Multiple sequence alignment - TraesCS4D01G221900

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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 TraesCS4D01G221900 chr4D 100.000 3104 0 0 1 3104 379153811 379156914 0.000000e+00 5733.0
1 TraesCS4D01G221900 chr4D 83.105 876 115 25 1167 2015 433220627 433221496 0.000000e+00 767.0
2 TraesCS4D01G221900 chr4B 92.888 3051 118 45 1 3013 465740847 465743836 0.000000e+00 4340.0
3 TraesCS4D01G221900 chr4B 82.763 876 118 25 1167 2015 531245777 531246646 0.000000e+00 750.0
4 TraesCS4D01G221900 chr4A 92.532 1848 69 38 442 2268 85893836 85892037 0.000000e+00 2584.0
5 TraesCS4D01G221900 chr4A 82.821 879 115 24 1167 2015 34669443 34670315 0.000000e+00 754.0
6 TraesCS4D01G221900 chr4A 90.463 367 29 5 2310 2674 85892046 85891684 2.170000e-131 479.0
7 TraesCS4D01G221900 chr4A 85.714 315 12 12 1 289 85896021 85895714 5.030000e-78 302.0
8 TraesCS4D01G221900 chr4A 87.417 151 5 8 300 446 85895533 85895393 8.910000e-36 161.0
9 TraesCS4D01G221900 chr4A 88.608 79 1 4 3034 3104 85891228 85891150 4.260000e-14 89.8


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 TraesCS4D01G221900 chr4D 379153811 379156914 3103 False 5733.00 5733 100.0000 1 3104 1 chr4D.!!$F1 3103
1 TraesCS4D01G221900 chr4D 433220627 433221496 869 False 767.00 767 83.1050 1167 2015 1 chr4D.!!$F2 848
2 TraesCS4D01G221900 chr4B 465740847 465743836 2989 False 4340.00 4340 92.8880 1 3013 1 chr4B.!!$F1 3012
3 TraesCS4D01G221900 chr4B 531245777 531246646 869 False 750.00 750 82.7630 1167 2015 1 chr4B.!!$F2 848
4 TraesCS4D01G221900 chr4A 34669443 34670315 872 False 754.00 754 82.8210 1167 2015 1 chr4A.!!$F1 848
5 TraesCS4D01G221900 chr4A 85891150 85896021 4871 True 723.16 2584 88.9468 1 3104 5 chr4A.!!$R1 3103

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
741 2528 0.106868 CAGATCAGGGGCAAGCATGA 60.107 55.0 0.0 0.0 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2711 4574 0.107945 GGTGAGACAGCAGGTGATCC 60.108 60.0 6.61 0.0 0.0 3.36 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
47 50 9.813446 TTAGATAATGATCTTCATCGATGATGG 57.187 33.333 30.19 23.86 39.56 3.51
52 55 3.480505 TCTTCATCGATGATGGCATGT 57.519 42.857 30.19 0.00 40.15 3.21
54 57 4.959723 TCTTCATCGATGATGGCATGTAA 58.040 39.130 30.19 13.83 40.15 2.41
55 58 5.554070 TCTTCATCGATGATGGCATGTAAT 58.446 37.500 30.19 0.00 40.15 1.89
56 59 6.700352 TCTTCATCGATGATGGCATGTAATA 58.300 36.000 30.19 12.79 40.15 0.98
57 60 7.160726 TCTTCATCGATGATGGCATGTAATAA 58.839 34.615 30.19 12.63 40.15 1.40
58 61 6.973229 TCATCGATGATGGCATGTAATAAG 57.027 37.500 23.99 0.00 40.15 1.73
59 62 6.466812 TCATCGATGATGGCATGTAATAAGT 58.533 36.000 23.99 0.00 40.15 2.24
60 63 7.610865 TCATCGATGATGGCATGTAATAAGTA 58.389 34.615 23.99 0.00 40.15 2.24
61 64 7.761249 TCATCGATGATGGCATGTAATAAGTAG 59.239 37.037 23.99 0.00 40.15 2.57
62 65 6.993079 TCGATGATGGCATGTAATAAGTAGT 58.007 36.000 3.81 0.00 34.11 2.73
104 107 5.935206 TCATTTCTCTGCCGTGTAATGTAAA 59.065 36.000 8.55 0.00 0.00 2.01
105 108 6.428465 TCATTTCTCTGCCGTGTAATGTAAAA 59.572 34.615 8.55 0.00 0.00 1.52
106 109 6.621316 TTTCTCTGCCGTGTAATGTAAAAA 57.379 33.333 0.00 0.00 0.00 1.94
107 110 5.856126 TCTCTGCCGTGTAATGTAAAAAG 57.144 39.130 0.00 0.00 0.00 2.27
156 167 1.598132 CGAAGAAGCAGAGCATCCATG 59.402 52.381 0.00 0.00 33.66 3.66
199 220 8.186821 CCTTTTATAGCTGATGAAGGTCAAAAG 58.813 37.037 0.00 12.64 41.96 2.27
281 317 0.943835 CATGCATGCCCAATGATGCG 60.944 55.000 14.93 0.00 46.66 4.73
289 325 1.201181 GCCCAATGATGCGTGTAAACA 59.799 47.619 0.00 0.00 0.00 2.83
293 329 4.326817 CCCAATGATGCGTGTAAACAAATG 59.673 41.667 0.00 0.00 0.00 2.32
298 504 3.699779 TGCGTGTAAACAAATGCTGAA 57.300 38.095 5.28 0.00 0.00 3.02
322 528 4.096984 CCAGCTTCATATTCTCACCAAACC 59.903 45.833 0.00 0.00 0.00 3.27
323 529 4.701651 CAGCTTCATATTCTCACCAAACCA 59.298 41.667 0.00 0.00 0.00 3.67
324 530 4.702131 AGCTTCATATTCTCACCAAACCAC 59.298 41.667 0.00 0.00 0.00 4.16
370 576 8.226543 TGACAAAAATCAAATCAAATACGAGC 57.773 30.769 0.00 0.00 0.00 5.03
610 2387 2.125147 ATCACCGCCACATGACCG 60.125 61.111 0.00 0.00 0.00 4.79
741 2528 0.106868 CAGATCAGGGGCAAGCATGA 60.107 55.000 0.00 0.00 0.00 3.07
781 2568 3.784202 TCCAGTTAAACCTTCCCTATCCC 59.216 47.826 0.00 0.00 0.00 3.85
797 2595 1.144057 CCCGATTCCAACTCCCTCG 59.856 63.158 0.00 0.00 0.00 4.63
901 2715 0.858139 AGGAGGAGGAGGAAGAGGGT 60.858 60.000 0.00 0.00 0.00 4.34
1040 2860 2.271497 GGACGACGGGAGAGGAGA 59.729 66.667 0.00 0.00 0.00 3.71
2035 3883 3.114616 CGGCAGTCGCAGTGGAAG 61.115 66.667 0.00 0.00 41.24 3.46
2073 3921 0.912528 GTCGTCTGATCGCCGTAAAC 59.087 55.000 0.00 0.00 0.00 2.01
2215 4069 2.365293 ACACAATGGGAAGAAAGGCAAC 59.635 45.455 0.00 0.00 0.00 4.17
2234 4088 5.221009 GGCAACAAATTCTGCAAAAATTCCA 60.221 36.000 7.07 0.00 40.46 3.53
2239 4093 5.549742 AATTCTGCAAAAATTCCACCTGA 57.450 34.783 1.78 0.00 0.00 3.86
2240 4094 5.549742 ATTCTGCAAAAATTCCACCTGAA 57.450 34.783 0.00 0.00 37.38 3.02
2241 4095 5.350504 TTCTGCAAAAATTCCACCTGAAA 57.649 34.783 0.00 0.00 36.33 2.69
2242 4096 4.692228 TCTGCAAAAATTCCACCTGAAAC 58.308 39.130 0.00 0.00 36.33 2.78
2283 4141 6.712241 TTCTGTCGATGAATCTTCAGAAAC 57.288 37.500 16.90 0.00 41.08 2.78
2284 4142 6.030548 TCTGTCGATGAATCTTCAGAAACT 57.969 37.500 9.98 0.00 41.08 2.66
2287 4145 5.106948 TGTCGATGAATCTTCAGAAACTTGC 60.107 40.000 0.00 0.00 41.08 4.01
2292 4150 1.981256 TCTTCAGAAACTTGCCCCAC 58.019 50.000 0.00 0.00 0.00 4.61
2303 4161 0.982704 TTGCCCCACCATTTTCCATG 59.017 50.000 0.00 0.00 0.00 3.66
2304 4162 1.221566 GCCCCACCATTTTCCATGC 59.778 57.895 0.00 0.00 0.00 4.06
2305 4163 1.906995 CCCCACCATTTTCCATGCC 59.093 57.895 0.00 0.00 0.00 4.40
2312 4170 4.566070 CCACCATTTTCCATGCCATCTTTT 60.566 41.667 0.00 0.00 0.00 2.27
2335 4193 3.628032 TGTCGGTCACATTGCAGTTTTTA 59.372 39.130 0.00 0.00 0.00 1.52
2431 4289 0.179084 ATTAGTGCATCGACGGTGGG 60.179 55.000 10.65 0.00 0.00 4.61
2432 4290 1.537814 TTAGTGCATCGACGGTGGGT 61.538 55.000 10.65 0.00 0.00 4.51
2433 4291 1.940883 TAGTGCATCGACGGTGGGTC 61.941 60.000 10.65 0.00 42.48 4.46
2496 4359 2.978018 GCCGGGTTCAGAAAAGCGG 61.978 63.158 2.18 0.00 0.00 5.52
2498 4361 1.574702 CCGGGTTCAGAAAAGCGGAC 61.575 60.000 0.00 0.00 0.00 4.79
2525 4388 1.388547 ACCAGCAACAACAATGTCGT 58.611 45.000 0.00 0.00 39.40 4.34
2531 4394 3.035942 GCAACAACAATGTCGTCTGTTC 58.964 45.455 0.00 0.00 39.40 3.18
2540 4403 1.202371 TGTCGTCTGTTCGCTTGTTCT 60.202 47.619 0.00 0.00 0.00 3.01
2635 4498 2.407090 TGCGATCTCTGACAGTTGTTG 58.593 47.619 1.59 0.00 0.00 3.33
2637 4500 1.728971 CGATCTCTGACAGTTGTTGCC 59.271 52.381 1.59 0.00 0.00 4.52
2638 4501 2.611473 CGATCTCTGACAGTTGTTGCCT 60.611 50.000 1.59 0.00 0.00 4.75
2640 4503 2.564771 TCTCTGACAGTTGTTGCCTTG 58.435 47.619 1.59 0.00 0.00 3.61
2641 4504 2.170397 TCTCTGACAGTTGTTGCCTTGA 59.830 45.455 1.59 0.00 0.00 3.02
2674 4537 9.247126 CTCTCTGTTGTCATCATCAGTTAATAG 57.753 37.037 6.30 0.00 40.36 1.73
2683 4546 8.821894 GTCATCATCAGTTAATAGTCCTTGTTC 58.178 37.037 0.00 0.00 0.00 3.18
2708 4571 1.294659 GAGAGCAAGTGGTTGGAGCG 61.295 60.000 0.00 0.00 33.87 5.03
2710 4573 1.152963 AGCAAGTGGTTGGAGCGTT 60.153 52.632 0.00 0.00 33.87 4.84
2711 4574 1.008538 GCAAGTGGTTGGAGCGTTG 60.009 57.895 0.00 0.00 33.87 4.10
2712 4575 1.654220 CAAGTGGTTGGAGCGTTGG 59.346 57.895 0.00 0.00 0.00 3.77
2713 4576 0.817634 CAAGTGGTTGGAGCGTTGGA 60.818 55.000 0.00 0.00 0.00 3.53
2721 4584 2.109126 GGAGCGTTGGATCACCTGC 61.109 63.158 0.00 0.00 37.04 4.85
2811 4674 7.039853 TGCAGTTTATCAAAGAATTGGTCATGA 60.040 33.333 0.00 0.00 37.15 3.07
2948 4811 5.754782 TGACTTGGTTGCATATACTCCATT 58.245 37.500 0.00 0.00 0.00 3.16
2950 4813 6.318648 TGACTTGGTTGCATATACTCCATTTC 59.681 38.462 0.00 0.00 0.00 2.17
2974 4837 3.753272 TCTTCGAATCTTGGCCTTCTTTG 59.247 43.478 3.32 0.00 0.00 2.77
3020 4883 0.179076 ATCATCGTGCGATTGCTGGA 60.179 50.000 6.47 3.77 43.34 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 37 6.936335 ACTTATTACATGCCATCATCGATGAA 59.064 34.615 30.41 15.56 42.09 2.57
36 39 6.732531 ACTTATTACATGCCATCATCGATG 57.267 37.500 19.61 19.61 39.52 3.84
47 50 8.839310 ATCATTCAGGACTACTTATTACATGC 57.161 34.615 0.00 0.00 0.00 4.06
52 55 8.585881 GGTGCTATCATTCAGGACTACTTATTA 58.414 37.037 0.00 0.00 34.99 0.98
54 57 6.554982 TGGTGCTATCATTCAGGACTACTTAT 59.445 38.462 0.00 0.00 34.99 1.73
55 58 5.897250 TGGTGCTATCATTCAGGACTACTTA 59.103 40.000 0.00 0.00 34.99 2.24
56 59 4.716784 TGGTGCTATCATTCAGGACTACTT 59.283 41.667 0.00 0.00 34.99 2.24
57 60 4.290093 TGGTGCTATCATTCAGGACTACT 58.710 43.478 0.00 0.00 34.99 2.57
58 61 4.672587 TGGTGCTATCATTCAGGACTAC 57.327 45.455 0.00 0.00 34.99 2.73
59 62 4.901250 TGATGGTGCTATCATTCAGGACTA 59.099 41.667 0.00 0.00 34.99 2.59
60 63 3.713248 TGATGGTGCTATCATTCAGGACT 59.287 43.478 0.00 0.00 34.99 3.85
61 64 4.077300 TGATGGTGCTATCATTCAGGAC 57.923 45.455 0.00 0.00 32.39 3.85
62 65 4.987963 ATGATGGTGCTATCATTCAGGA 57.012 40.909 5.38 0.00 43.41 3.86
156 167 2.717639 AGGTGAGTTGGTATCATGGC 57.282 50.000 0.00 0.00 0.00 4.40
256 292 2.894765 TCATTGGGCATGCATGATTAGG 59.105 45.455 30.64 13.61 32.13 2.69
298 504 4.574674 TTGGTGAGAATATGAAGCTGGT 57.425 40.909 0.00 0.00 0.00 4.00
304 510 4.340617 GGGTGGTTTGGTGAGAATATGAA 58.659 43.478 0.00 0.00 0.00 2.57
305 511 3.308832 GGGGTGGTTTGGTGAGAATATGA 60.309 47.826 0.00 0.00 0.00 2.15
322 528 0.820074 TACGCAGTTTGTTGGGGGTG 60.820 55.000 0.00 0.00 37.78 4.61
323 529 0.820482 GTACGCAGTTTGTTGGGGGT 60.820 55.000 0.00 0.00 37.78 4.95
324 530 0.536460 AGTACGCAGTTTGTTGGGGG 60.536 55.000 0.00 0.00 37.78 5.40
422 631 9.881649 TGGTACGTTGTATAATTTGGTGTATAA 57.118 29.630 0.00 0.00 0.00 0.98
741 2528 1.536662 AGGCTCGGAGGGAACTTGT 60.537 57.895 7.20 0.00 44.43 3.16
781 2568 2.000447 GAAACGAGGGAGTTGGAATCG 59.000 52.381 0.00 0.00 39.22 3.34
797 2595 5.989777 TGGAGTTGTAGCTTGTAGAAGAAAC 59.010 40.000 3.33 1.15 0.00 2.78
1031 2851 2.520741 CCGGCTCCTCTCCTCTCC 60.521 72.222 0.00 0.00 0.00 3.71
1162 2986 0.733150 TGAGTATCTGCCTCGTCACG 59.267 55.000 0.00 0.00 34.92 4.35
1669 3517 4.148825 CACTCCCCGGAGAAGCGG 62.149 72.222 17.73 0.00 44.53 5.52
2073 3921 1.202582 ACAGACGGACGGAAGAAGATG 59.797 52.381 0.00 0.00 0.00 2.90
2215 4069 5.759273 TCAGGTGGAATTTTTGCAGAATTTG 59.241 36.000 10.34 6.01 0.00 2.32
2234 4088 0.846693 AGGAGTGGCTTGTTTCAGGT 59.153 50.000 0.00 0.00 0.00 4.00
2239 4093 2.736670 AACAGAGGAGTGGCTTGTTT 57.263 45.000 0.00 0.00 0.00 2.83
2240 4094 2.736670 AAACAGAGGAGTGGCTTGTT 57.263 45.000 0.00 0.00 0.00 2.83
2241 4095 2.736670 AAAACAGAGGAGTGGCTTGT 57.263 45.000 0.00 0.00 0.00 3.16
2242 4096 3.004106 CAGAAAAACAGAGGAGTGGCTTG 59.996 47.826 0.00 0.00 0.00 4.01
2283 4141 1.065998 CATGGAAAATGGTGGGGCAAG 60.066 52.381 0.00 0.00 0.00 4.01
2284 4142 0.982704 CATGGAAAATGGTGGGGCAA 59.017 50.000 0.00 0.00 0.00 4.52
2287 4145 0.908656 TGGCATGGAAAATGGTGGGG 60.909 55.000 0.00 0.00 0.00 4.96
2292 4150 5.005094 ACAAAAAGATGGCATGGAAAATGG 58.995 37.500 3.81 0.00 0.00 3.16
2303 4161 1.606668 TGTGACCGACAAAAAGATGGC 59.393 47.619 0.00 0.00 0.00 4.40
2304 4162 4.229096 CAATGTGACCGACAAAAAGATGG 58.771 43.478 0.00 0.00 38.36 3.51
2305 4163 3.670055 GCAATGTGACCGACAAAAAGATG 59.330 43.478 0.00 0.00 38.36 2.90
2312 4170 1.674359 AACTGCAATGTGACCGACAA 58.326 45.000 0.00 0.00 38.36 3.18
2347 4205 7.922811 AGTACAGCCTTTTCTTTTTCTGATTTG 59.077 33.333 0.00 0.00 0.00 2.32
2496 4359 1.388547 TGTTGCTGGTTTGTCCTGTC 58.611 50.000 0.00 0.00 37.45 3.51
2498 4361 1.476085 TGTTGTTGCTGGTTTGTCCTG 59.524 47.619 0.00 0.00 38.06 3.86
2525 4388 0.250295 CCCCAGAACAAGCGAACAGA 60.250 55.000 0.00 0.00 0.00 3.41
2531 4394 1.903404 AAAGGCCCCAGAACAAGCG 60.903 57.895 0.00 0.00 0.00 4.68
2635 4498 3.608316 ACAGAGAGAACTCATCAAGGC 57.392 47.619 4.64 0.00 44.79 4.35
2637 4500 5.536260 TGACAACAGAGAGAACTCATCAAG 58.464 41.667 4.64 0.60 44.79 3.02
2638 4501 5.535753 TGACAACAGAGAGAACTCATCAA 57.464 39.130 4.64 0.00 44.79 2.57
2640 4503 5.718146 TGATGACAACAGAGAGAACTCATC 58.282 41.667 4.64 0.00 44.79 2.92
2641 4504 5.735285 TGATGACAACAGAGAGAACTCAT 57.265 39.130 4.64 0.00 44.79 2.90
2674 4537 1.531578 GCTCTCAAACCGAACAAGGAC 59.468 52.381 0.00 0.00 34.73 3.85
2683 4546 1.002468 CAACCACTTGCTCTCAAACCG 60.002 52.381 0.00 0.00 0.00 4.44
2708 4571 1.002430 TGAGACAGCAGGTGATCCAAC 59.998 52.381 6.61 0.00 35.89 3.77
2710 4573 0.610174 GTGAGACAGCAGGTGATCCA 59.390 55.000 6.61 0.00 35.89 3.41
2711 4574 0.107945 GGTGAGACAGCAGGTGATCC 60.108 60.000 6.61 0.00 0.00 3.36
2712 4575 0.107945 GGGTGAGACAGCAGGTGATC 60.108 60.000 6.61 4.72 33.07 2.92
2713 4576 0.837691 TGGGTGAGACAGCAGGTGAT 60.838 55.000 6.61 0.00 33.07 3.06
2744 4607 1.369321 GGTGCGGCAAATTTTGGGA 59.631 52.632 3.23 0.00 0.00 4.37
2776 4639 1.291132 GATAAACTGCAGTCCTCGGC 58.709 55.000 21.95 4.27 35.44 5.54
2948 4811 3.703001 AGGCCAAGATTCGAAGAAGAA 57.297 42.857 5.01 0.00 45.90 2.52
2950 4813 3.604582 AGAAGGCCAAGATTCGAAGAAG 58.395 45.455 5.01 0.00 45.90 2.85
3020 4883 2.699846 TGATGCAACTGGCCTTTTCTTT 59.300 40.909 3.32 0.00 43.89 2.52
3045 5067 1.639635 AAGGAAGGATGGCCGCATCT 61.640 55.000 0.00 0.00 39.96 2.90


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

AutoCloner maintained by Alex Coulton.