Multiple sequence alignment - TraesCS3B01G301600

Loading Multiple Alignment...

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 TraesCS3B01G301600 chr3B 100.000 3426 0 0 1 3426 483472209 483468784 0.000000e+00 6327
1 TraesCS3B01G301600 chr3B 85.417 96 14 0 1 96 402665389 402665484 2.180000e-17 100
2 TraesCS3B01G301600 chr2D 93.520 2392 113 16 1054 3407 463058130 463060517 0.000000e+00 3520
3 TraesCS3B01G301600 chr7B 93.364 2381 128 14 1054 3407 253135963 253138340 0.000000e+00 3494
4 TraesCS3B01G301600 chr7B 92.142 1069 74 8 1 1065 172904448 172903386 0.000000e+00 1500
5 TraesCS3B01G301600 chr7B 91.760 1068 77 7 1 1065 173012630 173011571 0.000000e+00 1474
6 TraesCS3B01G301600 chr5B 92.504 2388 157 14 1054 3426 221758503 221760883 0.000000e+00 3398
7 TraesCS3B01G301600 chr5B 93.924 1004 57 3 1 1003 98921525 98922525 0.000000e+00 1513
8 TraesCS3B01G301600 chr5B 90.815 1067 84 10 1 1063 221757408 221758464 0.000000e+00 1415
9 TraesCS3B01G301600 chr6D 91.838 2389 176 12 1055 3426 165562201 165564587 0.000000e+00 3314
10 TraesCS3B01G301600 chr7A 91.339 2390 180 18 1054 3426 231322590 231324969 0.000000e+00 3241
11 TraesCS3B01G301600 chr7A 90.886 2392 194 16 1054 3426 615841729 615839343 0.000000e+00 3188
12 TraesCS3B01G301600 chr6A 90.518 2394 201 16 1054 3425 343743209 343745598 0.000000e+00 3140
13 TraesCS3B01G301600 chr6A 88.286 2416 227 29 1055 3426 446429283 446431686 0.000000e+00 2843
14 TraesCS3B01G301600 chr4D 90.699 2376 172 24 1093 3426 166458472 166460840 0.000000e+00 3118
15 TraesCS3B01G301600 chr5D 89.376 2419 196 26 1055 3424 419890784 419893190 0.000000e+00 2987
16 TraesCS3B01G301600 chr2B 93.785 1062 60 3 1 1056 161613757 161612696 0.000000e+00 1591
17 TraesCS3B01G301600 chr2B 93.715 1066 59 5 1 1063 486048927 486047867 0.000000e+00 1591
18 TraesCS3B01G301600 chr4B 91.109 1091 87 7 1 1087 333761298 333762382 0.000000e+00 1469
19 TraesCS3B01G301600 chr6B 90.935 1070 87 9 1 1065 312791879 312790815 0.000000e+00 1430
20 TraesCS3B01G301600 chr1B 90.728 1003 82 10 64 1063 409880941 409881935 0.000000e+00 1327
21 TraesCS3B01G301600 chr2A 92.105 874 65 4 1054 1924 204483649 204484521 0.000000e+00 1229


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 TraesCS3B01G301600 chr3B 483468784 483472209 3425 True 6327.0 6327 100.0000 1 3426 1 chr3B.!!$R1 3425
1 TraesCS3B01G301600 chr2D 463058130 463060517 2387 False 3520.0 3520 93.5200 1054 3407 1 chr2D.!!$F1 2353
2 TraesCS3B01G301600 chr7B 253135963 253138340 2377 False 3494.0 3494 93.3640 1054 3407 1 chr7B.!!$F1 2353
3 TraesCS3B01G301600 chr7B 172903386 172904448 1062 True 1500.0 1500 92.1420 1 1065 1 chr7B.!!$R1 1064
4 TraesCS3B01G301600 chr7B 173011571 173012630 1059 True 1474.0 1474 91.7600 1 1065 1 chr7B.!!$R2 1064
5 TraesCS3B01G301600 chr5B 221757408 221760883 3475 False 2406.5 3398 91.6595 1 3426 2 chr5B.!!$F2 3425
6 TraesCS3B01G301600 chr5B 98921525 98922525 1000 False 1513.0 1513 93.9240 1 1003 1 chr5B.!!$F1 1002
7 TraesCS3B01G301600 chr6D 165562201 165564587 2386 False 3314.0 3314 91.8380 1055 3426 1 chr6D.!!$F1 2371
8 TraesCS3B01G301600 chr7A 231322590 231324969 2379 False 3241.0 3241 91.3390 1054 3426 1 chr7A.!!$F1 2372
9 TraesCS3B01G301600 chr7A 615839343 615841729 2386 True 3188.0 3188 90.8860 1054 3426 1 chr7A.!!$R1 2372
10 TraesCS3B01G301600 chr6A 343743209 343745598 2389 False 3140.0 3140 90.5180 1054 3425 1 chr6A.!!$F1 2371
11 TraesCS3B01G301600 chr6A 446429283 446431686 2403 False 2843.0 2843 88.2860 1055 3426 1 chr6A.!!$F2 2371
12 TraesCS3B01G301600 chr4D 166458472 166460840 2368 False 3118.0 3118 90.6990 1093 3426 1 chr4D.!!$F1 2333
13 TraesCS3B01G301600 chr5D 419890784 419893190 2406 False 2987.0 2987 89.3760 1055 3424 1 chr5D.!!$F1 2369
14 TraesCS3B01G301600 chr2B 161612696 161613757 1061 True 1591.0 1591 93.7850 1 1056 1 chr2B.!!$R1 1055
15 TraesCS3B01G301600 chr2B 486047867 486048927 1060 True 1591.0 1591 93.7150 1 1063 1 chr2B.!!$R2 1062
16 TraesCS3B01G301600 chr4B 333761298 333762382 1084 False 1469.0 1469 91.1090 1 1087 1 chr4B.!!$F1 1086
17 TraesCS3B01G301600 chr6B 312790815 312791879 1064 True 1430.0 1430 90.9350 1 1065 1 chr6B.!!$R1 1064
18 TraesCS3B01G301600 chr1B 409880941 409881935 994 False 1327.0 1327 90.7280 64 1063 1 chr1B.!!$F1 999
19 TraesCS3B01G301600 chr2A 204483649 204484521 872 False 1229.0 1229 92.1050 1054 1924 1 chr2A.!!$F1 870

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
358 374 1.621814 GTAAGGCCAGTCACACCACTA 59.378 52.381 5.01 0.0 0.00 2.74 F
1127 1194 1.119574 ACCAGCGTACCAGACAAGGT 61.120 55.000 0.00 0.0 45.72 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1245 1312 0.387929 AGAGTTCCTCGACGCACAAA 59.612 50.0 0.00 0.00 35.36 2.83 R
3039 3207 0.036732 ATGCGAACTGAAGCTTCCCA 59.963 50.0 23.42 5.82 0.00 4.37 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
332 346 8.565896 ACATATGACATCAGTTCTAAAAAGCA 57.434 30.769 10.38 0.00 0.00 3.91
340 356 6.169557 TCAGTTCTAAAAAGCAGGACAGTA 57.830 37.500 0.00 0.00 0.00 2.74
358 374 1.621814 GTAAGGCCAGTCACACCACTA 59.378 52.381 5.01 0.00 0.00 2.74
378 394 8.210265 ACCACTATGACACCAAATTTCAAAATT 58.790 29.630 0.00 0.00 40.15 1.82
412 428 9.051027 GTATGAAATTACAATTCAGTTCACACG 57.949 33.333 0.00 0.00 39.92 4.49
440 456 7.807907 CACTAAACCATAAGTGCACTAAAAAGG 59.192 37.037 22.01 18.94 36.96 3.11
465 481 7.979537 GGGAATACAAAAACTATAAAAGGCCTG 59.020 37.037 5.69 0.00 0.00 4.85
484 500 3.958798 CCTGACTTAGGTTCGGGAAGATA 59.041 47.826 0.00 0.00 42.00 1.98
491 507 9.557061 GACTTAGGTTCGGGAAGATAAAAATAT 57.443 33.333 0.00 0.00 0.00 1.28
567 583 8.613482 TGAGATCAACTAGTGTATAAGACTTCG 58.387 37.037 0.00 0.00 0.00 3.79
573 590 8.336806 CAACTAGTGTATAAGACTTCGGTAGAG 58.663 40.741 0.00 0.00 0.00 2.43
615 633 7.392113 TCCACACGGATAAACATCATAAAAAGT 59.608 33.333 0.00 0.00 35.91 2.66
617 635 9.485591 CACACGGATAAACATCATAAAAAGTAC 57.514 33.333 0.00 0.00 0.00 2.73
730 748 3.510531 TCAGTGTGACAGTAGAGACCT 57.489 47.619 0.00 0.00 0.00 3.85
741 759 4.841246 ACAGTAGAGACCTTTGACTTGGAT 59.159 41.667 0.00 0.00 0.00 3.41
963 982 2.094803 CACTGCAGACAAACCACAAACA 60.095 45.455 23.35 0.00 0.00 2.83
1012 1031 4.256180 GGGCGATGGCGGAGGAAT 62.256 66.667 0.00 0.00 41.24 3.01
1115 1182 2.125912 GATCGTCTGCACCAGCGT 60.126 61.111 0.00 0.00 46.23 5.07
1127 1194 1.119574 ACCAGCGTACCAGACAAGGT 61.120 55.000 0.00 0.00 45.72 3.50
1134 1201 1.267806 GTACCAGACAAGGTCGACGAA 59.732 52.381 9.92 0.00 42.06 3.85
1185 1252 2.565841 GGCTTGTATCCGAGCTTCATT 58.434 47.619 0.00 0.00 45.90 2.57
1513 1588 8.962884 TGCACTAGATTAGCATCTGAAAAATA 57.037 30.769 0.00 0.00 40.28 1.40
1636 1731 8.254508 GGTGAAGTGATATAGGTCCATATCTTC 58.745 40.741 16.10 13.61 38.30 2.87
1654 1749 5.366829 TCTTCATGCACATGTTTCTCAAG 57.633 39.130 10.27 5.98 39.72 3.02
1770 1865 7.444299 TGAAGTAAGCAGCACATATATCATCA 58.556 34.615 0.00 0.00 0.00 3.07
1917 2031 9.363763 CCATGACTTGTACTATATAAGCATCTG 57.636 37.037 0.00 0.00 30.97 2.90
1943 2058 7.467811 GCCTCATGGATTATCACTTGTAAACAG 60.468 40.741 0.00 0.00 34.57 3.16
1962 2079 6.809630 AACAGAAAGCAGGAGAACTAAATC 57.190 37.500 0.00 0.00 0.00 2.17
1965 2082 7.680730 ACAGAAAGCAGGAGAACTAAATCTTA 58.319 34.615 0.00 0.00 0.00 2.10
2107 2232 4.277476 TGTTGAACAAGTCTGGTTTGGAT 58.723 39.130 0.00 0.00 0.00 3.41
2137 2263 3.304592 CCAACAACTTCATCGACATGCAA 60.305 43.478 0.00 0.00 0.00 4.08
2200 2327 1.236616 TGGTCGATGTTGCAGCCAAG 61.237 55.000 0.00 0.00 0.00 3.61
2266 2393 2.421529 GGAGGAAGACCACAAACTGTGT 60.422 50.000 6.08 0.00 46.45 3.72
2302 2429 2.101582 GCCAGACAACCTCATCGAGTAT 59.898 50.000 0.00 0.00 0.00 2.12
2348 2475 6.756542 CACGTACAAGTCATGGAAGATAATCA 59.243 38.462 0.00 0.00 0.00 2.57
2456 2583 0.179045 AGTCTGCCTTCGTGTTGCTT 60.179 50.000 0.00 0.00 0.00 3.91
2462 2589 1.723542 CTTCGTGTTGCTTGCGCTG 60.724 57.895 9.73 2.28 36.97 5.18
2519 2646 7.703328 TGTAGTTTGCTTTCTTTAGGTTGAAG 58.297 34.615 0.00 0.00 0.00 3.02
2609 2736 4.983538 TGCTTATGTCGTTCGACAAGTTTA 59.016 37.500 27.07 14.82 46.37 2.01
2751 2903 4.771054 AGTGGTAGACGAACTAAGGACAAT 59.229 41.667 0.00 0.00 32.49 2.71
2776 2929 1.041437 ATAGTAGCCTTGGACGCTCC 58.959 55.000 0.00 0.00 37.79 4.70
2942 3106 3.784338 TGCAACAGGAAAAGCAAAGAAG 58.216 40.909 0.00 0.00 33.48 2.85
2944 3108 3.126073 CAACAGGAAAAGCAAAGAAGCC 58.874 45.455 0.00 0.00 34.23 4.35
3018 3183 3.065786 ACTTGAACACACAGTGCATTCAG 59.934 43.478 15.98 13.40 35.11 3.02
3027 3192 4.273480 ACACAGTGCATTCAGTCTACAAAC 59.727 41.667 0.00 0.00 0.00 2.93
3167 3337 7.289310 TGATGATACCAAATATTGCCTTGAGA 58.711 34.615 0.00 0.00 0.00 3.27
3233 3405 9.626045 CAAAAAGATATTAGTTCAACCAAGGAC 57.374 33.333 0.00 0.00 0.00 3.85
3246 3418 4.058721 ACCAAGGACAAAAATCACAAGC 57.941 40.909 0.00 0.00 0.00 4.01
3417 3603 4.023365 CCTTGAGAAAGAAAGCCAAGACTG 60.023 45.833 0.00 0.00 37.10 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
330 344 0.391793 GACTGGCCTTACTGTCCTGC 60.392 60.000 3.32 0.00 34.44 4.85
331 345 0.976641 TGACTGGCCTTACTGTCCTG 59.023 55.000 3.32 0.00 38.20 3.86
332 346 0.977395 GTGACTGGCCTTACTGTCCT 59.023 55.000 3.32 0.00 38.20 3.85
340 356 1.003580 CATAGTGGTGTGACTGGCCTT 59.996 52.381 3.32 0.00 0.00 4.35
347 363 2.831685 TGGTGTCATAGTGGTGTGAC 57.168 50.000 0.00 0.00 43.35 3.67
358 374 7.307101 GCGTACAATTTTGAAATTTGGTGTCAT 60.307 33.333 14.63 0.00 36.52 3.06
378 394 8.257830 TGAATTGTAATTTCATACAGCGTACA 57.742 30.769 0.00 0.00 37.13 2.90
440 456 8.745590 TCAGGCCTTTTATAGTTTTTGTATTCC 58.254 33.333 0.00 0.00 0.00 3.01
465 481 7.860918 ATTTTTATCTTCCCGAACCTAAGTC 57.139 36.000 0.00 0.00 0.00 3.01
491 507 8.780249 GTTGTTGCTCAAAACTAGGACTTATTA 58.220 33.333 0.00 0.00 37.81 0.98
567 583 6.107343 GGAGGTTATGTCTTGTTTCTCTACC 58.893 44.000 0.00 0.00 0.00 3.18
573 590 4.084013 CGTGTGGAGGTTATGTCTTGTTTC 60.084 45.833 0.00 0.00 0.00 2.78
730 748 6.831353 TGGAAGAACAAACTATCCAAGTCAAA 59.169 34.615 0.00 0.00 37.50 2.69
741 759 2.488347 GGTGGCCTGGAAGAACAAACTA 60.488 50.000 3.32 0.00 34.07 2.24
963 982 0.252881 TGTGGGCTTGGGAGAGAGAT 60.253 55.000 0.00 0.00 0.00 2.75
1115 1182 1.608055 TTCGTCGACCTTGTCTGGTA 58.392 50.000 10.58 0.00 41.00 3.25
1127 1194 1.926561 CCTGCTCATCATTTCGTCGA 58.073 50.000 0.00 0.00 0.00 4.20
1157 1224 2.270850 GATACAAGCCGCCACCCA 59.729 61.111 0.00 0.00 0.00 4.51
1185 1252 3.678056 GTGTACTCCACATCAACTCCA 57.322 47.619 0.00 0.00 43.92 3.86
1245 1312 0.387929 AGAGTTCCTCGACGCACAAA 59.612 50.000 0.00 0.00 35.36 2.83
1278 1345 0.527565 ATTTTGTGGCCGCTGTGATC 59.472 50.000 18.96 0.00 0.00 2.92
1636 1731 7.878477 AATTAACTTGAGAAACATGTGCATG 57.122 32.000 10.31 10.31 44.15 4.06
1770 1865 9.574516 AAGTTCAAGAACATATTTACCAGAGTT 57.425 29.630 14.69 0.00 43.47 3.01
1784 1884 3.128589 GTGCTTCACCAAGTTCAAGAACA 59.871 43.478 14.69 0.00 43.47 3.18
1917 2031 6.318648 TGTTTACAAGTGATAATCCATGAGGC 59.681 38.462 0.00 0.00 33.74 4.70
1972 2089 6.708054 GGGGAGACACATATTGAAGATTAGTG 59.292 42.308 0.00 0.00 0.00 2.74
2107 2232 4.006989 CGATGAAGTTGTTGGGGTTGATA 58.993 43.478 0.00 0.00 0.00 2.15
2158 2284 7.942341 ACCAAGGAGTCATAGAATTTGTTTGTA 59.058 33.333 0.00 0.00 0.00 2.41
2200 2327 3.644966 TTGTAGAATGGGTGGATGACC 57.355 47.619 0.00 0.00 45.28 4.02
2302 2429 1.075542 CGTACGCATCTTTTCCTGCA 58.924 50.000 0.52 0.00 38.30 4.41
2348 2475 2.892852 CCCAACCTGTCATGATGTTGTT 59.107 45.455 22.99 12.86 37.08 2.83
2462 2589 4.022849 ACAACAAGATTAAGGACAAGCAGC 60.023 41.667 0.00 0.00 0.00 5.25
2508 2635 3.508845 AGGAAGCTGCTTCAACCTAAA 57.491 42.857 35.27 0.00 41.77 1.85
2519 2646 4.396166 ACACACATAACATAAGGAAGCTGC 59.604 41.667 0.00 0.00 0.00 5.25
2609 2736 9.343539 GATGGATAAACAAAATAGGAAGCTAGT 57.656 33.333 0.00 0.00 0.00 2.57
2738 2890 8.766151 GCTACTATTTGCTATTGTCCTTAGTTC 58.234 37.037 0.00 0.00 0.00 3.01
2751 2903 3.740141 GCGTCCAAGGCTACTATTTGCTA 60.740 47.826 0.00 0.00 0.00 3.49
2942 3106 4.337555 TGACTAGGAAATACGTACTGAGGC 59.662 45.833 0.00 0.00 0.00 4.70
2944 3108 6.680874 AGTGACTAGGAAATACGTACTGAG 57.319 41.667 0.00 0.00 0.00 3.35
3018 3183 8.117813 TCCCATTCCTTTTTATGTTTGTAGAC 57.882 34.615 0.00 0.00 0.00 2.59
3027 3192 6.071165 ACTGAAGCTTCCCATTCCTTTTTATG 60.071 38.462 23.42 0.00 0.00 1.90
3039 3207 0.036732 ATGCGAACTGAAGCTTCCCA 59.963 50.000 23.42 5.82 0.00 4.37
3233 3405 5.806502 TCTGTTGTCTTGCTTGTGATTTTTG 59.193 36.000 0.00 0.00 0.00 2.44
3246 3418 2.095364 GGCTGATGCTTCTGTTGTCTTG 60.095 50.000 8.05 0.00 39.59 3.02
3323 3509 4.473196 TGAGATTCCAATTGGGCTAGTACA 59.527 41.667 24.29 12.66 36.21 2.90
3332 3518 6.824305 AAGTTGTACTGAGATTCCAATTGG 57.176 37.500 19.08 19.08 0.00 3.16
3365 3551 6.959606 ATTGGTATCATCATAGCCCTTACT 57.040 37.500 0.00 0.00 32.73 2.24
3371 3557 9.686683 AAGGTATTAATTGGTATCATCATAGCC 57.313 33.333 0.00 0.00 32.73 3.93
3393 3579 3.885901 GTCTTGGCTTTCTTTCTCAAGGT 59.114 43.478 0.00 0.00 36.45 3.50


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

AutoCloner maintained by Alex Coulton.