Multiple sequence alignment - TraesCS1B01G209800

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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 TraesCS1B01G209800 chr1B 100.000 4042 0 0 1 4042 380886703 380882662 0.000000e+00 7465
1 TraesCS1B01G209800 chr1D 93.947 1652 52 25 804 2447 280224015 280222404 0.000000e+00 2453
2 TraesCS1B01G209800 chr1D 96.176 863 27 5 2528 3385 280222405 280221544 0.000000e+00 1406
3 TraesCS1B01G209800 chr1D 95.449 813 23 5 1 806 280224846 280224041 0.000000e+00 1284
4 TraesCS1B01G209800 chr1D 81.006 616 62 32 3468 4042 280221337 280220736 4.800000e-119 438
5 TraesCS1B01G209800 chr1A 95.034 1470 59 8 804 2266 352139843 352138381 0.000000e+00 2298
6 TraesCS1B01G209800 chr1A 93.311 912 41 12 2528 3424 352137867 352136961 0.000000e+00 1328
7 TraesCS1B01G209800 chr1A 91.621 549 18 12 1 538 352140989 352140458 0.000000e+00 734
8 TraesCS1B01G209800 chr1A 93.069 202 4 5 601 801 352140066 352139874 1.840000e-73 287
9 TraesCS1B01G209800 chr1A 95.395 152 5 2 2265 2414 352138145 352137994 1.450000e-59 241
10 TraesCS1B01G209800 chr7B 94.505 91 3 2 2446 2534 639796283 639796193 5.450000e-29 139
11 TraesCS1B01G209800 chr5D 93.478 92 5 1 2446 2536 128577672 128577581 7.050000e-28 135
12 TraesCS1B01G209800 chr5D 94.382 89 4 1 2443 2530 357878345 357878433 7.050000e-28 135
13 TraesCS1B01G209800 chr5B 93.478 92 5 1 2446 2536 140966014 140965923 7.050000e-28 135
14 TraesCS1B01G209800 chr7A 92.473 93 5 2 2446 2536 98790410 98790318 9.120000e-27 132
15 TraesCS1B01G209800 chr6B 92.473 93 5 2 2446 2536 474189287 474189195 9.120000e-27 132
16 TraesCS1B01G209800 chr2D 91.579 95 6 2 2443 2536 54074023 54074116 3.280000e-26 130
17 TraesCS1B01G209800 chr2D 90.816 98 7 2 2443 2538 75255106 75255009 3.280000e-26 130
18 TraesCS1B01G209800 chr2A 86.441 118 12 4 2427 2541 258406412 258406528 4.240000e-25 126


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 TraesCS1B01G209800 chr1B 380882662 380886703 4041 True 7465.00 7465 100.0000 1 4042 1 chr1B.!!$R1 4041
1 TraesCS1B01G209800 chr1D 280220736 280224846 4110 True 1395.25 2453 91.6445 1 4042 4 chr1D.!!$R1 4041
2 TraesCS1B01G209800 chr1A 352136961 352140989 4028 True 977.60 2298 93.6860 1 3424 5 chr1A.!!$R1 3423

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
147 149 0.915364 GGAAGGAGCTCCAAGGTGAT 59.085 55.0 33.90 9.21 38.89 3.06 F
1802 2177 0.110295 TTGCTTCTGGCCAACTAGCA 59.890 50.0 24.44 24.44 39.85 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 2408 0.394938 TACGAGCCACCTCAAAAGCA 59.605 50.0 0.00 0.0 38.00 3.91 R
3450 4319 0.416231 TGGTAGGTACCCTCCAGCTT 59.584 55.0 18.22 0.0 45.87 3.74 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
80 81 4.331108 AGAAGAGGGAAAACAGCAATCTC 58.669 43.478 0.00 0.00 0.00 2.75
146 148 1.544825 CGGAAGGAGCTCCAAGGTGA 61.545 60.000 33.90 0.00 38.89 4.02
147 149 0.915364 GGAAGGAGCTCCAAGGTGAT 59.085 55.000 33.90 9.21 38.89 3.06
148 150 1.407989 GGAAGGAGCTCCAAGGTGATG 60.408 57.143 33.90 0.00 38.89 3.07
149 151 1.280421 GAAGGAGCTCCAAGGTGATGT 59.720 52.381 33.90 7.59 38.89 3.06
327 331 1.934220 GATCTCTGTCACCGCCGTCA 61.934 60.000 0.00 0.00 0.00 4.35
348 352 2.510238 CTCTTCGCTTCGGGCTGG 60.510 66.667 0.00 0.00 39.13 4.85
373 377 2.284921 TCCACCCTCCTCAGCCTG 60.285 66.667 0.00 0.00 0.00 4.85
374 378 4.106925 CCACCCTCCTCAGCCTGC 62.107 72.222 0.00 0.00 0.00 4.85
375 379 4.106925 CACCCTCCTCAGCCTGCC 62.107 72.222 0.00 0.00 0.00 4.85
376 380 4.345286 ACCCTCCTCAGCCTGCCT 62.345 66.667 0.00 0.00 0.00 4.75
401 407 1.346068 ACTCTTCTTCTTGCGCTTCCT 59.654 47.619 9.73 0.00 0.00 3.36
508 520 4.034048 GTCTAAACGCGATCAAACCATCAT 59.966 41.667 15.93 0.00 0.00 2.45
795 1136 5.105837 ACCGGTTCTAGTTTCTGTCAGATAC 60.106 44.000 13.77 13.77 0.00 2.24
801 1142 3.839293 AGTTTCTGTCAGATACGCTCAC 58.161 45.455 15.18 1.15 32.50 3.51
806 1175 1.810755 TGTCAGATACGCTCACGAACT 59.189 47.619 0.00 0.00 43.93 3.01
891 1263 5.292589 GCTGATAGTGAATTGCAATTTTGGG 59.707 40.000 24.81 11.29 0.00 4.12
892 1264 5.177326 TGATAGTGAATTGCAATTTTGGGC 58.823 37.500 24.81 12.66 0.00 5.36
893 1265 3.775261 AGTGAATTGCAATTTTGGGCT 57.225 38.095 24.81 15.00 0.00 5.19
895 1267 2.412770 GTGAATTGCAATTTTGGGCTCG 59.587 45.455 24.81 0.00 0.00 5.03
896 1268 2.298446 TGAATTGCAATTTTGGGCTCGA 59.702 40.909 24.81 0.66 0.00 4.04
897 1269 3.055963 TGAATTGCAATTTTGGGCTCGAT 60.056 39.130 24.81 0.00 0.00 3.59
899 1271 2.652941 TGCAATTTTGGGCTCGATTC 57.347 45.000 0.00 0.00 0.00 2.52
924 1299 7.766278 TCTTCTTTGCTATGTTATCTTGTCCTC 59.234 37.037 0.00 0.00 0.00 3.71
1033 1408 3.074412 CTCATGGACAAAGTTAACGCCT 58.926 45.455 0.00 0.00 0.00 5.52
1056 1431 1.140589 CGAGCGCCTCAAGATCAGT 59.859 57.895 2.29 0.00 0.00 3.41
1068 1443 1.741770 GATCAGTGGCGCGGAAGTT 60.742 57.895 8.83 0.00 0.00 2.66
1161 1536 1.529438 GCCGACAAGATTGTTGACGAA 59.471 47.619 17.17 0.00 43.74 3.85
1266 1641 2.340078 GAGCTCATCCGCGCCATA 59.660 61.111 9.40 0.00 34.40 2.74
1284 1659 3.058432 CCATAAAGAGGCGAATCATGCTG 60.058 47.826 0.00 0.00 0.00 4.41
1338 1713 2.028112 CCTCCTCGAGACCATTGTCAAA 60.028 50.000 15.71 0.00 44.33 2.69
1353 1728 0.951558 TCAAAAACTGCGAGAAGGCC 59.048 50.000 0.00 0.00 0.00 5.19
1482 1857 0.336737 GGGGAGAGTCAGGAGAGGAA 59.663 60.000 0.00 0.00 0.00 3.36
1576 1951 9.606631 CTCTCTGGTTAAACTAGCTGATTTAAT 57.393 33.333 15.82 0.00 33.92 1.40
1667 2042 9.227777 ACTTTGGTTAATTGTGGATAACTAGAC 57.772 33.333 0.00 0.00 0.00 2.59
1716 2091 7.325694 GGGGATAATTAGGATGCATTTTCATG 58.674 38.462 0.00 0.00 0.00 3.07
1738 2113 7.446931 TCATGAACATTCCTTTAGTGCAGTTTA 59.553 33.333 0.00 0.00 0.00 2.01
1739 2114 6.966021 TGAACATTCCTTTAGTGCAGTTTAC 58.034 36.000 0.00 0.00 0.00 2.01
1751 2126 2.880822 CAGTTTACACACTGCATCCG 57.119 50.000 0.00 0.00 37.96 4.18
1793 2168 7.031226 TGAAACTTATATCATTGCTTCTGGC 57.969 36.000 0.00 0.00 42.22 4.85
1802 2177 0.110295 TTGCTTCTGGCCAACTAGCA 59.890 50.000 24.44 24.44 39.85 3.49
1818 2193 4.072131 ACTAGCACTGTTAAACATGTGGG 58.928 43.478 0.00 0.00 32.07 4.61
1827 2202 6.603997 ACTGTTAAACATGTGGGTTTCAGTTA 59.396 34.615 0.00 0.00 40.21 2.24
1970 2345 2.434359 GCAGCACAGGACGGGTAC 60.434 66.667 0.00 0.00 0.00 3.34
2033 2408 2.163815 CCCTTCTGTACAAGTCGACGAT 59.836 50.000 10.46 0.00 0.00 3.73
2137 2512 3.445805 AGTCTTTTCTTTTGCCGGTCAAA 59.554 39.130 16.73 16.73 42.50 2.69
2142 2517 5.371115 TTTCTTTTGCCGGTCAAATAGAG 57.629 39.130 19.91 15.56 43.53 2.43
2171 2546 4.772624 AGCTTAGGTGAGTAGTTCATGTCA 59.227 41.667 0.00 0.00 38.29 3.58
2192 2567 2.014335 TCAGCGTGGAATCTGTGATG 57.986 50.000 0.00 0.00 0.00 3.07
2254 2630 5.461526 GCAGGGTTGAGTTTTGTTATCTTC 58.538 41.667 0.00 0.00 0.00 2.87
2312 2925 7.312154 TGGTTGCTAGCATTTGTTACATTTAG 58.688 34.615 20.13 0.00 0.00 1.85
2321 2934 8.082242 AGCATTTGTTACATTTAGTGGTCTTTC 58.918 33.333 0.00 0.00 0.00 2.62
2443 3155 8.281212 ACTGACAGTTTGTTAAGAACTTCATT 57.719 30.769 1.07 3.11 35.26 2.57
2444 3156 8.398665 ACTGACAGTTTGTTAAGAACTTCATTC 58.601 33.333 1.07 0.00 35.26 2.67
2455 3167 5.930837 AGAACTTCATTCTACTCCCTCTG 57.069 43.478 0.00 0.00 46.38 3.35
2456 3168 5.337788 AGAACTTCATTCTACTCCCTCTGT 58.662 41.667 0.00 0.00 46.38 3.41
2457 3169 6.494952 AGAACTTCATTCTACTCCCTCTGTA 58.505 40.000 0.00 0.00 46.38 2.74
2458 3170 6.954684 AGAACTTCATTCTACTCCCTCTGTAA 59.045 38.462 0.00 0.00 46.38 2.41
2459 3171 7.455008 AGAACTTCATTCTACTCCCTCTGTAAA 59.545 37.037 0.00 0.00 46.38 2.01
2460 3172 7.176589 ACTTCATTCTACTCCCTCTGTAAAG 57.823 40.000 0.00 0.00 0.00 1.85
2461 3173 6.954684 ACTTCATTCTACTCCCTCTGTAAAGA 59.045 38.462 0.00 0.00 0.00 2.52
2462 3174 7.455008 ACTTCATTCTACTCCCTCTGTAAAGAA 59.545 37.037 0.00 0.00 0.00 2.52
2463 3175 7.792364 TCATTCTACTCCCTCTGTAAAGAAA 57.208 36.000 0.00 0.00 0.00 2.52
2464 3176 8.380742 TCATTCTACTCCCTCTGTAAAGAAAT 57.619 34.615 0.00 0.00 0.00 2.17
2465 3177 9.488762 TCATTCTACTCCCTCTGTAAAGAAATA 57.511 33.333 0.00 0.00 0.00 1.40
2468 3180 9.488762 TTCTACTCCCTCTGTAAAGAAATATGA 57.511 33.333 0.00 0.00 0.00 2.15
2469 3181 9.137459 TCTACTCCCTCTGTAAAGAAATATGAG 57.863 37.037 0.00 0.00 0.00 2.90
2470 3182 7.979786 ACTCCCTCTGTAAAGAAATATGAGA 57.020 36.000 0.00 0.00 0.00 3.27
2471 3183 8.017418 ACTCCCTCTGTAAAGAAATATGAGAG 57.983 38.462 0.00 0.00 0.00 3.20
2472 3184 6.821388 TCCCTCTGTAAAGAAATATGAGAGC 58.179 40.000 0.00 0.00 0.00 4.09
2473 3185 5.694006 CCCTCTGTAAAGAAATATGAGAGCG 59.306 44.000 0.00 0.00 0.00 5.03
2474 3186 6.276847 CCTCTGTAAAGAAATATGAGAGCGT 58.723 40.000 0.00 0.00 0.00 5.07
2475 3187 6.758886 CCTCTGTAAAGAAATATGAGAGCGTT 59.241 38.462 0.00 0.00 0.00 4.84
2476 3188 7.278868 CCTCTGTAAAGAAATATGAGAGCGTTT 59.721 37.037 0.00 0.00 0.00 3.60
2477 3189 9.302345 CTCTGTAAAGAAATATGAGAGCGTTTA 57.698 33.333 0.00 0.00 0.00 2.01
2478 3190 9.302345 TCTGTAAAGAAATATGAGAGCGTTTAG 57.698 33.333 0.00 0.00 0.00 1.85
2479 3191 9.302345 CTGTAAAGAAATATGAGAGCGTTTAGA 57.698 33.333 0.00 0.00 0.00 2.10
2480 3192 9.817809 TGTAAAGAAATATGAGAGCGTTTAGAT 57.182 29.630 0.00 0.00 0.00 1.98
2482 3194 8.948631 AAAGAAATATGAGAGCGTTTAGATCA 57.051 30.769 0.00 0.00 37.82 2.92
2483 3195 7.938563 AGAAATATGAGAGCGTTTAGATCAC 57.061 36.000 0.00 0.00 37.82 3.06
2484 3196 7.721402 AGAAATATGAGAGCGTTTAGATCACT 58.279 34.615 0.00 0.00 37.82 3.41
2485 3197 8.851145 AGAAATATGAGAGCGTTTAGATCACTA 58.149 33.333 0.00 0.00 37.82 2.74
2486 3198 9.464714 GAAATATGAGAGCGTTTAGATCACTAA 57.535 33.333 0.00 0.00 37.82 2.24
2487 3199 9.817809 AAATATGAGAGCGTTTAGATCACTAAA 57.182 29.630 0.00 0.00 43.52 1.85
2488 3200 9.469807 AATATGAGAGCGTTTAGATCACTAAAG 57.530 33.333 0.00 0.00 45.42 1.85
2489 3201 6.268825 TGAGAGCGTTTAGATCACTAAAGT 57.731 37.500 0.00 0.00 45.42 2.66
2490 3202 7.387119 TGAGAGCGTTTAGATCACTAAAGTA 57.613 36.000 0.00 0.00 45.42 2.24
2491 3203 7.473366 TGAGAGCGTTTAGATCACTAAAGTAG 58.527 38.462 0.00 0.00 45.42 2.57
2492 3204 7.120873 TGAGAGCGTTTAGATCACTAAAGTAGT 59.879 37.037 0.00 0.00 45.42 2.73
2507 3219 8.817092 ACTAAAGTAGTGATCTAAGCTCTCTT 57.183 34.615 0.00 0.00 37.69 2.85
2508 3220 9.908747 ACTAAAGTAGTGATCTAAGCTCTCTTA 57.091 33.333 0.00 0.00 37.69 2.10
2521 3233 9.570468 TCTAAGCTCTCTTATATTTCTTACGGA 57.430 33.333 0.00 0.00 34.54 4.69
2522 3234 9.834628 CTAAGCTCTCTTATATTTCTTACGGAG 57.165 37.037 0.00 0.00 34.54 4.63
2523 3235 7.222000 AGCTCTCTTATATTTCTTACGGAGG 57.778 40.000 0.00 0.00 0.00 4.30
2524 3236 6.209788 AGCTCTCTTATATTTCTTACGGAGGG 59.790 42.308 0.00 0.00 0.00 4.30
2525 3237 6.208994 GCTCTCTTATATTTCTTACGGAGGGA 59.791 42.308 0.00 0.00 0.00 4.20
2526 3238 7.576098 GCTCTCTTATATTTCTTACGGAGGGAG 60.576 44.444 0.00 0.00 34.43 4.30
2596 3311 5.276461 ACAATGCTATCATCAACTCCGTA 57.724 39.130 0.00 0.00 31.27 4.02
2605 3320 4.948847 TCATCAACTCCGTATCCTGATTG 58.051 43.478 0.00 0.00 0.00 2.67
2729 3444 4.246458 GTGATAACGAGGCTCAACTCTTT 58.754 43.478 15.95 0.05 35.33 2.52
2792 3507 3.006537 CCAAGTACGAAGACCTCAAGGAA 59.993 47.826 2.30 0.00 38.94 3.36
2999 3714 0.911525 CCTCCTCCCAGCAGGAAAGA 60.912 60.000 0.00 0.00 46.94 2.52
3026 3741 0.108567 GGAAGGAGCAGAAGGACGAC 60.109 60.000 0.00 0.00 0.00 4.34
3186 3903 3.193479 TGCTGTACAGTGGTAGATGTCTG 59.807 47.826 23.44 0.00 0.00 3.51
3226 3943 4.431416 TGTGGCACTCCTTTTCTTTCTA 57.569 40.909 19.83 0.00 0.00 2.10
3275 3992 2.192443 CTGGGGCTGCTCTCATGG 59.808 66.667 0.00 0.00 0.00 3.66
3352 4080 4.848299 GTCTGCTCGTTCATCACAATTTTC 59.152 41.667 0.00 0.00 0.00 2.29
3426 4155 3.767230 CGACGCACGAAGGCACTG 61.767 66.667 0.00 0.00 45.77 3.66
3427 4156 3.414700 GACGCACGAAGGCACTGG 61.415 66.667 0.00 0.00 40.86 4.00
3428 4157 3.858868 GACGCACGAAGGCACTGGA 62.859 63.158 0.00 0.00 40.86 3.86
3429 4158 3.114616 CGCACGAAGGCACTGGAG 61.115 66.667 0.00 0.00 40.86 3.86
3430 4159 2.743928 GCACGAAGGCACTGGAGG 60.744 66.667 0.00 0.00 40.86 4.30
3432 4161 2.526873 ACGAAGGCACTGGAGGGT 60.527 61.111 0.00 0.00 40.86 4.34
3433 4162 1.229082 ACGAAGGCACTGGAGGGTA 60.229 57.895 0.00 0.00 40.86 3.69
3434 4163 1.218316 CGAAGGCACTGGAGGGTAC 59.782 63.158 0.00 0.00 40.86 3.34
3460 4329 3.005791 CCACTAAACAAAAAGCTGGAGGG 59.994 47.826 0.00 0.00 0.00 4.30
3555 4431 0.611896 TGATCTCCAGCGGTCACTCA 60.612 55.000 0.00 0.00 0.00 3.41
3556 4432 0.532573 GATCTCCAGCGGTCACTCAA 59.467 55.000 0.00 0.00 0.00 3.02
3566 4442 1.005630 GTCACTCAAGAGCGCACCT 60.006 57.895 11.47 2.70 0.00 4.00
3628 4504 4.308458 CCGGACGCACCCACAGAA 62.308 66.667 0.00 0.00 34.64 3.02
3629 4505 2.738521 CGGACGCACCCACAGAAG 60.739 66.667 0.00 0.00 34.64 2.85
3630 4506 3.050275 GGACGCACCCACAGAAGC 61.050 66.667 0.00 0.00 0.00 3.86
3631 4507 2.031163 GACGCACCCACAGAAGCT 59.969 61.111 0.00 0.00 0.00 3.74
3659 4535 8.672214 TTTTTGTACGTGTTTTAGGTTCTTTC 57.328 30.769 0.00 0.00 0.00 2.62
3660 4536 7.614124 TTTGTACGTGTTTTAGGTTCTTTCT 57.386 32.000 0.00 0.00 0.00 2.52
3663 4539 8.042944 TGTACGTGTTTTAGGTTCTTTCTTTT 57.957 30.769 0.00 0.00 0.00 2.27
3664 4540 8.513774 TGTACGTGTTTTAGGTTCTTTCTTTTT 58.486 29.630 0.00 0.00 0.00 1.94
3665 4541 7.806149 ACGTGTTTTAGGTTCTTTCTTTTTG 57.194 32.000 0.00 0.00 0.00 2.44
3746 4631 4.071423 CACACCATGTGGAAACATAGACA 58.929 43.478 5.96 0.00 44.27 3.41
3754 4639 4.455533 TGTGGAAACATAGACATGCTTCAC 59.544 41.667 0.00 0.00 46.14 3.18
3756 4641 3.063997 GGAAACATAGACATGCTTCACGG 59.936 47.826 0.00 0.00 38.47 4.94
3771 4656 0.583438 CACGGTGAAGAACAGTGCAG 59.417 55.000 0.74 0.00 45.82 4.41
3779 4664 3.505680 TGAAGAACAGTGCAGTTGTGTTT 59.494 39.130 4.66 3.24 34.55 2.83
3783 4668 3.398954 ACAGTGCAGTTGTGTTTTACG 57.601 42.857 3.13 0.00 0.00 3.18
3818 4730 7.414436 GTGCTTTTCACAAGTGTACTTATTGA 58.586 34.615 10.80 1.28 44.98 2.57
3829 4741 9.438291 CAAGTGTACTTATTGAAAAGTGAAGTG 57.562 33.333 0.00 0.00 39.95 3.16
3838 4750 3.064271 TGAAAAGTGAAGTGCGGTTGTAC 59.936 43.478 0.00 0.00 0.00 2.90
3853 4765 5.559608 GCGGTTGTACTTCTTAAAAGTGGAC 60.560 44.000 11.12 5.50 0.00 4.02
3856 4768 7.191551 GGTTGTACTTCTTAAAAGTGGACAAC 58.808 38.462 22.95 22.95 44.44 3.32
3875 4787 5.764131 ACAACACAGTTCACGAAAAAGAAA 58.236 33.333 0.00 0.00 0.00 2.52
3879 4791 6.210078 ACACAGTTCACGAAAAAGAAAAACA 58.790 32.000 0.00 0.00 0.00 2.83
3889 4801 3.608316 AAAGAAAAACAGTGCTTGGCA 57.392 38.095 0.00 0.00 35.60 4.92
3924 4837 4.026968 TGTGCTTTCGAAAAATGAAAAGCG 60.027 37.500 12.41 0.00 35.11 4.68
3949 4862 1.134848 TGTGCTTTTTGCTTCCCACAC 60.135 47.619 0.00 0.00 43.37 3.82
3982 4895 8.736751 TTCAAAAAGTGAAAAGTACAACACTC 57.263 30.769 12.14 0.00 43.43 3.51
4000 4913 2.146342 CTCCTCGTGAAGCACAATTGT 58.854 47.619 4.92 4.92 33.40 2.71
4002 4915 3.734463 TCCTCGTGAAGCACAATTGTAA 58.266 40.909 11.53 0.00 33.40 2.41
4017 4930 2.177394 TGTAATTGTGCTTCTCGCCA 57.823 45.000 0.00 0.00 38.05 5.69
4034 4947 3.067461 TCGCCAAAGCATAGTTGTGTTTT 59.933 39.130 0.00 0.00 39.83 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 91 8.784994 CCTTTTTCCCTCTTCTACTACTTTTTC 58.215 37.037 0.00 0.00 0.00 2.29
146 148 5.222007 GGTCTCAGGATGGAATGGATTACAT 60.222 44.000 0.00 0.00 43.81 2.29
147 149 4.103153 GGTCTCAGGATGGAATGGATTACA 59.897 45.833 0.00 0.00 36.16 2.41
148 150 4.349342 AGGTCTCAGGATGGAATGGATTAC 59.651 45.833 0.00 0.00 36.16 1.89
149 151 4.349048 CAGGTCTCAGGATGGAATGGATTA 59.651 45.833 0.00 0.00 36.16 1.75
244 246 2.285668 CCTCCTCCTTCTGCCCCA 60.286 66.667 0.00 0.00 0.00 4.96
249 251 0.398381 CCCTCCTCCTCCTCCTTCTG 60.398 65.000 0.00 0.00 0.00 3.02
252 256 2.023532 CTCCCTCCTCCTCCTCCTT 58.976 63.158 0.00 0.00 0.00 3.36
277 281 1.003118 CTCACCTTGTTCCCAATCCGA 59.997 52.381 0.00 0.00 0.00 4.55
348 352 1.909302 TGAGGAGGGTGGAGAAATCAC 59.091 52.381 0.00 0.00 34.61 3.06
373 377 2.626840 CAAGAAGAAGAGTAGGCAGGC 58.373 52.381 0.00 0.00 0.00 4.85
374 378 2.626840 GCAAGAAGAAGAGTAGGCAGG 58.373 52.381 0.00 0.00 0.00 4.85
375 379 2.266554 CGCAAGAAGAAGAGTAGGCAG 58.733 52.381 0.00 0.00 43.02 4.85
376 380 1.673033 GCGCAAGAAGAAGAGTAGGCA 60.673 52.381 0.30 0.00 43.02 4.75
401 407 3.067106 GCAGAAGCAGTGTTAGTAGCAA 58.933 45.455 0.00 0.00 41.58 3.91
722 1063 1.070601 GCTTGTTTGGTGCCCAGAAAT 59.929 47.619 0.00 0.00 33.81 2.17
795 1136 2.027625 GGTGGGAAGTTCGTGAGCG 61.028 63.158 0.00 0.00 39.92 5.03
801 1142 1.644786 GATTGCGGGTGGGAAGTTCG 61.645 60.000 0.00 0.00 0.00 3.95
806 1175 1.483415 GTAGTAGATTGCGGGTGGGAA 59.517 52.381 0.00 0.00 0.00 3.97
891 1263 5.476752 AACATAGCAAAGAAGAATCGAGC 57.523 39.130 0.00 0.00 0.00 5.03
892 1264 8.586570 AGATAACATAGCAAAGAAGAATCGAG 57.413 34.615 0.00 0.00 0.00 4.04
893 1265 8.820933 CAAGATAACATAGCAAAGAAGAATCGA 58.179 33.333 0.00 0.00 0.00 3.59
895 1267 9.928236 GACAAGATAACATAGCAAAGAAGAATC 57.072 33.333 0.00 0.00 0.00 2.52
896 1268 8.897752 GGACAAGATAACATAGCAAAGAAGAAT 58.102 33.333 0.00 0.00 0.00 2.40
897 1269 8.103305 AGGACAAGATAACATAGCAAAGAAGAA 58.897 33.333 0.00 0.00 0.00 2.52
899 1271 7.254252 CGAGGACAAGATAACATAGCAAAGAAG 60.254 40.741 0.00 0.00 0.00 2.85
1068 1443 1.220749 GGTGGACATCTTGCGGCTA 59.779 57.895 0.00 0.00 0.00 3.93
1161 1536 1.687612 CATGGTCTCCAAGGTGGCT 59.312 57.895 0.00 0.00 36.95 4.75
1266 1641 2.408271 TCAGCATGATTCGCCTCTTT 57.592 45.000 0.00 0.00 42.56 2.52
1284 1659 3.672295 CTGCACCCTCGGGCTCTTC 62.672 68.421 0.82 0.00 39.32 2.87
1338 1713 0.398318 AGAAGGCCTTCTCGCAGTTT 59.602 50.000 37.44 17.06 46.13 2.66
1353 1728 1.150567 CCGCAGCAATCTCGGAGAAG 61.151 60.000 12.40 8.95 45.53 2.85
1482 1857 2.036890 ACGGGAAGGTAGCGGAGT 59.963 61.111 0.00 0.00 0.00 3.85
1576 1951 2.902705 AGTAAAGCACTGTGTTCCGA 57.097 45.000 9.86 0.00 35.62 4.55
1691 2066 6.916360 TGAAAATGCATCCTAATTATCCCC 57.084 37.500 0.00 0.00 0.00 4.81
1716 2091 6.856426 GTGTAAACTGCACTAAAGGAATGTTC 59.144 38.462 0.00 0.00 34.30 3.18
1738 2113 0.670546 GTGCTACGGATGCAGTGTGT 60.671 55.000 0.00 0.00 41.41 3.72
1739 2114 0.670239 TGTGCTACGGATGCAGTGTG 60.670 55.000 0.00 0.00 41.41 3.82
1793 2168 5.451908 CACATGTTTAACAGTGCTAGTTGG 58.548 41.667 3.63 0.00 0.00 3.77
1802 2177 4.953579 ACTGAAACCCACATGTTTAACAGT 59.046 37.500 3.63 5.78 37.94 3.55
1818 2193 7.514573 ACGAAAACCAAATGTTAACTGAAAC 57.485 32.000 7.22 0.00 35.67 2.78
1827 2202 4.111916 CTCTGCAACGAAAACCAAATGTT 58.888 39.130 0.00 0.00 39.43 2.71
1970 2345 7.307573 GCAAAACTTTCATCTGGAATTTCTTGG 60.308 37.037 0.00 0.00 34.91 3.61
2033 2408 0.394938 TACGAGCCACCTCAAAAGCA 59.605 50.000 0.00 0.00 38.00 3.91
2137 2512 4.079443 ACTCACCTAAGCTGGAGTCTCTAT 60.079 45.833 0.00 0.00 35.85 1.98
2142 2517 3.358118 ACTACTCACCTAAGCTGGAGTC 58.642 50.000 8.07 0.00 40.76 3.36
2171 2546 2.768253 TCACAGATTCCACGCTGAAT 57.232 45.000 0.00 0.03 37.66 2.57
2192 2567 2.293122 TCACAAACTGCACATTGCCTAC 59.707 45.455 6.63 0.00 44.23 3.18
2208 2583 3.394674 TTTGAGATGCCTACGTCACAA 57.605 42.857 0.00 0.00 39.61 3.33
2214 2589 1.667724 CTGCCTTTTGAGATGCCTACG 59.332 52.381 0.00 0.00 0.00 3.51
2312 2925 6.395629 TGTTGCAGTATACTAGAAAGACCAC 58.604 40.000 4.74 0.00 0.00 4.16
2321 2934 3.815401 GGGCCATTGTTGCAGTATACTAG 59.185 47.826 4.39 1.71 0.00 2.57
2443 3155 9.137459 CTCATATTTCTTTACAGAGGGAGTAGA 57.863 37.037 0.00 0.00 0.00 2.59
2444 3156 9.137459 TCTCATATTTCTTTACAGAGGGAGTAG 57.863 37.037 0.00 0.00 0.00 2.57
2445 3157 9.137459 CTCTCATATTTCTTTACAGAGGGAGTA 57.863 37.037 0.00 0.00 0.00 2.59
2446 3158 7.418483 GCTCTCATATTTCTTTACAGAGGGAGT 60.418 40.741 0.00 0.00 0.00 3.85
2447 3159 6.928492 GCTCTCATATTTCTTTACAGAGGGAG 59.072 42.308 0.00 0.00 0.00 4.30
2448 3160 6.461648 CGCTCTCATATTTCTTTACAGAGGGA 60.462 42.308 4.55 0.00 40.23 4.20
2449 3161 5.694006 CGCTCTCATATTTCTTTACAGAGGG 59.306 44.000 0.00 0.00 34.42 4.30
2450 3162 6.276847 ACGCTCTCATATTTCTTTACAGAGG 58.723 40.000 0.00 0.00 0.00 3.69
2451 3163 7.763172 AACGCTCTCATATTTCTTTACAGAG 57.237 36.000 0.00 0.00 0.00 3.35
2452 3164 9.302345 CTAAACGCTCTCATATTTCTTTACAGA 57.698 33.333 0.00 0.00 0.00 3.41
2453 3165 9.302345 TCTAAACGCTCTCATATTTCTTTACAG 57.698 33.333 0.00 0.00 0.00 2.74
2454 3166 9.817809 ATCTAAACGCTCTCATATTTCTTTACA 57.182 29.630 0.00 0.00 0.00 2.41
2457 3169 8.821894 GTGATCTAAACGCTCTCATATTTCTTT 58.178 33.333 0.00 0.00 0.00 2.52
2458 3170 8.200792 AGTGATCTAAACGCTCTCATATTTCTT 58.799 33.333 0.00 0.00 0.00 2.52
2459 3171 7.721402 AGTGATCTAAACGCTCTCATATTTCT 58.279 34.615 0.00 0.00 0.00 2.52
2460 3172 7.938563 AGTGATCTAAACGCTCTCATATTTC 57.061 36.000 0.00 0.00 0.00 2.17
2461 3173 9.817809 TTTAGTGATCTAAACGCTCTCATATTT 57.182 29.630 0.00 0.00 40.05 1.40
2462 3174 9.469807 CTTTAGTGATCTAAACGCTCTCATATT 57.530 33.333 0.00 0.00 40.05 1.28
2463 3175 8.634444 ACTTTAGTGATCTAAACGCTCTCATAT 58.366 33.333 0.00 0.00 40.05 1.78
2464 3176 7.997482 ACTTTAGTGATCTAAACGCTCTCATA 58.003 34.615 0.00 0.00 40.05 2.15
2465 3177 6.868622 ACTTTAGTGATCTAAACGCTCTCAT 58.131 36.000 0.00 0.00 40.05 2.90
2466 3178 6.268825 ACTTTAGTGATCTAAACGCTCTCA 57.731 37.500 0.00 0.00 40.05 3.27
2467 3179 7.474190 ACTACTTTAGTGATCTAAACGCTCTC 58.526 38.462 0.00 0.00 40.05 3.20
2468 3180 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
2481 3193 8.682710 AAGAGAGCTTAGATCACTACTTTAGTG 58.317 37.037 0.00 6.97 43.89 2.74
2482 3194 8.817092 AAGAGAGCTTAGATCACTACTTTAGT 57.183 34.615 0.00 0.00 33.88 2.24
2495 3207 9.570468 TCCGTAAGAAATATAAGAGAGCTTAGA 57.430 33.333 0.00 0.00 38.87 2.10
2496 3208 9.834628 CTCCGTAAGAAATATAAGAGAGCTTAG 57.165 37.037 0.00 0.00 38.87 2.18
2497 3209 8.794553 CCTCCGTAAGAAATATAAGAGAGCTTA 58.205 37.037 0.00 0.00 39.51 3.09
2498 3210 7.256012 CCCTCCGTAAGAAATATAAGAGAGCTT 60.256 40.741 0.00 0.00 43.02 3.74
2499 3211 6.209788 CCCTCCGTAAGAAATATAAGAGAGCT 59.790 42.308 0.00 0.00 43.02 4.09
2500 3212 6.208994 TCCCTCCGTAAGAAATATAAGAGAGC 59.791 42.308 0.00 0.00 43.02 4.09
2501 3213 7.449086 ACTCCCTCCGTAAGAAATATAAGAGAG 59.551 40.741 0.00 0.00 43.02 3.20
2502 3214 7.296098 ACTCCCTCCGTAAGAAATATAAGAGA 58.704 38.462 0.00 0.00 43.02 3.10
2503 3215 7.527568 ACTCCCTCCGTAAGAAATATAAGAG 57.472 40.000 0.00 0.00 43.02 2.85
2504 3216 9.597681 AATACTCCCTCCGTAAGAAATATAAGA 57.402 33.333 0.00 0.00 43.02 2.10
2510 3222 9.916360 AAAAATAATACTCCCTCCGTAAGAAAT 57.084 29.630 0.00 0.00 43.02 2.17
2515 3227 9.991906 CAGATAAAAATAATACTCCCTCCGTAA 57.008 33.333 0.00 0.00 0.00 3.18
2516 3228 9.151177 ACAGATAAAAATAATACTCCCTCCGTA 57.849 33.333 0.00 0.00 0.00 4.02
2517 3229 8.030913 ACAGATAAAAATAATACTCCCTCCGT 57.969 34.615 0.00 0.00 0.00 4.69
2518 3230 8.904099 AACAGATAAAAATAATACTCCCTCCG 57.096 34.615 0.00 0.00 0.00 4.63
2576 3291 5.247110 AGGATACGGAGTTGATGATAGCATT 59.753 40.000 0.00 0.00 37.78 3.56
2596 3311 3.110705 AGGTGCAGTAGACAATCAGGAT 58.889 45.455 0.00 0.00 0.00 3.24
2605 3320 3.868757 TGTATGTGAGGTGCAGTAGAC 57.131 47.619 0.00 0.00 0.00 2.59
2729 3444 1.297689 GTGGATGCTCAGTGCCTCA 59.702 57.895 2.71 0.00 42.00 3.86
2792 3507 4.148825 GGCTCTGCGACGATGGGT 62.149 66.667 0.00 0.00 0.00 4.51
3026 3741 3.185188 CCGTTGATCATAAGCCGATGAAG 59.815 47.826 0.00 0.00 39.25 3.02
3186 3903 1.195448 CATGAAACTCACTGCCACGTC 59.805 52.381 0.00 0.00 0.00 4.34
3226 3943 1.774110 TTGGCCCGCATAACAATCAT 58.226 45.000 0.00 0.00 0.00 2.45
3275 3992 8.656849 CAAACTTATATACTTACCCATGCGATC 58.343 37.037 0.00 0.00 0.00 3.69
3306 4023 1.145803 GTCTTTGTACCACTGGACGC 58.854 55.000 0.71 0.00 0.00 5.19
3352 4080 8.916654 GTGACAACATATATACTCCAGATTTCG 58.083 37.037 0.00 0.00 0.00 3.46
3414 4143 1.541310 TACCCTCCAGTGCCTTCGTG 61.541 60.000 0.00 0.00 0.00 4.35
3424 4153 2.544844 TAGTGGAAGGTACCCTCCAG 57.455 55.000 29.37 0.00 33.71 3.86
3425 4154 2.908351 GTTTAGTGGAAGGTACCCTCCA 59.092 50.000 25.85 25.85 30.89 3.86
3426 4155 2.908351 TGTTTAGTGGAAGGTACCCTCC 59.092 50.000 21.19 21.19 30.89 4.30
3427 4156 4.628963 TTGTTTAGTGGAAGGTACCCTC 57.371 45.455 8.74 4.85 30.89 4.30
3428 4157 5.391577 TTTTGTTTAGTGGAAGGTACCCT 57.608 39.130 8.74 0.00 33.87 4.34
3429 4158 5.508489 GCTTTTTGTTTAGTGGAAGGTACCC 60.508 44.000 8.74 0.00 0.00 3.69
3430 4159 5.301045 AGCTTTTTGTTTAGTGGAAGGTACC 59.699 40.000 2.73 2.73 0.00 3.34
3432 4161 5.300792 CCAGCTTTTTGTTTAGTGGAAGGTA 59.699 40.000 0.00 0.00 0.00 3.08
3433 4162 4.099419 CCAGCTTTTTGTTTAGTGGAAGGT 59.901 41.667 0.00 0.00 0.00 3.50
3434 4163 4.340950 TCCAGCTTTTTGTTTAGTGGAAGG 59.659 41.667 0.00 0.00 29.63 3.46
3437 4166 3.888930 CCTCCAGCTTTTTGTTTAGTGGA 59.111 43.478 0.00 0.00 0.00 4.02
3438 4167 3.005791 CCCTCCAGCTTTTTGTTTAGTGG 59.994 47.826 0.00 0.00 0.00 4.00
3439 4168 3.636764 ACCCTCCAGCTTTTTGTTTAGTG 59.363 43.478 0.00 0.00 0.00 2.74
3440 4169 3.910989 ACCCTCCAGCTTTTTGTTTAGT 58.089 40.909 0.00 0.00 0.00 2.24
3441 4170 4.217767 GGTACCCTCCAGCTTTTTGTTTAG 59.782 45.833 0.00 0.00 0.00 1.85
3443 4172 2.963101 GGTACCCTCCAGCTTTTTGTTT 59.037 45.455 0.00 0.00 0.00 2.83
3447 4316 2.307980 GGTAGGTACCCTCCAGCTTTTT 59.692 50.000 8.74 0.00 40.53 1.94
3449 4318 1.203389 TGGTAGGTACCCTCCAGCTTT 60.203 52.381 18.22 0.00 45.87 3.51
3450 4319 0.416231 TGGTAGGTACCCTCCAGCTT 59.584 55.000 18.22 0.00 45.87 3.74
3452 4321 1.335882 GGTGGTAGGTACCCTCCAGC 61.336 65.000 27.54 27.54 45.87 4.85
3526 4402 1.667154 CTGGAGATCACCCGCGAAGA 61.667 60.000 8.23 1.95 0.00 2.87
3566 4442 3.353029 CACCACCGCATGTCGCAA 61.353 61.111 0.00 0.00 42.60 4.85
3570 4446 2.325082 GGACACACCACCGCATGTC 61.325 63.158 0.00 0.00 40.62 3.06
3612 4488 2.738521 CTTCTGTGGGTGCGTCCG 60.739 66.667 0.00 0.00 37.00 4.79
3614 4490 1.166531 AAAGCTTCTGTGGGTGCGTC 61.167 55.000 0.00 0.00 0.00 5.19
3639 4515 8.791605 CAAAAAGAAAGAACCTAAAACACGTAC 58.208 33.333 0.00 0.00 0.00 3.67
3640 4516 8.513774 ACAAAAAGAAAGAACCTAAAACACGTA 58.486 29.630 0.00 0.00 0.00 3.57
3706 4590 5.652891 TGGTGTGCTTCACTAAGGTTAAAAA 59.347 36.000 11.12 0.00 45.50 1.94
3707 4591 5.194432 TGGTGTGCTTCACTAAGGTTAAAA 58.806 37.500 11.12 0.00 45.50 1.52
3708 4592 4.783055 TGGTGTGCTTCACTAAGGTTAAA 58.217 39.130 11.12 0.00 45.50 1.52
3709 4593 4.425180 TGGTGTGCTTCACTAAGGTTAA 57.575 40.909 11.12 0.00 45.50 2.01
3710 4594 4.202419 ACATGGTGTGCTTCACTAAGGTTA 60.202 41.667 0.00 0.00 45.50 2.85
3711 4595 3.149196 CATGGTGTGCTTCACTAAGGTT 58.851 45.455 11.12 0.00 45.50 3.50
3712 4596 2.106511 ACATGGTGTGCTTCACTAAGGT 59.893 45.455 0.00 6.67 45.50 3.50
3713 4597 2.485426 CACATGGTGTGCTTCACTAAGG 59.515 50.000 0.00 6.20 41.89 2.69
3714 4598 2.485426 CCACATGGTGTGCTTCACTAAG 59.515 50.000 4.60 6.24 46.51 2.18
3715 4599 2.105649 TCCACATGGTGTGCTTCACTAA 59.894 45.455 4.60 3.08 46.51 2.24
3716 4600 1.696884 TCCACATGGTGTGCTTCACTA 59.303 47.619 4.60 6.80 46.51 2.74
3717 4601 0.473755 TCCACATGGTGTGCTTCACT 59.526 50.000 4.60 0.00 46.51 3.41
3718 4602 1.317613 TTCCACATGGTGTGCTTCAC 58.682 50.000 4.60 4.47 46.51 3.18
3729 4613 5.571784 AAGCATGTCTATGTTTCCACATG 57.428 39.130 6.54 6.54 43.92 3.21
3730 4614 5.824904 GAAGCATGTCTATGTTTCCACAT 57.175 39.130 5.81 0.00 44.18 3.21
3735 4619 9.663244 CTTCACCGTGAAGCATGTCTATGTTTC 62.663 44.444 24.62 9.12 46.03 2.78
3754 4639 1.003545 CAACTGCACTGTTCTTCACCG 60.004 52.381 0.00 0.00 0.00 4.94
3756 4641 2.420022 ACACAACTGCACTGTTCTTCAC 59.580 45.455 0.00 0.00 0.00 3.18
3762 4647 3.426963 CCGTAAAACACAACTGCACTGTT 60.427 43.478 0.00 0.00 0.00 3.16
3766 4651 3.408288 TTCCGTAAAACACAACTGCAC 57.592 42.857 0.00 0.00 0.00 4.57
3767 4652 4.416620 CTTTTCCGTAAAACACAACTGCA 58.583 39.130 0.00 0.00 31.37 4.41
3768 4653 3.242016 GCTTTTCCGTAAAACACAACTGC 59.758 43.478 0.00 0.00 31.37 4.40
3771 4656 4.801516 ACATGCTTTTCCGTAAAACACAAC 59.198 37.500 0.00 0.00 31.37 3.32
3811 4723 5.108385 ACCGCACTTCACTTTTCAATAAG 57.892 39.130 0.00 0.00 0.00 1.73
3812 4724 5.163602 ACAACCGCACTTCACTTTTCAATAA 60.164 36.000 0.00 0.00 0.00 1.40
3814 4726 3.130340 ACAACCGCACTTCACTTTTCAAT 59.870 39.130 0.00 0.00 0.00 2.57
3818 4730 3.275999 AGTACAACCGCACTTCACTTTT 58.724 40.909 0.00 0.00 0.00 2.27
3829 4741 4.512571 TCCACTTTTAAGAAGTACAACCGC 59.487 41.667 0.00 0.00 0.00 5.68
3838 4750 6.436843 ACTGTGTTGTCCACTTTTAAGAAG 57.563 37.500 0.00 0.00 44.81 2.85
3843 4755 4.093703 CGTGAACTGTGTTGTCCACTTTTA 59.906 41.667 0.00 0.00 44.81 1.52
3853 4765 6.683090 TTTTCTTTTTCGTGAACTGTGTTG 57.317 33.333 0.00 0.00 0.00 3.33
3856 4768 6.362283 ACTGTTTTTCTTTTTCGTGAACTGTG 59.638 34.615 0.00 0.00 0.00 3.66
3865 4777 4.492409 GCCAAGCACTGTTTTTCTTTTTCG 60.492 41.667 0.00 0.00 0.00 3.46
3866 4778 4.391523 TGCCAAGCACTGTTTTTCTTTTTC 59.608 37.500 0.00 0.00 31.71 2.29
3875 4787 1.269936 GCTTCATGCCAAGCACTGTTT 60.270 47.619 12.88 0.00 46.93 2.83
3909 4821 4.603960 CACAATTGCGCTTTTCATTTTTCG 59.396 37.500 9.73 0.00 0.00 3.46
3910 4822 4.376570 GCACAATTGCGCTTTTCATTTTTC 59.623 37.500 9.73 0.00 39.50 2.29
3979 4892 2.146342 CAATTGTGCTTCACGAGGAGT 58.854 47.619 0.00 0.00 37.14 3.85
3982 4895 4.685169 ATTACAATTGTGCTTCACGAGG 57.315 40.909 21.42 0.00 37.14 4.63
4017 4930 7.820044 TTTTCGAAAAACACAACTATGCTTT 57.180 28.000 20.56 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.