Multiple sequence alignment - TraesCS5D01G270500

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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 TraesCS5D01G270500 chr5D 100.000 3594 0 0 1 3594 374199075 374202668 0.000000e+00 6637.0
1 TraesCS5D01G270500 chr5B 94.698 2037 92 10 106 2130 445966163 445968195 0.000000e+00 3149.0
2 TraesCS5D01G270500 chr5B 90.848 1486 82 22 2123 3592 445968382 445969829 0.000000e+00 1941.0
3 TraesCS5D01G270500 chr5B 81.000 300 43 9 2125 2414 539929181 539928886 3.610000e-55 226.0
4 TraesCS5D01G270500 chr5B 80.435 92 15 3 1184 1274 685238819 685238730 2.320000e-07 67.6
5 TraesCS5D01G270500 chr5A 94.968 1570 63 6 562 2130 476023307 476024861 0.000000e+00 2447.0
6 TraesCS5D01G270500 chr5A 91.319 1486 87 17 2123 3594 476025049 476026506 0.000000e+00 1991.0
7 TraesCS5D01G270500 chr4B 81.164 292 49 5 2127 2413 663103373 663103663 2.790000e-56 230.0
8 TraesCS5D01G270500 chr7D 82.955 264 30 9 2125 2375 204256281 204256020 1.300000e-54 224.0
9 TraesCS5D01G270500 chr7A 82.955 264 30 8 2125 2375 216353640 216353379 1.300000e-54 224.0
10 TraesCS5D01G270500 chr7A 79.062 320 45 15 2125 2424 25338027 25337710 2.190000e-47 200.0
11 TraesCS5D01G270500 chr2B 77.841 352 64 8 2970 3311 679694115 679693768 4.700000e-49 206.0
12 TraesCS5D01G270500 chr2B 81.119 143 17 5 2125 2258 786215573 786215714 4.910000e-19 106.0
13 TraesCS5D01G270500 chr2B 79.231 130 17 7 3189 3311 713967251 713967377 8.270000e-12 82.4
14 TraesCS5D01G270500 chr1B 77.994 309 49 10 2123 2413 571693546 571693853 3.690000e-40 176.0
15 TraesCS5D01G270500 chr3B 78.218 303 44 15 3022 3314 472583305 472583015 1.330000e-39 174.0
16 TraesCS5D01G270500 chr6B 80.237 253 29 8 2139 2375 192354030 192353783 1.720000e-38 171.0
17 TraesCS5D01G270500 chr3D 76.571 350 54 21 2978 3314 362853960 362853626 2.220000e-37 167.0
18 TraesCS5D01G270500 chr6D 79.528 254 31 6 2139 2376 105823531 105823283 1.030000e-35 161.0
19 TraesCS5D01G270500 chr6D 81.928 83 13 1 1184 1266 24267264 24267344 6.440000e-08 69.4
20 TraesCS5D01G270500 chr7B 83.333 162 22 3 2219 2375 168324598 168324437 1.040000e-30 145.0
21 TraesCS5D01G270500 chr2D 75.987 304 58 9 3020 3311 566657677 566657977 3.740000e-30 143.0
22 TraesCS5D01G270500 chr2D 74.299 214 43 10 2125 2331 644671649 644671857 2.970000e-11 80.5
23 TraesCS5D01G270500 chr3A 82.877 146 15 7 3073 3210 124192623 124192766 4.870000e-24 122.0
24 TraesCS5D01G270500 chr2A 85.366 82 8 3 2127 2206 83423198 83423277 8.270000e-12 82.4
25 TraesCS5D01G270500 chrUn 95.122 41 2 0 60 100 213135791 213135751 8.330000e-07 65.8
26 TraesCS5D01G270500 chrUn 95.122 41 2 0 60 100 234811340 234811380 8.330000e-07 65.8
27 TraesCS5D01G270500 chrUn 95.122 41 2 0 60 100 234817094 234817134 8.330000e-07 65.8
28 TraesCS5D01G270500 chrUn 95.122 41 2 0 60 100 256789611 256789571 8.330000e-07 65.8
29 TraesCS5D01G270500 chrUn 95.122 41 2 0 60 100 256798937 256798897 8.330000e-07 65.8
30 TraesCS5D01G270500 chrUn 95.122 41 2 0 60 100 278882188 278882228 8.330000e-07 65.8
31 TraesCS5D01G270500 chrUn 95.122 41 2 0 60 100 310860935 310860975 8.330000e-07 65.8
32 TraesCS5D01G270500 chrUn 95.122 41 2 0 60 100 474352670 474352630 8.330000e-07 65.8
33 TraesCS5D01G270500 chr4D 95.122 41 2 0 60 100 413172127 413172087 8.330000e-07 65.8
34 TraesCS5D01G270500 chr6A 78.947 95 9 7 1123 1211 22807292 22807381 2.000000e-03 54.7


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 TraesCS5D01G270500 chr5D 374199075 374202668 3593 False 6637 6637 100.0000 1 3594 1 chr5D.!!$F1 3593
1 TraesCS5D01G270500 chr5B 445966163 445969829 3666 False 2545 3149 92.7730 106 3592 2 chr5B.!!$F1 3486
2 TraesCS5D01G270500 chr5A 476023307 476026506 3199 False 2219 2447 93.1435 562 3594 2 chr5A.!!$F1 3032

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
322 323 0.809636 CGATGGCGCAACAGGTCATA 60.81 55.0 10.83 0.0 0.0 2.15 F
1066 1076 0.999712 GGAGGGGGAGATGGTTTTCA 59.00 55.0 0.00 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1473 1484 0.589708 GTTGCCAGGAACGTACCAAC 59.410 55.000 0.00 0.0 0.0 3.77 R
2968 3192 1.138464 TGCAACGCGTGGGGTATTATA 59.862 47.619 14.98 0.0 0.0 0.98 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
28 29 5.475273 CGAAGCACACAGATAATGATTGT 57.525 39.130 0.00 0.00 0.00 2.71
29 30 5.872635 CGAAGCACACAGATAATGATTGTT 58.127 37.500 0.00 0.00 0.00 2.83
30 31 5.735892 CGAAGCACACAGATAATGATTGTTG 59.264 40.000 0.00 0.00 0.00 3.33
31 32 6.579666 AAGCACACAGATAATGATTGTTGT 57.420 33.333 0.00 0.00 0.00 3.32
32 33 6.579666 AGCACACAGATAATGATTGTTGTT 57.420 33.333 0.00 0.00 0.00 2.83
33 34 6.384224 AGCACACAGATAATGATTGTTGTTG 58.616 36.000 0.00 0.00 0.00 3.33
34 35 6.016024 AGCACACAGATAATGATTGTTGTTGT 60.016 34.615 0.00 0.00 0.00 3.32
35 36 6.306356 GCACACAGATAATGATTGTTGTTGTC 59.694 38.462 0.00 0.00 0.00 3.18
36 37 7.587629 CACACAGATAATGATTGTTGTTGTCT 58.412 34.615 0.00 0.00 0.00 3.41
37 38 7.536281 CACACAGATAATGATTGTTGTTGTCTG 59.464 37.037 8.79 8.79 42.87 3.51
38 39 7.750229 ACAGATAATGATTGTTGTTGTCTGT 57.250 32.000 9.83 9.83 44.26 3.41
39 40 7.747799 CACAGATAATGATTGTTGTTGTCTGTC 59.252 37.037 11.92 0.00 45.19 3.51
40 41 7.445096 ACAGATAATGATTGTTGTTGTCTGTCA 59.555 33.333 9.83 0.00 45.19 3.58
41 42 8.456471 CAGATAATGATTGTTGTTGTCTGTCAT 58.544 33.333 0.00 0.00 36.76 3.06
42 43 9.017509 AGATAATGATTGTTGTTGTCTGTCATT 57.982 29.630 0.00 0.00 38.14 2.57
43 44 8.975410 ATAATGATTGTTGTTGTCTGTCATTG 57.025 30.769 7.68 0.00 36.05 2.82
44 45 5.185668 TGATTGTTGTTGTCTGTCATTGG 57.814 39.130 0.00 0.00 0.00 3.16
45 46 4.644234 TGATTGTTGTTGTCTGTCATTGGT 59.356 37.500 0.00 0.00 0.00 3.67
46 47 5.825151 TGATTGTTGTTGTCTGTCATTGGTA 59.175 36.000 0.00 0.00 0.00 3.25
47 48 6.319911 TGATTGTTGTTGTCTGTCATTGGTAA 59.680 34.615 0.00 0.00 0.00 2.85
48 49 6.516739 TTGTTGTTGTCTGTCATTGGTAAA 57.483 33.333 0.00 0.00 0.00 2.01
49 50 6.707440 TGTTGTTGTCTGTCATTGGTAAAT 57.293 33.333 0.00 0.00 0.00 1.40
50 51 7.809546 TGTTGTTGTCTGTCATTGGTAAATA 57.190 32.000 0.00 0.00 0.00 1.40
51 52 8.402798 TGTTGTTGTCTGTCATTGGTAAATAT 57.597 30.769 0.00 0.00 0.00 1.28
52 53 9.508642 TGTTGTTGTCTGTCATTGGTAAATATA 57.491 29.630 0.00 0.00 0.00 0.86
53 54 9.769093 GTTGTTGTCTGTCATTGGTAAATATAC 57.231 33.333 0.00 0.00 0.00 1.47
54 55 9.508642 TTGTTGTCTGTCATTGGTAAATATACA 57.491 29.630 0.00 0.00 33.45 2.29
55 56 9.508642 TGTTGTCTGTCATTGGTAAATATACAA 57.491 29.630 0.00 0.00 33.45 2.41
56 57 9.988350 GTTGTCTGTCATTGGTAAATATACAAG 57.012 33.333 0.00 0.00 33.45 3.16
57 58 9.952030 TTGTCTGTCATTGGTAAATATACAAGA 57.048 29.630 0.00 0.00 33.45 3.02
85 86 9.880157 AATTACAAATGGAATGAGAAAGGATTG 57.120 29.630 0.00 0.00 0.00 2.67
86 87 8.648698 TTACAAATGGAATGAGAAAGGATTGA 57.351 30.769 0.00 0.00 0.00 2.57
87 88 7.543359 ACAAATGGAATGAGAAAGGATTGAA 57.457 32.000 0.00 0.00 0.00 2.69
88 89 7.965718 ACAAATGGAATGAGAAAGGATTGAAA 58.034 30.769 0.00 0.00 0.00 2.69
89 90 8.431222 ACAAATGGAATGAGAAAGGATTGAAAA 58.569 29.630 0.00 0.00 0.00 2.29
90 91 9.275398 CAAATGGAATGAGAAAGGATTGAAAAA 57.725 29.630 0.00 0.00 0.00 1.94
92 93 9.444600 AATGGAATGAGAAAGGATTGAAAAATG 57.555 29.630 0.00 0.00 0.00 2.32
93 94 8.192743 TGGAATGAGAAAGGATTGAAAAATGA 57.807 30.769 0.00 0.00 0.00 2.57
94 95 8.818860 TGGAATGAGAAAGGATTGAAAAATGAT 58.181 29.630 0.00 0.00 0.00 2.45
95 96 9.095065 GGAATGAGAAAGGATTGAAAAATGATG 57.905 33.333 0.00 0.00 0.00 3.07
96 97 9.865321 GAATGAGAAAGGATTGAAAAATGATGA 57.135 29.630 0.00 0.00 0.00 2.92
98 99 9.817809 ATGAGAAAGGATTGAAAAATGATGATG 57.182 29.630 0.00 0.00 0.00 3.07
99 100 8.809066 TGAGAAAGGATTGAAAAATGATGATGT 58.191 29.630 0.00 0.00 0.00 3.06
100 101 9.649167 GAGAAAGGATTGAAAAATGATGATGTT 57.351 29.630 0.00 0.00 0.00 2.71
101 102 9.431887 AGAAAGGATTGAAAAATGATGATGTTG 57.568 29.630 0.00 0.00 0.00 3.33
102 103 9.211485 GAAAGGATTGAAAAATGATGATGTTGT 57.789 29.630 0.00 0.00 0.00 3.32
103 104 8.767478 AAGGATTGAAAAATGATGATGTTGTC 57.233 30.769 0.00 0.00 0.00 3.18
104 105 8.130671 AGGATTGAAAAATGATGATGTTGTCT 57.869 30.769 0.00 0.00 0.00 3.41
108 109 7.274603 TGAAAAATGATGATGTTGTCTGTCA 57.725 32.000 0.00 0.00 0.00 3.58
143 144 1.895131 GGAAAGGCCAGAGCATCAAAA 59.105 47.619 5.01 0.00 42.56 2.44
147 148 1.203100 AGGCCAGAGCATCAAAAAGGT 60.203 47.619 5.01 0.00 42.56 3.50
152 153 2.417933 CAGAGCATCAAAAAGGTCGGAG 59.582 50.000 0.00 0.00 37.82 4.63
186 187 6.496338 AAATAGCCAAAGAAAGTTACGAGG 57.504 37.500 0.00 0.00 0.00 4.63
190 191 4.455877 AGCCAAAGAAAGTTACGAGGAATG 59.544 41.667 0.00 0.00 0.00 2.67
194 195 6.371548 CCAAAGAAAGTTACGAGGAATGATCA 59.628 38.462 0.00 0.00 0.00 2.92
204 205 6.425210 ACGAGGAATGATCATCATTAAGGA 57.575 37.500 13.09 0.00 46.20 3.36
218 219 9.166173 TCATCATTAAGGACAATAGAAACACTG 57.834 33.333 0.00 0.00 0.00 3.66
226 227 6.590292 AGGACAATAGAAACACTGTATGAACG 59.410 38.462 0.00 0.00 0.00 3.95
237 238 6.034591 ACACTGTATGAACGTAATCACTAGC 58.965 40.000 0.00 0.00 30.82 3.42
239 240 6.020599 CACTGTATGAACGTAATCACTAGCAC 60.021 42.308 0.00 0.00 30.82 4.40
249 250 2.724977 TCACTAGCACGAAGTTGAGG 57.275 50.000 0.00 0.00 41.61 3.86
260 261 5.736207 GCACGAAGTTGAGGAAAAATCCTTT 60.736 40.000 0.00 0.00 41.61 3.11
288 289 1.268625 TCGCTTAACTTCTGAGTCGCA 59.731 47.619 0.00 0.00 34.21 5.10
322 323 0.809636 CGATGGCGCAACAGGTCATA 60.810 55.000 10.83 0.00 0.00 2.15
336 337 7.686859 GCAACAGGTCATATAGTGGTGATAAGA 60.687 40.741 0.00 0.00 28.36 2.10
343 344 7.007116 TCATATAGTGGTGATAAGAGAGCAGT 58.993 38.462 0.00 0.00 0.00 4.40
356 357 1.064060 AGAGCAGTTGTTGTCGTTTGC 59.936 47.619 0.00 0.00 0.00 3.68
381 382 2.362717 GAGGGTATTGGTCTCTTCCTCG 59.637 54.545 0.00 0.00 31.47 4.63
382 383 1.413077 GGGTATTGGTCTCTTCCTCGG 59.587 57.143 0.00 0.00 0.00 4.63
416 417 1.880271 TCTACGATGGCCTAGTCGAG 58.120 55.000 25.18 18.55 40.11 4.04
440 441 4.728110 AGCCTGGAAGCGCATGCA 62.728 61.111 19.57 8.83 46.23 3.96
470 471 2.507058 AGTGCTTGCTATGGATCAGGAA 59.493 45.455 0.00 0.00 0.00 3.36
539 540 4.761739 AGTAGTGTCCAACATCAACAATGG 59.238 41.667 0.00 0.00 39.90 3.16
545 546 2.165030 CCAACATCAACAATGGAGCCTC 59.835 50.000 0.00 0.00 39.90 4.70
576 577 3.955471 TGGAGCGATCCTTGAAGAAATT 58.045 40.909 22.18 0.00 0.00 1.82
584 585 6.314784 CGATCCTTGAAGAAATTTACCACAC 58.685 40.000 0.00 0.00 0.00 3.82
600 601 2.483013 CCACACGAAGGAGTTCACTGAA 60.483 50.000 0.00 0.00 32.36 3.02
601 602 3.194861 CACACGAAGGAGTTCACTGAAA 58.805 45.455 0.00 0.00 32.36 2.69
658 659 3.056313 GCTCATGCGTGGGGAAAGC 62.056 63.158 8.15 4.30 0.00 3.51
788 789 5.184287 TGCCCCTAAAAATAACTAAGTGTGC 59.816 40.000 0.00 0.00 0.00 4.57
811 812 8.185505 GTGCTGGTTCGGTCATTAATTATAAAA 58.814 33.333 0.00 0.00 0.00 1.52
813 814 7.378728 GCTGGTTCGGTCATTAATTATAAAAGC 59.621 37.037 0.00 0.00 0.00 3.51
870 871 2.013400 TGTTGAATTGTATGCGGCGAT 58.987 42.857 12.98 3.86 0.00 4.58
912 913 1.815613 CCATGTGCAATCCGTGGTTTA 59.184 47.619 5.99 0.00 34.82 2.01
913 914 2.159393 CCATGTGCAATCCGTGGTTTAG 60.159 50.000 5.99 0.00 34.82 1.85
924 925 6.767524 ATCCGTGGTTTAGAAAAATGCATA 57.232 33.333 0.00 0.00 0.00 3.14
945 946 7.094032 TGCATAATGTGACATACCAAATGTTCA 60.094 33.333 0.00 0.00 31.52 3.18
953 954 8.122952 GTGACATACCAAATGTTCAGCTTATAC 58.877 37.037 0.00 0.00 31.52 1.47
962 963 4.093743 TGTTCAGCTTATACCTCACCAGA 58.906 43.478 0.00 0.00 0.00 3.86
1052 1062 2.386829 AACATGGGCAATATGGAGGG 57.613 50.000 0.00 0.00 0.00 4.30
1066 1076 0.999712 GGAGGGGGAGATGGTTTTCA 59.000 55.000 0.00 0.00 0.00 2.69
1214 1225 4.212636 CGGCTATTTCATAACTTTACCGGG 59.787 45.833 6.32 0.00 33.49 5.73
1238 1249 6.705825 GGCAATTCTACAAGAACACCATTTTT 59.294 34.615 0.00 0.00 37.00 1.94
1507 1518 0.312102 GCAACCACCTCAGACTTTGC 59.688 55.000 0.00 0.00 33.23 3.68
1595 1606 0.548031 CATGGACATGCCCCAGTACT 59.452 55.000 12.26 0.00 37.08 2.73
1689 1700 8.626526 TGTACTCAAAGTTGGTTTATTTCTTCC 58.373 33.333 0.00 0.00 0.00 3.46
1715 1726 2.064573 GCATTATTGCGCCAATACCC 57.935 50.000 4.18 0.00 39.49 3.69
1732 1743 1.617018 CCCGTCTGGATCCTTGCTCA 61.617 60.000 14.23 0.00 37.49 4.26
1743 1754 1.604378 CTTGCTCATCGGTTCCCCT 59.396 57.895 0.00 0.00 0.00 4.79
1811 1822 2.580815 GCCAAAATGCCTCCAGCC 59.419 61.111 0.00 0.00 42.71 4.85
2077 2089 1.710809 AGTTTATGTTGAGGGGTGCCT 59.289 47.619 0.00 0.00 0.00 4.75
2132 2339 7.730364 AGTTTTGTGGTACTAGTCTGAAATG 57.270 36.000 0.00 0.00 0.00 2.32
2135 2342 9.048446 GTTTTGTGGTACTAGTCTGAAATGTTA 57.952 33.333 0.00 0.00 0.00 2.41
2233 2441 4.418013 TGTTTCCTCAAATGTATGTGCG 57.582 40.909 0.00 0.00 0.00 5.34
2234 2442 3.818210 TGTTTCCTCAAATGTATGTGCGT 59.182 39.130 0.00 0.00 0.00 5.24
2332 2540 9.507280 CACCTATGACATTTGTTCATAATCAAC 57.493 33.333 0.00 0.00 0.00 3.18
2341 2549 3.498777 TGTTCATAATCAACGCCACGAAA 59.501 39.130 0.00 0.00 0.00 3.46
2423 2632 2.029649 GGTGTAGCCACTACGTTCTCAA 60.030 50.000 0.00 0.00 39.58 3.02
2475 2684 8.111545 AGCTAGGAATATGAATATTGCATGGAA 58.888 33.333 14.55 0.79 41.69 3.53
2537 2746 8.871629 ATAGGTGTGTCTATCTCTACCTAATG 57.128 38.462 0.00 0.00 42.23 1.90
2658 2867 3.122780 GTGGTTTTTGTTATGGCAATCGC 59.877 43.478 0.00 0.00 37.44 4.58
2716 2925 4.722526 TTCAAATCTTTCTCCCCACTCA 57.277 40.909 0.00 0.00 0.00 3.41
2719 2928 6.581388 TCAAATCTTTCTCCCCACTCATAT 57.419 37.500 0.00 0.00 0.00 1.78
2750 2959 8.998814 TCTCCAATCTCCACCTACATTATTTTA 58.001 33.333 0.00 0.00 0.00 1.52
2773 2982 1.072331 TGTGTCTGAGCCCTCTTTTCC 59.928 52.381 0.00 0.00 0.00 3.13
2875 3086 9.729281 AGTTAAATCTTCCGGAGTTGTAATTTA 57.271 29.630 3.34 7.42 34.01 1.40
2884 3095 6.819649 TCCGGAGTTGTAATTTAATCGTTCAT 59.180 34.615 0.00 0.00 0.00 2.57
2885 3096 7.334921 TCCGGAGTTGTAATTTAATCGTTCATT 59.665 33.333 0.00 0.00 0.00 2.57
2886 3097 7.966204 CCGGAGTTGTAATTTAATCGTTCATTT 59.034 33.333 0.00 0.00 0.00 2.32
2887 3098 9.337091 CGGAGTTGTAATTTAATCGTTCATTTT 57.663 29.630 0.00 0.00 0.00 1.82
2934 3157 9.778741 AGTCTATTAGTAGTCTTCTCTCATCTG 57.221 37.037 0.00 0.00 0.00 2.90
2968 3192 7.669427 TCCAGCATTGTCATTAAAAAGTTCAT 58.331 30.769 0.00 0.00 0.00 2.57
3015 3239 5.241728 GGGAATTGGGTGCAGATATTTCTAC 59.758 44.000 0.00 0.00 0.00 2.59
3016 3240 5.827797 GGAATTGGGTGCAGATATTTCTACA 59.172 40.000 0.00 0.00 0.00 2.74
3034 3258 2.758009 ACAACATTTGGCAGCATGAAC 58.242 42.857 13.91 0.00 38.34 3.18
3205 3429 3.070476 TGCCATAGTTGCATGTTGAGA 57.930 42.857 0.00 0.00 32.85 3.27
3206 3430 3.419943 TGCCATAGTTGCATGTTGAGAA 58.580 40.909 0.00 0.00 32.85 2.87
3209 3433 5.047164 TGCCATAGTTGCATGTTGAGAAAAT 60.047 36.000 0.00 0.00 32.85 1.82
3264 3488 2.565841 GTGAGTTGGCATAGGTCCATC 58.434 52.381 0.00 0.00 32.92 3.51
3470 3704 7.884816 TTGAGTTAGTAAATGGAAACTCGAG 57.115 36.000 11.84 11.84 46.94 4.04
3481 3715 8.842358 AAATGGAAACTCGAGTTAGTAAATGA 57.158 30.769 29.91 9.61 37.25 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.730761 CTGTGTGCTTCGCTGGCC 61.731 66.667 0.00 0.00 0.00 5.36
1 2 0.740868 TATCTGTGTGCTTCGCTGGC 60.741 55.000 0.00 0.00 0.00 4.85
2 3 1.725641 TTATCTGTGTGCTTCGCTGG 58.274 50.000 0.00 0.00 0.00 4.85
3 4 2.931969 TCATTATCTGTGTGCTTCGCTG 59.068 45.455 0.00 0.00 0.00 5.18
4 5 3.251479 TCATTATCTGTGTGCTTCGCT 57.749 42.857 0.00 0.00 0.00 4.93
5 6 4.201851 ACAATCATTATCTGTGTGCTTCGC 60.202 41.667 0.00 0.00 0.00 4.70
6 7 5.475273 ACAATCATTATCTGTGTGCTTCG 57.525 39.130 0.00 0.00 0.00 3.79
7 8 6.615088 ACAACAATCATTATCTGTGTGCTTC 58.385 36.000 0.00 0.00 0.00 3.86
8 9 6.579666 ACAACAATCATTATCTGTGTGCTT 57.420 33.333 0.00 0.00 0.00 3.91
9 10 6.016024 ACAACAACAATCATTATCTGTGTGCT 60.016 34.615 0.00 0.00 0.00 4.40
10 11 6.151691 ACAACAACAATCATTATCTGTGTGC 58.848 36.000 0.00 0.00 0.00 4.57
11 12 7.536281 CAGACAACAACAATCATTATCTGTGTG 59.464 37.037 0.00 0.00 0.00 3.82
12 13 7.229306 ACAGACAACAACAATCATTATCTGTGT 59.771 33.333 2.45 0.00 41.91 3.72
13 14 7.587629 ACAGACAACAACAATCATTATCTGTG 58.412 34.615 2.45 0.00 41.91 3.66
14 15 7.445096 TGACAGACAACAACAATCATTATCTGT 59.555 33.333 2.87 2.87 45.13 3.41
15 16 7.809665 TGACAGACAACAACAATCATTATCTG 58.190 34.615 0.00 0.00 37.62 2.90
16 17 7.984422 TGACAGACAACAACAATCATTATCT 57.016 32.000 0.00 0.00 0.00 1.98
17 18 9.069078 CAATGACAGACAACAACAATCATTATC 57.931 33.333 0.00 0.00 34.43 1.75
18 19 8.030692 CCAATGACAGACAACAACAATCATTAT 58.969 33.333 0.00 0.00 34.43 1.28
19 20 7.014134 ACCAATGACAGACAACAACAATCATTA 59.986 33.333 0.00 0.00 34.43 1.90
20 21 6.183360 ACCAATGACAGACAACAACAATCATT 60.183 34.615 0.00 0.00 36.10 2.57
21 22 5.302568 ACCAATGACAGACAACAACAATCAT 59.697 36.000 0.00 0.00 0.00 2.45
22 23 4.644234 ACCAATGACAGACAACAACAATCA 59.356 37.500 0.00 0.00 0.00 2.57
23 24 5.186996 ACCAATGACAGACAACAACAATC 57.813 39.130 0.00 0.00 0.00 2.67
24 25 6.707440 TTACCAATGACAGACAACAACAAT 57.293 33.333 0.00 0.00 0.00 2.71
25 26 6.516739 TTTACCAATGACAGACAACAACAA 57.483 33.333 0.00 0.00 0.00 2.83
26 27 6.707440 ATTTACCAATGACAGACAACAACA 57.293 33.333 0.00 0.00 0.00 3.33
27 28 9.769093 GTATATTTACCAATGACAGACAACAAC 57.231 33.333 0.00 0.00 0.00 3.32
28 29 9.508642 TGTATATTTACCAATGACAGACAACAA 57.491 29.630 0.00 0.00 0.00 2.83
29 30 9.508642 TTGTATATTTACCAATGACAGACAACA 57.491 29.630 0.00 0.00 0.00 3.33
30 31 9.988350 CTTGTATATTTACCAATGACAGACAAC 57.012 33.333 0.00 0.00 0.00 3.32
31 32 9.952030 TCTTGTATATTTACCAATGACAGACAA 57.048 29.630 0.00 0.00 0.00 3.18
59 60 9.880157 CAATCCTTTCTCATTCCATTTGTAATT 57.120 29.630 0.00 0.00 0.00 1.40
60 61 9.258629 TCAATCCTTTCTCATTCCATTTGTAAT 57.741 29.630 0.00 0.00 0.00 1.89
61 62 8.648698 TCAATCCTTTCTCATTCCATTTGTAA 57.351 30.769 0.00 0.00 0.00 2.41
62 63 8.648698 TTCAATCCTTTCTCATTCCATTTGTA 57.351 30.769 0.00 0.00 0.00 2.41
63 64 7.543359 TTCAATCCTTTCTCATTCCATTTGT 57.457 32.000 0.00 0.00 0.00 2.83
64 65 8.836268 TTTTCAATCCTTTCTCATTCCATTTG 57.164 30.769 0.00 0.00 0.00 2.32
66 67 9.444600 CATTTTTCAATCCTTTCTCATTCCATT 57.555 29.630 0.00 0.00 0.00 3.16
67 68 8.818860 TCATTTTTCAATCCTTTCTCATTCCAT 58.181 29.630 0.00 0.00 0.00 3.41
68 69 8.192743 TCATTTTTCAATCCTTTCTCATTCCA 57.807 30.769 0.00 0.00 0.00 3.53
69 70 9.095065 CATCATTTTTCAATCCTTTCTCATTCC 57.905 33.333 0.00 0.00 0.00 3.01
70 71 9.865321 TCATCATTTTTCAATCCTTTCTCATTC 57.135 29.630 0.00 0.00 0.00 2.67
72 73 9.817809 CATCATCATTTTTCAATCCTTTCTCAT 57.182 29.630 0.00 0.00 0.00 2.90
73 74 8.809066 ACATCATCATTTTTCAATCCTTTCTCA 58.191 29.630 0.00 0.00 0.00 3.27
74 75 9.649167 AACATCATCATTTTTCAATCCTTTCTC 57.351 29.630 0.00 0.00 0.00 2.87
75 76 9.431887 CAACATCATCATTTTTCAATCCTTTCT 57.568 29.630 0.00 0.00 0.00 2.52
76 77 9.211485 ACAACATCATCATTTTTCAATCCTTTC 57.789 29.630 0.00 0.00 0.00 2.62
77 78 9.211485 GACAACATCATCATTTTTCAATCCTTT 57.789 29.630 0.00 0.00 0.00 3.11
78 79 8.591072 AGACAACATCATCATTTTTCAATCCTT 58.409 29.630 0.00 0.00 0.00 3.36
79 80 8.033038 CAGACAACATCATCATTTTTCAATCCT 58.967 33.333 0.00 0.00 0.00 3.24
80 81 7.816031 ACAGACAACATCATCATTTTTCAATCC 59.184 33.333 0.00 0.00 0.00 3.01
81 82 8.752766 ACAGACAACATCATCATTTTTCAATC 57.247 30.769 0.00 0.00 0.00 2.67
82 83 8.361889 TGACAGACAACATCATCATTTTTCAAT 58.638 29.630 0.00 0.00 0.00 2.57
83 84 7.648908 GTGACAGACAACATCATCATTTTTCAA 59.351 33.333 0.00 0.00 30.02 2.69
84 85 7.140705 GTGACAGACAACATCATCATTTTTCA 58.859 34.615 0.00 0.00 30.02 2.69
85 86 7.140705 TGTGACAGACAACATCATCATTTTTC 58.859 34.615 0.00 0.00 30.02 2.29
86 87 7.041635 TGTGACAGACAACATCATCATTTTT 57.958 32.000 0.00 0.00 30.02 1.94
87 88 6.638096 TGTGACAGACAACATCATCATTTT 57.362 33.333 0.00 0.00 30.02 1.82
88 89 6.638096 TTGTGACAGACAACATCATCATTT 57.362 33.333 0.00 0.00 39.78 2.32
100 101 5.394224 TCGTATGGTAATTGTGACAGACA 57.606 39.130 0.00 0.00 0.00 3.41
101 102 4.804139 CCTCGTATGGTAATTGTGACAGAC 59.196 45.833 0.00 0.00 0.00 3.51
102 103 4.707934 TCCTCGTATGGTAATTGTGACAGA 59.292 41.667 0.00 0.00 0.00 3.41
103 104 5.006153 TCCTCGTATGGTAATTGTGACAG 57.994 43.478 0.00 0.00 0.00 3.51
104 105 5.408880 TTCCTCGTATGGTAATTGTGACA 57.591 39.130 0.00 0.00 0.00 3.58
108 109 4.196971 GCCTTTCCTCGTATGGTAATTGT 58.803 43.478 0.00 0.00 0.00 2.71
143 144 5.975693 TTTATTTTTGATGCTCCGACCTT 57.024 34.783 0.00 0.00 0.00 3.50
147 148 5.592282 TGGCTATTTATTTTTGATGCTCCGA 59.408 36.000 0.00 0.00 0.00 4.55
152 153 9.977762 CTTTCTTTGGCTATTTATTTTTGATGC 57.022 29.630 0.00 0.00 0.00 3.91
182 183 6.226052 TGTCCTTAATGATGATCATTCCTCG 58.774 40.000 22.70 10.14 43.03 4.63
204 205 8.821147 TTACGTTCATACAGTGTTTCTATTGT 57.179 30.769 0.00 0.00 0.00 2.71
218 219 5.268544 TCGTGCTAGTGATTACGTTCATAC 58.731 41.667 0.00 0.00 37.74 2.39
226 227 4.563184 CCTCAACTTCGTGCTAGTGATTAC 59.437 45.833 0.00 0.00 0.00 1.89
237 238 5.438761 AAGGATTTTTCCTCAACTTCGTG 57.561 39.130 0.00 0.00 39.65 4.35
239 240 6.072112 TCAAAGGATTTTTCCTCAACTTCG 57.928 37.500 0.00 0.00 39.65 3.79
249 250 9.620660 TTAAGCGAACTATTCAAAGGATTTTTC 57.379 29.630 0.00 0.00 35.03 2.29
288 289 0.456221 CATCGGCGTAGAGACCAACT 59.544 55.000 6.85 0.00 0.00 3.16
314 315 7.576666 GCTCTCTTATCACCACTATATGACCTG 60.577 44.444 0.00 0.00 0.00 4.00
322 323 5.423610 ACAACTGCTCTCTTATCACCACTAT 59.576 40.000 0.00 0.00 0.00 2.12
336 337 1.064060 GCAAACGACAACAACTGCTCT 59.936 47.619 0.00 0.00 0.00 4.09
343 344 2.159310 CCCTCTTTGCAAACGACAACAA 60.159 45.455 8.05 0.00 0.00 2.83
356 357 4.226168 AGGAAGAGACCAATACCCTCTTTG 59.774 45.833 0.00 0.00 44.53 2.77
381 382 6.366332 CCATCGTAGATTACAACATAAGCTCC 59.634 42.308 0.00 0.00 45.12 4.70
382 383 6.128795 GCCATCGTAGATTACAACATAAGCTC 60.129 42.308 0.00 0.00 45.12 4.09
422 423 3.885521 GCATGCGCTTCCAGGCTC 61.886 66.667 9.73 0.00 39.26 4.70
440 441 4.950744 GCAAGCACTTCGTTGCAT 57.049 50.000 8.68 0.00 46.83 3.96
443 444 2.076100 TCCATAGCAAGCACTTCGTTG 58.924 47.619 0.00 0.00 0.00 4.10
497 498 7.069085 ACACTACTTCAAGGTAGTTAGACACAA 59.931 37.037 2.48 0.00 46.88 3.33
502 503 6.309357 TGGACACTACTTCAAGGTAGTTAGA 58.691 40.000 2.48 0.00 46.88 2.10
539 540 2.546162 GCTCCATAAACTACCGAGGCTC 60.546 54.545 3.87 3.87 0.00 4.70
545 546 2.296471 AGGATCGCTCCATAAACTACCG 59.704 50.000 8.23 0.00 44.79 4.02
576 577 2.696707 AGTGAACTCCTTCGTGTGGTAA 59.303 45.455 0.00 0.00 0.00 2.85
584 585 3.187227 CACCATTTCAGTGAACTCCTTCG 59.813 47.826 4.68 0.00 37.42 3.79
600 601 0.598065 GCTCAAAGCGGAACACCATT 59.402 50.000 0.00 0.00 0.00 3.16
601 602 0.537143 TGCTCAAAGCGGAACACCAT 60.537 50.000 0.00 0.00 46.26 3.55
658 659 2.464157 AACTCAAGCGAGGAAGAAGG 57.536 50.000 0.00 0.00 44.17 3.46
788 789 8.621286 AGCTTTTATAATTAATGACCGAACCAG 58.379 33.333 0.00 0.00 0.00 4.00
811 812 4.284746 GGTATGCTCCAAGGTAGATAAGCT 59.715 45.833 0.00 0.00 37.60 3.74
813 814 4.810790 CGGTATGCTCCAAGGTAGATAAG 58.189 47.826 0.00 0.00 0.00 1.73
870 871 6.358178 TGGTTAGTCAAAATTGTGTGAGGTA 58.642 36.000 0.00 0.00 0.00 3.08
912 913 8.065473 TGGTATGTCACATTATGCATTTTTCT 57.935 30.769 3.54 0.00 0.00 2.52
913 914 8.700722 TTGGTATGTCACATTATGCATTTTTC 57.299 30.769 3.54 0.00 0.00 2.29
924 925 5.477984 AGCTGAACATTTGGTATGTCACATT 59.522 36.000 0.00 0.00 0.00 2.71
953 954 4.636206 GGTGTTTTAATAGCTCTGGTGAGG 59.364 45.833 0.00 0.00 40.53 3.86
1016 1020 5.073144 CCCATGTTATCCCCAATAGTACTGT 59.927 44.000 5.39 0.00 0.00 3.55
1052 1062 2.840651 TCTCTCCTGAAAACCATCTCCC 59.159 50.000 0.00 0.00 0.00 4.30
1214 1225 7.713764 AAAAATGGTGTTCTTGTAGAATTGC 57.286 32.000 0.00 0.00 36.50 3.56
1238 1249 1.892474 GGTTTGAGCAGGGCATTGTAA 59.108 47.619 0.00 0.00 0.00 2.41
1239 1250 1.544724 GGTTTGAGCAGGGCATTGTA 58.455 50.000 0.00 0.00 0.00 2.41
1242 1253 2.639327 GCGGTTTGAGCAGGGCATT 61.639 57.895 0.00 0.00 34.19 3.56
1301 1312 4.471904 TTCTTTGAGCTGTCGGACATAT 57.528 40.909 11.86 3.03 0.00 1.78
1473 1484 0.589708 GTTGCCAGGAACGTACCAAC 59.410 55.000 0.00 0.00 0.00 3.77
1507 1518 4.522405 TGGAAAATAACCACCATGTCACTG 59.478 41.667 0.00 0.00 32.03 3.66
1715 1726 1.863267 GATGAGCAAGGATCCAGACG 58.137 55.000 15.82 0.00 0.00 4.18
1743 1754 5.882557 GGATGAGCTTGATCCACTTCTTTTA 59.117 40.000 17.07 0.00 39.49 1.52
1811 1822 6.818644 ACCAACATATGTAGTTAACTGCTCTG 59.181 38.462 22.00 17.60 0.00 3.35
2077 2089 5.191426 ACTATGCTAGTTAGTGAACGAGGA 58.809 41.667 6.68 0.00 41.51 3.71
2156 2363 6.151817 ACCAAATTTTGCAAGCACCTTAAAAA 59.848 30.769 0.00 0.00 0.00 1.94
2157 2364 5.649831 ACCAAATTTTGCAAGCACCTTAAAA 59.350 32.000 0.00 0.00 0.00 1.52
2195 2403 3.685139 AACAAATTCAGAGCTCCTCGA 57.315 42.857 10.93 1.62 35.36 4.04
2269 2477 7.628234 TGGTGGCCAAATAACATCAAATTATT 58.372 30.769 7.24 0.00 34.42 1.40
2332 2540 3.935027 AAAAACCAAAATTTCGTGGCG 57.065 38.095 8.55 0.00 38.58 5.69
2392 2601 2.038837 GGCTACACCCAAGTTCGGC 61.039 63.158 0.00 0.00 0.00 5.54
2475 2684 6.946583 AGATATGTAATGCAATGCAATCTCCT 59.053 34.615 13.45 0.00 43.62 3.69
2511 2720 9.961264 CATTAGGTAGAGATAGACACACCTATA 57.039 37.037 0.00 0.00 38.19 1.31
2512 2721 7.394923 GCATTAGGTAGAGATAGACACACCTAT 59.605 40.741 0.00 0.00 38.19 2.57
2513 2722 6.715718 GCATTAGGTAGAGATAGACACACCTA 59.284 42.308 0.00 0.00 37.55 3.08
2514 2723 5.536916 GCATTAGGTAGAGATAGACACACCT 59.463 44.000 0.00 0.00 39.63 4.00
2515 2724 5.536916 AGCATTAGGTAGAGATAGACACACC 59.463 44.000 0.00 0.00 0.00 4.16
2516 2725 6.642707 AGCATTAGGTAGAGATAGACACAC 57.357 41.667 0.00 0.00 0.00 3.82
2517 2726 7.230913 GGTTAGCATTAGGTAGAGATAGACACA 59.769 40.741 0.00 0.00 0.00 3.72
2518 2727 7.573469 CGGTTAGCATTAGGTAGAGATAGACAC 60.573 44.444 0.00 0.00 0.00 3.67
2519 2728 6.430308 CGGTTAGCATTAGGTAGAGATAGACA 59.570 42.308 0.00 0.00 0.00 3.41
2520 2729 6.654161 TCGGTTAGCATTAGGTAGAGATAGAC 59.346 42.308 0.00 0.00 0.00 2.59
2537 2746 3.098555 CACGGGCATTCGGTTAGC 58.901 61.111 0.00 0.00 0.00 3.09
2658 2867 3.632145 GGTACAATGGTTAAGGAGCATGG 59.368 47.826 0.00 0.00 45.33 3.66
2699 2908 6.161170 AGGAAATATGAGTGGGGAGAAAGATT 59.839 38.462 0.00 0.00 0.00 2.40
2716 2925 5.230759 AGGTGGAGATTGGAGAGGAAATAT 58.769 41.667 0.00 0.00 0.00 1.28
2719 2928 2.921221 AGGTGGAGATTGGAGAGGAAA 58.079 47.619 0.00 0.00 0.00 3.13
2750 2959 3.515602 AAAGAGGGCTCAGACACAATT 57.484 42.857 0.00 0.00 0.00 2.32
2752 2961 2.487265 GGAAAAGAGGGCTCAGACACAA 60.487 50.000 0.00 0.00 0.00 3.33
2909 3129 8.504005 GCAGATGAGAGAAGACTACTAATAGAC 58.496 40.741 0.00 0.00 32.23 2.59
2968 3192 1.138464 TGCAACGCGTGGGGTATTATA 59.862 47.619 14.98 0.00 0.00 0.98
3015 3239 2.070783 GGTTCATGCTGCCAAATGTTG 58.929 47.619 0.00 0.00 0.00 3.33
3016 3240 1.972795 AGGTTCATGCTGCCAAATGTT 59.027 42.857 0.00 0.00 0.00 2.71
3206 3430 9.830975 GCATACCTCCACCAAATTTATTTATTT 57.169 29.630 0.00 0.00 0.00 1.40
3209 3433 7.962995 TGCATACCTCCACCAAATTTATTTA 57.037 32.000 0.00 0.00 0.00 1.40
3220 3444 1.901591 CCATCATGCATACCTCCACC 58.098 55.000 0.00 0.00 0.00 4.61
3398 3632 8.434589 TTCAAAATTTGAGGGTGGATAAGAAT 57.565 30.769 8.51 0.00 41.38 2.40
3404 3638 7.552050 TTACATTCAAAATTTGAGGGTGGAT 57.448 32.000 18.29 4.25 41.38 3.41
3525 3759 6.203530 GCATAGATTTTGCAGCTACATGACTA 59.796 38.462 0.00 0.00 39.90 2.59
3556 3790 6.431234 ACAGTAGATTCTTTGCCGAAAATCTT 59.569 34.615 2.18 0.00 38.86 2.40


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

AutoCloner maintained by Alex Coulton.