Multiple sequence alignment - TraesCS7D01G104600

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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 TraesCS7D01G104600 chr7D 100.000 4919 0 0 1 4919 63600496 63605414 0.000000e+00 9084.0
1 TraesCS7D01G104600 chr7D 83.683 1238 139 40 2549 3761 63556688 63555489 0.000000e+00 1109.0
2 TraesCS7D01G104600 chr7D 84.627 657 89 6 981 1627 63558683 63558029 1.150000e-180 643.0
3 TraesCS7D01G104600 chr7D 80.851 376 62 6 1244 1615 63608426 63608795 2.240000e-73 287.0
4 TraesCS7D01G104600 chr7D 88.889 189 21 0 4688 4876 63600518 63600706 2.960000e-57 233.0
5 TraesCS7D01G104600 chr7D 88.889 189 21 0 23 211 63605183 63605371 2.960000e-57 233.0
6 TraesCS7D01G104600 chr7D 87.435 191 23 1 3192 3382 63609393 63609582 8.290000e-53 219.0
7 TraesCS7D01G104600 chr7D 86.264 182 23 2 40 220 63564841 63564661 3.880000e-46 196.0
8 TraesCS7D01G104600 chr7D 86.550 171 22 1 976 1145 63643079 63643249 2.340000e-43 187.0
9 TraesCS7D01G104600 chr7D 88.679 53 4 2 2454 2506 631337065 631337115 4.110000e-06 63.9
10 TraesCS7D01G104600 chr7B 89.885 2096 102 53 1 2030 4087397 4089448 0.000000e+00 2595.0
11 TraesCS7D01G104600 chr7B 93.441 1677 90 14 2550 4218 4091603 4093267 0.000000e+00 2470.0
12 TraesCS7D01G104600 chr7B 91.433 712 36 15 4216 4919 4093313 4094007 0.000000e+00 953.0
13 TraesCS7D01G104600 chr7B 93.735 415 25 1 2028 2441 4091080 4091494 5.410000e-174 621.0
14 TraesCS7D01G104600 chr7B 80.371 377 60 9 1244 1615 4097846 4098213 1.740000e-69 274.0
15 TraesCS7D01G104600 chr7B 79.949 389 65 9 1244 1624 4148053 4148436 1.740000e-69 274.0
16 TraesCS7D01G104600 chr7B 92.063 189 15 0 23 211 4093776 4093964 2.920000e-67 267.0
17 TraesCS7D01G104600 chr7B 78.765 405 75 8 3533 3927 4012299 4012702 1.360000e-65 261.0
18 TraesCS7D01G104600 chr7B 90.116 172 17 0 3192 3363 4098781 4098952 1.780000e-54 224.0
19 TraesCS7D01G104600 chr7B 84.783 184 26 2 976 1157 4147829 4148012 3.020000e-42 183.0
20 TraesCS7D01G104600 chr7A 92.857 1694 97 15 2067 3757 66420757 66422429 0.000000e+00 2436.0
21 TraesCS7D01G104600 chr7A 92.274 1139 63 16 3787 4919 66422420 66423539 0.000000e+00 1592.0
22 TraesCS7D01G104600 chr7A 95.700 814 32 3 875 1687 66419946 66420757 0.000000e+00 1306.0
23 TraesCS7D01G104600 chr7A 92.072 391 23 3 1 383 66412604 66412994 1.200000e-150 544.0
24 TraesCS7D01G104600 chr7A 91.640 311 20 3 571 880 66418375 66418680 4.550000e-115 425.0
25 TraesCS7D01G104600 chr7A 81.841 391 60 7 1244 1627 66609160 66609546 7.950000e-83 318.0
26 TraesCS7D01G104600 chr7A 80.585 376 60 8 1244 1615 66427211 66427577 1.350000e-70 278.0
27 TraesCS7D01G104600 chr7A 91.176 170 15 0 3192 3361 66428174 66428343 1.060000e-56 231.0
28 TraesCS7D01G104600 chr7A 88.360 189 22 0 4688 4876 66412626 66412814 1.380000e-55 228.0
29 TraesCS7D01G104600 chr7A 87.831 189 23 0 23 211 66606281 66606469 6.410000e-54 222.0
30 TraesCS7D01G104600 chr7A 87.879 99 8 3 301 395 66425121 66425219 4.020000e-21 113.0
31 TraesCS7D01G104600 chr7A 100.000 28 0 0 2527 2554 608220049 608220076 9.000000e-03 52.8
32 TraesCS7D01G104600 chr5D 77.568 584 104 15 981 1542 519701913 519701335 1.320000e-85 327.0
33 TraesCS7D01G104600 chr5D 90.751 173 16 0 40 212 519702847 519702675 1.060000e-56 231.0
34 TraesCS7D01G104600 chr6A 87.435 191 23 1 3192 3382 74413176 74413365 8.290000e-53 219.0
35 TraesCS7D01G104600 chr1A 97.727 44 1 0 2455 2498 393463638 393463595 5.280000e-10 76.8
36 TraesCS7D01G104600 chr6D 93.333 45 3 0 2456 2500 24554516 24554560 3.180000e-07 67.6
37 TraesCS7D01G104600 chr6D 100.000 29 0 0 2527 2555 129165156 129165184 2.000000e-03 54.7
38 TraesCS7D01G104600 chr6B 79.798 99 11 6 2455 2551 546656567 546656658 4.110000e-06 63.9
39 TraesCS7D01G104600 chr6B 79.167 96 12 4 2458 2551 687414761 687414672 5.320000e-05 60.2
40 TraesCS7D01G104600 chr6B 100.000 28 0 0 2528 2555 507405845 507405872 9.000000e-03 52.8
41 TraesCS7D01G104600 chr1D 80.000 95 11 4 2459 2551 10263506 10263594 4.110000e-06 63.9
42 TraesCS7D01G104600 chr1D 100.000 29 0 0 2527 2555 483877570 483877598 2.000000e-03 54.7
43 TraesCS7D01G104600 chr1B 89.796 49 3 2 2441 2487 141843351 141843399 1.480000e-05 62.1
44 TraesCS7D01G104600 chr1B 89.796 49 3 2 2441 2487 142092304 142092352 1.480000e-05 62.1


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 TraesCS7D01G104600 chr7D 63600496 63605414 4918 False 9084.000000 9084 100.000000 1 4919 1 chr7D.!!$F1 4918
1 TraesCS7D01G104600 chr7D 63555489 63558683 3194 True 876.000000 1109 84.155000 981 3761 2 chr7D.!!$R2 2780
2 TraesCS7D01G104600 chr7D 63605183 63609582 4399 False 246.333333 287 85.725000 23 3382 3 chr7D.!!$F5 3359
3 TraesCS7D01G104600 chr7B 4087397 4098952 11555 False 1057.714286 2595 90.149143 1 4919 7 chr7B.!!$F2 4918
4 TraesCS7D01G104600 chr7B 4147829 4148436 607 False 228.500000 274 82.366000 976 1624 2 chr7B.!!$F3 648
5 TraesCS7D01G104600 chr7A 66418375 66428343 9968 False 911.571429 2436 90.301571 301 4919 7 chr7A.!!$F3 4618
6 TraesCS7D01G104600 chr7A 66606281 66609546 3265 False 270.000000 318 84.836000 23 1627 2 chr7A.!!$F4 1604
7 TraesCS7D01G104600 chr5D 519701335 519702847 1512 True 279.000000 327 84.159500 40 1542 2 chr5D.!!$R1 1502

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
344 349 0.332972 GGGGCAAGTGGAAGGAGATT 59.667 55.0 0.00 0.00 0.00 2.40 F
1687 13534 0.035152 TGAGCCATTTCAGCCGTCAT 60.035 50.0 0.00 0.00 0.00 3.06 F
1727 13574 0.107993 CTGGCCGTCAGATGTGATGT 60.108 55.0 10.87 0.00 46.18 3.06 F
1729 13576 0.176680 GGCCGTCAGATGTGATGTCT 59.823 55.0 10.87 0.00 37.94 3.41 F
1943 14386 0.179062 GAGATGGAAGCGGCATCACT 60.179 55.0 7.57 3.43 0.00 3.41 F
3643 16189 0.035458 GAGGCCCAACATATCCTCCG 59.965 60.0 0.00 0.00 39.27 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 13556 0.108186 GACATCACATCTGACGGCCA 60.108 55.000 2.24 0.0 0.00 5.36 R
3618 16164 0.466189 ATATGTTGGGCCTCGCTTGG 60.466 55.000 4.53 0.0 0.00 3.61 R
3619 16165 0.947244 GATATGTTGGGCCTCGCTTG 59.053 55.000 4.53 0.0 0.00 4.01 R
3643 16189 3.057315 CCACAGACAATGGGTTGAACATC 60.057 47.826 0.00 0.0 38.71 3.06 R
3856 16402 0.037590 TAAAGCCCGACAAGCACCAT 59.962 50.000 0.00 0.0 0.00 3.55 R
4796 17342 0.033504 GCGAGGAGGGCGAATATGAA 59.966 55.000 0.00 0.0 0.00 2.57 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)


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AutoCloner maintained by Alex Coulton.