Multiple sequence alignment - TraesCS7D01G278700

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 TraesCS7D01G278700 chr7D 100.000 2609 0 0 1 2609 268835699 268838307 0.000000e+00 4819.0
1 TraesCS7D01G278700 chr7D 79.583 240 37 10 147 378 27047352 27047117 7.470000e-36 161.0
2 TraesCS7D01G278700 chr7D 78.926 242 38 10 147 379 27093807 27093570 4.500000e-33 152.0
3 TraesCS7D01G278700 chr7D 76.446 242 46 8 147 379 26833835 26833596 1.270000e-23 121.0
4 TraesCS7D01G278700 chr7B 92.069 2030 82 34 625 2609 272750234 272748239 0.000000e+00 2784.0
5 TraesCS7D01G278700 chr7B 96.530 634 17 3 1 633 272753198 272752569 0.000000e+00 1044.0
6 TraesCS7D01G278700 chr7A 92.947 1900 80 21 751 2609 295212360 295214246 0.000000e+00 2717.0
7 TraesCS7D01G278700 chr7A 86.124 663 34 28 1 625 295099556 295100198 0.000000e+00 662.0
8 TraesCS7D01G278700 chr7A 78.750 240 43 8 147 379 27288846 27288608 1.250000e-33 154.0
9 TraesCS7D01G278700 chr1A 88.123 261 26 4 1090 1349 554933696 554933952 3.260000e-79 305.0
10 TraesCS7D01G278700 chr6B 84.942 259 27 8 1090 1348 558930467 558930713 4.310000e-63 252.0
11 TraesCS7D01G278700 chr4A 81.172 239 34 9 149 379 704629039 704628804 5.740000e-42 182.0
12 TraesCS7D01G278700 chr4A 80.913 241 34 10 147 379 704645112 704644876 2.060000e-41 180.0
13 TraesCS7D01G278700 chr3D 85.149 101 9 2 1113 1213 594957092 594956998 5.940000e-17 99.0
14 TraesCS7D01G278700 chr3B 88.158 76 9 0 1114 1189 798407012 798406937 9.940000e-15 91.6


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 TraesCS7D01G278700 chr7D 268835699 268838307 2608 False 4819 4819 100.0000 1 2609 1 chr7D.!!$F1 2608
1 TraesCS7D01G278700 chr7B 272748239 272753198 4959 True 1914 2784 94.2995 1 2609 2 chr7B.!!$R1 2608
2 TraesCS7D01G278700 chr7A 295212360 295214246 1886 False 2717 2717 92.9470 751 2609 1 chr7A.!!$F2 1858
3 TraesCS7D01G278700 chr7A 295099556 295100198 642 False 662 662 86.1240 1 625 1 chr7A.!!$F1 624

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
939 3348 1.036707 GCCCAACAGCCTAACACAAA 58.963 50.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2273 4715 1.225855 GTCAACACACATGCCGAGAA 58.774 50.0 0.0 0.0 0.0 2.87 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
39 40 3.118592 ACAGCCAGAACTCCTGTATAAGC 60.119 47.826 0.00 0.00 41.33 3.09
226 251 2.351738 CCTTTTCCAGGTTTGCATCGTC 60.352 50.000 0.00 0.00 37.99 4.20
275 300 5.560722 TTCTCCACATAACCTCTGTTTGA 57.439 39.130 0.00 0.00 35.87 2.69
354 380 1.805945 GTTCGAGAGCGCCGACATT 60.806 57.895 2.29 0.00 35.61 2.71
457 491 4.223700 TGCCATGTCTCTTCTCATGTAGTT 59.776 41.667 0.00 0.00 39.53 2.24
565 605 6.299141 TCTAAGAAACACTGAATTTGAGGCT 58.701 36.000 0.00 0.00 0.00 4.58
596 636 9.506018 AAAAGTGAAATAAAATCCAGAAATGGG 57.494 29.630 0.00 0.00 0.00 4.00
601 641 7.895429 TGAAATAAAATCCAGAAATGGGAGTCT 59.105 33.333 0.00 0.00 37.96 3.24
602 642 8.670521 AAATAAAATCCAGAAATGGGAGTCTT 57.329 30.769 0.00 0.00 37.96 3.01
603 643 5.990120 AAAATCCAGAAATGGGAGTCTTG 57.010 39.130 0.00 0.00 37.96 3.02
684 3068 9.880064 TTTTTCGATACAACGATTACATTCAAA 57.120 25.926 0.00 0.00 41.82 2.69
685 3069 9.880064 TTTTCGATACAACGATTACATTCAAAA 57.120 25.926 0.00 0.00 41.82 2.44
686 3070 9.880064 TTTCGATACAACGATTACATTCAAAAA 57.120 25.926 0.00 0.00 41.82 1.94
734 3119 5.404946 TGAGTAACACTAGCGTAACAATCC 58.595 41.667 0.00 0.00 0.00 3.01
737 3122 6.461640 AGTAACACTAGCGTAACAATCCTTT 58.538 36.000 0.00 0.00 0.00 3.11
835 3221 6.021596 CCAATAGTGACAAAATGTTAGCGTC 58.978 40.000 0.00 0.00 0.00 5.19
937 3346 4.492604 GCCCAACAGCCTAACACA 57.507 55.556 0.00 0.00 0.00 3.72
938 3347 2.727103 GCCCAACAGCCTAACACAA 58.273 52.632 0.00 0.00 0.00 3.33
939 3348 1.036707 GCCCAACAGCCTAACACAAA 58.963 50.000 0.00 0.00 0.00 2.83
940 3349 1.410882 GCCCAACAGCCTAACACAAAA 59.589 47.619 0.00 0.00 0.00 2.44
941 3350 2.545742 GCCCAACAGCCTAACACAAAAG 60.546 50.000 0.00 0.00 0.00 2.27
942 3351 2.693074 CCCAACAGCCTAACACAAAAGT 59.307 45.455 0.00 0.00 0.00 2.66
943 3352 3.490761 CCCAACAGCCTAACACAAAAGTG 60.491 47.826 0.00 0.00 0.00 3.16
944 3353 3.490761 CCAACAGCCTAACACAAAAGTGG 60.491 47.826 0.38 0.00 0.00 4.00
1032 3453 2.084546 GGAAACCAAATCCAGACCTCG 58.915 52.381 0.00 0.00 36.92 4.63
1648 4072 1.209747 GTATCACCACCTGAACCCTCC 59.790 57.143 0.00 0.00 30.60 4.30
1652 4076 1.538876 CCACCTGAACCCTCCCTCA 60.539 63.158 0.00 0.00 0.00 3.86
1670 4094 4.154195 CCCTCAAAACCTTATTCGTCTGTG 59.846 45.833 0.00 0.00 0.00 3.66
1676 4100 2.037251 ACCTTATTCGTCTGTGTGTGCT 59.963 45.455 0.00 0.00 0.00 4.40
1677 4101 3.067106 CCTTATTCGTCTGTGTGTGCTT 58.933 45.455 0.00 0.00 0.00 3.91
1678 4102 3.498397 CCTTATTCGTCTGTGTGTGCTTT 59.502 43.478 0.00 0.00 0.00 3.51
1679 4103 4.457810 CTTATTCGTCTGTGTGTGCTTTG 58.542 43.478 0.00 0.00 0.00 2.77
1680 4104 2.017138 TTCGTCTGTGTGTGCTTTGA 57.983 45.000 0.00 0.00 0.00 2.69
1681 4105 2.017138 TCGTCTGTGTGTGCTTTGAA 57.983 45.000 0.00 0.00 0.00 2.69
1701 4125 7.441890 TTGAAATGAAATGCAATGCAATCTT 57.558 28.000 13.45 9.27 43.62 2.40
1738 4162 6.036246 CAATGAAATGCAATGCAATCTCAG 57.964 37.500 13.45 4.45 43.62 3.35
1740 4164 5.592104 TGAAATGCAATGCAATCTCAGAT 57.408 34.783 13.45 0.00 43.62 2.90
1741 4165 5.972935 TGAAATGCAATGCAATCTCAGATT 58.027 33.333 13.45 0.00 43.62 2.40
1743 4167 4.585955 ATGCAATGCAATCTCAGATTCC 57.414 40.909 13.45 0.00 43.62 3.01
1744 4168 3.358118 TGCAATGCAATCTCAGATTCCA 58.642 40.909 5.01 0.00 34.76 3.53
1745 4169 3.764972 TGCAATGCAATCTCAGATTCCAA 59.235 39.130 5.01 0.00 34.76 3.53
1746 4170 4.404394 TGCAATGCAATCTCAGATTCCAAT 59.596 37.500 5.01 0.00 34.76 3.16
1747 4171 4.745125 GCAATGCAATCTCAGATTCCAATG 59.255 41.667 2.33 2.33 0.00 2.82
1757 4181 3.028850 CAGATTCCAATGCAATGTCCCT 58.971 45.455 0.21 0.00 0.00 4.20
1769 4194 6.455360 TGCAATGTCCCTTCATAGAATTTC 57.545 37.500 0.00 0.00 0.00 2.17
1770 4195 5.951148 TGCAATGTCCCTTCATAGAATTTCA 59.049 36.000 0.00 0.00 0.00 2.69
1786 4211 7.156876 AGAATTTCAACAAGAATAATCGGCA 57.843 32.000 0.00 0.00 35.83 5.69
1795 4220 2.092968 AGAATAATCGGCAGCTCCACAA 60.093 45.455 0.00 0.00 34.01 3.33
1882 4307 0.387239 GCTCGCATCCCACAAAACAC 60.387 55.000 0.00 0.00 0.00 3.32
1883 4308 0.950836 CTCGCATCCCACAAAACACA 59.049 50.000 0.00 0.00 0.00 3.72
1983 4408 2.201732 GTTTCTCAGTTGAGTGTCGCA 58.798 47.619 8.85 0.00 42.60 5.10
2166 4591 0.461548 TCGGCTCATAGTCCTGCAAG 59.538 55.000 0.00 0.00 0.00 4.01
2192 4617 0.912486 GCATGGTAGGGGAGTTCAGT 59.088 55.000 0.00 0.00 0.00 3.41
2221 4663 0.417035 TTGGGGCATTGGGGAAAGAT 59.583 50.000 0.00 0.00 0.00 2.40
2225 4667 1.619432 GGGCATTGGGGAAAGATGACA 60.619 52.381 0.00 0.00 30.25 3.58
2237 4679 5.300752 GGAAAGATGACAGTTCTTCACAGA 58.699 41.667 0.00 0.00 32.33 3.41
2329 4771 2.107204 AGAGTGGTTCTCCTGCAAATGT 59.893 45.455 0.00 0.00 43.71 2.71
2356 4798 1.066430 TCTACCGAATGTGCTTCCACC 60.066 52.381 0.00 0.00 41.35 4.61
2371 4813 0.663568 CCACCGTCGACACAACTCTC 60.664 60.000 17.16 0.00 0.00 3.20
2376 4818 1.399855 CGTCGACACAACTCTCGATGT 60.400 52.381 17.16 0.00 40.81 3.06
2377 4819 2.662700 GTCGACACAACTCTCGATGTT 58.337 47.619 11.55 0.00 40.81 2.71
2421 4867 0.108585 TCTGAGGCAAAGGGACACAC 59.891 55.000 0.00 0.00 0.00 3.82
2431 4877 0.546122 AGGGACACACAAGCAAGTCA 59.454 50.000 0.00 0.00 32.79 3.41
2446 4892 4.228210 AGCAAGTCAAGATTAGATGGGGAA 59.772 41.667 0.00 0.00 0.00 3.97
2448 4894 5.500234 CAAGTCAAGATTAGATGGGGAACA 58.500 41.667 0.00 0.00 0.00 3.18
2478 4926 4.325972 TGAATAAGCAGTCATGTTGAGCA 58.674 39.130 0.00 0.00 0.00 4.26
2567 5015 0.788995 CGCGAGATGATGCAATCTCC 59.211 55.000 18.50 12.18 46.66 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.470196 TTTAGCTGCTACGCTAGTCG 57.530 50.000 9.27 5.24 42.85 4.18
226 251 1.333524 CCAGCAGAAGCATAAATCGCG 60.334 52.381 0.00 0.00 45.49 5.87
275 300 5.585047 GCCTGTCAAGACGGTAAGATTAAAT 59.415 40.000 8.14 0.00 35.97 1.40
354 380 3.708451 TGTTGCCCTCAGATACTCTACA 58.292 45.455 0.00 0.00 0.00 2.74
457 491 9.177608 CCATTTTCCTAGTAAAGAATGTGATCA 57.822 33.333 0.00 0.00 0.00 2.92
596 636 4.495844 CCCGTGAAAGAAACAACAAGACTC 60.496 45.833 0.00 0.00 0.00 3.36
601 641 3.697045 ACATCCCGTGAAAGAAACAACAA 59.303 39.130 0.00 0.00 0.00 2.83
602 642 3.283751 ACATCCCGTGAAAGAAACAACA 58.716 40.909 0.00 0.00 0.00 3.33
603 643 3.982576 ACATCCCGTGAAAGAAACAAC 57.017 42.857 0.00 0.00 0.00 3.32
742 3127 8.339714 CAAGGTTCTAATTGTTACGTTCAAAGA 58.660 33.333 0.00 0.00 0.00 2.52
743 3128 8.339714 TCAAGGTTCTAATTGTTACGTTCAAAG 58.660 33.333 0.00 0.00 0.00 2.77
759 3144 3.954904 CTCGAGGGAATCTCAAGGTTCTA 59.045 47.826 3.91 0.00 42.55 2.10
810 3196 5.703592 ACGCTAACATTTTGTCACTATTGGA 59.296 36.000 0.00 0.00 0.00 3.53
835 3221 4.748144 GTTGGGAGCTGGGCTGGG 62.748 72.222 0.00 0.00 39.88 4.45
881 3290 0.392461 TTTGGATGTAGTGGGCTCGC 60.392 55.000 0.00 0.00 0.00 5.03
882 3291 2.009774 CTTTTGGATGTAGTGGGCTCG 58.990 52.381 0.00 0.00 0.00 5.03
1443 3864 2.821366 GCGTCCAGCTCCATGTGG 60.821 66.667 0.00 0.00 44.04 4.17
1461 3882 3.822192 CCCGCGATCTCCACGACA 61.822 66.667 8.23 0.00 0.00 4.35
1486 3907 2.807045 CGACCAGAGCAGCACGAC 60.807 66.667 0.00 0.00 0.00 4.34
1487 3908 4.724602 GCGACCAGAGCAGCACGA 62.725 66.667 0.00 0.00 34.19 4.35
1648 4072 4.755123 ACACAGACGAATAAGGTTTTGAGG 59.245 41.667 0.00 0.00 0.00 3.86
1652 4076 4.261031 GCACACACAGACGAATAAGGTTTT 60.261 41.667 0.00 0.00 0.00 2.43
1670 4094 5.406767 TTGCATTTCATTTCAAAGCACAC 57.593 34.783 0.00 0.00 0.00 3.82
1676 4100 7.441890 AGATTGCATTGCATTTCATTTCAAA 57.558 28.000 12.95 0.00 38.76 2.69
1677 4101 7.441890 AAGATTGCATTGCATTTCATTTCAA 57.558 28.000 12.95 0.00 38.76 2.69
1678 4102 7.361371 GGAAAGATTGCATTGCATTTCATTTCA 60.361 33.333 25.76 7.25 37.02 2.69
1679 4103 6.964934 GGAAAGATTGCATTGCATTTCATTTC 59.035 34.615 25.76 22.89 37.02 2.17
1680 4104 6.127842 GGGAAAGATTGCATTGCATTTCATTT 60.128 34.615 25.76 19.03 37.02 2.32
1681 4105 5.355910 GGGAAAGATTGCATTGCATTTCATT 59.644 36.000 25.76 18.63 37.02 2.57
1701 4125 4.970860 TTTCATTGCTTGGAATTGGGAA 57.029 36.364 0.00 0.00 0.00 3.97
1737 4161 3.393426 AGGGACATTGCATTGGAATCT 57.607 42.857 12.87 2.77 0.00 2.40
1738 4162 3.448301 TGAAGGGACATTGCATTGGAATC 59.552 43.478 12.87 2.02 0.00 2.52
1740 4164 2.886913 TGAAGGGACATTGCATTGGAA 58.113 42.857 12.87 0.00 0.00 3.53
1741 4165 2.601240 TGAAGGGACATTGCATTGGA 57.399 45.000 12.87 0.00 0.00 3.53
1743 4167 5.840243 TTCTATGAAGGGACATTGCATTG 57.160 39.130 7.04 7.04 0.00 2.82
1744 4168 7.124599 TGAAATTCTATGAAGGGACATTGCATT 59.875 33.333 0.00 0.00 0.00 3.56
1745 4169 6.608405 TGAAATTCTATGAAGGGACATTGCAT 59.392 34.615 0.00 0.00 0.00 3.96
1746 4170 5.951148 TGAAATTCTATGAAGGGACATTGCA 59.049 36.000 0.00 0.00 0.00 4.08
1747 4171 6.455360 TGAAATTCTATGAAGGGACATTGC 57.545 37.500 0.00 0.00 0.00 3.56
1769 4194 3.242870 GGAGCTGCCGATTATTCTTGTTG 60.243 47.826 0.00 0.00 0.00 3.33
1770 4195 2.945668 GGAGCTGCCGATTATTCTTGTT 59.054 45.455 0.00 0.00 0.00 2.83
1780 4205 1.417517 TGATATTGTGGAGCTGCCGAT 59.582 47.619 1.53 2.34 40.66 4.18
1783 4208 1.672881 GTGTGATATTGTGGAGCTGCC 59.327 52.381 1.53 0.00 37.10 4.85
1786 4211 4.019792 TGTTGTGTGATATTGTGGAGCT 57.980 40.909 0.00 0.00 0.00 4.09
1882 4307 5.375417 TTTGATGTCCTTGTTGTGCTATG 57.625 39.130 0.00 0.00 0.00 2.23
1883 4308 4.082571 GCTTTGATGTCCTTGTTGTGCTAT 60.083 41.667 0.00 0.00 0.00 2.97
1960 4385 3.544244 GCGACACTCAACTGAGAAACAAC 60.544 47.826 13.61 0.00 44.74 3.32
1983 4408 3.077556 ATCCCTCGCTCGCCACTT 61.078 61.111 0.00 0.00 0.00 3.16
2016 4441 3.038280 TCCCTATGAATCGAGCAAGGAA 58.962 45.455 14.83 0.49 0.00 3.36
2166 4591 2.290960 ACTCCCCTACCATGCTGTTTTC 60.291 50.000 0.00 0.00 0.00 2.29
2210 4652 4.141274 TGAAGAACTGTCATCTTTCCCCAA 60.141 41.667 0.00 0.00 37.26 4.12
2221 4663 7.500227 AGATGAAAATTCTGTGAAGAACTGTCA 59.500 33.333 0.00 0.00 0.00 3.58
2225 4667 7.040823 GGTGAGATGAAAATTCTGTGAAGAACT 60.041 37.037 0.00 0.00 0.00 3.01
2237 4679 4.946157 CAGCTACAGGGTGAGATGAAAATT 59.054 41.667 0.00 0.00 45.36 1.82
2273 4715 1.225855 GTCAACACACATGCCGAGAA 58.774 50.000 0.00 0.00 0.00 2.87
2329 4771 5.339008 AAGCACATTCGGTAGAGATACAA 57.661 39.130 0.00 0.00 0.00 2.41
2371 4813 2.930040 AGAGGCACGTAATTCAACATCG 59.070 45.455 0.00 0.00 0.00 3.84
2376 4818 3.244422 ACTGGAAGAGGCACGTAATTCAA 60.244 43.478 0.00 0.00 37.43 2.69
2377 4819 2.301870 ACTGGAAGAGGCACGTAATTCA 59.698 45.455 0.00 0.00 37.43 2.57
2421 4867 4.337555 CCCCATCTAATCTTGACTTGCTTG 59.662 45.833 0.00 0.00 0.00 4.01
2431 4877 7.698163 ATAAGAGTGTTCCCCATCTAATCTT 57.302 36.000 0.00 0.00 0.00 2.40
2446 4892 7.826252 ACATGACTGCTTATTCAATAAGAGTGT 59.174 33.333 19.66 13.47 43.85 3.55
2448 4894 8.671921 CAACATGACTGCTTATTCAATAAGAGT 58.328 33.333 19.66 17.58 43.85 3.24
2478 4926 8.361139 CCAGGATATCGACAGTAATTTCTAAGT 58.639 37.037 0.00 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.