Multiple sequence alignment - TraesCS4D01G283100

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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 TraesCS4D01G283100 chr4D 100.000 5243 0 0 1 5243 455247892 455253134 0.000000e+00 9683.0
1 TraesCS4D01G283100 chr4A 94.055 4912 203 30 1 4903 12685305 12680474 0.000000e+00 7371.0
2 TraesCS4D01G283100 chr4B 94.972 4316 208 5 1 4315 568333348 568337655 0.000000e+00 6759.0
3 TraesCS4D01G283100 chr4B 83.860 570 49 21 4349 4900 568337655 568338199 2.180000e-138 503.0
4 TraesCS4D01G283100 chr4B 83.554 377 27 11 4897 5241 568338240 568338613 2.360000e-83 320.0
5 TraesCS4D01G283100 chr7D 79.710 552 76 23 1043 1585 212242514 212241990 2.980000e-97 366.0
6 TraesCS4D01G283100 chr3D 79.710 552 74 24 1043 1585 141511776 141512298 1.070000e-96 364.0
7 TraesCS4D01G283100 chr7B 79.245 530 74 21 1010 1522 705023885 705024395 2.340000e-88 337.0
8 TraesCS4D01G283100 chr7B 96.491 57 2 0 3549 3605 459800388 459800332 1.550000e-15 95.3
9 TraesCS4D01G283100 chr7B 96.491 57 2 0 3549 3605 729406619 729406563 1.550000e-15 95.3
10 TraesCS4D01G283100 chr7A 81.517 422 58 11 1167 1585 577685086 577684682 3.910000e-86 329.0
11 TraesCS4D01G283100 chr6B 81.280 422 59 11 1167 1585 705321777 705322181 1.820000e-84 324.0
12 TraesCS4D01G283100 chr3B 79.773 440 73 11 1091 1522 661728731 661728300 6.600000e-79 305.0
13 TraesCS4D01G283100 chr3B 79.773 440 73 11 1091 1522 661761420 661760989 6.600000e-79 305.0
14 TraesCS4D01G283100 chr3B 96.491 57 2 0 3549 3605 598066772 598066828 1.550000e-15 95.3
15 TraesCS4D01G283100 chr1A 84.536 194 25 3 3549 3738 144629908 144629716 2.490000e-43 187.0
16 TraesCS4D01G283100 chr2B 81.532 222 30 5 794 1015 636760568 636760778 6.980000e-39 172.0
17 TraesCS4D01G283100 chr2B 97.959 49 1 0 1006 1054 636762553 636762601 9.350000e-13 86.1
18 TraesCS4D01G283100 chr1B 83.077 195 25 5 3549 3738 193880949 193881140 2.510000e-38 171.0
19 TraesCS4D01G283100 chr2D 85.185 162 24 0 810 971 535293654 535293815 3.250000e-37 167.0
20 TraesCS4D01G283100 chr1D 82.383 193 30 2 3549 3738 144457497 144457688 1.170000e-36 165.0
21 TraesCS4D01G283100 chr2A 79.679 187 22 12 1010 1195 218120849 218121020 2.560000e-23 121.0
22 TraesCS4D01G283100 chrUn 96.491 57 2 0 3549 3605 8464676 8464732 1.550000e-15 95.3


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 TraesCS4D01G283100 chr4D 455247892 455253134 5242 False 9683.000000 9683 100.000 1 5243 1 chr4D.!!$F1 5242
1 TraesCS4D01G283100 chr4A 12680474 12685305 4831 True 7371.000000 7371 94.055 1 4903 1 chr4A.!!$R1 4902
2 TraesCS4D01G283100 chr4B 568333348 568338613 5265 False 2527.333333 6759 87.462 1 5241 3 chr4B.!!$F1 5240
3 TraesCS4D01G283100 chr7D 212241990 212242514 524 True 366.000000 366 79.710 1043 1585 1 chr7D.!!$R1 542
4 TraesCS4D01G283100 chr3D 141511776 141512298 522 False 364.000000 364 79.710 1043 1585 1 chr3D.!!$F1 542
5 TraesCS4D01G283100 chr7B 705023885 705024395 510 False 337.000000 337 79.245 1010 1522 1 chr7B.!!$F1 512

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
463 468 0.250295 TTCAACCACTTCCAGCTCGG 60.250 55.000 0.0 0.00 0.00 4.63 F
686 691 0.743097 GAGGCTGATGTCCATTTGGC 59.257 55.000 0.0 0.00 34.44 4.52 F
1548 1568 1.583404 CTTGCGTCTTTGTGCACAAAC 59.417 47.619 35.1 27.12 41.57 2.93 F
2792 2812 0.393132 GTGGCAGAGGGCTTCCTAAC 60.393 60.000 0.0 0.00 41.93 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 2189 0.385223 GCAGAAGAGCACTTGCAACG 60.385 55.0 0.00 0.00 45.16 4.10 R
2593 2613 0.034670 AGCTGCAAGGATTCCTCCAC 60.035 55.0 5.48 0.00 44.79 4.02 R
2969 2989 1.592064 TTCGTTCACAATGCAGCTGA 58.408 45.0 20.43 2.70 0.00 4.26 R
4433 4453 0.387929 CCATGGGCTCAATGTGCATC 59.612 55.0 2.85 1.85 0.00 3.91 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
132 137 2.317040 CCTATCTTCCGCCACTCCTTA 58.683 52.381 0.00 0.00 0.00 2.69
133 138 2.698797 CCTATCTTCCGCCACTCCTTAA 59.301 50.000 0.00 0.00 0.00 1.85
142 147 4.814294 ACTCCTTAAGCGCGGCGG 62.814 66.667 25.03 6.56 0.00 6.13
322 327 3.502164 GGGGGAATCACATGTGGAG 57.498 57.895 25.16 0.11 0.00 3.86
377 382 3.403057 CGTCGACCAAGGTGCGTG 61.403 66.667 10.58 0.00 0.00 5.34
380 385 2.738521 CGACCAAGGTGCGTGAGG 60.739 66.667 0.00 0.00 0.00 3.86
463 468 0.250295 TTCAACCACTTCCAGCTCGG 60.250 55.000 0.00 0.00 0.00 4.63
524 529 2.874701 CCAATAATGCTCCGGAGTTGAG 59.125 50.000 31.43 16.45 0.00 3.02
546 551 2.294512 CTCCAACAAAGGGAGCTTGTTC 59.705 50.000 0.00 0.00 44.95 3.18
609 614 1.005340 CTCTCTGCAATTCAGCCGTC 58.995 55.000 0.00 0.00 42.56 4.79
641 646 3.840666 TCAGAGGAAGCTGGATTTAGTGT 59.159 43.478 0.00 0.00 36.55 3.55
686 691 0.743097 GAGGCTGATGTCCATTTGGC 59.257 55.000 0.00 0.00 34.44 4.52
729 734 5.620738 TTGGGAAATTGATTGTGTCCAAA 57.379 34.783 0.00 0.00 33.44 3.28
850 855 2.665185 GGTTCTGGCGTGCTTCGT 60.665 61.111 4.16 0.00 42.13 3.85
888 893 5.289434 GGATTTTCTTGACATTTTGATCGGC 59.711 40.000 0.00 0.00 0.00 5.54
942 947 5.569059 CGCAAGATTTCTGTGGAATTTGTAC 59.431 40.000 0.00 0.00 43.02 2.90
975 980 1.743252 GCAGAGCAAGGACTTCCGG 60.743 63.158 0.00 0.00 42.08 5.14
1089 1103 2.364842 AGGGCTCTGACCGATGCT 60.365 61.111 0.00 0.00 34.63 3.79
1176 1190 2.030805 GCTTTTTGATCGTGCAAGGTCT 60.031 45.455 14.13 0.00 0.00 3.85
1327 1346 7.000472 AGAAGGAGATGTTCTTGATTTTGTCA 59.000 34.615 0.00 0.00 29.57 3.58
1331 1350 7.120873 AGGAGATGTTCTTGATTTTGTCATCAG 59.879 37.037 0.00 0.00 36.54 2.90
1548 1568 1.583404 CTTGCGTCTTTGTGCACAAAC 59.417 47.619 35.10 27.12 41.57 2.93
2011 2031 3.712091 AGGTTAAGAGAGATAACGCCG 57.288 47.619 0.00 0.00 34.74 6.46
2074 2094 2.552155 GGCCTGTATTTGGACACTGACA 60.552 50.000 0.00 0.00 31.53 3.58
2100 2120 6.237808 CCAAAAAGTTTGAGATTTCGTTGGTG 60.238 38.462 2.30 0.00 28.40 4.17
2121 2141 5.277876 GGTGCAGATTCTTGATAATGCTCTG 60.278 44.000 0.00 0.00 33.70 3.35
2169 2189 2.050985 GCGTGTCAGCAAGGCAAC 60.051 61.111 0.00 0.00 37.05 4.17
2194 2214 2.350580 GCAAGTGCTCTTCTGCTGAAAG 60.351 50.000 7.48 8.73 38.21 2.62
2237 2257 4.637534 ACATTACATTTCACCAGCTAGCTG 59.362 41.667 33.58 33.58 43.26 4.24
2240 2260 3.490348 ACATTTCACCAGCTAGCTGTTT 58.510 40.909 36.14 23.45 42.15 2.83
2241 2261 3.254166 ACATTTCACCAGCTAGCTGTTTG 59.746 43.478 36.14 31.02 42.15 2.93
2273 2293 3.736483 CTTGTGCGCAAGTCCTGT 58.264 55.556 28.01 0.00 45.18 4.00
2388 2408 5.016051 TGAGTAAGAATGAGATGTCAGCC 57.984 43.478 0.00 0.00 35.66 4.85
2492 2512 4.866508 TCTGTACAGAAAGGAACATCGT 57.133 40.909 23.24 0.00 33.91 3.73
2505 2525 3.414269 GAACATCGTAGGGTTTTGGGAA 58.586 45.455 0.00 0.00 0.00 3.97
2554 2574 3.251484 TGGTCTCCTGACAAGAAGGATT 58.749 45.455 0.00 0.00 42.94 3.01
2559 2579 5.353678 GTCTCCTGACAAGAAGGATTTGATG 59.646 44.000 0.00 0.00 42.94 3.07
2593 2613 2.489329 CACTTGTGCAAATGGGGAGTAG 59.511 50.000 0.00 0.00 0.00 2.57
2602 2622 2.897823 ATGGGGAGTAGTGGAGGAAT 57.102 50.000 0.00 0.00 0.00 3.01
2688 2708 4.692625 GCACTTCTCAAAGAGTTATGCAGA 59.307 41.667 0.00 0.00 36.30 4.26
2792 2812 0.393132 GTGGCAGAGGGCTTCCTAAC 60.393 60.000 0.00 0.00 41.93 2.34
2796 2816 0.902531 CAGAGGGCTTCCTAACGGAA 59.097 55.000 0.00 0.00 46.90 4.30
2839 2859 3.118629 TGGACTGTATGACATCTGCCTTC 60.119 47.826 0.00 0.00 0.00 3.46
2846 2866 5.534278 TGTATGACATCTGCCTTCACAAAAA 59.466 36.000 0.00 0.00 0.00 1.94
2849 2869 4.341806 TGACATCTGCCTTCACAAAAACAT 59.658 37.500 0.00 0.00 0.00 2.71
2850 2870 5.163426 TGACATCTGCCTTCACAAAAACATT 60.163 36.000 0.00 0.00 0.00 2.71
2856 2876 6.040278 TCTGCCTTCACAAAAACATTGTATCA 59.960 34.615 0.00 0.00 0.00 2.15
2858 2878 5.119125 GCCTTCACAAAAACATTGTATCAGC 59.881 40.000 0.00 0.00 0.00 4.26
2893 2913 6.127535 CCACCAATTTGCATTCTCTTCACTAT 60.128 38.462 0.00 0.00 0.00 2.12
2938 2958 4.184629 CAAGGACTTGGTACAGTCTATGC 58.815 47.826 11.83 0.00 42.39 3.14
2969 2989 2.957402 TGTTCTGATGTCCCAGCTTT 57.043 45.000 0.00 0.00 34.28 3.51
2997 3017 4.082841 TGCATTGTGAACGAATTACTGCAT 60.083 37.500 0.00 0.00 32.65 3.96
3031 3051 2.756760 AGCCAGGCAATATCAGTTGTTG 59.243 45.455 15.80 0.00 0.00 3.33
3056 3076 5.196695 AGCATCCACTTTAGGGAAGAAATC 58.803 41.667 0.00 0.00 38.09 2.17
3069 3089 9.581289 TTAGGGAAGAAATCAAGTGACAAATTA 57.419 29.630 0.00 0.00 0.00 1.40
3460 3480 6.543465 AGTTACTATGCTTGATGCTTGCATTA 59.457 34.615 9.59 2.67 43.85 1.90
3521 3541 4.637534 AGTATTGAGTCACCATTGCATGTC 59.362 41.667 0.00 0.00 0.00 3.06
3634 3654 4.948621 CAGCTCTCCTTTCATTTGGAAGAT 59.051 41.667 0.00 0.00 36.72 2.40
3738 3758 2.172293 GGAATTCTGCAGACAGGGAGAT 59.828 50.000 18.03 1.94 44.59 2.75
3744 3764 0.835941 GCAGACAGGGAGATGTGGAT 59.164 55.000 0.00 0.00 32.25 3.41
3782 3802 7.916977 TCTGATAAATACAATGTTGAAGCATGC 59.083 33.333 10.51 10.51 0.00 4.06
3789 3809 5.491070 ACAATGTTGAAGCATGCTAGACTA 58.509 37.500 23.00 8.48 0.00 2.59
3885 3905 1.738350 CTTGCTGAGATGCAGTTGGAG 59.262 52.381 0.00 0.00 46.62 3.86
3903 3923 6.661805 AGTTGGAGAACTTAAAACCAAGTGAA 59.338 34.615 0.00 0.00 39.56 3.18
3906 3926 7.488322 TGGAGAACTTAAAACCAAGTGAAATG 58.512 34.615 0.00 0.00 38.74 2.32
3907 3927 6.923508 GGAGAACTTAAAACCAAGTGAAATGG 59.076 38.462 0.00 0.00 43.84 3.16
3983 4003 7.754924 CGCTAAGAAGATTTTGGAATTGCTAAA 59.245 33.333 8.78 8.78 0.00 1.85
3993 4013 4.479158 TGGAATTGCTAAAGACCTTTGGT 58.521 39.130 5.34 0.00 39.44 3.67
4000 4020 3.304726 GCTAAAGACCTTTGGTTCTGCAC 60.305 47.826 5.34 0.00 35.25 4.57
4104 4124 2.941333 CAGCAAGCAGGACACGTG 59.059 61.111 15.48 15.48 0.00 4.49
4244 4264 9.393512 CATGAAGGATAATAGGAGGAAATGATC 57.606 37.037 0.00 0.00 0.00 2.92
4314 4334 1.690219 ATGGCTGCCCTCCTACGAAG 61.690 60.000 17.53 0.00 0.00 3.79
4322 4342 0.535797 CCTCCTACGAAGAACCACCC 59.464 60.000 0.00 0.00 0.00 4.61
4405 4425 1.195115 AGAGATACGGCCTTCTGCAA 58.805 50.000 0.00 0.00 43.89 4.08
4421 4441 3.256879 TCTGCAACTCTGTAGAAGTGGAG 59.743 47.826 0.00 6.64 40.83 3.86
4428 4448 0.321671 TGTAGAAGTGGAGCAGTGGC 59.678 55.000 0.00 0.00 41.61 5.01
4429 4449 0.321671 GTAGAAGTGGAGCAGTGGCA 59.678 55.000 0.00 0.00 44.61 4.92
4431 4451 0.403271 AGAAGTGGAGCAGTGGCAAT 59.597 50.000 0.00 0.00 44.61 3.56
4432 4452 1.630369 AGAAGTGGAGCAGTGGCAATA 59.370 47.619 0.00 0.00 44.61 1.90
4433 4453 2.012673 GAAGTGGAGCAGTGGCAATAG 58.987 52.381 0.00 0.00 44.61 1.73
4449 4470 2.953648 CAATAGATGCACATTGAGCCCA 59.046 45.455 10.54 0.00 34.69 5.36
4476 4497 5.391736 GCAGGTCTCTTTCTGTTCATCATTG 60.392 44.000 0.00 0.00 33.81 2.82
4477 4498 4.699257 AGGTCTCTTTCTGTTCATCATTGC 59.301 41.667 0.00 0.00 0.00 3.56
4521 4543 2.195567 CATCCCGGCGAATTGGCAT 61.196 57.895 14.70 0.00 45.16 4.40
4522 4544 0.888736 CATCCCGGCGAATTGGCATA 60.889 55.000 14.70 0.00 45.16 3.14
4523 4545 0.038166 ATCCCGGCGAATTGGCATAT 59.962 50.000 14.70 0.00 45.16 1.78
4524 4546 0.687920 TCCCGGCGAATTGGCATATA 59.312 50.000 14.70 0.00 45.16 0.86
4525 4547 0.802494 CCCGGCGAATTGGCATATAC 59.198 55.000 14.70 0.00 45.16 1.47
4526 4548 0.802494 CCGGCGAATTGGCATATACC 59.198 55.000 14.70 0.00 45.16 2.73
4527 4549 1.610624 CCGGCGAATTGGCATATACCT 60.611 52.381 14.70 0.00 45.16 3.08
4528 4550 2.151202 CGGCGAATTGGCATATACCTT 58.849 47.619 14.70 0.00 45.16 3.50
4529 4551 2.159627 CGGCGAATTGGCATATACCTTC 59.840 50.000 14.70 0.00 45.16 3.46
4530 4552 2.159627 GGCGAATTGGCATATACCTTCG 59.840 50.000 14.70 10.57 44.08 3.79
4531 4553 2.806244 GCGAATTGGCATATACCTTCGT 59.194 45.455 14.50 0.00 38.77 3.85
4532 4554 3.363970 GCGAATTGGCATATACCTTCGTG 60.364 47.826 14.50 0.00 38.77 4.35
4533 4555 3.186409 CGAATTGGCATATACCTTCGTGG 59.814 47.826 7.78 0.00 42.93 4.94
4534 4556 4.385825 GAATTGGCATATACCTTCGTGGA 58.614 43.478 4.38 0.00 39.71 4.02
4535 4557 2.902705 TGGCATATACCTTCGTGGAC 57.097 50.000 4.38 0.00 39.71 4.02
4536 4558 2.112190 TGGCATATACCTTCGTGGACA 58.888 47.619 4.38 0.00 39.71 4.02
4537 4559 2.703536 TGGCATATACCTTCGTGGACAT 59.296 45.455 4.38 0.95 39.71 3.06
4538 4560 3.135712 TGGCATATACCTTCGTGGACATT 59.864 43.478 4.38 0.00 39.71 2.71
4542 4564 5.176958 GCATATACCTTCGTGGACATTACAC 59.823 44.000 4.38 0.00 39.71 2.90
4553 4575 6.072948 TCGTGGACATTACACAAAGGTAAATG 60.073 38.462 0.00 0.00 38.74 2.32
4597 4619 8.150296 ACAACATATTCTGGTCATATCGATTCA 58.850 33.333 1.71 0.00 0.00 2.57
4611 4633 3.581755 TCGATTCACGGAGTAGGTTTTG 58.418 45.455 0.00 0.00 41.61 2.44
4613 4635 3.612860 CGATTCACGGAGTAGGTTTTGAG 59.387 47.826 0.00 0.00 41.61 3.02
4625 4651 8.150945 GGAGTAGGTTTTGAGAGAATATGCATA 58.849 37.037 9.27 9.27 0.00 3.14
4626 4652 8.894768 AGTAGGTTTTGAGAGAATATGCATAC 57.105 34.615 8.99 0.00 0.00 2.39
4631 4657 8.125448 GGTTTTGAGAGAATATGCATACTTGTC 58.875 37.037 8.99 11.96 0.00 3.18
4642 4668 9.461312 AATATGCATACTTGTCTTCTTTTACCA 57.539 29.630 8.99 0.00 0.00 3.25
4712 4747 4.451629 TCAAGATGACCTTACTTCCGAC 57.548 45.455 0.00 0.00 32.86 4.79
4713 4748 3.194968 TCAAGATGACCTTACTTCCGACC 59.805 47.826 0.00 0.00 32.86 4.79
4714 4749 2.816411 AGATGACCTTACTTCCGACCA 58.184 47.619 0.00 0.00 0.00 4.02
4715 4750 3.375699 AGATGACCTTACTTCCGACCAT 58.624 45.455 0.00 0.00 0.00 3.55
4716 4751 3.385111 AGATGACCTTACTTCCGACCATC 59.615 47.826 0.00 0.00 0.00 3.51
4717 4752 1.829222 TGACCTTACTTCCGACCATCC 59.171 52.381 0.00 0.00 0.00 3.51
4718 4753 0.822164 ACCTTACTTCCGACCATCCG 59.178 55.000 0.00 0.00 0.00 4.18
4719 4754 1.108776 CCTTACTTCCGACCATCCGA 58.891 55.000 0.00 0.00 0.00 4.55
4730 4765 0.687757 ACCATCCGAAGCTGCTCCTA 60.688 55.000 1.00 0.00 0.00 2.94
4777 4812 4.278419 TCTCTCATGTTCTTCTCACACGAA 59.722 41.667 0.00 0.00 0.00 3.85
4838 4873 6.327626 ACCACAACAGTAATATCTCATAGCCT 59.672 38.462 0.00 0.00 0.00 4.58
4855 4890 2.101415 AGCCTTTTTCTTGTGTTCCTGC 59.899 45.455 0.00 0.00 0.00 4.85
4906 4996 2.028112 TGTTTTCGTCTGATCTCAGGGG 60.028 50.000 7.33 0.65 43.91 4.79
4907 4997 0.537188 TTTCGTCTGATCTCAGGGGC 59.463 55.000 7.33 0.00 43.91 5.80
4919 5009 1.474077 CTCAGGGGCATTGTTGTAAGC 59.526 52.381 0.00 0.00 0.00 3.09
4925 5015 0.521242 GCATTGTTGTAAGCGCCGAG 60.521 55.000 2.29 0.00 0.00 4.63
4928 5018 0.249531 TTGTTGTAAGCGCCGAGTCA 60.250 50.000 2.29 0.00 0.00 3.41
4930 5020 1.731613 TTGTAAGCGCCGAGTCACG 60.732 57.895 2.29 0.00 42.18 4.35
4938 5028 2.740714 GCCGAGTCACGATTGTGCC 61.741 63.158 8.34 0.00 46.01 5.01
4944 5034 0.743345 GTCACGATTGTGCCCCTACC 60.743 60.000 8.34 0.00 46.01 3.18
4965 5055 0.321564 TGCCACACTAGGTCATGTGC 60.322 55.000 5.83 3.34 44.01 4.57
4976 5066 3.367743 CATGTGCTGCCCGCTTGT 61.368 61.111 0.00 0.00 40.11 3.16
5049 5147 2.407798 GTCGTGTCGACGTTGTCTC 58.592 57.895 11.62 0.00 46.56 3.36
5050 5148 0.995731 GTCGTGTCGACGTTGTCTCC 60.996 60.000 11.62 0.00 46.56 3.71
5052 5150 1.728426 GTGTCGACGTTGTCTCCCG 60.728 63.158 11.62 0.00 0.00 5.14
5053 5151 2.126580 GTCGACGTTGTCTCCCGG 60.127 66.667 0.00 0.00 0.00 5.73
5084 5189 1.748879 CGTTACCCCACATGCCCTG 60.749 63.158 0.00 0.00 0.00 4.45
5088 5193 2.781258 TACCCCACATGCCCTGTCCT 62.781 60.000 0.00 0.00 35.29 3.85
5096 5201 1.856539 ATGCCCTGTCCTGGTCCTTG 61.857 60.000 0.00 0.00 0.00 3.61
5109 5214 0.321653 GTCCTTGGACCGATGCTTGT 60.322 55.000 8.54 0.00 0.00 3.16
5116 5221 1.880027 GGACCGATGCTTGTCTTTGTT 59.120 47.619 0.00 0.00 0.00 2.83
5118 5223 3.555518 GACCGATGCTTGTCTTTGTTTC 58.444 45.455 0.00 0.00 0.00 2.78
5139 5244 9.119418 TGTTTCATCTTTCTCTTCATGTTAACA 57.881 29.630 11.41 11.41 0.00 2.41
5171 5276 1.667830 CACGATCAACCCAGCGTGT 60.668 57.895 0.00 0.00 46.28 4.49
5175 5280 1.076332 GATCAACCCAGCGTGTGTAC 58.924 55.000 0.00 0.00 0.00 2.90
5235 5357 6.698008 TGTGCTGTTGCTTGCTTATATATT 57.302 33.333 0.00 0.00 40.48 1.28
5241 5363 3.000041 TGCTTGCTTATATATTCGCCGG 59.000 45.455 0.00 0.00 0.00 6.13
5242 5364 2.351726 GCTTGCTTATATATTCGCCGGG 59.648 50.000 2.18 0.00 0.00 5.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 113 1.049289 AGTGGCGGAAGATAGGGTCC 61.049 60.000 0.00 0.00 0.00 4.46
109 114 0.389757 GAGTGGCGGAAGATAGGGTC 59.610 60.000 0.00 0.00 0.00 4.46
114 119 2.102588 GCTTAAGGAGTGGCGGAAGATA 59.897 50.000 4.29 0.00 0.00 1.98
115 120 1.134371 GCTTAAGGAGTGGCGGAAGAT 60.134 52.381 4.29 0.00 0.00 2.40
203 208 0.754217 TCCTCACCCCGTATTCTCCG 60.754 60.000 0.00 0.00 0.00 4.63
377 382 1.003003 AGCAAAGAAGCTCTGTCCCTC 59.997 52.381 0.00 0.00 42.18 4.30
463 468 3.571590 TCTTGGGCTCTCTCCTTAGATC 58.428 50.000 0.00 0.00 0.00 2.75
546 551 0.735978 TGTAGCAGCGTTCACCATCG 60.736 55.000 0.00 0.00 0.00 3.84
609 614 2.897641 CTTCCTCTGAAGCTCCGGCG 62.898 65.000 0.00 0.00 41.45 6.46
630 635 4.805947 ATTTCGTGCTCCACACTAAATCCA 60.806 41.667 3.33 0.00 46.20 3.41
641 646 0.331278 ATCCCCAATTTCGTGCTCCA 59.669 50.000 0.00 0.00 0.00 3.86
686 691 2.576832 CCAGGGCCCAGTTTTGCTG 61.577 63.158 27.56 10.81 44.63 4.41
729 734 5.302568 TCCAGTGTCAAAAATGAAAGAGCAT 59.697 36.000 0.00 0.00 0.00 3.79
861 866 6.467047 CGATCAAAATGTCAAGAAAATCCTCG 59.533 38.462 0.00 0.00 0.00 4.63
888 893 1.572085 CTGCTGCACCTTGTCCGAAG 61.572 60.000 0.00 0.00 0.00 3.79
942 947 4.641645 TGCCACGAAGCCCACCTG 62.642 66.667 0.00 0.00 0.00 4.00
975 980 2.352960 GTCATTCGACCTTGGAAGATGC 59.647 50.000 0.00 0.00 36.02 3.91
1155 1169 2.030805 AGACCTTGCACGATCAAAAAGC 60.031 45.455 0.00 0.00 0.00 3.51
1176 1190 4.985538 AGGCTGAAGGAATCAAACACTTA 58.014 39.130 0.00 0.00 37.67 2.24
1259 1278 6.418101 ACTTCAAGCATGTCCACATATACTT 58.582 36.000 0.00 0.00 34.26 2.24
1327 1346 3.840666 TCTCCCTTGACTAAAGCACTGAT 59.159 43.478 0.00 0.00 34.24 2.90
1331 1350 3.402628 TGTCTCCCTTGACTAAAGCAC 57.597 47.619 0.00 0.00 37.79 4.40
1548 1568 0.537188 ATGCCTCGTCAGTACCAAGG 59.463 55.000 0.00 0.00 0.00 3.61
1899 1919 9.159254 AGATCATTTACACCATTAGTCTCCATA 57.841 33.333 0.00 0.00 0.00 2.74
1995 2015 1.337071 CCAGCGGCGTTATCTCTCTTA 59.663 52.381 9.37 0.00 0.00 2.10
2074 2094 5.810074 CCAACGAAATCTCAAACTTTTTGGT 59.190 36.000 0.00 0.00 0.00 3.67
2081 2101 2.948979 TGCACCAACGAAATCTCAAACT 59.051 40.909 0.00 0.00 0.00 2.66
2100 2120 6.073331 GGTACAGAGCATTATCAAGAATCTGC 60.073 42.308 0.00 0.00 36.92 4.26
2169 2189 0.385223 GCAGAAGAGCACTTGCAACG 60.385 55.000 0.00 0.00 45.16 4.10
2194 2214 3.511146 TGTCCCCATTGAAAAGCTTCATC 59.489 43.478 0.00 2.02 41.22 2.92
2237 2257 6.438763 CACAAGGACTTGATTAGTTCCAAAC 58.561 40.000 18.15 0.00 42.93 2.93
2240 2260 4.072131 GCACAAGGACTTGATTAGTTCCA 58.928 43.478 18.15 0.00 42.93 3.53
2241 2261 3.125316 CGCACAAGGACTTGATTAGTTCC 59.875 47.826 18.15 0.00 42.93 3.62
2268 2288 3.650281 ACATCCATAACATGCACAGGA 57.350 42.857 0.00 0.00 0.00 3.86
2273 2293 6.128486 AGGTCAATAACATCCATAACATGCA 58.872 36.000 0.00 0.00 0.00 3.96
2388 2408 3.252215 TGTCCAAAACTAATCTTGCACGG 59.748 43.478 0.00 0.00 0.00 4.94
2492 2512 3.905493 TCCAACATTCCCAAAACCCTA 57.095 42.857 0.00 0.00 0.00 3.53
2559 2579 0.326264 ACAAGTGACTGATGAGGGGC 59.674 55.000 0.00 0.00 0.00 5.80
2593 2613 0.034670 AGCTGCAAGGATTCCTCCAC 60.035 55.000 5.48 0.00 44.79 4.02
2688 2708 6.206634 CACATCCAACATTAGTGTAACCTGTT 59.793 38.462 0.00 0.00 37.67 3.16
2839 2859 5.978919 ACACAGCTGATACAATGTTTTTGTG 59.021 36.000 23.35 5.34 38.43 3.33
2846 2866 4.700213 GGGTAAACACAGCTGATACAATGT 59.300 41.667 23.35 10.36 0.00 2.71
2849 2869 4.069304 GTGGGTAAACACAGCTGATACAA 58.931 43.478 23.35 7.32 40.99 2.41
2850 2870 3.558321 GGTGGGTAAACACAGCTGATACA 60.558 47.826 23.35 4.72 43.87 2.29
2858 2878 3.181471 TGCAAATTGGTGGGTAAACACAG 60.181 43.478 0.00 0.00 43.08 3.66
2893 2913 2.777094 TCGTTCTGCATCAAACCATGA 58.223 42.857 0.00 0.00 43.67 3.07
2969 2989 1.592064 TTCGTTCACAATGCAGCTGA 58.408 45.000 20.43 2.70 0.00 4.26
2997 3017 2.373836 TGCCTGGCTTACTTTTCCTGTA 59.626 45.455 21.03 0.00 0.00 2.74
3031 3051 4.222124 TCTTCCCTAAAGTGGATGCTTC 57.778 45.455 0.00 0.00 36.31 3.86
3056 3076 9.573133 GGATGGAATTTAGTAATTTGTCACTTG 57.427 33.333 0.00 0.00 34.16 3.16
3069 3089 5.422214 ACGACTGAAGGATGGAATTTAGT 57.578 39.130 0.00 0.00 0.00 2.24
3460 3480 2.375174 TGCTTGGTGTTAATCCCTGAGT 59.625 45.455 0.00 0.00 0.00 3.41
3521 3541 1.882623 GTGCTTTCTCAAGGTTCCCTG 59.117 52.381 0.00 0.00 32.13 4.45
3531 3551 6.330004 TGAAATAATTGCAGTGCTTTCTCA 57.670 33.333 17.60 10.46 0.00 3.27
3604 3624 6.127423 CCAAATGAAAGGAGAGCTGAAATGAT 60.127 38.462 0.00 0.00 0.00 2.45
3634 3654 7.926674 TCAGACATGATTTTGCTTCAGAATA 57.073 32.000 0.00 0.00 0.00 1.75
3696 3716 6.258230 TCCTTGATTAGCACATCAAAACTG 57.742 37.500 10.74 1.69 41.59 3.16
3782 3802 4.642885 AGCTAGCTTCACTTGGTAGTCTAG 59.357 45.833 12.68 0.00 37.69 2.43
3789 3809 2.354203 GCTGTAGCTAGCTTCACTTGGT 60.354 50.000 24.88 0.00 40.52 3.67
3835 3855 3.442273 AGCGCCCGATCAAATTCTTTTAA 59.558 39.130 2.29 0.00 0.00 1.52
3837 3857 1.818674 AGCGCCCGATCAAATTCTTTT 59.181 42.857 2.29 0.00 0.00 2.27
3885 3905 5.465390 GGCCATTTCACTTGGTTTTAAGTTC 59.535 40.000 0.00 0.00 38.78 3.01
3903 3923 2.044650 AGCGCATCACAGGCCATT 60.045 55.556 11.47 0.00 0.00 3.16
3906 3926 2.515523 ATGAGCGCATCACAGGCC 60.516 61.111 11.47 0.00 41.91 5.19
3907 3927 2.713770 CATGAGCGCATCACAGGC 59.286 61.111 11.47 0.00 41.91 4.85
3993 4013 2.539338 GCCAAACGACGGTGCAGAA 61.539 57.895 0.00 0.00 0.00 3.02
4000 4020 2.816689 TCTATACATGCCAAACGACGG 58.183 47.619 0.00 0.00 0.00 4.79
4002 4022 4.630069 ACAGTTCTATACATGCCAAACGAC 59.370 41.667 0.00 0.00 0.00 4.34
4005 4025 7.865385 TCAAAAACAGTTCTATACATGCCAAAC 59.135 33.333 0.00 0.00 0.00 2.93
4104 4124 1.068055 CACTGCATCTCAAAGTTGGGC 60.068 52.381 0.00 0.00 0.00 5.36
4367 4387 3.118454 GCTTTAGCGTGCGAGCCA 61.118 61.111 0.00 0.00 38.01 4.75
4405 4425 2.560542 CACTGCTCCACTTCTACAGAGT 59.439 50.000 0.00 0.00 32.67 3.24
4428 4448 2.953648 TGGGCTCAATGTGCATCTATTG 59.046 45.455 9.57 12.43 36.00 1.90
4429 4449 3.301794 TGGGCTCAATGTGCATCTATT 57.698 42.857 9.57 0.00 0.00 1.73
4431 4451 2.578786 CATGGGCTCAATGTGCATCTA 58.421 47.619 9.57 0.00 0.00 1.98
4432 4452 1.399714 CATGGGCTCAATGTGCATCT 58.600 50.000 9.57 0.00 0.00 2.90
4433 4453 0.387929 CCATGGGCTCAATGTGCATC 59.612 55.000 2.85 1.85 0.00 3.91
4449 4470 2.373169 TGAACAGAAAGAGACCTGCCAT 59.627 45.455 0.00 0.00 33.90 4.40
4455 4476 4.699257 AGCAATGATGAACAGAAAGAGACC 59.301 41.667 0.00 0.00 0.00 3.85
4456 4477 5.410746 TCAGCAATGATGAACAGAAAGAGAC 59.589 40.000 0.00 0.00 0.00 3.36
4476 4497 1.336240 GGACTGCAATTTGTGGTCAGC 60.336 52.381 18.26 0.00 0.00 4.26
4477 4498 2.030540 CAGGACTGCAATTTGTGGTCAG 60.031 50.000 18.26 11.06 0.00 3.51
4521 4543 5.918426 TGTGTAATGTCCACGAAGGTATA 57.082 39.130 0.00 0.00 39.02 1.47
4522 4544 4.811969 TGTGTAATGTCCACGAAGGTAT 57.188 40.909 0.00 0.00 39.02 2.73
4523 4545 4.603989 TTGTGTAATGTCCACGAAGGTA 57.396 40.909 0.00 0.00 39.02 3.08
4524 4546 3.478857 TTGTGTAATGTCCACGAAGGT 57.521 42.857 0.00 0.00 39.02 3.50
4525 4547 4.404507 CTTTGTGTAATGTCCACGAAGG 57.595 45.455 11.12 0.00 44.91 3.46
4526 4548 3.813166 ACCTTTGTGTAATGTCCACGAAG 59.187 43.478 11.76 11.76 46.79 3.79
4527 4549 3.811083 ACCTTTGTGTAATGTCCACGAA 58.189 40.909 0.00 0.00 35.56 3.85
4528 4550 3.478857 ACCTTTGTGTAATGTCCACGA 57.521 42.857 0.00 0.00 35.56 4.35
4529 4551 5.676532 TTTACCTTTGTGTAATGTCCACG 57.323 39.130 0.00 0.00 35.56 4.94
4530 4552 5.861787 GCATTTACCTTTGTGTAATGTCCAC 59.138 40.000 0.00 0.00 33.69 4.02
4531 4553 5.047660 GGCATTTACCTTTGTGTAATGTCCA 60.048 40.000 0.00 0.00 33.69 4.02
4532 4554 5.185056 AGGCATTTACCTTTGTGTAATGTCC 59.815 40.000 0.00 0.00 36.28 4.02
4533 4555 6.267496 AGGCATTTACCTTTGTGTAATGTC 57.733 37.500 0.00 0.00 36.28 3.06
4553 4575 5.583495 TGTTGTACACAAACATAACAAGGC 58.417 37.500 0.00 0.00 37.63 4.35
4567 4589 7.865889 TCGATATGACCAGAATATGTTGTACAC 59.134 37.037 0.00 0.00 0.00 2.90
4597 4619 6.574350 CATATTCTCTCAAAACCTACTCCGT 58.426 40.000 0.00 0.00 0.00 4.69
4611 4633 8.885494 AAGAAGACAAGTATGCATATTCTCTC 57.115 34.615 10.16 9.41 0.00 3.20
4625 4651 5.133221 ACTGCATGGTAAAAGAAGACAAGT 58.867 37.500 0.00 0.00 0.00 3.16
4626 4652 5.695851 ACTGCATGGTAAAAGAAGACAAG 57.304 39.130 0.00 0.00 0.00 3.16
4631 4657 5.010282 ACCCTAACTGCATGGTAAAAGAAG 58.990 41.667 0.00 0.00 0.00 2.85
4642 4668 0.613260 TCGCAAGACCCTAACTGCAT 59.387 50.000 0.00 0.00 45.01 3.96
4712 4747 0.465705 TTAGGAGCAGCTTCGGATGG 59.534 55.000 0.00 0.00 0.00 3.51
4713 4748 2.315925 TTTAGGAGCAGCTTCGGATG 57.684 50.000 0.00 0.00 0.00 3.51
4714 4749 3.350219 TTTTTAGGAGCAGCTTCGGAT 57.650 42.857 0.00 0.00 0.00 4.18
4715 4750 2.851263 TTTTTAGGAGCAGCTTCGGA 57.149 45.000 0.00 0.00 0.00 4.55
4777 4812 6.062095 CACCGAACCCTCATATAAGGAAAAT 58.938 40.000 0.00 0.00 38.87 1.82
4813 4848 6.327626 AGGCTATGAGATATTACTGTTGTGGT 59.672 38.462 0.00 0.00 0.00 4.16
4838 4873 8.514594 CATCTATTAGCAGGAACACAAGAAAAA 58.485 33.333 0.00 0.00 0.00 1.94
4906 4996 0.521242 CTCGGCGCTTACAACAATGC 60.521 55.000 7.64 0.00 0.00 3.56
4907 4997 0.796312 ACTCGGCGCTTACAACAATG 59.204 50.000 7.64 0.00 0.00 2.82
4919 5009 3.071459 GCACAATCGTGACTCGGCG 62.071 63.158 0.00 0.00 46.80 6.46
4928 5018 1.615424 AGGGTAGGGGCACAATCGT 60.615 57.895 0.00 0.00 0.00 3.73
4930 5020 1.453928 GCAGGGTAGGGGCACAATC 60.454 63.158 0.00 0.00 0.00 2.67
4938 5028 1.338136 CCTAGTGTGGCAGGGTAGGG 61.338 65.000 7.73 0.00 0.00 3.53
4944 5034 0.615331 ACATGACCTAGTGTGGCAGG 59.385 55.000 0.00 0.00 37.97 4.85
4965 5055 4.389576 GTGCGAACAAGCGGGCAG 62.390 66.667 0.00 0.00 40.67 4.85
4996 5086 1.129811 GTATGAAGCCCGTTTTGGTCG 59.870 52.381 0.00 0.00 35.15 4.79
5053 5151 4.382320 TAACGGGCAGTGGACGGC 62.382 66.667 0.00 0.00 36.32 5.68
5096 5201 1.523758 ACAAAGACAAGCATCGGTCC 58.476 50.000 0.00 0.00 34.58 4.46
5105 5210 8.400947 TGAAGAGAAAGATGAAACAAAGACAAG 58.599 33.333 0.00 0.00 0.00 3.16
5109 5214 8.455903 ACATGAAGAGAAAGATGAAACAAAGA 57.544 30.769 0.00 0.00 0.00 2.52
5139 5244 6.378582 GGTTGATCGTGTGTTTAAATCACAT 58.621 36.000 19.48 13.84 45.43 3.21
5155 5260 0.389296 TACACACGCTGGGTTGATCG 60.389 55.000 11.71 0.00 34.65 3.69
5171 5276 3.005261 GCAACAACACATTGGATGGTACA 59.995 43.478 0.00 0.00 41.50 2.90
5175 5280 3.389925 AAGCAACAACACATTGGATGG 57.610 42.857 0.00 0.00 40.42 3.51
5215 5337 4.848299 GCGAATATATAAGCAAGCAACAGC 59.152 41.667 7.28 0.00 0.00 4.40
5216 5338 5.385617 GGCGAATATATAAGCAAGCAACAG 58.614 41.667 12.52 0.00 0.00 3.16
5219 5341 3.435327 CCGGCGAATATATAAGCAAGCAA 59.565 43.478 9.30 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.