Multiple sequence alignment - TraesCS1A01G391100

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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 TraesCS1A01G391100 chr1A 100.000 3041 0 0 1 3041 558320591 558323631 0.000000e+00 5616.0
1 TraesCS1A01G391100 chr1D 90.989 2497 163 25 137 2586 465978107 465980588 0.000000e+00 3308.0
2 TraesCS1A01G391100 chr1D 85.397 315 30 7 2600 2913 465980845 465981144 2.280000e-81 313.0
3 TraesCS1A01G391100 chr1D 81.994 311 47 8 2299 2606 57157354 57157050 3.890000e-64 255.0
4 TraesCS1A01G391100 chr1D 97.619 42 1 0 3000 3041 465981158 465981199 4.210000e-09 73.1
5 TraesCS1A01G391100 chr1B 89.289 2166 147 36 60 2180 642791186 642793311 0.000000e+00 2636.0
6 TraesCS1A01G391100 chr1B 91.859 651 40 6 1608 2255 642990583 642991223 0.000000e+00 896.0
7 TraesCS1A01G391100 chr1B 89.178 730 41 19 966 1683 642802672 642803375 0.000000e+00 876.0
8 TraesCS1A01G391100 chr1B 85.765 281 29 3 1866 2146 642811150 642811419 1.380000e-73 287.0
9 TraesCS1A01G391100 chr1B 86.747 249 16 6 2784 3016 643014646 643014893 8.360000e-66 261.0
10 TraesCS1A01G391100 chr1B 91.176 102 4 3 2187 2287 642795561 642795658 1.900000e-27 134.0
11 TraesCS1A01G391100 chr5A 87.525 497 32 2 809 1305 546208420 546207954 5.730000e-152 547.0
12 TraesCS1A01G391100 chr7A 83.959 293 38 9 2292 2580 521906036 521905749 3.860000e-69 272.0
13 TraesCS1A01G391100 chr7A 83.955 268 31 11 2299 2561 234853180 234853440 2.340000e-61 246.0
14 TraesCS1A01G391100 chr7A 85.981 107 14 1 1 107 718339046 718339151 2.480000e-21 113.0
15 TraesCS1A01G391100 chr7D 83.618 293 38 10 2299 2588 41928819 41929104 1.800000e-67 267.0
16 TraesCS1A01G391100 chr7D 82.562 281 41 8 2301 2576 625527236 625527513 1.090000e-59 241.0
17 TraesCS1A01G391100 chr7D 82.278 237 26 5 1330 1566 37427962 37427742 1.110000e-44 191.0
18 TraesCS1A01G391100 chr7D 85.185 108 14 2 1 107 4583804 4583910 3.210000e-20 110.0
19 TraesCS1A01G391100 chr2D 83.929 280 35 10 2299 2575 647435704 647435432 3.010000e-65 259.0
20 TraesCS1A01G391100 chr2D 85.849 106 13 2 2601 2705 572259298 572259402 8.910000e-21 111.0
21 TraesCS1A01G391100 chr2D 85.185 108 14 2 2595 2700 578935270 578935163 3.210000e-20 110.0
22 TraesCS1A01G391100 chr4A 83.636 275 41 4 2305 2576 540941252 540940979 3.890000e-64 255.0
23 TraesCS1A01G391100 chr6A 82.746 284 39 9 2301 2580 608315629 608315352 8.420000e-61 244.0
24 TraesCS1A01G391100 chr2A 82.909 275 43 4 2305 2576 66020585 66020312 8.420000e-61 244.0
25 TraesCS1A01G391100 chr6B 86.792 106 13 1 2 107 686812378 686812274 1.920000e-22 117.0
26 TraesCS1A01G391100 chr7B 84.167 120 16 2 2595 2713 577683155 577683038 2.480000e-21 113.0
27 TraesCS1A01G391100 chr7B 83.478 115 16 2 2600 2713 524226406 524226294 1.490000e-18 104.0
28 TraesCS1A01G391100 chr5D 85.047 107 15 1 1 107 462731455 462731560 1.150000e-19 108.0
29 TraesCS1A01G391100 chr5B 85.437 103 15 0 1 103 356181134 356181236 1.150000e-19 108.0
30 TraesCS1A01G391100 chr3D 83.929 112 18 0 2595 2706 1649285 1649174 1.150000e-19 108.0
31 TraesCS1A01G391100 chr2B 84.906 106 14 2 2594 2698 50246 50350 4.150000e-19 106.0
32 TraesCS1A01G391100 chrUn 85.859 99 13 1 2600 2697 42436787 42436885 1.490000e-18 104.0
33 TraesCS1A01G391100 chrUn 85.859 99 13 1 2600 2697 42534880 42534978 1.490000e-18 104.0
34 TraesCS1A01G391100 chrUn 86.813 91 11 1 18 107 243400521 243400431 1.930000e-17 100.0
35 TraesCS1A01G391100 chrUn 86.813 91 11 1 18 107 267334521 267334611 1.930000e-17 100.0
36 TraesCS1A01G391100 chr6D 82.243 107 16 3 1 107 289143346 289143449 4.180000e-14 89.8


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 TraesCS1A01G391100 chr1A 558320591 558323631 3040 False 5616.000000 5616 100.0000 1 3041 1 chr1A.!!$F1 3040
1 TraesCS1A01G391100 chr1D 465978107 465981199 3092 False 1231.366667 3308 91.3350 137 3041 3 chr1D.!!$F1 2904
2 TraesCS1A01G391100 chr1B 642791186 642795658 4472 False 1385.000000 2636 90.2325 60 2287 2 chr1B.!!$F5 2227
3 TraesCS1A01G391100 chr1B 642990583 642991223 640 False 896.000000 896 91.8590 1608 2255 1 chr1B.!!$F3 647
4 TraesCS1A01G391100 chr1B 642802672 642803375 703 False 876.000000 876 89.1780 966 1683 1 chr1B.!!$F1 717

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
155 157 0.036952 AGATGTCGACTGGCTTGGTG 60.037 55.0 17.92 0.00 0.00 4.17 F
836 883 0.319641 AGTCGCTTTCCAACTCCGAC 60.320 55.0 3.56 3.56 46.05 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1032 1088 3.077907 CGGAACATGAGGTGGGGT 58.922 61.111 0.0 0.0 0.0 4.95 R
2643 5222 1.270041 GCCACAGAAATTGCCCGAAAA 60.270 47.619 0.0 0.0 0.0 2.29 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
31 32 9.708092 TGAATGAAAATTATTTTCTCATGCACA 57.292 25.926 24.85 14.68 47.00 4.57
33 34 9.715121 AATGAAAATTATTTTCTCATGCACAGT 57.285 25.926 24.85 5.59 47.00 3.55
34 35 9.715121 ATGAAAATTATTTTCTCATGCACAGTT 57.285 25.926 24.85 0.00 47.00 3.16
35 36 8.980610 TGAAAATTATTTTCTCATGCACAGTTG 58.019 29.630 24.85 0.00 47.00 3.16
36 37 9.195411 GAAAATTATTTTCTCATGCACAGTTGA 57.805 29.630 19.61 0.00 44.29 3.18
37 38 9.545105 AAAATTATTTTCTCATGCACAGTTGAA 57.455 25.926 0.00 0.00 0.00 2.69
38 39 9.715121 AAATTATTTTCTCATGCACAGTTGAAT 57.285 25.926 0.00 0.00 0.00 2.57
39 40 8.697846 ATTATTTTCTCATGCACAGTTGAATG 57.302 30.769 0.00 0.00 39.95 2.67
40 41 5.518848 TTTTCTCATGCACAGTTGAATGT 57.481 34.783 0.00 0.00 39.60 2.71
41 42 5.518848 TTTCTCATGCACAGTTGAATGTT 57.481 34.783 0.00 0.00 39.60 2.71
42 43 4.492791 TCTCATGCACAGTTGAATGTTG 57.507 40.909 0.00 0.00 39.60 3.33
43 44 3.884693 TCTCATGCACAGTTGAATGTTGT 59.115 39.130 0.00 0.00 39.60 3.32
44 45 3.967401 TCATGCACAGTTGAATGTTGTG 58.033 40.909 0.00 0.00 39.60 3.33
45 46 2.867287 TGCACAGTTGAATGTTGTGG 57.133 45.000 6.05 0.00 41.81 4.17
46 47 2.098614 TGCACAGTTGAATGTTGTGGT 58.901 42.857 6.05 0.00 41.81 4.16
47 48 2.159268 TGCACAGTTGAATGTTGTGGTG 60.159 45.455 6.05 0.00 41.81 4.17
48 49 2.799207 GCACAGTTGAATGTTGTGGTGG 60.799 50.000 6.05 0.00 41.81 4.61
49 50 2.031120 ACAGTTGAATGTTGTGGTGGG 58.969 47.619 0.00 0.00 0.00 4.61
50 51 2.031120 CAGTTGAATGTTGTGGTGGGT 58.969 47.619 0.00 0.00 0.00 4.51
51 52 3.218453 CAGTTGAATGTTGTGGTGGGTA 58.782 45.455 0.00 0.00 0.00 3.69
52 53 3.826157 CAGTTGAATGTTGTGGTGGGTAT 59.174 43.478 0.00 0.00 0.00 2.73
53 54 4.280677 CAGTTGAATGTTGTGGTGGGTATT 59.719 41.667 0.00 0.00 0.00 1.89
54 55 4.898861 AGTTGAATGTTGTGGTGGGTATTT 59.101 37.500 0.00 0.00 0.00 1.40
55 56 5.365314 AGTTGAATGTTGTGGTGGGTATTTT 59.635 36.000 0.00 0.00 0.00 1.82
56 57 5.878406 TGAATGTTGTGGTGGGTATTTTT 57.122 34.783 0.00 0.00 0.00 1.94
82 83 2.536365 CATGATTGCATGTTGAGGTGC 58.464 47.619 0.00 0.00 45.41 5.01
94 96 4.617875 AGGTGCGCCTTATGACAC 57.382 55.556 14.67 0.00 44.18 3.67
107 109 7.307989 GCGCCTTATGACACTCATAATTGTATT 60.308 37.037 0.00 0.00 45.21 1.89
108 110 8.011673 CGCCTTATGACACTCATAATTGTATTG 58.988 37.037 5.38 0.00 45.21 1.90
130 132 2.174363 TGCCCATGAGCAATAGATCG 57.826 50.000 0.00 0.00 40.56 3.69
143 145 4.084849 GCAATAGATCGAAACCAGATGTCG 60.085 45.833 0.00 0.00 36.12 4.35
155 157 0.036952 AGATGTCGACTGGCTTGGTG 60.037 55.000 17.92 0.00 0.00 4.17
156 158 1.003355 ATGTCGACTGGCTTGGTGG 60.003 57.895 17.92 0.00 0.00 4.61
166 168 2.335712 GCTTGGTGGAAGGCGAAGG 61.336 63.158 0.00 0.00 31.56 3.46
168 170 3.860930 TTGGTGGAAGGCGAAGGGC 62.861 63.158 0.00 0.00 42.51 5.19
173 175 0.965363 TGGAAGGCGAAGGGCAATTC 60.965 55.000 0.00 0.00 46.16 2.17
248 250 2.813754 CCTTTGAGATTTTGCGAGTGGA 59.186 45.455 0.00 0.00 0.00 4.02
258 260 2.177394 TGCGAGTGGAAGTAATGCAA 57.823 45.000 0.00 0.00 0.00 4.08
286 288 4.951715 AGATTGCTGGATCTAAAACATGCA 59.048 37.500 0.00 0.00 34.68 3.96
289 291 2.223340 GCTGGATCTAAAACATGCACCG 60.223 50.000 0.00 0.00 0.00 4.94
292 294 3.438781 TGGATCTAAAACATGCACCGAAC 59.561 43.478 0.00 0.00 0.00 3.95
295 297 0.875728 TAAAACATGCACCGAACGGG 59.124 50.000 17.44 7.63 43.62 5.28
370 372 1.227205 GACGAGCCAGATGGAGCAG 60.227 63.158 2.18 0.00 37.39 4.24
396 398 2.511373 GCGACGCCACATGGATGA 60.511 61.111 9.14 0.00 37.39 2.92
400 402 0.739462 GACGCCACATGGATGACGAA 60.739 55.000 0.87 0.00 37.39 3.85
404 406 1.939974 CCACATGGATGACGAACGAT 58.060 50.000 0.00 0.00 37.39 3.73
488 495 1.135402 GCCGATGCAAACCGATCTTTT 60.135 47.619 7.88 0.00 37.47 2.27
493 500 4.672542 CGATGCAAACCGATCTTTTGATGT 60.673 41.667 16.76 5.31 39.67 3.06
494 501 4.582701 TGCAAACCGATCTTTTGATGTT 57.417 36.364 16.76 0.00 39.67 2.71
603 615 9.094578 TGGATAGAAATAAATGTGGACCAAAAA 57.905 29.630 0.00 0.00 0.00 1.94
630 642 0.887933 GGGCATTTTCCACGTGACAT 59.112 50.000 19.30 0.00 0.00 3.06
710 727 2.486982 CAGCCTGTGATTGTGAAAGAGG 59.513 50.000 0.00 0.00 0.00 3.69
711 728 1.815003 GCCTGTGATTGTGAAAGAGGG 59.185 52.381 0.00 0.00 0.00 4.30
741 758 1.597663 ACTGGAAAAGTGAAACGCGAG 59.402 47.619 15.93 0.00 45.86 5.03
797 844 2.045242 GGACGGCCCTTTCCTTCC 60.045 66.667 0.00 0.00 37.38 3.46
798 845 2.603652 GGACGGCCCTTTCCTTCCT 61.604 63.158 0.00 0.00 40.38 3.36
799 846 1.379146 GACGGCCCTTTCCTTCCTT 59.621 57.895 0.00 0.00 0.00 3.36
800 847 0.677098 GACGGCCCTTTCCTTCCTTC 60.677 60.000 0.00 0.00 0.00 3.46
806 853 1.550327 CCTTTCCTTCCTTCCTTGGC 58.450 55.000 0.00 0.00 0.00 4.52
807 854 1.076187 CCTTTCCTTCCTTCCTTGGCT 59.924 52.381 0.00 0.00 0.00 4.75
836 883 0.319641 AGTCGCTTTCCAACTCCGAC 60.320 55.000 3.56 3.56 46.05 4.79
841 888 0.400594 CTTTCCAACTCCGACCCCTT 59.599 55.000 0.00 0.00 0.00 3.95
845 892 1.215647 CAACTCCGACCCCTTCTCG 59.784 63.158 0.00 0.00 0.00 4.04
847 894 1.249469 AACTCCGACCCCTTCTCGTC 61.249 60.000 0.00 0.00 0.00 4.20
848 895 1.378778 CTCCGACCCCTTCTCGTCT 60.379 63.158 0.00 0.00 0.00 4.18
849 896 1.378124 CTCCGACCCCTTCTCGTCTC 61.378 65.000 0.00 0.00 0.00 3.36
850 897 1.378778 CCGACCCCTTCTCGTCTCT 60.379 63.158 0.00 0.00 0.00 3.10
851 898 1.378124 CCGACCCCTTCTCGTCTCTC 61.378 65.000 0.00 0.00 0.00 3.20
923 970 4.335647 CCGTGTCCTTGCCTGCCT 62.336 66.667 0.00 0.00 0.00 4.75
1121 1177 2.586079 CGCCGCTGGTATGGACAG 60.586 66.667 0.00 0.00 38.95 3.51
1155 1223 2.185350 CGGCTGAAGCTGTCCGAT 59.815 61.111 9.70 0.00 44.23 4.18
1156 1224 1.448540 CGGCTGAAGCTGTCCGATT 60.449 57.895 9.70 0.00 44.23 3.34
1212 1280 3.041940 GTCGTGACCAAGGTGCGG 61.042 66.667 0.00 0.00 0.00 5.69
1775 1858 0.680280 GTCACCGTCCTGGAGCTCTA 60.680 60.000 14.64 6.65 42.00 2.43
1860 1943 2.123854 TGCTACGGCGATCCTCCT 60.124 61.111 16.62 0.00 42.25 3.69
1933 2016 2.892425 GCGTGCAGAAGGATCCCG 60.892 66.667 8.55 3.87 0.00 5.14
2047 2130 3.826729 CGTGGAGACCATGTAGGATATCA 59.173 47.826 4.83 0.00 41.22 2.15
2154 2237 6.207417 TGGTGAAGATTTCTTTCATCAACCTC 59.793 38.462 0.00 0.00 36.11 3.85
2291 4618 9.439500 CAAATTTCCTGATTTATCAAATGGTGT 57.561 29.630 0.00 0.00 36.18 4.16
2387 4723 7.883229 AGTCACGAACAGTTTTTGAATTTTT 57.117 28.000 0.00 0.00 0.00 1.94
2389 4725 9.581099 AGTCACGAACAGTTTTTGAATTTTTAT 57.419 25.926 0.00 0.00 0.00 1.40
2415 4751 9.642327 TGACATTTTTCCTATCATGAACATTTG 57.358 29.630 0.00 0.00 0.00 2.32
2428 4764 4.297510 TGAACATTTGTTGAATTGGCGAG 58.702 39.130 0.00 0.00 38.56 5.03
2429 4765 4.037327 TGAACATTTGTTGAATTGGCGAGA 59.963 37.500 0.00 0.00 38.56 4.04
2443 4779 5.903764 TTGGCGAGATTTTGTTCAATTTG 57.096 34.783 0.00 0.00 0.00 2.32
2586 4922 7.939782 TCTGAACATCTTTTGTATCTGCAAAA 58.060 30.769 6.13 6.13 43.46 2.44
2628 5207 5.628797 TCACTTATAGGTGGCATTGATGA 57.371 39.130 14.38 0.00 37.75 2.92
2631 5210 6.326323 TCACTTATAGGTGGCATTGATGAGTA 59.674 38.462 14.38 0.00 37.75 2.59
2643 5222 8.205512 TGGCATTGATGAGTAATATTTTGCAAT 58.794 29.630 0.00 0.00 0.00 3.56
2654 5233 6.756299 AATATTTTGCAATTTTCGGGCAAT 57.244 29.167 0.00 0.00 45.81 3.56
2659 5238 3.065655 TGCAATTTTCGGGCAATTTCTG 58.934 40.909 0.00 0.00 34.05 3.02
2663 5242 0.316841 TTTCGGGCAATTTCTGTGGC 59.683 50.000 0.00 0.00 40.67 5.01
2665 5244 2.625823 CGGGCAATTTCTGTGGCGT 61.626 57.895 0.00 0.00 42.24 5.68
2670 5249 1.729149 GCAATTTCTGTGGCGTACTGC 60.729 52.381 1.72 1.72 45.38 4.40
2686 5265 1.075374 ACTGCCAGAAACAATAGCCCA 59.925 47.619 0.00 0.00 0.00 5.36
2800 5379 5.156649 TGGGGGTAGATATTGTCGGAAATA 58.843 41.667 0.00 0.00 0.00 1.40
2811 5390 9.371136 GATATTGTCGGAAATAGATATGAAGCA 57.629 33.333 0.00 0.00 0.00 3.91
2827 5406 5.172687 TGAAGCAAATATGGAGTGGTACA 57.827 39.130 0.00 0.00 0.00 2.90
2828 5407 5.565509 TGAAGCAAATATGGAGTGGTACAA 58.434 37.500 0.00 0.00 44.16 2.41
2829 5408 6.186957 TGAAGCAAATATGGAGTGGTACAAT 58.813 36.000 0.00 0.00 44.16 2.71
2834 5413 6.458751 GCAAATATGGAGTGGTACAATGACAG 60.459 42.308 0.00 0.00 44.16 3.51
2869 5449 9.812347 ATTGTCAATAATCCCTTAGAATATGCA 57.188 29.630 0.00 0.00 0.00 3.96
2913 5493 5.746990 AAACTAGTCATGAGTGGTTAGCT 57.253 39.130 26.74 13.03 34.89 3.32
2914 5494 6.852420 AAACTAGTCATGAGTGGTTAGCTA 57.148 37.500 26.74 8.56 34.89 3.32
2915 5495 7.425224 AAACTAGTCATGAGTGGTTAGCTAT 57.575 36.000 26.74 12.40 34.89 2.97
2916 5496 6.642707 ACTAGTCATGAGTGGTTAGCTATC 57.357 41.667 13.39 0.00 0.00 2.08
2917 5497 6.129874 ACTAGTCATGAGTGGTTAGCTATCA 58.870 40.000 13.39 0.00 0.00 2.15
2919 5499 7.945109 ACTAGTCATGAGTGGTTAGCTATCATA 59.055 37.037 13.39 0.00 0.00 2.15
2923 5503 9.109393 GTCATGAGTGGTTAGCTATCATAAAAA 57.891 33.333 6.49 0.00 0.00 1.94
2924 5504 9.330063 TCATGAGTGGTTAGCTATCATAAAAAG 57.670 33.333 6.49 0.00 0.00 2.27
2925 5505 8.562892 CATGAGTGGTTAGCTATCATAAAAAGG 58.437 37.037 6.49 0.00 0.00 3.11
2926 5506 7.857456 TGAGTGGTTAGCTATCATAAAAAGGA 58.143 34.615 0.00 0.00 0.00 3.36
2927 5507 8.325787 TGAGTGGTTAGCTATCATAAAAAGGAA 58.674 33.333 0.00 0.00 0.00 3.36
2928 5508 9.174166 GAGTGGTTAGCTATCATAAAAAGGAAA 57.826 33.333 0.00 0.00 0.00 3.13
2929 5509 9.528489 AGTGGTTAGCTATCATAAAAAGGAAAA 57.472 29.630 0.00 0.00 0.00 2.29
2945 5525 8.942338 AAAAGGAAAAACTAGTTCAACATTCC 57.058 30.769 8.95 15.91 36.25 3.01
2946 5526 7.654022 AAGGAAAAACTAGTTCAACATTCCA 57.346 32.000 23.99 0.00 38.00 3.53
2947 5527 7.654022 AGGAAAAACTAGTTCAACATTCCAA 57.346 32.000 23.99 0.00 38.00 3.53
2948 5528 7.489160 AGGAAAAACTAGTTCAACATTCCAAC 58.511 34.615 23.99 9.75 38.00 3.77
2949 5529 7.123547 AGGAAAAACTAGTTCAACATTCCAACA 59.876 33.333 23.99 0.00 38.00 3.33
2950 5530 7.926018 GGAAAAACTAGTTCAACATTCCAACAT 59.074 33.333 20.61 0.00 36.09 2.71
2951 5531 8.647143 AAAAACTAGTTCAACATTCCAACATG 57.353 30.769 8.95 0.00 0.00 3.21
2952 5532 7.581213 AAACTAGTTCAACATTCCAACATGA 57.419 32.000 8.95 0.00 0.00 3.07
2953 5533 7.581213 AACTAGTTCAACATTCCAACATGAA 57.419 32.000 1.12 0.00 0.00 2.57
2954 5534 7.765695 ACTAGTTCAACATTCCAACATGAAT 57.234 32.000 0.00 0.00 35.36 2.57
2966 5546 8.715998 CATTCCAACATGAATGTAGATAGTAGC 58.284 37.037 0.00 0.00 44.20 3.58
2967 5547 7.360113 TCCAACATGAATGTAGATAGTAGCA 57.640 36.000 0.00 0.00 40.80 3.49
2968 5548 7.791029 TCCAACATGAATGTAGATAGTAGCAA 58.209 34.615 0.00 0.00 40.80 3.91
2969 5549 7.710907 TCCAACATGAATGTAGATAGTAGCAAC 59.289 37.037 0.00 0.00 40.80 4.17
2970 5550 7.041780 CCAACATGAATGTAGATAGTAGCAACC 60.042 40.741 0.00 0.00 40.80 3.77
2971 5551 7.124573 ACATGAATGTAGATAGTAGCAACCA 57.875 36.000 0.00 0.00 39.68 3.67
2972 5552 6.986817 ACATGAATGTAGATAGTAGCAACCAC 59.013 38.462 0.00 0.00 39.68 4.16
2973 5553 5.588240 TGAATGTAGATAGTAGCAACCACG 58.412 41.667 0.00 0.00 0.00 4.94
2974 5554 5.126545 TGAATGTAGATAGTAGCAACCACGT 59.873 40.000 0.00 0.00 0.00 4.49
2975 5555 4.365899 TGTAGATAGTAGCAACCACGTG 57.634 45.455 9.08 9.08 0.00 4.49
2976 5556 2.961526 AGATAGTAGCAACCACGTGG 57.038 50.000 32.83 32.83 42.17 4.94
2994 5574 7.696755 CCACGTGGTAAGGTATTTAAATAACC 58.303 38.462 26.95 16.51 0.00 2.85
2995 5575 7.201723 CCACGTGGTAAGGTATTTAAATAACCC 60.202 40.741 26.95 13.03 0.00 4.11
2996 5576 7.336427 CACGTGGTAAGGTATTTAAATAACCCA 59.664 37.037 17.76 15.11 0.00 4.51
2997 5577 7.887495 ACGTGGTAAGGTATTTAAATAACCCAA 59.113 33.333 17.76 3.26 0.00 4.12
2998 5578 8.183536 CGTGGTAAGGTATTTAAATAACCCAAC 58.816 37.037 17.76 13.30 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 9.545105 TTCAACTGTGCATGAGAAAATAATTTT 57.455 25.926 0.00 0.00 35.12 1.82
12 13 9.715121 ATTCAACTGTGCATGAGAAAATAATTT 57.285 25.926 0.00 0.00 0.00 1.82
13 14 9.146984 CATTCAACTGTGCATGAGAAAATAATT 57.853 29.630 0.00 0.00 0.00 1.40
14 15 8.308931 ACATTCAACTGTGCATGAGAAAATAAT 58.691 29.630 0.00 0.00 0.00 1.28
15 16 7.660112 ACATTCAACTGTGCATGAGAAAATAA 58.340 30.769 0.00 0.00 0.00 1.40
16 17 7.218228 ACATTCAACTGTGCATGAGAAAATA 57.782 32.000 0.00 0.00 0.00 1.40
17 18 6.092955 ACATTCAACTGTGCATGAGAAAAT 57.907 33.333 0.00 0.00 0.00 1.82
18 19 5.518848 ACATTCAACTGTGCATGAGAAAA 57.481 34.783 0.00 0.00 0.00 2.29
19 20 5.163530 ACAACATTCAACTGTGCATGAGAAA 60.164 36.000 0.00 0.00 0.00 2.52
20 21 4.338964 ACAACATTCAACTGTGCATGAGAA 59.661 37.500 0.00 0.00 0.00 2.87
21 22 3.884693 ACAACATTCAACTGTGCATGAGA 59.115 39.130 0.00 0.00 0.00 3.27
22 23 3.978855 CACAACATTCAACTGTGCATGAG 59.021 43.478 0.00 0.00 34.55 2.90
23 24 3.243468 CCACAACATTCAACTGTGCATGA 60.243 43.478 0.00 0.00 39.30 3.07
24 25 3.054166 CCACAACATTCAACTGTGCATG 58.946 45.455 0.00 0.00 39.30 4.06
25 26 2.694628 ACCACAACATTCAACTGTGCAT 59.305 40.909 0.00 0.00 39.30 3.96
26 27 2.098614 ACCACAACATTCAACTGTGCA 58.901 42.857 0.00 0.00 39.30 4.57
27 28 2.462889 CACCACAACATTCAACTGTGC 58.537 47.619 0.00 0.00 39.30 4.57
28 29 2.223782 CCCACCACAACATTCAACTGTG 60.224 50.000 0.00 0.00 40.13 3.66
29 30 2.031120 CCCACCACAACATTCAACTGT 58.969 47.619 0.00 0.00 0.00 3.55
30 31 2.031120 ACCCACCACAACATTCAACTG 58.969 47.619 0.00 0.00 0.00 3.16
31 32 2.452600 ACCCACCACAACATTCAACT 57.547 45.000 0.00 0.00 0.00 3.16
32 33 4.864704 AATACCCACCACAACATTCAAC 57.135 40.909 0.00 0.00 0.00 3.18
33 34 5.878406 AAAATACCCACCACAACATTCAA 57.122 34.783 0.00 0.00 0.00 2.69
34 35 5.878406 AAAAATACCCACCACAACATTCA 57.122 34.783 0.00 0.00 0.00 2.57
76 77 5.849626 ATGAGTGTCATAAGGCGCACCTC 62.850 52.174 10.83 7.21 37.17 3.85
79 80 1.656652 ATGAGTGTCATAAGGCGCAC 58.343 50.000 10.83 0.00 34.88 5.34
90 92 7.141363 GGGCATTCAATACAATTATGAGTGTC 58.859 38.462 0.00 0.00 35.43 3.67
94 96 7.888424 TCATGGGCATTCAATACAATTATGAG 58.112 34.615 0.00 0.00 0.00 2.90
107 109 3.581265 TCTATTGCTCATGGGCATTCA 57.419 42.857 23.51 7.06 42.09 2.57
108 110 3.126514 CGATCTATTGCTCATGGGCATTC 59.873 47.826 23.51 12.21 42.09 2.67
124 126 3.945921 AGTCGACATCTGGTTTCGATCTA 59.054 43.478 19.50 0.00 43.22 1.98
143 145 1.973812 GCCTTCCACCAAGCCAGTC 60.974 63.158 0.00 0.00 0.00 3.51
155 157 1.809869 GAATTGCCCTTCGCCTTCC 59.190 57.895 0.00 0.00 36.24 3.46
156 158 1.024579 TCGAATTGCCCTTCGCCTTC 61.025 55.000 11.64 0.00 45.80 3.46
166 168 2.947448 AGCCTTCATTTCGAATTGCC 57.053 45.000 13.84 4.25 33.76 4.52
168 170 5.756195 TGGATAGCCTTCATTTCGAATTG 57.244 39.130 12.72 12.72 31.69 2.32
173 175 7.225523 CAATTTTTGGATAGCCTTCATTTCG 57.774 36.000 0.00 0.00 34.31 3.46
211 213 0.923358 AAGGCATGTATCCCCGGAAA 59.077 50.000 0.73 0.00 0.00 3.13
214 216 0.182537 TCAAAGGCATGTATCCCCGG 59.817 55.000 0.00 0.00 0.00 5.73
258 260 7.288810 TGTTTTAGATCCAGCAATCTTGTTT 57.711 32.000 2.17 0.00 37.24 2.83
289 291 1.912371 CTTCAAAGGCGAGCCCGTTC 61.912 60.000 10.95 0.00 39.21 3.95
292 294 3.804193 GCTTCAAAGGCGAGCCCG 61.804 66.667 10.95 0.00 39.21 6.13
295 297 1.738099 TCGAGCTTCAAAGGCGAGC 60.738 57.895 0.00 0.00 36.68 5.03
396 398 2.908817 GTGACCAACCATCGTTCGT 58.091 52.632 0.00 0.00 0.00 3.85
419 421 0.179089 CCAATGTCAGCCTCTCCTCG 60.179 60.000 0.00 0.00 0.00 4.63
432 434 2.598394 AACTGCTGCCGCCAATGT 60.598 55.556 0.00 0.00 34.43 2.71
547 556 3.608073 GCGTGCCTAAGCTTTTACAAATG 59.392 43.478 3.20 0.00 40.80 2.32
577 589 8.657387 TTTTGGTCCACATTTATTTCTATCCA 57.343 30.769 0.00 0.00 0.00 3.41
603 615 2.499693 CGTGGAAAATGCCCCCTTTTAT 59.500 45.455 0.00 0.00 0.00 1.40
606 618 0.471022 ACGTGGAAAATGCCCCCTTT 60.471 50.000 0.00 0.00 0.00 3.11
710 727 9.459640 GTTTCACTTTTCCAGTTTTATTACTCC 57.540 33.333 0.00 0.00 30.92 3.85
711 728 9.166126 CGTTTCACTTTTCCAGTTTTATTACTC 57.834 33.333 0.00 0.00 30.92 2.59
741 758 1.076332 CCAACCGAACCTCACGATTC 58.924 55.000 0.00 0.00 0.00 2.52
751 768 1.592830 CGTCGTTCAAACCAACCGAAC 60.593 52.381 0.00 0.00 36.51 3.95
753 770 0.179116 TCGTCGTTCAAACCAACCGA 60.179 50.000 0.00 0.00 0.00 4.69
754 771 0.042794 GTCGTCGTTCAAACCAACCG 60.043 55.000 0.00 0.00 0.00 4.44
797 844 3.703001 TTGGAGTAGAAGCCAAGGAAG 57.297 47.619 0.00 0.00 39.14 3.46
806 853 3.254892 GGAAAGCGACTTGGAGTAGAAG 58.745 50.000 0.00 0.00 0.00 2.85
807 854 2.631062 TGGAAAGCGACTTGGAGTAGAA 59.369 45.455 0.00 0.00 0.00 2.10
836 883 0.257616 AGAGGAGAGACGAGAAGGGG 59.742 60.000 0.00 0.00 0.00 4.79
841 888 0.176219 GTCGGAGAGGAGAGACGAGA 59.824 60.000 0.00 0.00 36.95 4.04
845 892 1.375551 GAGTGTCGGAGAGGAGAGAC 58.624 60.000 0.00 0.00 36.95 3.36
847 894 2.389386 CGAGTGTCGGAGAGGAGAG 58.611 63.158 0.00 0.00 36.95 3.20
848 895 4.619852 CGAGTGTCGGAGAGGAGA 57.380 61.111 0.00 0.00 36.95 3.71
906 953 4.335647 AGGCAGGCAAGGACACGG 62.336 66.667 0.00 0.00 0.00 4.94
922 969 3.093278 CTTCGGCTTTAGCGGCAG 58.907 61.111 1.45 0.09 43.26 4.85
923 970 3.124921 GCTTCGGCTTTAGCGGCA 61.125 61.111 1.45 0.00 43.26 5.69
1032 1088 3.077907 CGGAACATGAGGTGGGGT 58.922 61.111 0.00 0.00 0.00 4.95
1155 1223 3.172106 TCGGCCACCCACTCCAAA 61.172 61.111 2.24 0.00 0.00 3.28
1156 1224 3.948719 GTCGGCCACCCACTCCAA 61.949 66.667 2.24 0.00 0.00 3.53
2020 2103 3.889538 TCCTACATGGTCTCCACGATAAG 59.110 47.826 0.00 0.00 35.80 1.73
2047 2130 5.495926 ACAATTGATCTTGTCTCTGTCCT 57.504 39.130 13.59 0.00 34.26 3.85
2128 2211 6.015940 AGGTTGATGAAAGAAATCTTCACCAC 60.016 38.462 0.00 0.00 34.40 4.16
2154 2237 7.379750 AGAGTACCTAGCTTGTCTAAAAGTTG 58.620 38.462 0.00 0.00 0.00 3.16
2362 4689 7.883229 AAAATTCAAAAACTGTTCGTGACTT 57.117 28.000 5.81 4.99 0.00 3.01
2363 4690 7.883229 AAAAATTCAAAAACTGTTCGTGACT 57.117 28.000 5.81 0.00 0.00 3.41
2364 4691 9.618410 CATAAAAATTCAAAAACTGTTCGTGAC 57.382 29.630 5.81 0.00 0.00 3.67
2389 4725 9.642327 CAAATGTTCATGATAGGAAAAATGTCA 57.358 29.630 0.00 0.00 0.00 3.58
2399 4735 7.010738 GCCAATTCAACAAATGTTCATGATAGG 59.989 37.037 0.00 0.00 35.83 2.57
2401 4737 6.530887 CGCCAATTCAACAAATGTTCATGATA 59.469 34.615 0.00 0.00 35.83 2.15
2402 4738 5.349270 CGCCAATTCAACAAATGTTCATGAT 59.651 36.000 0.00 0.00 35.83 2.45
2415 4751 4.981674 TGAACAAAATCTCGCCAATTCAAC 59.018 37.500 0.00 0.00 0.00 3.18
2562 4898 8.578308 TTTTTGCAGATACAAAAGATGTTCAG 57.422 30.769 3.06 0.00 46.84 3.02
2628 5207 6.402222 TGCCCGAAAATTGCAAAATATTACT 58.598 32.000 1.71 0.00 30.85 2.24
2631 5210 6.756299 ATTGCCCGAAAATTGCAAAATATT 57.244 29.167 1.71 0.00 46.82 1.28
2643 5222 1.270041 GCCACAGAAATTGCCCGAAAA 60.270 47.619 0.00 0.00 0.00 2.29
2663 5242 2.351726 GGCTATTGTTTCTGGCAGTACG 59.648 50.000 15.27 3.20 0.00 3.67
2665 5244 2.307392 TGGGCTATTGTTTCTGGCAGTA 59.693 45.455 15.27 1.01 0.00 2.74
2756 5335 9.325248 CCCCCAACATATAATTTTCAAGGATAT 57.675 33.333 0.00 0.00 0.00 1.63
2757 5336 8.293216 ACCCCCAACATATAATTTTCAAGGATA 58.707 33.333 0.00 0.00 0.00 2.59
2758 5337 7.138934 ACCCCCAACATATAATTTTCAAGGAT 58.861 34.615 0.00 0.00 0.00 3.24
2759 5338 6.507568 ACCCCCAACATATAATTTTCAAGGA 58.492 36.000 0.00 0.00 0.00 3.36
2760 5339 6.806668 ACCCCCAACATATAATTTTCAAGG 57.193 37.500 0.00 0.00 0.00 3.61
2761 5340 8.760980 TCTACCCCCAACATATAATTTTCAAG 57.239 34.615 0.00 0.00 0.00 3.02
2789 5368 7.857734 TTTGCTTCATATCTATTTCCGACAA 57.142 32.000 0.00 0.00 0.00 3.18
2800 5379 6.845908 ACCACTCCATATTTGCTTCATATCT 58.154 36.000 0.00 0.00 0.00 1.98
2811 5390 6.957631 TCTGTCATTGTACCACTCCATATTT 58.042 36.000 0.00 0.00 0.00 1.40
2919 5499 9.378551 GGAATGTTGAACTAGTTTTTCCTTTTT 57.621 29.630 10.02 0.00 0.00 1.94
2923 5503 7.123547 TGTTGGAATGTTGAACTAGTTTTTCCT 59.876 33.333 22.12 6.72 34.00 3.36
2924 5504 7.262048 TGTTGGAATGTTGAACTAGTTTTTCC 58.738 34.615 10.02 15.78 33.58 3.13
2925 5505 8.755018 CATGTTGGAATGTTGAACTAGTTTTTC 58.245 33.333 10.02 8.22 0.00 2.29
2926 5506 8.474025 TCATGTTGGAATGTTGAACTAGTTTTT 58.526 29.630 10.02 0.00 0.00 1.94
2927 5507 8.006298 TCATGTTGGAATGTTGAACTAGTTTT 57.994 30.769 10.02 0.00 0.00 2.43
2928 5508 7.581213 TCATGTTGGAATGTTGAACTAGTTT 57.419 32.000 10.02 0.00 0.00 2.66
2929 5509 7.581213 TTCATGTTGGAATGTTGAACTAGTT 57.419 32.000 8.13 8.13 0.00 2.24
2930 5510 7.596494 CATTCATGTTGGAATGTTGAACTAGT 58.404 34.615 7.54 0.00 45.73 2.57
2941 5521 8.432013 TGCTACTATCTACATTCATGTTGGAAT 58.568 33.333 0.00 0.00 41.97 3.01
2942 5522 7.791029 TGCTACTATCTACATTCATGTTGGAA 58.209 34.615 0.00 0.00 41.97 3.53
2943 5523 7.360113 TGCTACTATCTACATTCATGTTGGA 57.640 36.000 0.00 0.00 41.97 3.53
2944 5524 7.041780 GGTTGCTACTATCTACATTCATGTTGG 60.042 40.741 0.00 0.00 41.97 3.77
2945 5525 7.495606 TGGTTGCTACTATCTACATTCATGTTG 59.504 37.037 0.00 0.00 41.97 3.33
2946 5526 7.495934 GTGGTTGCTACTATCTACATTCATGTT 59.504 37.037 0.00 0.00 41.97 2.71
2947 5527 6.986817 GTGGTTGCTACTATCTACATTCATGT 59.013 38.462 0.00 0.00 44.48 3.21
2948 5528 6.144563 CGTGGTTGCTACTATCTACATTCATG 59.855 42.308 0.00 0.00 0.00 3.07
2949 5529 6.183360 ACGTGGTTGCTACTATCTACATTCAT 60.183 38.462 0.00 0.00 0.00 2.57
2950 5530 5.126545 ACGTGGTTGCTACTATCTACATTCA 59.873 40.000 0.00 0.00 0.00 2.57
2951 5531 5.459107 CACGTGGTTGCTACTATCTACATTC 59.541 44.000 7.95 0.00 0.00 2.67
2952 5532 5.348986 CACGTGGTTGCTACTATCTACATT 58.651 41.667 7.95 0.00 0.00 2.71
2953 5533 4.202121 CCACGTGGTTGCTACTATCTACAT 60.202 45.833 26.95 0.00 0.00 2.29
2954 5534 3.129813 CCACGTGGTTGCTACTATCTACA 59.870 47.826 26.95 0.00 0.00 2.74
2955 5535 3.703420 CCACGTGGTTGCTACTATCTAC 58.297 50.000 26.95 0.00 0.00 2.59
2957 5537 2.961526 CCACGTGGTTGCTACTATCT 57.038 50.000 26.95 0.00 0.00 1.98
2969 5549 7.201723 GGGTTATTTAAATACCTTACCACGTGG 60.202 40.741 32.83 32.83 42.17 4.94
2970 5550 7.336427 TGGGTTATTTAAATACCTTACCACGTG 59.664 37.037 20.68 9.08 0.00 4.49
2971 5551 7.401246 TGGGTTATTTAAATACCTTACCACGT 58.599 34.615 20.68 0.00 0.00 4.49
2972 5552 7.862512 TGGGTTATTTAAATACCTTACCACG 57.137 36.000 20.68 0.00 0.00 4.94
2973 5553 9.022884 TGTTGGGTTATTTAAATACCTTACCAC 57.977 33.333 20.68 14.54 0.00 4.16
2974 5554 9.771140 ATGTTGGGTTATTTAAATACCTTACCA 57.229 29.630 20.68 15.14 0.00 3.25


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

AutoCloner maintained by Alex Coulton.