Multiple sequence alignment - TraesCS7B01G333800

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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 TraesCS7B01G333800 chr7B 100.000 2216 0 0 1 2216 588878217 588880432 0.000000e+00 4093.0
1 TraesCS7B01G333800 chr7B 99.248 133 1 0 279 411 589919621 589919489 7.910000e-60 241.0
2 TraesCS7B01G333800 chr7B 91.781 146 8 2 59 203 589919896 589919754 1.340000e-47 200.0
3 TraesCS7B01G333800 chr7B 87.821 156 8 2 68 223 498300093 498300237 2.930000e-39 172.0
4 TraesCS7B01G333800 chr7B 100.000 39 0 0 64 102 589735178 589735140 3.050000e-09 73.1
5 TraesCS7B01G333800 chr7B 100.000 28 0 0 384 411 589934849 589934822 4.000000e-03 52.8
6 TraesCS7B01G333800 chr1B 95.009 1062 45 3 279 1337 133124472 133125528 0.000000e+00 1661.0
7 TraesCS7B01G333800 chr1B 86.444 1468 143 46 774 2214 426497580 426499018 0.000000e+00 1557.0
8 TraesCS7B01G333800 chr1B 85.901 1454 151 43 786 2214 133111994 133113418 0.000000e+00 1500.0
9 TraesCS7B01G333800 chr1B 96.719 762 21 3 1458 2216 133125744 133126504 0.000000e+00 1266.0
10 TraesCS7B01G333800 chr1B 94.606 241 6 3 1 240 133124114 133124348 1.250000e-97 366.0
11 TraesCS7B01G333800 chr5D 92.851 1119 57 9 229 1335 289355583 289356690 0.000000e+00 1602.0
12 TraesCS7B01G333800 chr5D 90.053 1126 89 12 850 1962 289421540 289422655 0.000000e+00 1437.0
13 TraesCS7B01G333800 chr5D 90.167 956 79 11 933 1876 289727721 289728673 0.000000e+00 1230.0
14 TraesCS7B01G333800 chr5D 86.804 682 72 11 1051 1718 29905314 29904637 0.000000e+00 745.0
15 TraesCS7B01G333800 chr5D 88.272 162 10 2 59 219 289355340 289355493 3.760000e-43 185.0
16 TraesCS7B01G333800 chr5D 100.000 61 0 0 2156 2216 289498575 289498635 1.800000e-21 113.0
17 TraesCS7B01G333800 chr5D 94.286 35 2 0 59 93 289727204 289727238 1.000000e-03 54.7
18 TraesCS7B01G333800 chr7A 85.511 1477 162 44 761 2214 627045820 627047267 0.000000e+00 1495.0
19 TraesCS7B01G333800 chr7A 90.363 965 85 6 1004 1962 580505038 580506000 0.000000e+00 1260.0
20 TraesCS7B01G333800 chr7A 88.889 144 9 5 509 652 628386177 628386313 1.050000e-38 171.0
21 TraesCS7B01G333800 chr7A 96.970 99 2 1 324 422 627234131 627234228 4.900000e-37 165.0
22 TraesCS7B01G333800 chr7A 97.500 80 2 0 59 138 628385941 628386020 1.070000e-28 137.0
23 TraesCS7B01G333800 chr7A 80.000 100 11 6 382 476 580504607 580504702 5.110000e-07 65.8
24 TraesCS7B01G333800 chr7A 97.222 36 1 0 263 298 627234121 627234156 6.610000e-06 62.1
25 TraesCS7B01G333800 chr7A 97.143 35 1 0 59 93 627008738 627008772 2.380000e-05 60.2
26 TraesCS7B01G333800 chr7A 96.970 33 1 0 137 169 627232616 627232648 3.070000e-04 56.5
27 TraesCS7B01G333800 chr6A 89.972 1087 89 13 772 1851 107263818 107262745 0.000000e+00 1386.0
28 TraesCS7B01G333800 chr6A 80.838 167 15 6 1 150 107264421 107264255 5.000000e-22 115.0
29 TraesCS7B01G333800 chr6A 100.000 32 0 0 390 421 107264106 107264075 2.380000e-05 60.2
30 TraesCS7B01G333800 chr2B 95.288 764 30 4 1458 2216 127791356 127792118 0.000000e+00 1206.0
31 TraesCS7B01G333800 chr2B 89.504 867 77 12 840 1700 182134307 182135165 0.000000e+00 1085.0
32 TraesCS7B01G333800 chr2B 91.720 157 6 4 324 478 135512476 135512325 6.200000e-51 211.0
33 TraesCS7B01G333800 chr2B 100.000 45 0 0 65 109 135512573 135512529 1.410000e-12 84.2
34 TraesCS7B01G333800 chr2B 93.750 48 3 0 142 189 135512526 135512479 3.050000e-09 73.1
35 TraesCS7B01G333800 chr7D 84.783 184 19 5 516 690 509579870 509580053 2.260000e-40 176.0
36 TraesCS7B01G333800 chr7D 85.185 81 9 2 398 476 509598957 509599036 1.820000e-11 80.5
37 TraesCS7B01G333800 chr7D 96.875 32 0 1 599 629 545254753 545254722 4.000000e-03 52.8


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 TraesCS7B01G333800 chr7B 588878217 588880432 2215 False 4093.000000 4093 100.000000 1 2216 1 chr7B.!!$F2 2215
1 TraesCS7B01G333800 chr1B 426497580 426499018 1438 False 1557.000000 1557 86.444000 774 2214 1 chr1B.!!$F2 1440
2 TraesCS7B01G333800 chr1B 133111994 133113418 1424 False 1500.000000 1500 85.901000 786 2214 1 chr1B.!!$F1 1428
3 TraesCS7B01G333800 chr1B 133124114 133126504 2390 False 1097.666667 1661 95.444667 1 2216 3 chr1B.!!$F3 2215
4 TraesCS7B01G333800 chr5D 289421540 289422655 1115 False 1437.000000 1437 90.053000 850 1962 1 chr5D.!!$F1 1112
5 TraesCS7B01G333800 chr5D 289355340 289356690 1350 False 893.500000 1602 90.561500 59 1335 2 chr5D.!!$F3 1276
6 TraesCS7B01G333800 chr5D 29904637 29905314 677 True 745.000000 745 86.804000 1051 1718 1 chr5D.!!$R1 667
7 TraesCS7B01G333800 chr5D 289727204 289728673 1469 False 642.350000 1230 92.226500 59 1876 2 chr5D.!!$F4 1817
8 TraesCS7B01G333800 chr7A 627045820 627047267 1447 False 1495.000000 1495 85.511000 761 2214 1 chr7A.!!$F2 1453
9 TraesCS7B01G333800 chr7A 580504607 580506000 1393 False 662.900000 1260 85.181500 382 1962 2 chr7A.!!$F3 1580
10 TraesCS7B01G333800 chr6A 107262745 107264421 1676 True 520.400000 1386 90.270000 1 1851 3 chr6A.!!$R1 1850
11 TraesCS7B01G333800 chr2B 127791356 127792118 762 False 1206.000000 1206 95.288000 1458 2216 1 chr2B.!!$F1 758
12 TraesCS7B01G333800 chr2B 182134307 182135165 858 False 1085.000000 1085 89.504000 840 1700 1 chr2B.!!$F2 860

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
139 157 0.526096 CGGATTCAAATTGCCTGCCG 60.526 55.0 0.0 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1311 1640 0.630673 AGGCCTGGCATATGTGGAAA 59.369 50.0 22.05 0.0 0.0 3.13 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
39 41 2.367030 CGGCAAGCAATTTGAATCCA 57.633 45.000 0.00 0.00 39.21 3.41
51 53 3.380479 TTGAATCCAAGTCGAAGTCGT 57.620 42.857 0.00 0.00 40.80 4.34
52 54 3.380479 TGAATCCAAGTCGAAGTCGTT 57.620 42.857 0.00 0.00 40.80 3.85
53 55 3.314553 TGAATCCAAGTCGAAGTCGTTC 58.685 45.455 0.00 0.00 40.80 3.95
139 157 0.526096 CGGATTCAAATTGCCTGCCG 60.526 55.000 0.00 0.00 0.00 5.69
214 233 3.557228 AGCCCAGAAGAGCAAGATTAG 57.443 47.619 0.00 0.00 0.00 1.73
223 242 6.762187 CAGAAGAGCAAGATTAGACATGATGT 59.238 38.462 0.00 0.00 0.00 3.06
253 405 6.778821 TCAATTCTTGGATTGTAACTCCTCA 58.221 36.000 2.02 0.00 38.04 3.86
308 460 3.500448 TGTAGCATTGGGTTCACTTGA 57.500 42.857 0.00 0.00 0.00 3.02
639 847 9.557338 GAAGTTTGATGATTTCTCATTTCTCAG 57.443 33.333 0.00 0.00 42.27 3.35
696 904 3.550842 GCAAACAGTTGTTCTCATGTCCC 60.551 47.826 0.00 0.00 37.25 4.46
794 1061 7.083858 AGAAACATGAAACATCATACGTTTGG 58.916 34.615 0.00 0.00 36.72 3.28
835 1110 4.081087 GGAAAATCAGTCTGGTAGCTGGTA 60.081 45.833 0.00 0.00 33.81 3.25
836 1111 4.473477 AAATCAGTCTGGTAGCTGGTAC 57.527 45.455 8.46 8.46 33.81 3.34
889 1172 6.430925 CCACAAAACTGGTCTTTGATATCTCA 59.569 38.462 3.98 0.00 37.25 3.27
931 1217 4.644685 GCAGTAAAAAGCCCATAATCCTCA 59.355 41.667 0.00 0.00 0.00 3.86
1305 1634 0.524862 CCACAAGCTCATGCAACCTC 59.475 55.000 0.00 0.00 42.74 3.85
1311 1640 0.035630 GCTCATGCAACCTCTGGTCT 60.036 55.000 0.00 0.00 39.41 3.85
1444 1778 8.939929 TGTGAACTATAAGAAATCTTGCTTCAG 58.060 33.333 5.93 0.00 37.40 3.02
1466 1985 8.298729 TCAGACATATATTCAGTTCACTCACT 57.701 34.615 0.00 0.00 0.00 3.41
1857 2398 2.826488 AGTCTCTATGGACAAGGCAGT 58.174 47.619 0.00 0.00 38.57 4.40
1982 2538 9.667989 GCAAAAGATAATCAAATTGCAACTTTT 57.332 25.926 0.00 7.03 41.93 2.27
2087 2652 7.565398 AGATCTCTGTAGCCTTCCATTTAACTA 59.435 37.037 0.00 0.00 0.00 2.24
2115 2682 9.661563 AGATGTTTTGAATTCATGCACATTTAT 57.338 25.926 20.36 11.99 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 41 2.879646 AGTCTCAGAACGACTTCGACTT 59.120 45.455 5.47 0.00 38.52 3.01
51 53 6.371548 CGGATTCAAAAACCATAGTCTCAGAA 59.628 38.462 0.00 0.00 0.00 3.02
52 54 5.874810 CGGATTCAAAAACCATAGTCTCAGA 59.125 40.000 0.00 0.00 0.00 3.27
53 55 5.874810 TCGGATTCAAAAACCATAGTCTCAG 59.125 40.000 0.00 0.00 0.00 3.35
231 383 7.020827 TCTGAGGAGTTACAATCCAAGAATT 57.979 36.000 0.00 0.00 39.47 2.17
253 405 2.295349 CTGCAGGTCATTTGTGCTTTCT 59.705 45.455 5.57 0.00 38.09 2.52
308 460 1.608590 CTTCTGATTTTGGCACACCGT 59.391 47.619 0.00 0.00 39.29 4.83
639 847 0.451783 CTTAGCCGGCACATTCAACC 59.548 55.000 31.54 0.00 0.00 3.77
696 904 8.142994 ACAGTTATTCGCATGTCCTTTTATAG 57.857 34.615 0.00 0.00 0.00 1.31
770 1006 7.081349 TCCAAACGTATGATGTTTCATGTTTC 58.919 34.615 0.00 0.00 42.60 2.78
794 1061 6.463995 TTTTCCATGGGCTACATTGTAATC 57.536 37.500 13.02 0.00 37.84 1.75
835 1110 1.846007 AACATGTGTGTGTGGTTGGT 58.154 45.000 0.00 0.00 38.92 3.67
836 1111 2.957491 AAACATGTGTGTGTGGTTGG 57.043 45.000 0.00 0.00 38.92 3.77
837 1112 6.019961 GTGAAATAAACATGTGTGTGTGGTTG 60.020 38.462 0.00 0.00 38.92 3.77
838 1113 6.039616 GTGAAATAAACATGTGTGTGTGGTT 58.960 36.000 0.00 0.00 38.92 3.67
903 1189 2.949177 TGGGCTTTTTACTGCTCAGA 57.051 45.000 3.60 0.00 34.40 3.27
910 1196 6.079712 AGTGAGGATTATGGGCTTTTTACT 57.920 37.500 0.00 0.00 0.00 2.24
1311 1640 0.630673 AGGCCTGGCATATGTGGAAA 59.369 50.000 22.05 0.00 0.00 3.13
1352 1681 1.403914 CGCTGCAGTTCTCTCATGTCT 60.404 52.381 16.64 0.00 0.00 3.41
1444 1778 9.243637 GAGAAGTGAGTGAACTGAATATATGTC 57.756 37.037 0.00 0.00 0.00 3.06
1451 1787 4.592485 ACGAGAAGTGAGTGAACTGAAT 57.408 40.909 0.00 0.00 0.00 2.57
1466 1985 4.038763 ACTGTTGGTGATCTTGTACGAGAA 59.961 41.667 16.82 0.00 0.00 2.87
1512 2037 7.390718 GGTGATTATTAGTGGCCGAAAGAATAT 59.609 37.037 0.00 0.00 0.00 1.28
1857 2398 2.509548 ACCTGCATAAAGGCTCCATGTA 59.490 45.455 9.30 4.99 41.46 2.29
1982 2538 3.331150 AGCAATTCGTCAACCGTTGATA 58.669 40.909 16.80 6.25 42.47 2.15
1989 2545 3.500680 TGGTTTAGAGCAATTCGTCAACC 59.499 43.478 0.00 0.00 35.88 3.77
2087 2652 9.661563 AAATGTGCATGAATTCAAAACATCTAT 57.338 25.926 23.36 15.11 31.36 1.98
2115 2682 5.514500 AGCACACCTCCTTTAATTCCTAA 57.486 39.130 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.