Multiple sequence alignment - TraesCS1D01G193600

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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 TraesCS1D01G193600 chr1D 100.000 3587 0 0 1 3587 269428741 269425155 0.000000e+00 6625.0
1 TraesCS1D01G193600 chr1D 98.539 616 9 0 1 616 275776878 275777493 0.000000e+00 1088.0
2 TraesCS1D01G193600 chr4D 97.527 2992 55 5 615 3587 123348743 123351734 0.000000e+00 5097.0
3 TraesCS1D01G193600 chr4D 97.061 2994 67 4 615 3587 134978045 134981038 0.000000e+00 5022.0
4 TraesCS1D01G193600 chr4D 96.150 2987 94 7 615 3587 240996149 240993170 0.000000e+00 4859.0
5 TraesCS1D01G193600 chr4D 97.230 1011 24 4 2581 3587 123561662 123562672 0.000000e+00 1709.0
6 TraesCS1D01G193600 chr4D 94.925 1005 40 7 2586 3587 450897577 450896581 0.000000e+00 1563.0
7 TraesCS1D01G193600 chr4D 98.864 616 7 0 1 616 123348063 123348678 0.000000e+00 1099.0
8 TraesCS1D01G193600 chr4D 99.242 132 1 0 2249 2380 245098045 245097914 4.630000e-59 239.0
9 TraesCS1D01G193600 chr4D 89.024 164 3 1 2463 2611 18175130 18174967 4.730000e-44 189.0
10 TraesCS1D01G193600 chr4D 95.556 45 2 0 2416 2460 245097914 245097870 4.970000e-09 73.1
11 TraesCS1D01G193600 chr6D 97.211 2976 75 4 616 3587 370021144 370024115 0.000000e+00 5029.0
12 TraesCS1D01G193600 chr6D 98.864 616 7 0 1 616 370020461 370021076 0.000000e+00 1099.0
13 TraesCS1D01G193600 chr6D 98.539 616 9 0 1 616 369908046 369907431 0.000000e+00 1088.0
14 TraesCS1D01G193600 chr5D 97.090 2990 67 6 615 3587 301053022 301056008 0.000000e+00 5022.0
15 TraesCS1D01G193600 chr3D 95.567 3000 101 10 615 3587 308560030 308557036 0.000000e+00 4774.0
16 TraesCS1D01G193600 chr7B 97.917 2688 40 6 615 3286 742950116 742947429 0.000000e+00 4639.0
17 TraesCS1D01G193600 chr7B 95.250 2779 120 9 615 3383 247471736 247474512 0.000000e+00 4390.0
18 TraesCS1D01G193600 chr7B 98.864 616 7 0 1 616 742950797 742950182 0.000000e+00 1099.0
19 TraesCS1D01G193600 chr7A 97.952 2685 37 8 615 3283 60083560 60086242 0.000000e+00 4638.0
20 TraesCS1D01G193600 chr7A 97.879 2688 41 6 615 3286 60170145 60167458 0.000000e+00 4634.0
21 TraesCS1D01G193600 chr5A 97.877 2685 41 6 615 3283 16543176 16545860 0.000000e+00 4628.0
22 TraesCS1D01G193600 chr5A 97.840 2685 41 7 615 3283 420184325 420187008 0.000000e+00 4621.0
23 TraesCS1D01G193600 chr5A 98.539 616 9 0 1 616 238873944 238874559 0.000000e+00 1088.0
24 TraesCS1D01G193600 chr2A 97.877 2685 41 2 615 3283 755479171 755481855 0.000000e+00 4628.0
25 TraesCS1D01G193600 chr2A 99.188 616 5 0 1 616 755478489 755479104 0.000000e+00 1110.0
26 TraesCS1D01G193600 chr6A 97.255 2696 57 3 615 3293 155855921 155858616 0.000000e+00 4553.0
27 TraesCS1D01G193600 chr7D 98.864 616 7 0 1 616 579039711 579040326 0.000000e+00 1099.0
28 TraesCS1D01G193600 chr1B 98.701 616 8 0 1 616 583563607 583562992 0.000000e+00 1094.0
29 TraesCS1D01G193600 chr6B 92.357 314 18 2 3279 3587 606986076 606986388 3.290000e-120 442.0


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 TraesCS1D01G193600 chr1D 269425155 269428741 3586 True 6625 6625 100.0000 1 3587 1 chr1D.!!$R1 3586
1 TraesCS1D01G193600 chr1D 275776878 275777493 615 False 1088 1088 98.5390 1 616 1 chr1D.!!$F1 615
2 TraesCS1D01G193600 chr4D 134978045 134981038 2993 False 5022 5022 97.0610 615 3587 1 chr4D.!!$F2 2972
3 TraesCS1D01G193600 chr4D 240993170 240996149 2979 True 4859 4859 96.1500 615 3587 1 chr4D.!!$R2 2972
4 TraesCS1D01G193600 chr4D 123348063 123351734 3671 False 3098 5097 98.1955 1 3587 2 chr4D.!!$F3 3586
5 TraesCS1D01G193600 chr4D 123561662 123562672 1010 False 1709 1709 97.2300 2581 3587 1 chr4D.!!$F1 1006
6 TraesCS1D01G193600 chr4D 450896581 450897577 996 True 1563 1563 94.9250 2586 3587 1 chr4D.!!$R3 1001
7 TraesCS1D01G193600 chr6D 370020461 370024115 3654 False 3064 5029 98.0375 1 3587 2 chr6D.!!$F1 3586
8 TraesCS1D01G193600 chr6D 369907431 369908046 615 True 1088 1088 98.5390 1 616 1 chr6D.!!$R1 615
9 TraesCS1D01G193600 chr5D 301053022 301056008 2986 False 5022 5022 97.0900 615 3587 1 chr5D.!!$F1 2972
10 TraesCS1D01G193600 chr3D 308557036 308560030 2994 True 4774 4774 95.5670 615 3587 1 chr3D.!!$R1 2972
11 TraesCS1D01G193600 chr7B 247471736 247474512 2776 False 4390 4390 95.2500 615 3383 1 chr7B.!!$F1 2768
12 TraesCS1D01G193600 chr7B 742947429 742950797 3368 True 2869 4639 98.3905 1 3286 2 chr7B.!!$R1 3285
13 TraesCS1D01G193600 chr7A 60083560 60086242 2682 False 4638 4638 97.9520 615 3283 1 chr7A.!!$F1 2668
14 TraesCS1D01G193600 chr7A 60167458 60170145 2687 True 4634 4634 97.8790 615 3286 1 chr7A.!!$R1 2671
15 TraesCS1D01G193600 chr5A 16543176 16545860 2684 False 4628 4628 97.8770 615 3283 1 chr5A.!!$F1 2668
16 TraesCS1D01G193600 chr5A 420184325 420187008 2683 False 4621 4621 97.8400 615 3283 1 chr5A.!!$F3 2668
17 TraesCS1D01G193600 chr5A 238873944 238874559 615 False 1088 1088 98.5390 1 616 1 chr5A.!!$F2 615
18 TraesCS1D01G193600 chr2A 755478489 755481855 3366 False 2869 4628 98.5325 1 3283 2 chr2A.!!$F1 3282
19 TraesCS1D01G193600 chr6A 155855921 155858616 2695 False 4553 4553 97.2550 615 3293 1 chr6A.!!$F1 2678
20 TraesCS1D01G193600 chr7D 579039711 579040326 615 False 1099 1099 98.8640 1 616 1 chr7D.!!$F1 615
21 TraesCS1D01G193600 chr1B 583562992 583563607 615 True 1094 1094 98.7010 1 616 1 chr1B.!!$R1 615

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
896 965 0.036388 GTCTTTGTCCGAGATGCCCA 60.036 55.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2681 2769 0.107945 CCTGAACTACTGGAGCAGCC 60.108 60.0 0.0 0.0 39.52 4.85 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
198 199 8.849543 AAGTAGTGGGTTATTGGAAGTATAGA 57.150 34.615 0.00 0.00 0.00 1.98
297 298 5.589192 GATGAAAGCAATGGGAAATGAGAG 58.411 41.667 0.00 0.00 0.00 3.20
360 361 4.912766 CGAGAGCATAAAGAACGGTAGATC 59.087 45.833 0.00 0.00 0.00 2.75
458 459 7.888514 AATTCCACTATCAATATGGGTAGGA 57.111 36.000 2.38 0.00 34.03 2.94
585 586 1.353091 GGGTCTGGTCAGGAAGACTT 58.647 55.000 3.11 0.00 46.72 3.01
896 965 0.036388 GTCTTTGTCCGAGATGCCCA 60.036 55.000 0.00 0.00 0.00 5.36
941 1010 6.952935 ATCGAGATTGTGTGAAGTAAAGAC 57.047 37.500 0.00 0.00 0.00 3.01
1019 1088 4.366267 AGTATGGAATTCTCACCCAGAGT 58.634 43.478 5.23 0.00 44.98 3.24
1637 1706 3.510388 TGTTGCGATTGGACAAAAACA 57.490 38.095 0.00 0.00 0.00 2.83
2046 2115 4.385643 CCCACCAATGTGATCTCCATTACT 60.386 45.833 9.80 0.00 45.76 2.24
2111 2180 6.537660 GGAATTAGACCAGCTATTAACGTTGT 59.462 38.462 11.99 1.90 0.00 3.32
2385 2457 3.638627 TCTGTGATCGAATGCCACTAGAT 59.361 43.478 0.00 0.00 0.00 1.98
2567 2654 5.942826 CAGATGTAGGAAGAAGGCTTTTCTT 59.057 40.000 13.98 13.98 41.08 2.52
2671 2758 0.972983 GCTGAGAGTCTACCCCAGCA 60.973 60.000 20.88 1.80 46.68 4.41
2672 2759 1.110442 CTGAGAGTCTACCCCAGCAG 58.890 60.000 0.00 0.00 0.00 4.24
3324 3426 5.818136 TTGATTTTGACGATTGGATCTCC 57.182 39.130 0.00 0.00 0.00 3.71
3416 3520 2.430694 AGTCTAAGCGACATATGGCACA 59.569 45.455 9.77 0.00 45.32 4.57
3500 3611 6.884280 GGGGGACTTTTCATAGTTATCATG 57.116 41.667 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
198 199 7.004086 TCCTTGGTGACACTTGAGAAATAATT 58.996 34.615 5.39 0.00 42.67 1.40
297 298 4.901868 TGTACCAGTAATCAAACCCAGAC 58.098 43.478 0.00 0.00 0.00 3.51
360 361 3.347216 CTTGACCTACCAGTTGAATGGG 58.653 50.000 2.29 0.00 45.25 4.00
585 586 0.617935 TGGCCGTGAGAATGATTCCA 59.382 50.000 0.75 0.00 0.00 3.53
896 965 8.739039 TCGATTTGAATTATCATTTGGTGAACT 58.261 29.630 0.00 0.00 40.97 3.01
941 1010 5.532557 AGAAATCCGCTTTCAAGAAAAAGG 58.467 37.500 10.22 8.70 44.82 3.11
1030 1099 7.592164 GGTCATTCTACTTTCTAATAGAGTCGC 59.408 40.741 0.00 0.00 0.00 5.19
1637 1706 2.037251 ACTAATTGTGCCACAGTCGAGT 59.963 45.455 0.00 0.00 0.00 4.18
2046 2115 7.232330 TCTGTTTCCAAACATATTTGTCCATCA 59.768 33.333 5.35 0.00 46.71 3.07
2111 2180 0.376152 GACGCGACTGACGGATAAGA 59.624 55.000 15.93 0.00 42.83 2.10
2385 2457 8.821686 TGGCCTTTTCATATTGAGAAATTCTA 57.178 30.769 3.32 0.00 35.17 2.10
2406 2478 8.594550 TCAGGATTAATAGTACTTAGAATGGCC 58.405 37.037 0.00 0.00 0.00 5.36
2567 2654 1.272425 CCTATTGGGGTTCAGTTGGCA 60.272 52.381 0.00 0.00 0.00 4.92
2681 2769 0.107945 CCTGAACTACTGGAGCAGCC 60.108 60.000 0.00 0.00 39.52 4.85
2969 3069 3.057456 AGCACGTTCTAACATCTCGAGTT 60.057 43.478 13.13 0.15 0.00 3.01
2986 3086 2.032894 CGGCACCTATTGATTTAGCACG 60.033 50.000 0.00 0.00 0.00 5.34
3176 3276 6.881065 TCGGAAAATGAATGAGATCAGAAAGT 59.119 34.615 0.00 0.00 31.76 2.66
3324 3426 2.695147 GCACCCCTTTTCCATTCATAGG 59.305 50.000 0.00 0.00 0.00 2.57
3364 3467 0.605083 CCCTCTGCCCTTTCAAAAGC 59.395 55.000 0.00 0.00 34.69 3.51
3416 3520 7.870954 GTCTTACCGAAATTGGATTTCCTTTTT 59.129 33.333 7.58 0.00 44.40 1.94
3500 3611 6.636562 TCTACTACTAAAGCAGCTATCACC 57.363 41.667 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.