Multiple sequence alignment - TraesCS6D01G288500

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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 TraesCS6D01G288500 chr6D 100.000 8464 0 0 857 9320 398742797 398734334 0.000000e+00 15631.0
1 TraesCS6D01G288500 chr6D 83.960 1702 250 14 6056 7749 398228932 398227246 0.000000e+00 1609.0
2 TraesCS6D01G288500 chr6D 78.498 2530 439 60 2873 5344 398232005 398229523 0.000000e+00 1561.0
3 TraesCS6D01G288500 chr6D 100.000 554 0 0 1 554 398743653 398743100 0.000000e+00 1024.0
4 TraesCS6D01G288500 chr6A 96.183 6654 165 43 2684 9298 544479173 544472570 0.000000e+00 10798.0
5 TraesCS6D01G288500 chr6A 94.006 1852 50 17 860 2689 544481097 544479285 0.000000e+00 2748.0
6 TraesCS6D01G288500 chr6A 84.078 1702 248 15 6056 7749 544206265 544204579 0.000000e+00 1620.0
7 TraesCS6D01G288500 chr6A 78.230 2531 444 61 2873 5344 544209338 544206856 0.000000e+00 1522.0
8 TraesCS6D01G288500 chr6A 96.429 364 12 1 1 364 544481959 544481597 4.820000e-167 599.0
9 TraesCS6D01G288500 chr6B 95.588 6664 181 47 2684 9299 595956705 595950107 0.000000e+00 10573.0
10 TraesCS6D01G288500 chr6B 93.304 1837 65 25 860 2678 595958578 595956782 0.000000e+00 2658.0
11 TraesCS6D01G288500 chr6B 83.080 1844 264 34 5937 7749 595288799 595286973 0.000000e+00 1633.0
12 TraesCS6D01G288500 chr6B 78.357 2532 436 69 2873 5344 595291729 595289250 0.000000e+00 1537.0
13 TraesCS6D01G288500 chr6B 95.912 318 11 2 1 316 595959336 595959019 1.790000e-141 514.0
14 TraesCS6D01G288500 chr6B 95.745 47 2 0 508 554 595958664 595958618 1.000000e-09 76.8
15 TraesCS6D01G288500 chr3A 88.119 101 8 2 1523 1622 62269022 62268925 5.910000e-22 117.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G288500 chr6D 398734334 398743653 9319 True 8327.50 15631 100.000000 1 9320 2 chr6D.!!$R2 9319
1 TraesCS6D01G288500 chr6D 398227246 398232005 4759 True 1585.00 1609 81.229000 2873 7749 2 chr6D.!!$R1 4876
2 TraesCS6D01G288500 chr6A 544472570 544481959 9389 True 4715.00 10798 95.539333 1 9298 3 chr6A.!!$R2 9297
3 TraesCS6D01G288500 chr6A 544204579 544209338 4759 True 1571.00 1620 81.154000 2873 7749 2 chr6A.!!$R1 4876
4 TraesCS6D01G288500 chr6B 595950107 595959336 9229 True 3455.45 10573 95.137250 1 9299 4 chr6B.!!$R2 9298
5 TraesCS6D01G288500 chr6B 595286973 595291729 4756 True 1585.00 1633 80.718500 2873 7749 2 chr6B.!!$R1 4876

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
990 1279 0.739462 ATCTTCGTGCGCGGAAATGA 60.739 50.000 21.04 5.22 38.89 2.57 F
2006 2305 0.108851 GCTTGGTTTGGTAATGGCCG 60.109 55.000 0.00 0.00 0.00 6.13 F
2659 2964 0.180642 TACCTTTGCAACCCGACACA 59.819 50.000 0.00 0.00 0.00 3.72 F
2811 3303 3.390135 CGTTACACTTTCTCCTTCAGCA 58.610 45.455 0.00 0.00 0.00 4.41 F
4173 4668 0.737715 GACGAAGCGCCTCAAGTGAT 60.738 55.000 2.29 0.00 0.00 3.06 F
4716 5241 0.382158 GCTTTCCAAATCCTAGCCGC 59.618 55.000 0.00 0.00 0.00 6.53 F
5010 5547 0.957395 CATCACGGCCTGCAAGTTCT 60.957 55.000 0.00 0.00 0.00 3.01 F
5886 6438 0.037326 ACACGTGATGGCAGTACTGG 60.037 55.000 25.01 8.13 0.00 4.00 F
6932 7505 0.475906 AGAGCCTGCACAAAGGAGTT 59.524 50.000 0.00 0.00 40.02 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 2500 0.248054 CACAACACGACTTGCACCAC 60.248 55.000 0.00 0.00 0.00 4.16 R
3137 3629 1.195448 CAGCTCAACACCTTTGCGTAG 59.805 52.381 0.00 0.00 0.00 3.51 R
4173 4668 0.821711 CTGGGTTTTTCGGACTGGCA 60.822 55.000 0.00 0.00 0.00 4.92 R
4238 4754 1.895798 AGACAGAAGTGAGCGGATTCA 59.104 47.619 0.00 0.00 0.00 2.57 R
5421 5964 0.533032 GAGGTGACAGCCCAGTAGAC 59.467 60.000 0.00 0.00 0.00 2.59 R
5823 6366 1.175983 TACAACCCCAAGCGGCTTTG 61.176 55.000 13.53 9.83 0.00 2.77 R
6517 7090 1.499007 ACAGATGTCCCCACAACCTTT 59.501 47.619 0.00 0.00 35.64 3.11 R
7031 7604 0.106519 GGAGCATATGGGTTGGCAGT 60.107 55.000 4.56 0.00 0.00 4.40 R
8523 9123 0.036164 AGCAATGCCTACGACCAACA 59.964 50.000 0.00 0.00 0.00 3.33 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
85 86 3.530104 GGTACACGAACGCGAGCG 61.530 66.667 15.93 18.55 46.03 5.03
162 163 2.440247 CGGCCCATTTCCACTCCC 60.440 66.667 0.00 0.00 0.00 4.30
414 417 4.851179 GCCCGATCCCACCCGAAC 62.851 72.222 0.00 0.00 0.00 3.95
415 418 4.171103 CCCGATCCCACCCGAACC 62.171 72.222 0.00 0.00 0.00 3.62
416 419 4.171103 CCGATCCCACCCGAACCC 62.171 72.222 0.00 0.00 0.00 4.11
417 420 4.171103 CGATCCCACCCGAACCCC 62.171 72.222 0.00 0.00 0.00 4.95
418 421 3.805497 GATCCCACCCGAACCCCC 61.805 72.222 0.00 0.00 0.00 5.40
419 422 4.686437 ATCCCACCCGAACCCCCA 62.686 66.667 0.00 0.00 0.00 4.96
427 430 4.029809 CGAACCCCCACCCACCTC 62.030 72.222 0.00 0.00 0.00 3.85
428 431 3.658422 GAACCCCCACCCACCTCC 61.658 72.222 0.00 0.00 0.00 4.30
434 437 3.420482 CCACCCACCTCCCCCATC 61.420 72.222 0.00 0.00 0.00 3.51
435 438 2.613696 CACCCACCTCCCCCATCA 60.614 66.667 0.00 0.00 0.00 3.07
436 439 2.614013 ACCCACCTCCCCCATCAC 60.614 66.667 0.00 0.00 0.00 3.06
437 440 3.420482 CCCACCTCCCCCATCACC 61.420 72.222 0.00 0.00 0.00 4.02
438 441 3.797353 CCACCTCCCCCATCACCG 61.797 72.222 0.00 0.00 0.00 4.94
439 442 4.489771 CACCTCCCCCATCACCGC 62.490 72.222 0.00 0.00 0.00 5.68
474 477 2.102357 CGGATCCGGACGTCAGTG 59.898 66.667 26.95 7.80 35.56 3.66
475 478 2.494918 GGATCCGGACGTCAGTGG 59.505 66.667 18.91 15.49 0.00 4.00
476 479 2.202756 GATCCGGACGTCAGTGGC 60.203 66.667 18.91 0.00 0.00 5.01
477 480 2.994995 ATCCGGACGTCAGTGGCA 60.995 61.111 18.91 6.61 0.00 4.92
478 481 3.296709 ATCCGGACGTCAGTGGCAC 62.297 63.158 18.91 10.29 0.00 5.01
479 482 4.293648 CCGGACGTCAGTGGCACA 62.294 66.667 21.41 0.00 0.00 4.57
490 493 4.314440 TGGCACACCAGCGACCTC 62.314 66.667 0.00 0.00 42.67 3.85
492 495 4.357947 GCACACCAGCGACCTCGA 62.358 66.667 0.00 0.00 43.02 4.04
493 496 2.126307 CACACCAGCGACCTCGAG 60.126 66.667 5.13 5.13 43.02 4.04
494 497 4.057428 ACACCAGCGACCTCGAGC 62.057 66.667 6.99 0.00 43.02 5.03
495 498 4.803426 CACCAGCGACCTCGAGCC 62.803 72.222 6.99 0.00 43.02 4.70
497 500 4.504916 CCAGCGACCTCGAGCCAG 62.505 72.222 6.99 0.66 43.02 4.85
498 501 4.504916 CAGCGACCTCGAGCCAGG 62.505 72.222 6.99 0.00 43.02 4.45
990 1279 0.739462 ATCTTCGTGCGCGGAAATGA 60.739 50.000 21.04 5.22 38.89 2.57
1016 1305 3.002371 CCCCTGCCTCTTTCCTCC 58.998 66.667 0.00 0.00 0.00 4.30
1020 1309 1.631071 CCTGCCTCTTTCCTCCCTCC 61.631 65.000 0.00 0.00 0.00 4.30
1024 1315 1.045911 CCTCTTTCCTCCCTCCCTCG 61.046 65.000 0.00 0.00 0.00 4.63
1134 1429 1.329913 GCCCCCAAATCGCCATTTCT 61.330 55.000 0.00 0.00 28.97 2.52
1135 1430 0.746659 CCCCCAAATCGCCATTTCTC 59.253 55.000 0.00 0.00 28.97 2.87
1199 1494 3.147595 CAGATCGAGACCGGCCCA 61.148 66.667 0.00 0.00 36.24 5.36
1634 1932 3.213402 CCTCCCCGCTCGTCTCTC 61.213 72.222 0.00 0.00 0.00 3.20
1840 2139 2.773993 TGCTGCTCAAGTCATCATCA 57.226 45.000 0.00 0.00 0.00 3.07
1926 2225 2.027745 TGAGAGGTTACCGTAGTCTCGT 60.028 50.000 11.92 0.00 37.13 4.18
1931 2230 2.030805 GGTTACCGTAGTCTCGTGTTGT 60.031 50.000 0.00 0.00 0.00 3.32
1932 2231 3.229552 GTTACCGTAGTCTCGTGTTGTC 58.770 50.000 0.00 0.00 0.00 3.18
2006 2305 0.108851 GCTTGGTTTGGTAATGGCCG 60.109 55.000 0.00 0.00 0.00 6.13
2009 2308 0.402504 TGGTTTGGTAATGGCCGAGT 59.597 50.000 0.00 0.00 0.00 4.18
2030 2329 6.092122 CGAGTTATCTTCTAAATGGTGCAACA 59.908 38.462 7.04 7.04 39.98 3.33
2114 2414 0.317160 AGGCGTGTCAAAGATGTCGA 59.683 50.000 0.00 0.00 0.00 4.20
2173 2473 5.163550 TGTCGTTGGTCTATTGGATAGTGAG 60.164 44.000 0.00 0.00 34.47 3.51
2198 2498 5.813672 GCTATACCATTCGAAGGTGTTTACA 59.186 40.000 22.04 7.84 40.26 2.41
2200 2500 6.677781 ATACCATTCGAAGGTGTTTACATG 57.322 37.500 22.04 5.57 40.26 3.21
2216 2516 0.662619 CATGTGGTGCAAGTCGTGTT 59.337 50.000 0.00 0.00 0.00 3.32
2478 2783 4.004314 TGGAAGCCATTGCAATTTGATTG 58.996 39.130 9.83 0.00 43.06 2.67
2520 2825 5.387342 GCTTGACGTGCATTAATTTGTTGAC 60.387 40.000 0.00 0.00 0.00 3.18
2522 2827 5.448438 TGACGTGCATTAATTTGTTGACTC 58.552 37.500 0.00 0.00 0.00 3.36
2659 2964 0.180642 TACCTTTGCAACCCGACACA 59.819 50.000 0.00 0.00 0.00 3.72
2811 3303 3.390135 CGTTACACTTTCTCCTTCAGCA 58.610 45.455 0.00 0.00 0.00 4.41
3270 3762 7.670605 ATGTAAGTGCTATAGTTACCTTCCA 57.329 36.000 0.84 0.00 42.18 3.53
3598 4093 9.189156 ACTTAAAGGCAGAAAATATGAAGCATA 57.811 29.630 0.00 0.00 0.00 3.14
4077 4572 4.322804 GCTGAAATGAAGTCAAATGAAGCG 59.677 41.667 0.00 0.00 0.00 4.68
4173 4668 0.737715 GACGAAGCGCCTCAAGTGAT 60.738 55.000 2.29 0.00 0.00 3.06
4256 4772 2.037772 AGTTGAATCCGCTCACTTCTGT 59.962 45.455 0.00 0.00 0.00 3.41
4422 4947 1.489230 TCATGCTCCAGTGATCATGCT 59.511 47.619 0.00 0.00 42.28 3.79
4476 5001 2.920490 GAGAAGTTCTACTGCTGCTTCG 59.080 50.000 5.09 0.00 33.16 3.79
4554 5079 1.003233 GTCCGTCTTGGTTCTGGGATT 59.997 52.381 0.00 0.00 39.52 3.01
4716 5241 0.382158 GCTTTCCAAATCCTAGCCGC 59.618 55.000 0.00 0.00 0.00 6.53
4818 5349 4.590487 GAACAGAATGGTCGGCGA 57.410 55.556 4.99 4.99 46.44 5.54
5010 5547 0.957395 CATCACGGCCTGCAAGTTCT 60.957 55.000 0.00 0.00 0.00 3.01
5346 5889 1.609208 TGGTGAAGCAAGAGAAAGCC 58.391 50.000 0.00 0.00 0.00 4.35
5421 5964 3.795639 TGCATGACAACAAAATCACAACG 59.204 39.130 0.00 0.00 0.00 4.10
5506 6049 2.920076 AAACCAAGCGGAGGGTTGCA 62.920 55.000 5.38 0.00 46.33 4.08
5550 6093 1.168714 GGGCTGATTCACAAGGTGAC 58.831 55.000 0.00 0.00 42.60 3.67
5634 6177 4.452825 CATTCATCTGCAGGTCAAGATCT 58.547 43.478 15.13 0.00 0.00 2.75
5823 6366 5.768317 TGCCTTGTTAAAGCAAACTGATAC 58.232 37.500 0.00 0.00 31.51 2.24
5882 6434 2.104170 TGGATACACGTGATGGCAGTA 58.896 47.619 25.01 1.93 46.17 2.74
5883 6435 2.159156 TGGATACACGTGATGGCAGTAC 60.159 50.000 25.01 2.90 46.17 2.73
5884 6436 2.100916 GGATACACGTGATGGCAGTACT 59.899 50.000 25.01 0.00 0.00 2.73
5886 6438 0.037326 ACACGTGATGGCAGTACTGG 60.037 55.000 25.01 8.13 0.00 4.00
6067 6640 3.563808 TGCCGAATGGGATTAAAGAATCG 59.436 43.478 0.00 0.00 42.20 3.34
6074 6647 7.516198 AATGGGATTAAAGAATCGAAGGATG 57.484 36.000 0.00 0.00 42.20 3.51
6517 7090 1.740332 TTCGTCCTGCAGAACCACGA 61.740 55.000 17.39 18.82 37.69 4.35
6536 7109 2.162681 GAAAGGTTGTGGGGACATCTG 58.837 52.381 0.00 0.00 46.14 2.90
6572 7145 1.499368 TGTAGGATCTGATGCTGCCA 58.501 50.000 20.29 13.81 32.61 4.92
6706 7279 1.743958 AGTAGAAGTCGTGATGGTCCG 59.256 52.381 0.00 0.00 0.00 4.79
6832 7405 0.815734 CAGCAAGATCTTTGCCAGGG 59.184 55.000 19.67 4.77 45.98 4.45
6932 7505 0.475906 AGAGCCTGCACAAAGGAGTT 59.524 50.000 0.00 0.00 40.02 3.01
6994 7567 6.240894 TCAAGTTGCTGGTCTTAGAATGAAT 58.759 36.000 0.00 0.00 0.00 2.57
7031 7604 3.495331 AACATGTCACCATGGTTTGCTA 58.505 40.909 16.84 0.20 47.00 3.49
7174 7747 3.347216 CCAATTCGGAAGTGATTCAGGT 58.653 45.455 18.78 0.00 36.56 4.00
7196 7769 0.954452 GGCTCCAGTTGTTTCCACAG 59.046 55.000 0.00 0.00 33.22 3.66
7315 7888 2.479837 TCGACGTCATATGCCAATTCC 58.520 47.619 17.16 0.00 0.00 3.01
7331 7904 2.731691 TTCCGCACCTGCAGGAGTTC 62.732 60.000 39.19 21.07 41.80 3.01
7441 8014 2.168521 TGAAGGTAGCAGTAGTGATGGC 59.831 50.000 0.42 0.00 0.00 4.40
7769 8348 9.292195 TGTACCTAGAAAATCCAACTTTAAAGG 57.708 33.333 19.14 2.97 0.00 3.11
7944 8523 0.106519 GACATGGGATTGTGGGAGGG 60.107 60.000 0.00 0.00 0.00 4.30
8160 8741 1.665137 ATTAGTCCCGGTGGTTCCTT 58.335 50.000 0.00 0.00 0.00 3.36
8169 8750 3.118555 CCCGGTGGTTCCTTTTTCTTTTT 60.119 43.478 0.00 0.00 0.00 1.94
8170 8751 4.116961 CCGGTGGTTCCTTTTTCTTTTTC 58.883 43.478 0.00 0.00 0.00 2.29
8265 8846 0.179073 GCCGTGACATGTATCCTGCT 60.179 55.000 0.00 0.00 0.00 4.24
8280 8866 2.086869 CCTGCTGGGAAGTGTTACATG 58.913 52.381 0.71 0.00 37.23 3.21
8286 8872 4.322801 GCTGGGAAGTGTTACATGAGTAGT 60.323 45.833 0.00 0.00 0.00 2.73
8288 8874 5.547465 TGGGAAGTGTTACATGAGTAGTTG 58.453 41.667 0.00 0.00 0.00 3.16
8335 8923 1.201414 CCCTGTTATTTCCGTGTTGGC 59.799 52.381 0.00 0.00 37.80 4.52
8368 8960 3.441922 TGTGGCGCAAATGCTCTATTTTA 59.558 39.130 10.83 0.00 36.87 1.52
8394 8986 3.684788 CGACTTGTTTCTCCATTGTAGGG 59.315 47.826 0.00 0.00 0.00 3.53
8400 8992 0.694444 TCTCCATTGTAGGGGGAGGC 60.694 60.000 7.05 0.00 46.55 4.70
8404 8996 0.107017 CATTGTAGGGGGAGGCTGTG 60.107 60.000 0.00 0.00 0.00 3.66
8434 9034 1.673665 CTGCACCTTCCTGCTCACC 60.674 63.158 0.00 0.00 38.07 4.02
8436 9036 2.046892 CACCTTCCTGCTCACCGG 60.047 66.667 0.00 0.00 0.00 5.28
8506 9106 6.040278 TCTGTTGCATCAGTAATTTTTGACCA 59.960 34.615 21.24 0.00 36.85 4.02
8513 9113 6.012658 TCAGTAATTTTTGACCACTGCATC 57.987 37.500 0.00 0.00 37.20 3.91
8514 9114 5.048083 TCAGTAATTTTTGACCACTGCATCC 60.048 40.000 0.00 0.00 37.20 3.51
8515 9115 3.302365 AATTTTTGACCACTGCATCCG 57.698 42.857 0.00 0.00 0.00 4.18
8523 9123 1.067084 CACTGCATCCGCGATCTCT 59.933 57.895 8.23 0.00 42.97 3.10
8526 9126 0.529337 CTGCATCCGCGATCTCTGTT 60.529 55.000 8.23 0.00 42.97 3.16
8563 9163 1.540267 GATGCTGATGGATGATGGTGC 59.460 52.381 0.00 0.00 0.00 5.01
8621 9231 9.060347 CCATTTGTATTCTGCTACTTGTCATAT 57.940 33.333 0.00 0.00 0.00 1.78
8626 9236 9.665719 TGTATTCTGCTACTTGTCATATTTTGA 57.334 29.630 0.00 0.00 0.00 2.69
8701 9320 3.126001 AGTGAAGATGAAGCGGAACAA 57.874 42.857 0.00 0.00 0.00 2.83
8739 9375 2.418356 GGTTCACGGTCCGACACA 59.582 61.111 20.51 0.00 0.00 3.72
8863 9502 2.659016 GGGGAAAAAGCAGCAGCC 59.341 61.111 0.00 0.00 43.56 4.85
8883 9522 1.682087 CGAGGGGGAAAAGGATGGAAC 60.682 57.143 0.00 0.00 0.00 3.62
8986 9625 2.236395 CTCGCTTTCTTTCCCTTCCCTA 59.764 50.000 0.00 0.00 0.00 3.53
9009 9648 0.114954 TGCCATGCCTTCCTTCCTTT 59.885 50.000 0.00 0.00 0.00 3.11
9013 9652 1.084018 ATGCCTTCCTTCCTTTCCCA 58.916 50.000 0.00 0.00 0.00 4.37
9017 9656 1.303317 TTCCTTCCTTTCCCAGCGC 60.303 57.895 0.00 0.00 0.00 5.92
9084 9736 4.849329 CGTAGGCGCGTCCAGTCC 62.849 72.222 19.30 6.24 37.29 3.85
9085 9737 4.849329 GTAGGCGCGTCCAGTCCG 62.849 72.222 19.30 0.00 37.29 4.79
9091 9743 4.436998 GCGTCCAGTCCGGTCCAG 62.437 72.222 0.00 0.00 35.57 3.86
9092 9744 2.989824 CGTCCAGTCCGGTCCAGT 60.990 66.667 0.00 0.00 35.57 4.00
9093 9745 2.971452 GTCCAGTCCGGTCCAGTC 59.029 66.667 0.00 0.00 35.57 3.51
9121 9773 0.676151 CTTTCCTCAGCTGCCTGTCC 60.676 60.000 9.47 0.00 40.09 4.02
9123 9775 1.548357 TTCCTCAGCTGCCTGTCCTC 61.548 60.000 9.47 0.00 40.09 3.71
9207 9864 3.988379 TCCCGTTATTAATACGCGTCT 57.012 42.857 18.63 1.73 37.67 4.18
9299 9956 0.611200 TCCCGTCAACATCATCCGTT 59.389 50.000 0.00 0.00 0.00 4.44
9300 9957 1.006832 CCCGTCAACATCATCCGTTC 58.993 55.000 0.00 0.00 0.00 3.95
9301 9958 1.006832 CCGTCAACATCATCCGTTCC 58.993 55.000 0.00 0.00 0.00 3.62
9302 9959 1.674519 CCGTCAACATCATCCGTTCCA 60.675 52.381 0.00 0.00 0.00 3.53
9303 9960 2.279741 CGTCAACATCATCCGTTCCAT 58.720 47.619 0.00 0.00 0.00 3.41
9304 9961 3.453424 CGTCAACATCATCCGTTCCATA 58.547 45.455 0.00 0.00 0.00 2.74
9305 9962 3.868661 CGTCAACATCATCCGTTCCATAA 59.131 43.478 0.00 0.00 0.00 1.90
9306 9963 4.511454 CGTCAACATCATCCGTTCCATAAT 59.489 41.667 0.00 0.00 0.00 1.28
9307 9964 5.007626 CGTCAACATCATCCGTTCCATAATT 59.992 40.000 0.00 0.00 0.00 1.40
9308 9965 6.458206 CGTCAACATCATCCGTTCCATAATTT 60.458 38.462 0.00 0.00 0.00 1.82
9309 9966 7.257722 GTCAACATCATCCGTTCCATAATTTT 58.742 34.615 0.00 0.00 0.00 1.82
9310 9967 7.220683 GTCAACATCATCCGTTCCATAATTTTG 59.779 37.037 0.00 0.00 0.00 2.44
9311 9968 6.773976 ACATCATCCGTTCCATAATTTTGT 57.226 33.333 0.00 0.00 0.00 2.83
9312 9969 7.873719 ACATCATCCGTTCCATAATTTTGTA 57.126 32.000 0.00 0.00 0.00 2.41
9313 9970 8.463930 ACATCATCCGTTCCATAATTTTGTAT 57.536 30.769 0.00 0.00 0.00 2.29
9314 9971 8.912988 ACATCATCCGTTCCATAATTTTGTATT 58.087 29.630 0.00 0.00 0.00 1.89
9315 9972 9.748708 CATCATCCGTTCCATAATTTTGTATTT 57.251 29.630 0.00 0.00 0.00 1.40
9316 9973 9.965824 ATCATCCGTTCCATAATTTTGTATTTC 57.034 29.630 0.00 0.00 0.00 2.17
9317 9974 8.126074 TCATCCGTTCCATAATTTTGTATTTCG 58.874 33.333 0.00 0.00 0.00 3.46
9318 9975 7.380431 TCCGTTCCATAATTTTGTATTTCGT 57.620 32.000 0.00 0.00 0.00 3.85
9319 9976 7.244898 TCCGTTCCATAATTTTGTATTTCGTG 58.755 34.615 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
162 163 2.247267 GTCCGTGTTGTTTCGCCG 59.753 61.111 0.00 0.00 0.00 6.46
397 400 4.851179 GTTCGGGTGGGATCGGGC 62.851 72.222 0.00 0.00 0.00 6.13
398 401 4.171103 GGTTCGGGTGGGATCGGG 62.171 72.222 0.00 0.00 0.00 5.14
399 402 4.171103 GGGTTCGGGTGGGATCGG 62.171 72.222 0.00 0.00 0.00 4.18
400 403 4.171103 GGGGTTCGGGTGGGATCG 62.171 72.222 0.00 0.00 0.00 3.69
401 404 3.805497 GGGGGTTCGGGTGGGATC 61.805 72.222 0.00 0.00 0.00 3.36
402 405 4.686437 TGGGGGTTCGGGTGGGAT 62.686 66.667 0.00 0.00 0.00 3.85
410 413 4.029809 GAGGTGGGTGGGGGTTCG 62.030 72.222 0.00 0.00 0.00 3.95
411 414 3.658422 GGAGGTGGGTGGGGGTTC 61.658 72.222 0.00 0.00 0.00 3.62
417 420 3.420482 GATGGGGGAGGTGGGTGG 61.420 72.222 0.00 0.00 0.00 4.61
418 421 2.613696 TGATGGGGGAGGTGGGTG 60.614 66.667 0.00 0.00 0.00 4.61
419 422 2.614013 GTGATGGGGGAGGTGGGT 60.614 66.667 0.00 0.00 0.00 4.51
420 423 3.420482 GGTGATGGGGGAGGTGGG 61.420 72.222 0.00 0.00 0.00 4.61
421 424 3.797353 CGGTGATGGGGGAGGTGG 61.797 72.222 0.00 0.00 0.00 4.61
422 425 4.489771 GCGGTGATGGGGGAGGTG 62.490 72.222 0.00 0.00 0.00 4.00
457 460 2.102357 CACTGACGTCCGGATCCG 59.898 66.667 27.65 27.65 39.44 4.18
458 461 2.494918 CCACTGACGTCCGGATCC 59.505 66.667 14.12 0.00 0.00 3.36
459 462 2.202756 GCCACTGACGTCCGGATC 60.203 66.667 14.12 1.89 0.00 3.36
460 463 2.994995 TGCCACTGACGTCCGGAT 60.995 61.111 14.12 0.00 0.00 4.18
461 464 3.986006 GTGCCACTGACGTCCGGA 61.986 66.667 14.12 0.00 0.00 5.14
462 465 4.293648 TGTGCCACTGACGTCCGG 62.294 66.667 14.12 12.03 0.00 5.14
463 466 3.036084 GTGTGCCACTGACGTCCG 61.036 66.667 14.12 9.58 0.00 4.79
464 467 2.665185 GGTGTGCCACTGACGTCC 60.665 66.667 14.12 0.00 34.40 4.79
465 468 1.956170 CTGGTGTGCCACTGACGTC 60.956 63.158 9.11 9.11 40.46 4.34
466 469 2.108976 CTGGTGTGCCACTGACGT 59.891 61.111 0.00 0.00 40.46 4.34
467 470 3.349006 GCTGGTGTGCCACTGACG 61.349 66.667 0.00 0.00 40.46 4.35
468 471 3.349006 CGCTGGTGTGCCACTGAC 61.349 66.667 0.00 0.00 40.46 3.51
469 472 3.545574 TCGCTGGTGTGCCACTGA 61.546 61.111 0.00 0.00 40.46 3.41
470 473 3.349006 GTCGCTGGTGTGCCACTG 61.349 66.667 0.00 1.56 40.46 3.66
471 474 4.626081 GGTCGCTGGTGTGCCACT 62.626 66.667 0.00 0.00 40.46 4.00
472 475 4.626081 AGGTCGCTGGTGTGCCAC 62.626 66.667 0.00 0.00 40.46 5.01
473 476 4.314440 GAGGTCGCTGGTGTGCCA 62.314 66.667 0.00 0.00 43.73 4.92
475 478 4.357947 TCGAGGTCGCTGGTGTGC 62.358 66.667 0.00 0.00 39.60 4.57
476 479 2.126307 CTCGAGGTCGCTGGTGTG 60.126 66.667 3.91 0.00 39.60 3.82
477 480 4.057428 GCTCGAGGTCGCTGGTGT 62.057 66.667 15.58 0.00 39.60 4.16
478 481 4.803426 GGCTCGAGGTCGCTGGTG 62.803 72.222 15.58 0.00 39.60 4.17
480 483 4.504916 CTGGCTCGAGGTCGCTGG 62.505 72.222 15.58 0.00 39.60 4.85
481 484 4.504916 CCTGGCTCGAGGTCGCTG 62.505 72.222 15.58 0.00 39.60 5.18
856 1129 2.661866 GCACTGTTGACTCGCCGT 60.662 61.111 0.00 0.00 0.00 5.68
857 1130 3.414700 GGCACTGTTGACTCGCCG 61.415 66.667 0.00 0.00 32.14 6.46
858 1131 3.050275 GGGCACTGTTGACTCGCC 61.050 66.667 0.00 0.00 42.21 5.54
990 1279 3.645268 GAGGCAGGGGCATTTCCGT 62.645 63.158 0.00 0.00 43.71 4.69
1134 1429 1.518367 GGGGGAGAGAGAGAGAGAGA 58.482 60.000 0.00 0.00 0.00 3.10
1721 2019 4.154347 GAGTCTGCTGAGGGCGGG 62.154 72.222 0.00 0.00 46.69 6.13
1840 2139 2.750141 AGCAGAAATGATGGCCATCT 57.250 45.000 38.59 23.99 38.60 2.90
1926 2225 1.664649 CAGGAGCTTCGCGACAACA 60.665 57.895 9.15 0.00 0.00 3.33
1952 2251 5.395657 CCCGGCACAGATGATGTATATGTAT 60.396 44.000 0.00 0.00 39.11 2.29
2006 2305 7.377766 TGTTGCACCATTTAGAAGATAACTC 57.622 36.000 0.00 0.00 0.00 3.01
2009 2308 6.719370 ACCTTGTTGCACCATTTAGAAGATAA 59.281 34.615 0.00 0.00 0.00 1.75
2114 2414 5.710513 TTCTTATCATGCAAGCAACAAGT 57.289 34.783 0.00 0.00 0.00 3.16
2173 2473 3.470645 ACACCTTCGAATGGTATAGCC 57.529 47.619 15.86 0.00 35.80 3.93
2198 2498 0.662619 CAACACGACTTGCACCACAT 59.337 50.000 0.00 0.00 0.00 3.21
2200 2500 0.248054 CACAACACGACTTGCACCAC 60.248 55.000 0.00 0.00 0.00 4.16
2216 2516 7.148869 CGTTATCTTAATGAAGTCGTGAACACA 60.149 37.037 5.80 0.00 34.03 3.72
2478 2783 7.537306 ACGTCAAGCATGTAATAAAACATTCAC 59.463 33.333 0.00 0.00 38.01 3.18
2520 2825 8.698973 TGTTCTTATAAGGAGATACTCTGGAG 57.301 38.462 12.54 0.00 0.00 3.86
2729 3221 9.077885 AGCATAACTGAACCAAAAATAGAAAGA 57.922 29.630 0.00 0.00 0.00 2.52
2811 3303 6.166984 ACATCTTCATGTCACGAGGATAAT 57.833 37.500 0.00 0.00 39.15 1.28
3137 3629 1.195448 CAGCTCAACACCTTTGCGTAG 59.805 52.381 0.00 0.00 0.00 3.51
3412 3904 3.452990 TGGGCAGATGACGGACTATTTAA 59.547 43.478 0.00 0.00 0.00 1.52
3598 4093 6.894828 ACTTCGCGATAAACTTTGTAAATGT 58.105 32.000 10.88 0.00 35.51 2.71
4077 4572 6.092807 CAGCTTGACCAGATACTAAAGGTTTC 59.907 42.308 0.00 0.00 33.77 2.78
4173 4668 0.821711 CTGGGTTTTTCGGACTGGCA 60.822 55.000 0.00 0.00 0.00 4.92
4238 4754 1.895798 AGACAGAAGTGAGCGGATTCA 59.104 47.619 0.00 0.00 0.00 2.57
4256 4772 4.923893 CATGTGTTGCAACTTTGAAGAGA 58.076 39.130 28.61 7.11 0.00 3.10
4285 4801 2.425312 TCGAGTTGGTTGCAACATTTGT 59.575 40.909 29.55 10.79 37.52 2.83
4476 5001 3.181500 CGGAAGTTTTACTAGCATTGCCC 60.181 47.826 4.70 0.00 0.00 5.36
4554 5079 2.151202 CCCGCAGTAGCTTCTTTTTGA 58.849 47.619 0.00 0.00 39.10 2.69
4689 5214 3.165071 AGGATTTGGAAAGCGGACAATT 58.835 40.909 0.00 0.00 0.00 2.32
4716 5241 2.560542 ACTCACACTTCTAGCAGGACTG 59.439 50.000 0.00 0.00 0.00 3.51
4818 5349 9.403110 CGAGAATTTTCAATCTTCATTTTCACT 57.597 29.630 0.00 0.00 0.00 3.41
5010 5547 3.738982 TCCTTTCTCATTCACTTGCGAA 58.261 40.909 0.00 0.00 0.00 4.70
5346 5889 3.504863 CTTGGCAATCAAACAAGGATCG 58.495 45.455 0.00 0.00 38.29 3.69
5370 5913 0.896226 GAGCCCTCTGGTTACGTTCT 59.104 55.000 0.00 0.00 0.00 3.01
5421 5964 0.533032 GAGGTGACAGCCCAGTAGAC 59.467 60.000 0.00 0.00 0.00 2.59
5506 6049 4.080526 AGGTACAGGAAGACACTTGTTTGT 60.081 41.667 0.00 0.00 32.63 2.83
5634 6177 1.472082 CACGGCTGGAACATGCATTAA 59.528 47.619 0.00 0.00 38.20 1.40
5823 6366 1.175983 TACAACCCCAAGCGGCTTTG 61.176 55.000 13.53 9.83 0.00 2.77
5882 6434 5.838521 ACTTCAAATCCAATTTACCACCAGT 59.161 36.000 0.00 0.00 0.00 4.00
5883 6435 6.209391 AGACTTCAAATCCAATTTACCACCAG 59.791 38.462 0.00 0.00 0.00 4.00
5884 6436 6.074648 AGACTTCAAATCCAATTTACCACCA 58.925 36.000 0.00 0.00 0.00 4.17
5886 6438 7.657336 TGAAGACTTCAAATCCAATTTACCAC 58.343 34.615 15.58 0.00 36.59 4.16
6067 6640 2.939103 CGATTCACTGGAACCATCCTTC 59.061 50.000 0.00 0.00 46.70 3.46
6074 6647 3.192844 TGACTACTCGATTCACTGGAACC 59.807 47.826 0.00 0.00 35.46 3.62
6517 7090 1.499007 ACAGATGTCCCCACAACCTTT 59.501 47.619 0.00 0.00 35.64 3.11
6536 7109 4.122776 CCTACAATATCAGGTGCAGTCAC 58.877 47.826 0.00 0.00 42.40 3.67
6661 7234 3.519107 TGCCAGATTCAGATCCAACTGTA 59.481 43.478 0.00 0.00 38.79 2.74
6697 7270 2.264480 CTTCGCACCGGACCATCA 59.736 61.111 9.46 0.00 0.00 3.07
6832 7405 6.699575 TTCATACTAGTACTCGGTAAACCC 57.300 41.667 4.31 0.00 0.00 4.11
6932 7505 5.300752 GCTGCTAGCACCTTTAGATGATAA 58.699 41.667 14.93 0.00 41.89 1.75
6994 7567 3.761218 ACATGTTATTGATTTCGGTGCCA 59.239 39.130 0.00 0.00 0.00 4.92
7031 7604 0.106519 GGAGCATATGGGTTGGCAGT 60.107 55.000 4.56 0.00 0.00 4.40
7174 7747 1.073284 GTGGAAACAACTGGAGCCCTA 59.927 52.381 0.00 0.00 46.06 3.53
7315 7888 2.743928 GGAACTCCTGCAGGTGCG 60.744 66.667 31.58 22.06 45.83 5.34
7331 7904 2.168313 GGGCAATGGTTGGAAAGTATGG 59.832 50.000 0.00 0.00 0.00 2.74
7441 8014 4.513442 TCCATTTCCAATTACTGTCGAGG 58.487 43.478 0.00 0.00 0.00 4.63
7769 8348 5.715434 TTAACCAAACAAGATAACAGGGC 57.285 39.130 0.00 0.00 0.00 5.19
7801 8380 2.037121 GCAAACATAAAAGCACCCACCT 59.963 45.455 0.00 0.00 0.00 4.00
7876 8455 1.134965 GTATATCCTAGCCCAGCAGCG 60.135 57.143 0.00 0.00 38.01 5.18
7888 8467 6.753913 ATCCATGTGTGAGTTGTATATCCT 57.246 37.500 0.00 0.00 0.00 3.24
7944 8523 5.290158 CAGCAATTACAGCCATGTTTCATTC 59.710 40.000 0.00 0.00 41.01 2.67
8265 8846 5.305902 TCAACTACTCATGTAACACTTCCCA 59.694 40.000 0.00 0.00 0.00 4.37
8280 8866 8.417884 AGCAGATTATTAGTTCCTCAACTACTC 58.582 37.037 0.00 0.00 43.53 2.59
8286 8872 6.115446 CCACAGCAGATTATTAGTTCCTCAA 58.885 40.000 0.00 0.00 0.00 3.02
8288 8874 4.513318 GCCACAGCAGATTATTAGTTCCTC 59.487 45.833 0.00 0.00 39.53 3.71
8335 8923 1.159713 TGCGCCACACAGAACAGAAG 61.160 55.000 4.18 0.00 0.00 2.85
8368 8960 2.549754 CAATGGAGAAACAAGTCGCAGT 59.450 45.455 0.00 0.00 0.00 4.40
8394 8986 2.597510 AAAACGCCACAGCCTCCC 60.598 61.111 0.00 0.00 34.57 4.30
8400 8992 1.659335 CAGCTGCAAAACGCCACAG 60.659 57.895 0.00 0.00 41.33 3.66
8436 9036 0.452122 AATTTACAACAGACGCGCGC 60.452 50.000 32.58 23.91 0.00 6.86
8506 9106 1.067084 CAGAGATCGCGGATGCAGT 59.933 57.895 6.13 0.00 42.97 4.40
8513 9113 1.874019 CGACCAACAGAGATCGCGG 60.874 63.158 6.13 0.00 0.00 6.46
8514 9114 0.098200 TACGACCAACAGAGATCGCG 59.902 55.000 0.00 0.00 38.12 5.87
8515 9115 1.534175 CCTACGACCAACAGAGATCGC 60.534 57.143 0.00 0.00 38.12 4.58
8523 9123 0.036164 AGCAATGCCTACGACCAACA 59.964 50.000 0.00 0.00 0.00 3.33
8526 9126 0.541392 ATCAGCAATGCCTACGACCA 59.459 50.000 0.00 0.00 0.00 4.02
8555 9155 0.178995 TCAGCAAACAGGCACCATCA 60.179 50.000 0.00 0.00 35.83 3.07
8563 9163 2.355132 GAGATCAGCATCAGCAAACAGG 59.645 50.000 0.00 0.00 45.49 4.00
8621 9231 6.816136 TGTCAGACTGTAGAGATGTTCAAAA 58.184 36.000 1.59 0.00 0.00 2.44
8622 9232 6.405278 TGTCAGACTGTAGAGATGTTCAAA 57.595 37.500 1.59 0.00 0.00 2.69
8624 9234 5.711976 TCATGTCAGACTGTAGAGATGTTCA 59.288 40.000 14.98 0.00 36.99 3.18
8626 9236 5.478332 TGTCATGTCAGACTGTAGAGATGTT 59.522 40.000 14.98 0.00 39.27 2.71
8731 9367 1.299850 CTCTTGCGTGTGTGTCGGA 60.300 57.895 0.00 0.00 0.00 4.55
8839 9475 1.228429 TGCTTTTTCCCCCACCTCG 60.228 57.895 0.00 0.00 0.00 4.63
8863 9502 0.623723 TTCCATCCTTTTCCCCCTCG 59.376 55.000 0.00 0.00 0.00 4.63
8986 9625 2.505364 GAAGGAAGGCATGGCAGGGT 62.505 60.000 22.64 3.12 0.00 4.34
9013 9652 3.363844 GAAAGAGAGGAGGCGCGCT 62.364 63.158 32.29 17.27 0.00 5.92
9017 9656 2.202810 GCGGAAAGAGAGGAGGCG 60.203 66.667 0.00 0.00 0.00 5.52
9085 9737 4.131088 GCGACGGGAGACTGGACC 62.131 72.222 0.00 0.00 42.76 4.46
9086 9738 2.156051 AAAGCGACGGGAGACTGGAC 62.156 60.000 0.00 0.00 42.76 4.02
9087 9739 1.874345 GAAAGCGACGGGAGACTGGA 61.874 60.000 0.00 0.00 42.76 3.86
9088 9740 1.446272 GAAAGCGACGGGAGACTGG 60.446 63.158 0.00 0.00 42.76 4.00
9089 9741 1.446272 GGAAAGCGACGGGAGACTG 60.446 63.158 0.00 0.00 44.60 3.51
9090 9742 1.596895 GAGGAAAGCGACGGGAGACT 61.597 60.000 0.00 0.00 0.00 3.24
9091 9743 1.153804 GAGGAAAGCGACGGGAGAC 60.154 63.158 0.00 0.00 0.00 3.36
9092 9744 1.595993 CTGAGGAAAGCGACGGGAGA 61.596 60.000 0.00 0.00 0.00 3.71
9093 9745 1.153745 CTGAGGAAAGCGACGGGAG 60.154 63.158 0.00 0.00 0.00 4.30
9121 9773 2.103941 GGATGGAGCCCAAGTCTAAGAG 59.896 54.545 0.00 0.00 36.95 2.85
9123 9775 1.839994 TGGATGGAGCCCAAGTCTAAG 59.160 52.381 0.00 0.00 36.95 2.18
9207 9864 3.443925 CCTGCCGCTGTCGAGAGA 61.444 66.667 14.74 0.00 38.10 3.10


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

AutoCloner maintained by Alex Coulton.