Multiple sequence alignment - TraesCS2D01G519700

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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 TraesCS2D01G519700 chr2D 100.000 2903 0 0 1 2903 609430617 609433519 0.000000e+00 5361.0
1 TraesCS2D01G519700 chr2B 92.648 1197 44 15 1203 2363 743726814 743728002 0.000000e+00 1683.0
2 TraesCS2D01G519700 chr2B 89.067 997 46 20 336 1303 743726005 743726967 0.000000e+00 1179.0
3 TraesCS2D01G519700 chr2B 83.820 377 36 8 2550 2903 743728003 743728377 4.640000e-88 335.0
4 TraesCS2D01G519700 chr2B 77.907 258 33 16 1 244 743725585 743725832 3.900000e-29 139.0
5 TraesCS2D01G519700 chr2A 94.054 1009 38 10 1188 2180 741378821 741379823 0.000000e+00 1511.0
6 TraesCS2D01G519700 chr2A 91.704 892 36 8 1373 2261 742130631 742131487 0.000000e+00 1203.0
7 TraesCS2D01G519700 chr2A 87.073 1083 68 33 310 1362 741377901 741378941 0.000000e+00 1158.0
8 TraesCS2D01G519700 chr2A 91.808 354 11 3 2550 2903 742131829 742132164 7.280000e-131 477.0
9 TraesCS2D01G519700 chr2A 83.854 192 22 8 2378 2569 728402167 728401985 1.070000e-39 174.0
10 TraesCS2D01G519700 chr2A 96.262 107 3 1 2181 2287 742131692 742131797 1.070000e-39 174.0
11 TraesCS2D01G519700 chr2A 83.770 191 13 6 1 191 741377084 741377256 6.440000e-37 165.0
12 TraesCS2D01G519700 chr2A 90.323 124 12 0 2780 2903 741416071 741416194 2.310000e-36 163.0
13 TraesCS2D01G519700 chr2A 85.263 95 14 0 1160 1254 741378847 741378941 6.620000e-17 99.0
14 TraesCS2D01G519700 chr6B 87.861 173 15 5 2377 2548 583445979 583446146 6.350000e-47 198.0
15 TraesCS2D01G519700 chr6B 85.165 182 20 5 2372 2553 120226125 120226299 2.300000e-41 180.0
16 TraesCS2D01G519700 chr3D 87.135 171 16 5 2378 2548 87925997 87926161 3.820000e-44 189.0
17 TraesCS2D01G519700 chr5A 87.059 170 16 5 2379 2548 414776011 414776174 1.370000e-43 187.0
18 TraesCS2D01G519700 chr1B 86.705 173 15 7 2378 2549 521219541 521219376 4.940000e-43 185.0
19 TraesCS2D01G519700 chr5D 85.027 187 20 6 2364 2549 354813233 354813054 1.780000e-42 183.0
20 TraesCS2D01G519700 chr7B 84.699 183 22 4 2366 2548 382331915 382332091 8.270000e-41 178.0
21 TraesCS2D01G519700 chr4D 84.492 187 20 8 2364 2549 421405128 421404950 2.970000e-40 176.0
22 TraesCS2D01G519700 chrUn 75.568 176 29 12 1618 1783 279543423 279543594 1.120000e-09 75.0
23 TraesCS2D01G519700 chrUn 75.287 174 27 13 1621 1783 189561775 189561607 5.190000e-08 69.4
24 TraesCS2D01G519700 chrUn 75.281 178 26 13 1618 1783 201369286 201369457 5.190000e-08 69.4
25 TraesCS2D01G519700 chrUn 97.436 39 1 0 1618 1656 154542732 154542770 1.870000e-07 67.6
26 TraesCS2D01G519700 chrUn 97.436 39 1 0 1618 1656 363337004 363337042 1.870000e-07 67.6
27 TraesCS2D01G519700 chr4B 100.000 34 0 0 1623 1656 654707102 654707069 2.420000e-06 63.9


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 TraesCS2D01G519700 chr2D 609430617 609433519 2902 False 5361.00 5361 100.0000 1 2903 1 chr2D.!!$F1 2902
1 TraesCS2D01G519700 chr2B 743725585 743728377 2792 False 834.00 1683 85.8605 1 2903 4 chr2B.!!$F1 2902
2 TraesCS2D01G519700 chr2A 741377084 741379823 2739 False 733.25 1511 87.5400 1 2180 4 chr2A.!!$F2 2179
3 TraesCS2D01G519700 chr2A 742130631 742132164 1533 False 618.00 1203 93.2580 1373 2903 3 chr2A.!!$F3 1530

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
395 950 0.109532 TTCCACCCATCGTTTCTGCA 59.89 50.0 0.0 0.0 0.0 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2191 2923 1.065551 GCAACCATGGGTAGAAATCGC 59.934 52.381 18.09 3.08 33.12 4.58 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
46 48 0.602372 GAGGCATTGGGATCGAGCTC 60.602 60.000 2.73 2.73 0.00 4.09
47 49 1.053264 AGGCATTGGGATCGAGCTCT 61.053 55.000 12.85 0.00 0.00 4.09
48 50 0.602372 GGCATTGGGATCGAGCTCTC 60.602 60.000 12.85 3.05 0.00 3.20
49 51 0.392336 GCATTGGGATCGAGCTCTCT 59.608 55.000 12.85 0.00 0.00 3.10
50 52 1.202627 GCATTGGGATCGAGCTCTCTT 60.203 52.381 12.85 0.00 0.00 2.85
51 53 2.753296 CATTGGGATCGAGCTCTCTTC 58.247 52.381 12.85 5.57 0.00 2.87
52 54 1.115467 TTGGGATCGAGCTCTCTTCC 58.885 55.000 12.85 14.00 0.00 3.46
53 55 0.757188 TGGGATCGAGCTCTCTTCCC 60.757 60.000 26.72 26.72 43.95 3.97
54 56 0.469144 GGGATCGAGCTCTCTTCCCT 60.469 60.000 26.40 1.97 42.10 4.20
55 57 1.408969 GGATCGAGCTCTCTTCCCTT 58.591 55.000 12.85 0.00 0.00 3.95
59 61 1.819905 GAGCTCTCTTCCCTTCCCG 59.180 63.158 6.43 0.00 0.00 5.14
89 91 2.283529 GGGGGTCTTCGCTCAGTCA 61.284 63.158 0.00 0.00 0.00 3.41
93 95 1.751924 GGGTCTTCGCTCAGTCAGTAT 59.248 52.381 0.00 0.00 0.00 2.12
94 96 2.223618 GGGTCTTCGCTCAGTCAGTATC 60.224 54.545 0.00 0.00 0.00 2.24
96 98 1.671328 TCTTCGCTCAGTCAGTATCCG 59.329 52.381 0.00 0.00 0.00 4.18
100 102 1.069568 CGCTCAGTCAGTATCCGCTAG 60.070 57.143 0.00 0.00 0.00 3.42
101 103 1.335506 GCTCAGTCAGTATCCGCTAGC 60.336 57.143 4.06 4.06 0.00 3.42
102 104 2.226330 CTCAGTCAGTATCCGCTAGCT 58.774 52.381 13.93 0.00 0.00 3.32
103 105 3.403968 CTCAGTCAGTATCCGCTAGCTA 58.596 50.000 13.93 0.56 0.00 3.32
137 150 1.823169 TTGGAGTACTGGCCGGACAC 61.823 60.000 21.41 15.50 0.00 3.67
146 159 2.112297 GCCGGACACCTCCAAACA 59.888 61.111 5.05 0.00 36.12 2.83
147 160 1.303317 GCCGGACACCTCCAAACAT 60.303 57.895 5.05 0.00 36.12 2.71
148 161 1.586154 GCCGGACACCTCCAAACATG 61.586 60.000 5.05 0.00 36.12 3.21
151 164 1.542328 CGGACACCTCCAAACATGACA 60.542 52.381 0.00 0.00 36.12 3.58
155 168 2.172505 ACACCTCCAAACATGACACTGA 59.827 45.455 0.00 0.00 0.00 3.41
161 174 2.554032 CCAAACATGACACTGAAGGGAC 59.446 50.000 0.00 0.00 0.00 4.46
168 181 0.394565 ACACTGAAGGGACACAGCTC 59.605 55.000 0.00 0.00 38.22 4.09
208 427 3.497884 GACACCCAACTGGCCAGCT 62.498 63.158 33.06 19.23 37.83 4.24
210 429 4.335647 ACCCAACTGGCCAGCTCG 62.336 66.667 33.06 20.06 37.83 5.03
221 440 4.383861 CAGCTCGGCCACTCTGCA 62.384 66.667 2.24 0.00 0.00 4.41
244 468 2.033049 GCATGTAAGCAAGGCATCTCAG 59.967 50.000 0.00 0.00 0.00 3.35
245 469 3.538591 CATGTAAGCAAGGCATCTCAGA 58.461 45.455 0.00 0.00 0.00 3.27
249 483 5.118990 TGTAAGCAAGGCATCTCAGAATAC 58.881 41.667 0.00 0.00 0.00 1.89
256 490 3.319405 AGGCATCTCAGAATACGTACCTG 59.681 47.826 16.50 16.50 0.00 4.00
259 493 4.979197 GCATCTCAGAATACGTACCTGAAG 59.021 45.833 22.19 17.53 36.61 3.02
261 495 5.814764 TCTCAGAATACGTACCTGAAGTC 57.185 43.478 22.19 2.73 36.61 3.01
275 510 2.237143 CTGAAGTCCTGAACTGCCCATA 59.763 50.000 0.00 0.00 38.58 2.74
279 514 0.543277 TCCTGAACTGCCCATAGCTG 59.457 55.000 0.00 0.00 44.23 4.24
280 515 0.543277 CCTGAACTGCCCATAGCTGA 59.457 55.000 0.00 0.00 42.76 4.26
281 516 1.065199 CCTGAACTGCCCATAGCTGAA 60.065 52.381 0.00 0.00 42.76 3.02
282 517 2.618816 CCTGAACTGCCCATAGCTGAAA 60.619 50.000 0.00 0.00 42.76 2.69
283 518 2.681848 CTGAACTGCCCATAGCTGAAAG 59.318 50.000 0.00 0.00 42.76 2.62
284 519 2.040278 TGAACTGCCCATAGCTGAAAGT 59.960 45.455 0.00 0.00 42.76 2.66
285 520 2.119801 ACTGCCCATAGCTGAAAGTG 57.880 50.000 0.00 0.00 42.76 3.16
286 521 0.737219 CTGCCCATAGCTGAAAGTGC 59.263 55.000 0.00 0.00 42.76 4.40
288 523 0.737219 GCCCATAGCTGAAAGTGCAG 59.263 55.000 0.00 0.00 38.99 4.41
309 855 4.438797 CAGCTTGTGAAGTTGAAATGAACG 59.561 41.667 0.00 0.00 41.64 3.95
310 856 4.335315 AGCTTGTGAAGTTGAAATGAACGA 59.665 37.500 0.00 0.00 0.00 3.85
312 858 5.052370 GCTTGTGAAGTTGAAATGAACGAAC 60.052 40.000 0.00 0.00 0.00 3.95
314 860 6.130298 TGTGAAGTTGAAATGAACGAACAT 57.870 33.333 0.00 0.00 0.00 2.71
315 861 7.252965 TGTGAAGTTGAAATGAACGAACATA 57.747 32.000 0.00 0.00 0.00 2.29
316 862 7.870826 TGTGAAGTTGAAATGAACGAACATAT 58.129 30.769 0.00 0.00 0.00 1.78
317 863 7.802720 TGTGAAGTTGAAATGAACGAACATATG 59.197 33.333 0.00 0.00 0.00 1.78
318 864 6.801377 TGAAGTTGAAATGAACGAACATATGC 59.199 34.615 1.58 0.00 0.00 3.14
319 865 6.500684 AGTTGAAATGAACGAACATATGCT 57.499 33.333 1.58 0.00 0.00 3.79
320 866 6.317088 AGTTGAAATGAACGAACATATGCTG 58.683 36.000 1.58 0.00 0.00 4.41
321 867 5.878332 TGAAATGAACGAACATATGCTGT 57.122 34.783 1.58 0.00 40.84 4.40
322 868 5.630061 TGAAATGAACGAACATATGCTGTG 58.370 37.500 1.58 0.00 38.39 3.66
344 898 2.975732 TGAACTGCTCATAGCTCCTG 57.024 50.000 0.00 0.00 42.97 3.86
395 950 0.109532 TTCCACCCATCGTTTCTGCA 59.890 50.000 0.00 0.00 0.00 4.41
410 965 0.797542 CTGCACTCTTCTTGCTGAGC 59.202 55.000 0.00 0.00 40.36 4.26
411 966 0.395686 TGCACTCTTCTTGCTGAGCT 59.604 50.000 5.83 0.00 40.86 4.09
412 967 1.077915 GCACTCTTCTTGCTGAGCTC 58.922 55.000 6.82 6.82 37.00 4.09
505 1072 0.846401 CAGACAGAACACACGACACG 59.154 55.000 0.00 0.00 0.00 4.49
530 1097 5.007626 GGTACCTATCGATTACACGTACACA 59.992 44.000 1.71 0.00 34.70 3.72
540 1107 6.291427 CGATTACACGTACACAACACATATCC 60.291 42.308 0.00 0.00 0.00 2.59
550 1117 3.523564 ACAACACATATCCAGCCCTAGTT 59.476 43.478 0.00 0.00 0.00 2.24
616 1183 3.610477 CGCATCACGCTAGCTCAG 58.390 61.111 13.93 2.28 39.08 3.35
738 1309 2.435410 CAGCTGCACTGGCGATCA 60.435 61.111 0.00 0.00 45.35 2.92
798 1369 4.636435 CAGTCGGCCGGTTGGGTT 62.636 66.667 27.83 0.00 38.44 4.11
799 1370 4.636435 AGTCGGCCGGTTGGGTTG 62.636 66.667 27.83 0.00 38.44 3.77
1044 1660 3.200593 CTGGTGCTCGCCATGCTC 61.201 66.667 2.27 0.00 37.96 4.26
1154 1770 4.910585 CGTCAGCATACCCCCGGC 62.911 72.222 0.00 0.00 0.00 6.13
1155 1771 4.564110 GTCAGCATACCCCCGGCC 62.564 72.222 0.00 0.00 0.00 6.13
1239 1855 2.112297 GTCGGCAAAGTCACCCCA 59.888 61.111 0.00 0.00 0.00 4.96
1244 1872 2.617274 GCAAAGTCACCCCAGTCGC 61.617 63.158 0.00 0.00 0.00 5.19
1393 2084 1.043116 CGGTGGCATGGTCTCTCCTA 61.043 60.000 0.00 0.00 37.07 2.94
1898 2625 1.809619 CATTCCACATCCGACGCGT 60.810 57.895 13.85 13.85 0.00 6.01
1911 2638 2.160065 CCGACGCGTATAATTTAAGCCG 60.160 50.000 13.97 6.67 0.00 5.52
2096 2827 5.873179 AATTGTATTGTGTACCAACCTCG 57.127 39.130 0.00 0.00 35.44 4.63
2153 2885 1.614903 TGCAATGCTCCCTTGAACAAG 59.385 47.619 6.82 7.49 38.14 3.16
2191 2923 9.748708 TCTACTGATTTCAAATTCAAAAAGTGG 57.251 29.630 9.56 7.91 0.00 4.00
2300 3316 1.229951 TCCAACCTCCATGGAGCCT 60.230 57.895 32.97 20.04 41.98 4.58
2367 3383 6.639632 GGATGTGCTCCATGTATGTAAATT 57.360 37.500 0.00 0.00 44.26 1.82
2368 3384 7.042797 GGATGTGCTCCATGTATGTAAATTT 57.957 36.000 0.00 0.00 44.26 1.82
2369 3385 7.491682 GGATGTGCTCCATGTATGTAAATTTT 58.508 34.615 0.00 0.00 44.26 1.82
2370 3386 7.649306 GGATGTGCTCCATGTATGTAAATTTTC 59.351 37.037 0.00 0.00 44.26 2.29
2371 3387 7.459795 TGTGCTCCATGTATGTAAATTTTCA 57.540 32.000 0.00 0.00 0.00 2.69
2372 3388 7.312154 TGTGCTCCATGTATGTAAATTTTCAC 58.688 34.615 0.00 0.00 0.00 3.18
2373 3389 7.176515 TGTGCTCCATGTATGTAAATTTTCACT 59.823 33.333 0.00 0.00 0.00 3.41
2374 3390 8.673711 GTGCTCCATGTATGTAAATTTTCACTA 58.326 33.333 0.00 0.00 0.00 2.74
2375 3391 9.407380 TGCTCCATGTATGTAAATTTTCACTAT 57.593 29.630 0.00 0.00 0.00 2.12
2376 3392 9.884465 GCTCCATGTATGTAAATTTTCACTATC 57.116 33.333 0.00 0.00 0.00 2.08
2390 3406 9.712305 AATTTTCACTATCATATACTCCCTTCG 57.288 33.333 0.00 0.00 0.00 3.79
2391 3407 7.834881 TTTCACTATCATATACTCCCTTCGT 57.165 36.000 0.00 0.00 0.00 3.85
2392 3408 7.834881 TTCACTATCATATACTCCCTTCGTT 57.165 36.000 0.00 0.00 0.00 3.85
2393 3409 7.450124 TCACTATCATATACTCCCTTCGTTC 57.550 40.000 0.00 0.00 0.00 3.95
2394 3410 6.433404 TCACTATCATATACTCCCTTCGTTCC 59.567 42.308 0.00 0.00 0.00 3.62
2395 3411 6.434652 CACTATCATATACTCCCTTCGTTCCT 59.565 42.308 0.00 0.00 0.00 3.36
2396 3412 7.610692 CACTATCATATACTCCCTTCGTTCCTA 59.389 40.741 0.00 0.00 0.00 2.94
2397 3413 8.168725 ACTATCATATACTCCCTTCGTTCCTAA 58.831 37.037 0.00 0.00 0.00 2.69
2398 3414 7.850935 ATCATATACTCCCTTCGTTCCTAAA 57.149 36.000 0.00 0.00 0.00 1.85
2399 3415 7.850935 TCATATACTCCCTTCGTTCCTAAAT 57.149 36.000 0.00 0.00 0.00 1.40
2400 3416 8.945195 TCATATACTCCCTTCGTTCCTAAATA 57.055 34.615 0.00 0.00 0.00 1.40
2401 3417 9.543231 TCATATACTCCCTTCGTTCCTAAATAT 57.457 33.333 0.00 0.00 0.00 1.28
2405 3421 7.672122 ACTCCCTTCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
2406 3422 7.724287 ACTCCCTTCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
2407 3423 7.564292 ACTCCCTTCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
2408 3424 8.315220 TCCCTTCGTTCCTAAATATAAGTCTT 57.685 34.615 0.00 0.00 0.00 3.01
2409 3425 8.765517 TCCCTTCGTTCCTAAATATAAGTCTTT 58.234 33.333 0.00 0.00 0.00 2.52
2410 3426 9.392259 CCCTTCGTTCCTAAATATAAGTCTTTT 57.608 33.333 0.00 0.00 0.00 2.27
2452 3468 9.988350 ATAAAGAACTACATACGAAGCAAAATG 57.012 29.630 0.00 0.00 0.00 2.32
2453 3469 7.667043 AAGAACTACATACGAAGCAAAATGA 57.333 32.000 0.00 0.00 0.00 2.57
2454 3470 7.295952 AGAACTACATACGAAGCAAAATGAG 57.704 36.000 0.00 0.00 0.00 2.90
2455 3471 6.874134 AGAACTACATACGAAGCAAAATGAGT 59.126 34.615 0.00 0.00 0.00 3.41
2456 3472 6.408858 ACTACATACGAAGCAAAATGAGTG 57.591 37.500 0.00 0.00 0.00 3.51
2457 3473 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
2458 3474 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
2459 3475 6.312399 ACATACGAAGCAAAATGAGTGAAA 57.688 33.333 0.00 0.00 0.00 2.69
2460 3476 6.734137 ACATACGAAGCAAAATGAGTGAAAA 58.266 32.000 0.00 0.00 0.00 2.29
2461 3477 7.370383 ACATACGAAGCAAAATGAGTGAAAAT 58.630 30.769 0.00 0.00 0.00 1.82
2462 3478 8.511321 ACATACGAAGCAAAATGAGTGAAAATA 58.489 29.630 0.00 0.00 0.00 1.40
2463 3479 8.788813 CATACGAAGCAAAATGAGTGAAAATAC 58.211 33.333 0.00 0.00 0.00 1.89
2464 3480 6.734137 ACGAAGCAAAATGAGTGAAAATACA 58.266 32.000 0.00 0.00 0.00 2.29
2465 3481 6.636850 ACGAAGCAAAATGAGTGAAAATACAC 59.363 34.615 0.00 0.00 40.60 2.90
2510 3526 9.574577 ACATCCATATATAGTCCCTTATTGGAA 57.425 33.333 1.19 0.00 35.80 3.53
2522 3538 8.836735 AGTCCCTTATTGGAATCTCTAAAAAGA 58.163 33.333 0.00 0.00 35.80 2.52
2523 3539 9.114952 GTCCCTTATTGGAATCTCTAAAAAGAG 57.885 37.037 0.00 0.00 35.80 2.85
2524 3540 9.057911 TCCCTTATTGGAATCTCTAAAAAGAGA 57.942 33.333 7.51 7.51 42.76 3.10
2546 3562 9.851267 AGAGATATATTTAAGAATGGAGGGAGT 57.149 33.333 0.00 0.00 0.00 3.85
2685 3746 4.634883 TGCTACAAAAACGGTTACAACAGA 59.365 37.500 0.00 0.00 0.00 3.41
2686 3747 5.202640 GCTACAAAAACGGTTACAACAGAG 58.797 41.667 0.00 0.00 0.00 3.35
2687 3748 4.625972 ACAAAAACGGTTACAACAGAGG 57.374 40.909 0.00 0.00 0.00 3.69
2688 3749 4.263435 ACAAAAACGGTTACAACAGAGGA 58.737 39.130 0.00 0.00 0.00 3.71
2689 3750 4.095334 ACAAAAACGGTTACAACAGAGGAC 59.905 41.667 0.00 0.00 0.00 3.85
2690 3751 2.144482 AACGGTTACAACAGAGGACG 57.856 50.000 0.00 0.00 0.00 4.79
2691 3752 1.035139 ACGGTTACAACAGAGGACGT 58.965 50.000 0.00 0.00 0.00 4.34
2692 3753 1.269413 ACGGTTACAACAGAGGACGTG 60.269 52.381 0.00 0.00 31.60 4.49
2693 3754 1.792006 GGTTACAACAGAGGACGTGG 58.208 55.000 0.00 0.00 0.00 4.94
2694 3755 1.069668 GGTTACAACAGAGGACGTGGT 59.930 52.381 0.00 0.00 0.00 4.16
2695 3756 2.132762 GTTACAACAGAGGACGTGGTG 58.867 52.381 0.00 0.00 38.67 4.17
2696 3757 0.032952 TACAACAGAGGACGTGGTGC 59.967 55.000 0.00 0.00 35.93 5.01
2697 3758 1.227527 CAACAGAGGACGTGGTGCA 60.228 57.895 0.00 0.00 0.00 4.57
2698 3759 1.069765 AACAGAGGACGTGGTGCAG 59.930 57.895 0.00 0.00 0.00 4.41
2834 3897 9.235537 GAAAAGGAACTCGTAATATAGTGAGAC 57.764 37.037 5.34 0.00 38.49 3.36
2878 3941 1.069703 GGCACGACGGTAAAAGGTTTC 60.070 52.381 0.00 0.00 0.00 2.78
2879 3942 1.598601 GCACGACGGTAAAAGGTTTCA 59.401 47.619 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 0.319728 CTCGATCCCAATGCCTCGAT 59.680 55.000 0.00 0.00 39.19 3.59
25 26 1.742146 CTCGATCCCAATGCCTCGA 59.258 57.895 0.00 0.00 37.77 4.04
26 27 1.958205 GCTCGATCCCAATGCCTCG 60.958 63.158 0.00 0.00 0.00 4.63
27 28 0.602372 GAGCTCGATCCCAATGCCTC 60.602 60.000 0.00 0.00 0.00 4.70
28 29 1.053264 AGAGCTCGATCCCAATGCCT 61.053 55.000 8.37 0.00 0.00 4.75
31 32 2.547642 GGAAGAGAGCTCGATCCCAATG 60.548 54.545 19.08 0.00 35.68 2.82
46 48 1.341156 ATCTGCCGGGAAGGGAAGAG 61.341 60.000 2.18 0.00 45.11 2.85
47 49 1.306997 ATCTGCCGGGAAGGGAAGA 60.307 57.895 2.18 0.00 45.97 2.87
48 50 1.153086 CATCTGCCGGGAAGGGAAG 60.153 63.158 2.18 0.00 40.94 3.46
49 51 2.998097 CATCTGCCGGGAAGGGAA 59.002 61.111 2.18 0.00 40.94 3.97
50 52 3.797353 GCATCTGCCGGGAAGGGA 61.797 66.667 2.18 0.00 41.48 4.20
51 53 3.801997 AGCATCTGCCGGGAAGGG 61.802 66.667 2.18 0.00 43.38 3.95
52 54 2.515523 CAGCATCTGCCGGGAAGG 60.516 66.667 2.18 0.00 43.38 3.46
53 55 1.523258 CTCAGCATCTGCCGGGAAG 60.523 63.158 2.18 0.00 43.38 3.46
54 56 2.586245 CTCAGCATCTGCCGGGAA 59.414 61.111 2.18 0.00 43.38 3.97
55 57 3.473647 CCTCAGCATCTGCCGGGA 61.474 66.667 2.18 0.00 43.38 5.14
59 61 3.412624 GACCCCCTCAGCATCTGCC 62.413 68.421 0.00 0.00 43.38 4.85
89 91 3.414269 GACCTCTTAGCTAGCGGATACT 58.586 50.000 9.55 0.00 32.79 2.12
93 95 0.179702 TCGACCTCTTAGCTAGCGGA 59.820 55.000 9.55 8.36 32.79 5.54
94 96 0.589223 CTCGACCTCTTAGCTAGCGG 59.411 60.000 9.55 6.56 34.75 5.52
96 98 3.142951 TCATCTCGACCTCTTAGCTAGC 58.857 50.000 6.62 6.62 0.00 3.42
100 102 3.319405 TCCAATCATCTCGACCTCTTAGC 59.681 47.826 0.00 0.00 0.00 3.09
101 103 4.582656 ACTCCAATCATCTCGACCTCTTAG 59.417 45.833 0.00 0.00 0.00 2.18
102 104 4.537751 ACTCCAATCATCTCGACCTCTTA 58.462 43.478 0.00 0.00 0.00 2.10
103 105 3.370104 ACTCCAATCATCTCGACCTCTT 58.630 45.455 0.00 0.00 0.00 2.85
137 150 2.816087 CCTTCAGTGTCATGTTTGGAGG 59.184 50.000 0.00 0.00 0.00 4.30
146 159 1.271054 GCTGTGTCCCTTCAGTGTCAT 60.271 52.381 0.00 0.00 34.57 3.06
147 160 0.106708 GCTGTGTCCCTTCAGTGTCA 59.893 55.000 0.00 0.00 34.57 3.58
148 161 0.394565 AGCTGTGTCCCTTCAGTGTC 59.605 55.000 0.00 0.00 34.57 3.67
151 164 0.972883 GAGAGCTGTGTCCCTTCAGT 59.027 55.000 0.00 0.00 34.57 3.41
155 168 2.564947 CAGTAAGAGAGCTGTGTCCCTT 59.435 50.000 0.00 0.00 0.00 3.95
193 206 4.335647 CGAGCTGGCCAGTTGGGT 62.336 66.667 32.81 14.63 39.65 4.51
205 424 3.397439 ATGCAGAGTGGCCGAGCT 61.397 61.111 0.00 0.00 0.00 4.09
208 427 3.333899 ATGCATGCAGAGTGGCCGA 62.334 57.895 26.69 0.00 0.00 5.54
210 429 0.749091 TACATGCATGCAGAGTGGCC 60.749 55.000 28.77 0.00 0.00 5.36
214 433 2.118313 TGCTTACATGCATGCAGAGT 57.882 45.000 26.69 26.12 38.12 3.24
215 434 2.223502 CCTTGCTTACATGCATGCAGAG 60.224 50.000 26.69 22.00 42.96 3.35
216 435 1.746787 CCTTGCTTACATGCATGCAGA 59.253 47.619 26.69 11.04 42.96 4.26
218 437 0.173935 GCCTTGCTTACATGCATGCA 59.826 50.000 26.53 25.04 42.96 3.96
219 438 0.173935 TGCCTTGCTTACATGCATGC 59.826 50.000 26.53 11.82 42.96 4.06
221 440 2.621998 GAGATGCCTTGCTTACATGCAT 59.378 45.455 0.00 0.00 43.43 3.96
237 457 6.137794 ACTTCAGGTACGTATTCTGAGATG 57.862 41.667 22.05 19.01 38.55 2.90
244 468 4.978083 TCAGGACTTCAGGTACGTATTC 57.022 45.455 0.00 0.00 33.01 1.75
245 469 4.771054 AGTTCAGGACTTCAGGTACGTATT 59.229 41.667 0.00 0.00 33.92 1.89
249 483 2.927014 GCAGTTCAGGACTTCAGGTACG 60.927 54.545 0.00 0.00 36.10 3.67
256 490 2.911484 CTATGGGCAGTTCAGGACTTC 58.089 52.381 0.00 0.00 36.10 3.01
259 493 0.543749 AGCTATGGGCAGTTCAGGAC 59.456 55.000 0.00 0.00 44.79 3.85
261 495 0.543277 TCAGCTATGGGCAGTTCAGG 59.457 55.000 0.00 0.00 44.79 3.86
279 514 3.111098 CAACTTCACAAGCTGCACTTTC 58.889 45.455 1.02 0.00 36.04 2.62
280 515 2.754552 TCAACTTCACAAGCTGCACTTT 59.245 40.909 1.02 0.00 36.04 2.66
281 516 2.368439 TCAACTTCACAAGCTGCACTT 58.632 42.857 1.02 0.00 40.05 3.16
282 517 2.042686 TCAACTTCACAAGCTGCACT 57.957 45.000 1.02 0.00 0.00 4.40
283 518 2.849880 TTCAACTTCACAAGCTGCAC 57.150 45.000 1.02 0.00 0.00 4.57
284 519 3.380954 TCATTTCAACTTCACAAGCTGCA 59.619 39.130 1.02 0.00 0.00 4.41
285 520 3.968649 TCATTTCAACTTCACAAGCTGC 58.031 40.909 0.00 0.00 0.00 5.25
286 521 4.438797 CGTTCATTTCAACTTCACAAGCTG 59.561 41.667 0.00 0.00 0.00 4.24
288 523 4.597079 TCGTTCATTTCAACTTCACAAGC 58.403 39.130 0.00 0.00 0.00 4.01
289 524 6.027131 TGTTCGTTCATTTCAACTTCACAAG 58.973 36.000 0.00 0.00 0.00 3.16
290 525 5.944013 TGTTCGTTCATTTCAACTTCACAA 58.056 33.333 0.00 0.00 0.00 3.33
293 528 6.801377 GCATATGTTCGTTCATTTCAACTTCA 59.199 34.615 4.29 0.00 0.00 3.02
294 529 7.007725 CAGCATATGTTCGTTCATTTCAACTTC 59.992 37.037 4.29 0.00 0.00 3.01
296 531 6.072508 ACAGCATATGTTCGTTCATTTCAACT 60.073 34.615 4.29 0.00 39.96 3.16
344 898 2.102252 TGGTTTTGTGGCAGTGGAATTC 59.898 45.455 0.00 0.00 0.00 2.17
395 950 1.275856 CAGGAGCTCAGCAAGAAGAGT 59.724 52.381 17.19 0.00 34.39 3.24
448 1003 1.239347 GCTGGGTTCAGTTTCAGACC 58.761 55.000 0.00 0.00 42.78 3.85
505 1072 4.515191 TGTACGTGTAATCGATAGGTACCC 59.485 45.833 19.37 3.66 38.84 3.69
522 1089 3.259064 GCTGGATATGTGTTGTGTACGT 58.741 45.455 0.00 0.00 0.00 3.57
530 1097 4.040755 AGAACTAGGGCTGGATATGTGTT 58.959 43.478 0.00 0.00 0.00 3.32
550 1117 0.918983 CTTCCATGGTTGGGCCTAGA 59.081 55.000 12.58 0.00 43.81 2.43
616 1183 3.454960 GATTGCGTTGCGGCCTAGC 62.455 63.158 0.00 0.00 37.71 3.42
782 1353 4.636435 CAACCCAACCGGCCGACT 62.636 66.667 30.73 10.45 33.26 4.18
807 1378 2.827190 ATGCAGTGCGGATGGCTG 60.827 61.111 11.20 0.00 44.05 4.85
808 1379 2.827190 CATGCAGTGCGGATGGCT 60.827 61.111 11.20 0.00 44.05 4.75
1154 1770 3.487202 CAACGACACCGCCGATGG 61.487 66.667 0.00 0.00 39.95 3.51
1155 1771 3.487202 CCAACGACACCGCCGATG 61.487 66.667 0.00 0.00 39.95 3.84
1393 2084 4.203076 GCCTACGGTGCCGACGAT 62.203 66.667 18.16 0.00 42.83 3.73
1433 2124 3.307906 TGACAACTCCCCCGACGG 61.308 66.667 6.99 6.99 0.00 4.79
1898 2625 9.296400 GATTTCAAACTTGCGGCTTAAATTATA 57.704 29.630 0.00 0.00 0.00 0.98
1911 2638 5.351189 ACAACAACCTTGATTTCAAACTTGC 59.649 36.000 8.49 0.00 35.15 4.01
2175 2907 6.279882 AGAAATCGCCACTTTTTGAATTTGA 58.720 32.000 0.00 0.00 0.00 2.69
2176 2908 6.529463 AGAAATCGCCACTTTTTGAATTTG 57.471 33.333 0.00 0.00 0.00 2.32
2177 2909 6.645003 GGTAGAAATCGCCACTTTTTGAATTT 59.355 34.615 0.00 0.00 0.00 1.82
2178 2910 6.156519 GGTAGAAATCGCCACTTTTTGAATT 58.843 36.000 0.00 0.00 0.00 2.17
2179 2911 5.336451 GGGTAGAAATCGCCACTTTTTGAAT 60.336 40.000 0.00 0.00 0.00 2.57
2180 2912 4.022676 GGGTAGAAATCGCCACTTTTTGAA 60.023 41.667 0.00 0.00 0.00 2.69
2191 2923 1.065551 GCAACCATGGGTAGAAATCGC 59.934 52.381 18.09 3.08 33.12 4.58
2326 3342 8.815912 AGCACATCCATATGTACATGTAGATTA 58.184 33.333 19.49 7.51 44.70 1.75
2364 3380 9.712305 CGAAGGGAGTATATGATAGTGAAAATT 57.288 33.333 0.00 0.00 0.00 1.82
2365 3381 8.871125 ACGAAGGGAGTATATGATAGTGAAAAT 58.129 33.333 0.00 0.00 0.00 1.82
2366 3382 8.246430 ACGAAGGGAGTATATGATAGTGAAAA 57.754 34.615 0.00 0.00 0.00 2.29
2367 3383 7.834881 ACGAAGGGAGTATATGATAGTGAAA 57.165 36.000 0.00 0.00 0.00 2.69
2368 3384 7.039923 GGAACGAAGGGAGTATATGATAGTGAA 60.040 40.741 0.00 0.00 0.00 3.18
2369 3385 6.433404 GGAACGAAGGGAGTATATGATAGTGA 59.567 42.308 0.00 0.00 0.00 3.41
2370 3386 6.434652 AGGAACGAAGGGAGTATATGATAGTG 59.565 42.308 0.00 0.00 0.00 2.74
2371 3387 6.553857 AGGAACGAAGGGAGTATATGATAGT 58.446 40.000 0.00 0.00 0.00 2.12
2372 3388 8.577048 TTAGGAACGAAGGGAGTATATGATAG 57.423 38.462 0.00 0.00 0.00 2.08
2373 3389 8.945195 TTTAGGAACGAAGGGAGTATATGATA 57.055 34.615 0.00 0.00 0.00 2.15
2374 3390 7.850935 TTTAGGAACGAAGGGAGTATATGAT 57.149 36.000 0.00 0.00 0.00 2.45
2375 3391 7.850935 ATTTAGGAACGAAGGGAGTATATGA 57.149 36.000 0.00 0.00 0.00 2.15
2379 3395 9.377238 ACTTATATTTAGGAACGAAGGGAGTAT 57.623 33.333 0.00 0.00 0.00 2.12
2380 3396 8.773033 ACTTATATTTAGGAACGAAGGGAGTA 57.227 34.615 0.00 0.00 0.00 2.59
2381 3397 7.564292 AGACTTATATTTAGGAACGAAGGGAGT 59.436 37.037 0.00 0.00 0.00 3.85
2382 3398 7.953752 AGACTTATATTTAGGAACGAAGGGAG 58.046 38.462 0.00 0.00 0.00 4.30
2383 3399 7.909485 AGACTTATATTTAGGAACGAAGGGA 57.091 36.000 0.00 0.00 0.00 4.20
2384 3400 8.959705 AAAGACTTATATTTAGGAACGAAGGG 57.040 34.615 0.00 0.00 0.00 3.95
2426 3442 9.988350 CATTTTGCTTCGTATGTAGTTCTTTAT 57.012 29.630 0.00 0.00 0.00 1.40
2427 3443 9.210329 TCATTTTGCTTCGTATGTAGTTCTTTA 57.790 29.630 0.00 0.00 0.00 1.85
2428 3444 8.094798 TCATTTTGCTTCGTATGTAGTTCTTT 57.905 30.769 0.00 0.00 0.00 2.52
2429 3445 7.387948 ACTCATTTTGCTTCGTATGTAGTTCTT 59.612 33.333 0.00 0.00 0.00 2.52
2430 3446 6.874134 ACTCATTTTGCTTCGTATGTAGTTCT 59.126 34.615 0.00 0.00 0.00 3.01
2431 3447 6.955963 CACTCATTTTGCTTCGTATGTAGTTC 59.044 38.462 0.00 0.00 0.00 3.01
2432 3448 6.649141 TCACTCATTTTGCTTCGTATGTAGTT 59.351 34.615 0.00 0.00 0.00 2.24
2433 3449 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
2434 3450 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
2435 3451 7.428282 TTTCACTCATTTTGCTTCGTATGTA 57.572 32.000 0.00 0.00 0.00 2.29
2436 3452 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
2437 3453 7.801547 ATTTTCACTCATTTTGCTTCGTATG 57.198 32.000 0.00 0.00 0.00 2.39
2438 3454 8.511321 TGTATTTTCACTCATTTTGCTTCGTAT 58.489 29.630 0.00 0.00 0.00 3.06
2439 3455 7.801315 GTGTATTTTCACTCATTTTGCTTCGTA 59.199 33.333 0.00 0.00 35.68 3.43
2440 3456 6.636850 GTGTATTTTCACTCATTTTGCTTCGT 59.363 34.615 0.00 0.00 35.68 3.85
2441 3457 6.857964 AGTGTATTTTCACTCATTTTGCTTCG 59.142 34.615 0.00 0.00 44.07 3.79
2484 3500 9.574577 TTCCAATAAGGGACTATATATGGATGT 57.425 33.333 2.68 0.00 38.49 3.06
2497 3513 9.114952 CTCTTTTTAGAGATTCCAATAAGGGAC 57.885 37.037 0.00 0.00 38.13 4.46
2498 3514 9.057911 TCTCTTTTTAGAGATTCCAATAAGGGA 57.942 33.333 0.88 0.00 39.74 4.20
2520 3536 9.851267 ACTCCCTCCATTCTTAAATATATCTCT 57.149 33.333 0.00 0.00 0.00 3.10
2525 3541 9.548631 CTCCTACTCCCTCCATTCTTAAATATA 57.451 37.037 0.00 0.00 0.00 0.86
2526 3542 8.019652 ACTCCTACTCCCTCCATTCTTAAATAT 58.980 37.037 0.00 0.00 0.00 1.28
2527 3543 7.371043 ACTCCTACTCCCTCCATTCTTAAATA 58.629 38.462 0.00 0.00 0.00 1.40
2528 3544 6.213525 ACTCCTACTCCCTCCATTCTTAAAT 58.786 40.000 0.00 0.00 0.00 1.40
2529 3545 5.600749 ACTCCTACTCCCTCCATTCTTAAA 58.399 41.667 0.00 0.00 0.00 1.52
2530 3546 5.222278 ACTCCTACTCCCTCCATTCTTAA 57.778 43.478 0.00 0.00 0.00 1.85
2531 3547 4.901785 ACTCCTACTCCCTCCATTCTTA 57.098 45.455 0.00 0.00 0.00 2.10
2532 3548 3.786213 ACTCCTACTCCCTCCATTCTT 57.214 47.619 0.00 0.00 0.00 2.52
2533 3549 4.901785 TTACTCCTACTCCCTCCATTCT 57.098 45.455 0.00 0.00 0.00 2.40
2534 3550 6.502074 AAATTACTCCTACTCCCTCCATTC 57.498 41.667 0.00 0.00 0.00 2.67
2535 3551 7.849904 TCTTAAATTACTCCTACTCCCTCCATT 59.150 37.037 0.00 0.00 0.00 3.16
2536 3552 7.371043 TCTTAAATTACTCCTACTCCCTCCAT 58.629 38.462 0.00 0.00 0.00 3.41
2537 3553 6.748969 TCTTAAATTACTCCTACTCCCTCCA 58.251 40.000 0.00 0.00 0.00 3.86
2538 3554 7.290481 ACATCTTAAATTACTCCTACTCCCTCC 59.710 40.741 0.00 0.00 0.00 4.30
2539 3555 8.145122 CACATCTTAAATTACTCCTACTCCCTC 58.855 40.741 0.00 0.00 0.00 4.30
2540 3556 7.844779 TCACATCTTAAATTACTCCTACTCCCT 59.155 37.037 0.00 0.00 0.00 4.20
2541 3557 8.019656 TCACATCTTAAATTACTCCTACTCCC 57.980 38.462 0.00 0.00 0.00 4.30
2542 3558 7.654116 GCTCACATCTTAAATTACTCCTACTCC 59.346 40.741 0.00 0.00 0.00 3.85
2543 3559 8.417884 AGCTCACATCTTAAATTACTCCTACTC 58.582 37.037 0.00 0.00 0.00 2.59
2544 3560 8.312669 AGCTCACATCTTAAATTACTCCTACT 57.687 34.615 0.00 0.00 0.00 2.57
2545 3561 9.465985 GTAGCTCACATCTTAAATTACTCCTAC 57.534 37.037 0.00 0.00 0.00 3.18
2546 3562 9.197306 TGTAGCTCACATCTTAAATTACTCCTA 57.803 33.333 0.00 0.00 30.04 2.94
2547 3563 7.982354 GTGTAGCTCACATCTTAAATTACTCCT 59.018 37.037 10.30 0.00 45.51 3.69
2548 3564 8.132604 GTGTAGCTCACATCTTAAATTACTCC 57.867 38.462 10.30 0.00 45.51 3.85
2589 3605 8.723311 CATGTGCTAAAAATCCATGAATTTGTT 58.277 29.630 0.00 0.00 35.96 2.83
2598 3614 2.428171 AGCGCATGTGCTAAAAATCCAT 59.572 40.909 31.53 4.12 45.14 3.41
2685 3746 0.250166 GGTTTACTGCACCACGTCCT 60.250 55.000 0.00 0.00 34.04 3.85
2686 3747 0.250166 AGGTTTACTGCACCACGTCC 60.250 55.000 0.00 0.00 36.67 4.79
2687 3748 2.443887 TAGGTTTACTGCACCACGTC 57.556 50.000 0.00 0.00 36.67 4.34
2688 3749 3.071479 CAATAGGTTTACTGCACCACGT 58.929 45.455 0.00 0.00 36.67 4.49
2689 3750 3.331150 TCAATAGGTTTACTGCACCACG 58.669 45.455 0.00 0.00 36.67 4.94
2690 3751 3.127030 GCTCAATAGGTTTACTGCACCAC 59.873 47.826 0.00 0.00 36.67 4.16
2691 3752 3.244735 TGCTCAATAGGTTTACTGCACCA 60.245 43.478 0.00 0.00 36.67 4.17
2692 3753 3.343617 TGCTCAATAGGTTTACTGCACC 58.656 45.455 0.00 0.00 34.06 5.01
2693 3754 3.181506 GCTGCTCAATAGGTTTACTGCAC 60.182 47.826 0.00 0.00 0.00 4.57
2694 3755 3.009723 GCTGCTCAATAGGTTTACTGCA 58.990 45.455 0.00 0.00 0.00 4.41
2695 3756 3.274288 AGCTGCTCAATAGGTTTACTGC 58.726 45.455 0.00 0.00 0.00 4.40
2696 3757 4.509600 GCTAGCTGCTCAATAGGTTTACTG 59.490 45.833 4.91 0.00 38.95 2.74
2697 3758 4.162320 TGCTAGCTGCTCAATAGGTTTACT 59.838 41.667 17.23 0.00 43.37 2.24
2698 3759 4.442706 TGCTAGCTGCTCAATAGGTTTAC 58.557 43.478 17.23 0.00 43.37 2.01
2834 3897 4.223320 AGCAATTAATTTATGGACCGCG 57.777 40.909 0.00 0.00 0.00 6.46


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

AutoCloner maintained by Alex Coulton.