Multiple sequence alignment - TraesCS4B01G324700

Loading Multiple Alignment...

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 TraesCS4B01G324700 chr4B 100.000 2480 0 0 1 2480 615762497 615764976 0 4580
1 TraesCS4B01G324700 chr4B 91.574 985 69 9 1504 2480 113889581 113888603 0 1347
2 TraesCS4B01G324700 chr5B 95.850 1518 49 2 1 1505 45816299 45817815 0 2442
3 TraesCS4B01G324700 chr5B 95.839 1514 48 3 4 1504 704274419 704272908 0 2433
4 TraesCS4B01G324700 chr5B 95.446 1515 54 3 4 1505 314975391 314973879 0 2401
5 TraesCS4B01G324700 chr3B 95.781 1517 50 2 1 1504 828599740 828601255 0 2435
6 TraesCS4B01G324700 chr7B 95.655 1519 51 3 1 1506 367491389 367492905 0 2425
7 TraesCS4B01G324700 chr7B 91.988 986 65 8 1504 2480 116347336 116348316 0 1371
8 TraesCS4B01G324700 chr2B 95.512 1515 52 4 4 1505 588733449 588731938 0 2407
9 TraesCS4B01G324700 chr2B 95.260 1519 57 3 1 1506 409350698 409352214 0 2392
10 TraesCS4B01G324700 chr2B 95.812 1385 45 1 134 1505 141842568 141843952 0 2224
11 TraesCS4B01G324700 chr6B 95.449 1516 55 2 1 1503 80745604 80747118 0 2405
12 TraesCS4B01G324700 chr1D 92.758 1519 96 4 1 1506 298425607 298427124 0 2183
13 TraesCS4B01G324700 chr6D 91.818 990 63 11 1500 2480 114264550 114265530 0 1363
14 TraesCS4B01G324700 chr5D 91.565 984 71 7 1504 2479 300796700 300797679 0 1347
15 TraesCS4B01G324700 chr5D 91.472 985 71 8 1504 2480 404524134 404523155 0 1341
16 TraesCS4B01G324700 chr1B 91.574 985 69 9 1504 2480 159488496 159487518 0 1347
17 TraesCS4B01G324700 chr1B 91.463 984 71 8 1505 2480 299531451 299530473 0 1339
18 TraesCS4B01G324700 chr7D 91.313 990 67 11 1504 2480 429596144 429595161 0 1334
19 TraesCS4B01G324700 chrUn 91.287 987 70 11 1504 2480 236409105 236408125 0 1332


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 TraesCS4B01G324700 chr4B 615762497 615764976 2479 False 4580 4580 100.000 1 2480 1 chr4B.!!$F1 2479
1 TraesCS4B01G324700 chr4B 113888603 113889581 978 True 1347 1347 91.574 1504 2480 1 chr4B.!!$R1 976
2 TraesCS4B01G324700 chr5B 45816299 45817815 1516 False 2442 2442 95.850 1 1505 1 chr5B.!!$F1 1504
3 TraesCS4B01G324700 chr5B 704272908 704274419 1511 True 2433 2433 95.839 4 1504 1 chr5B.!!$R2 1500
4 TraesCS4B01G324700 chr5B 314973879 314975391 1512 True 2401 2401 95.446 4 1505 1 chr5B.!!$R1 1501
5 TraesCS4B01G324700 chr3B 828599740 828601255 1515 False 2435 2435 95.781 1 1504 1 chr3B.!!$F1 1503
6 TraesCS4B01G324700 chr7B 367491389 367492905 1516 False 2425 2425 95.655 1 1506 1 chr7B.!!$F2 1505
7 TraesCS4B01G324700 chr7B 116347336 116348316 980 False 1371 1371 91.988 1504 2480 1 chr7B.!!$F1 976
8 TraesCS4B01G324700 chr2B 588731938 588733449 1511 True 2407 2407 95.512 4 1505 1 chr2B.!!$R1 1501
9 TraesCS4B01G324700 chr2B 409350698 409352214 1516 False 2392 2392 95.260 1 1506 1 chr2B.!!$F2 1505
10 TraesCS4B01G324700 chr2B 141842568 141843952 1384 False 2224 2224 95.812 134 1505 1 chr2B.!!$F1 1371
11 TraesCS4B01G324700 chr6B 80745604 80747118 1514 False 2405 2405 95.449 1 1503 1 chr6B.!!$F1 1502
12 TraesCS4B01G324700 chr1D 298425607 298427124 1517 False 2183 2183 92.758 1 1506 1 chr1D.!!$F1 1505
13 TraesCS4B01G324700 chr6D 114264550 114265530 980 False 1363 1363 91.818 1500 2480 1 chr6D.!!$F1 980
14 TraesCS4B01G324700 chr5D 300796700 300797679 979 False 1347 1347 91.565 1504 2479 1 chr5D.!!$F1 975
15 TraesCS4B01G324700 chr5D 404523155 404524134 979 True 1341 1341 91.472 1504 2480 1 chr5D.!!$R1 976
16 TraesCS4B01G324700 chr1B 159487518 159488496 978 True 1347 1347 91.574 1504 2480 1 chr1B.!!$R1 976
17 TraesCS4B01G324700 chr1B 299530473 299531451 978 True 1339 1339 91.463 1505 2480 1 chr1B.!!$R2 975
18 TraesCS4B01G324700 chr7D 429595161 429596144 983 True 1334 1334 91.313 1504 2480 1 chr7D.!!$R1 976
19 TraesCS4B01G324700 chrUn 236408125 236409105 980 True 1332 1332 91.287 1504 2480 1 chrUn.!!$R1 976

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
446 460 0.748729 TGGAACCAACAACACGGGAC 60.749 55.0 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1798 1821 0.396435 AGTGTGTTTGCCGAGATCCA 59.604 50.0 0.0 0.0 0.0 3.41 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
27 28 6.318648 GTCCTGAATCTTTATGTGCAACCATA 59.681 38.462 0.00 0.00 34.36 2.74
54 55 7.749377 TGAGAGTTAAATATTTCCCTGAGGA 57.251 36.000 3.39 0.00 41.88 3.71
91 92 8.653328 ACGCAAGGTTAAAGAAGGGATCTTCA 62.653 42.308 8.56 0.00 45.51 3.02
146 147 9.396022 TGAACTCTTTGAGAAATGGTTATATCC 57.604 33.333 1.25 0.00 33.32 2.59
344 358 2.092375 GGGTCCTTGTGATTCCCCTTAG 60.092 54.545 0.00 0.00 32.66 2.18
446 460 0.748729 TGGAACCAACAACACGGGAC 60.749 55.000 0.00 0.00 0.00 4.46
573 587 1.346395 ACGTTGCATGGAACTCTACCA 59.654 47.619 25.01 0.00 41.83 3.25
766 781 1.235281 GGGTGAGGCGGTTCTTGAAC 61.235 60.000 5.03 5.03 0.00 3.18
833 848 5.677091 GCCAGAATGCAAGTGAATTAATCGT 60.677 40.000 0.00 0.00 31.97 3.73
923 938 1.212935 CCAGATTTCGATGGGGGTTCT 59.787 52.381 0.00 0.00 32.63 3.01
990 1005 6.095720 CGTCTAGTAGAAAAGAAGGATGGAGT 59.904 42.308 0.17 0.00 0.00 3.85
1076 1091 0.886563 ACGGTAGGTGCTGTACTCAC 59.113 55.000 9.42 9.42 0.00 3.51
1099 1114 8.423349 TCACAGATGACAAAGGAAAATTCATTT 58.577 29.630 0.32 0.32 41.28 2.32
1153 1168 3.676049 TGATGTACTAACAGCAGAAGCGG 60.676 47.826 0.00 0.00 46.59 5.52
1244 1259 8.892723 TGATAATATGGAAGTCATTGACACAAC 58.107 33.333 18.57 6.69 37.30 3.32
1375 1390 8.814038 AGATAATAAGGTTGCTCATGAACTTT 57.186 30.769 0.00 0.00 0.00 2.66
1595 1612 4.335416 ACAATACAGTACATGCCTTGCTT 58.665 39.130 0.00 0.00 30.46 3.91
1666 1683 2.494870 GCACTTCTCCCATTGCAAGAAT 59.505 45.455 4.94 0.00 34.97 2.40
1699 1720 6.824958 AGTAGGCCCTAAACTGATAATTCA 57.175 37.500 0.00 0.00 0.00 2.57
1706 1727 7.201741 GGCCCTAAACTGATAATTCAAAGAGAC 60.202 40.741 0.00 0.00 0.00 3.36
1707 1728 7.554476 GCCCTAAACTGATAATTCAAAGAGACT 59.446 37.037 0.00 0.00 0.00 3.24
1874 1898 5.359194 ACATCGAGGAGAACATGGTATTT 57.641 39.130 3.06 0.00 0.00 1.40
1992 2016 3.133542 TGATGTAGAAGCCCTCTGTGATG 59.866 47.826 0.00 0.00 35.41 3.07
2047 2072 3.085533 CCTAGATGGGATCTCACGGTAG 58.914 54.545 0.00 0.00 40.76 3.18
2074 2099 3.361977 CGGCGGTGGAAAAGTGGG 61.362 66.667 0.00 0.00 0.00 4.61
2081 2107 1.411074 GGTGGAAAAGTGGGTTCTGGT 60.411 52.381 0.00 0.00 0.00 4.00
2172 2198 2.844839 ATGAGGTAGGGGAGCGCC 60.845 66.667 2.29 0.00 0.00 6.53
2288 2322 4.901814 AGATCATCGCGAAAGTTTCATTG 58.098 39.130 15.24 3.09 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 9.413734 CCTCAGGGAAATATTTAACTCTCAATT 57.586 33.333 0.00 0.00 33.58 2.32
54 55 4.853924 AACCTTGCGTTCATCAAATCTT 57.146 36.364 0.00 0.00 0.00 2.40
91 92 5.118286 GCCATAATGCTTTGCCAAGTAAAT 58.882 37.500 0.00 0.00 31.86 1.40
146 147 0.953471 TGTCCATTTCCAACTCGCCG 60.953 55.000 0.00 0.00 0.00 6.46
173 174 7.114754 GGAATCCATGCATCTCTCCAAATATA 58.885 38.462 0.00 0.00 0.00 0.86
344 358 9.494479 CAATGAAATCCGACATATTATGCATAC 57.506 33.333 5.74 0.00 0.00 2.39
502 516 5.277345 CCGGACACGATAATTTCCAAATCTC 60.277 44.000 0.00 0.00 44.60 2.75
573 587 2.248280 TGGCAAGTGTAACACGACAT 57.752 45.000 0.00 0.00 41.43 3.06
671 685 3.005155 CCAAACCTCTTTTGCCTTCTCAG 59.995 47.826 0.00 0.00 43.03 3.35
766 781 4.832248 TGGTGTGGCATAAGAAGTAAGAG 58.168 43.478 0.00 0.00 0.00 2.85
833 848 5.529430 CACCATAAATACCAAGCGGTTATCA 59.471 40.000 0.00 0.00 46.31 2.15
990 1005 2.262637 ACAAAACCCATAGGAGGTCGA 58.737 47.619 0.00 0.00 36.27 4.20
1076 1091 9.872757 CAAAAATGAATTTTCCTTTGTCATCTG 57.127 29.630 1.67 0.00 39.20 2.90
1099 1114 2.754552 CGATCTTCCCATTTCTGCCAAA 59.245 45.455 0.00 0.00 0.00 3.28
1153 1168 1.692411 AAACCAAACCTCAGAGCCAC 58.308 50.000 0.00 0.00 0.00 5.01
1244 1259 2.477863 GCCGATTGTCCTCCATTTTTCG 60.478 50.000 0.00 0.00 0.00 3.46
1352 1367 8.814038 AGAAAGTTCATGAGCAACCTTATTAT 57.186 30.769 12.41 0.00 0.00 1.28
1375 1390 3.510360 ACAGAAACTTTCGCTAGCCTAGA 59.490 43.478 9.66 0.00 34.02 2.43
1565 1582 5.356751 GGCATGTACTGTATTGTTTCCATCA 59.643 40.000 0.00 0.00 0.00 3.07
1571 1588 4.766891 AGCAAGGCATGTACTGTATTGTTT 59.233 37.500 0.00 0.00 0.00 2.83
1595 1612 0.490017 TTCCCAGTGACAGTAGGGGA 59.510 55.000 14.32 10.07 45.84 4.81
1666 1683 6.099269 CAGTTTAGGGCCTACTAGATTGGTTA 59.901 42.308 14.17 0.00 0.00 2.85
1699 1720 7.334090 TGATATCTTTGCAAGCTAGTCTCTTT 58.666 34.615 3.98 0.00 0.00 2.52
1706 1727 7.326305 GCATGATTTGATATCTTTGCAAGCTAG 59.674 37.037 3.98 0.00 32.28 3.42
1707 1728 7.143340 GCATGATTTGATATCTTTGCAAGCTA 58.857 34.615 3.98 0.00 32.28 3.32
1708 1729 5.983720 GCATGATTTGATATCTTTGCAAGCT 59.016 36.000 3.98 0.00 32.28 3.74
1709 1730 5.751509 TGCATGATTTGATATCTTTGCAAGC 59.248 36.000 3.98 6.83 36.08 4.01
1798 1821 0.396435 AGTGTGTTTGCCGAGATCCA 59.604 50.000 0.00 0.00 0.00 3.41
1874 1898 6.438741 TGGCTTCTTCTCTCTCTTTGATTCTA 59.561 38.462 0.00 0.00 0.00 2.10
1992 2016 2.261729 GTCCTATCAGAGGGGGATTCC 58.738 57.143 0.00 0.00 46.70 3.01
2047 2072 3.423154 CACCGCCGCAACCTTCTC 61.423 66.667 0.00 0.00 0.00 2.87
2081 2107 2.603075 CCTGAAAACATCCAGGGGAA 57.397 50.000 0.00 0.00 44.68 3.97
2205 2239 2.637383 GGAGACTCAACGAGGCGGT 61.637 63.158 4.53 0.00 43.57 5.68
2288 2322 4.823790 ATACCAAACGAAGTCCAAACAC 57.176 40.909 0.00 0.00 45.00 3.32
2354 2389 3.967987 CCTATTAACCTAGAGCCCAGTGT 59.032 47.826 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.