Multiple sequence alignment - TraesCS4D01G127800

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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 TraesCS4D01G127800 chr4D 100.000 4500 0 0 1 4500 112076331 112071832 0.000000e+00 8311.0
1 TraesCS4D01G127800 chr4B 96.852 3939 96 13 569 4500 172737268 172733351 0.000000e+00 6562.0
2 TraesCS4D01G127800 chr4B 89.713 593 21 13 3 565 172751968 172751386 0.000000e+00 721.0
3 TraesCS4D01G127800 chr4A 92.530 1352 70 9 446 1782 465225386 465226721 0.000000e+00 1908.0
4 TraesCS4D01G127800 chr4A 93.693 1205 65 4 2405 3608 465227877 465229071 0.000000e+00 1794.0
5 TraesCS4D01G127800 chr4A 94.588 425 16 2 3612 4030 465229130 465229553 0.000000e+00 651.0
6 TraesCS4D01G127800 chr4A 95.376 173 8 0 4328 4500 465259490 465259662 4.430000e-70 276.0
7 TraesCS4D01G127800 chr4A 89.655 174 14 3 2066 2238 465227679 465227849 7.580000e-53 219.0
8 TraesCS4D01G127800 chr4A 95.283 106 5 0 4100 4205 465229546 465229651 7.740000e-38 169.0
9 TraesCS4D01G127800 chr4A 91.139 79 5 2 4023 4099 585545674 585545596 6.160000e-19 106.0
10 TraesCS4D01G127800 chr4A 100.000 30 0 0 504 533 584355351 584355322 6.290000e-04 56.5
11 TraesCS4D01G127800 chr7B 92.453 106 6 2 2247 2350 376359551 376359656 2.800000e-32 150.0
12 TraesCS4D01G127800 chr7B 100.000 43 0 0 2025 2067 540049007 540048965 3.730000e-11 80.5
13 TraesCS4D01G127800 chr5B 91.667 108 7 2 2241 2346 296853887 296853994 1.010000e-31 148.0
14 TraesCS4D01G127800 chr5A 93.137 102 5 2 2243 2343 524052482 524052582 1.010000e-31 148.0
15 TraesCS4D01G127800 chr5A 76.923 195 39 4 4102 4293 10199175 10198984 6.160000e-19 106.0
16 TraesCS4D01G127800 chr2D 92.308 104 6 2 2244 2345 367506499 367506396 3.630000e-31 147.0
17 TraesCS4D01G127800 chr2D 97.101 69 2 0 4031 4099 555946543 555946475 2.840000e-22 117.0
18 TraesCS4D01G127800 chr2D 77.160 162 27 9 4113 4271 492108289 492108135 8.020000e-13 86.1
19 TraesCS4D01G127800 chr5D 93.814 97 5 1 2247 2342 384468961 384468865 1.300000e-30 145.0
20 TraesCS4D01G127800 chr3D 92.079 101 6 2 2243 2342 426879575 426879674 1.690000e-29 141.0
21 TraesCS4D01G127800 chr7D 90.566 106 8 2 2239 2343 135974782 135974678 6.070000e-29 139.0
22 TraesCS4D01G127800 chr7D 100.000 41 0 0 2027 2067 511224103 511224063 4.830000e-10 76.8
23 TraesCS4D01G127800 chr2B 89.286 112 9 3 2235 2343 556697794 556697683 2.180000e-28 137.0
24 TraesCS4D01G127800 chr2B 93.421 76 4 1 4025 4099 37357069 37357144 1.320000e-20 111.0
25 TraesCS4D01G127800 chr6D 91.860 86 7 0 4014 4099 20107169 20107084 2.200000e-23 121.0
26 TraesCS4D01G127800 chr6D 78.205 156 30 3 4115 4269 456668428 456668580 3.710000e-16 97.1
27 TraesCS4D01G127800 chr7A 93.750 80 4 1 4022 4100 335980734 335980813 7.910000e-23 119.0
28 TraesCS4D01G127800 chr7A 97.561 41 1 0 2027 2067 583164407 583164367 2.250000e-08 71.3
29 TraesCS4D01G127800 chr6A 94.667 75 3 1 4026 4100 146554490 146554563 1.020000e-21 115.0
30 TraesCS4D01G127800 chr6A 94.521 73 4 0 4027 4099 23679308 23679380 3.680000e-21 113.0
31 TraesCS4D01G127800 chr6A 77.857 140 25 6 4115 4253 387992192 387992058 1.040000e-11 82.4
32 TraesCS4D01G127800 chr6B 90.588 85 7 1 4014 4098 34089133 34089050 1.320000e-20 111.0
33 TraesCS4D01G127800 chr6B 76.562 192 40 4 4113 4302 694519248 694519436 2.860000e-17 100.0
34 TraesCS4D01G127800 chr1D 80.597 134 22 3 4121 4253 311360022 311360152 2.860000e-17 100.0
35 TraesCS4D01G127800 chr1B 80.741 135 20 5 4121 4253 421094001 421094131 2.860000e-17 100.0


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 TraesCS4D01G127800 chr4D 112071832 112076331 4499 True 8311.0 8311 100.0000 1 4500 1 chr4D.!!$R1 4499
1 TraesCS4D01G127800 chr4B 172733351 172737268 3917 True 6562.0 6562 96.8520 569 4500 1 chr4B.!!$R1 3931
2 TraesCS4D01G127800 chr4B 172751386 172751968 582 True 721.0 721 89.7130 3 565 1 chr4B.!!$R2 562
3 TraesCS4D01G127800 chr4A 465225386 465229651 4265 False 948.2 1908 93.1498 446 4205 5 chr4A.!!$F2 3759

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
588 629 0.238289 CTTGTGCCAAGGTGCTTACG 59.762 55.000 6.96 0.0 0.00 3.18 F
1084 1126 0.381801 CTTTGCTTGTTGCTGTCGGT 59.618 50.000 0.00 0.0 43.37 4.69 F
1801 1847 3.011566 TGGTGCTACAATAACATGGGG 57.988 47.619 0.00 0.0 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1423 1469 1.072331 GTGGGCGATTATCCTGGACAT 59.928 52.381 0.00 0.00 0.00 3.06 R
2745 3466 0.390866 AGCTGATCACAACTGCCTCG 60.391 55.000 0.00 0.00 33.78 4.63 R
3503 4224 0.970640 TTGCCATTCAAGCATGCTGT 59.029 45.000 23.48 8.82 40.59 4.40 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
27 28 2.626780 CGTCGCAGGTGAGGTGAGA 61.627 63.158 0.00 0.00 0.00 3.27
28 29 1.080434 GTCGCAGGTGAGGTGAGAC 60.080 63.158 0.00 0.00 37.53 3.36
98 99 4.752879 GCGTTGCGGTAGCTCCCA 62.753 66.667 0.00 0.00 45.42 4.37
99 100 2.813908 CGTTGCGGTAGCTCCCAC 60.814 66.667 0.00 0.00 45.42 4.61
100 101 2.345991 GTTGCGGTAGCTCCCACA 59.654 61.111 0.00 0.00 45.42 4.17
101 102 2.033194 GTTGCGGTAGCTCCCACAC 61.033 63.158 0.00 0.00 45.42 3.82
102 103 2.214216 TTGCGGTAGCTCCCACACT 61.214 57.895 0.00 0.00 45.42 3.55
103 104 0.901114 TTGCGGTAGCTCCCACACTA 60.901 55.000 0.00 0.00 45.42 2.74
116 138 0.734253 CACACTACCTGCTCTGCGAC 60.734 60.000 0.00 0.00 0.00 5.19
183 205 4.899239 CCAGACCGAGGCCGCATC 62.899 72.222 7.44 3.24 0.00 3.91
184 206 4.899239 CAGACCGAGGCCGCATCC 62.899 72.222 7.44 0.00 0.00 3.51
201 223 4.131376 CGCATGCCTCGGATTCTT 57.869 55.556 13.15 0.00 0.00 2.52
204 226 0.665298 GCATGCCTCGGATTCTTTCC 59.335 55.000 6.36 0.00 41.59 3.13
293 319 3.521605 CGGTGCTACTCCGGATCA 58.478 61.111 3.57 0.00 43.68 2.92
321 347 7.491696 GGCTTGTTGAGGTAAATAGTACTACTG 59.508 40.741 4.31 0.00 0.00 2.74
338 364 5.166398 ACTACTGCTATGTCACGGTTTAAC 58.834 41.667 0.00 0.00 0.00 2.01
339 365 3.997762 ACTGCTATGTCACGGTTTAACA 58.002 40.909 0.00 0.00 0.00 2.41
381 412 6.093404 TGTGACGCTGTGAAAATTGTTAAAA 58.907 32.000 0.00 0.00 0.00 1.52
392 423 9.083080 GTGAAAATTGTTAAAATTATAGCGCCT 57.917 29.630 2.29 0.00 0.00 5.52
545 586 3.067461 ACACTAGCTCCGATCACTGATTC 59.933 47.826 0.00 0.00 0.00 2.52
588 629 0.238289 CTTGTGCCAAGGTGCTTACG 59.762 55.000 6.96 0.00 0.00 3.18
616 657 3.025262 GGGTCCAATTATTTTGGGCGTA 58.975 45.455 4.64 0.00 44.78 4.42
897 939 5.075493 TCCAAAGAGTAGTCTTCCGTAGTT 58.925 41.667 13.22 0.00 42.59 2.24
1020 1062 7.435192 GTCAATATGCCAATACTTTGCCTTTAC 59.565 37.037 0.00 0.00 0.00 2.01
1054 1096 4.084066 TCCAAATTCATTCGAACAGACACG 60.084 41.667 0.00 0.00 32.81 4.49
1068 1110 6.505044 AACAGACACGGTAAAAACTTCTTT 57.495 33.333 0.00 0.00 0.00 2.52
1084 1126 0.381801 CTTTGCTTGTTGCTGTCGGT 59.618 50.000 0.00 0.00 43.37 4.69
1145 1187 8.297426 TCTTAGACACGCTATCCTATAAATGTG 58.703 37.037 0.00 0.00 0.00 3.21
1365 1411 5.394005 CGAAGGATCTGTTGAGAAGACTGAT 60.394 44.000 0.00 0.00 38.07 2.90
1640 1686 3.750130 CAGGATCAAAAGGTCACACTCTG 59.250 47.826 0.00 0.00 0.00 3.35
1647 1693 5.827797 TCAAAAGGTCACACTCTGCTTTAAT 59.172 36.000 0.00 0.00 0.00 1.40
1770 1816 4.142116 TGAATGTGAAATGGCATGCCTAAG 60.142 41.667 35.53 0.00 36.94 2.18
1801 1847 3.011566 TGGTGCTACAATAACATGGGG 57.988 47.619 0.00 0.00 0.00 4.96
1860 1941 5.817816 GTCTTATGTACTGGTTTAGCATGCT 59.182 40.000 25.99 25.99 0.00 3.79
1879 1960 8.616076 AGCATGCTAAATTTAGTCTGTACATTC 58.384 33.333 21.21 12.57 33.32 2.67
1984 2065 4.927267 TCCCAGGATTATCAACAGTTGT 57.073 40.909 13.14 3.72 0.00 3.32
2277 2998 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
2646 3367 3.608662 TGCCTGTGCAAGCAAGCC 61.609 61.111 4.94 0.00 46.66 4.35
2745 3466 6.201234 GTGAGATCCTTAAGATAAACTTCGGC 59.799 42.308 3.36 0.00 39.72 5.54
2751 3472 0.535335 AGATAAACTTCGGCGAGGCA 59.465 50.000 19.50 4.98 0.00 4.75
3186 3907 2.808206 GGTATGCGAGGGGGTCCAG 61.808 68.421 0.00 0.00 34.83 3.86
3401 4122 0.036010 ATTTCAGCCTGGAGACCACG 60.036 55.000 0.00 0.00 0.00 4.94
3414 4135 3.120385 CCACGCAGCTCGAATGCA 61.120 61.111 19.04 0.00 44.05 3.96
3498 4219 2.762472 CGAATAAGACGCTGTTGCTTG 58.238 47.619 0.00 0.00 36.97 4.01
3503 4224 0.679505 AGACGCTGTTGCTTGAGGTA 59.320 50.000 0.00 0.00 36.97 3.08
3504 4225 0.790814 GACGCTGTTGCTTGAGGTAC 59.209 55.000 0.00 0.00 36.97 3.34
3505 4226 0.105964 ACGCTGTTGCTTGAGGTACA 59.894 50.000 0.00 0.00 36.97 2.90
3506 4227 0.792640 CGCTGTTGCTTGAGGTACAG 59.207 55.000 0.00 0.00 40.65 2.74
3545 4266 1.584761 CAAATTGATTGGTGCGATGCG 59.415 47.619 0.00 0.00 35.27 4.73
3678 4456 5.899278 AGGACATGGTTTAGGGTGTATTTT 58.101 37.500 0.00 0.00 0.00 1.82
3766 4550 5.731686 GCAAAGAAGCATAGTAAGATGGCAC 60.732 44.000 0.00 0.00 0.00 5.01
3767 4551 3.722147 AGAAGCATAGTAAGATGGCACG 58.278 45.455 0.00 0.00 0.00 5.34
3836 4620 8.156820 TGAATTAGGAATATACCCAGTGTGATG 58.843 37.037 0.00 0.00 0.00 3.07
4069 4853 6.738832 CATCTAGATGTGCCCTGAATATTG 57.261 41.667 22.42 0.00 34.23 1.90
4285 5069 6.718593 TGGATACATATGGGCCTTCTAAAT 57.281 37.500 4.53 0.00 46.17 1.40
4291 5075 3.662759 ATGGGCCTTCTAAATCGGAAA 57.337 42.857 4.53 0.00 0.00 3.13
4344 5128 5.433526 TGTTAACTAGTGGGCCATGATTAC 58.566 41.667 10.70 3.40 0.00 1.89
4432 5218 7.275888 ACTAGAAAACATTGTTTGCTGATCA 57.724 32.000 26.48 10.57 0.00 2.92
4471 5257 7.149015 GCGTGAAAACATATGTAGATAGTACCG 60.149 40.741 9.21 4.62 0.00 4.02
4473 5259 7.115947 GTGAAAACATATGTAGATAGTACCGCC 59.884 40.741 9.21 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 3.929948 GCTCCATTCTTCGCGGCG 61.930 66.667 17.70 17.70 0.00 6.46
52 53 1.131883 CCAAAGCTGCTCCATTCTTCG 59.868 52.381 1.00 0.00 0.00 3.79
97 98 0.734253 GTCGCAGAGCAGGTAGTGTG 60.734 60.000 0.00 0.00 36.95 3.82
98 99 1.587054 GTCGCAGAGCAGGTAGTGT 59.413 57.895 0.00 0.00 36.95 3.55
99 100 1.515088 CGTCGCAGAGCAGGTAGTG 60.515 63.158 0.00 0.00 36.95 2.74
100 101 2.701780 CCGTCGCAGAGCAGGTAGT 61.702 63.158 0.00 0.00 36.95 2.73
101 102 2.103143 CCGTCGCAGAGCAGGTAG 59.897 66.667 0.00 0.00 36.95 3.18
102 103 4.129737 GCCGTCGCAGAGCAGGTA 62.130 66.667 0.00 0.00 36.95 3.08
184 206 0.305922 GAAAGAATCCGAGGCATGCG 59.694 55.000 12.44 0.00 0.00 4.73
185 207 0.665298 GGAAAGAATCCGAGGCATGC 59.335 55.000 9.90 9.90 38.79 4.06
195 217 1.348594 CGCGCGAAGGGAAAGAATC 59.651 57.895 28.94 0.00 46.37 2.52
269 295 1.516423 GGAGTAGCACCGGGAGAAC 59.484 63.158 6.32 0.00 0.00 3.01
277 303 1.065928 CGTGATCCGGAGTAGCACC 59.934 63.158 11.34 0.60 0.00 5.01
293 319 4.281898 ACTATTTACCTCAACAAGCCGT 57.718 40.909 0.00 0.00 0.00 5.68
321 347 4.557301 GCAAATGTTAAACCGTGACATAGC 59.443 41.667 0.00 0.00 33.88 2.97
338 364 5.975344 GTCACATCATTCCACTATGCAAATG 59.025 40.000 0.00 0.00 0.00 2.32
339 365 5.220912 CGTCACATCATTCCACTATGCAAAT 60.221 40.000 0.00 0.00 0.00 2.32
381 412 2.094494 CGATCCACAGAGGCGCTATAAT 60.094 50.000 7.64 0.00 37.29 1.28
409 440 3.443681 ACACTCCCTTGAACAAACACTTG 59.556 43.478 0.00 0.00 38.61 3.16
588 629 4.564613 CCAAAATAATTGGACCCAACACCC 60.565 45.833 3.24 0.00 42.06 4.61
616 657 2.391724 AAACGCAGACCATGACGGGT 62.392 55.000 0.00 0.00 46.02 5.28
812 854 6.664384 TGGGTTAACAAGGTAACAAGAGTTTT 59.336 34.615 8.10 0.00 39.15 2.43
897 939 3.489355 ACATTGCAGTCAACCTGATCAA 58.511 40.909 0.00 0.00 44.49 2.57
917 959 3.191371 CCACTGGGCAGAAATAGACAAAC 59.809 47.826 0.00 0.00 0.00 2.93
1054 1096 5.795766 GCAACAAGCAAAGAAGTTTTTACC 58.204 37.500 0.00 0.00 44.79 2.85
1084 1126 7.201609 GGATTGCGTGTCTAAGACATAATTGAA 60.202 37.037 0.00 0.00 44.63 2.69
1365 1411 2.868583 GCTGATCTTCATAAAGCTGCGA 59.131 45.455 0.00 0.00 32.18 5.10
1423 1469 1.072331 GTGGGCGATTATCCTGGACAT 59.928 52.381 0.00 0.00 0.00 3.06
1770 1816 3.247006 TGTAGCACCAACTTAGCTAGC 57.753 47.619 6.62 6.62 41.11 3.42
1801 1847 4.438744 CCGATAAGAAAAGGACCAATGCAC 60.439 45.833 0.00 0.00 0.00 4.57
2646 3367 4.946784 AAAACATAGCTTGAGGTTAGCG 57.053 40.909 0.00 0.00 43.37 4.26
2745 3466 0.390866 AGCTGATCACAACTGCCTCG 60.391 55.000 0.00 0.00 33.78 4.63
3498 4219 2.357009 CCATTCAAGCATGCTGTACCTC 59.643 50.000 23.48 0.00 0.00 3.85
3503 4224 0.970640 TTGCCATTCAAGCATGCTGT 59.029 45.000 23.48 8.82 40.59 4.40
3504 4225 1.067142 AGTTGCCATTCAAGCATGCTG 60.067 47.619 23.48 15.40 40.59 4.41
3505 4226 1.203994 GAGTTGCCATTCAAGCATGCT 59.796 47.619 16.30 16.30 40.59 3.79
3506 4227 1.067425 TGAGTTGCCATTCAAGCATGC 60.067 47.619 10.51 10.51 40.59 4.06
3507 4228 3.306917 TTGAGTTGCCATTCAAGCATG 57.693 42.857 0.00 0.00 40.59 4.06
3545 4266 8.417884 ACTTTCATCTCTACATACCTAAGCTTC 58.582 37.037 0.00 0.00 0.00 3.86
3836 4620 1.609208 TGCAGGAAAAGACAAGGAGC 58.391 50.000 0.00 0.00 0.00 4.70
3994 4778 2.770164 AGGAGAGTCGACAATTTGGG 57.230 50.000 19.50 0.00 0.00 4.12
4233 5017 9.760660 GCTCGACAATTTGACCAATATAATATC 57.239 33.333 2.79 0.00 0.00 1.63
4234 5018 8.730680 GGCTCGACAATTTGACCAATATAATAT 58.269 33.333 2.79 0.00 0.00 1.28
4237 5021 5.883115 TGGCTCGACAATTTGACCAATATAA 59.117 36.000 2.79 0.00 0.00 0.98
4238 5022 5.432645 TGGCTCGACAATTTGACCAATATA 58.567 37.500 2.79 0.00 0.00 0.86
4239 5023 4.269183 TGGCTCGACAATTTGACCAATAT 58.731 39.130 2.79 0.00 0.00 1.28
4240 5024 3.680490 TGGCTCGACAATTTGACCAATA 58.320 40.909 2.79 0.00 0.00 1.90
4241 5025 2.513753 TGGCTCGACAATTTGACCAAT 58.486 42.857 2.79 0.00 0.00 3.16
4242 5026 1.974265 TGGCTCGACAATTTGACCAA 58.026 45.000 2.79 0.00 0.00 3.67
4243 5027 1.811965 CATGGCTCGACAATTTGACCA 59.188 47.619 2.79 3.34 0.00 4.02
4285 5069 6.208007 TGTTGTTAGATACTCACTCTTTCCGA 59.792 38.462 0.00 0.00 0.00 4.55
4291 5075 9.376075 CAATTCATGTTGTTAGATACTCACTCT 57.624 33.333 0.00 0.00 0.00 3.24
4329 5113 3.737559 TTGAAGTAATCATGGCCCACT 57.262 42.857 0.00 0.00 38.03 4.00
4432 5218 2.183478 TTCACGCATCAATGGTGACT 57.817 45.000 0.00 0.00 37.55 3.41
4471 5257 8.697187 TGGATACTCGGTCATCCATAAATGGC 62.697 46.154 3.98 0.00 44.55 4.40
4473 5259 5.793817 TGGATACTCGGTCATCCATAAATG 58.206 41.667 8.21 0.00 44.55 2.32


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

AutoCloner maintained by Alex Coulton.