Multiple sequence alignment - TraesCS2A01G172900

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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 TraesCS2A01G172900 chr2A 100.000 2207 0 0 1 2207 130179795 130177589 0.000000e+00 4076
1 TraesCS2A01G172900 chr5A 97.602 2210 49 3 1 2207 109299930 109302138 0.000000e+00 3784
2 TraesCS2A01G172900 chr2B 97.736 1767 37 2 443 2207 10667770 10669535 0.000000e+00 3038
3 TraesCS2A01G172900 chr2B 97.568 1768 39 3 443 2207 390975865 390974099 0.000000e+00 3024
4 TraesCS2A01G172900 chr2B 92.598 689 49 2 630 1317 588687074 588686387 0.000000e+00 989
5 TraesCS2A01G172900 chr2B 95.552 607 18 5 1391 1989 588686398 588685793 0.000000e+00 963
6 TraesCS2A01G172900 chr2B 92.908 564 34 5 755 1317 588685795 588685237 0.000000e+00 815
7 TraesCS2A01G172900 chr2B 96.573 321 11 0 1 321 10667453 10667773 1.160000e-147 532
8 TraesCS2A01G172900 chr2B 95.950 321 13 0 1 321 390976182 390975862 2.510000e-144 521
9 TraesCS2A01G172900 chr2B 92.798 361 25 1 1 361 406245957 406245598 2.510000e-144 521
10 TraesCS2A01G172900 chr2B 93.617 235 15 0 122 356 599848128 599847894 3.490000e-93 351
11 TraesCS2A01G172900 chr1B 97.631 1731 36 3 481 2207 674642150 674640421 0.000000e+00 2964
12 TraesCS2A01G172900 chr1B 93.711 318 19 1 1 318 198560107 198560423 1.980000e-130 475
13 TraesCS2A01G172900 chr1B 95.135 185 9 0 1 185 674654639 674654455 2.140000e-75 292
14 TraesCS2A01G172900 chr7D 90.975 1651 115 8 358 1995 301662742 301661113 0.000000e+00 2193
15 TraesCS2A01G172900 chr7D 94.192 637 25 1 927 1563 46096344 46096968 0.000000e+00 961
16 TraesCS2A01G172900 chr7D 92.813 654 37 5 1563 2207 46101977 46102629 0.000000e+00 939
17 TraesCS2A01G172900 chr7D 92.781 471 27 5 358 825 46086101 46086567 0.000000e+00 675
18 TraesCS2A01G172900 chr1D 93.925 1251 47 6 967 2207 252590495 252591726 0.000000e+00 1862
19 TraesCS2A01G172900 chr1D 91.542 402 13 9 358 744 252585942 252586337 3.230000e-148 534
20 TraesCS2A01G172900 chr7A 93.700 1254 49 7 967 2207 665832345 665831109 0.000000e+00 1851
21 TraesCS2A01G172900 chr7A 89.227 362 35 2 1 361 673020932 673021290 1.200000e-122 449
22 TraesCS2A01G172900 chr4A 92.308 1261 58 9 967 2207 713137572 713136331 0.000000e+00 1755
23 TraesCS2A01G172900 chr4A 91.629 442 27 3 1776 2207 504866808 504867249 8.720000e-169 603
24 TraesCS2A01G172900 chr6B 93.469 934 44 11 384 1314 26562138 26563057 0.000000e+00 1371
25 TraesCS2A01G172900 chr6A 91.796 963 44 11 358 1317 611535000 611534070 0.000000e+00 1308
26 TraesCS2A01G172900 chr6A 94.574 258 13 1 1951 2207 611533569 611533312 4.420000e-107 398
27 TraesCS2A01G172900 chr7B 92.179 358 26 1 1 358 620571908 620572263 2.530000e-139 505
28 TraesCS2A01G172900 chr5B 88.674 362 36 3 1 361 523137003 523137360 9.360000e-119 436
29 TraesCS2A01G172900 chr2D 96.104 77 3 0 285 361 628840856 628840932 2.300000e-25 126


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 TraesCS2A01G172900 chr2A 130177589 130179795 2206 True 4076.000000 4076 100.0000 1 2207 1 chr2A.!!$R1 2206
1 TraesCS2A01G172900 chr5A 109299930 109302138 2208 False 3784.000000 3784 97.6020 1 2207 1 chr5A.!!$F1 2206
2 TraesCS2A01G172900 chr2B 10667453 10669535 2082 False 1785.000000 3038 97.1545 1 2207 2 chr2B.!!$F1 2206
3 TraesCS2A01G172900 chr2B 390974099 390976182 2083 True 1772.500000 3024 96.7590 1 2207 2 chr2B.!!$R3 2206
4 TraesCS2A01G172900 chr2B 588685237 588687074 1837 True 922.333333 989 93.6860 630 1989 3 chr2B.!!$R4 1359
5 TraesCS2A01G172900 chr1B 674640421 674642150 1729 True 2964.000000 2964 97.6310 481 2207 1 chr1B.!!$R1 1726
6 TraesCS2A01G172900 chr7D 301661113 301662742 1629 True 2193.000000 2193 90.9750 358 1995 1 chr7D.!!$R1 1637
7 TraesCS2A01G172900 chr7D 46096344 46096968 624 False 961.000000 961 94.1920 927 1563 1 chr7D.!!$F2 636
8 TraesCS2A01G172900 chr7D 46101977 46102629 652 False 939.000000 939 92.8130 1563 2207 1 chr7D.!!$F3 644
9 TraesCS2A01G172900 chr1D 252590495 252591726 1231 False 1862.000000 1862 93.9250 967 2207 1 chr1D.!!$F2 1240
10 TraesCS2A01G172900 chr7A 665831109 665832345 1236 True 1851.000000 1851 93.7000 967 2207 1 chr7A.!!$R1 1240
11 TraesCS2A01G172900 chr4A 713136331 713137572 1241 True 1755.000000 1755 92.3080 967 2207 1 chr4A.!!$R1 1240
12 TraesCS2A01G172900 chr6B 26562138 26563057 919 False 1371.000000 1371 93.4690 384 1314 1 chr6B.!!$F1 930
13 TraesCS2A01G172900 chr6A 611533312 611535000 1688 True 853.000000 1308 93.1850 358 2207 2 chr6A.!!$R1 1849


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
748 772 1.887242 GTGTGTGCTTCCTGACGCA 60.887 57.895 0.0 0.0 0.0 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 1875 3.011517 CAGAGGACCACCAGGGGG 61.012 72.222 6.02 6.02 42.91 5.4 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
90 91 6.176183 ACCTCACATGTTTCCTTCTAATGAG 58.824 40.000 0.00 0.0 0.00 2.90
156 157 9.264719 AGTTTTAGAAGAAATGCAAGAAAATGG 57.735 29.630 0.00 0.0 0.00 3.16
324 325 2.488347 GGGGCTCCTTGTTACAGTTCAA 60.488 50.000 0.00 0.0 0.00 2.69
367 368 4.401022 ACTCAATTTCATCCTGAAGTGCA 58.599 39.130 0.00 0.0 37.70 4.57
548 549 2.555757 GTCTCAAAGCAGAGCAATGGTT 59.444 45.455 0.30 0.3 42.43 3.67
684 689 5.529581 AAGATTGTTTGTTTGTACCCAGG 57.470 39.130 0.00 0.0 0.00 4.45
748 772 1.887242 GTGTGTGCTTCCTGACGCA 60.887 57.895 0.00 0.0 0.00 5.24
1120 1144 1.676746 CATCATCTGGCACCTTGGAG 58.323 55.000 0.00 0.0 0.00 3.86
1176 1201 3.834489 TGTGATTTGTGCAATGGGTTT 57.166 38.095 0.00 0.0 0.00 3.27
1227 1252 1.211457 CAGGGGCTGCAAGTTCTATCT 59.789 52.381 0.50 0.0 35.30 1.98
1336 1366 8.592105 TTGATTCAAATTTTGTGTTCTGATCC 57.408 30.769 8.89 0.0 0.00 3.36
1359 1389 0.882484 TGTTGCGAGGTTTGCGATCA 60.882 50.000 0.00 0.0 34.24 2.92
1756 1875 0.883833 CCAGTCACAACAAGATGGGC 59.116 55.000 0.00 0.0 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 5.617528 TGTGAGGTTATCCGGCTTAATAA 57.382 39.130 0.00 0.00 39.05 1.40
90 91 2.965147 TTCAATGACGCACGGCTGC 61.965 57.895 0.00 0.00 40.38 5.25
101 102 7.665145 TCCAACAACATCTATCTTGTTCAATGA 59.335 33.333 0.00 0.00 38.30 2.57
156 157 3.449737 TGCATACCACCCTAGAACTACAC 59.550 47.826 0.00 0.00 0.00 2.90
198 199 0.550914 AACCAAACCAGCACTCAGGA 59.449 50.000 0.00 0.00 0.00 3.86
283 284 3.181455 CCCAGGACCATGAACGATCAATA 60.181 47.826 0.00 0.00 39.49 1.90
324 325 8.079211 TGAGTATTATGGACTAAACTCTTGCT 57.921 34.615 0.00 0.00 33.40 3.91
405 406 2.438254 CTGCCGCTGGGTTATGCA 60.438 61.111 0.00 0.00 34.97 3.96
548 549 6.587226 GCACATTCTGATAAAATTTGCAGTGA 59.413 34.615 12.76 6.57 38.85 3.41
684 689 1.006832 GGGCACATCACGTACACATC 58.993 55.000 0.00 0.00 0.00 3.06
936 960 9.903682 CTCTCATTAAATCAGAAACATTGTGTT 57.096 29.630 0.00 0.00 43.41 3.32
1120 1144 6.646240 ACTCCATGAACACATTTAATTTGCAC 59.354 34.615 0.00 0.00 0.00 4.57
1176 1201 0.116342 TGACAGCCCCTTCCACTCTA 59.884 55.000 0.00 0.00 0.00 2.43
1227 1252 2.481969 CGCTGCAAGTCAGGCTTATAGA 60.482 50.000 0.00 0.00 43.06 1.98
1336 1366 1.463056 TCGCAAACCTCGCAACATTAG 59.537 47.619 0.00 0.00 0.00 1.73
1359 1389 0.178068 GCAGTCCCGACCATACATGT 59.822 55.000 2.69 2.69 0.00 3.21
1756 1875 3.011517 CAGAGGACCACCAGGGGG 61.012 72.222 6.02 6.02 42.91 5.40
1802 1921 5.581126 ACATCAGACTTCAAAGCAAAACA 57.419 34.783 0.00 0.00 0.00 2.83



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

AutoCloner maintained by Alex Coulton.