Multiple sequence alignment - TraesCS1D01G394100

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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 TraesCS1D01G394100 chr1D 100.000 3215 0 0 1 3215 463340271 463343485 0.000000e+00 5938.0
1 TraesCS1D01G394100 chr1D 86.198 1536 140 42 796 2313 463283444 463281963 0.000000e+00 1596.0
2 TraesCS1D01G394100 chr1D 87.322 1262 127 16 1029 2269 463326510 463325261 0.000000e+00 1413.0
3 TraesCS1D01G394100 chr1D 91.133 203 14 3 2477 2679 463281799 463281601 4.090000e-69 272.0
4 TraesCS1D01G394100 chr1D 84.038 213 30 3 3006 3215 18761021 18760810 5.440000e-48 202.0
5 TraesCS1D01G394100 chr1D 100.000 32 0 0 2699 2730 463281603 463281572 3.460000e-05 60.2
6 TraesCS1D01G394100 chr1A 94.228 2443 93 24 777 3215 555533201 555535599 0.000000e+00 3687.0
7 TraesCS1D01G394100 chr1A 86.408 1545 143 39 802 2314 555485328 555483819 0.000000e+00 1628.0
8 TraesCS1D01G394100 chr1A 87.251 1255 128 12 1029 2269 555523215 555521979 0.000000e+00 1402.0
9 TraesCS1D01G394100 chr1A 93.377 302 13 5 2915 3215 555535804 555536099 1.060000e-119 440.0
10 TraesCS1D01G394100 chr1A 91.154 260 17 4 2477 2732 555483656 555483399 6.600000e-92 348.0
11 TraesCS1D01G394100 chr1B 96.159 1536 55 2 777 2312 638881733 638883264 0.000000e+00 2507.0
12 TraesCS1D01G394100 chr1B 86.319 1535 142 37 802 2313 638784107 638782618 0.000000e+00 1609.0
13 TraesCS1D01G394100 chr1B 87.381 1260 130 16 1027 2269 638821997 638820750 0.000000e+00 1419.0
14 TraesCS1D01G394100 chr1B 87.029 902 61 15 2330 3215 638883316 638884177 0.000000e+00 966.0
15 TraesCS1D01G394100 chr1B 83.984 256 11 12 2478 2732 638782460 638782234 5.400000e-53 219.0
16 TraesCS1D01G394100 chr1B 83.482 224 27 10 2996 3215 686917838 686917621 1.960000e-47 200.0
17 TraesCS1D01G394100 chr7D 97.683 777 16 2 1 776 242636899 242637674 0.000000e+00 1334.0
18 TraesCS1D01G394100 chr5D 97.555 777 17 2 1 776 270237438 270238213 0.000000e+00 1328.0
19 TraesCS1D01G394100 chr5D 88.660 97 9 2 2838 2933 347443724 347443819 2.030000e-22 117.0
20 TraesCS1D01G394100 chr7A 90.839 775 67 4 4 776 654808322 654809094 0.000000e+00 1035.0
21 TraesCS1D01G394100 chr7A 88.567 621 71 0 156 776 52893629 52894249 0.000000e+00 754.0
22 TraesCS1D01G394100 chr7A 82.909 275 31 9 2952 3215 19953643 19953374 1.930000e-57 233.0
23 TraesCS1D01G394100 chr7A 84.762 105 12 3 2838 2940 206959858 206959960 5.670000e-18 102.0
24 TraesCS1D01G394100 chr7A 84.615 104 12 4 2839 2940 547102786 547102887 2.040000e-17 100.0
25 TraesCS1D01G394100 chr6A 90.722 776 67 5 3 776 26890456 26889684 0.000000e+00 1029.0
26 TraesCS1D01G394100 chr6A 84.727 275 23 13 2953 3215 432533334 432533067 1.140000e-64 257.0
27 TraesCS1D01G394100 chr6A 80.282 284 35 12 2952 3215 18078480 18078198 9.100000e-46 195.0
28 TraesCS1D01G394100 chr7B 90.194 775 74 2 3 776 202762213 202762986 0.000000e+00 1009.0
29 TraesCS1D01G394100 chr5B 87.871 775 91 3 3 776 294148400 294149172 0.000000e+00 907.0
30 TraesCS1D01G394100 chr5B 86.727 776 97 6 1 773 539090721 539089949 0.000000e+00 857.0
31 TraesCS1D01G394100 chr4A 82.536 773 126 9 3 771 505437814 505437047 0.000000e+00 671.0
32 TraesCS1D01G394100 chr3D 86.207 464 56 4 1392 1849 5809086 5808625 2.230000e-136 496.0
33 TraesCS1D01G394100 chr3D 84.834 211 30 2 3006 3215 373599737 373599528 9.040000e-51 211.0
34 TraesCS1D01G394100 chrUn 84.038 213 30 3 3006 3215 161287 161076 5.440000e-48 202.0
35 TraesCS1D01G394100 chr3A 84.834 211 18 8 3005 3215 510852518 510852322 1.960000e-47 200.0
36 TraesCS1D01G394100 chr4D 85.417 192 22 5 3027 3215 49940455 49940267 9.100000e-46 195.0
37 TraesCS1D01G394100 chr6B 82.667 225 30 8 2996 3215 682657937 682657717 1.180000e-44 191.0
38 TraesCS1D01G394100 chr6B 76.842 285 27 17 2952 3215 39162708 39162442 1.210000e-24 124.0
39 TraesCS1D01G394100 chr2B 81.197 234 29 11 2950 3171 33544260 33544030 1.190000e-39 174.0
40 TraesCS1D01G394100 chr2D 88.889 99 9 2 2845 2943 124803412 124803316 1.570000e-23 121.0
41 TraesCS1D01G394100 chr5A 84.112 107 15 2 2838 2943 444533298 444533193 5.670000e-18 102.0
42 TraesCS1D01G394100 chr6D 83.333 108 16 2 2834 2940 289027680 289027574 7.340000e-17 99.0
43 TraesCS1D01G394100 chr2A 83.333 108 14 4 2836 2940 68155071 68154965 2.640000e-16 97.1


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 TraesCS1D01G394100 chr1D 463340271 463343485 3214 False 5938.000000 5938 100.000000 1 3215 1 chr1D.!!$F1 3214
1 TraesCS1D01G394100 chr1D 463325261 463326510 1249 True 1413.000000 1413 87.322000 1029 2269 1 chr1D.!!$R2 1240
2 TraesCS1D01G394100 chr1D 463281572 463283444 1872 True 642.733333 1596 92.443667 796 2730 3 chr1D.!!$R3 1934
3 TraesCS1D01G394100 chr1A 555533201 555536099 2898 False 2063.500000 3687 93.802500 777 3215 2 chr1A.!!$F1 2438
4 TraesCS1D01G394100 chr1A 555521979 555523215 1236 True 1402.000000 1402 87.251000 1029 2269 1 chr1A.!!$R1 1240
5 TraesCS1D01G394100 chr1A 555483399 555485328 1929 True 988.000000 1628 88.781000 802 2732 2 chr1A.!!$R2 1930
6 TraesCS1D01G394100 chr1B 638881733 638884177 2444 False 1736.500000 2507 91.594000 777 3215 2 chr1B.!!$F1 2438
7 TraesCS1D01G394100 chr1B 638820750 638821997 1247 True 1419.000000 1419 87.381000 1027 2269 1 chr1B.!!$R1 1242
8 TraesCS1D01G394100 chr1B 638782234 638784107 1873 True 914.000000 1609 85.151500 802 2732 2 chr1B.!!$R3 1930
9 TraesCS1D01G394100 chr7D 242636899 242637674 775 False 1334.000000 1334 97.683000 1 776 1 chr7D.!!$F1 775
10 TraesCS1D01G394100 chr5D 270237438 270238213 775 False 1328.000000 1328 97.555000 1 776 1 chr5D.!!$F1 775
11 TraesCS1D01G394100 chr7A 654808322 654809094 772 False 1035.000000 1035 90.839000 4 776 1 chr7A.!!$F4 772
12 TraesCS1D01G394100 chr7A 52893629 52894249 620 False 754.000000 754 88.567000 156 776 1 chr7A.!!$F1 620
13 TraesCS1D01G394100 chr6A 26889684 26890456 772 True 1029.000000 1029 90.722000 3 776 1 chr6A.!!$R2 773
14 TraesCS1D01G394100 chr7B 202762213 202762986 773 False 1009.000000 1009 90.194000 3 776 1 chr7B.!!$F1 773
15 TraesCS1D01G394100 chr5B 294148400 294149172 772 False 907.000000 907 87.871000 3 776 1 chr5B.!!$F1 773
16 TraesCS1D01G394100 chr5B 539089949 539090721 772 True 857.000000 857 86.727000 1 773 1 chr5B.!!$R1 772
17 TraesCS1D01G394100 chr4A 505437047 505437814 767 True 671.000000 671 82.536000 3 771 1 chr4A.!!$R1 768

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
651 653 0.038526 AATTCGCCGACTGTCGAGTT 60.039 50.0 29.93 11.43 43.74 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2631 2758 0.386113 AGCTAGCACGCTAACTAGGC 59.614 55.0 18.83 0.26 38.76 3.93 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
60 61 3.119136 GTCAATATATGTTCGACCGTCGC 59.881 47.826 16.24 3.90 40.21 5.19
61 62 3.004002 TCAATATATGTTCGACCGTCGCT 59.996 43.478 16.24 3.61 40.21 4.93
62 63 2.394545 TATATGTTCGACCGTCGCTG 57.605 50.000 16.24 0.00 40.21 5.18
124 125 2.016318 TCAAGCCGCACCTGAATATTG 58.984 47.619 0.00 0.00 0.00 1.90
157 158 5.127491 TCCCGTTTATTATCCCATGTGAAC 58.873 41.667 0.00 0.00 0.00 3.18
324 326 2.559440 GAGATCATCTTGTGCCCTCAC 58.441 52.381 0.00 0.00 43.40 3.51
409 411 2.762535 TCCTACAAAGCTTTCCCTCG 57.237 50.000 9.23 0.00 0.00 4.63
523 525 0.321210 CTACACAATCCACCGCCACA 60.321 55.000 0.00 0.00 0.00 4.17
651 653 0.038526 AATTCGCCGACTGTCGAGTT 60.039 50.000 29.93 11.43 43.74 3.01
739 741 2.965147 GCCGCTTCATCGTGTTGCA 61.965 57.895 0.00 0.00 0.00 4.08
838 840 2.311124 ATTGTAACTGACGCCTAGCC 57.689 50.000 0.00 0.00 0.00 3.93
949 952 2.449464 CTGGATGGCCTTTTGTGATCA 58.551 47.619 3.32 0.00 34.31 2.92
977 980 5.378332 TCTTCGTCCCCAACAAGAAAATTA 58.622 37.500 0.00 0.00 0.00 1.40
981 984 3.898741 GTCCCCAACAAGAAAATTACCCA 59.101 43.478 0.00 0.00 0.00 4.51
1482 1530 4.687215 TCGCTGCTGCTGTCCACC 62.687 66.667 14.03 0.00 36.97 4.61
2321 2440 6.884187 TGAAAATTTCTTAGTGTAGACGTGC 58.116 36.000 7.29 0.00 0.00 5.34
2325 2444 3.503827 TCTTAGTGTAGACGTGCCATG 57.496 47.619 0.00 0.00 0.00 3.66
2337 2456 4.119862 GACGTGCCATGTACTCATGTTAT 58.880 43.478 0.00 0.00 46.99 1.89
2399 2519 1.399440 CAAGAATGGCGTGGTGATGAG 59.601 52.381 0.00 0.00 0.00 2.90
2408 2528 0.824109 GTGGTGATGAGGACGGATGA 59.176 55.000 0.00 0.00 0.00 2.92
2439 2560 3.584406 TGGGCTGCTATGTATCTTGCTAT 59.416 43.478 0.00 0.00 0.00 2.97
2516 2639 2.094234 GGGTGTGTGAAAAACTTGCACT 60.094 45.455 0.00 0.00 33.83 4.40
2611 2738 1.164411 CCTGCGTTGTTCCTGCAATA 58.836 50.000 0.00 0.00 38.30 1.90
2625 2752 4.406326 TCCTGCAATACATCAATTGGCAAT 59.594 37.500 6.96 6.96 37.34 3.56
2631 2758 7.278203 TGCAATACATCAATTGGCAATAGTTTG 59.722 33.333 14.05 9.00 37.34 2.93
2841 2992 5.367060 AGAAAGATGATGGTTCCTAGGTACC 59.633 44.000 26.55 26.55 36.31 3.34
2869 3020 7.814107 ACTCCGTTCACAAATATAAGACGTTTA 59.186 33.333 0.00 0.00 0.00 2.01
2886 3037 7.383687 AGACGTTTAGGATATTTTCAGTGTGA 58.616 34.615 0.00 0.00 0.00 3.58
2924 3075 8.993121 ACTGAAATGAGTGAACAAATACACTAG 58.007 33.333 0.00 0.00 45.54 2.57
3061 3724 2.564062 AGAATGTTTGGGGTGCATGAAG 59.436 45.455 0.00 0.00 0.00 3.02
3172 3836 7.950512 TGGAGCTCTGAATTTGTTTTTATTGA 58.049 30.769 14.64 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 1.746615 CTGTCCACATTCCCGGCAG 60.747 63.158 0.00 0.00 0.00 4.85
61 62 1.773856 TTCTGTCCACATTCCCGGCA 61.774 55.000 0.00 0.00 0.00 5.69
62 63 0.608035 TTTCTGTCCACATTCCCGGC 60.608 55.000 0.00 0.00 0.00 6.13
124 125 5.469084 GGATAATAAACGGGATGGTCAAGAC 59.531 44.000 0.00 0.00 0.00 3.01
324 326 2.159435 TCATGGGATGCGATACGATACG 60.159 50.000 0.00 0.00 0.00 3.06
409 411 0.810648 TTGATGCGGAGGTTGAATGC 59.189 50.000 0.00 0.00 0.00 3.56
523 525 4.226168 TGGAGTTTGGGTTTTTCAAATGGT 59.774 37.500 0.00 0.00 36.64 3.55
589 591 2.596338 CCGGCGGTGGTTTTCCTT 60.596 61.111 19.97 0.00 41.38 3.36
591 593 4.960866 ACCCGGCGGTGGTTTTCC 62.961 66.667 26.32 0.00 42.48 3.13
651 653 2.111999 CTGTCGAGGCTTGGGGTTGA 62.112 60.000 0.97 0.00 0.00 3.18
838 840 2.485122 GCGGCCGGATGTGAAAAG 59.515 61.111 29.38 0.00 0.00 2.27
949 952 1.348064 TGTTGGGGACGAAGATCAGT 58.652 50.000 0.00 0.00 0.00 3.41
977 980 1.169765 TATATCGGGTAGGGGTGGGT 58.830 55.000 0.00 0.00 0.00 4.51
981 984 3.965347 GCATGTATATATCGGGTAGGGGT 59.035 47.826 0.00 0.00 0.00 4.95
1482 1530 4.749310 AGCGTGAAGGCGAGCTGG 62.749 66.667 0.00 0.00 38.67 4.85
2240 2306 2.288025 ATGGTTCGCACGTACCCCT 61.288 57.895 15.00 1.58 35.12 4.79
2290 2360 8.770828 TCTACACTAAGAAATTTTCAGTTTCCG 58.229 33.333 11.53 0.00 36.48 4.30
2325 2444 8.981724 TTGCCTAATCGATATAACATGAGTAC 57.018 34.615 0.00 0.00 0.00 2.73
2399 2519 1.472480 CCACCAAACAATCATCCGTCC 59.528 52.381 0.00 0.00 0.00 4.79
2408 2528 1.826720 CATAGCAGCCCACCAAACAAT 59.173 47.619 0.00 0.00 0.00 2.71
2439 2560 3.576861 TCCTGAAGAGAACCTCACAAGA 58.423 45.455 0.00 0.00 32.06 3.02
2516 2639 7.107542 GTCCCTGTTGATGGTACTACATTAAA 58.892 38.462 0.00 0.00 29.68 1.52
2625 2752 2.232941 AGCACGCTAACTAGGCAAACTA 59.767 45.455 0.00 0.00 0.00 2.24
2631 2758 0.386113 AGCTAGCACGCTAACTAGGC 59.614 55.000 18.83 0.26 38.76 3.93
2643 2770 1.221840 GCAGGCCAGTTAGCTAGCA 59.778 57.895 18.83 0.00 34.27 3.49
2699 2849 5.249393 ACAGTATAAGGATAAGGAGCCATGG 59.751 44.000 7.63 7.63 31.47 3.66
2841 2992 5.005394 CGTCTTATATTTGTGAACGGAGTGG 59.995 44.000 0.00 0.00 45.00 4.00
2881 3032 7.919091 TCATTTCAGTCCGTATATAGTTCACAC 59.081 37.037 0.00 0.00 0.00 3.82
2886 3037 8.234136 TCACTCATTTCAGTCCGTATATAGTT 57.766 34.615 0.00 0.00 0.00 2.24
2891 3042 6.275494 TGTTCACTCATTTCAGTCCGTATA 57.725 37.500 0.00 0.00 0.00 1.47
2924 3075 4.202161 CCAGAGGGTGTATGTAGACATGTC 60.202 50.000 18.47 18.47 37.15 3.06
3061 3724 5.061311 CCGATGTGATTTTGTGCTGAATTTC 59.939 40.000 0.00 0.00 0.00 2.17
3172 3836 1.150536 ACATTGGGGCAAGTCGTGT 59.849 52.632 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.