Multiple sequence alignment - TraesCS5D01G187600

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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 TraesCS5D01G187600 chr5D 100.000 2237 0 0 1 2237 289420692 289422928 0.000000e+00 4132.0
1 TraesCS5D01G187600 chr5D 96.680 994 15 4 1 978 289726736 289727727 0.000000e+00 1637.0
2 TraesCS5D01G187600 chr5D 96.421 950 27 2 936 1878 289727724 289728673 0.000000e+00 1559.0
3 TraesCS5D01G187600 chr5D 85.865 948 72 12 1097 1998 23823502 23824433 0.000000e+00 952.0
4 TraesCS5D01G187600 chr5D 95.528 492 17 2 1 492 289354877 289355363 0.000000e+00 782.0
5 TraesCS5D01G187600 chr5D 87.153 685 66 10 1051 1720 29905314 29904637 0.000000e+00 758.0
6 TraesCS5D01G187600 chr5D 91.304 46 2 1 590 635 289355781 289355824 6.670000e-06 62.1
7 TraesCS5D01G187600 chr1B 92.973 1423 84 8 828 2237 426497633 426499052 0.000000e+00 2060.0
8 TraesCS5D01G187600 chr1B 92.475 1422 93 7 828 2237 133112033 133113452 0.000000e+00 2021.0
9 TraesCS5D01G187600 chr1B 95.411 414 18 1 1 414 133123708 133124120 0.000000e+00 658.0
10 TraesCS5D01G187600 chr1B 86.561 253 13 8 570 812 133111699 133111940 2.200000e-65 259.0
11 TraesCS5D01G187600 chr1B 96.094 128 5 0 570 697 426482342 426482469 2.250000e-50 209.0
12 TraesCS5D01G187600 chr1B 82.199 191 11 8 570 751 426497242 426497418 2.320000e-30 143.0
13 TraesCS5D01G187600 chr1B 86.726 113 4 5 724 826 426497423 426497534 5.050000e-22 115.0
14 TraesCS5D01G187600 chr1B 98.246 57 1 0 495 551 398961783 398961727 1.410000e-17 100.0
15 TraesCS5D01G187600 chr1B 93.443 61 3 1 766 826 426482510 426482569 3.060000e-14 89.8
16 TraesCS5D01G187600 chr7A 92.762 1423 83 9 828 2237 627045886 627047301 0.000000e+00 2039.0
17 TraesCS5D01G187600 chr7A 93.906 1083 41 14 2 1070 627008265 627009336 0.000000e+00 1611.0
18 TraesCS5D01G187600 chr7A 91.900 1000 65 8 1004 1994 580505038 580506030 0.000000e+00 1384.0
19 TraesCS5D01G187600 chr7A 94.553 459 19 2 1 454 628385457 628385914 0.000000e+00 704.0
20 TraesCS5D01G187600 chr7A 82.395 835 104 28 1433 2237 627235191 627236012 0.000000e+00 688.0
21 TraesCS5D01G187600 chr7A 90.927 496 25 6 1 491 627232119 627232599 0.000000e+00 649.0
22 TraesCS5D01G187600 chr7A 89.200 500 41 8 1 491 628645947 628645452 1.470000e-171 612.0
23 TraesCS5D01G187600 chr7A 85.686 510 45 12 1 491 594434892 594434392 1.530000e-141 512.0
24 TraesCS5D01G187600 chr7A 98.454 194 3 0 2044 2237 627009339 627009532 2.130000e-90 342.0
25 TraesCS5D01G187600 chr7A 90.306 196 10 3 578 773 626992813 626992999 4.770000e-62 248.0
26 TraesCS5D01G187600 chr7A 80.783 281 22 17 565 826 627045520 627045787 8.150000e-45 191.0
27 TraesCS5D01G187600 chr7A 80.783 281 22 16 565 826 627119708 627119975 8.150000e-45 191.0
28 TraesCS5D01G187600 chr7A 100.000 43 0 0 509 551 627045398 627045440 1.840000e-11 80.5
29 TraesCS5D01G187600 chr7B 85.976 1419 149 34 849 2237 588879066 588880464 0.000000e+00 1472.0
30 TraesCS5D01G187600 chr7B 93.000 500 23 9 1 494 588823043 588823536 0.000000e+00 719.0
31 TraesCS5D01G187600 chr7B 91.781 511 17 10 1 495 589920371 589919870 0.000000e+00 688.0
32 TraesCS5D01G187600 chr7B 95.652 414 18 0 1 414 589735755 589735342 0.000000e+00 665.0
33 TraesCS5D01G187600 chr7B 95.122 82 3 1 617 697 588823713 588823794 6.480000e-26 128.0
34 TraesCS5D01G187600 chr7B 85.217 115 12 4 536 650 589735037 589734928 1.820000e-21 113.0
35 TraesCS5D01G187600 chr7B 100.000 57 0 0 495 551 589696390 589696446 3.040000e-19 106.0
36 TraesCS5D01G187600 chr7B 98.246 57 1 0 495 551 588823562 588823618 1.410000e-17 100.0
37 TraesCS5D01G187600 chr7B 96.667 60 1 1 766 825 588823824 588823882 5.080000e-17 99.0
38 TraesCS5D01G187600 chr7B 94.915 59 3 0 570 628 589696538 589696596 2.370000e-15 93.5
39 TraesCS5D01G187600 chr6A 91.473 1032 70 8 829 1853 107263765 107262745 0.000000e+00 1402.0
40 TraesCS5D01G187600 chr2B 90.374 883 66 10 838 1713 182134306 182135176 0.000000e+00 1142.0
41 TraesCS5D01G187600 chr2B 90.868 438 29 4 1744 2179 182135174 182135602 5.360000e-161 577.0
42 TraesCS5D01G187600 chr2B 83.475 236 16 9 604 826 127790332 127790557 4.870000e-47 198.0
43 TraesCS5D01G187600 chr2B 100.000 72 0 0 2166 2237 182140525 182140596 1.390000e-27 134.0
44 TraesCS5D01G187600 chr2B 90.196 102 0 5 735 826 182134121 182134222 8.390000e-25 124.0
45 TraesCS5D01G187600 chr3A 88.483 903 72 10 1097 1991 723440608 723439730 0.000000e+00 1062.0
46 TraesCS5D01G187600 chr7D 84.980 506 48 14 1 491 518769298 518768806 2.580000e-134 488.0
47 TraesCS5D01G187600 chr7D 97.990 199 4 0 2039 2237 545268176 545268374 1.640000e-91 346.0
48 TraesCS5D01G187600 chr7D 92.929 99 7 0 612 710 545267340 545267438 6.440000e-31 145.0
49 TraesCS5D01G187600 chr7D 100.000 57 0 0 495 551 545267188 545267244 3.040000e-19 106.0
50 TraesCS5D01G187600 chr7D 100.000 57 0 0 495 551 545650338 545650282 3.040000e-19 106.0


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 TraesCS5D01G187600 chr5D 289420692 289422928 2236 False 4132.000000 4132 100.000000 1 2237 1 chr5D.!!$F2 2236
1 TraesCS5D01G187600 chr5D 289726736 289728673 1937 False 1598.000000 1637 96.550500 1 1878 2 chr5D.!!$F4 1877
2 TraesCS5D01G187600 chr5D 23823502 23824433 931 False 952.000000 952 85.865000 1097 1998 1 chr5D.!!$F1 901
3 TraesCS5D01G187600 chr5D 29904637 29905314 677 True 758.000000 758 87.153000 1051 1720 1 chr5D.!!$R1 669
4 TraesCS5D01G187600 chr5D 289354877 289355824 947 False 422.050000 782 93.416000 1 635 2 chr5D.!!$F3 634
5 TraesCS5D01G187600 chr1B 133111699 133113452 1753 False 1140.000000 2021 89.518000 570 2237 2 chr1B.!!$F2 1667
6 TraesCS5D01G187600 chr1B 426497242 426499052 1810 False 772.666667 2060 87.299333 570 2237 3 chr1B.!!$F4 1667
7 TraesCS5D01G187600 chr7A 580505038 580506030 992 False 1384.000000 1384 91.900000 1004 1994 1 chr7A.!!$F1 990
8 TraesCS5D01G187600 chr7A 627008265 627009532 1267 False 976.500000 1611 96.180000 2 2237 2 chr7A.!!$F5 2235
9 TraesCS5D01G187600 chr7A 627045398 627047301 1903 False 770.166667 2039 91.181667 509 2237 3 chr7A.!!$F6 1728
10 TraesCS5D01G187600 chr7A 627232119 627236012 3893 False 668.500000 688 86.661000 1 2237 2 chr7A.!!$F7 2236
11 TraesCS5D01G187600 chr7A 594434392 594434892 500 True 512.000000 512 85.686000 1 491 1 chr7A.!!$R1 490
12 TraesCS5D01G187600 chr7B 588879066 588880464 1398 False 1472.000000 1472 85.976000 849 2237 1 chr7B.!!$F1 1388
13 TraesCS5D01G187600 chr7B 589919870 589920371 501 True 688.000000 688 91.781000 1 495 1 chr7B.!!$R1 494
14 TraesCS5D01G187600 chr7B 589734928 589735755 827 True 389.000000 665 90.434500 1 650 2 chr7B.!!$R2 649
15 TraesCS5D01G187600 chr7B 588823043 588823882 839 False 261.500000 719 95.758750 1 825 4 chr7B.!!$F2 824
16 TraesCS5D01G187600 chr6A 107262745 107263765 1020 True 1402.000000 1402 91.473000 829 1853 1 chr6A.!!$R1 1024
17 TraesCS5D01G187600 chr2B 182134121 182135602 1481 False 614.333333 1142 90.479333 735 2179 3 chr2B.!!$F3 1444
18 TraesCS5D01G187600 chr3A 723439730 723440608 878 True 1062.000000 1062 88.483000 1097 1991 1 chr3A.!!$R1 894

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
698 2583 3.193267 AGTTGCTGCTTGTCAAGTTGAAA 59.807 39.13 14.03 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1671 3921 5.825532 TCATCACAGATTCCCACCATTTTA 58.174 37.5 0.0 0.0 0.0 1.52 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
698 2583 3.193267 AGTTGCTGCTTGTCAAGTTGAAA 59.807 39.130 14.03 0.0 0.00 2.69
1352 3491 6.074142 GCCTGAAATAGTTTTTCAACAAGCTG 60.074 38.462 9.58 0.0 37.89 4.24
1429 3663 2.380084 TCCCGTGAATGTGAACTAGC 57.620 50.000 0.00 0.0 0.00 3.42
1643 3893 8.853345 CCACTGAAAATGAAACAAAAGATATCG 58.147 33.333 0.00 0.0 0.00 2.92
1755 4029 0.865218 CTCGTGCGCTCTTCTGCTAG 60.865 60.000 9.73 0.0 0.00 3.42
1756 4030 1.153939 CGTGCGCTCTTCTGCTAGT 60.154 57.895 9.73 0.0 0.00 2.57
2011 4318 8.641498 TTGGAATCTTTTCTTCTGCTCTAAAT 57.359 30.769 0.00 0.0 32.16 1.40
2064 4384 7.867921 TGATATGGAATTAGGGTTGTTGTAGT 58.132 34.615 0.00 0.0 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 75 4.436998 GTACGCGGTGCCTGCTCT 62.437 66.667 12.47 0.0 0.00 4.09
1352 3491 2.344950 CACTGCAGTTCTCTCATGTCC 58.655 52.381 18.94 0.0 0.00 4.02
1375 3514 6.924111 TGTTGCCAGATTATTTTCCTTCTTC 58.076 36.000 0.00 0.0 0.00 2.87
1671 3921 5.825532 TCATCACAGATTCCCACCATTTTA 58.174 37.500 0.00 0.0 0.00 1.52
2064 4384 6.183360 GCAAACCGTCTACGATTAAATCAAGA 60.183 38.462 3.65 0.0 43.02 3.02


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

AutoCloner maintained by Alex Coulton.