Multiple sequence alignment - TraesCS2A01G217400

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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 TraesCS2A01G217400 chr2A 100.000 2560 0 0 1 2560 204817190 204814631 0.000000e+00 4728.0
1 TraesCS2A01G217400 chr2A 92.012 989 62 7 585 1571 204626058 204625085 0.000000e+00 1373.0
2 TraesCS2A01G217400 chr2B 96.259 2352 77 7 1 2350 247364569 247362227 0.000000e+00 3845.0
3 TraesCS2A01G217400 chr2B 91.266 1351 102 8 759 2102 246954044 246952703 0.000000e+00 1827.0
4 TraesCS2A01G217400 chr2B 95.283 212 7 2 2349 2560 247362134 247361926 1.470000e-87 333.0
5 TraesCS2A01G217400 chr2B 93.590 156 8 2 575 730 246954198 246954045 5.510000e-57 231.0
6 TraesCS2A01G217400 chr2D 96.088 2352 82 6 1 2350 190327641 190325298 0.000000e+00 3825.0
7 TraesCS2A01G217400 chr2D 90.957 1526 114 15 585 2103 190214153 190212645 0.000000e+00 2032.0
8 TraesCS2A01G217400 chr2D 93.868 212 10 2 2349 2560 190325205 190324997 1.480000e-82 316.0
9 TraesCS2A01G217400 chr7D 86.182 550 71 3 3 550 237620644 237621190 7.890000e-165 590.0
10 TraesCS2A01G217400 chr7D 92.105 38 2 1 2349 2385 76534905 76534868 5.000000e-03 52.8
11 TraesCS2A01G217400 chr5D 85.484 558 78 3 5 561 515335517 515336072 1.710000e-161 579.0
12 TraesCS2A01G217400 chr7B 84.672 548 80 4 5 550 215011671 215012216 6.230000e-151 544.0
13 TraesCS2A01G217400 chr7A 84.601 552 78 5 5 550 557562694 557563244 2.240000e-150 542.0
14 TraesCS2A01G217400 chr7A 100.000 33 0 0 2350 2382 102495523 102495555 7.650000e-06 62.1
15 TraesCS2A01G217400 chr1B 84.220 564 81 7 1 561 642093322 642092764 2.240000e-150 542.0
16 TraesCS2A01G217400 chr1B 100.000 33 0 0 2350 2382 652257132 652257164 7.650000e-06 62.1
17 TraesCS2A01G217400 chr6B 84.420 552 83 3 3 553 591239481 591238932 8.060000e-150 540.0
18 TraesCS2A01G217400 chr5B 84.144 555 79 4 5 557 141461134 141461681 1.740000e-146 529.0
19 TraesCS2A01G217400 chr3D 100.000 33 0 0 2350 2382 601113895 601113863 7.650000e-06 62.1


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 TraesCS2A01G217400 chr2A 204814631 204817190 2559 True 4728.0 4728 100.000 1 2560 1 chr2A.!!$R2 2559
1 TraesCS2A01G217400 chr2A 204625085 204626058 973 True 1373.0 1373 92.012 585 1571 1 chr2A.!!$R1 986
2 TraesCS2A01G217400 chr2B 247361926 247364569 2643 True 2089.0 3845 95.771 1 2560 2 chr2B.!!$R2 2559
3 TraesCS2A01G217400 chr2B 246952703 246954198 1495 True 1029.0 1827 92.428 575 2102 2 chr2B.!!$R1 1527
4 TraesCS2A01G217400 chr2D 190324997 190327641 2644 True 2070.5 3825 94.978 1 2560 2 chr2D.!!$R2 2559
5 TraesCS2A01G217400 chr2D 190212645 190214153 1508 True 2032.0 2032 90.957 585 2103 1 chr2D.!!$R1 1518
6 TraesCS2A01G217400 chr7D 237620644 237621190 546 False 590.0 590 86.182 3 550 1 chr7D.!!$F1 547
7 TraesCS2A01G217400 chr5D 515335517 515336072 555 False 579.0 579 85.484 5 561 1 chr5D.!!$F1 556
8 TraesCS2A01G217400 chr7B 215011671 215012216 545 False 544.0 544 84.672 5 550 1 chr7B.!!$F1 545
9 TraesCS2A01G217400 chr7A 557562694 557563244 550 False 542.0 542 84.601 5 550 1 chr7A.!!$F2 545
10 TraesCS2A01G217400 chr1B 642092764 642093322 558 True 542.0 542 84.220 1 561 1 chr1B.!!$R1 560
11 TraesCS2A01G217400 chr6B 591238932 591239481 549 True 540.0 540 84.420 3 553 1 chr6B.!!$R1 550
12 TraesCS2A01G217400 chr5B 141461134 141461681 547 False 529.0 529 84.144 5 557 1 chr5B.!!$F1 552

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
59 60 2.781667 AGTTCTCAATCCCTAGCCCAT 58.218 47.619 0.0 0.0 0.0 4.00 F
1228 1258 3.428746 TCACAACGTTTTCCACCATTG 57.571 42.857 0.0 0.0 0.0 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1281 1311 1.497991 TTCACTTCGGCGAAGAACAG 58.502 50.0 45.12 31.58 41.71 3.16 R
2160 2200 1.712018 CGTACGACCGAGCCATGAGA 61.712 60.0 10.44 0.00 0.00 3.27 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
59 60 2.781667 AGTTCTCAATCCCTAGCCCAT 58.218 47.619 0.00 0.00 0.00 4.00
153 154 6.481313 TGCCAGAAAAATCGAGATCAATAGAG 59.519 38.462 0.00 0.00 0.00 2.43
507 523 3.705604 GCTCAAACAAGCAAAGCACTAA 58.294 40.909 0.00 0.00 42.05 2.24
753 771 7.279313 CAGTACGTATACCAACCTTAAAAGCAT 59.721 37.037 0.00 0.00 30.88 3.79
884 912 9.447040 CTTATCAATCATTGAACATGATGTCAC 57.553 33.333 3.63 0.00 43.95 3.67
892 920 6.603237 TTGAACATGATGTCACGATATTCC 57.397 37.500 0.00 0.00 0.00 3.01
987 1016 7.596749 TCCTGACGAAGAGATTATTCAAAAC 57.403 36.000 0.00 0.00 0.00 2.43
1214 1244 8.673711 TGCTTTAATGTGGAATACTATCACAAC 58.326 33.333 0.00 0.00 43.38 3.32
1228 1258 3.428746 TCACAACGTTTTCCACCATTG 57.571 42.857 0.00 0.00 0.00 2.82
1252 1282 7.939782 TGCAATTTCACTGTAAAGATTGAGAA 58.060 30.769 8.76 0.00 0.00 2.87
1281 1311 1.808945 CAAGTGATTCCAGAGTGGCAC 59.191 52.381 10.29 10.29 37.47 5.01
1337 1367 4.889995 AGAAAATACTATTTCTGCTGCCCC 59.110 41.667 0.00 0.00 45.47 5.80
1490 1524 9.565090 CATAACCAAGGATTTGATGATCTAAGA 57.435 33.333 0.00 0.00 36.36 2.10
1497 1531 7.986704 AGGATTTGATGATCTAAGACATCCAT 58.013 34.615 8.80 0.00 41.21 3.41
1941 1976 4.311606 GGAAGAAAGAATCCTCGGATAGC 58.688 47.826 0.00 0.00 33.97 2.97
2007 2042 6.984474 TCTTAAAAGTATTCGAGGTATGCCAG 59.016 38.462 1.54 0.00 37.19 4.85
2014 2049 4.746535 TTCGAGGTATGCCAGTTGAATA 57.253 40.909 1.54 0.00 37.19 1.75
2058 2096 5.587844 ACATCATCCTAATTGTGAGCAAGTC 59.412 40.000 0.00 0.00 38.10 3.01
2059 2097 5.164620 TCATCCTAATTGTGAGCAAGTCA 57.835 39.130 0.00 0.00 38.10 3.41
2073 2111 2.094675 CAAGTCATTCACCATGGGTCC 58.905 52.381 18.09 0.00 31.02 4.46
2130 2170 4.421131 ACACCCCTGATATGTATCTCCTC 58.579 47.826 2.08 0.00 33.88 3.71
2173 2213 0.324738 TCCTCTTCTCATGGCTCGGT 60.325 55.000 0.00 0.00 0.00 4.69
2174 2214 0.103937 CCTCTTCTCATGGCTCGGTC 59.896 60.000 0.00 0.00 0.00 4.79
2470 2606 0.753262 CTGGAGGGACGATTACCAGG 59.247 60.000 0.00 0.00 42.77 4.45
2499 2635 3.623510 GGTTGAGCTTTGCTACACCTATC 59.376 47.826 10.65 0.00 39.88 2.08
2524 2660 9.737427 TCAAAAATAATTACTCGAAACTTTGCA 57.263 25.926 0.00 0.00 0.00 4.08
2535 2671 6.657541 ACTCGAAACTTTGCATAAGGGATTAA 59.342 34.615 11.59 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
123 124 2.884012 TCTCGATTTTTCTGGCAAAGCA 59.116 40.909 0.00 0.00 0.00 3.91
153 154 3.453717 AGGGGTACGGAAAAGATTAGACC 59.546 47.826 0.00 0.00 0.00 3.85
240 245 2.181125 TGTCTTATGGTGGTCGGCTAA 58.819 47.619 0.00 0.00 0.00 3.09
241 246 1.855295 TGTCTTATGGTGGTCGGCTA 58.145 50.000 0.00 0.00 0.00 3.93
499 515 7.569240 AGGCTAGAAATATGAAGTTAGTGCTT 58.431 34.615 0.00 0.00 0.00 3.91
507 523 5.509498 TGGCAAAGGCTAGAAATATGAAGT 58.491 37.500 0.00 0.00 40.87 3.01
685 703 1.987807 CTCATGGCCCGTGATCCCTT 61.988 60.000 6.01 0.00 0.00 3.95
820 848 4.201910 CCCCAACACATATTAAGAAGCACG 60.202 45.833 0.00 0.00 0.00 5.34
884 912 7.478520 AGAACAAATAGAAACCGGAATATCG 57.521 36.000 9.46 0.00 0.00 2.92
892 920 8.752766 TCAAGTAGTAGAACAAATAGAAACCG 57.247 34.615 0.00 0.00 0.00 4.44
987 1016 3.689649 CCTTAGTCATCCAGTTTTTCCCG 59.310 47.826 0.00 0.00 0.00 5.14
1214 1244 3.806521 TGAAATTGCAATGGTGGAAAACG 59.193 39.130 13.82 0.00 38.70 3.60
1228 1258 7.327032 GGTTCTCAATCTTTACAGTGAAATTGC 59.673 37.037 0.00 0.00 0.00 3.56
1252 1282 2.840651 CTGGAATCACTTGACCTAGGGT 59.159 50.000 14.81 0.00 39.44 4.34
1281 1311 1.497991 TTCACTTCGGCGAAGAACAG 58.502 50.000 45.12 31.58 41.71 3.16
1337 1367 7.703058 AGTACCATTTTCATTTGGTTCTAGG 57.297 36.000 0.00 0.00 43.73 3.02
1497 1531 3.576861 CCTGGTCATATCCACCTGTAGA 58.423 50.000 2.66 0.00 34.66 2.59
1853 1888 4.351111 AGGTTTAGTTCCAGTCCAAGTGAT 59.649 41.667 0.00 0.00 0.00 3.06
2058 2096 2.120909 GCCGGACCCATGGTGAATG 61.121 63.158 5.05 0.00 35.25 2.67
2059 2097 2.275418 GCCGGACCCATGGTGAAT 59.725 61.111 5.05 0.00 35.25 2.57
2086 2126 8.114290 GGTGTTTATGTAAATGACATCTACGTG 58.886 37.037 0.00 0.00 46.33 4.49
2146 2186 5.388654 AGCCATGAGAAGAGGAAAAAGAAA 58.611 37.500 0.00 0.00 0.00 2.52
2160 2200 1.712018 CGTACGACCGAGCCATGAGA 61.712 60.000 10.44 0.00 0.00 3.27
2173 2213 2.032528 AGTCCCACGGTCGTACGA 59.967 61.111 15.28 15.28 37.61 3.43
2174 2214 2.177531 CAGTCCCACGGTCGTACG 59.822 66.667 9.53 9.53 40.31 3.67
2470 2606 2.597510 AAAGCTCAACCCGTGGCC 60.598 61.111 0.00 0.00 0.00 5.36
2511 2647 5.567138 AATCCCTTATGCAAAGTTTCGAG 57.433 39.130 0.00 0.00 0.00 4.04
2512 2648 7.639113 ATTAATCCCTTATGCAAAGTTTCGA 57.361 32.000 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.