Multiple sequence alignment - TraesCS1D01G276000

Loading Multiple Alignment...

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 TraesCS1D01G276000 chr1D 100.000 3287 0 0 2482 5768 371784723 371781437 0.000000e+00 6071.0
1 TraesCS1D01G276000 chr1D 100.000 1854 0 0 1 1854 371787204 371785351 0.000000e+00 3424.0
2 TraesCS1D01G276000 chr1B 92.253 1833 102 12 32 1847 496572866 496571057 0.000000e+00 2562.0
3 TraesCS1D01G276000 chr1B 93.924 1547 73 15 2482 4026 496571031 496569504 0.000000e+00 2316.0
4 TraesCS1D01G276000 chr1B 90.501 1158 68 22 4035 5190 496569383 496568266 0.000000e+00 1491.0
5 TraesCS1D01G276000 chr1B 100.000 32 0 0 1 32 496574959 496574928 6.240000e-05 60.2
6 TraesCS1D01G276000 chr1A 90.977 1873 122 27 1 1847 471508544 471506693 0.000000e+00 2479.0
7 TraesCS1D01G276000 chr1A 91.404 1524 83 22 3680 5190 471505154 471503666 0.000000e+00 2045.0
8 TraesCS1D01G276000 chr1A 89.467 788 53 18 2482 3251 471506667 471505892 0.000000e+00 968.0
9 TraesCS1D01G276000 chr1A 90.000 390 25 4 3205 3580 471505865 471505476 5.190000e-135 492.0
10 TraesCS1D01G276000 chr3D 96.735 582 19 0 5187 5768 4310671 4310090 0.000000e+00 970.0
11 TraesCS1D01G276000 chr3D 95.361 582 27 0 5187 5768 37550616 37551197 0.000000e+00 926.0
12 TraesCS1D01G276000 chr5D 96.386 581 21 0 5187 5767 107532584 107532004 0.000000e+00 957.0
13 TraesCS1D01G276000 chr3B 95.712 583 24 1 5187 5768 270512 271094 0.000000e+00 937.0
14 TraesCS1D01G276000 chr3A 95.392 586 25 2 5182 5766 1974418 1973834 0.000000e+00 931.0
15 TraesCS1D01G276000 chr3A 95.353 581 26 1 5188 5768 6509146 6508567 0.000000e+00 922.0
16 TraesCS1D01G276000 chr3A 94.889 587 29 1 5182 5768 6608846 6608261 0.000000e+00 917.0
17 TraesCS1D01G276000 chr3A 94.836 581 30 0 5188 5768 6347162 6346582 0.000000e+00 907.0
18 TraesCS1D01G276000 chr3A 94.330 582 31 1 5187 5768 6105293 6104714 0.000000e+00 891.0
19 TraesCS1D01G276000 chr6A 100.000 35 0 0 346 380 214328216 214328250 1.340000e-06 65.8
20 TraesCS1D01G276000 chr4D 93.182 44 2 1 1 43 418721831 418721874 4.830000e-06 63.9


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 TraesCS1D01G276000 chr1D 371781437 371787204 5767 True 4747.5 6071 100.0000 1 5768 2 chr1D.!!$R1 5767
1 TraesCS1D01G276000 chr1B 496568266 496574959 6693 True 1607.3 2562 94.1695 1 5190 4 chr1B.!!$R1 5189
2 TraesCS1D01G276000 chr1A 471503666 471508544 4878 True 1496.0 2479 90.4620 1 5190 4 chr1A.!!$R1 5189
3 TraesCS1D01G276000 chr3D 4310090 4310671 581 True 970.0 970 96.7350 5187 5768 1 chr3D.!!$R1 581
4 TraesCS1D01G276000 chr3D 37550616 37551197 581 False 926.0 926 95.3610 5187 5768 1 chr3D.!!$F1 581
5 TraesCS1D01G276000 chr5D 107532004 107532584 580 True 957.0 957 96.3860 5187 5767 1 chr5D.!!$R1 580
6 TraesCS1D01G276000 chr3B 270512 271094 582 False 937.0 937 95.7120 5187 5768 1 chr3B.!!$F1 581
7 TraesCS1D01G276000 chr3A 1973834 1974418 584 True 931.0 931 95.3920 5182 5766 1 chr3A.!!$R1 584
8 TraesCS1D01G276000 chr3A 6508567 6509146 579 True 922.0 922 95.3530 5188 5768 1 chr3A.!!$R4 580
9 TraesCS1D01G276000 chr3A 6608261 6608846 585 True 917.0 917 94.8890 5182 5768 1 chr3A.!!$R5 586
10 TraesCS1D01G276000 chr3A 6346582 6347162 580 True 907.0 907 94.8360 5188 5768 1 chr3A.!!$R3 580
11 TraesCS1D01G276000 chr3A 6104714 6105293 579 True 891.0 891 94.3300 5187 5768 1 chr3A.!!$R2 581

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
763 2856 0.254747 CGGCCACCCTCTCCATTTTA 59.745 55.000 2.24 0.0 0.00 1.52 F
1252 3356 0.836606 TGGAGAGGATAATGGCGCAA 59.163 50.000 10.83 0.0 0.00 4.85 F
2662 4766 0.967380 AAGGAATTGCGGCCTTGAGG 60.967 55.000 0.00 0.0 42.67 3.86 F
3384 5586 2.133641 GCAGGTGCCAGGTTTGGTT 61.134 57.895 0.00 0.0 46.80 3.67 F
4575 7139 0.034896 CAGGTACACCCTCTTGCGTT 59.965 55.000 0.00 0.0 43.86 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1645 3749 0.383590 TAAGCAACAGCAAAAGCGCA 59.616 45.0 11.47 0.0 0.00 6.09 R
2773 4877 0.108138 CTGAGATTCCACGGACACCC 60.108 60.0 0.00 0.0 0.00 4.61 R
4452 7015 0.250424 TAGCATGTGGGATGATGCCG 60.250 55.0 0.00 0.0 45.13 5.69 R
4745 7309 0.323451 GCCTCTGGAAAACCCCGAAT 60.323 55.0 0.00 0.0 0.00 3.34 R
5595 8181 0.601841 ACACCGCGGTTCGAATTTCT 60.602 50.0 32.11 0.0 41.67 2.52 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
75 2138 4.753107 TCCTGTACGAGTTGTTGGATTTTC 59.247 41.667 0.00 0.00 0.00 2.29
163 2232 1.078759 CGAACCAGTAGAGCCTTGCG 61.079 60.000 0.00 0.00 0.00 4.85
272 2341 4.816392 ACACAATACAATCGCAGACACTA 58.184 39.130 0.00 0.00 42.51 2.74
299 2368 4.847198 ACACTCATCCTTATGAATGCACA 58.153 39.130 0.00 0.00 41.91 4.57
302 2371 5.124297 CACTCATCCTTATGAATGCACACAA 59.876 40.000 0.00 0.00 41.57 3.33
322 2395 1.153369 CACGCACATCCACCCCTAG 60.153 63.158 0.00 0.00 0.00 3.02
344 2417 2.550606 GAGCACCTCCGAGATACAGTAG 59.449 54.545 0.00 0.00 0.00 2.57
348 2421 3.945921 CACCTCCGAGATACAGTAGTGAA 59.054 47.826 4.09 0.00 0.00 3.18
349 2422 3.946558 ACCTCCGAGATACAGTAGTGAAC 59.053 47.826 4.09 0.00 0.00 3.18
357 2430 4.705507 AGATACAGTAGTGAACCGACACAT 59.294 41.667 4.09 0.00 42.45 3.21
402 2475 1.002366 TAGGCGTCTCGTAAGTCGAC 58.998 55.000 7.70 7.70 44.01 4.20
419 2492 3.315749 GTCGACGAGAACATATCTTCCCT 59.684 47.826 0.00 0.00 38.96 4.20
423 2496 2.029828 CGAGAACATATCTTCCCTCCGG 60.030 54.545 0.00 0.00 38.96 5.14
443 2516 2.480419 GGACGAACATCACAGGAAAGTG 59.520 50.000 0.00 0.00 40.85 3.16
494 2568 9.349713 ACACCAGTGTCAAATCTAGAATTTAAA 57.650 29.630 0.00 0.00 40.24 1.52
498 2572 9.014297 CAGTGTCAAATCTAGAATTTAAACCCT 57.986 33.333 0.00 0.00 0.00 4.34
500 2574 9.010029 GTGTCAAATCTAGAATTTAAACCCTGA 57.990 33.333 0.00 0.00 0.00 3.86
506 2585 9.753674 AATCTAGAATTTAAACCCTGATGACAA 57.246 29.630 0.00 0.00 0.00 3.18
667 2749 3.572584 GACTCGGTAATCACGTGTTTCT 58.427 45.455 16.51 1.19 38.05 2.52
671 2753 3.495377 TCGGTAATCACGTGTTTCTTTGG 59.505 43.478 16.51 3.03 0.00 3.28
672 2754 3.495377 CGGTAATCACGTGTTTCTTTGGA 59.505 43.478 16.51 0.00 0.00 3.53
673 2755 4.153475 CGGTAATCACGTGTTTCTTTGGAT 59.847 41.667 16.51 0.00 0.00 3.41
674 2756 5.334569 CGGTAATCACGTGTTTCTTTGGATT 60.335 40.000 16.51 6.98 0.00 3.01
694 2780 7.428020 TGGATTGATTCGAAATCATCAAATCC 58.572 34.615 14.07 17.76 41.58 3.01
763 2856 0.254747 CGGCCACCCTCTCCATTTTA 59.745 55.000 2.24 0.00 0.00 1.52
767 2860 3.774766 GGCCACCCTCTCCATTTTATTTT 59.225 43.478 0.00 0.00 0.00 1.82
768 2861 4.959839 GGCCACCCTCTCCATTTTATTTTA 59.040 41.667 0.00 0.00 0.00 1.52
769 2862 5.602561 GGCCACCCTCTCCATTTTATTTTAT 59.397 40.000 0.00 0.00 0.00 1.40
770 2863 6.099701 GGCCACCCTCTCCATTTTATTTTATT 59.900 38.462 0.00 0.00 0.00 1.40
771 2864 7.365563 GGCCACCCTCTCCATTTTATTTTATTT 60.366 37.037 0.00 0.00 0.00 1.40
772 2865 8.046708 GCCACCCTCTCCATTTTATTTTATTTT 58.953 33.333 0.00 0.00 0.00 1.82
989 3093 3.617824 CCGCAATCTCGGTCATCG 58.382 61.111 0.00 0.00 44.18 3.84
994 3098 1.471676 GCAATCTCGGTCATCGGTTCT 60.472 52.381 0.00 0.00 39.77 3.01
1113 3217 1.615107 CGACGCGTTTCCTGAGGAAC 61.615 60.000 14.62 8.45 41.87 3.62
1215 3319 0.976073 CCATGTACGACCTCCACCCT 60.976 60.000 0.00 0.00 0.00 4.34
1252 3356 0.836606 TGGAGAGGATAATGGCGCAA 59.163 50.000 10.83 0.00 0.00 4.85
1446 3550 2.724977 TCTGGATCGTGAACACTGAC 57.275 50.000 3.51 0.00 0.00 3.51
1670 3774 4.375305 CGCTTTTGCTGTTGCTTAATTGAC 60.375 41.667 0.00 0.00 44.80 3.18
1693 3797 6.446318 ACGTAGAATTTGTGAATTGCAACAT 58.554 32.000 0.00 0.00 35.65 2.71
1844 3948 5.769662 TGTGCTTTGACTGAAAGGAATATGT 59.230 36.000 0.00 0.00 42.98 2.29
1845 3949 6.939730 TGTGCTTTGACTGAAAGGAATATGTA 59.060 34.615 0.00 0.00 42.98 2.29
1848 3952 8.855110 TGCTTTGACTGAAAGGAATATGTAAAA 58.145 29.630 0.00 0.00 38.91 1.52
1849 3953 9.691362 GCTTTGACTGAAAGGAATATGTAAAAA 57.309 29.630 0.00 0.00 41.41 1.94
2596 4700 3.928727 TTAACTGTCGGAATCGTGACT 57.071 42.857 5.98 0.00 36.10 3.41
2623 4727 4.518970 CCGTTTTCATTTGAGGGAAGAAGA 59.481 41.667 0.00 0.00 0.00 2.87
2662 4766 0.967380 AAGGAATTGCGGCCTTGAGG 60.967 55.000 0.00 0.00 42.67 3.86
2773 4877 2.344950 GCAGATGATATTCTCCGGCAG 58.655 52.381 0.00 0.00 0.00 4.85
2820 4924 7.895975 TCATCACTGTAAGATAATATGCTGC 57.104 36.000 0.00 0.00 37.43 5.25
2821 4925 7.674120 TCATCACTGTAAGATAATATGCTGCT 58.326 34.615 0.00 0.00 37.43 4.24
2832 4944 8.489676 AGATAATATGCTGCTATGCTATACCT 57.510 34.615 0.00 0.00 0.00 3.08
2834 4946 3.516981 ATGCTGCTATGCTATACCTCG 57.483 47.619 0.00 0.00 0.00 4.63
2855 4967 6.687105 CCTCGTGTTAGCTATTTTACATTTGC 59.313 38.462 0.00 0.00 0.00 3.68
2883 4995 3.916761 TGATTTGAAAGAAGTGGCATGC 58.083 40.909 9.90 9.90 0.00 4.06
2930 5043 5.008217 TGGTTTACAGTTTACACACTCATGC 59.992 40.000 0.00 0.00 0.00 4.06
2933 5046 4.552166 ACAGTTTACACACTCATGCAAC 57.448 40.909 0.00 0.00 0.00 4.17
2941 5054 4.194640 ACACACTCATGCAACTATGGATC 58.805 43.478 0.00 0.00 35.11 3.36
2953 5066 5.238214 GCAACTATGGATCAACAATCTCCTC 59.762 44.000 0.00 0.00 34.56 3.71
2965 5078 3.054065 ACAATCTCCTCTGACCATTTCCC 60.054 47.826 0.00 0.00 0.00 3.97
3005 5120 6.980593 TGTGTTCCAAAATTATCACCTTCAG 58.019 36.000 0.00 0.00 0.00 3.02
3031 5156 8.404107 ACTATGCAGCGGGTTTAAATTATTAT 57.596 30.769 0.00 0.00 0.00 1.28
3164 5289 6.547510 ACAGGATAAAAGTAGAATCCCATTGC 59.452 38.462 0.00 0.00 40.11 3.56
3165 5290 6.015940 CAGGATAAAAGTAGAATCCCATTGCC 60.016 42.308 0.00 0.00 40.11 4.52
3174 5303 3.136443 AGAATCCCATTGCCGACTATTGA 59.864 43.478 0.00 0.00 0.00 2.57
3347 5549 4.177165 TGCAGCTAAACATGTGATTTGG 57.823 40.909 0.00 0.00 0.00 3.28
3384 5586 2.133641 GCAGGTGCCAGGTTTGGTT 61.134 57.895 0.00 0.00 46.80 3.67
3478 5680 5.221441 GCAACAGGTTAAATTTCAGGGAACT 60.221 40.000 0.00 0.00 46.44 3.01
3502 5704 9.979578 ACTTTATTTGTTCAACATCAAATGCTA 57.020 25.926 11.66 0.00 42.01 3.49
3558 5763 7.100458 AGAGTTAATGCTTGTTGTGAAACTT 57.900 32.000 0.00 0.00 38.04 2.66
3626 6063 5.823045 ACTTGATTTTCTCCGTTGAAAGTCT 59.177 36.000 17.12 2.93 40.76 3.24
3627 6064 5.924475 TGATTTTCTCCGTTGAAAGTCTC 57.076 39.130 17.12 9.79 40.76 3.36
3628 6065 5.611374 TGATTTTCTCCGTTGAAAGTCTCT 58.389 37.500 17.12 0.00 40.76 3.10
3629 6066 5.696724 TGATTTTCTCCGTTGAAAGTCTCTC 59.303 40.000 17.12 6.68 40.76 3.20
3630 6067 4.939052 TTTCTCCGTTGAAAGTCTCTCT 57.061 40.909 0.00 0.00 32.82 3.10
3631 6068 4.506886 TTCTCCGTTGAAAGTCTCTCTC 57.493 45.455 0.00 0.00 0.00 3.20
3632 6069 3.757270 TCTCCGTTGAAAGTCTCTCTCT 58.243 45.455 0.00 0.00 0.00 3.10
3633 6070 3.754323 TCTCCGTTGAAAGTCTCTCTCTC 59.246 47.826 0.00 0.00 0.00 3.20
3634 6071 3.756434 CTCCGTTGAAAGTCTCTCTCTCT 59.244 47.826 0.00 0.00 0.00 3.10
3635 6072 3.754323 TCCGTTGAAAGTCTCTCTCTCTC 59.246 47.826 0.00 0.00 0.00 3.20
3636 6073 3.756434 CCGTTGAAAGTCTCTCTCTCTCT 59.244 47.826 0.00 0.00 0.00 3.10
3638 6075 4.695455 CGTTGAAAGTCTCTCTCTCTCTCT 59.305 45.833 0.00 0.00 0.00 3.10
3640 6077 5.762179 TGAAAGTCTCTCTCTCTCTCTCT 57.238 43.478 0.00 0.00 0.00 3.10
3641 6078 5.734720 TGAAAGTCTCTCTCTCTCTCTCTC 58.265 45.833 0.00 0.00 0.00 3.20
3642 6079 5.485353 TGAAAGTCTCTCTCTCTCTCTCTCT 59.515 44.000 0.00 0.00 0.00 3.10
3643 6080 5.606348 AAGTCTCTCTCTCTCTCTCTCTC 57.394 47.826 0.00 0.00 0.00 3.20
3645 6082 4.892934 AGTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.00 0.00 3.20
3646 6083 4.892934 GTCTCTCTCTCTCTCTCTCTCTCT 59.107 50.000 0.00 0.00 0.00 3.10
3647 6084 5.009610 GTCTCTCTCTCTCTCTCTCTCTCTC 59.990 52.000 0.00 0.00 0.00 3.20
3648 6085 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3649 6086 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3650 6087 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
3651 6088 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
3654 6091 6.857848 TCTCTCTCTCTCTCTCTCTCTCTAT 58.142 44.000 0.00 0.00 0.00 1.98
3655 6092 7.990055 TCTCTCTCTCTCTCTCTCTCTCTATA 58.010 42.308 0.00 0.00 0.00 1.31
3657 6094 9.913310 CTCTCTCTCTCTCTCTCTCTCTATATA 57.087 40.741 0.00 0.00 0.00 0.86
3963 6401 5.186021 AGTGACCTAACATTGACAGAGGTAG 59.814 44.000 0.00 0.00 40.65 3.18
4116 6679 3.864789 TCTAAATCAGGCCTCATTCCC 57.135 47.619 0.85 0.00 0.00 3.97
4437 7000 5.908341 TCAAAGACAATTAAAACACACCCC 58.092 37.500 0.00 0.00 0.00 4.95
4452 7015 1.283487 CCCCGGTAAACAAACGCAC 59.717 57.895 0.00 0.00 0.00 5.34
4463 7027 2.406616 AAACGCACGGCATCATCCC 61.407 57.895 0.00 0.00 0.00 3.85
4575 7139 0.034896 CAGGTACACCCTCTTGCGTT 59.965 55.000 0.00 0.00 43.86 4.84
4576 7140 0.320697 AGGTACACCCTCTTGCGTTC 59.679 55.000 0.00 0.00 40.71 3.95
4577 7141 0.672711 GGTACACCCTCTTGCGTTCC 60.673 60.000 0.00 0.00 0.00 3.62
4745 7309 1.485294 TTCCTACAGCGGAAAGGGCA 61.485 55.000 9.33 0.00 39.99 5.36
4770 7334 1.073923 GGGTTTTCCAGAGGCTGAAGA 59.926 52.381 0.00 0.00 42.91 2.87
4771 7335 2.155279 GGTTTTCCAGAGGCTGAAGAC 58.845 52.381 0.00 0.00 40.31 3.01
4807 7371 3.051081 AGCTCATCTTTCCAGTGTCAC 57.949 47.619 0.00 0.00 0.00 3.67
4843 7426 8.254508 CAGTAGACTCTTAGTTATGCCTTTCTT 58.745 37.037 0.00 0.00 0.00 2.52
4856 7439 5.675684 TGCCTTTCTTCTTTGTTTCCTTT 57.324 34.783 0.00 0.00 0.00 3.11
4858 7441 5.186797 TGCCTTTCTTCTTTGTTTCCTTTCA 59.813 36.000 0.00 0.00 0.00 2.69
4929 7512 8.554528 AGTGCATATGAAATCGTATCTTTTCAG 58.445 33.333 6.97 0.00 43.05 3.02
4930 7513 7.322222 GTGCATATGAAATCGTATCTTTTCAGC 59.678 37.037 6.97 3.67 43.05 4.26
4936 7519 5.950965 AATCGTATCTTTTCAGCGTGTAG 57.049 39.130 0.00 0.00 0.00 2.74
4967 7550 0.103937 CGGTCTCTTCTCAGCCATCC 59.896 60.000 0.00 0.00 0.00 3.51
4968 7551 0.103937 GGTCTCTTCTCAGCCATCCG 59.896 60.000 0.00 0.00 0.00 4.18
5000 7583 1.322442 GGAGCTTTGCTTGTTCCTGT 58.678 50.000 0.00 0.00 39.88 4.00
5003 7586 1.032014 GCTTTGCTTGTTCCTGTGGA 58.968 50.000 0.00 0.00 0.00 4.02
5011 7594 4.892934 TGCTTGTTCCTGTGGAAAATAAGT 59.107 37.500 0.12 0.00 43.86 2.24
5036 7619 5.785599 CGATTCTTGTGAAATTCTCGTGTTC 59.214 40.000 0.00 0.00 35.63 3.18
5072 7655 0.530870 GCTGGGTTACATCGAGCCTC 60.531 60.000 0.00 0.00 35.71 4.70
5135 7718 2.015587 GACGAGAGGTTGGTAGACGAT 58.984 52.381 0.00 0.00 0.00 3.73
5167 7750 7.786178 TGAACCATTGTATGTACTAGCATTC 57.214 36.000 0.00 0.00 0.00 2.67
5202 7785 6.235231 TCTCTTGCTTTAATCGATACCCTT 57.765 37.500 0.00 0.00 0.00 3.95
5338 7921 0.095935 CAAGGCTGATTCGCTCGTTG 59.904 55.000 0.00 0.00 0.00 4.10
5381 7965 7.408756 AATACTTTCAAATGCTAGCCAATGA 57.591 32.000 13.29 10.59 0.00 2.57
5386 7970 4.529897 TCAAATGCTAGCCAATGACAGAT 58.470 39.130 13.29 0.00 0.00 2.90
5418 8002 4.002906 ACGTATCTTTGCTCTTGACCAA 57.997 40.909 0.00 0.00 0.00 3.67
5545 8130 5.215069 AGTCTATCACTCATGACATCCCTT 58.785 41.667 0.00 0.00 37.79 3.95
5595 8181 7.745717 TCTTAACCTCTCCATTTTCTGAAGAA 58.254 34.615 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 2107 3.243336 CAACTCGTACAGGAGTAGTTGC 58.757 50.000 5.10 0.00 46.21 4.17
75 2138 4.034510 GCTACATCAACATTTCTCTTCGGG 59.965 45.833 0.00 0.00 0.00 5.14
163 2232 3.057174 TCATGGGTGTGGTTAATTTTCGC 60.057 43.478 0.00 0.00 0.00 4.70
248 2317 5.419542 AGTGTCTGCGATTGTATTGTGTAT 58.580 37.500 0.00 0.00 0.00 2.29
249 2318 4.816392 AGTGTCTGCGATTGTATTGTGTA 58.184 39.130 0.00 0.00 0.00 2.90
255 2324 8.577296 AGTGTATATTAGTGTCTGCGATTGTAT 58.423 33.333 0.00 0.00 0.00 2.29
272 2341 9.224267 GTGCATTCATAAGGATGAGTGTATATT 57.776 33.333 10.81 0.00 46.40 1.28
299 2368 2.260869 GGTGGATGTGCGTGCTTGT 61.261 57.895 0.00 0.00 0.00 3.16
302 2371 4.722700 GGGGTGGATGTGCGTGCT 62.723 66.667 0.00 0.00 0.00 4.40
322 2395 0.671251 CTGTATCTCGGAGGTGCTCC 59.329 60.000 7.86 0.00 46.44 4.70
344 2417 6.236017 TCTTAAAATGATGTGTCGGTTCAC 57.764 37.500 0.00 0.00 38.63 3.18
348 2421 7.390440 TCTTCAATCTTAAAATGATGTGTCGGT 59.610 33.333 0.00 0.00 0.00 4.69
349 2422 7.751732 TCTTCAATCTTAAAATGATGTGTCGG 58.248 34.615 0.00 0.00 0.00 4.79
402 2475 3.290308 CGGAGGGAAGATATGTTCTCG 57.710 52.381 11.96 7.78 31.60 4.04
419 2492 0.896479 TCCTGTGATGTTCGTCCGGA 60.896 55.000 0.00 0.00 0.00 5.14
423 2496 3.059597 CACACTTTCCTGTGATGTTCGTC 60.060 47.826 1.47 0.00 43.77 4.20
464 2538 6.605471 TCTAGATTTGACACTGGTGTACAT 57.395 37.500 6.35 0.00 45.05 2.29
891 2988 4.944372 GGATAGGCGGACGGTGCG 62.944 72.222 18.03 18.03 0.00 5.34
984 3088 2.362397 GCTCATACCTCAGAACCGATGA 59.638 50.000 0.00 0.00 0.00 2.92
989 3093 3.181470 GGAGAAGCTCATACCTCAGAACC 60.181 52.174 0.00 0.00 31.08 3.62
994 3098 2.820178 TGTGGAGAAGCTCATACCTCA 58.180 47.619 0.00 0.00 31.08 3.86
1041 3145 2.592861 GGATCCAGATGGCGTGCC 60.593 66.667 6.95 3.30 34.44 5.01
1215 3319 4.009002 CTCCATAGAGCATCGAGATCTCA 58.991 47.826 22.31 10.04 39.11 3.27
1446 3550 2.288702 CGACATCCTCATAGCCTGGAAG 60.289 54.545 0.00 0.00 33.20 3.46
1643 3747 1.147557 AGCAACAGCAAAAGCGCAAC 61.148 50.000 11.47 0.00 0.00 4.17
1645 3749 0.383590 TAAGCAACAGCAAAAGCGCA 59.616 45.000 11.47 0.00 0.00 6.09
1647 3751 3.735240 TCAATTAAGCAACAGCAAAAGCG 59.265 39.130 0.00 0.00 0.00 4.68
1670 3774 6.803320 AGATGTTGCAATTCACAAATTCTACG 59.197 34.615 0.59 0.00 32.69 3.51
1693 3797 7.544804 TCTCTATATTAGATGCCAAGCAAGA 57.455 36.000 0.00 0.00 43.62 3.02
2596 4700 4.627284 TCCCTCAAATGAAAACGGAGTA 57.373 40.909 0.00 0.00 45.00 2.59
2662 4766 4.568359 ACGATCAGTGTATCAACATTGCTC 59.432 41.667 0.00 0.00 41.69 4.26
2773 4877 0.108138 CTGAGATTCCACGGACACCC 60.108 60.000 0.00 0.00 0.00 4.61
2814 4918 2.828520 ACGAGGTATAGCATAGCAGCAT 59.171 45.455 4.48 0.00 36.85 3.79
2815 4919 2.029918 CACGAGGTATAGCATAGCAGCA 60.030 50.000 4.48 0.00 36.85 4.41
2816 4920 2.029828 ACACGAGGTATAGCATAGCAGC 60.030 50.000 4.48 0.00 0.00 5.25
2817 4921 3.924918 ACACGAGGTATAGCATAGCAG 57.075 47.619 4.48 4.71 0.00 4.24
2818 4922 4.321008 GCTAACACGAGGTATAGCATAGCA 60.321 45.833 4.48 0.00 36.73 3.49
2819 4923 4.082679 AGCTAACACGAGGTATAGCATAGC 60.083 45.833 4.48 7.88 37.97 2.97
2820 4924 5.630661 AGCTAACACGAGGTATAGCATAG 57.369 43.478 4.48 0.00 37.97 2.23
2821 4925 7.698506 AATAGCTAACACGAGGTATAGCATA 57.301 36.000 4.48 6.71 38.81 3.14
2829 4941 7.625606 GCAAATGTAAAATAGCTAACACGAGGT 60.626 37.037 0.00 0.00 0.00 3.85
2832 4944 6.149640 TGGCAAATGTAAAATAGCTAACACGA 59.850 34.615 0.00 0.00 0.00 4.35
2834 4946 7.812669 ACTTGGCAAATGTAAAATAGCTAACAC 59.187 33.333 0.00 0.00 0.00 3.32
2855 4967 6.095377 GCCACTTCTTTCAAATCATACTTGG 58.905 40.000 0.00 0.00 0.00 3.61
2868 4980 1.470098 ACATCGCATGCCACTTCTTTC 59.530 47.619 13.15 0.00 0.00 2.62
2883 4995 6.636850 CCAAACTTGGTTTTCTTAAGACATCG 59.363 38.462 4.18 0.00 43.43 3.84
2930 5043 6.482641 CAGAGGAGATTGTTGATCCATAGTTG 59.517 42.308 0.00 0.00 35.21 3.16
2933 5046 6.222389 GTCAGAGGAGATTGTTGATCCATAG 58.778 44.000 0.00 0.00 35.21 2.23
2941 5054 4.397417 GGAAATGGTCAGAGGAGATTGTTG 59.603 45.833 0.00 0.00 0.00 3.33
2953 5066 3.420893 TGCTAAACAGGGAAATGGTCAG 58.579 45.455 0.00 0.00 0.00 3.51
2982 5097 7.040409 AGTCTGAAGGTGATAATTTTGGAACAC 60.040 37.037 0.00 0.00 39.29 3.32
2994 5109 3.243535 CGCTGCATAGTCTGAAGGTGATA 60.244 47.826 0.00 0.00 30.11 2.15
3005 5120 4.632538 AATTTAAACCCGCTGCATAGTC 57.367 40.909 0.00 0.00 0.00 2.59
3031 5156 6.158520 TGGATCAGGAATGAACTAGGAATCAA 59.841 38.462 0.00 0.00 0.00 2.57
3384 5586 5.929415 TCGTACATCAGCAAAGTCAACATTA 59.071 36.000 0.00 0.00 0.00 1.90
3478 5680 9.755804 TGTAGCATTTGATGTTGAACAAATAAA 57.244 25.926 0.62 4.92 42.35 1.40
3618 5943 5.485353 AGAGAGAGAGAGAGAGAGACTTTCA 59.515 44.000 0.00 0.00 32.94 2.69
3626 6063 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3627 6064 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3628 6065 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
3629 6066 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
3630 6067 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
3631 6068 8.821686 ATATAGAGAGAGAGAGAGAGAGAGAG 57.178 42.308 0.00 0.00 0.00 3.20
3697 6134 6.601217 TCAATATAACTGCATAAAGCCACACA 59.399 34.615 0.00 0.00 44.83 3.72
3698 6135 6.912591 GTCAATATAACTGCATAAAGCCACAC 59.087 38.462 0.00 0.00 44.83 3.82
3963 6401 4.026475 GTCTAACAGAGATTGTGCGTATGC 60.026 45.833 0.00 0.00 40.74 3.14
4026 6464 4.215399 GCTTAGCTTGTTATGTTGGTCACA 59.785 41.667 0.00 0.00 40.71 3.58
4110 6673 5.464168 CAAGCTCAAAGTTACAAGGGAATG 58.536 41.667 0.00 0.00 0.00 2.67
4116 6679 4.035558 TCAGTGCAAGCTCAAAGTTACAAG 59.964 41.667 0.00 0.00 0.00 3.16
4422 6985 4.648307 TGTTTACCGGGGTGTGTTTTAATT 59.352 37.500 6.32 0.00 0.00 1.40
4423 6986 4.213513 TGTTTACCGGGGTGTGTTTTAAT 58.786 39.130 6.32 0.00 0.00 1.40
4437 7000 1.723197 GCCGTGCGTTTGTTTACCG 60.723 57.895 0.00 0.00 0.00 4.02
4452 7015 0.250424 TAGCATGTGGGATGATGCCG 60.250 55.000 0.00 0.00 45.13 5.69
4463 7027 4.037923 GGGGTTCCATGTTATTAGCATGTG 59.962 45.833 16.34 9.82 41.38 3.21
4575 7139 2.561419 CAGAAAGTAGTCGGTGGAAGGA 59.439 50.000 0.00 0.00 0.00 3.36
4576 7140 2.931320 GCAGAAAGTAGTCGGTGGAAGG 60.931 54.545 0.00 0.00 0.00 3.46
4577 7141 2.028930 AGCAGAAAGTAGTCGGTGGAAG 60.029 50.000 0.00 0.00 0.00 3.46
4745 7309 0.323451 GCCTCTGGAAAACCCCGAAT 60.323 55.000 0.00 0.00 0.00 3.34
4807 7371 3.840890 AGAGTCTACTGCAAGAACTCG 57.159 47.619 10.67 0.00 42.21 4.18
4843 7426 6.183360 GCTTTTGCAATGAAAGGAAACAAAGA 60.183 34.615 0.00 0.00 46.58 2.52
4858 7441 6.127619 GGTCTATCACCTAAAGCTTTTGCAAT 60.128 38.462 18.47 10.56 44.94 3.56
4967 7550 2.824041 CTCCAAACGGGGCCATCG 60.824 66.667 14.89 14.89 37.22 3.84
4968 7551 3.140814 GCTCCAAACGGGGCCATC 61.141 66.667 4.39 0.00 37.22 3.51
4976 7559 2.119457 GAACAAGCAAAGCTCCAAACG 58.881 47.619 0.00 0.00 38.25 3.60
5000 7583 7.737972 TTCACAAGAATCGACTTATTTTCCA 57.262 32.000 0.00 0.00 0.00 3.53
5011 7594 4.988540 ACACGAGAATTTCACAAGAATCGA 59.011 37.500 8.40 0.00 36.53 3.59
5072 7655 6.368791 TCTTATTTGAACACAACAGGAGATCG 59.631 38.462 0.00 0.00 0.00 3.69
5079 7662 8.724229 TCATCTGATCTTATTTGAACACAACAG 58.276 33.333 0.00 0.00 0.00 3.16
5118 7701 2.359531 CCTCATCGTCTACCAACCTCTC 59.640 54.545 0.00 0.00 0.00 3.20
5150 7733 6.317893 TGTCGAGAGAATGCTAGTACATACAA 59.682 38.462 0.00 0.00 45.01 2.41
5157 7740 7.067615 AGAGAAAATGTCGAGAGAATGCTAGTA 59.932 37.037 0.00 0.00 45.01 1.82
5158 7741 5.971763 AGAAAATGTCGAGAGAATGCTAGT 58.028 37.500 0.00 0.00 45.01 2.57
5159 7742 6.272318 AGAGAAAATGTCGAGAGAATGCTAG 58.728 40.000 0.00 0.00 45.01 3.42
5167 7750 5.604010 AAAGCAAGAGAAAATGTCGAGAG 57.396 39.130 0.00 0.00 0.00 3.20
5202 7785 3.278574 CCTCACCTCCGCAATTTTATCA 58.721 45.455 0.00 0.00 0.00 2.15
5386 7970 9.871238 AAGAGCAAAGATACGTTTCTTTCTATA 57.129 29.630 25.13 0.00 42.58 1.31
5418 8002 1.123928 CCTCAATACGGCCTTCCTCT 58.876 55.000 0.00 0.00 0.00 3.69
5545 8130 6.627395 TTCATTTTCCGCTTCTGAAACTTA 57.373 33.333 0.00 0.00 31.78 2.24
5595 8181 0.601841 ACACCGCGGTTCGAATTTCT 60.602 50.000 32.11 0.00 41.67 2.52
5651 8237 5.975693 TTGATAAAACTCTGCCGGAAAAT 57.024 34.783 5.05 0.00 0.00 1.82
5725 8311 6.296803 GGGAAATATCAAGGTCTTCGGTATT 58.703 40.000 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.