Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001090.1 Hibiscus syriacus cultivar Beakdansim tig00002151_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: 74018
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6176 original size:37 final size:37
Alignment explanation
Indices: 6123--6227 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
6113 CATTTTCGTC
6123 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * * *
6160 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
6197 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
6228 CCATAAGCAC
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:6605 original size:15 final size:14
Alignment explanation
Indices: 6585--6618 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
6575 TATGGATATT
*
6585 TTATTCATTTATTTA
1 TTATTCATGT-TTTA
6600 TTATTCATGTTTTA
1 TTATTCATGTTTTA
6614 TTATT
1 TTATT
6619 ATATGTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.68
Consensus pattern (14 bp):
TTATTCATGTTTTA
Found at i:6617 original size:17 final size:16
Alignment explanation
Indices: 6580--6620 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
6570 TATTATATGG
6580 ATATT-TTATTCATTT
1 ATATTATTATTCATTT
6595 AT-TTATTATTCATGTT
1 ATATTATTATTCAT-TT
*
6611 TTATTATTAT
1 ATATTATTAT
6621 ATGTATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.09
15 10 0.45
16 3 0.14
17 7 0.32
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (16 bp):
ATATTATTATTCATTT
Found at i:6670 original size:12 final size:12
Alignment explanation
Indices: 6580--6712 Score: 52
Period size: 12 Copynumber: 11.1 Consensus size: 12
6570 TATTATATGG
6580 ATATTTTATTCAT
1 ATATTTTATT-AT
*
6593 TTA-TTTATTAT
1 ATATTTTATTAT
*
6604 -TCATGTT-TTAT
1 AT-ATTTTATTAT
*
6615 -TATTATATGTAT
1 ATATTTTAT-TAT
* *
6627 ATATATATATTAA
1 ATAT-TTTATTAT
6640 ATTATTTTCATT-T
1 A-TATTTT-ATTAT
6653 AT-TTTT-TTACT
1 ATATTTTATTA-T
6664 ATATTTTATTAT
1 ATATTTTATTAT
*
6676 ATA-TATA-TAT
1 ATATTTTATTAT
6686 ATATATTTATT-T
1 ATAT-TTTATTAT
6698 AATATTTTACTTAT
1 -ATATTTTA-TTAT
6712 A
1 A
6713 AGTCTAATAT
Statistics
Matches: 93, Mismatches: 9, Indels: 36
0.67 0.07 0.26
Matches are distributed among these distances:
9 2 0.02
10 10 0.11
11 19 0.20
12 28 0.30
13 22 0.24
14 12 0.13
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (12 bp):
ATATTTTATTAT
Found at i:6806 original size:23 final size:22
Alignment explanation
Indices: 6780--6826 Score: 53
Period size: 21 Copynumber: 2.1 Consensus size: 22
6770 ATTTTTTCGT
6780 TATTTAATTTATTAATTTA-TATA
1 TATTTAATTT-TT-ATTTATTATA
*
6803 TA-TTACTTTTTATTTATTATA
1 TATTTAATTTTTATTTATTATA
6824 TAT
1 TAT
6827 ATATATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 6 0.29
23 2 0.10
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTAATTTTTATTTATTATA
Found at i:6820 original size:14 final size:14
Alignment explanation
Indices: 6781--6836 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
6771 TTTTTTCGTT
6781 ATTTA-ATTTATTA
1 ATTTATATTTATTA
*
6794 ATTTATATATATTA
1 ATTTATATTTATTA
* *
6808 CTTTTTATTTATTA
1 ATTTATATTTATTA
*
6822 TATATATATATTATT
1 -ATTTATAT-TTATT
6837 CGTACTTTGT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
13 5 0.15
14 18 0.55
15 5 0.15
16 5 0.15
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTTATATTTATTA
Found at i:8080 original size:20 final size:20
Alignment explanation
Indices: 8055--8092 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
8045 ACCTTACTAA
8055 CTCTTTTCATTTT-TTTCCCT
1 CTCTTTT-ATTTTATTTCCCT
8075 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
8093 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.66
Consensus pattern (20 bp):
CTCTTTTATTTTATTTCCCT
Found at i:11904 original size:183 final size:183
Alignment explanation
Indices: 11596--12132 Score: 941
Period size: 183 Copynumber: 2.9 Consensus size: 183
11586 ATTAAATCCG
** *
11596 TAAAGCTGAGCTATTATACTAAGGCAATTGGTTATATAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
11661 ATAGATTATGTTCAAACTATGACATTGCTCGGACACTTGGCAATTCGATGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
11726 TTGCCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
11779 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* * **
11844 ATAGATTATGTTCAAACTATGACACTGCTCAGACACTTGGCAATTCGGTGTTTGCTCCACTTATT
66 ATAGATTATGTTCAAACTATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
*
11909 TTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
11962 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
**
12027 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
12091 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
12133 TAAACCTGAT
Statistics
Matches: 335, Mismatches: 18, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
182 1 0.00
183 334 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:13328 original size:36 final size:34
Alignment explanation
Indices: 13288--13401 Score: 86
Period size: 36 Copynumber: 3.2 Consensus size: 34
13278 CACTCAAATT
13288 TGTTTTTCTTAAAACATACTTTGTCTCACTTGAGAC
1 TGTTTTTCTTAAAACA-A-TTTGTCTCACTTGAGAC
* * * ** *
13324 TGTTTTTCTCGAAAGA-AGATTTATTTCACTCAAGAT
1 TGTTTTTCT-TAAA-ACA-ATTTGTCTCACTTGAGAC
*
13360 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGAC
1 TGTTTTTCTTAAAAC-A-ATTTGTCTCACTTGAGAC
*
13396 CGTTTT
1 TGTTTT
13402 CACTCGAAAG
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
34 1 0.02
35 3 0.05
36 49 0.83
37 5 0.08
38 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (34 bp):
TGTTTTTCTTAAAACAATTTGTCTCACTTGAGAC
Found at i:13364 original size:72 final size:75
Alignment explanation
Indices: 13272--13446 Score: 218
Period size: 72 Copynumber: 2.4 Consensus size: 75
13262 ATGCAGATGA
* * * *
13272 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCGTTTTCACTC
13334 GAAAGAA-G-AT
64 GAAAGAAGGCAT
*
13344 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
13409 AAGAAGGCAT
66 AAGAAGGCAT
**
13419 TTCATTTCACTCAAGGCTGTTTTT-TTAA
1 TT-ATTTCACTCAAGATTGTTTTTCTTAA
13447 GAAGATTTTA
Statistics
Matches: 90, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
71 1 0.01
72 50 0.56
73 11 0.12
74 1 0.01
75 8 0.09
76 19 0.21
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (75 bp):
TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCGTTTTCACTCGA
AAGAAGGCAT
Found at i:13481 original size:73 final size:72
Alignment explanation
Indices: 13288--13483 Score: 177
Period size: 72 Copynumber: 2.7 Consensus size: 72
13278 CACTCAAATT
* * * * *
13288 TGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTCGAAAGAAGATTTATTTC
1 TGTTTTTCTT-AAACA-AGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAAGATTTATTTC
*
13351 ACTCAAGAT
64 ACTCAAGAC
* *
13360 TGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATT
1 TGTTTTTCTT-AAACAAGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAA-G-ATTT-ATT
*
13425 TCACTCAAGGC
62 TCACTCAAGAC
* * * *
13436 TGTTTTT-TT-AAGAAGATTTTATCTTGCTTGAGATAG-TTTCCCTCGAAA
1 TGTTTTTCTTAAACAAGA-TTTATCTCGCTTGAGACAGTTTTCACTCGAAA
13484 CAGAAAATTT
Statistics
Matches: 106, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
71 1 0.01
72 37 0.35
73 27 0.25
74 16 0.15
75 6 0.06
76 19 0.18
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.41
Consensus pattern (72 bp):
TGTTTTTCTTAAACAAGATTTATCTCGCTTGAGACAGTTTTCACTCGAAAGAAGATTTATTTCAC
TCAAGAC
Found at i:13568 original size:36 final size:36
Alignment explanation
Indices: 13526--13640 Score: 115
Period size: 36 Copynumber: 3.1 Consensus size: 36
13516 CTTGAAAACA
** *
13526 TTTCCCTTGAAATTAATTTTTTCTCTCC-TGAGATAG
1 TTTCCCTTGAAAAAAATTTTGTCTC-CCTTGAGATAG
* *
13562 TTTCCCTCGAAACAGAAAATTTTGTCTCCCTTGAGATAA
1 TTTCCCTTG-AA-A-AAAATTTTGTCTCCCTTGAGATAG
** *
13601 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAAAAAATTTTGTCTCCCTTGAGATAG
13637 TTTC
1 TTTC
13641 TCTCCAAACA
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
36 32 0.49
37 3 0.05
38 5 0.08
39 25 0.38
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAAAAAATTTTGTCTCCCTTGAGATAG
Found at i:13597 original size:39 final size:37
Alignment explanation
Indices: 13540--13650 Score: 127
Period size: 36 Copynumber: 3.0 Consensus size: 37
13530 CCTTGAAATT
*
13540 AATTTTTTCTCTCC-TGAGATAGTTTCCCTCGAAACAG
1 AATTTTGTCTC-CCTTGAGATAGTTTCCCTCGAAACAG
* *
13577 AAAATTTTGTCTCCCTTGAGATAATTTCCCTTGAAAC-G
1 --AATTTTGTCTCCCTTGAGATAGTTTCCCTCGAAACAG
* * *
13615 AATTTTGTCTCCCTTGAGACAGTTTCTCTCCAAACA
1 AATTTTGTCTCCCTTGAGATAGTTTCCCTCGAAACA
13651 TAAACTTTGA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
36 30 0.48
38 3 0.05
39 29 0.47
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (37 bp):
AATTTTGTCTCCCTTGAGATAGTTTCCCTCGAAACAG
Found at i:14035 original size:105 final size:105
Alignment explanation
Indices: 13854--14471 Score: 940
Period size: 105 Copynumber: 5.9 Consensus size: 105
13844 GAGACAGAGT
* * * *
13854 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
13919 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
65 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
13960 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCTAA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAA
*
14025 TTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACG
66 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
14065 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAA
14130 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
14170 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAA
*
14235 TTTCAACTTCACAACGAAGGATATTGGACTCCAGATAACG
66 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * *
14275 CAAGTTCAACTCCACGATGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGAGTCAA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAA
* * * *
14335 TTTCAACTTCACAGCGAAGGATATGGGACTCGAGACAACA
66 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * * ** *
14375 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* *
14440 ATTTCAACTTCACGACGGAGGATATTGGACTC
65 ATTTCAACTTCACAACGAAGGATATTGGACTC
14472 GGAACAATGC
Statistics
Matches: 473, Mismatches: 33, Indels: 12
0.91 0.06 0.02
Matches are distributed among these distances:
100 79 0.17
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 308 0.65
106 73 0.15
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (105 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCAA
TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
Found at i:15067 original size:37 final size:37
Alignment explanation
Indices: 15014--15118 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
15004 CATTTTCGTC
15014 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
15051 TTTCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
15088 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
15119 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:17825 original size:18 final size:19
Alignment explanation
Indices: 17791--17827 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
17781 GAATGCTAAT
*
17791 TTTGGATCAATATGGAAGA
1 TTTGGATCAAAATGGAAGA
17810 TTTGGAT-AAAATGGAAGA
1 TTTGGATCAAAATGGAAGA
17828 CTAATTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.41, C:0.03, G:0.27, T:0.30
Consensus pattern (19 bp):
TTTGGATCAAAATGGAAGA
Found at i:19011 original size:31 final size:31
Alignment explanation
Indices: 18976--19076 Score: 115
Period size: 31 Copynumber: 3.4 Consensus size: 31
18966 TTAGTGATGC
18976 TTTTATTTAATATTGTTTATTTTATATGTTA
1 TTTTATTTAATATTGTTTATTTTATATGTTA
* * * *
19007 TTTTATTTTATTTTATTT-TATTAATATGTTA
1 TTTTATTTAATATTGTTTAT-TTTATATGTTA
19038 TTTTATTT--TATTGTTTATTTTAT-T-TTA
1 TTTTATTTAATATTGTTTATTTTATATGTTA
19065 TTTTA-TTAATAT
1 TTTTATTTAATAT
19077 GTTGTCTCAT
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
26 2 0.03
27 8 0.14
28 4 0.07
29 10 0.17
30 2 0.03
31 33 0.56
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (31 bp):
TTTTATTTAATATTGTTTATTTTATATGTTA
Found at i:19012 original size:5 final size:5
Alignment explanation
Indices: 18991--19071 Score: 99
Period size: 5 Copynumber: 15.2 Consensus size: 5
18981 TTTAATATTG
* *
18991 TTTAT TTTAT ATGTTAT TTTAT TTTAT TTTAT TTTAT TAATAT GTTAT
1 TTTAT TTTAT -T-TTAT TTTAT TTTAT TTTAT TTTAT T-TTAT TTTAT
19039 TTTAT TTTATT GTTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTA-T -TTTAT TTTAT TTTAT TTTAT T
19072 AATATGTTGT
Statistics
Matches: 67, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
5 52 0.78
6 7 0.10
7 8 0.12
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:19039 original size:43 final size:43
Alignment explanation
Indices: 18976--19079 Score: 149
Period size: 43 Copynumber: 2.3 Consensus size: 43
18966 TTAGTGATGC
18976 TTTTATTTAATATTGTTTATTTTATATGTTA-T-TTTATTTTATTTTA
1 TTTTA-TTAATA-TG-TTATTTTAT-T-TTATTGTTTATTTTATTTTA
19022 TTTTATTAATATGTTATTTTATTTTATTGTTTATTTTATTTTA
1 TTTTATTAATATGTTATTTTATTTTATTGTTTATTTTATTTTA
19065 TTTTATTAATATGTT
1 TTTTATTAATATGTT
19080 GTCTCATATT
Statistics
Matches: 56, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
41 3 0.05
42 2 0.04
43 38 0.68
44 2 0.04
45 6 0.11
46 5 0.09
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (43 bp):
TTTTATTAATATGTTATTTTATTTTATTGTTTATTTTATTTTA
Found at i:19168 original size:2 final size:2
Alignment explanation
Indices: 19161--19216 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
19151 TAGTTGGCAG
19161 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19203 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
19217 CTTTTGATGC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20040 original size:18 final size:17
Alignment explanation
Indices: 19993--20043 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 17
19983 TTCTACCCTA
19993 TATTGTTTTATATT-TAAT
1 TATT-TTTTAT-TTATAAT
*
20011 TATTTTAATATTTATAAT
1 TATTTT-TTATTTATAAT
20029 TATTATTTTATTTAT
1 TATT-TTTTATTTAT
20044 TTTTAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 4 0.14
18 22 0.79
19 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTTTTTATTTATAAT
Found at i:20846 original size:7 final size:7
Alignment explanation
Indices: 20831--20870 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
20821 ATTTCATCCT
20831 TATATTA
1 TATATTA
*
20838 TATAATA
1 TATATTA
20845 TATATT-
1 TATATTA
20851 TATATTA
1 TATATTA
20858 TATATTA
1 TATATTA
20865 TATATT
1 TATATT
20871 TATTAACATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TATATTA
Found at i:20875 original size:18 final size:20
Alignment explanation
Indices: 20830--20873 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
20820 AATTTCATCC
20830 TTATATTATATAATATATAT
1 TTATATTATATAATATATAT
*
20850 TTATATTATATATTATATAT
1 TTATATTATATAATATATAT
20870 TTAT
1 TTAT
20874 TAACATTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATATTATATAATATATAT
Found at i:23767 original size:4 final size:4
Alignment explanation
Indices: 23758--23850 Score: 54
Period size: 4 Copynumber: 24.0 Consensus size: 4
23748 TTTCCTTACC
* *
23758 TTAT TTAT TTAT TTAT TTAT TT-T TCT-T CTT-T TTAT TTTT TTAT TTCCT
1 TTAT TTAT TTAT TTAT TTAT TTAT T-TAT -TTAT TTAT TTAT TTAT TT-AT
* * * * *
23806 TTAT CT-T TGAT TTAT TTAC TCA- TT-T TTAT TTAT TCAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
23851 GTATATATTG
Statistics
Matches: 69, Mismatches: 13, Indels: 14
0.72 0.14 0.15
Matches are distributed among these distances:
3 8 0.12
4 57 0.83
5 4 0.06
ACGTcount: A:0.18, C:0.09, G:0.01, T:0.72
Consensus pattern (4 bp):
TTAT
Found at i:35663 original size:99 final size:99
Alignment explanation
Indices: 35491--35684 Score: 291
Period size: 99 Copynumber: 2.0 Consensus size: 99
35481 AGCTTCCCAA
* * *
35491 TTTCAGAACCAATTTTAACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTC
1 TTTCAGAACCAATTTCAACTTCACAACGAAGGATATTAGACCCAAGACAACACAAGCTCAACTTC
* *
35556 ATGACGAAGGGGCGGCTGATTGTTAACAAACAAC
66 ATGACGAAGGGGCGGCTGACTGTCAACAAACAAC
** * *
35590 TTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCAAGACAGCACAAGCTCAACTTC
1 TTTCAGAACCAATTTCAACTTCACAACGAAGGATATTAGACCCAAGACAACACAAGCTCAACTTC
35655 AT-AGCGAAGGGGCGGCTGACTGTCAACAAA
66 ATGA-CGAAGGGGCGGCTGACTGTCAACAAA
35685 TAATTTCCCA
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
98 1 0.01
99 84 0.99
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (99 bp):
TTTCAGAACCAATTTCAACTTCACAACGAAGGATATTAGACCCAAGACAACACAAGCTCAACTTC
ATGACGAAGGGGCGGCTGACTGTCAACAAACAAC
Found at i:37674 original size:3 final size:3
Alignment explanation
Indices: 37666--37731 Score: 71
Period size: 3 Copynumber: 21.3 Consensus size: 3
37656 TTATAACTAA
*
37666 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAC TATT TAT GTAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA-T TAT -TAT
* *
37714 AAA TA- TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
37732 TTTTCTTTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
2 2 0.04
3 44 0.81
4 8 0.15
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:37830 original size:2 final size:2
Alignment explanation
Indices: 37817--37853 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
37807 CATGTTTAAT
*
37817 TA TA TG TA 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 TA TA TA TA T
37854 CTTTGTTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38360 original size:13 final size:13
Alignment explanation
Indices: 38338--38367 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
38328 AGGATCAGAG
*
38338 TTTTACCTTTCAA
1 TTTTAACTTTCAA
38351 TTTTAACTTTCAA
1 TTTTAACTTTCAA
38364 TTTT
1 TTTT
38368 TCTTAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAACTTTCAA
Found at i:40331 original size:2 final size:2
Alignment explanation
Indices: 40326--40388 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
40316 TAACACTAAA
40326 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
40368 AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG A
40389 TATGACATCT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:40940 original size:3 final size:3
Alignment explanation
Indices: 40932--40980 Score: 62
Period size: 3 Copynumber: 15.7 Consensus size: 3
40922 TCTACAAAAA
* *
40932 TAT TAT TAT TAT TAT TATT TATT TAT TAT TAT TAC TAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TAT
40979 TA
1 TA
40981 CATTTTGCAG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 34 0.83
4 7 0.17
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:42787 original size:59 final size:57
Alignment explanation
Indices: 42592--42808 Score: 213
Period size: 59 Copynumber: 3.7 Consensus size: 57
42582 TTAATACCAA
* * * * * *
42592 TTTAGTCTTTTAAATTTTTGTATTTGCTA-TTTAATCCTGTAATTTAATGTTTTT-CTAT
1 TTTAGTCCTTTAAGTTTATGT-TTTGCTATTTTAGTCCTTTAATTT--TTTTTTTGCTAT
* * *
42650 TTTAGTCCTTTAAGTTTTTGTTTGTGCTATTTTATTCCTTTAACTTTTTGTTATTGCTAT
1 TTTAGTCCTTTAAGTTTATGTTT-TGCTATTTTAGTCCTTTAA-TTTTT-TTTTTGCTAT
*
42710 TTTAGTCCTTTAAATTTATGTTATTGCTATTTTAGTCCTTTAATTTCTTTTTTTGCTAT
1 TTTAGTCCTTTAAGTTTATGTT-TTGCTATTTTAGTCCTTTAATTT-TTTTTTTGCTAT
** * *
42769 TTTAGTCCTTTGTGTTTATATTTTTGCTATTTTGGTCCTT
1 TTTAGTCCTTTAAGTTTAT-GTTTTGCTATTTTAGTCCTT
42809 GAAATTCCAA
Statistics
Matches: 136, Mismatches: 15, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
57 2 0.01
58 25 0.18
59 59 0.43
60 49 0.36
61 1 0.01
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.61
Consensus pattern (57 bp):
TTTAGTCCTTTAAGTTTATGTTTTGCTATTTTAGTCCTTTAATTTTTTTTTTGCTAT
Found at i:42795 original size:30 final size:30
Alignment explanation
Indices: 42592--42814 Score: 220
Period size: 30 Copynumber: 7.5 Consensus size: 30
42582 TTAATACCAA
* * *
42592 TTTAGTCTTTTAAATTTTTGTATTTGCTA-
1 TTTAGTCCTTTAAATTTATGTTTTTGCTAT
* *
42621 TTTAATCCTGT-AATTTAATGTTTTT-CTAT
1 TTTAGTCCTTTAAATTT-ATGTTTTTGCTAT
* * *
42650 TTTAGTCCTTTAAGTTTTTGTTTGTGCTAT
1 TTTAGTCCTTTAAATTTATGTTTTTGCTAT
* * * *
42680 TTTATTCCTTTAACTTTTTGTTATTGCTAT
1 TTTAGTCCTTTAAATTTATGTTTTTGCTAT
*
42710 TTTAGTCCTTTAAATTTATGTTATTGCTAT
1 TTTAGTCCTTTAAATTTATGTTTTTGCTAT
* *
42740 TTTAGTCCTTT-AATTTCTTTTTTTGCTAT
1 TTTAGTCCTTTAAATTTATGTTTTTGCTAT
*** *
42769 TTTAGTCCTTTGTGTTTATATTTTTGCTAT
1 TTTAGTCCTTTAAATTTATGTTTTTGCTAT
* *
42799 TTTGGTCCTTGAAATT
1 TTTAGTCCTTTAAATT
42815 CCAAATACTT
Statistics
Matches: 160, Mismatches: 29, Indels: 9
0.81 0.15 0.05
Matches are distributed among these distances:
28 8 0.05
29 55 0.34
30 97 0.61
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.61
Consensus pattern (30 bp):
TTTAGTCCTTTAAATTTATGTTTTTGCTAT
Found at i:42796 original size:89 final size:90
Alignment explanation
Indices: 42614--42814 Score: 232
Period size: 89 Copynumber: 2.3 Consensus size: 90
42604 AATTTTTGTA
* * *
42614 TTTGCTA-TTTAATCCTGT-AATTTAATGTTTTTCTATTTTAGTCCTTTAAGTTTTTGTTTGTGC
1 TTTGCTATTTTAGTCCTTTAAATTTAATGTTTTGCTATTTTAGTCCTTTAAGTTTTTGTTTGTGC
* * *
42677 TATTTTATTCCTTTAACTTTTTGTT
66 TATTTTAGTCCTTTAACTTTATATT
* *
42702 ATTGCTATTTTAGTCCTTTAAATTT-ATGTTATTGCTATTTTAGTCCTTTAA-TTTCTT-TTTTT
1 TTTGCTATTTTAGTCCTTTAAATTTAATGTT-TTGCTATTTTAGTCCTTTAAGTTT-TTGTTTGT
***
42764 GCTATTTTAGTCCTTTGTGTTTATATT
64 GCTATTTTAGTCCTTTAACTTTATATT
* *
42791 TTTGCTATTTTGGTCCTTGAAATT
1 TTTGCTATTTTAGTCCTTTAAATT
42815 CCAAATACTT
Statistics
Matches: 95, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
88 6 0.06
89 63 0.66
90 26 0.27
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.60
Consensus pattern (90 bp):
TTTGCTATTTTAGTCCTTTAAATTTAATGTTTTGCTATTTTAGTCCTTTAAGTTTTTGTTTGTGC
TATTTTAGTCCTTTAACTTTATATT
Found at i:43732 original size:23 final size:22
Alignment explanation
Indices: 43701--43743 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
43691 ATAAAAGTCA
*
43701 TAATCGTTTTTTAAATAAATATT
1 TAATCG-TTTTTAAAAAAATATT
*
43724 TAATTGTTTTTAAAAAAATA
1 TAATCGTTTTTAAAAAAATA
43744 GTTATGAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (22 bp):
TAATCGTTTTTAAAAAAATATT
Found at i:44770 original size:55 final size:54
Alignment explanation
Indices: 44722--44947 Score: 227
Period size: 55 Copynumber: 4.1 Consensus size: 54
44712 CTTCGAAGGG
* * *
44722 CGGGTTTGCTCCCTATTCTTTCAGGGAGTATAGGACTTGAAAAATCTTCGAAAAA
1 CGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCG-AAAA
* * * * * * * *
44777 CGAGTTTGCTCCATATTCTTTCAAGGAATATAAGACTCGAACAATCTTTGACAAC
1 CGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCGA-AAA
* * * * *
44832 CGGGTCCGCTCCCTATTCTTTTAGGGAGTATAGAACTCGAACTATCTTATGAAAA
1 CGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTT-CGAAAA
* * * *
44887 TGGGTTCACTCCCTATTCTTTCAGGGAGTATAGAACTCGAACAATCTACTGAAAA
1 CGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTC-GAAAA
*
44942 TGGGTT
1 CGGGTT
44948 TGCTTCCTCT
Statistics
Matches: 141, Mismatches: 27, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
54 1 0.01
55 137 0.97
56 3 0.02
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (54 bp):
CGGGTTCGCTCCCTATTCTTTCAGGGAGTATAGGACTCGAACAATCTTCGAAAA
Found at i:44904 original size:110 final size:110
Alignment explanation
Indices: 44729--44933 Score: 261
Period size: 110 Copynumber: 1.9 Consensus size: 110
44719 GGGCGGGTTT
* * **
44729 GCTCCCTATTCTTTCAGGGAGTATAGGACTTGAAAAATCTTCGAAAAACGAGTTTGCTCCATATT
1 GCTCCCTATTCTTTCAGGGAGTATAGAACTCGAAAAATCTTCGAAAAACGAGTTCACTCCATATT
44794 CTTTCAAGGAATATA-AGACTCGAACAATCTTTGACAACCGGGTCC
66 CTTTCAAGGAATATAGA-ACTCGAACAATCTTTGACAACCGGGTCC
* ** * * * *
44839 GCTCCCTATTCTTTTAGGGAGTATAGAACTCGAACTATCTTATG-AAAATGGGTTCACTCCCTAT
1 GCTCCCTATTCTTTCAGGGAGTATAGAACTCGAAAAATCTT-CGAAAAACGAGTTCACTCCATAT
* *
44903 TCTTTCAGGGAGTATAGAACTCGAACAATCT
65 TCTTTCAAGGAATATAGAACTCGAACAATCT
44934 ACTGAAAATG
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
110 78 0.98
111 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (110 bp):
GCTCCCTATTCTTTCAGGGAGTATAGAACTCGAAAAATCTTCGAAAAACGAGTTCACTCCATATT
CTTTCAAGGAATATAGAACTCGAACAATCTTTGACAACCGGGTCC
Found at i:44965 original size:55 final size:55
Alignment explanation
Indices: 44811--44969 Score: 160
Period size: 55 Copynumber: 2.9 Consensus size: 55
44801 GGAATATAAG
** * * * * *
44811 ACTCGAACAATCTT-TGACAACCGGGTCCGCTCCCTATTCTTTTAGGGAGTATAGA
1 ACTCGAACAATCTTATGA-AAATGGGTTCACTCCCTATACCTTCAGGGAGTATAGA
* * *
44866 ACTCGAACTATCTTATGAAAATGGGTTCACTCCCTATTCTTTCAGGGAGTATAGA
1 ACTCGAACAATCTTATGAAAATGGGTTCACTCCCTATACCTTCAGGGAGTATAGA
** * *
44921 ACTCGAACAATC-TACTGAAAATGGGTTTGCTTCCTCTACCTTCAGGGAG
1 ACTCGAACAATCTTA-TGAAAATGGGTTCACTCCCTATACCTTCAGGGAG
44970 ATCAGACTCG
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
54 2 0.02
55 84 0.94
56 3 0.03
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (55 bp):
ACTCGAACAATCTTATGAAAATGGGTTCACTCCCTATACCTTCAGGGAGTATAGA
Found at i:45023 original size:35 final size:37
Alignment explanation
Indices: 44988--45103 Score: 175
Period size: 37 Copynumber: 3.2 Consensus size: 37
44978 CGAGACTGAT
*
44988 TTGCTTCACTACTCTTCCGTGAAGGC-TAAGA-TGAT
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
*
45023 TTGCTTCACTACTCTTCTGTGAAGGCTTAAGATTGAC
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
*
45060 TCGCTTCACTACTCCTT-CGTGAAGGCTTAAGATTGAC
1 TTGCTTCACTACT-CTTCCGTGAAGGCTTAAGATTGAC
45097 TTGCTTC
1 TTGCTTC
45104 GAAGGAACCT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
35 25 0.34
36 5 0.07
37 40 0.55
38 3 0.04
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (37 bp):
TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAC
Found at i:48408 original size:35 final size:35
Alignment explanation
Indices: 48362--48430 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
48352 GGCATTCATG
* *
48362 GGGTATCGATACCTAGAAGG-TAGTATCTGTACCAA
1 GGGTACCGATACC-AGAAGGATAGTATCGGTACCAA
*
48397 GGGTACCGATACCATAAGGATAGTATCGGTACCA
1 GGGTACCGATACCAGAAGGATAGTATCGGTACCA
48431 TTTTTGAAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 5 0.17
35 25 0.83
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (35 bp):
GGGTACCGATACCAGAAGGATAGTATCGGTACCAA
Found at i:59203 original size:8 final size:8
Alignment explanation
Indices: 59190--59217 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
59180 AAGAGAATAT
59190 ATATATAC
1 ATATATAC
59198 ATATATAC
1 ATATATAC
59206 ATATATAC
1 ATATATAC
59214 ATAT
1 ATAT
59218 GGAGAATCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:64552 original size:11 final size:11
Alignment explanation
Indices: 64538--64562 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
64528 ATATAATAAT
64538 AAATAATATTA
1 AAATAATATTA
64549 AAATAATATTA
1 AAATAATATTA
64560 AAA
1 AAA
64563 ACAAATGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATAATATTA
Found at i:65094 original size:113 final size:113
Alignment explanation
Indices: 64890--65335 Score: 654
Period size: 113 Copynumber: 4.0 Consensus size: 113
64880 AGAATCAAAT
64890 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * * * *
64954 ATGAACTTTCTCTGGTAATG-TTGATCCATCAAATGAT-GAATTCAAACA
66 ATGAACTTTCTCTGGAAAAGCTT-ATCCATCAAGTGATGGATTTGAGA-A
* * ** * *
65002 AAAAGTTGAATAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
65067 ATGAACTTTCTCTGGAAAAGCTTATCCATCAAGTGATGGATTTGAGAA
66 ATGAACTTTCTCTGGAAAAGCTTATCCATCAAGTGATGGATTTGAGAA
*
65115 AAAGGTTGGACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
65180 ATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGGGAA
66 ATGAACTTTCTCTGGAAAAGCTTATCCATCAAGTGATGGATTTGAGAA
65228 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
65293 ATGAACTCTT-TCTGGAAATG-TTGATCCAT--TGTGATGGATTTGA
66 ATGAACT-TTCTCTGGAAAAGCTT-ATCCATCAAGTGATGGATTTGA
65336 ATCTTTGCTA
Statistics
Matches: 303, Mismatches: 26, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
111 12 0.04
112 37 0.12
113 244 0.81
114 10 0.03
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.39
Consensus pattern (113 bp):
AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGCTTATCCATCAAGTGATGGATTTGAGAA
Found at i:68366 original size:18 final size:19
Alignment explanation
Indices: 68338--68415 Score: 88
Period size: 19 Copynumber: 3.9 Consensus size: 19
68328 TTTACAAAAT
68338 AAAAGAATAAATTGAATTTC
1 AAAA-AATAAATTGAATTTC
*
68358 -AAAAATAAATTGAATCTC
1 AAAAAATAAATTGAATTTC
68376 AAAAAATAAATTGAATTT-
1 AAAAAATAAATTGAATTTC
68394 AGAGAAAATAAACTTAGAATTT
1 A-A-AAAATAAA-TT-GAATTT
68416 ATTAATAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
18 15 0.29
19 20 0.39
20 8 0.16
21 2 0.04
22 6 0.12
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.29
Consensus pattern (19 bp):
AAAAAATAAATTGAATTTC
Found at i:68756 original size:9 final size:9
Alignment explanation
Indices: 68744--68793 Score: 57
Period size: 9 Copynumber: 5.4 Consensus size: 9
68734 ATCTTGACCC
68744 TCTTTTTTT
1 TCTTTTTTT
68753 TCTTTTTTT
1 TCTTTTTTT
*
68762 T-TCTTTTT
1 TCTTTTTTT
*
68770 TCTCTTTATT
1 TCT-TTTTTT
68780 TCATTTTTTT
1 TC-TTTTTTT
68790 TCTT
1 TCTT
68794 AAAGCATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
8 7 0.21
9 13 0.38
10 13 0.38
11 1 0.03
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:68761 original size:10 final size:10
Alignment explanation
Indices: 68746--68770 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
68736 CTTGACCCTC
68746 TTTTTTTTCT
1 TTTTTTTTCT
68756 TTTTTTTTCT
1 TTTTTTTTCT
68766 TTTTT
1 TTTTT
68771 CTCTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:68768 original size:17 final size:18
Alignment explanation
Indices: 68748--68793 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
68738 TGACCCTCTT
* *
68748 TTTTTTCTTTTTTTTTC-
1 TTTTTTCTCTTTATTTCA
68765 TTTTTTCTCTTTATTTCA
1 TTTTTTCTCTTTATTTCA
*
68783 TTTTTTTTCTT
1 TTTTTTCTCTT
68794 AAAGCATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTCTCTTTATTTCA
Done.