Multiple sequence alignment - TraesCS5A01G264600

Loading Multiple Alignment...

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 TraesCS5A01G264600 chr5A 100.000 3666 0 0 1 3666 476757909 476761574 0.000000e+00 6770.0
1 TraesCS5A01G264600 chr5A 82.258 1240 118 55 1553 2750 476770389 476771568 0.000000e+00 977.0
2 TraesCS5A01G264600 chr5A 90.061 654 39 15 3032 3666 476818129 476818775 0.000000e+00 824.0
3 TraesCS5A01G264600 chr5A 81.001 1079 140 36 497 1536 476769280 476770332 0.000000e+00 797.0
4 TraesCS5A01G264600 chr5A 86.802 197 13 5 60 256 476769097 476769280 1.330000e-49 207.0
5 TraesCS5A01G264600 chr5A 89.691 97 6 3 2952 3044 476816785 476816881 1.790000e-23 121.0
6 TraesCS5A01G264600 chr5B 89.921 2153 133 39 60 2156 448302809 448304933 0.000000e+00 2697.0
7 TraesCS5A01G264600 chr5B 86.505 1445 105 44 2241 3665 448305610 448306984 0.000000e+00 1506.0
8 TraesCS5A01G264600 chr5B 92.448 768 39 10 2913 3666 448446968 448447730 0.000000e+00 1079.0
9 TraesCS5A01G264600 chr5B 87.768 793 62 19 2903 3666 448441411 448442197 0.000000e+00 894.0
10 TraesCS5A01G264600 chr5B 85.119 336 29 11 2412 2737 448440806 448441130 1.270000e-84 324.0
11 TraesCS5A01G264600 chr5B 89.655 58 6 0 2142 2199 448305479 448305536 1.410000e-09 75.0
12 TraesCS5A01G264600 chr5D 91.273 1249 72 17 1553 2794 375453034 375454252 0.000000e+00 1668.0
13 TraesCS5A01G264600 chr5D 82.686 1623 142 52 1 1536 375451407 375452977 0.000000e+00 1312.0
14 TraesCS5A01G264600 chr5D 87.414 874 72 25 2817 3666 375578150 375579009 0.000000e+00 970.0
15 TraesCS5A01G264600 chr5D 91.010 723 43 11 2961 3665 375464742 375465460 0.000000e+00 955.0
16 TraesCS5A01G264600 chr5D 93.410 607 32 3 1553 2156 375590903 375591504 0.000000e+00 893.0
17 TraesCS5A01G264600 chr5D 94.296 561 22 7 3107 3666 375592395 375592946 0.000000e+00 850.0
18 TraesCS5A01G264600 chr5D 91.321 530 38 5 1553 2077 375577516 375578042 0.000000e+00 717.0
19 TraesCS5A01G264600 chr5D 92.141 509 32 5 1553 2056 375590339 375590844 0.000000e+00 712.0
20 TraesCS5A01G264600 chr5D 82.019 862 111 24 700 1537 375589446 375590287 0.000000e+00 693.0
21 TraesCS5A01G264600 chr5D 86.192 478 52 8 1072 1537 375576989 375577464 4.220000e-139 505.0
22 TraesCS5A01G264600 chr5D 82.111 559 36 26 2121 2633 375591503 375592043 1.570000e-113 420.0
23 TraesCS5A01G264600 chr5D 81.746 378 30 24 2683 3052 375592044 375592390 2.790000e-71 279.0
24 TraesCS5A01G264600 chr5D 80.000 150 15 9 97 233 375588851 375588998 3.010000e-16 97.1
25 TraesCS5A01G264600 chr5D 90.164 61 3 2 2923 2982 375464673 375464731 3.930000e-10 76.8
26 TraesCS5A01G264600 chr6D 86.120 317 39 4 2290 2605 84558870 84559182 1.630000e-88 337.0
27 TraesCS5A01G264600 chr6D 89.641 251 22 2 1893 2143 84555744 84555990 2.120000e-82 316.0
28 TraesCS5A01G264600 chr6D 92.473 93 7 0 2140 2232 84558494 84558586 2.300000e-27 134.0
29 TraesCS5A01G264600 chr6D 92.308 65 4 1 817 881 374765896 374765833 1.400000e-14 91.6
30 TraesCS5A01G264600 chr6D 90.000 60 4 2 817 876 455466730 455466787 3.930000e-10 76.8
31 TraesCS5A01G264600 chr3A 89.320 103 9 2 614 715 184644076 184643975 1.070000e-25 128.0
32 TraesCS5A01G264600 chr3B 92.308 65 4 1 817 881 328606263 328606326 1.400000e-14 91.6
33 TraesCS5A01G264600 chr7B 90.769 65 5 1 817 881 394822411 394822348 6.520000e-13 86.1
34 TraesCS5A01G264600 chr7A 90.769 65 5 1 817 881 679418050 679418113 6.520000e-13 86.1
35 TraesCS5A01G264600 chr2B 90.769 65 5 1 817 881 118089625 118089562 6.520000e-13 86.1


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 TraesCS5A01G264600 chr5A 476757909 476761574 3665 False 6770.000000 6770 100.000000 1 3666 1 chr5A.!!$F1 3665
1 TraesCS5A01G264600 chr5A 476769097 476771568 2471 False 660.333333 977 83.353667 60 2750 3 chr5A.!!$F2 2690
2 TraesCS5A01G264600 chr5A 476816785 476818775 1990 False 472.500000 824 89.876000 2952 3666 2 chr5A.!!$F3 714
3 TraesCS5A01G264600 chr5B 448302809 448306984 4175 False 1426.000000 2697 88.693667 60 3665 3 chr5B.!!$F2 3605
4 TraesCS5A01G264600 chr5B 448446968 448447730 762 False 1079.000000 1079 92.448000 2913 3666 1 chr5B.!!$F1 753
5 TraesCS5A01G264600 chr5B 448440806 448442197 1391 False 609.000000 894 86.443500 2412 3666 2 chr5B.!!$F3 1254
6 TraesCS5A01G264600 chr5D 375451407 375454252 2845 False 1490.000000 1668 86.979500 1 2794 2 chr5D.!!$F1 2793
7 TraesCS5A01G264600 chr5D 375576989 375579009 2020 False 730.666667 970 88.309000 1072 3666 3 chr5D.!!$F3 2594
8 TraesCS5A01G264600 chr5D 375588851 375592946 4095 False 563.442857 893 86.531857 97 3666 7 chr5D.!!$F4 3569
9 TraesCS5A01G264600 chr5D 375464673 375465460 787 False 515.900000 955 90.587000 2923 3665 2 chr5D.!!$F2 742
10 TraesCS5A01G264600 chr6D 84555744 84559182 3438 False 262.333333 337 89.411333 1893 2605 3 chr6D.!!$F2 712

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
808 1190 0.038166 ATTCTGGGACATGCGTTGGT 59.962 50.000 0.0 0.0 38.2 3.67 F
809 1191 0.605319 TTCTGGGACATGCGTTGGTC 60.605 55.000 0.0 0.0 38.2 4.02 F
810 1192 1.003355 CTGGGACATGCGTTGGTCT 60.003 57.895 0.0 0.0 38.2 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1826 2294 1.200484 GTTCAGTCTCTGTCCGTCTCC 59.800 57.143 0.00 0.0 32.61 3.71 R
2530 6866 1.806623 GCGATCGCTATCAAACCACCT 60.807 52.381 31.94 0.0 38.26 4.00 R
2676 7012 3.445008 ACTATCTGGTTTCTGAGCTCCA 58.555 45.455 12.15 0.0 0.00 3.86 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
44 46 3.636929 ATTCGCCATGGCCCGTCAA 62.637 57.895 30.79 15.43 37.98 3.18
54 56 4.410400 CCCGTCAAGAGCCCACCC 62.410 72.222 0.00 0.00 0.00 4.61
55 57 3.636231 CCGTCAAGAGCCCACCCA 61.636 66.667 0.00 0.00 0.00 4.51
58 60 1.302832 GTCAAGAGCCCACCCACAG 60.303 63.158 0.00 0.00 0.00 3.66
93 112 3.090532 ACCAATCCCCTCCGCCTC 61.091 66.667 0.00 0.00 0.00 4.70
94 113 2.770048 CCAATCCCCTCCGCCTCT 60.770 66.667 0.00 0.00 0.00 3.69
95 114 2.507944 CAATCCCCTCCGCCTCTG 59.492 66.667 0.00 0.00 0.00 3.35
96 115 3.483869 AATCCCCTCCGCCTCTGC 61.484 66.667 0.00 0.00 0.00 4.26
177 232 2.515071 GCCCCATCCTCGCATCTCT 61.515 63.158 0.00 0.00 0.00 3.10
234 316 0.107945 GCCTGAAGGTGCGAATCTCT 60.108 55.000 0.00 0.00 37.57 3.10
244 326 3.103637 CGAATCTCTCGGTCCCTCT 57.896 57.895 0.00 0.00 44.20 3.69
264 351 0.817654 GGTGTCTAATTTGGGCTGCC 59.182 55.000 11.05 11.05 0.00 4.85
281 368 1.145945 TGCCCCCAAACAATCTGTACA 59.854 47.619 0.00 0.00 0.00 2.90
283 370 2.831526 GCCCCCAAACAATCTGTACAAT 59.168 45.455 0.00 0.00 0.00 2.71
284 371 4.020543 GCCCCCAAACAATCTGTACAATA 58.979 43.478 0.00 0.00 0.00 1.90
285 372 4.142249 GCCCCCAAACAATCTGTACAATAC 60.142 45.833 0.00 0.00 0.00 1.89
286 373 4.401202 CCCCCAAACAATCTGTACAATACC 59.599 45.833 0.00 0.00 0.00 2.73
287 374 5.261216 CCCCAAACAATCTGTACAATACCT 58.739 41.667 0.00 0.00 0.00 3.08
288 375 5.714806 CCCCAAACAATCTGTACAATACCTT 59.285 40.000 0.00 0.00 0.00 3.50
291 378 7.827236 CCCAAACAATCTGTACAATACCTTCTA 59.173 37.037 0.00 0.00 0.00 2.10
292 379 9.396022 CCAAACAATCTGTACAATACCTTCTAT 57.604 33.333 0.00 0.00 0.00 1.98
298 394 7.891498 TCTGTACAATACCTTCTATAGTGCA 57.109 36.000 0.00 0.00 0.00 4.57
300 396 6.812998 TGTACAATACCTTCTATAGTGCACC 58.187 40.000 14.63 0.00 0.00 5.01
308 404 3.520290 TCTATAGTGCACCGGAACTTG 57.480 47.619 14.63 0.00 33.80 3.16
311 407 4.891168 TCTATAGTGCACCGGAACTTGATA 59.109 41.667 14.63 4.04 33.80 2.15
312 408 2.851263 AGTGCACCGGAACTTGATAA 57.149 45.000 14.63 0.00 22.78 1.75
315 415 4.189231 AGTGCACCGGAACTTGATAATAC 58.811 43.478 14.63 0.00 22.78 1.89
321 421 3.493503 CCGGAACTTGATAATACGAAGCC 59.506 47.826 0.00 0.00 0.00 4.35
329 429 7.155328 ACTTGATAATACGAAGCCTAGATTGG 58.845 38.462 0.00 0.00 0.00 3.16
359 459 2.665185 GGTCCGGTGCTGTGTGTC 60.665 66.667 0.00 0.00 0.00 3.67
376 476 5.985530 TGTGTGTCATCTTTTGAGTACTCAG 59.014 40.000 23.97 14.00 41.13 3.35
377 477 5.406780 GTGTGTCATCTTTTGAGTACTCAGG 59.593 44.000 23.97 17.71 41.13 3.86
388 488 1.341531 AGTACTCAGGTGCAGTGTGTC 59.658 52.381 6.91 1.74 0.00 3.67
404 504 0.178932 TGTCTACTGGCCAGGTGACT 60.179 55.000 37.08 23.29 46.44 3.41
409 509 2.789409 ACTGGCCAGGTGACTTTATC 57.211 50.000 35.42 0.00 40.21 1.75
411 511 2.644798 ACTGGCCAGGTGACTTTATCTT 59.355 45.455 35.42 7.81 40.21 2.40
416 516 3.935828 GCCAGGTGACTTTATCTTCTGTC 59.064 47.826 0.00 0.00 40.21 3.51
417 517 4.177026 CCAGGTGACTTTATCTTCTGTCG 58.823 47.826 0.00 0.00 40.21 4.35
418 518 4.082190 CCAGGTGACTTTATCTTCTGTCGA 60.082 45.833 0.00 0.00 40.21 4.20
419 519 5.394663 CCAGGTGACTTTATCTTCTGTCGAT 60.395 44.000 0.00 0.00 40.21 3.59
420 520 6.183360 CCAGGTGACTTTATCTTCTGTCGATA 60.183 42.308 0.00 0.00 40.21 2.92
421 521 7.258441 CAGGTGACTTTATCTTCTGTCGATAA 58.742 38.462 0.00 0.00 40.21 1.75
422 522 7.221067 CAGGTGACTTTATCTTCTGTCGATAAC 59.779 40.741 0.00 0.00 40.21 1.89
423 523 7.033791 GGTGACTTTATCTTCTGTCGATAACA 58.966 38.462 0.00 0.00 34.18 2.41
435 535 3.615056 TGTCGATAACAGTTGCCATAACG 59.385 43.478 0.00 0.00 32.81 3.18
436 536 3.861113 GTCGATAACAGTTGCCATAACGA 59.139 43.478 0.00 0.00 0.00 3.85
437 537 4.506654 GTCGATAACAGTTGCCATAACGAT 59.493 41.667 0.00 0.00 0.00 3.73
438 538 4.506288 TCGATAACAGTTGCCATAACGATG 59.494 41.667 0.00 0.00 0.00 3.84
480 581 1.936547 GCATAGAGCTCGGTTTTCTGG 59.063 52.381 8.37 0.00 41.15 3.86
482 583 3.430374 GCATAGAGCTCGGTTTTCTGGTA 60.430 47.826 8.37 0.00 41.15 3.25
490 591 4.151867 GCTCGGTTTTCTGGTAACTAGTTG 59.848 45.833 18.56 1.24 37.61 3.16
560 912 8.742125 TTGTAGGATCATATTATGGGAAGTCT 57.258 34.615 3.89 0.00 0.00 3.24
576 935 4.691216 GGAAGTCTACAGGTTTAGCTTGTG 59.309 45.833 0.00 0.00 37.96 3.33
588 947 4.552166 TTAGCTTGTGTGCAGTTTCTTC 57.448 40.909 0.00 0.00 34.99 2.87
595 954 2.813754 GTGTGCAGTTTCTTCATAGCCA 59.186 45.455 0.00 0.00 0.00 4.75
596 955 3.441572 GTGTGCAGTTTCTTCATAGCCAT 59.558 43.478 0.00 0.00 0.00 4.40
597 956 4.635765 GTGTGCAGTTTCTTCATAGCCATA 59.364 41.667 0.00 0.00 0.00 2.74
599 958 5.887598 TGTGCAGTTTCTTCATAGCCATATT 59.112 36.000 0.00 0.00 0.00 1.28
601 960 6.261826 GTGCAGTTTCTTCATAGCCATATTCT 59.738 38.462 0.00 0.00 0.00 2.40
604 977 7.360776 GCAGTTTCTTCATAGCCATATTCTAGC 60.361 40.741 0.00 0.00 0.00 3.42
663 1036 5.598417 ACACCTTTCTTCCTGTTATTTTGCT 59.402 36.000 0.00 0.00 0.00 3.91
686 1059 7.194607 CTGTCAAAGCTCAAAAAGAGTGATA 57.805 36.000 0.00 0.00 46.47 2.15
690 1063 8.224437 GTCAAAGCTCAAAAAGAGTGATACTAC 58.776 37.037 0.00 0.00 46.47 2.73
693 1066 8.910351 AAGCTCAAAAAGAGTGATACTACTTT 57.090 30.769 0.00 0.00 46.47 2.66
695 1068 7.389053 AGCTCAAAAAGAGTGATACTACTTTGG 59.611 37.037 0.00 0.00 46.47 3.28
746 1121 0.829333 TCTCAATCTCCTGGCAGAGC 59.171 55.000 17.94 0.00 33.66 4.09
789 1171 6.227522 TGCAAAGTTGTACAATCTGTAGCTA 58.772 36.000 12.26 0.00 32.84 3.32
795 1177 7.268586 AGTTGTACAATCTGTAGCTATTCTGG 58.731 38.462 12.26 0.00 32.84 3.86
796 1178 6.161855 TGTACAATCTGTAGCTATTCTGGG 57.838 41.667 0.00 0.00 32.84 4.45
808 1190 0.038166 ATTCTGGGACATGCGTTGGT 59.962 50.000 0.00 0.00 38.20 3.67
809 1191 0.605319 TTCTGGGACATGCGTTGGTC 60.605 55.000 0.00 0.00 38.20 4.02
810 1192 1.003355 CTGGGACATGCGTTGGTCT 60.003 57.895 0.00 0.00 38.20 3.85
811 1193 1.003839 TGGGACATGCGTTGGTCTC 60.004 57.895 0.00 0.00 35.05 3.36
885 1268 6.937392 ACCTTGGATCAACTTACTCTTACTC 58.063 40.000 0.00 0.00 0.00 2.59
897 1280 3.225104 ACTCTTACTCCGGTGTGTTGTA 58.775 45.455 19.20 0.00 0.00 2.41
901 1284 5.713025 TCTTACTCCGGTGTGTTGTATTAC 58.287 41.667 19.20 0.00 0.00 1.89
929 1317 3.621953 GAGCTGAACCAGTGCTCTT 57.378 52.632 0.00 0.00 46.69 2.85
938 1326 4.263462 TGAACCAGTGCTCTTATGTTCCAT 60.263 41.667 14.87 0.00 33.04 3.41
959 1347 2.693267 AATTCTTAGCTGGTCGTCCC 57.307 50.000 0.00 0.00 0.00 4.46
966 1354 1.003839 GCTGGTCGTCCCAACATGA 60.004 57.895 0.00 0.00 44.65 3.07
985 1373 8.863049 CAACATGATTTTCAGTTTATACTTGGC 58.137 33.333 0.00 0.00 30.26 4.52
986 1374 8.121305 ACATGATTTTCAGTTTATACTTGGCA 57.879 30.769 0.00 0.00 30.26 4.92
1110 1504 2.176364 ACAGAGCATGGCCTTATGGAAT 59.824 45.455 3.32 0.00 34.57 3.01
1113 1507 2.555757 GAGCATGGCCTTATGGAATCAC 59.444 50.000 3.32 0.00 34.57 3.06
1181 1575 5.552870 AGTCTTTCTCCTAAGAGCACAAA 57.447 39.130 0.00 0.00 40.22 2.83
1249 1643 4.110482 ACAGTCTAAACGCGGATTATCAC 58.890 43.478 12.47 9.10 0.00 3.06
1251 1645 3.131577 AGTCTAAACGCGGATTATCACCA 59.868 43.478 12.47 0.00 0.00 4.17
1482 1906 4.082733 GCTCATGGGAAGAAAGTTTACACC 60.083 45.833 0.00 0.00 0.00 4.16
1789 2257 9.750882 GGTTAGTCGTTTCTGAAATTTGTATAC 57.249 33.333 6.06 0.00 0.00 1.47
1846 2314 1.200484 GGAGACGGACAGAGACTGAAC 59.800 57.143 5.76 0.18 35.18 3.18
1877 2346 7.502561 AGTTCCTTATACTGCTGTTGTTCTTTT 59.497 33.333 0.09 0.00 0.00 2.27
1924 2396 6.717540 ACATGCTTACCCTTTGTTGTAACATA 59.282 34.615 0.00 0.00 38.95 2.29
1927 2399 8.008513 TGCTTACCCTTTGTTGTAACATAAAA 57.991 30.769 0.00 0.00 38.95 1.52
1977 3005 9.853555 ATTTCGATACATATGTCTCTCAGATTC 57.146 33.333 12.68 0.00 0.00 2.52
2082 3110 8.730680 TCTGTTGAGATAGGCATTTTAAAAGAC 58.269 33.333 6.79 1.44 0.00 3.01
2207 6289 4.545823 TCACTTTTACCTTTGCAAGTCG 57.454 40.909 0.00 0.00 0.00 4.18
2232 6314 9.290483 CGGTAATACTGATGTAGCATAATACTG 57.710 37.037 0.00 0.00 31.51 2.74
2308 6417 1.610038 CTCAAGGTGCTGCAATTGTGA 59.390 47.619 21.28 14.19 0.00 3.58
2309 6418 2.230508 CTCAAGGTGCTGCAATTGTGAT 59.769 45.455 21.28 0.00 0.00 3.06
2373 6685 1.648681 GAAATGTTCCAATTGTCGCGC 59.351 47.619 0.00 0.00 0.00 6.86
2406 6721 9.871238 GAATCTATTACTGTAGTCCAACAAAGA 57.129 33.333 0.00 0.00 0.00 2.52
2430 6753 9.220767 AGATAGCTCTTTTGTAGGTTTAGTTTG 57.779 33.333 0.00 0.00 0.00 2.93
2530 6866 0.811219 ATATGCGCGAAGAAGCAGCA 60.811 50.000 12.10 9.80 44.57 4.41
2675 7011 5.063880 GGTCAAGACTGTAACATTTGGAGT 58.936 41.667 0.00 0.00 0.00 3.85
2676 7012 5.531287 GGTCAAGACTGTAACATTTGGAGTT 59.469 40.000 0.00 0.00 0.00 3.01
2677 7013 6.430451 GTCAAGACTGTAACATTTGGAGTTG 58.570 40.000 0.00 0.00 0.00 3.16
2678 7014 5.530915 TCAAGACTGTAACATTTGGAGTTGG 59.469 40.000 0.00 0.00 0.00 3.77
2679 7015 5.304686 AGACTGTAACATTTGGAGTTGGA 57.695 39.130 0.00 0.00 0.00 3.53
2680 7016 5.308825 AGACTGTAACATTTGGAGTTGGAG 58.691 41.667 0.00 0.00 0.00 3.86
2733 7070 8.958060 TCTTGGCCTATATATACTTTCTCTGT 57.042 34.615 3.32 0.00 0.00 3.41
2766 7127 9.846248 AAATGCATTTTCTGTCAAAGTATAGTC 57.154 29.630 18.99 0.00 0.00 2.59
2767 7128 7.977789 TGCATTTTCTGTCAAAGTATAGTCA 57.022 32.000 0.00 0.00 0.00 3.41
2768 7129 8.032952 TGCATTTTCTGTCAAAGTATAGTCAG 57.967 34.615 0.00 0.00 0.00 3.51
2800 7161 7.500227 TCATTGAGCTTCTTCCATTTACCTATG 59.500 37.037 0.00 0.00 0.00 2.23
2805 7166 7.349598 AGCTTCTTCCATTTACCTATGTGAAT 58.650 34.615 0.00 0.00 31.39 2.57
2806 7167 7.284034 AGCTTCTTCCATTTACCTATGTGAATG 59.716 37.037 8.19 8.19 44.08 2.67
2807 7168 7.283127 GCTTCTTCCATTTACCTATGTGAATGA 59.717 37.037 14.54 2.18 46.14 2.57
2808 7169 9.347240 CTTCTTCCATTTACCTATGTGAATGAT 57.653 33.333 14.54 0.00 46.14 2.45
2809 7170 9.699410 TTCTTCCATTTACCTATGTGAATGATT 57.301 29.630 14.54 0.00 46.14 2.57
2889 7284 0.534412 AGATAGCAGCGCTTGACAGT 59.466 50.000 7.50 0.00 40.44 3.55
2891 7286 1.061711 GATAGCAGCGCTTGACAGTTG 59.938 52.381 7.50 0.00 40.44 3.16
2892 7287 0.033366 TAGCAGCGCTTGACAGTTGA 59.967 50.000 7.50 0.00 40.44 3.18
2893 7288 1.082496 GCAGCGCTTGACAGTTGAC 60.082 57.895 7.50 0.00 0.00 3.18
2894 7289 1.775039 GCAGCGCTTGACAGTTGACA 61.775 55.000 7.50 0.00 0.00 3.58
2895 7290 0.234106 CAGCGCTTGACAGTTGACAG 59.766 55.000 7.50 0.00 0.00 3.51
2896 7291 0.104855 AGCGCTTGACAGTTGACAGA 59.895 50.000 2.64 0.00 0.00 3.41
2897 7292 1.151668 GCGCTTGACAGTTGACAGAT 58.848 50.000 0.00 0.00 0.00 2.90
2898 7293 1.532868 GCGCTTGACAGTTGACAGATT 59.467 47.619 0.00 0.00 0.00 2.40
2907 7302 3.265791 CAGTTGACAGATTCAGGTAGCC 58.734 50.000 0.00 0.00 34.94 3.93
2926 7392 1.079819 GAGTACCTGAGCGCTGCAA 60.080 57.895 18.48 0.00 0.00 4.08
2935 7401 1.227943 AGCGCTGCAAGAAAGTCCA 60.228 52.632 10.39 0.00 34.07 4.02
3019 7524 3.411446 TGCAAACGTCCAGATTCAGATT 58.589 40.909 0.00 0.00 0.00 2.40
3098 8885 1.252779 CGCACGTACACAATCTGATCG 59.747 52.381 0.00 0.00 0.00 3.69
3099 8886 2.526077 GCACGTACACAATCTGATCGA 58.474 47.619 0.00 0.00 0.00 3.59
3100 8887 3.116300 GCACGTACACAATCTGATCGAT 58.884 45.455 0.00 0.00 0.00 3.59
3101 8888 3.060940 GCACGTACACAATCTGATCGATG 60.061 47.826 0.54 0.00 31.20 3.84
3102 8889 4.351192 CACGTACACAATCTGATCGATGA 58.649 43.478 0.54 0.00 31.20 2.92
3103 8890 4.798387 CACGTACACAATCTGATCGATGAA 59.202 41.667 0.54 0.00 31.20 2.57
3104 8891 5.460091 CACGTACACAATCTGATCGATGAAT 59.540 40.000 0.54 0.00 31.20 2.57
3105 8892 5.687730 ACGTACACAATCTGATCGATGAATC 59.312 40.000 0.54 0.00 31.20 2.52
3419 9238 1.658686 GAGACGAGGAGTGGATGCGT 61.659 60.000 0.00 0.00 37.97 5.24
3599 9419 4.101448 GCGCAGGGGGACATGTCT 62.101 66.667 24.50 2.45 45.79 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 4.776322 TCTTGACGGGCCATGGCG 62.776 66.667 29.90 19.63 43.06 5.69
30 31 2.825836 CTCTTGACGGGCCATGGC 60.826 66.667 29.47 29.47 41.06 4.40
32 33 2.825836 GGCTCTTGACGGGCCATG 60.826 66.667 4.39 0.00 44.69 3.66
74 93 4.506255 GGCGGAGGGGATTGGTGG 62.506 72.222 0.00 0.00 0.00 4.61
75 94 3.406595 GAGGCGGAGGGGATTGGTG 62.407 68.421 0.00 0.00 0.00 4.17
234 316 0.406750 TTAGACACCAGAGGGACCGA 59.593 55.000 0.00 0.00 38.05 4.69
244 326 1.544724 GCAGCCCAAATTAGACACCA 58.455 50.000 0.00 0.00 0.00 4.17
264 351 5.261216 AGGTATTGTACAGATTGTTTGGGG 58.739 41.667 0.00 0.00 0.00 4.96
271 358 9.197694 GCACTATAGAAGGTATTGTACAGATTG 57.802 37.037 6.78 0.00 0.00 2.67
281 368 4.220724 TCCGGTGCACTATAGAAGGTATT 58.779 43.478 17.98 0.00 0.00 1.89
283 370 3.301794 TCCGGTGCACTATAGAAGGTA 57.698 47.619 17.98 0.00 0.00 3.08
284 371 2.154567 TCCGGTGCACTATAGAAGGT 57.845 50.000 17.98 0.00 0.00 3.50
285 372 2.431057 AGTTCCGGTGCACTATAGAAGG 59.569 50.000 17.98 8.96 0.00 3.46
286 373 3.802948 AGTTCCGGTGCACTATAGAAG 57.197 47.619 17.98 0.00 0.00 2.85
287 374 3.512329 TCAAGTTCCGGTGCACTATAGAA 59.488 43.478 17.98 11.43 0.00 2.10
288 375 3.093814 TCAAGTTCCGGTGCACTATAGA 58.906 45.455 17.98 5.71 0.00 1.98
291 378 4.481368 TTATCAAGTTCCGGTGCACTAT 57.519 40.909 17.98 0.00 0.00 2.12
292 379 3.965379 TTATCAAGTTCCGGTGCACTA 57.035 42.857 17.98 0.00 0.00 2.74
298 394 4.117685 GCTTCGTATTATCAAGTTCCGGT 58.882 43.478 0.00 0.00 0.00 5.28
300 396 4.369182 AGGCTTCGTATTATCAAGTTCCG 58.631 43.478 0.00 0.00 0.00 4.30
344 444 1.005037 GATGACACACAGCACCGGA 60.005 57.895 9.46 0.00 34.76 5.14
346 446 1.229428 AAAGATGACACACAGCACCG 58.771 50.000 0.00 0.00 37.37 4.94
347 447 2.618241 TCAAAAGATGACACACAGCACC 59.382 45.455 0.00 0.00 37.37 5.01
348 448 3.313526 ACTCAAAAGATGACACACAGCAC 59.686 43.478 0.00 0.00 37.37 4.40
349 449 3.544684 ACTCAAAAGATGACACACAGCA 58.455 40.909 0.00 0.00 37.37 4.41
350 450 4.752101 AGTACTCAAAAGATGACACACAGC 59.248 41.667 0.00 0.00 33.47 4.40
351 451 5.985530 TGAGTACTCAAAAGATGACACACAG 59.014 40.000 23.24 0.00 36.53 3.66
352 452 5.912892 TGAGTACTCAAAAGATGACACACA 58.087 37.500 23.24 0.00 36.53 3.72
353 453 5.406780 CCTGAGTACTCAAAAGATGACACAC 59.593 44.000 25.14 0.00 39.39 3.82
354 454 5.070446 ACCTGAGTACTCAAAAGATGACACA 59.930 40.000 25.14 0.00 39.39 3.72
355 455 5.406780 CACCTGAGTACTCAAAAGATGACAC 59.593 44.000 25.14 0.00 39.39 3.67
359 459 4.318332 TGCACCTGAGTACTCAAAAGATG 58.682 43.478 25.14 18.15 39.39 2.90
376 476 0.951040 GCCAGTAGACACACTGCACC 60.951 60.000 0.00 0.00 43.82 5.01
377 477 0.951040 GGCCAGTAGACACACTGCAC 60.951 60.000 0.00 0.00 43.82 4.57
388 488 3.452627 AGATAAAGTCACCTGGCCAGTAG 59.547 47.826 30.63 21.78 0.00 2.57
393 493 3.274288 CAGAAGATAAAGTCACCTGGCC 58.726 50.000 0.00 0.00 0.00 5.36
416 516 4.318760 CCATCGTTATGGCAACTGTTATCG 60.319 45.833 0.00 0.00 46.17 2.92
417 517 5.095691 CCATCGTTATGGCAACTGTTATC 57.904 43.478 0.00 0.00 46.17 1.75
429 529 1.270839 CCCTGTAGGCCCATCGTTATG 60.271 57.143 0.00 0.00 0.00 1.90
430 530 1.056660 CCCTGTAGGCCCATCGTTAT 58.943 55.000 0.00 0.00 0.00 1.89
431 531 0.031917 TCCCTGTAGGCCCATCGTTA 60.032 55.000 0.00 0.00 34.51 3.18
432 532 0.694444 ATCCCTGTAGGCCCATCGTT 60.694 55.000 0.00 0.00 34.51 3.85
433 533 1.074471 ATCCCTGTAGGCCCATCGT 60.074 57.895 0.00 0.00 34.51 3.73
434 534 1.674057 GATCCCTGTAGGCCCATCG 59.326 63.158 0.00 0.00 34.51 3.84
435 535 1.831652 CGGATCCCTGTAGGCCCATC 61.832 65.000 6.06 0.00 34.51 3.51
436 536 1.843376 CGGATCCCTGTAGGCCCAT 60.843 63.158 6.06 0.00 34.51 4.00
437 537 2.445845 CGGATCCCTGTAGGCCCA 60.446 66.667 6.06 0.00 34.51 5.36
438 538 2.446036 ACGGATCCCTGTAGGCCC 60.446 66.667 6.06 0.00 34.51 5.80
439 539 2.808206 CCACGGATCCCTGTAGGCC 61.808 68.421 6.06 0.00 34.51 5.19
440 540 0.757935 TACCACGGATCCCTGTAGGC 60.758 60.000 6.06 0.00 34.51 3.93
441 541 1.329256 CTACCACGGATCCCTGTAGG 58.671 60.000 16.74 11.69 0.00 3.18
474 575 3.072476 AGCAGCCAACTAGTTACCAGAAA 59.928 43.478 8.04 0.00 0.00 2.52
480 581 1.993370 CACGAGCAGCCAACTAGTTAC 59.007 52.381 8.04 3.72 0.00 2.50
482 583 0.951040 GCACGAGCAGCCAACTAGTT 60.951 55.000 1.12 1.12 41.58 2.24
560 912 3.138304 CTGCACACAAGCTAAACCTGTA 58.862 45.455 0.00 0.00 34.99 2.74
576 935 6.261826 AGAATATGGCTATGAAGAAACTGCAC 59.738 38.462 0.00 0.00 0.00 4.57
588 947 6.101997 TCGAACATGCTAGAATATGGCTATG 58.898 40.000 0.00 0.00 36.12 2.23
597 956 9.601217 AAATTACTAGTTCGAACATGCTAGAAT 57.399 29.630 28.78 17.27 35.96 2.40
599 958 8.248253 TGAAATTACTAGTTCGAACATGCTAGA 58.752 33.333 28.78 9.67 35.96 2.43
601 960 8.942338 ATGAAATTACTAGTTCGAACATGCTA 57.058 30.769 28.78 12.23 31.18 3.49
639 1012 5.598417 AGCAAAATAACAGGAAGAAAGGTGT 59.402 36.000 0.00 0.00 0.00 4.16
640 1013 5.922544 CAGCAAAATAACAGGAAGAAAGGTG 59.077 40.000 0.00 0.00 0.00 4.00
663 1036 6.767902 AGTATCACTCTTTTTGAGCTTTGACA 59.232 34.615 0.00 0.00 46.41 3.58
686 1059 5.479124 ACATCGACCTTTACCAAAGTAGT 57.521 39.130 0.00 0.00 36.77 2.73
690 1063 5.475719 TGACTACATCGACCTTTACCAAAG 58.524 41.667 0.00 0.00 38.24 2.77
693 1066 5.258456 GATGACTACATCGACCTTTACCA 57.742 43.478 0.00 0.00 42.45 3.25
789 1171 0.038166 ACCAACGCATGTCCCAGAAT 59.962 50.000 0.00 0.00 0.00 2.40
795 1177 0.247736 AGAGAGACCAACGCATGTCC 59.752 55.000 0.00 0.00 31.76 4.02
796 1178 1.996191 GAAGAGAGACCAACGCATGTC 59.004 52.381 0.00 0.00 0.00 3.06
808 1190 7.030165 CAGTAGCATCGTTTTAAGAAGAGAGA 58.970 38.462 0.00 0.00 0.00 3.10
809 1191 6.809196 ACAGTAGCATCGTTTTAAGAAGAGAG 59.191 38.462 0.00 0.00 0.00 3.20
810 1192 6.688578 ACAGTAGCATCGTTTTAAGAAGAGA 58.311 36.000 0.00 0.00 0.00 3.10
811 1193 6.586463 TGACAGTAGCATCGTTTTAAGAAGAG 59.414 38.462 0.00 0.00 0.00 2.85
885 1268 8.907685 CAAATAAAAAGTAATACAACACACCGG 58.092 33.333 0.00 0.00 0.00 5.28
897 1280 8.860088 ACTGGTTCAGCTCAAATAAAAAGTAAT 58.140 29.630 0.00 0.00 34.37 1.89
901 1284 5.403466 GCACTGGTTCAGCTCAAATAAAAAG 59.597 40.000 0.00 0.00 34.37 2.27
914 1301 3.686726 GGAACATAAGAGCACTGGTTCAG 59.313 47.826 18.27 0.00 35.83 3.02
938 1326 3.516300 TGGGACGACCAGCTAAGAATTAA 59.484 43.478 6.20 0.00 46.80 1.40
959 1347 8.863049 GCCAAGTATAAACTGAAAATCATGTTG 58.137 33.333 0.00 0.00 35.62 3.33
966 1354 6.493458 AGTGGTGCCAAGTATAAACTGAAAAT 59.507 34.615 0.00 0.00 35.62 1.82
985 1373 2.177950 GCATCTGCTTCCAGTGGTG 58.822 57.895 9.54 4.82 40.09 4.17
986 1374 4.730487 GCATCTGCTTCCAGTGGT 57.270 55.556 9.54 0.00 40.09 4.16
1110 1504 0.108945 CTGCATGTGAGCGAGAGTGA 60.109 55.000 0.00 0.00 37.31 3.41
1113 1507 0.108945 TGACTGCATGTGAGCGAGAG 60.109 55.000 0.00 0.00 37.31 3.20
1181 1575 3.379372 CCCATTTTGCAGACGAGATGATT 59.621 43.478 0.00 0.00 0.00 2.57
1249 1643 4.219507 AGCATGTAGGATACGATCTCTTGG 59.780 45.833 0.00 0.00 46.99 3.61
1251 1645 6.349777 GCTTAGCATGTAGGATACGATCTCTT 60.350 42.308 0.00 0.00 46.99 2.85
1316 1710 0.101040 TGTCGTCGTTCTCGGTTTGT 59.899 50.000 0.00 0.00 37.69 2.83
1317 1711 1.189446 CTTGTCGTCGTTCTCGGTTTG 59.811 52.381 0.00 0.00 37.69 2.93
1320 1714 0.383231 AACTTGTCGTCGTTCTCGGT 59.617 50.000 0.00 0.00 37.69 4.69
1321 1715 1.484356 AAACTTGTCGTCGTTCTCGG 58.516 50.000 0.00 0.00 37.69 4.63
1413 1807 2.979814 TGTCATTATCCACCAGACCG 57.020 50.000 0.00 0.00 0.00 4.79
1418 1812 5.764432 TGGAATCAATGTCATTATCCACCA 58.236 37.500 16.96 11.84 30.90 4.17
1482 1906 1.471287 TCACCGGTGACAGAATACTCG 59.529 52.381 33.23 2.97 34.14 4.18
1519 1943 8.950210 GCACATAGGCATAATGTATACAGAAAT 58.050 33.333 11.91 2.00 35.82 2.17
1542 1966 1.986378 GTCTCGTGTGACTACATGCAC 59.014 52.381 0.00 0.00 42.35 4.57
1789 2257 7.648142 TCAGCAACCTAACAATAGAAAAGTTG 58.352 34.615 0.00 0.00 33.92 3.16
1826 2294 1.200484 GTTCAGTCTCTGTCCGTCTCC 59.800 57.143 0.00 0.00 32.61 3.71
1846 2314 5.007385 ACAGCAGTATAAGGAACTAACCG 57.993 43.478 0.00 0.00 38.49 4.44
1927 2399 4.039124 CACCCTCAATAAACCTGCAGTTTT 59.961 41.667 14.08 14.08 46.79 2.43
1929 2401 3.157087 CACCCTCAATAAACCTGCAGTT 58.843 45.455 13.81 3.71 41.81 3.16
1930 2402 2.375174 TCACCCTCAATAAACCTGCAGT 59.625 45.455 13.81 0.00 0.00 4.40
2082 3110 6.372937 TCTGAGATCATGGCTAATACTACTCG 59.627 42.308 0.00 0.00 0.00 4.18
2232 6314 7.446001 AGAAGAAACAAGGTCAATGAGAATC 57.554 36.000 0.00 0.00 0.00 2.52
2301 6410 7.068593 TGGAGTGAAGACAGAAAAATCACAATT 59.931 33.333 6.94 0.00 42.12 2.32
2338 6650 7.004555 GGAACATTTCCCCTTGTTATCTTTT 57.995 36.000 0.00 0.00 44.30 2.27
2370 6682 3.610242 CAGTAATAGATTCTCATCGGCGC 59.390 47.826 0.00 0.00 34.17 6.53
2373 6685 7.175119 TGGACTACAGTAATAGATTCTCATCGG 59.825 40.741 0.00 0.00 34.17 4.18
2406 6721 9.569122 TTCAAACTAAACCTACAAAAGAGCTAT 57.431 29.630 0.00 0.00 0.00 2.97
2530 6866 1.806623 GCGATCGCTATCAAACCACCT 60.807 52.381 31.94 0.00 38.26 4.00
2675 7011 3.840666 ACTATCTGGTTTCTGAGCTCCAA 59.159 43.478 12.15 0.64 0.00 3.53
2676 7012 3.445008 ACTATCTGGTTTCTGAGCTCCA 58.555 45.455 12.15 0.00 0.00 3.86
2677 7013 4.187694 CAACTATCTGGTTTCTGAGCTCC 58.812 47.826 12.15 0.00 0.00 4.70
2678 7014 4.826556 ACAACTATCTGGTTTCTGAGCTC 58.173 43.478 6.82 6.82 0.00 4.09
2679 7015 4.899352 ACAACTATCTGGTTTCTGAGCT 57.101 40.909 0.00 0.00 0.00 4.09
2680 7016 5.725362 ACTACAACTATCTGGTTTCTGAGC 58.275 41.667 0.00 0.00 0.00 4.26
2733 7070 4.102210 TGACAGAAAATGCATTTGGGGAAA 59.898 37.500 24.74 7.90 0.00 3.13
2742 7079 8.565896 TGACTATACTTTGACAGAAAATGCAT 57.434 30.769 0.00 0.00 0.00 3.96
2842 7232 6.509418 AGAAGATCAAGTGACAGAGAGTAC 57.491 41.667 0.00 0.00 0.00 2.73
2845 7235 5.170021 CCAAGAAGATCAAGTGACAGAGAG 58.830 45.833 0.00 0.00 0.00 3.20
2846 7236 4.562347 GCCAAGAAGATCAAGTGACAGAGA 60.562 45.833 0.00 0.00 0.00 3.10
2847 7237 3.683822 GCCAAGAAGATCAAGTGACAGAG 59.316 47.826 0.00 0.00 0.00 3.35
2848 7238 3.071457 TGCCAAGAAGATCAAGTGACAGA 59.929 43.478 0.00 0.00 0.00 3.41
2849 7239 3.405831 TGCCAAGAAGATCAAGTGACAG 58.594 45.455 0.00 0.00 0.00 3.51
2851 7241 3.668447 TCTGCCAAGAAGATCAAGTGAC 58.332 45.455 0.00 0.00 0.00 3.67
2852 7242 4.564782 ATCTGCCAAGAAGATCAAGTGA 57.435 40.909 0.00 0.00 35.59 3.41
2853 7243 4.272991 GCTATCTGCCAAGAAGATCAAGTG 59.727 45.833 0.00 0.00 35.92 3.16
2889 7284 2.166459 CTCGGCTACCTGAATCTGTCAA 59.834 50.000 0.00 0.00 35.22 3.18
2891 7286 1.751924 ACTCGGCTACCTGAATCTGTC 59.248 52.381 0.00 0.00 0.00 3.51
2892 7287 1.853963 ACTCGGCTACCTGAATCTGT 58.146 50.000 0.00 0.00 0.00 3.41
2893 7288 2.034812 GGTACTCGGCTACCTGAATCTG 59.965 54.545 0.00 0.00 34.34 2.90
2894 7289 2.091775 AGGTACTCGGCTACCTGAATCT 60.092 50.000 10.25 0.00 44.25 2.40
2895 7290 2.308690 AGGTACTCGGCTACCTGAATC 58.691 52.381 10.25 0.00 44.25 2.52
2896 7291 2.456073 AGGTACTCGGCTACCTGAAT 57.544 50.000 10.25 0.00 44.25 2.57
2897 7292 3.994165 AGGTACTCGGCTACCTGAA 57.006 52.632 10.25 0.00 44.25 3.02
2907 7302 2.580867 GCAGCGCTCAGGTACTCG 60.581 66.667 7.13 0.00 34.60 4.18
2926 7392 0.976641 TGGCGTGATCTGGACTTTCT 59.023 50.000 0.00 0.00 0.00 2.52
2935 7401 4.479993 GCTGGGCTGGCGTGATCT 62.480 66.667 0.00 0.00 0.00 2.75
3019 7524 4.846779 GACAAGATTTGGCCAAGTACAA 57.153 40.909 19.48 3.35 30.38 2.41
3371 9190 3.791586 GAGTGGGCCTGCTCCTCC 61.792 72.222 14.87 0.00 0.00 4.30
3372 9191 3.791586 GGAGTGGGCCTGCTCCTC 61.792 72.222 28.49 15.81 45.78 3.71


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

AutoCloner maintained by Alex Coulton.