Multiple sequence alignment - TraesCS4B01G227700

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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 TraesCS4B01G227700 chr4B 100.000 4829 0 0 1 4829 476362536 476357708 0.000000e+00 8918.0
1 TraesCS4B01G227700 chr4B 93.333 90 5 1 4336 4425 512752816 512752904 1.090000e-26 132.0
2 TraesCS4B01G227700 chr4B 90.722 97 7 2 4336 4431 659147076 659147171 1.410000e-25 128.0
3 TraesCS4B01G227700 chr4A 93.179 3636 157 36 699 4290 69320509 69316921 0.000000e+00 5256.0
4 TraesCS4B01G227700 chr4A 88.702 655 23 14 1 645 69321133 69320520 0.000000e+00 752.0
5 TraesCS4B01G227700 chr4A 83.524 437 33 16 4417 4829 69316772 69316351 5.900000e-99 372.0
6 TraesCS4B01G227700 chr4A 86.364 88 10 2 175 262 614871662 614871747 1.430000e-15 95.3
7 TraesCS4B01G227700 chr4D 94.438 1852 68 16 2498 4337 388122813 388120985 0.000000e+00 2817.0
8 TraesCS4B01G227700 chr4D 89.970 2024 101 43 534 2499 388124875 388122896 0.000000e+00 2519.0
9 TraesCS4B01G227700 chr4D 94.900 549 13 7 1 545 388125434 388124897 0.000000e+00 845.0
10 TraesCS4B01G227700 chr4D 81.860 430 35 20 4425 4829 388120971 388120560 6.030000e-84 322.0
11 TraesCS4B01G227700 chr4D 94.505 91 5 0 4336 4426 469582274 469582364 1.810000e-29 141.0
12 TraesCS4B01G227700 chr3D 97.590 83 2 0 4336 4418 400683945 400684027 5.040000e-30 143.0
13 TraesCS4B01G227700 chr3D 88.043 92 8 2 172 263 418394890 418394802 6.610000e-19 106.0
14 TraesCS4B01G227700 chr5D 95.294 85 4 0 4336 4420 128577670 128577586 8.430000e-28 135.0
15 TraesCS4B01G227700 chr5D 87.755 98 7 4 173 269 288588511 288588418 5.110000e-20 110.0
16 TraesCS4B01G227700 chr5B 95.294 85 4 0 4336 4420 140966012 140965928 8.430000e-28 135.0
17 TraesCS4B01G227700 chr2A 94.253 87 5 0 4336 4422 539325660 539325574 3.030000e-27 134.0
18 TraesCS4B01G227700 chr3B 89.109 101 10 1 4336 4435 112281267 112281167 1.820000e-24 124.0
19 TraesCS4B01G227700 chr3B 83.696 92 13 2 172 262 778340622 778340712 8.610000e-13 86.1
20 TraesCS4B01G227700 chr3A 85.470 117 13 4 4336 4448 78732137 78732021 8.490000e-23 119.0
21 TraesCS4B01G227700 chr6D 85.870 92 10 2 172 263 78352686 78352774 1.430000e-15 95.3
22 TraesCS4B01G227700 chr5A 85.714 91 10 2 174 264 19105078 19104991 5.150000e-15 93.5
23 TraesCS4B01G227700 chr1B 87.805 82 7 2 175 256 85441708 85441630 5.150000e-15 93.5
24 TraesCS4B01G227700 chr1B 93.617 47 3 0 1067 1113 369190572 369190618 2.410000e-08 71.3
25 TraesCS4B01G227700 chr1D 95.455 44 2 0 1073 1116 237334627 237334584 2.410000e-08 71.3
26 TraesCS4B01G227700 chr1A 93.617 47 3 0 1067 1113 308202949 308202995 2.410000e-08 71.3
27 TraesCS4B01G227700 chr7D 100.000 28 0 0 4797 4824 31580350 31580377 9.000000e-03 52.8


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 TraesCS4B01G227700 chr4B 476357708 476362536 4828 True 8918.000000 8918 100.000000 1 4829 1 chr4B.!!$R1 4828
1 TraesCS4B01G227700 chr4A 69316351 69321133 4782 True 2126.666667 5256 88.468333 1 4829 3 chr4A.!!$R1 4828
2 TraesCS4B01G227700 chr4D 388120560 388125434 4874 True 1625.750000 2817 90.292000 1 4829 4 chr4D.!!$R1 4828

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
952 1040 0.309302 CCTACCGCTCTCGTGATCTG 59.691 60.0 0.0 0.0 0.00 2.90 F
1266 1372 0.106149 GTCACTGTCCGGTTCCACTT 59.894 55.0 0.0 0.0 0.00 3.16 F
1333 1439 0.179018 AGGAGGTGTTGTGAGTTGGC 60.179 55.0 0.0 0.0 0.00 4.52 F
2568 2775 0.393673 TGCAGCCGCTAATGCCTAAA 60.394 50.0 0.0 0.0 41.85 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 2010 0.472044 TGGGCAGTTGAGCACAGTTA 59.528 50.000 0.00 0.00 44.33 2.24 R
2814 3032 1.600413 GCTGAAAAGGTGCCTGTTTCG 60.600 52.381 14.77 12.16 34.63 3.46 R
3167 3385 1.670967 GCAGCCTGCAATCAAAGGTTC 60.671 52.381 12.82 0.00 44.26 3.62 R
4088 4315 0.462789 CCAGGATGCCATTTTCCAGC 59.537 55.000 0.00 0.00 34.27 4.85 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
144 148 9.885934 GTTTGGTAGAGAGATTTTCTTTCTTTC 57.114 33.333 3.27 0.00 38.65 2.62
152 156 5.004448 AGATTTTCTTTCTTTCGAGGGGTC 58.996 41.667 0.00 0.00 0.00 4.46
377 381 1.344763 ACTACTGTTTGGCTCGCTTCT 59.655 47.619 0.00 0.00 0.00 2.85
378 382 2.561419 ACTACTGTTTGGCTCGCTTCTA 59.439 45.455 0.00 0.00 0.00 2.10
379 383 2.086054 ACTGTTTGGCTCGCTTCTAG 57.914 50.000 0.00 0.00 0.00 2.43
380 384 1.344763 ACTGTTTGGCTCGCTTCTAGT 59.655 47.619 0.00 0.00 0.00 2.57
397 401 6.513720 GCTTCTAGTATTTCCTCGGTCAGTAG 60.514 46.154 0.00 0.00 0.00 2.57
443 447 2.557805 CGTGTGTGTGATGCAGGC 59.442 61.111 0.00 0.00 0.00 4.85
545 594 6.321321 TCCCAGTATCAGATCAGAATCAGAT 58.679 40.000 0.00 0.00 40.22 2.90
645 704 6.683861 GCATTCTTTAATCCAAGGTCAATCCC 60.684 42.308 0.00 0.00 36.75 3.85
646 705 5.528600 TCTTTAATCCAAGGTCAATCCCA 57.471 39.130 0.00 0.00 36.75 4.37
647 706 5.509498 TCTTTAATCCAAGGTCAATCCCAG 58.491 41.667 0.00 0.00 36.75 4.45
652 711 1.002134 AAGGTCAATCCCAGGCGTG 60.002 57.895 0.00 0.00 36.75 5.34
655 714 1.305930 GGTCAATCCCAGGCGTGAAC 61.306 60.000 8.24 0.00 0.00 3.18
662 721 0.949105 CCCAGGCGTGAACTGTGTAC 60.949 60.000 8.24 0.00 34.16 2.90
664 723 1.540363 CCAGGCGTGAACTGTGTACTT 60.540 52.381 8.24 0.00 34.16 2.24
671 743 3.662645 CGTGAACTGTGTACTTGTAGTCG 59.337 47.826 0.00 0.00 0.00 4.18
697 769 2.482721 GGATCAAACGAAAGAGCCGAAA 59.517 45.455 0.00 0.00 29.81 3.46
912 987 2.383855 CTGAGATTCCTTCCGTCTCCT 58.616 52.381 0.00 0.00 38.04 3.69
952 1040 0.309302 CCTACCGCTCTCGTGATCTG 59.691 60.000 0.00 0.00 0.00 2.90
954 1042 0.393944 TACCGCTCTCGTGATCTGGT 60.394 55.000 9.44 9.44 0.00 4.00
960 1048 1.329292 CTCTCGTGATCTGGTCTCGTC 59.671 57.143 11.56 0.00 42.67 4.20
1210 1306 4.683832 AGAACGTAGAATAGGCATGTGTC 58.316 43.478 0.00 0.00 0.00 3.67
1246 1352 6.264067 GTGAATTGCCTATTGAGAGCCTATTT 59.736 38.462 0.00 0.00 0.00 1.40
1251 1357 4.513318 GCCTATTGAGAGCCTATTTGTCAC 59.487 45.833 0.00 0.00 0.00 3.67
1263 1369 0.542333 TTTGTCACTGTCCGGTTCCA 59.458 50.000 0.00 0.00 0.00 3.53
1264 1370 0.179067 TTGTCACTGTCCGGTTCCAC 60.179 55.000 0.00 0.00 0.00 4.02
1265 1371 1.046472 TGTCACTGTCCGGTTCCACT 61.046 55.000 0.00 0.00 0.00 4.00
1266 1372 0.106149 GTCACTGTCCGGTTCCACTT 59.894 55.000 0.00 0.00 0.00 3.16
1267 1373 0.391597 TCACTGTCCGGTTCCACTTC 59.608 55.000 0.00 0.00 0.00 3.01
1268 1374 0.602905 CACTGTCCGGTTCCACTTCC 60.603 60.000 0.00 0.00 0.00 3.46
1269 1375 1.052124 ACTGTCCGGTTCCACTTCCA 61.052 55.000 0.00 0.00 0.00 3.53
1319 1425 4.822026 ACAAATCGAGTACAGAAAGGAGG 58.178 43.478 0.00 0.00 0.00 4.30
1333 1439 0.179018 AGGAGGTGTTGTGAGTTGGC 60.179 55.000 0.00 0.00 0.00 4.52
1336 1442 1.334869 GAGGTGTTGTGAGTTGGCTTG 59.665 52.381 0.00 0.00 0.00 4.01
1506 1612 8.170553 CGCCAATCAATTTTAGAAAATCCTTTG 58.829 33.333 0.86 5.53 37.62 2.77
1507 1613 8.453320 GCCAATCAATTTTAGAAAATCCTTTGG 58.547 33.333 19.17 19.17 39.77 3.28
1508 1614 8.949177 CCAATCAATTTTAGAAAATCCTTTGGG 58.051 33.333 17.50 7.86 37.62 4.12
1546 1653 4.344968 TCTGACTGAAAGATCACCAAGTGA 59.655 41.667 0.00 0.00 41.91 3.41
1593 1700 8.815565 TCAATGCACTTAATATTTGGGTCTTA 57.184 30.769 0.00 0.00 0.00 2.10
1601 1708 5.648330 AATATTTGGGTCTTAGAGGGGAC 57.352 43.478 0.00 0.00 0.00 4.46
1663 1772 7.388460 ACTATAGCCGTATTCAGTGGTATAC 57.612 40.000 0.00 0.00 0.00 1.47
1898 2010 5.995897 ACGCAACCTTCTACTGTATTTTCTT 59.004 36.000 0.00 0.00 0.00 2.52
1979 2091 3.331150 TGTATGCGTCTGAAAATCGGTT 58.669 40.909 0.00 0.00 0.00 4.44
1983 2095 1.461888 GCGTCTGAAAATCGGTTGTCG 60.462 52.381 0.00 0.00 40.90 4.35
2084 2206 3.119602 TCTCAGGTGTCGGTAAATCTTCG 60.120 47.826 0.00 0.00 0.00 3.79
2108 2230 3.137533 GGTGCATCTCATCTTAGAAGGC 58.862 50.000 0.00 0.00 33.10 4.35
2141 2263 1.551452 GACCAGCTCAGACAGTAGGT 58.449 55.000 0.00 0.00 35.00 3.08
2167 2289 2.617021 CGGTGGGCATTAAAGTAGGTGT 60.617 50.000 0.00 0.00 0.00 4.16
2177 2299 6.561614 CATTAAAGTAGGTGTTCTCGCTCTA 58.438 40.000 0.00 0.00 0.00 2.43
2204 2326 1.826720 CCCAGCTTGTACCATTTGCAT 59.173 47.619 0.00 0.00 0.00 3.96
2207 2329 4.081752 CCCAGCTTGTACCATTTGCATTTA 60.082 41.667 0.00 0.00 0.00 1.40
2336 2459 1.556911 GAGCTTTGGGATGTCTCAGGA 59.443 52.381 0.00 0.00 0.00 3.86
2366 2489 3.482112 GCTACAAAGCTTGTCGTTCGATC 60.482 47.826 0.00 0.00 45.85 3.69
2394 2517 9.607988 TCTATACACAAATCAATGGTAAACGAT 57.392 29.630 0.00 0.00 0.00 3.73
2421 2544 5.856126 TTCTCTTAATTACCAGCGTGTTG 57.144 39.130 0.00 0.00 0.00 3.33
2469 2592 4.874396 GCACGGCCTATCTTTAGTAGTTTT 59.126 41.667 0.00 0.00 0.00 2.43
2568 2775 0.393673 TGCAGCCGCTAATGCCTAAA 60.394 50.000 0.00 0.00 41.85 1.85
2668 2884 6.380274 ACACTCGTCCTTCTTTAGATCCATAA 59.620 38.462 0.00 0.00 0.00 1.90
2729 2947 2.357637 ACAACATTCACTGTTCCCAACG 59.642 45.455 0.00 0.00 44.99 4.10
2735 2953 1.208535 TCACTGTTCCCAACGTTGTCT 59.791 47.619 25.63 0.00 0.00 3.41
2926 3144 1.741401 CCAAGCGATGGCACTCGAA 60.741 57.895 18.84 0.00 43.80 3.71
2991 3209 3.696084 CGGGGTCTTCTTCCTCGT 58.304 61.111 0.00 0.00 43.13 4.18
3018 3236 6.391276 TGAAGAACTTCCACTCACAGAGAGT 61.391 44.000 11.30 0.00 46.20 3.24
3054 3272 2.758979 TGGTCTCATCTCGGTTAGGTTC 59.241 50.000 0.00 0.00 0.00 3.62
3132 3350 3.500680 TGGAACAGCCATCTTTTTACGTC 59.499 43.478 0.00 0.00 43.33 4.34
3245 3463 4.257731 AGTTTTTCCGCATGGTTTGTTTT 58.742 34.783 0.00 0.00 36.30 2.43
3434 3652 3.070446 ACCCGCAAAGATGATACCGATAA 59.930 43.478 0.00 0.00 0.00 1.75
3484 3706 4.132122 ACATGGAAAAATCAACTCCCCT 57.868 40.909 0.00 0.00 0.00 4.79
3485 3707 3.834231 ACATGGAAAAATCAACTCCCCTG 59.166 43.478 0.00 0.00 0.00 4.45
3545 3769 9.727859 AAGGAAAGTATAAAGGAGAACTCTTTC 57.272 33.333 0.00 0.00 38.86 2.62
3730 3954 3.424433 GCCGGTGTTTTCTTCAGATAACG 60.424 47.826 1.90 0.00 38.34 3.18
3807 4031 6.824305 ACAATAAGCAGCAATAGAACAAGT 57.176 33.333 0.00 0.00 0.00 3.16
3951 4178 1.538047 TCTGATGCCTTCCTTTGCAC 58.462 50.000 0.00 0.00 40.88 4.57
3994 4221 3.496160 GGTCTTCTTTGTTGGCCTAGTCA 60.496 47.826 3.32 0.00 0.00 3.41
4088 4315 5.794687 TGTCATTTCCGTAATGCAAGTAG 57.205 39.130 0.00 0.00 42.79 2.57
4102 4329 2.167075 GCAAGTAGCTGGAAAATGGCAT 59.833 45.455 0.00 0.00 41.15 4.40
4108 4335 0.462789 CTGGAAAATGGCATCCTGGC 59.537 55.000 0.00 0.00 44.03 4.85
4118 4345 0.942962 GCATCCTGGCTCGAGAAATG 59.057 55.000 18.75 11.81 0.00 2.32
4122 4349 0.661552 CCTGGCTCGAGAAATGCATG 59.338 55.000 18.75 0.00 0.00 4.06
4131 4358 3.444742 TCGAGAAATGCATGGCAAAAGAT 59.555 39.130 0.00 0.00 43.62 2.40
4152 4379 3.314693 TCAGGGGACAATGGACTATACC 58.685 50.000 0.00 0.00 0.00 2.73
4154 4381 1.346722 GGGGACAATGGACTATACCGG 59.653 57.143 0.00 0.00 0.00 5.28
4155 4382 2.044758 GGGACAATGGACTATACCGGT 58.955 52.381 13.98 13.98 0.00 5.28
4156 4383 2.224209 GGGACAATGGACTATACCGGTG 60.224 54.545 19.93 2.36 0.00 4.94
4157 4384 2.696707 GGACAATGGACTATACCGGTGA 59.303 50.000 19.93 3.75 0.00 4.02
4158 4385 3.323979 GGACAATGGACTATACCGGTGAT 59.676 47.826 19.93 9.49 0.00 3.06
4169 4396 9.447157 GGACTATACCGGTGATATATAGGATAC 57.553 40.741 19.93 8.86 34.51 2.24
4225 4452 0.919710 AGTAGGAATTGGAGTGGCCC 59.080 55.000 0.00 0.00 34.97 5.80
4228 4455 1.452108 GGAATTGGAGTGGCCCGAG 60.452 63.158 0.00 0.00 34.97 4.63
4233 4460 1.827399 TTGGAGTGGCCCGAGACTTC 61.827 60.000 0.00 0.00 34.97 3.01
4244 4471 1.407258 CCGAGACTTCTTAGGGCTGAG 59.593 57.143 0.00 0.00 0.00 3.35
4320 4644 2.779755 ATGTTTCCTCGCATGTGGTA 57.220 45.000 6.39 0.00 0.00 3.25
4341 4665 2.279517 CGCGTATGCACCTCCCTC 60.280 66.667 7.86 0.00 42.97 4.30
4342 4666 2.786495 CGCGTATGCACCTCCCTCT 61.786 63.158 7.86 0.00 42.97 3.69
4343 4667 1.227380 GCGTATGCACCTCCCTCTG 60.227 63.158 0.89 0.00 42.15 3.35
4344 4668 1.961180 GCGTATGCACCTCCCTCTGT 61.961 60.000 0.89 0.00 42.15 3.41
4345 4669 1.399714 CGTATGCACCTCCCTCTGTA 58.600 55.000 0.00 0.00 0.00 2.74
4346 4670 1.754803 CGTATGCACCTCCCTCTGTAA 59.245 52.381 0.00 0.00 0.00 2.41
4347 4671 2.167693 CGTATGCACCTCCCTCTGTAAA 59.832 50.000 0.00 0.00 0.00 2.01
4350 4674 2.334977 TGCACCTCCCTCTGTAAAGAA 58.665 47.619 0.00 0.00 0.00 2.52
4351 4675 2.708861 TGCACCTCCCTCTGTAAAGAAA 59.291 45.455 0.00 0.00 0.00 2.52
4352 4676 3.137544 TGCACCTCCCTCTGTAAAGAAAA 59.862 43.478 0.00 0.00 0.00 2.29
4353 4677 4.142038 GCACCTCCCTCTGTAAAGAAAAA 58.858 43.478 0.00 0.00 0.00 1.94
4354 4678 4.767409 GCACCTCCCTCTGTAAAGAAAAAT 59.233 41.667 0.00 0.00 0.00 1.82
4355 4679 5.944007 GCACCTCCCTCTGTAAAGAAAAATA 59.056 40.000 0.00 0.00 0.00 1.40
4356 4680 6.433093 GCACCTCCCTCTGTAAAGAAAAATAA 59.567 38.462 0.00 0.00 0.00 1.40
4357 4681 7.362142 GCACCTCCCTCTGTAAAGAAAAATAAG 60.362 40.741 0.00 0.00 0.00 1.73
4358 4682 7.883311 CACCTCCCTCTGTAAAGAAAAATAAGA 59.117 37.037 0.00 0.00 0.00 2.10
4359 4683 8.445588 ACCTCCCTCTGTAAAGAAAAATAAGAA 58.554 33.333 0.00 0.00 0.00 2.52
4360 4684 8.731605 CCTCCCTCTGTAAAGAAAAATAAGAAC 58.268 37.037 0.00 0.00 0.00 3.01
4361 4685 8.319143 TCCCTCTGTAAAGAAAAATAAGAACG 57.681 34.615 0.00 0.00 0.00 3.95
4362 4686 7.935210 TCCCTCTGTAAAGAAAAATAAGAACGT 59.065 33.333 0.00 0.00 0.00 3.99
4363 4687 8.565416 CCCTCTGTAAAGAAAAATAAGAACGTT 58.435 33.333 0.00 0.00 0.00 3.99
4364 4688 9.946165 CCTCTGTAAAGAAAAATAAGAACGTTT 57.054 29.630 0.46 0.00 0.00 3.60
4412 4736 8.608844 AATGCTCTTATATTTCTTTACGGAGG 57.391 34.615 0.00 0.00 0.00 4.30
4413 4737 7.356089 TGCTCTTATATTTCTTTACGGAGGA 57.644 36.000 0.00 0.00 0.00 3.71
4414 4738 7.788026 TGCTCTTATATTTCTTTACGGAGGAA 58.212 34.615 0.00 0.00 0.00 3.36
4415 4739 7.926555 TGCTCTTATATTTCTTTACGGAGGAAG 59.073 37.037 0.00 0.00 0.00 3.46
4416 4740 7.927092 GCTCTTATATTTCTTTACGGAGGAAGT 59.073 37.037 0.00 0.00 0.00 3.01
4421 4745 8.943909 ATATTTCTTTACGGAGGAAGTACTTG 57.056 34.615 14.14 0.12 0.00 3.16
4422 4746 5.796424 TTCTTTACGGAGGAAGTACTTGT 57.204 39.130 14.14 6.81 0.00 3.16
4423 4747 5.796424 TCTTTACGGAGGAAGTACTTGTT 57.204 39.130 14.14 0.00 0.00 2.83
4488 4813 4.032703 GCATCCGCAATAACACTTTGAT 57.967 40.909 0.00 0.00 38.36 2.57
4602 4946 1.961277 GTCCGTGTGTGCTCCCAAG 60.961 63.158 0.00 0.00 0.00 3.61
4637 4981 2.497273 GCCCCTAAACACAAGAATGCAT 59.503 45.455 0.00 0.00 0.00 3.96
4645 4989 8.341173 CCTAAACACAAGAATGCATATCTCTTC 58.659 37.037 8.80 0.00 0.00 2.87
4647 4991 7.692460 AACACAAGAATGCATATCTCTTCAA 57.308 32.000 8.80 0.00 0.00 2.69
4664 5008 0.750911 CAATGAGAAGGCCCCTGCTC 60.751 60.000 14.41 14.41 46.50 4.26
4666 5010 4.168291 GAGAAGGCCCCTGCTCGG 62.168 72.222 6.57 0.00 38.79 4.63
4703 5047 6.500336 TGGTAATTACTCCTTGGAGTACTCT 58.500 40.000 24.38 15.57 37.39 3.24
4705 5049 7.559170 TGGTAATTACTCCTTGGAGTACTCTAC 59.441 40.741 24.38 21.99 37.39 2.59
4719 5063 6.636562 AGTACTCTACTCATTCATAACCGG 57.363 41.667 0.00 0.00 32.47 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 140 2.224548 ACCAAGACCCCTCGAAAGAAAG 60.225 50.000 0.00 0.00 41.32 2.62
144 148 1.957877 GATCTCTACCAAGACCCCTCG 59.042 57.143 0.00 0.00 0.00 4.63
152 156 8.528044 AGTAGTTCCTAAAGATCTCTACCAAG 57.472 38.462 10.36 0.00 30.54 3.61
377 381 4.820716 GCTCTACTGACCGAGGAAATACTA 59.179 45.833 0.00 0.00 0.00 1.82
378 382 3.633065 GCTCTACTGACCGAGGAAATACT 59.367 47.826 0.00 0.00 0.00 2.12
379 383 3.380637 TGCTCTACTGACCGAGGAAATAC 59.619 47.826 0.00 0.00 0.00 1.89
380 384 3.628008 TGCTCTACTGACCGAGGAAATA 58.372 45.455 0.00 0.00 0.00 1.40
422 426 2.252260 GCATCACACACACGCACC 59.748 61.111 0.00 0.00 0.00 5.01
443 447 2.286294 GCACTGATTGATGTTAGGCTCG 59.714 50.000 0.00 0.00 0.00 5.03
545 594 0.401356 TGCAAGTCAGATTGGGAGCA 59.599 50.000 0.00 0.00 0.00 4.26
645 704 1.526887 CAAGTACACAGTTCACGCCTG 59.473 52.381 0.00 0.00 36.01 4.85
646 705 1.138266 ACAAGTACACAGTTCACGCCT 59.862 47.619 0.00 0.00 0.00 5.52
647 706 1.578583 ACAAGTACACAGTTCACGCC 58.421 50.000 0.00 0.00 0.00 5.68
652 711 2.985139 GGCGACTACAAGTACACAGTTC 59.015 50.000 0.00 0.00 0.00 3.01
655 714 2.987149 CAAGGCGACTACAAGTACACAG 59.013 50.000 0.00 0.00 42.68 3.66
662 721 2.672961 TGATCCAAGGCGACTACAAG 57.327 50.000 0.00 0.00 42.68 3.16
664 723 2.695359 GTTTGATCCAAGGCGACTACA 58.305 47.619 0.00 0.00 42.68 2.74
671 743 2.414691 GCTCTTTCGTTTGATCCAAGGC 60.415 50.000 0.00 0.00 0.00 4.35
697 769 3.067180 GGATTGTGATGGCGATGTGAATT 59.933 43.478 0.00 0.00 0.00 2.17
790 862 2.811317 CTGACGGGAGAGTTGCGC 60.811 66.667 0.00 0.00 0.00 6.09
792 864 2.811317 CGCTGACGGGAGAGTTGC 60.811 66.667 0.00 0.00 34.97 4.17
794 866 1.867919 CTGACGCTGACGGGAGAGTT 61.868 60.000 0.00 0.00 46.04 3.01
935 1023 0.393944 ACCAGATCACGAGAGCGGTA 60.394 55.000 11.37 0.00 43.17 4.02
989 1082 4.778143 AGAACATGGCCGGCGGTC 62.778 66.667 26.28 26.28 0.00 4.79
1210 1306 2.941064 AGGCAATTCACGATCATCAGTG 59.059 45.455 0.00 3.94 39.55 3.66
1246 1352 1.046472 AGTGGAACCGGACAGTGACA 61.046 55.000 9.46 0.00 37.80 3.58
1251 1357 0.602905 GTGGAAGTGGAACCGGACAG 60.603 60.000 9.46 0.00 37.80 3.51
1263 1369 1.533469 CCGAGGACGAAGGTGGAAGT 61.533 60.000 0.00 0.00 42.66 3.01
1264 1370 1.215647 CCGAGGACGAAGGTGGAAG 59.784 63.158 0.00 0.00 42.66 3.46
1265 1371 0.613853 ATCCGAGGACGAAGGTGGAA 60.614 55.000 0.00 0.00 42.66 3.53
1266 1372 1.000019 ATCCGAGGACGAAGGTGGA 60.000 57.895 0.00 0.00 42.66 4.02
1267 1373 1.320344 TGATCCGAGGACGAAGGTGG 61.320 60.000 0.00 0.00 42.66 4.61
1268 1374 0.179134 GTGATCCGAGGACGAAGGTG 60.179 60.000 0.00 0.00 42.66 4.00
1269 1375 0.611062 TGTGATCCGAGGACGAAGGT 60.611 55.000 0.00 0.00 42.66 3.50
1319 1425 0.385390 CCCAAGCCAACTCACAACAC 59.615 55.000 0.00 0.00 0.00 3.32
1465 1571 1.725641 TGGCGTGCTTACTGAATGAG 58.274 50.000 0.00 0.00 0.00 2.90
1593 1700 3.392616 CCTATTGCAGTTATGTCCCCTCT 59.607 47.826 0.00 0.00 0.00 3.69
1601 1708 5.343249 GCAAAACTCCCTATTGCAGTTATG 58.657 41.667 4.96 0.00 46.57 1.90
1663 1772 9.242477 GTTTCAGAAAAAGAGAGAAAATCCTTG 57.758 33.333 0.00 0.00 30.91 3.61
1838 1949 7.979444 TTTTCTATATTTCTAAGGATGGCGG 57.021 36.000 0.00 0.00 0.00 6.13
1875 1987 6.481954 AAGAAAATACAGTAGAAGGTTGCG 57.518 37.500 0.00 0.00 0.00 4.85
1898 2010 0.472044 TGGGCAGTTGAGCACAGTTA 59.528 50.000 0.00 0.00 44.33 2.24
1979 2091 5.524284 CAATTATGGTGTGGTTTTTCGACA 58.476 37.500 0.00 0.00 32.61 4.35
1983 2095 5.390779 GCATGCAATTATGGTGTGGTTTTTC 60.391 40.000 14.21 0.00 0.00 2.29
2084 2206 3.465742 TCTAAGATGAGATGCACCAGC 57.534 47.619 0.00 0.00 42.57 4.85
2108 2230 1.850377 CTGGTCGAGCAATAGCAGAG 58.150 55.000 19.16 0.07 45.49 3.35
2207 2329 8.635765 ACAGTGACAATGTAAGTGGATTAAAT 57.364 30.769 6.78 0.00 35.33 1.40
2303 2426 5.988287 TCCCAAAGCTCAACAAAGAAATTT 58.012 33.333 0.00 0.00 0.00 1.82
2366 2489 9.702726 CGTTTACCATTGATTTGTGTATAGAAG 57.297 33.333 0.00 0.00 0.00 2.85
2391 2514 6.682863 CGCTGGTAATTAAGAGAAAAACATCG 59.317 38.462 0.00 0.00 0.00 3.84
2394 2517 6.261381 ACACGCTGGTAATTAAGAGAAAAACA 59.739 34.615 0.00 0.00 0.00 2.83
2469 2592 4.403752 AGATCAGCTTGCTCATACAGTACA 59.596 41.667 0.00 0.00 0.00 2.90
2519 2726 6.933514 AAAATAAATCCTTCCCTTGAAGCA 57.066 33.333 0.00 0.00 45.53 3.91
2555 2762 3.995199 TCTCAGGATTTAGGCATTAGCG 58.005 45.455 0.00 0.00 43.41 4.26
2568 2775 5.690464 AAGAGCTGTTACAATCTCAGGAT 57.310 39.130 13.88 0.00 0.00 3.24
2729 2947 4.900635 AAAATGACACCTGACAGACAAC 57.099 40.909 3.32 0.00 0.00 3.32
2735 2953 7.340122 TCATAAACAAAAATGACACCTGACA 57.660 32.000 0.00 0.00 0.00 3.58
2814 3032 1.600413 GCTGAAAAGGTGCCTGTTTCG 60.600 52.381 14.77 12.16 34.63 3.46
2923 3141 3.865745 ACAATACTTCCGCTTCTGATTCG 59.134 43.478 0.00 0.00 0.00 3.34
2926 3144 4.832248 TCAACAATACTTCCGCTTCTGAT 58.168 39.130 0.00 0.00 0.00 2.90
2991 3209 4.893524 TCTGTGAGTGGAAGTTCTTCACTA 59.106 41.667 23.35 15.16 41.24 2.74
3018 3236 2.372172 GAGACCAGAGTTCCCAGGAAAA 59.628 50.000 0.00 0.00 35.75 2.29
3054 3272 4.326826 TGAGCAGAAGGTATTCAACAAGG 58.673 43.478 0.00 0.00 37.94 3.61
3128 3346 2.304751 ACTGAAACGACAAAGGACGT 57.695 45.000 0.00 0.00 46.76 4.34
3167 3385 1.670967 GCAGCCTGCAATCAAAGGTTC 60.671 52.381 12.82 0.00 44.26 3.62
3434 3652 4.023291 TGCTCACCTTTTCCTTTGAAAGT 58.977 39.130 4.02 0.00 41.31 2.66
3468 3686 5.301805 TCTTTGACAGGGGAGTTGATTTTTC 59.698 40.000 0.00 0.00 0.00 2.29
3484 3706 5.830457 TGTATGTGTTGGGATTTCTTTGACA 59.170 36.000 0.00 0.00 0.00 3.58
3485 3707 6.325919 TGTATGTGTTGGGATTTCTTTGAC 57.674 37.500 0.00 0.00 0.00 3.18
3525 3749 7.314393 GTGACGAAAGAGTTCTCCTTTATACT 58.686 38.462 0.00 0.00 34.33 2.12
3545 3769 1.203994 ACAGTTATCCTTCGGGTGACG 59.796 52.381 0.00 0.00 46.11 4.35
3557 3781 7.801716 TGTTTAATATGGGCTCACAGTTATC 57.198 36.000 0.00 0.00 0.00 1.75
3633 3857 3.829601 GTGGTACCCCATTGAACATGAAA 59.170 43.478 10.07 0.00 44.35 2.69
3660 3884 1.072505 GAGGTTCCTTTGTGCCGGA 59.927 57.895 5.05 0.00 0.00 5.14
3730 3954 5.698832 CGAGGAGAATCTGTGATATCTGTC 58.301 45.833 3.98 0.00 33.73 3.51
4053 4280 9.661563 TTACGGAAATGACAAGTAATCACTATT 57.338 29.630 0.00 0.00 33.48 1.73
4076 4303 5.343249 CCATTTTCCAGCTACTTGCATTAC 58.657 41.667 0.00 0.00 45.94 1.89
4088 4315 0.462789 CCAGGATGCCATTTTCCAGC 59.537 55.000 0.00 0.00 34.27 4.85
4102 4329 0.543277 ATGCATTTCTCGAGCCAGGA 59.457 50.000 7.81 0.00 0.00 3.86
4108 4335 2.925578 TTTGCCATGCATTTCTCGAG 57.074 45.000 5.93 5.93 38.76 4.04
4118 4345 0.462789 CCCCTGATCTTTTGCCATGC 59.537 55.000 0.00 0.00 0.00 4.06
4122 4349 1.923356 TTGTCCCCTGATCTTTTGCC 58.077 50.000 0.00 0.00 0.00 4.52
4131 4358 3.314693 GGTATAGTCCATTGTCCCCTGA 58.685 50.000 0.00 0.00 0.00 3.86
4207 4434 0.463833 CGGGCCACTCCAATTCCTAC 60.464 60.000 4.39 0.00 36.21 3.18
4225 4452 1.407258 CCTCAGCCCTAAGAAGTCTCG 59.593 57.143 0.00 0.00 0.00 4.04
4228 4455 0.905357 TGCCTCAGCCCTAAGAAGTC 59.095 55.000 0.00 0.00 38.69 3.01
4233 4460 2.725221 AATCTTGCCTCAGCCCTAAG 57.275 50.000 0.00 0.00 38.69 2.18
4244 4471 6.988522 TGTTCCTACCTTTTAAAATCTTGCC 58.011 36.000 0.09 0.00 0.00 4.52
4292 4520 3.701241 TGCGAGGAAACATTCAAACAAC 58.299 40.909 0.00 0.00 0.00 3.32
4337 4661 8.095937 ACGTTCTTATTTTTCTTTACAGAGGG 57.904 34.615 0.00 0.00 0.00 4.30
4338 4662 9.946165 AAACGTTCTTATTTTTCTTTACAGAGG 57.054 29.630 0.00 0.00 0.00 3.69
4386 4710 9.057089 CCTCCGTAAAGAAATATAAGAGCATTT 57.943 33.333 0.00 0.00 0.00 2.32
4387 4711 8.429641 TCCTCCGTAAAGAAATATAAGAGCATT 58.570 33.333 0.00 0.00 0.00 3.56
4388 4712 7.963532 TCCTCCGTAAAGAAATATAAGAGCAT 58.036 34.615 0.00 0.00 0.00 3.79
4389 4713 7.356089 TCCTCCGTAAAGAAATATAAGAGCA 57.644 36.000 0.00 0.00 0.00 4.26
4390 4714 7.927092 ACTTCCTCCGTAAAGAAATATAAGAGC 59.073 37.037 0.00 0.00 0.00 4.09
4396 4720 8.537858 ACAAGTACTTCCTCCGTAAAGAAATAT 58.462 33.333 4.77 0.00 0.00 1.28
4397 4721 7.899973 ACAAGTACTTCCTCCGTAAAGAAATA 58.100 34.615 4.77 0.00 0.00 1.40
4398 4722 6.766429 ACAAGTACTTCCTCCGTAAAGAAAT 58.234 36.000 4.77 0.00 0.00 2.17
4399 4723 6.165700 ACAAGTACTTCCTCCGTAAAGAAA 57.834 37.500 4.77 0.00 0.00 2.52
4400 4724 5.796424 ACAAGTACTTCCTCCGTAAAGAA 57.204 39.130 4.77 0.00 0.00 2.52
4401 4725 5.796424 AACAAGTACTTCCTCCGTAAAGA 57.204 39.130 4.77 0.00 0.00 2.52
4402 4726 6.856135 AAAACAAGTACTTCCTCCGTAAAG 57.144 37.500 4.77 0.00 0.00 1.85
4479 4804 7.670364 AGCTGGCTAAATAAAAATCAAAGTGT 58.330 30.769 0.00 0.00 0.00 3.55
4584 4928 1.961277 CTTGGGAGCACACACGGAC 60.961 63.158 0.00 0.00 0.00 4.79
4587 4931 3.357079 GCCTTGGGAGCACACACG 61.357 66.667 0.00 0.00 0.00 4.49
4602 4946 1.620822 AGGGGCATTATGAATTCGCC 58.379 50.000 11.61 11.61 42.21 5.54
4645 4989 0.750911 GAGCAGGGGCCTTCTCATTG 60.751 60.000 0.84 0.00 42.56 2.82
4647 4991 2.739996 CGAGCAGGGGCCTTCTCAT 61.740 63.158 0.84 0.00 42.56 2.90
4659 5003 2.508887 GTCTGAGCAGCCGAGCAG 60.509 66.667 0.00 0.00 36.85 4.24
4665 5009 2.507110 TTACCAGCGTCTGAGCAGCC 62.507 60.000 8.20 0.00 40.15 4.85
4666 5010 0.460987 ATTACCAGCGTCTGAGCAGC 60.461 55.000 8.20 0.00 40.15 5.25
4667 5011 2.015736 AATTACCAGCGTCTGAGCAG 57.984 50.000 8.20 0.00 40.15 4.24
4668 5012 2.496070 AGTAATTACCAGCGTCTGAGCA 59.504 45.455 12.05 0.00 40.15 4.26
4669 5013 3.117046 GAGTAATTACCAGCGTCTGAGC 58.883 50.000 12.05 0.00 32.44 4.26
4670 5014 3.381908 AGGAGTAATTACCAGCGTCTGAG 59.618 47.826 12.05 2.32 32.44 3.35
4671 5015 3.362706 AGGAGTAATTACCAGCGTCTGA 58.637 45.455 12.05 0.00 32.44 3.27
4703 5047 5.408880 TGTGTTCCGGTTATGAATGAGTA 57.591 39.130 0.00 0.00 0.00 2.59
4705 5049 4.094887 CCTTGTGTTCCGGTTATGAATGAG 59.905 45.833 0.00 0.00 0.00 2.90
4712 5056 7.571025 ACTAATATTCCTTGTGTTCCGGTTAT 58.429 34.615 0.00 0.00 0.00 1.89
4714 5058 5.812286 ACTAATATTCCTTGTGTTCCGGTT 58.188 37.500 0.00 0.00 0.00 4.44
4715 5059 5.431179 ACTAATATTCCTTGTGTTCCGGT 57.569 39.130 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.