Multiple sequence alignment - TraesCS4A01G174400

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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 TraesCS4A01G174400 chr4A 100.000 2522 0 0 1 2522 444863195 444865716 0.000000e+00 4658.0
1 TraesCS4A01G174400 chr4D 95.305 2492 53 19 1 2459 125232057 125229597 0.000000e+00 3895.0
2 TraesCS4A01G174400 chr4D 96.825 63 1 1 2461 2522 125227886 125227824 1.230000e-18 104.0
3 TraesCS4A01G174400 chr4B 96.849 1936 56 3 1 1935 189152832 189150901 0.000000e+00 3232.0
4 TraesCS4A01G174400 chr4B 92.693 479 25 8 2046 2522 189135727 189135257 0.000000e+00 682.0
5 TraesCS4A01G174400 chr4B 93.478 184 10 1 1752 1935 189150872 189150691 3.200000e-69 272.0
6 TraesCS4A01G174400 chr4B 95.489 133 4 2 1921 2053 189150676 189150546 7.070000e-51 211.0
7 TraesCS4A01G174400 chr6D 73.559 295 63 11 246 528 276903075 276903366 5.740000e-17 99.0
8 TraesCS4A01G174400 chr5D 73.401 297 60 14 246 528 103654432 103654141 2.670000e-15 93.5
9 TraesCS4A01G174400 chr5B 72.881 295 65 11 246 528 112586979 112586688 1.240000e-13 87.9


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 TraesCS4A01G174400 chr4A 444863195 444865716 2521 False 4658.000000 4658 100.000 1 2522 1 chr4A.!!$F1 2521
1 TraesCS4A01G174400 chr4D 125227824 125232057 4233 True 1999.500000 3895 96.065 1 2522 2 chr4D.!!$R1 2521
2 TraesCS4A01G174400 chr4B 189150546 189152832 2286 True 1238.333333 3232 95.272 1 2053 3 chr4B.!!$R2 2052

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
539 540 0.811616 CTTCTGCCCCGATTCTTCCG 60.812 60.000 0.0 0.0 0.0 4.30 F
740 744 3.198409 TGATCTCGCCATGTTTAGCAT 57.802 42.857 0.0 0.0 38.6 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1476 1487 0.106419 GGGAGATGTCGAGGGAGAGT 60.106 60.000 0.0 0.0 0.0 3.24 R
1901 2121 3.871006 TCCATAGAACATGCAGCTTTACG 59.129 43.478 0.0 0.0 0.0 3.18 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
161 162 3.430497 CCCCCTCCTCCTCCTCGA 61.430 72.222 0.00 0.0 0.00 4.04
539 540 0.811616 CTTCTGCCCCGATTCTTCCG 60.812 60.000 0.00 0.0 0.00 4.30
619 623 6.976349 CACGATGCCGGTTATATAATAAGCTA 59.024 38.462 1.90 0.0 40.78 3.32
740 744 3.198409 TGATCTCGCCATGTTTAGCAT 57.802 42.857 0.00 0.0 38.60 3.79
741 745 4.335400 TGATCTCGCCATGTTTAGCATA 57.665 40.909 0.00 0.0 35.74 3.14
742 746 4.309933 TGATCTCGCCATGTTTAGCATAG 58.690 43.478 0.00 0.0 35.74 2.23
762 767 9.489084 AGCATAGAAAAACAAGGAAAATAAACC 57.511 29.630 0.00 0.0 0.00 3.27
1290 1301 3.749064 GAGTGGAGCGAGCCGACA 61.749 66.667 0.00 0.0 0.00 4.35
1476 1487 2.813726 CGGGTCACTCCACCACCAA 61.814 63.158 0.00 0.0 38.32 3.67
1901 2121 9.036671 GCTTATTAGAGACAATGGAAGAGTTAC 57.963 37.037 0.00 0.0 0.00 2.50
1914 2134 4.201724 GGAAGAGTTACGTAAAGCTGCATG 60.202 45.833 10.11 0.0 0.00 4.06
1937 2157 5.839621 GTTCTATGGAACGTAATAGCCTGA 58.160 41.667 6.17 0.0 41.70 3.86
1939 2159 6.025749 TCTATGGAACGTAATAGCCTGATG 57.974 41.667 0.00 0.0 0.00 3.07
1940 2160 3.469008 TGGAACGTAATAGCCTGATGG 57.531 47.619 0.00 0.0 0.00 3.51
2034 2282 6.382869 AATATCAACATTGCTAGGCTGAAC 57.617 37.500 0.00 0.0 0.00 3.18
2073 2322 7.289084 ACTTTATCCCTAAAACAAAAGAAGCCA 59.711 33.333 0.00 0.0 0.00 4.75
2074 2323 7.604657 TTATCCCTAAAACAAAAGAAGCCAA 57.395 32.000 0.00 0.0 0.00 4.52
2075 2324 5.529581 TCCCTAAAACAAAAGAAGCCAAG 57.470 39.130 0.00 0.0 0.00 3.61
2076 2325 4.343814 TCCCTAAAACAAAAGAAGCCAAGG 59.656 41.667 0.00 0.0 0.00 3.61
2077 2326 4.343814 CCCTAAAACAAAAGAAGCCAAGGA 59.656 41.667 0.00 0.0 0.00 3.36
2078 2327 5.163353 CCCTAAAACAAAAGAAGCCAAGGAA 60.163 40.000 0.00 0.0 0.00 3.36
2079 2328 6.345298 CCTAAAACAAAAGAAGCCAAGGAAA 58.655 36.000 0.00 0.0 0.00 3.13
2175 2432 1.461268 TGAGGTGGTGGGCTCTTCA 60.461 57.895 0.00 0.0 0.00 3.02
2377 2649 5.573380 TGAAAGGATTCCCAGATAGATGG 57.427 43.478 0.00 0.0 40.29 3.51
2408 2680 4.099419 GGATTATTGGGACCATGTTGGAAC 59.901 45.833 0.00 0.0 40.96 3.62
2419 2691 6.331369 ACCATGTTGGAACAGAAGTTAATG 57.669 37.500 0.00 0.0 40.96 1.90
2426 2698 6.985188 TGGAACAGAAGTTAATGACTATGC 57.015 37.500 0.00 0.0 37.72 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
349 350 3.359523 TCCACGTCGAGGTCCACG 61.360 66.667 7.99 1.78 41.90 4.94
415 416 0.401738 CCTTGAAGAAGTGCCCCTGA 59.598 55.000 0.00 0.00 0.00 3.86
539 540 3.005472 TGTGTGGTAGCAAGTGACTAGTC 59.995 47.826 16.32 16.32 0.00 2.59
619 623 3.329743 CGAATCAGCAATCAATCGCTT 57.670 42.857 0.00 0.00 35.96 4.68
677 681 1.902508 AGATCAGTCCAAGCGGAAGAA 59.097 47.619 0.00 0.00 45.20 2.52
741 745 7.650504 GCTACGGTTTATTTTCCTTGTTTTTCT 59.349 33.333 0.00 0.00 0.00 2.52
742 746 7.435784 TGCTACGGTTTATTTTCCTTGTTTTTC 59.564 33.333 0.00 0.00 0.00 2.29
762 767 2.413837 ACACAAACTAAGCCTGCTACG 58.586 47.619 0.00 0.00 0.00 3.51
864 869 0.370273 CGATGGTTACGAAGCTGCAC 59.630 55.000 1.02 0.00 0.00 4.57
1176 1187 1.004560 CTCTTCCGGCTGCTGTTCA 60.005 57.895 7.82 0.00 0.00 3.18
1476 1487 0.106419 GGGAGATGTCGAGGGAGAGT 60.106 60.000 0.00 0.00 0.00 3.24
1901 2121 3.871006 TCCATAGAACATGCAGCTTTACG 59.129 43.478 0.00 0.00 0.00 3.18
1926 2146 8.150945 TCTATGAGAAAACCATCAGGCTATTAC 58.849 37.037 0.00 0.00 39.06 1.89
1935 2155 8.160765 TGGTAAAACTCTATGAGAAAACCATCA 58.839 33.333 1.25 0.00 32.12 3.07
1936 2156 8.561738 TGGTAAAACTCTATGAGAAAACCATC 57.438 34.615 1.25 0.00 32.12 3.51
1937 2157 8.383175 TCTGGTAAAACTCTATGAGAAAACCAT 58.617 33.333 1.25 0.00 34.37 3.55
1939 2159 8.617290 TTCTGGTAAAACTCTATGAGAAAACC 57.383 34.615 1.25 4.50 33.32 3.27
2071 2320 8.127150 AGTCTTCATATTTCCTTTTTCCTTGG 57.873 34.615 0.00 0.00 0.00 3.61
2219 2490 7.977293 CCTCATGCAAAATTATGACATCTTTCA 59.023 33.333 0.00 0.00 30.66 2.69
2221 2492 6.759827 GCCTCATGCAAAATTATGACATCTTT 59.240 34.615 0.00 0.00 40.77 2.52
2272 2544 9.832445 TCAACTTTGAAAAGAATAGTACTCTGT 57.168 29.630 9.71 0.00 39.31 3.41
2297 2569 9.890352 GATTTTATCATATGCTTTCTCCAAGTC 57.110 33.333 0.00 0.00 34.56 3.01
2368 2640 8.327271 CCAATAATCCAGTCATTCCATCTATCT 58.673 37.037 0.00 0.00 0.00 1.98
2377 2649 4.792068 TGGTCCCAATAATCCAGTCATTC 58.208 43.478 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.