Multiple sequence alignment - TraesCS7B01G477500

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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 TraesCS7B01G477500 chr7B 100.000 3494 0 0 1 3494 733218173 733214680 0.000000e+00 6453
1 TraesCS7B01G477500 chr7B 92.697 3341 167 43 1 3291 712607591 712610904 0.000000e+00 4747
2 TraesCS7B01G477500 chr7B 90.959 1272 64 33 2267 3494 712609874 712611138 0.000000e+00 1664
3 TraesCS7B01G477500 chr1B 97.061 3505 80 16 1 3494 621586893 621583401 0.000000e+00 5880
4 TraesCS7B01G477500 chr4B 92.970 3343 156 44 1 3294 638493811 638490499 0.000000e+00 4798
5 TraesCS7B01G477500 chr4B 90.859 1269 65 29 2267 3494 638491528 638490270 0.000000e+00 1653
6 TraesCS7B01G477500 chr3B 97.634 2071 43 5 1 2068 18008164 18006097 0.000000e+00 3548
7 TraesCS7B01G477500 chr7D 85.176 2678 283 78 652 3280 108301241 108298629 0.000000e+00 2641
8 TraesCS7B01G477500 chr7D 85.187 2680 277 81 652 3280 21681043 21678433 0.000000e+00 2639
9 TraesCS7B01G477500 chr7D 84.931 2681 289 76 652 3280 108264316 108261699 0.000000e+00 2606
10 TraesCS7B01G477500 chr7D 84.225 374 46 10 218 582 108264808 108264439 5.550000e-93 351
11 TraesCS7B01G477500 chr7D 86.341 205 25 3 3291 3494 108298577 108298375 1.630000e-53 220
12 TraesCS7B01G477500 chr7D 85.366 205 27 3 3291 3494 108261647 108261445 3.530000e-50 209
13 TraesCS7B01G477500 chr5D 85.102 2685 279 81 652 3280 30633316 30630697 0.000000e+00 2630
14 TraesCS7B01G477500 chr5D 84.636 371 48 8 218 582 420310003 420309636 9.220000e-96 361
15 TraesCS7B01G477500 chr5D 86.408 206 24 4 3291 3494 420306810 420306607 4.540000e-54 222
16 TraesCS7B01G477500 chr5D 84.878 205 28 3 3291 3494 30630645 30630443 1.640000e-48 204
17 TraesCS7B01G477500 chr6A 84.687 2475 267 70 653 3068 615412314 615409893 0.000000e+00 2368
18 TraesCS7B01G477500 chr6A 82.312 571 83 15 25 582 615412999 615412434 2.440000e-131 479
19 TraesCS7B01G477500 chr1D 85.340 2292 244 59 652 2904 66199545 66197307 0.000000e+00 2287
20 TraesCS7B01G477500 chr1D 83.632 446 47 18 2853 3282 66197303 66196868 2.530000e-106 396
21 TraesCS7B01G477500 chr1D 84.718 373 45 10 218 582 66200035 66199667 2.560000e-96 363
22 TraesCS7B01G477500 chr1D 86.829 205 24 3 3291 3494 66196826 66196624 3.510000e-55 226
23 TraesCS7B01G477500 chr3A 85.602 1014 88 31 2093 3068 735466924 735467917 0.000000e+00 1011
24 TraesCS7B01G477500 chr3A 80.903 576 83 18 25 577 735464881 735465452 2.490000e-116 429
25 TraesCS7B01G477500 chr2D 86.341 205 25 3 3291 3494 343139807 343139605 1.630000e-53 220


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 TraesCS7B01G477500 chr7B 733214680 733218173 3493 True 6453.000000 6453 100.000000 1 3494 1 chr7B.!!$R1 3493
1 TraesCS7B01G477500 chr7B 712607591 712611138 3547 False 3205.500000 4747 91.828000 1 3494 2 chr7B.!!$F1 3493
2 TraesCS7B01G477500 chr1B 621583401 621586893 3492 True 5880.000000 5880 97.061000 1 3494 1 chr1B.!!$R1 3493
3 TraesCS7B01G477500 chr4B 638490270 638493811 3541 True 3225.500000 4798 91.914500 1 3494 2 chr4B.!!$R1 3493
4 TraesCS7B01G477500 chr3B 18006097 18008164 2067 True 3548.000000 3548 97.634000 1 2068 1 chr3B.!!$R1 2067
5 TraesCS7B01G477500 chr7D 21678433 21681043 2610 True 2639.000000 2639 85.187000 652 3280 1 chr7D.!!$R1 2628
6 TraesCS7B01G477500 chr7D 108298375 108301241 2866 True 1430.500000 2641 85.758500 652 3494 2 chr7D.!!$R3 2842
7 TraesCS7B01G477500 chr7D 108261445 108264808 3363 True 1055.333333 2606 84.840667 218 3494 3 chr7D.!!$R2 3276
8 TraesCS7B01G477500 chr5D 30630443 30633316 2873 True 1417.000000 2630 84.990000 652 3494 2 chr5D.!!$R1 2842
9 TraesCS7B01G477500 chr5D 420306607 420310003 3396 True 291.500000 361 85.522000 218 3494 2 chr5D.!!$R2 3276
10 TraesCS7B01G477500 chr6A 615409893 615412999 3106 True 1423.500000 2368 83.499500 25 3068 2 chr6A.!!$R1 3043
11 TraesCS7B01G477500 chr1D 66196624 66200035 3411 True 818.000000 2287 85.129750 218 3494 4 chr1D.!!$R1 3276
12 TraesCS7B01G477500 chr3A 735464881 735467917 3036 False 720.000000 1011 83.252500 25 3068 2 chr3A.!!$F1 3043

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
519 551 0.035439 AACAACATGCTACTCCCCGG 60.035 55.000 0.0 0.0 0.0 5.73 F
2370 2555 2.184533 TGGGCTTCACGAAATCCTCTA 58.815 47.619 0.0 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2382 2567 1.198408 TCTGCTACGTCGTTCATCGTT 59.802 47.619 1.78 0.0 40.7 3.85 R
3348 3679 2.032290 GGGTCGTTTGTTGTCTTACTGC 60.032 50.000 0.00 0.0 0.0 4.40 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
261 280 3.898123 AGATTCGTCCATATACTGTGCCT 59.102 43.478 0.00 0.00 0.00 4.75
309 328 5.991328 TTGCAAGTACAGAGACTTTCTTG 57.009 39.130 0.00 0.00 37.57 3.02
344 363 0.103208 AGGATGGCATCGTCGACTTC 59.897 55.000 20.50 4.83 0.00 3.01
519 551 0.035439 AACAACATGCTACTCCCCGG 60.035 55.000 0.00 0.00 0.00 5.73
589 662 8.031277 GCACAAGAAGGTATCATCAAAATTCTT 58.969 33.333 0.00 0.00 36.29 2.52
650 740 4.732285 TCTCGAAATTTGTGCTTCACTC 57.268 40.909 0.00 0.00 35.11 3.51
659 749 8.496707 AAATTTGTGCTTCACTCTTTTGATTT 57.503 26.923 0.00 0.00 35.11 2.17
733 825 4.273969 CAGCAACATCAATTTTTGGCAAGT 59.726 37.500 0.00 0.00 0.00 3.16
827 920 9.739276 AGTGACTACCTTCATGAAAATTTGATA 57.261 29.630 9.88 0.00 0.00 2.15
1152 1253 3.298320 GAGAGGACCTCTTCAGCCT 57.702 57.895 25.04 0.70 41.35 4.58
1300 1406 4.323417 TGCCTTCACTAACAATACTGGTG 58.677 43.478 0.00 0.00 0.00 4.17
1603 1746 7.071414 GTGGAAGCTCAACAATTAAATTTTGC 58.929 34.615 0.00 0.00 0.00 3.68
1633 1777 6.147656 CCACAAAACCAGGATTATTTTCTTGC 59.852 38.462 0.00 0.00 0.00 4.01
1962 2110 7.838696 TCATATTATGAAGGGAACACACCATTT 59.161 33.333 3.84 0.00 36.11 2.32
2199 2354 3.649023 TGGTGTAGAGTACCCAAACATGT 59.351 43.478 0.00 0.00 37.40 3.21
2330 2515 2.542597 CGATGCATGTGGGATTTTTGG 58.457 47.619 2.46 0.00 0.00 3.28
2370 2555 2.184533 TGGGCTTCACGAAATCCTCTA 58.815 47.619 0.00 0.00 0.00 2.43
2382 2567 4.438336 CGAAATCCTCTACAGCGACAGTTA 60.438 45.833 0.00 0.00 0.00 2.24
2499 2684 4.568956 AGAACTTTGCATGGTAAATTGGC 58.431 39.130 0.00 0.00 0.00 4.52
2602 2790 9.354673 TGTTTATCTTTTTCTTCTGTCTTCCAT 57.645 29.630 0.00 0.00 0.00 3.41
2831 3034 3.070748 CAACATCACACAACATCCCGTA 58.929 45.455 0.00 0.00 0.00 4.02
2887 3154 8.766000 TTGAAAGCGAATACAAGTTGTATAGA 57.234 30.769 25.11 3.86 42.29 1.98
2915 3185 5.847514 GTCGTAGAAACTGGTCATTAACCGA 60.848 44.000 0.00 0.00 46.59 4.69
3068 3346 2.330440 ATGTATTCTGATGCGGCACA 57.670 45.000 4.03 4.92 0.00 4.57
3187 3476 5.636837 TCTACAACACAAGTGAAAAAGTGC 58.363 37.500 7.28 0.00 35.47 4.40
3348 3679 6.738114 TCATAGTTCCTTCTTGCTTTTTGTG 58.262 36.000 0.00 0.00 0.00 3.33
3384 3715 2.817844 ACGACCCAAACTTTAGCCAATC 59.182 45.455 0.00 0.00 0.00 2.67
3389 3720 5.580022 ACCCAAACTTTAGCCAATCTACAT 58.420 37.500 0.00 0.00 0.00 2.29
3446 3779 2.151502 TGAACTTCCAGCACCCAAAA 57.848 45.000 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
309 328 4.517075 GCCATCCTTTTCTATGAACTAGGC 59.483 45.833 0.00 0.00 0.00 3.93
519 551 0.539438 TCACTGTCCCATTTGCCCAC 60.539 55.000 0.00 0.00 0.00 4.61
650 740 6.018832 GGACATGTTCACCAACAAATCAAAAG 60.019 38.462 0.00 0.00 45.78 2.27
659 749 2.746279 AAGGGACATGTTCACCAACA 57.254 45.000 6.44 0.00 46.71 3.33
733 825 7.465353 TCAACATAATCATCTGAAAAAGCCA 57.535 32.000 0.00 0.00 0.00 4.75
775 868 5.222048 ACAGGGATTGGTTGCTCTTTAGTAA 60.222 40.000 0.00 0.00 0.00 2.24
776 869 4.288626 ACAGGGATTGGTTGCTCTTTAGTA 59.711 41.667 0.00 0.00 0.00 1.82
1152 1253 6.194967 TCCCTTGTGTAGTTCTATCTCATGA 58.805 40.000 0.00 0.00 0.00 3.07
1300 1406 0.825840 TGGCTGCAGGTGGTTTAACC 60.826 55.000 17.12 7.27 40.85 2.85
1603 1746 6.840780 AATAATCCTGGTTTTGTGGAAGAG 57.159 37.500 0.00 0.00 33.20 2.85
1633 1777 2.353208 CCTTCTTCAGAGGACCAACTCG 60.353 54.545 0.00 0.00 42.31 4.18
1962 2110 6.351626 CCATCAAATCTCTGATCCCGATATGA 60.352 42.308 0.00 0.00 33.66 2.15
2023 2173 6.693113 GGTATTAGCAGCTTAATTTGACAAGC 59.307 38.462 0.00 2.97 46.03 4.01
2151 2306 2.631384 TCTGAAACCCATCCCTCTCAA 58.369 47.619 0.00 0.00 0.00 3.02
2199 2354 8.245195 AGTTTTTACCTTCCTATTTGCTTTGA 57.755 30.769 0.00 0.00 0.00 2.69
2330 2515 4.321230 CCCAAGTTTGCATCCACTTAAGAC 60.321 45.833 10.09 0.00 31.78 3.01
2370 2555 2.717580 TCATCGTTAACTGTCGCTGT 57.282 45.000 3.71 0.00 0.00 4.40
2382 2567 1.198408 TCTGCTACGTCGTTCATCGTT 59.802 47.619 1.78 0.00 40.70 3.85
2499 2684 7.652909 TGCTTGAATGGAAGAAGTAAAAACATG 59.347 33.333 0.00 0.00 0.00 3.21
2658 2856 6.708949 AGTTAGTAACCTCAAAAATCGCAGAA 59.291 34.615 9.46 0.00 43.58 3.02
2800 3003 7.804614 TGTTGTGTGATGTTGTTAAACTTTC 57.195 32.000 0.00 0.00 37.19 2.62
2831 3034 9.872684 AGAAAATCATATTGTTCCTCCATGTAT 57.127 29.630 0.00 0.00 0.00 2.29
2887 3154 4.602340 ATGACCAGTTTCTACGACACTT 57.398 40.909 0.00 0.00 0.00 3.16
3059 3337 4.916983 AAATAATGTACATGTGCCGCAT 57.083 36.364 9.63 5.02 38.60 4.73
3114 3397 2.564062 CTGCACCAAAGAAATGATGGGT 59.436 45.455 0.00 0.00 38.58 4.51
3187 3476 7.546667 CAGTATGTCCCTTGGAAAATTTTCATG 59.453 37.037 27.53 17.48 38.92 3.07
3348 3679 2.032290 GGGTCGTTTGTTGTCTTACTGC 60.032 50.000 0.00 0.00 0.00 4.40
3384 3715 9.282247 GCAAGTGATGACTGAAATAAAATGTAG 57.718 33.333 0.00 0.00 30.61 2.74


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

AutoCloner maintained by Alex Coulton.