Multiple sequence alignment - TraesCS6D01G383000

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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 TraesCS6D01G383000 chr6D 100.000 3998 0 0 1 3998 462403899 462407896 0.000000e+00 7384.0
1 TraesCS6D01G383000 chr6D 98.126 2028 28 4 1 2023 452076246 452078268 0.000000e+00 3526.0
2 TraesCS6D01G383000 chr6D 98.203 1113 14 3 2888 3998 452079313 452080421 0.000000e+00 1940.0
3 TraesCS6D01G383000 chr6D 99.242 792 4 1 2024 2815 452078526 452079315 0.000000e+00 1428.0
4 TraesCS6D01G383000 chr6D 93.824 340 20 1 513 851 245042211 245041872 9.910000e-141 510.0
5 TraesCS6D01G383000 chr6B 93.814 1164 61 8 869 2023 704853152 704851991 0.000000e+00 1740.0
6 TraesCS6D01G383000 chr6B 93.471 628 29 8 3379 3998 704859088 704859711 0.000000e+00 922.0
7 TraesCS6D01G383000 chr6B 95.107 327 16 0 513 839 700192303 700192629 2.130000e-142 516.0
8 TraesCS6D01G383000 chr6B 88.889 225 17 4 2024 2248 704851733 704851517 1.830000e-68 270.0
9 TraesCS6D01G383000 chr6B 92.715 151 5 3 2975 3119 704858757 704858907 3.130000e-51 213.0
10 TraesCS6D01G383000 chr6B 85.714 91 7 2 2890 2978 704858592 704858678 1.530000e-14 91.6
11 TraesCS6D01G383000 chr6B 90.196 51 1 1 2550 2600 681924214 681924260 3.340000e-06 63.9
12 TraesCS6D01G383000 chr6A 93.317 1197 32 9 845 2023 609157298 609158464 0.000000e+00 1724.0
13 TraesCS6D01G383000 chr6A 95.652 345 11 3 3657 3998 609160737 609161080 5.840000e-153 551.0
14 TraesCS6D01G383000 chr6A 91.513 271 16 4 2024 2287 609158722 609158992 2.270000e-97 366.0
15 TraesCS6D01G383000 chr6A 84.739 249 26 5 3210 3457 609160388 609160625 5.160000e-59 239.0
16 TraesCS6D01G383000 chr6A 84.581 227 19 11 2890 3113 609160121 609160334 1.130000e-50 211.0
17 TraesCS6D01G383000 chr6A 91.860 86 7 0 1 86 359013878 359013963 1.950000e-23 121.0
18 TraesCS6D01G383000 chr6A 88.235 51 2 4 2550 2600 595481199 595481245 1.550000e-04 58.4
19 TraesCS6D01G383000 chr7D 95.413 327 15 0 513 839 545253802 545254128 4.580000e-144 521.0
20 TraesCS6D01G383000 chr7D 95.107 327 16 0 513 839 541816453 541816127 2.130000e-142 516.0
21 TraesCS6D01G383000 chr1D 95.413 327 15 0 513 839 490705950 490706276 4.580000e-144 521.0
22 TraesCS6D01G383000 chr1D 94.848 330 16 1 513 841 75466003 75466332 7.660000e-142 514.0
23 TraesCS6D01G383000 chr1D 98.837 86 1 0 1 86 176355954 176355869 1.920000e-33 154.0
24 TraesCS6D01G383000 chr1D 100.000 82 0 0 1 82 356876398 356876317 6.920000e-33 152.0
25 TraesCS6D01G383000 chr3D 95.107 327 16 0 513 839 127227917 127228243 2.130000e-142 516.0
26 TraesCS6D01G383000 chr3D 76.012 667 116 28 1385 2020 593236143 593236796 5.020000e-79 305.0
27 TraesCS6D01G383000 chr4D 94.562 331 18 0 512 842 55583311 55582981 2.760000e-141 512.0
28 TraesCS6D01G383000 chr3B 76.190 672 112 36 1385 2023 795839886 795840542 1.080000e-80 311.0
29 TraesCS6D01G383000 chr3A 75.785 669 120 30 1385 2023 724515610 724516266 2.340000e-77 300.0
30 TraesCS6D01G383000 chr5D 76.812 552 86 32 1383 1907 45379067 45378531 5.090000e-69 272.0
31 TraesCS6D01G383000 chr5D 71.988 689 138 36 1385 2034 1542432 1541760 6.920000e-33 152.0
32 TraesCS6D01G383000 chr5B 74.481 674 121 38 1383 2023 45393554 45394209 1.110000e-60 244.0
33 TraesCS6D01G383000 chr5A 76.275 510 83 29 1383 1867 36330859 36331355 1.860000e-58 237.0
34 TraesCS6D01G383000 chr7A 94.186 86 5 0 1 86 439781348 439781263 9.020000e-27 132.0
35 TraesCS6D01G383000 chr2B 94.186 86 5 0 1 86 484100666 484100581 9.020000e-27 132.0
36 TraesCS6D01G383000 chrUn 71.325 687 146 32 1385 2034 146272474 146271802 3.240000e-26 130.0
37 TraesCS6D01G383000 chr2A 93.023 86 6 0 1 86 77797630 77797545 4.190000e-25 126.0
38 TraesCS6D01G383000 chr2A 93.023 86 6 0 1 86 382860830 382860915 4.190000e-25 126.0
39 TraesCS6D01G383000 chr4A 100.000 30 0 0 2318 2347 708602998 708603027 5.580000e-04 56.5


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 TraesCS6D01G383000 chr6D 462403899 462407896 3997 False 7384.000000 7384 100.000000 1 3998 1 chr6D.!!$F1 3997
1 TraesCS6D01G383000 chr6D 452076246 452080421 4175 False 2298.000000 3526 98.523667 1 3998 3 chr6D.!!$F2 3997
2 TraesCS6D01G383000 chr6B 704851517 704853152 1635 True 1005.000000 1740 91.351500 869 2248 2 chr6B.!!$R1 1379
3 TraesCS6D01G383000 chr6B 704858592 704859711 1119 False 408.866667 922 90.633333 2890 3998 3 chr6B.!!$F3 1108
4 TraesCS6D01G383000 chr6A 609157298 609161080 3782 False 618.200000 1724 89.960400 845 3998 5 chr6A.!!$F3 3153
5 TraesCS6D01G383000 chr3D 593236143 593236796 653 False 305.000000 305 76.012000 1385 2020 1 chr3D.!!$F2 635
6 TraesCS6D01G383000 chr3B 795839886 795840542 656 False 311.000000 311 76.190000 1385 2023 1 chr3B.!!$F1 638
7 TraesCS6D01G383000 chr3A 724515610 724516266 656 False 300.000000 300 75.785000 1385 2023 1 chr3A.!!$F1 638
8 TraesCS6D01G383000 chr5D 45378531 45379067 536 True 272.000000 272 76.812000 1383 1907 1 chr5D.!!$R2 524
9 TraesCS6D01G383000 chr5B 45393554 45394209 655 False 244.000000 244 74.481000 1383 2023 1 chr5B.!!$F1 640

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
36 37 2.335011 CGACGGTCACTGTCAGCA 59.665 61.111 17.16 0.0 36.11 4.41 F
1311 1347 0.879400 GACATGCTGGAGGCGATGAG 60.879 60.000 0.00 0.0 45.43 2.90 F
2495 2892 0.904394 GCCCCAAAGAAGATGGCCAA 60.904 55.000 10.96 0.0 36.58 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1957 2011 1.033574 CGAAGAGGCCGAAGAGGTAT 58.966 55.000 0.00 0.0 43.7 2.73 R
2833 3391 0.251916 CTTGCCGGGGTGAGTTATGA 59.748 55.000 2.18 0.0 0.0 2.15 R
3927 4898 3.376636 TCCCCGTGTCCTGTTCATATAA 58.623 45.455 0.00 0.0 0.0 0.98 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
36 37 2.335011 CGACGGTCACTGTCAGCA 59.665 61.111 17.16 0.00 36.11 4.41
133 134 3.773560 TGGCCCTTAAACTGCAATACTT 58.226 40.909 0.00 0.00 0.00 2.24
224 225 2.844348 ACGAATGACTACCCCTGGAAAT 59.156 45.455 0.00 0.00 0.00 2.17
374 375 8.721133 TCATATATGAAGAGTGGCCTAACTAA 57.279 34.615 13.12 0.00 33.08 2.24
375 376 8.585881 TCATATATGAAGAGTGGCCTAACTAAC 58.414 37.037 13.12 0.00 33.08 2.34
376 377 8.589338 CATATATGAAGAGTGGCCTAACTAACT 58.411 37.037 6.92 0.00 0.00 2.24
377 378 4.803098 TGAAGAGTGGCCTAACTAACTC 57.197 45.455 3.32 7.49 39.47 3.01
378 379 4.157246 TGAAGAGTGGCCTAACTAACTCA 58.843 43.478 18.03 8.65 41.22 3.41
431 432 5.178797 CAATGTGTAGGTGGTAAAGGAGAG 58.821 45.833 0.00 0.00 0.00 3.20
494 495 7.491048 ACTCGTAAAATGTTTGAAGTTGCAAAT 59.509 29.630 0.00 0.00 39.65 2.32
495 496 8.190888 TCGTAAAATGTTTGAAGTTGCAAATT 57.809 26.923 12.63 12.63 39.65 1.82
496 497 8.660373 TCGTAAAATGTTTGAAGTTGCAAATTT 58.340 25.926 14.04 5.35 39.65 1.82
497 498 9.907576 CGTAAAATGTTTGAAGTTGCAAATTTA 57.092 25.926 14.04 6.81 39.65 1.40
565 566 4.935352 TCAAAAATCTCACCAACCAAGG 57.065 40.909 0.00 0.00 0.00 3.61
581 582 2.355108 CCAAGGTAGATGGTGAGTGGTG 60.355 54.545 0.00 0.00 33.08 4.17
604 605 9.644993 GGTGAAATACTTTTTGTAATTTGCAAC 57.355 29.630 0.00 0.00 34.45 4.17
704 705 7.656707 AAAGTACATGCATTGGTCAATTTTC 57.343 32.000 0.00 0.00 0.00 2.29
761 762 3.330405 TGGAATCTGAACTTGTGATGGGA 59.670 43.478 0.00 0.00 0.00 4.37
831 832 2.484602 AGCCCTATAAACCGGAAAGGA 58.515 47.619 9.46 0.00 45.00 3.36
1279 1315 2.242572 CGGCATCGAGGTCATGCTG 61.243 63.158 1.43 2.09 45.18 4.41
1311 1347 0.879400 GACATGCTGGAGGCGATGAG 60.879 60.000 0.00 0.00 45.43 2.90
1595 1643 2.706834 ATCGACGGCGTCATGACCA 61.707 57.895 35.62 14.61 38.98 4.02
1910 1961 1.595993 CGACGGCCTCCTCAAGAAGA 61.596 60.000 0.00 0.00 0.00 2.87
1957 2011 1.220749 GCAGGGCAAGATGGACGTA 59.779 57.895 0.00 0.00 0.00 3.57
2440 2833 7.754069 ATGCATAAATTGTGTAAACAATCCG 57.246 32.000 11.74 2.73 39.18 4.18
2495 2892 0.904394 GCCCCAAAGAAGATGGCCAA 60.904 55.000 10.96 0.00 36.58 4.52
2839 3397 2.042686 TGCCAGTGCAGGATCATAAC 57.957 50.000 0.00 0.00 44.23 1.89
2840 3398 1.561076 TGCCAGTGCAGGATCATAACT 59.439 47.619 0.00 0.00 44.23 2.24
2841 3399 2.216898 GCCAGTGCAGGATCATAACTC 58.783 52.381 0.00 0.00 37.47 3.01
2842 3400 2.420547 GCCAGTGCAGGATCATAACTCA 60.421 50.000 0.00 0.00 37.47 3.41
2844 3402 3.201290 CAGTGCAGGATCATAACTCACC 58.799 50.000 0.00 0.00 0.00 4.02
2845 3403 2.171448 AGTGCAGGATCATAACTCACCC 59.829 50.000 0.00 0.00 0.00 4.61
2852 3688 0.251916 TCATAACTCACCCCGGCAAG 59.748 55.000 0.00 0.00 0.00 4.01
2859 3695 2.852075 ACCCCGGCAAGTCTTCCA 60.852 61.111 0.00 0.00 0.00 3.53
2861 3697 2.359975 CCCGGCAAGTCTTCCACC 60.360 66.667 0.00 0.00 0.00 4.61
2865 3701 1.885871 GGCAAGTCTTCCACCATGC 59.114 57.895 0.00 0.00 37.53 4.06
2879 3715 1.888512 ACCATGCAAACACATGTCCTC 59.111 47.619 0.00 0.00 44.88 3.71
2885 3721 2.157668 GCAAACACATGTCCTCGTACTG 59.842 50.000 0.00 0.00 0.00 2.74
3114 4070 5.358442 ACATAGAGTCTCACAGTCCATGTAC 59.642 44.000 0.00 0.00 41.41 2.90
3127 4083 4.402793 AGTCCATGTACTCAGTGTGATACC 59.597 45.833 0.00 0.00 0.00 2.73
3128 4084 4.402793 GTCCATGTACTCAGTGTGATACCT 59.597 45.833 0.00 0.00 0.00 3.08
3129 4085 5.023452 TCCATGTACTCAGTGTGATACCTT 58.977 41.667 0.00 0.00 0.00 3.50
3208 4168 6.014925 TGGCACTTAATTACAGTCTAGTGACA 60.015 38.462 14.53 14.53 46.27 3.58
3267 4227 3.001634 CCAGTGGATCGAATTTCGTGATG 59.998 47.826 17.61 9.47 41.35 3.07
3315 4275 1.089920 CTGTGTGTGATTGGCTAGCC 58.910 55.000 27.71 27.71 0.00 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 7.716799 ACCTTAGCAATTTTGTGATATGGAA 57.283 32.000 8.77 0.00 37.03 3.53
431 432 6.000219 ACTGGTGCAGGTATATTGATCAATC 59.000 40.000 23.95 10.32 35.51 2.67
494 495 9.538508 GAGGGAGTAACTTATTTATTCGCTAAA 57.461 33.333 4.94 0.00 44.69 1.85
495 496 8.146412 GGAGGGAGTAACTTATTTATTCGCTAA 58.854 37.037 4.94 0.00 44.69 3.09
496 497 7.508296 AGGAGGGAGTAACTTATTTATTCGCTA 59.492 37.037 4.94 0.00 44.69 4.26
497 498 6.326843 AGGAGGGAGTAACTTATTTATTCGCT 59.673 38.462 4.69 4.69 46.25 4.93
565 566 5.978814 AGTATTTCACCACTCACCATCTAC 58.021 41.667 0.00 0.00 0.00 2.59
677 678 8.706492 AAATTGACCAATGCATGTACTTTATG 57.294 30.769 0.00 0.00 0.00 1.90
740 741 3.955471 TCCCATCACAAGTTCAGATTCC 58.045 45.455 0.00 0.00 0.00 3.01
761 762 9.791801 ATTTTATAAGGCTCAATTTGGTTGTTT 57.208 25.926 0.00 0.00 38.95 2.83
799 800 7.094762 CCGGTTTATAGGGCTTATCTCAAAATC 60.095 40.741 0.00 0.00 0.00 2.17
831 832 2.187946 GCATGCGCAGTACTCCCT 59.812 61.111 18.32 0.00 38.36 4.20
948 962 1.822186 GGTGCTCGTGGTTGGTGTT 60.822 57.895 0.00 0.00 0.00 3.32
1279 1315 2.120909 CATGTCGTTGGGGATGCCC 61.121 63.158 16.99 16.99 44.51 5.36
1595 1643 2.030893 CGTGCATGAACTTGACCATGTT 60.031 45.455 0.00 1.59 41.49 2.71
1910 1961 2.044946 GCCCTCGTTCTTGGCCAT 60.045 61.111 6.09 0.00 39.30 4.40
1957 2011 1.033574 CGAAGAGGCCGAAGAGGTAT 58.966 55.000 0.00 0.00 43.70 2.73
2495 2892 2.693591 TCTTCGTTCACTGTCTTCAGGT 59.306 45.455 0.47 0.00 45.14 4.00
2821 3379 2.216898 GAGTTATGATCCTGCACTGGC 58.783 52.381 0.00 0.00 41.68 4.85
2827 3385 1.541233 CGGGGTGAGTTATGATCCTGC 60.541 57.143 0.00 0.00 0.00 4.85
2828 3386 1.070758 CCGGGGTGAGTTATGATCCTG 59.929 57.143 0.00 0.00 0.00 3.86
2832 3390 0.916086 TTGCCGGGGTGAGTTATGAT 59.084 50.000 2.18 0.00 0.00 2.45
2833 3391 0.251916 CTTGCCGGGGTGAGTTATGA 59.748 55.000 2.18 0.00 0.00 2.15
2835 3393 0.252197 GACTTGCCGGGGTGAGTTAT 59.748 55.000 2.18 0.00 0.00 1.89
2836 3394 0.834687 AGACTTGCCGGGGTGAGTTA 60.835 55.000 2.18 0.00 0.00 2.24
2839 3397 1.376037 GAAGACTTGCCGGGGTGAG 60.376 63.158 2.18 0.00 0.00 3.51
2840 3398 2.747686 GAAGACTTGCCGGGGTGA 59.252 61.111 2.18 0.00 0.00 4.02
2841 3399 2.359975 GGAAGACTTGCCGGGGTG 60.360 66.667 2.18 0.00 0.00 4.61
2842 3400 2.852075 TGGAAGACTTGCCGGGGT 60.852 61.111 2.18 0.00 0.00 4.95
2844 3402 2.359975 GGTGGAAGACTTGCCGGG 60.360 66.667 2.18 0.00 0.00 5.73
2845 3403 1.002134 ATGGTGGAAGACTTGCCGG 60.002 57.895 4.07 0.00 0.00 6.13
2852 3688 1.680735 TGTGTTTGCATGGTGGAAGAC 59.319 47.619 0.00 0.00 0.00 3.01
2865 3701 2.157668 GCAGTACGAGGACATGTGTTTG 59.842 50.000 1.15 0.00 0.00 2.93
2885 3721 0.391130 TTCCAGCACCTGTATCACGC 60.391 55.000 0.00 0.00 0.00 5.34
3153 4109 5.675538 AGCAGTTCATTAGTCCAAGGTATC 58.324 41.667 0.00 0.00 0.00 2.24
3208 4168 1.203523 TCTTTTGCTGCACACGGTTTT 59.796 42.857 0.00 0.00 0.00 2.43
3927 4898 3.376636 TCCCCGTGTCCTGTTCATATAA 58.623 45.455 0.00 0.00 0.00 0.98


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

AutoCloner maintained by Alex Coulton.