Multiple sequence alignment - TraesCS2D01G085700

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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 TraesCS2D01G085700 chr2D 100.000 2339 0 0 1 2339 37042165 37039827 0.000000e+00 4320.0
1 TraesCS2D01G085700 chr2D 85.977 706 73 13 649 1334 37047245 37046546 0.000000e+00 732.0
2 TraesCS2D01G085700 chr2D 84.647 482 52 10 867 1334 37028302 37027829 5.890000e-126 460.0
3 TraesCS2D01G085700 chr2D 88.053 226 14 6 649 865 37028811 37028590 2.980000e-64 255.0
4 TraesCS2D01G085700 chr2B 95.575 1401 37 6 1 1376 63839138 63840538 0.000000e+00 2220.0
5 TraesCS2D01G085700 chr2B 89.221 1772 109 35 614 2339 64234047 64232312 0.000000e+00 2139.0
6 TraesCS2D01G085700 chr2B 92.563 874 52 10 1473 2339 64608053 64608920 0.000000e+00 1242.0
7 TraesCS2D01G085700 chr2B 92.839 782 46 9 1473 2251 64603661 64604435 0.000000e+00 1125.0
8 TraesCS2D01G085700 chr2B 92.378 761 44 11 1587 2339 64689276 64690030 0.000000e+00 1072.0
9 TraesCS2D01G085700 chr2B 94.661 487 19 5 1373 1856 63840698 63841180 0.000000e+00 749.0
10 TraesCS2D01G085700 chr2B 94.655 449 21 3 1854 2302 63841261 63841706 0.000000e+00 693.0
11 TraesCS2D01G085700 chr2B 85.085 704 69 17 649 1339 63849003 63849683 0.000000e+00 686.0
12 TraesCS2D01G085700 chr2B 83.810 525 63 12 865 1367 64764712 64764188 1.630000e-131 479.0
13 TraesCS2D01G085700 chr2B 89.973 369 37 0 966 1334 64212644 64212276 5.850000e-131 477.0
14 TraesCS2D01G085700 chr2B 93.548 310 19 1 2031 2339 64662698 64662389 5.890000e-126 460.0
15 TraesCS2D01G085700 chr2B 92.903 310 21 1 2031 2339 64601290 64600981 1.270000e-122 449.0
16 TraesCS2D01G085700 chr2B 94.410 161 6 1 1369 1529 64607898 64607741 6.460000e-61 244.0
17 TraesCS2D01G085700 chr2B 94.410 161 6 1 1369 1529 64664951 64664794 6.460000e-61 244.0
18 TraesCS2D01G085700 chr2B 93.789 161 7 1 1369 1529 64603508 64603351 3.000000e-59 239.0
19 TraesCS2D01G085700 chr2B 97.368 114 3 0 1473 1586 64665103 64665216 6.600000e-46 195.0
20 TraesCS2D01G085700 chr2B 82.906 234 20 7 649 877 64212931 64212713 2.370000e-45 193.0
21 TraesCS2D01G085700 chr2B 90.217 92 5 1 644 735 64620682 64620595 1.470000e-22 117.0
22 TraesCS2D01G085700 chr2B 90.217 92 5 1 644 735 64703355 64703268 1.470000e-22 117.0
23 TraesCS2D01G085700 chr2B 82.075 106 15 2 388 491 658489896 658489793 1.150000e-13 87.9
24 TraesCS2D01G085700 chr2B 81.176 85 9 7 386 468 673966886 673966807 6.980000e-06 62.1
25 TraesCS2D01G085700 chr2A 84.143 782 68 33 387 1138 41650601 41649846 0.000000e+00 706.0
26 TraesCS2D01G085700 chr2A 90.826 109 10 0 1980 2088 277141771 277141879 1.870000e-31 147.0
27 TraesCS2D01G085700 chr2A 87.037 108 8 3 650 757 41655811 41655710 1.470000e-22 117.0
28 TraesCS2D01G085700 chr7B 82.738 336 43 5 997 1332 137802144 137801824 3.800000e-73 285.0
29 TraesCS2D01G085700 chr7D 83.516 273 44 1 997 1269 171322222 171321951 1.070000e-63 254.0
30 TraesCS2D01G085700 chr6D 80.124 322 55 8 297 614 340856240 340855924 5.030000e-57 231.0
31 TraesCS2D01G085700 chr6D 79.913 229 40 5 387 612 115327595 115327370 1.860000e-36 163.0
32 TraesCS2D01G085700 chr6D 88.462 130 11 4 290 418 340856500 340856374 1.120000e-33 154.0
33 TraesCS2D01G085700 chr6D 87.597 129 13 3 290 417 340843342 340843216 1.870000e-31 147.0
34 TraesCS2D01G085700 chr6D 88.430 121 12 2 297 416 340843082 340842963 6.740000e-31 145.0
35 TraesCS2D01G085700 chr3B 83.978 181 27 2 322 500 823280817 823280637 3.090000e-39 172.0
36 TraesCS2D01G085700 chrUn 92.661 109 8 0 1980 2088 17536285 17536177 8.650000e-35 158.0
37 TraesCS2D01G085700 chrUn 78.448 232 40 8 367 594 127034434 127034209 2.420000e-30 143.0
38 TraesCS2D01G085700 chr6B 80.526 190 31 5 367 553 686189677 686189491 8.710000e-30 141.0
39 TraesCS2D01G085700 chr1D 90.385 104 10 0 317 420 381308571 381308468 1.130000e-28 137.0
40 TraesCS2D01G085700 chr5B 75.325 231 31 15 384 610 120303366 120303158 1.150000e-13 87.9


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 TraesCS2D01G085700 chr2D 37039827 37042165 2338 True 4320.000000 4320 100.000000 1 2339 1 chr2D.!!$R1 2338
1 TraesCS2D01G085700 chr2D 37046546 37047245 699 True 732.000000 732 85.977000 649 1334 1 chr2D.!!$R2 685
2 TraesCS2D01G085700 chr2D 37027829 37028811 982 True 357.500000 460 86.350000 649 1334 2 chr2D.!!$R3 685
3 TraesCS2D01G085700 chr2B 64232312 64234047 1735 True 2139.000000 2139 89.221000 614 2339 1 chr2B.!!$R1 1725
4 TraesCS2D01G085700 chr2B 63839138 63841706 2568 False 1220.666667 2220 94.963667 1 2302 3 chr2B.!!$F4 2301
5 TraesCS2D01G085700 chr2B 64603661 64608920 5259 False 1183.500000 1242 92.701000 1473 2339 2 chr2B.!!$F5 866
6 TraesCS2D01G085700 chr2B 64689276 64690030 754 False 1072.000000 1072 92.378000 1587 2339 1 chr2B.!!$F3 752
7 TraesCS2D01G085700 chr2B 63849003 63849683 680 False 686.000000 686 85.085000 649 1339 1 chr2B.!!$F1 690
8 TraesCS2D01G085700 chr2B 64764188 64764712 524 True 479.000000 479 83.810000 865 1367 1 chr2B.!!$R5 502
9 TraesCS2D01G085700 chr2B 64662389 64664951 2562 True 352.000000 460 93.979000 1369 2339 2 chr2B.!!$R10 970
10 TraesCS2D01G085700 chr2B 64600981 64603508 2527 True 344.000000 449 93.346000 1369 2339 2 chr2B.!!$R9 970
11 TraesCS2D01G085700 chr2B 64212276 64212931 655 True 335.000000 477 86.439500 649 1334 2 chr2B.!!$R8 685
12 TraesCS2D01G085700 chr2A 41649846 41650601 755 True 706.000000 706 84.143000 387 1138 1 chr2A.!!$R1 751

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
241 242 2.626088 GCACTAAGCTTCAGGCAAAG 57.374 50.0 0.0 0.0 44.79 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2060 8530 2.505777 CTCTCAGCGCAGTGGTCG 60.506 66.667 11.47 0.0 0.0 4.79 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
64 65 4.142687 CCCCGTACAATGAAGACAAATGTC 60.143 45.833 5.40 5.40 45.08 3.06
98 99 4.820775 ACTAAGGGATCATCTCCTAGCAA 58.179 43.478 0.00 0.00 44.28 3.91
110 111 7.628234 TCATCTCCTAGCAAAAAGAAGAGAAT 58.372 34.615 0.00 0.00 33.03 2.40
138 139 8.871686 TTATTTTGTTTGCTCTCTCTTTTTCC 57.128 30.769 0.00 0.00 0.00 3.13
148 149 3.657727 TCTCTCTTTTTCCCCTCACCAAT 59.342 43.478 0.00 0.00 0.00 3.16
153 154 5.898120 TCTTTTTCCCCTCACCAATTATCA 58.102 37.500 0.00 0.00 0.00 2.15
184 185 3.950397 TCCCAAAATTAGCGACATGTCT 58.050 40.909 22.95 8.49 0.00 3.41
185 186 5.092554 TCCCAAAATTAGCGACATGTCTA 57.907 39.130 22.95 7.46 0.00 2.59
203 204 7.175641 ACATGTCTATGCCCTTATAAATGCTTC 59.824 37.037 0.00 0.00 37.85 3.86
241 242 2.626088 GCACTAAGCTTCAGGCAAAG 57.374 50.000 0.00 0.00 44.79 2.77
256 257 7.259290 TCAGGCAAAGTTTTACTACTTGAAG 57.741 36.000 0.00 0.00 38.33 3.02
291 292 3.191371 ACTGCTTAATTTCTTCGCCTTGG 59.809 43.478 0.00 0.00 0.00 3.61
320 321 8.896722 TCCTATATACCTAAAAGACTCATCCC 57.103 38.462 0.00 0.00 0.00 3.85
690 726 5.983118 TGTAATATGCGTGAACTGTATCAGG 59.017 40.000 1.90 7.71 38.05 3.86
741 777 7.646526 CCATAAATCACATGTGCTCATAAAGTG 59.353 37.037 21.38 6.21 32.47 3.16
923 975 4.227197 ACCGATCTCCATATCTGAAGGTT 58.773 43.478 0.00 0.00 0.00 3.50
930 982 5.102953 TCCATATCTGAAGGTTCCAACTG 57.897 43.478 0.00 0.00 0.00 3.16
1078 1154 4.972875 AGGCATGCCTAGTTCAGC 57.027 55.556 37.99 7.11 46.14 4.26
1104 1180 2.008329 GAGACGTACGTCCTGATGAGT 58.992 52.381 37.43 21.06 45.59 3.41
1268 1350 2.671963 GGGGGTTCACTTCCGTGC 60.672 66.667 0.00 0.00 40.99 5.34
1425 1675 4.735822 CGATCTGAACCGTTTGTCTCTATC 59.264 45.833 0.00 0.00 0.00 2.08
1427 1677 5.723672 TCTGAACCGTTTGTCTCTATCTT 57.276 39.130 0.00 0.00 0.00 2.40
1428 1678 5.710984 TCTGAACCGTTTGTCTCTATCTTC 58.289 41.667 0.00 0.00 0.00 2.87
1587 6271 7.477494 CCTTGGGTATAATTTGGTTTTCGTAG 58.523 38.462 0.00 0.00 0.00 3.51
1760 6476 2.294791 CGCCCCTGACTATAAGTCTCAG 59.705 54.545 8.42 0.00 45.27 3.35
1884 6683 8.033038 TCATGTGTAAATGGTCTACAGTACTTC 58.967 37.037 0.00 0.00 30.04 3.01
1923 6722 4.095590 CCGTGGGTGGCAGATTTT 57.904 55.556 0.00 0.00 0.00 1.82
1977 6776 6.198029 CAGCAATACATTCACGTCTAGAAGAG 59.802 42.308 12.91 4.69 0.00 2.85
2105 8577 9.993454 TCATCCACAAAAATAAATGATCAACAA 57.007 25.926 0.00 0.00 0.00 2.83
2306 8783 8.554490 ACTTACTGGTAAATATCATCACCTCT 57.446 34.615 0.00 0.00 32.04 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 7.094377 GGTGCCTTCTCTAATTCACATGTTTTA 60.094 37.037 0.00 0.00 0.00 1.52
138 139 3.633525 CCACACATGATAATTGGTGAGGG 59.366 47.826 0.00 0.00 38.04 4.30
148 149 3.378861 TTGGGATGCCACACATGATAA 57.621 42.857 4.96 0.00 39.84 1.75
153 154 3.118665 GCTAATTTTGGGATGCCACACAT 60.119 43.478 4.96 0.00 43.54 3.21
184 185 8.476064 TCATTTGAAGCATTTATAAGGGCATA 57.524 30.769 11.52 0.00 0.00 3.14
185 186 7.364149 TCATTTGAAGCATTTATAAGGGCAT 57.636 32.000 11.52 1.64 0.00 4.40
203 204 1.407979 GCTTCCAGAGGCCATCATTTG 59.592 52.381 5.01 0.00 0.00 2.32
584 587 1.241315 ATGCCCTGCACGTTGTTACC 61.241 55.000 0.00 0.00 43.04 2.85
690 726 6.129088 GCTTGCAAACTTGTAATTAAGCTCAC 60.129 38.462 0.00 0.00 37.06 3.51
741 777 7.171337 TGTCGTTTATTTGGTGTACCTACTTTC 59.829 37.037 2.32 0.00 36.82 2.62
923 975 1.525077 GCGTGTCAACCCAGTTGGA 60.525 57.895 7.56 0.00 42.99 3.53
930 982 1.227853 AAGTCTGGCGTGTCAACCC 60.228 57.895 0.00 0.00 0.00 4.11
1078 1154 2.572647 GACGTACGTCTCGTGGCG 60.573 66.667 34.97 10.27 41.39 5.69
1389 1637 4.508124 GGTTCAGATCGCCACTAAGTATTG 59.492 45.833 0.00 0.00 0.00 1.90
1425 1675 5.163754 ACGGTTGAGTGTTCAAGAAAAGAAG 60.164 40.000 0.00 0.00 43.66 2.85
1427 1677 4.258543 ACGGTTGAGTGTTCAAGAAAAGA 58.741 39.130 0.00 0.00 43.66 2.52
1428 1678 4.616181 ACGGTTGAGTGTTCAAGAAAAG 57.384 40.909 0.00 0.00 43.66 2.27
1532 1783 2.622064 AGATCCGCCATTGGACTTAC 57.378 50.000 6.95 0.00 41.85 2.34
1760 6476 8.857216 GTCTGATCAAATTCACATTGTGATTTC 58.143 33.333 19.63 10.96 42.40 2.17
1806 6522 6.166279 ACTTGCTGTTCTAGATCGAATGAAA 58.834 36.000 0.00 0.00 0.00 2.69
1807 6523 5.724328 ACTTGCTGTTCTAGATCGAATGAA 58.276 37.500 0.00 0.00 0.00 2.57
1811 6527 4.155462 ACGTACTTGCTGTTCTAGATCGAA 59.845 41.667 0.00 0.00 0.00 3.71
1884 6683 3.820689 CAATACGGTGGTGTCATTTGTG 58.179 45.455 0.00 0.00 0.00 3.33
2060 8530 2.505777 CTCTCAGCGCAGTGGTCG 60.506 66.667 11.47 0.00 0.00 4.79
2131 8603 4.929819 TTCTTTTAGCTTTTGTGGGGAC 57.070 40.909 0.00 0.00 0.00 4.46
2306 8783 7.225784 ACACAAACATGCCTGAACAATTATA 57.774 32.000 0.00 0.00 0.00 0.98
2314 8791 2.553602 CAGCTACACAAACATGCCTGAA 59.446 45.455 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.