Multiple sequence alignment - TraesCS4A01G412300

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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 TraesCS4A01G412300 chr4A 100.000 2515 0 0 1 2515 684215397 684217911 0.000000e+00 4645.0
1 TraesCS4A01G412300 chr4A 99.316 585 4 0 1 585 684399939 684399355 0.000000e+00 1059.0
2 TraesCS4A01G412300 chr4A 86.061 330 17 14 1 319 684412077 684411766 6.710000e-86 327.0
3 TraesCS4A01G412300 chr4A 91.477 176 10 3 162 337 684398244 684398074 1.160000e-58 237.0
4 TraesCS4A01G412300 chr4A 86.275 204 24 1 382 585 684398076 684397877 4.210000e-53 219.0
5 TraesCS4A01G412300 chr6A 93.854 1871 86 14 584 2451 581971280 581969436 0.000000e+00 2791.0
6 TraesCS4A01G412300 chr6A 91.707 410 33 1 584 993 547338746 547339154 3.630000e-158 568.0
7 TraesCS4A01G412300 chr2A 93.152 1285 80 7 584 1864 87812064 87813344 0.000000e+00 1879.0
8 TraesCS4A01G412300 chr2A 95.688 858 35 2 1659 2515 87813190 87814046 0.000000e+00 1378.0
9 TraesCS4A01G412300 chr2A 92.513 374 26 2 584 957 617758063 617757692 3.680000e-148 534.0
10 TraesCS4A01G412300 chr2A 78.140 645 111 19 590 1214 705536579 705535945 1.410000e-102 383.0
11 TraesCS4A01G412300 chr7A 92.362 1283 91 5 584 1864 624797502 624798779 0.000000e+00 1820.0
12 TraesCS4A01G412300 chr7A 95.122 246 11 1 1670 1915 624798638 624798882 1.090000e-103 387.0
13 TraesCS4A01G412300 chr7A 89.011 91 8 2 1671 1760 624798743 624798832 7.350000e-21 111.0
14 TraesCS4A01G412300 chr2D 91.518 1285 96 8 584 1865 645767898 645766624 0.000000e+00 1757.0
15 TraesCS4A01G412300 chr2D 89.370 1223 108 9 585 1806 596256014 596257215 0.000000e+00 1519.0
16 TraesCS4A01G412300 chr2D 93.488 860 42 4 1669 2515 645766768 645765910 0.000000e+00 1266.0
17 TraesCS4A01G412300 chr2D 90.401 823 64 7 1694 2515 596257051 596257859 0.000000e+00 1068.0
18 TraesCS4A01G412300 chr2B 86.343 1296 146 13 584 1865 765756818 765755540 0.000000e+00 1384.0
19 TraesCS4A01G412300 chr2B 92.381 840 62 2 1676 2515 765755677 765754840 0.000000e+00 1195.0
20 TraesCS4A01G412300 chr2B 90.566 53 5 0 1198 1250 331371712 331371764 1.250000e-08 71.3
21 TraesCS4A01G412300 chr5A 91.794 524 43 0 585 1108 705355219 705355742 0.000000e+00 730.0
22 TraesCS4A01G412300 chr4B 84.679 483 41 16 104 585 602679978 602679528 3.810000e-123 451.0
23 TraesCS4A01G412300 chr4B 82.022 267 19 14 4 261 602731506 602731260 1.530000e-47 200.0
24 TraesCS4A01G412300 chr4B 80.882 204 27 3 382 585 602728865 602728674 1.560000e-32 150.0
25 TraesCS4A01G412300 chr4B 91.209 91 3 3 181 269 602406201 602406288 4.390000e-23 119.0
26 TraesCS4A01G412300 chr4D 85.348 273 20 12 70 334 477527244 477527504 5.330000e-67 265.0


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 TraesCS4A01G412300 chr4A 684215397 684217911 2514 False 4645.000000 4645 100.0000 1 2515 1 chr4A.!!$F1 2514
1 TraesCS4A01G412300 chr4A 684397877 684399939 2062 True 505.000000 1059 92.3560 1 585 3 chr4A.!!$R2 584
2 TraesCS4A01G412300 chr6A 581969436 581971280 1844 True 2791.000000 2791 93.8540 584 2451 1 chr6A.!!$R1 1867
3 TraesCS4A01G412300 chr2A 87812064 87814046 1982 False 1628.500000 1879 94.4200 584 2515 2 chr2A.!!$F1 1931
4 TraesCS4A01G412300 chr2A 705535945 705536579 634 True 383.000000 383 78.1400 590 1214 1 chr2A.!!$R2 624
5 TraesCS4A01G412300 chr7A 624797502 624798882 1380 False 772.666667 1820 92.1650 584 1915 3 chr7A.!!$F1 1331
6 TraesCS4A01G412300 chr2D 645765910 645767898 1988 True 1511.500000 1757 92.5030 584 2515 2 chr2D.!!$R1 1931
7 TraesCS4A01G412300 chr2D 596256014 596257859 1845 False 1293.500000 1519 89.8855 585 2515 2 chr2D.!!$F1 1930
8 TraesCS4A01G412300 chr2B 765754840 765756818 1978 True 1289.500000 1384 89.3620 584 2515 2 chr2B.!!$R1 1931
9 TraesCS4A01G412300 chr5A 705355219 705355742 523 False 730.000000 730 91.7940 585 1108 1 chr5A.!!$F1 523

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
892 1161 0.327095 TGCCCTAACCCTAGCCATGA 60.327 55.0 0.0 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 2155 0.665835 GATGATCGCCTCGACTGTCT 59.334 55.0 6.21 0.0 39.18 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
297 298 1.883084 CGCTTCCAGCCCATCGTAC 60.883 63.158 0.00 0.00 38.18 3.67
465 466 1.186200 TGACTGTCTTCATCCTCCCG 58.814 55.000 9.51 0.00 0.00 5.14
579 580 0.865769 GTCATGCTCGACCAACGTTT 59.134 50.000 0.00 0.00 43.13 3.60
829 1083 0.618458 TCTTCTTCACATTCCCCGGG 59.382 55.000 15.80 15.80 0.00 5.73
892 1161 0.327095 TGCCCTAACCCTAGCCATGA 60.327 55.000 0.00 0.00 0.00 3.07
912 1181 1.004560 CGGCACTTCAAGCTCCTCA 60.005 57.895 0.00 0.00 0.00 3.86
1026 1298 1.598130 GCTCGTGGCTTGTCCTTGT 60.598 57.895 0.00 0.00 38.06 3.16
1377 1650 3.432378 GAGGAGGAAGACAGAGGTGTTA 58.568 50.000 0.00 0.00 36.88 2.41
1456 1729 4.987912 GCTGATCTGCTTAGTTAGGATGTC 59.012 45.833 16.60 0.00 0.00 3.06
1491 1764 2.618241 GTCACTTTGTTGGCTGTGATGA 59.382 45.455 0.00 0.00 40.78 2.92
1558 1831 9.125026 ACTATTGGGATGAACTATTTGAATGAC 57.875 33.333 0.00 0.00 0.00 3.06
1783 2110 2.047655 GGTCAATGCGGACGGTCA 60.048 61.111 10.76 0.00 38.70 4.02
1787 2114 3.998672 AATGCGGACGGTCACGGT 61.999 61.111 10.76 0.00 46.48 4.83
1827 2155 4.261994 GGTTAGCTCATTTTTGGTCTTGCA 60.262 41.667 0.00 0.00 0.00 4.08
1847 2175 0.665835 GACAGTCGAGGCGATCATCT 59.334 55.000 0.00 0.00 38.42 2.90
1948 2276 4.397420 TCCAACATTGCATAGTTCACAGT 58.603 39.130 1.67 0.00 0.00 3.55
2124 2452 9.083080 GCTTTTTAGTTTTCAAGCTCAAACTAA 57.917 29.630 22.59 22.59 46.49 2.24
2163 2504 9.528018 CTTGTCTTCTTCTATACTTCAGGAATC 57.472 37.037 0.00 0.00 0.00 2.52
2327 2668 3.771479 TGAGACTGCTGAGTTGATATGGT 59.229 43.478 0.00 0.00 30.16 3.55
2377 2718 5.452078 TGAAATGGTTTGAGATCAACACC 57.548 39.130 14.69 14.69 37.45 4.16
2378 2719 4.892345 TGAAATGGTTTGAGATCAACACCA 59.108 37.500 21.23 21.23 43.75 4.17
2379 2720 5.539574 TGAAATGGTTTGAGATCAACACCAT 59.460 36.000 22.77 22.77 46.74 3.55
2435 2899 8.129496 TGTAGTATCTCCAACACTGAAACATA 57.871 34.615 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
297 298 0.999406 ACCGCGAAAGAACATCATCG 59.001 50.000 8.23 0.00 38.28 3.84
465 466 0.037326 TGCTATCGGCCCATTCGATC 60.037 55.000 0.00 0.00 44.82 3.69
504 505 2.743928 CAAGGTGGCTCTGGCGAC 60.744 66.667 0.00 0.00 44.59 5.19
579 580 7.027874 ACCTCCAATGTATTTAACTCTCCAA 57.972 36.000 0.00 0.00 0.00 3.53
829 1083 2.302260 GGGAAGAAATAGAGCAAGGGC 58.698 52.381 0.00 0.00 41.61 5.19
892 1161 2.032681 GGAGCTTGAAGTGCCGGT 59.967 61.111 1.90 0.00 0.00 5.28
912 1181 1.302832 CTTCAACTGCTTCCCCGCT 60.303 57.895 0.00 0.00 0.00 5.52
976 1245 2.030893 CAGACGAAATTGGAGCTTGCAA 60.031 45.455 0.00 0.00 30.73 4.08
1026 1298 1.599518 GGTGTCACGGACATGGCAA 60.600 57.895 0.00 0.00 44.63 4.52
1174 1447 4.023279 CCTGGACGAATTTGACACATTCAA 60.023 41.667 13.34 0.00 42.83 2.69
1377 1650 4.590222 ACCATTGCAAATCTTCTGGACTTT 59.410 37.500 18.92 0.00 0.00 2.66
1456 1729 7.201513 CCAACAAAGTGACAATACAAAACAAGG 60.202 37.037 0.00 0.00 0.00 3.61
1491 1764 8.627403 CATTCATTTCAGAGCCACTACATAAAT 58.373 33.333 0.00 0.00 0.00 1.40
1558 1831 7.621832 TGCTTTTCAATTCAGATTAAACACG 57.378 32.000 0.00 0.00 0.00 4.49
1659 1932 0.595567 CGACCGTCCACGAGACAAAA 60.596 55.000 0.00 0.00 46.69 2.44
1787 2114 3.348647 AACCATCATTGTGGACGATCA 57.651 42.857 10.89 0.00 42.02 2.92
1827 2155 0.665835 GATGATCGCCTCGACTGTCT 59.334 55.000 6.21 0.00 39.18 3.41
1889 2217 5.356751 TGTGAGCTTTGTTGTTCTACATGTT 59.643 36.000 2.30 0.00 0.00 2.71
1948 2276 8.003044 AGTACTAGTATGGCCAAGTGAACTATA 58.997 37.037 10.96 5.43 0.00 1.31
2124 2452 4.712476 AGAAGACAAGTGTTCTGATGCTT 58.288 39.130 11.28 0.00 41.00 3.91
2163 2504 2.135933 GTGAAGACCAAGGAGAACACG 58.864 52.381 0.00 0.00 0.00 4.49
2435 2899 3.743521 ACAACACATGTGTATGAGCAGT 58.256 40.909 30.75 16.80 44.13 4.40


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

AutoCloner maintained by Alex Coulton.