Multiple sequence alignment - TraesCS6D01G010900

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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 TraesCS6D01G010900 chr6D 100.000 4854 0 0 1 4854 4207549 4212402 0.000000e+00 8964
1 TraesCS6D01G010900 chr6D 93.244 3434 147 32 1491 4854 2134891 2138309 0.000000e+00 4977
2 TraesCS6D01G010900 chr6D 93.520 1497 88 8 3 1496 2133357 2134847 0.000000e+00 2218
3 TraesCS6D01G010900 chr6D 83.941 878 126 9 627 1494 439616067 439616939 0.000000e+00 826
4 TraesCS6D01G010900 chr6D 82.170 931 116 32 3948 4847 40499409 40498498 0.000000e+00 754
5 TraesCS6D01G010900 chr6D 82.647 680 85 23 4193 4847 297402865 297402194 5.450000e-159 571
6 TraesCS6D01G010900 chr6D 78.740 762 104 30 1491 2205 439661577 439660827 1.590000e-124 457
7 TraesCS6D01G010900 chr6D 78.329 766 100 30 1491 2205 439616984 439617734 7.460000e-118 435
8 TraesCS6D01G010900 chr6B 94.421 2653 122 14 2216 4854 4377187 4374547 0.000000e+00 4056
9 TraesCS6D01G010900 chr6B 94.311 2584 119 17 2288 4854 3836379 3838951 0.000000e+00 3932
10 TraesCS6D01G010900 chr6B 92.216 1503 98 8 1 1495 3834516 3836007 0.000000e+00 2109
11 TraesCS6D01G010900 chr6B 91.856 1498 108 6 1 1495 4379569 4378083 0.000000e+00 2078
12 TraesCS6D01G010900 chr6B 93.141 1283 81 5 216 1495 3799225 3800503 0.000000e+00 1875
13 TraesCS6D01G010900 chr6B 91.153 1232 70 19 1491 2684 3800549 3801779 0.000000e+00 1635
14 TraesCS6D01G010900 chr6B 91.840 723 41 14 1509 2215 4377935 4377215 0.000000e+00 992
15 TraesCS6D01G010900 chr6B 82.622 679 84 25 4193 4842 461429737 461429064 1.960000e-158 569
16 TraesCS6D01G010900 chr6B 95.133 226 11 0 1509 1734 3836155 3836380 1.660000e-94 357
17 TraesCS6D01G010900 chrUn 94.311 2004 93 12 2863 4854 355129168 355127174 0.000000e+00 3049
18 TraesCS6D01G010900 chrUn 94.009 1519 66 12 3353 4854 355695289 355693779 0.000000e+00 2278
19 TraesCS6D01G010900 chrUn 92.190 1498 102 7 1 1495 255513325 255514810 0.000000e+00 2104
20 TraesCS6D01G010900 chrUn 91.727 1233 87 7 1 1230 380679625 380680845 0.000000e+00 1698
21 TraesCS6D01G010900 chrUn 92.116 723 39 14 1509 2215 255514958 255515678 0.000000e+00 1003
22 TraesCS6D01G010900 chrUn 94.747 495 25 1 2863 3356 475068857 475068363 0.000000e+00 769
23 TraesCS6D01G010900 chrUn 96.774 403 13 0 3353 3755 478404781 478405183 0.000000e+00 673
24 TraesCS6D01G010900 chrUn 86.801 447 48 4 1 447 408243414 408242979 5.650000e-134 488
25 TraesCS6D01G010900 chrUn 97.938 97 2 0 2216 2312 255515706 255515802 8.360000e-38 169
26 TraesCS6D01G010900 chr6A 96.837 1328 31 5 1491 2809 774093 772768 0.000000e+00 2209
27 TraesCS6D01G010900 chr6A 97.029 1178 29 3 3062 4235 772748 771573 0.000000e+00 1977
28 TraesCS6D01G010900 chr6A 96.928 944 28 1 553 1495 775081 774138 0.000000e+00 1581
29 TraesCS6D01G010900 chr6A 94.050 521 30 1 1 521 775986 775467 0.000000e+00 789
30 TraesCS6D01G010900 chr6A 79.369 761 99 31 1491 2205 587971268 587970520 2.630000e-132 483
31 TraesCS6D01G010900 chr6A 79.161 763 99 27 1491 2205 587891221 587891971 1.580000e-129 473
32 TraesCS6D01G010900 chr3D 79.978 929 135 26 3948 4847 368835692 368834786 5.300000e-179 638
33 TraesCS6D01G010900 chr1B 84.466 309 46 2 8 314 544765308 544765000 2.200000e-78 303
34 TraesCS6D01G010900 chr7B 81.250 208 34 3 323 527 15229564 15229359 3.890000e-36 163
35 TraesCS6D01G010900 chr5B 79.500 200 35 5 3987 4181 711837876 711837678 2.360000e-28 137
36 TraesCS6D01G010900 chr3B 86.726 113 14 1 331 443 472943181 472943070 1.830000e-24 124
37 TraesCS6D01G010900 chr5A 83.898 118 18 1 4045 4162 555306645 555306529 1.430000e-20 111


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 TraesCS6D01G010900 chr6D 4207549 4212402 4853 False 8964.000000 8964 100.000000 1 4854 1 chr6D.!!$F1 4853
1 TraesCS6D01G010900 chr6D 2133357 2138309 4952 False 3597.500000 4977 93.382000 3 4854 2 chr6D.!!$F2 4851
2 TraesCS6D01G010900 chr6D 40498498 40499409 911 True 754.000000 754 82.170000 3948 4847 1 chr6D.!!$R1 899
3 TraesCS6D01G010900 chr6D 439616067 439617734 1667 False 630.500000 826 81.135000 627 2205 2 chr6D.!!$F3 1578
4 TraesCS6D01G010900 chr6D 297402194 297402865 671 True 571.000000 571 82.647000 4193 4847 1 chr6D.!!$R2 654
5 TraesCS6D01G010900 chr6D 439660827 439661577 750 True 457.000000 457 78.740000 1491 2205 1 chr6D.!!$R3 714
6 TraesCS6D01G010900 chr6B 4374547 4379569 5022 True 2375.333333 4056 92.705667 1 4854 3 chr6B.!!$R2 4853
7 TraesCS6D01G010900 chr6B 3834516 3838951 4435 False 2132.666667 3932 93.886667 1 4854 3 chr6B.!!$F2 4853
8 TraesCS6D01G010900 chr6B 3799225 3801779 2554 False 1755.000000 1875 92.147000 216 2684 2 chr6B.!!$F1 2468
9 TraesCS6D01G010900 chr6B 461429064 461429737 673 True 569.000000 569 82.622000 4193 4842 1 chr6B.!!$R1 649
10 TraesCS6D01G010900 chrUn 355127174 355129168 1994 True 3049.000000 3049 94.311000 2863 4854 1 chrUn.!!$R1 1991
11 TraesCS6D01G010900 chrUn 355693779 355695289 1510 True 2278.000000 2278 94.009000 3353 4854 1 chrUn.!!$R2 1501
12 TraesCS6D01G010900 chrUn 380679625 380680845 1220 False 1698.000000 1698 91.727000 1 1230 1 chrUn.!!$F1 1229
13 TraesCS6D01G010900 chrUn 255513325 255515802 2477 False 1092.000000 2104 94.081333 1 2312 3 chrUn.!!$F3 2311
14 TraesCS6D01G010900 chr6A 771573 775986 4413 True 1639.000000 2209 96.211000 1 4235 4 chr6A.!!$R2 4234
15 TraesCS6D01G010900 chr6A 587970520 587971268 748 True 483.000000 483 79.369000 1491 2205 1 chr6A.!!$R1 714
16 TraesCS6D01G010900 chr6A 587891221 587891971 750 False 473.000000 473 79.161000 1491 2205 1 chr6A.!!$F1 714
17 TraesCS6D01G010900 chr3D 368834786 368835692 906 True 638.000000 638 79.978000 3948 4847 1 chr3D.!!$R1 899

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
304 308 1.600023 GTGACATGTTTTCCCGGACA 58.400 50.0 0.73 0.0 0.0 4.02 F
1030 1408 0.521291 GCAAGCCATTAGTGCGACAA 59.479 50.0 0.00 0.0 0.0 3.18 F
2702 3303 1.234821 TTCCAACATTGAGTGGCGAC 58.765 50.0 6.34 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2145 2714 4.023963 GTCCAAGAGAGTGTTGCTAAAACC 60.024 45.833 0.00 0.0 0.00 3.27 R
2926 3530 0.034337 TAAACAGAGGGTGGTCGCAC 59.966 55.000 0.00 0.0 0.00 5.34 R
4499 5194 1.707427 ACTCAAACAGATGGAGGCCTT 59.293 47.619 6.77 0.0 32.98 4.35 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
72 73 2.589540 CAGGGGTGGCGCAAGATA 59.410 61.111 10.83 0.00 43.02 1.98
85 86 2.064581 AAGATAGAAGCCGCGGGGT 61.065 57.895 29.38 10.63 34.97 4.95
233 234 4.385754 GGAGGAAGAAGGGTTGATTAGCAT 60.386 45.833 0.00 0.00 0.00 3.79
304 308 1.600023 GTGACATGTTTTCCCGGACA 58.400 50.000 0.73 0.00 0.00 4.02
305 309 1.950909 GTGACATGTTTTCCCGGACAA 59.049 47.619 0.73 0.00 0.00 3.18
349 353 5.939883 TGTTGCAGTGAGCTGAAATAATAGT 59.060 36.000 0.00 0.00 41.92 2.12
383 388 7.202526 CCGAGGACACATAAATGCATATTTTT 58.797 34.615 0.00 0.00 37.64 1.94
385 390 9.385902 CGAGGACACATAAATGCATATTTTTAG 57.614 33.333 0.00 0.00 37.64 1.85
417 430 8.084073 CACTGTTGGATCATCTTTGTTACATTT 58.916 33.333 0.00 0.00 0.00 2.32
1029 1407 0.605050 TGCAAGCCATTAGTGCGACA 60.605 50.000 0.00 0.00 41.27 4.35
1030 1408 0.521291 GCAAGCCATTAGTGCGACAA 59.479 50.000 0.00 0.00 0.00 3.18
1579 2096 5.127519 CAGATGCAACCAAATCATTTCCCTA 59.872 40.000 0.00 0.00 0.00 3.53
2145 2714 7.839907 TGAAGGAATTCCAATTTCATTACCAG 58.160 34.615 26.22 0.00 38.89 4.00
2547 3148 5.186021 GGACTCATATACCAGGGTGATGTAG 59.814 48.000 0.06 7.01 0.00 2.74
2702 3303 1.234821 TTCCAACATTGAGTGGCGAC 58.765 50.000 6.34 0.00 0.00 5.19
2906 3510 3.516615 GTTTTGTGCAAGTTAGCCACAA 58.483 40.909 10.23 10.23 35.39 3.33
3665 4270 1.048601 TGCTTCCGAGGGATATGGAC 58.951 55.000 0.00 0.00 0.00 4.02
4188 4797 7.709613 CACCCCTATAGAATTGTTATATACCGC 59.290 40.741 0.00 0.00 0.00 5.68
4375 5047 6.137104 TGACAAGTACTAGGACCTACTCTT 57.863 41.667 0.00 0.27 0.00 2.85
4462 5154 1.144093 TCCACCGGTCTCCAATTTGTT 59.856 47.619 2.59 0.00 0.00 2.83
4494 5189 4.081697 CCCACTATTTTTCGCCATCCTTTT 60.082 41.667 0.00 0.00 0.00 2.27
4499 5194 9.796120 CACTATTTTTCGCCATCCTTTTATTTA 57.204 29.630 0.00 0.00 0.00 1.40
4757 5464 2.380084 TGTTACCATCGCTCAACTCC 57.620 50.000 0.00 0.00 0.00 3.85
4848 5556 7.703328 TCATTAACAAAGGTGACAAGAGAAAC 58.297 34.615 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
203 204 0.547712 CCCTTCTTCCTCCCCTGACA 60.548 60.000 0.00 0.00 0.00 3.58
260 261 8.565416 ACCAGCTTAGTTCAACTGTAATTTTAC 58.435 33.333 0.00 0.00 0.00 2.01
304 308 8.520351 GCAACATAATTAAACAGTACTCCCTTT 58.480 33.333 0.00 0.00 0.00 3.11
305 309 7.668052 TGCAACATAATTAAACAGTACTCCCTT 59.332 33.333 0.00 0.00 0.00 3.95
383 388 6.550938 AGATGATCCAACAGTGTGATTCTA 57.449 37.500 0.00 0.00 0.00 2.10
385 390 6.072286 ACAAAGATGATCCAACAGTGTGATTC 60.072 38.462 0.00 0.00 0.00 2.52
539 555 7.418368 CCTTGCCTCTCTACCCATATATATGTG 60.418 44.444 19.11 11.97 31.82 3.21
573 941 0.979665 TCTTTCTGGGTCTGCTCCTG 59.020 55.000 0.00 0.00 0.00 3.86
659 1028 5.343307 AATCTTCACAAGTGCCAAGTTTT 57.657 34.783 0.00 0.00 0.00 2.43
1029 1407 9.082313 ACCAGAACTAGAAATGACATGAAAATT 57.918 29.630 0.00 0.00 0.00 1.82
1030 1408 8.517878 CACCAGAACTAGAAATGACATGAAAAT 58.482 33.333 0.00 0.00 0.00 1.82
1462 1844 9.485206 GTTCTTAGTTCAGTACACTTCCAATAA 57.515 33.333 0.00 0.00 0.00 1.40
1945 2499 8.019656 ACGAACCTAGACCATTCATTATTACT 57.980 34.615 0.00 0.00 0.00 2.24
2145 2714 4.023963 GTCCAAGAGAGTGTTGCTAAAACC 60.024 45.833 0.00 0.00 0.00 3.27
2409 3010 4.724399 TCTTCTCCAAAATGTAAGGCACA 58.276 39.130 0.00 0.00 42.69 4.57
2547 3148 0.393808 AATACACCACGCACCCCATC 60.394 55.000 0.00 0.00 0.00 3.51
2876 3480 0.835941 TTGCACAAAACCAGGGCAAT 59.164 45.000 0.00 0.00 39.33 3.56
2880 3484 2.545742 GCTAACTTGCACAAAACCAGGG 60.546 50.000 0.00 0.00 0.00 4.45
2906 3510 2.173569 ACTCTTGCTCCAAGACCAACTT 59.826 45.455 3.69 0.00 44.27 2.66
2926 3530 0.034337 TAAACAGAGGGTGGTCGCAC 59.966 55.000 0.00 0.00 0.00 5.34
3056 3660 9.929722 TTATGCACACGAAATAAAATCAGATAC 57.070 29.630 0.00 0.00 0.00 2.24
3060 3664 7.008266 GTGGTTATGCACACGAAATAAAATCAG 59.992 37.037 0.00 0.00 0.00 2.90
3814 4420 6.153924 AGACCCTAATCCACCATAGAAGATT 58.846 40.000 0.00 0.00 33.66 2.40
4167 4775 8.926715 TGCTGCGGTATATAACAATTCTATAG 57.073 34.615 0.00 0.00 0.00 1.31
4188 4797 8.780249 TGATGATGAGTTGTTATATCATTGCTG 58.220 33.333 0.00 0.00 39.60 4.41
4375 5047 7.667575 ATGCTATTTTACCAGAGAGAGAGAA 57.332 36.000 0.00 0.00 0.00 2.87
4494 5189 6.073447 TCAAACAGATGGAGGCCTTAAATA 57.927 37.500 6.77 0.00 0.00 1.40
4499 5194 1.707427 ACTCAAACAGATGGAGGCCTT 59.293 47.619 6.77 0.00 32.98 4.35
4570 5276 3.801114 TGTATGTCGAAGGTGAGATGG 57.199 47.619 0.00 0.00 0.00 3.51
4757 5464 4.639310 AGTTGATACGTACCACTAGTCCAG 59.361 45.833 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.