Multiple sequence alignment - TraesCS1D01G159500

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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 TraesCS1D01G159500 chr1D 100.000 2915 0 0 1 2915 225430739 225433653 0.000000e+00 5384
1 TraesCS1D01G159500 chr1A 91.602 2572 115 29 160 2672 292747028 292744499 0.000000e+00 3459
2 TraesCS1D01G159500 chr1A 95.000 240 11 1 2676 2915 292744463 292744225 2.740000e-100 375
3 TraesCS1D01G159500 chr1A 95.652 230 10 0 1282 1511 97804967 97804738 1.280000e-98 370
4 TraesCS1D01G159500 chr1A 91.870 123 10 0 2 124 292747149 292747027 3.860000e-39 172
5 TraesCS1D01G159500 chr1B 93.164 1697 68 20 989 2671 325297278 325298940 0.000000e+00 2447
6 TraesCS1D01G159500 chr1B 91.477 880 34 18 38 907 325295945 325296793 0.000000e+00 1171
7 TraesCS1D01G159500 chr1B 96.034 353 13 1 1282 1634 612222931 612223282 9.060000e-160 573
8 TraesCS1D01G159500 chr1B 83.942 274 13 4 2673 2915 325298974 325299247 1.750000e-57 233
9 TraesCS1D01G159500 chr5B 96.601 353 11 1 1282 1634 96016973 96016622 4.190000e-163 584
10 TraesCS1D01G159500 chr6B 98.148 324 5 1 1311 1634 713457822 713457500 5.450000e-157 564
11 TraesCS1D01G159500 chr7A 97.538 325 7 1 1310 1634 642102217 642101894 3.280000e-154 555
12 TraesCS1D01G159500 chr3B 97.231 325 8 1 1310 1634 52652193 52651870 1.530000e-152 549
13 TraesCS1D01G159500 chr4A 99.259 135 1 0 1310 1444 730989590 730989724 8.070000e-61 244


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 TraesCS1D01G159500 chr1D 225430739 225433653 2914 False 5384.000000 5384 100.000000 1 2915 1 chr1D.!!$F1 2914
1 TraesCS1D01G159500 chr1A 292744225 292747149 2924 True 1335.333333 3459 92.824000 2 2915 3 chr1A.!!$R2 2913
2 TraesCS1D01G159500 chr1B 325295945 325299247 3302 False 1283.666667 2447 89.527667 38 2915 3 chr1B.!!$F2 2877

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
572 588 0.107831 ACTGCGGTTAAACCTGCTCA 59.892 50.0 0.0 0.0 38.17 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1990 2444 0.179037 CGTGCATCCATCCATCCTGT 60.179 55.0 0.0 0.0 0.0 4.0 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
22 23 3.504863 GTGTGATACGATAACACGGTGT 58.495 45.455 8.21 8.21 35.07 4.16
26 27 5.163632 TGTGATACGATAACACGGTGTACAT 60.164 40.000 15.11 10.83 37.35 2.29
56 57 1.271926 GCTAAAGAAGACCCAAGGCCA 60.272 52.381 5.01 0.00 0.00 5.36
57 58 2.817839 GCTAAAGAAGACCCAAGGCCAA 60.818 50.000 5.01 0.00 0.00 4.52
60 61 3.372440 AAGAAGACCCAAGGCCAATAG 57.628 47.619 5.01 0.00 0.00 1.73
123 124 8.942338 TCTCTTGTGTTAACCATCATACATAC 57.058 34.615 2.48 0.00 0.00 2.39
126 127 6.918892 TGTGTTAACCATCATACATACAGC 57.081 37.500 2.48 0.00 0.00 4.40
129 130 6.538742 GTGTTAACCATCATACATACAGCACT 59.461 38.462 2.48 0.00 0.00 4.40
247 255 1.014352 GGTGGGTATTGACACATCGC 58.986 55.000 0.00 0.00 42.26 4.58
281 289 4.831155 ACGTATGTATATATGGCGCCCTAT 59.169 41.667 26.77 25.62 31.36 2.57
282 290 5.303589 ACGTATGTATATATGGCGCCCTATT 59.696 40.000 26.29 16.89 31.36 1.73
283 291 6.183360 ACGTATGTATATATGGCGCCCTATTT 60.183 38.462 26.29 20.94 31.36 1.40
384 397 5.502153 AGTTATACTCGCTCTGTACAAGG 57.498 43.478 0.00 0.00 0.00 3.61
385 398 4.338682 AGTTATACTCGCTCTGTACAAGGG 59.661 45.833 12.67 12.67 0.00 3.95
386 399 1.471119 TACTCGCTCTGTACAAGGGG 58.529 55.000 16.36 11.57 0.00 4.79
479 495 6.686484 ATTCATCCACCATACTATGCACTA 57.314 37.500 0.00 0.00 0.00 2.74
481 497 4.528206 TCATCCACCATACTATGCACTAGG 59.472 45.833 0.00 0.00 0.00 3.02
569 585 0.948678 TCAACTGCGGTTAAACCTGC 59.051 50.000 11.38 0.00 37.95 4.85
570 586 0.951558 CAACTGCGGTTAAACCTGCT 59.048 50.000 11.38 0.00 38.17 4.24
571 587 1.069227 CAACTGCGGTTAAACCTGCTC 60.069 52.381 11.38 0.00 38.17 4.26
572 588 0.107831 ACTGCGGTTAAACCTGCTCA 59.892 50.000 0.00 0.00 38.17 4.26
573 589 1.271379 ACTGCGGTTAAACCTGCTCAT 60.271 47.619 0.00 0.00 38.17 2.90
574 590 1.812571 CTGCGGTTAAACCTGCTCATT 59.187 47.619 0.00 0.00 38.17 2.57
575 591 1.539388 TGCGGTTAAACCTGCTCATTG 59.461 47.619 0.00 0.00 38.17 2.82
576 592 1.732405 GCGGTTAAACCTGCTCATTGC 60.732 52.381 0.00 0.00 35.66 3.56
577 593 1.812571 CGGTTAAACCTGCTCATTGCT 59.187 47.619 0.00 0.00 35.66 3.91
578 594 2.228822 CGGTTAAACCTGCTCATTGCTT 59.771 45.455 0.00 0.00 35.66 3.91
696 722 2.288030 CCACTCAGTTAAGAACGGTCGT 60.288 50.000 0.00 0.00 36.23 4.34
745 780 4.162131 GGGTGCAACATTGGATATTCCTTT 59.838 41.667 3.06 0.00 39.98 3.11
874 915 2.162208 TGCGCTTTATGCTTTTGAGAGG 59.838 45.455 9.73 0.00 40.11 3.69
889 930 1.304217 GAGGGGTCAGTCCGTCAGA 60.304 63.158 0.00 0.00 40.37 3.27
895 936 0.109689 GTCAGTCCGTCAGAACCTCG 60.110 60.000 0.00 0.00 0.00 4.63
909 950 4.824515 CTCGGCTCCTCCTCCCGT 62.825 72.222 0.00 0.00 42.48 5.28
922 963 1.411216 CCTCCCGTCCCGGCTATATAT 60.411 57.143 0.00 0.00 46.86 0.86
923 964 2.158564 CCTCCCGTCCCGGCTATATATA 60.159 54.545 0.00 0.00 46.86 0.86
924 965 3.559069 CTCCCGTCCCGGCTATATATAA 58.441 50.000 0.00 0.00 46.86 0.98
926 967 2.035576 CCCGTCCCGGCTATATATAAGC 59.964 54.545 0.00 7.84 46.86 3.09
942 983 0.320771 AAGCACTCGACCCACACATC 60.321 55.000 0.00 0.00 0.00 3.06
977 1422 2.922503 TTGCACTCCCCTCTCGCA 60.923 61.111 0.00 0.00 0.00 5.10
981 1426 1.979155 CACTCCCCTCTCGCAGTCA 60.979 63.158 0.00 0.00 0.00 3.41
985 1430 1.216710 CCCCTCTCGCAGTCAAGTC 59.783 63.158 0.00 0.00 0.00 3.01
1086 1531 1.945776 GCGCAAACTCCTTCGTCTCG 61.946 60.000 0.30 0.00 0.00 4.04
1088 1533 1.627550 GCAAACTCCTTCGTCTCGGC 61.628 60.000 0.00 0.00 0.00 5.54
1090 1535 2.168666 AAACTCCTTCGTCTCGGCCC 62.169 60.000 0.00 0.00 0.00 5.80
1491 1939 2.762043 GAGAAGCCGAGGCCCTCT 60.762 66.667 19.94 17.27 43.17 3.69
1916 2370 1.360551 CTCCCATCCGCGTCTAGTG 59.639 63.158 4.92 0.00 0.00 2.74
1989 2443 2.480845 GTACGTGCTAATCCATCCACC 58.519 52.381 0.00 0.00 0.00 4.61
1990 2444 0.908910 ACGTGCTAATCCATCCACCA 59.091 50.000 0.00 0.00 0.00 4.17
1991 2445 1.299541 CGTGCTAATCCATCCACCAC 58.700 55.000 0.00 0.00 0.00 4.16
2010 2464 0.179037 CAGGATGGATGGATGCACGT 60.179 55.000 0.00 0.00 0.00 4.49
2031 2485 3.803082 CATGCACGCACGGAAGGG 61.803 66.667 0.00 0.00 37.78 3.95
2196 2657 1.138859 TGCACACTGAAGCAGTACTGT 59.861 47.619 23.44 5.15 43.43 3.55
2358 2823 7.903995 TCTTTGTTCTTTTGCTCAATTTTGT 57.096 28.000 0.00 0.00 0.00 2.83
2447 2913 3.819368 TCTCACTTGCCTTGTTCATCAA 58.181 40.909 0.00 0.00 34.61 2.57
2448 2914 4.401022 TCTCACTTGCCTTGTTCATCAAT 58.599 39.130 0.00 0.00 35.35 2.57
2449 2915 4.456911 TCTCACTTGCCTTGTTCATCAATC 59.543 41.667 0.00 0.00 35.35 2.67
2450 2916 4.143543 TCACTTGCCTTGTTCATCAATCA 58.856 39.130 0.00 0.00 35.35 2.57
2451 2917 4.768448 TCACTTGCCTTGTTCATCAATCAT 59.232 37.500 0.00 0.00 35.35 2.45
2452 2918 5.100259 CACTTGCCTTGTTCATCAATCATC 58.900 41.667 0.00 0.00 35.35 2.92
2453 2919 4.768448 ACTTGCCTTGTTCATCAATCATCA 59.232 37.500 0.00 0.00 35.35 3.07
2507 2973 3.628032 AGATGTGAGCATGCTTGAGATTG 59.372 43.478 23.61 0.00 35.07 2.67
2522 2988 1.287146 AGATTGAGGGCCTCTTGCATT 59.713 47.619 32.28 10.75 43.89 3.56
2526 2992 1.028130 GAGGGCCTCTTGCATTAAGC 58.972 55.000 26.44 0.00 43.89 3.09
2547 3013 3.249559 GCGGATTCTGGATTTCACTGATC 59.750 47.826 0.00 0.00 0.00 2.92
2716 3214 9.035607 ACAAGACAAGAATATAATAAGAGTGCG 57.964 33.333 0.00 0.00 0.00 5.34
2754 3252 4.963276 TGTAAAATGCGGGAATCTTGAG 57.037 40.909 0.00 0.00 0.00 3.02
2782 3280 4.887655 GGGTATTTGGTCCACAGAAATAGG 59.112 45.833 0.00 0.00 0.00 2.57
2889 3418 5.883661 TGTACGAATTACTAAAGGAGGTCG 58.116 41.667 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.192001 ACACCGTGTTATCGTATCACACT 59.808 43.478 0.00 0.00 38.97 3.55
13 14 2.076100 CAGCATCATGTACACCGTGTT 58.924 47.619 9.98 0.00 0.00 3.32
56 57 1.492176 CAGAGGTGCCCATGACCTATT 59.508 52.381 4.62 0.00 44.28 1.73
57 58 1.135094 CAGAGGTGCCCATGACCTAT 58.865 55.000 4.62 0.00 44.28 2.57
60 61 0.251341 AAACAGAGGTGCCCATGACC 60.251 55.000 0.00 0.00 0.00 4.02
69 70 6.540189 CCATGACTTATCCTAAAACAGAGGTG 59.460 42.308 0.00 0.00 35.40 4.00
126 127 9.776158 CTTGTCAATCAAGTACTAGTACTAGTG 57.224 37.037 35.52 25.68 44.96 2.74
174 175 1.762222 GACCGCGCGCATTATCACTT 61.762 55.000 32.61 2.83 0.00 3.16
247 255 2.223537 TACATACGTCAGCTGCATGG 57.776 50.000 9.47 0.00 0.00 3.66
282 290 1.703411 CAAGGGTGGAGCTGGAAAAA 58.297 50.000 0.00 0.00 0.00 1.94
283 291 3.437642 CAAGGGTGGAGCTGGAAAA 57.562 52.632 0.00 0.00 0.00 2.29
324 336 9.490379 AGACCATATATACGAAGAAATGGAAAC 57.510 33.333 14.60 7.85 37.80 2.78
361 374 5.505985 CCCTTGTACAGAGCGAGTATAACTC 60.506 48.000 0.00 0.00 41.71 3.01
381 394 1.001248 TCGTCGATCCCTTCCCCTT 59.999 57.895 0.00 0.00 0.00 3.95
382 395 1.757340 GTCGTCGATCCCTTCCCCT 60.757 63.158 0.00 0.00 0.00 4.79
383 396 1.757340 AGTCGTCGATCCCTTCCCC 60.757 63.158 0.00 0.00 0.00 4.81
384 397 1.437986 CAGTCGTCGATCCCTTCCC 59.562 63.158 0.00 0.00 0.00 3.97
385 398 1.321074 ACCAGTCGTCGATCCCTTCC 61.321 60.000 0.00 0.00 0.00 3.46
386 399 0.531200 AACCAGTCGTCGATCCCTTC 59.469 55.000 0.00 0.00 0.00 3.46
479 495 7.536625 ACACCCATATACTATCAACTACTCCT 58.463 38.462 0.00 0.00 0.00 3.69
481 497 9.477484 CAAACACCCATATACTATCAACTACTC 57.523 37.037 0.00 0.00 0.00 2.59
541 557 1.861982 ACCGCAGTTGATAGTAGGGT 58.138 50.000 0.00 0.00 0.00 4.34
569 585 3.451902 AGGAGGAAGAGAGAAGCAATGAG 59.548 47.826 0.00 0.00 0.00 2.90
570 586 3.448934 AGGAGGAAGAGAGAAGCAATGA 58.551 45.455 0.00 0.00 0.00 2.57
571 587 3.910568 AGGAGGAAGAGAGAAGCAATG 57.089 47.619 0.00 0.00 0.00 2.82
572 588 6.157645 TGATTAAGGAGGAAGAGAGAAGCAAT 59.842 38.462 0.00 0.00 0.00 3.56
573 589 5.485353 TGATTAAGGAGGAAGAGAGAAGCAA 59.515 40.000 0.00 0.00 0.00 3.91
574 590 5.026121 TGATTAAGGAGGAAGAGAGAAGCA 58.974 41.667 0.00 0.00 0.00 3.91
575 591 5.606348 TGATTAAGGAGGAAGAGAGAAGC 57.394 43.478 0.00 0.00 0.00 3.86
576 592 6.821160 GGTTTGATTAAGGAGGAAGAGAGAAG 59.179 42.308 0.00 0.00 0.00 2.85
577 593 6.272324 TGGTTTGATTAAGGAGGAAGAGAGAA 59.728 38.462 0.00 0.00 0.00 2.87
578 594 5.785423 TGGTTTGATTAAGGAGGAAGAGAGA 59.215 40.000 0.00 0.00 0.00 3.10
669 695 4.573201 CCGTTCTTAACTGAGTGGAACAAA 59.427 41.667 18.84 0.00 44.16 2.83
670 696 4.124238 CCGTTCTTAACTGAGTGGAACAA 58.876 43.478 18.84 0.00 44.16 2.83
745 780 5.907866 AGTTCCGAGGAAAAGAACAAAAA 57.092 34.783 6.09 0.00 41.86 1.94
777 812 5.109903 CCTCAACTGGTAGAGTAATTTCCG 58.890 45.833 0.00 0.00 33.09 4.30
831 866 6.355405 CGCACGCTAAAGATATTTTCATCTTG 59.645 38.462 0.00 0.00 43.01 3.02
874 915 1.186267 AGGTTCTGACGGACTGACCC 61.186 60.000 0.71 0.00 34.64 4.46
889 930 2.364448 GGAGGAGGAGCCGAGGTT 60.364 66.667 0.00 0.00 43.43 3.50
909 950 3.630769 CGAGTGCTTATATATAGCCGGGA 59.369 47.826 2.18 0.00 37.85 5.14
922 963 0.973632 ATGTGTGGGTCGAGTGCTTA 59.026 50.000 0.00 0.00 0.00 3.09
923 964 0.320771 GATGTGTGGGTCGAGTGCTT 60.321 55.000 0.00 0.00 0.00 3.91
924 965 1.293498 GATGTGTGGGTCGAGTGCT 59.707 57.895 0.00 0.00 0.00 4.40
926 967 0.250234 ATGGATGTGTGGGTCGAGTG 59.750 55.000 0.00 0.00 0.00 3.51
957 998 1.515020 CGAGAGGGGAGTGCAAGAG 59.485 63.158 0.00 0.00 0.00 2.85
958 999 2.650116 GCGAGAGGGGAGTGCAAGA 61.650 63.158 0.00 0.00 0.00 3.02
966 1007 1.228894 ACTTGACTGCGAGAGGGGA 60.229 57.895 0.00 0.00 0.00 4.81
981 1426 0.832135 TCTCGGGCAAGACCAGACTT 60.832 55.000 0.00 0.00 37.77 3.01
985 1430 0.250234 TTCATCTCGGGCAAGACCAG 59.750 55.000 0.00 0.00 42.05 4.00
1102 1547 0.691332 GGGGAGAAGAGGAAAACGGT 59.309 55.000 0.00 0.00 0.00 4.83
1147 1592 1.583967 GCGAGACGACGATGACCTG 60.584 63.158 0.00 0.00 35.09 4.00
1149 1594 1.297745 GAGCGAGACGACGATGACC 60.298 63.158 0.00 0.00 35.09 4.02
1451 1899 1.630244 CTCGCTGCGTTCCTTCTTGG 61.630 60.000 22.48 0.00 37.10 3.61
1530 1984 4.451150 TGCCACGCCGAGTCCATC 62.451 66.667 0.00 0.00 0.00 3.51
1989 2443 1.315690 GTGCATCCATCCATCCTGTG 58.684 55.000 0.00 0.00 0.00 3.66
1990 2444 0.179037 CGTGCATCCATCCATCCTGT 60.179 55.000 0.00 0.00 0.00 4.00
1991 2445 0.179037 ACGTGCATCCATCCATCCTG 60.179 55.000 0.00 0.00 0.00 3.86
2022 2476 1.202582 CTGTACAGTCTCCCTTCCGTG 59.797 57.143 15.06 0.00 0.00 4.94
2031 2485 4.551388 CTGACCAACTTCTGTACAGTCTC 58.449 47.826 21.99 8.07 0.00 3.36
2095 2549 4.137872 GCATGCAATGGCGGCAGT 62.138 61.111 19.29 13.15 46.86 4.40
2196 2657 2.741985 CGCGGTGCATGACCAGAA 60.742 61.111 0.00 0.00 46.55 3.02
2323 2788 3.202829 AGAACAAAGAAACGGCTACCA 57.797 42.857 0.00 0.00 0.00 3.25
2358 2823 4.647399 AGGGGTCTCGAAAATTTGAAACAA 59.353 37.500 0.00 0.00 0.00 2.83
2453 2919 5.048504 CAGTTATCAAGCACACATCCTTTGT 60.049 40.000 0.00 0.00 39.91 2.83
2507 2973 1.028130 GCTTAATGCAAGAGGCCCTC 58.972 55.000 1.26 1.26 43.89 4.30
2522 2988 4.081142 TCAGTGAAATCCAGAATCCGCTTA 60.081 41.667 0.00 0.00 0.00 3.09
2526 2992 4.701765 AGATCAGTGAAATCCAGAATCCG 58.298 43.478 0.00 0.00 0.00 4.18
2585 3051 4.567987 AATCCTCTACTCCCTCCAATCT 57.432 45.455 0.00 0.00 0.00 2.40
2638 3104 2.936498 CGAGGTTTGCAATCCTACGATT 59.064 45.455 25.58 6.27 39.39 3.34
2691 3189 9.035607 ACGCACTCTTATTATATTCTTGTCTTG 57.964 33.333 0.00 0.00 0.00 3.02
2754 3252 3.081804 CTGTGGACCAAATACCCAAGTC 58.918 50.000 0.00 0.00 0.00 3.01
2782 3280 7.970061 TGTGCTTATTAAGATCAACATGCTTTC 59.030 33.333 7.63 0.00 0.00 2.62
2866 3395 5.163622 CCGACCTCCTTTAGTAATTCGTACA 60.164 44.000 0.00 0.00 34.88 2.90
2889 3418 4.379204 CGCGAGAATTTTACGATCTACTCC 59.621 45.833 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.