Multiple sequence alignment - TraesCS1B01G069400

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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 TraesCS1B01G069400 chr1B 100.000 2755 0 0 1 2755 54963003 54965757 0.000000e+00 5088.0
1 TraesCS1B01G069400 chr1B 99.129 2755 16 3 1 2755 55006288 55009034 0.000000e+00 4948.0
2 TraesCS1B01G069400 chr1D 82.425 1229 99 47 636 1846 35786232 35787361 0.000000e+00 965.0
3 TraesCS1B01G069400 chr1D 91.692 650 38 8 1197 1841 35870505 35871143 0.000000e+00 887.0
4 TraesCS1B01G069400 chr1D 84.551 602 64 18 1197 1789 35917218 35917799 1.110000e-158 569.0
5 TraesCS1B01G069400 chr1D 84.114 598 74 17 1197 1789 35815642 35816223 2.400000e-155 558.0
6 TraesCS1B01G069400 chr1D 82.406 665 70 20 514 1157 35869768 35870406 1.120000e-148 536.0
7 TraesCS1B01G069400 chr1D 84.375 448 34 17 739 1161 35907673 35908109 9.190000e-110 407.0
8 TraesCS1B01G069400 chr1D 82.965 452 41 19 739 1170 35815125 35815560 2.590000e-100 375.0
9 TraesCS1B01G069400 chr1D 81.818 363 45 13 54 411 35754451 35754797 4.490000e-73 285.0
10 TraesCS1B01G069400 chr1D 87.791 172 16 4 2447 2613 202281894 202282065 2.160000e-46 196.0
11 TraesCS1B01G069400 chr1D 87.719 171 14 5 2447 2613 206038449 206038616 2.800000e-45 193.0
12 TraesCS1B01G069400 chr1A 86.071 840 70 26 998 1824 34534325 34535130 0.000000e+00 859.0
13 TraesCS1B01G069400 chr1A 80.832 1106 122 57 744 1789 34877715 34878790 0.000000e+00 785.0
14 TraesCS1B01G069400 chr1A 85.610 688 45 26 1197 1842 34857522 34858197 0.000000e+00 673.0
15 TraesCS1B01G069400 chr1A 86.795 621 37 21 1197 1780 34705222 34705834 0.000000e+00 651.0
16 TraesCS1B01G069400 chr1A 89.683 252 21 1 906 1157 34704876 34705122 1.590000e-82 316.0
17 TraesCS1B01G069400 chr1A 79.957 469 51 15 514 964 34851183 34851626 3.450000e-79 305.0
18 TraesCS1B01G069400 chr1A 88.384 198 18 1 960 1157 34857224 34857416 1.650000e-57 233.0
19 TraesCS1B01G069400 chr1A 77.922 385 34 14 512 876 34533888 34534241 2.800000e-45 193.0
20 TraesCS1B01G069400 chr1A 87.931 116 13 1 54 168 34520513 34520628 4.790000e-28 135.0
21 TraesCS1B01G069400 chr1A 87.654 81 10 0 58 138 34721738 34721818 8.120000e-16 95.3
22 TraesCS1B01G069400 chr7B 93.316 374 23 2 1848 2219 651336219 651335846 4.010000e-153 551.0
23 TraesCS1B01G069400 chr2B 93.103 377 22 2 1846 2218 775740771 775741147 1.440000e-152 549.0
24 TraesCS1B01G069400 chr2B 86.928 153 18 2 2605 2755 152752164 152752316 1.310000e-38 171.0
25 TraesCS1B01G069400 chr4B 92.761 373 26 1 1846 2217 643664192 643664564 3.120000e-149 538.0
26 TraesCS1B01G069400 chr4A 94.134 358 11 5 818 1173 521612720 521613069 1.120000e-148 536.0
27 TraesCS1B01G069400 chr4A 93.855 358 12 4 818 1173 536859297 536859646 5.220000e-147 531.0
28 TraesCS1B01G069400 chr7D 91.755 376 29 2 1846 2219 564139819 564140194 3.140000e-144 521.0
29 TraesCS1B01G069400 chr7D 90.667 150 11 2 2466 2613 107248344 107248196 2.160000e-46 196.0
30 TraesCS1B01G069400 chr7D 89.116 147 14 2 2605 2749 111350310 111350456 6.060000e-42 182.0
31 TraesCS1B01G069400 chrUn 92.141 369 25 2 1849 2216 141696955 141697320 4.070000e-143 518.0
32 TraesCS1B01G069400 chr6D 91.076 381 32 2 1846 2224 431057951 431057571 5.260000e-142 514.0
33 TraesCS1B01G069400 chr6D 90.411 146 14 0 2610 2755 336516133 336515988 2.800000e-45 193.0
34 TraesCS1B01G069400 chr2D 91.375 371 30 2 1849 2217 618645081 618645451 8.800000e-140 507.0
35 TraesCS1B01G069400 chr3D 90.860 372 32 2 1849 2218 38147847 38147476 5.300000e-137 497.0
36 TraesCS1B01G069400 chr3D 92.667 150 9 1 2466 2613 407812393 407812542 5.980000e-52 215.0
37 TraesCS1B01G069400 chr3D 90.667 150 12 1 2466 2613 246596427 246596278 6.020000e-47 198.0
38 TraesCS1B01G069400 chr3D 90.667 150 12 1 2466 2613 278512431 278512580 6.020000e-47 198.0
39 TraesCS1B01G069400 chr3D 88.889 153 15 2 2605 2755 565256092 565256244 1.300000e-43 187.0
40 TraesCS1B01G069400 chr3D 89.796 147 14 1 2610 2755 602717057 602716911 1.300000e-43 187.0
41 TraesCS1B01G069400 chr3D 89.041 146 16 0 2610 2755 405828016 405827871 6.060000e-42 182.0
42 TraesCS1B01G069400 chr3A 91.333 150 10 2 2466 2613 464244133 464243985 4.650000e-48 202.0
43 TraesCS1B01G069400 chr3A 88.356 146 17 0 2610 2755 464243942 464243797 2.820000e-40 176.0
44 TraesCS1B01G069400 chr3A 91.667 48 4 0 408 455 27015580 27015627 1.770000e-07 67.6
45 TraesCS1B01G069400 chr5D 90.132 152 13 1 2464 2613 377147854 377148005 2.160000e-46 196.0
46 TraesCS1B01G069400 chr5A 88.435 147 16 1 2610 2755 32052870 32053016 2.820000e-40 176.0
47 TraesCS1B01G069400 chr5A 92.000 50 2 2 411 459 495899226 495899178 4.920000e-08 69.4
48 TraesCS1B01G069400 chr6B 88.462 52 4 1 408 459 374977777 374977826 8.240000e-06 62.1
49 TraesCS1B01G069400 chr6A 90.476 42 4 0 418 459 317147352 317147311 3.830000e-04 56.5


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 TraesCS1B01G069400 chr1B 54963003 54965757 2754 False 5088.0 5088 100.0000 1 2755 1 chr1B.!!$F1 2754
1 TraesCS1B01G069400 chr1B 55006288 55009034 2746 False 4948.0 4948 99.1290 1 2755 1 chr1B.!!$F2 2754
2 TraesCS1B01G069400 chr1D 35786232 35787361 1129 False 965.0 965 82.4250 636 1846 1 chr1D.!!$F2 1210
3 TraesCS1B01G069400 chr1D 35869768 35871143 1375 False 711.5 887 87.0490 514 1841 2 chr1D.!!$F8 1327
4 TraesCS1B01G069400 chr1D 35917218 35917799 581 False 569.0 569 84.5510 1197 1789 1 chr1D.!!$F4 592
5 TraesCS1B01G069400 chr1D 35815125 35816223 1098 False 466.5 558 83.5395 739 1789 2 chr1D.!!$F7 1050
6 TraesCS1B01G069400 chr1A 34877715 34878790 1075 False 785.0 785 80.8320 744 1789 1 chr1A.!!$F4 1045
7 TraesCS1B01G069400 chr1A 34533888 34535130 1242 False 526.0 859 81.9965 512 1824 2 chr1A.!!$F5 1312
8 TraesCS1B01G069400 chr1A 34704876 34705834 958 False 483.5 651 88.2390 906 1780 2 chr1A.!!$F6 874
9 TraesCS1B01G069400 chr1A 34857224 34858197 973 False 453.0 673 86.9970 960 1842 2 chr1A.!!$F7 882

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
422 423 4.033358 CCACATGCGTCTAAGACTTGAATC 59.967 45.833 0.0 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 2288 2.522185 ACAGGAACTAGGTTGCTACGA 58.478 47.619 4.28 0.0 42.02 3.43 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
47 48 4.098349 CAGTGCAACACAGGGCAATTATAT 59.902 41.667 0.0 0.0 42.45 0.86
422 423 4.033358 CCACATGCGTCTAAGACTTGAATC 59.967 45.833 0.0 0.0 0.00 2.52
482 483 9.113876 CATTTGAGTTCGTGTTAATAAACCTTC 57.886 33.333 0.0 0.0 34.49 3.46
1803 2056 4.143094 GCGACTTCAGTTCATCCTTTGTAC 60.143 45.833 0.0 0.0 0.00 2.90
1804 2057 5.230942 CGACTTCAGTTCATCCTTTGTACT 58.769 41.667 0.0 0.0 36.49 2.73
1805 2058 6.387465 CGACTTCAGTTCATCCTTTGTACTA 58.613 40.000 0.0 0.0 34.08 1.82
1933 2188 5.105716 CCATCGATAAATCCTCATACCGAGT 60.106 44.000 0.0 0.0 40.48 4.18
2031 2286 3.615937 CCATGAGAGTTGATTCTGACGTG 59.384 47.826 0.0 0.0 0.00 4.49
2032 2287 4.240888 CATGAGAGTTGATTCTGACGTGT 58.759 43.478 0.0 0.0 0.00 4.49
2033 2288 4.322080 TGAGAGTTGATTCTGACGTGTT 57.678 40.909 0.0 0.0 0.00 3.32
2034 2289 4.299155 TGAGAGTTGATTCTGACGTGTTC 58.701 43.478 0.0 0.0 0.00 3.18
2035 2290 3.309388 AGAGTTGATTCTGACGTGTTCG 58.691 45.455 0.0 0.0 43.34 3.95
2199 2454 4.023291 TCCTGGGTAAAATTGCCTCATTC 58.977 43.478 0.0 0.0 33.03 2.67
2508 2763 1.817099 CCGGCCTCTGCATCTGAAC 60.817 63.158 0.0 0.0 40.13 3.18
2669 2924 2.024414 GACCCCAATCAAGCCACATAC 58.976 52.381 0.0 0.0 0.00 2.39
2719 2974 1.002430 ACTCTCATGTGTCGTTGCCAT 59.998 47.619 0.0 0.0 0.00 4.40
2734 2989 2.564771 TGCCATCATCTTCCACGAATC 58.435 47.619 0.0 0.0 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.204146 GCTACCTCATGGTCCCTTCA 58.796 55.000 0.00 0.0 44.78 3.02
422 423 3.165606 GTGGAACCAGCTCATCAGG 57.834 57.895 0.00 0.0 0.00 3.86
482 483 6.757010 GGCATGGTACCGATATATTTAGTGAG 59.243 42.308 7.57 0.0 0.00 3.51
866 905 1.141881 CGCCAACATAGAGACGGCT 59.858 57.895 0.00 0.0 40.72 5.52
2031 2286 3.251571 CAGGAACTAGGTTGCTACGAAC 58.748 50.000 4.28 0.0 42.02 3.95
2032 2287 2.895404 ACAGGAACTAGGTTGCTACGAA 59.105 45.455 4.28 0.0 42.02 3.85
2033 2288 2.522185 ACAGGAACTAGGTTGCTACGA 58.478 47.619 4.28 0.0 42.02 3.43
2034 2289 3.314541 AACAGGAACTAGGTTGCTACG 57.685 47.619 4.28 0.0 42.02 3.51
2035 2290 5.049612 GTCAAAACAGGAACTAGGTTGCTAC 60.050 44.000 4.28 0.0 42.02 3.58
2036 2291 5.061179 GTCAAAACAGGAACTAGGTTGCTA 58.939 41.667 4.28 0.0 42.02 3.49
2472 2727 1.864669 GGGGGCAATCCTCATTTTCA 58.135 50.000 0.00 0.0 35.56 2.69
2508 2763 6.825284 TTAATAAAATGGTTGCATGCATCG 57.175 33.333 23.37 0.0 0.00 3.84
2669 2924 1.636519 TGGTATGTACCCCAAACCCAG 59.363 52.381 6.74 0.0 45.87 4.45


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

AutoCloner maintained by Alex Coulton.