Multiple sequence alignment - TraesCS3B01G088600

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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 TraesCS3B01G088600 chr3B 100.000 3086 0 0 1 3086 56751379 56748294 0.000000e+00 5699.0
1 TraesCS3B01G088600 chr3B 83.085 804 103 22 3 778 631965185 631965983 0.000000e+00 701.0
2 TraesCS3B01G088600 chr3D 92.854 2337 94 15 1 2284 34689175 34691491 0.000000e+00 3323.0
3 TraesCS3B01G088600 chr3D 94.167 120 7 0 2280 2399 34691803 34691922 1.890000e-42 183.0
4 TraesCS3B01G088600 chr3A 91.204 1262 97 10 852 2110 477320894 477319644 0.000000e+00 1703.0
5 TraesCS3B01G088600 chr3A 93.361 241 14 2 1871 2110 477314324 477314085 3.780000e-94 355.0
6 TraesCS3B01G088600 chr7B 97.626 674 15 1 2414 3086 653064781 653064108 0.000000e+00 1155.0
7 TraesCS3B01G088600 chr7B 96.598 676 21 1 2413 3086 95012151 95011476 0.000000e+00 1120.0
8 TraesCS3B01G088600 chr7B 94.962 397 16 2 2411 2803 515415110 515414714 1.220000e-173 619.0
9 TraesCS3B01G088600 chr7B 85.895 475 57 10 333 804 590100893 590100426 5.940000e-137 497.0
10 TraesCS3B01G088600 chr7B 93.080 289 18 2 2800 3086 515414684 515414396 3.680000e-114 422.0
11 TraesCS3B01G088600 chr5B 96.889 675 19 2 2414 3086 122447170 122446496 0.000000e+00 1129.0
12 TraesCS3B01G088600 chr5B 86.260 262 29 5 2414 2668 697238485 697238224 8.430000e-71 278.0
13 TraesCS3B01G088600 chr5B 88.889 225 21 4 2864 3086 704906990 704906768 1.090000e-69 274.0
14 TraesCS3B01G088600 chr2B 96.889 675 18 3 2414 3086 639439358 639440031 0.000000e+00 1127.0
15 TraesCS3B01G088600 chr2B 97.415 619 15 1 2469 3086 730608775 730608157 0.000000e+00 1053.0
16 TraesCS3B01G088600 chr2B 86.028 773 87 3 3 757 105807066 105806297 0.000000e+00 809.0
17 TraesCS3B01G088600 chr2B 96.923 390 12 0 2414 2803 224655904 224656293 0.000000e+00 654.0
18 TraesCS3B01G088600 chr2B 94.444 288 15 1 2800 3086 224656323 224656610 2.820000e-120 442.0
19 TraesCS3B01G088600 chr2B 88.444 225 22 4 2864 3086 730608145 730607923 5.070000e-68 268.0
20 TraesCS3B01G088600 chr6D 84.456 772 87 8 3 756 337844066 337843310 0.000000e+00 730.0
21 TraesCS3B01G088600 chr5A 84.097 786 91 12 3 759 625908864 625908084 0.000000e+00 728.0
22 TraesCS3B01G088600 chr4D 84.184 784 88 22 3 756 442615874 442616651 0.000000e+00 728.0
23 TraesCS3B01G088600 chr4D 97.872 47 1 0 2666 2712 19885588 19885634 7.090000e-12 82.4
24 TraesCS3B01G088600 chr7D 85.099 604 70 2 3 588 45658562 45657961 1.580000e-167 599.0
25 TraesCS3B01G088600 chr7D 90.395 177 16 1 580 756 45657749 45657574 6.660000e-57 231.0
26 TraesCS3B01G088600 chr7D 82.028 217 37 1 344 558 590367835 590368051 1.890000e-42 183.0
27 TraesCS3B01G088600 chr7D 80.645 217 40 1 344 558 509830016 509829800 1.900000e-37 167.0
28 TraesCS3B01G088600 chr7A 90.355 197 18 1 554 750 579839335 579839530 1.100000e-64 257.0
29 TraesCS3B01G088600 chr5D 83.270 263 38 4 2412 2668 343655572 343655310 1.430000e-58 237.0
30 TraesCS3B01G088600 chr4B 83.206 262 38 4 2413 2668 613219856 613220117 5.140000e-58 235.0
31 TraesCS3B01G088600 chr2A 80.180 222 42 1 339 558 89599914 89600135 6.850000e-37 165.0
32 TraesCS3B01G088600 chr1B 97.872 47 1 0 2666 2712 633712326 633712372 7.090000e-12 82.4


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 TraesCS3B01G088600 chr3B 56748294 56751379 3085 True 5699.0 5699 100.0000 1 3086 1 chr3B.!!$R1 3085
1 TraesCS3B01G088600 chr3B 631965185 631965983 798 False 701.0 701 83.0850 3 778 1 chr3B.!!$F1 775
2 TraesCS3B01G088600 chr3D 34689175 34691922 2747 False 1753.0 3323 93.5105 1 2399 2 chr3D.!!$F1 2398
3 TraesCS3B01G088600 chr3A 477319644 477320894 1250 True 1703.0 1703 91.2040 852 2110 1 chr3A.!!$R2 1258
4 TraesCS3B01G088600 chr7B 653064108 653064781 673 True 1155.0 1155 97.6260 2414 3086 1 chr7B.!!$R3 672
5 TraesCS3B01G088600 chr7B 95011476 95012151 675 True 1120.0 1120 96.5980 2413 3086 1 chr7B.!!$R1 673
6 TraesCS3B01G088600 chr7B 515414396 515415110 714 True 520.5 619 94.0210 2411 3086 2 chr7B.!!$R4 675
7 TraesCS3B01G088600 chr5B 122446496 122447170 674 True 1129.0 1129 96.8890 2414 3086 1 chr5B.!!$R1 672
8 TraesCS3B01G088600 chr2B 639439358 639440031 673 False 1127.0 1127 96.8890 2414 3086 1 chr2B.!!$F1 672
9 TraesCS3B01G088600 chr2B 105806297 105807066 769 True 809.0 809 86.0280 3 757 1 chr2B.!!$R1 754
10 TraesCS3B01G088600 chr2B 730607923 730608775 852 True 660.5 1053 92.9295 2469 3086 2 chr2B.!!$R2 617
11 TraesCS3B01G088600 chr2B 224655904 224656610 706 False 548.0 654 95.6835 2414 3086 2 chr2B.!!$F2 672
12 TraesCS3B01G088600 chr6D 337843310 337844066 756 True 730.0 730 84.4560 3 756 1 chr6D.!!$R1 753
13 TraesCS3B01G088600 chr5A 625908084 625908864 780 True 728.0 728 84.0970 3 759 1 chr5A.!!$R1 756
14 TraesCS3B01G088600 chr4D 442615874 442616651 777 False 728.0 728 84.1840 3 756 1 chr4D.!!$F2 753
15 TraesCS3B01G088600 chr7D 45657574 45658562 988 True 415.0 599 87.7470 3 756 2 chr7D.!!$R2 753

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
35 36 0.405198 ACCACAATCATCCCACAGCA 59.595 50.000 0.0 0.00 0.0 4.41 F
713 1004 1.202651 ACGTGGCAAGTTCTAGTGCTT 60.203 47.619 0.0 0.35 40.7 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1073 1368 3.554692 CACCGTTGCCGATCTCGC 61.555 66.667 0.00 0.0 38.18 5.03 R
2120 2415 0.397254 CCCGGTAGATCACCAGGAGT 60.397 60.000 17.84 0.0 46.79 3.85 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
32 33 1.071434 TCCACCACAATCATCCCACA 58.929 50.000 0.00 0.00 0.00 4.17
35 36 0.405198 ACCACAATCATCCCACAGCA 59.595 50.000 0.00 0.00 0.00 4.41
42 43 1.288188 TCATCCCACAGCATTGGAGA 58.712 50.000 5.19 2.02 39.24 3.71
87 88 2.546494 CCCGCATCTTTCATCGCCC 61.546 63.158 0.00 0.00 0.00 6.13
100 101 3.385384 CGCCCTGCTCTCCTCACA 61.385 66.667 0.00 0.00 0.00 3.58
204 205 5.047306 CGTTAATCCCCATATGCTACTCTCA 60.047 44.000 0.00 0.00 0.00 3.27
259 260 4.704833 TTCGGCTCTGCTGCACCC 62.705 66.667 0.00 0.00 34.49 4.61
269 270 3.710722 CTGCACCCCCTCGAGCTT 61.711 66.667 6.99 0.00 0.00 3.74
365 404 1.370064 GACCTGGTTGTAGCCACGT 59.630 57.895 0.00 0.00 34.36 4.49
420 459 4.794439 CGGATGCGCGAGTGGTCA 62.794 66.667 12.10 0.00 0.00 4.02
421 460 2.202932 GGATGCGCGAGTGGTCAT 60.203 61.111 12.10 1.33 0.00 3.06
543 583 1.740285 GGCTTCGCCGGATTAGAGA 59.260 57.895 5.05 0.00 39.62 3.10
577 619 3.066481 GGACATAAGAGGAGTGACGTACC 59.934 52.174 0.00 0.00 0.00 3.34
713 1004 1.202651 ACGTGGCAAGTTCTAGTGCTT 60.203 47.619 0.00 0.35 40.70 3.91
728 1019 2.126467 GTGCTTCAAAATTTGCGCAGA 58.874 42.857 11.31 6.65 37.43 4.26
778 1069 5.703592 GGATGTGTTGATAAGTACCACACAA 59.296 40.000 7.46 2.38 38.70 3.33
783 1074 7.769507 TGTGTTGATAAGTACCACACAAGTAAA 59.230 33.333 1.03 0.00 34.31 2.01
829 1121 2.156891 CCACGTGTATCTTTTGTGACGG 59.843 50.000 15.65 0.00 32.39 4.79
847 1139 1.666700 CGGAACAAGACGTTTTCCACA 59.333 47.619 15.36 0.00 39.08 4.17
951 1243 3.579151 AGGACCAAAGAGTAGAGGACAAC 59.421 47.826 0.00 0.00 0.00 3.32
952 1244 3.323979 GGACCAAAGAGTAGAGGACAACA 59.676 47.826 0.00 0.00 0.00 3.33
1073 1368 1.233019 GGCATCAAGATCCATGTCGG 58.767 55.000 0.00 0.00 0.00 4.79
1252 1547 1.585006 CCGTCGTCCTACAGTGCTT 59.415 57.895 0.00 0.00 0.00 3.91
1605 1900 2.780924 AAAGAGTGGTGGGGCCCA 60.781 61.111 24.76 24.76 36.04 5.36
1607 1902 1.739608 AAAGAGTGGTGGGGCCCAAT 61.740 55.000 30.70 14.13 35.92 3.16
1756 2051 7.994194 ACTTCTACCGGAGTACAAATTAGTAG 58.006 38.462 9.46 1.66 0.00 2.57
1852 2147 0.768221 TTGGAGGAACTGGGAGCTGT 60.768 55.000 0.00 0.00 41.55 4.40
2110 2405 3.414272 GCAGCCTTGCGAGGTATG 58.586 61.111 21.55 19.70 45.44 2.39
2111 2406 2.182842 GCAGCCTTGCGAGGTATGG 61.183 63.158 21.55 9.50 45.44 2.74
2112 2407 1.524621 CAGCCTTGCGAGGTATGGG 60.525 63.158 21.55 3.29 45.44 4.00
2113 2408 2.203209 GCCTTGCGAGGTATGGGG 60.203 66.667 21.55 0.00 45.44 4.96
2114 2409 2.742116 GCCTTGCGAGGTATGGGGA 61.742 63.158 21.55 0.00 45.44 4.81
2115 2410 2.056906 GCCTTGCGAGGTATGGGGAT 62.057 60.000 21.55 0.00 45.44 3.85
2116 2411 0.474184 CCTTGCGAGGTATGGGGATT 59.526 55.000 12.40 0.00 38.32 3.01
2117 2412 1.697432 CCTTGCGAGGTATGGGGATTA 59.303 52.381 12.40 0.00 38.32 1.75
2118 2413 2.305927 CCTTGCGAGGTATGGGGATTAT 59.694 50.000 12.40 0.00 38.32 1.28
2119 2414 3.244911 CCTTGCGAGGTATGGGGATTATT 60.245 47.826 12.40 0.00 38.32 1.40
2120 2415 4.019681 CCTTGCGAGGTATGGGGATTATTA 60.020 45.833 12.40 0.00 38.32 0.98
2165 2460 1.135344 TGTTTGCGCACATGGATGATG 60.135 47.619 11.12 0.00 38.15 3.07
2174 2469 3.385433 GCACATGGATGATGGGAAATTCA 59.615 43.478 0.00 0.00 37.74 2.57
2210 2506 7.401484 TGTTTGAGTGTTTTTCTTCACAAAC 57.599 32.000 0.00 0.00 43.00 2.93
2213 2509 6.567687 TGAGTGTTTTTCTTCACAAACTGA 57.432 33.333 0.00 0.00 37.07 3.41
2216 2512 8.087750 TGAGTGTTTTTCTTCACAAACTGAAAT 58.912 29.630 0.00 0.00 38.47 2.17
2256 2552 8.846943 TCTAAACATATGATAATTCGCACCAT 57.153 30.769 10.38 0.00 0.00 3.55
2311 2923 3.947910 TCCCGTTATCAACTTCGTTCT 57.052 42.857 0.00 0.00 0.00 3.01
2347 2959 2.292016 TGTCACGGGCTTGTTTGTTATG 59.708 45.455 0.00 0.00 0.00 1.90
2377 2989 2.279517 GGGAGCTCATGTACGGCG 60.280 66.667 17.19 4.80 0.00 6.46
2402 3014 3.715854 GCGCTACGAAAGAAGGAGA 57.284 52.632 0.00 0.00 0.00 3.71
2403 3015 1.551145 GCGCTACGAAAGAAGGAGAG 58.449 55.000 0.00 0.00 0.00 3.20
2404 3016 1.551145 CGCTACGAAAGAAGGAGAGC 58.449 55.000 0.00 0.00 0.00 4.09
2405 3017 1.133407 CGCTACGAAAGAAGGAGAGCT 59.867 52.381 0.00 0.00 0.00 4.09
2406 3018 2.793237 CGCTACGAAAGAAGGAGAGCTC 60.793 54.545 5.27 5.27 0.00 4.09
2459 3074 1.945776 GCAAAGAGTCGTCGCTTCGG 61.946 60.000 0.00 0.00 32.86 4.30
2752 3369 1.537202 GGTGAACAAGGTAGCTTGCTG 59.463 52.381 29.70 12.02 37.83 4.41
2768 3385 3.584733 TGCTGACTATAGCTCCTGAGA 57.415 47.619 0.00 0.00 44.01 3.27
2811 3461 8.273780 AGCTTGTCCTATATGAAAGTTTGAAG 57.726 34.615 0.00 0.00 0.00 3.02
3030 3683 6.486657 TCTCCTAGTGAACACAATTTGAAAGG 59.513 38.462 2.79 0.00 0.00 3.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.242965 TCTCCAATGCTGTGGGATGATT 59.757 45.455 6.42 0.00 39.34 2.57
32 33 3.036429 GCTCGGGGTCTCCAATGCT 62.036 63.158 0.00 0.00 34.36 3.79
35 36 1.002274 AGAGCTCGGGGTCTCCAAT 59.998 57.895 12.19 0.00 45.88 3.16
67 68 1.819632 GCGATGAAAGATGCGGGGT 60.820 57.895 0.00 0.00 0.00 4.95
74 75 0.835941 AGAGCAGGGCGATGAAAGAT 59.164 50.000 0.00 0.00 0.00 2.40
87 88 2.172372 GCGCATGTGAGGAGAGCAG 61.172 63.158 11.26 0.00 0.00 4.24
172 173 2.076803 GGGGATTAACGGGGGCTCT 61.077 63.158 0.00 0.00 0.00 4.09
184 185 4.530161 GTCTGAGAGTAGCATATGGGGATT 59.470 45.833 4.56 0.00 0.00 3.01
269 270 2.761195 CGGAGATCACACGAGGCGA 61.761 63.158 0.00 0.00 0.00 5.54
324 325 3.818787 GTTCGCGCGGAGTCCCTA 61.819 66.667 31.69 4.34 0.00 3.53
443 482 1.674057 CGGTAGATGGCTGGATCCC 59.326 63.158 9.90 0.00 0.00 3.85
543 583 2.833151 TTATGTCCTCCCCCGCCAGT 62.833 60.000 0.00 0.00 0.00 4.00
577 619 4.329545 CCCCACTCACCCACACCG 62.330 72.222 0.00 0.00 0.00 4.94
685 976 2.360350 CTTGCCACGTCAGCCCAT 60.360 61.111 4.72 0.00 0.00 4.00
713 1004 3.567530 CATCACTCTGCGCAAATTTTGA 58.432 40.909 13.05 10.29 0.00 2.69
807 1098 2.411031 CGTCACAAAAGATACACGTGGC 60.411 50.000 21.57 8.85 0.00 5.01
808 1099 2.156891 CCGTCACAAAAGATACACGTGG 59.843 50.000 21.57 1.23 0.00 4.94
810 1101 3.374220 TCCGTCACAAAAGATACACGT 57.626 42.857 0.00 0.00 0.00 4.49
812 1103 5.235616 TCTTGTTCCGTCACAAAAGATACAC 59.764 40.000 0.00 0.00 36.22 2.90
829 1121 3.488553 CCCTTGTGGAAAACGTCTTGTTC 60.489 47.826 0.00 0.00 36.41 3.18
847 1139 3.436243 TGTTGTTCCTGTTTTGTCCCTT 58.564 40.909 0.00 0.00 0.00 3.95
884 1176 8.615705 TGTATCTAGAAGATGCTATTAGGAGGA 58.384 37.037 0.00 0.00 38.05 3.71
964 1259 0.942410 GCGTGACTGTGGCGTTTCTA 60.942 55.000 0.00 0.00 0.00 2.10
971 1266 1.436195 TTTGTGAGCGTGACTGTGGC 61.436 55.000 0.00 0.00 0.00 5.01
972 1267 0.583438 CTTTGTGAGCGTGACTGTGG 59.417 55.000 0.00 0.00 0.00 4.17
1073 1368 3.554692 CACCGTTGCCGATCTCGC 61.555 66.667 0.00 0.00 38.18 5.03
1756 2051 7.201232 CCGTATGAAATGAATGAAAAACACGAC 60.201 37.037 0.00 0.00 0.00 4.34
2110 2405 4.846940 AGATCACCAGGAGTAATAATCCCC 59.153 45.833 2.80 0.00 37.57 4.81
2111 2406 6.937392 GTAGATCACCAGGAGTAATAATCCC 58.063 44.000 2.80 0.00 37.57 3.85
2113 2408 9.192154 CCCGGTAGATCACCAGGAGTAATAATC 62.192 48.148 17.84 0.00 46.79 1.75
2114 2409 7.483016 CCCGGTAGATCACCAGGAGTAATAAT 61.483 46.154 17.84 0.00 46.79 1.28
2115 2410 6.218026 CCCGGTAGATCACCAGGAGTAATAA 61.218 48.000 17.84 0.00 46.79 1.40
2116 2411 4.751964 CCCGGTAGATCACCAGGAGTAATA 60.752 50.000 17.84 0.00 46.79 0.98
2117 2412 4.008406 CCCGGTAGATCACCAGGAGTAAT 61.008 52.174 17.84 0.00 46.79 1.89
2118 2413 2.688817 CCCGGTAGATCACCAGGAGTAA 60.689 54.545 17.84 0.00 46.79 2.24
2119 2414 1.133575 CCCGGTAGATCACCAGGAGTA 60.134 57.143 17.84 0.00 46.79 2.59
2120 2415 0.397254 CCCGGTAGATCACCAGGAGT 60.397 60.000 17.84 0.00 46.79 3.85
2256 2552 5.332743 AGAACCTTCCTGCCAAATGAATTA 58.667 37.500 0.00 0.00 0.00 1.40
2311 2923 2.159448 CGTGACAAACAAACAAGCCTGA 60.159 45.455 0.00 0.00 0.00 3.86
2347 2959 2.429610 TGAGCTCCCGACTAATACAACC 59.570 50.000 12.15 0.00 0.00 3.77
2377 2989 0.780002 TCTTTCGTAGCGCGTTGTTC 59.220 50.000 8.43 0.00 42.13 3.18
2399 3011 1.813192 CTCCCGAACAGGAGCTCTC 59.187 63.158 14.64 3.76 46.76 3.20
2400 3012 4.026300 CTCCCGAACAGGAGCTCT 57.974 61.111 14.64 0.00 46.76 4.09
2405 3017 0.683504 GTAGGAGCTCCCGAACAGGA 60.684 60.000 29.54 1.74 45.00 3.86
2406 3018 0.684805 AGTAGGAGCTCCCGAACAGG 60.685 60.000 29.54 0.00 40.87 4.00
2407 3019 0.741915 GAGTAGGAGCTCCCGAACAG 59.258 60.000 29.54 0.00 40.87 3.16
2408 3020 1.030488 CGAGTAGGAGCTCCCGAACA 61.030 60.000 29.54 6.82 40.87 3.18
2409 3021 1.728672 CGAGTAGGAGCTCCCGAAC 59.271 63.158 29.54 23.11 40.87 3.95
2622 3238 5.531659 TGCCACTATCGTTGGTTTCTTTAAA 59.468 36.000 0.00 0.00 0.00 1.52
2752 3369 6.472887 ACATAGACTCTCAGGAGCTATAGTC 58.527 44.000 0.84 7.45 42.98 2.59
2768 3385 3.652055 AGCTCCCATTGAGACATAGACT 58.348 45.455 0.00 0.00 44.42 3.24
2912 3563 9.743057 TTCATAAATTCAGAAAAATGTTCGTGT 57.257 25.926 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.