Multiple sequence alignment - TraesCS7B01G190900

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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 TraesCS7B01G190900 chr7B 100.000 7151 0 0 1 7151 328559894 328567044 0.000000e+00 13206.0
1 TraesCS7B01G190900 chr7B 90.807 533 32 6 2250 2779 328561892 328562410 0.000000e+00 697.0
2 TraesCS7B01G190900 chr7B 90.807 533 32 6 1999 2517 328562143 328562672 0.000000e+00 697.0
3 TraesCS7B01G190900 chr7B 87.636 275 21 8 2504 2777 328561892 328562154 2.510000e-79 307.0
4 TraesCS7B01G190900 chr7B 87.636 275 21 8 1999 2261 328562397 328562670 2.510000e-79 307.0
5 TraesCS7B01G190900 chr2B 98.114 7157 112 15 1 7151 84544208 84537069 0.000000e+00 12447.0
6 TraesCS7B01G190900 chr2B 88.010 784 86 7 6372 7151 26199743 26198964 0.000000e+00 920.0
7 TraesCS7B01G190900 chr2B 91.353 532 29 8 1999 2517 84541962 84541435 0.000000e+00 712.0
8 TraesCS7B01G190900 chr2B 90.977 532 32 6 2250 2779 84542214 84541697 0.000000e+00 702.0
9 TraesCS7B01G190900 chr2B 81.789 626 106 6 6530 7151 733830774 733830153 1.060000e-142 518.0
10 TraesCS7B01G190900 chr2B 71.257 1750 370 92 1 1708 733835469 733833811 8.950000e-84 322.0
11 TraesCS7B01G190900 chr2B 88.000 275 21 7 2504 2777 84542214 84541951 1.500000e-81 315.0
12 TraesCS7B01G190900 chr2B 88.000 275 20 8 1999 2261 84541710 84541437 5.390000e-81 313.0
13 TraesCS7B01G190900 chr2B 72.048 1338 279 73 1 1306 637752719 637751445 1.940000e-80 311.0
14 TraesCS7B01G190900 chr4D 83.757 2124 216 75 3801 5874 422226027 422223983 0.000000e+00 1892.0
15 TraesCS7B01G190900 chr4D 85.117 1747 181 56 1 1738 422228528 422226852 0.000000e+00 1712.0
16 TraesCS7B01G190900 chr4D 88.571 980 100 10 6175 7151 422223445 422222475 0.000000e+00 1179.0
17 TraesCS7B01G190900 chr4D 88.873 719 64 13 3084 3798 422226786 422226080 0.000000e+00 870.0
18 TraesCS7B01G190900 chr1D 83.310 2133 247 71 3801 5874 431416362 431418444 0.000000e+00 1866.0
19 TraesCS7B01G190900 chr1D 84.637 1751 209 49 1 1738 431413832 431415535 0.000000e+00 1688.0
20 TraesCS7B01G190900 chr1D 88.280 785 82 7 6372 7151 431419108 431419887 0.000000e+00 931.0
21 TraesCS7B01G190900 chr1D 87.000 700 76 14 3087 3781 431415608 431416297 0.000000e+00 774.0
22 TraesCS7B01G190900 chr7A 85.722 1765 201 41 1 1758 119520517 119522237 0.000000e+00 1816.0
23 TraesCS7B01G190900 chr7A 85.181 803 87 23 3016 3798 119523752 119524542 0.000000e+00 795.0
24 TraesCS7B01G190900 chr7A 87.117 163 21 0 2290 2452 119522623 119522785 1.230000e-42 185.0
25 TraesCS7B01G190900 chr7A 73.956 503 81 33 2542 3021 119522623 119523098 2.670000e-34 158.0
26 TraesCS7B01G190900 chr7D 82.802 2134 252 76 3800 5874 587281380 587283457 0.000000e+00 1801.0
27 TraesCS7B01G190900 chr7D 85.134 1749 202 46 1 1738 587278859 587280560 0.000000e+00 1736.0
28 TraesCS7B01G190900 chr7D 89.427 785 73 7 6372 7151 587284122 587284901 0.000000e+00 981.0
29 TraesCS7B01G190900 chr7D 85.571 700 76 15 3087 3781 587280633 587281312 0.000000e+00 710.0
30 TraesCS7B01G190900 chr5B 82.223 2132 262 84 3800 5875 170640612 170638542 0.000000e+00 1729.0
31 TraesCS7B01G190900 chr5B 83.400 1753 219 53 1 1738 170643142 170641447 0.000000e+00 1559.0
32 TraesCS7B01G190900 chr5B 84.765 978 130 13 6180 7151 170638033 170637069 0.000000e+00 963.0
33 TraesCS7B01G190900 chr5B 84.741 734 88 19 3084 3804 170641382 170640660 0.000000e+00 713.0
34 TraesCS7B01G190900 chr5B 83.721 86 10 4 2385 2469 657906513 657906595 2.140000e-10 78.7
35 TraesCS7B01G190900 chr5B 83.544 79 9 4 2138 2215 657906520 657906595 3.580000e-08 71.3
36 TraesCS7B01G190900 chr5B 83.562 73 8 4 2660 2731 657906526 657906595 1.670000e-06 65.8
37 TraesCS7B01G190900 chr6A 83.866 626 95 5 6530 7151 27217084 27217707 6.180000e-165 592.0
38 TraesCS7B01G190900 chr6A 81.405 242 35 8 3780 4013 27215016 27215255 9.470000e-44 189.0
39 TraesCS7B01G190900 chr1B 83.494 624 95 5 6530 7151 3169889 3169272 6.220000e-160 575.0


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 TraesCS7B01G190900 chr7B 328559894 328567044 7150 False 13206.00 13206 100.00000 1 7151 1 chr7B.!!$F1 7150
1 TraesCS7B01G190900 chr7B 328561892 328562672 780 False 502.00 697 89.22150 1999 2779 4 chr7B.!!$F2 780
2 TraesCS7B01G190900 chr2B 84537069 84544208 7139 True 2897.80 12447 91.28880 1 7151 5 chr2B.!!$R3 7150
3 TraesCS7B01G190900 chr2B 26198964 26199743 779 True 920.00 920 88.01000 6372 7151 1 chr2B.!!$R1 779
4 TraesCS7B01G190900 chr2B 733830153 733835469 5316 True 420.00 518 76.52300 1 7151 2 chr2B.!!$R4 7150
5 TraesCS7B01G190900 chr2B 637751445 637752719 1274 True 311.00 311 72.04800 1 1306 1 chr2B.!!$R2 1305
6 TraesCS7B01G190900 chr4D 422222475 422228528 6053 True 1413.25 1892 86.57950 1 7151 4 chr4D.!!$R1 7150
7 TraesCS7B01G190900 chr1D 431413832 431419887 6055 False 1314.75 1866 85.80675 1 7151 4 chr1D.!!$F1 7150
8 TraesCS7B01G190900 chr7A 119520517 119524542 4025 False 738.50 1816 82.99400 1 3798 4 chr7A.!!$F1 3797
9 TraesCS7B01G190900 chr7D 587278859 587284901 6042 False 1307.00 1801 85.73350 1 7151 4 chr7D.!!$F1 7150
10 TraesCS7B01G190900 chr5B 170637069 170643142 6073 True 1241.00 1729 83.78225 1 7151 4 chr5B.!!$R1 7150
11 TraesCS7B01G190900 chr6A 27215016 27217707 2691 False 390.50 592 82.63550 3780 7151 2 chr6A.!!$F1 3371
12 TraesCS7B01G190900 chr1B 3169272 3169889 617 True 575.00 575 83.49400 6530 7151 1 chr1B.!!$R1 621

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
660 673 3.381590 GGGGATTTTGTCAATCCAGTAGC 59.618 47.826 14.20 0.00 46.22 3.58 F
1016 1088 2.620115 CAACAATGCAGTGTCCACTTCT 59.380 45.455 21.44 0.00 40.20 2.85 F
1824 1923 3.134574 TGTATTCCGCCTTTTGTGAGT 57.865 42.857 0.00 0.00 0.00 3.41 F
2955 3067 4.409570 CGTCTACGCTGTAATTGTGTAGT 58.590 43.478 12.24 0.68 44.33 2.73 F
3944 4794 3.030291 TGTTCAAACAAGCTCACCCATT 58.970 40.909 0.00 0.00 35.67 3.16 F
4750 5673 4.300189 TGTGGTGTTTTTACTGTCATGC 57.700 40.909 0.00 0.00 0.00 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1621 1710 5.049267 GCAACTTCACCATTTCAATGCAAAT 60.049 36.000 0.00 0.0 35.08 2.32 R
2838 2950 3.005367 CCCACCAAAAATACAGTCCACAC 59.995 47.826 0.00 0.0 0.00 3.82 R
3477 4274 2.832129 GACCACCAGATGAACCACTAGA 59.168 50.000 0.00 0.0 0.00 2.43 R
4750 5673 0.321122 GGAGTCCAGTGCTTCAGGTG 60.321 60.000 3.60 0.0 0.00 4.00 R
5337 6330 1.538047 AGAACGTCCAACTACCGCTA 58.462 50.000 0.00 0.0 0.00 4.26 R
6283 7933 6.170506 AGGAGTGTTGCTACATAATTTCGAA 58.829 36.000 3.85 0.0 36.50 3.71 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
46 47 5.905480 ATGCCAAACTTTTCGAAATGAAC 57.095 34.783 25.41 11.30 35.97 3.18
62 63 6.582295 CGAAATGAACGTCCAGAAATCATTTT 59.418 34.615 18.20 7.15 45.61 1.82
633 646 7.441017 TCTAATTTTGCTGCTGGTGTTATTTT 58.559 30.769 0.00 0.00 0.00 1.82
660 673 3.381590 GGGGATTTTGTCAATCCAGTAGC 59.618 47.826 14.20 0.00 46.22 3.58
798 834 6.371809 TTGTTTTGATAGAGTGTGGTGAAC 57.628 37.500 0.00 0.00 0.00 3.18
1016 1088 2.620115 CAACAATGCAGTGTCCACTTCT 59.380 45.455 21.44 0.00 40.20 2.85
1819 1918 7.169982 TGTGTTTAATTTGTATTCCGCCTTTTG 59.830 33.333 0.00 0.00 0.00 2.44
1824 1923 3.134574 TGTATTCCGCCTTTTGTGAGT 57.865 42.857 0.00 0.00 0.00 3.41
1861 1960 6.813152 TGATGACTCTGTAATGTATGTGTGTG 59.187 38.462 0.00 0.00 0.00 3.82
1862 1961 6.096673 TGACTCTGTAATGTATGTGTGTGT 57.903 37.500 0.00 0.00 0.00 3.72
1990 2089 6.585416 AGTGCAAAATCTCCAGAATTTTTGT 58.415 32.000 13.29 0.00 36.83 2.83
2955 3067 4.409570 CGTCTACGCTGTAATTGTGTAGT 58.590 43.478 12.24 0.68 44.33 2.73
3248 4036 6.803154 AGTCGTTTCCCTAAGAATCAAAAG 57.197 37.500 0.00 0.00 33.44 2.27
3944 4794 3.030291 TGTTCAAACAAGCTCACCCATT 58.970 40.909 0.00 0.00 35.67 3.16
3962 4812 8.739039 TCACCCATTAGTATCAAAGAAACATTG 58.261 33.333 0.00 0.00 0.00 2.82
4067 4928 9.726438 TGGTTTTATCTTCCTTTTTGTTTTTCA 57.274 25.926 0.00 0.00 0.00 2.69
4195 5061 6.698380 TGTGGAGAAGTAATCTGGTTAGTTC 58.302 40.000 16.86 16.86 46.33 3.01
4750 5673 4.300189 TGTGGTGTTTTTACTGTCATGC 57.700 40.909 0.00 0.00 0.00 4.06
4832 5755 7.014134 TGTTGACAACATAACAATCAGATTGGT 59.986 33.333 24.22 21.25 39.42 3.67
4848 5771 8.918202 TCAGATTGGTAAATGAGTTGTACTTT 57.082 30.769 0.00 0.00 0.00 2.66
5207 6199 9.868277 TTTTCAATGTTGTGATTTAGTGACTTT 57.132 25.926 0.00 0.00 0.00 2.66
5661 6991 4.730966 TGCAGTGTAATTTTGGTCCCTTA 58.269 39.130 0.00 0.00 0.00 2.69
6157 7759 2.159338 TCTCGTCGATTTTAACTCCCGG 60.159 50.000 0.00 0.00 0.00 5.73
6283 7933 3.531262 GCGTAATTCGGTCAAAACAGT 57.469 42.857 0.00 0.00 40.26 3.55
7122 8895 4.448537 GCCACATGCACCAATTTACTTA 57.551 40.909 0.00 0.00 40.77 2.24
7131 8904 7.197071 TGCACCAATTTACTTACTAACACAG 57.803 36.000 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 4.161333 GAGCACAAAATGATTTCTGGACG 58.839 43.478 0.00 0.00 0.00 4.79
62 63 2.489971 CTCTAACCCAAAACGAGCACA 58.510 47.619 0.00 0.00 0.00 4.57
460 471 9.959749 GGATAAAGAAACAAACACTAAACATGA 57.040 29.630 0.00 0.00 0.00 3.07
633 646 3.245911 TGGATTGACAAAATCCCCATCCA 60.246 43.478 13.22 2.72 44.32 3.41
660 673 5.664294 AGCTGGAGATGAGCTAGATAATG 57.336 43.478 0.00 0.00 45.17 1.90
798 834 2.483877 TGCACCTTCAACATTAGCTTCG 59.516 45.455 0.00 0.00 0.00 3.79
954 1024 8.624776 ACAAAATGAAAACAAACAGGAAAACAA 58.375 25.926 0.00 0.00 0.00 2.83
1016 1088 2.360844 TCAACGAAGAACCAACAGCAA 58.639 42.857 0.00 0.00 0.00 3.91
1300 1386 0.938168 GCGTCAAACGAGTCGGAACT 60.938 55.000 18.30 0.00 46.05 3.01
1618 1707 7.230849 ACTTCACCATTTCAATGCAAATCTA 57.769 32.000 0.00 0.00 35.08 1.98
1621 1710 5.049267 GCAACTTCACCATTTCAATGCAAAT 60.049 36.000 0.00 0.00 35.08 2.32
1861 1960 7.376615 AGTCAAACATACTTACAGTGGACTAC 58.623 38.462 0.00 0.00 32.45 2.73
1862 1961 7.534723 AGTCAAACATACTTACAGTGGACTA 57.465 36.000 0.00 0.00 32.45 2.59
2838 2950 3.005367 CCCACCAAAAATACAGTCCACAC 59.995 47.826 0.00 0.00 0.00 3.82
2955 3067 7.604927 AGCTCATAAAAATTACGGTGTAGAACA 59.395 33.333 0.00 0.00 0.00 3.18
3248 4036 8.593492 AAAGCAAAAGAGAAAATGACATTACC 57.407 30.769 0.00 0.00 0.00 2.85
3477 4274 2.832129 GACCACCAGATGAACCACTAGA 59.168 50.000 0.00 0.00 0.00 2.43
3944 4794 9.507329 AGAAGAAGCAATGTTTCTTTGATACTA 57.493 29.630 22.48 0.00 43.07 1.82
3962 4812 4.875561 ACCCCGATATAAGAGAAGAAGC 57.124 45.455 0.00 0.00 0.00 3.86
4750 5673 0.321122 GGAGTCCAGTGCTTCAGGTG 60.321 60.000 3.60 0.00 0.00 4.00
4820 5743 8.950210 AGTACAACTCATTTACCAATCTGATTG 58.050 33.333 20.79 20.79 39.94 2.67
4848 5771 3.319689 TGTCGACACTGTTGAATCCACTA 59.680 43.478 15.76 0.00 0.00 2.74
4984 5949 3.182152 ACACCTAAGCCTTGACCTGTAT 58.818 45.455 0.00 0.00 0.00 2.29
5101 6090 6.117911 TGTCGCATTTAATCACACTATTGG 57.882 37.500 0.00 0.00 0.00 3.16
5337 6330 1.538047 AGAACGTCCAACTACCGCTA 58.462 50.000 0.00 0.00 0.00 4.26
5871 7230 7.612633 ACATAAAACCCAAGTATTTACACCGAT 59.387 33.333 0.00 0.00 0.00 4.18
6157 7759 6.313905 TGACAAAGACTGAAGAGAACAAAGAC 59.686 38.462 0.00 0.00 0.00 3.01
6283 7933 6.170506 AGGAGTGTTGCTACATAATTTCGAA 58.829 36.000 3.85 0.00 36.50 3.71
6370 8020 9.369904 CCTACCTATTTTTGAATTCATTGTTGG 57.630 33.333 9.40 10.03 0.00 3.77
7118 8891 7.286316 ACACTAAGGTACACTGTGTTAGTAAGT 59.714 37.037 19.73 13.91 38.51 2.24
7122 8895 5.221382 CCACACTAAGGTACACTGTGTTAGT 60.221 44.000 19.73 16.45 39.46 2.24


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

AutoCloner maintained by Alex Coulton.