Multiple sequence alignment - TraesCS2B01G119900

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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 TraesCS2B01G119900 chr2B 100.000 1794 0 0 1 1794 87757426 87755633 0.000000e+00 3314
1 TraesCS2B01G119900 chr2B 96.772 1363 41 3 1 1362 390803527 390802167 0.000000e+00 2270
2 TraesCS2B01G119900 chr2B 94.009 434 11 7 1362 1792 87745897 87745476 0.000000e+00 643
3 TraesCS2B01G119900 chr2B 100.000 313 0 0 2027 2339 87755400 87755088 1.560000e-161 579
4 TraesCS2B01G119900 chr2B 92.357 314 18 6 2027 2339 87745337 87745029 2.130000e-120 442
5 TraesCS2B01G119900 chr1B 96.628 1364 44 2 1 1363 92336397 92337759 0.000000e+00 2263
6 TraesCS2B01G119900 chr1B 86.347 271 35 2 2070 2339 17760929 17760660 6.320000e-76 294
7 TraesCS2B01G119900 chr3B 96.552 1363 46 1 1 1362 161678845 161677483 0.000000e+00 2255
8 TraesCS2B01G119900 chr3B 96.256 1362 49 2 1 1362 727124088 727122729 0.000000e+00 2231
9 TraesCS2B01G119900 chr3B 96.185 1363 52 0 1 1363 772414831 772413469 0.000000e+00 2230
10 TraesCS2B01G119900 chr3B 96.112 1363 51 2 1 1362 571263362 571262001 0.000000e+00 2222
11 TraesCS2B01G119900 chr5B 96.478 1363 47 1 1 1362 547493213 547491851 0.000000e+00 2250
12 TraesCS2B01G119900 chr5B 96.405 1363 48 1 1 1362 59780959 59779597 0.000000e+00 2244
13 TraesCS2B01G119900 chr6B 96.476 1362 47 1 1 1362 257594373 257595733 0.000000e+00 2248
14 TraesCS2B01G119900 chr1D 86.545 275 34 3 2066 2339 470719304 470719032 1.360000e-77 300
15 TraesCS2B01G119900 chr4B 90.950 221 18 2 2066 2285 27486105 27485886 1.760000e-76 296
16 TraesCS2B01G119900 chr2D 84.727 275 39 3 2066 2339 181352359 181352087 2.960000e-69 272
17 TraesCS2B01G119900 chr2D 83.394 277 37 6 2066 2337 599296923 599296651 4.990000e-62 248
18 TraesCS2B01G119900 chr7D 90.355 197 17 2 2144 2339 555609823 555610018 8.290000e-65 257
19 TraesCS2B01G119900 chr6A 86.932 176 22 1 2164 2339 22974828 22974654 1.830000e-46 196


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 TraesCS2B01G119900 chr2B 87755088 87757426 2338 True 1946.5 3314 100.000 1 2339 2 chr2B.!!$R3 2338
1 TraesCS2B01G119900 chr2B 390802167 390803527 1360 True 2270.0 2270 96.772 1 1362 1 chr2B.!!$R1 1361
2 TraesCS2B01G119900 chr2B 87745029 87745897 868 True 542.5 643 93.183 1362 2339 2 chr2B.!!$R2 977
3 TraesCS2B01G119900 chr1B 92336397 92337759 1362 False 2263.0 2263 96.628 1 1363 1 chr1B.!!$F1 1362
4 TraesCS2B01G119900 chr3B 161677483 161678845 1362 True 2255.0 2255 96.552 1 1362 1 chr3B.!!$R1 1361
5 TraesCS2B01G119900 chr3B 727122729 727124088 1359 True 2231.0 2231 96.256 1 1362 1 chr3B.!!$R3 1361
6 TraesCS2B01G119900 chr3B 772413469 772414831 1362 True 2230.0 2230 96.185 1 1363 1 chr3B.!!$R4 1362
7 TraesCS2B01G119900 chr3B 571262001 571263362 1361 True 2222.0 2222 96.112 1 1362 1 chr3B.!!$R2 1361
8 TraesCS2B01G119900 chr5B 547491851 547493213 1362 True 2250.0 2250 96.478 1 1362 1 chr5B.!!$R2 1361
9 TraesCS2B01G119900 chr5B 59779597 59780959 1362 True 2244.0 2244 96.405 1 1362 1 chr5B.!!$R1 1361
10 TraesCS2B01G119900 chr6B 257594373 257595733 1360 False 2248.0 2248 96.476 1 1362 1 chr6B.!!$F1 1361

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
862 863 0.105862 ATGGTCTAATCCCCCGACGA 60.106 55.0 0.0 0.0 0.0 4.2 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1704 1710 0.620556 AACAGCTCACGAATCCCCAT 59.379 50.0 0.0 0.0 0.0 4.0 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
217 218 4.081697 TCCCGATATCGCAACATGATATGT 60.082 41.667 19.78 0.00 38.74 2.29
294 295 4.162131 GCTTATTTTGTGGAATGGGACCAT 59.838 41.667 0.00 0.00 39.69 3.55
326 327 5.640357 GGAACAAGTTACGACATACCAATGA 59.360 40.000 0.00 0.00 36.54 2.57
373 374 1.544724 TTGGGCGAGGATTTGGAAAG 58.455 50.000 0.00 0.00 0.00 2.62
522 523 6.039616 GCCAGAAGACACAAAACATTTGTTA 58.960 36.000 5.77 0.00 37.25 2.41
579 580 5.652324 AGACTAGGGGTGGACGATATTATT 58.348 41.667 0.00 0.00 0.00 1.40
607 608 6.477033 CAGAGCTTGTAAAATAGACTATGCGT 59.523 38.462 0.00 0.00 0.00 5.24
736 737 1.480545 GGGAAAGGCGCAAATTGGTAT 59.519 47.619 10.83 0.00 0.00 2.73
862 863 0.105862 ATGGTCTAATCCCCCGACGA 60.106 55.000 0.00 0.00 0.00 4.20
906 907 4.265904 TGCTTCTTTTGATCACGACCTA 57.734 40.909 0.00 0.00 0.00 3.08
977 979 2.089201 CGGTGGGGAAAATGGTAAGAC 58.911 52.381 0.00 0.00 0.00 3.01
982 984 3.245122 TGGGGAAAATGGTAAGACTGACC 60.245 47.826 1.37 1.37 37.49 4.02
1061 1063 2.156098 GCAAAGGACGGGTTGTAATCA 58.844 47.619 0.00 0.00 0.00 2.57
1098 1100 5.014202 TCGGATAATATGGAGGTGATCGAA 58.986 41.667 0.00 0.00 0.00 3.71
1176 1179 5.587289 TGTTTTCACTTAGCTTGCGATTTT 58.413 33.333 0.00 0.00 0.00 1.82
1177 1180 6.039616 TGTTTTCACTTAGCTTGCGATTTTT 58.960 32.000 0.00 0.00 0.00 1.94
1182 1185 8.487313 TTCACTTAGCTTGCGATTTTTCTATA 57.513 30.769 0.00 0.00 0.00 1.31
1185 1188 8.551205 CACTTAGCTTGCGATTTTTCTATATCA 58.449 33.333 0.00 0.00 0.00 2.15
1390 1393 6.649141 GTCATACACTTTACATCAGGTGTTGA 59.351 38.462 0.00 0.00 42.29 3.18
1404 1407 2.486203 GGTGTTGATGTTATCACGGCAA 59.514 45.455 0.00 0.00 39.39 4.52
1434 1437 1.074752 CAAGAGCGACAAAGAGAGGC 58.925 55.000 0.00 0.00 0.00 4.70
1513 1519 2.543238 GCTATCGGAGACCAACCTAACG 60.543 54.545 0.00 0.00 42.51 3.18
1595 1601 3.578272 GCGTGTGCGGTCCAACAA 61.578 61.111 0.00 0.00 38.78 2.83
1596 1602 2.903547 GCGTGTGCGGTCCAACAAT 61.904 57.895 0.00 0.00 38.78 2.71
1597 1603 1.082169 CGTGTGCGGTCCAACAATG 60.082 57.895 0.00 0.00 0.00 2.82
1598 1604 1.502990 CGTGTGCGGTCCAACAATGA 61.503 55.000 0.00 0.00 0.00 2.57
1599 1605 0.238289 GTGTGCGGTCCAACAATGAG 59.762 55.000 0.00 0.00 0.00 2.90
1600 1606 1.210155 GTGCGGTCCAACAATGAGC 59.790 57.895 0.00 0.00 0.00 4.26
1601 1607 1.228094 TGCGGTCCAACAATGAGCA 60.228 52.632 0.00 0.00 0.00 4.26
1602 1608 1.210155 GCGGTCCAACAATGAGCAC 59.790 57.895 0.00 0.00 0.00 4.40
1603 1609 1.497278 CGGTCCAACAATGAGCACG 59.503 57.895 0.00 0.00 0.00 5.34
1671 1677 7.273457 TCTTGAAGTAAAATGGGGGTATACA 57.727 36.000 5.01 0.00 0.00 2.29
1689 1695 8.143193 GGGTATACATTCAAAATCATGCATCAA 58.857 33.333 5.01 0.00 0.00 2.57
1704 1710 8.184304 TCATGCATCAATGATATTTGAATGGA 57.816 30.769 0.00 0.00 38.98 3.41
2088 2094 3.450115 GTGCTCCTAGGCGACGGT 61.450 66.667 2.96 0.00 34.52 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 3.322828 TCTGCTACCTTCCGTAACAACTT 59.677 43.478 0.00 0.00 0.00 2.66
217 218 7.394077 TGTGAAATTCCAAGCTATGAAATCTGA 59.606 33.333 2.34 0.00 0.00 3.27
294 295 5.795972 TGTCGTAACTTGTTCCCATATTGA 58.204 37.500 0.00 0.00 0.00 2.57
326 327 1.120530 GACCATGGTACGTCCCATCT 58.879 55.000 19.80 0.00 43.46 2.90
522 523 7.446625 ACTTCTTTTGCTCTGTCACATAGAAAT 59.553 33.333 0.00 0.00 0.00 2.17
565 566 5.533482 AGCTCTGTCAATAATATCGTCCAC 58.467 41.667 0.00 0.00 0.00 4.02
579 580 7.492669 GCATAGTCTATTTTACAAGCTCTGTCA 59.507 37.037 5.04 0.00 39.64 3.58
607 608 7.118723 AGTAAATATTCCAAGATTGCCTCACA 58.881 34.615 0.00 0.00 0.00 3.58
862 863 8.349983 AGCATCAACGTTAAGTTTAACAAATCT 58.650 29.630 0.00 1.11 42.02 2.40
906 907 1.455217 CCCGATCGTACCCCTGAGT 60.455 63.158 15.09 0.00 0.00 3.41
977 979 1.004560 ACATCTGCACACCGGTCAG 60.005 57.895 2.59 10.16 0.00 3.51
982 984 1.135888 CATCAACACATCTGCACACCG 60.136 52.381 0.00 0.00 0.00 4.94
1098 1100 1.337823 CGTCCTCCTTCGTTCATGGTT 60.338 52.381 0.00 0.00 0.00 3.67
1176 1179 9.981114 TTACAATGCTCGAATCTTGATATAGAA 57.019 29.630 7.32 0.00 0.00 2.10
1182 1185 8.363390 TCTCTATTACAATGCTCGAATCTTGAT 58.637 33.333 7.32 0.00 0.00 2.57
1185 1188 7.170658 GCTTCTCTATTACAATGCTCGAATCTT 59.829 37.037 0.00 0.00 0.00 2.40
1296 1299 6.204688 TCATTACATCGTTTATGAGGATTGGC 59.795 38.462 0.00 0.00 39.07 4.52
1390 1393 2.945008 CCTGATGTTGCCGTGATAACAT 59.055 45.455 0.00 0.00 46.83 2.71
1434 1437 0.182537 TTTCATACATGGCCCCTCCG 59.817 55.000 0.00 0.00 37.80 4.63
1525 1531 0.105658 ATTAGGGGCAGAGTAGGCGA 60.106 55.000 0.00 0.00 34.40 5.54
1595 1601 2.988010 TAAGGAATCAGCGTGCTCAT 57.012 45.000 0.00 0.00 0.00 2.90
1596 1602 2.938451 CAATAAGGAATCAGCGTGCTCA 59.062 45.455 0.00 0.00 0.00 4.26
1597 1603 2.286654 GCAATAAGGAATCAGCGTGCTC 60.287 50.000 0.00 0.00 0.00 4.26
1598 1604 1.672881 GCAATAAGGAATCAGCGTGCT 59.327 47.619 0.00 0.00 0.00 4.40
1599 1605 1.401552 TGCAATAAGGAATCAGCGTGC 59.598 47.619 0.00 0.00 0.00 5.34
1600 1606 3.429085 GTTGCAATAAGGAATCAGCGTG 58.571 45.455 0.59 0.00 0.00 5.34
1601 1607 2.423538 GGTTGCAATAAGGAATCAGCGT 59.576 45.455 0.59 0.00 0.00 5.07
1602 1608 2.423185 TGGTTGCAATAAGGAATCAGCG 59.577 45.455 0.59 0.00 33.36 5.18
1603 1609 4.660789 ATGGTTGCAATAAGGAATCAGC 57.339 40.909 0.59 0.00 42.22 4.26
1689 1695 6.379133 CGAATCCCCATCCATTCAAATATCAT 59.621 38.462 0.00 0.00 0.00 2.45
1704 1710 0.620556 AACAGCTCACGAATCCCCAT 59.379 50.000 0.00 0.00 0.00 4.00
2067 2073 2.442272 TCGCCTAGGAGCACCCTC 60.442 66.667 14.75 0.00 43.31 4.30
2079 2085 3.450115 GCTAGACCACCGTCGCCT 61.450 66.667 0.00 0.00 44.28 5.52
2084 2090 2.283529 CCACCAGCTAGACCACCGT 61.284 63.158 0.00 0.00 0.00 4.83
2088 2094 1.229177 TCTGCCACCAGCTAGACCA 60.229 57.895 0.00 0.00 44.23 4.02
2190 2197 1.365633 CTAGATCTGGGCCGAGTGC 59.634 63.158 15.09 7.98 40.16 4.40
2192 2199 4.609098 CCTAGATCTGGGCCGAGT 57.391 61.111 12.76 2.01 0.00 4.18
2212 2219 2.041430 TCCAGATGGGCCCCGTAA 59.959 61.111 22.27 0.00 36.21 3.18
2264 2271 2.190578 CTGCCTCCCGGGAATCAC 59.809 66.667 26.68 14.36 37.23 3.06


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

AutoCloner maintained by Alex Coulton.