-AAAA-AAGAAAAGAAA
86004 AGAAAAA
1 AGAAAAA
86011 TTAATTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
17 12 0.32
18 5 0.13
19 7 0.18
20 14 0.37
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (18 bp):
AGAAAAAAAGAAAAGAAA
Found at i:89320 original size:8 final size:8
Alignment explanation
Indices: 89294--89327 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
89284 AAAAAATAAG
89294 ACTCTCAA
1 ACTCTCAA
*
89302 ATCTTTCAA
1 A-CTCTCAA
89311 ACTCTCAA
1 ACTCTCAA
89319 ACTCTCAA
1 ACTCTCAA
89327 A
1 A
89328 ATGAGGCGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.38, C:0.32, G:0.00, T:0.29
Consensus pattern (8 bp):
ACTCTCAA
Found at i:92557 original size:24 final size:26
Alignment explanation
Indices: 92524--92576 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
92514 ATTACAATTC
*
92524 AAACAATTAA-ATAATAAAAT-AATAA
1 AAACAATTAAGA-AACAAAATAAATAA
92549 AAAC-ATTAAGAAACAAAATAAATAA
1 AAACAATTAAGAAACAAAATAAATAA
92574 AAA
1 AAA
92577 GTACATCTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.74, C:0.06, G:0.02, T:0.19
Consensus pattern (26 bp):
AAACAATTAAGAAACAAAATAAATAA
Found at i:94176 original size:26 final size:26
Alignment explanation
Indices: 94147--94196 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
94137 AAAAATAGTA
94147 TATTAAAAT-ATAATAAAATAATAAGC
1 TATT-AAATGATAATAAAATAATAAGC
* *
94173 TATTAAATGATTATAATATAATAA
1 TATTAAATGATAATAAAATAATAA
94197 ATAATTTACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (26 bp):
TATTAAATGATAATAAAATAATAAGC
Found at i:96533 original size:12 final size:12
Alignment explanation
Indices: 96516--96540 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
96506 AAACAGTATC
96516 AATACCCAATGA
1 AATACCCAATGA
96528 AATACCCAATGA
1 AATACCCAATGA
96540 A
1 A
96541 CTAGTATCAA
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:0.24, G:0.08, T:0.16
Consensus pattern (12 bp):
AATACCCAATGA
Found at i:96629 original size:20 final size:20
Alignment explanation
Indices: 96600--96646 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
96590 AGAACAATAT
*
96600 CGATAGTGTTCATCTAGTAC
1 CGATACTGTTCATCTAGTAC
96620 CGATACTGTTCATCTAGTAC
1 CGATACTGTTCATCTAGTAC
*
96640 CTATACT
1 CGATACT
96647 CAAGCCCAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (20 bp):
CGATACTGTTCATCTAGTAC
Found at i:104199 original size:21 final size:21
Alignment explanation
Indices: 104174--104225 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
104164 GCCGTGCTGA
104174 TGTTGGTTGTTC-TTCAGTTGG
1 TGTTGGTTGTTCTTTCA-TTGG
104195 TGTTGGTTGTTCTTTCATTGG
1 TGTTGGTTGTTCTTTCATTGG
* *
104216 AGTGGGTTGT
1 TGTTGGTTGT
104226 ACATGAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 24 0.86
22 4 0.14
ACGTcount: A:0.06, C:0.08, G:0.35, T:0.52
Consensus pattern (21 bp):
TGTTGGTTGTTCTTTCATTGG
Found at i:107749 original size:336 final size:336
Alignment explanation
Indices: 107129--107800 Score: 1200
Period size: 336 Copynumber: 2.0 Consensus size: 336
107119 ACTAGAAATG
* * * *
107129 CATGGCCATGCTTGAATAAGTTGATATGTGATATCATATTCGTTAATTATAGTCTGCTCTAGATA
1 CATGGCCATGCTCGAATAAGTTGATATGTGATATCATATTCATTAATTATAGTATACTCTAGATA
* *
107194 TCAAGACACAATAGATGGGCTATACAAGTGTGACTATTCTAAGACTTGTGTCTATTCTAGATATA
66 TCAAGAAACAATAGATGGGCTATACAAGTGTGACTATTCTAAGACTTGTGCCTATTCTAGATATA
107259 AAGGAAAAAAGGATATAATAAATAAAAGAGTTAATCACAAAGATGATATGTCGAATCATAATTTC
131 AAGGAAAAAAGGATATAATAAATAAAAGAGTTAATCACAAAGATGATATGTCGAATCATAATTTC
107324 TTGTAACTTAGGTGACAATGATATATTGCTAGATGTCACTCATTGTATGTAATATTAGAATTGTT
196 TTGTAACTTAGGTGACAATGATATATTGCTAGATGTCACTCATTGTATGTAATATTAGAATTGTT
* * *
107389 CTAATAATTACTATTAATGTTACAAGAACCTATAGGGTCACACACTAGGATTGAAATGAGCAAAA
261 CTAATAATTACTACTAACGTTACAAGAACCTACAGGGTCACACACTAGGATTGAAATGAGCAAAA
*
107454 GTGTACAATTT
326 ATGTACAATTT
*
107465 CATGGCCATGCTCGAATAAGTTTATATGTGATATCATATTCATTAATTATAGTATACTCTAGATA
1 CATGGCCATGCTCGAATAAGTTGATATGTGATATCATATTCATTAATTATAGTATACTCTAGATA
107530 TCAAGAAACAATAGATGGGCTATACAAGTGTGACTATTCTAAGACTTGTGCCTATTCTAGATATA
66 TCAAGAAACAATAGATGGGCTATACAAGTGTGACTATTCTAAGACTTGTGCCTATTCTAGATATA
* * *
107595 AAGGAAAAAAGGATATAATACATAAAAGAGTTAATCACGAAGATGATTTGTCGAATCATAATTTC
131 AAGGAAAAAAGGATATAATAAATAAAAGAGTTAATCACAAAGATGATATGTCGAATCATAATTTC
*
107660 TTGTAACTTAGGTGACAATGATATATTTCTAGATGTCACTCATTGTATGTAATATTAGAATTGTT
196 TTGTAACTTAGGTGACAATGATATATTGCTAGATGTCACTCATTGTATGTAATATTAGAATTGTT
*
107725 CTAATAATTACTACTAACGTTACAAGAACCTACAGGGTCACACCCTAGGATTGAAATGAGCAAAA
261 CTAATAATTACTACTAACGTTACAAGAACCTACAGGGTCACACACTAGGATTGAAATGAGCAAAA
107790 ATGTACAATTT
326 ATGTACAATTT
107801 GTTGTATGTT
Statistics
Matches: 320, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
336 320 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.33
Consensus pattern (336 bp):
CATGGCCATGCTCGAATAAGTTGATATGTGATATCATATTCATTAATTATAGTATACTCTAGATA
TCAAGAAACAATAGATGGGCTATACAAGTGTGACTATTCTAAGACTTGTGCCTATTCTAGATATA
AAGGAAAAAAGGATATAATAAATAAAAGAGTTAATCACAAAGATGATATGTCGAATCATAATTTC
TTGTAACTTAGGTGACAATGATATATTGCTAGATGTCACTCATTGTATGTAATATTAGAATTGTT
CTAATAATTACTACTAACGTTACAAGAACCTACAGGGTCACACACTAGGATTGAAATGAGCAAAA
ATGTACAATTT
Found at i:112270 original size:20 final size:21
Alignment explanation
Indices: 112232--112270 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
112222 CATCAAGGCC
*
112232 TTTGTAGAAGTCATGAAATCT
1 TTTGTAGAAGGCATGAAATCT
*
112253 TTTGTCGAAGGCAT-AAAT
1 TTTGTAGAAGGCATGAAAT
112271 TCATTCAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (21 bp):
TTTGTAGAAGGCATGAAATCT
Found at i:115672 original size:3 final size:3
Alignment explanation
Indices: 115664--115751 Score: 65
Period size: 3 Copynumber: 30.3 Consensus size: 3
115654 TGGTTATAAA
* * * * *
115664 TAT TAT TA- TAT AAT TAT TAC GAT TA- TAT TAT TAT TAT TAT TAT AAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
115710 AAT TA- TAT TAT AAT AAT TAT TAG TAT TAT TAT TAG TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
115752 TATGTTTTCT
Statistics
Matches: 66, Mismatches: 16, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
2 6 0.09
3 60 0.91
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:115681 original size:14 final size:15
Alignment explanation
Indices: 115657--115750 Score: 75
Period size: 15 Copynumber: 6.3 Consensus size: 15
115647 TTTTGTCTGG
*
115657 TTATAAATATTATTA
1 TTATAATTATTATTA
**
115672 -TATAATTATTACGA
1 TTATAATTATTATTA
115686 TTATATTATTATTATTA
1 TTATA--ATTATTATTA
**
115703 TTATAACAATTA-TA
1 TTATAATTATTATTA
*
115717 TTATAATAATTATTA
1 TTATAATTATTATTA
* * *
115732 GTATTATTATTAGTA
1 TTATAATTATTATTA
115747 TTAT
1 TTAT
115751 TTATGTTTTC
Statistics
Matches: 62, Mismatches: 13, Indels: 8
0.75 0.16 0.10
Matches are distributed among these distances:
14 24 0.39
15 25 0.40
17 13 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (15 bp):
TTATAATTATTATTA
Found at i:115741 original size:26 final size:26
Alignment explanation
Indices: 115663--115731 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 26
115653 CTGGTTATAA
* * * *
115663 ATATTATTAT-ATAATTATTACGATT
1 ATATTATAATAATTATTATAACAATT
* *
115688 ATATTATTATTATTATTATAACAATT
1 ATATTATAATAATTATTATAACAATT
115714 ATATTATAATAATTATTA
1 ATATTATAATAATTATTA
115732 GTATTATTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
25 10 0.26
26 28 0.74
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.52
Consensus pattern (26 bp):
ATATTATAATAATTATTATAACAATT
Found at i:119161 original size:45 final size:45
Alignment explanation
Indices: 119094--119183 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
119084 CTTGAATTTA
* * * *
119094 TTTATTTTTACAAGAAGTATGTGAACTAGAGATCATGTGGTTAGG
1 TTTATTTTTACAACAAGCATGTGAACTAGAGACCATGAGGTTAGG
** *
119139 TTTATTTTTTGAACAAGCATGTGAATTAGAGACCATGAGGTTAGG
1 TTTATTTTTACAACAAGCATGTGAACTAGAGACCATGAGGTTAGG
119184 ATTTTTTGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.37
Consensus pattern (45 bp):
TTTATTTTTACAACAAGCATGTGAACTAGAGACCATGAGGTTAGG
Found at i:124147 original size:8 final size:8
Alignment explanation
Indices: 124134--124247 Score: 80
Period size: 8 Copynumber: 14.6 Consensus size: 8
124124 TTTGCTTGAA
124134 GAAAAAAT
1 GAAAAAAT
*
124142 GAAAAAAA
1 GAAAAAAT
*
124150 AAATGAAAAT
1 GAA--AAAAT
124160 G-AAAAAT
1 GAAAAAAT
*
124167 GAAAAAAAAG
1 G--AAAAAAT
*
124177 GAAAAAAG
1 GAAAAAAT
124185 GAAAAAA-
1 GAAAAAAT
* *
124192 G-GAAAAG
1 GAAAAAAT
124199 GAAAAAAT
1 GAAAAAAT
124207 G-AAAAAT
1 GAAAAAAT
124214 G-AAAAAT
1 GAAAAAAT
124221 G-AAAAAT
1 GAAAAAAT
124228 GAAAAAA-
1 GAAAAAAT
*
124235 GAAAAAAA
1 GAAAAAAT
124243 GAAAA
1 GAAAA
124248 TAAAATACAA
Statistics
Matches: 89, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
6 4 0.04
7 36 0.40
8 38 0.43
9 1 0.01
10 10 0.11
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (8 bp):
GAAAAAAT
Found at i:124158 original size:7 final size:7
Alignment explanation
Indices: 124136--124240 Score: 90
Period size: 7 Copynumber: 14.7 Consensus size: 7
124126 TGCTTGAAGA
124136 AAAAATG
1 AAAAATG
124143 AAAAA--
1 AAAAATG
124148 AAAAATG
1 AAAAATG
124155 -AAAATG
1 AAAAATG
124161 AAAAATG
1 AAAAATG
*
124168 AAAAAAAAGG
1 ---AAAAATG
*
124178 AAAAAAGG
1 -AAAAATG
*
124186 AAAAAAG
1 AAAAATG
* *
124193 GAAAAGG
1 AAAAATG
124200 AAAAAATG
1 -AAAAATG
124208 AAAAATG
1 AAAAATG
124215 AAAAATG
1 AAAAATG
124222 AAAAATG
1 AAAAATG
*
124229 AAAAAAG
1 AAAAATG
124236 AAAAA
1 AAAAA
124241 AAGAAAATAA
Statistics
Matches: 84, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
5 5 0.06
6 6 0.07
7 54 0.64
8 13 0.15
10 6 0.07
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (7 bp):
AAAAATG
Found at i:124247 original size:14 final size:14
Alignment explanation
Indices: 124132--124252 Score: 91
Period size: 14 Copynumber: 9.1 Consensus size: 14
124122 AATTTGCTTG
124132 AAGAAAAAATG-AA
1 AAGAAAAAATGAAA
124145 AA-AAAAAATGAAA
1 AAGAAAAAATGAAA
*
124158 ATG-AAAAATGAAA
1 AAGAAAAAATGAAA
*
124171 AA-AAAGGAA--AAA
1 AAGAAA-AAATGAAA
* *
124183 AGGAAAAAAGGAAA
1 AAGAAAAAATGAAA
*
124197 AGGAAAAAATGAAA
1 AAGAAAAAATGAAA
124211 AATG-AAAAATGAAA
1 AA-GAAAAAATGAAA
124225 AATGAAAAAA-GAAA
1 AA-GAAAAAATGAAA
124239 AA-AAGAAAAT-AAA
1 AAGAA-AAAATGAAA
124252 A
1 A
124253 TACAAAACAA
Statistics
Matches: 90, Mismatches: 7, Indels: 22
0.76 0.06 0.18
Matches are distributed among these distances:
12 16 0.18
13 29 0.32
14 39 0.43
15 6 0.07
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (14 bp):
AAGAAAAAATGAAA
Found at i:125578 original size:37 final size:37
Alignment explanation
Indices: 125528--125652 Score: 180
Period size: 37 Copynumber: 3.4 Consensus size: 37
125518 TTAAGAAGTG
*
125528 AATCCATCTTAAGCCTTCACTGAAGAGTAGTGAAGCA
1 AATCCATCATAAGCCTTCACTGAAGAGTAGTGAAGCA
*
125565 AATCCATCATAAGCCTTCACCGAAGAGTAGTGAAGCA
1 AATCCATCATAAGCCTTCACTGAAGAGTAGTGAAGCA
* * *
125602 AATCCATCTTAAGCATTTACAT-AAGAGTAGTGAAGCA
1 AATCCATCATAAGCCTTCAC-TGAAGAGTAGTGAAGCA
125639 AATCCATCAGTAAG
1 AATCCATCA-TAAG
125653 TCTTTCGAGC
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
37 75 0.95
38 4 0.05
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (37 bp):
AATCCATCATAAGCCTTCACTGAAGAGTAGTGAAGCA
Found at i:125723 original size:41 final size:41
Alignment explanation
Indices: 125646--125724 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
125636 GCAAATCCAT
* *
125646 CAGTAAGTCTTTCGAGCATGATAATGAAGTCTTTTGGGCCA
1 CAGTAAGTCTTTCGAGCATGATAATGAAATCCTTTGGGCCA
* *
125687 CAGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGG
1 CAGTAAGTCTTTCGAGCATGATAATGAAATCCTTTGGG
125725 TAATTTGTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (41 bp):
CAGTAAGTCTTTCGAGCATGATAATGAAATCCTTTGGGCCA
Found at i:125824 original size:42 final size:42
Alignment explanation
Indices: 125777--125874 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
125767 CAATAAGTGC
* * *
125777 CATCAGTAAGTCTTTCGAGTATGATGATGAAATCCTTCGGGT
1 CATCAGTAAGTCTTTCAAGCATGATGATGAAATCCATCGGGT
* * *
125819 CATCAGTAAGTCTTTCAAGCATGATTATTAAATTCATCGGGT
1 CATCAGTAAGTCTTTCAAGCATGATGATGAAATCCATCGGGT
*
125861 AATTCA-TAAGTCTT
1 CA-TCAGTAAGTCTT
125875 CACGGAAGAG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 45 0.94
43 3 0.06
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (42 bp):
CATCAGTAAGTCTTTCAAGCATGATGATGAAATCCATCGGGT
Found at i:125883 original size:135 final size:133
Alignment explanation
Indices: 125642--125908 Score: 381
Period size: 135 Copynumber: 2.0 Consensus size: 133
125632 TGAAGCAAAT
* * * *
125642 CCATCAGTAAGTCTTTCGAGCATGATAATGAAGTCTTTTGGGCCACAGTAAGTCTTTCGAGCATG
1 CCATCAGTAAGTCTTTCGAGCATGATAATGAAATCCTTCGGGCCACAGTAAGTCTTTCAAGCATG
* * **
125707 ATGATTAAATCCTTTGGGTAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGCAAATCCATCAATA
66 ATGATTAAATCCATCGGGTAATTCATAAGCCTTCACGGAAGAGTAGTGAAGCAAA-CCATCAATA
125772 AGTG
130 AGTG
* * *
125776 CCATCAGTAAGTCTTTCGAGTATGATGATGAAATCCTTCGGGTCATCAGTAAGTCTTTCAAGCAT
1 CCATCAGTAAGTCTTTCGAGCATGATAATGAAATCCTTCGGGCCA-CAGTAAGTCTTTCAAGCAT
* * * *
125841 GATTATTAAATTCATCGGGTAATTCATAAGTCTTCACGGAAGAGTAGTGAAGCAAACCATCAGTA
65 GATGATTAAATCCATCGGGTAATTCATAAGCCTTCACGGAAGAGTAGTGAAGCAAACCATCAATA
125906 AGT
130 AGT
125909 CTTTCAAACA
Statistics
Matches: 117, Mismatches: 15, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
134 50 0.43
135 67 0.57
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (133 bp):
CCATCAGTAAGTCTTTCGAGCATGATAATGAAATCCTTCGGGCCACAGTAAGTCTTTCAAGCATG
ATGATTAAATCCATCGGGTAATTCATAAGCCTTCACGGAAGAGTAGTGAAGCAAACCATCAATAA
GTG
Found at i:126591 original size:53 final size:53
Alignment explanation
Indices: 126506--127400 Score: 1115
Period size: 53 Copynumber: 16.8 Consensus size: 53
126496 ATCAAACCAT
* * *
126506 AAGATTGTTCCAGTTCTACTCCCTGAAGCAAGAGAGAGCGAACCCGTTGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * *
126559 AAGATTATTCGAGTTCTACTCCCTGAAACAAGAGGGAGTGAACCCGTAGGTAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
*
126612 AAGATTGTTCGAGTTCTACTCTCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * * *
126665 AAGATTGTTCAAATTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTTGGAAA
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * * * *
126718 AAGATTATTCGAGTTCTACTCCCTAAAGTAAGAGAGAGCCAACCCATAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * *
126771 AAGATTGTTCAAGTTCTACTCCCTGAAACAAGAGGGA-CTGAACCCGTTGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGC-GAACCCGTAGGCAG
* * * *
126824 AAGATTGCTT-GAGTTTTACTCCCTGAAGCAAGAGGGAACGAACCCATAGGTAG
1 AAGATTG-TTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * * *
126877 AAGA---TTCTAGTTCAACTCCCTGGAA-CAAGAGGGAGCAAACCTGTAGGAAG
1 AAGATTGTTCGAGTTCTACTCCCT-GAAGCAAGAGGGAGCGAACCCGTAGGCAG
*
126927 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGTAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * *
126980 TAGATTGTTCGAGTTCTACTCCCTTAAGCAAGAGGGAGTGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
*
127033 AAGATTGTTCGAGTTCTATACTCCCTGAAGCAAGAGGGTA-CGAACCCGTTGGCAG
1 AAGATTGTTCGAGTTC--TACTCCCTGAAGCAAGAGGG-AGCGAACCCGTAGGCAG
* * * *
127088 CAGATTGTTCGAGTTCGTACTCCCTGAAGCAAGAGGGAGTGAACTCGTAGGTAG
1 AAGATTGTTCGAGTTC-TACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * * * * *
127142 AAGATTGTTCTAGTTCTAATCACTGGAA-CAAAAGGGAGCAAACCCGTAGGTAG
1 AAGATTGTTCGAGTTCTACTCCCT-GAAGCAAGAGGGAGCGAACCCGTAGGCAG
*
127195 AAAATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * ** * *
127248 TAGATTGTTTGAGTTCTACTCCCTGAAGCAAGAGGGAATGAACCCATAGGAAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* *
127301 AAGATTGTTCGAGTTCTACACTCCCTGAAGCAATAGGGTA-CGAACCCGTTGGCAG
1 AAGATTGTTCGAGTTCT--ACTCCCTGAAGCAAGAGGG-AGCGAACCCGTAGGCAG
* *
127356 CAGATTGTTCGAGTTCTACTCCCTAAAGCAAGAGGGAGCGAACCC
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCC
127401 AAGCAGATTG
Statistics
Matches: 720, Mismatches: 103, Indels: 38
0.84 0.12 0.04
Matches are distributed among these distances:
49 2 0.00
50 35 0.05
51 3 0.00
52 8 0.01
53 527 0.73
54 51 0.07
55 92 0.13
56 2 0.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.22
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
Found at i:127612 original size:3 final size:3
Alignment explanation
Indices: 127588--127663 Score: 86
Period size: 3 Copynumber: 26.3 Consensus size: 3
127578 TAATTGTAAC
*
127588 TAT TA- TAT TAC TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
127634 AAT TA- TAT TAT AAT AAT TAT TAG TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
127664 TATGTTTTCT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
2 6 0.10
3 56 0.90
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:129054 original size:20 final size:20
Alignment explanation
Indices: 129031--129077 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
129021 ATTGGTTCAC
*
129031 GGAATGTAAGATTACCAGTG
1 GGAATATAAGATTACCAGTG
129051 GGAATATAAGATTACCA--G
1 GGAATATAAGATTACCAGTG
129069 GGAATATAA
1 GGAATATAA
129078 TTATTAGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 10 0.38
20 16 0.62
ACGTcount: A:0.43, C:0.09, G:0.26, T:0.23
Consensus pattern (20 bp):
GGAATATAAGATTACCAGTG
Found at i:142731 original size:12 final size:12
Alignment explanation
Indices: 142714--142753 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
142704 CTATTCAGGA
142714 TGATGTGCATGG
1 TGATGTGCATGG
* *
142726 TGATGTTCAAGG
1 TGATGTGCATGG
*
142738 TCATGTGCATGG
1 TGATGTGCATGG
142750 TGAT
1 TGAT
142754 CTTCATGATA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.20, C:0.10, G:0.35, T:0.35
Consensus pattern (12 bp):
TGATGTGCATGG
Found at i:149104 original size:12 final size:12
Alignment explanation
Indices: 149087--149133 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
149077 CTATTCAGGA
*
149087 TGATGTACATGG
1 TGATGTTCATGG
*
149099 TGATGTTCAAGG
1 TGATGTTCATGG
* *
149111 TCATGTGCATGG
1 TGATGTTCATGG
149123 TGATGTTCATG
1 TGATGTTCATG
149134 ATAACCAGCA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.21, C:0.11, G:0.32, T:0.36
Consensus pattern (12 bp):
TGATGTTCATGG
Found at i:150985 original size:31 final size:31
Alignment explanation
Indices: 150949--151010 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
150939 AAATGATAGA
150949 AAAATCAGATTTTGTTTAGAAGAGAAAAAAG
1 AAAATCAGATTTTGTTTAGAAGAGAAAAAAG
150980 AAAATCAGATTTTGTTTAGAAGAGAAAAAAG
1 AAAATCAGATTTTGTTTAGAAGAGAAAAAAG
151011 CTCATTTGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.52, C:0.03, G:0.19, T:0.26
Consensus pattern (31 bp):
AAAATCAGATTTTGTTTAGAAGAGAAAAAAG
Found at i:155775 original size:24 final size:23
Alignment explanation
Indices: 155748--155799 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
155738 CTAGATCCTA
155748 TTCAGGATGATGTGCATGATGATG
1 TTCAGG-TGATGTGCATGATGATG
* *
155772 TTCAAGGTGATGTGCATGGTGATT
1 TTC-AGGTGATGTGCATGATGATG
155796 TTCA
1 TTCA
155800 TATTAAACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.04
24 21 0.84
25 3 0.12
ACGTcount: A:0.23, C:0.10, G:0.31, T:0.37
Consensus pattern (23 bp):
TTCAGGTGATGTGCATGATGATG
Done.