Multiple sequence alignment - TraesCS5D01G374400

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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 TraesCS5D01G374400 chr5D 100.000 3298 0 0 1 3298 447318712 447315415 0.000000e+00 6091.0
1 TraesCS5D01G374400 chr4D 98.651 2669 35 1 630 3298 93441872 93444539 0.000000e+00 4728.0
2 TraesCS5D01G374400 chr6B 87.130 1181 143 5 2104 3283 36240685 36241857 0.000000e+00 1330.0
3 TraesCS5D01G374400 chr2B 86.299 1197 152 9 2104 3298 358777968 358776782 0.000000e+00 1291.0
4 TraesCS5D01G374400 chr2A 85.802 1134 152 8 2142 3271 711537872 711536744 0.000000e+00 1194.0
5 TraesCS5D01G374400 chr6D 80.631 1394 179 46 610 1986 414760754 414759435 0.000000e+00 994.0
6 TraesCS5D01G374400 chr6D 82.675 329 42 11 1874 2189 414759414 414759088 9.010000e-71 278.0
7 TraesCS5D01G374400 chr7D 82.230 1103 175 19 2179 3273 504351359 504350270 0.000000e+00 931.0
8 TraesCS5D01G374400 chr7D 94.286 35 2 0 608 642 504354349 504354315 2.000000e-03 54.7
9 TraesCS5D01G374400 chr5A 94.426 610 20 4 1 605 564761814 564762414 0.000000e+00 926.0
10 TraesCS5D01G374400 chr5A 84.013 638 79 15 608 1239 474494574 474495194 2.830000e-165 592.0
11 TraesCS5D01G374400 chr5A 82.787 244 33 5 1940 2174 474518017 474518260 3.330000e-50 209.0
12 TraesCS5D01G374400 chr3B 81.492 1086 182 18 2185 3259 452472019 452470942 0.000000e+00 874.0
13 TraesCS5D01G374400 chr3B 76.500 600 134 6 2635 3230 761922876 761922280 1.480000e-83 320.0
14 TraesCS5D01G374400 chr1B 79.275 1269 203 35 1811 3058 60483620 60484849 0.000000e+00 832.0
15 TraesCS5D01G374400 chr1B 79.841 878 151 21 608 1467 60482485 60483354 4.680000e-173 617.0
16 TraesCS5D01G374400 chr4B 78.690 1267 212 34 1811 3058 139527914 139526687 0.000000e+00 791.0
17 TraesCS5D01G374400 chr7A 79.485 1087 192 24 2185 3251 644610301 644611376 0.000000e+00 743.0
18 TraesCS5D01G374400 chr3A 84.714 700 100 6 2556 3251 67375300 67374604 0.000000e+00 693.0
19 TraesCS5D01G374400 chr5B 84.314 612 58 20 1 608 545270053 545270630 6.180000e-157 564.0
20 TraesCS5D01G374400 chr4A 75.799 657 151 7 2578 3230 661032647 661031995 3.170000e-85 326.0


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 TraesCS5D01G374400 chr5D 447315415 447318712 3297 True 6091.00 6091 100.000 1 3298 1 chr5D.!!$R1 3297
1 TraesCS5D01G374400 chr4D 93441872 93444539 2667 False 4728.00 4728 98.651 630 3298 1 chr4D.!!$F1 2668
2 TraesCS5D01G374400 chr6B 36240685 36241857 1172 False 1330.00 1330 87.130 2104 3283 1 chr6B.!!$F1 1179
3 TraesCS5D01G374400 chr2B 358776782 358777968 1186 True 1291.00 1291 86.299 2104 3298 1 chr2B.!!$R1 1194
4 TraesCS5D01G374400 chr2A 711536744 711537872 1128 True 1194.00 1194 85.802 2142 3271 1 chr2A.!!$R1 1129
5 TraesCS5D01G374400 chr6D 414759088 414760754 1666 True 636.00 994 81.653 610 2189 2 chr6D.!!$R1 1579
6 TraesCS5D01G374400 chr7D 504350270 504354349 4079 True 492.85 931 88.258 608 3273 2 chr7D.!!$R1 2665
7 TraesCS5D01G374400 chr5A 564761814 564762414 600 False 926.00 926 94.426 1 605 1 chr5A.!!$F3 604
8 TraesCS5D01G374400 chr5A 474494574 474495194 620 False 592.00 592 84.013 608 1239 1 chr5A.!!$F1 631
9 TraesCS5D01G374400 chr3B 452470942 452472019 1077 True 874.00 874 81.492 2185 3259 1 chr3B.!!$R1 1074
10 TraesCS5D01G374400 chr3B 761922280 761922876 596 True 320.00 320 76.500 2635 3230 1 chr3B.!!$R2 595
11 TraesCS5D01G374400 chr1B 60482485 60484849 2364 False 724.50 832 79.558 608 3058 2 chr1B.!!$F1 2450
12 TraesCS5D01G374400 chr4B 139526687 139527914 1227 True 791.00 791 78.690 1811 3058 1 chr4B.!!$R1 1247
13 TraesCS5D01G374400 chr7A 644610301 644611376 1075 False 743.00 743 79.485 2185 3251 1 chr7A.!!$F1 1066
14 TraesCS5D01G374400 chr3A 67374604 67375300 696 True 693.00 693 84.714 2556 3251 1 chr3A.!!$R1 695
15 TraesCS5D01G374400 chr5B 545270053 545270630 577 False 564.00 564 84.314 1 608 1 chr5B.!!$F1 607
16 TraesCS5D01G374400 chr4A 661031995 661032647 652 True 326.00 326 75.799 2578 3230 1 chr4A.!!$R1 652

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
126 133 0.179150 CACGTTTGTTGGGTGTGGTG 60.179 55.000 0.00 0.0 0.00 4.17 F
408 416 1.079127 CGAGCCCCACTACAGTTGG 60.079 63.158 0.00 0.0 0.00 3.77 F
588 600 1.267574 ATCCTTCGCTCCAGCCAGAA 61.268 55.000 0.00 0.0 37.91 3.02 F
1255 2788 1.612442 ACCCATGGCGACTGGTAGT 60.612 57.895 6.09 0.0 31.44 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1255 2788 1.606668 GCACAGATTTTCCCGTCAACA 59.393 47.619 0.00 0.0 0.00 3.33 R
2194 4263 1.669779 GTGCAGCTGCTCCAATTCTAG 59.330 52.381 36.61 0.0 42.66 2.43 R
2265 4334 1.881925 CGGGTTGATCAGCAAACTCCA 60.882 52.381 11.93 0.0 43.84 3.86 R
2973 5066 1.207089 CCGACCATCTTTGTCTGCCTA 59.793 52.381 0.00 0.0 0.00 3.93 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
99 106 7.286087 ACATGTGGTCTGCATTCATATACAATT 59.714 33.333 0.00 0.00 0.00 2.32
100 107 7.030075 TGTGGTCTGCATTCATATACAATTG 57.970 36.000 3.24 3.24 0.00 2.32
101 108 6.039605 TGTGGTCTGCATTCATATACAATTGG 59.960 38.462 10.83 0.00 0.00 3.16
102 109 5.009911 TGGTCTGCATTCATATACAATTGGC 59.990 40.000 10.83 0.50 0.00 4.52
103 110 5.009911 GGTCTGCATTCATATACAATTGGCA 59.990 40.000 10.83 5.31 0.00 4.92
104 111 6.294899 GGTCTGCATTCATATACAATTGGCAT 60.295 38.462 10.83 5.28 0.00 4.40
126 133 0.179150 CACGTTTGTTGGGTGTGGTG 60.179 55.000 0.00 0.00 0.00 4.17
155 162 7.335924 TCGACCTAACTTTTATTTTCCAGGATG 59.664 37.037 0.00 0.00 0.00 3.51
211 219 8.060689 TGGTACCAGTGTATTAGGTTAGTCATA 58.939 37.037 11.60 0.00 36.87 2.15
326 334 3.096092 TGTCCCAAAAACATGATAGCCC 58.904 45.455 0.00 0.00 0.00 5.19
327 335 3.245586 TGTCCCAAAAACATGATAGCCCT 60.246 43.478 0.00 0.00 0.00 5.19
328 336 3.131046 GTCCCAAAAACATGATAGCCCTG 59.869 47.826 0.00 0.00 0.00 4.45
408 416 1.079127 CGAGCCCCACTACAGTTGG 60.079 63.158 0.00 0.00 0.00 3.77
420 428 3.510360 ACTACAGTTGGCGATACTTCTGT 59.490 43.478 0.00 0.00 39.11 3.41
430 438 3.490933 GCGATACTTCTGTGCATCAGGTA 60.491 47.826 13.87 10.32 43.76 3.08
491 499 2.324014 TATGCACCCACTGCCGATCC 62.324 60.000 0.00 0.00 46.51 3.36
540 552 4.351874 TGGTCCACCTTGTTCTTTCTAG 57.648 45.455 0.00 0.00 36.82 2.43
544 556 5.245526 GGTCCACCTTGTTCTTTCTAGTCTA 59.754 44.000 0.00 0.00 0.00 2.59
545 557 6.239515 GGTCCACCTTGTTCTTTCTAGTCTAA 60.240 42.308 0.00 0.00 0.00 2.10
588 600 1.267574 ATCCTTCGCTCCAGCCAGAA 61.268 55.000 0.00 0.00 37.91 3.02
605 617 4.580868 CCAGAAGAAAAAGGAGGGTAGTC 58.419 47.826 0.00 0.00 0.00 2.59
606 618 4.287326 CCAGAAGAAAAAGGAGGGTAGTCT 59.713 45.833 0.00 0.00 0.00 3.24
1255 2788 1.612442 ACCCATGGCGACTGGTAGT 60.612 57.895 6.09 0.00 31.44 2.73
1434 2969 5.305902 TCCTGGACTGATTTTGTGTGTACTA 59.694 40.000 0.00 0.00 0.00 1.82
2098 4099 6.597832 AGTAGCTGACTTTGAGAATACTGT 57.402 37.500 0.00 0.00 33.13 3.55
2547 4621 1.284198 AGCTGTTTCTCCTGCATCCAT 59.716 47.619 0.00 0.00 0.00 3.41
2663 4738 4.486125 TGATTGGTACATAGCAGAGCAA 57.514 40.909 0.00 0.00 39.30 3.91
2753 4828 0.249120 TTGATGCGTACAGTGGGGAG 59.751 55.000 0.00 0.00 0.00 4.30
2870 4961 7.420800 TCACAAAAAGAGCTCTGAAGAATTTC 58.579 34.615 19.06 0.00 0.00 2.17
2964 5057 5.215160 GTTCACAAGATCCACATTTCACAC 58.785 41.667 0.00 0.00 0.00 3.82
2973 5066 2.483876 CACATTTCACACACCGAGTCT 58.516 47.619 0.00 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 7.087639 CCAGCCGAAAGATTACATTGTAAAAA 58.912 34.615 12.96 0.0 0.00 1.94
99 106 0.595588 CCAACAAACGTGCTATGCCA 59.404 50.000 0.00 0.0 0.00 4.92
100 107 0.109319 CCCAACAAACGTGCTATGCC 60.109 55.000 0.00 0.0 0.00 4.40
101 108 0.596082 ACCCAACAAACGTGCTATGC 59.404 50.000 0.00 0.0 0.00 3.14
102 109 1.606668 ACACCCAACAAACGTGCTATG 59.393 47.619 0.00 0.0 0.00 2.23
103 110 1.606668 CACACCCAACAAACGTGCTAT 59.393 47.619 0.00 0.0 0.00 2.97
104 111 1.018148 CACACCCAACAAACGTGCTA 58.982 50.000 0.00 0.0 0.00 3.49
126 133 5.413523 TGGAAAATAAAAGTTAGGTCGAGGC 59.586 40.000 0.00 0.0 0.00 4.70
155 162 7.870826 TGTGTTGCCATGCTATATATTGTTAC 58.129 34.615 0.00 0.0 0.00 2.50
211 219 3.511595 CGCGAGGCATGGCAATGT 61.512 61.111 22.64 0.0 36.08 2.71
241 249 2.027100 GCTACTTATAGGGACATGGGGC 60.027 54.545 0.00 0.0 0.00 5.80
326 334 6.385537 GCTGATTTTTCATTAACACAGCAG 57.614 37.500 0.00 0.0 45.48 4.24
328 336 6.617105 GCAAGCTGATTTTTCATTAACACAGC 60.617 38.462 0.00 0.0 46.18 4.40
430 438 1.186267 GGAGGAGACACCGGTCAGTT 61.186 60.000 2.59 0.0 46.80 3.16
434 442 0.034283 AGTAGGAGGAGACACCGGTC 60.034 60.000 2.59 0.0 46.96 4.79
491 499 0.881118 CACATTTGTCTGGTTCCCCG 59.119 55.000 0.00 0.0 0.00 5.73
540 552 2.303311 AGCAGGGGAGAAACTGTTAGAC 59.697 50.000 0.00 0.0 37.07 2.59
544 556 1.479389 CCAAGCAGGGGAGAAACTGTT 60.479 52.381 0.00 0.0 37.07 3.16
545 557 0.111253 CCAAGCAGGGGAGAAACTGT 59.889 55.000 0.00 0.0 37.07 3.55
588 600 3.583526 GTCCAGACTACCCTCCTTTTTCT 59.416 47.826 0.00 0.0 0.00 2.52
605 617 0.038526 ACTAGAACAACCGCGTCCAG 60.039 55.000 4.92 0.0 0.00 3.86
606 618 0.038892 GACTAGAACAACCGCGTCCA 60.039 55.000 4.92 0.0 0.00 4.02
1156 2689 2.158449 GCTGTCGTTCACTTCTTCCATG 59.842 50.000 0.00 0.0 0.00 3.66
1255 2788 1.606668 GCACAGATTTTCCCGTCAACA 59.393 47.619 0.00 0.0 0.00 3.33
1329 2862 6.119240 TGGGATCAATCTGTCCAATAGATC 57.881 41.667 0.00 0.0 33.92 2.75
1434 2969 2.371179 CCAGTCAGTCCATGCCATCTAT 59.629 50.000 0.00 0.0 0.00 1.98
2194 4263 1.669779 GTGCAGCTGCTCCAATTCTAG 59.330 52.381 36.61 0.0 42.66 2.43
2265 4334 1.881925 CGGGTTGATCAGCAAACTCCA 60.882 52.381 11.93 0.0 43.84 3.86
2663 4738 7.715657 ACAATGAATAGTTGTGTTGTTCATGT 58.284 30.769 0.00 0.0 38.93 3.21
2753 4828 3.414700 CGCAACTGCTCCACCGAC 61.415 66.667 0.00 0.0 39.32 4.79
2870 4961 2.156917 TCTCTGCTGATTTTGCCACAG 58.843 47.619 0.00 0.0 35.14 3.66
2973 5066 1.207089 CCGACCATCTTTGTCTGCCTA 59.793 52.381 0.00 0.0 0.00 3.93
3273 5366 7.239166 CCGTATGTATGCCATCAAGATAATC 57.761 40.000 0.00 0.0 34.86 1.75


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

AutoCloner maintained by Alex Coulton.