Multiple sequence alignment - TraesCS7D01G275300

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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 TraesCS7D01G275300 chr7D 100.000 2708 0 0 1 2708 264360362 264363069 0.000000e+00 5001
1 TraesCS7D01G275300 chr7D 96.882 1892 47 4 1 1887 264370233 264372117 0.000000e+00 3157
2 TraesCS7D01G275300 chr7D 92.504 1841 113 22 376 2206 264325902 264327727 0.000000e+00 2612
3 TraesCS7D01G275300 chr7D 95.958 1608 59 4 437 2044 264338738 264340339 0.000000e+00 2604
4 TraesCS7D01G275300 chr7D 91.304 414 28 2 1 409 264338330 264338740 2.350000e-155 558
5 TraesCS7D01G275300 chr7D 88.571 455 42 5 2084 2528 264340338 264340792 6.590000e-151 544
6 TraesCS7D01G275300 chr7D 83.025 324 19 16 47 370 264325488 264325775 7.440000e-66 261
7 TraesCS7D01G275300 chr7B 95.064 2269 81 14 322 2584 244644891 244647134 0.000000e+00 3541
8 TraesCS7D01G275300 chr7B 95.789 1995 61 6 1 1990 244692367 244694343 0.000000e+00 3197
9 TraesCS7D01G275300 chr7B 96.595 1762 50 4 131 1887 244715971 244717727 0.000000e+00 2913
10 TraesCS7D01G275300 chr7B 95.582 1358 59 1 687 2044 244651643 244652999 0.000000e+00 2174
11 TraesCS7D01G275300 chr7B 96.898 677 12 3 2041 2708 244694344 244695020 0.000000e+00 1125
12 TraesCS7D01G275300 chr7B 88.132 455 43 6 2084 2528 244652998 244653451 5.130000e-147 531
13 TraesCS7D01G275300 chr7B 92.145 331 17 3 1 323 244644276 244644605 2.460000e-125 459
14 TraesCS7D01G275300 chr7B 82.633 547 56 13 1 542 244651051 244651563 5.320000e-122 448
15 TraesCS7D01G275300 chr7B 92.308 104 8 0 1 104 244715877 244715980 6.040000e-32 148
16 TraesCS7D01G275300 chr7A 91.692 1661 113 22 404 2044 287889479 287891134 0.000000e+00 2279
17 TraesCS7D01G275300 chr7A 93.733 1085 64 4 1192 2274 287862649 287863731 0.000000e+00 1624
18 TraesCS7D01G275300 chr7A 87.692 455 45 6 2084 2528 287891133 287891586 1.110000e-143 520
19 TraesCS7D01G275300 chr7A 81.792 346 18 4 1 346 287889173 287889473 5.790000e-62 248
20 TraesCS7D01G275300 chr7A 94.839 155 7 1 2551 2704 287895920 287896074 9.690000e-60 241
21 TraesCS7D01G275300 chr7A 95.536 112 3 2 47 158 287862273 287862382 7.700000e-41 178


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 TraesCS7D01G275300 chr7D 264360362 264363069 2707 False 5001.000000 5001 100.000000 1 2708 1 chr7D.!!$F1 2707
1 TraesCS7D01G275300 chr7D 264370233 264372117 1884 False 3157.000000 3157 96.882000 1 1887 1 chr7D.!!$F2 1886
2 TraesCS7D01G275300 chr7D 264325488 264327727 2239 False 1436.500000 2612 87.764500 47 2206 2 chr7D.!!$F3 2159
3 TraesCS7D01G275300 chr7D 264338330 264340792 2462 False 1235.333333 2604 91.944333 1 2528 3 chr7D.!!$F4 2527
4 TraesCS7D01G275300 chr7B 244692367 244695020 2653 False 2161.000000 3197 96.343500 1 2708 2 chr7B.!!$F2 2707
5 TraesCS7D01G275300 chr7B 244715877 244717727 1850 False 1530.500000 2913 94.451500 1 1887 2 chr7B.!!$F3 1886
6 TraesCS7D01G275300 chr7B 244644276 244653451 9175 False 1430.600000 3541 90.711200 1 2584 5 chr7B.!!$F1 2583
7 TraesCS7D01G275300 chr7A 287889173 287891586 2413 False 1015.666667 2279 87.058667 1 2528 3 chr7A.!!$F3 2527
8 TraesCS7D01G275300 chr7A 287862273 287863731 1458 False 901.000000 1624 94.634500 47 2274 2 chr7A.!!$F2 2227

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
198 202 3.055747 TGATACATTGCCTACGGTTCACA 60.056 43.478 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1990 8834 0.251916 TTCGGACCTGGCATGTAAGG 59.748 55.0 12.71 12.71 39.65 2.69 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
34 35 4.527038 TGGTATCTCGTCTCCAAGAAGTTT 59.473 41.667 0.00 0.00 0.00 2.66
37 38 4.665833 TCTCGTCTCCAAGAAGTTTCAA 57.334 40.909 0.00 0.00 0.00 2.69
43 44 5.965918 CGTCTCCAAGAAGTTTCAAAAGAAC 59.034 40.000 0.00 0.00 0.00 3.01
198 202 3.055747 TGATACATTGCCTACGGTTCACA 60.056 43.478 0.00 0.00 0.00 3.58
323 629 7.062371 CCGACGGATCTTCAGAATATACAATTC 59.938 40.741 8.64 0.00 0.00 2.17
425 852 3.758554 GTCACTACAAGATGGCCATGTTT 59.241 43.478 26.56 17.52 0.00 2.83
486 914 4.797471 TCATTGTGCAGTGATTTTGCTAC 58.203 39.130 0.00 0.00 42.02 3.58
714 1165 7.319646 GCCAATTAAAGGAACATGACAATGTA 58.680 34.615 0.00 0.00 46.58 2.29
768 1219 7.942341 ACTAAAGAATTTGAACTACACATGGGA 59.058 33.333 0.00 0.00 39.63 4.37
785 1236 5.781818 ACATGGGAGAAGATTCCAAATGTTT 59.218 36.000 0.00 0.00 40.40 2.83
786 1237 6.270695 ACATGGGAGAAGATTCCAAATGTTTT 59.729 34.615 0.00 0.00 40.40 2.43
1990 8834 8.761575 TCATGATTTTGTTTTAGCATCTTTCC 57.238 30.769 0.00 0.00 0.00 3.13
2007 8851 1.153168 CCCTTACATGCCAGGTCCG 60.153 63.158 9.42 0.00 0.00 4.79
2023 8867 0.321298 TCCGAACTACAAGGCAAGCC 60.321 55.000 2.02 2.02 0.00 4.35
2042 8886 2.101917 GCCTGCAAATGGATAACATGCT 59.898 45.455 0.00 0.00 40.44 3.79
2043 8887 3.713288 CCTGCAAATGGATAACATGCTG 58.287 45.455 0.00 0.00 40.44 4.41
2062 8906 1.073125 TGGCCAGATTTTCTTCACGGA 59.927 47.619 0.00 0.00 0.00 4.69
2094 8979 4.314121 TGGCCTGTTATTGCATTGTTTTC 58.686 39.130 3.32 0.00 0.00 2.29
2485 9381 0.403655 TAGGTCACAAGGCATGGCAA 59.596 50.000 22.64 0.00 0.00 4.52
2544 9450 3.374058 CGGTGGCTTCAAAAGATAATCGT 59.626 43.478 0.00 0.00 0.00 3.73
2572 9478 5.298777 GGTGATGAATCTCTTGCTTATGCTT 59.701 40.000 1.96 0.00 40.48 3.91
2631 9537 0.251634 GAAGCCTTGGACTGGAGAGG 59.748 60.000 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 5.734855 TCTTTTGAAACTTCTTGGAGACG 57.265 39.130 0.00 0.00 0.00 4.18
34 35 4.206375 TGCATGGAAGTCTGTTCTTTTGA 58.794 39.130 0.00 0.00 0.00 2.69
37 38 3.953612 TGTTGCATGGAAGTCTGTTCTTT 59.046 39.130 0.00 0.00 0.00 2.52
43 44 2.486982 CTCCTTGTTGCATGGAAGTCTG 59.513 50.000 0.00 0.00 37.27 3.51
90 91 2.573462 TCTAAGCACTGCCCTCAAGAAT 59.427 45.455 0.00 0.00 0.00 2.40
198 202 1.372501 AAAGGTGGGTGCCTATCACT 58.627 50.000 0.00 0.00 44.98 3.41
236 240 4.070716 GTCCAAGCTATCAGCAGCATAAT 58.929 43.478 0.00 0.00 45.56 1.28
298 317 7.201274 CGAATTGTATATTCTGAAGATCCGTCG 60.201 40.741 0.03 2.41 0.00 5.12
332 638 2.223203 CCAGCAACGATGAGCATTTCTC 60.223 50.000 0.00 0.00 42.23 2.87
400 827 1.421410 GGCCATCTTGTAGTGACGCG 61.421 60.000 3.53 3.53 0.00 6.01
425 852 7.443879 TGTTGTGATAACAAGTAGCATCTGAAA 59.556 33.333 0.00 0.00 29.08 2.69
486 914 1.952296 CTGGCTTGCTTTAGCTATGGG 59.048 52.381 3.10 0.00 40.99 4.00
768 1219 6.550854 TCTGGTGAAAACATTTGGAATCTTCT 59.449 34.615 0.00 0.00 0.00 2.85
785 1236 5.034852 TCAAGTTTGTGAGATCTGGTGAA 57.965 39.130 0.00 0.00 0.00 3.18
786 1237 4.687901 TCAAGTTTGTGAGATCTGGTGA 57.312 40.909 0.00 0.00 0.00 4.02
911 1362 2.794350 GCCTTTCGGTTTGATGTGTTTG 59.206 45.455 0.00 0.00 0.00 2.93
1990 8834 0.251916 TTCGGACCTGGCATGTAAGG 59.748 55.000 12.71 12.71 39.65 2.69
2007 8851 0.523519 GCAGGCTTGCCTTGTAGTTC 59.476 55.000 10.18 0.00 44.74 3.01
2023 8867 3.713288 CCAGCATGTTATCCATTTGCAG 58.287 45.455 0.00 0.00 0.00 4.41
2042 8886 1.073125 TCCGTGAAGAAAATCTGGCCA 59.927 47.619 4.71 4.71 0.00 5.36
2043 8887 1.468914 GTCCGTGAAGAAAATCTGGCC 59.531 52.381 0.00 0.00 0.00 5.36
2062 8906 1.705002 TAACAGGCCAGGCTGTGTGT 61.705 55.000 25.35 13.75 33.66 3.72
2398 9294 5.747565 TGCAAAACTATTGAGTCGTCAAAG 58.252 37.500 0.00 0.00 45.88 2.77
2485 9381 6.007703 AGTTAGCTCTTAGTTCTCTGTCTGT 58.992 40.000 0.00 0.00 0.00 3.41
2544 9450 2.013563 GCAAGAGATTCATCACCGCCA 61.014 52.381 0.00 0.00 0.00 5.69
2572 9478 5.674525 AGCATGGACGAGATTATCTTTTGA 58.325 37.500 0.00 0.00 0.00 2.69
2631 9537 1.273327 CCAATCTTTCAGCCACCCAAC 59.727 52.381 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.