Multiple sequence alignment - TraesCS4D01G109800

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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 TraesCS4D01G109800 chr4D 100.000 6940 0 0 1 6940 89428287 89421348 0.000000e+00 12816.0
1 TraesCS4D01G109800 chr4A 95.692 2716 76 12 1542 4231 501966173 501963473 0.000000e+00 4329.0
2 TraesCS4D01G109800 chr4A 94.025 1590 58 16 1 1563 501967893 501966314 0.000000e+00 2375.0
3 TraesCS4D01G109800 chr4A 95.458 1475 52 7 5471 6940 501962342 501960878 0.000000e+00 2338.0
4 TraesCS4D01G109800 chr4A 94.941 1107 30 9 4388 5478 501963473 501962377 0.000000e+00 1711.0
5 TraesCS4D01G109800 chr4B 94.308 2530 104 13 1863 4368 126327101 126324588 0.000000e+00 3838.0
6 TraesCS4D01G109800 chr4B 93.957 2234 76 19 4709 6940 126323869 126321693 0.000000e+00 3323.0
7 TraesCS4D01G109800 chr4B 94.032 1642 55 13 1 1618 126328897 126327275 0.000000e+00 2449.0
8 TraesCS4D01G109800 chr4B 97.361 341 8 1 4370 4710 126324495 126324156 4.670000e-161 579.0
9 TraesCS4D01G109800 chr4B 89.617 183 12 4 1660 1837 126327278 126327098 7.000000e-55 226.0
10 TraesCS4D01G109800 chr3A 95.732 164 7 0 4228 4391 600921016 600920853 1.480000e-66 265.0
11 TraesCS4D01G109800 chr3A 94.578 166 9 0 4226 4391 627965085 627964920 2.480000e-64 257.0
12 TraesCS4D01G109800 chr7A 94.675 169 8 1 4223 4390 494786996 494786828 1.920000e-65 261.0
13 TraesCS4D01G109800 chr5A 95.092 163 8 0 4227 4389 320214243 320214405 2.480000e-64 257.0
14 TraesCS4D01G109800 chr5A 80.876 251 46 2 1124 1373 270177651 270177402 5.490000e-46 196.0
15 TraesCS4D01G109800 chr3D 95.092 163 8 0 4227 4389 87925999 87926161 2.480000e-64 257.0
16 TraesCS4D01G109800 chr3B 93.567 171 11 0 4219 4389 654649881 654649711 8.930000e-64 255.0
17 TraesCS4D01G109800 chr3B 94.048 168 9 1 4223 4390 529407785 529407951 3.210000e-63 254.0
18 TraesCS4D01G109800 chr7B 92.090 177 13 1 4214 4389 176002816 176002992 1.490000e-61 248.0
19 TraesCS4D01G109800 chr5D 81.275 251 45 2 1124 1373 209309671 209309422 1.180000e-47 202.0
20 TraesCS4D01G109800 chr5B 81.275 251 45 2 1124 1373 222367264 222367015 1.180000e-47 202.0
21 TraesCS4D01G109800 chr5B 90.698 43 1 3 1607 1648 280647973 280648013 3.000000e-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 TraesCS4D01G109800 chr4D 89421348 89428287 6939 True 12816.00 12816 100.000 1 6940 1 chr4D.!!$R1 6939
1 TraesCS4D01G109800 chr4A 501960878 501967893 7015 True 2688.25 4329 95.029 1 6940 4 chr4A.!!$R1 6939
2 TraesCS4D01G109800 chr4B 126321693 126328897 7204 True 2083.00 3838 93.855 1 6940 5 chr4B.!!$R1 6939

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
338 340 0.109597 CCAGCAGTGAAATTCCGCAC 60.110 55.000 0.00 0.0 35.30 5.34 F
539 542 0.329596 GGAGCACCAATGGAAGGAGT 59.670 55.000 6.16 0.0 35.97 3.85 F
2048 2257 0.250513 GACAGTGTAGGGAAGCCTGG 59.749 60.000 0.00 0.0 0.00 4.45 F
3297 3508 0.322456 CGAAGAATGGGAAGCCACCA 60.322 55.000 0.00 0.0 43.22 4.17 F
3303 3514 1.229131 ATGGGAAGCCACCATCATCT 58.771 50.000 0.00 0.0 45.33 2.90 F
4899 5692 1.005805 TGTATTGCCTGCCTGGTGATT 59.994 47.619 0.00 0.0 38.35 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1529 1570 1.136961 TCCCATAACACCCCACTGCA 61.137 55.000 0.00 0.0 0.00 4.41 R
2472 2683 0.738389 CCCACGGCCACATAATTGTC 59.262 55.000 2.24 0.0 32.34 3.18 R
3447 3673 1.473257 GCTTCCATATGACACGCAGGA 60.473 52.381 3.65 0.0 0.00 3.86 R
4485 4982 0.758734 TAGAAGGTGCCATGGGATCG 59.241 55.000 15.13 0.0 0.00 3.69 R
5246 6047 1.001641 CCAACTCCTCCCTGCCAAG 60.002 63.158 0.00 0.0 0.00 3.61 R
6583 7436 1.220206 CAGAGATCGCCAAGGTGCT 59.780 57.895 0.00 0.0 0.00 4.40 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
25 26 1.410004 CAAGCCATGGGAGATGCAAT 58.590 50.000 15.13 0.00 0.00 3.56
48 49 2.570302 ACCTTCGTATTGTGCTACCCTT 59.430 45.455 0.00 0.00 0.00 3.95
132 133 1.441311 TCTGCACGCAGACACAAGA 59.559 52.632 17.54 0.00 46.80 3.02
140 141 3.418619 CACGCAGACACAAGAAAATTTCG 59.581 43.478 0.00 0.00 34.02 3.46
166 167 7.816945 AAGAAATAATCAAATTTCACAGCGG 57.183 32.000 10.86 0.00 44.70 5.52
200 202 1.463553 AAAGGGGCGGAAGTTTGCAG 61.464 55.000 3.82 0.00 0.00 4.41
233 235 3.517100 TCCAAGAGGAATGGACAGAAGAG 59.483 47.826 0.00 0.00 41.98 2.85
338 340 0.109597 CCAGCAGTGAAATTCCGCAC 60.110 55.000 0.00 0.00 35.30 5.34
350 352 4.954092 AATTCCGCACAGAAATCTTCTC 57.046 40.909 0.00 0.00 38.11 2.87
363 365 9.709495 ACAGAAATCTTCTCTAATAGATGATGC 57.291 33.333 4.69 2.05 44.34 3.91
383 385 4.183865 TGCGCATGCTATATGTATTCTCC 58.816 43.478 17.13 0.00 43.34 3.71
443 446 4.201851 ACATTCATCTGAAGGAAAATCGCG 60.202 41.667 11.17 0.00 37.99 5.87
483 486 2.422231 CCCGACAGAGGCTCAGGAG 61.422 68.421 18.26 7.07 0.00 3.69
525 528 6.064060 TCAAGAATCAAGAAAAGAAGGAGCA 58.936 36.000 0.00 0.00 0.00 4.26
539 542 0.329596 GGAGCACCAATGGAAGGAGT 59.670 55.000 6.16 0.00 35.97 3.85
852 869 3.291611 GGCCACTTTGAGCCCATG 58.708 61.111 0.00 0.00 43.76 3.66
853 870 1.607467 GGCCACTTTGAGCCCATGT 60.607 57.895 0.00 0.00 43.76 3.21
854 871 1.598701 GGCCACTTTGAGCCCATGTC 61.599 60.000 0.00 0.00 43.76 3.06
855 872 0.610232 GCCACTTTGAGCCCATGTCT 60.610 55.000 0.00 0.00 0.00 3.41
856 873 1.171308 CCACTTTGAGCCCATGTCTG 58.829 55.000 0.00 0.00 0.00 3.51
857 874 1.546323 CCACTTTGAGCCCATGTCTGT 60.546 52.381 0.00 0.00 0.00 3.41
858 875 1.808945 CACTTTGAGCCCATGTCTGTC 59.191 52.381 0.00 0.00 0.00 3.51
859 876 1.701847 ACTTTGAGCCCATGTCTGTCT 59.298 47.619 0.00 0.00 0.00 3.41
1401 1442 2.369394 CAGCCACCATTTCCTTACTCC 58.631 52.381 0.00 0.00 0.00 3.85
1427 1468 5.009854 ACTGTCATTGTTTGGGTTTTCTG 57.990 39.130 0.00 0.00 0.00 3.02
1481 1522 2.100916 GCCTCAGAATGCATTGCAGAAT 59.899 45.455 18.59 5.81 43.65 2.40
1503 1544 3.884169 TGTTCGTCTGTTTTTATGCTGC 58.116 40.909 0.00 0.00 0.00 5.25
1505 1546 4.752604 TGTTCGTCTGTTTTTATGCTGCTA 59.247 37.500 0.00 0.00 0.00 3.49
1509 1550 4.627467 CGTCTGTTTTTATGCTGCTAGTCT 59.373 41.667 0.00 0.00 0.00 3.24
1514 1555 6.889198 TGTTTTTATGCTGCTAGTCTCCTAT 58.111 36.000 0.00 0.00 0.00 2.57
1529 1570 5.721960 AGTCTCCTATGTTGGATGTAGTTGT 59.278 40.000 0.00 0.00 35.30 3.32
1566 1770 5.815233 TGGGATTGGAAATTTGCTACAAA 57.185 34.783 11.22 0.00 0.00 2.83
1629 1837 0.561184 ATGATACTCCCTCCGTCCCA 59.439 55.000 0.00 0.00 0.00 4.37
1846 2055 9.739276 TCATCTCAGTTGACCTTACAATTATTT 57.261 29.630 0.00 0.00 32.36 1.40
1847 2056 9.778993 CATCTCAGTTGACCTTACAATTATTTG 57.221 33.333 0.00 0.00 38.86 2.32
1859 2068 4.944048 ACAATTATTTGGGCTTTATCGGC 58.056 39.130 2.66 0.00 37.15 5.54
1895 2104 4.004196 AGTTCTAGAAAAGTTGGGGTCG 57.996 45.455 6.78 0.00 0.00 4.79
1910 2119 3.637229 TGGGGTCGCTAAAACATGAAAAA 59.363 39.130 0.00 0.00 0.00 1.94
2048 2257 0.250513 GACAGTGTAGGGAAGCCTGG 59.749 60.000 0.00 0.00 0.00 4.45
2142 2351 5.179929 GCTAGTCTCGGAGTATTTCTAGTCC 59.820 48.000 4.69 0.00 42.10 3.85
2233 2443 6.173191 TGTAGTTTTTACTTATCTTGCGCC 57.827 37.500 4.18 0.00 0.00 6.53
2247 2458 1.512734 GCGCCGCTGTTTGATCTTG 60.513 57.895 0.00 0.00 0.00 3.02
2291 2502 5.110814 TGTATAGGTGGAAAGGATGGTTG 57.889 43.478 0.00 0.00 0.00 3.77
2418 2629 2.146342 CGCCTTCGGATGAGCAATTAT 58.854 47.619 0.00 0.00 0.00 1.28
2427 2638 8.534333 TTCGGATGAGCAATTATAACATACTC 57.466 34.615 0.00 0.00 0.00 2.59
2445 2656 3.847081 ACTCCTAGCCTGTCCTAATACC 58.153 50.000 0.00 0.00 0.00 2.73
2460 2671 0.394565 ATACCGAGCCCAGCATTCTC 59.605 55.000 0.00 0.00 0.00 2.87
2493 2704 1.024271 CAATTATGTGGCCGTGGGAG 58.976 55.000 0.00 0.00 0.00 4.30
2592 2803 3.636153 AATTACAGGGGAGCTCTTGAC 57.364 47.619 14.64 1.76 0.00 3.18
2635 2846 2.161609 CCAAAGCACTCCGGAAATGTAC 59.838 50.000 5.23 0.00 0.00 2.90
2701 2912 2.511600 CGGTCAACGGGCCTGATC 60.512 66.667 21.41 6.06 39.42 2.92
2783 2994 6.998968 AAGCTTTATGAGAATGAGTTCTGG 57.001 37.500 0.00 0.00 44.57 3.86
2802 3013 1.745653 GGGCAAAGTATTGGTGAGAGC 59.254 52.381 0.00 0.00 37.02 4.09
2817 3028 3.380637 GTGAGAGCAAATGCCTCATTGAT 59.619 43.478 21.27 0.00 44.19 2.57
2849 3060 1.002033 GAAGCCACGATCATCCAATGC 60.002 52.381 0.00 0.00 0.00 3.56
2851 3062 0.820891 GCCACGATCATCCAATGCCT 60.821 55.000 0.00 0.00 0.00 4.75
3002 3213 2.695585 GGAGACACCTAGAATCCCCAT 58.304 52.381 0.00 0.00 35.41 4.00
3031 3242 3.133721 GGTCAACTGTATCAGGAGAGCAT 59.866 47.826 13.55 0.00 37.09 3.79
3287 3498 2.611292 GCCTCATTGAGACGAAGAATGG 59.389 50.000 15.36 0.00 0.00 3.16
3294 3505 0.984230 AGACGAAGAATGGGAAGCCA 59.016 50.000 0.00 0.00 0.00 4.75
3295 3506 1.087501 GACGAAGAATGGGAAGCCAC 58.912 55.000 0.00 0.00 0.00 5.01
3296 3507 0.322546 ACGAAGAATGGGAAGCCACC 60.323 55.000 0.00 0.00 0.00 4.61
3297 3508 0.322456 CGAAGAATGGGAAGCCACCA 60.322 55.000 0.00 0.00 43.22 4.17
3302 3513 3.835810 ATGGGAAGCCACCATCATC 57.164 52.632 0.00 0.00 45.33 2.92
3303 3514 1.229131 ATGGGAAGCCACCATCATCT 58.771 50.000 0.00 0.00 45.33 2.90
3304 3515 1.891933 TGGGAAGCCACCATCATCTA 58.108 50.000 0.00 0.00 31.83 1.98
3305 3516 2.204463 TGGGAAGCCACCATCATCTAA 58.796 47.619 0.00 0.00 31.83 2.10
3306 3517 2.580322 TGGGAAGCCACCATCATCTAAA 59.420 45.455 0.00 0.00 31.83 1.85
3307 3518 3.217626 GGGAAGCCACCATCATCTAAAG 58.782 50.000 0.00 0.00 0.00 1.85
3308 3519 3.372025 GGGAAGCCACCATCATCTAAAGT 60.372 47.826 0.00 0.00 0.00 2.66
3418 3644 2.646798 AGAGACCAAAGGAAAGCTCCAT 59.353 45.455 0.00 0.00 45.24 3.41
3447 3673 9.343539 GTAGATTTTATTAAGCCATCTGAACCT 57.656 33.333 0.00 0.00 0.00 3.50
3491 3717 2.139323 ATGGTGATCACTGCTGCAAT 57.861 45.000 24.50 0.00 0.00 3.56
3672 3898 7.092716 GGCAACATAACAGACATTTGAGAAAT 58.907 34.615 0.00 0.00 0.00 2.17
3770 3996 6.594159 AGTTTGTCAAATGACCCGTCTAATAG 59.406 38.462 10.83 0.00 44.15 1.73
4122 4369 5.091261 TGTATCTTTCCTGCTTCTCCTTC 57.909 43.478 0.00 0.00 0.00 3.46
4234 4731 7.707467 ATAACCTGGATTAACAATACTCCCT 57.293 36.000 0.00 0.00 31.46 4.20
4235 4732 5.632034 ACCTGGATTAACAATACTCCCTC 57.368 43.478 0.00 0.00 31.46 4.30
4236 4733 4.412528 ACCTGGATTAACAATACTCCCTCC 59.587 45.833 0.00 0.00 31.46 4.30
4237 4734 4.503296 CCTGGATTAACAATACTCCCTCCG 60.503 50.000 0.00 0.00 31.46 4.63
4238 4735 4.035112 TGGATTAACAATACTCCCTCCGT 58.965 43.478 0.00 0.00 31.46 4.69
4239 4736 4.472108 TGGATTAACAATACTCCCTCCGTT 59.528 41.667 0.00 0.00 31.46 4.44
4240 4737 5.055144 GGATTAACAATACTCCCTCCGTTC 58.945 45.833 0.00 0.00 0.00 3.95
4241 4738 4.476628 TTAACAATACTCCCTCCGTTCC 57.523 45.455 0.00 0.00 0.00 3.62
4242 4739 2.249309 ACAATACTCCCTCCGTTCCT 57.751 50.000 0.00 0.00 0.00 3.36
4243 4740 3.393426 ACAATACTCCCTCCGTTCCTA 57.607 47.619 0.00 0.00 0.00 2.94
4244 4741 3.716431 ACAATACTCCCTCCGTTCCTAA 58.284 45.455 0.00 0.00 0.00 2.69
4245 4742 4.098894 ACAATACTCCCTCCGTTCCTAAA 58.901 43.478 0.00 0.00 0.00 1.85
4246 4743 4.720273 ACAATACTCCCTCCGTTCCTAAAT 59.280 41.667 0.00 0.00 0.00 1.40
4247 4744 5.901276 ACAATACTCCCTCCGTTCCTAAATA 59.099 40.000 0.00 0.00 0.00 1.40
4248 4745 6.557633 ACAATACTCCCTCCGTTCCTAAATAT 59.442 38.462 0.00 0.00 0.00 1.28
4249 4746 7.731688 ACAATACTCCCTCCGTTCCTAAATATA 59.268 37.037 0.00 0.00 0.00 0.86
4250 4747 8.591072 CAATACTCCCTCCGTTCCTAAATATAA 58.409 37.037 0.00 0.00 0.00 0.98
4251 4748 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
4252 4749 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
4253 4750 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
4254 4751 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
4255 4752 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
4256 4753 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
4257 4754 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
4258 4755 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
4288 4785 6.092955 TCCAATATGGACTACATACGGAAC 57.907 41.667 0.00 0.00 42.67 3.62
4289 4786 5.599242 TCCAATATGGACTACATACGGAACA 59.401 40.000 0.00 0.00 42.67 3.18
4290 4787 6.098552 TCCAATATGGACTACATACGGAACAA 59.901 38.462 0.00 0.00 42.67 2.83
4291 4788 6.764085 CCAATATGGACTACATACGGAACAAA 59.236 38.462 0.00 0.00 44.41 2.83
4292 4789 7.281324 CCAATATGGACTACATACGGAACAAAA 59.719 37.037 0.00 0.00 44.41 2.44
4293 4790 8.836413 CAATATGGACTACATACGGAACAAAAT 58.164 33.333 0.00 0.00 44.41 1.82
4294 4791 6.677781 ATGGACTACATACGGAACAAAATG 57.322 37.500 0.00 0.00 38.26 2.32
4295 4792 5.795972 TGGACTACATACGGAACAAAATGA 58.204 37.500 0.00 0.00 0.00 2.57
4296 4793 5.872617 TGGACTACATACGGAACAAAATGAG 59.127 40.000 0.00 0.00 0.00 2.90
4297 4794 5.873164 GGACTACATACGGAACAAAATGAGT 59.127 40.000 0.00 0.00 0.00 3.41
4298 4795 6.183360 GGACTACATACGGAACAAAATGAGTG 60.183 42.308 0.00 0.00 0.00 3.51
4299 4796 6.460781 ACTACATACGGAACAAAATGAGTGA 58.539 36.000 0.00 0.00 0.00 3.41
4300 4797 6.932400 ACTACATACGGAACAAAATGAGTGAA 59.068 34.615 0.00 0.00 0.00 3.18
4301 4798 6.817765 ACATACGGAACAAAATGAGTGAAT 57.182 33.333 0.00 0.00 0.00 2.57
4302 4799 6.842163 ACATACGGAACAAAATGAGTGAATC 58.158 36.000 0.00 0.00 0.00 2.52
4303 4800 6.655003 ACATACGGAACAAAATGAGTGAATCT 59.345 34.615 0.00 0.00 0.00 2.40
4304 4801 7.822334 ACATACGGAACAAAATGAGTGAATCTA 59.178 33.333 0.00 0.00 0.00 1.98
4305 4802 6.481954 ACGGAACAAAATGAGTGAATCTAC 57.518 37.500 0.00 0.00 0.00 2.59
4306 4803 5.995282 ACGGAACAAAATGAGTGAATCTACA 59.005 36.000 0.00 0.00 0.00 2.74
4307 4804 6.073222 ACGGAACAAAATGAGTGAATCTACAC 60.073 38.462 0.00 0.00 40.60 2.90
4321 4818 8.958506 AGTGAATCTACACTCTAAAATACGTCT 58.041 33.333 0.00 0.00 46.36 4.18
4383 4880 8.622948 AAAAGACTTACATTTAGGAACAGAGG 57.377 34.615 0.00 0.00 0.00 3.69
4384 4881 6.301169 AGACTTACATTTAGGAACAGAGGG 57.699 41.667 0.00 0.00 0.00 4.30
4385 4882 6.023603 AGACTTACATTTAGGAACAGAGGGA 58.976 40.000 0.00 0.00 0.00 4.20
4386 4883 6.155393 AGACTTACATTTAGGAACAGAGGGAG 59.845 42.308 0.00 0.00 0.00 4.30
4387 4884 5.785940 ACTTACATTTAGGAACAGAGGGAGT 59.214 40.000 0.00 0.00 0.00 3.85
4466 4963 1.706305 TGTCCGGAAAACTATGGGGTT 59.294 47.619 5.23 0.00 0.00 4.11
4509 5006 2.090210 TCCCATGGCACCTTCTAGGATA 60.090 50.000 6.09 0.00 37.67 2.59
4614 5111 4.154195 GTGGTAGTGTTTTGCTCATAGTGG 59.846 45.833 0.00 0.00 0.00 4.00
4733 5526 1.205417 ACCAATAAGCTGCATTGTGGC 59.795 47.619 16.19 0.00 32.55 5.01
4815 5608 5.708948 TGTATTACAAGCAAATGTCTTGCC 58.291 37.500 5.87 0.00 45.98 4.52
4834 5627 3.821600 TGCCCATAAGCGTTAACAGAAAA 59.178 39.130 6.39 0.00 34.65 2.29
4899 5692 1.005805 TGTATTGCCTGCCTGGTGATT 59.994 47.619 0.00 0.00 38.35 2.57
4991 5784 4.260170 ACTTTCCTTGTCTGCTCATGATC 58.740 43.478 0.00 0.00 0.00 2.92
5020 5813 9.981114 ATGATGTATATTGTTCTTATCGACACA 57.019 29.630 0.00 0.00 0.00 3.72
5099 5900 7.446106 AACATATATAGTCCAGGTCCAAACA 57.554 36.000 0.00 0.00 0.00 2.83
5137 5938 8.177119 TCAAGTTGCAGTAAAGTTATTCCATT 57.823 30.769 0.00 0.00 0.00 3.16
5311 6112 1.801178 CTTCTCAAAGGCCTTGACGAC 59.199 52.381 21.33 0.00 39.20 4.34
5706 6546 4.156556 TGCTGAATTTTCCGAGGATGAAAG 59.843 41.667 0.00 0.00 33.58 2.62
5740 6580 2.487986 CCAACAAGCAAGAAGAGACCCT 60.488 50.000 0.00 0.00 0.00 4.34
5890 6739 1.909141 CTTCGACCAAGCAGCAGCAG 61.909 60.000 3.17 0.00 45.49 4.24
5891 6740 4.099170 CGACCAAGCAGCAGCAGC 62.099 66.667 3.17 0.46 45.49 5.25
5892 6741 2.981909 GACCAAGCAGCAGCAGCA 60.982 61.111 12.92 0.00 45.49 4.41
5893 6742 2.979197 GACCAAGCAGCAGCAGCAG 61.979 63.158 12.92 3.98 45.49 4.24
5917 6766 4.389992 CAGCAACACTCGTGATATCAAGTT 59.610 41.667 16.71 9.74 0.00 2.66
6027 6877 8.109843 TGTCATTTTTAACATCAACACGTTTC 57.890 30.769 0.00 0.00 0.00 2.78
6070 6920 5.231357 GGCCTTTTGTAATTATGCTAAACGC 59.769 40.000 0.00 0.00 39.77 4.84
6179 7030 2.699809 GCTGCTTGCGATCGTCTG 59.300 61.111 17.81 7.90 0.00 3.51
6206 7057 0.331278 TCACCCAGCCCTACCAATTG 59.669 55.000 0.00 0.00 0.00 2.32
6243 7094 6.238566 CCGCATCAACATCTGATCTTAAACAT 60.239 38.462 0.00 0.00 43.28 2.71
6267 7119 0.704076 AGGCTTAACCATCTTGCCCA 59.296 50.000 0.00 0.00 44.19 5.36
6583 7436 9.052759 GGTTTACAGAGACAATAAGAGAAACAA 57.947 33.333 0.00 0.00 0.00 2.83
6636 7489 4.623932 ATTGTCTGTAGTCCTCAAGCAA 57.376 40.909 0.00 0.00 0.00 3.91
6703 7556 2.559998 ACCAAGTGAAACAAAGCGTG 57.440 45.000 0.00 0.00 41.43 5.34
6745 7598 3.211045 ACGCTAACCACACACAATTTCT 58.789 40.909 0.00 0.00 0.00 2.52
6797 7650 1.667212 GTTTGTACCTTAATCCGGCGG 59.333 52.381 22.51 22.51 0.00 6.13
6798 7651 1.193323 TTGTACCTTAATCCGGCGGA 58.807 50.000 33.10 33.10 35.55 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.770933 AGGGTAGCACAATACGAAGGTTA 59.229 43.478 0.00 0.00 0.00 2.85
140 141 8.375465 CCGCTGTGAAATTTGATTATTTCTTTC 58.625 33.333 0.00 0.00 42.39 2.62
166 167 0.670239 CCTTTTTCCCAACATGCGGC 60.670 55.000 0.00 0.00 0.00 6.53
200 202 0.462759 CCTCTTGGAGAACCATCCGC 60.463 60.000 0.00 0.00 46.34 5.54
214 216 2.909006 TGCTCTTCTGTCCATTCCTCTT 59.091 45.455 0.00 0.00 0.00 2.85
338 340 8.862074 CGCATCATCTATTAGAGAAGATTTCTG 58.138 37.037 0.00 0.00 39.11 3.02
350 352 7.384387 ACATATAGCATGCGCATCATCTATTAG 59.616 37.037 27.21 22.98 42.27 1.73
363 365 6.726258 TTTGGAGAATACATATAGCATGCG 57.274 37.500 13.01 0.00 0.00 4.73
392 394 2.632377 CTGTGACCATTTCTATGCGGT 58.368 47.619 0.00 0.00 0.00 5.68
443 446 5.393243 GGGTAGATAGAGATACGATTGGCAC 60.393 48.000 0.00 0.00 0.00 5.01
483 486 0.031178 GAATGGCGGCATGTGGATTC 59.969 55.000 26.50 14.80 0.00 2.52
525 528 3.875369 GCATCTTCACTCCTTCCATTGGT 60.875 47.826 1.86 0.00 0.00 3.67
539 542 0.040058 AAGGGCCATGTGCATCTTCA 59.960 50.000 6.18 0.00 43.89 3.02
850 867 3.701542 TGAGCCGAAAGATAGACAGACAT 59.298 43.478 0.00 0.00 0.00 3.06
851 868 3.089284 TGAGCCGAAAGATAGACAGACA 58.911 45.455 0.00 0.00 0.00 3.41
852 869 3.784701 TGAGCCGAAAGATAGACAGAC 57.215 47.619 0.00 0.00 0.00 3.51
853 870 3.509967 TGTTGAGCCGAAAGATAGACAGA 59.490 43.478 0.00 0.00 0.00 3.41
854 871 3.614616 GTGTTGAGCCGAAAGATAGACAG 59.385 47.826 0.00 0.00 0.00 3.51
855 872 3.585862 GTGTTGAGCCGAAAGATAGACA 58.414 45.455 0.00 0.00 0.00 3.41
856 873 2.930682 GGTGTTGAGCCGAAAGATAGAC 59.069 50.000 0.00 0.00 0.00 2.59
857 874 2.565391 TGGTGTTGAGCCGAAAGATAGA 59.435 45.455 0.00 0.00 0.00 1.98
858 875 2.932614 CTGGTGTTGAGCCGAAAGATAG 59.067 50.000 0.00 0.00 0.00 2.08
859 876 2.565391 TCTGGTGTTGAGCCGAAAGATA 59.435 45.455 0.00 0.00 0.00 1.98
1401 1442 3.154827 ACCCAAACAATGACAGTAGGG 57.845 47.619 0.00 0.00 39.22 3.53
1427 1468 3.915437 AACATTCCCAATTCGTGTGAC 57.085 42.857 0.00 0.00 0.00 3.67
1481 1522 4.036262 AGCAGCATAAAAACAGACGAACAA 59.964 37.500 0.00 0.00 0.00 2.83
1505 1546 5.721960 ACAACTACATCCAACATAGGAGACT 59.278 40.000 0.00 0.00 41.90 3.24
1509 1550 4.019771 TGCACAACTACATCCAACATAGGA 60.020 41.667 0.00 0.00 43.01 2.94
1514 1555 2.877786 CACTGCACAACTACATCCAACA 59.122 45.455 0.00 0.00 0.00 3.33
1529 1570 1.136961 TCCCATAACACCCCACTGCA 61.137 55.000 0.00 0.00 0.00 4.41
1629 1837 6.523840 TCCAGCAAAAATGCTCTTAAATTGT 58.476 32.000 0.00 0.00 44.30 2.71
1764 1972 7.822334 TGAAGAAGAAGACAAGAAAGTGTAACA 59.178 33.333 0.00 0.00 41.43 2.41
1838 2047 3.980775 CGCCGATAAAGCCCAAATAATTG 59.019 43.478 0.00 0.00 36.25 2.32
1846 2055 1.906105 AAGGACGCCGATAAAGCCCA 61.906 55.000 0.00 0.00 0.00 5.36
1847 2056 1.153229 AAGGACGCCGATAAAGCCC 60.153 57.895 0.00 0.00 0.00 5.19
2048 2257 3.612860 CACCATAACAGTAGACAAGCGAC 59.387 47.826 0.00 0.00 0.00 5.19
2142 2351 4.271049 TGAAGCGACAAAAGAAGAGTTGAG 59.729 41.667 0.00 0.00 0.00 3.02
2233 2443 3.067106 AGTACCACAAGATCAAACAGCG 58.933 45.455 0.00 0.00 0.00 5.18
2291 2502 5.749620 GATCAGCAATGAATGATCTGTCAC 58.250 41.667 16.62 0.00 45.45 3.67
2418 2629 4.537945 AGGACAGGCTAGGAGTATGTTA 57.462 45.455 0.00 0.00 0.00 2.41
2427 2638 2.820787 CTCGGTATTAGGACAGGCTAGG 59.179 54.545 0.00 0.00 0.00 3.02
2445 2656 4.121691 CAGAGAATGCTGGGCTCG 57.878 61.111 0.00 0.00 33.98 5.03
2472 2683 0.738389 CCCACGGCCACATAATTGTC 59.262 55.000 2.24 0.00 32.34 3.18
2493 2704 2.388735 CCCTCCCCTTTAATCAAAGCC 58.611 52.381 0.00 0.00 39.95 4.35
2592 2803 0.674895 CTGCTTTCTGGAAGGGGTCG 60.675 60.000 0.00 0.00 35.82 4.79
2635 2846 1.070445 TGGCTTCTTGGTTTGCAATGG 59.930 47.619 0.00 0.00 0.00 3.16
2782 2993 1.745653 GCTCTCACCAATACTTTGCCC 59.254 52.381 0.00 0.00 0.00 5.36
2783 2994 2.436417 TGCTCTCACCAATACTTTGCC 58.564 47.619 0.00 0.00 0.00 4.52
2802 3013 8.843262 TCATTCTTAGTATCAATGAGGCATTTG 58.157 33.333 0.00 0.00 32.72 2.32
2817 3028 5.359860 TGATCGTGGCTTCTCATTCTTAGTA 59.640 40.000 0.00 0.00 0.00 1.82
3002 3213 5.269189 TCCTGATACAGTTGACCACAGATA 58.731 41.667 0.00 0.00 0.00 1.98
3031 3242 5.788533 TGACCCCTTCAGGATAAGAGTTTAA 59.211 40.000 0.00 0.00 38.24 1.52
3128 3339 2.697654 CTTGGAGAAGAGCACTGAAGG 58.302 52.381 0.00 0.00 0.00 3.46
3287 3498 3.891049 ACTTTAGATGATGGTGGCTTCC 58.109 45.455 0.00 0.00 0.00 3.46
3294 3505 7.202047 GGAGAAGATGGTACTTTAGATGATGGT 60.202 40.741 0.00 0.00 0.00 3.55
3295 3506 7.158021 GGAGAAGATGGTACTTTAGATGATGG 58.842 42.308 0.00 0.00 0.00 3.51
3296 3507 7.730084 TGGAGAAGATGGTACTTTAGATGATG 58.270 38.462 0.00 0.00 0.00 3.07
3297 3508 7.921041 TGGAGAAGATGGTACTTTAGATGAT 57.079 36.000 0.00 0.00 0.00 2.45
3298 3509 7.565029 TGATGGAGAAGATGGTACTTTAGATGA 59.435 37.037 0.00 0.00 0.00 2.92
3299 3510 7.730084 TGATGGAGAAGATGGTACTTTAGATG 58.270 38.462 0.00 0.00 0.00 2.90
3300 3511 7.786943 TCTGATGGAGAAGATGGTACTTTAGAT 59.213 37.037 0.00 0.00 0.00 1.98
3301 3512 7.126061 TCTGATGGAGAAGATGGTACTTTAGA 58.874 38.462 0.00 0.00 0.00 2.10
3302 3513 7.353414 TCTGATGGAGAAGATGGTACTTTAG 57.647 40.000 0.00 0.00 0.00 1.85
3303 3514 7.921041 ATCTGATGGAGAAGATGGTACTTTA 57.079 36.000 0.00 0.00 33.12 1.85
3304 3515 6.821616 ATCTGATGGAGAAGATGGTACTTT 57.178 37.500 0.00 0.00 33.12 2.66
3305 3516 9.781425 ATATATCTGATGGAGAAGATGGTACTT 57.219 33.333 0.00 0.00 34.91 2.24
3306 3517 9.781425 AATATATCTGATGGAGAAGATGGTACT 57.219 33.333 0.00 0.00 34.91 2.73
3307 3518 9.814899 CAATATATCTGATGGAGAAGATGGTAC 57.185 37.037 0.00 0.00 34.91 3.34
3308 3519 9.552695 ACAATATATCTGATGGAGAAGATGGTA 57.447 33.333 0.00 0.00 34.91 3.25
3418 3644 7.732025 TCAGATGGCTTAATAAAATCTACGGA 58.268 34.615 0.00 0.00 0.00 4.69
3447 3673 1.473257 GCTTCCATATGACACGCAGGA 60.473 52.381 3.65 0.00 0.00 3.86
3672 3898 3.940209 GTGGAACAATTCTTCATGGCA 57.060 42.857 0.00 0.00 44.16 4.92
3857 4083 3.384467 TGCCCAGCTAAATATTCCTTTGC 59.616 43.478 0.00 0.00 0.00 3.68
4231 4728 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
4232 4729 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
4265 4762 5.599242 TGTTCCGTATGTAGTCCATATTGGA 59.401 40.000 0.00 0.00 45.98 3.53
4266 4763 5.849510 TGTTCCGTATGTAGTCCATATTGG 58.150 41.667 0.00 0.00 38.29 3.16
4267 4764 7.780008 TTTGTTCCGTATGTAGTCCATATTG 57.220 36.000 0.00 0.00 38.29 1.90
4268 4765 8.836413 CATTTTGTTCCGTATGTAGTCCATATT 58.164 33.333 0.00 0.00 38.29 1.28
4269 4766 8.208224 TCATTTTGTTCCGTATGTAGTCCATAT 58.792 33.333 0.00 0.00 38.29 1.78
4270 4767 7.557724 TCATTTTGTTCCGTATGTAGTCCATA 58.442 34.615 0.00 0.00 34.86 2.74
4271 4768 6.411376 TCATTTTGTTCCGTATGTAGTCCAT 58.589 36.000 0.00 0.00 37.58 3.41
4272 4769 5.795972 TCATTTTGTTCCGTATGTAGTCCA 58.204 37.500 0.00 0.00 0.00 4.02
4273 4770 5.873164 ACTCATTTTGTTCCGTATGTAGTCC 59.127 40.000 0.00 0.00 0.00 3.85
4274 4771 6.588756 TCACTCATTTTGTTCCGTATGTAGTC 59.411 38.462 0.00 0.00 0.00 2.59
4275 4772 6.460781 TCACTCATTTTGTTCCGTATGTAGT 58.539 36.000 0.00 0.00 0.00 2.73
4276 4773 6.961359 TCACTCATTTTGTTCCGTATGTAG 57.039 37.500 0.00 0.00 0.00 2.74
4277 4774 7.822334 AGATTCACTCATTTTGTTCCGTATGTA 59.178 33.333 0.00 0.00 0.00 2.29
4278 4775 6.655003 AGATTCACTCATTTTGTTCCGTATGT 59.345 34.615 0.00 0.00 0.00 2.29
4279 4776 7.076842 AGATTCACTCATTTTGTTCCGTATG 57.923 36.000 0.00 0.00 0.00 2.39
4280 4777 7.822334 TGTAGATTCACTCATTTTGTTCCGTAT 59.178 33.333 0.00 0.00 0.00 3.06
4281 4778 7.117236 GTGTAGATTCACTCATTTTGTTCCGTA 59.883 37.037 0.00 0.00 35.68 4.02
4282 4779 5.995282 TGTAGATTCACTCATTTTGTTCCGT 59.005 36.000 0.00 0.00 0.00 4.69
4283 4780 6.147821 AGTGTAGATTCACTCATTTTGTTCCG 59.852 38.462 0.00 0.00 44.07 4.30
4284 4781 7.440523 AGTGTAGATTCACTCATTTTGTTCC 57.559 36.000 0.00 0.00 44.07 3.62
4315 4812 9.875691 AACTACATACGGATGTATATAGACGTA 57.124 33.333 20.64 9.65 45.42 3.57
4316 4813 8.783833 AACTACATACGGATGTATATAGACGT 57.216 34.615 20.64 10.41 45.42 4.34
4317 4814 8.876790 TGAACTACATACGGATGTATATAGACG 58.123 37.037 20.64 9.79 45.42 4.18
4357 4854 9.067986 CCTCTGTTCCTAAATGTAAGTCTTTTT 57.932 33.333 0.00 0.00 0.00 1.94
4358 4855 7.665974 CCCTCTGTTCCTAAATGTAAGTCTTTT 59.334 37.037 0.00 0.00 0.00 2.27
4359 4856 7.017254 TCCCTCTGTTCCTAAATGTAAGTCTTT 59.983 37.037 0.00 0.00 0.00 2.52
4360 4857 6.500751 TCCCTCTGTTCCTAAATGTAAGTCTT 59.499 38.462 0.00 0.00 0.00 3.01
4361 4858 6.023603 TCCCTCTGTTCCTAAATGTAAGTCT 58.976 40.000 0.00 0.00 0.00 3.24
4362 4859 6.070710 ACTCCCTCTGTTCCTAAATGTAAGTC 60.071 42.308 0.00 0.00 0.00 3.01
4363 4860 5.785940 ACTCCCTCTGTTCCTAAATGTAAGT 59.214 40.000 0.00 0.00 0.00 2.24
4364 4861 6.301169 ACTCCCTCTGTTCCTAAATGTAAG 57.699 41.667 0.00 0.00 0.00 2.34
4365 4862 6.127140 GCTACTCCCTCTGTTCCTAAATGTAA 60.127 42.308 0.00 0.00 0.00 2.41
4366 4863 5.363005 GCTACTCCCTCTGTTCCTAAATGTA 59.637 44.000 0.00 0.00 0.00 2.29
4367 4864 4.162509 GCTACTCCCTCTGTTCCTAAATGT 59.837 45.833 0.00 0.00 0.00 2.71
4368 4865 4.407296 AGCTACTCCCTCTGTTCCTAAATG 59.593 45.833 0.00 0.00 0.00 2.32
4369 4866 4.625963 AGCTACTCCCTCTGTTCCTAAAT 58.374 43.478 0.00 0.00 0.00 1.40
4370 4867 4.024670 GAGCTACTCCCTCTGTTCCTAAA 58.975 47.826 0.00 0.00 0.00 1.85
4371 4868 3.269906 AGAGCTACTCCCTCTGTTCCTAA 59.730 47.826 0.00 0.00 38.21 2.69
4372 4869 2.853707 AGAGCTACTCCCTCTGTTCCTA 59.146 50.000 0.00 0.00 38.21 2.94
4373 4870 1.643811 AGAGCTACTCCCTCTGTTCCT 59.356 52.381 0.00 0.00 38.21 3.36
4374 4871 2.153034 AGAGCTACTCCCTCTGTTCC 57.847 55.000 0.00 0.00 38.21 3.62
4375 4872 3.368948 CCAAAGAGCTACTCCCTCTGTTC 60.369 52.174 0.00 0.00 39.50 3.18
4376 4873 2.569404 CCAAAGAGCTACTCCCTCTGTT 59.431 50.000 0.00 0.00 39.50 3.16
4377 4874 2.183679 CCAAAGAGCTACTCCCTCTGT 58.816 52.381 0.00 0.00 39.50 3.41
4378 4875 2.183679 ACCAAAGAGCTACTCCCTCTG 58.816 52.381 0.00 0.00 39.50 3.35
4379 4876 2.632763 ACCAAAGAGCTACTCCCTCT 57.367 50.000 0.00 0.00 41.25 3.69
4380 4877 4.466726 TCTTAACCAAAGAGCTACTCCCTC 59.533 45.833 0.00 0.00 39.36 4.30
4381 4878 4.426704 TCTTAACCAAAGAGCTACTCCCT 58.573 43.478 0.00 0.00 39.36 4.20
4382 4879 4.820894 TCTTAACCAAAGAGCTACTCCC 57.179 45.455 0.00 0.00 39.36 4.30
4485 4982 0.758734 TAGAAGGTGCCATGGGATCG 59.241 55.000 15.13 0.00 0.00 3.69
4509 5006 8.725148 TGTGTTTTTCTACAAAATTGCACAATT 58.275 25.926 2.77 2.77 42.35 2.32
4614 5111 5.230182 GGTTCATGAACAAAAGAATCCACC 58.770 41.667 33.42 13.64 42.85 4.61
4733 5526 3.443099 TTGTCGCTCCAGATATGACAG 57.557 47.619 0.00 0.00 40.31 3.51
4815 5608 9.221775 GTGATATTTTTCTGTTAACGCTTATGG 57.778 33.333 0.26 0.00 0.00 2.74
4834 5627 2.308570 TGGTGCTTCCACAGGTGATATT 59.691 45.455 0.00 0.00 43.88 1.28
4899 5692 3.965379 TTATCTACACGACCCAGCAAA 57.035 42.857 0.00 0.00 0.00 3.68
5137 5938 4.154176 CCATAGGATGGGAATTGCATGAA 58.846 43.478 0.00 0.00 46.86 2.57
5246 6047 1.001641 CCAACTCCTCCCTGCCAAG 60.002 63.158 0.00 0.00 0.00 3.61
5311 6112 9.770097 AGATGTACTAACTGATGGATATGTTTG 57.230 33.333 0.00 0.00 0.00 2.93
5447 6248 3.778954 AAGAGGAGAACTTGACCCTTG 57.221 47.619 0.00 0.00 0.00 3.61
5706 6546 2.669391 GCTTGTTGGCTTGCTGTATGAC 60.669 50.000 0.00 0.00 0.00 3.06
5890 6739 1.572085 ATCACGAGTGTTGCTGCTGC 61.572 55.000 8.89 8.89 40.20 5.25
5891 6740 1.713597 TATCACGAGTGTTGCTGCTG 58.286 50.000 0.00 0.00 0.00 4.41
5892 6741 2.094026 TGATATCACGAGTGTTGCTGCT 60.094 45.455 0.00 0.00 0.00 4.24
5893 6742 2.270923 TGATATCACGAGTGTTGCTGC 58.729 47.619 0.00 0.00 0.00 5.25
5894 6743 3.928992 ACTTGATATCACGAGTGTTGCTG 59.071 43.478 15.55 0.00 33.77 4.41
5895 6744 4.193826 ACTTGATATCACGAGTGTTGCT 57.806 40.909 15.55 0.00 33.77 3.91
5896 6745 4.928661 AACTTGATATCACGAGTGTTGC 57.071 40.909 15.55 0.00 35.06 4.17
5897 6746 5.576774 TGCTAACTTGATATCACGAGTGTTG 59.423 40.000 15.55 7.84 35.06 3.33
5898 6747 5.577164 GTGCTAACTTGATATCACGAGTGTT 59.423 40.000 15.55 12.27 35.06 3.32
6009 6859 5.821516 ACCAGAAACGTGTTGATGTTAAA 57.178 34.783 0.00 0.00 30.69 1.52
6027 6877 3.332919 GCCATCATCTAGTGCATACCAG 58.667 50.000 0.00 0.00 0.00 4.00
6179 7030 1.973812 GGGCTGGGTGAAGAAGCAC 60.974 63.158 0.00 0.00 38.73 4.40
6243 7094 3.347216 GCAAGATGGTTAAGCCTGAAGA 58.653 45.455 1.51 0.00 38.35 2.87
6267 7119 2.571653 TGAATGGAGTGGGAACGATCTT 59.428 45.455 0.00 0.00 0.00 2.40
6583 7436 1.220206 CAGAGATCGCCAAGGTGCT 59.780 57.895 0.00 0.00 0.00 4.40
6636 7489 2.146342 CAACGTGGACTGCTGAAGATT 58.854 47.619 0.00 0.00 0.00 2.40
6703 7556 5.659426 CGTTGTTTCAGTGATTTTTCATGC 58.341 37.500 0.00 0.00 0.00 4.06
6745 7598 2.158769 AGTTTCAGAGCACATGGACACA 60.159 45.455 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.