Multiple sequence alignment - TraesCS7D01G194000

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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 TraesCS7D01G194000 chr7D 100.000 4242 0 0 1 4242 150899550 150903791 0.000000e+00 7834.0
1 TraesCS7D01G194000 chr7B 89.537 2915 134 72 830 3663 113060207 113063031 0.000000e+00 3535.0
2 TraesCS7D01G194000 chr7B 83.908 522 20 15 3662 4133 113063065 113063572 1.400000e-119 440.0
3 TraesCS7D01G194000 chr7B 98.305 59 1 0 4153 4211 113068817 113068875 2.090000e-18 104.0
4 TraesCS7D01G194000 chr4B 89.082 2299 117 57 1312 3561 402965453 402967666 0.000000e+00 2732.0
5 TraesCS7D01G194000 chr4B 83.074 514 23 15 3662 4125 402967830 402968329 3.950000e-110 409.0
6 TraesCS7D01G194000 chr4B 89.041 292 11 9 743 1034 402965172 402965442 4.060000e-90 342.0
7 TraesCS7D01G194000 chr4B 98.305 59 1 0 4153 4211 402973162 402973220 2.090000e-18 104.0
8 TraesCS7D01G194000 chrUn 94.730 759 21 3 1 740 20493686 20492928 0.000000e+00 1162.0
9 TraesCS7D01G194000 chr7A 89.384 942 52 15 838 1742 150559482 150560412 0.000000e+00 1142.0
10 TraesCS7D01G194000 chr7A 90.670 836 53 16 1717 2535 150560430 150561257 0.000000e+00 1088.0
11 TraesCS7D01G194000 chr7A 91.734 738 53 4 1 733 16413174 16413908 0.000000e+00 1018.0
12 TraesCS7D01G194000 chr7A 89.871 543 18 17 2503 3022 150561281 150561809 0.000000e+00 664.0
13 TraesCS7D01G194000 chr7A 81.597 739 105 18 12 737 550308853 550309573 2.200000e-162 582.0
14 TraesCS7D01G194000 chr7A 88.081 495 24 12 3085 3561 150582142 150582619 4.790000e-154 555.0
15 TraesCS7D01G194000 chr7A 91.981 212 13 2 3965 4172 150585110 150585321 1.150000e-75 294.0
16 TraesCS7D01G194000 chr7A 89.950 199 8 9 3662 3858 150582781 150582969 3.280000e-61 246.0
17 TraesCS7D01G194000 chr7A 81.081 185 19 9 741 924 150451219 150451388 2.660000e-27 134.0
18 TraesCS7D01G194000 chr7A 100.000 60 0 0 3028 3087 150561790 150561849 1.250000e-20 111.0
19 TraesCS7D01G194000 chr2D 91.963 759 42 1 1 740 403768011 403767253 0.000000e+00 1046.0
20 TraesCS7D01G194000 chr2D 91.963 759 42 2 1 740 403777671 403776913 0.000000e+00 1046.0
21 TraesCS7D01G194000 chr2D 93.443 61 4 0 1371 1431 640618306 640618366 1.620000e-14 91.6
22 TraesCS7D01G194000 chr2B 91.903 741 52 4 1 736 517741517 517742254 0.000000e+00 1029.0
23 TraesCS7D01G194000 chr2B 90.658 760 51 2 1 740 8335196 8334437 0.000000e+00 992.0
24 TraesCS7D01G194000 chr3B 91.184 760 46 4 1 740 14522564 14523322 0.000000e+00 1013.0
25 TraesCS7D01G194000 chr3B 84.756 492 63 10 21 504 616234119 616233632 2.290000e-132 483.0
26 TraesCS7D01G194000 chr3A 86.928 459 57 2 42 497 355277988 355277530 2.930000e-141 512.0
27 TraesCS7D01G194000 chr1A 80.328 732 88 25 12 731 589427810 589427123 1.760000e-138 503.0
28 TraesCS7D01G194000 chr6A 83.755 277 33 7 1090 1357 545648068 545648341 7.040000e-63 252.0
29 TraesCS7D01G194000 chr6D 83.333 282 35 7 1085 1357 399759380 399759658 2.530000e-62 250.0
30 TraesCS7D01G194000 chr6B 82.979 282 36 7 1085 1357 598450938 598451216 1.180000e-60 244.0


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 TraesCS7D01G194000 chr7D 150899550 150903791 4241 False 7834.00 7834 100.000000 1 4242 1 chr7D.!!$F1 4241
1 TraesCS7D01G194000 chr7B 113060207 113063572 3365 False 1987.50 3535 86.722500 830 4133 2 chr7B.!!$F2 3303
2 TraesCS7D01G194000 chr4B 402965172 402968329 3157 False 1161.00 2732 87.065667 743 4125 3 chr4B.!!$F2 3382
3 TraesCS7D01G194000 chrUn 20492928 20493686 758 True 1162.00 1162 94.730000 1 740 1 chrUn.!!$R1 739
4 TraesCS7D01G194000 chr7A 16413174 16413908 734 False 1018.00 1018 91.734000 1 733 1 chr7A.!!$F1 732
5 TraesCS7D01G194000 chr7A 150559482 150561849 2367 False 751.25 1142 92.481250 838 3087 4 chr7A.!!$F4 2249
6 TraesCS7D01G194000 chr7A 550308853 550309573 720 False 582.00 582 81.597000 12 737 1 chr7A.!!$F3 725
7 TraesCS7D01G194000 chr7A 150582142 150585321 3179 False 365.00 555 90.004000 3085 4172 3 chr7A.!!$F5 1087
8 TraesCS7D01G194000 chr2D 403767253 403768011 758 True 1046.00 1046 91.963000 1 740 1 chr2D.!!$R1 739
9 TraesCS7D01G194000 chr2D 403776913 403777671 758 True 1046.00 1046 91.963000 1 740 1 chr2D.!!$R2 739
10 TraesCS7D01G194000 chr2B 517741517 517742254 737 False 1029.00 1029 91.903000 1 736 1 chr2B.!!$F1 735
11 TraesCS7D01G194000 chr2B 8334437 8335196 759 True 992.00 992 90.658000 1 740 1 chr2B.!!$R1 739
12 TraesCS7D01G194000 chr3B 14522564 14523322 758 False 1013.00 1013 91.184000 1 740 1 chr3B.!!$F1 739
13 TraesCS7D01G194000 chr1A 589427123 589427810 687 True 503.00 503 80.328000 12 731 1 chr1A.!!$R1 719

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
743 783 0.101759 CTAGCAGCGCCCTAAACGTA 59.898 55.0 2.29 0.0 0.00 3.57 F
820 860 0.315869 CGAAGACAAACACACACGGC 60.316 55.0 0.00 0.0 0.00 5.68 F
822 862 0.741574 AAGACAAACACACACGGCGA 60.742 50.0 16.62 0.0 0.00 5.54 F
1466 1538 0.891373 ACCAGTCACTCATGGACGAG 59.109 55.0 0.00 0.0 39.02 4.18 F
2772 2977 0.965866 ACCGGAAGATGAGCGTCTGA 60.966 55.0 9.46 0.0 33.78 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2034 2164 0.474854 TAGGAGGGTGGCCAACTGAA 60.475 55.0 22.79 0.0 0.00 3.02 R
2102 2239 0.544697 ATGGTTGGGCGGTTAGGTAG 59.455 55.0 0.00 0.0 0.00 3.18 R
2686 2880 0.732571 AAAATACAGGCCATGCGTCG 59.267 50.0 5.01 0.0 0.00 5.12 R
2975 3190 0.459411 GCACCACCACCAACAACAAC 60.459 55.0 0.00 0.0 0.00 3.32 R
4184 6593 0.179119 GCACCTCGCACGGTAACTAT 60.179 55.0 0.00 0.0 41.79 2.12 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
124 125 6.094603 ACTGCCTTGATTTTTGCTACATCTAG 59.905 38.462 0.00 0.00 0.00 2.43
156 158 7.301868 TGGAACCTCTTTTCATTTTTGCTAT 57.698 32.000 0.00 0.00 0.00 2.97
416 420 1.227853 GTGAGGGAGTTGCAACGGT 60.228 57.895 23.21 7.54 0.00 4.83
740 780 2.180862 GCCTAGCAGCGCCCTAAAC 61.181 63.158 2.29 0.00 0.00 2.01
741 781 1.883084 CCTAGCAGCGCCCTAAACG 60.883 63.158 2.29 0.00 0.00 3.60
742 782 1.153628 CTAGCAGCGCCCTAAACGT 60.154 57.895 2.29 0.00 0.00 3.99
743 783 0.101759 CTAGCAGCGCCCTAAACGTA 59.898 55.000 2.29 0.00 0.00 3.57
744 784 0.531657 TAGCAGCGCCCTAAACGTAA 59.468 50.000 2.29 0.00 0.00 3.18
745 785 1.017701 AGCAGCGCCCTAAACGTAAC 61.018 55.000 2.29 0.00 0.00 2.50
746 786 1.017701 GCAGCGCCCTAAACGTAACT 61.018 55.000 2.29 0.00 0.00 2.24
747 787 0.719465 CAGCGCCCTAAACGTAACTG 59.281 55.000 2.29 0.00 0.00 3.16
752 792 1.609841 GCCCTAAACGTAACTGTGCCT 60.610 52.381 0.00 0.00 0.00 4.75
816 856 4.587211 GTGTAACGAAGACAAACACACA 57.413 40.909 0.00 0.00 40.08 3.72
817 857 4.328667 GTGTAACGAAGACAAACACACAC 58.671 43.478 0.00 0.00 40.08 3.82
818 858 2.798834 AACGAAGACAAACACACACG 57.201 45.000 0.00 0.00 0.00 4.49
819 859 1.003851 ACGAAGACAAACACACACGG 58.996 50.000 0.00 0.00 0.00 4.94
820 860 0.315869 CGAAGACAAACACACACGGC 60.316 55.000 0.00 0.00 0.00 5.68
821 861 0.315869 GAAGACAAACACACACGGCG 60.316 55.000 4.80 4.80 0.00 6.46
822 862 0.741574 AAGACAAACACACACGGCGA 60.742 50.000 16.62 0.00 0.00 5.54
823 863 1.011574 GACAAACACACACGGCGAC 60.012 57.895 16.62 0.00 0.00 5.19
861 901 1.201647 CCAAACATCAAGAGCAGCAGG 59.798 52.381 0.00 0.00 0.00 4.85
1256 1313 2.202492 CGCGTCACCGAGGAAGAG 60.202 66.667 0.00 0.00 35.63 2.85
1264 1321 4.521062 CGAGGAAGAGGGCCAGCG 62.521 72.222 6.18 0.00 0.00 5.18
1466 1538 0.891373 ACCAGTCACTCATGGACGAG 59.109 55.000 0.00 0.00 39.02 4.18
1547 1628 1.807142 GGCAGCTCCTTGTTTCTGTAC 59.193 52.381 0.00 0.00 0.00 2.90
1559 1640 3.188254 TGTTTCTGTACCATGCATGTTCG 59.812 43.478 24.58 12.42 0.00 3.95
1675 1759 5.946942 TCATTCCAGCTCTTCACTAATCT 57.053 39.130 0.00 0.00 0.00 2.40
1679 1763 6.707440 TTCCAGCTCTTCACTAATCTCTAG 57.293 41.667 0.00 0.00 0.00 2.43
1680 1764 5.761205 TCCAGCTCTTCACTAATCTCTAGT 58.239 41.667 0.00 0.00 0.00 2.57
1686 1770 8.711170 AGCTCTTCACTAATCTCTAGTACTACT 58.289 37.037 0.00 0.00 0.00 2.57
1687 1771 9.985730 GCTCTTCACTAATCTCTAGTACTACTA 57.014 37.037 0.00 0.00 0.00 1.82
1714 1798 8.984891 TGCTTCATTATTAATTTGAACTGGTG 57.015 30.769 8.62 2.91 0.00 4.17
1753 1877 6.263344 CAATTGATCAAGACATGTCATCACC 58.737 40.000 27.02 13.29 0.00 4.02
1799 1923 2.354821 ACGAAATAAGGCAGGCGATTTC 59.645 45.455 19.38 19.38 35.75 2.17
1831 1956 8.682016 CATCGTTTGTTCTTCAGAAATTTGTAC 58.318 33.333 0.00 0.00 35.58 2.90
1838 1963 7.967854 TGTTCTTCAGAAATTTGTACTTGTGTG 59.032 33.333 0.00 0.00 35.58 3.82
1968 2093 6.579865 TGCCTAGTTAGTTAACCTGCTAATC 58.420 40.000 0.88 0.00 36.88 1.75
2024 2154 4.925054 CCATAAGACCATTTGCACTTGTTG 59.075 41.667 0.00 0.00 0.00 3.33
2102 2239 8.370493 AGTATGAGTTATGCATGACACAATAC 57.630 34.615 21.88 21.46 0.00 1.89
2259 2397 6.716934 TTCCCACTCAGAGCTAAACTATAG 57.283 41.667 0.00 0.00 0.00 1.31
2304 2442 1.150536 ACCACATGGAAACGGCAGT 59.849 52.632 4.53 0.00 38.94 4.40
2307 2445 1.167851 CACATGGAAACGGCAGTGAT 58.832 50.000 0.00 0.00 0.00 3.06
2439 2580 2.080286 AGTGGACAAGGAATCGTTCG 57.920 50.000 0.00 0.00 0.00 3.95
2450 2591 4.451900 AGGAATCGTTCGCCATTTATTCT 58.548 39.130 0.00 0.00 0.00 2.40
2451 2592 4.511826 AGGAATCGTTCGCCATTTATTCTC 59.488 41.667 0.00 0.00 0.00 2.87
2452 2593 4.511826 GGAATCGTTCGCCATTTATTCTCT 59.488 41.667 0.00 0.00 0.00 3.10
2463 2604 7.174946 TCGCCATTTATTCTCTTCTCAAAACTT 59.825 33.333 0.00 0.00 0.00 2.66
2711 2905 3.248602 CGCATGGCCTGTATTTTAGAGTC 59.751 47.826 3.32 0.00 0.00 3.36
2772 2977 0.965866 ACCGGAAGATGAGCGTCTGA 60.966 55.000 9.46 0.00 33.78 3.27
2973 3188 6.127451 TGCTGTTGCTGTGTACTATACTGTAT 60.127 38.462 5.53 5.53 40.48 2.29
2974 3189 6.757010 GCTGTTGCTGTGTACTATACTGTATT 59.243 38.462 5.52 0.00 36.03 1.89
2975 3190 7.254117 GCTGTTGCTGTGTACTATACTGTATTG 60.254 40.741 5.52 6.67 36.03 1.90
2985 3200 9.210329 TGTACTATACTGTATTGTTGTTGTTGG 57.790 33.333 17.54 0.00 0.00 3.77
3109 3326 2.427095 GTGTTGGAAGCAAAGTCCAGTT 59.573 45.455 0.00 0.00 45.79 3.16
3110 3327 2.687935 TGTTGGAAGCAAAGTCCAGTTC 59.312 45.455 0.00 0.00 45.79 3.01
3111 3328 1.981256 TGGAAGCAAAGTCCAGTTCC 58.019 50.000 0.00 0.00 40.33 3.62
3112 3329 1.214175 TGGAAGCAAAGTCCAGTTCCA 59.786 47.619 0.00 0.00 43.47 3.53
3113 3330 1.882623 GGAAGCAAAGTCCAGTTCCAG 59.117 52.381 0.00 0.00 37.27 3.86
3177 3409 2.158842 CCGAAAGATCCTTGATCAGGCT 60.159 50.000 0.00 0.00 43.55 4.58
3239 3471 5.341196 GTGTTGGAATAATTGTTCGTTTCGG 59.659 40.000 8.61 0.00 0.00 4.30
3240 3472 4.086199 TGGAATAATTGTTCGTTTCGGC 57.914 40.909 8.61 0.00 0.00 5.54
3241 3473 3.502595 TGGAATAATTGTTCGTTTCGGCA 59.497 39.130 8.61 0.00 0.00 5.69
3242 3474 4.156922 TGGAATAATTGTTCGTTTCGGCAT 59.843 37.500 8.61 0.00 0.00 4.40
3291 3529 1.824852 CTGCAACCCCCAAATAAGGAC 59.175 52.381 0.00 0.00 0.00 3.85
3295 3538 1.768265 ACCCCCAAATAAGGACACCT 58.232 50.000 0.00 0.00 33.87 4.00
3339 3585 1.379044 ATGCAAGTAGCCCACTGCC 60.379 57.895 0.00 0.00 44.83 4.85
3358 3604 2.483876 CCACTGCTGGTTACGATATGG 58.516 52.381 0.00 0.00 32.03 2.74
3376 3622 3.520290 TGGTCCATGAGTAATCGTGTC 57.480 47.619 11.18 4.42 0.00 3.67
3387 3633 6.786207 TGAGTAATCGTGTCATCTAAGTGAG 58.214 40.000 0.00 0.00 0.00 3.51
3388 3634 5.583495 AGTAATCGTGTCATCTAAGTGAGC 58.417 41.667 0.00 0.00 0.00 4.26
3455 3706 2.094494 AGCGGATTGTGATATCCTAGCG 60.094 50.000 0.00 0.00 41.65 4.26
3456 3707 2.094700 GCGGATTGTGATATCCTAGCGA 60.095 50.000 0.00 0.00 41.65 4.93
3457 3708 3.763902 CGGATTGTGATATCCTAGCGAG 58.236 50.000 0.00 0.00 41.65 5.03
3458 3709 3.191581 CGGATTGTGATATCCTAGCGAGT 59.808 47.826 0.00 0.00 41.65 4.18
3459 3710 4.395231 CGGATTGTGATATCCTAGCGAGTA 59.605 45.833 0.00 0.00 41.65 2.59
3460 3711 5.447954 CGGATTGTGATATCCTAGCGAGTAG 60.448 48.000 0.00 0.00 41.65 2.57
3461 3712 5.677598 GGATTGTGATATCCTAGCGAGTAGC 60.678 48.000 0.00 0.00 42.56 3.58
3462 3713 8.015777 GGATTGTGATATCCTAGCGAGTAGCA 62.016 46.154 0.00 0.00 43.59 3.49
3494 3745 1.062880 GAGTAAGAGAGACGGTCGCTG 59.937 57.143 19.20 0.00 35.14 5.18
3517 3771 2.149803 CTCGCCACGTTGACCTACCA 62.150 60.000 0.00 0.00 0.00 3.25
3542 3796 0.250338 AGCGGTTCTCCACTTTCACC 60.250 55.000 0.00 0.00 0.00 4.02
3545 3799 1.509703 GGTTCTCCACTTTCACCGAC 58.490 55.000 0.00 0.00 0.00 4.79
3546 3800 1.137513 GTTCTCCACTTTCACCGACG 58.862 55.000 0.00 0.00 0.00 5.12
3552 3810 1.301479 ACTTTCACCGACGGGCTTC 60.301 57.895 20.00 0.00 36.48 3.86
3553 3811 1.301401 CTTTCACCGACGGGCTTCA 60.301 57.895 20.00 0.00 36.48 3.02
3554 3812 1.291877 CTTTCACCGACGGGCTTCAG 61.292 60.000 20.00 3.44 36.48 3.02
3555 3813 2.035237 TTTCACCGACGGGCTTCAGT 62.035 55.000 20.00 0.00 36.48 3.41
3556 3814 2.430382 TTCACCGACGGGCTTCAGTC 62.430 60.000 20.00 0.00 36.48 3.51
3560 3818 2.507324 GACGGGCTTCAGTCGAGC 60.507 66.667 0.00 0.00 39.41 5.03
3561 3819 2.992114 ACGGGCTTCAGTCGAGCT 60.992 61.111 0.00 0.00 40.01 4.09
3562 3820 2.202676 CGGGCTTCAGTCGAGCTC 60.203 66.667 2.73 2.73 40.01 4.09
3580 3853 3.533691 GAGCAGCGCGACACGTAC 61.534 66.667 12.10 0.00 46.11 3.67
3642 3933 0.867753 CCTTGTCGATCTTCTCCGCG 60.868 60.000 0.00 0.00 0.00 6.46
3644 3935 3.019545 GTCGATCTTCTCCGCGCG 61.020 66.667 25.67 25.67 0.00 6.86
3712 4046 2.264794 CACCACGGCTCCACTACC 59.735 66.667 0.00 0.00 0.00 3.18
3759 4097 3.454573 CCCCGCCAGTACGCTGTA 61.455 66.667 0.00 0.00 41.02 2.74
3838 4176 2.642254 CGGTAGGGTCGCTGTTCCA 61.642 63.158 0.00 0.00 0.00 3.53
3861 4387 2.810032 GCATTTGGTTGGGTTCCTTTGG 60.810 50.000 0.00 0.00 0.00 3.28
3921 5880 3.571216 TTGGGTTGGGCGGCAGTA 61.571 61.111 12.47 0.00 0.00 2.74
4139 6548 1.265095 GGCATATGCGGTTCATCTGTG 59.735 52.381 21.04 0.00 43.26 3.66
4140 6549 1.334419 GCATATGCGGTTCATCTGTGC 60.334 52.381 12.82 0.00 36.63 4.57
4172 6581 2.416893 GCTACAAGTACAAAGCTGAGCC 59.583 50.000 0.00 0.00 32.18 4.70
4173 6582 2.638480 ACAAGTACAAAGCTGAGCCA 57.362 45.000 0.00 0.00 0.00 4.75
4174 6583 2.930950 ACAAGTACAAAGCTGAGCCAA 58.069 42.857 0.00 0.00 0.00 4.52
4175 6584 3.490348 ACAAGTACAAAGCTGAGCCAAT 58.510 40.909 0.00 0.00 0.00 3.16
4176 6585 3.891366 ACAAGTACAAAGCTGAGCCAATT 59.109 39.130 0.00 0.00 0.00 2.32
4177 6586 4.022849 ACAAGTACAAAGCTGAGCCAATTC 60.023 41.667 0.00 0.00 0.00 2.17
4178 6587 3.754965 AGTACAAAGCTGAGCCAATTCA 58.245 40.909 0.00 0.00 0.00 2.57
4179 6588 3.755378 AGTACAAAGCTGAGCCAATTCAG 59.245 43.478 0.00 0.00 45.85 3.02
4180 6589 2.590821 ACAAAGCTGAGCCAATTCAGT 58.409 42.857 0.00 0.00 45.07 3.41
4181 6590 2.555757 ACAAAGCTGAGCCAATTCAGTC 59.444 45.455 0.00 0.00 45.07 3.51
4182 6591 1.446907 AAGCTGAGCCAATTCAGTCG 58.553 50.000 0.00 0.00 45.07 4.18
4183 6592 0.610174 AGCTGAGCCAATTCAGTCGA 59.390 50.000 0.00 0.00 45.07 4.20
4184 6593 1.002430 AGCTGAGCCAATTCAGTCGAA 59.998 47.619 0.00 0.00 45.07 3.71
4185 6594 2.012673 GCTGAGCCAATTCAGTCGAAT 58.987 47.619 0.00 0.00 45.07 3.34
4186 6595 3.118629 AGCTGAGCCAATTCAGTCGAATA 60.119 43.478 0.00 0.00 45.07 1.75
4187 6596 3.247173 GCTGAGCCAATTCAGTCGAATAG 59.753 47.826 0.00 0.00 45.07 1.73
4188 6597 4.437239 CTGAGCCAATTCAGTCGAATAGT 58.563 43.478 0.00 0.00 41.12 2.12
4189 6598 4.832248 TGAGCCAATTCAGTCGAATAGTT 58.168 39.130 0.00 0.00 41.12 2.24
4190 6599 5.972935 TGAGCCAATTCAGTCGAATAGTTA 58.027 37.500 0.00 0.00 41.12 2.24
4191 6600 5.810587 TGAGCCAATTCAGTCGAATAGTTAC 59.189 40.000 0.00 0.00 41.12 2.50
4192 6601 5.116882 AGCCAATTCAGTCGAATAGTTACC 58.883 41.667 0.00 0.00 41.12 2.85
4193 6602 4.025979 GCCAATTCAGTCGAATAGTTACCG 60.026 45.833 0.00 0.00 41.12 4.02
4194 6603 5.107133 CCAATTCAGTCGAATAGTTACCGT 58.893 41.667 0.00 0.00 41.12 4.83
4195 6604 5.005394 CCAATTCAGTCGAATAGTTACCGTG 59.995 44.000 0.00 0.00 41.12 4.94
4196 6605 3.141002 TCAGTCGAATAGTTACCGTGC 57.859 47.619 0.00 0.00 0.00 5.34
4197 6606 1.844357 CAGTCGAATAGTTACCGTGCG 59.156 52.381 0.00 0.00 0.00 5.34
4198 6607 1.739466 AGTCGAATAGTTACCGTGCGA 59.261 47.619 0.00 0.00 0.00 5.10
4199 6608 2.107178 GTCGAATAGTTACCGTGCGAG 58.893 52.381 0.00 0.00 0.00 5.03
4200 6609 1.064505 TCGAATAGTTACCGTGCGAGG 59.935 52.381 0.00 0.00 37.30 4.63
4202 6611 2.190981 GAATAGTTACCGTGCGAGGTG 58.809 52.381 12.54 0.00 45.54 4.00
4203 6612 0.179119 ATAGTTACCGTGCGAGGTGC 60.179 55.000 12.54 6.06 45.54 5.01
4204 6613 1.246056 TAGTTACCGTGCGAGGTGCT 61.246 55.000 12.54 12.00 45.54 4.40
4205 6614 2.092882 GTTACCGTGCGAGGTGCTC 61.093 63.158 12.54 0.72 45.54 4.26
4206 6615 2.273179 TTACCGTGCGAGGTGCTCT 61.273 57.895 12.54 0.00 45.54 4.09
4207 6616 2.209064 TTACCGTGCGAGGTGCTCTC 62.209 60.000 12.54 0.00 45.54 3.20
4214 6623 3.706373 GAGGTGCTCTCGGGCCAA 61.706 66.667 4.39 0.00 32.18 4.52
4215 6624 3.959991 GAGGTGCTCTCGGGCCAAC 62.960 68.421 4.39 0.00 32.18 3.77
4216 6625 4.329545 GGTGCTCTCGGGCCAACA 62.330 66.667 4.39 0.00 0.00 3.33
4217 6626 2.743928 GTGCTCTCGGGCCAACAG 60.744 66.667 4.39 0.00 0.00 3.16
4218 6627 2.922503 TGCTCTCGGGCCAACAGA 60.923 61.111 4.39 0.59 0.00 3.41
4219 6628 2.125350 GCTCTCGGGCCAACAGAG 60.125 66.667 16.86 16.86 42.00 3.35
4220 6629 2.948720 GCTCTCGGGCCAACAGAGT 61.949 63.158 20.34 0.00 41.46 3.24
4221 6630 1.216710 CTCTCGGGCCAACAGAGTC 59.783 63.158 4.39 0.00 41.46 3.36
4222 6631 1.533033 TCTCGGGCCAACAGAGTCA 60.533 57.895 4.39 0.00 41.46 3.41
4223 6632 1.079543 CTCGGGCCAACAGAGTCAG 60.080 63.158 4.39 0.00 36.75 3.51
4224 6633 2.743928 CGGGCCAACAGAGTCAGC 60.744 66.667 4.39 0.00 0.00 4.26
4225 6634 2.753029 GGGCCAACAGAGTCAGCT 59.247 61.111 4.39 0.00 0.00 4.24
4226 6635 1.376553 GGGCCAACAGAGTCAGCTC 60.377 63.158 4.39 0.00 41.94 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 8.977505 GCAAAAACTAGATGTAGCAAAAATCAA 58.022 29.630 0.00 0.00 0.00 2.57
124 125 4.754322 TGAAAAGAGGTTCCAGCAAAAAC 58.246 39.130 0.00 0.00 0.00 2.43
156 158 2.235016 AGCTTTTGTGATTGCCGGTTA 58.765 42.857 1.90 0.00 0.00 2.85
416 420 3.866379 ATGCAGCAACTTCCGCCCA 62.866 57.895 0.00 0.00 0.00 5.36
590 622 3.751698 GGGAAAACGCATAGTTGACTCTT 59.248 43.478 0.00 0.00 43.37 2.85
635 674 4.393062 CCGCTCAATGTGTAACTTCTTCAT 59.607 41.667 0.00 0.00 38.04 2.57
740 780 3.179265 CGGCGAGGCACAGTTACG 61.179 66.667 0.00 0.00 0.00 3.18
741 781 3.488090 GCGGCGAGGCACAGTTAC 61.488 66.667 12.98 0.00 0.00 2.50
776 816 2.503375 CGTGACTCGTGGCGTACC 60.503 66.667 0.00 0.00 34.52 3.34
789 829 0.029167 TGTCTTCGTTACACGCGTGA 59.971 50.000 42.94 24.54 42.21 4.35
798 838 2.604011 CCGTGTGTGTTTGTCTTCGTTA 59.396 45.455 0.00 0.00 0.00 3.18
799 839 1.395608 CCGTGTGTGTTTGTCTTCGTT 59.604 47.619 0.00 0.00 0.00 3.85
800 840 1.003851 CCGTGTGTGTTTGTCTTCGT 58.996 50.000 0.00 0.00 0.00 3.85
803 843 0.741574 TCGCCGTGTGTGTTTGTCTT 60.742 50.000 0.00 0.00 0.00 3.01
807 847 2.053465 CGTCGCCGTGTGTGTTTG 60.053 61.111 0.00 0.00 0.00 2.93
809 849 2.958016 GTCGTCGCCGTGTGTGTT 60.958 61.111 0.00 0.00 35.01 3.32
812 852 2.657296 CTTGTCGTCGCCGTGTGT 60.657 61.111 0.00 0.00 35.01 3.72
813 853 2.354188 TCTTGTCGTCGCCGTGTG 60.354 61.111 0.00 0.00 35.01 3.82
814 854 2.354305 GTCTTGTCGTCGCCGTGT 60.354 61.111 0.00 0.00 35.01 4.49
815 855 3.103911 GGTCTTGTCGTCGCCGTG 61.104 66.667 0.00 0.00 35.01 4.94
816 856 4.353437 GGGTCTTGTCGTCGCCGT 62.353 66.667 0.00 0.00 35.01 5.68
823 863 4.796231 CTCGGCGGGGTCTTGTCG 62.796 72.222 7.21 0.00 0.00 4.35
935 975 0.453390 GGTACTAACGACCGAGGTGG 59.547 60.000 0.00 0.14 46.41 4.61
1062 1109 4.867599 CTACGCCGCCTCCCGAAC 62.868 72.222 0.00 0.00 40.02 3.95
1066 1117 4.893601 GCTTCTACGCCGCCTCCC 62.894 72.222 0.00 0.00 0.00 4.30
1067 1118 4.143333 TGCTTCTACGCCGCCTCC 62.143 66.667 0.00 0.00 0.00 4.30
1073 1124 2.202946 GCTCCCTGCTTCTACGCC 60.203 66.667 0.00 0.00 38.95 5.68
1076 1127 2.583593 CGCGCTCCCTGCTTCTAC 60.584 66.667 5.56 0.00 40.11 2.59
1077 1128 3.838271 CCGCGCTCCCTGCTTCTA 61.838 66.667 5.56 0.00 40.11 2.10
1443 1515 1.000955 GTCCATGAGTGACTGGTCGTT 59.999 52.381 0.00 0.00 34.03 3.85
1454 1526 2.889200 GAGACCCTCGTCCATGAGT 58.111 57.895 0.00 0.00 40.12 3.41
1466 1538 1.682323 GAAGGTACCTGATCGAGACCC 59.318 57.143 17.14 0.00 0.00 4.46
1513 1593 2.771435 CTGCCATCGATGAACAGCA 58.229 52.632 26.86 23.36 0.00 4.41
1547 1628 2.404789 GCGGACGAACATGCATGG 59.595 61.111 29.41 14.96 0.00 3.66
1559 1640 1.647346 TTATTGACCATCACGCGGAC 58.353 50.000 12.47 0.00 0.00 4.79
1688 1772 9.421806 CACCAGTTCAAATTAATAATGAAGCAA 57.578 29.630 13.88 0.00 34.02 3.91
1689 1773 8.034215 CCACCAGTTCAAATTAATAATGAAGCA 58.966 33.333 13.88 0.00 34.02 3.91
1690 1774 8.034804 ACCACCAGTTCAAATTAATAATGAAGC 58.965 33.333 13.88 10.31 34.02 3.86
1698 1782 5.772672 TGCACTACCACCAGTTCAAATTAAT 59.227 36.000 0.00 0.00 0.00 1.40
1753 1877 5.289675 CAGATACCAGCGTTTTAGAGACTTG 59.710 44.000 0.00 0.00 0.00 3.16
1799 1923 1.128692 GAAGAACAAACGATGGGAGCG 59.871 52.381 0.00 0.00 0.00 5.03
1831 1956 9.640974 CAAATTTCAAAATTAGAAGCACACAAG 57.359 29.630 1.36 0.00 37.62 3.16
1981 2107 3.244770 TGGTCAAAGCTACCCCAAGTTAG 60.245 47.826 1.64 0.00 36.06 2.34
2033 2163 1.142688 AGGAGGGTGGCCAACTGAAT 61.143 55.000 22.79 4.19 0.00 2.57
2034 2164 0.474854 TAGGAGGGTGGCCAACTGAA 60.475 55.000 22.79 0.00 0.00 3.02
2102 2239 0.544697 ATGGTTGGGCGGTTAGGTAG 59.455 55.000 0.00 0.00 0.00 3.18
2152 2290 4.763073 AGTCATCATTGTGTCATGATCGT 58.237 39.130 0.00 0.00 35.52 3.73
2259 2397 1.839424 AAGCAGGATGTGGCCTAAAC 58.161 50.000 3.32 0.00 39.31 2.01
2304 2442 5.221925 GGCAGGAAATTCTAGGTATCCATCA 60.222 44.000 0.00 0.00 32.47 3.07
2307 2445 3.071023 CGGCAGGAAATTCTAGGTATCCA 59.929 47.826 0.00 0.00 32.47 3.41
2450 2591 6.472887 ACGATTCCCATAAGTTTTGAGAAGA 58.527 36.000 0.00 0.00 0.00 2.87
2451 2592 6.371548 TGACGATTCCCATAAGTTTTGAGAAG 59.628 38.462 0.00 0.00 0.00 2.85
2452 2593 6.148811 GTGACGATTCCCATAAGTTTTGAGAA 59.851 38.462 0.00 0.00 0.00 2.87
2463 2604 4.581409 TCGTAATGAGTGACGATTCCCATA 59.419 41.667 0.00 0.00 42.80 2.74
2500 2641 4.221482 TGCCAATTTGCCATGTTGTACATA 59.779 37.500 0.00 0.00 36.53 2.29
2501 2642 3.007723 TGCCAATTTGCCATGTTGTACAT 59.992 39.130 0.00 0.00 39.91 2.29
2685 2879 1.095228 AAATACAGGCCATGCGTCGG 61.095 55.000 5.01 0.00 0.00 4.79
2686 2880 0.732571 AAAATACAGGCCATGCGTCG 59.267 50.000 5.01 0.00 0.00 5.12
2852 3063 1.699634 ACACCACACTGCTAGTCCAAT 59.300 47.619 0.00 0.00 0.00 3.16
2856 3067 1.419374 CGAACACCACACTGCTAGTC 58.581 55.000 0.00 0.00 0.00 2.59
2973 3188 1.273606 CACCACCACCAACAACAACAA 59.726 47.619 0.00 0.00 0.00 2.83
2974 3189 0.891373 CACCACCACCAACAACAACA 59.109 50.000 0.00 0.00 0.00 3.33
2975 3190 0.459411 GCACCACCACCAACAACAAC 60.459 55.000 0.00 0.00 0.00 3.32
2985 3200 2.867472 CGAATTCGGCACCACCAC 59.133 61.111 20.16 0.00 39.03 4.16
3109 3326 5.105752 GCACAAAACAATAACAACACTGGA 58.894 37.500 0.00 0.00 0.00 3.86
3110 3327 4.867047 TGCACAAAACAATAACAACACTGG 59.133 37.500 0.00 0.00 0.00 4.00
3111 3328 5.804473 TCTGCACAAAACAATAACAACACTG 59.196 36.000 0.00 0.00 0.00 3.66
3112 3329 5.960113 TCTGCACAAAACAATAACAACACT 58.040 33.333 0.00 0.00 0.00 3.55
3113 3330 6.292274 CCATCTGCACAAAACAATAACAACAC 60.292 38.462 0.00 0.00 0.00 3.32
3239 3471 4.285292 CAAATGCCTCTTGATTCGTATGC 58.715 43.478 0.00 0.00 0.00 3.14
3240 3472 4.790766 GCCAAATGCCTCTTGATTCGTATG 60.791 45.833 0.00 0.00 0.00 2.39
3241 3473 3.316308 GCCAAATGCCTCTTGATTCGTAT 59.684 43.478 0.00 0.00 0.00 3.06
3242 3474 2.682856 GCCAAATGCCTCTTGATTCGTA 59.317 45.455 0.00 0.00 0.00 3.43
3291 3529 1.471676 CGCCTAGCTACTTGGAAGGTG 60.472 57.143 1.75 0.00 0.00 4.00
3295 3538 4.831155 ACATATACGCCTAGCTACTTGGAA 59.169 41.667 1.75 0.00 0.00 3.53
3339 3585 3.123804 GACCATATCGTAACCAGCAGTG 58.876 50.000 0.00 0.00 0.00 3.66
3358 3604 4.938080 AGATGACACGATTACTCATGGAC 58.062 43.478 0.00 0.00 0.00 4.02
3415 3666 2.349886 GCTGTCTGAAATCAGTTAGGCG 59.650 50.000 10.06 0.00 44.12 5.52
3494 3745 3.712881 GTCAACGTGGCGAGCACC 61.713 66.667 0.00 0.00 0.00 5.01
3517 3771 2.331265 GTGGAGAACCGCTTTGCTT 58.669 52.632 0.00 0.00 42.77 3.91
3545 3799 2.202676 GAGCTCGACTGAAGCCCG 60.203 66.667 0.00 0.00 0.00 6.13
3546 3800 2.202676 CGAGCTCGACTGAAGCCC 60.203 66.667 32.06 0.00 43.02 5.19
3552 3810 2.579249 GCTGCTCGAGCTCGACTG 60.579 66.667 33.84 28.86 45.21 3.51
3553 3811 4.172772 CGCTGCTCGAGCTCGACT 62.173 66.667 33.84 0.00 46.64 4.18
3592 3865 3.110178 CGGGAGAACAACGGCGTC 61.110 66.667 15.17 0.00 0.00 5.19
3627 3918 3.019545 CGCGCGGAGAAGATCGAC 61.020 66.667 24.84 0.00 0.00 4.20
3758 4096 1.519013 GGTATGGGCGTCGCGTTTA 60.519 57.895 11.75 0.00 0.00 2.01
3759 4097 2.816520 GGTATGGGCGTCGCGTTT 60.817 61.111 11.75 0.24 0.00 3.60
3802 4140 0.656495 CGCAGCGTGCATGATCATTC 60.656 55.000 10.93 1.09 45.36 2.67
3838 4176 0.190815 AGGAACCCAACCAAATGCCT 59.809 50.000 0.00 0.00 0.00 4.75
3920 5879 3.066190 CCGTCCCAGTCCGTGCTA 61.066 66.667 0.00 0.00 0.00 3.49
4139 6548 2.230660 ACTTGTAGCAAAGTTGGAGGC 58.769 47.619 0.00 0.00 37.05 4.70
4140 6549 4.385825 TGTACTTGTAGCAAAGTTGGAGG 58.614 43.478 5.00 0.00 40.77 4.30
4172 6581 5.500290 GCACGGTAACTATTCGACTGAATTG 60.500 44.000 0.00 0.00 42.14 2.32
4173 6582 4.565564 GCACGGTAACTATTCGACTGAATT 59.434 41.667 0.00 0.00 42.14 2.17
4174 6583 4.110482 GCACGGTAACTATTCGACTGAAT 58.890 43.478 0.00 0.00 46.41 2.57
4175 6584 3.504863 GCACGGTAACTATTCGACTGAA 58.495 45.455 0.00 0.00 38.76 3.02
4176 6585 2.476686 CGCACGGTAACTATTCGACTGA 60.477 50.000 0.00 0.00 0.00 3.41
4177 6586 1.844357 CGCACGGTAACTATTCGACTG 59.156 52.381 0.00 0.00 0.00 3.51
4178 6587 1.739466 TCGCACGGTAACTATTCGACT 59.261 47.619 0.00 0.00 0.00 4.18
4179 6588 2.107178 CTCGCACGGTAACTATTCGAC 58.893 52.381 0.00 0.00 0.00 4.20
4180 6589 1.064505 CCTCGCACGGTAACTATTCGA 59.935 52.381 0.00 0.00 0.00 3.71
4181 6590 1.202222 ACCTCGCACGGTAACTATTCG 60.202 52.381 0.00 0.00 34.94 3.34
4182 6591 2.190981 CACCTCGCACGGTAACTATTC 58.809 52.381 0.00 0.00 34.94 1.75
4183 6592 1.738030 GCACCTCGCACGGTAACTATT 60.738 52.381 0.00 0.00 41.79 1.73
4184 6593 0.179119 GCACCTCGCACGGTAACTAT 60.179 55.000 0.00 0.00 41.79 2.12
4185 6594 1.213537 GCACCTCGCACGGTAACTA 59.786 57.895 0.00 0.00 41.79 2.24
4186 6595 2.048503 GCACCTCGCACGGTAACT 60.049 61.111 0.00 0.00 41.79 2.24
4187 6596 2.048503 AGCACCTCGCACGGTAAC 60.049 61.111 0.00 0.00 46.13 2.50
4188 6597 2.209064 GAGAGCACCTCGCACGGTAA 62.209 60.000 0.00 0.00 46.13 2.85
4189 6598 2.675423 AGAGCACCTCGCACGGTA 60.675 61.111 0.00 0.00 46.13 4.02
4190 6599 4.057428 GAGAGCACCTCGCACGGT 62.057 66.667 0.00 0.00 46.13 4.83
4197 6606 3.706373 TTGGCCCGAGAGCACCTC 61.706 66.667 0.00 0.00 38.55 3.85
4198 6607 4.021925 GTTGGCCCGAGAGCACCT 62.022 66.667 0.00 0.00 0.00 4.00
4199 6608 4.329545 TGTTGGCCCGAGAGCACC 62.330 66.667 0.00 0.00 0.00 5.01
4200 6609 2.743928 CTGTTGGCCCGAGAGCAC 60.744 66.667 0.00 0.00 0.00 4.40
4201 6610 2.922503 TCTGTTGGCCCGAGAGCA 60.923 61.111 0.00 0.00 0.00 4.26
4202 6611 2.125350 CTCTGTTGGCCCGAGAGC 60.125 66.667 0.00 0.00 0.00 4.09
4203 6612 1.216710 GACTCTGTTGGCCCGAGAG 59.783 63.158 17.22 17.22 39.38 3.20
4204 6613 1.533033 TGACTCTGTTGGCCCGAGA 60.533 57.895 0.00 0.00 0.00 4.04
4205 6614 1.079543 CTGACTCTGTTGGCCCGAG 60.080 63.158 0.00 3.46 0.00 4.63
4206 6615 3.059982 CTGACTCTGTTGGCCCGA 58.940 61.111 0.00 0.00 0.00 5.14
4207 6616 2.743928 GCTGACTCTGTTGGCCCG 60.744 66.667 0.00 0.00 0.00 6.13
4208 6617 1.376553 GAGCTGACTCTGTTGGCCC 60.377 63.158 0.00 0.00 40.03 5.80
4209 6618 4.292784 GAGCTGACTCTGTTGGCC 57.707 61.111 0.00 0.00 40.03 5.36


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

AutoCloner maintained by Alex Coulton.