Multiple sequence alignment - TraesCS4A01G287900

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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 TraesCS4A01G287900 chr4A 100.000 4000 0 0 699 4698 593112888 593116887 0.000000e+00 7387.0
1 TraesCS4A01G287900 chr4A 98.243 3814 42 3 743 4556 592544123 592547911 0.000000e+00 6649.0
2 TraesCS4A01G287900 chr4A 98.843 2679 27 3 711 3389 591499470 591496796 0.000000e+00 4772.0
3 TraesCS4A01G287900 chr4A 99.024 2458 24 0 743 3200 592830050 592832507 0.000000e+00 4407.0
4 TraesCS4A01G287900 chr4A 97.857 420 7 1 2340 2759 92375434 92375851 0.000000e+00 725.0
5 TraesCS4A01G287900 chr4A 100.000 273 0 0 1 273 593112190 593112462 5.430000e-139 505.0
6 TraesCS4A01G287900 chr4A 98.535 273 4 0 1 273 591500074 591499802 2.540000e-132 483.0
7 TraesCS4A01G287900 chr4A 98.540 274 3 1 1 273 592543821 592544094 2.540000e-132 483.0
8 TraesCS4A01G287900 chr4A 98.175 274 4 1 1 273 592829751 592830024 1.180000e-130 477.0
9 TraesCS4A01G287900 chr4A 91.582 297 3 1 4260 4556 592834007 592834281 1.590000e-104 390.0
10 TraesCS4A01G287900 chr4A 97.931 145 2 1 4554 4698 592548093 592548236 2.810000e-62 250.0
11 TraesCS4A01G287900 chr4A 97.241 145 3 1 4554 4698 592834463 592834606 1.310000e-60 244.0
12 TraesCS4A01G287900 chr4A 84.783 92 4 6 4381 4467 593116656 593116570 3.010000e-12 84.2
13 TraesCS4A01G287900 chrUn 98.243 3814 42 3 743 4556 308086280 308090068 0.000000e+00 6649.0
14 TraesCS4A01G287900 chrUn 99.633 545 2 0 743 1287 432033607 432034151 0.000000e+00 996.0
15 TraesCS4A01G287900 chrUn 98.175 274 4 1 1 273 432033308 432033581 1.180000e-130 477.0
16 TraesCS4A01G287900 chr4B 94.697 1603 67 8 2813 4402 20279711 20278114 0.000000e+00 2473.0
17 TraesCS4A01G287900 chr4B 88.542 1571 108 28 707 2263 20281254 20279742 0.000000e+00 1838.0
18 TraesCS4A01G287900 chr4B 91.246 297 4 1 4260 4556 20277709 20277435 7.370000e-103 385.0
19 TraesCS4A01G287900 chr4B 95.172 145 6 1 4554 4698 20277253 20277110 1.320000e-55 228.0
20 TraesCS4A01G287900 chr4B 91.971 137 5 4 1 134 20281441 20281308 2.230000e-43 187.0
21 TraesCS4A01G287900 chr4B 98.148 54 1 0 4411 4464 20278127 20278074 1.390000e-15 95.3
22 TraesCS4A01G287900 chr4D 94.636 1361 63 3 2813 4165 10766285 10764927 0.000000e+00 2100.0
23 TraesCS4A01G287900 chr4D 91.179 1179 73 17 1104 2263 10767482 10766316 0.000000e+00 1572.0
24 TraesCS4A01G287900 chr4D 86.802 394 26 8 700 1090 10767920 10767550 2.620000e-112 416.0
25 TraesCS4A01G287900 chr4D 98.561 139 2 0 4560 4698 10764093 10763955 3.630000e-61 246.0
26 TraesCS4A01G287900 chr4D 96.774 124 4 0 4433 4556 10764403 10764280 1.710000e-49 207.0
27 TraesCS4A01G287900 chr4D 100.000 55 0 0 4293 4347 10764621 10764567 8.320000e-18 102.0
28 TraesCS4A01G287900 chr6A 89.678 1521 125 18 2759 4258 117413343 117411834 0.000000e+00 1910.0
29 TraesCS4A01G287900 chr6A 86.801 1682 144 35 700 2334 117414987 117413337 0.000000e+00 1805.0
30 TraesCS4A01G287900 chr6A 98.349 424 6 1 2335 2758 471529457 471529879 0.000000e+00 743.0
31 TraesCS4A01G287900 chr6A 87.857 140 10 2 4559 4695 117403865 117403730 1.750000e-34 158.0
32 TraesCS4A01G287900 chr6D 87.262 1680 138 38 700 2334 98130403 98128755 0.000000e+00 1847.0
33 TraesCS4A01G287900 chr6D 89.281 1502 119 17 2759 4239 98128761 98127281 0.000000e+00 1844.0
34 TraesCS4A01G287900 chr6D 90.441 136 9 1 4560 4695 98126527 98126396 4.830000e-40 176.0
35 TraesCS4A01G287900 chr6B 87.224 1675 142 29 700 2334 183334903 183333261 0.000000e+00 1842.0
36 TraesCS4A01G287900 chr6B 89.271 1454 125 15 2759 4200 183333267 183331833 0.000000e+00 1792.0
37 TraesCS4A01G287900 chr6B 91.603 131 9 2 4554 4684 183331425 183331297 3.740000e-41 180.0
38 TraesCS4A01G287900 chr5A 99.054 423 2 2 2336 2758 383829990 383829570 0.000000e+00 758.0
39 TraesCS4A01G287900 chr5A 93.636 110 7 0 132 241 26132648 26132539 1.050000e-36 165.0
40 TraesCS4A01G287900 chr2A 98.582 423 6 0 2336 2758 408770258 408769836 0.000000e+00 749.0
41 TraesCS4A01G287900 chr2A 95.556 45 1 1 4425 4469 671704028 671703985 2.350000e-08 71.3
42 TraesCS4A01G287900 chr3A 98.345 423 6 1 2337 2758 599890797 599890375 0.000000e+00 741.0
43 TraesCS4A01G287900 chr7B 79.110 876 181 2 2847 3721 517625125 517625999 1.870000e-168 603.0
44 TraesCS4A01G287900 chr7B 85.517 145 17 4 131 273 521568102 521567960 1.050000e-31 148.0
45 TraesCS4A01G287900 chr7A 78.851 870 178 6 2855 3721 556319715 556320581 2.440000e-162 582.0
46 TraesCS4A01G287900 chr7A 94.495 109 6 0 132 240 709291313 709291205 8.080000e-38 169.0
47 TraesCS4A01G287900 chr7A 93.636 110 7 0 132 241 650030794 650030903 1.050000e-36 165.0
48 TraesCS4A01G287900 chr7D 93.694 111 7 0 129 239 615266719 615266609 2.910000e-37 167.0
49 TraesCS4A01G287900 chr7D 92.500 40 3 0 4183 4222 616766051 616766090 1.830000e-04 58.4
50 TraesCS4A01G287900 chr3D 82.796 93 6 6 4378 4469 389633130 389633213 1.810000e-09 75.0
51 TraesCS4A01G287900 chr2B 97.561 41 1 0 4429 4469 32892708 32892668 2.350000e-08 71.3


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 TraesCS4A01G287900 chr4A 593112190 593116887 4697 False 3946.000000 7387 100.000000 1 4698 2 chr4A.!!$F4 4697
1 TraesCS4A01G287900 chr4A 591496796 591500074 3278 True 2627.500000 4772 98.689000 1 3389 2 chr4A.!!$R2 3388
2 TraesCS4A01G287900 chr4A 592543821 592548236 4415 False 2460.666667 6649 98.238000 1 4698 3 chr4A.!!$F2 4697
3 TraesCS4A01G287900 chr4A 592829751 592834606 4855 False 1379.500000 4407 96.505500 1 4698 4 chr4A.!!$F3 4697
4 TraesCS4A01G287900 chrUn 308086280 308090068 3788 False 6649.000000 6649 98.243000 743 4556 1 chrUn.!!$F1 3813
5 TraesCS4A01G287900 chrUn 432033308 432034151 843 False 736.500000 996 98.904000 1 1287 2 chrUn.!!$F2 1286
6 TraesCS4A01G287900 chr4B 20277110 20281441 4331 True 867.716667 2473 93.296000 1 4698 6 chr4B.!!$R1 4697
7 TraesCS4A01G287900 chr4D 10763955 10767920 3965 True 773.833333 2100 94.658667 700 4698 6 chr4D.!!$R1 3998
8 TraesCS4A01G287900 chr6A 117411834 117414987 3153 True 1857.500000 1910 88.239500 700 4258 2 chr6A.!!$R2 3558
9 TraesCS4A01G287900 chr6D 98126396 98130403 4007 True 1289.000000 1847 88.994667 700 4695 3 chr6D.!!$R1 3995
10 TraesCS4A01G287900 chr6B 183331297 183334903 3606 True 1271.333333 1842 89.366000 700 4684 3 chr6B.!!$R1 3984
11 TraesCS4A01G287900 chr7B 517625125 517625999 874 False 603.000000 603 79.110000 2847 3721 1 chr7B.!!$F1 874
12 TraesCS4A01G287900 chr7A 556319715 556320581 866 False 582.000000 582 78.851000 2855 3721 1 chr7A.!!$F1 866

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
161 165 2.156117 CGTTCCAAATTACTCGTCGCAA 59.844 45.455 0.00 0.0 0.00 4.85 F
1785 1887 2.123428 GGGAGCGCTGGCATCAAAT 61.123 57.895 18.48 0.0 43.41 2.32 F
1832 1934 0.251653 AGTTCGACAGCAGGGACCTA 60.252 55.000 0.00 0.0 0.00 3.08 F
2100 2202 0.892755 CAGGAAGTGGCATGTGCAAT 59.107 50.000 7.36 0.0 44.36 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1824 1926 0.413832 TCCAGCTCTGTTAGGTCCCT 59.586 55.000 0.0 0.0 32.16 4.20 R
3129 3249 1.393539 CAATTAGGACGCTGAACACGG 59.606 52.381 0.0 0.0 34.00 4.94 R
3590 3710 4.388577 AGAAATAGTCCAAGTGCCCTTT 57.611 40.909 0.0 0.0 0.00 3.11 R
3945 4093 0.475906 GGGGCATAACCAGCTCATCT 59.524 55.000 0.0 0.0 42.05 2.90 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
161 165 2.156117 CGTTCCAAATTACTCGTCGCAA 59.844 45.455 0.00 0.00 0.00 4.85
223 227 5.404096 TCGATACTTGCGACAAGTAATTCA 58.596 37.500 25.44 12.66 36.45 2.57
1016 1039 2.267681 GACATGGAAGCAGCAGCAGC 62.268 60.000 3.17 0.46 45.49 5.25
1785 1887 2.123428 GGGAGCGCTGGCATCAAAT 61.123 57.895 18.48 0.00 43.41 2.32
1832 1934 0.251653 AGTTCGACAGCAGGGACCTA 60.252 55.000 0.00 0.00 0.00 3.08
2100 2202 0.892755 CAGGAAGTGGCATGTGCAAT 59.107 50.000 7.36 0.00 44.36 3.56
2341 2457 9.713740 GCACAAAAGATATCAGAAAATGAGTAG 57.286 33.333 5.32 0.00 42.53 2.57
2605 2723 4.788100 CAGCCTTCATTTCAACGTATTTCG 59.212 41.667 0.00 0.00 46.00 3.46
3129 3249 2.102252 CTGCCTCCCTCTCTATTGTCAC 59.898 54.545 0.00 0.00 0.00 3.67
3145 3265 1.174078 TCACCGTGTTCAGCGTCCTA 61.174 55.000 0.00 0.00 0.00 2.94
3590 3710 5.366768 GGATGGATCCCGGATAATCTGAATA 59.633 44.000 9.90 0.00 41.20 1.75
4003 4153 9.788889 AGATCATTTGATGCAAATCAGAGTATA 57.211 29.630 0.00 0.00 41.40 1.47
4353 5191 6.233434 TCGTCCGCTTATAATCTAGTAGGAA 58.767 40.000 0.00 0.00 0.00 3.36
4395 5233 2.158066 TGGTACCCCTCCGATCCATATT 60.158 50.000 10.07 0.00 0.00 1.28
4396 5234 3.077848 TGGTACCCCTCCGATCCATATTA 59.922 47.826 10.07 0.00 0.00 0.98
4397 5235 4.098894 GGTACCCCTCCGATCCATATTAA 58.901 47.826 0.00 0.00 0.00 1.40
4398 5236 4.720273 GGTACCCCTCCGATCCATATTAAT 59.280 45.833 0.00 0.00 0.00 1.40
4399 5237 5.191124 GGTACCCCTCCGATCCATATTAATT 59.809 44.000 0.00 0.00 0.00 1.40
4400 5238 5.179452 ACCCCTCCGATCCATATTAATTG 57.821 43.478 0.00 0.00 0.00 2.32
4401 5239 4.601857 ACCCCTCCGATCCATATTAATTGT 59.398 41.667 0.00 0.00 0.00 2.71
4402 5240 5.186198 CCCCTCCGATCCATATTAATTGTC 58.814 45.833 0.00 0.00 0.00 3.18
4403 5241 5.045578 CCCCTCCGATCCATATTAATTGTCT 60.046 44.000 0.00 0.00 0.00 3.41
4404 5242 6.109359 CCCTCCGATCCATATTAATTGTCTC 58.891 44.000 0.00 0.00 0.00 3.36
4405 5243 6.070538 CCCTCCGATCCATATTAATTGTCTCT 60.071 42.308 0.00 0.00 0.00 3.10
4406 5244 6.815641 CCTCCGATCCATATTAATTGTCTCTG 59.184 42.308 0.00 0.00 0.00 3.35
4407 5245 6.701340 TCCGATCCATATTAATTGTCTCTGG 58.299 40.000 0.00 0.00 0.00 3.86
4408 5246 6.270000 TCCGATCCATATTAATTGTCTCTGGT 59.730 38.462 0.00 0.00 0.00 4.00
4409 5247 6.936900 CCGATCCATATTAATTGTCTCTGGTT 59.063 38.462 0.00 0.00 0.00 3.67
4443 5281 8.891671 AATCGTTAACTTTGTACTAAACCAGA 57.108 30.769 3.71 0.00 0.00 3.86
4497 5335 3.541996 TTGTTCTGTGCACTTCTCTGA 57.458 42.857 19.41 4.02 0.00 3.27
4556 5396 5.177696 TGCACAAAACACAAACCTTGTAAAC 59.822 36.000 0.00 0.00 43.23 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
223 227 4.684484 ACTTTTGTACTCCTTCCGTTCT 57.316 40.909 0.00 0.00 0.00 3.01
698 702 1.524961 GACCCACGCCCATGACATA 59.475 57.895 0.00 0.00 0.00 2.29
702 706 3.716195 CAGGACCCACGCCCATGA 61.716 66.667 0.00 0.00 0.00 3.07
1144 1222 2.832838 TCACAGTACCAGGACATCCAT 58.167 47.619 0.00 0.00 38.89 3.41
1824 1926 0.413832 TCCAGCTCTGTTAGGTCCCT 59.586 55.000 0.00 0.00 32.16 4.20
1832 1934 1.627834 CCCTTCTTCTCCAGCTCTGTT 59.372 52.381 0.00 0.00 0.00 3.16
1865 1967 3.955650 TTGAGCAGGAAGTAGTACCAC 57.044 47.619 0.00 0.00 0.00 4.16
2100 2202 5.012046 ACAAGGACGATATATCATCTGGCAA 59.988 40.000 13.11 0.00 0.00 4.52
2341 2457 2.592287 TCGGTCACCAAAACGCCC 60.592 61.111 0.00 0.00 0.00 6.13
3129 3249 1.393539 CAATTAGGACGCTGAACACGG 59.606 52.381 0.00 0.00 34.00 4.94
3145 3265 5.359860 GGATTCGTAGATGAAAACCCCAATT 59.640 40.000 0.00 0.00 35.04 2.32
3590 3710 4.388577 AGAAATAGTCCAAGTGCCCTTT 57.611 40.909 0.00 0.00 0.00 3.11
3932 4080 1.619654 CTCATCTGCCCACACCAAAA 58.380 50.000 0.00 0.00 0.00 2.44
3945 4093 0.475906 GGGGCATAACCAGCTCATCT 59.524 55.000 0.00 0.00 42.05 2.90
4003 4153 8.944029 CACTTTGAATGATCTCATCAGTTAACT 58.056 33.333 1.12 1.12 43.53 2.24
4088 4251 5.343715 TCTATCACAACAACCCCCTAACTA 58.656 41.667 0.00 0.00 0.00 2.24
4396 5234 8.840321 CGATTAATATGGAAACCAGAGACAATT 58.160 33.333 0.00 0.00 36.75 2.32
4397 5235 7.993183 ACGATTAATATGGAAACCAGAGACAAT 59.007 33.333 0.00 0.00 36.75 2.71
4398 5236 7.335627 ACGATTAATATGGAAACCAGAGACAA 58.664 34.615 0.00 0.00 36.75 3.18
4399 5237 6.884832 ACGATTAATATGGAAACCAGAGACA 58.115 36.000 0.00 0.00 36.75 3.41
4400 5238 7.787725 AACGATTAATATGGAAACCAGAGAC 57.212 36.000 0.00 0.00 36.75 3.36
4401 5239 9.321562 GTTAACGATTAATATGGAAACCAGAGA 57.678 33.333 0.00 0.00 36.75 3.10
4402 5240 9.326413 AGTTAACGATTAATATGGAAACCAGAG 57.674 33.333 0.00 0.00 36.75 3.35
4403 5241 9.675464 AAGTTAACGATTAATATGGAAACCAGA 57.325 29.630 0.00 0.00 36.75 3.86
4443 5281 5.785423 TCCCTCCGATCCATATTAATTGTCT 59.215 40.000 0.00 0.00 0.00 3.41
4497 5335 6.766467 GCAGCCATACCTACAGTTTATAGTTT 59.234 38.462 0.00 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.