Multiple sequence alignment - TraesCS4A01G040200

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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 TraesCS4A01G040200 chr4A 100.000 5803 0 0 1 5803 33024488 33030290 0.000000e+00 10717.0
1 TraesCS4A01G040200 chr4A 95.995 824 33 0 4969 5792 11784378 11783555 0.000000e+00 1339.0
2 TraesCS4A01G040200 chr4A 89.815 216 20 2 3387 3600 33026398 33026613 5.730000e-70 276.0
3 TraesCS4A01G040200 chr4A 89.815 216 20 2 1911 2126 33027874 33028087 5.730000e-70 276.0
4 TraesCS4A01G040200 chr4A 88.333 60 7 0 475 534 635815828 635815769 8.070000e-09 73.1
5 TraesCS4A01G040200 chr2D 93.406 2290 96 27 784 3043 546865756 546868020 0.000000e+00 3341.0
6 TraesCS4A01G040200 chr2D 93.144 1765 58 21 3256 4968 546868423 546870176 0.000000e+00 2531.0
7 TraesCS4A01G040200 chr2D 81.140 456 71 7 6 458 546865025 546865468 9.250000e-93 351.0
8 TraesCS4A01G040200 chr2D 88.288 222 23 3 3382 3600 546866879 546867100 4.460000e-66 263.0
9 TraesCS4A01G040200 chr2D 87.387 222 26 2 1905 2126 546868549 546868768 2.680000e-63 254.0
10 TraesCS4A01G040200 chr2B 92.260 2248 109 33 772 2997 653603630 653605834 0.000000e+00 3127.0
11 TraesCS4A01G040200 chr2B 88.889 864 67 16 2996 3846 653605891 653606738 0.000000e+00 1037.0
12 TraesCS4A01G040200 chr2B 93.393 666 31 10 4315 4968 653607477 653608141 0.000000e+00 974.0
13 TraesCS4A01G040200 chr2B 95.536 448 20 0 3877 4324 653606739 653607186 0.000000e+00 717.0
14 TraesCS4A01G040200 chr2B 89.826 403 37 3 1 400 653602739 653603140 1.120000e-141 514.0
15 TraesCS4A01G040200 chr2B 90.950 221 18 2 3382 3600 653604747 653604967 4.400000e-76 296.0
16 TraesCS4A01G040200 chr2B 84.768 302 37 3 393 686 653603251 653603551 1.580000e-75 294.0
17 TraesCS4A01G040200 chr2B 83.796 216 26 4 1911 2126 653606291 653606497 4.590000e-46 196.0
18 TraesCS4A01G040200 chr2A 93.220 1534 84 10 1499 3018 689716427 689714900 0.000000e+00 2239.0
19 TraesCS4A01G040200 chr2A 92.819 1114 57 13 3873 4968 689713744 689712636 0.000000e+00 1592.0
20 TraesCS4A01G040200 chr2A 95.678 833 36 0 4969 5801 717844556 717843724 0.000000e+00 1339.0
21 TraesCS4A01G040200 chr2A 94.673 657 27 5 3211 3866 689714526 689713877 0.000000e+00 1013.0
22 TraesCS4A01G040200 chr2A 93.851 683 24 6 787 1456 689717100 689716423 0.000000e+00 1013.0
23 TraesCS4A01G040200 chr2A 91.928 223 14 3 3382 3600 689716022 689715800 5.650000e-80 309.0
24 TraesCS4A01G040200 chr2A 88.889 216 22 2 1911 2126 689714349 689714136 1.240000e-66 265.0
25 TraesCS4A01G040200 chr2A 94.118 68 4 0 3103 3170 689714594 689714527 2.860000e-18 104.0
26 TraesCS4A01G040200 chr3A 96.043 834 33 0 4968 5801 701931812 701930979 0.000000e+00 1358.0
27 TraesCS4A01G040200 chr3A 95.569 835 37 0 4969 5803 510173792 510172958 0.000000e+00 1338.0
28 TraesCS4A01G040200 chr1A 95.923 834 33 1 4969 5802 521346517 521345685 0.000000e+00 1351.0
29 TraesCS4A01G040200 chr7A 95.889 827 29 1 4968 5794 96003821 96003000 0.000000e+00 1334.0
30 TraesCS4A01G040200 chr7A 95.449 835 38 0 4969 5803 653372344 653373178 0.000000e+00 1332.0
31 TraesCS4A01G040200 chr5A 95.329 835 39 0 4969 5803 379961895 379962729 0.000000e+00 1327.0
32 TraesCS4A01G040200 chr5A 95.210 835 40 0 4969 5803 379967510 379968344 0.000000e+00 1321.0
33 TraesCS4A01G040200 chr7D 87.838 74 9 0 475 548 608479210 608479283 2.880000e-13 87.9
34 TraesCS4A01G040200 chr3B 87.838 74 6 3 475 548 661752490 661752560 3.730000e-12 84.2
35 TraesCS4A01G040200 chr3B 90.625 64 4 2 475 538 803850333 803850394 3.730000e-12 84.2
36 TraesCS4A01G040200 chr3B 89.062 64 5 2 475 538 437544944 437544883 1.730000e-10 78.7
37 TraesCS4A01G040200 chr7B 86.486 74 8 2 475 548 546378638 546378567 4.820000e-11 80.5
38 TraesCS4A01G040200 chr7B 91.667 48 4 0 475 522 717547713 717547666 3.750000e-07 67.6
39 TraesCS4A01G040200 chr6D 87.500 64 8 0 475 538 263042712 263042649 2.240000e-09 75.0
40 TraesCS4A01G040200 chr1B 92.000 50 3 1 475 524 431298713 431298665 1.040000e-07 69.4


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 TraesCS4A01G040200 chr4A 33024488 33030290 5802 False 3756.333333 10717 93.210000 1 5803 3 chr4A.!!$F1 5802
1 TraesCS4A01G040200 chr4A 11783555 11784378 823 True 1339.000000 1339 95.995000 4969 5792 1 chr4A.!!$R1 823
2 TraesCS4A01G040200 chr2D 546865025 546870176 5151 False 1348.000000 3341 88.673000 6 4968 5 chr2D.!!$F1 4962
3 TraesCS4A01G040200 chr2B 653602739 653608141 5402 False 894.375000 3127 89.927250 1 4968 8 chr2B.!!$F1 4967
4 TraesCS4A01G040200 chr2A 717843724 717844556 832 True 1339.000000 1339 95.678000 4969 5801 1 chr2A.!!$R1 832
5 TraesCS4A01G040200 chr2A 689712636 689717100 4464 True 933.571429 2239 92.785429 787 4968 7 chr2A.!!$R2 4181
6 TraesCS4A01G040200 chr3A 701930979 701931812 833 True 1358.000000 1358 96.043000 4968 5801 1 chr3A.!!$R2 833
7 TraesCS4A01G040200 chr3A 510172958 510173792 834 True 1338.000000 1338 95.569000 4969 5803 1 chr3A.!!$R1 834
8 TraesCS4A01G040200 chr1A 521345685 521346517 832 True 1351.000000 1351 95.923000 4969 5802 1 chr1A.!!$R1 833
9 TraesCS4A01G040200 chr7A 96003000 96003821 821 True 1334.000000 1334 95.889000 4968 5794 1 chr7A.!!$R1 826
10 TraesCS4A01G040200 chr7A 653372344 653373178 834 False 1332.000000 1332 95.449000 4969 5803 1 chr7A.!!$F1 834
11 TraesCS4A01G040200 chr5A 379961895 379962729 834 False 1327.000000 1327 95.329000 4969 5803 1 chr5A.!!$F1 834
12 TraesCS4A01G040200 chr5A 379967510 379968344 834 False 1321.000000 1321 95.210000 4969 5803 1 chr5A.!!$F2 834

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
723 941 0.105607 GAAGGGTAGAGATCGGGGGT 60.106 60.0 0.00 0.0 0.0 4.95 F
2622 2920 0.179015 TCTTTGTTGTAAGCCGGGCA 60.179 50.0 23.09 0.0 0.0 5.36 F
3036 3395 0.098200 CGCCGTCGTGTTCTCTGATA 59.902 55.0 0.00 0.0 0.0 2.15 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2659 2959 1.507140 CCTATGGTAGGTTCTGCCCA 58.493 55.000 0.00 0.0 41.18 5.36 R
3829 4414 1.068954 GTGTACCTTGAGCTTTGCTGC 60.069 52.381 0.00 0.0 39.88 5.25 R
4947 6017 0.041312 GCACTGCAGGTTACAACACG 60.041 55.000 19.93 0.0 0.00 4.49 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
51 52 3.430651 GGAAGGAGTTGATGCTCTCTCAG 60.431 52.174 0.00 0.00 35.89 3.35
83 84 0.687354 ACAGATCTTCGTTGGCTGGT 59.313 50.000 0.00 0.00 0.00 4.00
93 94 1.138859 CGTTGGCTGGTATGATGGAGA 59.861 52.381 0.00 0.00 0.00 3.71
125 126 1.224315 CCTGCATGGGATCCAACGA 59.776 57.895 15.23 0.00 36.95 3.85
142 143 0.725784 CGACATTGCTTTGTCCACGC 60.726 55.000 12.15 0.00 42.46 5.34
143 144 0.593128 GACATTGCTTTGTCCACGCT 59.407 50.000 8.01 0.00 40.11 5.07
182 187 2.178521 GCACACTGCATGCTCAGC 59.821 61.111 20.33 11.82 44.26 4.26
207 212 2.904866 TTGCTCCCAACACACGGC 60.905 61.111 0.00 0.00 0.00 5.68
209 214 3.660111 GCTCCCAACACACGGCAC 61.660 66.667 0.00 0.00 0.00 5.01
225 230 1.139853 GGCACTCTGGTTAGCTGCTAT 59.860 52.381 10.64 0.00 0.00 2.97
330 335 4.667858 ACCAATAATTGCCCCTACCTCATA 59.332 41.667 0.00 0.00 0.00 2.15
335 340 8.328758 CAATAATTGCCCCTACCTCATATCTTA 58.671 37.037 0.00 0.00 0.00 2.10
346 351 8.543774 CCTACCTCATATCTTAAAGGCATGTAT 58.456 37.037 0.00 0.00 31.79 2.29
481 612 7.272037 AGTAAAAATGTGGTGAGTTAACTGG 57.728 36.000 14.14 0.00 0.00 4.00
483 614 2.200373 ATGTGGTGAGTTAACTGGGC 57.800 50.000 14.14 0.00 0.00 5.36
488 619 3.057526 GTGGTGAGTTAACTGGGCAATTC 60.058 47.826 14.14 0.00 0.00 2.17
493 624 5.241728 GTGAGTTAACTGGGCAATTCTCTTT 59.758 40.000 14.14 0.00 0.00 2.52
500 631 4.588528 ACTGGGCAATTCTCTTTTGCTTAA 59.411 37.500 8.15 0.00 46.74 1.85
506 637 9.166173 GGGCAATTCTCTTTTGCTTAATTAATT 57.834 29.630 5.89 5.89 46.74 1.40
514 645 7.027161 TCTTTTGCTTAATTAATTGACGAGGC 58.973 34.615 11.05 3.67 0.00 4.70
515 646 4.893424 TGCTTAATTAATTGACGAGGCC 57.107 40.909 11.05 0.00 0.00 5.19
524 655 7.639113 ATTAATTGACGAGGCCAATCTTTTA 57.361 32.000 5.01 0.00 33.51 1.52
525 656 4.965119 ATTGACGAGGCCAATCTTTTAC 57.035 40.909 5.01 0.00 28.89 2.01
527 658 2.014857 GACGAGGCCAATCTTTTACCC 58.985 52.381 5.01 0.00 0.00 3.69
534 665 2.300723 GCCAATCTTTTACCCCCGTTTT 59.699 45.455 0.00 0.00 0.00 2.43
539 670 5.988310 ATCTTTTACCCCCGTTTTAAAGG 57.012 39.130 0.00 0.00 0.00 3.11
549 680 6.110033 CCCCCGTTTTAAAGGAAATAAATGG 58.890 40.000 0.00 0.00 36.73 3.16
561 692 7.592885 AGGAAATAAATGGGATGAGACATTG 57.407 36.000 0.00 0.00 37.38 2.82
648 780 9.218525 TCTCTTTCTCCACCTCATAAGATATTT 57.781 33.333 0.00 0.00 0.00 1.40
679 897 7.400339 TGACACTCTTAAGATAACCCATCTCTT 59.600 37.037 5.44 0.00 43.56 2.85
692 910 1.211212 CATCTCTTCTGGCCATGTGGA 59.789 52.381 5.51 0.00 37.39 4.02
712 930 2.413765 GAGAGGCGCGAAGGGTAG 59.586 66.667 12.10 0.00 44.71 3.18
713 931 2.044252 AGAGGCGCGAAGGGTAGA 60.044 61.111 12.10 0.00 44.71 2.59
715 933 2.044252 AGGCGCGAAGGGTAGAGA 60.044 61.111 12.10 0.00 44.71 3.10
716 934 1.455959 AGGCGCGAAGGGTAGAGAT 60.456 57.895 12.10 0.00 44.71 2.75
717 935 1.007154 GGCGCGAAGGGTAGAGATC 60.007 63.158 12.10 0.00 44.71 2.75
718 936 1.370657 GCGCGAAGGGTAGAGATCG 60.371 63.158 12.10 0.00 44.71 3.69
719 937 1.283181 CGCGAAGGGTAGAGATCGG 59.717 63.158 0.00 0.00 35.91 4.18
720 938 1.660917 GCGAAGGGTAGAGATCGGG 59.339 63.158 0.00 0.00 35.91 5.14
721 939 1.807495 GCGAAGGGTAGAGATCGGGG 61.807 65.000 0.00 0.00 35.91 5.73
722 940 1.179814 CGAAGGGTAGAGATCGGGGG 61.180 65.000 0.00 0.00 0.00 5.40
723 941 0.105607 GAAGGGTAGAGATCGGGGGT 60.106 60.000 0.00 0.00 0.00 4.95
724 942 0.398664 AAGGGTAGAGATCGGGGGTG 60.399 60.000 0.00 0.00 0.00 4.61
725 943 1.075450 GGGTAGAGATCGGGGGTGT 60.075 63.158 0.00 0.00 0.00 4.16
726 944 0.690077 GGGTAGAGATCGGGGGTGTT 60.690 60.000 0.00 0.00 0.00 3.32
727 945 1.201424 GGTAGAGATCGGGGGTGTTT 58.799 55.000 0.00 0.00 0.00 2.83
728 946 1.558294 GGTAGAGATCGGGGGTGTTTT 59.442 52.381 0.00 0.00 0.00 2.43
729 947 2.026542 GGTAGAGATCGGGGGTGTTTTT 60.027 50.000 0.00 0.00 0.00 1.94
781 1038 5.106317 GCGAAATGAAAACCAGTCCATAGAA 60.106 40.000 0.00 0.00 0.00 2.10
784 1041 7.521423 CGAAATGAAAACCAGTCCATAGAACAA 60.521 37.037 0.00 0.00 0.00 2.83
841 1098 0.391130 CCCAAACAGCCTTCGATCGA 60.391 55.000 15.15 15.15 0.00 3.59
842 1099 1.656652 CCAAACAGCCTTCGATCGAT 58.343 50.000 20.18 0.00 0.00 3.59
852 1109 4.616592 CGATCGATCGTCCCAGTG 57.383 61.111 33.95 8.77 44.74 3.66
853 1110 2.022520 CGATCGATCGTCCCAGTGA 58.977 57.895 33.95 0.00 44.74 3.41
854 1111 0.317103 CGATCGATCGTCCCAGTGAC 60.317 60.000 33.95 1.08 44.74 3.67
855 1112 0.738975 GATCGATCGTCCCAGTGACA 59.261 55.000 15.94 0.00 44.71 3.58
865 1122 1.164041 CCCAGTGACAACCACCGAAC 61.164 60.000 0.00 0.00 46.87 3.95
885 1142 1.270465 CCCCAAGAAAAGTACGGTCGT 60.270 52.381 0.69 0.69 0.00 4.34
888 1145 4.248058 CCCAAGAAAAGTACGGTCGTTAT 58.752 43.478 0.16 0.00 0.00 1.89
919 1176 0.323360 ACCATCGTTCACCCCCAATG 60.323 55.000 0.00 0.00 0.00 2.82
935 1192 0.329596 AATGCCACCTTCACCTCTCC 59.670 55.000 0.00 0.00 0.00 3.71
1265 1524 0.249398 CCACTGTACCTTCCCTTCCG 59.751 60.000 0.00 0.00 0.00 4.30
1286 1545 2.102757 GTCTCTTCCCTCCCGATTTACC 59.897 54.545 0.00 0.00 0.00 2.85
1327 1586 0.831307 AGGAATCTAACCGGGTGCTC 59.169 55.000 0.00 0.00 0.00 4.26
1354 1625 2.425668 AGCTGTTTTGGTGTTTAGCGTT 59.574 40.909 0.00 0.00 36.36 4.84
1355 1626 3.119280 AGCTGTTTTGGTGTTTAGCGTTT 60.119 39.130 0.00 0.00 36.36 3.60
1480 1755 1.663643 GTGTGGATTTCGATGCGCTAA 59.336 47.619 9.73 0.00 0.00 3.09
1481 1756 2.287915 GTGTGGATTTCGATGCGCTAAT 59.712 45.455 9.73 0.00 0.00 1.73
1482 1757 2.287644 TGTGGATTTCGATGCGCTAATG 59.712 45.455 9.73 0.00 0.00 1.90
1596 1871 2.275318 GAGCTGCGTTGATCTTTAGCT 58.725 47.619 0.00 0.00 43.52 3.32
1666 1941 0.179059 TTGCGAGCTTGGACTGTTGA 60.179 50.000 2.37 0.00 0.00 3.18
1795 2071 7.644157 GTGATTCTACTTTGGTGTTTGTTTCTC 59.356 37.037 0.00 0.00 0.00 2.87
1858 2134 6.872920 TGGTTGTTTCACTTGCTTTATCTTT 58.127 32.000 0.00 0.00 0.00 2.52
1873 2157 6.515035 GCTTTATCTTTTTGTACCAGCACAGT 60.515 38.462 0.00 0.00 0.00 3.55
1954 2238 3.950395 AGATTTGGGCTGTCTAATGCTTC 59.050 43.478 0.00 0.00 0.00 3.86
2117 2404 1.507562 TTTCGAACATCAGCTTGCGA 58.492 45.000 0.00 0.00 0.00 5.10
2128 2415 2.441378 GCTTGCGATCGTGCACGTA 61.441 57.895 35.74 23.61 46.25 3.57
2235 2523 0.467844 AGAAAGGCCATGTGTGTGCA 60.468 50.000 5.01 0.00 0.00 4.57
2276 2565 9.624373 AAGAAGATCATGATACTAAAATGCAGT 57.376 29.630 8.54 0.00 0.00 4.40
2316 2607 6.980397 CCAAGTTAATTTCACTTGCTGAAGTT 59.020 34.615 18.46 1.55 46.71 2.66
2323 2614 5.574891 TTCACTTGCTGAAGTTGCTTAAA 57.425 34.783 0.00 0.00 40.68 1.52
2557 2855 2.995258 CAACATAGCAACAAATGTGGGC 59.005 45.455 3.11 3.11 36.47 5.36
2618 2916 4.201724 GCTGATACTCTTTGTTGTAAGCCG 60.202 45.833 0.00 0.00 0.00 5.52
2620 2918 1.892209 ACTCTTTGTTGTAAGCCGGG 58.108 50.000 2.18 0.00 0.00 5.73
2621 2919 0.521735 CTCTTTGTTGTAAGCCGGGC 59.478 55.000 12.11 12.11 0.00 6.13
2622 2920 0.179015 TCTTTGTTGTAAGCCGGGCA 60.179 50.000 23.09 0.00 0.00 5.36
2624 2922 0.885196 TTTGTTGTAAGCCGGGCATC 59.115 50.000 23.09 11.18 0.00 3.91
2625 2923 0.250945 TTGTTGTAAGCCGGGCATCA 60.251 50.000 23.09 13.71 0.00 3.07
2659 2959 5.245531 TCTCAGCACGGTAGAAAAATTGAT 58.754 37.500 0.00 0.00 0.00 2.57
2702 3002 4.595762 ACAGAAGCAAATGAGCAAACAT 57.404 36.364 0.00 0.00 36.85 2.71
2721 3021 7.925483 GCAAACATCTAGAGTTACTCAGATGAT 59.075 37.037 34.15 27.49 42.11 2.45
2759 3059 0.827507 GCAAGCTGGGGTCCTTGAAA 60.828 55.000 4.70 0.00 40.59 2.69
2788 3088 4.777896 ACAGGATTACAGAAGAGCCTTACA 59.222 41.667 0.00 0.00 0.00 2.41
2862 3162 1.215647 CTACGCCAGTCTCGCCTTT 59.784 57.895 0.00 0.00 0.00 3.11
2876 3176 2.034879 CCTTTGCCTCGACGTGCAT 61.035 57.895 13.81 0.00 37.33 3.96
2982 3282 3.094062 GCTGATGGCTAGGACGGCA 62.094 63.158 0.00 0.00 43.95 5.69
3018 3377 2.027625 GTCTCCGTTGGCAGGTTCG 61.028 63.158 0.00 0.00 0.00 3.95
3036 3395 0.098200 CGCCGTCGTGTTCTCTGATA 59.902 55.000 0.00 0.00 0.00 2.15
3046 3413 0.187606 TTCTCTGATAGGGGCGGCTA 59.812 55.000 9.56 0.00 0.00 3.93
3076 3451 2.933287 TGACCCCAACCGAGGCAT 60.933 61.111 0.00 0.00 0.00 4.40
3086 3461 2.507944 CGAGGCATCAAGGGGAGG 59.492 66.667 0.00 0.00 0.00 4.30
3109 3689 2.811317 GGCAGCGACGAGACAAGG 60.811 66.667 0.00 0.00 0.00 3.61
3110 3690 2.049063 GCAGCGACGAGACAAGGT 60.049 61.111 0.00 0.00 0.00 3.50
3174 3754 0.735471 GCTGGGAGGCGATTTTTCTC 59.265 55.000 0.00 0.00 0.00 2.87
3198 3778 1.229951 AGAGATGGAAGTGGGGGCA 60.230 57.895 0.00 0.00 0.00 5.36
3202 3782 2.861271 GATGGAAGTGGGGGCAAGGG 62.861 65.000 0.00 0.00 0.00 3.95
3242 3826 1.304299 CATGGGATGTGTGGGTGCA 60.304 57.895 0.00 0.00 0.00 4.57
3254 3838 2.124570 GGTGCATGGCTGACGGAT 60.125 61.111 0.00 0.00 0.00 4.18
3258 3842 1.750399 GCATGGCTGACGGATTGGT 60.750 57.895 0.00 0.00 0.00 3.67
3265 3849 1.156736 CTGACGGATTGGTGGTTGTC 58.843 55.000 0.00 0.00 0.00 3.18
3338 3922 2.040779 GGACGGGGAGGGAAGGAT 60.041 66.667 0.00 0.00 0.00 3.24
3631 4216 3.121030 CCTGCCCGCAGTCTTTCG 61.121 66.667 15.22 0.00 42.15 3.46
3640 4225 2.921754 CCGCAGTCTTTCGGTTTACTAG 59.078 50.000 2.83 0.00 40.72 2.57
3643 4228 5.338365 CGCAGTCTTTCGGTTTACTAGTAT 58.662 41.667 2.79 0.00 0.00 2.12
3644 4229 5.454877 CGCAGTCTTTCGGTTTACTAGTATC 59.545 44.000 2.79 0.53 0.00 2.24
3645 4230 6.327934 GCAGTCTTTCGGTTTACTAGTATCA 58.672 40.000 2.79 0.00 0.00 2.15
3654 4239 8.510243 TCGGTTTACTAGTATCAGTATTCACA 57.490 34.615 2.79 0.00 31.24 3.58
3730 4315 7.727578 TGGATACTCTAGGTTGAATACACAA 57.272 36.000 0.00 0.00 37.61 3.33
3829 4414 2.183478 TGGTGCTGTATGGTCAACAG 57.817 50.000 0.00 0.00 45.80 3.16
3838 4423 0.316204 ATGGTCAACAGCAGCAAAGC 59.684 50.000 0.00 0.00 32.21 3.51
4031 4765 1.296715 CAGGTACACACTGGGGAGC 59.703 63.158 0.00 0.00 32.38 4.70
4237 4971 3.125316 CACCAGAAGTCGATAGCCAAAAC 59.875 47.826 0.00 0.00 0.00 2.43
4238 4972 2.678336 CCAGAAGTCGATAGCCAAAACC 59.322 50.000 0.00 0.00 0.00 3.27
4374 5408 7.440255 TCAAGCTGTAAACACTAGGAACTTAAC 59.560 37.037 0.00 0.00 41.75 2.01
4379 5413 7.567458 TGTAAACACTAGGAACTTAACAACCT 58.433 34.615 0.00 0.00 41.75 3.50
4590 5641 3.365868 GCTGAGCTCTATACTCATCACCG 60.366 52.174 16.19 0.00 42.99 4.94
4815 5866 4.919168 GGTTCTTGTAAAATGTAAACGGGC 59.081 41.667 0.00 0.00 0.00 6.13
4823 5874 1.024579 ATGTAAACGGGCTTCGGCAG 61.025 55.000 5.17 0.00 44.45 4.85
4853 5904 0.179018 ATAAGCCGATCCCCTTGTGC 60.179 55.000 3.45 0.00 0.00 4.57
4862 5913 0.981183 TCCCCTTGTGCGATGTAACT 59.019 50.000 0.00 0.00 0.00 2.24
4865 5916 3.199071 TCCCCTTGTGCGATGTAACTTAT 59.801 43.478 0.00 0.00 0.00 1.73
4866 5917 3.560068 CCCCTTGTGCGATGTAACTTATC 59.440 47.826 0.00 0.00 0.00 1.75
4867 5918 4.188462 CCCTTGTGCGATGTAACTTATCA 58.812 43.478 0.00 0.00 0.00 2.15
5259 6329 1.066858 GCAGCAGTAGCACTGGACTTA 60.067 52.381 15.16 0.00 46.01 2.24
5306 6376 1.168407 TCGAGGAGGTTGTCGACGTT 61.168 55.000 11.62 0.00 40.19 3.99
5402 6472 0.807496 GCAGAGCGCTCCTCAAAAAT 59.193 50.000 32.94 9.90 43.31 1.82
5506 6576 0.908198 GGGATGAGGAAGACAGCAGT 59.092 55.000 0.00 0.00 0.00 4.40
5590 6660 1.140252 GCGACCTCCCTTTTATAGGCA 59.860 52.381 0.00 0.00 43.27 4.75
5657 6727 3.563808 CGGGAGATGAAACAAACAGACAA 59.436 43.478 0.00 0.00 0.00 3.18
5659 6729 4.527564 GGAGATGAAACAAACAGACAACG 58.472 43.478 0.00 0.00 0.00 4.10
5717 6787 2.101249 CAGCAAAAACTTTCCAGCTCCA 59.899 45.455 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 6.110543 TGCAATCTAGTTCATTGATCAACG 57.889 37.500 11.07 1.83 33.69 4.10
51 52 5.299782 ACGAAGATCTGTTGATACTCCTACC 59.700 44.000 0.00 0.00 32.19 3.18
83 84 7.441890 GAGACTCTTCGTATTCTCCATCATA 57.558 40.000 0.00 0.00 0.00 2.15
93 94 3.181471 CCATGCAGGAGACTCTTCGTATT 60.181 47.826 0.00 0.00 40.21 1.89
125 126 1.032014 AAGCGTGGACAAAGCAATGT 58.968 45.000 0.00 0.00 35.90 2.71
142 143 0.029035 GCCATGCGCTCATCTTCAAG 59.971 55.000 9.73 0.00 0.00 3.02
143 144 2.100846 GCCATGCGCTCATCTTCAA 58.899 52.632 9.73 0.00 0.00 2.69
201 206 1.004918 GCTAACCAGAGTGCCGTGT 60.005 57.895 0.00 0.00 0.00 4.49
207 212 2.208431 GCATAGCAGCTAACCAGAGTG 58.792 52.381 6.13 0.00 0.00 3.51
209 214 1.139654 TGGCATAGCAGCTAACCAGAG 59.860 52.381 19.19 3.22 34.17 3.35
225 230 6.663093 ACAGATTTTACATAAACCATCTGGCA 59.337 34.615 20.19 0.00 40.93 4.92
309 314 6.725364 AGATATGAGGTAGGGGCAATTATTG 58.275 40.000 0.00 0.00 0.00 1.90
330 335 8.995027 TCAACCAATATACATGCCTTTAAGAT 57.005 30.769 0.00 0.00 0.00 2.40
335 340 8.995027 TCTTATCAACCAATATACATGCCTTT 57.005 30.769 0.00 0.00 0.00 3.11
410 415 9.367160 TGAGATAATCATTGTACTCCTACATCA 57.633 33.333 0.00 0.00 30.56 3.07
458 581 6.443792 CCCAGTTAACTCACCACATTTTTAC 58.556 40.000 4.77 0.00 0.00 2.01
466 597 1.975660 TTGCCCAGTTAACTCACCAC 58.024 50.000 4.77 0.00 0.00 4.16
488 619 7.218963 GCCTCGTCAATTAATTAAGCAAAAGAG 59.781 37.037 0.00 7.85 0.00 2.85
493 624 4.702612 TGGCCTCGTCAATTAATTAAGCAA 59.297 37.500 3.32 0.00 0.00 3.91
500 631 6.530019 AAAAGATTGGCCTCGTCAATTAAT 57.470 33.333 3.32 0.00 38.02 1.40
506 637 2.617021 GGGTAAAAGATTGGCCTCGTCA 60.617 50.000 3.32 0.00 0.00 4.35
514 645 5.725325 TTAAAACGGGGGTAAAAGATTGG 57.275 39.130 0.00 0.00 0.00 3.16
515 646 6.015265 TCCTTTAAAACGGGGGTAAAAGATTG 60.015 38.462 0.00 0.00 0.00 2.67
524 655 6.295973 CCATTTATTTCCTTTAAAACGGGGGT 60.296 38.462 0.00 0.00 0.00 4.95
525 656 6.110033 CCATTTATTTCCTTTAAAACGGGGG 58.890 40.000 0.00 0.00 0.00 5.40
527 658 6.937392 TCCCATTTATTTCCTTTAAAACGGG 58.063 36.000 0.00 0.00 37.03 5.28
534 665 9.713684 AATGTCTCATCCCATTTATTTCCTTTA 57.286 29.630 0.00 0.00 0.00 1.85
539 670 7.223387 GCAACAATGTCTCATCCCATTTATTTC 59.777 37.037 0.00 0.00 0.00 2.17
549 680 4.445452 ACATTGCAACAATGTCTCATCC 57.555 40.909 17.82 0.00 36.18 3.51
561 692 7.953710 GAAATGATTTCTTAGCAACATTGCAAC 59.046 33.333 18.31 0.00 44.94 4.17
618 749 6.549364 TCTTATGAGGTGGAGAAAGAGAGATC 59.451 42.308 0.00 0.00 0.00 2.75
619 750 6.439487 TCTTATGAGGTGGAGAAAGAGAGAT 58.561 40.000 0.00 0.00 0.00 2.75
621 752 6.729690 ATCTTATGAGGTGGAGAAAGAGAG 57.270 41.667 0.00 0.00 0.00 3.20
648 780 8.141298 TGGGTTATCTTAAGAGTGTCATGTAA 57.859 34.615 11.53 0.00 0.00 2.41
679 897 3.002583 TCGCTCCACATGGCCAGA 61.003 61.111 13.05 1.11 34.44 3.86
702 920 1.660917 CCCGATCTCTACCCTTCGC 59.339 63.158 0.00 0.00 0.00 4.70
705 923 0.398664 CACCCCCGATCTCTACCCTT 60.399 60.000 0.00 0.00 0.00 3.95
706 924 1.233369 CACCCCCGATCTCTACCCT 59.767 63.158 0.00 0.00 0.00 4.34
707 925 0.690077 AACACCCCCGATCTCTACCC 60.690 60.000 0.00 0.00 0.00 3.69
709 927 3.345508 AAAAACACCCCCGATCTCTAC 57.654 47.619 0.00 0.00 0.00 2.59
757 975 3.575965 ATGGACTGGTTTTCATTTCGC 57.424 42.857 0.00 0.00 0.00 4.70
784 1041 4.377021 TGTCAAGCTTAGTCAACGAATGT 58.623 39.130 0.00 0.00 0.00 2.71
844 1101 1.597027 CGGTGGTTGTCACTGGGAC 60.597 63.158 2.32 2.32 46.35 4.46
845 1102 2.825982 CGGTGGTTGTCACTGGGA 59.174 61.111 0.00 0.00 46.35 4.37
849 1106 1.147600 GGGTTCGGTGGTTGTCACT 59.852 57.895 0.00 0.00 45.38 3.41
850 1107 1.895231 GGGGTTCGGTGGTTGTCAC 60.895 63.158 0.00 0.00 45.34 3.67
851 1108 1.923006 TTGGGGTTCGGTGGTTGTCA 61.923 55.000 0.00 0.00 0.00 3.58
852 1109 1.152922 TTGGGGTTCGGTGGTTGTC 60.153 57.895 0.00 0.00 0.00 3.18
853 1110 1.152839 CTTGGGGTTCGGTGGTTGT 60.153 57.895 0.00 0.00 0.00 3.32
854 1111 0.466555 TTCTTGGGGTTCGGTGGTTG 60.467 55.000 0.00 0.00 0.00 3.77
855 1112 0.259356 TTTCTTGGGGTTCGGTGGTT 59.741 50.000 0.00 0.00 0.00 3.67
865 1122 1.270465 ACGACCGTACTTTTCTTGGGG 60.270 52.381 0.00 0.00 0.00 4.96
885 1142 0.630673 ATGGTTGGAGCTGGGCATAA 59.369 50.000 0.00 0.00 0.00 1.90
888 1145 2.356278 GATGGTTGGAGCTGGGCA 59.644 61.111 0.00 0.00 0.00 5.36
919 1176 2.671682 GGGAGAGGTGAAGGTGGC 59.328 66.667 0.00 0.00 0.00 5.01
1265 1524 2.102757 GGTAAATCGGGAGGGAAGAGAC 59.897 54.545 0.00 0.00 0.00 3.36
1286 1545 1.750399 CTCGGGAAACAGCATGGGG 60.750 63.158 0.00 0.00 43.62 4.96
1327 1586 5.458779 GCTAAACACCAAAACAGCTAACTTG 59.541 40.000 0.00 0.00 0.00 3.16
1354 1625 7.270757 TCACAAAATTTGCAGTAAGCTCTAA 57.729 32.000 5.52 0.00 45.94 2.10
1355 1626 6.875948 TCACAAAATTTGCAGTAAGCTCTA 57.124 33.333 5.52 0.00 45.94 2.43
1480 1755 1.915228 ACCCCAAGTGATAGCGCAT 59.085 52.632 11.47 0.06 0.00 4.73
1481 1756 3.399046 ACCCCAAGTGATAGCGCA 58.601 55.556 11.47 0.00 0.00 6.09
1491 1766 0.961019 CATCCAACACACACCCCAAG 59.039 55.000 0.00 0.00 0.00 3.61
1596 1871 3.736100 CGCCAGCAACCGCATCAA 61.736 61.111 0.00 0.00 42.27 2.57
1608 1883 2.124570 AGGCCTACAATGCGCCAG 60.125 61.111 1.29 0.00 45.56 4.85
1781 2057 5.105567 TCCACTAAGAGAAACAAACACCA 57.894 39.130 0.00 0.00 0.00 4.17
1795 2071 3.755378 ACATTTTGAGCTGCTCCACTAAG 59.245 43.478 25.61 13.79 0.00 2.18
1858 2134 2.700722 TGTCACTGTGCTGGTACAAA 57.299 45.000 2.12 0.00 38.70 2.83
1907 2191 2.799412 GGAGCTGAATGTGAGAATAGCG 59.201 50.000 0.00 0.00 36.36 4.26
1954 2238 8.530311 AGGTCTGCAGATATCATTATCAGTTAG 58.470 37.037 21.47 0.00 37.31 2.34
1971 2255 2.295349 ACAAAGCATGAAAGGTCTGCAG 59.705 45.455 7.63 7.63 38.37 4.41
1973 2257 3.667960 CGTACAAAGCATGAAAGGTCTGC 60.668 47.826 0.00 0.00 36.15 4.26
2117 2404 4.687018 TGTAAACTGAAATACGTGCACGAT 59.313 37.500 42.94 27.78 43.02 3.73
2299 2590 4.660789 AAGCAACTTCAGCAAGTGAAAT 57.339 36.364 0.00 0.00 44.83 2.17
2361 2652 5.779771 AGGTATGTGGGAATTGAACATGTTT 59.220 36.000 13.36 0.00 36.08 2.83
2505 2803 5.512753 TTGAGCAGTATTTTGCAGTCAAA 57.487 34.783 0.52 0.00 46.47 2.69
2618 2916 5.643379 TGAGAAGTACATTTTTGATGCCC 57.357 39.130 0.00 0.00 0.00 5.36
2620 2918 5.570589 GTGCTGAGAAGTACATTTTTGATGC 59.429 40.000 0.00 0.00 0.00 3.91
2621 2919 5.791974 CGTGCTGAGAAGTACATTTTTGATG 59.208 40.000 0.00 0.00 0.00 3.07
2622 2920 5.106555 CCGTGCTGAGAAGTACATTTTTGAT 60.107 40.000 0.00 0.00 0.00 2.57
2624 2922 4.024048 ACCGTGCTGAGAAGTACATTTTTG 60.024 41.667 0.00 0.00 0.00 2.44
2625 2923 4.134563 ACCGTGCTGAGAAGTACATTTTT 58.865 39.130 0.00 0.00 0.00 1.94
2659 2959 1.507140 CCTATGGTAGGTTCTGCCCA 58.493 55.000 0.00 0.00 41.18 5.36
2702 3002 8.986929 TGATTGATCATCTGAGTAACTCTAGA 57.013 34.615 0.00 0.00 32.34 2.43
2721 3021 3.954200 TGCTCAATAAGGTGCTGATTGA 58.046 40.909 0.00 0.00 37.27 2.57
2759 3059 5.337975 GGCTCTTCTGTAATCCTGTCTTCTT 60.338 44.000 0.00 0.00 0.00 2.52
2767 3067 5.485708 ACTTGTAAGGCTCTTCTGTAATCCT 59.514 40.000 0.00 0.00 0.00 3.24
2788 3088 4.398358 CCACAAGATCAGATGAATGCACTT 59.602 41.667 0.00 0.00 0.00 3.16
2862 3162 2.432456 GTCATGCACGTCGAGGCA 60.432 61.111 16.16 16.16 45.23 4.75
2876 3176 2.203401 CCGTTGAGTTTGTAACCGTCA 58.797 47.619 0.00 0.00 0.00 4.35
2884 3184 1.134340 TGGCAGTACCGTTGAGTTTGT 60.134 47.619 0.00 0.00 43.94 2.83
2886 3186 1.589803 GTGGCAGTACCGTTGAGTTT 58.410 50.000 0.00 0.00 43.94 2.66
2936 3236 2.435586 CCGACAGCAAGCCCTCTG 60.436 66.667 0.00 0.00 36.45 3.35
2944 3244 3.166490 TTACCGGCACCGACAGCAA 62.166 57.895 11.42 0.00 42.83 3.91
3012 3371 2.355481 GAACACGACGGCGAACCT 60.355 61.111 22.49 0.00 41.64 3.50
3018 3377 1.534175 CCTATCAGAGAACACGACGGC 60.534 57.143 0.00 0.00 0.00 5.68
3025 3384 1.686325 GCCGCCCCTATCAGAGAACA 61.686 60.000 0.00 0.00 0.00 3.18
3046 3413 3.239253 GGTCACCGGTGTGGGAGT 61.239 66.667 32.74 0.00 44.64 3.85
3071 3446 2.614969 TGCCTCCCCTTGATGCCT 60.615 61.111 0.00 0.00 34.05 4.75
3073 3448 2.123982 CCTGCCTCCCCTTGATGC 60.124 66.667 0.00 0.00 35.40 3.91
3076 3451 2.285668 CCTCCTGCCTCCCCTTGA 60.286 66.667 0.00 0.00 0.00 3.02
3089 3464 3.282745 TTGTCTCGTCGCTGCCTCC 62.283 63.158 0.00 0.00 0.00 4.30
3097 3472 2.805353 CCGCACCTTGTCTCGTCG 60.805 66.667 0.00 0.00 0.00 5.12
3157 3737 1.351017 ACTGAGAAAAATCGCCTCCCA 59.649 47.619 0.00 0.00 0.00 4.37
3174 3754 1.209019 CCCACTTCCATCTCTCCACTG 59.791 57.143 0.00 0.00 0.00 3.66
3202 3782 3.866582 CACGCCCCATCTCTCCCC 61.867 72.222 0.00 0.00 0.00 4.81
3225 3809 0.685131 CATGCACCCACACATCCCAT 60.685 55.000 0.00 0.00 0.00 4.00
3242 3826 1.077501 CCACCAATCCGTCAGCCAT 60.078 57.895 0.00 0.00 0.00 4.40
3314 3898 4.087892 CCTCCCCGTCCAGTGCAG 62.088 72.222 0.00 0.00 0.00 4.41
3318 3902 2.284699 CTTCCCTCCCCGTCCAGT 60.285 66.667 0.00 0.00 0.00 4.00
3324 3908 0.105658 TACTCATCCTTCCCTCCCCG 60.106 60.000 0.00 0.00 0.00 5.73
3338 3922 1.545136 TGCCGTCGTAATGGTTACTCA 59.455 47.619 0.00 0.00 33.98 3.41
3679 4264 7.122055 TCCACAACACAAGTGAGAAAAACTAAT 59.878 33.333 7.28 0.00 39.30 1.73
3682 4267 4.764823 TCCACAACACAAGTGAGAAAAACT 59.235 37.500 7.28 0.00 39.30 2.66
3829 4414 1.068954 GTGTACCTTGAGCTTTGCTGC 60.069 52.381 0.00 0.00 39.88 5.25
3838 4423 6.525578 TGTTCCATAGTAGTGTACCTTGAG 57.474 41.667 0.00 0.00 0.00 3.02
4031 4765 6.088824 GTCTGAATAAATGTCAGCTTTGGTG 58.911 40.000 0.00 0.00 41.94 4.17
4237 4971 4.639310 AGAGCAAATAAGAGCAATGAGTGG 59.361 41.667 0.00 0.00 0.00 4.00
4238 4972 5.448768 CCAGAGCAAATAAGAGCAATGAGTG 60.449 44.000 0.00 0.00 0.00 3.51
4379 5413 4.354662 AGTGACCCTTTTACCAACCAAAA 58.645 39.130 0.00 0.00 0.00 2.44
4590 5641 3.004944 CCTCGGAGGATTCTTACTGCTAC 59.995 52.174 19.57 0.00 37.67 3.58
4815 5866 6.347725 GGCTTATTTGATATACACTGCCGAAG 60.348 42.308 0.00 0.00 0.00 3.79
4823 5874 5.585047 GGGGATCGGCTTATTTGATATACAC 59.415 44.000 0.00 0.00 0.00 2.90
4853 5904 4.509230 AGCACAGCATGATAAGTTACATCG 59.491 41.667 0.00 0.00 39.69 3.84
4862 5913 4.152938 GCATATCGAAGCACAGCATGATAA 59.847 41.667 0.00 0.00 39.69 1.75
4865 5916 1.869132 GCATATCGAAGCACAGCATGA 59.131 47.619 0.00 0.00 39.69 3.07
4866 5917 1.398071 CGCATATCGAAGCACAGCATG 60.398 52.381 8.30 0.00 41.49 4.06
4867 5918 0.863799 CGCATATCGAAGCACAGCAT 59.136 50.000 8.30 0.00 41.67 3.79
4947 6017 0.041312 GCACTGCAGGTTACAACACG 60.041 55.000 19.93 0.00 0.00 4.49
4948 6018 1.021202 TGCACTGCAGGTTACAACAC 58.979 50.000 19.93 0.00 33.32 3.32
5068 6138 4.574421 GCAGAAGCTATTTTCCTTCTCTCC 59.426 45.833 0.27 0.00 44.30 3.71
5306 6376 1.859427 CGACGACGACTTCTTCCCCA 61.859 60.000 0.00 0.00 42.66 4.96
5395 6465 6.187682 GGGAGAAGGGTGATAAGATTTTTGA 58.812 40.000 0.00 0.00 0.00 2.69
5402 6472 2.544844 ACGGGAGAAGGGTGATAAGA 57.455 50.000 0.00 0.00 0.00 2.10
5506 6576 1.757118 CCGGTTCCAATCTCTGAGCTA 59.243 52.381 0.00 0.00 0.00 3.32
5590 6660 1.181786 CTCTCGCCTCCTTCTCTTGT 58.818 55.000 0.00 0.00 0.00 3.16
5717 6787 2.686915 CGGGTATACGAAAGGTCACTCT 59.313 50.000 0.00 0.00 35.47 3.24


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

AutoCloner maintained by Alex Coulton.