Multiple sequence alignment - TraesCS4A01G378800

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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 TraesCS4A01G378800 chr4A 100.000 2495 0 0 1 2495 656249415 656251909 0.000000e+00 4608.0
1 TraesCS4A01G378800 chr4A 97.464 1656 36 4 838 2487 656472923 656474578 0.000000e+00 2820.0
2 TraesCS4A01G378800 chr4A 96.042 1541 48 4 1 1540 656029665 656031193 0.000000e+00 2495.0
3 TraesCS4A01G378800 chr4A 98.839 603 6 1 1 603 656472315 656472916 0.000000e+00 1074.0
4 TraesCS4A01G378800 chr4A 94.487 653 19 5 1840 2487 656031283 656031923 0.000000e+00 990.0
5 TraesCS4A01G378800 chr4A 78.088 1360 235 37 265 1602 656499531 656498213 0.000000e+00 802.0
6 TraesCS4A01G378800 chr4A 77.703 1193 226 31 331 1502 650831042 650832215 0.000000e+00 693.0
7 TraesCS4A01G378800 chr4A 80.000 850 140 24 637 1476 655659102 655659931 3.550000e-168 601.0
8 TraesCS4A01G378800 chr4A 78.054 442 75 15 637 1072 656035610 656036035 2.460000e-65 259.0
9 TraesCS4A01G378800 chr4A 89.820 167 15 1 2179 2345 656486622 656486786 1.940000e-51 213.0
10 TraesCS4A01G378800 chr4A 94.444 54 3 0 1574 1627 656031193 656031246 1.590000e-12 84.2
11 TraesCS4A01G378800 chr4A 77.778 153 23 10 1710 1860 656854810 656854667 1.590000e-12 84.2
12 TraesCS4A01G378800 chr4A 100.000 35 0 0 1442 1476 656031244 656031278 5.760000e-07 65.8
13 TraesCS4A01G378800 chr7A 91.900 2210 129 19 146 2345 47007078 47009247 0.000000e+00 3044.0
14 TraesCS4A01G378800 chr7A 74.670 1287 236 59 331 1563 47256394 47255144 2.880000e-134 488.0
15 TraesCS4A01G378800 chr7A 88.571 70 6 2 1792 1860 47503099 47503031 1.590000e-12 84.2
16 TraesCS4A01G378800 chr7D 91.497 2211 117 23 149 2345 44538096 44540249 0.000000e+00 2976.0
17 TraesCS4A01G378800 chr7D 78.727 1194 212 34 331 1502 43169430 43168257 0.000000e+00 760.0
18 TraesCS4A01G378800 chrUn 77.722 1203 206 37 331 1502 289666304 289667475 0.000000e+00 680.0
19 TraesCS4A01G378800 chrUn 75.587 1278 231 48 331 1563 48987479 48986238 7.800000e-155 556.0
20 TraesCS4A01G378800 chr3D 75.598 1045 190 43 343 1358 9132093 9131085 8.130000e-125 457.0
21 TraesCS4A01G378800 chr3A 74.363 1139 196 64 343 1452 11865278 11866349 5.000000e-107 398.0
22 TraesCS4A01G378800 chr3B 74.822 981 195 36 343 1301 11475349 11474399 1.800000e-106 396.0
23 TraesCS4A01G378800 chr6B 96.947 131 2 2 2362 2490 211161476 211161606 4.180000e-53 219.0
24 TraesCS4A01G378800 chr5D 96.947 131 2 2 2362 2490 74461448 74461318 4.180000e-53 219.0
25 TraesCS4A01G378800 chr5D 95.968 124 4 1 2365 2487 507218742 507218619 1.510000e-47 200.0
26 TraesCS4A01G378800 chr2B 96.923 130 3 1 2362 2490 594834042 594833913 1.500000e-52 217.0
27 TraesCS4A01G378800 chr2B 94.928 138 4 3 2356 2490 155346677 155346814 1.940000e-51 213.0
28 TraesCS4A01G378800 chr1D 94.286 140 4 4 2353 2490 178466296 178466433 6.990000e-51 211.0
29 TraesCS4A01G378800 chr1A 92.000 150 8 4 2345 2490 573061945 573062094 9.040000e-50 207.0


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 TraesCS4A01G378800 chr4A 656249415 656251909 2494 False 4608.0 4608 100.0000 1 2495 1 chr4A.!!$F3 2494
1 TraesCS4A01G378800 chr4A 656472315 656474578 2263 False 1947.0 2820 98.1515 1 2487 2 chr4A.!!$F6 2486
2 TraesCS4A01G378800 chr4A 656498213 656499531 1318 True 802.0 802 78.0880 265 1602 1 chr4A.!!$R1 1337
3 TraesCS4A01G378800 chr4A 656029665 656036035 6370 False 778.8 2495 92.6054 1 2487 5 chr4A.!!$F5 2486
4 TraesCS4A01G378800 chr4A 650831042 650832215 1173 False 693.0 693 77.7030 331 1502 1 chr4A.!!$F1 1171
5 TraesCS4A01G378800 chr4A 655659102 655659931 829 False 601.0 601 80.0000 637 1476 1 chr4A.!!$F2 839
6 TraesCS4A01G378800 chr7A 47007078 47009247 2169 False 3044.0 3044 91.9000 146 2345 1 chr7A.!!$F1 2199
7 TraesCS4A01G378800 chr7A 47255144 47256394 1250 True 488.0 488 74.6700 331 1563 1 chr7A.!!$R1 1232
8 TraesCS4A01G378800 chr7D 44538096 44540249 2153 False 2976.0 2976 91.4970 149 2345 1 chr7D.!!$F1 2196
9 TraesCS4A01G378800 chr7D 43168257 43169430 1173 True 760.0 760 78.7270 331 1502 1 chr7D.!!$R1 1171
10 TraesCS4A01G378800 chrUn 289666304 289667475 1171 False 680.0 680 77.7220 331 1502 1 chrUn.!!$F1 1171
11 TraesCS4A01G378800 chrUn 48986238 48987479 1241 True 556.0 556 75.5870 331 1563 1 chrUn.!!$R1 1232
12 TraesCS4A01G378800 chr3D 9131085 9132093 1008 True 457.0 457 75.5980 343 1358 1 chr3D.!!$R1 1015
13 TraesCS4A01G378800 chr3A 11865278 11866349 1071 False 398.0 398 74.3630 343 1452 1 chr3A.!!$F1 1109
14 TraesCS4A01G378800 chr3B 11474399 11475349 950 True 396.0 396 74.8220 343 1301 1 chr3B.!!$R1 958

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
892 994 2.362503 TCACGGTGGGATCGAGCT 60.363 61.111 8.5 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2192 2372 1.299648 GCACCACTATCACCAGCCA 59.7 57.895 0.0 0.0 0.0 4.75 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
759 811 3.149196 ACGACCATGCTTCAGTTTCATT 58.851 40.909 0.00 0.00 0.00 2.57
892 994 2.362503 TCACGGTGGGATCGAGCT 60.363 61.111 8.50 0.00 0.00 4.09
1541 1709 6.554334 TGTTAATGCTTTGGACTAGTTGTC 57.446 37.500 0.00 0.00 44.63 3.18
1542 1710 5.178623 TGTTAATGCTTTGGACTAGTTGTCG 59.821 40.000 0.00 0.00 46.24 4.35
1616 1791 8.635765 ACCATTCAGTACTTCAATGTTGTAAT 57.364 30.769 17.48 0.00 0.00 1.89
1928 2106 0.592637 TGGCTGTGATTTTGTGCTCG 59.407 50.000 0.00 0.00 0.00 5.03
1939 2117 0.313672 TTGTGCTCGCCATGGTTTTC 59.686 50.000 14.67 1.46 0.00 2.29
2008 2186 7.050970 TCACTACTACTGTTTTGTGTCTGAT 57.949 36.000 0.00 0.00 0.00 2.90
2009 2187 6.923508 TCACTACTACTGTTTTGTGTCTGATG 59.076 38.462 0.00 0.00 0.00 3.07
2023 2203 3.570975 TGTCTGATGTTGCTGCTTCAATT 59.429 39.130 0.00 0.00 0.00 2.32
2052 2232 4.985538 TGTTAAAAAGAAACCGGCAAGA 57.014 36.364 0.00 0.00 0.00 3.02
2138 2318 8.253810 GGATTTCCTTTCTTTTGGAAGGAATAG 58.746 37.037 16.53 0.00 42.46 1.73
2192 2372 4.281657 TGTAGTGATGTAGTCTGCTGGAT 58.718 43.478 0.00 0.00 0.00 3.41
2249 2429 3.442273 GCAGGTAAAAATGTCCATTCGGA 59.558 43.478 0.00 0.00 39.79 4.55
2478 2660 5.483811 TCACTCATTTTGCTCCGTATGTAA 58.516 37.500 0.00 0.00 0.00 2.41
2484 2666 5.794687 TTTTGCTCCGTATGTAATCACTG 57.205 39.130 0.00 0.00 0.00 3.66
2485 2667 4.465632 TTGCTCCGTATGTAATCACTGT 57.534 40.909 0.00 0.00 0.00 3.55
2487 2669 5.585820 TGCTCCGTATGTAATCACTGTTA 57.414 39.130 0.00 0.00 0.00 2.41
2488 2670 5.968254 TGCTCCGTATGTAATCACTGTTAA 58.032 37.500 0.00 0.00 0.00 2.01
2490 2672 6.311935 TGCTCCGTATGTAATCACTGTTAAAC 59.688 38.462 0.00 0.00 0.00 2.01
2491 2673 6.238022 GCTCCGTATGTAATCACTGTTAAACC 60.238 42.308 0.00 0.00 0.00 3.27
2492 2674 6.699366 TCCGTATGTAATCACTGTTAAACCA 58.301 36.000 0.00 0.00 0.00 3.67
2494 2676 6.454583 CCGTATGTAATCACTGTTAAACCACG 60.455 42.308 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
892 994 2.589720 CCATTGGATGCATCTTGGCTA 58.410 47.619 25.28 6.94 34.04 3.93
1928 2106 3.760684 ACAATCAGAGAGAAAACCATGGC 59.239 43.478 13.04 0.00 0.00 4.40
1939 2117 8.594881 AGTGTAACAAACTAACAATCAGAGAG 57.405 34.615 0.00 0.00 41.43 3.20
2023 2203 6.674066 CCGGTTTCTTTTTAACAATAGCTGA 58.326 36.000 0.00 0.00 0.00 4.26
2052 2232 8.076178 CGAATGGTTAGTCAATGAAAGAAAGTT 58.924 33.333 0.00 0.00 0.00 2.66
2192 2372 1.299648 GCACCACTATCACCAGCCA 59.700 57.895 0.00 0.00 0.00 4.75
2249 2429 2.226437 CAGCTTTGATGCGTTTGGTAGT 59.774 45.455 0.00 0.00 38.13 2.73
2352 2532 3.192844 CAGAGGGAGTAGTTCGTAGCAAA 59.807 47.826 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.