Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002642.1 Hibiscus syriacus cultivar Beakdansim tig00005388_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: 54830
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Found at i:3629 original size:42 final size:42
Alignment explanation
Indices: 3580--3673 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 42
3570 CCTTTAAGGG
**
3580 AAGGGATCGAACCTTTTCATCGAGGTTTCGATCC-TTTTGGTA
1 AAGGGATCGAACCTTTTCATCGAGGGATCGATCCATTTT-GTA
* * *
3622 AAGGGATCGAGCCTTTTCCTTGAGGGATCGATCCATTTTGTA
1 AAGGGATCGAACCTTTTCATCGAGGGATCGATCCATTTTGTA
3664 AAGGGATCGA
1 AAGGGATCGA
3674 TTACAAACAC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 42 0.91
43 4 0.09
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (42 bp):
AAGGGATCGAACCTTTTCATCGAGGGATCGATCCATTTTGTA
Found at i:3631 original size:21 final size:20
Alignment explanation
Indices: 3607--3674 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 20
3597 CATCGAGGTT
3607 TCGATCCTTTTGGTAAAGGGA
1 TCGATCCTTTT-GTAAAGGGA
* * **
3628 TCGAGCCTTTTCCTTGAGGGA
1 TCGATCCTTTT-GTAAAGGGA
3649 TCGATCCATTTTGTAAAGGGA
1 TCGATCC-TTTTGTAAAGGGA
3670 TCGAT
1 TCGAT
3675 TACAAACACA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
21 33 0.89
22 4 0.11
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (20 bp):
TCGATCCTTTTGTAAAGGGA
Found at i:6394 original size:24 final size:24
Alignment explanation
Indices: 6362--6411 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
6352 ACATTTTAAC
6362 ATCATATTCTAAAAATCAACATAT
1 ATCATATTCTAAAAATCAACATAT
6386 ATCATATTCTAAAAATCAACATAT
1 ATCATATTCTAAAAATCAACATAT
6410 AT
1 AT
6412 AATCAATAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (24 bp):
ATCATATTCTAAAAATCAACATAT
Found at i:11345 original size:21 final size:21
Alignment explanation
Indices: 11320--11370 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
11310 CATCTAGGGG
11320 TATCGATACACATTCAAGGTA
1 TATCGATACACATTCAAGGTA
* *
11341 TATCGATACACATTCAATGTG
1 TATCGATACACATTCAAGGTA
11362 TATCGATAC
1 TATCGATAC
11371 CTAGCAAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (21 bp):
TATCGATACACATTCAAGGTA
Found at i:22804 original size:37 final size:37
Alignment explanation
Indices: 22754--22833 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
22744 TGATCAAGCT
*
22754 TTAAAAACAAGAAGATGAGAGAAGAGAAACTTGATAA
1 TTAAAAACAAGAAGAGGAGAGAAGAGAAACTTGATAA
22791 TTAAAAACAAGAAGAGGAGAGAAGAGAAACTTGATAA
1 TTAAAAACAAGAAGAGGAGAGAAGAGAAACTTGATAA
22828 TTAAAA
1 TTAAAA
22834 TCAAAATAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.16
Consensus pattern (37 bp):
TTAAAAACAAGAAGAGGAGAGAAGAGAAACTTGATAA
Found at i:31411 original size:40 final size:40
Alignment explanation
Indices: 31362--31484 Score: 160
Period size: 39 Copynumber: 3.1 Consensus size: 40
31352 TCAATGCAAT
31362 AGTGC-TTACACATAAGGTCGTGCCCACCATATGCACCGA
1 AGTGCATTACACATAAGGTCGTGCCCACCATATGCACCGA
* * * * *
31401 AGTGCATTACACATAAGGTCATGCCCTCTATATGCTCTGA
1 AGTGCATTACACATAAGGTCGTGCCCACCATATGCACCGA
* * *
31441 AGTG-AATACACATAAGGTCGTGCCTACCATATGCACCAA
1 AGTGCATTACACATAAGGTCGTGCCCACCATATGCACCGA
31480 AGTGC
1 AGTGC
31485 TTAATCGATA
Statistics
Matches: 69, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
39 36 0.52
40 33 0.48
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.24
Consensus pattern (40 bp):
AGTGCATTACACATAAGGTCGTGCCCACCATATGCACCGA
Found at i:34682 original size:11 final size:11
Alignment explanation
Indices: 34668--34701 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
34658 ATTTATATTC
34668 ATTTTAATTTT
1 ATTTTAATTTT
34679 ATTTTAATTTGT
1 ATTTTAATTT-T
*
34691 ATTTTACTTTT
1 ATTTTAATTTT
34702 TAAATATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (11 bp):
ATTTTAATTTT
Found at i:35118 original size:20 final size:20
Alignment explanation
Indices: 35093--35191 Score: 139
Period size: 20 Copynumber: 5.0 Consensus size: 20
35083 GTTTGGTTCA
*
35093 AGGAATGTAAGATTATCAGT
1 AGGAATGTAAGATTACCAGT
*
35113 AGGAATGTAAGATTACCTGT
1 AGGAATGTAAGATTACCAGT
35133 AGGAATGTAAGATTACCAGT
1 AGGAATGTAAGATTACCAGT
35153 -GAGAATGTAAGATTACC-GTT
1 AG-GAATGTAAGATTACCAG-T
*
35173 GGGAATGTAAGATTACCAG
1 AGGAATGTAAGATTACCAG
35192 GGAATATGAT
Statistics
Matches: 72, Mismatches: 3, Indels: 7
0.88 0.04 0.09
Matches are distributed among these distances:
19 2 0.03
20 68 0.94
21 2 0.03
ACGTcount: A:0.37, C:0.09, G:0.26, T:0.27
Consensus pattern (20 bp):
AGGAATGTAAGATTACCAGT
Found at i:35422 original size:37 final size:37
Alignment explanation
Indices: 35349--35423 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 37
35339 GTTGGAAAAT
* *
35349 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
35386 ATTTATATAATTCTT-TTTAAAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATT-TTCTTTAAAAAATTGAAAATCATAAA
35423 A
1 A
35424 GGTTTAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 14 0.41
38 18 0.53
39 2 0.06
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:38095 original size:49 final size:49
Alignment explanation
Indices: 37992--38316 Score: 395
Period size: 49 Copynumber: 6.6 Consensus size: 49
37982 AACTGCTCTA
* * *
37992 TAATGCAAGTTAAATGCATAATGGTGCATTTTTTTGCAGATAGGTGCCAC
1 TAATGCAAGTTAAATGCATAATGGTGCA-TTTTTGGCAGAAAGGTACCAC
* * *
38042 TAATGCAAGTTAAATTCATAATGGTGCATTTTTGGCAGAAAGGTTCCAA
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTACCAC
* *
38091 TAATGCAAGTTAAATGCATAATGGTGCACTTTTGGCAGAAAGGTGCCAC
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTACCAC
* * **
38140 TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGTATAAAGGTGTCAC
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTACCAC
* * *
38189 TAATGCAA-TTAAATGCATAATGGTGTATTTTTGGCATAAAGGTACCGC
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTACCAC
* * * * * *
38237 TAATGAAAATTTAATGCATAACGGTG--TATTTGAGCATAAAAGGTACCAC
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTG-GCA-GAAAGGTACCAC
* *
38286 TAATGAAAGTTAAATGCATAACGGTGCATTT
1 TAATGCAAGTTAAATGCATAATGGTGCATTT
38317 CAGCATAAAA
Statistics
Matches: 243, Mismatches: 27, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
47 5 0.02
48 45 0.19
49 164 0.67
50 27 0.11
51 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (49 bp):
TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTACCAC
Found at i:38279 original size:146 final size:146
Alignment explanation
Indices: 37992--38316 Score: 420
Period size: 146 Copynumber: 2.2 Consensus size: 146
37982 AACTGCTCTA
* *
37992 TAATGCAAGTTAAATGCATAATGGTGCATTTTTTTGCAGATAGGTGCCACTAATGCAAGTTAAAT
1 TAATGCAAGTTAAATGCATAATGGTGCA-TTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAAT
* * * * *
38057 TCATAATGGTGCATTTTTGGCAGAAAGGTTCCAATAATGCAAGTTAAATGCATAATGGTGCACTT
65 GCATAATGGTGCATTTTTGGCAGAAAGGTACCAATAATGAAAATTAAATGCATAACGGTGCAC-T
* *
38122 TTGGCAGAAAGGTGCCAC
129 TTGGCAAAAAGGTACCAC
* * *
38140 TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGTATAAAGGTGTCACTAATGCAA-TTAAATG
1 TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATG
* * ** * *
38204 CATAATGGTGTATTTTTGGCATAAAGGTACCGCTAATGAAAATTTAATGCATAACGGTGTA-TTT
66 CATAATGGTGCATTTTTGGCAGAAAGGTACCAATAATGAAAATTAAATGCATAACGGTGCACTTT
38268 GAGCATAAAAGGTACCAC
131 G-GCA-AAAAGGTACCAC
* *
38286 TAATGAAAGTTAAATGCATAACGGTGCATTT
1 TAATGCAAGTTAAATGCATAATGGTGCATTT
38317 CAGCATAAAA
Statistics
Matches: 155, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
144 4 0.03
145 3 0.02
146 96 0.62
147 24 0.15
148 28 0.18
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (146 bp):
TAATGCAAGTTAAATGCATAATGGTGCATTTTTGGCAGAAAGGTGCCACTAATGCAAGTTAAATG
CATAATGGTGCATTTTTGGCAGAAAGGTACCAATAATGAAAATTAAATGCATAACGGTGCACTTT
GGCAAAAAGGTACCAC
Found at i:41017 original size:18 final size:18
Alignment explanation
Indices: 40996--41043 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
40986 GTTTTTTTTA
* *
40996 AAATAAAAGATAACAATT
1 AAATAAAAAATAACAAAT
* *
41014 AAATAAAATA-AATAAAT
1 AAATAAAAAATAACAAAT
41031 AAATAAAAAATAA
1 AAATAAAAAATAA
41044 AAGAGATTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 14 0.56
18 11 0.44
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (18 bp):
AAATAAAAAATAACAAAT
Found at i:41695 original size:63 final size:62
Alignment explanation
Indices: 41623--41742 Score: 170
Period size: 63 Copynumber: 1.9 Consensus size: 62
41613 TAAAATATCT
41623 TAAATCCTAATAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAAAATAATATAATATTC
1 TAAATCCTAATAAAACAC-TAAAACCTATTTAAACTAAAATACCT-AAAAATAATATAATATTC
* ** * *
41686 TAAATCCTAATAAAATACTAAAACCTATTTAATTTAAAATATCTAAAACTAATATAA
1 TAAATCCTAATAAAACACTAAAACCTATTTAAACTAAAATACCTAAAAATAATATAA
41743 AATATAAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
62 17 0.33
63 34 0.67
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (62 bp):
TAAATCCTAATAAAACACTAAAACCTATTTAAACTAAAATACCTAAAAATAATATAATATTC
Found at i:41763 original size:31 final size:31
Alignment explanation
Indices: 41723--41783 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
41713 TTTAATTTAA
41723 AATATCTAAAAC-TAATATAAAATA-TAAAAT
1 AATATCTAAAACTTAAT-TAAAATACTAAAAT
41753 AATATCCTAAAACTTAATTAAAATACTAAAA
1 AATAT-CTAAAACTTAATTAAAATACTAAAA
41784 CCTATTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 5 0.18
31 14 0.50
32 9 0.32
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.30
Consensus pattern (31 bp):
AATATCTAAAACTTAATTAAAATACTAAAAT
Found at i:41763 original size:74 final size:74
Alignment explanation
Indices: 41666--41805 Score: 201
Period size: 74 Copynumber: 1.9 Consensus size: 74
41656 CTAAAATACC
* * * **
41666 TAAAAAATAATATAATATTCTAAATCCTAA-TAAAATACTAAAACCTATTTAATTTAAAATATCT
1 TAAAAAATAAAATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATA-CT
41730 AAAACTAATA
65 AAAACTAATA
* *
41740 TAAAATATAAAATAATATCCTAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACTA
1 TAAAAAATAAAATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACTA
41805 A
66 A
41806 GATAAAATAT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
74 29 0.50
75 29 0.50
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.32
Consensus pattern (74 bp):
TAAAAAATAAAATAATATCCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACTA
AAACTAATA
Found at i:41815 original size:75 final size:74
Alignment explanation
Indices: 41642--41838 Score: 200
Period size: 75 Copynumber: 2.6 Consensus size: 74
41632 ATAAAACACT
* * * * *
41642 TAAAACTATTTAAACTAAAATACCTAAAAAATAATATAATATTCTAAATCCTAATAAAATACTAA
1 TAAAA-TATCTAAA-TAAAATA--TAAAATATAAAATAATATCCTAAAACCTAATAAAATACTAA
**
41707 AACCTATTTAATT
62 AACCTATTTAAAC
* *
41720 TAAAATATCTAAA-ACTAATATAAAATATAAAATAATATCCTAAAACTTAATTAAAATACTAAAA
1 TAAAATATCTAAATA-AAATATAAAATATAAAATAATATCCTAAAACCTAA-TAAAATACTAAAA
41784 CCTATTTAAAC
64 CCTATTTAAAC
** * *
41795 TAAAATA-CTAAGATAAAATATAATGTTTAAAATATTATCCTAAA
1 TAAAATATCTAA-ATAAAATATAAAATATAAAATAATATCCTAAA
41839 CTTGAGTTTA
Statistics
Matches: 101, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
74 29 0.29
75 55 0.54
76 5 0.05
77 7 0.07
78 5 0.05
ACGTcount: A:0.55, C:0.11, G:0.01, T:0.32
Consensus pattern (74 bp):
TAAAATATCTAAATAAAATATAAAATATAAAATAATATCCTAAAACCTAATAAAATACTAAAACC
TATTTAAAC
Found at i:43683 original size:12 final size:12
Alignment explanation
Indices: 43661--43710 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
43651 ATGTTCGCTA
43661 AAAACATAAAACG
1 AAAA-ATAAAACG
*
43674 AAAAATAAAATG
1 AAAAATAAAACG
43686 -AAAATAAAAAC-
1 AAAAAT-AAAACG
*
43697 AAAAATATAACG
1 AAAAATAAAACG
43709 AA
1 AA
43711 TTGGGTTGCC
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 9 0.29
12 18 0.58
13 4 0.13
ACGTcount: A:0.74, C:0.08, G:0.06, T:0.12
Consensus pattern (12 bp):
AAAAATAAAACG
Found at i:49121 original size:12 final size:13
Alignment explanation
Indices: 49098--49126 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
49088 AGATAACAAT
49098 TAAATAAAATAAA
1 TAAATAAAATAAA
49111 TAAAT-AAATAAA
1 TAAATAAAATAAA
49123 TAAA
1 TAAA
49127 AGAGATGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAAATAAA
Found at i:49772 original size:60 final size:63
Alignment explanation
Indices: 49696--49820 Score: 170
Period size: 61 Copynumber: 2.0 Consensus size: 63
49686 AACAAGCTAA
49696 AATATCTTAAATCCTAATT-AAACACTTAAAA-CTATTTAAGCTAAAATACCTAAAA-ATAATAT
1 AATATCTTAAATCCTAATTAAAACAC-TAAAACCTATTTAAGCTAAAATACCTAAAACA-AATAT
* **
49758 AATATC-T-AATCCTAATTAAAATACTAAAACCTATTTAATTTAAAATACCTAAAACAAATAT
1 AATATCTTAAATCCTAATTAAAACACTAAAACCTATTTAAGCTAAAATACCTAAAACAAATAT
49819 AA
1 AA
49821 AATATAAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
60 15 0.26
61 35 0.61
62 7 0.12
ACGTcount: A:0.53, C:0.14, G:0.01, T:0.32
Consensus pattern (63 bp):
AATATCTTAAATCCTAATTAAAACACTAAAACCTATTTAAGCTAAAATACCTAAAACAAATAT
Found at i:50727 original size:15 final size:14
Alignment explanation
Indices: 50707--50737 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
50697 TGTATAAGTA
50707 GAAAATGAAGAGATT
1 GAAAATGAAGAG-TT
50722 GAAAATGAAGAGTT
1 GAAAATGAAGAGTT
50736 GA
1 GA
50738 TTATTAGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.52, C:0.00, G:0.29, T:0.19
Consensus pattern (14 bp):
GAAAATGAAGAGTT
Found at i:51116 original size:17 final size:17
Alignment explanation
Indices: 51094--51140 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
51084 ATTAAGCCTA
51094 GAATTTTAA-AATAGGAT
1 GAATTTTAAGAA-AGGAT
51111 GAATTTTAAGAAAGGAT
1 GAATTTTAAGAAAGGAT
*
51128 GAATTTTATGAAA
1 GAATTTTAAGAAA
51141 AATTGAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
17 26 0.93
18 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (17 bp):
GAATTTTAAGAAAGGAT
Found at i:51529 original size:48 final size:48
Alignment explanation
Indices: 51462--51765 Score: 321
Period size: 48 Copynumber: 6.3 Consensus size: 48
51452 ACTACTCTAT
* * *
51462 ATGC-AGTTAACTGCATAATGGTGCATTTTGGCATAAAGCTGCCACTA
1 ATGCAAGTTAAATGCATAATGGTGCATTTTGGCAGAAAGGTGCCACTA
* * *
51509 ATGCAAGTTGAATGCATAATGGTGCATTTTGGCAGAAAGGTGTCACCA
1 ATGCAAGTTAAATGCATAATGGTGCATTTTGGCAGAAAGGTGCCACTA
* *
51557 ATGCAAGTTAAATTCATAATGGTGCATATTT-GAAGAAAGGTGCCACTA
1 ATGCAAGTTAAATGCATAATGGTGCAT-TTTGGCAGAAAGGTGCCACTA
* *
51605 ATGCAAGTGAAATGCATAATGATGCATTTTTGGCAGAAAGGTGCCACTA
1 ATGCAAGTTAAATGCATAATGGTGCA-TTTTGGCAGAAAGGTGCCACTA
* ** * * *
51654 ATGCAAGTTAAATGCATAATGGTGTATTTTTTACA-TAAGGTACTACTA
1 ATGCAAGTTAAATGCATAATGGTGCA-TTTTGGCAGAAAGGTGCCACTA
* * * * *
51702 ATGAAAAAG-T-AATGCATAATGGTGCATTTCGACATAAAAGGTACCACTA
1 ATG--CAAGTTAAATGCATAATGGTGCATTTTGGCA-GAAAGGTGCCACTA
*
51751 ATGAAAGTTAAATGC
1 ATGCAAGTTAAATGC
51766 GTGCATTTCA
Statistics
Matches: 218, Mismatches: 29, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
47 14 0.06
48 131 0.60
49 70 0.32
50 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (48 bp):
ATGCAAGTTAAATGCATAATGGTGCATTTTGGCAGAAAGGTGCCACTA
Found at i:51694 original size:97 final size:95
Alignment explanation
Indices: 51462--51765 Score: 337
Period size: 97 Copynumber: 3.2 Consensus size: 95
51452 ACTACTCTAT
* * *
51462 ATGC-AGTTAACTGCATAATGGTGCA-TTTTGGCATAAAGCTGCCACTAATGCAAGTTGAATGCA
1 ATGCAAGTTAAATGCATAATGGTGCATTTTTGACAT-AAGGTGCCACTAATGCAAG-TGAATGCA
* *
51525 TAATGGTGCATTTTGGCAGAAAGGTGTCACCA
64 TAATGGTGCATTTTGGCAGAAAGGTGCCACTA
* * *
51557 ATGCAAGTTAAATTCATAATGGTGCATATTTGA-AGAAAGGTGCCACTAATGCAAGTGAAATGCA
1 ATGCAAGTTAAATGCATAATGGTGCATTTTTGACA-TAAGGTGCCACTAATGCAAGTG-AATGCA
*
51621 TAATGATGCATTTTTGGCAGAAAGGTGCCACTA
64 TAATGGTGCA-TTTTGGCAGAAAGGTGCCACTA
* * * * *
51654 ATGCAAGTTAAATGCATAATGGTGTATTTTTTACATAAGGTACTACTAATGAAAAAGT-AATGCA
1 ATGCAAGTTAAATGCATAATGGTGCATTTTTGACATAAGGTGCCACTAATG--CAAGTGAATGCA
* * * *
51718 TAATGGTGCATTTCGACATAAAAGGTACCACTA
64 TAATGGTGCATTTTGGCA-GAAAGGTGCCACTA
*
51751 ATGAAAGTTAAATGC
1 ATGCAAGTTAAATGC
51766 GTGCATTTCA
Statistics
Matches: 177, Mismatches: 23, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
95 6 0.03
96 59 0.33
97 107 0.60
98 1 0.01
99 4 0.02
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (95 bp):
ATGCAAGTTAAATGCATAATGGTGCATTTTTGACATAAGGTGCCACTAATGCAAGTGAATGCATA
ATGGTGCATTTTGGCAGAAAGGTGCCACTA
Found at i:54607 original size:26 final size:25
Alignment explanation
Indices: 54572--54622 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 25
54562 TTCTAAGGTT
54572 TTGCTCTTTTGCTGTAGATGAAGTA
1 TTGCTCTTTTGCTGTAGATGAAGTA
54597 TTGCATCTTTTGCTGTAGATGAAGTA
1 TTGC-TCTTTTGCTGTAGATGAAGTA
54623 ATGATAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.43
Consensus pattern (25 bp):
TTGCTCTTTTGCTGTAGATGAAGTA
Done.