Multiple sequence alignment - TraesCS1B01G214600

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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 TraesCS1B01G214600 chr1B 100.000 2189 0 0 1 2189 389551532 389553720 0.000000e+00 4043
1 TraesCS1B01G214600 chr1B 87.015 593 56 15 698 1276 389225004 389224419 0.000000e+00 649
2 TraesCS1B01G214600 chr1B 79.452 438 54 24 1451 1866 389224130 389223707 5.950000e-71 278
3 TraesCS1B01G214600 chr1B 82.857 245 26 8 1954 2189 389568285 389568522 2.850000e-49 206
4 TraesCS1B01G214600 chr1D 95.547 2201 72 14 1 2189 288081691 288083877 0.000000e+00 3498
5 TraesCS1B01G214600 chr1D 87.772 597 44 12 698 1274 287468288 287467701 0.000000e+00 671
6 TraesCS1B01G214600 chr1D 78.172 536 60 25 1660 2183 287467153 287466663 2.750000e-74 289
7 TraesCS1B01G214600 chr1D 75.595 336 49 27 377 702 100349686 100349998 3.790000e-28 135
8 TraesCS1B01G214600 chr1A 93.114 1670 71 13 546 2187 359228544 359230197 0.000000e+00 2407
9 TraesCS1B01G214600 chr1A 91.585 511 42 1 1 511 359228032 359228541 0.000000e+00 704
10 TraesCS1B01G214600 chr1A 86.921 604 43 12 698 1274 358772062 358771468 0.000000e+00 645
11 TraesCS1B01G214600 chr1A 89.118 340 37 0 1 340 566658916 566659255 7.220000e-115 424
12 TraesCS1B01G214600 chr1A 77.716 543 66 24 1660 2189 358770920 358770420 4.600000e-72 281
13 TraesCS1B01G214600 chr1A 86.391 169 23 0 1001 1169 458220109 458219941 3.710000e-43 185
14 TraesCS1B01G214600 chr1A 82.063 223 19 13 1451 1658 358771176 358770960 1.040000e-38 171
15 TraesCS1B01G214600 chr5A 89.415 359 34 3 1 359 345237149 345236795 1.190000e-122 449
16 TraesCS1B01G214600 chr5A 89.806 206 15 4 988 1192 678932021 678932221 2.160000e-65 259
17 TraesCS1B01G214600 chr2A 89.744 351 32 3 1 349 3883209 3883557 1.540000e-121 446
18 TraesCS1B01G214600 chr7B 89.143 350 37 1 1 349 152488744 152489093 3.340000e-118 435
19 TraesCS1B01G214600 chr4D 89.174 351 34 2 1 347 455347990 455348340 3.340000e-118 435
20 TraesCS1B01G214600 chr4D 89.213 343 37 0 1 343 66566800 66567142 1.550000e-116 429
21 TraesCS1B01G214600 chr4D 90.625 192 15 1 1001 1192 498384553 498384741 3.610000e-63 252
22 TraesCS1B01G214600 chr3D 88.636 352 37 1 1 349 516967664 516968015 2.010000e-115 425
23 TraesCS1B01G214600 chr4B 90.291 206 14 4 988 1192 640290049 640290249 4.630000e-67 265
24 TraesCS1B01G214600 chr7D 79.365 315 47 16 400 704 436107521 436107215 2.850000e-49 206
25 TraesCS1B01G214600 chr4A 78.249 354 48 15 352 699 706847918 706847588 1.330000e-47 200
26 TraesCS1B01G214600 chr3B 78.571 308 49 13 400 699 247500795 247500497 1.030000e-43 187


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 TraesCS1B01G214600 chr1B 389551532 389553720 2188 False 4043.000000 4043 100.000000 1 2189 1 chr1B.!!$F1 2188
1 TraesCS1B01G214600 chr1B 389223707 389225004 1297 True 463.500000 649 83.233500 698 1866 2 chr1B.!!$R1 1168
2 TraesCS1B01G214600 chr1D 288081691 288083877 2186 False 3498.000000 3498 95.547000 1 2189 1 chr1D.!!$F2 2188
3 TraesCS1B01G214600 chr1D 287466663 287468288 1625 True 480.000000 671 82.972000 698 2183 2 chr1D.!!$R1 1485
4 TraesCS1B01G214600 chr1A 359228032 359230197 2165 False 1555.500000 2407 92.349500 1 2187 2 chr1A.!!$F2 2186
5 TraesCS1B01G214600 chr1A 358770420 358772062 1642 True 365.666667 645 82.233333 698 2189 3 chr1A.!!$R2 1491

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
100 101 0.11456 TTCTCCTCCCTCTTGACGGT 59.885 55.0 0.0 0.0 0.0 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 1857 0.027455 CGCCTGCGCATTAATTTCGA 59.973 50.0 12.24 0.0 34.03 3.71 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
96 97 2.111384 CGGATTTCTCCTCCCTCTTGA 58.889 52.381 0.00 0.00 39.65 3.02
100 101 0.114560 TTCTCCTCCCTCTTGACGGT 59.885 55.000 0.00 0.00 0.00 4.83
255 256 0.682852 CGGGTTGTAGGTGTCCTTCA 59.317 55.000 0.00 0.00 34.61 3.02
269 270 0.538057 CCTTCACCTTGGCAAGAGCA 60.538 55.000 28.18 9.93 44.61 4.26
277 278 3.981308 GGCAAGAGCAAGCCGTAA 58.019 55.556 0.00 0.00 44.61 3.18
292 293 2.159198 GCCGTAACTCCGTCCATTTCTA 60.159 50.000 0.00 0.00 0.00 2.10
307 308 1.022735 TTCTAGCACGACTCGATCCC 58.977 55.000 5.20 0.00 0.00 3.85
326 327 2.436417 CCGGTGAACACATGAAGGAAT 58.564 47.619 0.00 0.00 0.00 3.01
471 472 2.044492 GGAGGGAAAGGGGGAAGAAAAT 59.956 50.000 0.00 0.00 0.00 1.82
564 565 4.776322 CCCGATGCGCTGGGTTCA 62.776 66.667 20.51 0.00 40.76 3.18
566 567 2.125552 CGATGCGCTGGGTTCAGA 60.126 61.111 9.73 0.00 43.49 3.27
629 630 4.933064 GGATCTCGGACGCGGCTG 62.933 72.222 16.77 16.77 0.00 4.85
905 929 1.287425 CCGGCTCGAATTTACTCACC 58.713 55.000 0.00 0.00 0.00 4.02
929 953 1.144565 TCGTTCGTTTTTCACCGCGA 61.145 50.000 8.23 0.00 0.00 5.87
1110 1143 2.103340 GCCTTCGAGCTCTCCGTC 59.897 66.667 12.85 0.00 0.00 4.79
1177 1210 0.811915 GCTCTACGAGTTCTCCAGCA 59.188 55.000 0.00 0.00 31.39 4.41
1282 1384 1.080569 GGTTCATGGGCGTTTGCAG 60.081 57.895 0.00 0.00 45.35 4.41
1395 1500 2.030274 ACGGGCTAATCAAAAAGCACAC 60.030 45.455 0.00 0.00 42.46 3.82
1427 1539 0.799393 GCTCTTCCTTTTGTCTCCGC 59.201 55.000 0.00 0.00 0.00 5.54
1563 1767 0.665369 TCTCCGTTCTTTCCGTTCGC 60.665 55.000 0.00 0.00 0.00 4.70
1644 1855 0.323360 GGCAGTACATGGAGCCCAAA 60.323 55.000 0.00 0.00 41.25 3.28
1646 1857 1.614317 GCAGTACATGGAGCCCAAAGT 60.614 52.381 0.00 3.64 36.95 2.66
1658 1869 4.105486 GAGCCCAAAGTCGAAATTAATGC 58.895 43.478 0.00 0.00 0.00 3.56
1720 1969 2.474816 GCTACGGCTACAAATGGAGAG 58.525 52.381 0.00 0.00 35.22 3.20
1916 2172 2.202878 GCCTGCGATTCGGCTGTA 60.203 61.111 8.34 0.00 42.98 2.74
2079 2340 7.184106 TCACATTTGACGAGTTTTAGTTTCAC 58.816 34.615 0.00 0.00 0.00 3.18
2080 2341 6.413818 CACATTTGACGAGTTTTAGTTTCACC 59.586 38.462 0.00 0.00 0.00 4.02
2122 2387 3.810687 TTGTCCTGGGCCTGGAGGT 62.811 63.158 30.29 0.00 37.57 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.516586 TGACCTTCTCAGGACCAACATA 58.483 45.455 0.00 0.00 44.19 2.29
13 14 1.801242 TGACCTTCTCAGGACCAACA 58.199 50.000 0.00 0.00 44.19 3.33
96 97 2.972505 CGCCAAGAGCAACACCGT 60.973 61.111 0.00 0.00 44.04 4.83
100 101 2.664851 CCGACGCCAAGAGCAACA 60.665 61.111 0.00 0.00 44.04 3.33
255 256 3.769201 GCTTGCTCTTGCCAAGGT 58.231 55.556 4.30 0.00 38.71 3.50
292 293 3.518998 CCGGGATCGAGTCGTGCT 61.519 66.667 13.12 0.00 39.00 4.40
307 308 4.023279 TCAAATTCCTTCATGTGTTCACCG 60.023 41.667 0.37 0.00 0.00 4.94
326 327 0.179067 ACGGCGACCAAGAGTTCAAA 60.179 50.000 16.62 0.00 0.00 2.69
364 365 0.746204 TGCCGCCGAAGAAATATGCA 60.746 50.000 0.00 0.00 0.00 3.96
549 550 1.091771 AATCTGAACCCAGCGCATCG 61.092 55.000 11.47 0.00 40.20 3.84
551 552 1.033746 CCAATCTGAACCCAGCGCAT 61.034 55.000 11.47 0.00 40.20 4.73
660 661 2.355837 TCAACAGGCTCACGACGC 60.356 61.111 0.00 0.00 0.00 5.19
663 664 2.583441 CCCCTCAACAGGCTCACGA 61.583 63.158 0.00 0.00 38.72 4.35
665 666 2.360475 GCCCCTCAACAGGCTCAC 60.360 66.667 0.00 0.00 46.14 3.51
905 929 3.596562 GCGGTGAAAAACGAACGAATTAG 59.403 43.478 0.14 0.00 0.00 1.73
929 953 3.751175 CGGACCAATCAACAACTACACAT 59.249 43.478 0.00 0.00 0.00 3.21
1282 1384 1.137404 CTAATGGCAACCGCAGCAC 59.863 57.895 0.00 0.00 41.24 4.40
1395 1500 2.093553 AGGAAGAGCAAGCTAGCAAGAG 60.094 50.000 18.83 4.43 36.85 2.85
1427 1539 1.956170 GTGTGGCGTGTGTGAGAGG 60.956 63.158 0.00 0.00 0.00 3.69
1563 1767 0.318275 GAATCGCTACCGCCTCTGAG 60.318 60.000 0.00 0.00 0.00 3.35
1627 1831 2.359900 GACTTTGGGCTCCATGTACTG 58.640 52.381 0.00 0.00 31.53 2.74
1644 1855 1.064060 GCCTGCGCATTAATTTCGACT 59.936 47.619 12.24 0.00 34.03 4.18
1646 1857 0.027455 CGCCTGCGCATTAATTTCGA 59.973 50.000 12.24 0.00 34.03 3.71
1720 1969 5.572896 GTCCGGACATCACATGAAATTTTTC 59.427 40.000 29.75 0.00 37.69 2.29
1869 2125 6.535150 CCTCGAACAGAACTGATGCTATTAAA 59.465 38.462 8.87 0.00 0.00 1.52
1904 2160 2.900528 GGGTCATACAGCCGAATCG 58.099 57.895 0.00 0.00 31.27 3.34
2079 2340 1.151668 CAGTTTTCCTGCTCACGAGG 58.848 55.000 0.00 0.00 33.59 4.63
2106 2367 2.081585 AAAACCTCCAGGCCCAGGAC 62.082 60.000 18.00 0.00 39.32 3.85


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

AutoCloner maintained by Alex Coulton.