Multiple sequence alignment - TraesCS1B01G384200

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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 TraesCS1B01G384200 chr1B 100.000 2549 0 0 1 2549 616704534 616701986 0.000000e+00 4708
1 TraesCS1B01G384200 chr1B 96.925 1984 54 5 569 2549 307939705 307941684 0.000000e+00 3319
2 TraesCS1B01G384200 chr1B 95.824 1748 69 3 563 2308 561526124 561527869 0.000000e+00 2820
3 TraesCS1B01G384200 chr1B 95.819 1746 65 6 568 2308 581717562 581715820 0.000000e+00 2813
4 TraesCS1B01G384200 chr1B 95.775 568 24 0 1 568 417618799 417618232 0.000000e+00 917
5 TraesCS1B01G384200 chr1B 97.551 245 5 1 2305 2549 442921411 442921654 3.920000e-113 418
6 TraesCS1B01G384200 chr2B 96.880 1987 56 6 564 2546 776161408 776163392 0.000000e+00 3321
7 TraesCS1B01G384200 chr2B 95.667 1754 67 9 558 2308 692955888 692957635 0.000000e+00 2809
8 TraesCS1B01G384200 chr2B 97.551 245 4 1 2305 2549 695138463 695138221 3.920000e-113 418
9 TraesCS1B01G384200 chr5B 95.312 1984 78 5 567 2549 523834973 523836942 0.000000e+00 3134
10 TraesCS1B01G384200 chr5B 96.730 1835 53 6 569 2399 81902666 81904497 0.000000e+00 3049
11 TraesCS1B01G384200 chr5B 97.011 1706 49 2 566 2270 682395999 682394295 0.000000e+00 2867
12 TraesCS1B01G384200 chr5B 95.599 568 25 0 1 568 32361513 32362080 0.000000e+00 911
13 TraesCS1B01G384200 chr5B 95.423 568 26 0 1 568 379093836 379093269 0.000000e+00 905
14 TraesCS1B01G384200 chr7B 94.644 1811 87 8 503 2308 602142372 602144177 0.000000e+00 2798
15 TraesCS1B01G384200 chr7B 97.007 568 17 0 1 568 356946420 356945853 0.000000e+00 955
16 TraesCS1B01G384200 chr7B 96.303 568 21 0 1 568 348455165 348455732 0.000000e+00 933
17 TraesCS1B01G384200 chr7B 95.951 568 23 0 1 568 286713190 286713757 0.000000e+00 922
18 TraesCS1B01G384200 chr7B 95.775 568 23 1 1 568 454259714 454260280 0.000000e+00 915
19 TraesCS1B01G384200 chr3B 96.127 568 22 0 1 568 102616621 102616054 0.000000e+00 928
20 TraesCS1B01G384200 chr3B 98.367 245 3 1 2305 2549 19703045 19703288 1.810000e-116 429
21 TraesCS1B01G384200 chr4B 95.599 568 25 0 1 568 123289634 123290201 0.000000e+00 911
22 TraesCS1B01G384200 chr6B 98.367 245 3 1 2305 2549 478989504 478989261 1.810000e-116 429
23 TraesCS1B01G384200 chr4A 97.959 245 4 1 2305 2549 610780018 610779775 8.430000e-115 424
24 TraesCS1B01G384200 chr4A 97.551 245 4 1 2305 2549 705527448 705527206 3.920000e-113 418


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 TraesCS1B01G384200 chr1B 616701986 616704534 2548 True 4708 4708 100.000 1 2549 1 chr1B.!!$R3 2548
1 TraesCS1B01G384200 chr1B 307939705 307941684 1979 False 3319 3319 96.925 569 2549 1 chr1B.!!$F1 1980
2 TraesCS1B01G384200 chr1B 561526124 561527869 1745 False 2820 2820 95.824 563 2308 1 chr1B.!!$F3 1745
3 TraesCS1B01G384200 chr1B 581715820 581717562 1742 True 2813 2813 95.819 568 2308 1 chr1B.!!$R2 1740
4 TraesCS1B01G384200 chr1B 417618232 417618799 567 True 917 917 95.775 1 568 1 chr1B.!!$R1 567
5 TraesCS1B01G384200 chr2B 776161408 776163392 1984 False 3321 3321 96.880 564 2546 1 chr2B.!!$F2 1982
6 TraesCS1B01G384200 chr2B 692955888 692957635 1747 False 2809 2809 95.667 558 2308 1 chr2B.!!$F1 1750
7 TraesCS1B01G384200 chr5B 523834973 523836942 1969 False 3134 3134 95.312 567 2549 1 chr5B.!!$F3 1982
8 TraesCS1B01G384200 chr5B 81902666 81904497 1831 False 3049 3049 96.730 569 2399 1 chr5B.!!$F2 1830
9 TraesCS1B01G384200 chr5B 682394295 682395999 1704 True 2867 2867 97.011 566 2270 1 chr5B.!!$R2 1704
10 TraesCS1B01G384200 chr5B 32361513 32362080 567 False 911 911 95.599 1 568 1 chr5B.!!$F1 567
11 TraesCS1B01G384200 chr5B 379093269 379093836 567 True 905 905 95.423 1 568 1 chr5B.!!$R1 567
12 TraesCS1B01G384200 chr7B 602142372 602144177 1805 False 2798 2798 94.644 503 2308 1 chr7B.!!$F4 1805
13 TraesCS1B01G384200 chr7B 356945853 356946420 567 True 955 955 97.007 1 568 1 chr7B.!!$R1 567
14 TraesCS1B01G384200 chr7B 348455165 348455732 567 False 933 933 96.303 1 568 1 chr7B.!!$F2 567
15 TraesCS1B01G384200 chr7B 286713190 286713757 567 False 922 922 95.951 1 568 1 chr7B.!!$F1 567
16 TraesCS1B01G384200 chr7B 454259714 454260280 566 False 915 915 95.775 1 568 1 chr7B.!!$F3 567
17 TraesCS1B01G384200 chr3B 102616054 102616621 567 True 928 928 96.127 1 568 1 chr3B.!!$R1 567
18 TraesCS1B01G384200 chr4B 123289634 123290201 567 False 911 911 95.599 1 568 1 chr4B.!!$F1 567

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
248 249 0.678366 TGGCCACAGTCGTTTTGTGT 60.678 50.0 0.0 0.0 43.37 3.72 F
939 942 0.689745 TTAGCTATGGAGGGCACGGT 60.690 55.0 0.0 0.0 0.00 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1102 1105 0.602905 CTCGGTGTGTGAGAAACCCC 60.603 60.000 0.00 0.0 35.43 4.95 R
1992 2007 2.190841 CCACGCGGTCTTGGGTTTT 61.191 57.895 12.47 0.0 32.02 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
78 79 1.661463 AGTGAGCAAGGGATGAAGGA 58.339 50.000 0.00 0.00 0.00 3.36
205 206 3.702048 CCTTCCCCAAGCGGACGA 61.702 66.667 0.00 0.00 0.00 4.20
248 249 0.678366 TGGCCACAGTCGTTTTGTGT 60.678 50.000 0.00 0.00 43.37 3.72
452 453 4.883083 TGGCTATATGAGACCGAATGAAC 58.117 43.478 0.00 0.00 28.20 3.18
454 455 5.773176 TGGCTATATGAGACCGAATGAACTA 59.227 40.000 0.00 0.00 28.20 2.24
463 464 2.229543 ACCGAATGAACTACTGCACGTA 59.770 45.455 0.00 0.00 0.00 3.57
605 606 2.116238 GCCCTTAGTGGTGTCCATCTA 58.884 52.381 0.00 0.00 35.28 1.98
695 696 1.615107 GAACTTTGGCGTCTCCGTCG 61.615 60.000 0.00 0.00 43.03 5.12
710 711 0.863144 CGTCGGGTCAACGTTTTGAT 59.137 50.000 0.00 0.00 43.72 2.57
764 765 3.442273 GGCGACCAATTTTATTCAGACCA 59.558 43.478 0.00 0.00 0.00 4.02
920 923 3.319198 ACGATGGCGGTGGGAAGT 61.319 61.111 0.00 0.00 43.17 3.01
939 942 0.689745 TTAGCTATGGAGGGCACGGT 60.690 55.000 0.00 0.00 0.00 4.83
1411 1414 3.441922 CACTGACAGAGAGCTAGCTGTTA 59.558 47.826 24.99 10.46 44.77 2.41
1718 1725 8.717821 CAGAAACTTTTGATCAATGAAATGCAT 58.282 29.630 9.40 0.00 39.43 3.96
1852 1860 7.992033 TCAAAGACCAAAATGTCATGGAAAATT 59.008 29.630 0.00 0.00 39.12 1.82
2119 2135 7.756722 AGTGAGACTGTGAAATTTGTCAAAAAG 59.243 33.333 1.31 0.00 32.41 2.27
2541 2562 1.782044 CTTGGGCACGGACATTTTTG 58.218 50.000 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 1.576451 TTGCTCACTACCGCGACGTA 61.576 55.000 8.23 0.43 0.00 3.57
78 79 0.106918 TCACAAAGCCGGTGAGGTTT 60.107 50.000 1.90 0.00 45.92 3.27
248 249 2.868899 TGCTCTCTTCACACTCTCTCA 58.131 47.619 0.00 0.00 0.00 3.27
581 582 1.244816 GGACACCACTAAGGGCAAAC 58.755 55.000 0.00 0.00 43.89 2.93
605 606 2.787994 CATCTGAGGGCAAAACTGAGT 58.212 47.619 0.00 0.00 0.00 3.41
669 670 2.808543 GAGACGCCAAAGTTCACAGAAT 59.191 45.455 0.00 0.00 0.00 2.40
695 696 1.664874 GCCGAATCAAAACGTTGACCC 60.665 52.381 0.00 0.00 46.40 4.46
746 747 6.165577 GTGCAATGGTCTGAATAAAATTGGT 58.834 36.000 0.00 0.00 0.00 3.67
814 815 2.411628 AATATAGCACACCCGCAACA 57.588 45.000 0.00 0.00 0.00 3.33
920 923 0.689745 ACCGTGCCCTCCATAGCTAA 60.690 55.000 0.00 0.00 0.00 3.09
939 942 1.679311 CACAGCTAGCTTCCCACCA 59.321 57.895 16.46 0.00 0.00 4.17
1102 1105 0.602905 CTCGGTGTGTGAGAAACCCC 60.603 60.000 0.00 0.00 35.43 4.95
1411 1414 5.942826 CCTTCTTCTTCAACATCCTAAGCTT 59.057 40.000 3.48 3.48 0.00 3.74
1718 1725 7.833682 TGTTTGGCTCTGGAATAATTCATTAGA 59.166 33.333 0.00 0.00 0.00 2.10
1852 1860 3.445008 ACATCTACCAGAGCTGAGGAAA 58.555 45.455 7.99 0.00 0.00 3.13
1973 1988 4.740822 GTCCCCAGCCGCACCAAT 62.741 66.667 0.00 0.00 0.00 3.16
1992 2007 2.190841 CCACGCGGTCTTGGGTTTT 61.191 57.895 12.47 0.00 32.02 2.43
2119 2135 3.006752 TGTGCATTTTTCCACCCTTCATC 59.993 43.478 0.00 0.00 0.00 2.92
2441 2462 2.285743 GGGGGTGAGAAGCCCTCT 60.286 66.667 12.46 0.00 43.38 3.69


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

AutoCloner maintained by Alex Coulton.