Multiple sequence alignment - TraesCS5D01G087000

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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 TraesCS5D01G087000 chr5D 100.000 3900 0 0 1 3900 92289707 92293606 0.000000e+00 7203
1 TraesCS5D01G087000 chr5D 95.455 3938 130 28 1 3900 437732650 437728724 0.000000e+00 6235
2 TraesCS5D01G087000 chr5D 94.996 3937 145 35 1 3900 51590018 51586097 0.000000e+00 6131
3 TraesCS5D01G087000 chr5D 94.203 69 4 0 907 975 92290506 92290574 5.330000e-19 106
4 TraesCS5D01G087000 chr1D 96.043 3917 117 14 1 3900 152472483 152476378 0.000000e+00 6340
5 TraesCS5D01G087000 chr1D 95.794 3947 117 13 1 3899 152621832 152625777 0.000000e+00 6324
6 TraesCS5D01G087000 chr1D 97.059 68 2 0 908 975 152473288 152473355 8.860000e-22 115
7 TraesCS5D01G087000 chr1D 95.652 69 3 0 907 975 152622646 152622714 1.150000e-20 111
8 TraesCS5D01G087000 chr2D 95.174 3937 142 27 1 3900 165659767 165663692 0.000000e+00 6174
9 TraesCS5D01G087000 chr2D 94.170 3396 149 32 236 3608 104550613 104547244 0.000000e+00 5129
10 TraesCS5D01G087000 chr7B 93.801 3694 190 25 233 3900 574617144 574620824 0.000000e+00 5517
11 TraesCS5D01G087000 chr7D 95.938 3102 96 20 822 3900 592034269 592037363 0.000000e+00 5003
12 TraesCS5D01G087000 chr7D 97.709 1746 35 3 2159 3900 509207834 509206090 0.000000e+00 2998
13 TraesCS5D01G087000 chr7D 92.155 2014 99 30 1 1976 107244683 107242691 0.000000e+00 2789
14 TraesCS5D01G087000 chr7D 92.956 1008 36 16 1 979 592033343 592034344 0.000000e+00 1435
15 TraesCS5D01G087000 chr7D 93.521 957 38 17 1 937 509209552 509208600 0.000000e+00 1402
16 TraesCS5D01G087000 chr5B 93.095 2404 130 28 233 2611 31741116 31738724 0.000000e+00 3487
17 TraesCS5D01G087000 chr3B 91.351 1480 77 26 1 1438 823898665 823897195 0.000000e+00 1977
18 TraesCS5D01G087000 chr4A 89.912 1130 62 28 1 1096 608901973 608903084 0.000000e+00 1408
19 TraesCS5D01G087000 chr6B 89.336 1144 65 28 4 1109 28131856 28130732 0.000000e+00 1384
20 TraesCS5D01G087000 chr7A 93.067 952 43 11 1 937 358382051 358382994 0.000000e+00 1371
21 TraesCS5D01G087000 chr7A 93.476 935 42 7 17 937 626865902 626866831 0.000000e+00 1371
22 TraesCS5D01G087000 chr6A 92.865 953 47 10 1 937 553574912 553573965 0.000000e+00 1363
23 TraesCS5D01G087000 chr1A 92.655 953 49 9 1 937 579142520 579141573 0.000000e+00 1352
24 TraesCS5D01G087000 chr5A 93.215 899 41 8 54 937 75981284 75980391 0.000000e+00 1304


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 TraesCS5D01G087000 chr5D 92289707 92293606 3899 False 3654.5 7203 97.1015 1 3900 2 chr5D.!!$F1 3899
1 TraesCS5D01G087000 chr5D 437728724 437732650 3926 True 6235.0 6235 95.4550 1 3900 1 chr5D.!!$R2 3899
2 TraesCS5D01G087000 chr5D 51586097 51590018 3921 True 6131.0 6131 94.9960 1 3900 1 chr5D.!!$R1 3899
3 TraesCS5D01G087000 chr1D 152472483 152476378 3895 False 3227.5 6340 96.5510 1 3900 2 chr1D.!!$F1 3899
4 TraesCS5D01G087000 chr1D 152621832 152625777 3945 False 3217.5 6324 95.7230 1 3899 2 chr1D.!!$F2 3898
5 TraesCS5D01G087000 chr2D 165659767 165663692 3925 False 6174.0 6174 95.1740 1 3900 1 chr2D.!!$F1 3899
6 TraesCS5D01G087000 chr2D 104547244 104550613 3369 True 5129.0 5129 94.1700 236 3608 1 chr2D.!!$R1 3372
7 TraesCS5D01G087000 chr7B 574617144 574620824 3680 False 5517.0 5517 93.8010 233 3900 1 chr7B.!!$F1 3667
8 TraesCS5D01G087000 chr7D 592033343 592037363 4020 False 3219.0 5003 94.4470 1 3900 2 chr7D.!!$F1 3899
9 TraesCS5D01G087000 chr7D 107242691 107244683 1992 True 2789.0 2789 92.1550 1 1976 1 chr7D.!!$R1 1975
10 TraesCS5D01G087000 chr7D 509206090 509209552 3462 True 2200.0 2998 95.6150 1 3900 2 chr7D.!!$R2 3899
11 TraesCS5D01G087000 chr5B 31738724 31741116 2392 True 3487.0 3487 93.0950 233 2611 1 chr5B.!!$R1 2378
12 TraesCS5D01G087000 chr3B 823897195 823898665 1470 True 1977.0 1977 91.3510 1 1438 1 chr3B.!!$R1 1437
13 TraesCS5D01G087000 chr4A 608901973 608903084 1111 False 1408.0 1408 89.9120 1 1096 1 chr4A.!!$F1 1095
14 TraesCS5D01G087000 chr6B 28130732 28131856 1124 True 1384.0 1384 89.3360 4 1109 1 chr6B.!!$R1 1105
15 TraesCS5D01G087000 chr7A 358382051 358382994 943 False 1371.0 1371 93.0670 1 937 1 chr7A.!!$F1 936
16 TraesCS5D01G087000 chr7A 626865902 626866831 929 False 1371.0 1371 93.4760 17 937 1 chr7A.!!$F2 920
17 TraesCS5D01G087000 chr6A 553573965 553574912 947 True 1363.0 1363 92.8650 1 937 1 chr6A.!!$R1 936
18 TraesCS5D01G087000 chr1A 579141573 579142520 947 True 1352.0 1352 92.6550 1 937 1 chr1A.!!$R1 936
19 TraesCS5D01G087000 chr5A 75980391 75981284 893 True 1304.0 1304 93.2150 54 937 1 chr5A.!!$R1 883

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
914 1157 0.390472 CTTTCTGTCACCGGCCTCTC 60.39 60.0 0.0 0.0 0.0 3.20 F
1315 1608 0.389817 CGCATGAGTTCGACCTGGAA 60.39 55.0 0.0 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2721 3025 2.167219 CGACCGCCGTACGTAGAGA 61.167 63.158 15.21 0.0 41.42 3.10 R
2953 3258 2.303175 AGCACGGCCAAAAGAAGTTAA 58.697 42.857 2.24 0.0 0.00 2.01 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
101 103 9.800572 TTGTGCATTAAATATGGCCTAGTATTA 57.199 29.630 3.32 0.00 0.00 0.98
370 406 5.026038 TCGACACTCCAAAGGTAGAAAAA 57.974 39.130 0.00 0.00 0.00 1.94
767 842 3.009115 CTCCCTTCCTTCCGCCCA 61.009 66.667 0.00 0.00 0.00 5.36
906 1149 1.978580 TCCTCCTTCCTTTCTGTCACC 59.021 52.381 0.00 0.00 0.00 4.02
914 1157 0.390472 CTTTCTGTCACCGGCCTCTC 60.390 60.000 0.00 0.00 0.00 3.20
1300 1593 2.046411 TGTTCCGGATGCACGCAT 60.046 55.556 4.15 3.71 39.69 4.73
1315 1608 0.389817 CGCATGAGTTCGACCTGGAA 60.390 55.000 0.00 0.00 0.00 3.53
1659 1953 2.434331 TTGCCGGGCAAAGCTAGT 59.566 55.556 31.03 0.00 45.96 2.57
1701 1995 1.586422 CCACTGATTGGCCTGTATCG 58.414 55.000 3.32 4.26 39.07 2.92
1806 2100 2.350804 CGGTTCTCGTCATCTCTTACGA 59.649 50.000 0.00 0.00 45.17 3.43
1927 2221 4.341235 AGCAGGATTAGTCTATGCGTGTAA 59.659 41.667 9.22 0.00 40.00 2.41
1933 2227 9.424319 AGGATTAGTCTATGCGTGTAATAATTG 57.576 33.333 0.00 0.00 0.00 2.32
1943 2237 6.213677 TGCGTGTAATAATTGAGCTACTAGG 58.786 40.000 0.00 0.00 0.00 3.02
2039 2333 6.591935 TGAAGTCAACTTAGAAGACCAATGT 58.408 36.000 0.00 0.00 36.11 2.71
2395 2699 6.763610 AGTGCTTAGTATACTCATGAAAAGGC 59.236 38.462 9.12 2.75 0.00 4.35
2419 2723 4.974645 ATTTCTCCACCTGTAGTTCACA 57.025 40.909 0.00 0.00 35.30 3.58
2433 2737 3.480470 AGTTCACAGTTTATGCAGCAGT 58.520 40.909 0.00 0.00 0.00 4.40
2585 2889 2.333462 CCCCTCCCTCTCACCCCTA 61.333 68.421 0.00 0.00 0.00 3.53
2721 3025 4.537688 TGAATCCTTCCTCCACTTCAAGAT 59.462 41.667 0.00 0.00 0.00 2.40
2740 3044 2.125713 TCTACGTACGGCGGTCGA 60.126 61.111 26.23 8.58 46.52 4.20
2927 3232 1.070445 CTGAGATCCAGTGGCATCTCC 59.930 57.143 29.42 19.86 43.09 3.71
3161 3469 2.359531 GCAGGTGTGGCTAGTACTCTAG 59.640 54.545 0.00 0.00 44.55 2.43
3219 3527 3.010420 GGCAAGTACTTGGATGACCTTC 58.990 50.000 31.42 14.61 40.74 3.46
3234 3542 4.578871 TGACCTTCACAACATCATACTGG 58.421 43.478 0.00 0.00 0.00 4.00
3588 3896 5.774690 ACTGGGCATTCTTTTATCAACTTGA 59.225 36.000 0.00 0.00 0.00 3.02
3831 4141 9.212593 TGCTTATCCTTGGTATCTATATGCATA 57.787 33.333 9.27 9.27 31.91 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 106 9.727627 GTTGCAAAATTGACCAAATCATTTTTA 57.272 25.926 0.00 0.00 43.83 1.52
284 316 3.193267 TGCAAAATGGCACCACTCTATTC 59.807 43.478 0.00 0.00 39.25 1.75
340 376 4.069304 CCTTTGGAGTGTCGAAAATGGTA 58.931 43.478 0.00 0.00 0.00 3.25
341 377 2.884639 CCTTTGGAGTGTCGAAAATGGT 59.115 45.455 0.00 0.00 0.00 3.55
568 624 7.357303 ACACACTTTGACGATTTTATAACCAC 58.643 34.615 0.00 0.00 0.00 4.16
617 673 1.016627 CATCGATCCGTGCCACAAAT 58.983 50.000 0.00 0.00 0.00 2.32
767 842 0.324275 GACAGAGAGAGGGAGGCAGT 60.324 60.000 0.00 0.00 0.00 4.40
804 879 4.796231 CGCGAACGGTGAGGGAGG 62.796 72.222 0.00 0.00 34.97 4.30
886 1129 1.978580 GGTGACAGAAAGGAAGGAGGA 59.021 52.381 0.00 0.00 0.00 3.71
967 1210 0.688087 ACTGGATCCGAGGGAAGGAC 60.688 60.000 7.39 0.00 41.10 3.85
1023 1307 0.249868 CTGGACGTGCTTGACCTTGA 60.250 55.000 8.99 0.00 0.00 3.02
1089 1373 2.181021 GATGACGAGGTCGCCGTT 59.819 61.111 0.00 0.00 44.43 4.44
1096 1380 1.381872 CCTCCAGGGATGACGAGGT 60.382 63.158 0.00 0.00 37.67 3.85
1300 1593 1.542547 GGCTTTTCCAGGTCGAACTCA 60.543 52.381 0.00 0.00 34.01 3.41
1433 1727 3.561310 CCAAATAGACACATCATCCCACG 59.439 47.826 0.00 0.00 0.00 4.94
1659 1953 2.149803 CTCTGGTGTTCCGCGTACCA 62.150 60.000 17.07 17.07 41.90 3.25
1806 2100 7.195374 TGGTATAAGCTGGAAAAGTCTATGT 57.805 36.000 0.00 0.00 0.00 2.29
1933 2227 6.764560 GCACTCCTATCTATACCTAGTAGCTC 59.235 46.154 0.00 0.00 0.00 4.09
1943 2237 4.180057 GCATGCTGCACTCCTATCTATAC 58.820 47.826 11.37 0.00 44.26 1.47
2000 2294 3.270877 GACTTCAACGCCAACCAGATAT 58.729 45.455 0.00 0.00 0.00 1.63
2395 2699 6.464222 TGTGAACTACAGGTGGAGAAATAAG 58.536 40.000 0.00 0.00 33.42 1.73
2419 2723 4.823989 AGAAGAACAACTGCTGCATAAACT 59.176 37.500 1.31 0.00 32.32 2.66
2433 2737 5.376625 AGCAACAGATTGGTAGAAGAACAA 58.623 37.500 0.00 0.00 44.67 2.83
2721 3025 2.167219 CGACCGCCGTACGTAGAGA 61.167 63.158 15.21 0.00 41.42 3.10
2953 3258 2.303175 AGCACGGCCAAAAGAAGTTAA 58.697 42.857 2.24 0.00 0.00 2.01
3126 3434 5.185454 CCACACCTGCTAGATGTATTTCAA 58.815 41.667 0.00 0.00 0.00 2.69
3219 3527 8.946085 AGTTATTACAACCAGTATGATGTTGTG 58.054 33.333 15.32 0.00 39.69 3.33
3234 3542 9.760660 CAGAGTCTTATGCAAAGTTATTACAAC 57.239 33.333 0.00 0.00 0.00 3.32
3588 3896 4.256920 CCTAAAGCAGAGCAAGTGTACAT 58.743 43.478 0.00 0.00 0.00 2.29
3831 4141 3.706086 AGAAAGCCTGAAACACAAATGGT 59.294 39.130 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.