Multiple sequence alignment - TraesCS2D01G347400

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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 TraesCS2D01G347400 chr2D 100.000 5385 0 0 1 5385 445402033 445396649 0.000000e+00 9945.0
1 TraesCS2D01G347400 chr2D 88.710 62 7 0 1743 1804 169639132 169639071 5.780000e-10 76.8
2 TraesCS2D01G347400 chr2B 92.676 4424 202 47 1030 5385 523765221 523760852 0.000000e+00 6263.0
3 TraesCS2D01G347400 chr2A 96.794 3493 86 10 1904 5385 587754539 587751062 0.000000e+00 5806.0
4 TraesCS2D01G347400 chr2A 97.634 2621 56 5 1904 4522 610714411 610711795 0.000000e+00 4492.0
5 TraesCS2D01G347400 chr2A 94.409 1395 59 11 377 1759 610716524 610715137 0.000000e+00 2126.0
6 TraesCS2D01G347400 chr2A 91.243 1553 102 18 383 1921 587756085 587754553 0.000000e+00 2084.0
7 TraesCS2D01G347400 chr2A 93.453 947 26 9 4462 5385 610711810 610710877 0.000000e+00 1373.0
8 TraesCS2D01G347400 chr2A 97.059 170 5 0 1752 1921 610714594 610714425 2.450000e-73 287.0
9 TraesCS2D01G347400 chr2A 83.843 229 32 5 1743 1970 70046382 70046606 4.220000e-51 213.0
10 TraesCS2D01G347400 chr2A 94.958 119 5 1 2 119 587756634 587756516 9.210000e-43 185.0
11 TraesCS2D01G347400 chr4D 92.025 163 13 0 1797 1959 145579679 145579517 4.200000e-56 230.0
12 TraesCS2D01G347400 chr3D 90.230 174 15 1 1797 1970 340340392 340340221 5.430000e-55 226.0
13 TraesCS2D01G347400 chr3D 94.231 52 3 0 1743 1794 248210770 248210719 4.470000e-11 80.5
14 TraesCS2D01G347400 chr3B 89.474 171 18 0 1789 1959 413810065 413810235 3.270000e-52 217.0
15 TraesCS2D01G347400 chr3B 82.234 197 25 7 5175 5365 452907505 452907697 1.550000e-35 161.0
16 TraesCS2D01G347400 chr1B 89.080 174 19 0 1797 1970 533803452 533803279 3.270000e-52 217.0
17 TraesCS2D01G347400 chr7A 83.871 217 33 1 1743 1957 40999100 40999316 7.070000e-49 206.0
18 TraesCS2D01G347400 chr7A 80.597 201 30 5 5175 5369 709417473 709417670 4.350000e-31 147.0
19 TraesCS2D01G347400 chr7A 79.845 129 17 4 5233 5355 53863353 53863228 9.610000e-13 86.1
20 TraesCS2D01G347400 chr7B 82.564 195 25 7 5175 5363 692827189 692827380 4.320000e-36 163.0
21 TraesCS2D01G347400 chr7B 81.188 202 25 11 5175 5370 692796784 692796978 3.360000e-32 150.0
22 TraesCS2D01G347400 chr7B 80.100 201 31 7 5175 5369 226424209 226424406 2.020000e-29 141.0
23 TraesCS2D01G347400 chr7B 89.231 65 7 0 1740 1804 193058977 193059041 1.240000e-11 82.4
24 TraesCS2D01G347400 chr3A 81.633 196 27 5 5175 5364 617439423 617439615 2.600000e-33 154.0
25 TraesCS2D01G347400 chr5A 79.602 201 32 7 5175 5369 33170685 33170882 9.410000e-28 135.0
26 TraesCS2D01G347400 chr4B 78.607 201 25 9 5175 5369 142427086 142426898 3.410000e-22 117.0
27 TraesCS2D01G347400 chr4B 77.114 201 28 7 5175 5369 142428239 142428051 3.430000e-17 100.0
28 TraesCS2D01G347400 chr5B 94.444 72 4 0 5173 5244 16855862 16855791 1.590000e-20 111.0
29 TraesCS2D01G347400 chr5B 94.444 72 4 0 5173 5244 17156964 17156893 1.590000e-20 111.0
30 TraesCS2D01G347400 chr5D 93.056 72 5 0 5173 5244 23170245 23170174 7.380000e-19 106.0
31 TraesCS2D01G347400 chr1A 97.727 44 1 0 5173 5216 254989199 254989156 5.780000e-10 76.8
32 TraesCS2D01G347400 chr6D 100.000 28 0 0 632 659 473361373 473361346 1.000000e-02 52.8


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 TraesCS2D01G347400 chr2D 445396649 445402033 5384 True 9945.000000 9945 100.000000 1 5385 1 chr2D.!!$R2 5384
1 TraesCS2D01G347400 chr2B 523760852 523765221 4369 True 6263.000000 6263 92.676000 1030 5385 1 chr2B.!!$R1 4355
2 TraesCS2D01G347400 chr2A 587751062 587756634 5572 True 2691.666667 5806 94.331667 2 5385 3 chr2A.!!$R1 5383
3 TraesCS2D01G347400 chr2A 610710877 610716524 5647 True 2069.500000 4492 95.638750 377 5385 4 chr2A.!!$R2 5008

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
550 751 3.537806 ACGCGAAAACATAAGTTTCGTG 58.462 40.909 23.49 23.49 46.79 4.35 F
1230 1455 0.326618 AGAGACCCCGAACCATCCAT 60.327 55.000 0.00 0.00 0.00 3.41 F
1754 2008 1.137675 GGCAAATGCTCCCTCCATTTC 59.862 52.381 5.25 0.00 40.00 2.17 F
2513 3350 1.203287 GCAAGCTGAATTTCCACCCTC 59.797 52.381 0.00 0.00 0.00 4.30 F
3313 4150 1.342174 CAACAAAAGGCATGGTCAGCT 59.658 47.619 0.00 0.00 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 2566 1.871039 CGGTCAAACCTAATATGCGGG 59.129 52.381 0.0 0.0 35.66 6.13 R
2092 2928 2.230508 GTCGACTGGTATGGACAGAACA 59.769 50.000 8.7 0.0 39.24 3.18 R
3705 4543 2.496470 ACAGGAGTTCGGATACAGTTCC 59.504 50.000 0.0 0.0 0.00 3.62 R
3757 4595 5.355071 TCATCAACCTCAGAATTTTCATCCG 59.645 40.000 0.0 0.0 0.00 4.18 R
5125 6062 1.277273 GGGCTAGGAAAACCACGTACT 59.723 52.381 0.0 0.0 0.00 2.73 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
79 80 6.697892 TGTGAAACGTGAATAAAAATGTTCCC 59.302 34.615 0.00 0.00 42.39 3.97
118 120 9.612066 AAATGTGAATGTTTAACTGGAAAATGT 57.388 25.926 0.00 0.00 0.00 2.71
119 121 9.612066 AATGTGAATGTTTAACTGGAAAATGTT 57.388 25.926 0.00 0.00 0.00 2.71
186 188 7.835634 TGATGTATACGCAAAATGTAGAACA 57.164 32.000 0.00 0.00 0.00 3.18
550 751 3.537806 ACGCGAAAACATAAGTTTCGTG 58.462 40.909 23.49 23.49 46.79 4.35
770 974 4.584327 ACGAAGAAAAATGAAACCCCAG 57.416 40.909 0.00 0.00 0.00 4.45
1104 1329 1.896694 CACTCTCTCTCAGTGCCCC 59.103 63.158 0.00 0.00 35.15 5.80
1138 1363 1.065782 CATTCACCACACCCGTATCCA 60.066 52.381 0.00 0.00 0.00 3.41
1230 1455 0.326618 AGAGACCCCGAACCATCCAT 60.327 55.000 0.00 0.00 0.00 3.41
1338 1563 4.431131 CCGGCAGGCCACAAGGAT 62.431 66.667 5.01 0.00 36.89 3.24
1396 1621 3.736482 CTCGTCCGGCAGCGTAGAC 62.736 68.421 0.00 0.00 0.00 2.59
1741 1995 1.398390 GTGGTTCTCGCTAGGCAAATG 59.602 52.381 0.00 0.00 0.00 2.32
1754 2008 1.137675 GGCAAATGCTCCCTCCATTTC 59.862 52.381 5.25 0.00 40.00 2.17
1762 2566 5.048846 TGCTCCCTCCATTTCTATTTACC 57.951 43.478 0.00 0.00 0.00 2.85
1971 2806 9.526286 GAGTAAATAAAAACAGAAAGAGTACGC 57.474 33.333 0.00 0.00 0.00 4.42
1983 2818 5.805994 AGAAAGAGTACGCTAATGTAACAGC 59.194 40.000 0.00 0.00 0.00 4.40
2092 2928 6.430000 ACGAAGTTATAACCTTCAAACATGCT 59.570 34.615 12.05 0.00 37.78 3.79
2469 3306 6.946340 TGATTTTCTAATACTGCTGGTCAGA 58.054 36.000 1.65 0.00 45.72 3.27
2513 3350 1.203287 GCAAGCTGAATTTCCACCCTC 59.797 52.381 0.00 0.00 0.00 4.30
2719 3556 5.981915 ACTTCTTGCAGCTTTGAAGAAAATC 59.018 36.000 21.11 0.00 39.17 2.17
3206 4043 4.022849 ACCGGCTTCAAGATTTCAAAGAAG 60.023 41.667 0.00 0.00 38.88 2.85
3306 4143 8.487176 GTTTAGAACATAACAACAAAAGGCATG 58.513 33.333 0.00 0.00 0.00 4.06
3313 4150 1.342174 CAACAAAAGGCATGGTCAGCT 59.658 47.619 0.00 0.00 0.00 4.24
3352 4189 4.559862 AGGAAGGGTGTTCTGTATTCTG 57.440 45.455 0.00 0.00 0.00 3.02
3481 4319 7.606839 GTGTTAGTACCCTGCTTTCTCTAAATT 59.393 37.037 0.00 0.00 0.00 1.82
3671 4509 4.645136 TCAGACTCTACAAACAGTGTGTCT 59.355 41.667 0.00 0.00 41.89 3.41
3705 4543 7.327214 AGATTCTTCTAGCTCAGTTTACAAGG 58.673 38.462 0.00 0.00 0.00 3.61
3757 4595 3.133141 AGAAAGGTCTGAGAAGTTGGC 57.867 47.619 0.00 0.00 30.83 4.52
4080 4918 5.537674 AGTTCATTGCTGAAGAAAAGGTGAT 59.462 36.000 0.00 0.00 41.96 3.06
4101 4939 9.744468 GGTGATGGTCAAATTAATTTGTATACC 57.256 33.333 30.50 28.93 45.49 2.73
4554 5444 5.764686 TGCATTATGATCGCCTCTTGTTTAT 59.235 36.000 0.00 0.00 0.00 1.40
4749 5669 2.070028 ACATGCACACACGCGTATTAA 58.930 42.857 13.44 0.00 33.35 1.40
4750 5670 2.093625 ACATGCACACACGCGTATTAAG 59.906 45.455 13.44 0.50 33.35 1.85
4751 5671 1.785768 TGCACACACGCGTATTAAGT 58.214 45.000 13.44 1.32 33.35 2.24
4752 5672 2.943993 TGCACACACGCGTATTAAGTA 58.056 42.857 13.44 0.00 33.35 2.24
4753 5673 2.918600 TGCACACACGCGTATTAAGTAG 59.081 45.455 13.44 0.00 33.35 2.57
4754 5674 2.919229 GCACACACGCGTATTAAGTAGT 59.081 45.455 13.44 0.00 0.00 2.73
4755 5675 3.365820 GCACACACGCGTATTAAGTAGTT 59.634 43.478 13.44 0.00 0.00 2.24
4756 5676 4.143263 GCACACACGCGTATTAAGTAGTTT 60.143 41.667 13.44 0.00 0.00 2.66
4757 5677 5.060816 GCACACACGCGTATTAAGTAGTTTA 59.939 40.000 13.44 0.00 0.00 2.01
4979 5904 3.680786 GTTCCGCCCCACTTTGGC 61.681 66.667 0.00 0.00 45.70 4.52
5125 6062 2.514160 TGGAGATAGCAGGGAGACAGTA 59.486 50.000 0.00 0.00 0.00 2.74
5137 6074 3.006217 GGGAGACAGTAGTACGTGGTTTT 59.994 47.826 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 8.424731 GGAACATTTTTATTCACGTTTCACATC 58.575 33.333 0.00 0.0 0.00 3.06
55 56 6.129300 CGGGAACATTTTTATTCACGTTTCAC 60.129 38.462 0.59 0.0 44.74 3.18
65 66 7.941431 TGTATACACCGGGAACATTTTTATT 57.059 32.000 6.32 0.0 0.00 1.40
480 681 4.206375 TCTTCACAAGCATCAGGAACAAA 58.794 39.130 0.00 0.0 0.00 2.83
488 689 6.041423 TGTTCTAGATCTTCACAAGCATCA 57.959 37.500 0.00 0.0 0.00 3.07
816 1020 8.476925 GTTCATATTCTTCGGTTTTGTTTTGTC 58.523 33.333 0.00 0.0 0.00 3.18
872 1077 3.639561 AGCTTTTTGTTCCCCACGTATTT 59.360 39.130 0.00 0.0 0.00 1.40
974 1196 0.680061 ACTGGACTGGGAAGTTCGTC 59.320 55.000 0.00 0.0 0.00 4.20
977 1199 3.633361 CCACTGGACTGGGAAGTTC 57.367 57.895 0.00 0.0 0.00 3.01
1741 1995 4.399219 GGGTAAATAGAAATGGAGGGAGC 58.601 47.826 0.00 0.0 0.00 4.70
1754 2008 6.938030 TCAAACCTAATATGCGGGGTAAATAG 59.062 38.462 0.00 0.0 0.00 1.73
1762 2566 1.871039 CGGTCAAACCTAATATGCGGG 59.129 52.381 0.00 0.0 35.66 6.13
1962 2797 5.125739 AGAGCTGTTACATTAGCGTACTCTT 59.874 40.000 0.00 0.0 44.43 2.85
2092 2928 2.230508 GTCGACTGGTATGGACAGAACA 59.769 50.000 8.70 0.0 39.24 3.18
2399 3236 8.553696 CAAGCAAACTTCATTCTTTTATGCTTT 58.446 29.630 6.45 0.0 46.11 3.51
2469 3306 9.845740 TGCAGTAATATACCTTACATGACAATT 57.154 29.630 0.00 0.0 34.66 2.32
2513 3350 5.923733 ATCTAATAAGATAGCCCACCTCG 57.076 43.478 0.00 0.0 40.82 4.63
2719 3556 2.910199 TCTGAAGGATCATTTGGCTCG 58.090 47.619 0.00 0.0 34.37 5.03
3206 4043 3.181470 GGAGGATCTTACTGAGCTTGTCC 60.181 52.174 0.00 0.0 33.73 4.02
3306 4143 7.158099 ACCAACTGAAAATAATTAGCTGACC 57.842 36.000 0.00 0.0 0.00 4.02
3313 4150 8.395605 ACCCTTCCTACCAACTGAAAATAATTA 58.604 33.333 0.00 0.0 0.00 1.40
3352 4189 3.703001 TTTGATCCTGACTTCCTGACC 57.297 47.619 0.00 0.0 0.00 4.02
3481 4319 4.883585 CCAGTGCCTGATTAGAAATGCTAA 59.116 41.667 4.00 0.0 42.92 3.09
3671 4509 8.535335 ACTGAGCTAGAAGAATCTTTATTCACA 58.465 33.333 0.00 0.0 43.44 3.58
3705 4543 2.496470 ACAGGAGTTCGGATACAGTTCC 59.504 50.000 0.00 0.0 0.00 3.62
3757 4595 5.355071 TCATCAACCTCAGAATTTTCATCCG 59.645 40.000 0.00 0.0 0.00 4.18
4101 4939 8.968242 GTTTAGGTAGAAAAACTCAAGCAAATG 58.032 33.333 0.00 0.0 33.71 2.32
4752 5672 9.314321 GTGTGATGCACTATGTAGTAATAAACT 57.686 33.333 0.00 0.0 44.41 2.66
5125 6062 1.277273 GGGCTAGGAAAACCACGTACT 59.723 52.381 0.00 0.0 0.00 2.73


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

AutoCloner maintained by Alex Coulton.