Multiple sequence alignment - TraesCS2A01G228300

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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 TraesCS2A01G228300 chr2A 100.000 6560 0 0 1 6560 249757022 249750463 0.000000e+00 12115.0
1 TraesCS2A01G228300 chr2A 92.442 172 12 1 2394 2564 655039289 655039118 1.830000e-60 244.0
2 TraesCS2A01G228300 chr2A 93.284 134 6 3 5145 5276 717816559 717816427 1.870000e-45 195.0
3 TraesCS2A01G228300 chr2A 96.491 114 3 1 5162 5274 313947725 313947612 3.120000e-43 187.0
4 TraesCS2A01G228300 chr2D 98.126 3416 47 12 878 4286 250632412 250629007 0.000000e+00 5938.0
5 TraesCS2A01G228300 chr2D 92.628 1343 36 8 5263 6560 250628703 250627379 0.000000e+00 1873.0
6 TraesCS2A01G228300 chr2D 96.273 322 9 2 4845 5163 250629019 250628698 5.830000e-145 525.0
7 TraesCS2A01G228300 chr2D 98.182 110 2 0 5158 5267 63660069 63660178 6.710000e-45 193.0
8 TraesCS2A01G228300 chr2D 96.429 56 2 0 2844 2899 217496952 217496897 7.000000e-15 93.5
9 TraesCS2A01G228300 chr2D 98.000 50 1 0 2844 2893 139109365 139109316 3.260000e-13 87.9
10 TraesCS2A01G228300 chr2D 77.215 158 15 9 5308 5450 645688711 645688560 9.120000e-09 73.1
11 TraesCS2A01G228300 chr2B 96.805 1972 42 5 878 2846 278435519 278437472 0.000000e+00 3273.0
12 TraesCS2A01G228300 chr2B 95.201 1417 51 12 2874 4286 278437532 278438935 0.000000e+00 2224.0
13 TraesCS2A01G228300 chr2B 97.491 877 22 0 1 877 445270337 445271213 0.000000e+00 1498.0
14 TraesCS2A01G228300 chr2B 95.603 614 23 3 5263 5874 278439227 278439838 0.000000e+00 981.0
15 TraesCS2A01G228300 chr2B 89.028 319 20 5 4845 5160 278438923 278439229 1.330000e-101 381.0
16 TraesCS2A01G228300 chr2B 94.492 236 13 0 5877 6112 278439942 278440177 1.340000e-96 364.0
17 TraesCS2A01G228300 chr2B 95.025 201 9 1 6361 6560 278440675 278440875 1.370000e-81 315.0
18 TraesCS2A01G228300 chr2B 96.970 33 1 0 2785 2817 278437517 278437485 1.000000e-03 56.5
19 TraesCS2A01G228300 chr1B 97.745 887 20 0 1 887 95486074 95485188 0.000000e+00 1528.0
20 TraesCS2A01G228300 chr1B 99.644 562 2 0 4283 4844 31897829 31897268 0.000000e+00 1027.0
21 TraesCS2A01G228300 chr1B 99.466 562 3 0 4283 4844 84872662 84873223 0.000000e+00 1022.0
22 TraesCS2A01G228300 chr3B 98.062 877 17 0 1 877 501981972 501981096 0.000000e+00 1526.0
23 TraesCS2A01G228300 chr3B 98.064 878 16 1 1 877 581680404 581679527 0.000000e+00 1526.0
24 TraesCS2A01G228300 chr3B 97.948 877 18 0 1 877 60268294 60269170 0.000000e+00 1520.0
25 TraesCS2A01G228300 chr3B 85.507 138 16 4 6231 6368 488531385 488531252 2.470000e-29 141.0
26 TraesCS2A01G228300 chr1A 97.834 877 18 1 1 877 589037882 589038757 0.000000e+00 1513.0
27 TraesCS2A01G228300 chr1A 98.131 107 2 0 5159 5265 523409000 523409106 3.120000e-43 187.0
28 TraesCS2A01G228300 chr1A 90.071 141 8 4 5129 5265 376145811 376145949 1.880000e-40 178.0
29 TraesCS2A01G228300 chr5A 97.611 879 20 1 1 878 578117525 578118403 0.000000e+00 1506.0
30 TraesCS2A01G228300 chr5A 97.605 877 16 1 1 877 23170071 23169200 0.000000e+00 1498.0
31 TraesCS2A01G228300 chr5A 99.645 564 2 0 4281 4844 371029275 371028712 0.000000e+00 1031.0
32 TraesCS2A01G228300 chr3A 97.605 877 21 0 1 877 605250314 605251190 0.000000e+00 1504.0
33 TraesCS2A01G228300 chr3A 99.645 564 1 1 4283 4846 340282174 340281612 0.000000e+00 1029.0
34 TraesCS2A01G228300 chr3A 98.754 562 7 0 4283 4844 204823787 204823226 0.000000e+00 1000.0
35 TraesCS2A01G228300 chr7B 99.823 564 1 0 4283 4846 394815722 394816285 0.000000e+00 1037.0
36 TraesCS2A01G228300 chr4B 99.822 563 1 0 4283 4845 206791756 206791194 0.000000e+00 1035.0
37 TraesCS2A01G228300 chr4B 93.210 162 11 0 2403 2564 517751220 517751059 8.500000e-59 239.0
38 TraesCS2A01G228300 chr6B 99.118 567 4 1 4278 4844 15393887 15393322 0.000000e+00 1018.0
39 TraesCS2A01G228300 chr7A 99.110 562 5 0 4283 4844 353203371 353203932 0.000000e+00 1011.0
40 TraesCS2A01G228300 chr7A 94.262 122 5 1 5159 5280 19217399 19217280 1.120000e-42 185.0
41 TraesCS2A01G228300 chr7A 96.154 52 2 0 2842 2893 162920378 162920327 1.170000e-12 86.1
42 TraesCS2A01G228300 chr6A 93.103 174 9 2 2391 2564 297641211 297641381 1.090000e-62 252.0
43 TraesCS2A01G228300 chr6A 96.552 116 4 0 5160 5275 130415779 130415894 6.710000e-45 193.0
44 TraesCS2A01G228300 chr7D 93.976 166 8 1 2399 2564 201885620 201885457 3.930000e-62 250.0
45 TraesCS2A01G228300 chr7D 98.198 111 2 0 5155 5265 610533494 610533384 1.870000e-45 195.0
46 TraesCS2A01G228300 chr7D 91.935 62 3 2 2831 2892 5068114 5068173 1.170000e-12 86.1
47 TraesCS2A01G228300 chr6D 94.444 162 9 0 2403 2564 93646226 93646387 3.930000e-62 250.0
48 TraesCS2A01G228300 chr6D 96.154 52 2 0 2844 2895 309072543 309072594 1.170000e-12 86.1
49 TraesCS2A01G228300 chr6D 90.625 64 3 3 2829 2892 472744286 472744346 1.520000e-11 82.4
50 TraesCS2A01G228300 chr5D 94.444 162 9 0 2403 2564 150835568 150835729 3.930000e-62 250.0
51 TraesCS2A01G228300 chr5D 96.154 52 2 0 2844 2895 111788689 111788638 1.170000e-12 86.1
52 TraesCS2A01G228300 chr3D 93.252 163 11 0 2403 2565 528611687 528611525 2.360000e-59 241.0
53 TraesCS2A01G228300 chr3D 98.039 51 1 0 2844 2894 338881604 338881554 9.060000e-14 89.8
54 TraesCS2A01G228300 chr4A 95.652 115 5 0 5156 5270 368568612 368568498 1.120000e-42 185.0
55 TraesCS2A01G228300 chr4A 84.783 92 11 3 5307 5396 470685904 470685814 9.060000e-14 89.8
56 TraesCS2A01G228300 chr4D 83.810 105 12 4 5300 5402 105141633 105141734 1.950000e-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 TraesCS2A01G228300 chr2A 249750463 249757022 6559 True 12115.000000 12115 100.000000 1 6560 1 chr2A.!!$R1 6559
1 TraesCS2A01G228300 chr2D 250627379 250632412 5033 True 2778.666667 5938 95.675667 878 6560 3 chr2D.!!$R4 5682
2 TraesCS2A01G228300 chr2B 445270337 445271213 876 False 1498.000000 1498 97.491000 1 877 1 chr2B.!!$F1 876
3 TraesCS2A01G228300 chr2B 278435519 278440875 5356 False 1256.333333 3273 94.359000 878 6560 6 chr2B.!!$F2 5682
4 TraesCS2A01G228300 chr1B 95485188 95486074 886 True 1528.000000 1528 97.745000 1 887 1 chr1B.!!$R2 886
5 TraesCS2A01G228300 chr1B 31897268 31897829 561 True 1027.000000 1027 99.644000 4283 4844 1 chr1B.!!$R1 561
6 TraesCS2A01G228300 chr1B 84872662 84873223 561 False 1022.000000 1022 99.466000 4283 4844 1 chr1B.!!$F1 561
7 TraesCS2A01G228300 chr3B 501981096 501981972 876 True 1526.000000 1526 98.062000 1 877 1 chr3B.!!$R2 876
8 TraesCS2A01G228300 chr3B 581679527 581680404 877 True 1526.000000 1526 98.064000 1 877 1 chr3B.!!$R3 876
9 TraesCS2A01G228300 chr3B 60268294 60269170 876 False 1520.000000 1520 97.948000 1 877 1 chr3B.!!$F1 876
10 TraesCS2A01G228300 chr1A 589037882 589038757 875 False 1513.000000 1513 97.834000 1 877 1 chr1A.!!$F3 876
11 TraesCS2A01G228300 chr5A 578117525 578118403 878 False 1506.000000 1506 97.611000 1 878 1 chr5A.!!$F1 877
12 TraesCS2A01G228300 chr5A 23169200 23170071 871 True 1498.000000 1498 97.605000 1 877 1 chr5A.!!$R1 876
13 TraesCS2A01G228300 chr5A 371028712 371029275 563 True 1031.000000 1031 99.645000 4281 4844 1 chr5A.!!$R2 563
14 TraesCS2A01G228300 chr3A 605250314 605251190 876 False 1504.000000 1504 97.605000 1 877 1 chr3A.!!$F1 876
15 TraesCS2A01G228300 chr3A 340281612 340282174 562 True 1029.000000 1029 99.645000 4283 4846 1 chr3A.!!$R2 563
16 TraesCS2A01G228300 chr3A 204823226 204823787 561 True 1000.000000 1000 98.754000 4283 4844 1 chr3A.!!$R1 561
17 TraesCS2A01G228300 chr7B 394815722 394816285 563 False 1037.000000 1037 99.823000 4283 4846 1 chr7B.!!$F1 563
18 TraesCS2A01G228300 chr4B 206791194 206791756 562 True 1035.000000 1035 99.822000 4283 4845 1 chr4B.!!$R1 562
19 TraesCS2A01G228300 chr6B 15393322 15393887 565 True 1018.000000 1018 99.118000 4278 4844 1 chr6B.!!$R1 566
20 TraesCS2A01G228300 chr7A 353203371 353203932 561 False 1011.000000 1011 99.110000 4283 4844 1 chr7A.!!$F1 561

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
617 619 0.683504 GCAGAAGACCTAGGGACCGA 60.684 60.0 14.81 0.0 0.0 4.69 F
957 959 1.679139 AGCAGGAGAGACAGAGATCG 58.321 55.0 0.00 0.0 0.0 3.69 F
1671 1673 0.035056 ATAGCCACCTGTTCCTGTGC 60.035 55.0 0.00 0.0 0.0 4.57 F
3210 3249 1.768684 GCTGGAAGGGACCTCACACA 61.769 60.0 0.00 0.0 0.0 3.72 F
5082 5127 1.668101 GGAGTGGTAGGCGTCAGAGG 61.668 65.0 0.00 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1548 1550 1.269448 CAAAGTTGCCCTGTTATGCGT 59.731 47.619 0.0 0.0 0.0 5.24 R
2923 2960 0.738389 ACAAAACCACACAGCGAAGG 59.262 50.000 0.0 0.0 0.0 3.46 R
3572 3613 1.471829 TTCTGTCGAGCCTCCTTGCA 61.472 55.000 0.0 0.0 0.0 4.08 R
5178 5223 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.0 0.0 0.0 4.18 R
6017 6187 0.663153 ACGCAGAGACAAAAGGCAAC 59.337 50.000 0.0 0.0 0.0 4.17 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
78 79 3.381590 AGTCTCGACAGTGCTATGCATTA 59.618 43.478 3.54 0.00 41.91 1.90
85 86 3.198635 ACAGTGCTATGCATTACTCCTGT 59.801 43.478 3.54 8.56 41.91 4.00
88 89 3.736252 GTGCTATGCATTACTCCTGTACG 59.264 47.826 3.54 0.00 41.91 3.67
617 619 0.683504 GCAGAAGACCTAGGGACCGA 60.684 60.000 14.81 0.00 0.00 4.69
802 804 7.523415 ACAACTTAGAAAGATTTAGGACCCAA 58.477 34.615 0.00 0.00 0.00 4.12
836 838 4.469945 TGAAAGAATTAGGACCCAGTCGAT 59.530 41.667 0.00 0.00 32.65 3.59
845 847 3.521937 AGGACCCAGTCGATATTTTTGGA 59.478 43.478 0.00 0.00 32.65 3.53
957 959 1.679139 AGCAGGAGAGACAGAGATCG 58.321 55.000 0.00 0.00 0.00 3.69
1548 1550 0.998928 TGCCCTGAAGCCCTAATGAA 59.001 50.000 0.00 0.00 0.00 2.57
1671 1673 0.035056 ATAGCCACCTGTTCCTGTGC 60.035 55.000 0.00 0.00 0.00 4.57
2110 2113 5.068987 CCCTTTCTTTGGACACAGAATGAAA 59.931 40.000 12.80 0.00 39.69 2.69
2379 2382 7.069950 ACAAAATTTCTGGGCCTATCTTTATCC 59.930 37.037 4.53 0.00 0.00 2.59
2754 2759 3.914426 ACTCAGTGAGTCCTTGTGTTT 57.086 42.857 20.34 0.00 38.71 2.83
2863 2868 5.798015 TTTAGTGTAGTGTCAAAAACGCA 57.202 34.783 0.00 0.00 41.03 5.24
2894 2931 2.237893 TGGGACGGAGGGAGTATTTTTC 59.762 50.000 0.00 0.00 0.00 2.29
3093 3130 5.727791 GCGGTGCTTTGAAGTAAGACATATG 60.728 44.000 0.00 0.00 0.00 1.78
3094 3131 5.573146 GGTGCTTTGAAGTAAGACATATGC 58.427 41.667 1.58 0.00 0.00 3.14
3210 3249 1.768684 GCTGGAAGGGACCTCACACA 61.769 60.000 0.00 0.00 0.00 3.72
3572 3613 6.317140 CCACTGTGCATTATGAAGTGACTATT 59.683 38.462 18.28 0.00 40.54 1.73
3579 3620 6.038603 GCATTATGAAGTGACTATTGCAAGGA 59.961 38.462 4.94 0.00 0.00 3.36
3600 3641 3.983741 AGGCTCGACAGAAGTATATTGC 58.016 45.455 0.00 0.00 0.00 3.56
3705 3746 2.354821 GGGCGGATACAACAAGTGAATC 59.645 50.000 0.00 0.00 0.00 2.52
4244 4286 4.395231 CCTCCGTTCCAAACTTTAAGATCC 59.605 45.833 0.00 0.00 0.00 3.36
5078 5123 2.029623 GATAAGGAGTGGTAGGCGTCA 58.970 52.381 0.00 0.00 0.00 4.35
5082 5127 1.668101 GGAGTGGTAGGCGTCAGAGG 61.668 65.000 0.00 0.00 0.00 3.69
5164 5209 9.642343 AAATTTAAATCCTATCAAGGTACTCCC 57.358 33.333 0.10 0.00 44.09 4.30
5166 5211 7.613551 TTAAATCCTATCAAGGTACTCCCTC 57.386 40.000 0.00 0.00 45.47 4.30
5167 5212 3.614568 TCCTATCAAGGTACTCCCTCC 57.385 52.381 0.00 0.00 45.47 4.30
5168 5213 2.863238 TCCTATCAAGGTACTCCCTCCA 59.137 50.000 0.00 0.00 45.47 3.86
5169 5214 3.471306 TCCTATCAAGGTACTCCCTCCAT 59.529 47.826 0.00 0.00 45.47 3.41
5170 5215 4.077982 TCCTATCAAGGTACTCCCTCCATT 60.078 45.833 0.00 0.00 45.47 3.16
5171 5216 4.284746 CCTATCAAGGTACTCCCTCCATTC 59.715 50.000 0.00 0.00 45.47 2.67
5172 5217 2.478292 TCAAGGTACTCCCTCCATTCC 58.522 52.381 0.00 0.00 45.47 3.01
5173 5218 2.196595 CAAGGTACTCCCTCCATTCCA 58.803 52.381 0.00 0.00 45.47 3.53
5174 5219 2.576191 CAAGGTACTCCCTCCATTCCAA 59.424 50.000 0.00 0.00 45.47 3.53
5175 5220 2.929301 AGGTACTCCCTCCATTCCAAA 58.071 47.619 0.00 0.00 40.71 3.28
5176 5221 3.474920 AGGTACTCCCTCCATTCCAAAT 58.525 45.455 0.00 0.00 40.71 2.32
5177 5222 3.858638 AGGTACTCCCTCCATTCCAAATT 59.141 43.478 0.00 0.00 40.71 1.82
5178 5223 5.043762 AGGTACTCCCTCCATTCCAAATTA 58.956 41.667 0.00 0.00 40.71 1.40
5179 5224 5.104067 AGGTACTCCCTCCATTCCAAATTAC 60.104 44.000 0.00 0.00 40.71 1.89
5180 5225 5.104067 GGTACTCCCTCCATTCCAAATTACT 60.104 44.000 0.00 0.00 0.00 2.24
5181 5226 5.117406 ACTCCCTCCATTCCAAATTACTC 57.883 43.478 0.00 0.00 0.00 2.59
5182 5227 4.130118 CTCCCTCCATTCCAAATTACTCG 58.870 47.826 0.00 0.00 0.00 4.18
5183 5228 3.521937 TCCCTCCATTCCAAATTACTCGT 59.478 43.478 0.00 0.00 0.00 4.18
5184 5229 3.877508 CCCTCCATTCCAAATTACTCGTC 59.122 47.826 0.00 0.00 0.00 4.20
5185 5230 3.555956 CCTCCATTCCAAATTACTCGTCG 59.444 47.826 0.00 0.00 0.00 5.12
5186 5231 2.933906 TCCATTCCAAATTACTCGTCGC 59.066 45.455 0.00 0.00 0.00 5.19
5187 5232 2.675844 CCATTCCAAATTACTCGTCGCA 59.324 45.455 0.00 0.00 0.00 5.10
5188 5233 3.242413 CCATTCCAAATTACTCGTCGCAG 60.242 47.826 0.00 0.00 0.00 5.18
5189 5234 3.306917 TTCCAAATTACTCGTCGCAGA 57.693 42.857 0.00 0.00 0.00 4.26
5190 5235 3.306917 TCCAAATTACTCGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
5191 5236 3.655486 TCCAAATTACTCGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
5192 5237 4.250464 TCCAAATTACTCGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
5193 5238 4.092821 TCCAAATTACTCGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
5194 5239 4.334443 CAAATTACTCGTCGCAGAAATGG 58.666 43.478 0.00 0.00 39.69 3.16
5195 5240 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
5196 5241 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
5197 5242 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
5198 5243 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
5199 5244 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
5200 5245 3.181475 ACTCGTCGCAGAAATGGATGTAT 60.181 43.478 0.00 0.00 39.69 2.29
5201 5246 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
5202 5247 3.068165 TCGTCGCAGAAATGGATGTATCT 59.932 43.478 0.00 0.00 39.69 1.98
5203 5248 4.277423 TCGTCGCAGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 39.69 1.98
5204 5249 4.618912 CGTCGCAGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 39.69 2.43
5205 5250 5.562890 CGTCGCAGAAATGGATGTATCTAGA 60.563 44.000 0.00 0.00 39.69 2.43
5206 5251 6.216569 GTCGCAGAAATGGATGTATCTAGAA 58.783 40.000 0.00 0.00 39.69 2.10
5207 5252 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
5208 5253 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
5209 5254 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
5210 5255 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
5211 5256 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
5240 5285 9.332502 ACATCTAGATACATCCATATCTACGAC 57.667 37.037 4.54 0.00 41.29 4.34
5241 5286 9.331282 CATCTAGATACATCCATATCTACGACA 57.669 37.037 4.54 0.00 41.29 4.35
5242 5287 9.907229 ATCTAGATACATCCATATCTACGACAA 57.093 33.333 2.53 0.00 41.29 3.18
5243 5288 9.384764 TCTAGATACATCCATATCTACGACAAG 57.615 37.037 0.00 0.00 41.29 3.16
5244 5289 9.168451 CTAGATACATCCATATCTACGACAAGT 57.832 37.037 0.00 0.00 41.29 3.16
5246 5291 9.516546 AGATACATCCATATCTACGACAAGTAA 57.483 33.333 0.00 0.00 39.63 2.24
5250 5295 7.808381 ACATCCATATCTACGACAAGTAATTCG 59.192 37.037 0.00 0.00 41.14 3.34
5251 5296 6.675026 TCCATATCTACGACAAGTAATTCGG 58.325 40.000 0.00 0.00 39.63 4.30
5252 5297 6.487668 TCCATATCTACGACAAGTAATTCGGA 59.512 38.462 0.00 0.00 39.63 4.55
5253 5298 7.013559 TCCATATCTACGACAAGTAATTCGGAA 59.986 37.037 0.00 0.00 39.63 4.30
5254 5299 7.114529 CCATATCTACGACAAGTAATTCGGAAC 59.885 40.741 0.00 0.00 39.63 3.62
5255 5300 4.406069 TCTACGACAAGTAATTCGGAACG 58.594 43.478 0.00 0.00 44.64 3.95
5256 5301 3.500982 TACGACAAGTAATTCGGAACGG 58.499 45.455 0.00 0.00 42.34 4.44
5316 5361 4.262851 GCCATGGGTCTGGTATTTGTTTTT 60.263 41.667 15.13 0.00 38.63 1.94
5403 5449 8.573035 GGAGGAGTGTATTTGTTTATTGTGAAA 58.427 33.333 0.00 0.00 0.00 2.69
5415 5461 1.145571 TTGTGAAACCTGGTAGGCCT 58.854 50.000 11.78 11.78 39.63 5.19
5603 5649 1.908299 TCCCTGCTCGCAGAAGTGA 60.908 57.895 19.78 8.08 46.30 3.41
5663 5709 2.084546 GAGCGTCAATTAGGGTGCTTT 58.915 47.619 0.00 0.00 31.88 3.51
5845 5893 3.748568 TCAGTTTGGTTTGGTTTTGTTGC 59.251 39.130 0.00 0.00 0.00 4.17
5972 6121 3.059188 CGAAAGTTTGACAACGCCACTAT 60.059 43.478 0.00 0.00 38.03 2.12
6050 6220 1.135660 TCTGCGTTTCAGCTAGTCTCG 60.136 52.381 0.00 0.00 42.56 4.04
6055 6225 2.033550 CGTTTCAGCTAGTCTCGGCTAT 59.966 50.000 0.00 0.00 37.00 2.97
6138 6329 6.040729 TGCACCTCAAATTTCTCATTTTCTGA 59.959 34.615 0.00 0.00 0.00 3.27
6162 6363 2.039084 GGTTGACCCTGATCTGACAAGT 59.961 50.000 0.38 0.00 0.00 3.16
6164 6365 4.262894 GGTTGACCCTGATCTGACAAGTTA 60.263 45.833 0.38 0.00 0.00 2.24
6166 6367 5.762179 TGACCCTGATCTGACAAGTTAAT 57.238 39.130 0.38 0.00 0.00 1.40
6187 6389 8.398665 GTTAATGACATTGATAAGTCCTGAACC 58.601 37.037 11.05 0.00 33.89 3.62
6189 6391 3.270877 ACATTGATAAGTCCTGAACCGC 58.729 45.455 0.00 0.00 0.00 5.68
6297 6510 1.501169 GCTTTTGCCACGAAATTGCT 58.499 45.000 0.00 0.00 40.15 3.91
6320 6533 3.020274 TGCTTGCCAACTAAACTTGTCA 58.980 40.909 0.00 0.00 0.00 3.58
6470 6902 8.654485 AAATTGGCTGCCATATATCTTCATTA 57.346 30.769 24.03 2.36 31.53 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.220989 GCAGAAGCAATGCAGAAGATGAATA 60.221 40.000 8.35 0.00 43.31 1.75
78 79 1.134965 GCAAGATGCTCGTACAGGAGT 60.135 52.381 0.00 0.00 40.96 3.85
85 86 2.029020 ACAGAAGTGCAAGATGCTCGTA 60.029 45.455 3.78 0.00 45.31 3.43
88 89 3.501445 AGAAACAGAAGTGCAAGATGCTC 59.499 43.478 3.78 0.00 45.31 4.26
101 102 5.125257 TGTCATTGCAAGTGAAGAAACAGAA 59.875 36.000 4.94 0.00 0.00 3.02
617 619 4.019771 GGAGTTTGTCCTCTCTTCATTCCT 60.020 45.833 0.00 0.00 42.99 3.36
802 804 7.603784 GGTCCTAATTCTTTCAAAATGCACATT 59.396 33.333 0.00 0.00 0.00 2.71
836 838 7.317390 GCGGTCCTAATTCTTTTCCAAAAATA 58.683 34.615 0.00 0.00 0.00 1.40
845 847 2.109425 AGCGCGGTCCTAATTCTTTT 57.891 45.000 4.23 0.00 0.00 2.27
957 959 1.524002 GTAGGGTTAGGGTTCGGGC 59.476 63.158 0.00 0.00 0.00 6.13
1548 1550 1.269448 CAAAGTTGCCCTGTTATGCGT 59.731 47.619 0.00 0.00 0.00 5.24
1671 1673 5.183713 TGGAAATTATCTGCAAAGGACACAG 59.816 40.000 0.00 0.00 0.00 3.66
1741 1744 3.752222 TGCTGCATAAAAAGGCAAATTGG 59.248 39.130 0.00 0.00 39.93 3.16
2110 2113 7.633621 CATGATTACATGCGAGTTTATCAAGT 58.366 34.615 0.00 0.00 45.51 3.16
2863 2868 5.019657 TCCCTCCGTCCCATAATATAAGT 57.980 43.478 0.00 0.00 0.00 2.24
2923 2960 0.738389 ACAAAACCACACAGCGAAGG 59.262 50.000 0.00 0.00 0.00 3.46
3093 3130 8.722480 TCAATGATGTAACATATATAGGCTGC 57.278 34.615 0.00 0.00 0.00 5.25
3210 3249 6.124340 TCAATCATGTTGGTTAGCTGATCAT 58.876 36.000 0.00 0.00 0.00 2.45
3545 3584 4.637534 GTCACTTCATAATGCACAGTGGAT 59.362 41.667 0.79 0.79 36.34 3.41
3572 3613 1.471829 TTCTGTCGAGCCTCCTTGCA 61.472 55.000 0.00 0.00 0.00 4.08
3579 3620 3.639094 AGCAATATACTTCTGTCGAGCCT 59.361 43.478 0.00 0.00 0.00 4.58
3600 3641 8.675705 TGTACACATTTGGATCATAATGGTAG 57.324 34.615 17.95 11.98 36.34 3.18
3705 3746 2.872245 TCTTTCTGGTGCTTCTTGTTCG 59.128 45.455 0.00 0.00 0.00 3.95
4863 4905 6.530019 AATGGATGGTTTCGCTAGAATTTT 57.470 33.333 0.00 0.00 36.09 1.82
4864 4906 6.530019 AAATGGATGGTTTCGCTAGAATTT 57.470 33.333 0.00 0.00 36.09 1.82
4866 4908 5.163519 CCAAAATGGATGGTTTCGCTAGAAT 60.164 40.000 0.00 0.00 40.96 2.40
5078 5123 5.997384 ACTACGGTCACTTAAAATCCTCT 57.003 39.130 0.00 0.00 0.00 3.69
5082 5127 7.766283 AGTACCTACTACGGTCACTTAAAATC 58.234 38.462 0.00 0.00 38.49 2.17
5160 5205 4.130118 CGAGTAATTTGGAATGGAGGGAG 58.870 47.826 0.00 0.00 0.00 4.30
5163 5208 3.555956 CGACGAGTAATTTGGAATGGAGG 59.444 47.826 0.00 0.00 0.00 4.30
5164 5209 3.001330 GCGACGAGTAATTTGGAATGGAG 59.999 47.826 0.00 0.00 0.00 3.86
5165 5210 2.933906 GCGACGAGTAATTTGGAATGGA 59.066 45.455 0.00 0.00 0.00 3.41
5166 5211 2.675844 TGCGACGAGTAATTTGGAATGG 59.324 45.455 0.00 0.00 0.00 3.16
5167 5212 3.616821 TCTGCGACGAGTAATTTGGAATG 59.383 43.478 0.00 0.00 0.00 2.67
5168 5213 3.857052 TCTGCGACGAGTAATTTGGAAT 58.143 40.909 0.00 0.00 0.00 3.01
5169 5214 3.306917 TCTGCGACGAGTAATTTGGAA 57.693 42.857 0.00 0.00 0.00 3.53
5170 5215 3.306917 TTCTGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
5171 5216 4.334443 CATTTCTGCGACGAGTAATTTGG 58.666 43.478 0.00 0.00 0.00 3.28
5172 5217 4.092821 TCCATTTCTGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
5173 5218 4.250464 TCCATTTCTGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
5174 5219 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
5175 5220 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
5176 5221 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
5177 5222 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
5178 5223 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
5179 5224 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
5180 5225 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
5181 5226 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
5182 5227 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
5183 5228 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
5184 5229 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
5185 5230 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
5214 5259 9.332502 GTCGTAGATATGGATGTATCTAGATGT 57.667 37.037 15.79 1.25 41.77 3.06
5215 5260 9.331282 TGTCGTAGATATGGATGTATCTAGATG 57.669 37.037 15.79 0.00 41.77 2.90
5216 5261 9.907229 TTGTCGTAGATATGGATGTATCTAGAT 57.093 33.333 10.73 10.73 41.77 1.98
5217 5262 9.384764 CTTGTCGTAGATATGGATGTATCTAGA 57.615 37.037 0.00 0.00 41.77 2.43
5218 5263 9.168451 ACTTGTCGTAGATATGGATGTATCTAG 57.832 37.037 4.37 0.00 41.77 2.43
5220 5265 9.516546 TTACTTGTCGTAGATATGGATGTATCT 57.483 33.333 2.43 2.43 42.50 1.98
5224 5269 7.808381 CGAATTACTTGTCGTAGATATGGATGT 59.192 37.037 0.00 0.00 40.67 3.06
5225 5270 7.273598 CCGAATTACTTGTCGTAGATATGGATG 59.726 40.741 0.00 0.00 40.67 3.51
5226 5271 7.176165 TCCGAATTACTTGTCGTAGATATGGAT 59.824 37.037 0.00 0.00 40.67 3.41
5227 5272 6.487668 TCCGAATTACTTGTCGTAGATATGGA 59.512 38.462 0.00 0.00 40.67 3.41
5228 5273 6.675026 TCCGAATTACTTGTCGTAGATATGG 58.325 40.000 0.00 0.00 40.67 2.74
5229 5274 7.149176 CGTTCCGAATTACTTGTCGTAGATATG 60.149 40.741 0.00 0.00 40.67 1.78
5230 5275 6.854892 CGTTCCGAATTACTTGTCGTAGATAT 59.145 38.462 0.00 0.00 40.67 1.63
5231 5276 6.194463 CGTTCCGAATTACTTGTCGTAGATA 58.806 40.000 0.00 0.00 40.67 1.98
5232 5277 5.032863 CGTTCCGAATTACTTGTCGTAGAT 58.967 41.667 0.00 0.00 40.67 1.98
5233 5278 4.406069 CGTTCCGAATTACTTGTCGTAGA 58.594 43.478 0.00 0.00 35.48 2.59
5234 5279 3.545078 CCGTTCCGAATTACTTGTCGTAG 59.455 47.826 0.00 0.00 35.48 3.51
5235 5280 3.190327 TCCGTTCCGAATTACTTGTCGTA 59.810 43.478 0.00 0.00 35.48 3.43
5236 5281 2.030007 TCCGTTCCGAATTACTTGTCGT 60.030 45.455 0.00 0.00 35.48 4.34
5237 5282 2.597305 CTCCGTTCCGAATTACTTGTCG 59.403 50.000 0.00 0.00 37.01 4.35
5238 5283 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
5239 5284 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
5240 5285 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
5241 5286 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
5242 5287 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
5243 5288 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
5244 5289 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
5245 5290 1.755380 CTACTCCCTCCGTTCCGAATT 59.245 52.381 0.00 0.00 0.00 2.17
5246 5291 1.341778 ACTACTCCCTCCGTTCCGAAT 60.342 52.381 0.00 0.00 0.00 3.34
5247 5292 0.038744 ACTACTCCCTCCGTTCCGAA 59.961 55.000 0.00 0.00 0.00 4.30
5248 5293 0.393537 GACTACTCCCTCCGTTCCGA 60.394 60.000 0.00 0.00 0.00 4.55
5249 5294 0.679002 TGACTACTCCCTCCGTTCCG 60.679 60.000 0.00 0.00 0.00 4.30
5250 5295 1.777941 ATGACTACTCCCTCCGTTCC 58.222 55.000 0.00 0.00 0.00 3.62
5251 5296 3.952967 ACTAATGACTACTCCCTCCGTTC 59.047 47.826 0.00 0.00 0.00 3.95
5252 5297 3.978610 ACTAATGACTACTCCCTCCGTT 58.021 45.455 0.00 0.00 0.00 4.44
5253 5298 3.666345 ACTAATGACTACTCCCTCCGT 57.334 47.619 0.00 0.00 0.00 4.69
5254 5299 5.131784 ACTTACTAATGACTACTCCCTCCG 58.868 45.833 0.00 0.00 0.00 4.63
5255 5300 6.606395 TCAACTTACTAATGACTACTCCCTCC 59.394 42.308 0.00 0.00 0.00 4.30
5256 5301 7.642082 TCAACTTACTAATGACTACTCCCTC 57.358 40.000 0.00 0.00 0.00 4.30
5257 5302 8.478877 CAATCAACTTACTAATGACTACTCCCT 58.521 37.037 0.00 0.00 0.00 4.20
5258 5303 7.224949 GCAATCAACTTACTAATGACTACTCCC 59.775 40.741 0.00 0.00 0.00 4.30
5259 5304 7.043325 CGCAATCAACTTACTAATGACTACTCC 60.043 40.741 0.00 0.00 0.00 3.85
5260 5305 7.043325 CCGCAATCAACTTACTAATGACTACTC 60.043 40.741 0.00 0.00 0.00 2.59
5261 5306 6.757010 CCGCAATCAACTTACTAATGACTACT 59.243 38.462 0.00 0.00 0.00 2.57
5262 5307 6.509677 GCCGCAATCAACTTACTAATGACTAC 60.510 42.308 0.00 0.00 0.00 2.73
5263 5308 5.522460 GCCGCAATCAACTTACTAATGACTA 59.478 40.000 0.00 0.00 0.00 2.59
5264 5309 4.332819 GCCGCAATCAACTTACTAATGACT 59.667 41.667 0.00 0.00 0.00 3.41
5265 5310 4.094294 TGCCGCAATCAACTTACTAATGAC 59.906 41.667 0.00 0.00 0.00 3.06
5403 5449 1.686325 CGCATGTAGGCCTACCAGGT 61.686 60.000 34.76 18.28 37.80 4.00
5415 5461 2.481289 TGGTGGTGAATTCGCATGTA 57.519 45.000 20.06 1.75 0.00 2.29
5603 5649 3.111853 TGTCTCAAGAACAGCATTCGT 57.888 42.857 0.00 0.00 0.00 3.85
5663 5709 1.618343 TCAACAGACTCGCTTCATGGA 59.382 47.619 0.00 0.00 0.00 3.41
5845 5893 2.492090 CCTTCGGGTCAGAGAGCG 59.508 66.667 0.00 0.00 0.00 5.03
5962 6111 1.705873 AGCTAGGCTATAGTGGCGTT 58.294 50.000 0.84 0.00 36.99 4.84
6017 6187 0.663153 ACGCAGAGACAAAAGGCAAC 59.337 50.000 0.00 0.00 0.00 4.17
6055 6225 1.065102 GATAAGACGTCGCACAGGCTA 59.935 52.381 10.46 0.00 38.10 3.93
6153 6354 9.725019 ACTTATCAATGTCATTAACTTGTCAGA 57.275 29.630 0.00 0.00 0.00 3.27
6158 6359 9.166173 TCAGGACTTATCAATGTCATTAACTTG 57.834 33.333 0.00 0.00 35.11 3.16
6162 6363 7.279981 CGGTTCAGGACTTATCAATGTCATTAA 59.720 37.037 0.00 0.00 35.11 1.40
6164 6365 5.586243 CGGTTCAGGACTTATCAATGTCATT 59.414 40.000 0.00 0.00 35.11 2.57
6166 6367 4.503910 CGGTTCAGGACTTATCAATGTCA 58.496 43.478 0.00 0.00 35.11 3.58
6187 6389 1.545582 ACATTGGTCAAATCCCAAGCG 59.454 47.619 0.00 0.00 44.74 4.68
6247 6460 2.097466 GGTGGATTTGTCATGCTTACCG 59.903 50.000 0.00 0.00 0.00 4.02
6297 6510 2.757868 ACAAGTTTAGTTGGCAAGCACA 59.242 40.909 0.00 0.00 0.00 4.57
6320 6533 5.356426 GCAATTTTAGTTGACACAAGGGTT 58.644 37.500 0.00 0.00 0.00 4.11
6358 6789 9.541143 TTTAAGCTTTGGAAAAGGTAAAATCTG 57.459 29.630 3.20 0.00 0.00 2.90
6526 6958 8.349983 GGTAATTGGGTGTACATATGATGTTTC 58.650 37.037 10.38 0.00 41.63 2.78


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

AutoCloner maintained by Alex Coulton.