Multiple sequence alignment - TraesCS1B01G222800

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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 TraesCS1B01G222800 chr1B 100.000 3547 0 0 1 3547 400419224 400415678 0.000000e+00 6551
1 TraesCS1B01G222800 chr1B 95.006 3384 125 20 2 3354 98650893 98654263 0.000000e+00 5273
2 TraesCS1B01G222800 chr1B 94.220 3391 141 19 2 3362 91432992 91429627 0.000000e+00 5125
3 TraesCS1B01G222800 chr1B 94.615 2804 132 5 452 3237 554927324 554930126 0.000000e+00 4324
4 TraesCS1B01G222800 chr1B 95.038 524 25 1 2 525 21723444 21722922 0.000000e+00 822
5 TraesCS1B01G222800 chr1B 94.724 398 18 2 3153 3547 98654101 98654498 1.810000e-172 616
6 TraesCS1B01G222800 chr1B 94.221 398 20 2 3153 3547 91429797 91429400 3.920000e-169 604
7 TraesCS1B01G222800 chr1B 92.911 395 23 3 3153 3547 613851050 613850661 1.430000e-158 569
8 TraesCS1B01G222800 chr2B 94.797 3575 153 11 2 3545 764626615 764630187 0.000000e+00 5541
9 TraesCS1B01G222800 chr2B 94.743 3367 144 15 2 3355 635824957 635828303 0.000000e+00 5206
10 TraesCS1B01G222800 chr2B 93.899 2852 155 8 452 3289 177298504 177295658 0.000000e+00 4285
11 TraesCS1B01G222800 chr2B 94.656 524 27 1 2 525 120664705 120665227 0.000000e+00 811
12 TraesCS1B01G222800 chr2B 92.932 382 26 1 3166 3547 635828156 635828536 4.000000e-154 555
13 TraesCS1B01G222800 chr2B 91.228 399 23 6 3159 3547 488089586 488089190 1.870000e-147 532
14 TraesCS1B01G222800 chr2B 90.609 394 34 1 3153 3546 775288707 775289097 1.460000e-143 520
15 TraesCS1B01G222800 chr2B 88.384 396 32 10 3153 3547 671840714 671841096 6.940000e-127 464
16 TraesCS1B01G222800 chr5B 95.641 3395 115 9 2 3365 419024693 419021301 0.000000e+00 5419
17 TraesCS1B01G222800 chr5B 94.993 2796 116 7 452 3237 92758939 92756158 0.000000e+00 4366
18 TraesCS1B01G222800 chr5B 94.923 2797 127 5 452 3237 230939116 230936324 0.000000e+00 4364
19 TraesCS1B01G222800 chr5B 91.414 396 27 4 3153 3547 584466583 584466194 1.450000e-148 536
20 TraesCS1B01G222800 chr6B 95.193 3391 123 16 2 3362 692886319 692882939 0.000000e+00 5323
21 TraesCS1B01G222800 chr4B 95.422 2796 117 4 452 3237 127610345 127607551 0.000000e+00 4444
22 TraesCS1B01G222800 chr4B 96.026 453 18 0 2 454 16598160 16597708 0.000000e+00 737
23 TraesCS1B01G222800 chr3B 94.594 2830 142 4 452 3270 746729923 746732752 0.000000e+00 4368
24 TraesCS1B01G222800 chr3B 93.214 2859 155 20 452 3293 729277506 729274670 0.000000e+00 4169
25 TraesCS1B01G222800 chr3B 94.177 395 18 4 3153 3547 729274578 729274189 6.550000e-167 597
26 TraesCS1B01G222800 chr7B 94.707 2796 138 3 452 3237 529760370 529763165 0.000000e+00 4335
27 TraesCS1B01G222800 chr4A 94.244 2832 147 5 452 3270 656384212 656381384 0.000000e+00 4313
28 TraesCS1B01G222800 chr4A 94.361 1667 84 5 452 2108 656176697 656175031 0.000000e+00 2549
29 TraesCS1B01G222800 chr2A 86.637 2013 215 30 452 2440 338675773 338673791 0.000000e+00 2178


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 TraesCS1B01G222800 chr1B 400415678 400419224 3546 True 6551.0 6551 100.0000 1 3547 1 chr1B.!!$R2 3546
1 TraesCS1B01G222800 chr1B 554927324 554930126 2802 False 4324.0 4324 94.6150 452 3237 1 chr1B.!!$F1 2785
2 TraesCS1B01G222800 chr1B 98650893 98654498 3605 False 2944.5 5273 94.8650 2 3547 2 chr1B.!!$F2 3545
3 TraesCS1B01G222800 chr1B 91429400 91432992 3592 True 2864.5 5125 94.2205 2 3547 2 chr1B.!!$R4 3545
4 TraesCS1B01G222800 chr1B 21722922 21723444 522 True 822.0 822 95.0380 2 525 1 chr1B.!!$R1 523
5 TraesCS1B01G222800 chr2B 764626615 764630187 3572 False 5541.0 5541 94.7970 2 3545 1 chr2B.!!$F3 3543
6 TraesCS1B01G222800 chr2B 177295658 177298504 2846 True 4285.0 4285 93.8990 452 3289 1 chr2B.!!$R1 2837
7 TraesCS1B01G222800 chr2B 635824957 635828536 3579 False 2880.5 5206 93.8375 2 3547 2 chr2B.!!$F5 3545
8 TraesCS1B01G222800 chr2B 120664705 120665227 522 False 811.0 811 94.6560 2 525 1 chr2B.!!$F1 523
9 TraesCS1B01G222800 chr5B 419021301 419024693 3392 True 5419.0 5419 95.6410 2 3365 1 chr5B.!!$R3 3363
10 TraesCS1B01G222800 chr5B 92756158 92758939 2781 True 4366.0 4366 94.9930 452 3237 1 chr5B.!!$R1 2785
11 TraesCS1B01G222800 chr5B 230936324 230939116 2792 True 4364.0 4364 94.9230 452 3237 1 chr5B.!!$R2 2785
12 TraesCS1B01G222800 chr6B 692882939 692886319 3380 True 5323.0 5323 95.1930 2 3362 1 chr6B.!!$R1 3360
13 TraesCS1B01G222800 chr4B 127607551 127610345 2794 True 4444.0 4444 95.4220 452 3237 1 chr4B.!!$R2 2785
14 TraesCS1B01G222800 chr3B 746729923 746732752 2829 False 4368.0 4368 94.5940 452 3270 1 chr3B.!!$F1 2818
15 TraesCS1B01G222800 chr3B 729274189 729277506 3317 True 2383.0 4169 93.6955 452 3547 2 chr3B.!!$R1 3095
16 TraesCS1B01G222800 chr7B 529760370 529763165 2795 False 4335.0 4335 94.7070 452 3237 1 chr7B.!!$F1 2785
17 TraesCS1B01G222800 chr4A 656381384 656384212 2828 True 4313.0 4313 94.2440 452 3270 1 chr4A.!!$R2 2818
18 TraesCS1B01G222800 chr4A 656175031 656176697 1666 True 2549.0 2549 94.3610 452 2108 1 chr4A.!!$R1 1656
19 TraesCS1B01G222800 chr2A 338673791 338675773 1982 True 2178.0 2178 86.6370 452 2440 1 chr2A.!!$R1 1988


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
128 129 0.108520 TTAGAATCACGTCCGTGCCC 60.109 55.0 14.64 6.43 45.04 5.36 F
1404 1427 0.037326 TGTCGGAGTTGATGTGGAGC 60.037 55.0 0.00 0.00 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1426 1449 0.670854 GACGAGGGCTGGTTTCTGAC 60.671 60.0 0.00 0.0 0.00 3.51 R
3060 3119 0.528924 CGTATGTGGAGTCCAACCGA 59.471 55.0 15.09 0.0 34.18 4.69 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
128 129 0.108520 TTAGAATCACGTCCGTGCCC 60.109 55.000 14.64 6.43 45.04 5.36
339 340 5.838531 AACATTCCGGAAAAACAGTAACA 57.161 34.783 23.08 0.00 0.00 2.41
691 692 3.068307 GTCCATCTGGTAGCGTCTATTGT 59.932 47.826 0.00 0.00 36.34 2.71
715 716 1.095228 CGGACACACAACAGTGCCTT 61.095 55.000 0.00 0.00 43.23 4.35
1081 1092 1.616159 AACCACGATCCAAAACCCAG 58.384 50.000 0.00 0.00 0.00 4.45
1383 1401 2.187946 CCTCGAATTGGAGCGCCT 59.812 61.111 11.70 0.00 32.57 5.52
1404 1427 0.037326 TGTCGGAGTTGATGTGGAGC 60.037 55.000 0.00 0.00 0.00 4.70
1426 1449 2.637025 CAACGACGTTGGCCAAGG 59.363 61.111 31.42 31.42 39.56 3.61
1488 1511 0.036732 TCCGGTGCTGCTCTTTCAAT 59.963 50.000 0.00 0.00 0.00 2.57
1610 1633 0.462047 GCCACGTCGGATTGGAGATT 60.462 55.000 11.67 0.00 36.56 2.40
1858 1882 1.219522 CTTCGTCGGGCAAAACTCGT 61.220 55.000 0.00 0.00 0.00 4.18
1993 2018 8.853077 TCTCATTAGATTTGCTTTCTCTCAAA 57.147 30.769 0.00 0.00 36.72 2.69
2303 2338 4.123506 TGAAAACGTGTGAATGACAGCTA 58.876 39.130 0.00 0.00 34.28 3.32
2304 2356 4.572795 TGAAAACGTGTGAATGACAGCTAA 59.427 37.500 0.00 0.00 34.28 3.09
2393 2445 2.741092 GTCCGTGCCTCCAGTTCA 59.259 61.111 0.00 0.00 0.00 3.18
2562 2614 9.866655 AAATCTCTAGAATAAAATATGTGCCCA 57.133 29.630 0.00 0.00 0.00 5.36
2591 2648 7.790000 TGAGACGTTTATTTTGTACTACTTGC 58.210 34.615 0.00 0.00 0.00 4.01
2851 2909 4.024387 GCTTGACATGGAAACGAAACTGTA 60.024 41.667 0.00 0.00 0.00 2.74
2947 3006 1.742880 CACTACTCCCCGTCGTCGA 60.743 63.158 2.98 0.00 39.71 4.20
3018 3077 2.755876 TCCGCATCCAGCTCGTCT 60.756 61.111 0.00 0.00 42.61 4.18
3110 3169 0.833834 ATGGACTCCAGGATAGCGGG 60.834 60.000 3.62 0.00 36.75 6.13
3150 3209 3.199677 CGACTCACCGAGATAGAACTCT 58.800 50.000 0.00 0.00 35.06 3.24
3217 3447 2.892425 CGTCCATGCCTTCCTCGC 60.892 66.667 0.00 0.00 0.00 5.03
3497 3898 2.554636 CCTGCAACTGAAAGCGGCA 61.555 57.895 1.45 0.00 42.88 5.69
3531 3932 6.309712 AGCATCGCGTAAGTAGTTATCTTA 57.690 37.500 5.77 0.00 41.68 2.10
3534 3935 6.581542 GCATCGCGTAAGTAGTTATCTTATGT 59.418 38.462 5.77 0.00 36.99 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.538287 GGGGCCATGGCTTATGAGTC 60.538 60.000 34.70 16.14 39.21 3.36
339 340 2.766263 TGAGGATTGACAATAGGCGTCT 59.234 45.455 0.00 0.00 34.37 4.18
691 692 2.272678 CACTGTTGTGTGTCCGTGTTA 58.727 47.619 0.00 0.00 39.24 2.41
715 716 3.128589 GGAGCAGTGTTGTGTTTCTTCAA 59.871 43.478 0.00 0.00 0.00 2.69
1383 1401 2.766313 CTCCACATCAACTCCGACAAA 58.234 47.619 0.00 0.00 0.00 2.83
1426 1449 0.670854 GACGAGGGCTGGTTTCTGAC 60.671 60.000 0.00 0.00 0.00 3.51
1858 1882 1.271054 GCTTCCTGGTCTGCTTCTTGA 60.271 52.381 0.00 0.00 0.00 3.02
1993 2018 8.751302 AAATTTGTAACAAGAAAACGACAGTT 57.249 26.923 0.00 0.00 43.50 3.16
2303 2338 3.500343 AGGTGTGCCTCTGCTTTAAATT 58.500 40.909 0.00 0.00 42.67 1.82
2304 2356 3.160679 AGGTGTGCCTCTGCTTTAAAT 57.839 42.857 0.00 0.00 42.67 1.40
2393 2445 1.542915 ACGTAGAGGCACACACGTAAT 59.457 47.619 11.66 0.00 45.04 1.89
2519 2571 9.653287 CTAGAGATTTCAGTGTGGTTACATTTA 57.347 33.333 0.00 0.00 39.39 1.40
2524 2576 9.871238 TTATTCTAGAGATTTCAGTGTGGTTAC 57.129 33.333 0.00 0.00 0.00 2.50
2562 2614 9.538508 AGTAGTACAAAATAAACGTCTCAACTT 57.461 29.630 2.52 0.00 0.00 2.66
2851 2909 5.301045 AGCAATCATCGATGTCAAAATGGAT 59.699 36.000 24.09 4.42 0.00 3.41
2947 3006 7.345653 TGTTAGAATGGAGATAGTGGACATCTT 59.654 37.037 0.00 0.00 32.86 2.40
3018 3077 4.037327 CAGGTGAAGATCGATGCTCTCTTA 59.963 45.833 0.54 0.00 29.64 2.10
3031 3090 3.251484 TCCAGGAAGAACAGGTGAAGAT 58.749 45.455 0.00 0.00 0.00 2.40
3060 3119 0.528924 CGTATGTGGAGTCCAACCGA 59.471 55.000 15.09 0.00 34.18 4.69
3150 3209 0.624254 TAGACGAGGAAGAGGAGGCA 59.376 55.000 0.00 0.00 0.00 4.75
3217 3447 1.448922 GACGAGGATGAGGAGGACGG 61.449 65.000 0.00 0.00 0.00 4.79
3497 3898 1.437986 GCGATGCTTACTCCCGAGT 59.562 57.895 2.41 2.41 45.02 4.18



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

AutoCloner maintained by Alex Coulton.