Multiple sequence alignment - TraesCS7D01G274600

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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 TraesCS7D01G274600 chr7D 100.000 2044 0 0 1 2044 264314398 264316441 0.000000e+00 3775.0
1 TraesCS7D01G274600 chr7D 100.000 232 0 0 2480 2711 264316877 264317108 1.930000e-116 429.0
2 TraesCS7D01G274600 chr7B 95.814 1481 45 5 492 1969 244631188 244632654 0.000000e+00 2375.0
3 TraesCS7D01G274600 chr7B 96.349 493 18 0 1 493 244630620 244631112 0.000000e+00 811.0
4 TraesCS7D01G274600 chr7B 96.070 229 9 0 2483 2711 244632953 244633181 9.170000e-100 374.0
5 TraesCS7D01G274600 chr6A 82.353 1258 186 30 620 1856 34280369 34279127 0.000000e+00 1061.0
6 TraesCS7D01G274600 chr6A 81.955 1258 189 32 620 1858 34282347 34281109 0.000000e+00 1031.0
7 TraesCS7D01G274600 chr6A 82.134 1237 185 30 641 1856 34392915 34391694 0.000000e+00 1027.0
8 TraesCS7D01G274600 chr6A 82.092 1195 182 26 681 1856 34275481 34274300 0.000000e+00 992.0
9 TraesCS7D01G274600 chrUn 82.259 1257 189 28 620 1856 101989814 101988572 0.000000e+00 1055.0
10 TraesCS7D01G274600 chr6B 81.717 1258 196 29 620 1857 62691102 62689859 0.000000e+00 1018.0
11 TraesCS7D01G274600 chr3B 82.431 1127 165 28 688 1798 780355613 780354504 0.000000e+00 953.0
12 TraesCS7D01G274600 chr3D 81.292 1192 186 29 688 1860 583289991 583288818 0.000000e+00 931.0
13 TraesCS7D01G274600 chr7A 96.040 505 19 1 492 995 287816616 287817120 0.000000e+00 821.0
14 TraesCS7D01G274600 chr7A 92.978 413 20 6 89 493 287816129 287816540 6.460000e-166 593.0
15 TraesCS7D01G274600 chr7A 93.013 229 16 0 2483 2711 287820712 287820940 4.330000e-88 335.0
16 TraesCS7D01G274600 chr7A 97.297 37 1 0 65 101 287809087 287809123 2.250000e-06 63.9


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 TraesCS7D01G274600 chr7D 264314398 264317108 2710 False 2102.000000 3775 100.000000 1 2711 2 chr7D.!!$F1 2710
1 TraesCS7D01G274600 chr7B 244630620 244633181 2561 False 1186.666667 2375 96.077667 1 2711 3 chr7B.!!$F1 2710
2 TraesCS7D01G274600 chr6A 34274300 34282347 8047 True 1028.000000 1061 82.133333 620 1858 3 chr6A.!!$R2 1238
3 TraesCS7D01G274600 chr6A 34391694 34392915 1221 True 1027.000000 1027 82.134000 641 1856 1 chr6A.!!$R1 1215
4 TraesCS7D01G274600 chrUn 101988572 101989814 1242 True 1055.000000 1055 82.259000 620 1856 1 chrUn.!!$R1 1236
5 TraesCS7D01G274600 chr6B 62689859 62691102 1243 True 1018.000000 1018 81.717000 620 1857 1 chr6B.!!$R1 1237
6 TraesCS7D01G274600 chr3B 780354504 780355613 1109 True 953.000000 953 82.431000 688 1798 1 chr3B.!!$R1 1110
7 TraesCS7D01G274600 chr3D 583288818 583289991 1173 True 931.000000 931 81.292000 688 1860 1 chr3D.!!$R1 1172
8 TraesCS7D01G274600 chr7A 287816129 287820940 4811 False 583.000000 821 94.010333 89 2711 3 chr7A.!!$F2 2622

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
533 620 1.050988 ATACATGGCAGCTCCGACCT 61.051 55.000 0.0 0.0 37.8 3.85 F
691 778 1.227823 CCACACGGCTGGTTCTTGA 60.228 57.895 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1378 5966 1.801178 CTTGGCCTTCTTCGTCAAGAC 59.199 52.381 3.32 0.0 38.44 3.01 R
2641 12267 0.622136 AGCAGCCATCTGGATTGACA 59.378 50.000 0.00 0.0 40.65 3.58 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
24 25 1.274167 CGGGTTACTTACAGGAGCACA 59.726 52.381 0.00 0.00 0.00 4.57
25 26 2.674177 CGGGTTACTTACAGGAGCACAG 60.674 54.545 0.00 0.00 0.00 3.66
126 127 6.767902 GGTTTCTAGTCTCCATGATATTGCAA 59.232 38.462 0.00 0.00 0.00 4.08
134 135 7.613022 AGTCTCCATGATATTGCAAAAGAGAAA 59.387 33.333 1.71 0.00 30.27 2.52
182 183 1.338105 ACTGCGCACATTAGAGAGCAA 60.338 47.619 5.66 0.00 40.11 3.91
383 389 2.998316 ATAGAACTGAGGCCTGCTTC 57.002 50.000 12.00 7.83 0.00 3.86
396 402 3.437049 GGCCTGCTTCTTTACAACTACAG 59.563 47.826 0.00 0.00 0.00 2.74
493 502 9.747898 AAAGTATAAGAACAATATGGTGACCAA 57.252 29.630 9.06 0.00 36.95 3.67
496 505 9.174166 GTATAAGAACAATATGGTGACCAAAGT 57.826 33.333 9.06 1.82 36.95 2.66
497 506 5.964958 AGAACAATATGGTGACCAAAGTG 57.035 39.130 9.06 9.29 36.95 3.16
498 507 4.766891 AGAACAATATGGTGACCAAAGTGG 59.233 41.667 9.06 0.00 45.02 4.00
499 508 4.380843 ACAATATGGTGACCAAAGTGGA 57.619 40.909 9.06 0.00 40.96 4.02
500 509 4.934356 ACAATATGGTGACCAAAGTGGAT 58.066 39.130 9.06 0.00 40.96 3.41
501 510 4.706476 ACAATATGGTGACCAAAGTGGATG 59.294 41.667 9.06 4.01 40.96 3.51
533 620 1.050988 ATACATGGCAGCTCCGACCT 61.051 55.000 0.00 0.00 37.80 3.85
691 778 1.227823 CCACACGGCTGGTTCTTGA 60.228 57.895 0.00 0.00 0.00 3.02
750 2817 2.882137 CGGGGACAACAAACACACTAAT 59.118 45.455 0.00 0.00 0.00 1.73
945 3028 2.669391 CGCATCAAACCAAAAGGCTCTC 60.669 50.000 0.00 0.00 0.00 3.20
1010 5598 4.978099 TCAAGATCAGATATGGCTTTCCC 58.022 43.478 0.00 0.00 0.00 3.97
1051 5639 2.102252 CCTTCTAGGCCTCACATCAGTC 59.898 54.545 9.68 0.00 0.00 3.51
1054 5642 1.411977 CTAGGCCTCACATCAGTCAGG 59.588 57.143 9.68 0.00 0.00 3.86
1300 5888 5.568685 AGAGATCTTCGTCGAGATGAAAA 57.431 39.130 8.81 0.00 36.54 2.29
1340 5928 2.784347 AGTGGCACTAAGAAAAGGAGC 58.216 47.619 20.61 0.00 0.00 4.70
1628 6216 0.926846 GAGTTAGAGTGCAGCATCGC 59.073 55.000 0.00 0.00 0.00 4.58
1938 11362 5.620206 TCCTTGTACATTATGTATGCCAGG 58.380 41.667 8.39 10.79 37.81 4.45
2512 12138 2.303022 TCAAGTTCTACCTGCTCTTGGG 59.697 50.000 0.00 0.00 36.94 4.12
2580 12206 6.639632 TTTGCTCCTTTCCATATAATGCTC 57.360 37.500 0.00 0.00 0.00 4.26
2595 12221 3.896648 ATGCTCAACAAACTAACACCG 57.103 42.857 0.00 0.00 0.00 4.94
2600 12226 3.142951 TCAACAAACTAACACCGATGGG 58.857 45.455 0.00 0.00 40.11 4.00
2641 12267 4.434545 AGCTGTGCCATGAAGATAGAAT 57.565 40.909 0.00 0.00 0.00 2.40
2665 12291 3.393609 TCAATCCAGATGGCTGCTAAGAT 59.606 43.478 0.00 0.00 40.91 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.586892 GTCCTGTGCTCCTGTAAGTAAC 58.413 50.000 0.00 0.0 0.00 2.50
24 25 2.145397 TCAAGTAGCGAGATGGTCCT 57.855 50.000 0.00 0.0 0.00 3.85
25 26 2.541556 GTTCAAGTAGCGAGATGGTCC 58.458 52.381 0.00 0.0 0.00 4.46
143 144 0.466543 TTGCTTCACCTGTACCGTGT 59.533 50.000 9.33 0.0 32.86 4.49
147 148 0.875059 GCAGTTGCTTCACCTGTACC 59.125 55.000 0.00 0.0 38.21 3.34
182 183 5.440610 ACAATTTGTGAACAGACTCTCCTT 58.559 37.500 0.15 0.0 0.00 3.36
362 368 3.265479 AGAAGCAGGCCTCAGTTCTATTT 59.735 43.478 16.04 0.0 0.00 1.40
365 371 1.944177 AGAAGCAGGCCTCAGTTCTA 58.056 50.000 16.04 0.0 0.00 2.10
476 485 4.764823 TCCACTTTGGTCACCATATTGTTC 59.235 41.667 0.00 0.0 39.03 3.18
509 596 1.152902 GAGCTGCCATGTATGCCCA 60.153 57.895 0.00 0.0 0.00 5.36
533 620 8.739039 CATGTTTAGGTGATGGAAAACAAGATA 58.261 33.333 3.87 0.0 42.98 1.98
750 2817 3.443681 TCGTCTCATGTTCAGTGCATCTA 59.556 43.478 0.00 0.0 0.00 1.98
945 3028 4.215185 GGTGAAGAAAGGAGCTGAAGAAAG 59.785 45.833 0.00 0.0 0.00 2.62
1010 5598 4.962155 AGGCAAACTTATCGATCTTAGGG 58.038 43.478 0.00 0.0 0.00 3.53
1051 5639 1.532868 CTCTTGTTCAACTTCCGCCTG 59.467 52.381 0.00 0.0 0.00 4.85
1054 5642 1.069636 CAGCTCTTGTTCAACTTCCGC 60.070 52.381 0.00 0.0 0.00 5.54
1300 5888 3.285484 CTTGCAGCTCTTGGATAATGGT 58.715 45.455 0.00 0.0 0.00 3.55
1378 5966 1.801178 CTTGGCCTTCTTCGTCAAGAC 59.199 52.381 3.32 0.0 38.44 3.01
1628 6216 2.538437 CTGCTCCGTTCTCAAGATCTG 58.462 52.381 0.00 0.0 0.00 2.90
1893 11317 3.196685 AGCAAGATCCACTAAGTGAGGTC 59.803 47.826 0.00 0.0 35.23 3.85
1938 11362 3.440522 CCTTAGCCCTTGTTAGCTTTGAC 59.559 47.826 0.00 0.0 40.56 3.18
1993 11417 5.817816 GGTATGGAGGTTGTTTCAGTGATAG 59.182 44.000 0.00 0.0 0.00 2.08
1996 11420 3.392947 TGGTATGGAGGTTGTTTCAGTGA 59.607 43.478 0.00 0.0 0.00 3.41
1997 11421 3.750371 TGGTATGGAGGTTGTTTCAGTG 58.250 45.455 0.00 0.0 0.00 3.66
1999 11423 4.582656 TGTTTGGTATGGAGGTTGTTTCAG 59.417 41.667 0.00 0.0 0.00 3.02
2000 11424 4.537751 TGTTTGGTATGGAGGTTGTTTCA 58.462 39.130 0.00 0.0 0.00 2.69
2002 11426 4.898861 ACATGTTTGGTATGGAGGTTGTTT 59.101 37.500 0.00 0.0 0.00 2.83
2003 11427 4.479158 ACATGTTTGGTATGGAGGTTGTT 58.521 39.130 0.00 0.0 0.00 2.83
2480 12106 6.151817 GCAGGTAGAACTTGAGATGGATTTTT 59.848 38.462 0.00 0.0 0.00 1.94
2481 12107 5.649831 GCAGGTAGAACTTGAGATGGATTTT 59.350 40.000 0.00 0.0 0.00 1.82
2580 12206 2.882137 ACCCATCGGTGTTAGTTTGTTG 59.118 45.455 0.00 0.0 42.48 3.33
2641 12267 0.622136 AGCAGCCATCTGGATTGACA 59.378 50.000 0.00 0.0 40.65 3.58
2678 12304 2.484417 GGCATTCCATCAGATCGTCACT 60.484 50.000 0.00 0.0 0.00 3.41


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

AutoCloner maintained by Alex Coulton.