Multiple sequence alignment - TraesCS4D01G145800

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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 TraesCS4D01G145800 chr4D 100.000 2396 0 0 1 2396 134685555 134687950 0.000000e+00 4425.0
1 TraesCS4D01G145800 chr4D 89.831 59 6 0 2039 2097 351735551 351735609 2.550000e-10 76.8
2 TraesCS4D01G145800 chr4D 93.617 47 3 0 2045 2091 78845903 78845949 1.190000e-08 71.3
3 TraesCS4D01G145800 chr4D 95.238 42 2 0 2050 2091 59066408 59066367 1.540000e-07 67.6
4 TraesCS4D01G145800 chr4B 93.348 1368 49 20 656 2018 193561958 193563288 0.000000e+00 1984.0
5 TraesCS4D01G145800 chr4B 95.455 308 13 1 2090 2396 193563283 193563590 7.700000e-135 490.0
6 TraesCS4D01G145800 chr4B 94.776 134 5 1 523 656 193560058 193560189 8.680000e-50 207.0
7 TraesCS4D01G145800 chr4A 92.734 812 25 10 658 1456 396756539 396757329 0.000000e+00 1142.0
8 TraesCS4D01G145800 chr4A 92.736 592 30 7 1455 2042 396757411 396757993 0.000000e+00 843.0
9 TraesCS4D01G145800 chr4A 94.325 511 25 2 1 507 699903142 699902632 0.000000e+00 780.0
10 TraesCS4D01G145800 chr4A 94.425 287 15 1 221 507 628945481 628945766 7.860000e-120 440.0
11 TraesCS4D01G145800 chr4A 93.455 275 15 2 2124 2396 396758145 396758418 2.870000e-109 405.0
12 TraesCS4D01G145800 chr4A 93.571 140 7 2 523 662 396756376 396756513 8.680000e-50 207.0
13 TraesCS4D01G145800 chr4A 87.037 54 7 0 2039 2092 559062552 559062499 7.150000e-06 62.1
14 TraesCS4D01G145800 chr4A 100.000 28 0 0 1360 1387 57438717 57438744 4.000000e-03 52.8
15 TraesCS4D01G145800 chr5B 96.063 508 20 0 1 508 539277906 539278413 0.000000e+00 828.0
16 TraesCS4D01G145800 chr6A 95.079 508 24 1 1 507 514491774 514492281 0.000000e+00 798.0
17 TraesCS4D01G145800 chr6A 89.412 510 52 2 1 510 558118562 558118055 2.010000e-180 641.0
18 TraesCS4D01G145800 chr1A 95.069 507 24 1 1 507 42628610 42629115 0.000000e+00 797.0
19 TraesCS4D01G145800 chr1B 91.583 499 41 1 9 507 332835821 332836318 0.000000e+00 688.0
20 TraesCS4D01G145800 chr5D 96.210 343 13 0 1 343 317212261 317212603 1.610000e-156 562.0
21 TraesCS4D01G145800 chr2D 85.600 500 70 2 7 504 561213123 561212624 7.590000e-145 523.0
22 TraesCS4D01G145800 chr2D 95.556 45 2 0 2050 2094 155977172 155977216 3.300000e-09 73.1
23 TraesCS4D01G145800 chr7B 85.429 501 71 2 7 507 679818337 679817839 9.820000e-144 520.0
24 TraesCS4D01G145800 chr7B 97.619 42 1 0 2050 2091 721287685 721287644 3.300000e-09 73.1
25 TraesCS4D01G145800 chr6B 93.750 48 3 0 2044 2091 635178948 635178995 3.300000e-09 73.1
26 TraesCS4D01G145800 chr2A 93.617 47 3 0 2050 2096 49937068 49937022 1.190000e-08 71.3
27 TraesCS4D01G145800 chr1D 89.583 48 5 0 2049 2096 31419415 31419368 7.150000e-06 62.1


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 TraesCS4D01G145800 chr4D 134685555 134687950 2395 False 4425.000000 4425 100.000000 1 2396 1 chr4D.!!$F2 2395
1 TraesCS4D01G145800 chr4B 193560058 193563590 3532 False 893.666667 1984 94.526333 523 2396 3 chr4B.!!$F1 1873
2 TraesCS4D01G145800 chr4A 699902632 699903142 510 True 780.000000 780 94.325000 1 507 1 chr4A.!!$R2 506
3 TraesCS4D01G145800 chr4A 396756376 396758418 2042 False 649.250000 1142 93.124000 523 2396 4 chr4A.!!$F3 1873
4 TraesCS4D01G145800 chr5B 539277906 539278413 507 False 828.000000 828 96.063000 1 508 1 chr5B.!!$F1 507
5 TraesCS4D01G145800 chr6A 514491774 514492281 507 False 798.000000 798 95.079000 1 507 1 chr6A.!!$F1 506
6 TraesCS4D01G145800 chr6A 558118055 558118562 507 True 641.000000 641 89.412000 1 510 1 chr6A.!!$R1 509
7 TraesCS4D01G145800 chr1A 42628610 42629115 505 False 797.000000 797 95.069000 1 507 1 chr1A.!!$F1 506

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
622 627 4.408821 TCACCCAGCCCGACATGC 62.409 66.667 0.0 0.0 0.0 4.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1551 3421 0.107993 CTGCTGCTGCTGCTACCTTA 60.108 55.0 27.67 9.42 40.48 2.69 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
36 37 4.501071 GTCAAATTGAATGCTGATGGCTT 58.499 39.130 0.00 0.00 42.39 4.35
259 260 6.022315 AGTATCCTTGATATCTTCTGGGGAG 58.978 44.000 3.98 0.00 0.00 4.30
289 290 4.585879 GTTCAGTTTATGCCTCCTTGGTA 58.414 43.478 0.00 0.00 38.35 3.25
497 502 5.471556 TTGAGTAATACAAGTGTTCCCGA 57.528 39.130 0.00 0.00 0.00 5.14
498 503 5.068234 TGAGTAATACAAGTGTTCCCGAG 57.932 43.478 0.00 0.00 0.00 4.63
622 627 4.408821 TCACCCAGCCCGACATGC 62.409 66.667 0.00 0.00 0.00 4.06
675 2449 5.067544 GCCCTCAGTACTAGTCGTAATTCTT 59.932 44.000 0.00 0.00 0.00 2.52
676 2450 6.727215 CCCTCAGTACTAGTCGTAATTCTTC 58.273 44.000 0.00 0.00 0.00 2.87
679 2453 7.254863 CCTCAGTACTAGTCGTAATTCTTCCTC 60.255 44.444 0.00 0.00 0.00 3.71
680 2454 7.337167 TCAGTACTAGTCGTAATTCTTCCTCT 58.663 38.462 0.00 0.00 0.00 3.69
681 2455 7.495279 TCAGTACTAGTCGTAATTCTTCCTCTC 59.505 40.741 0.00 0.00 0.00 3.20
682 2456 7.496591 CAGTACTAGTCGTAATTCTTCCTCTCT 59.503 40.741 0.00 0.00 0.00 3.10
683 2457 6.930667 ACTAGTCGTAATTCTTCCTCTCTC 57.069 41.667 0.00 0.00 0.00 3.20
684 2458 6.655930 ACTAGTCGTAATTCTTCCTCTCTCT 58.344 40.000 0.00 0.00 0.00 3.10
685 2459 6.764560 ACTAGTCGTAATTCTTCCTCTCTCTC 59.235 42.308 0.00 0.00 0.00 3.20
1103 2887 0.100146 GCGGACGGTTCGTAATCTCT 59.900 55.000 10.98 0.00 41.37 3.10
1105 2889 1.268437 CGGACGGTTCGTAATCTCTCC 60.268 57.143 0.00 0.00 41.37 3.71
1236 3023 3.669251 ACTTCAGAGGAGTGCAAGTAC 57.331 47.619 0.00 0.00 0.00 2.73
1248 3035 2.928116 GTGCAAGTACAGGATTCCGTAC 59.072 50.000 20.65 20.65 35.45 3.67
1398 3185 2.460669 GGGAAGCACCTCCAATGAAAT 58.539 47.619 2.38 0.00 37.20 2.17
1418 3205 8.797350 TGAAATACATACATCATCCATCCATC 57.203 34.615 0.00 0.00 0.00 3.51
1807 3684 9.807386 GGTTAATGTCAATTCTTGTATATACGC 57.193 33.333 8.33 0.00 0.00 4.42
1840 3717 4.021229 ACCATCCTACGTGTCACTTCATA 58.979 43.478 0.00 0.00 0.00 2.15
1842 3719 5.046878 ACCATCCTACGTGTCACTTCATAAA 60.047 40.000 0.00 0.00 0.00 1.40
1927 3804 4.274950 TGGAATCCAACAGAAGAAAACGTC 59.725 41.667 0.00 0.00 0.00 4.34
1957 3834 5.674052 ATCTTCATCCATAGATTCCTCCG 57.326 43.478 0.00 0.00 0.00 4.63
1964 3841 6.669591 TCATCCATAGATTCCTCCGTTCATAT 59.330 38.462 0.00 0.00 0.00 1.78
1994 3871 5.874810 AGCTTATTTTTAGCTCATCGTGTCA 59.125 36.000 0.00 0.00 45.52 3.58
2022 3899 2.730382 TCGACCATGCTACTTACTCCA 58.270 47.619 0.00 0.00 0.00 3.86
2029 3906 3.795623 TGCTACTTACTCCATCCGTTC 57.204 47.619 0.00 0.00 0.00 3.95
2031 3908 2.429610 GCTACTTACTCCATCCGTTCCA 59.570 50.000 0.00 0.00 0.00 3.53
2037 3914 6.113411 ACTTACTCCATCCGTTCCAAAATAG 58.887 40.000 0.00 0.00 0.00 1.73
2042 3919 4.457603 TCCATCCGTTCCAAAATAGTTGTG 59.542 41.667 0.00 0.00 0.00 3.33
2043 3920 3.907894 TCCGTTCCAAAATAGTTGTGC 57.092 42.857 0.00 0.00 0.00 4.57
2045 3922 4.643463 TCCGTTCCAAAATAGTTGTGCTA 58.357 39.130 0.00 0.00 0.00 3.49
2046 3923 5.064558 TCCGTTCCAAAATAGTTGTGCTAA 58.935 37.500 0.00 0.00 32.72 3.09
2047 3924 5.049267 TCCGTTCCAAAATAGTTGTGCTAAC 60.049 40.000 0.00 0.00 32.72 2.34
2049 3926 6.378582 CGTTCCAAAATAGTTGTGCTAACAT 58.621 36.000 7.08 0.00 35.83 2.71
2050 3927 6.861055 CGTTCCAAAATAGTTGTGCTAACATT 59.139 34.615 7.08 3.19 35.83 2.71
2051 3928 8.018520 CGTTCCAAAATAGTTGTGCTAACATTA 58.981 33.333 7.08 0.00 35.83 1.90
2061 3938 8.110860 AGTTGTGCTAACATTAATACAAAGCT 57.889 30.769 10.68 0.00 35.83 3.74
2062 3939 8.023128 AGTTGTGCTAACATTAATACAAAGCTG 58.977 33.333 10.68 0.00 35.83 4.24
2063 3940 7.680442 TGTGCTAACATTAATACAAAGCTGA 57.320 32.000 10.68 0.00 0.00 4.26
2064 3941 7.751732 TGTGCTAACATTAATACAAAGCTGAG 58.248 34.615 10.68 0.00 0.00 3.35
2065 3942 7.390440 TGTGCTAACATTAATACAAAGCTGAGT 59.610 33.333 10.68 0.00 0.00 3.41
2066 3943 8.237267 GTGCTAACATTAATACAAAGCTGAGTT 58.763 33.333 10.68 0.00 0.00 3.01
2067 3944 9.443323 TGCTAACATTAATACAAAGCTGAGTTA 57.557 29.630 10.68 0.00 0.00 2.24
2086 4051 8.726870 TGAGTTATCTATTTTAAAACGGAGGG 57.273 34.615 1.97 0.00 0.00 4.30
2093 4058 8.593945 TCTATTTTAAAACGGAGGGAGTACTA 57.406 34.615 1.97 0.00 0.00 1.82
2176 4141 1.956477 AGGAAATTCTGCACACACACC 59.044 47.619 0.00 0.00 0.00 4.16
2343 4310 2.229675 TCAGTGACAAGTGAGCACAG 57.770 50.000 3.19 0.00 35.08 3.66
2345 4312 0.467384 AGTGACAAGTGAGCACAGCT 59.533 50.000 3.19 0.00 43.88 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 2.159531 GCATCATCGCTTGCTACAAACA 60.160 45.455 0.00 0.00 35.95 2.83
259 260 3.689649 AGGCATAAACTGAACGATCAACC 59.310 43.478 0.00 0.00 34.49 3.77
509 514 4.362677 TCTATTTCAAGGGAGCCACTAGT 58.637 43.478 0.00 0.00 0.00 2.57
510 515 5.119694 GTTCTATTTCAAGGGAGCCACTAG 58.880 45.833 0.00 0.00 0.00 2.57
511 516 4.534500 TGTTCTATTTCAAGGGAGCCACTA 59.466 41.667 0.00 0.00 0.00 2.74
512 517 3.330701 TGTTCTATTTCAAGGGAGCCACT 59.669 43.478 0.00 0.00 0.00 4.00
513 518 3.686016 TGTTCTATTTCAAGGGAGCCAC 58.314 45.455 0.00 0.00 0.00 5.01
514 519 4.591321 ATGTTCTATTTCAAGGGAGCCA 57.409 40.909 0.00 0.00 0.00 4.75
515 520 5.921962 AAATGTTCTATTTCAAGGGAGCC 57.078 39.130 0.00 0.00 0.00 4.70
541 546 4.458295 ACGAGGAAAGACGTTCTATCTCAA 59.542 41.667 1.12 0.00 39.75 3.02
542 547 4.008330 ACGAGGAAAGACGTTCTATCTCA 58.992 43.478 1.12 0.00 39.75 3.27
555 560 3.389741 GCACAATGCACGAGGAAAG 57.610 52.632 0.00 0.00 44.26 2.62
717 2491 5.907197 ACGACTAGTCAAATCAACAACAG 57.093 39.130 22.37 4.11 0.00 3.16
1103 2887 2.441164 GGCGCAGAGAGAGAGGGA 60.441 66.667 10.83 0.00 0.00 4.20
1105 2889 0.249405 GAATGGCGCAGAGAGAGAGG 60.249 60.000 10.83 0.00 0.00 3.69
1178 2962 4.270834 ACTAGATCAGCGAGTAACTTGGA 58.729 43.478 0.00 0.00 30.10 3.53
1179 2963 4.640789 ACTAGATCAGCGAGTAACTTGG 57.359 45.455 0.00 0.00 30.10 3.61
1189 2973 5.120986 ACAGATGATACGTACTAGATCAGCG 59.879 44.000 0.00 1.20 40.17 5.18
1190 2974 6.147985 TCACAGATGATACGTACTAGATCAGC 59.852 42.308 0.00 0.86 36.48 4.26
1236 3023 1.396653 AGGGTACGTACGGAATCCTG 58.603 55.000 20.21 0.00 0.00 3.86
1398 3185 7.121611 GCAAATGATGGATGGATGATGTATGTA 59.878 37.037 0.00 0.00 0.00 2.29
1418 3205 2.319032 CGAGCGAGCGAGCAAATG 59.681 61.111 9.01 0.00 40.15 2.32
1500 3370 6.194796 TGAGAAAAGGAATTATTGGCTTCG 57.805 37.500 0.00 0.00 0.00 3.79
1549 3419 1.065199 TGCTGCTGCTGCTACCTTAAT 60.065 47.619 27.67 0.00 40.48 1.40
1550 3420 0.324614 TGCTGCTGCTGCTACCTTAA 59.675 50.000 27.67 7.14 40.48 1.85
1551 3421 0.107993 CTGCTGCTGCTGCTACCTTA 60.108 55.000 27.67 9.42 40.48 2.69
1552 3422 1.376942 CTGCTGCTGCTGCTACCTT 60.377 57.895 27.67 0.00 40.48 3.50
1553 3423 2.268280 CTGCTGCTGCTGCTACCT 59.732 61.111 27.67 0.00 40.48 3.08
1577 3447 2.949451 ACATCTGAAGCTCCTACGTG 57.051 50.000 0.00 0.00 0.00 4.49
1799 3676 8.372459 AGGATGGTTAATTGAGTTGCGTATATA 58.628 33.333 0.00 0.00 0.00 0.86
1800 3677 7.224297 AGGATGGTTAATTGAGTTGCGTATAT 58.776 34.615 0.00 0.00 0.00 0.86
1807 3684 5.642063 ACACGTAGGATGGTTAATTGAGTTG 59.358 40.000 0.00 0.00 0.00 3.16
1942 3819 6.935240 AATATGAACGGAGGAATCTATGGA 57.065 37.500 0.00 0.00 0.00 3.41
2022 3899 4.079253 AGCACAACTATTTTGGAACGGAT 58.921 39.130 0.00 0.00 0.00 4.18
2037 3914 8.020819 TCAGCTTTGTATTAATGTTAGCACAAC 58.979 33.333 0.00 0.00 36.16 3.32
2059 3936 8.336080 CCTCCGTTTTAAAATAGATAACTCAGC 58.664 37.037 3.52 0.00 0.00 4.26
2060 3937 8.827677 CCCTCCGTTTTAAAATAGATAACTCAG 58.172 37.037 3.52 0.00 0.00 3.35
2061 3938 8.542080 TCCCTCCGTTTTAAAATAGATAACTCA 58.458 33.333 3.52 0.00 0.00 3.41
2062 3939 8.953368 TCCCTCCGTTTTAAAATAGATAACTC 57.047 34.615 3.52 0.00 0.00 3.01
2063 3940 8.546322 ACTCCCTCCGTTTTAAAATAGATAACT 58.454 33.333 3.52 0.00 0.00 2.24
2064 3941 8.728337 ACTCCCTCCGTTTTAAAATAGATAAC 57.272 34.615 3.52 0.00 0.00 1.89
2065 3942 9.822185 GTACTCCCTCCGTTTTAAAATAGATAA 57.178 33.333 3.52 0.00 0.00 1.75
2066 3943 9.205513 AGTACTCCCTCCGTTTTAAAATAGATA 57.794 33.333 3.52 0.00 0.00 1.98
2067 3944 8.087303 AGTACTCCCTCCGTTTTAAAATAGAT 57.913 34.615 3.52 0.00 0.00 1.98
2068 3945 7.486407 AGTACTCCCTCCGTTTTAAAATAGA 57.514 36.000 3.52 3.61 0.00 1.98
2075 4040 6.375455 CAGTAACTAGTACTCCCTCCGTTTTA 59.625 42.308 0.00 0.00 41.37 1.52
2077 4042 4.704057 CAGTAACTAGTACTCCCTCCGTTT 59.296 45.833 0.00 0.00 41.37 3.60
2086 4051 9.816354 ACTAGTAGTAAGCAGTAACTAGTACTC 57.184 37.037 10.80 0.00 41.37 2.59
2093 4058 9.683870 ACTGAATACTAGTAGTAAGCAGTAACT 57.316 33.333 28.84 15.71 42.24 2.24
2164 4129 0.747644 TCTTGGTGGTGTGTGTGCAG 60.748 55.000 0.00 0.00 0.00 4.41
2176 4141 5.133221 CCATAGACCCCTTATTTCTTGGTG 58.867 45.833 0.00 0.00 0.00 4.17
2254 4219 5.156608 TGATCTCCGTCGGTACATCTATA 57.843 43.478 11.88 0.00 0.00 1.31
2261 4226 0.669077 AGCATGATCTCCGTCGGTAC 59.331 55.000 11.88 2.32 0.00 3.34
2263 4228 1.439228 CAGCATGATCTCCGTCGGT 59.561 57.895 11.88 0.00 39.69 4.69
2264 4229 1.953138 GCAGCATGATCTCCGTCGG 60.953 63.158 4.39 4.39 39.69 4.79
2343 4310 1.873591 ACACCACATTCGAACAAGAGC 59.126 47.619 0.00 0.00 0.00 4.09
2345 4312 5.301555 TGATTACACCACATTCGAACAAGA 58.698 37.500 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.