Multiple sequence alignment - TraesCS7B01G280100

Loading Multiple Alignment...

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 TraesCS7B01G280100 chr7B 100.000 4013 0 0 1 4013 513239133 513243145 0 7411
1 TraesCS7B01G280100 chr7D 94.206 3210 126 31 825 4011 485515266 485518438 0 4843
2 TraesCS7B01G280100 chr7A 90.790 3203 155 63 879 4011 553746426 553749558 0 4152
3 TraesCS7B01G280100 chr5B 95.146 824 36 4 1 822 543948701 543947880 0 1297
4 TraesCS7B01G280100 chr5A 90.012 821 78 4 2 819 169824707 169823888 0 1059
5 TraesCS7B01G280100 chr5A 85.194 824 114 7 1 819 481697320 481698140 0 839
6 TraesCS7B01G280100 chr3A 89.672 823 79 6 1 819 107940194 107939374 0 1044
7 TraesCS7B01G280100 chr6D 88.606 825 92 2 1 823 116948848 116948024 0 1002
8 TraesCS7B01G280100 chr6D 88.672 821 90 3 1 819 316510269 316511088 0 998
9 TraesCS7B01G280100 chr2D 88.672 821 91 2 1 819 78397824 78398644 0 1000
10 TraesCS7B01G280100 chr4D 87.956 822 96 3 1 819 306420612 306419791 0 966
11 TraesCS7B01G280100 chr2B 84.709 824 124 2 1 822 645480889 645480066 0 822


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 TraesCS7B01G280100 chr7B 513239133 513243145 4012 False 7411 7411 100.000 1 4013 1 chr7B.!!$F1 4012
1 TraesCS7B01G280100 chr7D 485515266 485518438 3172 False 4843 4843 94.206 825 4011 1 chr7D.!!$F1 3186
2 TraesCS7B01G280100 chr7A 553746426 553749558 3132 False 4152 4152 90.790 879 4011 1 chr7A.!!$F1 3132
3 TraesCS7B01G280100 chr5B 543947880 543948701 821 True 1297 1297 95.146 1 822 1 chr5B.!!$R1 821
4 TraesCS7B01G280100 chr5A 169823888 169824707 819 True 1059 1059 90.012 2 819 1 chr5A.!!$R1 817
5 TraesCS7B01G280100 chr5A 481697320 481698140 820 False 839 839 85.194 1 819 1 chr5A.!!$F1 818
6 TraesCS7B01G280100 chr3A 107939374 107940194 820 True 1044 1044 89.672 1 819 1 chr3A.!!$R1 818
7 TraesCS7B01G280100 chr6D 116948024 116948848 824 True 1002 1002 88.606 1 823 1 chr6D.!!$R1 822
8 TraesCS7B01G280100 chr6D 316510269 316511088 819 False 998 998 88.672 1 819 1 chr6D.!!$F1 818
9 TraesCS7B01G280100 chr2D 78397824 78398644 820 False 1000 1000 88.672 1 819 1 chr2D.!!$F1 818
10 TraesCS7B01G280100 chr4D 306419791 306420612 821 True 966 966 87.956 1 819 1 chr4D.!!$R1 818
11 TraesCS7B01G280100 chr2B 645480066 645480889 823 True 822 822 84.709 1 822 1 chr2B.!!$R1 821

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
921 929 0.968393 AACACCCGCCTCTCTCTCTC 60.968 60.0 0.00 0.00 0.00 3.20 F
1587 1608 0.109689 CCTAGATCCGATCGGCGAAC 60.110 60.0 29.62 18.19 44.57 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 1948 0.161658 CACAGCGCGTGTAAGTTCTG 59.838 55.0 19.58 6.25 41.03 3.02 R
3051 3149 0.178981 ATCTGTTGCCACTTGCCACT 60.179 50.0 0.00 0.00 40.16 4.00 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
231 233 1.607467 GGCACCCCTCACTTGCAAT 60.607 57.895 0.00 0.00 38.04 3.56
247 249 3.888583 TGCAATATCTTCATGTGGCTCA 58.111 40.909 0.00 0.00 0.00 4.26
268 270 6.311445 GCTCACGATACAACATAGAATATGGG 59.689 42.308 0.00 0.00 0.00 4.00
421 423 4.760047 CCTGCGTAAGGGCTGCGT 62.760 66.667 0.00 0.00 43.15 5.24
546 549 2.105649 TCTGGTGTGTTGGCACTTATGA 59.894 45.455 0.00 0.00 45.44 2.15
722 725 1.896660 GAGTTTGCCGTGGCCTCAA 60.897 57.895 8.69 0.00 41.09 3.02
775 782 7.865706 ACACTCTTGTACATTGTTTTCTCTT 57.134 32.000 0.00 0.00 32.60 2.85
803 810 9.439500 TCTATAAAGTTAAGGTACGCAATTTGT 57.561 29.630 0.00 0.00 0.00 2.83
837 844 4.351131 AAAGAACGAGTCGCTTTTGTTT 57.649 36.364 13.59 7.97 0.00 2.83
895 903 4.413565 TTAAACCGCCGGGCCTCC 62.414 66.667 14.55 0.00 36.48 4.30
921 929 0.968393 AACACCCGCCTCTCTCTCTC 60.968 60.000 0.00 0.00 0.00 3.20
961 970 3.522731 CCCAGCCGTCGGAGAGAG 61.523 72.222 17.49 0.00 36.95 3.20
1587 1608 0.109689 CCTAGATCCGATCGGCGAAC 60.110 60.000 29.62 18.19 44.57 3.95
1598 1619 3.340789 GGCGAACGAACCTTGCTT 58.659 55.556 0.00 0.00 0.00 3.91
1610 1631 1.555075 ACCTTGCTTCTGCCGATCTAA 59.445 47.619 0.00 0.00 38.71 2.10
1617 1638 1.048601 TCTGCCGATCTAACCCATCC 58.951 55.000 0.00 0.00 0.00 3.51
1681 1704 5.487488 ACCTGTCAATGTTACCCTCTCATTA 59.513 40.000 0.00 0.00 31.76 1.90
1682 1705 6.158695 ACCTGTCAATGTTACCCTCTCATTAT 59.841 38.462 0.00 0.00 31.76 1.28
1683 1706 6.708054 CCTGTCAATGTTACCCTCTCATTATC 59.292 42.308 0.00 0.00 31.76 1.75
1684 1707 7.194112 TGTCAATGTTACCCTCTCATTATCA 57.806 36.000 0.00 0.00 31.76 2.15
1685 1708 7.805163 TGTCAATGTTACCCTCTCATTATCAT 58.195 34.615 0.00 0.00 31.76 2.45
1686 1709 8.274322 TGTCAATGTTACCCTCTCATTATCATT 58.726 33.333 0.00 0.00 31.76 2.57
1687 1710 9.778741 GTCAATGTTACCCTCTCATTATCATTA 57.221 33.333 0.00 0.00 31.76 1.90
1707 1730 0.395173 ACCAAACGTGAAGGCAACCT 60.395 50.000 0.00 0.00 33.87 3.50
1784 1807 4.455190 GGAAACTAGACACTAGACGACACT 59.545 45.833 11.94 0.00 0.00 3.55
1812 1837 5.863965 TCTCACAACTTTCACATGACCATA 58.136 37.500 0.00 0.00 0.00 2.74
1827 1852 3.181486 TGACCATATCTTCTCGTGCAGAC 60.181 47.826 0.00 0.00 0.00 3.51
1832 1857 3.667497 ATCTTCTCGTGCAGACTTTGA 57.333 42.857 0.00 0.00 0.00 2.69
1837 1862 4.521130 TCTCGTGCAGACTTTGATTACT 57.479 40.909 0.00 0.00 0.00 2.24
1839 1864 4.923871 TCTCGTGCAGACTTTGATTACTTC 59.076 41.667 0.00 0.00 0.00 3.01
1846 1871 8.386606 GTGCAGACTTTGATTACTTCTTCATAG 58.613 37.037 0.00 0.00 0.00 2.23
1847 1872 8.097038 TGCAGACTTTGATTACTTCTTCATAGT 58.903 33.333 0.00 0.00 37.02 2.12
1848 1873 9.587772 GCAGACTTTGATTACTTCTTCATAGTA 57.412 33.333 0.00 0.00 35.28 1.82
1881 1906 6.930722 AGATGGAATTTGTTTCACAATTGTCC 59.069 34.615 8.48 3.42 38.00 4.02
1889 1933 1.896220 TCACAATTGTCCTCCTGTGC 58.104 50.000 8.48 0.00 39.21 4.57
1894 1938 0.537188 ATTGTCCTCCTGTGCCTACG 59.463 55.000 0.00 0.00 0.00 3.51
1903 1948 3.135994 TCCTGTGCCTACGTTTTTCTTC 58.864 45.455 0.00 0.00 0.00 2.87
1911 1956 6.018507 GTGCCTACGTTTTTCTTCAGAACTTA 60.019 38.462 0.00 0.00 33.13 2.24
1919 1964 1.000607 TCTTCAGAACTTACACGCGCT 60.001 47.619 5.73 0.00 0.00 5.92
1920 1965 1.125021 CTTCAGAACTTACACGCGCTG 59.875 52.381 5.73 6.58 0.00 5.18
1957 2002 5.426833 AGTCTAATCCCAGTTTGAGCACTAT 59.573 40.000 0.00 0.00 0.00 2.12
1960 2005 7.769044 GTCTAATCCCAGTTTGAGCACTATTAA 59.231 37.037 0.00 0.00 0.00 1.40
1961 2006 8.325787 TCTAATCCCAGTTTGAGCACTATTAAA 58.674 33.333 0.00 0.00 0.00 1.52
2085 2151 7.099266 ACAAGTGAATCTTTGTGAATTGTCA 57.901 32.000 3.62 0.00 33.63 3.58
2124 2190 3.610911 AGCAAAAGTAGCTGGTATCCAC 58.389 45.455 0.00 0.00 41.61 4.02
2145 2218 4.204978 CACAAATGCAAGAAACTGACGAAC 59.795 41.667 0.00 0.00 0.00 3.95
2251 2344 2.624838 GCATTCTTCACATACCCATGGG 59.375 50.000 30.23 30.23 36.86 4.00
2278 2371 4.252073 CTGATAAGATACTGCATCTGGCC 58.748 47.826 0.00 0.00 43.56 5.36
2620 2713 2.511373 GTCCATCGACATGCGCCA 60.511 61.111 4.18 0.00 38.99 5.69
2682 2775 1.301244 CTGCTGCAGTTCGTCAGGT 60.301 57.895 21.21 0.00 0.00 4.00
2784 2877 1.429463 GTACCTGGACAGCAAGAACG 58.571 55.000 0.00 0.00 0.00 3.95
2914 3007 8.674263 GACATGATCCAAGTCATTTTCTAGAT 57.326 34.615 0.00 0.00 36.72 1.98
3051 3149 1.148273 ACAGGAACCAAGCTGCGAA 59.852 52.632 0.00 0.00 0.00 4.70
3110 3208 6.044682 GCACCATTTATTTCTGATTGAAGGG 58.955 40.000 0.00 0.00 35.89 3.95
3136 3234 7.750903 GTGGTACTCTCAAGATTATTTTTGCAC 59.249 37.037 0.00 0.00 0.00 4.57
3181 3279 6.943718 ACTCCTAGCTTAGAGGACATACATAC 59.056 42.308 15.00 0.00 38.22 2.39
3290 3388 1.377202 CATGGAACTGGTCACCCCG 60.377 63.158 0.00 0.00 35.15 5.73
3444 3542 2.566833 CAGACCCATTCTGTTCACCA 57.433 50.000 0.00 0.00 46.12 4.17
3600 3698 0.184933 CTTGGTGGAAAGGGTGGTCA 59.815 55.000 0.00 0.00 0.00 4.02
3630 3728 0.174389 AGTCATCGACGCTGCTCAAT 59.826 50.000 0.00 0.00 37.67 2.57
3632 3730 0.807275 TCATCGACGCTGCTCAATGG 60.807 55.000 0.00 0.00 0.00 3.16
3634 3732 0.108186 ATCGACGCTGCTCAATGGAA 60.108 50.000 0.00 0.00 0.00 3.53
3651 3749 4.177537 TGGAACTTTTGATGAACCCTCA 57.822 40.909 0.00 0.00 35.56 3.86
3695 3793 2.658285 GGAATGGTCCATGATCTGCAA 58.342 47.619 4.74 0.00 44.26 4.08
3711 3809 4.819769 TCTGCAAAGTCCAAATAAATGGC 58.180 39.130 0.00 0.00 40.46 4.40
3724 3822 0.712380 AAATGGCCCATGGAGGTCTT 59.288 50.000 15.22 0.00 34.66 3.01
3731 3829 2.548920 GCCCATGGAGGTCTTATTCTCG 60.549 54.545 15.22 0.00 34.66 4.04
3736 3834 5.243954 CCATGGAGGTCTTATTCTCGTATCA 59.756 44.000 5.56 0.00 0.00 2.15
3750 3848 7.525688 TTCTCGTATCACTCTTGCTTAATTG 57.474 36.000 0.00 0.00 0.00 2.32
3780 3878 5.120674 CAGTAATGTCTTGATGAGCAACGAA 59.879 40.000 0.00 0.00 31.96 3.85
3970 4069 6.485171 ACTGGTACAATGAAAATCTTAGGCT 58.515 36.000 0.00 0.00 38.70 4.58
4007 4106 6.842437 ACACGCTGAGAATATATATGGAGT 57.158 37.500 0.00 0.00 0.00 3.85
4011 4110 9.809096 CACGCTGAGAATATATATGGAGTATTT 57.191 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 2.145397 TCATCGGTGGTAAGCTCTCT 57.855 50.000 0.00 0.00 0.00 3.10
231 233 4.340950 TGTATCGTGAGCCACATGAAGATA 59.659 41.667 0.00 0.00 45.86 1.98
247 249 6.109156 TGCCCATATTCTATGTTGTATCGT 57.891 37.500 0.00 0.00 0.00 3.73
268 270 0.943359 CGAAGCCTCCGATCAGATGC 60.943 60.000 0.00 0.00 0.00 3.91
546 549 4.853924 AACACGATCATTCCTTTGCTTT 57.146 36.364 0.00 0.00 0.00 3.51
649 652 1.343069 GTGTCAACTCCACTCCCTCT 58.657 55.000 0.00 0.00 0.00 3.69
722 725 0.250467 AGCCAACAGTCACAAGCGAT 60.250 50.000 0.00 0.00 0.00 4.58
841 848 7.366011 GGATTCTCCATTTCTCCTCTTTTAGGA 60.366 40.741 0.00 0.00 43.81 2.94
869 876 1.426041 CGGCGGTTTAAGATGGACGG 61.426 60.000 0.00 0.00 0.00 4.79
895 903 1.024579 AGAGGCGGGTGTTTAATGCG 61.025 55.000 0.00 0.00 0.00 4.73
945 954 1.595993 TTTCTCTCTCCGACGGCTGG 61.596 60.000 9.66 1.88 0.00 4.85
1566 1587 2.179517 GCCGATCGGATCTAGGCG 59.820 66.667 37.64 8.13 38.28 5.52
1587 1608 1.021390 ATCGGCAGAAGCAAGGTTCG 61.021 55.000 6.38 3.65 44.61 3.95
1594 1615 0.178068 GGGTTAGATCGGCAGAAGCA 59.822 55.000 0.00 0.00 44.61 3.91
1598 1619 1.048601 GGATGGGTTAGATCGGCAGA 58.951 55.000 0.00 0.00 0.00 4.26
1610 1631 1.141053 GAATTACTGGAGCGGATGGGT 59.859 52.381 0.00 0.00 0.00 4.51
1617 1638 0.107703 TGCTGGGAATTACTGGAGCG 60.108 55.000 0.00 0.00 0.00 5.03
1681 1704 3.823873 TGCCTTCACGTTTGGTTAATGAT 59.176 39.130 0.00 0.00 0.00 2.45
1682 1705 3.215151 TGCCTTCACGTTTGGTTAATGA 58.785 40.909 0.00 0.00 0.00 2.57
1683 1706 3.634568 TGCCTTCACGTTTGGTTAATG 57.365 42.857 0.00 0.00 0.00 1.90
1684 1707 3.243602 GGTTGCCTTCACGTTTGGTTAAT 60.244 43.478 0.00 0.00 0.00 1.40
1685 1708 2.099427 GGTTGCCTTCACGTTTGGTTAA 59.901 45.455 0.00 0.00 0.00 2.01
1686 1709 1.677052 GGTTGCCTTCACGTTTGGTTA 59.323 47.619 0.00 0.00 0.00 2.85
1687 1710 0.458260 GGTTGCCTTCACGTTTGGTT 59.542 50.000 0.00 0.00 0.00 3.67
1707 1730 2.590291 TGCTCAACCGAAAGCGCA 60.590 55.556 11.47 0.00 41.51 6.09
1784 1807 6.204688 GGTCATGTGAAAGTTGTGAGATGTTA 59.795 38.462 0.00 0.00 0.00 2.41
1812 1837 3.667497 TCAAAGTCTGCACGAGAAGAT 57.333 42.857 0.00 0.00 30.28 2.40
1869 1894 2.229792 GCACAGGAGGACAATTGTGAA 58.770 47.619 17.58 0.00 42.61 3.18
1875 1900 0.537188 CGTAGGCACAGGAGGACAAT 59.463 55.000 0.00 0.00 0.00 2.71
1881 1906 2.767505 AGAAAAACGTAGGCACAGGAG 58.232 47.619 0.00 0.00 0.00 3.69
1889 1933 7.342942 GTGTAAGTTCTGAAGAAAAACGTAGG 58.657 38.462 0.00 0.00 35.58 3.18
1894 1938 4.664851 CGCGTGTAAGTTCTGAAGAAAAAC 59.335 41.667 0.00 0.00 35.58 2.43
1903 1948 0.161658 CACAGCGCGTGTAAGTTCTG 59.838 55.000 19.58 6.25 41.03 3.02
1919 1964 1.460273 TAGACTGCTGCGTGGACACA 61.460 55.000 3.12 0.00 0.00 3.72
1920 1965 0.319555 TTAGACTGCTGCGTGGACAC 60.320 55.000 2.10 0.00 0.00 3.67
2085 2151 1.577736 CTTCCCTCATCACCAGGAGT 58.422 55.000 0.00 0.00 31.91 3.85
2124 2190 3.418619 CGTTCGTCAGTTTCTTGCATTTG 59.581 43.478 0.00 0.00 0.00 2.32
2145 2218 3.426963 CGGGTCATCCAAATAAAACACCG 60.427 47.826 0.00 0.00 34.36 4.94
2251 2344 6.426328 CCAGATGCAGTATCTTATCAGGAAAC 59.574 42.308 0.00 0.00 43.68 2.78
2278 2371 1.186267 GGGGACCGGGTAGCTATCTG 61.186 65.000 6.32 5.79 40.86 2.90
2682 2775 2.979676 CCCTCTGCACGCAAGCAA 60.980 61.111 1.52 0.00 45.13 3.91
2735 2828 0.526524 GCATGTCGAAGAGGAGACCG 60.527 60.000 0.00 0.00 36.95 4.79
2914 3007 9.884636 ACACAATTACATATCAGTAAGTAGCAA 57.115 29.630 0.00 0.00 37.39 3.91
3051 3149 0.178981 ATCTGTTGCCACTTGCCACT 60.179 50.000 0.00 0.00 40.16 4.00
3110 3208 7.750903 GTGCAAAAATAATCTTGAGAGTACCAC 59.249 37.037 0.00 0.00 0.00 4.16
3136 3234 5.765182 GGAGTAAATCATCCTGTAACATGGG 59.235 44.000 0.00 0.00 32.51 4.00
3181 3279 5.579119 TGTATACTTTGGCAATGTACTGTCG 59.421 40.000 23.26 0.00 0.00 4.35
3243 3341 2.972713 ACTGAGGTAGAAGAAGCAACCA 59.027 45.455 0.00 0.00 34.29 3.67
3290 3388 1.300388 CCAGCCTGCTGTTGTTTGC 60.300 57.895 17.23 0.00 42.15 3.68
3444 3542 0.179018 AGGCCGAGTTTCACAAGCTT 60.179 50.000 0.00 0.00 0.00 3.74
3600 3698 0.528017 TCGATGACTGCTTCTCGCTT 59.472 50.000 0.00 0.00 40.11 4.68
3630 3728 3.888930 GTGAGGGTTCATCAAAAGTTCCA 59.111 43.478 0.00 0.00 35.39 3.53
3632 3730 3.564225 ACGTGAGGGTTCATCAAAAGTTC 59.436 43.478 0.00 0.00 35.39 3.01
3634 3732 3.139077 GACGTGAGGGTTCATCAAAAGT 58.861 45.455 0.00 0.00 35.39 2.66
3651 3749 1.189524 TCCCCCATTTCTGTCGACGT 61.190 55.000 11.62 0.00 0.00 4.34
3687 3785 5.521372 GCCATTTATTTGGACTTTGCAGATC 59.479 40.000 0.00 0.00 39.25 2.75
3695 3793 3.455543 CCATGGGCCATTTATTTGGACTT 59.544 43.478 18.46 0.00 44.91 3.01
3711 3809 2.700897 ACGAGAATAAGACCTCCATGGG 59.299 50.000 13.02 2.26 41.11 4.00
3724 3822 9.249457 CAATTAAGCAAGAGTGATACGAGAATA 57.751 33.333 0.00 0.00 0.00 1.75
3736 3834 3.754965 TGCACTCCAATTAAGCAAGAGT 58.245 40.909 0.00 0.00 38.30 3.24
3750 3848 4.507710 TCATCAAGACATTACTGCACTCC 58.492 43.478 0.00 0.00 0.00 3.85
3780 3878 8.737168 TTACTTGCTAGTGCTATTTTCATCAT 57.263 30.769 11.27 0.00 40.48 2.45
3970 4069 2.811431 CAGCGTGTTGGAAGGTATTGAA 59.189 45.455 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.