Multiple sequence alignment - TraesCS5B01G331800

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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 TraesCS5B01G331800 chr5B 100.000 2624 0 0 1 2624 516040097 516037474 0.000000e+00 4846.0
1 TraesCS5B01G331800 chr5D 92.955 1093 46 14 642 1706 426167059 426165970 0.000000e+00 1563.0
2 TraesCS5B01G331800 chr5D 93.717 573 33 3 77 647 94510405 94510976 0.000000e+00 856.0
3 TraesCS5B01G331800 chr5D 94.434 557 28 3 86 641 421912344 421912898 0.000000e+00 854.0
4 TraesCS5B01G331800 chr5D 87.778 90 6 3 1699 1783 426165940 426165851 1.660000e-17 100.0
5 TraesCS5B01G331800 chr1A 96.812 847 17 2 1783 2624 511450303 511451144 0.000000e+00 1406.0
6 TraesCS5B01G331800 chr1A 96.686 845 21 3 1780 2624 38637013 38636176 0.000000e+00 1399.0
7 TraesCS5B01G331800 chr1A 96.331 845 25 5 1780 2624 38583939 38583101 0.000000e+00 1384.0
8 TraesCS5B01G331800 chr1A 83.401 247 36 1 1783 2029 38635095 38635336 9.450000e-55 224.0
9 TraesCS5B01G331800 chr1A 82.591 247 38 3 1783 2029 38581557 38581798 2.050000e-51 213.0
10 TraesCS5B01G331800 chr5A 91.847 1018 49 21 693 1699 540368500 540367506 0.000000e+00 1389.0
11 TraesCS5B01G331800 chr5A 93.023 86 3 1 4 86 540368614 540368529 3.550000e-24 122.0
12 TraesCS5B01G331800 chr5A 87.059 85 11 0 1699 1783 540367471 540367387 2.150000e-16 97.1
13 TraesCS5B01G331800 chr1B 90.095 737 59 7 1784 2520 435124655 435125377 0.000000e+00 944.0
14 TraesCS5B01G331800 chr1D 94.973 557 27 1 86 641 19875237 19874681 0.000000e+00 872.0
15 TraesCS5B01G331800 chr1D 94.624 558 29 1 87 643 250741386 250740829 0.000000e+00 863.0
16 TraesCS5B01G331800 chr3D 94.356 567 31 1 81 646 579568678 579568112 0.000000e+00 869.0
17 TraesCS5B01G331800 chr3D 94.004 567 33 1 81 646 579563166 579562600 0.000000e+00 857.0
18 TraesCS5B01G331800 chr3D 94.139 563 32 1 85 646 579557749 579557187 0.000000e+00 856.0
19 TraesCS5B01G331800 chr3D 82.992 488 69 9 1783 2264 254343121 254343600 1.870000e-116 429.0
20 TraesCS5B01G331800 chr3D 96.330 109 4 0 2516 2624 254343718 254343826 2.070000e-41 180.0
21 TraesCS5B01G331800 chr2D 94.275 559 31 1 88 645 534495009 534494451 0.000000e+00 854.0
22 TraesCS5B01G331800 chr2D 85.408 699 61 12 1854 2520 627142235 627142924 0.000000e+00 688.0
23 TraesCS5B01G331800 chr2D 93.694 111 6 1 2514 2624 627142952 627143061 5.810000e-37 165.0
24 TraesCS5B01G331800 chr4D 94.118 561 32 1 85 644 406229368 406229928 0.000000e+00 852.0
25 TraesCS5B01G331800 chr4D 94.643 112 5 1 2514 2624 437733532 437733421 3.470000e-39 172.0
26 TraesCS5B01G331800 chr7A 94.815 270 9 1 1783 2052 672472452 672472716 1.450000e-112 416.0
27 TraesCS5B01G331800 chr2B 83.333 264 38 4 1779 2042 390916742 390916999 3.380000e-59 239.0
28 TraesCS5B01G331800 chr3B 83.142 261 38 4 1782 2042 432690425 432690679 1.570000e-57 233.0
29 TraesCS5B01G331800 chr3B 93.694 111 7 0 2514 2624 432691575 432691465 1.620000e-37 167.0
30 TraesCS5B01G331800 chr7B 94.595 111 6 0 2514 2624 312431306 312431196 3.470000e-39 172.0
31 TraesCS5B01G331800 chr6A 92.793 111 8 0 2514 2624 605779479 605779589 7.520000e-36 161.0


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 TraesCS5B01G331800 chr5B 516037474 516040097 2623 True 4846.000000 4846 100.0000 1 2624 1 chr5B.!!$R1 2623
1 TraesCS5B01G331800 chr5D 94510405 94510976 571 False 856.000000 856 93.7170 77 647 1 chr5D.!!$F1 570
2 TraesCS5B01G331800 chr5D 421912344 421912898 554 False 854.000000 854 94.4340 86 641 1 chr5D.!!$F2 555
3 TraesCS5B01G331800 chr5D 426165851 426167059 1208 True 831.500000 1563 90.3665 642 1783 2 chr5D.!!$R1 1141
4 TraesCS5B01G331800 chr1A 511450303 511451144 841 False 1406.000000 1406 96.8120 1783 2624 1 chr1A.!!$F3 841
5 TraesCS5B01G331800 chr1A 38636176 38637013 837 True 1399.000000 1399 96.6860 1780 2624 1 chr1A.!!$R2 844
6 TraesCS5B01G331800 chr1A 38583101 38583939 838 True 1384.000000 1384 96.3310 1780 2624 1 chr1A.!!$R1 844
7 TraesCS5B01G331800 chr5A 540367387 540368614 1227 True 536.033333 1389 90.6430 4 1783 3 chr5A.!!$R1 1779
8 TraesCS5B01G331800 chr1B 435124655 435125377 722 False 944.000000 944 90.0950 1784 2520 1 chr1B.!!$F1 736
9 TraesCS5B01G331800 chr1D 19874681 19875237 556 True 872.000000 872 94.9730 86 641 1 chr1D.!!$R1 555
10 TraesCS5B01G331800 chr1D 250740829 250741386 557 True 863.000000 863 94.6240 87 643 1 chr1D.!!$R2 556
11 TraesCS5B01G331800 chr3D 579568112 579568678 566 True 869.000000 869 94.3560 81 646 1 chr3D.!!$R3 565
12 TraesCS5B01G331800 chr3D 579562600 579563166 566 True 857.000000 857 94.0040 81 646 1 chr3D.!!$R2 565
13 TraesCS5B01G331800 chr3D 579557187 579557749 562 True 856.000000 856 94.1390 85 646 1 chr3D.!!$R1 561
14 TraesCS5B01G331800 chr3D 254343121 254343826 705 False 304.500000 429 89.6610 1783 2624 2 chr3D.!!$F1 841
15 TraesCS5B01G331800 chr2D 534494451 534495009 558 True 854.000000 854 94.2750 88 645 1 chr2D.!!$R1 557
16 TraesCS5B01G331800 chr2D 627142235 627143061 826 False 426.500000 688 89.5510 1854 2624 2 chr2D.!!$F1 770
17 TraesCS5B01G331800 chr4D 406229368 406229928 560 False 852.000000 852 94.1180 85 644 1 chr4D.!!$F1 559

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
445 449 0.248843 AGCTCTTAGGCTCTGCACAC 59.751 55.0 0.0 0.0 38.24 3.82 F
685 697 0.251916 CTGCGGGTGGGAGAAATGTA 59.748 55.0 0.0 0.0 35.87 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1455 1488 0.176910 CGGCTCCTTCCTCTTCTTCC 59.823 60.0 0.0 0.0 0.0 3.46 R
2230 2341 0.739462 CGCGTGTTCTAATCCCTGCA 60.739 55.0 0.0 0.0 0.0 4.41 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
36 37 1.442857 CGGACTGTCACTGACGAGC 60.443 63.158 10.38 0.00 34.95 5.03
61 65 9.329913 GCAAAGTTTATTACTTACACATGACAG 57.670 33.333 0.00 0.00 46.34 3.51
76 80 1.881973 TGACAGAGAATTTGCTGCACC 59.118 47.619 0.00 0.00 35.57 5.01
77 81 0.877071 ACAGAGAATTTGCTGCACCG 59.123 50.000 0.00 0.00 35.57 4.94
78 82 0.455633 CAGAGAATTTGCTGCACCGC 60.456 55.000 0.00 0.00 0.00 5.68
79 83 1.512734 GAGAATTTGCTGCACCGCG 60.513 57.895 0.00 0.00 0.00 6.46
129 133 6.122277 ACCTATGGACGAAATCAAATCACAT 58.878 36.000 0.00 0.00 0.00 3.21
182 186 0.736053 GACCTTTTTGTGTGACGCCA 59.264 50.000 0.00 0.00 0.00 5.69
191 195 1.142097 TGTGACGCCAGACACGAAA 59.858 52.632 0.00 0.00 43.99 3.46
255 259 1.067084 CCTGATCAGCGTCGCATCT 59.933 57.895 21.09 2.24 0.00 2.90
329 333 2.732366 CACTATACAGTGTAGCGCCTG 58.268 52.381 2.29 6.84 46.03 4.85
445 449 0.248843 AGCTCTTAGGCTCTGCACAC 59.751 55.000 0.00 0.00 38.24 3.82
541 546 3.671008 ATGTAGTGTGACGCCTTTGTA 57.329 42.857 0.00 0.00 0.00 2.41
595 600 1.873698 TAGTTTCACGGGCAGTTCAC 58.126 50.000 0.00 0.00 0.00 3.18
665 670 4.025858 GCTGAGTGGCCCTGCAGA 62.026 66.667 17.39 0.00 0.00 4.26
683 695 1.002134 ACTGCGGGTGGGAGAAATG 60.002 57.895 0.00 0.00 37.56 2.32
684 696 1.002134 CTGCGGGTGGGAGAAATGT 60.002 57.895 0.00 0.00 35.87 2.71
685 697 0.251916 CTGCGGGTGGGAGAAATGTA 59.748 55.000 0.00 0.00 35.87 2.29
686 698 0.251916 TGCGGGTGGGAGAAATGTAG 59.748 55.000 0.00 0.00 0.00 2.74
687 699 0.252197 GCGGGTGGGAGAAATGTAGT 59.748 55.000 0.00 0.00 0.00 2.73
688 700 1.483415 GCGGGTGGGAGAAATGTAGTA 59.517 52.381 0.00 0.00 0.00 1.82
697 709 7.048512 GTGGGAGAAATGTAGTAGTAATGCTT 58.951 38.462 0.00 0.00 0.00 3.91
774 790 3.055719 GCGTGCTTTGCCCTGCTA 61.056 61.111 0.00 0.00 0.00 3.49
826 849 4.026300 CTCTCACGAGCCCTTCCT 57.974 61.111 0.00 0.00 0.00 3.36
831 854 2.635915 TCTCACGAGCCCTTCCTTTTTA 59.364 45.455 0.00 0.00 0.00 1.52
832 855 2.742589 CTCACGAGCCCTTCCTTTTTAC 59.257 50.000 0.00 0.00 0.00 2.01
925 948 2.416678 CGAGCAGAGGCAGCTAGG 59.583 66.667 0.00 0.00 43.58 3.02
1023 1050 2.371259 GGAGGTGGAGAGGAAGGCC 61.371 68.421 0.00 0.00 0.00 5.19
1188 1215 3.379445 TCGCCCGTCCTGTTCCTC 61.379 66.667 0.00 0.00 0.00 3.71
1221 1248 3.248171 GTCGCCTGCATCGTCGTC 61.248 66.667 8.11 0.00 0.00 4.20
1224 1251 3.248171 GCCTGCATCGTCGTCGTC 61.248 66.667 1.33 0.00 38.33 4.20
1686 1734 4.630894 TGTTCAAATCGCAGTCAGTTTT 57.369 36.364 0.00 0.00 0.00 2.43
1712 1796 4.399618 TCGCTTTCTTGATCTGTAGCTACT 59.600 41.667 23.84 4.56 0.00 2.57
1718 1802 5.756918 TCTTGATCTGTAGCTACTACTGGT 58.243 41.667 23.84 8.54 37.78 4.00
1770 1859 1.443194 GCATGCTTGCTTGGTCGTG 60.443 57.895 16.80 0.00 45.77 4.35
1897 1986 1.211949 AGTGGTGCATAACGGGCTAAT 59.788 47.619 0.00 0.00 0.00 1.73
1916 2005 7.639162 GCTAATGAGCGTATAACAGTGTATT 57.361 36.000 0.00 0.00 39.39 1.89
1917 2006 7.502339 GCTAATGAGCGTATAACAGTGTATTG 58.498 38.462 0.00 0.00 39.39 1.90
1918 2007 7.381408 GCTAATGAGCGTATAACAGTGTATTGA 59.619 37.037 0.00 0.00 39.39 2.57
1959 2048 2.203938 GGACCCCCTGTGAGGTGA 60.204 66.667 0.00 0.00 36.17 4.02
2054 2160 6.149633 CAGAAAAAGGTCCTACCAAAAATCG 58.850 40.000 0.00 0.00 41.95 3.34
2180 2290 4.329801 GCAAAGCTTTGTATACATTTGCCC 59.670 41.667 33.47 13.38 44.05 5.36
2230 2341 1.940883 TAGTTTGACCGCGCGATCCT 61.941 55.000 34.63 19.22 0.00 3.24
2498 2629 7.410800 ACGAAACAAGTTCATCGTATGTAAA 57.589 32.000 10.03 0.00 45.69 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 65 1.512734 CGCGGTGCAGCAAATTCTC 60.513 57.895 17.33 0.00 36.85 2.87
77 81 2.145905 CAATTTTGCCGCTCGACGC 61.146 57.895 0.00 0.09 41.76 5.19
78 82 0.789383 GTCAATTTTGCCGCTCGACG 60.789 55.000 0.00 0.00 43.15 5.12
79 83 0.237235 TGTCAATTTTGCCGCTCGAC 59.763 50.000 0.00 0.00 0.00 4.20
83 87 4.024977 GTCAAATTTGTCAATTTTGCCGCT 60.025 37.500 20.61 0.00 40.09 5.52
129 133 3.134574 AGTTTCACGGGCAGTTCATTA 57.865 42.857 0.00 0.00 0.00 1.90
182 186 2.108157 TGTGGCGCTTTCGTGTCT 59.892 55.556 7.64 0.00 38.14 3.41
191 195 1.300931 CACAGTGTAGTGTGGCGCT 60.301 57.895 7.64 0.00 43.56 5.92
241 245 1.080435 CACACAGATGCGACGCTGAT 61.080 55.000 22.08 6.91 36.07 2.90
242 246 1.734117 CACACAGATGCGACGCTGA 60.734 57.895 22.08 1.02 36.07 4.26
255 259 8.554835 TGATTTAGTAATTTTCGGATCACACA 57.445 30.769 0.00 0.00 0.00 3.72
329 333 0.108329 TAGTGCAACGCCTAGAAGCC 60.108 55.000 0.00 0.00 45.86 4.35
445 449 6.150140 AGACTGCCTAAAAATTGCTAAGTCAG 59.850 38.462 0.00 0.00 33.10 3.51
541 546 0.591170 CTTTTTGTGTGACGCCCGAT 59.409 50.000 0.00 0.00 0.00 4.18
595 600 3.484229 GCGGACGAAATCAAATCACAGAG 60.484 47.826 0.00 0.00 0.00 3.35
629 634 0.096976 CTCGACGCGGCAAATTTGAT 59.903 50.000 22.31 0.97 0.00 2.57
665 670 1.002134 CATTTCTCCCACCCGCAGT 60.002 57.895 0.00 0.00 0.00 4.40
672 684 6.583562 AGCATTACTACTACATTTCTCCCAC 58.416 40.000 0.00 0.00 0.00 4.61
683 695 3.001330 CAGCGGCAAAGCATTACTACTAC 59.999 47.826 1.45 0.00 40.15 2.73
684 696 3.194861 CAGCGGCAAAGCATTACTACTA 58.805 45.455 1.45 0.00 40.15 1.82
685 697 2.009774 CAGCGGCAAAGCATTACTACT 58.990 47.619 1.45 0.00 40.15 2.57
686 698 1.531883 GCAGCGGCAAAGCATTACTAC 60.532 52.381 3.18 0.00 40.72 2.73
687 699 0.732571 GCAGCGGCAAAGCATTACTA 59.267 50.000 3.18 0.00 40.72 1.82
688 700 1.508088 GCAGCGGCAAAGCATTACT 59.492 52.632 3.18 0.00 40.72 2.24
823 846 1.303806 GGGCAGGCGGTAAAAAGGA 60.304 57.895 0.00 0.00 0.00 3.36
826 849 1.605165 CCAGGGCAGGCGGTAAAAA 60.605 57.895 0.00 0.00 0.00 1.94
846 869 1.157585 TGTATAGAGGCGAGCTAGCG 58.842 55.000 12.91 1.09 38.18 4.26
850 873 4.787551 AGCTATATGTATAGAGGCGAGCT 58.212 43.478 10.48 0.00 38.30 4.09
856 879 5.361285 GGTGGTGGAGCTATATGTATAGAGG 59.639 48.000 10.48 0.00 38.30 3.69
925 948 2.127232 GCACGACGCTTTCTTGCC 60.127 61.111 0.00 0.00 42.42 4.52
961 984 3.316573 CTCTGCTCCCCGGTGGTTC 62.317 68.421 0.00 0.00 34.77 3.62
1182 1209 0.246910 GGACGTTGAGGAGGAGGAAC 59.753 60.000 0.00 0.00 0.00 3.62
1299 1326 3.916392 CTTCTTCGCCGCACCGTCT 62.916 63.158 0.00 0.00 0.00 4.18
1305 1332 2.029288 CTTCAGCTTCTTCGCCGCA 61.029 57.895 0.00 0.00 0.00 5.69
1455 1488 0.176910 CGGCTCCTTCCTCTTCTTCC 59.823 60.000 0.00 0.00 0.00 3.46
1686 1734 4.997395 AGCTACAGATCAAGAAAGCGAAAA 59.003 37.500 0.00 0.00 35.17 2.29
1712 1796 5.071250 ACCAGTTGATGTCAAAGTACCAGTA 59.929 40.000 0.00 0.00 37.63 2.74
1718 1802 5.042463 TCCAACCAGTTGATGTCAAAGTA 57.958 39.130 12.06 0.00 42.93 2.24
1767 1856 6.461698 GCAATTAACTCGTATTTCTTCACACG 59.538 38.462 0.00 0.00 35.78 4.49
1768 1857 7.295201 TGCAATTAACTCGTATTTCTTCACAC 58.705 34.615 0.00 0.00 0.00 3.82
1770 1859 7.962918 ACATGCAATTAACTCGTATTTCTTCAC 59.037 33.333 0.00 0.00 0.00 3.18
1897 1986 7.762159 TCAATTCAATACACTGTTATACGCTCA 59.238 33.333 0.00 0.00 0.00 4.26
1914 2003 5.237996 CGGTCAGATACAGCATCAATTCAAT 59.762 40.000 0.00 0.00 35.96 2.57
1915 2004 4.571984 CGGTCAGATACAGCATCAATTCAA 59.428 41.667 0.00 0.00 35.96 2.69
1916 2005 4.122046 CGGTCAGATACAGCATCAATTCA 58.878 43.478 0.00 0.00 35.96 2.57
1917 2006 3.496130 CCGGTCAGATACAGCATCAATTC 59.504 47.826 0.00 0.00 35.96 2.17
1918 2007 3.470709 CCGGTCAGATACAGCATCAATT 58.529 45.455 0.00 0.00 35.96 2.32
1953 2042 2.871022 GAGCATGACACATCATCACCTC 59.129 50.000 0.00 0.00 44.13 3.85
2054 2160 1.880027 AGTTGGTTCCTGCGAATGTTC 59.120 47.619 0.00 0.00 0.00 3.18
2230 2341 0.739462 CGCGTGTTCTAATCCCTGCA 60.739 55.000 0.00 0.00 0.00 4.41
2353 2484 2.277084 GCCCGAAGAATACACACGATT 58.723 47.619 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.