Multiple sequence alignment - TraesCS2D01G447700

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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 TraesCS2D01G447700 chr2D 100.000 2249 0 0 1 2249 557661166 557663414 0.000000e+00 4154
1 TraesCS2D01G447700 chr2D 94.437 773 33 4 551 1314 112173176 112173947 0.000000e+00 1181
2 TraesCS2D01G447700 chr3D 92.777 1329 85 5 1 1320 360942832 360941506 0.000000e+00 1912
3 TraesCS2D01G447700 chr3B 90.266 1202 102 9 88 1287 470353678 470352490 0.000000e+00 1557
4 TraesCS2D01G447700 chr3B 95.652 92 4 0 1 92 470478619 470478528 5.000000e-32 148
5 TraesCS2D01G447700 chr2B 84.049 978 58 37 1302 2248 665666767 665667677 0.000000e+00 852
6 TraesCS2D01G447700 chr2A 89.786 607 48 9 1653 2248 698079974 698080577 0.000000e+00 765
7 TraesCS2D01G447700 chr2A 86.319 307 10 12 1310 1613 698079695 698079972 2.810000e-79 305
8 TraesCS2D01G447700 chr7D 86.052 423 45 8 1647 2056 635099376 635099797 2.050000e-120 442
9 TraesCS2D01G447700 chr4A 83.294 425 42 12 1644 2056 688921096 688921503 4.560000e-97 364
10 TraesCS2D01G447700 chr4A 81.647 425 49 12 1644 2056 696397206 696397613 2.150000e-85 326
11 TraesCS2D01G447700 chr5B 82.824 425 44 12 1644 2056 380782284 380782691 9.880000e-94 353


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 TraesCS2D01G447700 chr2D 557661166 557663414 2248 False 4154 4154 100.0000 1 2249 1 chr2D.!!$F2 2248
1 TraesCS2D01G447700 chr2D 112173176 112173947 771 False 1181 1181 94.4370 551 1314 1 chr2D.!!$F1 763
2 TraesCS2D01G447700 chr3D 360941506 360942832 1326 True 1912 1912 92.7770 1 1320 1 chr3D.!!$R1 1319
3 TraesCS2D01G447700 chr3B 470352490 470353678 1188 True 1557 1557 90.2660 88 1287 1 chr3B.!!$R1 1199
4 TraesCS2D01G447700 chr2B 665666767 665667677 910 False 852 852 84.0490 1302 2248 1 chr2B.!!$F1 946
5 TraesCS2D01G447700 chr2A 698079695 698080577 882 False 535 765 88.0525 1310 2248 2 chr2A.!!$F1 938

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
408 410 0.915364 GTCTCCCCCTGAAGCTGAAT 59.085 55.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1846 1885 0.105039 GTCCTGATTGACGGCCCTAG 59.895 60.0 0.0 0.0 0.0 3.02 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
34 35 2.169352 TGGCTGAATAGAGAAGGAGTGC 59.831 50.000 0.00 0.00 0.00 4.40
84 85 1.403679 CTGTTGACCAAGGTTTGCGAA 59.596 47.619 0.00 0.00 0.00 4.70
109 110 3.054361 AGTTGATCCAGACACCCATAACC 60.054 47.826 0.00 0.00 0.00 2.85
244 245 2.549349 GGCCAGTTCTCGGTTAAGTCAA 60.549 50.000 0.00 0.00 0.00 3.18
305 306 1.338200 GGAAACGTCTGATCCACAGCT 60.338 52.381 0.00 0.00 45.38 4.24
333 334 3.845781 TGGGAGTGGAAAGAGATATGC 57.154 47.619 0.00 0.00 0.00 3.14
408 410 0.915364 GTCTCCCCCTGAAGCTGAAT 59.085 55.000 0.00 0.00 0.00 2.57
552 554 4.040936 AGAGGCAGTGAGAGAAAGACTA 57.959 45.455 0.00 0.00 0.00 2.59
720 722 5.241064 CAGCTTGCCTGCAGAGATTAATTAT 59.759 40.000 17.39 0.00 34.21 1.28
756 758 1.207488 TAACTCTGTGCAGGCCCCAT 61.207 55.000 0.00 0.00 0.00 4.00
888 890 2.550208 GGGTTTCGTTGTCAGAGACCAT 60.550 50.000 7.95 0.00 42.63 3.55
914 916 1.079503 GATGTTCGAGGTTCAGGTGC 58.920 55.000 0.00 0.00 0.00 5.01
1025 1027 2.125912 CGTCCAAGTCGAGCTGGG 60.126 66.667 11.81 7.33 39.80 4.45
1103 1105 7.464710 CGAAGGAATCTTGTTTAGAGAAATCCG 60.465 40.741 0.00 0.00 37.84 4.18
1117 1119 0.110486 AATCCGTGAGTTTGCCAGGT 59.890 50.000 0.00 0.00 0.00 4.00
1166 1168 1.152963 CCCCGAGGGCTTGTAATGG 60.153 63.158 1.76 0.00 35.35 3.16
1184 1186 0.108945 GGGTTAGCGCACGAGTTAGT 60.109 55.000 11.47 0.00 0.00 2.24
1198 1200 3.263261 GAGTTAGTAGCCTTTGGTGCTC 58.737 50.000 0.00 0.00 40.23 4.26
1263 1278 2.090524 GTAACTGTTCGTCGGGCCG 61.091 63.158 22.51 22.51 0.00 6.13
1287 1310 0.904649 TATGGCTGGACCTGTGTGAG 59.095 55.000 0.00 0.00 40.22 3.51
1364 1387 4.002506 TTGAGCGAGCCAGCCGAA 62.003 61.111 4.97 0.00 38.01 4.30
1365 1388 4.742201 TGAGCGAGCCAGCCGAAC 62.742 66.667 4.97 0.00 38.01 3.95
1571 1609 0.871057 GGCATCGCCTAGCTTCATTC 59.129 55.000 0.00 0.00 46.69 2.67
1630 1668 2.841988 GATCTCAGGCGCCCTCCT 60.842 66.667 26.15 0.00 36.78 3.69
1631 1669 2.841988 ATCTCAGGCGCCCTCCTC 60.842 66.667 26.15 0.00 33.25 3.71
1641 1679 4.179599 CCCTCCTCCCCTCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
1642 1680 4.179599 CCTCCTCCCCTCCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
1643 1681 4.179599 CTCCTCCCCTCCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
1646 1684 4.179599 CTCCCCTCCCCTCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
1737 1776 0.884704 TGCTCTGCTTTGTTCGGGTC 60.885 55.000 0.00 0.00 0.00 4.46
1759 1798 0.387622 TGCCGTTACGTTTCTCTCCG 60.388 55.000 3.52 0.00 0.00 4.63
1825 1864 2.258748 CTTCCTCGAGGCCTTTCCCC 62.259 65.000 27.39 0.00 34.51 4.81
1867 1917 1.224592 GGGCCGTCAATCAGGACAT 59.775 57.895 0.00 0.00 37.24 3.06
1931 1981 4.337274 TGATTTGTACGCTAGCTGCTAGTA 59.663 41.667 31.00 18.36 40.11 1.82
1965 2022 6.147821 CACTGTGAATAAGTGTTCTAAGGGTG 59.852 42.308 0.32 0.00 40.17 4.61
2172 2234 6.368791 GTCACAGTCACATAAATCTACAGCAA 59.631 38.462 0.00 0.00 0.00 3.91
2176 2238 8.454106 ACAGTCACATAAATCTACAGCAAATTC 58.546 33.333 0.00 0.00 0.00 2.17
2185 2247 5.885230 TCTACAGCAAATTCTCACCATTG 57.115 39.130 0.00 0.00 0.00 2.82
2199 2261 1.995542 ACCATTGTCTCCCCAACTCAT 59.004 47.619 0.00 0.00 0.00 2.90
2208 2270 4.164221 GTCTCCCCAACTCATTCTGGAATA 59.836 45.833 0.00 0.00 34.35 1.75
2209 2271 4.164221 TCTCCCCAACTCATTCTGGAATAC 59.836 45.833 0.00 0.00 34.35 1.89
2216 2287 8.355169 CCCAACTCATTCTGGAATACATTTATG 58.645 37.037 0.00 0.00 34.35 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 0.246635 CTTGGTGTACCTGGGACTCG 59.753 60.000 11.06 0.00 36.82 4.18
84 85 2.902608 TGGGTGTCTGGATCAACTAGT 58.097 47.619 0.00 0.00 0.00 2.57
109 110 0.958091 CTCACTAGCCTCTCATCCCG 59.042 60.000 0.00 0.00 0.00 5.14
118 119 4.249638 AGAAGATGTCTCTCACTAGCCT 57.750 45.455 0.00 0.00 0.00 4.58
291 292 1.753649 TCAGCTAGCTGTGGATCAGAC 59.246 52.381 36.99 0.00 46.27 3.51
305 306 3.181329 TCTTTCCACTCCCAATCAGCTA 58.819 45.455 0.00 0.00 0.00 3.32
333 334 0.397941 TGGGTTGACAAGGCAGAGAG 59.602 55.000 0.00 0.00 0.00 3.20
408 410 4.811024 CAGTTGATGCCTCTTCGCTTTATA 59.189 41.667 0.00 0.00 0.00 0.98
552 554 0.880441 TAGCGTTGTTGCATGCACAT 59.120 45.000 22.58 9.22 37.31 3.21
720 722 6.115446 CAGAGTTAGTGATTCAATAGCCCAA 58.885 40.000 4.64 0.00 0.00 4.12
888 890 1.825474 GAACCTCGAACATCTCCCAGA 59.175 52.381 0.00 0.00 0.00 3.86
1087 1089 6.512741 GCAAACTCACGGATTTCTCTAAACAA 60.513 38.462 0.00 0.00 0.00 2.83
1103 1105 2.024414 AGTTCAACCTGGCAAACTCAC 58.976 47.619 0.00 0.00 0.00 3.51
1117 1119 8.199449 AGAGAAAGAAATGCAATTGAAGTTCAA 58.801 29.630 24.59 20.14 41.09 2.69
1166 1168 2.448219 CTACTAACTCGTGCGCTAACC 58.552 52.381 9.73 0.00 0.00 2.85
1184 1186 1.080093 CGACGAGCACCAAAGGCTA 60.080 57.895 0.00 0.00 42.78 3.93
1198 1200 4.778415 CCGGCTCACAGGACGACG 62.778 72.222 0.00 0.00 40.66 5.12
1263 1278 1.153086 CAGGTCCAGCCATAGTGCC 60.153 63.158 0.00 0.00 40.61 5.01
1342 1365 2.259818 CTGGCTCGCTCAACTCGT 59.740 61.111 0.00 0.00 0.00 4.18
1343 1366 3.184683 GCTGGCTCGCTCAACTCG 61.185 66.667 0.00 0.00 0.00 4.18
1345 1368 4.749310 CGGCTGGCTCGCTCAACT 62.749 66.667 0.00 0.00 0.00 3.16
1346 1369 4.742201 TCGGCTGGCTCGCTCAAC 62.742 66.667 0.00 0.00 0.00 3.18
1347 1370 4.002506 TTCGGCTGGCTCGCTCAA 62.003 61.111 0.00 0.00 0.00 3.02
1417 1441 1.036707 CTCTCGCAAACCCCCAAAAA 58.963 50.000 0.00 0.00 0.00 1.94
1456 1482 3.626924 GAGGACAGGCACGGGTGT 61.627 66.667 0.25 0.00 0.00 4.16
1457 1483 4.394712 GGAGGACAGGCACGGGTG 62.395 72.222 0.00 0.00 0.00 4.61
1458 1484 4.954118 TGGAGGACAGGCACGGGT 62.954 66.667 0.00 0.00 0.00 5.28
1634 1672 4.179599 GAGGGGAGGGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
1639 1677 4.179599 GAGGGGAGGGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
1737 1776 1.719780 GAGAGAAACGTAACGGCAGTG 59.280 52.381 0.00 0.00 0.00 3.66
1759 1798 1.978712 GCGGCGAAGAAAAGTAGGCC 61.979 60.000 12.98 0.00 37.21 5.19
1791 1830 1.403687 GGAAGAGGGATCTGGTCGGG 61.404 65.000 0.00 0.00 0.00 5.14
1841 1880 0.529992 GATTGACGGCCCTAGGAACG 60.530 60.000 11.48 16.47 0.00 3.95
1842 1881 0.539986 TGATTGACGGCCCTAGGAAC 59.460 55.000 11.48 1.15 0.00 3.62
1843 1882 0.830648 CTGATTGACGGCCCTAGGAA 59.169 55.000 11.48 0.00 0.00 3.36
1844 1883 1.048724 CCTGATTGACGGCCCTAGGA 61.049 60.000 11.48 0.00 0.00 2.94
1845 1884 1.048724 TCCTGATTGACGGCCCTAGG 61.049 60.000 0.06 0.06 0.00 3.02
1846 1885 0.105039 GTCCTGATTGACGGCCCTAG 59.895 60.000 0.00 0.00 0.00 3.02
1847 1886 0.616395 TGTCCTGATTGACGGCCCTA 60.616 55.000 0.00 0.00 38.11 3.53
1848 1887 1.274703 ATGTCCTGATTGACGGCCCT 61.275 55.000 0.00 0.00 38.11 5.19
1849 1888 0.815615 GATGTCCTGATTGACGGCCC 60.816 60.000 0.00 0.00 38.11 5.80
1850 1889 1.154205 CGATGTCCTGATTGACGGCC 61.154 60.000 0.00 0.00 38.11 6.13
1851 1890 1.766143 GCGATGTCCTGATTGACGGC 61.766 60.000 0.00 0.00 38.11 5.68
1931 1981 8.627208 AACACTTATTCACAGTGAAATCTGAT 57.373 30.769 19.92 5.14 43.90 2.90
1952 2009 2.543777 TCTGTGCACCCTTAGAACAC 57.456 50.000 15.69 0.00 0.00 3.32
1965 2022 0.601311 ACGAGGTTGAGCTTCTGTGC 60.601 55.000 0.00 0.00 0.00 4.57
2044 2101 2.420058 GCACCCATGCCTACTAGTTT 57.580 50.000 0.00 0.00 46.97 2.66
2072 2129 6.654582 GGTTGAAAAATATCAATGGCAACCTT 59.345 34.615 0.20 0.00 46.33 3.50
2141 2203 7.194607 AGATTTATGTGACTGTGACTGTTTG 57.805 36.000 0.00 0.00 0.00 2.93
2142 2204 7.931407 TGTAGATTTATGTGACTGTGACTGTTT 59.069 33.333 0.00 0.00 0.00 2.83
2143 2205 7.441836 TGTAGATTTATGTGACTGTGACTGTT 58.558 34.615 0.00 0.00 0.00 3.16
2144 2206 6.993079 TGTAGATTTATGTGACTGTGACTGT 58.007 36.000 0.00 0.00 0.00 3.55
2145 2207 6.035435 GCTGTAGATTTATGTGACTGTGACTG 59.965 42.308 0.00 0.00 0.00 3.51
2172 2234 2.649312 TGGGGAGACAATGGTGAGAATT 59.351 45.455 0.00 0.00 0.00 2.17
2176 2238 1.352352 AGTTGGGGAGACAATGGTGAG 59.648 52.381 0.00 0.00 32.24 3.51
2185 2247 1.909302 TCCAGAATGAGTTGGGGAGAC 59.091 52.381 0.00 0.00 39.69 3.36
2199 2261 9.967451 TCTGTTAACCATAAATGTATTCCAGAA 57.033 29.630 2.48 0.00 0.00 3.02
2208 2270 7.994425 TGTGTGATCTGTTAACCATAAATGT 57.006 32.000 2.48 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.