Multiple sequence alignment - TraesCS6D01G252700

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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 TraesCS6D01G252700 chr6D 100.000 3665 0 0 1 3665 356772414 356768750 0.000000e+00 6769.0
1 TraesCS6D01G252700 chr6A 92.959 2457 120 29 782 3222 499287112 499284693 0.000000e+00 3530.0
2 TraesCS6D01G252700 chr6A 92.290 441 32 2 3223 3663 499217554 499217116 3.110000e-175 625.0
3 TraesCS6D01G252700 chr6A 77.494 862 136 38 2836 3663 13438876 13438039 7.170000e-127 464.0
4 TraesCS6D01G252700 chr6A 78.207 647 94 26 3020 3651 195134162 195134776 1.610000e-98 370.0
5 TraesCS6D01G252700 chr6A 91.743 109 5 1 635 743 499287218 499287114 8.200000e-32 148.0
6 TraesCS6D01G252700 chr6B 92.771 2075 91 37 635 2676 538172229 538170181 0.000000e+00 2946.0
7 TraesCS6D01G252700 chr6B 88.269 878 87 9 2794 3663 538162205 538161336 0.000000e+00 1037.0
8 TraesCS6D01G252700 chr6B 88.433 536 51 4 52 577 150831662 150831128 1.440000e-178 636.0
9 TraesCS6D01G252700 chr6B 95.714 140 6 0 2672 2811 538164474 538164335 3.680000e-55 226.0
10 TraesCS6D01G252700 chr1A 87.453 534 57 3 52 575 59836689 59837222 1.130000e-169 606.0
11 TraesCS6D01G252700 chrUn 86.704 534 61 3 52 575 3383165 3383698 5.270000e-163 584.0
12 TraesCS6D01G252700 chr1B 86.704 534 61 3 52 575 48010842 48011375 5.270000e-163 584.0
13 TraesCS6D01G252700 chr1B 87.027 370 37 5 52 412 302543631 302543264 1.230000e-109 407.0
14 TraesCS6D01G252700 chr1B 90.805 174 13 3 407 577 302523368 302523195 2.850000e-56 230.0
15 TraesCS6D01G252700 chr1B 96.875 64 1 1 1 64 121967015 121967077 5.010000e-19 106.0
16 TraesCS6D01G252700 chr2B 82.810 541 75 9 52 577 773821205 773820668 5.540000e-128 468.0
17 TraesCS6D01G252700 chr2B 100.000 59 0 0 1 59 234444753 234444811 3.870000e-20 110.0
18 TraesCS6D01G252700 chr2D 78.195 798 103 31 2884 3663 645964732 645963988 9.340000e-121 444.0
19 TraesCS6D01G252700 chr2D 82.060 301 41 8 287 575 647230943 647230644 1.020000e-60 244.0
20 TraesCS6D01G252700 chr4D 80.428 608 95 13 3066 3652 339476087 339475483 3.360000e-120 442.0
21 TraesCS6D01G252700 chr4D 94.030 67 1 2 2 67 220302788 220302852 8.380000e-17 99.0
22 TraesCS6D01G252700 chr4A 78.274 649 108 23 3000 3623 130975445 130976085 1.600000e-103 387.0
23 TraesCS6D01G252700 chr4A 80.236 339 58 7 3318 3652 685344942 685344609 2.830000e-61 246.0
24 TraesCS6D01G252700 chr4A 75.985 533 91 20 2860 3359 608228008 608227480 1.320000e-59 241.0
25 TraesCS6D01G252700 chr4A 92.857 70 4 1 1 69 452712156 452712087 2.330000e-17 100.0
26 TraesCS6D01G252700 chr7D 77.346 618 113 19 2985 3582 433874490 433875100 1.260000e-89 340.0
27 TraesCS6D01G252700 chr4B 75.890 730 131 23 2951 3665 427262505 427261806 7.590000e-87 331.0
28 TraesCS6D01G252700 chr7A 75.902 610 96 26 3072 3663 93030898 93030322 7.800000e-67 265.0
29 TraesCS6D01G252700 chr7A 83.019 212 32 4 367 575 227080455 227080245 4.830000e-44 189.0
30 TraesCS6D01G252700 chr7B 81.121 339 48 12 3318 3652 654924078 654923752 1.310000e-64 257.0
31 TraesCS6D01G252700 chr7B 90.667 75 3 3 1 72 437480444 437480371 3.010000e-16 97.1
32 TraesCS6D01G252700 chr7B 90.541 74 3 3 1 72 660272126 660272055 1.080000e-15 95.3
33 TraesCS6D01G252700 chr3D 75.413 545 107 17 52 577 274439745 274439209 4.730000e-59 239.0
34 TraesCS6D01G252700 chr3D 75.046 545 109 17 52 577 274651625 274651089 1.020000e-55 228.0
35 TraesCS6D01G252700 chr3D 75.415 301 54 13 289 577 33202671 33202379 1.070000e-25 128.0
36 TraesCS6D01G252700 chr3D 90.411 73 5 2 1 72 82248446 82248375 1.080000e-15 95.3
37 TraesCS6D01G252700 chr3A 81.481 297 43 6 287 572 33439839 33440134 2.200000e-57 233.0
38 TraesCS6D01G252700 chr5B 80.000 300 49 4 286 575 23348031 23347733 1.030000e-50 211.0
39 TraesCS6D01G252700 chr5B 76.879 173 27 8 2951 3114 576088832 576089000 6.520000e-13 86.1
40 TraesCS6D01G252700 chr3B 79.866 298 51 4 287 575 141971393 141971096 3.710000e-50 209.0
41 TraesCS6D01G252700 chr5A 78.689 305 53 4 284 577 291137131 291137434 3.730000e-45 193.0
42 TraesCS6D01G252700 chr5A 82.569 109 10 6 3066 3166 589299978 589300085 1.810000e-13 87.9
43 TraesCS6D01G252700 chr5D 98.361 61 0 1 1 60 70044140 70044080 5.010000e-19 106.0
44 TraesCS6D01G252700 chr5D 88.000 50 6 0 3063 3112 37634481 37634432 3.950000e-05 60.2
45 TraesCS6D01G252700 chr2A 92.754 69 3 2 1 68 602000053 601999986 8.380000e-17 99.0


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 TraesCS6D01G252700 chr6D 356768750 356772414 3664 True 6769.0 6769 100.0000 1 3665 1 chr6D.!!$R1 3664
1 TraesCS6D01G252700 chr6A 499284693 499287218 2525 True 1839.0 3530 92.3510 635 3222 2 chr6A.!!$R3 2587
2 TraesCS6D01G252700 chr6A 13438039 13438876 837 True 464.0 464 77.4940 2836 3663 1 chr6A.!!$R1 827
3 TraesCS6D01G252700 chr6A 195134162 195134776 614 False 370.0 370 78.2070 3020 3651 1 chr6A.!!$F1 631
4 TraesCS6D01G252700 chr6B 538170181 538172229 2048 True 2946.0 2946 92.7710 635 2676 1 chr6B.!!$R2 2041
5 TraesCS6D01G252700 chr6B 150831128 150831662 534 True 636.0 636 88.4330 52 577 1 chr6B.!!$R1 525
6 TraesCS6D01G252700 chr6B 538161336 538164474 3138 True 631.5 1037 91.9915 2672 3663 2 chr6B.!!$R3 991
7 TraesCS6D01G252700 chr1A 59836689 59837222 533 False 606.0 606 87.4530 52 575 1 chr1A.!!$F1 523
8 TraesCS6D01G252700 chrUn 3383165 3383698 533 False 584.0 584 86.7040 52 575 1 chrUn.!!$F1 523
9 TraesCS6D01G252700 chr1B 48010842 48011375 533 False 584.0 584 86.7040 52 575 1 chr1B.!!$F1 523
10 TraesCS6D01G252700 chr2B 773820668 773821205 537 True 468.0 468 82.8100 52 577 1 chr2B.!!$R1 525
11 TraesCS6D01G252700 chr2D 645963988 645964732 744 True 444.0 444 78.1950 2884 3663 1 chr2D.!!$R1 779
12 TraesCS6D01G252700 chr4D 339475483 339476087 604 True 442.0 442 80.4280 3066 3652 1 chr4D.!!$R1 586
13 TraesCS6D01G252700 chr4A 130975445 130976085 640 False 387.0 387 78.2740 3000 3623 1 chr4A.!!$F1 623
14 TraesCS6D01G252700 chr4A 608227480 608228008 528 True 241.0 241 75.9850 2860 3359 1 chr4A.!!$R2 499
15 TraesCS6D01G252700 chr7D 433874490 433875100 610 False 340.0 340 77.3460 2985 3582 1 chr7D.!!$F1 597
16 TraesCS6D01G252700 chr4B 427261806 427262505 699 True 331.0 331 75.8900 2951 3665 1 chr4B.!!$R1 714
17 TraesCS6D01G252700 chr7A 93030322 93030898 576 True 265.0 265 75.9020 3072 3663 1 chr7A.!!$R1 591
18 TraesCS6D01G252700 chr3D 274439209 274439745 536 True 239.0 239 75.4130 52 577 1 chr3D.!!$R3 525
19 TraesCS6D01G252700 chr3D 274651089 274651625 536 True 228.0 228 75.0460 52 577 1 chr3D.!!$R4 525

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
383 399 0.106149 GATGGGCGAATTACGGGACT 59.894 55.000 0.0 0.0 42.83 3.85 F
578 596 1.206132 CCGTGGTGCCAATACTACAGA 59.794 52.381 0.0 0.0 32.26 3.41 F
1436 1471 1.609501 CTTCTGGACGTGGAGGGGA 60.610 63.158 0.0 0.0 0.00 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1585 1620 0.106918 GTCACCCCGCATTCCCAATA 60.107 55.0 0.00 0.0 0.0 1.90 R
2200 2241 1.098129 TTGCGCTAGTGGTTGTTGCA 61.098 50.0 9.73 0.0 0.0 4.08 R
3266 5511 0.251073 TAGGCCAAACTAGCGGGAAC 59.749 55.0 5.01 0.0 0.0 3.62 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
20 21 2.892784 AAAAATTTCGTTCGGCCCAA 57.107 40.000 0.00 0.00 0.00 4.12
21 22 2.892784 AAAATTTCGTTCGGCCCAAA 57.107 40.000 0.00 0.00 0.00 3.28
22 23 2.892784 AAATTTCGTTCGGCCCAAAA 57.107 40.000 0.00 0.00 0.00 2.44
23 24 3.394674 AAATTTCGTTCGGCCCAAAAT 57.605 38.095 0.00 0.00 0.00 1.82
24 25 2.362169 ATTTCGTTCGGCCCAAAATG 57.638 45.000 0.00 0.00 0.00 2.32
25 26 1.033574 TTTCGTTCGGCCCAAAATGT 58.966 45.000 0.00 0.00 0.00 2.71
26 27 0.594110 TTCGTTCGGCCCAAAATGTC 59.406 50.000 0.00 0.00 0.00 3.06
27 28 0.535328 TCGTTCGGCCCAAAATGTCA 60.535 50.000 0.00 0.00 0.00 3.58
28 29 0.386731 CGTTCGGCCCAAAATGTCAC 60.387 55.000 0.00 0.00 0.00 3.67
29 30 0.386731 GTTCGGCCCAAAATGTCACG 60.387 55.000 0.00 0.00 0.00 4.35
30 31 1.519751 TTCGGCCCAAAATGTCACGG 61.520 55.000 0.00 0.00 0.00 4.94
31 32 1.969064 CGGCCCAAAATGTCACGGA 60.969 57.895 0.00 0.00 0.00 4.69
32 33 1.312371 CGGCCCAAAATGTCACGGAT 61.312 55.000 0.00 0.00 0.00 4.18
33 34 0.173255 GGCCCAAAATGTCACGGATG 59.827 55.000 0.00 0.00 0.00 3.51
34 35 0.887933 GCCCAAAATGTCACGGATGT 59.112 50.000 0.00 0.00 0.00 3.06
36 37 1.885887 CCCAAAATGTCACGGATGTGT 59.114 47.619 0.00 0.00 46.49 3.72
37 38 2.095263 CCCAAAATGTCACGGATGTGTC 60.095 50.000 0.00 0.00 46.49 3.67
38 39 2.813754 CCAAAATGTCACGGATGTGTCT 59.186 45.455 0.00 0.00 46.49 3.41
39 40 3.253188 CCAAAATGTCACGGATGTGTCTT 59.747 43.478 0.00 0.00 46.49 3.01
40 41 4.261572 CCAAAATGTCACGGATGTGTCTTT 60.262 41.667 0.00 0.00 46.49 2.52
41 42 5.280945 CAAAATGTCACGGATGTGTCTTTT 58.719 37.500 0.00 0.00 46.49 2.27
42 43 5.514274 AAATGTCACGGATGTGTCTTTTT 57.486 34.783 0.00 0.00 46.49 1.94
196 203 1.073098 GGAAACCAAAGGAGGGAGGA 58.927 55.000 0.00 0.00 0.00 3.71
201 208 2.765502 ACCAAAGGAGGGAGGAGATAC 58.234 52.381 0.00 0.00 0.00 2.24
266 274 7.816945 AAGACAACTTCAGTTTTTGAATGTG 57.183 32.000 2.03 1.44 44.48 3.21
276 284 7.484975 TCAGTTTTTGAATGTGTAACCGAATT 58.515 30.769 0.00 0.00 30.35 2.17
383 399 0.106149 GATGGGCGAATTACGGGACT 59.894 55.000 0.00 0.00 42.83 3.85
463 481 4.070716 GCGATGGAGAGATTGAAATGGAT 58.929 43.478 0.00 0.00 0.00 3.41
482 500 4.202398 TGGATTCTAGGATTCAGTCATGGC 60.202 45.833 0.00 0.00 0.00 4.40
577 595 1.651987 CCGTGGTGCCAATACTACAG 58.348 55.000 0.00 0.00 32.26 2.74
578 596 1.206132 CCGTGGTGCCAATACTACAGA 59.794 52.381 0.00 0.00 32.26 3.41
579 597 2.158957 CCGTGGTGCCAATACTACAGAT 60.159 50.000 0.00 0.00 32.26 2.90
580 598 2.866156 CGTGGTGCCAATACTACAGATG 59.134 50.000 0.00 0.00 32.26 2.90
581 599 3.430236 CGTGGTGCCAATACTACAGATGA 60.430 47.826 0.00 0.00 32.26 2.92
582 600 4.513442 GTGGTGCCAATACTACAGATGAA 58.487 43.478 0.00 0.00 32.91 2.57
583 601 4.941263 GTGGTGCCAATACTACAGATGAAA 59.059 41.667 0.00 0.00 32.91 2.69
584 602 5.590259 GTGGTGCCAATACTACAGATGAAAT 59.410 40.000 0.00 0.00 32.91 2.17
585 603 5.822519 TGGTGCCAATACTACAGATGAAATC 59.177 40.000 0.00 0.00 46.04 2.17
610 628 6.993079 CCAGCTTGGGAAACTTAAATAAAGT 58.007 36.000 0.00 0.00 41.28 2.66
611 629 7.441836 CCAGCTTGGGAAACTTAAATAAAGTT 58.558 34.615 0.00 0.00 45.78 2.66
612 630 7.384932 CCAGCTTGGGAAACTTAAATAAAGTTG 59.615 37.037 4.05 0.00 44.44 3.16
716 735 2.849294 TTCATTCCATCACGGTGTGA 57.151 45.000 8.17 1.65 46.90 3.58
717 736 2.849294 TCATTCCATCACGGTGTGAA 57.151 45.000 8.17 9.89 45.96 3.18
718 737 2.698803 TCATTCCATCACGGTGTGAAG 58.301 47.619 8.17 0.00 45.96 3.02
719 738 2.301583 TCATTCCATCACGGTGTGAAGA 59.698 45.455 8.17 1.76 45.96 2.87
905 926 2.565834 CAAGTAAAACTCTCTCCCCCGA 59.434 50.000 0.00 0.00 0.00 5.14
1109 1130 7.337436 GCACTTACTTCTCTCTACTTTCCTCTA 59.663 40.741 0.00 0.00 0.00 2.43
1313 1348 4.394610 GGCTCAAATCTTTCTTCAGAGTCC 59.605 45.833 0.00 0.00 0.00 3.85
1355 1390 5.335127 CCAATCAGAATTCATGTTCGTTCC 58.665 41.667 8.44 0.00 33.36 3.62
1357 1392 6.349611 CCAATCAGAATTCATGTTCGTTCCTT 60.350 38.462 8.44 0.00 33.36 3.36
1358 1393 5.862924 TCAGAATTCATGTTCGTTCCTTC 57.137 39.130 8.44 0.00 33.36 3.46
1359 1394 5.551233 TCAGAATTCATGTTCGTTCCTTCT 58.449 37.500 8.44 0.00 33.36 2.85
1436 1471 1.609501 CTTCTGGACGTGGAGGGGA 60.610 63.158 0.00 0.00 0.00 4.81
1647 1682 1.757682 TGGTTGGTGTTGTCTGAACC 58.242 50.000 0.00 0.00 37.23 3.62
1651 1686 2.036958 TGGTGTTGTCTGAACCACTG 57.963 50.000 0.00 0.00 39.05 3.66
1875 1911 4.559502 CGACACCATTCTTCAGAGTTCAGA 60.560 45.833 0.00 0.00 0.00 3.27
1884 1920 5.487433 TCTTCAGAGTTCAGAAACACACAA 58.513 37.500 0.00 0.00 37.88 3.33
2200 2241 3.927142 CGAGAAAGTCCTCAAAAGCGTAT 59.073 43.478 0.00 0.00 32.86 3.06
2206 2247 2.225491 GTCCTCAAAAGCGTATGCAACA 59.775 45.455 10.11 0.00 46.23 3.33
2207 2248 2.881513 TCCTCAAAAGCGTATGCAACAA 59.118 40.909 10.11 0.00 46.23 2.83
2208 2249 2.979813 CCTCAAAAGCGTATGCAACAAC 59.020 45.455 10.11 0.00 46.23 3.32
2209 2250 2.979813 CTCAAAAGCGTATGCAACAACC 59.020 45.455 10.11 0.00 46.23 3.77
2210 2251 2.359214 TCAAAAGCGTATGCAACAACCA 59.641 40.909 10.11 0.00 46.23 3.67
2212 2253 1.604604 AAGCGTATGCAACAACCACT 58.395 45.000 10.11 0.00 46.23 4.00
2214 2255 2.346803 AGCGTATGCAACAACCACTAG 58.653 47.619 10.11 0.00 46.23 2.57
2215 2256 1.202031 GCGTATGCAACAACCACTAGC 60.202 52.381 0.89 0.00 42.15 3.42
2218 2259 0.888736 ATGCAACAACCACTAGCGCA 60.889 50.000 11.47 0.00 0.00 6.09
2220 2261 0.030101 GCAACAACCACTAGCGCAAA 59.970 50.000 11.47 0.00 0.00 3.68
2222 2263 1.064803 CAACAACCACTAGCGCAAACA 59.935 47.619 11.47 0.00 0.00 2.83
2224 2265 1.225855 CAACCACTAGCGCAAACAGA 58.774 50.000 11.47 0.00 0.00 3.41
2225 2266 1.806542 CAACCACTAGCGCAAACAGAT 59.193 47.619 11.47 0.00 0.00 2.90
2226 2267 3.000041 CAACCACTAGCGCAAACAGATA 59.000 45.455 11.47 0.00 0.00 1.98
2229 2270 3.262420 CCACTAGCGCAAACAGATACTT 58.738 45.455 11.47 0.00 0.00 2.24
2230 2271 4.081862 ACCACTAGCGCAAACAGATACTTA 60.082 41.667 11.47 0.00 0.00 2.24
2235 2276 3.927142 AGCGCAAACAGATACTTACTGAC 59.073 43.478 11.47 0.00 38.55 3.51
2236 2277 3.678072 GCGCAAACAGATACTTACTGACA 59.322 43.478 0.30 0.00 38.55 3.58
2237 2278 4.330074 GCGCAAACAGATACTTACTGACAT 59.670 41.667 0.30 0.00 38.55 3.06
2239 2280 6.470160 CGCAAACAGATACTTACTGACATTC 58.530 40.000 0.00 0.00 38.55 2.67
2240 2281 6.311445 CGCAAACAGATACTTACTGACATTCT 59.689 38.462 0.00 0.00 38.55 2.40
2242 2296 9.151471 GCAAACAGATACTTACTGACATTCTTA 57.849 33.333 0.00 0.00 38.55 2.10
2247 2301 9.509855 CAGATACTTACTGACATTCTTACTCAC 57.490 37.037 0.00 0.00 37.54 3.51
2250 2304 5.243283 ACTTACTGACATTCTTACTCACCGT 59.757 40.000 0.00 0.00 0.00 4.83
2251 2305 4.175787 ACTGACATTCTTACTCACCGTC 57.824 45.455 0.00 0.00 0.00 4.79
2260 2315 5.060662 TCTTACTCACCGTCTCTTCATTG 57.939 43.478 0.00 0.00 0.00 2.82
2261 2316 4.523173 TCTTACTCACCGTCTCTTCATTGT 59.477 41.667 0.00 0.00 0.00 2.71
2264 2319 4.058817 ACTCACCGTCTCTTCATTGTTTC 58.941 43.478 0.00 0.00 0.00 2.78
2265 2320 4.058124 CTCACCGTCTCTTCATTGTTTCA 58.942 43.478 0.00 0.00 0.00 2.69
2266 2321 4.641396 TCACCGTCTCTTCATTGTTTCAT 58.359 39.130 0.00 0.00 0.00 2.57
2267 2322 5.063204 TCACCGTCTCTTCATTGTTTCATT 58.937 37.500 0.00 0.00 0.00 2.57
2268 2323 6.227522 TCACCGTCTCTTCATTGTTTCATTA 58.772 36.000 0.00 0.00 0.00 1.90
2269 2324 6.878923 TCACCGTCTCTTCATTGTTTCATTAT 59.121 34.615 0.00 0.00 0.00 1.28
2270 2325 8.038351 TCACCGTCTCTTCATTGTTTCATTATA 58.962 33.333 0.00 0.00 0.00 0.98
2271 2326 8.830580 CACCGTCTCTTCATTGTTTCATTATAT 58.169 33.333 0.00 0.00 0.00 0.86
2272 2327 9.046296 ACCGTCTCTTCATTGTTTCATTATATC 57.954 33.333 0.00 0.00 0.00 1.63
2273 2328 9.265901 CCGTCTCTTCATTGTTTCATTATATCT 57.734 33.333 0.00 0.00 0.00 1.98
2715 2773 2.003301 GGCGTTCCAGTGAAGAAGATC 58.997 52.381 0.00 0.00 0.00 2.75
2758 2816 5.061920 GAGGATCGTGAAGATGTATACCC 57.938 47.826 0.00 0.00 40.26 3.69
2759 2817 3.506455 AGGATCGTGAAGATGTATACCCG 59.494 47.826 0.00 0.00 40.26 5.28
2917 5122 4.896482 CCTCTAACCTACACCTAGCTGAAT 59.104 45.833 0.00 0.00 0.00 2.57
2925 5130 6.387220 ACCTACACCTAGCTGAATTCCTAAAT 59.613 38.462 2.27 0.00 0.00 1.40
3266 5511 0.816421 AGGTTTTTCCCACACGTCGG 60.816 55.000 0.00 0.00 36.75 4.79
3268 5513 0.734309 GTTTTTCCCACACGTCGGTT 59.266 50.000 0.00 0.00 0.00 4.44
3341 5586 1.202087 TGCAAGTGTTCGACGGTTTTG 60.202 47.619 0.00 0.00 0.00 2.44
3343 5588 1.063469 CAAGTGTTCGACGGTTTTGCT 59.937 47.619 0.00 0.00 0.00 3.91
3406 5660 5.640357 TCGTACAATTGAATTAAGCCGAGTT 59.360 36.000 13.59 0.00 0.00 3.01
3460 5714 5.533154 AGATAATCTTCGAGGACTCATCGTT 59.467 40.000 12.47 3.02 40.95 3.85
3481 5735 3.723554 CCGAAGAGGAAGAAGACGG 57.276 57.895 0.00 0.00 45.00 4.79
3483 5737 0.243907 CGAAGAGGAAGAAGACGGCA 59.756 55.000 0.00 0.00 0.00 5.69
3535 5789 2.079158 CAATGATGATATTCGGCGGCT 58.921 47.619 7.21 0.00 0.00 5.52
3610 5865 2.573369 CCATGCCAAGATCAAGAGAGG 58.427 52.381 0.00 0.00 0.00 3.69
3619 5874 6.405176 GCCAAGATCAAGAGAGGTTATTTTGG 60.405 42.308 0.00 0.00 34.73 3.28
3656 5911 6.775142 CCTATCTGGAGAAGTATCTTCACAGA 59.225 42.308 24.22 24.22 41.33 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.892784 TTGGGCCGAACGAAATTTTT 57.107 40.000 0.00 0.00 0.00 1.94
2 3 2.892784 TTTGGGCCGAACGAAATTTT 57.107 40.000 0.79 0.00 0.00 1.82
3 4 2.892784 TTTTGGGCCGAACGAAATTT 57.107 40.000 5.46 0.00 0.00 1.82
4 5 2.036604 ACATTTTGGGCCGAACGAAATT 59.963 40.909 5.46 0.00 31.28 1.82
5 6 1.616374 ACATTTTGGGCCGAACGAAAT 59.384 42.857 5.46 0.00 33.33 2.17
6 7 1.001158 GACATTTTGGGCCGAACGAAA 60.001 47.619 5.46 0.00 0.00 3.46
7 8 0.594110 GACATTTTGGGCCGAACGAA 59.406 50.000 5.46 0.00 0.00 3.85
8 9 0.535328 TGACATTTTGGGCCGAACGA 60.535 50.000 5.46 0.00 0.00 3.85
9 10 0.386731 GTGACATTTTGGGCCGAACG 60.387 55.000 5.46 3.01 0.00 3.95
10 11 0.386731 CGTGACATTTTGGGCCGAAC 60.387 55.000 5.46 0.00 0.00 3.95
11 12 1.519751 CCGTGACATTTTGGGCCGAA 61.520 55.000 0.79 0.79 0.00 4.30
12 13 1.969064 CCGTGACATTTTGGGCCGA 60.969 57.895 0.00 0.00 0.00 5.54
13 14 1.312371 ATCCGTGACATTTTGGGCCG 61.312 55.000 0.00 0.00 0.00 6.13
14 15 0.173255 CATCCGTGACATTTTGGGCC 59.827 55.000 0.00 0.00 0.00 5.80
15 16 0.887933 ACATCCGTGACATTTTGGGC 59.112 50.000 0.00 0.00 0.00 5.36
16 17 1.885887 ACACATCCGTGACATTTTGGG 59.114 47.619 0.00 0.00 46.80 4.12
17 18 2.813754 AGACACATCCGTGACATTTTGG 59.186 45.455 0.00 0.00 46.80 3.28
18 19 4.488126 AAGACACATCCGTGACATTTTG 57.512 40.909 0.00 0.00 46.80 2.44
19 20 5.514274 AAAAGACACATCCGTGACATTTT 57.486 34.783 0.00 1.58 46.80 1.82
20 21 5.514274 AAAAAGACACATCCGTGACATTT 57.486 34.783 0.00 0.00 46.80 2.32
40 41 6.993902 CCTTTCAGTAGGGTACACTACAAAAA 59.006 38.462 31.70 26.70 44.49 1.94
41 42 6.327104 TCCTTTCAGTAGGGTACACTACAAAA 59.673 38.462 31.70 26.97 44.49 2.44
42 43 5.840149 TCCTTTCAGTAGGGTACACTACAAA 59.160 40.000 31.70 23.15 44.49 2.83
43 44 5.396485 TCCTTTCAGTAGGGTACACTACAA 58.604 41.667 31.70 18.39 44.49 2.41
44 45 5.001833 TCCTTTCAGTAGGGTACACTACA 57.998 43.478 31.70 13.75 44.49 2.74
45 46 5.259632 TCTCCTTTCAGTAGGGTACACTAC 58.740 45.833 25.08 25.08 42.83 2.73
46 47 5.525454 TCTCCTTTCAGTAGGGTACACTA 57.475 43.478 0.00 0.00 35.90 2.74
47 48 4.399483 TCTCCTTTCAGTAGGGTACACT 57.601 45.455 1.68 1.68 35.90 3.55
48 49 4.771054 TCTTCTCCTTTCAGTAGGGTACAC 59.229 45.833 0.00 0.00 35.90 2.90
49 50 5.006896 TCTTCTCCTTTCAGTAGGGTACA 57.993 43.478 0.00 0.00 35.90 2.90
50 51 4.403113 CCTCTTCTCCTTTCAGTAGGGTAC 59.597 50.000 0.00 0.00 35.90 3.34
196 203 3.051940 TCATGCCCTTCCTGAGTATCT 57.948 47.619 0.00 0.00 34.92 1.98
201 208 3.853355 AAGTATCATGCCCTTCCTGAG 57.147 47.619 0.00 0.00 0.00 3.35
263 271 7.223193 CGATATACCTTCAAATTCGGTTACACA 59.777 37.037 0.00 0.00 32.36 3.72
266 274 6.347160 GCCGATATACCTTCAAATTCGGTTAC 60.347 42.308 9.82 0.00 44.79 2.50
276 284 1.342174 GGTCCGCCGATATACCTTCAA 59.658 52.381 0.00 0.00 0.00 2.69
365 381 0.544697 AAGTCCCGTAATTCGCCCAT 59.455 50.000 0.00 0.00 38.35 4.00
383 399 4.523083 GCTGGGTTGTATGACCTAATCAA 58.477 43.478 0.00 0.00 41.93 2.57
463 481 2.766263 ACGCCATGACTGAATCCTAGAA 59.234 45.455 0.00 0.00 0.00 2.10
482 500 2.789208 CCATTGCAATTCACAGCTACG 58.211 47.619 9.83 0.00 0.00 3.51
586 604 6.993079 ACTTTATTTAAGTTTCCCAAGCTGG 58.007 36.000 0.00 0.00 44.73 4.85
630 648 1.151908 TGTGGTAGCCCGGCTTTTT 59.848 52.632 19.35 0.00 40.44 1.94
631 649 1.602605 GTGTGGTAGCCCGGCTTTT 60.603 57.895 19.35 0.00 40.44 2.27
632 650 2.033602 GTGTGGTAGCCCGGCTTT 59.966 61.111 19.35 0.00 40.44 3.51
633 651 2.928396 AGTGTGGTAGCCCGGCTT 60.928 61.111 19.35 1.59 40.44 4.35
637 655 1.226974 CATCGAGTGTGGTAGCCCG 60.227 63.158 0.00 0.00 0.00 6.13
768 787 0.365859 GACGCGCTTAACTTCTTCGG 59.634 55.000 5.73 0.00 0.00 4.30
796 815 3.351794 AAGTTCGAAAGGGAGGGATTC 57.648 47.619 0.00 0.00 0.00 2.52
905 926 1.302511 GCTGGGTGATTCGTGGTGT 60.303 57.895 0.00 0.00 0.00 4.16
1084 1105 7.696992 AGAGGAAAGTAGAGAGAAGTAAGTG 57.303 40.000 0.00 0.00 0.00 3.16
1109 1130 1.305219 CCGAATCACCCACGCATGTT 61.305 55.000 0.00 0.00 0.00 2.71
1225 1247 4.863925 GAGCAGACGGAGAGCGCC 62.864 72.222 2.29 0.00 0.00 6.53
1290 1318 4.394610 GGACTCTGAAGAAAGATTTGAGCC 59.605 45.833 0.00 0.00 0.00 4.70
1294 1322 5.994054 TGTCTGGACTCTGAAGAAAGATTTG 59.006 40.000 2.38 0.00 0.00 2.32
1313 1348 2.560105 TGGCAGGATCTATCGATGTCTG 59.440 50.000 8.54 9.10 33.86 3.51
1334 1369 6.656693 AGAAGGAACGAACATGAATTCTGATT 59.343 34.615 7.05 0.00 0.00 2.57
1337 1372 5.180117 ACAGAAGGAACGAACATGAATTCTG 59.820 40.000 7.05 9.41 44.91 3.02
1338 1373 5.308825 ACAGAAGGAACGAACATGAATTCT 58.691 37.500 7.05 0.00 0.00 2.40
1355 1390 4.153986 CAAGCAAACGAGCATAACAGAAG 58.846 43.478 0.00 0.00 36.85 2.85
1357 1392 2.095768 GCAAGCAAACGAGCATAACAGA 60.096 45.455 0.00 0.00 36.85 3.41
1358 1393 2.245096 GCAAGCAAACGAGCATAACAG 58.755 47.619 0.00 0.00 36.85 3.16
1359 1394 1.606189 TGCAAGCAAACGAGCATAACA 59.394 42.857 0.00 0.00 36.85 2.41
1412 1447 1.478510 CTCCACGTCCAGAAGCTGTAT 59.521 52.381 0.00 0.00 0.00 2.29
1585 1620 0.106918 GTCACCCCGCATTCCCAATA 60.107 55.000 0.00 0.00 0.00 1.90
1594 1629 4.947147 GGCACTTGTCACCCCGCA 62.947 66.667 0.00 0.00 0.00 5.69
1647 1682 2.245942 CTGACGATCGAGTTCACAGTG 58.754 52.381 24.34 0.00 0.00 3.66
1651 1686 2.161012 TGTACCTGACGATCGAGTTCAC 59.839 50.000 24.34 12.09 0.00 3.18
1884 1920 4.208460 CAGTACGACGTTTGTTGAGAACAT 59.792 41.667 5.50 0.00 41.79 2.71
2200 2241 1.098129 TTGCGCTAGTGGTTGTTGCA 61.098 50.000 9.73 0.00 0.00 4.08
2206 2247 2.185004 ATCTGTTTGCGCTAGTGGTT 57.815 45.000 9.73 0.00 0.00 3.67
2207 2248 2.233922 AGTATCTGTTTGCGCTAGTGGT 59.766 45.455 9.73 0.00 0.00 4.16
2208 2249 2.893637 AGTATCTGTTTGCGCTAGTGG 58.106 47.619 9.73 0.00 0.00 4.00
2209 2250 5.004821 CAGTAAGTATCTGTTTGCGCTAGTG 59.995 44.000 9.73 0.00 0.00 2.74
2210 2251 5.103000 CAGTAAGTATCTGTTTGCGCTAGT 58.897 41.667 9.73 0.00 0.00 2.57
2212 2253 5.100259 GTCAGTAAGTATCTGTTTGCGCTA 58.900 41.667 9.73 0.00 34.86 4.26
2214 2255 3.678072 TGTCAGTAAGTATCTGTTTGCGC 59.322 43.478 0.00 0.00 34.86 6.09
2215 2256 6.311445 AGAATGTCAGTAAGTATCTGTTTGCG 59.689 38.462 0.00 0.00 34.86 4.85
2220 2261 9.244292 TGAGTAAGAATGTCAGTAAGTATCTGT 57.756 33.333 0.00 0.00 34.86 3.41
2222 2263 8.688151 GGTGAGTAAGAATGTCAGTAAGTATCT 58.312 37.037 0.00 0.00 0.00 1.98
2224 2265 7.122353 ACGGTGAGTAAGAATGTCAGTAAGTAT 59.878 37.037 0.00 0.00 0.00 2.12
2225 2266 6.432162 ACGGTGAGTAAGAATGTCAGTAAGTA 59.568 38.462 0.00 0.00 0.00 2.24
2226 2267 5.243283 ACGGTGAGTAAGAATGTCAGTAAGT 59.757 40.000 0.00 0.00 0.00 2.24
2229 2270 5.008331 AGACGGTGAGTAAGAATGTCAGTA 58.992 41.667 0.00 0.00 0.00 2.74
2230 2271 3.827302 AGACGGTGAGTAAGAATGTCAGT 59.173 43.478 0.00 0.00 0.00 3.41
2235 2276 5.060662 TGAAGAGACGGTGAGTAAGAATG 57.939 43.478 0.00 0.00 0.00 2.67
2236 2277 5.923733 ATGAAGAGACGGTGAGTAAGAAT 57.076 39.130 0.00 0.00 0.00 2.40
2237 2278 5.010719 ACAATGAAGAGACGGTGAGTAAGAA 59.989 40.000 0.00 0.00 0.00 2.52
2239 2280 4.810790 ACAATGAAGAGACGGTGAGTAAG 58.189 43.478 0.00 0.00 0.00 2.34
2240 2281 4.866508 ACAATGAAGAGACGGTGAGTAA 57.133 40.909 0.00 0.00 0.00 2.24
2242 2296 3.753294 AACAATGAAGAGACGGTGAGT 57.247 42.857 0.00 0.00 0.00 3.41
2247 2301 9.265901 AGATATAATGAAACAATGAAGAGACGG 57.734 33.333 0.00 0.00 0.00 4.79
2260 2315 8.958119 TTGTACACCTGGAGATATAATGAAAC 57.042 34.615 0.00 0.00 0.00 2.78
2261 2316 9.613428 CTTTGTACACCTGGAGATATAATGAAA 57.387 33.333 0.00 0.00 0.00 2.69
2264 2319 9.429359 GATCTTTGTACACCTGGAGATATAATG 57.571 37.037 0.00 0.00 0.00 1.90
2265 2320 8.598041 GGATCTTTGTACACCTGGAGATATAAT 58.402 37.037 0.00 0.00 0.00 1.28
2266 2321 7.255836 CGGATCTTTGTACACCTGGAGATATAA 60.256 40.741 0.00 0.00 0.00 0.98
2267 2322 6.208797 CGGATCTTTGTACACCTGGAGATATA 59.791 42.308 0.00 0.00 0.00 0.86
2268 2323 5.011125 CGGATCTTTGTACACCTGGAGATAT 59.989 44.000 0.00 0.00 0.00 1.63
2269 2324 4.341235 CGGATCTTTGTACACCTGGAGATA 59.659 45.833 0.00 0.00 0.00 1.98
2270 2325 3.133003 CGGATCTTTGTACACCTGGAGAT 59.867 47.826 0.00 0.00 0.00 2.75
2271 2326 2.496070 CGGATCTTTGTACACCTGGAGA 59.504 50.000 0.00 0.00 0.00 3.71
2272 2327 2.496070 TCGGATCTTTGTACACCTGGAG 59.504 50.000 0.00 0.00 0.00 3.86
2273 2328 2.496070 CTCGGATCTTTGTACACCTGGA 59.504 50.000 0.00 0.00 0.00 3.86
2274 2329 2.893637 CTCGGATCTTTGTACACCTGG 58.106 52.381 0.00 0.00 0.00 4.45
2715 2773 1.736645 CAGGTCCCGTAAGCACACG 60.737 63.158 3.35 3.35 41.59 4.49
2757 2815 2.737679 GCCACTTGTAAGCTAGTACCGG 60.738 54.545 0.00 0.00 0.00 5.28
2758 2816 2.094390 TGCCACTTGTAAGCTAGTACCG 60.094 50.000 0.00 0.00 0.00 4.02
2759 2817 3.604875 TGCCACTTGTAAGCTAGTACC 57.395 47.619 0.00 0.00 0.00 3.34
3135 5370 1.079127 CACCTCGATTCCGGCAACT 60.079 57.895 0.00 0.00 36.24 3.16
3252 5497 1.227615 GGAACCGACGTGTGGGAAA 60.228 57.895 8.11 0.00 32.36 3.13
3266 5511 0.251073 TAGGCCAAACTAGCGGGAAC 59.749 55.000 5.01 0.00 0.00 3.62
3268 5513 0.985760 TTTAGGCCAAACTAGCGGGA 59.014 50.000 5.01 0.00 0.00 5.14
3304 5549 4.284550 AAGGCGGTGGTGGTGCAT 62.285 61.111 0.00 0.00 0.00 3.96
3406 5660 6.596888 CAGCCTCTTCATCTTCAATTCAACTA 59.403 38.462 0.00 0.00 0.00 2.24
3460 5714 2.950309 CCGTCTTCTTCCTCTTCGGATA 59.050 50.000 0.00 0.00 42.70 2.59
3481 5735 4.474226 AGAACAGTTTCGAAGTCATTGC 57.526 40.909 0.00 0.00 36.78 3.56
3483 5737 4.881850 ACCAAGAACAGTTTCGAAGTCATT 59.118 37.500 0.00 0.00 36.78 2.57
3535 5789 3.623203 GCCAAATTGTGATCCTCTCCTCA 60.623 47.826 0.00 0.00 0.00 3.86
3604 5859 6.447084 TGGATTAGGACCAAAATAACCTCTCT 59.553 38.462 0.00 0.00 34.25 3.10
3610 5865 8.762481 ATAGGTTGGATTAGGACCAAAATAAC 57.238 34.615 0.00 0.00 46.77 1.89
3619 5874 5.148502 TCTCCAGATAGGTTGGATTAGGAC 58.851 45.833 0.00 0.00 43.46 3.85


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

AutoCloner maintained by Alex Coulton.