Multiple sequence alignment - TraesCS3D01G037600

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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 TraesCS3D01G037600 chr3D 100.000 3544 0 0 1 3544 13596771 13600314 0.000000e+00 6545.0
1 TraesCS3D01G037600 chr3D 82.698 1075 126 32 2102 3160 13630756 13631786 0.000000e+00 900.0
2 TraesCS3D01G037600 chr3D 81.735 438 35 21 911 1339 13629741 13630142 1.230000e-84 324.0
3 TraesCS3D01G037600 chr3D 89.157 166 18 0 3243 3408 13631947 13632112 1.290000e-49 207.0
4 TraesCS3D01G037600 chr3D 97.183 71 1 1 772 842 13597474 13597543 6.220000e-23 119.0
5 TraesCS3D01G037600 chr3B 88.704 2523 139 58 808 3241 19876765 19879230 0.000000e+00 2946.0
6 TraesCS3D01G037600 chr3B 85.223 1164 134 17 2018 3147 19933775 19934934 0.000000e+00 1162.0
7 TraesCS3D01G037600 chr3B 85.052 1164 136 17 2018 3147 19951617 19952776 0.000000e+00 1151.0
8 TraesCS3D01G037600 chr3B 82.684 1155 125 44 2030 3160 20022932 20024035 0.000000e+00 955.0
9 TraesCS3D01G037600 chr3B 91.730 653 47 4 1501 2153 19965681 19966326 0.000000e+00 900.0
10 TraesCS3D01G037600 chr3B 92.739 482 29 4 2151 2630 19976016 19976493 0.000000e+00 691.0
11 TraesCS3D01G037600 chr3B 85.299 619 58 19 2160 2749 19981917 19982531 3.030000e-170 608.0
12 TraesCS3D01G037600 chr3B 85.201 473 61 9 1515 1983 19919585 19920052 8.900000e-131 477.0
13 TraesCS3D01G037600 chr3B 84.375 480 59 11 55 524 795909752 795910225 1.160000e-124 457.0
14 TraesCS3D01G037600 chr3B 84.136 353 41 7 2748 3086 19977032 19977383 9.490000e-86 327.0
15 TraesCS3D01G037600 chr3B 95.556 180 8 0 3365 3544 19986068 19986247 4.480000e-74 289.0
16 TraesCS3D01G037600 chr3B 90.909 165 14 1 3244 3408 20024197 20024360 1.660000e-53 220.0
17 TraesCS3D01G037600 chr3B 82.061 262 27 9 1092 1339 20022087 20022342 4.640000e-49 206.0
18 TraesCS3D01G037600 chr3B 93.617 94 6 0 2652 2745 19976761 19976854 1.330000e-29 141.0
19 TraesCS3D01G037600 chr3B 85.938 64 7 1 993 1054 20022018 20022081 2.280000e-07 67.6
20 TraesCS3D01G037600 chr3B 94.737 38 1 1 772 809 72982315 72982351 1.370000e-04 58.4
21 TraesCS3D01G037600 chr3A 84.818 1785 176 52 1764 3477 23377676 23375916 0.000000e+00 1707.0
22 TraesCS3D01G037600 chr3A 84.540 1229 128 26 1964 3160 23309771 23308573 0.000000e+00 1160.0
23 TraesCS3D01G037600 chr3A 92.902 634 33 6 785 1415 23378848 23378224 0.000000e+00 911.0
24 TraesCS3D01G037600 chr3A 87.539 642 60 13 1778 2413 23367944 23367317 0.000000e+00 725.0
25 TraesCS3D01G037600 chr3A 93.103 261 13 4 1441 1700 23378232 23377976 9.290000e-101 377.0
26 TraesCS3D01G037600 chr3A 84.688 320 30 8 3244 3544 23351210 23350891 5.750000e-78 302.0
27 TraesCS3D01G037600 chr3A 81.043 211 21 9 3244 3452 23366475 23366282 2.200000e-32 150.0
28 TraesCS3D01G037600 chr3A 91.525 59 4 1 3251 3308 23325292 23325234 2.930000e-11 80.5
29 TraesCS3D01G037600 chr3A 91.228 57 5 0 1092 1148 23312153 23312097 1.050000e-10 78.7
30 TraesCS3D01G037600 chr3A 87.879 66 6 1 993 1056 23312222 23312157 3.790000e-10 76.8
31 TraesCS3D01G037600 chr3A 79.817 109 12 5 849 948 23312325 23312218 1.770000e-08 71.3
32 TraesCS3D01G037600 chr6D 81.275 737 79 25 56 744 343672435 343673160 3.110000e-150 542.0
33 TraesCS3D01G037600 chr6D 82.533 229 23 6 527 740 422221056 422221282 6.040000e-43 185.0
34 TraesCS3D01G037600 chr5A 80.417 720 94 25 54 740 548284225 548284930 4.080000e-139 505.0
35 TraesCS3D01G037600 chr5A 85.232 474 66 4 54 524 552476435 552475963 5.320000e-133 484.0
36 TraesCS3D01G037600 chr5A 82.214 551 72 18 2081 2627 334739818 334740346 5.400000e-123 451.0
37 TraesCS3D01G037600 chr5A 79.270 685 99 24 52 706 403599618 403600289 4.200000e-119 438.0
38 TraesCS3D01G037600 chr4D 82.297 627 68 18 54 642 57896742 57897363 1.470000e-138 503.0
39 TraesCS3D01G037600 chr1D 86.128 483 46 16 53 524 472298102 472298574 5.280000e-138 501.0
40 TraesCS3D01G037600 chr5D 85.863 481 50 13 57 524 37641097 37640622 2.460000e-136 496.0
41 TraesCS3D01G037600 chr5D 81.604 212 32 7 527 738 482401849 482402053 6.080000e-38 169.0
42 TraesCS3D01G037600 chr1A 85.870 460 56 7 2081 2540 566602290 566602740 6.880000e-132 481.0
43 TraesCS3D01G037600 chr1A 80.476 210 33 7 527 732 57745178 57745383 1.700000e-33 154.0
44 TraesCS3D01G037600 chrUn 84.929 491 53 14 52 524 143923127 143922640 8.900000e-131 477.0
45 TraesCS3D01G037600 chrUn 86.301 146 15 3 527 668 328078396 328078252 1.700000e-33 154.0
46 TraesCS3D01G037600 chr1B 82.790 552 73 13 2081 2630 657321522 657322053 1.150000e-129 473.0
47 TraesCS3D01G037600 chr7B 84.330 485 60 14 52 522 57052866 57053348 8.960000e-126 460.0
48 TraesCS3D01G037600 chr5B 82.278 553 74 14 2081 2630 283988113 283988644 1.160000e-124 457.0
49 TraesCS3D01G037600 chr2D 86.047 215 25 4 530 741 535732174 535731962 3.560000e-55 226.0
50 TraesCS3D01G037600 chr4A 83.951 243 23 5 520 747 486380513 486380272 5.960000e-53 219.0
51 TraesCS3D01G037600 chr7A 82.533 229 23 5 527 740 648747244 648747470 6.040000e-43 185.0
52 TraesCS3D01G037600 chr7A 81.068 206 32 5 535 739 617850056 617850255 1.320000e-34 158.0
53 TraesCS3D01G037600 chr2B 81.860 215 29 4 527 741 118598856 118599060 4.700000e-39 172.0
54 TraesCS3D01G037600 chr7D 81.545 233 15 9 527 746 120261700 120261483 2.190000e-37 167.0
55 TraesCS3D01G037600 chr6A 97.143 35 1 0 772 806 18070123 18070089 3.820000e-05 60.2


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 TraesCS3D01G037600 chr3D 13596771 13600314 3543 False 3332.000000 6545 98.591500 1 3544 2 chr3D.!!$F1 3543
1 TraesCS3D01G037600 chr3D 13629741 13632112 2371 False 477.000000 900 84.530000 911 3408 3 chr3D.!!$F2 2497
2 TraesCS3D01G037600 chr3B 19876765 19879230 2465 False 2946.000000 2946 88.704000 808 3241 1 chr3B.!!$F1 2433
3 TraesCS3D01G037600 chr3B 19933775 19934934 1159 False 1162.000000 1162 85.223000 2018 3147 1 chr3B.!!$F3 1129
4 TraesCS3D01G037600 chr3B 19951617 19952776 1159 False 1151.000000 1151 85.052000 2018 3147 1 chr3B.!!$F4 1129
5 TraesCS3D01G037600 chr3B 19965681 19966326 645 False 900.000000 900 91.730000 1501 2153 1 chr3B.!!$F5 652
6 TraesCS3D01G037600 chr3B 19981917 19986247 4330 False 448.500000 608 90.427500 2160 3544 2 chr3B.!!$F9 1384
7 TraesCS3D01G037600 chr3B 19976016 19977383 1367 False 386.333333 691 90.164000 2151 3086 3 chr3B.!!$F8 935
8 TraesCS3D01G037600 chr3B 20022018 20024360 2342 False 362.150000 955 85.398000 993 3408 4 chr3B.!!$F10 2415
9 TraesCS3D01G037600 chr3A 23375916 23378848 2932 True 998.333333 1707 90.274333 785 3477 3 chr3A.!!$R5 2692
10 TraesCS3D01G037600 chr3A 23366282 23367944 1662 True 437.500000 725 84.291000 1778 3452 2 chr3A.!!$R4 1674
11 TraesCS3D01G037600 chr3A 23308573 23312325 3752 True 346.700000 1160 85.866000 849 3160 4 chr3A.!!$R3 2311
12 TraesCS3D01G037600 chr6D 343672435 343673160 725 False 542.000000 542 81.275000 56 744 1 chr6D.!!$F1 688
13 TraesCS3D01G037600 chr5A 548284225 548284930 705 False 505.000000 505 80.417000 54 740 1 chr5A.!!$F3 686
14 TraesCS3D01G037600 chr5A 334739818 334740346 528 False 451.000000 451 82.214000 2081 2627 1 chr5A.!!$F1 546
15 TraesCS3D01G037600 chr5A 403599618 403600289 671 False 438.000000 438 79.270000 52 706 1 chr5A.!!$F2 654
16 TraesCS3D01G037600 chr4D 57896742 57897363 621 False 503.000000 503 82.297000 54 642 1 chr4D.!!$F1 588
17 TraesCS3D01G037600 chr1B 657321522 657322053 531 False 473.000000 473 82.790000 2081 2630 1 chr1B.!!$F1 549
18 TraesCS3D01G037600 chr5B 283988113 283988644 531 False 457.000000 457 82.278000 2081 2630 1 chr5B.!!$F1 549

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
30 31 0.389426 GACGTTCTGGCGCTTCCTTA 60.389 55.000 7.64 0.0 35.26 2.69 F
31 32 0.389948 ACGTTCTGGCGCTTCCTTAG 60.390 55.000 7.64 0.0 35.26 2.18 F
347 359 0.961019 GAGGCATGGTTGTGCTTTCA 59.039 50.000 0.00 0.0 44.45 2.69 F
424 444 1.067060 GAGAGGCACGGTTTTGCTTTT 59.933 47.619 0.00 0.0 42.56 2.27 F
1132 1222 1.214589 CCTACAGGTTCGTGTCGGG 59.785 63.158 7.88 6.0 31.12 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1476 3322 0.327924 TGCCATGGGTTTCGATGAGT 59.672 50.000 15.13 0.0 31.82 3.41 R
1547 3399 1.198637 GCAGGAGCTGTGCTGTTTAAG 59.801 52.381 9.92 0.0 43.87 1.85 R
1846 3939 7.504911 ACATCATCAGGGATAATTCTGAAAAGG 59.495 37.037 0.00 0.0 42.40 3.11 R
1884 3980 8.740123 TTTCAAGTCTAAATACAACCTGTGAA 57.260 30.769 0.00 0.0 0.00 3.18 R
2632 4918 0.035820 GTCCATCGGCTAACCAACCA 60.036 55.000 0.00 0.0 34.57 3.67 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
23 24 1.277440 TTTTTCGACGTTCTGGCGC 59.723 52.632 0.00 0.00 34.88 6.53
24 25 1.155424 TTTTTCGACGTTCTGGCGCT 61.155 50.000 7.64 0.00 34.88 5.92
25 26 1.155424 TTTTCGACGTTCTGGCGCTT 61.155 50.000 7.64 0.00 34.88 4.68
26 27 1.554042 TTTCGACGTTCTGGCGCTTC 61.554 55.000 7.64 0.00 34.88 3.86
27 28 3.479269 CGACGTTCTGGCGCTTCC 61.479 66.667 7.64 0.00 34.88 3.46
28 29 2.048127 GACGTTCTGGCGCTTCCT 60.048 61.111 7.64 0.00 35.26 3.36
29 30 1.668151 GACGTTCTGGCGCTTCCTT 60.668 57.895 7.64 0.00 35.26 3.36
30 31 0.389426 GACGTTCTGGCGCTTCCTTA 60.389 55.000 7.64 0.00 35.26 2.69
31 32 0.389948 ACGTTCTGGCGCTTCCTTAG 60.390 55.000 7.64 0.00 35.26 2.18
32 33 1.696832 CGTTCTGGCGCTTCCTTAGC 61.697 60.000 7.64 0.00 46.83 3.09
121 125 2.358737 CCGCGAGAGGCAAGGTTT 60.359 61.111 8.23 0.00 43.84 3.27
143 147 2.701780 ATTCGCGAGAGTCACGGCT 61.702 57.895 9.59 0.00 43.69 5.52
159 163 1.301716 GCTGTGCCTCTCGGAAACA 60.302 57.895 0.00 0.00 0.00 2.83
245 252 1.493311 GTTGTGCTTTCGCGAGAGG 59.507 57.895 25.84 13.55 43.69 3.69
347 359 0.961019 GAGGCATGGTTGTGCTTTCA 59.039 50.000 0.00 0.00 44.45 2.69
356 368 1.221466 TTGTGCTTTCACGAGAGGCG 61.221 55.000 0.00 0.00 46.01 5.52
424 444 1.067060 GAGAGGCACGGTTTTGCTTTT 59.933 47.619 0.00 0.00 42.56 2.27
474 494 2.600388 CACGAACGTGCCTCTTTCA 58.400 52.632 14.04 0.00 39.39 2.69
577 624 2.418628 GCGAGGAATCCAACGATGAAAA 59.581 45.455 19.24 0.00 0.00 2.29
580 627 3.670625 AGGAATCCAACGATGAAAACGA 58.329 40.909 0.61 0.00 34.88 3.85
583 630 5.028375 GGAATCCAACGATGAAAACGATTC 58.972 41.667 10.87 10.87 34.88 2.52
584 631 5.163754 GGAATCCAACGATGAAAACGATTCT 60.164 40.000 15.71 0.00 36.17 2.40
595 642 7.201522 CGATGAAAACGATTCTAGATTTGGACA 60.202 37.037 0.00 0.00 31.90 4.02
642 689 6.470557 TTGAATAAACGGACCTACGAAAAG 57.529 37.500 0.00 0.00 37.61 2.27
645 692 3.740631 AAACGGACCTACGAAAAGAGT 57.259 42.857 0.00 0.00 37.61 3.24
646 693 3.740631 AACGGACCTACGAAAAGAGTT 57.259 42.857 0.00 0.00 37.61 3.01
647 694 3.022607 ACGGACCTACGAAAAGAGTTG 57.977 47.619 0.00 0.00 37.61 3.16
649 696 1.725164 GGACCTACGAAAAGAGTTGCG 59.275 52.381 0.00 0.00 41.98 4.85
668 715 2.126618 CAAGTGGCGCACATGCAG 60.127 61.111 10.83 0.00 42.21 4.41
697 744 3.443681 ACTTGTCACAACCTGAAAAGGTG 59.556 43.478 0.00 0.00 45.58 4.00
706 753 5.067805 ACAACCTGAAAAGGTGAAAGTGATC 59.932 40.000 0.00 0.00 42.20 2.92
707 754 5.053978 ACCTGAAAAGGTGAAAGTGATCT 57.946 39.130 0.00 0.00 41.33 2.75
708 755 5.449553 ACCTGAAAAGGTGAAAGTGATCTT 58.550 37.500 0.00 0.00 41.33 2.40
709 756 5.893824 ACCTGAAAAGGTGAAAGTGATCTTT 59.106 36.000 0.00 0.00 41.33 2.52
710 757 6.183360 ACCTGAAAAGGTGAAAGTGATCTTTG 60.183 38.462 0.00 0.00 40.24 2.77
711 758 5.591099 TGAAAAGGTGAAAGTGATCTTTGC 58.409 37.500 0.00 0.00 42.99 3.68
712 759 5.126869 TGAAAAGGTGAAAGTGATCTTTGCA 59.873 36.000 0.00 0.00 42.99 4.08
713 760 5.596836 AAAGGTGAAAGTGATCTTTGCAA 57.403 34.783 0.00 0.00 42.99 4.08
714 761 5.796424 AAGGTGAAAGTGATCTTTGCAAT 57.204 34.783 0.00 0.00 42.99 3.56
715 762 5.130292 AGGTGAAAGTGATCTTTGCAATG 57.870 39.130 0.00 2.27 42.99 2.82
716 763 4.828939 AGGTGAAAGTGATCTTTGCAATGA 59.171 37.500 16.45 16.45 42.99 2.57
717 764 5.048224 AGGTGAAAGTGATCTTTGCAATGAG 60.048 40.000 18.58 6.50 42.99 2.90
718 765 5.278660 GGTGAAAGTGATCTTTGCAATGAGT 60.279 40.000 18.58 8.54 42.99 3.41
719 766 6.072508 GGTGAAAGTGATCTTTGCAATGAGTA 60.073 38.462 18.58 8.67 42.99 2.59
720 767 6.798959 GTGAAAGTGATCTTTGCAATGAGTAC 59.201 38.462 18.58 17.73 42.99 2.73
721 768 6.712095 TGAAAGTGATCTTTGCAATGAGTACT 59.288 34.615 18.58 19.25 42.99 2.73
722 769 7.877612 TGAAAGTGATCTTTGCAATGAGTACTA 59.122 33.333 22.97 12.60 42.99 1.82
723 770 7.602517 AAGTGATCTTTGCAATGAGTACTAC 57.397 36.000 22.97 15.62 0.00 2.73
724 771 6.940739 AGTGATCTTTGCAATGAGTACTACT 58.059 36.000 22.10 16.40 0.00 2.57
725 772 7.038659 AGTGATCTTTGCAATGAGTACTACTC 58.961 38.462 22.10 9.04 45.26 2.59
740 787 8.563289 GAGTACTACTCAATTAGTGATTTCGG 57.437 38.462 10.85 0.00 44.45 4.30
741 788 8.289939 AGTACTACTCAATTAGTGATTTCGGA 57.710 34.615 0.00 0.00 39.39 4.55
742 789 8.746530 AGTACTACTCAATTAGTGATTTCGGAA 58.253 33.333 0.00 0.00 39.39 4.30
743 790 9.362539 GTACTACTCAATTAGTGATTTCGGAAA 57.637 33.333 5.52 5.52 39.39 3.13
744 791 8.842358 ACTACTCAATTAGTGATTTCGGAAAA 57.158 30.769 7.33 0.00 39.39 2.29
745 792 9.280174 ACTACTCAATTAGTGATTTCGGAAAAA 57.720 29.630 7.33 0.00 39.39 1.94
767 814 8.546597 AAAAACCCATAAGATAAACAACATGC 57.453 30.769 0.00 0.00 0.00 4.06
768 815 7.480760 AAACCCATAAGATAAACAACATGCT 57.519 32.000 0.00 0.00 0.00 3.79
769 816 6.699575 ACCCATAAGATAAACAACATGCTC 57.300 37.500 0.00 0.00 0.00 4.26
770 817 5.296780 ACCCATAAGATAAACAACATGCTCG 59.703 40.000 0.00 0.00 0.00 5.03
771 818 5.277974 CCCATAAGATAAACAACATGCTCGG 60.278 44.000 0.00 0.00 0.00 4.63
772 819 5.527214 CCATAAGATAAACAACATGCTCGGA 59.473 40.000 0.00 0.00 0.00 4.55
773 820 6.205464 CCATAAGATAAACAACATGCTCGGAT 59.795 38.462 0.00 0.00 0.00 4.18
774 821 5.741388 AAGATAAACAACATGCTCGGATC 57.259 39.130 0.00 0.00 0.00 3.36
775 822 5.028549 AGATAAACAACATGCTCGGATCT 57.971 39.130 0.00 0.00 0.00 2.75
776 823 5.431765 AGATAAACAACATGCTCGGATCTT 58.568 37.500 0.00 0.00 0.00 2.40
777 824 5.882557 AGATAAACAACATGCTCGGATCTTT 59.117 36.000 0.00 0.00 0.00 2.52
778 825 3.837213 AACAACATGCTCGGATCTTTG 57.163 42.857 0.00 0.00 0.00 2.77
779 826 1.470098 ACAACATGCTCGGATCTTTGC 59.530 47.619 0.00 0.00 0.00 3.68
780 827 1.469703 CAACATGCTCGGATCTTTGCA 59.530 47.619 8.84 8.84 39.83 4.08
781 828 1.825090 ACATGCTCGGATCTTTGCAA 58.175 45.000 0.00 0.00 38.96 4.08
782 829 2.372264 ACATGCTCGGATCTTTGCAAT 58.628 42.857 0.00 0.00 38.96 3.56
783 830 2.098607 ACATGCTCGGATCTTTGCAATG 59.901 45.455 0.00 2.27 38.96 2.82
790 837 5.592054 CTCGGATCTTTGCAATGAGTACTA 58.408 41.667 18.58 5.01 0.00 1.82
870 918 3.796504 GCCCATGTGATATTGAAAAGCCG 60.797 47.826 0.00 0.00 0.00 5.52
871 919 3.374745 CCATGTGATATTGAAAAGCCGC 58.625 45.455 0.00 0.00 0.00 6.53
1038 1128 1.528341 TACCAGCTCCTCCCCCTCTT 61.528 60.000 0.00 0.00 0.00 2.85
1132 1222 1.214589 CCTACAGGTTCGTGTCGGG 59.785 63.158 7.88 6.00 31.12 5.14
1151 1241 2.644676 GGGCTATGGAAGAGGAAACAC 58.355 52.381 0.00 0.00 0.00 3.32
1286 1393 5.399892 GCGAGTAGTGTTATTCTGCTGTATC 59.600 44.000 0.00 0.00 0.00 2.24
1328 1436 1.469912 GCCGTTCGTTACTCTAGCGC 61.470 60.000 0.00 0.00 32.20 5.92
1346 1454 1.225855 GCGTGAAATGTGTCTGTGGA 58.774 50.000 0.00 0.00 0.00 4.02
1347 1455 1.806542 GCGTGAAATGTGTCTGTGGAT 59.193 47.619 0.00 0.00 0.00 3.41
1476 3322 5.814705 CGGGCATTAATTTGGCATAAAGAAA 59.185 36.000 6.09 0.00 43.56 2.52
1492 3338 5.376854 AAAGAAACTCATCGAAACCCATG 57.623 39.130 0.00 0.00 0.00 3.66
1523 3375 2.125024 GCCCATTTGCACATGGCC 60.125 61.111 23.96 11.67 42.39 5.36
1540 3392 2.231964 TGGCCACAATTTTCATCTCTGC 59.768 45.455 0.00 0.00 0.00 4.26
1547 3399 6.090358 CCACAATTTTCATCTCTGCAAACATC 59.910 38.462 0.00 0.00 0.00 3.06
1884 3980 6.070656 TCCCTGATGATGTTTGTCTTTTTCT 58.929 36.000 0.00 0.00 0.00 2.52
2546 4800 4.383770 GGTGGCCTGCTTAGACAGTAATTA 60.384 45.833 3.32 0.00 35.83 1.40
2618 4886 2.948979 ACGAAATGTTTCTCTTGTGGCA 59.051 40.909 4.20 0.00 35.07 4.92
2630 4916 5.809001 TCTCTTGTGGCAGTTGAATTATCT 58.191 37.500 0.00 0.00 0.00 1.98
2631 4917 5.877012 TCTCTTGTGGCAGTTGAATTATCTC 59.123 40.000 0.00 0.00 0.00 2.75
2632 4918 5.809001 TCTTGTGGCAGTTGAATTATCTCT 58.191 37.500 0.00 0.00 0.00 3.10
2708 5234 1.731720 CAGGTACAAGAGCTGCTTCC 58.268 55.000 2.53 0.63 46.16 3.46
2762 5534 8.117813 TCCAACTTATGTGGTTCTTAATTTCC 57.882 34.615 0.00 0.00 0.00 3.13
2786 5561 3.021695 TCCTGGTTATATCTATCGCGGG 58.978 50.000 6.13 0.00 0.00 6.13
2833 5615 7.928167 GGAGATGATGCCGATAATAATATGTGA 59.072 37.037 0.00 0.00 0.00 3.58
2915 5698 5.662674 AATCTCCGTTAGCCTGGATATAC 57.337 43.478 0.00 0.00 32.83 1.47
2925 5713 3.194542 AGCCTGGATATACGAGCTGAATC 59.805 47.826 0.00 0.00 0.00 2.52
2958 5758 7.147915 TGCATGGGAAATTAAGTAACTGAATCC 60.148 37.037 0.00 0.00 0.00 3.01
2979 6305 3.574396 CCGACTATCTATGTGTGGGTGAT 59.426 47.826 0.00 0.00 0.00 3.06
2985 6311 8.034313 ACTATCTATGTGTGGGTGATAATTGT 57.966 34.615 0.00 0.00 0.00 2.71
3094 6437 4.098914 TGCTTGATTGAGTACACCCTTT 57.901 40.909 0.00 0.00 0.00 3.11
3096 6439 4.072131 GCTTGATTGAGTACACCCTTTCA 58.928 43.478 0.00 0.00 0.00 2.69
3137 6605 2.428890 AGTCTTGTTCATAGCGGAGAGG 59.571 50.000 0.00 0.00 0.00 3.69
3166 6702 8.097038 GGCTGATAACAATGTTAGATCCATCTA 58.903 37.037 11.70 0.00 38.32 1.98
3167 6703 8.930760 GCTGATAACAATGTTAGATCCATCTAC 58.069 37.037 11.70 0.00 39.00 2.59
3208 6744 5.963176 TGCATGTGTTGTAATCTGACAAT 57.037 34.783 0.00 0.00 41.21 2.71
3361 6927 9.979578 TCATTAATTATTATGATTGGTTGGCAC 57.020 29.630 0.00 0.00 0.00 5.01
3416 9289 7.766219 AATATACAATCCAAGACGTGTACAC 57.234 36.000 16.32 16.32 29.71 2.90
3431 9304 9.042008 AGACGTGTACACATATTTGATAATTCC 57.958 33.333 24.98 0.00 0.00 3.01
3447 9320 1.886886 TTCCGGCCAAGTGAGTTTAC 58.113 50.000 2.24 0.00 0.00 2.01
3454 9327 4.638304 GGCCAAGTGAGTTTACTAAGACA 58.362 43.478 0.00 0.00 0.00 3.41
3490 9363 4.345257 GGAACATAGGCTTGAGAGGTATCA 59.655 45.833 0.00 0.00 0.00 2.15
3509 9382 6.974622 GGTATCAGGACAAATGTTGCTTTATG 59.025 38.462 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.155424 AGCGCCAGAACGTCGAAAAA 61.155 50.000 2.29 0.00 34.88 1.94
6 7 1.155424 AAGCGCCAGAACGTCGAAAA 61.155 50.000 2.29 0.00 34.88 2.29
7 8 1.554042 GAAGCGCCAGAACGTCGAAA 61.554 55.000 2.29 0.00 34.88 3.46
8 9 2.019951 GAAGCGCCAGAACGTCGAA 61.020 57.895 2.29 0.00 34.88 3.71
9 10 2.430244 GAAGCGCCAGAACGTCGA 60.430 61.111 2.29 0.00 34.88 4.20
10 11 3.479269 GGAAGCGCCAGAACGTCG 61.479 66.667 2.29 0.00 36.34 5.12
11 12 0.389426 TAAGGAAGCGCCAGAACGTC 60.389 55.000 2.29 0.00 40.02 4.34
12 13 0.389948 CTAAGGAAGCGCCAGAACGT 60.390 55.000 2.29 0.00 40.02 3.99
13 14 1.696832 GCTAAGGAAGCGCCAGAACG 61.697 60.000 2.29 0.00 42.53 3.95
14 15 2.090693 GCTAAGGAAGCGCCAGAAC 58.909 57.895 2.29 0.00 42.53 3.01
15 16 4.617875 GCTAAGGAAGCGCCAGAA 57.382 55.556 2.29 0.00 42.53 3.02
25 26 9.927668 CAAATTCTTTTATCCAAAAGCTAAGGA 57.072 29.630 4.41 4.41 46.84 3.36
26 27 9.927668 TCAAATTCTTTTATCCAAAAGCTAAGG 57.072 29.630 5.23 0.00 46.84 2.69
116 120 0.798776 CTCTCGCGAATGCAAAACCT 59.201 50.000 11.33 0.00 42.97 3.50
121 125 2.445274 GTGACTCTCGCGAATGCAA 58.555 52.632 11.33 0.00 42.97 4.08
185 192 1.237285 CCGTGCCTCTCACAAAAGGG 61.237 60.000 0.00 0.00 45.92 3.95
186 193 0.535102 ACCGTGCCTCTCACAAAAGG 60.535 55.000 0.00 0.00 45.92 3.11
191 198 1.444119 GCAAAACCGTGCCTCTCACA 61.444 55.000 0.00 0.00 45.92 3.58
305 317 1.739667 GGAAGCAAAACCGTGCCTT 59.260 52.632 0.00 0.00 46.14 4.35
409 429 1.142778 TCGCAAAAGCAAAACCGTGC 61.143 50.000 0.00 0.00 45.28 5.34
436 456 2.224281 TGCCTCTCACGAAATCACAACT 60.224 45.455 0.00 0.00 0.00 3.16
577 624 4.174009 CGTGTGTCCAAATCTAGAATCGT 58.826 43.478 0.00 0.00 0.00 3.73
580 627 4.553330 ACCGTGTGTCCAAATCTAGAAT 57.447 40.909 0.00 0.00 0.00 2.40
583 630 5.929992 TCTTAAACCGTGTGTCCAAATCTAG 59.070 40.000 0.00 0.00 0.00 2.43
584 631 5.856156 TCTTAAACCGTGTGTCCAAATCTA 58.144 37.500 0.00 0.00 0.00 1.98
632 679 2.400399 TGTCGCAACTCTTTTCGTAGG 58.600 47.619 0.00 0.00 0.00 3.18
642 689 2.551270 CGCCACTTGTCGCAACTC 59.449 61.111 0.00 0.00 0.00 3.01
649 696 2.126734 GCATGTGCGCCACTTGTC 60.127 61.111 4.18 5.08 40.25 3.18
668 715 3.947841 TTGTGACAAGTGCCGCGC 61.948 61.111 0.00 0.00 0.00 6.86
670 717 2.186826 AGGTTGTGACAAGTGCCGC 61.187 57.895 0.00 0.00 0.00 6.53
673 720 3.438360 CTTTTCAGGTTGTGACAAGTGC 58.562 45.455 0.00 0.00 37.93 4.40
682 729 8.504794 AAGATCACTTTCACCTTTTCAGGTTGT 61.505 37.037 0.00 0.00 41.21 3.32
697 744 7.138692 AGTACTCATTGCAAAGATCACTTTC 57.861 36.000 1.71 0.00 43.41 2.62
715 762 8.404000 TCCGAAATCACTAATTGAGTAGTACTC 58.596 37.037 21.35 21.35 45.26 2.59
716 763 8.289939 TCCGAAATCACTAATTGAGTAGTACT 57.710 34.615 1.37 1.37 37.77 2.73
717 764 8.922058 TTCCGAAATCACTAATTGAGTAGTAC 57.078 34.615 0.00 0.00 37.77 2.73
718 765 9.932207 TTTTCCGAAATCACTAATTGAGTAGTA 57.068 29.630 0.00 0.00 37.77 1.82
719 766 8.842358 TTTTCCGAAATCACTAATTGAGTAGT 57.158 30.769 0.00 0.00 37.77 2.73
742 789 8.374743 AGCATGTTGTTTATCTTATGGGTTTTT 58.625 29.630 0.00 0.00 0.00 1.94
743 790 7.906327 AGCATGTTGTTTATCTTATGGGTTTT 58.094 30.769 0.00 0.00 0.00 2.43
744 791 7.480760 AGCATGTTGTTTATCTTATGGGTTT 57.519 32.000 0.00 0.00 0.00 3.27
745 792 6.183360 CGAGCATGTTGTTTATCTTATGGGTT 60.183 38.462 0.00 0.00 0.00 4.11
746 793 5.296780 CGAGCATGTTGTTTATCTTATGGGT 59.703 40.000 0.00 0.00 0.00 4.51
747 794 5.277974 CCGAGCATGTTGTTTATCTTATGGG 60.278 44.000 0.00 0.00 0.00 4.00
748 795 5.527214 TCCGAGCATGTTGTTTATCTTATGG 59.473 40.000 0.00 0.00 0.00 2.74
749 796 6.603237 TCCGAGCATGTTGTTTATCTTATG 57.397 37.500 0.00 0.00 0.00 1.90
750 797 7.220030 AGATCCGAGCATGTTGTTTATCTTAT 58.780 34.615 0.00 0.00 0.00 1.73
751 798 6.582636 AGATCCGAGCATGTTGTTTATCTTA 58.417 36.000 0.00 0.00 0.00 2.10
752 799 5.431765 AGATCCGAGCATGTTGTTTATCTT 58.568 37.500 0.00 0.00 0.00 2.40
753 800 5.028549 AGATCCGAGCATGTTGTTTATCT 57.971 39.130 0.00 0.00 0.00 1.98
754 801 5.741388 AAGATCCGAGCATGTTGTTTATC 57.259 39.130 0.00 0.00 0.00 1.75
755 802 5.677091 GCAAAGATCCGAGCATGTTGTTTAT 60.677 40.000 0.00 0.00 0.00 1.40
756 803 4.379394 GCAAAGATCCGAGCATGTTGTTTA 60.379 41.667 0.00 0.00 0.00 2.01
757 804 3.612479 GCAAAGATCCGAGCATGTTGTTT 60.612 43.478 0.00 0.00 0.00 2.83
758 805 2.095059 GCAAAGATCCGAGCATGTTGTT 60.095 45.455 0.00 0.00 0.00 2.83
759 806 1.470098 GCAAAGATCCGAGCATGTTGT 59.530 47.619 0.00 0.00 0.00 3.32
760 807 1.469703 TGCAAAGATCCGAGCATGTTG 59.530 47.619 0.00 0.00 31.05 3.33
761 808 1.825090 TGCAAAGATCCGAGCATGTT 58.175 45.000 0.00 0.00 31.05 2.71
762 809 1.825090 TTGCAAAGATCCGAGCATGT 58.175 45.000 0.00 0.00 36.80 3.21
763 810 2.356695 TCATTGCAAAGATCCGAGCATG 59.643 45.455 1.71 0.00 36.80 4.06
764 811 2.617308 CTCATTGCAAAGATCCGAGCAT 59.383 45.455 1.71 0.00 36.80 3.79
765 812 2.011947 CTCATTGCAAAGATCCGAGCA 58.988 47.619 1.71 0.00 34.79 4.26
766 813 2.012673 ACTCATTGCAAAGATCCGAGC 58.987 47.619 1.71 0.00 0.00 5.03
767 814 4.437239 AGTACTCATTGCAAAGATCCGAG 58.563 43.478 1.71 5.61 0.00 4.63
768 815 4.471904 AGTACTCATTGCAAAGATCCGA 57.528 40.909 1.71 0.00 0.00 4.55
769 816 5.352284 AGTAGTACTCATTGCAAAGATCCG 58.648 41.667 1.71 0.00 0.00 4.18
770 817 6.836577 GAGTAGTACTCATTGCAAAGATCC 57.163 41.667 22.85 0.00 44.45 3.36
783 830 8.404000 TCCGAAATCACTAATTGAGTAGTACTC 58.596 37.037 21.35 21.35 45.26 2.59
825 873 2.508743 CGTCCGAGCACGTTGTTTA 58.491 52.632 2.18 0.00 37.88 2.01
870 918 2.830370 CTCATGGGCCGGGAAAGC 60.830 66.667 2.18 0.00 0.00 3.51
871 919 1.153086 CTCTCATGGGCCGGGAAAG 60.153 63.158 2.18 0.00 0.00 2.62
1132 1222 2.644676 GGTGTTTCCTCTTCCATAGCC 58.355 52.381 0.00 0.00 0.00 3.93
1214 1304 0.402121 GAGAGGGAAGCCAAACCTGT 59.598 55.000 0.00 0.00 34.02 4.00
1286 1393 1.135315 CGGCCGCACAGATCAAAAG 59.865 57.895 14.67 0.00 0.00 2.27
1328 1436 4.327357 GTCTATCCACAGACACATTTCACG 59.673 45.833 0.00 0.00 43.70 4.35
1346 1454 5.542635 TGTCACCTAAAACTGACCTGTCTAT 59.457 40.000 0.00 0.00 36.70 1.98
1347 1455 4.897076 TGTCACCTAAAACTGACCTGTCTA 59.103 41.667 0.00 0.00 36.70 2.59
1476 3322 0.327924 TGCCATGGGTTTCGATGAGT 59.672 50.000 15.13 0.00 31.82 3.41
1492 3338 1.856629 ATGGGCCATATGCTAATGCC 58.143 50.000 19.68 10.52 40.92 4.40
1523 3375 6.866770 AGATGTTTGCAGAGATGAAAATTGTG 59.133 34.615 0.00 0.00 0.00 3.33
1540 3392 4.863491 AGCTGTGCTGTTTAAGATGTTTG 58.137 39.130 0.00 0.00 37.57 2.93
1547 3399 1.198637 GCAGGAGCTGTGCTGTTTAAG 59.801 52.381 9.92 0.00 43.87 1.85
1786 3878 8.766000 AGACCGTGTTTAAACTTGAAATTTTT 57.234 26.923 18.72 0.00 0.00 1.94
1846 3939 7.504911 ACATCATCAGGGATAATTCTGAAAAGG 59.495 37.037 0.00 0.00 42.40 3.11
1884 3980 8.740123 TTTCAAGTCTAAATACAACCTGTGAA 57.260 30.769 0.00 0.00 0.00 3.18
2546 4800 0.396974 TGCCTTCTGTTTTGGCCTGT 60.397 50.000 3.32 0.00 45.56 4.00
2618 4886 6.599638 GCTAACCAACCAGAGATAATTCAACT 59.400 38.462 0.00 0.00 0.00 3.16
2630 4916 0.251916 CCATCGGCTAACCAACCAGA 59.748 55.000 0.00 0.00 34.57 3.86
2631 4917 0.251916 TCCATCGGCTAACCAACCAG 59.748 55.000 0.00 0.00 34.57 4.00
2632 4918 0.035820 GTCCATCGGCTAACCAACCA 60.036 55.000 0.00 0.00 34.57 3.67
2708 5234 1.326213 ACCTCAGGCTCAGATCACCG 61.326 60.000 0.00 0.00 0.00 4.94
2762 5534 4.528504 CGCGATAGATATAACCAGGATCG 58.471 47.826 0.00 0.00 38.14 3.69
2786 5561 6.601613 TCTCCAAAATACATACATGGTTCCAC 59.398 38.462 0.00 0.00 32.90 4.02
2833 5615 5.739935 GCAAGAACCAATGGTGTCTTGAATT 60.740 40.000 34.67 12.46 44.12 2.17
2898 5681 2.415625 GCTCGTATATCCAGGCTAACGG 60.416 54.545 0.00 0.00 0.00 4.44
2915 5698 2.547826 TGCATTCAGAGATTCAGCTCG 58.452 47.619 0.00 0.00 39.87 5.03
2925 5713 6.461110 ACTTAATTTCCCATGCATTCAGAG 57.539 37.500 0.00 0.00 0.00 3.35
2958 5758 4.855715 ATCACCCACACATAGATAGTCG 57.144 45.455 0.00 0.00 0.00 4.18
2979 6305 6.229936 AGCCGACTATAGGTGAAACAATTA 57.770 37.500 4.43 0.00 39.98 1.40
2985 6311 4.502604 GCCATTAGCCGACTATAGGTGAAA 60.503 45.833 4.43 0.00 34.35 2.69
2998 6326 1.155889 TATGCAATCGCCATTAGCCG 58.844 50.000 0.00 0.00 38.78 5.52
3009 6337 4.581824 ACTGTGTCAATCCCATATGCAATC 59.418 41.667 0.00 0.00 0.00 2.67
3094 6437 8.654094 AGACTACATAAATGACATGGATCATGA 58.346 33.333 13.96 0.00 43.81 3.07
3096 6439 9.281371 CAAGACTACATAAATGACATGGATCAT 57.719 33.333 0.00 0.00 41.20 2.45
3137 6605 7.217200 TGGATCTAACATTGTTATCAGCCTAC 58.783 38.462 17.37 2.81 0.00 3.18
3299 6865 1.406539 GGCCTTGTATGTTGCTCCATG 59.593 52.381 0.00 0.00 0.00 3.66
3354 6920 0.730494 GAGCAAATCGCAGTGCCAAC 60.730 55.000 10.11 0.00 46.13 3.77
3358 6924 1.136147 CTGGAGCAAATCGCAGTGC 59.864 57.895 4.58 4.58 46.13 4.40
3359 6925 0.445436 GACTGGAGCAAATCGCAGTG 59.555 55.000 0.00 0.00 46.13 3.66
3360 6926 0.035317 TGACTGGAGCAAATCGCAGT 59.965 50.000 0.00 0.00 46.13 4.40
3361 6927 1.376543 ATGACTGGAGCAAATCGCAG 58.623 50.000 0.00 0.00 46.13 5.18
3401 6967 5.785243 TCAAATATGTGTACACGTCTTGGA 58.215 37.500 26.87 22.09 30.42 3.53
3414 9287 5.703978 TGGCCGGAATTATCAAATATGTG 57.296 39.130 5.05 0.00 0.00 3.21
3416 9289 6.016360 TCACTTGGCCGGAATTATCAAATATG 60.016 38.462 5.05 0.00 0.00 1.78
3431 9304 3.678548 GTCTTAGTAAACTCACTTGGCCG 59.321 47.826 0.00 0.00 0.00 6.13
3447 9320 6.429692 TGTTCCATGTTGTATTGGTGTCTTAG 59.570 38.462 0.00 0.00 34.48 2.18
3454 9327 4.644685 GCCTATGTTCCATGTTGTATTGGT 59.355 41.667 0.00 0.00 34.48 3.67
3490 9363 6.909550 TTACCATAAAGCAACATTTGTCCT 57.090 33.333 0.00 0.00 0.00 3.85
3509 9382 2.370189 AGTGCTCCTCTATGCCATTACC 59.630 50.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.