Multiple sequence alignment - TraesCS1D01G001600

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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 TraesCS1D01G001600 chr1D 100.000 4403 0 0 1 4403 414385 418787 0.000000e+00 8131.0
1 TraesCS1D01G001600 chr1D 85.405 370 31 13 323 678 21844903 21845263 3.240000e-96 363.0
2 TraesCS1D01G001600 chr1D 90.511 137 10 3 3801 3935 481386483 481386618 1.260000e-40 178.0
3 TraesCS1D01G001600 chr7D 84.472 1230 169 8 2297 3510 399834009 399835232 0.000000e+00 1194.0
4 TraesCS1D01G001600 chr7D 91.556 675 55 2 1050 1723 399832945 399833618 0.000000e+00 929.0
5 TraesCS1D01G001600 chr7D 85.139 646 92 4 1080 1723 400185879 400185236 0.000000e+00 658.0
6 TraesCS1D01G001600 chr7D 86.994 346 34 7 340 678 8991691 8991350 3.210000e-101 379.0
7 TraesCS1D01G001600 chr7D 87.629 291 26 7 323 608 18920672 18920387 3.280000e-86 329.0
8 TraesCS1D01G001600 chr7A 84.372 1235 169 12 2297 3510 457684127 457685358 0.000000e+00 1190.0
9 TraesCS1D01G001600 chr7A 91.193 704 60 2 1050 1752 457683087 457683789 0.000000e+00 955.0
10 TraesCS1D01G001600 chr7A 81.159 621 111 6 1105 1722 203525581 203526198 1.100000e-135 494.0
11 TraesCS1D01G001600 chr7A 89.286 140 12 3 3801 3938 522496696 522496558 5.850000e-39 172.0
12 TraesCS1D01G001600 chr7A 97.222 36 1 0 2089 2124 528298873 528298838 1.320000e-05 62.1
13 TraesCS1D01G001600 chr7B 83.984 1230 175 8 2297 3510 409220901 409222124 0.000000e+00 1160.0
14 TraesCS1D01G001600 chr7B 90.588 680 54 4 1050 1729 409219860 409220529 0.000000e+00 893.0
15 TraesCS1D01G001600 chr7B 86.378 646 84 4 1080 1723 409750121 409749478 0.000000e+00 702.0
16 TraesCS1D01G001600 chr4D 84.475 657 97 5 1071 1723 503920962 503920307 1.030000e-180 643.0
17 TraesCS1D01G001600 chr4D 75.227 1102 233 26 2299 3372 491003141 491002052 1.840000e-133 486.0
18 TraesCS1D01G001600 chrUn 83.692 650 102 2 1076 1723 30086962 30087609 1.050000e-170 610.0
19 TraesCS1D01G001600 chr5A 76.377 1071 232 20 2299 3360 697068428 697069486 1.380000e-154 556.0
20 TraesCS1D01G001600 chr5A 76.377 1071 232 20 2299 3360 697200390 697201448 1.380000e-154 556.0
21 TraesCS1D01G001600 chr5A 76.421 1073 228 24 2299 3360 697282948 697284006 1.380000e-154 556.0
22 TraesCS1D01G001600 chr5A 83.705 583 93 1 1141 1723 706572683 706573263 2.310000e-152 549.0
23 TraesCS1D01G001600 chr5A 75.141 1066 239 20 2299 3360 697552563 697553606 1.110000e-130 477.0
24 TraesCS1D01G001600 chr5A 80.153 655 102 10 1072 1723 688614203 688613574 8.630000e-127 464.0
25 TraesCS1D01G001600 chr5A 78.291 585 123 4 2778 3360 697132988 697133570 1.500000e-99 374.0
26 TraesCS1D01G001600 chr5A 88.830 188 16 4 2089 2271 562386688 562386501 4.430000e-55 226.0
27 TraesCS1D01G001600 chr5A 96.364 55 2 0 623 677 505349224 505349170 1.690000e-14 91.6
28 TraesCS1D01G001600 chr4B 74.185 1073 257 18 2298 3360 649836201 649835139 3.150000e-116 429.0
29 TraesCS1D01G001600 chr3A 88.520 331 27 5 351 677 607224681 607224358 1.480000e-104 390.0
30 TraesCS1D01G001600 chr3A 94.872 39 2 0 3605 3643 732621753 732621715 1.320000e-05 62.1
31 TraesCS1D01G001600 chr4A 85.675 363 34 9 323 677 715877443 715877795 2.500000e-97 366.0
32 TraesCS1D01G001600 chr4A 85.337 341 29 9 350 678 622219443 622219112 2.540000e-87 333.0
33 TraesCS1D01G001600 chr4A 83.673 343 36 8 351 679 713367159 713367495 5.530000e-79 305.0
34 TraesCS1D01G001600 chr2B 89.789 284 20 8 323 600 779132002 779132282 5.420000e-94 355.0
35 TraesCS1D01G001600 chr2B 88.235 289 24 6 323 608 66552619 66552900 1.960000e-88 337.0
36 TraesCS1D01G001600 chr6D 84.469 367 33 11 323 677 461717117 461716763 1.520000e-89 340.0
37 TraesCS1D01G001600 chr6D 88.971 136 14 1 3801 3935 57999671 57999806 2.720000e-37 167.0
38 TraesCS1D01G001600 chr1B 84.127 378 30 14 323 680 656093053 656092686 5.450000e-89 339.0
39 TraesCS1D01G001600 chr1B 87.755 147 12 5 3800 3944 68290386 68290244 2.720000e-37 167.0
40 TraesCS1D01G001600 chr1A 85.088 342 37 8 351 690 591350242 591349913 1.960000e-88 337.0
41 TraesCS1D01G001600 chr3B 85.207 338 36 8 346 680 49874126 49873800 7.060000e-88 335.0
42 TraesCS1D01G001600 chr3B 94.872 39 2 0 3605 3643 810307993 810307955 1.320000e-05 62.1
43 TraesCS1D01G001600 chr5B 86.545 275 24 7 323 593 493285873 493285608 1.550000e-74 291.0
44 TraesCS1D01G001600 chr5B 89.630 135 11 3 3802 3933 570905874 570905740 7.570000e-38 169.0
45 TraesCS1D01G001600 chr5D 86.458 192 17 5 2089 2271 445106392 445106201 7.470000e-48 202.0
46 TraesCS1D01G001600 chr5D 78.736 174 23 5 2089 2262 461043803 461043962 2.170000e-18 104.0
47 TraesCS1D01G001600 chr5D 96.875 32 0 1 1953 1983 423246850 423246819 8.000000e-03 52.8
48 TraesCS1D01G001600 chr3D 85.354 198 22 4 2080 2271 418784969 418784773 9.660000e-47 198.0
49 TraesCS1D01G001600 chr6B 90.441 136 11 2 3801 3935 130075250 130075384 1.260000e-40 178.0
50 TraesCS1D01G001600 chr6A 89.362 141 13 2 3800 3938 112005147 112005007 4.530000e-40 176.0
51 TraesCS1D01G001600 chr6A 88.406 138 14 2 3800 3935 23496456 23496593 9.800000e-37 165.0
52 TraesCS1D01G001600 chr2D 88.194 144 13 4 3803 3944 37412737 37412596 7.570000e-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 TraesCS1D01G001600 chr1D 414385 418787 4402 False 8131.0 8131 100.0000 1 4403 1 chr1D.!!$F1 4402
1 TraesCS1D01G001600 chr7D 399832945 399835232 2287 False 1061.5 1194 88.0140 1050 3510 2 chr7D.!!$F1 2460
2 TraesCS1D01G001600 chr7D 400185236 400185879 643 True 658.0 658 85.1390 1080 1723 1 chr7D.!!$R3 643
3 TraesCS1D01G001600 chr7A 457683087 457685358 2271 False 1072.5 1190 87.7825 1050 3510 2 chr7A.!!$F2 2460
4 TraesCS1D01G001600 chr7A 203525581 203526198 617 False 494.0 494 81.1590 1105 1722 1 chr7A.!!$F1 617
5 TraesCS1D01G001600 chr7B 409219860 409222124 2264 False 1026.5 1160 87.2860 1050 3510 2 chr7B.!!$F1 2460
6 TraesCS1D01G001600 chr7B 409749478 409750121 643 True 702.0 702 86.3780 1080 1723 1 chr7B.!!$R1 643
7 TraesCS1D01G001600 chr4D 503920307 503920962 655 True 643.0 643 84.4750 1071 1723 1 chr4D.!!$R2 652
8 TraesCS1D01G001600 chr4D 491002052 491003141 1089 True 486.0 486 75.2270 2299 3372 1 chr4D.!!$R1 1073
9 TraesCS1D01G001600 chrUn 30086962 30087609 647 False 610.0 610 83.6920 1076 1723 1 chrUn.!!$F1 647
10 TraesCS1D01G001600 chr5A 697068428 697069486 1058 False 556.0 556 76.3770 2299 3360 1 chr5A.!!$F1 1061
11 TraesCS1D01G001600 chr5A 697200390 697201448 1058 False 556.0 556 76.3770 2299 3360 1 chr5A.!!$F3 1061
12 TraesCS1D01G001600 chr5A 697282948 697284006 1058 False 556.0 556 76.4210 2299 3360 1 chr5A.!!$F4 1061
13 TraesCS1D01G001600 chr5A 706572683 706573263 580 False 549.0 549 83.7050 1141 1723 1 chr5A.!!$F6 582
14 TraesCS1D01G001600 chr5A 697552563 697553606 1043 False 477.0 477 75.1410 2299 3360 1 chr5A.!!$F5 1061
15 TraesCS1D01G001600 chr5A 688613574 688614203 629 True 464.0 464 80.1530 1072 1723 1 chr5A.!!$R3 651
16 TraesCS1D01G001600 chr5A 697132988 697133570 582 False 374.0 374 78.2910 2778 3360 1 chr5A.!!$F2 582
17 TraesCS1D01G001600 chr4B 649835139 649836201 1062 True 429.0 429 74.1850 2298 3360 1 chr4B.!!$R1 1062


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
25 26 0.029567 CGTAAAAGCGTGCAACCCAA 59.970 50.0 0.0 0.0 0.00 4.12 F
1037 1038 0.034756 AGCGTTCCACAGCACATACA 59.965 50.0 0.0 0.0 35.48 2.29 F
1742 1752 0.033011 ATACCTGCTCCTCCGTGACT 60.033 55.0 0.0 0.0 0.00 3.41 F
1750 1760 0.179234 TCCTCCGTGACTTTGCACAA 59.821 50.0 0.0 0.0 38.69 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1723 1727 0.033011 AGTCACGGAGGAGCAGGTAT 60.033 55.0 0.00 0.00 0.00 2.73 R
2087 2238 0.315886 ACACGTGTGGCAGTTATCGA 59.684 50.0 22.71 0.00 34.19 3.59 R
3052 3203 0.179070 TCGTACTTGCACAGTGCCAA 60.179 50.0 23.06 15.07 44.23 4.52 R
3558 3747 0.183014 TGGTGCCCCTTCAAACGTTA 59.817 50.0 0.00 0.00 0.00 3.18 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.