Multiple sequence alignment - TraesCS2D01G543800

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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 TraesCS2D01G543800 chr2D 100.000 2873 0 0 1 2873 621361661 621364533 0.000000e+00 5306
1 TraesCS2D01G543800 chr2D 87.101 2318 240 43 1 2296 226333103 226335383 0.000000e+00 2569
2 TraesCS2D01G543800 chr2B 96.135 2225 60 4 1 2205 600080155 600082373 0.000000e+00 3609
3 TraesCS2D01G543800 chr2B 92.442 516 24 10 2019 2526 600082220 600082728 0.000000e+00 723
4 TraesCS2D01G543800 chr2B 90.171 234 21 2 2294 2525 776823663 776823896 1.290000e-78 303
5 TraesCS2D01G543800 chr2B 90.090 222 19 3 2608 2828 762118574 762118793 4.690000e-73 285
6 TraesCS2D01G543800 chr2B 89.157 83 4 3 2528 2610 762118476 762118553 6.550000e-17 99
7 TraesCS2D01G543800 chr1B 96.128 2221 67 16 1 2211 7321351 7319140 0.000000e+00 3607
8 TraesCS2D01G543800 chr1B 91.634 514 29 10 2019 2526 7319228 7318723 0.000000e+00 699
9 TraesCS2D01G543800 chr4B 95.856 2220 70 18 1 2205 411180455 411178243 0.000000e+00 3570
10 TraesCS2D01G543800 chr4B 90.286 525 37 13 2011 2526 411178376 411177857 0.000000e+00 675
11 TraesCS2D01G543800 chr3D 87.227 2560 246 58 1 2531 535143500 535146007 0.000000e+00 2841
12 TraesCS2D01G543800 chr3D 96.894 1288 21 5 990 2274 49963604 49964875 0.000000e+00 2139
13 TraesCS2D01G543800 chr3D 96.341 246 9 0 2281 2526 49967053 49967298 3.450000e-109 405
14 TraesCS2D01G543800 chr7A 91.242 1964 155 15 1 1956 683625613 683627567 0.000000e+00 2658
15 TraesCS2D01G543800 chr7A 90.928 1962 160 15 1 1956 683510221 683508272 0.000000e+00 2621
16 TraesCS2D01G543800 chr5B 91.362 1945 146 16 1 1938 567869163 567867234 0.000000e+00 2641
17 TraesCS2D01G543800 chr6D 87.543 2320 222 45 1 2296 61814074 61811798 0.000000e+00 2621
18 TraesCS2D01G543800 chr6D 88.797 241 23 4 2297 2534 61811716 61811477 2.800000e-75 292
19 TraesCS2D01G543800 chr2A 94.795 634 31 2 4 637 480692626 480691995 0.000000e+00 987
20 TraesCS2D01G543800 chr2A 89.389 311 24 6 2569 2873 753106641 753106948 1.620000e-102 383
21 TraesCS2D01G543800 chr6B 91.908 519 27 11 2019 2530 127847651 127847141 0.000000e+00 712
22 TraesCS2D01G543800 chr3B 90.675 504 30 12 2050 2538 652789367 652788866 0.000000e+00 654


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 TraesCS2D01G543800 chr2D 621361661 621364533 2872 False 5306.0 5306 100.0000 1 2873 1 chr2D.!!$F2 2872
1 TraesCS2D01G543800 chr2D 226333103 226335383 2280 False 2569.0 2569 87.1010 1 2296 1 chr2D.!!$F1 2295
2 TraesCS2D01G543800 chr2B 600080155 600082728 2573 False 2166.0 3609 94.2885 1 2526 2 chr2B.!!$F2 2525
3 TraesCS2D01G543800 chr1B 7318723 7321351 2628 True 2153.0 3607 93.8810 1 2526 2 chr1B.!!$R1 2525
4 TraesCS2D01G543800 chr4B 411177857 411180455 2598 True 2122.5 3570 93.0710 1 2526 2 chr4B.!!$R1 2525
5 TraesCS2D01G543800 chr3D 535143500 535146007 2507 False 2841.0 2841 87.2270 1 2531 1 chr3D.!!$F1 2530
6 TraesCS2D01G543800 chr3D 49963604 49967298 3694 False 1272.0 2139 96.6175 990 2526 2 chr3D.!!$F2 1536
7 TraesCS2D01G543800 chr7A 683625613 683627567 1954 False 2658.0 2658 91.2420 1 1956 1 chr7A.!!$F1 1955
8 TraesCS2D01G543800 chr7A 683508272 683510221 1949 True 2621.0 2621 90.9280 1 1956 1 chr7A.!!$R1 1955
9 TraesCS2D01G543800 chr5B 567867234 567869163 1929 True 2641.0 2641 91.3620 1 1938 1 chr5B.!!$R1 1937
10 TraesCS2D01G543800 chr6D 61811477 61814074 2597 True 1456.5 2621 88.1700 1 2534 2 chr6D.!!$R1 2533
11 TraesCS2D01G543800 chr2A 480691995 480692626 631 True 987.0 987 94.7950 4 637 1 chr2A.!!$R1 633
12 TraesCS2D01G543800 chr6B 127847141 127847651 510 True 712.0 712 91.9080 2019 2530 1 chr6B.!!$R1 511
13 TraesCS2D01G543800 chr3B 652788866 652789367 501 True 654.0 654 90.6750 2050 2538 1 chr3B.!!$R1 488

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
712 717 4.697352 CCAACTTCAGGAACCAACTATCTG 59.303 45.833 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2602 5146 0.179059 ACGGAACACATGTCAGTGCA 60.179 50.0 0.0 0.0 43.23 4.57 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
428 429 5.985781 TCGCACTCAAAGTTTCTTTGATAC 58.014 37.500 20.24 13.51 37.72 2.24
466 469 5.461032 TGTGTCCATTGGGTTTTCAATAC 57.539 39.130 2.09 0.00 35.78 1.89
607 612 7.611467 TGATGGACAACTTATTGCTACAAGAAT 59.389 33.333 0.00 0.00 39.66 2.40
712 717 4.697352 CCAACTTCAGGAACCAACTATCTG 59.303 45.833 0.00 0.00 0.00 2.90
1892 1908 9.121517 CATTTGAGTAGTTTCAAGTGCTTAATG 57.878 33.333 0.00 0.00 37.77 1.90
2061 2183 7.024171 TGTTGTTGTATGTGTTGTTGTTACTG 58.976 34.615 0.00 0.00 0.00 2.74
2133 2382 3.942829 AGTGCTGCTGTTGTATATGTGT 58.057 40.909 0.00 0.00 0.00 3.72
2139 2388 4.071423 TGCTGTTGTATATGTGTTGCTGT 58.929 39.130 0.00 0.00 0.00 4.40
2156 2408 2.291741 GCTGTTGCTAAGAAAGTGCTGT 59.708 45.455 0.00 0.00 36.03 4.40
2482 5026 4.808042 CCAAGGAGATTTGATATTGGGGT 58.192 43.478 0.00 0.00 34.80 4.95
2515 5059 3.257375 CCATGGCCCTGAATATCAACATG 59.743 47.826 9.96 0.00 35.48 3.21
2534 5078 1.215014 GCAAACAAAGCGCAAGGGAC 61.215 55.000 11.47 0.00 38.28 4.46
2538 5082 1.135315 CAAAGCGCAAGGGACATCG 59.865 57.895 11.47 0.00 38.28 3.84
2539 5083 1.302511 AAAGCGCAAGGGACATCGT 60.303 52.632 11.47 0.00 38.28 3.73
2540 5084 0.889186 AAAGCGCAAGGGACATCGTT 60.889 50.000 11.47 0.00 38.28 3.85
2541 5085 1.577328 AAGCGCAAGGGACATCGTTG 61.577 55.000 11.47 0.00 42.34 4.10
2542 5086 2.032634 GCGCAAGGGACATCGTTGA 61.033 57.895 0.30 0.00 42.11 3.18
2543 5087 1.369091 GCGCAAGGGACATCGTTGAT 61.369 55.000 0.30 0.00 42.11 2.57
2544 5088 0.374758 CGCAAGGGACATCGTTGATG 59.625 55.000 5.29 5.29 44.71 3.07
2545 5089 0.099436 GCAAGGGACATCGTTGATGC 59.901 55.000 6.70 0.68 43.15 3.91
2546 5090 0.374758 CAAGGGACATCGTTGATGCG 59.625 55.000 6.70 0.00 43.15 4.73
2547 5091 0.036388 AAGGGACATCGTTGATGCGT 60.036 50.000 6.70 0.00 43.15 5.24
2548 5092 0.460284 AGGGACATCGTTGATGCGTC 60.460 55.000 6.70 0.00 43.15 5.19
2549 5093 0.460284 GGGACATCGTTGATGCGTCT 60.460 55.000 7.58 0.00 43.15 4.18
2550 5094 1.202371 GGGACATCGTTGATGCGTCTA 60.202 52.381 7.58 0.00 43.15 2.59
2551 5095 2.545952 GGGACATCGTTGATGCGTCTAT 60.546 50.000 7.58 0.00 43.15 1.98
2552 5096 2.472861 GGACATCGTTGATGCGTCTATG 59.527 50.000 7.58 5.34 43.15 2.23
2553 5097 3.372060 GACATCGTTGATGCGTCTATGA 58.628 45.455 13.50 13.50 43.15 2.15
2554 5098 3.116300 ACATCGTTGATGCGTCTATGAC 58.884 45.455 13.42 3.95 43.15 3.06
2555 5099 3.181486 ACATCGTTGATGCGTCTATGACT 60.181 43.478 13.42 1.19 43.15 3.41
2556 5100 4.036380 ACATCGTTGATGCGTCTATGACTA 59.964 41.667 13.42 0.00 43.15 2.59
2557 5101 4.830826 TCGTTGATGCGTCTATGACTAT 57.169 40.909 7.58 0.00 0.00 2.12
2558 5102 5.934935 TCGTTGATGCGTCTATGACTATA 57.065 39.130 7.58 0.00 0.00 1.31
2559 5103 5.686834 TCGTTGATGCGTCTATGACTATAC 58.313 41.667 7.58 0.00 0.00 1.47
2560 5104 5.237779 TCGTTGATGCGTCTATGACTATACA 59.762 40.000 7.58 0.00 0.00 2.29
2561 5105 6.072673 TCGTTGATGCGTCTATGACTATACAT 60.073 38.462 7.58 0.00 0.00 2.29
2562 5106 6.032880 CGTTGATGCGTCTATGACTATACATG 59.967 42.308 7.58 0.00 0.00 3.21
2563 5107 6.575162 TGATGCGTCTATGACTATACATGT 57.425 37.500 7.58 2.69 0.00 3.21
2564 5108 7.681939 TGATGCGTCTATGACTATACATGTA 57.318 36.000 8.27 8.27 0.00 2.29
2565 5109 8.106247 TGATGCGTCTATGACTATACATGTAA 57.894 34.615 10.14 0.00 0.00 2.41
2566 5110 8.237267 TGATGCGTCTATGACTATACATGTAAG 58.763 37.037 10.14 10.86 0.00 2.34
2567 5111 7.506328 TGCGTCTATGACTATACATGTAAGT 57.494 36.000 10.14 13.79 0.00 2.24
2568 5112 7.582352 TGCGTCTATGACTATACATGTAAGTC 58.418 38.462 25.45 25.45 40.05 3.01
2583 5127 6.814954 ATGTAAGTCATGAGTGGGAACTAT 57.185 37.500 3.18 0.00 35.19 2.12
2584 5128 6.222038 TGTAAGTCATGAGTGGGAACTATC 57.778 41.667 3.18 0.00 0.00 2.08
2585 5129 5.958380 TGTAAGTCATGAGTGGGAACTATCT 59.042 40.000 3.18 0.00 0.00 1.98
2586 5130 7.123383 TGTAAGTCATGAGTGGGAACTATCTA 58.877 38.462 3.18 0.00 0.00 1.98
2587 5131 6.723298 AAGTCATGAGTGGGAACTATCTAG 57.277 41.667 3.18 0.00 0.00 2.43
2588 5132 6.019656 AGTCATGAGTGGGAACTATCTAGA 57.980 41.667 1.14 0.00 0.00 2.43
2589 5133 6.619464 AGTCATGAGTGGGAACTATCTAGAT 58.381 40.000 10.73 10.73 0.00 1.98
2590 5134 7.760607 AGTCATGAGTGGGAACTATCTAGATA 58.239 38.462 11.94 11.94 0.00 1.98
2591 5135 8.228206 AGTCATGAGTGGGAACTATCTAGATAA 58.772 37.037 13.41 0.00 0.00 1.75
2592 5136 9.030452 GTCATGAGTGGGAACTATCTAGATAAT 57.970 37.037 13.41 0.50 0.00 1.28
2593 5137 9.029368 TCATGAGTGGGAACTATCTAGATAATG 57.971 37.037 13.41 9.77 0.00 1.90
2594 5138 9.029368 CATGAGTGGGAACTATCTAGATAATGA 57.971 37.037 13.41 0.00 0.00 2.57
2595 5139 9.781425 ATGAGTGGGAACTATCTAGATAATGAT 57.219 33.333 13.41 0.00 0.00 2.45
2596 5140 9.607333 TGAGTGGGAACTATCTAGATAATGATT 57.393 33.333 13.41 6.04 0.00 2.57
2617 5161 4.717233 TTTTTCTGCACTGACATGTGTT 57.283 36.364 1.15 0.00 39.89 3.32
2618 5162 3.969117 TTTCTGCACTGACATGTGTTC 57.031 42.857 1.15 0.00 39.89 3.18
2619 5163 1.882912 TCTGCACTGACATGTGTTCC 58.117 50.000 1.15 0.00 39.89 3.62
2620 5164 0.514255 CTGCACTGACATGTGTTCCG 59.486 55.000 1.15 0.00 39.89 4.30
2621 5165 0.179059 TGCACTGACATGTGTTCCGT 60.179 50.000 1.15 0.00 39.89 4.69
2622 5166 0.512952 GCACTGACATGTGTTCCGTC 59.487 55.000 1.15 0.00 39.89 4.79
2623 5167 0.784178 CACTGACATGTGTTCCGTCG 59.216 55.000 1.15 0.00 33.61 5.12
2624 5168 0.944311 ACTGACATGTGTTCCGTCGC 60.944 55.000 1.15 0.00 32.17 5.19
2625 5169 0.667487 CTGACATGTGTTCCGTCGCT 60.667 55.000 1.15 0.00 32.17 4.93
2626 5170 0.599060 TGACATGTGTTCCGTCGCTA 59.401 50.000 1.15 0.00 32.17 4.26
2627 5171 1.203758 TGACATGTGTTCCGTCGCTAT 59.796 47.619 1.15 0.00 32.17 2.97
2628 5172 2.268298 GACATGTGTTCCGTCGCTATT 58.732 47.619 1.15 0.00 0.00 1.73
2629 5173 1.999735 ACATGTGTTCCGTCGCTATTG 59.000 47.619 0.00 0.00 0.00 1.90
2630 5174 1.999735 CATGTGTTCCGTCGCTATTGT 59.000 47.619 0.00 0.00 0.00 2.71
2631 5175 1.424403 TGTGTTCCGTCGCTATTGTG 58.576 50.000 0.00 0.00 0.00 3.33
2632 5176 1.000052 TGTGTTCCGTCGCTATTGTGA 60.000 47.619 0.00 0.00 0.00 3.58
2633 5177 1.654105 GTGTTCCGTCGCTATTGTGAG 59.346 52.381 0.00 0.00 32.87 3.51
2634 5178 1.542472 TGTTCCGTCGCTATTGTGAGA 59.458 47.619 0.00 0.00 32.87 3.27
2635 5179 2.165641 TGTTCCGTCGCTATTGTGAGAT 59.834 45.455 0.00 0.00 32.87 2.75
2636 5180 2.776312 TCCGTCGCTATTGTGAGATC 57.224 50.000 0.00 0.00 32.87 2.75
2637 5181 1.337071 TCCGTCGCTATTGTGAGATCC 59.663 52.381 0.00 0.00 32.87 3.36
2638 5182 1.399572 CGTCGCTATTGTGAGATCCG 58.600 55.000 0.00 0.00 32.87 4.18
2639 5183 1.268589 CGTCGCTATTGTGAGATCCGT 60.269 52.381 0.00 0.00 32.87 4.69
2640 5184 2.120232 GTCGCTATTGTGAGATCCGTG 58.880 52.381 0.00 0.00 32.87 4.94
2641 5185 0.855349 CGCTATTGTGAGATCCGTGC 59.145 55.000 0.00 0.00 0.00 5.34
2642 5186 1.221414 GCTATTGTGAGATCCGTGCC 58.779 55.000 0.00 0.00 0.00 5.01
2643 5187 1.473257 GCTATTGTGAGATCCGTGCCA 60.473 52.381 0.00 0.00 0.00 4.92
2644 5188 2.205074 CTATTGTGAGATCCGTGCCAC 58.795 52.381 0.00 0.00 0.00 5.01
2645 5189 0.392998 ATTGTGAGATCCGTGCCACC 60.393 55.000 0.00 0.00 0.00 4.61
2646 5190 2.125106 GTGAGATCCGTGCCACCC 60.125 66.667 0.00 0.00 0.00 4.61
2647 5191 2.606213 TGAGATCCGTGCCACCCA 60.606 61.111 0.00 0.00 0.00 4.51
2648 5192 1.995066 TGAGATCCGTGCCACCCAT 60.995 57.895 0.00 0.00 0.00 4.00
2649 5193 1.524621 GAGATCCGTGCCACCCATG 60.525 63.158 0.00 0.00 0.00 3.66
2650 5194 2.257409 GAGATCCGTGCCACCCATGT 62.257 60.000 0.00 0.00 0.00 3.21
2651 5195 1.378514 GATCCGTGCCACCCATGTT 60.379 57.895 0.00 0.00 0.00 2.71
2652 5196 0.965363 GATCCGTGCCACCCATGTTT 60.965 55.000 0.00 0.00 0.00 2.83
2653 5197 0.541764 ATCCGTGCCACCCATGTTTT 60.542 50.000 0.00 0.00 0.00 2.43
2654 5198 1.175983 TCCGTGCCACCCATGTTTTC 61.176 55.000 0.00 0.00 0.00 2.29
2655 5199 1.178534 CCGTGCCACCCATGTTTTCT 61.179 55.000 0.00 0.00 0.00 2.52
2656 5200 1.529226 CGTGCCACCCATGTTTTCTA 58.471 50.000 0.00 0.00 0.00 2.10
2657 5201 1.883275 CGTGCCACCCATGTTTTCTAA 59.117 47.619 0.00 0.00 0.00 2.10
2658 5202 2.294791 CGTGCCACCCATGTTTTCTAAA 59.705 45.455 0.00 0.00 0.00 1.85
2659 5203 3.243569 CGTGCCACCCATGTTTTCTAAAA 60.244 43.478 0.00 0.00 0.00 1.52
2660 5204 4.560513 CGTGCCACCCATGTTTTCTAAAAT 60.561 41.667 0.00 0.00 0.00 1.82
2661 5205 4.690280 GTGCCACCCATGTTTTCTAAAATG 59.310 41.667 0.00 0.00 0.00 2.32
2662 5206 4.590647 TGCCACCCATGTTTTCTAAAATGA 59.409 37.500 0.00 0.00 31.65 2.57
2663 5207 5.070981 TGCCACCCATGTTTTCTAAAATGAA 59.929 36.000 0.00 0.00 31.65 2.57
2664 5208 6.172630 GCCACCCATGTTTTCTAAAATGAAT 58.827 36.000 0.00 0.00 31.65 2.57
2665 5209 6.092533 GCCACCCATGTTTTCTAAAATGAATG 59.907 38.462 0.00 0.00 31.65 2.67
2666 5210 7.385267 CCACCCATGTTTTCTAAAATGAATGA 58.615 34.615 0.00 0.00 31.65 2.57
2667 5211 8.042515 CCACCCATGTTTTCTAAAATGAATGAT 58.957 33.333 0.00 0.00 31.65 2.45
2742 5286 9.685276 TCCTTATTTCAAAGTGTATCATGATGT 57.315 29.630 18.72 0.00 0.00 3.06
2749 5293 9.628746 TTCAAAGTGTATCATGATGTTTCATTG 57.371 29.630 18.72 14.61 40.70 2.82
2750 5294 8.795513 TCAAAGTGTATCATGATGTTTCATTGT 58.204 29.630 18.72 2.27 40.70 2.71
2751 5295 8.856247 CAAAGTGTATCATGATGTTTCATTGTG 58.144 33.333 18.72 9.83 40.70 3.33
2752 5296 6.558009 AGTGTATCATGATGTTTCATTGTGC 58.442 36.000 18.72 0.00 40.70 4.57
2753 5297 6.151480 AGTGTATCATGATGTTTCATTGTGCA 59.849 34.615 18.72 0.00 40.70 4.57
2754 5298 6.252015 GTGTATCATGATGTTTCATTGTGCAC 59.748 38.462 18.72 10.75 40.70 4.57
2755 5299 4.177165 TCATGATGTTTCATTGTGCACC 57.823 40.909 15.69 0.00 40.70 5.01
2756 5300 3.056678 TCATGATGTTTCATTGTGCACCC 60.057 43.478 15.69 0.00 40.70 4.61
2757 5301 1.269174 TGATGTTTCATTGTGCACCCG 59.731 47.619 15.69 2.37 0.00 5.28
2758 5302 0.038343 ATGTTTCATTGTGCACCCGC 60.038 50.000 15.69 0.00 39.24 6.13
2770 5314 2.878906 GCACCCGCAAATTCATTTTG 57.121 45.000 0.00 0.00 46.22 2.44
2771 5315 2.411904 GCACCCGCAAATTCATTTTGA 58.588 42.857 2.42 0.00 46.36 2.69
2772 5316 2.157474 GCACCCGCAAATTCATTTTGAC 59.843 45.455 2.42 0.00 46.36 3.18
2773 5317 3.388308 CACCCGCAAATTCATTTTGACA 58.612 40.909 2.42 0.00 46.36 3.58
2774 5318 3.184178 CACCCGCAAATTCATTTTGACAC 59.816 43.478 2.42 0.00 46.36 3.67
2775 5319 3.181471 ACCCGCAAATTCATTTTGACACA 60.181 39.130 2.42 0.00 46.36 3.72
2776 5320 3.806521 CCCGCAAATTCATTTTGACACAA 59.193 39.130 2.42 0.00 46.36 3.33
2777 5321 4.084433 CCCGCAAATTCATTTTGACACAAG 60.084 41.667 2.42 0.00 46.36 3.16
2778 5322 4.507388 CCGCAAATTCATTTTGACACAAGT 59.493 37.500 2.42 0.00 46.36 3.16
2779 5323 5.425398 CGCAAATTCATTTTGACACAAGTG 58.575 37.500 0.00 0.00 46.36 3.16
2780 5324 5.199726 GCAAATTCATTTTGACACAAGTGC 58.800 37.500 0.00 0.00 46.36 4.40
2781 5325 5.220624 GCAAATTCATTTTGACACAAGTGCA 60.221 36.000 0.00 0.00 46.36 4.57
2782 5326 5.971895 AATTCATTTTGACACAAGTGCAC 57.028 34.783 9.40 9.40 0.00 4.57
2783 5327 4.446994 TTCATTTTGACACAAGTGCACA 57.553 36.364 21.04 0.00 0.00 4.57
2784 5328 4.652421 TCATTTTGACACAAGTGCACAT 57.348 36.364 21.04 3.48 0.00 3.21
2785 5329 4.609947 TCATTTTGACACAAGTGCACATC 58.390 39.130 21.04 8.69 0.00 3.06
2786 5330 4.338964 TCATTTTGACACAAGTGCACATCT 59.661 37.500 21.04 0.00 0.00 2.90
2787 5331 4.717233 TTTTGACACAAGTGCACATCTT 57.283 36.364 21.04 1.11 0.00 2.40
2788 5332 4.717233 TTTGACACAAGTGCACATCTTT 57.283 36.364 21.04 0.68 0.00 2.52
2789 5333 3.696281 TGACACAAGTGCACATCTTTG 57.304 42.857 21.04 16.57 0.00 2.77
2790 5334 3.016031 TGACACAAGTGCACATCTTTGT 58.984 40.909 21.04 17.24 36.15 2.83
2791 5335 3.443329 TGACACAAGTGCACATCTTTGTT 59.557 39.130 21.04 10.87 32.34 2.83
2792 5336 3.772932 ACACAAGTGCACATCTTTGTTG 58.227 40.909 21.04 14.74 32.34 3.33
2793 5337 3.117794 CACAAGTGCACATCTTTGTTGG 58.882 45.455 21.04 6.17 32.34 3.77
2794 5338 2.760092 ACAAGTGCACATCTTTGTTGGT 59.240 40.909 21.04 0.00 32.34 3.67
2795 5339 3.951037 ACAAGTGCACATCTTTGTTGGTA 59.049 39.130 21.04 0.00 32.34 3.25
2796 5340 4.202010 ACAAGTGCACATCTTTGTTGGTAC 60.202 41.667 21.04 0.00 32.34 3.34
2797 5341 3.550820 AGTGCACATCTTTGTTGGTACA 58.449 40.909 21.04 0.00 32.34 2.90
2798 5342 3.315191 AGTGCACATCTTTGTTGGTACAC 59.685 43.478 21.04 0.00 39.29 2.90
2799 5343 3.066064 GTGCACATCTTTGTTGGTACACA 59.934 43.478 13.17 0.00 39.29 3.72
2800 5344 3.696548 TGCACATCTTTGTTGGTACACAA 59.303 39.130 0.00 0.00 39.29 3.33
2816 5360 9.490379 TTGGTACACAACAAAACATTAAACTTT 57.510 25.926 0.00 0.00 39.29 2.66
2817 5361 8.926710 TGGTACACAACAAAACATTAAACTTTG 58.073 29.630 0.00 5.99 36.37 2.77
2818 5362 9.141400 GGTACACAACAAAACATTAAACTTTGA 57.859 29.630 11.90 0.00 34.76 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
428 429 3.074412 GACACATGTACCTGGTCCTTTG 58.926 50.000 0.63 0.00 0.00 2.77
466 469 1.299468 GTCACTCCGCTAGGCATCG 60.299 63.158 0.00 0.00 37.47 3.84
607 612 6.051717 GCTGAGAAGCTAGTTCATTATCCAA 58.948 40.000 0.00 0.00 37.67 3.53
712 717 7.008901 CACAACATATTCAGCAAACATGTCATC 59.991 37.037 0.00 0.00 0.00 2.92
929 938 9.107367 GAACATATATTAATTGCTTTCTCGTGC 57.893 33.333 0.00 0.00 0.00 5.34
1100 1110 2.358090 CCATTTTGGCCCTGATCACCTA 60.358 50.000 0.00 0.00 0.00 3.08
1480 1493 1.176527 CCGGTTGCATGATCTTTGGT 58.823 50.000 0.00 0.00 0.00 3.67
1892 1908 4.097892 ACATGGAACCAAGAAACAACACTC 59.902 41.667 3.07 0.00 0.00 3.51
2061 2183 4.025396 CAGCACTTGTACAGCAGCATATAC 60.025 45.833 14.99 0.00 30.85 1.47
2122 2371 6.652900 TCTTAGCAACAGCAACACATATACAA 59.347 34.615 0.00 0.00 0.00 2.41
2133 2382 2.951642 AGCACTTTCTTAGCAACAGCAA 59.048 40.909 0.00 0.00 0.00 3.91
2139 2388 3.694072 ACACAACAGCACTTTCTTAGCAA 59.306 39.130 0.00 0.00 0.00 3.91
2156 2408 1.336440 GCAACACCAGCACATACACAA 59.664 47.619 0.00 0.00 0.00 3.33
2482 5026 2.767394 CAGGGCCATGGAATTGAATTGA 59.233 45.455 18.40 0.00 0.00 2.57
2515 5059 1.067250 TCCCTTGCGCTTTGTTTGC 59.933 52.632 9.73 0.00 0.00 3.68
2534 5078 3.375642 AGTCATAGACGCATCAACGATG 58.624 45.455 0.00 0.00 42.37 3.84
2538 5082 6.863645 ACATGTATAGTCATAGACGCATCAAC 59.136 38.462 0.00 0.00 37.67 3.18
2539 5083 6.981722 ACATGTATAGTCATAGACGCATCAA 58.018 36.000 0.00 0.00 37.67 2.57
2540 5084 6.575162 ACATGTATAGTCATAGACGCATCA 57.425 37.500 0.00 0.00 37.67 3.07
2541 5085 8.237949 ACTTACATGTATAGTCATAGACGCATC 58.762 37.037 6.36 0.00 37.67 3.91
2542 5086 8.112016 ACTTACATGTATAGTCATAGACGCAT 57.888 34.615 6.36 0.00 37.67 4.73
2543 5087 7.227910 TGACTTACATGTATAGTCATAGACGCA 59.772 37.037 28.20 15.38 42.31 5.24
2544 5088 7.582352 TGACTTACATGTATAGTCATAGACGC 58.418 38.462 28.20 13.88 42.31 5.19
2560 5104 6.613271 AGATAGTTCCCACTCATGACTTACAT 59.387 38.462 0.00 0.00 35.53 2.29
2561 5105 5.958380 AGATAGTTCCCACTCATGACTTACA 59.042 40.000 0.00 0.00 34.06 2.41
2562 5106 6.472686 AGATAGTTCCCACTCATGACTTAC 57.527 41.667 0.00 0.00 34.06 2.34
2563 5107 7.583625 TCTAGATAGTTCCCACTCATGACTTA 58.416 38.462 0.00 0.00 34.06 2.24
2564 5108 6.436027 TCTAGATAGTTCCCACTCATGACTT 58.564 40.000 0.00 0.00 34.06 3.01
2565 5109 6.019656 TCTAGATAGTTCCCACTCATGACT 57.980 41.667 0.00 0.00 34.06 3.41
2566 5110 6.909550 ATCTAGATAGTTCCCACTCATGAC 57.090 41.667 2.53 0.00 34.06 3.06
2567 5111 9.029368 CATTATCTAGATAGTTCCCACTCATGA 57.971 37.037 12.16 0.00 34.06 3.07
2568 5112 9.029368 TCATTATCTAGATAGTTCCCACTCATG 57.971 37.037 12.16 9.24 34.06 3.07
2569 5113 9.781425 ATCATTATCTAGATAGTTCCCACTCAT 57.219 33.333 12.16 0.00 34.06 2.90
2570 5114 9.607333 AATCATTATCTAGATAGTTCCCACTCA 57.393 33.333 12.16 0.00 34.06 3.41
2596 5140 4.439974 GGAACACATGTCAGTGCAGAAAAA 60.440 41.667 0.00 0.00 43.23 1.94
2597 5141 3.066621 GGAACACATGTCAGTGCAGAAAA 59.933 43.478 0.00 0.00 43.23 2.29
2598 5142 2.618241 GGAACACATGTCAGTGCAGAAA 59.382 45.455 0.00 0.00 43.23 2.52
2599 5143 2.221169 GGAACACATGTCAGTGCAGAA 58.779 47.619 0.00 0.00 43.23 3.02
2600 5144 1.873486 CGGAACACATGTCAGTGCAGA 60.873 52.381 0.00 0.00 43.23 4.26
2601 5145 0.514255 CGGAACACATGTCAGTGCAG 59.486 55.000 0.00 0.00 43.23 4.41
2602 5146 0.179059 ACGGAACACATGTCAGTGCA 60.179 50.000 0.00 0.00 43.23 4.57
2603 5147 0.512952 GACGGAACACATGTCAGTGC 59.487 55.000 0.00 0.00 43.23 4.40
2604 5148 0.784178 CGACGGAACACATGTCAGTG 59.216 55.000 0.00 0.00 44.93 3.66
2605 5149 0.944311 GCGACGGAACACATGTCAGT 60.944 55.000 0.00 0.00 32.91 3.41
2606 5150 0.667487 AGCGACGGAACACATGTCAG 60.667 55.000 0.00 0.00 32.91 3.51
2607 5151 0.599060 TAGCGACGGAACACATGTCA 59.401 50.000 0.00 0.00 32.91 3.58
2608 5152 1.922570 ATAGCGACGGAACACATGTC 58.077 50.000 0.00 0.00 0.00 3.06
2609 5153 1.999735 CAATAGCGACGGAACACATGT 59.000 47.619 0.00 0.00 0.00 3.21
2610 5154 1.999735 ACAATAGCGACGGAACACATG 59.000 47.619 0.00 0.00 0.00 3.21
2611 5155 1.999735 CACAATAGCGACGGAACACAT 59.000 47.619 0.00 0.00 0.00 3.21
2612 5156 1.000052 TCACAATAGCGACGGAACACA 60.000 47.619 0.00 0.00 0.00 3.72
2613 5157 1.654105 CTCACAATAGCGACGGAACAC 59.346 52.381 0.00 0.00 0.00 3.32
2614 5158 1.542472 TCTCACAATAGCGACGGAACA 59.458 47.619 0.00 0.00 0.00 3.18
2615 5159 2.273370 TCTCACAATAGCGACGGAAC 57.727 50.000 0.00 0.00 0.00 3.62
2616 5160 2.223735 GGATCTCACAATAGCGACGGAA 60.224 50.000 0.00 0.00 0.00 4.30
2617 5161 1.337071 GGATCTCACAATAGCGACGGA 59.663 52.381 0.00 0.00 0.00 4.69
2618 5162 1.772182 GGATCTCACAATAGCGACGG 58.228 55.000 0.00 0.00 0.00 4.79
2619 5163 1.268589 ACGGATCTCACAATAGCGACG 60.269 52.381 0.00 0.00 0.00 5.12
2620 5164 2.120232 CACGGATCTCACAATAGCGAC 58.880 52.381 0.00 0.00 0.00 5.19
2621 5165 1.536072 GCACGGATCTCACAATAGCGA 60.536 52.381 0.00 0.00 0.00 4.93
2622 5166 0.855349 GCACGGATCTCACAATAGCG 59.145 55.000 0.00 0.00 0.00 4.26
2623 5167 1.221414 GGCACGGATCTCACAATAGC 58.779 55.000 0.00 0.00 0.00 2.97
2624 5168 2.205074 GTGGCACGGATCTCACAATAG 58.795 52.381 0.00 0.00 0.00 1.73
2625 5169 1.134521 GGTGGCACGGATCTCACAATA 60.135 52.381 12.17 0.00 32.29 1.90
2626 5170 0.392998 GGTGGCACGGATCTCACAAT 60.393 55.000 12.17 0.00 32.29 2.71
2627 5171 1.003839 GGTGGCACGGATCTCACAA 60.004 57.895 12.17 0.00 32.29 3.33
2628 5172 2.662596 GGTGGCACGGATCTCACA 59.337 61.111 12.17 0.00 32.29 3.58
2629 5173 2.125106 GGGTGGCACGGATCTCAC 60.125 66.667 12.17 0.00 0.00 3.51
2630 5174 1.995066 ATGGGTGGCACGGATCTCA 60.995 57.895 12.17 3.50 0.00 3.27
2631 5175 1.524621 CATGGGTGGCACGGATCTC 60.525 63.158 12.17 0.00 0.00 2.75
2632 5176 1.852157 AACATGGGTGGCACGGATCT 61.852 55.000 12.17 0.00 0.00 2.75
2633 5177 0.965363 AAACATGGGTGGCACGGATC 60.965 55.000 12.17 1.91 0.00 3.36
2634 5178 0.541764 AAAACATGGGTGGCACGGAT 60.542 50.000 12.17 2.72 0.00 4.18
2635 5179 1.152652 AAAACATGGGTGGCACGGA 60.153 52.632 12.17 0.00 0.00 4.69
2636 5180 1.178534 AGAAAACATGGGTGGCACGG 61.179 55.000 12.17 3.67 0.00 4.94
2637 5181 1.529226 TAGAAAACATGGGTGGCACG 58.471 50.000 12.17 0.00 0.00 5.34
2638 5182 4.329462 TTTTAGAAAACATGGGTGGCAC 57.671 40.909 9.70 9.70 0.00 5.01
2639 5183 4.590647 TCATTTTAGAAAACATGGGTGGCA 59.409 37.500 0.00 0.00 0.00 4.92
2640 5184 5.146010 TCATTTTAGAAAACATGGGTGGC 57.854 39.130 0.00 0.00 0.00 5.01
2641 5185 7.385267 TCATTCATTTTAGAAAACATGGGTGG 58.615 34.615 0.00 0.00 0.00 4.61
2716 5260 9.685276 ACATCATGATACACTTTGAAATAAGGA 57.315 29.630 8.15 0.00 0.00 3.36
2723 5267 9.628746 CAATGAAACATCATGATACACTTTGAA 57.371 29.630 8.15 0.00 0.00 2.69
2724 5268 8.795513 ACAATGAAACATCATGATACACTTTGA 58.204 29.630 8.15 0.00 0.00 2.69
2725 5269 8.856247 CACAATGAAACATCATGATACACTTTG 58.144 33.333 8.15 14.82 0.00 2.77
2726 5270 7.543172 GCACAATGAAACATCATGATACACTTT 59.457 33.333 8.15 3.98 0.00 2.66
2727 5271 7.031372 GCACAATGAAACATCATGATACACTT 58.969 34.615 8.15 0.00 0.00 3.16
2728 5272 6.151480 TGCACAATGAAACATCATGATACACT 59.849 34.615 8.15 0.00 0.00 3.55
2729 5273 6.252015 GTGCACAATGAAACATCATGATACAC 59.748 38.462 13.17 1.55 0.00 2.90
2730 5274 6.324042 GTGCACAATGAAACATCATGATACA 58.676 36.000 13.17 7.13 0.00 2.29
2731 5275 5.745294 GGTGCACAATGAAACATCATGATAC 59.255 40.000 20.43 0.00 0.00 2.24
2732 5276 5.163530 GGGTGCACAATGAAACATCATGATA 60.164 40.000 20.43 0.00 0.00 2.15
2733 5277 4.382254 GGGTGCACAATGAAACATCATGAT 60.382 41.667 20.43 1.18 0.00 2.45
2734 5278 3.056678 GGGTGCACAATGAAACATCATGA 60.057 43.478 20.43 0.00 0.00 3.07
2735 5279 3.255725 GGGTGCACAATGAAACATCATG 58.744 45.455 20.43 0.00 0.00 3.07
2736 5280 2.094597 CGGGTGCACAATGAAACATCAT 60.095 45.455 20.43 0.00 0.00 2.45
2737 5281 1.269174 CGGGTGCACAATGAAACATCA 59.731 47.619 20.43 0.00 0.00 3.07
2738 5282 1.981254 CGGGTGCACAATGAAACATC 58.019 50.000 20.43 0.00 0.00 3.06
2739 5283 0.038343 GCGGGTGCACAATGAAACAT 60.038 50.000 20.43 0.00 42.15 2.71
2740 5284 1.361993 GCGGGTGCACAATGAAACA 59.638 52.632 20.43 0.00 42.15 2.83
2741 5285 4.243383 GCGGGTGCACAATGAAAC 57.757 55.556 20.43 0.00 42.15 2.78
2751 5295 2.157474 GTCAAAATGAATTTGCGGGTGC 59.843 45.455 0.00 0.00 46.53 5.01
2752 5296 3.184178 GTGTCAAAATGAATTTGCGGGTG 59.816 43.478 0.00 0.00 46.53 4.61
2753 5297 3.181471 TGTGTCAAAATGAATTTGCGGGT 60.181 39.130 0.00 0.00 46.53 5.28
2754 5298 3.388308 TGTGTCAAAATGAATTTGCGGG 58.612 40.909 0.00 0.00 46.53 6.13
2755 5299 4.507388 ACTTGTGTCAAAATGAATTTGCGG 59.493 37.500 0.00 0.00 46.53 5.69
2756 5300 5.425398 CACTTGTGTCAAAATGAATTTGCG 58.575 37.500 0.00 0.00 46.53 4.85
2757 5301 5.199726 GCACTTGTGTCAAAATGAATTTGC 58.800 37.500 2.61 0.00 46.53 3.68
2759 5303 5.873712 TGTGCACTTGTGTCAAAATGAATTT 59.126 32.000 19.41 0.00 0.00 1.82
2760 5304 5.417811 TGTGCACTTGTGTCAAAATGAATT 58.582 33.333 19.41 0.00 0.00 2.17
2761 5305 5.008619 TGTGCACTTGTGTCAAAATGAAT 57.991 34.783 19.41 0.00 0.00 2.57
2762 5306 4.446994 TGTGCACTTGTGTCAAAATGAA 57.553 36.364 19.41 0.00 0.00 2.57
2763 5307 4.338964 AGATGTGCACTTGTGTCAAAATGA 59.661 37.500 19.41 0.00 0.00 2.57
2764 5308 4.613944 AGATGTGCACTTGTGTCAAAATG 58.386 39.130 19.41 0.00 0.00 2.32
2765 5309 4.924305 AGATGTGCACTTGTGTCAAAAT 57.076 36.364 19.41 0.00 0.00 1.82
2766 5310 4.717233 AAGATGTGCACTTGTGTCAAAA 57.283 36.364 19.41 0.00 0.00 2.44
2767 5311 4.082300 ACAAAGATGTGCACTTGTGTCAAA 60.082 37.500 19.41 0.00 38.69 2.69
2768 5312 3.443329 ACAAAGATGTGCACTTGTGTCAA 59.557 39.130 19.41 0.00 38.69 3.18
2769 5313 3.016031 ACAAAGATGTGCACTTGTGTCA 58.984 40.909 19.41 0.00 38.69 3.58
2770 5314 3.698029 ACAAAGATGTGCACTTGTGTC 57.302 42.857 19.41 8.31 38.69 3.67
2771 5315 3.429272 CCAACAAAGATGTGCACTTGTGT 60.429 43.478 19.29 12.88 40.46 3.72
2772 5316 3.117794 CCAACAAAGATGTGCACTTGTG 58.882 45.455 19.29 12.34 40.46 3.33
2773 5317 2.760092 ACCAACAAAGATGTGCACTTGT 59.240 40.909 19.41 16.58 40.46 3.16
2774 5318 3.441496 ACCAACAAAGATGTGCACTTG 57.559 42.857 19.41 15.92 40.46 3.16
2775 5319 3.951037 TGTACCAACAAAGATGTGCACTT 59.049 39.130 19.41 12.28 40.46 3.16
2776 5320 3.315191 GTGTACCAACAAAGATGTGCACT 59.685 43.478 19.41 3.19 40.46 4.40
2777 5321 3.066064 TGTGTACCAACAAAGATGTGCAC 59.934 43.478 10.75 10.75 42.35 4.57
2778 5322 3.282885 TGTGTACCAACAAAGATGTGCA 58.717 40.909 0.00 0.00 40.46 4.57
2779 5323 3.980646 TGTGTACCAACAAAGATGTGC 57.019 42.857 0.00 0.00 40.46 4.57
2790 5334 9.490379 AAAGTTTAATGTTTTGTTGTGTACCAA 57.510 25.926 0.00 0.00 0.00 3.67
2791 5335 8.926710 CAAAGTTTAATGTTTTGTTGTGTACCA 58.073 29.630 0.00 0.00 0.00 3.25
2792 5336 9.141400 TCAAAGTTTAATGTTTTGTTGTGTACC 57.859 29.630 0.00 0.00 34.35 3.34


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

AutoCloner maintained by Alex Coulton.