Multiple sequence alignment - TraesCS2B01G438400

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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 TraesCS2B01G438400 chr2B 100.000 6495 0 0 1 6495 630727709 630734203 0.000000e+00 11995.0
1 TraesCS2B01G438400 chr2B 83.515 2105 238 43 1373 3387 630739833 630741918 0.000000e+00 1864.0
2 TraesCS2B01G438400 chr2B 84.526 1467 167 27 3981 5410 630741915 630743358 0.000000e+00 1397.0
3 TraesCS2B01G438400 chr2B 90.819 1013 58 15 1111 2116 630770607 630771591 0.000000e+00 1323.0
4 TraesCS2B01G438400 chr2B 94.737 703 25 10 1 695 489315630 489314932 0.000000e+00 1083.0
5 TraesCS2B01G438400 chr2B 94.034 704 28 9 1 691 374803946 374804648 0.000000e+00 1055.0
6 TraesCS2B01G438400 chr2B 93.644 708 27 10 1 691 51994933 51995639 0.000000e+00 1042.0
7 TraesCS2B01G438400 chr2B 87.125 567 50 9 2119 2676 630771799 630772351 7.150000e-174 621.0
8 TraesCS2B01G438400 chr2B 87.893 413 33 10 5453 5853 630743356 630743763 2.740000e-128 470.0
9 TraesCS2B01G438400 chr2B 81.768 362 37 11 3082 3439 630772394 630772730 6.410000e-70 276.0
10 TraesCS2B01G438400 chr2B 94.079 152 9 0 1111 1262 630739657 630739808 1.410000e-56 231.0
11 TraesCS2B01G438400 chr2B 79.755 326 30 21 794 1096 630739390 630739702 3.070000e-48 204.0
12 TraesCS2B01G438400 chr2B 93.421 76 5 0 1081 1156 630728759 630728834 5.320000e-21 113.0
13 TraesCS2B01G438400 chr2B 93.421 76 5 0 1051 1126 630728789 630728864 5.320000e-21 113.0
14 TraesCS2B01G438400 chr2B 83.065 124 15 4 6087 6204 110829762 110829639 2.480000e-19 108.0
15 TraesCS2B01G438400 chr2B 100.000 29 0 0 6087 6115 236042620 236042592 3.000000e-03 54.7
16 TraesCS2B01G438400 chr2D 95.390 4208 105 39 787 4981 530382708 530386839 0.000000e+00 6613.0
17 TraesCS2B01G438400 chr2D 89.224 1559 126 19 1136 2677 531201050 531202583 0.000000e+00 1910.0
18 TraesCS2B01G438400 chr2D 89.967 1495 79 26 5025 6495 530386836 530388283 0.000000e+00 1864.0
19 TraesCS2B01G438400 chr2D 83.592 1548 172 34 1373 2868 531043599 531045116 0.000000e+00 1376.0
20 TraesCS2B01G438400 chr2D 82.958 1420 145 42 4647 6032 531047043 531048399 0.000000e+00 1192.0
21 TraesCS2B01G438400 chr2D 84.108 925 93 28 3765 4663 531046091 531046987 0.000000e+00 845.0
22 TraesCS2B01G438400 chr2D 84.973 752 68 22 2975 3686 531045351 531046097 0.000000e+00 721.0
23 TraesCS2B01G438400 chr2D 84.857 350 36 5 3082 3429 531202624 531202958 2.900000e-88 337.0
24 TraesCS2B01G438400 chr2D 94.737 152 8 0 1111 1262 531043423 531043574 3.030000e-58 237.0
25 TraesCS2B01G438400 chr2D 91.026 156 3 6 693 837 530382644 530382799 3.970000e-47 200.0
26 TraesCS2B01G438400 chr2D 97.368 38 1 0 6192 6229 531048480 531048517 1.510000e-06 65.8
27 TraesCS2B01G438400 chr2D 94.737 38 2 0 1111 1148 531201013 531201050 7.030000e-05 60.2
28 TraesCS2B01G438400 chr2D 100.000 30 0 0 3737 3766 78531458 78531429 1.000000e-03 56.5
29 TraesCS2B01G438400 chr2A 88.868 1599 121 23 1111 2677 675582539 675584112 0.000000e+00 1914.0
30 TraesCS2B01G438400 chr2A 82.135 1920 202 49 1009 2868 675302103 675303941 0.000000e+00 1515.0
31 TraesCS2B01G438400 chr2A 83.451 1420 141 43 4647 6032 675305870 675307229 0.000000e+00 1234.0
32 TraesCS2B01G438400 chr2A 84.783 920 92 25 3765 4663 675304919 675305811 0.000000e+00 880.0
33 TraesCS2B01G438400 chr2A 85.734 743 70 17 2975 3686 675304188 675304925 0.000000e+00 752.0
34 TraesCS2B01G438400 chr2A 84.857 350 36 5 3082 3429 675584153 675584487 2.900000e-88 337.0
35 TraesCS2B01G438400 chr2A 89.474 95 9 1 6090 6183 721520777 721520871 1.140000e-22 119.0
36 TraesCS2B01G438400 chr2A 89.706 68 7 0 991 1058 675302034 675302101 3.230000e-13 87.9
37 TraesCS2B01G438400 chr2A 94.737 38 2 0 6192 6229 675307310 675307347 7.030000e-05 60.2
38 TraesCS2B01G438400 chr2A 97.059 34 1 0 3737 3770 92494449 92494416 2.530000e-04 58.4
39 TraesCS2B01G438400 chr7B 93.644 708 27 10 1 691 639080813 639081519 0.000000e+00 1042.0
40 TraesCS2B01G438400 chr7B 83.193 119 17 3 6089 6204 304125864 304125982 8.910000e-19 106.0
41 TraesCS2B01G438400 chr4A 93.608 704 29 10 1 691 444548405 444549105 0.000000e+00 1037.0
42 TraesCS2B01G438400 chr4A 89.655 87 7 2 6106 6190 36370509 36370423 6.890000e-20 110.0
43 TraesCS2B01G438400 chr3B 92.740 730 27 16 1 708 89378555 89379280 0.000000e+00 1031.0
44 TraesCS2B01G438400 chr3B 93.089 709 31 12 1 695 215310047 215309343 0.000000e+00 1022.0
45 TraesCS2B01G438400 chr5B 93.324 704 32 13 1 691 411229928 411229227 0.000000e+00 1026.0
46 TraesCS2B01G438400 chr1D 93.447 702 29 13 1 691 464380100 464380795 0.000000e+00 1026.0
47 TraesCS2B01G438400 chr1D 82.927 123 18 2 6089 6208 214849680 214849802 2.480000e-19 108.0
48 TraesCS2B01G438400 chr1D 96.970 33 0 1 3737 3769 240590285 240590254 3.000000e-03 54.7
49 TraesCS2B01G438400 chr1D 92.105 38 2 1 3727 3764 280717582 280717618 1.200000e-02 52.8
50 TraesCS2B01G438400 chr4D 88.119 101 11 1 6086 6185 505434783 505434683 1.140000e-22 119.0
51 TraesCS2B01G438400 chr4D 94.595 37 1 1 3729 3764 497653408 497653372 1.000000e-03 56.5
52 TraesCS2B01G438400 chr3A 89.583 96 5 5 6080 6173 680747532 680747440 4.110000e-22 117.0
53 TraesCS2B01G438400 chr6B 85.849 106 11 4 6106 6207 100906549 100906654 6.890000e-20 110.0
54 TraesCS2B01G438400 chr1A 85.526 76 7 1 3689 3764 352870998 352871069 6.980000e-10 76.8
55 TraesCS2B01G438400 chr6A 94.872 39 2 0 3692 3730 542237410 542237372 1.960000e-05 62.1
56 TraesCS2B01G438400 chr6D 100.000 30 0 0 3737 3766 351107268 351107239 1.000000e-03 56.5
57 TraesCS2B01G438400 chr4B 97.059 34 0 1 3737 3770 561643371 561643403 1.000000e-03 56.5


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 TraesCS2B01G438400 chr2B 630727709 630734203 6494 False 11995.000000 11995 100.000000 1 6495 1 chr2B.!!$F3 6494
1 TraesCS2B01G438400 chr2B 489314932 489315630 698 True 1083.000000 1083 94.737000 1 695 1 chr2B.!!$R3 694
2 TraesCS2B01G438400 chr2B 374803946 374804648 702 False 1055.000000 1055 94.034000 1 691 1 chr2B.!!$F2 690
3 TraesCS2B01G438400 chr2B 51994933 51995639 706 False 1042.000000 1042 93.644000 1 691 1 chr2B.!!$F1 690
4 TraesCS2B01G438400 chr2B 630739390 630743763 4373 False 833.200000 1864 85.953600 794 5853 5 chr2B.!!$F5 5059
5 TraesCS2B01G438400 chr2B 630770607 630772730 2123 False 740.000000 1323 86.570667 1111 3439 3 chr2B.!!$F6 2328
6 TraesCS2B01G438400 chr2D 530382644 530388283 5639 False 2892.333333 6613 92.127667 693 6495 3 chr2D.!!$F1 5802
7 TraesCS2B01G438400 chr2D 531201013 531202958 1945 False 769.066667 1910 89.606000 1111 3429 3 chr2D.!!$F3 2318
8 TraesCS2B01G438400 chr2D 531043423 531048517 5094 False 739.466667 1376 87.956000 1111 6229 6 chr2D.!!$F2 5118
9 TraesCS2B01G438400 chr2A 675582539 675584487 1948 False 1125.500000 1914 86.862500 1111 3429 2 chr2A.!!$F3 2318
10 TraesCS2B01G438400 chr2A 675302034 675307347 5313 False 754.850000 1515 86.757667 991 6229 6 chr2A.!!$F2 5238
11 TraesCS2B01G438400 chr7B 639080813 639081519 706 False 1042.000000 1042 93.644000 1 691 1 chr7B.!!$F2 690
12 TraesCS2B01G438400 chr4A 444548405 444549105 700 False 1037.000000 1037 93.608000 1 691 1 chr4A.!!$F1 690
13 TraesCS2B01G438400 chr3B 89378555 89379280 725 False 1031.000000 1031 92.740000 1 708 1 chr3B.!!$F1 707
14 TraesCS2B01G438400 chr3B 215309343 215310047 704 True 1022.000000 1022 93.089000 1 695 1 chr3B.!!$R1 694
15 TraesCS2B01G438400 chr5B 411229227 411229928 701 True 1026.000000 1026 93.324000 1 691 1 chr5B.!!$R1 690
16 TraesCS2B01G438400 chr1D 464380100 464380795 695 False 1026.000000 1026 93.447000 1 691 1 chr1D.!!$F3 690

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
404 413 0.741915 GTCGCAGGGGAAAACAACAA 59.258 50.000 0.00 0.00 0.00 2.83 F
951 993 0.839853 CCAAAGCCCCAAATCCCCAA 60.840 55.000 0.00 0.00 0.00 4.12 F
1937 2078 0.542232 CTAGCCGGCCCAGTACCTAT 60.542 60.000 26.15 2.07 0.00 2.57 F
3762 4379 0.337082 TTGGGACGGAGGGAGTATCA 59.663 55.000 0.00 0.00 36.25 2.15 F
4119 4748 1.666888 CGTGCCTTGAAAGTTCATGCC 60.667 52.381 11.38 0.00 37.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1302 1415 1.133216 TCGATGTCAAGAGAGAAGGCG 59.867 52.381 0.00 0.0 0.00 5.52 R
1984 2130 3.202906 TCTTCCGGAACAAACTGTCAAG 58.797 45.455 14.35 0.0 0.00 3.02 R
3797 4414 1.228552 GGGCAGCAAGGGAAGACAA 60.229 57.895 0.00 0.0 0.00 3.18 R
4998 5723 0.106268 TTTCAAGGCAGGCAACCAGA 60.106 50.000 0.00 0.0 37.17 3.86 R
5686 6489 0.883153 TAACAAGAGCGCCACGACTA 59.117 50.000 2.29 0.0 0.00 2.59 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
318 323 2.631580 GGCGACCCGGATTGCAAAA 61.632 57.895 11.17 0.00 0.00 2.44
345 350 9.638110 AAACACCCCACTATAATAATATAGGGA 57.362 33.333 8.44 0.00 44.92 4.20
404 413 0.741915 GTCGCAGGGGAAAACAACAA 59.258 50.000 0.00 0.00 0.00 2.83
436 448 1.466950 CGAGAGTGAGAGAAAGCGAGT 59.533 52.381 0.00 0.00 0.00 4.18
479 501 1.559682 AGAGAGGAAGAGAGAGACGCT 59.440 52.381 0.00 0.00 0.00 5.07
662 691 7.036220 AGAGTGTGTGTTATATTTTCTCTCCG 58.964 38.462 0.00 0.00 0.00 4.63
691 720 1.607148 GCACGGGTTCTTTTGCTAGTT 59.393 47.619 0.00 0.00 32.00 2.24
766 802 2.099592 GACTCTACGACGAGAGGAGAGA 59.900 54.545 19.82 5.39 46.22 3.10
794 830 3.591835 GCGAGAGGAGAGAGGCGG 61.592 72.222 0.00 0.00 0.00 6.13
795 831 2.904866 CGAGAGGAGAGAGGCGGG 60.905 72.222 0.00 0.00 0.00 6.13
796 832 2.520741 GAGAGGAGAGAGGCGGGG 60.521 72.222 0.00 0.00 0.00 5.73
797 833 4.150454 AGAGGAGAGAGGCGGGGG 62.150 72.222 0.00 0.00 0.00 5.40
798 834 4.144727 GAGGAGAGAGGCGGGGGA 62.145 72.222 0.00 0.00 0.00 4.81
806 842 3.680920 GAGGCGGGGGAGAAGAGGA 62.681 68.421 0.00 0.00 0.00 3.71
944 986 2.846754 GTGCCCCAAAGCCCCAAA 60.847 61.111 0.00 0.00 0.00 3.28
945 987 2.206612 TGCCCCAAAGCCCCAAAT 59.793 55.556 0.00 0.00 0.00 2.32
949 991 1.995066 CCCAAAGCCCCAAATCCCC 60.995 63.158 0.00 0.00 0.00 4.81
951 993 0.839853 CCAAAGCCCCAAATCCCCAA 60.840 55.000 0.00 0.00 0.00 4.12
960 1002 1.273781 CCAAATCCCCAATCCCCACTT 60.274 52.381 0.00 0.00 0.00 3.16
1081 1145 3.691342 TCGTGGTCTCCGGCAAGG 61.691 66.667 0.00 0.00 42.97 3.61
1102 1166 4.680537 AGGCCTCCGTCGTGGTCT 62.681 66.667 0.00 3.22 39.52 3.85
1105 1169 3.812019 CCTCCGTCGTGGTCTCCG 61.812 72.222 0.00 0.00 39.52 4.63
1937 2078 0.542232 CTAGCCGGCCCAGTACCTAT 60.542 60.000 26.15 2.07 0.00 2.57
1951 2092 6.273825 CCAGTACCTATATGACAGTGTCAAC 58.726 44.000 28.70 19.54 45.96 3.18
1984 2130 1.602771 GCCCTCCTGTCTGTAACCC 59.397 63.158 0.00 0.00 0.00 4.11
2229 2613 9.304731 TCAGAAAACATTATGATTAAGCAATGC 57.695 29.630 0.00 0.00 32.76 3.56
2446 2840 8.141268 CCAATCACTTTTGGTTACTGTTATGTT 58.859 33.333 0.00 0.00 41.09 2.71
2652 3063 1.168714 GGGCTCTTAACAGGCTGTTG 58.831 55.000 36.40 23.60 41.30 3.33
2970 3480 4.096382 AGCAATGAAAATCGCGGTAAATCT 59.904 37.500 6.13 0.00 0.00 2.40
3258 3852 5.279406 GCTGGATGCATCTACTGAGATACTT 60.279 44.000 25.28 0.00 40.68 2.24
3309 3907 1.550327 TCTTCTCATGCTCCGTCTGT 58.450 50.000 0.00 0.00 0.00 3.41
3458 4062 6.675413 ATTGGTCAATTGGCTATATGCATT 57.325 33.333 10.38 0.00 45.15 3.56
3560 4175 7.319646 TGCCACTTGTTATCATAATGTTTTCC 58.680 34.615 0.00 0.00 0.00 3.13
3614 4229 5.324409 TGGAGTCCTGCATTTCAAATAACT 58.676 37.500 11.33 0.00 0.00 2.24
3621 4236 5.512788 CCTGCATTTCAAATAACTTAGCACG 59.487 40.000 0.00 0.00 0.00 5.34
3701 4318 2.237392 GTTCTGCATTGTACTCCCTCCT 59.763 50.000 0.00 0.00 0.00 3.69
3714 4331 3.291584 CTCCCTCCTTCCCAAAATAAGC 58.708 50.000 0.00 0.00 0.00 3.09
3734 4351 5.041191 AGCATCTCAACTTTAGTATGGGG 57.959 43.478 0.00 0.00 0.00 4.96
3735 4352 4.475016 AGCATCTCAACTTTAGTATGGGGT 59.525 41.667 0.00 0.00 0.00 4.95
3749 4366 6.009908 AGTATGGGGTACTTATTTTGGGAC 57.990 41.667 0.00 0.00 40.80 4.46
3760 4377 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
3762 4379 0.337082 TTGGGACGGAGGGAGTATCA 59.663 55.000 0.00 0.00 36.25 2.15
3768 4385 4.508047 GGGACGGAGGGAGTATCATACTTA 60.508 50.000 0.00 0.00 39.59 2.24
3797 4414 7.861629 TCACAATTCTGTACCTATTCCATCTT 58.138 34.615 0.00 0.00 33.22 2.40
3924 4548 5.491982 CCTTAGGTTCTCTGTGCAGTTATT 58.508 41.667 0.00 0.00 0.00 1.40
3925 4549 6.351881 CCCTTAGGTTCTCTGTGCAGTTATTA 60.352 42.308 0.00 0.00 0.00 0.98
4099 4728 4.458397 TCCAATCTGCCAGATCATTTCTC 58.542 43.478 7.84 0.00 32.89 2.87
4119 4748 1.666888 CGTGCCTTGAAAGTTCATGCC 60.667 52.381 11.38 0.00 37.00 4.40
4164 4793 4.096382 CCGACAAATGCAGGTAATTAGCTT 59.904 41.667 14.43 0.00 30.45 3.74
4528 5173 5.819991 TCTTGCTAGGAACTCATGGATTTT 58.180 37.500 0.00 0.00 41.75 1.82
4530 5175 7.577303 TCTTGCTAGGAACTCATGGATTTTAT 58.423 34.615 0.00 0.00 41.75 1.40
4751 5473 2.033801 GTCATGCTCGGAATCAAATGGG 59.966 50.000 0.00 0.00 0.00 4.00
4892 5614 6.808704 TGAATAGCATAGTAGAATAGCTTGCG 59.191 38.462 0.00 0.00 36.80 4.85
4912 5634 5.956642 TGCGTAGACAAGTTGTGTATGATA 58.043 37.500 27.76 16.60 41.96 2.15
4968 5692 7.504911 AGATCTTAGTAGGGTGAGCGTTAAATA 59.495 37.037 0.00 0.00 0.00 1.40
4979 5703 4.569162 TGAGCGTTAAATATACAGCACCAC 59.431 41.667 0.00 0.00 0.00 4.16
4980 5704 4.509616 AGCGTTAAATATACAGCACCACA 58.490 39.130 0.00 0.00 0.00 4.17
4981 5705 4.331717 AGCGTTAAATATACAGCACCACAC 59.668 41.667 0.00 0.00 0.00 3.82
5010 5735 1.458639 AAGTTGCTCTGGTTGCCTGC 61.459 55.000 0.00 0.00 0.00 4.85
5082 5811 6.509418 TTTTGCATGGTAGAAATAGTGGTC 57.491 37.500 0.00 0.00 0.00 4.02
5083 5812 4.835284 TGCATGGTAGAAATAGTGGTCA 57.165 40.909 0.00 0.00 0.00 4.02
5102 5856 6.933521 GTGGTCATCAGCTTATTGAGACATAT 59.066 38.462 0.00 0.00 32.09 1.78
5127 5881 9.935241 ATATCGACTTTGATTGATACTTATGCT 57.065 29.630 0.00 0.00 29.47 3.79
5128 5882 7.468922 TCGACTTTGATTGATACTTATGCTG 57.531 36.000 0.00 0.00 0.00 4.41
5129 5883 6.018751 TCGACTTTGATTGATACTTATGCTGC 60.019 38.462 0.00 0.00 0.00 5.25
5130 5884 6.052840 ACTTTGATTGATACTTATGCTGCG 57.947 37.500 0.00 0.00 0.00 5.18
5131 5885 5.586243 ACTTTGATTGATACTTATGCTGCGT 59.414 36.000 0.00 0.00 0.00 5.24
5132 5886 6.761242 ACTTTGATTGATACTTATGCTGCGTA 59.239 34.615 0.00 0.00 0.00 4.42
5133 5887 6.525121 TTGATTGATACTTATGCTGCGTAC 57.475 37.500 0.05 0.00 0.00 3.67
5134 5888 5.596845 TGATTGATACTTATGCTGCGTACA 58.403 37.500 0.05 0.00 0.00 2.90
5135 5889 6.045955 TGATTGATACTTATGCTGCGTACAA 58.954 36.000 0.05 3.00 0.00 2.41
5136 5890 5.966636 TTGATACTTATGCTGCGTACAAG 57.033 39.130 0.05 2.03 0.00 3.16
5137 5891 5.006153 TGATACTTATGCTGCGTACAAGT 57.994 39.130 13.00 13.00 34.10 3.16
5138 5892 6.139048 TGATACTTATGCTGCGTACAAGTA 57.861 37.500 15.73 15.73 36.45 2.24
5139 5893 6.566141 TGATACTTATGCTGCGTACAAGTAA 58.434 36.000 16.80 4.07 35.84 2.24
5140 5894 7.036829 TGATACTTATGCTGCGTACAAGTAAA 58.963 34.615 16.80 9.02 35.84 2.01
5141 5895 5.526010 ACTTATGCTGCGTACAAGTAAAC 57.474 39.130 7.97 0.00 0.00 2.01
5142 5896 5.235516 ACTTATGCTGCGTACAAGTAAACT 58.764 37.500 7.97 0.00 0.00 2.66
5143 5897 5.120208 ACTTATGCTGCGTACAAGTAAACTG 59.880 40.000 7.97 0.00 0.00 3.16
5144 5898 2.139917 TGCTGCGTACAAGTAAACTGG 58.860 47.619 0.00 0.00 0.00 4.00
5154 5927 6.145048 CGTACAAGTAAACTGGTGACTAAAGG 59.855 42.308 0.15 0.00 31.39 3.11
5180 5953 5.858381 TCTTCAGCACTTCAGAACAAGTAT 58.142 37.500 0.00 0.00 34.70 2.12
5215 5996 1.681327 TAGTCTGGCGGGTGTCTCC 60.681 63.158 0.00 0.00 0.00 3.71
5274 6062 9.520204 ACTTTCATGAATTTGTAGTGTTTTCAG 57.480 29.630 9.40 0.19 30.56 3.02
5304 6092 3.314357 GCATTGCATTCTACAGCATGAGA 59.686 43.478 3.15 0.00 40.94 3.27
5400 6200 5.172687 TGGCTGATGGTATACTTGTTTCA 57.827 39.130 2.25 0.00 0.00 2.69
5401 6201 5.754782 TGGCTGATGGTATACTTGTTTCAT 58.245 37.500 2.25 0.00 0.00 2.57
5410 6210 5.183140 GGTATACTTGTTTCATGTGCAGGTT 59.817 40.000 2.25 0.00 0.00 3.50
5611 6414 2.042831 GCTTGCGCCCTGATTGTCT 61.043 57.895 4.18 0.00 0.00 3.41
5686 6489 6.759497 TGCTATGATGCGAGTACTATATGT 57.241 37.500 0.00 0.00 35.36 2.29
5726 6533 8.777865 TGTTAATTAGAGCTATATGGTGATGC 57.222 34.615 0.00 0.00 0.00 3.91
5727 6534 8.597167 TGTTAATTAGAGCTATATGGTGATGCT 58.403 33.333 0.00 0.00 36.63 3.79
5730 6537 7.969690 ATTAGAGCTATATGGTGATGCTAGT 57.030 36.000 0.00 0.00 33.83 2.57
5731 6538 9.480861 AATTAGAGCTATATGGTGATGCTAGTA 57.519 33.333 0.00 0.00 33.83 1.82
5732 6539 9.653516 ATTAGAGCTATATGGTGATGCTAGTAT 57.346 33.333 0.00 0.00 33.83 2.12
5733 6540 7.345422 AGAGCTATATGGTGATGCTAGTATG 57.655 40.000 0.00 0.00 33.83 2.39
5734 6541 6.894654 AGAGCTATATGGTGATGCTAGTATGT 59.105 38.462 0.00 0.00 33.83 2.29
5823 6646 6.239217 TGCTAATTGATCTAGCTCTTCCAA 57.761 37.500 12.23 0.00 41.96 3.53
5876 6699 7.651808 ACAGTTTTGAGTATGAAATTCAGTGG 58.348 34.615 1.10 0.00 0.00 4.00
5991 6823 9.509855 CTATATACTACCGAGATTGCTCAAATC 57.490 37.037 0.00 0.00 44.44 2.17
6001 6833 4.656041 GATTGCTCAAATCTTGACCGAAG 58.344 43.478 0.00 0.00 41.40 3.79
6002 6834 3.401033 TGCTCAAATCTTGACCGAAGA 57.599 42.857 0.00 0.00 45.03 2.87
6003 6835 3.067106 TGCTCAAATCTTGACCGAAGAC 58.933 45.455 0.00 0.00 43.71 3.01
6004 6836 3.067106 GCTCAAATCTTGACCGAAGACA 58.933 45.455 0.00 0.00 43.71 3.41
6006 6838 4.154918 GCTCAAATCTTGACCGAAGACAAT 59.845 41.667 0.00 0.00 43.71 2.71
6008 6840 6.128282 GCTCAAATCTTGACCGAAGACAATTA 60.128 38.462 0.00 0.00 43.71 1.40
6063 6909 6.783708 TTGAAATTACCAAAGTGGAAGTGT 57.216 33.333 0.18 0.00 40.96 3.55
6069 6915 2.775384 ACCAAAGTGGAAGTGTGGACTA 59.225 45.455 0.18 0.00 40.96 2.59
6084 6932 6.710744 AGTGTGGACTATTCTGTTTTTACCAG 59.289 38.462 0.00 0.00 0.00 4.00
6115 6963 8.329203 ACTTCCTTCATCTGAAAATACTTGTC 57.671 34.615 0.00 0.00 33.07 3.18
6116 6964 6.968131 TCCTTCATCTGAAAATACTTGTCG 57.032 37.500 0.00 0.00 33.07 4.35
6118 6966 7.158697 TCCTTCATCTGAAAATACTTGTCGAA 58.841 34.615 0.00 0.00 33.07 3.71
6119 6967 7.331934 TCCTTCATCTGAAAATACTTGTCGAAG 59.668 37.037 0.00 0.00 33.07 3.79
6120 6968 7.331934 CCTTCATCTGAAAATACTTGTCGAAGA 59.668 37.037 0.00 0.00 33.07 2.87
6121 6969 8.601845 TTCATCTGAAAATACTTGTCGAAGAA 57.398 30.769 0.00 0.00 39.69 2.52
6122 6970 8.601845 TCATCTGAAAATACTTGTCGAAGAAA 57.398 30.769 0.00 0.00 39.69 2.52
6123 6971 9.219603 TCATCTGAAAATACTTGTCGAAGAAAT 57.780 29.630 0.00 0.00 39.69 2.17
6124 6972 9.270576 CATCTGAAAATACTTGTCGAAGAAATG 57.729 33.333 0.00 0.00 39.69 2.32
6125 6973 7.806690 TCTGAAAATACTTGTCGAAGAAATGG 58.193 34.615 0.00 0.00 39.69 3.16
6126 6974 7.659799 TCTGAAAATACTTGTCGAAGAAATGGA 59.340 33.333 0.00 0.00 39.69 3.41
6127 6975 8.335532 TGAAAATACTTGTCGAAGAAATGGAT 57.664 30.769 0.00 0.00 39.69 3.41
6244 7095 5.409214 GCATAATTGTGTTGGCTTTGTTCAT 59.591 36.000 4.00 0.00 0.00 2.57
6292 7143 2.609459 CAGCGGTATCCATTCTTGTGTC 59.391 50.000 0.00 0.00 0.00 3.67
6294 7145 1.593006 CGGTATCCATTCTTGTGTCGC 59.407 52.381 0.00 0.00 0.00 5.19
6307 7160 0.389426 GTGTCGCGGTGTGGATAGTT 60.389 55.000 6.13 0.00 0.00 2.24
6341 7194 1.909700 TGTTTTGGACAGGGATGAGC 58.090 50.000 0.00 0.00 33.40 4.26
6349 7202 1.069823 GACAGGGATGAGCGATGACAT 59.930 52.381 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
278 282 2.095372 GCCGTACGAAAGGAAAATGGAG 59.905 50.000 18.76 0.00 0.00 3.86
436 448 1.221635 CTCCCTCCCTCTCTCTCTCA 58.778 60.000 0.00 0.00 0.00 3.27
514 543 1.745489 GATGGCCTCGGTGTTCACC 60.745 63.158 3.32 11.53 0.00 4.02
662 691 3.817274 GAACCCGTGCGTTGCAACC 62.817 63.158 23.42 16.11 41.47 3.77
766 802 2.238646 TCTCCTCTCGCTTCTCTCTTCT 59.761 50.000 0.00 0.00 0.00 2.85
794 830 3.108847 TCTCTCTTTCCTCTTCTCCCC 57.891 52.381 0.00 0.00 0.00 4.81
795 831 3.118775 GCTTCTCTCTTTCCTCTTCTCCC 60.119 52.174 0.00 0.00 0.00 4.30
796 832 3.428862 CGCTTCTCTCTTTCCTCTTCTCC 60.429 52.174 0.00 0.00 0.00 3.71
797 833 3.442273 TCGCTTCTCTCTTTCCTCTTCTC 59.558 47.826 0.00 0.00 0.00 2.87
798 834 3.426615 TCGCTTCTCTCTTTCCTCTTCT 58.573 45.455 0.00 0.00 0.00 2.85
806 842 3.016736 CTCCTCTCTCGCTTCTCTCTTT 58.983 50.000 0.00 0.00 0.00 2.52
944 986 1.296662 GGGAAGTGGGGATTGGGGAT 61.297 60.000 0.00 0.00 0.00 3.85
945 987 1.933812 GGGAAGTGGGGATTGGGGA 60.934 63.158 0.00 0.00 0.00 4.81
949 991 0.106015 GGATGGGGAAGTGGGGATTG 60.106 60.000 0.00 0.00 0.00 2.67
951 993 0.554865 TTGGATGGGGAAGTGGGGAT 60.555 55.000 0.00 0.00 0.00 3.85
960 1002 1.849692 TCGATTGGATTTGGATGGGGA 59.150 47.619 0.00 0.00 0.00 4.81
1084 1148 4.131088 GACCACGACGGAGGCCTC 62.131 72.222 25.59 25.59 38.63 4.70
1085 1149 4.680537 AGACCACGACGGAGGCCT 62.681 66.667 3.86 3.86 38.63 5.19
1086 1150 4.131088 GAGACCACGACGGAGGCC 62.131 72.222 8.33 0.00 38.63 5.19
1087 1151 4.131088 GGAGACCACGACGGAGGC 62.131 72.222 8.33 0.00 38.63 4.70
1088 1152 3.812019 CGGAGACCACGACGGAGG 61.812 72.222 0.00 3.16 38.63 4.30
1094 1158 3.691342 CCTTGCCGGAGACCACGA 61.691 66.667 5.05 0.00 33.16 4.35
1095 1159 4.760047 CCCTTGCCGGAGACCACG 62.760 72.222 5.05 0.00 33.16 4.94
1302 1415 1.133216 TCGATGTCAAGAGAGAAGGCG 59.867 52.381 0.00 0.00 0.00 5.52
1937 2078 8.753133 AGATGAGATTAAGTTGACACTGTCATA 58.247 33.333 12.71 0.13 42.40 2.15
1951 2092 3.393941 AGGAGGGCCAAGATGAGATTAAG 59.606 47.826 6.18 0.00 36.29 1.85
1984 2130 3.202906 TCTTCCGGAACAAACTGTCAAG 58.797 45.455 14.35 0.00 0.00 3.02
2229 2613 7.445402 CCAAACATATATGGAACCTAAGACCTG 59.555 40.741 16.96 0.00 39.12 4.00
2442 2836 6.207221 TCATGAGTGCAAACATAACAGAACAT 59.793 34.615 6.57 0.00 0.00 2.71
2446 2840 5.764686 AGTTCATGAGTGCAAACATAACAGA 59.235 36.000 17.51 7.85 0.00 3.41
2652 3063 5.532557 CCCAAAAGGACTCAAAACAGATTC 58.467 41.667 0.00 0.00 38.24 2.52
2959 3457 6.255020 ACAAAACTACTATCAGATTTACCGCG 59.745 38.462 0.00 0.00 0.00 6.46
2999 3572 2.580322 TGAAGTAGGGGCCATTGATTCA 59.420 45.455 4.39 7.08 0.00 2.57
3458 4062 9.649167 CATATCACTGAATGCTATCTATCAACA 57.351 33.333 0.00 0.00 0.00 3.33
3621 4236 3.577805 ACCATACAAATAGGGCAGGAC 57.422 47.619 0.00 0.00 35.52 3.85
3701 4318 6.916360 AAGTTGAGATGCTTATTTTGGGAA 57.084 33.333 0.00 0.00 0.00 3.97
3714 4331 7.125792 AGTACCCCATACTAAAGTTGAGATG 57.874 40.000 0.00 0.00 42.69 2.90
3732 4349 3.538591 CTCCGTCCCAAAATAAGTACCC 58.461 50.000 0.00 0.00 0.00 3.69
3734 4351 3.198417 TCCCTCCGTCCCAAAATAAGTAC 59.802 47.826 0.00 0.00 0.00 2.73
3735 4352 3.452878 TCCCTCCGTCCCAAAATAAGTA 58.547 45.455 0.00 0.00 0.00 2.24
3749 4366 6.208797 TGAACATAAGTATGATACTCCCTCCG 59.791 42.308 5.45 0.00 38.26 4.63
3760 4377 9.378551 GGTACAGAATTGTGAACATAAGTATGA 57.621 33.333 9.96 0.00 38.23 2.15
3768 4385 7.402054 TGGAATAGGTACAGAATTGTGAACAT 58.598 34.615 9.96 0.00 38.23 2.71
3797 4414 1.228552 GGGCAGCAAGGGAAGACAA 60.229 57.895 0.00 0.00 0.00 3.18
3925 4549 9.206870 CTTAATGTGAAGCAACCAACAAAATAT 57.793 29.630 0.00 0.00 0.00 1.28
4099 4728 1.666888 GGCATGAACTTTCAAGGCACG 60.667 52.381 13.91 0.00 46.51 5.34
4119 4748 4.081697 GGTGACAATATCCCAGGGTTTTTG 60.082 45.833 15.01 15.01 0.00 2.44
4751 5473 0.861837 CTCAACAGTTCGCAGTCCAC 59.138 55.000 0.00 0.00 0.00 4.02
4797 5519 1.451387 ATCAAATGCCCCGTCCGTC 60.451 57.895 0.00 0.00 0.00 4.79
4803 5525 0.531657 TTGCTTCATCAAATGCCCCG 59.468 50.000 0.00 0.00 0.00 5.73
4892 5614 8.630278 AACGATATCATACACAACTTGTCTAC 57.370 34.615 3.12 0.00 39.91 2.59
4968 5692 4.617253 TCAACTAAGTGTGGTGCTGTAT 57.383 40.909 0.00 0.00 0.00 2.29
4981 5705 6.621596 GCAACCAGAGCAACTTATCAACTAAG 60.622 42.308 0.00 0.00 42.26 2.18
4994 5719 2.598394 GGCAGGCAACCAGAGCAA 60.598 61.111 0.00 0.00 37.17 3.91
4998 5723 0.106268 TTTCAAGGCAGGCAACCAGA 60.106 50.000 0.00 0.00 37.17 3.86
5074 5803 6.098838 TGTCTCAATAAGCTGATGACCACTAT 59.901 38.462 0.00 0.00 0.00 2.12
5080 5809 9.018716 CGATATATGTCTCAATAAGCTGATGAC 57.981 37.037 0.00 0.00 0.00 3.06
5082 5811 9.018716 GTCGATATATGTCTCAATAAGCTGATG 57.981 37.037 0.00 0.00 0.00 3.07
5083 5812 8.965819 AGTCGATATATGTCTCAATAAGCTGAT 58.034 33.333 0.00 0.00 0.00 2.90
5102 5856 9.196552 CAGCATAAGTATCAATCAAAGTCGATA 57.803 33.333 0.00 0.00 0.00 2.92
5127 5881 3.125316 GTCACCAGTTTACTTGTACGCA 58.875 45.455 0.00 0.00 0.00 5.24
5128 5882 3.387397 AGTCACCAGTTTACTTGTACGC 58.613 45.455 0.00 0.00 0.00 4.42
5129 5883 6.145048 CCTTTAGTCACCAGTTTACTTGTACG 59.855 42.308 0.00 0.00 0.00 3.67
5130 5884 6.988580 ACCTTTAGTCACCAGTTTACTTGTAC 59.011 38.462 0.00 0.00 0.00 2.90
5131 5885 7.128234 ACCTTTAGTCACCAGTTTACTTGTA 57.872 36.000 0.00 0.00 0.00 2.41
5132 5886 5.997843 ACCTTTAGTCACCAGTTTACTTGT 58.002 37.500 0.00 0.00 0.00 3.16
5133 5887 6.937436 AACCTTTAGTCACCAGTTTACTTG 57.063 37.500 0.00 0.00 0.00 3.16
5134 5888 7.344134 AGAAACCTTTAGTCACCAGTTTACTT 58.656 34.615 0.00 0.00 0.00 2.24
5135 5889 6.896883 AGAAACCTTTAGTCACCAGTTTACT 58.103 36.000 0.00 0.00 0.00 2.24
5136 5890 7.281549 TGAAGAAACCTTTAGTCACCAGTTTAC 59.718 37.037 0.00 0.00 0.00 2.01
5137 5891 7.340256 TGAAGAAACCTTTAGTCACCAGTTTA 58.660 34.615 0.00 0.00 0.00 2.01
5138 5892 6.184789 TGAAGAAACCTTTAGTCACCAGTTT 58.815 36.000 0.00 0.00 0.00 2.66
5139 5893 5.751586 TGAAGAAACCTTTAGTCACCAGTT 58.248 37.500 0.00 0.00 0.00 3.16
5140 5894 5.367945 TGAAGAAACCTTTAGTCACCAGT 57.632 39.130 0.00 0.00 0.00 4.00
5141 5895 4.214332 GCTGAAGAAACCTTTAGTCACCAG 59.786 45.833 0.00 0.00 31.95 4.00
5142 5896 4.134563 GCTGAAGAAACCTTTAGTCACCA 58.865 43.478 0.00 0.00 31.95 4.17
5143 5897 4.023963 GTGCTGAAGAAACCTTTAGTCACC 60.024 45.833 0.00 0.00 33.57 4.02
5144 5898 4.816925 AGTGCTGAAGAAACCTTTAGTCAC 59.183 41.667 0.00 0.00 36.20 3.67
5154 5927 4.882671 TGTTCTGAAGTGCTGAAGAAAC 57.117 40.909 0.00 0.00 35.48 2.78
5215 5996 4.565166 TGTAAAGCCGTTACAGATCAATCG 59.435 41.667 6.51 0.00 45.76 3.34
5274 6062 3.248363 TGTAGAATGCAATGCGCTATGAC 59.752 43.478 9.73 4.90 43.06 3.06
5292 6080 2.674852 ACGTGCATTTCTCATGCTGTAG 59.325 45.455 8.22 0.60 44.79 2.74
5304 6092 3.402628 AAGGTACTCTCACGTGCATTT 57.597 42.857 11.67 0.00 38.49 2.32
5400 6200 3.842925 AACGCCGGAACCTGCACAT 62.843 57.895 5.05 0.00 0.00 3.21
5401 6201 4.555709 AACGCCGGAACCTGCACA 62.556 61.111 5.05 0.00 0.00 4.57
5410 6210 4.697756 CTGCCTCCAAACGCCGGA 62.698 66.667 5.05 0.00 0.00 5.14
5611 6414 1.113788 AAAGTTGCAAGCAAGCAGGA 58.886 45.000 7.88 0.00 46.54 3.86
5686 6489 0.883153 TAACAAGAGCGCCACGACTA 59.117 50.000 2.29 0.00 0.00 2.59
5722 6529 7.869937 ACACATGACATCTAACATACTAGCATC 59.130 37.037 0.00 0.00 0.00 3.91
5723 6530 7.730084 ACACATGACATCTAACATACTAGCAT 58.270 34.615 0.00 0.00 0.00 3.79
5724 6531 7.112452 ACACATGACATCTAACATACTAGCA 57.888 36.000 0.00 0.00 0.00 3.49
5725 6532 8.425577 AAACACATGACATCTAACATACTAGC 57.574 34.615 0.00 0.00 0.00 3.42
5731 6538 9.241919 TCCATTAAAACACATGACATCTAACAT 57.758 29.630 0.00 0.00 0.00 2.71
5732 6539 8.628630 TCCATTAAAACACATGACATCTAACA 57.371 30.769 0.00 0.00 0.00 2.41
5733 6540 9.341899 GTTCCATTAAAACACATGACATCTAAC 57.658 33.333 0.00 0.00 0.00 2.34
5734 6541 9.072375 TGTTCCATTAAAACACATGACATCTAA 57.928 29.630 0.00 0.00 31.90 2.10
5823 6646 5.861727 AGAATTGCTTTTCCAGATTTTGCT 58.138 33.333 0.00 0.00 0.00 3.91
5876 6699 2.055838 GGCCGAATTGAAAACCGAAAC 58.944 47.619 0.00 0.00 0.00 2.78
5959 6789 7.551262 AGCAATCTCGGTAGTATATAGAGTCAG 59.449 40.741 0.00 0.00 31.70 3.51
6057 6903 7.227910 TGGTAAAAACAGAATAGTCCACACTTC 59.772 37.037 0.00 0.00 33.62 3.01
6101 6949 7.806690 TCCATTTCTTCGACAAGTATTTTCAG 58.193 34.615 0.00 0.00 0.00 3.02
6102 6950 7.737972 TCCATTTCTTCGACAAGTATTTTCA 57.262 32.000 0.00 0.00 0.00 2.69
6229 7080 3.472283 AATGCATGAACAAAGCCAACA 57.528 38.095 0.00 0.00 0.00 3.33
6265 7116 2.628657 AGAATGGATACCGCTGAGTACC 59.371 50.000 0.00 0.00 0.00 3.34
6267 7118 3.704566 ACAAGAATGGATACCGCTGAGTA 59.295 43.478 0.00 0.00 0.00 2.59
6274 7125 1.593006 GCGACACAAGAATGGATACCG 59.407 52.381 0.00 0.00 0.00 4.02
6292 7143 0.108804 ACAGAACTATCCACACCGCG 60.109 55.000 0.00 0.00 0.00 6.46
6294 7145 2.417379 CCTCACAGAACTATCCACACCG 60.417 54.545 0.00 0.00 0.00 4.94
6307 7160 2.324014 AAACAGTGCCGCCTCACAGA 62.324 55.000 5.88 0.00 39.35 3.41
6334 7187 1.563435 CCGCATGTCATCGCTCATCC 61.563 60.000 0.00 0.00 0.00 3.51
6341 7194 1.062587 GAAAGGTTCCGCATGTCATCG 59.937 52.381 0.00 0.00 0.00 3.84
6452 7305 3.014304 TGTATCTCGGAGGCACTTAGT 57.986 47.619 4.96 0.00 41.55 2.24
6453 7306 4.592485 ATTGTATCTCGGAGGCACTTAG 57.408 45.455 4.96 0.00 41.55 2.18


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

AutoCloner maintained by Alex Coulton.