Multiple sequence alignment - TraesCS5A01G071300

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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 TraesCS5A01G071300 chr5A 100.000 3254 0 0 1 3254 80156961 80153708 0.000000e+00 6010
1 TraesCS5A01G071300 chr5A 82.716 162 28 0 1169 1330 523879581 523879420 9.410000e-31 145
2 TraesCS5A01G071300 chr5D 93.412 3294 121 28 2 3254 87174917 87171679 0.000000e+00 4793
3 TraesCS5A01G071300 chr5D 82.692 156 27 0 1175 1330 412147729 412147574 4.380000e-29 139
4 TraesCS5A01G071300 chr5B 91.331 3322 147 49 1 3254 93213656 93210408 0.000000e+00 4409
5 TraesCS5A01G071300 chr5B 82.099 162 29 0 1169 1330 495473502 495473341 4.380000e-29 139
6 TraesCS5A01G071300 chr4A 93.596 203 12 1 1137 1339 545106829 545106628 5.280000e-78 302
7 TraesCS5A01G071300 chr4D 94.595 185 10 0 1155 1339 51608637 51608821 1.480000e-73 287
8 TraesCS5A01G071300 chr6B 87.440 207 22 4 1162 1366 699018604 699018400 5.430000e-58 235
9 TraesCS5A01G071300 chr6D 86.957 207 23 4 1162 1366 459735469 459735265 2.530000e-56 230


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 TraesCS5A01G071300 chr5A 80153708 80156961 3253 True 6010 6010 100.000 1 3254 1 chr5A.!!$R1 3253
1 TraesCS5A01G071300 chr5D 87171679 87174917 3238 True 4793 4793 93.412 2 3254 1 chr5D.!!$R1 3252
2 TraesCS5A01G071300 chr5B 93210408 93213656 3248 True 4409 4409 91.331 1 3254 1 chr5B.!!$R1 3253

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
228 237 0.470268 TTTTAGGCTTTTGGGCGGGT 60.470 50.000 0.00 0.0 45.89 5.28 F
253 262 1.168714 AATTGGAGCTCAAAGCCGTC 58.831 50.000 17.19 0.0 43.77 4.79 F
2064 2126 1.079750 GTCCTCAGAACCAGCCGTC 60.080 63.158 0.00 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 1821 0.757188 ATCTCGAACGGGGAGCAGAT 60.757 55.00 0.0 0.0 0.00 2.90 R
2081 2143 0.905337 AGCTTTACCCTCCTCTGCGT 60.905 55.00 0.0 0.0 0.00 5.24 R
2980 3055 9.620660 CTAATAGCCGAAAACATTAACAAGTTT 57.379 29.63 0.0 0.0 39.46 2.66 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
21 26 1.955458 TTTTGACCCTGCCACCCCTT 61.955 55.000 0.00 0.00 0.00 3.95
37 42 2.486907 CCCCTTCCTCGTCGTACTAGAT 60.487 54.545 0.00 0.00 0.00 1.98
57 66 8.713036 ACTAGATCTGAATCATTTTCTTAGGCT 58.287 33.333 5.18 0.00 34.07 4.58
90 99 3.242011 ACCTGAAAATGCCAACCAATCT 58.758 40.909 0.00 0.00 0.00 2.40
106 115 2.100128 ATCTCATCTGACCAGAGGGG 57.900 55.000 11.14 8.36 40.82 4.79
228 237 0.470268 TTTTAGGCTTTTGGGCGGGT 60.470 50.000 0.00 0.00 45.89 5.28
251 260 2.730550 AAAATTGGAGCTCAAAGCCG 57.269 45.000 17.19 0.00 43.77 5.52
253 262 1.168714 AATTGGAGCTCAAAGCCGTC 58.831 50.000 17.19 0.00 43.77 4.79
389 398 6.866010 TGCATATACAGATCATTTCACACC 57.134 37.500 0.00 0.00 0.00 4.16
396 405 8.862325 ATACAGATCATTTCACACCAAAGTTA 57.138 30.769 0.00 0.00 0.00 2.24
401 410 4.892934 TCATTTCACACCAAAGTTAAGCCT 59.107 37.500 0.00 0.00 0.00 4.58
451 460 6.944862 ACTCAAAATTTCTTGGCTCTCATACT 59.055 34.615 0.00 0.00 0.00 2.12
474 483 8.037382 ACTATATTGAGTATGCATGCATCAAC 57.963 34.615 35.35 27.43 37.82 3.18
521 530 9.890629 AGCAAGATATACACTCATACTTTGAAA 57.109 29.630 0.00 0.00 32.78 2.69
561 570 4.273148 ACCTAGCTAGTTTCACACCAAG 57.727 45.455 19.31 2.20 0.00 3.61
631 640 1.553248 CGACCACACCCTCATCCTTAA 59.447 52.381 0.00 0.00 0.00 1.85
686 695 8.618677 CAGCATGAACACATGAATTAACTAGAT 58.381 33.333 13.30 0.00 42.56 1.98
740 749 2.472816 CCATTTGTTGAGCACCACAAC 58.527 47.619 0.22 0.00 45.07 3.32
745 754 5.392767 TTTGTTGAGCACCACAACTTAAA 57.607 34.783 0.00 0.00 45.08 1.52
783 792 4.901197 TTTGTACTCCCAATCAGTGCTA 57.099 40.909 0.00 0.00 0.00 3.49
784 793 3.887621 TGTACTCCCAATCAGTGCTAC 57.112 47.619 0.00 0.00 0.00 3.58
785 794 3.441101 TGTACTCCCAATCAGTGCTACT 58.559 45.455 0.00 0.00 0.00 2.57
786 795 4.606210 TGTACTCCCAATCAGTGCTACTA 58.394 43.478 0.00 0.00 0.00 1.82
787 796 5.020795 TGTACTCCCAATCAGTGCTACTAA 58.979 41.667 0.00 0.00 0.00 2.24
788 797 4.744795 ACTCCCAATCAGTGCTACTAAG 57.255 45.455 0.00 0.00 0.00 2.18
789 798 4.097418 ACTCCCAATCAGTGCTACTAAGT 58.903 43.478 0.00 0.00 0.00 2.24
812 821 6.882678 AGTACTAACCCATCACCATTAACAAC 59.117 38.462 0.00 0.00 0.00 3.32
825 834 7.383572 TCACCATTAACAACATAAATGCAACAC 59.616 33.333 0.00 0.00 30.81 3.32
844 853 6.985013 CAACACATTGCATGCAAATACTTAG 58.015 36.000 34.84 21.39 39.55 2.18
922 945 2.353109 GCAACAAAAGGCATCTTCCTCC 60.353 50.000 0.00 0.00 34.82 4.30
932 979 1.220236 CATCTTCCTCCTCTCCTCCCT 59.780 57.143 0.00 0.00 0.00 4.20
942 989 6.393440 TCCTCCTCTCCTCCCTTATATATACC 59.607 46.154 0.00 0.00 0.00 2.73
946 993 6.357015 TCTCCTCCCTTATATATACCCCTG 57.643 45.833 0.00 0.00 0.00 4.45
1123 1176 4.728102 CGTCCACGGTTGCGGCTA 62.728 66.667 0.00 0.00 35.37 3.93
1503 1559 2.125391 CAAGAGGCTGCGCTGCTA 60.125 61.111 33.50 1.62 0.00 3.49
1561 1617 1.255342 CGTCGTGCCAAGAATCATACG 59.745 52.381 0.00 0.00 0.00 3.06
1658 1717 2.112691 TGGAGGAGGAAGAAGAAGAGGT 59.887 50.000 0.00 0.00 0.00 3.85
1659 1718 2.499693 GGAGGAGGAAGAAGAAGAGGTG 59.500 54.545 0.00 0.00 0.00 4.00
1660 1719 2.499693 GAGGAGGAAGAAGAAGAGGTGG 59.500 54.545 0.00 0.00 0.00 4.61
1661 1720 2.112691 AGGAGGAAGAAGAAGAGGTGGA 59.887 50.000 0.00 0.00 0.00 4.02
1662 1721 2.499693 GGAGGAAGAAGAAGAGGTGGAG 59.500 54.545 0.00 0.00 0.00 3.86
1663 1722 2.499693 GAGGAAGAAGAAGAGGTGGAGG 59.500 54.545 0.00 0.00 0.00 4.30
1664 1723 2.112691 AGGAAGAAGAAGAGGTGGAGGA 59.887 50.000 0.00 0.00 0.00 3.71
1665 1724 2.907042 GGAAGAAGAAGAGGTGGAGGAA 59.093 50.000 0.00 0.00 0.00 3.36
1666 1725 3.055458 GGAAGAAGAAGAGGTGGAGGAAG 60.055 52.174 0.00 0.00 0.00 3.46
1667 1726 3.551635 AGAAGAAGAGGTGGAGGAAGA 57.448 47.619 0.00 0.00 0.00 2.87
1668 1727 3.863086 AGAAGAAGAGGTGGAGGAAGAA 58.137 45.455 0.00 0.00 0.00 2.52
1669 1728 3.837731 AGAAGAAGAGGTGGAGGAAGAAG 59.162 47.826 0.00 0.00 0.00 2.85
1670 1729 3.551635 AGAAGAGGTGGAGGAAGAAGA 57.448 47.619 0.00 0.00 0.00 2.87
1671 1730 3.440127 AGAAGAGGTGGAGGAAGAAGAG 58.560 50.000 0.00 0.00 0.00 2.85
1672 1731 2.246091 AGAGGTGGAGGAAGAAGAGG 57.754 55.000 0.00 0.00 0.00 3.69
1827 1886 3.217231 CCGGTGGAGGCTAACGAT 58.783 61.111 0.00 0.00 0.00 3.73
2018 2077 3.130160 CCGCAAGAAGCAGAGGGC 61.130 66.667 0.00 0.00 46.13 5.19
2046 2105 2.895865 CAGCCAGCATCGGAGCAG 60.896 66.667 3.00 0.00 36.85 4.24
2052 2111 1.683707 AGCATCGGAGCAGTCCTCA 60.684 57.895 3.00 0.00 42.62 3.86
2061 2123 1.376553 GCAGTCCTCAGAACCAGCC 60.377 63.158 0.00 0.00 0.00 4.85
2063 2125 1.534235 AGTCCTCAGAACCAGCCGT 60.534 57.895 0.00 0.00 0.00 5.68
2064 2126 1.079750 GTCCTCAGAACCAGCCGTC 60.080 63.158 0.00 0.00 0.00 4.79
2081 2143 0.808847 GTCGCTGCTGCTGATCATGA 60.809 55.000 14.03 0.00 36.97 3.07
2083 2145 1.642215 GCTGCTGCTGATCATGACG 59.358 57.895 10.92 0.00 36.03 4.35
2085 2147 1.078988 TGCTGCTGATCATGACGCA 60.079 52.632 13.49 13.49 0.00 5.24
2102 2167 1.740718 CGCAGAGGAGGGTAAAGCTTC 60.741 57.143 0.00 0.00 0.00 3.86
2104 2169 1.909302 CAGAGGAGGGTAAAGCTTCCA 59.091 52.381 12.20 0.00 32.02 3.53
2134 2199 2.981909 GTTCAGGCAGCAGCAGCA 60.982 61.111 12.41 0.00 45.49 4.41
2191 2259 2.202570 CGGAGGCTAACGTCACCG 60.203 66.667 0.00 0.00 40.83 4.94
2271 2339 2.435372 AGGCTGACCAGTTTTGTTGA 57.565 45.000 0.00 0.00 39.06 3.18
2272 2340 2.024414 AGGCTGACCAGTTTTGTTGAC 58.976 47.619 0.00 0.00 39.06 3.18
2310 2378 2.099098 ACTTGCAGTTAGGTTGTGTTGC 59.901 45.455 0.00 0.00 0.00 4.17
2363 2431 1.889545 GGCTCATATGAGAAGCCACC 58.110 55.000 32.38 19.84 44.74 4.61
2364 2432 1.544314 GGCTCATATGAGAAGCCACCC 60.544 57.143 32.38 19.20 44.74 4.61
2472 2540 5.989777 GGTAGTGCTTCAAAGTAGAACTCAA 59.010 40.000 0.00 0.00 0.00 3.02
2624 2698 2.095415 GGCACGAGTACCAATTTTCCAC 60.095 50.000 0.00 0.00 0.00 4.02
2649 2723 2.335681 TTCCCATGGACACCACTCTA 57.664 50.000 15.22 0.00 35.80 2.43
2720 2794 6.145535 GCTTACAAGAATCTTTCCACACTTG 58.854 40.000 0.00 0.00 39.98 3.16
2781 2856 5.279156 GCATGGAGTTGAATTCCTCAAGTTT 60.279 40.000 8.25 0.00 45.90 2.66
2800 2875 7.841729 TCAAGTTTAGATATTGGGGCCAAAATA 59.158 33.333 4.39 9.61 39.55 1.40
2801 2876 8.650490 CAAGTTTAGATATTGGGGCCAAAATAT 58.350 33.333 18.51 18.51 39.55 1.28
2802 2877 8.193953 AGTTTAGATATTGGGGCCAAAATATG 57.806 34.615 21.74 0.00 39.55 1.78
2980 3055 4.229639 ACCTCAGAATCTCCATCATGCTA 58.770 43.478 0.00 0.00 0.00 3.49
3102 3178 0.465460 AACCTTTGAGCACGCTTCCA 60.465 50.000 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 26 4.397481 TTCAGATCTAGTACGACGAGGA 57.603 45.455 0.00 0.00 0.00 3.71
37 42 6.715280 ACTCAGCCTAAGAAAATGATTCAGA 58.285 36.000 0.00 0.00 0.00 3.27
57 66 4.431809 CATTTTCAGGTTGTTGCAACTCA 58.568 39.130 28.61 13.88 0.00 3.41
90 99 2.060383 CGCCCCTCTGGTCAGATGA 61.060 63.158 0.75 0.00 36.76 2.92
130 139 8.836268 ACTAAACAAATCATTTCGTAGTACCA 57.164 30.769 0.00 0.00 0.00 3.25
202 211 4.754618 CGCCCAAAAGCCTAAAATTCTTTT 59.245 37.500 0.00 0.00 39.71 2.27
203 212 4.314961 CGCCCAAAAGCCTAAAATTCTTT 58.685 39.130 0.00 0.00 0.00 2.52
228 237 4.987912 CGGCTTTGAGCTCCAATTTTTAAA 59.012 37.500 12.15 1.33 41.99 1.52
253 262 2.819595 CCCGGCCGTCAAGTCATG 60.820 66.667 26.12 4.67 0.00 3.07
360 369 9.661187 GTGAAATGATCTGTATATGCAAGAAAG 57.339 33.333 0.00 0.00 0.00 2.62
389 398 5.649395 TGATTCCTCATCAGGCTTAACTTTG 59.351 40.000 0.00 0.00 40.12 2.77
396 405 4.525024 CTCTTTGATTCCTCATCAGGCTT 58.475 43.478 0.00 0.00 43.15 4.35
401 410 5.249163 TCAAGACCTCTTTGATTCCTCATCA 59.751 40.000 0.00 0.00 40.43 3.07
451 460 7.444792 TGTGTTGATGCATGCATACTCAATATA 59.555 33.333 32.27 23.80 36.70 0.86
463 472 1.171308 AGGAGTGTGTTGATGCATGC 58.829 50.000 11.82 11.82 0.00 4.06
470 479 4.124238 CCTTTTTCGTAGGAGTGTGTTGA 58.876 43.478 0.00 0.00 34.56 3.18
474 483 1.804748 GGCCTTTTTCGTAGGAGTGTG 59.195 52.381 0.00 0.00 34.56 3.82
521 530 3.272551 AGGTACACCTAGTCCTCTTGGAT 59.727 47.826 0.00 0.00 46.48 3.41
631 640 7.573968 AAGTTGTCTTTTGAATCTGCTTAGT 57.426 32.000 0.00 0.00 0.00 2.24
686 695 9.067963 AGGATATCTAGTGAGAGAGATTGGATA 57.932 37.037 2.05 0.00 34.35 2.59
740 749 9.021863 ACAAAAATTGCATTGCATTTGTTTAAG 57.978 25.926 25.27 14.89 42.61 1.85
745 754 7.261829 AGTACAAAAATTGCATTGCATTTGT 57.738 28.000 29.79 29.79 45.16 2.83
783 792 6.886178 AATGGTGATGGGTTAGTACTTAGT 57.114 37.500 0.00 0.00 0.00 2.24
784 793 8.262227 TGTTAATGGTGATGGGTTAGTACTTAG 58.738 37.037 0.00 0.00 0.00 2.18
785 794 8.148437 TGTTAATGGTGATGGGTTAGTACTTA 57.852 34.615 0.00 0.00 0.00 2.24
786 795 7.023171 TGTTAATGGTGATGGGTTAGTACTT 57.977 36.000 0.00 0.00 0.00 2.24
787 796 6.630203 TGTTAATGGTGATGGGTTAGTACT 57.370 37.500 0.00 0.00 0.00 2.73
788 797 6.655848 TGTTGTTAATGGTGATGGGTTAGTAC 59.344 38.462 0.00 0.00 0.00 2.73
789 798 6.780901 TGTTGTTAATGGTGATGGGTTAGTA 58.219 36.000 0.00 0.00 0.00 1.82
894 917 2.758736 TGCCTTTTGTTGCTTGTGTT 57.241 40.000 0.00 0.00 0.00 3.32
922 945 6.162420 TCAGGGGTATATATAAGGGAGGAGAG 59.838 46.154 0.00 0.00 0.00 3.20
932 979 8.578376 AGATGATCAGGTCAGGGGTATATATAA 58.422 37.037 0.09 0.00 40.92 0.98
942 989 4.080695 TGAAAAGAGATGATCAGGTCAGGG 60.081 45.833 0.09 0.00 40.92 4.45
946 993 3.876320 GGCTGAAAAGAGATGATCAGGTC 59.124 47.826 0.09 0.00 39.69 3.85
1152 1205 2.742372 CCCACGAACCGCTTCCTG 60.742 66.667 0.00 0.00 0.00 3.86
1561 1617 2.813908 GTCGTCACGGCCATGGAC 60.814 66.667 18.40 13.35 0.00 4.02
1658 1717 1.553417 CCTCCACCTCTTCTTCCTCCA 60.553 57.143 0.00 0.00 0.00 3.86
1659 1718 1.199615 CCTCCACCTCTTCTTCCTCC 58.800 60.000 0.00 0.00 0.00 4.30
1660 1719 2.239681 TCCTCCACCTCTTCTTCCTC 57.760 55.000 0.00 0.00 0.00 3.71
1661 1720 2.112691 TCTTCCTCCACCTCTTCTTCCT 59.887 50.000 0.00 0.00 0.00 3.36
1662 1721 2.541466 TCTTCCTCCACCTCTTCTTCC 58.459 52.381 0.00 0.00 0.00 3.46
1663 1722 3.835395 TCTTCTTCCTCCACCTCTTCTTC 59.165 47.826 0.00 0.00 0.00 2.87
1664 1723 3.863086 TCTTCTTCCTCCACCTCTTCTT 58.137 45.455 0.00 0.00 0.00 2.52
1665 1724 3.551635 TCTTCTTCCTCCACCTCTTCT 57.448 47.619 0.00 0.00 0.00 2.85
1666 1725 3.835395 TCTTCTTCTTCCTCCACCTCTTC 59.165 47.826 0.00 0.00 0.00 2.87
1667 1726 3.837731 CTCTTCTTCTTCCTCCACCTCTT 59.162 47.826 0.00 0.00 0.00 2.85
1668 1727 3.440127 CTCTTCTTCTTCCTCCACCTCT 58.560 50.000 0.00 0.00 0.00 3.69
1669 1728 2.499693 CCTCTTCTTCTTCCTCCACCTC 59.500 54.545 0.00 0.00 0.00 3.85
1670 1729 2.158081 ACCTCTTCTTCTTCCTCCACCT 60.158 50.000 0.00 0.00 0.00 4.00
1671 1730 2.027653 CACCTCTTCTTCTTCCTCCACC 60.028 54.545 0.00 0.00 0.00 4.61
1672 1731 2.027653 CCACCTCTTCTTCTTCCTCCAC 60.028 54.545 0.00 0.00 0.00 4.02
1762 1821 0.757188 ATCTCGAACGGGGAGCAGAT 60.757 55.000 0.00 0.00 0.00 2.90
1851 1910 2.729479 CCTCATCGCCTCCTGCACT 61.729 63.158 0.00 0.00 41.33 4.40
2046 2105 1.079750 GACGGCTGGTTCTGAGGAC 60.080 63.158 0.00 0.00 0.00 3.85
2081 2143 0.905337 AGCTTTACCCTCCTCTGCGT 60.905 55.000 0.00 0.00 0.00 5.24
2083 2145 1.407575 GGAAGCTTTACCCTCCTCTGC 60.408 57.143 0.00 0.00 0.00 4.26
2085 2147 2.344093 TGGAAGCTTTACCCTCCTCT 57.656 50.000 0.00 0.00 0.00 3.69
2102 2167 2.082231 CTGAACACTCCTCTTGCATGG 58.918 52.381 0.00 0.00 0.00 3.66
2104 2169 1.612726 GCCTGAACACTCCTCTTGCAT 60.613 52.381 0.00 0.00 0.00 3.96
2199 2267 2.740055 CTCCACAGCAGCACGTCC 60.740 66.667 0.00 0.00 0.00 4.79
2310 2378 2.293122 TGGAGCAAAACGAATTCCACAG 59.707 45.455 0.00 0.00 33.21 3.66
2361 2429 2.765969 CAAGTGATGGCCAGGGGT 59.234 61.111 13.05 0.00 0.00 4.95
2362 2430 2.757099 GCAAGTGATGGCCAGGGG 60.757 66.667 13.05 0.00 0.00 4.79
2363 2431 0.034186 TAAGCAAGTGATGGCCAGGG 60.034 55.000 13.05 0.00 0.00 4.45
2364 2432 1.838112 TTAAGCAAGTGATGGCCAGG 58.162 50.000 13.05 0.00 0.00 4.45
2562 2633 1.889530 GACCCCACCCTCTCAACTCG 61.890 65.000 0.00 0.00 0.00 4.18
2624 2698 1.256812 GGTGTCCATGGGAAAACTGG 58.743 55.000 13.02 0.00 31.38 4.00
2649 2723 0.755327 GTTGGTGGCCTTGAGGTTGT 60.755 55.000 3.32 0.00 37.57 3.32
2980 3055 9.620660 CTAATAGCCGAAAACATTAACAAGTTT 57.379 29.630 0.00 0.00 39.46 2.66
3049 3125 9.823098 CAGAAGTTTCATGAAGATTTCACTAAG 57.177 33.333 20.92 8.41 43.48 2.18


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

AutoCloner maintained by Alex Coulton.