Multiple sequence alignment - TraesCS3A01G421200

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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 TraesCS3A01G421200 chr3A 100.000 4007 0 0 1 4007 662574545 662570539 0.000000e+00 7400.0
1 TraesCS3A01G421200 chr3A 91.412 687 46 4 2340 3022 703816322 703816999 0.000000e+00 929.0
2 TraesCS3A01G421200 chr3A 100.000 44 0 0 3656 3699 662570821 662570778 9.230000e-12 82.4
3 TraesCS3A01G421200 chr3A 100.000 44 0 0 3725 3768 662570890 662570847 9.230000e-12 82.4
4 TraesCS3A01G421200 chr5A 97.730 4009 80 6 1 4007 470940718 470944717 0.000000e+00 6889.0
5 TraesCS3A01G421200 chr5A 92.191 461 35 1 1587 2047 3909851 3909392 0.000000e+00 651.0
6 TraesCS3A01G421200 chr5A 97.872 47 1 0 3653 3699 470944432 470944478 9.230000e-12 82.4
7 TraesCS3A01G421200 chr5A 100.000 33 0 0 3736 3768 470944377 470944409 1.200000e-05 62.1
8 TraesCS3A01G421200 chr2B 96.527 2188 71 3 940 3125 100092770 100090586 0.000000e+00 3615.0
9 TraesCS3A01G421200 chr2B 96.602 883 25 2 3127 4007 100090503 100089624 0.000000e+00 1459.0
10 TraesCS3A01G421200 chr2B 90.590 1084 80 9 1950 3022 392030684 392031756 0.000000e+00 1417.0
11 TraesCS3A01G421200 chr2B 91.142 858 68 4 940 1796 392029785 392030635 0.000000e+00 1157.0
12 TraesCS3A01G421200 chr2B 92.727 440 28 2 372 808 100093207 100092769 2.030000e-177 632.0
13 TraesCS3A01G421200 chr2B 92.027 439 31 2 373 808 392029349 392029786 7.360000e-172 614.0
14 TraesCS3A01G421200 chr2B 90.040 251 25 0 1797 2047 392030477 392030727 3.860000e-85 326.0
15 TraesCS3A01G421200 chr2B 100.000 44 0 0 3656 3699 100089903 100089860 9.230000e-12 82.4
16 TraesCS3A01G421200 chr2B 100.000 44 0 0 3725 3768 100089972 100089929 9.230000e-12 82.4
17 TraesCS3A01G421200 chr2B 94.595 37 1 1 101 137 13152854 13152819 5.590000e-04 56.5
18 TraesCS3A01G421200 chr5D 92.502 2014 126 7 994 2996 127930672 127928673 0.000000e+00 2859.0
19 TraesCS3A01G421200 chr5D 93.603 469 27 1 343 808 127931266 127930798 0.000000e+00 697.0
20 TraesCS3A01G421200 chr5D 93.899 377 22 1 3284 3659 510560153 510560529 5.810000e-158 568.0
21 TraesCS3A01G421200 chr5D 93.883 376 22 1 3284 3659 445018636 445018262 2.090000e-157 566.0
22 TraesCS3A01G421200 chr5D 91.781 146 12 0 3133 3278 445018831 445018686 1.890000e-48 204.0
23 TraesCS3A01G421200 chr5D 91.781 146 12 0 3133 3278 510559958 510560103 1.890000e-48 204.0
24 TraesCS3A01G421200 chr5D 94.898 98 2 2 6 101 7956327 7956423 2.490000e-32 150.0
25 TraesCS3A01G421200 chr5D 89.474 95 8 2 3032 3125 445019018 445018925 7.030000e-23 119.0
26 TraesCS3A01G421200 chr5D 89.474 95 8 2 3032 3125 510559771 510559864 7.030000e-23 119.0
27 TraesCS3A01G421200 chr6D 92.429 2021 120 12 994 2996 450179895 450177890 0.000000e+00 2854.0
28 TraesCS3A01G421200 chr6D 93.396 318 20 1 492 808 450180338 450180021 1.690000e-128 470.0
29 TraesCS3A01G421200 chr6D 83.434 332 38 11 150 467 450180648 450180320 3.920000e-75 292.0
30 TraesCS3A01G421200 chr6D 77.622 143 19 9 896 1037 25493339 25493209 1.540000e-09 75.0
31 TraesCS3A01G421200 chr6D 77.622 143 19 9 896 1037 413023622 413023492 1.540000e-09 75.0
32 TraesCS3A01G421200 chr1D 92.403 2014 127 8 994 2996 415604968 415606966 0.000000e+00 2848.0
33 TraesCS3A01G421200 chr7D 92.155 2014 133 7 994 2996 340191324 340193323 0.000000e+00 2820.0
34 TraesCS3A01G421200 chr7D 94.224 1108 63 1 940 2047 449485914 449484808 0.000000e+00 1690.0
35 TraesCS3A01G421200 chr7D 91.252 1086 73 9 1950 3022 449484851 449483775 0.000000e+00 1459.0
36 TraesCS3A01G421200 chr7D 93.603 469 27 1 343 808 340190730 340191198 0.000000e+00 697.0
37 TraesCS3A01G421200 chr7D 92.917 480 27 5 336 808 449486392 449485913 0.000000e+00 691.0
38 TraesCS3A01G421200 chr7D 86.498 237 15 9 150 386 340190526 340190745 1.110000e-60 244.0
39 TraesCS3A01G421200 chr7D 86.017 236 16 4 150 385 449486613 449486395 1.860000e-58 237.0
40 TraesCS3A01G421200 chr7D 95.918 98 1 2 6 101 135438960 135439056 5.360000e-34 156.0
41 TraesCS3A01G421200 chr7D 94.898 98 2 2 6 101 552304409 552304505 2.490000e-32 150.0
42 TraesCS3A01G421200 chr7D 93.204 103 4 2 1 101 7700509 7700408 8.970000e-32 148.0
43 TraesCS3A01G421200 chr7B 95.873 1163 45 2 1965 3125 593329040 593327879 0.000000e+00 1879.0
44 TraesCS3A01G421200 chr7B 94.170 892 51 1 681 1572 593330422 593329532 0.000000e+00 1358.0
45 TraesCS3A01G421200 chr7B 92.365 537 36 5 150 685 593339848 593339316 0.000000e+00 760.0
46 TraesCS3A01G421200 chr7B 98.295 176 3 0 3573 3748 593327417 593327242 3.890000e-80 309.0
47 TraesCS3A01G421200 chr7B 93.421 76 3 2 3847 3921 593327244 593327170 1.180000e-20 111.0
48 TraesCS3A01G421200 chr7B 100.000 44 0 0 3725 3768 593327334 593327291 9.230000e-12 82.4
49 TraesCS3A01G421200 chr7A 90.253 554 33 2 2574 3125 617600032 617600566 0.000000e+00 704.0
50 TraesCS3A01G421200 chr7A 89.531 554 37 2 2574 3125 41463266 41462732 0.000000e+00 682.0
51 TraesCS3A01G421200 chr7A 92.723 426 26 4 3235 3659 41462592 41462171 9.520000e-171 610.0
52 TraesCS3A01G421200 chr7A 92.471 425 28 3 3235 3659 617600706 617601126 4.430000e-169 604.0
53 TraesCS3A01G421200 chr7A 81.614 446 41 14 414 820 28987799 28987356 8.300000e-87 331.0
54 TraesCS3A01G421200 chr7A 81.755 433 42 17 417 819 28865324 28864899 1.070000e-85 327.0
55 TraesCS3A01G421200 chr7A 89.474 95 8 2 3032 3125 576789566 576789473 7.030000e-23 119.0
56 TraesCS3A01G421200 chr7A 92.857 42 3 0 3133 3174 41462637 41462596 1.200000e-05 62.1
57 TraesCS3A01G421200 chr1B 90.152 528 46 3 3133 3659 289696194 289696716 0.000000e+00 682.0
58 TraesCS3A01G421200 chr1B 91.781 146 12 0 3133 3278 680992476 680992621 1.890000e-48 204.0
59 TraesCS3A01G421200 chr3B 89.924 526 48 2 3134 3659 775656247 775655727 0.000000e+00 673.0
60 TraesCS3A01G421200 chrUn 92.826 460 29 2 2567 3022 314369261 314369720 0.000000e+00 664.0
61 TraesCS3A01G421200 chr2A 92.254 426 28 4 3235 3659 756526673 756527094 2.060000e-167 599.0
62 TraesCS3A01G421200 chr4D 94.898 98 2 2 6 101 25384189 25384093 2.490000e-32 150.0
63 TraesCS3A01G421200 chr3D 94.898 98 2 2 6 101 180622001 180621905 2.490000e-32 150.0
64 TraesCS3A01G421200 chr2D 94.792 96 2 2 8 101 176587353 176587447 3.230000e-31 147.0
65 TraesCS3A01G421200 chr2D 94.595 37 1 1 101 137 567056697 567056732 5.590000e-04 56.5
66 TraesCS3A01G421200 chr4B 92.233 103 5 2 1 101 552825445 552825546 4.170000e-30 143.0
67 TraesCS3A01G421200 chr6B 79.021 143 17 9 896 1037 123937575 123937445 7.140000e-13 86.1
68 TraesCS3A01G421200 chr4A 79.021 143 17 9 896 1037 648979495 648979365 7.140000e-13 86.1


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 TraesCS3A01G421200 chr3A 662570539 662574545 4006 True 2521.600000 7400 100.000000 1 4007 3 chr3A.!!$R1 4006
1 TraesCS3A01G421200 chr3A 703816322 703816999 677 False 929.000000 929 91.412000 2340 3022 1 chr3A.!!$F1 682
2 TraesCS3A01G421200 chr5A 470940718 470944717 3999 False 2344.500000 6889 98.534000 1 4007 3 chr5A.!!$F1 4006
3 TraesCS3A01G421200 chr2B 100089624 100093207 3583 True 1174.160000 3615 97.171200 372 4007 5 chr2B.!!$R2 3635
4 TraesCS3A01G421200 chr2B 392029349 392031756 2407 False 878.500000 1417 90.949750 373 3022 4 chr2B.!!$F1 2649
5 TraesCS3A01G421200 chr5D 127928673 127931266 2593 True 1778.000000 2859 93.052500 343 2996 2 chr5D.!!$R1 2653
6 TraesCS3A01G421200 chr5D 510559771 510560529 758 False 297.000000 568 91.718000 3032 3659 3 chr5D.!!$F2 627
7 TraesCS3A01G421200 chr5D 445018262 445019018 756 True 296.333333 566 91.712667 3032 3659 3 chr5D.!!$R2 627
8 TraesCS3A01G421200 chr6D 450177890 450180648 2758 True 1205.333333 2854 89.753000 150 2996 3 chr6D.!!$R3 2846
9 TraesCS3A01G421200 chr1D 415604968 415606966 1998 False 2848.000000 2848 92.403000 994 2996 1 chr1D.!!$F1 2002
10 TraesCS3A01G421200 chr7D 340190526 340193323 2797 False 1253.666667 2820 90.752000 150 2996 3 chr7D.!!$F3 2846
11 TraesCS3A01G421200 chr7D 449483775 449486613 2838 True 1019.250000 1690 91.102500 150 3022 4 chr7D.!!$R2 2872
12 TraesCS3A01G421200 chr7B 593339316 593339848 532 True 760.000000 760 92.365000 150 685 1 chr7B.!!$R1 535
13 TraesCS3A01G421200 chr7B 593327170 593330422 3252 True 747.880000 1879 96.351800 681 3921 5 chr7B.!!$R2 3240
14 TraesCS3A01G421200 chr7A 617600032 617601126 1094 False 654.000000 704 91.362000 2574 3659 2 chr7A.!!$F1 1085
15 TraesCS3A01G421200 chr7A 41462171 41463266 1095 True 451.366667 682 91.703667 2574 3659 3 chr7A.!!$R4 1085
16 TraesCS3A01G421200 chr1B 289696194 289696716 522 False 682.000000 682 90.152000 3133 3659 1 chr1B.!!$F1 526
17 TraesCS3A01G421200 chr3B 775655727 775656247 520 True 673.000000 673 89.924000 3134 3659 1 chr3B.!!$R1 525

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
252 253 0.107268 GTACTGGTGGGTGTTTCGGT 59.893 55.000 0.0 0.0 0.00 4.69 F
284 285 1.131883 CGTAGTGGTGAGTCCTAACGG 59.868 57.143 0.0 0.0 34.88 4.44 F
1666 1819 1.383109 ATGGAGGAGACCCGCATGA 60.383 57.895 0.0 0.0 37.58 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2115 2498 1.209128 CATACGGCTCGTTGACATCC 58.791 55.000 5.57 0.0 41.54 3.51 R
2419 2802 6.867816 GGAATGCACAATTCTTCACAATGTAA 59.132 34.615 0.00 0.0 43.71 2.41 R
3181 3660 1.272490 CTTGTACGGAAGGAGCACTGA 59.728 52.381 0.00 0.0 0.00 3.41 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
59 60 4.867599 CCGCGGTAGCTCGAACCC 62.868 72.222 19.50 0.00 42.32 4.11
129 130 1.388837 TAGCGCGGCTGTTGGAGATA 61.389 55.000 8.83 0.00 40.10 1.98
191 192 0.841289 ACCGAACCCAAAACTCCTGA 59.159 50.000 0.00 0.00 0.00 3.86
252 253 0.107268 GTACTGGTGGGTGTTTCGGT 59.893 55.000 0.00 0.00 0.00 4.69
284 285 1.131883 CGTAGTGGTGAGTCCTAACGG 59.868 57.143 0.00 0.00 34.88 4.44
292 293 2.093869 GTGAGTCCTAACGGGTAATGCA 60.094 50.000 0.00 0.00 36.25 3.96
524 597 1.609580 CCCAACTTAGCAGCCACGTAA 60.610 52.381 0.00 0.00 0.00 3.18
707 781 4.452455 CCAGTCAGATTCCATTAATACGGC 59.548 45.833 0.00 0.00 0.00 5.68
842 916 6.430000 ACAAGACCATGAAATGTGTTAGTACC 59.570 38.462 0.00 0.00 44.81 3.34
1506 1653 2.978978 TCACAAGACCAAGATGGAGGAA 59.021 45.455 2.85 0.00 40.96 3.36
1666 1819 1.383109 ATGGAGGAGACCCGCATGA 60.383 57.895 0.00 0.00 37.58 3.07
1861 2181 4.694760 TGATGCAAGACCATGCTAGTAT 57.305 40.909 0.00 0.00 46.54 2.12
1875 2195 4.209538 TGCTAGTATAGGCACGAAGGTAA 58.790 43.478 0.00 0.00 39.70 2.85
1983 2357 3.384168 ACATCCCTACACCAGAGCAATA 58.616 45.455 0.00 0.00 0.00 1.90
2005 2379 8.801299 CAATATGTCTCATCAGTACCTCTACAT 58.199 37.037 0.00 0.00 0.00 2.29
2115 2498 8.535592 TGAACACTTTAATATTGTGCAAAAACG 58.464 29.630 0.00 0.00 35.33 3.60
2945 3335 6.073331 TGGCTTTTACTATTTTTGCATTGCAC 60.073 34.615 11.66 0.00 38.71 4.57
2974 3364 6.535540 TGCACTAGTCCAAACCAGTTTTATA 58.464 36.000 0.00 0.00 0.00 0.98
3045 3435 8.798402 ACATTTTGGATTGATGCAAATTTTCAT 58.202 25.926 10.74 2.79 45.33 2.57
3069 3461 1.811965 CACATTTCATGAGACGGGCAA 59.188 47.619 0.00 0.00 0.00 4.52
3070 3462 1.812571 ACATTTCATGAGACGGGCAAC 59.187 47.619 0.00 0.00 0.00 4.17
3164 3643 7.857456 TCACCTATCAACAAGCTTAGGATAAA 58.143 34.615 16.00 0.00 35.74 1.40
3181 3660 5.016831 GGATAAACCCCAACATGAAGTCTT 58.983 41.667 0.00 0.00 0.00 3.01
3379 3904 1.126846 GAGTCTTGTTCATGGAACGCG 59.873 52.381 3.53 3.53 44.55 6.01
3383 3908 1.440145 TTGTTCATGGAACGCGCACA 61.440 50.000 5.73 2.56 44.55 4.57
3453 3978 7.758076 TGATTACGTAGCATCCTAATTAATCCG 59.242 37.037 5.10 0.00 33.54 4.18
3973 4500 3.309848 CCAGGTTATCATTTGGGAGGGTT 60.310 47.826 0.00 0.00 0.00 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.460311 CACCTACTCCGCCTCGATTT 59.540 55.000 0.00 0.00 0.00 2.17
106 107 1.167155 TCCAACAGCCGCGCTAAAAA 61.167 50.000 5.56 0.00 36.40 1.94
191 192 4.501071 AGACCGTTATAGAATTTGCGTGT 58.499 39.130 0.00 0.00 0.00 4.49
284 285 2.031683 GCGGACAACTACATGCATTACC 59.968 50.000 0.00 0.00 0.00 2.85
292 293 0.179084 CGGATGGCGGACAACTACAT 60.179 55.000 0.00 0.00 0.00 2.29
524 597 3.472652 TGCGTCTGTGATTTGGTTTACT 58.527 40.909 0.00 0.00 0.00 2.24
535 608 1.737838 GATGGGATTTGCGTCTGTGA 58.262 50.000 0.00 0.00 0.00 3.58
1155 1302 1.651987 GCGCCTGATGCAAGTACTTA 58.348 50.000 8.04 0.00 41.33 2.24
1208 1355 4.533707 TCAGATTCTTGTCCATCACCTCTT 59.466 41.667 0.00 0.00 0.00 2.85
1358 1505 2.192608 CTTGCGCTCCTGCTTCAACC 62.193 60.000 9.73 0.00 36.97 3.77
1481 1628 3.599343 TCCATCTTGGTCTTGTGATTCG 58.401 45.455 0.00 0.00 39.03 3.34
1506 1653 3.814504 ATATTCCCTTCCATGCGGATT 57.185 42.857 0.00 0.00 42.41 3.01
1666 1819 5.687166 TGGTCCTGTATCGTATTTCCTTT 57.313 39.130 0.00 0.00 0.00 3.11
1861 2181 8.514330 AATAATGAAATTTACCTTCGTGCCTA 57.486 30.769 0.00 0.00 37.87 3.93
1983 2357 6.132658 ACATGTAGAGGTACTGATGAGACAT 58.867 40.000 0.00 0.00 41.55 3.06
2005 2379 5.773176 TGGTGTACAGATCTCTTGTTCTACA 59.227 40.000 0.00 0.00 0.00 2.74
2063 2446 4.260743 CGTAGGATGTGCATACCATTTGTG 60.261 45.833 0.00 0.00 30.21 3.33
2115 2498 1.209128 CATACGGCTCGTTGACATCC 58.791 55.000 5.57 0.00 41.54 3.51
2419 2802 6.867816 GGAATGCACAATTCTTCACAATGTAA 59.132 34.615 0.00 0.00 43.71 2.41
2878 3268 7.543520 GCATCAAAGGAACCTTTCATCTAAAAG 59.456 37.037 14.89 2.84 43.56 2.27
2945 3335 1.470098 GGTTTGGACTAGTGCAGCATG 59.530 52.381 17.04 0.00 40.87 4.06
2974 3364 7.118680 ACTGGTCGTTTAATTGATGTTACGAAT 59.881 33.333 0.00 0.00 39.36 3.34
3045 3435 2.419990 CCCGTCTCATGAAATGTGCCTA 60.420 50.000 0.00 0.00 46.80 3.93
3069 3461 7.753580 GCACCAAAATTTTAAGCTAATACTCGT 59.246 33.333 2.44 0.00 0.00 4.18
3070 3462 7.753132 TGCACCAAAATTTTAAGCTAATACTCG 59.247 33.333 17.04 0.00 0.00 4.18
3164 3643 2.443255 ACTGAAGACTTCATGTTGGGGT 59.557 45.455 18.04 8.08 39.30 4.95
3181 3660 1.272490 CTTGTACGGAAGGAGCACTGA 59.728 52.381 0.00 0.00 0.00 3.41
3243 3722 1.446907 GAGTTGGTCGAGTCGTCCTA 58.553 55.000 25.52 17.62 36.17 2.94
3379 3904 3.000041 TGACTGATTACGACCAATGTGC 59.000 45.455 0.00 0.00 0.00 4.57
3383 3908 6.816136 TGTATCATGACTGATTACGACCAAT 58.184 36.000 0.00 0.00 42.23 3.16


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

AutoCloner maintained by Alex Coulton.