Multiple sequence alignment - TraesCS5B01G056200

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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 TraesCS5B01G056200 chr5B 100.000 3806 0 0 1 3806 62149399 62153204 0.000000e+00 7029
1 TraesCS5B01G056200 chr6A 95.009 3807 161 26 1 3796 554926825 554923037 0.000000e+00 5951
2 TraesCS5B01G056200 chr5A 94.878 3807 160 22 1 3796 398469595 398473377 0.000000e+00 5917
3 TraesCS5B01G056200 chr5A 94.978 3624 147 23 181 3794 524687471 524683873 0.000000e+00 5651
4 TraesCS5B01G056200 chr5A 94.762 420 11 6 1 420 33921461 33921053 0.000000e+00 643
5 TraesCS5B01G056200 chr5A 93.194 191 6 2 1 190 524705916 524705732 1.350000e-69 274
6 TraesCS5B01G056200 chr7A 94.791 3801 169 23 1 3796 299375351 299371575 0.000000e+00 5895
7 TraesCS5B01G056200 chr3A 94.563 3807 177 24 1 3796 32217110 32213323 0.000000e+00 5856
8 TraesCS5B01G056200 chrUn 94.119 3503 172 24 309 3796 82551933 82548450 0.000000e+00 5297
9 TraesCS5B01G056200 chr6B 90.964 3807 282 42 3 3796 718741022 718737265 0.000000e+00 5068
10 TraesCS5B01G056200 chr7B 90.993 3808 270 47 3 3796 709380656 709384404 0.000000e+00 5064
11 TraesCS5B01G056200 chr2B 90.673 3806 296 39 3 3793 626132146 626135907 0.000000e+00 5007


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 TraesCS5B01G056200 chr5B 62149399 62153204 3805 False 7029 7029 100.000 1 3806 1 chr5B.!!$F1 3805
1 TraesCS5B01G056200 chr6A 554923037 554926825 3788 True 5951 5951 95.009 1 3796 1 chr6A.!!$R1 3795
2 TraesCS5B01G056200 chr5A 398469595 398473377 3782 False 5917 5917 94.878 1 3796 1 chr5A.!!$F1 3795
3 TraesCS5B01G056200 chr5A 524683873 524687471 3598 True 5651 5651 94.978 181 3794 1 chr5A.!!$R2 3613
4 TraesCS5B01G056200 chr7A 299371575 299375351 3776 True 5895 5895 94.791 1 3796 1 chr7A.!!$R1 3795
5 TraesCS5B01G056200 chr3A 32213323 32217110 3787 True 5856 5856 94.563 1 3796 1 chr3A.!!$R1 3795
6 TraesCS5B01G056200 chrUn 82548450 82551933 3483 True 5297 5297 94.119 309 3796 1 chrUn.!!$R1 3487
7 TraesCS5B01G056200 chr6B 718737265 718741022 3757 True 5068 5068 90.964 3 3796 1 chr6B.!!$R1 3793
8 TraesCS5B01G056200 chr7B 709380656 709384404 3748 False 5064 5064 90.993 3 3796 1 chr7B.!!$F1 3793
9 TraesCS5B01G056200 chr2B 626132146 626135907 3761 False 5007 5007 90.673 3 3793 1 chr2B.!!$F1 3790

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
864 881 0.581053 CAGCGCGGTTTGCAAATTTT 59.419 45.000 16.21 0.0 46.97 1.82 F
1416 1436 1.066605 CAAACTGTCTGCTGCTGCTTT 59.933 47.619 17.00 4.9 40.48 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2776 2837 2.058829 CTTTTTGGAGCACGGCGTGT 62.059 55.0 36.68 24.91 35.75 4.49 R
2997 3061 0.553862 TGTCCTCCTCCTCCTCCTCT 60.554 60.0 0.00 0.00 0.00 3.69 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
55 57 5.946942 TTCTTAGGATGCTGATCAGTTCT 57.053 39.130 23.38 16.47 0.00 3.01
80 82 1.881973 TGTAAAGCGGACTAGACGTGT 59.118 47.619 0.00 0.00 0.00 4.49
186 189 4.395854 TCATGAAATTATGCAGCAGTTCGT 59.604 37.500 0.00 0.81 0.00 3.85
188 191 5.871465 TGAAATTATGCAGCAGTTCGTAA 57.129 34.783 0.00 0.00 0.00 3.18
224 227 8.962679 TGTTTTTAGTCTGTCAATAACAACCTT 58.037 29.630 0.00 0.00 37.45 3.50
459 467 8.593492 ATTTGAATAGTTCTTTGCAAACCTTC 57.407 30.769 8.05 6.73 0.00 3.46
576 592 2.708216 TTCTGAAGGTTGCACACTGA 57.292 45.000 0.00 0.00 0.00 3.41
864 881 0.581053 CAGCGCGGTTTGCAAATTTT 59.419 45.000 16.21 0.00 46.97 1.82
885 902 1.258445 ACGCCTCTCTAACCCCACTG 61.258 60.000 0.00 0.00 0.00 3.66
917 934 2.295349 AGCTAGTTTCGAGGTTGTTCGA 59.705 45.455 0.00 0.00 46.86 3.71
950 967 5.070446 TGAACTTATCAGACACACTTCCAGT 59.930 40.000 0.00 0.00 33.04 4.00
986 1003 1.536418 TGGTGCAGTCCTACCAGCT 60.536 57.895 0.00 0.00 41.80 4.24
1144 1163 6.109156 TCAGACAGGCTTTCAACATAACTA 57.891 37.500 3.13 0.00 0.00 2.24
1312 1332 6.791867 AGTGTTATGGACTTGTGCTAGATA 57.208 37.500 0.00 0.00 0.00 1.98
1366 1386 6.204688 CCTCTTTGTAGCAGAACACATTAACA 59.795 38.462 0.00 0.00 0.00 2.41
1374 1394 6.340522 AGCAGAACACATTAACAAAGCTTTT 58.659 32.000 9.53 0.00 0.00 2.27
1416 1436 1.066605 CAAACTGTCTGCTGCTGCTTT 59.933 47.619 17.00 4.90 40.48 3.51
1422 1442 3.349927 TGTCTGCTGCTGCTTTTATCAT 58.650 40.909 17.00 0.00 40.48 2.45
1447 1471 2.563702 TGGTTAGTGAAAACGACCACC 58.436 47.619 0.00 0.00 35.58 4.61
1462 1486 3.486383 GACCACCTTTTCCATCTGTTCA 58.514 45.455 0.00 0.00 0.00 3.18
1468 1492 5.242393 CACCTTTTCCATCTGTTCATGTTCT 59.758 40.000 0.00 0.00 0.00 3.01
1508 1533 9.846248 ATAGTTTGCTGAAATTCTCATAACAAC 57.154 29.630 0.00 0.00 32.14 3.32
1521 1546 6.119536 TCTCATAACAACAACTGAACTTGGT 58.880 36.000 0.00 0.00 0.00 3.67
1675 1703 3.779444 ACTATCTCTCCTGGTGTGTTCA 58.221 45.455 0.00 0.00 0.00 3.18
1934 1967 3.563808 TGTGTTGCATCACTTGGTAGAAC 59.436 43.478 24.36 0.00 38.90 3.01
2030 2071 5.186409 TGTCTACCCCAGTATCTTGTTGTAC 59.814 44.000 0.00 0.00 0.00 2.90
2065 2106 4.647424 AATGTGTGGTTTCGTTCAACAT 57.353 36.364 0.00 0.00 0.00 2.71
2067 2108 4.804608 TGTGTGGTTTCGTTCAACATAG 57.195 40.909 0.00 0.00 0.00 2.23
2265 2315 7.977293 ACAAAAACTTGTACCACTTACCAATTC 59.023 33.333 0.00 0.00 32.60 2.17
2277 2327 9.143155 ACCACTTACCAATTCTTTTTCTATTGT 57.857 29.630 0.00 0.00 0.00 2.71
2331 2382 6.854496 ACTTTTGTAGTTGCGAGAATACAA 57.146 33.333 7.20 7.20 36.59 2.41
2374 2425 4.598406 TGTTCAGTTGCACATATAAGCG 57.402 40.909 0.00 0.00 0.00 4.68
2401 2452 4.942761 AGTTGCACATGTTCTTTTGGAT 57.057 36.364 0.00 0.00 0.00 3.41
2419 2470 9.533253 CTTTTGGATAGTCAAAGTGTTCATTTT 57.467 29.630 0.00 0.00 37.82 1.82
2491 2543 3.073678 CAGTGCATGTGTAGTTGGCTAA 58.926 45.455 0.00 0.00 0.00 3.09
2575 2631 8.962679 TGGTCAGTTACAGACATTTTACTTTTT 58.037 29.630 9.94 0.00 37.74 1.94
2708 2769 2.035066 GCACCTTCATTGAAGCAGTTGT 59.965 45.455 19.04 9.54 38.24 3.32
2776 2837 0.611618 ATCAATGCAAACTGGGGCGA 60.612 50.000 0.00 0.00 0.00 5.54
2805 2866 4.214119 CGTGCTCCAAAAAGAAAGAGATGA 59.786 41.667 0.00 0.00 0.00 2.92
2851 2912 5.296151 AGAGTTTGTTGAGGATGAGTCAA 57.704 39.130 0.00 0.00 0.00 3.18
2868 2929 9.388506 GATGAGTCAAAAGAAGATGAGGAAATA 57.611 33.333 0.00 0.00 0.00 1.40
2895 2956 2.491298 AGCGATAGATGCTGACGATGAT 59.509 45.455 0.00 0.00 42.14 2.45
2944 3005 3.438668 GGAGGAGGACAAGGATGAGGATA 60.439 52.174 0.00 0.00 0.00 2.59
2997 3061 2.292587 GGAAGAGGAAGAGGAGGAGGAA 60.293 54.545 0.00 0.00 0.00 3.36
3094 3167 3.436243 GAGGAGGAAGAAGAAGGTGAGA 58.564 50.000 0.00 0.00 0.00 3.27
3118 3191 2.450897 AGGGGGACGGGGACAAAA 60.451 61.111 0.00 0.00 0.00 2.44
3160 3233 0.693049 GAGGGGAGAAGACAAAGGCA 59.307 55.000 0.00 0.00 0.00 4.75
3348 3424 3.177884 ACTTCTGCCACCCCTGCA 61.178 61.111 0.00 0.00 37.17 4.41
3404 3480 8.077991 CACACTACAGATGTTGATTGACAAAAT 58.922 33.333 1.43 0.00 38.94 1.82
3466 3542 1.153667 GAAGCAGAGTCTCAGGGCG 60.154 63.158 1.94 0.00 0.00 6.13
3496 3572 1.677576 TGTTCAAGCTCTGCAACTTGG 59.322 47.619 18.50 5.80 42.82 3.61
3539 3615 0.809385 CCTGTGCCAGATTTCAGCAG 59.191 55.000 4.00 0.00 37.15 4.24
3542 3618 0.815734 GTGCCAGATTTCAGCAGCAT 59.184 50.000 0.00 0.00 37.15 3.79
3583 3659 2.590821 ACTTTGCCATTGACAAGAGCT 58.409 42.857 12.06 0.00 0.00 4.09
3658 3734 2.915869 AGGGTCTTGACTGGGTTCATA 58.084 47.619 0.61 0.00 0.00 2.15
3716 3793 1.552792 AGACCTAAGCTCCAGCAAGAC 59.447 52.381 0.48 0.00 45.16 3.01
3757 3834 1.293498 CCTCACGTGGTCCAGAAGG 59.707 63.158 17.00 9.30 0.00 3.46
3765 3842 1.053424 TGGTCCAGAAGGCGTAAAGT 58.947 50.000 0.00 0.00 33.74 2.66
3796 3873 2.574006 AGAAGAATCTGCAGTTGCCA 57.426 45.000 14.67 0.00 41.18 4.92
3797 3874 2.867624 AGAAGAATCTGCAGTTGCCAA 58.132 42.857 14.67 0.00 41.18 4.52
3798 3875 2.555757 AGAAGAATCTGCAGTTGCCAAC 59.444 45.455 14.67 0.00 41.18 3.77
3799 3876 2.283145 AGAATCTGCAGTTGCCAACT 57.717 45.000 14.67 3.74 44.06 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 57 3.645884 GTCTAGTCCGCTTTACAACACA 58.354 45.455 0.00 0.00 0.00 3.72
80 82 0.771127 AGCTCCCTTGCCAAGTGTTA 59.229 50.000 3.37 0.00 0.00 2.41
164 167 4.665212 ACGAACTGCTGCATAATTTCATG 58.335 39.130 1.31 0.00 0.00 3.07
292 296 5.865085 AGATGCCAACTAGTGAACTACAAA 58.135 37.500 0.00 0.00 0.00 2.83
371 377 1.153765 CTGCGGAAGATGCGACAGA 60.154 57.895 8.95 0.00 37.46 3.41
554 570 3.953612 TCAGTGTGCAACCTTCAGAAAAT 59.046 39.130 0.00 0.00 34.36 1.82
559 575 1.600957 CTGTCAGTGTGCAACCTTCAG 59.399 52.381 0.00 0.00 34.36 3.02
576 592 1.486310 TGAGGACAACTGCAAGACTGT 59.514 47.619 0.00 0.00 36.51 3.55
673 689 4.652881 ACTAGCAGTCATCATCTGGATCAA 59.347 41.667 0.00 0.00 32.57 2.57
864 881 1.188863 GTGGGGTTAGAGAGGCGTTA 58.811 55.000 0.00 0.00 0.00 3.18
885 902 2.920490 CGAAACTAGCTCTGACTTCTGC 59.080 50.000 0.00 0.00 0.00 4.26
917 934 4.721776 TGTCTGATAAGTTCAATAGCCCCT 59.278 41.667 0.00 0.00 32.78 4.79
1045 1062 4.788075 TGGGAGATCAAATACCCTCTGAAA 59.212 41.667 0.00 0.00 42.49 2.69
1144 1163 4.725810 AGTGATCTGGGGATGAGAATTTCT 59.274 41.667 0.00 0.00 31.46 2.52
1366 1386 3.960102 TGGTCCATGTTCTGAAAAGCTTT 59.040 39.130 5.69 5.69 0.00 3.51
1374 1394 2.325661 TCTCCTGGTCCATGTTCTGA 57.674 50.000 0.00 0.00 0.00 3.27
1416 1436 9.004717 TCGTTTTCACTAACCATCAAATGATAA 57.995 29.630 0.00 0.00 32.63 1.75
1422 1442 4.882427 TGGTCGTTTTCACTAACCATCAAA 59.118 37.500 0.00 0.00 33.59 2.69
1447 1471 8.139989 AGAAAAGAACATGAACAGATGGAAAAG 58.860 33.333 0.00 0.00 0.00 2.27
1462 1486 7.986085 ACTATAACTGCACAGAAAAGAACAT 57.014 32.000 4.31 0.00 0.00 2.71
1468 1492 6.262049 TCAGCAAACTATAACTGCACAGAAAA 59.738 34.615 4.31 0.00 38.58 2.29
1599 1627 3.401033 TCCCATGCATTCGATCGTATT 57.599 42.857 15.94 0.00 0.00 1.89
1709 1738 4.202357 ACATAGAAGGAAGACACTGTTGCA 60.202 41.667 0.00 0.00 0.00 4.08
1710 1739 4.319177 ACATAGAAGGAAGACACTGTTGC 58.681 43.478 0.00 0.00 0.00 4.17
1844 1877 6.426328 TGGTGTGCCAATTTAAAATGAACATC 59.574 34.615 4.78 9.32 42.83 3.06
1994 2034 6.180472 ACTGGGGTAGACAAAATCAACTATG 58.820 40.000 0.00 0.00 0.00 2.23
2003 2043 5.836024 ACAAGATACTGGGGTAGACAAAA 57.164 39.130 0.00 0.00 0.00 2.44
2030 2071 3.550639 CCACACATTACAACCTGTGCAAG 60.551 47.826 2.77 0.00 45.22 4.01
2265 2315 8.511604 ACATACATCCCAGACAATAGAAAAAG 57.488 34.615 0.00 0.00 0.00 2.27
2277 2327 5.192927 GTCCAATTGAACATACATCCCAGA 58.807 41.667 7.12 0.00 0.00 3.86
2331 2382 9.423061 GAACATACATCAAAGCCAACTAAATTT 57.577 29.630 0.00 0.00 0.00 1.82
2374 2425 5.424121 AAAGAACATGTGCAACTACAGAC 57.576 39.130 6.60 0.00 38.04 3.51
2401 2452 7.397892 TGGTTGAAAATGAACACTTTGACTA 57.602 32.000 0.00 0.00 0.00 2.59
2419 2470 5.599732 CCAAAAGTTGATGACAATGGTTGA 58.400 37.500 0.00 0.00 38.32 3.18
2491 2543 6.418057 TCTGGCCAACTAAAAACATGATTT 57.582 33.333 7.01 0.00 0.00 2.17
2708 2769 2.099263 GGTTCCTCGTCATCGATCTTGA 59.901 50.000 0.00 0.00 45.21 3.02
2776 2837 2.058829 CTTTTTGGAGCACGGCGTGT 62.059 55.000 36.68 24.91 35.75 4.49
2805 2866 7.455008 TCTTCTTCTTCTTGTATAGTTGACCCT 59.545 37.037 0.00 0.00 0.00 4.34
2851 2912 7.708752 CGCTACTTCTATTTCCTCATCTTCTTT 59.291 37.037 0.00 0.00 0.00 2.52
2868 2929 3.058570 CGTCAGCATCTATCGCTACTTCT 60.059 47.826 0.00 0.00 37.72 2.85
2895 2956 2.181975 TCATCTGCATCTGTGTCCTCA 58.818 47.619 0.00 0.00 0.00 3.86
2944 3005 4.914983 TCCTCTGCATCTTCTTCATTGTT 58.085 39.130 0.00 0.00 0.00 2.83
2997 3061 0.553862 TGTCCTCCTCCTCCTCCTCT 60.554 60.000 0.00 0.00 0.00 3.69
3094 3167 2.933834 CCCGTCCCCCTCTTTGGT 60.934 66.667 0.00 0.00 0.00 3.67
3118 3191 2.362120 GCCATCAACTGCTGCCCT 60.362 61.111 0.00 0.00 0.00 5.19
3348 3424 2.561419 ACTCAATGAATTGCTGCTGCTT 59.439 40.909 17.00 3.39 40.48 3.91
3404 3480 4.740334 GCAAATCCTTGTCTTTCCAGCAAA 60.740 41.667 0.00 0.00 34.79 3.68
3466 3542 4.792057 GCAGAGCTTGAACATATCAATGCC 60.792 45.833 0.00 1.16 46.62 4.40
3539 3615 7.871973 AGTTGATCTTCTCACACATATCTATGC 59.128 37.037 0.00 0.00 33.53 3.14
3542 3618 9.591792 CAAAGTTGATCTTCTCACACATATCTA 57.408 33.333 0.00 0.00 35.02 1.98
3583 3659 7.566760 TTTCAGCTTCACTTGATAAGAACAA 57.433 32.000 0.00 0.00 0.00 2.83
3716 3793 3.533720 CCATGGATGCTGCCTTGG 58.466 61.111 5.56 13.27 44.00 3.61
3757 3834 7.793902 TCTTCTTCATTGAAACTACTTTACGC 58.206 34.615 0.01 0.00 0.00 4.42
3765 3842 7.663081 ACTGCAGATTCTTCTTCATTGAAACTA 59.337 33.333 23.35 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.