Multiple sequence alignment - TraesCS4D01G319900

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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 TraesCS4D01G319900 chr4D 100.000 2578 0 0 1 2578 483449542 483446965 0.000000e+00 4761.0
1 TraesCS4D01G319900 chr4D 96.643 983 31 1 1596 2578 25354697 25353717 0.000000e+00 1631.0
2 TraesCS4D01G319900 chr4D 91.536 319 13 2 1048 1366 483458138 483457834 6.590000e-116 427.0
3 TraesCS4D01G319900 chr4D 89.333 300 29 2 260 556 483461062 483460763 8.710000e-100 374.0
4 TraesCS4D01G319900 chr4D 76.031 388 54 14 691 1046 483458605 483458225 5.710000e-37 165.0
5 TraesCS4D01G319900 chr4D 90.476 126 5 3 1405 1523 483457474 483457349 2.660000e-35 159.0
6 TraesCS4D01G319900 chr3D 96.881 1026 25 2 1559 2578 451221845 451220821 0.000000e+00 1711.0
7 TraesCS4D01G319900 chr3D 95.652 1035 27 9 1556 2578 134848088 134849116 0.000000e+00 1646.0
8 TraesCS4D01G319900 chr3D 95.289 1019 38 4 1567 2578 132562768 132561753 0.000000e+00 1607.0
9 TraesCS4D01G319900 chr5D 96.607 943 28 3 1638 2578 423204423 423203483 0.000000e+00 1561.0
10 TraesCS4D01G319900 chr5D 79.075 411 51 20 967 1355 483659053 483658656 1.530000e-62 250.0
11 TraesCS4D01G319900 chr2D 94.747 1009 39 4 1577 2578 152634809 152635810 0.000000e+00 1557.0
12 TraesCS4D01G319900 chr2D 92.375 1036 58 10 1553 2578 79376004 79374980 0.000000e+00 1456.0
13 TraesCS4D01G319900 chr7B 94.575 977 47 3 1605 2578 703296768 703297741 0.000000e+00 1506.0
14 TraesCS4D01G319900 chr7B 78.095 210 36 8 352 555 161865265 161865470 9.690000e-25 124.0
15 TraesCS4D01G319900 chr2B 93.564 1010 48 8 1581 2578 16986251 16987255 0.000000e+00 1489.0
16 TraesCS4D01G319900 chr5A 81.826 1216 107 50 374 1523 663386772 663385605 0.000000e+00 917.0
17 TraesCS4D01G319900 chr5A 82.550 149 22 4 429 574 71498001 71497854 7.490000e-26 128.0
18 TraesCS4D01G319900 chr4B 93.408 622 33 6 1 618 613710853 613711470 0.000000e+00 915.0
19 TraesCS4D01G319900 chr4B 92.414 580 40 3 911 1489 613714755 613715331 0.000000e+00 824.0
20 TraesCS4D01G319900 chr4B 96.642 268 6 2 640 904 613712828 613713095 2.350000e-120 442.0
21 TraesCS4D01G319900 chr4B 89.024 164 15 1 1222 1385 613755677 613755837 1.560000e-47 200.0
22 TraesCS4D01G319900 chr5B 79.540 391 52 15 967 1337 594760081 594759699 1.180000e-63 254.0
23 TraesCS4D01G319900 chr5B 80.702 114 21 1 486 598 477556838 477556725 1.270000e-13 87.9
24 TraesCS4D01G319900 chr6D 78.431 204 31 10 352 548 11766922 11766725 1.250000e-23 121.0
25 TraesCS4D01G319900 chr6D 75.449 167 32 8 395 555 133708692 133708529 3.560000e-09 73.1
26 TraesCS4D01G319900 chr3B 75.709 247 43 14 353 589 701735534 701735295 9.750000e-20 108.0
27 TraesCS4D01G319900 chr1B 82.692 104 15 3 482 583 440745885 440745783 3.530000e-14 89.8
28 TraesCS4D01G319900 chr7A 76.667 150 31 4 371 517 696654216 696654364 2.130000e-11 80.5


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 TraesCS4D01G319900 chr4D 483446965 483449542 2577 True 4761.00 4761 100.000000 1 2578 1 chr4D.!!$R2 2577
1 TraesCS4D01G319900 chr4D 25353717 25354697 980 True 1631.00 1631 96.643000 1596 2578 1 chr4D.!!$R1 982
2 TraesCS4D01G319900 chr4D 483457349 483461062 3713 True 281.25 427 86.844000 260 1523 4 chr4D.!!$R3 1263
3 TraesCS4D01G319900 chr3D 451220821 451221845 1024 True 1711.00 1711 96.881000 1559 2578 1 chr3D.!!$R2 1019
4 TraesCS4D01G319900 chr3D 134848088 134849116 1028 False 1646.00 1646 95.652000 1556 2578 1 chr3D.!!$F1 1022
5 TraesCS4D01G319900 chr3D 132561753 132562768 1015 True 1607.00 1607 95.289000 1567 2578 1 chr3D.!!$R1 1011
6 TraesCS4D01G319900 chr5D 423203483 423204423 940 True 1561.00 1561 96.607000 1638 2578 1 chr5D.!!$R1 940
7 TraesCS4D01G319900 chr2D 152634809 152635810 1001 False 1557.00 1557 94.747000 1577 2578 1 chr2D.!!$F1 1001
8 TraesCS4D01G319900 chr2D 79374980 79376004 1024 True 1456.00 1456 92.375000 1553 2578 1 chr2D.!!$R1 1025
9 TraesCS4D01G319900 chr7B 703296768 703297741 973 False 1506.00 1506 94.575000 1605 2578 1 chr7B.!!$F2 973
10 TraesCS4D01G319900 chr2B 16986251 16987255 1004 False 1489.00 1489 93.564000 1581 2578 1 chr2B.!!$F1 997
11 TraesCS4D01G319900 chr5A 663385605 663386772 1167 True 917.00 917 81.826000 374 1523 1 chr5A.!!$R2 1149
12 TraesCS4D01G319900 chr4B 613710853 613715331 4478 False 727.00 915 94.154667 1 1489 3 chr4B.!!$F2 1488

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
35 36 1.539827 CCATTGGTTGGTCTTTCGTCC 59.460 52.381 0.00 0.0 40.99 4.79 F
171 172 1.783140 GTACTTTTTCTCACGCGTCGT 59.217 47.619 9.86 0.0 42.36 4.34 F
1480 6973 2.093973 CAGTGATAGGTATCCATCGGCC 60.094 54.545 0.00 0.0 31.71 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1530 7030 0.107081 TGGTGGTGGTTGTACCGAAG 59.893 55.000 0.0 0.0 42.58 3.79 R
1531 7031 0.179051 GTGGTGGTGGTTGTACCGAA 60.179 55.000 0.0 0.0 42.58 4.30 R
2298 7825 1.745087 ACATTCCACAACATCATCGCC 59.255 47.619 0.0 0.0 0.00 5.54 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
28 29 2.445155 GGCCCCATTGGTTGGTCT 59.555 61.111 1.20 0.00 44.83 3.85
35 36 1.539827 CCATTGGTTGGTCTTTCGTCC 59.460 52.381 0.00 0.00 40.99 4.79
53 54 3.691498 GTCCGTTTTTGCAGGTATATGC 58.309 45.455 0.00 0.00 46.68 3.14
133 134 3.872511 TGGCTGAATGCAATAACCAAG 57.127 42.857 0.00 0.00 45.15 3.61
171 172 1.783140 GTACTTTTTCTCACGCGTCGT 59.217 47.619 9.86 0.00 42.36 4.34
192 193 4.432345 CGTGTATGTCGTACAATCACGTAG 59.568 45.833 22.72 9.64 45.00 3.51
193 194 4.731961 GTGTATGTCGTACAATCACGTAGG 59.268 45.833 6.48 0.00 44.52 3.18
194 195 4.635324 TGTATGTCGTACAATCACGTAGGA 59.365 41.667 2.25 0.00 40.27 2.94
195 196 3.752412 TGTCGTACAATCACGTAGGAG 57.248 47.619 0.00 0.00 42.51 3.69
231 232 7.512426 CGTTAGTGTTAGTTTTTCTTTTTGGCG 60.512 37.037 0.00 0.00 0.00 5.69
232 233 5.106442 AGTGTTAGTTTTTCTTTTTGGCGG 58.894 37.500 0.00 0.00 0.00 6.13
240 241 5.793030 TTTTCTTTTTGGCGGGAATCTAA 57.207 34.783 0.00 0.00 0.00 2.10
312 314 4.397417 CCCATCAAACAGGACTTGAGATTC 59.603 45.833 0.00 0.00 36.30 2.52
368 370 2.426024 GCATGTACTACCTCCGTTCTGA 59.574 50.000 0.00 0.00 0.00 3.27
409 411 6.915843 CGTATTTAGGGCCATATTTTGACAAC 59.084 38.462 6.18 0.00 0.00 3.32
410 412 6.865834 ATTTAGGGCCATATTTTGACAACA 57.134 33.333 6.18 0.00 0.00 3.33
564 570 3.262405 TGGCACTAAATACGGAAAGGACT 59.738 43.478 0.00 0.00 0.00 3.85
624 1021 9.599322 GACATGTTGTCTTATTTGTAGAAAGTG 57.401 33.333 0.00 0.00 43.73 3.16
965 6045 3.569194 TCTTTTAGCAGTCCAACACCA 57.431 42.857 0.00 0.00 0.00 4.17
1431 6924 4.077822 CCAGGCAATAATCTTCCTGATCC 58.922 47.826 8.56 0.00 46.80 3.36
1440 6933 2.307768 TCTTCCTGATCCGTCGCTTAT 58.692 47.619 0.00 0.00 0.00 1.73
1480 6973 2.093973 CAGTGATAGGTATCCATCGGCC 60.094 54.545 0.00 0.00 31.71 6.13
1489 6982 2.775911 ATCCATCGGCCTCATGTATG 57.224 50.000 0.00 0.00 0.00 2.39
1535 7035 9.745880 AGTATTCACAATAATGTAGTACTTCGG 57.254 33.333 0.00 0.00 37.82 4.30
1536 7036 9.525409 GTATTCACAATAATGTAGTACTTCGGT 57.475 33.333 0.00 0.00 37.82 4.69
1538 7038 8.915871 TTCACAATAATGTAGTACTTCGGTAC 57.084 34.615 0.00 0.00 43.27 3.34
1539 7039 8.054152 TCACAATAATGTAGTACTTCGGTACA 57.946 34.615 0.00 0.00 44.29 2.90
1540 7040 8.522003 TCACAATAATGTAGTACTTCGGTACAA 58.478 33.333 0.00 0.00 44.29 2.41
1541 7041 8.589629 CACAATAATGTAGTACTTCGGTACAAC 58.410 37.037 0.00 0.00 44.29 3.32
1542 7042 7.761249 ACAATAATGTAGTACTTCGGTACAACC 59.239 37.037 0.00 0.00 42.90 3.77
1547 7047 2.818130 TACTTCGGTACAACCACCAC 57.182 50.000 0.00 0.00 38.47 4.16
1548 7048 0.107268 ACTTCGGTACAACCACCACC 59.893 55.000 0.00 0.00 38.47 4.61
1549 7049 0.107081 CTTCGGTACAACCACCACCA 59.893 55.000 0.00 0.00 38.47 4.17
1550 7050 0.179051 TTCGGTACAACCACCACCAC 60.179 55.000 0.00 0.00 38.47 4.16
1551 7051 1.598685 CGGTACAACCACCACCACC 60.599 63.158 0.00 0.00 38.47 4.61
1562 7062 3.814906 CACCACCACCACCACCCA 61.815 66.667 0.00 0.00 0.00 4.51
1686 7196 1.299544 CCGCGTCGTATGCATACCA 60.300 57.895 27.08 15.17 0.00 3.25
1703 7213 1.739929 CATGCGGTTCGGTAGTGCA 60.740 57.895 0.00 0.00 40.23 4.57
2005 7518 2.740826 CCGTGTCGCCGGTGAAAT 60.741 61.111 21.49 0.00 43.07 2.17
2298 7825 7.740346 GTCACTGTTGACGAATTTACTGTATTG 59.260 37.037 0.00 0.00 42.86 1.90
2453 7980 2.891580 TCCCGGAGACAACTATATGAGC 59.108 50.000 0.73 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.096416 ACCTGCAAAAACGGACGAAA 58.904 45.000 0.00 0.00 0.00 3.46
35 36 3.376859 TGAGGCATATACCTGCAAAAACG 59.623 43.478 0.00 0.00 44.12 3.60
53 54 0.814457 CGGGAGAGTCAAGAGTGAGG 59.186 60.000 0.00 0.00 33.27 3.86
116 117 3.872511 TGCCTTGGTTATTGCATTCAG 57.127 42.857 0.00 0.00 0.00 3.02
133 134 1.601166 ACCAACTAAGGTTCGTTGCC 58.399 50.000 2.38 0.00 39.34 4.52
145 146 3.737266 CGCGTGAGAAAAAGTACCAACTA 59.263 43.478 0.00 0.00 33.75 2.24
171 172 4.635324 TCCTACGTGATTGTACGACATACA 59.365 41.667 0.00 0.00 46.46 2.29
231 232 4.037446 TGCGCATTAACCAATTAGATTCCC 59.963 41.667 5.66 0.00 0.00 3.97
232 233 5.181690 TGCGCATTAACCAATTAGATTCC 57.818 39.130 5.66 0.00 0.00 3.01
240 241 8.725148 TCAATTTTTATTTGCGCATTAACCAAT 58.275 25.926 12.75 9.64 0.00 3.16
346 348 2.165641 CAGAACGGAGGTAGTACATGCA 59.834 50.000 7.25 0.00 0.00 3.96
564 570 9.381038 AGCTACCTCCTCTGTTATGATTTATTA 57.619 33.333 0.00 0.00 0.00 0.98
612 618 6.433847 TCCATCTCTTCCACTTTCTACAAA 57.566 37.500 0.00 0.00 0.00 2.83
624 1021 6.581171 ACAACTTTCATTTCCATCTCTTCC 57.419 37.500 0.00 0.00 0.00 3.46
965 6045 4.657969 AGCAAGAGAGGAGCATTTATAGGT 59.342 41.667 0.00 0.00 0.00 3.08
1020 6100 4.635223 TGATAGCTAAACCTATGCAGCTG 58.365 43.478 10.11 10.11 43.91 4.24
1361 6533 6.653320 GTGGATTGGTGACTTTCTAATGTGTA 59.347 38.462 0.00 0.00 0.00 2.90
1431 6924 2.398903 GTCGTGTTCAATAAGCGACG 57.601 50.000 0.00 0.00 41.53 5.12
1440 6933 1.608109 TGTACGCCTAGTCGTGTTCAA 59.392 47.619 9.44 0.00 43.21 2.69
1480 6973 2.133553 CTCTTGCCGAGCATACATGAG 58.866 52.381 0.00 0.00 38.76 2.90
1489 6982 4.877282 ACTAATATCTTCTCTTGCCGAGC 58.123 43.478 0.00 0.00 39.70 5.03
1528 7028 1.344114 GGTGGTGGTTGTACCGAAGTA 59.656 52.381 0.00 0.00 42.58 2.24
1529 7029 0.107268 GGTGGTGGTTGTACCGAAGT 59.893 55.000 0.00 0.00 42.58 3.01
1530 7030 0.107081 TGGTGGTGGTTGTACCGAAG 59.893 55.000 0.00 0.00 42.58 3.79
1531 7031 0.179051 GTGGTGGTGGTTGTACCGAA 60.179 55.000 0.00 0.00 42.58 4.30
1532 7032 1.446791 GTGGTGGTGGTTGTACCGA 59.553 57.895 0.00 0.00 42.58 4.69
1533 7033 1.598685 GGTGGTGGTGGTTGTACCG 60.599 63.158 0.00 0.00 42.58 4.02
1534 7034 0.820482 GTGGTGGTGGTGGTTGTACC 60.820 60.000 0.00 0.00 41.24 3.34
1535 7035 0.820482 GGTGGTGGTGGTGGTTGTAC 60.820 60.000 0.00 0.00 0.00 2.90
1536 7036 1.279749 TGGTGGTGGTGGTGGTTGTA 61.280 55.000 0.00 0.00 0.00 2.41
1537 7037 2.277404 GGTGGTGGTGGTGGTTGT 59.723 61.111 0.00 0.00 0.00 3.32
1538 7038 2.124693 GTGGTGGTGGTGGTGGTTG 61.125 63.158 0.00 0.00 0.00 3.77
1539 7039 2.277404 GTGGTGGTGGTGGTGGTT 59.723 61.111 0.00 0.00 0.00 3.67
1540 7040 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
1541 7041 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.00 0.00 4.61
1542 7042 2.518349 GTGGTGGTGGTGGTGGTG 60.518 66.667 0.00 0.00 0.00 4.17
1543 7043 3.816090 GGTGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
1544 7044 4.596585 GGGTGGTGGTGGTGGTGG 62.597 72.222 0.00 0.00 0.00 4.61
1545 7045 3.814906 TGGGTGGTGGTGGTGGTG 61.815 66.667 0.00 0.00 0.00 4.17
1546 7046 3.816090 GTGGGTGGTGGTGGTGGT 61.816 66.667 0.00 0.00 0.00 4.16
1547 7047 4.596585 GGTGGGTGGTGGTGGTGG 62.597 72.222 0.00 0.00 0.00 4.61
1548 7048 4.596585 GGGTGGGTGGTGGTGGTG 62.597 72.222 0.00 0.00 0.00 4.17
1686 7196 0.392461 ATTGCACTACCGAACCGCAT 60.392 50.000 0.00 0.00 31.67 4.73
2021 7534 2.352421 CGTACCAGGACAGAACGTTGAT 60.352 50.000 5.00 0.00 0.00 2.57
2177 7704 8.725256 TCTCCTCTCTAATTTAGCTAAGTAGGA 58.275 37.037 18.88 16.40 35.61 2.94
2242 7769 4.496360 TGTGGCATGCATACAAATTTGAG 58.504 39.130 24.64 13.95 0.00 3.02
2298 7825 1.745087 ACATTCCACAACATCATCGCC 59.255 47.619 0.00 0.00 0.00 5.54
2453 7980 2.168521 ACCACTGTACGATTCATCCTGG 59.831 50.000 0.00 0.00 0.00 4.45


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

AutoCloner maintained by Alex Coulton.