Multiple sequence alignment - TraesCS3B01G524500

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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 TraesCS3B01G524500 chr3B 100.000 3030 0 0 1 3030 766630235 766633264 0.000000e+00 5596.0
1 TraesCS3B01G524500 chr3B 86.414 1266 96 28 894 2127 769056478 769055257 0.000000e+00 1315.0
2 TraesCS3B01G524500 chr3B 86.125 1218 119 13 898 2075 768904995 768903788 0.000000e+00 1267.0
3 TraesCS3B01G524500 chr3B 87.721 961 85 8 898 1835 768929703 768928753 0.000000e+00 1090.0
4 TraesCS3B01G524500 chr3B 91.275 149 12 1 681 829 769071979 769071832 5.120000e-48 202.0
5 TraesCS3B01G524500 chr3B 84.916 179 7 5 714 888 768988471 768988309 2.420000e-36 163.0
6 TraesCS3B01G524500 chr3B 94.872 39 2 0 201 239 768988917 768988879 9.070000e-06 62.1
7 TraesCS3B01G524500 chr3B 94.872 39 2 0 201 239 769072430 769072392 9.070000e-06 62.1
8 TraesCS3B01G524500 chr3A 91.956 1268 60 11 892 2128 711217682 711218938 0.000000e+00 1738.0
9 TraesCS3B01G524500 chr3A 88.983 1062 95 17 1078 2128 711203009 711204059 0.000000e+00 1293.0
10 TraesCS3B01G524500 chr3A 91.833 551 38 4 1486 2031 712571794 712571246 0.000000e+00 761.0
11 TraesCS3B01G524500 chr3A 84.325 689 45 33 1 665 711216631 711217280 1.540000e-172 616.0
12 TraesCS3B01G524500 chr3A 84.000 600 57 20 1130 1701 712572380 712571792 9.560000e-150 540.0
13 TraesCS3B01G524500 chr3A 82.031 512 54 16 2257 2765 711220010 711220486 4.710000e-108 401.0
14 TraesCS3B01G524500 chr3A 84.951 412 38 13 2633 3030 711220548 711220949 2.190000e-106 396.0
15 TraesCS3B01G524500 chr3A 87.375 301 33 4 2258 2554 711204211 711204510 1.040000e-89 340.0
16 TraesCS3B01G524500 chr3A 92.825 223 5 8 677 890 711217428 711217648 2.270000e-81 313.0
17 TraesCS3B01G524500 chr3A 75.735 544 61 36 360 889 711202274 711202760 1.100000e-49 207.0
18 TraesCS3B01G524500 chr3A 78.125 192 30 5 901 1086 711202806 711202991 8.880000e-21 111.0
19 TraesCS3B01G524500 chr3A 94.118 51 0 1 2176 2223 711219035 711219085 1.170000e-09 75.0
20 TraesCS3B01G524500 chr3D 92.006 1251 66 15 892 2123 575725738 575726973 0.000000e+00 1725.0
21 TraesCS3B01G524500 chr3D 85.852 1039 108 29 1020 2034 577255856 577254833 0.000000e+00 1068.0
22 TraesCS3B01G524500 chr3D 93.088 217 10 2 669 884 575725466 575725678 2.270000e-81 313.0
23 TraesCS3B01G524500 chr3D 90.043 231 9 5 892 1116 577264605 577264383 1.370000e-73 287.0
24 TraesCS3B01G524500 chr3D 85.490 255 17 13 640 890 577264877 577264639 6.490000e-62 248.0
25 TraesCS3B01G524500 chr3D 78.188 298 39 16 1930 2211 577263863 577263576 1.870000e-37 167.0
26 TraesCS3B01G524500 chr3D 93.902 82 4 1 2129 2210 575727019 575727099 4.100000e-24 122.0
27 TraesCS3B01G524500 chr3D 94.118 51 3 0 244 294 575725159 575725209 9.010000e-11 78.7
28 TraesCS3B01G524500 chr3D 93.023 43 3 0 568 610 575725406 575725448 2.520000e-06 63.9
29 TraesCS3B01G524500 chr6B 85.887 992 90 25 1172 2127 438386790 438385813 0.000000e+00 1011.0
30 TraesCS3B01G524500 chr6A 85.204 1007 83 35 1161 2127 399722103 399723083 0.000000e+00 974.0
31 TraesCS3B01G524500 chr6A 80.220 91 12 6 2809 2894 22431638 22431549 2.520000e-06 63.9
32 TraesCS3B01G524500 chr5B 84.012 344 43 6 1695 2026 96764631 96764288 1.360000e-83 320.0


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 TraesCS3B01G524500 chr3B 766630235 766633264 3029 False 5596.000000 5596 100.000000 1 3030 1 chr3B.!!$F1 3029
1 TraesCS3B01G524500 chr3B 769055257 769056478 1221 True 1315.000000 1315 86.414000 894 2127 1 chr3B.!!$R3 1233
2 TraesCS3B01G524500 chr3B 768903788 768904995 1207 True 1267.000000 1267 86.125000 898 2075 1 chr3B.!!$R1 1177
3 TraesCS3B01G524500 chr3B 768928753 768929703 950 True 1090.000000 1090 87.721000 898 1835 1 chr3B.!!$R2 937
4 TraesCS3B01G524500 chr3A 712571246 712572380 1134 True 650.500000 761 87.916500 1130 2031 2 chr3A.!!$R1 901
5 TraesCS3B01G524500 chr3A 711216631 711220949 4318 False 589.833333 1738 88.367667 1 3030 6 chr3A.!!$F2 3029
6 TraesCS3B01G524500 chr3A 711202274 711204510 2236 False 487.750000 1293 82.554500 360 2554 4 chr3A.!!$F1 2194
7 TraesCS3B01G524500 chr3D 577254833 577255856 1023 True 1068.000000 1068 85.852000 1020 2034 1 chr3D.!!$R1 1014
8 TraesCS3B01G524500 chr3D 575725159 575727099 1940 False 460.520000 1725 93.227400 244 2210 5 chr3D.!!$F1 1966
9 TraesCS3B01G524500 chr3D 577263576 577264877 1301 True 234.000000 287 84.573667 640 2211 3 chr3D.!!$R2 1571
10 TraesCS3B01G524500 chr6B 438385813 438386790 977 True 1011.000000 1011 85.887000 1172 2127 1 chr6B.!!$R1 955
11 TraesCS3B01G524500 chr6A 399722103 399723083 980 False 974.000000 974 85.204000 1161 2127 1 chr6A.!!$F1 966

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
936 1191 0.033601 ATGCTCCCCAACGGCATTAA 60.034 50.0 0.0 0.0 43.02 1.4 F
943 1198 0.525761 CCAACGGCATTAACCACCAG 59.474 55.0 0.0 0.0 0.00 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 2497 0.179073 CCAGGATCGCCAGGTAGTTG 60.179 60.0 0.0 0.0 36.15 3.16 R
2536 4358 0.735471 TAGCTCAGTCGCACAGCTAG 59.265 55.0 0.0 0.0 41.84 3.42 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
31 32 5.366477 AGGTTTTTCATCATGAGGGTTTTGT 59.634 36.000 7.64 0.00 0.00 2.83
35 36 5.452078 TTCATCATGAGGGTTTTGTTGTC 57.548 39.130 7.64 0.00 0.00 3.18
87 88 6.667007 AAGCTTTTGTTGAACATTTTCCAG 57.333 33.333 0.00 0.00 0.00 3.86
88 89 5.733676 AGCTTTTGTTGAACATTTTCCAGT 58.266 33.333 0.00 0.00 0.00 4.00
91 92 6.960992 GCTTTTGTTGAACATTTTCCAGTTTC 59.039 34.615 0.00 0.00 0.00 2.78
116 117 8.464404 TCAATATCTGGAAAAATGCTCTGAAAG 58.536 33.333 0.00 0.00 0.00 2.62
126 127 2.057922 TGCTCTGAAAGGGGAAGAACT 58.942 47.619 0.00 0.00 23.25 3.01
127 128 2.443255 TGCTCTGAAAGGGGAAGAACTT 59.557 45.455 0.00 0.00 23.25 2.66
128 129 3.117512 TGCTCTGAAAGGGGAAGAACTTT 60.118 43.478 0.00 0.00 39.45 2.66
129 130 3.891977 GCTCTGAAAGGGGAAGAACTTTT 59.108 43.478 0.00 0.00 37.07 2.27
165 167 2.600470 GTTGCCCCCTGTCCCAAC 60.600 66.667 0.00 0.00 0.00 3.77
255 283 1.946768 CATTTCACACAACACCGAGGT 59.053 47.619 0.00 0.00 0.00 3.85
284 312 1.374758 GTGGCCGGAGAGAAGTGTG 60.375 63.158 5.05 0.00 0.00 3.82
306 334 1.743623 CCGTTCTACGCAATGGGCA 60.744 57.895 0.00 0.00 45.17 5.36
336 364 5.301551 TGCAGATGTTCCAACAATTTGTACT 59.698 36.000 1.76 0.00 43.03 2.73
337 365 6.488344 TGCAGATGTTCCAACAATTTGTACTA 59.512 34.615 1.76 0.00 43.03 1.82
338 366 7.023575 GCAGATGTTCCAACAATTTGTACTAG 58.976 38.462 1.76 0.00 43.03 2.57
339 367 7.308589 GCAGATGTTCCAACAATTTGTACTAGT 60.309 37.037 1.76 0.00 43.03 2.57
340 368 8.230486 CAGATGTTCCAACAATTTGTACTAGTC 58.770 37.037 0.00 0.00 43.03 2.59
341 369 8.157476 AGATGTTCCAACAATTTGTACTAGTCT 58.843 33.333 0.00 1.40 43.03 3.24
342 370 8.691661 ATGTTCCAACAATTTGTACTAGTCTT 57.308 30.769 0.00 0.00 43.03 3.01
343 371 8.149973 TGTTCCAACAATTTGTACTAGTCTTC 57.850 34.615 0.00 0.00 35.67 2.87
344 372 7.990886 TGTTCCAACAATTTGTACTAGTCTTCT 59.009 33.333 0.00 0.00 35.67 2.85
345 373 9.485206 GTTCCAACAATTTGTACTAGTCTTCTA 57.515 33.333 0.00 0.00 0.00 2.10
346 374 9.706691 TTCCAACAATTTGTACTAGTCTTCTAG 57.293 33.333 0.00 1.37 46.43 2.43
371 399 1.867166 TTGTACGTTTCGGTGCATCA 58.133 45.000 0.00 0.00 32.55 3.07
390 418 7.280876 GTGCATCATTATTATGTCACCGGATAT 59.719 37.037 9.46 0.00 33.34 1.63
391 419 8.482128 TGCATCATTATTATGTCACCGGATATA 58.518 33.333 9.46 0.00 33.34 0.86
430 469 3.106407 GTGTCACGGACTCGCAGC 61.106 66.667 5.77 0.00 40.63 5.25
431 470 4.357947 TGTCACGGACTCGCAGCC 62.358 66.667 5.77 0.00 40.63 4.85
432 471 4.057428 GTCACGGACTCGCAGCCT 62.057 66.667 0.00 0.00 40.63 4.58
433 472 3.749064 TCACGGACTCGCAGCCTC 61.749 66.667 0.00 0.00 40.63 4.70
434 473 4.056125 CACGGACTCGCAGCCTCA 62.056 66.667 0.00 0.00 40.63 3.86
435 474 4.057428 ACGGACTCGCAGCCTCAC 62.057 66.667 0.00 0.00 40.63 3.51
473 512 4.802039 CACTTTGTGATTATCTTGGCATGC 59.198 41.667 9.90 9.90 35.23 4.06
503 543 0.948623 TGCGATGCACACGTAGCTTT 60.949 50.000 14.78 1.75 34.78 3.51
505 545 1.392168 GCGATGCACACGTAGCTTTAA 59.608 47.619 14.78 0.00 31.37 1.52
506 546 2.534939 GCGATGCACACGTAGCTTTAAG 60.535 50.000 14.78 0.00 31.37 1.85
507 547 2.921121 CGATGCACACGTAGCTTTAAGA 59.079 45.455 12.59 0.00 0.00 2.10
509 549 4.032900 CGATGCACACGTAGCTTTAAGATT 59.967 41.667 12.59 0.00 0.00 2.40
511 551 3.435327 TGCACACGTAGCTTTAAGATTGG 59.565 43.478 12.59 0.00 0.00 3.16
512 552 3.727970 GCACACGTAGCTTTAAGATTGGC 60.728 47.826 0.00 0.00 0.00 4.52
513 553 3.435327 CACACGTAGCTTTAAGATTGGCA 59.565 43.478 0.00 0.00 0.00 4.92
544 584 8.184304 AGTTTGGTATTTTGGCAGTACATAAA 57.816 30.769 0.00 6.68 0.00 1.40
545 585 8.085909 AGTTTGGTATTTTGGCAGTACATAAAC 58.914 33.333 18.08 18.08 32.81 2.01
546 586 7.768807 TTGGTATTTTGGCAGTACATAAACT 57.231 32.000 0.00 0.00 0.00 2.66
573 625 3.027412 ACACAGCATTGGTGGTTACAAA 58.973 40.909 19.20 0.00 40.54 2.83
578 632 4.507388 CAGCATTGGTGGTTACAAAACAAG 59.493 41.667 7.98 0.00 37.34 3.16
628 682 4.260132 GCGTGATGCTATATATGCTTGCTC 60.260 45.833 0.00 0.00 41.73 4.26
633 687 2.743183 GCTATATATGCTTGCTCCGGGG 60.743 54.545 0.00 0.00 0.00 5.73
647 701 0.316204 CCGGGGATACGTACATGGAC 59.684 60.000 0.00 0.00 37.60 4.02
665 719 7.655490 ACATGGACGAAGTACCTGTAATATAC 58.345 38.462 0.00 0.00 43.89 1.47
800 993 1.683011 CCTCCATCCACATGTGAACCC 60.683 57.143 27.46 0.00 0.00 4.11
862 1060 0.252057 TTCTCCACCCGTCATCTCCA 60.252 55.000 0.00 0.00 0.00 3.86
863 1061 0.252057 TCTCCACCCGTCATCTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
866 1064 0.833287 CCACCCGTCATCTCCAATCT 59.167 55.000 0.00 0.00 0.00 2.40
867 1065 1.202580 CCACCCGTCATCTCCAATCTC 60.203 57.143 0.00 0.00 0.00 2.75
874 1073 3.749226 GTCATCTCCAATCTCCATTCCC 58.251 50.000 0.00 0.00 0.00 3.97
890 1100 3.739401 TTCCCTCCTTCCTTTTGATCC 57.261 47.619 0.00 0.00 0.00 3.36
896 1151 5.518367 CCCTCCTTCCTTTTGATCCCTTAAA 60.518 44.000 0.00 0.00 0.00 1.52
918 1173 2.816087 CTGCTGGCCTATAAATTCGCAT 59.184 45.455 3.32 0.00 0.00 4.73
936 1191 0.033601 ATGCTCCCCAACGGCATTAA 60.034 50.000 0.00 0.00 43.02 1.40
937 1192 0.963355 TGCTCCCCAACGGCATTAAC 60.963 55.000 0.00 0.00 0.00 2.01
938 1193 1.663379 GCTCCCCAACGGCATTAACC 61.663 60.000 0.00 0.00 0.00 2.85
940 1195 0.609681 TCCCCAACGGCATTAACCAC 60.610 55.000 0.00 0.00 0.00 4.16
943 1198 0.525761 CCAACGGCATTAACCACCAG 59.474 55.000 0.00 0.00 0.00 4.00
1106 1406 3.797353 CACACCTGCCCCCGCTAT 61.797 66.667 0.00 0.00 35.36 2.97
1107 1407 3.480133 ACACCTGCCCCCGCTATC 61.480 66.667 0.00 0.00 35.36 2.08
1108 1408 4.256180 CACCTGCCCCCGCTATCC 62.256 72.222 0.00 0.00 35.36 2.59
1119 1422 3.942439 GCTATCCCCAGCCCCGTC 61.942 72.222 0.00 0.00 35.40 4.79
1127 1430 3.476419 CAGCCCCGTCCCCGTTAT 61.476 66.667 0.00 0.00 0.00 1.89
1128 1431 3.476419 AGCCCCGTCCCCGTTATG 61.476 66.667 0.00 0.00 0.00 1.90
1429 1898 0.605589 GGTCAGCTACTTTTGCCGGT 60.606 55.000 1.90 0.00 0.00 5.28
1469 1977 0.539051 ACAGTAGAGTGCTGATGGGC 59.461 55.000 0.00 0.00 37.40 5.36
1473 1981 0.833287 TAGAGTGCTGATGGGCCTTC 59.167 55.000 12.30 12.30 0.00 3.46
1702 2435 1.228245 GCAGTTCAAGAGGGTGCCA 60.228 57.895 0.00 0.00 0.00 4.92
1978 2731 4.530857 GACCAGGTCATCCCCGCG 62.531 72.222 15.43 0.00 32.09 6.46
1980 2733 4.227134 CCAGGTCATCCCCGCGAG 62.227 72.222 8.23 0.00 0.00 5.03
1981 2734 3.461773 CAGGTCATCCCCGCGAGT 61.462 66.667 8.23 0.00 0.00 4.18
2060 2821 0.757935 GACCCATGGAAGGCATGCAT 60.758 55.000 21.36 10.32 41.32 3.96
2128 2908 2.029073 CTTGTGACGTCCGGTGCT 59.971 61.111 14.12 0.00 0.00 4.40
2129 2909 1.287815 CTTGTGACGTCCGGTGCTA 59.712 57.895 14.12 0.00 0.00 3.49
2130 2910 1.007038 TTGTGACGTCCGGTGCTAC 60.007 57.895 14.12 2.88 0.00 3.58
2131 2911 2.503375 GTGACGTCCGGTGCTACG 60.503 66.667 14.12 11.47 44.47 3.51
2147 3044 7.544566 CCGGTGCTACGTATTTATCATTTATCT 59.455 37.037 0.00 0.00 0.00 1.98
2223 3150 4.533815 TGGAGGAGGCTGGTATATATACG 58.466 47.826 15.15 5.36 34.11 3.06
2224 3151 4.228895 TGGAGGAGGCTGGTATATATACGA 59.771 45.833 15.15 11.26 34.11 3.43
2229 3156 5.994054 GGAGGCTGGTATATATACGATACGA 59.006 44.000 15.15 0.00 34.11 3.43
2230 3157 6.073331 GGAGGCTGGTATATATACGATACGAC 60.073 46.154 15.15 4.10 34.11 4.34
2231 3158 6.351711 AGGCTGGTATATATACGATACGACA 58.648 40.000 15.15 6.28 34.11 4.35
2232 3159 6.259608 AGGCTGGTATATATACGATACGACAC 59.740 42.308 15.15 1.13 34.11 3.67
2234 3161 6.237942 GCTGGTATATATACGATACGACACGT 60.238 42.308 15.15 1.91 44.72 4.49
2235 3162 7.043391 GCTGGTATATATACGATACGACACGTA 60.043 40.741 15.15 6.48 46.18 3.57
2245 3172 1.964552 ACGACACGTATAGGCTAGCT 58.035 50.000 15.72 3.22 38.73 3.32
2246 3173 3.117491 ACGACACGTATAGGCTAGCTA 57.883 47.619 15.72 5.54 38.73 3.32
2249 3176 5.426504 ACGACACGTATAGGCTAGCTATAT 58.573 41.667 15.72 15.03 38.73 0.86
2250 3177 5.879223 ACGACACGTATAGGCTAGCTATATT 59.121 40.000 15.72 4.21 38.73 1.28
2251 3178 6.036953 ACGACACGTATAGGCTAGCTATATTC 59.963 42.308 15.72 10.13 38.73 1.75
2252 3179 6.258287 CGACACGTATAGGCTAGCTATATTCT 59.742 42.308 15.72 4.36 0.00 2.40
2253 3180 7.323049 ACACGTATAGGCTAGCTATATTCTG 57.677 40.000 15.72 12.19 0.00 3.02
2254 3181 6.183360 ACACGTATAGGCTAGCTATATTCTGC 60.183 42.308 15.72 0.00 0.00 4.26
2255 3182 5.299782 ACGTATAGGCTAGCTATATTCTGCC 59.700 44.000 15.72 10.65 40.54 4.85
2348 4168 9.075678 TCAGTTTAGCTATATGTAAGGTACCTC 57.924 37.037 16.64 4.00 0.00 3.85
2370 4190 5.070001 TCAAAAATGAATTCGGGTCAGTCT 58.930 37.500 0.04 0.00 0.00 3.24
2374 4194 8.673711 CAAAAATGAATTCGGGTCAGTCTATTA 58.326 33.333 0.04 0.00 0.00 0.98
2404 4225 5.484715 CCATTGATTGTTGCTCCAAGATTT 58.515 37.500 0.00 0.00 0.00 2.17
2446 4268 9.116054 CTGTTTTGGTTTTGAGAAATTTTTGTG 57.884 29.630 0.00 0.00 0.00 3.33
2451 4273 8.833231 TGGTTTTGAGAAATTTTTGTGTGTTA 57.167 26.923 0.00 0.00 0.00 2.41
2503 4325 4.864704 TTTGACTGACCTAAATTTGGGC 57.135 40.909 19.69 12.19 30.94 5.36
2513 4335 4.280929 ACCTAAATTTGGGCTTCAGTCAAC 59.719 41.667 19.69 0.00 30.94 3.18
2549 4371 2.575993 CCAGCTAGCTGTGCGACT 59.424 61.111 36.14 3.39 42.15 4.18
2567 4389 6.470877 GTGCGACTGAGCTATATCTATTTAGC 59.529 42.308 4.76 4.76 40.90 3.09
2577 4399 7.621285 AGCTATATCTATTTAGCCCATCTGACA 59.379 37.037 8.30 0.00 41.40 3.58
2610 4432 7.801783 CCATTACGTCTCTTCCTTTGTTTTTAC 59.198 37.037 0.00 0.00 0.00 2.01
2611 4433 5.399604 ACGTCTCTTCCTTTGTTTTTACG 57.600 39.130 0.00 0.00 0.00 3.18
2612 4434 4.209112 CGTCTCTTCCTTTGTTTTTACGC 58.791 43.478 0.00 0.00 0.00 4.42
2691 4523 8.224720 TCTTCTATCCTTATGGGTATTTTTGGG 58.775 37.037 0.00 0.00 36.25 4.12
2692 4524 7.715267 TCTATCCTTATGGGTATTTTTGGGA 57.285 36.000 0.00 0.00 36.25 4.37
2693 4525 8.300752 TCTATCCTTATGGGTATTTTTGGGAT 57.699 34.615 0.00 0.00 35.57 3.85
2694 4526 8.170061 TCTATCCTTATGGGTATTTTTGGGATG 58.830 37.037 0.00 0.00 33.75 3.51
2695 4527 6.098716 TCCTTATGGGTATTTTTGGGATGT 57.901 37.500 0.00 0.00 36.25 3.06
2696 4528 6.507568 TCCTTATGGGTATTTTTGGGATGTT 58.492 36.000 0.00 0.00 36.25 2.71
2697 4529 7.653503 TCCTTATGGGTATTTTTGGGATGTTA 58.346 34.615 0.00 0.00 36.25 2.41
2698 4530 8.123130 TCCTTATGGGTATTTTTGGGATGTTAA 58.877 33.333 0.00 0.00 36.25 2.01
2699 4531 8.421002 CCTTATGGGTATTTTTGGGATGTTAAG 58.579 37.037 0.00 0.00 0.00 1.85
2700 4532 8.903059 TTATGGGTATTTTTGGGATGTTAAGT 57.097 30.769 0.00 0.00 0.00 2.24
2837 4865 9.696917 ACCAATTTCACTAATTCATTTGTTCTC 57.303 29.630 0.00 0.00 34.19 2.87
2921 4950 1.237285 ACAATCAGCGTCAACTGGCC 61.237 55.000 0.00 0.00 38.26 5.36
2925 4954 2.034879 CAGCGTCAACTGGCCGAAT 61.035 57.895 0.00 0.00 33.85 3.34
2926 4955 2.034879 AGCGTCAACTGGCCGAATG 61.035 57.895 0.00 0.00 0.00 2.67
2941 4970 1.536766 CGAATGCCTTCTCTGTGCAAA 59.463 47.619 0.00 0.00 38.69 3.68
2942 4971 2.666619 CGAATGCCTTCTCTGTGCAAAC 60.667 50.000 0.00 0.00 38.69 2.93
2943 4972 1.985473 ATGCCTTCTCTGTGCAAACA 58.015 45.000 0.00 0.00 38.69 2.83
2960 4990 1.065410 ACATGTCCTTGTGGGTCCCA 61.065 55.000 6.47 6.47 36.25 4.37
2974 5004 1.122019 GTCCCACACACTCTCCACCT 61.122 60.000 0.00 0.00 0.00 4.00
2994 5024 6.447162 CACCTCCCTTAATTTCTGAAACAAC 58.553 40.000 4.73 0.00 0.00 3.32
3023 5053 2.103941 GCCAACATTTTCTTCCCCACAA 59.896 45.455 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 6.772233 TGAATTTTGGACATCTCTCTTGACAA 59.228 34.615 0.00 0.00 0.00 3.18
35 36 6.814506 ACTGAATTTTGGACATCTCTCTTG 57.185 37.500 0.00 0.00 0.00 3.02
87 88 8.246180 TCAGAGCATTTTTCCAGATATTGAAAC 58.754 33.333 0.00 0.00 30.64 2.78
88 89 8.352137 TCAGAGCATTTTTCCAGATATTGAAA 57.648 30.769 0.00 0.00 0.00 2.69
91 92 7.705325 CCTTTCAGAGCATTTTTCCAGATATTG 59.295 37.037 0.00 0.00 0.00 1.90
102 103 4.118168 TCTTCCCCTTTCAGAGCATTTT 57.882 40.909 0.00 0.00 0.00 1.82
150 151 1.955458 AAAAGTTGGGACAGGGGGCA 61.955 55.000 0.00 0.00 42.39 5.36
157 158 7.125792 TGCCTTTTTAATAAAAGTTGGGACA 57.874 32.000 8.92 8.01 45.69 4.02
158 159 7.172532 CCTTGCCTTTTTAATAAAAGTTGGGAC 59.827 37.037 8.92 6.47 45.69 4.46
159 160 7.220740 CCTTGCCTTTTTAATAAAAGTTGGGA 58.779 34.615 8.92 8.99 45.69 4.37
194 196 1.421646 CACACCAAGTCCTTCCTTCCT 59.578 52.381 0.00 0.00 0.00 3.36
195 197 1.897560 CACACCAAGTCCTTCCTTCC 58.102 55.000 0.00 0.00 0.00 3.46
196 198 1.239347 GCACACCAAGTCCTTCCTTC 58.761 55.000 0.00 0.00 0.00 3.46
197 199 0.178990 GGCACACCAAGTCCTTCCTT 60.179 55.000 0.00 0.00 35.26 3.36
198 200 1.456287 GGCACACCAAGTCCTTCCT 59.544 57.895 0.00 0.00 35.26 3.36
204 206 0.884704 ATCACACGGCACACCAAGTC 60.885 55.000 0.00 0.00 34.57 3.01
209 211 1.732259 CTAAAGATCACACGGCACACC 59.268 52.381 0.00 0.00 0.00 4.16
210 212 1.128692 GCTAAAGATCACACGGCACAC 59.871 52.381 0.00 0.00 0.00 3.82
255 283 1.611977 CTCCGGCCACGTCATAATCTA 59.388 52.381 2.24 0.00 38.78 1.98
284 312 0.928229 CCATTGCGTAGAACGGTAGC 59.072 55.000 1.25 0.00 42.82 3.58
306 334 3.489355 TGTTGGAACATCTGCACAATCT 58.511 40.909 0.00 0.00 39.30 2.40
336 364 7.928307 AACGTACAATGGTACTAGAAGACTA 57.072 36.000 8.76 0.00 46.20 2.59
337 365 6.830873 AACGTACAATGGTACTAGAAGACT 57.169 37.500 8.76 0.00 46.20 3.24
338 366 6.250104 CGAAACGTACAATGGTACTAGAAGAC 59.750 42.308 8.76 0.00 46.20 3.01
339 367 6.317088 CGAAACGTACAATGGTACTAGAAGA 58.683 40.000 8.76 0.00 46.20 2.87
340 368 5.514204 CCGAAACGTACAATGGTACTAGAAG 59.486 44.000 8.76 0.00 46.20 2.85
341 369 5.048083 ACCGAAACGTACAATGGTACTAGAA 60.048 40.000 8.76 0.00 46.20 2.10
342 370 4.458989 ACCGAAACGTACAATGGTACTAGA 59.541 41.667 8.76 0.00 46.20 2.43
343 371 4.560035 CACCGAAACGTACAATGGTACTAG 59.440 45.833 8.76 0.00 46.20 2.57
344 372 4.484236 CACCGAAACGTACAATGGTACTA 58.516 43.478 8.76 0.00 46.20 1.82
345 373 3.319755 CACCGAAACGTACAATGGTACT 58.680 45.455 8.76 0.00 46.20 2.73
346 374 2.159801 GCACCGAAACGTACAATGGTAC 60.160 50.000 0.00 0.00 45.18 3.34
347 375 2.067766 GCACCGAAACGTACAATGGTA 58.932 47.619 0.00 0.00 0.00 3.25
348 376 0.869730 GCACCGAAACGTACAATGGT 59.130 50.000 0.00 0.00 0.00 3.55
349 377 0.869068 TGCACCGAAACGTACAATGG 59.131 50.000 0.00 0.00 0.00 3.16
358 386 6.632834 GTGACATAATAATGATGCACCGAAAC 59.367 38.462 0.00 0.00 36.54 2.78
390 418 4.890088 GGCATGAACCCGACAAGTATATA 58.110 43.478 0.00 0.00 0.00 0.86
391 419 3.740115 GGCATGAACCCGACAAGTATAT 58.260 45.455 0.00 0.00 0.00 0.86
435 474 4.173971 GTGGTTACACGCTACCCG 57.826 61.111 0.00 0.00 44.21 5.28
503 543 9.914834 AATACCAAACTAGTATTGCCAATCTTA 57.085 29.630 0.00 0.00 38.63 2.10
505 545 8.823220 AAATACCAAACTAGTATTGCCAATCT 57.177 30.769 0.00 0.00 39.69 2.40
506 546 9.301153 CAAAATACCAAACTAGTATTGCCAATC 57.699 33.333 0.00 0.00 39.69 2.67
507 547 8.257306 CCAAAATACCAAACTAGTATTGCCAAT 58.743 33.333 0.00 0.00 39.69 3.16
509 549 6.350612 GCCAAAATACCAAACTAGTATTGCCA 60.351 38.462 0.00 0.00 39.69 4.92
511 551 6.626302 TGCCAAAATACCAAACTAGTATTGC 58.374 36.000 0.00 0.00 39.69 3.56
512 552 7.826690 ACTGCCAAAATACCAAACTAGTATTG 58.173 34.615 0.00 3.46 39.69 1.90
513 553 8.953313 GTACTGCCAAAATACCAAACTAGTATT 58.047 33.333 0.00 0.00 41.13 1.89
544 584 3.507233 CCACCAATGCTGTGTTTATCAGT 59.493 43.478 0.00 0.00 35.60 3.41
545 585 3.507233 ACCACCAATGCTGTGTTTATCAG 59.493 43.478 0.00 0.00 36.18 2.90
546 586 3.495331 ACCACCAATGCTGTGTTTATCA 58.505 40.909 0.00 0.00 31.71 2.15
547 587 4.519540 AACCACCAATGCTGTGTTTATC 57.480 40.909 0.00 0.00 31.71 1.75
548 588 4.830046 TGTAACCACCAATGCTGTGTTTAT 59.170 37.500 0.00 0.00 31.71 1.40
549 589 4.207955 TGTAACCACCAATGCTGTGTTTA 58.792 39.130 0.00 0.00 31.71 2.01
550 590 3.027412 TGTAACCACCAATGCTGTGTTT 58.973 40.909 0.00 0.00 31.71 2.83
551 591 2.660572 TGTAACCACCAATGCTGTGTT 58.339 42.857 0.00 0.00 31.71 3.32
557 597 4.688021 TCTTGTTTTGTAACCACCAATGC 58.312 39.130 0.00 0.00 33.15 3.56
573 625 2.691526 CCATATGCAGCCACATCTTGTT 59.308 45.455 0.00 0.00 0.00 2.83
578 632 0.870393 CGACCATATGCAGCCACATC 59.130 55.000 0.00 0.00 0.00 3.06
628 682 0.316204 GTCCATGTACGTATCCCCGG 59.684 60.000 0.00 0.00 0.00 5.73
633 687 4.274459 AGGTACTTCGTCCATGTACGTATC 59.726 45.833 10.78 0.00 43.31 2.24
692 882 3.252974 ACTCATCTTCCGTTCCATCAC 57.747 47.619 0.00 0.00 0.00 3.06
800 993 1.623542 AACCTAGCTTGGGCCCTACG 61.624 60.000 25.70 12.30 39.73 3.51
862 1060 3.157556 AGGAAGGAGGGAATGGAGATT 57.842 47.619 0.00 0.00 0.00 2.40
863 1061 2.906169 AGGAAGGAGGGAATGGAGAT 57.094 50.000 0.00 0.00 0.00 2.75
866 1064 2.993146 TCAAAAGGAAGGAGGGAATGGA 59.007 45.455 0.00 0.00 0.00 3.41
867 1065 3.456380 TCAAAAGGAAGGAGGGAATGG 57.544 47.619 0.00 0.00 0.00 3.16
874 1073 6.151817 CAGTTTAAGGGATCAAAAGGAAGGAG 59.848 42.308 0.00 0.00 0.00 3.69
890 1100 6.513393 CGAATTTATAGGCCAGCAGTTTAAGG 60.513 42.308 5.01 0.00 0.00 2.69
896 1151 2.222027 GCGAATTTATAGGCCAGCAGT 58.778 47.619 5.01 0.00 0.00 4.40
918 1173 0.963355 GTTAATGCCGTTGGGGAGCA 60.963 55.000 0.00 0.00 36.93 4.26
936 1191 0.190069 TACTCTGGTGGTCTGGTGGT 59.810 55.000 0.00 0.00 0.00 4.16
937 1192 0.898320 CTACTCTGGTGGTCTGGTGG 59.102 60.000 0.00 0.00 0.00 4.61
938 1193 0.898320 CCTACTCTGGTGGTCTGGTG 59.102 60.000 0.00 0.00 0.00 4.17
940 1195 1.617947 GCCCTACTCTGGTGGTCTGG 61.618 65.000 0.00 0.00 0.00 3.86
943 1198 0.910088 AAGGCCCTACTCTGGTGGTC 60.910 60.000 0.00 0.00 0.00 4.02
1102 1402 3.942439 GACGGGGCTGGGGATAGC 61.942 72.222 0.00 0.00 42.94 2.97
1104 1404 4.892291 GGGACGGGGCTGGGGATA 62.892 72.222 0.00 0.00 0.00 2.59
1119 1422 2.192175 GGTGGAGGCATAACGGGG 59.808 66.667 0.00 0.00 0.00 5.73
1124 1427 2.689691 GGGGCAGGTGGAGGCATAA 61.690 63.158 0.00 0.00 0.00 1.90
1429 1898 3.250762 GTCAGTGTCAAGCAACTGCAATA 59.749 43.478 4.22 0.00 45.16 1.90
1469 1977 1.225745 GCAACGCGACAATCGAAGG 60.226 57.895 15.93 0.00 43.74 3.46
1473 1981 0.452618 ACAATGCAACGCGACAATCG 60.453 50.000 15.93 3.64 43.89 3.34
1549 2282 0.741326 CCGTGATGATCACCGTCTCT 59.259 55.000 19.01 0.00 44.20 3.10
1756 2497 0.179073 CCAGGATCGCCAGGTAGTTG 60.179 60.000 0.00 0.00 36.15 3.16
1998 2751 2.099831 GGACGTCGGAGCTGTACG 59.900 66.667 9.92 9.77 42.17 3.67
2147 3044 9.871175 TGTATATGTACAAGGATAGTAGGACAA 57.129 33.333 0.00 0.00 37.86 3.18
2229 3156 6.183360 GCAGAATATAGCTAGCCTATACGTGT 60.183 42.308 12.13 0.00 40.77 4.49
2230 3157 6.202937 GCAGAATATAGCTAGCCTATACGTG 58.797 44.000 12.13 11.16 40.77 4.49
2231 3158 5.299782 GGCAGAATATAGCTAGCCTATACGT 59.700 44.000 12.13 0.00 40.77 3.57
2232 3159 5.561145 CGGCAGAATATAGCTAGCCTATACG 60.561 48.000 12.13 7.82 40.77 3.06
2234 3161 5.446860 ACGGCAGAATATAGCTAGCCTATA 58.553 41.667 12.13 12.73 41.85 1.31
2235 3162 4.282496 ACGGCAGAATATAGCTAGCCTAT 58.718 43.478 12.13 10.97 39.91 2.57
2236 3163 3.698289 ACGGCAGAATATAGCTAGCCTA 58.302 45.455 12.13 3.93 39.91 3.93
2237 3164 2.530701 ACGGCAGAATATAGCTAGCCT 58.469 47.619 12.13 1.34 39.91 4.58
2238 3165 4.451629 TTACGGCAGAATATAGCTAGCC 57.548 45.455 12.13 8.94 38.73 3.93
2239 3166 5.411781 ACATTACGGCAGAATATAGCTAGC 58.588 41.667 6.62 6.62 0.00 3.42
2240 3167 9.239002 GATAACATTACGGCAGAATATAGCTAG 57.761 37.037 0.00 0.00 0.00 3.42
2241 3168 8.745590 TGATAACATTACGGCAGAATATAGCTA 58.254 33.333 0.00 0.00 0.00 3.32
2242 3169 7.611770 TGATAACATTACGGCAGAATATAGCT 58.388 34.615 0.00 0.00 0.00 3.32
2243 3170 7.827819 TGATAACATTACGGCAGAATATAGC 57.172 36.000 0.00 0.00 0.00 2.97
2244 3171 8.331022 GCATGATAACATTACGGCAGAATATAG 58.669 37.037 0.00 0.00 34.15 1.31
2245 3172 7.821846 TGCATGATAACATTACGGCAGAATATA 59.178 33.333 0.00 0.00 34.15 0.86
2246 3173 6.654582 TGCATGATAACATTACGGCAGAATAT 59.345 34.615 0.00 0.00 34.15 1.28
2249 3176 4.195416 TGCATGATAACATTACGGCAGAA 58.805 39.130 0.00 0.00 34.15 3.02
2250 3177 3.802866 TGCATGATAACATTACGGCAGA 58.197 40.909 0.00 0.00 34.15 4.26
2251 3178 4.550577 TTGCATGATAACATTACGGCAG 57.449 40.909 0.00 0.00 34.73 4.85
2252 3179 4.972514 TTTGCATGATAACATTACGGCA 57.027 36.364 0.00 0.00 34.15 5.69
2344 4164 4.148838 TGACCCGAATTCATTTTTGAGGT 58.851 39.130 6.22 0.00 0.00 3.85
2348 4168 5.376854 AGACTGACCCGAATTCATTTTTG 57.623 39.130 6.22 0.00 0.00 2.44
2353 4173 7.875041 CAGAATAATAGACTGACCCGAATTCAT 59.125 37.037 6.22 0.00 34.07 2.57
2370 4190 6.324512 AGCAACAATCAATGGCCAGAATAATA 59.675 34.615 13.05 0.00 0.00 0.98
2374 4194 2.835764 AGCAACAATCAATGGCCAGAAT 59.164 40.909 13.05 0.90 0.00 2.40
2427 4249 9.701355 CATAACACACAAAAATTTCTCAAAACC 57.299 29.630 0.00 0.00 0.00 3.27
2432 4254 7.551585 ACCACATAACACACAAAAATTTCTCA 58.448 30.769 0.00 0.00 0.00 3.27
2446 4268 6.304126 CGAAACAAGACATACCACATAACAC 58.696 40.000 0.00 0.00 0.00 3.32
2451 4273 3.343617 CCCGAAACAAGACATACCACAT 58.656 45.455 0.00 0.00 0.00 3.21
2503 4325 3.341823 CCCATGAAGGAGTTGACTGAAG 58.658 50.000 0.00 0.00 41.22 3.02
2513 4335 2.716814 GCATCAGCCCATGAAGGAG 58.283 57.895 0.00 0.00 42.53 3.69
2536 4358 0.735471 TAGCTCAGTCGCACAGCTAG 59.265 55.000 0.00 0.00 41.84 3.42
2567 4389 2.133281 TGGCTGATTTGTCAGATGGG 57.867 50.000 9.47 0.00 39.99 4.00
2577 4399 4.080863 AGGAAGAGACGTAATGGCTGATTT 60.081 41.667 0.00 0.00 0.00 2.17
2586 4408 7.570161 CGTAAAAACAAAGGAAGAGACGTAAT 58.430 34.615 0.00 0.00 0.00 1.89
2589 4411 4.260497 GCGTAAAAACAAAGGAAGAGACGT 60.260 41.667 0.00 0.00 0.00 4.34
2591 4413 5.419760 AGCGTAAAAACAAAGGAAGAGAC 57.580 39.130 0.00 0.00 0.00 3.36
2670 4502 7.831955 ACATCCCAAAAATACCCATAAGGATA 58.168 34.615 0.00 0.00 39.89 2.59
2671 4503 6.692588 ACATCCCAAAAATACCCATAAGGAT 58.307 36.000 0.00 0.00 39.89 3.24
2689 4521 8.612619 CATACATTTACAGTCACTTAACATCCC 58.387 37.037 0.00 0.00 0.00 3.85
2691 4523 8.664798 TGCATACATTTACAGTCACTTAACATC 58.335 33.333 0.00 0.00 0.00 3.06
2692 4524 8.560355 TGCATACATTTACAGTCACTTAACAT 57.440 30.769 0.00 0.00 0.00 2.71
2693 4525 7.971183 TGCATACATTTACAGTCACTTAACA 57.029 32.000 0.00 0.00 0.00 2.41
2694 4526 7.429340 GCATGCATACATTTACAGTCACTTAAC 59.571 37.037 14.21 0.00 32.87 2.01
2695 4527 7.120432 TGCATGCATACATTTACAGTCACTTAA 59.880 33.333 18.46 0.00 32.87 1.85
2696 4528 6.597280 TGCATGCATACATTTACAGTCACTTA 59.403 34.615 18.46 0.00 32.87 2.24
2697 4529 5.415389 TGCATGCATACATTTACAGTCACTT 59.585 36.000 18.46 0.00 32.87 3.16
2698 4530 4.943093 TGCATGCATACATTTACAGTCACT 59.057 37.500 18.46 0.00 32.87 3.41
2699 4531 5.233957 TGCATGCATACATTTACAGTCAC 57.766 39.130 18.46 0.00 32.87 3.67
2700 4532 5.415389 ACTTGCATGCATACATTTACAGTCA 59.585 36.000 23.37 0.00 32.87 3.41
2818 4846 9.897744 GTTTCATGAGAACAAATGAATTAGTGA 57.102 29.630 12.84 0.00 41.23 3.41
2895 4924 4.614284 CAGTTGACGCTGATTGTTTTCATC 59.386 41.667 0.00 0.00 38.70 2.92
2897 4926 3.243035 CCAGTTGACGCTGATTGTTTTCA 60.243 43.478 0.00 0.00 38.70 2.69
2904 4933 2.034879 CGGCCAGTTGACGCTGATT 61.035 57.895 2.24 0.00 38.70 2.57
2905 4934 2.434884 CGGCCAGTTGACGCTGAT 60.435 61.111 2.24 0.00 38.70 2.90
2909 4938 2.480555 CATTCGGCCAGTTGACGC 59.519 61.111 2.24 0.00 0.00 5.19
2921 4950 1.159285 TTGCACAGAGAAGGCATTCG 58.841 50.000 5.31 0.00 40.58 3.34
2925 4954 1.610038 CATGTTTGCACAGAGAAGGCA 59.390 47.619 0.00 0.00 35.94 4.75
2926 4955 1.610522 ACATGTTTGCACAGAGAAGGC 59.389 47.619 0.00 0.00 35.94 4.35
2934 4963 1.408340 CCACAAGGACATGTTTGCACA 59.592 47.619 9.67 0.00 36.89 4.57
2941 4970 1.065410 TGGGACCCACAAGGACATGT 61.065 55.000 9.95 0.00 39.89 3.21
2942 4971 1.767036 TGGGACCCACAAGGACATG 59.233 57.895 9.95 0.00 39.89 3.21
2943 4972 4.348684 TGGGACCCACAAGGACAT 57.651 55.556 9.95 0.00 39.89 3.06
2960 4990 0.104934 AAGGGAGGTGGAGAGTGTGT 60.105 55.000 0.00 0.00 0.00 3.72
2974 5004 4.022676 GGCGTTGTTTCAGAAATTAAGGGA 60.023 41.667 0.00 0.00 0.00 4.20
2994 5024 1.281566 GAAAATGTTGGCGTTGGGCG 61.282 55.000 0.00 0.00 44.92 6.13
3002 5032 1.691434 TGTGGGGAAGAAAATGTTGGC 59.309 47.619 0.00 0.00 0.00 4.52
3006 5036 4.141158 AGAGAGTTGTGGGGAAGAAAATGT 60.141 41.667 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.