Multiple sequence alignment - TraesCS3D01G213900

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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 TraesCS3D01G213900 chr3D 100.000 5494 0 0 1 5494 288114566 288109073 0.000000e+00 10146.0
1 TraesCS3D01G213900 chr3D 97.661 513 10 2 1 512 459099159 459098648 0.000000e+00 880.0
2 TraesCS3D01G213900 chr3A 91.261 4051 131 89 1578 5480 377802506 377798531 0.000000e+00 5313.0
3 TraesCS3D01G213900 chr3A 85.606 924 32 32 705 1577 377803423 377802550 0.000000e+00 876.0
4 TraesCS3D01G213900 chr3A 91.150 113 9 1 544 655 377803550 377803438 9.530000e-33 152.0
5 TraesCS3D01G213900 chr3A 93.182 44 3 0 503 546 16292855 16292812 1.280000e-06 65.8
6 TraesCS3D01G213900 chr3B 91.651 2683 108 45 2846 5480 380893478 380890864 0.000000e+00 3607.0
7 TraesCS3D01G213900 chr3B 88.518 1167 31 33 1677 2773 380894618 380893485 0.000000e+00 1317.0
8 TraesCS3D01G213900 chr3B 86.303 1044 45 26 544 1557 380895805 380894830 0.000000e+00 1046.0
9 TraesCS3D01G213900 chr3B 94.253 87 1 1 1575 1657 380894775 380894689 4.470000e-26 130.0
10 TraesCS3D01G213900 chr4D 97.679 517 11 1 1 516 183193594 183193078 0.000000e+00 887.0
11 TraesCS3D01G213900 chr4D 97.665 514 11 1 1 513 442399476 442398963 0.000000e+00 881.0
12 TraesCS3D01G213900 chr6D 98.039 510 9 1 1 509 11162911 11163420 0.000000e+00 885.0
13 TraesCS3D01G213900 chr6D 97.843 510 10 1 1 509 291374420 291373911 0.000000e+00 880.0
14 TraesCS3D01G213900 chr6D 97.843 510 10 1 1 509 340563154 340562645 0.000000e+00 880.0
15 TraesCS3D01G213900 chr2D 98.039 510 9 1 1 509 487266978 487266469 0.000000e+00 885.0
16 TraesCS3D01G213900 chr2D 95.238 42 1 1 510 550 271248 271207 1.280000e-06 65.8
17 TraesCS3D01G213900 chr2D 88.889 54 3 3 510 562 56075001 56075052 4.590000e-06 63.9
18 TraesCS3D01G213900 chr5D 97.852 512 10 1 1 511 65112790 65113301 0.000000e+00 883.0
19 TraesCS3D01G213900 chr5D 97.847 511 9 2 1 509 530609825 530609315 0.000000e+00 881.0
20 TraesCS3D01G213900 chr5D 95.455 44 2 0 1141 1184 435933403 435933446 2.750000e-08 71.3
21 TraesCS3D01G213900 chr5D 100.000 36 0 0 514 549 287021685 287021650 3.550000e-07 67.6
22 TraesCS3D01G213900 chr1A 92.079 101 7 1 1083 1183 586283229 586283328 2.060000e-29 141.0
23 TraesCS3D01G213900 chr1D 88.889 108 10 2 1076 1183 487807911 487808016 1.240000e-26 132.0
24 TraesCS3D01G213900 chr1D 97.368 38 0 1 510 546 493757938 493757901 4.590000e-06 63.9
25 TraesCS3D01G213900 chr1B 88.889 108 10 2 1076 1183 679567481 679567586 1.240000e-26 132.0
26 TraesCS3D01G213900 chr1B 85.714 105 15 0 3080 3184 679569826 679569930 1.620000e-20 111.0
27 TraesCS3D01G213900 chr7A 91.837 49 3 1 503 550 547550508 547550460 3.550000e-07 67.6
28 TraesCS3D01G213900 chr7A 91.489 47 2 2 510 554 726986170 726986216 4.590000e-06 63.9
29 TraesCS3D01G213900 chr5A 93.182 44 3 0 503 546 55264581 55264538 1.280000e-06 65.8
30 TraesCS3D01G213900 chr5A 93.182 44 3 0 1141 1184 549953324 549953367 1.280000e-06 65.8
31 TraesCS3D01G213900 chr4B 100.000 31 0 0 4889 4919 518086837 518086867 2.140000e-04 58.4
32 TraesCS3D01G213900 chr4A 94.737 38 1 1 510 546 740583274 740583311 2.140000e-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 TraesCS3D01G213900 chr3D 288109073 288114566 5493 True 10146.000000 10146 100.00000 1 5494 1 chr3D.!!$R1 5493
1 TraesCS3D01G213900 chr3D 459098648 459099159 511 True 880.000000 880 97.66100 1 512 1 chr3D.!!$R2 511
2 TraesCS3D01G213900 chr3A 377798531 377803550 5019 True 2113.666667 5313 89.33900 544 5480 3 chr3A.!!$R2 4936
3 TraesCS3D01G213900 chr3B 380890864 380895805 4941 True 1525.000000 3607 90.18125 544 5480 4 chr3B.!!$R1 4936
4 TraesCS3D01G213900 chr4D 183193078 183193594 516 True 887.000000 887 97.67900 1 516 1 chr4D.!!$R1 515
5 TraesCS3D01G213900 chr4D 442398963 442399476 513 True 881.000000 881 97.66500 1 513 1 chr4D.!!$R2 512
6 TraesCS3D01G213900 chr6D 11162911 11163420 509 False 885.000000 885 98.03900 1 509 1 chr6D.!!$F1 508
7 TraesCS3D01G213900 chr6D 291373911 291374420 509 True 880.000000 880 97.84300 1 509 1 chr6D.!!$R1 508
8 TraesCS3D01G213900 chr6D 340562645 340563154 509 True 880.000000 880 97.84300 1 509 1 chr6D.!!$R2 508
9 TraesCS3D01G213900 chr2D 487266469 487266978 509 True 885.000000 885 98.03900 1 509 1 chr2D.!!$R2 508
10 TraesCS3D01G213900 chr5D 65112790 65113301 511 False 883.000000 883 97.85200 1 511 1 chr5D.!!$F1 510
11 TraesCS3D01G213900 chr5D 530609315 530609825 510 True 881.000000 881 97.84700 1 509 1 chr5D.!!$R2 508

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
541 544 0.185175 AGTCCCTGAACCAAACACCC 59.815 55.000 0.00 0.00 0.00 4.61 F
774 787 0.250901 CAGTTGTGGGGAAGACAGGG 60.251 60.000 0.00 0.00 0.00 4.45 F
887 926 0.472471 GGTCTCCAAGTCACAACCCA 59.528 55.000 0.00 0.00 0.00 4.51 F
925 967 0.613777 ACCTACCCGAAGCCAAGAAG 59.386 55.000 0.00 0.00 0.00 2.85 F
1483 1562 1.138661 TGCATGATCATACCTCACGCA 59.861 47.619 8.15 9.12 39.27 5.24 F
2658 2967 1.235281 GCCTTTGGACTTCACCGGAC 61.235 60.000 9.46 0.00 0.00 4.79 F
3107 3450 1.276622 GAGAGCCTGTTGGGGAAGTA 58.723 55.000 0.00 0.00 35.12 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2305 2591 0.474184 ACACAGTAAGGCCACAGCTT 59.526 50.000 5.01 0.00 39.73 3.74 R
2500 2800 0.809636 TGAAGTGGATATGGCACGCG 60.810 55.000 3.53 3.53 0.00 6.01 R
2722 3046 3.571590 ACTCCTCCTATGTTCAGCTAGG 58.428 50.000 0.00 0.00 36.60 3.02 R
2908 3250 1.738432 TTTGCATGCAAAGCACGGA 59.262 47.368 35.80 17.12 43.04 4.69 R
3009 3352 0.590682 TGCGCATTTCAGCTTCGAAA 59.409 45.000 5.66 2.05 39.13 3.46 R
4142 4522 0.816825 CCCGATCTGCCCAGTCAATG 60.817 60.000 0.00 0.00 0.00 2.82 R
4774 5174 0.179124 GATCCACACAGAGCGAGACC 60.179 60.000 0.00 0.00 0.00 3.85 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
123 124 2.290641 CCAATGGTAGTAGTTGTGGGCA 60.291 50.000 0.00 0.00 0.00 5.36
142 143 3.491619 GGCAGCGAGATCAAGAACTATGA 60.492 47.826 0.00 0.00 0.00 2.15
472 475 4.286808 GGGGTAGGGTACAAAACTGACTTA 59.713 45.833 0.00 0.00 0.00 2.24
521 524 9.970553 TGACTACTCTAACATCTAGGACTAAAA 57.029 33.333 0.00 0.00 0.00 1.52
537 540 5.828747 GACTAAAAAGTCCCTGAACCAAAC 58.171 41.667 0.00 0.00 32.97 2.93
538 541 5.265989 ACTAAAAAGTCCCTGAACCAAACA 58.734 37.500 0.00 0.00 0.00 2.83
539 542 4.465632 AAAAAGTCCCTGAACCAAACAC 57.534 40.909 0.00 0.00 0.00 3.32
540 543 2.067365 AAGTCCCTGAACCAAACACC 57.933 50.000 0.00 0.00 0.00 4.16
541 544 0.185175 AGTCCCTGAACCAAACACCC 59.815 55.000 0.00 0.00 0.00 4.61
542 545 0.826256 GTCCCTGAACCAAACACCCC 60.826 60.000 0.00 0.00 0.00 4.95
578 581 8.586570 TGAACAAAAATTAGCACTAAATGTGG 57.413 30.769 0.00 0.00 46.27 4.17
633 636 5.726980 TGGAAAGATCCCAAACAAATGAG 57.273 39.130 0.00 0.00 45.95 2.90
641 644 5.867903 TCCCAAACAAATGAGACACAAAT 57.132 34.783 0.00 0.00 0.00 2.32
651 654 3.804036 TGAGACACAAATCCACGAAACT 58.196 40.909 0.00 0.00 0.00 2.66
652 655 3.807622 TGAGACACAAATCCACGAAACTC 59.192 43.478 0.00 0.00 0.00 3.01
658 661 4.976116 CACAAATCCACGAAACTCTTTTCC 59.024 41.667 0.00 0.00 38.35 3.13
659 662 4.037565 ACAAATCCACGAAACTCTTTTCCC 59.962 41.667 0.00 0.00 38.35 3.97
660 663 2.265589 TCCACGAAACTCTTTTCCCC 57.734 50.000 0.00 0.00 38.35 4.81
661 664 1.772453 TCCACGAAACTCTTTTCCCCT 59.228 47.619 0.00 0.00 38.35 4.79
662 665 1.880027 CCACGAAACTCTTTTCCCCTG 59.120 52.381 0.00 0.00 38.35 4.45
663 666 1.266989 CACGAAACTCTTTTCCCCTGC 59.733 52.381 0.00 0.00 38.35 4.85
664 667 1.133915 ACGAAACTCTTTTCCCCTGCA 60.134 47.619 0.00 0.00 38.35 4.41
665 668 1.953686 CGAAACTCTTTTCCCCTGCAA 59.046 47.619 0.00 0.00 38.35 4.08
666 669 2.360801 CGAAACTCTTTTCCCCTGCAAA 59.639 45.455 0.00 0.00 38.35 3.68
668 671 4.679372 CGAAACTCTTTTCCCCTGCAAAAA 60.679 41.667 0.00 0.00 38.35 1.94
741 747 7.604657 ACCAGAGAAAGAGAGAGAAAAGTAA 57.395 36.000 0.00 0.00 0.00 2.24
774 787 0.250901 CAGTTGTGGGGAAGACAGGG 60.251 60.000 0.00 0.00 0.00 4.45
834 856 7.019964 ACCCATCCATCCATTCCTCTATAAATT 59.980 37.037 0.00 0.00 0.00 1.82
840 862 5.305585 TCCATTCCTCTATAAATTGACGCC 58.694 41.667 0.00 0.00 0.00 5.68
886 925 0.765510 AGGTCTCCAAGTCACAACCC 59.234 55.000 0.00 0.00 0.00 4.11
887 926 0.472471 GGTCTCCAAGTCACAACCCA 59.528 55.000 0.00 0.00 0.00 4.51
925 967 0.613777 ACCTACCCGAAGCCAAGAAG 59.386 55.000 0.00 0.00 0.00 2.85
975 1017 2.359975 GAACCACCAGCCTTCCCG 60.360 66.667 0.00 0.00 0.00 5.14
976 1018 2.852075 AACCACCAGCCTTCCCGA 60.852 61.111 0.00 0.00 0.00 5.14
1245 1310 2.809601 CTCACGCGCGTAAGGCTT 60.810 61.111 37.24 8.36 40.44 4.35
1348 1427 1.879380 CATGTTGGCCTTCTTGTTCGA 59.121 47.619 3.32 0.00 0.00 3.71
1462 1541 3.589881 GCATGGATCACGCCTGCC 61.590 66.667 0.00 0.00 0.00 4.85
1463 1542 2.191375 CATGGATCACGCCTGCCT 59.809 61.111 0.00 0.00 0.00 4.75
1464 1543 2.184830 CATGGATCACGCCTGCCTG 61.185 63.158 0.00 0.00 0.00 4.85
1465 1544 4.783621 TGGATCACGCCTGCCTGC 62.784 66.667 0.00 0.00 0.00 4.85
1483 1562 1.138661 TGCATGATCATACCTCACGCA 59.861 47.619 8.15 9.12 39.27 5.24
1557 1636 4.618227 GCTGGACAAATCACAAATGGTACC 60.618 45.833 4.43 4.43 0.00 3.34
1805 2013 1.670811 GACGCCATGTGATTGGGTAAG 59.329 52.381 0.00 0.00 37.24 2.34
1838 2081 3.885901 TCTCTCTCTCTCTCTCTCTCTCG 59.114 52.174 0.00 0.00 0.00 4.04
1849 2092 2.623416 TCTCTCTCTCGTGCTTGTTTGA 59.377 45.455 0.00 0.00 0.00 2.69
2137 2392 2.206900 TCCTCTTGGAGTGCCCCA 59.793 61.111 0.00 0.00 37.46 4.96
2226 2499 1.594397 CTATACATGCACAGCACGGTG 59.406 52.381 3.15 3.15 43.04 4.94
2244 2522 2.805099 GGTGCAGCTAGATTAGATGTGC 59.195 50.000 9.07 0.00 43.74 4.57
2332 2620 2.092646 TGGCCTTACTGTGTTTGACTGT 60.093 45.455 3.32 0.00 39.80 3.55
2381 2669 5.431765 TCTGTTTGCTCTTCTCTTTTGTCT 58.568 37.500 0.00 0.00 0.00 3.41
2433 2721 1.269448 GAGAGGTGAGCGATCCATCTC 59.731 57.143 14.67 14.67 41.00 2.75
2437 2733 1.327303 GTGAGCGATCCATCTCCTCT 58.673 55.000 0.00 0.00 0.00 3.69
2438 2734 2.509569 GTGAGCGATCCATCTCCTCTA 58.490 52.381 0.00 0.00 0.00 2.43
2439 2735 2.227865 GTGAGCGATCCATCTCCTCTAC 59.772 54.545 0.00 0.00 0.00 2.59
2440 2736 2.107378 TGAGCGATCCATCTCCTCTACT 59.893 50.000 0.00 0.00 0.00 2.57
2441 2737 2.747446 GAGCGATCCATCTCCTCTACTC 59.253 54.545 0.00 0.00 0.00 2.59
2442 2738 2.375174 AGCGATCCATCTCCTCTACTCT 59.625 50.000 0.00 0.00 0.00 3.24
2443 2739 3.585289 AGCGATCCATCTCCTCTACTCTA 59.415 47.826 0.00 0.00 0.00 2.43
2444 2740 3.687698 GCGATCCATCTCCTCTACTCTAC 59.312 52.174 0.00 0.00 0.00 2.59
2445 2741 4.564821 GCGATCCATCTCCTCTACTCTACT 60.565 50.000 0.00 0.00 0.00 2.57
2446 2742 5.175859 CGATCCATCTCCTCTACTCTACTC 58.824 50.000 0.00 0.00 0.00 2.59
2491 2791 1.717194 TTACTCCGTTTTGCTAGGCG 58.283 50.000 0.00 0.00 0.00 5.52
2658 2967 1.235281 GCCTTTGGACTTCACCGGAC 61.235 60.000 9.46 0.00 0.00 4.79
2737 3061 7.225725 ACTAGTACTACCTAGCTGAACATAGG 58.774 42.308 0.00 0.00 43.61 2.57
2738 3062 6.263412 AGTACTACCTAGCTGAACATAGGA 57.737 41.667 4.95 0.00 41.00 2.94
2739 3063 6.300703 AGTACTACCTAGCTGAACATAGGAG 58.699 44.000 4.95 1.51 41.00 3.69
2740 3064 4.475345 ACTACCTAGCTGAACATAGGAGG 58.525 47.826 4.95 0.00 41.00 4.30
2796 3123 9.532494 TTGTTATTGACCAAGGTACTAGTACTA 57.468 33.333 27.71 10.07 38.49 1.82
2797 3124 9.705103 TGTTATTGACCAAGGTACTAGTACTAT 57.295 33.333 27.71 16.58 38.49 2.12
2908 3250 3.737266 CGTACCGTACAGAAATGTGTGTT 59.263 43.478 9.34 0.00 32.56 3.32
2910 3252 3.135994 ACCGTACAGAAATGTGTGTTCC 58.864 45.455 0.00 0.00 32.56 3.62
3000 3343 5.823045 AGTTTCAGTAGAGGGTTTTGAACAG 59.177 40.000 0.00 0.00 0.00 3.16
3009 3352 7.205515 AGAGGGTTTTGAACAGATGATCTAT 57.794 36.000 0.00 0.00 0.00 1.98
3107 3450 1.276622 GAGAGCCTGTTGGGGAAGTA 58.723 55.000 0.00 0.00 35.12 2.24
3467 3821 4.623002 TGCGCGATAGTTTAACCATCATA 58.377 39.130 12.10 0.00 39.35 2.15
3725 4088 6.092670 CGATCCGCAATCTCCATTGTTTATAT 59.907 38.462 0.00 0.00 41.51 0.86
3875 4243 7.961283 GTGGACGGTTTGAATAATCTCTTTAAC 59.039 37.037 0.00 0.00 0.00 2.01
3876 4244 7.881232 TGGACGGTTTGAATAATCTCTTTAACT 59.119 33.333 0.00 0.00 0.00 2.24
3901 4272 3.576982 AGTAACGAATGTCCTCCACTTCA 59.423 43.478 0.00 0.00 0.00 3.02
3999 4371 8.658499 GAACGGATCCATGTTAGTAGTATTTT 57.342 34.615 13.41 0.00 0.00 1.82
4000 4372 9.106070 GAACGGATCCATGTTAGTAGTATTTTT 57.894 33.333 13.41 0.00 0.00 1.94
4108 4488 7.994194 AGTACTAGTACACATTAGCAGTAACC 58.006 38.462 29.87 2.04 38.48 2.85
4142 4522 2.996621 CGACTGATCTCTTTTGGTGGAC 59.003 50.000 0.00 0.00 0.00 4.02
4151 4531 3.221771 TCTTTTGGTGGACATTGACTGG 58.778 45.455 0.00 0.00 0.00 4.00
4281 4661 2.282180 GCTCCAACCGCCAAGGAA 60.282 61.111 0.00 0.00 45.00 3.36
4296 4676 4.322801 GCCAAGGAACTAGTTCTCAAGCTA 60.323 45.833 29.66 0.00 38.49 3.32
4409 4793 2.628657 GCAGGAGTATGTTCCGGACTAT 59.371 50.000 1.83 3.96 42.29 2.12
4650 5044 0.682852 AGCAAGTAGTGGTGCGGTTA 59.317 50.000 0.00 0.00 45.62 2.85
4684 5079 5.012239 TCTTTTGGTCGTAGCTTAGGTAGA 58.988 41.667 0.00 0.00 0.00 2.59
4687 5082 3.285484 TGGTCGTAGCTTAGGTAGAAGG 58.715 50.000 0.00 0.00 0.00 3.46
4689 5084 3.950395 GGTCGTAGCTTAGGTAGAAGGAA 59.050 47.826 0.00 0.00 0.00 3.36
4691 5086 4.036616 GTCGTAGCTTAGGTAGAAGGAAGG 59.963 50.000 0.00 0.00 0.00 3.46
4698 5093 5.627272 GCTTAGGTAGAAGGAAGGAAAGGAC 60.627 48.000 0.00 0.00 0.00 3.85
4739 5139 0.907486 TAGGAGCAGCAGCAGATGTT 59.093 50.000 3.17 0.00 45.49 2.71
4812 5212 0.866906 CTGTTTGCTTGCACGTGTGG 60.867 55.000 18.38 8.65 0.00 4.17
4814 5214 3.423162 TTTGCTTGCACGTGTGGGC 62.423 57.895 18.38 17.65 0.00 5.36
5022 5441 3.461773 CGGCGATGGGACCTGTCT 61.462 66.667 0.00 0.00 0.00 3.41
5029 5448 2.760385 GGGACCTGTCTCTCCCGG 60.760 72.222 0.00 0.00 36.97 5.73
5190 5627 2.224314 CGCGCTTCCTTCTTTCTTTCTT 59.776 45.455 5.56 0.00 0.00 2.52
5193 5630 4.023622 GCGCTTCCTTCTTTCTTTCTTTCT 60.024 41.667 0.00 0.00 0.00 2.52
5196 5633 6.634837 CGCTTCCTTCTTTCTTTCTTTCTTTC 59.365 38.462 0.00 0.00 0.00 2.62
5238 5675 1.597663 ACGCCGTTTTCTCTTGTCTTG 59.402 47.619 0.00 0.00 0.00 3.02
5315 5752 0.609131 TTTGGCTGGACTGGCTAAGC 60.609 55.000 4.55 0.76 32.25 3.09
5333 5770 1.683385 AGCTTTCAACTTCAACAGGCC 59.317 47.619 0.00 0.00 0.00 5.19
5357 5794 1.412710 CTTCCTTAGTCTATGCGGCCA 59.587 52.381 2.24 0.00 0.00 5.36
5480 5921 7.787623 TCTCTTCATTCAGCATAGGATATGA 57.212 36.000 0.99 0.00 0.00 2.15
5481 5922 8.376803 TCTCTTCATTCAGCATAGGATATGAT 57.623 34.615 0.99 0.00 0.00 2.45
5482 5923 8.823794 TCTCTTCATTCAGCATAGGATATGATT 58.176 33.333 0.99 0.00 0.00 2.57
5483 5924 9.451002 CTCTTCATTCAGCATAGGATATGATTT 57.549 33.333 0.99 0.00 0.00 2.17
5484 5925 9.803507 TCTTCATTCAGCATAGGATATGATTTT 57.196 29.630 0.99 0.00 0.00 1.82
5485 5926 9.841880 CTTCATTCAGCATAGGATATGATTTTG 57.158 33.333 0.99 0.00 0.00 2.44
5486 5927 8.344446 TCATTCAGCATAGGATATGATTTTGG 57.656 34.615 0.99 0.00 0.00 3.28
5487 5928 8.165397 TCATTCAGCATAGGATATGATTTTGGA 58.835 33.333 0.99 0.00 0.00 3.53
5488 5929 7.991084 TTCAGCATAGGATATGATTTTGGAG 57.009 36.000 0.99 0.00 0.00 3.86
5489 5930 6.479006 TCAGCATAGGATATGATTTTGGAGG 58.521 40.000 0.99 0.00 0.00 4.30
5490 5931 5.651139 CAGCATAGGATATGATTTTGGAGGG 59.349 44.000 0.99 0.00 0.00 4.30
5491 5932 5.314306 AGCATAGGATATGATTTTGGAGGGT 59.686 40.000 0.99 0.00 0.00 4.34
5492 5933 6.505344 AGCATAGGATATGATTTTGGAGGGTA 59.495 38.462 0.99 0.00 0.00 3.69
5493 5934 6.825721 GCATAGGATATGATTTTGGAGGGTAG 59.174 42.308 0.99 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 124 4.211125 TCCTCATAGTTCTTGATCTCGCT 58.789 43.478 0.00 0.00 0.00 4.93
142 143 1.001760 ACGTCAGCCCCTACATCCT 59.998 57.895 0.00 0.00 0.00 3.24
318 319 2.359850 GCTCCGCCAACATCACCA 60.360 61.111 0.00 0.00 0.00 4.17
442 443 2.419457 TGTACCCTACCCCAAGTTGA 57.581 50.000 3.87 0.00 0.00 3.18
472 475 9.001542 GTCATTATGGTATACGACTTCTAGTCT 57.998 37.037 5.41 0.00 42.92 3.24
516 519 5.451381 GGTGTTTGGTTCAGGGACTTTTTAG 60.451 44.000 0.00 0.00 34.60 1.85
517 520 4.403113 GGTGTTTGGTTCAGGGACTTTTTA 59.597 41.667 0.00 0.00 34.60 1.52
518 521 3.196901 GGTGTTTGGTTCAGGGACTTTTT 59.803 43.478 0.00 0.00 34.60 1.94
519 522 2.764010 GGTGTTTGGTTCAGGGACTTTT 59.236 45.455 0.00 0.00 34.60 2.27
520 523 2.384828 GGTGTTTGGTTCAGGGACTTT 58.615 47.619 0.00 0.00 34.60 2.66
521 524 1.411074 GGGTGTTTGGTTCAGGGACTT 60.411 52.381 0.00 0.00 34.60 3.01
522 525 0.185175 GGGTGTTTGGTTCAGGGACT 59.815 55.000 0.00 0.00 43.88 3.85
523 526 0.826256 GGGGTGTTTGGTTCAGGGAC 60.826 60.000 0.00 0.00 0.00 4.46
524 527 0.996762 AGGGGTGTTTGGTTCAGGGA 60.997 55.000 0.00 0.00 0.00 4.20
525 528 0.105709 AAGGGGTGTTTGGTTCAGGG 60.106 55.000 0.00 0.00 0.00 4.45
526 529 2.158519 AGTAAGGGGTGTTTGGTTCAGG 60.159 50.000 0.00 0.00 0.00 3.86
527 530 3.146847 GAGTAAGGGGTGTTTGGTTCAG 58.853 50.000 0.00 0.00 0.00 3.02
528 531 2.781174 AGAGTAAGGGGTGTTTGGTTCA 59.219 45.455 0.00 0.00 0.00 3.18
529 532 3.503800 AGAGTAAGGGGTGTTTGGTTC 57.496 47.619 0.00 0.00 0.00 3.62
530 533 4.414514 AGTTAGAGTAAGGGGTGTTTGGTT 59.585 41.667 0.00 0.00 0.00 3.67
531 534 3.978672 AGTTAGAGTAAGGGGTGTTTGGT 59.021 43.478 0.00 0.00 0.00 3.67
532 535 4.041198 TCAGTTAGAGTAAGGGGTGTTTGG 59.959 45.833 0.00 0.00 0.00 3.28
533 536 5.223449 TCAGTTAGAGTAAGGGGTGTTTG 57.777 43.478 0.00 0.00 0.00 2.93
534 537 5.131475 TGTTCAGTTAGAGTAAGGGGTGTTT 59.869 40.000 0.00 0.00 0.00 2.83
535 538 4.657039 TGTTCAGTTAGAGTAAGGGGTGTT 59.343 41.667 0.00 0.00 0.00 3.32
536 539 4.228824 TGTTCAGTTAGAGTAAGGGGTGT 58.771 43.478 0.00 0.00 0.00 4.16
537 540 4.884668 TGTTCAGTTAGAGTAAGGGGTG 57.115 45.455 0.00 0.00 0.00 4.61
538 541 5.899631 TTTGTTCAGTTAGAGTAAGGGGT 57.100 39.130 0.00 0.00 0.00 4.95
539 542 7.761038 ATTTTTGTTCAGTTAGAGTAAGGGG 57.239 36.000 0.00 0.00 0.00 4.79
541 544 9.827411 GCTAATTTTTGTTCAGTTAGAGTAAGG 57.173 33.333 0.00 0.00 0.00 2.69
578 581 1.156736 TAGCGGCTTTGCTGAGTTTC 58.843 50.000 8.26 0.00 46.70 2.78
612 615 5.243730 TGTCTCATTTGTTTGGGATCTTTCC 59.756 40.000 0.00 0.00 41.77 3.13
619 622 5.221422 GGATTTGTGTCTCATTTGTTTGGGA 60.221 40.000 0.00 0.00 0.00 4.37
633 636 4.813296 AAGAGTTTCGTGGATTTGTGTC 57.187 40.909 0.00 0.00 0.00 3.67
641 644 1.772453 AGGGGAAAAGAGTTTCGTGGA 59.228 47.619 0.00 0.00 43.56 4.02
673 676 7.039722 TGATATGAAAAAGGGTTTCCTACCT 57.960 36.000 0.00 0.00 46.86 3.08
674 677 7.898014 ATGATATGAAAAAGGGTTTCCTACC 57.102 36.000 0.00 0.00 44.07 3.18
741 747 3.493350 CCACAACTGCTGAGAGTACTGTT 60.493 47.826 0.00 0.00 0.00 3.16
774 787 1.004679 CAACATTGTTGGGGCCTGC 60.005 57.895 19.66 0.00 0.00 4.85
886 925 2.049627 GCTGATGGTAGGGGAGGCTG 62.050 65.000 0.00 0.00 0.00 4.85
887 926 1.768077 GCTGATGGTAGGGGAGGCT 60.768 63.158 0.00 0.00 0.00 4.58
975 1017 2.847435 GATCCGTCGGTGTTGGGGTC 62.847 65.000 11.88 0.00 0.00 4.46
976 1018 2.926242 ATCCGTCGGTGTTGGGGT 60.926 61.111 11.88 0.00 0.00 4.95
1236 1301 1.412710 TCTATGGAGCCAAGCCTTACG 59.587 52.381 0.00 0.00 0.00 3.18
1237 1302 3.560636 TTCTATGGAGCCAAGCCTTAC 57.439 47.619 0.00 0.00 0.00 2.34
1238 1303 4.796110 ATTTCTATGGAGCCAAGCCTTA 57.204 40.909 0.00 0.00 0.00 2.69
1245 1310 8.055181 AGAAAAGATTGTATTTCTATGGAGCCA 58.945 33.333 0.00 0.00 42.47 4.75
1348 1427 1.047801 GTGCCATCCCCAAACAAACT 58.952 50.000 0.00 0.00 0.00 2.66
1465 1544 2.138320 GGTGCGTGAGGTATGATCATG 58.862 52.381 18.72 0.46 36.87 3.07
1557 1636 1.662629 CGGATGCAGCAACTTCTAGTG 59.337 52.381 3.51 0.00 0.00 2.74
1805 2013 5.983540 AGAGAGAGAGAGAGAGAGAGAAAC 58.016 45.833 0.00 0.00 0.00 2.78
1838 2081 1.523934 GCATGCTGTTCAAACAAGCAC 59.476 47.619 11.37 6.96 41.88 4.40
2137 2392 4.463050 AATTAGAGGGAGGACGAGAGAT 57.537 45.455 0.00 0.00 0.00 2.75
2305 2591 0.474184 ACACAGTAAGGCCACAGCTT 59.526 50.000 5.01 0.00 39.73 3.74
2321 2607 9.083080 AGTTTTTAGCATAAAACAGTCAAACAC 57.917 29.630 21.14 7.22 45.81 3.32
2332 2620 7.254227 AGACACGTCAGTTTTTAGCATAAAA 57.746 32.000 0.00 0.00 0.00 1.52
2433 2721 3.621682 AATGGGGGAGTAGAGTAGAGG 57.378 52.381 0.00 0.00 0.00 3.69
2437 2733 3.130734 AGCAAATGGGGGAGTAGAGTA 57.869 47.619 0.00 0.00 0.00 2.59
2438 2734 1.972588 AGCAAATGGGGGAGTAGAGT 58.027 50.000 0.00 0.00 0.00 3.24
2439 2735 2.239654 TGAAGCAAATGGGGGAGTAGAG 59.760 50.000 0.00 0.00 0.00 2.43
2440 2736 2.274542 TGAAGCAAATGGGGGAGTAGA 58.725 47.619 0.00 0.00 0.00 2.59
2441 2737 2.806945 TGAAGCAAATGGGGGAGTAG 57.193 50.000 0.00 0.00 0.00 2.57
2442 2738 2.311542 ACATGAAGCAAATGGGGGAGTA 59.688 45.455 0.00 0.00 0.00 2.59
2443 2739 1.077663 ACATGAAGCAAATGGGGGAGT 59.922 47.619 0.00 0.00 0.00 3.85
2444 2740 1.856629 ACATGAAGCAAATGGGGGAG 58.143 50.000 0.00 0.00 0.00 4.30
2445 2741 2.323999 AACATGAAGCAAATGGGGGA 57.676 45.000 0.00 0.00 0.00 4.81
2446 2742 2.568509 AGAAACATGAAGCAAATGGGGG 59.431 45.455 0.00 0.00 0.00 5.40
2500 2800 0.809636 TGAAGTGGATATGGCACGCG 60.810 55.000 3.53 3.53 0.00 6.01
2658 2967 3.808466 TCAGCTAGAGTAGGTTGCATG 57.192 47.619 0.00 0.00 33.57 4.06
2716 3040 5.474189 CCTCCTATGTTCAGCTAGGTAGTAC 59.526 48.000 0.00 0.00 36.64 2.73
2717 3041 5.371769 TCCTCCTATGTTCAGCTAGGTAGTA 59.628 44.000 0.00 0.00 36.64 1.82
2718 3042 4.168283 TCCTCCTATGTTCAGCTAGGTAGT 59.832 45.833 0.00 0.00 36.64 2.73
2719 3043 4.730966 TCCTCCTATGTTCAGCTAGGTAG 58.269 47.826 0.00 0.00 36.64 3.18
2720 3044 4.168283 ACTCCTCCTATGTTCAGCTAGGTA 59.832 45.833 0.00 0.00 36.64 3.08
2722 3046 3.571590 ACTCCTCCTATGTTCAGCTAGG 58.428 50.000 0.00 0.00 36.60 3.02
2723 3047 4.217550 GCTACTCCTCCTATGTTCAGCTAG 59.782 50.000 0.00 0.00 0.00 3.42
2737 3061 6.689554 ACAGTTAGTAAAAGTGCTACTCCTC 58.310 40.000 0.00 0.00 31.98 3.71
2738 3062 6.295180 GGACAGTTAGTAAAAGTGCTACTCCT 60.295 42.308 1.72 0.00 31.98 3.69
2739 3063 5.868258 GGACAGTTAGTAAAAGTGCTACTCC 59.132 44.000 1.72 0.00 31.98 3.85
2740 3064 6.689554 AGGACAGTTAGTAAAAGTGCTACTC 58.310 40.000 7.83 0.00 31.98 2.59
2796 3123 6.670027 ACCAGTTCTACTTCTCCATAGTGAAT 59.330 38.462 0.00 0.00 0.00 2.57
2797 3124 6.017192 ACCAGTTCTACTTCTCCATAGTGAA 58.983 40.000 0.00 0.00 0.00 3.18
2798 3125 5.580998 ACCAGTTCTACTTCTCCATAGTGA 58.419 41.667 0.00 0.00 0.00 3.41
2799 3126 5.163499 GGACCAGTTCTACTTCTCCATAGTG 60.163 48.000 0.00 0.00 0.00 2.74
2908 3250 1.738432 TTTGCATGCAAAGCACGGA 59.262 47.368 35.80 17.12 43.04 4.69
3000 3343 6.796072 GCATTTCAGCTTCGAAATAGATCATC 59.204 38.462 10.70 0.00 42.36 2.92
3009 3352 0.590682 TGCGCATTTCAGCTTCGAAA 59.409 45.000 5.66 2.05 39.13 3.46
3264 3611 7.763356 CAAGAGATGCAGATTTTCAGATCTTT 58.237 34.615 0.00 0.00 34.20 2.52
3875 4243 6.636562 AGTGGAGGACATTCGTTACTATAG 57.363 41.667 0.00 0.00 0.00 1.31
3876 4244 6.604396 TGAAGTGGAGGACATTCGTTACTATA 59.396 38.462 0.00 0.00 0.00 1.31
3891 4262 9.381033 GATAGATATGATGAATTGAAGTGGAGG 57.619 37.037 0.00 0.00 0.00 4.30
3998 4370 6.493115 TCAGCATAACAGATTTCTTCCCAAAA 59.507 34.615 0.00 0.00 0.00 2.44
3999 4371 6.009589 TCAGCATAACAGATTTCTTCCCAAA 58.990 36.000 0.00 0.00 0.00 3.28
4000 4372 5.569355 TCAGCATAACAGATTTCTTCCCAA 58.431 37.500 0.00 0.00 0.00 4.12
4001 4373 5.178096 TCAGCATAACAGATTTCTTCCCA 57.822 39.130 0.00 0.00 0.00 4.37
4002 4374 6.545298 AGATTCAGCATAACAGATTTCTTCCC 59.455 38.462 0.00 0.00 0.00 3.97
4040 4412 9.847224 GTATTGATTGAGAATAGTAAAAGGGGA 57.153 33.333 0.00 0.00 0.00 4.81
4087 4463 6.864342 ACTGGTTACTGCTAATGTGTACTAG 58.136 40.000 0.00 0.00 0.00 2.57
4091 4467 5.128171 CCCTACTGGTTACTGCTAATGTGTA 59.872 44.000 0.00 0.00 0.00 2.90
4092 4468 4.081087 CCCTACTGGTTACTGCTAATGTGT 60.081 45.833 0.00 0.00 0.00 3.72
4093 4469 4.442706 CCCTACTGGTTACTGCTAATGTG 58.557 47.826 0.00 0.00 0.00 3.21
4094 4470 3.454812 CCCCTACTGGTTACTGCTAATGT 59.545 47.826 0.00 0.00 0.00 2.71
4108 4488 3.700038 AGATCAGTCGTTAACCCCTACTG 59.300 47.826 14.34 14.34 39.10 2.74
4142 4522 0.816825 CCCGATCTGCCCAGTCAATG 60.817 60.000 0.00 0.00 0.00 2.82
4281 4661 7.964666 AATTACCTCTAGCTTGAGAACTAGT 57.035 36.000 24.33 15.60 37.67 2.57
4296 4676 9.615660 TGATTGGGTCTGTATATAATTACCTCT 57.384 33.333 7.99 0.00 0.00 3.69
4409 4793 2.659063 CCACACCAGCCCGATCTCA 61.659 63.158 0.00 0.00 0.00 3.27
4505 4889 4.058817 ACTTAGTTCAGAAACGCTTCCAG 58.941 43.478 0.00 0.00 40.48 3.86
4650 5044 2.095263 CGACCAAAAGAACGCCATCATT 60.095 45.455 0.00 0.00 0.00 2.57
4684 5079 2.108952 ACATGCAGTCCTTTCCTTCCTT 59.891 45.455 0.00 0.00 0.00 3.36
4687 5082 3.674997 TGTACATGCAGTCCTTTCCTTC 58.325 45.455 0.00 0.00 0.00 3.46
4689 5084 3.788227 TTGTACATGCAGTCCTTTCCT 57.212 42.857 0.00 0.00 0.00 3.36
4691 5086 5.156355 CACATTTGTACATGCAGTCCTTTC 58.844 41.667 0.00 0.00 0.00 2.62
4698 5093 7.065683 TCCTACATAACACATTTGTACATGCAG 59.934 37.037 0.00 4.17 33.55 4.41
4774 5174 0.179124 GATCCACACAGAGCGAGACC 60.179 60.000 0.00 0.00 0.00 3.85
4812 5212 1.594194 TTTGCACATCGTCCATGGCC 61.594 55.000 6.96 0.00 36.72 5.36
4814 5214 0.880441 TGTTTGCACATCGTCCATGG 59.120 50.000 4.97 4.97 36.72 3.66
4878 5285 2.783609 TCTAGTCTAGGACGCACTGT 57.216 50.000 7.05 0.00 37.67 3.55
4884 5291 6.072728 CCTTCATCTTCATCTAGTCTAGGACG 60.073 46.154 7.05 0.00 37.67 4.79
5047 5466 1.555967 GACCTCTCTCAGTGCCTCTT 58.444 55.000 0.00 0.00 0.00 2.85
5190 5627 7.335924 TCAACCGAAAGAAAGAAAGAGAAAGAA 59.664 33.333 0.00 0.00 0.00 2.52
5193 5630 6.821665 TCTCAACCGAAAGAAAGAAAGAGAAA 59.178 34.615 0.00 0.00 0.00 2.52
5196 5633 5.332656 CGTCTCAACCGAAAGAAAGAAAGAG 60.333 44.000 0.00 0.00 0.00 2.85
5238 5675 0.679321 CTTCCTGCCTTTGGAGGAGC 60.679 60.000 3.03 0.00 46.74 4.70
5315 5752 1.600413 GCGGCCTGTTGAAGTTGAAAG 60.600 52.381 0.00 0.00 0.00 2.62
5333 5770 1.603172 CGCATAGACTAAGGAAGGGCG 60.603 57.143 0.00 0.00 35.87 6.13
5357 5794 2.362120 GGCCATTCCTGCTGCACT 60.362 61.111 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.