Multiple sequence alignment - TraesCS4B01G011000

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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 TraesCS4B01G011000 chr4B 100.000 4819 0 0 1 4819 7307627 7312445 0.000000e+00 8900.0
1 TraesCS4B01G011000 chr4B 98.895 4254 41 2 572 4819 7170126 7174379 0.000000e+00 7590.0
2 TraesCS4B01G011000 chr4B 98.637 4255 46 6 572 4819 7217087 7221336 0.000000e+00 7526.0
3 TraesCS4B01G011000 chr4B 98.003 4257 73 8 572 4819 7262700 7266953 0.000000e+00 7380.0
4 TraesCS4B01G011000 chr4B 94.493 4013 151 24 572 4568 7353144 7357102 0.000000e+00 6122.0
5 TraesCS4B01G011000 chr4B 98.427 572 9 0 1 572 7169367 7169938 0.000000e+00 1007.0
6 TraesCS4B01G011000 chr4B 98.252 572 10 0 1 572 7216326 7216897 0.000000e+00 1002.0
7 TraesCS4B01G011000 chr4B 79.689 965 128 32 902 1820 7381436 7382378 6.800000e-178 634.0
8 TraesCS4B01G011000 chr4B 88.630 343 33 5 3490 3827 7378265 7378606 3.470000e-111 412.0
9 TraesCS4B01G011000 chr4B 87.126 334 15 5 369 674 7262310 7262643 2.130000e-93 353.0
10 TraesCS4B01G011000 chr4B 87.048 332 17 4 369 674 7352755 7353086 7.670000e-93 351.0
11 TraesCS4B01G011000 chr4B 81.873 331 38 12 369 684 415342162 415342485 4.780000e-65 259.0
12 TraesCS4B01G011000 chr4B 88.462 156 14 3 572 723 415342540 415342695 8.240000e-43 185.0
13 TraesCS4B01G011000 chr4D 91.037 4117 298 29 731 4819 4416804 4420877 0.000000e+00 5493.0
14 TraesCS4B01G011000 chr4D 87.051 919 87 17 731 1639 4458675 4459571 0.000000e+00 1009.0
15 TraesCS4B01G011000 chr4A 90.109 3579 254 38 729 4280 599102645 599099140 0.000000e+00 4556.0
16 TraesCS4B01G011000 chr4A 90.028 3580 256 39 729 4280 599180024 599176518 0.000000e+00 4540.0
17 TraesCS4B01G011000 chr4A 89.997 3579 258 39 729 4280 599223451 599219946 0.000000e+00 4534.0
18 TraesCS4B01G011000 chr4A 90.554 3176 243 24 1142 4287 598910263 598907115 0.000000e+00 4150.0
19 TraesCS4B01G011000 chr4A 90.457 3175 252 21 1142 4287 598960634 598957482 0.000000e+00 4137.0
20 TraesCS4B01G011000 chr4A 90.965 2103 132 20 2186 4280 599246791 599244739 0.000000e+00 2778.0
21 TraesCS4B01G011000 chr4A 90.424 1629 120 16 769 2380 599084875 599083266 0.000000e+00 2111.0
22 TraesCS4B01G011000 chr4A 92.703 370 25 2 1 368 689504865 689505234 2.550000e-147 532.0
23 TraesCS4B01G011000 chrUn 91.060 2103 130 20 2186 4280 216674910 216672858 0.000000e+00 2789.0
24 TraesCS4B01G011000 chrUn 89.486 1655 128 22 729 2358 360633261 360631628 0.000000e+00 2050.0
25 TraesCS4B01G011000 chrUn 88.007 567 43 11 729 1283 216652332 216651779 0.000000e+00 647.0
26 TraesCS4B01G011000 chr6A 90.587 733 48 8 3549 4280 593024590 593023878 0.000000e+00 952.0
27 TraesCS4B01G011000 chr1B 94.580 369 19 1 1 368 100313035 100312667 1.950000e-158 569.0
28 TraesCS4B01G011000 chr6B 93.716 366 21 2 4 368 586516034 586516398 9.120000e-152 547.0
29 TraesCS4B01G011000 chr2B 93.664 363 22 1 7 368 690910317 690909955 4.240000e-150 542.0
30 TraesCS4B01G011000 chr2B 100.000 51 0 0 662 712 179261021 179261071 1.430000e-15 95.3
31 TraesCS4B01G011000 chr7B 92.935 368 26 0 1 368 727986005 727986372 1.970000e-148 536.0
32 TraesCS4B01G011000 chr3A 93.388 363 23 1 7 368 61453384 61453022 1.970000e-148 536.0
33 TraesCS4B01G011000 chr3A 90.541 148 10 3 575 719 691379495 691379349 4.920000e-45 193.0
34 TraesCS4B01G011000 chr3A 85.714 112 12 3 464 572 683200399 683200509 1.100000e-21 115.0
35 TraesCS4B01G011000 chr1D 92.935 368 26 0 1 368 469078026 469077659 1.970000e-148 536.0
36 TraesCS4B01G011000 chr3B 89.796 147 11 3 575 717 154038842 154038696 8.240000e-43 185.0
37 TraesCS4B01G011000 chr3B 88.194 144 14 2 575 716 685579307 685579165 8.290000e-38 169.0


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 TraesCS4B01G011000 chr4B 7307627 7312445 4818 False 8900.0 8900 100.0000 1 4819 1 chr4B.!!$F1 4818
1 TraesCS4B01G011000 chr4B 7169367 7174379 5012 False 4298.5 7590 98.6610 1 4819 2 chr4B.!!$F2 4818
2 TraesCS4B01G011000 chr4B 7216326 7221336 5010 False 4264.0 7526 98.4445 1 4819 2 chr4B.!!$F3 4818
3 TraesCS4B01G011000 chr4B 7262310 7266953 4643 False 3866.5 7380 92.5645 369 4819 2 chr4B.!!$F4 4450
4 TraesCS4B01G011000 chr4B 7352755 7357102 4347 False 3236.5 6122 90.7705 369 4568 2 chr4B.!!$F5 4199
5 TraesCS4B01G011000 chr4B 7378265 7382378 4113 False 523.0 634 84.1595 902 3827 2 chr4B.!!$F6 2925
6 TraesCS4B01G011000 chr4B 415342162 415342695 533 False 222.0 259 85.1675 369 723 2 chr4B.!!$F7 354
7 TraesCS4B01G011000 chr4D 4416804 4420877 4073 False 5493.0 5493 91.0370 731 4819 1 chr4D.!!$F1 4088
8 TraesCS4B01G011000 chr4D 4458675 4459571 896 False 1009.0 1009 87.0510 731 1639 1 chr4D.!!$F2 908
9 TraesCS4B01G011000 chr4A 599099140 599102645 3505 True 4556.0 4556 90.1090 729 4280 1 chr4A.!!$R4 3551
10 TraesCS4B01G011000 chr4A 599176518 599180024 3506 True 4540.0 4540 90.0280 729 4280 1 chr4A.!!$R5 3551
11 TraesCS4B01G011000 chr4A 599219946 599223451 3505 True 4534.0 4534 89.9970 729 4280 1 chr4A.!!$R6 3551
12 TraesCS4B01G011000 chr4A 598907115 598910263 3148 True 4150.0 4150 90.5540 1142 4287 1 chr4A.!!$R1 3145
13 TraesCS4B01G011000 chr4A 598957482 598960634 3152 True 4137.0 4137 90.4570 1142 4287 1 chr4A.!!$R2 3145
14 TraesCS4B01G011000 chr4A 599244739 599246791 2052 True 2778.0 2778 90.9650 2186 4280 1 chr4A.!!$R7 2094
15 TraesCS4B01G011000 chr4A 599083266 599084875 1609 True 2111.0 2111 90.4240 769 2380 1 chr4A.!!$R3 1611
16 TraesCS4B01G011000 chrUn 216672858 216674910 2052 True 2789.0 2789 91.0600 2186 4280 1 chrUn.!!$R2 2094
17 TraesCS4B01G011000 chrUn 360631628 360633261 1633 True 2050.0 2050 89.4860 729 2358 1 chrUn.!!$R3 1629
18 TraesCS4B01G011000 chrUn 216651779 216652332 553 True 647.0 647 88.0070 729 1283 1 chrUn.!!$R1 554
19 TraesCS4B01G011000 chr6A 593023878 593024590 712 True 952.0 952 90.5870 3549 4280 1 chr6A.!!$R1 731

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
399 400 0.036010 CTCGAGTGGAAGGGCAATGT 60.036 55.000 3.62 0.00 0.00 2.71 F
520 534 1.449246 GCGCTGGCAGAAGAGATGT 60.449 57.895 20.86 0.00 39.62 3.06 F
1694 1961 6.774354 AGAATCAAGTTTAGTCGCGTTTAA 57.226 33.333 5.77 3.36 0.00 1.52 F
2360 2652 1.796459 GTCGTGTGTAGCGGAATTGTT 59.204 47.619 0.00 0.00 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2343 2635 1.877443 ACCAACAATTCCGCTACACAC 59.123 47.619 0.0 0.0 0.00 3.82 R
2344 2636 2.264005 ACCAACAATTCCGCTACACA 57.736 45.000 0.0 0.0 0.00 3.72 R
3419 3723 4.957759 TTCGTGAAGCTTAATTTAGGCC 57.042 40.909 0.0 0.0 0.00 5.19 R
4109 4498 2.040412 ACAGACCATCCCCTCTGTTTTC 59.960 50.000 0.0 0.0 43.81 2.29 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
77 78 3.399181 GCCATGGGTCAGGTCCGA 61.399 66.667 15.13 0.00 0.00 4.55
92 93 0.976641 TCCGAGTGCTTCATGTTCCT 59.023 50.000 0.00 0.00 0.00 3.36
170 171 3.009033 TGGATTTTCGGTCCAGTCTCAAT 59.991 43.478 0.00 0.00 40.72 2.57
399 400 0.036010 CTCGAGTGGAAGGGCAATGT 60.036 55.000 3.62 0.00 0.00 2.71
520 534 1.449246 GCGCTGGCAGAAGAGATGT 60.449 57.895 20.86 0.00 39.62 3.06
1694 1961 6.774354 AGAATCAAGTTTAGTCGCGTTTAA 57.226 33.333 5.77 3.36 0.00 1.52
2343 2635 3.914312 AGACCTCATTGTAGTTGTGTCG 58.086 45.455 0.00 0.00 0.00 4.35
2344 2636 3.321111 AGACCTCATTGTAGTTGTGTCGT 59.679 43.478 0.00 0.00 0.00 4.34
2360 2652 1.796459 GTCGTGTGTAGCGGAATTGTT 59.204 47.619 0.00 0.00 0.00 2.83
2938 3237 8.831550 GTTCTCTTGTAATTTATTGGCTCTAGG 58.168 37.037 0.00 0.00 0.00 3.02
3065 3365 6.317789 TCTTCAGAATTTGACAATGTGGTC 57.682 37.500 0.00 0.00 34.94 4.02
3419 3723 3.010420 GGGAGAAATTCTCTGTTTCCCG 58.990 50.000 20.82 0.00 42.95 5.14
3422 3726 1.472878 GAAATTCTCTGTTTCCCGGCC 59.527 52.381 0.00 0.00 31.08 6.13
3438 3742 2.031683 CCGGCCTAAATTAAGCTTCACG 59.968 50.000 0.00 0.00 0.00 4.35
3730 4064 3.473625 CCGTTTTCAAAGGGTGTCTAGT 58.526 45.455 3.28 0.00 38.71 2.57
4288 4677 5.563085 CGCTGGAACATCATACTACTCCTAC 60.563 48.000 0.00 0.00 38.20 3.18
4624 6105 1.665679 GTACAACCATGCTCCACATCG 59.334 52.381 0.00 0.00 36.64 3.84
4689 7620 6.633500 TGTGGGACTTTCAGTAGAAAATTG 57.367 37.500 0.00 0.00 42.78 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 2.224281 TGACGAAGGAACATGAAGCACT 60.224 45.455 0.00 0.00 0.00 4.40
170 171 0.679505 CAACAGGAGGAGAACGGACA 59.320 55.000 0.00 0.00 0.00 4.02
338 339 6.719370 AGATTTAGGAATTGTTGCCACACTTA 59.281 34.615 0.00 0.00 30.32 2.24
1694 1961 5.068723 CGGGATACTGGTAACTCTGTTACAT 59.931 44.000 18.39 6.82 40.24 2.29
2103 2386 5.681437 GCCCGAAGAACAGACATGATAGTAA 60.681 44.000 0.00 0.00 0.00 2.24
2343 2635 1.877443 ACCAACAATTCCGCTACACAC 59.123 47.619 0.00 0.00 0.00 3.82
2344 2636 2.264005 ACCAACAATTCCGCTACACA 57.736 45.000 0.00 0.00 0.00 3.72
3029 3329 7.773224 TCAAATTCTGAAGAGGTTAACAGAACA 59.227 33.333 8.10 0.43 46.87 3.18
3065 3365 6.252015 CGAGACACCTGAAATAATGCAAAATG 59.748 38.462 0.00 0.00 0.00 2.32
3419 3723 4.957759 TTCGTGAAGCTTAATTTAGGCC 57.042 40.909 0.00 0.00 0.00 5.19
3422 3726 7.981142 TGGGTATTTCGTGAAGCTTAATTTAG 58.019 34.615 0.00 0.00 0.00 1.85
3730 4064 3.381272 AGTTTTACGCGCACCCTATAGTA 59.619 43.478 5.73 0.00 0.00 1.82
4109 4498 2.040412 ACAGACCATCCCCTCTGTTTTC 59.960 50.000 0.00 0.00 43.81 2.29
4288 4677 8.361139 CAGGGTAGTCTAAATAACTATGTGGAG 58.639 40.741 0.00 0.00 32.19 3.86
4624 6105 9.103861 CCACTCTGGAAAAATAAGATAGAGTTC 57.896 37.037 0.00 0.00 40.96 3.01
4689 7620 4.946478 AGGTGCTTCTATCTGTATGGAC 57.054 45.455 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.