Multiple sequence alignment - TraesCS2B01G426400

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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 TraesCS2B01G426400 chr2B 100.000 6294 0 0 1 6294 612697520 612691227 0.000000e+00 11623
1 TraesCS2B01G426400 chr2B 91.588 2865 186 27 2351 5203 619642560 619645381 0.000000e+00 3904
2 TraesCS2B01G426400 chr2B 91.096 2875 211 29 2347 5203 727941179 727938332 0.000000e+00 3849
3 TraesCS2B01G426400 chr2B 93.745 1151 64 4 1201 2350 557751893 557753036 0.000000e+00 1720
4 TraesCS2B01G426400 chr2B 91.825 526 33 5 5204 5719 636459630 636459105 0.000000e+00 725
5 TraesCS2B01G426400 chr2B 95.238 231 11 0 2347 2577 790391393 790391623 3.590000e-97 366
6 TraesCS2B01G426400 chr1D 92.643 2868 188 17 2347 5203 30179559 30182414 0.000000e+00 4106
7 TraesCS2B01G426400 chr1D 91.113 1204 98 4 1 1201 429020144 429021341 0.000000e+00 1622
8 TraesCS2B01G426400 chr2D 92.581 2871 166 14 2347 5203 429573822 429570985 0.000000e+00 4078
9 TraesCS2B01G426400 chr2D 92.536 2867 177 12 2347 5203 7594123 7591284 0.000000e+00 4074
10 TraesCS2B01G426400 chr2D 94.005 1151 63 2 1201 2350 611733747 611734892 0.000000e+00 1738
11 TraesCS2B01G426400 chr2D 93.761 1154 65 6 1201 2353 640528798 640527651 0.000000e+00 1725
12 TraesCS2B01G426400 chr2D 85.740 547 38 9 5749 6282 520529051 520528532 5.550000e-150 542
13 TraesCS2B01G426400 chr5B 92.078 2878 191 18 2347 5201 25527750 25530613 0.000000e+00 4017
14 TraesCS2B01G426400 chr5B 91.211 2890 201 27 2347 5203 561007578 561010447 0.000000e+00 3880
15 TraesCS2B01G426400 chr5B 93.772 1156 60 6 1200 2353 563585394 563584249 0.000000e+00 1725
16 TraesCS2B01G426400 chr5B 91.013 879 77 2 1 877 410846017 410846895 0.000000e+00 1184
17 TraesCS2B01G426400 chr5B 93.018 487 30 4 5204 5686 407223736 407224222 0.000000e+00 708
18 TraesCS2B01G426400 chr5B 90.751 519 42 6 5204 5718 562074938 562074422 0.000000e+00 688
19 TraesCS2B01G426400 chr5B 90.154 518 40 6 5204 5718 327195677 327196186 0.000000e+00 664
20 TraesCS2B01G426400 chr7D 92.107 2876 184 17 2347 5203 583821798 583824649 0.000000e+00 4013
21 TraesCS2B01G426400 chr7D 92.091 2870 184 20 2352 5203 255282340 255285184 0.000000e+00 4002
22 TraesCS2B01G426400 chr7D 91.942 2358 139 22 2863 5205 265681390 265683711 0.000000e+00 3254
23 TraesCS2B01G426400 chr7D 90.916 1409 104 17 3808 5204 107401551 107402947 0.000000e+00 1871
24 TraesCS2B01G426400 chr7D 93.465 1163 60 4 1199 2352 529846277 529847432 0.000000e+00 1712
25 TraesCS2B01G426400 chr7B 91.929 2887 187 21 2354 5203 292159226 292162103 0.000000e+00 3999
26 TraesCS2B01G426400 chr3B 91.762 2889 191 25 2347 5203 570038654 570041527 0.000000e+00 3973
27 TraesCS2B01G426400 chr3B 93.414 1154 67 4 1200 2350 327749637 327750784 0.000000e+00 1701
28 TraesCS2B01G426400 chr3B 93.351 1158 63 7 1200 2353 739913139 739914286 0.000000e+00 1700
29 TraesCS2B01G426400 chr3B 91.255 526 31 7 5204 5718 61876071 61875550 0.000000e+00 702
30 TraesCS2B01G426400 chr3B 90.787 521 40 6 5204 5718 478549761 478549243 0.000000e+00 689
31 TraesCS2B01G426400 chr4B 91.884 2871 187 20 2347 5203 202940732 202943570 0.000000e+00 3969
32 TraesCS2B01G426400 chr4B 91.774 2869 175 28 2347 5203 634919427 634916608 0.000000e+00 3934
33 TraesCS2B01G426400 chr1B 91.371 2874 221 20 2347 5205 575434257 575437118 0.000000e+00 3908
34 TraesCS2B01G426400 chr1B 93.207 1163 62 13 1200 2353 114512722 114513876 0.000000e+00 1694
35 TraesCS2B01G426400 chr1A 93.121 1163 67 4 1197 2353 592347249 592346094 0.000000e+00 1692
36 TraesCS2B01G426400 chr1A 90.557 879 76 3 1 877 327011959 327011086 0.000000e+00 1157
37 TraesCS2B01G426400 chr1A 92.547 322 23 1 879 1199 327011051 327010730 1.600000e-125 460
38 TraesCS2B01G426400 chr1A 91.950 323 26 0 879 1201 238075832 238076154 2.680000e-123 453
39 TraesCS2B01G426400 chr4D 91.308 1208 96 6 1 1201 442390546 442391751 0.000000e+00 1640
40 TraesCS2B01G426400 chr4D 91.240 879 71 6 1 875 48683969 48683093 0.000000e+00 1192
41 TraesCS2B01G426400 chr4D 91.250 880 69 4 1 877 116524598 116523724 0.000000e+00 1192
42 TraesCS2B01G426400 chr4D 90.568 880 80 3 1 877 421048677 421047798 0.000000e+00 1162
43 TraesCS2B01G426400 chr4D 92.500 320 24 0 882 1201 116523686 116523367 5.750000e-125 459
44 TraesCS2B01G426400 chr3A 91.591 880 71 3 1 877 418765701 418764822 0.000000e+00 1212
45 TraesCS2B01G426400 chr5A 90.682 880 79 3 1 877 392040555 392041434 0.000000e+00 1168
46 TraesCS2B01G426400 chr5A 93.808 323 20 0 879 1201 10322793 10323115 2.640000e-133 486
47 TraesCS2B01G426400 chr5A 92.523 321 24 0 881 1201 604231187 604230867 1.600000e-125 460
48 TraesCS2B01G426400 chr6B 91.255 526 36 5 5204 5719 81982255 81982780 0.000000e+00 708
49 TraesCS2B01G426400 chr6B 92.000 325 26 0 877 1201 81981934 81982258 2.070000e-124 457
50 TraesCS2B01G426400 chr7A 90.661 514 41 7 5204 5710 63380357 63379844 0.000000e+00 676
51 TraesCS2B01G426400 chr6D 90.600 500 33 12 5204 5696 469236408 469236900 0.000000e+00 651
52 TraesCS2B01G426400 chr2A 83.828 606 57 25 5716 6294 665713776 665713185 7.180000e-149 538
53 TraesCS2B01G426400 chr5D 92.260 323 25 0 879 1201 460217072 460217394 5.750000e-125 459


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 TraesCS2B01G426400 chr2B 612691227 612697520 6293 True 11623.0 11623 100.0000 1 6294 1 chr2B.!!$R1 6293
1 TraesCS2B01G426400 chr2B 619642560 619645381 2821 False 3904.0 3904 91.5880 2351 5203 1 chr2B.!!$F2 2852
2 TraesCS2B01G426400 chr2B 727938332 727941179 2847 True 3849.0 3849 91.0960 2347 5203 1 chr2B.!!$R3 2856
3 TraesCS2B01G426400 chr2B 557751893 557753036 1143 False 1720.0 1720 93.7450 1201 2350 1 chr2B.!!$F1 1149
4 TraesCS2B01G426400 chr2B 636459105 636459630 525 True 725.0 725 91.8250 5204 5719 1 chr2B.!!$R2 515
5 TraesCS2B01G426400 chr1D 30179559 30182414 2855 False 4106.0 4106 92.6430 2347 5203 1 chr1D.!!$F1 2856
6 TraesCS2B01G426400 chr1D 429020144 429021341 1197 False 1622.0 1622 91.1130 1 1201 1 chr1D.!!$F2 1200
7 TraesCS2B01G426400 chr2D 429570985 429573822 2837 True 4078.0 4078 92.5810 2347 5203 1 chr2D.!!$R2 2856
8 TraesCS2B01G426400 chr2D 7591284 7594123 2839 True 4074.0 4074 92.5360 2347 5203 1 chr2D.!!$R1 2856
9 TraesCS2B01G426400 chr2D 611733747 611734892 1145 False 1738.0 1738 94.0050 1201 2350 1 chr2D.!!$F1 1149
10 TraesCS2B01G426400 chr2D 640527651 640528798 1147 True 1725.0 1725 93.7610 1201 2353 1 chr2D.!!$R4 1152
11 TraesCS2B01G426400 chr2D 520528532 520529051 519 True 542.0 542 85.7400 5749 6282 1 chr2D.!!$R3 533
12 TraesCS2B01G426400 chr5B 25527750 25530613 2863 False 4017.0 4017 92.0780 2347 5201 1 chr5B.!!$F1 2854
13 TraesCS2B01G426400 chr5B 561007578 561010447 2869 False 3880.0 3880 91.2110 2347 5203 1 chr5B.!!$F5 2856
14 TraesCS2B01G426400 chr5B 563584249 563585394 1145 True 1725.0 1725 93.7720 1200 2353 1 chr5B.!!$R2 1153
15 TraesCS2B01G426400 chr5B 410846017 410846895 878 False 1184.0 1184 91.0130 1 877 1 chr5B.!!$F4 876
16 TraesCS2B01G426400 chr5B 562074422 562074938 516 True 688.0 688 90.7510 5204 5718 1 chr5B.!!$R1 514
17 TraesCS2B01G426400 chr5B 327195677 327196186 509 False 664.0 664 90.1540 5204 5718 1 chr5B.!!$F2 514
18 TraesCS2B01G426400 chr7D 583821798 583824649 2851 False 4013.0 4013 92.1070 2347 5203 1 chr7D.!!$F5 2856
19 TraesCS2B01G426400 chr7D 255282340 255285184 2844 False 4002.0 4002 92.0910 2352 5203 1 chr7D.!!$F2 2851
20 TraesCS2B01G426400 chr7D 265681390 265683711 2321 False 3254.0 3254 91.9420 2863 5205 1 chr7D.!!$F3 2342
21 TraesCS2B01G426400 chr7D 107401551 107402947 1396 False 1871.0 1871 90.9160 3808 5204 1 chr7D.!!$F1 1396
22 TraesCS2B01G426400 chr7D 529846277 529847432 1155 False 1712.0 1712 93.4650 1199 2352 1 chr7D.!!$F4 1153
23 TraesCS2B01G426400 chr7B 292159226 292162103 2877 False 3999.0 3999 91.9290 2354 5203 1 chr7B.!!$F1 2849
24 TraesCS2B01G426400 chr3B 570038654 570041527 2873 False 3973.0 3973 91.7620 2347 5203 1 chr3B.!!$F2 2856
25 TraesCS2B01G426400 chr3B 327749637 327750784 1147 False 1701.0 1701 93.4140 1200 2350 1 chr3B.!!$F1 1150
26 TraesCS2B01G426400 chr3B 739913139 739914286 1147 False 1700.0 1700 93.3510 1200 2353 1 chr3B.!!$F3 1153
27 TraesCS2B01G426400 chr3B 61875550 61876071 521 True 702.0 702 91.2550 5204 5718 1 chr3B.!!$R1 514
28 TraesCS2B01G426400 chr3B 478549243 478549761 518 True 689.0 689 90.7870 5204 5718 1 chr3B.!!$R2 514
29 TraesCS2B01G426400 chr4B 202940732 202943570 2838 False 3969.0 3969 91.8840 2347 5203 1 chr4B.!!$F1 2856
30 TraesCS2B01G426400 chr4B 634916608 634919427 2819 True 3934.0 3934 91.7740 2347 5203 1 chr4B.!!$R1 2856
31 TraesCS2B01G426400 chr1B 575434257 575437118 2861 False 3908.0 3908 91.3710 2347 5205 1 chr1B.!!$F2 2858
32 TraesCS2B01G426400 chr1B 114512722 114513876 1154 False 1694.0 1694 93.2070 1200 2353 1 chr1B.!!$F1 1153
33 TraesCS2B01G426400 chr1A 592346094 592347249 1155 True 1692.0 1692 93.1210 1197 2353 1 chr1A.!!$R1 1156
34 TraesCS2B01G426400 chr1A 327010730 327011959 1229 True 808.5 1157 91.5520 1 1199 2 chr1A.!!$R2 1198
35 TraesCS2B01G426400 chr4D 442390546 442391751 1205 False 1640.0 1640 91.3080 1 1201 1 chr4D.!!$F1 1200
36 TraesCS2B01G426400 chr4D 48683093 48683969 876 True 1192.0 1192 91.2400 1 875 1 chr4D.!!$R1 874
37 TraesCS2B01G426400 chr4D 421047798 421048677 879 True 1162.0 1162 90.5680 1 877 1 chr4D.!!$R2 876
38 TraesCS2B01G426400 chr4D 116523367 116524598 1231 True 825.5 1192 91.8750 1 1201 2 chr4D.!!$R3 1200
39 TraesCS2B01G426400 chr3A 418764822 418765701 879 True 1212.0 1212 91.5910 1 877 1 chr3A.!!$R1 876
40 TraesCS2B01G426400 chr5A 392040555 392041434 879 False 1168.0 1168 90.6820 1 877 1 chr5A.!!$F2 876
41 TraesCS2B01G426400 chr6B 81981934 81982780 846 False 582.5 708 91.6275 877 5719 2 chr6B.!!$F1 4842
42 TraesCS2B01G426400 chr7A 63379844 63380357 513 True 676.0 676 90.6610 5204 5710 1 chr7A.!!$R1 506
43 TraesCS2B01G426400 chr2A 665713185 665713776 591 True 538.0 538 83.8280 5716 6294 1 chr2A.!!$R1 578

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
841 850 0.321671 CAAGAAGGACAAGGAGCCGA 59.678 55.0 0.0 0.0 0.00 5.54 F
1927 1982 0.039472 TCACTCCTGCTGCTCTCTCT 59.961 55.0 0.0 0.0 0.00 3.10 F
1928 1983 0.457035 CACTCCTGCTGCTCTCTCTC 59.543 60.0 0.0 0.0 0.00 3.20 F
3170 3247 0.673437 CACACAAATTCGGGGCACTT 59.327 50.0 0.0 0.0 0.00 3.16 F
3980 4071 0.036952 ATGAGGATGCGGGATAAGCG 60.037 55.0 0.0 0.0 37.44 4.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1970 2025 1.159285 TGCTCCAACTTGATGAAGCG 58.841 50.000 0.00 0.0 31.68 4.68 R
2985 3061 0.598419 TGATAGGCGCTTCAGCATCG 60.598 55.000 7.64 0.0 42.21 3.84 R
3331 3408 1.298340 CCAAGTGGCCGGTCATGTA 59.702 57.895 14.23 0.0 0.00 2.29 R
4746 4910 3.056313 GCACTTCCTGGAATGCGCC 62.056 63.158 20.26 0.0 0.00 6.53 R
5558 5753 0.106521 GGTGTTTGGTTGCCTGCATT 59.893 50.000 0.00 0.0 0.00 3.56 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
82 83 4.621510 CGACCTTCATCTTCTTGTCCATCA 60.622 45.833 0.00 0.00 0.00 3.07
113 114 2.595463 TGGGTCGTCGTCGTCCTT 60.595 61.111 16.18 0.00 42.88 3.36
118 119 1.893335 TCGTCGTCGTCCTTGGTGA 60.893 57.895 1.33 0.00 38.33 4.02
315 320 2.569404 CCACCTCTTCCTCTGTTTAGCT 59.431 50.000 0.00 0.00 0.00 3.32
318 323 3.904339 ACCTCTTCCTCTGTTTAGCTTCA 59.096 43.478 0.00 0.00 0.00 3.02
355 361 1.105457 ATGGCCCAACGAATGATGTG 58.895 50.000 0.00 0.00 0.00 3.21
372 379 4.408821 GGACTGCCATCGTGCCCA 62.409 66.667 0.00 0.00 0.00 5.36
376 383 4.094646 TGCCATCGTGCCCATCGT 62.095 61.111 0.00 0.00 0.00 3.73
391 398 3.820557 CCATCGTTGGGTTAGGAATCAT 58.179 45.455 4.47 0.00 39.56 2.45
393 400 3.553828 TCGTTGGGTTAGGAATCATCC 57.446 47.619 0.00 0.00 46.98 3.51
499 506 3.444388 ACCTCCATAGTGTTCTCGAACTC 59.556 47.826 10.75 7.41 41.67 3.01
574 581 1.231928 GGAAGGGGTTGGTGTTGGT 59.768 57.895 0.00 0.00 0.00 3.67
577 584 0.396556 AAGGGGTTGGTGTTGGTGTC 60.397 55.000 0.00 0.00 0.00 3.67
691 700 1.388065 CGCGATGGAGAGGAGGAAGT 61.388 60.000 0.00 0.00 0.00 3.01
701 710 0.962489 AGGAGGAAGTGTGACAGTCG 59.038 55.000 0.00 0.00 0.00 4.18
777 786 4.084287 ACTCCATGAATTGTGTGCAGATT 58.916 39.130 0.00 0.00 0.00 2.40
785 794 2.462456 TGTGTGCAGATTGAGGAGAC 57.538 50.000 0.00 0.00 0.00 3.36
841 850 0.321671 CAAGAAGGACAAGGAGCCGA 59.678 55.000 0.00 0.00 0.00 5.54
848 857 1.139853 GGACAAGGAGCCGATTCATCT 59.860 52.381 0.00 0.00 0.00 2.90
867 876 2.635915 TCTAATGTCCGAGGTGGTGTTT 59.364 45.455 0.00 0.00 39.52 2.83
887 929 4.980805 GCCCACCAACGACGAGCA 62.981 66.667 0.00 0.00 0.00 4.26
968 1010 0.595095 CCAACTCACTTCTGCAAGGC 59.405 55.000 0.00 0.00 33.37 4.35
1027 1071 1.239347 GGACTTCACCAAGCACTTCC 58.761 55.000 0.00 0.00 32.09 3.46
1031 1075 1.990160 TTCACCAAGCACTTCCCCGT 61.990 55.000 0.00 0.00 0.00 5.28
1050 1094 2.975799 GTGCCGGCGGAGTTCAAA 60.976 61.111 33.44 0.00 0.00 2.69
1116 1160 1.122632 TGAACGGCAGGTTGACCCTA 61.123 55.000 0.00 0.00 43.86 3.53
1138 1182 2.780924 AGGGTTGGGCCACCTTCA 60.781 61.111 19.97 0.00 39.65 3.02
1139 1183 2.169810 AGGGTTGGGCCACCTTCAT 61.170 57.895 19.97 1.42 39.65 2.57
1194 1238 0.605589 CGTTCAAGCTCCTGACTCCT 59.394 55.000 0.00 0.00 0.00 3.69
1277 1321 1.753073 ACACCGCGCTACTAATAAGGT 59.247 47.619 5.56 0.00 0.00 3.50
1564 1619 7.109501 TGTGGTGCATGTCAAAAGTATACTAT 58.890 34.615 5.65 0.00 0.00 2.12
1733 1788 8.468399 AGTCATAGTGTAGCATATCATCATCTG 58.532 37.037 0.00 0.00 0.00 2.90
1762 1817 6.015519 ACTCATTCTAGCTAGCTAATCACCAG 60.016 42.308 24.20 16.93 0.00 4.00
1852 1907 9.695155 ATTACCACCAACACTAGCTATTTAATT 57.305 29.630 0.00 0.00 0.00 1.40
1927 1982 0.039472 TCACTCCTGCTGCTCTCTCT 59.961 55.000 0.00 0.00 0.00 3.10
1928 1983 0.457035 CACTCCTGCTGCTCTCTCTC 59.543 60.000 0.00 0.00 0.00 3.20
1970 2025 4.700213 ACATAAAACATGTGTAGCACTCCC 59.300 41.667 0.00 0.00 35.11 4.30
2012 2067 3.055819 TGCAGATGAACCTGTCTCCTAAC 60.056 47.826 0.00 0.00 36.57 2.34
2168 2226 4.475051 TGGCCGTAAGCTAACAATTCTA 57.525 40.909 0.00 0.00 43.05 2.10
2216 2274 0.734889 GCACAACATTCATCGGGAGG 59.265 55.000 0.00 0.00 0.00 4.30
2217 2275 1.950484 GCACAACATTCATCGGGAGGT 60.950 52.381 0.00 0.00 0.00 3.85
2312 2370 7.989826 AGATGCATTGAGGACAAATAGTAAAC 58.010 34.615 0.00 0.00 39.54 2.01
2478 2536 2.532531 CAAGCGCTGGACATGTTTAG 57.467 50.000 12.58 2.72 0.00 1.85
2484 2542 3.810373 CGCTGGACATGTTTAGTTGAAC 58.190 45.455 0.00 0.00 0.00 3.18
2838 2898 8.095452 AGGACTGAAACATATCTTATCCAAGT 57.905 34.615 0.00 0.00 33.20 3.16
2856 2916 4.441913 CCAAGTCAAAAACTCTTGCATGGT 60.442 41.667 0.00 0.00 37.17 3.55
2985 3061 2.440539 TCAAAGTTCTCGTCCAGCTC 57.559 50.000 0.00 0.00 0.00 4.09
3030 3106 3.701542 TCTAGGAAGATTCTGTCGCACAT 59.298 43.478 0.00 0.00 0.00 3.21
3094 3170 6.347725 CCTTTTCGTTGTCAGACATTTCCTAG 60.348 42.308 3.45 0.00 0.00 3.02
3170 3247 0.673437 CACACAAATTCGGGGCACTT 59.327 50.000 0.00 0.00 0.00 3.16
3385 3462 7.558161 TCCTATTTGAGCAACACAAGATATG 57.442 36.000 0.00 0.00 0.00 1.78
3511 3588 5.858581 GCAAAAGTAAATCATCTCTTGCGTT 59.141 36.000 0.00 0.00 0.00 4.84
3930 4015 2.146724 CCCGGACATGGCCCATCTA 61.147 63.158 13.45 0.00 0.00 1.98
3977 4068 1.272490 GACGATGAGGATGCGGGATAA 59.728 52.381 0.00 0.00 0.00 1.75
3980 4071 0.036952 ATGAGGATGCGGGATAAGCG 60.037 55.000 0.00 0.00 37.44 4.68
3981 4072 2.029844 GAGGATGCGGGATAAGCGC 61.030 63.158 0.00 0.00 37.44 5.92
4014 4105 4.031652 CGATGCGGGAAAAATTGCTTTAAG 59.968 41.667 0.00 0.00 0.00 1.85
4047 4139 8.939201 ATAACAACAAATGTGACATGTTCAAA 57.061 26.923 0.00 0.00 42.99 2.69
4050 4142 9.545105 AACAACAAATGTGACATGTTCAAATAT 57.455 25.926 0.00 0.00 42.99 1.28
4379 4505 2.359900 GCATCTGATTCGTTTCCACCT 58.640 47.619 0.00 0.00 0.00 4.00
4388 4514 6.513180 TGATTCGTTTCCACCTATAGATGAC 58.487 40.000 0.00 0.00 0.00 3.06
4442 4569 3.878358 CCTAGGCAGAGGTAGGGC 58.122 66.667 0.00 0.00 33.34 5.19
4624 4784 2.048503 GCGTAGAAGGTGTGCGGT 60.049 61.111 0.00 0.00 0.00 5.68
4626 4786 1.736645 CGTAGAAGGTGTGCGGTGG 60.737 63.158 0.00 0.00 0.00 4.61
4707 4869 2.969300 TTTGGGGGAAGTGGTCGTGC 62.969 60.000 0.00 0.00 0.00 5.34
4746 4910 3.921021 CGGTTAAGTCAGAAGTAGCAGTG 59.079 47.826 0.00 0.00 0.00 3.66
4765 4929 2.334946 GCGCATTCCAGGAAGTGCA 61.335 57.895 24.56 0.00 37.44 4.57
4820 4984 3.166489 ACACGCTACTGCTATTCCTTC 57.834 47.619 0.00 0.00 36.97 3.46
4821 4985 2.761208 ACACGCTACTGCTATTCCTTCT 59.239 45.455 0.00 0.00 36.97 2.85
5062 5237 5.365619 CCATGGGAATTTTAGTAGTAGCGT 58.634 41.667 2.85 0.00 0.00 5.07
5230 5411 3.381590 TCAAGGTCATCATCTTCGACGAT 59.618 43.478 0.00 0.00 0.00 3.73
5320 5501 3.263489 GGCACCTCCTTCTTAAGTACC 57.737 52.381 1.63 0.00 0.00 3.34
5345 5526 5.730550 TCGAGTCTGCTTTATGGTTTATGT 58.269 37.500 0.00 0.00 0.00 2.29
5355 5536 7.013750 TGCTTTATGGTTTATGTGTTGAACTGA 59.986 33.333 0.00 0.00 0.00 3.41
5366 5547 9.725019 TTATGTGTTGAACTGATTGAACTATCT 57.275 29.630 0.00 0.00 33.51 1.98
5367 5548 7.425577 TGTGTTGAACTGATTGAACTATCTG 57.574 36.000 0.00 0.00 33.51 2.90
5433 5620 9.083422 AGTAGTTGATGCTCTATTTATGCTCTA 57.917 33.333 0.00 0.00 0.00 2.43
5436 5623 7.758980 AGTTGATGCTCTATTTATGCTCTATCG 59.241 37.037 0.00 0.00 0.00 2.92
5437 5624 6.567959 TGATGCTCTATTTATGCTCTATCGG 58.432 40.000 0.00 0.00 0.00 4.18
5558 5753 1.044611 GCCTTGGGTTTGCCACTAAA 58.955 50.000 0.00 0.00 36.17 1.85
5697 5896 4.678044 GCAATGCAGCTACTGTAGACTACA 60.678 45.833 18.64 14.53 37.13 2.74
5710 5909 3.275617 AGACTACAGCAACCAAACACA 57.724 42.857 0.00 0.00 0.00 3.72
5802 6001 3.323979 GGGTCGCCTTAATGAATCCTCTA 59.676 47.826 0.00 0.00 0.00 2.43
5804 6003 4.561105 GTCGCCTTAATGAATCCTCTAGG 58.439 47.826 0.00 0.00 0.00 3.02
5825 6024 8.842764 TCTAGGAATAGTAAAACCTGGGAAAAT 58.157 33.333 0.00 0.00 34.42 1.82
5826 6025 7.956328 AGGAATAGTAAAACCTGGGAAAATC 57.044 36.000 0.00 0.00 0.00 2.17
5827 6026 6.602009 AGGAATAGTAAAACCTGGGAAAATCG 59.398 38.462 0.00 0.00 0.00 3.34
5837 6037 4.586841 ACCTGGGAAAATCGTTTTGATGAA 59.413 37.500 0.00 0.00 37.39 2.57
5950 6153 7.630082 AGAGCTACTAAACAATGTAATCCCAA 58.370 34.615 0.00 0.00 0.00 4.12
5951 6154 7.553044 AGAGCTACTAAACAATGTAATCCCAAC 59.447 37.037 0.00 0.00 0.00 3.77
5952 6155 7.402862 AGCTACTAAACAATGTAATCCCAACT 58.597 34.615 0.00 0.00 0.00 3.16
5953 6156 8.545472 AGCTACTAAACAATGTAATCCCAACTA 58.455 33.333 0.00 0.00 0.00 2.24
5954 6157 9.169592 GCTACTAAACAATGTAATCCCAACTAA 57.830 33.333 0.00 0.00 0.00 2.24
5957 6160 9.185680 ACTAAACAATGTAATCCCAACTAATCC 57.814 33.333 0.00 0.00 0.00 3.01
5958 6161 9.184523 CTAAACAATGTAATCCCAACTAATCCA 57.815 33.333 0.00 0.00 0.00 3.41
5959 6162 7.645058 AACAATGTAATCCCAACTAATCCAG 57.355 36.000 0.00 0.00 0.00 3.86
5960 6163 6.129179 ACAATGTAATCCCAACTAATCCAGG 58.871 40.000 0.00 0.00 0.00 4.45
5961 6164 6.069088 ACAATGTAATCCCAACTAATCCAGGA 60.069 38.462 0.00 0.00 0.00 3.86
5962 6165 6.786843 ATGTAATCCCAACTAATCCAGGAT 57.213 37.500 0.00 0.00 39.02 3.24
5963 6166 7.888514 ATGTAATCCCAACTAATCCAGGATA 57.111 36.000 1.02 0.00 36.30 2.59
5964 6167 7.888514 TGTAATCCCAACTAATCCAGGATAT 57.111 36.000 1.02 0.00 36.30 1.63
5965 6168 7.689299 TGTAATCCCAACTAATCCAGGATATG 58.311 38.462 1.02 1.12 36.30 1.78
5966 6169 7.515861 TGTAATCCCAACTAATCCAGGATATGA 59.484 37.037 1.02 0.00 36.30 2.15
5967 6170 7.594849 AATCCCAACTAATCCAGGATATGAT 57.405 36.000 1.02 0.00 36.30 2.45
5968 6171 7.594849 ATCCCAACTAATCCAGGATATGATT 57.405 36.000 1.02 0.00 35.56 2.57
5969 6172 8.700145 ATCCCAACTAATCCAGGATATGATTA 57.300 34.615 1.02 0.00 35.56 1.75
5970 6173 8.518720 TCCCAACTAATCCAGGATATGATTAA 57.481 34.615 1.02 0.00 34.12 1.40
5971 6174 8.954729 TCCCAACTAATCCAGGATATGATTAAA 58.045 33.333 1.02 0.00 34.12 1.52
5972 6175 9.586732 CCCAACTAATCCAGGATATGATTAAAA 57.413 33.333 1.02 0.00 34.12 1.52
6039 6270 4.932200 AGAAGCTCAAAAACTGTCTATCCG 59.068 41.667 0.00 0.00 0.00 4.18
6047 6278 3.802948 AACTGTCTATCCGTGATCCAC 57.197 47.619 0.00 0.00 0.00 4.02
6057 6290 3.884895 TCCGTGATCCACTGCATTTATT 58.115 40.909 0.00 0.00 31.34 1.40
6073 6306 8.686397 TGCATTTATTTAAACATACAGCACAG 57.314 30.769 0.00 0.00 0.00 3.66
6080 6313 0.322648 ACATACAGCACAGCTCAGCA 59.677 50.000 0.00 0.00 36.40 4.41
6109 6350 3.573229 AGACAGCCAGCCAGCCAA 61.573 61.111 0.00 0.00 0.00 4.52
6198 6443 1.284982 CGTAGGCCTATGATGCGCAC 61.285 60.000 25.48 7.75 0.00 5.34
6216 6461 2.233271 CACACAGGCCAATCAAGAGTT 58.767 47.619 5.01 0.00 0.00 3.01
6274 6522 7.117397 TGTACTCCTGCTAGAATTAGTAGTGT 58.883 38.462 0.00 1.84 37.78 3.55
6277 6531 7.348033 ACTCCTGCTAGAATTAGTAGTGTACT 58.652 38.462 0.00 0.00 37.78 2.73
6278 6532 7.283580 ACTCCTGCTAGAATTAGTAGTGTACTG 59.716 40.741 0.00 0.00 37.78 2.74
6279 6533 6.039493 TCCTGCTAGAATTAGTAGTGTACTGC 59.961 42.308 0.00 0.00 37.78 4.40
6280 6534 6.183360 CCTGCTAGAATTAGTAGTGTACTGCA 60.183 42.308 0.00 0.00 37.78 4.41
6281 6535 7.348080 TGCTAGAATTAGTAGTGTACTGCAT 57.652 36.000 0.00 0.00 39.81 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 0.904865 AGATGAAGGTCGGCCACTCA 60.905 55.000 9.71 11.49 37.19 3.41
59 60 3.319137 TGGACAAGAAGATGAAGGTCG 57.681 47.619 0.00 0.00 0.00 4.79
61 62 4.566488 GGTGATGGACAAGAAGATGAAGGT 60.566 45.833 0.00 0.00 0.00 3.50
113 114 4.486887 TCGACCTCGACTTCACCA 57.513 55.556 0.00 0.00 44.22 4.17
166 171 2.056481 GAACCGATGCAGATGCCAGC 62.056 60.000 1.72 0.00 41.18 4.85
233 238 1.310933 CGTAGTGTACTGGGAGGCGT 61.311 60.000 0.00 0.00 0.00 5.68
315 320 0.834612 AATTAGGCCGTCCCGATGAA 59.165 50.000 0.00 0.00 39.21 2.57
318 323 1.056660 ATGAATTAGGCCGTCCCGAT 58.943 50.000 0.00 0.00 39.21 4.18
331 337 2.455557 TCATTCGTTGGGCCATGAATT 58.544 42.857 24.13 12.23 0.00 2.17
355 361 3.704231 ATGGGCACGATGGCAGTCC 62.704 63.158 12.19 0.00 45.76 3.85
372 379 4.086706 GGATGATTCCTAACCCAACGAT 57.913 45.455 0.00 0.00 39.14 3.73
391 398 2.435805 ACTGCACAAGAGTTGAAGAGGA 59.564 45.455 0.00 0.00 0.00 3.71
393 400 2.547211 CCACTGCACAAGAGTTGAAGAG 59.453 50.000 0.00 0.00 0.00 2.85
691 700 1.999048 AAAACGACACGACTGTCACA 58.001 45.000 8.73 0.00 46.47 3.58
701 710 5.840940 AGAGCATGTAGTTAAAACGACAC 57.159 39.130 10.37 1.00 45.03 3.67
777 786 2.121948 CCCATCTCATTGGTCTCCTCA 58.878 52.381 0.00 0.00 34.77 3.86
785 794 0.816825 CTCCGTGCCCATCTCATTGG 60.817 60.000 0.00 0.00 36.46 3.16
813 822 0.468226 TGTCCTTCTTGTCAACGGCT 59.532 50.000 0.00 0.00 0.00 5.52
841 850 3.711704 ACCACCTCGGACATTAGATGAAT 59.288 43.478 0.00 0.00 38.63 2.57
848 857 2.289819 GGAAACACCACCTCGGACATTA 60.290 50.000 0.00 0.00 38.63 1.90
887 929 1.074167 CTAGGGGGCTCCTCCATGT 60.074 63.158 10.64 0.00 44.06 3.21
916 958 1.330234 TGGTAGTGGTCGTAGTTGCA 58.670 50.000 0.00 0.00 0.00 4.08
968 1010 2.364970 TCAAACTTTGGTGCAAGGATGG 59.635 45.455 1.62 0.00 0.00 3.51
1050 1094 2.424302 CCGGTGTTGTTCCTCGGT 59.576 61.111 0.00 0.00 36.38 4.69
1116 1160 2.616458 GGTGGCCCAACCCTGATCT 61.616 63.158 0.00 0.00 37.83 2.75
1138 1182 2.101415 TCTTGATCTGATGAACGGCGAT 59.899 45.455 16.62 0.00 0.00 4.58
1139 1183 1.476488 TCTTGATCTGATGAACGGCGA 59.524 47.619 16.62 0.00 0.00 5.54
1194 1238 3.325716 GGTTTTCCCTAGTAGTGGTGTCA 59.674 47.826 0.00 0.00 0.00 3.58
1722 1777 7.387122 GCTAGAATGAGTTTGCAGATGATGATA 59.613 37.037 0.00 0.00 0.00 2.15
1733 1788 6.703607 TGATTAGCTAGCTAGAATGAGTTTGC 59.296 38.462 25.15 5.56 0.00 3.68
1762 1817 2.373938 CTACCGCAGCTAGTGTTGC 58.626 57.895 0.00 6.10 45.13 4.17
1870 1925 6.694877 ATGAGTTTGAAGATGATGATGTGG 57.305 37.500 0.00 0.00 0.00 4.17
1970 2025 1.159285 TGCTCCAACTTGATGAAGCG 58.841 50.000 0.00 0.00 31.68 4.68
2216 2274 6.331061 ACTATACGATGTTCTTCAACAGGAC 58.669 40.000 0.00 0.00 45.85 3.85
2217 2275 6.525578 ACTATACGATGTTCTTCAACAGGA 57.474 37.500 0.00 0.00 45.85 3.86
2294 2352 9.444600 GGTAAGATGTTTACTATTTGTCCTCAA 57.555 33.333 0.00 0.00 0.00 3.02
2477 2535 6.371809 TTGACAGCTTATTTTCGTTCAACT 57.628 33.333 0.00 0.00 0.00 3.16
2478 2536 8.227791 TCTATTGACAGCTTATTTTCGTTCAAC 58.772 33.333 0.00 0.00 0.00 3.18
2619 2678 8.648557 ATTCGTTCGAAAGATGATATTGAAGA 57.351 30.769 14.54 0.00 41.60 2.87
2635 2694 6.477688 GGTTATCACCTTTGATATTCGTTCGA 59.522 38.462 0.00 0.00 43.02 3.71
2667 2726 4.367386 GCAAGACTTATGCATTTGAGCT 57.633 40.909 3.54 0.00 43.29 4.09
2721 2780 3.671008 ATACAACGCAGACACCTACAA 57.329 42.857 0.00 0.00 0.00 2.41
2774 2834 7.798071 TGGAGGTAAAGAGAGTTTACTTGAAA 58.202 34.615 7.40 0.00 35.73 2.69
2838 2898 3.826157 CCCTACCATGCAAGAGTTTTTGA 59.174 43.478 0.00 0.00 0.00 2.69
2856 2916 6.633325 ACTATTCTACTAGCGTATCCCCTA 57.367 41.667 0.00 0.00 0.00 3.53
2959 3035 2.801111 GGACGAGAACTTTGAAGTGGAC 59.199 50.000 0.00 0.00 39.66 4.02
2985 3061 0.598419 TGATAGGCGCTTCAGCATCG 60.598 55.000 7.64 0.00 42.21 3.84
3030 3106 3.403057 GCAAAGACGAGCGCGACA 61.403 61.111 19.05 0.00 41.64 4.35
3094 3170 9.959749 TTTCAGTTAATGTTTCAACTATGAACC 57.040 29.630 0.00 0.00 45.01 3.62
3170 3247 7.744733 TGTGCCAGAATATGTAGGAAATATCA 58.255 34.615 0.00 0.00 0.00 2.15
3331 3408 1.298340 CCAAGTGGCCGGTCATGTA 59.702 57.895 14.23 0.00 0.00 2.29
3356 3433 5.756195 TGTGTTGCTCAAATAGGATATGC 57.244 39.130 0.00 0.00 0.00 3.14
3511 3588 7.125536 AGTGATAATATTCGACGATGTACGA 57.874 36.000 0.00 0.00 45.77 3.43
3592 3675 2.491152 GCCGATACCCGTCGTTCA 59.509 61.111 0.00 0.00 39.89 3.18
3768 3852 4.344865 GGCTTGAGGACCCCGCAA 62.345 66.667 2.41 2.41 40.75 4.85
3930 4015 1.203441 TGGAGGATGCCTGCTTGACT 61.203 55.000 6.54 0.00 42.66 3.41
4388 4514 7.639113 TTAGTTGCATCAAATTAGTTAGGGG 57.361 36.000 0.00 0.00 0.00 4.79
4529 4661 3.064324 GATGCCGCCCTTTGCTGT 61.064 61.111 0.00 0.00 38.05 4.40
4531 4663 4.408821 TCGATGCCGCCCTTTGCT 62.409 61.111 0.00 0.00 38.05 3.91
4534 4666 3.682292 GACCTCGATGCCGCCCTTT 62.682 63.158 0.00 0.00 35.37 3.11
4535 4667 4.162690 GACCTCGATGCCGCCCTT 62.163 66.667 0.00 0.00 35.37 3.95
4611 4771 4.643387 GCCCACCGCACACCTTCT 62.643 66.667 0.00 0.00 37.47 2.85
4746 4910 3.056313 GCACTTCCTGGAATGCGCC 62.056 63.158 20.26 0.00 0.00 6.53
5062 5237 4.391830 CAGTAGCACGCCTGAAGATAAAAA 59.608 41.667 0.00 0.00 0.00 1.94
5230 5411 0.697658 TGACCACCTCAATGCCATCA 59.302 50.000 0.00 0.00 0.00 3.07
5320 5501 6.258727 ACATAAACCATAAAGCAGACTCGATG 59.741 38.462 0.00 0.00 0.00 3.84
5345 5526 9.154847 CATACAGATAGTTCAATCAGTTCAACA 57.845 33.333 0.00 0.00 29.57 3.33
5355 5536 7.568349 ACCACACATCATACAGATAGTTCAAT 58.432 34.615 0.00 0.00 34.43 2.57
5366 5547 9.143155 AGATAACATAGTACCACACATCATACA 57.857 33.333 0.00 0.00 0.00 2.29
5367 5548 9.411801 CAGATAACATAGTACCACACATCATAC 57.588 37.037 0.00 0.00 0.00 2.39
5433 5620 4.503123 CCATGTACCACACATCATACCGAT 60.503 45.833 0.00 0.00 44.99 4.18
5435 5622 3.130633 CCATGTACCACACATCATACCG 58.869 50.000 0.00 0.00 44.99 4.02
5436 5623 4.150897 ACCATGTACCACACATCATACC 57.849 45.455 0.00 0.00 44.99 2.73
5437 5624 4.941263 ACAACCATGTACCACACATCATAC 59.059 41.667 0.00 0.00 44.99 2.39
5558 5753 0.106521 GGTGTTTGGTTGCCTGCATT 59.893 50.000 0.00 0.00 0.00 3.56
5645 5841 2.906389 TCTCAACTCAGCCTGGTTATGT 59.094 45.455 0.00 0.00 0.00 2.29
5697 5896 2.238521 CTATGGGTGTGTTTGGTTGCT 58.761 47.619 0.00 0.00 0.00 3.91
5710 5909 3.866656 CCGTCTGGATCCCCTATGGGT 62.867 61.905 9.90 0.00 45.69 4.51
5723 5922 2.093181 TCATGAATTACCACCCGTCTGG 60.093 50.000 0.00 0.00 41.37 3.86
5727 5926 1.406341 CGGTCATGAATTACCACCCGT 60.406 52.381 0.00 0.00 35.35 5.28
5728 5927 1.295792 CGGTCATGAATTACCACCCG 58.704 55.000 0.00 0.00 35.35 5.28
5802 6001 6.602009 CGATTTTCCCAGGTTTTACTATTCCT 59.398 38.462 0.00 0.00 0.00 3.36
5804 6003 7.387119 ACGATTTTCCCAGGTTTTACTATTC 57.613 36.000 0.00 0.00 0.00 1.75
5827 6026 7.267600 CACTCGTATTTAACCGTTCATCAAAAC 59.732 37.037 0.00 0.00 0.00 2.43
5837 6037 4.708726 AGTAGCACTCGTATTTAACCGT 57.291 40.909 0.00 0.00 0.00 4.83
5882 6082 7.915508 TCTATAAAAATATGGCACTTGACGTG 58.084 34.615 0.00 0.00 46.58 4.49
5884 6084 8.826710 TCTTCTATAAAAATATGGCACTTGACG 58.173 33.333 0.00 0.00 0.00 4.35
5923 6126 7.769044 TGGGATTACATTGTTTAGTAGCTCTTC 59.231 37.037 0.00 0.00 0.00 2.87
5972 6175 6.663523 CAGGGTGTTATCCTGGATTAGTTTTT 59.336 38.462 15.55 0.00 45.95 1.94
5973 6176 6.187682 CAGGGTGTTATCCTGGATTAGTTTT 58.812 40.000 15.55 0.00 45.95 2.43
5974 6177 5.755849 CAGGGTGTTATCCTGGATTAGTTT 58.244 41.667 15.55 0.00 45.95 2.66
5975 6178 5.373812 CAGGGTGTTATCCTGGATTAGTT 57.626 43.478 15.55 0.00 45.95 2.24
6029 6257 2.544694 GCAGTGGATCACGGATAGACAG 60.545 54.545 0.00 0.00 39.64 3.51
6030 6261 1.409064 GCAGTGGATCACGGATAGACA 59.591 52.381 0.00 0.00 39.64 3.41
6039 6270 8.931385 ATGTTTAAATAAATGCAGTGGATCAC 57.069 30.769 0.00 0.00 34.10 3.06
6047 6278 8.686397 TGTGCTGTATGTTTAAATAAATGCAG 57.314 30.769 15.74 15.74 0.00 4.41
6057 6290 3.436704 GCTGAGCTGTGCTGTATGTTTAA 59.563 43.478 0.00 0.00 39.88 1.52
6073 6306 0.604780 TGACTGGCTTCTTGCTGAGC 60.605 55.000 0.00 0.00 42.39 4.26
6080 6313 0.036022 GGCTGTCTGACTGGCTTCTT 59.964 55.000 26.49 0.00 39.07 2.52
6109 6350 1.814634 GCTGATGATGCCTGCTAAGCT 60.815 52.381 0.00 0.00 0.00 3.74
6171 6416 3.156288 TCATAGGCCTACGATGTAGCT 57.844 47.619 16.61 0.00 34.28 3.32
6198 6443 1.542915 CCAACTCTTGATTGGCCTGTG 59.457 52.381 3.32 0.00 40.25 3.66


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

AutoCloner maintained by Alex Coulton.