Multiple sequence alignment - TraesCS2A01G340200

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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 TraesCS2A01G340200 chr2A 100.000 2479 0 0 1 2479 575062871 575060393 0 4578
1 TraesCS2A01G340200 chr7D 96.022 2489 76 9 1 2477 155686979 155689456 0 4026
2 TraesCS2A01G340200 chrUn 87.922 977 56 27 1511 2478 504592 503669 0 1094


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 TraesCS2A01G340200 chr2A 575060393 575062871 2478 True 4578 4578 100.000 1 2479 1 chr2A.!!$R1 2478
1 TraesCS2A01G340200 chr7D 155686979 155689456 2477 False 4026 4026 96.022 1 2477 1 chr7D.!!$F1 2476
2 TraesCS2A01G340200 chrUn 503669 504592 923 True 1094 1094 87.922 1511 2478 1 chrUn.!!$R1 967

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
85 86 0.104120 TGCGTAGTGGCGATTGCTAT 59.896 50.0 4.59 0.00 42.25 2.97 F
97 98 0.740737 ATTGCTATGCGTTTGGGCTC 59.259 50.0 0.00 0.00 0.00 4.70 F
180 181 0.966875 AATGGGATGCATGCACGTGT 60.967 50.0 25.37 6.94 0.00 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1095 1099 0.035630 AGTCTGCCTGCTGTCCATTC 60.036 55.0 0.00 0.00 0.00 2.67 R
1153 1157 0.178068 ACAACACGACAGCTGTTCCT 59.822 50.0 22.65 3.26 29.02 3.36 R
2082 2097 0.322456 TGCCAGGCAGATACAACACC 60.322 55.0 11.22 0.00 33.32 4.16 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
34 35 5.831702 ATATCTCTTGCCTTGAAGCTTTG 57.168 39.130 0.00 0.00 0.00 2.77
38 39 2.620115 TCTTGCCTTGAAGCTTTGTCTG 59.380 45.455 0.00 0.00 0.00 3.51
85 86 0.104120 TGCGTAGTGGCGATTGCTAT 59.896 50.000 4.59 0.00 42.25 2.97
97 98 0.740737 ATTGCTATGCGTTTGGGCTC 59.259 50.000 0.00 0.00 0.00 4.70
157 158 2.548875 CTAGAAGCAGCTTCAATCGCT 58.451 47.619 32.20 15.98 42.37 4.93
180 181 0.966875 AATGGGATGCATGCACGTGT 60.967 50.000 25.37 6.94 0.00 4.49
181 182 1.659622 ATGGGATGCATGCACGTGTG 61.660 55.000 25.37 9.68 0.00 3.82
229 230 6.594788 AATAAATTCAGAGCACAACCATGT 57.405 33.333 0.00 0.00 41.61 3.21
230 231 4.942761 AAATTCAGAGCACAACCATGTT 57.057 36.364 0.00 0.00 37.82 2.71
353 354 2.930040 CAACATCGTAGATGGTTCGCTT 59.070 45.455 13.69 0.00 45.12 4.68
354 355 2.810650 ACATCGTAGATGGTTCGCTTC 58.189 47.619 13.69 0.00 45.12 3.86
392 393 5.838531 ATGTTTTCTTTGGTCCGTTGTTA 57.161 34.783 0.00 0.00 0.00 2.41
431 432 6.986250 AGGGAATCATCTTTTGTGTTCTTTC 58.014 36.000 0.00 0.00 0.00 2.62
436 437 4.574421 TCATCTTTTGTGTTCTTTCGCAGA 59.426 37.500 0.00 0.00 0.00 4.26
527 529 9.123709 GTTTAAAGAAATTGCGTGTGATATGAA 57.876 29.630 0.00 0.00 0.00 2.57
530 532 3.698029 AATTGCGTGTGATATGAAGGC 57.302 42.857 0.00 0.00 0.00 4.35
553 555 6.071728 GGCCAGATTAATTAAGATGTGGGATG 60.072 42.308 13.86 1.00 37.23 3.51
599 601 8.429641 ACTTACTTGATGAAGAGGTCAGTTTTA 58.570 33.333 0.00 0.00 40.43 1.52
604 606 7.854557 TGATGAAGAGGTCAGTTTTATGATG 57.145 36.000 0.00 0.00 40.43 3.07
696 700 9.550406 AAATTATTATTGTTTCAGGGCATGATG 57.450 29.630 1.35 0.00 37.89 3.07
720 724 8.978874 TGCATGAGAAGGTAATGTAACATATT 57.021 30.769 0.00 0.00 0.00 1.28
767 771 7.974504 TCCAAGAAGGTTCAGTCTAAGTTTAT 58.025 34.615 0.00 0.00 39.02 1.40
860 864 6.136541 ACTATTGGCGGAGATTGAATTTTC 57.863 37.500 0.00 0.00 0.00 2.29
982 986 7.962373 TCATTAAAGCATACAAATGTCGAACAG 59.038 33.333 0.00 0.00 35.38 3.16
1163 1167 7.872113 AAAATTCTAGGAATAGGAACAGCTG 57.128 36.000 13.48 13.48 0.00 4.24
1191 1195 6.481976 GTGTTGTACATTCCGATGGATAATCA 59.518 38.462 0.00 0.00 37.60 2.57
1216 1220 7.995488 CAGAAAATGAGGGTAGTATGGAGAAAT 59.005 37.037 0.00 0.00 0.00 2.17
1278 1282 8.657387 AGTATATAATAGCTCACAGATGTGGT 57.343 34.615 12.77 1.65 45.65 4.16
1365 1369 7.928908 TGCATGTTCTTTCATAGTTTTTCAC 57.071 32.000 0.00 0.00 0.00 3.18
1369 1373 7.548196 TGTTCTTTCATAGTTTTTCACGTCT 57.452 32.000 0.00 0.00 0.00 4.18
1370 1374 7.627340 TGTTCTTTCATAGTTTTTCACGTCTC 58.373 34.615 0.00 0.00 0.00 3.36
1371 1375 7.494625 TGTTCTTTCATAGTTTTTCACGTCTCT 59.505 33.333 0.00 0.00 0.00 3.10
1372 1376 8.975439 GTTCTTTCATAGTTTTTCACGTCTCTA 58.025 33.333 0.00 0.00 0.00 2.43
1373 1377 9.537192 TTCTTTCATAGTTTTTCACGTCTCTAA 57.463 29.630 0.00 0.00 0.00 2.10
1472 1476 3.724478 TGATGAACTCCACCTCCATACT 58.276 45.455 0.00 0.00 0.00 2.12
1676 1686 6.569127 TGGTCCAGATATAGCACCTTTTTA 57.431 37.500 0.00 0.00 0.00 1.52
1746 1757 0.103937 GCATCTCTCAGTTCCCCTCG 59.896 60.000 0.00 0.00 0.00 4.63
2056 2071 7.013655 GGAAACTAGCCAATGTGATTCATATGT 59.986 37.037 1.90 0.00 35.48 2.29
2082 2097 8.788806 TCCACAGTACAACAATAACCATTTTAG 58.211 33.333 0.00 0.00 0.00 1.85
2177 2192 7.813087 AAAATGAAAGGAGGTTTGGGATAAT 57.187 32.000 0.00 0.00 0.00 1.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 0.818296 ATCCGGTAGCTCACACAGAC 59.182 55.000 0.00 0.00 0.00 3.51
38 39 0.179108 GGTCATCCGGTAGCTCACAC 60.179 60.000 0.00 0.00 0.00 3.82
104 105 3.184628 TCCTATAATGAGGGCCATGAGG 58.815 50.000 6.18 2.20 37.20 3.86
157 158 1.395635 GTGCATGCATCCCATTCTCA 58.604 50.000 25.64 0.00 29.71 3.27
180 181 0.106918 AGGTGTCGAAAAACTGCCCA 60.107 50.000 0.00 0.00 0.00 5.36
181 182 0.591659 GAGGTGTCGAAAAACTGCCC 59.408 55.000 0.00 0.00 0.00 5.36
229 230 4.350368 TTGTGTAAGCTCACCTGATGAA 57.650 40.909 3.31 0.00 36.69 2.57
230 231 4.350368 TTTGTGTAAGCTCACCTGATGA 57.650 40.909 3.31 0.00 37.51 2.92
353 354 5.499004 AAACATTGGCACCTAGTTAGAGA 57.501 39.130 0.00 0.00 0.00 3.10
354 355 5.940470 AGAAAACATTGGCACCTAGTTAGAG 59.060 40.000 0.00 0.00 0.00 2.43
385 386 3.811722 ACATGCACAGTGATAACAACG 57.188 42.857 4.15 0.00 0.00 4.10
392 393 3.719268 TTCCCTAACATGCACAGTGAT 57.281 42.857 4.15 0.00 0.00 3.06
509 511 3.181487 GGCCTTCATATCACACGCAATTT 60.181 43.478 0.00 0.00 0.00 1.82
517 519 9.288576 CTTAATTAATCTGGCCTTCATATCACA 57.711 33.333 3.32 0.00 0.00 3.58
527 529 5.134339 TCCCACATCTTAATTAATCTGGCCT 59.866 40.000 3.32 0.00 0.00 5.19
530 532 6.071728 GGCATCCCACATCTTAATTAATCTGG 60.072 42.308 0.00 1.84 0.00 3.86
553 555 5.352643 AGTTCACTGTTAACGTTAATGGC 57.647 39.130 22.65 11.40 32.00 4.40
604 606 9.236691 CTGATTGTATAATGTTTATGTTGGCAC 57.763 33.333 0.00 0.00 0.00 5.01
696 700 8.840321 ACAATATGTTACATTACCTTCTCATGC 58.160 33.333 2.23 0.00 0.00 4.06
720 724 4.251543 TCAGCGACTGAACTTGATAACA 57.748 40.909 7.02 0.00 37.57 2.41
731 735 1.205655 CCTTCTTGGATCAGCGACTGA 59.794 52.381 11.12 11.12 44.99 3.41
767 771 4.594123 TGATGGAAATACGGCGAAGATA 57.406 40.909 16.62 0.00 0.00 1.98
845 849 8.034058 AGTCTAAACTGAAAATTCAATCTCCG 57.966 34.615 0.00 0.00 36.64 4.63
935 939 5.116180 TGACGTGTCTTCTTCAAAATCTGT 58.884 37.500 0.00 0.00 0.00 3.41
982 986 4.332819 CCTCATGGTCGAAATAACAGAACC 59.667 45.833 0.00 0.00 0.00 3.62
996 1000 6.543831 ACAAAACAATATAGAGCCTCATGGTC 59.456 38.462 0.00 0.00 41.93 4.02
1095 1099 0.035630 AGTCTGCCTGCTGTCCATTC 60.036 55.000 0.00 0.00 0.00 2.67
1153 1157 0.178068 ACAACACGACAGCTGTTCCT 59.822 50.000 22.65 3.26 29.02 3.36
1163 1167 2.347452 CCATCGGAATGTACAACACGAC 59.653 50.000 17.43 0.00 29.20 4.34
1191 1195 7.510675 TTTCTCCATACTACCCTCATTTTCT 57.489 36.000 0.00 0.00 0.00 2.52
1278 1282 4.746535 TTCTGGTATTCTACGAATGCCA 57.253 40.909 20.19 20.19 39.55 4.92
1373 1377 8.895737 CCCTGCAAAATCATTTTTAGCAATTAT 58.104 29.630 8.70 0.00 37.86 1.28
1380 1384 4.577875 TGCCCCTGCAAAATCATTTTTAG 58.422 39.130 0.00 0.00 46.66 1.85
1429 1433 2.972713 TCCTCCGGCTCTTGCTTTATAT 59.027 45.455 0.00 0.00 39.59 0.86
1472 1476 5.868662 TCCTTCCCCTAATCCTTTTAGGTA 58.131 41.667 9.83 0.00 39.86 3.08
1676 1686 4.347583 ACACATGGATGGTGGAACAATTTT 59.652 37.500 0.00 0.00 44.16 1.82
1746 1757 6.072563 ACCATGCTCACAAATAAAATTTTGCC 60.073 34.615 13.76 0.00 39.65 4.52
1861 1872 8.777413 TCTTGATTGTCTGAAATCAGTTGTTAG 58.223 33.333 10.06 8.19 44.96 2.34
2025 2040 7.395772 TGAATCACATTGGCTAGTTTCCATTTA 59.604 33.333 0.00 0.00 32.92 1.40
2026 2041 6.211184 TGAATCACATTGGCTAGTTTCCATTT 59.789 34.615 0.00 0.00 32.92 2.32
2027 2042 5.716228 TGAATCACATTGGCTAGTTTCCATT 59.284 36.000 0.00 0.00 32.92 3.16
2039 2054 5.591472 ACTGTGGACATATGAATCACATTGG 59.409 40.000 21.11 15.58 40.07 3.16
2056 2071 7.589958 AAAATGGTTATTGTTGTACTGTGGA 57.410 32.000 0.00 0.00 0.00 4.02
2082 2097 0.322456 TGCCAGGCAGATACAACACC 60.322 55.000 11.22 0.00 33.32 4.16
2177 2192 3.446310 TGTCAAACAACGCTCTCTACA 57.554 42.857 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.