Multiple sequence alignment - TraesCS5A01G143000

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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 TraesCS5A01G143000 chr5A 100.000 4689 0 0 998 5686 317230685 317235373 0.000000e+00 8660
1 TraesCS5A01G143000 chr5A 100.000 688 0 0 1 688 317229688 317230375 0.000000e+00 1271
2 TraesCS5A01G143000 chr5B 95.021 4137 162 22 998 5126 267752397 267756497 0.000000e+00 6458
3 TraesCS5A01G143000 chr5B 87.550 498 28 11 5195 5686 267756841 267757310 3.870000e-151 545
4 TraesCS5A01G143000 chr5D 92.876 2288 109 26 3419 5686 238118917 238116664 0.000000e+00 3273
5 TraesCS5A01G143000 chr5D 92.209 1399 85 9 998 2393 238121274 238119897 0.000000e+00 1958
6 TraesCS5A01G143000 chr5D 91.513 919 65 10 2509 3420 238119868 238118956 0.000000e+00 1253
7 TraesCS5A01G143000 chr5D 92.830 265 19 0 1 265 238133800 238133536 8.940000e-103 385
8 TraesCS5A01G143000 chr5D 84.615 338 50 2 90 427 320370228 320370563 9.130000e-88 335
9 TraesCS5A01G143000 chr5D 90.351 228 20 2 38 265 371632245 371632470 1.200000e-76 298
10 TraesCS5A01G143000 chr5D 83.388 307 48 2 220 523 238133533 238133227 1.210000e-71 281
11 TraesCS5A01G143000 chr5D 89.655 145 14 1 520 664 238124499 238124356 3.500000e-42 183
12 TraesCS5A01G143000 chr4A 85.969 449 59 4 38 484 134220677 134221123 1.430000e-130 477
13 TraesCS5A01G143000 chr4A 76.092 916 160 39 3330 4207 469241903 469242797 1.890000e-114 424
14 TraesCS5A01G143000 chr4A 74.481 337 65 17 2736 3061 469241371 469241697 5.980000e-25 126
15 TraesCS5A01G143000 chr7D 83.698 503 62 13 38 522 130922872 130923372 1.870000e-124 457
16 TraesCS5A01G143000 chr7D 84.510 439 48 11 38 457 417368782 417368345 3.170000e-112 416
17 TraesCS5A01G143000 chr7A 84.110 472 72 2 38 507 167789331 167788861 2.420000e-123 453
18 TraesCS5A01G143000 chr7A 81.667 300 52 3 269 565 449448439 449448738 4.400000e-61 246
19 TraesCS5A01G143000 chr4D 76.413 920 158 38 3326 4207 106683337 106682439 5.230000e-120 442
20 TraesCS5A01G143000 chr4D 85.120 457 36 13 38 471 488176688 488177135 6.760000e-119 438
21 TraesCS5A01G143000 chr4D 73.373 338 71 15 2736 3063 106683869 106683541 2.170000e-19 108
22 TraesCS5A01G143000 chr4B 76.279 919 159 39 3326 4207 169928752 169929648 8.750000e-118 435
23 TraesCS5A01G143000 chr4B 89.623 106 11 0 2746 2851 169928231 169928336 9.940000e-28 135
24 TraesCS5A01G143000 chr6B 79.298 541 81 12 45 564 258755126 258754596 3.260000e-92 350
25 TraesCS5A01G143000 chr1D 86.254 291 38 1 268 556 425562727 425562437 1.190000e-81 315
26 TraesCS5A01G143000 chr7B 92.166 217 16 1 38 254 646378032 646378247 7.160000e-79 305
27 TraesCS5A01G143000 chr7B 88.259 247 27 2 221 465 19958937 19959183 1.550000e-75 294
28 TraesCS5A01G143000 chr2D 86.275 255 32 2 268 519 458507680 458507934 2.020000e-69 274


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 TraesCS5A01G143000 chr5A 317229688 317235373 5685 False 4965.50 8660 100.00000 1 5686 2 chr5A.!!$F1 5685
1 TraesCS5A01G143000 chr5B 267752397 267757310 4913 False 3501.50 6458 91.28550 998 5686 2 chr5B.!!$F1 4688
2 TraesCS5A01G143000 chr5D 238116664 238124499 7835 True 1666.75 3273 91.56325 520 5686 4 chr5D.!!$R1 5166
3 TraesCS5A01G143000 chr5D 238133227 238133800 573 True 333.00 385 88.10900 1 523 2 chr5D.!!$R2 522
4 TraesCS5A01G143000 chr4A 469241371 469242797 1426 False 275.00 424 75.28650 2736 4207 2 chr4A.!!$F2 1471
5 TraesCS5A01G143000 chr7D 130922872 130923372 500 False 457.00 457 83.69800 38 522 1 chr7D.!!$F1 484
6 TraesCS5A01G143000 chr4D 106682439 106683869 1430 True 275.00 442 74.89300 2736 4207 2 chr4D.!!$R1 1471
7 TraesCS5A01G143000 chr4B 169928231 169929648 1417 False 285.00 435 82.95100 2746 4207 2 chr4B.!!$F1 1461
8 TraesCS5A01G143000 chr6B 258754596 258755126 530 True 350.00 350 79.29800 45 564 1 chr6B.!!$R1 519

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
557 629 0.036732 TGCAAAGTCCAGCTGTAGGG 59.963 55.000 13.81 0.00 0.00 3.53 F
678 3736 0.528901 TTCACAAGGTCGGACACGTG 60.529 55.000 15.48 15.48 41.85 4.49 F
1397 4456 1.343789 ACTATGATGCGCATCTCTGCT 59.656 47.619 40.90 25.43 46.65 4.24 F
2435 5505 0.659427 CTGTGTAATGCATCCAGGCG 59.341 55.000 0.00 0.00 36.28 5.52 F
4325 7486 0.673333 TGCGTAATCTGCAGGGTGTG 60.673 55.000 15.13 2.82 37.44 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2315 5385 0.177604 CTTCAGCTTCGAGGCCAGAT 59.822 55.000 16.77 0.0 0.00 2.90 R
2435 5505 1.682323 GTGACCTAGGTAGCAGGTAGC 59.318 57.143 16.29 0.0 46.60 3.58 R
3375 6469 0.876342 CCGCTAAAGCAGGATCGACC 60.876 60.000 2.44 0.0 42.21 4.79 R
4382 7543 0.609406 GGGGAGCCTCAAACCTTGAC 60.609 60.000 0.00 0.0 35.46 3.18 R
5293 8757 0.756294 TCCGGGATATGCAATGACGT 59.244 50.000 0.00 0.0 0.00 4.34 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
32 33 1.869690 GACTTGCAAGGCGAAGGAC 59.130 57.895 29.18 7.26 0.00 3.85
73 74 5.163713 GCGACATAAAGCTTGAGAAGGAAAT 60.164 40.000 0.00 0.00 0.00 2.17
188 189 1.835494 AGAAGGAGATCAACGACCGA 58.165 50.000 0.00 0.00 0.00 4.69
190 191 2.561419 AGAAGGAGATCAACGACCGAAA 59.439 45.455 0.00 0.00 0.00 3.46
276 325 0.680280 GGAGTAGGACGAGCAGGACA 60.680 60.000 0.00 0.00 0.00 4.02
293 363 0.322816 ACACATTCCGCTTGGAGCAT 60.323 50.000 0.50 0.00 44.35 3.79
301 371 3.063704 CTTGGAGCATGCGCCCAA 61.064 61.111 33.75 32.39 42.56 4.12
327 397 3.770040 CCGAGGCCATCCGTCACA 61.770 66.667 5.01 0.00 37.47 3.58
374 444 8.735315 TGTCATGTCCGATTTGTTAAATTATGT 58.265 29.630 0.00 0.00 0.00 2.29
401 471 4.326009 GCTTTGCTTTGTTTCGAACTTTGA 59.674 37.500 0.00 0.00 0.00 2.69
419 489 7.016361 ACTTTGACATTCAGACAGTTTGTAC 57.984 36.000 0.00 0.00 0.00 2.90
427 497 5.055642 TCAGACAGTTTGTACCGTATGAG 57.944 43.478 0.00 0.00 30.24 2.90
428 498 4.082408 TCAGACAGTTTGTACCGTATGAGG 60.082 45.833 0.00 0.00 30.24 3.86
429 499 2.928116 GACAGTTTGTACCGTATGAGGC 59.072 50.000 0.00 0.00 33.69 4.70
465 537 5.241506 GCATGGATTTGAGGATCGGAATTTA 59.758 40.000 0.00 0.00 38.61 1.40
468 540 4.213482 GGATTTGAGGATCGGAATTTACGG 59.787 45.833 0.31 0.00 38.61 4.02
471 543 4.311816 TGAGGATCGGAATTTACGGTAC 57.688 45.455 0.31 0.00 38.61 3.34
472 544 3.700539 TGAGGATCGGAATTTACGGTACA 59.299 43.478 0.00 0.00 38.61 2.90
484 556 7.814107 GGAATTTACGGTACATGAATATACGGA 59.186 37.037 0.00 0.00 0.00 4.69
510 582 0.179023 TTTAAAAGGTGCCCGGTCGT 60.179 50.000 0.00 0.00 0.00 4.34
525 597 2.801996 CGTGTCCGCGAGCGTTTA 60.802 61.111 8.23 0.00 37.81 2.01
528 600 1.005294 GTGTCCGCGAGCGTTTAAGA 61.005 55.000 8.23 3.12 37.81 2.10
529 601 0.318869 TGTCCGCGAGCGTTTAAGAA 60.319 50.000 8.23 0.00 37.81 2.52
534 606 1.349259 GCGAGCGTTTAAGAAGCCGA 61.349 55.000 0.00 0.00 0.00 5.54
548 620 1.327303 AGCCGAATTTGCAAAGTCCA 58.673 45.000 28.20 1.98 29.78 4.02
556 628 1.896220 TTGCAAAGTCCAGCTGTAGG 58.104 50.000 13.81 0.00 0.00 3.18
557 629 0.036732 TGCAAAGTCCAGCTGTAGGG 59.963 55.000 13.81 0.00 0.00 3.53
575 647 1.547372 GGGGCTCTAACACGACTGTTA 59.453 52.381 0.00 0.00 41.15 2.41
612 684 6.899393 ATTTGTGAACATAGGAAGCAGAAA 57.101 33.333 0.00 0.00 0.00 2.52
613 685 5.947228 TTGTGAACATAGGAAGCAGAAAG 57.053 39.130 0.00 0.00 0.00 2.62
614 686 5.227569 TGTGAACATAGGAAGCAGAAAGA 57.772 39.130 0.00 0.00 0.00 2.52
616 688 6.240894 TGTGAACATAGGAAGCAGAAAGATT 58.759 36.000 0.00 0.00 0.00 2.40
617 689 6.149973 TGTGAACATAGGAAGCAGAAAGATTG 59.850 38.462 0.00 0.00 0.00 2.67
618 690 5.124457 TGAACATAGGAAGCAGAAAGATTGC 59.876 40.000 0.00 0.00 41.83 3.56
619 691 4.592942 ACATAGGAAGCAGAAAGATTGCA 58.407 39.130 0.00 0.00 43.92 4.08
620 692 4.639310 ACATAGGAAGCAGAAAGATTGCAG 59.361 41.667 0.00 0.00 43.92 4.41
621 693 3.151912 AGGAAGCAGAAAGATTGCAGT 57.848 42.857 0.00 0.00 43.92 4.40
622 694 3.080319 AGGAAGCAGAAAGATTGCAGTC 58.920 45.455 0.00 0.00 43.92 3.51
632 704 3.252974 AGATTGCAGTCCCTCGTTAAG 57.747 47.619 5.47 0.00 0.00 1.85
638 710 3.813166 TGCAGTCCCTCGTTAAGAAAAAG 59.187 43.478 0.00 0.00 0.00 2.27
668 3726 3.672808 CAGCTCTTGATCTTCACAAGGT 58.327 45.455 0.00 0.00 43.11 3.50
678 3736 0.528901 TTCACAAGGTCGGACACGTG 60.529 55.000 15.48 15.48 41.85 4.49
1066 4124 2.128035 GACCAGCAGAAATCGGTATCG 58.872 52.381 0.00 0.00 37.82 2.92
1150 4209 3.488721 CGAGGTAAGATCCGTTCACGATT 60.489 47.826 0.00 0.00 43.02 3.34
1203 4262 3.250521 CAGCAATTTCCCGCAATTTTGTT 59.749 39.130 0.00 0.00 0.00 2.83
1397 4456 1.343789 ACTATGATGCGCATCTCTGCT 59.656 47.619 40.90 25.43 46.65 4.24
1457 4516 5.636903 ATCTTAGCCTGGAATTCTGCTTA 57.363 39.130 18.15 11.25 35.34 3.09
1566 4628 6.373216 GGTACCATGTTGCTTCATACAACTAA 59.627 38.462 7.15 0.00 46.03 2.24
1594 4656 8.023021 TGACATGAAATCAGTATAAGCCTACT 57.977 34.615 0.00 0.00 32.10 2.57
1600 4662 8.421784 TGAAATCAGTATAAGCCTACTAGTTGG 58.578 37.037 17.92 17.92 30.78 3.77
1629 4691 3.370953 GCATGGGATAGTCACCTCAAGTT 60.371 47.826 0.00 0.00 0.00 2.66
1679 4741 5.760253 ACTTTATGGTGTATCTGTATGCTGC 59.240 40.000 0.00 0.00 0.00 5.25
1691 4753 4.146058 TGCTGCGGAATAGCATGG 57.854 55.556 0.00 0.00 45.52 3.66
1712 4774 3.431207 GGTTCATTGGAAGGCAATCATGG 60.431 47.826 0.00 0.00 32.62 3.66
1820 4882 7.047891 TCTCTCCAACCATAATTGTGTATGTC 58.952 38.462 1.26 0.00 30.72 3.06
1899 4961 6.506500 AATTCACTCATCCTTGTGACAATC 57.493 37.500 0.00 0.00 42.06 2.67
1906 4968 6.373774 ACTCATCCTTGTGACAATCTTCAATC 59.626 38.462 0.00 0.00 0.00 2.67
1909 4971 5.624159 TCCTTGTGACAATCTTCAATCTGT 58.376 37.500 0.00 0.00 0.00 3.41
2204 5273 1.494721 TCTCAGGGGAAGTTGCACTTT 59.505 47.619 0.00 0.00 38.80 2.66
2205 5274 2.091885 TCTCAGGGGAAGTTGCACTTTT 60.092 45.455 0.00 0.00 38.80 2.27
2206 5275 2.695147 CTCAGGGGAAGTTGCACTTTTT 59.305 45.455 0.00 0.00 38.80 1.94
2207 5276 2.430332 TCAGGGGAAGTTGCACTTTTTG 59.570 45.455 0.00 0.00 38.80 2.44
2208 5277 2.168313 CAGGGGAAGTTGCACTTTTTGT 59.832 45.455 0.00 0.00 38.80 2.83
2224 5293 6.520447 CACTTTTTGTGTTGCAAATTGAACAG 59.480 34.615 0.00 0.00 45.38 3.16
2282 5351 7.843490 TTGTATACCTCAAGTAGAAACATGC 57.157 36.000 0.00 0.00 33.42 4.06
2382 5452 5.140747 AGATATGACAATCGCCTTCTACC 57.859 43.478 0.00 0.00 0.00 3.18
2435 5505 0.659427 CTGTGTAATGCATCCAGGCG 59.341 55.000 0.00 0.00 36.28 5.52
2586 5670 4.039004 CCTGATCAGTCTTACTCCTGGATG 59.961 50.000 21.11 0.00 0.00 3.51
2610 5695 7.107542 TGTTTGGTTACTTGTTGACTAGTTCT 58.892 34.615 0.00 0.00 34.09 3.01
2933 6019 6.314018 TCTTCGTATGCACAAATTTAAGCAG 58.686 36.000 18.01 8.38 40.71 4.24
3040 6126 8.153221 TCAAAGGTATTTCTTGGACTACCATA 57.847 34.615 0.00 0.00 46.34 2.74
3244 6333 5.738619 TTCTCCATGCTTTAGTCTGTGTA 57.261 39.130 0.00 0.00 0.00 2.90
3900 7049 4.976864 TCAGAAGGTTGGGTAAAGTAACC 58.023 43.478 0.00 0.00 43.22 2.85
4030 7188 5.121142 GGCTAAATACACAGTTCTTTACGCA 59.879 40.000 0.00 0.00 0.00 5.24
4138 7299 3.960755 TCCTAGAGAAATGCGATGGAGAA 59.039 43.478 0.00 0.00 0.00 2.87
4141 7302 4.148128 AGAGAAATGCGATGGAGAATGT 57.852 40.909 0.00 0.00 0.00 2.71
4186 7347 5.126545 GGAAGGAGTTTTTGTGGTAAGTTGT 59.873 40.000 0.00 0.00 0.00 3.32
4215 7376 5.399301 CGCACTCTGTTTTGTTTATTCCAAG 59.601 40.000 0.00 0.00 0.00 3.61
4222 7383 6.991938 TGTTTTGTTTATTCCAAGCTATGCT 58.008 32.000 0.00 0.00 42.56 3.79
4225 7386 6.588719 TTGTTTATTCCAAGCTATGCTGTT 57.411 33.333 0.00 0.00 39.62 3.16
4228 7389 6.208402 TGTTTATTCCAAGCTATGCTGTTGAA 59.792 34.615 0.00 0.00 39.62 2.69
4325 7486 0.673333 TGCGTAATCTGCAGGGTGTG 60.673 55.000 15.13 2.82 37.44 3.82
4379 7540 1.278985 TGCATGATGGGGATCGATACC 59.721 52.381 19.30 19.30 0.00 2.73
4410 7571 1.979809 TGAGGCTCCCCAGGATTAAA 58.020 50.000 12.86 0.00 0.00 1.52
4422 7583 4.884164 CCCAGGATTAAACTTGGTCTGATC 59.116 45.833 12.07 0.00 35.64 2.92
4517 7678 4.148838 AGGTGCCTTGCTTGTGTATTTTA 58.851 39.130 0.00 0.00 0.00 1.52
4542 7703 6.998673 ACTAAGCCAAACTTCTGTTTAGTGAT 59.001 34.615 0.00 0.00 43.75 3.06
4617 7783 2.742053 CAAACTACTACATGCGCAAGGT 59.258 45.455 17.11 18.86 38.28 3.50
4657 7823 5.276461 ACCAGAATTGTTTCCAGTTTTCC 57.724 39.130 0.00 0.00 31.84 3.13
4797 7963 1.886542 GGACACAAGGCTACTTTTGGG 59.113 52.381 0.00 0.00 38.42 4.12
4798 7964 1.886542 GACACAAGGCTACTTTTGGGG 59.113 52.381 0.00 0.00 38.42 4.96
4803 7969 0.033109 AGGCTACTTTTGGGGGCATC 60.033 55.000 0.00 0.00 0.00 3.91
4846 8012 4.256920 GCTGAGGATGTGTAATTGTCAGT 58.743 43.478 0.00 0.00 33.88 3.41
4902 8068 0.031449 GGAGTAGTGATCGCTCTGCC 59.969 60.000 13.11 8.62 0.00 4.85
4904 8070 2.222886 GAGTAGTGATCGCTCTGCCTA 58.777 52.381 13.11 0.00 0.00 3.93
4959 8126 3.389656 CCCCAGTATCTTTTCCTCCTCTC 59.610 52.174 0.00 0.00 0.00 3.20
5012 8179 1.728971 CTTGTCTTGGCTTAGCACTCG 59.271 52.381 6.53 0.00 0.00 4.18
5033 8201 3.181530 CGAGTGAGTAGAAAATTGTGGCG 60.182 47.826 0.00 0.00 0.00 5.69
5072 8240 1.538047 ATGCGTGCTCCATTTTGTCT 58.462 45.000 0.00 0.00 0.00 3.41
5083 8251 7.545265 GTGCTCCATTTTGTCTTTTATAATGCA 59.455 33.333 0.00 0.00 0.00 3.96
5110 8278 0.385473 ACGCAACTGAAATTTCGCGG 60.385 50.000 29.03 18.03 46.47 6.46
5128 8296 2.810400 GCGGGCATATAGATTGTGTGGT 60.810 50.000 0.00 0.00 0.00 4.16
5160 8624 4.095782 GCGTTTCATATCCCAACTTGCTTA 59.904 41.667 0.00 0.00 0.00 3.09
5186 8650 5.106357 GGCAAAAGGATTTGTTGTTGTTGTT 60.106 36.000 3.55 0.00 46.19 2.83
5187 8651 5.794448 GCAAAAGGATTTGTTGTTGTTGTTG 59.206 36.000 3.55 0.00 46.19 3.33
5188 8652 6.567511 GCAAAAGGATTTGTTGTTGTTGTTGT 60.568 34.615 3.55 0.00 46.19 3.32
5189 8653 7.358830 CAAAAGGATTTGTTGTTGTTGTTGTT 58.641 30.769 0.00 0.00 39.02 2.83
5190 8654 6.479095 AAGGATTTGTTGTTGTTGTTGTTG 57.521 33.333 0.00 0.00 0.00 3.33
5191 8655 5.546526 AGGATTTGTTGTTGTTGTTGTTGT 58.453 33.333 0.00 0.00 0.00 3.32
5192 8656 5.994668 AGGATTTGTTGTTGTTGTTGTTGTT 59.005 32.000 0.00 0.00 0.00 2.83
5193 8657 6.073331 AGGATTTGTTGTTGTTGTTGTTGTTG 60.073 34.615 0.00 0.00 0.00 3.33
5194 8658 6.293135 GGATTTGTTGTTGTTGTTGTTGTTGT 60.293 34.615 0.00 0.00 0.00 3.32
5195 8659 6.422776 TTTGTTGTTGTTGTTGTTGTTGTT 57.577 29.167 0.00 0.00 0.00 2.83
5196 8660 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
5197 8661 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
5198 8662 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
5199 8663 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
5200 8664 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
5201 8665 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
5202 8666 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
5203 8667 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
5204 8668 5.351465 TGTTGTTGTTGTTGTTGTTGTTGTT 59.649 32.000 0.00 0.00 0.00 2.83
5205 8669 5.395325 TGTTGTTGTTGTTGTTGTTGTTG 57.605 34.783 0.00 0.00 0.00 3.33
5206 8670 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
5209 8673 7.224753 TGTTGTTGTTGTTGTTGTTGTTGTATT 59.775 29.630 0.00 0.00 0.00 1.89
5256 8720 2.910482 CCGATGCGACATTTTTGTTCTG 59.090 45.455 0.00 0.00 0.00 3.02
5261 8725 2.034053 GCGACATTTTTGTTCTGGACCA 59.966 45.455 0.00 0.00 0.00 4.02
5263 8727 4.677584 CGACATTTTTGTTCTGGACCAAA 58.322 39.130 0.00 0.00 0.00 3.28
5264 8728 4.502645 CGACATTTTTGTTCTGGACCAAAC 59.497 41.667 0.00 4.28 0.00 2.93
5265 8729 5.413309 ACATTTTTGTTCTGGACCAAACA 57.587 34.783 14.47 14.47 33.74 2.83
5266 8730 5.988287 ACATTTTTGTTCTGGACCAAACAT 58.012 33.333 17.42 5.73 35.46 2.71
5267 8731 7.118496 ACATTTTTGTTCTGGACCAAACATA 57.882 32.000 17.42 12.56 35.46 2.29
5269 8733 8.865090 ACATTTTTGTTCTGGACCAAACATATA 58.135 29.630 17.42 11.32 35.46 0.86
5270 8734 9.874205 CATTTTTGTTCTGGACCAAACATATAT 57.126 29.630 17.42 12.50 35.46 0.86
5293 8757 1.685765 ATAGTCAGGCCGAGGCACA 60.686 57.895 16.65 0.00 44.11 4.57
5310 8774 1.261354 CACACGTCATTGCATATCCCG 59.739 52.381 0.00 0.00 0.00 5.14
5313 8777 1.270305 ACGTCATTGCATATCCCGGAG 60.270 52.381 0.73 0.00 0.00 4.63
5325 8789 3.164479 CCGGAGGCCCATGATGAT 58.836 61.111 0.00 0.00 46.14 2.45
5330 8794 2.093973 CGGAGGCCCATGATGATAGTAC 60.094 54.545 0.00 0.00 0.00 2.73
5440 8904 1.029408 TGCCAAGTCAGTGCGTGTTT 61.029 50.000 0.00 0.00 0.00 2.83
5528 8992 2.356382 TCTTTGACGTTTGCGGATTGTT 59.644 40.909 0.00 0.00 43.45 2.83
5589 9054 2.551856 TAGCATGACTCTGGGGGCCT 62.552 60.000 0.84 0.00 0.00 5.19
5600 9065 4.564110 GGGGCCTGGGATGCGTAC 62.564 72.222 0.84 0.00 0.00 3.67
5680 9150 3.794270 CGCCACGGTGGAGTAATG 58.206 61.111 30.65 8.25 40.96 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.964438 TTCGCCTTGCAAGTCGTCGT 62.964 55.000 26.87 0.00 0.00 4.34
38 39 3.669557 GCTTTATGTCGCCAAATGTCGTT 60.670 43.478 0.00 0.00 0.00 3.85
39 40 2.159572 GCTTTATGTCGCCAAATGTCGT 60.160 45.455 0.00 0.00 0.00 4.34
188 189 2.577593 GCCGCCTCGTAGTCCTTT 59.422 61.111 0.00 0.00 0.00 3.11
190 191 4.790962 TCGCCGCCTCGTAGTCCT 62.791 66.667 0.00 0.00 0.00 3.85
254 255 3.456431 CTGCTCGTCCTACTCCGCG 62.456 68.421 0.00 0.00 0.00 6.46
261 310 1.476891 GAATGTGTCCTGCTCGTCCTA 59.523 52.381 0.00 0.00 0.00 2.94
276 325 1.660560 GCATGCTCCAAGCGGAATGT 61.661 55.000 11.37 0.00 46.26 2.71
293 363 2.359850 GATCACTGGTTGGGCGCA 60.360 61.111 10.83 0.00 0.00 6.09
301 371 1.690219 GATGGCCTCGGATCACTGGT 61.690 60.000 3.32 0.00 0.00 4.00
327 397 7.944061 TGACAAAATGAAATCAATGTCTGAGT 58.056 30.769 19.21 0.00 37.52 3.41
374 444 4.688413 AGTTCGAAACAAAGCAAAGCAAAA 59.312 33.333 0.00 0.00 0.00 2.44
401 471 4.067972 ACGGTACAAACTGTCTGAATGT 57.932 40.909 0.00 0.00 41.57 2.71
419 489 0.250424 TCCATGCATGCCTCATACGG 60.250 55.000 21.69 4.32 0.00 4.02
510 582 0.318869 TTCTTAAACGCTCGCGGACA 60.319 50.000 16.18 0.00 44.69 4.02
514 586 1.058903 GGCTTCTTAAACGCTCGCG 59.941 57.895 10.06 10.06 46.03 5.87
516 588 1.065358 TTCGGCTTCTTAAACGCTCG 58.935 50.000 0.00 0.00 0.00 5.03
518 590 3.821841 CAAATTCGGCTTCTTAAACGCT 58.178 40.909 0.00 0.00 0.00 5.07
525 597 3.552890 GGACTTTGCAAATTCGGCTTCTT 60.553 43.478 19.56 0.00 0.00 2.52
528 600 1.686052 TGGACTTTGCAAATTCGGCTT 59.314 42.857 19.56 0.00 0.00 4.35
529 601 1.270550 CTGGACTTTGCAAATTCGGCT 59.729 47.619 19.56 0.00 0.00 5.52
534 606 3.256631 CCTACAGCTGGACTTTGCAAATT 59.743 43.478 19.93 7.10 0.00 1.82
548 620 1.196012 GTGTTAGAGCCCCTACAGCT 58.804 55.000 0.00 0.00 45.23 4.24
556 628 3.908737 AACAGTCGTGTTAGAGCCC 57.091 52.632 0.00 0.00 45.48 5.19
575 647 5.046159 TGTTCACAAATATTACCTCCGTCCT 60.046 40.000 0.00 0.00 0.00 3.85
612 684 2.832129 TCTTAACGAGGGACTGCAATCT 59.168 45.455 0.00 0.00 41.55 2.40
613 685 3.247006 TCTTAACGAGGGACTGCAATC 57.753 47.619 0.00 0.00 41.55 2.67
614 686 3.695830 TTCTTAACGAGGGACTGCAAT 57.304 42.857 0.00 0.00 41.55 3.56
616 688 3.478857 TTTTCTTAACGAGGGACTGCA 57.521 42.857 0.00 0.00 41.55 4.41
617 689 3.813724 ACTTTTTCTTAACGAGGGACTGC 59.186 43.478 0.00 0.00 41.55 4.40
618 690 7.486802 TTTACTTTTTCTTAACGAGGGACTG 57.513 36.000 0.00 0.00 41.55 3.51
620 692 9.177304 CAATTTTACTTTTTCTTAACGAGGGAC 57.823 33.333 0.00 0.00 0.00 4.46
621 693 7.863877 GCAATTTTACTTTTTCTTAACGAGGGA 59.136 33.333 0.00 0.00 0.00 4.20
622 694 7.650104 TGCAATTTTACTTTTTCTTAACGAGGG 59.350 33.333 0.00 0.00 0.00 4.30
632 704 7.698836 TCAAGAGCTGCAATTTTACTTTTTC 57.301 32.000 1.02 0.00 0.00 2.29
638 710 6.525976 GTGAAGATCAAGAGCTGCAATTTTAC 59.474 38.462 1.02 0.00 33.56 2.01
668 3726 3.281395 TGTCTCGCACGTGTCCGA 61.281 61.111 18.38 16.87 37.88 4.55
1001 4059 4.463879 CGTGGCAGGGGCAGAGAG 62.464 72.222 0.00 0.00 43.71 3.20
1010 4068 0.304705 GTATTGCGAATCGTGGCAGG 59.695 55.000 4.07 0.00 39.84 4.85
1150 4209 2.016393 CTGGAGTATCTGGCGCGGAA 62.016 60.000 8.83 0.00 33.73 4.30
1237 4296 1.010935 CCGCCATCTGATCGAATCGG 61.011 60.000 1.76 0.00 36.99 4.18
1397 4456 6.926826 ACAAGAACGTATCACATCTAACACAA 59.073 34.615 0.00 0.00 0.00 3.33
1457 4516 4.217118 CCAACTTGCAATAGTTTCAGAGCT 59.783 41.667 0.00 0.00 36.24 4.09
1538 4599 1.518325 TGAAGCAACATGGTACCACG 58.482 50.000 19.09 12.66 0.00 4.94
1566 4628 7.743749 AGGCTTATACTGATTTCATGTCAGAT 58.256 34.615 16.38 9.21 44.57 2.90
1594 4656 1.702401 TCCCATGCACTGAACCAACTA 59.298 47.619 0.00 0.00 0.00 2.24
1600 4662 2.939103 GTGACTATCCCATGCACTGAAC 59.061 50.000 0.00 0.00 0.00 3.18
1629 4691 3.496160 GGTGAGAGGCCTTCAAGTAACAA 60.496 47.826 6.77 0.00 0.00 2.83
1657 4719 4.749598 CGCAGCATACAGATACACCATAAA 59.250 41.667 0.00 0.00 0.00 1.40
1658 4720 4.306600 CGCAGCATACAGATACACCATAA 58.693 43.478 0.00 0.00 0.00 1.90
1679 4741 3.213506 TCCAATGAACCATGCTATTCCG 58.786 45.455 0.00 0.00 0.00 4.30
1689 4751 2.886913 TGATTGCCTTCCAATGAACCA 58.113 42.857 0.00 0.00 44.02 3.67
1691 4753 3.196254 ACCATGATTGCCTTCCAATGAAC 59.804 43.478 0.00 0.00 44.02 3.18
1712 4774 9.988815 ATGTAGATATCAATCTTGAGGTAACAC 57.011 33.333 5.32 0.00 39.55 3.32
1767 4829 5.757320 GCAGCTGACATAAATCTACTGTGAT 59.243 40.000 20.43 0.00 0.00 3.06
1820 4882 0.828022 TTCCACGGGTAGCTGTATGG 59.172 55.000 5.98 5.07 0.00 2.74
1899 4961 5.398603 ACTCTACACTCCACAGATTGAAG 57.601 43.478 0.00 0.00 0.00 3.02
1906 4968 3.088789 ACCCTACTCTACACTCCACAG 57.911 52.381 0.00 0.00 0.00 3.66
1909 4971 4.569228 CCAACTACCCTACTCTACACTCCA 60.569 50.000 0.00 0.00 0.00 3.86
2205 5274 4.624882 GTCACTGTTCAATTTGCAACACAA 59.375 37.500 0.00 0.00 36.13 3.33
2206 5275 4.082300 AGTCACTGTTCAATTTGCAACACA 60.082 37.500 0.00 0.00 0.00 3.72
2207 5276 4.423732 AGTCACTGTTCAATTTGCAACAC 58.576 39.130 0.00 0.00 0.00 3.32
2208 5277 4.717233 AGTCACTGTTCAATTTGCAACA 57.283 36.364 0.00 11.36 0.00 3.33
2209 5278 5.230726 CAGAAGTCACTGTTCAATTTGCAAC 59.769 40.000 0.00 0.00 33.73 4.17
2210 5279 5.342433 CAGAAGTCACTGTTCAATTTGCAA 58.658 37.500 0.00 0.00 33.73 4.08
2211 5280 4.923893 CAGAAGTCACTGTTCAATTTGCA 58.076 39.130 0.00 0.00 33.73 4.08
2224 5293 2.802816 AGCGTGATTGAACAGAAGTCAC 59.197 45.455 0.00 0.00 36.67 3.67
2315 5385 0.177604 CTTCAGCTTCGAGGCCAGAT 59.822 55.000 16.77 0.00 0.00 2.90
2382 5452 2.101415 TCACAGGTAAGGATGCATCTCG 59.899 50.000 25.28 9.21 0.00 4.04
2435 5505 1.682323 GTGACCTAGGTAGCAGGTAGC 59.318 57.143 16.29 0.00 46.60 3.58
2490 5560 7.048629 AGTAACACTGGAGATGTATGAGATG 57.951 40.000 0.00 0.00 0.00 2.90
2586 5670 7.549615 AGAACTAGTCAACAAGTAACCAAAC 57.450 36.000 0.00 0.00 0.00 2.93
2671 5756 9.301153 GACGGCAAATATATCAAAAATGAACTT 57.699 29.630 0.00 0.00 0.00 2.66
2933 6019 4.676849 ACAAAACCAAAACATTGTGTGC 57.323 36.364 0.00 0.00 34.88 4.57
3275 6366 9.453572 ACAAAATAGAGATAGCATCTTCAACAA 57.546 29.630 1.06 0.00 40.38 2.83
3375 6469 0.876342 CCGCTAAAGCAGGATCGACC 60.876 60.000 2.44 0.00 42.21 4.79
3900 7049 4.651778 TGAAGGTGATGGAACTAAACCTG 58.348 43.478 0.00 0.00 40.37 4.00
4138 7299 7.890127 TCCAGGAGAGTTGATTTTAATTGACAT 59.110 33.333 0.00 0.00 0.00 3.06
4141 7302 7.394359 CCTTCCAGGAGAGTTGATTTTAATTGA 59.606 37.037 0.00 0.00 37.67 2.57
4186 7347 6.854496 ATAAACAAAACAGAGTGCGAGTAA 57.146 33.333 0.00 0.00 0.00 2.24
4215 7376 4.397417 AGAGGACAAATTCAACAGCATAGC 59.603 41.667 0.00 0.00 0.00 2.97
4222 7383 6.064060 ACAGATGAAGAGGACAAATTCAACA 58.936 36.000 0.00 0.00 36.59 3.33
4225 7386 9.958180 TTTATACAGATGAAGAGGACAAATTCA 57.042 29.630 0.00 0.00 37.36 2.57
4228 7389 9.388506 CAGTTTATACAGATGAAGAGGACAAAT 57.611 33.333 0.00 0.00 0.00 2.32
4325 7486 5.936372 TGATATCAAGATGATAAGCAGCACC 59.064 40.000 1.98 0.00 42.05 5.01
4379 7540 0.955919 GAGCCTCAAACCTTGACGGG 60.956 60.000 0.00 0.00 35.46 5.28
4382 7543 0.609406 GGGGAGCCTCAAACCTTGAC 60.609 60.000 0.00 0.00 35.46 3.18
4410 7571 3.777106 TGCTTCAAGATCAGACCAAGT 57.223 42.857 0.00 0.00 0.00 3.16
4422 7583 1.068333 CCACATCGGGTTTGCTTCAAG 60.068 52.381 0.00 0.00 0.00 3.02
4517 7678 6.354130 TCACTAAACAGAAGTTTGGCTTAGT 58.646 36.000 4.02 0.00 46.50 2.24
4553 7714 4.649218 GGGTTTGGGAATGCAATAGTACAT 59.351 41.667 0.00 0.00 0.00 2.29
4558 7719 2.159254 CGTGGGTTTGGGAATGCAATAG 60.159 50.000 0.00 0.00 0.00 1.73
4568 7732 0.392998 CAGATCTCCGTGGGTTTGGG 60.393 60.000 0.00 0.00 0.00 4.12
4657 7823 3.881688 CTGAATTCCAGGCTATTCACAGG 59.118 47.826 7.01 0.00 39.23 4.00
4731 7897 8.988934 TGTGCTTCAAGTTATGACTACTAAAAG 58.011 33.333 0.00 0.00 37.92 2.27
4797 7963 1.202698 ACATAGAAAGGAGCGATGCCC 60.203 52.381 0.00 0.00 0.00 5.36
4798 7964 2.246719 ACATAGAAAGGAGCGATGCC 57.753 50.000 0.00 0.00 0.00 4.40
4803 7969 1.398390 GGTGCAACATAGAAAGGAGCG 59.602 52.381 0.00 0.00 39.98 5.03
4815 7981 1.672030 CATCCTCAGCGGTGCAACA 60.672 57.895 10.38 0.00 39.98 3.33
4846 8012 1.270274 TCACTTGCGCGGTAAGTCTAA 59.730 47.619 8.83 0.00 36.42 2.10
4904 8070 7.011109 CCGACTATCCATCGTTTTAAATGAAGT 59.989 37.037 3.59 2.74 37.90 3.01
4938 8105 3.068873 CGAGAGGAGGAAAAGATACTGGG 59.931 52.174 0.00 0.00 0.00 4.45
4959 8126 5.046910 AGCATAAAGGACAAATTGACACG 57.953 39.130 0.00 0.00 0.00 4.49
5012 8179 3.746492 ACGCCACAATTTTCTACTCACTC 59.254 43.478 0.00 0.00 0.00 3.51
5033 8201 8.234546 CACGCATTAAACCATATATAAAGGGAC 58.765 37.037 8.85 0.00 0.00 4.46
5072 8240 7.439655 AGTTGCGTTTCCTTTTGCATTATAAAA 59.560 29.630 0.00 0.00 37.17 1.52
5083 8251 5.005299 CGAAATTTCAGTTGCGTTTCCTTTT 59.995 36.000 17.99 0.00 0.00 2.27
5110 8278 8.792830 ATATAACACCACACAATCTATATGCC 57.207 34.615 0.00 0.00 0.00 4.40
5128 8296 5.785243 TGGGATATGAAACGCGATATAACA 58.215 37.500 15.93 5.43 0.00 2.41
5160 8624 3.199727 ACAACAACAAATCCTTTTGCCCT 59.800 39.130 0.00 0.00 45.01 5.19
5186 8650 7.715265 AAATACAACAACAACAACAACAACA 57.285 28.000 0.00 0.00 0.00 3.33
5187 8651 7.058920 GCAAAATACAACAACAACAACAACAAC 59.941 33.333 0.00 0.00 0.00 3.32
5188 8652 7.041780 AGCAAAATACAACAACAACAACAACAA 60.042 29.630 0.00 0.00 0.00 2.83
5189 8653 6.425114 AGCAAAATACAACAACAACAACAACA 59.575 30.769 0.00 0.00 0.00 3.33
5190 8654 6.826612 AGCAAAATACAACAACAACAACAAC 58.173 32.000 0.00 0.00 0.00 3.32
5191 8655 7.426929 AAGCAAAATACAACAACAACAACAA 57.573 28.000 0.00 0.00 0.00 2.83
5192 8656 7.815068 AGTAAGCAAAATACAACAACAACAACA 59.185 29.630 0.00 0.00 0.00 3.33
5193 8657 8.107564 CAGTAAGCAAAATACAACAACAACAAC 58.892 33.333 0.00 0.00 0.00 3.32
5194 8658 7.815068 ACAGTAAGCAAAATACAACAACAACAA 59.185 29.630 0.00 0.00 0.00 2.83
5195 8659 7.316640 ACAGTAAGCAAAATACAACAACAACA 58.683 30.769 0.00 0.00 0.00 3.33
5196 8660 7.749539 ACAGTAAGCAAAATACAACAACAAC 57.250 32.000 0.00 0.00 0.00 3.32
5197 8661 7.815068 ACAACAGTAAGCAAAATACAACAACAA 59.185 29.630 0.00 0.00 0.00 2.83
5198 8662 7.274468 CACAACAGTAAGCAAAATACAACAACA 59.726 33.333 0.00 0.00 0.00 3.33
5199 8663 7.608755 CACAACAGTAAGCAAAATACAACAAC 58.391 34.615 0.00 0.00 0.00 3.32
5200 8664 6.254589 GCACAACAGTAAGCAAAATACAACAA 59.745 34.615 0.00 0.00 0.00 2.83
5201 8665 5.746245 GCACAACAGTAAGCAAAATACAACA 59.254 36.000 0.00 0.00 0.00 3.33
5202 8666 5.108405 CGCACAACAGTAAGCAAAATACAAC 60.108 40.000 0.00 0.00 0.00 3.32
5203 8667 4.973051 CGCACAACAGTAAGCAAAATACAA 59.027 37.500 0.00 0.00 0.00 2.41
5204 8668 4.273724 TCGCACAACAGTAAGCAAAATACA 59.726 37.500 0.00 0.00 0.00 2.29
5205 8669 4.778904 TCGCACAACAGTAAGCAAAATAC 58.221 39.130 0.00 0.00 0.00 1.89
5206 8670 5.621197 ATCGCACAACAGTAAGCAAAATA 57.379 34.783 0.00 0.00 0.00 1.40
5209 8673 3.304391 GGAATCGCACAACAGTAAGCAAA 60.304 43.478 0.00 0.00 0.00 3.68
5236 8700 2.910482 CCAGAACAAAAATGTCGCATCG 59.090 45.455 0.00 0.00 0.00 3.84
5256 8720 7.907389 TGACTATGAGGATATATGTTTGGTCC 58.093 38.462 0.00 0.00 0.00 4.46
5261 8725 6.351371 CGGCCTGACTATGAGGATATATGTTT 60.351 42.308 0.00 0.00 31.48 2.83
5263 8727 4.646945 CGGCCTGACTATGAGGATATATGT 59.353 45.833 0.00 0.00 31.48 2.29
5264 8728 4.889995 TCGGCCTGACTATGAGGATATATG 59.110 45.833 0.00 0.00 31.48 1.78
5265 8729 5.130705 TCGGCCTGACTATGAGGATATAT 57.869 43.478 0.00 0.00 31.48 0.86
5266 8730 4.527944 CTCGGCCTGACTATGAGGATATA 58.472 47.826 0.00 0.00 31.48 0.86
5267 8731 3.360867 CTCGGCCTGACTATGAGGATAT 58.639 50.000 0.00 0.00 31.48 1.63
5269 8733 1.626686 CTCGGCCTGACTATGAGGAT 58.373 55.000 0.00 0.00 31.48 3.24
5270 8734 3.117657 CTCGGCCTGACTATGAGGA 57.882 57.895 0.00 0.00 31.48 3.71
5271 8735 2.045280 CCTCGGCCTGACTATGAGG 58.955 63.158 0.00 3.37 40.19 3.86
5293 8757 0.756294 TCCGGGATATGCAATGACGT 59.244 50.000 0.00 0.00 0.00 4.34
5310 8774 3.177228 AGTACTATCATCATGGGCCTCC 58.823 50.000 4.53 0.00 0.00 4.30
5313 8777 7.796054 ACATTATAGTACTATCATCATGGGCC 58.204 38.462 18.68 0.00 0.00 5.80
5314 8778 8.700051 AGACATTATAGTACTATCATCATGGGC 58.300 37.037 18.68 12.25 0.00 5.36
5325 8789 7.280428 GCTCAGCGGATAGACATTATAGTACTA 59.720 40.741 4.77 4.77 0.00 1.82
5330 8794 4.400884 AGGCTCAGCGGATAGACATTATAG 59.599 45.833 0.00 0.00 0.00 1.31
5528 8992 4.269183 TCAGAAAGGAAAAACTGCTCACA 58.731 39.130 0.00 0.00 0.00 3.58
5589 9054 0.821517 AACTCATCGTACGCATCCCA 59.178 50.000 11.24 0.00 0.00 4.37
5600 9065 7.507733 AGGTAGGTACATAACTAACTCATCG 57.492 40.000 2.63 0.00 31.86 3.84


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

AutoCloner maintained by Alex Coulton.