Multiple sequence alignment - TraesCS5B01G264600

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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 TraesCS5B01G264600 chr5B 100.000 4032 0 0 1 4032 448600333 448604364 0.000000e+00 7446.0
1 TraesCS5B01G264600 chr5A 92.087 4107 207 55 1 4032 476850963 476855026 0.000000e+00 5675.0
2 TraesCS5B01G264600 chr5D 93.845 2226 94 15 1 2193 375747523 375749738 0.000000e+00 3312.0
3 TraesCS5B01G264600 chr5D 96.378 1850 56 8 2188 4032 375749762 375751605 0.000000e+00 3035.0
4 TraesCS5B01G264600 chr7A 84.884 86 5 2 1252 1329 202520927 202520842 3.340000e-11 80.5
5 TraesCS5B01G264600 chr7D 100.000 29 0 0 1252 1280 192929259 192929231 2.000000e-03 54.7


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 TraesCS5B01G264600 chr5B 448600333 448604364 4031 False 7446.0 7446 100.0000 1 4032 1 chr5B.!!$F1 4031
1 TraesCS5B01G264600 chr5A 476850963 476855026 4063 False 5675.0 5675 92.0870 1 4032 1 chr5A.!!$F1 4031
2 TraesCS5B01G264600 chr5D 375747523 375751605 4082 False 3173.5 3312 95.1115 1 4032 2 chr5D.!!$F1 4031

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
976 994 0.178975 ACACAGCCGGAAAAATCCCA 60.179 50.000 5.05 0.00 0.00 4.37 F
1505 1562 0.818296 CTCCACCTCCACTAAGACGG 59.182 60.000 0.00 0.00 0.00 4.79 F
1782 1846 2.968697 TGTGCGTGCTCACAGCTG 60.969 61.111 13.48 13.48 42.97 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2026 2090 0.252197 AGTTACCTGATTGTCCCCGC 59.748 55.000 0.0 0.0 0.00 6.13 R
2763 2863 0.967380 AGTGGGCTGCACATTAAGGC 60.967 55.000 8.3 0.0 38.21 4.35 R
3441 3541 1.406887 GGGTCTAGGCATTTCGCTCAA 60.407 52.381 0.0 0.0 41.91 3.02 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
46 50 0.958091 TGCGGAACATTTTGACCTGG 59.042 50.000 0.00 0.00 0.00 4.45
156 161 3.829886 TGAGAGCAAACCATAAAAGCG 57.170 42.857 0.00 0.00 0.00 4.68
168 173 5.040635 ACCATAAAAGCGCAAATTATTCCG 58.959 37.500 11.47 4.00 0.00 4.30
173 178 1.062002 AGCGCAAATTATTCCGTCACG 59.938 47.619 11.47 0.00 0.00 4.35
185 190 9.706691 AATTATTCCGTCACGTTTCATAGATAT 57.293 29.630 0.00 0.00 0.00 1.63
219 224 3.012518 CAGCTAGAAAACATCACCAGGG 58.987 50.000 0.00 0.00 0.00 4.45
239 244 1.272212 GAGAGATCCATCCGAGAAGGC 59.728 57.143 0.00 0.00 40.77 4.35
285 290 2.169352 CCATCTGGACGTTCTTCTCCAT 59.831 50.000 0.00 0.00 35.95 3.41
322 327 4.332543 AACCCCCTCAGCTCCGGA 62.333 66.667 2.93 2.93 0.00 5.14
337 342 2.688446 CTCCGGAGTGCAGTTCAGTATA 59.312 50.000 24.04 0.00 0.00 1.47
358 363 2.925706 TTGTAGCACCCCCTCGCA 60.926 61.111 0.00 0.00 0.00 5.10
439 444 2.920912 TCCACCACCACGTCCTCC 60.921 66.667 0.00 0.00 0.00 4.30
803 814 2.375146 GGACGTCAAATAAGGCCCAAT 58.625 47.619 18.91 0.00 0.00 3.16
816 827 2.097036 GGCCCAATTGGTGTTAGTACC 58.903 52.381 22.91 7.36 41.24 3.34
846 857 6.295575 CCTGTTACATTTTGATTGGGCCTTTA 60.296 38.462 4.53 0.00 0.00 1.85
893 911 2.172851 ACAAAGATTCGCCCGTTACA 57.827 45.000 0.00 0.00 0.00 2.41
894 912 1.802365 ACAAAGATTCGCCCGTTACAC 59.198 47.619 0.00 0.00 0.00 2.90
895 913 1.801771 CAAAGATTCGCCCGTTACACA 59.198 47.619 0.00 0.00 0.00 3.72
976 994 0.178975 ACACAGCCGGAAAAATCCCA 60.179 50.000 5.05 0.00 0.00 4.37
1134 1158 2.567049 CTCTCGAGCCGTTTCCGT 59.433 61.111 7.81 0.00 0.00 4.69
1382 1406 5.565439 CGATTCATTTCAGGGTTTGCTTCTT 60.565 40.000 0.00 0.00 0.00 2.52
1385 1409 4.520492 TCATTTCAGGGTTTGCTTCTTCTC 59.480 41.667 0.00 0.00 0.00 2.87
1391 1415 3.586618 AGGGTTTGCTTCTTCTCATCTCT 59.413 43.478 0.00 0.00 0.00 3.10
1395 1419 3.516981 TGCTTCTTCTCATCTCTTCCG 57.483 47.619 0.00 0.00 0.00 4.30
1429 1453 1.682849 GATACACAGTGGCCACCCA 59.317 57.895 32.29 13.23 39.32 4.51
1500 1557 3.757947 TGAGATCTCCACCTCCACTAA 57.242 47.619 20.03 0.00 0.00 2.24
1501 1558 3.636679 TGAGATCTCCACCTCCACTAAG 58.363 50.000 20.03 0.00 0.00 2.18
1505 1562 0.818296 CTCCACCTCCACTAAGACGG 59.182 60.000 0.00 0.00 0.00 4.79
1520 1577 4.419522 AAGACGGTGCACATTTGTATTC 57.580 40.909 20.43 2.46 0.00 1.75
1523 1580 4.870426 AGACGGTGCACATTTGTATTCTAG 59.130 41.667 20.43 0.00 0.00 2.43
1524 1581 3.374058 ACGGTGCACATTTGTATTCTAGC 59.626 43.478 20.43 0.00 0.00 3.42
1525 1582 3.373748 CGGTGCACATTTGTATTCTAGCA 59.626 43.478 20.43 0.00 0.00 3.49
1526 1583 4.142708 CGGTGCACATTTGTATTCTAGCAA 60.143 41.667 20.43 0.00 32.03 3.91
1527 1584 5.449041 CGGTGCACATTTGTATTCTAGCAAT 60.449 40.000 20.43 0.00 32.03 3.56
1528 1585 6.332630 GGTGCACATTTGTATTCTAGCAATT 58.667 36.000 20.43 0.00 32.03 2.32
1529 1586 6.813152 GGTGCACATTTGTATTCTAGCAATTT 59.187 34.615 20.43 0.00 32.03 1.82
1530 1587 7.331687 GGTGCACATTTGTATTCTAGCAATTTT 59.668 33.333 20.43 0.00 32.03 1.82
1531 1588 8.711457 GTGCACATTTGTATTCTAGCAATTTTT 58.289 29.630 13.17 0.00 32.03 1.94
1562 1625 4.346734 AAATAGCGTGTTGAATCAGCAG 57.653 40.909 0.00 0.00 0.00 4.24
1575 1638 5.122519 TGAATCAGCAGTACAAGTGAACAA 58.877 37.500 0.00 0.00 0.00 2.83
1580 1644 5.182190 TCAGCAGTACAAGTGAACAACAAAA 59.818 36.000 0.00 0.00 0.00 2.44
1645 1709 3.607741 CAGAAGCTGGATGATCTGTTGT 58.392 45.455 3.15 0.00 35.65 3.32
1646 1710 3.622163 CAGAAGCTGGATGATCTGTTGTC 59.378 47.826 3.15 0.00 35.65 3.18
1782 1846 2.968697 TGTGCGTGCTCACAGCTG 60.969 61.111 13.48 13.48 42.97 4.24
2154 2218 4.061357 TGTTTCCATGGCATATGCATTG 57.939 40.909 28.07 22.21 44.36 2.82
2213 2306 8.766000 TTCTTAGTGATGACGCTTGTAAATTA 57.234 30.769 0.00 0.00 37.97 1.40
2263 2359 9.208022 CAGAACAAGAGTTGTATAACATTCAGA 57.792 33.333 5.08 0.00 44.59 3.27
2264 2360 9.778741 AGAACAAGAGTTGTATAACATTCAGAA 57.221 29.630 5.08 0.00 44.59 3.02
2395 2491 4.865905 TGTGGGTGGCATATTCTTACAAT 58.134 39.130 0.00 0.00 0.00 2.71
2753 2853 4.082190 CGGATTCTGAGTCTCCTGTAACAA 60.082 45.833 0.00 0.00 0.00 2.83
2763 2863 4.859798 GTCTCCTGTAACAACGAGAGAATG 59.140 45.833 0.00 0.00 32.20 2.67
2794 2894 4.394712 CCCACTGACGGCACTCCC 62.395 72.222 0.00 0.00 0.00 4.30
2880 2980 2.507992 ATCAGTGCGCTCGACTGC 60.508 61.111 18.70 0.00 40.64 4.40
2908 3008 7.538678 CCACTCAAAGAGAAATGTTTAAATCCG 59.461 37.037 0.31 0.00 33.32 4.18
3002 3102 5.529060 AGAAGACAAAGTCACCAAGATTCAC 59.471 40.000 0.00 0.00 34.60 3.18
3060 3160 5.012664 TGGACTGCAAGAACTTATTACCAGA 59.987 40.000 0.00 0.00 37.43 3.86
3115 3215 6.479990 TCATCTCATTATGCCACGAAGTTTAG 59.520 38.462 0.00 0.00 41.61 1.85
3118 3218 5.242434 TCATTATGCCACGAAGTTTAGTGT 58.758 37.500 10.28 0.00 41.61 3.55
3132 3232 9.661187 CGAAGTTTAGTGTATATCTTACGTCAT 57.339 33.333 0.00 0.00 0.00 3.06
3347 3447 2.863809 TCCACTCAGAAAAGGAAAGGC 58.136 47.619 0.00 0.00 0.00 4.35
3385 3485 8.950007 ACCAATTAGATACCCTTTTTCAAGAA 57.050 30.769 0.00 0.00 30.57 2.52
3427 3527 9.681692 CTTTGATTATTCTGTCAAATGAACACA 57.318 29.630 1.55 0.00 41.80 3.72
3487 3589 3.328931 CCCCTGATACTCTGCATATTGGT 59.671 47.826 0.00 0.00 0.00 3.67
3500 3602 4.415179 TGCATATTGGTTCCTTCCCTGATA 59.585 41.667 0.00 0.00 0.00 2.15
3572 3674 5.349817 CGACACTTCTATGAATTCAACAGCT 59.650 40.000 13.09 0.00 0.00 4.24
3602 3704 3.214328 TCCTTTCTTGTTTGCTCACCTC 58.786 45.455 0.00 0.00 0.00 3.85
3624 3726 8.322091 ACCTCTTATGTAAGTGCATTCTACTTT 58.678 33.333 0.00 0.00 39.06 2.66
3689 3791 6.131961 CCAGTTATCTTCATTCCCCATCTTT 58.868 40.000 0.00 0.00 0.00 2.52
3768 3873 8.742777 CCATTTTCTTACATTTCAGATCAGGAA 58.257 33.333 0.00 0.00 0.00 3.36
3769 3874 9.784680 CATTTTCTTACATTTCAGATCAGGAAG 57.215 33.333 0.00 0.00 0.00 3.46
3770 3875 7.928307 TTTCTTACATTTCAGATCAGGAAGG 57.072 36.000 0.00 0.00 0.00 3.46
3850 3955 3.756434 TGTCCGGTGAAAGAAAATGGATC 59.244 43.478 0.00 0.00 0.00 3.36
3855 3960 4.158394 CGGTGAAAGAAAATGGATCCATGT 59.842 41.667 27.97 20.37 36.68 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 35 8.788325 ATAACTACTACCAGGTCAAAATGTTC 57.212 34.615 0.00 0.00 0.00 3.18
46 50 5.080969 TGGGTTGCACTGATAACTACTAC 57.919 43.478 0.00 0.00 0.00 2.73
139 143 2.346099 TGCGCTTTTATGGTTTGCTC 57.654 45.000 9.73 0.00 0.00 4.26
156 161 4.468643 TGAAACGTGACGGAATAATTTGC 58.531 39.130 10.66 0.00 0.00 3.68
168 173 9.776158 CCTGTATCTATATCTATGAAACGTGAC 57.224 37.037 0.00 0.00 0.00 3.67
173 178 9.929180 TGTTGCCTGTATCTATATCTATGAAAC 57.071 33.333 0.00 0.00 0.00 2.78
185 190 5.932619 TTTCTAGCTGTTGCCTGTATCTA 57.067 39.130 0.00 0.00 40.80 1.98
219 224 1.272212 GCCTTCTCGGATGGATCTCTC 59.728 57.143 9.17 0.00 33.16 3.20
239 244 5.009610 GGCTCTACTTCTGATCTAGGTTCAG 59.990 48.000 14.16 14.16 41.61 3.02
322 327 5.228945 ACAAGGTTATACTGAACTGCACT 57.771 39.130 0.00 0.00 0.00 4.40
337 342 1.838073 CGAGGGGGTGCTACAAGGTT 61.838 60.000 0.00 0.00 0.00 3.50
816 827 4.497300 CAATCAAAATGTAACAGGGCCTG 58.503 43.478 31.62 31.62 37.52 4.85
846 857 0.987294 CCCATGAGTTCAGTCCCTGT 59.013 55.000 0.00 0.00 32.61 4.00
857 869 0.398522 TGTAGATCCGGCCCATGAGT 60.399 55.000 0.00 0.00 0.00 3.41
860 872 1.140852 TCTTTGTAGATCCGGCCCATG 59.859 52.381 0.00 0.00 0.00 3.66
893 911 1.772063 GCCAAGTTGAAGCGACGTGT 61.772 55.000 3.87 0.00 0.00 4.49
894 912 1.082756 GCCAAGTTGAAGCGACGTG 60.083 57.895 3.87 0.00 0.00 4.49
895 913 0.884704 ATGCCAAGTTGAAGCGACGT 60.885 50.000 3.87 0.00 0.00 4.34
902 920 4.116238 GGTTTTCGAAATGCCAAGTTGAA 58.884 39.130 20.45 0.00 0.00 2.69
976 994 3.338603 CGTGACGCGTTTCGATTTT 57.661 47.368 24.79 0.00 41.67 1.82
1074 1098 2.490685 GAGGAGGAGCGAACGGAC 59.509 66.667 0.00 0.00 0.00 4.79
1083 1107 1.820481 GGAGGACGACGAGGAGGAG 60.820 68.421 0.00 0.00 0.00 3.69
1362 1386 4.473444 AGAAGAAGCAAACCCTGAAATGA 58.527 39.130 0.00 0.00 0.00 2.57
1382 1406 3.948473 AGATCGAAACGGAAGAGATGAGA 59.052 43.478 0.00 0.00 0.00 3.27
1385 1409 7.340699 CAAATAAGATCGAAACGGAAGAGATG 58.659 38.462 0.00 0.00 0.00 2.90
1391 1415 7.010738 GTGTATCCAAATAAGATCGAAACGGAA 59.989 37.037 0.00 0.00 0.00 4.30
1395 1419 8.116753 CACTGTGTATCCAAATAAGATCGAAAC 58.883 37.037 0.00 0.00 0.00 2.78
1429 1453 6.595682 ACTTATACAGGCACTTGATAGCATT 58.404 36.000 0.00 0.00 34.60 3.56
1500 1557 3.674997 AGAATACAAATGTGCACCGTCT 58.325 40.909 15.69 2.43 0.00 4.18
1501 1558 4.494199 GCTAGAATACAAATGTGCACCGTC 60.494 45.833 15.69 0.07 0.00 4.79
1505 1562 7.816945 AAATTGCTAGAATACAAATGTGCAC 57.183 32.000 10.75 10.75 0.00 4.57
1539 1596 5.119931 TGCTGATTCAACACGCTATTTTT 57.880 34.783 0.00 0.00 0.00 1.94
1541 1598 3.753272 ACTGCTGATTCAACACGCTATTT 59.247 39.130 0.00 0.00 0.00 1.40
1542 1599 3.338249 ACTGCTGATTCAACACGCTATT 58.662 40.909 0.00 0.00 0.00 1.73
1548 1611 4.511454 TCACTTGTACTGCTGATTCAACAC 59.489 41.667 0.00 0.00 0.00 3.32
1575 1638 6.019156 CCTGCACAACGAAAACATTATTTTGT 60.019 34.615 0.00 0.00 38.30 2.83
1580 1644 5.182950 TCATCCTGCACAACGAAAACATTAT 59.817 36.000 0.00 0.00 0.00 1.28
1645 1709 3.621225 CAGGGAGTGCATCTCGGA 58.379 61.111 9.29 0.00 43.60 4.55
1779 1843 0.739112 GAGTAGCAGCAGTCACCAGC 60.739 60.000 0.00 0.00 0.00 4.85
1781 1845 0.542938 AGGAGTAGCAGCAGTCACCA 60.543 55.000 0.00 0.00 0.00 4.17
1782 1846 0.610687 AAGGAGTAGCAGCAGTCACC 59.389 55.000 0.00 0.00 0.00 4.02
2026 2090 0.252197 AGTTACCTGATTGTCCCCGC 59.748 55.000 0.00 0.00 0.00 6.13
2061 2125 3.869246 ACAAAATAGATACTTCCGCCACG 59.131 43.478 0.00 0.00 0.00 4.94
2154 2218 7.253422 AGAGCACATTTGACATTAGCATAAAC 58.747 34.615 0.00 0.00 0.00 2.01
2199 2292 6.787085 AGCTGGATATAATTTACAAGCGTC 57.213 37.500 0.00 0.00 0.00 5.19
2200 2293 7.931948 ACTTAGCTGGATATAATTTACAAGCGT 59.068 33.333 0.00 0.00 0.00 5.07
2263 2359 4.263639 TGCATCCTTCTCTTCACATTCCTT 60.264 41.667 0.00 0.00 0.00 3.36
2264 2360 3.265221 TGCATCCTTCTCTTCACATTCCT 59.735 43.478 0.00 0.00 0.00 3.36
2265 2361 3.614092 TGCATCCTTCTCTTCACATTCC 58.386 45.455 0.00 0.00 0.00 3.01
2569 2668 3.062763 AGACACGAGAAGTCAGCATTTG 58.937 45.455 0.00 0.00 38.46 2.32
2753 2853 2.939103 GCACATTAAGGCATTCTCTCGT 59.061 45.455 0.00 0.00 0.00 4.18
2763 2863 0.967380 AGTGGGCTGCACATTAAGGC 60.967 55.000 8.30 0.00 38.21 4.35
2880 2980 6.648879 TTAAACATTTCTCTTTGAGTGGGG 57.351 37.500 0.00 0.00 0.00 4.96
2908 3008 4.629634 CCAACCAAACTTGTTTCCACTTTC 59.370 41.667 0.00 0.00 0.00 2.62
3002 3102 6.049149 TCCATCTCTTTGTAGCTTTATTCCG 58.951 40.000 0.00 0.00 0.00 4.30
3060 3160 8.807948 AATTCAAGCATAAACAGTGTACCTAT 57.192 30.769 0.00 0.00 0.00 2.57
3385 3485 4.521130 TCAAAGTGCTAGATTCTCACGT 57.479 40.909 0.00 0.00 35.97 4.49
3427 3527 7.221452 GCATTTCGCTCAATCAATTAGTTCAAT 59.779 33.333 0.00 0.00 37.77 2.57
3441 3541 1.406887 GGGTCTAGGCATTTCGCTCAA 60.407 52.381 0.00 0.00 41.91 3.02
3487 3589 9.320295 ACATTAAAAATTGTATCAGGGAAGGAA 57.680 29.630 0.00 0.00 0.00 3.36
3500 3602 7.038373 AGGGTGGCTAATGACATTAAAAATTGT 60.038 33.333 9.14 0.00 31.55 2.71
3572 3674 1.745232 ACAAGAAAGGAACGTGTGCA 58.255 45.000 0.00 0.00 0.00 4.57
3624 3726 9.365906 ACTATGCAATGGATATCATTACCAAAA 57.634 29.630 4.83 0.00 43.70 2.44
3768 3873 3.181433 CCTAACCAACCAACTTCCTTCCT 60.181 47.826 0.00 0.00 0.00 3.36
3769 3874 3.154710 CCTAACCAACCAACTTCCTTCC 58.845 50.000 0.00 0.00 0.00 3.46
3770 3875 4.094830 TCCTAACCAACCAACTTCCTTC 57.905 45.455 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.