Multiple sequence alignment - TraesCS4B01G176600

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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 TraesCS4B01G176600 chr4B 100.000 2729 0 0 1 2729 386746880 386749608 0.000000e+00 5040.0
1 TraesCS4B01G176600 chr4B 100.000 29 0 0 2575 2603 386749421 386749449 1.000000e-03 54.7
2 TraesCS4B01G176600 chr4B 100.000 29 0 0 2542 2570 386749454 386749482 1.000000e-03 54.7
3 TraesCS4B01G176600 chr4A 93.488 2718 85 28 40 2720 165359018 165356356 0.000000e+00 3954.0
4 TraesCS4B01G176600 chr4D 93.970 1592 43 16 295 1841 309700434 309702017 0.000000e+00 2359.0
5 TraesCS4B01G176600 chr4D 93.240 858 21 13 1873 2729 309702018 309702839 0.000000e+00 1229.0
6 TraesCS4B01G176600 chr4D 96.753 308 6 2 1 306 309698911 309699216 6.740000e-141 510.0
7 TraesCS4B01G176600 chr7D 90.090 111 9 1 2609 2717 609974296 609974186 2.830000e-30 143.0
8 TraesCS4B01G176600 chr7D 88.136 118 10 3 2603 2717 607916556 607916672 1.320000e-28 137.0
9 TraesCS4B01G176600 chr7D 88.136 118 10 3 2603 2717 609746015 609746131 1.320000e-28 137.0
10 TraesCS4B01G176600 chr7B 89.908 109 9 1 2611 2717 694102716 694102824 3.660000e-29 139.0


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 TraesCS4B01G176600 chr4B 386746880 386749608 2728 False 1716.466667 5040 100.000000 1 2729 3 chr4B.!!$F1 2728
1 TraesCS4B01G176600 chr4A 165356356 165359018 2662 True 3954.000000 3954 93.488000 40 2720 1 chr4A.!!$R1 2680
2 TraesCS4B01G176600 chr4D 309698911 309702839 3928 False 1366.000000 2359 94.654333 1 2729 3 chr4D.!!$F1 2728

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
242 245 1.152756 AGGCACGCTTTCCAAGGTT 60.153 52.632 0.0 0.0 0.0 3.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1980 3260 0.036875 CAAGGTGTTCTCCCAGTCCC 59.963 60.0 0.0 0.0 0.0 4.46 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
242 245 1.152756 AGGCACGCTTTCCAAGGTT 60.153 52.632 0.00 0.00 0.00 3.50
380 1612 1.376543 CTGCTACACTCATTGGCCTG 58.623 55.000 3.32 0.00 0.00 4.85
389 1621 1.451387 CATTGGCCTGTACCGGGTC 60.451 63.158 6.32 2.65 34.60 4.46
468 1700 2.745482 GCATGTGCAGGATGATCTGAGT 60.745 50.000 9.40 0.00 39.69 3.41
488 1720 8.244802 TCTGAGTATGAAGCTACTCTACAAAAC 58.755 37.037 14.00 1.12 45.19 2.43
502 1734 7.149307 ACTCTACAAAACTAGTTTCAGAGAGC 58.851 38.462 34.02 0.00 36.92 4.09
604 1849 2.030401 CGCAATCCGTGGGAACGAA 61.030 57.895 0.00 0.00 42.76 3.85
887 2153 6.404708 GGACGTCTAGGTTTCTCCTTATTTT 58.595 40.000 16.46 0.00 45.67 1.82
888 2154 6.877855 GGACGTCTAGGTTTCTCCTTATTTTT 59.122 38.462 16.46 0.00 45.67 1.94
889 2155 7.064371 GGACGTCTAGGTTTCTCCTTATTTTTC 59.936 40.741 16.46 0.00 45.67 2.29
890 2156 6.877855 ACGTCTAGGTTTCTCCTTATTTTTCC 59.122 38.462 0.00 0.00 45.67 3.13
891 2157 6.035758 CGTCTAGGTTTCTCCTTATTTTTCCG 59.964 42.308 0.00 0.00 45.67 4.30
1269 2546 2.048503 GACGTCACCTTCCACGGG 60.049 66.667 11.55 0.00 40.43 5.28
1305 2582 0.468214 TCTACCCCATCCTCTCGCTG 60.468 60.000 0.00 0.00 0.00 5.18
1447 2724 1.271840 CGGGGACAGGAAGATTGGGA 61.272 60.000 0.00 0.00 0.00 4.37
1473 2750 0.684805 GGGTCAGGATCTCGTCAGGT 60.685 60.000 0.00 0.00 0.00 4.00
1693 2970 3.708403 AGGATGATTCAGAGTGTGCAA 57.292 42.857 0.00 0.00 0.00 4.08
1732 3009 3.278574 GCAACTGGGCAACACTGATATA 58.721 45.455 0.00 0.00 39.74 0.86
1733 3010 3.885297 GCAACTGGGCAACACTGATATAT 59.115 43.478 0.00 0.00 39.74 0.86
1782 3059 1.313091 GGGATTTTGCCTCGACACCC 61.313 60.000 0.00 0.00 0.00 4.61
1801 3078 6.612741 ACACCCTGTTATAAACTTTTGGGTA 58.387 36.000 0.00 0.00 38.48 3.69
1830 3107 8.655935 AAAATTTCCTCTGATAATGTTGGTCT 57.344 30.769 0.00 0.00 0.00 3.85
1906 3183 2.332063 AGTGTGGTGTCTTCTTGGTG 57.668 50.000 0.00 0.00 0.00 4.17
1984 3264 6.942532 TCAGCTTGTTGAAATATATGGGAC 57.057 37.500 0.00 0.00 0.00 4.46
2163 3443 6.373774 GGAGATGGCAAATTCTGTGGATATAG 59.626 42.308 0.00 0.00 0.00 1.31
2167 3447 7.136822 TGGCAAATTCTGTGGATATAGTACT 57.863 36.000 0.00 0.00 0.00 2.73
2168 3448 8.257602 TGGCAAATTCTGTGGATATAGTACTA 57.742 34.615 4.77 4.77 0.00 1.82
2169 3449 8.148351 TGGCAAATTCTGTGGATATAGTACTAC 58.852 37.037 4.31 0.00 0.00 2.73
2170 3450 7.328737 GGCAAATTCTGTGGATATAGTACTACG 59.671 40.741 4.31 0.00 0.00 3.51
2392 3672 6.782298 TTCATGTGTAAATTTGCACCAATG 57.218 33.333 29.06 25.53 42.16 2.82
2433 3713 9.720769 GGAATATAATCTATTTTCGTTCCTCCA 57.279 33.333 0.00 0.00 32.06 3.86
2444 3724 2.028112 TCGTTCCTCCAACTTCATCAGG 60.028 50.000 0.00 0.00 32.09 3.86
2445 3725 2.087646 GTTCCTCCAACTTCATCAGGC 58.912 52.381 0.00 0.00 31.50 4.85
2446 3726 1.361204 TCCTCCAACTTCATCAGGCA 58.639 50.000 0.00 0.00 0.00 4.75
2447 3727 1.704628 TCCTCCAACTTCATCAGGCAA 59.295 47.619 0.00 0.00 0.00 4.52
2448 3728 2.108075 TCCTCCAACTTCATCAGGCAAA 59.892 45.455 0.00 0.00 0.00 3.68
2449 3729 2.490903 CCTCCAACTTCATCAGGCAAAG 59.509 50.000 0.00 0.00 0.00 2.77
2450 3730 3.415212 CTCCAACTTCATCAGGCAAAGA 58.585 45.455 0.00 0.00 0.00 2.52
2451 3731 3.415212 TCCAACTTCATCAGGCAAAGAG 58.585 45.455 0.00 0.00 0.00 2.85
2536 3816 5.900425 ACGCCATGCACAAATAAAATGATA 58.100 33.333 0.00 0.00 0.00 2.15
2545 3825 9.800433 TGCACAAATAAAATGATATTACACTGG 57.200 29.630 0.00 0.00 0.00 4.00
2559 3839 9.185192 GATATTACACTGGATTTTGCTTATTGC 57.815 33.333 0.00 0.00 43.25 3.56
2669 3949 3.633525 GCTGCCCATCTTTCATGTTCATA 59.366 43.478 0.00 0.00 0.00 2.15
2674 3955 6.712095 TGCCCATCTTTCATGTTCATATACTC 59.288 38.462 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.135489 TCGAGTCGTCTTGCATGGTAC 60.135 52.381 13.12 0.00 0.00 3.34
232 235 1.152860 TGGCGCTGAACCTTGGAAA 60.153 52.632 7.64 0.00 0.00 3.13
242 245 1.811266 GCTTCGAATCTGGCGCTGA 60.811 57.895 7.64 6.74 0.00 4.26
334 1566 6.555812 AACGTTAAGGCCTTCTTAAGAAAG 57.444 37.500 24.49 14.11 45.47 2.62
355 1587 3.568538 CCAATGAGTGTAGCAGCAAAAC 58.431 45.455 0.00 0.00 0.00 2.43
380 1612 0.104855 GGGTTAATCGGACCCGGTAC 59.895 60.000 8.73 0.00 46.71 3.34
488 1720 4.377839 TTCATCGGCTCTCTGAAACTAG 57.622 45.455 0.00 0.00 0.00 2.57
585 1817 2.433491 CGTTCCCACGGATTGCGA 60.433 61.111 4.05 0.00 43.16 5.10
604 1849 4.329545 ATGTGGCGTCGGGCTTGT 62.330 61.111 0.00 0.00 42.94 3.16
788 2045 1.026718 CGCTGACCCTTCCAATGTCC 61.027 60.000 0.00 0.00 0.00 4.02
887 2153 7.328737 CCTAAATAAAGAGAGAAGGAACGGAA 58.671 38.462 0.00 0.00 0.00 4.30
888 2154 6.629739 GCCTAAATAAAGAGAGAAGGAACGGA 60.630 42.308 0.00 0.00 0.00 4.69
889 2155 5.524281 GCCTAAATAAAGAGAGAAGGAACGG 59.476 44.000 0.00 0.00 0.00 4.44
890 2156 5.524281 GGCCTAAATAAAGAGAGAAGGAACG 59.476 44.000 0.00 0.00 0.00 3.95
891 2157 5.524281 CGGCCTAAATAAAGAGAGAAGGAAC 59.476 44.000 0.00 0.00 0.00 3.62
1251 2528 2.732016 CCGTGGAAGGTGACGTCA 59.268 61.111 15.76 15.76 40.97 4.35
1305 2582 2.203209 CCTAGCCCAATGTCCCGC 60.203 66.667 0.00 0.00 0.00 6.13
1473 2750 0.614415 CCAGGCCATGGCAGGTAAAA 60.614 55.000 36.56 0.00 43.83 1.52
1494 2771 3.119849 CCAAATCAGGGTCGATGTTGAAC 60.120 47.826 0.00 0.00 0.00 3.18
1653 2930 4.753107 TCCTTGACTTTAACATCACCGAAC 59.247 41.667 0.00 0.00 0.00 3.95
1657 2934 7.121168 TGAATCATCCTTGACTTTAACATCACC 59.879 37.037 0.00 0.00 33.85 4.02
1693 2970 2.995283 TGCAGCTGAGCTAATCATGTT 58.005 42.857 20.43 0.00 36.40 2.71
1801 3078 9.880157 CCAACATTATCAGAGGAAATTTTTGAT 57.120 29.630 0.00 3.40 33.44 2.57
1808 3085 6.962182 TGAGACCAACATTATCAGAGGAAAT 58.038 36.000 0.00 0.00 0.00 2.17
1830 3107 2.673775 TGGGAAGCACCTTCATTTGA 57.326 45.000 7.22 0.00 41.77 2.69
1979 3259 0.401395 AAGGTGTTCTCCCAGTCCCA 60.401 55.000 0.00 0.00 0.00 4.37
1980 3260 0.036875 CAAGGTGTTCTCCCAGTCCC 59.963 60.000 0.00 0.00 0.00 4.46
1981 3261 0.606673 GCAAGGTGTTCTCCCAGTCC 60.607 60.000 0.00 0.00 0.00 3.85
1982 3262 0.606673 GGCAAGGTGTTCTCCCAGTC 60.607 60.000 0.00 0.00 0.00 3.51
1983 3263 1.352622 TGGCAAGGTGTTCTCCCAGT 61.353 55.000 0.00 0.00 0.00 4.00
1984 3264 0.038744 ATGGCAAGGTGTTCTCCCAG 59.961 55.000 0.00 0.00 0.00 4.45
2163 3443 7.201410 CCACATCATCTGTTAACAACGTAGTAC 60.201 40.741 10.03 0.00 35.78 2.73
2167 3447 4.932799 CCCACATCATCTGTTAACAACGTA 59.067 41.667 10.03 0.00 35.29 3.57
2168 3448 3.751175 CCCACATCATCTGTTAACAACGT 59.249 43.478 10.03 0.00 35.29 3.99
2169 3449 3.751175 ACCCACATCATCTGTTAACAACG 59.249 43.478 10.03 0.00 35.29 4.10
2170 3450 4.518970 ACACCCACATCATCTGTTAACAAC 59.481 41.667 10.03 0.00 35.29 3.32
2331 3611 2.163815 CTCTTTGCCTTCAAGCATCCTG 59.836 50.000 0.00 0.00 43.64 3.86
2433 3713 3.073650 AGACCTCTTTGCCTGATGAAGTT 59.926 43.478 0.00 0.00 0.00 2.66
2444 3724 5.449725 GCAATATTTCAGGAGACCTCTTTGC 60.450 44.000 0.00 0.00 0.00 3.68
2445 3725 5.649395 TGCAATATTTCAGGAGACCTCTTTG 59.351 40.000 0.00 0.00 0.00 2.77
2446 3726 5.819991 TGCAATATTTCAGGAGACCTCTTT 58.180 37.500 0.00 0.00 0.00 2.52
2447 3727 5.441718 TGCAATATTTCAGGAGACCTCTT 57.558 39.130 0.00 0.00 0.00 2.85
2448 3728 5.643421 ATGCAATATTTCAGGAGACCTCT 57.357 39.130 0.00 0.00 0.00 3.69
2449 3729 7.992754 ATTATGCAATATTTCAGGAGACCTC 57.007 36.000 0.00 0.00 0.00 3.85
2558 3838 0.458669 CAGTTCAGGGATGCCAATGC 59.541 55.000 5.86 0.00 38.26 3.56
2559 3839 1.108776 CCAGTTCAGGGATGCCAATG 58.891 55.000 5.86 0.00 0.00 2.82
2560 3840 1.002069 TCCAGTTCAGGGATGCCAAT 58.998 50.000 5.86 0.00 0.00 3.16
2561 3841 1.002069 ATCCAGTTCAGGGATGCCAA 58.998 50.000 5.86 0.00 43.44 4.52
2562 3842 1.002069 AATCCAGTTCAGGGATGCCA 58.998 50.000 5.86 0.00 44.30 4.92
2563 3843 2.149973 AAATCCAGTTCAGGGATGCC 57.850 50.000 0.00 0.00 44.30 4.40
2564 3844 2.417787 GCAAAATCCAGTTCAGGGATGC 60.418 50.000 0.00 0.00 44.30 3.91
2565 3845 3.094572 AGCAAAATCCAGTTCAGGGATG 58.905 45.455 0.00 0.00 44.30 3.51
2566 3846 9.462955 GCAATAAGCAAAATCCAGTTCAGGGAT 62.463 40.741 0.00 0.00 44.52 3.85
2567 3847 2.978156 AGCAAAATCCAGTTCAGGGA 57.022 45.000 0.00 0.00 39.14 4.20
2669 3949 6.590292 CACAACATAGAAAAGACCACGAGTAT 59.410 38.462 0.00 0.00 0.00 2.12
2674 3955 3.498397 AGCACAACATAGAAAAGACCACG 59.502 43.478 0.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.