Multiple sequence alignment - TraesCS1D01G164700

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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 TraesCS1D01G164700 chr1D 100.000 3792 0 0 1 3792 235668663 235672454 0.000000e+00 7003.0
1 TraesCS1D01G164700 chr1D 80.899 445 70 5 3023 3453 382212497 382212054 1.690000e-88 337.0
2 TraesCS1D01G164700 chr1B 93.593 1389 54 4 867 2243 340992666 340994031 0.000000e+00 2039.0
3 TraesCS1D01G164700 chr1B 95.301 1213 55 2 1056 2268 341128564 341129774 0.000000e+00 1923.0
4 TraesCS1D01G164700 chr1B 87.288 354 35 4 2795 3145 341134885 341135231 2.750000e-106 396.0
5 TraesCS1D01G164700 chr1B 80.401 449 74 7 3019 3453 651552129 651552577 2.820000e-86 329.0
6 TraesCS1D01G164700 chr1B 84.241 349 42 9 2366 2708 340994369 340994710 1.020000e-85 327.0
7 TraesCS1D01G164700 chr1B 89.354 263 22 2 2294 2550 341129759 341130021 3.650000e-85 326.0
8 TraesCS1D01G164700 chr1B 88.000 225 18 2 2550 2774 341133743 341133958 1.350000e-64 257.0
9 TraesCS1D01G164700 chr1B 92.727 55 4 0 2702 2756 341022300 341022354 3.140000e-11 80.5
10 TraesCS1D01G164700 chr1A 87.666 1435 143 24 1080 2509 311059506 311060911 0.000000e+00 1639.0
11 TraesCS1D01G164700 chr1A 94.937 1027 29 1 1080 2083 310258636 310257610 0.000000e+00 1587.0
12 TraesCS1D01G164700 chr1A 85.881 1374 113 35 2460 3785 310256923 310255583 0.000000e+00 1387.0
13 TraesCS1D01G164700 chr1A 94.272 419 24 0 1080 1498 311058322 311058740 3.190000e-180 641.0
14 TraesCS1D01G164700 chr1A 92.124 419 32 1 1080 1498 311057139 311057556 1.170000e-164 590.0
15 TraesCS1D01G164700 chr1A 90.566 424 34 3 1078 1495 311055947 311056370 1.190000e-154 556.0
16 TraesCS1D01G164700 chr1A 96.970 198 5 1 2072 2269 310257259 310257063 7.850000e-87 331.0
17 TraesCS1D01G164700 chr1A 82.759 261 32 10 782 1031 310259003 310258745 1.770000e-53 220.0
18 TraesCS1D01G164700 chr1A 81.855 248 35 7 792 1031 311059152 311059397 2.310000e-47 200.0
19 TraesCS1D01G164700 chr1A 81.226 261 36 10 782 1031 311056772 311057030 8.310000e-47 198.0
20 TraesCS1D01G164700 chr1A 81.226 261 36 10 782 1031 311057955 311058213 8.310000e-47 198.0
21 TraesCS1D01G164700 chr4B 96.460 791 26 1 1 789 64814168 64814958 0.000000e+00 1304.0
22 TraesCS1D01G164700 chr3A 96.334 791 28 1 1 790 734026462 734027252 0.000000e+00 1299.0
23 TraesCS1D01G164700 chr3A 86.047 129 18 0 2866 2994 414312165 414312037 5.110000e-29 139.0
24 TraesCS1D01G164700 chr3A 86.047 129 18 0 2866 2994 431057846 431057974 5.110000e-29 139.0
25 TraesCS1D01G164700 chr5D 96.329 790 28 1 1 789 501410795 501410006 0.000000e+00 1297.0
26 TraesCS1D01G164700 chr5D 95.828 791 32 1 1 790 378908696 378907906 0.000000e+00 1277.0
27 TraesCS1D01G164700 chr6B 95.729 796 31 2 1 794 35080085 35080879 0.000000e+00 1279.0
28 TraesCS1D01G164700 chr6B 81.208 447 72 4 3019 3453 65095230 65095676 2.170000e-92 350.0
29 TraesCS1D01G164700 chr3B 95.718 794 32 2 1 792 125801383 125802176 0.000000e+00 1277.0
30 TraesCS1D01G164700 chr3B 87.597 129 16 0 2866 2994 353878171 353878043 2.360000e-32 150.0
31 TraesCS1D01G164700 chr4D 95.702 791 32 2 1 789 291656426 291655636 0.000000e+00 1271.0
32 TraesCS1D01G164700 chr4D 95.477 796 29 3 1 789 320243772 320242977 0.000000e+00 1264.0
33 TraesCS1D01G164700 chr7B 95.346 795 35 1 1 793 89823 89029 0.000000e+00 1262.0
34 TraesCS1D01G164700 chr7B 80.717 446 71 8 3022 3453 228334641 228334197 2.180000e-87 333.0
35 TraesCS1D01G164700 chr7B 86.047 129 18 0 2866 2994 722474132 722474004 5.110000e-29 139.0
36 TraesCS1D01G164700 chr5B 80.846 449 72 5 3019 3453 397412468 397412916 1.300000e-89 340.0
37 TraesCS1D01G164700 chr2A 80.942 446 71 3 3022 3453 776425872 776425427 1.300000e-89 340.0
38 TraesCS1D01G164700 chr6A 80.690 435 69 4 3033 3453 596150214 596150647 1.310000e-84 324.0
39 TraesCS1D01G164700 chr6A 86.822 129 17 0 2866 2994 91457646 91457518 1.100000e-30 145.0
40 TraesCS1D01G164700 chr7D 80.000 450 75 6 3022 3456 566035093 566034644 6.110000e-83 318.0
41 TraesCS1D01G164700 chr7D 86.822 129 17 0 2866 2994 396007428 396007556 1.100000e-30 145.0
42 TraesCS1D01G164700 chr5A 86.047 129 18 0 2866 2994 347274176 347274304 5.110000e-29 139.0
43 TraesCS1D01G164700 chr2D 100.000 30 0 0 2527 2556 101438909 101438880 5.290000e-04 56.5


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 TraesCS1D01G164700 chr1D 235668663 235672454 3791 False 7003.000000 7003 100.000000 1 3792 1 chr1D.!!$F1 3791
1 TraesCS1D01G164700 chr1B 340992666 340994710 2044 False 1183.000000 2039 88.917000 867 2708 2 chr1B.!!$F3 1841
2 TraesCS1D01G164700 chr1B 341128564 341135231 6667 False 725.500000 1923 89.985750 1056 3145 4 chr1B.!!$F4 2089
3 TraesCS1D01G164700 chr1A 310255583 310259003 3420 True 881.250000 1587 90.136750 782 3785 4 chr1A.!!$R1 3003
4 TraesCS1D01G164700 chr1A 311055947 311060911 4964 False 574.571429 1639 86.990714 782 2509 7 chr1A.!!$F1 1727
5 TraesCS1D01G164700 chr4B 64814168 64814958 790 False 1304.000000 1304 96.460000 1 789 1 chr4B.!!$F1 788
6 TraesCS1D01G164700 chr3A 734026462 734027252 790 False 1299.000000 1299 96.334000 1 790 1 chr3A.!!$F2 789
7 TraesCS1D01G164700 chr5D 501410006 501410795 789 True 1297.000000 1297 96.329000 1 789 1 chr5D.!!$R2 788
8 TraesCS1D01G164700 chr5D 378907906 378908696 790 True 1277.000000 1277 95.828000 1 790 1 chr5D.!!$R1 789
9 TraesCS1D01G164700 chr6B 35080085 35080879 794 False 1279.000000 1279 95.729000 1 794 1 chr6B.!!$F1 793
10 TraesCS1D01G164700 chr3B 125801383 125802176 793 False 1277.000000 1277 95.718000 1 792 1 chr3B.!!$F1 791
11 TraesCS1D01G164700 chr4D 291655636 291656426 790 True 1271.000000 1271 95.702000 1 789 1 chr4D.!!$R1 788
12 TraesCS1D01G164700 chr4D 320242977 320243772 795 True 1264.000000 1264 95.477000 1 789 1 chr4D.!!$R2 788
13 TraesCS1D01G164700 chr7B 89029 89823 794 True 1262.000000 1262 95.346000 1 793 1 chr7B.!!$R1 792

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
218 219 0.956633 ACACTCGTCGCTCCACTTTA 59.043 50.000 0.00 0.0 0.00 1.85 F
980 3409 1.685355 GCACCACCTTTTGCCCAGTT 61.685 55.000 0.00 0.0 32.21 3.16 F
1669 4181 1.349627 CTGCATCGACGGCATGTTC 59.650 57.895 13.32 0.0 41.06 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1051 3523 0.247736 TTTCCTCTCTGCTTCTCCGC 59.752 55.0 0.00 0.0 0.0 5.54 R
2399 5558 0.037303 ATCCACTGGAAGGTGTGCTG 59.963 55.0 0.66 0.0 39.3 4.41 R
3379 11197 0.240945 CATCGCAACTCCCACCAAAC 59.759 55.0 0.00 0.0 0.0 2.93 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
218 219 0.956633 ACACTCGTCGCTCCACTTTA 59.043 50.000 0.00 0.00 0.00 1.85
277 278 2.190578 GTCCAAGCGGCAGCCTAT 59.809 61.111 10.54 0.00 46.67 2.57
703 711 2.434702 CCGCCTCCTAGTTCCTTGTATT 59.565 50.000 0.00 0.00 0.00 1.89
806 3221 8.901472 ATTCTACATCTATCATAGGGCTTGTA 57.099 34.615 0.00 0.00 0.00 2.41
807 3222 7.704578 TCTACATCTATCATAGGGCTTGTAC 57.295 40.000 0.00 0.00 0.00 2.90
821 3236 5.073691 AGGGCTTGTACATATCCAGCTTTAT 59.926 40.000 14.43 0.00 0.00 1.40
823 3238 6.595716 GGGCTTGTACATATCCAGCTTTATAG 59.404 42.308 14.43 0.00 0.00 1.31
837 3252 5.223225 GCTTTATAGCACAAAGGTCTGTC 57.777 43.478 0.00 0.00 46.95 3.51
847 3263 3.643320 ACAAAGGTCTGTCAGACATCTCA 59.357 43.478 29.50 0.00 46.79 3.27
851 3267 5.495926 AGGTCTGTCAGACATCTCATTTT 57.504 39.130 29.50 5.24 46.79 1.82
885 3302 9.531942 TTTTATGCAATAATTAAGGCACATCAG 57.468 29.630 14.37 0.00 38.83 2.90
917 3334 6.376299 CCTAGTTAAACCCAAACATTAGTCCC 59.624 42.308 0.00 0.00 0.00 4.46
980 3409 1.685355 GCACCACCTTTTGCCCAGTT 61.685 55.000 0.00 0.00 32.21 3.16
1003 3432 8.258708 AGTTAGAAGCCGAATCAAACTAACTAT 58.741 33.333 0.00 0.00 43.23 2.12
1033 3462 2.839975 TCAAACGATTACTGTGCCACA 58.160 42.857 0.00 0.00 0.00 4.17
1035 3464 3.002862 TCAAACGATTACTGTGCCACAAC 59.997 43.478 0.00 0.00 0.00 3.32
1051 3523 2.598192 CACAACAAAACAGCTGGAAACG 59.402 45.455 19.93 4.78 0.00 3.60
1669 4181 1.349627 CTGCATCGACGGCATGTTC 59.650 57.895 13.32 0.00 41.06 3.18
2013 4525 3.300032 AGGAGTACCCTGCGATCAA 57.700 52.632 2.43 0.00 45.61 2.57
2034 4546 1.353076 GGGAACTGCGTTTACTACCG 58.647 55.000 0.00 0.00 0.00 4.02
2230 5103 8.934825 GCAATAAGCATGGACTTTGAAAATTAA 58.065 29.630 0.00 0.00 44.79 1.40
2269 5376 9.797556 GAAATTCCTGTTGTAACTGTTTTAACT 57.202 29.630 15.67 0.85 0.00 2.24
2273 5380 9.984190 TTCCTGTTGTAACTGTTTTAACTTTTT 57.016 25.926 15.67 0.00 0.00 1.94
2343 5450 9.878667 TCGTTATCACATTCCTAATTTCTAACA 57.121 29.630 0.00 0.00 0.00 2.41
2367 5522 3.922171 AAGACTGCAGGATTTCCTAGG 57.078 47.619 19.93 0.82 46.65 3.02
2406 5565 9.840427 ATTATTATCAAAACTGTTACAGCACAC 57.160 29.630 12.80 0.00 34.37 3.82
2521 5690 5.468409 TGATTTGCTGATCGAAAGTGTTACA 59.532 36.000 0.00 0.00 0.00 2.41
2567 9458 4.641989 CCTCATGAACAGTAAATTCCAGGG 59.358 45.833 0.00 0.00 0.00 4.45
2568 9459 4.599041 TCATGAACAGTAAATTCCAGGGG 58.401 43.478 0.00 0.00 0.00 4.79
2569 9460 3.449746 TGAACAGTAAATTCCAGGGGG 57.550 47.619 0.00 0.00 0.00 5.40
2592 9490 8.260114 GGGGAAAATGAAATGTTGATTATCTGT 58.740 33.333 0.00 0.00 0.00 3.41
2593 9491 9.657419 GGGAAAATGAAATGTTGATTATCTGTT 57.343 29.630 0.00 0.00 0.00 3.16
2662 9564 8.565416 TGAAGAATGCTGATGTGATTAATGATC 58.435 33.333 0.00 0.00 35.21 2.92
2696 9598 4.854399 ACCGTTGTATTGATTGTGTGTTG 58.146 39.130 0.00 0.00 0.00 3.33
2711 9613 7.987750 TTGTGTGTTGTGGTACAATGTATAT 57.012 32.000 0.00 0.00 44.16 0.86
2736 9638 2.719556 CGGAATAGACGCGACATTACAG 59.280 50.000 15.93 2.93 0.00 2.74
2757 9659 1.080093 GGATGTGTCGGTTGCTCGA 60.080 57.895 0.00 0.00 36.76 4.04
2833 10641 7.750947 AGTTGTAACACTCCCTCCTAATAAT 57.249 36.000 0.00 0.00 0.00 1.28
2834 10642 8.849543 AGTTGTAACACTCCCTCCTAATAATA 57.150 34.615 0.00 0.00 0.00 0.98
2835 10643 9.275572 AGTTGTAACACTCCCTCCTAATAATAA 57.724 33.333 0.00 0.00 0.00 1.40
2862 10671 3.757745 AAAAACACTCATAATCCCGCG 57.242 42.857 0.00 0.00 0.00 6.46
2886 10695 5.242795 AGCATAGTTTAGTGGTGGAAAGT 57.757 39.130 0.00 0.00 0.00 2.66
2889 10698 3.945640 AGTTTAGTGGTGGAAAGTGGT 57.054 42.857 0.00 0.00 0.00 4.16
2907 10716 1.747355 GGTTGATGTCTTGCCATCCAG 59.253 52.381 0.00 0.00 40.43 3.86
2918 10727 0.899717 GCCATCCAGCCAGGTTCAAA 60.900 55.000 0.00 0.00 39.02 2.69
2923 10732 0.245539 CCAGCCAGGTTCAAAGCATG 59.754 55.000 0.00 0.00 0.00 4.06
2945 10754 7.063308 GCATGGTACTTGTAATTTGGATTTGTG 59.937 37.037 0.00 0.00 0.00 3.33
2950 10759 4.944619 TGTAATTTGGATTTGTGGCACA 57.055 36.364 17.96 17.96 0.00 4.57
3017 10826 4.640201 GGGGTCCCTTTAATTAAACCGTAC 59.360 45.833 8.15 3.70 0.00 3.67
3019 10828 5.252547 GGTCCCTTTAATTAAACCGTACCA 58.747 41.667 6.54 0.00 0.00 3.25
3031 10840 1.358725 CCGTACCATCACAAGCCACG 61.359 60.000 0.00 0.00 0.00 4.94
3081 10890 4.450976 TCGATAGAACCAATTCCACATGG 58.549 43.478 0.00 0.00 46.15 3.66
3086 10895 2.307496 ACCAATTCCACATGGCTGAA 57.693 45.000 0.00 0.00 40.51 3.02
3159 10968 8.593492 TCATATAATGAGACTGTTTCGGAATG 57.407 34.615 0.00 0.00 33.59 2.67
3184 10993 5.435686 TGGTAGATATTGCCACAAGAGTT 57.564 39.130 0.00 0.00 36.55 3.01
3199 11008 6.528072 CCACAAGAGTTTGTTTTGAAGACTTC 59.472 38.462 8.34 8.34 45.01 3.01
3209 11018 8.634335 TTGTTTTGAAGACTTCCATGATATGA 57.366 30.769 12.66 0.00 0.00 2.15
3212 11021 7.615582 TTTGAAGACTTCCATGATATGACAC 57.384 36.000 12.66 0.00 0.00 3.67
3213 11022 5.674525 TGAAGACTTCCATGATATGACACC 58.325 41.667 12.66 0.00 0.00 4.16
3214 11023 5.189539 TGAAGACTTCCATGATATGACACCA 59.810 40.000 12.66 0.00 0.00 4.17
3215 11024 5.028549 AGACTTCCATGATATGACACCAC 57.971 43.478 0.00 0.00 0.00 4.16
3217 11026 3.782523 ACTTCCATGATATGACACCACCT 59.217 43.478 0.00 0.00 0.00 4.00
3235 11047 4.582656 CCACCTTGTAGGAACACAAAATCA 59.417 41.667 0.00 0.00 37.67 2.57
3261 11073 4.654915 TGTGATCTCGTATTACGGGGATA 58.345 43.478 15.70 0.00 43.50 2.59
3263 11075 5.535783 TGTGATCTCGTATTACGGGGATAAA 59.464 40.000 15.70 9.03 43.50 1.40
3264 11076 6.209986 TGTGATCTCGTATTACGGGGATAAAT 59.790 38.462 15.70 1.85 43.50 1.40
3265 11077 7.394077 TGTGATCTCGTATTACGGGGATAAATA 59.606 37.037 15.70 7.85 43.50 1.40
3266 11078 7.914346 GTGATCTCGTATTACGGGGATAAATAG 59.086 40.741 15.70 3.32 43.50 1.73
3267 11079 7.613022 TGATCTCGTATTACGGGGATAAATAGT 59.387 37.037 15.70 0.00 43.50 2.12
3268 11080 7.383102 TCTCGTATTACGGGGATAAATAGTC 57.617 40.000 15.70 0.00 43.50 2.59
3269 11081 6.092670 TCTCGTATTACGGGGATAAATAGTCG 59.907 42.308 15.70 0.00 43.50 4.18
3270 11082 5.123820 TCGTATTACGGGGATAAATAGTCGG 59.876 44.000 15.69 0.00 42.81 4.79
3271 11083 5.106157 CGTATTACGGGGATAAATAGTCGGT 60.106 44.000 8.36 0.00 38.08 4.69
3272 11084 6.093495 CGTATTACGGGGATAAATAGTCGGTA 59.907 42.308 8.36 0.00 38.08 4.02
3273 11085 7.201732 CGTATTACGGGGATAAATAGTCGGTAT 60.202 40.741 8.36 0.00 38.08 2.73
3274 11086 6.515272 TTACGGGGATAAATAGTCGGTATC 57.485 41.667 0.00 0.00 0.00 2.24
3275 11087 4.670765 ACGGGGATAAATAGTCGGTATCT 58.329 43.478 0.00 0.00 0.00 1.98
3276 11088 4.461781 ACGGGGATAAATAGTCGGTATCTG 59.538 45.833 0.00 0.00 0.00 2.90
3300 11117 6.443849 TGGGTATCCAATCATATTAGAGTCCC 59.556 42.308 0.00 0.00 40.73 4.46
3311 11128 7.004691 TCATATTAGAGTCCCGATTTCTCTGA 58.995 38.462 0.00 0.00 38.71 3.27
3378 11196 1.003580 TCTTGACTCCTGACCAATGGC 59.996 52.381 0.00 0.00 0.00 4.40
3379 11197 0.321564 TTGACTCCTGACCAATGGCG 60.322 55.000 0.00 0.00 0.00 5.69
3395 11213 2.637025 CGTTTGGTGGGAGTTGCG 59.363 61.111 0.00 0.00 0.00 4.85
3396 11214 1.890041 CGTTTGGTGGGAGTTGCGA 60.890 57.895 0.00 0.00 0.00 5.10
3434 11252 3.850122 TTGACTACAGATGTGAGGTCG 57.150 47.619 0.00 0.00 34.13 4.79
3443 11261 1.595993 ATGTGAGGTCGGGTCTCGTG 61.596 60.000 0.00 0.00 40.32 4.35
3465 11283 3.096461 CAATTTGCAGAAGAATCTCGCG 58.904 45.455 0.00 0.00 34.47 5.87
3466 11284 0.443869 TTTGCAGAAGAATCTCGCGC 59.556 50.000 0.00 0.00 34.47 6.86
3500 11318 5.573219 CCATATCTCCCATGGAATTAGCAA 58.427 41.667 15.22 0.00 44.95 3.91
3501 11319 5.651139 CCATATCTCCCATGGAATTAGCAAG 59.349 44.000 15.22 0.00 44.95 4.01
3502 11320 2.936202 TCTCCCATGGAATTAGCAAGC 58.064 47.619 15.22 0.00 0.00 4.01
3543 11377 2.575279 AGATGAAGGAAGACATGCCACT 59.425 45.455 0.00 0.00 0.00 4.00
3552 11386 2.481441 AGACATGCCACTAATCCCTCA 58.519 47.619 0.00 0.00 0.00 3.86
3582 11416 1.824230 TCATTGCCCAACTTGCCATAC 59.176 47.619 0.00 0.00 0.00 2.39
3583 11417 0.817013 ATTGCCCAACTTGCCATACG 59.183 50.000 0.00 0.00 0.00 3.06
3634 11468 5.750352 AGGCAAGATTTCATTCCAAATGT 57.250 34.783 0.04 0.00 0.00 2.71
3639 11473 6.456449 GCAAGATTTCATTCCAAATGTGCATC 60.456 38.462 0.00 1.72 35.41 3.91
3664 11498 6.956047 GTGAAACGACATTAGAAAAGAAGGT 58.044 36.000 0.00 0.00 0.00 3.50
3669 11503 3.081804 ACATTAGAAAAGAAGGTGGGCG 58.918 45.455 0.00 0.00 0.00 6.13
3692 11526 0.670162 GACTCTTGGCTTTGCTTGCA 59.330 50.000 0.00 0.00 0.00 4.08
3705 11539 2.518112 TTGCAGAGCGGGCACAAA 60.518 55.556 0.00 0.00 41.75 2.83
3708 11542 2.042831 GCAGAGCGGGCACAAAGAT 61.043 57.895 0.00 0.00 0.00 2.40
3720 11554 4.929211 GGGCACAAAGATCACAAATTTACC 59.071 41.667 0.00 0.00 0.00 2.85
3727 11561 7.893302 ACAAAGATCACAAATTTACCATCCCTA 59.107 33.333 0.00 0.00 0.00 3.53
3729 11563 8.469309 AAGATCACAAATTTACCATCCCTATG 57.531 34.615 0.00 0.00 0.00 2.23
3756 11590 1.698506 ACCGCCAAAAGTCCAAATCA 58.301 45.000 0.00 0.00 0.00 2.57
3773 11607 6.873076 TCCAAATCATGTTTTGAATTACCAGC 59.127 34.615 24.43 0.00 38.58 4.85
3785 11619 2.656947 TTACCAGCCAAGCAAAGACT 57.343 45.000 0.00 0.00 0.00 3.24
3786 11620 2.656947 TACCAGCCAAGCAAAGACTT 57.343 45.000 0.00 0.00 0.00 3.01
3787 11621 1.322442 ACCAGCCAAGCAAAGACTTC 58.678 50.000 0.00 0.00 0.00 3.01
3788 11622 0.239347 CCAGCCAAGCAAAGACTTCG 59.761 55.000 0.00 0.00 0.00 3.79
3789 11623 0.947244 CAGCCAAGCAAAGACTTCGT 59.053 50.000 0.00 0.00 0.00 3.85
3790 11624 2.143122 CAGCCAAGCAAAGACTTCGTA 58.857 47.619 0.00 0.00 0.00 3.43
3791 11625 2.744202 CAGCCAAGCAAAGACTTCGTAT 59.256 45.455 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
166 167 0.249238 CCAGTCTGCATCGGAGTAGC 60.249 60.000 0.00 0.00 0.00 3.58
218 219 3.197983 GTCCAAGGTAGACACAATAGCCT 59.802 47.826 0.00 0.00 34.27 4.58
277 278 0.827925 AGCACTGGAACGAGAGACCA 60.828 55.000 0.00 0.00 38.67 4.02
703 711 3.948719 GGGCCACGGACCTCAACA 61.949 66.667 4.39 0.00 41.04 3.33
800 3215 7.066374 GCTATAAAGCTGGATATGTACAAGC 57.934 40.000 8.18 8.18 45.85 4.01
821 3236 2.698274 TGTCTGACAGACCTTTGTGCTA 59.302 45.455 28.47 7.63 44.44 3.49
823 3238 1.953559 TGTCTGACAGACCTTTGTGC 58.046 50.000 28.47 5.90 44.44 4.57
826 3241 4.263018 TGAGATGTCTGACAGACCTTTG 57.737 45.455 28.47 0.00 44.44 2.77
865 3281 6.742109 ACATCTGATGTGCCTTAATTATTGC 58.258 36.000 21.71 0.94 43.01 3.56
885 3302 3.359695 TGGGTTTAACTAGGGCACATC 57.640 47.619 0.00 0.00 0.00 3.06
891 3308 6.376299 GGACTAATGTTTGGGTTTAACTAGGG 59.624 42.308 0.00 0.00 0.00 3.53
917 3334 2.260844 TCCACTCAGAGTGCTTTTGG 57.739 50.000 23.46 10.25 44.63 3.28
980 3409 7.778083 TCATAGTTAGTTTGATTCGGCTTCTA 58.222 34.615 0.00 0.00 0.00 2.10
1033 3462 1.797348 CGCGTTTCCAGCTGTTTTGTT 60.797 47.619 13.81 0.00 0.00 2.83
1035 3464 0.934436 CCGCGTTTCCAGCTGTTTTG 60.934 55.000 13.81 0.00 0.00 2.44
1051 3523 0.247736 TTTCCTCTCTGCTTCTCCGC 59.752 55.000 0.00 0.00 0.00 5.54
1424 3913 2.722201 GGATCTCGGTGCCGGAGTT 61.722 63.158 5.05 2.75 40.25 3.01
1519 4008 2.401766 CCATCTGTGCTTGGTCGCC 61.402 63.158 0.00 0.00 0.00 5.54
1669 4181 3.181500 TGAGATCGTAGATGGACACGTTG 60.181 47.826 0.00 0.00 45.12 4.10
1770 4282 1.626321 TGTCCTTCCAATACTTGCGGA 59.374 47.619 0.00 0.00 0.00 5.54
1989 4501 1.377333 GCAGGGTACTCCTTGGCAC 60.377 63.158 0.52 0.00 45.47 5.01
2285 5392 5.363292 TGGTTAAAAGTTAAAACAGTCCCCC 59.637 40.000 0.00 0.00 0.00 5.40
2286 5393 6.468333 TGGTTAAAAGTTAAAACAGTCCCC 57.532 37.500 0.00 0.00 0.00 4.81
2287 5394 9.070179 TCTATGGTTAAAAGTTAAAACAGTCCC 57.930 33.333 0.00 0.00 0.00 4.46
2305 5412 8.621286 GGAATGTGATAACGAAATTCTATGGTT 58.379 33.333 0.00 0.00 0.00 3.67
2306 5413 7.993183 AGGAATGTGATAACGAAATTCTATGGT 59.007 33.333 0.00 0.00 0.00 3.55
2307 5414 8.383318 AGGAATGTGATAACGAAATTCTATGG 57.617 34.615 0.00 0.00 0.00 2.74
2338 5445 8.010589 AGGAAATCCTGCAGTCTTAACTGTTAG 61.011 40.741 13.81 6.30 45.81 2.34
2343 5450 4.917906 AGGAAATCCTGCAGTCTTAACT 57.082 40.909 13.81 1.11 46.55 2.24
2399 5558 0.037303 ATCCACTGGAAGGTGTGCTG 59.963 55.000 0.66 0.00 39.30 4.41
2406 5565 2.228822 CGGTCAAAAATCCACTGGAAGG 59.771 50.000 0.66 0.00 39.30 3.46
2521 5690 2.017049 GCATTTGTGCTCGGGATTAGT 58.983 47.619 0.00 0.00 0.00 2.24
2567 9458 9.657419 AACAGATAATCAACATTTCATTTTCCC 57.343 29.630 0.00 0.00 0.00 3.97
2595 9493 9.539825 GACAAGATGATCTACACATAAGTTCAT 57.460 33.333 0.00 0.00 36.54 2.57
2596 9494 8.753133 AGACAAGATGATCTACACATAAGTTCA 58.247 33.333 0.00 0.00 0.00 3.18
2597 9495 9.243637 GAGACAAGATGATCTACACATAAGTTC 57.756 37.037 0.00 0.00 0.00 3.01
2598 9496 8.753133 TGAGACAAGATGATCTACACATAAGTT 58.247 33.333 0.00 0.00 0.00 2.66
2599 9497 8.298729 TGAGACAAGATGATCTACACATAAGT 57.701 34.615 0.00 0.00 0.00 2.24
2600 9498 8.628280 TCTGAGACAAGATGATCTACACATAAG 58.372 37.037 0.00 0.00 0.00 1.73
2604 9502 6.840780 TTCTGAGACAAGATGATCTACACA 57.159 37.500 0.00 0.00 0.00 3.72
2608 9506 7.724490 TTCCTTTCTGAGACAAGATGATCTA 57.276 36.000 0.00 0.00 0.00 1.98
2662 9564 6.847400 TCAATACAACGGTTATGGTTCATTG 58.153 36.000 0.00 0.00 32.93 2.82
2696 9598 5.204409 TCCGGACATATACATTGTACCAC 57.796 43.478 0.00 0.00 0.00 4.16
2711 9613 1.307355 TGTCGCGTCTATTCCGGACA 61.307 55.000 1.83 0.00 35.04 4.02
2736 9638 1.079503 GAGCAACCGACACATCCTTC 58.920 55.000 0.00 0.00 0.00 3.46
2757 9659 1.613437 CCCCGCATTGTTGAAACTTCT 59.387 47.619 0.00 0.00 0.00 2.85
2852 10661 1.267121 ACTATGCTCCGCGGGATTAT 58.733 50.000 27.83 16.67 0.00 1.28
2862 10671 3.906720 TCCACCACTAAACTATGCTCC 57.093 47.619 0.00 0.00 0.00 4.70
2907 10716 1.202348 GTACCATGCTTTGAACCTGGC 59.798 52.381 0.00 0.00 0.00 4.85
2918 10727 7.039082 ACAAATCCAAATTACAAGTACCATGCT 60.039 33.333 0.00 0.00 0.00 3.79
2923 10732 5.867174 GCCACAAATCCAAATTACAAGTACC 59.133 40.000 0.00 0.00 0.00 3.34
2945 10754 3.303229 GCGCTTACAATACAATTTGTGCC 59.697 43.478 12.30 0.00 40.00 5.01
2950 10759 3.380320 GGGAGGCGCTTACAATACAATTT 59.620 43.478 7.64 0.00 0.00 1.82
2955 10764 2.327200 AAGGGAGGCGCTTACAATAC 57.673 50.000 7.64 0.00 34.91 1.89
3013 10822 0.669318 ACGTGGCTTGTGATGGTACG 60.669 55.000 0.00 0.00 36.28 3.67
3017 10826 2.632377 AGATAACGTGGCTTGTGATGG 58.368 47.619 0.00 0.00 0.00 3.51
3019 10828 3.937814 TGAAGATAACGTGGCTTGTGAT 58.062 40.909 0.00 0.00 0.00 3.06
3081 10890 7.493743 AGAATGATCAATCACATACTTCAGC 57.506 36.000 13.19 0.00 40.03 4.26
3086 10895 7.383572 GCTTCGTAGAATGATCAATCACATACT 59.616 37.037 13.19 0.00 45.90 2.12
3145 10954 5.175859 TCTACCAATCATTCCGAAACAGTC 58.824 41.667 0.00 0.00 0.00 3.51
3147 10956 7.969536 ATATCTACCAATCATTCCGAAACAG 57.030 36.000 0.00 0.00 0.00 3.16
3159 10968 6.058183 ACTCTTGTGGCAATATCTACCAATC 58.942 40.000 0.00 0.00 34.63 2.67
3184 10993 8.514594 GTCATATCATGGAAGTCTTCAAAACAA 58.485 33.333 14.49 0.00 0.00 2.83
3199 11008 3.889815 ACAAGGTGGTGTCATATCATGG 58.110 45.455 0.00 0.00 0.00 3.66
3209 11018 1.841277 TGTGTTCCTACAAGGTGGTGT 59.159 47.619 0.00 0.00 36.53 4.16
3212 11021 4.582656 TGATTTTGTGTTCCTACAAGGTGG 59.417 41.667 0.00 0.00 41.18 4.61
3213 11022 5.299279 ACTGATTTTGTGTTCCTACAAGGTG 59.701 40.000 0.00 0.00 41.18 4.00
3214 11023 5.445964 ACTGATTTTGTGTTCCTACAAGGT 58.554 37.500 0.00 0.00 41.18 3.50
3215 11024 6.391227 AACTGATTTTGTGTTCCTACAAGG 57.609 37.500 0.00 0.00 41.18 3.61
3235 11047 4.441079 CCCCGTAATACGAGATCACAAACT 60.441 45.833 15.03 0.00 46.05 2.66
3241 11053 6.845758 ATTTATCCCCGTAATACGAGATCA 57.154 37.500 15.03 5.18 46.05 2.92
3248 11060 6.272822 ACCGACTATTTATCCCCGTAATAC 57.727 41.667 0.00 0.00 0.00 1.89
3261 11073 5.399991 TGGATACCCAGATACCGACTATTT 58.600 41.667 0.00 0.00 37.58 1.40
3263 11075 4.669866 TGGATACCCAGATACCGACTAT 57.330 45.455 0.00 0.00 37.58 2.12
3264 11076 4.458256 TTGGATACCCAGATACCGACTA 57.542 45.455 0.00 0.00 44.60 2.59
3265 11077 3.323774 TTGGATACCCAGATACCGACT 57.676 47.619 0.00 0.00 44.60 4.18
3266 11078 3.576982 TGATTGGATACCCAGATACCGAC 59.423 47.826 0.00 0.00 44.60 4.79
3267 11079 3.851979 TGATTGGATACCCAGATACCGA 58.148 45.455 0.00 0.00 44.60 4.69
3268 11080 4.826274 ATGATTGGATACCCAGATACCG 57.174 45.455 0.00 0.00 44.60 4.02
3269 11081 9.213777 TCTAATATGATTGGATACCCAGATACC 57.786 37.037 0.00 0.00 44.60 2.73
3272 11084 8.923838 ACTCTAATATGATTGGATACCCAGAT 57.076 34.615 0.00 0.00 44.60 2.90
3273 11085 7.400339 GGACTCTAATATGATTGGATACCCAGA 59.600 40.741 0.00 0.00 44.60 3.86
3274 11086 7.365117 GGGACTCTAATATGATTGGATACCCAG 60.365 44.444 15.49 0.00 44.60 4.45
3275 11087 6.443849 GGGACTCTAATATGATTGGATACCCA 59.556 42.308 15.49 0.00 41.64 4.51
3276 11088 6.407074 CGGGACTCTAATATGATTGGATACCC 60.407 46.154 12.69 12.69 0.00 3.69
3378 11196 1.234615 ATCGCAACTCCCACCAAACG 61.235 55.000 0.00 0.00 0.00 3.60
3379 11197 0.240945 CATCGCAACTCCCACCAAAC 59.759 55.000 0.00 0.00 0.00 2.93
3395 11213 6.568869 AGTCAATCTACTTGCTAGACACATC 58.431 40.000 1.04 0.00 34.08 3.06
3396 11214 6.537453 AGTCAATCTACTTGCTAGACACAT 57.463 37.500 1.04 0.00 34.08 3.21
3434 11252 4.868195 GCAAATTGCACGAGACCC 57.132 55.556 13.73 0.00 44.26 4.46
3443 11261 2.850647 GCGAGATTCTTCTGCAAATTGC 59.149 45.455 11.58 11.58 45.29 3.56
3452 11270 4.100981 GCAGCGCGAGATTCTTCT 57.899 55.556 12.10 0.00 33.88 2.85
3473 11291 1.200760 TCCATGGGAGATATGGCCGG 61.201 60.000 13.02 0.00 43.81 6.13
3543 11377 1.416401 GATGGCTTCGGTGAGGGATTA 59.584 52.381 0.00 0.00 0.00 1.75
3639 11473 6.071463 CCTTCTTTTCTAATGTCGTTTCACG 58.929 40.000 0.00 0.00 44.19 4.35
3654 11488 1.574702 CGGACGCCCACCTTCTTTTC 61.575 60.000 0.00 0.00 0.00 2.29
3664 11498 3.691342 CCAAGAGTCGGACGCCCA 61.691 66.667 8.30 0.00 0.00 5.36
3669 11503 0.603975 AGCAAAGCCAAGAGTCGGAC 60.604 55.000 0.00 0.00 0.00 4.79
3692 11526 0.674895 GTGATCTTTGTGCCCGCTCT 60.675 55.000 0.00 0.00 0.00 4.09
3696 11530 3.302365 AATTTGTGATCTTTGTGCCCG 57.698 42.857 0.00 0.00 0.00 6.13
3705 11539 7.006509 CCATAGGGATGGTAAATTTGTGATCT 58.993 38.462 0.00 0.00 46.80 2.75
3720 11554 1.949525 CGGTTTGCTTCCATAGGGATG 59.050 52.381 0.00 0.00 44.48 3.51
3727 11561 0.755686 TTTTGGCGGTTTGCTTCCAT 59.244 45.000 0.00 0.00 45.43 3.41
3729 11563 0.104120 ACTTTTGGCGGTTTGCTTCC 59.896 50.000 0.00 0.00 45.43 3.46
3730 11564 1.487482 GACTTTTGGCGGTTTGCTTC 58.513 50.000 0.00 0.00 45.43 3.86
3756 11590 4.040217 TGCTTGGCTGGTAATTCAAAACAT 59.960 37.500 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.