Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008608.1 Hibiscus syriacus cultivar Beakdansim tig00111564_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: 114760
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2647 original size:2 final size:2
Alignment explanation
Indices: 2642--2693 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2632 TTAATAAAAC
2642 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2684 TA TA TA TA TA
1 TA TA TA TA TA
2694 GTGTGTGTGT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2916 original size:22 final size:22
Alignment explanation
Indices: 2891--2934 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2881 GTAGTATTCT
*
2891 TATGCCTTTATGACATATTTTC
1 TATGCCTTTATGACACATTTTC
*
2913 TATGTCTTTATGACACATTTTC
1 TATGCCTTTATGACACATTTTC
2935 GATCGTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.18, G:0.09, T:0.50
Consensus pattern (22 bp):
TATGCCTTTATGACACATTTTC
Found at i:5260 original size:16 final size:15
Alignment explanation
Indices: 5230--5263 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
5220 ATGGATATCT
5230 AAATATTAATTTTAA
1 AAATATTAATTTTAA
*
5245 AAATATTAATTTTTA
1 AAATATTAATTTTAA
5260 AAAT
1 AAAT
5264 TAATGGCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAATATTAATTTTAA
Found at i:5267 original size:13 final size:15
Alignment explanation
Indices: 5229--5267 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
5219 AATGGATATC
5229 TAAATATTAATTTTA
1 TAAATATTAATTTTA
*
5244 AAAATATTAATTTT-
1 TAAATATTAATTTTA
5258 TAAA-ATTAAT
1 TAAATATTAAT
5268 GGCAGAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 6 0.27
14 3 0.14
15 13 0.59
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TAAATATTAATTTTA
Found at i:13241 original size:22 final size:22
Alignment explanation
Indices: 13216--13261 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
13206 ATTTTGAGGA
13216 AGAATTAGGTGTTATATGATTT
1 AGAATTAGGTGTTATATGATTT
*
13238 AGAATTGGGTGTTATATGATTT
1 AGAATTAGGTGTTATATGATTT
13260 AG
1 AG
13262 GTATGATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.26, T:0.43
Consensus pattern (22 bp):
AGAATTAGGTGTTATATGATTT
Found at i:13353 original size:2 final size:2
Alignment explanation
Indices: 13293--13337 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
13283 ATAAATTAAG
13293 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13335 TA T
1 TA T
13338 GTTATAAGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15720 original size:23 final size:23
Alignment explanation
Indices: 15685--15742 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
15675 AATCTTATAT
*
15685 GGCACTACGGTGCATTTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
15708 GGCACTTCTGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
15731 GGCACTCCGGTG
1 GGCACTACGGTG
15743 TATTTATAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.16, C:0.29, G:0.28, T:0.28
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:16085 original size:2 final size:2
Alignment explanation
Indices: 16080--16105 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16070 TTGTGAAGCA
16080 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
16106 GTGTGTTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19596 original size:24 final size:24
Alignment explanation
Indices: 19564--19619 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
19554 CTATTCTTTC
19564 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
19588 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
19612 GCTTCAAT
1 GCTTCAAT
19620 CGAACTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:19888 original size:30 final size:30
Alignment explanation
Indices: 19854--19910 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
19844 GCGGTTCAAA
* *
19854 CTGGTTTTGCCTATTTTCAGCCAGTTCACC
1 CTGGTTTTCCCGATTTTCAGCCAGTTCACC
*
19884 CTGGTTTTCCCGGTTTTCAGCCAGTTC
1 CTGGTTTTCCCGATTTTCAGCCAGTTC
19911 TTCCGGTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.11, C:0.30, G:0.19, T:0.40
Consensus pattern (30 bp):
CTGGTTTTCCCGATTTTCAGCCAGTTCACC
Found at i:23999 original size:23 final size:23
Alignment explanation
Indices: 23949--24024 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
23939 AACTTACCAT
* *
23949 AAAGGTAGAGATAAAAGTG-CTAC
1 AAAGGCAGAGATAAACGTGTC-AC
* *
23972 AAAGGCAGGGATAAATGTGTCAC
1 AAAGGCAGAGATAAACGTGTCAC
* *
23995 CAAGGAAGAGATAAACGTGTCAC
1 AAAGGCAGAGATAAACGTGTCAC
24018 AAAGGCA
1 AAAGGCA
24025 TAATTATTCT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.45, C:0.13, G:0.28, T:0.14
Consensus pattern (23 bp):
AAAGGCAGAGATAAACGTGTCAC
Found at i:24336 original size:41 final size:40
Alignment explanation
Indices: 24287--24784 Score: 236
Period size: 41 Copynumber: 12.1 Consensus size: 40
24277 CATTAACGGT
*
24287 GTTTTTCAATAAACGCCGCTAAAACTCATACTTTAGTGGC
1 GTTTTTCAACAAACGCCGCTAAAACTCATACTTTAGTGGC
*
24327 GTTTATTCAACAAACGCCGCTAAAGA-TAAGTACTTTAGTGGC
1 GTTT-TTCAACAAACGCCGCTAAA-ACTCA-TACTTTAGTGGC
* * * *
24369 GTTTTTAAACAAACGCCGCCATAGAA-TCGTTCTTTAGTGGC
1 GTTTTTCAACAAACGCCG-C-TAAAACTCATACTTTAGTGGC
* * * * **
24410 GTTTTTAAACAAAAGTCAC-AATAGGGTACATA-TATT-GTGGC
1 GTTTTTCAACAAACGCCGCTAA-A-ACT-CATACT-TTAGTGGC
* * *
24451 ATTTTT-AGATAAACGCCGCTAAAAC-CTAGTACTTTAGAGGC
1 GTTTTTCA-ACAAACGCCGCTAAAACTC-A-TACTTTAGTGGC
* ** **
24492 ATTTTATGCAA-AAACGTTGCTAAAACTTGTACTTTAGTGGC
1 GTTTT-T-CAACAAACGCCGCTAAAACTCATACTTTAGTGGC
* *
24533 GTTTATTCGACAAACGCCGCTAAAGA-TAAGTACTTTAGTGGC
1 GTTT-TTCAACAAACGCCGCTAAA-ACTCA-TACTTTAGTGGC
* * * *
24575 GTTTGTT-TACAAACGCCGTCATAGAA-TCGTTCTTTAGTGGC
1 GTTT-TTCAACAAACGCCG-C-TAAAACTCATACTTTAGTGGC
* * * ** * * *
24616 GTTTTTAAATAAACGACGC-AATAGGGTACATA-TATCGTTGC
1 GTTTTTCAACAAACGCCGCTAA-A-ACT-CATACTTTAGTGGC
* * * *
24657 GTTTTTAAATAAATGCCGCTAAAACCTAATACTTTAGTGGC
1 GTTTTTCAACAAACGCCGCTAAAA-CTCATACTTTAGTGGC
*
24698 GTTTTATTCAA-AAACGCCGCTAAATACTCATACTTTAGTGAC
1 G-TTT-TTCAACAAACGCCGCTAAA-ACTCATACTTTAGTGGC
** *
24740 AATTTT-AGACAAACGCCGCTAAAAC-CTAGTACTTTATTGGC
1 GTTTTTCA-ACAAACGCCGCTAAAACTC-A-TACTTTAGTGGC
24781 GTTT
1 GTTT
24785 AACCCTTTCT
Statistics
Matches: 350, Mismatches: 67, Indels: 81
0.70 0.13 0.16
Matches are distributed among these distances:
38 3 0.01
39 5 0.01
40 24 0.07
41 209 0.60
42 96 0.27
43 12 0.03
44 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (40 bp):
GTTTTTCAACAAACGCCGCTAAAACTCATACTTTAGTGGC
Found at i:24677 original size:206 final size:206
Alignment explanation
Indices: 24297--24784 Score: 687
Period size: 206 Copynumber: 2.4 Consensus size: 206
24287 GTTTTTCAAT
*
24297 AAACGCCGCTAAAACTCATACTTTAGTGGCGTTTATTCAACAAACGCCGCTAAAGATAAGTACTT
1 AAACGCCGCTAAAACTCATACTTTAGTGGCGTTTATTCGACAAACGCCGCTAAAGATAAGTACTT
*
24362 TAGTGGCGTTTTTAAACAAACGCCGCCATAGAATCGTTCTTTAGTGGCGTTTTTAAACAAAAGTC
66 TAGTGGCGTTTTTAAACAAACGCCGCCATAGAATCGTTCTTTAGTGGCGTTTTTAAACAAAAGAC
* * *
24427 ACAATAGGGTACATATATTGTGGCATTTTTAGATAAACGCCGCTAAAACCTAGTACTTTAGAGGC
131 ACAATAGGGTACATATATCGTGGCATTTTTAAATAAACGCCGCTAAAACCTAATACTTTAGAGGC
24492 ATTTTATGCAA
196 ATTTTATGCAA
** **
24503 AAACGTTGCTAAAACTTGTACTTTAGTGGCGTTTATTCGACAAACGCCGCTAAAGATAAGTACTT
1 AAACGCCGCTAAAACTCATACTTTAGTGGCGTTTATTCGACAAACGCCGCTAAAGATAAGTACTT
* * * *
24568 TAGTGGCGTTTGTT-TACAAACGCCGTCATAGAATCGTTCTTTAGTGGCGTTTTTAAATAAACGA
66 TAGTGGCGTTT-TTAAACAAACGCCGCCATAGAATCGTTCTTTAGTGGCGTTTTTAAACAAAAGA
* * * * *
24632 CGCAATAGGGTACATATATCGTTGCGTTTTTAAATAAATGCCGCTAAAACCTAATACTTTAGTGG
130 CACAATAGGGTACATATATCGTGGCATTTTTAAATAAACGCCGCTAAAACCTAATACTTTAGAGG
* *
24697 CGTTTTATTCAA
195 CATTTTATGCAA
* ** *
24709 AAACGCCGCTAAATACTCATACTTTAGTGACAATT-TTAGACAAACGCCGCTAAA-ACCT-AGTA
1 AAACGCCGCTAAA-ACTCATACTTTAGTGGCGTTTATTCGACAAACGCCGCTAAAGA--TAAGTA
*
24771 CTTTATTGGCGTTT
63 CTTTAGTGGCGTTT
24785 AACCCTTTCT
Statistics
Matches: 249, Mismatches: 29, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
205 1 0.00
206 229 0.92
207 19 0.08
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (206 bp):
AAACGCCGCTAAAACTCATACTTTAGTGGCGTTTATTCGACAAACGCCGCTAAAGATAAGTACTT
TAGTGGCGTTTTTAAACAAACGCCGCCATAGAATCGTTCTTTAGTGGCGTTTTTAAACAAAAGAC
ACAATAGGGTACATATATCGTGGCATTTTTAAATAAACGCCGCTAAAACCTAATACTTTAGAGGC
ATTTTATGCAA
Found at i:25251 original size:19 final size:20
Alignment explanation
Indices: 25206--25251 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
25196 AAATGTTTGG
*
25206 GTTTTC-TAGCTTTTTACAC
1 GTTTTCTTAGCTTTTTAAAC
25225 GTTTTCTTA-CTTTTTAAAC
1 GTTTTCTTAGCTTTTTAAAC
25244 GTTTTCTT
1 GTTTTCTT
25252 GATCTGGGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 23 0.92
20 2 0.08
ACGTcount: A:0.15, C:0.17, G:0.09, T:0.59
Consensus pattern (20 bp):
GTTTTCTTAGCTTTTTAAAC
Found at i:29676 original size:42 final size:43
Alignment explanation
Indices: 29598--29825 Score: 318
Period size: 43 Copynumber: 5.3 Consensus size: 43
29588 GTTTGTATAG
*
29598 AAAAACGCCGCTATAAAT-TCCGACCTTTTGCAGCATTTGTTCC
1 AAAAACGCCGCTATAAATCT-CGACCTTTTGCGGCATTTGTTCC
* * *
29641 AAAAACGCCGCTATAGATAT-GACCTTTTGCGGCATTTGTTTC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
*
29683 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
* * * *
29726 AAAATCGCCGCTATAGATCT-AACCTTTTACGGCATTTGTTCC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
* * *
29768 AAAAATGCCGCTATAAATCTCGACCTTTAGCGGCGTTTGTTCC
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
29811 AAAAACGCCGCTATA
1 AAAAACGCCGCTATA
29826 TATCACTACC
Statistics
Matches: 162, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
42 74 0.46
43 87 0.54
44 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (43 bp):
AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCATTTGTTCC
Found at i:29741 original size:85 final size:85
Alignment explanation
Indices: 29598--29825 Score: 359
Period size: 85 Copynumber: 2.7 Consensus size: 85
29588 GTTTGTATAG
* * *
29598 AAAAACGCCGCTATAAAT-TCCGACCTTTTGCAGCATTTGTTCCAAAAACGCCGCTATAGATATG
1 AAAAACGCCGCTATAAATCT-CGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATATA
* *
29662 ACCTTTTGCGGCATTTGTTTC
65 ACCTTTTACGGCATTTGTTCC
* *
29683 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAATCGCCGCTATAGATCTAA
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATATAA
29748 CCTTTTACGGCATTTGTTCC
66 CCTTTTACGGCATTTGTTCC
* *
29768 AAAAATGCCGCTATAAATCTCGACCTTTAGCGGCGTTTGTTCCAAAAACGCCGCTATA
1 AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATA
29826 TATCACTACC
Statistics
Matches: 132, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
85 131 0.99
86 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (85 bp):
AAAAACGCCGCTATAAATCTCGACCTTTTGCGGCGTTTGTTCCAAAAACGCCGCTATAGATATAA
CCTTTTACGGCATTTGTTCC
Found at i:36931 original size:3 final size:3
Alignment explanation
Indices: 36916--36990 Score: 105
Period size: 3 Copynumber: 25.0 Consensus size: 3
36906 GCAAAAAATG
* * * * *
36916 TAA TAA TAT TAA TAA TCA TAA TAA AAA TAA TGA TAA TGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
36964 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
36991 AACCCATACA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:42039 original size:2 final size:2
Alignment explanation
Indices: 42034--42069 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
42024 CCTAAATGAA
42034 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
42070 GGTTATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49244 original size:21 final size:19
Alignment explanation
Indices: 49218--49355 Score: 105
Period size: 21 Copynumber: 6.6 Consensus size: 19
49208 TTCCAAATTT
49218 GTTGCGATAGTCCAAGTTCGC
1 GTTGCGATAGTCCAAGTT--C
* *
49239 GTTGCGATTTATTCCAAATTC
1 GTTGCGA--TAGTCCAAGTTC
*
49260 GTTGCGATAGTCGAAGTTCGC
1 GTTGCGATAGTCCAAGTT--C
*
49281 GTTGCGATTTATTCCAAGTTC
1 GTTGCGA--TAGTCCAAGTTC
*
49302 GTTGCGATAGTCGAAGTTCGC
1 GTTGCGATAGTCCAAGTT--C
* *
49323 GTTGCGATTTATTCCAAATTC
1 GTTGCGA--TAGTCCAAGTTC
49344 GTTGCGATAGTC
1 GTTGCGATAGTC
49356 TAAAATCGCA
Statistics
Matches: 94, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
19 21 0.22
21 47 0.50
23 26 0.28
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (19 bp):
GTTGCGATAGTCCAAGTTC
Found at i:49267 original size:42 final size:42
Alignment explanation
Indices: 49208--49355 Score: 269
Period size: 42 Copynumber: 3.5 Consensus size: 42
49198 CAACGCGAAC
* *
49208 TTCCAAATTTGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
1 TTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
49250 TTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
1 TTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
*
49292 TTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
1 TTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
49334 TTCCAAATTCGTTGCGATAGTC
1 TTCCAAATTCGTTGCGATAGTC
49356 TAAAATCGCA
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 102 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (42 bp):
TTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
Found at i:50090 original size:6 final size:6
Alignment explanation
Indices: 50081--50105 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
50071 GCCGTTCGTC
50081 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
50106 AATACGTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:50221 original size:21 final size:21
Alignment explanation
Indices: 50195--50359 Score: 117
Period size: 21 Copynumber: 8.0 Consensus size: 21
50185 CGTTGCGATT
*
50195 TTGGACTATCGCAACGCAAAC
1 TTGGACTATCGCAACGCGAAC
*
50216 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* * * *
50235 TTGTAATAAATCGTAACACGAAC
1 TTGGACT--ATCGCAACGCGAAC
* *
50258 TTGGACTATCGCAA--CAAAT
1 TTGGACTATCGCAACGCGAAC
** *
50277 TTAAAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
50300 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
**
50319 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
50340 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAACGCGAA
50360 TATGTAAATC
Statistics
Matches: 108, Mismatches: 26, Indels: 20
0.70 0.17 0.13
Matches are distributed among these distances:
19 31 0.29
21 61 0.56
23 16 0.15
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:50272 original size:42 final size:41
Alignment explanation
Indices: 50202--50378 Score: 225
Period size: 42 Copynumber: 4.3 Consensus size: 41
50192 ATTTTGGACT
*
50202 ATCGCAACGCAAACTTGGACTATCGCAACGAATTTGTAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTG-AATAA
* * * *
50244 ATCGTAACACGAACTTGGACTATCGCAACAAATTTAAAATAA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTT-GAATAA
*
50286 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGA-AA
1 ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAATAA
*
50326 ATCGCAACGCGAACTTGGACTATCGCAATGCGAATATG--TAA
1 ATCGCAACGCGAACTTGGACTATCGCAA--CGAATTTGAATAA
*
50367 ATCGCAATGCGA
1 ATCGCAACGCGA
50379 TAGTCGAAGT
Statistics
Matches: 119, Mismatches: 12, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
40 30 0.25
41 14 0.12
42 75 0.63
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGAACTTGGACTATCGCAACGAATTTGAATAA
Found at i:61730 original size:2 final size:2
Alignment explanation
Indices: 61723--61749 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
61713 AAACATAATG
61723 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
61750 GATAATAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62851 original size:2 final size:2
Alignment explanation
Indices: 62844--62870 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
62834 ATATTTCTTG
62844 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
62871 CATGTCTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65670 original size:33 final size:33
Alignment explanation
Indices: 65618--65699 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
65608 AATTTTATAT
* *
65618 TTATTTATTAATGATTATAATTTGAATCTTAAAA
1 TTATTTTTTAATGATTATAATTTGAATATT-AAA
65652 TT-TTTTCTT-ATGATTATAATTTGAATATTAAA
1 TTATTTT-TTAATGATTATAATTTGAATATTAAA
65684 TTATTTTTTAATGATT
1 TTATTTTTTAATGATT
65700 TCATATATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 7 0.16
33 32 0.74
34 4 0.09
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.56
Consensus pattern (33 bp):
TTATTTTTTAATGATTATAATTTGAATATTAAA
Found at i:67363 original size:23 final size:23
Alignment explanation
Indices: 67332--67385 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
67322 GATGCACCAT
*
67332 TGACGATAGAGAGAACTAGTCAA
1 TGACAATAGAGAGAACTAGTCAA
67355 TGACAATAGAGAGAACTAGTCAA
1 TGACAATAGAGAGAACTAGTCAA
67378 TGACAATA
1 TGACAATA
67386 AAATAAGATC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.46, C:0.13, G:0.22, T:0.19
Consensus pattern (23 bp):
TGACAATAGAGAGAACTAGTCAA
Found at i:74982 original size:43 final size:43
Alignment explanation
Indices: 74934--75016 Score: 157
Period size: 43 Copynumber: 1.9 Consensus size: 43
74924 GGATCGAAAG
*
74934 TTCGATATGATACCATGTAGAAAATAGGTATTAGGAAAAACTC
1 TTCGATATGATACCATGTAGAAAATAGGTATTAGAAAAAACTC
74977 TTCGATATGATACCATGTAGAAAATAGGTATTAGAAAAAA
1 TTCGATATGATACCATGTAGAAAATAGGTATTAGAAAAAA
75017 TTCTCTCTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.28
Consensus pattern (43 bp):
TTCGATATGATACCATGTAGAAAATAGGTATTAGAAAAAACTC
Found at i:81290 original size:18 final size:17
Alignment explanation
Indices: 81267--81317 Score: 84
Period size: 18 Copynumber: 2.9 Consensus size: 17
81257 CGGTCACGAC
81267 CCGTTTACCCGACCCGA
1 CCGTTTACCCGACCCGA
81284 CCAGTTTACCCGACCCGA
1 CC-GTTTACCCGACCCGA
*
81302 CCGTTGACCCGACCCG
1 CCGTTTACCCGACCCG
81318 TTGACCGATG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 15 0.47
18 17 0.53
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.16
Consensus pattern (17 bp):
CCGTTTACCCGACCCGA
Found at i:81312 original size:12 final size:13
Alignment explanation
Indices: 81295--81323 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
81285 CAGTTTACCC
81295 GACCCGA-CCGTT
1 GACCCGACCCGTT
81307 GACCCGACCCGTT
1 GACCCGACCCGTT
81320 GACC
1 GACC
81324 GATGACCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.17, C:0.45, G:0.24, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:81406 original size:29 final size:29
Alignment explanation
Indices: 81345--81411 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
81335 ACCGTTGACC
*** *
81345 GGTGCTATTCTGGGAATTAATTCGGTTTT
1 GGTGCTATTCTGGGAATTAATTCGAAATG
81374 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTCTGGGAATTAATTCGAAATG
81403 GGTGCTATT
1 GGTGCTATT
81412 ATAGTAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.21, C:0.10, G:0.28, T:0.40
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCGAAATG
Found at i:81420 original size:29 final size:27
Alignment explanation
Indices: 81374--81427 Score: 63
Period size: 29 Copynumber: 1.9 Consensus size: 27
81364 ATTCGGTTTT
* *
81374 GGTGCTATTCTGGGAATTAATTCGAAATG
1 GGTGCTATTATAGGAATT--TTCGAAATG
*
81403 GGTGCTATTATAGTAATTTTCGAAA
1 GGTGCTATTATAGGAATTTTCGAAA
81428 CAAAATGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 7 0.32
29 15 0.68
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.37
Consensus pattern (27 bp):
GGTGCTATTATAGGAATTTTCGAAATG
Found at i:86404 original size:51 final size:51
Alignment explanation
Indices: 86344--86445 Score: 195
Period size: 51 Copynumber: 2.0 Consensus size: 51
86334 ACTCGTTGCT
*
86344 TCCCATTATTCAACAAGTTAAGCAAGGATCGAGTTTGGAGTATACTGTGGA
1 TCCCATTATTCAACAAGTTAAGCAAGGATCGAGTTCGGAGTATACTGTGGA
86395 TCCCATTATTCAACAAGTTAAGCAAGGATCGAGTTCGGAGTATACTGTGGA
1 TCCCATTATTCAACAAGTTAAGCAAGGATCGAGTTCGGAGTATACTGTGGA
86446 CCAGGATGGT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (51 bp):
TCCCATTATTCAACAAGTTAAGCAAGGATCGAGTTCGGAGTATACTGTGGA
Found at i:88556 original size:10 final size:10
Alignment explanation
Indices: 88541--88595 Score: 60
Period size: 9 Copynumber: 5.6 Consensus size: 10
88531 AACGCTGGAA
88541 ACCGGTTTTG
1 ACCGGTTTTG
*
88551 ACCGG-TTTA
1 ACCGGTTTTG
*
88560 ACCGG-TTTA
1 ACCGGTTTTG
88569 ACCGGTTTTG
1 ACCGGTTTTG
*
88579 AACCGGGTTTG
1 -ACCGGTTTTG
88590 ACCGGT
1 ACCGGT
88596 CACGACCCGT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
9 17 0.44
10 13 0.33
11 9 0.23
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:88616 original size:13 final size:13
Alignment explanation
Indices: 88613--88637 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88603 CGTTTACCCG
88613 ACCCGACCCGTTT
1 ACCCGACCCGTTT
88626 ACCCGACCCGTT
1 ACCCGACCCGTT
88638 GACCGATGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.48, G:0.16, T:0.20
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:88621 original size:18 final size:18
Alignment explanation
Indices: 88598--88635 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
88588 TGACCGGTCA
88598 CGACCCGTTTACCCGACC
1 CGACCCGTTTACCCGACC
88616 CGACCCGTTTACCCGACC
1 CGACCCGTTTACCCGACC
88634 CG
1 CG
88636 TTGACCGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.16, C:0.50, G:0.18, T:0.16
Consensus pattern (18 bp):
CGACCCGTTTACCCGACC
Found at i:88724 original size:29 final size:29
Alignment explanation
Indices: 88663--88745 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 29
88653 ACCGTTGACC
*** *
88663 GGTGCTATTCTAGGAATTAATTCGGTTTT
1 GGTGCTATTCTAGGAATTAATTCGAAATG
* *
88692 GGTGCTATTCTGGGAATTAATTTGAAATG
1 GGTGCTATTCTAGGAATTAATTCGAAATG
* *
88721 GGTGCTATTATAGTAATT--TTCGAAA
1 GGTGCTATTCTAGGAATTAATTCGAAA
88746 CAAAATGATA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
27 6 0.14
29 38 0.86
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.41
Consensus pattern (29 bp):
GGTGCTATTCTAGGAATTAATTCGAAATG
Found at i:94376 original size:21 final size:19
Alignment explanation
Indices: 94340--94383 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 19
94330 CAAAAACCTT
94340 AAAAGATACATTTAAAATTA
1 AAAAGATACATTTAAAA-TA
94360 AAAAGATA-ATTTCTAAAATA
1 AAAAGATACA-TT-TAAAATA
94380 AAAA
1 AAAA
94384 TAAAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.05
20 16 0.73
21 5 0.23
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (19 bp):
AAAAGATACATTTAAAATA
Found at i:108825 original size:25 final size:25
Alignment explanation
Indices: 108797--108844 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
108787 ATTAAAGTTT
*
108797 TTTCTT-TTTACTTTTTAAGTTTTTA
1 TTTCTTCTTTA-TTTTCAAGTTTTTA
108822 TTTCTTCTTTATTTTCAAGTTTT
1 TTTCTTCTTTATTTTCAAGTTTT
108845 GTTTTTATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.15, C:0.10, G:0.04, T:0.71
Consensus pattern (25 bp):
TTTCTTCTTTATTTTCAAGTTTTTA
Done.