Multiple sequence alignment - TraesCS5D01G475200

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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 TraesCS5D01G475200 chr5D 100.000 2635 0 0 1 2635 514975315 514972681 0.000000e+00 4867.0
1 TraesCS5D01G475200 chr5D 93.842 2647 148 9 1 2635 514948907 514946264 0.000000e+00 3971.0
2 TraesCS5D01G475200 chr5D 93.608 2644 159 7 1 2635 515026109 515023467 0.000000e+00 3938.0
3 TraesCS5D01G475200 chr5D 93.381 2644 164 8 1 2635 514996752 514994111 0.000000e+00 3903.0
4 TraesCS5D01G475200 chr5B 89.387 2563 223 27 1 2539 647699127 647696590 0.000000e+00 3181.0
5 TraesCS5D01G475200 chr5B 89.371 2559 228 25 1 2539 647781505 647778971 0.000000e+00 3179.0
6 TraesCS5D01G475200 chr5B 91.201 2057 162 9 1 2041 647405859 647403806 0.000000e+00 2778.0
7 TraesCS5D01G475200 chr5B 87.069 116 12 3 2516 2630 460169258 460169145 7.660000e-26 128.0
8 TraesCS5D01G475200 chr5A 89.175 2217 215 18 332 2534 643034528 643032323 0.000000e+00 2741.0
9 TraesCS5D01G475200 chr5A 88.141 2302 250 17 249 2534 643042713 643040419 0.000000e+00 2717.0
10 TraesCS5D01G475200 chr5A 88.702 2142 217 20 249 2372 643029622 643027488 0.000000e+00 2591.0
11 TraesCS5D01G475200 chr5A 83.333 138 19 3 2497 2630 643037819 643037682 9.900000e-25 124.0
12 TraesCS5D01G475200 chr5A 88.333 60 7 0 249 308 643034869 643034810 3.640000e-09 73.1
13 TraesCS5D01G475200 chr1D 91.892 222 18 0 21 242 8737634 8737413 7.080000e-81 311.0
14 TraesCS5D01G475200 chr4D 89.256 242 26 0 1 242 348455850 348455609 1.190000e-78 303.0
15 TraesCS5D01G475200 chr4B 89.256 242 26 0 1 242 131751589 131751830 1.190000e-78 303.0
16 TraesCS5D01G475200 chr3A 86.992 123 13 3 2509 2630 707195865 707195745 4.570000e-28 135.0
17 TraesCS5D01G475200 chr6B 86.508 126 12 5 2508 2630 37105565 37105442 1.650000e-27 134.0
18 TraesCS5D01G475200 chr2B 83.453 139 20 3 2492 2629 608227289 608227153 2.750000e-25 126.0


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 TraesCS5D01G475200 chr5D 514972681 514975315 2634 True 4867.00 4867 100.0000 1 2635 1 chr5D.!!$R2 2634
1 TraesCS5D01G475200 chr5D 514946264 514948907 2643 True 3971.00 3971 93.8420 1 2635 1 chr5D.!!$R1 2634
2 TraesCS5D01G475200 chr5D 515023467 515026109 2642 True 3938.00 3938 93.6080 1 2635 1 chr5D.!!$R4 2634
3 TraesCS5D01G475200 chr5D 514994111 514996752 2641 True 3903.00 3903 93.3810 1 2635 1 chr5D.!!$R3 2634
4 TraesCS5D01G475200 chr5B 647696590 647699127 2537 True 3181.00 3181 89.3870 1 2539 1 chr5B.!!$R3 2538
5 TraesCS5D01G475200 chr5B 647778971 647781505 2534 True 3179.00 3179 89.3710 1 2539 1 chr5B.!!$R4 2538
6 TraesCS5D01G475200 chr5B 647403806 647405859 2053 True 2778.00 2778 91.2010 1 2041 1 chr5B.!!$R2 2040
7 TraesCS5D01G475200 chr5A 643027488 643042713 15225 True 1649.22 2741 87.5368 249 2630 5 chr5A.!!$R1 2381

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
354 365 1.340308 TGAGGTAATCGTCTCCGTCCA 60.34 52.381 0.0 0.0 35.01 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2242 10375 0.472925 TGGGTGAAGTGGAGCAGGTA 60.473 55.0 0.0 0.0 0.0 3.08 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
139 140 4.439974 GGTTGAATTGACAACTCAACTGCA 60.440 41.667 30.54 3.63 45.33 4.41
285 287 2.932261 CAGGATGGTTAGTTTAGGGCC 58.068 52.381 0.00 0.00 0.00 5.80
314 316 1.476891 TGATCAGGAGTAGTTGCGGAC 59.523 52.381 0.00 0.00 0.00 4.79
318 320 2.029290 TCAGGAGTAGTTGCGGACTTTC 60.029 50.000 0.00 0.00 39.86 2.62
354 365 1.340308 TGAGGTAATCGTCTCCGTCCA 60.340 52.381 0.00 0.00 35.01 4.02
397 408 7.741785 TGGTAAGTCTCACAAATTTTCCTCTA 58.258 34.615 0.00 0.00 0.00 2.43
955 9074 8.655970 GTCCACATTAAAACAATGATTTTAGCC 58.344 33.333 4.10 0.00 35.88 3.93
1018 9137 2.677902 GCCATCACTTGAGGAATCGACA 60.678 50.000 0.00 0.00 0.00 4.35
1072 9196 5.243060 TCGGTATCAACAAGAAGTCAAGAGA 59.757 40.000 0.00 0.00 0.00 3.10
1157 9281 3.041940 GCAACCACCGTCGTCCAG 61.042 66.667 0.00 0.00 0.00 3.86
1170 9294 2.935481 TCCAGGGCAAGGAGTGGG 60.935 66.667 0.00 0.00 0.00 4.61
1171 9295 3.260100 CCAGGGCAAGGAGTGGGT 61.260 66.667 0.00 0.00 0.00 4.51
1172 9296 2.845345 CCAGGGCAAGGAGTGGGTT 61.845 63.158 0.00 0.00 0.00 4.11
1227 9351 1.225704 GGATGGGAGAGTGGCAAGG 59.774 63.158 0.00 0.00 0.00 3.61
1282 9406 8.697507 AACTCTAAAGATCAAGTGATTGGTTT 57.302 30.769 0.00 0.20 34.37 3.27
1375 9499 2.076100 CGAGTATGCACAATGTGGTGT 58.924 47.619 15.78 0.00 40.89 4.16
1440 9564 1.305623 GAGGACCTACACCTCCGGA 59.694 63.158 2.93 2.93 45.64 5.14
1488 9612 3.428532 AGGCAAAGCATTCTTCATCTGT 58.571 40.909 0.00 0.00 0.00 3.41
1534 9658 2.005451 GCATGAAGATCGCTGTCACTT 58.995 47.619 0.00 0.00 0.00 3.16
1547 9671 6.499172 TCGCTGTCACTTCTTAATAGATCTG 58.501 40.000 5.18 0.00 0.00 2.90
1579 9705 6.423862 TGTGCGTCTTTGTATTTGTACTTTC 58.576 36.000 0.00 0.00 0.00 2.62
1582 9708 8.277713 GTGCGTCTTTGTATTTGTACTTTCTTA 58.722 33.333 0.00 0.00 0.00 2.10
1651 9781 9.905713 AAGAAATAAATTGATCCTAGTGCAGTA 57.094 29.630 0.37 0.37 0.00 2.74
1689 9819 8.421249 TTTCATGGAATCTTGATAAACCAACT 57.579 30.769 0.00 0.00 0.00 3.16
1698 9828 9.860898 AATCTTGATAAACCAACTTCTATTTGC 57.139 29.630 0.00 0.00 0.00 3.68
1759 9891 8.523915 TCTACAATTCTACCGACCATACTTTA 57.476 34.615 0.00 0.00 0.00 1.85
1776 9908 8.311109 CCATACTTTAAACATAAAGGGCAAACT 58.689 33.333 11.71 0.00 40.39 2.66
1859 9991 4.517952 TGTACAAAGCATCCCAAACATG 57.482 40.909 0.00 0.00 0.00 3.21
1937 10069 4.273257 TCACGCGCTGGTTGTCGA 62.273 61.111 5.73 0.00 0.00 4.20
2028 10160 0.179169 GCCCTAGTCGTCGAGTCAAC 60.179 60.000 5.70 0.00 0.00 3.18
2146 10279 5.105635 GGACTGCTCCAATTCATGATTTCAA 60.106 40.000 0.00 0.00 36.42 2.69
2151 10284 8.473358 TGCTCCAATTCATGATTTCAATAGAT 57.527 30.769 0.00 0.00 0.00 1.98
2242 10375 2.560105 GGAGCAGAGAAATGGTTGCTTT 59.440 45.455 0.00 0.00 46.12 3.51
2502 10642 8.109634 TCATTTGGGCTAGAAAAGTAAGAGATT 58.890 33.333 0.00 0.00 0.00 2.40
2503 10643 8.743714 CATTTGGGCTAGAAAAGTAAGAGATTT 58.256 33.333 0.00 0.00 0.00 2.17
2618 10809 7.489574 TTTATCAAAAACCAATTGCACCTTC 57.510 32.000 0.00 0.00 0.00 3.46
2631 10822 8.519526 CCAATTGCACCTTCTATTAAGTAACAA 58.480 33.333 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 8.685838 AACAGTAGCAATAGTAACAGGAAAAA 57.314 30.769 0.00 0.00 0.00 1.94
139 140 7.201947 GGAGCCAAAGAATATTTATGAGCCTTT 60.202 37.037 0.00 0.00 0.00 3.11
200 201 5.163152 GGGATCATGATAGTCTTCAAGGGTT 60.163 44.000 8.54 0.00 0.00 4.11
242 244 4.564821 GGCACAAACTGGAATGACCTACTA 60.565 45.833 0.00 0.00 39.86 1.82
285 287 6.537566 CAACTACTCCTGATCAACGAAATTG 58.462 40.000 0.00 0.00 39.94 2.32
354 365 3.898482 ACCAAGAACTTGTAGCCACTTT 58.102 40.909 12.54 0.00 38.85 2.66
397 408 6.920758 CGACGAGATTCTGAAGGATCTAATTT 59.079 38.462 0.88 0.00 0.00 1.82
411 422 2.416972 GCAGTAAACCCGACGAGATTCT 60.417 50.000 0.00 0.00 0.00 2.40
635 649 5.701290 AGTCCCTAATCTTGACTTTTCAACG 59.299 40.000 0.00 0.00 36.79 4.10
930 9049 7.543868 CGGCTAAAATCATTGTTTTAATGTGGA 59.456 33.333 0.00 0.00 34.26 4.02
931 9050 7.543868 TCGGCTAAAATCATTGTTTTAATGTGG 59.456 33.333 0.00 0.00 34.26 4.17
955 9074 6.589139 TCTCGTATGATATATATAGGCGGTCG 59.411 42.308 0.00 0.53 0.00 4.79
1046 9170 6.285224 TCTTGACTTCTTGTTGATACCGAAA 58.715 36.000 0.00 0.00 0.00 3.46
1157 9281 1.152546 AACAACCCACTCCTTGCCC 60.153 57.895 0.00 0.00 0.00 5.36
1227 9351 2.202756 GTCGCCGGACTGGATGTC 60.203 66.667 5.05 0.00 44.63 3.06
1298 9422 7.164122 ACACAAGAATACAGATCAGAACACAT 58.836 34.615 0.00 0.00 0.00 3.21
1375 9499 0.627451 TAGTCGCCTTCTCCCACCTA 59.373 55.000 0.00 0.00 0.00 3.08
1440 9564 1.742761 CGAGCTGGATGTGGTCATTT 58.257 50.000 0.00 0.00 34.06 2.32
1476 9600 4.065321 CGGAAGGCTACAGATGAAGAAT 57.935 45.455 0.00 0.00 0.00 2.40
1534 9658 6.101997 CACATATGCGCCAGATCTATTAAGA 58.898 40.000 4.18 0.00 35.80 2.10
1579 9705 6.183360 GCTAGCACACCATAAAGACTTGTAAG 60.183 42.308 10.63 0.00 0.00 2.34
1582 9708 4.003648 GCTAGCACACCATAAAGACTTGT 58.996 43.478 10.63 0.00 0.00 3.16
1651 9781 5.925506 TTCCATGAAAACATGATGCAGAT 57.074 34.783 11.10 0.00 34.66 2.90
1765 9897 6.435164 AGACCATCATAATAGTTTGCCCTTT 58.565 36.000 0.00 0.00 0.00 3.11
1784 9916 6.313658 CGAATTCAATTGACTGTGATAGACCA 59.686 38.462 7.89 0.00 0.00 4.02
1876 10008 4.039973 TGGTCGTTTGATGGTCTAAGAACT 59.960 41.667 0.00 0.00 0.00 3.01
1883 10015 2.028385 GGTAGTGGTCGTTTGATGGTCT 60.028 50.000 0.00 0.00 0.00 3.85
1930 10062 3.423154 CAGGCCGGCTTCGACAAC 61.423 66.667 28.56 6.68 35.61 3.32
1937 10069 3.553095 GACAAGGTCAGGCCGGCTT 62.553 63.158 28.56 18.19 43.70 4.35
2028 10160 6.884295 TGGATTGGTGGATCTAGTTTGTTAAG 59.116 38.462 0.00 0.00 0.00 1.85
2146 10279 8.237811 AGTTGAGGTGTTTGAAACAAATCTAT 57.762 30.769 12.89 2.27 44.16 1.98
2151 10284 6.090483 TGAAGTTGAGGTGTTTGAAACAAA 57.910 33.333 12.89 0.41 44.16 2.83
2242 10375 0.472925 TGGGTGAAGTGGAGCAGGTA 60.473 55.000 0.00 0.00 0.00 3.08
2502 10642 3.220110 AGTATCTCTCCCGATTGCGTAA 58.780 45.455 0.00 0.00 35.23 3.18
2503 10643 2.860009 AGTATCTCTCCCGATTGCGTA 58.140 47.619 0.00 0.00 35.23 4.42
2605 10796 8.050778 TGTTACTTAATAGAAGGTGCAATTGG 57.949 34.615 7.72 0.00 0.00 3.16
2609 10800 8.106247 CCTTTGTTACTTAATAGAAGGTGCAA 57.894 34.615 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.