Multiple sequence alignment - TraesCS2A01G367600

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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 TraesCS2A01G367600 chr2A 100.000 3116 0 0 1 3116 611309397 611312512 0.000000e+00 5755.0
1 TraesCS2A01G367600 chr2A 96.809 94 3 0 2673 2766 758604226 758604133 1.160000e-34 158.0
2 TraesCS2A01G367600 chr2B 89.543 2735 147 58 1 2619 548649677 548652388 0.000000e+00 3338.0
3 TraesCS2A01G367600 chr2B 80.795 604 62 22 1 581 548629912 548630484 1.030000e-114 424.0
4 TraesCS2A01G367600 chr2B 94.059 101 6 0 2673 2773 13713112 13713012 1.500000e-33 154.0
5 TraesCS2A01G367600 chr2B 91.525 59 5 0 2624 2682 760299870 760299928 7.160000e-12 82.4
6 TraesCS2A01G367600 chr2D 93.401 2182 101 21 302 2447 469999276 470001450 0.000000e+00 3192.0
7 TraesCS2A01G367600 chr2D 87.692 325 23 9 2796 3113 470001757 470002071 2.280000e-96 363.0
8 TraesCS2A01G367600 chr2D 83.273 275 17 9 2428 2682 470001463 470001728 3.130000e-55 226.0
9 TraesCS2A01G367600 chr7D 88.834 609 50 10 690 1288 418398831 418398231 0.000000e+00 732.0
10 TraesCS2A01G367600 chr7D 81.731 104 5 5 530 620 418398951 418398849 1.200000e-09 75.0
11 TraesCS2A01G367600 chr5D 80.249 724 111 29 1045 1750 292698750 292698041 1.660000e-142 516.0
12 TraesCS2A01G367600 chr5D 83.832 334 49 3 1784 2116 292695793 292695464 2.330000e-81 313.0
13 TraesCS2A01G367600 chr5D 83.594 128 10 8 2796 2914 519340311 519340186 3.290000e-20 110.0
14 TraesCS2A01G367600 chr5D 87.879 66 8 0 2617 2682 551242265 551242330 9.260000e-11 78.7
15 TraesCS2A01G367600 chr5A 82.439 615 84 20 1146 1750 385398457 385397857 1.660000e-142 516.0
16 TraesCS2A01G367600 chr5A 82.991 341 51 6 1778 2116 385395798 385395463 5.050000e-78 302.0
17 TraesCS2A01G367600 chr5A 95.000 100 5 0 2669 2768 584680893 584680794 1.160000e-34 158.0
18 TraesCS2A01G367600 chr5B 81.833 611 94 15 1146 1750 333256470 333255871 6.000000e-137 497.0
19 TraesCS2A01G367600 chr5B 82.934 334 52 3 1784 2116 333252579 333252250 2.350000e-76 296.0
20 TraesCS2A01G367600 chr5B 88.060 67 8 0 2616 2682 677345486 677345420 2.580000e-11 80.5
21 TraesCS2A01G367600 chrUn 94.286 105 5 1 2664 2767 35713238 35713342 3.220000e-35 159.0
22 TraesCS2A01G367600 chrUn 89.076 119 7 5 2675 2792 17061962 17061849 3.240000e-30 143.0
23 TraesCS2A01G367600 chrUn 94.565 92 5 0 2675 2766 394816392 394816483 3.240000e-30 143.0
24 TraesCS2A01G367600 chrUn 88.406 69 7 1 2615 2682 303756334 303756266 7.160000e-12 82.4
25 TraesCS2A01G367600 chr1B 97.826 92 2 0 2676 2767 668678533 668678442 3.220000e-35 159.0
26 TraesCS2A01G367600 chr1B 93.750 64 4 0 2842 2905 552952383 552952446 2.560000e-16 97.1
27 TraesCS2A01G367600 chr6A 95.833 96 4 0 2671 2766 563250872 563250967 4.160000e-34 156.0
28 TraesCS2A01G367600 chr7A 94.949 99 4 1 2678 2775 126943130 126943032 1.500000e-33 154.0
29 TraesCS2A01G367600 chr7A 93.548 62 4 0 2620 2681 450374712 450374773 3.310000e-15 93.5
30 TraesCS2A01G367600 chr3B 87.129 101 6 4 2820 2913 16048314 16048414 1.180000e-19 108.0
31 TraesCS2A01G367600 chr3B 95.082 61 3 0 2842 2902 670028685 670028625 2.560000e-16 97.1
32 TraesCS2A01G367600 chr3B 86.765 68 8 1 2616 2682 627198181 627198114 1.200000e-09 75.0
33 TraesCS2A01G367600 chr3D 85.294 102 9 2 2810 2905 523299163 523299264 1.980000e-17 100.0
34 TraesCS2A01G367600 chr3D 82.759 116 12 5 2792 2900 556988586 556988472 2.560000e-16 97.1
35 TraesCS2A01G367600 chr1D 82.857 105 13 4 2796 2900 476713198 476713297 4.280000e-14 89.8
36 TraesCS2A01G367600 chr1A 80.672 119 17 1 2789 2901 107521044 107521162 1.540000e-13 87.9
37 TraesCS2A01G367600 chr1A 88.406 69 7 1 2615 2682 579533049 579532981 7.160000e-12 82.4
38 TraesCS2A01G367600 chr1A 88.406 69 7 1 2615 2682 579552185 579552117 7.160000e-12 82.4
39 TraesCS2A01G367600 chr4A 84.932 73 11 0 2620 2692 27649173 27649245 1.200000e-09 75.0


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 TraesCS2A01G367600 chr2A 611309397 611312512 3115 False 5755.000000 5755 100.0000 1 3116 1 chr2A.!!$F1 3115
1 TraesCS2A01G367600 chr2B 548649677 548652388 2711 False 3338.000000 3338 89.5430 1 2619 1 chr2B.!!$F2 2618
2 TraesCS2A01G367600 chr2B 548629912 548630484 572 False 424.000000 424 80.7950 1 581 1 chr2B.!!$F1 580
3 TraesCS2A01G367600 chr2D 469999276 470002071 2795 False 1260.333333 3192 88.1220 302 3113 3 chr2D.!!$F1 2811
4 TraesCS2A01G367600 chr7D 418398231 418398951 720 True 403.500000 732 85.2825 530 1288 2 chr7D.!!$R1 758
5 TraesCS2A01G367600 chr5D 292695464 292698750 3286 True 414.500000 516 82.0405 1045 2116 2 chr5D.!!$R2 1071
6 TraesCS2A01G367600 chr5A 385395463 385398457 2994 True 409.000000 516 82.7150 1146 2116 2 chr5A.!!$R2 970
7 TraesCS2A01G367600 chr5B 333252250 333256470 4220 True 396.500000 497 82.3835 1146 2116 2 chr5B.!!$R2 970

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
152 163 0.033601 TTGAGCCATGGCCCGTAATT 60.034 50.0 33.14 13.08 43.17 1.40 F
516 554 0.249398 ACGTCAATGGCTGTAGGTCC 59.751 55.0 0.00 0.00 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1496 1576 1.992667 TGATCTGCACGTCAATTCGTC 59.007 47.619 0.0 0.0 42.27 4.2 R
2271 5799 2.967362 CATCACAATGCACAAAGCCAT 58.033 42.857 0.0 0.0 44.83 4.4 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
36 37 1.066257 CCAATAGCATGCGCCAACC 59.934 57.895 13.01 0.00 39.83 3.77
38 39 1.308047 CAATAGCATGCGCCAACCTA 58.692 50.000 13.01 0.38 39.83 3.08
68 69 1.663702 GTTGTCCAGCACGCTACGT 60.664 57.895 0.00 0.00 42.36 3.57
83 94 4.110482 CGCTACGTGCTAAATAGAAGGTT 58.890 43.478 0.00 0.00 40.11 3.50
112 123 0.035820 TGACGGTGAATGGTAAGGGC 60.036 55.000 0.00 0.00 0.00 5.19
151 162 0.185901 ATTGAGCCATGGCCCGTAAT 59.814 50.000 33.14 22.73 43.17 1.89
152 163 0.033601 TTGAGCCATGGCCCGTAATT 60.034 50.000 33.14 13.08 43.17 1.40
163 175 6.239289 CCATGGCCCGTAATTTTGAAGAATAT 60.239 38.462 0.00 0.00 0.00 1.28
179 191 3.769300 AGAATATTGACAAAACTGGGCCC 59.231 43.478 17.59 17.59 0.00 5.80
185 197 0.558712 ACAAAACTGGGCCCCAAGTA 59.441 50.000 22.27 0.00 30.80 2.24
186 198 1.149077 ACAAAACTGGGCCCCAAGTAT 59.851 47.619 22.27 6.99 30.80 2.12
220 232 0.608130 TTCAGTCAGACACCGGATGG 59.392 55.000 9.46 0.00 42.84 3.51
268 282 2.351706 TTCGCTACAAAACAACCCCT 57.648 45.000 0.00 0.00 0.00 4.79
273 287 2.352715 GCTACAAAACAACCCCTGATGC 60.353 50.000 0.00 0.00 0.00 3.91
339 354 1.106285 GGGGCATGTTCCTTTAGCAG 58.894 55.000 0.00 0.00 0.00 4.24
420 441 4.634004 TCGGCACACCTAAATTGTCATAAG 59.366 41.667 0.00 0.00 0.00 1.73
438 459 8.184848 TGTCATAAGAAACGTTCAATTTGTCAA 58.815 29.630 0.00 0.00 0.00 3.18
473 496 7.120138 ACCTGACGTCGGATTTTTAACATTATT 59.880 33.333 26.01 0.00 0.00 1.40
476 499 7.958567 TGACGTCGGATTTTTAACATTATTGAC 59.041 33.333 11.62 0.00 0.00 3.18
491 514 6.712095 ACATTATTGACCGCTTATGTGATGAT 59.288 34.615 0.00 0.00 0.00 2.45
511 535 3.326836 TTGATGACGTCAATGGCTGTA 57.673 42.857 24.13 0.00 41.79 2.74
515 539 1.067142 TGACGTCAATGGCTGTAGGTC 60.067 52.381 17.62 0.00 0.00 3.85
516 554 0.249398 ACGTCAATGGCTGTAGGTCC 59.751 55.000 0.00 0.00 0.00 4.46
552 590 7.976734 CAGTTTTACTGTCTCTTCGATTAGGAT 59.023 37.037 0.00 0.00 41.19 3.24
681 736 4.408821 TCACCCCGACATGGCAGC 62.409 66.667 0.00 0.00 35.87 5.25
726 782 3.803082 GCAGCGGCGCATTTCTCA 61.803 61.111 35.02 0.00 0.00 3.27
738 803 1.857217 CATTTCTCAGTGCTCGATCCG 59.143 52.381 0.00 0.00 0.00 4.18
793 859 8.948853 ATTTACTGTCGTGTTGTTGATTAATG 57.051 30.769 0.00 0.00 0.00 1.90
803 869 7.558137 GTGTTGTTGATTAATGAGCTTGTTTG 58.442 34.615 0.00 0.00 0.00 2.93
805 871 7.222417 TGTTGTTGATTAATGAGCTTGTTTGTG 59.778 33.333 0.00 0.00 0.00 3.33
863 930 2.559668 AGTTGCATGGTTTCCATCACAG 59.440 45.455 0.00 0.00 43.15 3.66
917 984 6.978659 CACCGTATCGCTGTATAAATATCCAT 59.021 38.462 0.00 0.00 0.00 3.41
958 1025 2.066262 CACGCACTACCAAGTACCAAG 58.934 52.381 0.00 0.00 33.48 3.61
961 1028 3.512724 ACGCACTACCAAGTACCAAGTAT 59.487 43.478 0.00 0.00 33.48 2.12
975 1042 2.221749 CCAAGTATCAATCCACGCATCG 59.778 50.000 0.00 0.00 0.00 3.84
981 1048 1.091771 CAATCCACGCATCGGAGCTT 61.092 55.000 0.00 0.00 35.56 3.74
1428 1508 1.446907 CACCTCGATCTTGCTTGCTT 58.553 50.000 0.00 0.00 0.00 3.91
1496 1576 1.586042 GCCGCTGTGTTGTTGTGTG 60.586 57.895 0.00 0.00 0.00 3.82
1557 1637 2.031012 CTGTTCTGCGAGGTGCCA 59.969 61.111 0.00 0.00 45.60 4.92
2229 5752 0.974010 CTGGGGATGCTGCATTTGGT 60.974 55.000 17.36 0.00 0.00 3.67
2236 5759 3.696051 GGATGCTGCATTTGGTTCTTCTA 59.304 43.478 17.36 0.00 0.00 2.10
2237 5760 4.201990 GGATGCTGCATTTGGTTCTTCTAG 60.202 45.833 17.36 0.00 0.00 2.43
2238 5761 3.754965 TGCTGCATTTGGTTCTTCTAGT 58.245 40.909 0.00 0.00 0.00 2.57
2271 5799 6.421801 GCTGTCTTCAGTTACTACGGTAAAAA 59.578 38.462 0.00 0.00 43.05 1.94
2415 5947 1.078637 GGTGCGGTAGTTTCTCCCC 60.079 63.158 0.00 0.00 0.00 4.81
2422 5954 4.100498 TGCGGTAGTTTCTCCCCTAATTAG 59.900 45.833 5.43 5.43 0.00 1.73
2423 5955 4.629092 CGGTAGTTTCTCCCCTAATTAGC 58.371 47.826 6.99 0.00 0.00 3.09
2479 6044 7.694388 TGCATTACGACATGTAAGACTTATC 57.306 36.000 0.00 0.00 45.79 1.75
2480 6045 6.700081 TGCATTACGACATGTAAGACTTATCC 59.300 38.462 0.00 0.00 45.79 2.59
2499 6088 9.439500 ACTTATCCTCTTCGAGTGATATAGTAC 57.561 37.037 0.00 0.00 29.25 2.73
2544 6136 9.671279 TGTTGTCTCTATGTTCATGAATACATT 57.329 29.630 16.22 0.89 36.46 2.71
2634 6237 5.216614 ACAAAAAGGAGTGTCTAGGTCTC 57.783 43.478 0.00 0.00 0.00 3.36
2641 6244 3.537580 GAGTGTCTAGGTCTCAGTCGAT 58.462 50.000 0.00 0.00 0.00 3.59
2642 6245 3.537580 AGTGTCTAGGTCTCAGTCGATC 58.462 50.000 0.00 0.00 0.00 3.69
2685 6288 6.648725 GTCAAGTGACATAACATGTACTCC 57.351 41.667 0.00 0.00 45.03 3.85
2686 6289 5.581085 GTCAAGTGACATAACATGTACTCCC 59.419 44.000 0.00 0.00 45.03 4.30
2687 6290 5.483937 TCAAGTGACATAACATGTACTCCCT 59.516 40.000 0.00 0.00 45.03 4.20
2688 6291 5.599999 AGTGACATAACATGTACTCCCTC 57.400 43.478 0.00 0.00 45.03 4.30
2689 6292 4.406003 AGTGACATAACATGTACTCCCTCC 59.594 45.833 0.00 0.00 45.03 4.30
2690 6293 3.383505 TGACATAACATGTACTCCCTCCG 59.616 47.826 0.00 0.00 45.03 4.63
2691 6294 3.371965 ACATAACATGTACTCCCTCCGT 58.628 45.455 0.00 0.00 42.78 4.69
2692 6295 3.773119 ACATAACATGTACTCCCTCCGTT 59.227 43.478 0.00 0.00 42.78 4.44
2693 6296 4.142004 ACATAACATGTACTCCCTCCGTTC 60.142 45.833 0.00 0.00 42.78 3.95
2695 6298 1.191535 CATGTACTCCCTCCGTTCCA 58.808 55.000 0.00 0.00 0.00 3.53
2696 6299 1.553248 CATGTACTCCCTCCGTTCCAA 59.447 52.381 0.00 0.00 0.00 3.53
2697 6300 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
2698 6301 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
2700 6303 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
2702 6305 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2703 6306 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2704 6307 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2706 6309 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2707 6310 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
2708 6311 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
2709 6312 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
2711 6314 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
2712 6315 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
2713 6316 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
2714 6317 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
2715 6318 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
2716 6319 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
2717 6320 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
2718 6321 7.893302 TCCAAAATAGATGACCCAACTTTGTAT 59.107 33.333 0.00 0.00 0.00 2.29
2719 6322 8.531146 CCAAAATAGATGACCCAACTTTGTATT 58.469 33.333 0.00 0.00 0.00 1.89
2723 6326 9.975218 AATAGATGACCCAACTTTGTATTAACT 57.025 29.630 0.00 0.00 0.00 2.24
2724 6327 9.975218 ATAGATGACCCAACTTTGTATTAACTT 57.025 29.630 0.00 0.00 0.00 2.66
2725 6328 8.706322 AGATGACCCAACTTTGTATTAACTTT 57.294 30.769 0.00 0.00 0.00 2.66
2726 6329 9.802039 AGATGACCCAACTTTGTATTAACTTTA 57.198 29.630 0.00 0.00 0.00 1.85
2728 6331 8.983702 TGACCCAACTTTGTATTAACTTTAGT 57.016 30.769 0.00 0.00 0.00 2.24
2731 6334 9.850198 ACCCAACTTTGTATTAACTTTAGTACA 57.150 29.630 0.00 1.37 35.09 2.90
2752 6355 9.003658 AGTACAAAGTTGAGTCATCTATTTTGG 57.996 33.333 14.35 0.00 40.00 3.28
2753 6356 8.999431 GTACAAAGTTGAGTCATCTATTTTGGA 58.001 33.333 14.35 6.88 40.00 3.53
2754 6357 8.463930 ACAAAGTTGAGTCATCTATTTTGGAA 57.536 30.769 14.35 0.00 40.00 3.53
2755 6358 8.352942 ACAAAGTTGAGTCATCTATTTTGGAAC 58.647 33.333 14.35 0.00 40.00 3.62
2756 6359 6.727824 AGTTGAGTCATCTATTTTGGAACG 57.272 37.500 1.70 0.00 0.00 3.95
2757 6360 5.643777 AGTTGAGTCATCTATTTTGGAACGG 59.356 40.000 1.70 0.00 0.00 4.44
2758 6361 5.414789 TGAGTCATCTATTTTGGAACGGA 57.585 39.130 0.00 0.00 0.00 4.69
2759 6362 5.419542 TGAGTCATCTATTTTGGAACGGAG 58.580 41.667 0.00 0.00 0.00 4.63
2760 6363 4.770795 AGTCATCTATTTTGGAACGGAGG 58.229 43.478 0.00 0.00 0.00 4.30
2761 6364 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2762 6365 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2763 6366 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2764 6367 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2765 6368 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
2766 6369 4.966805 TCTATTTTGGAACGGAGGGAGTAT 59.033 41.667 0.00 0.00 0.00 2.12
2767 6370 3.622166 TTTTGGAACGGAGGGAGTATC 57.378 47.619 0.00 0.00 0.00 2.24
2768 6371 2.241281 TTGGAACGGAGGGAGTATCA 57.759 50.000 0.00 0.00 36.25 2.15
2769 6372 1.481871 TGGAACGGAGGGAGTATCAC 58.518 55.000 0.00 0.00 40.51 3.06
2783 6386 7.710766 GGGAGTATCACTTATTTTAAGACGG 57.289 40.000 1.47 0.00 33.91 4.79
2784 6387 6.704937 GGGAGTATCACTTATTTTAAGACGGG 59.295 42.308 1.47 0.00 33.91 5.28
2785 6388 6.704937 GGAGTATCACTTATTTTAAGACGGGG 59.295 42.308 1.47 0.00 36.25 5.73
2786 6389 6.589135 AGTATCACTTATTTTAAGACGGGGG 58.411 40.000 1.47 0.00 0.00 5.40
2844 6453 7.680442 TTTGAACGGATCTTCATGTAAATGA 57.320 32.000 0.00 0.00 30.19 2.57
2849 6458 9.817365 GAACGGATCTTCATGTAAATGAATATG 57.183 33.333 8.80 0.00 39.52 1.78
2852 6461 7.094677 CGGATCTTCATGTAAATGAATATGGCA 60.095 37.037 8.80 0.00 39.52 4.92
2867 6476 6.040054 TGAATATGGCATTGATTGAGACTTGG 59.960 38.462 4.78 0.00 0.00 3.61
2871 6480 5.076182 TGGCATTGATTGAGACTTGGTTAA 58.924 37.500 0.00 0.00 0.00 2.01
2872 6481 5.183713 TGGCATTGATTGAGACTTGGTTAAG 59.816 40.000 0.00 0.00 39.86 1.85
2883 6492 4.240175 ACTTGGTTAAGTCTCAGTCGAC 57.760 45.455 7.70 7.70 43.53 4.20
2910 6519 7.040340 TGAGATTTAGCAATCCCGTAACAAAAA 60.040 33.333 0.00 0.00 39.95 1.94
3027 6637 5.414454 AGCTGAATCCGCACTACAAAATAAA 59.586 36.000 0.00 0.00 0.00 1.40
3049 6659 1.588239 TGAGGCCTGGTCTCAATGAT 58.412 50.000 27.77 0.00 41.56 2.45
3055 6665 3.558746 GGCCTGGTCTCAATGATATCCTG 60.559 52.174 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 4.439700 CGAGACGGAACCTTCTATTTAGCA 60.440 45.833 0.00 0.00 0.00 3.49
96 107 1.817941 CCGCCCTTACCATTCACCG 60.818 63.158 0.00 0.00 0.00 4.94
112 123 0.389817 TTTGTCTCATCGTGGCTCCG 60.390 55.000 0.00 0.00 0.00 4.63
151 162 7.440856 GCCCAGTTTTGTCAATATTCTTCAAAA 59.559 33.333 13.31 13.31 36.23 2.44
152 163 6.928492 GCCCAGTTTTGTCAATATTCTTCAAA 59.072 34.615 5.60 5.60 0.00 2.69
163 175 0.325671 TTGGGGCCCAGTTTTGTCAA 60.326 50.000 27.05 13.12 33.81 3.18
220 232 2.104170 CTCCACACCCTCTAGTCCTTC 58.896 57.143 0.00 0.00 0.00 3.46
273 287 7.429636 AAAAATGTTTGATTTCCATGCTGAG 57.570 32.000 0.00 0.00 0.00 3.35
399 420 6.509418 TTCTTATGACAATTTAGGTGTGCC 57.491 37.500 0.00 0.00 0.00 5.01
401 422 7.581476 ACGTTTCTTATGACAATTTAGGTGTG 58.419 34.615 0.00 0.00 0.00 3.82
420 441 7.444558 TTTAGCTTGACAAATTGAACGTTTC 57.555 32.000 0.46 0.00 0.00 2.78
448 471 4.939509 ATGTTAAAAATCCGACGTCAGG 57.060 40.909 17.16 17.07 0.00 3.86
473 496 4.135747 TCAATCATCACATAAGCGGTCA 57.864 40.909 0.00 0.00 0.00 4.02
476 499 4.376717 CGTCATCAATCATCACATAAGCGG 60.377 45.833 0.00 0.00 0.00 5.52
511 535 0.542232 AACTGAGCCACGTAGGACCT 60.542 55.000 0.00 0.00 41.22 3.85
515 539 3.314541 AGTAAAACTGAGCCACGTAGG 57.685 47.619 0.00 0.00 41.84 3.18
573 611 0.249114 GATCGGAGTTCGGAGCCTTC 60.249 60.000 0.00 0.00 39.77 3.46
630 685 0.527113 TCCTTTGCATTGCATCGTGG 59.473 50.000 12.95 11.83 38.76 4.94
695 750 2.588877 CTGCTATTGACCGGGCGG 60.589 66.667 6.32 0.00 42.03 6.13
720 776 0.173481 CCGGATCGAGCACTGAGAAA 59.827 55.000 1.84 0.00 0.00 2.52
725 781 0.389817 TTTGTCCGGATCGAGCACTG 60.390 55.000 7.81 0.00 0.00 3.66
726 782 0.320374 TTTTGTCCGGATCGAGCACT 59.680 50.000 7.81 0.00 0.00 4.40
738 803 4.380841 AAGTTCCGTTTTCCTTTTGTCC 57.619 40.909 0.00 0.00 0.00 4.02
790 856 2.887152 GGGAGACACAAACAAGCTCATT 59.113 45.455 0.00 0.00 0.00 2.57
793 859 1.967319 TGGGAGACACAAACAAGCTC 58.033 50.000 0.00 0.00 0.00 4.09
803 869 0.393820 TTGGTTACCGTGGGAGACAC 59.606 55.000 0.00 0.00 46.78 3.67
805 871 0.672711 GCTTGGTTACCGTGGGAGAC 60.673 60.000 0.00 0.00 0.00 3.36
917 984 3.578282 TGCCTGACTGACTCTGAATACAA 59.422 43.478 0.00 0.00 0.00 2.41
924 991 1.735920 GCGTGCCTGACTGACTCTG 60.736 63.158 0.00 0.00 0.00 3.35
926 993 2.024319 GTGCGTGCCTGACTGACTC 61.024 63.158 0.00 0.00 0.00 3.36
929 996 1.289066 GTAGTGCGTGCCTGACTGA 59.711 57.895 0.00 0.00 0.00 3.41
958 1025 2.061773 CTCCGATGCGTGGATTGATAC 58.938 52.381 0.00 0.00 34.32 2.24
961 1028 1.521457 GCTCCGATGCGTGGATTGA 60.521 57.895 0.00 0.00 34.32 2.57
981 1048 3.912907 GCGCCGGCCTAGCTTCTA 61.913 66.667 23.46 0.00 0.00 2.10
994 1061 4.496336 AGCTTCTCCCATGGCGCC 62.496 66.667 22.73 22.73 0.00 6.53
1428 1508 2.572095 AATGGCGAACGAGCGATGGA 62.572 55.000 5.91 0.00 35.75 3.41
1483 1563 3.437049 TCAATTCGTCACACAACAACACA 59.563 39.130 0.00 0.00 0.00 3.72
1496 1576 1.992667 TGATCTGCACGTCAATTCGTC 59.007 47.619 0.00 0.00 42.27 4.20
2254 5777 6.490566 AAGCCATTTTTACCGTAGTAACTG 57.509 37.500 0.00 0.00 38.19 3.16
2271 5799 2.967362 CATCACAATGCACAAAGCCAT 58.033 42.857 0.00 0.00 44.83 4.40
2335 5867 7.596494 TGATCAAACCTTCAGCTCTTATTTTG 58.404 34.615 0.00 0.00 0.00 2.44
2415 5947 6.798482 TGATGGATGCAAAACTGCTAATTAG 58.202 36.000 8.20 8.20 35.49 1.73
2422 5954 3.513680 TGATGATGGATGCAAAACTGC 57.486 42.857 0.00 0.00 0.00 4.40
2423 5955 3.802139 GCATGATGATGGATGCAAAACTG 59.198 43.478 0.00 0.00 43.75 3.16
2499 6088 7.332926 AGACAACAGTAAACAGAAGATGCATAG 59.667 37.037 0.00 0.00 0.00 2.23
2544 6136 1.511318 CCATGCCCAACGACAACGAA 61.511 55.000 0.00 0.00 42.66 3.85
2569 6168 2.661718 ACCGATGAAGTTGTTTTGGGT 58.338 42.857 0.00 0.00 0.00 4.51
2570 6169 3.726291 AACCGATGAAGTTGTTTTGGG 57.274 42.857 0.00 0.00 0.00 4.12
2571 6170 5.432885 AGTAACCGATGAAGTTGTTTTGG 57.567 39.130 0.00 0.00 0.00 3.28
2572 6171 7.111041 CGTAAAGTAACCGATGAAGTTGTTTTG 59.889 37.037 0.00 0.00 0.00 2.44
2573 6172 7.127686 CGTAAAGTAACCGATGAAGTTGTTTT 58.872 34.615 0.00 0.00 0.00 2.43
2574 6173 6.258507 ACGTAAAGTAACCGATGAAGTTGTTT 59.741 34.615 0.00 0.00 0.00 2.83
2575 6174 5.754890 ACGTAAAGTAACCGATGAAGTTGTT 59.245 36.000 0.00 0.00 0.00 2.83
2576 6175 5.291971 ACGTAAAGTAACCGATGAAGTTGT 58.708 37.500 0.00 0.00 0.00 3.32
2577 6176 5.834239 ACGTAAAGTAACCGATGAAGTTG 57.166 39.130 0.00 0.00 0.00 3.16
2578 6177 6.446318 TGTACGTAAAGTAACCGATGAAGTT 58.554 36.000 0.00 0.00 37.02 2.66
2634 6237 5.574082 ACTTGATTAAGTCTCGATCGACTG 58.426 41.667 15.15 5.81 43.53 3.51
2656 6259 7.891183 ACATGTTATGTCACTTGACTTAGAC 57.109 36.000 10.63 9.45 44.99 2.59
2682 6285 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2683 6286 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2684 6287 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2685 6288 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
2686 6289 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
2687 6290 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
2688 6291 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
2689 6292 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
2690 6293 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
2691 6294 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
2692 6295 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
2693 6296 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
2697 6300 9.975218 AGTTAATACAAAGTTGGGTCATCTATT 57.025 29.630 0.00 0.00 0.00 1.73
2698 6301 9.975218 AAGTTAATACAAAGTTGGGTCATCTAT 57.025 29.630 0.00 0.00 0.00 1.98
2700 6303 8.706322 AAAGTTAATACAAAGTTGGGTCATCT 57.294 30.769 0.00 0.00 0.00 2.90
2702 6305 9.582648 ACTAAAGTTAATACAAAGTTGGGTCAT 57.417 29.630 0.00 0.00 0.00 3.06
2703 6306 8.983702 ACTAAAGTTAATACAAAGTTGGGTCA 57.016 30.769 0.00 0.00 0.00 4.02
2726 6329 9.003658 CCAAAATAGATGACTCAACTTTGTACT 57.996 33.333 0.00 0.00 0.00 2.73
2727 6330 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
2728 6331 9.567776 TTCCAAAATAGATGACTCAACTTTGTA 57.432 29.630 0.00 0.00 0.00 2.41
2729 6332 8.352942 GTTCCAAAATAGATGACTCAACTTTGT 58.647 33.333 0.00 0.00 0.00 2.83
2730 6333 7.535258 CGTTCCAAAATAGATGACTCAACTTTG 59.465 37.037 0.00 0.00 0.00 2.77
2731 6334 7.308589 CCGTTCCAAAATAGATGACTCAACTTT 60.309 37.037 0.00 0.00 0.00 2.66
2732 6335 6.149474 CCGTTCCAAAATAGATGACTCAACTT 59.851 38.462 0.00 0.00 0.00 2.66
2733 6336 5.643777 CCGTTCCAAAATAGATGACTCAACT 59.356 40.000 0.00 0.00 0.00 3.16
2734 6337 5.642063 TCCGTTCCAAAATAGATGACTCAAC 59.358 40.000 0.00 0.00 0.00 3.18
2735 6338 5.800296 TCCGTTCCAAAATAGATGACTCAA 58.200 37.500 0.00 0.00 0.00 3.02
2736 6339 5.414789 TCCGTTCCAAAATAGATGACTCA 57.585 39.130 0.00 0.00 0.00 3.41
2737 6340 4.811557 CCTCCGTTCCAAAATAGATGACTC 59.188 45.833 0.00 0.00 0.00 3.36
2738 6341 4.384208 CCCTCCGTTCCAAAATAGATGACT 60.384 45.833 0.00 0.00 0.00 3.41
2739 6342 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2740 6343 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2741 6344 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2742 6345 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2743 6346 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2744 6347 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2745 6348 4.717778 TGATACTCCCTCCGTTCCAAAATA 59.282 41.667 0.00 0.00 0.00 1.40
2746 6349 3.521937 TGATACTCCCTCCGTTCCAAAAT 59.478 43.478 0.00 0.00 0.00 1.82
2747 6350 2.907696 TGATACTCCCTCCGTTCCAAAA 59.092 45.455 0.00 0.00 0.00 2.44
2748 6351 2.235402 GTGATACTCCCTCCGTTCCAAA 59.765 50.000 0.00 0.00 0.00 3.28
2749 6352 1.829222 GTGATACTCCCTCCGTTCCAA 59.171 52.381 0.00 0.00 0.00 3.53
2750 6353 1.006758 AGTGATACTCCCTCCGTTCCA 59.993 52.381 0.00 0.00 0.00 3.53
2751 6354 1.777941 AGTGATACTCCCTCCGTTCC 58.222 55.000 0.00 0.00 0.00 3.62
2752 6355 5.532664 AATAAGTGATACTCCCTCCGTTC 57.467 43.478 0.00 0.00 0.00 3.95
2753 6356 5.952347 AAATAAGTGATACTCCCTCCGTT 57.048 39.130 0.00 0.00 0.00 4.44
2754 6357 5.952347 AAAATAAGTGATACTCCCTCCGT 57.048 39.130 0.00 0.00 0.00 4.69
2755 6358 7.652507 GTCTTAAAATAAGTGATACTCCCTCCG 59.347 40.741 0.00 0.00 0.00 4.63
2756 6359 7.652507 CGTCTTAAAATAAGTGATACTCCCTCC 59.347 40.741 0.00 0.00 0.00 4.30
2757 6360 7.652507 CCGTCTTAAAATAAGTGATACTCCCTC 59.347 40.741 0.00 0.00 0.00 4.30
2758 6361 7.418712 CCCGTCTTAAAATAAGTGATACTCCCT 60.419 40.741 0.00 0.00 0.00 4.20
2759 6362 6.704937 CCCGTCTTAAAATAAGTGATACTCCC 59.295 42.308 0.00 0.00 0.00 4.30
2760 6363 6.704937 CCCCGTCTTAAAATAAGTGATACTCC 59.295 42.308 0.00 0.00 0.00 3.85
2761 6364 6.704937 CCCCCGTCTTAAAATAAGTGATACTC 59.295 42.308 0.00 0.00 0.00 2.59
2762 6365 6.589135 CCCCCGTCTTAAAATAAGTGATACT 58.411 40.000 0.00 0.00 0.00 2.12
2763 6366 6.856135 CCCCCGTCTTAAAATAAGTGATAC 57.144 41.667 0.00 0.00 0.00 2.24
2834 6437 9.699703 TCAATCAATGCCATATTCATTTACATG 57.300 29.630 0.00 0.00 32.30 3.21
2844 6453 5.895534 ACCAAGTCTCAATCAATGCCATATT 59.104 36.000 0.00 0.00 0.00 1.28
2849 6458 5.183904 ACTTAACCAAGTCTCAATCAATGCC 59.816 40.000 0.00 0.00 41.25 4.40
2876 6485 4.505922 GGATTGCTAAATCTCAGTCGACTG 59.494 45.833 34.76 34.76 41.74 3.51
2883 6492 5.116180 TGTTACGGGATTGCTAAATCTCAG 58.884 41.667 0.00 0.00 42.61 3.35
2948 6558 9.299465 TGCCAATTATTTAGATGCATCATAAGA 57.701 29.630 27.81 15.22 0.00 2.10
2977 6587 6.589907 GCTTGGTTTGGTTTCACTATATTTGG 59.410 38.462 0.00 0.00 0.00 3.28
2985 6595 1.136891 GCTGCTTGGTTTGGTTTCACT 59.863 47.619 0.00 0.00 0.00 3.41
2986 6596 1.136891 AGCTGCTTGGTTTGGTTTCAC 59.863 47.619 0.00 0.00 0.00 3.18
2990 6600 1.484038 TTCAGCTGCTTGGTTTGGTT 58.516 45.000 9.47 0.00 0.00 3.67
3027 6637 1.064906 CATTGAGACCAGGCCTCATGT 60.065 52.381 6.25 0.00 40.02 3.21
3046 6656 8.727149 AGTGATTAAGGGAAAATCAGGATATCA 58.273 33.333 4.83 0.00 42.43 2.15
3049 6659 8.101309 TGAGTGATTAAGGGAAAATCAGGATA 57.899 34.615 0.00 0.00 42.43 2.59


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

AutoCloner maintained by Alex Coulton.