Multiple sequence alignment - TraesCS1B01G435100

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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 TraesCS1B01G435100 chr1B 100.000 2267 0 0 1 2267 659285060 659287326 0.000000e+00 4187.0
1 TraesCS1B01G435100 chr1B 96.725 1374 39 5 1 1373 659181519 659182887 0.000000e+00 2283.0
2 TraesCS1B01G435100 chr1B 94.461 1354 37 8 837 2155 659294562 659295912 0.000000e+00 2050.0
3 TraesCS1B01G435100 chr1B 94.404 1358 29 12 837 2155 659033653 659035002 0.000000e+00 2043.0
4 TraesCS1B01G435100 chr1B 93.455 1207 39 9 978 2148 659073582 659074784 0.000000e+00 1755.0
5 TraesCS1B01G435100 chr1B 90.500 1379 52 29 837 2155 659002555 659003914 0.000000e+00 1748.0
6 TraesCS1B01G435100 chr1B 89.020 1357 61 31 834 2155 658969028 658970331 0.000000e+00 1600.0
7 TraesCS1B01G435100 chr1B 92.931 679 29 11 1 673 659293730 659294395 0.000000e+00 970.0
8 TraesCS1B01G435100 chr1B 82.556 900 52 39 1 836 659072569 659073427 0.000000e+00 695.0
9 TraesCS1B01G435100 chr1B 86.513 608 50 13 244 836 658968395 658968985 6.830000e-180 640.0
10 TraesCS1B01G435100 chr1B 84.810 395 26 13 456 836 659033241 659033615 1.280000e-97 366.0
11 TraesCS1B01G435100 chr1B 82.386 352 41 9 1645 1986 659327166 659327506 1.020000e-73 287.0
12 TraesCS1B01G435100 chr1B 96.774 124 3 1 717 840 659294395 659294517 2.950000e-49 206.0
13 TraesCS1B01G435100 chr1B 97.479 119 3 0 2149 2267 659296516 659296634 1.060000e-48 204.0
14 TraesCS1B01G435100 chr1B 96.610 118 4 0 2150 2267 658970899 658971016 1.780000e-46 196.0
15 TraesCS1B01G435100 chr1B 95.763 118 5 0 2150 2267 659004482 659004599 8.260000e-45 191.0
16 TraesCS1B01G435100 chr1B 95.763 118 5 0 2150 2267 659191620 659191737 8.260000e-45 191.0
17 TraesCS1B01G435100 chr1B 94.915 118 6 0 2150 2267 659083808 659083925 3.850000e-43 185.0
18 TraesCS1B01G435100 chr1B 84.659 176 11 6 1984 2157 659318282 659318443 6.480000e-36 161.0
19 TraesCS1B01G435100 chr1B 94.286 105 5 1 834 937 659073466 659073570 2.330000e-35 159.0
20 TraesCS1B01G435100 chr1B 90.426 94 6 2 2151 2244 659319053 659319143 1.100000e-23 121.0
21 TraesCS1B01G435100 chr1B 90.741 54 3 2 1 54 658968321 658968372 1.120000e-08 71.3
22 TraesCS1B01G435100 chr1A 87.597 1540 116 31 82 1578 568265148 568266655 0.000000e+00 1716.0
23 TraesCS1B01G435100 chr1A 89.535 602 42 12 94 692 568327020 568327603 0.000000e+00 743.0
24 TraesCS1B01G435100 chr1A 88.312 616 45 15 834 1432 568327855 568328460 0.000000e+00 713.0
25 TraesCS1B01G435100 chr1A 93.956 364 18 3 1623 1985 568266926 568267286 4.260000e-152 547.0
26 TraesCS1B01G435100 chr1A 83.140 344 37 9 1653 1986 568399455 568399787 6.120000e-76 294.0
27 TraesCS1B01G435100 chr1A 82.857 350 37 6 1651 1985 568377871 568378212 2.200000e-75 292.0
28 TraesCS1B01G435100 chr1A 93.367 196 13 0 641 836 568327619 568327814 7.920000e-75 291.0
29 TraesCS1B01G435100 chr1A 92.157 204 14 1 1784 1985 568334079 568334282 1.020000e-73 287.0
30 TraesCS1B01G435100 chr1A 90.173 173 10 1 1983 2155 568378242 568378407 3.790000e-53 219.0
31 TraesCS1B01G435100 chr1A 96.639 119 4 0 2149 2267 568267996 568268114 4.940000e-47 198.0
32 TraesCS1B01G435100 chr1A 87.209 172 8 4 1984 2155 568390083 568390240 1.380000e-42 183.0
33 TraesCS1B01G435100 chr1A 93.043 115 8 0 2149 2263 568335457 568335571 3.870000e-38 169.0
34 TraesCS1B01G435100 chr1A 95.876 97 4 0 1983 2079 568334305 568334401 8.380000e-35 158.0
35 TraesCS1B01G435100 chr1A 90.756 119 7 2 1446 1564 568328598 568328712 3.010000e-34 156.0
36 TraesCS1B01G435100 chr1A 85.906 149 13 3 1446 1594 568383884 568384024 3.900000e-33 152.0
37 TraesCS1B01G435100 chr1A 91.781 73 4 2 840 911 568393396 568393467 1.430000e-17 100.0
38 TraesCS1B01G435100 chr1D 87.701 1366 63 35 837 2155 473961080 473962387 0.000000e+00 1495.0
39 TraesCS1B01G435100 chr1D 85.079 697 49 22 938 1597 473879765 473880443 0.000000e+00 660.0
40 TraesCS1B01G435100 chr1D 80.759 790 84 31 82 836 473960287 473961043 2.540000e-154 555.0
41 TraesCS1B01G435100 chr1D 79.965 564 43 30 1645 2155 473993099 473993645 3.580000e-93 351.0
42 TraesCS1B01G435100 chr1D 96.581 117 3 1 2151 2267 473962959 473963074 2.300000e-45 193.0
43 TraesCS1B01G435100 chr1D 86.047 172 10 4 1984 2155 473988331 473988488 2.990000e-39 172.0
44 TraesCS1B01G435100 chr1D 80.645 217 18 9 1394 1597 473987712 473987917 1.810000e-31 147.0


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 TraesCS1B01G435100 chr1B 659285060 659287326 2266 False 4187.000000 4187 100.000000 1 2267 1 chr1B.!!$F4 2266
1 TraesCS1B01G435100 chr1B 659181519 659182887 1368 False 2283.000000 2283 96.725000 1 1373 1 chr1B.!!$F2 1372
2 TraesCS1B01G435100 chr1B 659033241 659035002 1761 False 1204.500000 2043 89.607000 456 2155 2 chr1B.!!$F8 1699
3 TraesCS1B01G435100 chr1B 659002555 659004599 2044 False 969.500000 1748 93.131500 837 2267 2 chr1B.!!$F7 1430
4 TraesCS1B01G435100 chr1B 659072569 659074784 2215 False 869.666667 1755 90.099000 1 2148 3 chr1B.!!$F9 2147
5 TraesCS1B01G435100 chr1B 659293730 659296634 2904 False 857.500000 2050 95.411250 1 2267 4 chr1B.!!$F10 2266
6 TraesCS1B01G435100 chr1B 658968321 658971016 2695 False 626.825000 1600 90.721000 1 2267 4 chr1B.!!$F6 2266
7 TraesCS1B01G435100 chr1A 568265148 568268114 2966 False 820.333333 1716 92.730667 82 2267 3 chr1A.!!$F3 2185
8 TraesCS1B01G435100 chr1A 568327020 568328712 1692 False 475.750000 743 90.492500 94 1564 4 chr1A.!!$F4 1470
9 TraesCS1B01G435100 chr1A 568377871 568378407 536 False 255.500000 292 86.515000 1651 2155 2 chr1A.!!$F6 504
10 TraesCS1B01G435100 chr1A 568334079 568335571 1492 False 204.666667 287 93.692000 1784 2263 3 chr1A.!!$F5 479
11 TraesCS1B01G435100 chr1D 473960287 473963074 2787 False 747.666667 1495 88.347000 82 2267 3 chr1D.!!$F3 2185
12 TraesCS1B01G435100 chr1D 473879765 473880443 678 False 660.000000 660 85.079000 938 1597 1 chr1D.!!$F1 659
13 TraesCS1B01G435100 chr1D 473993099 473993645 546 False 351.000000 351 79.965000 1645 2155 1 chr1D.!!$F2 510

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
712 907 3.109547 GACGTCGGCATGCGTTGA 61.11 61.111 12.44 6.71 41.7 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2083 3243 1.149288 AGGAGGAAGGTAGTGGTGACA 59.851 52.381 0.0 0.0 38.7 3.58 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
623 749 6.754209 AGCACTAATTCAGATTTAGACACGAG 59.246 38.462 15.92 0.00 0.00 4.18
624 750 6.508721 GCACTAATTCAGATTTAGACACGAGC 60.509 42.308 15.92 8.03 0.00 5.03
645 771 7.924412 ACGAGCGGATTTAAGAGTTAATTATGA 59.076 33.333 0.00 0.00 0.00 2.15
712 907 3.109547 GACGTCGGCATGCGTTGA 61.110 61.111 12.44 6.71 41.70 3.18
1536 2003 3.222603 CCACCCTAGCCCAATTTATCAC 58.777 50.000 0.00 0.00 0.00 3.06
2081 3241 0.798776 GCACACCGAATCCTTGTCAG 59.201 55.000 0.00 0.00 0.00 3.51
2083 3243 2.494059 CACACCGAATCCTTGTCAGTT 58.506 47.619 0.00 0.00 0.00 3.16
2090 3251 3.476552 GAATCCTTGTCAGTTGTCACCA 58.523 45.455 0.00 0.00 0.00 4.17
2221 4101 4.984785 GGAAAAGAAAGCTCGCTTTGAATT 59.015 37.500 20.40 11.79 45.16 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
273 326 8.210946 TCCAAAACATATTCTGTCTGGTATAGG 58.789 37.037 6.42 0.0 39.83 2.57
712 907 2.268076 GGGTCCATTTGCGCACTGT 61.268 57.895 11.12 0.0 0.00 3.55
1278 1552 5.021033 AGCATCCTATGTCTGTTGAGAAG 57.979 43.478 0.00 0.0 0.00 2.85
1536 2003 7.066163 TGTCTGATTGTGCTATGATTAAACCAG 59.934 37.037 0.00 0.0 0.00 4.00
1700 2410 3.436704 TGCTTCATCGATCCTGAAAACAC 59.563 43.478 0.00 0.0 32.53 3.32
2081 3241 2.289506 GGAGGAAGGTAGTGGTGACAAC 60.290 54.545 0.00 0.0 46.06 3.32
2083 3243 1.149288 AGGAGGAAGGTAGTGGTGACA 59.851 52.381 0.00 0.0 38.70 3.58
2090 3251 5.662597 TCTTTTAGGAAGGAGGAAGGTAGT 58.337 41.667 0.00 0.0 0.00 2.73
2221 4101 4.393155 AGCGTCGCAATGCTGGGA 62.393 61.111 21.09 0.0 46.11 4.37


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

AutoCloner maintained by Alex Coulton.