Multiple sequence alignment - TraesCS3A01G193900

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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 TraesCS3A01G193900 chr3A 100.000 4802 0 0 1 4802 266688314 266693115 0.000000e+00 8868.0
1 TraesCS3A01G193900 chr3A 100.000 2067 0 0 4917 6983 266693230 266695296 0.000000e+00 3818.0
2 TraesCS3A01G193900 chr3A 84.942 518 42 20 3907 4424 725881201 725881682 6.290000e-135 492.0
3 TraesCS3A01G193900 chr3A 85.201 473 35 19 4026 4498 365962900 365962463 2.970000e-123 453.0
4 TraesCS3A01G193900 chr3A 88.926 298 30 3 4917 5214 629690731 629691025 1.430000e-96 364.0
5 TraesCS3A01G193900 chr3D 96.957 3122 53 8 1 3102 191094476 191097575 0.000000e+00 5201.0
6 TraesCS3A01G193900 chr3D 98.220 1685 17 5 3118 4802 191097563 191099234 0.000000e+00 2933.0
7 TraesCS3A01G193900 chr3D 96.667 900 19 3 5456 6345 191099842 191100740 0.000000e+00 1485.0
8 TraesCS3A01G193900 chr3D 98.810 588 6 1 4917 5504 191099258 191099844 0.000000e+00 1046.0
9 TraesCS3A01G193900 chr3D 96.774 155 2 2 6342 6493 191100831 191100985 8.990000e-64 255.0
10 TraesCS3A01G193900 chr3D 100.000 61 0 0 6521 6581 191100986 191101046 5.720000e-21 113.0
11 TraesCS3A01G193900 chr3B 96.938 1698 30 5 3118 4802 277032007 277033695 0.000000e+00 2828.0
12 TraesCS3A01G193900 chr3B 95.897 1755 47 9 939 2677 277029330 277031075 0.000000e+00 2819.0
13 TraesCS3A01G193900 chr3B 95.661 945 31 7 1 942 277028271 277029208 0.000000e+00 1509.0
14 TraesCS3A01G193900 chr3B 94.643 896 25 6 5453 6348 277034301 277035173 0.000000e+00 1367.0
15 TraesCS3A01G193900 chr3B 98.639 588 8 0 4917 5504 277033719 277034306 0.000000e+00 1042.0
16 TraesCS3A01G193900 chr3B 86.930 658 48 21 3907 4564 755228340 755228959 0.000000e+00 704.0
17 TraesCS3A01G193900 chr3B 96.901 355 11 0 2748 3102 277031665 277032019 4.660000e-166 595.0
18 TraesCS3A01G193900 chr3B 97.059 238 5 1 6342 6577 277035261 277035498 3.920000e-107 399.0
19 TraesCS3A01G193900 chr3B 84.740 308 37 6 6606 6911 350463677 350463976 4.090000e-77 300.0
20 TraesCS3A01G193900 chr3B 90.541 222 19 2 3242 3463 96859544 96859763 6.850000e-75 292.0
21 TraesCS3A01G193900 chr7A 89.409 2030 160 34 2797 4802 596685775 596687773 0.000000e+00 2507.0
22 TraesCS3A01G193900 chr7A 91.325 853 60 6 877 1718 596684739 596685588 0.000000e+00 1153.0
23 TraesCS3A01G193900 chr7A 91.938 583 41 5 4917 5497 596687797 596688375 0.000000e+00 811.0
24 TraesCS3A01G193900 chr7A 85.179 641 64 21 3907 4542 651433102 651433716 4.600000e-176 628.0
25 TraesCS3A01G193900 chr7A 84.839 653 48 31 5485 6112 596688399 596689025 1.670000e-170 610.0
26 TraesCS3A01G193900 chr7A 87.778 270 25 5 1725 1994 42978898 42979159 6.800000e-80 309.0
27 TraesCS3A01G193900 chr7B 89.328 2024 165 35 2797 4802 553443250 553445240 0.000000e+00 2494.0
28 TraesCS3A01G193900 chr7B 91.192 931 54 10 803 1718 553441503 553442420 0.000000e+00 1240.0
29 TraesCS3A01G193900 chr7B 90.655 931 53 14 4917 5814 553445264 553446193 0.000000e+00 1206.0
30 TraesCS3A01G193900 chr7B 85.028 354 32 7 203 556 122291692 122291360 2.410000e-89 340.0
31 TraesCS3A01G193900 chr7B 82.042 284 24 16 5842 6112 553446293 553446562 4.240000e-52 217.0
32 TraesCS3A01G193900 chr7B 100.000 30 0 0 6578 6607 712258312 712258283 1.000000e-03 56.5
33 TraesCS3A01G193900 chr7B 100.000 29 0 0 6579 6607 156077420 156077392 4.000000e-03 54.7
34 TraesCS3A01G193900 chr7D 88.746 2026 155 41 2797 4802 520387472 520389444 0.000000e+00 2410.0
35 TraesCS3A01G193900 chr7D 93.168 849 48 5 877 1718 520386345 520387190 0.000000e+00 1238.0
36 TraesCS3A01G193900 chr7D 91.798 573 43 4 4927 5497 520389469 520390039 0.000000e+00 795.0
37 TraesCS3A01G193900 chr7D 88.444 450 42 5 1725 2165 43134513 43134961 1.030000e-147 534.0
38 TraesCS3A01G193900 chr7D 94.562 331 17 1 5485 5814 520390063 520390393 1.740000e-140 510.0
39 TraesCS3A01G193900 chr4B 86.993 592 40 20 3907 4498 462782773 462782219 3.550000e-177 632.0
40 TraesCS3A01G193900 chr4A 89.066 439 31 10 1738 2166 650844358 650843927 4.800000e-146 529.0
41 TraesCS3A01G193900 chr4A 100.000 28 0 0 6580 6607 606542042 606542069 1.300000e-02 52.8
42 TraesCS3A01G193900 chr6D 91.029 379 33 1 6606 6983 231251897 231252275 1.740000e-140 510.0
43 TraesCS3A01G193900 chr6D 100.000 28 0 0 6580 6607 130193177 130193204 1.300000e-02 52.8
44 TraesCS3A01G193900 chr1A 90.551 381 33 2 6606 6983 522307961 522308341 1.050000e-137 501.0
45 TraesCS3A01G193900 chr1A 88.714 381 39 3 6606 6983 522305899 522306278 4.930000e-126 462.0
46 TraesCS3A01G193900 chr2D 87.143 420 52 2 4917 5336 278879804 278880221 6.340000e-130 475.0
47 TraesCS3A01G193900 chr2D 90.868 219 20 0 6606 6824 313806022 313806240 1.900000e-75 294.0
48 TraesCS3A01G193900 chr2D 90.411 219 21 0 6606 6824 313804008 313804226 8.860000e-74 289.0
49 TraesCS3A01G193900 chr2D 83.436 326 32 7 200 525 453571733 453572036 4.120000e-72 283.0
50 TraesCS3A01G193900 chr2D 82.972 323 29 13 5338 5634 278880297 278880619 1.150000e-67 268.0
51 TraesCS3A01G193900 chr2D 91.139 79 6 1 582 660 5765646 5765723 9.580000e-19 106.0
52 TraesCS3A01G193900 chr2D 87.500 80 10 0 581 660 488235994 488236073 7.460000e-15 93.5
53 TraesCS3A01G193900 chr2D 90.769 65 6 0 581 645 569200942 569200878 3.470000e-13 87.9
54 TraesCS3A01G193900 chr2D 87.838 74 9 0 579 652 624184916 624184989 3.470000e-13 87.9
55 TraesCS3A01G193900 chr2B 91.562 320 24 3 3242 3561 770585709 770586025 8.320000e-119 438.0
56 TraesCS3A01G193900 chr2B 87.500 72 9 0 581 652 788011183 788011112 4.490000e-12 84.2
57 TraesCS3A01G193900 chr2B 94.737 38 2 0 1806 1843 427102413 427102450 7.560000e-05 60.2
58 TraesCS3A01G193900 chr2B 100.000 30 0 0 6578 6607 58078082 58078053 1.000000e-03 56.5
59 TraesCS3A01G193900 chr1B 90.938 320 25 4 3242 3561 345535815 345535500 1.800000e-115 427.0
60 TraesCS3A01G193900 chr1B 96.875 32 0 1 6576 6607 498075251 498075281 1.300000e-02 52.8
61 TraesCS3A01G193900 chr5D 91.633 251 20 1 3400 3650 333076590 333076839 5.180000e-91 346.0
62 TraesCS3A01G193900 chr5D 89.961 259 24 2 3400 3657 492284771 492284514 4.040000e-87 333.0
63 TraesCS3A01G193900 chr5D 89.868 227 23 0 6606 6832 163924805 163925031 6.850000e-75 292.0
64 TraesCS3A01G193900 chr5D 90.141 71 7 0 582 652 340948780 340948850 7.460000e-15 93.5
65 TraesCS3A01G193900 chr6B 84.857 350 31 8 200 549 404123847 404124174 4.040000e-87 333.0
66 TraesCS3A01G193900 chr6B 100.000 28 0 0 6580 6607 114378106 114378079 1.300000e-02 52.8
67 TraesCS3A01G193900 chr2A 90.222 225 21 1 6606 6830 71423336 71423113 6.850000e-75 292.0
68 TraesCS3A01G193900 chr2A 90.000 80 7 1 581 660 4218524 4218446 1.240000e-17 102.0
69 TraesCS3A01G193900 chr5B 81.383 376 52 15 1806 2177 292750134 292749773 2.460000e-74 291.0
70 TraesCS3A01G193900 chr5A 90.455 220 19 2 6606 6824 106169567 106169785 8.860000e-74 289.0
71 TraesCS3A01G193900 chr5A 94.643 56 3 0 4509 4564 565381987 565381932 3.470000e-13 87.9
72 TraesCS3A01G193900 chr4D 100.000 28 0 0 6580 6607 246657354 246657327 1.300000e-02 52.8


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 TraesCS3A01G193900 chr3A 266688314 266695296 6982 False 6343.000000 8868 100.000000 1 6983 2 chr3A.!!$F3 6982
1 TraesCS3A01G193900 chr3D 191094476 191101046 6570 False 1838.833333 5201 97.904667 1 6581 6 chr3D.!!$F1 6580
2 TraesCS3A01G193900 chr3B 277028271 277035498 7227 False 1508.428571 2828 96.534000 1 6577 7 chr3B.!!$F4 6576
3 TraesCS3A01G193900 chr3B 755228340 755228959 619 False 704.000000 704 86.930000 3907 4564 1 chr3B.!!$F3 657
4 TraesCS3A01G193900 chr7A 596684739 596689025 4286 False 1270.250000 2507 89.377750 877 6112 4 chr7A.!!$F3 5235
5 TraesCS3A01G193900 chr7A 651433102 651433716 614 False 628.000000 628 85.179000 3907 4542 1 chr7A.!!$F2 635
6 TraesCS3A01G193900 chr7B 553441503 553446562 5059 False 1289.250000 2494 88.304250 803 6112 4 chr7B.!!$F1 5309
7 TraesCS3A01G193900 chr7D 520386345 520390393 4048 False 1238.250000 2410 92.068500 877 5814 4 chr7D.!!$F2 4937
8 TraesCS3A01G193900 chr4B 462782219 462782773 554 True 632.000000 632 86.993000 3907 4498 1 chr4B.!!$R1 591
9 TraesCS3A01G193900 chr1A 522305899 522308341 2442 False 481.500000 501 89.632500 6606 6983 2 chr1A.!!$F1 377
10 TraesCS3A01G193900 chr2D 278879804 278880619 815 False 371.500000 475 85.057500 4917 5634 2 chr2D.!!$F5 717
11 TraesCS3A01G193900 chr2D 313804008 313806240 2232 False 291.500000 294 90.639500 6606 6824 2 chr2D.!!$F6 218

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
496 497 5.479306 TGATTTAGTCACCAGAAGTAGTGC 58.521 41.667 0.00 0.0 33.90 4.40 F
1460 1609 0.600782 CTTGCAATGCACACCCAACC 60.601 55.000 7.72 0.0 38.71 3.77 F
2254 2419 2.241685 AGCAGGAAGAAGCATGAAGGAT 59.758 45.455 0.00 0.0 0.00 3.24 F
3834 5244 1.466950 GTTTGGCGCACAAGTATGCTA 59.533 47.619 10.83 0.0 43.80 3.49 F
4021 5431 2.809446 GTTCAGAAACCTGTTGTTGCC 58.191 47.619 0.00 0.0 37.23 4.52 F
5961 7681 0.178926 TCTACCGTCACCCTTGGGAA 60.179 55.000 13.39 0.0 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2254 2419 1.003051 GCACCTCCCCTCTTCCCTA 59.997 63.158 0.00 0.00 0.00 3.53 R
2442 2607 2.217847 CCGACATACAAGTTAATCGGCG 59.782 50.000 0.00 0.00 42.23 6.46 R
4021 5431 1.950484 GCACATGTCCCACTAACCCAG 60.950 57.143 0.00 0.00 0.00 4.45 R
5515 7158 6.149973 TGTTGTCTCTGCTTTTGATCCTAATG 59.850 38.462 0.00 0.00 0.00 1.90 R
5970 7690 1.145803 GTCGGCTTCACTTGGTGTAC 58.854 55.000 0.00 0.00 34.79 2.90 R
6891 8741 2.632996 TGAACTAGGAGTCCAGGTTGTG 59.367 50.000 19.81 2.59 0.00 3.33 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
341 342 9.059260 TGTTAAAATGTTCCTTTGTACTCCTAC 57.941 33.333 0.00 0.00 0.00 3.18
496 497 5.479306 TGATTTAGTCACCAGAAGTAGTGC 58.521 41.667 0.00 0.00 33.90 4.40
1005 1142 2.949963 GCAGGGGAAGTAAATCATGGCA 60.950 50.000 0.00 0.00 0.00 4.92
1460 1609 0.600782 CTTGCAATGCACACCCAACC 60.601 55.000 7.72 0.00 38.71 3.77
1790 1940 5.556915 TGAATAGGGATTAATCGGCGAATT 58.443 37.500 15.93 11.51 0.00 2.17
2254 2419 2.241685 AGCAGGAAGAAGCATGAAGGAT 59.758 45.455 0.00 0.00 0.00 3.24
2415 2580 2.303890 ACGAGAAGGGGGTTTTCGTATT 59.696 45.455 1.90 0.00 42.05 1.89
2586 2882 2.948979 TGGACAGTGTAAAAGTTGCCAG 59.051 45.455 0.00 0.00 0.00 4.85
2663 2959 1.527311 GCGATAGGGAAAATGCGACTC 59.473 52.381 0.00 0.00 0.00 3.36
2982 4340 4.822036 TGGTTTTGTGTCTAAATCGGTG 57.178 40.909 0.00 0.00 0.00 4.94
3097 4459 2.987149 CCAGTGTGTCTGTAATGACGAC 59.013 50.000 0.00 0.00 42.19 4.34
3098 4460 3.305403 CCAGTGTGTCTGTAATGACGACT 60.305 47.826 0.00 0.00 42.19 4.18
3099 4461 4.299155 CAGTGTGTCTGTAATGACGACTT 58.701 43.478 0.00 0.00 39.64 3.01
3100 4462 4.745125 CAGTGTGTCTGTAATGACGACTTT 59.255 41.667 0.00 0.00 39.64 2.66
3101 4463 5.234329 CAGTGTGTCTGTAATGACGACTTTT 59.766 40.000 0.00 0.00 39.64 2.27
3102 4464 5.462398 AGTGTGTCTGTAATGACGACTTTTC 59.538 40.000 0.00 0.00 39.64 2.29
3103 4465 5.233476 GTGTGTCTGTAATGACGACTTTTCA 59.767 40.000 0.00 0.00 39.64 2.69
3104 4466 5.233476 TGTGTCTGTAATGACGACTTTTCAC 59.767 40.000 0.00 0.00 39.64 3.18
3105 4467 5.233476 GTGTCTGTAATGACGACTTTTCACA 59.767 40.000 0.00 0.00 39.64 3.58
3106 4468 5.462068 TGTCTGTAATGACGACTTTTCACAG 59.538 40.000 8.89 8.89 39.64 3.66
3107 4469 5.462398 GTCTGTAATGACGACTTTTCACAGT 59.538 40.000 12.53 0.00 0.00 3.55
3108 4470 5.690409 TCTGTAATGACGACTTTTCACAGTC 59.310 40.000 12.53 0.00 40.02 3.51
3109 4471 5.353111 TGTAATGACGACTTTTCACAGTCA 58.647 37.500 0.00 0.00 43.11 3.41
3110 4472 5.813157 TGTAATGACGACTTTTCACAGTCAA 59.187 36.000 0.66 0.00 43.11 3.18
3111 4473 5.811399 AATGACGACTTTTCACAGTCAAA 57.189 34.783 0.66 0.00 43.11 2.69
3112 4474 5.811399 ATGACGACTTTTCACAGTCAAAA 57.189 34.783 0.66 0.00 43.11 2.44
3113 4475 5.614923 TGACGACTTTTCACAGTCAAAAA 57.385 34.783 0.00 0.00 43.11 1.94
3163 4556 3.064134 GGTGCTTCGGCTTTATCTTCTTC 59.936 47.826 0.00 0.00 42.37 2.87
3164 4557 3.935828 GTGCTTCGGCTTTATCTTCTTCT 59.064 43.478 0.00 0.00 42.37 2.85
3165 4558 4.393371 GTGCTTCGGCTTTATCTTCTTCTT 59.607 41.667 0.00 0.00 42.37 2.52
3633 5039 4.491676 GTCTTTGTCGCATAAGTGTCCTA 58.508 43.478 0.00 0.00 0.00 2.94
3706 5115 7.011950 TGTCACTGTAACATGTTCCTTTGTTAG 59.988 37.037 15.85 5.72 38.58 2.34
3834 5244 1.466950 GTTTGGCGCACAAGTATGCTA 59.533 47.619 10.83 0.00 43.80 3.49
4021 5431 2.809446 GTTCAGAAACCTGTTGTTGCC 58.191 47.619 0.00 0.00 37.23 4.52
4086 5496 3.505680 CAGTTTGGCCATGCTGTAAGTTA 59.494 43.478 22.05 0.00 35.30 2.24
4138 5548 6.476378 AGTTCCAGTTAGCTGAACAATACAT 58.524 36.000 8.34 0.00 45.28 2.29
5282 6717 6.737608 AGCCATCTTATTTCCTGTCCCTATAT 59.262 38.462 0.00 0.00 0.00 0.86
5466 7026 6.434028 TCATAATAAGCTTGCACCTGAAAAGT 59.566 34.615 9.86 0.00 0.00 2.66
5515 7158 9.129209 GTTTCTAAATTTCACTTGCATACCTTC 57.871 33.333 0.00 0.00 0.00 3.46
5734 7377 2.957680 TGGAATGTTCAGCAAGCAAGAA 59.042 40.909 0.00 0.00 0.00 2.52
5758 7401 9.334947 GAAATTGATGAGATTGTAGAGATTGGA 57.665 33.333 0.00 0.00 0.00 3.53
5961 7681 0.178926 TCTACCGTCACCCTTGGGAA 60.179 55.000 13.39 0.00 0.00 3.97
5970 7690 0.995024 ACCCTTGGGAAGATGTCCTG 59.005 55.000 13.39 0.00 46.92 3.86
5983 7703 3.646162 AGATGTCCTGTACACCAAGTGAA 59.354 43.478 0.96 0.00 42.09 3.18
6003 7723 2.182791 CGACTCAGCACGGCATCT 59.817 61.111 0.00 0.00 0.00 2.90
6210 7951 3.119029 GCATGAAAGCTTTAGGGCATCAA 60.119 43.478 12.68 0.00 35.28 2.57
6264 8005 9.460019 TTCATGTTATCATCAATTAAGTGACCA 57.540 29.630 7.92 0.00 31.15 4.02
6269 8010 8.519526 GTTATCATCAATTAAGTGACCACCAAA 58.480 33.333 7.92 0.00 0.00 3.28
6440 8286 6.883756 TGGATGTTACTTGAGTTGCATGATAA 59.116 34.615 0.00 0.00 0.00 1.75
6581 8428 4.444056 CCTAAATTCAACTGGCAAAACGTG 59.556 41.667 0.00 0.00 0.00 4.49
6582 8429 3.791973 AATTCAACTGGCAAAACGTGA 57.208 38.095 0.00 0.00 0.00 4.35
6583 8430 4.320608 AATTCAACTGGCAAAACGTGAT 57.679 36.364 0.00 0.00 0.00 3.06
6584 8431 2.772568 TCAACTGGCAAAACGTGATG 57.227 45.000 0.00 0.00 0.00 3.07
6585 8432 2.293170 TCAACTGGCAAAACGTGATGA 58.707 42.857 5.11 0.00 0.00 2.92
6586 8433 2.685388 TCAACTGGCAAAACGTGATGAA 59.315 40.909 5.11 0.00 0.00 2.57
6587 8434 3.044986 CAACTGGCAAAACGTGATGAAG 58.955 45.455 5.11 4.34 0.00 3.02
6588 8435 1.001378 ACTGGCAAAACGTGATGAAGC 60.001 47.619 5.11 0.00 0.00 3.86
6589 8436 1.001487 CTGGCAAAACGTGATGAAGCA 60.001 47.619 5.11 0.00 0.00 3.91
6590 8437 1.268999 TGGCAAAACGTGATGAAGCAC 60.269 47.619 5.11 0.00 35.46 4.40
6598 8445 1.281899 GTGATGAAGCACGGACTAGC 58.718 55.000 0.00 0.00 0.00 3.42
6599 8446 0.179137 TGATGAAGCACGGACTAGCG 60.179 55.000 0.00 0.00 35.48 4.26
6600 8447 0.100682 GATGAAGCACGGACTAGCGA 59.899 55.000 0.00 0.00 35.48 4.93
6601 8448 0.101399 ATGAAGCACGGACTAGCGAG 59.899 55.000 0.00 0.00 35.48 5.03
6602 8449 0.958876 TGAAGCACGGACTAGCGAGA 60.959 55.000 0.00 0.00 35.48 4.04
6603 8450 0.382515 GAAGCACGGACTAGCGAGAT 59.617 55.000 0.00 0.00 35.48 2.75
6604 8451 0.101399 AAGCACGGACTAGCGAGATG 59.899 55.000 0.00 0.00 35.48 2.90
6605 8452 1.946650 GCACGGACTAGCGAGATGC 60.947 63.158 0.00 1.39 46.98 3.91
6671 8518 5.261216 ACACGAATGAAAATAATGACCCCT 58.739 37.500 0.00 0.00 0.00 4.79
6689 8536 1.066143 CCTTTGGATCAGCACGTAGGT 60.066 52.381 0.00 0.00 0.00 3.08
6732 8579 3.056678 TCCGTCGCTAGTAAATTTCCACA 60.057 43.478 0.00 0.00 0.00 4.17
6737 8584 6.401688 CGTCGCTAGTAAATTTCCACAATGAA 60.402 38.462 0.00 0.00 0.00 2.57
6780 8627 2.022764 TATGACCGTCCGTAACTCGA 57.977 50.000 0.00 0.00 42.86 4.04
6841 8690 6.515272 AAAACTAATTTGATCGGATGCACT 57.485 33.333 0.00 0.00 0.00 4.40
6905 8755 1.172812 GCCAACACAACCTGGACTCC 61.173 60.000 0.00 0.00 34.35 3.85
6935 8785 4.517285 ACTTGGTCATCACGCTCATTATT 58.483 39.130 0.00 0.00 0.00 1.40
6937 8787 6.291377 ACTTGGTCATCACGCTCATTATTAT 58.709 36.000 0.00 0.00 0.00 1.28
6941 8791 5.106948 GGTCATCACGCTCATTATTATGTGG 60.107 44.000 0.00 0.00 33.34 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.363341 TTTTCGCCACCAAGATTCAAC 57.637 42.857 0.00 0.00 0.00 3.18
220 221 5.499004 TCTAAAACCTCCAGTACAAGCAT 57.501 39.130 0.00 0.00 0.00 3.79
341 342 5.576774 TCACACGCAGACAAACTATAATGAG 59.423 40.000 0.00 0.00 0.00 2.90
496 497 3.283256 CGCATATTAAGTTCTTGCTGCG 58.717 45.455 13.52 13.52 44.02 5.18
639 643 5.635120 AGGAAAGAGCTAACACAGGAAAAT 58.365 37.500 0.00 0.00 0.00 1.82
735 742 8.032952 TGATTTCAAACAAGCTACTGACATAG 57.967 34.615 0.00 0.00 0.00 2.23
1005 1142 4.904253 TTTCGAGAAAATTTGACCCGTT 57.096 36.364 0.00 0.00 0.00 4.44
1460 1609 4.670621 GCAAAGTTGATAAATACATCCGCG 59.329 41.667 0.00 0.00 0.00 6.46
1790 1940 9.268268 CTACCGATAAATTCAGTTAAATGGCTA 57.732 33.333 2.65 0.00 0.00 3.93
1816 1966 1.810455 TGGTATGGCCCTAGGTAACC 58.190 55.000 8.29 6.90 36.04 2.85
1819 1969 2.848242 TGTTTGGTATGGCCCTAGGTA 58.152 47.619 8.29 0.00 36.04 3.08
1820 1970 1.676248 TGTTTGGTATGGCCCTAGGT 58.324 50.000 8.29 0.00 36.04 3.08
1821 1971 4.657814 ATATGTTTGGTATGGCCCTAGG 57.342 45.455 0.06 0.06 36.04 3.02
1908 2073 1.745087 AGCCCAAATGTGACTTATGCG 59.255 47.619 0.00 0.00 0.00 4.73
2166 2331 1.517361 CCAGTGCATCCTACAGCGA 59.483 57.895 0.00 0.00 0.00 4.93
2254 2419 1.003051 GCACCTCCCCTCTTCCCTA 59.997 63.158 0.00 0.00 0.00 3.53
2415 2580 2.363795 CTACTCGGAGGGTGGCCA 60.364 66.667 0.00 0.00 0.00 5.36
2442 2607 2.217847 CCGACATACAAGTTAATCGGCG 59.782 50.000 0.00 0.00 42.23 6.46
2623 2919 3.553511 CGCTCTGTTGGATCATCTTACAC 59.446 47.826 0.00 0.00 0.00 2.90
2663 2959 4.624364 TCCGCACAGGGCACACAG 62.624 66.667 0.00 0.00 45.17 3.66
2739 3035 9.060347 AGCAATCATTTCAACTCATTACGATAT 57.940 29.630 0.00 0.00 0.00 1.63
2742 3038 6.741992 AGCAATCATTTCAACTCATTACGA 57.258 33.333 0.00 0.00 0.00 3.43
2982 4340 9.341899 AGATTATTAACAACGAAATTGAAGCAC 57.658 29.630 0.00 0.00 41.23 4.40
3116 4478 9.405587 CCATATGTAAACAAAAAGTCGTCATTT 57.594 29.630 1.24 0.00 0.00 2.32
3117 4479 8.573035 ACCATATGTAAACAAAAAGTCGTCATT 58.427 29.630 1.24 0.00 0.00 2.57
3118 4480 8.020819 CACCATATGTAAACAAAAAGTCGTCAT 58.979 33.333 1.24 0.00 0.00 3.06
3119 4481 7.356540 CACCATATGTAAACAAAAAGTCGTCA 58.643 34.615 1.24 0.00 0.00 4.35
3120 4482 6.304683 GCACCATATGTAAACAAAAAGTCGTC 59.695 38.462 1.24 0.00 0.00 4.20
3121 4483 6.016610 AGCACCATATGTAAACAAAAAGTCGT 60.017 34.615 1.24 0.00 0.00 4.34
3122 4484 6.378582 AGCACCATATGTAAACAAAAAGTCG 58.621 36.000 1.24 0.00 0.00 4.18
3163 4556 5.050567 GCTCTCCACATTTTTGCAAGAAAAG 60.051 40.000 6.49 5.39 32.54 2.27
3164 4557 4.810491 GCTCTCCACATTTTTGCAAGAAAA 59.190 37.500 6.49 2.56 33.46 2.29
3165 4558 4.141981 TGCTCTCCACATTTTTGCAAGAAA 60.142 37.500 6.49 7.71 0.00 2.52
3834 5244 3.262842 TCAGGGATGGCATTATCCTGAT 58.737 45.455 28.39 7.86 44.90 2.90
4021 5431 1.950484 GCACATGTCCCACTAACCCAG 60.950 57.143 0.00 0.00 0.00 4.45
4086 5496 9.366216 GAAGAAAAGAACACCAATTTGTTTACT 57.634 29.630 0.00 0.00 39.88 2.24
4138 5548 8.995027 AATAAACCAGATCCATGCATACTAAA 57.005 30.769 0.00 0.00 0.00 1.85
4562 5995 5.105351 GCAGGGCAAAGGACAATTATAAAGT 60.105 40.000 0.00 0.00 0.00 2.66
4563 5996 5.127682 AGCAGGGCAAAGGACAATTATAAAG 59.872 40.000 0.00 0.00 0.00 1.85
4564 5997 5.022787 AGCAGGGCAAAGGACAATTATAAA 58.977 37.500 0.00 0.00 0.00 1.40
4565 5998 4.609301 AGCAGGGCAAAGGACAATTATAA 58.391 39.130 0.00 0.00 0.00 0.98
4566 5999 4.249638 AGCAGGGCAAAGGACAATTATA 57.750 40.909 0.00 0.00 0.00 0.98
4753 6187 6.877611 ACATTTAGCCCATAAATTACCTCG 57.122 37.500 0.00 0.00 41.25 4.63
5466 7026 9.868277 AAACAACAAACTTATGTCTTGAAATCA 57.132 25.926 9.20 0.00 31.81 2.57
5515 7158 6.149973 TGTTGTCTCTGCTTTTGATCCTAATG 59.850 38.462 0.00 0.00 0.00 1.90
5758 7401 7.201767 GCAAGCACAAAGAGTCCATTAAGATAT 60.202 37.037 0.00 0.00 0.00 1.63
5961 7681 3.239449 TCACTTGGTGTACAGGACATCT 58.761 45.455 0.00 0.00 40.17 2.90
5970 7690 1.145803 GTCGGCTTCACTTGGTGTAC 58.854 55.000 0.00 0.00 34.79 2.90
6172 7912 9.059260 AGCTTTCATGCTTGAACAATAAAAATT 57.941 25.926 14.11 0.00 41.50 1.82
6173 7913 8.611654 AGCTTTCATGCTTGAACAATAAAAAT 57.388 26.923 14.11 0.00 41.50 1.82
6264 8005 6.290605 CCCAAATGTCTGAAGAAAATTTGGT 58.709 36.000 27.32 2.98 46.36 3.67
6269 8010 5.244626 CACTCCCCAAATGTCTGAAGAAAAT 59.755 40.000 0.00 0.00 0.00 1.82
6334 8084 6.479972 AGACGGATACCATTACAGAATTCA 57.520 37.500 8.44 0.00 0.00 2.57
6581 8428 0.100682 TCGCTAGTCCGTGCTTCATC 59.899 55.000 0.00 0.00 0.00 2.92
6582 8429 0.101399 CTCGCTAGTCCGTGCTTCAT 59.899 55.000 0.00 0.00 0.00 2.57
6583 8430 0.958876 TCTCGCTAGTCCGTGCTTCA 60.959 55.000 0.00 0.00 0.00 3.02
6584 8431 0.382515 ATCTCGCTAGTCCGTGCTTC 59.617 55.000 0.00 0.00 0.00 3.86
6585 8432 0.101399 CATCTCGCTAGTCCGTGCTT 59.899 55.000 0.00 0.00 0.00 3.91
6586 8433 1.730487 CATCTCGCTAGTCCGTGCT 59.270 57.895 0.00 0.00 0.00 4.40
6587 8434 1.946650 GCATCTCGCTAGTCCGTGC 60.947 63.158 0.00 0.00 37.77 5.34
6588 8435 4.310672 GCATCTCGCTAGTCCGTG 57.689 61.111 0.00 0.00 37.77 4.94
6605 8452 9.278734 GAAAATTATCTTAAAGTTTGCGAGGAG 57.721 33.333 0.00 0.00 27.70 3.69
6606 8453 8.788806 TGAAAATTATCTTAAAGTTTGCGAGGA 58.211 29.630 0.00 0.00 27.70 3.71
6607 8454 8.850452 GTGAAAATTATCTTAAAGTTTGCGAGG 58.150 33.333 0.00 0.00 27.70 4.63
6608 8455 8.850452 GGTGAAAATTATCTTAAAGTTTGCGAG 58.150 33.333 0.00 0.00 27.70 5.03
6609 8456 7.810759 GGGTGAAAATTATCTTAAAGTTTGCGA 59.189 33.333 0.00 0.00 27.70 5.10
6615 8462 5.413523 ACGCGGGTGAAAATTATCTTAAAGT 59.586 36.000 12.47 0.00 0.00 2.66
6619 8466 4.503734 CGTACGCGGGTGAAAATTATCTTA 59.496 41.667 16.34 0.00 0.00 2.10
6671 8518 3.490249 CGATACCTACGTGCTGATCCAAA 60.490 47.826 0.00 0.00 0.00 3.28
6689 8536 4.021104 GGAGGGTTGATCATCACATCGATA 60.021 45.833 8.70 0.00 31.20 2.92
6743 8590 7.820386 ACGGTCATATCTTGTGTATTGTTTGTA 59.180 33.333 0.00 0.00 0.00 2.41
6749 8596 4.444388 CGGACGGTCATATCTTGTGTATTG 59.556 45.833 10.76 0.00 0.00 1.90
6836 8685 5.734720 GCTAATATAATAGCCAGGAGTGCA 58.265 41.667 8.41 0.00 41.98 4.57
6891 8741 2.632996 TGAACTAGGAGTCCAGGTTGTG 59.367 50.000 19.81 2.59 0.00 3.33
6905 8755 3.123621 GCGTGATGACCAAGTTGAACTAG 59.876 47.826 3.87 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.