Multiple sequence alignment - TraesCS1B01G121200

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 TraesCS1B01G121200 chr1B 100.000 2591 0 0 1 2591 143060168 143057578 0.000000e+00 4785
1 TraesCS1B01G121200 chr1B 81.223 229 40 2 2355 2583 145359790 145360015 5.700000e-42 182
2 TraesCS1B01G121200 chr1A 95.062 1600 73 5 685 2280 85822831 85824428 0.000000e+00 2512
3 TraesCS1B01G121200 chr1A 83.983 693 103 7 1 691 10236315 10235629 0.000000e+00 658
4 TraesCS1B01G121200 chr1A 94.000 150 9 0 2442 2591 85826390 85826539 7.210000e-56 228
5 TraesCS1B01G121200 chr1A 80.786 229 41 2 2355 2583 86636878 86637103 2.650000e-40 176
6 TraesCS1B01G121200 chr1D 94.154 1129 43 12 685 1809 89517430 89518539 0.000000e+00 1698
7 TraesCS1B01G121200 chr1D 92.212 321 23 2 2273 2591 89533154 89533474 1.090000e-123 453
8 TraesCS1B01G121200 chr1D 91.597 119 9 1 2026 2143 89520552 89520670 2.060000e-36 163
9 TraesCS1B01G121200 chr3A 84.985 686 96 6 1 684 674254962 674254282 0.000000e+00 689
10 TraesCS1B01G121200 chr4B 87.919 447 49 3 243 689 358171358 358170917 2.950000e-144 521
11 TraesCS1B01G121200 chr4B 88.980 245 26 1 1 245 358182794 358182551 4.190000e-78 302
12 TraesCS1B01G121200 chr6A 80.580 690 121 11 2 685 510882548 510883230 1.060000e-143 520
13 TraesCS1B01G121200 chr7B 79.395 694 118 21 1 684 24121752 24122430 1.400000e-127 466
14 TraesCS1B01G121200 chr4D 76.818 220 48 3 469 686 403912356 403912574 1.260000e-23 121


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 TraesCS1B01G121200 chr1B 143057578 143060168 2590 True 4785.0 4785 100.0000 1 2591 1 chr1B.!!$R1 2590
1 TraesCS1B01G121200 chr1A 85822831 85826539 3708 False 1370.0 2512 94.5310 685 2591 2 chr1A.!!$F2 1906
2 TraesCS1B01G121200 chr1A 10235629 10236315 686 True 658.0 658 83.9830 1 691 1 chr1A.!!$R1 690
3 TraesCS1B01G121200 chr1D 89517430 89520670 3240 False 930.5 1698 92.8755 685 2143 2 chr1D.!!$F2 1458
4 TraesCS1B01G121200 chr3A 674254282 674254962 680 True 689.0 689 84.9850 1 684 1 chr3A.!!$R1 683
5 TraesCS1B01G121200 chr6A 510882548 510883230 682 False 520.0 520 80.5800 2 685 1 chr6A.!!$F1 683
6 TraesCS1B01G121200 chr7B 24121752 24122430 678 False 466.0 466 79.3950 1 684 1 chr7B.!!$F1 683

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
299 304 0.096976 CTCGTTATTGCCGCCAACTG 59.903 55.0 0.0 0.0 32.95 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 3645 1.937546 CTTGGGCCAAGAACATCGCC 61.938 60.0 37.45 0.0 43.42 5.54 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
28 29 1.227674 GTATCCTGCCGCTTCCTGG 60.228 63.158 0.00 0.00 0.00 4.45
72 73 2.281484 GTGCAGAACCGGCCTGAA 60.281 61.111 23.80 13.75 33.65 3.02
75 76 3.121030 CAGAACCGGCCTGAAGCG 61.121 66.667 16.93 0.00 45.17 4.68
115 116 3.699894 CGGGAGAGGTGCTGCACT 61.700 66.667 29.54 17.00 36.54 4.40
131 132 2.813474 CTCGACGGCGCCAATTCA 60.813 61.111 28.98 4.43 37.46 2.57
132 133 3.083600 CTCGACGGCGCCAATTCAC 62.084 63.158 28.98 9.19 37.46 3.18
137 141 2.988684 GGCGCCAATTCACACCCA 60.989 61.111 24.80 0.00 0.00 4.51
139 143 2.993471 GCGCCAATTCACACCCAGG 61.993 63.158 0.00 0.00 0.00 4.45
146 150 0.617413 ATTCACACCCAGGAGAGCAG 59.383 55.000 0.00 0.00 0.00 4.24
148 152 2.203907 ACACCCAGGAGAGCAGCT 60.204 61.111 0.00 0.00 0.00 4.24
156 160 4.200283 GAGAGCAGCTCGACCCCG 62.200 72.222 16.99 0.00 35.36 5.73
219 224 0.486879 TTGATGGGTCCTTTTGCCCT 59.513 50.000 0.00 0.00 45.06 5.19
220 225 1.377690 TGATGGGTCCTTTTGCCCTA 58.622 50.000 0.00 0.00 45.06 3.53
225 230 1.017701 GGTCCTTTTGCCCTACGACG 61.018 60.000 0.00 0.00 0.00 5.12
229 234 3.256824 TTTTGCCCTACGACGGGGG 62.257 63.158 19.60 19.60 44.83 5.40
263 268 0.180171 CATGGTGCTCCGGGATAACA 59.820 55.000 0.00 0.00 36.30 2.41
286 291 2.223735 GGGCACGATCATCTTCTCGTTA 60.224 50.000 0.00 0.00 45.15 3.18
299 304 0.096976 CTCGTTATTGCCGCCAACTG 59.903 55.000 0.00 0.00 32.95 3.16
318 323 1.939597 CGATCTTGCGCAGATGCAT 59.060 52.632 21.70 0.00 45.78 3.96
357 362 2.158608 GCATGTATGGAGGGCCTAAACT 60.159 50.000 5.73 0.00 34.31 2.66
378 383 3.680786 CACTCCAGTGGACGCCGA 61.681 66.667 8.12 0.00 42.10 5.54
410 415 0.888619 TTGAGACCGACTGCCTAGTG 59.111 55.000 0.00 0.00 37.25 2.74
490 495 3.394674 TCAAACCAAGCGTCTCATGTA 57.605 42.857 0.00 0.00 0.00 2.29
491 496 3.937814 TCAAACCAAGCGTCTCATGTAT 58.062 40.909 0.00 0.00 0.00 2.29
508 513 3.632333 TGTATGGAGGACGAGAAGTGAT 58.368 45.455 0.00 0.00 0.00 3.06
510 515 5.386060 TGTATGGAGGACGAGAAGTGATAT 58.614 41.667 0.00 0.00 0.00 1.63
521 526 7.308649 GGACGAGAAGTGATATTAGCTCACATA 60.309 40.741 5.90 0.00 44.37 2.29
524 529 7.700234 CGAGAAGTGATATTAGCTCACATATCC 59.300 40.741 13.89 8.31 44.37 2.59
542 547 8.070171 CACATATCCCGTGATCAAAATAAAGTC 58.930 37.037 0.00 0.00 36.43 3.01
546 551 6.001460 TCCCGTGATCAAAATAAAGTCAGTT 58.999 36.000 0.00 0.00 0.00 3.16
565 570 8.250332 AGTCAGTTATTTTCTTGCAAACTTTGA 58.750 29.630 5.65 0.00 0.00 2.69
639 644 2.166459 CCGGATCTCTGTAAGCAAGACA 59.834 50.000 0.00 0.00 0.00 3.41
642 647 5.451937 CCGGATCTCTGTAAGCAAGACATTA 60.452 44.000 0.00 0.00 0.00 1.90
643 648 6.219473 CGGATCTCTGTAAGCAAGACATTAT 58.781 40.000 0.00 0.00 0.00 1.28
644 649 6.703607 CGGATCTCTGTAAGCAAGACATTATT 59.296 38.462 0.00 0.00 0.00 1.40
675 681 7.553760 GGTAATCAATAAAGTTTTACCCTCCGA 59.446 37.037 0.00 0.00 37.09 4.55
740 746 1.608717 ATGAGTGCTCCGAGTCACCC 61.609 60.000 15.21 7.91 33.90 4.61
790 796 0.250295 TCAGTCACCTGGCCGAAAAG 60.250 55.000 0.00 0.00 39.31 2.27
856 862 1.254026 CCACCTCTTCTCCACACGTA 58.746 55.000 0.00 0.00 0.00 3.57
865 871 4.137872 CCACACGTATCCCGGCGT 62.138 66.667 6.01 0.00 42.24 5.68
997 1005 5.552178 GAGTTAGGATCCATAACCCATCAC 58.448 45.833 15.82 0.00 34.34 3.06
1608 1616 3.076182 TGTAGAAGGGAGGAGAGACAGTT 59.924 47.826 0.00 0.00 0.00 3.16
1612 1620 4.044825 AGAAGGGAGGAGAGACAGTTAGAA 59.955 45.833 0.00 0.00 0.00 2.10
1686 1694 3.759550 CAGTACACTGTACACGCGA 57.240 52.632 15.93 0.00 39.09 5.87
1715 1723 3.781341 TGTTGTATCTCGTCGCAAAAC 57.219 42.857 0.00 0.00 0.00 2.43
1718 1726 2.063266 TGTATCTCGTCGCAAAACACC 58.937 47.619 0.00 0.00 0.00 4.16
1837 1890 6.983910 TCAAATGTTCGGTTTTTCTTTTTCG 58.016 32.000 0.00 0.00 0.00 3.46
1952 3556 5.468072 CCCAGATAGAATCGGAATTGAGTTG 59.532 44.000 0.00 0.00 0.00 3.16
1970 3574 5.652014 TGAGTTGGTTCAAATTCTGTTCTGT 59.348 36.000 0.00 0.00 0.00 3.41
2041 3645 4.035208 CGATTAAACCCCTCTTGGAAATCG 59.965 45.833 0.00 0.00 38.42 3.34
2149 3954 3.387091 AGGCGGCCACACGACATA 61.387 61.111 23.09 0.00 46.48 2.29
2150 3955 3.192922 GGCGGCCACACGACATAC 61.193 66.667 15.62 0.00 42.70 2.39
2307 4148 3.990092 TGAGTGCTGACAATCGTTTACT 58.010 40.909 0.00 0.00 43.80 2.24
2308 4149 4.377021 TGAGTGCTGACAATCGTTTACTT 58.623 39.130 0.00 0.00 43.80 2.24
2309 4150 5.534407 TGAGTGCTGACAATCGTTTACTTA 58.466 37.500 0.00 0.00 43.80 2.24
2311 4152 6.073980 TGAGTGCTGACAATCGTTTACTTAAC 60.074 38.462 0.00 0.00 43.80 2.01
2325 4166 5.646467 TTACTTAACGTTGTTCAGTGAGC 57.354 39.130 11.99 0.00 0.00 4.26
2334 4175 1.669115 TTCAGTGAGCAAGCGAGCC 60.669 57.895 0.00 0.00 34.23 4.70
2378 4219 3.895025 CACCATCGTGGCCTCTTG 58.105 61.111 3.32 0.74 42.67 3.02
2390 4231 2.642311 TGGCCTCTTGTGTCTTCCAATA 59.358 45.455 3.32 0.00 0.00 1.90
2413 4254 5.885881 ACAAAGTTGATTACGAACAAAGCA 58.114 33.333 0.00 0.00 0.00 3.91
2428 4269 4.904466 GCAAGCAGCTTCCCATTG 57.096 55.556 4.07 0.00 41.15 2.82
2463 6073 4.570663 GACATCGTCTCCGCCGGG 62.571 72.222 1.90 0.00 0.00 5.73
2481 6091 1.216990 GGGGACATCTGTGGAGGATT 58.783 55.000 0.00 0.00 0.00 3.01
2483 6093 2.370189 GGGGACATCTGTGGAGGATTAG 59.630 54.545 0.00 0.00 0.00 1.73
2491 6101 3.034635 CTGTGGAGGATTAGGTGCTACT 58.965 50.000 0.00 0.00 28.74 2.57
2517 6127 0.388649 GCGACACAGAGGACGACAAT 60.389 55.000 0.00 0.00 0.00 2.71
2580 6190 3.268103 AAGCGTCGGGGCCATCTTT 62.268 57.895 4.39 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.491022 GCGGCAGGATACCTCGACT 61.491 63.158 0.00 0.00 37.17 4.18
15 16 2.435586 CTCACCAGGAAGCGGCAG 60.436 66.667 1.45 0.00 0.00 4.85
28 29 0.818296 ATGGACTCCACGTAGCTCAC 59.182 55.000 0.00 0.00 35.80 3.51
69 70 3.691342 CTCACCGGGTCCGCTTCA 61.691 66.667 6.32 0.00 38.24 3.02
101 102 1.445238 GTCGAGTGCAGCACCTCTC 60.445 63.158 22.41 12.23 34.49 3.20
102 103 2.653702 GTCGAGTGCAGCACCTCT 59.346 61.111 22.41 3.33 34.49 3.69
115 116 3.115892 GTGAATTGGCGCCGTCGA 61.116 61.111 23.90 8.11 38.10 4.20
128 129 2.061220 CTGCTCTCCTGGGTGTGAA 58.939 57.895 0.00 0.00 0.00 3.18
131 132 2.203907 AGCTGCTCTCCTGGGTGT 60.204 61.111 0.00 0.00 0.00 4.16
132 133 2.583520 GAGCTGCTCTCCTGGGTG 59.416 66.667 21.93 0.00 35.77 4.61
137 141 2.757917 GGGTCGAGCTGCTCTCCT 60.758 66.667 25.59 0.00 38.62 3.69
139 143 4.200283 CGGGGTCGAGCTGCTCTC 62.200 72.222 25.59 17.83 39.00 3.20
156 160 4.129148 GGTGGGGCCCATCTGACC 62.129 72.222 31.48 21.31 35.28 4.02
263 268 0.103208 GAGAAGATGATCGTGCCCGT 59.897 55.000 0.00 0.00 35.01 5.28
303 308 0.677414 TCCAATGCATCTGCGCAAGA 60.677 50.000 13.05 11.87 46.87 3.02
311 316 1.147824 CTCCGCCTCCAATGCATCT 59.852 57.895 0.00 0.00 0.00 2.90
338 343 3.117512 CCAAGTTTAGGCCCTCCATACAT 60.118 47.826 0.00 0.00 33.74 2.29
357 362 2.425592 CGTCCACTGGAGTGCCAA 59.574 61.111 0.00 0.00 45.41 4.52
377 382 0.465705 TCTCAATCTCCACCGGCATC 59.534 55.000 0.00 0.00 0.00 3.91
378 383 0.179000 GTCTCAATCTCCACCGGCAT 59.821 55.000 0.00 0.00 0.00 4.40
429 434 4.081862 TCGGGATCGATCAACAAAGTTACT 60.082 41.667 25.93 0.00 40.88 2.24
456 461 6.258727 CGCTTGGTTTGATCTATCAACATAGT 59.741 38.462 4.89 0.00 45.63 2.12
479 484 1.600663 CGTCCTCCATACATGAGACGC 60.601 57.143 0.00 0.00 38.10 5.19
482 487 3.577805 TCTCGTCCTCCATACATGAGA 57.422 47.619 0.00 0.00 0.00 3.27
490 495 5.047660 GCTAATATCACTTCTCGTCCTCCAT 60.048 44.000 0.00 0.00 0.00 3.41
491 496 4.278669 GCTAATATCACTTCTCGTCCTCCA 59.721 45.833 0.00 0.00 0.00 3.86
521 526 6.180472 ACTGACTTTATTTTGATCACGGGAT 58.820 36.000 0.00 0.00 36.13 3.85
524 529 9.840427 AAATAACTGACTTTATTTTGATCACGG 57.160 29.630 0.00 0.00 38.09 4.94
565 570 2.034053 GCAGTGCGCTCTTCTACTCTAT 59.966 50.000 9.70 0.00 37.77 1.98
697 703 2.488153 ACTCGTGTGATCTTGTCATCGA 59.512 45.455 0.00 0.00 40.71 3.59
740 746 0.695347 AAAGGAGCTTCTGGAGTGGG 59.305 55.000 0.00 0.00 0.00 4.61
790 796 4.534103 AGGGGCTCAGTAATCTATCCATTC 59.466 45.833 0.00 0.00 0.00 2.67
844 850 1.952102 GCCGGGATACGTGTGGAGAA 61.952 60.000 2.18 0.00 42.24 2.87
881 887 1.138047 CGCGGCGAGTGGTTAAGTAG 61.138 60.000 19.16 0.00 0.00 2.57
997 1005 4.489771 GGTGGCGGTCTCCATGGG 62.490 72.222 13.02 2.57 38.57 4.00
1116 1124 2.437359 CGGCCCAGCTTCCTCTTG 60.437 66.667 0.00 0.00 0.00 3.02
1567 1575 6.567959 TCTACAGCATCTTGTAGTTCATCAG 58.432 40.000 11.61 0.00 46.75 2.90
1608 1616 2.806244 GACAACTCGCAAAGCCTTTCTA 59.194 45.455 0.00 0.00 0.00 2.10
1612 1620 1.941812 CGACAACTCGCAAAGCCTT 59.058 52.632 0.00 0.00 31.91 4.35
1686 1694 4.164294 GACGAGATACAACAAACTACGCT 58.836 43.478 0.00 0.00 0.00 5.07
1696 1704 3.466836 GTGTTTTGCGACGAGATACAAC 58.533 45.455 0.00 0.00 0.00 3.32
1715 1723 7.148474 ACAGTAATACACAAAAAGATAGCGGTG 60.148 37.037 0.00 0.00 0.00 4.94
1718 1726 8.227791 ACAACAGTAATACACAAAAAGATAGCG 58.772 33.333 0.00 0.00 0.00 4.26
1803 1839 2.981805 CCGAACATTTGAGCACAACATG 59.018 45.455 13.31 13.31 35.63 3.21
1837 1890 5.176590 CCTAGTCGATCAAAAGCAGCTAATC 59.823 44.000 0.00 0.00 0.00 1.75
1952 3556 6.706270 TGACTCTACAGAACAGAATTTGAACC 59.294 38.462 0.00 0.00 0.00 3.62
1970 3574 3.484721 CGAACTAACACGCGATGACTCTA 60.485 47.826 15.93 0.00 0.00 2.43
2041 3645 1.937546 CTTGGGCCAAGAACATCGCC 61.938 60.000 37.45 0.00 43.42 5.54
2170 3975 3.414700 CCGCGTGTTGACCTCTGC 61.415 66.667 4.92 0.00 0.00 4.26
2225 4032 2.899339 GCTGCCGGAGATTGAGCC 60.899 66.667 5.05 0.00 0.00 4.70
2228 4035 2.586245 CCAGCTGCCGGAGATTGA 59.414 61.111 5.05 0.00 0.00 2.57
2288 4129 6.224420 GTTAAGTAAACGATTGTCAGCACT 57.776 37.500 0.00 0.00 0.00 4.40
2307 4148 3.242608 GCTTGCTCACTGAACAACGTTAA 60.243 43.478 0.00 0.00 0.00 2.01
2308 4149 2.286833 GCTTGCTCACTGAACAACGTTA 59.713 45.455 0.00 0.00 0.00 3.18
2309 4150 1.064060 GCTTGCTCACTGAACAACGTT 59.936 47.619 0.00 0.00 0.00 3.99
2311 4152 0.383491 CGCTTGCTCACTGAACAACG 60.383 55.000 0.00 0.00 0.00 4.10
2312 4153 0.937304 TCGCTTGCTCACTGAACAAC 59.063 50.000 0.00 0.00 0.00 3.32
2313 4154 1.220529 CTCGCTTGCTCACTGAACAA 58.779 50.000 0.00 0.00 0.00 2.83
2315 4156 1.495069 GCTCGCTTGCTCACTGAAC 59.505 57.895 0.00 0.00 0.00 3.18
2316 4157 1.669115 GGCTCGCTTGCTCACTGAA 60.669 57.895 0.00 0.00 0.00 3.02
2318 4159 1.909141 CTTGGCTCGCTTGCTCACTG 61.909 60.000 0.00 0.00 0.00 3.66
2319 4160 1.670406 CTTGGCTCGCTTGCTCACT 60.670 57.895 0.00 0.00 0.00 3.41
2320 4161 1.023513 ATCTTGGCTCGCTTGCTCAC 61.024 55.000 0.00 0.00 0.00 3.51
2321 4162 1.022982 CATCTTGGCTCGCTTGCTCA 61.023 55.000 0.00 0.00 0.00 4.26
2322 4163 1.712977 CCATCTTGGCTCGCTTGCTC 61.713 60.000 0.00 0.00 0.00 4.26
2378 4219 7.744715 CGTAATCAACTTTGTATTGGAAGACAC 59.255 37.037 0.00 0.00 28.56 3.67
2390 4231 5.885881 TGCTTTGTTCGTAATCAACTTTGT 58.114 33.333 0.00 0.00 0.00 2.83
2413 4254 1.891150 CTTGTCAATGGGAAGCTGCTT 59.109 47.619 15.92 15.92 0.00 3.91
2428 4269 2.158957 TGTCGGAATAGATGGCCTTGTC 60.159 50.000 3.32 0.00 0.00 3.18
2463 6073 2.370189 CCTAATCCTCCACAGATGTCCC 59.630 54.545 0.00 0.00 0.00 4.46
2496 6106 3.733960 TCGTCCTCTGTGTCGCCG 61.734 66.667 0.00 0.00 0.00 6.46
2502 6112 1.354337 CGCCATTGTCGTCCTCTGTG 61.354 60.000 0.00 0.00 0.00 3.66
2505 6115 1.251527 ACTCGCCATTGTCGTCCTCT 61.252 55.000 0.00 0.00 0.00 3.69
2517 6127 5.138276 AGGTAGACAGAAATATACTCGCCA 58.862 41.667 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.