Multiple sequence alignment - TraesCS6B01G280100

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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 TraesCS6B01G280100 chr6B 100.000 4016 0 0 1 4016 506272381 506268366 0.000000e+00 7417.0
1 TraesCS6B01G280100 chr6B 87.206 383 43 4 3354 3735 135939112 135939489 7.970000e-117 431.0
2 TraesCS6B01G280100 chr6B 79.245 318 42 11 1341 1654 70512032 70512329 2.450000e-47 200.0
3 TraesCS6B01G280100 chr6D 95.851 940 25 5 819 1748 318085314 318086249 0.000000e+00 1507.0
4 TraesCS6B01G280100 chr6D 94.595 925 36 4 2426 3343 318087309 318088226 0.000000e+00 1419.0
5 TraesCS6B01G280100 chr6D 91.000 700 34 16 2 695 318084499 318085175 0.000000e+00 917.0
6 TraesCS6B01G280100 chr6D 88.290 649 48 13 1759 2398 318086452 318087081 0.000000e+00 752.0
7 TraesCS6B01G280100 chr6D 86.784 681 54 17 1320 1993 294414687 294414036 0.000000e+00 726.0
8 TraesCS6B01G280100 chr6D 94.189 413 24 0 2638 3050 294413475 294413063 7.320000e-177 630.0
9 TraesCS6B01G280100 chr6D 92.092 392 24 5 2007 2398 294414049 294413665 2.730000e-151 545.0
10 TraesCS6B01G280100 chr6D 91.292 356 24 4 942 1297 294423667 294423319 2.810000e-131 479.0
11 TraesCS6B01G280100 chr6D 91.209 273 21 3 3746 4016 371581015 371580744 6.340000e-98 368.0
12 TraesCS6B01G280100 chr6D 95.238 84 3 1 858 940 294423804 294423721 9.060000e-27 132.0
13 TraesCS6B01G280100 chr6D 93.056 72 5 0 3050 3121 294412994 294412923 5.490000e-19 106.0
14 TraesCS6B01G280100 chr6D 90.123 81 4 2 714 791 318085238 318085317 7.100000e-18 102.0
15 TraesCS6B01G280100 chr6D 83.333 120 4 10 3121 3240 294412495 294412392 3.300000e-16 97.1
16 TraesCS6B01G280100 chr6D 94.737 57 3 0 3292 3348 294412394 294412338 5.530000e-14 89.8
17 TraesCS6B01G280100 chr6A 94.725 872 19 6 819 1683 455644402 455645253 0.000000e+00 1330.0
18 TraesCS6B01G280100 chr6A 94.725 872 19 6 819 1683 455651550 455652401 0.000000e+00 1330.0
19 TraesCS6B01G280100 chr6A 92.128 940 37 13 2426 3348 455645977 455646896 0.000000e+00 1291.0
20 TraesCS6B01G280100 chr6A 92.128 940 37 13 2426 3348 455653125 455654044 0.000000e+00 1291.0
21 TraesCS6B01G280100 chr6A 93.646 661 39 3 3357 4016 176988656 176987998 0.000000e+00 985.0
22 TraesCS6B01G280100 chr6A 89.045 639 42 14 1725 2361 455645249 455645861 0.000000e+00 767.0
23 TraesCS6B01G280100 chr6A 89.045 639 42 14 1725 2361 455652397 455653009 0.000000e+00 767.0
24 TraesCS6B01G280100 chr6A 92.053 151 11 1 1 151 455643970 455644119 1.130000e-50 211.0
25 TraesCS6B01G280100 chr6A 88.235 85 6 2 710 791 455644316 455644399 9.190000e-17 99.0
26 TraesCS6B01G280100 chr6A 88.235 85 6 2 710 791 455651464 455651547 9.190000e-17 99.0
27 TraesCS6B01G280100 chr7D 95.310 661 29 2 3356 4016 10721773 10721115 0.000000e+00 1048.0
28 TraesCS6B01G280100 chr7D 94.454 577 31 1 3440 4016 409487524 409486949 0.000000e+00 887.0
29 TraesCS6B01G280100 chr7D 90.616 341 30 2 3354 3694 20489349 20489687 6.120000e-123 451.0
30 TraesCS6B01G280100 chr7A 95.023 663 32 1 3354 4016 159554001 159553340 0.000000e+00 1040.0
31 TraesCS6B01G280100 chr1A 93.414 577 35 3 3440 4016 576226543 576227116 0.000000e+00 852.0
32 TraesCS6B01G280100 chr5B 87.559 426 45 5 3354 3778 429186051 429186469 1.680000e-133 486.0
33 TraesCS6B01G280100 chr3B 90.265 339 33 0 3409 3747 267229820 267229482 1.020000e-120 444.0
34 TraesCS6B01G280100 chr5D 90.842 273 22 3 3746 4016 398905966 398906237 2.950000e-96 363.0
35 TraesCS6B01G280100 chr5D 90.741 270 22 3 3746 4013 564297780 564298048 1.370000e-94 357.0
36 TraesCS6B01G280100 chr5D 90.110 273 24 3 3746 4016 398425682 398425411 6.390000e-93 351.0
37 TraesCS6B01G280100 chr2B 86.164 318 36 6 1341 1654 625542253 625542566 1.790000e-88 337.0
38 TraesCS6B01G280100 chr2D 85.714 315 43 2 1341 1654 527904716 527905029 8.320000e-87 331.0
39 TraesCS6B01G280100 chr2A 80.615 423 74 6 1234 1654 672770977 672771393 1.800000e-83 320.0
40 TraesCS6B01G280100 chr4B 92.857 126 7 2 3355 3480 636044605 636044482 8.870000e-42 182.0


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 TraesCS6B01G280100 chr6B 506268366 506272381 4015 True 7417.00 7417 100.00000 1 4016 1 chr6B.!!$R1 4015
1 TraesCS6B01G280100 chr6D 318084499 318088226 3727 False 939.40 1507 91.97180 2 3343 5 chr6D.!!$F1 3341
2 TraesCS6B01G280100 chr6D 294412338 294414687 2349 True 365.65 726 90.69850 1320 3348 6 chr6D.!!$R2 2028
3 TraesCS6B01G280100 chr6A 176987998 176988656 658 True 985.00 985 93.64600 3357 4016 1 chr6A.!!$R1 659
4 TraesCS6B01G280100 chr6A 455651464 455654044 2580 False 871.75 1330 91.03325 710 3348 4 chr6A.!!$F2 2638
5 TraesCS6B01G280100 chr6A 455643970 455646896 2926 False 739.60 1330 91.23720 1 3348 5 chr6A.!!$F1 3347
6 TraesCS6B01G280100 chr7D 10721115 10721773 658 True 1048.00 1048 95.31000 3356 4016 1 chr7D.!!$R1 660
7 TraesCS6B01G280100 chr7D 409486949 409487524 575 True 887.00 887 94.45400 3440 4016 1 chr7D.!!$R2 576
8 TraesCS6B01G280100 chr7A 159553340 159554001 661 True 1040.00 1040 95.02300 3354 4016 1 chr7A.!!$R1 662
9 TraesCS6B01G280100 chr1A 576226543 576227116 573 False 852.00 852 93.41400 3440 4016 1 chr1A.!!$F1 576

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
519 520 0.036448 CGGCGATCCTCCTACTCCTA 59.964 60.0 0.00 0.00 0.00 2.94 F
1008 1080 0.248907 CAGGTACGTACATGGAGCCG 60.249 60.0 27.99 5.69 34.62 5.52 F
1794 2065 0.235665 CGTCAAAAGCGCACATGAGT 59.764 50.0 11.47 0.00 0.00 3.41 F
2264 2546 0.670162 GCAATCGTGATCATTGGGGG 59.330 55.0 0.00 0.00 32.66 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1667 1746 0.032540 GGCAACCAAAGCAAGAGTGG 59.967 55.0 0.0 0.0 38.46 4.00 R
2587 3103 0.179062 TAGAGGCCGTAGTCCGAGAC 60.179 60.0 0.0 0.0 39.56 3.36 R
2898 3414 1.063806 CGTTGAGCTTCCTCTCGTTG 58.936 55.0 0.0 0.0 38.93 4.10 R
3523 4544 1.293924 CAATCTGACGCATCCTGTCC 58.706 55.0 0.0 0.0 35.46 4.02 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
65 66 4.912187 GCTCCGATTTTGTGTTTTCTCTTC 59.088 41.667 0.00 0.00 0.00 2.87
70 71 4.364415 TTTTGTGTTTTCTCTTCACGGG 57.636 40.909 0.00 0.00 35.20 5.28
87 88 0.985490 GGGGCTCCTCCTGAAGTCAT 60.985 60.000 0.00 0.00 34.39 3.06
159 160 5.789512 CCGCAAACAAAATCATATGTTTTGC 59.210 36.000 26.22 21.86 44.91 3.68
161 162 6.347563 CGCAAACAAAATCATATGTTTTGCCT 60.348 34.615 26.22 18.11 44.91 4.75
162 163 7.148672 CGCAAACAAAATCATATGTTTTGCCTA 60.149 33.333 26.22 2.40 44.91 3.93
201 202 2.289072 ACTGTTCACGCTGTAGCAGATT 60.289 45.455 4.59 0.00 42.21 2.40
203 204 4.115516 CTGTTCACGCTGTAGCAGATTAT 58.884 43.478 4.59 0.00 42.21 1.28
235 236 2.818130 TTTGAATCCAAAGCAGCCAC 57.182 45.000 0.00 0.00 37.36 5.01
236 237 1.702182 TTGAATCCAAAGCAGCCACA 58.298 45.000 0.00 0.00 0.00 4.17
242 243 0.890542 CCAAAGCAGCCACACAGCTA 60.891 55.000 0.00 0.00 40.82 3.32
247 248 2.242043 AGCAGCCACACAGCTAAAAAT 58.758 42.857 0.00 0.00 42.61 1.82
275 276 1.682854 CACCAAAGCTCAAAAGGCAGA 59.317 47.619 0.00 0.00 0.00 4.26
296 297 1.202952 AGTGAAAATTACCCGCCACCA 60.203 47.619 0.00 0.00 0.00 4.17
314 315 5.737635 GCCACCAAATACAACTGTGCTAAAA 60.738 40.000 0.00 0.00 0.00 1.52
323 324 2.222953 CTGTGCTAAAACCGCGGACG 62.223 60.000 35.90 15.32 39.67 4.79
334 335 2.025418 CGCGGACGGTAGCACTTTT 61.025 57.895 0.00 0.00 34.97 2.27
362 363 3.764160 AAGCCGGCCATAGAGCAGC 62.764 63.158 26.15 0.00 34.69 5.25
373 374 3.434167 CCATAGAGCAGCCACCAAACTAT 60.434 47.826 0.00 0.00 0.00 2.12
377 378 0.727398 GCAGCCACCAAACTATCGTC 59.273 55.000 0.00 0.00 0.00 4.20
381 382 0.461339 CCACCAAACTATCGTCGGGG 60.461 60.000 0.00 0.00 0.00 5.73
382 383 1.087771 CACCAAACTATCGTCGGGGC 61.088 60.000 0.00 0.00 0.00 5.80
383 384 1.523032 CCAAACTATCGTCGGGGCC 60.523 63.158 0.00 0.00 0.00 5.80
384 385 1.881252 CAAACTATCGTCGGGGCCG 60.881 63.158 0.00 0.00 41.35 6.13
385 386 3.085119 AAACTATCGTCGGGGCCGG 62.085 63.158 4.42 4.42 40.25 6.13
386 387 4.828296 ACTATCGTCGGGGCCGGT 62.828 66.667 11.18 0.00 40.25 5.28
387 388 3.974757 CTATCGTCGGGGCCGGTC 61.975 72.222 11.18 0.00 40.25 4.79
417 418 1.598130 GCCGCCCATCTGTATGTCC 60.598 63.158 0.00 0.00 0.00 4.02
418 419 1.071471 CCGCCCATCTGTATGTCCC 59.929 63.158 0.00 0.00 0.00 4.46
492 493 2.352805 CCTTCCACTCCAGGCCAC 59.647 66.667 5.01 0.00 0.00 5.01
493 494 2.528818 CCTTCCACTCCAGGCCACA 61.529 63.158 5.01 0.00 0.00 4.17
515 516 2.203509 CCCGGCGATCCTCCTACT 60.204 66.667 9.30 0.00 0.00 2.57
518 519 1.228306 CGGCGATCCTCCTACTCCT 60.228 63.158 0.00 0.00 0.00 3.69
519 520 0.036448 CGGCGATCCTCCTACTCCTA 59.964 60.000 0.00 0.00 0.00 2.94
520 521 1.536940 GGCGATCCTCCTACTCCTAC 58.463 60.000 0.00 0.00 0.00 3.18
521 522 1.536940 GCGATCCTCCTACTCCTACC 58.463 60.000 0.00 0.00 0.00 3.18
522 523 1.887522 GCGATCCTCCTACTCCTACCC 60.888 61.905 0.00 0.00 0.00 3.69
523 524 1.272037 CGATCCTCCTACTCCTACCCC 60.272 61.905 0.00 0.00 0.00 4.95
524 525 2.075383 GATCCTCCTACTCCTACCCCT 58.925 57.143 0.00 0.00 0.00 4.79
525 526 1.532038 TCCTCCTACTCCTACCCCTC 58.468 60.000 0.00 0.00 0.00 4.30
576 577 1.750193 GCCATGGATTCTCAACGGAA 58.250 50.000 18.40 0.00 0.00 4.30
702 712 0.250467 GGAAGCTGGACTCACTGCAA 60.250 55.000 0.00 0.00 37.72 4.08
703 713 1.155042 GAAGCTGGACTCACTGCAAG 58.845 55.000 0.00 0.00 42.29 4.01
704 714 0.888285 AAGCTGGACTCACTGCAAGC 60.888 55.000 0.00 0.00 37.60 4.01
705 715 1.598962 GCTGGACTCACTGCAAGCA 60.599 57.895 0.00 0.00 37.60 3.91
707 717 0.873054 CTGGACTCACTGCAAGCAAG 59.127 55.000 0.00 0.00 37.60 4.01
708 718 1.168407 TGGACTCACTGCAAGCAAGC 61.168 55.000 0.00 0.00 37.60 4.01
712 766 1.449726 CTCACTGCAAGCAAGCCACA 61.450 55.000 0.00 0.00 37.60 4.17
729 783 1.670406 CACTCCCACAGTGCTCAGC 60.670 63.158 0.00 0.00 46.30 4.26
785 842 0.341258 TCTCAAGCCATCCTCCTCCT 59.659 55.000 0.00 0.00 0.00 3.69
786 843 0.758123 CTCAAGCCATCCTCCTCCTC 59.242 60.000 0.00 0.00 0.00 3.71
787 844 1.045350 TCAAGCCATCCTCCTCCTCG 61.045 60.000 0.00 0.00 0.00 4.63
788 845 2.439104 AAGCCATCCTCCTCCTCGC 61.439 63.158 0.00 0.00 0.00 5.03
789 846 2.841988 GCCATCCTCCTCCTCGCT 60.842 66.667 0.00 0.00 0.00 4.93
790 847 2.866726 GCCATCCTCCTCCTCGCTC 61.867 68.421 0.00 0.00 0.00 5.03
791 848 2.560119 CCATCCTCCTCCTCGCTCG 61.560 68.421 0.00 0.00 0.00 5.03
792 849 2.203422 ATCCTCCTCCTCGCTCGG 60.203 66.667 0.00 0.00 0.00 4.63
796 853 4.761058 TCCTCCTCGCTCGGCCTT 62.761 66.667 0.00 0.00 0.00 4.35
797 854 4.214327 CCTCCTCGCTCGGCCTTC 62.214 72.222 0.00 0.00 0.00 3.46
798 855 4.214327 CTCCTCGCTCGGCCTTCC 62.214 72.222 0.00 0.00 0.00 3.46
799 856 4.761058 TCCTCGCTCGGCCTTCCT 62.761 66.667 0.00 0.00 0.00 3.36
800 857 3.775654 CCTCGCTCGGCCTTCCTT 61.776 66.667 0.00 0.00 0.00 3.36
810 873 1.610327 GCCTTCCTTTCCTCCTCCC 59.390 63.158 0.00 0.00 0.00 4.30
811 874 1.908483 CCTTCCTTTCCTCCTCCCG 59.092 63.158 0.00 0.00 0.00 5.14
812 875 1.627297 CCTTCCTTTCCTCCTCCCGG 61.627 65.000 0.00 0.00 0.00 5.73
813 876 2.258748 CTTCCTTTCCTCCTCCCGGC 62.259 65.000 0.00 0.00 0.00 6.13
814 877 4.162690 CCTTTCCTCCTCCCGGCG 62.163 72.222 0.00 0.00 0.00 6.46
815 878 3.391382 CTTTCCTCCTCCCGGCGT 61.391 66.667 6.01 0.00 0.00 5.68
816 879 2.926242 TTTCCTCCTCCCGGCGTT 60.926 61.111 6.01 0.00 0.00 4.84
817 880 2.854187 CTTTCCTCCTCCCGGCGTTC 62.854 65.000 6.01 0.00 0.00 3.95
1007 1079 3.661745 CAGGTACGTACATGGAGCC 57.338 57.895 27.99 9.93 34.62 4.70
1008 1080 0.248907 CAGGTACGTACATGGAGCCG 60.249 60.000 27.99 5.69 34.62 5.52
1009 1081 1.066918 GGTACGTACATGGAGCCGG 59.933 63.158 26.02 0.00 0.00 6.13
1667 1746 1.672356 AAGGTCAGTGCGCATCACC 60.672 57.895 15.91 19.66 46.81 4.02
1720 1799 6.218019 CAAGAAATCACAAAAATGCTCCTGA 58.782 36.000 0.00 0.00 0.00 3.86
1753 1832 4.112634 ACATGTTCATCCTGATTCGTACG 58.887 43.478 9.53 9.53 0.00 3.67
1754 1833 3.861276 TGTTCATCCTGATTCGTACGT 57.139 42.857 16.05 0.00 0.00 3.57
1755 1834 4.968812 TGTTCATCCTGATTCGTACGTA 57.031 40.909 16.05 6.02 0.00 3.57
1784 2055 4.606012 GCACAATTTTGCTACGTCAAAAGC 60.606 41.667 17.00 10.45 45.55 3.51
1794 2065 0.235665 CGTCAAAAGCGCACATGAGT 59.764 50.000 11.47 0.00 0.00 3.41
1836 2109 9.612620 AACTTTTCTTATTCTATTTGTTGCGAG 57.387 29.630 0.00 0.00 0.00 5.03
1855 2134 3.369147 CGAGGAGATCACACATGAAACAC 59.631 47.826 0.00 0.00 38.69 3.32
1856 2135 3.679389 AGGAGATCACACATGAAACACC 58.321 45.455 0.00 0.00 38.69 4.16
1865 2147 4.919168 CACACATGAAACACCATAAGCTTG 59.081 41.667 9.86 0.00 0.00 4.01
1867 2149 4.919168 CACATGAAACACCATAAGCTTGTG 59.081 41.667 15.71 15.71 36.11 3.33
1868 2150 4.826733 ACATGAAACACCATAAGCTTGTGA 59.173 37.500 23.29 3.03 34.18 3.58
1870 2152 6.015180 ACATGAAACACCATAAGCTTGTGAAT 60.015 34.615 23.29 9.15 34.18 2.57
1874 2156 8.417106 TGAAACACCATAAGCTTGTGAATTTAA 58.583 29.630 23.29 10.99 34.18 1.52
1876 2158 9.606631 AAACACCATAAGCTTGTGAATTTAAAA 57.393 25.926 23.29 0.00 34.18 1.52
1877 2159 9.606631 AACACCATAAGCTTGTGAATTTAAAAA 57.393 25.926 23.29 0.00 34.18 1.94
1954 2236 1.461559 AAAGGCAGATCAGCAGCTTC 58.538 50.000 12.54 0.00 35.83 3.86
1958 2240 1.605992 CAGATCAGCAGCTTCCCCA 59.394 57.895 0.00 0.00 0.00 4.96
1993 2275 2.151202 TCGGCCATCAGTTTCAACTTC 58.849 47.619 2.24 0.00 37.08 3.01
1999 2281 5.359756 GCCATCAGTTTCAACTTCCTTTTT 58.640 37.500 0.00 0.00 37.08 1.94
2040 2322 0.889994 TGAGGCAATGTGGAATGTGC 59.110 50.000 0.00 0.00 36.24 4.57
2060 2342 6.338146 TGTGCTACACAGATAGTTATGTTCC 58.662 40.000 0.00 0.00 39.62 3.62
2063 2345 5.686397 GCTACACAGATAGTTATGTTCCGTC 59.314 44.000 0.00 0.00 0.00 4.79
2221 2503 3.897239 TGGTCCTGGCCATTAATGTTAG 58.103 45.455 5.51 8.78 32.81 2.34
2223 2505 3.883489 GGTCCTGGCCATTAATGTTAGAC 59.117 47.826 5.51 12.00 0.00 2.59
2245 2527 4.122776 CAAGGTCATTAGATCACCCTTCG 58.877 47.826 0.00 0.00 30.08 3.79
2264 2546 0.670162 GCAATCGTGATCATTGGGGG 59.330 55.000 0.00 0.00 32.66 5.40
2287 2569 4.142816 GCATACAATCAGTCCTGTGTGTTC 60.143 45.833 9.67 0.00 37.10 3.18
2335 2617 3.365220 GCATAGTCGTCTGTCAAACAGTC 59.635 47.826 6.96 1.18 46.03 3.51
2353 2635 6.946229 ACAGTCGTAAACATAGTCATTGTC 57.054 37.500 0.00 0.00 0.00 3.18
2374 2689 4.441087 GTCGTGCCTTGTTTCAAAGAAATC 59.559 41.667 0.00 0.00 0.00 2.17
2398 2713 5.736951 AAGCCATTGTTGTGCCTTAATTA 57.263 34.783 0.00 0.00 0.00 1.40
2399 2714 5.937975 AGCCATTGTTGTGCCTTAATTAT 57.062 34.783 0.00 0.00 0.00 1.28
2401 2716 6.805713 AGCCATTGTTGTGCCTTAATTATAC 58.194 36.000 0.00 0.00 0.00 1.47
2402 2717 6.379703 AGCCATTGTTGTGCCTTAATTATACA 59.620 34.615 0.00 0.00 0.00 2.29
2403 2718 7.069826 AGCCATTGTTGTGCCTTAATTATACAT 59.930 33.333 0.00 0.00 0.00 2.29
2408 2723 9.456147 TTGTTGTGCCTTAATTATACATACACT 57.544 29.630 0.00 0.00 0.00 3.55
2409 2724 8.888716 TGTTGTGCCTTAATTATACATACACTG 58.111 33.333 0.00 0.00 0.00 3.66
2410 2725 7.490962 TGTGCCTTAATTATACATACACTGC 57.509 36.000 0.00 0.00 0.00 4.40
2411 2726 6.201997 TGTGCCTTAATTATACATACACTGCG 59.798 38.462 0.00 0.00 0.00 5.18
2412 2727 6.202188 GTGCCTTAATTATACATACACTGCGT 59.798 38.462 0.00 0.00 0.00 5.24
2413 2728 6.201997 TGCCTTAATTATACATACACTGCGTG 59.798 38.462 7.07 7.07 39.75 5.34
2415 2730 7.568861 GCCTTAATTATACATACACTGCGTGTC 60.569 40.741 15.75 0.00 43.92 3.67
2416 2731 7.652105 CCTTAATTATACATACACTGCGTGTCT 59.348 37.037 15.75 5.90 43.92 3.41
2417 2732 9.673454 CTTAATTATACATACACTGCGTGTCTA 57.327 33.333 15.75 2.91 43.92 2.59
2421 2736 4.294416 ACATACACTGCGTGTCTATCTC 57.706 45.455 15.75 0.00 43.92 2.75
2422 2737 3.694566 ACATACACTGCGTGTCTATCTCA 59.305 43.478 15.75 0.42 43.92 3.27
2423 2738 4.339530 ACATACACTGCGTGTCTATCTCAT 59.660 41.667 15.75 2.48 43.92 2.90
2448 2964 4.508128 GGGATCGCCGACTCGCAA 62.508 66.667 0.00 0.00 33.83 4.85
2451 2967 2.509336 ATCGCCGACTCGCAAAGG 60.509 61.111 0.00 0.00 0.00 3.11
2587 3103 2.185350 CCAGCTACGAGTGCAGGG 59.815 66.667 0.00 0.00 34.10 4.45
2711 3227 4.083862 GGACGCCACCAGGGAGAC 62.084 72.222 0.00 0.00 39.08 3.36
2868 3384 1.176619 TCTCCGACGCCTTCAACTCA 61.177 55.000 0.00 0.00 0.00 3.41
2898 3414 2.125350 CAGAGCAGGAAGTCGGGC 60.125 66.667 0.00 0.00 0.00 6.13
2913 3429 1.448717 GGGCAACGAGAGGAAGCTC 60.449 63.158 0.00 0.00 37.60 4.09
2997 3513 3.069443 CCAAGGAGATACTCAGAAGGCTC 59.931 52.174 0.00 0.00 31.08 4.70
3017 3533 4.388469 GCTCGAGGAGATAGCAAAATGATC 59.612 45.833 15.58 0.00 36.26 2.92
3079 3664 1.301716 GCACGAGACAGGGCTGAAA 60.302 57.895 0.00 0.00 37.60 2.69
3108 3697 0.036858 GACTGAACCTCTGCTGGACC 60.037 60.000 0.00 0.00 0.00 4.46
3497 4518 4.070552 GCTTCTCCTCCACCGCGT 62.071 66.667 4.92 0.00 0.00 6.01
3523 4544 0.171455 CGTTTCGTCAGAGGAGGGAG 59.829 60.000 0.00 0.00 0.00 4.30
3547 4568 1.764723 AGGATGCGTCAGATTGGATCA 59.235 47.619 8.47 0.00 34.95 2.92
3709 4731 1.281925 GGGCTTCCTTCCCAGATCCA 61.282 60.000 0.00 0.00 43.37 3.41
3811 4833 2.831284 GGCGGTGGGTGTTGTTGT 60.831 61.111 0.00 0.00 0.00 3.32
3852 4874 1.905512 CCGGTTTTCGATCTCCCCT 59.094 57.895 0.00 0.00 42.43 4.79
3978 5000 3.319198 GGTGGTTCCTGGCCTCGA 61.319 66.667 3.32 0.00 0.00 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.440371 CCGAAGCTGCTCGAGTTTTC 59.560 55.000 15.13 11.31 41.44 2.29
65 66 3.003173 TTCAGGAGGAGCCCCGTG 61.003 66.667 0.00 0.00 37.37 4.94
70 71 1.412343 GAGATGACTTCAGGAGGAGCC 59.588 57.143 0.00 0.00 0.00 4.70
168 169 6.018994 ACAGCGTGAACAGTACTTTCTTTAAG 60.019 38.462 14.65 0.00 39.87 1.85
174 175 3.121445 GCTACAGCGTGAACAGTACTTTC 59.879 47.826 0.00 1.89 0.00 2.62
176 177 2.035449 TGCTACAGCGTGAACAGTACTT 59.965 45.455 0.00 0.00 45.83 2.24
178 179 1.986378 CTGCTACAGCGTGAACAGTAC 59.014 52.381 0.00 0.00 45.83 2.73
201 202 1.485124 TCAAAGCTGAGCCCGAGATA 58.515 50.000 0.00 0.00 0.00 1.98
203 204 0.615331 ATTCAAAGCTGAGCCCGAGA 59.385 50.000 0.00 0.00 31.69 4.04
231 232 2.480037 GGCAAATTTTTAGCTGTGTGGC 59.520 45.455 0.00 0.00 0.00 5.01
234 235 4.990426 GTGATGGCAAATTTTTAGCTGTGT 59.010 37.500 0.00 0.00 0.00 3.72
235 236 4.389687 GGTGATGGCAAATTTTTAGCTGTG 59.610 41.667 0.00 0.00 0.00 3.66
236 237 4.040217 TGGTGATGGCAAATTTTTAGCTGT 59.960 37.500 0.00 0.00 0.00 4.40
242 243 4.463070 AGCTTTGGTGATGGCAAATTTTT 58.537 34.783 0.00 0.00 0.00 1.94
247 248 1.702182 TGAGCTTTGGTGATGGCAAA 58.298 45.000 0.00 0.00 0.00 3.68
275 276 1.890489 GGTGGCGGGTAATTTTCACTT 59.110 47.619 0.00 0.00 0.00 3.16
296 297 4.542735 GCGGTTTTAGCACAGTTGTATTT 58.457 39.130 0.00 0.00 34.19 1.40
323 324 0.935196 CGCCGGATAAAAGTGCTACC 59.065 55.000 5.05 0.00 0.00 3.18
325 326 0.108089 TGCGCCGGATAAAAGTGCTA 60.108 50.000 5.05 0.00 37.87 3.49
403 404 2.288666 CAAACGGGACATACAGATGGG 58.711 52.381 0.00 0.00 37.39 4.00
411 412 0.108774 TGTGGTGCAAACGGGACATA 59.891 50.000 0.00 0.00 40.06 2.29
417 418 1.358759 GGAGTTGTGGTGCAAACGG 59.641 57.895 0.00 0.00 39.03 4.44
418 419 0.248458 GTGGAGTTGTGGTGCAAACG 60.248 55.000 0.00 0.00 39.03 3.60
506 507 1.532038 GAGGGGTAGGAGTAGGAGGA 58.468 60.000 0.00 0.00 0.00 3.71
515 516 0.031414 GGCAGTTAGGAGGGGTAGGA 60.031 60.000 0.00 0.00 0.00 2.94
518 519 2.062177 GCGGCAGTTAGGAGGGGTA 61.062 63.158 0.00 0.00 0.00 3.69
519 520 3.400054 GCGGCAGTTAGGAGGGGT 61.400 66.667 0.00 0.00 0.00 4.95
520 521 3.083997 AGCGGCAGTTAGGAGGGG 61.084 66.667 1.45 0.00 0.00 4.79
521 522 2.187946 CAGCGGCAGTTAGGAGGG 59.812 66.667 1.45 0.00 0.00 4.30
522 523 2.512515 GCAGCGGCAGTTAGGAGG 60.513 66.667 3.18 0.00 40.72 4.30
523 524 2.512515 GGCAGCGGCAGTTAGGAG 60.513 66.667 11.88 0.00 43.71 3.69
524 525 3.318384 TGGCAGCGGCAGTTAGGA 61.318 61.111 11.88 0.00 43.71 2.94
525 526 3.127533 GTGGCAGCGGCAGTTAGG 61.128 66.667 11.88 0.00 43.71 2.69
576 577 0.901114 TGCTGTGCATGGCCATTTCT 60.901 50.000 17.92 0.00 31.71 2.52
671 681 4.084888 GCTTCCGTCGCGTTTGGG 62.085 66.667 5.77 3.44 0.00 4.12
677 687 4.421479 AGTCCAGCTTCCGTCGCG 62.421 66.667 0.00 0.00 0.00 5.87
702 712 2.113986 GTGGGAGTGTGGCTTGCT 59.886 61.111 0.00 0.00 0.00 3.91
703 713 2.203337 TGTGGGAGTGTGGCTTGC 60.203 61.111 0.00 0.00 0.00 4.01
704 714 1.149174 ACTGTGGGAGTGTGGCTTG 59.851 57.895 0.00 0.00 31.75 4.01
705 715 1.149174 CACTGTGGGAGTGTGGCTT 59.851 57.895 0.00 0.00 46.30 4.35
712 766 2.746359 GCTGAGCACTGTGGGAGT 59.254 61.111 10.21 0.00 34.02 3.85
729 783 5.385509 AGGTTTTTATCATCAACCAACCG 57.614 39.130 3.27 0.00 42.25 4.44
785 842 2.264794 GAAAGGAAGGCCGAGCGA 59.735 61.111 0.00 0.00 39.96 4.93
786 843 2.820037 GGAAAGGAAGGCCGAGCG 60.820 66.667 0.00 0.00 39.96 5.03
787 844 1.450491 GAGGAAAGGAAGGCCGAGC 60.450 63.158 0.00 0.00 39.96 5.03
788 845 1.222113 GGAGGAAAGGAAGGCCGAG 59.778 63.158 0.00 0.00 39.96 4.63
789 846 1.229529 AGGAGGAAAGGAAGGCCGA 60.230 57.895 0.00 0.00 39.96 5.54
790 847 1.222113 GAGGAGGAAAGGAAGGCCG 59.778 63.158 0.00 0.00 39.96 6.13
791 848 1.610327 GGAGGAGGAAAGGAAGGCC 59.390 63.158 0.00 0.00 0.00 5.19
792 849 1.610327 GGGAGGAGGAAAGGAAGGC 59.390 63.158 0.00 0.00 0.00 4.35
793 850 1.908483 CGGGAGGAGGAAAGGAAGG 59.092 63.158 0.00 0.00 0.00 3.46
813 876 4.636435 AACTGCCGGGTGGGAACG 62.636 66.667 2.18 0.00 38.47 3.95
814 877 2.203437 AAACTGCCGGGTGGGAAC 60.203 61.111 2.18 0.00 38.47 3.62
815 878 2.114411 GAAACTGCCGGGTGGGAA 59.886 61.111 2.18 0.00 38.47 3.97
816 879 3.961414 GGAAACTGCCGGGTGGGA 61.961 66.667 2.18 0.00 38.47 4.37
817 880 3.920093 GAGGAAACTGCCGGGTGGG 62.920 68.421 2.18 0.00 44.43 4.61
818 881 2.359975 GAGGAAACTGCCGGGTGG 60.360 66.667 2.18 0.00 44.43 4.61
819 882 2.359975 GGAGGAAACTGCCGGGTG 60.360 66.667 2.18 0.00 44.13 4.61
854 917 0.823356 TTGCTCAGTTGGCTTGGGTC 60.823 55.000 0.00 0.00 0.00 4.46
855 918 0.396974 TTTGCTCAGTTGGCTTGGGT 60.397 50.000 0.00 0.00 0.00 4.51
984 1047 1.546923 TCCATGTACGTACCTGGTGTG 59.453 52.381 34.66 18.81 41.14 3.82
985 1048 1.822990 CTCCATGTACGTACCTGGTGT 59.177 52.381 34.66 10.98 41.14 4.16
987 1050 0.822164 GCTCCATGTACGTACCTGGT 59.178 55.000 34.66 14.51 41.14 4.00
989 1052 0.248907 CGGCTCCATGTACGTACCTG 60.249 60.000 22.43 21.25 0.00 4.00
990 1053 1.389609 CCGGCTCCATGTACGTACCT 61.390 60.000 22.43 10.54 0.00 3.08
1667 1746 0.032540 GGCAACCAAAGCAAGAGTGG 59.967 55.000 0.00 0.00 38.46 4.00
1720 1799 2.198827 TGAACATGTCGCCCAATTCT 57.801 45.000 0.00 0.00 0.00 2.40
1784 2055 1.904852 GCAGTGTGGACTCATGTGCG 61.905 60.000 0.00 0.00 37.34 5.34
1794 2065 4.734398 AAAGTTTCATTTGCAGTGTGGA 57.266 36.364 0.00 0.00 0.00 4.02
1836 2109 3.411446 TGGTGTTTCATGTGTGATCTCC 58.589 45.455 0.00 0.00 33.56 3.71
1876 2158 9.657419 CATGCTTTTCCCTTTGTTATAAGAATT 57.343 29.630 0.00 0.00 0.00 2.17
1877 2159 8.260114 CCATGCTTTTCCCTTTGTTATAAGAAT 58.740 33.333 0.00 0.00 0.00 2.40
1879 2161 6.350949 GCCATGCTTTTCCCTTTGTTATAAGA 60.351 38.462 0.00 0.00 0.00 2.10
1880 2162 5.812127 GCCATGCTTTTCCCTTTGTTATAAG 59.188 40.000 0.00 0.00 0.00 1.73
1882 2164 4.142271 CGCCATGCTTTTCCCTTTGTTATA 60.142 41.667 0.00 0.00 0.00 0.98
1883 2165 3.368323 CGCCATGCTTTTCCCTTTGTTAT 60.368 43.478 0.00 0.00 0.00 1.89
1884 2166 2.029470 CGCCATGCTTTTCCCTTTGTTA 60.029 45.455 0.00 0.00 0.00 2.41
1885 2167 1.270252 CGCCATGCTTTTCCCTTTGTT 60.270 47.619 0.00 0.00 0.00 2.83
1913 2195 6.764877 TTTTGTAGTCTTCGAACTAGCTTG 57.235 37.500 0.00 0.00 32.52 4.01
1918 2200 5.603596 TGCCTTTTTGTAGTCTTCGAACTA 58.396 37.500 0.00 0.00 0.00 2.24
1954 2236 4.244862 CCGAAATGATTCTTGTTTTGGGG 58.755 43.478 0.00 0.00 34.25 4.96
1958 2240 4.599047 TGGCCGAAATGATTCTTGTTTT 57.401 36.364 0.00 0.00 33.17 2.43
2014 2296 5.304101 ACATTCCACATTGCCTCAAAAGTTA 59.696 36.000 0.00 0.00 0.00 2.24
2040 2322 6.691818 GTGACGGAACATAACTATCTGTGTAG 59.308 42.308 0.00 0.00 32.98 2.74
2060 2342 2.631418 ATGAACTCTGTACCGTGACG 57.369 50.000 0.00 0.00 0.00 4.35
2063 2345 6.157211 AGTAAGAAATGAACTCTGTACCGTG 58.843 40.000 0.00 0.00 0.00 4.94
2221 2503 4.762289 AGGGTGATCTAATGACCTTGTC 57.238 45.455 0.00 0.00 0.00 3.18
2223 2505 4.122776 CGAAGGGTGATCTAATGACCTTG 58.877 47.826 0.00 0.00 38.36 3.61
2245 2527 0.670162 CCCCCAATGATCACGATTGC 59.330 55.000 0.00 0.00 30.66 3.56
2264 2546 3.338249 ACACACAGGACTGATTGTATGC 58.662 45.455 6.29 0.00 31.06 3.14
2287 2569 5.277828 GCACTAACCACTGTTTTAACTGAGG 60.278 44.000 12.15 12.15 41.78 3.86
2335 2617 4.491924 GGCACGACAATGACTATGTTTACG 60.492 45.833 0.00 0.00 0.00 3.18
2353 2635 4.358851 TGATTTCTTTGAAACAAGGCACG 58.641 39.130 0.00 0.00 0.00 5.34
2407 2722 5.175090 TCTGTAATGAGATAGACACGCAG 57.825 43.478 0.00 0.00 0.00 5.18
2408 2723 4.036852 CCTCTGTAATGAGATAGACACGCA 59.963 45.833 0.00 0.00 36.23 5.24
2409 2724 4.541779 CCTCTGTAATGAGATAGACACGC 58.458 47.826 0.00 0.00 36.23 5.34
2410 2725 4.022762 CCCCTCTGTAATGAGATAGACACG 60.023 50.000 0.00 0.00 36.23 4.49
2411 2726 5.141182 TCCCCTCTGTAATGAGATAGACAC 58.859 45.833 0.00 0.00 36.23 3.67
2412 2727 5.403558 TCCCCTCTGTAATGAGATAGACA 57.596 43.478 0.00 0.00 36.23 3.41
2413 2728 5.124776 CGATCCCCTCTGTAATGAGATAGAC 59.875 48.000 0.00 0.00 36.23 2.59
2414 2729 5.257262 CGATCCCCTCTGTAATGAGATAGA 58.743 45.833 0.00 0.00 36.23 1.98
2415 2730 4.142271 GCGATCCCCTCTGTAATGAGATAG 60.142 50.000 0.00 0.00 36.23 2.08
2416 2731 3.764434 GCGATCCCCTCTGTAATGAGATA 59.236 47.826 0.00 0.00 36.23 1.98
2417 2732 2.564947 GCGATCCCCTCTGTAATGAGAT 59.435 50.000 0.00 0.00 36.23 2.75
2418 2733 1.964223 GCGATCCCCTCTGTAATGAGA 59.036 52.381 0.00 0.00 36.23 3.27
2421 2736 0.319900 CGGCGATCCCCTCTGTAATG 60.320 60.000 0.00 0.00 0.00 1.90
2422 2737 0.469331 TCGGCGATCCCCTCTGTAAT 60.469 55.000 4.99 0.00 0.00 1.89
2423 2738 1.076559 TCGGCGATCCCCTCTGTAA 60.077 57.895 4.99 0.00 0.00 2.41
2451 2967 1.020437 GCTTGCAGATTAGGCTCCAC 58.980 55.000 0.00 0.00 0.00 4.02
2587 3103 0.179062 TAGAGGCCGTAGTCCGAGAC 60.179 60.000 0.00 0.00 39.56 3.36
2711 3227 2.126071 CCAGGCTGTACACGTCGG 60.126 66.667 14.43 0.00 0.00 4.79
2868 3384 2.347322 GCTCTGCCTGACGAGGTCT 61.347 63.158 0.00 0.00 42.15 3.85
2898 3414 1.063806 CGTTGAGCTTCCTCTCGTTG 58.936 55.000 0.00 0.00 38.93 4.10
2913 3429 1.630244 CCAGCTCGAAGAAGGCGTTG 61.630 60.000 0.00 0.00 34.09 4.10
2997 3513 5.295950 AGTGATCATTTTGCTATCTCCTCG 58.704 41.667 0.00 0.00 0.00 4.63
3079 3664 2.900546 AGAGGTTCAGTCGTTCCTTCAT 59.099 45.455 0.00 0.00 0.00 2.57
3108 3697 6.002082 TGATATCTGAAGCCATTCTCCAATG 58.998 40.000 3.98 0.00 39.45 2.82
3348 4369 4.758251 CCCGTGTCGCCAGCATGA 62.758 66.667 0.00 0.00 39.69 3.07
3497 4518 2.280524 CTGACGAAACGGTGGCCA 60.281 61.111 0.00 0.00 0.00 5.36
3523 4544 1.293924 CAATCTGACGCATCCTGTCC 58.706 55.000 0.00 0.00 35.46 4.02
3585 4606 3.606065 GACACAGGGACGACGTCGG 62.606 68.421 37.89 23.54 44.95 4.79
3588 4609 3.300765 GGGACACAGGGACGACGT 61.301 66.667 0.00 0.00 0.00 4.34
3695 4717 2.066393 CGGCTGGATCTGGGAAGGA 61.066 63.158 0.00 0.00 0.00 3.36
3811 4833 1.827789 GCAGTCCACCAAGCACCAA 60.828 57.895 0.00 0.00 0.00 3.67
3852 4874 1.614051 CCATAGCACTGACCAAAGGCA 60.614 52.381 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.