Multiple sequence alignment - TraesCS3A01G066500

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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 TraesCS3A01G066500 chr3A 100.000 2389 0 0 1 2389 39697694 39700082 0.000000e+00 4412.0
1 TraesCS3A01G066500 chr3A 94.588 2291 91 10 4 2279 39677466 39679738 0.000000e+00 3513.0
2 TraesCS3A01G066500 chr3A 94.041 2299 96 19 2 2279 39657804 39660082 0.000000e+00 3448.0
3 TraesCS3A01G066500 chr3A 93.818 1844 80 9 443 2279 39307172 39308988 0.000000e+00 2743.0
4 TraesCS3A01G066500 chr3A 93.709 1844 82 9 443 2279 39323904 39325720 0.000000e+00 2732.0
5 TraesCS3A01G066500 chr3A 94.459 1534 56 7 756 2279 39574114 39575628 0.000000e+00 2335.0
6 TraesCS3A01G066500 chr3A 94.615 1467 69 5 823 2279 39858604 39860070 0.000000e+00 2263.0
7 TraesCS3A01G066500 chr3A 92.862 1541 88 11 753 2279 39185334 39186866 0.000000e+00 2217.0
8 TraesCS3A01G066500 chr3A 93.400 1500 66 19 806 2279 38692378 38693870 0.000000e+00 2191.0
9 TraesCS3A01G066500 chr3A 93.981 731 38 4 2 726 39442590 39443320 0.000000e+00 1101.0
10 TraesCS3A01G066500 chr3A 94.457 451 17 4 2 447 39573272 39573719 0.000000e+00 688.0
11 TraesCS3A01G066500 chr3A 94.040 453 19 5 2 447 39857674 39858125 0.000000e+00 680.0
12 TraesCS3A01G066500 chr3A 93.488 430 22 3 2 425 39248347 39248776 3.350000e-178 634.0
13 TraesCS3A01G066500 chr3A 92.239 451 27 5 2 447 39183986 39184433 1.200000e-177 632.0
14 TraesCS3A01G066500 chr3A 92.035 452 23 7 2 447 38691008 38691452 7.250000e-175 623.0
15 TraesCS3A01G066500 chr3A 93.333 315 19 1 443 757 38692084 38692396 4.650000e-127 464.0
16 TraesCS3A01G066500 chr3A 93.226 310 21 0 443 752 39185054 39185363 7.780000e-125 457.0
17 TraesCS3A01G066500 chr3A 100.000 67 0 0 2321 2387 39660741 39660807 8.970000e-25 124.0
18 TraesCS3A01G066500 chr3A 98.507 67 1 0 2321 2387 39680403 39680469 4.170000e-23 119.0
19 TraesCS3A01G066500 chr3A 98.507 67 1 0 2321 2387 39860734 39860800 4.170000e-23 119.0
20 TraesCS3A01G066500 chr3A 97.015 67 2 0 2321 2387 39576292 39576358 1.940000e-21 113.0
21 TraesCS3A01G066500 chr3A 96.970 66 2 0 2321 2386 39309653 39309718 6.980000e-21 111.0
22 TraesCS3A01G066500 chr3A 96.970 66 2 0 2321 2386 39326385 39326450 6.980000e-21 111.0
23 TraesCS3A01G066500 chr3A 95.522 67 3 0 2321 2387 39187533 39187599 9.030000e-20 108.0
24 TraesCS3A01G066500 chr3A 94.030 67 4 0 2321 2387 38694536 38694602 4.200000e-18 102.0
25 TraesCS3A01G066500 chr3D 86.024 830 80 15 1485 2279 29371740 29372568 0.000000e+00 857.0
26 TraesCS3A01G066500 chr3D 80.292 822 107 34 834 1630 29377050 29377841 9.580000e-159 569.0
27 TraesCS3A01G066500 chr3D 85.271 258 15 8 447 704 29285280 29285514 6.600000e-61 244.0
28 TraesCS3A01G066500 chr3D 90.141 71 7 0 634 704 29361599 29361669 2.530000e-15 93.5
29 TraesCS3A01G066500 chr4A 88.968 281 31 0 149 429 466960250 466959970 4.890000e-92 348.0


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 TraesCS3A01G066500 chr3A 39697694 39700082 2388 False 4412.000000 4412 100.000000 1 2389 1 chr3A.!!$F3 2388
1 TraesCS3A01G066500 chr3A 39677466 39680469 3003 False 1816.000000 3513 96.547500 4 2387 2 chr3A.!!$F10 2383
2 TraesCS3A01G066500 chr3A 39657804 39660807 3003 False 1786.000000 3448 97.020500 2 2387 2 chr3A.!!$F9 2385
3 TraesCS3A01G066500 chr3A 39307172 39309718 2546 False 1427.000000 2743 95.394000 443 2386 2 chr3A.!!$F6 1943
4 TraesCS3A01G066500 chr3A 39323904 39326450 2546 False 1421.500000 2732 95.339500 443 2386 2 chr3A.!!$F7 1943
5 TraesCS3A01G066500 chr3A 39442590 39443320 730 False 1101.000000 1101 93.981000 2 726 1 chr3A.!!$F2 724
6 TraesCS3A01G066500 chr3A 39573272 39576358 3086 False 1045.333333 2335 95.310333 2 2387 3 chr3A.!!$F8 2385
7 TraesCS3A01G066500 chr3A 39857674 39860800 3126 False 1020.666667 2263 95.720667 2 2387 3 chr3A.!!$F11 2385
8 TraesCS3A01G066500 chr3A 39183986 39187599 3613 False 853.500000 2217 93.462250 2 2387 4 chr3A.!!$F5 2385
9 TraesCS3A01G066500 chr3A 38691008 38694602 3594 False 845.000000 2191 93.199500 2 2387 4 chr3A.!!$F4 2385
10 TraesCS3A01G066500 chr3D 29371740 29372568 828 False 857.000000 857 86.024000 1485 2279 1 chr3D.!!$F3 794
11 TraesCS3A01G066500 chr3D 29377050 29377841 791 False 569.000000 569 80.292000 834 1630 1 chr3D.!!$F4 796

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
544 1232 0.833287 GGTGATTCCCAGCTAGCAGA 59.167 55.0 18.83 7.79 40.01 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1712 2459 1.134551 ACGCAAGCAACCACCATTTTT 60.135 42.857 0.0 0.0 45.62 1.94 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
27 28 9.537192 TTATTAGGTGACTATGTAAATTGTCCG 57.463 33.333 5.21 0.00 43.94 4.79
36 37 8.780846 ACTATGTAAATTGTCCGTTGATTGTA 57.219 30.769 0.00 0.00 0.00 2.41
174 182 2.827322 CTGAAATGGCAATGGTCCAAGA 59.173 45.455 0.00 0.00 37.13 3.02
208 218 2.621998 AGTAGCTACGTCCGTGCATATT 59.378 45.455 17.99 0.00 0.00 1.28
500 1154 6.407752 GCAAAAGCATCTACTACCCCTTACTA 60.408 42.308 0.00 0.00 0.00 1.82
535 1223 1.001503 GGGCCATTGGTGATTCCCA 59.998 57.895 4.39 0.00 32.76 4.37
544 1232 0.833287 GGTGATTCCCAGCTAGCAGA 59.167 55.000 18.83 7.79 40.01 4.26
545 1233 1.419387 GGTGATTCCCAGCTAGCAGAT 59.581 52.381 18.83 2.79 40.01 2.90
1042 1768 2.248431 GCGTCCTGTGTTTCGTGC 59.752 61.111 0.00 0.00 0.00 5.34
1043 1769 2.530497 GCGTCCTGTGTTTCGTGCA 61.530 57.895 0.00 0.00 0.00 4.57
1073 1799 2.189521 GGTCATGGCTACCACCCG 59.810 66.667 0.00 0.00 35.80 5.28
1305 2039 3.608456 GACGACAAGTGCAAGAAGTTTC 58.392 45.455 0.00 0.00 0.00 2.78
1314 2048 0.581529 CAAGAAGTTTCGCGACAGCA 59.418 50.000 9.15 0.00 45.49 4.41
1325 2059 1.811266 CGACAGCATAGGCAAGCGT 60.811 57.895 0.67 0.00 44.61 5.07
1421 2155 5.703592 TGAAGCAACCGAGCTAAGAAATAAA 59.296 36.000 0.00 0.00 45.89 1.40
1526 2261 9.465985 TTTAAATCATTGTAAACCGACTTTTCC 57.534 29.630 0.00 0.00 0.00 3.13
1547 2282 4.038042 TCCATAATTTGTTGTGTTCGGCAA 59.962 37.500 0.00 0.00 0.00 4.52
1671 2418 1.134007 CCCCAGCATCTACATCAAGCA 60.134 52.381 0.00 0.00 0.00 3.91
1822 2589 3.088532 AGCCTTTCAAACTTGACACACA 58.911 40.909 0.00 0.00 36.83 3.72
1927 2701 9.553064 TGTTTACTTGCCAATTATGTCAAAATT 57.447 25.926 0.00 0.00 0.00 1.82
2019 2793 2.198827 TGTCGAACTGATGGGCATTT 57.801 45.000 0.00 0.00 0.00 2.32
2115 2891 4.437239 CGAAGTCCTTGTCAGCATTATCT 58.563 43.478 0.00 0.00 0.00 1.98
2279 3061 4.576873 TGCAATCGTTCTTCAACAAGGTTA 59.423 37.500 0.00 0.00 32.14 2.85
2280 3062 5.066634 TGCAATCGTTCTTCAACAAGGTTAA 59.933 36.000 0.00 0.00 32.14 2.01
2284 3066 9.030301 CAATCGTTCTTCAACAAGGTTAAATTT 57.970 29.630 0.00 0.00 32.14 1.82
2297 3140 9.178758 ACAAGGTTAAATTTATTTTTGCAACCA 57.821 25.926 14.54 0.00 37.23 3.67
2387 3794 4.038162 GTGACGAGCAGATAATAACTCCCT 59.962 45.833 0.00 0.00 0.00 4.20
2388 3795 4.038042 TGACGAGCAGATAATAACTCCCTG 59.962 45.833 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 118 6.144886 CACATGTGTCAAAAGAATGTTCATGG 59.855 38.462 18.03 0.00 29.20 3.66
174 182 8.930760 CGGACGTAGCTACTACTACTTAATTAT 58.069 37.037 21.20 0.00 40.36 1.28
500 1154 3.849951 CGGGCCGACTAGCATGGT 61.850 66.667 24.41 1.62 0.00 3.55
535 1223 3.710209 AAACCTCACAATCTGCTAGCT 57.290 42.857 17.23 0.00 0.00 3.32
544 1232 5.510179 CCATCTGCAAAGAAAACCTCACAAT 60.510 40.000 0.00 0.00 0.00 2.71
545 1233 4.202141 CCATCTGCAAAGAAAACCTCACAA 60.202 41.667 0.00 0.00 0.00 3.33
610 1298 9.575783 AGAGATTTTATCTAGAAGAACGTGAAC 57.424 33.333 0.00 0.00 40.38 3.18
638 1326 7.804843 ATCTTTGGCAATTTGATTCAAACAA 57.195 28.000 13.80 10.52 36.13 2.83
685 1373 8.175069 CGAATTCCTGTCAATCGAAGAAATTTA 58.825 33.333 0.00 0.00 43.58 1.40
686 1374 7.023575 CGAATTCCTGTCAATCGAAGAAATTT 58.976 34.615 0.00 0.00 43.58 1.82
704 1392 2.406130 TGTGACCACGTAACGAATTCC 58.594 47.619 0.00 0.00 0.00 3.01
1073 1799 0.454196 GTCGCAGGAGGAGAGAAGAC 59.546 60.000 0.00 0.00 0.00 3.01
1305 2039 3.009140 CTTGCCTATGCTGTCGCG 58.991 61.111 0.00 0.00 39.65 5.87
1314 2048 4.547367 GGCCGGACGCTTGCCTAT 62.547 66.667 5.05 0.00 42.01 2.57
1526 2261 5.249336 GTTGCCGAACACAACAAATTATG 57.751 39.130 1.95 0.00 45.35 1.90
1547 2282 8.157476 AGAGATACACACAGGATAAACAAAAGT 58.843 33.333 0.00 0.00 0.00 2.66
1701 2448 6.717413 CAACCACCATTTTTGTTTGAGATTG 58.283 36.000 0.00 0.00 0.00 2.67
1712 2459 1.134551 ACGCAAGCAACCACCATTTTT 60.135 42.857 0.00 0.00 45.62 1.94
1822 2589 7.560368 CACTGGACCTATAGAAAGACTTGATT 58.440 38.462 0.00 0.00 0.00 2.57
1946 2720 9.918630 GTCTGCCAATATTTCATTTATAGCAAT 57.081 29.630 0.00 0.00 0.00 3.56
1966 2740 2.113860 TGAGCAACCATTAGTCTGCC 57.886 50.000 0.00 0.00 34.80 4.85
2019 2793 1.766496 ACTCCAACAAGGACTTCCGAA 59.234 47.619 0.00 0.00 43.07 4.30
2284 3066 9.167311 AGTACAAATTGTTTGGTTGCAAAAATA 57.833 25.926 3.17 0.00 44.81 1.40
2286 3068 7.440523 AGTACAAATTGTTTGGTTGCAAAAA 57.559 28.000 3.17 0.00 44.81 1.94
2288 3070 7.063544 GTGTAGTACAAATTGTTTGGTTGCAAA 59.936 33.333 3.17 0.00 44.81 3.68
2289 3071 6.531948 GTGTAGTACAAATTGTTTGGTTGCAA 59.468 34.615 3.17 0.00 44.81 4.08


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

AutoCloner maintained by Alex Coulton.