Multiple sequence alignment - TraesCS6B01G433400

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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 TraesCS6B01G433400 chr6B 100.000 3806 0 0 1 3806 702242531 702246336 0.000000e+00 7029
1 TraesCS6B01G433400 chr6A 93.793 3818 196 22 9 3806 607053929 607057725 0.000000e+00 5699
2 TraesCS6B01G433400 chr6A 85.366 205 17 9 2891 3092 607059415 607059609 2.320000e-47 200
3 TraesCS6B01G433400 chr6D 90.945 3534 210 57 1 3495 460787709 460791171 0.000000e+00 4652
4 TraesCS6B01G433400 chr6D 84.971 346 44 7 3187 3527 460792915 460793257 1.010000e-90 344
5 TraesCS6B01G433400 chr6D 85.809 303 21 12 3524 3806 460791160 460791460 6.180000e-78 302
6 TraesCS6B01G433400 chr3B 94.585 591 30 2 2548 3138 739118322 739117734 0.000000e+00 913
7 TraesCS6B01G433400 chr3B 93.909 591 34 2 2548 3138 13127140 13127728 0.000000e+00 891
8 TraesCS6B01G433400 chr3B 94.565 92 3 2 3271 3362 739117733 739117644 1.430000e-29 141
9 TraesCS6B01G433400 chr3B 90.526 95 6 2 3268 3362 13127726 13127817 5.160000e-24 122


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 TraesCS6B01G433400 chr6B 702242531 702246336 3805 False 7029.0 7029 100.000000 1 3806 1 chr6B.!!$F1 3805
1 TraesCS6B01G433400 chr6A 607053929 607059609 5680 False 2949.5 5699 89.579500 9 3806 2 chr6A.!!$F1 3797
2 TraesCS6B01G433400 chr6D 460787709 460793257 5548 False 1766.0 4652 87.241667 1 3806 3 chr6D.!!$F1 3805
3 TraesCS6B01G433400 chr3B 739117644 739118322 678 True 527.0 913 94.575000 2548 3362 2 chr3B.!!$R1 814
4 TraesCS6B01G433400 chr3B 13127140 13127817 677 False 506.5 891 92.217500 2548 3362 2 chr3B.!!$F1 814

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
576 599 0.102120 GGAGCATGACGACCTGAGAG 59.898 60.0 0.0 0.0 0.00 3.20 F
1560 1590 0.179119 CGACAAGGGACACCGTATCC 60.179 60.0 0.0 0.0 43.47 2.59 F
2009 2039 0.313672 GGATTCGTGCAGTTTGGCAA 59.686 50.0 0.0 0.0 46.93 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2394 2424 0.460722 TGCATGCACACAAAACTGCT 59.539 45.000 18.46 0.0 34.29 4.24 R
2418 2448 0.537143 CTTGTGCCACTAAGCCACCA 60.537 55.000 0.00 0.0 0.00 4.17 R
3260 3290 1.072806 AGGTCAGCTGTCAATCTGCAA 59.927 47.619 14.67 0.0 42.26 4.08 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
61 62 1.780860 GCAATCCACGATTTATTGCGC 59.219 47.619 0.00 0.00 44.09 6.09
82 83 3.607741 CTCAACATTCCTCATGAGCAGT 58.392 45.455 17.76 9.16 36.24 4.40
85 86 1.022735 CATTCCTCATGAGCAGTGGC 58.977 55.000 17.76 0.00 41.61 5.01
143 144 1.331756 CGAGCAATGCCATACCTGAAC 59.668 52.381 0.00 0.00 0.00 3.18
146 147 1.064060 GCAATGCCATACCTGAACGAC 59.936 52.381 0.00 0.00 0.00 4.34
150 151 3.066291 TGCCATACCTGAACGACAAAT 57.934 42.857 0.00 0.00 0.00 2.32
208 210 9.077885 AGATCTAGATATCTCTGAAAGGACAAC 57.922 37.037 8.95 0.00 30.09 3.32
211 213 6.531503 AGATATCTCTGAAAGGACAACGAA 57.468 37.500 0.00 0.00 0.00 3.85
214 216 8.043710 AGATATCTCTGAAAGGACAACGAAATT 58.956 33.333 0.00 0.00 0.00 1.82
281 283 1.694150 GCCCTTTTCCCTTTCAGCTTT 59.306 47.619 0.00 0.00 0.00 3.51
330 332 9.578576 TGCTATTCTTTTCCTGCAGATATAAAT 57.421 29.630 17.39 9.90 0.00 1.40
404 409 6.071278 ACTGTAAAAGAGAGCTCGGAACTAAT 60.071 38.462 8.37 2.90 34.09 1.73
405 410 6.100004 TGTAAAAGAGAGCTCGGAACTAATG 58.900 40.000 8.37 0.00 34.09 1.90
439 445 2.029110 CAGGAATTTGGCGAACACCATT 60.029 45.455 12.34 0.00 40.13 3.16
478 484 1.214589 GCCGAGGTGCTTCGAGTTA 59.785 57.895 5.28 0.00 43.03 2.24
518 541 3.754188 AAATTCAGACTTCATGCGAGC 57.246 42.857 0.00 0.00 0.00 5.03
540 563 1.367659 CAGCACAGAAGAAGCTAGGC 58.632 55.000 0.00 0.00 36.73 3.93
556 579 1.063649 GGCAAGCACATCGCATCAG 59.936 57.895 0.00 0.00 46.13 2.90
576 599 0.102120 GGAGCATGACGACCTGAGAG 59.898 60.000 0.00 0.00 0.00 3.20
642 665 4.785453 GGGGAGTTCAGCCTGCCG 62.785 72.222 0.00 0.00 43.43 5.69
650 673 1.830587 TTCAGCCTGCCGTCAGATGT 61.831 55.000 0.00 0.00 42.95 3.06
657 680 2.094659 GCCGTCAGATGTCACCGTG 61.095 63.158 0.00 0.00 0.00 4.94
659 682 2.436539 CGTCAGATGTCACCGTGCG 61.437 63.158 0.00 0.00 0.00 5.34
681 705 4.390603 CGTGAGACCGGAATACATGAAAAA 59.609 41.667 9.46 0.00 0.00 1.94
714 738 6.623767 GCAGCCCAAAATCTCTACTAAAACTG 60.624 42.308 0.00 0.00 0.00 3.16
825 849 3.258228 AATCCGGTGAGCTGCTGCA 62.258 57.895 18.42 0.88 42.74 4.41
1143 1173 3.151022 CACCTCTCCCTCCTCGCC 61.151 72.222 0.00 0.00 0.00 5.54
1197 1227 3.535962 CAGCTCCTCCTCCTCGGC 61.536 72.222 0.00 0.00 0.00 5.54
1504 1534 0.522915 CTTCTACGCGTCCTTCGGTC 60.523 60.000 18.63 0.00 40.26 4.79
1506 1536 1.226323 CTACGCGTCCTTCGGTCTG 60.226 63.158 18.63 0.00 40.26 3.51
1543 1573 0.726827 GCTGTTCGATGAAATGCCGA 59.273 50.000 0.00 0.00 0.00 5.54
1545 1575 1.731709 CTGTTCGATGAAATGCCGACA 59.268 47.619 0.00 0.00 31.60 4.35
1560 1590 0.179119 CGACAAGGGACACCGTATCC 60.179 60.000 0.00 0.00 43.47 2.59
1588 1618 2.036475 ACTCTGATCGGGTCATATGTGC 59.964 50.000 0.62 0.00 35.97 4.57
1691 1721 4.759096 GTTGTCGGGCGCATGTGC 62.759 66.667 23.05 23.05 37.78 4.57
1789 1819 1.667830 CAACAGGTGGCGATCGTGT 60.668 57.895 17.81 9.74 35.83 4.49
1878 1908 1.966451 GGCAAGGGACGTGAGGTTG 60.966 63.158 0.00 0.00 41.23 3.77
2009 2039 0.313672 GGATTCGTGCAGTTTGGCAA 59.686 50.000 0.00 0.00 46.93 4.52
2112 2142 2.888594 TCAGCTTGTATTCAGTACCGC 58.111 47.619 0.00 0.00 32.03 5.68
2113 2143 1.588404 CAGCTTGTATTCAGTACCGCG 59.412 52.381 0.00 0.00 35.27 6.46
2123 2153 4.261495 GTACCGCGCGTTCGATGC 62.261 66.667 29.95 8.25 38.10 3.91
2168 2198 4.514066 TGTGATGCATAATGAGCTGATCAC 59.486 41.667 0.00 0.00 41.91 3.06
2394 2424 6.156775 TCCATCCTGATAAGATCACTTTCACA 59.843 38.462 0.00 0.00 37.53 3.58
2418 2448 2.014064 TTTTGTGTGCATGCAGCCGT 62.014 50.000 23.41 0.00 44.83 5.68
2448 2478 1.541588 GTGGCACAAGGGTTTGAGATC 59.458 52.381 13.86 0.00 44.16 2.75
2520 2550 1.202734 GCTTGCATGGCTGATCTCCTA 60.203 52.381 1.34 0.00 0.00 2.94
2644 2674 4.067896 CCGTGGAAATATGAGGATTGGAG 58.932 47.826 0.00 0.00 0.00 3.86
2790 2820 5.377478 GTTATAGGCCTCAAACCTAAGCAT 58.623 41.667 9.68 0.00 42.93 3.79
2885 2915 3.330701 AGATGGTTTCTGTAGCCTTTGGA 59.669 43.478 0.00 0.00 31.79 3.53
2996 3026 4.825422 TCTGTGAAGATTTACAGCAGAGG 58.175 43.478 11.50 0.00 43.02 3.69
3008 3038 8.668510 ATTTACAGCAGAGGTATATGTTTGAG 57.331 34.615 0.00 0.00 0.00 3.02
3070 3100 2.165167 CTTGCATGGACAACTGGTGAT 58.835 47.619 0.00 0.00 0.00 3.06
3218 3248 4.082125 AGATCCAAAACAATCCACCTGTC 58.918 43.478 0.00 0.00 0.00 3.51
3227 3257 6.723298 AACAATCCACCTGTCAAACATAAA 57.277 33.333 0.00 0.00 0.00 1.40
3260 3290 9.260002 GATCAAAACCAACAACTCACAATTTAT 57.740 29.630 0.00 0.00 0.00 1.40
3636 3675 2.627699 GGTGATGACCAACCACAACAAT 59.372 45.455 0.00 0.00 42.59 2.71
3648 3687 6.462347 CCAACCACAACAATAGCTACCTTTTT 60.462 38.462 0.00 0.00 0.00 1.94
3701 3753 5.928976 TCACACTCTTTCTGGAGAATCAAA 58.071 37.500 0.00 0.00 36.25 2.69
3758 3810 5.798125 TCATGGCAAAGGTATGTTTTTCA 57.202 34.783 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 3.374367 CACTGCTCATGAGGAATGTTGAG 59.626 47.826 23.89 10.01 38.86 3.02
82 83 2.113774 CAGGTTGAGGTGCTGCCA 59.886 61.111 0.00 0.00 40.61 4.92
85 86 0.604780 CTGACCAGGTTGAGGTGCTG 60.605 60.000 0.00 0.00 40.09 4.41
124 125 1.331756 CGTTCAGGTATGGCATTGCTC 59.668 52.381 4.78 0.00 0.00 4.26
143 144 9.722056 CTCAAGGGAAATAATCTTTATTTGTCG 57.278 33.333 9.34 0.00 0.00 4.35
150 151 9.892130 GTTCTCTCTCAAGGGAAATAATCTTTA 57.108 33.333 0.00 0.00 43.64 1.85
281 283 4.105697 AGGAAAGGTAGGTTTTGTCCATCA 59.894 41.667 0.00 0.00 0.00 3.07
330 332 5.528690 GCTGGTGCTAATGTCAATATCTGAA 59.471 40.000 0.00 0.00 34.04 3.02
337 339 4.463539 TGATTTGCTGGTGCTAATGTCAAT 59.536 37.500 2.85 0.00 42.76 2.57
338 340 3.825585 TGATTTGCTGGTGCTAATGTCAA 59.174 39.130 2.85 0.00 42.76 3.18
351 353 5.387752 GCGTTTTCTAAGCTTTGATTTGCTG 60.388 40.000 11.41 2.15 39.71 4.41
405 410 0.106015 ATTCCTGGTAATGGCCTGCC 60.106 55.000 3.32 0.00 0.00 4.85
439 445 3.055080 GACGGTATGGGACGCGTCA 62.055 63.158 37.26 21.69 44.44 4.35
478 484 0.904865 TTCGATGTCTGCAGGACCCT 60.905 55.000 15.13 1.52 43.89 4.34
493 499 4.450757 TCGCATGAAGTCTGAATTTTTCGA 59.549 37.500 0.00 0.00 0.00 3.71
518 541 0.390340 TAGCTTCTTCTGTGCTGCCG 60.390 55.000 0.00 0.00 37.62 5.69
540 563 0.745486 TCCCTGATGCGATGTGCTTG 60.745 55.000 0.00 0.00 46.63 4.01
556 579 1.142748 CTCAGGTCGTCATGCTCCC 59.857 63.158 0.00 0.00 0.00 4.30
642 665 1.372997 ACGCACGGTGACATCTGAC 60.373 57.895 13.29 0.00 0.00 3.51
657 680 1.202371 TCATGTATTCCGGTCTCACGC 60.202 52.381 0.00 0.00 0.00 5.34
659 682 5.180492 TGTTTTTCATGTATTCCGGTCTCAC 59.820 40.000 0.00 0.00 0.00 3.51
681 705 0.178953 ATTTTGGGCTGCTCCACTGT 60.179 50.000 9.02 0.00 36.38 3.55
714 738 1.156645 CCGTTCCTGCATCTAGCTGC 61.157 60.000 11.65 11.65 45.94 5.25
748 772 1.001631 TCCCCTCCTCTCGCAATCA 59.998 57.895 0.00 0.00 0.00 2.57
749 773 1.045911 ACTCCCCTCCTCTCGCAATC 61.046 60.000 0.00 0.00 0.00 2.67
750 774 1.002274 ACTCCCCTCCTCTCGCAAT 59.998 57.895 0.00 0.00 0.00 3.56
892 919 2.655364 CCATCGCTAGACGCCACG 60.655 66.667 0.00 0.00 43.23 4.94
905 932 2.005960 CTCCGACAGTCCGACCCATC 62.006 65.000 0.00 0.00 0.00 3.51
906 933 2.036731 TCCGACAGTCCGACCCAT 59.963 61.111 0.00 0.00 0.00 4.00
907 934 2.675423 CTCCGACAGTCCGACCCA 60.675 66.667 0.00 0.00 0.00 4.51
909 936 4.131088 GCCTCCGACAGTCCGACC 62.131 72.222 0.00 0.00 0.00 4.79
910 937 4.131088 GGCCTCCGACAGTCCGAC 62.131 72.222 0.00 0.00 0.00 4.79
913 940 1.760875 TATGGGCCTCCGACAGTCC 60.761 63.158 4.53 0.00 35.24 3.85
915 942 0.617820 AAGTATGGGCCTCCGACAGT 60.618 55.000 4.53 0.00 35.24 3.55
916 943 0.105039 GAAGTATGGGCCTCCGACAG 59.895 60.000 4.53 0.00 35.24 3.51
919 946 0.325296 ACAGAAGTATGGGCCTCCGA 60.325 55.000 4.53 0.00 35.24 4.55
1520 1550 1.470098 GCATTTCATCGAACAGCCTGT 59.530 47.619 0.00 0.00 0.00 4.00
1543 1573 1.553704 GAAGGATACGGTGTCCCTTGT 59.446 52.381 18.93 3.87 46.39 3.16
1545 1575 1.946984 TGAAGGATACGGTGTCCCTT 58.053 50.000 18.93 13.67 46.39 3.95
1560 1590 2.029020 TGACCCGATCAGAGTGTTGAAG 60.029 50.000 0.00 0.00 31.91 3.02
1588 1618 1.803922 CGCCAACACAGCATGCATG 60.804 57.895 22.70 22.70 42.53 4.06
1625 1655 1.580059 TCCTCTGTCCACCATAACCC 58.420 55.000 0.00 0.00 0.00 4.11
1691 1721 1.407437 CCCTCAAATCCTTCAGTCCCG 60.407 57.143 0.00 0.00 0.00 5.14
1789 1819 2.290008 ACTTCGCATACATGTCCACCAA 60.290 45.455 0.00 0.00 0.00 3.67
1920 1950 3.636764 TGAATAACGCTCTAGCCATCTCA 59.363 43.478 0.00 0.00 37.91 3.27
2029 2059 3.007831 GCCTCCTCCATCTCCTCAAATAG 59.992 52.174 0.00 0.00 0.00 1.73
2113 2143 2.574212 CTTTGCCGCATCGAACGC 60.574 61.111 5.74 3.05 0.00 4.84
2123 2153 1.332997 GATGATGAAGCCTCTTTGCCG 59.667 52.381 0.00 0.00 0.00 5.69
2394 2424 0.460722 TGCATGCACACAAAACTGCT 59.539 45.000 18.46 0.00 34.29 4.24
2418 2448 0.537143 CTTGTGCCACTAAGCCACCA 60.537 55.000 0.00 0.00 0.00 4.17
2431 2461 5.705609 TTAAAGATCTCAAACCCTTGTGC 57.294 39.130 0.00 0.00 33.94 4.57
2448 2478 3.443681 ACTTGCCCACCATCGAATTAAAG 59.556 43.478 0.00 0.00 0.00 1.85
2520 2550 2.976490 AAGCCGCCCATCTCTTGCT 61.976 57.895 0.00 0.00 0.00 3.91
2532 2562 1.348594 GTAAGCATCGTCAAGCCGC 59.651 57.895 0.00 0.00 0.00 6.53
2644 2674 2.849294 AGTTCCTCCTCTGCAAGTTC 57.151 50.000 0.00 0.00 33.76 3.01
2790 2820 4.247267 ACACTGCTACTTTGTACGCTTA 57.753 40.909 0.00 0.00 0.00 3.09
2885 2915 9.654919 TTAGGGCCTTAGAATAAATTTAGCAAT 57.345 29.630 13.45 0.00 0.00 3.56
2996 3026 6.260936 CCTGGTTCCATCACTCAAACATATAC 59.739 42.308 0.00 0.00 0.00 1.47
3008 3038 1.685224 TGGAGCCTGGTTCCATCAC 59.315 57.895 26.25 2.67 37.99 3.06
3104 3134 4.177165 TGCCTGCAATTTGTGAACATAG 57.823 40.909 0.00 0.00 0.00 2.23
3218 3248 9.258826 TGGTTTTGATCAACTCATTTATGTTTG 57.741 29.630 7.89 0.00 32.72 2.93
3227 3257 6.469782 AGTTGTTGGTTTTGATCAACTCAT 57.530 33.333 7.89 0.00 42.98 2.90
3260 3290 1.072806 AGGTCAGCTGTCAATCTGCAA 59.927 47.619 14.67 0.00 42.26 4.08
3343 3373 7.047891 TGAGCTTCTCTCAGTGTTTTCTTTTA 58.952 34.615 0.00 0.00 46.34 1.52
3346 3376 5.028549 TGAGCTTCTCTCAGTGTTTTCTT 57.971 39.130 0.00 0.00 46.34 2.52
3347 3377 4.679373 TGAGCTTCTCTCAGTGTTTTCT 57.321 40.909 0.00 0.00 46.34 2.52
3636 3675 5.130350 AGAGCACAAACAAAAAGGTAGCTA 58.870 37.500 0.00 0.00 0.00 3.32
3648 3687 8.011844 AGTATGATATACAGAGAGCACAAACA 57.988 34.615 2.24 0.00 0.00 2.83
3701 3753 3.704566 TGTCTTAAGCCTGGTCGTGATAT 59.295 43.478 0.00 0.00 0.00 1.63
3758 3810 8.803235 TGGATCTGTATATACGTTTAGATGCTT 58.197 33.333 22.05 3.99 35.09 3.91


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

AutoCloner maintained by Alex Coulton.