Multiple sequence alignment - TraesCS3B01G348400

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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 TraesCS3B01G348400 chr3B 100.000 2786 0 0 1 2786 557704315 557707100 0.000000e+00 5145
1 TraesCS3B01G348400 chr3B 94.711 2817 97 15 1 2786 751900620 751897825 0.000000e+00 4329
2 TraesCS3B01G348400 chr3B 94.646 2092 78 11 724 2783 766268394 766270483 0.000000e+00 3212
3 TraesCS3B01G348400 chr3B 87.909 397 14 6 1 364 517884030 517883635 1.180000e-118 436
4 TraesCS3B01G348400 chr4A 95.029 2756 106 13 61 2786 660540612 660543366 0.000000e+00 4301
5 TraesCS3B01G348400 chr4A 96.279 215 8 0 1 215 691941346 691941560 1.230000e-93 353
6 TraesCS3B01G348400 chr5B 94.705 2493 97 17 324 2786 492520713 492518226 0.000000e+00 3840
7 TraesCS3B01G348400 chr1B 94.494 2488 125 10 309 2786 627378457 627375972 0.000000e+00 3825
8 TraesCS3B01G348400 chr1B 93.436 2605 110 24 236 2786 600347580 600344983 0.000000e+00 3807
9 TraesCS3B01G348400 chr1B 96.537 1155 33 7 1637 2786 6174572 6175724 0.000000e+00 1905
10 TraesCS3B01G348400 chr1B 94.419 215 12 0 1 215 600347847 600347633 5.750000e-87 331
11 TraesCS3B01G348400 chr1B 94.419 215 8 1 1 215 337579824 337579614 7.440000e-86 327
12 TraesCS3B01G348400 chr2B 95.392 2257 80 10 1 2235 700669614 700671868 0.000000e+00 3570
13 TraesCS3B01G348400 chr2B 90.505 495 18 8 1 495 796942831 796943296 6.550000e-176 627
14 TraesCS3B01G348400 chr2B 89.516 496 22 9 1 495 750608093 750608559 3.970000e-168 601
15 TraesCS3B01G348400 chrUn 95.902 2123 55 11 1 2113 236924716 236926816 0.000000e+00 3410
16 TraesCS3B01G348400 chrUn 93.744 2094 83 11 724 2786 290561338 290559262 0.000000e+00 3097
17 TraesCS3B01G348400 chrUn 95.350 1527 42 8 1 1520 35192606 35191102 0.000000e+00 2399
18 TraesCS3B01G348400 chrUn 89.495 495 23 3 1 495 290561792 290561327 1.430000e-167 599
19 TraesCS3B01G348400 chrUn 96.135 207 8 0 1 207 264980718 264980924 3.440000e-89 339
20 TraesCS3B01G348400 chrUn 96.875 192 5 1 304 495 264980973 264981163 1.250000e-83 320
21 TraesCS3B01G348400 chr4B 94.556 2094 67 10 725 2786 668352629 668350551 0.000000e+00 3192
22 TraesCS3B01G348400 chr4B 94.286 1785 84 5 1 1768 263067658 263065875 0.000000e+00 2715
23 TraesCS3B01G348400 chr4B 89.600 500 18 5 1 495 668353089 668352619 3.070000e-169 604
24 TraesCS3B01G348400 chr4B 93.953 215 9 1 1 215 613127412 613127622 3.460000e-84 322
25 TraesCS3B01G348400 chr7B 94.012 1386 51 9 1432 2786 749266896 749268280 0.000000e+00 2071
26 TraesCS3B01G348400 chr6B 89.113 496 12 4 1 495 630184798 630184344 1.860000e-161 579
27 TraesCS3B01G348400 chr3D 97.000 200 6 0 263 462 330477837 330477638 1.240000e-88 337
28 TraesCS3B01G348400 chr3D 91.176 204 10 3 1 200 57605980 57606179 1.270000e-68 270
29 TraesCS3B01G348400 chr4D 96.000 200 8 0 263 462 222630779 222630580 2.680000e-85 326
30 TraesCS3B01G348400 chr4D 92.019 213 9 4 1 209 125862128 125861920 2.710000e-75 292
31 TraesCS3B01G348400 chr4D 92.157 204 8 3 1 200 125871860 125872059 5.880000e-72 281
32 TraesCS3B01G348400 chr4D 90.686 204 11 3 1 200 261240324 261240125 5.920000e-67 265
33 TraesCS3B01G348400 chr4D 88.263 213 11 6 1 209 125937716 125937514 2.770000e-60 243
34 TraesCS3B01G348400 chr6D 95.000 200 10 0 263 462 46527962 46527763 5.790000e-82 315
35 TraesCS3B01G348400 chr6D 86.224 196 13 4 1 192 297180008 297179823 1.690000e-47 200
36 TraesCS3B01G348400 chr1D 89.732 224 10 8 1 215 428056569 428056350 9.830000e-70 274


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 TraesCS3B01G348400 chr3B 557704315 557707100 2785 False 5145 5145 100.0000 1 2786 1 chr3B.!!$F1 2785
1 TraesCS3B01G348400 chr3B 751897825 751900620 2795 True 4329 4329 94.7110 1 2786 1 chr3B.!!$R2 2785
2 TraesCS3B01G348400 chr3B 766268394 766270483 2089 False 3212 3212 94.6460 724 2783 1 chr3B.!!$F2 2059
3 TraesCS3B01G348400 chr4A 660540612 660543366 2754 False 4301 4301 95.0290 61 2786 1 chr4A.!!$F1 2725
4 TraesCS3B01G348400 chr5B 492518226 492520713 2487 True 3840 3840 94.7050 324 2786 1 chr5B.!!$R1 2462
5 TraesCS3B01G348400 chr1B 627375972 627378457 2485 True 3825 3825 94.4940 309 2786 1 chr1B.!!$R2 2477
6 TraesCS3B01G348400 chr1B 600344983 600347847 2864 True 2069 3807 93.9275 1 2786 2 chr1B.!!$R3 2785
7 TraesCS3B01G348400 chr1B 6174572 6175724 1152 False 1905 1905 96.5370 1637 2786 1 chr1B.!!$F1 1149
8 TraesCS3B01G348400 chr2B 700669614 700671868 2254 False 3570 3570 95.3920 1 2235 1 chr2B.!!$F1 2234
9 TraesCS3B01G348400 chrUn 236924716 236926816 2100 False 3410 3410 95.9020 1 2113 1 chrUn.!!$F1 2112
10 TraesCS3B01G348400 chrUn 35191102 35192606 1504 True 2399 2399 95.3500 1 1520 1 chrUn.!!$R1 1519
11 TraesCS3B01G348400 chrUn 290559262 290561792 2530 True 1848 3097 91.6195 1 2786 2 chrUn.!!$R2 2785
12 TraesCS3B01G348400 chr4B 263065875 263067658 1783 True 2715 2715 94.2860 1 1768 1 chr4B.!!$R1 1767
13 TraesCS3B01G348400 chr4B 668350551 668353089 2538 True 1898 3192 92.0780 1 2786 2 chr4B.!!$R2 2785
14 TraesCS3B01G348400 chr7B 749266896 749268280 1384 False 2071 2071 94.0120 1432 2786 1 chr7B.!!$F1 1354

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
645 734 1.214175 TCTGAAACTTGGGCCTGTTCA 59.786 47.619 4.53 8.19 0.0 3.18 F
1446 1544 1.135915 CGATGCCAGTAAGCTCTCTGT 59.864 52.381 14.24 0.25 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1481 1579 0.168788 CATGGTGTTGTCGTCATGCC 59.831 55.0 0.0 0.0 32.04 4.40 R
2614 2850 2.617276 CCATCACAAGACAGAGGCATGT 60.617 50.0 0.0 0.0 35.68 3.21 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
138 139 1.266178 TGAATCCGCTGACTCCTTCA 58.734 50.000 0.00 0.00 0.00 3.02
274 322 7.715266 AGATTAGGGTTCTTTTAGTACGAGT 57.285 36.000 0.00 0.00 0.00 4.18
349 416 7.554118 GGTTACCATGTAGTACTGTACTAGTGA 59.446 40.741 24.09 14.04 41.59 3.41
445 534 7.814264 AATTAAAGTATCAGGAATGCTCAGG 57.186 36.000 0.00 0.00 28.96 3.86
532 621 8.061920 TGGGGTTACATTTTGATATACCATCAA 58.938 33.333 0.00 0.00 36.37 2.57
596 685 6.261381 GGTTGTGTAAGATTTGTTGGTGTCTA 59.739 38.462 0.00 0.00 0.00 2.59
645 734 1.214175 TCTGAAACTTGGGCCTGTTCA 59.786 47.619 4.53 8.19 0.00 3.18
674 763 9.496873 TTCATTTTTAGTCGAGATAAGTTTCCA 57.503 29.630 0.00 0.00 0.00 3.53
901 998 3.617706 TGCTGTTGCTGTTGATGTTTTTG 59.382 39.130 0.00 0.00 40.48 2.44
906 1003 2.168106 TGCTGTTGATGTTTTTGCCACT 59.832 40.909 0.00 0.00 0.00 4.00
966 1064 5.105310 TCCTATTTCTGTCTAGTCCTGTTGC 60.105 44.000 0.00 0.00 0.00 4.17
1008 1106 1.829849 CAGAGAAGTGAGATGGCTGGA 59.170 52.381 0.00 0.00 0.00 3.86
1358 1456 1.684450 TCCTTGTGTTCTGCTACGACA 59.316 47.619 0.00 0.00 0.00 4.35
1390 1488 2.798283 GTTCACCGTGAAGATGTTCGAA 59.202 45.455 14.35 0.00 37.00 3.71
1446 1544 1.135915 CGATGCCAGTAAGCTCTCTGT 59.864 52.381 14.24 0.25 0.00 3.41
1481 1579 1.278127 TCCTTTTGGCTTCCTCTACCG 59.722 52.381 0.00 0.00 40.12 4.02
1485 1583 1.271840 TTGGCTTCCTCTACCGGCAT 61.272 55.000 0.00 0.00 0.00 4.40
1520 1618 5.752472 CCATGTTCACACTTTGTTGCATTTA 59.248 36.000 0.00 0.00 0.00 1.40
1552 1650 4.783621 GCAGCAGCGGGGATGACA 62.784 66.667 0.00 0.00 0.00 3.58
1843 2049 3.385749 ATCCGCGTTGGGATTCGCT 62.386 57.895 4.92 0.00 44.44 4.93
1852 2058 2.145397 TGGGATTCGCTACTCTGAGT 57.855 50.000 15.57 15.57 0.00 3.41
2113 2344 0.031857 TGGGTTTTTGTGCATGCTCG 59.968 50.000 20.33 0.00 0.00 5.03
2115 2346 1.537990 GGGTTTTTGTGCATGCTCGTT 60.538 47.619 20.33 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 2.504244 GAGTGGTTCGCCGTCGAG 60.504 66.667 0.00 0.00 46.34 4.04
76 77 2.052690 CCGTCGATGGAGGAGTGGT 61.053 63.158 19.48 0.00 0.00 4.16
249 297 8.814038 ACTCGTACTAAAAGAACCCTAATCTA 57.186 34.615 0.00 0.00 0.00 1.98
274 322 5.705441 CAGAAACACCAATTAGCTACTCCAA 59.295 40.000 0.00 0.00 0.00 3.53
327 394 7.120873 CACTTCACTAGTACAGTACTACATGGT 59.879 40.741 15.43 9.76 40.14 3.55
349 416 3.290948 TGGCAAGTCAAACCTACACTT 57.709 42.857 0.00 0.00 0.00 3.16
532 621 1.545651 GCCAGCAGACAACCTAAACCT 60.546 52.381 0.00 0.00 0.00 3.50
674 763 3.756933 ATGCTTTCAAACAGCCAACAT 57.243 38.095 0.00 0.00 36.33 2.71
966 1064 8.746922 TCTGAAAAGCAGCATTGTAAATTAAG 57.253 30.769 0.00 0.00 44.52 1.85
1154 1252 1.001487 CTTCGCAAACATGTCAGGCAA 60.001 47.619 14.26 8.23 0.00 4.52
1358 1456 2.742372 GGTGAACATGGCGTCGCT 60.742 61.111 18.11 0.00 0.00 4.93
1390 1488 3.776158 ATGCGGCACATGGTGTTT 58.224 50.000 4.03 0.00 37.70 2.83
1446 1544 4.040952 CCAAAAGGACAGGAAGAAGAGAGA 59.959 45.833 0.00 0.00 0.00 3.10
1481 1579 0.168788 CATGGTGTTGTCGTCATGCC 59.831 55.000 0.00 0.00 32.04 4.40
1485 1583 1.937223 GTGAACATGGTGTTGTCGTCA 59.063 47.619 0.00 0.00 41.28 4.35
1552 1650 2.366167 ATCCCCGCTCTGCTCCTT 60.366 61.111 0.00 0.00 0.00 3.36
1783 1989 3.075005 GGTCCTGTCGCCCAGCTA 61.075 66.667 0.00 0.00 40.06 3.32
2614 2850 2.617276 CCATCACAAGACAGAGGCATGT 60.617 50.000 0.00 0.00 35.68 3.21
2623 2859 3.384146 ACATTGTTTGCCATCACAAGACA 59.616 39.130 0.00 0.00 36.36 3.41


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

AutoCloner maintained by Alex Coulton.