Multiple sequence alignment - TraesCS5A01G083400

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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 TraesCS5A01G083400 chr5A 100.000 2207 0 0 1 2207 109299931 109302137 0.000000e+00 4076
1 TraesCS5A01G083400 chr2A 97.600 2208 49 3 1 2207 130179794 130177590 0.000000e+00 3781
2 TraesCS5A01G083400 chr2B 97.961 1766 35 1 442 2207 10667770 10669534 0.000000e+00 3061
3 TraesCS5A01G083400 chr2B 97.623 1767 40 2 442 2207 390975865 390974100 0.000000e+00 3029
4 TraesCS5A01G083400 chr2B 93.033 689 46 2 630 1317 588687074 588686387 0.000000e+00 1005
5 TraesCS5A01G083400 chr2B 95.066 608 20 5 1391 1990 588686398 588685793 0.000000e+00 948
6 TraesCS5A01G083400 chr2B 93.262 564 32 5 755 1317 588685795 588685237 0.000000e+00 826
7 TraesCS5A01G083400 chr2B 94.150 359 20 1 1 359 406245956 406245599 1.490000e-151 545
8 TraesCS5A01G083400 chr2B 97.188 320 9 0 1 320 10667454 10667773 1.930000e-150 542
9 TraesCS5A01G083400 chr2B 96.562 320 11 0 1 320 390976181 390975862 4.170000e-147 531
10 TraesCS5A01G083400 chr1B 97.803 1730 35 2 480 2207 674642150 674640422 0.000000e+00 2981
11 TraesCS5A01G083400 chr1B 94.322 317 17 1 1 317 198560108 198560423 3.290000e-133 484
12 TraesCS5A01G083400 chr7D 91.157 1651 114 7 357 1996 301662742 301661113 0.000000e+00 2211
13 TraesCS5A01G083400 chr7D 94.192 637 25 1 927 1563 46096344 46096968 0.000000e+00 961
14 TraesCS5A01G083400 chr7D 92.508 654 38 5 1563 2207 46101977 46102628 0.000000e+00 926
15 TraesCS5A01G083400 chr7D 94.043 470 24 3 357 825 46086101 46086567 0.000000e+00 710
16 TraesCS5A01G083400 chr7D 91.136 361 29 3 1 359 559672356 559671997 9.160000e-134 486
17 TraesCS5A01G083400 chr1D 93.520 1250 53 6 967 2207 252590495 252591725 0.000000e+00 1834
18 TraesCS5A01G083400 chr1D 92.519 401 12 7 357 744 252585942 252586337 1.910000e-155 558
19 TraesCS5A01G083400 chr1D 92.784 388 12 5 361 737 252573379 252573761 4.140000e-152 547
20 TraesCS5A01G083400 chr7A 93.142 1254 55 8 967 2207 665832345 665831110 0.000000e+00 1810
21 TraesCS5A01G083400 chr7A 90.278 360 31 2 1 359 673020933 673021289 3.320000e-128 468
22 TraesCS5A01G083400 chr4A 91.911 1261 62 10 967 2207 713137572 713136332 0.000000e+00 1727
23 TraesCS5A01G083400 chr4A 91.610 441 28 2 1776 2207 504866808 504867248 3.140000e-168 601
24 TraesCS5A01G083400 chr6B 94.105 933 41 9 383 1314 26562138 26563057 0.000000e+00 1406
25 TraesCS5A01G083400 chr6A 92.620 962 39 14 357 1317 611535000 611534070 0.000000e+00 1354
26 TraesCS5A01G083400 chr6A 94.163 257 14 1 1952 2207 611533569 611533313 7.390000e-105 390
27 TraesCS5A01G083400 chr7B 92.437 357 25 1 1 357 620571909 620572263 1.950000e-140 508
28 TraesCS5A01G083400 chr5B 90.556 360 29 3 1 359 523137004 523137359 2.560000e-129 472


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 TraesCS5A01G083400 chr5A 109299931 109302137 2206 False 4076.000000 4076 100.0000 1 2207 1 chr5A.!!$F1 2206
1 TraesCS5A01G083400 chr2A 130177590 130179794 2204 True 3781.000000 3781 97.6000 1 2207 1 chr2A.!!$R1 2206
2 TraesCS5A01G083400 chr2B 10667454 10669534 2080 False 1801.500000 3061 97.5745 1 2207 2 chr2B.!!$F1 2206
3 TraesCS5A01G083400 chr2B 390974100 390976181 2081 True 1780.000000 3029 97.0925 1 2207 2 chr2B.!!$R2 2206
4 TraesCS5A01G083400 chr2B 588685237 588687074 1837 True 926.333333 1005 93.7870 630 1990 3 chr2B.!!$R3 1360
5 TraesCS5A01G083400 chr1B 674640422 674642150 1728 True 2981.000000 2981 97.8030 480 2207 1 chr1B.!!$R1 1727
6 TraesCS5A01G083400 chr7D 301661113 301662742 1629 True 2211.000000 2211 91.1570 357 1996 1 chr7D.!!$R1 1639
7 TraesCS5A01G083400 chr7D 46096344 46096968 624 False 961.000000 961 94.1920 927 1563 1 chr7D.!!$F2 636
8 TraesCS5A01G083400 chr7D 46101977 46102628 651 False 926.000000 926 92.5080 1563 2207 1 chr7D.!!$F3 644
9 TraesCS5A01G083400 chr1D 252590495 252591725 1230 False 1834.000000 1834 93.5200 967 2207 1 chr1D.!!$F3 1240
10 TraesCS5A01G083400 chr7A 665831110 665832345 1235 True 1810.000000 1810 93.1420 967 2207 1 chr7A.!!$R1 1240
11 TraesCS5A01G083400 chr4A 713136332 713137572 1240 True 1727.000000 1727 91.9110 967 2207 1 chr4A.!!$R1 1240
12 TraesCS5A01G083400 chr6B 26562138 26563057 919 False 1406.000000 1406 94.1050 383 1314 1 chr6B.!!$F1 931
13 TraesCS5A01G083400 chr6A 611533313 611535000 1687 True 872.000000 1354 93.3915 357 2207 2 chr6A.!!$R1 1850

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
323 324 2.427506 GGGCTCCTTGTTACAGTTCAG 58.572 52.381 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1482 1598 1.408702 GTGAGGATGGAGTCAGAGCTC 59.591 57.143 5.27 5.27 34.89 4.09 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
95 96 3.073798 TGTTTCCTTCTAATGACCAGCCA 59.926 43.478 0.00 0.00 0.00 4.75
299 300 9.784531 AAATATCTAGATTGATCGTTCATGGTT 57.215 29.630 11.25 0.00 0.00 3.67
323 324 2.427506 GGGCTCCTTGTTACAGTTCAG 58.572 52.381 0.00 0.00 0.00 3.02
893 916 7.173218 TGAACTTAGTTTTAGCTCTCATGTTGG 59.827 37.037 0.00 0.00 0.00 3.77
899 922 7.168219 AGTTTTAGCTCTCATGTTGGTCAATA 58.832 34.615 0.00 0.00 0.00 1.90
988 1011 4.344865 GCGTTCCTGGCTTCCCCA 62.345 66.667 0.00 0.00 42.79 4.96
1084 1107 1.473257 GCTTCATCATCTACGGCCACA 60.473 52.381 2.24 0.00 0.00 4.17
1190 1214 1.134438 GGGTTCAGAGTGGAAGGGGT 61.134 60.000 0.00 0.00 0.00 4.95
1503 1619 1.189752 GCTCTGACTCCATCCTCACA 58.810 55.000 0.00 0.00 0.00 3.58
1589 1705 1.990799 CGTGCATGTCTCTTCGGTTA 58.009 50.000 0.00 0.00 0.00 2.85
2100 2371 6.266103 TCAGGAATCAAGCTTGTGAAGAAAAT 59.734 34.615 25.19 6.76 0.00 1.82
2185 2715 3.123620 GCCAAGCTCAGAGCCACG 61.124 66.667 19.40 7.53 43.77 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 3.544684 TCTATCTTGTTCAATGCCGCAT 58.455 40.909 0.00 0.00 0.00 4.73
230 231 1.273606 CCCTCGAGTTTCTTGAGAGCA 59.726 52.381 12.31 0.00 42.88 4.26
299 300 0.984230 CTGTAACAAGGAGCCCCAGA 59.016 55.000 0.00 0.00 33.88 3.86
323 324 7.272978 TGAGTATTATGGACTAAACTCTTGCC 58.727 38.462 0.00 0.00 33.40 4.52
359 360 3.884774 TCAGGGGGCACGCACTTT 61.885 61.111 5.55 0.00 45.96 2.66
899 922 8.095792 TCCATGCAAAACATTACTTGATGATTT 58.904 29.630 0.00 0.00 36.64 2.17
1084 1107 2.281276 GCCGACGACAAAGGGGTT 60.281 61.111 0.00 0.00 0.00 4.11
1141 1164 4.657814 AATCACAATTACACCCCACTCT 57.342 40.909 0.00 0.00 0.00 3.24
1190 1214 3.826157 CCCCTGCTAAACAAGAATGACAA 59.174 43.478 0.00 0.00 0.00 3.18
1482 1598 1.408702 GTGAGGATGGAGTCAGAGCTC 59.591 57.143 5.27 5.27 34.89 4.09
1503 1619 4.780815 TCATCAAGACAGGTTTGAGTGTT 58.219 39.130 0.00 0.00 37.91 3.32
1619 1735 4.714632 ACACTGCATGTTACCTACAAAGT 58.285 39.130 0.00 0.00 38.98 2.66
2100 2371 9.915629 AAGTGTGTGTCATTAAAGTAACAAAAA 57.084 25.926 0.00 0.00 0.00 1.94


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

AutoCloner maintained by Alex Coulton.