Multiple sequence alignment - TraesCS5A01G233700

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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 TraesCS5A01G233700 chr5A 100.000 3893 0 0 857 4749 449254823 449258715 0.000000e+00 7190
1 TraesCS5A01G233700 chr5A 100.000 523 0 0 1 523 449253967 449254489 0.000000e+00 966
2 TraesCS5A01G233700 chr5D 92.958 3181 114 43 857 3978 349376766 349379895 0.000000e+00 4532
3 TraesCS5A01G233700 chr5D 89.286 812 59 7 3962 4749 349379915 349380722 0.000000e+00 992
4 TraesCS5A01G233700 chr5D 92.180 422 15 10 106 523 349376329 349376736 8.860000e-162 580
5 TraesCS5A01G233700 chr5B 93.316 2274 115 18 2342 4599 409874723 409876975 0.000000e+00 3323
6 TraesCS5A01G233700 chr5B 91.000 1500 64 35 857 2329 409872683 409874138 0.000000e+00 1956
7 TraesCS5A01G233700 chr5B 89.899 495 23 10 37 523 409872182 409872657 3.140000e-171 612
8 TraesCS5A01G233700 chr4A 91.016 256 21 2 1495 1748 74009958 74010213 1.270000e-90 344
9 TraesCS5A01G233700 chr4B 90.625 256 22 2 1495 1748 482137849 482138104 5.890000e-89 339
10 TraesCS5A01G233700 chr4B 90.323 155 15 0 1339 1493 482137641 482137795 2.240000e-48 204
11 TraesCS5A01G233700 chr4D 90.234 256 23 2 1495 1748 392537963 392538218 2.740000e-87 333
12 TraesCS5A01G233700 chr4D 90.323 155 15 0 1339 1493 392537755 392537909 2.240000e-48 204
13 TraesCS5A01G233700 chr3B 80.098 407 73 6 1336 1741 222318456 222318855 3.590000e-76 296
14 TraesCS5A01G233700 chr3B 90.708 226 15 1 1337 1562 821233075 821232856 3.590000e-76 296
15 TraesCS5A01G233700 chr3B 76.961 408 89 4 1339 1745 372896587 372896184 1.330000e-55 228
16 TraesCS5A01G233700 chr3D 77.206 408 88 4 1339 1745 277222115 277222518 2.860000e-57 233
17 TraesCS5A01G233700 chr3A 76.961 408 89 4 1339 1745 362202181 362201778 1.330000e-55 228


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 TraesCS5A01G233700 chr5A 449253967 449258715 4748 False 4078.000000 7190 100.000000 1 4749 2 chr5A.!!$F1 4748
1 TraesCS5A01G233700 chr5D 349376329 349380722 4393 False 2034.666667 4532 91.474667 106 4749 3 chr5D.!!$F1 4643
2 TraesCS5A01G233700 chr5B 409872182 409876975 4793 False 1963.666667 3323 91.405000 37 4599 3 chr5B.!!$F1 4562

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
455 467 0.047176 TCCCTCTCCCTCTCTCCTCT 59.953 60.0 0.00 0.00 0.00 3.69 F
1278 1309 0.035317 TTGCATGATAGCCCGGCTAG 59.965 55.0 23.37 11.52 44.66 3.42 F
2331 2407 0.109153 ACTCACAAGTCATGGCAGCA 59.891 50.0 0.00 0.00 0.00 4.41 F
2569 3225 0.035439 AACTAATGGGTGGGCTCGTG 60.035 55.0 0.00 0.00 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2180 2235 0.029300 CGTGCGCAGATTAAATGGGG 59.971 55.0 12.22 0.0 0.00 4.96 R
2569 3225 1.535204 CCACCCTGCACCACATTTCC 61.535 60.0 0.00 0.0 0.00 3.13 R
3612 4271 0.176680 ACTCCGGCAGCATCTAACTG 59.823 55.0 0.00 0.0 38.22 3.16 R
4469 5178 0.240945 CACAACAAGCCCGCCTAAAG 59.759 55.0 0.00 0.0 0.00 1.85 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
85 86 6.578023 AGCTCATTGTACAGTATTCTTCTCC 58.422 40.000 0.00 0.00 0.00 3.71
87 88 6.235231 TCATTGTACAGTATTCTTCTCCCC 57.765 41.667 0.00 0.00 0.00 4.81
114 121 5.960113 TCTCTCTCTGTAGCATTTGTTCTC 58.040 41.667 0.00 0.00 0.00 2.87
144 151 1.518929 GCTAGCTAGACAACGATTGCG 59.481 52.381 25.15 0.00 44.79 4.85
188 195 1.542915 CCATCTGTGCAAACTCCCTTG 59.457 52.381 0.00 0.00 0.00 3.61
200 207 5.278512 GCAAACTCCCTTGAAAAGTCCTTAG 60.279 44.000 0.00 0.00 44.25 2.18
239 246 1.453762 GCCAGCCATGCATCTTCCTC 61.454 60.000 0.00 0.00 0.00 3.71
251 258 1.456705 CTTCCTCCTCCCTCCCTCG 60.457 68.421 0.00 0.00 0.00 4.63
253 260 4.150454 CCTCCTCCCTCCCTCGCT 62.150 72.222 0.00 0.00 0.00 4.93
254 261 2.520741 CTCCTCCCTCCCTCGCTC 60.521 72.222 0.00 0.00 0.00 5.03
255 262 4.507916 TCCTCCCTCCCTCGCTCG 62.508 72.222 0.00 0.00 0.00 5.03
286 298 1.142748 CTCCTGTCCTTAGCTGCGG 59.857 63.158 0.00 0.00 0.00 5.69
372 384 2.654863 CTCTCACTCCCTCTCTCTTCC 58.345 57.143 0.00 0.00 0.00 3.46
413 425 4.464947 AGAAAGCTGCTGAAACCTAAAGT 58.535 39.130 1.35 0.00 0.00 2.66
444 456 2.445654 CCTGCCTCCTCCCTCTCC 60.446 72.222 0.00 0.00 0.00 3.71
445 457 2.445654 CTGCCTCCTCCCTCTCCC 60.446 72.222 0.00 0.00 0.00 4.30
446 458 2.955246 TGCCTCCTCCCTCTCCCT 60.955 66.667 0.00 0.00 0.00 4.20
447 459 2.123033 GCCTCCTCCCTCTCCCTC 60.123 72.222 0.00 0.00 0.00 4.30
448 460 2.710826 GCCTCCTCCCTCTCCCTCT 61.711 68.421 0.00 0.00 0.00 3.69
449 461 1.541672 CCTCCTCCCTCTCCCTCTC 59.458 68.421 0.00 0.00 0.00 3.20
450 462 0.998945 CCTCCTCCCTCTCCCTCTCT 60.999 65.000 0.00 0.00 0.00 3.10
451 463 0.478507 CTCCTCCCTCTCCCTCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
452 464 0.996762 TCCTCCCTCTCCCTCTCTCC 60.997 65.000 0.00 0.00 0.00 3.71
453 465 0.998945 CCTCCCTCTCCCTCTCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
454 466 0.478507 CTCCCTCTCCCTCTCTCCTC 59.521 65.000 0.00 0.00 0.00 3.71
455 467 0.047176 TCCCTCTCCCTCTCTCCTCT 59.953 60.000 0.00 0.00 0.00 3.69
456 468 0.478507 CCCTCTCCCTCTCTCCTCTC 59.521 65.000 0.00 0.00 0.00 3.20
457 469 0.108585 CCTCTCCCTCTCTCCTCTCG 59.891 65.000 0.00 0.00 0.00 4.04
458 470 0.837272 CTCTCCCTCTCTCCTCTCGT 59.163 60.000 0.00 0.00 0.00 4.18
459 471 0.834612 TCTCCCTCTCTCCTCTCGTC 59.165 60.000 0.00 0.00 0.00 4.20
460 472 0.531974 CTCCCTCTCTCCTCTCGTCG 60.532 65.000 0.00 0.00 0.00 5.12
502 516 0.523519 TGTCTCTGTAGCAGCTCACG 59.476 55.000 0.00 0.00 0.00 4.35
515 529 1.901650 GCTCACGAAAGCCAACTCCG 61.902 60.000 0.00 0.00 36.22 4.63
896 913 2.814183 TTCCTTCCGAACGCTCGCTC 62.814 60.000 1.91 0.00 44.04 5.03
912 929 4.260132 GCTCGCTCTTGTTGTAGATCATTG 60.260 45.833 0.00 0.00 0.00 2.82
951 971 1.580059 TACCACTCCCCATCTGGTTC 58.420 55.000 0.00 0.00 39.16 3.62
982 1002 1.115467 CTCCCTATATAGGCAGCCCG 58.885 60.000 21.75 8.44 42.26 6.13
986 1006 1.460504 CTATATAGGCAGCCCGACGA 58.539 55.000 8.22 0.00 35.76 4.20
1010 1031 5.531122 TTCCTTTCCATCGTGTAGATAGG 57.469 43.478 0.00 0.00 37.52 2.57
1039 1060 2.197324 AGGCGAGCTAGAGAGGGG 59.803 66.667 0.00 0.00 0.00 4.79
1051 1077 1.943860 AGAGAGGGGAAGGAGGATTCT 59.056 52.381 0.00 0.00 0.00 2.40
1052 1078 2.320675 AGAGAGGGGAAGGAGGATTCTT 59.679 50.000 0.00 0.00 0.00 2.52
1071 1097 5.779241 TCTTTCTCTCTCTCTCCTCTTCT 57.221 43.478 0.00 0.00 0.00 2.85
1143 1169 3.136123 CCGCCTACCGACGAGGAA 61.136 66.667 6.77 0.00 45.00 3.36
1239 1265 2.264794 GGGACACCAGGTACGCAG 59.735 66.667 0.00 0.00 36.50 5.18
1274 1305 3.057969 TCTAATTGCATGATAGCCCGG 57.942 47.619 0.00 0.00 0.00 5.73
1275 1306 1.470098 CTAATTGCATGATAGCCCGGC 59.530 52.381 0.00 0.00 0.00 6.13
1276 1307 0.178981 AATTGCATGATAGCCCGGCT 60.179 50.000 18.05 18.05 43.41 5.52
1277 1308 0.692476 ATTGCATGATAGCCCGGCTA 59.308 50.000 21.55 21.55 45.55 3.93
1278 1309 0.035317 TTGCATGATAGCCCGGCTAG 59.965 55.000 23.37 11.52 44.66 3.42
1279 1310 1.743252 GCATGATAGCCCGGCTAGC 60.743 63.158 25.02 25.02 44.66 3.42
1280 1311 1.978473 CATGATAGCCCGGCTAGCT 59.022 57.895 29.86 13.57 46.16 3.32
1281 1312 1.186200 CATGATAGCCCGGCTAGCTA 58.814 55.000 29.86 18.95 46.16 3.32
1282 1313 1.134965 CATGATAGCCCGGCTAGCTAC 60.135 57.143 29.86 18.09 46.16 3.58
1283 1314 0.112606 TGATAGCCCGGCTAGCTACT 59.887 55.000 29.86 12.15 46.16 2.57
1284 1315 0.528470 GATAGCCCGGCTAGCTACTG 59.472 60.000 24.60 2.33 44.66 2.74
1285 1316 0.900647 ATAGCCCGGCTAGCTACTGG 60.901 60.000 23.37 11.29 44.66 4.00
1286 1317 2.294170 TAGCCCGGCTAGCTACTGGT 62.294 60.000 15.59 9.05 41.83 4.00
1287 1318 1.831286 GCCCGGCTAGCTACTGGTA 60.831 63.158 15.72 0.00 0.00 3.25
1288 1319 1.807495 GCCCGGCTAGCTACTGGTAG 61.807 65.000 15.72 3.62 44.55 3.18
1289 1320 1.179814 CCCGGCTAGCTACTGGTAGG 61.180 65.000 15.72 5.54 42.66 3.18
1290 1321 0.467659 CCGGCTAGCTACTGGTAGGT 60.468 60.000 15.72 15.25 44.92 3.08
1291 1322 1.202855 CCGGCTAGCTACTGGTAGGTA 60.203 57.143 15.72 15.75 42.99 3.08
1292 1323 1.878734 CGGCTAGCTACTGGTAGGTAC 59.121 57.143 15.72 10.99 42.99 3.34
1311 1342 0.958091 CGCAATGGTGGAGTGGAAAA 59.042 50.000 0.00 0.00 0.00 2.29
1317 1348 2.858745 TGGTGGAGTGGAAAAACTAGC 58.141 47.619 0.00 0.00 0.00 3.42
1319 1350 1.197036 GTGGAGTGGAAAAACTAGCGC 59.803 52.381 0.00 0.00 0.00 5.92
1320 1351 1.071699 TGGAGTGGAAAAACTAGCGCT 59.928 47.619 17.26 17.26 0.00 5.92
1322 1353 3.244284 TGGAGTGGAAAAACTAGCGCTAA 60.244 43.478 19.37 2.45 0.00 3.09
1324 1355 2.735134 AGTGGAAAAACTAGCGCTAACG 59.265 45.455 19.37 10.39 44.07 3.18
1362 1410 3.681835 GACGCGGAGGTGGTGTCT 61.682 66.667 12.47 0.00 40.74 3.41
1746 1794 2.101770 CGCGTCTTCTCCCGGTAC 59.898 66.667 0.00 0.00 0.00 3.34
1760 1808 2.776659 GGTACGCAATCAACCTCCC 58.223 57.895 0.00 0.00 0.00 4.30
1761 1809 0.746923 GGTACGCAATCAACCTCCCC 60.747 60.000 0.00 0.00 0.00 4.81
1781 1829 0.820871 CTCTCTCTTCTTCCCCACCG 59.179 60.000 0.00 0.00 0.00 4.94
1834 1886 3.130164 TCTTTACAACAAGCAAGCAAGCA 59.870 39.130 3.19 0.00 36.85 3.91
1836 1888 2.607631 ACAACAAGCAAGCAAGCAAT 57.392 40.000 3.19 0.00 36.85 3.56
1837 1889 2.476821 ACAACAAGCAAGCAAGCAATC 58.523 42.857 3.19 0.00 36.85 2.67
1838 1890 2.159071 ACAACAAGCAAGCAAGCAATCA 60.159 40.909 3.19 0.00 36.85 2.57
1839 1891 2.867368 CAACAAGCAAGCAAGCAATCAA 59.133 40.909 3.19 0.00 36.85 2.57
1840 1892 2.750948 ACAAGCAAGCAAGCAATCAAG 58.249 42.857 3.19 0.00 36.85 3.02
1841 1893 1.459592 CAAGCAAGCAAGCAATCAAGC 59.540 47.619 3.19 0.00 36.85 4.01
1843 1895 1.067776 AGCAAGCAAGCAATCAAGCTC 60.068 47.619 3.19 0.00 45.89 4.09
1931 1986 4.288366 CCCCCTTTCTTTCTTTCTCTCTCT 59.712 45.833 0.00 0.00 0.00 3.10
1932 1987 5.487433 CCCCTTTCTTTCTTTCTCTCTCTC 58.513 45.833 0.00 0.00 0.00 3.20
1933 1988 5.487433 CCCTTTCTTTCTTTCTCTCTCTCC 58.513 45.833 0.00 0.00 0.00 3.71
1934 1989 5.167845 CCTTTCTTTCTTTCTCTCTCTCCG 58.832 45.833 0.00 0.00 0.00 4.63
1935 1990 4.792521 TTCTTTCTTTCTCTCTCTCCGG 57.207 45.455 0.00 0.00 0.00 5.14
2107 2162 1.541670 GCACACCTCCGTTGGTTTCTA 60.542 52.381 0.00 0.00 38.45 2.10
2329 2405 3.325293 ACTACTCACAAGTCATGGCAG 57.675 47.619 0.00 0.00 36.92 4.85
2330 2406 2.005451 CTACTCACAAGTCATGGCAGC 58.995 52.381 0.00 0.00 36.92 5.25
2331 2407 0.109153 ACTCACAAGTCATGGCAGCA 59.891 50.000 0.00 0.00 0.00 4.41
2332 2408 1.241165 CTCACAAGTCATGGCAGCAA 58.759 50.000 0.00 0.00 0.00 3.91
2333 2409 0.953727 TCACAAGTCATGGCAGCAAC 59.046 50.000 0.00 0.00 0.00 4.17
2334 2410 0.669619 CACAAGTCATGGCAGCAACA 59.330 50.000 0.00 0.00 0.00 3.33
2335 2411 1.271379 CACAAGTCATGGCAGCAACAT 59.729 47.619 0.00 0.00 0.00 2.71
2337 2413 1.271379 CAAGTCATGGCAGCAACATGT 59.729 47.619 0.00 0.00 44.57 3.21
2338 2414 2.488937 CAAGTCATGGCAGCAACATGTA 59.511 45.455 0.00 0.00 44.57 2.29
2339 2415 2.362736 AGTCATGGCAGCAACATGTAG 58.637 47.619 0.00 0.00 44.57 2.74
2340 2416 2.026915 AGTCATGGCAGCAACATGTAGA 60.027 45.455 0.00 0.00 44.57 2.59
2389 3037 3.242870 CCGAGCAGCAACATAAATTCCTC 60.243 47.826 0.00 0.00 0.00 3.71
2426 3074 1.271102 AGTCTCTTTTCTCGCTCGCTT 59.729 47.619 0.00 0.00 0.00 4.68
2439 3095 1.009829 CTCGCTTGCTGTTGGTATCC 58.990 55.000 0.00 0.00 0.00 2.59
2446 3102 1.555075 TGCTGTTGGTATCCTCAGTCC 59.445 52.381 10.79 0.00 32.40 3.85
2449 3105 3.866651 CTGTTGGTATCCTCAGTCCTTG 58.133 50.000 0.00 0.00 0.00 3.61
2453 3109 3.719871 TGGTATCCTCAGTCCTTGCTAA 58.280 45.455 0.00 0.00 0.00 3.09
2481 3137 3.570550 GCTCCTCTTGACCATACGAGTAT 59.429 47.826 0.00 0.00 0.00 2.12
2482 3138 4.760715 GCTCCTCTTGACCATACGAGTATA 59.239 45.833 0.00 0.00 0.00 1.47
2528 3184 5.888412 TCGTCGATGTGAATATGTGATTG 57.112 39.130 4.21 0.00 0.00 2.67
2569 3225 0.035439 AACTAATGGGTGGGCTCGTG 60.035 55.000 0.00 0.00 0.00 4.35
2782 3441 3.248171 GTCGTCATCAGCGCCGTC 61.248 66.667 2.29 0.00 0.00 4.79
2819 3478 2.480555 CAATGCGCAGTCCGAACC 59.519 61.111 18.32 0.00 40.02 3.62
3515 4174 0.394938 ACACGCCACAATGGACACTA 59.605 50.000 0.00 0.00 40.96 2.74
3604 4263 2.826702 GGTTGTCCCACGGTGAGT 59.173 61.111 10.28 0.00 0.00 3.41
3660 4323 1.404748 TCTTCTGATCGAGCTGCAGAG 59.595 52.381 20.43 7.97 39.56 3.35
3856 4520 5.804473 TGCATGCAACTGGAAATATTTAACG 59.196 36.000 20.30 0.00 0.00 3.18
3880 4544 7.067129 ACGAACTCAGATACAGAAATGCTAGTA 59.933 37.037 0.00 0.00 0.00 1.82
3883 4547 7.711846 ACTCAGATACAGAAATGCTAGTAGTG 58.288 38.462 0.00 0.00 0.00 2.74
4041 4743 0.966179 ACACACGCCTACATCTGACA 59.034 50.000 0.00 0.00 0.00 3.58
4051 4753 6.823689 ACGCCTACATCTGACAAAGATAAATT 59.176 34.615 0.00 0.00 44.24 1.82
4099 4801 0.948678 AAACGTGTACATGTGGGTGC 59.051 50.000 21.12 0.00 0.00 5.01
4144 4846 0.321653 ACCGCAATTCACCTCCTCAC 60.322 55.000 0.00 0.00 0.00 3.51
4181 4883 2.100584 GTCACCAAACCATTGTGCTTGA 59.899 45.455 0.00 0.00 34.60 3.02
4186 4888 2.991190 CAAACCATTGTGCTTGATGCTC 59.009 45.455 0.00 0.00 43.37 4.26
4227 4929 7.480810 TGAATGCTTCAGATCAGATTTCATTG 58.519 34.615 11.75 0.00 34.08 2.82
4237 4939 6.765036 AGATCAGATTTCATTGTATTCGTGCT 59.235 34.615 0.00 0.00 0.00 4.40
4295 5004 9.421399 TCCATAATAGACTGAGAACAATAGTCA 57.579 33.333 0.00 0.00 42.44 3.41
4348 5057 5.506317 GCACTATTACAAGATTGGCATCACC 60.506 44.000 0.00 0.00 39.84 4.02
4365 5074 5.302568 GCATCACCAAATTCCAATCCATCTA 59.697 40.000 0.00 0.00 0.00 1.98
4379 5088 3.609853 TCCATCTAATGTGTCTGCAACC 58.390 45.455 0.00 0.00 0.00 3.77
4380 5089 3.008923 TCCATCTAATGTGTCTGCAACCA 59.991 43.478 0.00 0.00 0.00 3.67
4382 5091 4.218200 CCATCTAATGTGTCTGCAACCAAA 59.782 41.667 0.00 0.00 0.00 3.28
4384 5093 5.375417 TCTAATGTGTCTGCAACCAAATG 57.625 39.130 0.00 0.00 0.00 2.32
4400 5109 3.193903 CCAAATGCTCACACATGAATGGA 59.806 43.478 0.00 0.00 33.88 3.41
4436 5145 3.827722 TGTAAAGGAGAAGGGTTTGGTG 58.172 45.455 0.00 0.00 0.00 4.17
4440 5149 1.355720 AGGAGAAGGGTTTGGTGATGG 59.644 52.381 0.00 0.00 0.00 3.51
4441 5150 1.177401 GAGAAGGGTTTGGTGATGGC 58.823 55.000 0.00 0.00 0.00 4.40
4469 5178 4.459089 GCGTCCCAGCTGAGTCCC 62.459 72.222 17.39 0.00 0.00 4.46
4489 5198 0.466555 TTTAGGCGGGCTTGTTGTGT 60.467 50.000 10.13 0.00 0.00 3.72
4492 5201 2.658268 GCGGGCTTGTTGTGTTGC 60.658 61.111 0.00 0.00 0.00 4.17
4504 5213 2.856494 TGTTGCTGCCCCCTACCA 60.856 61.111 0.00 0.00 0.00 3.25
4511 5220 0.611896 CTGCCCCCTACCAAAACCTG 60.612 60.000 0.00 0.00 0.00 4.00
4554 5263 4.518970 GTGTTCCTATGTGGTTGTGTGATT 59.481 41.667 0.00 0.00 37.07 2.57
4558 5267 5.136828 TCCTATGTGGTTGTGTGATTTGTT 58.863 37.500 0.00 0.00 37.07 2.83
4564 5273 3.507622 TGGTTGTGTGATTTGTTGTGTCA 59.492 39.130 0.00 0.00 0.00 3.58
4583 5292 7.543756 TGTGTCATTTCGATGAGACTTATGTA 58.456 34.615 14.98 0.00 42.99 2.29
4585 5294 8.483218 GTGTCATTTCGATGAGACTTATGTATG 58.517 37.037 8.60 0.00 40.43 2.39
4616 5325 9.944376 TTTGATGCTATATGTATAAAGGGAGAC 57.056 33.333 0.00 0.00 0.00 3.36
4628 5337 2.233305 AGGGAGACGAGAGCCTTTTA 57.767 50.000 0.00 0.00 0.00 1.52
4630 5339 1.469423 GGGAGACGAGAGCCTTTTACG 60.469 57.143 0.00 0.00 0.00 3.18
4638 5347 3.982058 CGAGAGCCTTTTACGGTATGATC 59.018 47.826 0.00 0.00 0.00 2.92
4652 5376 5.048921 ACGGTATGATCACGGAGTAGTATTG 60.049 44.000 0.00 0.00 41.61 1.90
4653 5377 5.180680 CGGTATGATCACGGAGTAGTATTGA 59.819 44.000 0.00 0.00 41.61 2.57
4687 5411 1.241315 CCTACTTGTGCCCCAAACGG 61.241 60.000 0.00 0.00 31.20 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 1.342474 TGCTACAGAGAGAGAAGGGGG 60.342 57.143 0.00 0.00 0.00 5.40
87 88 4.081198 ACAAATGCTACAGAGAGAGAAGGG 60.081 45.833 0.00 0.00 0.00 3.95
89 90 6.397272 AGAACAAATGCTACAGAGAGAGAAG 58.603 40.000 0.00 0.00 0.00 2.85
90 91 6.210385 AGAGAACAAATGCTACAGAGAGAGAA 59.790 38.462 0.00 0.00 0.00 2.87
98 105 4.470462 GCACAAGAGAACAAATGCTACAG 58.530 43.478 0.00 0.00 0.00 2.74
99 106 3.058983 CGCACAAGAGAACAAATGCTACA 60.059 43.478 0.00 0.00 0.00 2.74
100 107 3.058914 ACGCACAAGAGAACAAATGCTAC 60.059 43.478 0.00 0.00 0.00 3.58
114 121 0.173481 TCTAGCTAGCCACGCACAAG 59.827 55.000 16.35 0.00 0.00 3.16
144 151 3.322828 TGGATATACGTTTGGGGTAGCTC 59.677 47.826 0.00 0.00 0.00 4.09
188 195 7.235080 GCGTCTCAATAAACTAAGGACTTTTC 58.765 38.462 0.00 0.00 0.00 2.29
200 207 1.398390 CTGGCTGGCGTCTCAATAAAC 59.602 52.381 0.00 0.00 0.00 2.01
251 258 1.605202 GGAGGAAGATGATGAGCGAGC 60.605 57.143 0.00 0.00 0.00 5.03
253 260 1.685517 CAGGAGGAAGATGATGAGCGA 59.314 52.381 0.00 0.00 0.00 4.93
254 261 1.411977 ACAGGAGGAAGATGATGAGCG 59.588 52.381 0.00 0.00 0.00 5.03
255 262 2.224257 GGACAGGAGGAAGATGATGAGC 60.224 54.545 0.00 0.00 0.00 4.26
259 271 3.645687 GCTAAGGACAGGAGGAAGATGAT 59.354 47.826 0.00 0.00 0.00 2.45
286 298 1.478105 CCTTAATTGTCCTTGCAGGGC 59.522 52.381 10.65 6.16 41.40 5.19
372 384 5.599048 TTCTTTGGGATTATATGGGGAGG 57.401 43.478 0.00 0.00 0.00 4.30
413 425 2.032528 CAGGCAGCTTTCCACCGA 59.967 61.111 4.72 0.00 0.00 4.69
444 456 0.817634 ATGCGACGAGAGGAGAGAGG 60.818 60.000 0.00 0.00 0.00 3.69
445 457 0.586319 GATGCGACGAGAGGAGAGAG 59.414 60.000 0.00 0.00 0.00 3.20
446 458 0.179234 AGATGCGACGAGAGGAGAGA 59.821 55.000 0.00 0.00 0.00 3.10
447 459 0.586319 GAGATGCGACGAGAGGAGAG 59.414 60.000 0.00 0.00 0.00 3.20
448 460 0.179234 AGAGATGCGACGAGAGGAGA 59.821 55.000 0.00 0.00 0.00 3.71
449 461 0.586319 GAGAGATGCGACGAGAGGAG 59.414 60.000 0.00 0.00 0.00 3.69
450 462 0.179234 AGAGAGATGCGACGAGAGGA 59.821 55.000 0.00 0.00 0.00 3.71
451 463 0.586319 GAGAGAGATGCGACGAGAGG 59.414 60.000 0.00 0.00 0.00 3.69
452 464 0.586319 GGAGAGAGATGCGACGAGAG 59.414 60.000 0.00 0.00 0.00 3.20
453 465 0.179234 AGGAGAGAGATGCGACGAGA 59.821 55.000 0.00 0.00 0.00 4.04
454 466 0.586319 GAGGAGAGAGATGCGACGAG 59.414 60.000 0.00 0.00 0.00 4.18
455 467 0.816018 GGAGGAGAGAGATGCGACGA 60.816 60.000 0.00 0.00 0.00 4.20
456 468 0.817634 AGGAGGAGAGAGATGCGACG 60.818 60.000 0.00 0.00 0.00 5.12
457 469 1.398692 AAGGAGGAGAGAGATGCGAC 58.601 55.000 0.00 0.00 0.00 5.19
458 470 1.753649 CAAAGGAGGAGAGAGATGCGA 59.246 52.381 0.00 0.00 0.00 5.10
459 471 1.202510 CCAAAGGAGGAGAGAGATGCG 60.203 57.143 0.00 0.00 0.00 4.73
460 472 1.836802 ACCAAAGGAGGAGAGAGATGC 59.163 52.381 0.00 0.00 0.00 3.91
502 516 0.673956 GGGTCTCGGAGTTGGCTTTC 60.674 60.000 4.69 0.00 0.00 2.62
896 913 2.689983 GGGGCCAATGATCTACAACAAG 59.310 50.000 4.39 0.00 0.00 3.16
923 940 1.297689 GGGAGTGGTAACGGGTTCC 59.702 63.158 0.00 0.00 42.51 3.62
924 941 1.297689 GGGGAGTGGTAACGGGTTC 59.702 63.158 0.00 0.00 42.51 3.62
925 942 0.843343 ATGGGGAGTGGTAACGGGTT 60.843 55.000 0.00 0.00 42.51 4.11
926 943 1.229723 ATGGGGAGTGGTAACGGGT 60.230 57.895 0.00 0.00 42.51 5.28
930 947 1.286248 ACCAGATGGGGAGTGGTAAC 58.714 55.000 3.48 0.00 42.99 2.50
951 971 6.372931 CCTATATAGGGAGGGAGAAGAGATG 58.627 48.000 19.74 0.00 39.86 2.90
982 1002 3.000727 ACACGATGGAAAGGAATTCGTC 58.999 45.455 0.30 0.00 40.72 4.20
986 1006 6.525629 CCTATCTACACGATGGAAAGGAATT 58.474 40.000 0.00 0.00 32.75 2.17
1010 1031 0.875474 GCTCGCCTGATCAAGAGAGC 60.875 60.000 27.18 27.18 43.82 4.09
1039 1060 5.893824 AGAGAGAGAGAAAGAATCCTCCTTC 59.106 44.000 0.00 0.00 0.00 3.46
1051 1077 5.500234 CTCAGAAGAGGAGAGAGAGAGAAA 58.500 45.833 0.00 0.00 38.26 2.52
1052 1078 4.626287 GCTCAGAAGAGGAGAGAGAGAGAA 60.626 50.000 0.00 0.00 42.33 2.87
1218 1244 4.091939 GTACCTGGTGTCCCGGCC 62.092 72.222 10.23 0.00 35.58 6.13
1239 1265 0.934496 TTAGATGCAATGGCGTACGC 59.066 50.000 31.54 31.54 45.35 4.42
1270 1301 1.179814 CCTACCAGTAGCTAGCCGGG 61.180 65.000 12.13 9.82 31.95 5.73
1271 1302 0.467659 ACCTACCAGTAGCTAGCCGG 60.468 60.000 12.13 9.76 31.95 6.13
1274 1305 1.266446 GCGTACCTACCAGTAGCTAGC 59.734 57.143 6.62 6.62 31.95 3.42
1275 1306 2.569059 TGCGTACCTACCAGTAGCTAG 58.431 52.381 0.00 0.00 31.95 3.42
1276 1307 2.715749 TGCGTACCTACCAGTAGCTA 57.284 50.000 0.00 0.00 31.95 3.32
1277 1308 1.843368 TTGCGTACCTACCAGTAGCT 58.157 50.000 0.00 0.00 31.95 3.32
1278 1309 2.470821 CATTGCGTACCTACCAGTAGC 58.529 52.381 0.00 0.00 31.95 3.58
1279 1310 2.429610 ACCATTGCGTACCTACCAGTAG 59.570 50.000 0.00 0.00 0.00 2.57
1280 1311 2.166870 CACCATTGCGTACCTACCAGTA 59.833 50.000 0.00 0.00 0.00 2.74
1281 1312 1.066430 CACCATTGCGTACCTACCAGT 60.066 52.381 0.00 0.00 0.00 4.00
1282 1313 1.651987 CACCATTGCGTACCTACCAG 58.348 55.000 0.00 0.00 0.00 4.00
1283 1314 0.250793 CCACCATTGCGTACCTACCA 59.749 55.000 0.00 0.00 0.00 3.25
1284 1315 0.538118 TCCACCATTGCGTACCTACC 59.462 55.000 0.00 0.00 0.00 3.18
1285 1316 1.206371 ACTCCACCATTGCGTACCTAC 59.794 52.381 0.00 0.00 0.00 3.18
1286 1317 1.206132 CACTCCACCATTGCGTACCTA 59.794 52.381 0.00 0.00 0.00 3.08
1287 1318 0.036388 CACTCCACCATTGCGTACCT 60.036 55.000 0.00 0.00 0.00 3.08
1288 1319 1.024579 CCACTCCACCATTGCGTACC 61.025 60.000 0.00 0.00 0.00 3.34
1289 1320 0.036765 TCCACTCCACCATTGCGTAC 60.037 55.000 0.00 0.00 0.00 3.67
1290 1321 0.687920 TTCCACTCCACCATTGCGTA 59.312 50.000 0.00 0.00 0.00 4.42
1291 1322 0.179004 TTTCCACTCCACCATTGCGT 60.179 50.000 0.00 0.00 0.00 5.24
1292 1323 0.958091 TTTTCCACTCCACCATTGCG 59.042 50.000 0.00 0.00 0.00 4.85
1319 1350 2.931969 TCTGCAACATCATCAGCGTTAG 59.068 45.455 0.00 0.00 0.00 2.34
1320 1351 2.672874 GTCTGCAACATCATCAGCGTTA 59.327 45.455 0.00 0.00 0.00 3.18
1322 1353 1.081892 GTCTGCAACATCATCAGCGT 58.918 50.000 0.00 0.00 0.00 5.07
1324 1355 0.737219 GGGTCTGCAACATCATCAGC 59.263 55.000 0.00 0.00 0.00 4.26
1329 1360 1.003839 GTCCGGGTCTGCAACATCA 60.004 57.895 0.00 0.00 0.00 3.07
1330 1361 2.100631 CGTCCGGGTCTGCAACATC 61.101 63.158 0.00 0.00 0.00 3.06
1331 1362 2.047274 CGTCCGGGTCTGCAACAT 60.047 61.111 0.00 0.00 0.00 2.71
1746 1794 1.452108 GAGGGGGAGGTTGATTGCG 60.452 63.158 0.00 0.00 0.00 4.85
1747 1795 0.106967 GAGAGGGGGAGGTTGATTGC 60.107 60.000 0.00 0.00 0.00 3.56
1759 1807 0.043334 TGGGGAAGAAGAGAGAGGGG 59.957 60.000 0.00 0.00 0.00 4.79
1760 1808 1.199615 GTGGGGAAGAAGAGAGAGGG 58.800 60.000 0.00 0.00 0.00 4.30
1761 1809 1.199615 GGTGGGGAAGAAGAGAGAGG 58.800 60.000 0.00 0.00 0.00 3.69
1781 1829 0.744771 GTTCGATGAGTTGGAGGGGC 60.745 60.000 0.00 0.00 0.00 5.80
1834 1886 1.677217 GGGAACTGCTCGAGCTTGATT 60.677 52.381 35.27 23.33 42.66 2.57
1836 1888 1.293498 GGGAACTGCTCGAGCTTGA 59.707 57.895 35.27 16.86 42.66 3.02
1837 1889 2.097038 CGGGAACTGCTCGAGCTTG 61.097 63.158 35.27 28.28 45.56 4.01
1838 1890 2.262915 CGGGAACTGCTCGAGCTT 59.737 61.111 35.27 23.67 45.56 3.74
1839 1891 3.764466 CCGGGAACTGCTCGAGCT 61.764 66.667 35.27 18.16 45.56 4.09
1841 1893 4.821589 GGCCGGGAACTGCTCGAG 62.822 72.222 8.45 8.45 45.56 4.04
1870 1922 1.200020 CCTTTCTGTCCCGCATTGAAC 59.800 52.381 0.00 0.00 0.00 3.18
1926 1981 2.769095 AGAAATCCTTTCCCGGAGAGAG 59.231 50.000 0.73 3.07 40.54 3.20
1931 1986 3.518992 ACAAAGAAATCCTTTCCCGGA 57.481 42.857 0.73 0.00 42.88 5.14
1932 1987 3.826729 AGAACAAAGAAATCCTTTCCCGG 59.173 43.478 0.00 0.00 42.88 5.73
1933 1988 4.762251 AGAGAACAAAGAAATCCTTTCCCG 59.238 41.667 0.00 0.00 42.88 5.14
1934 1989 5.565637 GCAGAGAACAAAGAAATCCTTTCCC 60.566 44.000 0.00 0.00 42.88 3.97
1935 1990 5.010012 TGCAGAGAACAAAGAAATCCTTTCC 59.990 40.000 0.00 0.00 42.88 3.13
2058 2113 4.066139 CAGGGAAAGGGGCTGGGG 62.066 72.222 0.00 0.00 0.00 4.96
2059 2114 3.268032 ACAGGGAAAGGGGCTGGG 61.268 66.667 0.00 0.00 0.00 4.45
2060 2115 2.036256 CACAGGGAAAGGGGCTGG 59.964 66.667 0.00 0.00 0.00 4.85
2061 2116 1.303643 GACACAGGGAAAGGGGCTG 60.304 63.158 0.00 0.00 0.00 4.85
2179 2234 0.385390 GTGCGCAGATTAAATGGGGG 59.615 55.000 12.22 0.00 0.00 5.40
2180 2235 0.029300 CGTGCGCAGATTAAATGGGG 59.971 55.000 12.22 0.00 0.00 4.96
2329 2405 4.509600 GCTTGGATCTACTCTACATGTTGC 59.490 45.833 2.30 0.00 0.00 4.17
2330 2406 5.053145 GGCTTGGATCTACTCTACATGTTG 58.947 45.833 2.30 1.19 0.00 3.33
2331 2407 4.965532 AGGCTTGGATCTACTCTACATGTT 59.034 41.667 2.30 0.00 0.00 2.71
2332 2408 4.551671 AGGCTTGGATCTACTCTACATGT 58.448 43.478 2.69 2.69 0.00 3.21
2333 2409 5.543507 AAGGCTTGGATCTACTCTACATG 57.456 43.478 0.00 0.00 0.00 3.21
2334 2410 5.923204 CAAAGGCTTGGATCTACTCTACAT 58.077 41.667 0.00 0.00 0.00 2.29
2335 2411 5.344743 CAAAGGCTTGGATCTACTCTACA 57.655 43.478 0.00 0.00 0.00 2.74
2370 3018 4.592942 TGAGAGGAATTTATGTTGCTGCT 58.407 39.130 0.00 0.00 29.32 4.24
2389 3037 4.634883 AGAGACTTTATTGCATGTGCTGAG 59.365 41.667 6.55 0.52 42.66 3.35
2426 3074 1.555075 GGACTGAGGATACCAACAGCA 59.445 52.381 12.09 0.00 35.09 4.41
2439 3095 4.197750 AGCATGAATTAGCAAGGACTGAG 58.802 43.478 0.00 0.00 0.00 3.35
2446 3102 4.880120 TCAAGAGGAGCATGAATTAGCAAG 59.120 41.667 0.00 0.00 0.00 4.01
2449 3105 3.563390 GGTCAAGAGGAGCATGAATTAGC 59.437 47.826 0.00 0.00 43.54 3.09
2481 3137 5.048573 TCAATCACAACAGCACTAGTACGTA 60.049 40.000 0.00 0.00 0.00 3.57
2482 3138 3.936372 ATCACAACAGCACTAGTACGT 57.064 42.857 0.00 0.00 0.00 3.57
2569 3225 1.535204 CCACCCTGCACCACATTTCC 61.535 60.000 0.00 0.00 0.00 3.13
2893 3552 2.281761 AGCTCAAGGTTGTGCCCG 60.282 61.111 12.01 0.00 45.84 6.13
3397 4056 4.463879 CTGCAGGCCACCTCCGAG 62.464 72.222 5.01 0.00 0.00 4.63
3515 4174 2.441001 AGATGGCTTAGCTTGGCTACAT 59.559 45.455 3.59 0.00 41.12 2.29
3604 4263 1.809619 GCATCTAACTGCGCCACGA 60.810 57.895 4.18 0.00 31.49 4.35
3612 4271 0.176680 ACTCCGGCAGCATCTAACTG 59.823 55.000 0.00 0.00 38.22 3.16
3660 4323 1.470458 GCCAGCCATGCTTAGCTTTTC 60.470 52.381 5.60 0.00 36.40 2.29
3856 4520 8.410141 ACTACTAGCATTTCTGTATCTGAGTTC 58.590 37.037 0.00 0.00 0.00 3.01
3880 4544 4.002906 TGTCCGAGAAAAATAGTGCACT 57.997 40.909 25.12 25.12 0.00 4.40
3883 4547 5.358298 AGTTTGTCCGAGAAAAATAGTGC 57.642 39.130 0.00 0.00 0.00 4.40
4099 4801 7.599621 TCCATTTTGATTTAGTGCTCACATTTG 59.400 33.333 2.63 0.00 0.00 2.32
4118 4820 2.231235 GAGGTGAATTGCGGTCCATTTT 59.769 45.455 0.00 0.00 0.00 1.82
4144 4846 2.135933 GTGACCGTGACTTTCTCTTGG 58.864 52.381 0.00 0.00 0.00 3.61
4227 4929 3.770666 TGCTTGACTAGAGCACGAATAC 58.229 45.455 0.00 0.00 44.63 1.89
4237 4939 5.917462 TGCTATGCTTAATGCTTGACTAGA 58.083 37.500 0.00 0.00 43.37 2.43
4280 4989 7.905604 TTAATGGTGTGACTATTGTTCTCAG 57.094 36.000 0.00 0.00 31.57 3.35
4282 4991 8.492673 TGATTAATGGTGTGACTATTGTTCTC 57.507 34.615 0.00 0.00 31.57 2.87
4295 5004 5.646215 TGTTAGGGGTTTGATTAATGGTGT 58.354 37.500 0.00 0.00 0.00 4.16
4348 5057 7.919091 CAGACACATTAGATGGATTGGAATTTG 59.081 37.037 0.00 0.00 33.60 2.32
4365 5074 2.366266 AGCATTTGGTTGCAGACACATT 59.634 40.909 0.00 0.00 45.23 2.71
4379 5088 4.421058 CTCCATTCATGTGTGAGCATTTG 58.579 43.478 0.00 0.00 35.39 2.32
4380 5089 3.446161 CCTCCATTCATGTGTGAGCATTT 59.554 43.478 0.00 0.00 35.39 2.32
4382 5091 2.240414 TCCTCCATTCATGTGTGAGCAT 59.760 45.455 0.00 0.00 35.39 3.79
4384 5093 2.408271 TCCTCCATTCATGTGTGAGC 57.592 50.000 0.00 0.00 35.39 4.26
4400 5109 4.163458 TCCTTTACAATCGCCATACTTCCT 59.837 41.667 0.00 0.00 0.00 3.36
4436 5145 2.709475 GCCGTTGTCATCGCCATC 59.291 61.111 0.00 0.00 0.00 3.51
4440 5149 3.849953 GGACGCCGTTGTCATCGC 61.850 66.667 0.00 0.00 40.72 4.58
4441 5150 3.186047 GGGACGCCGTTGTCATCG 61.186 66.667 0.00 0.00 40.72 3.84
4455 5164 1.573108 CTAAAGGGACTCAGCTGGGA 58.427 55.000 23.49 0.00 38.49 4.37
4469 5178 0.240945 CACAACAAGCCCGCCTAAAG 59.759 55.000 0.00 0.00 0.00 1.85
4489 5198 0.830023 GTTTTGGTAGGGGGCAGCAA 60.830 55.000 0.00 0.00 0.00 3.91
4492 5201 0.611896 CAGGTTTTGGTAGGGGGCAG 60.612 60.000 0.00 0.00 0.00 4.85
4517 5226 6.264292 ACATAGGAACACACAAAGCAACAATA 59.736 34.615 0.00 0.00 0.00 1.90
4518 5227 5.068987 ACATAGGAACACACAAAGCAACAAT 59.931 36.000 0.00 0.00 0.00 2.71
4519 5228 4.400884 ACATAGGAACACACAAAGCAACAA 59.599 37.500 0.00 0.00 0.00 2.83
4554 5263 5.056480 AGTCTCATCGAAATGACACAACAA 58.944 37.500 14.41 0.00 36.98 2.83
4558 5267 6.398095 ACATAAGTCTCATCGAAATGACACA 58.602 36.000 14.41 5.12 36.98 3.72
4588 5297 9.950496 CTCCCTTTATACATATAGCATCAAACT 57.050 33.333 0.00 0.00 0.00 2.66
4603 5312 3.224269 AGGCTCTCGTCTCCCTTTATAC 58.776 50.000 0.00 0.00 0.00 1.47
4616 5325 3.431922 TCATACCGTAAAAGGCTCTCG 57.568 47.619 0.00 0.00 33.69 4.04
4628 5337 2.928334 ACTACTCCGTGATCATACCGT 58.072 47.619 0.00 0.00 0.00 4.83
4630 5339 6.570672 TCAATACTACTCCGTGATCATACC 57.429 41.667 0.00 0.00 0.00 2.73
4653 5377 9.338622 GGCACAAGTAGGTCATTTATAGTATTT 57.661 33.333 0.00 0.00 0.00 1.40
4660 5384 3.268334 TGGGGCACAAGTAGGTCATTTAT 59.732 43.478 0.00 0.00 0.00 1.40
4687 5411 7.787725 CCAAGATTGGTAACCTCACTATAAC 57.212 40.000 3.30 0.00 43.43 1.89


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

AutoCloner maintained by Alex Coulton.