Multiple sequence alignment - TraesCS7D01G013400

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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 TraesCS7D01G013400 chr7D 100.000 4796 0 0 1 4796 5649607 5644812 0.000000e+00 8857.0
1 TraesCS7D01G013400 chr7D 83.466 3756 550 53 557 4275 5486537 5482816 0.000000e+00 3430.0
2 TraesCS7D01G013400 chr7D 81.785 1367 216 22 2843 4189 5798370 5797017 0.000000e+00 1114.0
3 TraesCS7D01G013400 chr7D 89.066 503 45 5 4303 4796 5523208 5522707 2.450000e-172 616.0
4 TraesCS7D01G013400 chr7D 92.079 303 22 1 103 405 5777902 5777602 4.440000e-115 425.0
5 TraesCS7D01G013400 chr4A 95.242 4624 184 14 100 4704 734585011 734589617 0.000000e+00 7287.0
6 TraesCS7D01G013400 chr4A 95.099 4448 200 9 269 4704 735747182 735751623 0.000000e+00 6990.0
7 TraesCS7D01G013400 chr4A 85.779 3966 524 33 200 4145 735316288 735320233 0.000000e+00 4163.0
8 TraesCS7D01G013400 chr4A 85.363 4065 543 39 100 4145 736147165 736151196 0.000000e+00 4163.0
9 TraesCS7D01G013400 chr4A 85.157 4103 546 35 49 4136 735488125 735484071 0.000000e+00 4145.0
10 TraesCS7D01G013400 chr4A 84.039 4179 594 57 40 4193 736756152 736760282 0.000000e+00 3954.0
11 TraesCS7D01G013400 chr4A 84.809 3976 555 27 200 4145 735562732 735558776 0.000000e+00 3951.0
12 TraesCS7D01G013400 chr4A 84.130 4058 549 53 266 4275 736884006 736888016 0.000000e+00 3838.0
13 TraesCS7D01G013400 chr4A 83.162 4193 617 62 123 4275 734730569 734734712 0.000000e+00 3749.0
14 TraesCS7D01G013400 chr4A 82.995 4193 625 61 123 4275 736570643 736574787 0.000000e+00 3712.0
15 TraesCS7D01G013400 chr4A 82.784 4246 635 60 346 4549 736470575 736466384 0.000000e+00 3703.0
16 TraesCS7D01G013400 chr4A 82.917 3524 557 35 673 4169 735689506 735693011 0.000000e+00 3131.0
17 TraesCS7D01G013400 chr4A 82.609 2553 322 55 2178 4684 734848672 734851148 0.000000e+00 2143.0
18 TraesCS7D01G013400 chr4A 90.678 118 10 1 4680 4796 734589632 734589749 6.430000e-34 156.0
19 TraesCS7D01G013400 chr4A 97.826 46 1 0 1 46 734582444 734582489 3.980000e-11 80.5
20 TraesCS7D01G013400 chr7A 83.303 4378 652 47 207 4549 6928676 6924343 0.000000e+00 3962.0


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 TraesCS7D01G013400 chr7D 5644812 5649607 4795 True 8857.000000 8857 100.000 1 4796 1 chr7D.!!$R3 4795
1 TraesCS7D01G013400 chr7D 5482816 5486537 3721 True 3430.000000 3430 83.466 557 4275 1 chr7D.!!$R1 3718
2 TraesCS7D01G013400 chr7D 5797017 5798370 1353 True 1114.000000 1114 81.785 2843 4189 1 chr7D.!!$R5 1346
3 TraesCS7D01G013400 chr7D 5522707 5523208 501 True 616.000000 616 89.066 4303 4796 1 chr7D.!!$R2 493
4 TraesCS7D01G013400 chr4A 735747182 735751623 4441 False 6990.000000 6990 95.099 269 4704 1 chr4A.!!$F5 4435
5 TraesCS7D01G013400 chr4A 735316288 735320233 3945 False 4163.000000 4163 85.779 200 4145 1 chr4A.!!$F3 3945
6 TraesCS7D01G013400 chr4A 736147165 736151196 4031 False 4163.000000 4163 85.363 100 4145 1 chr4A.!!$F6 4045
7 TraesCS7D01G013400 chr4A 735484071 735488125 4054 True 4145.000000 4145 85.157 49 4136 1 chr4A.!!$R1 4087
8 TraesCS7D01G013400 chr4A 736756152 736760282 4130 False 3954.000000 3954 84.039 40 4193 1 chr4A.!!$F8 4153
9 TraesCS7D01G013400 chr4A 735558776 735562732 3956 True 3951.000000 3951 84.809 200 4145 1 chr4A.!!$R2 3945
10 TraesCS7D01G013400 chr4A 736884006 736888016 4010 False 3838.000000 3838 84.130 266 4275 1 chr4A.!!$F9 4009
11 TraesCS7D01G013400 chr4A 734730569 734734712 4143 False 3749.000000 3749 83.162 123 4275 1 chr4A.!!$F1 4152
12 TraesCS7D01G013400 chr4A 736570643 736574787 4144 False 3712.000000 3712 82.995 123 4275 1 chr4A.!!$F7 4152
13 TraesCS7D01G013400 chr4A 736466384 736470575 4191 True 3703.000000 3703 82.784 346 4549 1 chr4A.!!$R3 4203
14 TraesCS7D01G013400 chr4A 735689506 735693011 3505 False 3131.000000 3131 82.917 673 4169 1 chr4A.!!$F4 3496
15 TraesCS7D01G013400 chr4A 734582444 734589749 7305 False 2507.833333 7287 94.582 1 4796 3 chr4A.!!$F10 4795
16 TraesCS7D01G013400 chr4A 734848672 734851148 2476 False 2143.000000 2143 82.609 2178 4684 1 chr4A.!!$F2 2506
17 TraesCS7D01G013400 chr7A 6924343 6928676 4333 True 3962.000000 3962 83.303 207 4549 1 chr7A.!!$R1 4342

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
545 557 1.340991 GGGAAGGATTACTTGCTGGCA 60.341 52.381 0.00 0.00 45.79 4.92 F
1042 1066 0.387202 ATCATTGAGTCGGCCTCTCG 59.613 55.000 16.33 6.24 41.11 4.04 F
1071 1095 2.639065 TGCCCACGAATTGATAACCTC 58.361 47.619 0.00 0.00 0.00 3.85 F
1338 3876 3.189080 TCTTCAAACACCATGCATTCTCG 59.811 43.478 0.00 0.00 0.00 4.04 F
2690 5272 3.891366 AGTGCTTTGCAAAGACTACCATT 59.109 39.130 37.14 20.70 41.47 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1941 4522 0.882042 CCATCAGCGGGTCTATGCAC 60.882 60.000 0.00 0.0 0.00 4.57 R
2764 5346 6.711645 AGTAACGTTTTAAGGCATAGTGGAAA 59.288 34.615 5.91 0.0 0.00 3.13 R
3222 5804 5.242393 CACCAAGACCAATCTTTTGAGTGAT 59.758 40.000 0.00 0.0 46.32 3.06 R
3474 6057 1.268899 CAAAGGAAGTCAGCTGCAAGG 59.731 52.381 9.47 0.0 0.00 3.61 R
4594 7234 0.250858 TGTGGCAGAACAGGACCATG 60.251 55.000 0.00 0.0 34.04 3.66 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
46 47 3.205733 TGTTTTCCTCCTTAAACACCCCT 59.794 43.478 0.00 0.00 38.82 4.79
47 48 4.220724 GTTTTCCTCCTTAAACACCCCTT 58.779 43.478 0.00 0.00 35.02 3.95
57 58 7.627311 TCCTTAAACACCCCTTAACTATCTTC 58.373 38.462 0.00 0.00 0.00 2.87
64 65 3.181450 CCCCTTAACTATCTTCCAGCCTG 60.181 52.174 0.00 0.00 0.00 4.85
119 120 7.680730 TGCTTAGGAGAAGTCTGTTCTTTTAT 58.319 34.615 0.00 0.00 0.00 1.40
386 398 2.351418 CACTATCTTGCCGCAATTCGAA 59.649 45.455 6.19 0.00 41.67 3.71
470 482 5.046520 GGAACTCAAAGAAGGCTTCTACCTA 60.047 44.000 28.78 14.14 39.93 3.08
535 547 2.888069 GCCAAGCAAAGGGGAAGGATTA 60.888 50.000 0.00 0.00 0.00 1.75
541 553 3.701664 CAAAGGGGAAGGATTACTTGCT 58.298 45.455 0.00 0.00 45.79 3.91
545 557 1.340991 GGGAAGGATTACTTGCTGGCA 60.341 52.381 0.00 0.00 45.79 4.92
549 561 4.081476 GGAAGGATTACTTGCTGGCAAATT 60.081 41.667 9.32 2.52 43.46 1.82
572 584 2.486982 CTCCTCCATCAGCAACACTTTG 59.513 50.000 0.00 0.00 35.62 2.77
623 635 2.158928 GCTGTCCAATCTGAGCTCTGAT 60.159 50.000 25.58 25.58 36.31 2.90
1042 1066 0.387202 ATCATTGAGTCGGCCTCTCG 59.613 55.000 16.33 6.24 41.11 4.04
1071 1095 2.639065 TGCCCACGAATTGATAACCTC 58.361 47.619 0.00 0.00 0.00 3.85
1204 3735 4.595781 TGTTAGCTCCTCTAGTTTCCCAAA 59.404 41.667 0.00 0.00 0.00 3.28
1272 3804 3.242870 CCACTGCTCTTTGTTGTGAAGAC 60.243 47.826 0.00 0.00 0.00 3.01
1338 3876 3.189080 TCTTCAAACACCATGCATTCTCG 59.811 43.478 0.00 0.00 0.00 4.04
1941 4522 8.244494 AGCTACATCATTTACGCACTATAATG 57.756 34.615 0.00 0.00 0.00 1.90
2690 5272 3.891366 AGTGCTTTGCAAAGACTACCATT 59.109 39.130 37.14 20.70 41.47 3.16
2764 5346 6.239204 GCCAAACCTAAAGACATTACCTTGTT 60.239 38.462 0.00 0.00 0.00 2.83
2967 5549 7.014134 TCACAGGAACATTCATTTCTAAAGCAA 59.986 33.333 0.00 0.00 0.00 3.91
3022 5604 7.886191 CATGTTCAAAAACTTGAAAATGCTG 57.114 32.000 14.63 0.00 44.73 4.41
3029 5611 9.598517 TCAAAAACTTGAAAATGCTGTAGAAAT 57.401 25.926 0.00 0.00 0.00 2.17
3474 6057 3.982058 GCCTCAGTATATACAACTGCGTC 59.018 47.826 15.18 0.00 43.30 5.19
3492 6075 0.767375 TCCTTGCAGCTGACTTCCTT 59.233 50.000 20.43 0.00 0.00 3.36
3559 6164 2.046314 GCCCCGCAAGCTTGTCTA 60.046 61.111 26.55 0.00 0.00 2.59
3774 6379 0.318441 TCTCAGCTGAAGGTTCCACG 59.682 55.000 18.85 2.53 0.00 4.94
3814 6421 3.992643 TGACAAATGCAAGGAACCATTG 58.007 40.909 0.00 0.00 32.40 2.82
3860 6467 0.251354 CACATCTGTCAGGACCCTGG 59.749 60.000 15.43 0.84 43.75 4.45
3905 6512 1.067354 CCCTGCCAACAAATCTGAAGC 60.067 52.381 0.00 0.00 0.00 3.86
4122 6731 3.681593 TCAAATTCCCACCTGCAAATG 57.318 42.857 0.00 0.00 0.00 2.32
4229 6865 6.920569 TCTATCTTTCAAATACGCCCTTTC 57.079 37.500 0.00 0.00 0.00 2.62
4297 6936 6.165577 CCATAAAGGAAATTCAACCAAGTGG 58.834 40.000 0.00 0.00 41.22 4.00
4298 6937 6.239572 CCATAAAGGAAATTCAACCAAGTGGT 60.240 38.462 0.00 0.00 46.50 4.16
4440 7079 2.300723 TGCTTTGCTGATTGGCTCATTT 59.699 40.909 0.00 0.00 32.10 2.32
4454 7093 1.528586 CTCATTTATTGCCCTCTCGCG 59.471 52.381 0.00 0.00 0.00 5.87
4495 7135 1.001860 TGATGCCACAATCACTGACGA 59.998 47.619 0.00 0.00 31.58 4.20
4505 7145 3.559238 ATCACTGACGATGGTTTTTGC 57.441 42.857 0.00 0.00 0.00 3.68
4568 7208 2.908688 AACTGGACAATTGCCCAAAC 57.091 45.000 14.86 0.00 31.11 2.93
4610 7250 2.945668 GTTATCATGGTCCTGTTCTGCC 59.054 50.000 0.00 0.00 0.00 4.85
4612 7252 0.036732 TCATGGTCCTGTTCTGCCAC 59.963 55.000 0.00 0.00 33.42 5.01
4616 7256 0.685097 GGTCCTGTTCTGCCACAGTA 59.315 55.000 6.95 0.00 42.45 2.74
4660 7300 4.406456 TGGTTTGTACTGGATTGCAATCT 58.594 39.130 32.48 19.25 35.73 2.40
4661 7301 4.832266 TGGTTTGTACTGGATTGCAATCTT 59.168 37.500 32.48 21.38 35.73 2.40
4710 7389 7.464710 CGCCATGTAACTGAAGATCTCTTTTAC 60.465 40.741 0.00 2.96 36.11 2.01
4713 7392 8.660373 CATGTAACTGAAGATCTCTTTTACCAC 58.340 37.037 0.00 0.00 36.11 4.16
4719 7398 7.451877 ACTGAAGATCTCTTTTACCACTCACTA 59.548 37.037 0.00 0.00 36.11 2.74
4764 7443 7.458397 TGTATTTGGAGTACTCTGGTTTCATT 58.542 34.615 21.88 4.78 0.00 2.57
4772 7451 2.158475 ACTCTGGTTTCATTCCTGGCAA 60.158 45.455 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.264294 AGGAGGAAAACAAGAGAACAGATAT 57.736 36.000 0.00 0.00 0.00 1.63
46 47 4.081087 GTCACCAGGCTGGAAGATAGTTAA 60.081 45.833 38.99 10.66 40.96 2.01
47 48 3.451178 GTCACCAGGCTGGAAGATAGTTA 59.549 47.826 38.99 11.33 40.96 2.24
57 58 2.930019 TGAGGGTCACCAGGCTGG 60.930 66.667 31.62 31.62 45.02 4.85
88 89 4.021544 ACAGACTTCTCCTAAGCAGACTTG 60.022 45.833 0.00 0.00 36.57 3.16
119 120 9.010029 GTAGAAAGACAAATTATGGGAAACAGA 57.990 33.333 0.00 0.00 0.00 3.41
386 398 2.854963 TCTGCTGCTTCAATCAACAGT 58.145 42.857 0.00 0.00 31.56 3.55
470 482 0.320247 CGTCCAGCAAGTCTTCAGCT 60.320 55.000 0.00 0.00 39.63 4.24
535 547 1.203100 AGGAGGAATTTGCCAGCAAGT 60.203 47.619 5.08 0.00 37.24 3.16
541 553 1.640149 TGATGGAGGAGGAATTTGCCA 59.360 47.619 0.00 0.00 0.00 4.92
545 557 3.245371 TGTTGCTGATGGAGGAGGAATTT 60.245 43.478 0.00 0.00 0.00 1.82
549 561 0.615331 GTGTTGCTGATGGAGGAGGA 59.385 55.000 0.00 0.00 0.00 3.71
572 584 1.449246 AGCACGCAGAGGCTTCATC 60.449 57.895 0.00 0.00 38.34 2.92
623 635 8.846943 TCAGATGTTGAATTAGCTTTCTGTTA 57.153 30.769 0.00 0.00 31.34 2.41
721 739 0.105964 TGTTTTGGTGGGGCTTGCTA 60.106 50.000 0.00 0.00 0.00 3.49
1059 1083 6.161855 TGCAGAGTATCGAGGTTATCAATT 57.838 37.500 0.00 0.00 42.67 2.32
1071 1095 0.933097 ATTTGCGCTGCAGAGTATCG 59.067 50.000 20.43 12.30 42.67 2.92
1157 3688 1.846439 GGTCCCATTCCCTCTGATTGA 59.154 52.381 0.00 0.00 0.00 2.57
1204 3735 2.100749 CCAAAACTTTGCTTCCCGTCTT 59.899 45.455 0.00 0.00 36.86 3.01
1272 3804 3.679980 CCATGTTTTCTAGAGGACACACG 59.320 47.826 11.16 5.11 0.00 4.49
1338 3876 2.034878 GGATTTCTGATTTCTGGCCCC 58.965 52.381 0.00 0.00 0.00 5.80
1555 4105 1.681166 GCACCTCTGCAGATGTGGATT 60.681 52.381 37.12 13.87 43.62 3.01
1941 4522 0.882042 CCATCAGCGGGTCTATGCAC 60.882 60.000 0.00 0.00 0.00 4.57
2583 5165 7.178451 CCTGGGTATTTTGAAGATTTGTAACCT 59.822 37.037 0.00 0.00 0.00 3.50
2764 5346 6.711645 AGTAACGTTTTAAGGCATAGTGGAAA 59.288 34.615 5.91 0.00 0.00 3.13
3222 5804 5.242393 CACCAAGACCAATCTTTTGAGTGAT 59.758 40.000 0.00 0.00 46.32 3.06
3283 5866 6.098124 TCAAGTTTTGTCAAATGTTGGAGGAT 59.902 34.615 15.21 0.00 0.00 3.24
3474 6057 1.268899 CAAAGGAAGTCAGCTGCAAGG 59.731 52.381 9.47 0.00 0.00 3.61
3492 6075 1.488812 ACTTGTGGCCAGTCAGTACAA 59.511 47.619 5.11 3.76 0.00 2.41
3559 6164 1.958288 ACAGAGGTGAGGCTACCAAT 58.042 50.000 13.32 1.86 43.37 3.16
3860 6467 3.521560 TCATTAGACAGTCACCGAATGC 58.478 45.455 2.66 0.00 30.24 3.56
3905 6512 1.907739 TCCTCAGATTGGGGAAGCG 59.092 57.895 0.00 0.00 45.82 4.68
4122 6731 7.387643 AGTGGATCTAAGTTACCTTTCTGTTC 58.612 38.462 0.00 0.00 31.89 3.18
4141 6751 4.464008 TCTTTGAGAGTGCAAAAGTGGAT 58.536 39.130 7.50 0.00 37.32 3.41
4259 6898 6.757173 TCCTTTATGGCCTGCTATAAAGTA 57.243 37.500 29.82 20.49 46.63 2.24
4454 7093 2.025898 GAGGACAGTAGGTGGTAGAGC 58.974 57.143 0.00 0.00 0.00 4.09
4495 7135 3.791245 ACAACACGATTGCAAAAACCAT 58.209 36.364 1.71 0.00 0.00 3.55
4505 7145 6.820470 AAAACATAACCAACAACACGATTG 57.180 33.333 0.00 0.00 0.00 2.67
4594 7234 0.250858 TGTGGCAGAACAGGACCATG 60.251 55.000 0.00 0.00 34.04 3.66
4597 7237 4.386413 CTGTGGCAGAACAGGACC 57.614 61.111 5.72 0.00 43.22 4.46
4616 7256 7.182060 ACCAAAAATACAACATACTCCAGGAT 58.818 34.615 0.00 0.00 0.00 3.24
4660 7300 5.673337 GTGACAGCACACAAGAGATAAAA 57.327 39.130 0.00 0.00 44.51 1.52
4713 7392 6.145338 ACCATTACTCATTACGGTAGTGAG 57.855 41.667 28.58 28.58 45.01 3.51
4719 7398 9.841295 AAATACATAACCATTACTCATTACGGT 57.159 29.630 0.00 0.00 0.00 4.83
4747 7426 4.508662 CCAGGAATGAAACCAGAGTACTC 58.491 47.826 15.41 15.41 0.00 2.59
4754 7433 2.629617 ACTTTGCCAGGAATGAAACCAG 59.370 45.455 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.