Multiple sequence alignment - TraesCS2B01G035100

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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 TraesCS2B01G035100 chr2B 100.000 3648 0 0 1 3648 16961707 16958060 0.000000e+00 6737.0
1 TraesCS2B01G035100 chr2B 96.963 3655 81 3 1 3648 16929127 16925496 0.000000e+00 6107.0
2 TraesCS2B01G035100 chr2A 87.475 1988 204 26 1690 3645 11845033 11847007 0.000000e+00 2250.0
3 TraesCS2B01G035100 chr2A 89.058 658 36 7 784 1405 11839702 11840359 0.000000e+00 784.0
4 TraesCS2B01G035100 chr2A 92.063 126 8 2 1531 1655 11840373 11840497 3.740000e-40 176.0
5 TraesCS2B01G035100 chr2D 88.528 1508 128 24 1404 2885 11149448 11147960 0.000000e+00 1784.0
6 TraesCS2B01G035100 chr2D 94.823 792 36 3 1 790 11150730 11149942 0.000000e+00 1230.0
7 TraesCS2B01G035100 chr2D 85.811 592 45 17 780 1344 11149988 11149409 3.140000e-165 592.0
8 TraesCS2B01G035100 chr2D 85.885 503 53 12 3156 3645 11147480 11146983 1.500000e-143 520.0
9 TraesCS2B01G035100 chrUn 95.777 663 23 3 1 661 313033891 313033232 0.000000e+00 1064.0
10 TraesCS2B01G035100 chrUn 95.777 663 23 3 1 661 313037686 313037027 0.000000e+00 1064.0
11 TraesCS2B01G035100 chrUn 95.777 663 23 3 1 661 327964362 327963703 0.000000e+00 1064.0
12 TraesCS2B01G035100 chrUn 83.576 688 96 12 2149 2827 329646756 329647435 2.390000e-176 628.0
13 TraesCS2B01G035100 chrUn 89.842 443 43 2 784 1226 313033228 313032788 5.290000e-158 568.0
14 TraesCS2B01G035100 chrUn 89.842 443 43 2 784 1226 313037023 313036583 5.290000e-158 568.0
15 TraesCS2B01G035100 chrUn 89.842 443 43 2 784 1226 327963699 327963259 5.290000e-158 568.0
16 TraesCS2B01G035100 chrUn 88.631 431 45 3 1694 2120 313032199 313031769 4.170000e-144 521.0
17 TraesCS2B01G035100 chrUn 88.631 431 45 3 1694 2120 313035994 313035564 4.170000e-144 521.0
18 TraesCS2B01G035100 chrUn 88.631 431 45 3 1694 2120 327962670 327962240 4.170000e-144 521.0
19 TraesCS2B01G035100 chrUn 90.217 92 7 1 1256 1345 313032720 313032629 6.400000e-23 119.0
20 TraesCS2B01G035100 chrUn 90.217 92 7 1 1256 1345 313036515 313036424 6.400000e-23 119.0
21 TraesCS2B01G035100 chrUn 90.217 92 7 1 1256 1345 327963191 327963100 6.400000e-23 119.0
22 TraesCS2B01G035100 chr4D 76.396 788 157 20 1830 2592 507423642 507422859 7.340000e-107 398.0
23 TraesCS2B01G035100 chr4D 78.059 237 52 0 1015 1251 507423907 507423671 2.270000e-32 150.0
24 TraesCS2B01G035100 chr7D 73.390 823 174 23 1812 2592 3094866 3094047 7.770000e-67 265.0
25 TraesCS2B01G035100 chr7D 73.439 817 172 23 1812 2586 3168886 3169699 7.770000e-67 265.0
26 TraesCS2B01G035100 chr6D 76.023 513 88 21 2109 2590 32640360 32639852 2.190000e-57 233.0
27 TraesCS2B01G035100 chr6B 80.913 241 46 0 2335 2575 68393852 68393612 1.340000e-44 191.0
28 TraesCS2B01G035100 chr6B 89.474 133 12 2 5 135 67469216 67469348 2.250000e-37 167.0
29 TraesCS2B01G035100 chr6B 83.030 165 28 0 2102 2266 68394112 68393948 2.270000e-32 150.0
30 TraesCS2B01G035100 chr6B 86.667 60 8 0 132 191 26023113 26023172 2.350000e-07 67.6
31 TraesCS2B01G035100 chr5B 91.339 127 9 2 11 135 237976722 237976848 4.840000e-39 172.0
32 TraesCS2B01G035100 chr1B 91.339 127 9 2 11 135 625168326 625168452 4.840000e-39 172.0
33 TraesCS2B01G035100 chr3B 90.551 127 10 2 11 135 8549185 8549059 2.250000e-37 167.0
34 TraesCS2B01G035100 chr7A 85.470 117 14 3 135 248 219402588 219402472 6.400000e-23 119.0
35 TraesCS2B01G035100 chr1A 79.851 134 18 7 133 261 248875308 248875437 5.020000e-14 89.8
36 TraesCS2B01G035100 chr4B 100.000 30 0 0 133 162 595238319 595238348 5.090000e-04 56.5


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 TraesCS2B01G035100 chr2B 16958060 16961707 3647 True 6737.0 6737 100.00000 1 3648 1 chr2B.!!$R2 3647
1 TraesCS2B01G035100 chr2B 16925496 16929127 3631 True 6107.0 6107 96.96300 1 3648 1 chr2B.!!$R1 3647
2 TraesCS2B01G035100 chr2A 11845033 11847007 1974 False 2250.0 2250 87.47500 1690 3645 1 chr2A.!!$F1 1955
3 TraesCS2B01G035100 chr2A 11839702 11840497 795 False 480.0 784 90.56050 784 1655 2 chr2A.!!$F2 871
4 TraesCS2B01G035100 chr2D 11146983 11150730 3747 True 1031.5 1784 88.76175 1 3645 4 chr2D.!!$R1 3644
5 TraesCS2B01G035100 chrUn 329646756 329647435 679 False 628.0 628 83.57600 2149 2827 1 chrUn.!!$F1 678
6 TraesCS2B01G035100 chrUn 313031769 313037686 5917 True 568.0 1064 91.11675 1 2120 8 chrUn.!!$R1 2119
7 TraesCS2B01G035100 chrUn 327962240 327964362 2122 True 568.0 1064 91.11675 1 2120 4 chrUn.!!$R2 2119
8 TraesCS2B01G035100 chr4D 507422859 507423907 1048 True 274.0 398 77.22750 1015 2592 2 chr4D.!!$R1 1577
9 TraesCS2B01G035100 chr7D 3094047 3094866 819 True 265.0 265 73.39000 1812 2592 1 chr7D.!!$R1 780
10 TraesCS2B01G035100 chr7D 3168886 3169699 813 False 265.0 265 73.43900 1812 2586 1 chr7D.!!$F1 774
11 TraesCS2B01G035100 chr6D 32639852 32640360 508 True 233.0 233 76.02300 2109 2590 1 chr6D.!!$R1 481

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
468 471 1.416243 ACCACGGACTTACCTTGTCA 58.584 50.0 0.00 0.00 36.35 3.58 F
1132 1142 2.004583 TGCTTTTATCACGGACGAGG 57.995 50.0 0.00 0.00 0.00 4.63 F
2043 2325 1.095228 ACACGTGTTTCACTGCAGGG 61.095 55.0 17.22 15.69 31.34 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 2309 1.042003 TTTTGCTTGCCCTGCAGTGA 61.042 50.000 13.81 0.0 40.61 3.41 R
2576 4174 2.751259 GGACGGGGATGTTTACCTTTTC 59.249 50.000 0.00 0.0 0.00 2.29 R
3615 6960 3.535561 CGCCAACTGGATAATTGACTCT 58.464 45.455 0.00 0.0 37.39 3.24 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
31 32 2.170187 AGGCCTTGTTTGTTTGCATTGA 59.830 40.909 0.00 0.00 0.00 2.57
49 50 5.363580 GCATTGATTTGAGGGGGATTAAAGA 59.636 40.000 0.00 0.00 0.00 2.52
455 458 3.302870 CGAAACTCAAACACTTACCACGG 60.303 47.826 0.00 0.00 0.00 4.94
468 471 1.416243 ACCACGGACTTACCTTGTCA 58.584 50.000 0.00 0.00 36.35 3.58
603 606 4.500499 AATCTCTTAGACTTGCAGGCAT 57.500 40.909 0.00 0.00 0.00 4.40
703 706 5.376625 AGTTCAAATACAACTCTGGCAGAA 58.623 37.500 19.29 3.17 27.00 3.02
823 833 5.072741 AGTTGTGAAGACTTGGCACATATT 58.927 37.500 9.75 0.00 41.60 1.28
884 894 9.998106 TTTTAAGAGAAGTTAGCTTACTGATGT 57.002 29.630 6.07 0.00 34.61 3.06
1132 1142 2.004583 TGCTTTTATCACGGACGAGG 57.995 50.000 0.00 0.00 0.00 4.63
1185 1195 2.433604 ACATGAGAAGCGAGATGACCAT 59.566 45.455 0.00 0.00 0.00 3.55
1219 1229 2.281484 GGGTGAAGCAAGTCCGCA 60.281 61.111 0.00 0.00 0.00 5.69
2016 2290 3.446161 ACCGAAGTACAAATCCAGATCGA 59.554 43.478 0.00 0.00 0.00 3.59
2033 2309 1.271379 TCGATGAGGCTACACGTGTTT 59.729 47.619 28.55 10.39 0.00 2.83
2043 2325 1.095228 ACACGTGTTTCACTGCAGGG 61.095 55.000 17.22 15.69 31.34 4.45
2308 2615 3.571590 TGTTAAAAGAACAGGGGTGCAT 58.428 40.909 0.00 0.00 0.00 3.96
2495 3638 5.008613 TCCACTCAGCAATTTGAAGTTACAC 59.991 40.000 0.00 0.00 0.00 2.90
2775 5800 2.493278 CAATTGGCTTCGACCCAAGAAT 59.507 45.455 18.42 7.89 44.85 2.40
2993 6165 9.754382 AACATACCAAATCATATCATTTTGCTC 57.246 29.630 0.00 0.00 0.00 4.26
2994 6166 8.916062 ACATACCAAATCATATCATTTTGCTCA 58.084 29.630 0.00 0.00 0.00 4.26
2995 6167 9.923143 CATACCAAATCATATCATTTTGCTCAT 57.077 29.630 0.00 0.00 0.00 2.90
2997 6169 8.014070 ACCAAATCATATCATTTTGCTCATCA 57.986 30.769 0.00 0.00 0.00 3.07
2998 6170 8.647796 ACCAAATCATATCATTTTGCTCATCAT 58.352 29.630 0.00 0.00 0.00 2.45
2999 6171 9.489084 CCAAATCATATCATTTTGCTCATCATT 57.511 29.630 0.00 0.00 0.00 2.57
3004 6176 9.524106 TCATATCATTTTGCTCATCATTCAAAC 57.476 29.630 0.00 0.00 30.45 2.93
3005 6177 9.308318 CATATCATTTTGCTCATCATTCAAACA 57.692 29.630 0.00 0.00 30.45 2.83
3007 6179 7.589574 TCATTTTGCTCATCATTCAAACATG 57.410 32.000 0.00 0.00 30.45 3.21
3008 6180 7.156000 TCATTTTGCTCATCATTCAAACATGT 58.844 30.769 0.00 0.00 30.45 3.21
3009 6181 7.658167 TCATTTTGCTCATCATTCAAACATGTT 59.342 29.630 4.92 4.92 30.45 2.71
3010 6182 7.789273 TTTTGCTCATCATTCAAACATGTTT 57.211 28.000 18.13 18.13 30.45 2.83
3011 6183 7.789273 TTTGCTCATCATTCAAACATGTTTT 57.211 28.000 21.10 4.59 0.00 2.43
3347 6666 1.608025 GGTGAACTCATTGACCGAGCA 60.608 52.381 0.00 0.00 32.01 4.26
3536 6855 1.269621 CCTCACGTTCTTTCACCGAGT 60.270 52.381 0.00 0.00 0.00 4.18
3538 6857 2.978489 CTCACGTTCTTTCACCGAGTAC 59.022 50.000 0.00 0.00 0.00 2.73
3615 6960 2.034687 GGCTCTGGCTCTGGCAAA 59.965 61.111 0.00 0.00 37.73 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 6.138967 CAATCCTCTTTAATCCCCCTCAAAT 58.861 40.000 0.00 0.00 0.00 2.32
380 383 4.577152 CCGGCCATGGCATTCTAA 57.423 55.556 36.56 0.00 44.11 2.10
455 458 3.493503 CGTGGAAACTGACAAGGTAAGTC 59.506 47.826 0.00 0.00 36.55 3.01
468 471 1.873591 GCATGTGAGTTCGTGGAAACT 59.126 47.619 0.00 0.00 42.10 2.66
644 647 3.139850 CTGCATGGTTCATTTGCCAAAA 58.860 40.909 0.00 0.00 38.38 2.44
739 742 0.320421 TGACCAGGCTGTACGCTTTC 60.320 55.000 14.43 0.00 39.13 2.62
894 904 5.762711 TGTTATTAGAAAGTGAAGCTGTGCA 59.237 36.000 0.00 0.00 0.00 4.57
1132 1142 3.442977 AGGAAAGCTTGCATCATCTCAAC 59.557 43.478 6.80 0.00 0.00 3.18
1185 1195 1.358152 CCCAGGTCTTGACCACCTTA 58.642 55.000 20.36 0.00 41.95 2.69
1219 1229 3.009723 CCTCAACATCGTAGGCAACATT 58.990 45.455 0.00 0.00 41.41 2.71
1474 1538 9.737844 TTTGGAGCTACATATTGCATATCATTA 57.262 29.630 0.00 0.00 0.00 1.90
1808 2067 8.458843 CCAGGAATAATTTTCAATACGAACAGT 58.541 33.333 0.00 0.00 31.73 3.55
1850 2112 4.299547 ACAGCGCCAGTCGAGCAA 62.300 61.111 2.29 0.00 41.67 3.91
2016 2290 2.037251 AGTGAAACACGTGTAGCCTCAT 59.963 45.455 23.69 0.34 41.43 2.90
2033 2309 1.042003 TTTTGCTTGCCCTGCAGTGA 61.042 50.000 13.81 0.00 40.61 3.41
2043 2325 3.084786 ACCAGATCTACCTTTTGCTTGC 58.915 45.455 0.00 0.00 0.00 4.01
2308 2615 4.321899 GGTGCTTCCATATGCTTCAAAACA 60.322 41.667 0.00 0.00 35.97 2.83
2576 4174 2.751259 GGACGGGGATGTTTACCTTTTC 59.249 50.000 0.00 0.00 0.00 2.29
2747 5771 3.181500 GGGTCGAAGCCAATTGTAATCAC 60.181 47.826 4.43 1.62 35.40 3.06
2775 5800 5.784578 AAGGATGCGTATGACATACACTA 57.215 39.130 22.30 10.17 35.48 2.74
3536 6855 6.156602 TGGAGTAAGTCCCCAATAAATTCGTA 59.843 38.462 0.00 0.00 46.31 3.43
3538 6857 5.433526 TGGAGTAAGTCCCCAATAAATTCG 58.566 41.667 0.00 0.00 46.31 3.34
3615 6960 3.535561 CGCCAACTGGATAATTGACTCT 58.464 45.455 0.00 0.00 37.39 3.24


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

AutoCloner maintained by Alex Coulton.