Multiple sequence alignment - TraesCS2B01G481800

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 TraesCS2B01G481800 chr2B 100.000 3092 0 0 1 3092 679902698 679905789 0.000000e+00 5710.0
1 TraesCS2B01G481800 chr2B 97.452 157 3 1 456 611 679902999 679903155 1.830000e-67 267.0
2 TraesCS2B01G481800 chr2B 97.452 157 3 1 302 458 679903153 679903308 1.830000e-67 267.0
3 TraesCS2B01G481800 chr2B 98.780 82 1 0 601 682 793534789 793534708 2.480000e-31 147.0
4 TraesCS2B01G481800 chr2B 94.118 34 2 0 2883 2916 567074593 567074560 6.000000e-03 52.8
5 TraesCS2B01G481800 chr2A 93.424 1840 98 15 585 2410 706758369 706760199 0.000000e+00 2706.0
6 TraesCS2B01G481800 chr2A 78.740 381 54 15 46 421 706757394 706757752 2.400000e-56 230.0
7 TraesCS2B01G481800 chr2A 94.681 94 2 2 601 694 768211242 768211332 3.210000e-30 143.0
8 TraesCS2B01G481800 chr2D 93.344 1818 89 14 595 2409 566993367 566995155 0.000000e+00 2658.0
9 TraesCS2B01G481800 chr2D 84.225 374 36 9 1 359 566992957 566993322 2.950000e-90 342.0
10 TraesCS2B01G481800 chr3B 95.157 702 13 2 2411 3092 698193790 698194490 0.000000e+00 1088.0
11 TraesCS2B01G481800 chr3B 97.701 87 1 1 601 687 544794497 544794582 6.910000e-32 148.0
12 TraesCS2B01G481800 chr3D 91.619 704 37 2 2409 3092 445845416 445846117 0.000000e+00 953.0
13 TraesCS2B01G481800 chr3D 87.225 728 52 11 2404 3092 200465009 200464284 0.000000e+00 791.0
14 TraesCS2B01G481800 chr3D 85.953 719 59 16 2412 3092 114072961 114073675 0.000000e+00 730.0
15 TraesCS2B01G481800 chr3D 98.851 87 0 1 601 687 418398132 418398217 1.480000e-33 154.0
16 TraesCS2B01G481800 chr3D 94.792 96 5 0 2808 2903 445845937 445846032 1.920000e-32 150.0
17 TraesCS2B01G481800 chr3D 93.750 96 6 0 2808 2903 200464463 200464368 8.940000e-31 145.0
18 TraesCS2B01G481800 chr7A 87.926 704 41 13 2409 3092 544293663 544292984 0.000000e+00 789.0
19 TraesCS2B01G481800 chr7A 100.000 28 0 0 2883 2910 594890916 594890943 6.000000e-03 52.8
20 TraesCS2B01G481800 chr1A 91.379 116 10 0 2414 2529 589673726 589673611 3.190000e-35 159.0
21 TraesCS2B01G481800 chr5D 96.552 87 3 0 601 687 449271489 449271575 8.940000e-31 145.0
22 TraesCS2B01G481800 chr5B 92.308 104 5 3 608 710 548735790 548735689 8.940000e-31 145.0
23 TraesCS2B01G481800 chr5A 95.652 92 1 3 601 689 568156544 568156635 8.940000e-31 145.0
24 TraesCS2B01G481800 chr7D 97.436 39 1 0 2808 2846 127702243 127702281 1.990000e-07 67.6


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 TraesCS2B01G481800 chr2B 679902698 679905789 3091 False 2081.333333 5710 98.301333 1 3092 3 chr2B.!!$F1 3091
1 TraesCS2B01G481800 chr2A 706757394 706760199 2805 False 1468.000000 2706 86.082000 46 2410 2 chr2A.!!$F2 2364
2 TraesCS2B01G481800 chr2D 566992957 566995155 2198 False 1500.000000 2658 88.784500 1 2409 2 chr2D.!!$F1 2408
3 TraesCS2B01G481800 chr3B 698193790 698194490 700 False 1088.000000 1088 95.157000 2411 3092 1 chr3B.!!$F2 681
4 TraesCS2B01G481800 chr3D 114072961 114073675 714 False 730.000000 730 85.953000 2412 3092 1 chr3D.!!$F1 680
5 TraesCS2B01G481800 chr3D 445845416 445846117 701 False 551.500000 953 93.205500 2409 3092 2 chr3D.!!$F3 683
6 TraesCS2B01G481800 chr3D 200464284 200465009 725 True 468.000000 791 90.487500 2404 3092 2 chr3D.!!$R1 688
7 TraesCS2B01G481800 chr7A 544292984 544293663 679 True 789.000000 789 87.926000 2409 3092 1 chr7A.!!$R1 683

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
304 322 0.179001 AGAAACCCAAACCCAGGACG 60.179 55.0 0.00 0.0 0.00 4.79 F
468 933 0.249911 AAAAGCGACTGAGGCTCGTT 60.250 50.0 10.42 0.0 40.53 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1680 2175 1.284198 AGCTGAAATGCCTCATCCACT 59.716 47.619 0.00 0.0 0.00 4.00 R
2317 2824 1.301677 GAGCTTCAAGCCAACCGAGG 61.302 60.000 5.53 0.0 43.77 4.63 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
27 28 4.024048 CACAGAAGTATGAACAACCACCAC 60.024 45.833 0.00 0.00 0.00 4.16
36 37 2.197324 AACCACCACCAACGCCAT 59.803 55.556 0.00 0.00 0.00 4.40
40 41 0.962489 CCACCACCAACGCCATAAAA 59.038 50.000 0.00 0.00 0.00 1.52
44 45 4.061596 CACCACCAACGCCATAAAATTTT 58.938 39.130 8.75 8.75 0.00 1.82
51 52 5.406780 CCAACGCCATAAAATTTTGTAGCAA 59.593 36.000 13.76 0.00 0.00 3.91
61 62 3.296322 TTTTGTAGCAAAATGAGGCGG 57.704 42.857 3.26 0.00 34.54 6.13
63 64 1.164411 TGTAGCAAAATGAGGCGGTG 58.836 50.000 0.00 0.00 34.54 4.94
66 67 1.181098 AGCAAAATGAGGCGGTGCTT 61.181 50.000 0.00 0.00 42.77 3.91
67 68 0.525761 GCAAAATGAGGCGGTGCTTA 59.474 50.000 0.00 0.00 32.43 3.09
122 123 3.265479 CCTCTTCCTTGGGTTCTTGATCT 59.735 47.826 0.00 0.00 0.00 2.75
131 132 6.434028 CCTTGGGTTCTTGATCTGATTTGTAA 59.566 38.462 0.00 0.00 0.00 2.41
159 160 8.985694 GTTTCAAAAATGATTATGTCTACGTCG 58.014 33.333 0.00 0.00 0.00 5.12
165 166 8.516811 AAATGATTATGTCTACGTCGTAATCC 57.483 34.615 18.04 0.00 40.32 3.01
182 183 7.952101 GTCGTAATCCTAACCGTTTAAAGTTTC 59.048 37.037 0.00 0.00 0.00 2.78
188 189 8.744568 TCCTAACCGTTTAAAGTTTCCTTAAA 57.255 30.769 0.00 0.00 0.00 1.52
203 204 8.227731 GTTTCCTTAAACTTCAATCAATTCCG 57.772 34.615 0.00 0.00 41.52 4.30
217 218 8.413229 TCAATCAATTCCGAAAAGAAAAGTTCT 58.587 29.630 0.00 0.00 43.15 3.01
254 268 1.137282 GGAGTTCGAAGGGGATGAGTC 59.863 57.143 0.00 0.00 0.00 3.36
292 310 1.614583 GCAAGAGGGGAAGAGAAACCC 60.615 57.143 0.00 0.00 45.06 4.11
300 318 2.239400 GGAAGAGAAACCCAAACCCAG 58.761 52.381 0.00 0.00 0.00 4.45
301 319 2.239400 GAAGAGAAACCCAAACCCAGG 58.761 52.381 0.00 0.00 0.00 4.45
302 320 1.529744 AGAGAAACCCAAACCCAGGA 58.470 50.000 0.00 0.00 0.00 3.86
303 321 1.145119 AGAGAAACCCAAACCCAGGAC 59.855 52.381 0.00 0.00 0.00 3.85
304 322 0.179001 AGAAACCCAAACCCAGGACG 60.179 55.000 0.00 0.00 0.00 4.79
315 333 2.651361 CAGGACGTGAGGCTCGTT 59.349 61.111 10.42 0.00 41.64 3.85
325 343 1.140052 TGAGGCTCGTTTCAGGAACAA 59.860 47.619 10.42 0.00 38.18 2.83
348 366 7.281324 ACAAAAACCCTTAACCAAATTAGCAAC 59.719 33.333 0.00 0.00 0.00 4.17
359 377 5.977129 ACCAAATTAGCAACGAAGAAGTTTG 59.023 36.000 0.00 0.00 30.96 2.93
373 391 1.826385 AGTTTGCAAAGGAGATCCCG 58.174 50.000 13.26 0.00 40.87 5.14
379 397 1.613255 GCAAAGGAGATCCCGGTTCAA 60.613 52.381 0.00 0.00 40.87 2.69
395 413 5.291614 CCGGTTCAAATGAAAATATGCCAAG 59.708 40.000 0.00 0.00 35.58 3.61
414 432 1.006162 AGGAAAGACTAGCGAGGAGGT 59.994 52.381 0.00 0.00 0.00 3.85
417 435 1.187087 AAGACTAGCGAGGAGGTTGG 58.813 55.000 0.00 0.00 0.00 3.77
421 439 1.689233 TAGCGAGGAGGTTGGCCAT 60.689 57.895 6.09 0.00 37.19 4.40
424 442 0.393808 GCGAGGAGGTTGGCCATAAA 60.394 55.000 6.09 0.00 37.19 1.40
426 444 2.442413 CGAGGAGGTTGGCCATAAAAA 58.558 47.619 6.09 0.00 37.19 1.94
468 933 0.249911 AAAAGCGACTGAGGCTCGTT 60.250 50.000 10.42 0.00 40.53 3.85
482 947 3.113322 GGCTCGTTTCAGGAACAAAAAC 58.887 45.455 0.00 0.00 38.18 2.43
483 948 3.113322 GCTCGTTTCAGGAACAAAAACC 58.887 45.455 0.00 0.00 38.18 3.27
489 954 5.517411 CGTTTCAGGAACAAAAACCCTTAAC 59.483 40.000 0.00 0.00 38.18 2.01
493 958 5.484290 TCAGGAACAAAAACCCTTAACCAAA 59.516 36.000 0.00 0.00 0.00 3.28
495 960 6.826231 CAGGAACAAAAACCCTTAACCAAATT 59.174 34.615 0.00 0.00 0.00 1.82
498 963 7.041644 GGAACAAAAACCCTTAACCAAATTAGC 60.042 37.037 0.00 0.00 0.00 3.09
500 965 7.339482 ACAAAAACCCTTAACCAAATTAGCAA 58.661 30.769 0.00 0.00 0.00 3.91
501 966 7.281324 ACAAAAACCCTTAACCAAATTAGCAAC 59.719 33.333 0.00 0.00 0.00 4.17
502 967 4.776795 ACCCTTAACCAAATTAGCAACG 57.223 40.909 0.00 0.00 0.00 4.10
503 968 4.400120 ACCCTTAACCAAATTAGCAACGA 58.600 39.130 0.00 0.00 0.00 3.85
504 969 4.828387 ACCCTTAACCAAATTAGCAACGAA 59.172 37.500 0.00 0.00 0.00 3.85
505 970 5.048294 ACCCTTAACCAAATTAGCAACGAAG 60.048 40.000 0.00 0.00 0.00 3.79
506 971 5.182380 CCCTTAACCAAATTAGCAACGAAGA 59.818 40.000 0.00 0.00 0.00 2.87
507 972 6.294286 CCCTTAACCAAATTAGCAACGAAGAA 60.294 38.462 0.00 0.00 0.00 2.52
508 973 6.801862 CCTTAACCAAATTAGCAACGAAGAAG 59.198 38.462 0.00 0.00 0.00 2.85
509 974 5.767816 AACCAAATTAGCAACGAAGAAGT 57.232 34.783 0.00 0.00 0.00 3.01
510 975 5.767816 ACCAAATTAGCAACGAAGAAGTT 57.232 34.783 0.00 0.00 34.15 2.66
511 976 6.144078 ACCAAATTAGCAACGAAGAAGTTT 57.856 33.333 0.00 0.00 30.96 2.66
512 977 5.977129 ACCAAATTAGCAACGAAGAAGTTTG 59.023 36.000 0.00 0.00 30.96 2.93
513 978 5.107875 CCAAATTAGCAACGAAGAAGTTTGC 60.108 40.000 0.00 0.00 30.96 3.68
514 979 4.829064 ATTAGCAACGAAGAAGTTTGCA 57.171 36.364 8.15 0.00 33.66 4.08
515 980 4.624336 TTAGCAACGAAGAAGTTTGCAA 57.376 36.364 8.15 0.00 33.66 4.08
516 981 3.502191 AGCAACGAAGAAGTTTGCAAA 57.498 38.095 8.05 8.05 33.66 3.68
517 982 3.438360 AGCAACGAAGAAGTTTGCAAAG 58.562 40.909 13.26 1.16 33.66 2.77
518 983 3.128589 AGCAACGAAGAAGTTTGCAAAGA 59.871 39.130 13.26 0.00 33.66 2.52
519 984 3.857093 GCAACGAAGAAGTTTGCAAAGAA 59.143 39.130 13.26 0.00 32.48 2.52
520 985 4.027377 GCAACGAAGAAGTTTGCAAAGAAG 60.027 41.667 13.26 2.95 32.48 2.85
521 986 5.331902 CAACGAAGAAGTTTGCAAAGAAGA 58.668 37.500 13.26 0.00 30.96 2.87
522 987 5.757850 ACGAAGAAGTTTGCAAAGAAGAT 57.242 34.783 13.26 0.00 0.00 2.40
523 988 5.752712 ACGAAGAAGTTTGCAAAGAAGATC 58.247 37.500 13.26 7.98 0.00 2.75
524 989 5.149977 CGAAGAAGTTTGCAAAGAAGATCC 58.850 41.667 13.26 0.00 0.00 3.36
525 990 5.459536 AAGAAGTTTGCAAAGAAGATCCC 57.540 39.130 13.26 0.00 0.00 3.85
534 999 3.193479 GCAAAGAAGATCCCGGTTCAAAT 59.807 43.478 0.00 0.00 0.00 2.32
535 1000 4.737054 CAAAGAAGATCCCGGTTCAAATG 58.263 43.478 0.00 0.00 0.00 2.32
541 1006 6.889722 AGAAGATCCCGGTTCAAATGAAAATA 59.110 34.615 0.00 0.00 35.58 1.40
542 1007 7.561356 AGAAGATCCCGGTTCAAATGAAAATAT 59.439 33.333 0.00 0.00 35.58 1.28
544 1009 5.004922 TCCCGGTTCAAATGAAAATATGC 57.995 39.130 0.00 0.00 35.58 3.14
545 1010 4.119136 CCCGGTTCAAATGAAAATATGCC 58.881 43.478 0.00 0.00 35.58 4.40
549 1014 5.291614 CGGTTCAAATGAAAATATGCCAAGG 59.708 40.000 0.00 0.00 35.58 3.61
553 1018 8.445493 GTTCAAATGAAAATATGCCAAGGAAAG 58.555 33.333 0.00 0.00 35.58 2.62
556 1021 7.486407 AATGAAAATATGCCAAGGAAAGACT 57.514 32.000 0.00 0.00 0.00 3.24
558 1023 7.630242 TGAAAATATGCCAAGGAAAGACTAG 57.370 36.000 0.00 0.00 0.00 2.57
559 1024 6.095440 TGAAAATATGCCAAGGAAAGACTAGC 59.905 38.462 0.00 0.00 0.00 3.42
560 1025 2.029838 ATGCCAAGGAAAGACTAGCG 57.970 50.000 0.00 0.00 0.00 4.26
561 1026 0.973632 TGCCAAGGAAAGACTAGCGA 59.026 50.000 0.00 0.00 0.00 4.93
562 1027 1.066858 TGCCAAGGAAAGACTAGCGAG 60.067 52.381 0.00 0.00 0.00 5.03
563 1028 1.740718 GCCAAGGAAAGACTAGCGAGG 60.741 57.143 0.00 0.00 0.00 4.63
564 1029 1.825474 CCAAGGAAAGACTAGCGAGGA 59.175 52.381 0.00 0.00 0.00 3.71
565 1030 2.159170 CCAAGGAAAGACTAGCGAGGAG 60.159 54.545 0.00 0.00 0.00 3.69
566 1031 1.770294 AGGAAAGACTAGCGAGGAGG 58.230 55.000 0.00 0.00 0.00 4.30
567 1032 1.006162 AGGAAAGACTAGCGAGGAGGT 59.994 52.381 0.00 0.00 0.00 3.85
568 1033 1.826096 GGAAAGACTAGCGAGGAGGTT 59.174 52.381 0.00 0.00 0.00 3.50
569 1034 2.417515 GGAAAGACTAGCGAGGAGGTTG 60.418 54.545 0.00 0.00 0.00 3.77
570 1035 1.187087 AAGACTAGCGAGGAGGTTGG 58.813 55.000 0.00 0.00 0.00 3.77
571 1036 1.142097 GACTAGCGAGGAGGTTGGC 59.858 63.158 0.00 0.00 0.00 4.52
572 1037 2.299503 GACTAGCGAGGAGGTTGGCC 62.300 65.000 0.00 0.00 0.00 5.36
573 1038 2.284331 TAGCGAGGAGGTTGGCCA 60.284 61.111 0.00 0.00 37.19 5.36
574 1039 1.689233 TAGCGAGGAGGTTGGCCAT 60.689 57.895 6.09 0.00 37.19 4.40
576 1041 1.223487 GCGAGGAGGTTGGCCATAA 59.777 57.895 6.09 0.00 37.19 1.90
577 1042 0.393808 GCGAGGAGGTTGGCCATAAA 60.394 55.000 6.09 0.00 37.19 1.40
578 1043 1.953311 GCGAGGAGGTTGGCCATAAAA 60.953 52.381 6.09 0.00 37.19 1.52
579 1044 2.442413 CGAGGAGGTTGGCCATAAAAA 58.558 47.619 6.09 0.00 37.19 1.94
689 1184 1.298157 CCACGCGGTCATGTTGTGAT 61.298 55.000 12.47 0.00 39.48 3.06
695 1190 1.129251 CGGTCATGTTGTGATCACTGC 59.871 52.381 25.55 17.81 37.86 4.40
697 1192 1.470098 GTCATGTTGTGATCACTGCCC 59.530 52.381 25.55 11.51 39.48 5.36
706 1201 3.072330 TGTGATCACTGCCCTACTGAAAA 59.928 43.478 25.55 0.00 0.00 2.29
725 1220 8.458843 ACTGAAAACTATACATACATTTGTGCC 58.541 33.333 0.00 0.00 0.00 5.01
743 1238 1.525995 CAACCACACGAGTTGGGCT 60.526 57.895 0.00 0.00 40.73 5.19
778 1273 2.595095 CCAAGGCCCGCCATTCTA 59.405 61.111 8.74 0.00 38.92 2.10
781 1276 1.097547 CAAGGCCCGCCATTCTACTG 61.098 60.000 8.74 0.00 38.92 2.74
783 1278 2.742116 GGCCCGCCATTCTACTGGA 61.742 63.158 0.00 0.00 38.69 3.86
916 1411 1.523758 CTTCCTTGCTACACACACCC 58.476 55.000 0.00 0.00 0.00 4.61
919 1414 1.761174 CTTGCTACACACACCCCCT 59.239 57.895 0.00 0.00 0.00 4.79
920 1415 0.606401 CTTGCTACACACACCCCCTG 60.606 60.000 0.00 0.00 0.00 4.45
921 1416 1.057275 TTGCTACACACACCCCCTGA 61.057 55.000 0.00 0.00 0.00 3.86
922 1417 1.057275 TGCTACACACACCCCCTGAA 61.057 55.000 0.00 0.00 0.00 3.02
962 1457 1.433879 CACTTCTCGAGTAGCCCCG 59.566 63.158 17.94 2.13 36.65 5.73
963 1458 2.413765 CTTCTCGAGTAGCCCCGC 59.586 66.667 13.13 0.00 0.00 6.13
1391 1886 2.202987 GGCCATGGAGACGCTCTG 60.203 66.667 18.40 0.00 0.00 3.35
1440 1935 3.264450 CCTCCACCAAGACCTTCAACTAT 59.736 47.826 0.00 0.00 0.00 2.12
1553 2048 3.002042 CGCTGCTTCAACATCCTTATCAG 59.998 47.826 0.00 0.00 0.00 2.90
1634 2129 2.902343 GGAGTGCCGGCCTAATGC 60.902 66.667 26.77 7.03 40.16 3.56
1680 2175 2.636412 CCTCTGCCGGAACTGTCGA 61.636 63.158 5.05 0.00 0.00 4.20
1695 2190 1.278985 TGTCGAGTGGATGAGGCATTT 59.721 47.619 0.00 0.00 0.00 2.32
1696 2191 1.936547 GTCGAGTGGATGAGGCATTTC 59.063 52.381 0.00 0.00 0.00 2.17
1728 2223 2.424956 GAGAATGCGCAAGGAGGAAATT 59.575 45.455 17.11 0.00 45.13 1.82
1968 2463 4.082190 AGTTTCTCATCGTACAAGCTGCTA 60.082 41.667 0.90 0.00 0.00 3.49
1977 2472 3.871006 CGTACAAGCTGCTAATTGATGGA 59.129 43.478 0.90 0.00 0.00 3.41
1987 2482 6.299805 TGCTAATTGATGGACTCTGTAGTT 57.700 37.500 0.00 0.00 35.56 2.24
2050 2545 3.558033 GTGGACCAAGGTTTTGTTCCTA 58.442 45.455 0.00 0.00 44.01 2.94
2106 2604 7.557358 TCCTTATGCTGAAATGTATGTTCATGT 59.443 33.333 0.00 0.00 34.59 3.21
2117 2622 6.795098 TGTATGTTCATGTCAGTGGTTTAC 57.205 37.500 0.00 0.00 0.00 2.01
2193 2698 0.538057 CAACCTGCCTGCCTTTCTGA 60.538 55.000 0.00 0.00 0.00 3.27
2238 2743 5.598417 CGGATCTTTTTCCTTATGGGGATTT 59.402 40.000 0.00 0.00 35.07 2.17
2257 2764 6.410388 GGGATTTAGGAATATTGGGTCTCACA 60.410 42.308 0.00 0.00 0.00 3.58
2258 2765 6.486993 GGATTTAGGAATATTGGGTCTCACAC 59.513 42.308 0.00 0.00 0.00 3.82
2271 2778 4.585955 GTCTCACACTGACCAAGTTCTA 57.414 45.455 0.00 0.00 36.83 2.10
2286 2793 7.036220 ACCAAGTTCTATTTACTGATGACTCG 58.964 38.462 0.00 0.00 0.00 4.18
2317 2824 1.226717 CCTGAGAACCGAGCGCTAC 60.227 63.158 11.50 2.92 0.00 3.58
2338 2845 0.036732 TCGGTTGGCTTGAAGCTCAT 59.963 50.000 17.59 0.00 41.99 2.90
2369 2876 4.752879 CCCACCCGCGTTCGATGT 62.753 66.667 4.92 0.00 38.10 3.06
2474 2981 2.997897 GTCCTGGGTGAGCTCGGT 60.998 66.667 9.64 0.00 0.00 4.69
2484 2991 2.526873 AGCTCGGTCTGGTTGGGT 60.527 61.111 0.00 0.00 0.00 4.51
2499 3006 1.855295 TGGGTTGATGCAAGCATGAT 58.145 45.000 12.94 0.00 42.72 2.45
3075 3639 2.801111 GAGAAGAAAAGCGAAGGAACGT 59.199 45.455 0.00 0.00 35.59 3.99
3083 3647 2.250939 CGAAGGAACGTGCCTGCAA 61.251 57.895 21.49 0.00 38.58 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.482436 TGGTGGTGGTTGTTCATACTTC 58.518 45.455 0.00 0.00 0.00 3.01
12 13 2.222886 CGTTGGTGGTGGTTGTTCATA 58.777 47.619 0.00 0.00 0.00 2.15
27 28 4.926238 TGCTACAAAATTTTATGGCGTTGG 59.074 37.500 12.13 0.00 0.00 3.77
36 37 6.367422 CCGCCTCATTTTGCTACAAAATTTTA 59.633 34.615 14.00 4.54 0.00 1.52
40 41 3.258123 ACCGCCTCATTTTGCTACAAAAT 59.742 39.130 11.49 11.49 0.00 1.82
44 45 1.164411 CACCGCCTCATTTTGCTACA 58.836 50.000 0.00 0.00 0.00 2.74
51 52 2.418368 TCATAAGCACCGCCTCATTT 57.582 45.000 0.00 0.00 0.00 2.32
61 62 7.588512 AGTTTGTGAAGATTCTTCATAAGCAC 58.411 34.615 33.11 27.35 34.80 4.40
155 156 5.572896 ACTTTAAACGGTTAGGATTACGACG 59.427 40.000 0.00 0.00 0.00 5.12
159 160 8.327941 AGGAAACTTTAAACGGTTAGGATTAC 57.672 34.615 0.00 0.00 37.44 1.89
182 183 8.810652 TTTTCGGAATTGATTGAAGTTTAAGG 57.189 30.769 0.00 0.00 0.00 2.69
188 189 8.197439 ACTTTTCTTTTCGGAATTGATTGAAGT 58.803 29.630 0.00 2.72 0.00 3.01
203 204 9.573133 TTGATTGAAGTCAGAACTTTTCTTTTC 57.427 29.630 0.00 0.00 45.80 2.29
217 218 2.290260 ACTCCGCCATTGATTGAAGTCA 60.290 45.455 0.00 0.00 0.00 3.41
270 284 2.431454 GTTTCTCTTCCCCTCTTGCAG 58.569 52.381 0.00 0.00 0.00 4.41
292 310 1.966451 GCCTCACGTCCTGGGTTTG 60.966 63.158 0.00 0.00 0.00 2.93
293 311 2.113243 GAGCCTCACGTCCTGGGTTT 62.113 60.000 4.54 0.00 0.00 3.27
294 312 2.526873 AGCCTCACGTCCTGGGTT 60.527 61.111 0.00 0.00 0.00 4.11
296 314 4.135153 CGAGCCTCACGTCCTGGG 62.135 72.222 0.00 0.00 0.00 4.45
297 315 2.436087 AAACGAGCCTCACGTCCTGG 62.436 60.000 0.00 0.00 43.16 4.45
300 318 1.006571 TGAAACGAGCCTCACGTCC 60.007 57.895 0.00 0.00 43.16 4.79
301 319 1.009389 CCTGAAACGAGCCTCACGTC 61.009 60.000 0.00 0.00 43.16 4.34
302 320 1.006102 CCTGAAACGAGCCTCACGT 60.006 57.895 0.00 0.00 45.89 4.49
303 321 0.319555 TTCCTGAAACGAGCCTCACG 60.320 55.000 0.00 0.00 0.00 4.35
304 322 1.149148 GTTCCTGAAACGAGCCTCAC 58.851 55.000 0.00 0.00 0.00 3.51
315 333 5.024118 TGGTTAAGGGTTTTTGTTCCTGAA 58.976 37.500 0.00 0.00 0.00 3.02
325 343 5.986741 CGTTGCTAATTTGGTTAAGGGTTTT 59.013 36.000 0.00 0.00 0.00 2.43
348 366 4.378874 GGATCTCCTTTGCAAACTTCTTCG 60.379 45.833 8.05 0.00 0.00 3.79
359 377 0.035439 TGAACCGGGATCTCCTTTGC 60.035 55.000 6.32 0.00 35.95 3.68
373 391 6.405538 TCCTTGGCATATTTTCATTTGAACC 58.594 36.000 0.00 0.00 33.13 3.62
379 397 7.486407 AGTCTTTCCTTGGCATATTTTCATT 57.514 32.000 0.00 0.00 0.00 2.57
395 413 1.476477 ACCTCCTCGCTAGTCTTTCC 58.524 55.000 0.00 0.00 0.00 3.13
424 442 9.768662 TTTTACTCACCTTCGAGTTATACTTTT 57.231 29.630 0.00 0.00 43.84 2.27
449 739 0.249911 AACGAGCCTCAGTCGCTTTT 60.250 50.000 0.00 0.00 41.26 2.27
452 742 1.080434 GAAACGAGCCTCAGTCGCT 60.080 57.895 0.00 0.00 41.26 4.93
453 743 1.347817 CTGAAACGAGCCTCAGTCGC 61.348 60.000 0.00 0.00 41.26 5.19
468 933 5.024118 TGGTTAAGGGTTTTTGTTCCTGAA 58.976 37.500 0.00 0.00 0.00 3.02
482 947 5.182380 TCTTCGTTGCTAATTTGGTTAAGGG 59.818 40.000 0.00 0.00 0.00 3.95
483 948 6.249035 TCTTCGTTGCTAATTTGGTTAAGG 57.751 37.500 0.00 0.00 0.00 2.69
489 954 5.107875 GCAAACTTCTTCGTTGCTAATTTGG 60.108 40.000 0.53 0.00 0.00 3.28
493 958 4.829064 TGCAAACTTCTTCGTTGCTAAT 57.171 36.364 8.84 0.00 0.00 1.73
495 960 4.334203 TCTTTGCAAACTTCTTCGTTGCTA 59.666 37.500 8.05 0.00 0.00 3.49
498 963 5.331902 TCTTCTTTGCAAACTTCTTCGTTG 58.668 37.500 8.05 0.00 0.00 4.10
500 965 5.278022 GGATCTTCTTTGCAAACTTCTTCGT 60.278 40.000 8.05 0.00 0.00 3.85
501 966 5.149977 GGATCTTCTTTGCAAACTTCTTCG 58.850 41.667 8.05 0.00 0.00 3.79
502 967 5.465051 GGGATCTTCTTTGCAAACTTCTTC 58.535 41.667 8.05 3.23 0.00 2.87
503 968 4.022849 CGGGATCTTCTTTGCAAACTTCTT 60.023 41.667 8.05 0.00 0.00 2.52
504 969 3.503748 CGGGATCTTCTTTGCAAACTTCT 59.496 43.478 8.05 0.00 0.00 2.85
505 970 3.366374 CCGGGATCTTCTTTGCAAACTTC 60.366 47.826 8.05 1.15 0.00 3.01
506 971 2.558359 CCGGGATCTTCTTTGCAAACTT 59.442 45.455 8.05 0.00 0.00 2.66
507 972 2.162681 CCGGGATCTTCTTTGCAAACT 58.837 47.619 8.05 0.00 0.00 2.66
508 973 1.886542 ACCGGGATCTTCTTTGCAAAC 59.113 47.619 8.05 0.00 0.00 2.93
509 974 2.286365 ACCGGGATCTTCTTTGCAAA 57.714 45.000 12.14 12.14 0.00 3.68
510 975 2.159382 GAACCGGGATCTTCTTTGCAA 58.841 47.619 6.32 0.00 0.00 4.08
511 976 1.073125 TGAACCGGGATCTTCTTTGCA 59.927 47.619 6.32 0.00 0.00 4.08
512 977 1.821216 TGAACCGGGATCTTCTTTGC 58.179 50.000 6.32 0.00 0.00 3.68
513 978 4.458989 TCATTTGAACCGGGATCTTCTTTG 59.541 41.667 6.32 0.63 0.00 2.77
514 979 4.662278 TCATTTGAACCGGGATCTTCTTT 58.338 39.130 6.32 0.00 0.00 2.52
515 980 4.301072 TCATTTGAACCGGGATCTTCTT 57.699 40.909 6.32 0.00 0.00 2.52
516 981 4.301072 TTCATTTGAACCGGGATCTTCT 57.699 40.909 6.32 0.00 0.00 2.85
517 982 5.385509 TTTTCATTTGAACCGGGATCTTC 57.614 39.130 6.32 0.07 33.13 2.87
518 983 7.491682 CATATTTTCATTTGAACCGGGATCTT 58.508 34.615 6.32 0.00 33.13 2.40
519 984 6.461509 GCATATTTTCATTTGAACCGGGATCT 60.462 38.462 6.32 0.00 33.13 2.75
520 985 5.691754 GCATATTTTCATTTGAACCGGGATC 59.308 40.000 6.32 4.19 33.13 3.36
521 986 5.453198 GGCATATTTTCATTTGAACCGGGAT 60.453 40.000 6.32 0.00 33.13 3.85
522 987 4.142049 GGCATATTTTCATTTGAACCGGGA 60.142 41.667 6.32 0.00 33.13 5.14
523 988 4.119136 GGCATATTTTCATTTGAACCGGG 58.881 43.478 6.32 0.00 33.13 5.73
524 989 4.753233 TGGCATATTTTCATTTGAACCGG 58.247 39.130 0.00 0.00 33.13 5.28
525 990 5.291614 CCTTGGCATATTTTCATTTGAACCG 59.708 40.000 0.00 0.00 33.13 4.44
534 999 6.095440 GCTAGTCTTTCCTTGGCATATTTTCA 59.905 38.462 0.00 0.00 0.00 2.69
535 1000 6.499172 GCTAGTCTTTCCTTGGCATATTTTC 58.501 40.000 0.00 0.00 0.00 2.29
541 1006 1.555075 TCGCTAGTCTTTCCTTGGCAT 59.445 47.619 0.00 0.00 0.00 4.40
542 1007 0.973632 TCGCTAGTCTTTCCTTGGCA 59.026 50.000 0.00 0.00 0.00 4.92
544 1009 1.825474 TCCTCGCTAGTCTTTCCTTGG 59.175 52.381 0.00 0.00 0.00 3.61
545 1010 2.159170 CCTCCTCGCTAGTCTTTCCTTG 60.159 54.545 0.00 0.00 0.00 3.61
549 1014 2.417515 CCAACCTCCTCGCTAGTCTTTC 60.418 54.545 0.00 0.00 0.00 2.62
553 1018 1.142097 GCCAACCTCCTCGCTAGTC 59.858 63.158 0.00 0.00 0.00 2.59
556 1021 0.397957 TATGGCCAACCTCCTCGCTA 60.398 55.000 10.96 0.00 36.63 4.26
558 1023 0.393808 TTTATGGCCAACCTCCTCGC 60.394 55.000 10.96 0.00 36.63 5.03
559 1024 2.122783 TTTTATGGCCAACCTCCTCG 57.877 50.000 10.96 0.00 36.63 4.63
581 1046 8.827677 GCATTTTTACTCACCTTCGAGTTATAT 58.172 33.333 0.00 0.00 43.84 0.86
583 1048 6.183360 CGCATTTTTACTCACCTTCGAGTTAT 60.183 38.462 0.00 0.00 43.84 1.89
587 1081 3.678072 TCGCATTTTTACTCACCTTCGAG 59.322 43.478 0.00 0.00 39.05 4.04
590 1084 3.500680 TGGTCGCATTTTTACTCACCTTC 59.499 43.478 0.00 0.00 0.00 3.46
689 1184 5.482526 TGTATAGTTTTCAGTAGGGCAGTGA 59.517 40.000 0.00 0.00 34.66 3.41
725 1220 1.101049 AAGCCCAACTCGTGTGGTTG 61.101 55.000 0.00 0.00 42.35 3.77
743 1238 4.407365 CTTGGGCTCTTTCTTAGGGAAAA 58.593 43.478 0.00 0.00 42.52 2.29
783 1278 3.637273 GTGCCCGGACAGGAAGGT 61.637 66.667 0.73 0.00 45.00 3.50
871 1366 2.282462 CTGCGCTGGGGGAGTTTT 60.282 61.111 9.73 0.00 0.00 2.43
916 1411 0.106894 GCTTATCGGGGAGTTCAGGG 59.893 60.000 0.00 0.00 0.00 4.45
919 1414 2.032620 GAGAGCTTATCGGGGAGTTCA 58.967 52.381 0.00 0.00 0.00 3.18
920 1415 1.341852 GGAGAGCTTATCGGGGAGTTC 59.658 57.143 0.00 0.00 0.00 3.01
921 1416 1.343075 TGGAGAGCTTATCGGGGAGTT 60.343 52.381 0.00 0.00 0.00 3.01
922 1417 0.261991 TGGAGAGCTTATCGGGGAGT 59.738 55.000 0.00 0.00 0.00 3.85
968 1463 4.360405 CTGGGAAACGGGTGGGGG 62.360 72.222 0.00 0.00 0.00 5.40
1059 1554 1.520787 CCATTGTCCGTCGTAGCCC 60.521 63.158 0.00 0.00 0.00 5.19
1063 1558 0.382873 CCGATCCATTGTCCGTCGTA 59.617 55.000 0.00 0.00 0.00 3.43
1071 1566 3.797353 AGCCGGCCGATCCATTGT 61.797 61.111 30.73 0.00 34.01 2.71
1531 2026 2.938451 TGATAAGGATGTTGAAGCAGCG 59.062 45.455 0.00 0.00 0.00 5.18
1566 2061 3.303049 GGCCTCATTGAATCTCCCAAAT 58.697 45.455 0.00 0.00 0.00 2.32
1680 2175 1.284198 AGCTGAAATGCCTCATCCACT 59.716 47.619 0.00 0.00 0.00 4.00
1695 2190 2.071540 CGCATTCTCTCAAACAGCTGA 58.928 47.619 23.35 0.00 0.00 4.26
1696 2191 1.465354 GCGCATTCTCTCAAACAGCTG 60.465 52.381 13.48 13.48 0.00 4.24
1728 2223 2.102070 AAACAACCGTATCCGCATCA 57.898 45.000 0.00 0.00 0.00 3.07
1881 2376 2.287009 CGCCTCCACAAACTTCTTTGAC 60.287 50.000 0.27 0.00 39.43 3.18
1968 2463 9.003658 CAGTTAAAACTACAGAGTCCATCAATT 57.996 33.333 0.00 0.00 37.08 2.32
1977 2472 8.585881 TCATCTAAGCAGTTAAAACTACAGAGT 58.414 33.333 0.00 0.00 37.08 3.24
1987 2482 7.019774 GATGTGCATCATCTAAGCAGTTAAA 57.980 36.000 17.00 0.00 46.64 1.52
2012 2507 3.068024 GTCCACCATTTGCTTCAAGACAA 59.932 43.478 0.00 0.00 0.00 3.18
2050 2545 3.397955 AGTTTTGTCCAAGTACCCATCCT 59.602 43.478 0.00 0.00 0.00 3.24
2117 2622 4.248859 CTCAAGTGTATTGTCAGGTCCAG 58.751 47.826 0.00 0.00 0.00 3.86
2159 2664 2.105821 CAGGTTGGTCCACTAGTTCCAA 59.894 50.000 15.63 15.63 39.02 3.53
2193 2698 2.880890 GACTTCAACATGCAAGTCCACT 59.119 45.455 16.65 0.00 41.83 4.00
2238 2743 5.128827 GTCAGTGTGAGACCCAATATTCCTA 59.871 44.000 0.00 0.00 0.00 2.94
2257 2764 7.819900 GTCATCAGTAAATAGAACTTGGTCAGT 59.180 37.037 0.00 0.00 37.30 3.41
2258 2765 8.037758 AGTCATCAGTAAATAGAACTTGGTCAG 58.962 37.037 0.00 0.00 0.00 3.51
2271 2778 8.851145 ACATCAGTATACGAGTCATCAGTAAAT 58.149 33.333 0.00 0.00 0.00 1.40
2286 2793 5.530171 TCGGTTCTCAGGTACATCAGTATAC 59.470 44.000 0.00 0.00 31.84 1.47
2317 2824 1.301677 GAGCTTCAAGCCAACCGAGG 61.302 60.000 5.53 0.00 43.77 4.63
2338 2845 2.283604 TGGGCGAGCTCACACCTA 60.284 61.111 15.40 6.96 0.00 3.08
2369 2876 4.567747 GGAAGAAAATGAGCCTTCCCTGTA 60.568 45.833 8.73 0.00 46.27 2.74
2474 2981 1.619654 CTTGCATCAACCCAACCAGA 58.380 50.000 0.00 0.00 0.00 3.86
2484 2991 3.881220 TCTCTGATCATGCTTGCATCAA 58.119 40.909 4.99 0.00 0.00 2.57
2499 3006 4.104102 AGTTAACCAAACACCCATCTCTGA 59.896 41.667 0.88 0.00 40.83 3.27
2913 3477 4.680237 CAAGCGTCGCCTCCCACA 62.680 66.667 14.86 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.