Multiple sequence alignment - TraesCS4A01G477700

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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 TraesCS4A01G477700 chr4A 100.000 3305 0 0 1 3305 735368923 735365619 0.000000e+00 6104.0
1 TraesCS4A01G477700 chr4A 94.566 2742 124 9 581 3305 734996318 734999051 0.000000e+00 4215.0
2 TraesCS4A01G477700 chr4A 92.715 2759 172 18 572 3305 735775982 735778736 0.000000e+00 3954.0
3 TraesCS4A01G477700 chr4A 85.794 2499 307 29 834 3305 735562883 735560406 0.000000e+00 2604.0
4 TraesCS4A01G477700 chr4A 85.808 1987 271 7 1031 3013 734876248 734878227 0.000000e+00 2097.0
5 TraesCS4A01G477700 chr4A 86.042 1963 261 8 1031 2989 736119761 736121714 0.000000e+00 2095.0
6 TraesCS4A01G477700 chr4A 84.265 2040 293 21 976 3006 735818692 735820712 0.000000e+00 1964.0
7 TraesCS4A01G477700 chr4A 85.722 1786 221 25 1531 3305 736724763 736726525 0.000000e+00 1855.0
8 TraesCS4A01G477700 chr4A 96.082 536 15 3 1 534 735775381 735775912 0.000000e+00 869.0
9 TraesCS4A01G477700 chr4A 86.343 659 82 4 2277 2935 736611694 736612344 0.000000e+00 712.0
10 TraesCS4A01G477700 chr4A 91.873 283 22 1 127 409 736895360 736895641 8.600000e-106 394.0
11 TraesCS4A01G477700 chr4A 86.047 258 36 0 3048 3305 734878229 734878486 9.030000e-71 278.0
12 TraesCS4A01G477700 chr4A 92.571 175 12 1 411 585 734478713 734478886 1.970000e-62 250.0
13 TraesCS4A01G477700 chr4A 91.111 180 14 2 410 589 736895696 736895873 3.290000e-60 243.0
14 TraesCS4A01G477700 chr4A 83.333 258 42 1 3048 3305 734848744 734849000 1.530000e-58 237.0
15 TraesCS4A01G477700 chr4A 90.556 180 16 1 410 589 736471524 736471346 1.530000e-58 237.0
16 TraesCS4A01G477700 chr4A 87.952 166 13 3 412 577 734384550 734384708 4.350000e-44 189.0
17 TraesCS4A01G477700 chr4A 89.844 128 13 0 1 128 736894295 736894422 7.340000e-37 165.0
18 TraesCS4A01G477700 chr4A 89.231 130 8 3 1 125 734995831 734995959 1.230000e-34 158.0
19 TraesCS4A01G477700 chr4A 88.976 127 13 1 281 406 734384356 734384482 4.420000e-34 156.0
20 TraesCS4A01G477700 chr4A 78.138 247 36 8 3061 3305 735027185 735027415 1.240000e-29 141.0
21 TraesCS4A01G477700 chr4A 94.595 74 3 1 333 406 734996079 734996151 2.700000e-21 113.0
22 TraesCS4A01G477700 chr4A 93.651 63 4 0 344 406 736471654 736471592 9.760000e-16 95.3
23 TraesCS4A01G477700 chr4A 93.750 48 2 1 141 188 735664142 735664096 1.650000e-08 71.3
24 TraesCS4A01G477700 chr7D 93.601 2735 168 5 573 3305 5638511 5635782 0.000000e+00 4074.0
25 TraesCS4A01G477700 chr7D 88.368 2751 273 27 572 3305 5449544 5446824 0.000000e+00 3264.0
26 TraesCS4A01G477700 chr7D 91.758 182 12 2 410 589 5449755 5449575 1.970000e-62 250.0
27 TraesCS4A01G477700 chr7D 86.408 103 11 3 417 518 5639427 5639327 3.490000e-20 110.0
28 TraesCS4A01G477700 chr7D 93.651 63 4 0 344 406 5449885 5449823 9.760000e-16 95.3
29 TraesCS4A01G477700 chr7A 88.457 2755 267 29 572 3305 6929085 6926361 0.000000e+00 3278.0
30 TraesCS4A01G477700 chr7A 82.359 2738 390 53 589 3305 7045875 7043210 0.000000e+00 2294.0
31 TraesCS4A01G477700 chr7A 89.091 220 22 1 127 346 6929588 6929371 4.200000e-69 272.0
32 TraesCS4A01G477700 chr7A 92.571 175 13 0 411 585 6929287 6929113 5.470000e-63 252.0
33 TraesCS4A01G477700 chr7A 87.597 129 12 2 3 128 6930731 6930604 2.660000e-31 147.0
34 TraesCS4A01G477700 chr7A 97.778 45 1 0 368 412 6929374 6929330 9.830000e-11 78.7


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 TraesCS4A01G477700 chr4A 735365619 735368923 3304 True 6104.000000 6104 100.000000 1 3305 1 chr4A.!!$R1 3304
1 TraesCS4A01G477700 chr4A 735560406 735562883 2477 True 2604.000000 2604 85.794000 834 3305 1 chr4A.!!$R2 2471
2 TraesCS4A01G477700 chr4A 735775381 735778736 3355 False 2411.500000 3954 94.398500 1 3305 2 chr4A.!!$F11 3304
3 TraesCS4A01G477700 chr4A 736119761 736121714 1953 False 2095.000000 2095 86.042000 1031 2989 1 chr4A.!!$F5 1958
4 TraesCS4A01G477700 chr4A 735818692 735820712 2020 False 1964.000000 1964 84.265000 976 3006 1 chr4A.!!$F4 2030
5 TraesCS4A01G477700 chr4A 736724763 736726525 1762 False 1855.000000 1855 85.722000 1531 3305 1 chr4A.!!$F7 1774
6 TraesCS4A01G477700 chr4A 734995831 734999051 3220 False 1495.333333 4215 92.797333 1 3305 3 chr4A.!!$F10 3304
7 TraesCS4A01G477700 chr4A 734876248 734878486 2238 False 1187.500000 2097 85.927500 1031 3305 2 chr4A.!!$F9 2274
8 TraesCS4A01G477700 chr4A 736611694 736612344 650 False 712.000000 712 86.343000 2277 2935 1 chr4A.!!$F6 658
9 TraesCS4A01G477700 chr4A 736894295 736895873 1578 False 267.333333 394 90.942667 1 589 3 chr4A.!!$F12 588
10 TraesCS4A01G477700 chr7D 5635782 5639427 3645 True 2092.000000 4074 90.004500 417 3305 2 chr7D.!!$R2 2888
11 TraesCS4A01G477700 chr7D 5446824 5449885 3061 True 1203.100000 3264 91.259000 344 3305 3 chr7D.!!$R1 2961
12 TraesCS4A01G477700 chr7A 7043210 7045875 2665 True 2294.000000 2294 82.359000 589 3305 1 chr7A.!!$R1 2716
13 TraesCS4A01G477700 chr7A 6926361 6930731 4370 True 805.540000 3278 91.098800 3 3305 5 chr7A.!!$R2 3302

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
539 2474 0.247460 GCTGTTTGGGGATTTCTGCC 59.753 55.0 0.0 0.0 0.0 4.85 F
1375 3424 0.039798 GCGTGTTGTGTCGAGTAGGA 60.040 55.0 0.0 0.0 0.0 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1496 3553 0.398318 GGATGGTATGGTGGAGCTCC 59.602 60.000 26.78 26.78 0.0 4.70 R
3040 5137 3.181493 GGTGCATCTTTGTATGGCTTGAG 60.181 47.826 0.00 0.00 0.0 3.02 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
54 59 2.222027 GCGATGGGGTGAGATAAAAGG 58.778 52.381 0.00 0.00 0.00 3.11
75 83 3.181500 GGATTTTGATGGGCTAACACGAC 60.181 47.826 0.00 0.00 0.00 4.34
117 127 3.515502 TGTTGATAGTTCTCCACTCCTGG 59.484 47.826 0.00 0.00 36.88 4.45
206 1346 6.796426 GTTGAAAACTTAGAAGGAAGCACTT 58.204 36.000 0.00 0.00 45.32 3.16
223 1363 3.602265 GCACTTCGTCAAATTTTGCTTGC 60.602 43.478 4.19 3.35 0.00 4.01
451 1655 6.895782 TGGCTACTGGTTAGTTTATTAGCAT 58.104 36.000 0.00 0.00 35.95 3.79
465 1671 2.904697 TAGCATGTCCATCTCAGCTG 57.095 50.000 7.63 7.63 33.83 4.24
534 2469 1.133199 TGACCTGCTGTTTGGGGATTT 60.133 47.619 0.00 0.00 0.00 2.17
535 2470 1.546029 GACCTGCTGTTTGGGGATTTC 59.454 52.381 0.00 0.00 0.00 2.17
536 2471 1.147817 ACCTGCTGTTTGGGGATTTCT 59.852 47.619 0.00 0.00 0.00 2.52
537 2472 1.547372 CCTGCTGTTTGGGGATTTCTG 59.453 52.381 0.00 0.00 0.00 3.02
538 2473 0.968405 TGCTGTTTGGGGATTTCTGC 59.032 50.000 0.00 0.00 0.00 4.26
539 2474 0.247460 GCTGTTTGGGGATTTCTGCC 59.753 55.000 0.00 0.00 0.00 4.85
540 2475 1.928868 CTGTTTGGGGATTTCTGCCT 58.071 50.000 0.00 0.00 32.40 4.75
541 2476 1.821136 CTGTTTGGGGATTTCTGCCTC 59.179 52.381 0.00 0.00 32.40 4.70
542 2477 1.186200 GTTTGGGGATTTCTGCCTCC 58.814 55.000 0.00 0.00 32.40 4.30
548 2483 2.744352 GGATTTCTGCCTCCCATTCT 57.256 50.000 0.00 0.00 0.00 2.40
557 2492 1.615384 GCCTCCCATTCTCTTGCAACT 60.615 52.381 0.00 0.00 0.00 3.16
570 2505 5.822519 TCTCTTGCAACTCAACATTGTTAGT 59.177 36.000 0.86 4.17 0.00 2.24
604 2609 2.806745 GCTTCTGTGTAAGCTCACCACA 60.807 50.000 11.23 11.23 46.74 4.17
711 2720 3.068024 TGATTTTTCAGTCCAACAGGTGC 59.932 43.478 0.00 0.00 0.00 5.01
765 2774 3.008330 CCTCTGATCCAGAAGCACTTTG 58.992 50.000 0.00 0.00 40.18 2.77
779 2788 5.814764 AGCACTTTGAATTGCTCATCTAG 57.185 39.130 3.10 0.00 46.31 2.43
927 2940 5.138125 TGCTTCAACAGATTTTTCATCCC 57.862 39.130 0.00 0.00 0.00 3.85
1022 3053 2.280628 GGAAGTTGCATTAGCTAGCGT 58.719 47.619 9.55 0.21 42.74 5.07
1292 3338 0.108585 AACCTTCTCAAGCGCCAAGA 59.891 50.000 2.29 1.04 0.00 3.02
1375 3424 0.039798 GCGTGTTGTGTCGAGTAGGA 60.040 55.000 0.00 0.00 0.00 2.94
1434 3485 5.592282 TCAACAGTTAAATGAACTCAAGGCA 59.408 36.000 10.35 0.00 45.81 4.75
1515 3572 0.398318 GGAGCTCCACCATACCATCC 59.602 60.000 28.43 0.00 35.64 3.51
1582 3642 2.760374 GTGACAAGGATCGGGATCATC 58.240 52.381 10.57 3.59 39.54 2.92
1584 3644 3.041211 TGACAAGGATCGGGATCATCTT 58.959 45.455 10.57 3.32 39.54 2.40
1625 3685 9.856488 CAAGACAACTGCTACTACTAAATCTAA 57.144 33.333 0.00 0.00 0.00 2.10
1714 3774 7.704472 CACAACTTGTTTACAATAGCAAAAGGA 59.296 33.333 0.00 0.00 35.02 3.36
1750 3810 2.093306 TGTGAGAATGTGGGTAAGCG 57.907 50.000 0.00 0.00 0.00 4.68
1933 3995 3.260100 AACCTGGCAGTGAGGGGG 61.260 66.667 14.43 0.00 34.56 5.40
1986 4048 2.489971 CAACAGTCGGGAAGCAAAGTA 58.510 47.619 0.00 0.00 0.00 2.24
2002 4065 6.228258 AGCAAAGTATTGGTAACTTCTCGAA 58.772 36.000 0.00 0.00 45.01 3.71
2033 4096 4.076244 AGCTGCTCTTTGCTGTGG 57.924 55.556 0.00 0.00 43.37 4.17
2304 4379 1.277273 CCCATGAGAGCTCTGTTGTGA 59.723 52.381 23.91 0.00 0.00 3.58
2655 4752 2.107366 TCCACTGTTCGGCATCTATCA 58.893 47.619 0.00 0.00 0.00 2.15
3040 5137 8.296713 ACCGTGATTGGCATAATGATTTAATAC 58.703 33.333 0.00 0.00 0.00 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 59 3.485216 CGTCGTGTTAGCCCATCAAAATC 60.485 47.826 0.00 0.00 0.00 2.17
75 83 2.049433 GTGGTGGTCTGGTCGACG 60.049 66.667 9.92 0.00 43.79 5.12
117 127 5.054477 ACCACTAAATACATACCATGCGTC 58.946 41.667 0.00 0.00 0.00 5.19
206 1346 2.857152 GTGTGCAAGCAAAATTTGACGA 59.143 40.909 10.26 0.00 0.00 4.20
329 1469 1.569493 CGTTCCACACGCCAAGAAG 59.431 57.895 0.00 0.00 43.37 2.85
415 1619 0.466543 AGTAGCCAACGTGGACACAA 59.533 50.000 8.04 0.00 40.96 3.33
451 1655 4.890158 TTAAGTTCAGCTGAGATGGACA 57.110 40.909 17.43 0.00 0.00 4.02
465 1671 6.879276 ACTACTTGCCCTTTCTTTAAGTTC 57.121 37.500 0.00 0.00 33.93 3.01
534 2469 0.254178 GCAAGAGAATGGGAGGCAGA 59.746 55.000 0.00 0.00 0.00 4.26
535 2470 0.034767 TGCAAGAGAATGGGAGGCAG 60.035 55.000 0.00 0.00 0.00 4.85
536 2471 0.405198 TTGCAAGAGAATGGGAGGCA 59.595 50.000 0.00 0.00 0.00 4.75
537 2472 0.813821 GTTGCAAGAGAATGGGAGGC 59.186 55.000 0.00 0.00 0.00 4.70
538 2473 2.290514 TGAGTTGCAAGAGAATGGGAGG 60.291 50.000 0.00 0.00 0.00 4.30
539 2474 3.063510 TGAGTTGCAAGAGAATGGGAG 57.936 47.619 0.00 0.00 0.00 4.30
540 2475 3.149196 GTTGAGTTGCAAGAGAATGGGA 58.851 45.455 0.00 0.00 37.12 4.37
541 2476 2.886523 TGTTGAGTTGCAAGAGAATGGG 59.113 45.455 0.00 0.00 37.12 4.00
542 2477 4.778534 ATGTTGAGTTGCAAGAGAATGG 57.221 40.909 0.00 0.00 37.12 3.16
543 2478 5.526115 ACAATGTTGAGTTGCAAGAGAATG 58.474 37.500 0.00 0.00 37.12 2.67
544 2479 5.779529 ACAATGTTGAGTTGCAAGAGAAT 57.220 34.783 0.00 0.00 37.12 2.40
545 2480 5.581126 AACAATGTTGAGTTGCAAGAGAA 57.419 34.783 0.00 0.00 37.12 2.87
546 2481 5.822519 ACTAACAATGTTGAGTTGCAAGAGA 59.177 36.000 9.15 0.00 37.12 3.10
547 2482 6.064846 ACTAACAATGTTGAGTTGCAAGAG 57.935 37.500 9.15 0.00 37.12 2.85
548 2483 6.449635 AACTAACAATGTTGAGTTGCAAGA 57.550 33.333 9.15 0.00 37.12 3.02
557 2492 7.441157 CAGAGTTGTAGGAACTAACAATGTTGA 59.559 37.037 9.15 0.00 45.48 3.18
570 2505 3.388024 ACACAGAAGCAGAGTTGTAGGAA 59.612 43.478 0.00 0.00 0.00 3.36
711 2720 8.455903 AACCAGTCAATATAACAATGGATGAG 57.544 34.615 0.00 0.00 0.00 2.90
765 2774 7.877097 ACCTGAATATCACTAGATGAGCAATTC 59.123 37.037 0.00 8.25 41.91 2.17
779 2788 3.248602 GTGCGGAATGACCTGAATATCAC 59.751 47.826 0.00 0.00 36.31 3.06
927 2940 4.576053 TGAATTGTTTCTGGACACAGTGAG 59.424 41.667 7.81 0.00 45.14 3.51
1022 3053 5.528320 ACTTTTAAGCTAACACTTACGGCAA 59.472 36.000 0.00 0.00 31.94 4.52
1292 3338 3.954258 CGATAAGGAATCCTTGCCCTTTT 59.046 43.478 23.89 0.00 44.44 2.27
1495 3552 1.131638 GATGGTATGGTGGAGCTCCA 58.868 55.000 32.00 32.00 45.30 3.86
1496 3553 0.398318 GGATGGTATGGTGGAGCTCC 59.602 60.000 26.78 26.78 0.00 4.70
1515 3572 4.174411 TGATGTAGTCTCAGGAACAACG 57.826 45.455 0.00 0.00 0.00 4.10
1625 3685 5.970023 GCGAAACTCGAGTACATAGTTGTAT 59.030 40.000 20.39 0.00 43.74 2.29
1647 3707 1.656652 CTCCAGGTCCAACAATAGCG 58.343 55.000 0.00 0.00 0.00 4.26
1750 3810 4.090930 ACGTACATCAAGTTTGCGTGATAC 59.909 41.667 0.00 0.00 40.83 2.24
1933 3995 3.883489 GGTGCTAATAGTTGGTCCCATTC 59.117 47.826 0.00 0.00 0.00 2.67
1986 4048 5.424252 TGTATCCCTTCGAGAAGTTACCAAT 59.576 40.000 11.38 0.22 36.72 3.16
2002 4065 1.849039 AGCAGCTGGAAATGTATCCCT 59.151 47.619 17.12 0.00 38.82 4.20
2154 4229 5.183904 TCCAAGCCTTTTAGCAATCTTCTTC 59.816 40.000 0.00 0.00 34.23 2.87
2655 4752 5.967088 AGCTTCATACTATCAACACGAACT 58.033 37.500 0.00 0.00 0.00 3.01
3040 5137 3.181493 GGTGCATCTTTGTATGGCTTGAG 60.181 47.826 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.