Multiple sequence alignment - TraesCS5D01G285800

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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 TraesCS5D01G285800 chr5D 100.000 2547 0 0 1 2547 386169259 386171805 0 4704
1 TraesCS5D01G285800 chr5D 93.115 1496 89 6 972 2458 257136745 257138235 0 2180
2 TraesCS5D01G285800 chr5D 91.263 1591 108 12 972 2547 353835247 353833673 0 2139
3 TraesCS5D01G285800 chr5D 90.464 1594 118 13 974 2547 18407627 18406048 0 2071
4 TraesCS5D01G285800 chr3D 92.308 1586 105 11 972 2547 80249202 80250780 0 2237
5 TraesCS5D01G285800 chr2D 91.766 1591 112 11 972 2547 590929418 590927832 0 2194
6 TraesCS5D01G285800 chr2D 91.541 1596 110 11 972 2547 12543718 12542128 0 2176
7 TraesCS5D01G285800 chr2D 93.115 1467 92 8 1084 2544 551247277 551248740 0 2141
8 TraesCS5D01G285800 chr2D 92.740 978 59 11 1 972 1330897 1329926 0 1402
9 TraesCS5D01G285800 chr2D 92.434 978 62 12 1 972 1450047 1449076 0 1386
10 TraesCS5D01G285800 chr2D 91.612 763 52 5 1792 2544 604092952 604093712 0 1044
11 TraesCS5D01G285800 chr7D 91.165 1596 115 12 972 2547 625237014 625235425 0 2143
12 TraesCS5D01G285800 chr7D 90.744 1599 107 17 972 2547 565949255 565947675 0 2095
13 TraesCS5D01G285800 chr5B 91.011 1602 116 9 972 2547 548479320 548477721 0 2135
14 TraesCS5D01G285800 chr5B 85.363 977 123 16 5 971 369758535 369757569 0 994
15 TraesCS5D01G285800 chr5B 84.560 978 133 12 5 971 369740237 369739267 0 953
16 TraesCS5D01G285800 chr7B 91.022 1604 111 11 972 2544 27463673 27465274 0 2134
17 TraesCS5D01G285800 chr7B 90.731 1586 130 9 974 2547 685253987 685252407 0 2098
18 TraesCS5D01G285800 chrUn 92.177 1355 75 8 1217 2544 110637312 110638662 0 1886
19 TraesCS5D01G285800 chr3A 91.098 1348 103 9 972 2308 47285284 47286625 0 1808
20 TraesCS5D01G285800 chr6D 93.756 977 52 7 1 972 271334924 271333952 0 1458
21 TraesCS5D01G285800 chr6D 93.271 966 60 4 4 967 271342902 271341940 0 1419
22 TraesCS5D01G285800 chr6D 92.828 976 60 9 1 971 271350910 271349940 0 1406
23 TraesCS5D01G285800 chr3B 83.996 956 117 25 29 971 335369764 335370696 0 885
24 TraesCS5D01G285800 chr3B 83.682 956 119 28 29 973 335386886 335387815 0 867


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 TraesCS5D01G285800 chr5D 386169259 386171805 2546 False 4704 4704 100.000 1 2547 1 chr5D.!!$F2 2546
1 TraesCS5D01G285800 chr5D 257136745 257138235 1490 False 2180 2180 93.115 972 2458 1 chr5D.!!$F1 1486
2 TraesCS5D01G285800 chr5D 353833673 353835247 1574 True 2139 2139 91.263 972 2547 1 chr5D.!!$R2 1575
3 TraesCS5D01G285800 chr5D 18406048 18407627 1579 True 2071 2071 90.464 974 2547 1 chr5D.!!$R1 1573
4 TraesCS5D01G285800 chr3D 80249202 80250780 1578 False 2237 2237 92.308 972 2547 1 chr3D.!!$F1 1575
5 TraesCS5D01G285800 chr2D 590927832 590929418 1586 True 2194 2194 91.766 972 2547 1 chr2D.!!$R4 1575
6 TraesCS5D01G285800 chr2D 12542128 12543718 1590 True 2176 2176 91.541 972 2547 1 chr2D.!!$R3 1575
7 TraesCS5D01G285800 chr2D 551247277 551248740 1463 False 2141 2141 93.115 1084 2544 1 chr2D.!!$F1 1460
8 TraesCS5D01G285800 chr2D 1329926 1330897 971 True 1402 1402 92.740 1 972 1 chr2D.!!$R1 971
9 TraesCS5D01G285800 chr2D 1449076 1450047 971 True 1386 1386 92.434 1 972 1 chr2D.!!$R2 971
10 TraesCS5D01G285800 chr2D 604092952 604093712 760 False 1044 1044 91.612 1792 2544 1 chr2D.!!$F2 752
11 TraesCS5D01G285800 chr7D 625235425 625237014 1589 True 2143 2143 91.165 972 2547 1 chr7D.!!$R2 1575
12 TraesCS5D01G285800 chr7D 565947675 565949255 1580 True 2095 2095 90.744 972 2547 1 chr7D.!!$R1 1575
13 TraesCS5D01G285800 chr5B 548477721 548479320 1599 True 2135 2135 91.011 972 2547 1 chr5B.!!$R3 1575
14 TraesCS5D01G285800 chr5B 369757569 369758535 966 True 994 994 85.363 5 971 1 chr5B.!!$R2 966
15 TraesCS5D01G285800 chr5B 369739267 369740237 970 True 953 953 84.560 5 971 1 chr5B.!!$R1 966
16 TraesCS5D01G285800 chr7B 27463673 27465274 1601 False 2134 2134 91.022 972 2544 1 chr7B.!!$F1 1572
17 TraesCS5D01G285800 chr7B 685252407 685253987 1580 True 2098 2098 90.731 974 2547 1 chr7B.!!$R1 1573
18 TraesCS5D01G285800 chrUn 110637312 110638662 1350 False 1886 1886 92.177 1217 2544 1 chrUn.!!$F1 1327
19 TraesCS5D01G285800 chr3A 47285284 47286625 1341 False 1808 1808 91.098 972 2308 1 chr3A.!!$F1 1336
20 TraesCS5D01G285800 chr6D 271333952 271334924 972 True 1458 1458 93.756 1 972 1 chr6D.!!$R1 971
21 TraesCS5D01G285800 chr6D 271341940 271342902 962 True 1419 1419 93.271 4 967 1 chr6D.!!$R2 963
22 TraesCS5D01G285800 chr6D 271349940 271350910 970 True 1406 1406 92.828 1 971 1 chr6D.!!$R3 970
23 TraesCS5D01G285800 chr3B 335369764 335370696 932 False 885 885 83.996 29 971 1 chr3B.!!$F1 942
24 TraesCS5D01G285800 chr3B 335386886 335387815 929 False 867 867 83.682 29 973 1 chr3B.!!$F2 944

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
331 344 1.385347 ACCTTGGGGACACAGTGGA 60.385 57.895 5.31 0.0 42.67 4.02 F
1211 1246 0.250234 TGGTCGGGATCTTTGAGCAG 59.750 55.000 9.21 0.0 35.42 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1260 1295 1.078918 TTGGCCAGAGCATCGACTG 60.079 57.895 5.11 0.0 42.67 3.51 R
2215 2344 1.379044 GCAGCCCTAACAGCCACAT 60.379 57.895 0.00 0.0 0.00 3.21 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
245 258 3.839432 GAGGAGGAAGACGGCGGG 61.839 72.222 13.24 0.00 0.00 6.13
290 303 4.572571 TCCAACGGGGTGCACCAC 62.573 66.667 35.78 32.70 42.91 4.16
331 344 1.385347 ACCTTGGGGACACAGTGGA 60.385 57.895 5.31 0.00 42.67 4.02
425 438 3.224324 GGGAGCGGCGTGGATCTA 61.224 66.667 9.37 0.00 0.00 1.98
451 465 3.386237 GGGAGAGGCGCAGTGACT 61.386 66.667 10.83 0.00 0.00 3.41
452 466 2.052690 GGGAGAGGCGCAGTGACTA 61.053 63.158 10.83 0.00 0.00 2.59
459 473 2.509336 CGCAGTGACTAAGGGCGG 60.509 66.667 7.09 0.00 43.63 6.13
590 605 2.204244 GGGGGAACAGGGAAGGGA 60.204 66.667 0.00 0.00 0.00 4.20
897 931 4.520179 ACGGGTTTTGAACTAACAAGAGT 58.480 39.130 0.00 0.00 0.00 3.24
902 936 7.201670 CGGGTTTTGAACTAACAAGAGTTTAGT 60.202 37.037 0.00 0.00 39.79 2.24
981 1016 1.670674 GGGCGTTACACGTTGAGATCA 60.671 52.381 0.00 0.00 44.73 2.92
1020 1055 1.048601 TGTCTTCTTCAAGCTCCCGT 58.951 50.000 0.00 0.00 0.00 5.28
1021 1056 2.244695 TGTCTTCTTCAAGCTCCCGTA 58.755 47.619 0.00 0.00 0.00 4.02
1074 1109 1.328680 CAAATGCCGATCTTCGTCTGG 59.671 52.381 0.00 0.00 38.40 3.86
1080 1115 3.411418 GATCTTCGTCTGGCCGCGA 62.411 63.158 8.23 11.92 35.17 5.87
1139 1174 3.243168 CCGAAGAACCATAATCGTCCGTA 60.243 47.826 0.00 0.00 33.65 4.02
1211 1246 0.250234 TGGTCGGGATCTTTGAGCAG 59.750 55.000 9.21 0.00 35.42 4.24
1215 1250 2.094182 GTCGGGATCTTTGAGCAGTACA 60.094 50.000 0.00 0.00 0.00 2.90
1260 1295 4.984785 GCAGGTGAAATGTTTCTTCCTTTC 59.015 41.667 14.90 9.56 38.81 2.62
1451 1486 4.468153 AGAAGAAGGTTAGGAAGCTCGAAT 59.532 41.667 0.00 0.00 38.49 3.34
1462 1503 3.247173 GGAAGCTCGAATATCAAGCACAG 59.753 47.826 0.00 0.00 38.51 3.66
1488 1535 4.349342 ACCCATTTGCAATTACTTTTGGGA 59.651 37.500 21.16 0.00 44.36 4.37
1694 1784 6.788218 AGGGAGAAGAAATGAGAAATTCAGT 58.212 36.000 0.00 0.00 39.68 3.41
1723 1814 2.969990 TCAATGAACTGCAGCTCTCTC 58.030 47.619 15.27 3.58 0.00 3.20
1729 1820 0.971959 ACTGCAGCTCTCTCCTCTGG 60.972 60.000 15.27 0.00 0.00 3.86
1799 1897 2.420129 CCAAGTGCCGGCTAGACTAATT 60.420 50.000 29.70 8.71 0.00 1.40
1810 1908 1.453155 AGACTAATTGGCCAACTGCG 58.547 50.000 23.27 12.12 42.61 5.18
1818 1916 1.112315 TGGCCAACTGCGTCCAATTT 61.112 50.000 0.61 0.00 42.61 1.82
2222 2351 4.467084 CCGCGTGGGTATGTGGCT 62.467 66.667 7.26 0.00 36.73 4.75
2223 2352 3.195002 CGCGTGGGTATGTGGCTG 61.195 66.667 0.00 0.00 0.00 4.85
2393 2523 9.628746 GTTTTCCTTTGTTTTGTACTGAACTTA 57.371 29.630 11.42 0.87 0.00 2.24
2513 2646 6.084326 TGACTTGGTTTAGGAAAGAAATGC 57.916 37.500 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
425 438 2.370633 GCCTCTCCCTCTCCCCTT 59.629 66.667 0.00 0.00 0.00 3.95
451 465 4.733725 ACCCTGCTCCCGCCCTTA 62.734 66.667 0.00 0.00 34.43 2.69
459 473 2.607750 TCCCACTCACCCTGCTCC 60.608 66.667 0.00 0.00 0.00 4.70
464 479 1.751143 TTCCTCCTCCCACTCACCCT 61.751 60.000 0.00 0.00 0.00 4.34
552 567 2.928396 CAGGGTCGGAACAGGGGT 60.928 66.667 0.00 0.00 0.00 4.95
590 605 4.377760 TCCCTCGGTCGCTCCCTT 62.378 66.667 0.00 0.00 0.00 3.95
865 899 4.461431 AGTTCAAAACCCGTTCAAAAGTCT 59.539 37.500 0.00 0.00 0.00 3.24
868 902 6.094061 TGTTAGTTCAAAACCCGTTCAAAAG 58.906 36.000 0.00 0.00 0.00 2.27
877 911 7.993101 ACTAAACTCTTGTTAGTTCAAAACCC 58.007 34.615 0.00 0.00 38.76 4.11
902 936 6.521162 TGCTTGTCATCTCTGTTTACTGTTA 58.479 36.000 0.00 0.00 0.00 2.41
1089 1124 1.838073 AAACCCTCCGATCAACGCCT 61.838 55.000 0.00 0.00 41.07 5.52
1215 1250 5.068234 CATGAATGCCAAACAGATCAACT 57.932 39.130 0.00 0.00 33.31 3.16
1260 1295 1.078918 TTGGCCAGAGCATCGACTG 60.079 57.895 5.11 0.00 42.67 3.51
1420 1455 6.207614 GCTTCCTAACCTTCTTCTTCAACATT 59.792 38.462 0.00 0.00 0.00 2.71
1451 1486 4.580167 GCAAATGGGTATCTGTGCTTGATA 59.420 41.667 0.00 0.00 0.00 2.15
1462 1503 6.538381 CCCAAAAGTAATTGCAAATGGGTATC 59.462 38.462 16.95 0.00 41.08 2.24
1488 1535 6.260050 CAGTGCGATTACCATACCTACAAATT 59.740 38.462 0.00 0.00 0.00 1.82
1694 1784 5.474532 AGCTGCAGTTCATTGATCAAAGTTA 59.525 36.000 16.64 0.00 0.00 2.24
1711 1802 1.817881 CCAGAGGAGAGAGCTGCAG 59.182 63.158 10.11 10.11 34.49 4.41
1818 1916 4.374584 CCACCCCCGAATTGGCCA 62.375 66.667 0.00 0.00 35.87 5.36
2029 2147 5.452078 TCCATGACATTTTGGTCTTTGAC 57.548 39.130 0.00 0.00 38.61 3.18
2215 2344 1.379044 GCAGCCCTAACAGCCACAT 60.379 57.895 0.00 0.00 0.00 3.21
2393 2523 2.307686 ACATACGTTTCCAACCCTCCAT 59.692 45.455 0.00 0.00 0.00 3.41
2513 2646 2.332063 ATGTCCGTGCCCAAAGATAG 57.668 50.000 0.00 0.00 0.00 2.08


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

AutoCloner maintained by Alex Coulton.