Multiple sequence alignment - TraesCS1B01G098400

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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 TraesCS1B01G098400 chr1B 100.000 3134 0 0 1 3134 104783271 104780138 0.000000e+00 5788.0
1 TraesCS1B01G098400 chr1B 73.935 775 157 27 1007 1765 630820149 630820894 1.430000e-68 270.0
2 TraesCS1B01G098400 chr1B 80.205 293 48 7 1842 2128 630821040 630821328 8.810000e-51 211.0
3 TraesCS1B01G098400 chr1A 92.650 1864 90 13 479 2318 63087705 63085865 0.000000e+00 2639.0
4 TraesCS1B01G098400 chr1A 92.791 652 39 4 2488 3134 63085652 63085004 0.000000e+00 937.0
5 TraesCS1B01G098400 chr1A 83.099 497 40 20 7 478 63089164 63088687 2.250000e-111 412.0
6 TraesCS1B01G098400 chr1A 74.679 778 159 27 1007 1765 551311311 551312069 8.440000e-81 311.0
7 TraesCS1B01G098400 chr1A 78.425 292 55 6 1842 2128 551312215 551312503 1.920000e-42 183.0
8 TraesCS1B01G098400 chr1A 94.624 93 5 0 2332 2424 19416612 19416704 9.060000e-31 145.0
9 TraesCS1B01G098400 chr1A 94.624 93 4 1 2332 2424 19363119 19363210 3.260000e-30 143.0
10 TraesCS1B01G098400 chr1A 94.624 93 4 1 2332 2424 19469524 19469615 3.260000e-30 143.0
11 TraesCS1B01G098400 chr1A 100.000 29 0 0 136 164 139629438 139629410 2.000000e-03 54.7
12 TraesCS1B01G098400 chr1D 93.941 1535 66 6 621 2149 64118962 64117449 0.000000e+00 2294.0
13 TraesCS1B01G098400 chr1D 98.225 676 12 0 2457 3132 64117083 64116408 0.000000e+00 1182.0
14 TraesCS1B01G098400 chr1D 92.405 158 10 2 466 623 64119087 64118932 1.130000e-54 224.0
15 TraesCS1B01G098400 chr1D 77.937 349 64 8 1789 2128 458876692 458877036 4.100000e-49 206.0
16 TraesCS1B01G098400 chr1D 87.500 112 8 4 2213 2318 64117358 64117247 1.180000e-24 124.0
17 TraesCS1B01G098400 chr1D 87.879 66 6 1 2172 2235 64117446 64117381 3.350000e-10 76.8
18 TraesCS1B01G098400 chr1D 100.000 29 0 0 2423 2451 64117251 64117223 2.000000e-03 54.7
19 TraesCS1B01G098400 chr5D 88.501 487 39 4 877 1362 317162929 317162459 9.750000e-160 573.0
20 TraesCS1B01G098400 chr5D 76.792 293 57 6 1842 2127 47531993 47532281 1.510000e-33 154.0
21 TraesCS1B01G098400 chr7B 73.753 762 153 29 1410 2128 594122272 594123029 4.010000e-64 255.0
22 TraesCS1B01G098400 chr7B 74.375 640 128 23 1409 2013 594119195 594119833 1.120000e-59 241.0
23 TraesCS1B01G098400 chr7B 75.904 332 68 8 1791 2113 620678176 620677848 3.240000e-35 159.0
24 TraesCS1B01G098400 chr7B 75.945 291 63 5 1842 2127 661723554 661723266 3.260000e-30 143.0
25 TraesCS1B01G098400 chr7D 74.766 642 119 26 1411 2013 549795006 549795643 6.710000e-62 248.0
26 TraesCS1B01G098400 chr6A 75.000 448 74 22 1293 1717 616903408 616902976 4.160000e-39 172.0
27 TraesCS1B01G098400 chr5A 77.431 288 58 5 1842 2124 37936046 37936331 6.950000e-37 165.0
28 TraesCS1B01G098400 chr3B 95.556 90 4 0 2337 2426 67967261 67967172 9.060000e-31 145.0
29 TraesCS1B01G098400 chrUn 93.684 95 6 0 2334 2428 60492571 60492665 3.260000e-30 143.0
30 TraesCS1B01G098400 chrUn 94.565 92 5 0 2337 2428 318520577 318520486 3.260000e-30 143.0
31 TraesCS1B01G098400 chrUn 94.624 93 4 1 2332 2424 331152177 331152268 3.260000e-30 143.0
32 TraesCS1B01G098400 chr6D 92.857 98 7 0 2334 2431 95373338 95373435 3.260000e-30 143.0
33 TraesCS1B01G098400 chr6D 100.000 28 0 0 137 164 266462747 266462720 6.000000e-03 52.8
34 TraesCS1B01G098400 chr4D 87.719 114 12 2 2315 2427 47897582 47897470 7.050000e-27 132.0
35 TraesCS1B01G098400 chr4B 100.000 29 0 0 136 164 587855663 587855691 2.000000e-03 54.7


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 TraesCS1B01G098400 chr1B 104780138 104783271 3133 True 5788.000000 5788 100.000000 1 3134 1 chr1B.!!$R1 3133
1 TraesCS1B01G098400 chr1B 630820149 630821328 1179 False 240.500000 270 77.070000 1007 2128 2 chr1B.!!$F1 1121
2 TraesCS1B01G098400 chr1A 63085004 63089164 4160 True 1329.333333 2639 89.513333 7 3134 3 chr1A.!!$R2 3127
3 TraesCS1B01G098400 chr1A 551311311 551312503 1192 False 247.000000 311 76.552000 1007 2128 2 chr1A.!!$F4 1121
4 TraesCS1B01G098400 chr1D 64116408 64119087 2679 True 659.250000 2294 93.325000 466 3132 6 chr1D.!!$R1 2666
5 TraesCS1B01G098400 chr7B 594119195 594123029 3834 False 248.000000 255 74.064000 1409 2128 2 chr7B.!!$F1 719
6 TraesCS1B01G098400 chr7D 549795006 549795643 637 False 248.000000 248 74.766000 1411 2013 1 chr7D.!!$F1 602

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
296 321 0.034670 GGAACCTTGCCATCTGAGCT 60.035 55.0 0.0 0.0 0.00 4.09 F
299 324 0.176680 ACCTTGCCATCTGAGCTACG 59.823 55.0 0.0 0.0 0.00 3.51 F
728 1752 0.250467 TGGTGCAGAGAAAGCAGACC 60.250 55.0 0.0 0.0 43.63 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1135 2159 1.478916 CATGATGTGCTTGCCATTGGA 59.521 47.619 6.95 0.0 0.0 3.53 R
1272 2302 1.529010 CACCTTCACAGCCTTGGCA 60.529 57.895 14.54 0.0 0.0 4.92 R
2416 6669 0.603569 CGCCGAGCAATATACTCCCT 59.396 55.000 0.00 0.0 0.0 4.20 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
30 31 7.593875 TTTTTCCAGAATTTTGTTGACACAG 57.406 32.000 0.00 0.00 33.22 3.66
53 54 2.416547 ACAAACGCAGATGCTCACATAC 59.583 45.455 2.95 0.00 36.35 2.39
82 83 3.362986 GCACACTCACTTGTATGAACACG 60.363 47.826 0.00 0.00 34.61 4.49
83 84 2.800544 ACACTCACTTGTATGAACACGC 59.199 45.455 0.00 0.00 34.61 5.34
84 85 2.058798 ACTCACTTGTATGAACACGCG 58.941 47.619 3.53 3.53 34.61 6.01
85 86 2.058798 CTCACTTGTATGAACACGCGT 58.941 47.619 5.58 5.58 34.61 6.01
86 87 1.790043 TCACTTGTATGAACACGCGTG 59.210 47.619 35.99 35.99 34.61 5.34
87 88 0.511221 ACTTGTATGAACACGCGTGC 59.489 50.000 37.35 23.10 34.61 5.34
88 89 0.510790 CTTGTATGAACACGCGTGCA 59.489 50.000 37.35 27.82 34.61 4.57
89 90 0.233590 TTGTATGAACACGCGTGCAC 59.766 50.000 37.35 29.22 31.72 4.57
90 91 0.876342 TGTATGAACACGCGTGCACA 60.876 50.000 37.35 33.23 31.72 4.57
91 92 0.450482 GTATGAACACGCGTGCACAC 60.450 55.000 37.35 23.59 31.72 3.82
92 93 0.876342 TATGAACACGCGTGCACACA 60.876 50.000 37.35 28.66 31.72 3.72
93 94 2.350760 GAACACGCGTGCACACAC 60.351 61.111 37.35 18.36 43.76 3.82
104 105 1.135431 GTGCACACACACACACACATT 60.135 47.619 13.17 0.00 46.61 2.71
111 112 3.436704 CACACACACACACATTCTATCCC 59.563 47.826 0.00 0.00 0.00 3.85
131 133 2.982488 CCTACCCCCAAGATATTGAGCT 59.018 50.000 0.54 0.00 0.00 4.09
132 134 4.168101 CCTACCCCCAAGATATTGAGCTA 58.832 47.826 0.54 0.00 0.00 3.32
136 138 6.128138 ACCCCCAAGATATTGAGCTAATAC 57.872 41.667 0.54 0.00 34.22 1.89
141 143 9.911788 CCCCAAGATATTGAGCTAATACAATAT 57.088 33.333 14.85 14.85 45.92 1.28
168 170 7.672983 TGAGATTGATAAAGTCACCAAAGAC 57.327 36.000 0.00 0.00 36.32 3.01
172 174 4.951254 TGATAAAGTCACCAAAGACGTCA 58.049 39.130 19.50 0.00 43.24 4.35
173 175 5.361427 TGATAAAGTCACCAAAGACGTCAA 58.639 37.500 19.50 0.00 43.24 3.18
176 178 4.552166 AAGTCACCAAAGACGTCAAATG 57.448 40.909 19.50 12.75 43.24 2.32
177 179 3.541632 AGTCACCAAAGACGTCAAATGT 58.458 40.909 19.50 6.66 43.24 2.71
178 180 3.560068 AGTCACCAAAGACGTCAAATGTC 59.440 43.478 19.50 6.42 43.24 3.06
179 181 2.875933 TCACCAAAGACGTCAAATGTCC 59.124 45.455 19.50 0.00 34.73 4.02
180 182 2.031157 CACCAAAGACGTCAAATGTCCC 60.031 50.000 19.50 0.00 34.73 4.46
189 205 2.162681 GTCAAATGTCCCTTCCCACTG 58.837 52.381 0.00 0.00 0.00 3.66
194 210 1.444933 TGTCCCTTCCCACTGAACAT 58.555 50.000 0.00 0.00 0.00 2.71
199 215 3.199946 TCCCTTCCCACTGAACATACATC 59.800 47.826 0.00 0.00 0.00 3.06
204 220 1.470805 CCACTGAACATACATCGCCGA 60.471 52.381 0.00 0.00 0.00 5.54
212 228 2.930040 ACATACATCGCCGAAAAGTCTG 59.070 45.455 0.00 0.00 0.00 3.51
215 231 2.489971 ACATCGCCGAAAAGTCTGAAA 58.510 42.857 0.00 0.00 0.00 2.69
278 303 0.754957 TGGGCTGTTTCACCACAAGG 60.755 55.000 0.00 0.00 42.21 3.61
294 319 2.089980 CAAGGAACCTTGCCATCTGAG 58.910 52.381 18.61 0.00 45.38 3.35
296 321 0.034670 GGAACCTTGCCATCTGAGCT 60.035 55.000 0.00 0.00 0.00 4.09
297 322 1.210478 GGAACCTTGCCATCTGAGCTA 59.790 52.381 0.00 0.00 0.00 3.32
298 323 2.284190 GAACCTTGCCATCTGAGCTAC 58.716 52.381 0.00 0.00 0.00 3.58
299 324 0.176680 ACCTTGCCATCTGAGCTACG 59.823 55.000 0.00 0.00 0.00 3.51
313 338 1.945776 GCTACGCTCAGTTCGCACAC 61.946 60.000 0.00 0.00 0.00 3.82
330 355 6.499172 TCGCACACTTTTTGAAATTCACATA 58.501 32.000 0.00 0.00 0.00 2.29
387 413 5.348164 AGAAACCGAAAACAAATTGGACTG 58.652 37.500 0.00 0.00 0.00 3.51
390 416 3.118956 ACCGAAAACAAATTGGACTGCAA 60.119 39.130 0.00 0.00 0.00 4.08
416 442 1.001487 CTGGCATTTTGACGCACTGAA 60.001 47.619 0.00 0.00 0.00 3.02
467 515 7.903995 AATCTTCACAGTTTCAAAAGCAAAA 57.096 28.000 0.00 0.00 0.00 2.44
643 1651 1.299648 CCCACGATTGCCTCCTCAA 59.700 57.895 0.00 0.00 0.00 3.02
644 1652 0.322456 CCCACGATTGCCTCCTCAAA 60.322 55.000 0.00 0.00 0.00 2.69
645 1653 1.533625 CCACGATTGCCTCCTCAAAA 58.466 50.000 0.00 0.00 0.00 2.44
728 1752 0.250467 TGGTGCAGAGAAAGCAGACC 60.250 55.000 0.00 0.00 43.63 3.85
771 1795 2.432628 GTCTTGGTGTCTCCGGCG 60.433 66.667 0.00 0.00 39.52 6.46
772 1796 3.691342 TCTTGGTGTCTCCGGCGG 61.691 66.667 22.51 22.51 39.52 6.13
813 1837 1.005748 CAGAGTCTTCGTGCTGCCA 60.006 57.895 0.00 0.00 0.00 4.92
935 1959 6.238211 CGCGATCTCAACTCTGGAATTTTAAT 60.238 38.462 0.00 0.00 0.00 1.40
1135 2159 5.003804 ACTCGCAAACAAAAGAGATGGTAT 58.996 37.500 0.00 0.00 34.98 2.73
1203 2227 1.298157 GCTGGTGCATCAGTTACGCA 61.298 55.000 27.18 0.00 39.41 5.24
1221 2245 1.227853 ACCAAACGGTGACAGCTCC 60.228 57.895 2.72 0.00 34.62 4.70
1222 2246 1.071471 CCAAACGGTGACAGCTCCT 59.929 57.895 2.72 0.00 0.00 3.69
1230 2254 0.605589 GTGACAGCTCCTACAGTGCT 59.394 55.000 0.00 0.00 46.09 4.40
1272 2302 4.271696 TGTCCTTCTTGATGACGATGTT 57.728 40.909 0.00 0.00 0.00 2.71
1279 2309 1.452110 TGATGACGATGTTGCCAAGG 58.548 50.000 0.00 0.00 0.00 3.61
1553 5665 2.162208 ACATACAGCAGCATTTGAACCG 59.838 45.455 0.00 0.00 0.00 4.44
1678 5790 1.888512 CACAACTCTTTGGTCCCATGG 59.111 52.381 4.14 4.14 37.00 3.66
1738 5856 2.584835 AGCAAATGTGTTCAGGGCTA 57.415 45.000 0.00 0.00 0.00 3.93
1825 6018 6.147985 GGAAGAACAAGAAGTGGATGAAGTAC 59.852 42.308 0.00 0.00 0.00 2.73
2114 6310 1.825090 TTGAACGAGCTCATTGCCAT 58.175 45.000 15.40 0.00 44.23 4.40
2147 6343 8.812147 TCGAAAGCGTAATTACATCTGATAAT 57.188 30.769 15.67 0.00 38.98 1.28
2148 6344 9.902196 TCGAAAGCGTAATTACATCTGATAATA 57.098 29.630 15.67 0.00 38.98 0.98
2174 6370 2.820728 TATGAGGTTCCTGAGACCGA 57.179 50.000 0.00 0.00 42.11 4.69
2247 6500 6.902771 ATGATCTTGTAGGTATAAGCGTCT 57.097 37.500 0.00 0.00 0.00 4.18
2266 6519 4.692155 CGTCTATATTGATCTGCATTGCCA 59.308 41.667 6.12 0.00 0.00 4.92
2280 6533 0.894141 TTGCCACACTGTGCAAGTTT 59.106 45.000 7.90 0.00 36.83 2.66
2357 6610 7.878477 CACTTTAAGTGTGCATTCATTCATT 57.122 32.000 16.22 0.00 41.19 2.57
2358 6611 8.301730 CACTTTAAGTGTGCATTCATTCATTT 57.698 30.769 16.22 0.00 41.19 2.32
2359 6612 8.767085 CACTTTAAGTGTGCATTCATTCATTTT 58.233 29.630 16.22 0.00 41.19 1.82
2360 6613 8.767085 ACTTTAAGTGTGCATTCATTCATTTTG 58.233 29.630 0.00 0.00 0.00 2.44
2361 6614 5.600908 AAGTGTGCATTCATTCATTTTGC 57.399 34.783 0.00 0.00 0.00 3.68
2362 6615 4.890088 AGTGTGCATTCATTCATTTTGCT 58.110 34.783 0.00 0.00 34.47 3.91
2363 6616 5.302360 AGTGTGCATTCATTCATTTTGCTT 58.698 33.333 0.00 0.00 34.47 3.91
2364 6617 5.407387 AGTGTGCATTCATTCATTTTGCTTC 59.593 36.000 0.00 0.00 34.47 3.86
2365 6618 4.386350 TGTGCATTCATTCATTTTGCTTCG 59.614 37.500 0.00 0.00 34.47 3.79
2366 6619 4.386652 GTGCATTCATTCATTTTGCTTCGT 59.613 37.500 0.00 0.00 34.47 3.85
2367 6620 5.572511 GTGCATTCATTCATTTTGCTTCGTA 59.427 36.000 0.00 0.00 34.47 3.43
2368 6621 6.254157 GTGCATTCATTCATTTTGCTTCGTAT 59.746 34.615 0.00 0.00 34.47 3.06
2369 6622 6.253942 TGCATTCATTCATTTTGCTTCGTATG 59.746 34.615 0.00 0.00 34.47 2.39
2370 6623 6.254157 GCATTCATTCATTTTGCTTCGTATGT 59.746 34.615 0.00 0.00 0.00 2.29
2371 6624 7.431960 GCATTCATTCATTTTGCTTCGTATGTA 59.568 33.333 0.00 0.00 0.00 2.29
2372 6625 8.950961 CATTCATTCATTTTGCTTCGTATGTAG 58.049 33.333 0.00 0.00 0.00 2.74
2373 6626 7.609760 TCATTCATTTTGCTTCGTATGTAGT 57.390 32.000 0.00 0.00 0.00 2.73
2374 6627 7.684670 TCATTCATTTTGCTTCGTATGTAGTC 58.315 34.615 0.00 0.00 0.00 2.59
2375 6628 6.417191 TTCATTTTGCTTCGTATGTAGTCC 57.583 37.500 0.00 0.00 0.00 3.85
2376 6629 5.483811 TCATTTTGCTTCGTATGTAGTCCA 58.516 37.500 0.00 0.00 0.00 4.02
2377 6630 5.350365 TCATTTTGCTTCGTATGTAGTCCAC 59.650 40.000 0.00 0.00 0.00 4.02
2378 6631 2.953466 TGCTTCGTATGTAGTCCACC 57.047 50.000 0.00 0.00 0.00 4.61
2379 6632 2.453521 TGCTTCGTATGTAGTCCACCT 58.546 47.619 0.00 0.00 0.00 4.00
2380 6633 3.623703 TGCTTCGTATGTAGTCCACCTA 58.376 45.455 0.00 0.00 0.00 3.08
2381 6634 3.630769 TGCTTCGTATGTAGTCCACCTAG 59.369 47.826 0.00 0.00 0.00 3.02
2382 6635 3.631227 GCTTCGTATGTAGTCCACCTAGT 59.369 47.826 0.00 0.00 0.00 2.57
2383 6636 4.497674 GCTTCGTATGTAGTCCACCTAGTG 60.498 50.000 0.00 0.00 0.00 2.74
2384 6637 4.492494 TCGTATGTAGTCCACCTAGTGA 57.508 45.455 0.00 0.00 35.23 3.41
2385 6638 4.847198 TCGTATGTAGTCCACCTAGTGAA 58.153 43.478 0.00 0.00 35.23 3.18
2386 6639 5.255687 TCGTATGTAGTCCACCTAGTGAAA 58.744 41.667 0.00 0.00 35.23 2.69
2387 6640 5.889853 TCGTATGTAGTCCACCTAGTGAAAT 59.110 40.000 0.00 0.00 35.23 2.17
2388 6641 6.039047 TCGTATGTAGTCCACCTAGTGAAATC 59.961 42.308 0.00 0.00 35.23 2.17
2389 6642 6.039493 CGTATGTAGTCCACCTAGTGAAATCT 59.961 42.308 0.00 0.00 35.23 2.40
2390 6643 5.916661 TGTAGTCCACCTAGTGAAATCTC 57.083 43.478 0.00 0.00 35.23 2.75
2391 6644 5.580998 TGTAGTCCACCTAGTGAAATCTCT 58.419 41.667 0.00 0.00 35.23 3.10
2392 6645 6.728411 TGTAGTCCACCTAGTGAAATCTCTA 58.272 40.000 0.00 0.00 35.23 2.43
2393 6646 6.602406 TGTAGTCCACCTAGTGAAATCTCTAC 59.398 42.308 0.00 0.00 35.23 2.59
2394 6647 5.580998 AGTCCACCTAGTGAAATCTCTACA 58.419 41.667 0.00 0.00 35.23 2.74
2395 6648 6.017192 AGTCCACCTAGTGAAATCTCTACAA 58.983 40.000 0.00 0.00 35.23 2.41
2396 6649 6.497259 AGTCCACCTAGTGAAATCTCTACAAA 59.503 38.462 0.00 0.00 35.23 2.83
2397 6650 6.814146 GTCCACCTAGTGAAATCTCTACAAAG 59.186 42.308 0.00 0.00 35.23 2.77
2398 6651 6.724441 TCCACCTAGTGAAATCTCTACAAAGA 59.276 38.462 0.00 0.00 35.23 2.52
2399 6652 6.814146 CCACCTAGTGAAATCTCTACAAAGAC 59.186 42.308 0.00 0.00 35.23 3.01
2400 6653 7.310113 CCACCTAGTGAAATCTCTACAAAGACT 60.310 40.741 0.00 0.00 35.23 3.24
2401 6654 8.091449 CACCTAGTGAAATCTCTACAAAGACTT 58.909 37.037 0.00 0.00 35.23 3.01
2402 6655 9.310449 ACCTAGTGAAATCTCTACAAAGACTTA 57.690 33.333 0.00 0.00 0.00 2.24
2403 6656 9.575783 CCTAGTGAAATCTCTACAAAGACTTAC 57.424 37.037 0.00 0.00 0.00 2.34
2418 6671 9.057089 ACAAAGACTTACATTTAAGAACAGAGG 57.943 33.333 5.64 0.00 37.49 3.69
2419 6672 8.507249 CAAAGACTTACATTTAAGAACAGAGGG 58.493 37.037 5.64 0.00 37.49 4.30
2420 6673 7.554959 AGACTTACATTTAAGAACAGAGGGA 57.445 36.000 5.64 0.00 37.49 4.20
2421 6674 7.616313 AGACTTACATTTAAGAACAGAGGGAG 58.384 38.462 5.64 0.00 37.49 4.30
2451 6704 1.368641 GGCGCATTGTCTCATGTACA 58.631 50.000 10.83 0.00 0.00 2.90
2452 6705 1.328680 GGCGCATTGTCTCATGTACAG 59.671 52.381 10.83 0.00 0.00 2.74
2454 6707 2.001872 CGCATTGTCTCATGTACAGCA 58.998 47.619 0.33 0.00 0.00 4.41
2455 6708 2.416202 CGCATTGTCTCATGTACAGCAA 59.584 45.455 0.33 2.29 0.00 3.91
2478 6865 0.317799 TTTGGTGATGTGTGCCATGC 59.682 50.000 0.00 0.00 32.56 4.06
2882 7293 7.167924 TGGTATTTCTGCTTGCAAATTGATA 57.832 32.000 0.00 0.00 0.00 2.15
2980 7391 4.074970 ACACAACCAAAGTCCATCTCATC 58.925 43.478 0.00 0.00 0.00 2.92
3106 7517 5.496387 CATGCTGCGTTCAATAGTCTAAAG 58.504 41.667 0.00 0.00 0.00 1.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.382110 TCTGTGTCAACAAAATTCTGGAAAAA 58.618 30.769 0.00 0.00 35.37 1.94
7 8 6.929625 TCTGTGTCAACAAAATTCTGGAAAA 58.070 32.000 0.00 0.00 35.37 2.29
8 9 6.522625 TCTGTGTCAACAAAATTCTGGAAA 57.477 33.333 0.00 0.00 35.37 3.13
9 10 6.071672 TGTTCTGTGTCAACAAAATTCTGGAA 60.072 34.615 0.00 0.00 35.37 3.53
10 11 5.417266 TGTTCTGTGTCAACAAAATTCTGGA 59.583 36.000 0.00 0.00 35.37 3.86
11 12 5.649557 TGTTCTGTGTCAACAAAATTCTGG 58.350 37.500 0.00 0.00 35.37 3.86
12 13 7.579589 TTTGTTCTGTGTCAACAAAATTCTG 57.420 32.000 7.99 0.00 46.03 3.02
53 54 3.909776 ACAAGTGAGTGTGCATTCATG 57.090 42.857 0.00 0.00 29.78 3.07
84 85 0.451383 ATGTGTGTGTGTGTGTGCAC 59.549 50.000 10.75 10.75 45.44 4.57
85 86 1.132073 GAATGTGTGTGTGTGTGTGCA 59.868 47.619 0.00 0.00 0.00 4.57
86 87 1.401552 AGAATGTGTGTGTGTGTGTGC 59.598 47.619 0.00 0.00 0.00 4.57
87 88 4.083855 GGATAGAATGTGTGTGTGTGTGTG 60.084 45.833 0.00 0.00 0.00 3.82
88 89 4.065088 GGATAGAATGTGTGTGTGTGTGT 58.935 43.478 0.00 0.00 0.00 3.72
89 90 3.436704 GGGATAGAATGTGTGTGTGTGTG 59.563 47.826 0.00 0.00 0.00 3.82
90 91 3.327757 AGGGATAGAATGTGTGTGTGTGT 59.672 43.478 0.00 0.00 0.00 3.72
91 92 3.942829 AGGGATAGAATGTGTGTGTGTG 58.057 45.455 0.00 0.00 0.00 3.82
92 93 4.081087 GGTAGGGATAGAATGTGTGTGTGT 60.081 45.833 0.00 0.00 0.00 3.72
93 94 4.442706 GGTAGGGATAGAATGTGTGTGTG 58.557 47.826 0.00 0.00 0.00 3.82
104 105 5.078715 TCAATATCTTGGGGGTAGGGATAGA 59.921 44.000 0.00 0.00 32.95 1.98
111 112 5.825593 TTAGCTCAATATCTTGGGGGTAG 57.174 43.478 0.00 0.00 33.12 3.18
141 143 8.156820 TCTTTGGTGACTTTATCAATCTCAAGA 58.843 33.333 0.00 0.00 39.72 3.02
142 144 8.233190 GTCTTTGGTGACTTTATCAATCTCAAG 58.767 37.037 0.00 0.00 39.72 3.02
153 155 5.587043 ACATTTGACGTCTTTGGTGACTTTA 59.413 36.000 17.92 0.00 35.00 1.85
161 163 2.504367 AGGGACATTTGACGTCTTTGG 58.496 47.619 17.92 6.71 33.73 3.28
162 164 3.058224 GGAAGGGACATTTGACGTCTTTG 60.058 47.826 17.92 13.33 33.73 2.77
168 170 1.165270 GTGGGAAGGGACATTTGACG 58.835 55.000 0.00 0.00 0.00 4.35
172 174 2.176798 TGTTCAGTGGGAAGGGACATTT 59.823 45.455 0.00 0.00 35.82 2.32
173 175 1.780309 TGTTCAGTGGGAAGGGACATT 59.220 47.619 0.00 0.00 35.82 2.71
176 178 2.304761 TGTATGTTCAGTGGGAAGGGAC 59.695 50.000 0.00 0.00 35.82 4.46
177 179 2.626785 TGTATGTTCAGTGGGAAGGGA 58.373 47.619 0.00 0.00 35.82 4.20
178 180 3.545703 GATGTATGTTCAGTGGGAAGGG 58.454 50.000 0.00 0.00 35.82 3.95
179 181 3.198068 CGATGTATGTTCAGTGGGAAGG 58.802 50.000 0.00 0.00 35.82 3.46
180 182 2.609459 GCGATGTATGTTCAGTGGGAAG 59.391 50.000 0.00 0.00 35.82 3.46
189 205 3.617263 AGACTTTTCGGCGATGTATGTTC 59.383 43.478 11.76 1.33 0.00 3.18
194 210 3.306917 TTCAGACTTTTCGGCGATGTA 57.693 42.857 11.76 0.00 0.00 2.29
199 215 9.318041 CATATATTTATTTCAGACTTTTCGGCG 57.682 33.333 0.00 0.00 0.00 6.46
252 277 1.150536 TGAAACAGCCCACCAGGAC 59.849 57.895 0.00 0.00 38.24 3.85
259 284 0.754957 CCTTGTGGTGAAACAGCCCA 60.755 55.000 0.00 0.00 39.98 5.36
278 303 2.284190 GTAGCTCAGATGGCAAGGTTC 58.716 52.381 0.00 0.00 0.00 3.62
296 321 0.031585 AAGTGTGCGAACTGAGCGTA 59.968 50.000 0.00 0.00 37.44 4.42
297 322 0.810031 AAAGTGTGCGAACTGAGCGT 60.810 50.000 0.00 0.00 37.44 5.07
298 323 0.304705 AAAAGTGTGCGAACTGAGCG 59.695 50.000 0.00 0.00 37.44 5.03
299 324 2.111756 CAAAAAGTGTGCGAACTGAGC 58.888 47.619 0.00 0.00 0.00 4.26
387 413 0.952010 CAAAATGCCAGCCCACTTGC 60.952 55.000 0.00 0.00 35.15 4.01
390 416 1.526575 CGTCAAAATGCCAGCCCACT 61.527 55.000 0.00 0.00 0.00 4.00
394 420 1.734117 GTGCGTCAAAATGCCAGCC 60.734 57.895 0.00 0.00 36.52 4.85
399 425 2.405892 AGTTCAGTGCGTCAAAATGC 57.594 45.000 0.00 0.00 37.95 3.56
416 442 7.833285 TTCTTTGGCAGTTCCTTTATTAAGT 57.167 32.000 0.00 0.00 35.26 2.24
467 515 8.076178 GTGTAATTACTGATTGTGTGAAGCTTT 58.924 33.333 16.33 0.00 0.00 3.51
470 518 6.898041 TGTGTAATTACTGATTGTGTGAAGC 58.102 36.000 16.33 0.00 0.00 3.86
700 1712 4.746309 TCTGCACCATGCTGCCCC 62.746 66.667 10.45 0.00 45.31 5.80
798 1822 2.031163 GGTGGCAGCACGAAGACT 59.969 61.111 12.58 0.00 0.00 3.24
821 1845 4.389576 CTTGCACTTGCCGCGTCC 62.390 66.667 4.92 0.00 41.18 4.79
836 1860 3.446570 GCTTGCATGCTCCGGCTT 61.447 61.111 20.33 0.00 39.59 4.35
840 1864 2.689785 TTTCCGCTTGCATGCTCCG 61.690 57.895 20.33 17.17 0.00 4.63
935 1959 3.880490 AGTGAACTGAACGTTGGCATTTA 59.120 39.130 5.00 0.00 35.56 1.40
941 1965 4.569162 TGAAACTAGTGAACTGAACGTTGG 59.431 41.667 5.00 0.23 35.56 3.77
1135 2159 1.478916 CATGATGTGCTTGCCATTGGA 59.521 47.619 6.95 0.00 0.00 3.53
1230 2254 4.101585 ACAAGATGGAGAGAAACACAGTCA 59.898 41.667 0.00 0.00 0.00 3.41
1272 2302 1.529010 CACCTTCACAGCCTTGGCA 60.529 57.895 14.54 0.00 0.00 4.92
1279 2309 2.946762 GAACCGCACCTTCACAGC 59.053 61.111 0.00 0.00 0.00 4.40
1375 2405 5.152623 TCGAAGCCCCTAATAGAATCATG 57.847 43.478 0.00 0.00 0.00 3.07
1553 5665 5.408909 GCACCTACCTTAGTTTCAAAGAGAC 59.591 44.000 0.00 0.00 0.00 3.36
1678 5790 4.643387 ACACGTTGCAGCCCCCTC 62.643 66.667 0.00 0.00 0.00 4.30
1738 5856 6.940739 AGTCTGTGTAGATGAAACTAAGCAT 58.059 36.000 0.00 0.00 34.94 3.79
1986 6179 4.539726 TCAAGCATGCCTCCTTCAAATAT 58.460 39.130 15.66 0.00 0.00 1.28
1987 6180 3.966979 TCAAGCATGCCTCCTTCAAATA 58.033 40.909 15.66 0.00 0.00 1.40
2147 6343 7.556635 CGGTCTCAGGAACCTCATATATACATA 59.443 40.741 0.00 0.00 0.00 2.29
2148 6344 6.378564 CGGTCTCAGGAACCTCATATATACAT 59.621 42.308 0.00 0.00 0.00 2.29
2156 6352 2.035632 GATCGGTCTCAGGAACCTCAT 58.964 52.381 0.00 0.00 0.00 2.90
2166 6362 2.555325 ACACAAACTACGATCGGTCTCA 59.445 45.455 20.98 0.00 0.00 3.27
2174 6370 7.493320 TCAAAAGTAAGACACACAAACTACGAT 59.507 33.333 0.00 0.00 0.00 3.73
2247 6500 5.239963 CAGTGTGGCAATGCAGATCAATATA 59.760 40.000 7.79 0.00 0.00 0.86
2280 6533 9.880157 AATAAAAGTATAAAACGACTGCTAGGA 57.120 29.630 0.00 0.00 0.00 2.94
2334 6587 8.767085 CAAAATGAATGAATGCACACTTAAAGT 58.233 29.630 0.00 0.00 0.00 2.66
2335 6588 7.742963 GCAAAATGAATGAATGCACACTTAAAG 59.257 33.333 0.00 0.00 37.00 1.85
2336 6589 7.441760 AGCAAAATGAATGAATGCACACTTAAA 59.558 29.630 0.00 0.00 39.42 1.52
2337 6590 6.930164 AGCAAAATGAATGAATGCACACTTAA 59.070 30.769 0.00 0.00 39.42 1.85
2338 6591 6.457355 AGCAAAATGAATGAATGCACACTTA 58.543 32.000 0.00 0.00 39.42 2.24
2339 6592 5.302360 AGCAAAATGAATGAATGCACACTT 58.698 33.333 0.00 0.00 39.42 3.16
2340 6593 4.890088 AGCAAAATGAATGAATGCACACT 58.110 34.783 0.00 0.00 39.42 3.55
2341 6594 5.600908 AAGCAAAATGAATGAATGCACAC 57.399 34.783 0.00 0.00 39.42 3.82
2342 6595 4.386350 CGAAGCAAAATGAATGAATGCACA 59.614 37.500 0.00 0.00 39.42 4.57
2343 6596 4.386652 ACGAAGCAAAATGAATGAATGCAC 59.613 37.500 0.00 0.00 39.42 4.57
2344 6597 4.558178 ACGAAGCAAAATGAATGAATGCA 58.442 34.783 0.00 0.00 39.42 3.96
2345 6598 6.254157 ACATACGAAGCAAAATGAATGAATGC 59.746 34.615 0.00 0.00 37.28 3.56
2346 6599 7.745022 ACATACGAAGCAAAATGAATGAATG 57.255 32.000 0.00 0.00 0.00 2.67
2347 6600 8.677300 ACTACATACGAAGCAAAATGAATGAAT 58.323 29.630 0.00 0.00 0.00 2.57
2348 6601 8.039603 ACTACATACGAAGCAAAATGAATGAA 57.960 30.769 0.00 0.00 0.00 2.57
2349 6602 7.201609 GGACTACATACGAAGCAAAATGAATGA 60.202 37.037 0.00 0.00 0.00 2.57
2350 6603 6.907212 GGACTACATACGAAGCAAAATGAATG 59.093 38.462 0.00 0.00 0.00 2.67
2351 6604 6.597672 TGGACTACATACGAAGCAAAATGAAT 59.402 34.615 0.00 0.00 0.00 2.57
2352 6605 5.935206 TGGACTACATACGAAGCAAAATGAA 59.065 36.000 0.00 0.00 0.00 2.57
2353 6606 5.350365 GTGGACTACATACGAAGCAAAATGA 59.650 40.000 0.00 0.00 0.00 2.57
2354 6607 5.447279 GGTGGACTACATACGAAGCAAAATG 60.447 44.000 0.00 0.00 0.00 2.32
2355 6608 4.634443 GGTGGACTACATACGAAGCAAAAT 59.366 41.667 0.00 0.00 0.00 1.82
2356 6609 3.998341 GGTGGACTACATACGAAGCAAAA 59.002 43.478 0.00 0.00 0.00 2.44
2357 6610 3.259876 AGGTGGACTACATACGAAGCAAA 59.740 43.478 0.00 0.00 0.00 3.68
2358 6611 2.829720 AGGTGGACTACATACGAAGCAA 59.170 45.455 0.00 0.00 0.00 3.91
2359 6612 2.453521 AGGTGGACTACATACGAAGCA 58.546 47.619 0.00 0.00 0.00 3.91
2360 6613 3.631227 ACTAGGTGGACTACATACGAAGC 59.369 47.826 0.00 0.00 0.00 3.86
2361 6614 4.880120 TCACTAGGTGGACTACATACGAAG 59.120 45.833 0.00 0.00 33.87 3.79
2362 6615 4.847198 TCACTAGGTGGACTACATACGAA 58.153 43.478 0.00 0.00 33.87 3.85
2363 6616 4.492494 TCACTAGGTGGACTACATACGA 57.508 45.455 0.00 0.00 33.87 3.43
2364 6617 5.571784 TTTCACTAGGTGGACTACATACG 57.428 43.478 0.00 0.00 33.87 3.06
2365 6618 7.285858 AGAGATTTCACTAGGTGGACTACATAC 59.714 40.741 0.00 0.00 33.87 2.39
2366 6619 7.355101 AGAGATTTCACTAGGTGGACTACATA 58.645 38.462 0.00 0.00 33.87 2.29
2367 6620 6.198639 AGAGATTTCACTAGGTGGACTACAT 58.801 40.000 0.00 0.00 33.87 2.29
2368 6621 5.580998 AGAGATTTCACTAGGTGGACTACA 58.419 41.667 0.00 0.00 33.87 2.74
2369 6622 6.602406 TGTAGAGATTTCACTAGGTGGACTAC 59.398 42.308 0.00 0.00 33.87 2.73
2370 6623 6.728411 TGTAGAGATTTCACTAGGTGGACTA 58.272 40.000 0.00 0.00 33.87 2.59
2371 6624 5.580998 TGTAGAGATTTCACTAGGTGGACT 58.419 41.667 0.00 0.00 33.87 3.85
2372 6625 5.916661 TGTAGAGATTTCACTAGGTGGAC 57.083 43.478 0.00 0.00 33.87 4.02
2373 6626 6.724441 TCTTTGTAGAGATTTCACTAGGTGGA 59.276 38.462 0.00 0.00 33.87 4.02
2374 6627 6.814146 GTCTTTGTAGAGATTTCACTAGGTGG 59.186 42.308 0.00 0.00 33.87 4.61
2375 6628 7.607250 AGTCTTTGTAGAGATTTCACTAGGTG 58.393 38.462 0.00 0.00 34.45 4.00
2376 6629 7.784470 AGTCTTTGTAGAGATTTCACTAGGT 57.216 36.000 0.00 0.00 0.00 3.08
2377 6630 9.575783 GTAAGTCTTTGTAGAGATTTCACTAGG 57.424 37.037 0.00 0.00 29.76 3.02
2392 6645 9.057089 CCTCTGTTCTTAAATGTAAGTCTTTGT 57.943 33.333 2.53 0.00 38.33 2.83
2393 6646 8.507249 CCCTCTGTTCTTAAATGTAAGTCTTTG 58.493 37.037 2.53 0.00 38.33 2.77
2394 6647 8.437575 TCCCTCTGTTCTTAAATGTAAGTCTTT 58.562 33.333 2.53 0.00 38.33 2.52
2395 6648 7.974504 TCCCTCTGTTCTTAAATGTAAGTCTT 58.025 34.615 2.53 0.00 38.33 3.01
2396 6649 7.235812 ACTCCCTCTGTTCTTAAATGTAAGTCT 59.764 37.037 2.53 0.00 38.33 3.24
2397 6650 7.387643 ACTCCCTCTGTTCTTAAATGTAAGTC 58.612 38.462 2.53 0.00 38.33 3.01
2398 6651 7.317722 ACTCCCTCTGTTCTTAAATGTAAGT 57.682 36.000 2.53 0.00 38.33 2.24
2402 6655 9.838339 CAATATACTCCCTCTGTTCTTAAATGT 57.162 33.333 0.00 0.00 0.00 2.71
2403 6656 8.778358 GCAATATACTCCCTCTGTTCTTAAATG 58.222 37.037 0.00 0.00 0.00 2.32
2404 6657 8.718656 AGCAATATACTCCCTCTGTTCTTAAAT 58.281 33.333 0.00 0.00 0.00 1.40
2405 6658 8.090788 AGCAATATACTCCCTCTGTTCTTAAA 57.909 34.615 0.00 0.00 0.00 1.52
2406 6659 7.470147 CGAGCAATATACTCCCTCTGTTCTTAA 60.470 40.741 0.00 0.00 0.00 1.85
2407 6660 6.016192 CGAGCAATATACTCCCTCTGTTCTTA 60.016 42.308 0.00 0.00 0.00 2.10
2408 6661 5.221342 CGAGCAATATACTCCCTCTGTTCTT 60.221 44.000 0.00 0.00 0.00 2.52
2409 6662 4.279671 CGAGCAATATACTCCCTCTGTTCT 59.720 45.833 0.00 0.00 0.00 3.01
2410 6663 4.551388 CGAGCAATATACTCCCTCTGTTC 58.449 47.826 0.00 0.00 0.00 3.18
2411 6664 3.322254 CCGAGCAATATACTCCCTCTGTT 59.678 47.826 0.00 0.00 0.00 3.16
2412 6665 2.894126 CCGAGCAATATACTCCCTCTGT 59.106 50.000 0.00 0.00 0.00 3.41
2413 6666 2.353208 GCCGAGCAATATACTCCCTCTG 60.353 54.545 0.00 0.00 0.00 3.35
2414 6667 1.896465 GCCGAGCAATATACTCCCTCT 59.104 52.381 0.00 0.00 0.00 3.69
2415 6668 1.402984 CGCCGAGCAATATACTCCCTC 60.403 57.143 0.00 0.00 0.00 4.30
2416 6669 0.603569 CGCCGAGCAATATACTCCCT 59.396 55.000 0.00 0.00 0.00 4.20
2417 6670 3.123674 CGCCGAGCAATATACTCCC 57.876 57.895 0.00 0.00 0.00 4.30
2451 6704 2.559668 CACACATCACCAAAGGATTGCT 59.440 45.455 0.00 0.00 35.10 3.91
2452 6705 2.927871 GCACACATCACCAAAGGATTGC 60.928 50.000 0.00 0.00 35.10 3.56
2454 6707 1.895131 GGCACACATCACCAAAGGATT 59.105 47.619 0.00 0.00 0.00 3.01
2455 6708 1.203038 TGGCACACATCACCAAAGGAT 60.203 47.619 0.00 0.00 0.00 3.24
2478 6865 2.358737 GCACGACACCTCCCCTTG 60.359 66.667 0.00 0.00 0.00 3.61
2712 7119 1.935799 TGGCCAACCAAAGCATACAT 58.064 45.000 0.61 0.00 45.37 2.29
2931 7342 2.787473 TCCAACATCGCTTTGGATCT 57.213 45.000 7.81 0.00 46.23 2.75
2980 7391 3.339253 TCAGGACATGATGGTCAAGTG 57.661 47.619 0.00 0.00 39.59 3.16
3106 7517 3.882888 TGTCCATCACAAAGGTTGAGAAC 59.117 43.478 0.00 0.00 34.05 3.01


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

AutoCloner maintained by Alex Coulton.