Multiple sequence alignment - TraesCS6A01G256100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6A01G256100 chr6A 100.000 4413 0 0 1 4413 475259431 475263843 0.000000e+00 8150.0
1 TraesCS6A01G256100 chr6B 89.560 2749 155 60 172 2897 484990680 484988041 0.000000e+00 3365.0
2 TraesCS6A01G256100 chr6B 95.482 996 28 3 2953 3948 484987954 484986976 0.000000e+00 1574.0
3 TraesCS6A01G256100 chr6D 94.434 1545 50 17 471 2012 335979789 335981300 0.000000e+00 2344.0
4 TraesCS6A01G256100 chr6D 97.992 996 20 0 2953 3948 335984466 335985461 0.000000e+00 1729.0
5 TraesCS6A01G256100 chr6D 89.111 900 59 11 2008 2897 335983509 335984379 0.000000e+00 1083.0
6 TraesCS6A01G256100 chr6D 94.709 378 13 6 4041 4413 335985690 335986065 8.230000e-162 580.0
7 TraesCS6A01G256100 chr6D 81.000 300 30 19 172 471 335979418 335979690 3.460000e-51 213.0
8 TraesCS6A01G256100 chr6D 89.189 111 4 2 3944 4046 335985421 335985531 9.960000e-27 132.0
9 TraesCS6A01G256100 chr5A 97.101 69 2 0 16 84 40096853 40096785 2.790000e-22 117.0
10 TraesCS6A01G256100 chr7A 93.506 77 2 3 11 84 628670545 628670469 1.300000e-20 111.0
11 TraesCS6A01G256100 chr1D 92.424 66 5 0 19 84 13037365 13037300 1.310000e-15 95.3
12 TraesCS6A01G256100 chr1D 84.146 82 13 0 19 100 423270278 423270197 3.660000e-11 80.5
13 TraesCS6A01G256100 chr7D 90.000 70 6 1 15 84 127220625 127220693 6.080000e-14 89.8
14 TraesCS6A01G256100 chr3B 90.909 66 6 0 19 84 236509957 236510022 6.080000e-14 89.8
15 TraesCS6A01G256100 chr3A 90.909 66 6 0 19 84 714426792 714426727 6.080000e-14 89.8
16 TraesCS6A01G256100 chr2D 90.909 66 6 0 19 84 629532572 629532507 6.080000e-14 89.8
17 TraesCS6A01G256100 chr2A 90.909 66 6 0 19 84 342543865 342543800 6.080000e-14 89.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6A01G256100 chr6A 475259431 475263843 4412 False 8150.0 8150 100.0000 1 4413 1 chr6A.!!$F1 4412
1 TraesCS6A01G256100 chr6B 484986976 484990680 3704 True 2469.5 3365 92.5210 172 3948 2 chr6B.!!$R1 3776
2 TraesCS6A01G256100 chr6D 335979418 335986065 6647 False 1013.5 2344 91.0725 172 4413 6 chr6D.!!$F1 4241

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
297 303 0.025001 CTCGTTTAAGCGACCGCATG 59.975 55.0 16.97 1.54 44.88 4.06 F
831 948 0.168128 GCGCAAAGGCTTGTATTCGT 59.832 50.0 0.30 0.00 38.10 3.85 F
922 1041 0.178068 GCTCCAATCCTACCTTCGCA 59.822 55.0 0.00 0.00 0.00 5.10 F
928 1047 0.179108 ATCCTACCTTCGCAGTTCGC 60.179 55.0 0.00 0.00 38.27 4.70 F
1621 1750 0.392998 TCTCCTCAAAAGCGATGGCC 60.393 55.0 0.00 0.00 41.24 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1248 1367 1.080093 GACATTGCCGTCTCCGTCA 60.080 57.895 0.00 0.00 32.92 4.35 R
2270 4617 1.222567 ATACGGGAATTTCCAGCCCT 58.777 50.000 17.08 0.63 38.64 5.19 R
2452 4800 1.668419 ATTCCATACGCTCAAGGCAC 58.332 50.000 0.00 0.00 41.91 5.01 R
2732 5085 3.327757 ACACTCCAAGATAAGCACTTCCA 59.672 43.478 0.00 0.00 0.00 3.53 R
3449 5851 0.813210 CTCCCTCTGAATTGCCTCGC 60.813 60.000 0.00 0.00 0.00 5.03 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 7.463961 AATACAGTATAACATACTCCCTCCG 57.536 40.000 0.00 0.00 0.00 4.63
29 30 4.801164 ACAGTATAACATACTCCCTCCGT 58.199 43.478 0.00 0.00 0.00 4.69
30 31 4.826183 ACAGTATAACATACTCCCTCCGTC 59.174 45.833 0.00 0.00 0.00 4.79
31 32 4.217983 CAGTATAACATACTCCCTCCGTCC 59.782 50.000 0.00 0.00 0.00 4.79
32 33 3.614568 ATAACATACTCCCTCCGTCCT 57.385 47.619 0.00 0.00 0.00 3.85
33 34 4.736611 ATAACATACTCCCTCCGTCCTA 57.263 45.455 0.00 0.00 0.00 2.94
34 35 3.393426 AACATACTCCCTCCGTCCTAA 57.607 47.619 0.00 0.00 0.00 2.69
35 36 3.393426 ACATACTCCCTCCGTCCTAAA 57.607 47.619 0.00 0.00 0.00 1.85
36 37 3.716431 ACATACTCCCTCCGTCCTAAAA 58.284 45.455 0.00 0.00 0.00 1.52
37 38 4.296056 ACATACTCCCTCCGTCCTAAAAT 58.704 43.478 0.00 0.00 0.00 1.82
38 39 5.461327 ACATACTCCCTCCGTCCTAAAATA 58.539 41.667 0.00 0.00 0.00 1.40
39 40 6.082707 ACATACTCCCTCCGTCCTAAAATAT 58.917 40.000 0.00 0.00 0.00 1.28
40 41 7.243824 ACATACTCCCTCCGTCCTAAAATATA 58.756 38.462 0.00 0.00 0.00 0.86
41 42 7.731688 ACATACTCCCTCCGTCCTAAAATATAA 59.268 37.037 0.00 0.00 0.00 0.98
42 43 6.667558 ACTCCCTCCGTCCTAAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
43 44 6.379579 ACTCCCTCCGTCCTAAAATATAAGA 58.620 40.000 0.00 0.00 0.00 2.10
44 45 6.494146 ACTCCCTCCGTCCTAAAATATAAGAG 59.506 42.308 0.00 0.00 0.00 2.85
45 46 5.245526 TCCCTCCGTCCTAAAATATAAGAGC 59.754 44.000 0.00 0.00 0.00 4.09
46 47 5.162075 CCTCCGTCCTAAAATATAAGAGCG 58.838 45.833 0.00 0.00 0.00 5.03
47 48 5.278858 CCTCCGTCCTAAAATATAAGAGCGT 60.279 44.000 0.00 0.00 0.00 5.07
48 49 6.152932 TCCGTCCTAAAATATAAGAGCGTT 57.847 37.500 0.00 0.00 0.00 4.84
49 50 6.576185 TCCGTCCTAAAATATAAGAGCGTTT 58.424 36.000 0.00 0.00 0.00 3.60
50 51 7.043565 TCCGTCCTAAAATATAAGAGCGTTTT 58.956 34.615 0.00 0.00 0.00 2.43
51 52 7.010738 TCCGTCCTAAAATATAAGAGCGTTTTG 59.989 37.037 0.00 0.00 0.00 2.44
52 53 7.201582 CCGTCCTAAAATATAAGAGCGTTTTGT 60.202 37.037 0.00 0.00 0.00 2.83
53 54 8.810427 CGTCCTAAAATATAAGAGCGTTTTGTA 58.190 33.333 0.00 0.00 0.00 2.41
64 65 9.947669 ATAAGAGCGTTTTGTATACTAGTGTAG 57.052 33.333 5.39 0.00 31.51 2.74
65 66 7.388460 AGAGCGTTTTGTATACTAGTGTAGT 57.612 36.000 5.39 0.00 42.68 2.73
66 67 7.249147 AGAGCGTTTTGTATACTAGTGTAGTG 58.751 38.462 5.39 0.00 39.81 2.74
67 68 6.917533 AGCGTTTTGTATACTAGTGTAGTGT 58.082 36.000 5.39 0.00 39.81 3.55
68 69 7.025963 AGCGTTTTGTATACTAGTGTAGTGTC 58.974 38.462 5.39 0.00 39.81 3.67
69 70 6.803320 GCGTTTTGTATACTAGTGTAGTGTCA 59.197 38.462 5.39 0.00 39.81 3.58
70 71 7.326789 GCGTTTTGTATACTAGTGTAGTGTCAA 59.673 37.037 5.39 1.21 39.81 3.18
71 72 9.184062 CGTTTTGTATACTAGTGTAGTGTCAAA 57.816 33.333 5.39 7.26 39.81 2.69
75 76 8.732413 TGTATACTAGTGTAGTGTCAAAAACG 57.268 34.615 5.39 0.00 39.81 3.60
76 77 8.352201 TGTATACTAGTGTAGTGTCAAAAACGT 58.648 33.333 5.39 0.00 39.81 3.99
77 78 9.185192 GTATACTAGTGTAGTGTCAAAAACGTT 57.815 33.333 5.39 0.00 39.81 3.99
78 79 6.973229 ACTAGTGTAGTGTCAAAAACGTTT 57.027 33.333 7.96 7.96 37.69 3.60
79 80 7.368480 ACTAGTGTAGTGTCAAAAACGTTTT 57.632 32.000 20.26 20.26 37.69 2.43
80 81 7.809665 ACTAGTGTAGTGTCAAAAACGTTTTT 58.190 30.769 28.62 28.62 37.99 1.94
81 82 8.934825 ACTAGTGTAGTGTCAAAAACGTTTTTA 58.065 29.630 32.12 18.43 36.61 1.52
82 83 9.925268 CTAGTGTAGTGTCAAAAACGTTTTTAT 57.075 29.630 32.12 19.76 38.23 1.40
89 90 9.843334 AGTGTCAAAAACGTTTTTATAAACAGA 57.157 25.926 32.12 22.06 43.05 3.41
91 92 9.291664 TGTCAAAAACGTTTTTATAAACAGAGG 57.708 29.630 32.12 18.65 43.05 3.69
92 93 9.505995 GTCAAAAACGTTTTTATAAACAGAGGA 57.494 29.630 32.12 20.28 43.05 3.71
98 99 9.551734 AACGTTTTTATAAACAGAGGAAGTAGT 57.448 29.630 9.09 0.00 43.05 2.73
99 100 9.551734 ACGTTTTTATAAACAGAGGAAGTAGTT 57.448 29.630 9.09 0.00 43.05 2.24
107 108 7.939784 AAACAGAGGAAGTAGTTCTTTGTTT 57.060 32.000 21.29 21.29 36.60 2.83
108 109 7.555306 AACAGAGGAAGTAGTTCTTTGTTTC 57.445 36.000 10.10 0.50 36.40 2.78
109 110 6.650120 ACAGAGGAAGTAGTTCTTTGTTTCA 58.350 36.000 10.10 0.00 36.40 2.69
110 111 6.763610 ACAGAGGAAGTAGTTCTTTGTTTCAG 59.236 38.462 10.10 0.42 36.40 3.02
111 112 5.760743 AGAGGAAGTAGTTCTTTGTTTCAGC 59.239 40.000 10.10 0.00 36.40 4.26
112 113 5.685728 AGGAAGTAGTTCTTTGTTTCAGCT 58.314 37.500 10.10 0.00 36.40 4.24
113 114 5.529060 AGGAAGTAGTTCTTTGTTTCAGCTG 59.471 40.000 7.63 7.63 36.40 4.24
114 115 4.820284 AGTAGTTCTTTGTTTCAGCTGC 57.180 40.909 9.47 0.00 0.00 5.25
115 116 4.199310 AGTAGTTCTTTGTTTCAGCTGCA 58.801 39.130 9.47 0.00 0.00 4.41
116 117 4.640201 AGTAGTTCTTTGTTTCAGCTGCAA 59.360 37.500 9.47 0.30 0.00 4.08
117 118 4.660789 AGTTCTTTGTTTCAGCTGCAAT 57.339 36.364 9.47 0.00 0.00 3.56
118 119 5.014808 AGTTCTTTGTTTCAGCTGCAATT 57.985 34.783 9.47 0.00 0.00 2.32
119 120 4.807304 AGTTCTTTGTTTCAGCTGCAATTG 59.193 37.500 9.47 0.00 0.00 2.32
120 121 3.125316 TCTTTGTTTCAGCTGCAATTGC 58.875 40.909 23.69 23.69 42.50 3.56
165 166 9.730420 ACTATACCAAAACATAATTTCATTCGC 57.270 29.630 0.00 0.00 0.00 4.70
166 167 9.729023 CTATACCAAAACATAATTTCATTCGCA 57.271 29.630 0.00 0.00 0.00 5.10
167 168 8.994429 ATACCAAAACATAATTTCATTCGCAA 57.006 26.923 0.00 0.00 0.00 4.85
168 169 7.350110 ACCAAAACATAATTTCATTCGCAAG 57.650 32.000 0.00 0.00 0.00 4.01
275 281 8.567948 CGGATTTTATCAGTTTAATACCAGCAT 58.432 33.333 0.00 0.00 0.00 3.79
279 285 9.905713 TTTTATCAGTTTAATACCAGCATCTCT 57.094 29.630 0.00 0.00 0.00 3.10
281 287 5.592054 TCAGTTTAATACCAGCATCTCTCG 58.408 41.667 0.00 0.00 0.00 4.04
283 289 5.812642 CAGTTTAATACCAGCATCTCTCGTT 59.187 40.000 0.00 0.00 0.00 3.85
284 290 6.313905 CAGTTTAATACCAGCATCTCTCGTTT 59.686 38.462 0.00 0.00 0.00 3.60
285 291 7.491372 CAGTTTAATACCAGCATCTCTCGTTTA 59.509 37.037 0.00 0.00 0.00 2.01
287 293 8.328864 GTTTAATACCAGCATCTCTCGTTTAAG 58.671 37.037 0.00 0.00 0.00 1.85
288 294 2.622436 ACCAGCATCTCTCGTTTAAGC 58.378 47.619 0.00 0.00 0.00 3.09
289 295 1.590238 CCAGCATCTCTCGTTTAAGCG 59.410 52.381 5.23 5.23 0.00 4.68
290 296 2.530177 CAGCATCTCTCGTTTAAGCGA 58.470 47.619 13.89 13.89 39.22 4.93
291 297 2.280183 CAGCATCTCTCGTTTAAGCGAC 59.720 50.000 10.56 0.18 36.80 5.19
292 298 1.588861 GCATCTCTCGTTTAAGCGACC 59.411 52.381 10.56 0.00 36.80 4.79
293 299 1.846782 CATCTCTCGTTTAAGCGACCG 59.153 52.381 10.56 2.58 36.80 4.79
294 300 0.455633 TCTCTCGTTTAAGCGACCGC 60.456 55.000 10.56 6.25 42.33 5.68
295 301 0.731514 CTCTCGTTTAAGCGACCGCA 60.732 55.000 16.97 0.00 44.88 5.69
296 302 0.108992 TCTCGTTTAAGCGACCGCAT 60.109 50.000 16.97 7.29 44.88 4.73
297 303 0.025001 CTCGTTTAAGCGACCGCATG 59.975 55.000 16.97 1.54 44.88 4.06
299 305 1.427819 GTTTAAGCGACCGCATGGG 59.572 57.895 16.97 2.06 44.88 4.00
300 306 1.022451 GTTTAAGCGACCGCATGGGA 61.022 55.000 16.97 0.00 44.88 4.37
301 307 1.022451 TTTAAGCGACCGCATGGGAC 61.022 55.000 16.97 4.23 44.88 4.46
302 308 2.173758 TTAAGCGACCGCATGGGACA 62.174 55.000 16.97 0.00 44.88 4.02
303 309 1.966901 TAAGCGACCGCATGGGACAT 61.967 55.000 16.97 0.00 44.88 3.06
317 323 4.098914 TGGGACATGTTCTTAGCAAACT 57.901 40.909 3.62 0.00 0.00 2.66
318 324 4.072131 TGGGACATGTTCTTAGCAAACTC 58.928 43.478 3.62 0.00 0.00 3.01
319 325 4.072131 GGGACATGTTCTTAGCAAACTCA 58.928 43.478 3.62 0.00 0.00 3.41
320 326 4.518970 GGGACATGTTCTTAGCAAACTCAA 59.481 41.667 3.62 0.00 0.00 3.02
321 327 5.009610 GGGACATGTTCTTAGCAAACTCAAA 59.990 40.000 3.62 0.00 0.00 2.69
322 328 6.460953 GGGACATGTTCTTAGCAAACTCAAAA 60.461 38.462 3.62 0.00 0.00 2.44
323 329 7.147976 GGACATGTTCTTAGCAAACTCAAAAT 58.852 34.615 0.00 0.00 0.00 1.82
324 330 7.653311 GGACATGTTCTTAGCAAACTCAAAATT 59.347 33.333 0.00 0.00 0.00 1.82
325 331 8.579682 ACATGTTCTTAGCAAACTCAAAATTC 57.420 30.769 0.00 0.00 0.00 2.17
326 332 8.196771 ACATGTTCTTAGCAAACTCAAAATTCA 58.803 29.630 0.00 0.00 0.00 2.57
327 333 7.985634 TGTTCTTAGCAAACTCAAAATTCAC 57.014 32.000 0.00 0.00 0.00 3.18
328 334 7.542890 TGTTCTTAGCAAACTCAAAATTCACA 58.457 30.769 0.00 0.00 0.00 3.58
329 335 8.196771 TGTTCTTAGCAAACTCAAAATTCACAT 58.803 29.630 0.00 0.00 0.00 3.21
330 336 9.677567 GTTCTTAGCAAACTCAAAATTCACATA 57.322 29.630 0.00 0.00 0.00 2.29
331 337 9.677567 TTCTTAGCAAACTCAAAATTCACATAC 57.322 29.630 0.00 0.00 0.00 2.39
349 366 7.431249 TCACATACAGTACTAAATTCGATCCC 58.569 38.462 0.00 0.00 0.00 3.85
353 370 9.273016 CATACAGTACTAAATTCGATCCCAATT 57.727 33.333 0.00 0.00 0.00 2.32
371 388 4.977963 CCAATTCAATCGAATCAAATCCGG 59.022 41.667 0.00 0.00 41.12 5.14
408 425 4.160814 ACGTAAATGTGCCACTATCCTACA 59.839 41.667 0.00 0.00 0.00 2.74
473 490 3.257624 CGGGGCCGAAGATAATAACTACT 59.742 47.826 0.00 0.00 42.83 2.57
474 491 4.617762 CGGGGCCGAAGATAATAACTACTC 60.618 50.000 0.00 0.00 42.83 2.59
518 634 5.086058 GCAATGTTTGTTATACGGTCAGTG 58.914 41.667 0.00 0.00 0.00 3.66
555 671 2.561478 ATGGCCGTGTATCAATACCC 57.439 50.000 0.00 0.00 32.33 3.69
746 862 1.161843 GCGAAAGTTGGGAATTCGGA 58.838 50.000 8.90 0.00 44.42 4.55
756 872 2.495669 TGGGAATTCGGAAGCATTTTCC 59.504 45.455 10.29 10.29 35.27 3.13
807 924 2.546778 GTGCGACCCTTTGATCGAATA 58.453 47.619 0.00 0.00 40.86 1.75
831 948 0.168128 GCGCAAAGGCTTGTATTCGT 59.832 50.000 0.30 0.00 38.10 3.85
841 958 8.447833 CAAAGGCTTGTATTCGTCTGTAATTTA 58.552 33.333 0.00 0.00 0.00 1.40
922 1041 0.178068 GCTCCAATCCTACCTTCGCA 59.822 55.000 0.00 0.00 0.00 5.10
923 1042 1.808133 GCTCCAATCCTACCTTCGCAG 60.808 57.143 0.00 0.00 0.00 5.18
924 1043 1.482593 CTCCAATCCTACCTTCGCAGT 59.517 52.381 0.00 0.00 0.00 4.40
925 1044 1.906574 TCCAATCCTACCTTCGCAGTT 59.093 47.619 0.00 0.00 0.00 3.16
926 1045 2.093658 TCCAATCCTACCTTCGCAGTTC 60.094 50.000 0.00 0.00 0.00 3.01
927 1046 1.927174 CAATCCTACCTTCGCAGTTCG 59.073 52.381 0.00 0.00 40.15 3.95
928 1047 0.179108 ATCCTACCTTCGCAGTTCGC 60.179 55.000 0.00 0.00 38.27 4.70
1122 1241 4.598894 CCGCCGGAGATCTGCCAG 62.599 72.222 5.05 1.56 0.00 4.85
1248 1367 0.395686 CTGATGATGAGGGCGATGGT 59.604 55.000 0.00 0.00 0.00 3.55
1386 1515 4.825546 AATCTTTTATGGCAGCTGATCG 57.174 40.909 20.43 0.00 0.00 3.69
1390 1519 4.751600 TCTTTTATGGCAGCTGATCGTATG 59.248 41.667 20.43 7.87 0.00 2.39
1588 1717 0.608640 TCGAGAAGAACAAGGGAGGC 59.391 55.000 0.00 0.00 0.00 4.70
1621 1750 0.392998 TCTCCTCAAAAGCGATGGCC 60.393 55.000 0.00 0.00 41.24 5.36
1681 1810 5.338708 CCTTGTCACAGAGGAATCAAGGTAT 60.339 44.000 11.96 0.00 43.66 2.73
1682 1811 5.089970 TGTCACAGAGGAATCAAGGTATG 57.910 43.478 0.00 0.00 0.00 2.39
1703 1832 3.117888 TGTTCTTCCTCTTGCTGACCTTT 60.118 43.478 0.00 0.00 0.00 3.11
1704 1833 3.864789 TCTTCCTCTTGCTGACCTTTT 57.135 42.857 0.00 0.00 0.00 2.27
1705 1834 4.170468 TCTTCCTCTTGCTGACCTTTTT 57.830 40.909 0.00 0.00 0.00 1.94
1706 1835 4.137543 TCTTCCTCTTGCTGACCTTTTTC 58.862 43.478 0.00 0.00 0.00 2.29
1707 1836 3.864789 TCCTCTTGCTGACCTTTTTCT 57.135 42.857 0.00 0.00 0.00 2.52
1708 1837 3.744660 TCCTCTTGCTGACCTTTTTCTC 58.255 45.455 0.00 0.00 0.00 2.87
1709 1838 3.392616 TCCTCTTGCTGACCTTTTTCTCT 59.607 43.478 0.00 0.00 0.00 3.10
1710 1839 3.501445 CCTCTTGCTGACCTTTTTCTCTG 59.499 47.826 0.00 0.00 0.00 3.35
1748 1877 8.981659 TCTCTGAGATGTGATTTCCAATAGTTA 58.018 33.333 2.58 0.00 0.00 2.24
1799 1928 6.323739 TGGTTTTCTGATTCAGGTTTAAAGCT 59.676 34.615 14.07 14.07 37.19 3.74
1825 1954 2.467838 CACTGGAGTATCGCTGACATG 58.532 52.381 0.00 0.00 34.37 3.21
1833 1962 4.184629 AGTATCGCTGACATGTTCTTTCC 58.815 43.478 0.00 0.00 0.00 3.13
1844 1973 7.386851 TGACATGTTCTTTCCTAACTCCTAAG 58.613 38.462 0.00 0.00 0.00 2.18
1845 1974 7.234782 TGACATGTTCTTTCCTAACTCCTAAGA 59.765 37.037 0.00 0.00 0.00 2.10
1847 1976 8.606830 ACATGTTCTTTCCTAACTCCTAAGAAT 58.393 33.333 0.00 0.00 37.23 2.40
1882 2012 9.593134 TTTTGCATACTGTTTTTACTTCATTGT 57.407 25.926 0.00 0.00 0.00 2.71
1885 2015 8.194104 TGCATACTGTTTTTACTTCATTGTTGT 58.806 29.630 0.00 0.00 0.00 3.32
1886 2016 9.030301 GCATACTGTTTTTACTTCATTGTTGTT 57.970 29.630 0.00 0.00 0.00 2.83
1983 2113 4.437682 AGCTGGTTAGGCTATTGCATAA 57.562 40.909 2.14 2.14 42.17 1.90
2014 4357 6.554982 TGGTATACTTAGTTGATGAGAGCCAT 59.445 38.462 2.25 0.00 38.43 4.40
2060 4403 2.762535 TAGCCAGCAGTTAACCTCAC 57.237 50.000 0.88 0.00 0.00 3.51
2087 4430 4.034975 GCCTAAATGTTGCTGTTTTTGCAA 59.965 37.500 0.00 0.00 46.48 4.08
2102 4445 5.726980 TTTTGCAAGCTACTTGATTCCAT 57.273 34.783 11.38 0.00 43.42 3.41
2108 4451 5.747197 GCAAGCTACTTGATTCCATTCATTG 59.253 40.000 11.38 0.00 43.42 2.82
2168 4511 7.928307 AGTCAAGTGAAATATGCAACACTAT 57.072 32.000 11.84 0.00 41.73 2.12
2197 4540 6.372104 TCAGGAGATAGTGATCAGTGAGAAT 58.628 40.000 13.54 0.00 34.17 2.40
2198 4541 6.264970 TCAGGAGATAGTGATCAGTGAGAATG 59.735 42.308 13.54 5.44 34.17 2.67
2211 4554 7.587037 TCAGTGAGAATGAAAACATTTCCTT 57.413 32.000 0.00 0.00 0.00 3.36
2218 4561 6.697019 AGAATGAAAACATTTCCTTTGACACG 59.303 34.615 0.00 0.00 0.00 4.49
2225 4568 4.935808 ACATTTCCTTTGACACGGATCTAC 59.064 41.667 0.00 0.00 0.00 2.59
2232 4579 5.923114 CCTTTGACACGGATCTACTATGATG 59.077 44.000 0.00 0.00 0.00 3.07
2238 4585 7.501225 TGACACGGATCTACTATGATGTAAGAA 59.499 37.037 0.00 0.00 0.00 2.52
2240 4587 8.353684 ACACGGATCTACTATGATGTAAGAAAG 58.646 37.037 0.00 0.00 0.00 2.62
2241 4588 7.810282 CACGGATCTACTATGATGTAAGAAAGG 59.190 40.741 0.00 0.00 0.00 3.11
2301 4648 7.444183 TGGAAATTCCCGTATTAATCAGCTAAG 59.556 37.037 9.87 0.00 35.03 2.18
2354 4702 4.515944 CCCACATTAACCGACTACAAACAA 59.484 41.667 0.00 0.00 0.00 2.83
2366 4714 8.041323 ACCGACTACAAACAAAGATAGATCAAT 58.959 33.333 0.00 0.00 0.00 2.57
2393 4741 6.253946 AGAGGTTCTCTGAAAGGAAAAGAA 57.746 37.500 0.00 0.00 39.62 2.52
2488 4836 9.091784 CGTATGGAATATGGAGAGTGAATAATG 57.908 37.037 0.00 0.00 32.11 1.90
2536 4884 3.650281 GGGGGAATTTTGGATGCATTT 57.350 42.857 0.00 0.00 0.00 2.32
2552 4900 9.639563 TGGATGCATTTATAAGGTATTTGAAGA 57.360 29.630 0.00 0.00 0.00 2.87
2632 4985 9.014297 AGTATTTATCCCTTTGTCTCAAAGTTG 57.986 33.333 17.18 10.35 0.00 3.16
2667 5020 8.787852 TGATGTACATTGTAGCAATTTGTGTTA 58.212 29.630 10.30 0.00 0.00 2.41
2715 5068 9.890629 TTCATAAGTGAGCTATTTGTCAAGTAT 57.109 29.630 0.00 0.00 35.39 2.12
2734 5087 9.706691 TCAAGTATGTTTCTAAGTTCTAACTGG 57.293 33.333 0.00 0.00 39.66 4.00
2735 5088 9.706691 CAAGTATGTTTCTAAGTTCTAACTGGA 57.293 33.333 0.00 0.00 39.66 3.86
2737 5090 9.930693 AGTATGTTTCTAAGTTCTAACTGGAAG 57.069 33.333 0.00 0.00 39.66 3.46
2790 5144 7.982919 TCCATTATAAAGCGTTGTATGTACTGT 59.017 33.333 0.00 0.00 0.00 3.55
2872 5226 7.428282 TGTGACTTATGAAACGCTTGATTAA 57.572 32.000 0.00 0.00 0.00 1.40
2883 5237 4.787598 ACGCTTGATTAAAAGTTCTGCTG 58.212 39.130 0.00 0.00 0.00 4.41
2885 5239 5.215160 CGCTTGATTAAAAGTTCTGCTGTT 58.785 37.500 0.00 0.00 0.00 3.16
3118 5520 3.490759 CACAGACGCATGGGTCGC 61.491 66.667 30.26 14.12 41.81 5.19
3250 5652 2.708325 GGGAAGCTGGATTCTCTACCAT 59.292 50.000 0.00 0.00 35.54 3.55
3253 5655 4.384647 GGAAGCTGGATTCTCTACCATGTT 60.385 45.833 0.00 0.00 35.54 2.71
3331 5733 3.272574 CAGATTGACTGCACCCATACT 57.727 47.619 0.00 0.00 39.86 2.12
3361 5763 1.442017 GTGCGTTGATTCGGTTGCC 60.442 57.895 0.00 0.00 0.00 4.52
3770 6172 8.592998 CGTCGCCCTATGATTATAACTAATTTC 58.407 37.037 0.00 0.00 0.00 2.17
3771 6173 9.654663 GTCGCCCTATGATTATAACTAATTTCT 57.345 33.333 0.00 0.00 0.00 2.52
3835 6237 2.009051 TGCGTCAGCTTGAATGTATGG 58.991 47.619 0.00 0.00 45.42 2.74
3873 6275 1.550072 TGATGTTGATGTGCTCGGAGA 59.450 47.619 9.69 0.00 0.00 3.71
3894 6296 3.395630 GGTGCCTAACCTCGGGAA 58.604 61.111 0.00 0.00 46.55 3.97
3957 6359 8.579850 TCTAAATTGGATGCTATCAAACTTGT 57.420 30.769 0.00 0.00 0.00 3.16
3958 6360 9.023962 TCTAAATTGGATGCTATCAAACTTGTT 57.976 29.630 0.00 0.00 0.00 2.83
3959 6361 7.894376 AAATTGGATGCTATCAAACTTGTTG 57.106 32.000 0.00 0.00 0.00 3.33
3960 6362 6.839124 ATTGGATGCTATCAAACTTGTTGA 57.161 33.333 0.00 0.00 0.00 3.18
3961 6363 6.647334 TTGGATGCTATCAAACTTGTTGAA 57.353 33.333 0.00 0.00 31.55 2.69
3962 6364 6.839124 TGGATGCTATCAAACTTGTTGAAT 57.161 33.333 0.00 0.00 31.55 2.57
3963 6365 7.936496 TGGATGCTATCAAACTTGTTGAATA 57.064 32.000 0.00 0.00 31.55 1.75
3964 6366 8.523915 TGGATGCTATCAAACTTGTTGAATAT 57.476 30.769 0.00 0.00 31.55 1.28
3965 6367 9.625747 TGGATGCTATCAAACTTGTTGAATATA 57.374 29.630 0.00 0.00 31.55 0.86
4099 6665 2.171448 GGCTCCCATGTGTCTATTGTCT 59.829 50.000 0.00 0.00 0.00 3.41
4129 6695 6.961359 TTATATCCGTCTCAAGTTGTTGTG 57.039 37.500 2.11 0.00 34.98 3.33
4148 6714 1.102978 GGGTCGATGGGTTTCATTGG 58.897 55.000 0.00 0.00 37.74 3.16
4253 6822 2.407090 TGAGTGAGCAAGTTCGTGATG 58.593 47.619 0.00 0.00 0.00 3.07
4256 6825 3.668447 AGTGAGCAAGTTCGTGATGATT 58.332 40.909 0.00 0.00 0.00 2.57
4266 6835 5.313712 AGTTCGTGATGATTTTAACCTGGT 58.686 37.500 0.00 0.00 0.00 4.00
4271 6840 7.142680 TCGTGATGATTTTAACCTGGTTTTTC 58.857 34.615 18.58 9.98 0.00 2.29
4282 6851 4.851010 ACCTGGTTTTTCGTCAATTAACG 58.149 39.130 0.00 0.00 43.92 3.18
4283 6852 4.223659 CCTGGTTTTTCGTCAATTAACGG 58.776 43.478 0.32 0.00 42.80 4.44
4312 6881 9.853177 AACTTTATCCTTCCTAACTAATGGATG 57.147 33.333 0.00 0.00 36.02 3.51
4320 6889 7.281100 CCTTCCTAACTAATGGATGTCTTTCAC 59.719 40.741 0.00 0.00 31.76 3.18
4404 6973 1.811558 GCGCCTCATATCTCCAAAGCA 60.812 52.381 0.00 0.00 0.00 3.91
4405 6974 1.869767 CGCCTCATATCTCCAAAGCAC 59.130 52.381 0.00 0.00 0.00 4.40
4406 6975 2.484417 CGCCTCATATCTCCAAAGCACT 60.484 50.000 0.00 0.00 0.00 4.40
4409 6978 4.378774 CCTCATATCTCCAAAGCACTCTG 58.621 47.826 0.00 0.00 0.00 3.35
4410 6979 3.801698 TCATATCTCCAAAGCACTCTGC 58.198 45.455 0.00 0.00 45.46 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.017509 CGGAGGGAGTATGTTATACTGTATTTA 57.982 37.037 5.52 0.00 0.00 1.40
3 4 7.508296 ACGGAGGGAGTATGTTATACTGTATTT 59.492 37.037 5.52 0.00 0.00 1.40
4 5 7.008941 ACGGAGGGAGTATGTTATACTGTATT 58.991 38.462 5.52 0.00 0.00 1.89
5 6 6.550163 ACGGAGGGAGTATGTTATACTGTAT 58.450 40.000 6.24 5.53 0.00 2.29
6 7 5.945310 ACGGAGGGAGTATGTTATACTGTA 58.055 41.667 6.24 0.00 0.00 2.74
7 8 4.801164 ACGGAGGGAGTATGTTATACTGT 58.199 43.478 6.24 0.00 0.00 3.55
8 9 4.217983 GGACGGAGGGAGTATGTTATACTG 59.782 50.000 6.24 0.00 0.00 2.74
9 10 4.106019 AGGACGGAGGGAGTATGTTATACT 59.894 45.833 1.34 1.34 0.00 2.12
10 11 4.405548 AGGACGGAGGGAGTATGTTATAC 58.594 47.826 0.00 0.00 0.00 1.47
11 12 4.736611 AGGACGGAGGGAGTATGTTATA 57.263 45.455 0.00 0.00 0.00 0.98
12 13 3.614568 AGGACGGAGGGAGTATGTTAT 57.385 47.619 0.00 0.00 0.00 1.89
13 14 4.524802 TTAGGACGGAGGGAGTATGTTA 57.475 45.455 0.00 0.00 0.00 2.41
14 15 3.393426 TTAGGACGGAGGGAGTATGTT 57.607 47.619 0.00 0.00 0.00 2.71
15 16 3.393426 TTTAGGACGGAGGGAGTATGT 57.607 47.619 0.00 0.00 0.00 2.29
16 17 4.957684 ATTTTAGGACGGAGGGAGTATG 57.042 45.455 0.00 0.00 0.00 2.39
17 18 8.175431 TCTTATATTTTAGGACGGAGGGAGTAT 58.825 37.037 0.00 0.00 0.00 2.12
18 19 7.529555 TCTTATATTTTAGGACGGAGGGAGTA 58.470 38.462 0.00 0.00 0.00 2.59
19 20 6.379579 TCTTATATTTTAGGACGGAGGGAGT 58.620 40.000 0.00 0.00 0.00 3.85
20 21 6.572703 GCTCTTATATTTTAGGACGGAGGGAG 60.573 46.154 0.00 0.00 0.00 4.30
21 22 5.245526 GCTCTTATATTTTAGGACGGAGGGA 59.754 44.000 0.00 0.00 0.00 4.20
22 23 5.480205 GCTCTTATATTTTAGGACGGAGGG 58.520 45.833 0.00 0.00 0.00 4.30
23 24 5.162075 CGCTCTTATATTTTAGGACGGAGG 58.838 45.833 0.00 0.00 0.00 4.30
24 25 5.770417 ACGCTCTTATATTTTAGGACGGAG 58.230 41.667 0.00 0.00 0.00 4.63
25 26 5.779529 ACGCTCTTATATTTTAGGACGGA 57.220 39.130 0.00 0.00 0.00 4.69
26 27 6.839820 AAACGCTCTTATATTTTAGGACGG 57.160 37.500 0.00 0.00 0.00 4.79
27 28 7.681903 ACAAAACGCTCTTATATTTTAGGACG 58.318 34.615 0.00 0.00 0.00 4.79
38 39 9.947669 CTACACTAGTATACAAAACGCTCTTAT 57.052 33.333 5.50 0.00 0.00 1.73
39 40 8.950210 ACTACACTAGTATACAAAACGCTCTTA 58.050 33.333 5.50 0.00 37.23 2.10
40 41 7.754027 CACTACACTAGTATACAAAACGCTCTT 59.246 37.037 5.50 0.00 37.23 2.85
41 42 7.094463 ACACTACACTAGTATACAAAACGCTCT 60.094 37.037 5.50 0.00 37.23 4.09
42 43 7.025963 ACACTACACTAGTATACAAAACGCTC 58.974 38.462 5.50 0.00 37.23 5.03
43 44 6.917533 ACACTACACTAGTATACAAAACGCT 58.082 36.000 5.50 0.00 37.23 5.07
44 45 6.803320 TGACACTACACTAGTATACAAAACGC 59.197 38.462 5.50 0.00 37.23 4.84
45 46 8.732413 TTGACACTACACTAGTATACAAAACG 57.268 34.615 5.50 0.00 37.23 3.60
49 50 9.184062 CGTTTTTGACACTACACTAGTATACAA 57.816 33.333 5.50 0.00 37.23 2.41
50 51 8.352201 ACGTTTTTGACACTACACTAGTATACA 58.648 33.333 5.50 0.00 37.23 2.29
51 52 8.733857 ACGTTTTTGACACTACACTAGTATAC 57.266 34.615 0.00 0.00 37.23 1.47
52 53 9.748708 AAACGTTTTTGACACTACACTAGTATA 57.251 29.630 7.96 0.00 37.23 1.47
53 54 8.652810 AAACGTTTTTGACACTACACTAGTAT 57.347 30.769 7.96 0.00 37.23 2.12
54 55 8.477984 AAAACGTTTTTGACACTACACTAGTA 57.522 30.769 20.26 0.00 37.23 1.82
55 56 6.973229 AAACGTTTTTGACACTACACTAGT 57.027 33.333 7.96 0.00 40.28 2.57
56 57 9.925268 ATAAAAACGTTTTTGACACTACACTAG 57.075 29.630 36.92 0.00 40.33 2.57
63 64 9.843334 TCTGTTTATAAAAACGTTTTTGACACT 57.157 25.926 36.92 22.37 46.63 3.55
65 66 9.291664 CCTCTGTTTATAAAAACGTTTTTGACA 57.708 29.630 36.92 30.72 46.63 3.58
66 67 9.505995 TCCTCTGTTTATAAAAACGTTTTTGAC 57.494 29.630 36.92 28.82 46.63 3.18
72 73 9.551734 ACTACTTCCTCTGTTTATAAAAACGTT 57.448 29.630 0.00 0.00 46.63 3.99
73 74 9.551734 AACTACTTCCTCTGTTTATAAAAACGT 57.448 29.630 0.00 0.00 46.63 3.99
81 82 9.628500 AAACAAAGAACTACTTCCTCTGTTTAT 57.372 29.630 0.00 0.00 40.69 1.40
82 83 9.106070 GAAACAAAGAACTACTTCCTCTGTTTA 57.894 33.333 0.00 0.00 41.61 2.01
83 84 7.610305 TGAAACAAAGAACTACTTCCTCTGTTT 59.390 33.333 0.00 0.00 42.91 2.83
84 85 7.110155 TGAAACAAAGAACTACTTCCTCTGTT 58.890 34.615 0.00 0.00 37.40 3.16
85 86 6.650120 TGAAACAAAGAACTACTTCCTCTGT 58.350 36.000 0.00 0.00 37.93 3.41
86 87 6.293135 GCTGAAACAAAGAACTACTTCCTCTG 60.293 42.308 0.00 0.00 37.93 3.35
87 88 5.760743 GCTGAAACAAAGAACTACTTCCTCT 59.239 40.000 0.00 0.00 37.93 3.69
88 89 5.760743 AGCTGAAACAAAGAACTACTTCCTC 59.239 40.000 0.00 0.00 37.93 3.71
89 90 5.529060 CAGCTGAAACAAAGAACTACTTCCT 59.471 40.000 8.42 0.00 37.93 3.36
90 91 5.752712 CAGCTGAAACAAAGAACTACTTCC 58.247 41.667 8.42 0.00 37.93 3.46
91 92 5.208503 GCAGCTGAAACAAAGAACTACTTC 58.791 41.667 20.43 0.00 37.93 3.01
92 93 4.640201 TGCAGCTGAAACAAAGAACTACTT 59.360 37.500 20.43 0.00 40.98 2.24
93 94 4.199310 TGCAGCTGAAACAAAGAACTACT 58.801 39.130 20.43 0.00 0.00 2.57
94 95 4.552166 TGCAGCTGAAACAAAGAACTAC 57.448 40.909 20.43 0.00 0.00 2.73
95 96 5.772825 ATTGCAGCTGAAACAAAGAACTA 57.227 34.783 20.43 0.00 0.00 2.24
96 97 4.660789 ATTGCAGCTGAAACAAAGAACT 57.339 36.364 20.43 0.00 0.00 3.01
97 98 4.551410 GCAATTGCAGCTGAAACAAAGAAC 60.551 41.667 25.36 0.00 41.59 3.01
98 99 3.556775 GCAATTGCAGCTGAAACAAAGAA 59.443 39.130 25.36 0.00 41.59 2.52
99 100 3.125316 GCAATTGCAGCTGAAACAAAGA 58.875 40.909 25.36 0.00 41.59 2.52
100 101 3.515071 GCAATTGCAGCTGAAACAAAG 57.485 42.857 25.36 10.32 41.59 2.77
139 140 9.730420 GCGAATGAAATTATGTTTTGGTATAGT 57.270 29.630 0.00 0.00 36.07 2.12
140 141 9.729023 TGCGAATGAAATTATGTTTTGGTATAG 57.271 29.630 0.00 0.00 36.07 1.31
142 143 8.994429 TTGCGAATGAAATTATGTTTTGGTAT 57.006 26.923 0.00 0.00 36.07 2.73
143 144 8.300286 TCTTGCGAATGAAATTATGTTTTGGTA 58.700 29.630 0.00 0.00 36.07 3.25
144 145 7.151308 TCTTGCGAATGAAATTATGTTTTGGT 58.849 30.769 0.00 0.00 36.07 3.67
145 146 7.579589 TCTTGCGAATGAAATTATGTTTTGG 57.420 32.000 0.00 0.00 36.07 3.28
149 150 9.853555 TGTTTATCTTGCGAATGAAATTATGTT 57.146 25.926 0.00 0.00 36.07 2.71
150 151 9.289303 GTGTTTATCTTGCGAATGAAATTATGT 57.711 29.630 0.00 0.00 36.07 2.29
151 152 9.288124 TGTGTTTATCTTGCGAATGAAATTATG 57.712 29.630 0.00 0.00 36.07 1.90
152 153 9.853555 TTGTGTTTATCTTGCGAATGAAATTAT 57.146 25.926 0.00 0.00 36.07 1.28
153 154 9.853555 ATTGTGTTTATCTTGCGAATGAAATTA 57.146 25.926 0.00 0.00 36.07 1.40
154 155 8.761575 ATTGTGTTTATCTTGCGAATGAAATT 57.238 26.923 0.00 0.00 40.93 1.82
155 156 8.761575 AATTGTGTTTATCTTGCGAATGAAAT 57.238 26.923 0.00 0.00 0.00 2.17
156 157 9.123709 GTAATTGTGTTTATCTTGCGAATGAAA 57.876 29.630 0.00 0.00 0.00 2.69
157 158 8.293157 TGTAATTGTGTTTATCTTGCGAATGAA 58.707 29.630 0.00 0.00 0.00 2.57
158 159 7.811653 TGTAATTGTGTTTATCTTGCGAATGA 58.188 30.769 0.00 0.00 0.00 2.57
159 160 8.619146 ATGTAATTGTGTTTATCTTGCGAATG 57.381 30.769 0.00 0.00 0.00 2.67
247 248 8.784043 GCTGGTATTAAACTGATAAAATCCGAT 58.216 33.333 0.00 0.00 0.00 4.18
248 249 7.771361 TGCTGGTATTAAACTGATAAAATCCGA 59.229 33.333 0.00 0.00 0.00 4.55
249 250 7.925993 TGCTGGTATTAAACTGATAAAATCCG 58.074 34.615 0.00 0.00 0.00 4.18
250 251 9.899226 GATGCTGGTATTAAACTGATAAAATCC 57.101 33.333 0.00 0.00 0.00 3.01
260 266 5.599999 ACGAGAGATGCTGGTATTAAACT 57.400 39.130 0.00 0.00 33.43 2.66
269 275 1.590238 CGCTTAAACGAGAGATGCTGG 59.410 52.381 0.00 0.00 34.06 4.85
271 277 2.531206 GTCGCTTAAACGAGAGATGCT 58.469 47.619 0.27 0.00 43.89 3.79
275 281 0.455633 GCGGTCGCTTAAACGAGAGA 60.456 55.000 8.20 0.00 43.89 3.10
279 285 1.355796 CCATGCGGTCGCTTAAACGA 61.356 55.000 16.36 0.00 42.51 3.85
281 287 1.022451 TCCCATGCGGTCGCTTAAAC 61.022 55.000 16.36 0.00 42.51 2.01
283 289 1.448893 GTCCCATGCGGTCGCTTAA 60.449 57.895 16.36 0.00 42.51 1.85
284 290 1.966901 ATGTCCCATGCGGTCGCTTA 61.967 55.000 16.36 0.00 42.51 3.09
285 291 3.329542 ATGTCCCATGCGGTCGCTT 62.330 57.895 16.36 7.40 42.51 4.68
287 293 3.576356 CATGTCCCATGCGGTCGC 61.576 66.667 8.54 8.54 42.35 5.19
288 294 1.705337 GAACATGTCCCATGCGGTCG 61.705 60.000 0.00 0.00 0.00 4.79
289 295 0.392998 AGAACATGTCCCATGCGGTC 60.393 55.000 0.00 0.00 0.00 4.79
290 296 0.038166 AAGAACATGTCCCATGCGGT 59.962 50.000 0.00 0.00 0.00 5.68
291 297 1.942657 CTAAGAACATGTCCCATGCGG 59.057 52.381 0.00 0.00 0.00 5.69
292 298 1.331756 GCTAAGAACATGTCCCATGCG 59.668 52.381 0.00 0.00 0.00 4.73
293 299 2.368439 TGCTAAGAACATGTCCCATGC 58.632 47.619 0.00 2.46 0.00 4.06
294 300 4.460382 AGTTTGCTAAGAACATGTCCCATG 59.540 41.667 0.00 2.77 0.00 3.66
295 301 4.666512 AGTTTGCTAAGAACATGTCCCAT 58.333 39.130 0.00 0.00 0.00 4.00
296 302 4.072131 GAGTTTGCTAAGAACATGTCCCA 58.928 43.478 0.00 0.00 0.00 4.37
297 303 4.072131 TGAGTTTGCTAAGAACATGTCCC 58.928 43.478 0.00 0.00 0.00 4.46
299 305 8.579682 AATTTTGAGTTTGCTAAGAACATGTC 57.420 30.769 0.00 0.00 0.00 3.06
300 306 8.196771 TGAATTTTGAGTTTGCTAAGAACATGT 58.803 29.630 0.00 0.00 0.00 3.21
301 307 8.482429 GTGAATTTTGAGTTTGCTAAGAACATG 58.518 33.333 0.00 0.00 0.00 3.21
302 308 8.196771 TGTGAATTTTGAGTTTGCTAAGAACAT 58.803 29.630 0.00 0.00 0.00 2.71
303 309 7.542890 TGTGAATTTTGAGTTTGCTAAGAACA 58.457 30.769 0.00 0.00 0.00 3.18
304 310 7.985634 TGTGAATTTTGAGTTTGCTAAGAAC 57.014 32.000 0.00 0.00 0.00 3.01
305 311 9.677567 GTATGTGAATTTTGAGTTTGCTAAGAA 57.322 29.630 0.00 0.00 0.00 2.52
306 312 8.845227 TGTATGTGAATTTTGAGTTTGCTAAGA 58.155 29.630 0.00 0.00 0.00 2.10
307 313 9.121517 CTGTATGTGAATTTTGAGTTTGCTAAG 57.878 33.333 0.00 0.00 0.00 2.18
308 314 8.629158 ACTGTATGTGAATTTTGAGTTTGCTAA 58.371 29.630 0.00 0.00 0.00 3.09
309 315 8.165239 ACTGTATGTGAATTTTGAGTTTGCTA 57.835 30.769 0.00 0.00 0.00 3.49
310 316 7.042797 ACTGTATGTGAATTTTGAGTTTGCT 57.957 32.000 0.00 0.00 0.00 3.91
311 317 8.076178 AGTACTGTATGTGAATTTTGAGTTTGC 58.924 33.333 0.00 0.00 0.00 3.68
322 328 9.477484 GGATCGAATTTAGTACTGTATGTGAAT 57.523 33.333 5.39 0.00 0.00 2.57
323 329 7.924412 GGGATCGAATTTAGTACTGTATGTGAA 59.076 37.037 5.39 0.00 0.00 3.18
324 330 7.068962 TGGGATCGAATTTAGTACTGTATGTGA 59.931 37.037 5.39 0.00 0.00 3.58
325 331 7.207383 TGGGATCGAATTTAGTACTGTATGTG 58.793 38.462 5.39 0.00 0.00 3.21
326 332 7.356089 TGGGATCGAATTTAGTACTGTATGT 57.644 36.000 5.39 0.00 0.00 2.29
327 333 8.833231 ATTGGGATCGAATTTAGTACTGTATG 57.167 34.615 5.39 0.00 0.00 2.39
328 334 9.490379 GAATTGGGATCGAATTTAGTACTGTAT 57.510 33.333 5.39 0.00 0.00 2.29
329 335 8.479689 TGAATTGGGATCGAATTTAGTACTGTA 58.520 33.333 5.39 0.00 0.00 2.74
330 336 7.335627 TGAATTGGGATCGAATTTAGTACTGT 58.664 34.615 5.39 0.00 0.00 3.55
331 337 7.786178 TGAATTGGGATCGAATTTAGTACTG 57.214 36.000 5.39 0.00 0.00 2.74
349 366 4.977963 CCCGGATTTGATTCGATTGAATTG 59.022 41.667 0.73 0.00 44.79 2.32
353 370 1.946768 GCCCGGATTTGATTCGATTGA 59.053 47.619 0.73 0.00 0.00 2.57
387 404 8.848474 ATAATGTAGGATAGTGGCACATTTAC 57.152 34.615 21.41 13.95 44.52 2.01
473 490 3.142951 CGTTTGGGTCCAATTGTGTAGA 58.857 45.455 4.43 0.00 35.70 2.59
474 491 2.227865 CCGTTTGGGTCCAATTGTGTAG 59.772 50.000 4.43 0.00 35.70 2.74
583 699 3.581332 TCGGAGGCCTTTTAAAGAAGAGA 59.419 43.478 6.77 0.00 0.00 3.10
584 700 3.939066 TCGGAGGCCTTTTAAAGAAGAG 58.061 45.455 6.77 0.00 0.00 2.85
585 701 4.360951 TTCGGAGGCCTTTTAAAGAAGA 57.639 40.909 6.77 0.00 0.00 2.87
746 862 2.817258 TCAAATCGACCGGAAAATGCTT 59.183 40.909 9.46 0.00 0.00 3.91
756 872 2.890474 CCGGCCTCAAATCGACCG 60.890 66.667 0.00 1.67 43.44 4.79
922 1041 0.037326 TCAGATTTGCCGAGCGAACT 60.037 50.000 1.28 0.11 34.53 3.01
923 1042 0.371645 CTCAGATTTGCCGAGCGAAC 59.628 55.000 1.28 0.00 34.53 3.95
924 1043 0.740868 CCTCAGATTTGCCGAGCGAA 60.741 55.000 1.70 1.70 36.30 4.70
925 1044 1.153568 CCTCAGATTTGCCGAGCGA 60.154 57.895 0.00 0.00 0.00 4.93
926 1045 2.817423 GCCTCAGATTTGCCGAGCG 61.817 63.158 0.00 0.00 0.00 5.03
927 1046 2.817423 CGCCTCAGATTTGCCGAGC 61.817 63.158 0.00 0.00 0.00 5.03
928 1047 2.817423 GCGCCTCAGATTTGCCGAG 61.817 63.158 0.00 0.00 0.00 4.63
968 1087 3.357079 CGCGGATTATGGCAGCCC 61.357 66.667 9.64 0.00 0.00 5.19
1122 1241 2.125106 CGGTTGAGGCAGGCTACC 60.125 66.667 5.94 5.94 0.00 3.18
1248 1367 1.080093 GACATTGCCGTCTCCGTCA 60.080 57.895 0.00 0.00 32.92 4.35
1386 1515 7.329471 TCTGCTCAATTAATCATCTACGCATAC 59.671 37.037 0.00 0.00 0.00 2.39
1390 1519 6.718454 ATCTGCTCAATTAATCATCTACGC 57.282 37.500 0.00 0.00 0.00 4.42
1588 1717 4.760530 TGAGGAGATGGACATACAAAGG 57.239 45.455 0.00 0.00 0.00 3.11
1621 1750 5.241728 TCTTCGGTCATCTATACCTGTGATG 59.758 44.000 0.00 0.00 38.97 3.07
1681 1810 2.050144 AGGTCAGCAAGAGGAAGAACA 58.950 47.619 0.00 0.00 0.00 3.18
1682 1811 2.849294 AGGTCAGCAAGAGGAAGAAC 57.151 50.000 0.00 0.00 0.00 3.01
1721 1850 8.032045 ACTATTGGAAATCACATCTCAGAGAT 57.968 34.615 7.15 7.15 34.74 2.75
1736 1865 8.581578 GGTTTCTTCAATGGTAACTATTGGAAA 58.418 33.333 7.32 7.27 36.42 3.13
1748 1877 3.760684 GCTGAGATGGTTTCTTCAATGGT 59.239 43.478 0.00 0.00 33.74 3.55
1799 1928 2.031870 AGCGATACTCCAGTGCATACA 58.968 47.619 0.00 0.00 0.00 2.29
1943 2073 5.578727 CCAGCTACAGAGAACTACAACATTC 59.421 44.000 0.00 0.00 0.00 2.67
1948 2078 5.185249 CCTAACCAGCTACAGAGAACTACAA 59.815 44.000 0.00 0.00 0.00 2.41
1953 2083 2.498078 AGCCTAACCAGCTACAGAGAAC 59.502 50.000 0.00 0.00 39.29 3.01
1955 2085 2.534042 AGCCTAACCAGCTACAGAGA 57.466 50.000 0.00 0.00 39.29 3.10
2028 4371 6.780457 ACTGCTGGCTATAAAATGATTTGT 57.220 33.333 0.00 0.00 0.00 2.83
2029 4372 9.023967 GTTAACTGCTGGCTATAAAATGATTTG 57.976 33.333 0.00 0.00 0.00 2.32
2041 4384 1.974957 TGTGAGGTTAACTGCTGGCTA 59.025 47.619 5.42 0.00 0.00 3.93
2044 4387 2.095059 GCAATGTGAGGTTAACTGCTGG 60.095 50.000 5.42 0.00 0.00 4.85
2060 4403 9.527095 TGCAAAAACAGCAACATTTAGGCAATG 62.527 37.037 0.00 0.00 41.65 2.82
2078 4421 5.288804 TGGAATCAAGTAGCTTGCAAAAAC 58.711 37.500 0.00 0.00 40.84 2.43
2079 4422 5.528043 TGGAATCAAGTAGCTTGCAAAAA 57.472 34.783 0.00 0.00 40.84 1.94
2102 4445 9.184523 CTAATACAAGGTTAACATCCCAATGAA 57.815 33.333 8.10 0.00 36.67 2.57
2108 4451 8.685838 TTATGCTAATACAAGGTTAACATCCC 57.314 34.615 8.10 0.00 0.00 3.85
2140 4483 7.228507 AGTGTTGCATATTTCACTTGACTAACA 59.771 33.333 0.00 0.00 37.81 2.41
2141 4484 7.584987 AGTGTTGCATATTTCACTTGACTAAC 58.415 34.615 0.00 0.00 37.81 2.34
2142 4485 7.744087 AGTGTTGCATATTTCACTTGACTAA 57.256 32.000 0.00 0.00 37.81 2.24
2143 4486 9.448438 AATAGTGTTGCATATTTCACTTGACTA 57.552 29.630 11.84 0.00 40.77 2.59
2144 4487 7.928307 ATAGTGTTGCATATTTCACTTGACT 57.072 32.000 11.84 0.00 40.77 3.41
2168 4511 8.539117 TCACTGATCACTATCTCCTGAATTAA 57.461 34.615 0.00 0.00 32.93 1.40
2197 4540 4.399618 TCCGTGTCAAAGGAAATGTTTTCA 59.600 37.500 2.74 0.00 30.19 2.69
2198 4541 4.927422 TCCGTGTCAAAGGAAATGTTTTC 58.073 39.130 0.00 0.00 30.19 2.29
2211 4554 7.501225 TCTTACATCATAGTAGATCCGTGTCAA 59.499 37.037 0.00 0.00 0.00 3.18
2251 4598 4.823989 GCCCTACAGAGCAAATATGAACAT 59.176 41.667 0.00 0.00 0.00 2.71
2270 4617 1.222567 ATACGGGAATTTCCAGCCCT 58.777 50.000 17.08 0.63 38.64 5.19
2354 4702 9.881773 AGAGAACCTCTTCTATTGATCTATCTT 57.118 33.333 0.00 0.00 37.60 2.40
2366 4714 6.996180 TTTCCTTTCAGAGAACCTCTTCTA 57.004 37.500 0.00 0.00 38.99 2.10
2393 4741 7.180766 CCAGGCCACCATATATTTTCCAATATT 59.819 37.037 5.01 0.00 36.95 1.28
2444 4792 1.869690 GCTCAAGGCACGAAGGTTC 59.130 57.895 0.00 0.00 41.35 3.62
2452 4800 1.668419 ATTCCATACGCTCAAGGCAC 58.332 50.000 0.00 0.00 41.91 5.01
2594 4942 9.541884 AAAGGGATAAATACTCTTTTAAGGCAA 57.458 29.630 0.00 0.00 34.90 4.52
2656 5009 6.269315 TGCCAGTACAAAGTAACACAAATTG 58.731 36.000 0.00 0.00 0.00 2.32
2715 5068 6.482308 GCACTTCCAGTTAGAACTTAGAAACA 59.518 38.462 0.00 0.00 37.08 2.83
2724 5077 6.092807 CCAAGATAAGCACTTCCAGTTAGAAC 59.907 42.308 0.00 0.00 0.00 3.01
2726 5079 5.483937 TCCAAGATAAGCACTTCCAGTTAGA 59.516 40.000 0.00 0.00 0.00 2.10
2727 5080 5.734720 TCCAAGATAAGCACTTCCAGTTAG 58.265 41.667 0.00 0.00 0.00 2.34
2728 5081 5.248477 ACTCCAAGATAAGCACTTCCAGTTA 59.752 40.000 0.00 0.00 0.00 2.24
2729 5082 4.042187 ACTCCAAGATAAGCACTTCCAGTT 59.958 41.667 0.00 0.00 0.00 3.16
2730 5083 3.584848 ACTCCAAGATAAGCACTTCCAGT 59.415 43.478 0.00 0.00 0.00 4.00
2731 5084 3.937706 CACTCCAAGATAAGCACTTCCAG 59.062 47.826 0.00 0.00 0.00 3.86
2732 5085 3.327757 ACACTCCAAGATAAGCACTTCCA 59.672 43.478 0.00 0.00 0.00 3.53
2733 5086 3.944087 ACACTCCAAGATAAGCACTTCC 58.056 45.455 0.00 0.00 0.00 3.46
2734 5087 4.870991 GGTACACTCCAAGATAAGCACTTC 59.129 45.833 0.00 0.00 0.00 3.01
2735 5088 4.532521 AGGTACACTCCAAGATAAGCACTT 59.467 41.667 0.00 0.00 0.00 3.16
2736 5089 4.097418 AGGTACACTCCAAGATAAGCACT 58.903 43.478 0.00 0.00 0.00 4.40
2737 5090 4.473477 AGGTACACTCCAAGATAAGCAC 57.527 45.455 0.00 0.00 0.00 4.40
2738 5091 5.269991 ACTAGGTACACTCCAAGATAAGCA 58.730 41.667 0.00 0.00 0.00 3.91
2739 5092 5.855740 ACTAGGTACACTCCAAGATAAGC 57.144 43.478 0.00 0.00 0.00 3.09
2740 5093 8.578151 GGAATACTAGGTACACTCCAAGATAAG 58.422 40.741 0.00 0.00 0.00 1.73
2741 5094 8.063153 TGGAATACTAGGTACACTCCAAGATAA 58.937 37.037 0.00 0.00 28.34 1.75
2787 5141 6.744537 GCTGACTATATGCAAGAAAACAACAG 59.255 38.462 0.00 0.00 0.00 3.16
2790 5144 5.709631 TGGCTGACTATATGCAAGAAAACAA 59.290 36.000 0.00 0.00 0.00 2.83
2872 5226 8.919777 AACTAATAACCTAACAGCAGAACTTT 57.080 30.769 0.00 0.00 0.00 2.66
2947 5340 5.049405 CACGGAAGAAACTCAGCAAAAGTAT 60.049 40.000 0.00 0.00 0.00 2.12
2949 5342 3.065371 CACGGAAGAAACTCAGCAAAAGT 59.935 43.478 0.00 0.00 0.00 2.66
2950 5343 3.065371 ACACGGAAGAAACTCAGCAAAAG 59.935 43.478 0.00 0.00 0.00 2.27
3118 5520 1.515521 GCTCAGTTCCACAAACCCGG 61.516 60.000 0.00 0.00 38.76 5.73
3250 5652 4.384940 TCGAGATGACAAAATCACCAACA 58.615 39.130 0.00 0.00 41.24 3.33
3253 5655 4.641396 AGTTCGAGATGACAAAATCACCA 58.359 39.130 0.00 0.00 41.24 4.17
3331 5733 2.366533 TCAACGCACAAACCACCTTTA 58.633 42.857 0.00 0.00 0.00 1.85
3449 5851 0.813210 CTCCCTCTGAATTGCCTCGC 60.813 60.000 0.00 0.00 0.00 5.03
3835 6237 2.317040 TCACCCCGAGAGTATCATTCC 58.683 52.381 0.00 0.00 37.82 3.01
3894 6296 0.965363 GATGGCAAACATGTCCCCGT 60.965 55.000 0.00 1.02 40.72 5.28
3967 6369 8.202137 CCATCTTTTTCAGCATCCAATTTAGAT 58.798 33.333 0.00 0.00 0.00 1.98
3968 6370 7.178983 ACCATCTTTTTCAGCATCCAATTTAGA 59.821 33.333 0.00 0.00 0.00 2.10
3969 6371 7.325694 ACCATCTTTTTCAGCATCCAATTTAG 58.674 34.615 0.00 0.00 0.00 1.85
3970 6372 7.243604 ACCATCTTTTTCAGCATCCAATTTA 57.756 32.000 0.00 0.00 0.00 1.40
3971 6373 6.117975 ACCATCTTTTTCAGCATCCAATTT 57.882 33.333 0.00 0.00 0.00 1.82
3972 6374 5.750352 ACCATCTTTTTCAGCATCCAATT 57.250 34.783 0.00 0.00 0.00 2.32
3973 6375 5.484715 CAACCATCTTTTTCAGCATCCAAT 58.515 37.500 0.00 0.00 0.00 3.16
3974 6376 4.262549 CCAACCATCTTTTTCAGCATCCAA 60.263 41.667 0.00 0.00 0.00 3.53
3975 6377 3.258872 CCAACCATCTTTTTCAGCATCCA 59.741 43.478 0.00 0.00 0.00 3.41
3976 6378 3.511146 TCCAACCATCTTTTTCAGCATCC 59.489 43.478 0.00 0.00 0.00 3.51
3977 6379 4.789012 TCCAACCATCTTTTTCAGCATC 57.211 40.909 0.00 0.00 0.00 3.91
3978 6380 4.622220 GCATCCAACCATCTTTTTCAGCAT 60.622 41.667 0.00 0.00 0.00 3.79
3979 6381 3.306225 GCATCCAACCATCTTTTTCAGCA 60.306 43.478 0.00 0.00 0.00 4.41
3980 6382 3.256558 GCATCCAACCATCTTTTTCAGC 58.743 45.455 0.00 0.00 0.00 4.26
3981 6383 3.512724 AGGCATCCAACCATCTTTTTCAG 59.487 43.478 0.00 0.00 0.00 3.02
3982 6384 3.509442 AGGCATCCAACCATCTTTTTCA 58.491 40.909 0.00 0.00 0.00 2.69
3983 6385 3.766051 AGAGGCATCCAACCATCTTTTTC 59.234 43.478 0.00 0.00 0.00 2.29
3989 6391 2.425143 TCAAGAGGCATCCAACCATC 57.575 50.000 0.00 0.00 0.00 3.51
4099 6665 9.661563 ACAACTTGAGACGGATATAATAACAAA 57.338 29.630 0.00 0.00 0.00 2.83
4114 6680 1.597663 CGACCCACAACAACTTGAGAC 59.402 52.381 0.00 0.00 0.00 3.36
4129 6695 1.102978 CCAATGAAACCCATCGACCC 58.897 55.000 0.00 0.00 33.53 4.46
4165 6732 1.531423 CAACAGACTCAATGCAGCCT 58.469 50.000 0.00 0.00 0.00 4.58
4253 6822 7.940178 ATTGACGAAAAACCAGGTTAAAATC 57.060 32.000 4.87 1.18 0.00 2.17
4256 6825 7.431668 CGTTAATTGACGAAAAACCAGGTTAAA 59.568 33.333 17.02 0.00 45.47 1.52
4266 6835 3.984508 TGCCCGTTAATTGACGAAAAA 57.015 38.095 22.77 4.18 45.47 1.94
4271 6840 2.981400 AAGTTGCCCGTTAATTGACG 57.019 45.000 15.24 15.24 42.43 4.35
4282 6851 4.856509 AGTTAGGAAGGATAAAGTTGCCC 58.143 43.478 0.00 0.00 0.00 5.36
4283 6852 7.013369 CCATTAGTTAGGAAGGATAAAGTTGCC 59.987 40.741 0.00 0.00 0.00 4.52
4381 6950 1.123077 TTGGAGATATGAGGCGCTGT 58.877 50.000 7.64 0.00 0.00 4.40


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.