Multiple sequence alignment - TraesCS6A01G414200

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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 TraesCS6A01G414200 chr6A 100.000 8657 0 0 1 8657 614698825 614690169 0.000000e+00 15987.0
1 TraesCS6A01G414200 chr6A 84.397 282 34 7 5035 5311 591378799 591379075 1.430000e-67 268.0
2 TraesCS6A01G414200 chr6A 75.818 550 113 18 3399 3941 594863010 594863546 2.400000e-65 261.0
3 TraesCS6A01G414200 chr6A 82.482 274 41 3 5035 5306 7307661 7307929 5.230000e-57 233.0
4 TraesCS6A01G414200 chr6A 92.405 79 6 0 5402 5480 409090522 409090600 7.100000e-21 113.0
5 TraesCS6A01G414200 chr6A 91.463 82 7 0 5405 5486 451606408 451606327 7.100000e-21 113.0
6 TraesCS6A01G414200 chrUn 98.939 4714 32 5 3945 8657 297826686 297821990 0.000000e+00 8412.0
7 TraesCS6A01G414200 chrUn 97.311 3793 58 25 1 3756 305404268 305408053 0.000000e+00 6399.0
8 TraesCS6A01G414200 chrUn 79.436 1843 344 26 6766 8598 62091362 62093179 0.000000e+00 1271.0
9 TraesCS6A01G414200 chrUn 84.615 845 120 8 996 1835 331544486 331545325 0.000000e+00 832.0
10 TraesCS6A01G414200 chrUn 84.460 843 125 4 996 1835 291937667 291936828 0.000000e+00 826.0
11 TraesCS6A01G414200 chrUn 84.460 843 125 4 996 1835 328964784 328963945 0.000000e+00 826.0
12 TraesCS6A01G414200 chrUn 83.749 843 131 5 996 1835 62146649 62147488 0.000000e+00 793.0
13 TraesCS6A01G414200 chrUn 83.966 817 128 1 995 1811 75076689 75075876 0.000000e+00 780.0
14 TraesCS6A01G414200 chrUn 76.635 1254 267 25 6832 8070 62149025 62150267 0.000000e+00 669.0
15 TraesCS6A01G414200 chrUn 75.128 587 111 25 3378 3950 32093951 32094516 8.680000e-60 243.0
16 TraesCS6A01G414200 chrUn 92.405 79 6 0 5402 5480 252262181 252262259 7.100000e-21 113.0
17 TraesCS6A01G414200 chr6B 90.656 1905 158 11 6707 8597 715968107 715966209 0.000000e+00 2514.0
18 TraesCS6A01G414200 chr6B 83.775 1812 268 22 6796 8595 716226286 716224489 0.000000e+00 1694.0
19 TraesCS6A01G414200 chr6B 83.113 1812 262 29 6796 8595 715900311 715898532 0.000000e+00 1611.0
20 TraesCS6A01G414200 chr6B 82.748 1965 182 64 7 1847 715981350 715979419 0.000000e+00 1605.0
21 TraesCS6A01G414200 chr6B 85.181 911 132 1 999 1909 715971060 715970153 0.000000e+00 931.0
22 TraesCS6A01G414200 chr6B 77.874 1157 225 24 6834 7974 715860638 715859497 0.000000e+00 689.0
23 TraesCS6A01G414200 chr6B 75.920 652 131 20 3303 3941 519311752 519312390 2.350000e-80 311.0
24 TraesCS6A01G414200 chr6B 81.191 319 40 8 5780 6080 715969057 715968741 1.120000e-58 239.0
25 TraesCS6A01G414200 chr6B 90.476 84 8 0 5405 5488 218030169 218030086 2.550000e-20 111.0
26 TraesCS6A01G414200 chr6D 79.825 1829 337 22 6778 8598 469790147 469788343 0.000000e+00 1304.0
27 TraesCS6A01G414200 chr6D 86.347 813 108 1 999 1811 469813088 469812279 0.000000e+00 883.0
28 TraesCS6A01G414200 chr6D 77.243 1226 247 26 6832 8039 469917772 469918983 0.000000e+00 689.0
29 TraesCS6A01G414200 chr6D 75.891 589 110 28 3378 3952 455630080 455630650 1.110000e-68 272.0
30 TraesCS6A01G414200 chr6D 89.247 93 7 1 5388 5480 321163239 321163328 7.100000e-21 113.0
31 TraesCS6A01G414200 chr7D 78.243 717 134 15 3237 3941 542846492 542845786 2.870000e-119 440.0
32 TraesCS6A01G414200 chr7D 78.689 671 119 15 3293 3950 542907173 542906514 8.030000e-115 425.0
33 TraesCS6A01G414200 chr7D 77.759 598 101 23 3365 3949 633521970 633522548 1.080000e-88 339.0
34 TraesCS6A01G414200 chr7D 80.255 157 23 7 7 160 191574489 191574640 2.550000e-20 111.0
35 TraesCS6A01G414200 chr5D 76.529 605 104 20 3326 3920 421537734 421537158 6.570000e-76 296.0
36 TraesCS6A01G414200 chr5D 87.097 62 6 1 5329 5388 411595128 411595067 1.560000e-07 69.4
37 TraesCS6A01G414200 chr3D 75.776 644 125 22 3324 3950 338496329 338496958 6.570000e-76 296.0
38 TraesCS6A01G414200 chr3D 82.545 275 40 5 5035 5305 599298620 599298350 1.450000e-57 235.0
39 TraesCS6A01G414200 chr3D 89.091 55 5 1 110 164 190259187 190259134 5.610000e-07 67.6
40 TraesCS6A01G414200 chr2A 79.475 419 72 11 3543 3951 447371054 447370640 1.420000e-72 285.0
41 TraesCS6A01G414200 chr2A 84.364 275 33 5 5035 5306 28828408 28828141 2.400000e-65 261.0
42 TraesCS6A01G414200 chr2A 83.813 278 38 4 5035 5309 59560501 59560228 3.100000e-64 257.0
43 TraesCS6A01G414200 chr2A 77.860 271 46 10 3412 3679 654008655 654008914 1.160000e-33 156.0
44 TraesCS6A01G414200 chr2A 92.683 82 6 0 5405 5486 676458254 676458173 1.530000e-22 119.0
45 TraesCS6A01G414200 chr5A 75.299 668 119 34 3299 3951 566046684 566047320 2.380000e-70 278.0
46 TraesCS6A01G414200 chr5A 83.154 279 37 7 5035 5308 60122527 60122800 6.710000e-61 246.0
47 TraesCS6A01G414200 chr5A 87.500 80 8 2 5313 5390 529907976 529907897 3.330000e-14 91.6
48 TraesCS6A01G414200 chr4D 84.532 278 36 3 5035 5309 15155275 15155548 1.430000e-67 268.0
49 TraesCS6A01G414200 chr4D 80.588 170 25 6 1 167 78688892 78689056 3.280000e-24 124.0
50 TraesCS6A01G414200 chr4D 89.873 79 8 0 7 85 468514478 468514400 1.540000e-17 102.0
51 TraesCS6A01G414200 chr3A 77.000 500 88 18 3464 3951 709466172 709465688 2.400000e-65 261.0
52 TraesCS6A01G414200 chr3A 76.923 390 77 6 3363 3745 380903671 380904054 8.810000e-50 209.0
53 TraesCS6A01G414200 chr3A 74.631 339 73 9 3380 3713 747564067 747564397 4.210000e-28 137.0
54 TraesCS6A01G414200 chr3A 90.278 72 5 1 5326 5395 481654831 481654760 9.250000e-15 93.5
55 TraesCS6A01G414200 chr3A 82.692 104 12 5 5307 5406 641803855 641803754 4.310000e-13 87.9
56 TraesCS6A01G414200 chr7A 83.929 280 35 7 5035 5309 275024228 275023954 8.620000e-65 259.0
57 TraesCS6A01G414200 chr7A 80.451 133 16 6 29 160 690367836 690367713 9.250000e-15 93.5
58 TraesCS6A01G414200 chr7B 77.619 420 82 8 3543 3956 246503954 246503541 2.410000e-60 244.0
59 TraesCS6A01G414200 chr4B 75.610 369 70 15 3380 3738 520227560 520227918 1.930000e-36 165.0
60 TraesCS6A01G414200 chr4B 82.353 153 22 4 7 157 587467710 587467561 2.540000e-25 128.0
61 TraesCS6A01G414200 chr4B 89.394 66 5 1 5326 5389 647036036 647035971 2.000000e-11 82.4
62 TraesCS6A01G414200 chr1D 91.463 82 7 0 5405 5486 492177887 492177806 7.100000e-21 113.0
63 TraesCS6A01G414200 chr1D 92.593 54 4 0 107 160 104576819 104576872 2.590000e-10 78.7
64 TraesCS6A01G414200 chr1A 92.405 79 4 2 5402 5480 319887520 319887596 2.550000e-20 111.0
65 TraesCS6A01G414200 chr1A 79.699 133 17 6 29 160 307055765 307055888 4.310000e-13 87.9
66 TraesCS6A01G414200 chr1A 92.593 54 4 0 110 163 107468647 107468594 2.590000e-10 78.7
67 TraesCS6A01G414200 chr4A 92.857 42 1 1 5353 5392 5201392 5201351 9.390000e-05 60.2
68 TraesCS6A01G414200 chr2B 100.000 28 0 0 5368 5395 598566852 598566825 1.600000e-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 TraesCS6A01G414200 chr6A 614690169 614698825 8656 True 15987 15987 100.000 1 8657 1 chr6A.!!$R2 8656
1 TraesCS6A01G414200 chr6A 594863010 594863546 536 False 261 261 75.818 3399 3941 1 chr6A.!!$F4 542
2 TraesCS6A01G414200 chrUn 297821990 297826686 4696 True 8412 8412 98.939 3945 8657 1 chrUn.!!$R3 4712
3 TraesCS6A01G414200 chrUn 305404268 305408053 3785 False 6399 6399 97.311 1 3756 1 chrUn.!!$F4 3755
4 TraesCS6A01G414200 chrUn 62091362 62093179 1817 False 1271 1271 79.436 6766 8598 1 chrUn.!!$F2 1832
5 TraesCS6A01G414200 chrUn 331544486 331545325 839 False 832 832 84.615 996 1835 1 chrUn.!!$F5 839
6 TraesCS6A01G414200 chrUn 291936828 291937667 839 True 826 826 84.460 996 1835 1 chrUn.!!$R2 839
7 TraesCS6A01G414200 chrUn 328963945 328964784 839 True 826 826 84.460 996 1835 1 chrUn.!!$R4 839
8 TraesCS6A01G414200 chrUn 75075876 75076689 813 True 780 780 83.966 995 1811 1 chrUn.!!$R1 816
9 TraesCS6A01G414200 chrUn 62146649 62150267 3618 False 731 793 80.192 996 8070 2 chrUn.!!$F6 7074
10 TraesCS6A01G414200 chrUn 32093951 32094516 565 False 243 243 75.128 3378 3950 1 chrUn.!!$F1 572
11 TraesCS6A01G414200 chr6B 716224489 716226286 1797 True 1694 1694 83.775 6796 8595 1 chr6B.!!$R5 1799
12 TraesCS6A01G414200 chr6B 715898532 715900311 1779 True 1611 1611 83.113 6796 8595 1 chr6B.!!$R3 1799
13 TraesCS6A01G414200 chr6B 715979419 715981350 1931 True 1605 1605 82.748 7 1847 1 chr6B.!!$R4 1840
14 TraesCS6A01G414200 chr6B 715966209 715971060 4851 True 1228 2514 85.676 999 8597 3 chr6B.!!$R6 7598
15 TraesCS6A01G414200 chr6B 715859497 715860638 1141 True 689 689 77.874 6834 7974 1 chr6B.!!$R2 1140
16 TraesCS6A01G414200 chr6B 519311752 519312390 638 False 311 311 75.920 3303 3941 1 chr6B.!!$F1 638
17 TraesCS6A01G414200 chr6D 469788343 469790147 1804 True 1304 1304 79.825 6778 8598 1 chr6D.!!$R1 1820
18 TraesCS6A01G414200 chr6D 469812279 469813088 809 True 883 883 86.347 999 1811 1 chr6D.!!$R2 812
19 TraesCS6A01G414200 chr6D 469917772 469918983 1211 False 689 689 77.243 6832 8039 1 chr6D.!!$F3 1207
20 TraesCS6A01G414200 chr6D 455630080 455630650 570 False 272 272 75.891 3378 3952 1 chr6D.!!$F2 574
21 TraesCS6A01G414200 chr7D 542845786 542846492 706 True 440 440 78.243 3237 3941 1 chr7D.!!$R1 704
22 TraesCS6A01G414200 chr7D 542906514 542907173 659 True 425 425 78.689 3293 3950 1 chr7D.!!$R2 657
23 TraesCS6A01G414200 chr7D 633521970 633522548 578 False 339 339 77.759 3365 3949 1 chr7D.!!$F2 584
24 TraesCS6A01G414200 chr5D 421537158 421537734 576 True 296 296 76.529 3326 3920 1 chr5D.!!$R2 594
25 TraesCS6A01G414200 chr3D 338496329 338496958 629 False 296 296 75.776 3324 3950 1 chr3D.!!$F1 626
26 TraesCS6A01G414200 chr5A 566046684 566047320 636 False 278 278 75.299 3299 3951 1 chr5A.!!$F2 652

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
311 319 0.029567 CTCGACTGGCACTCGGATAC 59.970 60.000 14.95 0.00 0.00 2.24 F
473 520 0.032678 CTCCACCCCATTCTCGATCG 59.967 60.000 9.36 9.36 0.00 3.69 F
519 582 0.970937 TCCGAGCTTCACCCCTACTG 60.971 60.000 0.00 0.00 0.00 2.74 F
892 1046 1.171308 ACTTCTTCGGCGCACTAGTA 58.829 50.000 10.83 0.00 0.00 1.82 F
2544 3490 5.232838 GCATAGAATTTTGCAGCATAACCAC 59.767 40.000 0.00 0.00 38.72 4.16 F
3875 4889 0.105504 TCCTAGCTATGCAGAGGCCA 60.106 55.000 10.92 0.00 40.13 5.36 F
4185 5204 0.322975 TGAGCAGTTTGAGGAGCCTC 59.677 55.000 9.61 9.61 43.01 4.70 F
4186 5205 0.392327 GAGCAGTTTGAGGAGCCTCC 60.392 60.000 13.69 1.26 42.09 4.30 F
4685 5705 1.197721 CTTCAATGGAGTCGTGTTGGC 59.802 52.381 2.30 0.00 0.00 4.52 F
5905 6926 2.768492 GCTCCTGGGCTCAAATGCG 61.768 63.158 0.00 0.00 0.00 4.73 F
6530 7602 1.913403 GCGTCTTTTCATCATTTGCCG 59.087 47.619 0.00 0.00 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 1863 5.453567 TCGTCATATCTGGATTTCGTGAT 57.546 39.130 0.00 0.00 0.00 3.06 R
2060 2254 9.929722 TGCGTGATATTGTATTTTATTTCTCAC 57.070 29.630 0.00 0.00 0.00 3.51 R
2544 3490 8.857694 TGTCACTTTTAGGAATTAAACCCTAG 57.142 34.615 6.40 0.00 36.49 3.02 R
2894 3841 5.125900 TGTGGCAATGTGATTTGATCTAAGG 59.874 40.000 0.00 0.00 0.00 2.69 R
4555 5575 0.037734 TCCTAGCACGACACTCCTCA 59.962 55.000 0.00 0.00 0.00 3.86 R
4879 5899 2.785357 AGCTAGCTACATCCCTCCTT 57.215 50.000 17.69 0.00 0.00 3.36 R
6143 7213 0.681887 TTGTGATGCAGAGGCCATGG 60.682 55.000 7.63 7.63 40.13 3.66 R
6369 7439 2.103373 GCCTACAGAGTGATCTGGACA 58.897 52.381 9.85 0.00 41.76 4.02 R
6511 7583 3.163594 GTCGGCAAATGATGAAAAGACG 58.836 45.455 0.00 0.00 0.00 4.18 R
7617 8922 3.446873 TCATCAACTTGGAGAGAGAGAGC 59.553 47.826 0.00 0.00 0.00 4.09 R
8349 9666 0.798776 CGCAACAGCTGGAGGTTTAG 59.201 55.000 19.93 0.00 0.00 1.85 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
166 172 3.244009 CGGATGTAGATGCTCTGAATGGT 60.244 47.826 0.00 0.00 0.00 3.55
212 218 1.184431 TGGTCATGGCAATCGCAATT 58.816 45.000 0.00 0.00 41.24 2.32
293 301 2.751259 CACAATGACAATAGGCTGCACT 59.249 45.455 0.50 0.00 0.00 4.40
311 319 0.029567 CTCGACTGGCACTCGGATAC 59.970 60.000 14.95 0.00 0.00 2.24
369 412 1.134521 CAGGTACACACACACCACACT 60.135 52.381 0.00 0.00 37.28 3.55
464 511 2.448542 CGGATCCCTCCACCCCAT 60.449 66.667 6.06 0.00 42.19 4.00
470 517 1.689233 CCCTCCACCCCATTCTCGA 60.689 63.158 0.00 0.00 0.00 4.04
471 518 1.056700 CCCTCCACCCCATTCTCGAT 61.057 60.000 0.00 0.00 0.00 3.59
473 520 0.032678 CTCCACCCCATTCTCGATCG 59.967 60.000 9.36 9.36 0.00 3.69
499 562 1.077930 CCTCGTCTCTCCGTGGGTA 60.078 63.158 0.00 0.00 37.72 3.69
519 582 0.970937 TCCGAGCTTCACCCCTACTG 60.971 60.000 0.00 0.00 0.00 2.74
643 732 2.345560 AGGTTTAGGTTGGCTACACCT 58.654 47.619 8.39 8.39 40.22 4.00
680 789 5.530519 TCAACGCAGAATTATTGACAGAC 57.469 39.130 0.00 0.00 0.00 3.51
798 935 1.968255 GCTAGGCTAGGTACACCCCAA 60.968 57.143 22.40 0.00 36.42 4.12
892 1046 1.171308 ACTTCTTCGGCGCACTAGTA 58.829 50.000 10.83 0.00 0.00 1.82
1698 1863 7.847096 TCAAGTGTAAGGCTTTCATATCTGTA 58.153 34.615 4.45 0.00 0.00 2.74
1852 2034 5.684550 AAGGTTCGGTTCTATTTGTGTTC 57.315 39.130 0.00 0.00 0.00 3.18
2060 2254 9.726232 CAAATATGACCATGTTGATGTCTAAAG 57.274 33.333 0.00 0.00 0.00 1.85
2544 3490 5.232838 GCATAGAATTTTGCAGCATAACCAC 59.767 40.000 0.00 0.00 38.72 4.16
2894 3841 3.512516 GGCGCATCTGGGTCAAGC 61.513 66.667 10.83 0.00 32.43 4.01
2951 3898 1.271001 CCTGGATCTGTGTGACAAGCA 60.271 52.381 0.00 0.00 0.00 3.91
3003 3950 2.050836 TTGCCGAGTTTCAGGAGCCA 62.051 55.000 0.00 0.00 0.00 4.75
3031 3978 3.000819 CTGGGACACGTGCCCCTA 61.001 66.667 35.70 23.44 45.40 3.53
3106 4053 3.379240 TCAACATCGTTTTGCAACCATG 58.621 40.909 0.00 1.58 37.48 3.66
3279 4226 2.159430 CGATGTTTTCGGATGCAACAGA 59.841 45.455 0.00 0.00 44.28 3.41
3519 4473 4.887071 TGGTTATACCTGGCAATGACAATC 59.113 41.667 0.00 0.00 39.58 2.67
3774 4773 9.814899 TTTTGATTGCTTGAGTTTTTCTTCATA 57.185 25.926 0.00 0.00 0.00 2.15
3780 4779 8.165239 TGCTTGAGTTTTTCTTCATAGCTTAA 57.835 30.769 0.00 0.00 0.00 1.85
3798 4798 4.923281 GCTTAAGCATAGTTTTGGTGTTGG 59.077 41.667 22.59 0.00 41.59 3.77
3800 4800 4.584327 AAGCATAGTTTTGGTGTTGGAC 57.416 40.909 0.00 0.00 0.00 4.02
3816 4816 6.238925 GGTGTTGGACAACTTTACTATTTGCT 60.239 38.462 15.37 0.00 41.67 3.91
3819 4822 7.934665 TGTTGGACAACTTTACTATTTGCTAGA 59.065 33.333 15.37 0.00 41.67 2.43
3839 4850 4.920376 AGAGTGTTTATTTGTGTGTGTGC 58.080 39.130 0.00 0.00 0.00 4.57
3840 4851 4.397730 AGAGTGTTTATTTGTGTGTGTGCA 59.602 37.500 0.00 0.00 0.00 4.57
3844 4855 5.518128 GTGTTTATTTGTGTGTGTGCATTGA 59.482 36.000 0.00 0.00 0.00 2.57
3845 4856 6.200665 GTGTTTATTTGTGTGTGTGCATTGAT 59.799 34.615 0.00 0.00 0.00 2.57
3875 4889 0.105504 TCCTAGCTATGCAGAGGCCA 60.106 55.000 10.92 0.00 40.13 5.36
3943 4962 6.183361 TGAGCCAATAAAATTCACCCTTTGTT 60.183 34.615 0.00 0.00 0.00 2.83
4183 5202 1.163554 CTTGAGCAGTTTGAGGAGCC 58.836 55.000 0.00 0.00 0.00 4.70
4184 5203 0.767375 TTGAGCAGTTTGAGGAGCCT 59.233 50.000 0.00 0.00 0.00 4.58
4185 5204 0.322975 TGAGCAGTTTGAGGAGCCTC 59.677 55.000 9.61 9.61 43.01 4.70
4186 5205 0.392327 GAGCAGTTTGAGGAGCCTCC 60.392 60.000 13.69 1.26 42.09 4.30
4194 5213 2.665603 AGGAGCCTCCTCAAACGC 59.334 61.111 7.68 0.00 45.66 4.84
4216 5235 1.202879 TCCTCAAATTTCAGCCACCGT 60.203 47.619 0.00 0.00 0.00 4.83
4427 5446 2.316792 CTGTCCAAGACTCGTTACACG 58.683 52.381 0.00 0.00 44.19 4.49
4555 5575 1.606480 CGACAACATGGAGTGCTCACT 60.606 52.381 1.62 1.62 45.84 3.41
4677 5697 4.132336 TGCATCATAGCTTCAATGGAGTC 58.868 43.478 0.00 0.00 34.99 3.36
4685 5705 1.197721 CTTCAATGGAGTCGTGTTGGC 59.802 52.381 2.30 0.00 0.00 4.52
5090 6110 7.814587 TGTCATGCATATAACACTAGTATGAGC 59.185 37.037 0.00 2.41 0.00 4.26
5509 6529 3.012502 TCCCCACTATGACTAGTCCAAGT 59.987 47.826 20.11 18.47 35.99 3.16
5521 6541 5.352284 ACTAGTCCAAGTTTGATAGATGCG 58.648 41.667 0.00 0.00 0.00 4.73
5905 6926 2.768492 GCTCCTGGGCTCAAATGCG 61.768 63.158 0.00 0.00 0.00 4.73
5978 7013 8.641541 ACATCTTTTGTGGAATCTTTTACATGT 58.358 29.630 2.69 2.69 37.11 3.21
6143 7213 6.695713 AGTTCTTTGTTTTGAAAGGCGATTAC 59.304 34.615 0.00 0.00 34.27 1.89
6369 7439 4.577283 ACTTGGTGTACGCACAATAGTTTT 59.423 37.500 8.97 0.00 46.95 2.43
6530 7602 1.913403 GCGTCTTTTCATCATTTGCCG 59.087 47.619 0.00 0.00 0.00 5.69
7617 8922 0.991770 CGCAAAGCAAAGTTCGTCGG 60.992 55.000 0.00 0.00 0.00 4.79
7618 8923 1.268778 GCAAAGCAAAGTTCGTCGGC 61.269 55.000 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 3.836562 ACAACCGGATACCTCAGTTAAGT 59.163 43.478 9.46 0.00 0.00 2.24
116 117 2.357952 GCAAATCCGACCCCTCAAATAC 59.642 50.000 0.00 0.00 0.00 1.89
118 119 1.005924 AGCAAATCCGACCCCTCAAAT 59.994 47.619 0.00 0.00 0.00 2.32
166 172 1.614051 CCCAACTACTCCAGCATGCAA 60.614 52.381 21.98 3.72 31.97 4.08
293 301 1.381928 GGTATCCGAGTGCCAGTCGA 61.382 60.000 22.87 9.65 43.33 4.20
311 319 2.048597 TACGCGAGTTGTGGCTGG 60.049 61.111 15.93 0.00 46.40 4.85
369 412 5.080337 AGAGGATGGAAGTTATCTATGCGA 58.920 41.667 0.00 0.00 41.38 5.10
417 460 0.178975 ATCCCCTTCACCAAAACGCA 60.179 50.000 0.00 0.00 0.00 5.24
464 511 0.814410 AGGAGTAGCGCGATCGAGAA 60.814 55.000 23.47 6.64 38.10 2.87
470 517 1.500512 GAGACGAGGAGTAGCGCGAT 61.501 60.000 12.10 5.99 0.00 4.58
471 518 2.125229 AGACGAGGAGTAGCGCGA 60.125 61.111 12.10 0.00 0.00 5.87
473 520 1.644913 GAGAGACGAGGAGTAGCGC 59.355 63.158 0.00 0.00 0.00 5.92
499 562 0.032017 AGTAGGGGTGAAGCTCGGAT 60.032 55.000 0.00 0.00 0.00 4.18
643 732 0.594110 GTTGAACCCGCGGAATTCAA 59.406 50.000 34.74 34.74 39.42 2.69
798 935 0.397816 AAGAGGCATACGAGGGAGCT 60.398 55.000 0.00 0.00 0.00 4.09
846 984 3.222354 GAACACCGACGTGGGAGCT 62.222 63.158 24.54 6.63 44.86 4.09
892 1046 0.834687 TTAAGCCACTCACCCGAGGT 60.835 55.000 0.00 0.00 44.17 3.85
1698 1863 5.453567 TCGTCATATCTGGATTTCGTGAT 57.546 39.130 0.00 0.00 0.00 3.06
2060 2254 9.929722 TGCGTGATATTGTATTTTATTTCTCAC 57.070 29.630 0.00 0.00 0.00 3.51
2544 3490 8.857694 TGTCACTTTTAGGAATTAAACCCTAG 57.142 34.615 6.40 0.00 36.49 3.02
2894 3841 5.125900 TGTGGCAATGTGATTTGATCTAAGG 59.874 40.000 0.00 0.00 0.00 2.69
2951 3898 1.227645 CCATCATGCACCGTCCGAT 60.228 57.895 0.00 0.00 0.00 4.18
3003 3950 1.305297 TGTCCCAGTCGCTCAGGAT 60.305 57.895 0.00 0.00 0.00 3.24
3031 3978 0.396435 TGTTGTCAATGAGGGCGAGT 59.604 50.000 0.00 0.00 0.00 4.18
3106 4053 4.971125 GCCTCATAGGTCGGGCGC 62.971 72.222 0.00 0.00 37.80 6.53
3279 4226 1.002087 CACTACCAGAACGGAGCCTTT 59.998 52.381 0.00 0.00 38.63 3.11
3519 4473 7.491048 ACAACAACAAGGTAATACTGCAAAAAG 59.509 33.333 0.00 0.00 0.00 2.27
3753 4742 7.224522 AGCTATGAAGAAAAACTCAAGCAAT 57.775 32.000 0.00 0.00 0.00 3.56
3754 4743 6.639632 AGCTATGAAGAAAAACTCAAGCAA 57.360 33.333 0.00 0.00 0.00 3.91
3761 4750 9.454859 ACTATGCTTAAGCTATGAAGAAAAACT 57.545 29.630 26.90 0.01 42.66 2.66
3774 4773 5.278957 CCAACACCAAAACTATGCTTAAGCT 60.279 40.000 26.90 15.25 42.66 3.74
3780 4779 3.561143 TGTCCAACACCAAAACTATGCT 58.439 40.909 0.00 0.00 0.00 3.79
3798 4798 8.535690 ACACTCTAGCAAATAGTAAAGTTGTC 57.464 34.615 0.00 0.00 32.85 3.18
3816 4816 5.586643 TGCACACACACAAATAAACACTCTA 59.413 36.000 0.00 0.00 0.00 2.43
3819 4822 4.710423 TGCACACACACAAATAAACACT 57.290 36.364 0.00 0.00 0.00 3.55
3839 4850 3.861276 AGGATGCACACAACATCAATG 57.139 42.857 6.13 0.00 44.68 2.82
3840 4851 3.379372 GCTAGGATGCACACAACATCAAT 59.621 43.478 6.13 0.00 44.68 2.57
3844 4855 2.795231 AGCTAGGATGCACACAACAT 57.205 45.000 0.00 0.00 34.99 2.71
3845 4856 3.534554 CATAGCTAGGATGCACACAACA 58.465 45.455 0.00 0.00 34.99 3.33
3875 4889 0.183492 AACACCATGAGCACACACCT 59.817 50.000 0.00 0.00 0.00 4.00
3964 4983 7.160049 CACTCTTCCATACAATAGATCTGCAT 58.840 38.462 5.18 0.00 0.00 3.96
3968 4987 7.921041 TTCCACTCTTCCATACAATAGATCT 57.079 36.000 0.00 0.00 0.00 2.75
4183 5202 0.321671 TTGAGGAGGCGTTTGAGGAG 59.678 55.000 0.00 0.00 0.00 3.69
4184 5203 0.762418 TTTGAGGAGGCGTTTGAGGA 59.238 50.000 0.00 0.00 0.00 3.71
4185 5204 1.826385 ATTTGAGGAGGCGTTTGAGG 58.174 50.000 0.00 0.00 0.00 3.86
4186 5205 3.253188 TGAAATTTGAGGAGGCGTTTGAG 59.747 43.478 0.00 0.00 0.00 3.02
4187 5206 3.218453 TGAAATTTGAGGAGGCGTTTGA 58.782 40.909 0.00 0.00 0.00 2.69
4188 5207 3.568538 CTGAAATTTGAGGAGGCGTTTG 58.431 45.455 0.00 0.00 0.00 2.93
4189 5208 2.029918 GCTGAAATTTGAGGAGGCGTTT 60.030 45.455 6.79 0.00 0.00 3.60
4190 5209 1.541588 GCTGAAATTTGAGGAGGCGTT 59.458 47.619 6.79 0.00 0.00 4.84
4191 5210 1.168714 GCTGAAATTTGAGGAGGCGT 58.831 50.000 6.79 0.00 0.00 5.68
4192 5211 0.453390 GGCTGAAATTTGAGGAGGCG 59.547 55.000 6.79 0.00 0.00 5.52
4193 5212 1.203287 GTGGCTGAAATTTGAGGAGGC 59.797 52.381 6.79 5.07 0.00 4.70
4194 5213 1.821136 GGTGGCTGAAATTTGAGGAGG 59.179 52.381 6.79 0.00 0.00 4.30
4427 5446 0.394488 GGAGGTTAGCTCCCAAAGGC 60.394 60.000 18.87 0.00 35.03 4.35
4555 5575 0.037734 TCCTAGCACGACACTCCTCA 59.962 55.000 0.00 0.00 0.00 3.86
4677 5697 2.954753 GAGGAGCAACGCCAACACG 61.955 63.158 0.00 0.00 39.50 4.49
4878 5898 3.053359 AGCTAGCTACATCCCTCCTTT 57.947 47.619 17.69 0.00 0.00 3.11
4879 5899 2.785357 AGCTAGCTACATCCCTCCTT 57.215 50.000 17.69 0.00 0.00 3.36
5090 6110 9.431887 TGTTACTTTGCACTATAAAGGTTCTAG 57.568 33.333 0.00 0.00 38.99 2.43
5509 6529 8.404765 TCAAATTTTAGATGCGCATCTATCAAA 58.595 29.630 44.23 39.64 46.38 2.69
6015 7051 6.238320 CGAGCATCAATTCTTTTTCCTCCTAG 60.238 42.308 0.00 0.00 33.17 3.02
6143 7213 0.681887 TTGTGATGCAGAGGCCATGG 60.682 55.000 7.63 7.63 40.13 3.66
6369 7439 2.103373 GCCTACAGAGTGATCTGGACA 58.897 52.381 9.85 0.00 41.76 4.02
6511 7583 3.163594 GTCGGCAAATGATGAAAAGACG 58.836 45.455 0.00 0.00 0.00 4.18
7539 8841 6.093495 TGACAAAGTTCACTTCGATTGACTTT 59.907 34.615 13.40 13.40 34.61 2.66
7617 8922 3.446873 TCATCAACTTGGAGAGAGAGAGC 59.553 47.826 0.00 0.00 0.00 4.09
7618 8923 4.098349 CCTCATCAACTTGGAGAGAGAGAG 59.902 50.000 10.97 0.00 0.00 3.20
7928 9236 6.370442 CGAGGTTCACAATAGTTGATGGTAAA 59.630 38.462 0.00 0.00 0.00 2.01
8349 9666 0.798776 CGCAACAGCTGGAGGTTTAG 59.201 55.000 19.93 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.