Multiple sequence alignment - TraesCS6D01G117500

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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 TraesCS6D01G117500 chr6D 100.000 5835 0 0 1 5835 83159857 83165691 0.000000e+00 10776.0
1 TraesCS6D01G117500 chr6D 86.185 637 87 1 1 637 83046322 83046957 0.000000e+00 688.0
2 TraesCS6D01G117500 chr6D 88.868 521 58 0 2 522 83124186 83124706 4.930000e-180 641.0
3 TraesCS6D01G117500 chr6D 82.451 359 45 12 1514 1862 83524136 83523786 1.230000e-76 298.0
4 TraesCS6D01G117500 chr6D 78.000 200 28 11 1262 1451 83047998 83048191 1.720000e-20 111.0
5 TraesCS6D01G117500 chr6B 92.010 4443 249 38 1471 5835 158165250 158169664 0.000000e+00 6141.0
6 TraesCS6D01G117500 chr6B 97.138 1118 28 3 1 1114 158162467 158163584 0.000000e+00 1884.0
7 TraesCS6D01G117500 chr6B 89.060 521 57 0 2 522 158149255 158149775 0.000000e+00 647.0
8 TraesCS6D01G117500 chr6B 87.194 531 63 5 1 529 159402615 159402088 3.010000e-167 599.0
9 TraesCS6D01G117500 chr6B 95.467 353 10 1 1099 1451 158164835 158165181 5.110000e-155 558.0
10 TraesCS6D01G117500 chr6B 78.088 251 51 4 2715 2963 51918838 51919086 7.830000e-34 156.0
11 TraesCS6D01G117500 chr6B 90.323 62 4 1 1390 1451 159394481 159394422 4.850000e-11 80.5
12 TraesCS6D01G117500 chr6A 89.817 3722 281 42 2179 5835 100262447 100266135 0.000000e+00 4684.0
13 TraesCS6D01G117500 chr6A 96.281 1452 43 4 1 1451 100228327 100229768 0.000000e+00 2372.0
14 TraesCS6D01G117500 chr6A 87.739 522 64 0 1 522 100184543 100185064 1.390000e-170 610.0
15 TraesCS6D01G117500 chr6A 87.194 531 63 5 1 529 100761521 100760994 3.010000e-167 599.0
16 TraesCS6D01G117500 chr6A 82.835 635 102 5 61 695 100743693 100743066 3.950000e-156 562.0
17 TraesCS6D01G117500 chr6A 90.343 321 22 5 1451 1763 100229806 100230125 4.210000e-111 412.0
18 TraesCS6D01G117500 chr6A 82.440 336 14 18 1869 2188 100234155 100234461 9.710000e-63 252.0
19 TraesCS6D01G117500 chr6A 77.807 383 48 18 1514 1862 100754298 100753919 9.910000e-48 202.0
20 TraesCS6D01G117500 chr6A 73.114 517 74 44 961 1451 100357723 100358200 2.210000e-24 124.0
21 TraesCS6D01G117500 chr6A 79.747 158 22 9 1304 1451 100074039 100074196 8.000000e-19 106.0
22 TraesCS6D01G117500 chr5A 82.403 2114 289 43 2697 4748 18762802 18764894 0.000000e+00 1766.0
23 TraesCS6D01G117500 chr5A 78.444 900 164 14 4835 5725 18764898 18765776 1.420000e-155 560.0
24 TraesCS6D01G117500 chr2B 83.403 1681 242 15 3100 4743 754921157 754922837 0.000000e+00 1524.0
25 TraesCS6D01G117500 chr2B 77.887 918 178 16 4835 5741 754922846 754923749 1.110000e-151 547.0
26 TraesCS6D01G117500 chr2B 78.125 128 26 2 2881 3007 8636140 8636014 4.850000e-11 80.5
27 TraesCS6D01G117500 chr2B 81.188 101 17 2 2881 2980 8666547 8666646 4.850000e-11 80.5
28 TraesCS6D01G117500 chr7B 81.302 1690 274 19 3101 4750 747197088 747198775 0.000000e+00 1332.0
29 TraesCS6D01G117500 chr7B 80.055 727 128 10 4836 5552 747198778 747199497 1.860000e-144 523.0
30 TraesCS6D01G117500 chr7A 81.165 1683 273 21 3101 4742 708362089 708363768 0.000000e+00 1312.0
31 TraesCS6D01G117500 chr7A 80.758 686 117 8 4832 5508 708363775 708364454 6.700000e-144 521.0
32 TraesCS6D01G117500 chr7A 96.970 33 1 0 2365 2397 708361117 708361149 8.170000e-04 56.5
33 TraesCS6D01G117500 chr3D 81.273 1618 256 24 3101 4675 600154336 600155949 0.000000e+00 1266.0
34 TraesCS6D01G117500 chr3D 76.950 859 159 31 4882 5725 600156100 600156934 2.480000e-123 453.0
35 TraesCS6D01G117500 chr1D 75.799 1376 285 31 3264 4606 79141577 79140217 0.000000e+00 652.0
36 TraesCS6D01G117500 chr1B 74.787 1408 303 36 3234 4606 130023877 130022487 2.340000e-163 586.0
37 TraesCS6D01G117500 chr5D 100.000 111 0 0 1238 1348 455825298 455825408 7.660000e-49 206.0


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 TraesCS6D01G117500 chr6D 83159857 83165691 5834 False 10776.000000 10776 100.000000 1 5835 1 chr6D.!!$F2 5834
1 TraesCS6D01G117500 chr6D 83124186 83124706 520 False 641.000000 641 88.868000 2 522 1 chr6D.!!$F1 520
2 TraesCS6D01G117500 chr6D 83046322 83048191 1869 False 399.500000 688 82.092500 1 1451 2 chr6D.!!$F3 1450
3 TraesCS6D01G117500 chr6B 158162467 158169664 7197 False 2861.000000 6141 94.871667 1 5835 3 chr6B.!!$F3 5834
4 TraesCS6D01G117500 chr6B 158149255 158149775 520 False 647.000000 647 89.060000 2 522 1 chr6B.!!$F2 520
5 TraesCS6D01G117500 chr6B 159402088 159402615 527 True 599.000000 599 87.194000 1 529 1 chr6B.!!$R2 528
6 TraesCS6D01G117500 chr6A 100262447 100266135 3688 False 4684.000000 4684 89.817000 2179 5835 1 chr6A.!!$F4 3656
7 TraesCS6D01G117500 chr6A 100228327 100230125 1798 False 1392.000000 2372 93.312000 1 1763 2 chr6A.!!$F6 1762
8 TraesCS6D01G117500 chr6A 100184543 100185064 521 False 610.000000 610 87.739000 1 522 1 chr6A.!!$F2 521
9 TraesCS6D01G117500 chr6A 100760994 100761521 527 True 599.000000 599 87.194000 1 529 1 chr6A.!!$R3 528
10 TraesCS6D01G117500 chr6A 100743066 100743693 627 True 562.000000 562 82.835000 61 695 1 chr6A.!!$R1 634
11 TraesCS6D01G117500 chr5A 18762802 18765776 2974 False 1163.000000 1766 80.423500 2697 5725 2 chr5A.!!$F1 3028
12 TraesCS6D01G117500 chr2B 754921157 754923749 2592 False 1035.500000 1524 80.645000 3100 5741 2 chr2B.!!$F2 2641
13 TraesCS6D01G117500 chr7B 747197088 747199497 2409 False 927.500000 1332 80.678500 3101 5552 2 chr7B.!!$F1 2451
14 TraesCS6D01G117500 chr7A 708361117 708364454 3337 False 629.833333 1312 86.297667 2365 5508 3 chr7A.!!$F1 3143
15 TraesCS6D01G117500 chr3D 600154336 600156934 2598 False 859.500000 1266 79.111500 3101 5725 2 chr3D.!!$F1 2624
16 TraesCS6D01G117500 chr1D 79140217 79141577 1360 True 652.000000 652 75.799000 3264 4606 1 chr1D.!!$R1 1342
17 TraesCS6D01G117500 chr1B 130022487 130023877 1390 True 586.000000 586 74.787000 3234 4606 1 chr1B.!!$R1 1372

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
342 343 1.800805 CCAGCGAAACATCAGTGACT 58.199 50.0 0.00 0.00 0.00 3.41 F
2108 3585 0.036952 TTTCTCTTGCGCAGGGAGAG 60.037 55.0 29.80 27.71 37.41 3.20 F
2148 3625 0.188342 ATTGGTGGCTTGGTGTTCCT 59.812 50.0 0.00 0.00 34.23 3.36 F
2398 3904 0.323178 CTTGGTTGCTCTGCCTCCAT 60.323 55.0 0.00 0.00 32.60 3.41 F
3213 4998 0.747255 GATCTAGAGCTCCGCAACCA 59.253 55.0 10.93 0.00 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2188 3666 0.250901 AATGGAGCGAAGTTGGCTGT 60.251 50.000 17.77 0.34 41.72 4.40 R
2977 4552 1.072173 TGCTTATCGGCTGCATGGTAT 59.928 47.619 0.50 0.00 0.00 2.73 R
3334 5125 1.977594 GCACGGTAAGTCCATTGGCG 61.978 60.000 0.00 0.00 35.57 5.69 R
3821 5639 2.173356 CCTTCAGATGCCCCACTATTGA 59.827 50.000 0.00 0.00 0.00 2.57 R
4857 6729 0.670162 CACCAAAGTCTGCCAACTGG 59.330 55.000 0.00 0.00 38.53 4.00 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
342 343 1.800805 CCAGCGAAACATCAGTGACT 58.199 50.000 0.00 0.00 0.00 3.41
343 344 2.930887 GCCAGCGAAACATCAGTGACTA 60.931 50.000 0.00 0.00 0.00 2.59
714 717 5.682943 TCTTTAGTTTGTTTGATCCGGTG 57.317 39.130 0.00 0.00 0.00 4.94
863 899 3.769844 TCTGACCATTTCTCCTACCAGTC 59.230 47.826 0.00 0.00 0.00 3.51
1093 1211 5.594317 GGTTGATGGAATAGGTGCAGTTATT 59.406 40.000 0.00 0.00 0.00 1.40
1160 2544 6.650390 AGTTGGTTGATGGAATAATTTGTTGC 59.350 34.615 0.00 0.00 0.00 4.17
1187 2571 1.279271 GATCAGTAAGTGGCCACTGGT 59.721 52.381 38.35 25.90 41.58 4.00
1316 2711 0.962356 GCACTTGCAGGGTGTATGCT 60.962 55.000 18.53 0.00 44.17 3.79
1335 2730 1.216710 GTGCGAGCTAGCTTGGTCT 59.783 57.895 29.27 2.61 38.13 3.85
1454 2897 0.040157 CCCACAACAGCAACATGACG 60.040 55.000 0.00 0.00 0.00 4.35
1549 3005 2.426522 TCAGCAGGAGGTTGAAATTCG 58.573 47.619 0.00 0.00 33.43 3.34
1644 3103 8.045507 AGAAGCAGTCTCATTTCATTCTAATCA 58.954 33.333 0.00 0.00 0.00 2.57
1645 3104 8.571461 AAGCAGTCTCATTTCATTCTAATCAA 57.429 30.769 0.00 0.00 0.00 2.57
1693 3165 8.807118 TCTAAGACTTGAATCACTGTCACTTAT 58.193 33.333 14.82 2.76 32.41 1.73
1723 3195 6.560253 AATCAATAATCAAGGTATCCACGC 57.440 37.500 0.00 0.00 0.00 5.34
1780 3252 9.878667 TGATCTTATACAACAATAGGAAACGAA 57.121 29.630 0.00 0.00 0.00 3.85
1870 3345 3.632145 AGGGTGAATGAACAGTTGAACAC 59.368 43.478 0.00 0.00 0.00 3.32
1955 3432 5.006941 GCATGATTTTTCCATGTGGTAATGC 59.993 40.000 0.00 0.00 42.39 3.56
2108 3585 0.036952 TTTCTCTTGCGCAGGGAGAG 60.037 55.000 29.80 27.71 37.41 3.20
2148 3625 0.188342 ATTGGTGGCTTGGTGTTCCT 59.812 50.000 0.00 0.00 34.23 3.36
2188 3666 3.648067 ACTCCATTCAGACTTCCAGACAA 59.352 43.478 0.00 0.00 0.00 3.18
2337 3816 3.303189 GCAGGAGCAGCAGGAGTA 58.697 61.111 0.00 0.00 41.58 2.59
2338 3817 1.143620 GCAGGAGCAGCAGGAGTAG 59.856 63.158 0.00 0.00 41.58 2.57
2349 3855 4.302455 CAGCAGGAGTAGATGTATTTCCG 58.698 47.826 0.00 0.00 33.16 4.30
2352 3858 5.597182 AGCAGGAGTAGATGTATTTCCGTTA 59.403 40.000 0.00 0.00 33.16 3.18
2354 3860 6.461231 GCAGGAGTAGATGTATTTCCGTTACT 60.461 42.308 0.00 0.00 33.16 2.24
2355 3861 7.255381 GCAGGAGTAGATGTATTTCCGTTACTA 60.255 40.741 0.00 0.00 33.16 1.82
2356 3862 8.074972 CAGGAGTAGATGTATTTCCGTTACTAC 58.925 40.741 0.00 0.00 33.16 2.73
2362 3868 5.587388 TGTATTTCCGTTACTACCAGAGG 57.413 43.478 0.00 0.00 0.00 3.69
2366 3872 3.719268 TCCGTTACTACCAGAGGTGTA 57.281 47.619 0.00 0.00 36.19 2.90
2398 3904 0.323178 CTTGGTTGCTCTGCCTCCAT 60.323 55.000 0.00 0.00 32.60 3.41
2515 4070 1.089920 CAAGATCTGAAGCCCCAACG 58.910 55.000 0.00 0.00 0.00 4.10
2592 4147 2.167075 AGTGTTGCTGCTGCTTCTTTTT 59.833 40.909 17.00 0.00 40.48 1.94
2597 4152 1.625511 CTGCTGCTTCTTTTTCCCCT 58.374 50.000 0.00 0.00 0.00 4.79
2621 4176 7.174253 CCTTTTGCTATTTGGTAGTGACTAACA 59.826 37.037 6.20 6.20 31.17 2.41
2680 4235 1.149174 CAACCCACTCACCAGCAGT 59.851 57.895 0.00 0.00 0.00 4.40
2685 4257 2.029666 ACTCACCAGCAGTGCGAC 59.970 61.111 10.00 0.00 46.81 5.19
2713 4285 4.208632 GCTATCAGTGCGGCTGTT 57.791 55.556 0.00 3.20 45.23 3.16
2757 4329 1.134220 TCCCATTACGGATGACTTGCC 60.134 52.381 2.95 0.00 38.03 4.52
2799 4371 1.002624 GTCTCGGCCCCAACATCAA 60.003 57.895 0.00 0.00 0.00 2.57
3184 4969 6.328934 TGGATCCTATATGTGCTAAGGTGAAA 59.671 38.462 14.23 0.00 0.00 2.69
3213 4998 0.747255 GATCTAGAGCTCCGCAACCA 59.253 55.000 10.93 0.00 0.00 3.67
3214 4999 0.749649 ATCTAGAGCTCCGCAACCAG 59.250 55.000 10.93 0.00 0.00 4.00
3241 5032 1.477923 GCCCAAGGTAACAACAGACCA 60.478 52.381 0.00 0.00 38.27 4.02
3387 5178 1.534338 CCAGGGGGTATTGGGAAGAT 58.466 55.000 0.00 0.00 0.00 2.40
3423 5214 8.421784 ACAACACGTATATCAAGAGGTGAATAT 58.578 33.333 3.67 0.00 40.50 1.28
3488 5279 8.883954 TTTTGATGCAAATAGATTGACACAAA 57.116 26.923 0.00 0.00 41.85 2.83
3519 5310 8.303876 TGTGAAAAAGATCCCTAAAGTTAATGC 58.696 33.333 0.00 0.00 0.00 3.56
3526 5317 8.056407 AGATCCCTAAAGTTAATGCTGAAAAC 57.944 34.615 0.00 0.00 0.00 2.43
3776 5594 3.188254 TGAAGCATGTGTATTTGGTCACG 59.812 43.478 0.00 0.00 37.38 4.35
3810 5628 7.338710 TGGAAAGACTATCCTGAATTACTTGG 58.661 38.462 0.00 0.00 37.85 3.61
3821 5639 6.553100 TCCTGAATTACTTGGTGTTGGAAAAT 59.447 34.615 0.00 0.00 0.00 1.82
3880 5698 7.094762 GCAGCAAAAACTGTAGGTAGATTACTT 60.095 37.037 0.00 0.00 39.96 2.24
3893 5711 7.919151 AGGTAGATTACTTAGAAACCAGCTTT 58.081 34.615 0.00 0.00 0.00 3.51
4058 5876 7.040478 TGTTTCCTGAAGATTATGAGTTTGGTG 60.040 37.037 0.00 0.00 0.00 4.17
4062 5888 4.458989 TGAAGATTATGAGTTTGGTGGCAC 59.541 41.667 9.70 9.70 0.00 5.01
4325 6151 0.974010 TCCCCCATCTGTACGTCACC 60.974 60.000 0.00 0.00 0.00 4.02
4341 6167 6.576662 ACGTCACCTGTCTATCATTATAGG 57.423 41.667 0.00 0.00 36.49 2.57
4418 6244 7.338196 TGAGTACACTGGATGAAAAACTGAAAA 59.662 33.333 0.00 0.00 0.00 2.29
4429 6255 9.706846 GATGAAAAACTGAAAATTGAAAACCTG 57.293 29.630 0.00 0.00 0.00 4.00
4472 6298 1.780503 ATACCAAGGATGCTTTGCCC 58.219 50.000 0.00 0.00 0.00 5.36
4480 6306 1.067354 GGATGCTTTGCCCAGACTTTG 60.067 52.381 0.00 0.00 0.00 2.77
4564 6390 4.079253 GGTATGTTGTGGAGGATGTGTTT 58.921 43.478 0.00 0.00 0.00 2.83
4570 6396 0.396435 TGGAGGATGTGTTTCGCAGT 59.604 50.000 0.00 0.00 0.00 4.40
4594 6420 6.936279 TCTTCCAAGACTTATTCATCTTCGT 58.064 36.000 0.00 0.00 32.77 3.85
4614 6440 4.436332 CGTTACCTAAGGATAACGCCTTT 58.564 43.478 12.44 0.00 45.85 3.11
4624 6462 3.687698 GGATAACGCCTTTTGCAAGACTA 59.312 43.478 0.00 0.00 41.33 2.59
4687 6525 6.061441 AGATGTTGAACAATACAGTGTCCAA 58.939 36.000 0.62 0.00 0.00 3.53
4690 6528 6.350103 TGTTGAACAATACAGTGTCCAACTA 58.650 36.000 12.04 0.00 36.83 2.24
4719 6584 5.918608 TCCAAGAGATATGAGCAACCTTAC 58.081 41.667 0.00 0.00 0.00 2.34
4750 6615 3.191371 GCCATTTTCTTGTCCGAGACATT 59.809 43.478 7.43 0.00 42.40 2.71
4756 6621 2.029020 TCTTGTCCGAGACATTGACCTG 60.029 50.000 7.43 0.00 42.40 4.00
4764 6629 4.262207 CCGAGACATTGACCTGCAGTATAT 60.262 45.833 13.81 0.00 0.00 0.86
4767 6632 6.923508 CGAGACATTGACCTGCAGTATATAAA 59.076 38.462 13.81 0.00 0.00 1.40
4774 6645 8.662781 TTGACCTGCAGTATATAAATTCTGAC 57.337 34.615 13.81 0.00 33.55 3.51
4777 6648 7.272978 ACCTGCAGTATATAAATTCTGACGTT 58.727 34.615 13.81 0.00 33.55 3.99
4795 6666 7.662258 TCTGACGTTGGAAAACTGGAATTATTA 59.338 33.333 0.00 0.00 0.00 0.98
4830 6701 8.435931 AGAAGCTTTATGGTTAAAAGGGAAAT 57.564 30.769 0.00 0.00 36.40 2.17
4831 6702 9.541884 AGAAGCTTTATGGTTAAAAGGGAAATA 57.458 29.630 0.00 0.00 36.40 1.40
4845 6717 7.625828 AAAGGGAAATATAGGTTTCGAACTG 57.374 36.000 0.00 0.00 38.64 3.16
4854 6726 2.003301 GGTTTCGAACTGAGGCAGATC 58.997 52.381 0.00 0.00 35.18 2.75
4857 6729 4.116878 GAACTGAGGCAGATCGGC 57.883 61.111 9.58 9.58 41.61 5.54
4937 6812 6.129273 CGACAAGAAGTGAATGAAGCAAAATG 60.129 38.462 0.00 0.00 0.00 2.32
5053 6928 4.938226 GTCTTAAGCCACATAGCAGTCTTT 59.062 41.667 0.00 0.00 34.23 2.52
5055 6930 5.412594 TCTTAAGCCACATAGCAGTCTTTTG 59.587 40.000 0.00 0.00 34.23 2.44
5162 7046 3.264193 TGTCTGGTTGATGTAGCTTGGAT 59.736 43.478 0.00 0.00 0.00 3.41
5182 7066 3.366052 TCAAATTTCCACCTCTAGGGC 57.634 47.619 0.20 0.00 40.27 5.19
5394 7278 2.731572 CCATTTCCAGGCTGTCAATCT 58.268 47.619 14.43 0.00 0.00 2.40
5435 7322 5.105473 TGACTTGGTTTCCTAGATTACGGAG 60.105 44.000 4.48 0.00 31.18 4.63
5441 7328 3.028094 TCCTAGATTACGGAGGCTTGT 57.972 47.619 0.00 0.00 0.00 3.16
5494 7381 0.684535 TCATGTTCCTTGGACTCGCA 59.315 50.000 0.00 0.00 0.00 5.10
5544 7431 1.001633 GGGTCACGTTTTGAGGAGCTA 59.998 52.381 0.00 0.00 33.71 3.32
5546 7433 3.335579 GGTCACGTTTTGAGGAGCTAAT 58.664 45.455 0.00 0.00 33.71 1.73
5552 7439 7.330208 GTCACGTTTTGAGGAGCTAATTTACTA 59.670 37.037 0.00 0.00 33.71 1.82
5553 7440 8.038944 TCACGTTTTGAGGAGCTAATTTACTAT 58.961 33.333 0.00 0.00 0.00 2.12
5554 7441 8.116753 CACGTTTTGAGGAGCTAATTTACTATG 58.883 37.037 0.00 0.00 0.00 2.23
5589 7485 3.733337 GGAGTTGAGCTTGAGAGTTGAA 58.267 45.455 0.00 0.00 0.00 2.69
5622 7518 5.246307 GGTGGTCTAACTGATAGCAAGTTT 58.754 41.667 2.07 0.00 0.00 2.66
5766 7665 4.156556 TCAGATAATGTTTTGCCACTGAGC 59.843 41.667 0.00 0.00 0.00 4.26
5774 7679 0.250252 TTGCCACTGAGCGATGTTGA 60.250 50.000 0.00 0.00 34.65 3.18
5793 7698 2.571202 TGAGAGTGATGGCATGTACCAA 59.429 45.455 3.81 0.00 44.65 3.67
5822 7727 4.706842 TTGATACCCTAGAGATTTGGCC 57.293 45.455 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
342 343 4.037222 TCACCTGCAACCAAGATAGGATA 58.963 43.478 0.00 0.00 32.86 2.59
343 344 2.846206 TCACCTGCAACCAAGATAGGAT 59.154 45.455 0.00 0.00 32.86 3.24
714 717 2.526304 TCACTGCTCACTACAACCAC 57.474 50.000 0.00 0.00 0.00 4.16
863 899 4.038162 GTCAGTACCTCAGGGCATAGTAAG 59.962 50.000 0.00 0.00 35.63 2.34
1093 1211 9.378551 CACTTACTGCTGATAGGTATTTTAACA 57.621 33.333 0.00 0.00 0.00 2.41
1160 2544 3.187700 GGCCACTTACTGATCGTAGTTG 58.812 50.000 0.00 0.00 32.19 3.16
1187 2571 1.142667 TCCATCAACCAACTGCACTGA 59.857 47.619 0.00 0.00 0.00 3.41
1300 2695 0.806868 CACAGCATACACCCTGCAAG 59.193 55.000 0.00 0.00 42.15 4.01
1301 2696 1.243342 GCACAGCATACACCCTGCAA 61.243 55.000 0.00 0.00 42.15 4.08
1302 2697 1.675310 GCACAGCATACACCCTGCA 60.675 57.895 0.00 0.00 42.15 4.41
1303 2698 2.753966 CGCACAGCATACACCCTGC 61.754 63.158 0.00 0.00 39.97 4.85
1304 2699 1.079197 TCGCACAGCATACACCCTG 60.079 57.895 0.00 0.00 35.26 4.45
1305 2700 1.219124 CTCGCACAGCATACACCCT 59.781 57.895 0.00 0.00 0.00 4.34
1316 2711 1.079819 GACCAAGCTAGCTCGCACA 60.080 57.895 19.65 0.00 0.00 4.57
1335 2730 6.139679 ACAAGACTTCTGGGGAAATCATTA 57.860 37.500 0.00 0.00 31.01 1.90
1454 2897 2.674796 AATAGTTCCGACCTGCTCAC 57.325 50.000 0.00 0.00 0.00 3.51
1549 3005 3.906720 TGGTAAAGACTAGATGCCACC 57.093 47.619 0.00 0.00 0.00 4.61
1663 3122 8.279103 GTGACAGTGATTCAAGTCTTAGAAAAG 58.721 37.037 16.74 0.00 32.41 2.27
1710 3182 1.016627 CACATGGCGTGGATACCTTG 58.983 55.000 12.05 0.00 42.34 3.61
1723 3195 1.477553 AAAGGCCATAGTGCACATGG 58.522 50.000 29.18 29.18 44.94 3.66
1780 3252 4.818546 GCAGCTTGACATGTATTACAGGAT 59.181 41.667 14.87 0.12 33.56 3.24
1841 3316 6.605594 TCAACTGTTCATTCACCCTAAAAAGT 59.394 34.615 0.00 0.00 0.00 2.66
1848 3323 3.632145 GTGTTCAACTGTTCATTCACCCT 59.368 43.478 0.00 0.00 0.00 4.34
1870 3345 3.319031 AGATTGGGAGGCCCTTATTTG 57.681 47.619 0.00 0.00 45.70 2.32
1933 3410 5.126869 TCGCATTACCACATGGAAAAATCAT 59.873 36.000 4.53 0.00 38.94 2.45
1934 3411 4.460731 TCGCATTACCACATGGAAAAATCA 59.539 37.500 4.53 0.00 38.94 2.57
2044 3521 1.748403 GTGTGCAGGTCACCAGAGA 59.252 57.895 0.00 0.00 45.03 3.10
2108 3585 3.282021 TGAGTGGAGGCTGAATTATTGC 58.718 45.455 0.00 0.00 0.00 3.56
2188 3666 0.250901 AATGGAGCGAAGTTGGCTGT 60.251 50.000 17.77 0.34 41.72 4.40
2302 3781 1.612950 TGCACAAAGATGATTGGCGTT 59.387 42.857 0.00 0.00 34.56 4.84
2334 3813 7.776969 TCTGGTAGTAACGGAAATACATCTACT 59.223 37.037 0.00 0.00 0.00 2.57
2335 3814 7.934457 TCTGGTAGTAACGGAAATACATCTAC 58.066 38.462 0.00 0.00 0.00 2.59
2336 3815 7.230108 CCTCTGGTAGTAACGGAAATACATCTA 59.770 40.741 0.00 0.00 0.00 1.98
2337 3816 6.040616 CCTCTGGTAGTAACGGAAATACATCT 59.959 42.308 0.00 0.00 0.00 2.90
2338 3817 6.183360 ACCTCTGGTAGTAACGGAAATACATC 60.183 42.308 0.00 0.00 32.11 3.06
2349 3855 7.772757 AGTACACTATACACCTCTGGTAGTAAC 59.227 40.741 0.00 0.00 32.11 2.50
2352 3858 6.069789 TCAGTACACTATACACCTCTGGTAGT 60.070 42.308 0.00 0.00 32.11 2.73
2354 3860 6.317663 TCAGTACACTATACACCTCTGGTA 57.682 41.667 0.00 0.00 32.11 3.25
2355 3861 5.188988 TCAGTACACTATACACCTCTGGT 57.811 43.478 0.00 0.00 35.62 4.00
2356 3862 5.652891 AGTTCAGTACACTATACACCTCTGG 59.347 44.000 0.00 0.00 0.00 3.86
2362 3868 6.128634 GCAACCAAGTTCAGTACACTATACAC 60.129 42.308 0.00 0.00 0.00 2.90
2366 3872 5.012148 AGAGCAACCAAGTTCAGTACACTAT 59.988 40.000 0.00 0.00 0.00 2.12
2398 3904 1.477700 GCTGCAAAACCCATCTGCATA 59.522 47.619 0.00 0.00 44.59 3.14
2515 4070 3.821033 AGAATGGTTCACTTACACAAGGC 59.179 43.478 0.00 0.00 35.97 4.35
2592 4147 4.043561 TCACTACCAAATAGCAAAAGGGGA 59.956 41.667 0.00 0.00 33.73 4.81
2597 4152 7.308348 GCTGTTAGTCACTACCAAATAGCAAAA 60.308 37.037 2.74 0.00 36.78 2.44
2621 4176 4.036027 CGCATCAATAGGAATGTTCTTGCT 59.964 41.667 0.00 0.00 0.00 3.91
2685 4257 1.665916 CTGATAGCGGTGGCCATCG 60.666 63.158 34.08 34.08 39.75 3.84
2710 4282 3.136345 CTTGCGCAGTGCCCAAACA 62.136 57.895 15.62 1.48 45.60 2.83
2741 4313 2.643551 CTTGGGCAAGTCATCCGTAAT 58.356 47.619 0.00 0.00 33.87 1.89
2799 4371 1.992277 AGCTCCATCTTGAGGGCGT 60.992 57.895 0.00 0.00 32.81 5.68
2826 4398 1.204146 GTTGTAGAGGATCCCCTGCA 58.796 55.000 10.06 10.06 44.53 4.41
2977 4552 1.072173 TGCTTATCGGCTGCATGGTAT 59.928 47.619 0.50 0.00 0.00 2.73
3184 4969 4.280677 CGGAGCTCTAGATCAAGGATTTCT 59.719 45.833 14.64 0.00 30.87 2.52
3229 5020 3.757493 ACGTGGTTTTTGGTCTGTTGTTA 59.243 39.130 0.00 0.00 0.00 2.41
3230 5021 2.559231 ACGTGGTTTTTGGTCTGTTGTT 59.441 40.909 0.00 0.00 0.00 2.83
3231 5022 2.162809 GACGTGGTTTTTGGTCTGTTGT 59.837 45.455 0.00 0.00 0.00 3.32
3241 5032 6.622896 GCTCTATTATTGCTGACGTGGTTTTT 60.623 38.462 0.00 0.00 0.00 1.94
3334 5125 1.977594 GCACGGTAAGTCCATTGGCG 61.978 60.000 0.00 0.00 35.57 5.69
3387 5178 6.217294 TGATATACGTGTTGTGTGAAAGTCA 58.783 36.000 0.00 0.00 0.00 3.41
3488 5279 8.712228 ACTTTAGGGATCTTTTTCACAATCTT 57.288 30.769 0.00 0.00 0.00 2.40
3519 5310 6.092670 TCCTTCAATAGCATTCTCGTTTTCAG 59.907 38.462 0.00 0.00 0.00 3.02
3526 5317 3.740321 GCTCTCCTTCAATAGCATTCTCG 59.260 47.826 0.00 0.00 35.05 4.04
3776 5594 3.879892 GGATAGTCTTTCCATGGCTGTTC 59.120 47.826 6.96 0.34 33.21 3.18
3810 5628 4.620567 GCCCCACTATTGATTTTCCAACAC 60.621 45.833 0.00 0.00 0.00 3.32
3821 5639 2.173356 CCTTCAGATGCCCCACTATTGA 59.827 50.000 0.00 0.00 0.00 2.57
3880 5698 4.724399 TGTCCAATGAAAGCTGGTTTCTA 58.276 39.130 26.68 16.51 44.45 2.10
3893 5711 4.728772 ACTCTTGTCCAATTGTCCAATGA 58.271 39.130 4.43 5.79 0.00 2.57
4058 5876 4.380867 CCATAATTGAACCAACTCTGTGCC 60.381 45.833 0.00 0.00 0.00 5.01
4062 5888 6.488006 CCCTATCCATAATTGAACCAACTCTG 59.512 42.308 0.00 0.00 0.00 3.35
4325 6151 8.628630 TCTCTGTCACCTATAATGATAGACAG 57.371 38.462 12.12 12.12 38.82 3.51
4418 6244 8.791327 AACATCAAAGTTTTCAGGTTTTCAAT 57.209 26.923 0.00 0.00 0.00 2.57
4472 6298 3.370672 GCAAACAAAACACCCAAAGTCTG 59.629 43.478 0.00 0.00 0.00 3.51
4480 6306 1.933181 GCTTCTGCAAACAAAACACCC 59.067 47.619 0.00 0.00 39.41 4.61
4510 6336 4.783242 CACCAGACAAAAGAATAACACGG 58.217 43.478 0.00 0.00 0.00 4.94
4570 6396 6.936279 ACGAAGATGAATAAGTCTTGGAAGA 58.064 36.000 0.00 0.00 34.97 2.87
4594 6420 4.637091 GCAAAAGGCGTTATCCTTAGGTAA 59.363 41.667 0.00 0.00 45.25 2.85
4614 6440 4.580167 AGATGTTGCTGTTTAGTCTTGCAA 59.420 37.500 0.00 0.00 40.65 4.08
4624 6462 8.579006 TGATAAAATCTTGAGATGTTGCTGTTT 58.421 29.630 6.66 0.00 34.12 2.83
4687 6525 8.027524 TGCTCATATCTCTTGGAAAATCTAGT 57.972 34.615 0.00 0.00 0.00 2.57
4690 6528 6.545298 GGTTGCTCATATCTCTTGGAAAATCT 59.455 38.462 0.00 0.00 0.00 2.40
4719 6584 2.865551 ACAAGAAAATGGCGCAGTTTTG 59.134 40.909 21.61 13.30 31.79 2.44
4750 6615 6.923508 CGTCAGAATTTATATACTGCAGGTCA 59.076 38.462 19.93 2.72 0.00 4.02
4756 6621 7.709269 TCCAACGTCAGAATTTATATACTGC 57.291 36.000 0.00 0.00 0.00 4.40
4764 6629 5.823570 TCCAGTTTTCCAACGTCAGAATTTA 59.176 36.000 0.00 0.00 38.03 1.40
4767 6632 3.815809 TCCAGTTTTCCAACGTCAGAAT 58.184 40.909 0.00 0.00 38.03 2.40
4774 6645 8.293867 TCTTGTAATAATTCCAGTTTTCCAACG 58.706 33.333 0.00 0.00 38.03 4.10
4777 6648 8.934023 AGTCTTGTAATAATTCCAGTTTTCCA 57.066 30.769 0.00 0.00 0.00 3.53
4795 6666 9.569122 TTAACCATAAAGCTTCTTAAGTCTTGT 57.431 29.630 0.00 0.00 0.00 3.16
4824 6695 5.758784 CCTCAGTTCGAAACCTATATTTCCC 59.241 44.000 0.00 0.00 35.52 3.97
4830 6701 4.021229 TCTGCCTCAGTTCGAAACCTATA 58.979 43.478 0.00 0.00 32.61 1.31
4831 6702 2.832129 TCTGCCTCAGTTCGAAACCTAT 59.168 45.455 0.00 0.00 32.61 2.57
4832 6703 2.244695 TCTGCCTCAGTTCGAAACCTA 58.755 47.619 0.00 0.00 32.61 3.08
4833 6704 1.048601 TCTGCCTCAGTTCGAAACCT 58.951 50.000 0.00 0.00 32.61 3.50
4857 6729 0.670162 CACCAAAGTCTGCCAACTGG 59.330 55.000 0.00 0.00 38.53 4.00
4906 6778 6.618287 TTCATTCACTTCTTGTCGTTCAAT 57.382 33.333 0.00 0.00 35.35 2.57
4937 6812 3.138304 TGTAAGTGGATATTGCGCATCC 58.862 45.455 19.46 19.46 42.08 3.51
4947 6822 9.197306 TCTAACATTAGCTTCTGTAAGTGGATA 57.803 33.333 0.00 0.00 34.99 2.59
5053 6928 2.092429 GCCCTCCAATGTGTAGATCCAA 60.092 50.000 0.00 0.00 0.00 3.53
5055 6930 1.490490 TGCCCTCCAATGTGTAGATCC 59.510 52.381 0.00 0.00 0.00 3.36
5124 7008 8.700051 TCAACCAGACAAAGAAATTCCAATTTA 58.300 29.630 0.00 0.00 38.64 1.40
5135 7019 4.973168 AGCTACATCAACCAGACAAAGAA 58.027 39.130 0.00 0.00 0.00 2.52
5162 7046 2.647299 TGCCCTAGAGGTGGAAATTTGA 59.353 45.455 0.00 0.00 38.26 2.69
5182 7066 5.186996 AGCTCATTAACAAACCACAACTG 57.813 39.130 0.00 0.00 0.00 3.16
5394 7278 3.151554 AGTCATGTTTGCATCTTGCTCA 58.848 40.909 0.75 0.00 45.31 4.26
5403 7287 3.030291 AGGAAACCAAGTCATGTTTGCA 58.970 40.909 8.85 0.00 42.90 4.08
5435 7322 1.200948 GGCAGTCTTCAATCACAAGCC 59.799 52.381 0.00 0.00 0.00 4.35
5441 7328 1.888512 GCTTTGGGCAGTCTTCAATCA 59.111 47.619 0.00 0.00 41.35 2.57
5477 7364 0.687354 ACTGCGAGTCCAAGGAACAT 59.313 50.000 0.00 0.00 0.00 2.71
5494 7381 2.100128 ATCCTAGCAGAGCATGGACT 57.900 50.000 0.00 0.00 35.75 3.85
5517 7404 3.109592 AAAACGTGACCCTGCCCGA 62.110 57.895 0.00 0.00 0.00 5.14
5552 7439 7.178274 AGCTCAACTCCGATCTATAATTCTCAT 59.822 37.037 0.00 0.00 0.00 2.90
5553 7440 6.491745 AGCTCAACTCCGATCTATAATTCTCA 59.508 38.462 0.00 0.00 0.00 3.27
5554 7441 6.919721 AGCTCAACTCCGATCTATAATTCTC 58.080 40.000 0.00 0.00 0.00 2.87
5589 7485 0.797579 TTAGACCACCCTCCTTCCCT 59.202 55.000 0.00 0.00 0.00 4.20
5622 7518 1.415289 TGCAATGCCAACACATTCCAA 59.585 42.857 1.53 0.00 38.19 3.53
5766 7665 2.014335 TGCCATCACTCTCAACATCG 57.986 50.000 0.00 0.00 0.00 3.84
5774 7679 3.939740 ATTGGTACATGCCATCACTCT 57.060 42.857 0.00 0.00 39.30 3.24
5793 7698 9.799106 CAAATCTCTAGGGTATCAATTGGTAAT 57.201 33.333 5.42 0.00 0.00 1.89
5811 7716 0.606401 CACCACACGGCCAAATCTCT 60.606 55.000 2.24 0.00 34.57 3.10
5812 7717 1.875963 CACCACACGGCCAAATCTC 59.124 57.895 2.24 0.00 34.57 2.75
5814 7719 0.958382 TAGCACCACACGGCCAAATC 60.958 55.000 2.24 0.00 34.57 2.17


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

AutoCloner maintained by Alex Coulton.