Multiple sequence alignment - TraesCS5D01G112700

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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 TraesCS5D01G112700 chr5D 100.000 2810 0 0 1 2810 128643818 128641009 0.000000e+00 5190.0
1 TraesCS5D01G112700 chr5B 98.398 1810 26 2 1 1808 141149335 141147527 0.000000e+00 3179.0
2 TraesCS5D01G112700 chr5B 95.620 274 5 2 2288 2554 141147152 141146879 1.550000e-117 433.0
3 TraesCS5D01G112700 chr5B 98.718 234 2 1 1810 2042 141147558 141147325 5.600000e-112 414.0
4 TraesCS5D01G112700 chr5B 92.576 229 16 1 2583 2810 141146878 141146650 7.510000e-86 327.0
5 TraesCS5D01G112700 chr5B 99.429 175 1 0 2081 2255 141147325 141147151 4.520000e-83 318.0
6 TraesCS5D01G112700 chr5B 90.123 81 7 1 2000 2079 65592606 65592686 1.380000e-18 104.0
7 TraesCS5D01G112700 chr5A 98.011 1810 32 2 1 1808 143660104 143658297 0.000000e+00 3140.0
8 TraesCS5D01G112700 chr5A 91.945 869 18 9 1809 2627 143658329 143657463 0.000000e+00 1170.0
9 TraesCS5D01G112700 chr5A 90.000 70 5 2 2729 2796 567208338 567208407 3.860000e-14 89.8
10 TraesCS5D01G112700 chr3B 76.873 1388 284 32 399 1762 72715464 72716838 0.000000e+00 750.0
11 TraesCS5D01G112700 chr3B 80.858 606 105 8 1161 1762 72923375 72923973 1.520000e-127 466.0
12 TraesCS5D01G112700 chr3D 75.577 1474 319 36 315 1762 46485703 46487161 0.000000e+00 689.0
13 TraesCS5D01G112700 chr3D 74.909 1375 302 31 390 1731 560024577 560023213 3.120000e-164 588.0
14 TraesCS5D01G112700 chr3D 91.139 79 6 1 1989 2066 13182038 13182116 3.830000e-19 106.0
15 TraesCS5D01G112700 chr6D 73.472 1391 315 42 402 1767 411470789 411469428 2.530000e-130 475.0
16 TraesCS5D01G112700 chr6D 92.308 39 3 0 2548 2586 471329407 471329369 3.910000e-04 56.5
17 TraesCS5D01G112700 chr6A 73.517 1382 313 42 402 1758 556038300 556036947 2.530000e-130 475.0
18 TraesCS5D01G112700 chr6A 87.234 94 11 1 1990 2082 529566730 529566823 3.830000e-19 106.0
19 TraesCS5D01G112700 chr3A 80.066 607 111 8 1161 1762 57905489 57906090 2.570000e-120 442.0
20 TraesCS5D01G112700 chr6B 72.411 1381 327 42 402 1758 618670090 618668740 9.440000e-105 390.0
21 TraesCS5D01G112700 chr6B 88.421 95 10 1 1990 2083 284652753 284652659 2.290000e-21 113.0
22 TraesCS5D01G112700 chr2A 90.426 94 8 1 1990 2082 364478313 364478406 3.800000e-24 122.0
23 TraesCS5D01G112700 chr2A 95.000 40 0 2 2548 2586 19695529 19695567 8.400000e-06 62.1
24 TraesCS5D01G112700 chr4B 90.110 91 7 2 1990 2079 552857558 552857647 1.770000e-22 117.0
25 TraesCS5D01G112700 chr7D 87.500 96 11 1 1988 2082 262364692 262364787 2.960000e-20 110.0
26 TraesCS5D01G112700 chr7A 84.211 76 10 2 2723 2796 324948651 324948726 3.880000e-09 73.1
27 TraesCS5D01G112700 chr2B 94.872 39 0 1 2539 2577 724741900 724741936 3.020000e-05 60.2
28 TraesCS5D01G112700 chrUn 92.308 39 3 0 2548 2586 85478500 85478462 3.910000e-04 56.5
29 TraesCS5D01G112700 chrUn 92.308 39 3 0 2548 2586 236205803 236205765 3.910000e-04 56.5
30 TraesCS5D01G112700 chrUn 84.211 57 6 2 2531 2586 272975751 272975697 5.000000e-03 52.8
31 TraesCS5D01G112700 chrUn 84.211 57 6 2 2531 2586 292016212 292016158 5.000000e-03 52.8
32 TraesCS5D01G112700 chr1D 92.308 39 3 0 2548 2586 486090779 486090741 3.910000e-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 TraesCS5D01G112700 chr5D 128641009 128643818 2809 True 5190.0 5190 100.0000 1 2810 1 chr5D.!!$R1 2809
1 TraesCS5D01G112700 chr5B 141146650 141149335 2685 True 934.2 3179 96.9482 1 2810 5 chr5B.!!$R1 2809
2 TraesCS5D01G112700 chr5A 143657463 143660104 2641 True 2155.0 3140 94.9780 1 2627 2 chr5A.!!$R1 2626
3 TraesCS5D01G112700 chr3B 72715464 72716838 1374 False 750.0 750 76.8730 399 1762 1 chr3B.!!$F1 1363
4 TraesCS5D01G112700 chr3B 72923375 72923973 598 False 466.0 466 80.8580 1161 1762 1 chr3B.!!$F2 601
5 TraesCS5D01G112700 chr3D 46485703 46487161 1458 False 689.0 689 75.5770 315 1762 1 chr3D.!!$F2 1447
6 TraesCS5D01G112700 chr3D 560023213 560024577 1364 True 588.0 588 74.9090 390 1731 1 chr3D.!!$R1 1341
7 TraesCS5D01G112700 chr6D 411469428 411470789 1361 True 475.0 475 73.4720 402 1767 1 chr6D.!!$R1 1365
8 TraesCS5D01G112700 chr6A 556036947 556038300 1353 True 475.0 475 73.5170 402 1758 1 chr6A.!!$R1 1356
9 TraesCS5D01G112700 chr3A 57905489 57906090 601 False 442.0 442 80.0660 1161 1762 1 chr3A.!!$F1 601
10 TraesCS5D01G112700 chr6B 618668740 618670090 1350 True 390.0 390 72.4110 402 1758 1 chr6B.!!$R2 1356

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
653 656 0.324552 CCAGTGGCCATGGGAATCAA 60.325 55.0 18.3 0.0 33.94 2.57 F
1794 1823 0.036577 GATCAGCTCAGTGCCACACT 60.037 55.0 0.0 0.0 46.51 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1808 1837 0.036577 AGTGTGGCACTGAGCTGATC 60.037 55.000 19.83 0.0 43.63 2.92 R
2745 2826 3.558418 TGACGGATTAATAAAGGCTTCGC 59.442 43.478 0.00 0.0 0.00 4.70 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
285 286 9.489084 GTTGGTATACATATGCTTCTTGATGTA 57.511 33.333 1.58 0.00 38.70 2.29
369 371 6.169094 GCAGTATGATGTATACCTGCTGAAT 58.831 40.000 17.28 0.00 42.18 2.57
468 471 2.787994 AGGTTGCCAAGAGAAGTGATG 58.212 47.619 0.00 0.00 0.00 3.07
653 656 0.324552 CCAGTGGCCATGGGAATCAA 60.325 55.000 18.30 0.00 33.94 2.57
1254 1268 4.274459 GGCCTAAATGACAGTGACATGATC 59.726 45.833 8.86 0.00 0.00 2.92
1540 1569 1.361204 TGCAGACAAGGGGATGAAGA 58.639 50.000 0.00 0.00 0.00 2.87
1794 1823 0.036577 GATCAGCTCAGTGCCACACT 60.037 55.000 0.00 0.00 46.51 3.55
1795 1824 0.399454 ATCAGCTCAGTGCCACACTT 59.601 50.000 0.00 0.00 42.59 3.16
1796 1825 0.250038 TCAGCTCAGTGCCACACTTC 60.250 55.000 0.00 0.00 42.59 3.01
1797 1826 1.072159 AGCTCAGTGCCACACTTCC 59.928 57.895 0.00 0.00 42.59 3.46
1798 1827 1.227943 GCTCAGTGCCACACTTCCA 60.228 57.895 0.00 0.00 42.59 3.53
1799 1828 0.819259 GCTCAGTGCCACACTTCCAA 60.819 55.000 0.00 0.00 42.59 3.53
1800 1829 1.679139 CTCAGTGCCACACTTCCAAA 58.321 50.000 0.00 0.00 42.59 3.28
1801 1830 2.023673 CTCAGTGCCACACTTCCAAAA 58.976 47.619 0.00 0.00 42.59 2.44
1802 1831 2.426738 CTCAGTGCCACACTTCCAAAAA 59.573 45.455 0.00 0.00 42.59 1.94
1821 1850 4.698583 AAAAAGATGATCAGCTCAGTGC 57.301 40.909 14.98 0.00 37.28 4.40
1822 1851 2.328819 AAGATGATCAGCTCAGTGCC 57.671 50.000 14.98 0.00 44.23 5.01
1823 1852 1.201424 AGATGATCAGCTCAGTGCCA 58.799 50.000 7.89 0.00 44.23 4.92
1824 1853 1.134461 AGATGATCAGCTCAGTGCCAC 60.134 52.381 7.89 0.00 44.23 5.01
1825 1854 0.616891 ATGATCAGCTCAGTGCCACA 59.383 50.000 0.09 0.00 44.23 4.17
1826 1855 0.321034 TGATCAGCTCAGTGCCACAC 60.321 55.000 0.00 0.00 44.23 3.82
2386 2435 6.342111 TGTTTTGTTTAAGTTAGCAAAGGGG 58.658 36.000 11.75 0.00 33.25 4.79
2642 2722 2.140839 AAACGGGACTATCGAGGAGT 57.859 50.000 2.53 2.53 0.00 3.85
2691 2771 6.127730 TGAGGTTGACTTTTCCTTTGACTTTC 60.128 38.462 0.00 0.00 0.00 2.62
2692 2772 5.127194 AGGTTGACTTTTCCTTTGACTTTCC 59.873 40.000 0.00 0.00 0.00 3.13
2698 2778 2.543777 TCCTTTGACTTTCCGGTGAG 57.456 50.000 0.00 3.03 0.00 3.51
2716 2796 4.299978 GTGAGCATCTATCGAGGTTTACC 58.700 47.826 0.00 0.00 34.92 2.85
2783 2864 1.275291 CGTCACCACAGTTACAGGGAT 59.725 52.381 0.00 0.00 0.00 3.85
2792 2873 5.182001 CCACAGTTACAGGGATGAAAGAAAG 59.818 44.000 0.00 0.00 0.00 2.62
2797 2878 9.401058 CAGTTACAGGGATGAAAGAAAGATTAT 57.599 33.333 0.00 0.00 0.00 1.28
2798 2879 9.981460 AGTTACAGGGATGAAAGAAAGATTATT 57.019 29.630 0.00 0.00 0.00 1.40
2800 2881 7.651027 ACAGGGATGAAAGAAAGATTATTGG 57.349 36.000 0.00 0.00 0.00 3.16
2801 2882 6.608808 ACAGGGATGAAAGAAAGATTATTGGG 59.391 38.462 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
233 234 2.616842 GTGAACCTTTCCGTGTTGACAT 59.383 45.455 0.00 0.00 30.35 3.06
285 286 8.605325 AGATTATTAGGTTACAGTACCACAGT 57.395 34.615 0.00 0.00 40.82 3.55
369 371 5.414454 GCTGTGTTGATGGGTAATCTTAACA 59.586 40.000 0.00 0.00 36.15 2.41
423 425 2.827921 TGACAATCTCTGCTAGCAGTGA 59.172 45.455 37.70 37.70 46.20 3.41
468 471 4.201970 TGACACAAGGGAAAACGAATTCAC 60.202 41.667 6.22 0.00 32.72 3.18
1254 1268 1.020861 TGCAGCACTTGGATAGCGTG 61.021 55.000 0.00 0.00 0.00 5.34
1540 1569 1.890552 AATGGAGCAGATGAGAGGGT 58.109 50.000 0.00 0.00 0.00 4.34
1800 1829 3.442977 GGCACTGAGCTGATCATCTTTTT 59.557 43.478 0.00 0.00 44.79 1.94
1801 1830 3.015327 GGCACTGAGCTGATCATCTTTT 58.985 45.455 0.00 0.00 44.79 2.27
1802 1831 2.026542 TGGCACTGAGCTGATCATCTTT 60.027 45.455 0.00 0.00 44.79 2.52
1803 1832 1.558294 TGGCACTGAGCTGATCATCTT 59.442 47.619 0.00 0.00 44.79 2.40
1804 1833 1.134461 GTGGCACTGAGCTGATCATCT 60.134 52.381 11.13 0.00 44.79 2.90
1805 1834 1.297664 GTGGCACTGAGCTGATCATC 58.702 55.000 11.13 0.00 44.79 2.92
1806 1835 0.616891 TGTGGCACTGAGCTGATCAT 59.383 50.000 19.83 0.00 44.79 2.45
1807 1836 0.321034 GTGTGGCACTGAGCTGATCA 60.321 55.000 19.83 0.00 44.79 2.92
1808 1837 0.036577 AGTGTGGCACTGAGCTGATC 60.037 55.000 19.83 0.00 43.63 2.92
1809 1838 0.399454 AAGTGTGGCACTGAGCTGAT 59.601 50.000 19.83 0.00 44.62 2.90
1810 1839 0.250038 GAAGTGTGGCACTGAGCTGA 60.250 55.000 19.83 0.00 44.62 4.26
1811 1840 1.233285 GGAAGTGTGGCACTGAGCTG 61.233 60.000 19.83 0.00 44.62 4.24
1812 1841 1.072159 GGAAGTGTGGCACTGAGCT 59.928 57.895 19.83 8.76 44.62 4.09
1813 1842 0.819259 TTGGAAGTGTGGCACTGAGC 60.819 55.000 19.83 6.58 44.62 4.26
1814 1843 1.679139 TTTGGAAGTGTGGCACTGAG 58.321 50.000 19.83 0.00 44.62 3.35
1815 1844 2.136298 TTTTGGAAGTGTGGCACTGA 57.864 45.000 19.83 0.00 44.62 3.41
1816 1845 2.957491 TTTTTGGAAGTGTGGCACTG 57.043 45.000 19.83 0.00 44.62 3.66
1977 2007 1.104630 AGGGAGTAGCAACGTAGAGC 58.895 55.000 0.00 0.00 0.00 4.09
2061 2092 4.897051 AGTACTCCCTCTGTCCCATAATT 58.103 43.478 0.00 0.00 0.00 1.40
2259 2290 4.858692 CAGCCATATTCAAAACTGTTTCCG 59.141 41.667 6.20 1.53 0.00 4.30
2386 2435 1.911057 AAACCAGCTAGGCCTTCAAC 58.089 50.000 12.58 0.00 43.14 3.18
2651 2731 4.019411 TCAACCTCAATAGATGCTCAACCA 60.019 41.667 0.00 0.00 0.00 3.67
2745 2826 3.558418 TGACGGATTAATAAAGGCTTCGC 59.442 43.478 0.00 0.00 0.00 4.70
2746 2827 4.025145 GGTGACGGATTAATAAAGGCTTCG 60.025 45.833 0.00 0.00 0.00 3.79
2783 2864 4.466015 GCCACCCCAATAATCTTTCTTTCA 59.534 41.667 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.