Multiple sequence alignment - TraesCS4A01G383900

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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 TraesCS4A01G383900 chr4A 100.000 3262 0 0 1 3262 661819076 661822337 0.000000e+00 6024.0
1 TraesCS4A01G383900 chr7B 90.710 2917 188 36 384 3262 699136637 699139508 0.000000e+00 3808.0
2 TraesCS4A01G383900 chr7B 90.369 2928 190 31 375 3262 693617497 693620372 0.000000e+00 3760.0
3 TraesCS4A01G383900 chr7B 89.686 2928 192 38 392 3262 698649995 698652869 0.000000e+00 3633.0
4 TraesCS4A01G383900 chr7B 92.165 2272 130 16 395 2639 699177493 699179743 0.000000e+00 3166.0
5 TraesCS4A01G383900 chr7B 90.779 2169 154 18 375 2516 694359374 694361523 0.000000e+00 2856.0
6 TraesCS4A01G383900 chr7B 88.931 1328 107 11 392 1693 696140169 696141482 0.000000e+00 1602.0
7 TraesCS4A01G383900 chr7B 83.934 1027 140 17 1394 2408 697027539 697026526 0.000000e+00 959.0
8 TraesCS4A01G383900 chr7B 85.675 733 49 19 2553 3262 694361517 694362216 0.000000e+00 721.0
9 TraesCS4A01G383900 chr7B 87.621 412 29 5 2872 3262 699180016 699180426 2.970000e-125 459.0
10 TraesCS4A01G383900 chr7B 85.560 464 29 10 2820 3262 699142733 699143179 4.960000e-123 451.0
11 TraesCS4A01G383900 chr7B 82.589 448 34 15 2785 3209 636073389 636073815 4.000000e-94 355.0
12 TraesCS4A01G383900 chr7B 83.651 367 33 5 2869 3209 12863777 12863412 1.460000e-83 320.0
13 TraesCS4A01G383900 chr7B 88.601 193 19 2 215 406 384970641 384970831 7.040000e-57 231.0
14 TraesCS4A01G383900 chr7B 91.875 160 9 3 18 176 699176565 699176721 1.520000e-53 220.0
15 TraesCS4A01G383900 chr7B 87.634 186 9 7 1 176 693616241 693616422 1.530000e-48 204.0
16 TraesCS4A01G383900 chr7B 86.022 186 10 8 1 176 699135370 699135549 5.560000e-43 185.0
17 TraesCS4A01G383900 chr7B 87.195 164 7 7 23 176 694358139 694358298 1.200000e-39 174.0
18 TraesCS4A01G383900 chr7B 87.313 134 8 4 49 177 698648982 698649111 9.430000e-31 145.0
19 TraesCS4A01G383900 chr7B 89.908 109 6 3 1 109 696139612 696139715 5.680000e-28 135.0
20 TraesCS4A01G383900 chr7B 88.889 72 2 4 5 75 696123838 696123904 2.090000e-12 84.2
21 TraesCS4A01G383900 chr7B 94.118 51 1 2 176 224 699177436 699177486 3.490000e-10 76.8
22 TraesCS4A01G383900 chr7B 87.143 70 4 1 108 177 696123903 696123967 1.260000e-09 75.0
23 TraesCS4A01G383900 chr7B 100.000 35 0 0 144 178 696140036 696140070 7.550000e-07 65.8
24 TraesCS4A01G383900 chr7D 86.612 2196 201 42 395 2547 610537469 610535324 0.000000e+00 2340.0
25 TraesCS4A01G383900 chr7D 92.758 1519 90 6 894 2409 608194801 608196302 0.000000e+00 2178.0
26 TraesCS4A01G383900 chr7D 89.887 1325 104 12 395 1693 600237981 600236661 0.000000e+00 1677.0
27 TraesCS4A01G383900 chr7D 89.886 1315 95 10 401 1693 514744254 514745552 0.000000e+00 1657.0
28 TraesCS4A01G383900 chr7D 89.989 879 63 9 579 1436 79325957 79326831 0.000000e+00 1112.0
29 TraesCS4A01G383900 chr7D 88.737 879 74 8 579 1436 79260319 79261193 0.000000e+00 1051.0
30 TraesCS4A01G383900 chr7D 84.047 1028 139 20 1394 2406 609333457 609334474 0.000000e+00 966.0
31 TraesCS4A01G383900 chr7D 87.321 836 86 10 1722 2544 514745551 514746379 0.000000e+00 939.0
32 TraesCS4A01G383900 chr7D 87.129 606 35 13 2589 3176 610535322 610534742 0.000000e+00 647.0
33 TraesCS4A01G383900 chr7D 87.961 515 36 5 2769 3257 514746523 514747037 4.690000e-163 584.0
34 TraesCS4A01G383900 chr7D 88.432 389 28 2 2891 3262 608196757 608197145 1.380000e-123 453.0
35 TraesCS4A01G383900 chr7D 84.910 444 54 8 2443 2885 609669211 609668780 1.390000e-118 436.0
36 TraesCS4A01G383900 chr7D 88.779 303 17 6 2891 3176 600235580 600235278 4.000000e-94 355.0
37 TraesCS4A01G383900 chr7D 91.968 249 20 0 2589 2837 600235833 600235585 1.860000e-92 350.0
38 TraesCS4A01G383900 chr7D 83.815 173 13 9 5 177 610538042 610537885 2.030000e-32 150.0
39 TraesCS4A01G383900 chr7D 91.489 94 6 1 1 94 514744012 514744103 9.500000e-26 128.0
40 TraesCS4A01G383900 chr7D 80.791 177 17 9 5 177 608191773 608191936 4.420000e-24 122.0
41 TraesCS4A01G383900 chr7D 96.226 53 1 1 172 224 514744197 514744248 5.800000e-13 86.1
42 TraesCS4A01G383900 chr7A 88.644 1814 128 26 782 2547 700508867 700507084 0.000000e+00 2137.0
43 TraesCS4A01G383900 chr7A 88.276 1578 136 17 1722 3262 700205612 700207177 0.000000e+00 1844.0
44 TraesCS4A01G383900 chr7A 85.530 698 61 18 2589 3262 700507082 700506401 0.000000e+00 693.0
45 TraesCS4A01G383900 chr7A 90.127 395 21 8 395 785 700509517 700509137 6.290000e-137 497.0
46 TraesCS4A01G383900 chr7A 87.151 179 21 2 231 409 1528631 1528807 5.520000e-48 202.0
47 TraesCS4A01G383900 chr7A 91.837 49 2 2 178 224 700509572 700509524 2.100000e-07 67.6
48 TraesCS4A01G383900 chr7A 100.000 31 0 0 196 226 700204172 700204202 1.260000e-04 58.4
49 TraesCS4A01G383900 chr1D 90.443 858 61 4 579 1436 16257678 16258514 0.000000e+00 1110.0
50 TraesCS4A01G383900 chr5D 89.545 880 63 12 579 1436 385871469 385870597 0.000000e+00 1088.0
51 TraesCS4A01G383900 chr2B 85.337 341 28 6 2891 3209 135994940 135994600 1.880000e-87 333.0
52 TraesCS4A01G383900 chr2B 93.789 161 10 0 233 393 486633196 486633356 3.250000e-60 243.0
53 TraesCS4A01G383900 chr6B 78.774 424 45 20 2298 2687 309066091 309065679 3.250000e-60 243.0
54 TraesCS4A01G383900 chr6B 90.449 178 13 3 217 393 314546972 314547146 7.040000e-57 231.0
55 TraesCS4A01G383900 chr6B 92.500 160 12 0 234 393 119526809 119526968 2.530000e-56 230.0
56 TraesCS4A01G383900 chr6B 85.714 189 21 6 234 418 120647843 120647657 9.230000e-46 195.0
57 TraesCS4A01G383900 chr4B 92.814 167 11 1 227 393 502957291 502957126 1.170000e-59 241.0
58 TraesCS4A01G383900 chr2D 91.429 175 14 1 233 406 87407363 87407537 4.210000e-59 239.0
59 TraesCS4A01G383900 chr2D 88.649 185 19 2 223 405 11039582 11039766 1.180000e-54 224.0
60 TraesCS4A01G383900 chr2D 87.363 182 21 2 234 415 63737098 63736919 1.190000e-49 207.0
61 TraesCS4A01G383900 chr2D 87.151 179 18 4 234 408 52690227 52690404 7.140000e-47 198.0
62 TraesCS4A01G383900 chr2A 91.329 173 15 0 234 406 12003273 12003445 1.510000e-58 237.0
63 TraesCS4A01G383900 chr2A 90.857 175 15 1 234 408 734270036 734269863 1.960000e-57 233.0
64 TraesCS4A01G383900 chr4D 90.909 176 15 1 219 393 474374136 474374311 5.440000e-58 235.0
65 TraesCS4A01G383900 chr3D 88.832 197 15 5 211 406 459077447 459077257 5.440000e-58 235.0
66 TraesCS4A01G383900 chr3A 89.011 182 16 3 231 411 13540977 13541155 4.240000e-54 222.0
67 TraesCS4A01G383900 chr1B 84.974 193 24 5 235 425 673969370 673969181 1.190000e-44 191.0


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 TraesCS4A01G383900 chr4A 661819076 661822337 3261 False 6024.000000 6024 100.000000 1 3262 1 chr4A.!!$F1 3261
1 TraesCS4A01G383900 chr7B 693616241 693620372 4131 False 1982.000000 3760 89.001500 1 3262 2 chr7B.!!$F3 3261
2 TraesCS4A01G383900 chr7B 698648982 698652869 3887 False 1889.000000 3633 88.499500 49 3262 2 chr7B.!!$F7 3213
3 TraesCS4A01G383900 chr7B 699135370 699143179 7809 False 1481.333333 3808 87.430667 1 3262 3 chr7B.!!$F8 3261
4 TraesCS4A01G383900 chr7B 694358139 694362216 4077 False 1250.333333 2856 87.883000 23 3262 3 chr7B.!!$F4 3239
5 TraesCS4A01G383900 chr7B 699176565 699180426 3861 False 980.450000 3166 91.444750 18 3262 4 chr7B.!!$F9 3244
6 TraesCS4A01G383900 chr7B 697026526 697027539 1013 True 959.000000 959 83.934000 1394 2408 1 chr7B.!!$R2 1014
7 TraesCS4A01G383900 chr7B 696139612 696141482 1870 False 600.933333 1602 92.946333 1 1693 3 chr7B.!!$F6 1692
8 TraesCS4A01G383900 chr7D 79325957 79326831 874 False 1112.000000 1112 89.989000 579 1436 1 chr7D.!!$F2 857
9 TraesCS4A01G383900 chr7D 79260319 79261193 874 False 1051.000000 1051 88.737000 579 1436 1 chr7D.!!$F1 857
10 TraesCS4A01G383900 chr7D 610534742 610538042 3300 True 1045.666667 2340 85.852000 5 3176 3 chr7D.!!$R3 3171
11 TraesCS4A01G383900 chr7D 609333457 609334474 1017 False 966.000000 966 84.047000 1394 2406 1 chr7D.!!$F3 1012
12 TraesCS4A01G383900 chr7D 608191773 608197145 5372 False 917.666667 2178 87.327000 5 3262 3 chr7D.!!$F5 3257
13 TraesCS4A01G383900 chr7D 600235278 600237981 2703 True 794.000000 1677 90.211333 395 3176 3 chr7D.!!$R2 2781
14 TraesCS4A01G383900 chr7D 514744012 514747037 3025 False 678.820000 1657 90.576600 1 3257 5 chr7D.!!$F4 3256
15 TraesCS4A01G383900 chr7A 700204172 700207177 3005 False 951.200000 1844 94.138000 196 3262 2 chr7A.!!$F2 3066
16 TraesCS4A01G383900 chr7A 700506401 700509572 3171 True 848.650000 2137 89.034500 178 3262 4 chr7A.!!$R1 3084
17 TraesCS4A01G383900 chr1D 16257678 16258514 836 False 1110.000000 1110 90.443000 579 1436 1 chr1D.!!$F1 857
18 TraesCS4A01G383900 chr5D 385870597 385871469 872 True 1088.000000 1088 89.545000 579 1436 1 chr5D.!!$R1 857

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
526 2603 0.5312 AAGTACGGTAGCTGCTCACC 59.469 55.0 4.91 11.42 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2313 6359 0.320374 CTCTTGTTGCGGGGTCACTA 59.68 55.0 0.0 0.0 0.0 2.74 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
50 51 9.708092 ACTTCTTCATTTACCTTGTACTCTTAC 57.292 33.333 0.00 0.00 0.00 2.34
52 53 9.706691 TTCTTCATTTACCTTGTACTCTTACTG 57.293 33.333 0.00 0.00 0.00 2.74
75 88 8.865090 ACTGTAGTTTATCTGATTGCTAGCTAT 58.135 33.333 17.23 14.36 0.00 2.97
79 92 7.961351 AGTTTATCTGATTGCTAGCTATCTGT 58.039 34.615 30.38 22.86 32.45 3.41
94 107 6.051717 AGCTATCTGTACTGGCTTTTATGTG 58.948 40.000 0.00 0.00 0.00 3.21
145 463 7.593875 AATTTGTTGCACGCATACATTAATT 57.406 28.000 0.00 2.88 0.00 1.40
240 2106 2.618709 GCATGCATGTAAAGTACTCCCC 59.381 50.000 26.79 2.60 0.00 4.81
241 2107 3.214328 CATGCATGTAAAGTACTCCCCC 58.786 50.000 18.91 0.00 0.00 5.40
261 2127 6.720217 CCCCCATTCCTAAATATAAGTCCT 57.280 41.667 0.00 0.00 0.00 3.85
262 2128 7.103745 CCCCCATTCCTAAATATAAGTCCTT 57.896 40.000 0.00 0.00 0.00 3.36
263 2129 7.535738 CCCCCATTCCTAAATATAAGTCCTTT 58.464 38.462 0.00 0.00 0.00 3.11
264 2130 8.010697 CCCCCATTCCTAAATATAAGTCCTTTT 58.989 37.037 0.00 0.00 0.00 2.27
302 2168 7.615582 TTGACTACATAGGAAGCAAAATGAG 57.384 36.000 0.00 0.00 0.00 2.90
305 2171 6.711277 ACTACATAGGAAGCAAAATGAGTGA 58.289 36.000 0.00 0.00 0.00 3.41
311 2177 6.749923 AGGAAGCAAAATGAGTGAATCTAC 57.250 37.500 0.00 0.00 0.00 2.59
313 2179 6.150140 AGGAAGCAAAATGAGTGAATCTACAC 59.850 38.462 0.00 0.00 40.60 2.90
356 2331 7.395190 ACATCCGTATGTAGTTTGTAGTGTA 57.605 36.000 0.00 0.00 44.66 2.90
357 2332 7.829725 ACATCCGTATGTAGTTTGTAGTGTAA 58.170 34.615 0.00 0.00 44.66 2.41
358 2333 8.472413 ACATCCGTATGTAGTTTGTAGTGTAAT 58.528 33.333 0.00 0.00 44.66 1.89
359 2334 8.965172 CATCCGTATGTAGTTTGTAGTGTAATC 58.035 37.037 0.00 0.00 0.00 1.75
360 2335 8.284945 TCCGTATGTAGTTTGTAGTGTAATCT 57.715 34.615 0.00 0.00 0.00 2.40
361 2336 8.400947 TCCGTATGTAGTTTGTAGTGTAATCTC 58.599 37.037 0.00 0.00 0.00 2.75
362 2337 8.404000 CCGTATGTAGTTTGTAGTGTAATCTCT 58.596 37.037 0.00 0.00 0.00 3.10
393 2368 1.209747 ACATTTAGGAACGGAGGGAGC 59.790 52.381 0.00 0.00 0.00 4.70
486 2555 8.893727 ACACATTAACTCTAGCCATTATTTCAC 58.106 33.333 0.00 0.00 0.00 3.18
511 2581 8.822805 ACTTTCCTATATTGGACAAGTGAAGTA 58.177 33.333 21.12 0.23 36.76 2.24
526 2603 0.531200 AAGTACGGTAGCTGCTCACC 59.469 55.000 4.91 11.42 0.00 4.02
595 2674 4.324254 CCTCTTCCAAGCCAACAGGTATTA 60.324 45.833 0.00 0.00 0.00 0.98
610 2689 7.145932 ACAGGTATTAACTTTGTTGATCAGC 57.854 36.000 2.05 2.05 0.00 4.26
710 2817 7.820872 GCCGGCCTATATGTCTAAACTATAAAA 59.179 37.037 18.11 0.00 0.00 1.52
734 2841 9.930693 AAATCGTAAGTTATCTGAAAGAAGAGT 57.069 29.630 0.00 0.00 43.74 3.24
811 3191 6.928492 TGGTTCATTCAAGCTTCATTTTAACC 59.072 34.615 14.69 14.69 33.27 2.85
967 4873 2.159043 TCTTGATGACAGGCGGAGATTC 60.159 50.000 0.00 0.00 0.00 2.52
982 4888 4.084328 CGGAGATTCAAGTTCACTCAACAC 60.084 45.833 0.00 0.00 37.48 3.32
1051 4969 0.394216 TGATTTGGACGGATGGCTGG 60.394 55.000 0.00 0.00 0.00 4.85
1069 4987 4.035208 GGCTGGAAGGTACGATGTTTAATG 59.965 45.833 0.00 0.00 0.00 1.90
1114 5032 7.405469 TTGTTACACAAGCAAGCAATTTATG 57.595 32.000 0.00 0.00 32.34 1.90
1135 5053 3.163594 GCATGATTCGACTTTGAAACCG 58.836 45.455 0.00 0.00 0.00 4.44
1225 5143 2.991190 GGCAAGATTTTCACACATGCAG 59.009 45.455 0.00 0.00 34.14 4.41
1275 5193 1.731709 GGCAAATGGCGTTGAAAATCC 59.268 47.619 5.03 0.00 46.16 3.01
1345 5263 7.493320 GTGATCATGGCATGAAAATACAAACAT 59.507 33.333 31.81 12.46 43.50 2.71
1361 5363 5.564550 ACAAACATCTATGCCTGAGAAAGT 58.435 37.500 0.00 0.00 0.00 2.66
1506 5531 3.555967 CCATCGGAGGAGGGGAAG 58.444 66.667 0.00 0.00 40.45 3.46
1666 5692 1.203523 GAAGTGCACGTGAGAGAGGAT 59.796 52.381 22.23 0.00 0.00 3.24
1702 5728 3.699134 GAACCATGCTCCCGGGACC 62.699 68.421 22.63 15.26 0.00 4.46
1817 5843 1.283613 TGTACATGGGGTTGGACCATC 59.716 52.381 0.00 0.00 45.33 3.51
1857 5883 5.414454 TGAAAGGTTTCCAATATCAGTTCGG 59.586 40.000 0.05 0.00 36.36 4.30
1872 5898 0.894835 TTCGGACAGCAGTGCATCTA 59.105 50.000 19.20 4.63 35.57 1.98
1882 5908 4.450419 CAGCAGTGCATCTAAAGGTATAGC 59.550 45.833 19.20 0.00 0.00 2.97
2294 6340 3.435327 GTGAATGCTACACGGAACATCAA 59.565 43.478 0.00 0.00 0.00 2.57
2313 6359 7.259290 CATCAAACAGTACTTTTGGTGTAGT 57.741 36.000 22.42 4.10 39.33 2.73
2347 6399 6.912591 CGCAACAAGAGTTCTGTTATTTTTCT 59.087 34.615 0.00 0.00 35.28 2.52
2348 6400 8.067784 CGCAACAAGAGTTCTGTTATTTTTCTA 58.932 33.333 0.00 0.00 35.28 2.10
2349 6401 9.387123 GCAACAAGAGTTCTGTTATTTTTCTAG 57.613 33.333 0.00 0.00 35.28 2.43
2389 6441 4.081642 AGGCTGTCATATTAAGTGTGTCGT 60.082 41.667 0.00 0.00 0.00 4.34
2409 6461 6.314152 TGTCGTGAGTAGAGAGTAGATTGAAG 59.686 42.308 0.00 0.00 0.00 3.02
2418 6482 3.118811 AGAGTAGATTGAAGTGGAGCAGC 60.119 47.826 0.00 0.00 0.00 5.25
2419 6483 2.836981 AGTAGATTGAAGTGGAGCAGCT 59.163 45.455 0.00 0.00 0.00 4.24
2423 6487 3.517100 AGATTGAAGTGGAGCAGCTTCTA 59.483 43.478 1.29 0.00 41.05 2.10
2439 6503 2.634639 TCTACTGCCTAACTTCCCCA 57.365 50.000 0.00 0.00 0.00 4.96
2497 6593 0.464735 TGCCGGTTTTGCTACAGTGT 60.465 50.000 1.90 0.00 0.00 3.55
2672 6978 0.392706 AATCGAGCACCTGTGACACA 59.607 50.000 8.26 8.26 0.00 3.72
2677 6983 1.146041 GCACCTGTGACACACCTCA 59.854 57.895 3.56 0.00 32.73 3.86
2691 7002 2.224402 ACACCTCAACCTGAAGAAGCTC 60.224 50.000 0.00 0.00 0.00 4.09
2692 7003 2.050144 ACCTCAACCTGAAGAAGCTCA 58.950 47.619 0.00 0.00 0.00 4.26
2728 7039 3.091633 AGCAGCAGGTTTATTCACCAT 57.908 42.857 0.00 0.00 39.62 3.55
2743 7054 4.901197 TCACCATTCTGCTTGTACCTTA 57.099 40.909 0.00 0.00 0.00 2.69
2756 7067 4.901197 TGTACCTTAAGCCATTGTGAGA 57.099 40.909 0.00 0.00 0.00 3.27
2845 7160 1.890876 TGCTGTTGTATGGTGTGGTC 58.109 50.000 0.00 0.00 0.00 4.02
2860 7175 1.347707 GTGGTCTGTTGTGGATCCTGA 59.652 52.381 14.23 0.00 0.00 3.86
2864 7179 3.244561 GGTCTGTTGTGGATCCTGAGAAA 60.245 47.826 14.23 0.00 0.00 2.52
2866 7181 5.006386 GTCTGTTGTGGATCCTGAGAAAAT 58.994 41.667 14.23 0.00 0.00 1.82
2881 7196 7.069826 TCCTGAGAAAATTTTTGGTTGATGACT 59.930 33.333 4.63 0.00 0.00 3.41
2882 7197 7.383300 CCTGAGAAAATTTTTGGTTGATGACTC 59.617 37.037 4.63 3.82 0.00 3.36
2921 7270 3.668757 CGGTCTGATTGTTTGCACTGATG 60.669 47.826 0.00 0.00 0.00 3.07
2936 7285 2.290577 ACTGATGCTCTCTTGGGTTTCC 60.291 50.000 0.00 0.00 0.00 3.13
2943 7292 3.615155 CTCTCTTGGGTTTCCTCCATTC 58.385 50.000 0.00 0.00 33.82 2.67
2944 7293 3.260205 TCTCTTGGGTTTCCTCCATTCT 58.740 45.455 0.00 0.00 33.82 2.40
2945 7294 3.009473 TCTCTTGGGTTTCCTCCATTCTG 59.991 47.826 0.00 0.00 33.82 3.02
2946 7295 1.821136 CTTGGGTTTCCTCCATTCTGC 59.179 52.381 0.00 0.00 33.82 4.26
2947 7296 0.776810 TGGGTTTCCTCCATTCTGCA 59.223 50.000 0.00 0.00 0.00 4.41
2948 7297 1.146774 TGGGTTTCCTCCATTCTGCAA 59.853 47.619 0.00 0.00 0.00 4.08
2949 7298 2.247358 GGGTTTCCTCCATTCTGCAAA 58.753 47.619 0.00 0.00 0.00 3.68
2950 7299 2.632512 GGGTTTCCTCCATTCTGCAAAA 59.367 45.455 0.00 0.00 0.00 2.44
2951 7300 3.070878 GGGTTTCCTCCATTCTGCAAAAA 59.929 43.478 0.00 0.00 0.00 1.94
2952 7301 4.263025 GGGTTTCCTCCATTCTGCAAAAAT 60.263 41.667 0.00 0.00 0.00 1.82
2953 7302 5.308014 GGTTTCCTCCATTCTGCAAAAATT 58.692 37.500 0.00 0.00 0.00 1.82
2954 7303 5.179929 GGTTTCCTCCATTCTGCAAAAATTG 59.820 40.000 0.00 0.00 0.00 2.32
2955 7304 4.540359 TCCTCCATTCTGCAAAAATTGG 57.460 40.909 0.00 0.00 0.00 3.16
2956 7305 4.158786 TCCTCCATTCTGCAAAAATTGGA 58.841 39.130 0.00 0.00 0.00 3.53
2967 7343 3.195396 GCAAAAATTGGAGCCAGGATACA 59.805 43.478 0.00 0.00 41.41 2.29
2992 7368 5.362430 TCCCTCTTGATCTTCTCTAGAAAGC 59.638 44.000 0.00 0.00 35.69 3.51
3088 11136 7.668052 ACCATAAAAGGTTTATAGTTCAGCACA 59.332 33.333 0.00 0.00 39.34 4.57
3128 11194 7.033185 ACACAATTGTTCAGGTGTAAAACTTC 58.967 34.615 8.77 0.00 42.24 3.01
3142 11208 1.542492 AACTTCTGCTCAATGCCTGG 58.458 50.000 0.00 0.00 42.00 4.45
3149 11215 0.747283 GCTCAATGCCTGGACCTGAG 60.747 60.000 0.00 6.44 37.23 3.35
3183 11249 5.999205 ATTGTTCATCAGAGTCAGAGACT 57.001 39.130 0.00 0.00 46.42 3.24
3250 11316 6.703319 TCTCACCACCTGATTTAATCGTAAA 58.297 36.000 0.23 0.00 33.76 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 9.352784 GATAGCTAGCAATCAGATAAACTACAG 57.647 37.037 18.83 0.00 0.00 2.74
52 53 9.352784 CAGATAGCTAGCAATCAGATAAACTAC 57.647 37.037 18.83 0.00 0.00 2.73
75 88 4.202419 ACACCACATAAAAGCCAGTACAGA 60.202 41.667 0.00 0.00 0.00 3.41
79 92 3.331150 CGACACCACATAAAAGCCAGTA 58.669 45.455 0.00 0.00 0.00 2.74
274 2140 9.113838 CATTTTGCTTCCTATGTAGTCAATAGT 57.886 33.333 0.00 0.00 0.00 2.12
275 2141 9.330063 TCATTTTGCTTCCTATGTAGTCAATAG 57.670 33.333 0.00 0.00 0.00 1.73
276 2142 9.330063 CTCATTTTGCTTCCTATGTAGTCAATA 57.670 33.333 0.00 0.00 0.00 1.90
277 2143 7.831193 ACTCATTTTGCTTCCTATGTAGTCAAT 59.169 33.333 0.00 0.00 0.00 2.57
278 2144 7.119699 CACTCATTTTGCTTCCTATGTAGTCAA 59.880 37.037 0.00 0.00 0.00 3.18
279 2145 6.595326 CACTCATTTTGCTTCCTATGTAGTCA 59.405 38.462 0.00 0.00 0.00 3.41
280 2146 6.818644 TCACTCATTTTGCTTCCTATGTAGTC 59.181 38.462 0.00 0.00 0.00 2.59
281 2147 6.711277 TCACTCATTTTGCTTCCTATGTAGT 58.289 36.000 0.00 0.00 0.00 2.73
282 2148 7.615582 TTCACTCATTTTGCTTCCTATGTAG 57.384 36.000 0.00 0.00 0.00 2.74
283 2149 8.049117 AGATTCACTCATTTTGCTTCCTATGTA 58.951 33.333 0.00 0.00 0.00 2.29
284 2150 6.888632 AGATTCACTCATTTTGCTTCCTATGT 59.111 34.615 0.00 0.00 0.00 2.29
285 2151 7.330900 AGATTCACTCATTTTGCTTCCTATG 57.669 36.000 0.00 0.00 0.00 2.23
286 2152 8.049117 TGTAGATTCACTCATTTTGCTTCCTAT 58.951 33.333 0.00 0.00 0.00 2.57
287 2153 7.334421 GTGTAGATTCACTCATTTTGCTTCCTA 59.666 37.037 0.00 0.00 35.68 2.94
288 2154 6.150140 GTGTAGATTCACTCATTTTGCTTCCT 59.850 38.462 0.00 0.00 35.68 3.36
289 2155 6.150140 AGTGTAGATTCACTCATTTTGCTTCC 59.850 38.462 0.00 0.00 44.07 3.46
290 2156 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
329 2304 9.123902 ACACTACAAACTACATACGGATGTATA 57.876 33.333 20.64 9.08 45.42 1.47
360 2335 9.211485 CCGTTCCTAAATGTAAGTCTTTTTAGA 57.789 33.333 13.43 2.40 0.00 2.10
361 2336 9.211485 TCCGTTCCTAAATGTAAGTCTTTTTAG 57.789 33.333 7.75 7.75 0.00 1.85
362 2337 9.211485 CTCCGTTCCTAAATGTAAGTCTTTTTA 57.789 33.333 0.00 0.00 0.00 1.52
363 2338 7.174426 CCTCCGTTCCTAAATGTAAGTCTTTTT 59.826 37.037 0.00 0.00 0.00 1.94
364 2339 6.653740 CCTCCGTTCCTAAATGTAAGTCTTTT 59.346 38.462 0.00 0.00 0.00 2.27
365 2340 6.171213 CCTCCGTTCCTAAATGTAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
366 2341 5.338137 CCCTCCGTTCCTAAATGTAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
367 2342 4.161754 CCCTCCGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
368 2343 4.161001 TCCCTCCGTTCCTAAATGTAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
369 2344 4.098894 TCCCTCCGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
370 2345 4.694339 CTCCCTCCGTTCCTAAATGTAAG 58.306 47.826 0.00 0.00 0.00 2.34
371 2346 3.118519 GCTCCCTCCGTTCCTAAATGTAA 60.119 47.826 0.00 0.00 0.00 2.41
372 2347 2.433239 GCTCCCTCCGTTCCTAAATGTA 59.567 50.000 0.00 0.00 0.00 2.29
373 2348 1.209747 GCTCCCTCCGTTCCTAAATGT 59.790 52.381 0.00 0.00 0.00 2.71
374 2349 1.209504 TGCTCCCTCCGTTCCTAAATG 59.790 52.381 0.00 0.00 0.00 2.32
375 2350 1.580059 TGCTCCCTCCGTTCCTAAAT 58.420 50.000 0.00 0.00 0.00 1.40
376 2351 1.580059 ATGCTCCCTCCGTTCCTAAA 58.420 50.000 0.00 0.00 0.00 1.85
377 2352 2.464796 TATGCTCCCTCCGTTCCTAA 57.535 50.000 0.00 0.00 0.00 2.69
378 2353 2.696526 ATATGCTCCCTCCGTTCCTA 57.303 50.000 0.00 0.00 0.00 2.94
379 2354 2.696526 TATATGCTCCCTCCGTTCCT 57.303 50.000 0.00 0.00 0.00 3.36
380 2355 3.983044 AATATATGCTCCCTCCGTTCC 57.017 47.619 0.00 0.00 0.00 3.62
381 2356 5.662674 AGTAATATATGCTCCCTCCGTTC 57.337 43.478 0.00 0.00 0.00 3.95
382 2357 5.542635 TCAAGTAATATATGCTCCCTCCGTT 59.457 40.000 0.00 0.00 0.00 4.44
385 2360 6.156949 TCCATCAAGTAATATATGCTCCCTCC 59.843 42.308 0.00 0.00 0.00 4.30
486 2555 9.099454 GTACTTCACTTGTCCAATATAGGAAAG 57.901 37.037 0.00 0.00 39.92 2.62
526 2603 3.003171 TGTCAACATGTTCCATTGTGTCG 59.997 43.478 8.48 0.00 0.00 4.35
541 2620 2.569354 GGGCGCCCAAATGTCAACA 61.569 57.895 40.73 0.00 35.81 3.33
595 2674 6.883217 AGATATGTGAGCTGATCAACAAAGTT 59.117 34.615 0.00 0.00 40.43 2.66
610 2689 8.940952 TCATCGTCTCTAACATAGATATGTGAG 58.059 37.037 10.13 10.13 45.55 3.51
733 2840 6.025280 CCATTTTGGTTGTGCTTATACGTAC 58.975 40.000 0.00 0.00 31.35 3.67
734 2841 6.184580 CCATTTTGGTTGTGCTTATACGTA 57.815 37.500 0.00 0.00 31.35 3.57
735 2842 5.054390 CCATTTTGGTTGTGCTTATACGT 57.946 39.130 0.00 0.00 31.35 3.57
791 3171 7.816031 ACATCAGGTTAAAATGAAGCTTGAATG 59.184 33.333 2.10 0.00 34.99 2.67
884 3264 6.525629 ACGAGCCTATTGCAAACTCTATATT 58.474 36.000 1.71 0.00 44.83 1.28
895 3275 2.201732 GATTTCGACGAGCCTATTGCA 58.798 47.619 0.00 0.00 44.83 4.08
967 4873 3.627123 TCCACATGTGTTGAGTGAACTTG 59.373 43.478 23.79 4.49 35.33 3.16
982 4888 2.297880 CCATGGTGCCATAATCCACATG 59.702 50.000 2.57 0.00 34.91 3.21
1051 4969 5.329493 GCAACCATTAAACATCGTACCTTC 58.671 41.667 0.00 0.00 0.00 3.46
1069 4987 2.433436 AGTTTGGAATAGACCGCAACC 58.567 47.619 0.00 0.00 0.00 3.77
1114 5032 3.120338 TCGGTTTCAAAGTCGAATCATGC 60.120 43.478 0.00 0.00 0.00 4.06
1225 5143 7.958674 TCATTTGTTTTGCAAGTTTGTACTTC 58.041 30.769 0.00 0.00 42.67 3.01
1275 5193 3.557577 TCATTCTGCAATGGTGAAACG 57.442 42.857 0.00 0.00 40.08 3.60
1345 5263 2.768527 CCTCCACTTTCTCAGGCATAGA 59.231 50.000 0.00 0.00 0.00 1.98
1376 5378 2.050351 CGCCGTTGAGAGTCGTGT 60.050 61.111 0.00 0.00 0.00 4.49
1456 5481 1.066858 CGCAAGCCTTCTACTTCTCCA 60.067 52.381 0.00 0.00 0.00 3.86
1505 5530 6.902771 AATTCATACCTAGTAGATCGCACT 57.097 37.500 0.00 7.94 0.00 4.40
1506 5531 8.459635 TCATAATTCATACCTAGTAGATCGCAC 58.540 37.037 0.00 0.00 0.00 5.34
1628 5654 1.184970 TCTCACACGACCTCCATGCA 61.185 55.000 0.00 0.00 0.00 3.96
1666 5692 6.228616 TGGTTCTATGTTTATCGACCATGA 57.771 37.500 0.00 0.00 0.00 3.07
1817 5843 6.787085 ACCTTTCATTCTTCAACTTAGTCG 57.213 37.500 0.00 0.00 0.00 4.18
1857 5883 2.704572 ACCTTTAGATGCACTGCTGTC 58.295 47.619 1.98 1.01 0.00 3.51
1872 5898 8.782137 ATTAATCACCAATTGGCTATACCTTT 57.218 30.769 24.79 9.26 40.22 3.11
1882 5908 7.201548 GCTTTAGTGCAATTAATCACCAATTGG 60.202 37.037 23.31 23.31 41.57 3.16
2294 6340 6.982724 GTCACTACTACACCAAAAGTACTGTT 59.017 38.462 0.00 0.00 0.00 3.16
2313 6359 0.320374 CTCTTGTTGCGGGGTCACTA 59.680 55.000 0.00 0.00 0.00 2.74
2347 6399 5.263968 GCCTATGCTTCACAGTTCTACTA 57.736 43.478 0.00 0.00 33.53 1.82
2348 6400 4.130286 GCCTATGCTTCACAGTTCTACT 57.870 45.455 0.00 0.00 33.53 2.57
2389 6441 6.722328 TCCACTTCAATCTACTCTCTACTCA 58.278 40.000 0.00 0.00 0.00 3.41
2418 6482 2.838202 TGGGGAAGTTAGGCAGTAGAAG 59.162 50.000 0.00 0.00 0.00 2.85
2419 6483 2.910544 TGGGGAAGTTAGGCAGTAGAA 58.089 47.619 0.00 0.00 0.00 2.10
2423 6487 1.668826 TCATGGGGAAGTTAGGCAGT 58.331 50.000 0.00 0.00 0.00 4.40
2439 6503 1.800805 CGAGCGCTATTCCCATTCAT 58.199 50.000 11.50 0.00 0.00 2.57
2672 6978 2.038295 CTGAGCTTCTTCAGGTTGAGGT 59.962 50.000 0.00 0.00 40.69 3.85
2692 7003 4.711949 CTTGGAGGCAGCGGCACT 62.712 66.667 11.88 5.30 43.71 4.40
2743 7054 1.033746 CCGGCATCTCACAATGGCTT 61.034 55.000 8.51 0.00 46.85 4.35
2747 7058 1.335810 CCATTCCGGCATCTCACAATG 59.664 52.381 0.00 0.00 0.00 2.82
2750 7061 4.961637 CCATTCCGGCATCTCACA 57.038 55.556 0.00 0.00 0.00 3.58
2831 7146 3.210227 CACAACAGACCACACCATACAA 58.790 45.455 0.00 0.00 0.00 2.41
2845 7160 5.972107 AATTTTCTCAGGATCCACAACAG 57.028 39.130 15.82 1.87 0.00 3.16
2864 7179 7.671398 ACAGGATAGAGTCATCAACCAAAAATT 59.329 33.333 0.00 0.00 0.00 1.82
2866 7181 6.542821 ACAGGATAGAGTCATCAACCAAAAA 58.457 36.000 0.00 0.00 0.00 1.94
2881 7196 1.393603 CGGCTGAGTGACAGGATAGA 58.606 55.000 0.00 0.00 45.82 1.98
2882 7197 0.387202 CCGGCTGAGTGACAGGATAG 59.613 60.000 0.00 0.00 45.82 2.08
2921 7270 0.693049 TGGAGGAAACCCAAGAGAGC 59.307 55.000 0.00 0.00 0.00 4.09
2936 7285 3.930848 GCTCCAATTTTTGCAGAATGGAG 59.069 43.478 25.04 25.04 38.09 3.86
2943 7292 1.619827 TCCTGGCTCCAATTTTTGCAG 59.380 47.619 0.00 0.00 0.00 4.41
2944 7293 1.714541 TCCTGGCTCCAATTTTTGCA 58.285 45.000 0.00 0.00 0.00 4.08
2945 7294 3.195396 TGTATCCTGGCTCCAATTTTTGC 59.805 43.478 0.00 0.00 0.00 3.68
2946 7295 5.452356 GGATGTATCCTGGCTCCAATTTTTG 60.452 44.000 3.63 0.00 43.73 2.44
2947 7296 4.651045 GGATGTATCCTGGCTCCAATTTTT 59.349 41.667 3.63 0.00 43.73 1.94
2948 7297 4.218312 GGATGTATCCTGGCTCCAATTTT 58.782 43.478 3.63 0.00 43.73 1.82
2949 7298 3.437052 GGGATGTATCCTGGCTCCAATTT 60.437 47.826 10.53 0.00 46.35 1.82
2950 7299 2.108952 GGGATGTATCCTGGCTCCAATT 59.891 50.000 10.53 0.00 46.35 2.32
2951 7300 1.707427 GGGATGTATCCTGGCTCCAAT 59.293 52.381 10.53 0.00 46.35 3.16
2952 7301 1.140312 GGGATGTATCCTGGCTCCAA 58.860 55.000 10.53 0.00 46.35 3.53
2953 7302 0.268869 AGGGATGTATCCTGGCTCCA 59.731 55.000 10.53 0.00 46.35 3.86
2954 7303 0.980423 GAGGGATGTATCCTGGCTCC 59.020 60.000 10.53 0.00 46.35 4.70
2955 7304 2.022718 AGAGGGATGTATCCTGGCTC 57.977 55.000 10.53 8.68 46.35 4.70
2956 7305 2.053244 CAAGAGGGATGTATCCTGGCT 58.947 52.381 10.53 0.00 46.35 4.75
2957 7306 2.050144 TCAAGAGGGATGTATCCTGGC 58.950 52.381 10.53 1.52 46.35 4.85
2958 7307 4.166539 AGATCAAGAGGGATGTATCCTGG 58.833 47.826 10.53 0.00 46.35 4.45
2967 7343 6.041979 GCTTTCTAGAGAAGATCAAGAGGGAT 59.958 42.308 14.88 0.00 35.21 3.85
2992 7368 5.551233 TCTTCAAGGGTACAGACTGAATTG 58.449 41.667 10.08 6.51 0.00 2.32
3088 11136 3.883830 TTGTGTTGTTTCTGCACCATT 57.116 38.095 0.00 0.00 32.62 3.16
3142 11208 5.675538 ACAATAGTAGCATTTCCTCAGGTC 58.324 41.667 0.00 0.00 0.00 3.85
3149 11215 7.497249 ACTCTGATGAACAATAGTAGCATTTCC 59.503 37.037 0.00 0.00 0.00 3.13
3183 11249 5.163281 AGGCAATTGAACCAAAATGCATA 57.837 34.783 10.34 0.00 39.95 3.14


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

AutoCloner maintained by Alex Coulton.