Multiple sequence alignment - TraesCS4B01G119100

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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 TraesCS4B01G119100 chr4B 100.000 4035 0 0 1 4035 139573175 139569141 0.000000e+00 7452.0
1 TraesCS4B01G119100 chr4B 85.192 2323 252 48 897 3164 139549317 139547032 0.000000e+00 2300.0
2 TraesCS4B01G119100 chr4B 81.412 1232 192 24 1415 2620 139593660 139592440 0.000000e+00 972.0
3 TraesCS4B01G119100 chr4B 94.697 528 28 0 3508 4035 523009986 523010513 0.000000e+00 821.0
4 TraesCS4B01G119100 chr4B 83.045 926 133 19 1415 2329 460156617 460155705 0.000000e+00 819.0
5 TraesCS4B01G119100 chr4B 89.572 537 54 2 3499 4035 398166577 398166043 0.000000e+00 680.0
6 TraesCS4B01G119100 chr4B 89.385 537 55 2 3499 4035 398132209 398131675 0.000000e+00 675.0
7 TraesCS4B01G119100 chr4B 89.199 537 56 2 3499 4035 398201490 398200956 0.000000e+00 669.0
8 TraesCS4B01G119100 chr4D 97.007 2005 47 2 934 2937 97970281 97968289 0.000000e+00 3358.0
9 TraesCS4B01G119100 chr4D 86.236 2216 234 38 892 3070 97962541 97960360 0.000000e+00 2337.0
10 TraesCS4B01G119100 chr4D 92.562 726 34 10 232 947 97971993 97971278 0.000000e+00 1024.0
11 TraesCS4B01G119100 chr4D 93.264 579 25 6 2935 3508 97967196 97966627 0.000000e+00 841.0
12 TraesCS4B01G119100 chr4D 82.639 720 99 18 1621 2329 374041175 374040471 7.410000e-172 614.0
13 TraesCS4B01G119100 chr4D 95.333 150 6 1 1 149 97972686 97972537 1.870000e-58 237.0
14 TraesCS4B01G119100 chr1B 84.326 2501 289 43 935 3396 487405524 487407960 0.000000e+00 2351.0
15 TraesCS4B01G119100 chr1D 85.259 2320 261 37 1003 3285 363861164 363863439 0.000000e+00 2314.0
16 TraesCS4B01G119100 chr1D 86.174 528 72 1 3508 4035 360108586 360108060 1.630000e-158 569.0
17 TraesCS4B01G119100 chr1D 91.667 48 2 2 262 307 58619964 58620011 9.360000e-07 65.8
18 TraesCS4B01G119100 chr1A 84.329 2227 285 27 925 3112 463218523 463220724 0.000000e+00 2121.0
19 TraesCS4B01G119100 chr4A 86.019 1688 173 42 637 2280 478209189 478210857 0.000000e+00 1751.0
20 TraesCS4B01G119100 chr4A 81.260 1254 191 31 1397 2620 478191393 478192632 0.000000e+00 974.0
21 TraesCS4B01G119100 chr4A 79.310 1218 162 47 2276 3440 478216299 478217479 0.000000e+00 771.0
22 TraesCS4B01G119100 chr4A 90.833 240 12 8 1 233 478199504 478199740 3.030000e-81 313.0
23 TraesCS4B01G119100 chr4A 85.019 267 24 8 303 563 478200096 478200352 1.440000e-64 257.0
24 TraesCS4B01G119100 chr6B 79.666 1436 218 46 913 2317 134838183 134839575 0.000000e+00 966.0
25 TraesCS4B01G119100 chr6B 93.333 45 0 3 266 307 2202366 2202322 3.370000e-06 63.9
26 TraesCS4B01G119100 chr5B 95.833 528 22 0 3508 4035 320638170 320638697 0.000000e+00 854.0
27 TraesCS4B01G119100 chr3B 95.833 528 22 0 3508 4035 284652511 284653038 0.000000e+00 854.0
28 TraesCS4B01G119100 chr7B 94.886 528 27 0 3508 4035 81050375 81049848 0.000000e+00 826.0
29 TraesCS4B01G119100 chr6D 82.685 745 86 20 913 1646 61002816 61003528 4.430000e-174 621.0
30 TraesCS4B01G119100 chr6D 95.556 45 0 2 265 307 4187342 4187386 2.010000e-08 71.3
31 TraesCS4B01G119100 chr6D 95.349 43 2 0 265 307 16081306 16081264 7.240000e-08 69.4
32 TraesCS4B01G119100 chr7A 79.886 527 97 8 3511 4035 43530035 43529516 1.060000e-100 377.0
33 TraesCS4B01G119100 chr5D 77.698 278 43 13 479 751 450609190 450609453 6.980000e-33 152.0
34 TraesCS4B01G119100 chr5D 93.333 45 1 2 265 307 331068937 331068893 9.360000e-07 65.8
35 TraesCS4B01G119100 chr2D 84.848 99 12 3 478 575 66116012 66115916 3.320000e-16 97.1
36 TraesCS4B01G119100 chr3D 95.745 47 1 1 262 307 158449439 158449393 1.560000e-09 75.0


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 TraesCS4B01G119100 chr4B 139569141 139573175 4034 True 7452 7452 100.0000 1 4035 1 chr4B.!!$R2 4034
1 TraesCS4B01G119100 chr4B 139547032 139549317 2285 True 2300 2300 85.1920 897 3164 1 chr4B.!!$R1 2267
2 TraesCS4B01G119100 chr4B 139592440 139593660 1220 True 972 972 81.4120 1415 2620 1 chr4B.!!$R3 1205
3 TraesCS4B01G119100 chr4B 523009986 523010513 527 False 821 821 94.6970 3508 4035 1 chr4B.!!$F1 527
4 TraesCS4B01G119100 chr4B 460155705 460156617 912 True 819 819 83.0450 1415 2329 1 chr4B.!!$R7 914
5 TraesCS4B01G119100 chr4B 398166043 398166577 534 True 680 680 89.5720 3499 4035 1 chr4B.!!$R5 536
6 TraesCS4B01G119100 chr4B 398131675 398132209 534 True 675 675 89.3850 3499 4035 1 chr4B.!!$R4 536
7 TraesCS4B01G119100 chr4B 398200956 398201490 534 True 669 669 89.1990 3499 4035 1 chr4B.!!$R6 536
8 TraesCS4B01G119100 chr4D 97960360 97962541 2181 True 2337 2337 86.2360 892 3070 1 chr4D.!!$R1 2178
9 TraesCS4B01G119100 chr4D 97966627 97972686 6059 True 1365 3358 94.5415 1 3508 4 chr4D.!!$R3 3507
10 TraesCS4B01G119100 chr4D 374040471 374041175 704 True 614 614 82.6390 1621 2329 1 chr4D.!!$R2 708
11 TraesCS4B01G119100 chr1B 487405524 487407960 2436 False 2351 2351 84.3260 935 3396 1 chr1B.!!$F1 2461
12 TraesCS4B01G119100 chr1D 363861164 363863439 2275 False 2314 2314 85.2590 1003 3285 1 chr1D.!!$F2 2282
13 TraesCS4B01G119100 chr1D 360108060 360108586 526 True 569 569 86.1740 3508 4035 1 chr1D.!!$R1 527
14 TraesCS4B01G119100 chr1A 463218523 463220724 2201 False 2121 2121 84.3290 925 3112 1 chr1A.!!$F1 2187
15 TraesCS4B01G119100 chr4A 478209189 478210857 1668 False 1751 1751 86.0190 637 2280 1 chr4A.!!$F2 1643
16 TraesCS4B01G119100 chr4A 478191393 478192632 1239 False 974 974 81.2600 1397 2620 1 chr4A.!!$F1 1223
17 TraesCS4B01G119100 chr4A 478216299 478217479 1180 False 771 771 79.3100 2276 3440 1 chr4A.!!$F3 1164
18 TraesCS4B01G119100 chr4A 478199504 478200352 848 False 285 313 87.9260 1 563 2 chr4A.!!$F4 562
19 TraesCS4B01G119100 chr6B 134838183 134839575 1392 False 966 966 79.6660 913 2317 1 chr6B.!!$F1 1404
20 TraesCS4B01G119100 chr5B 320638170 320638697 527 False 854 854 95.8330 3508 4035 1 chr5B.!!$F1 527
21 TraesCS4B01G119100 chr3B 284652511 284653038 527 False 854 854 95.8330 3508 4035 1 chr3B.!!$F1 527
22 TraesCS4B01G119100 chr7B 81049848 81050375 527 True 826 826 94.8860 3508 4035 1 chr7B.!!$R1 527
23 TraesCS4B01G119100 chr6D 61002816 61003528 712 False 621 621 82.6850 913 1646 1 chr6D.!!$F2 733
24 TraesCS4B01G119100 chr7A 43529516 43530035 519 True 377 377 79.8860 3511 4035 1 chr7A.!!$R1 524

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
452 1263 1.674962 GTTCTGATCATGAGCTTGGGC 59.325 52.381 12.92 0.0 39.06 5.36 F
2156 4107 2.879907 CAATTGCAGGCTGGGACG 59.120 61.111 17.64 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2198 4149 0.100325 CACAACGCACTTCCAAAGCA 59.900 50.0 0.00 0.0 0.00 3.91 R
3396 6496 1.333177 AACCATTTTTAGGCACGCCA 58.667 45.0 11.35 0.0 38.92 5.69 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
217 223 3.525537 ACTTCTACAGTGCATCAATCGG 58.474 45.455 0.00 0.00 32.83 4.18
276 1081 5.944599 GCCTATGTGGATCATTGAGATGAAT 59.055 40.000 0.00 0.00 39.91 2.57
366 1177 5.764131 TGTAAATTGTTTCGTTCCACATCC 58.236 37.500 0.00 0.00 0.00 3.51
375 1186 2.569853 TCGTTCCACATCCATGTTAGGT 59.430 45.455 0.00 0.00 39.39 3.08
441 1252 2.239400 AGGACACGACTGTTCTGATCA 58.761 47.619 0.00 0.00 34.57 2.92
448 1259 3.056250 ACGACTGTTCTGATCATGAGCTT 60.056 43.478 12.92 0.00 0.00 3.74
452 1263 1.674962 GTTCTGATCATGAGCTTGGGC 59.325 52.381 12.92 0.00 39.06 5.36
467 1278 3.425758 GCTTGGGCGAACAGTAACATAAC 60.426 47.826 0.00 0.00 0.00 1.89
472 1283 5.049267 TGGGCGAACAGTAACATAACTTTTC 60.049 40.000 0.00 0.00 34.34 2.29
563 1376 7.742464 ATCACCGGATGATATTCACGGAAAATA 60.742 37.037 9.46 0.00 46.80 1.40
591 1404 6.036408 GCAAAGAAAACAATATCAATGCTCCC 59.964 38.462 0.00 0.00 31.05 4.30
634 1447 4.599047 TTTCGGAGCATCAATTTTTGGT 57.401 36.364 0.00 0.00 36.25 3.67
698 1511 9.881529 TGAAATTTTGCAAGCTATCAAATTTTC 57.118 25.926 28.05 28.05 43.63 2.29
1378 3237 4.414956 TCCCACATCCTCCCCGCT 62.415 66.667 0.00 0.00 0.00 5.52
2156 4107 2.879907 CAATTGCAGGCTGGGACG 59.120 61.111 17.64 0.00 0.00 4.79
2167 4118 3.649277 CTGGGACGAAGGTGAGCCG 62.649 68.421 0.00 0.00 40.50 5.52
2198 4149 2.572104 GGTACCAAGTGTGAGGATCCTT 59.428 50.000 17.42 0.00 0.00 3.36
2207 4158 2.108075 TGTGAGGATCCTTGCTTTGGAA 59.892 45.455 17.42 0.00 37.13 3.53
2313 4264 3.584947 AAGCCCCTGATGCTTCTTC 57.415 52.632 0.88 0.00 45.58 2.87
2642 4600 2.315176 TGGAAGTTTCACCACAATGGG 58.685 47.619 0.00 0.00 43.37 4.00
2814 4788 3.806625 AGGTGCATGTTTATTCATGGC 57.193 42.857 8.41 0.00 43.54 4.40
2826 4800 0.833287 TTCATGGCCTCTACCTCTGC 59.167 55.000 3.32 0.00 0.00 4.26
2896 4874 0.254747 TTTGATGATCCACCCCGACC 59.745 55.000 0.00 0.00 0.00 4.79
3117 6193 1.005097 AGGAATGTGGCTTGATGCTGA 59.995 47.619 0.00 0.00 42.39 4.26
3363 6463 1.456544 TGGTTATTTTCGCGACGTGTC 59.543 47.619 9.15 0.00 0.00 3.67
3441 6541 3.149196 CAGGCGGGCAAACTATGATATT 58.851 45.455 3.78 0.00 0.00 1.28
3442 6542 4.323417 CAGGCGGGCAAACTATGATATTA 58.677 43.478 3.78 0.00 0.00 0.98
3443 6543 4.759693 CAGGCGGGCAAACTATGATATTAA 59.240 41.667 3.78 0.00 0.00 1.40
3444 6544 5.415701 CAGGCGGGCAAACTATGATATTAAT 59.584 40.000 3.78 0.00 0.00 1.40
3445 6545 5.415701 AGGCGGGCAAACTATGATATTAATG 59.584 40.000 3.78 0.00 0.00 1.90
3446 6546 5.414454 GGCGGGCAAACTATGATATTAATGA 59.586 40.000 0.00 0.00 0.00 2.57
3447 6547 6.095440 GGCGGGCAAACTATGATATTAATGAT 59.905 38.462 0.00 0.00 0.00 2.45
3448 6548 7.282224 GGCGGGCAAACTATGATATTAATGATA 59.718 37.037 0.00 0.00 0.00 2.15
3449 6549 8.840321 GCGGGCAAACTATGATATTAATGATAT 58.160 33.333 0.00 0.00 33.58 1.63
3452 6552 9.956720 GGCAAACTATGATATTAATGATATGCC 57.043 33.333 0.00 0.00 31.85 4.40
3532 6636 3.627395 TTTCGAGAGTATGCCAATGGT 57.373 42.857 0.00 0.00 0.00 3.55
3576 6680 6.578023 GGCAGAGAGATATGTACAAGAGTTT 58.422 40.000 0.00 0.00 0.00 2.66
3577 6681 7.468768 CGGCAGAGAGATATGTACAAGAGTTTA 60.469 40.741 0.00 0.00 0.00 2.01
3599 6704 0.541392 TACAATCGCAGGCCTCACAT 59.459 50.000 0.00 0.00 0.00 3.21
3716 6821 4.511527 GCTCTCTCATGATGACCTCAAAA 58.488 43.478 0.00 0.00 37.44 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
217 223 4.630069 CAGCCCATTTAGTGTGTAGTGTAC 59.370 45.833 0.00 0.00 0.00 2.90
276 1081 4.394729 AGAAAACTCGCCCACTTTATTGA 58.605 39.130 0.00 0.00 0.00 2.57
336 1145 8.813282 GTGGAACGAAACAATTTACAGAAAAAT 58.187 29.630 0.00 0.00 0.00 1.82
337 1146 7.813148 TGTGGAACGAAACAATTTACAGAAAAA 59.187 29.630 0.00 0.00 42.39 1.94
338 1147 7.313646 TGTGGAACGAAACAATTTACAGAAAA 58.686 30.769 0.00 0.00 42.39 2.29
344 1153 5.764131 TGGATGTGGAACGAAACAATTTAC 58.236 37.500 0.00 0.00 42.39 2.01
366 1177 6.266168 TGGTCATAAGCAAAACCTAACATG 57.734 37.500 0.00 0.00 32.82 3.21
441 1252 0.613260 TACTGTTCGCCCAAGCTCAT 59.387 50.000 0.00 0.00 36.60 2.90
448 1259 3.688694 AGTTATGTTACTGTTCGCCCA 57.311 42.857 0.00 0.00 0.00 5.36
452 1263 5.390145 CGGGGAAAAGTTATGTTACTGTTCG 60.390 44.000 0.00 0.00 41.38 3.95
467 1278 7.728847 AAAATCAGAATTTTTCGGGGAAAAG 57.271 32.000 4.02 0.00 41.27 2.27
563 1376 7.107542 AGCATTGATATTGTTTTCTTTGCCAT 58.892 30.769 0.00 0.00 0.00 4.40
583 1396 6.418057 TGAAAATAACAGTTTGGGAGCATT 57.582 33.333 0.00 0.00 0.00 3.56
698 1511 8.915871 TTTTCTTCTTCTGAAACATTGACAAG 57.084 30.769 0.00 0.00 33.77 3.16
734 1547 8.784043 CGAGCTAGGGCAAATAGTAAAATAAAT 58.216 33.333 0.00 0.00 41.70 1.40
832 1656 9.478768 TGTTTCTATTTCTGAATACAACGTACA 57.521 29.630 0.00 0.00 0.00 2.90
833 1657 9.737025 GTGTTTCTATTTCTGAATACAACGTAC 57.263 33.333 0.00 0.00 0.00 3.67
834 1658 8.928733 GGTGTTTCTATTTCTGAATACAACGTA 58.071 33.333 0.00 0.00 0.00 3.57
1464 3359 2.523168 TGCTGGTGAGGTGGACGA 60.523 61.111 0.00 0.00 0.00 4.20
1681 3599 3.572661 AGGAGGTTAGGGAAACAGGTA 57.427 47.619 0.00 0.00 40.08 3.08
2156 4107 2.035442 GGTGCTTCGGCTCACCTTC 61.035 63.158 11.75 0.00 46.90 3.46
2167 4118 1.880027 CACTTGGTACCTTGGTGCTTC 59.120 52.381 14.36 0.00 0.00 3.86
2198 4149 0.100325 CACAACGCACTTCCAAAGCA 59.900 50.000 0.00 0.00 0.00 3.91
2207 4158 4.988598 CGGCCTCCACAACGCACT 62.989 66.667 0.00 0.00 0.00 4.40
2313 4264 2.093921 TGATGGTGCAAATGAATGCCAG 60.094 45.455 0.00 0.00 45.83 4.85
2516 4474 2.417243 CGGAAATCATGGAAAACCAGCC 60.417 50.000 0.00 0.00 0.00 4.85
2554 4512 7.729116 TCAAAGAAGAATTTGAGGAAAGCAAT 58.271 30.769 0.00 0.00 42.68 3.56
2642 4600 4.201920 GCTTCACTTTGGAACGAATATCCC 60.202 45.833 0.00 0.00 36.04 3.85
2781 4754 3.815401 ACATGCACCTTTGACTTCAGTAC 59.185 43.478 0.00 0.00 0.00 2.73
2814 4788 3.409026 AACAACTTGCAGAGGTAGAGG 57.591 47.619 0.00 0.00 0.00 3.69
2826 4800 4.457810 CGACAACAGAGCATAACAACTTG 58.542 43.478 0.00 0.00 0.00 3.16
2913 4891 5.931441 AACTTCAACACTTAAGCTAGCTG 57.069 39.130 20.16 8.64 0.00 4.24
2914 4892 6.647067 CACTAACTTCAACACTTAAGCTAGCT 59.353 38.462 12.68 12.68 28.70 3.32
2985 6058 8.579850 TCTGTAATTGCCAACAGAAGAAATAT 57.420 30.769 6.36 0.00 46.82 1.28
2987 6060 6.899393 TCTGTAATTGCCAACAGAAGAAAT 57.101 33.333 6.36 0.00 46.82 2.17
3041 6115 6.528321 TCAGCAGACCAAATCTAGATAATGG 58.472 40.000 25.36 25.36 35.15 3.16
3117 6193 4.168101 TGTCACTAATTCTCCCCAGTCTT 58.832 43.478 0.00 0.00 0.00 3.01
3196 6288 3.442977 AGAGCATCAAAATCTTCAGCCAC 59.557 43.478 0.00 0.00 37.82 5.01
3363 6463 3.438087 CAGCTCAAGTTACCATCACCTTG 59.562 47.826 0.00 0.00 36.49 3.61
3396 6496 1.333177 AACCATTTTTAGGCACGCCA 58.667 45.000 11.35 0.00 38.92 5.69
3464 6564 4.946772 TGGACATATCATTCCTCGCAAAAA 59.053 37.500 0.00 0.00 32.55 1.94
3472 6576 6.939163 GCATTAAGACTGGACATATCATTCCT 59.061 38.462 0.00 0.00 32.55 3.36
3523 6627 1.633432 AGCTAAGGTACACCATTGGCA 59.367 47.619 1.54 0.00 38.89 4.92
3532 6636 4.646040 TGCCGTCTATAAAGCTAAGGTACA 59.354 41.667 0.00 0.00 0.00 2.90
3576 6680 3.202906 GTGAGGCCTGCGATTGTAAATA 58.797 45.455 12.00 0.00 0.00 1.40
3577 6681 2.017049 GTGAGGCCTGCGATTGTAAAT 58.983 47.619 12.00 0.00 0.00 1.40
3599 6704 3.142838 GTGGGTAGGCTCGCCGTA 61.143 66.667 1.69 0.00 41.95 4.02


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

AutoCloner maintained by Alex Coulton.