Multiple sequence alignment - TraesCS5D01G426700

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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 TraesCS5D01G426700 chr5D 100.000 3539 0 0 1 3539 485061938 485058400 0.000000e+00 6536.0
1 TraesCS5D01G426700 chr5D 77.254 1675 333 35 1889 3537 246012369 246010717 0.000000e+00 939.0
2 TraesCS5D01G426700 chr5D 79.611 976 128 34 277 1195 485092586 485091625 4.980000e-178 634.0
3 TraesCS5D01G426700 chr5D 79.461 891 149 24 2660 3532 77017252 77016378 5.060000e-168 601.0
4 TraesCS5D01G426700 chr5D 78.079 406 69 15 56 447 485118373 485117974 4.570000e-59 239.0
5 TraesCS5D01G426700 chr5D 82.927 123 19 2 1575 1696 501365809 501365688 3.740000e-20 110.0
6 TraesCS5D01G426700 chr5B 95.965 3544 106 12 16 3539 596826356 596822830 0.000000e+00 5718.0
7 TraesCS5D01G426700 chr5B 96.754 2403 71 4 1143 3539 596223409 596225810 0.000000e+00 3999.0
8 TraesCS5D01G426700 chr5B 94.557 1819 89 6 1724 3539 596393698 596395509 0.000000e+00 2802.0
9 TraesCS5D01G426700 chr5B 94.224 883 39 7 291 1171 596210870 596211742 0.000000e+00 1338.0
10 TraesCS5D01G426700 chr5B 77.135 1710 350 31 1853 3537 280650159 280648466 0.000000e+00 953.0
11 TraesCS5D01G426700 chr5B 90.541 296 22 2 10 300 596205457 596205751 1.540000e-103 387.0
12 TraesCS5D01G426700 chr5B 95.102 245 10 2 1482 1726 596388706 596388948 5.540000e-103 385.0
13 TraesCS5D01G426700 chr5B 75.832 691 104 42 89 749 596349466 596350123 3.460000e-75 292.0
14 TraesCS5D01G426700 chr5B 82.000 350 56 4 3188 3532 85946172 85945825 1.240000e-74 291.0
15 TraesCS5D01G426700 chr5B 82.857 245 30 8 260 501 596199142 596198907 3.580000e-50 209.0
16 TraesCS5D01G426700 chr5B 88.462 156 18 0 1040 1195 596204059 596204214 4.660000e-44 189.0
17 TraesCS5D01G426700 chr5B 80.000 210 40 2 1453 1661 280650559 280650351 1.700000e-33 154.0
18 TraesCS5D01G426700 chr5B 87.500 72 9 0 770 841 596723391 596723320 2.260000e-12 84.2
19 TraesCS5D01G426700 chr5A 95.613 3123 110 7 423 3539 606354318 606351217 0.000000e+00 4983.0
20 TraesCS5D01G426700 chr5A 76.649 1713 352 38 1853 3537 329994849 329993157 0.000000e+00 904.0
21 TraesCS5D01G426700 chr5A 88.462 286 15 6 1 280 606354811 606354538 2.630000e-86 329.0
22 TraesCS5D01G426700 chr5A 80.417 240 41 4 298 535 606392633 606392398 1.010000e-40 178.0
23 TraesCS5D01G426700 chr5A 94.690 113 6 0 277 389 606354425 606354313 3.630000e-40 176.0
24 TraesCS5D01G426700 chr4A 76.965 1997 425 28 1562 3537 733990966 733992948 0.000000e+00 1107.0
25 TraesCS5D01G426700 chr4A 76.692 1995 434 25 1562 3537 741159908 741161890 0.000000e+00 1079.0
26 TraesCS5D01G426700 chr4A 77.578 223 48 2 1570 1792 740183331 740183551 2.220000e-27 134.0
27 TraesCS5D01G426700 chr4A 76.316 228 52 2 1577 1803 740603553 740603327 1.730000e-23 121.0


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 TraesCS5D01G426700 chr5D 485058400 485061938 3538 True 6536.000000 6536 100.000000 1 3539 1 chr5D.!!$R3 3538
1 TraesCS5D01G426700 chr5D 246010717 246012369 1652 True 939.000000 939 77.254000 1889 3537 1 chr5D.!!$R2 1648
2 TraesCS5D01G426700 chr5D 485091625 485092586 961 True 634.000000 634 79.611000 277 1195 1 chr5D.!!$R4 918
3 TraesCS5D01G426700 chr5D 77016378 77017252 874 True 601.000000 601 79.461000 2660 3532 1 chr5D.!!$R1 872
4 TraesCS5D01G426700 chr5B 596822830 596826356 3526 True 5718.000000 5718 95.965000 16 3539 1 chr5B.!!$R4 3523
5 TraesCS5D01G426700 chr5B 596223409 596225810 2401 False 3999.000000 3999 96.754000 1143 3539 1 chr5B.!!$F2 2396
6 TraesCS5D01G426700 chr5B 596393698 596395509 1811 False 2802.000000 2802 94.557000 1724 3539 1 chr5B.!!$F5 1815
7 TraesCS5D01G426700 chr5B 596210870 596211742 872 False 1338.000000 1338 94.224000 291 1171 1 chr5B.!!$F1 880
8 TraesCS5D01G426700 chr5B 280648466 280650559 2093 True 553.500000 953 78.567500 1453 3537 2 chr5B.!!$R5 2084
9 TraesCS5D01G426700 chr5B 596349466 596350123 657 False 292.000000 292 75.832000 89 749 1 chr5B.!!$F3 660
10 TraesCS5D01G426700 chr5B 596204059 596205751 1692 False 288.000000 387 89.501500 10 1195 2 chr5B.!!$F6 1185
11 TraesCS5D01G426700 chr5A 606351217 606354811 3594 True 1829.333333 4983 92.921667 1 3539 3 chr5A.!!$R3 3538
12 TraesCS5D01G426700 chr5A 329993157 329994849 1692 True 904.000000 904 76.649000 1853 3537 1 chr5A.!!$R1 1684
13 TraesCS5D01G426700 chr4A 733990966 733992948 1982 False 1107.000000 1107 76.965000 1562 3537 1 chr4A.!!$F1 1975
14 TraesCS5D01G426700 chr4A 741159908 741161890 1982 False 1079.000000 1079 76.692000 1562 3537 1 chr4A.!!$F3 1975

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
802 2379 0.179032 TGATGTGAACCACCGCACTT 60.179 50.0 0.0 0.0 36.05 3.16 F
856 2440 0.538287 AACAAGCAGGGGCACTTCTC 60.538 55.0 0.0 0.0 44.61 2.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2379 4111 1.370064 GTAACACTCACCCCAGCGT 59.63 57.895 0.0 0.0 0.00 5.07 R
2810 4550 0.610174 CAAGCCACCTAGCTGACTCA 59.39 55.000 0.0 0.0 44.11 3.41 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
28 1418 4.764336 CGACGACGGCGCTGGTAA 62.764 66.667 22.44 0.00 42.48 2.85
49 1439 1.470098 CGCTAGCAATTGAAGCCAGTT 59.530 47.619 20.95 0.00 32.50 3.16
53 1443 1.142474 GCAATTGAAGCCAGTTGTGC 58.858 50.000 10.34 0.00 40.71 4.57
84 1474 6.266168 TCAAAACTGCCCATGTATGTAAAG 57.734 37.500 0.00 0.00 0.00 1.85
85 1475 5.772672 TCAAAACTGCCCATGTATGTAAAGT 59.227 36.000 0.00 0.00 0.00 2.66
86 1476 6.266558 TCAAAACTGCCCATGTATGTAAAGTT 59.733 34.615 0.00 0.00 0.00 2.66
87 1477 5.643379 AACTGCCCATGTATGTAAAGTTG 57.357 39.130 0.00 0.00 0.00 3.16
167 1565 3.367607 GCTCGACATCACAGACTACATC 58.632 50.000 0.00 0.00 0.00 3.06
258 1667 3.241530 TGCCTCTTGCGGTGGACT 61.242 61.111 2.43 0.00 45.60 3.85
328 1856 1.725557 CTGGGTGAGCAGCATCATGC 61.726 60.000 0.00 0.00 46.88 4.06
454 1985 1.266989 GCACCTTCTTTCTGGTTTCCG 59.733 52.381 0.00 0.00 33.75 4.30
790 2367 6.239515 CCTCTCTCACCATATTGATGATGTGA 60.240 42.308 0.00 0.00 34.79 3.58
802 2379 0.179032 TGATGTGAACCACCGCACTT 60.179 50.000 0.00 0.00 36.05 3.16
856 2440 0.538287 AACAAGCAGGGGCACTTCTC 60.538 55.000 0.00 0.00 44.61 2.87
898 2482 2.815647 CGAAGCCAAGACGCCCTC 60.816 66.667 0.00 0.00 0.00 4.30
981 2568 2.663188 GGTGATCGCCGCCATCTC 60.663 66.667 10.09 0.00 44.82 2.75
982 2569 2.663188 GTGATCGCCGCCATCTCC 60.663 66.667 0.00 0.00 0.00 3.71
983 2570 3.928779 TGATCGCCGCCATCTCCC 61.929 66.667 0.00 0.00 0.00 4.30
984 2571 3.620785 GATCGCCGCCATCTCCCT 61.621 66.667 0.00 0.00 0.00 4.20
985 2572 3.873026 GATCGCCGCCATCTCCCTG 62.873 68.421 0.00 0.00 0.00 4.45
1160 2747 5.364735 TCCTGCATGACAATCAGATAAGAGA 59.635 40.000 0.00 0.00 0.00 3.10
1191 2778 4.321230 CCACCTGTTTTAGCAAATCTCACC 60.321 45.833 0.00 0.00 0.00 4.02
1199 2786 2.309613 AGCAAATCTCACCAAACTGCA 58.690 42.857 0.00 0.00 0.00 4.41
1200 2787 2.694628 AGCAAATCTCACCAAACTGCAA 59.305 40.909 0.00 0.00 0.00 4.08
1275 2862 3.722147 CGAGATGGGTAATCTTGTGAGG 58.278 50.000 0.00 0.00 46.12 3.86
1714 3445 2.653726 TGAGGCTCAACAACAACACAT 58.346 42.857 16.28 0.00 0.00 3.21
1926 3657 3.525199 AGATCTTGTACCTTGGCCAGAAT 59.475 43.478 5.11 0.00 0.00 2.40
1934 3665 4.112634 ACCTTGGCCAGAATCAACTTTA 57.887 40.909 5.11 0.00 0.00 1.85
2110 3841 7.671398 ACATTCCTCAAGAAATTGGTGAGTTAT 59.329 33.333 10.66 3.64 38.21 1.89
2249 3980 2.397549 CTTGCCAACAAGCTTGCTAAC 58.602 47.619 26.27 13.91 46.38 2.34
2267 3998 3.990318 AACTTGCAAAAGCCTAGTCAC 57.010 42.857 0.00 0.00 0.00 3.67
2379 4111 8.918202 ACAAACTATTTGGTCAACTATCTCAA 57.082 30.769 6.28 0.00 44.81 3.02
2454 4186 2.902608 ACTGGAGTCATACCACCAAGA 58.097 47.619 0.00 0.00 33.57 3.02
2537 4269 1.643286 TCCACTGGGGATTGGCAATTA 59.357 47.619 14.93 1.14 42.15 1.40
2810 4550 7.835682 TGATAATTCATTTCCTGGTGTCATTCT 59.164 33.333 0.00 0.00 0.00 2.40
2826 4566 0.898320 TTCTGAGTCAGCTAGGTGGC 59.102 55.000 18.68 18.68 0.00 5.01
2889 4629 0.469917 AAGGTAGCATCCCACCATCG 59.530 55.000 0.00 0.00 37.28 3.84
2900 4640 1.154413 CACCATCGTTTCAGCGCAC 60.154 57.895 11.47 0.00 0.00 5.34
3007 4747 5.185454 TCGAATGGTTCATGCAGAATAAGT 58.815 37.500 0.00 0.00 38.76 2.24
3113 4856 8.882415 TTACTAGCTATAATACCTGTTGTTGC 57.118 34.615 0.00 0.00 0.00 4.17
3239 4994 7.805163 TGGAACTTTCATGGAGATATGTACAT 58.195 34.615 13.93 13.93 0.00 2.29
3249 5004 7.263100 TGGAGATATGTACATGCAAATTGTC 57.737 36.000 18.81 5.19 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.177249 GTTACCAGCGCCGTCGTC 61.177 66.667 2.29 0.00 38.14 4.20
22 1412 3.485877 GCTTCAATTGCTAGCGTTACCAG 60.486 47.826 10.77 3.42 0.00 4.00
28 1418 1.089920 CTGGCTTCAATTGCTAGCGT 58.910 50.000 19.51 0.00 35.77 5.07
49 1439 2.033299 GCAGTTTTGAGCTGTTAGCACA 59.967 45.455 0.00 0.01 45.56 4.57
53 1443 2.229792 TGGGCAGTTTTGAGCTGTTAG 58.770 47.619 0.00 0.00 36.42 2.34
258 1667 6.365247 GCACTACTTTCTGAGTCGATTAAACA 59.635 38.462 0.00 0.00 39.86 2.83
328 1856 2.060980 CCACCGGAGAAGAGAGGGG 61.061 68.421 9.46 0.00 0.00 4.79
454 1985 1.519408 ACATGTACGCACCCAGAAAC 58.481 50.000 0.00 0.00 0.00 2.78
790 2367 0.532862 CTGAGACAAGTGCGGTGGTT 60.533 55.000 0.00 0.00 0.00 3.67
802 2379 4.074526 GCTCCAGCGGCTGAGACA 62.075 66.667 30.52 10.61 32.44 3.41
882 2466 2.436824 GGAGGGCGTCTTGGCTTC 60.437 66.667 7.19 0.00 46.99 3.86
898 2482 0.839946 AGATGTTTCCCCAGGATCGG 59.160 55.000 0.00 0.00 0.00 4.18
929 2513 4.738998 CCGGATGCCCTGCCAACA 62.739 66.667 0.00 0.00 0.00 3.33
1160 2747 6.418057 TTGCTAAAACAGGTGGAATTGAAT 57.582 33.333 0.00 0.00 0.00 2.57
1191 2778 3.119708 GGAGCATTAGGAGTTGCAGTTTG 60.120 47.826 0.00 0.00 41.35 2.93
1199 2786 4.265073 GTTGTCATGGAGCATTAGGAGTT 58.735 43.478 0.00 0.00 0.00 3.01
1200 2787 3.370953 GGTTGTCATGGAGCATTAGGAGT 60.371 47.826 0.00 0.00 0.00 3.85
1275 2862 8.129211 ACTAAGTAATTGTTTGACAAGTTCAGC 58.871 33.333 0.00 0.00 41.94 4.26
1356 2943 1.089920 CGGAAAGGTCATTGCTGGAG 58.910 55.000 0.00 0.00 0.00 3.86
1714 3445 4.314522 TGCTTGGAATGGAACCAGATAA 57.685 40.909 0.00 0.00 38.70 1.75
2110 3841 6.070656 AGACTCCAAACATTTCCAGATTCAA 58.929 36.000 0.00 0.00 0.00 2.69
2379 4111 1.370064 GTAACACTCACCCCAGCGT 59.630 57.895 0.00 0.00 0.00 5.07
2454 4186 4.141390 CCCAACTGAGATAACTGCCCTATT 60.141 45.833 0.00 0.00 0.00 1.73
2537 4269 2.088423 TCAAGTTGAACAGCACCGTTT 58.912 42.857 2.20 0.00 0.00 3.60
2622 4354 9.308000 AGGTTGTTTGATGATAAATCCAAGTAA 57.692 29.630 0.00 0.00 0.00 2.24
2797 4537 2.934364 GCTGACTCAGAATGACACCAGG 60.934 54.545 10.45 0.00 42.56 4.45
2810 4550 0.610174 CAAGCCACCTAGCTGACTCA 59.390 55.000 0.00 0.00 44.11 3.41
2826 4566 3.058708 TCAAAACTTCGAGCATGCTCAAG 60.059 43.478 38.97 36.07 42.86 3.02
2889 4629 1.722507 GCTGAACGTGCGCTGAAAC 60.723 57.895 9.73 0.00 0.00 2.78
2900 4640 2.103094 TCAATGGATAGGAGGCTGAACG 59.897 50.000 0.00 0.00 0.00 3.95
3007 4747 5.686753 ACCTTTCACTACACCACACAATTA 58.313 37.500 0.00 0.00 0.00 1.40
3113 4856 6.860080 AGTGCCATGATAAACAGAAAAGATG 58.140 36.000 0.00 0.00 0.00 2.90
3239 4994 1.281353 GTGGCGTCGACAATTTGCA 59.719 52.632 17.16 0.00 0.00 4.08
3249 5004 3.906008 CACTAAAATTTTCTGTGGCGTCG 59.094 43.478 20.36 0.00 0.00 5.12
3329 5084 7.926018 TCTTCTTTACTGCAAATATCTCGCATA 59.074 33.333 0.00 0.00 34.63 3.14
3515 5270 1.981256 TGCAGTTTCCTTGGTCCTTC 58.019 50.000 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.