Multiple sequence alignment - TraesCS2A01G026000

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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 TraesCS2A01G026000 chr2A 100.000 4090 0 0 1 4090 12163710 12159621 0.000000e+00 7553.0
1 TraesCS2A01G026000 chr2A 85.934 2147 279 16 223 2361 12181076 12178945 0.000000e+00 2270.0
2 TraesCS2A01G026000 chr2A 100.000 512 0 0 4544 5055 12159167 12158656 0.000000e+00 946.0
3 TraesCS2A01G026000 chr2A 85.000 460 42 15 4544 4995 12178472 12178032 4.640000e-120 442.0
4 TraesCS2A01G026000 chr2A 87.805 82 6 2 3233 3314 12160430 12160353 5.390000e-15 93.5
5 TraesCS2A01G026000 chr2A 87.805 82 6 2 3281 3358 12160478 12160397 5.390000e-15 93.5
6 TraesCS2A01G026000 chr2B 87.879 2376 273 10 6 2377 18013075 18010711 0.000000e+00 2778.0
7 TraesCS2A01G026000 chr2B 83.849 2390 315 49 52 2406 17928410 17926057 0.000000e+00 2209.0
8 TraesCS2A01G026000 chr2B 75.794 1888 371 58 131 1975 18139978 18138134 0.000000e+00 876.0
9 TraesCS2A01G026000 chr2B 77.571 1507 277 38 131 1606 17936744 17935268 0.000000e+00 854.0
10 TraesCS2A01G026000 chr2B 94.937 237 10 1 4544 4780 17925361 17925127 2.220000e-98 370.0
11 TraesCS2A01G026000 chr2B 90.756 238 17 4 4544 4780 18004630 18004397 3.800000e-81 313.0
12 TraesCS2A01G026000 chr2B 90.977 133 7 3 4863 4995 17925101 17924974 1.870000e-39 174.0
13 TraesCS2A01G026000 chr2B 90.769 65 5 1 4990 5053 17994535 17994471 9.020000e-13 86.1
14 TraesCS2A01G026000 chr2D 88.204 2077 216 20 248 2311 11552437 11550377 0.000000e+00 2451.0
15 TraesCS2A01G026000 chr2D 75.286 2011 416 48 215 2188 11578105 11576139 0.000000e+00 885.0
16 TraesCS2A01G026000 chr2D 76.841 1507 288 42 131 1606 11611135 11609659 0.000000e+00 793.0
17 TraesCS2A01G026000 chr2D 78.067 652 121 15 1049 1686 2260622 2261265 4.740000e-105 392.0
18 TraesCS2A01G026000 chr2D 90.213 235 16 4 4547 4780 11549553 11549325 2.960000e-77 300.0
19 TraesCS2A01G026000 chr2D 96.078 51 2 0 4544 4594 2262500 2262550 3.240000e-12 84.2
20 TraesCS2A01G026000 chrUn 85.973 1768 236 10 223 1980 2013897 2012132 0.000000e+00 1881.0
21 TraesCS2A01G026000 chrUn 82.173 1638 220 44 1 1588 1981393 1979778 0.000000e+00 1341.0
22 TraesCS2A01G026000 chrUn 85.156 896 73 23 2407 3294 348207947 348208790 0.000000e+00 863.0
23 TraesCS2A01G026000 chrUn 85.275 455 50 11 4544 4995 2010968 2010528 2.150000e-123 453.0
24 TraesCS2A01G026000 chrUn 79.286 280 32 12 4716 4995 331372325 331372072 6.730000e-39 172.0
25 TraesCS2A01G026000 chrUn 73.519 287 61 12 1797 2075 1979581 1979302 1.500000e-15 95.3
26 TraesCS2A01G026000 chrUn 87.879 66 7 1 4989 5053 2010367 2010302 5.430000e-10 76.8
27 TraesCS2A01G026000 chrUn 100.000 36 0 0 4553 4588 111116208 111116173 3.270000e-07 67.6
28 TraesCS2A01G026000 chr1D 90.352 1420 58 25 2404 3818 33992271 33990926 0.000000e+00 1790.0
29 TraesCS2A01G026000 chr1D 76.339 2016 388 59 228 2200 363122738 363124707 0.000000e+00 998.0
30 TraesCS2A01G026000 chr1D 100.000 36 0 0 4553 4588 37516259 37516224 3.270000e-07 67.6
31 TraesCS2A01G026000 chr6D 95.291 1083 40 9 2729 3809 334232282 334233355 0.000000e+00 1707.0
32 TraesCS2A01G026000 chr6D 87.600 871 75 13 2427 3287 448416615 448417462 0.000000e+00 979.0
33 TraesCS2A01G026000 chr6D 83.426 899 91 20 2407 3294 448161785 448160934 0.000000e+00 782.0
34 TraesCS2A01G026000 chr6D 93.633 267 17 0 2405 2671 334231645 334231911 2.840000e-107 399.0
35 TraesCS2A01G026000 chr1B 75.926 1998 387 62 228 2181 486480451 486482398 0.000000e+00 939.0
36 TraesCS2A01G026000 chr1B 92.125 546 28 11 3281 3824 361801503 361800971 0.000000e+00 756.0
37 TraesCS2A01G026000 chr1B 89.813 589 38 19 3234 3809 338429495 338430074 0.000000e+00 736.0
38 TraesCS2A01G026000 chr1B 100.000 36 0 0 4553 4588 152828853 152828888 3.270000e-07 67.6
39 TraesCS2A01G026000 chr1A 79.030 1402 254 20 228 1603 462393286 462394673 0.000000e+00 924.0
40 TraesCS2A01G026000 chr5B 93.548 589 28 10 3231 3814 572543778 572543195 0.000000e+00 869.0
41 TraesCS2A01G026000 chr3A 85.142 848 77 18 2445 3291 701310236 701309437 0.000000e+00 822.0
42 TraesCS2A01G026000 chr5A 84.746 826 74 25 2470 3288 658678000 658678780 0.000000e+00 780.0
43 TraesCS2A01G026000 chr5A 90.437 481 33 11 3335 3810 482683274 482682802 5.560000e-174 621.0
44 TraesCS2A01G026000 chr5A 90.426 282 26 1 2408 2689 482718664 482718384 2.220000e-98 370.0
45 TraesCS2A01G026000 chr4B 92.551 537 31 9 3281 3812 384296094 384296626 0.000000e+00 761.0
46 TraesCS2A01G026000 chr4B 79.070 559 60 23 2740 3287 658000832 658001344 1.050000e-86 331.0
47 TraesCS2A01G026000 chr4B 92.609 230 15 2 2408 2636 634416428 634416200 3.770000e-86 329.0
48 TraesCS2A01G026000 chr4B 86.029 272 30 5 2411 2676 449189237 449188968 8.280000e-73 285.0
49 TraesCS2A01G026000 chr4B 88.584 219 11 7 2405 2622 16385433 16385228 2.340000e-63 254.0
50 TraesCS2A01G026000 chr5D 89.765 596 41 17 3234 3818 438043502 438042916 0.000000e+00 745.0
51 TraesCS2A01G026000 chr5D 94.340 53 3 0 2718 2770 545983204 545983152 1.170000e-11 82.4
52 TraesCS2A01G026000 chr3D 95.127 472 17 4 2817 3287 566966622 566966156 0.000000e+00 739.0
53 TraesCS2A01G026000 chr3D 92.013 313 20 1 2407 2719 566967294 566966987 7.770000e-118 435.0
54 TraesCS2A01G026000 chr3D 100.000 28 0 0 2785 2812 566966988 566966961 9.000000e-03 52.8
55 TraesCS2A01G026000 chr3B 91.969 523 20 14 3301 3821 70119737 70119235 0.000000e+00 713.0
56 TraesCS2A01G026000 chr7A 91.147 497 29 12 3323 3809 232391131 232391622 0.000000e+00 660.0
57 TraesCS2A01G026000 chr7A 95.115 348 15 2 2940 3287 232390842 232391187 9.570000e-152 547.0
58 TraesCS2A01G026000 chr7A 74.926 1017 201 39 1044 2033 32019086 32018097 2.820000e-112 416.0
59 TraesCS2A01G026000 chr7A 80.851 141 24 3 1482 1621 32014445 32014307 1.920000e-19 108.0
60 TraesCS2A01G026000 chr7B 94.872 117 6 0 2408 2524 632869923 632869807 3.110000e-42 183.0
61 TraesCS2A01G026000 chr6A 91.667 132 10 1 2428 2559 45329656 45329526 1.120000e-41 182.0
62 TraesCS2A01G026000 chr4A 82.400 125 14 2 2702 2818 17031882 17031758 8.950000e-18 102.0
63 TraesCS2A01G026000 chr7D 74.394 289 39 14 2530 2806 21098686 21098951 1.940000e-14 91.6


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 TraesCS2A01G026000 chr2A 12158656 12163710 5054 True 2171.500000 7553 93.902500 1 5055 4 chr2A.!!$R1 5054
1 TraesCS2A01G026000 chr2A 12178032 12181076 3044 True 1356.000000 2270 85.467000 223 4995 2 chr2A.!!$R2 4772
2 TraesCS2A01G026000 chr2B 18010711 18013075 2364 True 2778.000000 2778 87.879000 6 2377 1 chr2B.!!$R4 2371
3 TraesCS2A01G026000 chr2B 17924974 17928410 3436 True 917.666667 2209 89.921000 52 4995 3 chr2B.!!$R6 4943
4 TraesCS2A01G026000 chr2B 18138134 18139978 1844 True 876.000000 876 75.794000 131 1975 1 chr2B.!!$R5 1844
5 TraesCS2A01G026000 chr2B 17935268 17936744 1476 True 854.000000 854 77.571000 131 1606 1 chr2B.!!$R1 1475
6 TraesCS2A01G026000 chr2D 11549325 11552437 3112 True 1375.500000 2451 89.208500 248 4780 2 chr2D.!!$R3 4532
7 TraesCS2A01G026000 chr2D 11576139 11578105 1966 True 885.000000 885 75.286000 215 2188 1 chr2D.!!$R1 1973
8 TraesCS2A01G026000 chr2D 11609659 11611135 1476 True 793.000000 793 76.841000 131 1606 1 chr2D.!!$R2 1475
9 TraesCS2A01G026000 chr2D 2260622 2262550 1928 False 238.100000 392 87.072500 1049 4594 2 chr2D.!!$F1 3545
10 TraesCS2A01G026000 chrUn 348207947 348208790 843 False 863.000000 863 85.156000 2407 3294 1 chrUn.!!$F1 887
11 TraesCS2A01G026000 chrUn 2010302 2013897 3595 True 803.600000 1881 86.375667 223 5053 3 chrUn.!!$R4 4830
12 TraesCS2A01G026000 chrUn 1979302 1981393 2091 True 718.150000 1341 77.846000 1 2075 2 chrUn.!!$R3 2074
13 TraesCS2A01G026000 chr1D 33990926 33992271 1345 True 1790.000000 1790 90.352000 2404 3818 1 chr1D.!!$R1 1414
14 TraesCS2A01G026000 chr1D 363122738 363124707 1969 False 998.000000 998 76.339000 228 2200 1 chr1D.!!$F1 1972
15 TraesCS2A01G026000 chr6D 334231645 334233355 1710 False 1053.000000 1707 94.462000 2405 3809 2 chr6D.!!$F2 1404
16 TraesCS2A01G026000 chr6D 448416615 448417462 847 False 979.000000 979 87.600000 2427 3287 1 chr6D.!!$F1 860
17 TraesCS2A01G026000 chr6D 448160934 448161785 851 True 782.000000 782 83.426000 2407 3294 1 chr6D.!!$R1 887
18 TraesCS2A01G026000 chr1B 486480451 486482398 1947 False 939.000000 939 75.926000 228 2181 1 chr1B.!!$F3 1953
19 TraesCS2A01G026000 chr1B 361800971 361801503 532 True 756.000000 756 92.125000 3281 3824 1 chr1B.!!$R1 543
20 TraesCS2A01G026000 chr1B 338429495 338430074 579 False 736.000000 736 89.813000 3234 3809 1 chr1B.!!$F2 575
21 TraesCS2A01G026000 chr1A 462393286 462394673 1387 False 924.000000 924 79.030000 228 1603 1 chr1A.!!$F1 1375
22 TraesCS2A01G026000 chr5B 572543195 572543778 583 True 869.000000 869 93.548000 3231 3814 1 chr5B.!!$R1 583
23 TraesCS2A01G026000 chr3A 701309437 701310236 799 True 822.000000 822 85.142000 2445 3291 1 chr3A.!!$R1 846
24 TraesCS2A01G026000 chr5A 658678000 658678780 780 False 780.000000 780 84.746000 2470 3288 1 chr5A.!!$F1 818
25 TraesCS2A01G026000 chr4B 384296094 384296626 532 False 761.000000 761 92.551000 3281 3812 1 chr4B.!!$F1 531
26 TraesCS2A01G026000 chr4B 658000832 658001344 512 False 331.000000 331 79.070000 2740 3287 1 chr4B.!!$F2 547
27 TraesCS2A01G026000 chr5D 438042916 438043502 586 True 745.000000 745 89.765000 3234 3818 1 chr5D.!!$R1 584
28 TraesCS2A01G026000 chr3D 566966156 566967294 1138 True 408.933333 739 95.713333 2407 3287 3 chr3D.!!$R1 880
29 TraesCS2A01G026000 chr3B 70119235 70119737 502 True 713.000000 713 91.969000 3301 3821 1 chr3B.!!$R1 520
30 TraesCS2A01G026000 chr7A 232390842 232391622 780 False 603.500000 660 93.131000 2940 3809 2 chr7A.!!$F1 869
31 TraesCS2A01G026000 chr7A 32014307 32019086 4779 True 262.000000 416 77.888500 1044 2033 2 chr7A.!!$R1 989

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
654 671 0.459078 GACTTACCGCAGACCCTACC 59.541 60.000 0.00 0.00 0.00 3.18 F
1041 1082 1.039856 GCAGGCTGTCCCTTCAAAAA 58.960 50.000 17.16 0.00 43.06 1.94 F
2007 2116 1.442148 GCTCCATACCGGTCTGTCC 59.558 63.158 12.40 0.00 35.57 4.02 F
2547 2964 0.755698 TCTTCTTCCTCCCGATCCCG 60.756 60.000 0.00 0.00 0.00 5.14 F
2599 3028 1.107945 CTCTTCTTCCTCCCTCGGAC 58.892 60.000 0.00 0.00 31.44 4.79 F
2962 4053 1.641577 AGCTTCGATCGTAGTTTGCC 58.358 50.000 20.79 6.01 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2131 2267 0.247695 GCAGACGTCGCTTTATTGGC 60.248 55.000 20.14 7.49 0.00 4.52 R
2228 2391 1.072331 AGGAAAGACAAGCATCACCGT 59.928 47.619 0.00 0.00 0.00 4.83 R
3097 4200 0.322322 TTCCAAGCCGACGGTTGTAT 59.678 50.000 16.73 0.00 44.35 2.29 R
3984 5187 1.131126 CAAGTGCCGTTGATCCATGTC 59.869 52.381 0.00 0.00 0.00 3.06 R
3998 5206 2.489329 TGCCAAGAAAGATAGCAAGTGC 59.511 45.455 0.00 0.00 42.49 4.40 R
4949 8694 1.174783 GAACCGTCTCCACTGCTCTA 58.825 55.000 0.00 0.00 0.00 2.43 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
46 47 2.544903 GGCTCTCTCCGACTCAAATAGC 60.545 54.545 0.00 0.00 0.00 2.97
116 119 7.761409 TGTTAATCTAGCAATTGTAGCCTTTG 58.239 34.615 7.40 0.00 0.00 2.77
377 394 3.973135 CGTATAGCCAGTGTAGCTAAACG 59.027 47.826 8.44 3.99 45.46 3.60
393 410 2.821366 CGGTGCTGCTCATCCACC 60.821 66.667 0.00 0.00 44.28 4.61
415 432 7.384115 CCACCAATGATTCAATCTATCAAATGC 59.616 37.037 0.00 0.00 35.77 3.56
440 457 7.042187 GCAACCACTTAGTGATGATGATTCTAG 60.042 40.741 14.66 0.00 35.23 2.43
501 518 4.397417 GGGTGTCCTCATGAATTTGAAGAG 59.603 45.833 0.00 0.00 0.00 2.85
579 596 1.953686 GCTGGTGTTTTGGCTAGTGAA 59.046 47.619 0.00 0.00 0.00 3.18
654 671 0.459078 GACTTACCGCAGACCCTACC 59.541 60.000 0.00 0.00 0.00 3.18
660 677 2.577593 GCAGACCCTACCGTGGAC 59.422 66.667 0.00 0.00 0.00 4.02
724 741 1.339438 GCCCTCTGAAGACATGCTTGA 60.339 52.381 6.60 0.00 36.83 3.02
809 826 2.650322 TGCCGAGGGTTTTATCCAATC 58.350 47.619 0.00 0.00 0.00 2.67
820 837 9.492730 AGGGTTTTATCCAATCTGAAACAATAT 57.507 29.630 0.00 0.00 33.17 1.28
821 838 9.533253 GGGTTTTATCCAATCTGAAACAATATG 57.467 33.333 0.00 0.00 33.17 1.78
948 971 2.007608 CATGACAGTGTGCTGGATCTG 58.992 52.381 0.00 3.69 46.62 2.90
1041 1082 1.039856 GCAGGCTGTCCCTTCAAAAA 58.960 50.000 17.16 0.00 43.06 1.94
1066 1107 9.831737 AAATTATCAAAGAAGAACATCAAGACG 57.168 29.630 0.00 0.00 0.00 4.18
1196 1249 4.216257 GGATTTGAGTACATGTGCACTTGT 59.784 41.667 32.80 32.80 37.83 3.16
1404 1488 7.630082 TGTGCCTACTTTATAAGGAAAGATGT 58.370 34.615 0.98 0.00 38.48 3.06
1463 1550 6.648192 CAATGGAAGAGTTGAGTTCTATCCT 58.352 40.000 0.00 0.00 0.00 3.24
2007 2116 1.442148 GCTCCATACCGGTCTGTCC 59.558 63.158 12.40 0.00 35.57 4.02
2031 2146 2.685388 GGCAAAAGAGGAAGTAGATGGC 59.315 50.000 0.00 0.00 0.00 4.40
2032 2147 3.347216 GCAAAAGAGGAAGTAGATGGCA 58.653 45.455 0.00 0.00 0.00 4.92
2033 2148 3.758554 GCAAAAGAGGAAGTAGATGGCAA 59.241 43.478 0.00 0.00 0.00 4.52
2136 2272 3.082579 GCGAGAGGAGGACGCCAAT 62.083 63.158 0.00 0.00 45.35 3.16
2228 2391 7.148573 CGTAGAAGGTACGTAACTAAAGAGTGA 60.149 40.741 14.76 0.00 34.65 3.41
2251 2576 3.941483 CGGTGATGCTTGTCTTTCCTTAT 59.059 43.478 0.00 0.00 0.00 1.73
2260 2585 8.650143 TGCTTGTCTTTCCTTATTTTCCTTAT 57.350 30.769 0.00 0.00 0.00 1.73
2261 2586 9.088987 TGCTTGTCTTTCCTTATTTTCCTTATT 57.911 29.630 0.00 0.00 0.00 1.40
2307 2660 5.866207 TCAACCTTTACTCCCTCTTTCTTC 58.134 41.667 0.00 0.00 0.00 2.87
2365 2781 1.597854 TGGCTGTGAAGAACCTGCG 60.598 57.895 0.00 0.00 0.00 5.18
2494 2911 4.201679 CCCATCGTACGCCTCGCA 62.202 66.667 11.24 0.00 0.00 5.10
2521 2938 2.408565 CCTGGCCCACCTTATCTTCTA 58.591 52.381 0.00 0.00 36.63 2.10
2547 2964 0.755698 TCTTCTTCCTCCCGATCCCG 60.756 60.000 0.00 0.00 0.00 5.14
2569 2986 1.388547 CTTCTCTCTCAGCCTAGCGT 58.611 55.000 0.00 0.00 0.00 5.07
2599 3028 1.107945 CTCTTCTTCCTCCCTCGGAC 58.892 60.000 0.00 0.00 31.44 4.79
2831 3916 2.339556 GGCGCCTGCACCAATGTTA 61.340 57.895 22.15 0.00 45.35 2.41
2906 3997 6.647067 GCTCGTATATAAAGCTTCAACTGGAT 59.353 38.462 0.00 0.00 33.23 3.41
2962 4053 1.641577 AGCTTCGATCGTAGTTTGCC 58.358 50.000 20.79 6.01 0.00 4.52
3053 4147 3.430333 TTGAAAAAGCTTCAACCGACC 57.570 42.857 0.00 0.00 33.90 4.79
3190 4294 8.318412 TCAACCAACTATATAGAAAGCTTCACA 58.682 33.333 16.79 0.00 0.00 3.58
3321 4432 6.385649 TCTGAAAAGCTTCAACCGTAATTT 57.614 33.333 0.00 0.00 41.05 1.82
3517 4658 1.909459 TTGCTGCATAAGAGGGGCGA 61.909 55.000 1.84 0.00 0.00 5.54
3654 4814 3.983420 CCATGGCTGGGTGTGGGT 61.983 66.667 0.00 0.00 39.04 4.51
3822 4985 4.142038 TCACTGCCCTTAGAAAAAGAACC 58.858 43.478 0.00 0.00 0.00 3.62
3826 4989 4.086457 TGCCCTTAGAAAAAGAACCCATC 58.914 43.478 0.00 0.00 0.00 3.51
3838 5001 6.347061 AAAGAACCCATCTAAAGATCCCAT 57.653 37.500 0.00 0.00 37.42 4.00
3953 5154 7.918076 AGGTTCTGTCATTATTTACTGGAGAA 58.082 34.615 0.00 0.00 0.00 2.87
3998 5206 2.525248 CGGCGACATGGATCAACGG 61.525 63.158 0.00 0.00 0.00 4.44
4019 5238 2.489329 GCACTTGCTATCTTTCTTGGCA 59.511 45.455 0.00 0.00 38.21 4.92
4022 5241 5.163622 GCACTTGCTATCTTTCTTGGCATAA 60.164 40.000 0.00 0.00 38.21 1.90
4025 5244 6.886459 ACTTGCTATCTTTCTTGGCATAAAGA 59.114 34.615 20.94 20.94 43.72 2.52
4026 5245 7.394359 ACTTGCTATCTTTCTTGGCATAAAGAA 59.606 33.333 21.94 11.58 43.05 2.52
4684 8289 6.255020 CCTATTGCTCATTTCTGTTTTGATGC 59.745 38.462 0.00 0.00 0.00 3.91
4712 8317 9.102757 GTTGTCATTACATTGATACACATCTCT 57.897 33.333 0.00 0.00 34.97 3.10
4733 8338 8.985315 TCTCTATCATAATGTTTCAAAGGCAT 57.015 30.769 0.00 0.00 0.00 4.40
4764 8395 6.966021 TGTTAGGTTTTCATTGTTAGTCTGC 58.034 36.000 0.00 0.00 0.00 4.26
4781 8412 8.512138 GTTAGTCTGCCATTTGTACAGTTTTAT 58.488 33.333 0.00 0.00 33.12 1.40
4787 8418 7.312154 TGCCATTTGTACAGTTTTATAGCTTG 58.688 34.615 0.00 0.00 0.00 4.01
4794 8425 4.794169 ACAGTTTTATAGCTTGCAAACCG 58.206 39.130 0.00 0.00 30.72 4.44
4829 8460 1.126079 CGTCGGTGTTGAGTGTGTAC 58.874 55.000 0.00 0.00 0.00 2.90
4840 8471 5.356751 TGTTGAGTGTGTACTTTGCAAGATT 59.643 36.000 0.00 0.00 37.25 2.40
4906 8651 8.567948 TGGTAGAAGATCAACAATCAAAGTTTC 58.432 33.333 0.00 0.00 36.79 2.78
4949 8694 1.346062 TTGCAGAGGAAGAGCAGAGT 58.654 50.000 0.00 0.00 39.72 3.24
4957 8709 2.099405 GGAAGAGCAGAGTAGAGCAGT 58.901 52.381 0.00 0.00 0.00 4.40
4982 8734 0.102120 CGGTTCCAAACTTGCAAGCA 59.898 50.000 26.27 2.53 0.00 3.91
4985 8737 2.195922 GTTCCAAACTTGCAAGCAGTG 58.804 47.619 26.27 19.50 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.201956 GGAGAGAGCCTATTTCTTCATGACTAA 60.202 40.741 0.00 0.00 0.00 2.24
11 12 5.296748 GGAGAGAGCCTATTTCTTCATGAC 58.703 45.833 0.00 0.00 0.00 3.06
116 119 2.802247 GCAATGGACAAAAAGACAAGGC 59.198 45.455 0.00 0.00 0.00 4.35
288 302 8.611654 ATGCCAAATTGATAATTTTCCATAGC 57.388 30.769 0.00 0.00 38.97 2.97
377 394 0.682209 ATTGGTGGATGAGCAGCACC 60.682 55.000 0.00 0.00 36.53 5.01
393 410 8.761497 GGTTGCATTTGATAGATTGAATCATTG 58.239 33.333 8.03 0.00 33.52 2.82
415 432 8.200120 TCTAGAATCATCATCACTAAGTGGTTG 58.800 37.037 0.00 0.00 33.87 3.77
579 596 8.509690 CACTCATCATGTGAATTTACTTTCTGT 58.490 33.333 1.75 0.00 37.60 3.41
654 671 0.526211 TCCTCAACATCTCGTCCACG 59.474 55.000 0.00 0.00 41.45 4.94
724 741 9.716556 ATCCTCCGGAAACATACTTAGATATAT 57.283 33.333 5.23 0.00 34.34 0.86
820 837 7.122048 TCTCCAATCTCAAAGAGACTAGATCA 58.878 38.462 0.00 0.00 41.76 2.92
821 838 7.581213 TCTCCAATCTCAAAGAGACTAGATC 57.419 40.000 0.00 0.00 41.76 2.75
913 936 0.461870 TCATGTACACGGCAGGCATC 60.462 55.000 0.00 0.00 0.00 3.91
948 971 6.207417 TCTCTTCCCTTGACAATTGACAAATC 59.793 38.462 20.79 5.58 30.22 2.17
1041 1082 7.965107 GCGTCTTGATGTTCTTCTTTGATAATT 59.035 33.333 0.00 0.00 0.00 1.40
1066 1107 3.051081 ACTCACAGATTCAAGAGGTGC 57.949 47.619 0.00 0.00 32.52 5.01
1196 1249 5.887598 CACAACCCCTGAAGATTATGATCAA 59.112 40.000 0.00 0.00 34.60 2.57
1332 1415 4.875544 TGATGGCAGTTTTCTAATACGC 57.124 40.909 0.00 0.00 0.00 4.42
1333 1416 6.128282 ACACTTGATGGCAGTTTTCTAATACG 60.128 38.462 0.00 0.00 0.00 3.06
1338 1421 6.296026 AGTAACACTTGATGGCAGTTTTCTA 58.704 36.000 0.00 0.00 0.00 2.10
1404 1488 1.987855 CCCACCTGGAAGCCGAGTA 60.988 63.158 0.00 0.00 37.39 2.59
1430 1517 1.093159 CTCTTCCATTGCTGTCAGGC 58.907 55.000 1.14 0.00 0.00 4.85
1463 1550 2.028112 ACAATGCTTAGAGAGTCGCCAA 60.028 45.455 0.00 0.00 0.00 4.52
1594 1681 8.786826 TCAATACTAATGGTTACACTTTGGAG 57.213 34.615 0.00 0.00 0.00 3.86
2007 2116 3.040147 TCTACTTCCTCTTTTGCCACG 57.960 47.619 0.00 0.00 0.00 4.94
2031 2146 1.081509 CCAATCACCGCCGTTGTTG 60.082 57.895 0.00 0.00 0.00 3.33
2032 2147 1.104577 AACCAATCACCGCCGTTGTT 61.105 50.000 0.00 0.00 0.00 2.83
2033 2148 1.104577 AAACCAATCACCGCCGTTGT 61.105 50.000 0.00 0.00 0.00 3.32
2131 2267 0.247695 GCAGACGTCGCTTTATTGGC 60.248 55.000 20.14 7.49 0.00 4.52
2144 2280 1.801913 GTAGTCACCAGCGCAGACG 60.802 63.158 11.47 0.00 44.07 4.18
2228 2391 1.072331 AGGAAAGACAAGCATCACCGT 59.928 47.619 0.00 0.00 0.00 4.83
2230 2393 5.904362 AATAAGGAAAGACAAGCATCACC 57.096 39.130 0.00 0.00 0.00 4.02
2231 2394 6.808704 GGAAAATAAGGAAAGACAAGCATCAC 59.191 38.462 0.00 0.00 0.00 3.06
2251 2576 7.915293 TGAAGACGAGCATTAATAAGGAAAA 57.085 32.000 0.00 0.00 0.00 2.29
2260 2585 8.576442 TGATCAGTATATGAAGACGAGCATTAA 58.424 33.333 0.00 0.00 42.53 1.40
2261 2586 8.110860 TGATCAGTATATGAAGACGAGCATTA 57.889 34.615 0.00 0.00 42.53 1.90
2262 2587 6.986250 TGATCAGTATATGAAGACGAGCATT 58.014 36.000 0.00 0.00 42.53 3.56
2268 2593 8.969267 GTAAAGGTTGATCAGTATATGAAGACG 58.031 37.037 0.00 0.00 42.53 4.18
2307 2660 9.717942 CTGTATATATCTTGGGAAGAAGAAAGG 57.282 37.037 0.00 0.00 41.63 3.11
2350 2766 1.159713 TGCACGCAGGTTCTTCACAG 61.160 55.000 0.00 0.00 0.00 3.66
2351 2767 1.153269 TGCACGCAGGTTCTTCACA 60.153 52.632 0.00 0.00 0.00 3.58
2365 2781 2.878406 ACTGTATGTGACAAACCTGCAC 59.122 45.455 0.00 0.00 37.70 4.57
2372 2788 6.334202 GGGAAAACAAACTGTATGTGACAAA 58.666 36.000 0.00 0.00 37.70 2.83
2377 2793 4.561735 ACGGGAAAACAAACTGTATGTG 57.438 40.909 0.00 0.00 0.00 3.21
2494 2911 3.661648 GGTGGGCCAGGGTGATGT 61.662 66.667 6.40 0.00 34.09 3.06
2521 2938 2.709397 TCGGGAGGAAGAAGAAAAAGGT 59.291 45.455 0.00 0.00 0.00 3.50
2547 2964 1.681264 GCTAGGCTGAGAGAGAAGGAC 59.319 57.143 0.00 0.00 0.00 3.85
2569 2986 2.475371 GAAGAAGAGGGCCAGCAGCA 62.475 60.000 6.18 0.00 46.50 4.41
2611 3040 1.971505 CTGCACGGGATTAGGGCTGA 61.972 60.000 0.00 0.00 38.94 4.26
2695 3126 3.607871 GGGGGAACTTGTATTGGGG 57.392 57.895 0.00 0.00 0.00 4.96
2831 3916 2.661718 ACTTTTTGGGTCATCGGTTGT 58.338 42.857 0.00 0.00 0.00 3.32
2962 4053 2.757868 TGGGTGGTCTGTTGAAACTTTG 59.242 45.455 0.00 0.00 0.00 2.77
3053 4147 8.177663 AGTGTTCGCATGAAACTTATCTATTTG 58.822 33.333 0.00 0.00 35.46 2.32
3097 4200 0.322322 TTCCAAGCCGACGGTTGTAT 59.678 50.000 16.73 0.00 44.35 2.29
3190 4294 3.425577 TTTCGTTGTGTACTCGTGAGT 57.574 42.857 7.77 7.77 45.02 3.41
3321 4432 6.038825 TCAGAAATACGGTTGAAGCTTTTCAA 59.961 34.615 0.00 0.00 38.49 2.69
3812 4975 6.663523 TGGGATCTTTAGATGGGTTCTTTTTC 59.336 38.462 0.00 0.00 35.79 2.29
3838 5001 8.132995 GCATGTGGCACGTATATATACATAGTA 58.867 37.037 20.24 3.60 43.97 1.82
3878 5074 6.359804 AGCATGGCTTTATGAATAACAGAGA 58.640 36.000 0.00 0.00 33.89 3.10
3953 5154 1.369091 GATTCCAGACGCACCGCAAT 61.369 55.000 0.00 0.00 0.00 3.56
3984 5187 1.131126 CAAGTGCCGTTGATCCATGTC 59.869 52.381 0.00 0.00 0.00 3.06
3998 5206 2.489329 TGCCAAGAAAGATAGCAAGTGC 59.511 45.455 0.00 0.00 42.49 4.40
4651 8256 9.466497 AACAGAAATGAGCAATAGGATAAGAAA 57.534 29.630 0.00 0.00 0.00 2.52
4652 8257 9.466497 AAACAGAAATGAGCAATAGGATAAGAA 57.534 29.630 0.00 0.00 0.00 2.52
4684 8289 6.415798 TGTGTATCAATGTAATGACAACCG 57.584 37.500 0.00 0.00 39.59 4.44
4764 8395 7.312154 TGCAAGCTATAAAACTGTACAAATGG 58.688 34.615 0.00 0.00 0.00 3.16
4781 8412 3.997762 TCTAGTTTCGGTTTGCAAGCTA 58.002 40.909 13.27 0.00 0.00 3.32
4787 8418 5.388111 GGTTGTTATCTAGTTTCGGTTTGC 58.612 41.667 0.00 0.00 0.00 3.68
4794 8425 4.325472 CACCGACGGTTGTTATCTAGTTTC 59.675 45.833 19.02 0.00 31.02 2.78
4906 8651 9.565213 CAATTTCTCTCTGGTATAAGCTTTTTG 57.435 33.333 3.20 0.00 0.00 2.44
4949 8694 1.174783 GAACCGTCTCCACTGCTCTA 58.825 55.000 0.00 0.00 0.00 2.43
4957 8709 1.961793 CAAGTTTGGAACCGTCTCCA 58.038 50.000 0.00 0.00 43.99 3.86
4997 8749 4.111016 TCAGCCGTGCGGTCGTAG 62.111 66.667 12.46 0.00 37.65 3.51
4998 8750 4.111016 CTCAGCCGTGCGGTCGTA 62.111 66.667 12.46 0.00 37.65 3.43


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

AutoCloner maintained by Alex Coulton.