Multiple sequence alignment - TraesCS3B01G216700

Loading Multiple Alignment...

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 TraesCS3B01G216700 chr3B 100.000 2336 0 0 1 2336 257549135 257546800 0.000000e+00 4314
1 TraesCS3B01G216700 chr3B 99.735 755 2 0 1582 2336 254161249 254162003 0.000000e+00 1384
2 TraesCS3B01G216700 chr3B 99.602 754 3 0 1583 2336 236939682 236940435 0.000000e+00 1376
3 TraesCS3B01G216700 chr3B 99.602 754 3 0 1583 2336 250852724 250851971 0.000000e+00 1376
4 TraesCS3B01G216700 chr3B 99.602 754 3 0 1583 2336 250893884 250893131 0.000000e+00 1376
5 TraesCS3B01G216700 chr3B 99.470 755 4 0 1582 2336 258990951 258990197 0.000000e+00 1373
6 TraesCS3B01G216700 chr3B 99.469 754 4 0 1583 2336 250859560 250858807 0.000000e+00 1371
7 TraesCS3B01G216700 chr3B 99.469 754 4 0 1583 2336 254418458 254419211 0.000000e+00 1371
8 TraesCS3B01G216700 chr3B 99.469 754 4 0 1583 2336 261950555 261949802 0.000000e+00 1371
9 TraesCS3B01G216700 chr3B 99.337 754 5 0 1583 2336 245766084 245766837 0.000000e+00 1365
10 TraesCS3B01G216700 chr6B 95.403 1588 68 2 1 1583 460300398 460298811 0.000000e+00 2523
11 TraesCS3B01G216700 chr6B 94.579 1605 63 6 1 1583 281828590 281826988 0.000000e+00 2460
12 TraesCS3B01G216700 chr6B 84.469 1262 152 25 2 1239 327557454 327558695 0.000000e+00 1205
13 TraesCS3B01G216700 chr7D 95.087 1486 64 5 1 1483 213609593 213608114 0.000000e+00 2331
14 TraesCS3B01G216700 chr7D 95.890 73 3 0 1511 1583 213608112 213608040 4.080000e-23 119
15 TraesCS3B01G216700 chr6A 89.241 1608 133 13 1 1583 39927646 39926054 0.000000e+00 1975
16 TraesCS3B01G216700 chr4B 82.360 1610 186 34 2 1583 300483880 300482341 0.000000e+00 1310
17 TraesCS3B01G216700 chr4D 87.682 1031 100 8 572 1583 239764364 239765386 0.000000e+00 1175
18 TraesCS3B01G216700 chr4A 88.972 934 88 9 38 959 228656700 228657630 0.000000e+00 1140
19 TraesCS3B01G216700 chr4A 82.460 821 106 20 2 803 334265549 334266350 0.000000e+00 684
20 TraesCS3B01G216700 chr4A 86.653 472 46 10 1128 1583 228657844 228658314 7.450000e-140 507
21 TraesCS3B01G216700 chr4A 85.327 443 51 8 800 1239 334267177 334267608 1.650000e-121 446
22 TraesCS3B01G216700 chr4A 83.794 253 28 6 1269 1510 334267608 334267858 6.490000e-56 228
23 TraesCS3B01G216700 chr2D 79.886 527 82 19 922 1440 413281278 413280768 4.740000e-97 364
24 TraesCS3B01G216700 chr7B 79.576 519 78 20 932 1440 192739913 192740413 1.720000e-91 346
25 TraesCS3B01G216700 chr2A 78.070 570 99 18 882 1440 266135903 266136457 1.030000e-88 337
26 TraesCS3B01G216700 chr7A 78.053 565 98 18 885 1440 399875585 399875038 1.340000e-87 333
27 TraesCS3B01G216700 chr5B 90.625 128 12 0 458 585 330122381 330122508 1.110000e-38 171
28 TraesCS3B01G216700 chr5B 89.844 128 13 0 458 585 330431937 330432064 5.160000e-37 165


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 TraesCS3B01G216700 chr3B 257546800 257549135 2335 True 4314.000000 4314 100.000000 1 2336 1 chr3B.!!$R4 2335
1 TraesCS3B01G216700 chr3B 254161249 254162003 754 False 1384.000000 1384 99.735000 1582 2336 1 chr3B.!!$F3 754
2 TraesCS3B01G216700 chr3B 236939682 236940435 753 False 1376.000000 1376 99.602000 1583 2336 1 chr3B.!!$F1 753
3 TraesCS3B01G216700 chr3B 250851971 250852724 753 True 1376.000000 1376 99.602000 1583 2336 1 chr3B.!!$R1 753
4 TraesCS3B01G216700 chr3B 250893131 250893884 753 True 1376.000000 1376 99.602000 1583 2336 1 chr3B.!!$R3 753
5 TraesCS3B01G216700 chr3B 258990197 258990951 754 True 1373.000000 1373 99.470000 1582 2336 1 chr3B.!!$R5 754
6 TraesCS3B01G216700 chr3B 250858807 250859560 753 True 1371.000000 1371 99.469000 1583 2336 1 chr3B.!!$R2 753
7 TraesCS3B01G216700 chr3B 254418458 254419211 753 False 1371.000000 1371 99.469000 1583 2336 1 chr3B.!!$F4 753
8 TraesCS3B01G216700 chr3B 261949802 261950555 753 True 1371.000000 1371 99.469000 1583 2336 1 chr3B.!!$R6 753
9 TraesCS3B01G216700 chr3B 245766084 245766837 753 False 1365.000000 1365 99.337000 1583 2336 1 chr3B.!!$F2 753
10 TraesCS3B01G216700 chr6B 460298811 460300398 1587 True 2523.000000 2523 95.403000 1 1583 1 chr6B.!!$R2 1582
11 TraesCS3B01G216700 chr6B 281826988 281828590 1602 True 2460.000000 2460 94.579000 1 1583 1 chr6B.!!$R1 1582
12 TraesCS3B01G216700 chr6B 327557454 327558695 1241 False 1205.000000 1205 84.469000 2 1239 1 chr6B.!!$F1 1237
13 TraesCS3B01G216700 chr7D 213608040 213609593 1553 True 1225.000000 2331 95.488500 1 1583 2 chr7D.!!$R1 1582
14 TraesCS3B01G216700 chr6A 39926054 39927646 1592 True 1975.000000 1975 89.241000 1 1583 1 chr6A.!!$R1 1582
15 TraesCS3B01G216700 chr4B 300482341 300483880 1539 True 1310.000000 1310 82.360000 2 1583 1 chr4B.!!$R1 1581
16 TraesCS3B01G216700 chr4D 239764364 239765386 1022 False 1175.000000 1175 87.682000 572 1583 1 chr4D.!!$F1 1011
17 TraesCS3B01G216700 chr4A 228656700 228658314 1614 False 823.500000 1140 87.812500 38 1583 2 chr4A.!!$F1 1545
18 TraesCS3B01G216700 chr4A 334265549 334267858 2309 False 452.666667 684 83.860333 2 1510 3 chr4A.!!$F2 1508
19 TraesCS3B01G216700 chr2D 413280768 413281278 510 True 364.000000 364 79.886000 922 1440 1 chr2D.!!$R1 518
20 TraesCS3B01G216700 chr7B 192739913 192740413 500 False 346.000000 346 79.576000 932 1440 1 chr7B.!!$F1 508
21 TraesCS3B01G216700 chr2A 266135903 266136457 554 False 337.000000 337 78.070000 882 1440 1 chr2A.!!$F1 558
22 TraesCS3B01G216700 chr7A 399875038 399875585 547 True 333.000000 333 78.053000 885 1440 1 chr7A.!!$R1 555

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
51 52 0.878523 CGTTCTTCCTCCGCACAACA 60.879 55.000 0.0 0.0 0.0 3.33 F
114 115 0.900421 GTTCAGTAGTACGCCCCCTT 59.100 55.000 0.0 0.0 0.0 3.95 F
145 153 1.134220 TCCTTGTTTGTTCCTCGCTGT 60.134 47.619 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1291 2286 0.482446 TGGAACCCCAAACAGCTCAT 59.518 50.000 0.00 0.0 40.09 2.90 R
1318 2314 2.357009 GACATCATGACCCACATTCTGC 59.643 50.000 0.00 0.0 37.07 4.26 R
1538 2620 3.748083 TGAAGGGATGCATGATCTAAGC 58.252 45.455 2.46 0.0 0.00 3.09 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
49 50 1.301401 CCGTTCTTCCTCCGCACAA 60.301 57.895 0.00 0.0 0.00 3.33
51 52 0.878523 CGTTCTTCCTCCGCACAACA 60.879 55.000 0.00 0.0 0.00 3.33
69 70 3.165160 AAGGGACGACGCAAGCACT 62.165 57.895 4.64 0.0 45.62 4.40
114 115 0.900421 GTTCAGTAGTACGCCCCCTT 59.100 55.000 0.00 0.0 0.00 3.95
143 151 2.154462 CATCCTTGTTTGTTCCTCGCT 58.846 47.619 0.00 0.0 0.00 4.93
145 153 1.134220 TCCTTGTTTGTTCCTCGCTGT 60.134 47.619 0.00 0.0 0.00 4.40
147 155 1.939934 CTTGTTTGTTCCTCGCTGTCA 59.060 47.619 0.00 0.0 0.00 3.58
204 212 4.555709 AGGCACCGACCAACGCAA 62.556 61.111 0.00 0.0 41.07 4.85
280 296 1.404181 CCTCTCCAAAATCGCGAGTCA 60.404 52.381 16.66 0.0 0.00 3.41
657 698 6.801539 TGTTAACATGAGAACAATCTGACC 57.198 37.500 3.59 0.0 35.54 4.02
698 739 2.957402 TCCACAGTGCCTCAAAAGAT 57.043 45.000 0.00 0.0 0.00 2.40
890 1764 4.126520 TCCAAACAGGCCCTTAGATTTT 57.873 40.909 0.00 0.0 37.29 1.82
1089 2053 2.561478 TTTGCTTAGTGTGTCCCCTC 57.439 50.000 0.00 0.0 0.00 4.30
1108 2100 3.323403 CCTCCTCTCTCTCTCTCTCTCTC 59.677 56.522 0.00 0.0 0.00 3.20
1109 2101 4.222336 CTCCTCTCTCTCTCTCTCTCTCT 58.778 52.174 0.00 0.0 0.00 3.10
1110 2102 4.219115 TCCTCTCTCTCTCTCTCTCTCTC 58.781 52.174 0.00 0.0 0.00 3.20
1111 2103 4.078922 TCCTCTCTCTCTCTCTCTCTCTCT 60.079 50.000 0.00 0.0 0.00 3.10
1112 2104 4.280677 CCTCTCTCTCTCTCTCTCTCTCTC 59.719 54.167 0.00 0.0 0.00 3.20
1114 2106 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.0 0.00 3.20
1116 2108 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.0 0.00 3.20
1117 2109 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.0 0.00 3.10
1118 2110 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.0 0.00 3.20
1120 2112 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.0 0.00 3.20
1318 2314 3.292460 TGTTTGGGGTTCCAGTTTAGTG 58.708 45.455 0.00 0.0 45.04 2.74
1381 2389 7.584847 AACATGAAAGTTGTTTGACGTTATACG 59.415 33.333 0.00 0.0 39.76 3.06
1483 2501 0.255318 CTGGCAGGCTCATCTTTCCT 59.745 55.000 6.61 0.0 0.00 3.36
2046 3128 3.052944 AGGTACATGTTGGGTTGGCATAT 60.053 43.478 2.30 0.0 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 2.665185 GCTTGCGTCGTCCCTTGT 60.665 61.111 0.00 0.00 0.00 3.16
51 52 2.665185 GTGCTTGCGTCGTCCCTT 60.665 61.111 0.00 0.00 0.00 3.95
69 70 2.609299 TTGAGGACGGGGGCATCA 60.609 61.111 0.00 0.00 0.00 3.07
114 115 0.984230 AAACAAGGATGAGCGAGGGA 59.016 50.000 0.00 0.00 0.00 4.20
215 223 2.281484 GGTTGAGGCGCTGGTTGA 60.281 61.111 7.64 0.00 0.00 3.18
280 296 1.269206 CGCAAATCAAACACTGGCAGT 60.269 47.619 15.88 15.88 0.00 4.40
349 366 6.013898 TGCAAATAATGTCCATGAAAAAGGGA 60.014 34.615 0.00 0.00 36.03 4.20
657 698 5.851177 GGATATAAATTGGAAATGTGACGCG 59.149 40.000 3.53 3.53 0.00 6.01
869 1743 3.825908 AAATCTAAGGGCCTGTTTGGA 57.174 42.857 6.92 0.00 38.35 3.53
890 1764 3.598299 TCAATGATGCGTGTGAATCAGA 58.402 40.909 0.00 0.00 43.51 3.27
1089 2053 4.222336 AGAGAGAGAGAGAGAGAGAGAGG 58.778 52.174 0.00 0.00 0.00 3.69
1108 2100 1.064505 CGCAAGCAGAGAGAGAGAGAG 59.935 57.143 0.00 0.00 0.00 3.20
1109 2101 1.093972 CGCAAGCAGAGAGAGAGAGA 58.906 55.000 0.00 0.00 0.00 3.10
1110 2102 3.628005 CGCAAGCAGAGAGAGAGAG 57.372 57.895 0.00 0.00 0.00 3.20
1291 2286 0.482446 TGGAACCCCAAACAGCTCAT 59.518 50.000 0.00 0.00 40.09 2.90
1318 2314 2.357009 GACATCATGACCCACATTCTGC 59.643 50.000 0.00 0.00 37.07 4.26
1381 2389 8.713271 GTTTCATGGCTTATAGAGTAGCATTAC 58.287 37.037 0.00 0.00 39.15 1.89
1538 2620 3.748083 TGAAGGGATGCATGATCTAAGC 58.252 45.455 2.46 0.00 0.00 3.09
2046 3128 6.106673 GGAGTGACAAATCCTAATCTCGAAA 58.893 40.000 1.45 0.00 32.51 3.46


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

AutoCloner maintained by Alex Coulton.