Multiple sequence alignment - TraesCS1B01G223800

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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 TraesCS1B01G223800 chr1B 100.000 2432 0 0 1 2432 401993366 401990935 0.000000e+00 4492.0
1 TraesCS1B01G223800 chr1B 94.339 1837 80 6 600 2431 401763967 401762150 0.000000e+00 2795.0
2 TraesCS1B01G223800 chr1B 91.607 977 55 16 644 1609 402039921 402038961 0.000000e+00 1325.0
3 TraesCS1B01G223800 chr1B 98.507 268 3 1 336 602 401764299 401764032 2.830000e-129 472.0
4 TraesCS1B01G223800 chr1B 97.500 240 6 0 101 340 401765701 401765462 6.260000e-111 411.0
5 TraesCS1B01G223800 chr1B 89.167 240 26 0 1664 1903 2770258 2770497 1.410000e-77 300.0
6 TraesCS1B01G223800 chr1B 94.828 116 6 0 474 589 402040038 402039923 5.340000e-42 182.0
7 TraesCS1B01G223800 chr1B 92.857 112 8 0 1 112 401766225 401766114 1.930000e-36 163.0
8 TraesCS1B01G223800 chr1D 92.395 1052 57 13 602 1637 298604698 298603654 0.000000e+00 1478.0
9 TraesCS1B01G223800 chr1D 85.921 554 50 19 1901 2432 298598676 298598129 1.260000e-157 566.0
10 TraesCS1B01G223800 chr1D 94.488 127 7 0 474 600 298604892 298604766 1.910000e-46 196.0
11 TraesCS1B01G223800 chr1D 92.373 118 7 1 1550 1665 298598792 298598675 1.500000e-37 167.0
12 TraesCS1B01G223800 chr1D 96.774 31 1 0 600 630 298599862 298599832 4.000000e-03 52.8
13 TraesCS1B01G223800 chr1A 91.392 1092 58 16 600 1665 372287997 372286916 0.000000e+00 1463.0
14 TraesCS1B01G223800 chr1A 90.169 1007 72 16 602 1591 372316468 372315472 0.000000e+00 1286.0
15 TraesCS1B01G223800 chr1A 92.193 602 23 2 1 602 372288639 372288062 0.000000e+00 830.0
16 TraesCS1B01G223800 chr1A 88.608 237 23 4 366 600 372316770 372316536 3.960000e-73 285.0
17 TraesCS1B01G223800 chr1A 89.773 176 16 2 2259 2432 372285910 372285735 8.750000e-55 224.0
18 TraesCS1B01G223800 chr4B 82.604 983 116 29 677 1628 602873972 602873014 0.000000e+00 817.0
19 TraesCS1B01G223800 chr4B 83.333 924 113 25 627 1529 603037675 603038578 0.000000e+00 815.0
20 TraesCS1B01G223800 chr4B 89.669 242 22 3 1664 1904 139755999 139756238 3.040000e-79 305.0
21 TraesCS1B01G223800 chr4D 83.808 877 106 22 773 1628 477543741 477542880 0.000000e+00 800.0
22 TraesCS1B01G223800 chr4D 83.620 873 91 27 627 1473 477558660 477559506 0.000000e+00 773.0
23 TraesCS1B01G223800 chr5B 90.717 237 22 0 1666 1902 64626076 64626312 1.400000e-82 316.0
24 TraesCS1B01G223800 chr3D 89.540 239 25 0 1664 1902 209677726 209677488 1.090000e-78 303.0
25 TraesCS1B01G223800 chr3D 89.344 244 23 2 1663 1905 593241647 593241406 1.090000e-78 303.0
26 TraesCS1B01G223800 chr7A 89.121 239 26 0 1664 1902 383095996 383096234 5.080000e-77 298.0
27 TraesCS1B01G223800 chr2A 88.142 253 27 3 1650 1902 468294297 468294048 5.080000e-77 298.0
28 TraesCS1B01G223800 chr2B 86.923 260 31 2 1664 1923 557173662 557173918 3.060000e-74 289.0


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 TraesCS1B01G223800 chr1B 401990935 401993366 2431 True 4492.00 4492 100.000000 1 2432 1 chr1B.!!$R1 2431
1 TraesCS1B01G223800 chr1B 401762150 401766225 4075 True 960.25 2795 95.800750 1 2431 4 chr1B.!!$R2 2430
2 TraesCS1B01G223800 chr1B 402038961 402040038 1077 True 753.50 1325 93.217500 474 1609 2 chr1B.!!$R3 1135
3 TraesCS1B01G223800 chr1D 298598129 298604892 6763 True 491.96 1478 92.390200 474 2432 5 chr1D.!!$R1 1958
4 TraesCS1B01G223800 chr1A 372285735 372288639 2904 True 839.00 1463 91.119333 1 2432 3 chr1A.!!$R1 2431
5 TraesCS1B01G223800 chr1A 372315472 372316770 1298 True 785.50 1286 89.388500 366 1591 2 chr1A.!!$R2 1225
6 TraesCS1B01G223800 chr4B 602873014 602873972 958 True 817.00 817 82.604000 677 1628 1 chr4B.!!$R1 951
7 TraesCS1B01G223800 chr4B 603037675 603038578 903 False 815.00 815 83.333000 627 1529 1 chr4B.!!$F2 902
8 TraesCS1B01G223800 chr4D 477542880 477543741 861 True 800.00 800 83.808000 773 1628 1 chr4D.!!$R1 855
9 TraesCS1B01G223800 chr4D 477558660 477559506 846 False 773.00 773 83.620000 627 1473 1 chr4D.!!$F1 846


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
998 2728 1.066215 TCTAGCACGCCACACAATCAT 60.066 47.619 0.0 0.0 0.0 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2339 9781 1.219124 GCGGCTTGGACTCTCATCA 59.781 57.895 0.0 0.0 0.0 3.07 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
47 48 1.421646 AGCTAGGTCACATAATGGGGC 59.578 52.381 0.00 0.00 0.00 5.80
159 584 1.135286 GCAGATTGTAAGCCTGTTGCC 60.135 52.381 0.00 0.00 42.71 4.52
359 1952 9.317936 GCCTATCATATCGAAATGACAATGATA 57.682 33.333 0.00 0.00 40.68 2.15
423 2017 4.903054 TGACTATCAATGGATGGATCTGC 58.097 43.478 0.00 0.00 35.70 4.26
441 2035 4.635223 TCTGCAGAACCAGCATATCATAC 58.365 43.478 15.67 0.00 41.82 2.39
442 2036 4.346127 TCTGCAGAACCAGCATATCATACT 59.654 41.667 15.67 0.00 41.82 2.12
443 2037 4.383173 TGCAGAACCAGCATATCATACTG 58.617 43.478 0.00 0.00 37.02 2.74
690 2374 1.523501 GCGTGTAACATGCATGAACG 58.476 50.000 32.75 29.66 44.78 3.95
693 2377 2.096466 CGTGTAACATGCATGAACGTGT 60.096 45.455 32.75 8.26 41.53 4.49
733 2421 4.209538 TGTTGCCATATCTCCAGAATTGG 58.790 43.478 4.50 4.50 46.49 3.16
884 2597 2.596452 ACTACGTCAAACAGCTCGATG 58.404 47.619 0.00 0.00 0.00 3.84
891 2607 1.985447 AAACAGCTCGATGCCATGCG 61.985 55.000 3.66 0.00 44.23 4.73
998 2728 1.066215 TCTAGCACGCCACACAATCAT 60.066 47.619 0.00 0.00 0.00 2.45
1012 2742 4.710865 ACACAATCATAATGGCATCCAACA 59.289 37.500 0.00 0.00 36.95 3.33
1239 2986 2.348998 CTGCTCCGCCTCAAGGTT 59.651 61.111 0.00 0.00 37.57 3.50
1483 3246 5.358298 AGATTTGCTTTCCGTACTTTGTC 57.642 39.130 0.00 0.00 0.00 3.18
1541 3307 5.920273 CCACATTTCAATTGTGTAACCAGTC 59.080 40.000 10.71 0.00 34.36 3.51
1562 3342 3.640967 TCCTGCTTATTTGGCAAACAAGT 59.359 39.130 26.48 10.37 40.82 3.16
1644 8374 7.435068 TTGTCCAATTGTAGCTTCTTACTTC 57.565 36.000 4.43 0.00 0.00 3.01
1672 8402 7.148373 TGCGAATTTGTACAAAATACTACCTCC 60.148 37.037 23.97 1.85 33.56 4.30
1691 8421 1.609841 CCGTCCTGGTTTGTTAGTCCC 60.610 57.143 0.00 0.00 0.00 4.46
1692 8422 1.609841 CGTCCTGGTTTGTTAGTCCCC 60.610 57.143 0.00 0.00 0.00 4.81
1800 8530 9.004717 TCGTATTTGAACATAGTTTTCAATGGA 57.995 29.630 0.00 0.00 41.45 3.41
2044 8780 1.672356 CAGGGAAGGTGCTCCAACG 60.672 63.158 7.70 0.00 37.20 4.10
2135 9567 5.470047 TTCACCCTTGAAGAGAAGTCTAC 57.530 43.478 0.00 0.00 36.79 2.59
2253 9694 2.035442 GGAGCTCGTGACCCAAAGC 61.035 63.158 7.83 0.00 34.95 3.51
2339 9781 2.762887 ACTGTCGACACTGATCCATGAT 59.237 45.455 15.76 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 7.073883 CACATAATTTGCGAGATAATGAGGTG 58.926 38.462 0.00 0.00 0.00 4.00
99 100 1.729267 AATCCGGGCCCCTATGCAAT 61.729 55.000 18.66 0.00 0.00 3.56
159 584 7.267857 GGGGAATCAAAGAGTTTTATTCCATG 58.732 38.462 19.68 0.00 44.85 3.66
290 715 1.133199 TCAAGGGGAACTTTGCCACAT 60.133 47.619 1.61 0.00 46.22 3.21
359 1952 7.882271 GGAATGATAGAGATTAATCAGGTGCTT 59.118 37.037 17.56 3.11 35.67 3.91
447 2041 3.316308 GCCATGTCCATCTTTGATGGTAC 59.684 47.826 21.54 18.15 40.06 3.34
460 2054 1.001764 CAAGCTGGAGCCATGTCCA 60.002 57.895 5.05 5.05 44.82 4.02
462 2056 0.807496 GAACAAGCTGGAGCCATGTC 59.193 55.000 0.00 0.86 43.38 3.06
690 2374 2.572290 AGTTGAGCAACACCCTTACAC 58.428 47.619 14.99 0.00 43.47 2.90
693 2377 3.290948 ACAAGTTGAGCAACACCCTTA 57.709 42.857 10.54 0.00 43.47 2.69
803 2507 4.389077 GTGATTCGATCGGTTTCAAGACTT 59.611 41.667 16.41 0.00 0.00 3.01
891 2607 2.228103 CTGGTGATATGGATGCATGCAC 59.772 50.000 25.37 16.53 0.00 4.57
1012 2742 4.070552 GGCGACGAAGAGGGCAGT 62.071 66.667 0.00 0.00 0.00 4.40
1435 3186 2.485122 GCCCATGCAACAGTACGC 59.515 61.111 0.00 0.00 37.47 4.42
1508 3272 4.840115 ACAATTGAAATGTGGGAGTGGATT 59.160 37.500 13.59 0.00 0.00 3.01
1509 3273 4.221262 CACAATTGAAATGTGGGAGTGGAT 59.779 41.667 13.59 0.00 43.45 3.41
1541 3307 3.993920 ACTTGTTTGCCAAATAAGCAGG 58.006 40.909 21.93 6.38 41.57 4.85
1644 8374 8.234546 AGGTAGTATTTTGTACAAATTCGCAAG 58.765 33.333 21.17 0.00 0.00 4.01
1672 8402 1.609841 GGGGACTAACAAACCAGGACG 60.610 57.143 0.00 0.00 0.00 4.79
1729 8459 6.141560 TCACATGCAGTAACATTTTGTCAA 57.858 33.333 0.00 0.00 0.00 3.18
1743 8473 8.619146 ACGATATAATTTTTGTTCACATGCAG 57.381 30.769 0.00 0.00 0.00 4.41
1854 8584 7.188381 TGGCCCTTATTATAATATGTGCCAAT 58.812 34.615 29.15 1.38 42.31 3.16
1863 8593 9.762381 CCTGGTTTATTGGCCCTTATTATAATA 57.238 33.333 0.00 0.81 0.00 0.98
1872 8602 1.615919 CGTCCTGGTTTATTGGCCCTT 60.616 52.381 0.00 0.00 0.00 3.95
1876 8606 1.379527 CTCCGTCCTGGTTTATTGGC 58.620 55.000 0.00 0.00 39.52 4.52
1967 8700 3.124466 TGTTGCAACTATTCCGTTGATCG 59.876 43.478 28.61 0.00 45.40 3.69
1969 8702 4.699735 TGATGTTGCAACTATTCCGTTGAT 59.300 37.500 28.61 10.89 45.40 2.57
1979 8714 4.006989 GGTGTATGGTGATGTTGCAACTA 58.993 43.478 28.61 16.22 0.00 2.24
2044 8780 2.479566 TCTTTCATGGAGGTGCTGTC 57.520 50.000 0.00 0.00 0.00 3.51
2109 9541 4.855340 ACTTCTCTTCAAGGGTGAAAACA 58.145 39.130 0.00 0.00 43.18 2.83
2135 9567 3.854286 AAACACTGCTCGAAGTTTACG 57.146 42.857 0.00 0.00 32.88 3.18
2184 9618 7.396055 CCCTTTATTGGTTGAACCTAGAAATGA 59.604 37.037 16.44 3.00 39.58 2.57
2253 9694 1.278238 GACTTCGATTAGGTGGCACG 58.722 55.000 12.17 0.00 0.00 5.34
2282 9723 4.334203 ACGTTGCTCAAACTCAACAACATA 59.666 37.500 0.00 0.00 41.80 2.29
2320 9761 2.760092 TCATCATGGATCAGTGTCGACA 59.240 45.455 15.76 15.76 0.00 4.35
2339 9781 1.219124 GCGGCTTGGACTCTCATCA 59.781 57.895 0.00 0.00 0.00 3.07
2379 9821 3.891977 GTCAGAGATGCCCTACATGACTA 59.108 47.826 0.00 0.00 39.84 2.59



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

AutoCloner maintained by Alex Coulton.