Multiple sequence alignment - TraesCS2A01G496300

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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 TraesCS2A01G496300 chr2A 100.000 3593 0 0 1 3593 727303787 727307379 0.000000e+00 6599.0
1 TraesCS2A01G496300 chr2A 99.166 3478 9 2 1 3476 727349077 727352536 0.000000e+00 6244.0
2 TraesCS2A01G496300 chr2A 95.155 2683 93 11 755 3434 727429963 727432611 0.000000e+00 4200.0
3 TraesCS2A01G496300 chr2A 90.483 2690 196 27 752 3439 727436634 727439265 0.000000e+00 3494.0
4 TraesCS2A01G496300 chr2A 89.231 2693 189 41 752 3434 727412952 727415553 0.000000e+00 3273.0
5 TraesCS2A01G496300 chr2A 91.368 2201 138 26 1242 3439 727384876 727387027 0.000000e+00 2964.0
6 TraesCS2A01G496300 chr2A 91.176 2176 140 26 1267 3439 727335640 727337766 0.000000e+00 2907.0
7 TraesCS2A01G496300 chr2A 81.050 2285 299 66 752 2978 727390973 727393181 0.000000e+00 1698.0
8 TraesCS2A01G496300 chr2A 93.478 460 23 4 303 755 727429419 727429878 0.000000e+00 676.0
9 TraesCS2A01G496300 chr2A 90.167 478 21 12 2958 3434 727394611 727395063 1.850000e-167 599.0
10 TraesCS2A01G496300 chr2A 97.049 305 9 0 3 307 727426763 727427067 6.880000e-142 514.0
11 TraesCS2A01G496300 chr2A 100.000 107 0 0 3487 3593 727337377 727337483 7.870000e-47 198.0
12 TraesCS2A01G496300 chr2A 100.000 107 0 0 3487 3593 727386638 727386744 7.870000e-47 198.0
13 TraesCS2A01G496300 chr2A 92.381 105 7 1 3488 3592 727306832 727306935 8.040000e-32 148.0
14 TraesCS2A01G496300 chr2A 91.429 105 8 1 3488 3592 727352104 727352207 3.740000e-30 143.0
15 TraesCS2A01G496300 chr2A 90.566 106 6 2 3488 3591 727432222 727432325 1.740000e-28 137.0
16 TraesCS2A01G496300 chr2A 100.000 40 0 0 3437 3476 727438982 727439021 1.380000e-09 75.0
17 TraesCS2A01G496300 chr2A 97.500 40 1 0 3437 3476 727394808 727394847 6.440000e-08 69.4
18 TraesCS2A01G496300 chr2A 97.500 40 1 0 3437 3476 727415298 727415337 6.440000e-08 69.4
19 TraesCS2A01G496300 chr2A 97.500 40 1 0 3437 3476 727432332 727432371 6.440000e-08 69.4
20 TraesCS2A01G496300 chr2A 100.000 30 0 0 2067 2096 727305911 727305940 5.010000e-04 56.5
21 TraesCS2A01G496300 chr2A 100.000 30 0 0 2067 2096 727336469 727336498 5.010000e-04 56.5
22 TraesCS2A01G496300 chr2A 100.000 30 0 0 2067 2096 727351183 727351212 5.010000e-04 56.5
23 TraesCS2A01G496300 chr2A 100.000 30 0 0 2067 2096 727385730 727385759 5.010000e-04 56.5
24 TraesCS2A01G496300 chr2D 94.129 2708 106 20 741 3434 592993443 592996111 0.000000e+00 4071.0
25 TraesCS2A01G496300 chr2D 92.512 2484 136 21 923 3396 593003014 593005457 0.000000e+00 3511.0
26 TraesCS2A01G496300 chr2D 89.908 2705 207 34 752 3434 593107636 593110296 0.000000e+00 3422.0
27 TraesCS2A01G496300 chr2D 85.795 1056 129 9 752 1804 593023271 593024308 0.000000e+00 1099.0
28 TraesCS2A01G496300 chr2D 94.934 454 20 3 1 453 592991631 592992082 0.000000e+00 708.0
29 TraesCS2A01G496300 chr2D 91.319 288 18 4 475 755 570988538 570988825 1.560000e-103 387.0
30 TraesCS2A01G496300 chr2D 88.321 274 27 2 752 1024 593113792 593114061 1.240000e-84 324.0
31 TraesCS2A01G496300 chr2D 95.283 106 4 1 3488 3593 593109906 593110010 2.220000e-37 167.0
32 TraesCS2A01G496300 chr2D 94.444 108 3 3 3488 3593 592995723 592995829 2.870000e-36 163.0
33 TraesCS2A01G496300 chr2D 97.500 40 1 0 3437 3476 592995832 592995871 6.440000e-08 69.4
34 TraesCS2A01G496300 chr2D 100.000 31 0 0 2067 2097 593108988 593109018 1.390000e-04 58.4
35 TraesCS2A01G496300 chr2D 100.000 30 0 0 2067 2096 592994815 592994844 5.010000e-04 56.5
36 TraesCS2A01G496300 chr2D 100.000 30 0 0 2067 2096 593004188 593004217 5.010000e-04 56.5
37 TraesCS2A01G496300 chr2B 89.092 2741 211 39 741 3433 719124279 719126979 0.000000e+00 3325.0
38 TraesCS2A01G496300 chr2B 89.546 507 27 8 1 481 719123798 719124304 1.420000e-173 619.0
39 TraesCS2A01G496300 chr2B 86.435 317 28 9 755 1063 719151028 719151337 2.070000e-87 333.0
40 TraesCS2A01G496300 chrUn 91.277 2201 140 26 1242 3439 340445120 340442969 0.000000e+00 2953.0
41 TraesCS2A01G496300 chrUn 100.000 107 0 0 3487 3593 340443358 340443252 7.870000e-47 198.0
42 TraesCS2A01G496300 chrUn 100.000 30 0 0 2067 2096 340444266 340444237 5.010000e-04 56.5
43 TraesCS2A01G496300 chr4B 92.527 281 15 3 481 755 432821300 432821580 7.230000e-107 398.0
44 TraesCS2A01G496300 chr7A 92.171 281 16 3 481 755 58987120 58986840 3.360000e-105 392.0
45 TraesCS2A01G496300 chr6B 92.143 280 16 3 482 755 18732753 18732474 1.210000e-104 390.0
46 TraesCS2A01G496300 chr6D 92.115 279 16 3 481 753 116858278 116858556 4.350000e-104 388.0
47 TraesCS2A01G496300 chr5D 91.549 284 18 4 478 755 115973106 115973389 1.560000e-103 387.0
48 TraesCS2A01G496300 chr1D 91.815 281 17 2 481 755 43194360 43194640 1.560000e-103 387.0


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 TraesCS2A01G496300 chr2A 727303787 727307379 3592 False 2267.833333 6599 97.460333 1 3593 3 chr2A.!!$F1 3592
1 TraesCS2A01G496300 chr2A 727349077 727352536 3459 False 2147.833333 6244 96.865000 1 3592 3 chr2A.!!$F3 3591
2 TraesCS2A01G496300 chr2A 727436634 727439265 2631 False 1784.500000 3494 95.241500 752 3476 2 chr2A.!!$F8 2724
3 TraesCS2A01G496300 chr2A 727412952 727415553 2601 False 1671.200000 3273 93.365500 752 3476 2 chr2A.!!$F6 2724
4 TraesCS2A01G496300 chr2A 727426763 727432611 5848 False 1119.280000 4200 94.749600 3 3591 5 chr2A.!!$F7 3588
5 TraesCS2A01G496300 chr2A 727384876 727387027 2151 False 1072.833333 2964 97.122667 1242 3593 3 chr2A.!!$F4 2351
6 TraesCS2A01G496300 chr2A 727335640 727337766 2126 False 1053.833333 2907 97.058667 1267 3593 3 chr2A.!!$F2 2326
7 TraesCS2A01G496300 chr2A 727390973 727395063 4090 False 788.800000 1698 89.572333 752 3476 3 chr2A.!!$F5 2724
8 TraesCS2A01G496300 chr2D 593003014 593005457 2443 False 1783.750000 3511 96.256000 923 3396 2 chr2D.!!$F4 2473
9 TraesCS2A01G496300 chr2D 593023271 593024308 1037 False 1099.000000 1099 85.795000 752 1804 1 chr2D.!!$F2 1052
10 TraesCS2A01G496300 chr2D 592991631 592996111 4480 False 1013.580000 4071 96.201400 1 3593 5 chr2D.!!$F3 3592
11 TraesCS2A01G496300 chr2D 593107636 593114061 6425 False 992.850000 3422 93.378000 752 3593 4 chr2D.!!$F5 2841
12 TraesCS2A01G496300 chr2B 719123798 719126979 3181 False 1972.000000 3325 89.319000 1 3433 2 chr2B.!!$F2 3432
13 TraesCS2A01G496300 chrUn 340442969 340445120 2151 True 1069.166667 2953 97.092333 1242 3593 3 chrUn.!!$R1 2351

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
1312 5160 2.046892 CTGCCTTAGCTGTGCCGT 60.047 61.111 0.0 0.0 40.8 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3237 8679 6.435277 AGAAATGGTGATTGCTGAAACTACAT 59.565 34.615 0.0 0.0 0.0 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
1312 5160 2.046892 CTGCCTTAGCTGTGCCGT 60.047 61.111 0.00 0.00 40.80 5.68
2304 6203 1.962100 ACCGAAGAAGAAGAAGACGGT 59.038 47.619 0.00 0.00 45.51 4.83
2573 6512 0.250252 TGTGTCAGCATGCCTCGAAA 60.250 50.000 15.66 0.57 34.76 3.46
3537 9230 7.753309 TTTGTCATTATATAAACCGATGGGG 57.247 36.000 0.00 0.00 43.62 4.96
3538 9231 5.811190 TGTCATTATATAAACCGATGGGGG 58.189 41.667 0.00 0.00 41.60 5.40
3539 9232 4.638865 GTCATTATATAAACCGATGGGGGC 59.361 45.833 0.00 0.00 41.60 5.80
3540 9233 4.538490 TCATTATATAAACCGATGGGGGCT 59.462 41.667 0.00 0.00 41.60 5.19
3541 9234 5.727279 TCATTATATAAACCGATGGGGGCTA 59.273 40.000 0.00 0.00 41.60 3.93
3542 9235 3.994931 ATATAAACCGATGGGGGCTAC 57.005 47.619 0.00 0.00 41.60 3.58
3543 9236 1.513858 ATAAACCGATGGGGGCTACA 58.486 50.000 0.00 0.00 41.60 2.74
3544 9237 1.287217 TAAACCGATGGGGGCTACAA 58.713 50.000 0.00 0.00 41.60 2.41
3545 9238 0.629058 AAACCGATGGGGGCTACAAT 59.371 50.000 0.00 0.00 41.60 2.71
3546 9239 1.513858 AACCGATGGGGGCTACAATA 58.486 50.000 0.00 0.00 41.60 1.90
3547 9240 1.056660 ACCGATGGGGGCTACAATAG 58.943 55.000 0.00 0.00 41.60 1.73
3548 9241 1.348064 CCGATGGGGGCTACAATAGA 58.652 55.000 0.00 0.00 0.00 1.98
3549 9242 1.909302 CCGATGGGGGCTACAATAGAT 59.091 52.381 0.00 0.00 0.00 1.98
3550 9243 3.104512 CCGATGGGGGCTACAATAGATA 58.895 50.000 0.00 0.00 0.00 1.98
3551 9244 3.517901 CCGATGGGGGCTACAATAGATAA 59.482 47.826 0.00 0.00 0.00 1.75
3552 9245 4.019681 CCGATGGGGGCTACAATAGATAAA 60.020 45.833 0.00 0.00 0.00 1.40
3553 9246 5.514136 CCGATGGGGGCTACAATAGATAAAA 60.514 44.000 0.00 0.00 0.00 1.52
3555 11357 7.335627 CGATGGGGGCTACAATAGATAAAATA 58.664 38.462 0.00 0.00 0.00 1.40
3558 11360 7.686434 TGGGGGCTACAATAGATAAAATAGTC 58.314 38.462 0.00 0.00 0.00 2.59
3560 11362 7.310237 GGGGGCTACAATAGATAAAATAGTCGA 60.310 40.741 0.00 0.00 0.00 4.20
3565 11367 9.587772 CTACAATAGATAAAATAGTCGATGGGG 57.412 37.037 0.00 0.00 0.00 4.96
3589 11391 6.206438 GGGGCAAAATAAGCAAAATGAGAAAA 59.794 34.615 0.00 0.00 0.00 2.29
3590 11392 7.255416 GGGGCAAAATAAGCAAAATGAGAAAAA 60.255 33.333 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
594 4330 0.467290 ACGGTGTTGCCAAGATGGTT 60.467 50.000 0.00 0.0 40.46 3.67
1312 5160 1.289066 CAGACGGCGTTCTCCTCAA 59.711 57.895 16.19 0.0 0.00 3.02
3237 8679 6.435277 AGAAATGGTGATTGCTGAAACTACAT 59.565 34.615 0.00 0.0 0.00 2.29
3511 9204 8.802267 CCCCATCGGTTTATATAATGACAAAAT 58.198 33.333 0.00 0.0 0.00 1.82
3512 9205 7.231722 CCCCCATCGGTTTATATAATGACAAAA 59.768 37.037 0.00 0.0 0.00 2.44
3513 9206 6.717540 CCCCCATCGGTTTATATAATGACAAA 59.282 38.462 0.00 0.0 0.00 2.83
3514 9207 6.242396 CCCCCATCGGTTTATATAATGACAA 58.758 40.000 0.00 0.0 0.00 3.18
3515 9208 5.805098 GCCCCCATCGGTTTATATAATGACA 60.805 44.000 0.00 0.0 0.00 3.58
3516 9209 4.638865 GCCCCCATCGGTTTATATAATGAC 59.361 45.833 0.00 0.0 0.00 3.06
3517 9210 4.538490 AGCCCCCATCGGTTTATATAATGA 59.462 41.667 0.00 0.0 0.00 2.57
3518 9211 4.855340 AGCCCCCATCGGTTTATATAATG 58.145 43.478 0.00 0.0 0.00 1.90
3519 9212 5.489637 TGTAGCCCCCATCGGTTTATATAAT 59.510 40.000 0.00 0.0 0.00 1.28
3520 9213 4.845225 TGTAGCCCCCATCGGTTTATATAA 59.155 41.667 0.00 0.0 0.00 0.98
3521 9214 4.427637 TGTAGCCCCCATCGGTTTATATA 58.572 43.478 0.00 0.0 0.00 0.86
3522 9215 3.253220 TGTAGCCCCCATCGGTTTATAT 58.747 45.455 0.00 0.0 0.00 0.86
3523 9216 2.692024 TGTAGCCCCCATCGGTTTATA 58.308 47.619 0.00 0.0 0.00 0.98
3524 9217 1.513858 TGTAGCCCCCATCGGTTTAT 58.486 50.000 0.00 0.0 0.00 1.40
3525 9218 1.287217 TTGTAGCCCCCATCGGTTTA 58.713 50.000 0.00 0.0 0.00 2.01
3526 9219 0.629058 ATTGTAGCCCCCATCGGTTT 59.371 50.000 0.00 0.0 0.00 3.27
3527 9220 1.420138 CTATTGTAGCCCCCATCGGTT 59.580 52.381 0.00 0.0 0.00 4.44
3528 9221 1.056660 CTATTGTAGCCCCCATCGGT 58.943 55.000 0.00 0.0 0.00 4.69
3529 9222 1.348064 TCTATTGTAGCCCCCATCGG 58.652 55.000 0.00 0.0 0.00 4.18
3530 9223 4.819105 TTATCTATTGTAGCCCCCATCG 57.181 45.455 0.00 0.0 0.00 3.84
3531 9224 8.329502 ACTATTTTATCTATTGTAGCCCCCATC 58.670 37.037 0.00 0.0 0.00 3.51
3532 9225 8.232098 ACTATTTTATCTATTGTAGCCCCCAT 57.768 34.615 0.00 0.0 0.00 4.00
3533 9226 7.526526 CGACTATTTTATCTATTGTAGCCCCCA 60.527 40.741 0.00 0.0 0.00 4.96
3534 9227 6.817140 CGACTATTTTATCTATTGTAGCCCCC 59.183 42.308 0.00 0.0 0.00 5.40
3535 9228 7.609056 TCGACTATTTTATCTATTGTAGCCCC 58.391 38.462 0.00 0.0 0.00 5.80
3536 9229 9.088512 CATCGACTATTTTATCTATTGTAGCCC 57.911 37.037 0.00 0.0 0.00 5.19
3537 9230 9.088512 CCATCGACTATTTTATCTATTGTAGCC 57.911 37.037 0.00 0.0 0.00 3.93
3538 9231 9.088512 CCCATCGACTATTTTATCTATTGTAGC 57.911 37.037 0.00 0.0 0.00 3.58
3539 9232 9.587772 CCCCATCGACTATTTTATCTATTGTAG 57.412 37.037 0.00 0.0 0.00 2.74
3540 9233 8.537016 CCCCCATCGACTATTTTATCTATTGTA 58.463 37.037 0.00 0.0 0.00 2.41
3541 9234 7.394816 CCCCCATCGACTATTTTATCTATTGT 58.605 38.462 0.00 0.0 0.00 2.71
3542 9235 7.849804 CCCCCATCGACTATTTTATCTATTG 57.150 40.000 0.00 0.0 0.00 1.90
3565 11367 6.799926 TTTCTCATTTTGCTTATTTTGCCC 57.200 33.333 0.00 0.0 0.00 5.36


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

AutoCloner maintained by Alex Coulton.