Multiple sequence alignment - TraesCS7D01G116000

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 TraesCS7D01G116000 chr7D 100.000 5353 0 0 1 5353 71321652 71316300 0.000000e+00 9886.0
1 TraesCS7D01G116000 chr7D 86.643 3676 408 53 599 4222 71218274 71214630 0.000000e+00 3991.0
2 TraesCS7D01G116000 chr7D 86.435 3133 323 59 826 3928 71353509 71356569 0.000000e+00 3338.0
3 TraesCS7D01G116000 chr7D 86.114 2499 282 42 2640 5109 71548771 71546309 0.000000e+00 2632.0
4 TraesCS7D01G116000 chr7D 84.536 2412 281 53 2639 5023 72169217 72171563 0.000000e+00 2303.0
5 TraesCS7D01G116000 chr7D 89.203 954 89 11 3279 4229 70830392 70829450 0.000000e+00 1179.0
6 TraesCS7D01G116000 chr7D 86.010 822 99 11 3923 4736 71361794 71362607 0.000000e+00 867.0
7 TraesCS7D01G116000 chr7D 77.183 355 52 14 2 327 71218947 71218593 4.260000e-41 180.0
8 TraesCS7D01G116000 chr7D 83.060 183 18 7 4827 4997 71362659 71362840 2.580000e-33 154.0
9 TraesCS7D01G116000 chr7B 94.197 4274 204 21 1 4252 13811549 13807298 0.000000e+00 6479.0
10 TraesCS7D01G116000 chr7B 86.886 3401 361 57 865 4209 13881473 13878102 0.000000e+00 3731.0
11 TraesCS7D01G116000 chr7B 85.600 2500 290 42 2656 5131 14068548 14066095 0.000000e+00 2558.0
12 TraesCS7D01G116000 chr7B 84.650 2469 300 52 2584 5023 14996092 14998510 0.000000e+00 2386.0
13 TraesCS7D01G116000 chr7B 88.276 1723 171 20 826 2529 13870903 13869193 0.000000e+00 2034.0
14 TraesCS7D01G116000 chr7B 88.159 1689 174 20 2584 4257 13117196 13115519 0.000000e+00 1988.0
15 TraesCS7D01G116000 chr7B 93.043 963 40 9 4289 5239 13805929 13804982 0.000000e+00 1382.0
16 TraesCS7D01G116000 chr7B 82.785 517 56 16 597 1086 13630792 13630282 1.070000e-116 431.0
17 TraesCS7D01G116000 chr7B 80.328 427 43 20 663 1056 13827395 13826977 8.770000e-73 285.0
18 TraesCS7D01G116000 chr7B 76.404 356 54 9 2 328 13631461 13631107 1.190000e-36 165.0
19 TraesCS7D01G116000 chr7B 83.889 180 19 7 4827 4997 13866899 13866721 4.290000e-36 163.0
20 TraesCS7D01G116000 chr7B 97.619 84 2 0 5270 5353 13803325 13803242 1.550000e-30 145.0
21 TraesCS7D01G116000 chr7B 97.143 35 1 0 597 631 13827542 13827508 5.790000e-05 60.2
22 TraesCS7D01G116000 chrUn 86.294 3896 436 51 865 4730 82520576 82516749 0.000000e+00 4146.0
23 TraesCS7D01G116000 chrUn 97.854 2376 47 1 2529 4900 84435464 84437839 0.000000e+00 4102.0
24 TraesCS7D01G116000 chrUn 95.159 2541 107 10 1 2529 84432847 84435383 0.000000e+00 3997.0
25 TraesCS7D01G116000 chrUn 84.685 3846 451 67 1062 4832 84239904 84236122 0.000000e+00 3712.0
26 TraesCS7D01G116000 chrUn 86.344 3200 358 47 1059 4222 84288250 84285094 0.000000e+00 3415.0
27 TraesCS7D01G116000 chrUn 86.344 3200 358 47 1059 4222 226941575 226938419 0.000000e+00 3415.0
28 TraesCS7D01G116000 chrUn 87.041 2068 206 31 2639 4689 82528721 82526699 0.000000e+00 2278.0
29 TraesCS7D01G116000 chrUn 98.904 456 5 0 4898 5353 84437921 84438376 0.000000e+00 815.0
30 TraesCS7D01G116000 chrUn 81.818 627 78 23 488 1086 84289146 84288528 1.340000e-135 494.0
31 TraesCS7D01G116000 chrUn 81.818 627 78 23 488 1086 226942471 226941853 1.340000e-135 494.0
32 TraesCS7D01G116000 chrUn 79.176 437 41 27 663 1056 260166597 260167026 1.910000e-64 257.0
33 TraesCS7D01G116000 chrUn 76.685 356 53 9 2 328 84289691 84289337 2.560000e-38 171.0
34 TraesCS7D01G116000 chrUn 76.685 356 53 9 2 328 226943016 226942662 2.560000e-38 171.0
35 TraesCS7D01G116000 chrUn 81.081 111 12 6 4833 4934 82516689 82516579 4.440000e-11 80.5
36 TraesCS7D01G116000 chrUn 100.000 32 0 0 597 628 260166452 260166483 5.790000e-05 60.2
37 TraesCS7D01G116000 chr2B 86.631 3396 377 48 865 4209 723405399 723402030 0.000000e+00 3685.0
38 TraesCS7D01G116000 chr2B 87.073 2398 247 39 826 3190 723397083 723394716 0.000000e+00 2652.0
39 TraesCS7D01G116000 chr2B 85.959 1517 172 26 3233 4739 723394703 723393218 0.000000e+00 1583.0
40 TraesCS7D01G116000 chr2B 84.536 194 14 5 738 919 723405571 723405382 1.530000e-40 178.0
41 TraesCS7D01G116000 chr2B 85.000 180 17 7 4827 4997 723393169 723392991 1.980000e-39 174.0
42 TraesCS7D01G116000 chr7A 86.185 2186 263 27 2584 4754 77159254 77161415 0.000000e+00 2327.0
43 TraesCS7D01G116000 chr7A 86.842 152 18 2 179 328 76990223 76990072 9.220000e-38 169.0
44 TraesCS7D01G116000 chr1A 79.881 2182 340 56 3075 5210 21775079 21772951 0.000000e+00 1506.0


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 TraesCS7D01G116000 chr7D 71316300 71321652 5352 True 9886.000000 9886 100.000000 1 5353 1 chr7D.!!$R2 5352
1 TraesCS7D01G116000 chr7D 71353509 71356569 3060 False 3338.000000 3338 86.435000 826 3928 1 chr7D.!!$F1 3102
2 TraesCS7D01G116000 chr7D 71546309 71548771 2462 True 2632.000000 2632 86.114000 2640 5109 1 chr7D.!!$R3 2469
3 TraesCS7D01G116000 chr7D 72169217 72171563 2346 False 2303.000000 2303 84.536000 2639 5023 1 chr7D.!!$F2 2384
4 TraesCS7D01G116000 chr7D 71214630 71218947 4317 True 2085.500000 3991 81.913000 2 4222 2 chr7D.!!$R4 4220
5 TraesCS7D01G116000 chr7D 70829450 70830392 942 True 1179.000000 1179 89.203000 3279 4229 1 chr7D.!!$R1 950
6 TraesCS7D01G116000 chr7D 71361794 71362840 1046 False 510.500000 867 84.535000 3923 4997 2 chr7D.!!$F3 1074
7 TraesCS7D01G116000 chr7B 13878102 13881473 3371 True 3731.000000 3731 86.886000 865 4209 1 chr7B.!!$R2 3344
8 TraesCS7D01G116000 chr7B 13803242 13811549 8307 True 2668.666667 6479 94.953000 1 5353 3 chr7B.!!$R5 5352
9 TraesCS7D01G116000 chr7B 14066095 14068548 2453 True 2558.000000 2558 85.600000 2656 5131 1 chr7B.!!$R3 2475
10 TraesCS7D01G116000 chr7B 14996092 14998510 2418 False 2386.000000 2386 84.650000 2584 5023 1 chr7B.!!$F1 2439
11 TraesCS7D01G116000 chr7B 13115519 13117196 1677 True 1988.000000 1988 88.159000 2584 4257 1 chr7B.!!$R1 1673
12 TraesCS7D01G116000 chr7B 13866721 13870903 4182 True 1098.500000 2034 86.082500 826 4997 2 chr7B.!!$R7 4171
13 TraesCS7D01G116000 chr7B 13630282 13631461 1179 True 298.000000 431 79.594500 2 1086 2 chr7B.!!$R4 1084
14 TraesCS7D01G116000 chrUn 84236122 84239904 3782 True 3712.000000 3712 84.685000 1062 4832 1 chrUn.!!$R2 3770
15 TraesCS7D01G116000 chrUn 84432847 84438376 5529 False 2971.333333 4102 97.305667 1 5353 3 chrUn.!!$F1 5352
16 TraesCS7D01G116000 chrUn 82526699 82528721 2022 True 2278.000000 2278 87.041000 2639 4689 1 chrUn.!!$R1 2050
17 TraesCS7D01G116000 chrUn 82516579 82520576 3997 True 2113.250000 4146 83.687500 865 4934 2 chrUn.!!$R3 4069
18 TraesCS7D01G116000 chrUn 84285094 84289691 4597 True 1360.000000 3415 81.615667 2 4222 3 chrUn.!!$R4 4220
19 TraesCS7D01G116000 chrUn 226938419 226943016 4597 True 1360.000000 3415 81.615667 2 4222 3 chrUn.!!$R5 4220
20 TraesCS7D01G116000 chr2B 723402030 723405571 3541 True 1931.500000 3685 85.583500 738 4209 2 chr2B.!!$R2 3471
21 TraesCS7D01G116000 chr2B 723392991 723397083 4092 True 1469.666667 2652 86.010667 826 4997 3 chr2B.!!$R1 4171
22 TraesCS7D01G116000 chr7A 77159254 77161415 2161 False 2327.000000 2327 86.185000 2584 4754 1 chr7A.!!$F1 2170
23 TraesCS7D01G116000 chr1A 21772951 21775079 2128 True 1506.000000 1506 79.881000 3075 5210 1 chr1A.!!$R1 2135

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
227 255 0.394762 TGGATCTGATGGTTGCCTGC 60.395 55.00 0.00 0.00 0.00 4.85 F
248 277 0.912486 AAGGCATGTAGGAGTGGACC 59.088 55.00 0.00 0.00 0.00 4.46 F
631 722 1.189752 CAGCCTAGAGAGGTCAGCAA 58.810 55.00 0.00 0.00 45.78 3.91 F
2268 2770 1.009829 CATCTGAGCTTAACGGGCAC 58.990 55.00 0.00 0.00 0.00 5.01 F
2744 3385 4.087907 TCAGAATGCATGGATCCAAACAA 58.912 39.13 20.67 5.35 34.76 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 2545 1.357137 TAGGTGATGCCCAACACAGA 58.643 50.000 10.22 0.00 38.57 3.41 R
2112 2614 3.943381 TGAAGACATTGCTAGCATCAAGG 59.057 43.478 20.13 8.21 0.00 3.61 R
2300 2803 2.168496 TCATCGCTATAGGTACAGGGC 58.832 52.381 1.04 0.00 0.00 5.19 R
3091 3735 5.597594 TCTTGTCTGATAGAGCACTCATGAT 59.402 40.000 0.00 0.00 0.00 2.45 R
4740 6801 1.538276 GTAGCAATGTCAATGCACGC 58.462 50.000 15.13 1.28 46.22 5.34 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
88 90 1.284982 CGAAGAACCACACTCCTGCG 61.285 60.000 0.00 0.00 0.00 5.18
155 157 0.833287 TGCTCAGGGTTATCTCTGCC 59.167 55.000 0.00 0.00 0.00 4.85
227 255 0.394762 TGGATCTGATGGTTGCCTGC 60.395 55.000 0.00 0.00 0.00 4.85
248 277 0.912486 AAGGCATGTAGGAGTGGACC 59.088 55.000 0.00 0.00 0.00 4.46
278 308 4.774124 TGCTCTGTTTCTATGAATGGGAG 58.226 43.478 0.00 0.00 0.00 4.30
444 515 2.085320 TGCGGCGTGTATTTAAATGGT 58.915 42.857 9.37 0.00 0.00 3.55
445 516 3.063725 GTGCGGCGTGTATTTAAATGGTA 59.936 43.478 9.37 0.00 0.00 3.25
487 564 3.511934 AGAAGATTTGACTCAGGCTACGT 59.488 43.478 0.00 0.00 0.00 3.57
631 722 1.189752 CAGCCTAGAGAGGTCAGCAA 58.810 55.000 0.00 0.00 45.78 3.91
674 767 2.168521 TGTCGATCCTTTCTAGCCAAGG 59.831 50.000 12.35 12.35 42.16 3.61
735 831 2.159282 GGTACTTGATGATGACCGACGT 60.159 50.000 0.00 0.00 0.00 4.34
757 866 2.627699 GTTCAGCTTTGGGTTTCCATGA 59.372 45.455 0.00 0.00 43.63 3.07
758 867 3.173953 TCAGCTTTGGGTTTCCATGAT 57.826 42.857 0.00 0.00 43.63 2.45
759 868 2.827322 TCAGCTTTGGGTTTCCATGATG 59.173 45.455 0.00 0.00 43.63 3.07
763 872 4.161001 AGCTTTGGGTTTCCATGATGATTC 59.839 41.667 0.00 0.00 43.63 2.52
817 938 8.030692 TGAGCAAACATTCAAATTTCTGGATAG 58.969 33.333 0.00 0.00 0.00 2.08
852 982 2.344950 GACTCTGATGTTGCTCCAGTG 58.655 52.381 0.00 0.00 0.00 3.66
862 992 3.244735 TGTTGCTCCAGTGCCAGTATTTA 60.245 43.478 0.00 0.00 0.00 1.40
944 1120 5.769662 ACTAGTTTCTTGTTCATGATTGGCA 59.230 36.000 0.00 0.00 0.00 4.92
1276 1775 1.935873 CATGCAACCAGTACTCGATGG 59.064 52.381 1.14 1.14 42.60 3.51
1731 2233 2.385013 TCCATCAGACATGGACAACG 57.615 50.000 0.00 0.00 42.81 4.10
2043 2545 5.987019 TTAGGAGGGCATACCATAGTTTT 57.013 39.130 0.00 0.00 43.89 2.43
2112 2614 3.366052 TGCTATCTTTTGAAGACCCCC 57.634 47.619 0.00 0.00 41.01 5.40
2268 2770 1.009829 CATCTGAGCTTAACGGGCAC 58.990 55.000 0.00 0.00 0.00 5.01
2300 2803 7.424227 AAAAATACAACATTGGCACTGATTG 57.576 32.000 12.15 13.36 0.00 2.67
2510 3013 9.577110 CACGGTATGTTCTTTTCTACTAACATA 57.423 33.333 0.00 0.00 41.48 2.29
2580 3173 8.665643 TTAGAGACGTTTAAAAGAAACATGGA 57.334 30.769 8.18 0.00 0.00 3.41
2744 3385 4.087907 TCAGAATGCATGGATCCAAACAA 58.912 39.130 20.67 5.35 34.76 2.83
3135 3779 3.117512 AGACTGTTCTTTTGGTGACCCAT 60.118 43.478 0.00 0.00 41.49 4.00
3403 4066 6.293955 CCTTGTAAATGCCCATAAAGATACGG 60.294 42.308 0.00 0.00 0.00 4.02
3451 4114 5.321102 ACTCAGACTCTCAAAGAGCTAAGA 58.679 41.667 3.90 0.00 46.12 2.10
3643 4318 8.939929 TCTCTTTTTGTGCTATTTCTCACATAG 58.060 33.333 0.00 0.00 42.07 2.23
3861 4536 4.855715 TTCATTTTTCCGTGCACCAATA 57.144 36.364 12.15 0.00 0.00 1.90
4148 4829 1.676014 GCTCTGTTTGTATCCGTGCCT 60.676 52.381 0.00 0.00 0.00 4.75
4740 6801 6.895607 TGCATCTGATTTGCATAAATGTTG 57.104 33.333 1.96 0.00 44.73 3.33
5263 9043 7.542130 GCCAAAGTCAAGTGAATAAGTATTTGG 59.458 37.037 0.00 0.00 43.57 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 0.511653 GTGGTTCTTCGTTCCTTCGC 59.488 55.000 0.00 0.00 0.00 4.70
135 137 1.474143 GGCAGAGATAACCCTGAGCAC 60.474 57.143 0.00 0.00 32.37 4.40
155 157 3.529252 CTGAAGGGAGACACAGCAG 57.471 57.895 0.00 0.00 0.00 4.24
227 255 0.911769 TCCACTCCTACATGCCTTGG 59.088 55.000 0.00 0.00 0.00 3.61
248 277 5.181009 TCATAGAAACAGAGCAACATCCAG 58.819 41.667 0.00 0.00 0.00 3.86
292 322 6.392354 CAGTGCCACATTTTGTAGATCAAAT 58.608 36.000 0.00 0.00 44.15 2.32
334 384 5.546621 AGCTCACCAGTAGACTTGTTAAA 57.453 39.130 0.00 0.00 0.00 1.52
487 564 2.723273 TCTCCTGTCGTATGCTGAGAA 58.277 47.619 0.00 0.00 0.00 2.87
631 722 2.158696 GGGAAAGCTACAGAGATGCCAT 60.159 50.000 0.00 0.00 0.00 4.40
674 767 2.032178 AGACGCTGCAAGAACTGTTTTC 59.968 45.455 0.00 0.00 34.07 2.29
730 826 1.157870 ACCCAAAGCTGAACACGTCG 61.158 55.000 0.00 0.00 0.00 5.12
735 831 2.151502 TGGAAACCCAAAGCTGAACA 57.848 45.000 0.00 0.00 0.00 3.18
759 868 0.376152 CACAGTGCCGCATGAGAATC 59.624 55.000 0.00 0.00 0.00 2.52
763 872 0.461516 AGATCACAGTGCCGCATGAG 60.462 55.000 0.00 0.00 0.00 2.90
817 938 4.335416 TCAGAGTCCAAATCCCATGAAAC 58.665 43.478 0.00 0.00 0.00 2.78
862 992 6.382570 AGGAGCAGACAAAGAACAGATACTAT 59.617 38.462 0.00 0.00 0.00 2.12
1276 1775 3.548770 TGCCATTCATCTTCTCCATGAC 58.451 45.455 0.00 0.00 29.70 3.06
1731 2233 2.056577 GCAATGCAAAGCTGAACACTC 58.943 47.619 0.00 0.00 0.00 3.51
2043 2545 1.357137 TAGGTGATGCCCAACACAGA 58.643 50.000 10.22 0.00 38.57 3.41
2112 2614 3.943381 TGAAGACATTGCTAGCATCAAGG 59.057 43.478 20.13 8.21 0.00 3.61
2300 2803 2.168496 TCATCGCTATAGGTACAGGGC 58.832 52.381 1.04 0.00 0.00 5.19
2560 3150 6.492254 ACAGTCCATGTTTCTTTTAAACGTC 58.508 36.000 0.00 0.00 39.96 4.34
2744 3385 4.579869 AGAATATTGTCTTGCACGGTTCT 58.420 39.130 0.00 0.00 0.00 3.01
3091 3735 5.597594 TCTTGTCTGATAGAGCACTCATGAT 59.402 40.000 0.00 0.00 0.00 2.45
3135 3779 9.567776 TCAAATACAGGTAGAAAATCAACTTGA 57.432 29.630 0.00 0.00 0.00 3.02
3403 4066 5.644636 TGTTATTAAGATCCGAAACACCCAC 59.355 40.000 0.00 0.00 0.00 4.61
3451 4114 5.923733 ACTGTCTCCTTGATCGATACTTT 57.076 39.130 0.00 0.00 0.00 2.66
3643 4318 5.979517 GTGATATTTGCCCAGCTATGAAAAC 59.020 40.000 0.00 0.00 0.00 2.43
4148 4829 9.535170 TGTAACCAAATTCCCAAAACTATCATA 57.465 29.630 0.00 0.00 0.00 2.15
4631 6683 8.658992 ATGGTGTCCATATAATTGCTTACCAGC 61.659 40.741 0.00 0.00 43.19 4.85
4740 6801 1.538276 GTAGCAATGTCAATGCACGC 58.462 50.000 15.13 1.28 46.22 5.34


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

AutoCloner maintained by Alex Coulton.