Multiple sequence alignment - TraesCS6B01G088100

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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 TraesCS6B01G088100 chr6B 100.000 2582 0 0 1 2582 63998858 63996277 0.000000e+00 4769.0
1 TraesCS6B01G088100 chr6B 95.801 1667 69 1 1 1667 63768805 63767140 0.000000e+00 2689.0
2 TraesCS6B01G088100 chr6B 94.272 838 43 4 1738 2573 63753237 63752403 0.000000e+00 1277.0
3 TraesCS6B01G088100 chr6B 84.458 489 67 8 1182 1667 77616039 77616521 8.360000e-130 473.0
4 TraesCS6B01G088100 chr6B 80.931 451 33 30 1883 2308 77397051 77396629 8.970000e-80 307.0
5 TraesCS6B01G088100 chr6B 80.505 277 23 17 2312 2581 77396463 77396211 1.580000e-42 183.0
6 TraesCS6B01G088100 chr6B 77.652 264 47 6 75 326 84491347 84491610 1.600000e-32 150.0
7 TraesCS6B01G088100 chr6B 98.750 80 1 0 1665 1744 63767106 63767027 2.680000e-30 143.0
8 TraesCS6B01G088100 chr6B 76.042 192 42 3 1803 1993 84135151 84135339 2.110000e-16 97.1
9 TraesCS6B01G088100 chrUn 95.196 2602 96 22 1 2581 102652062 102649469 0.000000e+00 4085.0
10 TraesCS6B01G088100 chrUn 78.582 1326 239 26 356 1663 98357393 98356095 0.000000e+00 833.0
11 TraesCS6B01G088100 chrUn 79.265 1225 209 30 462 1655 143908680 143909890 0.000000e+00 813.0
12 TraesCS6B01G088100 chrUn 75.063 1576 320 53 91 1626 153494816 153493274 0.000000e+00 665.0
13 TraesCS6B01G088100 chrUn 80.676 828 127 26 1182 1987 113108878 113108062 1.700000e-171 612.0
14 TraesCS6B01G088100 chrUn 74.775 1554 294 61 91 1618 26732840 26734321 2.200000e-170 608.0
15 TraesCS6B01G088100 chrUn 79.778 811 131 25 1199 1987 113158393 113157594 2.240000e-155 558.0
16 TraesCS6B01G088100 chrUn 83.673 588 61 22 1705 2264 104484711 104484131 2.940000e-144 521.0
17 TraesCS6B01G088100 chrUn 82.618 489 76 8 1182 1667 350654140 350653658 8.540000e-115 424.0
18 TraesCS6B01G088100 chrUn 86.479 355 45 3 1665 2018 104795907 104795555 1.120000e-103 387.0
19 TraesCS6B01G088100 chrUn 85.673 349 47 3 1671 2018 104679609 104679263 5.250000e-97 364.0
20 TraesCS6B01G088100 chrUn 78.042 337 66 6 84 416 26573649 26573317 3.370000e-49 206.0
21 TraesCS6B01G088100 chrUn 88.439 173 17 2 2311 2481 104484133 104483962 3.370000e-49 206.0
22 TraesCS6B01G088100 chrUn 80.408 245 43 5 91 334 153436432 153436192 5.680000e-42 182.0
23 TraesCS6B01G088100 chrUn 88.732 71 3 4 1671 1740 153493194 153493128 5.920000e-12 82.4
24 TraesCS6B01G088100 chr6A 90.876 1655 144 6 18 1667 61815037 61813385 0.000000e+00 2213.0
25 TraesCS6B01G088100 chr6A 78.785 1202 216 32 469 1655 47956548 47957725 0.000000e+00 771.0
26 TraesCS6B01G088100 chr6A 74.889 1577 315 54 69 1618 48036685 48038207 0.000000e+00 643.0
27 TraesCS6B01G088100 chr6A 87.033 455 52 5 2117 2568 61812718 61812268 8.240000e-140 507.0
28 TraesCS6B01G088100 chr6A 86.446 332 37 6 1665 1990 61813348 61813019 8.790000e-95 357.0
29 TraesCS6B01G088100 chr6A 71.536 801 165 34 91 888 47701949 47702689 9.560000e-35 158.0
30 TraesCS6B01G088100 chr6A 90.141 71 5 2 1671 1740 48038297 48038366 9.840000e-15 91.6
31 TraesCS6B01G088100 chr6A 86.111 72 8 2 1672 1742 47959394 47959464 2.760000e-10 76.8
32 TraesCS6B01G088100 chr5D 82.609 138 22 2 1786 1922 556048931 556048795 1.250000e-23 121.0


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 TraesCS6B01G088100 chr6B 63996277 63998858 2581 True 4769.000000 4769 100.000000 1 2582 1 chr6B.!!$R2 2581
1 TraesCS6B01G088100 chr6B 63767027 63768805 1778 True 1416.000000 2689 97.275500 1 1744 2 chr6B.!!$R3 1743
2 TraesCS6B01G088100 chr6B 63752403 63753237 834 True 1277.000000 1277 94.272000 1738 2573 1 chr6B.!!$R1 835
3 TraesCS6B01G088100 chr6B 77396211 77397051 840 True 245.000000 307 80.718000 1883 2581 2 chr6B.!!$R4 698
4 TraesCS6B01G088100 chrUn 102649469 102652062 2593 True 4085.000000 4085 95.196000 1 2581 1 chrUn.!!$R3 2580
5 TraesCS6B01G088100 chrUn 98356095 98357393 1298 True 833.000000 833 78.582000 356 1663 1 chrUn.!!$R2 1307
6 TraesCS6B01G088100 chrUn 143908680 143909890 1210 False 813.000000 813 79.265000 462 1655 1 chrUn.!!$F2 1193
7 TraesCS6B01G088100 chrUn 113108062 113108878 816 True 612.000000 612 80.676000 1182 1987 1 chrUn.!!$R6 805
8 TraesCS6B01G088100 chrUn 26732840 26734321 1481 False 608.000000 608 74.775000 91 1618 1 chrUn.!!$F1 1527
9 TraesCS6B01G088100 chrUn 113157594 113158393 799 True 558.000000 558 79.778000 1199 1987 1 chrUn.!!$R7 788
10 TraesCS6B01G088100 chrUn 153493128 153494816 1688 True 373.700000 665 81.897500 91 1740 2 chrUn.!!$R11 1649
11 TraesCS6B01G088100 chrUn 104483962 104484711 749 True 363.500000 521 86.056000 1705 2481 2 chrUn.!!$R10 776
12 TraesCS6B01G088100 chr6A 61812268 61815037 2769 True 1025.666667 2213 88.118333 18 2568 3 chr6A.!!$R1 2550
13 TraesCS6B01G088100 chr6A 47956548 47959464 2916 False 423.900000 771 82.448000 469 1742 2 chr6A.!!$F2 1273
14 TraesCS6B01G088100 chr6A 48036685 48038366 1681 False 367.300000 643 82.515000 69 1740 2 chr6A.!!$F3 1671

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
60 61 0.758734 CGACCAGCCAGAATCCCATA 59.241 55.000 0.0 0.0 0.0 2.74 F
761 781 1.552337 TCAGAGCTGGTGATTGAGGAC 59.448 52.381 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 3027 1.212935 GGCATCAACCCTGTCTATGGT 59.787 52.381 0.00 0.0 36.06 3.55 R
2473 4608 5.070446 TCCATGAAAAGAGATACGTATGGCT 59.930 40.000 13.97 4.5 35.09 4.75 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
60 61 0.758734 CGACCAGCCAGAATCCCATA 59.241 55.000 0.00 0.00 0.00 2.74
99 100 3.067320 TGAGATCGCGAGTGATTTCATCT 59.933 43.478 16.66 9.02 35.33 2.90
100 101 4.275936 TGAGATCGCGAGTGATTTCATCTA 59.724 41.667 16.66 0.00 35.33 1.98
103 104 3.435566 TCGCGAGTGATTTCATCTACAC 58.564 45.455 3.71 0.00 0.00 2.90
123 124 2.849162 TCCCCGATGCCATCCTCC 60.849 66.667 0.00 0.00 0.00 4.30
459 479 4.206375 TCAATGTTCTGAGCCAAGAAACA 58.794 39.130 0.48 3.06 37.90 2.83
502 522 3.746949 CTGCATCCACCCTCCTCGC 62.747 68.421 0.00 0.00 0.00 5.03
504 524 2.134287 GCATCCACCCTCCTCGCTA 61.134 63.158 0.00 0.00 0.00 4.26
575 595 2.038863 TTCCCCTCCTCAAGCAACTA 57.961 50.000 0.00 0.00 0.00 2.24
710 730 2.797786 AGCTCACGGACTCTTAGAAGT 58.202 47.619 0.00 0.00 0.00 3.01
761 781 1.552337 TCAGAGCTGGTGATTGAGGAC 59.448 52.381 0.00 0.00 0.00 3.85
1480 2924 5.373222 TGCTAAAAGTGGAAAACAGAGCTA 58.627 37.500 0.00 0.00 0.00 3.32
1752 3531 0.250209 AGTGCACTGCAGAGAGGTTG 60.250 55.000 23.35 8.15 40.08 3.77
1865 3646 7.026562 TGCATGTATTGGAAACTTAATTGTCG 58.973 34.615 0.00 0.00 0.00 4.35
2161 4131 9.487790 GGTTGAATTTAGTGAAATGAAATTGGA 57.512 29.630 0.00 0.00 36.10 3.53
2182 4152 6.530019 GGATCCATCCTTGTACAAATTTGT 57.470 37.500 25.99 25.99 43.73 2.83
2185 4155 8.695456 GGATCCATCCTTGTACAAATTTGTAAT 58.305 33.333 28.05 16.84 42.90 1.89
2347 4479 6.479095 TCTTTGTTGCTTTCAAAACCTTTG 57.521 33.333 0.00 0.00 34.96 2.77
2351 4483 5.794894 TGTTGCTTTCAAAACCTTTGGTTA 58.205 33.333 2.15 0.00 46.20 2.85
2354 4487 7.391833 TGTTGCTTTCAAAACCTTTGGTTATTT 59.608 29.630 2.15 0.00 46.20 1.40
2473 4608 1.880271 TTGGTCGCATTTCGTTACCA 58.120 45.000 0.00 0.00 41.49 3.25
2481 4616 2.286184 GCATTTCGTTACCAGCCATACG 60.286 50.000 0.00 0.00 35.46 3.06
2581 4722 4.128925 TCTTCTGCATCTGTGGTATGAC 57.871 45.455 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 6.243811 GATCTCATCGTAGACGGTAATTCT 57.756 41.667 1.67 0.0 42.51 2.40
99 100 3.845259 GGCATCGGGGAGCGTGTA 61.845 66.667 0.00 0.0 0.00 2.90
103 104 4.996434 GGATGGCATCGGGGAGCG 62.996 72.222 20.50 0.0 0.00 5.03
123 124 1.342819 GAGGAGGGAGATGATGGTTCG 59.657 57.143 0.00 0.0 0.00 3.95
502 522 6.992063 AATCACAATAGCTGAACTTGGTAG 57.008 37.500 0.00 0.0 0.00 3.18
504 524 5.183904 GGAAATCACAATAGCTGAACTTGGT 59.816 40.000 0.00 0.0 0.00 3.67
710 730 0.034574 AGGCATTGCGGACACCAATA 60.035 50.000 1.91 0.0 32.03 1.90
761 781 2.046285 CCTTACAAGGCAAGGGGCG 61.046 63.158 0.00 0.0 46.16 6.13
984 1032 3.804036 TGACATAACTGGGCTTATTCCG 58.196 45.455 0.00 0.0 0.00 4.30
1480 2924 3.667497 TTCAAACTGAGCATCTCGAGT 57.333 42.857 13.13 0.0 34.92 4.18
1575 3027 1.212935 GGCATCAACCCTGTCTATGGT 59.787 52.381 0.00 0.0 36.06 3.55
2200 4170 7.386851 AGTCCATAATTATCCCAATACGACAG 58.613 38.462 0.00 0.0 0.00 3.51
2354 4487 8.740906 TGACAAAAGTCCAACAAGTAAATGTTA 58.259 29.630 0.00 0.0 41.44 2.41
2399 4532 9.069082 GTATCTCAAGCCTCTCTTATGTAAGTA 57.931 37.037 0.16 0.0 34.93 2.24
2473 4608 5.070446 TCCATGAAAAGAGATACGTATGGCT 59.930 40.000 13.97 4.5 35.09 4.75


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

AutoCloner maintained by Alex Coulton.