Multiple sequence alignment - TraesCS5B01G453700

Loading Multiple Alignment...

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 TraesCS5B01G453700 chr5B 100.000 2831 0 0 1 2831 626252111 626249281 0.000000e+00 5228.0
1 TraesCS5B01G453700 chr5B 92.506 2829 117 30 6 2798 631392890 631390121 0.000000e+00 3962.0
2 TraesCS5B01G453700 chr5A 95.792 1307 50 2 911 2212 631277370 631276064 0.000000e+00 2104.0
3 TraesCS5B01G453700 chr5A 92.051 629 30 7 2215 2823 631268281 631267653 0.000000e+00 867.0
4 TraesCS5B01G453700 chr5A 89.151 636 36 15 4 619 631278838 631278216 0.000000e+00 761.0
5 TraesCS5B01G453700 chr5A 93.827 162 9 1 743 904 631277723 631277563 2.820000e-60 243.0
6 TraesCS5B01G453700 chr1D 81.246 1413 199 33 1068 2433 71639747 71638354 0.000000e+00 1081.0
7 TraesCS5B01G453700 chr1D 78.295 1267 203 50 960 2179 71770093 71768852 0.000000e+00 750.0
8 TraesCS5B01G453700 chr1A 80.793 1437 203 34 1068 2444 71724985 71723562 0.000000e+00 1057.0
9 TraesCS5B01G453700 chr1A 77.387 398 50 22 2455 2831 71723581 71723203 1.720000e-47 200.0
10 TraesCS5B01G453700 chr1B 80.611 1408 200 31 1085 2444 112865985 112864603 0.000000e+00 1020.0
11 TraesCS5B01G453700 chr1B 77.656 1280 202 57 960 2179 113026363 113025108 0.000000e+00 702.0
12 TraesCS5B01G453700 chr1B 74.821 1116 225 43 1085 2164 113516574 113515479 1.200000e-123 453.0
13 TraesCS5B01G453700 chr1B 78.141 398 60 17 2455 2831 112864622 112864231 7.890000e-56 228.0
14 TraesCS5B01G453700 chr1B 80.165 121 23 1 2290 2410 63218018 63217899 3.880000e-14 89.8
15 TraesCS5B01G453700 chr6D 79.216 255 45 7 1080 1330 71053203 71052953 1.350000e-38 171.0
16 TraesCS5B01G453700 chr6B 79.216 255 45 7 1080 1330 145576129 145575879 1.350000e-38 171.0
17 TraesCS5B01G453700 chr6B 77.731 238 39 9 1086 1316 145570263 145570033 1.770000e-27 134.0
18 TraesCS5B01G453700 chr7B 82.222 135 19 3 324 458 712738820 712738949 8.290000e-21 111.0
19 TraesCS5B01G453700 chr7D 81.343 134 20 4 322 455 603189523 603189395 1.390000e-18 104.0
20 TraesCS5B01G453700 chr4A 82.906 117 19 1 335 450 40265183 40265299 1.390000e-18 104.0
21 TraesCS5B01G453700 chr4A 91.667 48 2 2 1832 1878 613681380 613681426 6.550000e-07 65.8
22 TraesCS5B01G453700 chr3B 80.328 122 19 4 310 429 605480832 605480950 1.400000e-13 87.9
23 TraesCS5B01G453700 chr3A 82.192 73 12 1 343 414 600677395 600677467 8.470000e-06 62.1
24 TraesCS5B01G453700 chr2D 94.286 35 2 0 2360 2394 34541533 34541567 1.000000e-03 54.7


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 TraesCS5B01G453700 chr5B 626249281 626252111 2830 True 5228.0 5228 100.000000 1 2831 1 chr5B.!!$R1 2830
1 TraesCS5B01G453700 chr5B 631390121 631392890 2769 True 3962.0 3962 92.506000 6 2798 1 chr5B.!!$R2 2792
2 TraesCS5B01G453700 chr5A 631276064 631278838 2774 True 1036.0 2104 92.923333 4 2212 3 chr5A.!!$R2 2208
3 TraesCS5B01G453700 chr5A 631267653 631268281 628 True 867.0 867 92.051000 2215 2823 1 chr5A.!!$R1 608
4 TraesCS5B01G453700 chr1D 71638354 71639747 1393 True 1081.0 1081 81.246000 1068 2433 1 chr1D.!!$R1 1365
5 TraesCS5B01G453700 chr1D 71768852 71770093 1241 True 750.0 750 78.295000 960 2179 1 chr1D.!!$R2 1219
6 TraesCS5B01G453700 chr1A 71723203 71724985 1782 True 628.5 1057 79.090000 1068 2831 2 chr1A.!!$R1 1763
7 TraesCS5B01G453700 chr1B 113025108 113026363 1255 True 702.0 702 77.656000 960 2179 1 chr1B.!!$R2 1219
8 TraesCS5B01G453700 chr1B 112864231 112865985 1754 True 624.0 1020 79.376000 1085 2831 2 chr1B.!!$R4 1746
9 TraesCS5B01G453700 chr1B 113515479 113516574 1095 True 453.0 453 74.821000 1085 2164 1 chr1B.!!$R3 1079

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
643 692 1.179814 AGAGAGAAACCCGCTCACGT 61.180 55.000 0.0 0.0 43.13 4.49 F
997 1578 1.227380 CCATCTCGCCAGCCACTAC 60.227 63.158 0.0 0.0 0.00 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1752 2381 0.521735 GGGCGTCCTCAATGAACAAC 59.478 55.0 0.00 0.0 0.0 3.32 R
2036 2703 1.071605 CTCGAGAGCCAAAACCTTCG 58.928 55.0 6.58 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
74 77 7.919091 CGAGCAGATAACCACTATAACTAACAA 59.081 37.037 0.00 0.00 0.00 2.83
77 80 7.494625 GCAGATAACCACTATAACTAACAAGCA 59.505 37.037 0.00 0.00 0.00 3.91
102 105 4.776349 TGTGCCTACTTCAAAGAAGTTGA 58.224 39.130 16.53 0.66 44.74 3.18
173 176 9.443323 TTTTTAAGAATAGCATGTACTGTAGCA 57.557 29.630 0.00 0.00 0.00 3.49
444 466 7.485913 CGAACAAAATTATGGAATCCTGAACAG 59.514 37.037 0.00 0.00 0.00 3.16
455 477 7.390027 TGGAATCCTGAACAGTTTTTGAAAAA 58.610 30.769 0.00 0.00 0.00 1.94
568 590 3.699779 TCAGACTGCATCATCGTCTAC 57.300 47.619 5.34 0.00 36.33 2.59
569 591 2.032178 TCAGACTGCATCATCGTCTACG 59.968 50.000 5.34 0.00 36.33 3.51
570 592 2.017782 AGACTGCATCATCGTCTACGT 58.982 47.619 3.88 0.00 36.33 3.57
571 593 2.423892 AGACTGCATCATCGTCTACGTT 59.576 45.455 3.88 0.00 36.33 3.99
597 619 5.991328 TGCATAGCAGTGCTCTTAATAAC 57.009 39.130 23.64 5.94 45.27 1.89
643 692 1.179814 AGAGAGAAACCCGCTCACGT 61.180 55.000 0.00 0.00 43.13 4.49
717 770 2.122989 ATACGACCGGGGCTGGAT 60.123 61.111 6.32 0.00 0.00 3.41
838 1229 4.699522 GCGTGGCTCCCTCCGTTT 62.700 66.667 0.00 0.00 0.00 3.60
995 1576 2.685017 TCCATCTCGCCAGCCACT 60.685 61.111 0.00 0.00 0.00 4.00
996 1577 1.381191 TCCATCTCGCCAGCCACTA 60.381 57.895 0.00 0.00 0.00 2.74
997 1578 1.227380 CCATCTCGCCAGCCACTAC 60.227 63.158 0.00 0.00 0.00 2.73
1247 1852 2.359169 CCCTCTGCTCCAACGCCTA 61.359 63.158 0.00 0.00 0.00 3.93
1409 2014 1.630244 CGAGCCCTTGACAAGCTTCG 61.630 60.000 9.85 13.12 36.87 3.79
1482 2102 2.268076 GCTGCCACCATCCGTGTTT 61.268 57.895 0.00 0.00 41.26 2.83
1752 2381 4.614946 CTTGTTTTTCAGGCAAAGGAGAG 58.385 43.478 0.00 0.00 0.00 3.20
1871 2510 4.307259 AGATATTAGGCCCTTTGTCTCCA 58.693 43.478 0.00 0.00 0.00 3.86
2024 2691 8.537728 TTGATCCCAACAAGCTTGAATAATAT 57.462 30.769 32.50 16.88 0.00 1.28
2252 2947 4.770010 ACTTTTTCAGTGGGAGAAACACAA 59.230 37.500 0.00 0.00 41.21 3.33
2254 2949 2.341846 TCAGTGGGAGAAACACAACC 57.658 50.000 0.00 0.00 41.21 3.77
2480 3191 1.747355 CAGCAAGGAATGGTTGGCTAG 59.253 52.381 0.00 0.00 37.77 3.42
2489 3200 4.947388 GGAATGGTTGGCTAGTCAATACAA 59.053 41.667 13.85 0.00 0.00 2.41
2491 3202 4.634012 TGGTTGGCTAGTCAATACAAGT 57.366 40.909 13.85 0.00 0.00 3.16
2669 3389 0.887247 TGGTTTGTCAATGGCCGATG 59.113 50.000 0.00 0.00 0.00 3.84
2739 3462 8.260114 TGTCTTTTACTCAGATTGATATGCTCA 58.740 33.333 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.887854 GAATCCTCGCCTAGTACTCCC 59.112 57.143 0.00 0.00 0.00 4.30
1 2 1.536331 CGAATCCTCGCCTAGTACTCC 59.464 57.143 0.00 0.00 38.45 3.85
2 3 2.492012 TCGAATCCTCGCCTAGTACTC 58.508 52.381 0.00 0.00 45.04 2.59
77 80 4.781934 ACTTCTTTGAAGTAGGCACAAGT 58.218 39.130 10.76 0.00 0.00 3.16
267 271 7.480229 ACAATGTTTGCTTTTTAAAAAGTTCGC 59.520 29.630 31.25 22.31 45.48 4.70
268 272 8.873242 ACAATGTTTGCTTTTTAAAAAGTTCG 57.127 26.923 31.25 15.12 45.48 3.95
353 374 8.961294 TTGTTCCAAATTTTGTTCACATTTTG 57.039 26.923 8.26 0.00 0.00 2.44
354 375 9.007901 TCTTGTTCCAAATTTTGTTCACATTTT 57.992 25.926 8.26 0.00 0.00 1.82
405 427 9.152851 CATAATTTTGTTCGCGTTTTGAAAAAT 57.847 25.926 5.77 8.60 0.00 1.82
509 531 8.703336 GCATGGAACTTTTCTTCTGTTTTATTC 58.297 33.333 0.00 0.00 0.00 1.75
533 555 2.240414 AGTCTGAACCATCATCCATGCA 59.760 45.455 0.00 0.00 34.37 3.96
539 561 3.538591 TGATGCAGTCTGAACCATCATC 58.461 45.455 14.23 11.25 37.43 2.92
540 562 3.639672 TGATGCAGTCTGAACCATCAT 57.360 42.857 14.23 3.57 37.43 2.45
541 563 3.538591 GATGATGCAGTCTGAACCATCA 58.461 45.455 18.28 18.28 37.43 3.07
568 590 2.373735 GCACTGCTATGCATACAACG 57.626 50.000 1.16 0.00 45.39 4.10
622 671 0.603569 GTGAGCGGGTTTCTCTCTCA 59.396 55.000 0.00 0.00 0.00 3.27
623 672 0.456995 CGTGAGCGGGTTTCTCTCTC 60.457 60.000 0.00 0.00 0.00 3.20
643 692 0.630673 ATGGAATAACAGCAGGGCCA 59.369 50.000 6.18 0.00 0.00 5.36
736 789 1.298339 GGGCGCACGTCATTATTGC 60.298 57.895 10.83 0.00 0.00 3.56
995 1576 5.473504 GCCTTCTTTTTCCTCTTCATGTGTA 59.526 40.000 0.00 0.00 0.00 2.90
996 1577 4.279420 GCCTTCTTTTTCCTCTTCATGTGT 59.721 41.667 0.00 0.00 0.00 3.72
997 1578 4.614535 CGCCTTCTTTTTCCTCTTCATGTG 60.615 45.833 0.00 0.00 0.00 3.21
1163 1768 2.733301 ATCTGCGAGAGATGGCCG 59.267 61.111 0.00 0.00 40.19 6.13
1247 1852 2.430921 CGACGGAGAAGCGCTTGT 60.431 61.111 30.47 25.67 0.00 3.16
1409 2014 0.107945 AAAGCTGATGTCGAGCTCCC 60.108 55.000 8.47 0.00 46.32 4.30
1482 2102 1.456196 CGAGGAGGGATGCTAAGCGA 61.456 60.000 0.00 0.00 0.00 4.93
1752 2381 0.521735 GGGCGTCCTCAATGAACAAC 59.478 55.000 0.00 0.00 0.00 3.32
1871 2510 6.371278 AGCAATCTCAATTTCAGGGATACAT 58.629 36.000 0.00 0.00 39.74 2.29
2024 2691 4.513692 CCAAAACCTTCGTTGTGTCTATGA 59.486 41.667 0.00 0.00 35.69 2.15
2036 2703 1.071605 CTCGAGAGCCAAAACCTTCG 58.928 55.000 6.58 0.00 0.00 3.79
2128 2795 9.334693 CAGAAAGCAAAGATGAATACTTACAAC 57.665 33.333 0.00 0.00 0.00 3.32
2254 2949 7.653713 ACGTGCATCTTTCATACCTATCTTTAG 59.346 37.037 0.00 0.00 0.00 1.85
2318 3028 4.525100 TGGCTAGGTAATTTTTCAACACCC 59.475 41.667 0.00 0.00 0.00 4.61
2480 3191 7.377766 TCCATTTCTAGCAACTTGTATTGAC 57.622 36.000 0.00 0.00 0.00 3.18
2489 3200 7.115414 AGCTCTATTTTCCATTTCTAGCAACT 58.885 34.615 0.00 0.00 0.00 3.16
2491 3202 7.831193 AGAAGCTCTATTTTCCATTTCTAGCAA 59.169 33.333 0.00 0.00 0.00 3.91
2642 3362 3.677190 CCATTGACAAACCATTGCCATT 58.323 40.909 0.00 0.00 40.34 3.16
2669 3389 2.602878 CTTGTCTGCAACATCAATGGC 58.397 47.619 3.15 0.00 37.82 4.40
2739 3462 2.545742 GGCCAAAGACAACGCAATCTTT 60.546 45.455 0.00 3.29 44.19 2.52


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

AutoCloner maintained by Alex Coulton.