Multiple sequence alignment - TraesCS2B01G502800

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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 TraesCS2B01G502800 chr2B 100.000 2601 0 0 1 2601 697399838 697397238 0.000000e+00 4804.0
1 TraesCS2B01G502800 chr2B 94.701 2038 95 9 1 2031 697380021 697377990 0.000000e+00 3153.0
2 TraesCS2B01G502800 chr2B 94.652 2038 98 7 1 2031 697342513 697340480 0.000000e+00 3149.0
3 TraesCS2B01G502800 chr2B 94.502 2037 91 4 1 2031 697143607 697141586 0.000000e+00 3121.0
4 TraesCS2B01G502800 chr2B 94.651 1720 83 4 320 2031 697295970 697294252 0.000000e+00 2658.0
5 TraesCS2B01G502800 chr2B 95.210 1545 72 2 402 1945 697015566 697014023 0.000000e+00 2442.0
6 TraesCS2B01G502800 chr2B 95.481 1527 68 1 505 2031 697158080 697156555 0.000000e+00 2436.0
7 TraesCS2B01G502800 chr2B 95.589 1519 65 2 505 2023 697229315 697227799 0.000000e+00 2433.0
8 TraesCS2B01G502800 chr2B 96.194 578 18 3 2028 2601 697359033 697358456 0.000000e+00 942.0
9 TraesCS2B01G502800 chr2B 96.194 578 18 3 2028 2601 697377898 697377321 0.000000e+00 942.0
10 TraesCS2B01G502800 chr2B 96.021 578 19 3 2028 2601 697340388 697339811 0.000000e+00 937.0
11 TraesCS2B01G502800 chr2B 92.642 598 17 6 2028 2598 697156463 697155866 0.000000e+00 835.0
12 TraesCS2B01G502800 chr2B 94.118 510 26 2 1 509 697257859 697257353 0.000000e+00 773.0
13 TraesCS2B01G502800 chr2B 93.725 510 28 2 1 509 697186135 697185629 0.000000e+00 761.0
14 TraesCS2B01G502800 chr2B 96.659 449 14 1 2154 2601 697141390 697140942 0.000000e+00 745.0
15 TraesCS2B01G502800 chr2B 96.429 448 16 0 2154 2601 697010516 697010069 0.000000e+00 739.0
16 TraesCS2B01G502800 chr2B 97.229 397 11 0 2205 2601 697227251 697226855 0.000000e+00 673.0
17 TraesCS2B01G502800 chr2B 95.077 325 16 0 1 325 697324216 697323892 1.790000e-141 512.0
18 TraesCS2B01G502800 chr2B 97.753 267 6 0 2335 2601 697289903 697289637 6.560000e-126 460.0
19 TraesCS2B01G502800 chr2B 96.377 138 5 0 2028 2165 697010678 697010541 7.240000e-56 228.0
20 TraesCS2B01G502800 chr2B 95.652 138 6 0 2028 2165 697294160 697294023 3.370000e-54 222.0
21 TraesCS2B01G502800 chr2B 94.215 121 7 0 2166 2286 697290022 697289902 4.420000e-43 185.0
22 TraesCS2B01G502800 chr2B 97.753 89 2 0 1943 2031 697010858 697010770 1.250000e-33 154.0
23 TraesCS2B01G502800 chr2B 96.825 63 2 0 2028 2090 697141494 697141432 3.540000e-19 106.0
24 TraesCS2B01G502800 chr2D 88.655 1428 137 8 327 1738 579511873 579510455 0.000000e+00 1716.0
25 TraesCS2B01G502800 chr2D 90.570 509 42 5 2095 2601 579510165 579509661 0.000000e+00 669.0
26 TraesCS2B01G502800 chr2D 97.222 36 1 0 2063 2098 579510457 579510422 7.770000e-06 62.1
27 TraesCS2B01G502800 chr2A 77.793 707 150 7 930 1633 773563499 773562797 1.850000e-116 429.0


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 TraesCS2B01G502800 chr2B 697397238 697399838 2600 True 4804.00 4804 100.000000 1 2601 1 chr2B.!!$R5 2600
1 TraesCS2B01G502800 chr2B 697377321 697380021 2700 True 2047.50 3153 95.447500 1 2601 2 chr2B.!!$R13 2600
2 TraesCS2B01G502800 chr2B 697339811 697342513 2702 True 2043.00 3149 95.336500 1 2601 2 chr2B.!!$R12 2600
3 TraesCS2B01G502800 chr2B 697155866 697158080 2214 True 1635.50 2436 94.061500 505 2598 2 chr2B.!!$R8 2093
4 TraesCS2B01G502800 chr2B 697226855 697229315 2460 True 1553.00 2433 96.409000 505 2601 2 chr2B.!!$R9 2096
5 TraesCS2B01G502800 chr2B 697294023 697295970 1947 True 1440.00 2658 95.151500 320 2165 2 chr2B.!!$R11 1845
6 TraesCS2B01G502800 chr2B 697140942 697143607 2665 True 1324.00 3121 95.995333 1 2601 3 chr2B.!!$R7 2600
7 TraesCS2B01G502800 chr2B 697358456 697359033 577 True 942.00 942 96.194000 2028 2601 1 chr2B.!!$R4 573
8 TraesCS2B01G502800 chr2B 697010069 697015566 5497 True 890.75 2442 96.442250 402 2601 4 chr2B.!!$R6 2199
9 TraesCS2B01G502800 chr2B 697257353 697257859 506 True 773.00 773 94.118000 1 509 1 chr2B.!!$R2 508
10 TraesCS2B01G502800 chr2B 697185629 697186135 506 True 761.00 761 93.725000 1 509 1 chr2B.!!$R1 508
11 TraesCS2B01G502800 chr2D 579509661 579511873 2212 True 815.70 1716 92.149000 327 2601 3 chr2D.!!$R1 2274
12 TraesCS2B01G502800 chr2A 773562797 773563499 702 True 429.00 429 77.793000 930 1633 1 chr2A.!!$R1 703

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
575 587 2.091775 ACCACCTTCTCTAGCGGTAGAT 60.092 50.0 23.55 6.83 34.63 1.98 F
1156 1170 0.687920 TACGCCATGAGGACAACCAA 59.312 50.0 0.00 0.00 38.94 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1519 1533 0.543410 TCCTCCCGCTTAGTTCACCA 60.543 55.000 0.0 0.0 0.0 4.17 R
2392 5984 7.395489 ACAACTATGCAGGAAATGAGAAAGATT 59.605 33.333 0.0 0.0 0.0 2.40 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
36 38 6.317140 TCAATTCTAGACACCATCATCAAAGC 59.683 38.462 0.00 0.00 0.00 3.51
84 86 7.507829 AGCTCTCAGTATATTTGCTCTTGATT 58.492 34.615 0.00 0.00 0.00 2.57
205 208 6.231211 CAACATCCCAGGTAATACTATCCAC 58.769 44.000 0.00 0.00 0.00 4.02
308 311 9.450807 GGTAATAATTGATGCAACATGACTAAC 57.549 33.333 0.00 0.00 0.00 2.34
362 365 8.251721 ACTCATGTCATAGAACAAGTTACTACC 58.748 37.037 0.00 0.00 31.81 3.18
371 374 6.597562 AGAACAAGTTACTACCCAAACATCA 58.402 36.000 0.00 0.00 0.00 3.07
373 376 7.558444 AGAACAAGTTACTACCCAAACATCAAA 59.442 33.333 0.00 0.00 0.00 2.69
375 378 7.712797 ACAAGTTACTACCCAAACATCAAAAG 58.287 34.615 0.00 0.00 0.00 2.27
575 587 2.091775 ACCACCTTCTCTAGCGGTAGAT 60.092 50.000 23.55 6.83 34.63 1.98
582 594 6.151985 ACCTTCTCTAGCGGTAGATCATATTG 59.848 42.308 23.55 10.99 34.63 1.90
584 596 4.950475 TCTCTAGCGGTAGATCATATTGGG 59.050 45.833 23.55 9.64 34.63 4.12
610 622 9.967346 GCTACTTCACTTTTTAAGATTTTTCCT 57.033 29.630 0.00 0.00 0.00 3.36
786 798 8.948853 ATTGTTGAATATTTGTGTAACTGTCG 57.051 30.769 0.00 0.00 38.04 4.35
860 873 4.837896 TGTGTCCAATTAATGTTCGCAA 57.162 36.364 0.00 0.00 0.00 4.85
871 884 8.987729 CAATTAATGTTCGCAATAAAATGTTGC 58.012 29.630 2.20 2.20 46.37 4.17
893 906 9.944663 GTTGCTTTAAATTCATGTTCGGATATA 57.055 29.630 0.00 0.00 0.00 0.86
1041 1055 3.831323 TGATTGTTGTGGAACCACTCAT 58.169 40.909 21.98 10.31 46.30 2.90
1049 1063 3.088532 GTGGAACCACTCATATTGCCAA 58.911 45.455 15.69 0.00 43.12 4.52
1053 1067 4.498009 GGAACCACTCATATTGCCAATTCG 60.498 45.833 0.00 0.00 0.00 3.34
1070 1084 1.149174 CGCCAGAGCCCCACATAAT 59.851 57.895 0.00 0.00 34.57 1.28
1096 1110 4.499183 ACTCGTTATCTCAAGCTCCAAAG 58.501 43.478 0.00 0.00 0.00 2.77
1115 1129 5.453198 CCAAAGCCTCACTAACAAACCAAAT 60.453 40.000 0.00 0.00 0.00 2.32
1127 1141 9.829507 ACTAACAAACCAAATTTTTCATCATCA 57.170 25.926 0.00 0.00 0.00 3.07
1156 1170 0.687920 TACGCCATGAGGACAACCAA 59.312 50.000 0.00 0.00 38.94 3.67
1170 1184 5.014123 AGGACAACCAATTTCCTACTCATCA 59.986 40.000 0.00 0.00 38.03 3.07
1183 1197 5.700832 TCCTACTCATCATTGTTGTTGTGAC 59.299 40.000 0.00 0.00 0.00 3.67
1452 1466 4.349636 TGACACACTTTGAGGGGAAAGATA 59.650 41.667 0.00 0.00 36.58 1.98
1519 1533 3.681034 CGCCAACTTCTCTCCTTCATGAT 60.681 47.826 0.00 0.00 0.00 2.45
1742 1776 5.640218 TGTTACCTTCGTTGTAAAACTCG 57.360 39.130 0.00 0.00 30.52 4.18
1752 1786 2.758009 TGTAAAACTCGGGAAGGTTCG 58.242 47.619 0.00 0.00 32.14 3.95
1776 1810 6.220201 GTGATATTTCTCCCAGCTAGACTTC 58.780 44.000 0.00 0.00 0.00 3.01
1782 1816 5.130705 TCTCCCAGCTAGACTTCAGAATA 57.869 43.478 0.00 0.00 0.00 1.75
1836 1870 7.945134 ACTAACAAGTGCTTCAGAATCAAAAT 58.055 30.769 0.00 0.00 0.00 1.82
2124 5680 4.750833 TTTCCCTCATAAAAGGTTGGGA 57.249 40.909 0.00 0.00 41.46 4.37
2227 5819 3.915437 ACAAATTTCACCACTTAGCCG 57.085 42.857 0.00 0.00 0.00 5.52
2295 5887 8.307582 TCTAAGAGTTTCACCCTCTATTAAGG 57.692 38.462 0.00 0.00 38.32 2.69
2392 5984 6.070596 AGCGAATGAATATGATCATCAGGGTA 60.071 38.462 12.53 0.00 39.08 3.69
2415 6007 7.500559 GGTAATCTTTCTCATTTCCTGCATAGT 59.499 37.037 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 38 3.006859 TGCATAGGTGGATCGATTACCAG 59.993 47.826 25.47 18.21 36.82 4.00
84 86 3.844211 ACCTTACTTTGCTAGGTCATGGA 59.156 43.478 0.00 0.00 37.78 3.41
174 176 8.057246 AGTATTACCTGGGATGTTGGAATATT 57.943 34.615 0.00 0.00 0.00 1.28
220 223 9.136323 CCCAAAAAGGCATCTAGAAATATACTT 57.864 33.333 0.00 0.00 35.39 2.24
232 235 5.306678 TCAAAATACACCCAAAAAGGCATCT 59.693 36.000 0.00 0.00 35.39 2.90
373 376 9.790344 CCTCTAATGATTTATCACATCCTTCTT 57.210 33.333 0.00 0.00 40.03 2.52
375 378 9.566432 AACCTCTAATGATTTATCACATCCTTC 57.434 33.333 0.00 0.00 40.03 3.46
575 587 8.871629 TTAAAAAGTGAAGTAGCCCAATATGA 57.128 30.769 0.00 0.00 0.00 2.15
582 594 9.193133 GAAAAATCTTAAAAAGTGAAGTAGCCC 57.807 33.333 0.00 0.00 0.00 5.19
584 596 9.967346 AGGAAAAATCTTAAAAAGTGAAGTAGC 57.033 29.630 0.00 0.00 0.00 3.58
610 622 9.094578 TGTTGGAATATTTGGGTCAAAGAAATA 57.905 29.630 0.00 0.00 36.76 1.40
786 798 6.509418 TGACTACAAGATTTTATTGGGTGC 57.491 37.500 0.00 0.00 31.76 5.01
835 848 5.645929 TGCGAACATTAATTGGACACATACT 59.354 36.000 0.00 0.00 0.00 2.12
979 993 3.327757 AGACATCACTACAGGAGGCAAAA 59.672 43.478 0.00 0.00 0.00 2.44
1049 1063 1.344953 TATGTGGGGCTCTGGCGAAT 61.345 55.000 0.00 0.00 39.81 3.34
1053 1067 0.538287 GGATTATGTGGGGCTCTGGC 60.538 60.000 0.00 0.00 37.82 4.85
1070 1084 2.355132 GAGCTTGAGATAACGAGTCGGA 59.645 50.000 18.30 4.54 0.00 4.55
1096 1110 6.536941 TGAAAAATTTGGTTTGTTAGTGAGGC 59.463 34.615 0.00 0.00 0.00 4.70
1115 1129 9.123709 GCGTATAAACTTTGTGATGATGAAAAA 57.876 29.630 0.00 0.00 0.00 1.94
1127 1141 4.634443 GTCCTCATGGCGTATAAACTTTGT 59.366 41.667 0.00 0.00 0.00 2.83
1156 1170 7.448161 TCACAACAACAATGATGAGTAGGAAAT 59.552 33.333 0.00 0.00 33.82 2.17
1170 1184 3.304391 GCATACACGGTCACAACAACAAT 60.304 43.478 0.00 0.00 0.00 2.71
1183 1197 0.103390 TACACCGATGGCATACACGG 59.897 55.000 20.65 20.65 44.16 4.94
1452 1466 4.773323 GCAACTCTGCCTTGTATTTTCT 57.227 40.909 0.00 0.00 43.26 2.52
1519 1533 0.543410 TCCTCCCGCTTAGTTCACCA 60.543 55.000 0.00 0.00 0.00 4.17
1742 1776 4.127907 GGAGAAATATCACGAACCTTCCC 58.872 47.826 0.00 0.00 0.00 3.97
1752 1786 5.799827 AGTCTAGCTGGGAGAAATATCAC 57.200 43.478 0.00 0.00 0.00 3.06
1861 1895 1.000955 ACTTTCACTGGAACTCGCGAT 59.999 47.619 10.36 0.00 31.35 4.58
1935 1969 4.724279 ACTTCCAACAACTAAGGGTGAT 57.276 40.909 0.00 0.00 0.00 3.06
2008 5209 8.887717 CAAATACTTGATAGTTCTTTCTGAGGG 58.112 37.037 0.00 0.00 35.78 4.30
2309 5901 7.548075 GGGTTATCTCGTAATGACTTGAAGAAA 59.452 37.037 0.00 0.00 0.00 2.52
2392 5984 7.395489 ACAACTATGCAGGAAATGAGAAAGATT 59.605 33.333 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.