Multiple sequence alignment - TraesCS6B01G065100

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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 TraesCS6B01G065100 chr6B 100.000 4988 0 0 1 4988 43226287 43221300 0.000000e+00 9212.0
1 TraesCS6B01G065100 chr6B 81.643 1656 240 35 2292 3904 41456885 41455251 0.000000e+00 1315.0
2 TraesCS6B01G065100 chr6B 85.495 717 86 10 3289 3994 41447460 41446751 0.000000e+00 732.0
3 TraesCS6B01G065100 chr6B 80.595 639 117 6 68 703 51383409 51384043 2.090000e-133 486.0
4 TraesCS6B01G065100 chr6B 87.415 294 26 7 2491 2774 41448346 41448054 1.340000e-85 327.0
5 TraesCS6B01G065100 chr6B 79.651 344 36 17 1606 1920 41449073 41448735 3.020000e-52 217.0
6 TraesCS6B01G065100 chr6B 84.862 218 27 6 2337 2551 41448563 41448349 1.090000e-51 215.0
7 TraesCS6B01G065100 chr6B 79.430 316 39 11 1070 1365 41449499 41449190 3.050000e-47 200.0
8 TraesCS6B01G065100 chr6A 96.190 3963 62 25 1070 4988 24773535 24769618 0.000000e+00 6399.0
9 TraesCS6B01G065100 chr6A 81.834 1745 247 45 2292 3991 23678643 23676924 0.000000e+00 1402.0
10 TraesCS6B01G065100 chr6A 86.427 722 76 17 3286 3994 23652307 23651595 0.000000e+00 771.0
11 TraesCS6B01G065100 chr6A 85.929 732 83 14 3275 3994 23636307 23635584 0.000000e+00 763.0
12 TraesCS6B01G065100 chr6A 83.060 732 101 15 3276 3991 24458021 24458745 1.170000e-180 643.0
13 TraesCS6B01G065100 chr6A 84.405 513 72 4 2749 3254 23636867 23636356 9.640000e-137 497.0
14 TraesCS6B01G065100 chr6A 87.415 294 26 7 2491 2774 23637173 23636881 1.340000e-85 327.0
15 TraesCS6B01G065100 chr6A 88.492 252 13 8 833 1070 24773976 24773727 1.760000e-74 291.0
16 TraesCS6B01G065100 chr6A 84.429 289 36 6 2491 2770 23653187 23652899 4.920000e-70 276.0
17 TraesCS6B01G065100 chr6A 86.328 256 28 7 2300 2551 23637428 23637176 6.360000e-69 272.0
18 TraesCS6B01G065100 chr6A 78.310 355 38 17 1601 1919 23637978 23637627 5.100000e-45 193.0
19 TraesCS6B01G065100 chr6A 75.419 358 39 18 1070 1384 23638339 23637988 1.460000e-25 128.0
20 TraesCS6B01G065100 chr6A 81.503 173 15 5 1076 1235 23654203 23654035 5.240000e-25 126.0
21 TraesCS6B01G065100 chrUn 97.697 3344 60 8 1546 4881 94024731 94021397 0.000000e+00 5733.0
22 TraesCS6B01G065100 chrUn 94.844 1571 57 7 1 1550 94026498 94024931 0.000000e+00 2431.0
23 TraesCS6B01G065100 chrUn 82.688 2016 237 58 2028 3973 93844360 93846333 0.000000e+00 1687.0
24 TraesCS6B01G065100 chrUn 98.000 50 1 0 4939 4988 94021123 94021074 2.470000e-13 87.9
25 TraesCS6B01G065100 chr6D 82.126 1740 242 38 2296 3991 25648952 25647238 0.000000e+00 1426.0
26 TraesCS6B01G065100 chr6D 86.115 713 81 12 3293 3994 25640456 25639751 0.000000e+00 752.0
27 TraesCS6B01G065100 chr6D 87.075 294 27 7 2491 2774 25641343 25641051 6.230000e-84 322.0
28 TraesCS6B01G065100 chr6D 80.057 351 46 14 2218 2551 25641689 25641346 6.450000e-59 239.0
29 TraesCS6B01G065100 chr6D 79.456 331 42 12 1075 1384 25642465 25642140 1.410000e-50 211.0
30 TraesCS6B01G065100 chr6D 78.470 353 38 17 1601 1920 25642130 25641783 3.940000e-46 196.0
31 TraesCS6B01G065100 chr7D 82.126 621 108 3 85 703 199080494 199081113 3.420000e-146 529.0
32 TraesCS6B01G065100 chr7D 80.414 628 121 2 76 702 136414293 136414919 1.260000e-130 477.0
33 TraesCS6B01G065100 chr5B 81.761 636 110 5 70 704 711257489 711258119 1.230000e-145 527.0
34 TraesCS6B01G065100 chr5B 79.969 639 120 7 68 703 606279663 606280296 9.780000e-127 464.0
35 TraesCS6B01G065100 chr5D 82.082 586 101 4 113 697 220673986 220674568 9.640000e-137 497.0
36 TraesCS6B01G065100 chr1B 80.811 641 112 7 68 705 68177845 68177213 4.490000e-135 492.0
37 TraesCS6B01G065100 chr1D 80.160 625 123 1 81 704 306222288 306222912 2.720000e-127 466.0


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 TraesCS6B01G065100 chr6B 43221300 43226287 4987 True 9212.000000 9212 100.000000 1 4988 1 chr6B.!!$R2 4987
1 TraesCS6B01G065100 chr6B 41455251 41456885 1634 True 1315.000000 1315 81.643000 2292 3904 1 chr6B.!!$R1 1612
2 TraesCS6B01G065100 chr6B 51383409 51384043 634 False 486.000000 486 80.595000 68 703 1 chr6B.!!$F1 635
3 TraesCS6B01G065100 chr6B 41446751 41449499 2748 True 338.200000 732 83.370600 1070 3994 5 chr6B.!!$R3 2924
4 TraesCS6B01G065100 chr6A 24769618 24773976 4358 True 3345.000000 6399 92.341000 833 4988 2 chr6A.!!$R4 4155
5 TraesCS6B01G065100 chr6A 23676924 23678643 1719 True 1402.000000 1402 81.834000 2292 3991 1 chr6A.!!$R1 1699
6 TraesCS6B01G065100 chr6A 24458021 24458745 724 False 643.000000 643 83.060000 3276 3991 1 chr6A.!!$F1 715
7 TraesCS6B01G065100 chr6A 23651595 23654203 2608 True 391.000000 771 84.119667 1076 3994 3 chr6A.!!$R3 2918
8 TraesCS6B01G065100 chr6A 23635584 23638339 2755 True 363.333333 763 82.967667 1070 3994 6 chr6A.!!$R2 2924
9 TraesCS6B01G065100 chrUn 94021074 94026498 5424 True 2750.633333 5733 96.847000 1 4988 3 chrUn.!!$R1 4987
10 TraesCS6B01G065100 chrUn 93844360 93846333 1973 False 1687.000000 1687 82.688000 2028 3973 1 chrUn.!!$F1 1945
11 TraesCS6B01G065100 chr6D 25647238 25648952 1714 True 1426.000000 1426 82.126000 2296 3991 1 chr6D.!!$R1 1695
12 TraesCS6B01G065100 chr6D 25639751 25642465 2714 True 344.000000 752 82.234600 1075 3994 5 chr6D.!!$R2 2919
13 TraesCS6B01G065100 chr7D 199080494 199081113 619 False 529.000000 529 82.126000 85 703 1 chr7D.!!$F2 618
14 TraesCS6B01G065100 chr7D 136414293 136414919 626 False 477.000000 477 80.414000 76 702 1 chr7D.!!$F1 626
15 TraesCS6B01G065100 chr5B 711257489 711258119 630 False 527.000000 527 81.761000 70 704 1 chr5B.!!$F2 634
16 TraesCS6B01G065100 chr5B 606279663 606280296 633 False 464.000000 464 79.969000 68 703 1 chr5B.!!$F1 635
17 TraesCS6B01G065100 chr5D 220673986 220674568 582 False 497.000000 497 82.082000 113 697 1 chr5D.!!$F1 584
18 TraesCS6B01G065100 chr1B 68177213 68177845 632 True 492.000000 492 80.811000 68 705 1 chr1B.!!$R1 637
19 TraesCS6B01G065100 chr1D 306222288 306222912 624 False 466.000000 466 80.160000 81 704 1 chr1D.!!$F1 623

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
108 109 0.103208 CTTTATCTCCTGCCGACGCT 59.897 55.000 0.00 0.0 35.36 5.07 F
137 138 1.129917 CCACCTCATCTCTCATGGCT 58.870 55.000 0.00 0.0 0.00 4.75 F
900 903 1.718757 GGCGCCTGCTCGAATTTGAT 61.719 55.000 22.15 0.0 42.25 2.57 F
903 906 2.223249 GCGCCTGCTCGAATTTGATTTA 60.223 45.455 0.00 0.0 38.39 1.40 F
1920 2549 2.365293 AGTTGCCCAGGTTCATGTTTTC 59.635 45.455 0.00 0.0 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1123 1338 1.022982 CCCTTCCTTTTACCCGTCGC 61.023 60.000 0.00 0.0 0.00 5.19 R
1920 2549 3.861276 AATGACACTGACATTGCATGG 57.139 42.857 6.01 0.0 36.74 3.66 R
2408 3113 2.414559 GCAATATGTCCTGCACACACAC 60.415 50.000 0.00 0.0 38.04 3.82 R
3880 4759 9.708092 AGTTAACTTAACTGTAGATGGAACTTC 57.292 33.333 12.55 0.0 46.58 3.01 R
4712 5602 1.000274 GTGAAAGCAGGGCGTCATTTT 60.000 47.619 0.00 0.0 32.19 1.82 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
104 105 1.485066 GGTTCCTTTATCTCCTGCCGA 59.515 52.381 0.00 0.00 0.00 5.54
108 109 0.103208 CTTTATCTCCTGCCGACGCT 59.897 55.000 0.00 0.00 35.36 5.07
137 138 1.129917 CCACCTCATCTCTCATGGCT 58.870 55.000 0.00 0.00 0.00 4.75
444 446 8.254508 AGATCTTTTCAATCTACGCTACTCTTT 58.745 33.333 0.00 0.00 31.71 2.52
476 478 3.730761 CTGTTCTGGTGCGCTGGC 61.731 66.667 9.73 0.00 40.52 4.85
650 652 9.834628 TGATTTTTATTATTTCCTGTGTTCGTC 57.165 29.630 0.00 0.00 0.00 4.20
675 677 9.914131 TCGTAGTAGGATAAATGAAGATGAATG 57.086 33.333 0.00 0.00 0.00 2.67
794 796 1.789523 TAGGAAAGATAGCCGCACCT 58.210 50.000 0.00 0.00 0.00 4.00
900 903 1.718757 GGCGCCTGCTCGAATTTGAT 61.719 55.000 22.15 0.00 42.25 2.57
903 906 2.223249 GCGCCTGCTCGAATTTGATTTA 60.223 45.455 0.00 0.00 38.39 1.40
1361 1703 9.479549 AGATCCTTTTGGTCACATATTAATGTT 57.520 29.630 0.00 0.00 41.65 2.71
1620 2201 2.748461 TGCGCTGTAACAAAGTTCAC 57.252 45.000 9.73 0.00 0.00 3.18
1920 2549 2.365293 AGTTGCCCAGGTTCATGTTTTC 59.635 45.455 0.00 0.00 0.00 2.29
2031 2681 7.173218 ACATATTCATTTCTGTTTCGTCACTGT 59.827 33.333 0.00 0.00 0.00 3.55
2525 3230 4.056740 CTGGAGATGTCATTCCAATCTCG 58.943 47.826 14.04 3.64 42.61 4.04
3880 4759 7.359849 CGGCTATCAGAACATACATTGAGAATG 60.360 40.741 0.00 0.00 44.48 2.67
4185 5067 4.458989 GGCCAGTGTTGAAATATTCAGTCA 59.541 41.667 0.00 0.00 41.38 3.41
4228 5110 8.780249 GTTTTGTTTCTCAGGCTATTGTTACTA 58.220 33.333 0.00 0.00 0.00 1.82
4229 5111 9.515226 TTTTGTTTCTCAGGCTATTGTTACTAT 57.485 29.630 0.00 0.00 0.00 2.12
4476 5362 6.091169 CCAACATGACACTTTATTTTGCATCC 59.909 38.462 0.00 0.00 0.00 3.51
4525 5411 7.970614 GTCTTCCAACATTACAATTTCATCCTC 59.029 37.037 0.00 0.00 0.00 3.71
4712 5602 4.517075 TCAGGATTTGCATTCGTACAACAA 59.483 37.500 0.00 0.00 0.00 2.83
4716 5606 6.928492 AGGATTTGCATTCGTACAACAAAAAT 59.072 30.769 0.00 0.00 34.25 1.82
4729 5619 1.412343 ACAAAAATGACGCCCTGCTTT 59.588 42.857 0.00 0.00 0.00 3.51
4775 5665 9.045223 TCCAAATCATTATGTTACGAATCTGAG 57.955 33.333 0.00 0.00 0.00 3.35
4839 5729 0.251742 CACCCCCTGAATTTCAGCCA 60.252 55.000 19.04 0.00 42.98 4.75
4840 5730 0.712380 ACCCCCTGAATTTCAGCCAT 59.288 50.000 19.04 3.49 42.98 4.40
4843 5733 1.620524 CCCCTGAATTTCAGCCATGGT 60.621 52.381 19.04 0.00 42.98 3.55
4869 5759 1.289160 CAACCTCCCCCAATCTCTCA 58.711 55.000 0.00 0.00 0.00 3.27
4884 5774 6.878389 CCAATCTCTCAAATCCTATTAGCCTC 59.122 42.308 0.00 0.00 0.00 4.70
4899 5789 9.660180 CCTATTAGCCTCTGATTAATTAAGTCC 57.340 37.037 3.94 0.00 0.00 3.85
4906 5796 7.254692 GCCTCTGATTAATTAAGTCCGTAAACC 60.255 40.741 3.94 0.00 0.00 3.27
4937 5827 1.149174 CCCCGTGGCTCATTATGCT 59.851 57.895 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
111 112 2.039624 AGATGAGGTGGACCGGCT 59.960 61.111 0.00 0.00 42.08 5.52
137 138 2.044451 CACCGCCATGGCCCTAAA 60.044 61.111 30.79 0.00 43.94 1.85
159 161 2.285368 TGGCAAGGACCGGGATCT 60.285 61.111 6.32 0.00 0.00 2.75
312 314 0.179119 ACGCCTACCAACGATGCTAC 60.179 55.000 0.00 0.00 0.00 3.58
444 446 3.805422 CAGAACAGTTACCGCAGTTGTTA 59.195 43.478 0.00 0.00 32.58 2.41
476 478 2.719739 CCATGCTAAGCCATCATAGGG 58.280 52.381 0.00 0.00 0.00 3.53
650 652 9.144747 CCATTCATCTTCATTTATCCTACTACG 57.855 37.037 0.00 0.00 0.00 3.51
811 814 0.759346 CCCTAGGTGCGGCTATCTTT 59.241 55.000 8.29 0.00 0.00 2.52
887 890 5.410132 TCCGTTTCTAAATCAAATTCGAGCA 59.590 36.000 0.00 0.00 0.00 4.26
900 903 7.376615 TCTTTGTTTTTGGTTCCGTTTCTAAA 58.623 30.769 0.00 0.00 0.00 1.85
903 906 5.394224 TCTTTGTTTTTGGTTCCGTTTCT 57.606 34.783 0.00 0.00 0.00 2.52
938 941 1.859302 TTTCTCCAGCTCTCCTCTCC 58.141 55.000 0.00 0.00 0.00 3.71
1123 1338 1.022982 CCCTTCCTTTTACCCGTCGC 61.023 60.000 0.00 0.00 0.00 5.19
1313 1568 9.535270 GATCTTTTCTCTGTTTTCAAATCGTAG 57.465 33.333 0.00 0.00 0.00 3.51
1361 1703 8.974060 ACCAAAAATAACTTCTCTCTGTTACA 57.026 30.769 0.00 0.00 32.43 2.41
1620 2201 6.421377 TGAATATCCCAATCAATTATCGCG 57.579 37.500 0.00 0.00 0.00 5.87
1822 2450 8.975410 CAGAAAATGCAGAGTTCAATTCATAA 57.025 30.769 8.88 0.00 0.00 1.90
1920 2549 3.861276 AATGACACTGACATTGCATGG 57.139 42.857 6.01 0.00 36.74 3.66
2407 3112 2.813172 CAATATGTCCTGCACACACACA 59.187 45.455 0.00 0.00 38.04 3.72
2408 3113 2.414559 GCAATATGTCCTGCACACACAC 60.415 50.000 0.00 0.00 38.04 3.82
3880 4759 9.708092 AGTTAACTTAACTGTAGATGGAACTTC 57.292 33.333 12.55 0.00 46.58 3.01
4185 5067 4.021544 ACAAAACACAACACCACATCTTGT 60.022 37.500 0.00 0.00 0.00 3.16
4427 5311 8.693542 GGATACAAATCTCACCAAATTGAAAG 57.306 34.615 0.00 0.00 32.29 2.62
4712 5602 1.000274 GTGAAAGCAGGGCGTCATTTT 60.000 47.619 0.00 0.00 32.19 1.82
4716 5606 1.597854 CTGTGAAAGCAGGGCGTCA 60.598 57.895 0.00 0.00 33.11 4.35
4775 5665 6.294397 GGATGCAAATCCTGATTTCTATGGAC 60.294 42.308 2.19 0.00 38.84 4.02
4839 5729 3.672503 GAGGTTGGGCCCCACCAT 61.673 66.667 39.20 26.71 40.91 3.55
4884 5774 7.490402 ACGAGGTTTACGGACTTAATTAATCAG 59.510 37.037 0.00 3.08 34.93 2.90
4899 5789 4.805719 GGGGATTAGTTTACGAGGTTTACG 59.194 45.833 0.00 0.00 0.00 3.18
4906 5796 2.817901 CCACGGGGATTAGTTTACGAG 58.182 52.381 0.00 0.00 35.59 4.18
4937 5827 5.334260 CCTTTTGTTAGCGAACATTTCCGTA 60.334 40.000 13.36 0.00 44.96 4.02


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

AutoCloner maintained by Alex Coulton.