Multiple sequence alignment - TraesCS4A01G233100

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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 TraesCS4A01G233100 chr4A 100.000 3729 0 0 1 3729 542251602 542247874 0.000000e+00 6887.0
1 TraesCS4A01G233100 chr4A 96.171 2220 64 4 1527 3729 439299279 439301494 0.000000e+00 3609.0
2 TraesCS4A01G233100 chr4A 92.456 2121 154 4 548 2667 573107189 573109304 0.000000e+00 3025.0
3 TraesCS4A01G233100 chr4A 95.118 553 25 2 1 552 573096457 573097008 0.000000e+00 870.0
4 TraesCS4A01G233100 chr4A 82.424 495 52 25 2653 3124 573110759 573111241 2.090000e-107 399.0
5 TraesCS4A01G233100 chr7A 94.896 3135 141 11 4 3124 61920692 61917563 0.000000e+00 4885.0
6 TraesCS4A01G233100 chr7A 93.780 418 26 0 3312 3729 61904680 61904263 2.440000e-176 628.0
7 TraesCS4A01G233100 chr7A 92.941 170 12 0 3090 3259 61917540 61917371 8.000000e-62 248.0
8 TraesCS4A01G233100 chr7A 91.525 59 1 1 3254 3312 61904751 61904697 1.110000e-10 78.7
9 TraesCS4A01G233100 chr5D 93.962 3031 173 5 4 3029 166262227 166259202 0.000000e+00 4575.0
10 TraesCS4A01G233100 chr5D 95.455 418 19 0 3312 3729 166258641 166258224 0.000000e+00 667.0
11 TraesCS4A01G233100 chr5D 88.830 188 16 5 3090 3276 88281803 88281620 3.750000e-55 226.0
12 TraesCS4A01G233100 chr5D 88.360 189 16 5 3090 3277 166258826 166258643 4.850000e-54 222.0
13 TraesCS4A01G233100 chr5D 92.222 90 5 2 3036 3124 166258994 166258906 3.910000e-25 126.0
14 TraesCS4A01G233100 chr6D 93.740 3035 165 9 1 3029 137228901 137231916 0.000000e+00 4529.0
15 TraesCS4A01G233100 chr7B 92.836 3029 196 13 4 3028 164833389 164830378 0.000000e+00 4372.0
16 TraesCS4A01G233100 chr3B 90.909 3278 264 27 4 3276 751582617 751579369 0.000000e+00 4372.0
17 TraesCS4A01G233100 chr3B 94.139 2696 150 6 1 2693 462250808 462253498 0.000000e+00 4096.0
18 TraesCS4A01G233100 chr3B 93.768 2391 145 3 4 2393 79243362 79240975 0.000000e+00 3587.0
19 TraesCS4A01G233100 chr6A 95.907 2590 99 5 4 2593 405315 402733 0.000000e+00 4189.0
20 TraesCS4A01G233100 chr6A 93.465 658 20 3 3090 3729 402335 401683 0.000000e+00 955.0
21 TraesCS4A01G233100 chr6A 93.469 245 4 6 2892 3124 402602 402358 1.650000e-93 353.0
22 TraesCS4A01G233100 chr6B 88.377 1910 160 31 1435 3309 423110549 423108667 0.000000e+00 2241.0
23 TraesCS4A01G233100 chr6B 93.303 657 22 3 3090 3729 3517216 3516565 0.000000e+00 950.0
24 TraesCS4A01G233100 chr6B 94.931 434 11 5 2702 3124 3517672 3517239 0.000000e+00 669.0
25 TraesCS4A01G233100 chr2D 86.212 747 68 8 3008 3729 465845970 465846706 0.000000e+00 776.0
26 TraesCS4A01G233100 chr2D 85.564 665 48 16 3093 3729 264000362 263999718 0.000000e+00 652.0
27 TraesCS4A01G233100 chr3D 87.690 658 52 6 3091 3727 161346497 161347146 0.000000e+00 739.0
28 TraesCS4A01G233100 chr3D 81.613 310 41 9 3008 3312 501958091 501958389 3.720000e-60 243.0
29 TraesCS4A01G233100 chr4D 90.778 553 27 8 3194 3729 437765886 437766431 0.000000e+00 717.0
30 TraesCS4A01G233100 chr1A 87.197 578 36 10 3175 3729 84820882 84821444 1.140000e-174 623.0
31 TraesCS4A01G233100 chr2B 89.686 223 16 4 3090 3312 666046529 666046314 1.020000e-70 278.0
32 TraesCS4A01G233100 chr1B 83.111 225 27 7 3091 3312 44039147 44039363 1.060000e-45 195.0
33 TraesCS4A01G233100 chr5B 78.400 250 35 15 3030 3269 336150028 336150268 1.080000e-30 145.0


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 TraesCS4A01G233100 chr4A 542247874 542251602 3728 True 6887.000000 6887 100.000000 1 3729 1 chr4A.!!$R1 3728
1 TraesCS4A01G233100 chr4A 439299279 439301494 2215 False 3609.000000 3609 96.171000 1527 3729 1 chr4A.!!$F1 2202
2 TraesCS4A01G233100 chr4A 573107189 573111241 4052 False 1712.000000 3025 87.440000 548 3124 2 chr4A.!!$F3 2576
3 TraesCS4A01G233100 chr4A 573096457 573097008 551 False 870.000000 870 95.118000 1 552 1 chr4A.!!$F2 551
4 TraesCS4A01G233100 chr7A 61917371 61920692 3321 True 2566.500000 4885 93.918500 4 3259 2 chr7A.!!$R2 3255
5 TraesCS4A01G233100 chr5D 166258224 166262227 4003 True 1397.500000 4575 92.499750 4 3729 4 chr5D.!!$R2 3725
6 TraesCS4A01G233100 chr6D 137228901 137231916 3015 False 4529.000000 4529 93.740000 1 3029 1 chr6D.!!$F1 3028
7 TraesCS4A01G233100 chr7B 164830378 164833389 3011 True 4372.000000 4372 92.836000 4 3028 1 chr7B.!!$R1 3024
8 TraesCS4A01G233100 chr3B 751579369 751582617 3248 True 4372.000000 4372 90.909000 4 3276 1 chr3B.!!$R2 3272
9 TraesCS4A01G233100 chr3B 462250808 462253498 2690 False 4096.000000 4096 94.139000 1 2693 1 chr3B.!!$F1 2692
10 TraesCS4A01G233100 chr3B 79240975 79243362 2387 True 3587.000000 3587 93.768000 4 2393 1 chr3B.!!$R1 2389
11 TraesCS4A01G233100 chr6A 401683 405315 3632 True 1832.333333 4189 94.280333 4 3729 3 chr6A.!!$R1 3725
12 TraesCS4A01G233100 chr6B 423108667 423110549 1882 True 2241.000000 2241 88.377000 1435 3309 1 chr6B.!!$R1 1874
13 TraesCS4A01G233100 chr6B 3516565 3517672 1107 True 809.500000 950 94.117000 2702 3729 2 chr6B.!!$R2 1027
14 TraesCS4A01G233100 chr2D 465845970 465846706 736 False 776.000000 776 86.212000 3008 3729 1 chr2D.!!$F1 721
15 TraesCS4A01G233100 chr2D 263999718 264000362 644 True 652.000000 652 85.564000 3093 3729 1 chr2D.!!$R1 636
16 TraesCS4A01G233100 chr3D 161346497 161347146 649 False 739.000000 739 87.690000 3091 3727 1 chr3D.!!$F1 636
17 TraesCS4A01G233100 chr4D 437765886 437766431 545 False 717.000000 717 90.778000 3194 3729 1 chr4D.!!$F1 535
18 TraesCS4A01G233100 chr1A 84820882 84821444 562 False 623.000000 623 87.197000 3175 3729 1 chr1A.!!$F1 554

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
869 872 0.234884 GTCAGCGTGTACACAAAGGC 59.765 55.0 24.98 18.99 0.0 4.35 F
1897 1905 0.623723 GTTATCCACCTTCCAGCCCA 59.376 55.0 0.00 0.00 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2330 2339 0.321653 GTGAATTCGGTCTGGCCACT 60.322 55.0 0.00 0.00 36.97 4.00 R
3145 4749 0.320247 CGCTCCATACCCTCATGAGC 60.320 60.0 17.76 2.42 0.00 4.26 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
539 542 5.215160 CAAAGTGAAAGGGAAACATCTTCG 58.785 41.667 0.00 0.00 0.00 3.79
869 872 0.234884 GTCAGCGTGTACACAAAGGC 59.765 55.000 24.98 18.99 0.00 4.35
931 934 0.905337 CTCGGACCAAGGGGAGTTCT 60.905 60.000 0.00 0.00 38.05 3.01
1066 1070 7.491372 GCATCTCGAATGGTCCGAATTATAATA 59.509 37.037 0.00 0.00 35.48 0.98
1067 1071 9.025020 CATCTCGAATGGTCCGAATTATAATAG 57.975 37.037 0.00 0.00 35.48 1.73
1208 1212 6.346096 CAGCCATCAAATTGAATGGAAAGAT 58.654 36.000 20.70 5.41 36.31 2.40
1225 1229 6.069088 TGGAAAGATAATTATGGACCACTGGT 60.069 38.462 1.78 0.00 39.44 4.00
1275 1279 8.236586 TCAAATGATGAACCTTTAATCAACTCG 58.763 33.333 0.00 0.00 34.30 4.18
1421 1428 5.674525 TGCTACTCAACCCATGAAATCTAG 58.325 41.667 0.00 0.00 37.67 2.43
1529 1537 1.926511 GCTGCAGCAAAGTGGCGTAT 61.927 55.000 33.36 0.00 41.59 3.06
1641 1649 5.728255 CGGACAGAAGCGTAGAAATTTATG 58.272 41.667 0.00 0.00 0.00 1.90
1660 1668 1.375908 GCCCACTCATGCTGACGAA 60.376 57.895 0.00 0.00 0.00 3.85
1843 1851 5.648092 CCTTGGTGACCTTTTCGATTTATCT 59.352 40.000 2.11 0.00 0.00 1.98
1880 1888 2.186826 GGCGAGTGTGGCACAAGTT 61.187 57.895 23.90 11.13 44.16 2.66
1897 1905 0.623723 GTTATCCACCTTCCAGCCCA 59.376 55.000 0.00 0.00 0.00 5.36
2076 2085 1.200020 CCAAGAAATTCGCCACTCACC 59.800 52.381 0.00 0.00 0.00 4.02
2183 2192 2.176045 TCATAGTGAAACGAGCCCTCA 58.824 47.619 0.00 0.00 45.86 3.86
2398 2407 9.630098 CATGTTGTTGCTGAAATAGAACTTAAT 57.370 29.630 0.00 0.00 0.00 1.40
2458 2468 3.279434 GGACTTATCTGCCGTGGAAAAT 58.721 45.455 0.00 0.00 0.00 1.82
2886 4390 3.521560 CATGATGTGTTAGTACGCCAGT 58.478 45.455 0.00 0.00 33.79 4.00
3145 4749 0.322997 TTGGTCTGCCCCGGTTTATG 60.323 55.000 0.00 0.00 0.00 1.90
3149 4753 1.077787 CTGCCCCGGTTTATGCTCA 60.078 57.895 0.00 0.00 0.00 4.26
3178 4782 1.502163 GGAGCGCCCTCGATGATTTG 61.502 60.000 2.29 0.00 39.06 2.32
3183 4787 2.096819 GCGCCCTCGATGATTTGTTTTA 59.903 45.455 0.00 0.00 38.10 1.52
3253 5278 4.823442 TGTGTCCTAGTTTAGACTCGTGAA 59.177 41.667 0.00 0.00 37.33 3.18
3413 5460 6.643770 CGCCGCTAGAATAAACCTCTTTTATA 59.356 38.462 0.00 0.00 39.14 0.98
3456 5504 9.631257 ATTTTGGTTCAAATTTTCCTTTCATCT 57.369 25.926 0.00 0.00 33.19 2.90
3548 5596 1.369625 GTTTGTCGAATGCTCGGGAT 58.630 50.000 0.00 0.00 45.49 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.005740 ACATTAGAAGCATGTCAAGCAGAA 58.994 37.500 2.46 0.00 27.99 3.02
69 70 9.488762 TTTGAAGGTTCTAGGTCATCTATAGAA 57.511 33.333 6.52 0.00 34.10 2.10
539 542 2.346803 TCGGCAGTTGCTTAACATCTC 58.653 47.619 3.88 0.00 41.70 2.75
667 670 2.347731 CCCGACTAAGTTCTTTGGAGC 58.652 52.381 0.00 0.00 0.00 4.70
869 872 3.181517 CGCATATGCAACTCCAATATCCG 60.182 47.826 26.52 2.00 42.21 4.18
931 934 3.129113 TGCGCATCGTTAAGAAGGTACTA 59.871 43.478 5.66 0.00 38.49 1.82
1084 1088 1.345415 GTACTCCTCCCCACGTTTCAA 59.655 52.381 0.00 0.00 0.00 2.69
1421 1428 3.526534 GCAGACCATTAACTCACCTCTC 58.473 50.000 0.00 0.00 0.00 3.20
1505 1513 1.952296 GCCACTTTGCTGCAGCTATAT 59.048 47.619 36.61 18.81 42.66 0.86
1507 1515 1.651240 CGCCACTTTGCTGCAGCTAT 61.651 55.000 36.61 18.03 42.66 2.97
1508 1516 2.327343 CGCCACTTTGCTGCAGCTA 61.327 57.895 36.61 28.48 42.66 3.32
1509 1517 3.667282 CGCCACTTTGCTGCAGCT 61.667 61.111 36.61 16.43 42.66 4.24
1529 1537 3.119531 CCAACTGCAACAACAGACTTTGA 60.120 43.478 0.00 0.00 40.25 2.69
1660 1668 0.415429 TGAAGGGGAGCCTCTCTTCT 59.585 55.000 20.39 0.00 37.21 2.85
1843 1851 3.491964 CGCCAAAGGTATAATCCTCGACA 60.492 47.826 0.00 0.00 36.74 4.35
1880 1888 0.988145 CCTGGGCTGGAAGGTGGATA 60.988 60.000 0.00 0.00 0.00 2.59
1897 1905 1.226746 GCACAACTTTAGTCGCACCT 58.773 50.000 0.00 0.00 0.00 4.00
2076 2085 0.987294 AACCATCACCTCAGGGTCTG 59.013 55.000 0.00 0.00 45.41 3.51
2183 2192 2.561858 GGGTAGAGTCGTTCAGTCCTTT 59.438 50.000 0.00 0.00 0.00 3.11
2330 2339 0.321653 GTGAATTCGGTCTGGCCACT 60.322 55.000 0.00 0.00 36.97 4.00
2398 2407 6.495181 TGGAAACTTCATGGCCAAACTTAATA 59.505 34.615 10.96 0.00 0.00 0.98
2406 2415 1.969923 CCTTGGAAACTTCATGGCCAA 59.030 47.619 10.96 0.00 37.13 4.52
2458 2468 2.224744 TGCCTCCATTTCAGTGCACTTA 60.225 45.455 18.94 6.64 0.00 2.24
2886 4390 2.839486 AGGATGCTTCAACGTCAAGA 57.161 45.000 10.63 0.00 0.00 3.02
3085 4632 3.006967 ACGAGTCTAAACTGTGGCAGATT 59.993 43.478 2.91 0.24 35.28 2.40
3145 4749 0.320247 CGCTCCATACCCTCATGAGC 60.320 60.000 17.76 2.42 0.00 4.26
3149 4753 2.520536 GGGCGCTCCATACCCTCAT 61.521 63.158 7.64 0.00 40.75 2.90
3183 4787 6.985188 ACGAGTATAAACTGTGATGCAAAT 57.015 33.333 0.00 0.00 35.56 2.32
3456 5504 1.538075 TCCTATGAATATCGCGCGACA 59.462 47.619 37.37 27.38 0.00 4.35
3548 5596 6.291648 CTTGAGGCATATCAAGCTAGGATA 57.708 41.667 11.22 9.66 46.95 2.59


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

AutoCloner maintained by Alex Coulton.