Multiple sequence alignment - TraesCS4D01G357000

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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 TraesCS4D01G357000 chr4D 100.000 2384 0 0 1 2384 505434054 505431671 0.000000e+00 4403.0
1 TraesCS4D01G357000 chr4B 90.160 1880 108 36 529 2384 652284980 652283154 0.000000e+00 2375.0
2 TraesCS4D01G357000 chr4B 94.578 498 27 0 3 500 652288949 652288452 0.000000e+00 771.0
3 TraesCS4D01G357000 chr4B 78.309 272 53 5 93 364 661186238 661185973 1.130000e-38 171.0
4 TraesCS4D01G357000 chr5A 86.607 1665 120 32 739 2365 689916033 689914434 0.000000e+00 1744.0
5 TraesCS4D01G357000 chr5A 89.756 859 55 14 1532 2384 689891799 689890968 0.000000e+00 1068.0
6 TraesCS4D01G357000 chr5A 95.190 499 23 1 3 500 689916919 689916421 0.000000e+00 787.0
7 TraesCS4D01G357000 chr5A 83.920 199 15 9 937 1134 689892147 689891965 8.760000e-40 174.0
8 TraesCS4D01G357000 chr5A 97.619 42 1 0 699 740 689916089 689916048 3.290000e-09 73.1
9 TraesCS4D01G357000 chr3B 78.249 354 69 6 3 355 19041571 19041225 1.110000e-53 220.0
10 TraesCS4D01G357000 chr7D 83.333 192 32 0 60 251 112117554 112117363 6.770000e-41 178.0
11 TraesCS4D01G357000 chrUn 77.941 272 54 5 93 364 111192774 111192509 5.270000e-37 165.0


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 TraesCS4D01G357000 chr4D 505431671 505434054 2383 True 4403.000000 4403 100.000000 1 2384 1 chr4D.!!$R1 2383
1 TraesCS4D01G357000 chr4B 652283154 652288949 5795 True 1573.000000 2375 92.369000 3 2384 2 chr4B.!!$R2 2381
2 TraesCS4D01G357000 chr5A 689914434 689916919 2485 True 868.033333 1744 93.138667 3 2365 3 chr5A.!!$R2 2362
3 TraesCS4D01G357000 chr5A 689890968 689892147 1179 True 621.000000 1068 86.838000 937 2384 2 chr5A.!!$R1 1447

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
481 482 0.734889 GGACGCCATCTCCAATTGTG 59.265 55.0 4.43 0.0 0.00 3.33 F
750 4317 0.863144 GCAGTGCAATGCCAAAAGTG 59.137 50.0 27.88 0.0 40.43 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1294 4882 0.119155 TCCACAGATCCCCTTCCACT 59.881 55.0 0.0 0.0 0.0 4.00 R
1838 5492 0.179062 GGGCGATCAACTCAGAGCAT 60.179 55.0 0.0 0.0 0.0 3.79 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
53 54 3.041211 TCCAGCTTCTACTACATGGCAT 58.959 45.455 0.00 0.00 0.00 4.40
58 59 4.592351 AGCTTCTACTACATGGCATCAGAT 59.408 41.667 11.56 0.00 0.00 2.90
88 89 1.069765 CGACAGTGAGGCCACAAGT 59.930 57.895 3.76 6.85 45.54 3.16
202 203 4.274700 GCCGACGCGCCCTACATA 62.275 66.667 5.73 0.00 0.00 2.29
211 212 1.679944 GCGCCCTACATATGCATGGAT 60.680 52.381 10.16 4.68 36.39 3.41
230 231 4.417183 TGGATCTCATCTACCAGTACTCCT 59.583 45.833 0.00 0.00 0.00 3.69
237 238 0.815734 TACCAGTACTCCTTGCTCGC 59.184 55.000 0.00 0.00 0.00 5.03
295 296 2.558313 GCGCAGAAGGTGAAGCAC 59.442 61.111 0.30 0.00 33.18 4.40
340 341 2.512515 GCGCTCGGAGAAGCCATT 60.513 61.111 9.69 0.00 34.84 3.16
419 420 1.064758 TCCCTCGCAATAAGGTGCAAT 60.065 47.619 0.00 0.00 45.19 3.56
481 482 0.734889 GGACGCCATCTCCAATTGTG 59.265 55.000 4.43 0.00 0.00 3.33
496 498 7.503566 TCTCCAATTGTGATCCTTTTATCATCC 59.496 37.037 4.43 0.00 38.13 3.51
512 554 9.797642 TTTTATCATCCTTGCATATAGATGTGT 57.202 29.630 12.63 7.86 37.84 3.72
567 4012 7.959733 TCATTCACATGTCGTTTACTGAATAC 58.040 34.615 0.00 0.00 31.96 1.89
617 4062 3.812156 ATGTCACGATTATCCGGTTCA 57.188 42.857 0.00 0.00 0.00 3.18
621 4066 4.390603 TGTCACGATTATCCGGTTCAAAAG 59.609 41.667 0.00 0.00 0.00 2.27
676 4121 4.527564 CCATGAAGAATAATCCGCGAAAC 58.472 43.478 8.23 0.00 0.00 2.78
701 4252 2.162208 ACATGCGATAAGGTGCAAACAG 59.838 45.455 0.00 0.00 45.45 3.16
750 4317 0.863144 GCAGTGCAATGCCAAAAGTG 59.137 50.000 27.88 0.00 40.43 3.16
770 4337 6.246420 AGTGAAGTTCAAATTGAGGATTCG 57.754 37.500 7.25 0.00 0.00 3.34
772 4339 6.148480 AGTGAAGTTCAAATTGAGGATTCGAG 59.852 38.462 7.25 0.00 0.00 4.04
786 4353 3.683340 GGATTCGAGGGTGTAAGTTTCAC 59.317 47.826 4.16 4.16 35.36 3.18
842 4412 2.258591 CCCGGCCGAGATCATACG 59.741 66.667 30.73 5.91 0.00 3.06
862 4432 2.954868 CGATGCAGCCGTCGTACC 60.955 66.667 0.00 0.00 43.65 3.34
909 4479 1.503994 GCTTTTCTGCCTTCCGAGC 59.496 57.895 0.00 0.00 0.00 5.03
1083 4656 1.840737 CGAAGGGAGAAGAGAGGACA 58.159 55.000 0.00 0.00 0.00 4.02
1254 4827 2.202146 CTCACCGACGACGACGAC 60.202 66.667 20.63 7.02 42.66 4.34
1309 4897 0.761802 GGCTAGTGGAAGGGGATCTG 59.238 60.000 0.00 0.00 0.00 2.90
1325 4913 0.251832 TCTGTGGAGGAGGACAGGTC 60.252 60.000 0.00 0.00 40.11 3.85
1417 5028 2.301583 TCGGTTGATTGGTGACTGATCA 59.698 45.455 0.00 0.00 33.71 2.92
1498 5112 7.402054 TGGGTATGTTCTGTTCTATCATGTTT 58.598 34.615 0.00 0.00 0.00 2.83
1555 5196 4.460263 TGTTATGGGTATGACTGGAATGC 58.540 43.478 0.00 0.00 0.00 3.56
1560 5201 2.880890 GGGTATGACTGGAATGCATGAC 59.119 50.000 0.00 0.00 0.00 3.06
1657 5303 6.954944 TGACAGTATTTTGCACAACTAACTC 58.045 36.000 0.00 0.00 0.00 3.01
1721 5374 4.072131 AGGCACAAGAACAACATCGTAAT 58.928 39.130 0.00 0.00 0.00 1.89
1743 5396 1.396301 GTCAGCTGCACACTATCAAGC 59.604 52.381 9.47 0.00 0.00 4.01
1744 5397 1.277273 TCAGCTGCACACTATCAAGCT 59.723 47.619 9.47 0.00 0.00 3.74
1745 5398 2.082231 CAGCTGCACACTATCAAGCTT 58.918 47.619 0.00 0.00 0.00 3.74
1746 5399 2.486982 CAGCTGCACACTATCAAGCTTT 59.513 45.455 0.00 0.00 0.00 3.51
1747 5400 2.746362 AGCTGCACACTATCAAGCTTTC 59.254 45.455 1.02 0.00 0.00 2.62
1748 5401 2.746362 GCTGCACACTATCAAGCTTTCT 59.254 45.455 0.00 0.00 0.00 2.52
1749 5402 3.190118 GCTGCACACTATCAAGCTTTCTT 59.810 43.478 0.00 0.00 0.00 2.52
1750 5403 4.671250 GCTGCACACTATCAAGCTTTCTTC 60.671 45.833 0.00 0.00 0.00 2.87
1751 5404 4.388485 TGCACACTATCAAGCTTTCTTCA 58.612 39.130 0.00 0.00 0.00 3.02
1752 5405 4.214119 TGCACACTATCAAGCTTTCTTCAC 59.786 41.667 0.00 0.00 0.00 3.18
1753 5406 4.214119 GCACACTATCAAGCTTTCTTCACA 59.786 41.667 0.00 0.00 0.00 3.58
1754 5407 5.277974 GCACACTATCAAGCTTTCTTCACAA 60.278 40.000 0.00 0.00 0.00 3.33
1755 5408 6.369005 CACACTATCAAGCTTTCTTCACAAG 58.631 40.000 0.00 0.00 0.00 3.16
1756 5409 6.203530 CACACTATCAAGCTTTCTTCACAAGA 59.796 38.462 0.00 0.00 35.26 3.02
1757 5410 6.426328 ACACTATCAAGCTTTCTTCACAAGAG 59.574 38.462 0.00 0.00 39.03 2.85
1758 5411 5.936956 ACTATCAAGCTTTCTTCACAAGAGG 59.063 40.000 0.00 0.00 39.03 3.69
1759 5412 3.480470 TCAAGCTTTCTTCACAAGAGGG 58.520 45.455 0.00 0.00 39.03 4.30
1760 5413 2.555757 CAAGCTTTCTTCACAAGAGGGG 59.444 50.000 0.00 0.00 39.03 4.79
1761 5414 1.074566 AGCTTTCTTCACAAGAGGGGG 59.925 52.381 0.00 0.00 39.03 5.40
1838 5492 5.261209 ACTCAAATTAGCAAGCACACAAA 57.739 34.783 0.00 0.00 0.00 2.83
1867 5521 2.363680 AGTTGATCGCCCTGATAGACTG 59.636 50.000 0.00 0.00 37.47 3.51
1878 5532 4.502259 CCCTGATAGACTGTATCCACAAGC 60.502 50.000 0.00 0.00 33.22 4.01
1967 5621 2.529632 TCCGATCGGAGATTCATCCAT 58.470 47.619 32.59 0.00 45.12 3.41
1998 5652 3.708451 TCCAGATCCACACTAACTAGCA 58.292 45.455 0.00 0.00 0.00 3.49
2233 5887 1.032014 TGCAGTTCTTCAAACAGGCC 58.968 50.000 0.00 0.00 0.00 5.19
2281 5935 8.184304 AGATACCATACATCTAAGTTCTGGTC 57.816 38.462 0.00 0.00 37.45 4.02
2306 5960 3.963374 TGCATAGTTCTGATAGCTCCAGT 59.037 43.478 13.65 1.04 33.57 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 2.028203 TGTCGATCAAGCCAACATCTGA 60.028 45.455 0.00 0.00 0.00 3.27
58 59 1.069978 TCACTGTCGATCAAGCCAACA 59.930 47.619 0.00 0.00 0.00 3.33
88 89 3.256960 GCAGGGGTGGTCTTCCCA 61.257 66.667 3.37 0.00 46.26 4.37
186 187 1.733041 CATATGTAGGGCGCGTCGG 60.733 63.158 8.43 0.00 0.00 4.79
202 203 3.908733 ACTGGTAGATGAGATCCATGCAT 59.091 43.478 0.00 0.00 35.17 3.96
211 212 3.954904 GCAAGGAGTACTGGTAGATGAGA 59.045 47.826 0.00 0.00 0.00 3.27
230 231 3.039588 GAAACCGTCCGCGAGCAA 61.040 61.111 8.23 0.00 41.33 3.91
237 238 2.431942 CCAGACCGAAACCGTCCG 60.432 66.667 0.00 0.00 0.00 4.79
295 296 1.536284 GCTTCGATGAAGTACTCCCCG 60.536 57.143 8.23 0.00 41.27 5.73
355 356 1.741770 ATCGTTGAGCCGCTTGGTC 60.742 57.895 0.00 0.00 41.96 4.02
419 420 8.600449 TGCAATTAATCGTATGATACACATGA 57.400 30.769 0.00 0.00 39.77 3.07
481 482 9.896645 TCTATATGCAAGGATGATAAAAGGATC 57.103 33.333 0.00 0.00 0.00 3.36
496 498 2.096069 GGCGCACACATCTATATGCAAG 60.096 50.000 10.83 0.00 37.97 4.01
567 4012 0.666577 GTGAAGAACCACGACTCCGG 60.667 60.000 0.00 0.00 40.78 5.14
648 4093 4.129380 CGGATTATTCTTCATGGCAGACA 58.871 43.478 0.00 0.00 0.00 3.41
676 4121 1.498865 GCACCTTATCGCATGTCCCG 61.499 60.000 0.00 0.00 0.00 5.14
678 4123 1.378531 TTGCACCTTATCGCATGTCC 58.621 50.000 0.00 0.00 38.10 4.02
701 4252 0.999406 CGATGGAATGTCCGTGTGTC 59.001 55.000 0.00 0.00 40.17 3.67
750 4317 5.163713 CCCTCGAATCCTCAATTTGAACTTC 60.164 44.000 0.01 3.59 37.33 3.01
770 4337 3.460103 TCGTTGTGAAACTTACACCCTC 58.540 45.455 0.00 0.00 38.04 4.30
772 4339 4.619437 TTTCGTTGTGAAACTTACACCC 57.381 40.909 0.00 0.00 41.59 4.61
805 4375 1.412343 GCCCAACAAATCACTGGTTGT 59.588 47.619 0.00 0.00 40.10 3.32
922 4492 2.267961 CGGTAACCCTGGGTCAGC 59.732 66.667 20.85 14.24 33.12 4.26
1060 4633 2.202810 CTCTTCTCCCTTCGCGGC 60.203 66.667 6.13 0.00 0.00 6.53
1065 4638 3.835395 TCTTTGTCCTCTCTTCTCCCTTC 59.165 47.826 0.00 0.00 0.00 3.46
1083 4656 2.300437 CACCCTCGTCTTCTCCTTCTTT 59.700 50.000 0.00 0.00 0.00 2.52
1209 4782 1.079057 GACGAAGCCCTTCTGTCCC 60.079 63.158 15.58 1.67 37.26 4.46
1254 4827 3.203412 CCCTCCTCCTCGTCGTCG 61.203 72.222 0.00 0.00 38.55 5.12
1260 4833 1.668101 CGTTTCCTCCCTCCTCCTCG 61.668 65.000 0.00 0.00 0.00 4.63
1294 4882 0.119155 TCCACAGATCCCCTTCCACT 59.881 55.000 0.00 0.00 0.00 4.00
1309 4897 3.715015 GGACCTGTCCTCCTCCAC 58.285 66.667 9.11 0.00 46.16 4.02
1417 5028 0.765510 GGACAGGAGGCCGGATTAAT 59.234 55.000 5.05 0.00 0.00 1.40
1498 5112 6.511121 GCAGTTTCAGAATTCGACAACAGTAA 60.511 38.462 14.97 0.00 0.00 2.24
1555 5196 7.425577 AATCAACACCGATACATATGTCATG 57.574 36.000 12.68 7.32 0.00 3.07
1560 5201 6.469322 CGCATAATCAACACCGATACATATG 58.531 40.000 0.00 0.00 0.00 1.78
1637 5283 6.542370 AGTGTGAGTTAGTTGTGCAAAATACT 59.458 34.615 0.00 0.00 0.00 2.12
1657 5303 7.010697 TGTGATTTGTGTAACTTGTAGTGTG 57.989 36.000 0.00 0.00 38.04 3.82
1721 5374 0.887933 TGATAGTGTGCAGCTGACGA 59.112 50.000 20.43 3.32 0.00 4.20
1743 5396 3.508845 TTCCCCCTCTTGTGAAGAAAG 57.491 47.619 0.00 0.00 37.02 2.62
1744 5397 3.963476 TTTCCCCCTCTTGTGAAGAAA 57.037 42.857 0.00 0.00 37.02 2.52
1745 5398 3.963476 TTTTCCCCCTCTTGTGAAGAA 57.037 42.857 0.00 0.00 37.02 2.52
1746 5399 3.963476 TTTTTCCCCCTCTTGTGAAGA 57.037 42.857 0.00 0.00 35.87 2.87
1838 5492 0.179062 GGGCGATCAACTCAGAGCAT 60.179 55.000 0.00 0.00 0.00 3.79
1867 5521 2.544267 GTCGCTTATGGCTTGTGGATAC 59.456 50.000 0.00 0.00 39.13 2.24
1878 5532 3.982475 TGCTAGAAGATGTCGCTTATGG 58.018 45.455 0.00 0.00 0.00 2.74
1998 5652 4.344679 TGAATTTCCAAGCACATTGAACCT 59.655 37.500 0.00 0.00 41.83 3.50
2108 5762 2.039418 GGAAACCCCCATTGCTTATCC 58.961 52.381 0.00 0.00 0.00 2.59
2281 5935 4.202192 TGGAGCTATCAGAACTATGCACAG 60.202 45.833 0.00 0.00 0.00 3.66
2306 5960 8.526147 GTCAGGTTAGGTTACATAGAAACAGTA 58.474 37.037 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.