Multiple sequence alignment - TraesCS6A01G100500

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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 TraesCS6A01G100500 chr6A 100.000 7689 0 0 1 7689 68125853 68133541 0.000000e+00 14200.0
1 TraesCS6A01G100500 chr6A 85.556 180 26 0 3668 3847 4234174 4233995 1.020000e-43 189.0
2 TraesCS6A01G100500 chr6A 85.556 180 26 0 3668 3847 4354569 4354390 1.020000e-43 189.0
3 TraesCS6A01G100500 chr6A 84.884 86 11 2 5511 5594 163161190 163161275 1.370000e-12 86.1
4 TraesCS6A01G100500 chr6D 96.282 5998 152 24 1 5960 47627439 47621475 0.000000e+00 9775.0
5 TraesCS6A01G100500 chr6D 94.741 1331 34 12 6007 7322 47621371 47620062 0.000000e+00 2037.0
6 TraesCS6A01G100500 chr6D 90.801 337 22 7 7354 7687 47620063 47619733 7.080000e-120 442.0
7 TraesCS6A01G100500 chr6D 79.412 204 38 4 4773 4973 5044095 5044297 2.890000e-29 141.0
8 TraesCS6A01G100500 chr5A 84.038 4899 573 109 506 5274 655075521 655070702 0.000000e+00 4521.0
9 TraesCS6A01G100500 chr5A 86.047 86 6 4 5511 5594 3896127 3896208 3.820000e-13 87.9
10 TraesCS6A01G100500 chr5A 84.884 86 11 2 5511 5594 655070484 655070399 1.370000e-12 86.1
11 TraesCS6A01G100500 chr6B 94.595 2627 94 23 3369 5960 124083946 124086559 0.000000e+00 4021.0
12 TraesCS6A01G100500 chr6B 97.337 1014 21 4 3 1016 124080331 124081338 0.000000e+00 1718.0
13 TraesCS6A01G100500 chr6B 96.663 959 28 3 6007 6961 124086663 124087621 0.000000e+00 1591.0
14 TraesCS6A01G100500 chr6B 93.842 341 18 2 7350 7689 124088780 124089118 1.910000e-140 510.0
15 TraesCS6A01G100500 chr6B 92.276 246 17 1 6986 7231 124087615 124087858 1.590000e-91 348.0
16 TraesCS6A01G100500 chr6B 89.844 128 4 3 7240 7358 124087943 124088070 1.030000e-33 156.0
17 TraesCS6A01G100500 chr6B 96.364 55 2 0 5957 6011 124086577 124086631 2.950000e-14 91.6
18 TraesCS6A01G100500 chr5B 85.365 3191 378 44 1840 4985 664379253 664376107 0.000000e+00 3223.0
19 TraesCS6A01G100500 chr5B 85.307 946 94 26 571 1484 664380533 664379601 0.000000e+00 935.0
20 TraesCS6A01G100500 chr3D 83.617 2643 315 65 1030 3610 161712629 161710043 0.000000e+00 2374.0
21 TraesCS6A01G100500 chr3D 77.690 381 47 20 7269 7625 67651294 67651660 1.690000e-46 198.0
22 TraesCS6A01G100500 chr3A 83.618 2637 314 58 1030 3605 191534206 191531627 0.000000e+00 2368.0
23 TraesCS6A01G100500 chr3A 75.815 368 69 15 7272 7625 79189974 79189613 1.330000e-37 169.0
24 TraesCS6A01G100500 chr3B 83.598 2646 306 72 1030 3610 238313877 238311295 0.000000e+00 2364.0
25 TraesCS6A01G100500 chr3B 78.370 319 54 13 7269 7582 114728367 114728675 7.870000e-45 193.0
26 TraesCS6A01G100500 chr5D 86.027 2011 202 32 1847 3822 527606104 527604138 0.000000e+00 2084.0
27 TraesCS6A01G100500 chr5D 85.927 2011 204 32 1847 3822 527576499 527574533 0.000000e+00 2073.0
28 TraesCS6A01G100500 chr5D 83.309 1390 175 31 506 1855 527607501 527606129 0.000000e+00 1229.0
29 TraesCS6A01G100500 chr5D 83.237 1390 176 31 506 1855 527577896 527576524 0.000000e+00 1223.0
30 TraesCS6A01G100500 chr5D 84.327 1174 167 13 3824 4985 527573896 527572728 0.000000e+00 1133.0
31 TraesCS6A01G100500 chr5D 84.327 1174 167 13 3824 4985 527603459 527602291 0.000000e+00 1133.0
32 TraesCS6A01G100500 chr5D 86.695 233 22 7 5047 5274 527572607 527572379 4.610000e-62 250.0
33 TraesCS6A01G100500 chr5D 86.695 233 22 7 5047 5274 527602170 527601942 4.610000e-62 250.0
34 TraesCS6A01G100500 chr5D 84.884 86 11 2 5511 5594 527572157 527572072 1.370000e-12 86.1
35 TraesCS6A01G100500 chr5D 84.884 86 11 2 5511 5594 527601720 527601635 1.370000e-12 86.1
36 TraesCS6A01G100500 chr5D 83.721 86 12 2 5511 5594 127927733 127927818 6.400000e-11 80.5
37 TraesCS6A01G100500 chr7B 81.825 2564 367 63 2311 4847 736138536 736141027 0.000000e+00 2061.0
38 TraesCS6A01G100500 chr7B 83.421 1146 124 34 1024 2149 736137396 736138495 0.000000e+00 1003.0
39 TraesCS6A01G100500 chr7B 79.285 811 90 40 1100 1890 736090760 736091512 5.360000e-136 496.0
40 TraesCS6A01G100500 chrUn 84.771 2075 251 38 1021 3059 62647021 62649066 0.000000e+00 2021.0
41 TraesCS6A01G100500 chrUn 84.477 1224 180 4 3624 4847 62649172 62650385 0.000000e+00 1199.0
42 TraesCS6A01G100500 chrUn 85.876 177 25 0 3668 3844 62408926 62409102 1.020000e-43 189.0
43 TraesCS6A01G100500 chrUn 85.876 177 25 0 3668 3844 62593206 62593382 1.020000e-43 189.0
44 TraesCS6A01G100500 chr1A 84.681 1286 160 24 1027 2285 576355375 576354100 0.000000e+00 1249.0
45 TraesCS6A01G100500 chr1A 85.653 697 75 17 4488 5170 576352993 576352308 0.000000e+00 710.0
46 TraesCS6A01G100500 chr1D 89.000 100 9 2 583 682 41173230 41173133 1.050000e-23 122.0
47 TraesCS6A01G100500 chr7D 83.721 86 12 2 5511 5594 340194263 340194178 6.400000e-11 80.5


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 TraesCS6A01G100500 chr6A 68125853 68133541 7688 False 14200.000000 14200 100.000000 1 7689 1 chr6A.!!$F1 7688
1 TraesCS6A01G100500 chr6D 47619733 47627439 7706 True 4084.666667 9775 93.941333 1 7687 3 chr6D.!!$R1 7686
2 TraesCS6A01G100500 chr5A 655070399 655075521 5122 True 2303.550000 4521 84.461000 506 5594 2 chr5A.!!$R1 5088
3 TraesCS6A01G100500 chr6B 124080331 124089118 8787 False 1205.085714 4021 94.417286 3 7689 7 chr6B.!!$F1 7686
4 TraesCS6A01G100500 chr5B 664376107 664380533 4426 True 2079.000000 3223 85.336000 571 4985 2 chr5B.!!$R1 4414
5 TraesCS6A01G100500 chr3D 161710043 161712629 2586 True 2374.000000 2374 83.617000 1030 3610 1 chr3D.!!$R1 2580
6 TraesCS6A01G100500 chr3A 191531627 191534206 2579 True 2368.000000 2368 83.618000 1030 3605 1 chr3A.!!$R2 2575
7 TraesCS6A01G100500 chr3B 238311295 238313877 2582 True 2364.000000 2364 83.598000 1030 3610 1 chr3B.!!$R1 2580
8 TraesCS6A01G100500 chr5D 527601635 527607501 5866 True 956.420000 2084 85.048400 506 5594 5 chr5D.!!$R2 5088
9 TraesCS6A01G100500 chr5D 527572072 527577896 5824 True 953.020000 2073 85.014000 506 5594 5 chr5D.!!$R1 5088
10 TraesCS6A01G100500 chr7B 736137396 736141027 3631 False 1532.000000 2061 82.623000 1024 4847 2 chr7B.!!$F2 3823
11 TraesCS6A01G100500 chr7B 736090760 736091512 752 False 496.000000 496 79.285000 1100 1890 1 chr7B.!!$F1 790
12 TraesCS6A01G100500 chrUn 62647021 62650385 3364 False 1610.000000 2021 84.624000 1021 4847 2 chrUn.!!$F3 3826
13 TraesCS6A01G100500 chr1A 576352308 576355375 3067 True 979.500000 1249 85.167000 1027 5170 2 chr1A.!!$R1 4143

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
310 313 5.105635 CGTACAGGGTTCCAAACATCTACTA 60.106 44.000 0.00 0.0 0.00 1.82 F
815 836 5.302823 CCTCTGTTTTTGACCTTGATTCCTT 59.697 40.000 0.00 0.0 0.00 3.36 F
2577 4947 2.094700 TGCTCACTAGAAGCGTTTCGAT 60.095 45.455 6.35 0.0 38.38 3.59 F
3811 6249 0.603707 CTTCCTCTGCCGTTTCTGCA 60.604 55.000 0.00 0.0 37.17 4.41 F
4806 7927 1.111116 AGATGATTTGGCCGCCCATG 61.111 55.000 7.03 0.0 41.78 3.66 F
5573 8839 3.010138 TGAGGGCATTTAAGCTTACAGGT 59.990 43.478 5.45 0.0 34.17 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1525 3787 1.278238 GGATCTTTAGCCACGACACG 58.722 55.000 0.00 0.00 0.00 4.49 R
2720 5105 2.832129 CACCCTGTACTACACCAGATGT 59.168 50.000 0.00 0.00 46.06 3.06 R
4466 7587 1.153005 CCAGAAGCATCCTGAGCCC 60.153 63.158 0.00 0.00 33.65 5.19 R
5802 9068 0.108138 AGTCACTATCAGCCGGCAAC 60.108 55.000 31.54 12.53 0.00 4.17 R
5803 9069 0.613260 AAGTCACTATCAGCCGGCAA 59.387 50.000 31.54 17.44 0.00 4.52 R
6962 10294 0.676466 TAATGCCAACACTGCCGGAG 60.676 55.000 5.05 1.84 0.00 4.63 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
281 284 6.048509 GGAAGAAATTCCTTTGCTTTCACAA 58.951 36.000 0.00 0.00 38.09 3.33
310 313 5.105635 CGTACAGGGTTCCAAACATCTACTA 60.106 44.000 0.00 0.00 0.00 1.82
379 382 8.716646 TCGAGCTTCATCAAATTAATTAGACA 57.283 30.769 0.01 0.00 0.00 3.41
380 383 9.161629 TCGAGCTTCATCAAATTAATTAGACAA 57.838 29.630 0.01 0.00 0.00 3.18
491 498 5.937540 TGGATACTGATTTGTGTTTGATCGT 59.062 36.000 0.00 0.00 37.61 3.73
569 587 8.934023 TTTTTATATCAAAGGACCTGTGAGTT 57.066 30.769 19.34 11.50 30.61 3.01
815 836 5.302823 CCTCTGTTTTTGACCTTGATTCCTT 59.697 40.000 0.00 0.00 0.00 3.36
1248 3481 7.995488 TGTAATTTGGGTGAATGTTTGGATTTT 59.005 29.630 0.00 0.00 0.00 1.82
1253 3486 6.284459 TGGGTGAATGTTTGGATTTTAACAC 58.716 36.000 0.00 0.00 37.11 3.32
1738 4010 8.030692 CACAAAACATTTGATCCATCTGTATGT 58.969 33.333 9.62 0.00 0.00 2.29
2129 4468 5.829924 CCTGTGTATTCTATTTGCCCTCATT 59.170 40.000 0.00 0.00 0.00 2.57
2167 4506 6.398095 TCAGGTATGTGTTGTCTGAATACAG 58.602 40.000 0.00 0.00 44.66 2.74
2219 4560 2.225068 ATATCGACGGTTGCTCCTTG 57.775 50.000 0.00 0.00 0.00 3.61
2373 4743 6.425114 GCCTTTATCTGGTGTACTGATACATG 59.575 42.308 0.00 0.00 43.21 3.21
2374 4744 7.686859 GCCTTTATCTGGTGTACTGATACATGA 60.687 40.741 0.00 0.00 43.21 3.07
2375 4745 8.370940 CCTTTATCTGGTGTACTGATACATGAT 58.629 37.037 0.00 0.00 43.21 2.45
2376 4746 9.770097 CTTTATCTGGTGTACTGATACATGATT 57.230 33.333 0.00 0.00 43.21 2.57
2378 4748 9.546428 TTATCTGGTGTACTGATACATGATTTG 57.454 33.333 0.00 0.00 43.21 2.32
2379 4749 7.181569 TCTGGTGTACTGATACATGATTTGA 57.818 36.000 0.00 0.00 43.21 2.69
2380 4750 7.795047 TCTGGTGTACTGATACATGATTTGAT 58.205 34.615 0.00 0.00 43.21 2.57
2381 4751 8.923270 TCTGGTGTACTGATACATGATTTGATA 58.077 33.333 0.00 0.00 43.21 2.15
2382 4752 8.887036 TGGTGTACTGATACATGATTTGATAC 57.113 34.615 0.00 0.00 43.21 2.24
2383 4753 8.482128 TGGTGTACTGATACATGATTTGATACA 58.518 33.333 0.00 0.00 43.21 2.29
2384 4754 9.494271 GGTGTACTGATACATGATTTGATACAT 57.506 33.333 0.00 0.00 43.21 2.29
2419 4789 7.147976 GTGTTCCTTGCAGTTTATTTTCTCAT 58.852 34.615 0.00 0.00 0.00 2.90
2492 4862 2.224769 GGGTGGACTTTGATGTTCCAGA 60.225 50.000 0.00 0.00 0.00 3.86
2569 4939 4.695455 TGTGGTATTTTGCTCACTAGAAGC 59.305 41.667 12.92 12.92 0.00 3.86
2577 4947 2.094700 TGCTCACTAGAAGCGTTTCGAT 60.095 45.455 6.35 0.00 38.38 3.59
3100 5493 4.524328 TCAGATCGCCATATGAAGCTTCTA 59.476 41.667 26.09 16.00 26.81 2.10
3103 5496 2.061773 CGCCATATGAAGCTTCTACGG 58.938 52.381 26.09 20.26 0.00 4.02
3166 5559 1.669265 GGTTGCGGGTATAGTTTCAGC 59.331 52.381 0.00 0.00 0.00 4.26
3614 6023 7.724305 TTGTTTGTACTTCTTATCACAGACC 57.276 36.000 0.00 0.00 0.00 3.85
3811 6249 0.603707 CTTCCTCTGCCGTTTCTGCA 60.604 55.000 0.00 0.00 37.17 4.41
3996 7111 1.280457 ACTTTCTCTGCTCCCGGAAT 58.720 50.000 0.73 0.00 0.00 3.01
4443 7564 1.285280 CACAAGGGGTGGAGTATGGA 58.715 55.000 0.00 0.00 44.04 3.41
4466 7587 2.315925 AGAGATACCATGTTGGCACG 57.684 50.000 0.00 0.00 42.67 5.34
4806 7927 1.111116 AGATGATTTGGCCGCCCATG 61.111 55.000 7.03 0.00 41.78 3.66
5227 8428 5.869649 AATTTTTCACTGCCTACCTTTGT 57.130 34.783 0.00 0.00 0.00 2.83
5402 8667 8.450578 TGATTTTACATGGTCAGGTATGATTC 57.549 34.615 0.00 0.00 37.87 2.52
5404 8669 9.071276 GATTTTACATGGTCAGGTATGATTCAT 57.929 33.333 4.28 4.28 37.87 2.57
5465 8730 4.202010 GGTAGTTTGTGCTTGTGTGTGAAT 60.202 41.667 0.00 0.00 0.00 2.57
5485 8750 7.120285 TGTGAATCACATCTTTCTCTTTGGATC 59.880 37.037 12.63 0.00 39.62 3.36
5486 8751 7.336427 GTGAATCACATCTTTCTCTTTGGATCT 59.664 37.037 8.74 0.00 34.08 2.75
5488 8753 8.647256 AATCACATCTTTCTCTTTGGATCTTT 57.353 30.769 0.00 0.00 0.00 2.52
5489 8754 7.444629 TCACATCTTTCTCTTTGGATCTTTG 57.555 36.000 0.00 0.00 0.00 2.77
5494 8759 6.476378 TCTTTCTCTTTGGATCTTTGGGTAG 58.524 40.000 0.00 0.00 0.00 3.18
5500 8765 7.829211 TCTCTTTGGATCTTTGGGTAGTTTATG 59.171 37.037 0.00 0.00 0.00 1.90
5504 8769 5.593909 TGGATCTTTGGGTAGTTTATGCATG 59.406 40.000 10.16 0.00 0.00 4.06
5505 8770 5.827797 GGATCTTTGGGTAGTTTATGCATGA 59.172 40.000 10.16 0.00 0.00 3.07
5506 8771 6.321181 GGATCTTTGGGTAGTTTATGCATGAA 59.679 38.462 10.16 4.23 0.00 2.57
5507 8772 6.509418 TCTTTGGGTAGTTTATGCATGAAC 57.491 37.500 22.98 22.98 0.00 3.18
5508 8773 6.245408 TCTTTGGGTAGTTTATGCATGAACT 58.755 36.000 31.80 31.80 39.52 3.01
5509 8774 5.895636 TTGGGTAGTTTATGCATGAACTG 57.104 39.130 34.75 0.00 37.23 3.16
5573 8839 3.010138 TGAGGGCATTTAAGCTTACAGGT 59.990 43.478 5.45 0.00 34.17 4.00
5579 8845 4.459337 GCATTTAAGCTTACAGGTTGGAGT 59.541 41.667 5.45 0.00 36.49 3.85
5646 8912 7.291411 TGCTGAATTAACTCTACTCTATCCC 57.709 40.000 0.00 0.00 0.00 3.85
5658 8924 3.798202 ACTCTATCCCGATGCTTTTGTC 58.202 45.455 0.00 0.00 0.00 3.18
5677 8943 6.659745 TTGTCTACAGCTCTTAACACCTAA 57.340 37.500 0.00 0.00 0.00 2.69
5698 8964 7.147966 ACCTAATGACGAACATACATACTCACA 60.148 37.037 0.00 0.00 38.38 3.58
5701 8967 6.944557 TGACGAACATACATACTCACAAAG 57.055 37.500 0.00 0.00 0.00 2.77
5729 8995 9.829507 ATAATTAGCTGCTAACTCCATATCATC 57.170 33.333 23.20 0.00 0.00 2.92
5775 9041 4.338400 GTGGGTTTAGGCACTCCAATTATC 59.662 45.833 0.00 0.00 41.75 1.75
5802 9068 4.556104 GCATAGTTGCTAATCAGGTGCATG 60.556 45.833 0.00 0.00 45.77 4.06
5803 9069 3.077484 AGTTGCTAATCAGGTGCATGT 57.923 42.857 0.00 0.00 36.55 3.21
5821 9087 0.108138 GTTGCCGGCTGATAGTGACT 60.108 55.000 29.70 0.00 0.00 3.41
5822 9088 0.613260 TTGCCGGCTGATAGTGACTT 59.387 50.000 29.70 0.00 0.00 3.01
5823 9089 0.108186 TGCCGGCTGATAGTGACTTG 60.108 55.000 29.70 0.00 0.00 3.16
5824 9090 0.175760 GCCGGCTGATAGTGACTTGA 59.824 55.000 22.15 0.00 0.00 3.02
5826 9092 2.743183 GCCGGCTGATAGTGACTTGATT 60.743 50.000 22.15 0.00 0.00 2.57
5827 9093 3.492656 GCCGGCTGATAGTGACTTGATTA 60.493 47.826 22.15 0.00 0.00 1.75
5832 9099 5.931146 GGCTGATAGTGACTTGATTATGAGG 59.069 44.000 0.00 0.00 0.00 3.86
5954 9221 4.702131 ACTCTGCTTCAGTTTCAGTTTTGT 59.298 37.500 0.00 0.00 32.61 2.83
5981 9269 3.326880 AGTTAGTTTCAGTCCCGGATGTT 59.673 43.478 0.73 0.00 0.00 2.71
6011 9335 3.151554 TCAGTTCCGTCACTTAGCTGTA 58.848 45.455 0.00 0.00 0.00 2.74
6146 9470 5.129634 TGAAACAACCTGTCAGCTCATTTA 58.870 37.500 0.00 0.00 0.00 1.40
6464 9792 4.816925 GTGTAGTTTAGGGATGGAGCAATC 59.183 45.833 0.00 0.00 0.00 2.67
6475 9803 4.756642 GGATGGAGCAATCATCGTTTATCA 59.243 41.667 7.52 0.00 41.24 2.15
6551 9879 3.360249 ACTTCAGTGATGCACTTTTGC 57.640 42.857 5.95 0.00 42.59 3.68
6562 9890 2.946564 GCACTTTTGCCATGTTCTACC 58.053 47.619 0.00 0.00 43.66 3.18
6815 10143 7.334090 AGATTGCACAGTAGTCATGTAAGAAT 58.666 34.615 0.00 0.00 0.00 2.40
6849 10177 1.133668 AGGCCAAGCTAGCATTTAGGG 60.134 52.381 18.83 9.46 0.00 3.53
6850 10178 1.133792 GGCCAAGCTAGCATTTAGGGA 60.134 52.381 18.83 0.00 0.00 4.20
6851 10179 2.489802 GGCCAAGCTAGCATTTAGGGAT 60.490 50.000 18.83 0.00 0.00 3.85
6876 10207 1.696884 GGATAGAAGAGCTGGAAGGGG 59.303 57.143 0.00 0.00 0.00 4.79
6962 10294 2.726821 TCAGATTTTCAGTGGCATCCC 58.273 47.619 0.00 0.00 0.00 3.85
7059 10391 7.424803 TCAACAAGTGATTATGTGAAAAGTGG 58.575 34.615 0.00 0.00 0.00 4.00
7107 10439 5.547465 TGTGAATAACAACTCTGTCCGAAT 58.453 37.500 0.00 0.00 35.24 3.34
7111 10443 6.257849 TGAATAACAACTCTGTCCGAATATGC 59.742 38.462 0.00 0.00 33.45 3.14
7164 10496 5.620738 AGATATGTACTTGCAGTCCATGT 57.379 39.130 0.00 0.00 36.06 3.21
7168 10500 8.046708 AGATATGTACTTGCAGTCCATGTTTTA 58.953 33.333 0.00 0.00 34.15 1.52
7267 10675 6.413269 CAAGCAAAGTAAATCAAAACTGCAC 58.587 36.000 0.00 0.00 0.00 4.57
7313 10730 3.027412 TCCCATAAGAGTCACTCAGAGC 58.973 50.000 7.77 0.00 32.06 4.09
7405 11540 1.078709 TACATTCAAGCACAGCGAGC 58.921 50.000 0.00 0.00 0.00 5.03
7484 11619 1.002468 CCGCTCAAACTGGAACTTGTG 60.002 52.381 0.00 0.00 0.00 3.33
7595 11730 4.909696 TCCGATTCTAAGAGAGCAAGAG 57.090 45.455 0.00 0.00 0.00 2.85
7598 11733 4.278858 CGATTCTAAGAGAGCAAGAGACG 58.721 47.826 0.00 0.00 0.00 4.18
7600 11735 2.717390 TCTAAGAGAGCAAGAGACGCT 58.283 47.619 0.00 0.00 44.10 5.07
7684 11827 8.782533 AAATTGACAAGAATCGAACTGTAAAC 57.217 30.769 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
281 284 3.071892 TGTTTGGAACCCTGTACGATTCT 59.928 43.478 0.00 0.00 0.00 2.40
325 328 3.518634 GGGCATCCGCAAATTTTAAGA 57.481 42.857 0.00 0.00 41.24 2.10
377 380 2.958355 CTGGGGTGATGAGTTTGTTTGT 59.042 45.455 0.00 0.00 0.00 2.83
378 381 2.288395 GCTGGGGTGATGAGTTTGTTTG 60.288 50.000 0.00 0.00 0.00 2.93
379 382 1.963515 GCTGGGGTGATGAGTTTGTTT 59.036 47.619 0.00 0.00 0.00 2.83
380 383 1.620822 GCTGGGGTGATGAGTTTGTT 58.379 50.000 0.00 0.00 0.00 2.83
569 587 3.431486 GGATTGAACCAAAAGCACCAACA 60.431 43.478 0.00 0.00 0.00 3.33
742 763 3.451141 TGGTCATTTGGTTTGCAGAAC 57.549 42.857 0.00 0.00 0.00 3.01
1197 3428 7.840342 TGAAACACATTTTGTACTTGCAAAT 57.160 28.000 0.00 0.00 37.51 2.32
1248 3481 8.698973 TGACAAGAAAATCAATAAGGGTGTTA 57.301 30.769 0.00 0.00 0.00 2.41
1525 3787 1.278238 GGATCTTTAGCCACGACACG 58.722 55.000 0.00 0.00 0.00 4.49
1598 3860 7.415095 CCGGCTAAAGATTGAAATATTGACACA 60.415 37.037 0.00 0.00 0.00 3.72
1738 4010 6.473131 ACGTGTTTTATTTCGATGCTCGTATA 59.527 34.615 0.00 3.58 41.35 1.47
1750 4022 7.181143 TCTACCACTTCACGTGTTTTATTTC 57.819 36.000 16.51 0.00 42.20 2.17
2129 4468 8.631480 ACACATACCTGAATATCGTCTATGTA 57.369 34.615 0.00 0.00 0.00 2.29
2219 4560 6.166982 AGTAGACTTTTGAAGCATACAGACC 58.833 40.000 0.00 0.00 0.00 3.85
2374 4744 9.651913 GGAACACAATAAAACCATGTATCAAAT 57.348 29.630 0.00 0.00 0.00 2.32
2375 4745 8.865090 AGGAACACAATAAAACCATGTATCAAA 58.135 29.630 0.00 0.00 0.00 2.69
2376 4746 8.415950 AGGAACACAATAAAACCATGTATCAA 57.584 30.769 0.00 0.00 0.00 2.57
2377 4747 8.303156 CAAGGAACACAATAAAACCATGTATCA 58.697 33.333 0.00 0.00 0.00 2.15
2378 4748 7.275560 GCAAGGAACACAATAAAACCATGTATC 59.724 37.037 0.00 0.00 0.00 2.24
2379 4749 7.096551 GCAAGGAACACAATAAAACCATGTAT 58.903 34.615 0.00 0.00 0.00 2.29
2380 4750 6.040955 TGCAAGGAACACAATAAAACCATGTA 59.959 34.615 0.00 0.00 0.00 2.29
2381 4751 5.163364 TGCAAGGAACACAATAAAACCATGT 60.163 36.000 0.00 0.00 0.00 3.21
2382 4752 5.295950 TGCAAGGAACACAATAAAACCATG 58.704 37.500 0.00 0.00 0.00 3.66
2383 4753 5.070313 ACTGCAAGGAACACAATAAAACCAT 59.930 36.000 0.00 0.00 39.30 3.55
2384 4754 4.404073 ACTGCAAGGAACACAATAAAACCA 59.596 37.500 0.00 0.00 39.30 3.67
2492 4862 8.807948 ATAGAGCATTGTAGTACACCATTTTT 57.192 30.769 1.43 0.00 0.00 1.94
2720 5105 2.832129 CACCCTGTACTACACCAGATGT 59.168 50.000 0.00 0.00 46.06 3.06
2904 5291 5.355350 ACAGAGGTTAGATTGCTACAAATGC 59.645 40.000 0.00 0.00 0.00 3.56
3100 5493 3.906720 ATATGTGCTTACCTTCACCGT 57.093 42.857 0.00 0.00 32.51 4.83
3103 5496 5.448632 CCGGAAAATATGTGCTTACCTTCAC 60.449 44.000 0.00 0.00 0.00 3.18
3981 7096 2.735772 GCCATTCCGGGAGCAGAGA 61.736 63.158 0.00 0.00 34.06 3.10
3996 7111 1.273759 AGCTGATGAAGACTCTGCCA 58.726 50.000 0.00 0.00 38.06 4.92
4135 7256 3.726607 AGAAGAGATCATTCATCGTGCC 58.273 45.455 11.82 0.00 36.50 5.01
4407 7528 4.521146 CTTGTGGGAGCTGAAACATAGAT 58.479 43.478 0.00 0.00 0.00 1.98
4443 7564 4.262207 CGTGCCAACATGGTATCTCTATCT 60.262 45.833 0.00 0.00 40.46 1.98
4466 7587 1.153005 CCAGAAGCATCCTGAGCCC 60.153 63.158 0.00 0.00 33.65 5.19
4806 7927 2.347490 TCCTTGAGCGCAGGGAAC 59.653 61.111 18.93 0.00 46.13 3.62
4854 7976 8.745837 CGAACAAAAGCAATATACAAATCATCC 58.254 33.333 0.00 0.00 0.00 3.51
4973 8106 9.987272 TCTATGTCGCTAAACTAGTATACTGTA 57.013 33.333 15.90 0.00 0.00 2.74
5227 8428 2.928801 TAAGCTTGAGGTTCACAGCA 57.071 45.000 9.86 0.00 34.92 4.41
5253 8455 5.293324 TCGCATACATAAGTTCAGCGAAAAT 59.707 36.000 4.01 0.00 42.61 1.82
5402 8667 4.880886 TTCACGGTTCATGCATAAGATG 57.119 40.909 0.00 0.00 0.00 2.90
5404 8669 4.323417 ACTTTCACGGTTCATGCATAAGA 58.677 39.130 0.00 0.00 0.00 2.10
5465 8730 6.432162 CCAAAGATCCAAAGAGAAAGATGTGA 59.568 38.462 0.00 0.00 0.00 3.58
5470 8735 5.324832 ACCCAAAGATCCAAAGAGAAAGA 57.675 39.130 0.00 0.00 0.00 2.52
5485 8750 6.071952 ACAGTTCATGCATAAACTACCCAAAG 60.072 38.462 14.99 3.91 34.05 2.77
5486 8751 5.772672 ACAGTTCATGCATAAACTACCCAAA 59.227 36.000 14.99 0.00 34.05 3.28
5488 8753 4.699735 CACAGTTCATGCATAAACTACCCA 59.300 41.667 14.99 0.00 34.05 4.51
5489 8754 4.096382 CCACAGTTCATGCATAAACTACCC 59.904 45.833 14.99 0.00 34.05 3.69
5494 8759 4.563976 GCATTCCACAGTTCATGCATAAAC 59.436 41.667 4.39 4.39 41.47 2.01
5500 8765 2.029649 AGTTGCATTCCACAGTTCATGC 60.030 45.455 0.00 0.00 42.07 4.06
5504 8769 5.627499 TTCATAGTTGCATTCCACAGTTC 57.373 39.130 0.00 0.00 0.00 3.01
5505 8770 6.392354 CATTTCATAGTTGCATTCCACAGTT 58.608 36.000 0.00 0.00 0.00 3.16
5506 8771 5.105635 CCATTTCATAGTTGCATTCCACAGT 60.106 40.000 0.00 0.00 0.00 3.55
5507 8772 5.125900 TCCATTTCATAGTTGCATTCCACAG 59.874 40.000 0.00 0.00 0.00 3.66
5508 8773 5.015515 TCCATTTCATAGTTGCATTCCACA 58.984 37.500 0.00 0.00 0.00 4.17
5509 8774 5.581126 TCCATTTCATAGTTGCATTCCAC 57.419 39.130 0.00 0.00 0.00 4.02
5538 8803 2.763039 TGCCCTCATATTCCAGTCTGA 58.237 47.619 0.00 0.00 0.00 3.27
5542 8807 4.829492 GCTTAAATGCCCTCATATTCCAGT 59.171 41.667 0.00 0.00 31.46 4.00
5546 8811 7.308830 CCTGTAAGCTTAAATGCCCTCATATTC 60.309 40.741 7.99 0.00 31.46 1.75
5617 8883 7.175347 AGAGTAGAGTTAATTCAGCATCACA 57.825 36.000 0.44 0.00 0.00 3.58
5618 8884 9.405587 GATAGAGTAGAGTTAATTCAGCATCAC 57.594 37.037 0.44 0.00 0.00 3.06
5646 8912 3.257393 AGAGCTGTAGACAAAAGCATCG 58.743 45.455 0.00 0.00 39.47 3.84
5658 8924 5.744345 CGTCATTAGGTGTTAAGAGCTGTAG 59.256 44.000 14.10 4.20 0.00 2.74
5677 8943 7.097192 ACTTTGTGAGTATGTATGTTCGTCAT 58.903 34.615 2.17 2.17 36.65 3.06
5743 9009 4.949856 AGTGCCTAAACCCACATAATCAAG 59.050 41.667 0.00 0.00 34.48 3.02
5753 9019 2.990740 AATTGGAGTGCCTAAACCCA 57.009 45.000 0.00 0.00 34.31 4.51
5754 9020 4.532834 TGATAATTGGAGTGCCTAAACCC 58.467 43.478 0.00 0.00 34.31 4.11
5802 9068 0.108138 AGTCACTATCAGCCGGCAAC 60.108 55.000 31.54 12.53 0.00 4.17
5803 9069 0.613260 AAGTCACTATCAGCCGGCAA 59.387 50.000 31.54 17.44 0.00 4.52
5821 9087 5.869649 TGTAGCAGCTACCTCATAATCAA 57.130 39.130 26.65 4.17 36.24 2.57
5822 9088 6.041979 TGAATGTAGCAGCTACCTCATAATCA 59.958 38.462 26.65 14.73 36.24 2.57
5823 9089 6.459066 TGAATGTAGCAGCTACCTCATAATC 58.541 40.000 26.65 12.57 36.24 1.75
5824 9090 6.042552 ACTGAATGTAGCAGCTACCTCATAAT 59.957 38.462 26.65 11.72 36.24 1.28
5826 9092 4.895889 ACTGAATGTAGCAGCTACCTCATA 59.104 41.667 26.65 10.64 36.24 2.15
5827 9093 3.708631 ACTGAATGTAGCAGCTACCTCAT 59.291 43.478 26.65 13.11 36.24 2.90
5832 9099 6.504398 TGTGTATACTGAATGTAGCAGCTAC 58.496 40.000 23.74 23.74 36.86 3.58
5954 9221 5.324409 TCCGGGACTGAAACTAACTACTAA 58.676 41.667 0.00 0.00 0.00 2.24
5981 9269 6.687081 AAGTGACGGAACTGAATAAAAACA 57.313 33.333 0.00 0.00 0.00 2.83
6011 9335 7.316640 GCAGATATCTGGTTACGAGAATATGT 58.683 38.462 29.43 0.00 43.94 2.29
6163 9487 7.174946 AGGGAGTATTTATACCATCAAAATGCG 59.825 37.037 0.00 0.00 32.55 4.73
6353 9681 6.567050 AGCCATACTAAATGCAGAACAAATG 58.433 36.000 0.00 0.00 0.00 2.32
6354 9682 6.604795 AGAGCCATACTAAATGCAGAACAAAT 59.395 34.615 0.00 0.00 0.00 2.32
6464 9792 8.970691 AAAAATTCCTTGACTGATAAACGATG 57.029 30.769 0.00 0.00 0.00 3.84
6551 9879 3.262420 CGAGGAAGTTGGTAGAACATGG 58.738 50.000 0.00 0.00 0.00 3.66
6562 9890 6.574350 ACCTTCTAATGATACGAGGAAGTTG 58.426 40.000 0.00 0.00 0.00 3.16
6815 10143 3.861840 CTTGGCCTCGAGTTGAATCTTA 58.138 45.455 12.31 0.00 0.00 2.10
6827 10155 1.869767 CTAAATGCTAGCTTGGCCTCG 59.130 52.381 17.23 0.00 0.00 4.63
6849 10177 2.566724 CCAGCTCTTCTATCCTCCCATC 59.433 54.545 0.00 0.00 0.00 3.51
6850 10178 2.180973 TCCAGCTCTTCTATCCTCCCAT 59.819 50.000 0.00 0.00 0.00 4.00
6851 10179 1.575788 TCCAGCTCTTCTATCCTCCCA 59.424 52.381 0.00 0.00 0.00 4.37
6876 10207 7.106239 TCCTTCTTATCATGTTCTTCAACCTC 58.894 38.462 0.00 0.00 0.00 3.85
6962 10294 0.676466 TAATGCCAACACTGCCGGAG 60.676 55.000 5.05 1.84 0.00 4.63
7267 10675 1.347707 TGGACCCAAGTGACTGCTAAG 59.652 52.381 0.00 0.00 0.00 2.18
7313 10730 0.947244 GTGTTCAGGCTGGACTGTTG 59.053 55.000 25.63 0.00 39.48 3.33
7405 11540 4.336153 TGTTGGCTGTATATGTTGATGCAG 59.664 41.667 0.00 0.00 41.12 4.41
7501 11636 3.548770 CAGATGATGTACCATTGCCTGT 58.451 45.455 0.00 0.00 0.00 4.00
7595 11730 0.859232 TCGCTTTCTTGTGAAGCGTC 59.141 50.000 24.56 0.00 43.39 5.19
7598 11733 2.644078 CAAGTCGCTTTCTTGTGAAGC 58.356 47.619 0.00 0.00 37.90 3.86
7600 11735 1.333619 GGCAAGTCGCTTTCTTGTGAA 59.666 47.619 11.77 0.00 42.67 3.18


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

AutoCloner maintained by Alex Coulton.