Multiple sequence alignment - TraesCS6A01G375800

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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 TraesCS6A01G375800 chr6A 100.000 3426 0 0 1 3426 597941035 597937610 0.000000e+00 6327.0
1 TraesCS6A01G375800 chr6A 84.048 1586 164 47 1050 2590 598024344 598025885 0.000000e+00 1445.0
2 TraesCS6A01G375800 chr6A 93.458 214 14 0 2936 3149 597932644 597932431 5.520000e-83 318.0
3 TraesCS6A01G375800 chr6A 93.578 109 7 0 3303 3411 597931854 597931746 2.740000e-36 163.0
4 TraesCS6A01G375800 chr6B 91.273 1925 100 34 772 2681 687017045 687015174 0.000000e+00 2562.0
5 TraesCS6A01G375800 chr6B 91.040 1038 75 7 1026 2057 687083364 687084389 0.000000e+00 1386.0
6 TraesCS6A01G375800 chr6B 81.361 676 76 36 2788 3426 687004905 687004243 3.950000e-139 505.0
7 TraesCS6A01G375800 chr6B 81.356 531 56 21 48 574 687017770 687017279 3.210000e-105 392.0
8 TraesCS6A01G375800 chr6B 89.130 276 13 9 3008 3281 687014867 687014607 9.170000e-86 327.0
9 TraesCS6A01G375800 chr6B 92.481 133 9 1 3295 3426 687009465 687009333 4.510000e-44 189.0
10 TraesCS6A01G375800 chr6B 89.333 75 7 1 214 288 687082404 687082477 3.640000e-15 93.5
11 TraesCS6A01G375800 chr6D 90.661 1799 96 38 951 2735 452406302 452404562 0.000000e+00 2326.0
12 TraesCS6A01G375800 chr6D 88.314 1489 108 35 1051 2502 452454903 452456362 0.000000e+00 1725.0
13 TraesCS6A01G375800 chr6D 89.744 468 33 9 2734 3191 452404403 452403941 4.930000e-163 584.0
14 TraesCS6A01G375800 chr6D 89.130 184 17 3 397 580 452407008 452406828 3.440000e-55 226.0
15 TraesCS6A01G375800 chr6D 90.533 169 9 3 772 940 452406836 452406675 2.070000e-52 217.0
16 TraesCS6A01G375800 chr6D 100.000 74 0 0 3215 3288 452403880 452403807 1.660000e-28 137.0
17 TraesCS6A01G375800 chr6D 92.754 69 5 0 214 282 452454350 452454418 2.180000e-17 100.0
18 TraesCS6A01G375800 chr6D 97.872 47 0 1 3295 3340 452397347 452397301 2.830000e-11 80.5
19 TraesCS6A01G375800 chrUn 92.118 406 26 4 1265 1669 306829854 306830254 4.960000e-158 568.0
20 TraesCS6A01G375800 chr3B 92.118 406 26 4 1265 1669 809102338 809102738 4.960000e-158 568.0
21 TraesCS6A01G375800 chr3B 92.079 404 23 7 1270 1669 783880986 783881384 8.300000e-156 560.0
22 TraesCS6A01G375800 chr3A 91.872 406 27 4 1265 1669 736251651 736252051 2.310000e-156 562.0
23 TraesCS6A01G375800 chr3A 85.759 323 24 10 2102 2419 92676792 92676487 4.270000e-84 322.0
24 TraesCS6A01G375800 chr1A 86.538 364 28 8 2102 2460 515828524 515828177 6.940000e-102 381.0
25 TraesCS6A01G375800 chr2D 87.629 291 26 6 2635 2923 305470168 305469886 2.550000e-86 329.0
26 TraesCS6A01G375800 chr2D 87.640 267 19 7 2102 2363 305470460 305470203 7.190000e-77 298.0
27 TraesCS6A01G375800 chr1D 87.285 291 27 6 2635 2923 155903661 155903943 1.190000e-84 324.0
28 TraesCS6A01G375800 chr1D 87.037 270 21 6 2099 2363 155903366 155903626 3.340000e-75 292.0
29 TraesCS6A01G375800 chr3D 86.897 290 28 7 2635 2923 544189417 544189697 1.980000e-82 316.0
30 TraesCS6A01G375800 chr3D 86.598 291 29 6 2635 2923 126256693 126256411 2.570000e-81 313.0
31 TraesCS6A01G375800 chr3D 87.407 270 20 6 2099 2363 544189122 544189382 7.190000e-77 298.0
32 TraesCS6A01G375800 chr3D 83.571 280 18 14 2102 2363 126256997 126256728 1.590000e-58 237.0
33 TraesCS6A01G375800 chr5A 88.439 173 9 4 2102 2268 691285526 691285359 7.500000e-47 198.0


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 TraesCS6A01G375800 chr6A 597937610 597941035 3425 True 6327.000000 6327 100.0000 1 3426 1 chr6A.!!$R1 3425
1 TraesCS6A01G375800 chr6A 598024344 598025885 1541 False 1445.000000 1445 84.0480 1050 2590 1 chr6A.!!$F1 1540
2 TraesCS6A01G375800 chr6A 597931746 597932644 898 True 240.500000 318 93.5180 2936 3411 2 chr6A.!!$R2 475
3 TraesCS6A01G375800 chr6B 687014607 687017770 3163 True 1093.666667 2562 87.2530 48 3281 3 chr6B.!!$R3 3233
4 TraesCS6A01G375800 chr6B 687082404 687084389 1985 False 739.750000 1386 90.1865 214 2057 2 chr6B.!!$F1 1843
5 TraesCS6A01G375800 chr6B 687004243 687004905 662 True 505.000000 505 81.3610 2788 3426 1 chr6B.!!$R1 638
6 TraesCS6A01G375800 chr6D 452454350 452456362 2012 False 912.500000 1725 90.5340 214 2502 2 chr6D.!!$F1 2288
7 TraesCS6A01G375800 chr6D 452403807 452407008 3201 True 698.000000 2326 92.0136 397 3288 5 chr6D.!!$R2 2891
8 TraesCS6A01G375800 chr2D 305469886 305470460 574 True 313.500000 329 87.6345 2102 2923 2 chr2D.!!$R1 821
9 TraesCS6A01G375800 chr1D 155903366 155903943 577 False 308.000000 324 87.1610 2099 2923 2 chr1D.!!$F1 824
10 TraesCS6A01G375800 chr3D 544189122 544189697 575 False 307.000000 316 87.1520 2099 2923 2 chr3D.!!$F1 824
11 TraesCS6A01G375800 chr3D 126256411 126256997 586 True 275.000000 313 85.0845 2102 2923 2 chr3D.!!$R1 821

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
87 88 0.035598 TCGCGGATCAAAGAAACCCA 59.964 50.0 6.13 0.0 0.00 4.51 F
776 1343 0.038892 GGCAAGTCTCGTCCGTAACA 60.039 55.0 0.00 0.0 0.00 2.41 F
1931 2894 0.784778 GAGTTCCTCGCTGACGTTTG 59.215 55.0 0.00 0.0 41.18 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2083 3054 0.514691 CACAGAAGAGCCGCAGAAAC 59.485 55.0 0.0 0.0 0.0 2.78 R
2207 3182 0.248843 CAGCTTCACCAGAGACCTCC 59.751 60.0 0.0 0.0 0.0 4.30 R
3337 5077 0.032017 AGGATGGCTCGGTTAGGTCT 60.032 55.0 0.0 0.0 0.0 3.85 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
24 25 7.946655 TTCGTAGCACATTCTATAGGAAATG 57.053 36.000 10.97 10.97 37.49 2.32
25 26 7.050970 TCGTAGCACATTCTATAGGAAATGT 57.949 36.000 11.99 11.99 37.49 2.71
26 27 8.173542 TCGTAGCACATTCTATAGGAAATGTA 57.826 34.615 15.68 3.14 37.49 2.29
27 28 8.297426 TCGTAGCACATTCTATAGGAAATGTAG 58.703 37.037 15.68 12.30 37.49 2.74
28 29 8.082852 CGTAGCACATTCTATAGGAAATGTAGT 58.917 37.037 15.68 10.47 37.49 2.73
29 30 9.765795 GTAGCACATTCTATAGGAAATGTAGTT 57.234 33.333 15.68 11.83 37.49 2.24
31 32 9.331282 AGCACATTCTATAGGAAATGTAGTTTC 57.669 33.333 15.68 6.87 44.43 2.78
32 33 9.109393 GCACATTCTATAGGAAATGTAGTTTCA 57.891 33.333 15.68 0.00 46.49 2.69
41 42 9.840427 ATAGGAAATGTAGTTTCAATTCAAACG 57.160 29.630 0.00 0.00 46.49 3.60
42 43 7.712797 AGGAAATGTAGTTTCAATTCAAACGT 58.287 30.769 0.00 0.00 46.49 3.99
43 44 8.194769 AGGAAATGTAGTTTCAATTCAAACGTT 58.805 29.630 0.00 0.00 46.49 3.99
44 45 8.813282 GGAAATGTAGTTTCAATTCAAACGTTT 58.187 29.630 7.96 7.96 46.49 3.60
45 46 9.618410 GAAATGTAGTTTCAATTCAAACGTTTG 57.382 29.630 30.63 30.63 44.53 2.93
46 47 8.696410 AATGTAGTTTCAATTCAAACGTTTGT 57.304 26.923 33.42 17.81 40.60 2.83
54 55 6.806751 TCAATTCAAACGTTTGTTATTCCCA 58.193 32.000 33.42 18.62 37.31 4.37
80 81 2.806288 AACGATTTCGCGGATCAAAG 57.194 45.000 18.73 8.75 44.43 2.77
82 83 2.343101 ACGATTTCGCGGATCAAAGAA 58.657 42.857 18.73 0.00 44.43 2.52
87 88 0.035598 TCGCGGATCAAAGAAACCCA 59.964 50.000 6.13 0.00 0.00 4.51
89 90 1.243902 GCGGATCAAAGAAACCCACA 58.756 50.000 0.00 0.00 0.00 4.17
101 103 7.947890 TCAAAGAAACCCACATAGTAGGATTTT 59.052 33.333 0.00 0.00 0.00 1.82
102 104 9.238368 CAAAGAAACCCACATAGTAGGATTTTA 57.762 33.333 0.00 0.00 0.00 1.52
103 105 8.803397 AAGAAACCCACATAGTAGGATTTTAC 57.197 34.615 0.00 0.00 0.00 2.01
110 112 9.601217 CCCACATAGTAGGATTTTACTATATGC 57.399 37.037 6.13 0.00 42.24 3.14
134 136 5.726980 TTAAGCATGCAAACAGAGGAAAT 57.273 34.783 21.98 0.00 0.00 2.17
139 141 4.802039 GCATGCAAACAGAGGAAATATGTG 59.198 41.667 14.21 0.00 32.45 3.21
140 142 5.622914 GCATGCAAACAGAGGAAATATGTGT 60.623 40.000 14.21 0.00 32.45 3.72
143 145 4.142381 GCAAACAGAGGAAATATGTGTCCC 60.142 45.833 0.00 0.00 32.45 4.46
145 147 2.213499 CAGAGGAAATATGTGTCCCGC 58.787 52.381 0.00 0.00 34.13 6.13
171 173 5.341872 TTCCAAATGGCCATAATGACTTG 57.658 39.130 25.57 20.78 34.44 3.16
173 175 3.133362 CCAAATGGCCATAATGACTTGCT 59.867 43.478 25.57 3.48 0.00 3.91
174 176 4.365723 CAAATGGCCATAATGACTTGCTC 58.634 43.478 21.15 0.00 0.00 4.26
177 179 2.953648 TGGCCATAATGACTTGCTCATG 59.046 45.455 0.00 0.00 38.82 3.07
181 183 4.261072 GCCATAATGACTTGCTCATGAGTG 60.261 45.833 23.38 15.69 38.82 3.51
182 184 4.880120 CCATAATGACTTGCTCATGAGTGT 59.120 41.667 23.38 18.47 38.82 3.55
183 185 6.051074 CCATAATGACTTGCTCATGAGTGTA 58.949 40.000 23.38 8.30 38.82 2.90
185 187 7.228108 CCATAATGACTTGCTCATGAGTGTATT 59.772 37.037 23.38 16.07 38.82 1.89
186 188 9.264719 CATAATGACTTGCTCATGAGTGTATTA 57.735 33.333 23.38 17.36 38.82 0.98
188 190 8.743085 AATGACTTGCTCATGAGTGTATTATT 57.257 30.769 23.38 14.26 38.82 1.40
189 191 9.836864 AATGACTTGCTCATGAGTGTATTATTA 57.163 29.630 23.38 3.79 38.82 0.98
190 192 8.648557 TGACTTGCTCATGAGTGTATTATTAC 57.351 34.615 23.38 3.85 0.00 1.89
191 193 8.478066 TGACTTGCTCATGAGTGTATTATTACT 58.522 33.333 23.38 0.00 0.00 2.24
192 194 9.967346 GACTTGCTCATGAGTGTATTATTACTA 57.033 33.333 23.38 0.00 0.00 1.82
193 195 9.973450 ACTTGCTCATGAGTGTATTATTACTAG 57.027 33.333 23.38 10.95 0.00 2.57
194 196 9.973450 CTTGCTCATGAGTGTATTATTACTAGT 57.027 33.333 23.38 0.00 0.00 2.57
196 198 9.750125 TGCTCATGAGTGTATTATTACTAGTTG 57.250 33.333 23.38 0.00 0.00 3.16
197 199 8.704234 GCTCATGAGTGTATTATTACTAGTTGC 58.296 37.037 23.38 0.00 0.00 4.17
198 200 9.750125 CTCATGAGTGTATTATTACTAGTTGCA 57.250 33.333 14.95 0.00 0.00 4.08
219 221 9.746711 GTTGCATTATCTTATCGTAAGCATTAG 57.253 33.333 0.00 0.00 37.18 1.73
220 222 9.489084 TTGCATTATCTTATCGTAAGCATTAGT 57.511 29.630 0.00 0.00 37.18 2.24
239 241 8.860088 GCATTAGTTTATCCTAAACCCATCAAT 58.140 33.333 6.23 0.00 31.09 2.57
285 287 4.256920 CAACTCATCCACTTCCCTTGTAG 58.743 47.826 0.00 0.00 0.00 2.74
286 288 3.521727 ACTCATCCACTTCCCTTGTAGT 58.478 45.455 0.00 0.00 0.00 2.73
289 291 6.441222 ACTCATCCACTTCCCTTGTAGTATA 58.559 40.000 0.00 0.00 0.00 1.47
291 293 7.569111 ACTCATCCACTTCCCTTGTAGTATAAT 59.431 37.037 0.00 0.00 0.00 1.28
292 294 9.090103 CTCATCCACTTCCCTTGTAGTATAATA 57.910 37.037 0.00 0.00 0.00 0.98
293 295 9.442062 TCATCCACTTCCCTTGTAGTATAATAA 57.558 33.333 0.00 0.00 0.00 1.40
295 297 8.849543 TCCACTTCCCTTGTAGTATAATAACT 57.150 34.615 0.00 0.00 0.00 2.24
344 346 2.754472 GACCCAAGCAAATGACAAACC 58.246 47.619 0.00 0.00 0.00 3.27
345 347 2.365293 GACCCAAGCAAATGACAAACCT 59.635 45.455 0.00 0.00 0.00 3.50
376 379 4.023963 GTCGGAGAGACCTTTTTCCTTTTG 60.024 45.833 0.00 0.00 43.95 2.44
395 821 2.302260 TGAAAAAGGTTGATCGGCACA 58.698 42.857 0.00 0.00 0.00 4.57
407 833 6.318628 GTTGATCGGCACAATTTTGTATGTA 58.681 36.000 0.00 0.00 39.91 2.29
460 897 5.277683 CGGTTAGAGAAGGCAATCATTCATG 60.278 44.000 0.00 0.00 0.00 3.07
464 901 3.544684 AGAAGGCAATCATTCATGCGTA 58.455 40.909 0.00 0.00 43.47 4.42
501 976 7.621832 TTGAAAAACAAGATGAAATGCGTAG 57.378 32.000 0.00 0.00 34.20 3.51
502 977 6.734137 TGAAAAACAAGATGAAATGCGTAGT 58.266 32.000 0.00 0.00 0.00 2.73
503 978 7.866729 TGAAAAACAAGATGAAATGCGTAGTA 58.133 30.769 0.00 0.00 0.00 1.82
504 979 7.801315 TGAAAAACAAGATGAAATGCGTAGTAC 59.199 33.333 0.00 0.00 0.00 2.73
510 985 2.980568 TGAAATGCGTAGTACCTTGGG 58.019 47.619 0.00 0.00 0.00 4.12
531 1031 2.933260 GTTTCTCTCTGCCTCGGATTTC 59.067 50.000 0.00 0.00 0.00 2.17
536 1036 3.944015 CTCTCTGCCTCGGATTTCATTTT 59.056 43.478 0.00 0.00 0.00 1.82
574 1074 9.461312 AACCAATTGATTGACTAATAGCAGTAA 57.539 29.630 7.12 0.00 40.14 2.24
575 1075 8.893727 ACCAATTGATTGACTAATAGCAGTAAC 58.106 33.333 7.12 0.00 40.14 2.50
581 1081 8.892723 TGATTGACTAATAGCAGTAACAAATGG 58.107 33.333 0.00 0.00 0.00 3.16
582 1082 9.109393 GATTGACTAATAGCAGTAACAAATGGA 57.891 33.333 0.00 0.00 0.00 3.41
586 1086 7.573710 ACTAATAGCAGTAACAAATGGATCCA 58.426 34.615 18.88 18.88 0.00 3.41
588 1088 3.019564 AGCAGTAACAAATGGATCCAGC 58.980 45.455 21.33 14.13 0.00 4.85
591 1091 4.676196 GCAGTAACAAATGGATCCAGCTTG 60.676 45.833 26.68 26.68 0.00 4.01
592 1092 3.445096 AGTAACAAATGGATCCAGCTTGC 59.555 43.478 27.61 17.25 0.00 4.01
593 1093 1.188863 ACAAATGGATCCAGCTTGCC 58.811 50.000 27.61 0.00 0.00 4.52
596 1096 1.041447 AATGGATCCAGCTTGCCTGC 61.041 55.000 21.33 0.00 40.36 4.85
598 1098 1.823041 GGATCCAGCTTGCCTGCTC 60.823 63.158 6.95 0.00 41.98 4.26
602 1102 1.605738 CCAGCTTGCCTGCTCCTTT 60.606 57.895 0.00 0.00 41.98 3.11
603 1103 1.593296 CCAGCTTGCCTGCTCCTTTC 61.593 60.000 0.00 0.00 41.98 2.62
605 1105 0.322366 AGCTTGCCTGCTCCTTTCTC 60.322 55.000 0.00 0.00 39.34 2.87
606 1106 0.607489 GCTTGCCTGCTCCTTTCTCA 60.607 55.000 0.00 0.00 0.00 3.27
607 1107 1.954258 GCTTGCCTGCTCCTTTCTCAT 60.954 52.381 0.00 0.00 0.00 2.90
608 1108 1.743958 CTTGCCTGCTCCTTTCTCATG 59.256 52.381 0.00 0.00 0.00 3.07
609 1109 0.679002 TGCCTGCTCCTTTCTCATGC 60.679 55.000 0.00 0.00 0.00 4.06
612 1112 2.444421 CCTGCTCCTTTCTCATGCTTT 58.556 47.619 0.00 0.00 0.00 3.51
613 1113 2.422832 CCTGCTCCTTTCTCATGCTTTC 59.577 50.000 0.00 0.00 0.00 2.62
614 1114 3.079578 CTGCTCCTTTCTCATGCTTTCA 58.920 45.455 0.00 0.00 0.00 2.69
615 1115 3.693807 TGCTCCTTTCTCATGCTTTCAT 58.306 40.909 0.00 0.00 0.00 2.57
616 1116 4.084287 TGCTCCTTTCTCATGCTTTCATT 58.916 39.130 0.00 0.00 0.00 2.57
617 1117 4.525487 TGCTCCTTTCTCATGCTTTCATTT 59.475 37.500 0.00 0.00 0.00 2.32
618 1118 4.863131 GCTCCTTTCTCATGCTTTCATTTG 59.137 41.667 0.00 0.00 0.00 2.32
619 1119 5.566230 GCTCCTTTCTCATGCTTTCATTTGT 60.566 40.000 0.00 0.00 0.00 2.83
620 1120 5.775686 TCCTTTCTCATGCTTTCATTTGTG 58.224 37.500 0.00 0.00 0.00 3.33
621 1121 4.387862 CCTTTCTCATGCTTTCATTTGTGC 59.612 41.667 0.00 0.00 0.00 4.57
623 1123 5.963176 TTCTCATGCTTTCATTTGTGCTA 57.037 34.783 0.00 0.00 0.00 3.49
624 1124 6.519679 TTCTCATGCTTTCATTTGTGCTAT 57.480 33.333 0.00 0.00 0.00 2.97
625 1125 6.127810 TCTCATGCTTTCATTTGTGCTATC 57.872 37.500 0.00 0.00 0.00 2.08
626 1126 5.648960 TCTCATGCTTTCATTTGTGCTATCA 59.351 36.000 0.00 0.00 0.00 2.15
628 1128 5.416639 TCATGCTTTCATTTGTGCTATCACT 59.583 36.000 0.00 0.00 43.49 3.41
630 1130 6.088016 TGCTTTCATTTGTGCTATCACTTT 57.912 33.333 0.00 0.00 43.49 2.66
631 1131 7.213216 TGCTTTCATTTGTGCTATCACTTTA 57.787 32.000 0.00 0.00 43.49 1.85
632 1132 7.829725 TGCTTTCATTTGTGCTATCACTTTAT 58.170 30.769 0.00 0.00 43.49 1.40
633 1133 7.970061 TGCTTTCATTTGTGCTATCACTTTATC 59.030 33.333 0.00 0.00 43.49 1.75
634 1134 7.433425 GCTTTCATTTGTGCTATCACTTTATCC 59.567 37.037 0.00 0.00 43.49 2.59
635 1135 8.579850 TTTCATTTGTGCTATCACTTTATCCT 57.420 30.769 0.00 0.00 43.49 3.24
637 1137 8.662781 TCATTTGTGCTATCACTTTATCCTAC 57.337 34.615 0.00 0.00 43.49 3.18
638 1138 7.438160 TCATTTGTGCTATCACTTTATCCTACG 59.562 37.037 0.00 0.00 43.49 3.51
639 1139 5.196341 TGTGCTATCACTTTATCCTACGG 57.804 43.478 0.00 0.00 43.49 4.02
640 1140 3.988517 GTGCTATCACTTTATCCTACGGC 59.011 47.826 0.00 0.00 40.03 5.68
641 1141 3.895656 TGCTATCACTTTATCCTACGGCT 59.104 43.478 0.00 0.00 0.00 5.52
642 1142 4.238514 GCTATCACTTTATCCTACGGCTG 58.761 47.826 0.00 0.00 0.00 4.85
643 1143 4.262079 GCTATCACTTTATCCTACGGCTGT 60.262 45.833 2.42 2.42 0.00 4.40
644 1144 4.755266 ATCACTTTATCCTACGGCTGTT 57.245 40.909 1.99 0.00 0.00 3.16
645 1145 4.546829 TCACTTTATCCTACGGCTGTTT 57.453 40.909 1.99 0.00 0.00 2.83
646 1146 4.901868 TCACTTTATCCTACGGCTGTTTT 58.098 39.130 1.99 0.00 0.00 2.43
680 1180 6.578163 TTTCCTTTGATTTTAACGGGGTAG 57.422 37.500 0.00 0.00 0.00 3.18
682 1182 5.247862 TCCTTTGATTTTAACGGGGTAGAC 58.752 41.667 0.00 0.00 0.00 2.59
683 1183 4.397103 CCTTTGATTTTAACGGGGTAGACC 59.603 45.833 0.00 0.00 39.11 3.85
684 1184 4.637387 TTGATTTTAACGGGGTAGACCA 57.363 40.909 0.21 0.00 42.91 4.02
685 1185 3.941573 TGATTTTAACGGGGTAGACCAC 58.058 45.455 0.21 0.00 42.91 4.16
692 1192 3.007323 GGGTAGACCACGGGCCTT 61.007 66.667 0.84 0.00 39.85 4.35
694 1194 1.052694 GGGTAGACCACGGGCCTTAT 61.053 60.000 0.84 0.00 39.85 1.73
696 1196 1.211212 GGTAGACCACGGGCCTTATTT 59.789 52.381 0.84 0.00 35.64 1.40
697 1197 2.356432 GGTAGACCACGGGCCTTATTTT 60.356 50.000 0.84 0.00 35.64 1.82
699 1199 0.172578 GACCACGGGCCTTATTTTGC 59.827 55.000 0.84 0.00 0.00 3.68
700 1200 0.251608 ACCACGGGCCTTATTTTGCT 60.252 50.000 0.84 0.00 0.00 3.91
701 1201 0.455815 CCACGGGCCTTATTTTGCTC 59.544 55.000 0.84 0.00 0.00 4.26
702 1202 0.455815 CACGGGCCTTATTTTGCTCC 59.544 55.000 0.84 0.00 0.00 4.70
703 1203 0.039035 ACGGGCCTTATTTTGCTCCA 59.961 50.000 0.84 0.00 0.00 3.86
705 1205 1.756538 CGGGCCTTATTTTGCTCCAAT 59.243 47.619 0.84 0.00 0.00 3.16
706 1206 2.223805 CGGGCCTTATTTTGCTCCAATC 60.224 50.000 0.84 0.00 0.00 2.67
707 1207 2.765699 GGGCCTTATTTTGCTCCAATCA 59.234 45.455 0.84 0.00 0.00 2.57
711 1278 5.882000 GGCCTTATTTTGCTCCAATCAAATT 59.118 36.000 0.00 0.00 33.94 1.82
715 1282 9.657419 CCTTATTTTGCTCCAATCAAATTAAGT 57.343 29.630 18.44 0.00 40.81 2.24
719 1286 5.295431 TGCTCCAATCAAATTAAGTCACG 57.705 39.130 0.00 0.00 0.00 4.35
722 1289 6.128391 TGCTCCAATCAAATTAAGTCACGTAC 60.128 38.462 0.00 0.00 0.00 3.67
723 1290 6.397831 TCCAATCAAATTAAGTCACGTACG 57.602 37.500 15.01 15.01 0.00 3.67
724 1291 5.019498 CCAATCAAATTAAGTCACGTACGC 58.981 41.667 16.72 0.00 0.00 4.42
736 1303 2.202570 GTACGCACGAGCACGGAT 60.203 61.111 8.74 0.00 44.46 4.18
738 1305 3.693382 TACGCACGAGCACGGATGG 62.693 63.158 8.74 0.00 44.46 3.51
763 1330 4.335647 CGAGGGGCACAGGCAAGT 62.336 66.667 0.00 0.00 43.71 3.16
764 1331 2.360475 GAGGGGCACAGGCAAGTC 60.360 66.667 0.00 0.00 43.71 3.01
765 1332 2.856000 AGGGGCACAGGCAAGTCT 60.856 61.111 0.00 0.00 43.71 3.24
766 1333 2.360475 GGGGCACAGGCAAGTCTC 60.360 66.667 0.00 0.00 43.71 3.36
767 1334 2.743928 GGGCACAGGCAAGTCTCG 60.744 66.667 0.00 0.00 43.71 4.04
768 1335 2.031163 GGCACAGGCAAGTCTCGT 59.969 61.111 0.00 0.00 43.71 4.18
769 1336 2.029844 GGCACAGGCAAGTCTCGTC 61.030 63.158 0.00 0.00 43.71 4.20
770 1337 2.029844 GCACAGGCAAGTCTCGTCC 61.030 63.158 0.00 0.00 40.72 4.79
776 1343 0.038892 GGCAAGTCTCGTCCGTAACA 60.039 55.000 0.00 0.00 0.00 2.41
844 1418 4.687901 ATTTAAGTATGCAAATGGGGGC 57.312 40.909 0.00 0.00 0.00 5.80
879 1453 1.402968 CCAGCGGATTCCAAATGACTG 59.597 52.381 3.09 0.57 0.00 3.51
1017 1953 3.582120 CCACACCGCACACCACAC 61.582 66.667 0.00 0.00 0.00 3.82
1048 1989 2.095978 AACAACAGAGACGGACCCGG 62.096 60.000 13.43 0.00 44.69 5.73
1876 2837 4.832608 GTAAGCAGCGACCCCCGG 62.833 72.222 0.00 0.00 39.04 5.73
1931 2894 0.784778 GAGTTCCTCGCTGACGTTTG 59.215 55.000 0.00 0.00 41.18 2.93
1950 2913 1.074727 TGTGGATCGGGTGGTGATTTT 59.925 47.619 0.00 0.00 0.00 1.82
2028 2997 2.044053 ATGGACCAACATGCGGGG 60.044 61.111 0.00 2.61 0.00 5.73
2057 3026 6.350110 GCTCCATCCATCTGTAGATAGAAGAC 60.350 46.154 0.00 0.00 32.63 3.01
2070 3039 1.551452 AGAAGACCTTCTCCACGGAG 58.449 55.000 6.77 6.77 46.13 4.63
2097 3068 1.374758 CTCGGTTTCTGCGGCTCTT 60.375 57.895 0.00 0.00 0.00 2.85
2100 3071 1.630244 CGGTTTCTGCGGCTCTTCTG 61.630 60.000 0.00 0.00 0.00 3.02
2162 3135 1.149148 GCCGGAGTTGAGTTGAGTTC 58.851 55.000 5.05 0.00 0.00 3.01
2163 3136 1.540363 GCCGGAGTTGAGTTGAGTTCA 60.540 52.381 5.05 0.00 0.00 3.18
2164 3137 2.408050 CCGGAGTTGAGTTGAGTTCAG 58.592 52.381 0.00 0.00 0.00 3.02
2165 3138 2.224066 CCGGAGTTGAGTTGAGTTCAGT 60.224 50.000 0.00 0.00 0.00 3.41
2166 3139 3.005472 CCGGAGTTGAGTTGAGTTCAGTA 59.995 47.826 0.00 0.00 0.00 2.74
2197 3171 2.826128 AGTGCTAGTTCCTTCGTGATCA 59.174 45.455 0.00 0.00 0.00 2.92
2207 3182 2.874701 CCTTCGTGATCATTTAGGCCTG 59.125 50.000 17.99 0.00 0.00 4.85
2297 3289 3.981416 TCGTGTTTGTTCTCTGAATCTCG 59.019 43.478 0.00 0.00 0.00 4.04
2299 3291 3.067106 TGTTTGTTCTCTGAATCTCGGC 58.933 45.455 0.00 0.00 0.00 5.54
2325 3317 5.566826 GCAGTCCTTGTACATACAGTCTTGA 60.567 44.000 0.00 0.00 37.52 3.02
2365 3357 6.218107 AGAGGAAGAGAGGGTTTAGTAGTACT 59.782 42.308 8.14 8.14 0.00 2.73
2372 3364 7.037008 AGAGAGGGTTTAGTAGTACTTAGTGGA 60.037 40.741 8.40 0.00 0.00 4.02
2410 3413 6.925165 GGCTTTGTTCAGAAGAATGAAAATGA 59.075 34.615 9.44 0.00 40.72 2.57
2467 3476 2.913975 GCGTGCTGCTTCAGTTTAACTG 60.914 50.000 18.12 18.12 43.45 3.16
2487 3497 1.404391 GGCCATCATCTTCTGTGCTTG 59.596 52.381 0.00 0.00 0.00 4.01
2569 3591 1.005662 GTGCGATGTCATGTGTGATCG 60.006 52.381 11.45 11.45 38.97 3.69
2627 3652 3.950087 TGATGCGTGCTGATAATGAAC 57.050 42.857 0.00 0.00 0.00 3.18
2633 3658 4.749598 TGCGTGCTGATAATGAACGAATAT 59.250 37.500 0.00 0.00 38.65 1.28
2671 3726 3.030291 AGATACTAGCAGCAGAGCAGTT 58.970 45.455 0.00 0.00 36.85 3.16
2675 3730 0.672711 TAGCAGCAGAGCAGTTGCAG 60.673 55.000 13.28 5.55 46.51 4.41
2676 3731 2.259439 GCAGCAGAGCAGTTGCAGT 61.259 57.895 6.90 0.00 43.99 4.40
2677 3732 1.793134 GCAGCAGAGCAGTTGCAGTT 61.793 55.000 6.90 0.00 43.99 3.16
2678 3733 0.040336 CAGCAGAGCAGTTGCAGTTG 60.040 55.000 6.90 2.98 43.92 3.16
2679 3734 1.371389 GCAGAGCAGTTGCAGTTGC 60.371 57.895 14.58 14.58 45.16 4.17
2715 3770 2.929531 TTCAGTCGCAACTTGCAAAA 57.070 40.000 14.10 0.00 45.36 2.44
2718 3773 2.618241 TCAGTCGCAACTTGCAAAATCT 59.382 40.909 14.10 1.88 45.36 2.40
2719 3774 3.066621 TCAGTCGCAACTTGCAAAATCTT 59.933 39.130 14.10 0.00 45.36 2.40
2720 3775 3.180980 CAGTCGCAACTTGCAAAATCTTG 59.819 43.478 14.10 1.29 45.36 3.02
2721 3776 3.115554 GTCGCAACTTGCAAAATCTTGT 58.884 40.909 14.10 0.00 45.36 3.16
2722 3777 4.036262 AGTCGCAACTTGCAAAATCTTGTA 59.964 37.500 14.10 0.00 45.36 2.41
2756 3972 3.452990 TGTATGTATCCCGTGGATGTTGT 59.547 43.478 13.77 2.92 43.06 3.32
2757 3973 2.684001 TGTATCCCGTGGATGTTGTC 57.316 50.000 13.77 3.00 43.06 3.18
2771 3989 5.885352 TGGATGTTGTCTCTGAACTTTTTCA 59.115 36.000 0.00 0.00 39.55 2.69
2786 4004 2.957491 TTTCAGCAACTTGTGGGTTG 57.043 45.000 3.36 3.36 46.41 3.77
2813 4031 5.493133 TCACCATTAACCAATCGCATTAC 57.507 39.130 0.00 0.00 0.00 1.89
2841 4059 2.240414 AGTCACATGATGGATGGCTCAA 59.760 45.455 0.00 0.00 36.23 3.02
2844 4062 1.325355 CATGATGGATGGCTCAACCC 58.675 55.000 0.00 0.00 37.83 4.11
2846 4064 0.703488 TGATGGATGGCTCAACCCAA 59.297 50.000 0.00 0.00 38.61 4.12
2905 4123 0.603975 AGAGCCGAAAACACTCTGCC 60.604 55.000 0.00 0.00 39.29 4.85
2929 4147 7.012610 GCCACCTAACTGAAAACACTTTTACTA 59.987 37.037 0.00 0.00 31.94 1.82
2931 4149 9.106070 CACCTAACTGAAAACACTTTTACTACT 57.894 33.333 0.00 0.00 31.94 2.57
2932 4150 9.676861 ACCTAACTGAAAACACTTTTACTACTT 57.323 29.630 0.00 0.00 31.94 2.24
2958 4188 6.581166 CCGTTGCTTTAATAACTTCTGAAACC 59.419 38.462 0.00 0.00 0.00 3.27
2964 4194 7.060748 GCTTTAATAACTTCTGAAACCGAAAGC 59.939 37.037 13.48 13.48 37.71 3.51
3153 4458 4.135153 CCTCCTCCGTCCTGTGCG 62.135 72.222 0.00 0.00 0.00 5.34
3289 4631 5.128205 TGAAACCATGCAGATAATGAGGAG 58.872 41.667 0.00 0.00 0.00 3.69
3292 4634 3.072184 ACCATGCAGATAATGAGGAGGAC 59.928 47.826 0.00 0.00 0.00 3.85
3293 4635 3.327172 CCATGCAGATAATGAGGAGGACT 59.673 47.826 0.00 0.00 0.00 3.85
3298 4640 4.125703 CAGATAATGAGGAGGACTGTTGC 58.874 47.826 0.00 0.00 0.00 4.17
3305 5045 1.671379 GAGGACTGTTGCCGGGAAC 60.671 63.158 29.91 29.91 0.00 3.62
3337 5077 4.284178 CTGTAGCCACCTTACCTACCTAA 58.716 47.826 0.00 0.00 32.47 2.69
3408 5153 1.981256 TCTGTTGCTCCTTTGGGTTC 58.019 50.000 0.00 0.00 0.00 3.62
3417 5163 1.149627 CTTTGGGTTCGGGTGGTGA 59.850 57.895 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.497595 ACATTTCCTATAGAATGTGCTACGAA 58.502 34.615 15.46 0.00 33.44 3.85
1 2 7.050970 ACATTTCCTATAGAATGTGCTACGA 57.949 36.000 15.46 0.00 33.44 3.43
2 3 8.082852 ACTACATTTCCTATAGAATGTGCTACG 58.917 37.037 21.55 11.69 33.44 3.51
3 4 9.765795 AACTACATTTCCTATAGAATGTGCTAC 57.234 33.333 21.55 0.00 33.44 3.58
5 6 9.331282 GAAACTACATTTCCTATAGAATGTGCT 57.669 33.333 21.55 9.66 40.88 4.40
6 7 9.109393 TGAAACTACATTTCCTATAGAATGTGC 57.891 33.333 21.55 11.19 45.40 4.57
15 16 9.840427 CGTTTGAATTGAAACTACATTTCCTAT 57.160 29.630 16.76 0.00 45.40 2.57
16 17 8.842280 ACGTTTGAATTGAAACTACATTTCCTA 58.158 29.630 16.76 0.00 45.40 2.94
17 18 7.712797 ACGTTTGAATTGAAACTACATTTCCT 58.287 30.769 16.76 0.00 45.40 3.36
18 19 7.924103 ACGTTTGAATTGAAACTACATTTCC 57.076 32.000 16.76 0.00 45.40 3.13
19 20 9.618410 CAAACGTTTGAATTGAAACTACATTTC 57.382 29.630 32.36 0.00 42.43 2.17
20 21 9.145865 ACAAACGTTTGAATTGAAACTACATTT 57.854 25.926 39.63 14.18 40.55 2.32
21 22 8.696410 ACAAACGTTTGAATTGAAACTACATT 57.304 26.923 39.63 14.53 40.55 2.71
22 23 8.696410 AACAAACGTTTGAATTGAAACTACAT 57.304 26.923 39.63 15.14 40.55 2.29
23 24 9.790389 ATAACAAACGTTTGAATTGAAACTACA 57.210 25.926 39.63 13.07 40.55 2.74
26 27 8.813282 GGAATAACAAACGTTTGAATTGAAACT 58.187 29.630 39.63 19.23 40.55 2.66
27 28 8.059502 GGGAATAACAAACGTTTGAATTGAAAC 58.940 33.333 39.63 24.42 40.55 2.78
28 29 7.764443 TGGGAATAACAAACGTTTGAATTGAAA 59.236 29.630 39.63 22.19 40.55 2.69
29 30 7.222999 GTGGGAATAACAAACGTTTGAATTGAA 59.777 33.333 39.63 22.45 40.55 2.69
30 31 6.697892 GTGGGAATAACAAACGTTTGAATTGA 59.302 34.615 39.63 22.17 40.55 2.57
31 32 6.345408 CGTGGGAATAACAAACGTTTGAATTG 60.345 38.462 39.63 22.35 40.55 2.32
32 33 5.688176 CGTGGGAATAACAAACGTTTGAATT 59.312 36.000 39.63 33.54 40.55 2.17
33 34 5.216648 CGTGGGAATAACAAACGTTTGAAT 58.783 37.500 39.63 29.01 40.55 2.57
34 35 4.096081 ACGTGGGAATAACAAACGTTTGAA 59.904 37.500 39.63 28.28 44.38 2.69
35 36 3.626670 ACGTGGGAATAACAAACGTTTGA 59.373 39.130 39.63 23.41 44.38 2.69
36 37 3.954999 ACGTGGGAATAACAAACGTTTG 58.045 40.909 33.52 33.52 44.38 2.93
40 41 5.113826 CGTTAAAACGTGGGAATAACAAACG 59.886 40.000 7.07 0.00 46.63 3.60
41 42 6.423188 CGTTAAAACGTGGGAATAACAAAC 57.577 37.500 7.07 0.00 46.63 2.93
64 65 3.426323 GGTTTCTTTGATCCGCGAAATC 58.574 45.455 8.23 11.22 0.00 2.17
68 69 0.035598 TGGGTTTCTTTGATCCGCGA 59.964 50.000 8.23 0.00 0.00 5.87
71 72 4.261801 ACTATGTGGGTTTCTTTGATCCG 58.738 43.478 0.00 0.00 0.00 4.18
72 73 5.823045 CCTACTATGTGGGTTTCTTTGATCC 59.177 44.000 0.00 0.00 29.23 3.36
110 112 4.771590 TCCTCTGTTTGCATGCTTAAAG 57.228 40.909 20.33 11.01 0.00 1.85
134 136 1.199615 TGGAATCTGCGGGACACATA 58.800 50.000 0.00 0.00 0.00 2.29
139 141 0.740737 CCATTTGGAATCTGCGGGAC 59.259 55.000 0.00 0.00 37.39 4.46
140 142 1.037030 GCCATTTGGAATCTGCGGGA 61.037 55.000 0.00 0.00 37.39 5.14
143 145 0.748450 ATGGCCATTTGGAATCTGCG 59.252 50.000 14.09 0.00 37.39 5.18
145 147 5.303589 AGTCATTATGGCCATTTGGAATCTG 59.696 40.000 26.37 8.29 37.39 2.90
171 173 8.704234 GCAACTAGTAATAATACACTCATGAGC 58.296 37.037 22.83 2.17 34.29 4.26
188 190 9.622004 GCTTACGATAAGATAATGCAACTAGTA 57.378 33.333 0.00 0.00 0.00 1.82
189 191 8.141909 TGCTTACGATAAGATAATGCAACTAGT 58.858 33.333 0.00 0.00 0.00 2.57
190 192 8.520835 TGCTTACGATAAGATAATGCAACTAG 57.479 34.615 0.00 0.00 0.00 2.57
191 193 9.489084 AATGCTTACGATAAGATAATGCAACTA 57.511 29.630 0.00 0.00 0.00 2.24
192 194 7.969536 ATGCTTACGATAAGATAATGCAACT 57.030 32.000 0.00 0.00 0.00 3.16
193 195 9.746711 CTAATGCTTACGATAAGATAATGCAAC 57.253 33.333 0.00 0.00 0.00 4.17
194 196 9.489084 ACTAATGCTTACGATAAGATAATGCAA 57.511 29.630 0.00 0.00 0.00 4.08
195 197 9.489084 AACTAATGCTTACGATAAGATAATGCA 57.511 29.630 8.39 0.00 0.00 3.96
206 208 9.269453 GGTTTAGGATAAACTAATGCTTACGAT 57.731 33.333 11.11 0.00 33.31 3.73
207 209 7.712205 GGGTTTAGGATAAACTAATGCTTACGA 59.288 37.037 11.11 0.00 33.31 3.43
208 210 7.496591 TGGGTTTAGGATAAACTAATGCTTACG 59.503 37.037 11.11 0.00 33.31 3.18
209 211 8.741603 TGGGTTTAGGATAAACTAATGCTTAC 57.258 34.615 11.11 0.00 33.31 2.34
210 212 9.569122 GATGGGTTTAGGATAAACTAATGCTTA 57.431 33.333 11.11 0.00 33.31 3.09
211 213 8.058847 TGATGGGTTTAGGATAAACTAATGCTT 58.941 33.333 11.11 0.00 33.31 3.91
212 214 7.582719 TGATGGGTTTAGGATAAACTAATGCT 58.417 34.615 11.11 0.00 33.31 3.79
239 241 6.441924 TGGTTTTGGCCCATCTTAATTGATAA 59.558 34.615 0.00 0.00 0.00 1.75
250 252 1.337118 TGAGTTGGTTTTGGCCCATC 58.663 50.000 0.00 0.00 0.00 3.51
289 291 7.643569 TGCATACAACATGGATGAAGTTATT 57.356 32.000 6.74 0.00 41.23 1.40
291 293 6.262944 GGATGCATACAACATGGATGAAGTTA 59.737 38.462 3.28 0.00 41.23 2.24
292 294 5.068198 GGATGCATACAACATGGATGAAGTT 59.932 40.000 3.28 0.00 41.23 2.66
293 295 4.581824 GGATGCATACAACATGGATGAAGT 59.418 41.667 3.28 0.00 41.23 3.01
295 297 4.581409 CAGGATGCATACAACATGGATGAA 59.419 41.667 12.53 0.00 41.23 2.57
324 326 2.365293 AGGTTTGTCATTTGCTTGGGTC 59.635 45.455 0.00 0.00 0.00 4.46
344 346 0.528470 GTCTCTCCGACCAGACCAAG 59.472 60.000 0.00 0.00 36.62 3.61
345 347 2.654802 GTCTCTCCGACCAGACCAA 58.345 57.895 0.00 0.00 36.62 3.67
376 379 3.363341 TTGTGCCGATCAACCTTTTTC 57.637 42.857 0.00 0.00 0.00 2.29
390 816 8.082334 ACAAATTGTACATACAAAATTGTGCC 57.918 30.769 24.07 0.00 46.52 5.01
464 901 5.276963 CTTGTTTTTCAATGCATTTCGTGCT 60.277 36.000 9.83 0.00 41.81 4.40
467 904 6.700960 TCATCTTGTTTTTCAATGCATTTCGT 59.299 30.769 9.83 0.00 35.35 3.85
501 976 2.615747 GGCAGAGAGAAACCCAAGGTAC 60.616 54.545 0.00 0.00 33.12 3.34
502 977 1.628846 GGCAGAGAGAAACCCAAGGTA 59.371 52.381 0.00 0.00 33.12 3.08
503 978 0.402121 GGCAGAGAGAAACCCAAGGT 59.598 55.000 0.00 0.00 37.65 3.50
504 979 0.695347 AGGCAGAGAGAAACCCAAGG 59.305 55.000 0.00 0.00 0.00 3.61
510 985 2.682155 AATCCGAGGCAGAGAGAAAC 57.318 50.000 0.00 0.00 0.00 2.78
536 1036 8.141268 GTCAATCAATTGGTTGACTTAGGAAAA 58.859 33.333 39.24 15.13 46.43 2.29
565 1065 4.823989 GCTGGATCCATTTGTTACTGCTAT 59.176 41.667 16.63 0.00 0.00 2.97
574 1074 1.188863 GGCAAGCTGGATCCATTTGT 58.811 50.000 27.05 10.08 0.00 2.83
575 1075 1.136305 CAGGCAAGCTGGATCCATTTG 59.864 52.381 24.53 24.53 0.00 2.32
577 1077 1.041447 GCAGGCAAGCTGGATCCATT 61.041 55.000 16.63 4.60 0.00 3.16
578 1078 1.455217 GCAGGCAAGCTGGATCCAT 60.455 57.895 16.63 0.00 0.00 3.41
580 1080 1.823041 GAGCAGGCAAGCTGGATCC 60.823 63.158 4.20 4.20 46.75 3.36
581 1081 1.823041 GGAGCAGGCAAGCTGGATC 60.823 63.158 9.25 0.00 46.75 3.36
582 1082 1.860944 AAGGAGCAGGCAAGCTGGAT 61.861 55.000 9.25 0.00 46.75 3.41
588 1088 1.743958 CATGAGAAAGGAGCAGGCAAG 59.256 52.381 0.00 0.00 0.00 4.01
591 1091 0.394080 AGCATGAGAAAGGAGCAGGC 60.394 55.000 0.00 0.00 39.38 4.85
592 1092 2.125773 AAGCATGAGAAAGGAGCAGG 57.874 50.000 0.00 0.00 0.00 4.85
593 1093 3.079578 TGAAAGCATGAGAAAGGAGCAG 58.920 45.455 0.00 0.00 0.00 4.24
596 1096 5.862323 CACAAATGAAAGCATGAGAAAGGAG 59.138 40.000 0.00 0.00 34.26 3.69
598 1098 4.387862 GCACAAATGAAAGCATGAGAAAGG 59.612 41.667 0.00 0.00 34.26 3.11
602 1102 5.648960 TGATAGCACAAATGAAAGCATGAGA 59.351 36.000 0.00 0.00 34.26 3.27
603 1103 5.742453 GTGATAGCACAAATGAAAGCATGAG 59.258 40.000 6.17 0.00 44.51 2.90
605 1105 5.944049 GTGATAGCACAAATGAAAGCATG 57.056 39.130 6.17 0.00 44.51 4.06
655 1155 6.236558 ACCCCGTTAAAATCAAAGGAAAAA 57.763 33.333 0.00 0.00 0.00 1.94
656 1156 5.873146 ACCCCGTTAAAATCAAAGGAAAA 57.127 34.783 0.00 0.00 0.00 2.29
658 1158 5.706833 GTCTACCCCGTTAAAATCAAAGGAA 59.293 40.000 0.00 0.00 0.00 3.36
661 1161 5.005094 TGGTCTACCCCGTTAAAATCAAAG 58.995 41.667 0.00 0.00 34.29 2.77
662 1162 4.761227 GTGGTCTACCCCGTTAAAATCAAA 59.239 41.667 0.00 0.00 34.29 2.69
663 1163 4.325972 GTGGTCTACCCCGTTAAAATCAA 58.674 43.478 0.00 0.00 34.29 2.57
664 1164 3.617045 CGTGGTCTACCCCGTTAAAATCA 60.617 47.826 0.00 0.00 34.29 2.57
665 1165 2.931969 CGTGGTCTACCCCGTTAAAATC 59.068 50.000 0.00 0.00 34.29 2.17
667 1167 1.001860 CCGTGGTCTACCCCGTTAAAA 59.998 52.381 3.39 0.00 34.29 1.52
668 1168 0.607620 CCGTGGTCTACCCCGTTAAA 59.392 55.000 3.39 0.00 34.29 1.52
675 1175 1.052694 ATAAGGCCCGTGGTCTACCC 61.053 60.000 0.00 0.00 36.17 3.69
676 1176 0.835276 AATAAGGCCCGTGGTCTACC 59.165 55.000 0.00 0.00 36.17 3.18
677 1177 2.681344 CAAAATAAGGCCCGTGGTCTAC 59.319 50.000 0.00 0.00 36.17 2.59
680 1180 0.172578 GCAAAATAAGGCCCGTGGTC 59.827 55.000 0.00 0.00 0.00 4.02
682 1182 0.455815 GAGCAAAATAAGGCCCGTGG 59.544 55.000 0.00 0.00 0.00 4.94
683 1183 0.455815 GGAGCAAAATAAGGCCCGTG 59.544 55.000 0.00 0.00 0.00 4.94
684 1184 0.039035 TGGAGCAAAATAAGGCCCGT 59.961 50.000 0.00 0.00 0.00 5.28
685 1185 1.181786 TTGGAGCAAAATAAGGCCCG 58.818 50.000 0.00 0.00 0.00 6.13
686 1186 2.765699 TGATTGGAGCAAAATAAGGCCC 59.234 45.455 0.00 0.00 0.00 5.80
687 1187 4.470334 TTGATTGGAGCAAAATAAGGCC 57.530 40.909 0.00 0.00 0.00 5.19
689 1189 9.657419 ACTTAATTTGATTGGAGCAAAATAAGG 57.343 29.630 21.03 10.26 44.79 2.69
692 1192 9.638239 GTGACTTAATTTGATTGGAGCAAAATA 57.362 29.630 0.00 0.00 38.57 1.40
694 1194 6.640499 CGTGACTTAATTTGATTGGAGCAAAA 59.360 34.615 0.00 0.00 38.57 2.44
696 1196 5.240623 ACGTGACTTAATTTGATTGGAGCAA 59.759 36.000 0.00 0.00 0.00 3.91
697 1197 4.759693 ACGTGACTTAATTTGATTGGAGCA 59.240 37.500 0.00 0.00 0.00 4.26
699 1199 6.466812 CGTACGTGACTTAATTTGATTGGAG 58.533 40.000 7.22 0.00 0.00 3.86
700 1200 5.163933 GCGTACGTGACTTAATTTGATTGGA 60.164 40.000 17.90 0.00 0.00 3.53
701 1201 5.019498 GCGTACGTGACTTAATTTGATTGG 58.981 41.667 17.90 0.00 0.00 3.16
702 1202 5.503376 GTGCGTACGTGACTTAATTTGATTG 59.497 40.000 17.90 0.00 0.00 2.67
703 1203 5.614760 GTGCGTACGTGACTTAATTTGATT 58.385 37.500 17.90 0.00 0.00 2.57
705 1205 3.119956 CGTGCGTACGTGACTTAATTTGA 59.880 43.478 18.32 0.00 44.99 2.69
706 1206 3.392141 CGTGCGTACGTGACTTAATTTG 58.608 45.455 18.32 0.00 44.99 2.32
707 1207 3.693300 CGTGCGTACGTGACTTAATTT 57.307 42.857 18.32 0.00 44.99 1.82
719 1286 2.202570 ATCCGTGCTCGTGCGTAC 60.203 61.111 7.47 0.00 43.34 3.67
746 1313 4.335647 ACTTGCCTGTGCCCCTCG 62.336 66.667 0.00 0.00 36.33 4.63
747 1314 2.360475 GACTTGCCTGTGCCCCTC 60.360 66.667 0.00 0.00 36.33 4.30
748 1315 2.856000 AGACTTGCCTGTGCCCCT 60.856 61.111 0.00 0.00 36.33 4.79
749 1316 2.360475 GAGACTTGCCTGTGCCCC 60.360 66.667 0.00 0.00 36.33 5.80
750 1317 2.743928 CGAGACTTGCCTGTGCCC 60.744 66.667 0.00 0.00 36.33 5.36
751 1318 2.029844 GACGAGACTTGCCTGTGCC 61.030 63.158 0.00 0.00 36.33 5.01
752 1319 2.029844 GGACGAGACTTGCCTGTGC 61.030 63.158 0.00 0.00 38.26 4.57
753 1320 1.734477 CGGACGAGACTTGCCTGTG 60.734 63.158 0.00 0.00 0.00 3.66
754 1321 0.892358 TACGGACGAGACTTGCCTGT 60.892 55.000 0.00 0.00 0.00 4.00
755 1322 0.242825 TTACGGACGAGACTTGCCTG 59.757 55.000 0.00 0.00 0.00 4.85
756 1323 0.243095 GTTACGGACGAGACTTGCCT 59.757 55.000 0.00 0.00 0.00 4.75
757 1324 0.038892 TGTTACGGACGAGACTTGCC 60.039 55.000 0.00 0.00 0.00 4.52
758 1325 1.774639 TTGTTACGGACGAGACTTGC 58.225 50.000 0.00 0.00 0.00 4.01
759 1326 5.442390 CGTTATTTGTTACGGACGAGACTTG 60.442 44.000 0.00 0.00 34.30 3.16
760 1327 4.618489 CGTTATTTGTTACGGACGAGACTT 59.382 41.667 0.00 0.00 34.30 3.01
761 1328 4.161333 CGTTATTTGTTACGGACGAGACT 58.839 43.478 0.00 0.00 34.30 3.24
762 1329 3.241458 GCGTTATTTGTTACGGACGAGAC 60.241 47.826 0.00 0.00 38.17 3.36
763 1330 2.916716 GCGTTATTTGTTACGGACGAGA 59.083 45.455 0.00 0.00 38.17 4.04
764 1331 2.919229 AGCGTTATTTGTTACGGACGAG 59.081 45.455 0.00 0.00 38.17 4.18
765 1332 2.916716 GAGCGTTATTTGTTACGGACGA 59.083 45.455 0.00 0.00 38.17 4.20
766 1333 2.919229 AGAGCGTTATTTGTTACGGACG 59.081 45.455 0.00 0.00 38.17 4.79
767 1334 3.305361 GGAGAGCGTTATTTGTTACGGAC 59.695 47.826 0.00 0.00 38.17 4.79
768 1335 3.514645 GGAGAGCGTTATTTGTTACGGA 58.485 45.455 0.00 0.00 38.17 4.69
769 1336 2.606272 GGGAGAGCGTTATTTGTTACGG 59.394 50.000 0.00 0.00 38.17 4.02
770 1337 2.606272 GGGGAGAGCGTTATTTGTTACG 59.394 50.000 0.00 0.00 40.55 3.18
776 1343 3.366052 AATGTGGGGAGAGCGTTATTT 57.634 42.857 0.00 0.00 0.00 1.40
816 1386 7.497579 CCCCATTTGCATACTTAAATAAAACCC 59.502 37.037 0.00 0.00 0.00 4.11
852 1426 1.788229 TGGAATCCGCTGGAGACATA 58.212 50.000 0.00 0.00 41.51 2.29
879 1453 1.746991 CTCCTCTCTTTTGGCCGCC 60.747 63.158 1.04 1.04 0.00 6.13
998 1934 3.582120 GTGGTGTGCGGTGTGGTG 61.582 66.667 0.00 0.00 0.00 4.17
999 1935 4.102815 TGTGGTGTGCGGTGTGGT 62.103 61.111 0.00 0.00 0.00 4.16
1000 1936 3.582120 GTGTGGTGTGCGGTGTGG 61.582 66.667 0.00 0.00 0.00 4.17
1001 1937 3.582120 GGTGTGGTGTGCGGTGTG 61.582 66.667 0.00 0.00 0.00 3.82
1002 1938 4.868116 GGGTGTGGTGTGCGGTGT 62.868 66.667 0.00 0.00 0.00 4.16
1200 2141 2.680352 GCCAGGTCGAGAGGGTCA 60.680 66.667 0.00 0.00 0.00 4.02
1470 2411 2.029964 TTGTCGGGCTTGACGTCC 59.970 61.111 14.12 0.00 41.87 4.79
1621 2562 2.408022 CTTCTCGCCGTACTCCCG 59.592 66.667 0.00 0.00 0.00 5.14
1876 2837 3.730715 CGTTTTTGTTTCAGTGGATCTGC 59.269 43.478 0.00 0.00 43.32 4.26
1931 2894 1.743394 GAAAATCACCACCCGATCCAC 59.257 52.381 0.00 0.00 0.00 4.02
2028 2997 2.699576 TACAGATGGATGGAGCGCGC 62.700 60.000 26.66 26.66 0.00 6.86
2070 3039 2.808321 GAAACCGAGCCGTCGTCC 60.808 66.667 0.00 0.00 45.30 4.79
2082 3053 0.603975 ACAGAAGAGCCGCAGAAACC 60.604 55.000 0.00 0.00 0.00 3.27
2083 3054 0.514691 CACAGAAGAGCCGCAGAAAC 59.485 55.000 0.00 0.00 0.00 2.78
2097 3068 2.151202 GATTTGCCGGAGAAACACAGA 58.849 47.619 5.05 0.00 0.00 3.41
2100 3071 3.676091 CGATTTGCCGGAGAAACAC 57.324 52.632 5.05 0.84 0.00 3.32
2178 3151 4.471904 AATGATCACGAAGGAACTAGCA 57.528 40.909 0.00 0.00 38.49 3.49
2197 3171 2.122768 CAGAGACCTCCAGGCCTAAAT 58.877 52.381 3.98 0.00 39.32 1.40
2207 3182 0.248843 CAGCTTCACCAGAGACCTCC 59.751 60.000 0.00 0.00 0.00 4.30
2297 3289 2.280628 GTATGTACAAGGACTGCTGCC 58.719 52.381 0.00 0.00 0.00 4.85
2299 3291 4.081972 AGACTGTATGTACAAGGACTGCTG 60.082 45.833 0.00 0.00 35.50 4.41
2325 3317 5.268387 TCTTCCTCTTCAGCTAGAACTGAT 58.732 41.667 0.00 0.00 45.75 2.90
2365 3357 3.367703 GCCTGCGTACTAAGTTCCACTAA 60.368 47.826 0.00 0.00 0.00 2.24
2372 3364 3.121738 ACAAAGCCTGCGTACTAAGTT 57.878 42.857 0.00 0.00 0.00 2.66
2380 3379 0.947244 CTTCTGAACAAAGCCTGCGT 59.053 50.000 0.00 0.00 0.00 5.24
2381 3380 1.229428 TCTTCTGAACAAAGCCTGCG 58.771 50.000 0.00 0.00 0.00 5.18
2410 3413 7.261829 ACAAAACATGCACATATTTTTGCTT 57.738 28.000 19.66 7.58 39.62 3.91
2467 3476 1.404391 CAAGCACAGAAGATGATGGCC 59.596 52.381 0.00 0.00 0.00 5.36
2487 3497 4.036262 TGTCCATTTGTAAGAGTGTTGTGC 59.964 41.667 0.00 0.00 0.00 4.57
2569 3591 2.830370 CCAAATCTCCAGCCCCGC 60.830 66.667 0.00 0.00 0.00 6.13
2627 3652 7.787084 TCTGAATCAAAAGCGTATCATATTCG 58.213 34.615 0.00 0.00 0.00 3.34
2633 3658 7.382488 GCTAGTATCTGAATCAAAAGCGTATCA 59.618 37.037 0.00 0.00 0.00 2.15
2683 3738 2.127251 CGACTGAAAAGGCCAAAAAGC 58.873 47.619 5.01 0.00 0.00 3.51
2684 3739 2.127251 GCGACTGAAAAGGCCAAAAAG 58.873 47.619 5.01 0.00 0.00 2.27
2685 3740 1.478510 TGCGACTGAAAAGGCCAAAAA 59.521 42.857 5.01 0.00 0.00 1.94
2721 3776 9.910267 ACGGGATACATACATACATACATAGTA 57.090 33.333 0.00 0.00 39.74 1.82
2722 3777 8.683615 CACGGGATACATACATACATACATAGT 58.316 37.037 0.00 0.00 39.74 2.12
2813 4031 1.004595 CCATCATGTGACTGACTGCG 58.995 55.000 0.00 0.00 0.00 5.18
2841 4059 8.215736 GTGGTTTCAGTTAGGTATATATTGGGT 58.784 37.037 0.00 0.00 0.00 4.51
2905 4123 9.106070 AGTAGTAAAAGTGTTTTCAGTTAGGTG 57.894 33.333 0.00 0.00 41.95 4.00
2931 4149 7.499321 TTCAGAAGTTATTAAAGCAACGGAA 57.501 32.000 0.00 0.00 0.00 4.30
2932 4150 7.357303 GTTTCAGAAGTTATTAAAGCAACGGA 58.643 34.615 0.00 0.00 0.00 4.69
2933 4151 6.581166 GGTTTCAGAAGTTATTAAAGCAACGG 59.419 38.462 2.38 0.00 0.00 4.44
2934 4152 6.302313 CGGTTTCAGAAGTTATTAAAGCAACG 59.698 38.462 7.03 0.00 0.00 4.10
2964 4194 0.519077 GCAGAGGAAGCGTTTTCAGG 59.481 55.000 0.00 0.00 0.00 3.86
3153 4458 2.262915 CACTCACCTCACGGGAGC 59.737 66.667 9.89 0.00 39.96 4.70
3289 4631 3.047877 CGTTCCCGGCAACAGTCC 61.048 66.667 9.37 0.00 0.00 3.85
3305 5045 2.870372 GGCTACAGCACAAAGCCG 59.130 61.111 3.24 0.00 45.82 5.52
3319 5059 3.372897 GTCTTAGGTAGGTAAGGTGGCT 58.627 50.000 0.00 0.00 31.82 4.75
3337 5077 0.032017 AGGATGGCTCGGTTAGGTCT 60.032 55.000 0.00 0.00 0.00 3.85
3408 5153 2.184322 CTCACCGATCACCACCCG 59.816 66.667 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.