Multiple sequence alignment - TraesCS1B01G409000

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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 TraesCS1B01G409000 chr1B 100.000 2573 0 0 1 2573 636680928 636678356 0.000000e+00 4752.0
1 TraesCS1B01G409000 chr1B 99.433 705 4 0 1658 2362 636661697 636660993 0.000000e+00 1280.0
2 TraesCS1B01G409000 chr1B 98.755 482 5 1 827 1308 636662518 636662038 0.000000e+00 856.0
3 TraesCS1B01G409000 chr1B 93.772 562 22 2 5 553 636665383 636664822 0.000000e+00 832.0
4 TraesCS1B01G409000 chr1B 95.392 217 10 0 2357 2573 636659017 636658801 1.900000e-91 346.0
5 TraesCS1B01G409000 chr1B 91.964 224 7 4 545 757 636663541 636663318 1.160000e-78 303.0
6 TraesCS1B01G409000 chr1B 98.485 66 1 0 757 822 636663229 636663164 1.620000e-22 117.0
7 TraesCS1B01G409000 chr1A 92.267 1319 66 16 1260 2573 553903117 553901830 0.000000e+00 1838.0
8 TraesCS1B01G409000 chr1A 94.432 449 23 2 232 679 553912977 553912530 0.000000e+00 689.0
9 TraesCS1B01G409000 chr1A 95.115 348 9 5 872 1213 553903459 553903114 2.250000e-150 542.0
10 TraesCS1B01G409000 chr1A 94.091 220 11 1 5 224 553933237 553933020 1.480000e-87 333.0
11 TraesCS1B01G409000 chr1A 92.727 220 16 0 5 224 553907373 553907154 4.130000e-83 318.0
12 TraesCS1B01G409000 chr1A 93.785 177 9 2 701 875 553903891 553903715 5.460000e-67 265.0
13 TraesCS1B01G409000 chr3D 89.033 693 63 8 884 1569 26643153 26642467 0.000000e+00 846.0
14 TraesCS1B01G409000 chr3D 82.933 791 99 19 887 1656 26649649 26648874 0.000000e+00 680.0
15 TraesCS1B01G409000 chr3D 78.218 404 57 13 2005 2408 602720480 602720108 1.990000e-56 230.0
16 TraesCS1B01G409000 chr3D 81.308 214 15 3 693 882 26643397 26643185 1.590000e-32 150.0
17 TraesCS1B01G409000 chr5A 88.051 703 55 9 5 679 456102782 456103483 0.000000e+00 806.0
18 TraesCS1B01G409000 chr4B 87.983 699 59 10 5 679 147351661 147350964 0.000000e+00 802.0
19 TraesCS1B01G409000 chr3A 87.983 699 58 8 5 679 684053429 684052733 0.000000e+00 802.0
20 TraesCS1B01G409000 chr3B 86.160 737 82 14 884 1611 44857651 44856926 0.000000e+00 778.0
21 TraesCS1B01G409000 chr3B 82.828 792 99 20 887 1656 45198810 45198034 0.000000e+00 675.0
22 TraesCS1B01G409000 chr3B 81.027 896 113 23 729 1569 45272018 45271125 0.000000e+00 660.0
23 TraesCS1B01G409000 chr3B 81.997 711 79 22 889 1585 44848249 44847574 2.240000e-155 558.0
24 TraesCS1B01G409000 chr4A 86.876 701 57 13 5 679 485135113 485134422 0.000000e+00 752.0
25 TraesCS1B01G409000 chr4A 85.405 692 50 14 5 670 542232549 542231883 0.000000e+00 671.0
26 TraesCS1B01G409000 chr4A 82.158 241 35 3 249 481 743700907 743700667 1.560000e-47 200.0
27 TraesCS1B01G409000 chrUn 82.299 757 102 16 884 1623 38820901 38821642 6.040000e-176 627.0
28 TraesCS1B01G409000 chrUn 83.019 477 52 14 223 679 92696443 92695976 3.080000e-109 405.0
29 TraesCS1B01G409000 chrUn 90.395 177 13 2 5 179 92696623 92696449 1.990000e-56 230.0
30 TraesCS1B01G409000 chr7D 83.019 477 52 14 223 679 577252988 577252521 3.080000e-109 405.0
31 TraesCS1B01G409000 chr2B 85.455 330 29 10 242 556 359273055 359273380 2.470000e-85 326.0
32 TraesCS1B01G409000 chr2D 79.458 443 66 17 1943 2374 538780691 538780263 9.010000e-75 291.0
33 TraesCS1B01G409000 chr7A 86.667 270 21 7 223 483 669494287 669494024 4.190000e-73 285.0
34 TraesCS1B01G409000 chr5D 81.185 287 53 1 2212 2498 544769209 544769494 1.990000e-56 230.0
35 TraesCS1B01G409000 chr5B 87.059 85 11 0 2281 2365 166644489 166644405 2.110000e-16 97.1


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 TraesCS1B01G409000 chr1B 636678356 636680928 2572 True 4752.000000 4752 100.000000 1 2573 1 chr1B.!!$R1 2572
1 TraesCS1B01G409000 chr1B 636658801 636665383 6582 True 622.333333 1280 96.300167 5 2573 6 chr1B.!!$R2 2568
2 TraesCS1B01G409000 chr1A 553901830 553907373 5543 True 740.750000 1838 93.473500 5 2573 4 chr1A.!!$R3 2568
3 TraesCS1B01G409000 chr3D 26648874 26649649 775 True 680.000000 680 82.933000 887 1656 1 chr3D.!!$R1 769
4 TraesCS1B01G409000 chr3D 26642467 26643397 930 True 498.000000 846 85.170500 693 1569 2 chr3D.!!$R3 876
5 TraesCS1B01G409000 chr5A 456102782 456103483 701 False 806.000000 806 88.051000 5 679 1 chr5A.!!$F1 674
6 TraesCS1B01G409000 chr4B 147350964 147351661 697 True 802.000000 802 87.983000 5 679 1 chr4B.!!$R1 674
7 TraesCS1B01G409000 chr3A 684052733 684053429 696 True 802.000000 802 87.983000 5 679 1 chr3A.!!$R1 674
8 TraesCS1B01G409000 chr3B 44856926 44857651 725 True 778.000000 778 86.160000 884 1611 1 chr3B.!!$R2 727
9 TraesCS1B01G409000 chr3B 45198034 45198810 776 True 675.000000 675 82.828000 887 1656 1 chr3B.!!$R3 769
10 TraesCS1B01G409000 chr3B 45271125 45272018 893 True 660.000000 660 81.027000 729 1569 1 chr3B.!!$R4 840
11 TraesCS1B01G409000 chr3B 44847574 44848249 675 True 558.000000 558 81.997000 889 1585 1 chr3B.!!$R1 696
12 TraesCS1B01G409000 chr4A 485134422 485135113 691 True 752.000000 752 86.876000 5 679 1 chr4A.!!$R1 674
13 TraesCS1B01G409000 chr4A 542231883 542232549 666 True 671.000000 671 85.405000 5 670 1 chr4A.!!$R2 665
14 TraesCS1B01G409000 chrUn 38820901 38821642 741 False 627.000000 627 82.299000 884 1623 1 chrUn.!!$F1 739
15 TraesCS1B01G409000 chrUn 92695976 92696623 647 True 317.500000 405 86.707000 5 679 2 chrUn.!!$R1 674

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
122 125 1.500474 CATCTGCTTCCCCCTCACTA 58.5 55.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1770 9437 1.153107 CCGATCAATGCCAGCAGGA 60.153 57.895 0.0 0.0 36.89 3.86 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
122 125 1.500474 CATCTGCTTCCCCCTCACTA 58.500 55.000 0.00 0.00 0.00 2.74
140 143 2.846827 ACTATTGCACTAGAGGCCCTTT 59.153 45.455 17.19 0.00 0.00 3.11
164 170 6.544928 TGGAGCTAACTGAGATATTGTCAA 57.455 37.500 0.00 0.00 0.00 3.18
363 603 3.875134 GGTACAAATGGACTACCCGATTG 59.125 47.826 0.00 0.00 38.40 2.67
378 618 3.563808 CCCGATTGTATACATGTGTTGGG 59.436 47.826 9.11 11.55 0.00 4.12
381 621 5.124776 CCGATTGTATACATGTGTTGGGTTT 59.875 40.000 9.11 0.00 0.00 3.27
681 4681 9.487790 AATTCAAAAATGAATTGTATTGTCCGT 57.512 25.926 14.17 0.00 44.14 4.69
682 4682 7.865875 TCAAAAATGAATTGTATTGTCCGTG 57.134 32.000 0.00 0.00 0.00 4.94
683 4683 7.429633 TCAAAAATGAATTGTATTGTCCGTGT 58.570 30.769 0.00 0.00 0.00 4.49
684 4684 7.380870 TCAAAAATGAATTGTATTGTCCGTGTG 59.619 33.333 0.00 0.00 0.00 3.82
686 4686 3.142174 TGAATTGTATTGTCCGTGTGCA 58.858 40.909 0.00 0.00 0.00 4.57
687 4687 3.058570 TGAATTGTATTGTCCGTGTGCAC 60.059 43.478 10.75 10.75 0.00 4.57
808 5012 5.077134 TGGAGATATGGCGTATGATCTTG 57.923 43.478 3.45 0.00 0.00 3.02
1458 8377 1.067212 GCCTATAGGGACGTGTCACAG 59.933 57.143 20.58 0.00 34.87 3.66
1604 8698 2.465010 TAACCCGCTCTTCCCCTCCA 62.465 60.000 0.00 0.00 0.00 3.86
1657 9324 1.921982 TGCAATGCTGTATTGTGGGT 58.078 45.000 17.69 0.00 46.35 4.51
1678 9345 9.043079 GTGGGTTTATGAGTATTAGCTAAACTC 57.957 37.037 25.77 25.77 40.05 3.01
1744 9411 7.161404 CCATAGTTGGCATATCTAAGCACTTA 58.839 38.462 0.00 0.00 35.85 2.24
1760 9427 3.000376 GCACTTATACGTTTACAGACGCC 60.000 47.826 0.00 0.00 46.47 5.68
1770 9437 2.759641 TACAGACGCCTCCGGACACT 62.760 60.000 0.00 0.00 39.22 3.55
1844 9511 3.689649 CCCGCACCTAAATCCATATAAGC 59.310 47.826 0.00 0.00 0.00 3.09
1847 9514 4.943705 CGCACCTAAATCCATATAAGCCAT 59.056 41.667 0.00 0.00 0.00 4.40
1860 9527 2.660189 AAGCCATGCAGCAATGTAAC 57.340 45.000 0.00 0.00 34.23 2.50
1931 9598 6.442952 ACAGATTCGAGCATAGATAGTTGAC 58.557 40.000 0.00 0.00 0.00 3.18
1937 9604 2.628657 AGCATAGATAGTTGACCCGACC 59.371 50.000 0.00 0.00 0.00 4.79
1967 9634 8.631480 AATCGGACCTAAAATAGACAAAGTTT 57.369 30.769 0.00 0.00 0.00 2.66
2050 9718 2.580815 GCCCTTGCCTTTGCCATC 59.419 61.111 0.00 0.00 36.33 3.51
2081 9749 2.835431 CGGCCGTCCATCTCCTCT 60.835 66.667 19.50 0.00 0.00 3.69
2093 9761 1.136984 CTCCTCTGTGTACGCGTCC 59.863 63.158 18.63 4.27 0.00 4.79
2127 9795 0.392998 GGTGTCATCATTGCCGTCCT 60.393 55.000 0.00 0.00 0.00 3.85
2155 9823 1.153066 TGCCGCTTTCCAACACAGA 60.153 52.632 0.00 0.00 0.00 3.41
2165 9833 6.145209 CGCTTTCCAACACAGATGAGATATAG 59.855 42.308 0.00 0.00 0.00 1.31
2166 9834 6.073331 GCTTTCCAACACAGATGAGATATAGC 60.073 42.308 0.00 0.00 0.00 2.97
2167 9835 5.474578 TCCAACACAGATGAGATATAGCC 57.525 43.478 0.00 0.00 0.00 3.93
2168 9836 4.284490 TCCAACACAGATGAGATATAGCCC 59.716 45.833 0.00 0.00 0.00 5.19
2171 9839 2.232208 CACAGATGAGATATAGCCCGCA 59.768 50.000 0.00 0.00 0.00 5.69
2176 9847 3.667497 TGAGATATAGCCCGCAAAGAG 57.333 47.619 0.00 0.00 0.00 2.85
2246 9917 2.811799 GCTCTCCTTCTCCCTCGC 59.188 66.667 0.00 0.00 0.00 5.03
2248 9919 1.608717 GCTCTCCTTCTCCCTCGCAA 61.609 60.000 0.00 0.00 0.00 4.85
2278 9949 2.669240 TCTCGAGCCTGAGACGGA 59.331 61.111 7.81 0.00 40.01 4.69
2280 9951 3.119709 CTCGAGCCTGAGACGGAGC 62.120 68.421 0.00 0.00 38.28 4.70
2282 9953 4.863925 GAGCCTGAGACGGAGCGC 62.864 72.222 0.00 0.00 0.00 5.92
2285 9956 3.764466 CCTGAGACGGAGCGCCTT 61.764 66.667 2.29 0.00 0.00 4.35
2286 9957 2.202676 CTGAGACGGAGCGCCTTC 60.203 66.667 2.29 4.71 32.81 3.46
2287 9958 4.116328 TGAGACGGAGCGCCTTCG 62.116 66.667 2.29 8.58 37.51 3.79
2297 9968 2.703409 CGCCTTCGCATTCTTCCG 59.297 61.111 0.00 0.00 34.03 4.30
2298 9969 2.405191 GCCTTCGCATTCTTCCGC 59.595 61.111 0.00 0.00 34.03 5.54
2299 9970 3.102097 CCTTCGCATTCTTCCGCC 58.898 61.111 0.00 0.00 0.00 6.13
2379 10050 0.811616 GCGCCTCATTCGAATCCACT 60.812 55.000 7.92 0.00 0.00 4.00
2543 10214 2.896443 CCGGAGCCAGAGGAGAAC 59.104 66.667 0.00 0.00 0.00 3.01
2544 10215 1.984570 CCGGAGCCAGAGGAGAACA 60.985 63.158 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.028131 ACCAGAATAATCACGGGAGTACA 58.972 43.478 0.00 0.00 44.67 2.90
1 2 4.142004 ACACCAGAATAATCACGGGAGTAC 60.142 45.833 0.00 0.00 44.67 2.73
2 3 4.028131 ACACCAGAATAATCACGGGAGTA 58.972 43.478 0.00 0.00 44.67 2.59
84 87 4.692625 AGATGCACAACAAGCTACAACTAG 59.307 41.667 0.00 0.00 0.00 2.57
122 125 2.450476 CAAAAGGGCCTCTAGTGCAAT 58.550 47.619 6.46 0.00 0.00 3.56
140 143 6.544928 TGACAATATCTCAGTTAGCTCCAA 57.455 37.500 0.00 0.00 0.00 3.53
363 603 6.751514 TCATCAAACCCAACACATGTATAC 57.248 37.500 0.00 0.00 0.00 1.47
378 618 8.975439 GGCTCAAATCATCAAATATCATCAAAC 58.025 33.333 0.00 0.00 0.00 2.93
381 621 8.357402 CAAGGCTCAAATCATCAAATATCATCA 58.643 33.333 0.00 0.00 0.00 3.07
599 4592 5.473796 TGTTTGTTCGTCTACACCTTTTC 57.526 39.130 0.00 0.00 0.00 2.29
680 4680 5.858049 TGTATGTACTAGTAAACGTGCACAC 59.142 40.000 18.64 7.33 0.00 3.82
681 4681 6.011476 TGTATGTACTAGTAAACGTGCACA 57.989 37.500 18.64 0.00 0.00 4.57
682 4682 6.932901 TTGTATGTACTAGTAAACGTGCAC 57.067 37.500 6.82 6.82 28.74 4.57
683 4683 7.943413 TTTTGTATGTACTAGTAAACGTGCA 57.057 32.000 3.61 4.50 0.00 4.57
727 4834 6.780198 ATCACTTATTATTGGGAGCCCTTA 57.220 37.500 7.16 0.00 36.94 2.69
1629 9292 5.882000 ACAATACAGCATTGCATGTTAGAGA 59.118 36.000 11.91 0.00 46.85 3.10
1645 9312 8.774586 GCTAATACTCATAAACCCACAATACAG 58.225 37.037 0.00 0.00 0.00 2.74
1657 9324 9.731819 CACGAGAGTTTAGCTAATACTCATAAA 57.268 33.333 29.70 9.08 46.40 1.40
1678 9345 6.414408 AAAGAGATGAATAAACAGCACGAG 57.586 37.500 0.00 0.00 0.00 4.18
1744 9411 1.202222 CGGAGGCGTCTGTAAACGTAT 60.202 52.381 0.00 0.00 44.38 3.06
1760 9427 2.575993 CAGCAGGAGTGTCCGGAG 59.424 66.667 3.06 0.00 42.75 4.63
1770 9437 1.153107 CCGATCAATGCCAGCAGGA 60.153 57.895 0.00 0.00 36.89 3.86
1844 9511 1.199789 ACGTGTTACATTGCTGCATGG 59.800 47.619 1.84 0.85 0.00 3.66
1847 9514 1.943340 TCAACGTGTTACATTGCTGCA 59.057 42.857 0.00 0.00 0.00 4.41
1860 9527 6.690957 ACTTGTTTGTGATGTTAATCAACGTG 59.309 34.615 0.00 0.00 44.40 4.49
1908 9575 5.861251 GGTCAACTATCTATGCTCGAATCTG 59.139 44.000 0.00 0.00 0.00 2.90
1910 9577 5.164954 GGGTCAACTATCTATGCTCGAATC 58.835 45.833 0.00 0.00 0.00 2.52
1912 9579 3.004419 CGGGTCAACTATCTATGCTCGAA 59.996 47.826 0.00 0.00 0.00 3.71
1937 9604 5.808540 TGTCTATTTTAGGTCCGATTTGTCG 59.191 40.000 0.00 0.00 0.00 4.35
2003 9671 2.254152 AGTGGTGATCTTGCCCTCTA 57.746 50.000 0.00 0.00 0.00 2.43
2042 9710 2.560861 GCAGAACGCGATGGCAAA 59.439 55.556 15.93 0.00 39.92 3.68
2065 9733 2.060980 ACAGAGGAGATGGACGGCC 61.061 63.158 0.00 0.00 0.00 6.13
2109 9777 2.309528 TAGGACGGCAATGATGACAC 57.690 50.000 0.00 0.00 32.33 3.67
2127 9795 0.392461 GAAAGCGGCACCACCAGATA 60.392 55.000 1.45 0.00 39.03 1.98
2155 9823 3.055530 CCTCTTTGCGGGCTATATCTCAT 60.056 47.826 0.00 0.00 0.00 2.90
2246 9917 0.734253 CGAGACTTCGGAGTGCCTTG 60.734 60.000 0.00 0.00 43.05 3.61
2248 9919 1.303398 TCGAGACTTCGGAGTGCCT 60.303 57.895 0.00 0.00 46.67 4.75
2270 9941 4.116328 CGAAGGCGCTCCGTCTCA 62.116 66.667 7.64 0.00 42.48 3.27
2280 9951 2.703409 CGGAAGAATGCGAAGGCG 59.297 61.111 0.00 0.00 43.91 5.52
2282 9953 2.813179 CGGCGGAAGAATGCGAAGG 61.813 63.158 0.00 0.00 43.91 3.46
2283 9954 2.703409 CGGCGGAAGAATGCGAAG 59.297 61.111 0.00 0.00 43.91 3.79
2284 9955 2.817834 CCGGCGGAAGAATGCGAA 60.818 61.111 24.41 0.00 43.91 4.70
2285 9956 3.716539 CTCCGGCGGAAGAATGCGA 62.717 63.158 30.59 3.78 43.91 5.10
2286 9957 3.264897 CTCCGGCGGAAGAATGCG 61.265 66.667 30.59 12.56 44.03 4.73
2287 9958 2.897350 CCTCCGGCGGAAGAATGC 60.897 66.667 30.59 0.00 0.00 3.56
2288 9959 2.897350 GCCTCCGGCGGAAGAATG 60.897 66.667 30.59 17.39 39.62 2.67
2367 10038 0.744414 CCGTGCCAGTGGATTCGAAT 60.744 55.000 15.20 11.20 0.00 3.34
2402 10073 2.286523 CGGAGCCCTGTCTTGTCCT 61.287 63.158 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.