Multiple sequence alignment - TraesCS6D01G129100

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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 TraesCS6D01G129100 chr6D 100.000 2930 0 0 1 2930 93676825 93679754 0.000000e+00 5411.0
1 TraesCS6D01G129100 chr6A 95.944 2342 68 8 10 2343 115015308 115012986 0.000000e+00 3773.0
2 TraesCS6D01G129100 chr6A 87.457 582 64 8 2351 2926 115012480 115011902 0.000000e+00 662.0
3 TraesCS6D01G129100 chr6B 96.583 2195 59 10 156 2343 179356587 179354402 0.000000e+00 3624.0
4 TraesCS6D01G129100 chr6B 87.931 580 64 5 2351 2926 179354061 179353484 0.000000e+00 678.0
5 TraesCS6D01G129100 chr6B 94.872 156 8 0 1 156 179357213 179357058 8.110000e-61 244.0
6 TraesCS6D01G129100 chr2B 95.095 734 32 3 700 1430 305762567 305761835 0.000000e+00 1153.0
7 TraesCS6D01G129100 chr2B 92.346 601 33 6 1433 2030 305759449 305758859 0.000000e+00 843.0
8 TraesCS6D01G129100 chr2B 93.277 119 8 0 1135 1253 616454558 616454440 3.000000e-40 176.0
9 TraesCS6D01G129100 chr2D 93.142 627 34 6 1517 2137 19266344 19265721 0.000000e+00 911.0
10 TraesCS6D01G129100 chr2D 92.675 628 35 9 1517 2137 406698160 406697537 0.000000e+00 894.0
11 TraesCS6D01G129100 chr7D 92.834 628 32 9 1517 2137 109362733 109362112 0.000000e+00 898.0
12 TraesCS6D01G129100 chr7D 92.185 627 40 7 1517 2137 631742020 631742643 0.000000e+00 878.0
13 TraesCS6D01G129100 chr7D 92.667 600 31 6 1433 2028 521632627 521632037 0.000000e+00 852.0
14 TraesCS6D01G129100 chr7D 97.306 297 8 0 700 996 521642066 521641770 3.370000e-139 505.0
15 TraesCS6D01G129100 chr5D 92.663 627 37 6 1517 2137 517971384 517972007 0.000000e+00 894.0
16 TraesCS6D01G129100 chr5D 92.487 599 33 5 1433 2028 423852352 423852941 0.000000e+00 846.0
17 TraesCS6D01G129100 chr4B 93.771 594 35 2 1102 1693 535114129 535113536 0.000000e+00 891.0
18 TraesCS6D01G129100 chr4B 92.763 152 11 0 1102 1253 630968987 630969138 1.370000e-53 220.0
19 TraesCS6D01G129100 chr4B 84.337 83 10 3 2801 2881 488893583 488893664 8.710000e-11 78.7
20 TraesCS6D01G129100 chr5A 92.185 627 40 8 1517 2137 512779129 512779752 0.000000e+00 878.0
21 TraesCS6D01G129100 chr5A 94.118 119 7 0 1135 1253 539080152 539080270 6.450000e-42 182.0
22 TraesCS6D01G129100 chr4A 92.026 627 41 7 1517 2137 7329512 7328889 0.000000e+00 872.0
23 TraesCS6D01G129100 chr4A 81.429 70 13 0 2802 2871 78765805 78765874 1.130000e-04 58.4
24 TraesCS6D01G129100 chr1D 92.654 599 32 6 1433 2028 110584313 110584902 0.000000e+00 852.0
25 TraesCS6D01G129100 chr3A 92.450 596 33 5 1433 2025 726010171 726010757 0.000000e+00 841.0
26 TraesCS6D01G129100 chr3A 97.643 297 7 0 700 996 726003093 726003389 7.240000e-141 510.0
27 TraesCS6D01G129100 chr7B 94.079 152 8 1 1102 1253 36976839 36976989 2.270000e-56 230.0
28 TraesCS6D01G129100 chr2A 94.118 119 7 0 1135 1253 605007468 605007586 6.450000e-42 182.0
29 TraesCS6D01G129100 chr4D 85.135 74 8 3 2800 2871 396938509 396938581 4.050000e-09 73.1


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 TraesCS6D01G129100 chr6D 93676825 93679754 2929 False 5411.000000 5411 100.000000 1 2930 1 chr6D.!!$F1 2929
1 TraesCS6D01G129100 chr6A 115011902 115015308 3406 True 2217.500000 3773 91.700500 10 2926 2 chr6A.!!$R1 2916
2 TraesCS6D01G129100 chr6B 179353484 179357213 3729 True 1515.333333 3624 93.128667 1 2926 3 chr6B.!!$R1 2925
3 TraesCS6D01G129100 chr2B 305758859 305762567 3708 True 998.000000 1153 93.720500 700 2030 2 chr2B.!!$R2 1330
4 TraesCS6D01G129100 chr2D 19265721 19266344 623 True 911.000000 911 93.142000 1517 2137 1 chr2D.!!$R1 620
5 TraesCS6D01G129100 chr2D 406697537 406698160 623 True 894.000000 894 92.675000 1517 2137 1 chr2D.!!$R2 620
6 TraesCS6D01G129100 chr7D 109362112 109362733 621 True 898.000000 898 92.834000 1517 2137 1 chr7D.!!$R1 620
7 TraesCS6D01G129100 chr7D 631742020 631742643 623 False 878.000000 878 92.185000 1517 2137 1 chr7D.!!$F1 620
8 TraesCS6D01G129100 chr7D 521632037 521632627 590 True 852.000000 852 92.667000 1433 2028 1 chr7D.!!$R2 595
9 TraesCS6D01G129100 chr5D 517971384 517972007 623 False 894.000000 894 92.663000 1517 2137 1 chr5D.!!$F2 620
10 TraesCS6D01G129100 chr5D 423852352 423852941 589 False 846.000000 846 92.487000 1433 2028 1 chr5D.!!$F1 595
11 TraesCS6D01G129100 chr4B 535113536 535114129 593 True 891.000000 891 93.771000 1102 1693 1 chr4B.!!$R1 591
12 TraesCS6D01G129100 chr5A 512779129 512779752 623 False 878.000000 878 92.185000 1517 2137 1 chr5A.!!$F1 620
13 TraesCS6D01G129100 chr4A 7328889 7329512 623 True 872.000000 872 92.026000 1517 2137 1 chr4A.!!$R1 620
14 TraesCS6D01G129100 chr1D 110584313 110584902 589 False 852.000000 852 92.654000 1433 2028 1 chr1D.!!$F1 595
15 TraesCS6D01G129100 chr3A 726010171 726010757 586 False 841.000000 841 92.450000 1433 2025 1 chr3A.!!$F2 592

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
313 785 0.18135 GGGCCTGGAATCCTACAGTG 59.819 60.0 0.84 0.0 32.9 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2302 5175 0.322975 AGCAGGTACAACAGCCTCAG 59.677 55.0 0.0 0.0 31.73 3.35 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
27 28 7.396623 TCCTAGTTAAGTTCTCTCCTTACCTTG 59.603 40.741 0.00 0.00 0.00 3.61
189 661 5.885230 TTGAAGTCAAATGGTAGCAGATG 57.115 39.130 0.00 2.09 32.11 2.90
211 683 8.978472 AGATGCATACTACACTTAAGTAGGAAA 58.022 33.333 8.04 0.00 44.49 3.13
308 780 0.470080 CTCGAGGGCCTGGAATCCTA 60.470 60.000 19.31 0.00 0.00 2.94
313 785 0.181350 GGGCCTGGAATCCTACAGTG 59.819 60.000 0.84 0.00 32.90 3.66
377 849 8.106247 TGTTAGAAAATTCAGGTTAATTCGCT 57.894 30.769 0.00 0.00 0.00 4.93
404 876 5.499004 TCACTCACTAGGGCAAAGTAAAT 57.501 39.130 0.00 0.00 0.00 1.40
563 1035 7.429920 GCTAGTATGTCTTCTCGTTTAAGTCTG 59.570 40.741 0.00 0.00 0.00 3.51
867 1339 5.482908 CCTGGGTGTTATCACATAGATAGC 58.517 45.833 6.28 0.00 45.45 2.97
1050 1523 4.829492 ACATATTGCATAAGGGGAAGCTTC 59.171 41.667 18.54 18.54 0.00 3.86
1226 1704 5.990668 ACCATAGAAGGTGGAATCAACTAC 58.009 41.667 0.00 0.00 40.66 2.73
1244 1722 9.744468 ATCAACTACAATAAAAGTTTGGTTGAC 57.256 29.630 16.00 0.00 41.63 3.18
1341 1820 8.200364 AGACAAAATTTGAAAACCTGTTCATG 57.800 30.769 13.19 0.00 37.36 3.07
1346 1825 3.940209 TGAAAACCTGTTCATGGCATC 57.060 42.857 0.00 0.00 32.56 3.91
1349 1828 1.549203 AACCTGTTCATGGCATCCAC 58.451 50.000 0.00 0.00 35.80 4.02
1365 1844 2.559698 CCACGCCATGGGTCATTATA 57.440 50.000 15.13 0.00 45.95 0.98
1417 1896 2.980476 CGTTCATCGGATTCGGATACAG 59.020 50.000 6.42 0.00 36.95 2.74
1586 4449 4.356405 AAGTGACAGACATTGATCACCA 57.644 40.909 0.00 0.00 37.97 4.17
2302 5175 5.121454 CCACTTTATTCAGAGAACAGACAGC 59.879 44.000 0.00 0.00 0.00 4.40
2344 5217 3.368822 CGGGTGACGGACAGGTAA 58.631 61.111 0.00 0.00 39.42 2.85
2346 5219 0.033781 CGGGTGACGGACAGGTAAAA 59.966 55.000 0.00 0.00 39.42 1.52
2358 5733 5.640732 GGACAGGTAAAATACAATGTGCAG 58.359 41.667 0.00 0.00 37.81 4.41
2455 5831 2.358984 GGCGGCGACACCCTTTAA 60.359 61.111 12.98 0.00 33.26 1.52
2456 5832 1.967494 GGCGGCGACACCCTTTAAA 60.967 57.895 12.98 0.00 33.26 1.52
2468 5844 5.816682 ACACCCTTTAAAAGATCGATTCCT 58.183 37.500 0.00 0.00 0.00 3.36
2478 5854 3.148340 TCGATTCCTCTCGACGACA 57.852 52.632 0.00 0.00 42.38 4.35
2487 5863 2.420372 CCTCTCGACGACATTTCTCTCA 59.580 50.000 0.00 0.00 0.00 3.27
2536 5912 7.327518 TGTGAAACGGAGAAAAAGAAGAAAAAC 59.672 33.333 0.00 0.00 42.39 2.43
2541 5917 6.972901 ACGGAGAAAAAGAAGAAAAACATGTC 59.027 34.615 0.00 0.00 0.00 3.06
2544 5920 7.222805 GGAGAAAAAGAAGAAAAACATGTCACC 59.777 37.037 0.00 0.00 0.00 4.02
2657 6033 7.615403 AGTTCAGATTGCTAACTCTATTCACA 58.385 34.615 0.00 0.00 0.00 3.58
2666 6042 1.273098 ACTCTATTCACACGGGGAGGT 60.273 52.381 0.00 0.00 0.00 3.85
2689 6066 4.701651 TGGATGCATTGATCTCGAAGTTTT 59.298 37.500 0.00 0.00 0.00 2.43
2697 6074 9.643652 GCATTGATCTCGAAGTTTTAATCTAAG 57.356 33.333 0.00 0.00 0.00 2.18
2716 6095 8.988546 ATCTAAGTGAGTATTCTCTTAGCTCA 57.011 34.615 22.56 12.48 46.85 4.26
2785 6164 0.161658 CTGATGTGCACACGACGTTC 59.838 55.000 24.37 15.22 0.00 3.95
2799 6178 3.242608 ACGACGTTCTTTTGTGTCCAATG 60.243 43.478 0.00 0.00 0.00 2.82
2806 6185 3.005684 TCTTTTGTGTCCAATGTGCATCC 59.994 43.478 0.00 0.00 0.00 3.51
2825 6204 1.290203 CGATAAATGCTCTGCACCGT 58.710 50.000 0.00 0.00 43.04 4.83
2829 6208 0.957395 AAATGCTCTGCACCGTCAGG 60.957 55.000 0.00 0.00 43.04 3.86
2853 6232 8.784043 AGGTGATGTAAGAACAGAATTACAAAC 58.216 33.333 2.28 4.51 43.14 2.93
2856 6235 7.442969 TGATGTAAGAACAGAATTACAAACGGT 59.557 33.333 2.28 0.00 43.14 4.83
2871 6251 0.107081 ACGGTTGGATGGAAACGTCA 59.893 50.000 0.00 0.00 46.07 4.35
2872 6252 1.876416 ACGGTTGGATGGAAACGTCAG 60.876 52.381 0.00 0.00 46.07 3.51
2885 6265 2.363788 ACGTCAGATGCGTGTTGTAT 57.636 45.000 2.36 0.00 41.33 2.29
2893 6273 7.464358 GTCAGATGCGTGTTGTATAAAAAGAT 58.536 34.615 0.00 0.00 0.00 2.40
2926 6306 5.012328 AGTAGTGCTCTAATAACAGCCAC 57.988 43.478 0.00 0.00 34.47 5.01
2927 6307 3.268023 AGTGCTCTAATAACAGCCACC 57.732 47.619 0.00 0.00 34.47 4.61
2928 6308 1.933853 GTGCTCTAATAACAGCCACCG 59.066 52.381 0.00 0.00 34.47 4.94
2929 6309 1.553248 TGCTCTAATAACAGCCACCGT 59.447 47.619 0.00 0.00 34.47 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 6.436532 ACGATCAAGGTAAGGAGAGAACTTAA 59.563 38.462 0.00 0.00 32.68 1.85
8 9 5.950549 ACGATCAAGGTAAGGAGAGAACTTA 59.049 40.000 0.00 0.00 0.00 2.24
39 40 0.536006 AAGGCCAGTCTGTGAACAGC 60.536 55.000 5.01 1.74 43.46 4.40
211 683 6.223120 GTTTGTTGGTCTTCCATTAGCAAAT 58.777 36.000 0.00 0.00 43.91 2.32
377 849 4.286032 ACTTTGCCCTAGTGAGTGATGTTA 59.714 41.667 0.00 0.00 0.00 2.41
404 876 8.212312 TGGGTGTAGTGAACTTTTGTAGATAAA 58.788 33.333 0.00 0.00 0.00 1.40
563 1035 5.125578 CCAAGAACTAAAGGCTAATTCACCC 59.874 44.000 0.00 0.00 0.00 4.61
871 1343 6.664816 AGGCTAATTTCCTTTTCATGACATCA 59.335 34.615 0.00 0.00 0.00 3.07
1050 1523 0.949397 CACAGATGAATGATGCCCGG 59.051 55.000 0.00 0.00 0.00 5.73
1226 1704 6.528423 TGACAACGTCAACCAAACTTTTATTG 59.472 34.615 0.00 0.00 39.78 1.90
1244 1722 6.951256 TCTTCTGATTGTAGATTGACAACG 57.049 37.500 0.00 0.00 41.93 4.10
1253 1731 8.762645 ACCATTTGTAGATCTTCTGATTGTAGA 58.237 33.333 0.00 0.00 32.19 2.59
1349 1828 4.578871 TGAGAATATAATGACCCATGGCG 58.421 43.478 6.09 2.02 0.00 5.69
1394 1873 3.254903 TGTATCCGAATCCGATGAACGAT 59.745 43.478 0.00 0.00 45.77 3.73
1417 1896 3.817647 GGATCTGTAAATGGTCCATCTGC 59.182 47.826 4.39 0.00 0.00 4.26
2007 4877 4.264638 GCCGGCGAGCTCTCTCTC 62.265 72.222 12.58 0.00 37.19 3.20
2302 5175 0.322975 AGCAGGTACAACAGCCTCAG 59.677 55.000 0.00 0.00 31.73 3.35
2336 5209 5.095490 GCTGCACATTGTATTTTACCTGTC 58.905 41.667 0.00 0.00 0.00 3.51
2358 5733 2.623173 GACTAGCGCGAATGCAGC 59.377 61.111 12.10 0.00 42.97 5.25
2388 5763 4.816385 TCTTTCATTGCGTTTCTGACTTCT 59.184 37.500 0.00 0.00 0.00 2.85
2421 5796 1.005037 CCGCTGTTGTGCACTCCTA 60.005 57.895 19.41 0.00 0.00 2.94
2422 5797 2.281070 CCGCTGTTGTGCACTCCT 60.281 61.111 19.41 0.00 0.00 3.69
2423 5798 4.030452 GCCGCTGTTGTGCACTCC 62.030 66.667 19.41 8.86 0.00 3.85
2468 5844 3.075148 AGTGAGAGAAATGTCGTCGAGA 58.925 45.455 0.00 0.00 0.00 4.04
2473 5849 4.082136 GGGAACTAGTGAGAGAAATGTCGT 60.082 45.833 0.00 0.00 0.00 4.34
2477 5853 4.440802 CGAGGGGAACTAGTGAGAGAAATG 60.441 50.000 0.00 0.00 0.00 2.32
2478 5854 3.702045 CGAGGGGAACTAGTGAGAGAAAT 59.298 47.826 0.00 0.00 0.00 2.17
2487 5863 2.758737 CCGCCGAGGGGAACTAGT 60.759 66.667 7.83 0.00 37.91 2.57
2514 5890 7.817478 ACATGTTTTTCTTCTTTTTCTCCGTTT 59.183 29.630 0.00 0.00 0.00 3.60
2515 5891 7.320399 ACATGTTTTTCTTCTTTTTCTCCGTT 58.680 30.769 0.00 0.00 0.00 4.44
2518 5894 7.222805 GGTGACATGTTTTTCTTCTTTTTCTCC 59.777 37.037 0.00 0.00 0.00 3.71
2519 5895 7.759433 TGGTGACATGTTTTTCTTCTTTTTCTC 59.241 33.333 0.00 0.00 33.40 2.87
2541 5917 7.287466 TGACTATCCCAAATTTTATCCATGGTG 59.713 37.037 12.58 0.00 0.00 4.17
2544 5920 9.081204 TGATGACTATCCCAAATTTTATCCATG 57.919 33.333 0.00 0.00 32.09 3.66
2587 5963 7.330262 ACAGAAACTGGTTGAAACATTTCATT 58.670 30.769 15.36 0.00 40.10 2.57
2638 6014 4.508124 CCCGTGTGAATAGAGTTAGCAATC 59.492 45.833 0.00 0.00 0.00 2.67
2657 6033 2.308722 AATGCATCCACCTCCCCGT 61.309 57.895 0.00 0.00 0.00 5.28
2666 6042 3.548745 ACTTCGAGATCAATGCATCCA 57.451 42.857 0.00 0.00 0.00 3.41
2698 6075 9.265901 GCATAAAATGAGCTAAGAGAATACTCA 57.734 33.333 0.00 0.00 44.79 3.41
2745 6124 7.414222 TCAGTTCCGTTATTATCACTAACCT 57.586 36.000 0.00 0.00 0.00 3.50
2746 6125 7.709613 ACATCAGTTCCGTTATTATCACTAACC 59.290 37.037 0.00 0.00 0.00 2.85
2785 6164 3.319755 GGATGCACATTGGACACAAAAG 58.680 45.455 0.00 0.00 40.55 2.27
2806 6185 1.258982 GACGGTGCAGAGCATTTATCG 59.741 52.381 0.00 0.00 41.91 2.92
2825 6204 7.676004 TGTAATTCTGTTCTTACATCACCTGA 58.324 34.615 0.00 0.00 33.96 3.86
2829 6208 7.744715 CCGTTTGTAATTCTGTTCTTACATCAC 59.255 37.037 0.00 0.00 37.60 3.06
2837 6216 5.127491 TCCAACCGTTTGTAATTCTGTTCT 58.873 37.500 0.00 0.00 0.00 3.01
2839 6218 5.278758 CCATCCAACCGTTTGTAATTCTGTT 60.279 40.000 0.00 0.00 0.00 3.16
2853 6232 0.796312 CTGACGTTTCCATCCAACCG 59.204 55.000 0.00 0.00 0.00 4.44
2856 6235 2.083774 GCATCTGACGTTTCCATCCAA 58.916 47.619 0.00 0.00 0.00 3.53
2871 6251 8.511321 TCAAATCTTTTTATACAACACGCATCT 58.489 29.630 0.00 0.00 0.00 2.90
2872 6252 8.667987 TCAAATCTTTTTATACAACACGCATC 57.332 30.769 0.00 0.00 0.00 3.91
2908 6288 1.933853 CGGTGGCTGTTATTAGAGCAC 59.066 52.381 3.13 0.10 42.22 4.40


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

AutoCloner maintained by Alex Coulton.