Multiple sequence alignment - TraesCS4D01G073500

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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 TraesCS4D01G073500 chr4D 100.000 2558 0 0 1 2558 47989978 47992535 0.000000e+00 4724.0
1 TraesCS4D01G073500 chr4B 96.510 1662 49 5 900 2558 70575731 70577386 0.000000e+00 2739.0
2 TraesCS4D01G073500 chr4B 91.395 674 41 11 121 789 70574641 70575302 0.000000e+00 907.0
3 TraesCS4D01G073500 chr4B 96.748 123 3 1 1 123 70574485 70574606 1.200000e-48 204.0
4 TraesCS4D01G073500 chr4A 96.050 886 30 3 908 1790 549800229 549799346 0.000000e+00 1437.0
5 TraesCS4D01G073500 chr4A 89.337 347 28 8 121 464 549801199 549800859 6.540000e-116 427.0
6 TraesCS4D01G073500 chr4A 94.872 117 6 0 1 117 549801356 549801240 1.560000e-42 183.0
7 TraesCS4D01G073500 chr5A 83.929 112 11 3 434 538 51459508 51459619 1.620000e-17 100.0
8 TraesCS4D01G073500 chr5D 83.929 112 9 4 434 537 546298269 546298159 5.820000e-17 99.0
9 TraesCS4D01G073500 chr1D 81.818 121 18 3 652 772 371254105 371253989 5.820000e-17 99.0
10 TraesCS4D01G073500 chr1D 93.333 45 2 1 538 582 211684123 211684080 5.910000e-07 65.8
11 TraesCS4D01G073500 chr2B 81.301 123 17 4 652 773 13634446 13634563 7.530000e-16 95.3
12 TraesCS4D01G073500 chr2B 92.188 64 5 0 434 497 445257286 445257223 9.750000e-15 91.6
13 TraesCS4D01G073500 chr2B 80.000 130 16 6 644 772 134253608 134253728 1.260000e-13 87.9
14 TraesCS4D01G073500 chr7B 80.147 136 15 8 644 777 380073196 380073321 9.750000e-15 91.6
15 TraesCS4D01G073500 chr7B 80.488 123 16 4 650 772 648273618 648273504 1.260000e-13 87.9
16 TraesCS4D01G073500 chr3B 81.148 122 15 6 652 771 16102371 16102486 9.750000e-15 91.6
17 TraesCS4D01G073500 chr3B 79.851 134 16 7 644 776 534159546 534159669 1.260000e-13 87.9
18 TraesCS4D01G073500 chr3B 97.222 36 1 0 512 547 440135777 440135742 7.640000e-06 62.1
19 TraesCS4D01G073500 chr5B 80.488 123 16 4 650 772 710235736 710235622 1.260000e-13 87.9
20 TraesCS4D01G073500 chr7A 82.243 107 12 4 435 538 22917681 22917579 4.530000e-13 86.1
21 TraesCS4D01G073500 chr2D 91.803 61 5 0 434 494 195298071 195298131 4.530000e-13 86.1
22 TraesCS4D01G073500 chr2D 88.732 71 7 1 434 504 375149126 375149057 4.530000e-13 86.1
23 TraesCS4D01G073500 chr2D 84.722 72 6 3 472 538 539004513 539004584 1.640000e-07 67.6
24 TraesCS4D01G073500 chr2D 91.111 45 2 1 538 582 629976871 629976913 2.750000e-05 60.2
25 TraesCS4D01G073500 chr2D 91.111 45 2 1 538 582 630044609 630044651 2.750000e-05 60.2
26 TraesCS4D01G073500 chr6D 87.692 65 8 0 434 498 415495583 415495519 2.730000e-10 76.8
27 TraesCS4D01G073500 chr1A 94.118 51 2 1 532 582 267144022 267143973 2.730000e-10 76.8
28 TraesCS4D01G073500 chr6B 85.135 74 10 1 434 507 16960332 16960404 9.820000e-10 75.0
29 TraesCS4D01G073500 chr7D 100.000 30 0 0 551 580 22527634 22527605 3.560000e-04 56.5


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 TraesCS4D01G073500 chr4D 47989978 47992535 2557 False 4724.000000 4724 100.000000 1 2558 1 chr4D.!!$F1 2557
1 TraesCS4D01G073500 chr4B 70574485 70577386 2901 False 1283.333333 2739 94.884333 1 2558 3 chr4B.!!$F1 2557
2 TraesCS4D01G073500 chr4A 549799346 549801356 2010 True 682.333333 1437 93.419667 1 1790 3 chr4A.!!$R1 1789

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
879 1539 0.032678 CTCAGGTGTGCGCTATAGGG 59.967 60.0 9.73 12.3 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2423 3101 1.345415 TCTTTCCGTGGTTACCCTGTC 59.655 52.381 0.0 0.0 0.0 3.51 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
59 60 2.681152 AGGCGTTTGATTGTCGTTTC 57.319 45.000 0.00 0.0 0.00 2.78
281 322 8.816640 AAATTCGCAAATACTTGTTCAATTCT 57.183 26.923 0.00 0.0 34.79 2.40
507 549 7.494298 ACATCATCAAAAAGTGGGTTTTTACAC 59.506 33.333 0.00 0.0 44.93 2.90
567 617 4.515567 CACTAGAAAACCTCCAACTCCAAC 59.484 45.833 0.00 0.0 0.00 3.77
570 620 3.202151 AGAAAACCTCCAACTCCAACAGA 59.798 43.478 0.00 0.0 0.00 3.41
580 631 6.303054 TCCAACTCCAACAGATGATGTAAAA 58.697 36.000 0.00 0.0 43.00 1.52
621 672 3.490031 ATGGTGAGGTGCGGTGCAA 62.490 57.895 0.00 0.0 41.47 4.08
636 688 1.957186 GCAACGACGTTAGTGGCCA 60.957 57.895 13.77 0.0 32.58 5.36
719 1057 7.390823 TGTTACTTCTCATGTTATTGGTGCTA 58.609 34.615 0.00 0.0 0.00 3.49
740 1078 6.058183 GCTACCAGGATGTTTGATGAATACT 58.942 40.000 0.00 0.0 0.00 2.12
746 1084 7.330454 CCAGGATGTTTGATGAATACTAGATCG 59.670 40.741 0.00 0.0 0.00 3.69
791 1129 5.950544 AAAGCTACTGGTTTTTCCCTTTT 57.049 34.783 0.00 0.0 40.50 2.27
792 1130 5.950544 AAGCTACTGGTTTTTCCCTTTTT 57.049 34.783 0.00 0.0 34.77 1.94
832 1210 0.398318 GGAGCCAAAGAGTGAGTGGT 59.602 55.000 0.00 0.0 34.71 4.16
851 1511 3.077556 ACCGAGCCAGTGCCCTAG 61.078 66.667 0.00 0.0 38.69 3.02
874 1534 4.435436 CGGCTCAGGTGTGCGCTA 62.435 66.667 9.73 0.0 34.63 4.26
877 1537 0.598680 GGCTCAGGTGTGCGCTATAG 60.599 60.000 9.73 0.0 34.63 1.31
878 1538 0.598680 GCTCAGGTGTGCGCTATAGG 60.599 60.000 9.73 0.0 31.29 2.57
879 1539 0.032678 CTCAGGTGTGCGCTATAGGG 59.967 60.000 9.73 12.3 0.00 3.53
880 1540 1.069765 CAGGTGTGCGCTATAGGGG 59.930 63.158 17.62 1.1 0.00 4.79
896 1556 4.483243 GGCGCCTCCCGATTGGAA 62.483 66.667 22.15 0.0 44.57 3.53
897 1557 2.897350 GCGCCTCCCGATTGGAAG 60.897 66.667 0.00 0.0 44.57 3.46
898 1558 2.897350 CGCCTCCCGATTGGAAGC 60.897 66.667 0.00 0.0 45.67 3.86
974 1649 3.120108 TGACCCCGAGGATAGGATTTTT 58.880 45.455 0.00 0.0 36.73 1.94
1050 1725 1.083895 TTCCCTCCCCACCATAGCA 59.916 57.895 0.00 0.0 0.00 3.49
1251 1926 1.300620 CGTGAAGAAGGTGTCGGCA 60.301 57.895 0.00 0.0 0.00 5.69
1255 1930 0.238553 GAAGAAGGTGTCGGCAAAGC 59.761 55.000 0.00 0.0 0.00 3.51
1392 2067 2.383527 CGAGGACAGCGCCTTGTTC 61.384 63.158 2.29 0.8 38.73 3.18
1545 2220 2.967599 TGGTCAGGAACATCATCGAG 57.032 50.000 0.00 0.0 0.00 4.04
1548 2223 3.452264 TGGTCAGGAACATCATCGAGAAT 59.548 43.478 0.00 0.0 0.00 2.40
1585 2260 4.283467 TGTCTAGGCAACATAGTGTCTGTT 59.717 41.667 0.00 0.0 33.48 3.16
1836 2514 5.771469 TGTATGCACTGGATTTTGTCTTTG 58.229 37.500 0.00 0.0 0.00 2.77
1842 2520 5.860716 GCACTGGATTTTGTCTTTGATCTTC 59.139 40.000 0.00 0.0 0.00 2.87
1907 2585 0.246635 AAATACCTCACGTCGCTGCT 59.753 50.000 0.00 0.0 0.00 4.24
2204 2882 0.572590 GCGATCATCGTTGTCCTTCG 59.427 55.000 9.23 0.0 42.81 3.79
2221 2899 3.207669 GCGCCCTCTTGGATGCAG 61.208 66.667 0.00 0.0 35.39 4.41
2224 2902 1.817099 GCCCTCTTGGATGCAGTCG 60.817 63.158 0.00 0.0 35.39 4.18
2227 2905 1.078918 CTCTTGGATGCAGTCGCCA 60.079 57.895 0.00 0.0 37.32 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
487 529 5.740290 TGGTGTAAAAACCCACTTTTTGA 57.260 34.783 1.84 0.00 41.34 2.69
507 549 4.582869 TCATCTGTTGAAGTTGGAGATGG 58.417 43.478 0.00 0.00 40.23 3.51
541 591 5.179533 GGAGTTGGAGGTTTTCTAGTGATC 58.820 45.833 0.00 0.00 0.00 2.92
546 596 4.714632 TGTTGGAGTTGGAGGTTTTCTAG 58.285 43.478 0.00 0.00 0.00 2.43
580 631 1.473965 CCGCCTCTGCAGTGATGTAAT 60.474 52.381 17.19 0.00 37.32 1.89
593 644 3.790437 CTCACCATGGCCGCCTCT 61.790 66.667 13.04 0.00 0.00 3.69
616 667 1.203313 GCCACTAACGTCGTTGCAC 59.797 57.895 20.62 2.22 0.00 4.57
621 672 2.049802 CGTGGCCACTAACGTCGT 60.050 61.111 32.28 0.00 35.13 4.34
645 697 0.377554 AGCGACGACTACAATCCTCG 59.622 55.000 0.00 0.00 32.41 4.63
719 1057 7.437713 TCTAGTATTCATCAAACATCCTGGT 57.562 36.000 0.00 0.00 0.00 4.00
723 1061 7.378966 TCCGATCTAGTATTCATCAAACATCC 58.621 38.462 0.00 0.00 0.00 3.51
803 1141 4.038402 CACTCTTTGGCTCCATCACTTTTT 59.962 41.667 0.00 0.00 0.00 1.94
804 1142 3.571401 CACTCTTTGGCTCCATCACTTTT 59.429 43.478 0.00 0.00 0.00 2.27
805 1143 3.152341 CACTCTTTGGCTCCATCACTTT 58.848 45.455 0.00 0.00 0.00 2.66
806 1144 2.373169 TCACTCTTTGGCTCCATCACTT 59.627 45.455 0.00 0.00 0.00 3.16
818 1196 1.068588 TCGGTCACCACTCACTCTTTG 59.931 52.381 0.00 0.00 0.00 2.77
821 1199 1.528292 GCTCGGTCACCACTCACTCT 61.528 60.000 0.00 0.00 0.00 3.24
894 1554 2.550180 GACTCCTTTCACTGGTTGCTTC 59.450 50.000 0.00 0.00 0.00 3.86
895 1555 2.576615 GACTCCTTTCACTGGTTGCTT 58.423 47.619 0.00 0.00 0.00 3.91
896 1556 1.202818 GGACTCCTTTCACTGGTTGCT 60.203 52.381 0.00 0.00 0.00 3.91
897 1557 1.202818 AGGACTCCTTTCACTGGTTGC 60.203 52.381 0.00 0.00 0.00 4.17
898 1558 2.370189 AGAGGACTCCTTTCACTGGTTG 59.630 50.000 0.00 0.00 31.76 3.77
974 1649 0.909610 AGAGATTTGGGGGACGAGCA 60.910 55.000 0.00 0.00 0.00 4.26
1392 2067 1.663702 GTCCGTGTCCACCTTGACG 60.664 63.158 0.00 0.00 38.11 4.35
1545 2220 3.924144 AGACAGAACTCACAGCTCATTC 58.076 45.455 0.00 0.00 0.00 2.67
1548 2223 2.822561 CCTAGACAGAACTCACAGCTCA 59.177 50.000 0.00 0.00 0.00 4.26
1651 2326 3.791789 GCAACACAAAGCTCGAATCAACA 60.792 43.478 0.00 0.00 0.00 3.33
1736 2414 8.383619 CAATAGAGAACCAATTTGTTAGTCTCG 58.616 37.037 9.04 0.00 0.00 4.04
1810 2488 6.403866 AGACAAAATCCAGTGCATACAAAA 57.596 33.333 0.00 0.00 0.00 2.44
1836 2514 7.484035 AAGTCAATTTATACGCAGGAAGATC 57.516 36.000 0.00 0.00 0.00 2.75
1842 2520 7.072030 GCATCTAAAGTCAATTTATACGCAGG 58.928 38.462 0.00 0.00 32.93 4.85
1891 2569 1.969589 TGAGCAGCGACGTGAGGTA 60.970 57.895 0.00 0.00 0.00 3.08
2204 2882 3.207669 CTGCATCCAAGAGGGCGC 61.208 66.667 0.00 0.00 36.21 6.53
2221 2899 3.660111 GCAAGTGGTGGTGGCGAC 61.660 66.667 0.00 0.00 0.00 5.19
2227 2905 2.700185 AACAGGGGCAAGTGGTGGT 61.700 57.895 0.00 0.00 0.00 4.16
2292 2970 2.300437 GCGGATATAAGAGGAAGGCTGT 59.700 50.000 0.00 0.00 0.00 4.40
2327 3005 3.555324 TCAAGCAGCCCACGGACA 61.555 61.111 0.00 0.00 0.00 4.02
2423 3101 1.345415 TCTTTCCGTGGTTACCCTGTC 59.655 52.381 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.