Multiple sequence alignment - TraesCS1A01G310800

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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 TraesCS1A01G310800 chr1A 100.000 2966 0 0 1 2966 501889130 501886165 0.000000e+00 5478
1 TraesCS1A01G310800 chr1A 95.569 1828 51 8 952 2773 501994096 501992293 0.000000e+00 2900
2 TraesCS1A01G310800 chr1A 92.780 651 40 5 1 648 517822779 517823425 0.000000e+00 935
3 TraesCS1A01G310800 chr1A 92.473 651 43 4 1 648 517855388 517856035 0.000000e+00 926
4 TraesCS1A01G310800 chr1A 98.722 313 4 0 647 959 501997241 501996929 9.290000e-155 556
5 TraesCS1A01G310800 chr1A 89.474 133 14 0 2834 2966 501989687 501989555 5.080000e-38 169
6 TraesCS1A01G310800 chr1B 91.615 1920 125 13 700 2595 546861153 546859246 0.000000e+00 2621
7 TraesCS1A01G310800 chr1B 91.697 1915 121 18 701 2595 546968126 546966230 0.000000e+00 2621
8 TraesCS1A01G310800 chr1B 92.540 1126 68 7 647 1763 547178777 547177659 0.000000e+00 1600
9 TraesCS1A01G310800 chr1B 95.988 673 25 2 701 1373 546702461 546701791 0.000000e+00 1092
10 TraesCS1A01G310800 chr1B 90.291 618 40 8 1987 2595 547175868 547175262 0.000000e+00 791
11 TraesCS1A01G310800 chr1B 93.491 507 24 5 2091 2595 546700226 546699727 0.000000e+00 745
12 TraesCS1A01G310800 chr1B 89.802 353 27 6 2619 2966 547175129 547174781 7.540000e-121 444
13 TraesCS1A01G310800 chr1B 89.224 232 25 0 2369 2600 546963235 546963004 1.040000e-74 291
14 TraesCS1A01G310800 chr1B 88.841 233 24 2 2369 2600 546856183 546855952 4.840000e-73 285
15 TraesCS1A01G310800 chr1B 94.737 152 5 2 2817 2966 546693179 546693029 1.780000e-57 233
16 TraesCS1A01G310800 chr1B 95.556 135 6 0 2832 2966 546966017 546965883 1.790000e-52 217
17 TraesCS1A01G310800 chr1B 94.815 135 7 0 2832 2966 546859033 546858899 8.330000e-51 211
18 TraesCS1A01G310800 chr1B 92.568 148 6 3 2666 2812 546699560 546699417 1.080000e-49 207
19 TraesCS1A01G310800 chr1B 89.706 136 13 1 2831 2966 547222326 547222192 3.930000e-39 172
20 TraesCS1A01G310800 chr1B 88.889 135 15 0 2832 2966 546689857 546689723 1.830000e-37 167
21 TraesCS1A01G310800 chr1B 95.098 102 5 0 1992 2093 546701787 546701686 8.510000e-36 161
22 TraesCS1A01G310800 chr1B 94.805 77 2 1 2624 2700 546859098 546859024 5.190000e-23 119
23 TraesCS1A01G310800 chr1B 93.506 77 3 1 2624 2700 546966082 546966008 2.420000e-21 113
24 TraesCS1A01G310800 chr1D 91.032 1550 93 12 647 2186 406677362 406675849 0.000000e+00 2050
25 TraesCS1A01G310800 chr1D 91.262 412 31 5 2189 2599 406675690 406675283 9.290000e-155 556
26 TraesCS1A01G310800 chr1D 93.123 349 17 2 2619 2966 406675164 406674822 3.410000e-139 505
27 TraesCS1A01G310800 chr1D 90.830 229 21 0 2369 2597 406671162 406670934 1.030000e-79 307
28 TraesCS1A01G310800 chr1D 91.176 136 12 0 2831 2966 406829463 406829328 5.050000e-43 185
29 TraesCS1A01G310800 chr7A 96.804 657 14 5 1 651 670304108 670303453 0.000000e+00 1090
30 TraesCS1A01G310800 chr7A 94.037 654 29 8 1 647 488777006 488776356 0.000000e+00 983
31 TraesCS1A01G310800 chr5A 95.833 624 18 6 25 647 632888093 632887477 0.000000e+00 1002
32 TraesCS1A01G310800 chr5A 93.405 652 36 3 1 647 440279843 440280492 0.000000e+00 959
33 TraesCS1A01G310800 chr6A 94.009 651 33 5 1 648 73527107 73526460 0.000000e+00 981
34 TraesCS1A01G310800 chr6A 86.897 145 14 3 2700 2842 147983635 147983494 1.100000e-34 158
35 TraesCS1A01G310800 chr3A 93.553 667 24 9 1 648 706219489 706218823 0.000000e+00 976
36 TraesCS1A01G310800 chr4A 92.802 653 38 5 1 647 564658353 564657704 0.000000e+00 937
37 TraesCS1A01G310800 chr4A 88.652 141 12 3 2700 2836 575432170 575432310 5.080000e-38 169
38 TraesCS1A01G310800 chr6D 89.051 137 12 3 2700 2834 119818218 119818083 1.830000e-37 167
39 TraesCS1A01G310800 chr3D 88.406 138 11 3 2700 2835 577649546 577649412 8.510000e-36 161
40 TraesCS1A01G310800 chr2B 87.857 140 12 3 2700 2837 678557160 678557024 3.060000e-35 159


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 TraesCS1A01G310800 chr1A 501886165 501889130 2965 True 5478.000000 5478 100.000000 1 2966 1 chr1A.!!$R1 2965
1 TraesCS1A01G310800 chr1A 501989555 501997241 7686 True 1208.333333 2900 94.588333 647 2966 3 chr1A.!!$R2 2319
2 TraesCS1A01G310800 chr1A 517822779 517823425 646 False 935.000000 935 92.780000 1 648 1 chr1A.!!$F1 647
3 TraesCS1A01G310800 chr1A 517855388 517856035 647 False 926.000000 926 92.473000 1 648 1 chr1A.!!$F2 647
4 TraesCS1A01G310800 chr1B 547174781 547178777 3996 True 945.000000 1600 90.877667 647 2966 3 chr1B.!!$R6 2319
5 TraesCS1A01G310800 chr1B 546963004 546968126 5122 True 810.500000 2621 92.495750 701 2966 4 chr1B.!!$R5 2265
6 TraesCS1A01G310800 chr1B 546855952 546861153 5201 True 809.000000 2621 92.519000 700 2966 4 chr1B.!!$R4 2266
7 TraesCS1A01G310800 chr1B 546699417 546702461 3044 True 551.250000 1092 94.286250 701 2812 4 chr1B.!!$R3 2111
8 TraesCS1A01G310800 chr1D 406670934 406677362 6428 True 854.500000 2050 91.561750 647 2966 4 chr1D.!!$R2 2319
9 TraesCS1A01G310800 chr7A 670303453 670304108 655 True 1090.000000 1090 96.804000 1 651 1 chr7A.!!$R2 650
10 TraesCS1A01G310800 chr7A 488776356 488777006 650 True 983.000000 983 94.037000 1 647 1 chr7A.!!$R1 646
11 TraesCS1A01G310800 chr5A 632887477 632888093 616 True 1002.000000 1002 95.833000 25 647 1 chr5A.!!$R1 622
12 TraesCS1A01G310800 chr5A 440279843 440280492 649 False 959.000000 959 93.405000 1 647 1 chr5A.!!$F1 646
13 TraesCS1A01G310800 chr6A 73526460 73527107 647 True 981.000000 981 94.009000 1 648 1 chr6A.!!$R1 647
14 TraesCS1A01G310800 chr3A 706218823 706219489 666 True 976.000000 976 93.553000 1 648 1 chr3A.!!$R1 647
15 TraesCS1A01G310800 chr4A 564657704 564658353 649 True 937.000000 937 92.802000 1 647 1 chr4A.!!$R1 646

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
653 681 2.669113 CGTTTTCCGGTAGTGTCGATGA 60.669 50.0 0.0 0.0 0.0 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2039 6891 0.675633 ACAGAACAATGCAAGCCACC 59.324 50.0 0.0 0.0 0.0 4.61 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
530 558 4.674623 GCCGTCGGTATAGATCCATGTAAG 60.675 50.000 13.94 0.00 0.00 2.34
653 681 2.669113 CGTTTTCCGGTAGTGTCGATGA 60.669 50.000 0.00 0.00 0.00 2.92
783 825 5.531287 CACCATCTCATCATGTCATCAATGT 59.469 40.000 0.00 0.00 0.00 2.71
1143 4033 4.203076 GTGGCCGCCGTCGTCTAT 62.203 66.667 4.45 0.00 0.00 1.98
1470 4363 1.147824 CATGGCTTCGCTGAGGGAT 59.852 57.895 0.00 0.00 0.00 3.85
1597 4490 3.491652 GCGGTCGCTTTGAGCTCC 61.492 66.667 12.15 0.00 43.02 4.70
1709 4779 1.689273 GATGGAGGAGCTAATGACGGT 59.311 52.381 0.00 0.00 0.00 4.83
1739 4809 4.020617 CGGTGGGCTTGAGCTGGA 62.021 66.667 0.00 0.00 41.70 3.86
1746 4816 1.378250 GCTTGAGCTGGATGGCACT 60.378 57.895 0.00 0.00 38.21 4.40
1763 4833 2.053244 CACTAGCCTGAATGGAGGGAT 58.947 52.381 0.00 0.00 38.35 3.85
1851 4921 2.281484 TTTGAGCTCGGTGGCACC 60.281 61.111 26.95 26.95 34.05 5.01
1881 4951 1.224069 GCCGGATGGATGACGTGATG 61.224 60.000 5.05 0.00 37.49 3.07
1882 4952 0.389025 CCGGATGGATGACGTGATGA 59.611 55.000 0.00 0.00 37.49 2.92
1883 4953 1.491670 CGGATGGATGACGTGATGAC 58.508 55.000 0.00 0.00 0.00 3.06
1922 4992 1.607467 GGTTTGAGCTGGGTGGCAT 60.607 57.895 0.00 0.00 34.17 4.40
1990 6842 7.008021 TCTGGATGCAGCATATGTATTTCTA 57.992 36.000 8.22 0.00 33.94 2.10
2039 6891 1.153784 GCATCGGCAACCCAACATG 60.154 57.895 0.00 0.00 40.72 3.21
2214 8697 5.689383 TGCTTAAACAGGAAAGATGTCAC 57.311 39.130 0.00 0.00 0.00 3.67
2240 8723 9.292195 CGGGGAAAATATACCAATAAACATACT 57.708 33.333 0.00 0.00 0.00 2.12
2260 8743 9.231297 ACATACTTTAGCATTTGTCTATTGTGT 57.769 29.630 0.00 0.00 0.00 3.72
2261 8744 9.708222 CATACTTTAGCATTTGTCTATTGTGTC 57.292 33.333 0.00 0.00 0.00 3.67
2282 8771 9.546428 TGTGTCAATCGATGAATCATACTAAAT 57.454 29.630 0.00 0.00 40.50 1.40
2363 8855 3.179443 AGATCATATGTGGAAACGCGT 57.821 42.857 5.58 5.58 46.31 6.01
2635 11823 3.925630 ATGCCCGGTCTGCCACAAG 62.926 63.158 0.00 0.00 34.09 3.16
2757 11958 1.807814 AAGCACTCATAGGGGTAGGG 58.192 55.000 0.00 0.00 0.00 3.53
2758 11959 0.642710 AGCACTCATAGGGGTAGGGT 59.357 55.000 0.00 0.00 0.00 4.34
2759 11960 0.759346 GCACTCATAGGGGTAGGGTG 59.241 60.000 0.00 0.00 0.00 4.61
2781 11983 2.096614 GTGTGCGTGTTTGCGTTATAGT 60.097 45.455 0.00 0.00 37.81 2.12
2796 11998 4.679662 GTTATAGTGGTGAGTGTATGCGT 58.320 43.478 0.00 0.00 0.00 5.24
2940 12146 6.163135 ACTAGCAAACATAGTAGGCTTAGG 57.837 41.667 0.00 0.00 36.10 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
425 451 4.630069 GCATAAATCAGCCGTCGGTATAAT 59.370 41.667 13.94 0.00 0.00 1.28
783 825 1.137086 GCTTCACGGATGAGCTAGGAA 59.863 52.381 0.00 0.00 35.83 3.36
1495 4388 2.702093 CCTGGAGGACCTGGTTGAT 58.298 57.895 0.00 0.00 46.11 2.57
1597 4490 4.838152 CATCTGCCCCGTCCCACG 62.838 72.222 0.00 0.00 42.11 4.94
1643 4536 4.323477 CAAACCCGCCTCCGACCA 62.323 66.667 0.00 0.00 36.29 4.02
1709 4779 2.125552 CACCGAAGCCTGCGATCA 60.126 61.111 0.00 0.00 0.00 2.92
1746 4816 1.061424 TCCATCCCTCCATTCAGGCTA 60.061 52.381 0.00 0.00 37.29 3.93
1857 4927 4.240103 TCATCCATCCGGCCGCTG 62.240 66.667 22.85 19.02 0.00 5.18
1864 4934 1.491670 GTCATCACGTCATCCATCCG 58.508 55.000 0.00 0.00 0.00 4.18
1872 4942 3.620300 GACCGCCGTCATCACGTCA 62.620 63.158 0.00 0.00 45.17 4.35
1922 4992 1.596934 GTCCCTCCATTCACGCTGA 59.403 57.895 0.00 0.00 0.00 4.26
1990 6842 7.423844 ACAAGAGAAACAAAGAGGGAAAAAT 57.576 32.000 0.00 0.00 0.00 1.82
2000 6852 3.108144 CACCGCAACAAGAGAAACAAAG 58.892 45.455 0.00 0.00 0.00 2.77
2039 6891 0.675633 ACAGAACAATGCAAGCCACC 59.324 50.000 0.00 0.00 0.00 4.61
2214 8697 9.292195 AGTATGTTTATTGGTATATTTTCCCCG 57.708 33.333 0.00 0.00 0.00 5.73
2240 8723 7.962373 CGATTGACACAATAGACAAATGCTAAA 59.038 33.333 0.00 0.00 0.00 1.85
2246 8729 7.848223 TCATCGATTGACACAATAGACAAAT 57.152 32.000 0.00 0.00 0.00 2.32
2363 8855 3.471680 TGCTATTACTTGTGTGTGTGCA 58.528 40.909 0.00 0.00 0.00 4.57
2382 8874 8.981724 TTTCTCGGACTATATATGTATGTTGC 57.018 34.615 0.00 0.00 0.00 4.17
2595 9089 5.934402 TTGCCTTACCCTGTTTTGTTTTA 57.066 34.783 0.00 0.00 0.00 1.52
2598 9092 3.494223 GCATTGCCTTACCCTGTTTTGTT 60.494 43.478 0.00 0.00 0.00 2.83
2635 11823 4.036144 GCAATCCTTTCATAGCTTGACTCC 59.964 45.833 0.00 0.00 32.84 3.85
2757 11958 2.650602 CGCAAACACGCACACCAC 60.651 61.111 0.00 0.00 0.00 4.16
2758 11959 1.366854 TAACGCAAACACGCACACCA 61.367 50.000 0.00 0.00 36.19 4.17
2759 11960 0.040781 ATAACGCAAACACGCACACC 60.041 50.000 0.00 0.00 36.19 4.16
2781 11983 2.232696 ACATACACGCATACACTCACCA 59.767 45.455 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.