Multiple sequence alignment - TraesCS1D01G033600

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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 TraesCS1D01G033600 chr1D 100.000 3760 0 0 1 3760 13729514 13725755 0.000000e+00 6944.0
1 TraesCS1D01G033600 chr1D 99.174 2664 21 1 510 3173 13818154 13815492 0.000000e+00 4796.0
2 TraesCS1D01G033600 chr1D 97.363 493 13 0 3268 3760 13815489 13814997 0.000000e+00 839.0
3 TraesCS1D01G033600 chr1D 91.165 532 41 5 3230 3760 349531740 349532266 0.000000e+00 717.0
4 TraesCS1D01G033600 chr1D 93.681 364 18 3 2853 3215 13721548 13721189 1.190000e-149 540.0
5 TraesCS1D01G033600 chr1D 93.681 364 18 3 2853 3215 13810307 13809948 1.190000e-149 540.0
6 TraesCS1D01G033600 chr1D 86.053 380 23 15 58 429 13508954 13508597 7.620000e-102 381.0
7 TraesCS1D01G033600 chr1D 88.925 307 28 4 125 425 13819065 13818759 1.280000e-99 374.0
8 TraesCS1D01G033600 chr1D 87.692 260 26 3 125 379 13975430 13975172 7.900000e-77 298.0
9 TraesCS1D01G033600 chr1D 87.692 260 26 3 125 379 14007246 14006988 7.900000e-77 298.0
10 TraesCS1D01G033600 chr1D 95.455 88 4 0 1 88 13848978 13848891 1.410000e-29 141.0
11 TraesCS1D01G033600 chr1D 95.455 88 4 0 1 88 13886114 13886027 1.410000e-29 141.0
12 TraesCS1D01G033600 chr1D 95.455 88 4 0 1 88 13996710 13996623 1.410000e-29 141.0
13 TraesCS1D01G033600 chr1D 96.429 84 3 0 1 84 13965490 13965407 5.060000e-29 139.0
14 TraesCS1D01G033600 chr1D 97.826 46 1 0 422 467 13818206 13818161 3.110000e-11 80.5
15 TraesCS1D01G033600 chr1B 92.569 2799 154 24 424 3215 20048333 20045582 0.000000e+00 3967.0
16 TraesCS1D01G033600 chr1B 93.911 2447 131 12 424 2860 19620563 19618125 0.000000e+00 3677.0
17 TraesCS1D01G033600 chr1B 93.666 2447 138 11 424 2860 19951993 19949554 0.000000e+00 3644.0
18 TraesCS1D01G033600 chr1B 93.625 2447 138 12 424 2860 19840116 19837678 0.000000e+00 3639.0
19 TraesCS1D01G033600 chr1B 93.295 2461 132 16 424 2860 19720522 19718071 0.000000e+00 3600.0
20 TraesCS1D01G033600 chr1B 93.053 2447 143 13 424 2860 19781143 19778714 0.000000e+00 3552.0
21 TraesCS1D01G033600 chr1B 92.638 2119 119 22 424 2534 20554706 20556795 0.000000e+00 3014.0
22 TraesCS1D01G033600 chr1B 94.442 1925 90 11 946 2860 19892022 19890105 0.000000e+00 2946.0
23 TraesCS1D01G033600 chr1B 90.789 532 45 4 3230 3760 338675575 338675047 0.000000e+00 708.0
24 TraesCS1D01G033600 chr1B 93.855 358 19 2 2853 3209 20557041 20557396 1.540000e-148 536.0
25 TraesCS1D01G033600 chr1B 89.078 412 25 10 24 429 20553947 20554344 9.380000e-136 494.0
26 TraesCS1D01G033600 chr1B 90.782 358 30 2 2853 3209 19890084 19889729 3.400000e-130 475.0
27 TraesCS1D01G033600 chr1B 90.503 358 31 2 2853 3209 19949533 19949178 1.580000e-128 470.0
28 TraesCS1D01G033600 chr1B 90.223 358 32 2 2853 3209 19778693 19778338 7.360000e-127 464.0
29 TraesCS1D01G033600 chr1B 85.323 402 23 14 28 423 19952629 19952258 2.120000e-102 383.0
30 TraesCS1D01G033600 chr1B 84.759 374 22 13 56 423 19621172 19620828 3.600000e-90 342.0
31 TraesCS1D01G033600 chr1B 84.759 374 22 15 56 423 19840725 19840381 3.600000e-90 342.0
32 TraesCS1D01G033600 chr1A 93.423 2296 97 7 570 2864 14792339 14790097 0.000000e+00 3354.0
33 TraesCS1D01G033600 chr1A 97.454 432 7 2 1 429 14795825 14795395 0.000000e+00 734.0
34 TraesCS1D01G033600 chr1A 92.308 364 25 2 2853 3215 14790079 14789718 7.200000e-142 514.0
35 TraesCS1D01G033600 chr1A 87.013 231 28 1 146 374 14852320 14852090 3.730000e-65 259.0
36 TraesCS1D01G033600 chr1A 97.959 98 2 0 477 574 14795047 14794950 1.800000e-38 171.0
37 TraesCS1D01G033600 chr5D 92.045 528 41 1 3230 3757 561438402 561438928 0.000000e+00 741.0
38 TraesCS1D01G033600 chr5D 89.908 545 48 7 3220 3760 431109471 431110012 0.000000e+00 695.0
39 TraesCS1D01G033600 chr2B 91.525 531 42 3 3230 3760 239686424 239685897 0.000000e+00 728.0
40 TraesCS1D01G033600 chr3B 91.337 531 46 0 3230 3760 620688648 620688118 0.000000e+00 726.0
41 TraesCS1D01G033600 chr7B 90.019 531 52 1 3230 3760 189188074 189188603 0.000000e+00 686.0
42 TraesCS1D01G033600 chr6D 89.831 531 54 0 3230 3760 318128190 318127660 0.000000e+00 682.0


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 TraesCS1D01G033600 chr1D 13725755 13729514 3759 True 6944.000 6944 100.000000 1 3760 1 chr1D.!!$R3 3759
1 TraesCS1D01G033600 chr1D 13814997 13819065 4068 True 1522.375 4796 95.822000 125 3760 4 chr1D.!!$R11 3635
2 TraesCS1D01G033600 chr1D 349531740 349532266 526 False 717.000 717 91.165000 3230 3760 1 chr1D.!!$F1 530
3 TraesCS1D01G033600 chr1B 20045582 20048333 2751 True 3967.000 3967 92.569000 424 3215 1 chr1B.!!$R2 2791
4 TraesCS1D01G033600 chr1B 19718071 19720522 2451 True 3600.000 3600 93.295000 424 2860 1 chr1B.!!$R1 2436
5 TraesCS1D01G033600 chr1B 19618125 19621172 3047 True 2009.500 3677 89.335000 56 2860 2 chr1B.!!$R4 2804
6 TraesCS1D01G033600 chr1B 19778338 19781143 2805 True 2008.000 3552 91.638000 424 3209 2 chr1B.!!$R5 2785
7 TraesCS1D01G033600 chr1B 19837678 19840725 3047 True 1990.500 3639 89.192000 56 2860 2 chr1B.!!$R6 2804
8 TraesCS1D01G033600 chr1B 19889729 19892022 2293 True 1710.500 2946 92.612000 946 3209 2 chr1B.!!$R7 2263
9 TraesCS1D01G033600 chr1B 19949178 19952629 3451 True 1499.000 3644 89.830667 28 3209 3 chr1B.!!$R8 3181
10 TraesCS1D01G033600 chr1B 20553947 20557396 3449 False 1348.000 3014 91.857000 24 3209 3 chr1B.!!$F1 3185
11 TraesCS1D01G033600 chr1B 338675047 338675575 528 True 708.000 708 90.789000 3230 3760 1 chr1B.!!$R3 530
12 TraesCS1D01G033600 chr1A 14789718 14795825 6107 True 1193.250 3354 95.286000 1 3215 4 chr1A.!!$R2 3214
13 TraesCS1D01G033600 chr5D 561438402 561438928 526 False 741.000 741 92.045000 3230 3757 1 chr5D.!!$F2 527
14 TraesCS1D01G033600 chr5D 431109471 431110012 541 False 695.000 695 89.908000 3220 3760 1 chr5D.!!$F1 540
15 TraesCS1D01G033600 chr2B 239685897 239686424 527 True 728.000 728 91.525000 3230 3760 1 chr2B.!!$R1 530
16 TraesCS1D01G033600 chr3B 620688118 620688648 530 True 726.000 726 91.337000 3230 3760 1 chr3B.!!$R1 530
17 TraesCS1D01G033600 chr7B 189188074 189188603 529 False 686.000 686 90.019000 3230 3760 1 chr7B.!!$F1 530
18 TraesCS1D01G033600 chr6D 318127660 318128190 530 True 682.000 682 89.831000 3230 3760 1 chr6D.!!$R1 530

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
504 1183 0.963962 TCGTCTACCACCCTGTGTTC 59.036 55.0 0.00 0.0 0.0 3.18 F
1962 5276 2.039879 GGTTGAGGAGAAAGTTGGCCTA 59.960 50.0 3.32 0.0 0.0 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 5394 1.978580 CTTACCCTCTCCAGTGGTTGT 59.021 52.381 9.54 3.34 33.55 3.32 R
2976 6361 0.935898 CGAGAGCATGCTCAACATCC 59.064 55.000 40.91 23.46 44.99 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
255 261 4.268359 TGTTCACCATGCTATGTTATGCA 58.732 39.130 0.00 0.00 43.67 3.96
449 1122 3.334691 CTTAGATGGAACTCGGCAAACA 58.665 45.455 0.00 0.00 0.00 2.83
504 1183 0.963962 TCGTCTACCACCCTGTGTTC 59.036 55.000 0.00 0.00 0.00 3.18
1962 5276 2.039879 GGTTGAGGAGAAAGTTGGCCTA 59.960 50.000 3.32 0.00 0.00 3.93
2297 5612 5.385198 TGGCTGTTCTGAGTTTCCTTTATT 58.615 37.500 0.00 0.00 0.00 1.40
2410 5728 7.599998 ACCTCGTGTATTTTAGTAACGTTCAAT 59.400 33.333 2.82 0.00 35.79 2.57
2714 6034 6.479990 TCAGGACATTATTTTGATCAGCGTAG 59.520 38.462 0.00 0.00 0.00 3.51
2802 6122 5.703978 TTGTACTGTTTGCATGCATACTT 57.296 34.783 32.04 23.69 0.00 2.24
2976 6361 4.014406 GGACTTGGGTGTTATGGTTTAGG 58.986 47.826 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.349503 TGGCCGGCTGCAACATCT 62.350 61.111 28.56 0.00 43.89 2.90
255 261 2.890311 TGAAACCATGACCGCTTGATTT 59.110 40.909 0.00 0.00 0.00 2.17
480 1159 0.959372 CAGGGTGGTAGACGAGACGT 60.959 60.000 0.00 0.00 45.10 4.34
504 1183 3.303406 ACGTAAAAAGGAGAACTCGTCG 58.697 45.455 0.00 0.00 0.00 5.12
1962 5276 2.680913 GCGCATGCGTTCCTTGTCT 61.681 57.895 37.54 0.00 42.09 3.41
2080 5394 1.978580 CTTACCCTCTCCAGTGGTTGT 59.021 52.381 9.54 3.34 33.55 3.32
2297 5612 5.221541 ACACAACAAAAAGTGAAAACCAGGA 60.222 36.000 0.00 0.00 39.03 3.86
2563 5883 5.171339 AGCATCCCAGACATATGGATTAC 57.829 43.478 7.80 0.00 43.57 1.89
2759 6079 0.798776 CACAAACGGATGGAGCTGTC 59.201 55.000 0.00 0.00 0.00 3.51
2802 6122 3.440173 GTCTCGATTGATGGCTGGAAAAA 59.560 43.478 0.00 0.00 0.00 1.94
2937 6321 2.021457 GTCCGTCATAATTTGTGGGGG 58.979 52.381 0.00 0.00 0.00 5.40
2976 6361 0.935898 CGAGAGCATGCTCAACATCC 59.064 55.000 40.91 23.46 44.99 3.51


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

AutoCloner maintained by Alex Coulton.