Multiple sequence alignment - TraesCS5D01G254900

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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 TraesCS5D01G254900 chr5D 100.000 3179 0 0 1 3179 361405953 361402775 0.000000e+00 5871.0
1 TraesCS5D01G254900 chr5D 89.474 57 3 2 2568 2622 532806402 532806457 5.690000e-08 69.4
2 TraesCS5D01G254900 chr5A 90.555 2488 147 43 1 2434 461940033 461937580 0.000000e+00 3212.0
3 TraesCS5D01G254900 chr5A 88.889 450 19 14 2001 2427 461932642 461932201 2.810000e-145 525.0
4 TraesCS5D01G254900 chr5A 91.477 352 27 1 2831 3179 464133988 464133637 6.170000e-132 481.0
5 TraesCS5D01G254900 chr5A 89.224 232 19 4 2570 2799 464134214 464133987 5.190000e-73 285.0
6 TraesCS5D01G254900 chr5A 85.430 151 15 2 1875 2024 428809490 428809346 1.980000e-32 150.0
7 TraesCS5D01G254900 chr5B 89.682 1919 96 51 499 2384 426995466 426993617 0.000000e+00 2353.0
8 TraesCS5D01G254900 chr3D 94.498 618 27 5 2566 3179 580319311 580319925 0.000000e+00 946.0
9 TraesCS5D01G254900 chr3D 80.119 1343 159 52 898 2189 587608115 587609400 0.000000e+00 902.0
10 TraesCS5D01G254900 chr3A 83.088 1088 112 30 1144 2189 716988170 716989227 0.000000e+00 924.0
11 TraesCS5D01G254900 chr6B 92.557 618 32 5 2567 3179 162618762 162619370 0.000000e+00 874.0
12 TraesCS5D01G254900 chr6B 78.750 640 93 29 1289 1899 152108732 152108107 3.850000e-104 388.0
13 TraesCS5D01G254900 chr1B 92.084 619 35 6 2566 3179 15207127 15207736 0.000000e+00 859.0
14 TraesCS5D01G254900 chr3B 94.343 495 20 6 2568 3058 784527231 784527721 0.000000e+00 752.0
15 TraesCS5D01G254900 chr3B 93.535 495 24 4 2568 3058 784456094 784456584 0.000000e+00 730.0
16 TraesCS5D01G254900 chr3B 81.001 779 88 22 1434 2189 784926604 784927345 5.950000e-157 564.0
17 TraesCS5D01G254900 chr3B 80.610 557 59 25 922 1444 784925598 784926139 4.970000e-103 385.0
18 TraesCS5D01G254900 chr3B 92.045 88 7 0 3092 3179 784456584 784456671 1.200000e-24 124.0
19 TraesCS5D01G254900 chr7D 75.278 449 75 25 1126 1549 131269803 131269366 7.000000e-42 182.0
20 TraesCS5D01G254900 chr7D 87.324 71 3 5 2566 2633 46850785 46850852 3.400000e-10 76.8
21 TraesCS5D01G254900 chr4A 92.913 127 6 3 2069 2192 2701376 2701502 7.000000e-42 182.0
22 TraesCS5D01G254900 chr2A 91.339 127 8 2 2069 2192 614570545 614570671 1.520000e-38 171.0
23 TraesCS5D01G254900 chr7A 74.236 458 76 29 1126 1549 130091934 130091485 1.530000e-33 154.0
24 TraesCS5D01G254900 chr7B 81.215 181 27 5 1369 1549 92063165 92062992 4.280000e-29 139.0
25 TraesCS5D01G254900 chr7B 88.525 61 1 6 2566 2622 351005797 351005855 5.690000e-08 69.4
26 TraesCS5D01G254900 chr4D 97.059 34 1 0 2478 2511 473169704 473169737 1.230000e-04 58.4


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 TraesCS5D01G254900 chr5D 361402775 361405953 3178 True 5871.0 5871 100.0000 1 3179 1 chr5D.!!$R1 3178
1 TraesCS5D01G254900 chr5A 461937580 461940033 2453 True 3212.0 3212 90.5550 1 2434 1 chr5A.!!$R3 2433
2 TraesCS5D01G254900 chr5A 464133637 464134214 577 True 383.0 481 90.3505 2570 3179 2 chr5A.!!$R4 609
3 TraesCS5D01G254900 chr5B 426993617 426995466 1849 True 2353.0 2353 89.6820 499 2384 1 chr5B.!!$R1 1885
4 TraesCS5D01G254900 chr3D 580319311 580319925 614 False 946.0 946 94.4980 2566 3179 1 chr3D.!!$F1 613
5 TraesCS5D01G254900 chr3D 587608115 587609400 1285 False 902.0 902 80.1190 898 2189 1 chr3D.!!$F2 1291
6 TraesCS5D01G254900 chr3A 716988170 716989227 1057 False 924.0 924 83.0880 1144 2189 1 chr3A.!!$F1 1045
7 TraesCS5D01G254900 chr6B 162618762 162619370 608 False 874.0 874 92.5570 2567 3179 1 chr6B.!!$F1 612
8 TraesCS5D01G254900 chr6B 152108107 152108732 625 True 388.0 388 78.7500 1289 1899 1 chr6B.!!$R1 610
9 TraesCS5D01G254900 chr1B 15207127 15207736 609 False 859.0 859 92.0840 2566 3179 1 chr1B.!!$F1 613
10 TraesCS5D01G254900 chr3B 784925598 784927345 1747 False 474.5 564 80.8055 922 2189 2 chr3B.!!$F3 1267
11 TraesCS5D01G254900 chr3B 784456094 784456671 577 False 427.0 730 92.7900 2568 3179 2 chr3B.!!$F2 611

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
450 452 0.034756 AGCATGGCGAGTGTGTGTAA 59.965 50.0 0.00 0.00 0.0 2.41 F
895 920 0.852777 ATATAAACGCGCTGCACTCG 59.147 50.0 5.73 2.34 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2169 2800 0.236449 CCCGGTCAAACTAAACACGC 59.764 55.0 0.0 0.0 0.0 5.34 R
2466 3125 0.251121 TTCGGTGGTTCATGGTGCAT 60.251 50.0 0.0 0.0 0.0 3.96 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 9.305555 AGTAGTACCAGTAGACACATTTCTAAA 57.694 33.333 0.00 0.00 29.70 1.85
106 108 1.214424 GGTACCCACAGCCATAACCAT 59.786 52.381 0.00 0.00 0.00 3.55
112 114 3.371487 CCCACAGCCATAACCATAGAACA 60.371 47.826 0.00 0.00 0.00 3.18
224 226 1.408422 GGCTTTGTGCAAACTAAGCG 58.592 50.000 15.35 0.00 44.97 4.68
254 256 6.778069 TCAGATGATTAGGTTCCTACTAGTGG 59.222 42.308 5.39 1.52 0.00 4.00
255 257 6.015010 CAGATGATTAGGTTCCTACTAGTGGG 60.015 46.154 18.89 18.89 0.00 4.61
288 290 3.763897 CAGGGTTTTAATCCCAGACTTGG 59.236 47.826 13.04 0.00 46.82 3.61
291 293 3.056821 GGTTTTAATCCCAGACTTGGCAC 60.057 47.826 0.00 0.00 43.58 5.01
292 294 3.806949 TTTAATCCCAGACTTGGCACT 57.193 42.857 0.00 0.00 43.58 4.40
293 295 2.787473 TAATCCCAGACTTGGCACTG 57.213 50.000 0.00 0.00 43.58 3.66
297 299 1.149174 CCAGACTTGGCACTGGTGT 59.851 57.895 13.10 0.00 45.82 4.16
300 302 0.546122 AGACTTGGCACTGGTGTTCA 59.454 50.000 2.64 0.00 0.00 3.18
364 366 6.562825 CGTTTTCTTAGTGGGAGTAAACGTTC 60.563 42.308 15.69 0.00 44.99 3.95
365 367 5.796424 TTCTTAGTGGGAGTAAACGTTCT 57.204 39.130 0.00 0.00 0.00 3.01
386 388 2.502163 TCGACAACGAAGAACGCAG 58.498 52.632 0.00 0.00 45.74 5.18
387 389 0.937699 TCGACAACGAAGAACGCAGG 60.938 55.000 0.00 0.00 45.74 4.85
391 393 1.663702 AACGAAGAACGCAGGGTCG 60.664 57.895 0.00 0.00 46.94 4.79
398 400 0.526524 GAACGCAGGGTCGATCTCAG 60.527 60.000 0.00 0.00 0.00 3.35
400 402 0.965866 ACGCAGGGTCGATCTCAGAA 60.966 55.000 0.00 0.00 0.00 3.02
405 407 3.181475 GCAGGGTCGATCTCAGAATGTTA 60.181 47.826 0.00 0.00 37.40 2.41
430 432 6.717540 AGACCATATCTCGAAAGTGCTATAGT 59.282 38.462 0.84 0.00 28.16 2.12
448 450 0.670546 GTAGCATGGCGAGTGTGTGT 60.671 55.000 0.00 0.00 0.00 3.72
449 451 0.892063 TAGCATGGCGAGTGTGTGTA 59.108 50.000 0.00 0.00 0.00 2.90
450 452 0.034756 AGCATGGCGAGTGTGTGTAA 59.965 50.000 0.00 0.00 0.00 2.41
451 453 0.871722 GCATGGCGAGTGTGTGTAAA 59.128 50.000 0.00 0.00 0.00 2.01
455 459 2.566913 TGGCGAGTGTGTGTAAATGTT 58.433 42.857 0.00 0.00 0.00 2.71
468 472 5.048364 TGTGTAAATGTTTGTGGGCATCTAC 60.048 40.000 0.00 0.00 0.00 2.59
473 477 2.746904 TGTTTGTGGGCATCTACGATTG 59.253 45.455 0.00 0.00 0.00 2.67
475 479 2.022764 TGTGGGCATCTACGATTGTG 57.977 50.000 0.00 0.00 0.00 3.33
476 480 1.277842 TGTGGGCATCTACGATTGTGT 59.722 47.619 0.00 0.00 0.00 3.72
479 483 2.290008 TGGGCATCTACGATTGTGTTGT 60.290 45.455 0.00 0.00 0.00 3.32
484 488 6.259167 GGGCATCTACGATTGTGTTGTATTAA 59.741 38.462 0.00 0.00 0.00 1.40
485 489 7.201661 GGGCATCTACGATTGTGTTGTATTAAA 60.202 37.037 0.00 0.00 0.00 1.52
487 491 9.210426 GCATCTACGATTGTGTTGTATTAAAAG 57.790 33.333 0.00 0.00 0.00 2.27
521 525 5.600696 ACAAACATGAGTTTTGCTTTAGGG 58.399 37.500 0.00 0.00 45.32 3.53
560 564 2.022240 GCCCCCGTGCACTTCAAAAA 62.022 55.000 16.19 0.00 0.00 1.94
592 596 6.294176 GCACACTTAATTCTGTCATTTGACCT 60.294 38.462 8.16 0.00 44.15 3.85
624 628 1.949525 CCCCCGCATGAAAGTATGAAG 59.050 52.381 0.00 0.00 0.00 3.02
654 658 7.599998 GCACCATTCAAGATGTAAAAGACAAAT 59.400 33.333 0.00 0.00 42.78 2.32
658 662 9.903682 CATTCAAGATGTAAAAGACAAATGAGT 57.096 29.630 0.00 0.00 42.78 3.41
725 732 2.451132 CACTACTCCATTCGCTACGTG 58.549 52.381 0.00 0.00 0.00 4.49
759 766 2.775032 TTCGCGGTGGACCTAGCAAC 62.775 60.000 6.13 0.00 0.00 4.17
782 789 3.322466 ACCCTTCCCGCTCCACAG 61.322 66.667 0.00 0.00 0.00 3.66
783 790 3.322466 CCCTTCCCGCTCCACAGT 61.322 66.667 0.00 0.00 0.00 3.55
784 791 2.266055 CCTTCCCGCTCCACAGTC 59.734 66.667 0.00 0.00 0.00 3.51
785 792 2.266055 CTTCCCGCTCCACAGTCC 59.734 66.667 0.00 0.00 0.00 3.85
786 793 2.525629 TTCCCGCTCCACAGTCCA 60.526 61.111 0.00 0.00 0.00 4.02
787 794 2.788191 CTTCCCGCTCCACAGTCCAC 62.788 65.000 0.00 0.00 0.00 4.02
788 795 3.625897 CCCGCTCCACAGTCCACA 61.626 66.667 0.00 0.00 0.00 4.17
795 802 1.223211 CCACAGTCCACACACACCA 59.777 57.895 0.00 0.00 0.00 4.17
797 804 1.016627 CACAGTCCACACACACCAAG 58.983 55.000 0.00 0.00 0.00 3.61
805 812 2.415357 CCACACACACCAAGAACAACAC 60.415 50.000 0.00 0.00 0.00 3.32
814 830 4.638421 CACCAAGAACAACACCTACTCAAA 59.362 41.667 0.00 0.00 0.00 2.69
856 881 2.187946 GGCCGTCATCCACCTCTG 59.812 66.667 0.00 0.00 0.00 3.35
860 885 1.599047 CGTCATCCACCTCTGCCTT 59.401 57.895 0.00 0.00 0.00 4.35
865 890 1.558756 CATCCACCTCTGCCTTCTTCT 59.441 52.381 0.00 0.00 0.00 2.85
866 891 1.270907 TCCACCTCTGCCTTCTTCTC 58.729 55.000 0.00 0.00 0.00 2.87
895 920 0.852777 ATATAAACGCGCTGCACTCG 59.147 50.000 5.73 2.34 0.00 4.18
933 959 3.486383 TCCCAGTTCACAACTCCATTTC 58.514 45.455 0.00 0.00 40.46 2.17
1047 1085 1.761667 CCTCTGGCTCCTCCTCCTG 60.762 68.421 0.00 0.00 35.26 3.86
1049 1087 3.478274 CTGGCTCCTCCTCCTGGC 61.478 72.222 0.00 0.00 35.26 4.85
1098 1136 2.359975 CAGAACCAGAACCCGCCC 60.360 66.667 0.00 0.00 0.00 6.13
2257 2899 0.660300 CGGCTGTTGCTTTCCGTTTC 60.660 55.000 0.00 0.00 39.59 2.78
2258 2900 0.660300 GGCTGTTGCTTTCCGTTTCG 60.660 55.000 0.00 0.00 39.59 3.46
2259 2901 0.306533 GCTGTTGCTTTCCGTTTCGA 59.693 50.000 0.00 0.00 36.03 3.71
2260 2902 1.069227 GCTGTTGCTTTCCGTTTCGAT 60.069 47.619 0.00 0.00 36.03 3.59
2261 2903 2.604614 GCTGTTGCTTTCCGTTTCGATT 60.605 45.455 0.00 0.00 36.03 3.34
2262 2904 3.226347 CTGTTGCTTTCCGTTTCGATTC 58.774 45.455 0.00 0.00 0.00 2.52
2396 3053 6.791303 TCACACACAAAACATTAAAGGAGAC 58.209 36.000 0.00 0.00 0.00 3.36
2423 3082 9.635404 ATTCCTATCAATTTTATCCGGTTTGTA 57.365 29.630 0.00 0.00 0.00 2.41
2429 3088 8.458573 TCAATTTTATCCGGTTTGTAGCATAT 57.541 30.769 0.00 0.00 0.00 1.78
2434 3093 2.237643 TCCGGTTTGTAGCATATGGTGT 59.762 45.455 17.58 0.00 0.00 4.16
2435 3094 3.013921 CCGGTTTGTAGCATATGGTGTT 58.986 45.455 17.58 0.00 0.00 3.32
2436 3095 3.442273 CCGGTTTGTAGCATATGGTGTTT 59.558 43.478 17.58 0.00 0.00 2.83
2437 3096 4.082463 CCGGTTTGTAGCATATGGTGTTTT 60.082 41.667 17.58 0.00 0.00 2.43
2438 3097 5.465935 CGGTTTGTAGCATATGGTGTTTTT 58.534 37.500 17.58 0.00 0.00 1.94
2482 3141 5.789643 ATAAATATGCACCATGAACCACC 57.210 39.130 0.00 0.00 0.00 4.61
2483 3142 1.679139 ATATGCACCATGAACCACCG 58.321 50.000 0.00 0.00 0.00 4.94
2484 3143 0.615850 TATGCACCATGAACCACCGA 59.384 50.000 0.00 0.00 0.00 4.69
2485 3144 0.251121 ATGCACCATGAACCACCGAA 60.251 50.000 0.00 0.00 0.00 4.30
2486 3145 1.169661 TGCACCATGAACCACCGAAC 61.170 55.000 0.00 0.00 0.00 3.95
2487 3146 1.866237 CACCATGAACCACCGAACG 59.134 57.895 0.00 0.00 0.00 3.95
2488 3147 1.302192 ACCATGAACCACCGAACGG 60.302 57.895 11.83 11.83 42.03 4.44
2489 3148 2.686816 CCATGAACCACCGAACGGC 61.687 63.158 13.32 0.00 39.32 5.68
2490 3149 2.359478 ATGAACCACCGAACGGCC 60.359 61.111 13.32 0.00 39.32 6.13
2491 3150 3.185299 ATGAACCACCGAACGGCCA 62.185 57.895 13.32 4.60 39.32 5.36
2492 3151 3.351416 GAACCACCGAACGGCCAC 61.351 66.667 13.32 0.00 39.32 5.01
2493 3152 3.819877 GAACCACCGAACGGCCACT 62.820 63.158 13.32 0.00 39.32 4.00
2494 3153 2.438951 GAACCACCGAACGGCCACTA 62.439 60.000 13.32 0.00 39.32 2.74
2495 3154 2.433664 CCACCGAACGGCCACTAC 60.434 66.667 13.32 0.00 39.32 2.73
2496 3155 2.433664 CACCGAACGGCCACTACC 60.434 66.667 13.32 0.00 39.32 3.18
2506 3165 4.077184 CCACTACCGCCGGCAGAA 62.077 66.667 28.98 9.50 0.00 3.02
2507 3166 2.186903 CACTACCGCCGGCAGAAT 59.813 61.111 28.98 10.73 0.00 2.40
2508 3167 2.173669 CACTACCGCCGGCAGAATG 61.174 63.158 28.98 13.66 40.87 2.67
2509 3168 2.355986 ACTACCGCCGGCAGAATGA 61.356 57.895 28.98 3.63 39.69 2.57
2510 3169 1.592669 CTACCGCCGGCAGAATGAG 60.593 63.158 28.98 10.24 39.69 2.90
2511 3170 3.733344 TACCGCCGGCAGAATGAGC 62.733 63.158 28.98 0.00 39.69 4.26
2517 3176 2.184322 GGCAGAATGAGCCGACGA 59.816 61.111 0.00 0.00 43.15 4.20
2518 3177 2.167861 GGCAGAATGAGCCGACGAC 61.168 63.158 0.00 0.00 43.15 4.34
2519 3178 2.508891 GCAGAATGAGCCGACGACG 61.509 63.158 0.00 0.00 39.69 5.12
2520 3179 2.202623 AGAATGAGCCGACGACGC 60.203 61.111 0.64 0.00 38.29 5.19
2521 3180 2.202623 GAATGAGCCGACGACGCT 60.203 61.111 0.64 2.80 38.29 5.07
2522 3181 2.202623 AATGAGCCGACGACGCTC 60.203 61.111 16.33 16.33 40.33 5.03
2523 3182 3.701604 AATGAGCCGACGACGCTCC 62.702 63.158 19.20 6.26 39.73 4.70
2528 3187 4.175489 CCGACGACGCTCCGATGT 62.175 66.667 0.64 0.00 38.29 3.06
2529 3188 2.648102 CGACGACGCTCCGATGTC 60.648 66.667 0.00 0.00 33.82 3.06
2530 3189 2.483745 GACGACGCTCCGATGTCA 59.516 61.111 0.00 0.00 35.78 3.58
2531 3190 1.868251 GACGACGCTCCGATGTCAC 60.868 63.158 0.00 0.00 35.78 3.67
2532 3191 2.944557 CGACGCTCCGATGTCACG 60.945 66.667 0.00 0.00 34.78 4.35
2539 3198 2.264480 CCGATGTCACGGCTTCCA 59.736 61.111 0.00 0.00 46.20 3.53
2540 3199 1.153369 CCGATGTCACGGCTTCCAT 60.153 57.895 0.00 0.00 46.20 3.41
2541 3200 0.104120 CCGATGTCACGGCTTCCATA 59.896 55.000 0.00 0.00 46.20 2.74
2542 3201 1.270305 CCGATGTCACGGCTTCCATAT 60.270 52.381 0.00 0.00 46.20 1.78
2543 3202 2.061773 CGATGTCACGGCTTCCATATC 58.938 52.381 0.00 0.00 0.00 1.63
2544 3203 2.061773 GATGTCACGGCTTCCATATCG 58.938 52.381 0.00 0.00 0.00 2.92
2545 3204 1.107945 TGTCACGGCTTCCATATCGA 58.892 50.000 0.00 0.00 0.00 3.59
2546 3205 1.478916 TGTCACGGCTTCCATATCGAA 59.521 47.619 0.00 0.00 0.00 3.71
2547 3206 2.128035 GTCACGGCTTCCATATCGAAG 58.872 52.381 5.77 5.77 41.88 3.79
2553 3212 1.517242 CTTCCATATCGAAGCCAGCC 58.483 55.000 0.00 0.00 33.33 4.85
2554 3213 1.071385 CTTCCATATCGAAGCCAGCCT 59.929 52.381 0.00 0.00 33.33 4.58
2555 3214 0.394192 TCCATATCGAAGCCAGCCTG 59.606 55.000 0.00 0.00 0.00 4.85
2556 3215 0.394192 CCATATCGAAGCCAGCCTGA 59.606 55.000 0.00 0.00 0.00 3.86
2557 3216 1.506493 CATATCGAAGCCAGCCTGAC 58.494 55.000 0.00 0.00 0.00 3.51
2558 3217 0.394565 ATATCGAAGCCAGCCTGACC 59.605 55.000 0.00 0.00 0.00 4.02
2559 3218 0.687757 TATCGAAGCCAGCCTGACCT 60.688 55.000 0.00 0.00 0.00 3.85
2560 3219 1.557269 ATCGAAGCCAGCCTGACCTT 61.557 55.000 0.00 0.00 0.00 3.50
2561 3220 2.037136 CGAAGCCAGCCTGACCTTG 61.037 63.158 0.00 0.00 0.00 3.61
2562 3221 1.073897 GAAGCCAGCCTGACCTTGT 59.926 57.895 0.00 0.00 0.00 3.16
2563 3222 0.538287 GAAGCCAGCCTGACCTTGTT 60.538 55.000 0.00 0.00 0.00 2.83
2564 3223 0.825010 AAGCCAGCCTGACCTTGTTG 60.825 55.000 0.00 0.00 0.00 3.33
2651 3311 2.317530 GGCCCACCTTATCCCTTCA 58.682 57.895 0.00 0.00 0.00 3.02
2676 3336 3.057245 GGTGTCTTCTTCCTCAATTTGCC 60.057 47.826 0.00 0.00 0.00 4.52
2702 3362 1.305930 CCTTTTCCCCTTCTTCGCCG 61.306 60.000 0.00 0.00 0.00 6.46
2703 3363 1.923227 CTTTTCCCCTTCTTCGCCGC 61.923 60.000 0.00 0.00 0.00 6.53
2704 3364 2.406002 TTTTCCCCTTCTTCGCCGCT 62.406 55.000 0.00 0.00 0.00 5.52
2705 3365 1.546589 TTTCCCCTTCTTCGCCGCTA 61.547 55.000 0.00 0.00 0.00 4.26
2706 3366 1.335132 TTCCCCTTCTTCGCCGCTAT 61.335 55.000 0.00 0.00 0.00 2.97
2707 3367 0.468585 TCCCCTTCTTCGCCGCTATA 60.469 55.000 0.00 0.00 0.00 1.31
2964 3627 0.388659 GTGGAACCATGTTTGCTGCA 59.611 50.000 0.00 0.00 0.00 4.41
2973 3636 1.377987 GTTTGCTGCATACCCCGGA 60.378 57.895 0.73 0.00 0.00 5.14
3098 3762 1.122019 AGTTGTCCTGCGAGGGAAGT 61.122 55.000 0.00 0.00 37.10 3.01
3101 3765 1.371558 GTCCTGCGAGGGAAGTTGT 59.628 57.895 0.00 0.00 37.10 3.32
3130 3794 4.935352 ATGCAAGAAAAGCTACAACCAA 57.065 36.364 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 8.874744 TTAGAAATGTGTCTACTGGTACTACT 57.125 34.615 0.00 0.00 29.70 2.57
88 90 3.659841 TCTATGGTTATGGCTGTGGGTA 58.340 45.455 0.00 0.00 0.00 3.69
103 105 6.829229 ATCATATGCCACAATGTTCTATGG 57.171 37.500 0.00 0.00 35.17 2.74
214 216 4.424626 TCATCTGAGCTACGCTTAGTTTG 58.575 43.478 7.39 7.08 41.93 2.93
215 217 4.720649 TCATCTGAGCTACGCTTAGTTT 57.279 40.909 7.39 0.00 41.93 2.66
224 226 5.799827 AGGAACCTAATCATCTGAGCTAC 57.200 43.478 0.00 0.00 0.00 3.58
230 232 6.015010 CCCACTAGTAGGAACCTAATCATCTG 60.015 46.154 0.22 0.00 0.00 2.90
264 266 2.993863 AGTCTGGGATTAAAACCCTGGT 59.006 45.455 19.81 10.54 46.82 4.00
270 272 3.826729 AGTGCCAAGTCTGGGATTAAAAC 59.173 43.478 0.00 0.00 45.98 2.43
273 275 2.290896 CCAGTGCCAAGTCTGGGATTAA 60.291 50.000 0.00 0.00 45.98 1.40
332 334 4.515361 TCCCACTAAGAAAACGTTGACAA 58.485 39.130 0.00 0.00 0.00 3.18
334 336 4.124970 ACTCCCACTAAGAAAACGTTGAC 58.875 43.478 0.00 0.00 0.00 3.18
335 337 4.411256 ACTCCCACTAAGAAAACGTTGA 57.589 40.909 0.00 0.00 0.00 3.18
336 338 6.424683 GTTTACTCCCACTAAGAAAACGTTG 58.575 40.000 0.00 0.00 0.00 4.10
337 339 5.234972 CGTTTACTCCCACTAAGAAAACGTT 59.765 40.000 0.00 0.00 41.42 3.99
338 340 4.746611 CGTTTACTCCCACTAAGAAAACGT 59.253 41.667 8.74 0.00 41.42 3.99
339 341 5.260027 CGTTTACTCCCACTAAGAAAACG 57.740 43.478 0.00 0.00 40.83 3.60
340 342 6.481313 AGAACGTTTACTCCCACTAAGAAAAC 59.519 38.462 0.46 0.00 0.00 2.43
343 345 5.563475 CGAGAACGTTTACTCCCACTAAGAA 60.563 44.000 0.46 0.00 34.56 2.52
344 346 4.083110 CGAGAACGTTTACTCCCACTAAGA 60.083 45.833 0.46 0.00 34.56 2.10
345 347 4.164294 CGAGAACGTTTACTCCCACTAAG 58.836 47.826 0.46 0.00 34.56 2.18
346 348 4.164822 CGAGAACGTTTACTCCCACTAA 57.835 45.455 0.46 0.00 34.56 2.24
382 384 0.387202 ATTCTGAGATCGACCCTGCG 59.613 55.000 0.00 0.00 0.00 5.18
386 388 4.500035 GGTCTAACATTCTGAGATCGACCC 60.500 50.000 0.00 0.00 33.96 4.46
387 389 4.098044 TGGTCTAACATTCTGAGATCGACC 59.902 45.833 0.00 0.00 39.00 4.79
391 393 7.967854 CGAGATATGGTCTAACATTCTGAGATC 59.032 40.741 0.00 0.00 37.29 2.75
398 400 7.306866 GCACTTTCGAGATATGGTCTAACATTC 60.307 40.741 0.00 0.00 37.29 2.67
400 402 5.986135 GCACTTTCGAGATATGGTCTAACAT 59.014 40.000 0.00 0.00 37.29 2.71
405 407 6.717540 ACTATAGCACTTTCGAGATATGGTCT 59.282 38.462 0.00 0.00 40.81 3.85
430 432 0.892063 TACACACACTCGCCATGCTA 59.108 50.000 0.00 0.00 0.00 3.49
435 437 2.248280 ACATTTACACACACTCGCCA 57.752 45.000 0.00 0.00 0.00 5.69
438 440 4.278858 CCACAAACATTTACACACACTCG 58.721 43.478 0.00 0.00 0.00 4.18
448 450 4.580868 TCGTAGATGCCCACAAACATTTA 58.419 39.130 0.00 0.00 0.00 1.40
449 451 3.417101 TCGTAGATGCCCACAAACATTT 58.583 40.909 0.00 0.00 0.00 2.32
450 452 3.066291 TCGTAGATGCCCACAAACATT 57.934 42.857 0.00 0.00 0.00 2.71
451 453 2.779755 TCGTAGATGCCCACAAACAT 57.220 45.000 0.00 0.00 0.00 2.71
455 459 2.290008 ACACAATCGTAGATGCCCACAA 60.290 45.455 0.00 0.00 45.12 3.33
488 492 9.553418 GCAAAACTCATGTTTGTTTGTTTTTAT 57.447 25.926 12.28 0.00 44.70 1.40
490 494 7.647228 AGCAAAACTCATGTTTGTTTGTTTTT 58.353 26.923 12.28 0.00 44.70 1.94
491 495 7.200778 AGCAAAACTCATGTTTGTTTGTTTT 57.799 28.000 12.28 0.00 44.70 2.43
492 496 6.799926 AGCAAAACTCATGTTTGTTTGTTT 57.200 29.167 12.28 0.00 44.70 2.83
493 497 6.799926 AAGCAAAACTCATGTTTGTTTGTT 57.200 29.167 8.06 4.03 44.70 2.83
494 498 6.799926 AAAGCAAAACTCATGTTTGTTTGT 57.200 29.167 9.18 0.80 44.70 2.83
495 499 7.401080 CCTAAAGCAAAACTCATGTTTGTTTG 58.599 34.615 9.18 8.84 44.70 2.93
496 500 6.538381 CCCTAAAGCAAAACTCATGTTTGTTT 59.462 34.615 8.54 6.40 44.70 2.83
497 501 6.048509 CCCTAAAGCAAAACTCATGTTTGTT 58.951 36.000 8.54 1.16 44.70 2.83
507 511 2.235891 CCGGTTCCCTAAAGCAAAACT 58.764 47.619 0.00 0.00 34.98 2.66
509 513 2.362717 CAACCGGTTCCCTAAAGCAAAA 59.637 45.455 19.24 0.00 34.98 2.44
521 525 1.302271 GAGTGACCCCAACCGGTTC 60.302 63.158 19.24 6.56 35.79 3.62
592 596 0.840617 TGCGGGGGTCATATGCTTTA 59.159 50.000 0.00 0.00 0.00 1.85
624 628 4.782019 TTACATCTTGAATGGTGCCAAC 57.218 40.909 0.00 0.00 0.00 3.77
725 732 1.736249 GCGAATTCATTGCTGCACGC 61.736 55.000 14.13 14.13 38.23 5.34
782 789 1.745232 TGTTCTTGGTGTGTGTGGAC 58.255 50.000 0.00 0.00 0.00 4.02
783 790 2.088423 GTTGTTCTTGGTGTGTGTGGA 58.912 47.619 0.00 0.00 0.00 4.02
784 791 1.815613 TGTTGTTCTTGGTGTGTGTGG 59.184 47.619 0.00 0.00 0.00 4.17
785 792 2.415357 GGTGTTGTTCTTGGTGTGTGTG 60.415 50.000 0.00 0.00 0.00 3.82
786 793 1.816224 GGTGTTGTTCTTGGTGTGTGT 59.184 47.619 0.00 0.00 0.00 3.72
787 794 2.091541 AGGTGTTGTTCTTGGTGTGTG 58.908 47.619 0.00 0.00 0.00 3.82
788 795 2.507407 AGGTGTTGTTCTTGGTGTGT 57.493 45.000 0.00 0.00 0.00 3.72
821 846 1.066454 GCCGGCTTGTTGTTGTACTTT 59.934 47.619 22.15 0.00 0.00 2.66
822 847 0.666374 GCCGGCTTGTTGTTGTACTT 59.334 50.000 22.15 0.00 0.00 2.24
829 854 3.842925 ATGACGGCCGGCTTGTTGT 62.843 57.895 34.65 16.81 0.00 3.32
856 881 2.663826 ACGTGAGATGAGAAGAAGGC 57.336 50.000 0.00 0.00 0.00 4.35
860 885 7.076362 GCGTTTATATACGTGAGATGAGAAGA 58.924 38.462 15.58 0.00 43.22 2.87
933 959 3.768633 AGCTGACGCTTTATGGGAG 57.231 52.632 0.00 0.00 46.47 4.30
995 1030 4.875713 GTGCCGGCCCCATCGATT 62.876 66.667 26.77 0.00 0.00 3.34
2169 2800 0.236449 CCCGGTCAAACTAAACACGC 59.764 55.000 0.00 0.00 0.00 5.34
2224 2861 2.282180 GCCGTTTCCTTCCCAGCA 60.282 61.111 0.00 0.00 0.00 4.41
2225 2862 2.034221 AGCCGTTTCCTTCCCAGC 59.966 61.111 0.00 0.00 0.00 4.85
2226 2863 0.537371 AACAGCCGTTTCCTTCCCAG 60.537 55.000 0.00 0.00 28.09 4.45
2257 2899 1.940613 GAAATTCCACCGGGAGAATCG 59.059 52.381 18.31 0.00 46.01 3.34
2258 2900 3.118223 AGAGAAATTCCACCGGGAGAATC 60.118 47.826 18.31 10.27 46.01 2.52
2259 2901 2.846827 AGAGAAATTCCACCGGGAGAAT 59.153 45.455 13.76 13.76 46.01 2.40
2260 2902 2.027192 CAGAGAAATTCCACCGGGAGAA 60.027 50.000 6.32 8.84 46.01 2.87
2261 2903 1.555075 CAGAGAAATTCCACCGGGAGA 59.445 52.381 6.32 0.00 46.01 3.71
2262 2904 2.014068 GCAGAGAAATTCCACCGGGAG 61.014 57.143 6.32 0.00 46.01 4.30
2372 3027 6.375736 TGTCTCCTTTAATGTTTTGTGTGTGA 59.624 34.615 0.00 0.00 0.00 3.58
2373 3028 6.559810 TGTCTCCTTTAATGTTTTGTGTGTG 58.440 36.000 0.00 0.00 0.00 3.82
2374 3029 6.767524 TGTCTCCTTTAATGTTTTGTGTGT 57.232 33.333 0.00 0.00 0.00 3.72
2396 3053 8.413229 ACAAACCGGATAAAATTGATAGGAATG 58.587 33.333 9.46 0.00 0.00 2.67
2415 3072 4.695217 AAACACCATATGCTACAAACCG 57.305 40.909 0.00 0.00 0.00 4.44
2456 3115 9.019656 GGTGGTTCATGGTGCATATTTATAATA 57.980 33.333 0.00 0.00 0.00 0.98
2457 3116 7.309133 CGGTGGTTCATGGTGCATATTTATAAT 60.309 37.037 0.00 0.00 0.00 1.28
2458 3117 6.016693 CGGTGGTTCATGGTGCATATTTATAA 60.017 38.462 0.00 0.00 0.00 0.98
2459 3118 5.471797 CGGTGGTTCATGGTGCATATTTATA 59.528 40.000 0.00 0.00 0.00 0.98
2460 3119 4.278170 CGGTGGTTCATGGTGCATATTTAT 59.722 41.667 0.00 0.00 0.00 1.40
2461 3120 3.629855 CGGTGGTTCATGGTGCATATTTA 59.370 43.478 0.00 0.00 0.00 1.40
2462 3121 2.426738 CGGTGGTTCATGGTGCATATTT 59.573 45.455 0.00 0.00 0.00 1.40
2463 3122 2.023673 CGGTGGTTCATGGTGCATATT 58.976 47.619 0.00 0.00 0.00 1.28
2464 3123 1.211703 TCGGTGGTTCATGGTGCATAT 59.788 47.619 0.00 0.00 0.00 1.78
2465 3124 0.615850 TCGGTGGTTCATGGTGCATA 59.384 50.000 0.00 0.00 0.00 3.14
2466 3125 0.251121 TTCGGTGGTTCATGGTGCAT 60.251 50.000 0.00 0.00 0.00 3.96
2467 3126 1.149401 TTCGGTGGTTCATGGTGCA 59.851 52.632 0.00 0.00 0.00 4.57
2468 3127 1.579429 GTTCGGTGGTTCATGGTGC 59.421 57.895 0.00 0.00 0.00 5.01
2469 3128 1.573829 CCGTTCGGTGGTTCATGGTG 61.574 60.000 2.82 0.00 0.00 4.17
2470 3129 1.302192 CCGTTCGGTGGTTCATGGT 60.302 57.895 2.82 0.00 0.00 3.55
2471 3130 2.686816 GCCGTTCGGTGGTTCATGG 61.687 63.158 12.81 0.00 0.00 3.66
2472 3131 2.686816 GGCCGTTCGGTGGTTCATG 61.687 63.158 12.81 0.00 0.00 3.07
2473 3132 2.359478 GGCCGTTCGGTGGTTCAT 60.359 61.111 12.81 0.00 0.00 2.57
2474 3133 3.862991 TGGCCGTTCGGTGGTTCA 61.863 61.111 12.81 2.16 0.00 3.18
2475 3134 2.438951 TAGTGGCCGTTCGGTGGTTC 62.439 60.000 12.81 0.00 0.00 3.62
2476 3135 2.509651 TAGTGGCCGTTCGGTGGTT 61.510 57.895 12.81 0.41 0.00 3.67
2477 3136 2.918802 TAGTGGCCGTTCGGTGGT 60.919 61.111 12.81 0.00 0.00 4.16
2478 3137 2.433664 GTAGTGGCCGTTCGGTGG 60.434 66.667 12.81 0.00 0.00 4.61
2479 3138 2.433664 GGTAGTGGCCGTTCGGTG 60.434 66.667 12.81 0.00 0.00 4.94
2480 3139 4.060038 CGGTAGTGGCCGTTCGGT 62.060 66.667 12.81 0.00 46.11 4.69
2489 3148 3.385749 ATTCTGCCGGCGGTAGTGG 62.386 63.158 36.81 18.44 36.77 4.00
2490 3149 2.173669 CATTCTGCCGGCGGTAGTG 61.174 63.158 36.81 27.05 36.77 2.74
2491 3150 2.186903 CATTCTGCCGGCGGTAGT 59.813 61.111 36.81 20.94 36.77 2.73
2492 3151 1.592669 CTCATTCTGCCGGCGGTAG 60.593 63.158 34.25 34.25 36.75 3.18
2493 3152 2.499205 CTCATTCTGCCGGCGGTA 59.501 61.111 33.59 26.02 0.00 4.02
2500 3159 2.167861 GTCGTCGGCTCATTCTGCC 61.168 63.158 0.00 0.00 46.42 4.85
2501 3160 2.508891 CGTCGTCGGCTCATTCTGC 61.509 63.158 0.00 0.00 0.00 4.26
2502 3161 2.508891 GCGTCGTCGGCTCATTCTG 61.509 63.158 3.90 0.00 37.56 3.02
2503 3162 2.202623 GCGTCGTCGGCTCATTCT 60.203 61.111 3.90 0.00 37.56 2.40
2504 3163 2.202623 AGCGTCGTCGGCTCATTC 60.203 61.111 3.90 0.00 37.56 2.67
2505 3164 2.202623 GAGCGTCGTCGGCTCATT 60.203 61.111 15.83 0.00 38.78 2.57
2506 3165 4.194720 GGAGCGTCGTCGGCTCAT 62.195 66.667 20.39 0.00 39.78 2.90
2511 3170 4.175489 ACATCGGAGCGTCGTCGG 62.175 66.667 3.90 0.00 37.56 4.79
2512 3171 2.648102 GACATCGGAGCGTCGTCG 60.648 66.667 0.00 0.00 40.37 5.12
2513 3172 1.868251 GTGACATCGGAGCGTCGTC 60.868 63.158 0.00 0.00 33.35 4.20
2514 3173 2.178521 GTGACATCGGAGCGTCGT 59.821 61.111 0.00 0.00 33.35 4.34
2515 3174 2.944557 CGTGACATCGGAGCGTCG 60.945 66.667 6.03 0.00 33.35 5.12
2523 3182 2.061773 GATATGGAAGCCGTGACATCG 58.938 52.381 0.00 0.00 0.00 3.84
2524 3183 2.061773 CGATATGGAAGCCGTGACATC 58.938 52.381 0.00 0.00 0.00 3.06
2525 3184 1.686587 TCGATATGGAAGCCGTGACAT 59.313 47.619 0.00 0.00 0.00 3.06
2526 3185 1.107945 TCGATATGGAAGCCGTGACA 58.892 50.000 0.00 0.00 0.00 3.58
2527 3186 2.128035 CTTCGATATGGAAGCCGTGAC 58.872 52.381 13.66 0.00 37.24 3.67
2528 3187 2.509052 CTTCGATATGGAAGCCGTGA 57.491 50.000 13.66 0.00 37.24 4.35
2534 3193 1.071385 AGGCTGGCTTCGATATGGAAG 59.929 52.381 19.88 19.88 44.92 3.46
2535 3194 1.131638 AGGCTGGCTTCGATATGGAA 58.868 50.000 0.00 0.00 0.00 3.53
2536 3195 0.394192 CAGGCTGGCTTCGATATGGA 59.606 55.000 6.61 0.00 0.00 3.41
2537 3196 0.394192 TCAGGCTGGCTTCGATATGG 59.606 55.000 15.73 0.00 0.00 2.74
2538 3197 1.506493 GTCAGGCTGGCTTCGATATG 58.494 55.000 12.82 0.00 0.00 1.78
2539 3198 0.394565 GGTCAGGCTGGCTTCGATAT 59.605 55.000 19.90 0.00 0.00 1.63
2540 3199 0.687757 AGGTCAGGCTGGCTTCGATA 60.688 55.000 19.90 0.00 0.00 2.92
2541 3200 1.557269 AAGGTCAGGCTGGCTTCGAT 61.557 55.000 19.90 0.00 0.00 3.59
2542 3201 2.217038 AAGGTCAGGCTGGCTTCGA 61.217 57.895 19.90 0.00 0.00 3.71
2543 3202 2.037136 CAAGGTCAGGCTGGCTTCG 61.037 63.158 19.90 0.00 0.00 3.79
2544 3203 0.538287 AACAAGGTCAGGCTGGCTTC 60.538 55.000 19.90 2.82 0.00 3.86
2545 3204 0.825010 CAACAAGGTCAGGCTGGCTT 60.825 55.000 19.90 8.87 0.00 4.35
2546 3205 1.228367 CAACAAGGTCAGGCTGGCT 60.228 57.895 19.90 0.00 0.00 4.75
2547 3206 0.610232 ATCAACAAGGTCAGGCTGGC 60.610 55.000 15.73 13.70 0.00 4.85
2548 3207 2.636830 CTATCAACAAGGTCAGGCTGG 58.363 52.381 15.73 0.00 0.00 4.85
2549 3208 2.636830 CCTATCAACAAGGTCAGGCTG 58.363 52.381 8.58 8.58 0.00 4.85
2550 3209 1.561542 CCCTATCAACAAGGTCAGGCT 59.438 52.381 0.00 0.00 31.70 4.58
2551 3210 1.559682 TCCCTATCAACAAGGTCAGGC 59.440 52.381 0.00 0.00 31.70 4.85
2552 3211 4.010349 GTTTCCCTATCAACAAGGTCAGG 58.990 47.826 0.00 0.00 31.70 3.86
2553 3212 3.684788 CGTTTCCCTATCAACAAGGTCAG 59.315 47.826 0.00 0.00 31.70 3.51
2554 3213 3.071892 ACGTTTCCCTATCAACAAGGTCA 59.928 43.478 0.00 0.00 31.70 4.02
2555 3214 3.671716 ACGTTTCCCTATCAACAAGGTC 58.328 45.455 0.00 0.00 31.70 3.85
2556 3215 3.782656 ACGTTTCCCTATCAACAAGGT 57.217 42.857 0.00 0.00 31.70 3.50
2557 3216 5.704053 AGTAAACGTTTCCCTATCAACAAGG 59.296 40.000 18.42 0.00 0.00 3.61
2558 3217 6.796705 AGTAAACGTTTCCCTATCAACAAG 57.203 37.500 18.42 0.00 0.00 3.16
2559 3218 6.365789 CGTAGTAAACGTTTCCCTATCAACAA 59.634 38.462 18.42 0.00 46.72 2.83
2560 3219 5.863397 CGTAGTAAACGTTTCCCTATCAACA 59.137 40.000 18.42 0.00 46.72 3.33
2561 3220 6.323197 CGTAGTAAACGTTTCCCTATCAAC 57.677 41.667 18.42 7.50 46.72 3.18
2651 3311 4.664688 AATTGAGGAAGAAGACACCCAT 57.335 40.909 0.00 0.00 0.00 4.00
2676 3336 0.393132 GAAGGGGAAAAGGAGAGGCG 60.393 60.000 0.00 0.00 0.00 5.52
2702 3362 4.250116 AGCTAGCGCATGGATATATAGC 57.750 45.455 11.47 10.86 39.10 2.97
2703 3363 6.319141 TGTAGCTAGCGCATGGATATATAG 57.681 41.667 11.47 0.00 39.10 1.31
2704 3364 6.096282 TGTTGTAGCTAGCGCATGGATATATA 59.904 38.462 11.47 0.00 39.10 0.86
2705 3365 5.105351 TGTTGTAGCTAGCGCATGGATATAT 60.105 40.000 11.47 0.00 39.10 0.86
2706 3366 4.219725 TGTTGTAGCTAGCGCATGGATATA 59.780 41.667 11.47 0.00 39.10 0.86
2707 3367 3.006859 TGTTGTAGCTAGCGCATGGATAT 59.993 43.478 11.47 0.00 39.10 1.63
2776 3436 0.757188 CGGATGTGAGAGGGGCTAGT 60.757 60.000 0.00 0.00 0.00 2.57
2976 3639 0.689412 TCTCCGGTGATGCATGGGTA 60.689 55.000 2.46 0.00 0.00 3.69
3076 3740 2.583441 CCCTCGCAGGACAACTCCA 61.583 63.158 4.00 0.00 37.67 3.86
3098 3762 2.284754 TTCTTGCATACAGGGCACAA 57.715 45.000 0.00 0.00 41.75 3.33
3101 3765 1.545582 GCTTTTCTTGCATACAGGGCA 59.454 47.619 0.00 0.00 40.00 5.36
3130 3794 2.721167 TTCTAGCTCCGCCGCATGT 61.721 57.895 0.00 0.00 0.00 3.21
3145 3809 2.661718 ACATTTTCCACCGTTGGTTCT 58.338 42.857 0.00 0.00 44.35 3.01


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

AutoCloner maintained by Alex Coulton.