Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005067.1 Hibiscus syriacus cultivar Beakdansim tig00011372_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: 61337
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:9611 original size:19 final size:19
Alignment explanation
Indices: 9587--9625 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
9577 ATGAGTTAGA
9587 TCCCGAACATGCTTTGAGT
1 TCCCGAACATGCTTTGAGT
9606 TCCCGAACATGCTTTGAGT
1 TCCCGAACATGCTTTGAGT
9625 T
1 T
9626 GGATCCCGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.33
Consensus pattern (19 bp):
TCCCGAACATGCTTTGAGT
Found at i:9636 original size:23 final size:22
Alignment explanation
Indices: 9578--9643 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 22
9568 TGACCGTGAA
9578 TGAGTTAGATCCCGAACATGCTT
1 TGAGTT-GATCCCGAACATGCTT
9601 TGAG-T--TCCCGAACATGCTT
1 TGAGTTGATCCCGAACATGCTT
9620 TGAGTTGGATCCCGAACATGCTT
1 TGAGTT-GATCCCGAACATGCTT
9643 T
1 T
9644 TTCATTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
19 18 0.46
20 1 0.03
22 1 0.03
23 19 0.49
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.32
Consensus pattern (22 bp):
TGAGTTGATCCCGAACATGCTT
Found at i:16854 original size:35 final size:35
Alignment explanation
Indices: 16803--16926 Score: 133
Period size: 35 Copynumber: 3.5 Consensus size: 35
16793 CCTTAGGTCC
* *
16803 ATAAGGAATTATCAGCTGATCATTGTTGAACCTAT
1 ATAAGGAATTACCAGCTGATCATTGCTGAACCTAT
**
16838 ATAAGGAATTACCAGCTTGATCATAACTGAACCTGCA-
1 ATAAGGAATTACCAGC-TGATCATTGCTGAACCT--AT
** * **
16875 ATAAGGAATTATTAGTTGATCGGTGCTGAACCTAT
1 ATAAGGAATTACCAGCTGATCATTGCTGAACCTAT
16910 ATAAGGAATTACCAGCT
1 ATAAGGAATTACCAGCT
16927 TGATTAGAAC
Statistics
Matches: 71, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
34 1 0.01
35 29 0.41
36 27 0.38
37 13 0.18
38 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (35 bp):
ATAAGGAATTACCAGCTGATCATTGCTGAACCTAT
Found at i:16869 original size:36 final size:36
Alignment explanation
Indices: 16803--16943 Score: 137
Period size: 36 Copynumber: 3.9 Consensus size: 36
16793 CCTTAGGTCC
* ***
16803 ATAAGGAATTATCAGC-TGATCATTGTTGAACCTAT
1 ATAAGGAATTACCAGCTTGATCATAACTGAACCTAT
16838 ATAAGGAATTACCAGCTTGATCATAACTGAACCTGCA-
1 ATAAGGAATTACCAGCTTGATCATAACTGAACCT--AT
** * *
16875 ATAAGGAATTATTAG-TTGATCGGT-GCTGAACCTAT
1 ATAAGGAATTACCAGCTTGATC-ATAACTGAACCTAT
* *
16910 ATAAGGAATTACCAGCTTGATTAGAACTGAACCT
1 ATAAGGAATTACCAGCTTGATCATAACTGAACCT
16944 GCAGAGACTT
Statistics
Matches: 85, Mismatches: 14, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
34 1 0.01
35 28 0.33
36 41 0.48
37 14 0.16
38 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.30
Consensus pattern (36 bp):
ATAAGGAATTACCAGCTTGATCATAACTGAACCTAT
Found at i:16920 original size:72 final size:72
Alignment explanation
Indices: 16803--16946 Score: 225
Period size: 72 Copynumber: 2.0 Consensus size: 72
16793 CCTTAGGTCC
* * *
16803 ATAAGGAATTATCAGCTGATCATTGTTGAACCTATATAAGGAATTACCAGCTTGATCATAACTGA
1 ATAAGGAATTATCAGCTGATCAGTGCTGAACCTATATAAGGAATTACCAGCTTGATCAGAACTGA
16868 ACCTGCA
66 ACCTGCA
* * * *
16875 ATAAGGAATTATTAGTTGATCGGTGCTGAACCTATATAAGGAATTACCAGCTTGATTAGAACTGA
1 ATAAGGAATTATCAGCTGATCAGTGCTGAACCTATATAAGGAATTACCAGCTTGATCAGAACTGA
16940 ACCTGCA
66 ACCTGCA
16947 GAGACTTCAT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (72 bp):
ATAAGGAATTATCAGCTGATCAGTGCTGAACCTATATAAGGAATTACCAGCTTGATCAGAACTGA
ACCTGCA
Found at i:26067 original size:18 final size:19
Alignment explanation
Indices: 26044--26083 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
26034 CGGGCAGGCT
26044 AACGG-TCAGGTCAAAGTC
1 AACGGTTCAGGTCAAAGTC
* *
26062 AACGGTTCGGGTCAAGGTC
1 AACGGTTCAGGTCAAAGTC
26081 AAC
1 AAC
26084 AAGTCAGACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.30, C:0.23, G:0.30, T:0.17
Consensus pattern (19 bp):
AACGGTTCAGGTCAAAGTC
Found at i:27942 original size:21 final size:20
Alignment explanation
Indices: 27914--27954 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
27904 TTCAGGGGTT
27914 TCTTTTTTTGGTTTTATGCA
1 TCTTTTTTTGGTTTTATGCA
27934 TCTTTTTTTGGTTTTATGCA
1 TCTTTTTTTGGTTTTATGCA
27954 T
1 T
27955 GGAGGAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.10, G:0.15, T:0.66
Consensus pattern (20 bp):
TCTTTTTTTGGTTTTATGCA
Found at i:28088 original size:44 final size:44
Alignment explanation
Indices: 28021--28234 Score: 398
Period size: 44 Copynumber: 4.9 Consensus size: 44
28011 ACGAACGAAT
*
28021 AACGTGTGGTCGAGAAAAAAGAGTAAGTCTAATTTGAGATGAAG
1 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAG
28065 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAG
1 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAG
28109 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAG
1 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAG
28153 AAC--GT-GTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAG
1 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAG
28194 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATG
1 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATG
28235 GGACAAACTC
Statistics
Matches: 166, Mismatches: 1, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
41 39 0.23
42 2 0.01
43 2 0.01
44 123 0.74
ACGTcount: A:0.39, C:0.07, G:0.29, T:0.25
Consensus pattern (44 bp):
AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAG
Found at i:28207 original size:85 final size:87
Alignment explanation
Indices: 28021--28234 Score: 396
Period size: 85 Copynumber: 2.5 Consensus size: 87
28011 ACGAACGAAT
*
28021 AACGTGTGGTCGAGAAAAAAGAGTAAGTCTAATTTGAGATGAAGAACGTGTGGTCGAGAAAATAG
1 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAGAACG-GTGGTCGAGAAAATAG
28086 AGTAAGTCTAATTTGAGATGAAG
65 AGTAAGTCTAATTTGAGATGAAG
28109 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAGAAC-GT-GTCGAGAAAATAGA
1 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAGAACGGTGGTCGAGAAAATAGA
28172 GTAAGTCTAATTTGAGATGAAG
66 GTAAGTCTAATTTGAGATGAAG
28194 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATG
1 AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATG
28235 GGACAAACTC
Statistics
Matches: 125, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
85 77 0.62
86 2 0.02
88 46 0.37
ACGTcount: A:0.39, C:0.07, G:0.29, T:0.25
Consensus pattern (87 bp):
AACGTGTGGTCGAGAAAATAGAGTAAGTCTAATTTGAGATGAAGAACGGTGGTCGAGAAAATAGA
GTAAGTCTAATTTGAGATGAAG
Found at i:28562 original size:2 final size:2
Alignment explanation
Indices: 28555--28587 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
28545 ATTAATGAGT
28555 TA 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 T
28588 GAAGGATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28980 original size:17 final size:18
Alignment explanation
Indices: 28958--29000 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
28948 TCCGAGTTGA
* *
28958 GTCGGGTCAAC-TGTCGG
1 GTCGGGTCAACGGGTCAG
28975 GTCGGGTCAACGGGTCAG
1 GTCGGGTCAACGGGTCAG
28993 GTCGGGTC
1 GTCGGGTC
29001 GTGACCGGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.12, C:0.23, G:0.44, T:0.21
Consensus pattern (18 bp):
GTCGGGTCAACGGGTCAG
Found at i:34977 original size:52 final size:54
Alignment explanation
Indices: 34909--35015 Score: 173
Period size: 52 Copynumber: 2.0 Consensus size: 54
34899 TTTATCACGA
* * *
34909 TGTTAGACTTGTTTGTTTTGGGTCTATATG-AAAAGC-TATAAATTATTTATTG
1 TGTTAGACTTGTTTGTTTGGGGTCTACATGAAAAAGCTTACAAATTATTTATTG
34961 TGTTAGACTTGTTTGTTTGGGGTCTACATGAAAAAGCTTACAAATTATTTATTG
1 TGTTAGACTTGTTTGTTTGGGGTCTACATGAAAAAGCTTACAAATTATTTATTG
35015 T
1 T
35016 AAAGCTCAGC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
52 28 0.56
53 6 0.12
54 16 0.32
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.46
Consensus pattern (54 bp):
TGTTAGACTTGTTTGTTTGGGGTCTACATGAAAAAGCTTACAAATTATTTATTG
Found at i:35975 original size:29 final size:30
Alignment explanation
Indices: 35930--36005 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
35920 TAAAGGACTG
* * *
35930 AAATGTAAAT-GCTGAAAATT-AAAGGCAC
1 AAATGTAAATAACAGAAAATTAAAAGGAAC
* *
35958 AAAT-TAAAATAACAGAAATTTAAAAGGAAG
1 AAATGT-AAATAACAGAAAATTAAAAGGAAC
35988 AAATGTAAATAACAGAAA
1 AAATGTAAATAACAGAAA
36006 GTAAATCAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 1 0.03
28 8 0.21
29 7 0.18
30 22 0.56
31 1 0.03
ACGTcount: A:0.59, C:0.07, G:0.14, T:0.20
Consensus pattern (30 bp):
AAATGTAAATAACAGAAAATTAAAAGGAAC
Found at i:38287 original size:29 final size:29
Alignment explanation
Indices: 38232--38288 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
38222 CCGAAATTTA
* **
38232 TTCGGTTCGGTTAATATGTTCGAAAAAAG
1 TTCGGTTCGGTTAATAGGTTAAAAAAAAG
38261 TTCGGTTCGGTTAAT-GGTTAAAGAAAAA
1 TTCGGTTCGGTTAATAGGTTAAA-AAAAA
38289 AAAGTTTGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.33, C:0.09, G:0.25, T:0.33
Consensus pattern (29 bp):
TTCGGTTCGGTTAATAGGTTAAAAAAAAG
Found at i:38316 original size:15 final size:15
Alignment explanation
Indices: 38293--38324 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
38283 GAAAAAAAAG
*
38293 TTTGGTTAATTCGGT
1 TTTGATTAATTCGGT
38308 TTTGATTAATTCGGT
1 TTTGATTAATTCGGT
38323 TT
1 TT
38325 GGTTCGGTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.22, T:0.56
Consensus pattern (15 bp):
TTTGATTAATTCGGT
Found at i:38767 original size:19 final size:20
Alignment explanation
Indices: 38745--38784 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
38735 TATTTCCTTA
38745 AATTAAACA-TATTTTACAT
1 AATTAAACAGTATTTTACAT
* *
38764 AATTAATCAGTATTTTTCAT
1 AATTAAACAGTATTTTACAT
38784 A
1 A
38785 TACGCAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (20 bp):
AATTAAACAGTATTTTACAT
Found at i:42283 original size:21 final size:21
Alignment explanation
Indices: 42238--42283 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
42228 AGCTACTTGA
*
42238 TTCTGGCACGTATCATCATAC
1 TTCTGGCACGTATCATCAGAC
*
42259 TTCTGGCACGT-TCATTCAGAG
1 TTCTGGCACGTATCA-TCAGAC
42280 TTCT
1 TTCT
42284 ATTCATGCGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (21 bp):
TTCTGGCACGTATCATCAGAC
Found at i:45554 original size:15 final size:15
Alignment explanation
Indices: 45536--45564 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
45526 GGATCTGATA
45536 AAAAAAT-TATTTTT
1 AAAAAATATATTTTT
45550 AAAAAATATATTTTT
1 AAAAAATATATTTTT
45565 TATTCAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAAAATATATTTTT
Found at i:50795 original size:2 final size:2
Alignment explanation
Indices: 50788--50812 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50778 CTATAAAAAG
50788 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
50813 GAATGCATAA
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:51352 original size:2 final size:2
Alignment explanation
Indices: 51345--51376 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
51335 CAACTTGATG
51345 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
51377 TCACACACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51482 original size:7 final size:7
Alignment explanation
Indices: 51470--51494 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
51460 ATACTATCAA
51470 ATTTAAT
1 ATTTAAT
51477 ATTTAAT
1 ATTTAAT
51484 ATTTAAT
1 ATTTAAT
51491 ATTT
1 ATTT
51495 GATTAGGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTAAT
Found at i:54470 original size:26 final size:26
Alignment explanation
Indices: 54434--54573 Score: 176
Period size: 26 Copynumber: 5.5 Consensus size: 26
54424 GAGTGGTTGG
* *
54434 AAGCAGTGGTGGCTGTTGAGTGGTCC
1 AAGCGGTGGTGGTTGTTGAGTGGTCC
* *
54460 AAGCGATGGTGGTTGTCGAGTGGTCC
1 AAGCGGTGGTGGTTGTTGAGTGGTCC
54486 AAGCGGTGGTGGTTGTTGAGTGGTCC
1 AAGCGGTGGTGGTTGTTGAGTGGTCC
*
54512 AAGTGGTGGTGGTTGTTGAGTGGTCC
1 AAGCGGTGGTGGTTGTTGAGTGGTCC
** **
54538 AAGCGGAAGTGG--CATGAGTGGTCC
1 AAGCGGTGGTGGTTGTTGAGTGGTCC
*
54562 AAGTGGTGGTGG
1 AAGCGGTGGTGG
54574 CCTATTCTGG
Statistics
Matches: 99, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
24 19 0.19
26 80 0.81
ACGTcount: A:0.16, C:0.12, G:0.45, T:0.27
Consensus pattern (26 bp):
AAGCGGTGGTGGTTGTTGAGTGGTCC
Found at i:54823 original size:17 final size:16
Alignment explanation
Indices: 54801--54847 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 16
54791 ATTATTTTTA
54801 ATATTATTAATAATA-
1 ATATTATTAATAATAT
54816 ATA-TATTAATAATAT
1 ATATTATTAATAATAT
54831 A-ATTA-TAATAATA-
1 ATATTATTAATAATAT
54844 ATAT
1 ATAT
54848 AAATAATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
13 1 0.03
14 22 0.76
15 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATTATTAATAATAT
Found at i:54827 original size:11 final size:12
Alignment explanation
Indices: 54799--54845 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
54789 TTATTATTTT
*
54799 TAATATTATTAA
1 TAATATAATTAA
54811 TAATAATATATTAA
1 TAAT-ATA-ATTAA
54825 TAATATAATT-A
1 TAATATAATTAA
54836 TAATAATAAT
1 TAAT-ATAAT
54846 ATAAATAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
11 5 0.16
12 12 0.39
13 5 0.16
14 9 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAATATAATTAA
Found at i:54848 original size:11 final size:11
Alignment explanation
Indices: 54808--54854 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
54798 TTAATATTAT
54808 TAATAATAATA
1 TAATAATAATA
*
54819 TATTAATAATA
1 TAATAATAATA
*
54830 TAATTATAATAA
1 TAATAATAAT-A
54842 TAAT-ATAA-A
1 TAATAATAATA
54851 TAAT
1 TAAT
54855 GAAAGAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
9 5 0.16
11 22 0.69
12 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAATAATAATA
Found at i:54848 original size:17 final size:16
Alignment explanation
Indices: 54808--54854 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
54798 TTAATATTAT
*
54808 TAATAATAATATATTAA
1 TAAT-ATAATATAATAA
54825 TAATATAATTATAATAA
1 TAATATAA-TATAATAA
54842 TAATATAA-ATAAT
1 TAATATAATATAAT
54855 GAAAGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 5 0.18
16 4 0.14
17 19 0.68
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATATAATATAATAA
Found at i:55340 original size:115 final size:115
Alignment explanation
Indices: 55115--55936 Score: 1195
Period size: 115 Copynumber: 7.2 Consensus size: 115
55105 ATTGAATTGA
* * * * *
55115 GGCAGACTTGTTCCACTTACTCAGAAGGGAATATCAAATCTT-GAAAAAAAAGACCTGTTCCACT
1 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
*
55179 TACTCTGAAGGAAATATCAGATCTT-AGAGGAGTTTGATCCACTGAATGGG
66 TACTCTGAAGGGAATATCAGATCTTGA-AGGAGTTTGATCCACTGAATGGG
* * * * * **
55229 GGAAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATATTGGGAAAGAGATATCTATTTTGCT
1 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
* * * * **
55294 TACTCTGAAAGGAATATCAGATCTTTAAGGAGTTCGATTCC-TTGAATCAG
66 TACTCTGAAGGGAATATCAGATCTTGAAGGAGTTTGA-TCCACTGAATGGG
55344 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
1 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
* *
55409 TACTCTGAAAGGAATATCAGATCTTAAAGGAGTTTGATCCACTGAATGGG
66 TACTCTGAAGGGAATATCAGATCTTGAAGGAGTTTGATCCACTGAATGGG
**
55459 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGATATGTTCCGCT
1 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
*
55524 TACTCTGAAGGGAATATCAGATCTTGGAGGAGTTTGATCCACTGAATGGG
66 TACTCTGAAGGGAATATCAGATCTTGAAGGAGTTTGATCCACTGAATGGG
* * * *
55574 GGCAAACTTGTTCCACTTACTCTTAAGGGAATATCAAATCTTGGGAAAGAGATACATGTTCCGCT
1 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
* * * **
55639 TACTCTGAAGGGAATATCAGATCTTGAAGTAGTTCGATTCC-TTGAATCAG
66 TACTCTGAAGGGAATATCAGATCTTGAAGGAGTTTGA-TCCACTGAATGGG
*
55689 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAAAGAGACCTGTTCCGCT
1 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
55754 TACTCTGAAGGGAATATCAGATCTT-ACAGGAGTTTGATCCACTGAATGGG
66 TACTCTGAAGGGAATATCAGATCTTGA-AGGAGTTTGATCCACTGAATGGG
* *
55804 GGCAGACTTGTTCCACTTACTTTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTACGCT
1 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
* * * * *
55869 TACTATGAAGGGAATATCAAATATTGGAGGAGCTTGATCCACTGAATGGG
66 TACTCTGAAGGGAATATCAGATCTTGAAGGAGTTTGATCCACTGAATGGG
*
55919 GGCAGAGTTGTTCCACTT
1 GGCAGACTTGTTCCACTT
55937 GTCTTTAAAA
Statistics
Matches: 636, Mismatches: 64, Indels: 15
0.89 0.09 0.02
Matches are distributed among these distances:
114 46 0.07
115 583 0.92
116 7 0.01
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (115 bp):
GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
TACTCTGAAGGGAATATCAGATCTTGAAGGAGTTTGATCCACTGAATGGG
Found at i:55745 original size:345 final size:345
Alignment explanation
Indices: 55115--55936 Score: 1355
Period size: 345 Copynumber: 2.4 Consensus size: 345
55105 ATTGAATTGA
* * * * *
55115 GGCAGACTTGTTCCACTTACTCAGAAGGGAATATCAAATCTT-GAAAAAAAAGACCTGTTCCACT
1 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
* *
55179 TACTCTGAAGGAAATATCAGATCTTAGAGGAGTTTGATCCACTGAATGGGGG-AAGACTTGTTCC
66 TACTCTGAAGGGAATATCAGATCTTGGAGGAGTTTGATCCACTGAATGGGGGCAA-ACTTGTTCC
*
55243 ACTTACTCTGAAGGGAATATCAAATATTGGGAAAGAGATATCTATTTTGCTTACTCTGAAAGGAA
130 ACTTACTCTGAAGGGAATATCAAATATTGGGAAAGAGATATCTATTTCGCTTACTCTGAAAGGAA
*
55308 TATCAGATCTTTAAGGAGTTCGATTCCTTGAATCAGGGCAGACTTGTTCCACTTACTCTGAAGGG
195 TATCAGATCTTGAAGGAGTTCGATTCCTTGAATCAGGGCAGACTTGTTCCACTTACTCTGAAGGG
*
55373 AATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCTTACTCTGAAAGGAATATCAGATCTTAAAG
260 AATATCAAATCTTGGGAAAAAGAGACCTGTTCCGCTTACTCTGAAAGGAATATCAGATCTTAAAG
55438 GAGTTTGATCCACTGAATGGG
325 GAGTTTGATCCACTGAATGGG
**
55459 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGATATGTTCCGCT
1 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
55524 TACTCTGAAGGGAATATCAGATCTTGGAGGAGTTTGATCCACTGAATGGGGGCAAACTTGTTCCA
66 TACTCTGAAGGGAATATCAGATCTTGGAGGAGTTTGATCCACTGAATGGGGGCAAACTTGTTCCA
* * *
55589 CTTACTCTTAAGGGAATATCAAATCTTGGGAAAGAGATA-C-ATGTTCCGCTTACTCTGAAGGGA
131 CTTACTCTGAAGGGAATATCAAATATTGGGAAAGAGATATCTAT-TT-CGCTTACTCTGAAAGGA
*
55652 ATATCAGATCTTGAAGTAGTTCGATTCCTTGAATCAGGGCAGACTTGTTCCACTTACTCTGAAGG
194 ATATCAGATCTTGAAGGAGTTCGATTCCTTGAATCAGGGCAGACTTGTTCCACTTACTCTGAAGG
* *
55717 GAATATCAAATCTTGGGAAAAAGAGACCTGTTCCGCTTACTCTGAAGGGAATATCAGATCTTACA
259 GAATATCAAATCTTGGGAAAAAGAGACCTGTTCCGCTTACTCTGAAAGGAATATCAGATCTTAAA
55782 GGAGTTTGATCCACTGAATGGG
324 GGAGTTTGATCCACTGAATGGG
* *
55804 GGCAGACTTGTTCCACTTACTTTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTACGCT
1 GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
* * * * * *
55869 TACTATGAAGGGAATATCAAATATTGGAGGAGCTTGATCCACTGAATGGGGGCAGAGTTGTTCCA
66 TACTCTGAAGGGAATATCAGATCTTGGAGGAGTTTGATCCACTGAATGGGGGCAAACTTGTTCCA
55934 CTT
131 CTT
55937 GTCTTTAAAA
Statistics
Matches: 446, Mismatches: 28, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
343 2 0.00
344 44 0.10
345 398 0.89
346 2 0.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (345 bp):
GGCAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGGAAAGAGAGACCTGTTCCGCT
TACTCTGAAGGGAATATCAGATCTTGGAGGAGTTTGATCCACTGAATGGGGGCAAACTTGTTCCA
CTTACTCTGAAGGGAATATCAAATATTGGGAAAGAGATATCTATTTCGCTTACTCTGAAAGGAAT
ATCAGATCTTGAAGGAGTTCGATTCCTTGAATCAGGGCAGACTTGTTCCACTTACTCTGAAGGGA
ATATCAAATCTTGGGAAAAAGAGACCTGTTCCGCTTACTCTGAAAGGAATATCAGATCTTAAAGG
AGTTTGATCCACTGAATGGG
Done.