Multiple sequence alignment - TraesCS4B01G134300

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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 TraesCS4B01G134300 chr4B 100.000 2931 0 0 1 2931 175309594 175306664 0.000000e+00 5413.0
1 TraesCS4B01G134300 chr4B 97.389 1800 47 0 1 1800 531339287 531341086 0.000000e+00 3064.0
2 TraesCS4B01G134300 chr4B 95.325 1583 62 7 1355 2931 609105459 609103883 0.000000e+00 2503.0
3 TraesCS4B01G134300 chr4B 96.292 809 30 0 1 809 357795610 357794802 0.000000e+00 1328.0
4 TraesCS4B01G134300 chr4B 83.905 845 83 21 1 809 289622409 289623236 0.000000e+00 758.0
5 TraesCS4B01G134300 chr4B 94.819 386 16 2 2544 2929 172482537 172482918 1.500000e-167 599.0
6 TraesCS4B01G134300 chr4B 93.830 389 21 3 2544 2931 316994408 316994794 1.510000e-162 582.0
7 TraesCS4B01G134300 chr4B 93.995 383 21 2 2549 2931 491006787 491006407 1.960000e-161 579.0
8 TraesCS4B01G134300 chr7D 96.510 1748 48 5 809 2551 311619004 311620743 0.000000e+00 2878.0
9 TraesCS4B01G134300 chr7D 89.610 77 6 1 559 633 46354311 46354235 2.400000e-16 97.1
10 TraesCS4B01G134300 chr3A 96.294 1727 57 5 814 2535 361576865 361575141 0.000000e+00 2828.0
11 TraesCS4B01G134300 chr5B 96.912 1684 46 4 809 2487 209633858 209632176 0.000000e+00 2817.0
12 TraesCS4B01G134300 chr6A 95.757 1744 66 6 814 2551 197861226 197859485 0.000000e+00 2804.0
13 TraesCS4B01G134300 chr3B 95.538 1748 72 4 809 2551 371039713 371037967 0.000000e+00 2791.0
14 TraesCS4B01G134300 chr3B 85.885 836 86 18 1 808 9161158 9161989 0.000000e+00 861.0
15 TraesCS4B01G134300 chr5D 95.974 1689 56 9 809 2487 199084299 199085985 0.000000e+00 2732.0
16 TraesCS4B01G134300 chr5A 95.616 1688 64 8 809 2487 216692021 216693707 0.000000e+00 2699.0
17 TraesCS4B01G134300 chr4D 96.558 1627 50 4 906 2527 366045591 366047216 0.000000e+00 2689.0
18 TraesCS4B01G134300 chr4D 78.906 256 34 11 549 800 353417693 353417932 3.910000e-34 156.0
19 TraesCS4B01G134300 chr4D 77.912 249 34 11 557 800 194082388 194082156 5.100000e-28 135.0
20 TraesCS4B01G134300 chr4D 98.182 55 1 0 814 868 366045531 366045585 2.400000e-16 97.1
21 TraesCS4B01G134300 chr7B 96.044 809 31 1 1 809 397594023 397593216 0.000000e+00 1315.0
22 TraesCS4B01G134300 chr1B 86.374 844 72 20 1 809 646214099 646214934 0.000000e+00 881.0
23 TraesCS4B01G134300 chr1B 95.361 388 17 1 2544 2931 148510266 148510652 1.490000e-172 616.0
24 TraesCS4B01G134300 chr1B 94.588 388 19 2 2544 2931 358387001 358386616 1.500000e-167 599.0
25 TraesCS4B01G134300 chr1B 93.557 388 22 3 2544 2931 359605877 359606261 2.530000e-160 575.0
26 TraesCS4B01G134300 chr1B 93.299 388 24 2 2544 2931 193412123 193411738 3.280000e-159 571.0


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 TraesCS4B01G134300 chr4B 175306664 175309594 2930 True 5413.00 5413 100.000 1 2931 1 chr4B.!!$R1 2930
1 TraesCS4B01G134300 chr4B 531339287 531341086 1799 False 3064.00 3064 97.389 1 1800 1 chr4B.!!$F4 1799
2 TraesCS4B01G134300 chr4B 609103883 609105459 1576 True 2503.00 2503 95.325 1355 2931 1 chr4B.!!$R4 1576
3 TraesCS4B01G134300 chr4B 357794802 357795610 808 True 1328.00 1328 96.292 1 809 1 chr4B.!!$R2 808
4 TraesCS4B01G134300 chr4B 289622409 289623236 827 False 758.00 758 83.905 1 809 1 chr4B.!!$F2 808
5 TraesCS4B01G134300 chr7D 311619004 311620743 1739 False 2878.00 2878 96.510 809 2551 1 chr7D.!!$F1 1742
6 TraesCS4B01G134300 chr3A 361575141 361576865 1724 True 2828.00 2828 96.294 814 2535 1 chr3A.!!$R1 1721
7 TraesCS4B01G134300 chr5B 209632176 209633858 1682 True 2817.00 2817 96.912 809 2487 1 chr5B.!!$R1 1678
8 TraesCS4B01G134300 chr6A 197859485 197861226 1741 True 2804.00 2804 95.757 814 2551 1 chr6A.!!$R1 1737
9 TraesCS4B01G134300 chr3B 371037967 371039713 1746 True 2791.00 2791 95.538 809 2551 1 chr3B.!!$R1 1742
10 TraesCS4B01G134300 chr3B 9161158 9161989 831 False 861.00 861 85.885 1 808 1 chr3B.!!$F1 807
11 TraesCS4B01G134300 chr5D 199084299 199085985 1686 False 2732.00 2732 95.974 809 2487 1 chr5D.!!$F1 1678
12 TraesCS4B01G134300 chr5A 216692021 216693707 1686 False 2699.00 2699 95.616 809 2487 1 chr5A.!!$F1 1678
13 TraesCS4B01G134300 chr4D 366045531 366047216 1685 False 1393.05 2689 97.370 814 2527 2 chr4D.!!$F2 1713
14 TraesCS4B01G134300 chr7B 397593216 397594023 807 True 1315.00 1315 96.044 1 809 1 chr7B.!!$R1 808
15 TraesCS4B01G134300 chr1B 646214099 646214934 835 False 881.00 881 86.374 1 809 1 chr1B.!!$F3 808


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
698 729 0.034756 TCTCCCATGTTGGTGTCGTG 59.965 55.0 0.0 0.0 35.17 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 2377 0.335019 GGGGTATGCCAGAGGGTTTT 59.665 55.0 1.04 0.0 36.17 2.43 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
303 334 8.527810 CCAATTTGTTACCTGTACCAATGTATT 58.472 33.333 0.00 0.00 0.00 1.89
492 523 3.306088 CGAAAACTGCTCCTCTTGACCTA 60.306 47.826 0.00 0.00 0.00 3.08
508 539 2.164422 GACCTATTTCAGCTTTGTGGGC 59.836 50.000 0.00 0.00 0.00 5.36
541 572 1.547372 GATGATGGCAGCTTGGTGTTT 59.453 47.619 3.69 0.00 0.00 2.83
542 573 0.675083 TGATGGCAGCTTGGTGTTTG 59.325 50.000 3.69 0.00 0.00 2.93
616 647 4.006319 GCTGAAAGAGGTCAAGTGCTAAT 58.994 43.478 0.00 0.00 34.07 1.73
698 729 0.034756 TCTCCCATGTTGGTGTCGTG 59.965 55.000 0.00 0.00 35.17 4.35
709 740 4.703093 TGTTGGTGTCGTGACTATCAGATA 59.297 41.667 1.23 0.00 0.00 1.98
739 770 9.734620 TGTGTCTTTGAAACTTTATGAATTCTG 57.265 29.630 7.05 0.00 0.00 3.02
762 793 6.785076 TGGGATTTTCTTTGTACTGGTATCA 58.215 36.000 0.00 0.00 0.00 2.15
783 814 7.741027 ATCATGAAATTAGTATGGCTCTGTG 57.259 36.000 0.00 0.00 0.00 3.66
831 862 7.472945 GCCTAGGCCTGTTATACTAGAATTGAA 60.473 40.741 24.19 0.00 35.99 2.69
1191 1225 2.599032 CCAGCCATCCCATCAGCA 59.401 61.111 0.00 0.00 0.00 4.41
1441 1478 5.469479 AGGGAATGCAAAGACAATAAAACG 58.531 37.500 0.00 0.00 0.00 3.60
1442 1479 5.010617 AGGGAATGCAAAGACAATAAAACGT 59.989 36.000 0.00 0.00 0.00 3.99
1721 2007 6.239217 TGACCTTCACATACATGCTCTAAT 57.761 37.500 0.00 0.00 0.00 1.73
1958 2247 5.924475 GCGTTAGCATACATAATTGAGGT 57.076 39.130 0.00 0.00 44.35 3.85
1972 2261 9.271921 ACATAATTGAGGTATGCATATCCTCTA 57.728 33.333 32.45 29.10 45.46 2.43
2022 2311 3.503363 ACGACATTGTTGACTGCATGATT 59.497 39.130 11.07 0.00 0.00 2.57
2088 2377 3.713003 TGGTGCTTCTCAGGAGATTCTA 58.287 45.455 0.00 0.00 37.29 2.10
2182 2471 9.347240 GAATTCCATAGGATCAGAAATTGAGAA 57.653 33.333 0.00 0.00 39.68 2.87
2268 2558 5.680619 TGTTCAATCTGTCTGTAGGTTGTT 58.319 37.500 0.00 0.00 39.31 2.83
2564 2857 5.593909 TGATTGTGATGTTTGTGGTCTTCTT 59.406 36.000 0.00 0.00 0.00 2.52
2602 2895 9.586435 TTTGATATGTATTGGATATGCTACTCG 57.414 33.333 0.00 0.00 0.00 4.18
2622 2915 3.313249 TCGCATCTTTGAACATGCATAGG 59.687 43.478 0.00 0.00 44.88 2.57
2641 2934 1.065345 GGGCCTCTCAGTCTTTAACCC 60.065 57.143 0.84 0.00 0.00 4.11
2649 2942 6.834451 CCTCTCAGTCTTTAACCCTGACTATA 59.166 42.308 0.00 0.00 38.80 1.31
2678 2971 3.424105 ATGGAAGCTGGGGAGGGC 61.424 66.667 0.00 0.00 0.00 5.19
2756 3049 3.609853 TCCATGTCATTTACTCCAGCAC 58.390 45.455 0.00 0.00 0.00 4.40
2802 3095 3.983420 CCTTTGCTCCCCAGGCCA 61.983 66.667 5.01 0.00 0.00 5.36
2814 3107 1.205417 CCCAGGCCACAAAATGATCAC 59.795 52.381 5.01 0.00 0.00 3.06
2823 3116 5.775686 CCACAAAATGATCACAGTGATGTT 58.224 37.500 21.26 12.08 37.20 2.71
2826 3119 7.326789 CCACAAAATGATCACAGTGATGTTTAC 59.673 37.037 21.26 6.51 37.20 2.01
2851 3144 6.659668 CGACCTCCTCCTAGATGTATTAATCA 59.340 42.308 0.00 0.00 0.00 2.57
2877 3170 4.344104 TCTCATGATTGGTTTTCTTCCCC 58.656 43.478 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
492 523 0.883833 CTCGCCCACAAAGCTGAAAT 59.116 50.000 0.00 0.00 0.00 2.17
508 539 2.350484 GCCATCATCATGCATTCACTCG 60.350 50.000 0.00 0.00 0.00 4.18
541 572 3.459598 AGCTCCTTCCCTTGTATTATGCA 59.540 43.478 0.00 0.00 0.00 3.96
542 573 3.817647 CAGCTCCTTCCCTTGTATTATGC 59.182 47.826 0.00 0.00 0.00 3.14
635 666 9.638176 AGAGGAAAAATACTGATGAATGCTTAT 57.362 29.630 0.00 0.00 0.00 1.73
698 729 8.932945 TCAAAGACACACAATATCTGATAGTC 57.067 34.615 3.48 4.37 0.00 2.59
739 770 7.556275 TCATGATACCAGTACAAAGAAAATCCC 59.444 37.037 0.00 0.00 0.00 3.85
762 793 6.540189 GTGACACAGAGCCATACTAATTTCAT 59.460 38.462 0.00 0.00 0.00 2.57
783 814 5.005299 GGCAAACATTACAAAACACAGTGAC 59.995 40.000 7.81 0.00 0.00 3.67
831 862 5.043248 GCATCACAAACTAAGCAACAAACT 58.957 37.500 0.00 0.00 0.00 2.66
886 918 0.251354 AGAGACGCAACTGATGGCAT 59.749 50.000 0.00 0.00 0.00 4.40
1191 1225 3.627395 TTCGGAACAACATCCAGCTAT 57.373 42.857 0.00 0.00 39.61 2.97
1441 1478 0.586802 GACCAGCTTCCGTTTGTCAC 59.413 55.000 0.00 0.00 0.00 3.67
1442 1479 0.468226 AGACCAGCTTCCGTTTGTCA 59.532 50.000 0.00 0.00 0.00 3.58
1692 1978 4.494484 CATGTATGTGAAGGTCAACTCGA 58.506 43.478 0.00 0.00 0.00 4.04
1721 2007 6.603940 AGTTAAGCAAAGATGGGCAAATAA 57.396 33.333 0.00 0.00 0.00 1.40
1958 2247 5.071653 TGCACAAAGGTAGAGGATATGCATA 59.928 40.000 9.27 9.27 35.74 3.14
2022 2311 7.835682 AGTTTTCATCATGACCATCAAATCCTA 59.164 33.333 0.00 0.00 0.00 2.94
2088 2377 0.335019 GGGGTATGCCAGAGGGTTTT 59.665 55.000 1.04 0.00 36.17 2.43
2182 2471 8.164070 ACTAACTTTACAAAATCCCTCACATCT 58.836 33.333 0.00 0.00 0.00 2.90
2268 2558 6.106673 CCCAATCTCGTAGCTCTTTTCTTTA 58.893 40.000 0.00 0.00 0.00 1.85
2343 2636 4.915704 TCCTTTCTTTGTTGTTGTTAGCG 58.084 39.130 0.00 0.00 0.00 4.26
2371 2664 6.210385 AGCACTGAGGAGTAATGATATACTGG 59.790 42.308 0.00 0.00 36.28 4.00
2388 2681 1.436600 ATGCGAGAACAAGCACTGAG 58.563 50.000 0.00 0.00 46.83 3.35
2576 2869 9.586435 CGAGTAGCATATCCAATACATATCAAA 57.414 33.333 0.00 0.00 0.00 2.69
2622 2915 1.909986 AGGGTTAAAGACTGAGAGGCC 59.090 52.381 0.00 0.00 0.00 5.19
2678 2971 0.598680 GAGCCGGATGTTCATCTCGG 60.599 60.000 24.32 24.32 43.13 4.63
2682 2975 0.533755 CAGGGAGCCGGATGTTCATC 60.534 60.000 5.05 4.41 0.00 2.92
2745 3038 1.122632 TTGTCCGGGTGCTGGAGTAA 61.123 55.000 0.00 0.00 39.90 2.24
2756 3049 3.067601 GGTTTTTATATGCCTTGTCCGGG 59.932 47.826 0.00 0.00 0.00 5.73
2802 3095 7.041440 TCGTAAACATCACTGTGATCATTTTGT 60.041 33.333 23.89 16.52 34.28 2.83
2814 3107 3.512680 GAGGAGGTCGTAAACATCACTG 58.487 50.000 0.00 0.00 40.48 3.66
2823 3116 3.947612 ACATCTAGGAGGAGGTCGTAA 57.052 47.619 0.00 0.00 0.00 3.18
2826 3119 6.659668 TGATTAATACATCTAGGAGGAGGTCG 59.340 42.308 0.00 0.00 32.42 4.79
2862 3155 5.079998 AGAGAAAGGGGAAGAAAACCAAT 57.920 39.130 0.00 0.00 0.00 3.16



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

AutoCloner maintained by Alex Coulton.