Multiple sequence alignment - TraesCS4A01G059700

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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 TraesCS4A01G059700 chr4A 100.000 2342 0 0 1 2342 56252754 56250413 0.000000e+00 4325.0
1 TraesCS4A01G059700 chr4A 94.683 489 26 0 1854 2342 125962568 125962080 0.000000e+00 760.0
2 TraesCS4A01G059700 chr2A 97.197 2355 52 4 1 2342 55468235 55465882 0.000000e+00 3971.0
3 TraesCS4A01G059700 chr7A 95.183 2346 83 5 1 2342 90543774 90541455 0.000000e+00 3679.0
4 TraesCS4A01G059700 chr7A 82.248 952 123 26 112 1040 81231491 81230563 0.000000e+00 780.0
5 TraesCS4A01G059700 chr7A 89.773 88 7 2 1582 1668 350571876 350571790 6.840000e-21 111.0
6 TraesCS4A01G059700 chr7A 90.698 43 3 1 1526 1567 130500456 130500414 3.250000e-04 56.5
7 TraesCS4A01G059700 chr1A 95.074 1685 54 3 1 1681 562587211 562588870 0.000000e+00 2625.0
8 TraesCS4A01G059700 chr1A 94.946 653 33 0 1680 2332 562589130 562589782 0.000000e+00 1024.0
9 TraesCS4A01G059700 chr1A 78.666 1289 172 48 104 1365 2763533 2764745 0.000000e+00 761.0
10 TraesCS4A01G059700 chr5D 94.288 1418 48 9 1 1402 527622613 527624013 0.000000e+00 2139.0
11 TraesCS4A01G059700 chr5D 94.218 1401 47 10 1 1385 527593101 527594483 0.000000e+00 2108.0
12 TraesCS4A01G059700 chr5D 92.487 945 65 3 1400 2342 527624116 527625056 0.000000e+00 1347.0
13 TraesCS4A01G059700 chr5A 93.701 1413 60 8 1 1402 17810730 17812124 0.000000e+00 2089.0
14 TraesCS4A01G059700 chr5A 91.966 946 73 2 1400 2342 17812229 17813174 0.000000e+00 1323.0
15 TraesCS4A01G059700 chr2D 93.583 1418 58 9 1 1402 35586617 35588017 0.000000e+00 2084.0
16 TraesCS4A01G059700 chr2D 92.211 950 70 3 1397 2342 35588118 35589067 0.000000e+00 1341.0
17 TraesCS4A01G059700 chrUn 94.382 1157 33 8 1 1142 331175080 331176219 0.000000e+00 1748.0
18 TraesCS4A01G059700 chr6A 94.710 964 42 2 440 1402 557348885 557349840 0.000000e+00 1489.0
19 TraesCS4A01G059700 chr6A 90.360 944 67 11 1400 2342 557349944 557350864 0.000000e+00 1218.0
20 TraesCS4A01G059700 chr7D 83.090 958 113 22 209 1147 32111309 32110382 0.000000e+00 826.0
21 TraesCS4A01G059700 chr7D 89.504 524 52 2 1821 2342 375308413 375307891 0.000000e+00 660.0
22 TraesCS4A01G059700 chr7D 80.214 187 24 7 1181 1365 89810247 89810422 6.790000e-26 128.0
23 TraesCS4A01G059700 chr1B 82.117 973 114 24 209 1147 77276713 77275767 0.000000e+00 778.0
24 TraesCS4A01G059700 chr3B 79.059 1127 157 41 104 1214 713137531 713136468 0.000000e+00 701.0
25 TraesCS4A01G059700 chr6B 90.698 86 6 1 1590 1673 55676142 55676057 1.900000e-21 113.0


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 TraesCS4A01G059700 chr4A 56250413 56252754 2341 True 4325.0 4325 100.0000 1 2342 1 chr4A.!!$R1 2341
1 TraesCS4A01G059700 chr2A 55465882 55468235 2353 True 3971.0 3971 97.1970 1 2342 1 chr2A.!!$R1 2341
2 TraesCS4A01G059700 chr7A 90541455 90543774 2319 True 3679.0 3679 95.1830 1 2342 1 chr7A.!!$R2 2341
3 TraesCS4A01G059700 chr7A 81230563 81231491 928 True 780.0 780 82.2480 112 1040 1 chr7A.!!$R1 928
4 TraesCS4A01G059700 chr1A 562587211 562589782 2571 False 1824.5 2625 95.0100 1 2332 2 chr1A.!!$F2 2331
5 TraesCS4A01G059700 chr1A 2763533 2764745 1212 False 761.0 761 78.6660 104 1365 1 chr1A.!!$F1 1261
6 TraesCS4A01G059700 chr5D 527593101 527594483 1382 False 2108.0 2108 94.2180 1 1385 1 chr5D.!!$F1 1384
7 TraesCS4A01G059700 chr5D 527622613 527625056 2443 False 1743.0 2139 93.3875 1 2342 2 chr5D.!!$F2 2341
8 TraesCS4A01G059700 chr5A 17810730 17813174 2444 False 1706.0 2089 92.8335 1 2342 2 chr5A.!!$F1 2341
9 TraesCS4A01G059700 chr2D 35586617 35589067 2450 False 1712.5 2084 92.8970 1 2342 2 chr2D.!!$F1 2341
10 TraesCS4A01G059700 chrUn 331175080 331176219 1139 False 1748.0 1748 94.3820 1 1142 1 chrUn.!!$F1 1141
11 TraesCS4A01G059700 chr6A 557348885 557350864 1979 False 1353.5 1489 92.5350 440 2342 2 chr6A.!!$F1 1902
12 TraesCS4A01G059700 chr7D 32110382 32111309 927 True 826.0 826 83.0900 209 1147 1 chr7D.!!$R1 938
13 TraesCS4A01G059700 chr7D 375307891 375308413 522 True 660.0 660 89.5040 1821 2342 1 chr7D.!!$R2 521
14 TraesCS4A01G059700 chr1B 77275767 77276713 946 True 778.0 778 82.1170 209 1147 1 chr1B.!!$R1 938
15 TraesCS4A01G059700 chr3B 713136468 713137531 1063 True 701.0 701 79.0590 104 1214 1 chr3B.!!$R1 1110

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
483 505 1.273048 GCCTTGACCAAACATGCATGA 59.727 47.619 32.75 5.74 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1349 1470 0.618458 ATGTACGTGGCCATGTCCTT 59.382 50.0 33.57 18.01 0.0 3.36 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
52 53 1.851053 CTTGACGAGCATCATCTCACG 59.149 52.381 0.00 0.00 33.41 4.35
64 65 2.154462 CATCTCACGCCCTTTCAAAGT 58.846 47.619 0.00 0.00 0.00 2.66
483 505 1.273048 GCCTTGACCAAACATGCATGA 59.727 47.619 32.75 5.74 0.00 3.07
754 815 5.592282 TCAACTTGAACAACAGGAGCAAATA 59.408 36.000 0.00 0.00 0.00 1.40
842 906 4.848562 ATATGACCTGCTCGACGAATTA 57.151 40.909 0.00 0.00 0.00 1.40
1058 1162 0.182537 CACCTATTGAATGGGGGCGA 59.817 55.000 12.38 0.00 34.79 5.54
1059 1163 0.182775 ACCTATTGAATGGGGGCGAC 59.817 55.000 12.38 0.00 34.79 5.19
1060 1164 0.884704 CCTATTGAATGGGGGCGACG 60.885 60.000 0.00 0.00 0.00 5.12
1061 1165 0.105964 CTATTGAATGGGGGCGACGA 59.894 55.000 0.00 0.00 0.00 4.20
1062 1166 0.105964 TATTGAATGGGGGCGACGAG 59.894 55.000 0.00 0.00 0.00 4.18
1078 1190 2.992114 AGCCGACGAGGTCAAGCT 60.992 61.111 0.00 4.89 43.70 3.74
1217 1332 0.398381 GCTGGACCAGGGAGAGAGAT 60.398 60.000 23.09 0.00 31.21 2.75
1349 1470 1.354368 GAAAAGGGGGTGAGACATGGA 59.646 52.381 0.00 0.00 0.00 3.41
1824 2317 1.202604 ACAACTCCACGGAACAACGAT 60.203 47.619 0.00 0.00 37.61 3.73
1852 2345 2.433604 AGATCATGTCATCAACGGCTCT 59.566 45.455 0.00 0.00 0.00 4.09
1903 2398 0.545309 CCACACTCTCCCTCCCAAGA 60.545 60.000 0.00 0.00 0.00 3.02
1928 2423 3.454587 TTGTTGTCCCGTCGCTGCT 62.455 57.895 0.00 0.00 0.00 4.24
2015 2510 1.450312 CTCACCCCCGAGCATGAAC 60.450 63.158 0.00 0.00 0.00 3.18
2179 2674 4.320456 CACCACTGCACCGAGCCT 62.320 66.667 0.00 0.00 44.83 4.58
2225 2720 3.006217 GGCACCTTCAAGAAGAAAGCAAT 59.994 43.478 11.25 0.00 40.79 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 4.081050 AGGCGACTTTGAAAGGGC 57.919 55.556 10.02 11.62 37.44 5.19
64 65 2.419159 CCACATCAGATTCTGAAGGCGA 60.419 50.000 19.73 0.00 44.04 5.54
483 505 1.815003 GCTGGCTAGCTTGTGTTGATT 59.185 47.619 15.78 0.00 46.57 2.57
630 667 7.840342 TGATTGTTTGCATGTTTGTTTAGTT 57.160 28.000 0.00 0.00 0.00 2.24
631 668 7.041916 CCATGATTGTTTGCATGTTTGTTTAGT 60.042 33.333 0.00 0.00 40.11 2.24
639 676 2.303600 AGGCCATGATTGTTTGCATGTT 59.696 40.909 5.01 0.00 40.11 2.71
652 689 4.404394 TCAAGTTCTATAACGAGGCCATGA 59.596 41.667 5.01 0.00 40.73 3.07
754 815 3.425014 TGGTGGTTGGGGTGCAGT 61.425 61.111 0.00 0.00 0.00 4.40
842 906 0.467290 TCTTCCTTTGGGCTTTGCGT 60.467 50.000 0.00 0.00 0.00 5.24
1058 1162 2.979197 CTTGACCTCGTCGGCTCGT 61.979 63.158 0.00 0.00 34.95 4.18
1059 1163 2.202492 CTTGACCTCGTCGGCTCG 60.202 66.667 0.00 0.00 34.95 5.03
1060 1164 2.507324 GCTTGACCTCGTCGGCTC 60.507 66.667 0.00 0.00 34.95 4.70
1061 1165 2.992114 AGCTTGACCTCGTCGGCT 60.992 61.111 6.34 6.34 38.57 5.52
1062 1166 2.811317 CAGCTTGACCTCGTCGGC 60.811 66.667 0.00 0.00 34.95 5.54
1063 1167 2.125912 CCAGCTTGACCTCGTCGG 60.126 66.667 0.00 0.00 34.95 4.79
1064 1168 2.811317 GCCAGCTTGACCTCGTCG 60.811 66.667 0.00 0.00 34.95 5.12
1065 1169 2.435059 GGCCAGCTTGACCTCGTC 60.435 66.667 0.00 0.00 0.00 4.20
1217 1332 4.680237 CGCGCAGTTCCACCCTCA 62.680 66.667 8.75 0.00 0.00 3.86
1349 1470 0.618458 ATGTACGTGGCCATGTCCTT 59.382 50.000 33.57 18.01 0.00 3.36
1574 1806 9.186837 CGGAGGGAGTATTATTAAATAGAGCTA 57.813 37.037 0.00 0.00 0.00 3.32
1765 2258 5.838531 TTTTCCGTTTCTTGTTGTATGGT 57.161 34.783 0.00 0.00 0.00 3.55
1824 2317 4.678840 CGTTGATGACATGATCTGAGGTCA 60.679 45.833 0.00 0.00 43.61 4.02
1852 2345 1.207089 CGGTGAATAGCTCCCTTGTCA 59.793 52.381 0.00 0.00 0.00 3.58
1903 2398 1.871039 CGACGGGACAACAAGTTTGAT 59.129 47.619 0.00 0.00 0.00 2.57
1928 2423 3.327404 GGGGTGCCCTCTTCGGAA 61.327 66.667 7.26 0.00 41.34 4.30
2015 2510 2.113139 AACTGGTTGCCCTGTCCG 59.887 61.111 0.00 0.00 41.62 4.79
2179 2674 0.756294 TGGAAGCTCTTCGTGGTCAA 59.244 50.000 3.81 0.00 40.37 3.18


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

AutoCloner maintained by Alex Coulton.