Multiple sequence alignment - TraesCS7D01G274700

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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 TraesCS7D01G274700 chr7D 100.000 2942 0 0 1 2942 264318784 264321725 0.000000e+00 5433.0
1 TraesCS7D01G274700 chr7A 94.323 1550 67 12 1159 2697 287848810 287850349 0.000000e+00 2355.0
2 TraesCS7D01G274700 chr7A 99.355 155 1 0 2778 2932 735617740 735617586 6.210000e-72 281.0
3 TraesCS7D01G274700 chr4D 97.664 1156 25 2 1 1154 467596809 467595654 0.000000e+00 1984.0
4 TraesCS7D01G274700 chr4D 97.165 1164 32 1 1 1163 3273628 3274791 0.000000e+00 1965.0
5 TraesCS7D01G274700 chr4D 96.129 155 6 0 2778 2932 333462715 333462561 1.350000e-63 254.0
6 TraesCS7D01G274700 chr5D 97.502 1161 27 2 1 1160 27352425 27353584 0.000000e+00 1982.0
7 TraesCS7D01G274700 chr5D 97.246 1162 31 1 1 1161 432155343 432156504 0.000000e+00 1967.0
8 TraesCS7D01G274700 chr2D 96.954 1149 33 2 11 1157 377505792 377506940 0.000000e+00 1927.0
9 TraesCS7D01G274700 chr2D 98.026 152 3 0 2781 2932 346097452 346097603 6.250000e-67 265.0
10 TraesCS7D01G274700 chr5B 96.389 1163 37 4 1 1160 316618123 316616963 0.000000e+00 1910.0
11 TraesCS7D01G274700 chr5B 92.529 174 10 3 2766 2939 434912037 434912207 2.260000e-61 246.0
12 TraesCS7D01G274700 chr4B 96.752 1139 35 2 23 1160 400687270 400686133 0.000000e+00 1897.0
13 TraesCS7D01G274700 chr7B 91.101 1326 81 17 1159 2473 244635842 244637141 0.000000e+00 1760.0
14 TraesCS7D01G274700 chr7B 93.610 1158 69 5 1 1156 695340452 695339298 0.000000e+00 1724.0
15 TraesCS7D01G274700 chr7B 87.349 166 16 2 2617 2777 244640300 244640465 5.010000e-43 185.0
16 TraesCS7D01G274700 chr7B 88.496 113 11 2 2504 2614 244637141 244637253 5.110000e-28 135.0
17 TraesCS7D01G274700 chr6A 93.643 1164 71 3 1 1162 464505650 464506812 0.000000e+00 1736.0
18 TraesCS7D01G274700 chr6A 87.013 1001 124 5 1204 2199 34281996 34280997 0.000000e+00 1123.0
19 TraesCS7D01G274700 chr6A 85.563 1039 144 6 1164 2199 34284054 34283019 0.000000e+00 1083.0
20 TraesCS7D01G274700 chr6A 95.062 162 8 0 2781 2942 522344032 522344193 3.760000e-64 255.0
21 TraesCS7D01G274700 chr6A 83.654 104 12 2 2203 2306 34280948 34280850 3.120000e-15 93.5
22 TraesCS7D01G274700 chr6A 83.516 91 10 2 2216 2306 34393522 34393437 2.430000e-11 80.5
23 TraesCS7D01G274700 chr6B 86.230 1024 127 6 1189 2199 62692718 62691696 0.000000e+00 1098.0
24 TraesCS7D01G274700 chr6B 86.037 1017 135 4 1189 2199 62635904 62634889 0.000000e+00 1085.0
25 TraesCS7D01G274700 chr3D 85.308 1055 141 13 1164 2209 583289750 583288701 0.000000e+00 1077.0
26 TraesCS7D01G274700 chr3D 85.135 1036 148 6 1166 2197 583181382 583180349 0.000000e+00 1055.0
27 TraesCS7D01G274700 chr3D 83.477 1047 144 22 1166 2208 583224694 583223673 0.000000e+00 948.0
28 TraesCS7D01G274700 chr3D 85.621 153 21 1 2615 2766 583222012 583221860 3.030000e-35 159.0
29 TraesCS7D01G274700 chr3D 78.818 203 36 5 2215 2415 583288642 583288445 2.380000e-26 130.0
30 TraesCS7D01G274700 chr3D 83.333 96 13 1 2215 2310 583276891 583276799 5.220000e-13 86.1
31 TraesCS7D01G274700 chr3D 81.373 102 16 2 2215 2316 583168758 583168660 2.430000e-11 80.5
32 TraesCS7D01G274700 chr3D 100.000 33 0 0 2205 2237 583180301 583180269 8.800000e-06 62.1
33 TraesCS7D01G274700 chr3D 100.000 33 0 0 2205 2237 583283171 583283139 8.800000e-06 62.1
34 TraesCS7D01G274700 chr3B 85.535 1037 142 8 1166 2197 780301827 780300794 0.000000e+00 1077.0
35 TraesCS7D01G274700 chr3B 84.314 153 23 1 2615 2766 780299047 780298895 6.570000e-32 148.0
36 TraesCS7D01G274700 chr3B 80.296 203 33 4 2215 2415 780354286 780354089 2.360000e-31 147.0
37 TraesCS7D01G274700 chr3B 83.019 159 26 1 2618 2775 780201073 780200915 3.060000e-30 143.0
38 TraesCS7D01G274700 chr3B 86.614 127 16 1 2620 2745 780317726 780317600 3.950000e-29 139.0
39 TraesCS7D01G274700 chr3B 86.614 127 16 1 2620 2745 780323100 780322974 3.950000e-29 139.0
40 TraesCS7D01G274700 chr3B 86.614 127 16 1 2620 2745 780327705 780327579 3.950000e-29 139.0
41 TraesCS7D01G274700 chr3B 85.827 127 17 1 2620 2745 780313120 780312994 1.840000e-27 134.0
42 TraesCS7D01G274700 chr3A 94.186 172 9 1 2771 2942 357576746 357576576 8.090000e-66 261.0
43 TraesCS7D01G274700 chr4A 95.062 162 8 0 2781 2942 596753514 596753353 3.760000e-64 255.0
44 TraesCS7D01G274700 chr4A 93.939 165 10 0 2778 2942 5929776 5929940 1.750000e-62 250.0
45 TraesCS7D01G274700 chr6D 96.129 155 6 0 2778 2932 328353433 328353279 1.350000e-63 254.0
46 TraesCS7D01G274700 chrUn 86.154 130 17 1 2617 2745 352586707 352586836 3.950000e-29 139.0


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 TraesCS7D01G274700 chr7D 264318784 264321725 2941 False 5433.000000 5433 100.0000 1 2942 1 chr7D.!!$F1 2941
1 TraesCS7D01G274700 chr7A 287848810 287850349 1539 False 2355.000000 2355 94.3230 1159 2697 1 chr7A.!!$F1 1538
2 TraesCS7D01G274700 chr4D 467595654 467596809 1155 True 1984.000000 1984 97.6640 1 1154 1 chr4D.!!$R2 1153
3 TraesCS7D01G274700 chr4D 3273628 3274791 1163 False 1965.000000 1965 97.1650 1 1163 1 chr4D.!!$F1 1162
4 TraesCS7D01G274700 chr5D 27352425 27353584 1159 False 1982.000000 1982 97.5020 1 1160 1 chr5D.!!$F1 1159
5 TraesCS7D01G274700 chr5D 432155343 432156504 1161 False 1967.000000 1967 97.2460 1 1161 1 chr5D.!!$F2 1160
6 TraesCS7D01G274700 chr2D 377505792 377506940 1148 False 1927.000000 1927 96.9540 11 1157 1 chr2D.!!$F2 1146
7 TraesCS7D01G274700 chr5B 316616963 316618123 1160 True 1910.000000 1910 96.3890 1 1160 1 chr5B.!!$R1 1159
8 TraesCS7D01G274700 chr4B 400686133 400687270 1137 True 1897.000000 1897 96.7520 23 1160 1 chr4B.!!$R1 1137
9 TraesCS7D01G274700 chr7B 695339298 695340452 1154 True 1724.000000 1724 93.6100 1 1156 1 chr7B.!!$R1 1155
10 TraesCS7D01G274700 chr7B 244635842 244640465 4623 False 693.333333 1760 88.9820 1159 2777 3 chr7B.!!$F1 1618
11 TraesCS7D01G274700 chr6A 464505650 464506812 1162 False 1736.000000 1736 93.6430 1 1162 1 chr6A.!!$F1 1161
12 TraesCS7D01G274700 chr6A 34280850 34284054 3204 True 766.500000 1123 85.4100 1164 2306 3 chr6A.!!$R2 1142
13 TraesCS7D01G274700 chr6B 62691696 62692718 1022 True 1098.000000 1098 86.2300 1189 2199 1 chr6B.!!$R2 1010
14 TraesCS7D01G274700 chr6B 62634889 62635904 1015 True 1085.000000 1085 86.0370 1189 2199 1 chr6B.!!$R1 1010
15 TraesCS7D01G274700 chr3D 583288445 583289750 1305 True 603.500000 1077 82.0630 1164 2415 2 chr3D.!!$R6 1251
16 TraesCS7D01G274700 chr3D 583180269 583181382 1113 True 558.550000 1055 92.5675 1166 2237 2 chr3D.!!$R4 1071
17 TraesCS7D01G274700 chr3D 583221860 583224694 2834 True 553.500000 948 84.5490 1166 2766 2 chr3D.!!$R5 1600
18 TraesCS7D01G274700 chr3B 780298895 780301827 2932 True 612.500000 1077 84.9245 1166 2766 2 chr3B.!!$R7 1600

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
249 251 2.033911 TTGGCGGATCTGCTTGCA 59.966 55.556 25.27 12.74 34.52 4.08 F
1740 1766 1.075536 TCTCTGCTGGAGTCCACACTA 59.924 52.381 8.12 0.73 42.40 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 1854 0.935898 CTAGCTCCTGCAATTGCTCG 59.064 55.0 29.37 19.83 42.74 5.03 R
2868 9425 0.031515 TCCCTCTTCGGCCAATAGGA 60.032 55.0 16.10 6.54 36.89 2.94 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
205 207 3.770040 CCGGCGGTGATGGACTCA 61.770 66.667 19.97 0.00 0.00 3.41
249 251 2.033911 TTGGCGGATCTGCTTGCA 59.966 55.556 25.27 12.74 34.52 4.08
368 370 2.666098 GGCCCTTTCCCAGCTACGA 61.666 63.158 0.00 0.00 0.00 3.43
1182 1188 3.568007 TGGTACATCAAACCAGAAGTTGC 59.432 43.478 0.00 0.00 42.10 4.17
1217 1236 8.035394 TCTCCTCTCTTTCACAACAATACATAC 58.965 37.037 0.00 0.00 0.00 2.39
1448 1474 1.474478 TCAAGTTAGCTCCTCTCAGCG 59.526 52.381 0.00 0.00 44.82 5.18
1490 1516 4.121317 GAGATGGAATGCTCTCTTGAGTG 58.879 47.826 0.00 0.00 42.13 3.51
1495 1521 3.557898 GGAATGCTCTCTTGAGTGGTTGA 60.558 47.826 0.00 0.00 42.13 3.18
1525 1551 5.798132 ACAGTAACATGCAAGAGATCTTCA 58.202 37.500 0.00 0.00 33.11 3.02
1557 1583 1.669779 GTCATCATCCAAGAGCTGCAC 59.330 52.381 1.02 0.00 0.00 4.57
1558 1584 1.279846 TCATCATCCAAGAGCTGCACA 59.720 47.619 1.02 0.00 0.00 4.57
1641 1667 1.812571 GCGAAGAAGGCCAAGAATCAA 59.187 47.619 5.01 0.00 0.00 2.57
1740 1766 1.075536 TCTCTGCTGGAGTCCACACTA 59.924 52.381 8.12 0.73 42.40 2.74
1744 1770 1.977854 TGCTGGAGTCCACACTACATT 59.022 47.619 8.12 0.00 43.08 2.71
1776 1802 6.073873 CGAAGCAAATTGAAATGCCTAAACAA 60.074 34.615 0.00 0.00 43.57 2.83
2013 2043 9.770097 TTAAGGAATAGCTGATCTTCATACAAG 57.230 33.333 0.00 0.00 0.00 3.16
2168 4231 3.628008 TGGTTAGTCGATCTTGCTCCTA 58.372 45.455 0.00 0.00 0.00 2.94
2288 4407 7.439056 CAGAATGCAACAAAGTCCAAATTAGTT 59.561 33.333 0.00 0.00 0.00 2.24
2289 4408 8.637986 AGAATGCAACAAAGTCCAAATTAGTTA 58.362 29.630 0.00 0.00 0.00 2.24
2416 4537 7.038373 ACAGGATTAACAATAATTTGGGCAAGT 60.038 33.333 0.00 0.00 37.15 3.16
2423 4544 7.494922 ACAATAATTTGGGCAAGTCCTAATT 57.505 32.000 15.34 15.34 42.10 1.40
2424 4545 8.602472 ACAATAATTTGGGCAAGTCCTAATTA 57.398 30.769 17.96 17.96 43.28 1.40
2425 4546 9.041354 ACAATAATTTGGGCAAGTCCTAATTAA 57.959 29.630 19.02 7.77 42.81 1.40
2426 4547 9.533253 CAATAATTTGGGCAAGTCCTAATTAAG 57.467 33.333 19.02 13.12 42.81 1.85
2427 4548 9.487442 AATAATTTGGGCAAGTCCTAATTAAGA 57.513 29.630 19.02 4.81 42.81 2.10
2428 4549 7.790782 AATTTGGGCAAGTCCTAATTAAGAA 57.209 32.000 10.60 0.00 39.31 2.52
2429 4550 7.978099 ATTTGGGCAAGTCCTAATTAAGAAT 57.022 32.000 0.00 0.00 35.09 2.40
2430 4551 7.790782 TTTGGGCAAGTCCTAATTAAGAATT 57.209 32.000 0.00 0.00 35.09 2.17
2502 4654 5.184096 TCAGTACACAAACAACAACCAATGT 59.816 36.000 0.00 0.00 46.82 2.71
2539 4790 2.602660 GCACACATCAAAAGCGTGTTTT 59.397 40.909 0.00 0.00 41.79 2.43
2595 6102 7.364144 GGAGCAGGAAATTGTTCAGGAAATTAT 60.364 37.037 0.00 0.00 35.25 1.28
2629 9181 2.103537 TCTCGATACTCCACGTCACA 57.896 50.000 0.00 0.00 0.00 3.58
2745 9302 9.237846 CTGTAGAAAGAGAAACCAAATTTTGAC 57.762 33.333 10.72 0.00 0.00 3.18
2747 9304 7.423844 AGAAAGAGAAACCAAATTTTGACCT 57.576 32.000 10.72 2.28 0.00 3.85
2748 9305 7.267857 AGAAAGAGAAACCAAATTTTGACCTG 58.732 34.615 10.72 0.00 0.00 4.00
2766 9323 9.829507 TTTGACCTGTTTCAAATTTTGTGATAT 57.170 25.926 8.89 0.00 39.94 1.63
2767 9324 9.474920 TTGACCTGTTTCAAATTTTGTGATATC 57.525 29.630 8.89 0.00 32.42 1.63
2769 9326 9.474920 GACCTGTTTCAAATTTTGTGATATCAA 57.525 29.630 7.07 0.00 0.00 2.57
2830 9387 5.813080 AGCAAATTCGGAAACTATACACC 57.187 39.130 0.00 0.00 0.00 4.16
2831 9388 4.638865 AGCAAATTCGGAAACTATACACCC 59.361 41.667 0.00 0.00 0.00 4.61
2832 9389 4.638865 GCAAATTCGGAAACTATACACCCT 59.361 41.667 0.00 0.00 0.00 4.34
2833 9390 5.818857 GCAAATTCGGAAACTATACACCCTA 59.181 40.000 0.00 0.00 0.00 3.53
2834 9391 6.316890 GCAAATTCGGAAACTATACACCCTAA 59.683 38.462 0.00 0.00 0.00 2.69
2835 9392 7.012989 GCAAATTCGGAAACTATACACCCTAAT 59.987 37.037 0.00 0.00 0.00 1.73
2836 9393 8.342634 CAAATTCGGAAACTATACACCCTAATG 58.657 37.037 0.00 0.00 0.00 1.90
2837 9394 4.952460 TCGGAAACTATACACCCTAATGC 58.048 43.478 0.00 0.00 0.00 3.56
2838 9395 4.406326 TCGGAAACTATACACCCTAATGCA 59.594 41.667 0.00 0.00 0.00 3.96
2839 9396 4.750098 CGGAAACTATACACCCTAATGCAG 59.250 45.833 0.00 0.00 0.00 4.41
2840 9397 5.452776 CGGAAACTATACACCCTAATGCAGA 60.453 44.000 0.00 0.00 0.00 4.26
2841 9398 6.354130 GGAAACTATACACCCTAATGCAGAA 58.646 40.000 0.00 0.00 0.00 3.02
2842 9399 6.826741 GGAAACTATACACCCTAATGCAGAAA 59.173 38.462 0.00 0.00 0.00 2.52
2843 9400 7.338449 GGAAACTATACACCCTAATGCAGAAAA 59.662 37.037 0.00 0.00 0.00 2.29
2844 9401 8.644374 AAACTATACACCCTAATGCAGAAAAA 57.356 30.769 0.00 0.00 0.00 1.94
2845 9402 8.823220 AACTATACACCCTAATGCAGAAAAAT 57.177 30.769 0.00 0.00 0.00 1.82
2846 9403 8.451908 ACTATACACCCTAATGCAGAAAAATC 57.548 34.615 0.00 0.00 0.00 2.17
2847 9404 8.052748 ACTATACACCCTAATGCAGAAAAATCA 58.947 33.333 0.00 0.00 0.00 2.57
2848 9405 7.716799 ATACACCCTAATGCAGAAAAATCAA 57.283 32.000 0.00 0.00 0.00 2.57
2849 9406 6.418057 ACACCCTAATGCAGAAAAATCAAA 57.582 33.333 0.00 0.00 0.00 2.69
2850 9407 6.825610 ACACCCTAATGCAGAAAAATCAAAA 58.174 32.000 0.00 0.00 0.00 2.44
2851 9408 6.930722 ACACCCTAATGCAGAAAAATCAAAAG 59.069 34.615 0.00 0.00 0.00 2.27
2852 9409 6.930722 CACCCTAATGCAGAAAAATCAAAAGT 59.069 34.615 0.00 0.00 0.00 2.66
2853 9410 8.087750 CACCCTAATGCAGAAAAATCAAAAGTA 58.912 33.333 0.00 0.00 0.00 2.24
2854 9411 8.815912 ACCCTAATGCAGAAAAATCAAAAGTAT 58.184 29.630 0.00 0.00 0.00 2.12
2855 9412 9.305925 CCCTAATGCAGAAAAATCAAAAGTATC 57.694 33.333 0.00 0.00 0.00 2.24
2856 9413 9.859427 CCTAATGCAGAAAAATCAAAAGTATCA 57.141 29.630 0.00 0.00 0.00 2.15
2858 9415 8.538409 AATGCAGAAAAATCAAAAGTATCACC 57.462 30.769 0.00 0.00 0.00 4.02
2859 9416 6.454795 TGCAGAAAAATCAAAAGTATCACCC 58.545 36.000 0.00 0.00 0.00 4.61
2860 9417 6.267471 TGCAGAAAAATCAAAAGTATCACCCT 59.733 34.615 0.00 0.00 0.00 4.34
2861 9418 6.587608 GCAGAAAAATCAAAAGTATCACCCTG 59.412 38.462 0.00 0.00 0.00 4.45
2862 9419 7.661040 CAGAAAAATCAAAAGTATCACCCTGT 58.339 34.615 0.00 0.00 0.00 4.00
2863 9420 7.809806 CAGAAAAATCAAAAGTATCACCCTGTC 59.190 37.037 0.00 0.00 0.00 3.51
2864 9421 5.880054 AAATCAAAAGTATCACCCTGTCG 57.120 39.130 0.00 0.00 0.00 4.35
2865 9422 3.328382 TCAAAAGTATCACCCTGTCGG 57.672 47.619 0.00 0.00 37.81 4.79
2866 9423 1.737793 CAAAAGTATCACCCTGTCGGC 59.262 52.381 0.00 0.00 33.26 5.54
2867 9424 0.252197 AAAGTATCACCCTGTCGGCC 59.748 55.000 0.00 0.00 33.26 6.13
2868 9425 0.617820 AAGTATCACCCTGTCGGCCT 60.618 55.000 0.00 0.00 33.26 5.19
2869 9426 1.043673 AGTATCACCCTGTCGGCCTC 61.044 60.000 0.00 0.00 33.26 4.70
2870 9427 1.760875 TATCACCCTGTCGGCCTCC 60.761 63.158 0.00 0.00 33.26 4.30
2871 9428 2.238319 TATCACCCTGTCGGCCTCCT 62.238 60.000 0.00 0.00 33.26 3.69
2872 9429 2.238319 ATCACCCTGTCGGCCTCCTA 62.238 60.000 0.00 0.00 33.26 2.94
2873 9430 1.762460 CACCCTGTCGGCCTCCTAT 60.762 63.158 0.00 0.00 33.26 2.57
2874 9431 1.003051 ACCCTGTCGGCCTCCTATT 59.997 57.895 0.00 0.00 33.26 1.73
2875 9432 1.338136 ACCCTGTCGGCCTCCTATTG 61.338 60.000 0.00 0.00 33.26 1.90
2876 9433 1.447643 CCTGTCGGCCTCCTATTGG 59.552 63.158 0.00 0.00 0.00 3.16
2882 9439 4.464262 GCCTCCTATTGGCCGAAG 57.536 61.111 0.00 0.00 44.32 3.79
2883 9440 1.830145 GCCTCCTATTGGCCGAAGA 59.170 57.895 0.00 0.00 44.32 2.87
2884 9441 0.250081 GCCTCCTATTGGCCGAAGAG 60.250 60.000 0.00 3.85 44.32 2.85
2885 9442 0.394565 CCTCCTATTGGCCGAAGAGG 59.605 60.000 18.13 18.13 43.55 3.69
2886 9443 0.394565 CTCCTATTGGCCGAAGAGGG 59.605 60.000 21.15 11.35 42.58 4.30
2887 9444 0.031515 TCCTATTGGCCGAAGAGGGA 60.032 55.000 21.15 13.03 42.58 4.20
2888 9445 0.106894 CCTATTGGCCGAAGAGGGAC 59.893 60.000 16.46 0.00 39.14 4.46
2889 9446 4.639674 TCCTATTGGCCGAAGAGGGACT 62.640 54.545 21.15 0.00 42.58 3.85
2890 9447 1.486726 CTATTGGCCGAAGAGGGACTT 59.513 52.381 0.00 0.00 41.55 3.01
2891 9448 0.698818 ATTGGCCGAAGAGGGACTTT 59.301 50.000 0.00 0.00 41.55 2.66
2892 9449 0.476771 TTGGCCGAAGAGGGACTTTT 59.523 50.000 0.00 0.00 41.55 2.27
2893 9450 0.476771 TGGCCGAAGAGGGACTTTTT 59.523 50.000 0.00 0.00 41.55 1.94
2894 9451 0.881796 GGCCGAAGAGGGACTTTTTG 59.118 55.000 0.00 0.00 41.55 2.44
2896 9453 0.881796 CCGAAGAGGGACTTTTTGGC 59.118 55.000 0.00 0.00 45.37 4.52
2897 9454 0.881796 CGAAGAGGGACTTTTTGGCC 59.118 55.000 0.00 0.00 41.55 5.36
2898 9455 1.545651 CGAAGAGGGACTTTTTGGCCT 60.546 52.381 3.32 0.00 45.52 5.19
2899 9456 2.290071 CGAAGAGGGACTTTTTGGCCTA 60.290 50.000 3.32 0.00 45.52 3.93
2900 9457 2.881111 AGAGGGACTTTTTGGCCTAC 57.119 50.000 3.32 0.00 45.52 3.18
2901 9458 1.354705 AGAGGGACTTTTTGGCCTACC 59.645 52.381 3.32 0.00 45.52 3.18
2902 9459 1.074889 GAGGGACTTTTTGGCCTACCA 59.925 52.381 3.32 0.00 45.52 3.25
2903 9460 1.716503 AGGGACTTTTTGGCCTACCAT 59.283 47.619 3.32 0.00 41.34 3.55
2904 9461 2.111792 AGGGACTTTTTGGCCTACCATT 59.888 45.455 3.32 0.00 41.34 3.16
2905 9462 4.071680 AGGGACTTTTTGGCCTACCATTG 61.072 47.826 3.32 0.00 41.34 2.82
2912 9469 3.827634 GCCTACCATTGGCCGAAG 58.172 61.111 1.54 0.00 44.32 3.79
2913 9470 1.223487 GCCTACCATTGGCCGAAGA 59.777 57.895 1.54 0.00 44.32 2.87
2914 9471 0.815615 GCCTACCATTGGCCGAAGAG 60.816 60.000 1.54 0.00 44.32 2.85
2915 9472 0.179045 CCTACCATTGGCCGAAGAGG 60.179 60.000 1.54 1.95 44.97 3.69
2916 9473 0.179045 CTACCATTGGCCGAAGAGGG 60.179 60.000 1.54 7.81 41.48 4.30
2917 9474 0.619255 TACCATTGGCCGAAGAGGGA 60.619 55.000 1.54 2.88 41.48 4.20
2918 9475 1.452108 CCATTGGCCGAAGAGGGAC 60.452 63.158 0.00 0.00 41.48 4.46
2920 9477 0.035056 CATTGGCCGAAGAGGGACTT 60.035 55.000 0.00 0.00 41.55 3.01
2921 9478 0.698818 ATTGGCCGAAGAGGGACTTT 59.301 50.000 0.00 0.00 41.55 2.66
2922 9479 0.476771 TTGGCCGAAGAGGGACTTTT 59.523 50.000 0.00 0.00 41.55 2.27
2923 9480 0.036306 TGGCCGAAGAGGGACTTTTC 59.964 55.000 0.00 0.00 44.82 2.29
2927 9484 2.855887 GAAGAGGGACTTTTCGGCC 58.144 57.895 0.00 0.00 39.71 6.13
2928 9485 0.325272 GAAGAGGGACTTTTCGGCCT 59.675 55.000 0.00 0.00 39.71 5.19
2929 9486 1.553704 GAAGAGGGACTTTTCGGCCTA 59.446 52.381 0.00 0.00 39.71 3.93
2930 9487 0.903236 AGAGGGACTTTTCGGCCTAC 59.097 55.000 0.00 0.00 41.55 3.18
2931 9488 0.107800 GAGGGACTTTTCGGCCTACC 60.108 60.000 0.00 0.00 41.55 3.18
2932 9489 0.838987 AGGGACTTTTCGGCCTACCA 60.839 55.000 0.00 0.00 27.25 3.25
2933 9490 0.255033 GGGACTTTTCGGCCTACCAT 59.745 55.000 0.00 0.00 34.57 3.55
2934 9491 1.340697 GGGACTTTTCGGCCTACCATT 60.341 52.381 0.00 0.00 34.57 3.16
2935 9492 2.014857 GGACTTTTCGGCCTACCATTC 58.985 52.381 0.00 0.00 34.57 2.67
2936 9493 1.664151 GACTTTTCGGCCTACCATTCG 59.336 52.381 0.00 0.00 34.57 3.34
2937 9494 0.377203 CTTTTCGGCCTACCATTCGC 59.623 55.000 0.00 0.00 34.57 4.70
2938 9495 1.027792 TTTTCGGCCTACCATTCGCC 61.028 55.000 0.00 0.00 39.41 5.54
2941 9498 2.188469 GGCCTACCATTCGCCGAA 59.812 61.111 0.33 0.33 35.26 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
175 177 4.309950 GCCGGACCTCCACACGTT 62.310 66.667 5.05 0.00 35.14 3.99
368 370 4.310672 GCGAGACGAGCGATGAAT 57.689 55.556 0.00 0.00 0.00 2.57
1182 1188 4.399303 GTGAAAGAGAGGAGAAGAGGAGAG 59.601 50.000 0.00 0.00 0.00 3.20
1217 1236 6.489361 AGCCATATCTAATCTGGAAGCTTTTG 59.511 38.462 0.00 0.00 31.38 2.44
1329 1355 5.279506 GCCGATGGTAATGGAAGAAGAGATA 60.280 44.000 0.00 0.00 0.00 1.98
1448 1474 2.774234 TCTCCATCCAACATCTTCCTCC 59.226 50.000 0.00 0.00 0.00 4.30
1490 1516 4.392138 GCATGTTACTGTAGAGGTTCAACC 59.608 45.833 0.00 0.00 38.99 3.77
1495 1521 5.246203 TCTCTTGCATGTTACTGTAGAGGTT 59.754 40.000 6.46 0.00 32.55 3.50
1525 1551 5.039920 TGGATGATGACCTTCATTTCGAT 57.960 39.130 0.00 0.00 37.20 3.59
1557 1583 1.283029 TCCCCTTTTCTCAGAGCCATG 59.717 52.381 0.00 0.00 0.00 3.66
1558 1584 1.673767 TCCCCTTTTCTCAGAGCCAT 58.326 50.000 0.00 0.00 0.00 4.40
1641 1667 5.823045 AGTCTTTTTCGTGGTCTTCTTGAAT 59.177 36.000 0.00 0.00 0.00 2.57
1744 1770 5.175491 GCATTTCAATTTGCTTCGACAAGAA 59.825 36.000 0.00 0.00 35.95 2.52
1827 1854 0.935898 CTAGCTCCTGCAATTGCTCG 59.064 55.000 29.37 19.83 42.74 5.03
2168 4231 3.449377 TGATCTGGCATGTTTCATGCATT 59.551 39.130 27.76 14.07 46.21 3.56
2306 4426 5.361571 TGCTTAAATGATGCAGATGGTGATT 59.638 36.000 0.00 0.00 33.49 2.57
2416 4537 8.330466 TCGCAAGTTTGAATTCTTAATTAGGA 57.670 30.769 7.05 0.00 39.48 2.94
2423 4544 3.190535 GCCCTCGCAAGTTTGAATTCTTA 59.809 43.478 7.05 0.00 39.48 2.10
2424 4545 2.029918 GCCCTCGCAAGTTTGAATTCTT 60.030 45.455 7.05 0.00 39.48 2.52
2425 4546 1.541588 GCCCTCGCAAGTTTGAATTCT 59.458 47.619 7.05 0.00 39.48 2.40
2426 4547 1.729149 CGCCCTCGCAAGTTTGAATTC 60.729 52.381 0.00 0.00 39.48 2.17
2427 4548 0.240945 CGCCCTCGCAAGTTTGAATT 59.759 50.000 0.00 0.00 39.48 2.17
2428 4549 1.875963 CGCCCTCGCAAGTTTGAAT 59.124 52.632 0.00 0.00 39.48 2.57
2429 4550 3.339731 CGCCCTCGCAAGTTTGAA 58.660 55.556 0.00 0.00 39.48 2.69
2502 4654 8.005192 TGATGTGTGCCAATAAGCATATAAAA 57.995 30.769 0.00 0.00 46.24 1.52
2539 4790 7.785033 TGAAGATCTCTTATGAGCATGTACAA 58.215 34.615 0.00 0.00 40.03 2.41
2550 6056 6.522946 TGCTCCATTCTGAAGATCTCTTATG 58.477 40.000 0.00 0.00 36.11 1.90
2553 6059 4.141665 CCTGCTCCATTCTGAAGATCTCTT 60.142 45.833 0.00 0.00 39.23 2.85
2595 6102 6.982852 AGTATCGAGAAACTCTGTTCTGAAA 58.017 36.000 0.00 0.00 37.98 2.69
2629 9181 4.885426 CCAATCGCAGGGCATAGT 57.115 55.556 0.00 0.00 0.00 2.12
2649 9201 1.405463 GCTAATCCTCAAAAAGGCGGG 59.595 52.381 0.00 0.00 45.78 6.13
2719 9271 9.237846 GTCAAAATTTGGTTTCTCTTTCTACAG 57.762 33.333 5.83 0.00 0.00 2.74
2721 9273 8.414003 AGGTCAAAATTTGGTTTCTCTTTCTAC 58.586 33.333 5.83 0.00 0.00 2.59
2804 9361 9.048446 GGTGTATAGTTTCCGAATTTGCTATAA 57.952 33.333 0.00 0.00 0.00 0.98
2805 9362 7.658575 GGGTGTATAGTTTCCGAATTTGCTATA 59.341 37.037 0.00 0.00 0.00 1.31
2806 9363 6.485648 GGGTGTATAGTTTCCGAATTTGCTAT 59.514 38.462 0.00 0.00 0.00 2.97
2807 9364 5.818857 GGGTGTATAGTTTCCGAATTTGCTA 59.181 40.000 0.00 0.00 0.00 3.49
2808 9365 4.638865 GGGTGTATAGTTTCCGAATTTGCT 59.361 41.667 0.00 0.00 0.00 3.91
2809 9366 4.638865 AGGGTGTATAGTTTCCGAATTTGC 59.361 41.667 0.00 0.00 0.00 3.68
2810 9367 7.852971 TTAGGGTGTATAGTTTCCGAATTTG 57.147 36.000 0.00 0.00 0.00 2.32
2811 9368 7.012989 GCATTAGGGTGTATAGTTTCCGAATTT 59.987 37.037 0.00 0.00 0.00 1.82
2812 9369 6.485648 GCATTAGGGTGTATAGTTTCCGAATT 59.514 38.462 0.00 0.00 0.00 2.17
2813 9370 5.995897 GCATTAGGGTGTATAGTTTCCGAAT 59.004 40.000 0.00 0.00 0.00 3.34
2814 9371 5.104859 TGCATTAGGGTGTATAGTTTCCGAA 60.105 40.000 0.00 0.00 0.00 4.30
2815 9372 4.406326 TGCATTAGGGTGTATAGTTTCCGA 59.594 41.667 0.00 0.00 0.00 4.55
2816 9373 4.699637 TGCATTAGGGTGTATAGTTTCCG 58.300 43.478 0.00 0.00 0.00 4.30
2817 9374 5.925509 TCTGCATTAGGGTGTATAGTTTCC 58.074 41.667 0.00 0.00 0.00 3.13
2818 9375 7.859325 TTTCTGCATTAGGGTGTATAGTTTC 57.141 36.000 0.00 0.00 0.00 2.78
2819 9376 8.644374 TTTTTCTGCATTAGGGTGTATAGTTT 57.356 30.769 0.00 0.00 0.00 2.66
2820 9377 8.823220 ATTTTTCTGCATTAGGGTGTATAGTT 57.177 30.769 0.00 0.00 0.00 2.24
2821 9378 8.052748 TGATTTTTCTGCATTAGGGTGTATAGT 58.947 33.333 0.00 0.00 0.00 2.12
2822 9379 8.450578 TGATTTTTCTGCATTAGGGTGTATAG 57.549 34.615 0.00 0.00 0.00 1.31
2823 9380 8.815565 TTGATTTTTCTGCATTAGGGTGTATA 57.184 30.769 0.00 0.00 0.00 1.47
2824 9381 7.716799 TTGATTTTTCTGCATTAGGGTGTAT 57.283 32.000 0.00 0.00 0.00 2.29
2825 9382 7.531857 TTTGATTTTTCTGCATTAGGGTGTA 57.468 32.000 0.00 0.00 0.00 2.90
2826 9383 6.418057 TTTGATTTTTCTGCATTAGGGTGT 57.582 33.333 0.00 0.00 0.00 4.16
2827 9384 6.930722 ACTTTTGATTTTTCTGCATTAGGGTG 59.069 34.615 0.00 0.00 0.00 4.61
2828 9385 7.066307 ACTTTTGATTTTTCTGCATTAGGGT 57.934 32.000 0.00 0.00 0.00 4.34
2829 9386 9.305925 GATACTTTTGATTTTTCTGCATTAGGG 57.694 33.333 0.00 0.00 0.00 3.53
2830 9387 9.859427 TGATACTTTTGATTTTTCTGCATTAGG 57.141 29.630 0.00 0.00 0.00 2.69
2832 9389 9.638239 GGTGATACTTTTGATTTTTCTGCATTA 57.362 29.630 0.00 0.00 0.00 1.90
2833 9390 7.603784 GGGTGATACTTTTGATTTTTCTGCATT 59.396 33.333 0.00 0.00 0.00 3.56
2834 9391 7.038799 AGGGTGATACTTTTGATTTTTCTGCAT 60.039 33.333 0.00 0.00 0.00 3.96
2835 9392 6.267471 AGGGTGATACTTTTGATTTTTCTGCA 59.733 34.615 0.00 0.00 0.00 4.41
2836 9393 6.587608 CAGGGTGATACTTTTGATTTTTCTGC 59.412 38.462 0.00 0.00 0.00 4.26
2837 9394 7.661040 ACAGGGTGATACTTTTGATTTTTCTG 58.339 34.615 0.00 0.00 0.00 3.02
2838 9395 7.308589 CGACAGGGTGATACTTTTGATTTTTCT 60.309 37.037 0.00 0.00 0.00 2.52
2839 9396 6.801862 CGACAGGGTGATACTTTTGATTTTTC 59.198 38.462 0.00 0.00 0.00 2.29
2840 9397 6.294508 CCGACAGGGTGATACTTTTGATTTTT 60.295 38.462 0.00 0.00 0.00 1.94
2841 9398 5.183140 CCGACAGGGTGATACTTTTGATTTT 59.817 40.000 0.00 0.00 0.00 1.82
2842 9399 4.700213 CCGACAGGGTGATACTTTTGATTT 59.300 41.667 0.00 0.00 0.00 2.17
2843 9400 4.261801 CCGACAGGGTGATACTTTTGATT 58.738 43.478 0.00 0.00 0.00 2.57
2844 9401 3.873910 CCGACAGGGTGATACTTTTGAT 58.126 45.455 0.00 0.00 0.00 2.57
2845 9402 2.614481 GCCGACAGGGTGATACTTTTGA 60.614 50.000 0.00 0.00 38.44 2.69
2846 9403 1.737793 GCCGACAGGGTGATACTTTTG 59.262 52.381 0.00 0.00 38.44 2.44
2847 9404 1.339727 GGCCGACAGGGTGATACTTTT 60.340 52.381 0.00 0.00 38.44 2.27
2848 9405 0.252197 GGCCGACAGGGTGATACTTT 59.748 55.000 0.00 0.00 38.44 2.66
2849 9406 0.617820 AGGCCGACAGGGTGATACTT 60.618 55.000 0.00 0.00 38.44 2.24
2850 9407 1.001760 AGGCCGACAGGGTGATACT 59.998 57.895 0.00 0.00 38.44 2.12
2851 9408 1.442148 GAGGCCGACAGGGTGATAC 59.558 63.158 0.00 0.00 38.44 2.24
2852 9409 1.760875 GGAGGCCGACAGGGTGATA 60.761 63.158 0.00 0.00 38.44 2.15
2853 9410 2.238319 TAGGAGGCCGACAGGGTGAT 62.238 60.000 0.00 0.00 38.44 3.06
2854 9411 2.238319 ATAGGAGGCCGACAGGGTGA 62.238 60.000 0.00 0.00 38.44 4.02
2855 9412 1.338136 AATAGGAGGCCGACAGGGTG 61.338 60.000 0.00 0.00 38.44 4.61
2856 9413 1.003051 AATAGGAGGCCGACAGGGT 59.997 57.895 0.00 0.00 38.44 4.34
2857 9414 1.447643 CAATAGGAGGCCGACAGGG 59.552 63.158 0.00 0.00 38.20 4.45
2858 9415 1.447643 CCAATAGGAGGCCGACAGG 59.552 63.158 0.00 0.00 37.64 4.00
2859 9416 1.227674 GCCAATAGGAGGCCGACAG 60.228 63.158 0.00 0.00 46.50 3.51
2860 9417 2.908015 GCCAATAGGAGGCCGACA 59.092 61.111 0.00 0.00 46.50 4.35
2866 9423 0.394565 CCTCTTCGGCCAATAGGAGG 59.605 60.000 11.93 11.93 36.89 4.30
2867 9424 0.394565 CCCTCTTCGGCCAATAGGAG 59.605 60.000 16.10 10.11 36.89 3.69
2868 9425 0.031515 TCCCTCTTCGGCCAATAGGA 60.032 55.000 16.10 6.54 36.89 2.94
2869 9426 0.106894 GTCCCTCTTCGGCCAATAGG 59.893 60.000 2.24 7.86 38.23 2.57
2870 9427 1.123928 AGTCCCTCTTCGGCCAATAG 58.876 55.000 2.24 0.00 0.00 1.73
2871 9428 1.580059 AAGTCCCTCTTCGGCCAATA 58.420 50.000 2.24 0.00 0.00 1.90
2872 9429 0.698818 AAAGTCCCTCTTCGGCCAAT 59.301 50.000 2.24 0.00 35.02 3.16
2873 9430 0.476771 AAAAGTCCCTCTTCGGCCAA 59.523 50.000 2.24 0.00 35.02 4.52
2874 9431 0.476771 AAAAAGTCCCTCTTCGGCCA 59.523 50.000 2.24 0.00 35.02 5.36
2875 9432 0.881796 CAAAAAGTCCCTCTTCGGCC 59.118 55.000 0.00 0.00 35.02 6.13
2876 9433 0.881796 CCAAAAAGTCCCTCTTCGGC 59.118 55.000 0.00 0.00 35.02 5.54
2877 9434 0.881796 GCCAAAAAGTCCCTCTTCGG 59.118 55.000 0.00 0.00 35.02 4.30
2878 9435 0.881796 GGCCAAAAAGTCCCTCTTCG 59.118 55.000 0.00 0.00 35.02 3.79
2879 9436 2.294449 AGGCCAAAAAGTCCCTCTTC 57.706 50.000 5.01 0.00 35.02 2.87
2880 9437 2.225041 GGTAGGCCAAAAAGTCCCTCTT 60.225 50.000 5.01 0.00 34.56 2.85
2881 9438 1.354705 GGTAGGCCAAAAAGTCCCTCT 59.645 52.381 5.01 0.00 34.09 3.69
2882 9439 1.074889 TGGTAGGCCAAAAAGTCCCTC 59.925 52.381 5.01 0.00 42.83 4.30
2883 9440 1.154430 TGGTAGGCCAAAAAGTCCCT 58.846 50.000 5.01 0.00 42.83 4.20
2884 9441 3.757836 TGGTAGGCCAAAAAGTCCC 57.242 52.632 5.01 0.00 42.83 4.46
2896 9453 0.179045 CCTCTTCGGCCAATGGTAGG 60.179 60.000 2.24 0.00 0.00 3.18
2897 9454 0.179045 CCCTCTTCGGCCAATGGTAG 60.179 60.000 2.24 0.00 0.00 3.18
2898 9455 0.619255 TCCCTCTTCGGCCAATGGTA 60.619 55.000 2.24 0.00 0.00 3.25
2899 9456 1.923395 TCCCTCTTCGGCCAATGGT 60.923 57.895 2.24 0.00 0.00 3.55
2900 9457 1.452108 GTCCCTCTTCGGCCAATGG 60.452 63.158 2.24 0.00 0.00 3.16
2901 9458 0.035056 AAGTCCCTCTTCGGCCAATG 60.035 55.000 2.24 0.00 0.00 2.82
2902 9459 0.698818 AAAGTCCCTCTTCGGCCAAT 59.301 50.000 2.24 0.00 35.02 3.16
2903 9460 0.476771 AAAAGTCCCTCTTCGGCCAA 59.523 50.000 2.24 0.00 35.02 4.52
2904 9461 0.036306 GAAAAGTCCCTCTTCGGCCA 59.964 55.000 2.24 0.00 35.02 5.36
2905 9462 1.019805 CGAAAAGTCCCTCTTCGGCC 61.020 60.000 0.00 0.00 38.57 6.13
2906 9463 2.457080 CGAAAAGTCCCTCTTCGGC 58.543 57.895 0.00 0.00 38.57 5.54
2908 9465 1.019805 GGCCGAAAAGTCCCTCTTCG 61.020 60.000 0.00 0.00 41.18 3.79
2909 9466 0.325272 AGGCCGAAAAGTCCCTCTTC 59.675 55.000 0.00 0.00 35.02 2.87
2910 9467 1.278413 GTAGGCCGAAAAGTCCCTCTT 59.722 52.381 0.00 0.00 38.10 2.85
2911 9468 0.903236 GTAGGCCGAAAAGTCCCTCT 59.097 55.000 0.00 0.00 0.00 3.69
2912 9469 0.107800 GGTAGGCCGAAAAGTCCCTC 60.108 60.000 0.00 0.00 0.00 4.30
2913 9470 0.838987 TGGTAGGCCGAAAAGTCCCT 60.839 55.000 0.00 0.00 37.67 4.20
2914 9471 0.255033 ATGGTAGGCCGAAAAGTCCC 59.745 55.000 0.00 0.00 37.67 4.46
2915 9472 2.014857 GAATGGTAGGCCGAAAAGTCC 58.985 52.381 0.00 0.00 37.67 3.85
2916 9473 1.664151 CGAATGGTAGGCCGAAAAGTC 59.336 52.381 0.00 0.00 37.67 3.01
2917 9474 1.734163 CGAATGGTAGGCCGAAAAGT 58.266 50.000 0.00 0.00 37.67 2.66
2918 9475 0.377203 GCGAATGGTAGGCCGAAAAG 59.623 55.000 0.00 0.00 37.67 2.27
2919 9476 1.027792 GGCGAATGGTAGGCCGAAAA 61.028 55.000 0.00 0.00 37.06 2.29
2920 9477 1.450669 GGCGAATGGTAGGCCGAAA 60.451 57.895 0.00 0.00 37.06 3.46
2921 9478 2.188469 GGCGAATGGTAGGCCGAA 59.812 61.111 0.00 0.00 37.06 4.30
2924 9481 2.188469 TTCGGCGAATGGTAGGCC 59.812 61.111 19.83 0.00 43.42 5.19


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

AutoCloner maintained by Alex Coulton.