Multiple sequence alignment - TraesCS4A01G334100

Loading Multiple Alignment...

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 TraesCS4A01G334100 chr4A 100.000 3520 0 0 1 3520 617287987 617291506 0.000000e+00 6501.0
1 TraesCS4A01G334100 chr4A 98.534 2592 31 6 1 2591 617348056 617350641 0.000000e+00 4569.0
2 TraesCS4A01G334100 chr4A 86.299 1467 171 21 802 2254 617281328 617282778 0.000000e+00 1568.0
3 TraesCS4A01G334100 chr4A 83.998 1631 192 33 838 2456 617360181 617361754 0.000000e+00 1502.0
4 TraesCS4A01G334100 chr4A 84.364 275 34 5 2324 2589 617282770 617283044 9.690000e-66 261.0
5 TraesCS4A01G334100 chr5B 89.065 2460 166 41 169 2593 702553471 702551080 0.000000e+00 2957.0
6 TraesCS4A01G334100 chr5B 84.560 1658 212 24 759 2401 702479648 702478020 0.000000e+00 1604.0
7 TraesCS4A01G334100 chr5B 95.371 929 43 0 2592 3520 625489819 625490747 0.000000e+00 1478.0
8 TraesCS4A01G334100 chr5B 83.117 1694 208 32 835 2510 702558067 702556434 0.000000e+00 1472.0
9 TraesCS4A01G334100 chr5D 88.624 2391 149 51 181 2536 550375281 550372979 0.000000e+00 2795.0
10 TraesCS4A01G334100 chr5D 84.355 1713 216 28 759 2456 550301309 550299634 0.000000e+00 1631.0
11 TraesCS4A01G334100 chr5D 96.233 929 35 0 2592 3520 416990707 416989779 0.000000e+00 1522.0
12 TraesCS4A01G334100 chr5D 95.371 929 43 0 2592 3520 501747017 501747945 0.000000e+00 1478.0
13 TraesCS4A01G334100 chr5D 85.366 1435 158 20 835 2264 550402717 550401330 0.000000e+00 1439.0
14 TraesCS4A01G334100 chr5D 85.083 181 13 5 178 344 550403434 550403254 4.670000e-39 172.0
15 TraesCS4A01G334100 chr5D 77.311 357 32 26 204 543 550301966 550301642 7.820000e-37 165.0
16 TraesCS4A01G334100 chr4D 95.582 928 41 0 2592 3519 361074309 361075236 0.000000e+00 1487.0
17 TraesCS4A01G334100 chr4D 95.264 929 43 1 2592 3520 340346183 340347110 0.000000e+00 1471.0
18 TraesCS4A01G334100 chr6D 95.676 925 39 1 2592 3516 418715351 418714428 0.000000e+00 1485.0
19 TraesCS4A01G334100 chr6D 95.264 929 44 0 2592 3520 304826765 304827693 0.000000e+00 1472.0
20 TraesCS4A01G334100 chr1D 95.371 929 43 0 2592 3520 302833349 302834277 0.000000e+00 1478.0
21 TraesCS4A01G334100 chr3D 95.366 928 43 0 2592 3519 93241021 93241948 0.000000e+00 1476.0
22 TraesCS4A01G334100 chr1A 100.000 32 0 0 612 643 249773929 249773960 3.790000e-05 60.2


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 TraesCS4A01G334100 chr4A 617287987 617291506 3519 False 6501.0 6501 100.0000 1 3520 1 chr4A.!!$F1 3519
1 TraesCS4A01G334100 chr4A 617348056 617350641 2585 False 4569.0 4569 98.5340 1 2591 1 chr4A.!!$F2 2590
2 TraesCS4A01G334100 chr4A 617360181 617361754 1573 False 1502.0 1502 83.9980 838 2456 1 chr4A.!!$F3 1618
3 TraesCS4A01G334100 chr4A 617281328 617283044 1716 False 914.5 1568 85.3315 802 2589 2 chr4A.!!$F4 1787
4 TraesCS4A01G334100 chr5B 702551080 702558067 6987 True 2214.5 2957 86.0910 169 2593 2 chr5B.!!$R2 2424
5 TraesCS4A01G334100 chr5B 702478020 702479648 1628 True 1604.0 1604 84.5600 759 2401 1 chr5B.!!$R1 1642
6 TraesCS4A01G334100 chr5B 625489819 625490747 928 False 1478.0 1478 95.3710 2592 3520 1 chr5B.!!$F1 928
7 TraesCS4A01G334100 chr5D 550372979 550375281 2302 True 2795.0 2795 88.6240 181 2536 1 chr5D.!!$R2 2355
8 TraesCS4A01G334100 chr5D 416989779 416990707 928 True 1522.0 1522 96.2330 2592 3520 1 chr5D.!!$R1 928
9 TraesCS4A01G334100 chr5D 501747017 501747945 928 False 1478.0 1478 95.3710 2592 3520 1 chr5D.!!$F1 928
10 TraesCS4A01G334100 chr5D 550299634 550301966 2332 True 898.0 1631 80.8330 204 2456 2 chr5D.!!$R3 2252
11 TraesCS4A01G334100 chr5D 550401330 550403434 2104 True 805.5 1439 85.2245 178 2264 2 chr5D.!!$R4 2086
12 TraesCS4A01G334100 chr4D 361074309 361075236 927 False 1487.0 1487 95.5820 2592 3519 1 chr4D.!!$F2 927
13 TraesCS4A01G334100 chr4D 340346183 340347110 927 False 1471.0 1471 95.2640 2592 3520 1 chr4D.!!$F1 928
14 TraesCS4A01G334100 chr6D 418714428 418715351 923 True 1485.0 1485 95.6760 2592 3516 1 chr6D.!!$R1 924
15 TraesCS4A01G334100 chr6D 304826765 304827693 928 False 1472.0 1472 95.2640 2592 3520 1 chr6D.!!$F1 928
16 TraesCS4A01G334100 chr1D 302833349 302834277 928 False 1478.0 1478 95.3710 2592 3520 1 chr1D.!!$F1 928
17 TraesCS4A01G334100 chr3D 93241021 93241948 927 False 1476.0 1476 95.3660 2592 3519 1 chr3D.!!$F1 927

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
1928 7476 0.928505 ATGGTGGAGGCAATGGATCA 59.071 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
3429 9002 0.878961 GCGAGTTCCGTGACCTTGTT 60.879 55.0 0.0 0.0 41.15 2.83 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
1921 7469 1.607178 CTGGCAATGGTGGAGGCAA 60.607 57.895 0.00 0.00 37.38 4.52
1928 7476 0.928505 ATGGTGGAGGCAATGGATCA 59.071 50.000 0.00 0.00 0.00 2.92
2031 7579 8.725405 TTTCCATCATTTTACTAGCATTACGA 57.275 30.769 0.00 0.00 0.00 3.43
2070 7618 2.429610 GTGCACTAAAGGGACGATCCTA 59.570 50.000 10.32 0.00 36.57 2.94
2137 7687 0.107945 CTCCTACAGCTGTTCAGGCC 60.108 60.000 27.06 0.00 0.00 5.19
2381 7947 9.603921 TCTATTTAAAATAACCCCTCGTGTAAG 57.396 33.333 0.00 0.00 0.00 2.34
2421 7987 8.605746 TGAATCGGTATTAACAAAATAGTTCCG 58.394 33.333 0.00 0.00 36.84 4.30
2640 8213 9.490379 CTACTACACAACCTTTTTCTTGTAGAT 57.510 33.333 12.31 1.84 39.06 1.98
2647 8220 8.962679 ACAACCTTTTTCTTGTAGATGTTGTTA 58.037 29.630 0.00 0.00 40.37 2.41
2654 8227 4.777896 TCTTGTAGATGTTGTTAGGCCTCT 59.222 41.667 9.68 0.00 0.00 3.69
2664 8237 2.903784 TGTTAGGCCTCTAAGTGCAGAA 59.096 45.455 9.68 0.00 36.27 3.02
2672 8245 4.938226 GCCTCTAAGTGCAGAAGTTTGTAT 59.062 41.667 0.00 0.00 0.00 2.29
2704 8277 7.000472 AGAAAATTTCTCTCAAGTGGATGACA 59.000 34.615 1.80 0.00 34.07 3.58
2760 8333 4.963318 AGATGGTCTCTCTCAAACAACA 57.037 40.909 0.00 0.00 0.00 3.33
2768 8341 3.342719 TCTCTCAAACAACACTGCAACA 58.657 40.909 0.00 0.00 0.00 3.33
2847 8420 0.315886 TGCACTAGTTCGGCGAAGAA 59.684 50.000 24.41 12.93 0.00 2.52
2965 8538 3.214328 CGGTATTGCAAGGCTAGGAAAT 58.786 45.455 4.94 0.00 0.00 2.17
3008 8581 5.474578 TCACTAGTGCAAGTTCTCTCAAT 57.525 39.130 18.45 0.00 0.00 2.57
3246 8819 4.583073 ACACCTTAAGACACAAATCAACCC 59.417 41.667 3.36 0.00 0.00 4.11
3259 8832 5.368230 ACAAATCAACCCAAACCCTAATGTT 59.632 36.000 0.00 0.00 0.00 2.71
3354 8927 9.028284 AGATTCATCTATTCAACCAACACAAAT 57.972 29.630 0.00 0.00 34.85 2.32
3364 8937 8.833231 TTCAACCAACACAAATAACTTCAAAA 57.167 26.923 0.00 0.00 0.00 2.44
3380 8953 4.293662 TCAAAAAGTGCCCCAAAGTTTT 57.706 36.364 0.00 0.00 32.77 2.43
3429 9002 3.203263 TGCCAACCCCTATGCATAAGTTA 59.797 43.478 8.00 0.00 0.00 2.24
3477 9050 6.912082 TGATCACCAAAACATACATCAAGTG 58.088 36.000 0.00 0.00 0.00 3.16
3502 9075 5.034852 TCACGTGAATATCCCATTGTCAT 57.965 39.130 17.62 0.00 0.00 3.06
3507 9080 5.471116 CGTGAATATCCCATTGTCATCACAT 59.529 40.000 0.00 0.00 36.59 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1921 7469 1.773052 CACCACCAGATCCTGATCCAT 59.227 52.381 3.55 0.00 38.58 3.41
1928 7476 3.402681 CCGCCACCACCAGATCCT 61.403 66.667 0.00 0.00 0.00 3.24
2031 7579 0.039618 ACGCCCCATGTCCTTCAATT 59.960 50.000 0.00 0.00 0.00 2.32
2070 7618 1.972588 AGTTCCCTCCACCTATGCTT 58.027 50.000 0.00 0.00 0.00 3.91
2381 7947 3.047093 CCGATTCAAAAACGAACCCAAC 58.953 45.455 0.00 0.00 0.00 3.77
2421 7987 7.772332 ACGTTCTATGTTGATGGTTAAGATC 57.228 36.000 0.00 0.00 0.00 2.75
2640 8213 2.370519 TGCACTTAGAGGCCTAACAACA 59.629 45.455 4.42 0.00 31.94 3.33
2647 8220 1.650528 ACTTCTGCACTTAGAGGCCT 58.349 50.000 3.86 3.86 0.00 5.19
2654 8227 6.288294 ACTGTCATACAAACTTCTGCACTTA 58.712 36.000 0.00 0.00 0.00 2.24
2672 8245 7.442364 CCACTTGAGAGAAATTTTCTACTGTCA 59.558 37.037 11.55 9.43 40.87 3.58
2704 8277 5.456186 CCTCCCACGGATTGATAAACCTTAT 60.456 44.000 0.00 0.00 0.00 1.73
2760 8333 7.067494 AGAGACTCTTTGTTATTTTGTTGCAGT 59.933 33.333 0.00 0.00 0.00 4.40
2768 8341 7.013369 GGGACACAAGAGACTCTTTGTTATTTT 59.987 37.037 22.64 8.73 33.78 1.82
2847 8420 6.128486 TCCATATTGCACTTGTATCACCATT 58.872 36.000 0.00 0.00 0.00 3.16
2913 8486 6.177310 TCACTTTTACCACTTGCTACCTTA 57.823 37.500 0.00 0.00 0.00 2.69
2955 8528 3.394940 ACCTTAGGCCTTATTTCCTAGCC 59.605 47.826 12.58 0.00 44.20 3.93
2965 8538 6.214819 AGTGAAAGTATGAACCTTAGGCCTTA 59.785 38.462 12.58 0.00 0.00 2.69
2974 8547 5.483685 TGCACTAGTGAAAGTATGAACCT 57.516 39.130 27.08 0.00 0.00 3.50
3246 8819 8.148999 GGAGTATCTAGGTAACATTAGGGTTTG 58.851 40.741 0.00 0.00 34.38 2.93
3259 8832 6.027025 AGGTGACATTGGAGTATCTAGGTA 57.973 41.667 0.00 0.00 33.73 3.08
3354 8927 4.468153 ACTTTGGGGCACTTTTTGAAGTTA 59.532 37.500 0.00 0.00 0.00 2.24
3364 8937 2.101750 CGGTAAAAACTTTGGGGCACTT 59.898 45.455 0.00 0.00 0.00 3.16
3380 8953 2.189594 TCGTCTTGACTCTCCGGTAA 57.810 50.000 0.00 0.00 0.00 2.85
3429 9002 0.878961 GCGAGTTCCGTGACCTTGTT 60.879 55.000 0.00 0.00 41.15 2.83
3477 9050 4.389374 ACAATGGGATATTCACGTGATCC 58.611 43.478 22.96 22.96 38.78 3.36


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

AutoCloner maintained by Alex Coulton.