Multiple sequence alignment - TraesCS5D01G559000

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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 TraesCS5D01G559000 chr5D 100.000 3659 0 0 1 3659 560476617 560480275 0.000000e+00 6758
1 TraesCS5D01G559000 chr5D 97.891 569 12 0 3091 3659 307447621 307447053 0.000000e+00 985
2 TraesCS5D01G559000 chr5D 95.487 421 15 1 145 561 503986716 503986296 0.000000e+00 669
3 TraesCS5D01G559000 chr4A 94.846 2464 68 17 668 3091 603787366 603784922 0.000000e+00 3792
4 TraesCS5D01G559000 chr4A 93.482 2608 74 26 561 3091 603840407 603837819 0.000000e+00 3786
5 TraesCS5D01G559000 chr4A 94.829 2456 73 18 668 3091 603799926 603797493 0.000000e+00 3783
6 TraesCS5D01G559000 chr4A 92.420 2612 76 29 561 3091 603918229 603915659 0.000000e+00 3615
7 TraesCS5D01G559000 chr4A 92.343 2612 77 30 561 3091 603852338 603849769 0.000000e+00 3602
8 TraesCS5D01G559000 chr4A 94.388 2370 65 22 561 2881 603911691 603909341 0.000000e+00 3578
9 TraesCS5D01G559000 chr4A 94.304 2370 67 22 561 2881 603781298 603778948 0.000000e+00 3567
10 TraesCS5D01G559000 chr4A 95.890 1898 43 14 1229 3091 603793085 603791188 0.000000e+00 3040
11 TraesCS5D01G559000 chr4A 92.701 1507 42 29 1632 3091 603884414 603882929 0.000000e+00 2111
12 TraesCS5D01G559000 chr4A 93.362 919 40 8 690 1608 603885306 603884409 0.000000e+00 1339
13 TraesCS5D01G559000 chr4A 93.311 882 40 6 690 1571 603920653 603919791 0.000000e+00 1284
14 TraesCS5D01G559000 chr4A 93.197 882 41 6 690 1571 603854783 603853921 0.000000e+00 1279
15 TraesCS5D01G559000 chr4A 92.541 791 16 9 2344 3091 603804166 603803376 0.000000e+00 1094
16 TraesCS5D01G559000 chr4A 88.091 613 20 17 561 1139 603846204 603845611 0.000000e+00 678
17 TraesCS5D01G559000 chr4A 88.091 613 20 17 561 1139 603880040 603879447 0.000000e+00 678
18 TraesCS5D01G559000 chr4A 96.596 235 3 4 2862 3091 603778936 603778702 5.730000e-103 385
19 TraesCS5D01G559000 chr4A 95.745 141 6 0 4 144 603801211 603801071 1.020000e-55 228
20 TraesCS5D01G559000 chr4A 95.745 141 6 0 4 144 603841553 603841413 1.020000e-55 228
21 TraesCS5D01G559000 chr4A 95.745 141 6 0 4 144 603906229 603906089 1.020000e-55 228
22 TraesCS5D01G559000 chr4A 95.745 141 6 0 4 144 603912839 603912699 1.020000e-55 228
23 TraesCS5D01G559000 chr4A 95.714 140 6 0 5 144 603853504 603853365 3.680000e-55 226
24 TraesCS5D01G559000 chr4A 95.035 141 7 0 4 144 603788651 603788511 4.760000e-54 222
25 TraesCS5D01G559000 chr4A 95.035 141 7 0 4 144 603847352 603847212 4.760000e-54 222
26 TraesCS5D01G559000 chr4A 95.070 142 6 1 4 144 603881189 603881048 4.760000e-54 222
27 TraesCS5D01G559000 chr4A 95.000 140 7 0 5 144 603919374 603919235 1.710000e-53 220
28 TraesCS5D01G559000 chr4A 96.639 119 3 1 561 678 603787506 603787388 2.880000e-46 196
29 TraesCS5D01G559000 chrUn 96.101 2026 55 7 824 2833 358267448 358269465 0.000000e+00 3282
30 TraesCS5D01G559000 chrUn 93.838 1915 62 18 561 2441 338456024 338454132 0.000000e+00 2832
31 TraesCS5D01G559000 chrUn 95.058 1214 25 9 1913 3091 359587586 359586373 0.000000e+00 1877
32 TraesCS5D01G559000 chrUn 94.163 1028 40 8 668 1694 449594326 449593318 0.000000e+00 1548
33 TraesCS5D01G559000 chrUn 91.207 671 9 9 2468 3091 430211918 430212585 0.000000e+00 867
34 TraesCS5D01G559000 chrUn 97.021 235 2 4 2862 3091 374445341 374445575 1.230000e-104 390
35 TraesCS5D01G559000 chr7D 97.887 568 12 0 3092 3659 162356259 162355692 0.000000e+00 983
36 TraesCS5D01G559000 chr7D 97.552 572 13 1 3088 3659 489502221 489502791 0.000000e+00 977
37 TraesCS5D01G559000 chr7D 95.581 430 13 4 137 561 590083897 590084325 0.000000e+00 684
38 TraesCS5D01G559000 chr7D 95.952 420 15 1 144 561 46701814 46701395 0.000000e+00 680
39 TraesCS5D01G559000 chr2D 97.887 568 12 0 3092 3659 496715765 496716332 0.000000e+00 983
40 TraesCS5D01G559000 chr2D 95.962 421 14 1 145 562 21191378 21191798 0.000000e+00 680
41 TraesCS5D01G559000 chr2D 95.529 425 15 1 141 561 620148797 620148373 0.000000e+00 676
42 TraesCS5D01G559000 chr2D 95.261 422 18 2 141 561 611204961 611205381 0.000000e+00 667
43 TraesCS5D01G559000 chr1D 97.723 571 13 0 3089 3659 396750133 396750703 0.000000e+00 983
44 TraesCS5D01G559000 chr1D 97.711 568 13 0 3092 3659 30148737 30148170 0.000000e+00 977
45 TraesCS5D01G559000 chr4D 97.887 568 11 1 3092 3659 480540983 480541549 0.000000e+00 981
46 TraesCS5D01G559000 chr4D 96.271 590 20 2 3072 3659 418440383 418440972 0.000000e+00 966
47 TraesCS5D01G559000 chr4D 94.964 417 20 1 145 561 25396529 25396944 0.000000e+00 652
48 TraesCS5D01G559000 chr6D 97.552 572 13 1 3088 3659 189558283 189558853 0.000000e+00 977
49 TraesCS5D01G559000 chr3D 94.811 424 14 4 145 561 576576678 576577100 0.000000e+00 654
50 TraesCS5D01G559000 chr3D 93.968 431 20 4 135 561 2304463 2304891 0.000000e+00 647


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 TraesCS5D01G559000 chr5D 560476617 560480275 3658 False 6758.000000 6758 100.000000 1 3659 1 chr5D.!!$F1 3658
1 TraesCS5D01G559000 chr5D 307447053 307447621 568 True 985.000000 985 97.891000 3091 3659 1 chr5D.!!$R1 568
2 TraesCS5D01G559000 chr4A 603837819 603841553 3734 True 2007.000000 3786 94.613500 4 3091 2 chr4A.!!$R3 3087
3 TraesCS5D01G559000 chr4A 603778702 603793085 14383 True 1867.000000 3792 95.551667 4 3091 6 chr4A.!!$R1 3087
4 TraesCS5D01G559000 chr4A 603797493 603804166 6673 True 1701.666667 3783 94.371667 4 3091 3 chr4A.!!$R2 3087
5 TraesCS5D01G559000 chr4A 603906089 603920653 14564 True 1525.500000 3615 94.434833 4 3091 6 chr4A.!!$R6 3087
6 TraesCS5D01G559000 chr4A 603845611 603854783 9172 True 1201.400000 3602 92.876000 4 3091 5 chr4A.!!$R4 3087
7 TraesCS5D01G559000 chr4A 603879447 603885306 5859 True 1087.500000 2111 92.306000 4 3091 4 chr4A.!!$R5 3087
8 TraesCS5D01G559000 chrUn 358267448 358269465 2017 False 3282.000000 3282 96.101000 824 2833 1 chrUn.!!$F1 2009
9 TraesCS5D01G559000 chrUn 338454132 338456024 1892 True 2832.000000 2832 93.838000 561 2441 1 chrUn.!!$R1 1880
10 TraesCS5D01G559000 chrUn 359586373 359587586 1213 True 1877.000000 1877 95.058000 1913 3091 1 chrUn.!!$R2 1178
11 TraesCS5D01G559000 chrUn 449593318 449594326 1008 True 1548.000000 1548 94.163000 668 1694 1 chrUn.!!$R3 1026
12 TraesCS5D01G559000 chrUn 430211918 430212585 667 False 867.000000 867 91.207000 2468 3091 1 chrUn.!!$F3 623
13 TraesCS5D01G559000 chr7D 162355692 162356259 567 True 983.000000 983 97.887000 3092 3659 1 chr7D.!!$R2 567
14 TraesCS5D01G559000 chr7D 489502221 489502791 570 False 977.000000 977 97.552000 3088 3659 1 chr7D.!!$F1 571
15 TraesCS5D01G559000 chr2D 496715765 496716332 567 False 983.000000 983 97.887000 3092 3659 1 chr2D.!!$F2 567
16 TraesCS5D01G559000 chr1D 396750133 396750703 570 False 983.000000 983 97.723000 3089 3659 1 chr1D.!!$F1 570
17 TraesCS5D01G559000 chr1D 30148170 30148737 567 True 977.000000 977 97.711000 3092 3659 1 chr1D.!!$R1 567
18 TraesCS5D01G559000 chr4D 480540983 480541549 566 False 981.000000 981 97.887000 3092 3659 1 chr4D.!!$F3 567
19 TraesCS5D01G559000 chr4D 418440383 418440972 589 False 966.000000 966 96.271000 3072 3659 1 chr4D.!!$F2 587
20 TraesCS5D01G559000 chr6D 189558283 189558853 570 False 977.000000 977 97.552000 3088 3659 1 chr6D.!!$F1 571

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
735 12895 0.034059 ACACAAGCAACTCCTCCTCG 59.966 55.0 0.00 0.00 0.00 4.63 F
852 13012 0.520404 CTTGCTAGTGCCACAAGCTG 59.480 55.0 0.00 0.00 44.23 4.24 F
1971 14138 0.543277 ATGTCATCGATGTGGGCAGT 59.457 50.0 24.09 3.34 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 14252 0.386113 GAGTGTACATCCGAGCTCCC 59.614 60.0 8.47 0.0 0.0 4.30 R
2308 14475 0.666913 CCATTGCAGGCATACTCAGC 59.333 55.0 0.00 0.0 0.0 4.26 R
3298 15566 1.663695 CCAAAGCACCTGGGTATACG 58.336 55.0 0.00 0.0 0.0 3.06 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
94 11607 9.838975 CAATATAAGTTTGCTTATGTGACAACA 57.161 29.630 9.39 0.00 44.88 3.33
101 11614 9.195411 AGTTTGCTTATGTGACAACAATTAATG 57.805 29.630 0.00 0.00 40.46 1.90
162 11675 3.503800 ACCACCAGTAGAAAAAGGACC 57.496 47.619 0.00 0.00 0.00 4.46
163 11676 3.053826 ACCACCAGTAGAAAAAGGACCT 58.946 45.455 0.00 0.00 0.00 3.85
167 11680 5.648092 CCACCAGTAGAAAAAGGACCTAATG 59.352 44.000 0.00 0.00 0.00 1.90
168 11681 6.238648 CACCAGTAGAAAAAGGACCTAATGT 58.761 40.000 0.00 0.00 29.54 2.71
170 11683 6.043938 ACCAGTAGAAAAAGGACCTAATGTGA 59.956 38.462 0.00 0.00 29.54 3.58
172 11685 7.386851 CAGTAGAAAAAGGACCTAATGTGAGA 58.613 38.462 0.00 0.00 0.00 3.27
186 11699 1.548719 TGTGAGACACATTAGTCCCGG 59.451 52.381 0.00 0.00 39.62 5.73
188 11701 2.028385 GTGAGACACATTAGTCCCGGTT 60.028 50.000 0.00 0.00 39.34 4.44
189 11702 2.635915 TGAGACACATTAGTCCCGGTTT 59.364 45.455 0.00 0.00 39.34 3.27
190 11703 3.000727 GAGACACATTAGTCCCGGTTTG 58.999 50.000 0.00 0.00 39.34 2.93
192 11705 3.263425 AGACACATTAGTCCCGGTTTGAT 59.737 43.478 0.00 0.00 39.34 2.57
193 11706 4.007659 GACACATTAGTCCCGGTTTGATT 58.992 43.478 0.00 0.00 32.36 2.57
194 11707 4.403734 ACACATTAGTCCCGGTTTGATTT 58.596 39.130 0.00 0.00 0.00 2.17
195 11708 4.830600 ACACATTAGTCCCGGTTTGATTTT 59.169 37.500 0.00 0.00 0.00 1.82
196 11709 5.160641 CACATTAGTCCCGGTTTGATTTTG 58.839 41.667 0.00 0.00 0.00 2.44
197 11710 4.219725 ACATTAGTCCCGGTTTGATTTTGG 59.780 41.667 0.00 0.00 0.00 3.28
198 11711 0.966179 AGTCCCGGTTTGATTTTGGC 59.034 50.000 0.00 0.00 0.00 4.52
200 11713 1.188871 TCCCGGTTTGATTTTGGCCC 61.189 55.000 0.00 0.00 0.00 5.80
201 11714 1.080161 CCGGTTTGATTTTGGCCCG 60.080 57.895 0.00 0.00 35.32 6.13
202 11715 1.080161 CGGTTTGATTTTGGCCCGG 60.080 57.895 0.00 0.00 0.00 5.73
204 11717 1.258676 GGTTTGATTTTGGCCCGGTA 58.741 50.000 0.00 0.00 0.00 4.02
205 11718 1.067425 GGTTTGATTTTGGCCCGGTAC 60.067 52.381 0.00 0.00 0.00 3.34
207 11720 3.083293 GTTTGATTTTGGCCCGGTACTA 58.917 45.455 0.00 0.00 0.00 1.82
208 11721 3.436577 TTGATTTTGGCCCGGTACTAA 57.563 42.857 0.00 0.00 0.00 2.24
209 11722 3.655615 TGATTTTGGCCCGGTACTAAT 57.344 42.857 0.00 0.00 0.00 1.73
210 11723 3.283751 TGATTTTGGCCCGGTACTAATG 58.716 45.455 0.00 0.00 0.00 1.90
211 11724 2.131776 TTTTGGCCCGGTACTAATGG 57.868 50.000 0.00 0.00 0.00 3.16
212 11725 0.993470 TTTGGCCCGGTACTAATGGT 59.007 50.000 0.00 0.00 0.00 3.55
213 11726 1.876849 TTGGCCCGGTACTAATGGTA 58.123 50.000 0.00 0.00 0.00 3.25
214 11727 2.106187 TGGCCCGGTACTAATGGTAT 57.894 50.000 0.00 0.00 32.56 2.73
215 11728 1.972795 TGGCCCGGTACTAATGGTATC 59.027 52.381 0.00 0.00 32.56 2.24
217 11730 2.570302 GGCCCGGTACTAATGGTATCAT 59.430 50.000 0.00 0.00 31.28 2.45
218 11731 3.008704 GGCCCGGTACTAATGGTATCATT 59.991 47.826 6.44 6.44 44.87 2.57
228 11741 3.857157 ATGGTATCATTAGTGGCGGTT 57.143 42.857 0.00 0.00 0.00 4.44
229 11742 3.188159 TGGTATCATTAGTGGCGGTTC 57.812 47.619 0.00 0.00 0.00 3.62
230 11743 2.132762 GGTATCATTAGTGGCGGTTCG 58.867 52.381 0.00 0.00 0.00 3.95
232 11745 2.684001 ATCATTAGTGGCGGTTCGAA 57.316 45.000 0.00 0.00 0.00 3.71
233 11746 1.717194 TCATTAGTGGCGGTTCGAAC 58.283 50.000 20.14 20.14 0.00 3.95
234 11747 0.368907 CATTAGTGGCGGTTCGAACG 59.631 55.000 21.34 16.92 0.00 3.95
235 11748 0.738412 ATTAGTGGCGGTTCGAACGG 60.738 55.000 26.33 26.33 0.00 4.44
241 11754 3.003478 CGGTTCGAACGGCTATGC 58.997 61.111 21.34 5.39 0.00 3.14
242 11755 1.807981 CGGTTCGAACGGCTATGCA 60.808 57.895 21.34 0.00 0.00 3.96
243 11756 1.151777 CGGTTCGAACGGCTATGCAT 61.152 55.000 21.34 3.79 0.00 3.96
244 11757 1.014352 GGTTCGAACGGCTATGCATT 58.986 50.000 21.34 0.00 0.00 3.56
245 11758 2.206750 GGTTCGAACGGCTATGCATTA 58.793 47.619 21.34 0.00 0.00 1.90
246 11759 2.610374 GGTTCGAACGGCTATGCATTAA 59.390 45.455 21.34 0.00 0.00 1.40
247 11760 3.250040 GGTTCGAACGGCTATGCATTAAT 59.750 43.478 21.34 0.00 0.00 1.40
248 11761 4.211389 GTTCGAACGGCTATGCATTAATG 58.789 43.478 13.36 11.27 0.00 1.90
260 11773 2.911819 CATTAATGCCGGTTCGTGTT 57.088 45.000 1.90 0.00 0.00 3.32
261 11774 2.514902 CATTAATGCCGGTTCGTGTTG 58.485 47.619 1.90 0.00 0.00 3.33
262 11775 1.880271 TTAATGCCGGTTCGTGTTGA 58.120 45.000 1.90 0.00 0.00 3.18
276 11789 2.410730 CGTGTTGAACCTTTAGTAGCGG 59.589 50.000 0.00 0.00 0.00 5.52
277 11790 3.396560 GTGTTGAACCTTTAGTAGCGGT 58.603 45.455 0.00 0.00 0.00 5.68
278 11791 3.431233 GTGTTGAACCTTTAGTAGCGGTC 59.569 47.826 0.00 0.00 0.00 4.79
279 11792 2.998670 GTTGAACCTTTAGTAGCGGTCC 59.001 50.000 0.00 0.00 0.00 4.46
280 11793 1.203052 TGAACCTTTAGTAGCGGTCCG 59.797 52.381 6.99 6.99 0.00 4.79
284 11797 0.804933 CTTTAGTAGCGGTCCGTGCC 60.805 60.000 13.94 0.51 0.00 5.01
286 11799 2.216750 TTAGTAGCGGTCCGTGCCAC 62.217 60.000 13.94 5.92 0.00 5.01
297 11810 2.341176 GTGCCACGAACCGGTACT 59.659 61.111 8.00 0.00 36.33 2.73
299 11812 0.038343 GTGCCACGAACCGGTACTAA 60.038 55.000 8.00 0.00 36.33 2.24
300 11813 0.678395 TGCCACGAACCGGTACTAAA 59.322 50.000 8.00 0.00 0.00 1.85
302 11815 2.000429 CCACGAACCGGTACTAAAGG 58.000 55.000 8.00 1.40 0.00 3.11
303 11816 1.404583 CCACGAACCGGTACTAAAGGG 60.405 57.143 8.00 0.00 0.00 3.95
304 11817 0.897621 ACGAACCGGTACTAAAGGGG 59.102 55.000 8.00 0.00 0.00 4.79
305 11818 0.897621 CGAACCGGTACTAAAGGGGT 59.102 55.000 8.00 0.00 0.00 4.95
306 11819 1.404583 CGAACCGGTACTAAAGGGGTG 60.405 57.143 8.00 0.00 0.00 4.61
307 11820 0.986527 AACCGGTACTAAAGGGGTGG 59.013 55.000 8.00 0.00 0.00 4.61
309 11822 0.251073 CCGGTACTAAAGGGGTGGTG 59.749 60.000 0.00 0.00 0.00 4.17
310 11823 0.251073 CGGTACTAAAGGGGTGGTGG 59.749 60.000 0.00 0.00 0.00 4.61
311 11824 0.034767 GGTACTAAAGGGGTGGTGGC 60.035 60.000 0.00 0.00 0.00 5.01
312 11825 0.694196 GTACTAAAGGGGTGGTGGCA 59.306 55.000 0.00 0.00 0.00 4.92
313 11826 0.988832 TACTAAAGGGGTGGTGGCAG 59.011 55.000 0.00 0.00 0.00 4.85
314 11827 1.000896 CTAAAGGGGTGGTGGCAGG 60.001 63.158 0.00 0.00 0.00 4.85
315 11828 3.218386 TAAAGGGGTGGTGGCAGGC 62.218 63.158 0.00 0.00 0.00 4.85
346 11859 3.728373 GGGCCCCACGATCACCTT 61.728 66.667 12.23 0.00 0.00 3.50
348 11861 1.605453 GGCCCCACGATCACCTTTA 59.395 57.895 0.00 0.00 0.00 1.85
350 11863 0.252197 GCCCCACGATCACCTTTAGT 59.748 55.000 0.00 0.00 0.00 2.24
351 11864 1.483415 GCCCCACGATCACCTTTAGTA 59.517 52.381 0.00 0.00 0.00 1.82
352 11865 2.740904 GCCCCACGATCACCTTTAGTAC 60.741 54.545 0.00 0.00 0.00 2.73
354 11867 2.480759 CCCACGATCACCTTTAGTACCG 60.481 54.545 0.00 0.00 0.00 4.02
355 11868 2.480759 CCACGATCACCTTTAGTACCGG 60.481 54.545 0.00 0.00 0.00 5.28
356 11869 2.165030 CACGATCACCTTTAGTACCGGT 59.835 50.000 13.98 13.98 0.00 5.28
357 11870 2.827921 ACGATCACCTTTAGTACCGGTT 59.172 45.455 15.04 0.00 0.00 4.44
358 11871 3.119352 ACGATCACCTTTAGTACCGGTTC 60.119 47.826 15.04 8.12 0.00 3.62
360 11873 2.238521 TCACCTTTAGTACCGGTTCGT 58.761 47.619 15.04 0.00 0.00 3.85
361 11874 2.030007 TCACCTTTAGTACCGGTTCGTG 60.030 50.000 15.04 11.08 0.00 4.35
364 11877 0.678395 TTTAGTACCGGTTCGTGGCA 59.322 50.000 15.04 0.00 0.00 4.92
366 11879 1.177895 TAGTACCGGTTCGTGGCACA 61.178 55.000 15.04 1.83 0.00 4.57
367 11880 1.594836 GTACCGGTTCGTGGCACAA 60.595 57.895 15.04 8.34 44.16 3.33
368 11881 1.145598 TACCGGTTCGTGGCACAAA 59.854 52.632 15.04 1.67 44.16 2.83
369 11882 1.159098 TACCGGTTCGTGGCACAAAC 61.159 55.000 15.04 15.95 44.16 2.93
371 11884 2.330041 GGTTCGTGGCACAAACCG 59.670 61.111 23.48 6.41 44.16 4.44
372 11885 2.330041 GTTCGTGGCACAAACCGG 59.670 61.111 19.09 0.00 44.16 5.28
374 11887 1.145598 TTCGTGGCACAAACCGGTA 59.854 52.632 19.09 0.00 44.16 4.02
376 11889 1.595929 CGTGGCACAAACCGGTACT 60.596 57.895 19.09 0.00 44.16 2.73
378 11891 1.873069 CGTGGCACAAACCGGTACTAA 60.873 52.381 19.09 0.00 44.16 2.24
379 11892 2.220313 GTGGCACAAACCGGTACTAAA 58.780 47.619 8.00 0.00 44.16 1.85
381 11894 1.808343 GGCACAAACCGGTACTAAAGG 59.192 52.381 8.00 0.00 0.00 3.11
382 11895 1.808343 GCACAAACCGGTACTAAAGGG 59.192 52.381 8.00 0.00 0.00 3.95
384 11897 1.701292 ACAAACCGGTACTAAAGGGCT 59.299 47.619 8.00 0.00 0.00 5.19
386 11899 3.327464 ACAAACCGGTACTAAAGGGCTAA 59.673 43.478 8.00 0.00 0.00 3.09
387 11900 3.616956 AACCGGTACTAAAGGGCTAAC 57.383 47.619 8.00 0.00 0.00 2.34
388 11901 1.833630 ACCGGTACTAAAGGGCTAACC 59.166 52.381 4.49 0.00 40.67 2.85
399 11912 2.609427 GGGCTAACCTTTAGTACCGG 57.391 55.000 0.00 0.00 35.85 5.28
402 11915 3.525537 GGCTAACCTTTAGTACCGGTTC 58.474 50.000 15.04 8.12 41.09 3.62
403 11916 3.182182 GCTAACCTTTAGTACCGGTTCG 58.818 50.000 15.04 0.00 41.09 3.95
404 11917 3.367395 GCTAACCTTTAGTACCGGTTCGT 60.367 47.826 15.04 0.00 41.09 3.85
406 11919 1.337167 ACCTTTAGTACCGGTTCGTGC 60.337 52.381 15.04 0.00 0.00 5.34
407 11920 1.353076 CTTTAGTACCGGTTCGTGCC 58.647 55.000 15.04 0.00 0.00 5.01
408 11921 0.678395 TTTAGTACCGGTTCGTGCCA 59.322 50.000 15.04 0.00 0.00 4.92
409 11922 0.896923 TTAGTACCGGTTCGTGCCAT 59.103 50.000 15.04 0.00 0.00 4.40
412 11925 0.671163 GTACCGGTTCGTGCCATGAA 60.671 55.000 15.04 0.00 0.00 2.57
413 11926 0.671163 TACCGGTTCGTGCCATGAAC 60.671 55.000 15.04 19.30 42.00 3.18
416 11929 2.867472 GTTCGTGCCATGAACCGG 59.133 61.111 17.21 0.00 37.98 5.28
419 11932 3.124921 CGTGCCATGAACCGGGAC 61.125 66.667 6.32 0.00 41.17 4.46
421 11934 1.600107 GTGCCATGAACCGGGACTA 59.400 57.895 6.32 0.00 41.35 2.59
422 11935 0.035820 GTGCCATGAACCGGGACTAA 60.036 55.000 6.32 0.00 41.35 2.24
423 11936 0.693622 TGCCATGAACCGGGACTAAA 59.306 50.000 6.32 0.00 0.00 1.85
424 11937 1.339631 TGCCATGAACCGGGACTAAAG 60.340 52.381 6.32 0.00 0.00 1.85
425 11938 2.017113 GCCATGAACCGGGACTAAAGG 61.017 57.143 6.32 0.00 0.00 3.11
428 11941 0.474273 TGAACCGGGACTAAAGGGGT 60.474 55.000 6.32 0.00 0.00 4.95
429 11942 0.251354 GAACCGGGACTAAAGGGGTC 59.749 60.000 6.32 0.00 0.00 4.46
433 11946 0.535797 CGGGACTAAAGGGGTCTGAC 59.464 60.000 0.00 0.00 34.47 3.51
434 11947 0.910338 GGGACTAAAGGGGTCTGACC 59.090 60.000 18.65 18.65 37.60 4.02
435 11948 1.555058 GGGACTAAAGGGGTCTGACCT 60.555 57.143 25.01 9.03 38.64 3.85
437 11950 3.632906 GGGACTAAAGGGGTCTGACCTAT 60.633 52.174 25.01 12.03 38.64 2.57
438 11951 4.388346 GGGACTAAAGGGGTCTGACCTATA 60.388 50.000 25.01 12.36 38.64 1.31
439 11952 4.833938 GGACTAAAGGGGTCTGACCTATAG 59.166 50.000 25.01 20.89 38.64 1.31
440 11953 5.456779 GACTAAAGGGGTCTGACCTATAGT 58.543 45.833 25.01 23.27 38.64 2.12
441 11954 5.456779 ACTAAAGGGGTCTGACCTATAGTC 58.543 45.833 25.01 8.25 46.51 2.59
442 11955 3.331718 AAGGGGTCTGACCTATAGTCC 57.668 52.381 25.01 16.47 45.68 3.85
445 11958 1.618487 GGTCTGACCTATAGTCCCGG 58.382 60.000 19.53 0.00 45.68 5.73
446 11959 1.133544 GGTCTGACCTATAGTCCCGGT 60.134 57.143 19.53 0.00 45.68 5.28
447 11960 2.664015 GTCTGACCTATAGTCCCGGTT 58.336 52.381 0.00 0.00 45.68 4.44
450 11963 1.288633 TGACCTATAGTCCCGGTTGGA 59.711 52.381 0.00 0.00 45.68 3.53
453 11966 1.962100 CCTATAGTCCCGGTTGGAGAC 59.038 57.143 0.00 0.00 46.38 3.36
454 11967 2.662866 CTATAGTCCCGGTTGGAGACA 58.337 52.381 9.96 0.00 46.38 3.41
456 11969 0.178955 TAGTCCCGGTTGGAGACACA 60.179 55.000 9.96 0.00 46.38 3.72
457 11970 1.052124 AGTCCCGGTTGGAGACACAA 61.052 55.000 9.96 0.00 46.38 3.33
460 11973 1.170290 CCCGGTTGGAGACACAAACC 61.170 60.000 0.00 0.00 42.67 3.27
461 11974 1.503818 CCGGTTGGAGACACAAACCG 61.504 60.000 20.93 20.93 42.67 4.44
463 11976 1.170290 GGTTGGAGACACAAACCGGG 61.170 60.000 6.32 0.00 42.67 5.73
464 11977 0.179040 GTTGGAGACACAAACCGGGA 60.179 55.000 6.32 0.00 42.67 5.14
465 11978 0.179040 TTGGAGACACAAACCGGGAC 60.179 55.000 6.32 0.00 42.67 4.46
466 11979 1.052124 TGGAGACACAAACCGGGACT 61.052 55.000 6.32 0.00 33.40 3.85
467 11980 0.971386 GGAGACACAAACCGGGACTA 59.029 55.000 6.32 0.00 0.00 2.59
468 11981 1.553704 GGAGACACAAACCGGGACTAT 59.446 52.381 6.32 0.00 0.00 2.12
469 11982 2.762327 GGAGACACAAACCGGGACTATA 59.238 50.000 6.32 0.00 0.00 1.31
470 11983 3.181478 GGAGACACAAACCGGGACTATAG 60.181 52.174 6.32 0.00 0.00 1.31
471 11984 2.764572 AGACACAAACCGGGACTATAGG 59.235 50.000 6.32 0.00 0.00 2.57
472 11985 1.835531 ACACAAACCGGGACTATAGGG 59.164 52.381 6.32 0.00 0.00 3.53
473 11986 0.835276 ACAAACCGGGACTATAGGGC 59.165 55.000 6.32 0.00 0.00 5.19
474 11987 0.834612 CAAACCGGGACTATAGGGCA 59.165 55.000 6.32 0.00 0.00 5.36
475 11988 1.210967 CAAACCGGGACTATAGGGCAA 59.789 52.381 6.32 0.00 0.00 4.52
477 11990 1.815757 ACCGGGACTATAGGGCAATT 58.184 50.000 6.32 0.00 0.00 2.32
479 11992 2.512476 ACCGGGACTATAGGGCAATTTT 59.488 45.455 6.32 0.00 0.00 1.82
480 11993 3.146847 CCGGGACTATAGGGCAATTTTC 58.853 50.000 4.43 0.00 0.00 2.29
481 11994 3.434453 CCGGGACTATAGGGCAATTTTCA 60.434 47.826 4.43 0.00 0.00 2.69
482 11995 4.204012 CGGGACTATAGGGCAATTTTCAA 58.796 43.478 4.43 0.00 0.00 2.69
483 11996 4.642885 CGGGACTATAGGGCAATTTTCAAA 59.357 41.667 4.43 0.00 0.00 2.69
484 11997 5.449999 CGGGACTATAGGGCAATTTTCAAAC 60.450 44.000 4.43 0.00 0.00 2.93
485 11998 5.656859 GGGACTATAGGGCAATTTTCAAACT 59.343 40.000 4.43 0.00 0.00 2.66
486 11999 6.183360 GGGACTATAGGGCAATTTTCAAACTC 60.183 42.308 4.43 0.00 0.00 3.01
487 12000 6.603599 GGACTATAGGGCAATTTTCAAACTCT 59.396 38.462 4.43 0.00 0.00 3.24
488 12001 7.773690 GGACTATAGGGCAATTTTCAAACTCTA 59.226 37.037 4.43 0.00 0.00 2.43
489 12002 8.507524 ACTATAGGGCAATTTTCAAACTCTAC 57.492 34.615 4.43 0.00 0.00 2.59
490 12003 6.775594 ATAGGGCAATTTTCAAACTCTACC 57.224 37.500 0.00 0.00 0.00 3.18
491 12004 3.832490 AGGGCAATTTTCAAACTCTACCC 59.168 43.478 0.00 0.00 0.00 3.69
493 12006 3.056107 GGCAATTTTCAAACTCTACCCCC 60.056 47.826 0.00 0.00 0.00 5.40
509 12022 2.677228 CCCCCTCGCCATTTCAGT 59.323 61.111 0.00 0.00 0.00 3.41
510 12023 1.000896 CCCCCTCGCCATTTCAGTT 60.001 57.895 0.00 0.00 0.00 3.16
511 12024 0.611896 CCCCCTCGCCATTTCAGTTT 60.612 55.000 0.00 0.00 0.00 2.66
512 12025 1.256812 CCCCTCGCCATTTCAGTTTT 58.743 50.000 0.00 0.00 0.00 2.43
513 12026 1.067635 CCCCTCGCCATTTCAGTTTTG 60.068 52.381 0.00 0.00 0.00 2.44
514 12027 1.885887 CCCTCGCCATTTCAGTTTTGA 59.114 47.619 0.00 0.00 0.00 2.69
612 12740 0.740737 GACCCTCATTTTGCCCATCG 59.259 55.000 0.00 0.00 0.00 3.84
688 12848 4.131088 GGCCGTCCCTCGTCACTC 62.131 72.222 0.00 0.00 37.94 3.51
689 12849 4.477975 GCCGTCCCTCGTCACTCG 62.478 72.222 0.00 0.00 41.41 4.18
722 12882 2.358737 GGGCGAGGTGGACACAAG 60.359 66.667 4.69 0.00 0.00 3.16
730 12890 0.179018 GGTGGACACAAGCAACTCCT 60.179 55.000 4.69 0.00 0.00 3.69
731 12891 1.230324 GTGGACACAAGCAACTCCTC 58.770 55.000 0.00 0.00 0.00 3.71
735 12895 0.034059 ACACAAGCAACTCCTCCTCG 59.966 55.000 0.00 0.00 0.00 4.63
741 12901 1.079543 CAACTCCTCCTCGTGCCTG 60.080 63.158 0.00 0.00 0.00 4.85
742 12902 2.948720 AACTCCTCCTCGTGCCTGC 61.949 63.158 0.00 0.00 0.00 4.85
743 12903 3.385384 CTCCTCCTCGTGCCTGCA 61.385 66.667 0.00 0.00 0.00 4.41
744 12904 2.922503 TCCTCCTCGTGCCTGCAA 60.923 61.111 0.00 0.00 0.00 4.08
745 12905 2.249413 CTCCTCCTCGTGCCTGCAAT 62.249 60.000 0.00 0.00 0.00 3.56
746 12906 1.817099 CCTCCTCGTGCCTGCAATC 60.817 63.158 0.00 0.00 0.00 2.67
747 12907 1.817099 CTCCTCGTGCCTGCAATCC 60.817 63.158 0.00 0.00 0.00 3.01
748 12908 2.249413 CTCCTCGTGCCTGCAATCCT 62.249 60.000 0.00 0.00 0.00 3.24
749 12909 2.110967 CCTCGTGCCTGCAATCCTG 61.111 63.158 0.00 0.00 0.00 3.86
750 12910 2.046023 TCGTGCCTGCAATCCTGG 60.046 61.111 0.00 0.00 35.75 4.45
751 12911 2.046023 CGTGCCTGCAATCCTGGA 60.046 61.111 0.00 0.00 34.66 3.86
821 12981 9.833894 CAATAAGAAGAAAACAATCAAAACGTG 57.166 29.630 0.00 0.00 0.00 4.49
822 12982 5.949233 AGAAGAAAACAATCAAAACGTGC 57.051 34.783 0.00 0.00 0.00 5.34
835 12995 0.882474 AACGTGCGTCTCTCTAGCTT 59.118 50.000 0.00 0.00 0.00 3.74
842 13002 2.540769 GCGTCTCTCTAGCTTGCTAGTG 60.541 54.545 23.70 21.60 0.00 2.74
848 13008 1.623311 TCTAGCTTGCTAGTGCCACAA 59.377 47.619 23.70 5.47 38.71 3.33
852 13012 0.520404 CTTGCTAGTGCCACAAGCTG 59.480 55.000 0.00 0.00 44.23 4.24
873 13033 4.992688 TGAAGCTTGTACAAAAACCACTG 58.007 39.130 2.10 0.00 0.00 3.66
894 13054 1.130054 TGAGAGGAAGCCAGCCTTGT 61.130 55.000 0.00 0.00 35.44 3.16
931 13091 0.698238 AGCTGCTGGGGAATACACAA 59.302 50.000 0.00 0.00 0.00 3.33
932 13092 0.811281 GCTGCTGGGGAATACACAAC 59.189 55.000 0.00 0.00 0.00 3.32
933 13093 1.614317 GCTGCTGGGGAATACACAACT 60.614 52.381 0.00 0.00 0.00 3.16
934 13094 2.355716 GCTGCTGGGGAATACACAACTA 60.356 50.000 0.00 0.00 0.00 2.24
935 13095 3.270877 CTGCTGGGGAATACACAACTAC 58.729 50.000 0.00 0.00 0.00 2.73
936 13096 2.640332 TGCTGGGGAATACACAACTACA 59.360 45.455 0.00 0.00 0.00 2.74
937 13097 3.007635 GCTGGGGAATACACAACTACAC 58.992 50.000 0.00 0.00 0.00 2.90
938 13098 3.558321 GCTGGGGAATACACAACTACACA 60.558 47.826 0.00 0.00 0.00 3.72
978 13138 4.034510 CGAGAAGTCCATTACCTGCATTTC 59.965 45.833 0.00 0.00 0.00 2.17
1130 13297 4.394712 GGACACTGTCCCTGGCGG 62.395 72.222 16.54 0.00 46.19 6.13
1161 13328 1.017387 GGCTAGTTGCAATCCCTTCG 58.983 55.000 0.59 0.00 45.15 3.79
1167 13334 5.163652 GCTAGTTGCAATCCCTTCGTATTTT 60.164 40.000 0.59 0.00 42.31 1.82
1173 13340 1.842052 TCCCTTCGTATTTTTGGGGC 58.158 50.000 0.00 0.00 38.43 5.80
1202 13369 2.176273 CGAAGCGGCAAGATGGAGG 61.176 63.158 1.45 0.00 0.00 4.30
1255 13422 4.740822 CCTTGGTCGGCAAGGGGG 62.741 72.222 9.55 0.00 44.02 5.40
1574 13741 3.207669 CCTGCTGATTGGCGCCTC 61.208 66.667 29.70 18.70 34.52 4.70
1623 13790 2.426738 CGTGGTGGACATGGCATTTTAT 59.573 45.455 0.00 0.00 32.27 1.40
1971 14138 0.543277 ATGTCATCGATGTGGGCAGT 59.457 50.000 24.09 3.34 0.00 4.40
2157 14324 1.961793 TCACCTTGTACACTTGGCAC 58.038 50.000 0.00 0.00 0.00 5.01
2190 14357 2.047274 CACATGTTCCTCCGCCGT 60.047 61.111 0.00 0.00 0.00 5.68
2308 14475 3.551496 TTCAGCAGGCCCCTTGACG 62.551 63.158 0.00 0.00 0.00 4.35
2731 14916 1.110876 GATCGATCCGAACGAACGTC 58.889 55.000 14.76 0.00 42.80 4.34
2732 14917 0.248377 ATCGATCCGAACGAACGTCC 60.248 55.000 4.76 0.00 42.80 4.79
2764 14949 5.365403 CATGCATGCATGTTTTCCTTTTT 57.635 34.783 40.30 13.48 46.20 1.94
2767 14952 7.531716 CATGCATGCATGTTTTCCTTTTTAAT 58.468 30.769 40.30 12.04 46.20 1.40
2812 15012 3.381590 GGAATCCCCTTTCTTTCCAATCG 59.618 47.826 0.00 0.00 38.01 3.34
2958 15222 2.649312 TGGTGTCCTCTCCAAATTCCAT 59.351 45.455 0.00 0.00 34.78 3.41
2999 15263 3.401033 TCGTCCAAGAAGCAAATCTCA 57.599 42.857 0.00 0.00 0.00 3.27
3177 15445 2.020720 CCATTAGTGCCACGCCATTAA 58.979 47.619 0.00 0.00 0.00 1.40
3219 15487 2.288666 CACTGGTGCGCCATTAGTATT 58.711 47.619 21.54 0.00 45.05 1.89
3242 15510 0.319083 TATACTAATGGCGCACCCCG 59.681 55.000 10.83 0.00 40.75 5.73
3246 15514 2.958578 CTAATGGCGCACCCCGGATT 62.959 60.000 10.83 0.00 37.44 3.01
3293 15561 2.338809 CATTAGTATGCCTCCCAGGGA 58.661 52.381 8.35 8.35 41.08 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.907474 TCTAACAGAGGTCCAATGGAACA 59.093 43.478 20.74 0.00 42.91 3.18
9 11522 8.334734 ACTATAAGTAGTCTAACAGAGGTCCAA 58.665 37.037 0.00 0.00 36.41 3.53
56 11569 6.978080 GCAAACTTATATTGGGGTGTGTAATG 59.022 38.462 0.00 0.00 0.00 1.90
60 11573 4.672899 AGCAAACTTATATTGGGGTGTGT 58.327 39.130 0.00 0.00 0.00 3.72
94 11607 8.954350 CCAGAAACACATCTCTTCTCATTAATT 58.046 33.333 0.00 0.00 0.00 1.40
95 11608 8.105829 ACCAGAAACACATCTCTTCTCATTAAT 58.894 33.333 0.00 0.00 0.00 1.40
101 11614 5.346281 CGTTACCAGAAACACATCTCTTCTC 59.654 44.000 0.00 0.00 0.00 2.87
144 11657 6.149474 CACATTAGGTCCTTTTTCTACTGGTG 59.851 42.308 0.00 0.00 0.00 4.17
145 11658 6.043938 TCACATTAGGTCCTTTTTCTACTGGT 59.956 38.462 0.00 0.00 0.00 4.00
147 11660 7.332182 GTCTCACATTAGGTCCTTTTTCTACTG 59.668 40.741 0.00 0.00 0.00 2.74
148 11661 7.016268 TGTCTCACATTAGGTCCTTTTTCTACT 59.984 37.037 0.00 0.00 0.00 2.57
149 11662 7.117956 GTGTCTCACATTAGGTCCTTTTTCTAC 59.882 40.741 0.00 0.00 34.08 2.59
150 11663 7.159372 GTGTCTCACATTAGGTCCTTTTTCTA 58.841 38.462 0.00 0.00 34.08 2.10
151 11664 5.998363 GTGTCTCACATTAGGTCCTTTTTCT 59.002 40.000 0.00 0.00 34.08 2.52
152 11665 5.763204 TGTGTCTCACATTAGGTCCTTTTTC 59.237 40.000 0.00 0.00 39.62 2.29
154 11667 5.304686 TGTGTCTCACATTAGGTCCTTTT 57.695 39.130 0.00 0.00 39.62 2.27
155 11668 4.974645 TGTGTCTCACATTAGGTCCTTT 57.025 40.909 0.00 0.00 39.62 3.11
167 11680 1.549170 ACCGGGACTAATGTGTCTCAC 59.451 52.381 6.32 0.00 37.29 3.51
168 11681 1.933021 ACCGGGACTAATGTGTCTCA 58.067 50.000 6.32 0.00 37.29 3.27
170 11683 2.635915 TCAAACCGGGACTAATGTGTCT 59.364 45.455 6.32 0.00 37.16 3.41
172 11685 3.713826 ATCAAACCGGGACTAATGTGT 57.286 42.857 6.32 0.00 0.00 3.72
179 11692 0.966179 GCCAAAATCAAACCGGGACT 59.034 50.000 6.32 0.00 0.00 3.85
180 11693 0.037697 GGCCAAAATCAAACCGGGAC 60.038 55.000 6.32 0.00 0.00 4.46
181 11694 1.188871 GGGCCAAAATCAAACCGGGA 61.189 55.000 6.32 0.00 0.00 5.14
184 11697 1.080161 CCGGGCCAAAATCAAACCG 60.080 57.895 4.39 0.00 40.89 4.44
185 11698 1.067425 GTACCGGGCCAAAATCAAACC 60.067 52.381 6.32 0.00 0.00 3.27
186 11699 1.890489 AGTACCGGGCCAAAATCAAAC 59.110 47.619 6.32 0.00 0.00 2.93
188 11701 3.436577 TTAGTACCGGGCCAAAATCAA 57.563 42.857 6.32 0.00 0.00 2.57
189 11702 3.283751 CATTAGTACCGGGCCAAAATCA 58.716 45.455 6.32 0.00 0.00 2.57
190 11703 2.621526 CCATTAGTACCGGGCCAAAATC 59.378 50.000 6.32 0.00 0.00 2.17
192 11705 1.355043 ACCATTAGTACCGGGCCAAAA 59.645 47.619 6.32 0.00 0.00 2.44
193 11706 0.993470 ACCATTAGTACCGGGCCAAA 59.007 50.000 6.32 0.00 0.00 3.28
194 11707 1.876849 TACCATTAGTACCGGGCCAA 58.123 50.000 6.32 0.00 0.00 4.52
195 11708 1.972795 GATACCATTAGTACCGGGCCA 59.027 52.381 6.32 0.00 32.46 5.36
196 11709 1.972795 TGATACCATTAGTACCGGGCC 59.027 52.381 6.32 0.00 32.46 5.80
197 11710 3.975168 ATGATACCATTAGTACCGGGC 57.025 47.619 6.32 0.00 32.46 6.13
207 11720 3.857157 ACCGCCACTAATGATACCATT 57.143 42.857 0.00 0.00 44.56 3.16
208 11721 3.740115 GAACCGCCACTAATGATACCAT 58.260 45.455 0.00 0.00 33.66 3.55
209 11722 2.482316 CGAACCGCCACTAATGATACCA 60.482 50.000 0.00 0.00 0.00 3.25
210 11723 2.132762 CGAACCGCCACTAATGATACC 58.867 52.381 0.00 0.00 0.00 2.73
211 11724 3.088194 TCGAACCGCCACTAATGATAC 57.912 47.619 0.00 0.00 0.00 2.24
212 11725 3.450578 GTTCGAACCGCCACTAATGATA 58.549 45.455 17.68 0.00 0.00 2.15
213 11726 2.277084 GTTCGAACCGCCACTAATGAT 58.723 47.619 17.68 0.00 0.00 2.45
214 11727 1.717194 GTTCGAACCGCCACTAATGA 58.283 50.000 17.68 0.00 0.00 2.57
215 11728 0.368907 CGTTCGAACCGCCACTAATG 59.631 55.000 22.07 0.54 0.00 1.90
217 11730 1.373246 CCGTTCGAACCGCCACTAA 60.373 57.895 22.07 0.00 0.00 2.24
218 11731 2.259204 CCGTTCGAACCGCCACTA 59.741 61.111 22.07 0.00 0.00 2.74
220 11733 3.919973 TAGCCGTTCGAACCGCCAC 62.920 63.158 29.59 13.31 34.37 5.01
221 11734 3.009192 ATAGCCGTTCGAACCGCCA 62.009 57.895 29.59 21.21 34.37 5.69
222 11735 2.202837 ATAGCCGTTCGAACCGCC 60.203 61.111 29.59 15.96 34.37 6.13
223 11736 3.003478 CATAGCCGTTCGAACCGC 58.997 61.111 27.26 27.26 34.11 5.68
225 11738 1.014352 AATGCATAGCCGTTCGAACC 58.986 50.000 22.07 9.45 0.00 3.62
241 11754 2.160615 TCAACACGAACCGGCATTAATG 59.839 45.455 11.27 11.27 0.00 1.90
242 11755 2.428491 TCAACACGAACCGGCATTAAT 58.572 42.857 0.00 0.00 0.00 1.40
243 11756 1.880271 TCAACACGAACCGGCATTAA 58.120 45.000 0.00 0.00 0.00 1.40
244 11757 1.880271 TTCAACACGAACCGGCATTA 58.120 45.000 0.00 0.00 0.00 1.90
245 11758 2.709170 TTCAACACGAACCGGCATT 58.291 47.368 0.00 0.00 0.00 3.56
246 11759 4.466133 TTCAACACGAACCGGCAT 57.534 50.000 0.00 0.00 0.00 4.40
253 11766 3.737266 CGCTACTAAAGGTTCAACACGAA 59.263 43.478 0.00 0.00 0.00 3.85
254 11767 3.311106 CGCTACTAAAGGTTCAACACGA 58.689 45.455 0.00 0.00 0.00 4.35
255 11768 2.410730 CCGCTACTAAAGGTTCAACACG 59.589 50.000 0.00 0.00 0.00 4.49
256 11769 3.396560 ACCGCTACTAAAGGTTCAACAC 58.603 45.455 0.00 0.00 33.96 3.32
257 11770 3.555586 GGACCGCTACTAAAGGTTCAACA 60.556 47.826 0.00 0.00 38.57 3.33
258 11771 2.998670 GGACCGCTACTAAAGGTTCAAC 59.001 50.000 0.00 0.00 38.57 3.18
259 11772 2.353011 CGGACCGCTACTAAAGGTTCAA 60.353 50.000 0.00 0.00 38.57 2.69
260 11773 1.203052 CGGACCGCTACTAAAGGTTCA 59.797 52.381 0.00 0.00 38.57 3.18
261 11774 1.203287 ACGGACCGCTACTAAAGGTTC 59.797 52.381 15.39 0.00 38.57 3.62
262 11775 1.067354 CACGGACCGCTACTAAAGGTT 60.067 52.381 15.39 0.00 38.57 3.50
265 11778 0.804933 GGCACGGACCGCTACTAAAG 60.805 60.000 15.39 0.00 0.00 1.85
266 11779 1.216178 GGCACGGACCGCTACTAAA 59.784 57.895 15.39 0.00 0.00 1.85
267 11780 1.978080 TGGCACGGACCGCTACTAA 60.978 57.895 15.39 0.00 0.00 2.24
268 11781 2.361483 TGGCACGGACCGCTACTA 60.361 61.111 15.39 0.00 0.00 1.82
279 11792 2.198906 TAGTACCGGTTCGTGGCACG 62.199 60.000 32.75 32.75 44.19 5.34
280 11793 0.038343 TTAGTACCGGTTCGTGGCAC 60.038 55.000 15.04 7.79 0.00 5.01
284 11797 1.404583 CCCCTTTAGTACCGGTTCGTG 60.405 57.143 15.04 0.51 0.00 4.35
286 11799 0.897621 ACCCCTTTAGTACCGGTTCG 59.102 55.000 15.04 0.00 0.00 3.95
287 11800 1.065926 CCACCCCTTTAGTACCGGTTC 60.066 57.143 15.04 8.12 0.00 3.62
288 11801 0.986527 CCACCCCTTTAGTACCGGTT 59.013 55.000 15.04 0.00 0.00 4.44
289 11802 0.178894 ACCACCCCTTTAGTACCGGT 60.179 55.000 13.98 13.98 0.00 5.28
290 11803 0.251073 CACCACCCCTTTAGTACCGG 59.749 60.000 0.00 0.00 0.00 5.28
291 11804 0.251073 CCACCACCCCTTTAGTACCG 59.749 60.000 0.00 0.00 0.00 4.02
292 11805 0.034767 GCCACCACCCCTTTAGTACC 60.035 60.000 0.00 0.00 0.00 3.34
294 11807 0.988832 CTGCCACCACCCCTTTAGTA 59.011 55.000 0.00 0.00 0.00 1.82
297 11810 3.176297 CCTGCCACCACCCCTTTA 58.824 61.111 0.00 0.00 0.00 1.85
329 11842 1.917336 TAAAGGTGATCGTGGGGCCC 61.917 60.000 18.17 18.17 0.00 5.80
330 11843 0.463833 CTAAAGGTGATCGTGGGGCC 60.464 60.000 0.00 0.00 0.00 5.80
337 11850 3.442100 GAACCGGTACTAAAGGTGATCG 58.558 50.000 8.00 0.00 38.44 3.69
338 11851 3.119352 ACGAACCGGTACTAAAGGTGATC 60.119 47.826 8.00 0.00 38.44 2.92
344 11857 1.337074 TGCCACGAACCGGTACTAAAG 60.337 52.381 8.00 0.00 0.00 1.85
345 11858 0.678395 TGCCACGAACCGGTACTAAA 59.322 50.000 8.00 0.00 0.00 1.85
346 11859 0.038343 GTGCCACGAACCGGTACTAA 60.038 55.000 8.00 0.00 36.33 2.24
348 11861 2.030490 TTGTGCCACGAACCGGTACT 62.030 55.000 8.00 0.00 39.62 2.73
350 11863 1.145598 TTTGTGCCACGAACCGGTA 59.854 52.632 8.00 0.00 0.00 4.02
351 11864 2.124653 TTTGTGCCACGAACCGGT 60.125 55.556 0.00 0.00 0.00 5.28
352 11865 2.330041 GTTTGTGCCACGAACCGG 59.670 61.111 15.77 0.00 36.68 5.28
355 11868 1.159098 TACCGGTTTGTGCCACGAAC 61.159 55.000 15.04 17.94 40.84 3.95
356 11869 1.145598 TACCGGTTTGTGCCACGAA 59.854 52.632 15.04 0.00 0.00 3.85
357 11870 1.594836 GTACCGGTTTGTGCCACGA 60.595 57.895 15.04 0.00 0.00 4.35
358 11871 0.319727 TAGTACCGGTTTGTGCCACG 60.320 55.000 15.04 0.00 0.00 4.94
360 11873 2.496111 CTTTAGTACCGGTTTGTGCCA 58.504 47.619 15.04 0.00 0.00 4.92
361 11874 1.808343 CCTTTAGTACCGGTTTGTGCC 59.192 52.381 15.04 0.00 0.00 5.01
364 11877 1.701292 AGCCCTTTAGTACCGGTTTGT 59.299 47.619 15.04 0.00 0.00 2.83
366 11879 3.307691 GGTTAGCCCTTTAGTACCGGTTT 60.308 47.826 15.04 4.12 0.00 3.27
367 11880 2.237143 GGTTAGCCCTTTAGTACCGGTT 59.763 50.000 15.04 0.00 0.00 4.44
368 11881 1.833630 GGTTAGCCCTTTAGTACCGGT 59.166 52.381 13.98 13.98 0.00 5.28
369 11882 2.113807 AGGTTAGCCCTTTAGTACCGG 58.886 52.381 0.00 0.00 42.73 5.28
381 11894 3.616956 AACCGGTACTAAAGGTTAGCC 57.383 47.619 8.00 0.00 45.44 3.93
386 11899 1.337167 GCACGAACCGGTACTAAAGGT 60.337 52.381 8.00 0.00 40.50 3.50
387 11900 1.353076 GCACGAACCGGTACTAAAGG 58.647 55.000 8.00 0.00 0.00 3.11
388 11901 1.337074 TGGCACGAACCGGTACTAAAG 60.337 52.381 8.00 0.00 0.00 1.85
390 11903 0.896923 ATGGCACGAACCGGTACTAA 59.103 50.000 8.00 0.00 0.00 2.24
391 11904 0.173935 CATGGCACGAACCGGTACTA 59.826 55.000 8.00 0.00 0.00 1.82
392 11905 1.079405 CATGGCACGAACCGGTACT 60.079 57.895 8.00 0.00 0.00 2.73
393 11906 0.671163 TTCATGGCACGAACCGGTAC 60.671 55.000 8.00 0.00 0.00 3.34
394 11907 0.671163 GTTCATGGCACGAACCGGTA 60.671 55.000 15.10 0.00 37.40 4.02
395 11908 1.964373 GTTCATGGCACGAACCGGT 60.964 57.895 15.10 0.00 37.40 5.28
396 11909 2.867472 GTTCATGGCACGAACCGG 59.133 61.111 15.10 0.00 37.40 5.28
399 11912 2.686816 CCCGGTTCATGGCACGAAC 61.687 63.158 17.48 17.48 41.66 3.95
402 11915 2.233605 TAGTCCCGGTTCATGGCACG 62.234 60.000 0.00 0.00 0.00 5.34
403 11916 0.035820 TTAGTCCCGGTTCATGGCAC 60.036 55.000 0.00 0.00 0.00 5.01
404 11917 0.693622 TTTAGTCCCGGTTCATGGCA 59.306 50.000 0.00 0.00 0.00 4.92
406 11919 1.408266 CCCTTTAGTCCCGGTTCATGG 60.408 57.143 0.00 0.00 0.00 3.66
407 11920 1.408266 CCCCTTTAGTCCCGGTTCATG 60.408 57.143 0.00 0.00 0.00 3.07
408 11921 0.916809 CCCCTTTAGTCCCGGTTCAT 59.083 55.000 0.00 0.00 0.00 2.57
409 11922 0.474273 ACCCCTTTAGTCCCGGTTCA 60.474 55.000 0.00 0.00 0.00 3.18
412 11925 0.908180 CAGACCCCTTTAGTCCCGGT 60.908 60.000 0.00 0.00 34.67 5.28
413 11926 0.616679 TCAGACCCCTTTAGTCCCGG 60.617 60.000 0.00 0.00 34.67 5.73
415 11928 0.910338 GGTCAGACCCCTTTAGTCCC 59.090 60.000 8.65 0.00 34.67 4.46
416 11929 1.954035 AGGTCAGACCCCTTTAGTCC 58.046 55.000 16.72 0.00 39.75 3.85
419 11932 4.833938 GGACTATAGGTCAGACCCCTTTAG 59.166 50.000 16.72 13.46 46.16 1.85
421 11934 3.632906 GGGACTATAGGTCAGACCCCTTT 60.633 52.174 16.72 0.00 46.16 3.11
422 11935 2.090663 GGGACTATAGGTCAGACCCCTT 60.091 54.545 16.72 3.93 46.16 3.95
423 11936 1.504221 GGGACTATAGGTCAGACCCCT 59.496 57.143 16.72 6.36 46.16 4.79
424 11937 1.822457 CGGGACTATAGGTCAGACCCC 60.822 61.905 16.72 8.79 46.16 4.95
425 11938 1.618487 CGGGACTATAGGTCAGACCC 58.382 60.000 16.72 0.35 46.16 4.46
428 11941 2.662866 CAACCGGGACTATAGGTCAGA 58.337 52.381 6.32 0.00 46.16 3.27
429 11942 1.687123 CCAACCGGGACTATAGGTCAG 59.313 57.143 6.32 0.00 46.16 3.51
433 11946 1.962100 GTCTCCAACCGGGACTATAGG 59.038 57.143 6.32 0.00 42.15 2.57
434 11947 2.361438 GTGTCTCCAACCGGGACTATAG 59.639 54.545 6.32 0.00 42.15 1.31
435 11948 2.291735 TGTGTCTCCAACCGGGACTATA 60.292 50.000 6.32 0.00 42.15 1.31
437 11950 0.178955 TGTGTCTCCAACCGGGACTA 60.179 55.000 6.32 0.00 42.15 2.59
438 11951 1.052124 TTGTGTCTCCAACCGGGACT 61.052 55.000 6.32 0.00 42.15 3.85
439 11952 0.179040 TTTGTGTCTCCAACCGGGAC 60.179 55.000 6.32 3.26 42.15 4.46
440 11953 0.179040 GTTTGTGTCTCCAACCGGGA 60.179 55.000 6.32 0.00 45.89 5.14
441 11954 1.170290 GGTTTGTGTCTCCAACCGGG 61.170 60.000 6.32 0.00 38.37 5.73
442 11955 1.503818 CGGTTTGTGTCTCCAACCGG 61.504 60.000 17.93 0.00 36.37 5.28
445 11958 0.179040 TCCCGGTTTGTGTCTCCAAC 60.179 55.000 0.00 0.00 0.00 3.77
446 11959 0.179040 GTCCCGGTTTGTGTCTCCAA 60.179 55.000 0.00 0.00 0.00 3.53
447 11960 1.052124 AGTCCCGGTTTGTGTCTCCA 61.052 55.000 0.00 0.00 0.00 3.86
450 11963 2.764572 CCTATAGTCCCGGTTTGTGTCT 59.235 50.000 0.00 0.00 0.00 3.41
453 11966 1.474498 GCCCTATAGTCCCGGTTTGTG 60.474 57.143 0.00 0.00 0.00 3.33
454 11967 0.835276 GCCCTATAGTCCCGGTTTGT 59.165 55.000 0.00 0.00 0.00 2.83
456 11969 1.587066 TTGCCCTATAGTCCCGGTTT 58.413 50.000 0.00 0.00 0.00 3.27
457 11970 1.815757 ATTGCCCTATAGTCCCGGTT 58.184 50.000 0.00 0.00 0.00 4.44
460 11973 3.815809 TGAAAATTGCCCTATAGTCCCG 58.184 45.455 0.00 0.00 0.00 5.14
461 11974 5.656859 AGTTTGAAAATTGCCCTATAGTCCC 59.343 40.000 0.00 0.00 0.00 4.46
463 11976 7.631717 AGAGTTTGAAAATTGCCCTATAGTC 57.368 36.000 0.00 0.00 0.00 2.59
464 11977 7.556635 GGTAGAGTTTGAAAATTGCCCTATAGT 59.443 37.037 0.00 0.00 0.00 2.12
465 11978 7.013369 GGGTAGAGTTTGAAAATTGCCCTATAG 59.987 40.741 0.00 0.00 0.00 1.31
466 11979 6.831868 GGGTAGAGTTTGAAAATTGCCCTATA 59.168 38.462 6.51 0.00 0.00 1.31
467 11980 5.656859 GGGTAGAGTTTGAAAATTGCCCTAT 59.343 40.000 6.51 0.00 0.00 2.57
468 11981 5.014202 GGGTAGAGTTTGAAAATTGCCCTA 58.986 41.667 6.51 0.00 0.00 3.53
469 11982 3.832490 GGGTAGAGTTTGAAAATTGCCCT 59.168 43.478 6.51 0.00 0.00 5.19
470 11983 3.056107 GGGGTAGAGTTTGAAAATTGCCC 60.056 47.826 5.61 5.61 0.00 5.36
471 11984 3.056107 GGGGGTAGAGTTTGAAAATTGCC 60.056 47.826 0.00 0.00 0.00 4.52
472 11985 4.188247 GGGGGTAGAGTTTGAAAATTGC 57.812 45.455 0.00 0.00 0.00 3.56
493 12006 1.067635 CAAAACTGAAATGGCGAGGGG 60.068 52.381 0.00 0.00 0.00 4.79
494 12007 1.885887 TCAAAACTGAAATGGCGAGGG 59.114 47.619 0.00 0.00 0.00 4.30
495 12008 3.641437 TTCAAAACTGAAATGGCGAGG 57.359 42.857 0.00 0.00 0.00 4.63
552 12674 7.810260 AGCTCTATTAGTGGAATGAAGGATTT 58.190 34.615 0.00 0.00 0.00 2.17
555 12677 7.014711 CACTAGCTCTATTAGTGGAATGAAGGA 59.985 40.741 5.78 0.00 42.63 3.36
556 12678 7.151308 CACTAGCTCTATTAGTGGAATGAAGG 58.849 42.308 5.78 0.00 42.63 3.46
612 12740 4.153957 AGGGTCCATGGTCCTGAC 57.846 61.111 24.71 9.75 0.00 3.51
714 12874 0.398318 AGGAGGAGTTGCTTGTGTCC 59.602 55.000 0.00 0.00 0.00 4.02
722 12882 2.435059 GGCACGAGGAGGAGTTGC 60.435 66.667 0.00 0.00 0.00 4.17
730 12890 2.268920 GGATTGCAGGCACGAGGA 59.731 61.111 0.00 0.00 0.00 3.71
731 12891 2.110967 CAGGATTGCAGGCACGAGG 61.111 63.158 0.00 0.00 0.00 4.63
735 12895 2.413142 GCTCCAGGATTGCAGGCAC 61.413 63.158 0.00 0.00 0.00 5.01
741 12901 1.502163 CGATTCCGCTCCAGGATTGC 61.502 60.000 0.00 0.00 40.48 3.56
742 12902 0.179073 ACGATTCCGCTCCAGGATTG 60.179 55.000 0.00 0.00 40.48 2.67
743 12903 0.179073 CACGATTCCGCTCCAGGATT 60.179 55.000 0.00 0.00 40.48 3.01
744 12904 1.330655 ACACGATTCCGCTCCAGGAT 61.331 55.000 0.00 0.00 40.48 3.24
745 12905 1.541310 AACACGATTCCGCTCCAGGA 61.541 55.000 0.00 0.00 39.95 3.86
746 12906 0.174845 TAACACGATTCCGCTCCAGG 59.825 55.000 0.00 0.00 39.95 4.45
747 12907 1.135083 AGTAACACGATTCCGCTCCAG 60.135 52.381 0.00 0.00 39.95 3.86
748 12908 0.892755 AGTAACACGATTCCGCTCCA 59.107 50.000 0.00 0.00 39.95 3.86
749 12909 2.005971 AAGTAACACGATTCCGCTCC 57.994 50.000 0.00 0.00 39.95 4.70
750 12910 3.251571 AGAAAGTAACACGATTCCGCTC 58.748 45.455 0.00 0.00 39.95 5.03
751 12911 3.314541 AGAAAGTAACACGATTCCGCT 57.685 42.857 0.00 0.00 39.95 5.52
821 12981 1.673920 ACTAGCAAGCTAGAGAGACGC 59.326 52.381 29.95 0.00 46.56 5.19
822 12982 2.540769 GCACTAGCAAGCTAGAGAGACG 60.541 54.545 29.95 14.22 46.56 4.18
835 12995 0.108396 TTCAGCTTGTGGCACTAGCA 59.892 50.000 40.54 26.44 46.76 3.49
852 13012 3.796717 GCAGTGGTTTTTGTACAAGCTTC 59.203 43.478 8.56 1.83 0.00 3.86
931 13091 1.318576 GTTTGCCAGCCTTGTGTAGT 58.681 50.000 0.00 0.00 0.00 2.73
932 13092 1.001378 GTGTTTGCCAGCCTTGTGTAG 60.001 52.381 0.00 0.00 0.00 2.74
933 13093 1.028905 GTGTTTGCCAGCCTTGTGTA 58.971 50.000 0.00 0.00 0.00 2.90
934 13094 1.675720 GGTGTTTGCCAGCCTTGTGT 61.676 55.000 0.00 0.00 35.48 3.72
935 13095 1.067916 GGTGTTTGCCAGCCTTGTG 59.932 57.895 0.00 0.00 35.48 3.33
936 13096 1.381056 TGGTGTTTGCCAGCCTTGT 60.381 52.632 0.00 0.00 40.95 3.16
937 13097 1.067916 GTGGTGTTTGCCAGCCTTG 59.932 57.895 0.00 0.00 40.95 3.61
938 13098 2.489275 CGTGGTGTTTGCCAGCCTT 61.489 57.895 0.00 0.00 40.95 4.35
1040 13201 4.614036 GGGTTGGGGTGGGTGGTG 62.614 72.222 0.00 0.00 0.00 4.17
1130 13297 3.799755 CTAGCCCGTTGCCGTTGC 61.800 66.667 0.00 0.00 42.71 4.17
1139 13306 1.077716 GGGATTGCAACTAGCCCGT 60.078 57.895 0.00 0.00 44.83 5.28
1143 13310 1.739067 ACGAAGGGATTGCAACTAGC 58.261 50.000 0.00 0.00 45.96 3.42
1161 13328 2.492560 CGGGCGCCCCAAAAATAC 59.507 61.111 39.24 11.89 45.83 1.89
1202 13369 4.296265 CCGTGTACAAGGGGAAGC 57.704 61.111 19.07 0.00 0.00 3.86
1269 13436 1.066908 CGAGACAGCCTTCTCAGATCC 59.933 57.143 11.65 0.00 42.03 3.36
1379 13546 4.379243 CCAGCTCCGGCGACAGTT 62.379 66.667 9.30 0.00 44.37 3.16
1623 13790 1.177895 TGTGGTACCCGTGCTCGTAA 61.178 55.000 10.07 0.00 35.01 3.18
1971 14138 1.263356 CCTCGGAGTTTACCAGGTCA 58.737 55.000 0.00 0.00 0.00 4.02
2029 14196 4.363990 CTCGCTCACCACGCCTGT 62.364 66.667 0.00 0.00 0.00 4.00
2085 14252 0.386113 GAGTGTACATCCGAGCTCCC 59.614 60.000 8.47 0.00 0.00 4.30
2241 14408 2.359602 TCGTCGAAGTCGGCCTCT 60.360 61.111 0.00 0.00 41.58 3.69
2308 14475 0.666913 CCATTGCAGGCATACTCAGC 59.333 55.000 0.00 0.00 0.00 4.26
2999 15263 9.995003 GAGTAGGAGATGAAACATATCATTTCT 57.005 33.333 8.28 4.34 40.08 2.52
3068 15332 7.554835 AGTGCTATTTTTACCGTTCCATATGAA 59.445 33.333 3.65 0.00 0.00 2.57
3069 15333 7.051623 AGTGCTATTTTTACCGTTCCATATGA 58.948 34.615 3.65 0.00 0.00 2.15
3142 15410 2.033294 TGGCGCACCACTAATGCA 59.967 55.556 10.83 0.00 42.67 3.96
3219 15487 2.485835 GGGTGCGCCATTAGTATACCAA 60.486 50.000 19.98 0.00 36.17 3.67
3242 15510 9.909644 ACTGTTGTATATACTAATGACGAATCC 57.090 33.333 13.89 0.00 0.00 3.01
3246 15514 6.854381 CGCACTGTTGTATATACTAATGACGA 59.146 38.462 13.89 0.00 0.00 4.20
3293 15561 1.968050 GCACCTGGGTATACGTGGCT 61.968 60.000 0.00 0.00 0.00 4.75
3298 15566 1.663695 CCAAAGCACCTGGGTATACG 58.336 55.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.