Multiple sequence alignment - TraesCS4B01G170200

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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 TraesCS4B01G170200 chr4B 100.000 2549 0 0 1 2549 372353685 372351137 0.000000e+00 4708
1 TraesCS4B01G170200 chr4B 95.150 2000 78 11 556 2549 17791865 17789879 0.000000e+00 3138
2 TraesCS4B01G170200 chr4A 95.646 1998 74 10 558 2549 705529263 705527273 0.000000e+00 3195
3 TraesCS4B01G170200 chr7B 95.628 1990 74 10 567 2549 720989192 720987209 0.000000e+00 3181
4 TraesCS4B01G170200 chr7B 89.032 465 48 3 1 464 162350543 162351005 7.910000e-160 573
5 TraesCS4B01G170200 chr7B 88.806 402 34 7 1 399 447448315 447447922 1.370000e-132 483
6 TraesCS4B01G170200 chr7B 92.381 105 7 1 463 566 162351058 162351162 5.680000e-32 148
7 TraesCS4B01G170200 chr1B 95.585 1993 70 14 568 2549 581717562 581715577 0.000000e+00 3177
8 TraesCS4B01G170200 chr1B 95.622 1987 72 11 569 2549 520844119 520842142 0.000000e+00 3173
9 TraesCS4B01G170200 chr1B 95.250 2000 81 10 556 2549 561526116 561528107 0.000000e+00 3155
10 TraesCS4B01G170200 chr3B 95.393 1997 74 13 564 2549 19701232 19703221 0.000000e+00 3162
11 TraesCS4B01G170200 chr2B 95.243 1997 83 9 558 2549 458657412 458659401 0.000000e+00 3151
12 TraesCS4B01G170200 chr2B 95.112 2005 78 15 557 2549 492636654 492638650 0.000000e+00 3142
13 TraesCS4B01G170200 chr2D 91.944 571 40 6 1 568 131639321 131638754 0.000000e+00 795
14 TraesCS4B01G170200 chr2D 88.337 403 41 5 1 400 125425000 125425399 1.770000e-131 479
15 TraesCS4B01G170200 chr5B 91.068 571 47 4 1 568 276795964 276795395 0.000000e+00 769
16 TraesCS4B01G170200 chr6D 88.834 403 39 5 1 400 226761549 226761948 8.200000e-135 490
17 TraesCS4B01G170200 chr2A 88.586 403 40 5 1 400 100197820 100197421 3.810000e-133 484
18 TraesCS4B01G170200 chr3D 88.500 400 43 2 1 400 297661592 297661196 4.930000e-132 481
19 TraesCS4B01G170200 chr3D 88.366 404 40 6 1 400 453169208 453169608 1.770000e-131 479


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 TraesCS4B01G170200 chr4B 372351137 372353685 2548 True 4708.0 4708 100.0000 1 2549 1 chr4B.!!$R2 2548
1 TraesCS4B01G170200 chr4B 17789879 17791865 1986 True 3138.0 3138 95.1500 556 2549 1 chr4B.!!$R1 1993
2 TraesCS4B01G170200 chr4A 705527273 705529263 1990 True 3195.0 3195 95.6460 558 2549 1 chr4A.!!$R1 1991
3 TraesCS4B01G170200 chr7B 720987209 720989192 1983 True 3181.0 3181 95.6280 567 2549 1 chr7B.!!$R2 1982
4 TraesCS4B01G170200 chr7B 162350543 162351162 619 False 360.5 573 90.7065 1 566 2 chr7B.!!$F1 565
5 TraesCS4B01G170200 chr1B 581715577 581717562 1985 True 3177.0 3177 95.5850 568 2549 1 chr1B.!!$R2 1981
6 TraesCS4B01G170200 chr1B 520842142 520844119 1977 True 3173.0 3173 95.6220 569 2549 1 chr1B.!!$R1 1980
7 TraesCS4B01G170200 chr1B 561526116 561528107 1991 False 3155.0 3155 95.2500 556 2549 1 chr1B.!!$F1 1993
8 TraesCS4B01G170200 chr3B 19701232 19703221 1989 False 3162.0 3162 95.3930 564 2549 1 chr3B.!!$F1 1985
9 TraesCS4B01G170200 chr2B 458657412 458659401 1989 False 3151.0 3151 95.2430 558 2549 1 chr2B.!!$F1 1991
10 TraesCS4B01G170200 chr2B 492636654 492638650 1996 False 3142.0 3142 95.1120 557 2549 1 chr2B.!!$F2 1992
11 TraesCS4B01G170200 chr2D 131638754 131639321 567 True 795.0 795 91.9440 1 568 1 chr2D.!!$R1 567
12 TraesCS4B01G170200 chr5B 276795395 276795964 569 True 769.0 769 91.0680 1 568 1 chr5B.!!$R1 567

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
988 1049 0.179171 GGCGTTGAGATCTCGTTCGA 60.179 55.0 26.3 6.85 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2184 2260 0.184933 AGTGCAGCCCTAAACACCAA 59.815 50.0 0.0 0.0 33.46 3.67 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
31 32 2.283476 GGAGGTGATGACCACATGCAC 61.283 57.143 3.51 0.00 45.33 4.57
60 61 8.579850 AGTGCCATTTTCATACTTTTGATAGA 57.420 30.769 0.00 0.00 0.00 1.98
127 128 9.698309 AATGAGTTGACTCCGTTCATATATTAG 57.302 33.333 8.56 0.00 42.20 1.73
134 135 7.232737 TGACTCCGTTCATATATTAGTGGTGAT 59.767 37.037 0.00 0.00 0.00 3.06
173 174 6.620678 ACTATTGTGACGCTTAATTGCATTT 58.379 32.000 0.00 0.00 0.00 2.32
271 273 4.022155 ACTGTTGTAAATGATGTGCATGCA 60.022 37.500 18.46 18.46 37.28 3.96
276 278 1.182667 AATGATGTGCATGCAGCTGT 58.817 45.000 23.41 7.22 45.94 4.40
408 411 7.227314 TCGTACTATTATGTTTAGAGCCGAAGA 59.773 37.037 0.00 0.00 0.00 2.87
432 435 8.015658 AGAAAATGATTCTAAAAACGAACCGAG 58.984 33.333 0.00 0.00 0.00 4.63
478 535 9.836076 GTTATCCTTTTAACCAACTGATACAAC 57.164 33.333 0.00 0.00 0.00 3.32
692 751 0.179234 TGTGAACTTTGGCGTCTCCA 59.821 50.000 0.00 0.00 44.85 3.86
735 794 0.840722 CCTTACAGGTGGGACCAGGT 60.841 60.000 0.00 0.00 41.95 4.00
813 872 1.678627 GAGAGCCGTTGAGCATAGAGA 59.321 52.381 0.00 0.00 34.23 3.10
846 907 1.067776 GCTATATTAGCGGGCGACAGT 60.068 52.381 0.00 0.00 42.62 3.55
915 976 3.268965 GAGAGCACGACGGCAGTGA 62.269 63.158 15.83 0.00 41.83 3.41
955 1016 1.676678 CGGCAGTGGGAAGCTAGCTA 61.677 60.000 19.70 0.00 0.00 3.32
967 1028 2.203437 TAGCTATGGAGGGCGCGA 60.203 61.111 12.10 0.00 0.00 5.87
988 1049 0.179171 GGCGTTGAGATCTCGTTCGA 60.179 55.000 26.30 6.85 0.00 3.71
1075 1136 1.620819 AGATGCCTGTCTTCGTCTGTT 59.379 47.619 0.00 0.00 0.00 3.16
1082 1143 1.081641 TCTTCGTCTGTTCGCGGTC 60.082 57.895 6.13 0.00 0.00 4.79
1101 1162 4.847516 CGGGCGAGCGTTGATCGA 62.848 66.667 8.79 0.00 44.55 3.59
1124 1185 1.002087 GGTTTCTCACACACCGAGGAT 59.998 52.381 0.00 0.00 0.00 3.24
1133 1194 1.066215 CACACCGAGGATCCACAATCA 60.066 52.381 15.82 0.00 35.96 2.57
1175 1236 1.772453 GAATGGGGTAAGAATCGGGGA 59.228 52.381 0.00 0.00 0.00 4.81
1237 1298 3.401033 TGATCTGTTCCGTGTTCATGT 57.599 42.857 0.00 0.00 0.00 3.21
1306 1367 7.389232 TCTGATAAATGAACTGCAAGAAGAGA 58.611 34.615 0.00 0.00 37.43 3.10
1491 1552 3.439825 CCATTTGCAAATACTTTTGGGCC 59.560 43.478 23.69 0.00 42.09 5.80
2004 2076 2.434359 CTCGAACCCAAGACCGCC 60.434 66.667 0.00 0.00 0.00 6.13
2116 2189 7.756722 AGTGAGACTGTGAAATTTGTCAAAAAG 59.243 33.333 1.31 0.00 32.41 2.27
2346 2425 5.046950 AGTGGTTTTCCTTTGTTTTGCACTA 60.047 36.000 0.00 0.00 41.38 2.74
2488 2569 8.524870 AATTTGCATGTTAGTTCATGACTTTC 57.475 30.769 10.28 0.00 45.41 2.62
2516 2599 2.762535 TAAAACGGAGGGCTTCTCAG 57.237 50.000 9.20 7.73 44.19 3.35
2527 2610 0.107459 GCTTCTCAGCCCTCCGATTT 60.107 55.000 0.00 0.00 40.61 2.17
2528 2611 1.680249 GCTTCTCAGCCCTCCGATTTT 60.680 52.381 0.00 0.00 40.61 1.82
2529 2612 2.284190 CTTCTCAGCCCTCCGATTTTC 58.716 52.381 0.00 0.00 0.00 2.29
2530 2613 1.275666 TCTCAGCCCTCCGATTTTCA 58.724 50.000 0.00 0.00 0.00 2.69
2531 2614 1.839994 TCTCAGCCCTCCGATTTTCAT 59.160 47.619 0.00 0.00 0.00 2.57
2532 2615 2.239654 TCTCAGCCCTCCGATTTTCATT 59.760 45.455 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.035152 TGCATGTGGTCATCACCTCC 60.035 55.000 0.00 0.00 45.48 4.30
31 32 3.492421 AGTATGAAAATGGCACTTGCG 57.508 42.857 0.00 0.00 43.26 4.85
104 105 7.595502 CCACTAATATATGAACGGAGTCAACTC 59.404 40.741 1.37 1.37 45.00 3.01
105 106 7.069578 ACCACTAATATATGAACGGAGTCAACT 59.930 37.037 0.00 0.00 45.00 3.16
127 128 5.354234 AGTTCGAACAAATATCCATCACCAC 59.646 40.000 28.78 0.00 0.00 4.16
134 135 7.201487 CGTCACAATAGTTCGAACAAATATCCA 60.201 37.037 28.78 4.83 0.00 3.41
143 144 5.505165 TTAAGCGTCACAATAGTTCGAAC 57.495 39.130 20.71 20.71 0.00 3.95
173 174 3.065233 GCTTCAATATGGATGTCGTTGCA 59.935 43.478 0.00 0.00 0.00 4.08
237 238 9.844790 CATCATTTACAACAGTACATCAAACAT 57.155 29.630 0.00 0.00 0.00 2.71
238 239 8.845227 ACATCATTTACAACAGTACATCAAACA 58.155 29.630 0.00 0.00 0.00 2.83
239 240 9.117145 CACATCATTTACAACAGTACATCAAAC 57.883 33.333 0.00 0.00 0.00 2.93
240 241 7.807433 GCACATCATTTACAACAGTACATCAAA 59.193 33.333 0.00 0.00 0.00 2.69
256 258 1.548719 ACAGCTGCATGCACATCATTT 59.451 42.857 18.46 0.00 45.94 2.32
402 405 8.627428 GTTCGTTTTTAGAATCATTTTCTTCGG 58.373 33.333 0.00 0.00 0.00 4.30
408 411 7.645402 ACTCGGTTCGTTTTTAGAATCATTTT 58.355 30.769 0.00 0.00 0.00 1.82
813 872 2.638480 ATATAGCACACCCGCAATGT 57.362 45.000 0.00 0.00 0.00 2.71
915 976 1.621672 GCCCTCCACAGCTAGCTTCT 61.622 60.000 16.46 0.00 0.00 2.85
940 1001 2.324541 CTCCATAGCTAGCTTCCCACT 58.675 52.381 24.88 0.00 0.00 4.00
967 1028 0.456312 GAACGAGATCTCAACGCCGT 60.456 55.000 22.31 11.00 0.00 5.68
988 1049 0.820871 GAAGACATGGAGCTCGGAGT 59.179 55.000 7.83 5.42 0.00 3.85
1101 1162 0.834612 TCGGTGTGTGAGAAACCCTT 59.165 50.000 0.00 0.00 0.00 3.95
1124 1185 3.924073 CACGTAGAACGAATGATTGTGGA 59.076 43.478 6.44 0.00 46.05 4.02
1133 1194 1.068474 GCTGCACACGTAGAACGAAT 58.932 50.000 6.44 0.00 46.05 3.34
1237 1298 4.761739 CCAAAGAAAGAAGCATGTCACCTA 59.238 41.667 0.00 0.00 0.00 3.08
1306 1367 2.339418 CATGCGCAACCATTTGTCATT 58.661 42.857 17.11 0.00 34.90 2.57
1491 1552 5.234329 CAGTGCGATTACCATACCTACAAAG 59.766 44.000 0.00 0.00 0.00 2.77
2004 2076 1.960689 CCCTAAACACCACAAACCCAG 59.039 52.381 0.00 0.00 0.00 4.45
2116 2189 2.562298 TGTGCATTTTCCACCCTTCATC 59.438 45.455 0.00 0.00 32.30 2.92
2184 2260 0.184933 AGTGCAGCCCTAAACACCAA 59.815 50.000 0.00 0.00 33.46 3.67
2346 2425 4.044308 ACCTTCCAACCCTCCAAAATTTT 58.956 39.130 0.00 0.00 0.00 1.82
2488 2569 5.134202 AGCCCTCCGTTTTATTCAAAAAG 57.866 39.130 0.00 0.00 35.46 2.27
2516 2599 4.338118 TGTCATTAATGAAAATCGGAGGGC 59.662 41.667 19.55 3.85 38.75 5.19
2521 2604 6.385843 TGTGGTTGTCATTAATGAAAATCGG 58.614 36.000 21.24 0.00 37.84 4.18
2523 2606 8.816640 ACTTGTGGTTGTCATTAATGAAAATC 57.183 30.769 21.24 20.89 36.49 2.17


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

AutoCloner maintained by Alex Coulton.