Multiple sequence alignment - TraesCS2B01G490900

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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 TraesCS2B01G490900 chr2B 100.000 4607 0 0 1 4607 688459100 688463706 0.000000e+00 8508.0
1 TraesCS2B01G490900 chr2B 92.697 1520 72 18 2503 4008 689105252 689106746 0.000000e+00 2156.0
2 TraesCS2B01G490900 chr2B 92.775 692 34 3 3305 3988 689310781 689311464 0.000000e+00 987.0
3 TraesCS2B01G490900 chr2B 88.684 433 26 7 2091 2501 689104576 689105007 1.480000e-139 507.0
4 TraesCS2B01G490900 chr2B 91.420 338 22 5 1314 1649 689089160 689089492 1.510000e-124 457.0
5 TraesCS2B01G490900 chr2B 86.624 314 27 6 1663 1963 689104272 689104583 2.660000e-87 333.0
6 TraesCS2B01G490900 chr2B 88.142 253 22 6 4083 4330 689120173 689120422 1.250000e-75 294.0
7 TraesCS2B01G490900 chr2A 87.322 2311 136 67 310 2522 711976509 711978760 0.000000e+00 2499.0
8 TraesCS2B01G490900 chr2A 93.606 1517 60 13 2520 4008 711978839 711980346 0.000000e+00 2230.0
9 TraesCS2B01G490900 chr2A 83.015 524 72 10 4087 4607 333732696 333732187 4.200000e-125 459.0
10 TraesCS2B01G490900 chr2A 82.927 410 61 9 4201 4605 769061629 769061224 1.220000e-95 361.0
11 TraesCS2B01G490900 chr2A 87.197 289 27 8 2 289 711976176 711976455 2.070000e-83 320.0
12 TraesCS2B01G490900 chr2A 79.391 427 72 9 4190 4602 49764468 49764044 2.100000e-73 287.0
13 TraesCS2B01G490900 chr2D 93.758 1634 70 12 2277 3899 572788506 572790118 0.000000e+00 2423.0
14 TraesCS2B01G490900 chr2D 90.364 1702 84 26 649 2276 572786785 572788480 0.000000e+00 2161.0
15 TraesCS2B01G490900 chr2D 82.562 562 77 14 4050 4607 284574058 284574602 4.170000e-130 475.0
16 TraesCS2B01G490900 chr2D 93.312 314 13 5 4068 4374 572791343 572791655 1.510000e-124 457.0
17 TraesCS2B01G490900 chr2D 93.644 236 14 1 4372 4607 572808169 572808403 7.330000e-93 351.0
18 TraesCS2B01G490900 chr2D 90.041 241 18 5 2 240 572786216 572786452 1.610000e-79 307.0
19 TraesCS2B01G490900 chr2D 93.077 130 2 4 3897 4019 572791213 572791342 2.830000e-42 183.0
20 TraesCS2B01G490900 chr2D 79.032 124 16 9 4050 4166 75376036 75375916 4.940000e-10 76.8
21 TraesCS2B01G490900 chr5D 85.211 568 71 11 4051 4607 356334223 356334788 5.170000e-159 571.0
22 TraesCS2B01G490900 chr5D 82.446 507 83 5 4105 4607 291930993 291930489 5.470000e-119 438.0
23 TraesCS2B01G490900 chr5A 82.914 556 76 17 4053 4599 457922141 457922686 2.490000e-132 483.0
24 TraesCS2B01G490900 chrUn 80.928 388 65 7 4197 4579 48828011 48828394 9.690000e-77 298.0
25 TraesCS2B01G490900 chr6B 78.534 382 74 7 4231 4607 153353959 153353581 1.280000e-60 244.0
26 TraesCS2B01G490900 chr6B 100.000 30 0 0 3979 4008 437845761 437845790 6.440000e-04 56.5
27 TraesCS2B01G490900 chr4A 87.736 106 10 3 4050 4154 57517807 57517910 2.250000e-23 121.0
28 TraesCS2B01G490900 chr4A 95.000 40 1 1 3976 4015 57517789 57517827 1.380000e-05 62.1
29 TraesCS2B01G490900 chr4B 81.818 110 14 6 4049 4153 122857348 122857456 2.280000e-13 87.9
30 TraesCS2B01G490900 chr4D 97.059 34 0 1 3977 4010 9338713 9338745 6.440000e-04 56.5
31 TraesCS2B01G490900 chr5B 100.000 28 0 0 3979 4006 16529263 16529236 8.000000e-03 52.8
32 TraesCS2B01G490900 chr5B 100.000 28 0 0 3979 4006 16572863 16572836 8.000000e-03 52.8
33 TraesCS2B01G490900 chr5B 100.000 28 0 0 3979 4006 16611434 16611407 8.000000e-03 52.8
34 TraesCS2B01G490900 chr5B 100.000 28 0 0 3979 4006 16643810 16643783 8.000000e-03 52.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G490900 chr2B 688459100 688463706 4606 False 8508.000000 8508 100.0000 1 4607 1 chr2B.!!$F1 4606
1 TraesCS2B01G490900 chr2B 689104272 689106746 2474 False 998.666667 2156 89.3350 1663 4008 3 chr2B.!!$F5 2345
2 TraesCS2B01G490900 chr2B 689310781 689311464 683 False 987.000000 987 92.7750 3305 3988 1 chr2B.!!$F4 683
3 TraesCS2B01G490900 chr2A 711976176 711980346 4170 False 1683.000000 2499 89.3750 2 4008 3 chr2A.!!$F1 4006
4 TraesCS2B01G490900 chr2A 333732187 333732696 509 True 459.000000 459 83.0150 4087 4607 1 chr2A.!!$R2 520
5 TraesCS2B01G490900 chr2D 572786216 572791655 5439 False 1106.200000 2423 92.1104 2 4374 5 chr2D.!!$F3 4372
6 TraesCS2B01G490900 chr2D 284574058 284574602 544 False 475.000000 475 82.5620 4050 4607 1 chr2D.!!$F1 557
7 TraesCS2B01G490900 chr5D 356334223 356334788 565 False 571.000000 571 85.2110 4051 4607 1 chr5D.!!$F1 556
8 TraesCS2B01G490900 chr5D 291930489 291930993 504 True 438.000000 438 82.4460 4105 4607 1 chr5D.!!$R1 502
9 TraesCS2B01G490900 chr5A 457922141 457922686 545 False 483.000000 483 82.9140 4053 4599 1 chr5A.!!$F1 546

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
387 430 0.107361 GCGGGTTAGGTATGTTGCCT 60.107 55.0 0.0 0.0 40.0 4.75 F
754 820 0.250553 GTCACCATCCACCACCGAAA 60.251 55.0 0.0 0.0 0.0 3.46 F
990 1095 0.914417 CCCACCACCACTCCTACCAT 60.914 60.0 0.0 0.0 0.0 3.55 F
2415 2613 0.748005 CGATTGCGGGGGAAGTGATT 60.748 55.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2030 2194 0.179103 AAGCAAGCAAGCACCACAAC 60.179 50.000 3.19 0.0 36.85 3.32 R
2396 2594 0.748005 AATCACTTCCCCCGCAATCG 60.748 55.000 0.00 0.0 0.00 3.34 R
2898 3462 3.042887 GCGTTTAAGCAAAAGTCACCAG 58.957 45.455 0.00 0.0 37.05 4.00 R
3702 4271 0.038251 CGACAGAGGTTACAGCTGCA 60.038 55.000 15.27 0.0 33.03 4.41 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
40 41 6.115448 AGTGAGGTACTTGCAGAATTTACT 57.885 37.500 0.00 0.00 41.55 2.24
142 144 6.183360 CCTGTGAATACCTATATAGAGACGCC 60.183 46.154 11.53 0.00 0.00 5.68
168 171 1.270465 GCCTGGCATTTTTGAAGCAGT 60.270 47.619 15.17 0.00 0.00 4.40
190 193 3.131400 TGTTTTGTTCTGGTTGTAAGCCC 59.869 43.478 0.00 0.00 0.00 5.19
192 195 0.847373 TGTTCTGGTTGTAAGCCCCA 59.153 50.000 0.00 0.00 0.00 4.96
196 199 1.776710 TGGTTGTAAGCCCCACCCT 60.777 57.895 0.00 0.00 0.00 4.34
197 200 1.365105 TGGTTGTAAGCCCCACCCTT 61.365 55.000 0.00 0.00 0.00 3.95
198 201 0.898326 GGTTGTAAGCCCCACCCTTG 60.898 60.000 0.00 0.00 0.00 3.61
199 202 1.228737 TTGTAAGCCCCACCCTTGC 60.229 57.895 0.00 0.00 0.00 4.01
200 203 2.362503 GTAAGCCCCACCCTTGCC 60.363 66.667 0.00 0.00 0.00 4.52
201 204 2.534272 TAAGCCCCACCCTTGCCT 60.534 61.111 0.00 0.00 0.00 4.75
204 207 3.015145 GCCCCACCCTTGCCTCTA 61.015 66.667 0.00 0.00 0.00 2.43
206 209 1.306997 CCCCACCCTTGCCTCTAGA 60.307 63.158 0.00 0.00 0.00 2.43
207 210 0.914417 CCCCACCCTTGCCTCTAGAA 60.914 60.000 0.00 0.00 0.00 2.10
208 211 0.991920 CCCACCCTTGCCTCTAGAAA 59.008 55.000 0.00 0.00 0.00 2.52
209 212 1.354368 CCCACCCTTGCCTCTAGAAAA 59.646 52.381 0.00 0.00 0.00 2.29
240 243 5.728637 TTCTTGAACTGCTAGATCTGACA 57.271 39.130 5.18 2.26 0.00 3.58
242 245 6.291648 TCTTGAACTGCTAGATCTGACAAT 57.708 37.500 5.18 0.00 0.00 2.71
243 246 6.705302 TCTTGAACTGCTAGATCTGACAATT 58.295 36.000 5.18 0.00 0.00 2.32
244 247 6.592994 TCTTGAACTGCTAGATCTGACAATTG 59.407 38.462 5.18 3.24 0.00 2.32
247 250 6.592994 TGAACTGCTAGATCTGACAATTGAAG 59.407 38.462 13.59 9.36 0.00 3.02
248 251 4.874966 ACTGCTAGATCTGACAATTGAAGC 59.125 41.667 13.59 3.35 0.00 3.86
249 252 4.194640 TGCTAGATCTGACAATTGAAGCC 58.805 43.478 13.59 5.07 0.00 4.35
250 253 4.080695 TGCTAGATCTGACAATTGAAGCCT 60.081 41.667 13.59 11.19 0.00 4.58
251 254 5.129320 TGCTAGATCTGACAATTGAAGCCTA 59.871 40.000 13.59 11.63 0.00 3.93
252 255 5.695816 GCTAGATCTGACAATTGAAGCCTAG 59.304 44.000 13.59 18.86 0.00 3.02
253 256 5.690464 AGATCTGACAATTGAAGCCTAGT 57.310 39.130 13.59 0.00 0.00 2.57
254 257 6.798427 AGATCTGACAATTGAAGCCTAGTA 57.202 37.500 13.59 0.00 0.00 1.82
258 261 7.476540 TCTGACAATTGAAGCCTAGTAAGTA 57.523 36.000 13.59 0.00 0.00 2.24
261 264 7.446769 TGACAATTGAAGCCTAGTAAGTACAA 58.553 34.615 13.59 0.00 0.00 2.41
266 269 6.737254 TGAAGCCTAGTAAGTACAATTTGC 57.263 37.500 0.00 0.00 0.00 3.68
274 277 8.303876 CCTAGTAAGTACAATTTGCAATGGTTT 58.696 33.333 0.00 0.00 0.00 3.27
275 278 9.341899 CTAGTAAGTACAATTTGCAATGGTTTC 57.658 33.333 0.00 0.00 0.00 2.78
305 331 5.809001 TGATGGTGAAGAATCTGTAGCTTT 58.191 37.500 0.00 0.00 0.00 3.51
307 333 4.326826 TGGTGAAGAATCTGTAGCTTTGG 58.673 43.478 0.00 0.00 0.00 3.28
323 362 3.677424 GCTTTGGTTGCTGGTGTGTTTTA 60.677 43.478 0.00 0.00 0.00 1.52
335 374 3.746492 GGTGTGTTTTAGCTTCGTGATCT 59.254 43.478 0.00 0.00 0.00 2.75
352 395 1.511850 TCTCATGTCAAGTGGTTGCG 58.488 50.000 0.00 0.00 33.23 4.85
369 412 6.020678 GTGGTTGCGAGAATATTGTTATTTGC 60.021 38.462 0.00 0.00 0.00 3.68
384 427 5.124138 TGTTATTTGCGGGTTAGGTATGTTG 59.876 40.000 0.00 0.00 0.00 3.33
385 428 1.455248 TTGCGGGTTAGGTATGTTGC 58.545 50.000 0.00 0.00 0.00 4.17
386 429 0.393267 TGCGGGTTAGGTATGTTGCC 60.393 55.000 0.00 0.00 0.00 4.52
387 430 0.107361 GCGGGTTAGGTATGTTGCCT 60.107 55.000 0.00 0.00 40.00 4.75
389 432 2.420408 GCGGGTTAGGTATGTTGCCTAA 60.420 50.000 0.60 0.60 43.88 2.69
390 433 3.876341 CGGGTTAGGTATGTTGCCTAAA 58.124 45.455 5.78 0.00 46.46 1.85
391 434 3.875134 CGGGTTAGGTATGTTGCCTAAAG 59.125 47.826 5.78 0.00 46.46 1.85
392 435 4.383335 CGGGTTAGGTATGTTGCCTAAAGA 60.383 45.833 5.78 0.00 46.46 2.52
393 436 5.503002 GGGTTAGGTATGTTGCCTAAAGAA 58.497 41.667 5.78 0.00 46.46 2.52
394 437 5.947566 GGGTTAGGTATGTTGCCTAAAGAAA 59.052 40.000 5.78 0.00 46.46 2.52
395 438 6.605995 GGGTTAGGTATGTTGCCTAAAGAAAT 59.394 38.462 5.78 0.00 46.46 2.17
396 439 7.416326 GGGTTAGGTATGTTGCCTAAAGAAATG 60.416 40.741 5.78 0.00 46.46 2.32
397 440 7.416326 GGTTAGGTATGTTGCCTAAAGAAATGG 60.416 40.741 5.78 0.00 46.46 3.16
398 441 4.402474 AGGTATGTTGCCTAAAGAAATGGC 59.598 41.667 0.00 0.00 46.26 4.40
479 522 7.373617 TGCCATCCTTCTATGTTTGTCTATA 57.626 36.000 0.00 0.00 0.00 1.31
480 523 7.445121 TGCCATCCTTCTATGTTTGTCTATAG 58.555 38.462 0.00 0.00 0.00 1.31
481 524 7.071196 TGCCATCCTTCTATGTTTGTCTATAGT 59.929 37.037 0.00 0.00 0.00 2.12
482 525 7.934120 GCCATCCTTCTATGTTTGTCTATAGTT 59.066 37.037 0.00 0.00 0.00 2.24
508 551 1.123077 TCTTGGATGCCGTATCTGCT 58.877 50.000 0.00 0.00 36.03 4.24
511 554 0.815213 TGGATGCCGTATCTGCTTGC 60.815 55.000 0.00 0.00 36.03 4.01
607 650 2.356665 TTTGTTAGCCTCTGTGCCAA 57.643 45.000 0.00 0.00 0.00 4.52
608 651 1.896220 TTGTTAGCCTCTGTGCCAAG 58.104 50.000 0.00 0.00 0.00 3.61
612 655 2.623416 GTTAGCCTCTGTGCCAAGTTTT 59.377 45.455 0.00 0.00 0.00 2.43
613 656 1.035139 AGCCTCTGTGCCAAGTTTTG 58.965 50.000 0.00 0.00 0.00 2.44
618 661 1.203523 TCTGTGCCAAGTTTTGCGTTT 59.796 42.857 0.00 0.00 0.00 3.60
625 668 3.668656 GCCAAGTTTTGCGTTTAGATCAC 59.331 43.478 0.00 0.00 0.00 3.06
630 673 6.072112 AGTTTTGCGTTTAGATCACAATGT 57.928 33.333 0.00 0.00 0.00 2.71
631 674 6.503524 AGTTTTGCGTTTAGATCACAATGTT 58.496 32.000 0.00 0.00 0.00 2.71
751 817 2.434185 CGTCACCATCCACCACCG 60.434 66.667 0.00 0.00 0.00 4.94
754 820 0.250553 GTCACCATCCACCACCGAAA 60.251 55.000 0.00 0.00 0.00 3.46
835 912 3.064408 CACTGATCCATCATCACCAAACG 59.936 47.826 0.00 0.00 36.51 3.60
959 1054 7.256083 CCCTCAAAATCTCATCTTTTGTTTCCT 60.256 37.037 8.00 0.00 41.88 3.36
986 1081 2.124085 CCCCCACCACCACTCCTA 59.876 66.667 0.00 0.00 0.00 2.94
990 1095 0.914417 CCCACCACCACTCCTACCAT 60.914 60.000 0.00 0.00 0.00 3.55
991 1096 1.624113 CCCACCACCACTCCTACCATA 60.624 57.143 0.00 0.00 0.00 2.74
999 1104 1.047034 ACTCCTACCATACCGCCACC 61.047 60.000 0.00 0.00 0.00 4.61
1329 1434 1.403687 CCATCCCCTTCCTCGAGTCC 61.404 65.000 12.31 0.00 0.00 3.85
1590 1695 4.025858 GCCCTGCAGGTCAGCTGA 62.026 66.667 30.63 13.74 41.50 4.26
1699 1838 8.910351 ATTTCTAAGATTAGGGAATGCACTAC 57.090 34.615 0.00 0.00 27.29 2.73
1701 1840 7.676683 TCTAAGATTAGGGAATGCACTACTT 57.323 36.000 0.00 0.00 27.29 2.24
1708 1853 2.619074 GGGAATGCACTACTTGGAGCTT 60.619 50.000 0.00 0.00 0.00 3.74
1716 1861 2.039084 ACTACTTGGAGCTTCAAGGGTG 59.961 50.000 33.20 24.32 46.04 4.61
1787 1939 8.613060 ACATTATGATGGAGTGTTGATACATC 57.387 34.615 0.00 0.00 37.60 3.06
1801 1953 3.617824 CATCGCGATTCGGTGGAG 58.382 61.111 21.14 1.05 45.16 3.86
1802 1954 1.226974 CATCGCGATTCGGTGGAGT 60.227 57.895 21.14 0.00 45.16 3.85
1811 1968 3.930229 CGATTCGGTGGAGTTCATTGTTA 59.070 43.478 0.00 0.00 0.00 2.41
1844 2001 8.853077 TGAGTTTCAATGTGATTAGTTCAGAT 57.147 30.769 0.00 0.00 39.90 2.90
1874 2033 2.567169 AGCTTTATTGGGGAAAAGGCAC 59.433 45.455 0.00 0.00 34.07 5.01
1889 2048 7.502561 GGGAAAAGGCACTAATAGTATCATTGT 59.497 37.037 0.00 0.00 38.49 2.71
1924 2083 9.522804 GTTTATGGTTTGTTGTTGATCTTGTAA 57.477 29.630 0.00 0.00 0.00 2.41
2025 2189 4.637534 GCTGCTTGGTGAGATTTCTTGATA 59.362 41.667 0.00 0.00 0.00 2.15
2030 2194 4.774124 TGGTGAGATTTCTTGATAGGCAG 58.226 43.478 0.00 0.00 0.00 4.85
2034 2198 5.645497 GTGAGATTTCTTGATAGGCAGTTGT 59.355 40.000 0.00 0.00 0.00 3.32
2063 2227 2.418609 GCTTGCTTGGTCAAGTTTTGGT 60.419 45.455 11.71 0.00 43.92 3.67
2070 2234 6.103330 GCTTGGTCAAGTTTTGGTTTCTTAA 58.897 36.000 11.71 0.00 40.45 1.85
2072 2236 7.042725 GCTTGGTCAAGTTTTGGTTTCTTAATC 60.043 37.037 11.71 0.00 40.45 1.75
2104 2268 6.999272 AGATGCAATGCTCTATCTGAATTCTT 59.001 34.615 6.82 0.00 0.00 2.52
2127 2291 3.901844 AGGTAGTAGTTGAGCAGGTTTGA 59.098 43.478 0.00 0.00 0.00 2.69
2156 2320 2.685106 TCTCAGTTGGTGGACTCTCT 57.315 50.000 0.00 0.00 0.00 3.10
2171 2335 6.152154 GTGGACTCTCTAGCTAAAGTTTCTCT 59.848 42.308 0.00 0.00 0.00 3.10
2271 2437 1.813513 CTCCTGCCAGTTTTCGTCAT 58.186 50.000 0.00 0.00 0.00 3.06
2300 2494 7.431376 CACTATGAAATTATGAAAGCAGTGCAG 59.569 37.037 19.20 2.09 0.00 4.41
2396 2594 8.175716 CCTTCACAACGTAGGATTTTTATTCTC 58.824 37.037 0.00 0.00 34.07 2.87
2415 2613 0.748005 CGATTGCGGGGGAAGTGATT 60.748 55.000 0.00 0.00 0.00 2.57
2464 2666 8.691797 ACTATTTGTGTGGTTTTGTTGAAGTAT 58.308 29.630 0.00 0.00 0.00 2.12
2469 2671 9.877178 TTGTGTGGTTTTGTTGAAGTATTAAAT 57.123 25.926 0.00 0.00 0.00 1.40
2510 2960 9.884636 CGATTATGTATATTTGATACTTCCCCA 57.115 33.333 0.00 0.00 0.00 4.96
2604 3135 1.673665 GCTGCACCAACTCTCCAGG 60.674 63.158 0.00 0.00 0.00 4.45
2745 3307 8.738645 ACTTCCAGTTTTCATATTATGACTCC 57.261 34.615 5.86 0.00 39.39 3.85
2759 3321 3.594603 TGACTCCGCTCCTTTCTTTAG 57.405 47.619 0.00 0.00 0.00 1.85
2898 3462 5.568620 AAGTGGGTCTATGGGATGTTATC 57.431 43.478 0.00 0.00 0.00 1.75
3339 3903 0.037303 TGAAGCAGCTCAAGGAAGGG 59.963 55.000 0.00 0.00 0.00 3.95
3349 3913 0.332632 CAAGGAAGGGCCCAAGATCA 59.667 55.000 27.56 0.00 37.37 2.92
3426 3990 2.355115 GGCACCGGGGAGAACATT 59.645 61.111 8.67 0.00 0.00 2.71
3630 4194 6.260936 AGGTTGTGTACAGAAGAGAAACAATG 59.739 38.462 5.55 0.00 0.00 2.82
3631 4195 6.430451 GTTGTGTACAGAAGAGAAACAATGG 58.570 40.000 5.55 0.00 0.00 3.16
3632 4196 5.924356 TGTGTACAGAAGAGAAACAATGGA 58.076 37.500 0.00 0.00 0.00 3.41
3633 4197 6.533730 TGTGTACAGAAGAGAAACAATGGAT 58.466 36.000 0.00 0.00 0.00 3.41
3674 4243 0.388649 TTTTCTCTCGCGACTCTGCC 60.389 55.000 3.71 0.00 0.00 4.85
3702 4271 1.228644 TTGTTCATGGCAGGCTGCT 60.229 52.632 35.73 17.41 44.28 4.24
3870 4457 1.373497 CGAGCTTTCGACCTGTGCT 60.373 57.895 0.00 0.00 36.63 4.40
3884 4472 2.354259 CTGTGCTCCTTTGAGATGTCC 58.646 52.381 0.00 0.00 41.42 4.02
4154 5850 7.498443 CCGAGTCCTAAATTTAGTGGAGTAAT 58.502 38.462 20.99 3.35 32.90 1.89
4379 6082 3.195610 ACGAAGTGCTATGGAGATGTCAA 59.804 43.478 0.00 0.00 42.51 3.18
4394 6097 4.398358 AGATGTCAATGATGCTCAACAAGG 59.602 41.667 0.00 0.00 0.00 3.61
4400 6103 1.814394 TGATGCTCAACAAGGTCATGC 59.186 47.619 0.00 0.00 0.00 4.06
4406 6109 1.171308 CAACAAGGTCATGCTGGAGG 58.829 55.000 0.00 0.00 0.00 4.30
4408 6111 1.656587 ACAAGGTCATGCTGGAGGTA 58.343 50.000 0.00 0.00 0.00 3.08
4416 6119 2.965831 TCATGCTGGAGGTAGGTATGAC 59.034 50.000 0.00 0.00 29.82 3.06
4451 6154 0.821517 TCCTCCGATGCGCTTTAAGA 59.178 50.000 9.73 0.00 0.00 2.10
4457 6160 2.223340 CCGATGCGCTTTAAGAAATGCT 60.223 45.455 9.73 0.00 34.46 3.79
4465 6168 4.800471 CGCTTTAAGAAATGCTTGAATCCC 59.200 41.667 0.00 0.00 37.42 3.85
4466 6169 5.393461 CGCTTTAAGAAATGCTTGAATCCCT 60.393 40.000 0.00 0.00 37.42 4.20
4486 6189 0.036732 TTTGGATCGTGCTCTGGCTT 59.963 50.000 0.00 0.00 39.59 4.35
4525 6231 5.657474 GGTGATGTACCGAATGTTCTTAGA 58.343 41.667 0.00 0.00 40.26 2.10
4547 6253 7.446001 AGACATTTCTTTCTCATCTTCAACC 57.554 36.000 0.00 0.00 0.00 3.77
4585 6291 7.634671 AGATGATGCAACAAGTCATGATTTA 57.365 32.000 0.00 0.00 33.03 1.40
4599 6305 7.633789 AGTCATGATTTACCATAGAACCTTGT 58.366 34.615 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 4.942363 AGTACCTCACTACTTAGACCCA 57.058 45.455 0.00 0.00 34.98 4.51
40 41 0.181587 TGTGGGCGAAAAAGGTCTCA 59.818 50.000 0.00 0.00 0.00 3.27
69 70 1.292992 AAAACGGGTGACAACGTCTC 58.707 50.000 5.11 0.00 43.31 3.36
142 144 0.454957 CAAAAATGCCAGGCGACGAG 60.455 55.000 7.03 0.00 0.00 4.18
168 171 3.131400 GGGCTTACAACCAGAACAAAACA 59.869 43.478 0.00 0.00 0.00 2.83
190 193 2.619074 CCTTTTCTAGAGGCAAGGGTGG 60.619 54.545 15.24 0.00 33.37 4.61
199 202 4.268359 AGAAAGCATGCCTTTTCTAGAGG 58.732 43.478 25.34 0.00 43.64 3.69
200 203 5.413833 TCAAGAAAGCATGCCTTTTCTAGAG 59.586 40.000 26.26 20.37 43.64 2.43
201 204 5.316167 TCAAGAAAGCATGCCTTTTCTAGA 58.684 37.500 26.26 14.58 43.64 2.43
203 206 5.536161 AGTTCAAGAAAGCATGCCTTTTCTA 59.464 36.000 26.26 14.68 43.64 2.10
204 207 4.343239 AGTTCAAGAAAGCATGCCTTTTCT 59.657 37.500 22.57 22.57 43.64 2.52
206 209 4.374399 CAGTTCAAGAAAGCATGCCTTTT 58.626 39.130 15.66 9.54 43.64 2.27
207 210 3.801293 GCAGTTCAAGAAAGCATGCCTTT 60.801 43.478 15.66 13.95 46.19 3.11
208 211 2.288640 GCAGTTCAAGAAAGCATGCCTT 60.289 45.455 15.66 7.90 34.51 4.35
209 212 1.271656 GCAGTTCAAGAAAGCATGCCT 59.728 47.619 15.66 0.00 0.00 4.75
240 243 8.244113 GCAAATTGTACTTACTAGGCTTCAATT 58.756 33.333 0.00 1.59 36.34 2.32
242 245 6.712998 TGCAAATTGTACTTACTAGGCTTCAA 59.287 34.615 0.00 0.00 0.00 2.69
243 246 6.234920 TGCAAATTGTACTTACTAGGCTTCA 58.765 36.000 0.00 0.00 0.00 3.02
244 247 6.737254 TGCAAATTGTACTTACTAGGCTTC 57.263 37.500 0.00 0.00 0.00 3.86
247 250 6.127730 ACCATTGCAAATTGTACTTACTAGGC 60.128 38.462 1.71 0.00 0.00 3.93
248 251 7.391148 ACCATTGCAAATTGTACTTACTAGG 57.609 36.000 1.71 0.00 0.00 3.02
249 252 9.341899 GAAACCATTGCAAATTGTACTTACTAG 57.658 33.333 1.71 0.00 0.00 2.57
250 253 9.073475 AGAAACCATTGCAAATTGTACTTACTA 57.927 29.630 1.71 0.00 0.00 1.82
251 254 7.951591 AGAAACCATTGCAAATTGTACTTACT 58.048 30.769 1.71 0.00 0.00 2.24
252 255 7.060633 CGAGAAACCATTGCAAATTGTACTTAC 59.939 37.037 1.71 0.00 0.00 2.34
253 256 7.081349 CGAGAAACCATTGCAAATTGTACTTA 58.919 34.615 1.71 0.00 0.00 2.24
254 257 5.920273 CGAGAAACCATTGCAAATTGTACTT 59.080 36.000 1.71 0.00 0.00 2.24
258 261 3.069443 ACCGAGAAACCATTGCAAATTGT 59.931 39.130 1.71 0.00 0.00 2.71
261 264 4.057432 CAAACCGAGAAACCATTGCAAAT 58.943 39.130 1.71 0.00 0.00 2.32
266 269 3.255642 ACCATCAAACCGAGAAACCATTG 59.744 43.478 0.00 0.00 0.00 2.82
274 277 3.762407 TTCTTCACCATCAAACCGAGA 57.238 42.857 0.00 0.00 0.00 4.04
275 278 4.093998 CAGATTCTTCACCATCAAACCGAG 59.906 45.833 0.00 0.00 0.00 4.63
305 331 1.407258 GCTAAAACACACCAGCAACCA 59.593 47.619 0.00 0.00 34.13 3.67
307 333 3.372060 GAAGCTAAAACACACCAGCAAC 58.628 45.455 0.00 0.00 36.47 4.17
323 362 3.056250 ACTTGACATGAGATCACGAAGCT 60.056 43.478 0.00 0.00 0.00 3.74
335 374 1.069978 TCTCGCAACCACTTGACATGA 59.930 47.619 0.00 0.00 0.00 3.07
352 395 7.012989 ACCTAACCCGCAAATAACAATATTCTC 59.987 37.037 0.00 0.00 31.28 2.87
369 412 3.547054 TTAGGCAACATACCTAACCCG 57.453 47.619 0.00 0.00 43.31 5.28
385 428 3.690460 AGAGGTGTGCCATTTCTTTAGG 58.310 45.455 0.00 0.00 37.19 2.69
386 429 4.583871 AGAGAGGTGTGCCATTTCTTTAG 58.416 43.478 0.00 0.00 37.19 1.85
387 430 4.287067 AGAGAGAGGTGTGCCATTTCTTTA 59.713 41.667 0.00 0.00 37.19 1.85
389 432 2.641815 AGAGAGAGGTGTGCCATTTCTT 59.358 45.455 0.00 0.00 37.19 2.52
390 433 2.027377 CAGAGAGAGGTGTGCCATTTCT 60.027 50.000 0.00 0.00 37.19 2.52
391 434 2.354259 CAGAGAGAGGTGTGCCATTTC 58.646 52.381 0.00 0.00 37.19 2.17
392 435 1.612726 GCAGAGAGAGGTGTGCCATTT 60.613 52.381 0.00 0.00 37.19 2.32
393 436 0.035630 GCAGAGAGAGGTGTGCCATT 60.036 55.000 0.00 0.00 37.19 3.16
394 437 1.196766 TGCAGAGAGAGGTGTGCCAT 61.197 55.000 0.00 0.00 35.88 4.40
395 438 1.824224 CTGCAGAGAGAGGTGTGCCA 61.824 60.000 8.42 0.00 35.88 4.92
396 439 1.079266 CTGCAGAGAGAGGTGTGCC 60.079 63.158 8.42 0.00 35.88 5.01
397 440 1.741032 GCTGCAGAGAGAGGTGTGC 60.741 63.158 20.43 0.00 37.24 4.57
398 441 0.390078 CAGCTGCAGAGAGAGGTGTG 60.390 60.000 20.43 0.00 33.83 3.82
399 442 1.973760 CAGCTGCAGAGAGAGGTGT 59.026 57.895 20.43 0.00 33.83 4.16
400 443 1.448189 GCAGCTGCAGAGAGAGGTG 60.448 63.158 33.36 7.08 41.59 4.00
479 522 3.055094 ACGGCATCCAAGACTGATTAACT 60.055 43.478 0.00 0.00 0.00 2.24
480 523 3.270877 ACGGCATCCAAGACTGATTAAC 58.729 45.455 0.00 0.00 0.00 2.01
481 524 3.627395 ACGGCATCCAAGACTGATTAA 57.373 42.857 0.00 0.00 0.00 1.40
482 525 4.588951 AGATACGGCATCCAAGACTGATTA 59.411 41.667 0.00 0.00 33.75 1.75
483 526 3.389329 AGATACGGCATCCAAGACTGATT 59.611 43.478 0.00 0.00 33.75 2.57
484 527 2.968574 AGATACGGCATCCAAGACTGAT 59.031 45.455 0.00 0.00 33.75 2.90
485 528 2.101415 CAGATACGGCATCCAAGACTGA 59.899 50.000 0.00 0.00 33.75 3.41
486 529 2.477825 CAGATACGGCATCCAAGACTG 58.522 52.381 0.00 0.00 33.75 3.51
508 551 2.594303 CAACAGCGGTGAGGGCAA 60.594 61.111 23.44 0.00 0.00 4.52
511 554 2.281761 AAGCAACAGCGGTGAGGG 60.282 61.111 23.44 10.83 0.00 4.30
588 631 2.229792 CTTGGCACAGAGGCTAACAAA 58.770 47.619 0.00 0.00 42.39 2.83
589 632 1.142870 ACTTGGCACAGAGGCTAACAA 59.857 47.619 0.00 0.00 42.39 2.83
591 634 1.897560 AACTTGGCACAGAGGCTAAC 58.102 50.000 0.00 0.00 42.39 2.34
592 635 2.622942 CAAAACTTGGCACAGAGGCTAA 59.377 45.455 0.00 0.00 42.39 3.09
593 636 2.229792 CAAAACTTGGCACAGAGGCTA 58.770 47.619 0.00 0.00 42.39 3.93
594 637 1.035139 CAAAACTTGGCACAGAGGCT 58.965 50.000 0.00 0.00 42.39 4.58
595 638 0.598419 GCAAAACTTGGCACAGAGGC 60.598 55.000 0.00 0.00 42.39 4.70
596 639 0.318107 CGCAAAACTTGGCACAGAGG 60.318 55.000 0.00 0.00 42.39 3.69
599 642 1.639280 AAACGCAAAACTTGGCACAG 58.361 45.000 0.00 0.00 42.39 3.66
600 643 2.423892 TCTAAACGCAAAACTTGGCACA 59.576 40.909 0.00 0.00 0.00 4.57
601 644 3.073144 TCTAAACGCAAAACTTGGCAC 57.927 42.857 0.00 0.00 0.00 5.01
602 645 3.316588 TGATCTAAACGCAAAACTTGGCA 59.683 39.130 0.00 0.00 0.00 4.92
603 646 3.668656 GTGATCTAAACGCAAAACTTGGC 59.331 43.478 0.00 0.00 0.00 4.52
607 650 6.072112 ACATTGTGATCTAAACGCAAAACT 57.928 33.333 0.00 0.00 40.29 2.66
608 651 6.747659 AACATTGTGATCTAAACGCAAAAC 57.252 33.333 0.00 0.00 40.29 2.43
700 753 1.573829 GGCAAAGATTCGTGTGCGGA 61.574 55.000 0.00 0.00 37.89 5.54
751 817 2.094130 TGTTGGGTTTTTGTCCGGTTTC 60.094 45.455 0.00 0.00 0.00 2.78
754 820 1.558233 TTGTTGGGTTTTTGTCCGGT 58.442 45.000 0.00 0.00 0.00 5.28
860 938 1.306226 AAAGGGAGGGGACGAGGAG 60.306 63.158 0.00 0.00 0.00 3.69
861 939 1.612442 CAAAGGGAGGGGACGAGGA 60.612 63.158 0.00 0.00 0.00 3.71
862 940 2.990479 CAAAGGGAGGGGACGAGG 59.010 66.667 0.00 0.00 0.00 4.63
920 1015 3.966543 GAGGGGTGGTGGTGGTGG 61.967 72.222 0.00 0.00 0.00 4.61
921 1016 2.291402 TTTGAGGGGTGGTGGTGGTG 62.291 60.000 0.00 0.00 0.00 4.17
922 1017 1.585651 TTTTGAGGGGTGGTGGTGGT 61.586 55.000 0.00 0.00 0.00 4.16
959 1054 2.286121 GGTGGGGGAGTGGGATGA 60.286 66.667 0.00 0.00 0.00 2.92
986 1081 0.980754 TCTCATGGTGGCGGTATGGT 60.981 55.000 0.00 0.00 0.00 3.55
990 1095 2.731571 GCCTCTCATGGTGGCGGTA 61.732 63.158 10.26 0.00 43.37 4.02
991 1096 4.101448 GCCTCTCATGGTGGCGGT 62.101 66.667 10.26 0.00 43.37 5.68
1368 1473 2.606826 AAGACGGTGAGGGACCCC 60.607 66.667 7.00 1.17 42.62 4.95
1371 1476 1.292541 GGTGAAGACGGTGAGGGAC 59.707 63.158 0.00 0.00 0.00 4.46
1590 1695 1.003233 GAAGAGGGCAAGGAAGCGT 60.003 57.895 0.00 0.00 34.64 5.07
1638 1752 6.309389 CCAACCTTGGGAGTACTATTAACT 57.691 41.667 0.00 0.00 44.70 2.24
1681 1820 4.721776 TCCAAGTAGTGCATTCCCTAATCT 59.278 41.667 0.00 0.00 0.00 2.40
1696 1835 2.704572 CACCCTTGAAGCTCCAAGTAG 58.295 52.381 12.09 5.25 41.34 2.57
1699 1838 1.246737 GGCACCCTTGAAGCTCCAAG 61.247 60.000 5.58 5.58 42.28 3.61
1701 1840 1.792757 ATGGCACCCTTGAAGCTCCA 61.793 55.000 0.00 0.00 0.00 3.86
1708 1853 5.867903 CCATTTATTTATGGCACCCTTGA 57.132 39.130 0.00 0.00 38.75 3.02
1787 1939 0.806102 ATGAACTCCACCGAATCGCG 60.806 55.000 0.00 0.00 40.47 5.87
1798 1950 7.875971 ACTCAATTTCACTAACAATGAACTCC 58.124 34.615 0.00 0.00 35.82 3.85
1799 1951 9.736023 AAACTCAATTTCACTAACAATGAACTC 57.264 29.630 0.00 0.00 35.82 3.01
1800 1952 9.736023 GAAACTCAATTTCACTAACAATGAACT 57.264 29.630 0.00 0.00 45.32 3.01
1844 2001 9.936759 CTTTTCCCCAATAAAGCTAAATGTTAA 57.063 29.630 0.00 0.00 0.00 2.01
1860 2019 4.668138 ACTATTAGTGCCTTTTCCCCAA 57.332 40.909 0.00 0.00 0.00 4.12
1862 2021 5.937111 TGATACTATTAGTGCCTTTTCCCC 58.063 41.667 6.60 0.00 0.00 4.81
1889 2048 7.106439 ACAACAAACCATAAACTGACATCAA 57.894 32.000 0.00 0.00 0.00 2.57
1924 2083 4.142049 GCCATACTAGCTGAACTCAGTCTT 60.142 45.833 8.46 0.00 45.45 3.01
1954 2115 3.119602 CCATCTGCACACCATCAAAAGAG 60.120 47.826 0.00 0.00 0.00 2.85
1995 2159 2.977914 TCTCACCAAGCAGCAAGATAC 58.022 47.619 0.00 0.00 0.00 2.24
2025 2189 2.492773 GCAAGCACCACAACTGCCT 61.493 57.895 0.00 0.00 35.01 4.75
2030 2194 0.179103 AAGCAAGCAAGCACCACAAC 60.179 50.000 3.19 0.00 36.85 3.32
2034 2198 1.737355 GACCAAGCAAGCAAGCACCA 61.737 55.000 3.19 0.00 36.85 4.17
2063 2227 7.975616 GCATTGCATCTTGTAAGGATTAAGAAA 59.024 33.333 3.15 0.00 34.47 2.52
2070 2234 4.789807 AGAGCATTGCATCTTGTAAGGAT 58.210 39.130 11.91 0.00 0.00 3.24
2072 2236 5.996513 AGATAGAGCATTGCATCTTGTAAGG 59.003 40.000 11.91 0.00 0.00 2.69
2104 2268 5.081728 TCAAACCTGCTCAACTACTACCTA 58.918 41.667 0.00 0.00 0.00 3.08
2127 2291 3.947834 CCACCAACTGAGAAAAAGACACT 59.052 43.478 0.00 0.00 0.00 3.55
2156 2320 7.280356 AGTGAAACCAAGAGAAACTTTAGCTA 58.720 34.615 0.00 0.00 37.80 3.32
2171 2335 6.549364 ACTGGATTACATCAAAGTGAAACCAA 59.451 34.615 0.00 0.00 37.80 3.67
2271 2437 8.615211 CACTGCTTTCATAATTTCATAGTGCTA 58.385 33.333 0.00 0.00 0.00 3.49
2300 2494 4.507756 GCTGAAACTTGAATTGGGTTGTTC 59.492 41.667 0.00 0.00 0.00 3.18
2396 2594 0.748005 AATCACTTCCCCCGCAATCG 60.748 55.000 0.00 0.00 0.00 3.34
2415 2613 6.772716 AGTGCCAAGAAGTTCAGAATAGAAAA 59.227 34.615 5.50 0.00 0.00 2.29
2507 2957 5.860611 TCGGGAAATAGTACATATGTTGGG 58.139 41.667 14.77 0.00 0.00 4.12
2538 3069 9.003658 AGGAACAGAGTTACAATAATGTCTTTG 57.996 33.333 0.00 0.00 41.05 2.77
2539 3070 9.574516 AAGGAACAGAGTTACAATAATGTCTTT 57.425 29.630 0.00 0.00 41.05 2.52
2604 3135 4.791974 CTCAAATCTTCCTTTGTCAGCAC 58.208 43.478 0.00 0.00 37.39 4.40
2731 3262 5.540337 AGAAAGGAGCGGAGTCATAATATGA 59.460 40.000 0.00 0.00 36.84 2.15
2745 3307 3.194968 TCCTGGTACTAAAGAAAGGAGCG 59.805 47.826 0.00 0.00 29.93 5.03
2898 3462 3.042887 GCGTTTAAGCAAAAGTCACCAG 58.957 45.455 0.00 0.00 37.05 4.00
3396 3960 2.181777 GTGCCGCTCACGATCTCA 59.818 61.111 0.00 0.00 43.93 3.27
3674 4243 1.140161 CATGAACAAGCCGCCATGG 59.860 57.895 7.63 7.63 42.50 3.66
3702 4271 0.038251 CGACAGAGGTTACAGCTGCA 60.038 55.000 15.27 0.00 33.03 4.41
3773 4345 1.518133 GCAAACAACGCACTGGCAA 60.518 52.632 0.00 0.00 41.24 4.52
3830 4402 4.023107 CGTCCGTGGTATGTCTGATAGATT 60.023 45.833 0.00 0.00 0.00 2.40
3870 4457 7.403231 ACCTTTATAAGAGGACATCTCAAAGGA 59.597 37.037 27.42 3.30 44.57 3.36
4064 5756 3.338249 AGCTTACTCGACGGTTACTGTA 58.662 45.455 0.00 0.00 0.00 2.74
4065 5757 2.157738 AGCTTACTCGACGGTTACTGT 58.842 47.619 0.00 0.00 0.00 3.55
4066 5758 2.915738 AGCTTACTCGACGGTTACTG 57.084 50.000 0.00 0.00 0.00 2.74
4067 5759 5.363939 ACTATAGCTTACTCGACGGTTACT 58.636 41.667 0.00 0.00 0.00 2.24
4069 5761 7.495934 ACTTTACTATAGCTTACTCGACGGTTA 59.504 37.037 0.00 0.00 0.00 2.85
4192 5888 7.852945 GTCTGCTAATATGTAGTTGCAATGAAC 59.147 37.037 0.59 1.98 0.00 3.18
4194 5890 7.047271 TGTCTGCTAATATGTAGTTGCAATGA 58.953 34.615 0.59 0.00 0.00 2.57
4332 6032 9.301153 GTAGTTGTGATTTTATTAGGCCATTTG 57.699 33.333 5.01 0.00 0.00 2.32
4337 6040 6.913873 TCGTAGTTGTGATTTTATTAGGCC 57.086 37.500 0.00 0.00 0.00 5.19
4379 6082 5.935173 CAGCATGACCTTGTTGAGCATCAT 61.935 45.833 0.00 0.00 43.13 2.45
4394 6097 2.965831 TCATACCTACCTCCAGCATGAC 59.034 50.000 0.00 0.00 39.69 3.06
4465 6168 0.449388 GCCAGAGCACGATCCAAAAG 59.551 55.000 0.00 0.00 39.53 2.27
4466 6169 0.036732 AGCCAGAGCACGATCCAAAA 59.963 50.000 0.00 0.00 43.56 2.44
4486 6189 5.579047 ACATCACCAATGGGAATCTTGTTA 58.421 37.500 3.55 0.00 39.90 2.41
4516 6222 9.784531 AAGATGAGAAAGAAATGTCTAAGAACA 57.215 29.630 0.00 0.00 32.16 3.18
4522 6228 8.156820 TGGTTGAAGATGAGAAAGAAATGTCTA 58.843 33.333 0.00 0.00 32.16 2.59
4525 6231 7.449395 TGATGGTTGAAGATGAGAAAGAAATGT 59.551 33.333 0.00 0.00 0.00 2.71
4533 6239 7.201758 GCATAACATGATGGTTGAAGATGAGAA 60.202 37.037 0.00 0.00 32.29 2.87


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

AutoCloner maintained by Alex Coulton.