Multiple sequence alignment - TraesCS4B01G273700

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 TraesCS4B01G273700 chr4B 100.000 2288 0 0 1 2288 551730107 551732394 0.000000e+00 4226.0
1 TraesCS4B01G273700 chr4B 97.727 2288 51 1 1 2288 551784715 551787001 0.000000e+00 3936.0
2 TraesCS4B01G273700 chr7B 93.503 1724 102 7 2 1724 150842115 150843829 0.000000e+00 2555.0
3 TraesCS4B01G273700 chr7B 88.858 359 40 0 1723 2081 141013494 141013136 2.090000e-120 442.0
4 TraesCS4B01G273700 chr6D 93.318 1721 108 6 4 1723 450905965 450907679 0.000000e+00 2534.0
5 TraesCS4B01G273700 chr7D 93.210 1723 115 2 2 1723 463975826 463974105 0.000000e+00 2532.0
6 TraesCS4B01G273700 chr7D 93.151 1723 113 2 2 1719 107722767 107721045 0.000000e+00 2523.0
7 TraesCS4B01G273700 chr7D 88.462 78 9 0 2079 2156 531068874 531068951 6.730000e-16 95.3
8 TraesCS4B01G273700 chr2B 92.290 1725 124 6 2 1723 459481020 459479302 0.000000e+00 2440.0
9 TraesCS4B01G273700 chr2B 87.465 359 44 1 1723 2081 154531251 154530894 1.640000e-111 412.0
10 TraesCS4B01G273700 chr5B 91.773 1726 129 5 2 1723 641300599 641298883 0.000000e+00 2388.0
11 TraesCS4B01G273700 chr5B 87.500 192 24 0 1890 2081 41260468 41260277 2.960000e-54 222.0
12 TraesCS4B01G273700 chr5B 91.339 127 11 0 1723 1849 592834328 592834202 8.400000e-40 174.0
13 TraesCS4B01G273700 chr6B 91.652 1725 127 8 2 1721 189103565 189105277 0.000000e+00 2372.0
14 TraesCS4B01G273700 chr2A 91.183 1724 138 11 2 1723 504065954 504067665 0.000000e+00 2329.0
15 TraesCS4B01G273700 chr4D 94.708 359 19 0 1723 2081 442882788 442882430 1.990000e-155 558.0
16 TraesCS4B01G273700 chr4D 94.429 359 20 0 1723 2081 442878644 442879002 9.240000e-154 553.0
17 TraesCS4B01G273700 chr4D 97.143 210 6 0 2079 2288 442879049 442879258 2.800000e-94 355.0
18 TraesCS4B01G273700 chr4D 97.101 207 6 0 2082 2288 442882380 442882174 1.300000e-92 350.0
19 TraesCS4B01G273700 chr4A 93.872 359 22 0 1723 2081 24812148 24811790 2.000000e-150 542.0
20 TraesCS4B01G273700 chr4A 90.028 361 33 3 1723 2081 656482781 656482422 4.450000e-127 464.0
21 TraesCS4B01G273700 chr4A 93.839 211 9 1 2082 2288 24811740 24811530 4.740000e-82 315.0
22 TraesCS4B01G273700 chr5A 90.251 359 35 0 1723 2081 689900346 689900704 9.570000e-129 470.0


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 TraesCS4B01G273700 chr4B 551730107 551732394 2287 False 4226.0 4226 100.0000 1 2288 1 chr4B.!!$F1 2287
1 TraesCS4B01G273700 chr4B 551784715 551787001 2286 False 3936.0 3936 97.7270 1 2288 1 chr4B.!!$F2 2287
2 TraesCS4B01G273700 chr7B 150842115 150843829 1714 False 2555.0 2555 93.5030 2 1724 1 chr7B.!!$F1 1722
3 TraesCS4B01G273700 chr6D 450905965 450907679 1714 False 2534.0 2534 93.3180 4 1723 1 chr6D.!!$F1 1719
4 TraesCS4B01G273700 chr7D 463974105 463975826 1721 True 2532.0 2532 93.2100 2 1723 1 chr7D.!!$R2 1721
5 TraesCS4B01G273700 chr7D 107721045 107722767 1722 True 2523.0 2523 93.1510 2 1719 1 chr7D.!!$R1 1717
6 TraesCS4B01G273700 chr2B 459479302 459481020 1718 True 2440.0 2440 92.2900 2 1723 1 chr2B.!!$R2 1721
7 TraesCS4B01G273700 chr5B 641298883 641300599 1716 True 2388.0 2388 91.7730 2 1723 1 chr5B.!!$R3 1721
8 TraesCS4B01G273700 chr6B 189103565 189105277 1712 False 2372.0 2372 91.6520 2 1721 1 chr6B.!!$F1 1719
9 TraesCS4B01G273700 chr2A 504065954 504067665 1711 False 2329.0 2329 91.1830 2 1723 1 chr2A.!!$F1 1721
10 TraesCS4B01G273700 chr4D 442878644 442879258 614 False 454.0 553 95.7860 1723 2288 2 chr4D.!!$F1 565
11 TraesCS4B01G273700 chr4D 442882174 442882788 614 True 454.0 558 95.9045 1723 2288 2 chr4D.!!$R1 565
12 TraesCS4B01G273700 chr4A 24811530 24812148 618 True 428.5 542 93.8555 1723 2288 2 chr4A.!!$R2 565

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
75 76 0.746923 TCGTCGTCATCATCCTCGGT 60.747 55.0 0.0 0.0 0.0 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1941 1960 0.529833 CCGATGCTGCTATCCGAGAT 59.47 55.0 0.0 0.0 0.0 2.75 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
67 68 2.571757 GGCAGGTCGTCGTCATCA 59.428 61.111 0.00 0.00 0.00 3.07
75 76 0.746923 TCGTCGTCATCATCCTCGGT 60.747 55.000 0.00 0.00 0.00 4.69
176 180 2.763215 GCTCCCCACCAATGACCA 59.237 61.111 0.00 0.00 0.00 4.02
234 238 1.067582 GACGGTCATTAGGAGCCCG 59.932 63.158 2.62 0.00 40.99 6.13
316 320 1.451927 GGCCCAGCGAATGATGTCA 60.452 57.895 0.00 0.00 0.00 3.58
576 587 2.192263 GATGGAGAGGAGGAAGGTTGT 58.808 52.381 0.00 0.00 0.00 3.32
693 704 7.688578 GTCGTTTTAACTACATGCTCTTCAATC 59.311 37.037 0.00 0.00 0.00 2.67
962 977 1.559682 GGATGGCCCAACTCACTTCTA 59.440 52.381 0.00 0.00 34.14 2.10
1194 1211 0.605589 CGTTCAAGCTCCTCACTCCT 59.394 55.000 0.00 0.00 0.00 3.69
1424 1441 7.726033 AGTTGATCCTCTGTTTATACTCTGT 57.274 36.000 0.00 0.00 0.00 3.41
1841 1860 3.055719 CCTTGGATTGCGCACCGT 61.056 61.111 11.12 0.00 0.00 4.83
1960 1979 0.529833 ATCTCGGATAGCAGCATCGG 59.470 55.000 0.00 0.95 0.00 4.18
1972 1991 0.037882 AGCATCGGAGCGTGATATGG 60.038 55.000 0.00 0.00 40.15 2.74
1985 2004 1.206132 TGATATGGTCCGCAGTTTCGT 59.794 47.619 0.00 0.00 0.00 3.85
2241 2313 0.106149 AAGCAACCGTCCGAAAGAGT 59.894 50.000 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.407139 AAGATGAAGGCCAGCCACTT 59.593 50.000 12.03 1.82 38.92 3.16
75 76 0.532573 GCAGATTGACCTCGACTCCA 59.467 55.000 0.00 0.00 0.00 3.86
234 238 6.038997 AGTGATCCAAGTACAAGAACTACC 57.961 41.667 0.00 0.00 0.00 3.18
576 587 1.006519 CCCCCTCTCTTCTCTCACTGA 59.993 57.143 0.00 0.00 0.00 3.41
693 704 2.031420 CACAACACAGAGTTCATGGCTG 60.031 50.000 0.00 0.00 38.74 4.85
775 786 1.301401 CCTTGTCTTCAACGGCCGA 60.301 57.895 35.90 6.51 0.00 5.54
980 995 0.034670 GGGGATGCACTCAAGCTTCT 60.035 55.000 0.00 0.00 38.37 2.85
1276 1293 2.378634 CCCAGCCCTAGTCCTTGGG 61.379 68.421 9.20 9.20 46.45 4.12
1424 1441 4.831107 TGTAGCACACATCATAAGCAGAA 58.169 39.130 0.00 0.00 30.04 3.02
1841 1860 3.647590 TGGAACAGGCTCTATATGCATCA 59.352 43.478 0.19 0.00 0.00 3.07
1941 1960 0.529833 CCGATGCTGCTATCCGAGAT 59.470 55.000 0.00 0.00 0.00 2.75
1947 1966 1.006805 ACGCTCCGATGCTGCTATC 60.007 57.895 0.00 1.79 0.00 2.08
1960 1979 0.941463 CTGCGGACCATATCACGCTC 60.941 60.000 9.32 0.00 43.37 5.03
1972 1991 2.668280 GGAGCACGAAACTGCGGAC 61.668 63.158 0.00 0.00 42.42 4.79
1985 2004 1.297689 GGCTGTGTGATCAGGAGCA 59.702 57.895 17.82 1.92 36.12 4.26
2241 2313 4.564821 GCTCCAACTACACCCATCTAACAA 60.565 45.833 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.