Multiple sequence alignment - TraesCS1A01G163800

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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 TraesCS1A01G163800 chr1A 100.000 2435 0 0 1 2435 295023968 295021534 0.000000e+00 4497.0
1 TraesCS1A01G163800 chr1A 93.653 646 41 0 1790 2435 487209695 487210340 0.000000e+00 966.0
2 TraesCS1A01G163800 chr1A 95.192 312 15 0 83 394 295022176 295022487 6.050000e-136 494.0
3 TraesCS1A01G163800 chr1A 95.192 312 15 0 1482 1793 295023575 295023886 6.050000e-136 494.0
4 TraesCS1A01G163800 chr6A 95.138 1090 44 4 409 1491 203599965 203598878 0.000000e+00 1711.0
5 TraesCS1A01G163800 chr6A 95.046 646 32 0 1790 2435 309761662 309761017 0.000000e+00 1016.0
6 TraesCS1A01G163800 chr6A 93.944 644 38 1 1792 2435 396024218 396024860 0.000000e+00 972.0
7 TraesCS1A01G163800 chr6A 93.811 307 17 2 83 388 203597968 203598273 6.130000e-126 460.0
8 TraesCS1A01G163800 chr6A 92.994 314 20 2 1481 1793 203598280 203597968 7.940000e-125 457.0
9 TraesCS1A01G163800 chr6A 96.591 88 1 2 1 87 203600052 203599966 7.020000e-31 145.0
10 TraesCS1A01G163800 chr2A 95.046 646 32 0 1790 2435 614515965 614516610 0.000000e+00 1016.0
11 TraesCS1A01G163800 chr7A 94.272 646 37 0 1790 2435 497018891 497018246 0.000000e+00 989.0
12 TraesCS1A01G163800 chr7A 93.529 649 39 1 1790 2435 490883803 490883155 0.000000e+00 963.0
13 TraesCS1A01G163800 chr4A 93.963 646 39 0 1790 2435 555425132 555425777 0.000000e+00 977.0
14 TraesCS1A01G163800 chr6D 93.683 649 35 2 1790 2435 122531785 122532430 0.000000e+00 966.0
15 TraesCS1A01G163800 chr3D 93.529 649 39 1 1790 2435 8004460 8003812 0.000000e+00 963.0
16 TraesCS1A01G163800 chr6B 83.518 995 124 16 813 1791 431794286 431795256 0.000000e+00 893.0
17 TraesCS1A01G163800 chr6B 89.394 330 25 6 430 749 431792147 431792476 8.110000e-110 407.0
18 TraesCS1A01G163800 chr6B 100.000 68 0 0 1 68 431792082 431792149 2.540000e-25 126.0
19 TraesCS1A01G163800 chr3B 88.866 485 36 8 634 1116 462045683 462045215 4.510000e-162 580.0
20 TraesCS1A01G163800 chr3B 88.475 295 29 5 1505 1794 462042655 462042361 3.850000e-93 351.0
21 TraesCS1A01G163800 chr3B 91.005 189 14 2 409 597 462045876 462045691 4.020000e-63 252.0
22 TraesCS1A01G163800 chr3B 95.385 65 3 0 8 72 462045998 462045934 1.190000e-18 104.0
23 TraesCS1A01G163800 chr5D 86.022 558 52 13 627 1182 116616062 116615529 2.100000e-160 575.0
24 TraesCS1A01G163800 chr5D 82.306 633 71 18 1179 1794 116610590 116609982 6.010000e-141 510.0
25 TraesCS1A01G163800 chr5D 88.213 263 26 4 83 340 116609983 116610245 2.350000e-80 309.0
26 TraesCS1A01G163800 chr5D 91.220 205 15 3 430 633 116618215 116618013 2.380000e-70 276.0
27 TraesCS1A01G163800 chr5D 95.775 71 0 1 1 68 116618283 116618213 7.120000e-21 111.0
28 TraesCS1A01G163800 chr1D 100.000 29 0 0 409 437 441190264 441190236 1.000000e-03 54.7


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 TraesCS1A01G163800 chr1A 295021534 295023968 2434 True 4497.000000 4497 100.000000 1 2435 1 chr1A.!!$R1 2434
1 TraesCS1A01G163800 chr1A 487209695 487210340 645 False 966.000000 966 93.653000 1790 2435 1 chr1A.!!$F1 645
2 TraesCS1A01G163800 chr1A 295022176 295023886 1710 False 494.000000 494 95.192000 83 1793 2 chr1A.!!$F2 1710
3 TraesCS1A01G163800 chr6A 309761017 309761662 645 True 1016.000000 1016 95.046000 1790 2435 1 chr6A.!!$R1 645
4 TraesCS1A01G163800 chr6A 396024218 396024860 642 False 972.000000 972 93.944000 1792 2435 1 chr6A.!!$F2 643
5 TraesCS1A01G163800 chr6A 203597968 203600052 2084 True 771.000000 1711 94.907667 1 1793 3 chr6A.!!$R2 1792
6 TraesCS1A01G163800 chr2A 614515965 614516610 645 False 1016.000000 1016 95.046000 1790 2435 1 chr2A.!!$F1 645
7 TraesCS1A01G163800 chr7A 497018246 497018891 645 True 989.000000 989 94.272000 1790 2435 1 chr7A.!!$R2 645
8 TraesCS1A01G163800 chr7A 490883155 490883803 648 True 963.000000 963 93.529000 1790 2435 1 chr7A.!!$R1 645
9 TraesCS1A01G163800 chr4A 555425132 555425777 645 False 977.000000 977 93.963000 1790 2435 1 chr4A.!!$F1 645
10 TraesCS1A01G163800 chr6D 122531785 122532430 645 False 966.000000 966 93.683000 1790 2435 1 chr6D.!!$F1 645
11 TraesCS1A01G163800 chr3D 8003812 8004460 648 True 963.000000 963 93.529000 1790 2435 1 chr3D.!!$R1 645
12 TraesCS1A01G163800 chr6B 431792082 431795256 3174 False 475.333333 893 90.970667 1 1791 3 chr6B.!!$F1 1790
13 TraesCS1A01G163800 chr3B 462042361 462045998 3637 True 321.750000 580 90.932750 8 1794 4 chr3B.!!$R1 1786
14 TraesCS1A01G163800 chr5D 116609982 116610590 608 True 510.000000 510 82.306000 1179 1794 1 chr5D.!!$R1 615
15 TraesCS1A01G163800 chr5D 116615529 116618283 2754 True 320.666667 575 91.005667 1 1182 3 chr5D.!!$R2 1181

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
259 305 2.046892 GGCTGACCATGCGTCACT 60.047 61.111 11.56 0.0 46.8 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1445 8310 0.729116 CACGACATCCTGATTGCACC 59.271 55.0 0.0 0.0 0.0 5.01 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
72 118 8.838365 AGATAGTAAAGATTGTACTGTACTCCG 58.162 37.037 17.98 0.00 39.35 4.63
92 138 4.583489 TCCGGTGATCTAAATCTCCACTAC 59.417 45.833 0.00 0.00 43.03 2.73
192 238 9.756571 TTAGGCCCACTAATTTTAATCTAACAA 57.243 29.630 0.00 0.00 36.76 2.83
218 264 6.927294 AGCTTTACCCTGATCTATTTTTCG 57.073 37.500 0.00 0.00 0.00 3.46
225 271 3.689161 CCTGATCTATTTTTCGGTGTGCA 59.311 43.478 0.00 0.00 0.00 4.57
243 289 3.911964 GTGCACTTAGTATTTTGCGTTGG 59.088 43.478 10.32 0.00 37.82 3.77
244 290 2.914838 GCACTTAGTATTTTGCGTTGGC 59.085 45.455 0.00 0.00 40.52 4.52
259 305 2.046892 GGCTGACCATGCGTCACT 60.047 61.111 11.56 0.00 46.80 3.41
260 306 2.103042 GGCTGACCATGCGTCACTC 61.103 63.158 11.56 7.63 46.80 3.51
276 322 4.261031 CGTCACTCGGAGGAAAACAAATTT 60.261 41.667 10.23 0.00 33.18 1.82
394 440 4.555348 AAAACGCGTCATTAGAAAACCA 57.445 36.364 14.44 0.00 0.00 3.67
395 441 4.759516 AAACGCGTCATTAGAAAACCAT 57.240 36.364 14.44 0.00 0.00 3.55
396 442 4.759516 AACGCGTCATTAGAAAACCATT 57.240 36.364 14.44 0.00 0.00 3.16
397 443 4.078363 ACGCGTCATTAGAAAACCATTG 57.922 40.909 5.58 0.00 0.00 2.82
398 444 3.749088 ACGCGTCATTAGAAAACCATTGA 59.251 39.130 5.58 0.00 0.00 2.57
399 445 4.214545 ACGCGTCATTAGAAAACCATTGAA 59.785 37.500 5.58 0.00 0.00 2.69
400 446 5.150683 CGCGTCATTAGAAAACCATTGAAA 58.849 37.500 0.00 0.00 0.00 2.69
402 448 5.059221 GCGTCATTAGAAAACCATTGAAACG 59.941 40.000 0.00 0.00 0.00 3.60
404 450 5.918011 GTCATTAGAAAACCATTGAAACGCA 59.082 36.000 0.00 0.00 0.00 5.24
405 451 6.586082 GTCATTAGAAAACCATTGAAACGCAT 59.414 34.615 0.00 0.00 0.00 4.73
475 1412 5.820131 TCCATTGAAACGCATCATGATAAC 58.180 37.500 8.15 2.81 0.00 1.89
592 1529 5.529289 ACTGGATGGAGTCTTGACCTATAA 58.471 41.667 0.00 0.00 0.00 0.98
601 1539 5.030147 AGTCTTGACCTATAATGTGTGGGA 58.970 41.667 0.00 0.00 0.00 4.37
606 1544 7.893302 TCTTGACCTATAATGTGTGGGATTTTT 59.107 33.333 0.00 0.00 0.00 1.94
731 3634 5.918576 CACGAACAACACAAGTACTGATAGA 59.081 40.000 0.00 0.00 0.00 1.98
923 5593 4.039973 TCACGGAAGAAAGTACAGTTCCAT 59.960 41.667 13.03 0.00 38.76 3.41
944 5614 4.736126 TCTTCATGATGTAAGAAGCCGA 57.264 40.909 8.33 0.00 38.83 5.54
945 5615 5.282055 TCTTCATGATGTAAGAAGCCGAT 57.718 39.130 8.33 0.00 38.83 4.18
1024 5695 2.529136 CCACCTCCACCAGTCCCA 60.529 66.667 0.00 0.00 0.00 4.37
1112 5783 0.617820 GGCTCCACTCCAGGGACTTA 60.618 60.000 0.00 0.00 34.60 2.24
1117 7686 2.044492 TCCACTCCAGGGACTTACATCT 59.956 50.000 0.00 0.00 34.60 2.90
1170 7739 4.436998 CTCGTTCTCGCCCGCCTT 62.437 66.667 0.00 0.00 36.96 4.35
1233 7802 1.459348 TCTGGCTGCCGATGGGATA 60.459 57.895 14.98 0.00 34.06 2.59
1308 7877 2.070650 GGAGATACAGGGGCCGGTT 61.071 63.158 1.90 0.00 0.00 4.44
1351 7933 0.520404 GTACTTCTCTCACGTCGGCA 59.480 55.000 0.00 0.00 0.00 5.69
1353 7935 0.171455 ACTTCTCTCACGTCGGCATC 59.829 55.000 0.00 0.00 0.00 3.91
1445 8310 3.125376 GCAGGTAGGGGAGGGCATG 62.125 68.421 0.00 0.00 0.00 4.06
1472 8337 3.327404 GGATGTCGTGGGTGGGGT 61.327 66.667 0.00 0.00 0.00 4.95
1582 9058 2.831685 TGCGTGATTGTAGGAGTTGT 57.168 45.000 0.00 0.00 0.00 3.32
1622 9098 3.662759 TTGTTTTCCTCCAGGTGAAGT 57.337 42.857 0.00 0.00 36.34 3.01
1630 9106 2.571653 CCTCCAGGTGAAGTATGGTCAA 59.428 50.000 0.00 0.00 35.51 3.18
1649 9125 5.511729 GGTCAATCAACGCAAAATACTAAGC 59.488 40.000 0.00 0.00 0.00 3.09
1656 9132 2.159707 CGCAAAATACTAAGCGCACACT 60.160 45.455 11.47 0.00 43.80 3.55
1838 9316 7.356680 TCATAACCATGGAAAGGATCAGATTT 58.643 34.615 21.47 0.00 32.61 2.17
2014 9492 7.545362 TCTTTGCAAGCAAGAATATCTCTAC 57.455 36.000 7.60 0.00 37.24 2.59
2042 9520 9.349713 TGTTTCTTCACTCATAACATAACCTTT 57.650 29.630 0.00 0.00 0.00 3.11
2060 9538 4.014406 CCTTTCGGTACCTTAGGCAATTT 58.986 43.478 10.90 0.00 0.00 1.82
2061 9539 4.142469 CCTTTCGGTACCTTAGGCAATTTG 60.142 45.833 10.90 0.00 0.00 2.32
2063 9541 4.023726 TCGGTACCTTAGGCAATTTGTT 57.976 40.909 10.90 0.00 0.00 2.83
2067 9545 5.048294 CGGTACCTTAGGCAATTTGTTTCTT 60.048 40.000 10.90 0.00 0.00 2.52
2073 9551 2.037641 AGGCAATTTGTTTCTTGGAGGC 59.962 45.455 0.00 0.00 0.00 4.70
2097 9575 4.529109 AGTTCTAGCAGGAGTTTCAGTC 57.471 45.455 0.00 0.00 0.00 3.51
2331 9815 5.774690 TGAATTTAAAGCAGAACTGGATGGT 59.225 36.000 3.99 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
190 236 8.738645 AAAATAGATCAGGGTAAAGCTAGTTG 57.261 34.615 0.00 0.0 0.00 3.16
192 238 7.711339 CGAAAAATAGATCAGGGTAAAGCTAGT 59.289 37.037 0.00 0.0 0.00 2.57
196 242 5.589050 ACCGAAAAATAGATCAGGGTAAAGC 59.411 40.000 0.00 0.0 0.00 3.51
218 264 3.058501 ACGCAAAATACTAAGTGCACACC 60.059 43.478 21.04 0.0 36.80 4.16
225 271 4.069304 TCAGCCAACGCAAAATACTAAGT 58.931 39.130 0.00 0.0 37.52 2.24
252 298 0.599204 TGTTTTCCTCCGAGTGACGC 60.599 55.000 0.00 0.0 41.07 5.19
254 300 4.830826 AATTTGTTTTCCTCCGAGTGAC 57.169 40.909 0.00 0.0 0.00 3.67
259 305 4.555262 GCATGAAATTTGTTTTCCTCCGA 58.445 39.130 0.00 0.0 42.63 4.55
260 306 3.364621 CGCATGAAATTTGTTTTCCTCCG 59.635 43.478 0.00 0.0 42.63 4.63
292 338 1.438651 TGCGTGATTGTAGGAGTTGC 58.561 50.000 0.00 0.0 0.00 4.17
592 1529 3.196254 GCCAGATCAAAAATCCCACACAT 59.804 43.478 0.00 0.0 0.00 3.21
601 1539 3.491964 CGCCATGATGCCAGATCAAAAAT 60.492 43.478 0.00 0.0 0.00 1.82
606 1544 0.816421 CACGCCATGATGCCAGATCA 60.816 55.000 0.00 0.0 0.00 2.92
673 3576 0.693049 ACCTGGGATGTGGTCTTCAC 59.307 55.000 0.00 0.0 46.23 3.18
731 3634 4.034975 GCGTCGTAAGTTCCTACTCTACAT 59.965 45.833 0.00 0.0 39.48 2.29
882 5551 3.216800 GTGATGATATCCAGCTTTGCCA 58.783 45.455 0.00 0.0 31.20 4.92
923 5593 4.736126 TCGGCTTCTTACATCATGAAGA 57.264 40.909 4.68 0.0 39.61 2.87
936 5606 1.257750 GCCCCCAAAAATCGGCTTCT 61.258 55.000 0.00 0.0 38.41 2.85
944 5614 2.582493 CGCACAGGCCCCCAAAAAT 61.582 57.895 0.00 0.0 36.38 1.82
945 5615 3.230245 CGCACAGGCCCCCAAAAA 61.230 61.111 0.00 0.0 36.38 1.94
1024 5695 1.048601 ATTGGTGTCACTCGTGGAGT 58.951 50.000 2.35 0.0 44.44 3.85
1112 5783 2.373707 GCCTGCTCCTCCCAGATGT 61.374 63.158 0.00 0.0 32.03 3.06
1308 7877 2.342279 CTCCTGACGCCGGACAAA 59.658 61.111 5.05 0.0 0.00 2.83
1429 8017 2.039405 CCATGCCCTCCCCTACCT 60.039 66.667 0.00 0.0 0.00 3.08
1445 8310 0.729116 CACGACATCCTGATTGCACC 59.271 55.000 0.00 0.0 0.00 5.01
1472 8337 3.938963 GTCATTAGAAAACCTCCATCGCA 59.061 43.478 0.00 0.0 0.00 5.10
1476 8341 2.936498 CGCGTCATTAGAAAACCTCCAT 59.064 45.455 0.00 0.0 0.00 3.41
1622 9098 6.751514 AGTATTTTGCGTTGATTGACCATA 57.248 33.333 0.00 0.0 0.00 2.74
1649 9125 4.201851 CCCTGATCTATTTTTCAGTGTGCG 60.202 45.833 0.00 0.0 38.12 5.34
1656 9132 7.773690 GCTACCTTTACCCTGATCTATTTTTCA 59.226 37.037 0.00 0.0 0.00 2.69
1782 9260 4.284490 ACTGTTGTGTCACATCTCCACTAT 59.716 41.667 6.48 0.0 0.00 2.12
1796 9274 6.151985 TGGTTATGAAACTGAAACTGTTGTGT 59.848 34.615 0.00 0.0 35.81 3.72
1888 9366 8.398665 GTTTGCTACTTCACCTATCTTTATTGG 58.601 37.037 0.00 0.0 34.51 3.16
2014 9492 9.003658 AGGTTATGTTATGAGTGAAGAAACAAG 57.996 33.333 0.00 0.0 34.08 3.16
2042 9520 3.706600 ACAAATTGCCTAAGGTACCGA 57.293 42.857 6.18 0.0 0.00 4.69
2060 9538 2.979678 AGAACTAGGCCTCCAAGAAACA 59.020 45.455 9.68 0.0 0.00 2.83
2061 9539 3.704800 AGAACTAGGCCTCCAAGAAAC 57.295 47.619 9.68 0.0 0.00 2.78
2063 9541 2.766828 GCTAGAACTAGGCCTCCAAGAA 59.233 50.000 9.68 0.0 33.87 2.52
2067 9545 1.689575 CCTGCTAGAACTAGGCCTCCA 60.690 57.143 9.68 0.0 33.87 3.86
2073 9551 4.464597 ACTGAAACTCCTGCTAGAACTAGG 59.535 45.833 10.30 0.0 33.87 3.02
2097 9575 5.585047 TGTTGAATCTGATGATGAGCTTGAG 59.415 40.000 0.00 0.0 32.44 3.02
2312 9796 5.499004 ACTACCATCCAGTTCTGCTTTAA 57.501 39.130 0.00 0.0 0.00 1.52
2331 9815 1.642762 ACGAGGGGAGGTAAGGAACTA 59.357 52.381 0.00 0.0 38.49 2.24


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

AutoCloner maintained by Alex Coulton.