Multiple sequence alignment - TraesCS7D01G216700

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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 TraesCS7D01G216700 chr7D 100.000 2648 0 0 1 2648 176573203 176570556 0.000000e+00 4891.0
1 TraesCS7D01G216700 chr7D 93.539 1393 64 12 1263 2648 176768061 176766688 0.000000e+00 2050.0
2 TraesCS7D01G216700 chr7D 92.857 910 48 6 3 896 176584003 176583095 0.000000e+00 1304.0
3 TraesCS7D01G216700 chr7D 89.256 121 12 1 706 825 219717827 219717947 1.640000e-32 150.0
4 TraesCS7D01G216700 chr7D 81.437 167 26 2 2123 2285 5481975 5481810 5.950000e-27 132.0
5 TraesCS7D01G216700 chr7D 85.149 101 9 5 2125 2225 540508315 540508409 6.030000e-17 99.0
6 TraesCS7D01G216700 chr7A 92.095 2201 115 20 1 2160 179531558 179529376 0.000000e+00 3046.0
7 TraesCS7D01G216700 chr7A 89.483 1664 129 28 1022 2648 180161708 180160054 0.000000e+00 2061.0
8 TraesCS7D01G216700 chr7A 89.505 1658 122 24 1022 2648 180342200 180340564 0.000000e+00 2050.0
9 TraesCS7D01G216700 chr7A 88.246 1659 92 34 754 2374 179890086 179888493 0.000000e+00 1888.0
10 TraesCS7D01G216700 chr7A 93.023 903 44 6 1 886 180164251 180163351 0.000000e+00 1301.0
11 TraesCS7D01G216700 chr7A 91.208 944 55 13 1 925 180344954 180344020 0.000000e+00 1258.0
12 TraesCS7D01G216700 chr7A 94.959 615 29 2 143 756 179904355 179903742 0.000000e+00 963.0
13 TraesCS7D01G216700 chr7A 85.644 202 28 1 2448 2648 179888152 179887951 7.430000e-51 211.0
14 TraesCS7D01G216700 chr7A 91.453 117 9 1 30 146 674076631 674076516 2.730000e-35 159.0
15 TraesCS7D01G216700 chr7B 90.714 1863 116 18 707 2523 143155632 143153781 0.000000e+00 2429.0
16 TraesCS7D01G216700 chr7B 86.512 734 65 16 1 716 143156713 143155996 0.000000e+00 776.0
17 TraesCS7D01G216700 chr7B 82.143 420 50 12 1535 1929 143180400 143179981 1.170000e-88 337.0
18 TraesCS7D01G216700 chr7B 96.078 51 2 0 144 194 143156724 143156674 1.690000e-12 84.2
19 TraesCS7D01G216700 chr2D 81.107 524 89 9 2127 2648 352121112 352120597 6.820000e-111 411.0
20 TraesCS7D01G216700 chr2D 89.256 121 13 0 26 146 498472985 498473105 4.570000e-33 152.0
21 TraesCS7D01G216700 chr1B 80.077 522 82 14 2127 2648 105038350 105037851 4.160000e-98 368.0
22 TraesCS7D01G216700 chr1B 87.597 258 29 3 2125 2381 555781658 555781403 1.990000e-76 296.0
23 TraesCS7D01G216700 chr6B 82.985 335 45 7 2125 2450 638429304 638429635 2.580000e-75 292.0
24 TraesCS7D01G216700 chr6B 82.934 334 46 7 2125 2450 638417958 638418288 9.270000e-75 291.0
25 TraesCS7D01G216700 chr6B 91.964 112 9 0 35 146 82007387 82007498 9.810000e-35 158.0
26 TraesCS7D01G216700 chr6D 78.788 462 65 23 264 709 363447064 363446620 2.010000e-71 279.0
27 TraesCS7D01G216700 chr2A 92.593 108 8 0 38 145 249754459 249754566 3.530000e-34 156.0
28 TraesCS7D01G216700 chr2B 89.256 121 13 0 26 146 585712482 585712602 4.570000e-33 152.0
29 TraesCS7D01G216700 chr2B 89.286 112 10 2 715 826 16928988 16929097 3.550000e-29 139.0
30 TraesCS7D01G216700 chrUn 90.179 112 10 1 715 826 313033751 313033861 7.640000e-31 145.0
31 TraesCS7D01G216700 chrUn 90.179 112 10 1 715 826 313037546 313037656 7.640000e-31 145.0
32 TraesCS7D01G216700 chrUn 90.179 112 10 1 715 826 327964222 327964332 7.640000e-31 145.0


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 TraesCS7D01G216700 chr7D 176570556 176573203 2647 True 4891.0 4891 100.000000 1 2648 1 chr7D.!!$R2 2647
1 TraesCS7D01G216700 chr7D 176766688 176768061 1373 True 2050.0 2050 93.539000 1263 2648 1 chr7D.!!$R4 1385
2 TraesCS7D01G216700 chr7D 176583095 176584003 908 True 1304.0 1304 92.857000 3 896 1 chr7D.!!$R3 893
3 TraesCS7D01G216700 chr7A 179529376 179531558 2182 True 3046.0 3046 92.095000 1 2160 1 chr7A.!!$R1 2159
4 TraesCS7D01G216700 chr7A 180160054 180164251 4197 True 1681.0 2061 91.253000 1 2648 2 chr7A.!!$R5 2647
5 TraesCS7D01G216700 chr7A 180340564 180344954 4390 True 1654.0 2050 90.356500 1 2648 2 chr7A.!!$R6 2647
6 TraesCS7D01G216700 chr7A 179887951 179890086 2135 True 1049.5 1888 86.945000 754 2648 2 chr7A.!!$R4 1894
7 TraesCS7D01G216700 chr7A 179903742 179904355 613 True 963.0 963 94.959000 143 756 1 chr7A.!!$R2 613
8 TraesCS7D01G216700 chr7B 143153781 143156724 2943 True 1096.4 2429 91.101333 1 2523 3 chr7B.!!$R2 2522
9 TraesCS7D01G216700 chr2D 352120597 352121112 515 True 411.0 411 81.107000 2127 2648 1 chr2D.!!$R1 521

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
576 746 1.078918 CGCCTCATGCTCTGTTGGA 60.079 57.895 0.0 0.0 38.05 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2531 5188 0.035881 CAGCCACCAGAGAAGCTTCA 59.964 55.0 27.57 0.0 31.93 3.02 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
441 611 4.223255 AGGCAGGAGAAGGTAAAAGTAGAC 59.777 45.833 0.00 0.00 0.00 2.59
487 657 7.665145 TCAAATCATCTGTGTGAAGTATTTGGA 59.335 33.333 0.00 0.00 35.35 3.53
566 736 9.950680 ACAAGTTATTTAAAATATCGCCTCATG 57.049 29.630 0.00 0.00 0.00 3.07
576 746 1.078918 CGCCTCATGCTCTGTTGGA 60.079 57.895 0.00 0.00 38.05 3.53
580 750 1.489649 CCTCATGCTCTGTTGGATCCT 59.510 52.381 14.23 0.00 0.00 3.24
596 766 4.101585 TGGATCCTGCGTAATTTCAGATCT 59.898 41.667 14.23 0.00 32.26 2.75
597 767 4.450419 GGATCCTGCGTAATTTCAGATCTG 59.550 45.833 17.07 17.07 32.26 2.90
687 857 7.444558 TTTTAAAAGAAGTTGCACAACGATC 57.555 32.000 7.81 10.17 45.50 3.69
964 3269 1.082117 GTATAACGCACACGCAGGCT 61.082 55.000 0.00 0.00 45.53 4.58
1111 3428 3.235481 TCACCGTCCAGGCCGAAA 61.235 61.111 0.00 0.00 46.52 3.46
1254 3571 1.277273 GTTAAGGGCTACGTGGGAGTT 59.723 52.381 0.00 0.00 0.00 3.01
1481 3800 2.594592 GGTGCAAGGTCAGGCGTT 60.595 61.111 0.00 0.00 0.00 4.84
1485 3804 2.281761 CAAGGTCAGGCGTTGGCT 60.282 61.111 0.00 0.00 38.79 4.75
1506 3825 4.338539 ACTGTGACGACGGCGACC 62.339 66.667 22.49 9.67 41.64 4.79
1699 4018 6.101734 GGCTATAGATGGGATGGGAATATCAA 59.898 42.308 3.21 0.00 0.00 2.57
1959 4303 2.722201 GGCGAGGTGGAAGACGGAT 61.722 63.158 0.00 0.00 0.00 4.18
1970 4314 2.163815 GGAAGACGGATGAGAACGAGAA 59.836 50.000 0.00 0.00 0.00 2.87
2028 4372 7.333672 CCTTATTTAAGTAGCGTGGAGAAAGTT 59.666 37.037 0.00 0.00 0.00 2.66
2268 4652 2.034432 TGTAAACTACAACACCTCGCGA 59.966 45.455 9.26 9.26 35.38 5.87
2357 4741 2.740714 CCTTTCCCTTTCGCGCGAG 61.741 63.158 32.74 21.84 0.00 5.03
2517 5173 0.741221 GAGCCGCCGATTCACTTTCT 60.741 55.000 0.00 0.00 0.00 2.52
2531 5188 3.825160 TTTCTGCCGCCGCTGAGTT 62.825 57.895 6.71 0.00 42.98 3.01
2542 5199 1.337635 CCGCTGAGTTGAAGCTTCTCT 60.338 52.381 26.09 22.21 38.57 3.10
2554 5211 3.241530 TTCTCTGGTGGCTGCGGT 61.242 61.111 0.00 0.00 0.00 5.68
2565 5222 1.971695 GCTGCGGTTGGCCTAAACT 60.972 57.895 3.32 0.00 42.61 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 9.120538 GAGGGAGTAATACAAAAGATATGCAAA 57.879 33.333 0.00 0.00 0.00 3.68
123 124 7.132213 CGTATACGGAGCAAAATGATTGAATT 58.868 34.615 17.61 0.00 35.37 2.17
129 130 5.220777 CCAAACGTATACGGAGCAAAATGAT 60.221 40.000 27.62 0.56 44.95 2.45
204 374 9.582431 CGAGAAACATAAGGACATTAGTAGAAA 57.418 33.333 0.00 0.00 0.00 2.52
338 508 8.834465 GTTACTAGATCTATGTTGTCCTTACGA 58.166 37.037 2.11 0.00 0.00 3.43
464 634 8.585471 AATCCAAATACTTCACACAGATGATT 57.415 30.769 0.00 0.00 0.00 2.57
566 736 0.175760 TACGCAGGATCCAACAGAGC 59.824 55.000 15.82 6.86 0.00 4.09
576 746 5.282055 TCAGATCTGAAATTACGCAGGAT 57.718 39.130 23.17 0.00 36.53 3.24
580 750 6.741992 ACAAATCAGATCTGAAATTACGCA 57.258 33.333 28.40 3.40 43.58 5.24
666 836 4.819630 AGGATCGTTGTGCAACTTCTTTTA 59.180 37.500 12.44 0.00 39.08 1.52
740 1285 3.492102 TCCACTTCAAACCTCTCCAAG 57.508 47.619 0.00 0.00 0.00 3.61
985 3302 3.310774 CCTCGCATGATGTTTTCTAGGTG 59.689 47.826 0.00 0.00 0.00 4.00
1111 3428 4.736896 GTCCTTTCCGCGCTCCGT 62.737 66.667 5.56 0.00 34.38 4.69
1238 3555 2.291043 CCAACTCCCACGTAGCCCT 61.291 63.158 0.00 0.00 0.00 5.19
1350 3668 2.360350 CCTTGCACCGTGATGCCT 60.360 61.111 1.65 0.00 45.50 4.75
1481 3800 3.545574 TCGTCACAGTGGCAGCCA 61.546 61.111 11.22 11.22 0.00 4.75
1485 3804 4.961511 GCCGTCGTCACAGTGGCA 62.962 66.667 5.87 0.00 45.06 4.92
1506 3825 2.190578 GCTGGTTCCATCTCCCCG 59.809 66.667 0.00 0.00 0.00 5.73
1699 4018 6.245408 TGCCAAGTTTACAATAACCTCTCAT 58.755 36.000 0.00 0.00 0.00 2.90
1959 4303 1.248785 CCCCCGACTTCTCGTTCTCA 61.249 60.000 0.00 0.00 38.32 3.27
2028 4372 1.508632 GCACCGCTACACTTTCTTCA 58.491 50.000 0.00 0.00 0.00 3.02
2268 4652 7.611467 TCTGTAAGTGGAGATACAAATTTGCAT 59.389 33.333 18.12 10.95 32.05 3.96
2517 5173 4.617520 TTCAACTCAGCGGCGGCA 62.618 61.111 19.21 0.00 43.41 5.69
2531 5188 0.035881 CAGCCACCAGAGAAGCTTCA 59.964 55.000 27.57 0.00 31.93 3.02
2554 5211 0.702316 GGGGAAGGAGTTTAGGCCAA 59.298 55.000 5.01 0.00 0.00 4.52
2565 5222 2.003212 TAGATCTCGCCGGGGAAGGA 62.003 60.000 22.77 17.00 0.00 3.36
2623 5281 1.592223 GTGCGCCTCCAGTAACTCT 59.408 57.895 4.18 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.