Multiple sequence alignment - TraesCS1B01G208000

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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 TraesCS1B01G208000 chr1B 100.000 4082 0 0 1 4082 376070131 376074212 0.000000e+00 7539.0
1 TraesCS1B01G208000 chr1B 94.737 38 0 2 44 81 376055614 376055649 1.580000e-04 58.4
2 TraesCS1B01G208000 chr1D 95.884 3669 88 28 452 4082 277092326 277095969 0.000000e+00 5880.0
3 TraesCS1B01G208000 chr1D 90.400 500 36 9 1 492 277091834 277092329 0.000000e+00 647.0
4 TraesCS1B01G208000 chr1A 95.142 2985 78 23 1154 4082 349358923 349361896 0.000000e+00 4647.0
5 TraesCS1B01G208000 chr1A 88.868 1078 90 15 1 1050 349357439 349358514 0.000000e+00 1299.0
6 TraesCS1B01G208000 chr3D 91.371 197 17 0 2486 2682 355319164 355318968 1.870000e-68 270.0
7 TraesCS1B01G208000 chr3D 89.781 137 9 4 318 449 313908606 313908742 1.950000e-38 171.0
8 TraesCS1B01G208000 chr3D 84.211 171 17 6 303 464 104025897 104026066 1.520000e-34 158.0
9 TraesCS1B01G208000 chr3B 91.371 197 17 0 2486 2682 456323865 456323669 1.870000e-68 270.0
10 TraesCS1B01G208000 chr3B 92.063 189 15 0 2486 2674 463204071 463204259 2.420000e-67 267.0
11 TraesCS1B01G208000 chr3A 90.909 187 17 0 2496 2682 474209620 474209434 6.770000e-63 252.0
12 TraesCS1B01G208000 chr5A 88.125 160 8 5 318 466 322584168 322584009 3.240000e-41 180.0
13 TraesCS1B01G208000 chr7B 88.435 147 11 5 309 449 627977207 627977353 5.420000e-39 172.0
14 TraesCS1B01G208000 chr4A 86.420 162 16 5 309 464 651826333 651826172 5.420000e-39 172.0
15 TraesCS1B01G208000 chr5B 88.732 142 10 5 313 449 417444086 417443946 7.020000e-38 169.0
16 TraesCS1B01G208000 chr2B 84.795 171 16 5 310 471 590855789 590855620 3.260000e-36 163.0
17 TraesCS1B01G208000 chr2B 86.905 84 11 0 1670 1753 788803903 788803820 1.210000e-15 95.3
18 TraesCS1B01G208000 chr2D 100.000 29 0 0 2550 2578 477238249 477238277 2.000000e-03 54.7


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 TraesCS1B01G208000 chr1B 376070131 376074212 4081 False 7539.0 7539 100.000 1 4082 1 chr1B.!!$F2 4081
1 TraesCS1B01G208000 chr1D 277091834 277095969 4135 False 3263.5 5880 93.142 1 4082 2 chr1D.!!$F1 4081
2 TraesCS1B01G208000 chr1A 349357439 349361896 4457 False 2973.0 4647 92.005 1 4082 2 chr1A.!!$F1 4081

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
689 747 0.034616 CCAAAATTCGGGCAGCCAAA 59.965 50.0 15.19 7.41 0.00 3.28 F
920 982 0.921256 CCCACCTTTCCCATCTCCCT 60.921 60.0 0.00 0.00 0.00 4.20 F
1809 2195 1.264749 CCGGGGACATGAAGGAGTCA 61.265 60.0 0.00 0.00 41.67 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2402 1.526917 GTTGTGCTGGTGCTGGAGT 60.527 57.895 0.00 0.0 40.48 3.85 R
3006 3398 1.139947 GAGCTGGTCCTGCGAGTAC 59.860 63.158 14.44 3.0 33.59 2.73 R
3479 3912 0.667487 CGCTCTGCCAAGACGAGAAA 60.667 55.000 0.00 0.0 32.26 2.52 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
26 27 5.056480 TGCACTCCGATCGATTTATTCATT 58.944 37.500 18.66 0.00 0.00 2.57
163 164 8.506168 AGGACGTCATAAATGTGAATTAACAT 57.494 30.769 18.91 2.22 42.62 2.71
181 182 2.919602 ACATGACCCAAAGATACCACCT 59.080 45.455 0.00 0.00 0.00 4.00
189 190 6.741724 ACCCAAAGATACCACCTTCATTTAT 58.258 36.000 0.00 0.00 0.00 1.40
227 228 3.244561 ACGGTCACATGTTCTGGATCTTT 60.245 43.478 0.00 0.00 0.00 2.52
254 255 3.864789 CCCCCTATGCTTACAGTGAAT 57.135 47.619 0.00 0.00 0.00 2.57
255 256 4.974645 CCCCCTATGCTTACAGTGAATA 57.025 45.455 0.00 0.00 0.00 1.75
316 317 5.398603 TGGGTCGTGATTGCAAAATAATT 57.601 34.783 1.71 0.00 0.00 1.40
423 436 5.571741 CACTCATTTTGTCGTATGTAGTCGT 59.428 40.000 0.00 0.00 0.00 4.34
430 443 6.874297 TTGTCGTATGTAGTCGTTTATTGG 57.126 37.500 0.00 0.00 0.00 3.16
434 447 8.404765 TGTCGTATGTAGTCGTTTATTGGAATA 58.595 33.333 0.00 0.00 0.00 1.75
493 510 9.406828 GTTTGAGGGACACATAATTAAAAAGAC 57.593 33.333 0.00 0.00 0.00 3.01
611 669 8.364894 GGCTAAATCCGATTAATGGGTTAAATT 58.635 33.333 15.30 5.98 33.76 1.82
689 747 0.034616 CCAAAATTCGGGCAGCCAAA 59.965 50.000 15.19 7.41 0.00 3.28
920 982 0.921256 CCCACCTTTCCCATCTCCCT 60.921 60.000 0.00 0.00 0.00 4.20
981 1056 3.711782 CCTTCCTCCCCCTCCCCT 61.712 72.222 0.00 0.00 0.00 4.79
1074 1155 4.424711 GACATGCCGGCCTTCCCA 62.425 66.667 26.77 3.54 0.00 4.37
1152 1233 2.974148 CAGGACACGCTGCAGCAA 60.974 61.111 36.03 0.00 42.21 3.91
1809 2195 1.264749 CCGGGGACATGAAGGAGTCA 61.265 60.000 0.00 0.00 41.67 3.41
1917 2303 3.322466 ACGGAGAACCCCAGCCTG 61.322 66.667 0.00 0.00 0.00 4.85
3006 3398 3.995506 GAAGATGGCCACCCGGGTG 62.996 68.421 41.60 41.60 45.02 4.61
3012 3404 4.446413 GCCACCCGGGTGTACTCG 62.446 72.222 43.47 31.39 44.02 4.18
3085 3477 2.226437 GCGATGCAAATCCGGTAATGAT 59.774 45.455 0.00 0.00 0.00 2.45
3091 3483 4.213270 TGCAAATCCGGTAATGATCGAATC 59.787 41.667 0.00 0.00 0.00 2.52
3097 3489 3.055819 CCGGTAATGATCGAATCCCATCT 60.056 47.826 0.00 0.00 0.00 2.90
3113 3505 3.322254 CCCATCTACCAGGTAGTAGCAAG 59.678 52.174 23.79 9.73 39.71 4.01
3121 3513 1.066358 AGGTAGTAGCAAGGAAACCGC 60.066 52.381 1.58 0.00 32.18 5.68
3183 3578 0.731855 GCCGTCGTTATAGCCCGATC 60.732 60.000 0.00 0.00 35.30 3.69
3215 3611 1.135083 GGAGAAAGAAGGCGACGATCA 60.135 52.381 0.00 0.00 0.00 2.92
3256 3660 1.661463 TAGGAGGATGGATGGATGGC 58.339 55.000 0.00 0.00 0.00 4.40
3366 3794 2.670939 TCTCATGACCCTGTGATCGAT 58.329 47.619 0.00 0.00 0.00 3.59
3404 3832 2.033236 CGTAGCGCTGTTGAACTGAAAA 60.033 45.455 22.90 0.00 0.00 2.29
3454 3882 0.323957 GCCGTTCTCCCCTAGTGTTT 59.676 55.000 0.00 0.00 0.00 2.83
3455 3883 1.944430 GCCGTTCTCCCCTAGTGTTTG 60.944 57.143 0.00 0.00 0.00 2.93
3462 3895 2.293399 CTCCCCTAGTGTTTGTTGTTGC 59.707 50.000 0.00 0.00 0.00 4.17
3539 3976 5.477510 TGGTATCGCTTGCAAAATGAAATT 58.522 33.333 0.00 0.00 38.98 1.82
3578 4015 8.487313 TTTTTATCTGCTCGTATGCTCTTAAA 57.513 30.769 0.00 0.00 0.00 1.52
3579 4016 8.662781 TTTTATCTGCTCGTATGCTCTTAAAT 57.337 30.769 0.00 0.00 0.00 1.40
3580 4017 7.875316 TTATCTGCTCGTATGCTCTTAAATC 57.125 36.000 0.00 0.00 0.00 2.17
3581 4018 5.521906 TCTGCTCGTATGCTCTTAAATCT 57.478 39.130 0.00 0.00 0.00 2.40
3602 4039 6.564709 TCTTTGATTGTGTTCTCATCTTGG 57.435 37.500 0.00 0.00 0.00 3.61
3719 4156 2.962421 AGAAGAGAAGGATTAGCGAGGG 59.038 50.000 0.00 0.00 0.00 4.30
3720 4157 2.757894 AGAGAAGGATTAGCGAGGGA 57.242 50.000 0.00 0.00 0.00 4.20
3721 4158 2.593026 AGAGAAGGATTAGCGAGGGAG 58.407 52.381 0.00 0.00 0.00 4.30
3722 4159 1.616374 GAGAAGGATTAGCGAGGGAGG 59.384 57.143 0.00 0.00 0.00 4.30
3723 4160 1.218196 AGAAGGATTAGCGAGGGAGGA 59.782 52.381 0.00 0.00 0.00 3.71
3724 4161 1.341852 GAAGGATTAGCGAGGGAGGAC 59.658 57.143 0.00 0.00 0.00 3.85
3730 4181 2.285889 TAGCGAGGGAGGACAGGAGG 62.286 65.000 0.00 0.00 0.00 4.30
3778 4229 4.986622 GCTCTTGGCATAACAAAAGGTAG 58.013 43.478 0.00 0.00 41.35 3.18
3822 4274 0.250727 CCGTCCTTCTTTGGCAAGGA 60.251 55.000 8.09 8.09 46.05 3.36
3846 4305 3.373830 AGAAGAGAAGTGGATGAGGAGG 58.626 50.000 0.00 0.00 0.00 4.30
3847 4306 3.012274 AGAAGAGAAGTGGATGAGGAGGA 59.988 47.826 0.00 0.00 0.00 3.71
3848 4307 3.030873 AGAGAAGTGGATGAGGAGGAG 57.969 52.381 0.00 0.00 0.00 3.69
3849 4308 1.412343 GAGAAGTGGATGAGGAGGAGC 59.588 57.143 0.00 0.00 0.00 4.70
3927 4386 1.734477 CGAACCAGGCAGACAGACG 60.734 63.158 0.00 0.00 0.00 4.18
3929 4388 0.667792 GAACCAGGCAGACAGACGTC 60.668 60.000 7.70 7.70 42.95 4.34
4008 4467 1.068281 CCACCTGATCCATGTCGAGAG 59.932 57.143 0.00 0.00 0.00 3.20
4032 4491 3.672241 CGCCTAATTTTGTTGTACCCTGC 60.672 47.826 0.00 0.00 0.00 4.85
4035 4494 5.469479 CCTAATTTTGTTGTACCCTGCTTG 58.531 41.667 0.00 0.00 0.00 4.01
4036 4495 2.880963 TTTTGTTGTACCCTGCTTGC 57.119 45.000 0.00 0.00 0.00 4.01
4039 4498 1.317613 TGTTGTACCCTGCTTGCTTG 58.682 50.000 0.00 0.00 0.00 4.01
4056 4515 3.999663 TGCTTGTTTGTTTGTTTTCCAGG 59.000 39.130 0.00 0.00 0.00 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 9.663904 ATTAAACACAATGAATAAATCGATCGG 57.336 29.630 16.41 0.00 0.00 4.18
26 27 4.902443 TTCTGGCAACGAATTAAACACA 57.098 36.364 0.00 0.00 42.51 3.72
39 40 3.118482 TGCACTTTCCAAATTTCTGGCAA 60.118 39.130 0.00 0.00 36.32 4.52
117 118 0.108138 AGCTGGTACGCAGTGATTCC 60.108 55.000 11.47 0.00 45.73 3.01
163 164 2.983192 TGAAGGTGGTATCTTTGGGTCA 59.017 45.455 0.00 0.00 0.00 4.02
196 197 6.293955 CCAGAACATGTGACCGTTAGATTTTT 60.294 38.462 0.00 0.00 0.00 1.94
199 200 4.020573 TCCAGAACATGTGACCGTTAGATT 60.021 41.667 0.00 0.00 0.00 2.40
216 217 3.551259 GGCGACCAAAGATCCAGAA 57.449 52.632 0.00 0.00 0.00 3.02
254 255 5.011227 GGGGAACAAGGTAAACAAGCAAATA 59.989 40.000 0.00 0.00 0.00 1.40
255 256 4.202315 GGGGAACAAGGTAAACAAGCAAAT 60.202 41.667 0.00 0.00 0.00 2.32
294 295 5.398603 AATTATTTTGCAATCACGACCCA 57.601 34.783 0.00 0.00 0.00 4.51
296 297 5.650543 AGGAATTATTTTGCAATCACGACC 58.349 37.500 0.00 0.00 0.00 4.79
395 403 8.547967 ACTACATACGACAAAATGAGTGAATT 57.452 30.769 0.00 0.00 0.00 2.17
410 421 9.616634 GATATTCCAATAAACGACTACATACGA 57.383 33.333 0.00 0.00 0.00 3.43
411 422 9.622004 AGATATTCCAATAAACGACTACATACG 57.378 33.333 0.00 0.00 0.00 3.06
430 443 9.813446 TCCGTTCCTAAGTCTTTTTAGATATTC 57.187 33.333 0.00 0.00 33.42 1.75
434 447 6.351966 CCCTCCGTTCCTAAGTCTTTTTAGAT 60.352 42.308 0.00 0.00 33.42 1.98
493 510 6.432783 TGGGGTTTATCTGTGTAAATGAGTTG 59.567 38.462 0.00 0.00 0.00 3.16
611 669 2.813726 CCCGGGTTGTCAGTGACCA 61.814 63.158 20.43 6.90 37.68 4.02
636 694 0.259065 TCGTAGCCTCCTGTCTGGAT 59.741 55.000 0.00 0.00 45.16 3.41
639 697 0.888619 TGTTCGTAGCCTCCTGTCTG 59.111 55.000 0.00 0.00 0.00 3.51
689 747 3.443145 TCTTCTCTCTTTCCTCCTCGT 57.557 47.619 0.00 0.00 0.00 4.18
920 982 4.075793 CGGGGGAGGGTGGAGAGA 62.076 72.222 0.00 0.00 0.00 3.10
949 1024 1.522900 GAAGGGGAATGGATGGGAGA 58.477 55.000 0.00 0.00 0.00 3.71
2010 2402 1.526917 GTTGTGCTGGTGCTGGAGT 60.527 57.895 0.00 0.00 40.48 3.85
3006 3398 1.139947 GAGCTGGTCCTGCGAGTAC 59.860 63.158 14.44 3.00 33.59 2.73
3012 3404 3.426568 GCGTTGAGCTGGTCCTGC 61.427 66.667 12.66 12.66 44.04 4.85
3085 3477 2.471815 ACCTGGTAGATGGGATTCGA 57.528 50.000 0.00 0.00 0.00 3.71
3091 3483 2.958818 TGCTACTACCTGGTAGATGGG 58.041 52.381 34.43 21.61 40.98 4.00
3097 3489 3.516700 GGTTTCCTTGCTACTACCTGGTA 59.483 47.826 6.36 6.36 0.00 3.25
3113 3505 3.243636 TGAGTAATAGGATCGCGGTTTCC 60.244 47.826 6.13 10.93 0.00 3.13
3121 3513 2.621998 ACGGTGGTGAGTAATAGGATCG 59.378 50.000 0.00 0.00 0.00 3.69
3183 3578 3.699779 TCTTTCTCCATCTCGATGTCG 57.300 47.619 6.20 0.00 37.11 4.35
3215 3611 9.793259 TCCTAAAGAGAGATTTTACAACAACAT 57.207 29.630 0.00 0.00 0.00 2.71
3256 3660 5.468746 TGATGATGATGATGTACACATGCAG 59.531 40.000 13.42 0.00 36.57 4.41
3371 3799 3.401577 CGCTACGCCGATACATCAT 57.598 52.632 0.00 0.00 0.00 2.45
3404 3832 7.831193 GGCAATCCATCTTTGTCCTATATACAT 59.169 37.037 0.00 0.00 0.00 2.29
3445 3873 2.096819 ACACGCAACAACAAACACTAGG 59.903 45.455 0.00 0.00 0.00 3.02
3454 3882 1.665448 GCATGCATACACGCAACAACA 60.665 47.619 14.21 0.00 46.87 3.33
3455 3883 0.984109 GCATGCATACACGCAACAAC 59.016 50.000 14.21 0.00 46.87 3.32
3462 3895 2.030823 AGAAACGATGCATGCATACACG 59.969 45.455 32.27 30.06 36.70 4.49
3479 3912 0.667487 CGCTCTGCCAAGACGAGAAA 60.667 55.000 0.00 0.00 32.26 2.52
3576 4013 8.086522 CCAAGATGAGAACACAATCAAAGATTT 58.913 33.333 0.00 0.00 0.00 2.17
3577 4014 7.309621 CCCAAGATGAGAACACAATCAAAGATT 60.310 37.037 0.00 0.00 0.00 2.40
3578 4015 6.152323 CCCAAGATGAGAACACAATCAAAGAT 59.848 38.462 0.00 0.00 0.00 2.40
3579 4016 5.474532 CCCAAGATGAGAACACAATCAAAGA 59.525 40.000 0.00 0.00 0.00 2.52
3580 4017 5.706916 CCCAAGATGAGAACACAATCAAAG 58.293 41.667 0.00 0.00 0.00 2.77
3581 4018 4.022068 GCCCAAGATGAGAACACAATCAAA 60.022 41.667 0.00 0.00 0.00 2.69
3602 4039 2.087646 CCTTCTCTTAGCCAAGTTGCC 58.912 52.381 0.00 0.00 33.20 4.52
3719 4156 1.075600 CCTCTCCCCTCCTGTCCTC 60.076 68.421 0.00 0.00 0.00 3.71
3720 4157 3.114390 CCTCTCCCCTCCTGTCCT 58.886 66.667 0.00 0.00 0.00 3.85
3721 4158 2.766229 GCCTCTCCCCTCCTGTCC 60.766 72.222 0.00 0.00 0.00 4.02
3722 4159 1.201429 TTTGCCTCTCCCCTCCTGTC 61.201 60.000 0.00 0.00 0.00 3.51
3723 4160 1.151810 TTTGCCTCTCCCCTCCTGT 60.152 57.895 0.00 0.00 0.00 4.00
3724 4161 1.606531 CTTTGCCTCTCCCCTCCTG 59.393 63.158 0.00 0.00 0.00 3.86
3730 4181 1.301677 CGTCTTGCTTTGCCTCTCCC 61.302 60.000 0.00 0.00 0.00 4.30
3778 4229 3.471806 GGGTTCCCCTCTCCTCGC 61.472 72.222 0.00 0.00 41.34 5.03
3812 4264 4.141390 ACTTCTCTTCTTCTCCTTGCCAAA 60.141 41.667 0.00 0.00 0.00 3.28
3822 4274 4.682563 TCCTCATCCACTTCTCTTCTTCT 58.317 43.478 0.00 0.00 0.00 2.85
3823 4275 4.141959 CCTCCTCATCCACTTCTCTTCTTC 60.142 50.000 0.00 0.00 0.00 2.87
3824 4276 3.774216 CCTCCTCATCCACTTCTCTTCTT 59.226 47.826 0.00 0.00 0.00 2.52
3849 4308 4.075793 TGTCCCCTCCCTCCCTCG 62.076 72.222 0.00 0.00 0.00 4.63
3929 4388 3.793144 GCCTTCTTGTCGCCAGCG 61.793 66.667 5.50 5.50 41.35 5.18
3931 4390 2.037136 CCTGCCTTCTTGTCGCCAG 61.037 63.158 0.00 0.00 0.00 4.85
3960 4419 3.397439 ATGTGGAGAGGCAGCGCT 61.397 61.111 2.64 2.64 0.00 5.92
4008 4467 3.754850 AGGGTACAACAAAATTAGGCGAC 59.245 43.478 0.00 0.00 0.00 5.19
4032 4491 5.390779 CCTGGAAAACAAACAAACAAGCAAG 60.391 40.000 0.00 0.00 0.00 4.01
4035 4494 4.000325 ACCTGGAAAACAAACAAACAAGC 59.000 39.130 0.00 0.00 0.00 4.01
4036 4495 7.841915 ATTACCTGGAAAACAAACAAACAAG 57.158 32.000 0.00 0.00 0.00 3.16
4056 4515 6.673154 ACCGCCTGTGAAAACTTATATTAC 57.327 37.500 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.