Multiple sequence alignment - TraesCS3B01G050100

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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 TraesCS3B01G050100 chr3B 100.000 6645 0 0 1 6645 25166167 25172811 0.000000e+00 12272.0
1 TraesCS3B01G050100 chr3B 97.308 5350 104 21 706 6034 16137743 16132413 0.000000e+00 9046.0
2 TraesCS3B01G050100 chr3B 98.282 582 6 1 1 578 16138747 16138166 0.000000e+00 1016.0
3 TraesCS3B01G050100 chr3B 93.047 489 25 6 6067 6547 16132413 16131926 0.000000e+00 706.0
4 TraesCS3B01G050100 chr3B 95.238 42 1 1 3211 3251 16135279 16135238 1.550000e-06 65.8
5 TraesCS3B01G050100 chr3B 95.238 42 1 1 3211 3251 25169341 25169382 1.550000e-06 65.8
6 TraesCS3B01G050100 chr3B 95.238 42 1 1 3175 3216 25169377 25169417 1.550000e-06 65.8
7 TraesCS3B01G050100 chr3A 92.017 5086 331 44 688 5725 25871687 25876745 0.000000e+00 7073.0
8 TraesCS3B01G050100 chr3A 89.800 500 40 8 1 494 25870907 25871401 1.220000e-176 630.0
9 TraesCS3B01G050100 chr3A 92.689 383 20 6 5800 6176 25877653 25878033 4.530000e-151 545.0
10 TraesCS3B01G050100 chr3A 87.850 321 29 5 6231 6547 25878033 25878347 1.050000e-97 368.0
11 TraesCS3B01G050100 chr3A 98.990 99 1 0 6547 6645 733280687 733280589 1.900000e-40 178.0
12 TraesCS3B01G050100 chr3A 97.674 43 0 1 3175 3217 25874224 25874265 9.240000e-09 73.1
13 TraesCS3B01G050100 chr3D 91.291 5190 354 58 599 5735 11450304 11445160 0.000000e+00 6990.0
14 TraesCS3B01G050100 chr3D 91.733 629 45 5 5800 6422 11444177 11443550 0.000000e+00 867.0
15 TraesCS3B01G050100 chr3D 87.849 502 35 6 1 494 11450994 11450511 3.480000e-157 566.0
16 TraesCS3B01G050100 chr3D 93.056 144 7 2 6406 6547 11443385 11443243 2.430000e-49 207.0
17 TraesCS3B01G050100 chr3D 88.462 78 4 5 6170 6244 564316160 564316235 9.180000e-14 89.8
18 TraesCS3B01G050100 chr3D 97.619 42 0 1 3175 3216 11447685 11447645 3.320000e-08 71.3
19 TraesCS3B01G050100 chr7B 91.864 762 47 7 5800 6547 165707847 165708607 0.000000e+00 1050.0
20 TraesCS3B01G050100 chr7B 98.990 99 1 0 6547 6645 538386163 538386065 1.900000e-40 178.0
21 TraesCS3B01G050100 chr1A 79.624 319 40 11 6252 6545 563173170 563173488 8.730000e-49 206.0
22 TraesCS3B01G050100 chr6B 98.990 99 1 0 6547 6645 42601861 42601959 1.900000e-40 178.0
23 TraesCS3B01G050100 chr6B 98.990 99 1 0 6547 6645 252458769 252458867 1.900000e-40 178.0
24 TraesCS3B01G050100 chr6B 82.258 124 12 6 6407 6525 157161719 157161837 1.520000e-16 99.0
25 TraesCS3B01G050100 chr5A 98.990 99 1 0 6547 6645 600074635 600074537 1.900000e-40 178.0
26 TraesCS3B01G050100 chr5A 85.714 84 6 5 6160 6239 36365728 36365647 4.270000e-12 84.2
27 TraesCS3B01G050100 chr4D 96.226 106 4 0 6540 6645 477747209 477747314 2.460000e-39 174.0
28 TraesCS3B01G050100 chr4A 96.226 106 4 0 6540 6645 618931459 618931564 2.460000e-39 174.0
29 TraesCS3B01G050100 chr1B 95.413 109 4 1 6538 6645 279907081 279906973 8.860000e-39 172.0
30 TraesCS3B01G050100 chr2B 96.970 99 3 0 6547 6645 794668010 794667912 4.120000e-37 167.0
31 TraesCS3B01G050100 chr2B 86.792 106 10 3 6421 6525 741514878 741514980 1.510000e-21 115.0
32 TraesCS3B01G050100 chr6D 84.314 153 24 0 6251 6403 19119916 19120068 4.150000e-32 150.0
33 TraesCS3B01G050100 chr6D 83.448 145 16 6 6408 6546 19120126 19120268 1.940000e-25 128.0
34 TraesCS3B01G050100 chr6D 92.424 66 4 1 6177 6242 86643239 86643303 7.100000e-15 93.5
35 TraesCS3B01G050100 chr5B 85.366 123 13 3 6408 6525 14286762 14286640 9.050000e-24 122.0
36 TraesCS3B01G050100 chr5B 86.275 102 14 0 6237 6338 14286962 14286861 1.960000e-20 111.0
37 TraesCS3B01G050100 chr5B 81.295 139 21 2 6237 6375 429017720 429017853 2.530000e-19 108.0
38 TraesCS3B01G050100 chr6A 93.939 66 4 0 6177 6242 104308492 104308557 4.240000e-17 100.0
39 TraesCS3B01G050100 chr7A 92.188 64 5 0 6176 6239 460754581 460754644 2.550000e-14 91.6
40 TraesCS3B01G050100 chr5D 87.342 79 6 3 6167 6245 469062814 469062740 3.300000e-13 87.9
41 TraesCS3B01G050100 chr2D 83.146 89 12 3 1520 1607 412713616 412713530 1.990000e-10 78.7


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 TraesCS3B01G050100 chr3B 25166167 25172811 6644 False 4134.533333 12272 96.825333 1 6645 3 chr3B.!!$F1 6644
1 TraesCS3B01G050100 chr3B 16131926 16138747 6821 True 2708.450000 9046 95.968750 1 6547 4 chr3B.!!$R1 6546
2 TraesCS3B01G050100 chr3A 25870907 25878347 7440 False 1737.820000 7073 92.006000 1 6547 5 chr3A.!!$F1 6546
3 TraesCS3B01G050100 chr3D 11443243 11450994 7751 True 1740.260000 6990 92.309600 1 6547 5 chr3D.!!$R1 6546
4 TraesCS3B01G050100 chr7B 165707847 165708607 760 False 1050.000000 1050 91.864000 5800 6547 1 chr7B.!!$F1 747

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
675 918 2.686405 GGGGGCGTAACCATTAAAGAAG 59.314 50.000 0.00 0.0 42.05 2.85 F
1141 1680 0.033109 TCTGCTTCGATCCCCTCAGA 60.033 55.000 0.00 0.0 0.00 3.27 F
2019 2586 3.307975 GGTATGGCATCACTAGCATCCAT 60.308 47.826 1.65 0.0 37.92 3.41 F
2020 2587 4.080919 GGTATGGCATCACTAGCATCCATA 60.081 45.833 1.65 0.0 35.99 2.74 F
3965 4559 1.366319 AGAGCAACCCAGATTCACCT 58.634 50.000 0.00 0.0 0.00 4.00 F
4094 4688 1.297968 TTCAATCATGAGCCCTCCCA 58.702 50.000 0.09 0.0 36.78 4.37 F
4917 5513 1.522092 CCAACTCCAGCGCCATCTA 59.478 57.895 2.29 0.0 0.00 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2093 2661 2.817844 GAGTTATGGTTTGGTCACCCAC 59.182 50.000 0.00 0.0 41.67 4.61 R
2466 3037 5.840243 TGCTAAAGCTAATTCATGCACAT 57.160 34.783 3.26 0.0 42.66 3.21 R
3965 4559 3.576118 GCTTAGATGACCTCCTATGCAGA 59.424 47.826 0.00 0.0 36.58 4.26 R
4073 4667 2.236766 GGGAGGGCTCATGATTGAATG 58.763 52.381 0.00 0.0 0.00 2.67 R
5090 5686 0.247460 CTCCGTCACAGCATGAGGAA 59.753 55.000 11.11 0.0 44.50 3.36 R
5348 5944 0.487772 ATATGCGGTAGAGACCCCCT 59.512 55.000 0.00 0.0 43.64 4.79 R
6572 8305 0.250381 CATCTCCCAGATGCAGAGGC 60.250 60.000 0.61 0.0 44.69 4.70 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
108 109 7.173218 ACTGACCAAACACTTAACATCTATGTG 59.827 37.037 0.00 0.00 41.61 3.21
675 918 2.686405 GGGGGCGTAACCATTAAAGAAG 59.314 50.000 0.00 0.00 42.05 2.85
676 919 3.613030 GGGGCGTAACCATTAAAGAAGA 58.387 45.455 0.00 0.00 42.05 2.87
677 920 4.011698 GGGGCGTAACCATTAAAGAAGAA 58.988 43.478 0.00 0.00 42.05 2.52
678 921 4.095932 GGGGCGTAACCATTAAAGAAGAAG 59.904 45.833 0.00 0.00 42.05 2.85
679 922 4.939439 GGGCGTAACCATTAAAGAAGAAGA 59.061 41.667 0.00 0.00 42.05 2.87
680 923 5.413523 GGGCGTAACCATTAAAGAAGAAGAA 59.586 40.000 0.00 0.00 42.05 2.52
681 924 6.072342 GGGCGTAACCATTAAAGAAGAAGAAA 60.072 38.462 0.00 0.00 42.05 2.52
682 925 7.364970 GGCGTAACCATTAAAGAAGAAGAAAA 58.635 34.615 0.00 0.00 38.86 2.29
683 926 7.325338 GGCGTAACCATTAAAGAAGAAGAAAAC 59.675 37.037 0.00 0.00 38.86 2.43
684 927 7.858879 GCGTAACCATTAAAGAAGAAGAAAACA 59.141 33.333 0.00 0.00 0.00 2.83
685 928 9.166126 CGTAACCATTAAAGAAGAAGAAAACAC 57.834 33.333 0.00 0.00 0.00 3.32
686 929 9.166126 GTAACCATTAAAGAAGAAGAAAACACG 57.834 33.333 0.00 0.00 0.00 4.49
979 1518 9.317936 CATATATCTAGCGATAAAATTGAGGCA 57.682 33.333 0.00 0.00 35.84 4.75
1059 1598 2.158385 AGAGTATGGAGGCGAAGAGGAT 60.158 50.000 0.00 0.00 0.00 3.24
1084 1623 2.266055 GAGAAGTCCGCCACCAGG 59.734 66.667 0.00 0.00 38.23 4.45
1141 1680 0.033109 TCTGCTTCGATCCCCTCAGA 60.033 55.000 0.00 0.00 0.00 3.27
1334 1874 4.853924 ACATCTTAGGCACCAAACAAAG 57.146 40.909 0.00 0.00 0.00 2.77
1561 2107 5.308014 TGTGCACTTTCATAGTCATCTTGT 58.692 37.500 19.41 0.00 33.85 3.16
2019 2586 3.307975 GGTATGGCATCACTAGCATCCAT 60.308 47.826 1.65 0.00 37.92 3.41
2020 2587 4.080919 GGTATGGCATCACTAGCATCCATA 60.081 45.833 1.65 0.00 35.99 2.74
2052 2619 7.918076 ACCTACTCATAAGGATCTTCACAAAA 58.082 34.615 0.00 0.00 37.57 2.44
2276 2845 5.777802 TGCTGCAATTTTAATTTCCTTCGA 58.222 33.333 0.00 0.00 0.00 3.71
2353 2923 7.519032 TTTCCACCTCAAAGTAAATTGTAGG 57.481 36.000 0.00 0.00 35.51 3.18
3066 3648 9.028284 TCAATTCATCTTAATTTCTCCAAAGCT 57.972 29.630 0.00 0.00 0.00 3.74
3112 3694 6.702329 AGATACAAAACTCTAGTGTCCAAGG 58.298 40.000 0.00 0.00 0.00 3.61
3119 3701 5.266709 ACTCTAGTGTCCAAGGGTTACTA 57.733 43.478 0.00 0.00 0.00 1.82
3244 3826 5.549742 AAATCATGCAGAACCCTTGAAAA 57.450 34.783 0.00 0.00 0.00 2.29
3614 4199 5.244851 ACTCTCTCATGTTCTAAGAAGCACA 59.755 40.000 0.00 0.00 33.29 4.57
3620 4205 6.647229 TCATGTTCTAAGAAGCACATCTCAT 58.353 36.000 0.00 0.00 37.47 2.90
3965 4559 1.366319 AGAGCAACCCAGATTCACCT 58.634 50.000 0.00 0.00 0.00 4.00
4073 4667 2.755103 CCAACCCTATCTTTGGCAAGAC 59.245 50.000 0.00 0.00 42.05 3.01
4094 4688 1.297968 TTCAATCATGAGCCCTCCCA 58.702 50.000 0.09 0.00 36.78 4.37
4450 5046 3.825014 ACTAGGAGTACAAAGAGCGAACA 59.175 43.478 0.00 0.00 0.00 3.18
4782 5378 2.022718 AGGTCTCTTGCTCCAACTCT 57.977 50.000 0.00 0.00 0.00 3.24
4917 5513 1.522092 CCAACTCCAGCGCCATCTA 59.478 57.895 2.29 0.00 0.00 1.98
5090 5686 3.144657 TGTCTCCATCTTGTGCATTGT 57.855 42.857 0.00 0.00 0.00 2.71
5341 5937 3.825014 AGTGACTAGCGTTGGAGAAGTTA 59.175 43.478 0.00 0.00 0.00 2.24
5348 5944 3.825014 AGCGTTGGAGAAGTTAGTAGTCA 59.175 43.478 0.00 0.00 0.00 3.41
5504 6104 6.377712 TGATAATTTGGTCATGTGCATCTTCA 59.622 34.615 0.00 0.00 0.00 3.02
5537 6137 6.842437 TCGCTTTTATCATAGCTAGGATCT 57.158 37.500 23.25 5.47 35.25 2.75
5576 6176 3.641437 TGAAAACTTGCATAGTGGTGC 57.359 42.857 0.00 0.00 45.25 5.01
5617 6218 2.829043 GATACCGGCAGCACACGTGA 62.829 60.000 25.01 0.00 0.00 4.35
5755 6363 2.539476 CCTTTGTTGAACCAAGTGCAC 58.461 47.619 9.40 9.40 0.00 4.57
5837 7365 9.796120 TTGTTGAACCAAGTGAAGTAAATTTAG 57.204 29.630 0.00 0.00 0.00 1.85
5894 7422 4.593206 AGTGAATTAGAGTTCCACCTGTCA 59.407 41.667 0.00 0.00 0.00 3.58
5902 7430 5.690865 AGAGTTCCACCTGTCAACAATTTA 58.309 37.500 0.00 0.00 0.00 1.40
5996 7524 4.014406 TCATACCACTGACGTGTGTATCT 58.986 43.478 0.00 0.00 39.55 1.98
6002 7530 5.168569 CCACTGACGTGTGTATCTAAACAT 58.831 41.667 0.00 0.00 39.55 2.71
6003 7531 5.288712 CCACTGACGTGTGTATCTAAACATC 59.711 44.000 0.00 0.00 39.55 3.06
6034 7562 5.583061 CCAGCAATGTAACATTGATTTGCAT 59.417 36.000 17.05 0.00 41.33 3.96
6055 7583 5.335191 GCATTGTGGCTAGCTTTATGGATAC 60.335 44.000 15.72 0.00 0.00 2.24
6172 7705 7.274904 GTGTAATTCGTCTGTCTGCATTTACTA 59.725 37.037 0.00 0.00 0.00 1.82
6232 7767 9.871238 AAACGCTCTTATATTTCTTTACAGAGA 57.129 29.630 0.00 0.00 0.00 3.10
6333 7871 4.072131 ACATACAACATGGTCAAGGTGAC 58.928 43.478 0.00 0.00 46.23 3.67
6498 8225 7.124573 TGCCAATGTACTATCAGTCTAACAT 57.875 36.000 0.00 0.00 28.98 2.71
6523 8256 6.092670 TCAATGCATAACTTACTCTCAGCAAC 59.907 38.462 0.00 0.00 34.15 4.17
6530 8263 3.243907 ACTTACTCTCAGCAACCACTGTC 60.244 47.826 0.00 0.00 38.84 3.51
6538 8271 1.514678 GCAACCACTGTCGCATTCCA 61.515 55.000 0.00 0.00 0.00 3.53
6547 8280 2.744202 CTGTCGCATTCCAAGCTTACTT 59.256 45.455 0.00 0.00 36.19 2.24
6548 8281 3.146066 TGTCGCATTCCAAGCTTACTTT 58.854 40.909 0.00 0.00 32.29 2.66
6549 8282 3.568007 TGTCGCATTCCAAGCTTACTTTT 59.432 39.130 0.00 0.00 32.29 2.27
6550 8283 4.037446 TGTCGCATTCCAAGCTTACTTTTT 59.963 37.500 0.00 0.00 32.29 1.94
6551 8284 5.239744 TGTCGCATTCCAAGCTTACTTTTTA 59.760 36.000 0.00 0.00 32.29 1.52
6552 8285 5.795441 GTCGCATTCCAAGCTTACTTTTTAG 59.205 40.000 0.00 0.00 32.29 1.85
6553 8286 5.703592 TCGCATTCCAAGCTTACTTTTTAGA 59.296 36.000 0.00 0.00 32.29 2.10
6554 8287 6.205853 TCGCATTCCAAGCTTACTTTTTAGAA 59.794 34.615 0.00 0.00 32.29 2.10
6555 8288 6.861055 CGCATTCCAAGCTTACTTTTTAGAAA 59.139 34.615 0.00 0.00 32.29 2.52
6556 8289 7.381139 CGCATTCCAAGCTTACTTTTTAGAAAA 59.619 33.333 0.00 0.00 32.29 2.29
6557 8290 8.703336 GCATTCCAAGCTTACTTTTTAGAAAAG 58.297 33.333 0.00 10.67 32.29 2.27
6558 8291 9.196552 CATTCCAAGCTTACTTTTTAGAAAAGG 57.803 33.333 15.27 5.74 32.29 3.11
6559 8292 8.528044 TTCCAAGCTTACTTTTTAGAAAAGGA 57.472 30.769 15.27 6.12 32.29 3.36
6560 8293 8.166422 TCCAAGCTTACTTTTTAGAAAAGGAG 57.834 34.615 15.27 13.06 32.29 3.69
6561 8294 7.230712 TCCAAGCTTACTTTTTAGAAAAGGAGG 59.769 37.037 15.27 9.73 32.29 4.30
6562 8295 7.230712 CCAAGCTTACTTTTTAGAAAAGGAGGA 59.769 37.037 15.27 0.00 32.29 3.71
6563 8296 8.797438 CAAGCTTACTTTTTAGAAAAGGAGGAT 58.203 33.333 15.27 5.51 32.29 3.24
6564 8297 8.341892 AGCTTACTTTTTAGAAAAGGAGGATG 57.658 34.615 15.27 0.14 0.00 3.51
6565 8298 8.164070 AGCTTACTTTTTAGAAAAGGAGGATGA 58.836 33.333 15.27 0.00 0.00 2.92
6566 8299 8.237949 GCTTACTTTTTAGAAAAGGAGGATGAC 58.762 37.037 15.27 0.00 0.00 3.06
6567 8300 8.631480 TTACTTTTTAGAAAAGGAGGATGACC 57.369 34.615 15.27 0.00 0.00 4.02
6568 8301 6.010850 ACTTTTTAGAAAAGGAGGATGACCC 58.989 40.000 15.27 0.00 36.73 4.46
6569 8302 4.586306 TTTAGAAAAGGAGGATGACCCC 57.414 45.455 0.00 0.00 36.73 4.95
6570 8303 1.299939 AGAAAAGGAGGATGACCCCC 58.700 55.000 0.00 0.00 36.73 5.40
6571 8304 0.107165 GAAAAGGAGGATGACCCCCG 60.107 60.000 0.00 0.00 36.73 5.73
6572 8305 1.571773 AAAAGGAGGATGACCCCCGG 61.572 60.000 0.00 0.00 36.73 5.73
6578 8311 3.866582 GATGACCCCCGGCCTCTG 61.867 72.222 0.00 0.00 0.00 3.35
6584 8317 4.559063 CCCCGGCCTCTGCATCTG 62.559 72.222 0.00 0.00 40.13 2.90
6585 8318 4.559063 CCCGGCCTCTGCATCTGG 62.559 72.222 0.00 0.00 40.13 3.86
6586 8319 4.559063 CCGGCCTCTGCATCTGGG 62.559 72.222 0.00 0.00 40.13 4.45
6587 8320 3.473647 CGGCCTCTGCATCTGGGA 61.474 66.667 0.00 0.00 40.13 4.37
6588 8321 2.509916 GGCCTCTGCATCTGGGAG 59.490 66.667 0.00 0.00 40.13 4.30
6589 8322 2.068821 GGCCTCTGCATCTGGGAGA 61.069 63.158 0.00 0.00 42.24 3.71
6590 8323 1.417288 GGCCTCTGCATCTGGGAGAT 61.417 60.000 0.00 0.00 43.58 2.75
6600 8333 3.144506 CATCTGGGAGATGCATACAACC 58.855 50.000 0.00 0.30 44.69 3.77
6601 8334 2.195727 TCTGGGAGATGCATACAACCA 58.804 47.619 0.00 5.45 0.00 3.67
6602 8335 2.092968 TCTGGGAGATGCATACAACCAC 60.093 50.000 0.00 0.00 0.00 4.16
6603 8336 1.915489 TGGGAGATGCATACAACCACT 59.085 47.619 0.00 0.00 0.00 4.00
6604 8337 2.308570 TGGGAGATGCATACAACCACTT 59.691 45.455 0.00 0.00 0.00 3.16
6605 8338 3.245229 TGGGAGATGCATACAACCACTTT 60.245 43.478 0.00 0.00 0.00 2.66
6606 8339 4.018870 TGGGAGATGCATACAACCACTTTA 60.019 41.667 0.00 0.00 0.00 1.85
6607 8340 5.133221 GGGAGATGCATACAACCACTTTAT 58.867 41.667 0.00 0.00 0.00 1.40
6608 8341 5.594317 GGGAGATGCATACAACCACTTTATT 59.406 40.000 0.00 0.00 0.00 1.40
6609 8342 6.460123 GGGAGATGCATACAACCACTTTATTG 60.460 42.308 0.00 0.00 0.00 1.90
6610 8343 6.318648 GGAGATGCATACAACCACTTTATTGA 59.681 38.462 0.00 0.00 0.00 2.57
6611 8344 7.013655 GGAGATGCATACAACCACTTTATTGAT 59.986 37.037 0.00 0.00 0.00 2.57
6612 8345 8.297470 AGATGCATACAACCACTTTATTGATT 57.703 30.769 0.00 0.00 0.00 2.57
6613 8346 9.407380 AGATGCATACAACCACTTTATTGATTA 57.593 29.630 0.00 0.00 0.00 1.75
6620 8353 8.786826 ACAACCACTTTATTGATTATTCTCGA 57.213 30.769 0.00 0.00 0.00 4.04
6621 8354 8.883731 ACAACCACTTTATTGATTATTCTCGAG 58.116 33.333 5.93 5.93 0.00 4.04
6622 8355 8.338259 CAACCACTTTATTGATTATTCTCGAGG 58.662 37.037 13.56 0.00 0.00 4.63
6623 8356 7.792032 ACCACTTTATTGATTATTCTCGAGGA 58.208 34.615 13.56 3.44 0.00 3.71
6624 8357 7.711339 ACCACTTTATTGATTATTCTCGAGGAC 59.289 37.037 13.56 0.00 0.00 3.85
6625 8358 7.171678 CCACTTTATTGATTATTCTCGAGGACC 59.828 40.741 13.56 0.00 0.00 4.46
6626 8359 7.928706 CACTTTATTGATTATTCTCGAGGACCT 59.071 37.037 13.56 0.00 0.00 3.85
6627 8360 8.487028 ACTTTATTGATTATTCTCGAGGACCTT 58.513 33.333 13.56 0.00 0.00 3.50
6628 8361 9.982651 CTTTATTGATTATTCTCGAGGACCTTA 57.017 33.333 13.56 0.00 0.00 2.69
6629 8362 9.760077 TTTATTGATTATTCTCGAGGACCTTAC 57.240 33.333 13.56 0.40 0.00 2.34
6630 8363 6.785337 TTGATTATTCTCGAGGACCTTACA 57.215 37.500 13.56 3.04 0.00 2.41
6631 8364 6.785337 TGATTATTCTCGAGGACCTTACAA 57.215 37.500 13.56 0.00 0.00 2.41
6632 8365 7.177832 TGATTATTCTCGAGGACCTTACAAA 57.822 36.000 13.56 0.00 0.00 2.83
6633 8366 7.265673 TGATTATTCTCGAGGACCTTACAAAG 58.734 38.462 13.56 0.00 0.00 2.77
6634 8367 6.600882 TTATTCTCGAGGACCTTACAAAGT 57.399 37.500 13.56 0.00 0.00 2.66
6635 8368 7.707624 TTATTCTCGAGGACCTTACAAAGTA 57.292 36.000 13.56 0.00 0.00 2.24
6636 8369 6.793505 ATTCTCGAGGACCTTACAAAGTAT 57.206 37.500 13.56 0.00 0.00 2.12
6637 8370 6.600882 TTCTCGAGGACCTTACAAAGTATT 57.399 37.500 13.56 0.00 0.00 1.89
6638 8371 7.707624 TTCTCGAGGACCTTACAAAGTATTA 57.292 36.000 13.56 0.00 0.00 0.98
6639 8372 7.093322 TCTCGAGGACCTTACAAAGTATTAC 57.907 40.000 13.56 0.00 0.00 1.89
6640 8373 6.660521 TCTCGAGGACCTTACAAAGTATTACA 59.339 38.462 13.56 0.00 0.00 2.41
6641 8374 7.177216 TCTCGAGGACCTTACAAAGTATTACAA 59.823 37.037 13.56 0.00 0.00 2.41
6642 8375 7.092716 TCGAGGACCTTACAAAGTATTACAAC 58.907 38.462 0.00 0.00 0.00 3.32
6643 8376 6.869913 CGAGGACCTTACAAAGTATTACAACA 59.130 38.462 0.00 0.00 0.00 3.33
6644 8377 7.385752 CGAGGACCTTACAAAGTATTACAACAA 59.614 37.037 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
108 109 2.596419 CGTCTTGACGATGAAGCTCTTC 59.404 50.000 17.00 2.80 36.33 2.87
624 867 9.065798 CCCCACATCAATTTTCTTTTTACAAAT 57.934 29.630 0.00 0.00 0.00 2.32
625 868 7.500559 CCCCCACATCAATTTTCTTTTTACAAA 59.499 33.333 0.00 0.00 0.00 2.83
626 869 6.995091 CCCCCACATCAATTTTCTTTTTACAA 59.005 34.615 0.00 0.00 0.00 2.41
627 870 6.529220 CCCCCACATCAATTTTCTTTTTACA 58.471 36.000 0.00 0.00 0.00 2.41
655 898 3.613030 TCTTCTTTAATGGTTACGCCCC 58.387 45.455 0.00 0.00 36.04 5.80
656 899 4.939439 TCTTCTTCTTTAATGGTTACGCCC 59.061 41.667 0.00 0.00 36.04 6.13
657 900 6.490566 TTCTTCTTCTTTAATGGTTACGCC 57.509 37.500 0.00 0.00 37.90 5.68
659 902 9.166126 GTGTTTTCTTCTTCTTTAATGGTTACG 57.834 33.333 0.00 0.00 0.00 3.18
660 903 9.166126 CGTGTTTTCTTCTTCTTTAATGGTTAC 57.834 33.333 0.00 0.00 0.00 2.50
693 936 5.627135 AGGTTTCGGTCCAATTTTTCTCTA 58.373 37.500 0.00 0.00 0.00 2.43
694 937 4.470602 AGGTTTCGGTCCAATTTTTCTCT 58.529 39.130 0.00 0.00 0.00 3.10
696 939 4.893524 AGAAGGTTTCGGTCCAATTTTTCT 59.106 37.500 0.00 0.00 34.02 2.52
703 957 4.139038 CCTTTTAGAAGGTTTCGGTCCAA 58.861 43.478 3.82 0.00 46.16 3.53
979 1518 0.108585 ATGTGGACCTCGTGCTTGTT 59.891 50.000 0.00 0.00 0.00 2.83
1084 1623 2.105806 CTAGAGGGATGGCGCCTTCC 62.106 65.000 40.25 40.25 38.93 3.46
1561 2107 7.256494 TGCATATGACACCATATTCCTGATA 57.744 36.000 6.97 0.00 41.83 2.15
2093 2661 2.817844 GAGTTATGGTTTGGTCACCCAC 59.182 50.000 0.00 0.00 41.67 4.61
2191 2760 6.092807 GGACTCACTTCAACATTCTATCAACC 59.907 42.308 0.00 0.00 0.00 3.77
2466 3037 5.840243 TGCTAAAGCTAATTCATGCACAT 57.160 34.783 3.26 0.00 42.66 3.21
3141 3723 8.538701 TGGTGGATATTTTAACAGCATTCAATT 58.461 29.630 0.00 0.00 36.54 2.32
3142 3724 8.076910 TGGTGGATATTTTAACAGCATTCAAT 57.923 30.769 0.00 0.00 36.54 2.57
3244 3826 7.124573 AGGAAAGTTGGCTTTTTGTCTAAAT 57.875 32.000 0.00 0.00 44.25 1.40
3965 4559 3.576118 GCTTAGATGACCTCCTATGCAGA 59.424 47.826 0.00 0.00 36.58 4.26
4073 4667 2.236766 GGGAGGGCTCATGATTGAATG 58.763 52.381 0.00 0.00 0.00 2.67
4094 4688 2.037772 AGGTGCGACAGATTGAAGTCTT 59.962 45.455 0.00 0.00 32.68 3.01
4350 4944 5.253330 AGTCAAAAGACAACAAGAGTTCCA 58.747 37.500 0.00 0.00 35.28 3.53
4450 5046 1.303317 GAACGATGGCTTGGTGGGT 60.303 57.895 0.00 0.00 0.00 4.51
4725 5321 4.128388 TCGAAGGCGATGCAGCGA 62.128 61.111 30.90 1.97 42.51 4.93
4782 5378 1.783071 TGACGGTGCACCCATAGATA 58.217 50.000 29.95 6.89 0.00 1.98
4917 5513 1.806542 GGCAACATGTGATCGACAGTT 59.193 47.619 0.00 6.03 38.23 3.16
5090 5686 0.247460 CTCCGTCACAGCATGAGGAA 59.753 55.000 11.11 0.00 44.50 3.36
5341 5937 1.570024 GGTAGAGACCCCCTGACTACT 59.430 57.143 0.00 0.00 40.23 2.57
5348 5944 0.487772 ATATGCGGTAGAGACCCCCT 59.512 55.000 0.00 0.00 43.64 4.79
5504 6104 6.258947 GCTATGATAAAAGCGAACCTTCTTCT 59.741 38.462 0.00 0.00 31.99 2.85
5537 6137 7.387397 AGTTTTCAAGCATCAAAGTTCAACAAA 59.613 29.630 0.00 0.00 0.00 2.83
5602 6202 3.716006 CTTCACGTGTGCTGCCGG 61.716 66.667 16.51 0.00 0.00 6.13
5837 7365 3.058224 GTGACATGCAGGGTACACTTTTC 60.058 47.826 2.31 0.00 0.00 2.29
5996 7524 2.535012 TGCTGGTGTGACGATGTTTA 57.465 45.000 0.00 0.00 0.00 2.01
6002 7530 2.139917 GTTACATTGCTGGTGTGACGA 58.860 47.619 0.00 0.00 0.00 4.20
6003 7531 1.870402 TGTTACATTGCTGGTGTGACG 59.130 47.619 6.95 0.00 38.48 4.35
6034 7562 5.366482 TGTATCCATAAAGCTAGCCACAA 57.634 39.130 12.13 0.00 0.00 3.33
6055 7583 7.894376 AAATGTTGCAACCTTCAGATTTATG 57.106 32.000 26.14 0.00 0.00 1.90
6057 7585 8.584157 ACATAAATGTTGCAACCTTCAGATTTA 58.416 29.630 26.14 23.83 37.90 1.40
6103 7631 1.111277 ACAACTTTGTGCTTGGGACC 58.889 50.000 0.00 0.00 40.49 4.46
6157 7690 8.589338 AGGGAGTATATTAGTAAATGCAGACAG 58.411 37.037 0.00 0.00 0.00 3.51
6186 7719 8.251721 AGCGTTTAGATCACTGTAGTTCTTTAT 58.748 33.333 0.00 0.00 0.00 1.40
6197 7730 9.469807 AGAAATATAAGAGCGTTTAGATCACTG 57.530 33.333 0.00 0.00 37.82 3.66
6228 7763 7.389330 CACTCCGTTATGATATGTACTCTCTCT 59.611 40.741 0.00 0.00 0.00 3.10
6232 7767 7.094720 GCTACACTCCGTTATGATATGTACTCT 60.095 40.741 0.00 0.00 0.00 3.24
6248 7784 1.810755 TGTCTACTGTGCTACACTCCG 59.189 52.381 0.00 0.00 35.11 4.63
6498 8225 5.733676 TGCTGAGAGTAAGTTATGCATTGA 58.266 37.500 3.54 0.00 0.00 2.57
6523 8256 0.957395 AGCTTGGAATGCGACAGTGG 60.957 55.000 0.00 0.00 42.59 4.00
6530 8263 5.938322 TCTAAAAAGTAAGCTTGGAATGCG 58.062 37.500 9.86 0.00 42.59 4.73
6538 8271 8.797438 CATCCTCCTTTTCTAAAAAGTAAGCTT 58.203 33.333 3.48 3.48 36.30 3.74
6547 8280 4.930696 GGGGTCATCCTCCTTTTCTAAAA 58.069 43.478 0.00 0.00 35.33 1.52
6548 8281 4.586306 GGGGTCATCCTCCTTTTCTAAA 57.414 45.455 0.00 0.00 35.33 1.85
6561 8294 3.866582 CAGAGGCCGGGGGTCATC 61.867 72.222 2.18 0.00 0.00 2.92
6567 8300 4.559063 CAGATGCAGAGGCCGGGG 62.559 72.222 2.18 0.00 40.13 5.73
6568 8301 4.559063 CCAGATGCAGAGGCCGGG 62.559 72.222 2.18 0.00 40.13 5.73
6569 8302 4.559063 CCCAGATGCAGAGGCCGG 62.559 72.222 0.00 0.00 40.13 6.13
6570 8303 3.457625 CTCCCAGATGCAGAGGCCG 62.458 68.421 0.00 0.00 40.13 6.13
6571 8304 1.417288 ATCTCCCAGATGCAGAGGCC 61.417 60.000 0.00 0.00 40.13 5.19
6572 8305 0.250381 CATCTCCCAGATGCAGAGGC 60.250 60.000 0.61 0.00 44.69 4.70
6580 8313 2.779430 TGGTTGTATGCATCTCCCAGAT 59.221 45.455 0.19 0.00 34.74 2.90
6581 8314 2.092968 GTGGTTGTATGCATCTCCCAGA 60.093 50.000 0.19 0.00 0.00 3.86
6582 8315 2.092753 AGTGGTTGTATGCATCTCCCAG 60.093 50.000 0.19 0.00 0.00 4.45
6583 8316 1.915489 AGTGGTTGTATGCATCTCCCA 59.085 47.619 0.19 2.59 0.00 4.37
6584 8317 2.717639 AGTGGTTGTATGCATCTCCC 57.282 50.000 0.19 0.00 0.00 4.30
6585 8318 6.318648 TCAATAAAGTGGTTGTATGCATCTCC 59.681 38.462 0.19 2.39 0.00 3.71
6586 8319 7.320443 TCAATAAAGTGGTTGTATGCATCTC 57.680 36.000 0.19 0.00 0.00 2.75
6587 8320 7.886629 ATCAATAAAGTGGTTGTATGCATCT 57.113 32.000 0.19 0.00 0.00 2.90
6594 8327 9.878667 TCGAGAATAATCAATAAAGTGGTTGTA 57.121 29.630 0.00 0.00 0.00 2.41
6595 8328 8.786826 TCGAGAATAATCAATAAAGTGGTTGT 57.213 30.769 0.00 0.00 0.00 3.32
6596 8329 8.338259 CCTCGAGAATAATCAATAAAGTGGTTG 58.662 37.037 15.71 0.00 0.00 3.77
6597 8330 8.265055 TCCTCGAGAATAATCAATAAAGTGGTT 58.735 33.333 15.71 0.00 0.00 3.67
6598 8331 7.711339 GTCCTCGAGAATAATCAATAAAGTGGT 59.289 37.037 15.71 0.00 0.00 4.16
6599 8332 7.171678 GGTCCTCGAGAATAATCAATAAAGTGG 59.828 40.741 15.71 0.00 0.00 4.00
6600 8333 7.928706 AGGTCCTCGAGAATAATCAATAAAGTG 59.071 37.037 15.71 0.00 0.00 3.16
6601 8334 8.024145 AGGTCCTCGAGAATAATCAATAAAGT 57.976 34.615 15.71 0.00 0.00 2.66
6602 8335 8.894768 AAGGTCCTCGAGAATAATCAATAAAG 57.105 34.615 15.71 0.00 0.00 1.85
6603 8336 9.760077 GTAAGGTCCTCGAGAATAATCAATAAA 57.240 33.333 15.71 0.00 0.00 1.40
6604 8337 8.920174 TGTAAGGTCCTCGAGAATAATCAATAA 58.080 33.333 15.71 0.00 0.00 1.40
6605 8338 8.473358 TGTAAGGTCCTCGAGAATAATCAATA 57.527 34.615 15.71 0.00 0.00 1.90
6606 8339 7.361457 TGTAAGGTCCTCGAGAATAATCAAT 57.639 36.000 15.71 0.00 0.00 2.57
6607 8340 6.785337 TGTAAGGTCCTCGAGAATAATCAA 57.215 37.500 15.71 0.00 0.00 2.57
6608 8341 6.785337 TTGTAAGGTCCTCGAGAATAATCA 57.215 37.500 15.71 2.16 0.00 2.57
6609 8342 7.266400 ACTTTGTAAGGTCCTCGAGAATAATC 58.734 38.462 15.71 0.00 0.00 1.75
6610 8343 7.184067 ACTTTGTAAGGTCCTCGAGAATAAT 57.816 36.000 15.71 0.00 0.00 1.28
6611 8344 6.600882 ACTTTGTAAGGTCCTCGAGAATAA 57.399 37.500 15.71 0.00 0.00 1.40
6612 8345 7.893124 ATACTTTGTAAGGTCCTCGAGAATA 57.107 36.000 15.71 0.00 0.00 1.75
6613 8346 6.793505 ATACTTTGTAAGGTCCTCGAGAAT 57.206 37.500 15.71 0.00 0.00 2.40
6614 8347 6.600882 AATACTTTGTAAGGTCCTCGAGAA 57.399 37.500 15.71 0.00 0.00 2.87
6615 8348 6.660521 TGTAATACTTTGTAAGGTCCTCGAGA 59.339 38.462 15.71 0.00 0.00 4.04
6616 8349 6.860080 TGTAATACTTTGTAAGGTCCTCGAG 58.140 40.000 5.13 5.13 0.00 4.04
6617 8350 6.839124 TGTAATACTTTGTAAGGTCCTCGA 57.161 37.500 0.00 0.00 0.00 4.04
6618 8351 6.869913 TGTTGTAATACTTTGTAAGGTCCTCG 59.130 38.462 0.00 0.00 0.00 4.63
6619 8352 8.611654 TTGTTGTAATACTTTGTAAGGTCCTC 57.388 34.615 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.