Multiple sequence alignment - TraesCS4B01G210900

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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 TraesCS4B01G210900 chr4B 100.000 6350 0 0 1 6350 449501804 449508153 0.000000e+00 11727
1 TraesCS4B01G210900 chr4A 94.206 4246 172 34 271 4475 100969503 100965291 0.000000e+00 6410
2 TraesCS4B01G210900 chr4A 95.874 1115 21 5 4504 5604 100965293 100964190 0.000000e+00 1781
3 TraesCS4B01G210900 chr4A 98.916 369 4 0 5982 6350 650063507 650063875 0.000000e+00 660
4 TraesCS4B01G210900 chr4A 93.120 407 8 2 5599 5986 663370967 663371372 4.270000e-161 579
5 TraesCS4B01G210900 chr4A 93.573 389 20 2 5598 5986 652190954 652190571 5.520000e-160 575
6 TraesCS4B01G210900 chr4D 94.325 3119 117 24 1381 4475 364028529 364031611 0.000000e+00 4724
7 TraesCS4B01G210900 chr4D 96.256 1095 28 4 4504 5596 364031609 364032692 0.000000e+00 1783
8 TraesCS4B01G210900 chr4D 89.927 1092 37 22 278 1339 364027484 364028532 0.000000e+00 1339
9 TraesCS4B01G210900 chr4D 95.181 83 4 0 25 107 364025817 364025899 1.440000e-26 132
10 TraesCS4B01G210900 chr3B 99.458 369 2 0 5982 6350 532669160 532669528 0.000000e+00 671
11 TraesCS4B01G210900 chr6B 99.187 369 3 0 5982 6350 134104575 134104207 0.000000e+00 665
12 TraesCS4B01G210900 chr6B 98.919 370 3 1 5982 6350 560194581 560194950 0.000000e+00 660
13 TraesCS4B01G210900 chr6B 98.916 369 4 0 5982 6350 667085963 667085595 0.000000e+00 660
14 TraesCS4B01G210900 chr6B 96.354 384 14 0 5602 5985 293100077 293099694 3.230000e-177 632
15 TraesCS4B01G210900 chr6B 93.684 380 19 2 5607 5986 116213192 116212818 1.200000e-156 564
16 TraesCS4B01G210900 chr6B 95.794 214 7 2 5774 5986 165301176 165300964 1.690000e-90 344
17 TraesCS4B01G210900 chr1B 99.187 369 3 0 5982 6350 664978148 664978516 0.000000e+00 665
18 TraesCS4B01G210900 chr1B 95.584 385 14 1 5602 5986 664977288 664977669 1.170000e-171 614
19 TraesCS4B01G210900 chr5B 98.916 369 4 0 5982 6350 425661963 425661595 0.000000e+00 660
20 TraesCS4B01G210900 chr5B 95.052 384 18 1 5602 5985 578999893 578999511 2.530000e-168 603
21 TraesCS4B01G210900 chr2B 98.916 369 4 0 5982 6350 2546440 2546072 0.000000e+00 660
22 TraesCS4B01G210900 chr2B 94.737 399 18 2 5588 5986 507805764 507805369 9.040000e-173 617
23 TraesCS4B01G210900 chr2B 91.687 409 14 2 5597 5986 711127990 711128397 3.350000e-152 549
24 TraesCS4B01G210900 chr7B 98.645 369 5 0 5982 6350 700437274 700437642 0.000000e+00 654
25 TraesCS4B01G210900 chr7B 93.716 366 18 2 5621 5986 700436435 700436795 1.560000e-150 544
26 TraesCS4B01G210900 chr5D 95.161 186 6 3 5802 5986 255684225 255684042 2.240000e-74 291


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 TraesCS4B01G210900 chr4B 449501804 449508153 6349 False 11727.0 11727 100.00000 1 6350 1 chr4B.!!$F1 6349
1 TraesCS4B01G210900 chr4A 100964190 100969503 5313 True 4095.5 6410 95.04000 271 5604 2 chr4A.!!$R2 5333
2 TraesCS4B01G210900 chr4D 364025817 364032692 6875 False 1994.5 4724 93.92225 25 5596 4 chr4D.!!$F1 5571
3 TraesCS4B01G210900 chr1B 664977288 664978516 1228 False 639.5 665 97.38550 5602 6350 2 chr1B.!!$F1 748
4 TraesCS4B01G210900 chr7B 700436435 700437642 1207 False 599.0 654 96.18050 5621 6350 2 chr7B.!!$F1 729

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
180 1222 0.322648 ACGGGCTTTACACCAGTACC 59.677 55.000 0.0 0.0 33.56 3.34 F
1340 2811 1.006102 CAGCCGTCGTTCTCCTTGT 60.006 57.895 0.0 0.0 0.00 3.16 F
2960 4456 0.806492 GAACGATGAAGACCTCGCCC 60.806 60.000 0.0 0.0 37.60 6.13 F
3859 5361 0.108585 GAACTGCCTCTCCAACCACA 59.891 55.000 0.0 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1378 2849 0.515564 ACGGTTCAAATCGAAAGGCG 59.484 50.0 1.86 0.0 42.69 5.52 R
3205 4701 0.321122 AGGAAGAGCAACGGAAGCAG 60.321 55.0 0.00 0.0 0.00 4.24 R
3977 5479 0.118346 TGATGGAGTGGTACAGGGGT 59.882 55.0 0.00 0.0 41.80 4.95 R
5652 7170 1.061324 AACCCCTACCCAAACGGACA 61.061 55.0 0.00 0.0 34.64 4.02 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
17 18 3.541072 CCCAAATGATGCGGCCAT 58.459 55.556 2.24 0.00 0.00 4.40
18 19 1.824658 CCCAAATGATGCGGCCATT 59.175 52.632 2.24 0.00 35.92 3.16
19 20 0.531090 CCCAAATGATGCGGCCATTG 60.531 55.000 2.24 0.00 34.75 2.82
20 21 0.460722 CCAAATGATGCGGCCATTGA 59.539 50.000 2.24 0.00 34.75 2.57
21 22 1.134759 CCAAATGATGCGGCCATTGAA 60.135 47.619 2.24 0.00 34.75 2.69
22 23 2.619147 CAAATGATGCGGCCATTGAAA 58.381 42.857 2.24 0.00 34.75 2.69
23 24 3.199677 CAAATGATGCGGCCATTGAAAT 58.800 40.909 2.24 0.00 34.75 2.17
24 25 3.547054 AATGATGCGGCCATTGAAATT 57.453 38.095 2.24 0.00 33.41 1.82
25 26 2.582728 TGATGCGGCCATTGAAATTC 57.417 45.000 2.24 0.00 0.00 2.17
26 27 1.202279 TGATGCGGCCATTGAAATTCG 60.202 47.619 2.24 0.00 0.00 3.34
37 38 6.020995 GGCCATTGAAATTCGTTTAATGTACG 60.021 38.462 0.00 0.00 40.11 3.67
150 1192 3.086282 ACCGGAACATCAAATAACACCC 58.914 45.455 9.46 0.00 0.00 4.61
151 1193 2.096819 CCGGAACATCAAATAACACCCG 59.903 50.000 0.00 0.00 34.76 5.28
154 1196 4.392445 CGGAACATCAAATAACACCCGTAA 59.608 41.667 0.00 0.00 0.00 3.18
155 1197 5.446741 CGGAACATCAAATAACACCCGTAAG 60.447 44.000 0.00 0.00 0.00 2.34
180 1222 0.322648 ACGGGCTTTACACCAGTACC 59.677 55.000 0.00 0.00 33.56 3.34
197 1239 4.578928 CAGTACCTGGGTATTACAAATGGC 59.421 45.833 2.63 0.00 32.82 4.40
198 1240 3.748645 ACCTGGGTATTACAAATGGCA 57.251 42.857 0.00 0.00 0.00 4.92
199 1241 4.264373 ACCTGGGTATTACAAATGGCAT 57.736 40.909 0.00 0.00 0.00 4.40
200 1242 3.960102 ACCTGGGTATTACAAATGGCATG 59.040 43.478 0.00 0.00 0.00 4.06
201 1243 3.321682 CCTGGGTATTACAAATGGCATGG 59.678 47.826 0.00 0.00 0.00 3.66
249 1292 2.109425 AAACCCCTCATGCTACGTTC 57.891 50.000 0.00 0.00 0.00 3.95
255 1298 3.190874 CCCTCATGCTACGTTCTCTTTC 58.809 50.000 0.00 0.00 0.00 2.62
258 1301 3.254060 TCATGCTACGTTCTCTTTCTGC 58.746 45.455 0.00 0.00 0.00 4.26
272 1315 6.476378 TCTCTTTCTGCTGCCTTACTTTTAT 58.524 36.000 0.00 0.00 0.00 1.40
273 1316 6.372659 TCTCTTTCTGCTGCCTTACTTTTATG 59.627 38.462 0.00 0.00 0.00 1.90
274 1317 6.003950 TCTTTCTGCTGCCTTACTTTTATGT 58.996 36.000 0.00 0.00 0.00 2.29
275 1318 5.880054 TTCTGCTGCCTTACTTTTATGTC 57.120 39.130 0.00 0.00 0.00 3.06
276 1319 3.932710 TCTGCTGCCTTACTTTTATGTCG 59.067 43.478 0.00 0.00 0.00 4.35
290 1712 7.960793 ACTTTTATGTCGATTGTTACTAGTGC 58.039 34.615 5.39 0.00 0.00 4.40
294 1716 5.892160 TGTCGATTGTTACTAGTGCTACT 57.108 39.130 5.39 0.00 0.00 2.57
337 1759 4.334759 GTGTGATCAATGGTGGAGAATCTG 59.665 45.833 0.00 0.00 33.73 2.90
341 1763 2.507058 TCAATGGTGGAGAATCTGAGGG 59.493 50.000 0.00 0.00 33.73 4.30
372 1798 3.942439 GGATGACCCTAGCCCGGC 61.942 72.222 0.00 0.00 0.00 6.13
394 1820 1.078759 CTACCACCAAAGCTCGCTCG 61.079 60.000 0.00 0.00 0.00 5.03
519 1945 1.098129 GCTGCTTTCGGGGGAGAATC 61.098 60.000 0.00 0.00 0.00 2.52
856 2309 1.625565 AGGAGAGGAGAGGAGGGCT 60.626 63.158 0.00 0.00 0.00 5.19
1247 2718 1.075374 ACTCTCTGCTCCTCTGTGTCT 59.925 52.381 0.00 0.00 0.00 3.41
1262 2733 5.955488 TCTGTGTCTCCTCTTCTATTTTCG 58.045 41.667 0.00 0.00 0.00 3.46
1340 2811 1.006102 CAGCCGTCGTTCTCCTTGT 60.006 57.895 0.00 0.00 0.00 3.16
1342 2813 1.179814 AGCCGTCGTTCTCCTTGTCT 61.180 55.000 0.00 0.00 0.00 3.41
1347 2818 3.551454 CCGTCGTTCTCCTTGTCTTTGTA 60.551 47.826 0.00 0.00 0.00 2.41
1373 2844 5.221382 TGTCTCGCTAGAGGTTAACTTTTGT 60.221 40.000 5.42 0.00 44.47 2.83
1378 2849 5.220381 GCTAGAGGTTAACTTTTGTTTGCC 58.780 41.667 5.42 0.00 43.32 4.52
1380 2851 2.792674 GAGGTTAACTTTTGTTTGCCGC 59.207 45.455 5.42 0.00 43.32 6.53
1403 2874 1.970092 TCGATTTGAACCGTGGGTTT 58.030 45.000 0.97 0.00 46.95 3.27
1408 2879 3.679824 TTTGAACCGTGGGTTTGTTTT 57.320 38.095 0.97 0.00 46.95 2.43
1414 2885 4.374843 ACCGTGGGTTTGTTTTAACTTC 57.625 40.909 0.00 0.00 27.29 3.01
1594 3065 7.051000 GTCTATCCCTTTCATAGCAAACTTCT 58.949 38.462 0.00 0.00 0.00 2.85
1595 3066 7.011857 GTCTATCCCTTTCATAGCAAACTTCTG 59.988 40.741 0.00 0.00 0.00 3.02
1614 3085 2.864343 CTGTTGATTTACCGGTCGATCC 59.136 50.000 12.40 5.00 0.00 3.36
1652 3123 3.120041 ACCATTTTGTTTACGCACTTGC 58.880 40.909 0.00 0.00 37.78 4.01
2064 3543 2.602257 ATTCCGCATTCGTCATCTGA 57.398 45.000 0.00 0.00 0.00 3.27
2070 3549 2.416547 CGCATTCGTCATCTGACCTTTT 59.583 45.455 4.81 0.00 41.86 2.27
2107 3586 4.387862 CCCATTAAGCGCCTAATAGTAACG 59.612 45.833 10.82 0.00 0.00 3.18
2112 3591 7.858052 TTAAGCGCCTAATAGTAACGATAAC 57.142 36.000 2.29 0.00 0.00 1.89
2193 3673 3.669251 AGAACAGTTCCTGTAGTCTGC 57.331 47.619 9.85 0.00 44.62 4.26
2196 3676 1.000163 ACAGTTCCTGTAGTCTGCACG 60.000 52.381 0.00 0.00 43.46 5.34
2257 3737 1.072331 AGTGTCGGCTCATGAAGGTTT 59.928 47.619 0.00 0.00 0.00 3.27
2281 3761 5.743117 AGAGCTGCTCATGAAAGTTCTAAT 58.257 37.500 29.49 2.54 30.76 1.73
2297 3781 7.661536 AGTTCTAATGCTTCTGACCATAGTA 57.338 36.000 0.00 0.00 0.00 1.82
2299 3783 8.709308 AGTTCTAATGCTTCTGACCATAGTAAT 58.291 33.333 0.00 0.00 0.00 1.89
2394 3878 1.442769 TCCTGCTGACATTTCGCTTC 58.557 50.000 0.00 0.00 0.00 3.86
2623 4107 6.376864 TCCGCCATTTTTCTTTCATATCTTCA 59.623 34.615 0.00 0.00 0.00 3.02
2659 4154 6.183360 GCATTCAATTCACCCCCACATTTATA 60.183 38.462 0.00 0.00 0.00 0.98
2678 4173 6.656314 TTATACAAGCACTTCATGTTACCG 57.344 37.500 0.00 0.00 0.00 4.02
2832 4327 1.728425 GCCAAACGTCCTAAAGGTACG 59.272 52.381 15.06 15.06 41.28 3.67
2960 4456 0.806492 GAACGATGAAGACCTCGCCC 60.806 60.000 0.00 0.00 37.60 6.13
3010 4506 2.040947 TCCTTACATGCCACACAATCCA 59.959 45.455 0.00 0.00 0.00 3.41
3106 4602 2.613977 CCCCTGAAAGAGCTAGTGTGTG 60.614 54.545 0.00 0.00 34.07 3.82
3205 4701 2.565841 GGAATGTACTGGCATCCTCAC 58.434 52.381 0.00 0.00 0.00 3.51
3223 4719 0.603975 ACTGCTTCCGTTGCTCTTCC 60.604 55.000 0.00 0.00 0.00 3.46
3229 4725 1.302033 CCGTTGCTCTTCCTGCACT 60.302 57.895 0.00 0.00 40.40 4.40
3271 4767 2.434702 GGTAACCATCCTACACTCCCTG 59.565 54.545 0.00 0.00 0.00 4.45
3272 4768 2.344093 AACCATCCTACACTCCCTGT 57.656 50.000 0.00 0.00 36.82 4.00
3275 4771 3.375699 ACCATCCTACACTCCCTGTAAG 58.624 50.000 0.00 0.00 34.80 2.34
3276 4772 3.246021 ACCATCCTACACTCCCTGTAAGT 60.246 47.826 0.00 0.00 34.80 2.24
3279 4775 5.280521 CCATCCTACACTCCCTGTAAGTTTT 60.281 44.000 0.00 0.00 34.80 2.43
3280 4776 5.899631 TCCTACACTCCCTGTAAGTTTTT 57.100 39.130 0.00 0.00 34.80 1.94
3299 4795 3.750639 TTTGTGAATTCGGCGGTAATC 57.249 42.857 7.21 1.34 0.00 1.75
3310 4806 2.380081 CGGTAATCGCACTGGTTCC 58.620 57.895 0.00 0.00 0.00 3.62
3340 4836 9.565213 GAAATTCTTGTATTTCAGTCAATCCTG 57.435 33.333 7.51 0.00 41.81 3.86
3350 4846 7.962964 TTTCAGTCAATCCTGTAAACTGTAG 57.037 36.000 0.00 0.00 38.71 2.74
3351 4847 6.665992 TCAGTCAATCCTGTAAACTGTAGT 57.334 37.500 0.00 0.00 38.71 2.73
3352 4848 7.770366 TCAGTCAATCCTGTAAACTGTAGTA 57.230 36.000 0.00 0.00 38.71 1.82
3353 4849 7.600065 TCAGTCAATCCTGTAAACTGTAGTAC 58.400 38.462 0.00 0.00 38.71 2.73
3360 4856 6.782986 TCCTGTAAACTGTAGTACTCAGGTA 58.217 40.000 17.73 10.90 38.67 3.08
3579 5081 6.572519 AGCATGTAACTTGATTTTTGTGTGT 58.427 32.000 0.00 0.00 0.00 3.72
3584 5086 3.520569 ACTTGATTTTTGTGTGTGTGCC 58.479 40.909 0.00 0.00 0.00 5.01
3720 5222 4.702131 GCTGTGAGAAAATGGAGGTACAAT 59.298 41.667 0.00 0.00 0.00 2.71
3733 5235 5.077564 GGAGGTACAATTTTTCCCTTCTGT 58.922 41.667 0.00 0.00 0.00 3.41
3843 5345 6.091305 GCTCCTGCATTTTAATTTCCTTGAAC 59.909 38.462 0.00 0.00 39.41 3.18
3859 5361 0.108585 GAACTGCCTCTCCAACCACA 59.891 55.000 0.00 0.00 0.00 4.17
3977 5479 1.602323 GGACACGGGTGAATGCCAA 60.602 57.895 0.00 0.00 0.00 4.52
3998 5500 0.833287 CCCTGTACCACTCCATCAGG 59.167 60.000 0.00 0.00 43.46 3.86
4138 5640 1.659098 GATCGGTCGAAGCAAATCGTT 59.341 47.619 0.00 0.00 43.19 3.85
4263 5765 4.262079 GCAGTGTAAGTACAACCTCTCAGT 60.262 45.833 0.00 0.00 38.04 3.41
4306 5808 9.171877 GGATCAAATTATCCAGTAGATGATTCC 57.828 37.037 2.81 0.00 44.26 3.01
4308 5810 9.736414 ATCAAATTATCCAGTAGATGATTCCTG 57.264 33.333 0.00 0.00 39.57 3.86
4311 5813 9.927081 AAATTATCCAGTAGATGATTCCTGTTT 57.073 29.630 0.00 0.00 39.57 2.83
4312 5814 9.927081 AATTATCCAGTAGATGATTCCTGTTTT 57.073 29.630 0.00 0.00 36.69 2.43
4473 5975 4.689812 CAGGTCAGTTCATTCTTCACTGAG 59.310 45.833 1.48 0.00 45.91 3.35
4474 5976 4.590647 AGGTCAGTTCATTCTTCACTGAGA 59.409 41.667 1.48 0.00 45.91 3.27
4475 5977 4.928615 GGTCAGTTCATTCTTCACTGAGAG 59.071 45.833 1.48 0.00 45.91 3.20
4476 5978 5.279206 GGTCAGTTCATTCTTCACTGAGAGA 60.279 44.000 1.48 0.00 45.91 3.10
4477 5979 5.863397 GTCAGTTCATTCTTCACTGAGAGAG 59.137 44.000 1.48 0.00 45.91 3.20
4478 5980 5.538053 TCAGTTCATTCTTCACTGAGAGAGT 59.462 40.000 0.00 0.00 41.60 3.24
4479 5981 5.863397 CAGTTCATTCTTCACTGAGAGAGTC 59.137 44.000 0.00 0.00 40.43 3.36
4480 5982 5.774690 AGTTCATTCTTCACTGAGAGAGTCT 59.225 40.000 0.00 0.00 29.75 3.24
4481 5983 5.641783 TCATTCTTCACTGAGAGAGTCTG 57.358 43.478 0.00 0.00 29.75 3.51
4482 5984 5.320277 TCATTCTTCACTGAGAGAGTCTGA 58.680 41.667 0.00 0.00 29.75 3.27
4483 5985 5.415389 TCATTCTTCACTGAGAGAGTCTGAG 59.585 44.000 0.00 0.00 33.77 3.35
4484 5986 4.632327 TCTTCACTGAGAGAGTCTGAGA 57.368 45.455 0.00 0.00 31.90 3.27
4485 5987 4.323417 TCTTCACTGAGAGAGTCTGAGAC 58.677 47.826 3.98 3.98 31.90 3.36
4486 5988 4.041567 TCTTCACTGAGAGAGTCTGAGACT 59.958 45.833 16.14 16.14 46.42 3.24
4487 5989 3.673902 TCACTGAGAGAGTCTGAGACTG 58.326 50.000 21.45 6.83 43.53 3.51
4488 5990 3.326297 TCACTGAGAGAGTCTGAGACTGA 59.674 47.826 21.45 6.33 43.53 3.41
4489 5991 3.686241 CACTGAGAGAGTCTGAGACTGAG 59.314 52.174 21.45 9.72 43.53 3.35
4490 5992 2.679837 CTGAGAGAGTCTGAGACTGAGC 59.320 54.545 21.45 5.72 43.53 4.26
4491 5993 2.039613 TGAGAGAGTCTGAGACTGAGCA 59.960 50.000 21.45 9.60 43.53 4.26
4492 5994 2.420022 GAGAGAGTCTGAGACTGAGCAC 59.580 54.545 21.45 4.92 43.53 4.40
4493 5995 2.040278 AGAGAGTCTGAGACTGAGCACT 59.960 50.000 21.45 10.20 43.53 4.40
4494 5996 2.819608 GAGAGTCTGAGACTGAGCACTT 59.180 50.000 21.45 0.00 43.53 3.16
4495 5997 2.819608 AGAGTCTGAGACTGAGCACTTC 59.180 50.000 21.45 2.88 43.53 3.01
4496 5998 2.556189 GAGTCTGAGACTGAGCACTTCA 59.444 50.000 21.45 0.00 43.53 3.02
4497 5999 2.961741 AGTCTGAGACTGAGCACTTCAA 59.038 45.455 15.39 0.00 41.76 2.69
4498 6000 3.056304 GTCTGAGACTGAGCACTTCAAC 58.944 50.000 5.12 0.00 34.81 3.18
4499 6001 2.695147 TCTGAGACTGAGCACTTCAACA 59.305 45.455 0.00 0.00 34.81 3.33
4500 6002 3.323115 TCTGAGACTGAGCACTTCAACAT 59.677 43.478 0.00 0.00 34.81 2.71
4501 6003 4.524328 TCTGAGACTGAGCACTTCAACATA 59.476 41.667 0.00 0.00 34.81 2.29
4502 6004 5.186603 TCTGAGACTGAGCACTTCAACATAT 59.813 40.000 0.00 0.00 34.81 1.78
4503 6005 6.378280 TCTGAGACTGAGCACTTCAACATATA 59.622 38.462 0.00 0.00 34.81 0.86
4513 6015 7.790027 AGCACTTCAACATATAGATCAGAACT 58.210 34.615 0.00 0.00 0.00 3.01
4523 6025 8.099537 ACATATAGATCAGAACTAAATGCTGGG 58.900 37.037 0.00 0.00 0.00 4.45
4561 6063 7.056006 TCTATGACTGGTGCATCATTTGTATT 58.944 34.615 0.00 0.00 36.87 1.89
4562 6064 5.981088 TGACTGGTGCATCATTTGTATTT 57.019 34.783 0.00 0.00 0.00 1.40
4603 6105 2.837591 TGATTGCAGGCTACTAACTGGA 59.162 45.455 0.00 0.00 35.30 3.86
4948 6450 1.989430 CTCACACCGAGAAGAAGCTC 58.011 55.000 0.00 0.00 45.45 4.09
5209 6711 3.817084 CAGTGACCTTGCATTTTCAGAGA 59.183 43.478 0.00 0.00 0.00 3.10
5284 6786 6.483640 GGATGGAAGGTGTAATAAGATGACAC 59.516 42.308 0.00 0.00 42.22 3.67
5291 6795 8.324163 AGGTGTAATAAGATGACACAAGAAAC 57.676 34.615 8.92 0.00 44.26 2.78
5516 7022 4.407296 AGAAGGCTTCACTAACCTATCCAG 59.593 45.833 27.70 0.00 32.08 3.86
5598 7116 2.166050 TGGAACCAAATGGCATCATTCG 59.834 45.455 0.00 0.00 42.29 3.34
5616 7134 2.038837 GTAAGGCCAACTCCACCGC 61.039 63.158 5.01 0.00 0.00 5.68
5872 7390 5.067023 CCAGCCTCCAAAATGAATAGTTCTC 59.933 44.000 0.00 0.00 0.00 2.87
5926 7444 3.027292 TTTTTCGCCGGCACACTC 58.973 55.556 28.98 0.00 0.00 3.51
5927 7445 1.525077 TTTTTCGCCGGCACACTCT 60.525 52.632 28.98 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.531090 CAATGGCCGCATCATTTGGG 60.531 55.000 0.00 0.00 37.99 4.12
2 3 2.296831 TTCAATGGCCGCATCATTTG 57.703 45.000 0.00 0.00 33.08 2.32
3 4 3.547054 ATTTCAATGGCCGCATCATTT 57.453 38.095 0.00 0.00 33.08 2.32
4 5 3.460103 GAATTTCAATGGCCGCATCATT 58.540 40.909 0.00 0.00 35.45 2.57
5 6 2.544277 CGAATTTCAATGGCCGCATCAT 60.544 45.455 0.00 0.00 0.00 2.45
6 7 1.202279 CGAATTTCAATGGCCGCATCA 60.202 47.619 0.00 0.00 0.00 3.07
7 8 1.202290 ACGAATTTCAATGGCCGCATC 60.202 47.619 0.00 0.00 0.00 3.91
8 9 0.817013 ACGAATTTCAATGGCCGCAT 59.183 45.000 0.00 0.00 0.00 4.73
9 10 0.600557 AACGAATTTCAATGGCCGCA 59.399 45.000 0.00 0.00 0.00 5.69
10 11 1.708822 AAACGAATTTCAATGGCCGC 58.291 45.000 0.00 0.00 0.00 6.53
11 12 4.862018 ACATTAAACGAATTTCAATGGCCG 59.138 37.500 0.00 0.00 30.81 6.13
12 13 6.020995 CGTACATTAAACGAATTTCAATGGCC 60.021 38.462 0.00 0.00 42.90 5.36
13 14 6.743627 TCGTACATTAAACGAATTTCAATGGC 59.256 34.615 10.28 4.38 45.62 4.40
107 108 9.712305 CCGGTGAGTTCATTTAGAGATATTTAT 57.288 33.333 0.00 0.00 0.00 1.40
108 109 8.920174 TCCGGTGAGTTCATTTAGAGATATTTA 58.080 33.333 0.00 0.00 0.00 1.40
109 110 7.792032 TCCGGTGAGTTCATTTAGAGATATTT 58.208 34.615 0.00 0.00 0.00 1.40
111 112 6.978674 TCCGGTGAGTTCATTTAGAGATAT 57.021 37.500 0.00 0.00 0.00 1.63
112 113 6.153851 TGTTCCGGTGAGTTCATTTAGAGATA 59.846 38.462 0.00 0.00 0.00 1.98
122 1164 2.920724 TTGATGTTCCGGTGAGTTCA 57.079 45.000 0.00 0.00 0.00 3.18
180 1222 3.243839 GCCATGCCATTTGTAATACCCAG 60.244 47.826 0.00 0.00 0.00 4.45
184 1226 5.199024 TCATGCCATGCCATTTGTAATAC 57.801 39.130 0.00 0.00 0.00 1.89
197 1239 4.702020 CGTGTGCATCATGCCATG 57.298 55.556 7.30 6.55 44.23 3.66
249 1292 6.150140 ACATAAAAGTAAGGCAGCAGAAAGAG 59.850 38.462 0.00 0.00 0.00 2.85
255 1298 3.932710 TCGACATAAAAGTAAGGCAGCAG 59.067 43.478 0.00 0.00 0.00 4.24
258 1301 6.422776 ACAATCGACATAAAAGTAAGGCAG 57.577 37.500 0.00 0.00 0.00 4.85
272 1315 5.646793 AGAGTAGCACTAGTAACAATCGACA 59.353 40.000 0.00 0.00 0.00 4.35
273 1316 5.966503 CAGAGTAGCACTAGTAACAATCGAC 59.033 44.000 0.00 0.00 0.00 4.20
274 1317 5.066117 CCAGAGTAGCACTAGTAACAATCGA 59.934 44.000 0.00 0.00 0.00 3.59
275 1318 5.274718 CCAGAGTAGCACTAGTAACAATCG 58.725 45.833 0.00 0.00 0.00 3.34
276 1319 5.044558 GCCAGAGTAGCACTAGTAACAATC 58.955 45.833 0.00 0.00 0.00 2.67
290 1712 5.866633 CAGTTAAACAAGAGAGCCAGAGTAG 59.133 44.000 0.00 0.00 0.00 2.57
294 1716 4.141711 ACACAGTTAAACAAGAGAGCCAGA 60.142 41.667 0.00 0.00 0.00 3.86
337 1759 3.194005 TCCACGAATTTCATAGCCCTC 57.806 47.619 0.00 0.00 0.00 4.30
341 1763 3.251004 GGGTCATCCACGAATTTCATAGC 59.749 47.826 0.00 0.00 35.00 2.97
372 1798 2.100631 CGAGCTTTGGTGGTAGCCG 61.101 63.158 0.00 0.00 38.14 5.52
502 1928 1.204786 TGGATTCTCCCCCGAAAGCA 61.205 55.000 0.00 0.00 35.03 3.91
519 1945 1.398390 GAGTACGCTTGCTTGGAATGG 59.602 52.381 0.00 0.00 0.00 3.16
571 1997 2.285144 GGGAACGGGGGAGAGGAA 60.285 66.667 0.00 0.00 0.00 3.36
1026 2489 1.385206 GGAGCAGGGGAGGAGGATT 60.385 63.158 0.00 0.00 0.00 3.01
1121 2590 1.973138 ATATATACACGACGCACCGC 58.027 50.000 0.00 0.00 0.00 5.68
1125 2594 3.487879 CCGGCATATATATACACGACGCA 60.488 47.826 11.81 0.00 0.00 5.24
1247 2718 8.253113 ACGGTAATTAACGAAAATAGAAGAGGA 58.747 33.333 28.63 0.00 0.00 3.71
1340 2811 4.705507 ACCTCTAGCGAGACAATACAAAGA 59.294 41.667 0.00 0.00 39.74 2.52
1342 2813 5.401531 AACCTCTAGCGAGACAATACAAA 57.598 39.130 0.00 0.00 39.74 2.83
1347 2818 5.662674 AAGTTAACCTCTAGCGAGACAAT 57.337 39.130 0.88 0.00 39.74 2.71
1373 2844 0.955178 TCAAATCGAAAGGCGGCAAA 59.045 45.000 13.08 0.00 41.33 3.68
1378 2849 0.515564 ACGGTTCAAATCGAAAGGCG 59.484 50.000 1.86 0.00 42.69 5.52
1380 2851 1.199097 CCCACGGTTCAAATCGAAAGG 59.801 52.381 1.86 1.56 35.73 3.11
1403 2874 9.136952 GCGTTCTCTAATCTAGAAGTTAAAACA 57.863 33.333 0.00 0.00 33.75 2.83
1408 2879 7.553402 ACTCTGCGTTCTCTAATCTAGAAGTTA 59.447 37.037 0.00 0.00 33.75 2.24
1414 2885 7.642194 CAGTTTACTCTGCGTTCTCTAATCTAG 59.358 40.741 0.00 0.00 0.00 2.43
1594 3065 2.234168 TGGATCGACCGGTAAATCAACA 59.766 45.455 23.18 13.87 42.61 3.33
1595 3066 2.896168 TGGATCGACCGGTAAATCAAC 58.104 47.619 23.18 12.02 42.61 3.18
1652 3123 7.756395 AATGGATATCAGCCTCAAAATACAG 57.244 36.000 4.83 0.00 0.00 2.74
1895 3373 0.861837 GTTCAGTCACCGACAGCAAG 59.138 55.000 0.00 0.00 34.60 4.01
2257 3737 4.815533 AGAACTTTCATGAGCAGCTCTA 57.184 40.909 23.15 10.19 0.00 2.43
2281 3761 5.692115 TGGAATTACTATGGTCAGAAGCA 57.308 39.130 0.00 0.00 37.29 3.91
2297 3781 4.342092 CCTGTCAGGTGAAAGTTTGGAATT 59.658 41.667 11.09 0.00 0.00 2.17
2299 3783 3.287222 CCTGTCAGGTGAAAGTTTGGAA 58.713 45.455 11.09 0.00 0.00 3.53
2394 3878 5.495502 GTTACGTTAACATCAAATAGGCCG 58.504 41.667 6.39 0.00 38.52 6.13
2559 4043 1.228367 CAGCACCTTTGGCCTGACT 60.228 57.895 3.32 0.00 30.24 3.41
2623 4107 5.577945 GGTGAATTGAATGCGACAATTTCAT 59.422 36.000 13.72 0.00 44.46 2.57
2659 4154 2.846193 ACGGTAACATGAAGTGCTTGT 58.154 42.857 0.00 0.00 36.53 3.16
2678 4173 4.892655 TGTTCGATGATCGCACAAAATAC 58.107 39.130 17.24 2.97 42.44 1.89
2721 4216 9.297037 TCCCTCTGGAAATAGTAAAAGAAAAAG 57.703 33.333 0.00 0.00 37.86 2.27
2727 4222 6.561519 TCCTCCCTCTGGAAATAGTAAAAG 57.438 41.667 0.00 0.00 41.17 2.27
2832 4327 6.391227 AACAGGGTTAAATGCTGTATATGC 57.609 37.500 0.00 0.00 0.00 3.14
2960 4456 1.748122 GACTGTCCTGCATGGCCTG 60.748 63.158 3.32 0.34 35.26 4.85
3010 4506 2.860971 GCCTGGGAGGGGGCATAT 60.861 66.667 0.00 0.00 46.84 1.78
3106 4602 4.697514 TGCAGGATGTACATAGCTTCTTC 58.302 43.478 21.04 5.02 39.31 2.87
3205 4701 0.321122 AGGAAGAGCAACGGAAGCAG 60.321 55.000 0.00 0.00 0.00 4.24
3223 4719 1.227380 GCGGATAGGGTGAGTGCAG 60.227 63.158 0.00 0.00 0.00 4.41
3229 4725 1.826921 GGTCTCGCGGATAGGGTGA 60.827 63.158 6.13 0.00 33.77 4.02
3279 4775 2.094575 CGATTACCGCCGAATTCACAAA 59.905 45.455 6.22 0.00 0.00 2.83
3280 4776 1.661617 CGATTACCGCCGAATTCACAA 59.338 47.619 6.22 0.00 0.00 3.33
3281 4777 1.282817 CGATTACCGCCGAATTCACA 58.717 50.000 6.22 0.00 0.00 3.58
3295 4791 1.001068 TCAACGGAACCAGTGCGATTA 59.999 47.619 0.00 0.00 45.26 1.75
3301 4797 4.202010 ACAAGAATTTCAACGGAACCAGTG 60.202 41.667 0.00 0.00 31.35 3.66
3332 4828 7.093902 CCTGAGTACTACAGTTTACAGGATTGA 60.094 40.741 14.76 0.00 39.75 2.57
3382 4878 4.600062 ACACAAAGAGAAAAAGGGTGACT 58.400 39.130 0.00 0.00 0.00 3.41
3394 4890 3.945285 GTGAACTGGGAAACACAAAGAGA 59.055 43.478 0.00 0.00 34.05 3.10
3395 4891 3.066760 GGTGAACTGGGAAACACAAAGAG 59.933 47.826 0.00 0.00 35.33 2.85
3579 5081 1.300971 GCGATCTGCAGAAAGGCACA 61.301 55.000 22.50 0.00 45.45 4.57
3720 5222 6.613153 TGAAGGAAAAACAGAAGGGAAAAA 57.387 33.333 0.00 0.00 0.00 1.94
3733 5235 8.248904 TCATCTCCTGAAAATTGAAGGAAAAA 57.751 30.769 5.74 0.00 39.59 1.94
3843 5345 1.338020 GTTTTGTGGTTGGAGAGGCAG 59.662 52.381 0.00 0.00 0.00 4.85
3977 5479 0.118346 TGATGGAGTGGTACAGGGGT 59.882 55.000 0.00 0.00 41.80 4.95
3998 5500 3.698040 TGTTCATCCCTTCGTAGTAGTCC 59.302 47.826 0.00 0.00 0.00 3.85
4138 5640 3.367992 AACATTTGCAAAGATCACGCA 57.632 38.095 18.19 0.00 0.00 5.24
4143 5645 7.912250 AGATGATCGTTAACATTTGCAAAGATC 59.088 33.333 18.19 19.44 37.55 2.75
4263 5765 8.884124 ATTTGATCCCTGAAAGTCAATTTAGA 57.116 30.769 0.00 0.00 31.39 2.10
4306 5808 3.489813 GCCGCAAAGGGTAAAACAG 57.510 52.632 0.00 0.00 41.48 3.16
4473 5975 2.436417 AGTGCTCAGTCTCAGACTCTC 58.564 52.381 3.60 0.00 41.37 3.20
4474 5976 2.584835 AGTGCTCAGTCTCAGACTCT 57.415 50.000 3.60 0.00 41.37 3.24
4475 5977 2.556189 TGAAGTGCTCAGTCTCAGACTC 59.444 50.000 3.60 0.00 41.37 3.36
4476 5978 2.591923 TGAAGTGCTCAGTCTCAGACT 58.408 47.619 0.00 0.00 44.44 3.24
4477 5979 3.056304 GTTGAAGTGCTCAGTCTCAGAC 58.944 50.000 0.00 0.00 34.81 3.51
4478 5980 2.695147 TGTTGAAGTGCTCAGTCTCAGA 59.305 45.455 0.00 0.00 34.81 3.27
4479 5981 3.103447 TGTTGAAGTGCTCAGTCTCAG 57.897 47.619 0.00 0.00 34.81 3.35
4480 5982 3.758755 ATGTTGAAGTGCTCAGTCTCA 57.241 42.857 0.00 0.00 34.81 3.27
4481 5983 6.800543 TCTATATGTTGAAGTGCTCAGTCTC 58.199 40.000 0.00 0.00 34.81 3.36
4482 5984 6.782082 TCTATATGTTGAAGTGCTCAGTCT 57.218 37.500 0.00 0.00 34.81 3.24
4483 5985 7.205992 TGATCTATATGTTGAAGTGCTCAGTC 58.794 38.462 0.00 0.00 34.81 3.51
4484 5986 7.069208 TCTGATCTATATGTTGAAGTGCTCAGT 59.931 37.037 0.00 0.00 34.81 3.41
4485 5987 7.432059 TCTGATCTATATGTTGAAGTGCTCAG 58.568 38.462 0.00 0.00 34.81 3.35
4486 5988 7.352079 TCTGATCTATATGTTGAAGTGCTCA 57.648 36.000 0.00 0.00 0.00 4.26
4487 5989 7.925483 AGTTCTGATCTATATGTTGAAGTGCTC 59.075 37.037 0.00 0.00 0.00 4.26
4488 5990 7.790027 AGTTCTGATCTATATGTTGAAGTGCT 58.210 34.615 0.00 0.00 0.00 4.40
4489 5991 9.534565 TTAGTTCTGATCTATATGTTGAAGTGC 57.465 33.333 0.00 0.00 0.00 4.40
4496 5998 9.499479 CCAGCATTTAGTTCTGATCTATATGTT 57.501 33.333 18.78 13.97 33.04 2.71
4497 5999 8.099537 CCCAGCATTTAGTTCTGATCTATATGT 58.900 37.037 18.78 9.52 33.04 2.29
4498 6000 7.551974 CCCCAGCATTTAGTTCTGATCTATATG 59.448 40.741 15.83 15.83 33.35 1.78
4499 6001 7.238514 ACCCCAGCATTTAGTTCTGATCTATAT 59.761 37.037 0.00 0.00 0.00 0.86
4500 6002 6.558775 ACCCCAGCATTTAGTTCTGATCTATA 59.441 38.462 0.00 0.00 0.00 1.31
4501 6003 5.370880 ACCCCAGCATTTAGTTCTGATCTAT 59.629 40.000 0.00 0.00 0.00 1.98
4502 6004 4.721776 ACCCCAGCATTTAGTTCTGATCTA 59.278 41.667 0.00 0.00 0.00 1.98
4503 6005 3.525199 ACCCCAGCATTTAGTTCTGATCT 59.475 43.478 0.00 0.00 0.00 2.75
4513 6015 3.838565 TGACAAAGAACCCCAGCATTTA 58.161 40.909 0.00 0.00 0.00 1.40
4562 6064 9.970395 GCAATCATGTGGAGAATATTTTGATTA 57.030 29.630 0.00 0.00 32.82 1.75
4603 6105 2.969950 CAATTCATGGGCAAGGATGGAT 59.030 45.455 0.00 0.00 0.00 3.41
4948 6450 2.349590 TGATGCATGAAGAACTCACCG 58.650 47.619 2.46 0.00 36.69 4.94
4951 6453 4.095932 GCAATCTGATGCATGAAGAACTCA 59.904 41.667 2.46 0.00 45.70 3.41
5209 6711 4.099633 TCCTGATTCACTCTGAATGACCT 58.900 43.478 2.17 0.00 46.20 3.85
5284 6786 6.312399 TGCTAGTTACATTGGTGTTTCTTG 57.688 37.500 0.00 0.00 39.77 3.02
5291 6795 4.665212 CAATGCTGCTAGTTACATTGGTG 58.335 43.478 18.34 3.03 43.51 4.17
5451 6957 6.422701 CGAGGTTAATGGTTTTTCCCTTTTTC 59.577 38.462 0.00 0.00 34.77 2.29
5452 6958 6.098552 TCGAGGTTAATGGTTTTTCCCTTTTT 59.901 34.615 0.00 0.00 34.77 1.94
5453 6959 5.599242 TCGAGGTTAATGGTTTTTCCCTTTT 59.401 36.000 0.00 0.00 34.77 2.27
5454 6960 5.141910 TCGAGGTTAATGGTTTTTCCCTTT 58.858 37.500 0.00 0.00 34.77 3.11
5455 6961 4.732065 TCGAGGTTAATGGTTTTTCCCTT 58.268 39.130 0.00 0.00 34.77 3.95
5456 6962 4.376225 TCGAGGTTAATGGTTTTTCCCT 57.624 40.909 0.00 0.00 34.77 4.20
5457 6963 5.393787 GGATTCGAGGTTAATGGTTTTTCCC 60.394 44.000 0.00 0.00 34.77 3.97
5458 6964 5.417894 AGGATTCGAGGTTAATGGTTTTTCC 59.582 40.000 0.00 0.00 0.00 3.13
5598 7116 2.038837 GCGGTGGAGTTGGCCTTAC 61.039 63.158 3.32 1.81 0.00 2.34
5652 7170 1.061324 AACCCCTACCCAAACGGACA 61.061 55.000 0.00 0.00 34.64 4.02
5792 7310 3.071837 TGTAGGCCGGCGTGATGA 61.072 61.111 30.94 8.72 0.00 2.92
5793 7311 2.890474 GTGTAGGCCGGCGTGATG 60.890 66.667 30.94 0.00 0.00 3.07
5794 7312 4.508128 CGTGTAGGCCGGCGTGAT 62.508 66.667 30.94 14.22 0.00 3.06


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

AutoCloner maintained by Alex Coulton.