Multiple sequence alignment - TraesCS4D01G165000

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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 TraesCS4D01G165000 chr4D 100.000 2399 0 0 1 2399 270688059 270690457 0.000000e+00 4431.0
1 TraesCS4D01G165000 chr7D 98.074 1506 19 4 1 1500 274862411 274860910 0.000000e+00 2612.0
2 TraesCS4D01G165000 chr7D 91.753 97 7 1 1925 2021 80504224 80504129 1.500000e-27 134.0
3 TraesCS4D01G165000 chr7D 90.099 101 10 0 1927 2027 581296260 581296360 5.380000e-27 132.0
4 TraesCS4D01G165000 chr6D 97.400 1500 35 4 1 1498 153176520 153175023 0.000000e+00 2551.0
5 TraesCS4D01G165000 chr6D 98.300 1412 20 2 1 1408 69504182 69502771 0.000000e+00 2471.0
6 TraesCS4D01G165000 chr6D 92.929 99 5 2 1931 2028 91845415 91845512 2.490000e-30 143.0
7 TraesCS4D01G165000 chr6D 93.548 93 5 1 1930 2021 461690114 461690206 1.160000e-28 137.0
8 TraesCS4D01G165000 chr1D 96.966 1483 39 3 1 1477 480940198 480938716 0.000000e+00 2484.0
9 TraesCS4D01G165000 chr1D 85.942 1508 190 20 1 1497 452581295 452579799 0.000000e+00 1591.0
10 TraesCS4D01G165000 chr1D 96.667 90 3 0 1935 2024 205088311 205088222 1.490000e-32 150.0
11 TraesCS4D01G165000 chr1D 95.402 87 4 0 1936 2022 253197536 253197622 3.220000e-29 139.0
12 TraesCS4D01G165000 chr4A 93.559 1506 90 5 1 1502 521299090 521300592 0.000000e+00 2237.0
13 TraesCS4D01G165000 chr4A 90.727 1499 134 3 1 1496 429502171 429503667 0.000000e+00 1993.0
14 TraesCS4D01G165000 chr4A 93.103 290 17 2 2041 2330 278325716 278325430 2.850000e-114 422.0
15 TraesCS4D01G165000 chr4A 93.889 180 10 1 1751 1929 278326065 278325886 1.090000e-68 270.0
16 TraesCS4D01G165000 chr2D 86.770 1489 183 10 20 1498 10068180 10069664 0.000000e+00 1646.0
17 TraesCS4D01G165000 chr1A 86.212 1494 192 13 12 1497 544569056 544570543 0.000000e+00 1605.0
18 TraesCS4D01G165000 chr4B 93.750 384 18 3 2019 2399 237900838 237900458 2.680000e-159 571.0
19 TraesCS4D01G165000 chr4B 92.000 400 16 4 1602 2001 237901372 237900989 4.510000e-152 547.0
20 TraesCS4D01G165000 chr4B 96.739 92 3 0 1498 1589 237901448 237901357 1.150000e-33 154.0
21 TraesCS4D01G165000 chr3A 93.548 93 5 1 1928 2020 574287982 574288073 1.160000e-28 137.0
22 TraesCS4D01G165000 chr3A 92.553 94 6 1 1935 2027 465214564 465214471 1.500000e-27 134.0
23 TraesCS4D01G165000 chr7B 89.524 105 8 3 1928 2030 482820035 482820138 1.940000e-26 130.0
24 TraesCS4D01G165000 chr5A 93.182 44 3 0 2354 2397 294260181 294260224 5.540000e-07 65.8


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 TraesCS4D01G165000 chr4D 270688059 270690457 2398 False 4431 4431 100.000 1 2399 1 chr4D.!!$F1 2398
1 TraesCS4D01G165000 chr7D 274860910 274862411 1501 True 2612 2612 98.074 1 1500 1 chr7D.!!$R2 1499
2 TraesCS4D01G165000 chr6D 153175023 153176520 1497 True 2551 2551 97.400 1 1498 1 chr6D.!!$R2 1497
3 TraesCS4D01G165000 chr6D 69502771 69504182 1411 True 2471 2471 98.300 1 1408 1 chr6D.!!$R1 1407
4 TraesCS4D01G165000 chr1D 480938716 480940198 1482 True 2484 2484 96.966 1 1477 1 chr1D.!!$R3 1476
5 TraesCS4D01G165000 chr1D 452579799 452581295 1496 True 1591 1591 85.942 1 1497 1 chr1D.!!$R2 1496
6 TraesCS4D01G165000 chr4A 521299090 521300592 1502 False 2237 2237 93.559 1 1502 1 chr4A.!!$F2 1501
7 TraesCS4D01G165000 chr4A 429502171 429503667 1496 False 1993 1993 90.727 1 1496 1 chr4A.!!$F1 1495
8 TraesCS4D01G165000 chr4A 278325430 278326065 635 True 346 422 93.496 1751 2330 2 chr4A.!!$R1 579
9 TraesCS4D01G165000 chr2D 10068180 10069664 1484 False 1646 1646 86.770 20 1498 1 chr2D.!!$F1 1478
10 TraesCS4D01G165000 chr1A 544569056 544570543 1487 False 1605 1605 86.212 12 1497 1 chr1A.!!$F1 1485
11 TraesCS4D01G165000 chr4B 237900458 237901448 990 True 424 571 94.163 1498 2399 3 chr4B.!!$R1 901

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
357 359 0.872388 GTCTGGTCGCGTGGAAAAAT 59.128 50.000 5.77 0.0 0.00 1.82 F
530 532 2.703536 CAACAAAAACCCCTAGGCCTTT 59.296 45.455 12.58 0.0 36.11 3.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1244 1254 0.666577 GTCCTCGTTCCTGAACACGG 60.667 60.0 10.38 8.95 41.2 4.94 R
1734 1750 2.543777 AGGCACATCAACACGTTAGT 57.456 45.0 0.00 0.00 0.0 2.24 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
357 359 0.872388 GTCTGGTCGCGTGGAAAAAT 59.128 50.000 5.77 0.0 0.00 1.82
530 532 2.703536 CAACAAAAACCCCTAGGCCTTT 59.296 45.455 12.58 0.0 36.11 3.11
1011 1019 3.552684 CGAAGGCCAACATGTTTCACAAT 60.553 43.478 8.77 0.0 0.00 2.71
1244 1254 2.026822 TCTGGGACTCAAGAAATGCTCC 60.027 50.000 0.00 0.0 0.00 4.70
1350 1364 2.978156 AAAATGAGGACAGGGCTTCA 57.022 45.000 0.00 0.0 0.00 3.02
1379 1393 5.635120 ACAGTGGCTAAATTTTCTCTCCTT 58.365 37.500 0.00 0.0 0.00 3.36
1441 1457 3.399644 TGTATTCCCCTGAACCCTTTGAA 59.600 43.478 0.00 0.0 32.13 2.69
1490 1506 1.964373 CCCCCGTTGACCGTTCAAG 60.964 63.158 0.00 0.0 42.60 3.02
1566 1582 7.857569 TGTAAATACTGACAAAACACTACAGC 58.142 34.615 0.00 0.0 32.67 4.40
1573 1589 5.507077 TGACAAAACACTACAGCGATTTTC 58.493 37.500 0.00 0.0 0.00 2.29
1574 1590 4.855531 ACAAAACACTACAGCGATTTTCC 58.144 39.130 0.00 0.0 0.00 3.13
1575 1591 4.578928 ACAAAACACTACAGCGATTTTCCT 59.421 37.500 0.00 0.0 0.00 3.36
1576 1592 5.067283 ACAAAACACTACAGCGATTTTCCTT 59.933 36.000 0.00 0.0 0.00 3.36
1577 1593 4.749245 AACACTACAGCGATTTTCCTTG 57.251 40.909 0.00 0.0 0.00 3.61
1578 1594 3.740115 ACACTACAGCGATTTTCCTTGT 58.260 40.909 0.00 0.0 0.00 3.16
1579 1595 4.890088 ACACTACAGCGATTTTCCTTGTA 58.110 39.130 0.00 0.0 0.00 2.41
1580 1596 5.488341 ACACTACAGCGATTTTCCTTGTAT 58.512 37.500 0.00 0.0 0.00 2.29
1581 1597 6.636705 ACACTACAGCGATTTTCCTTGTATA 58.363 36.000 0.00 0.0 0.00 1.47
1582 1598 7.101054 ACACTACAGCGATTTTCCTTGTATAA 58.899 34.615 0.00 0.0 0.00 0.98
1583 1599 7.277981 ACACTACAGCGATTTTCCTTGTATAAG 59.722 37.037 0.00 0.0 0.00 1.73
1584 1600 7.491372 CACTACAGCGATTTTCCTTGTATAAGA 59.509 37.037 0.00 0.0 35.92 2.10
1585 1601 8.204836 ACTACAGCGATTTTCCTTGTATAAGAT 58.795 33.333 0.00 0.0 35.92 2.40
1586 1602 7.865706 ACAGCGATTTTCCTTGTATAAGATT 57.134 32.000 0.00 0.0 35.92 2.40
1587 1603 8.281212 ACAGCGATTTTCCTTGTATAAGATTT 57.719 30.769 0.00 0.0 35.92 2.17
1588 1604 8.739972 ACAGCGATTTTCCTTGTATAAGATTTT 58.260 29.630 0.00 0.0 35.92 1.82
1589 1605 9.573133 CAGCGATTTTCCTTGTATAAGATTTTT 57.427 29.630 0.00 0.0 35.92 1.94
1631 1647 9.106070 GTATAAGAATTTGTACCCTTGTACTGG 57.894 37.037 4.68 0.0 46.19 4.00
1682 1698 0.246635 CCTCGGTGGAGTACTGGTTG 59.753 60.000 0.00 0.0 38.70 3.77
1746 1762 6.680874 AATGGTTACAAACTAACGTGTTGA 57.319 33.333 8.11 0.0 0.00 3.18
1913 1930 7.051623 ACACTCTTTTGGTTATGTGTCAGTAA 58.948 34.615 0.00 0.0 34.10 2.24
1927 1944 7.485418 TGTGTCAGTAACGACAATGTTTAAT 57.515 32.000 0.00 0.0 46.99 1.40
1928 1945 8.590719 TGTGTCAGTAACGACAATGTTTAATA 57.409 30.769 0.00 0.0 46.99 0.98
1929 1946 9.043079 TGTGTCAGTAACGACAATGTTTAATAA 57.957 29.630 0.00 0.0 46.99 1.40
2076 2247 3.454375 ACAAGTGGTCTTACGTCAACAG 58.546 45.455 0.00 0.0 32.07 3.16
2266 2437 9.651718 GTCACTAAAGAAATAAGAACAACACAG 57.348 33.333 0.00 0.0 0.00 3.66
2346 2517 8.839343 CAAATGGAGGCTGAATTTAAAAACTTT 58.161 29.630 0.00 0.0 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
357 359 2.622942 CAGTTCTTTAGGCCTGCAAACA 59.377 45.455 17.99 0.00 0.00 2.83
1011 1019 1.065491 ACTGCGGATTGAGCCACATTA 60.065 47.619 0.00 0.00 0.00 1.90
1120 1128 2.234661 TGAGAGATGTCGGAGCAAACAT 59.765 45.455 0.00 0.00 38.78 2.71
1124 1132 1.203287 CAGTGAGAGATGTCGGAGCAA 59.797 52.381 0.00 0.00 0.00 3.91
1244 1254 0.666577 GTCCTCGTTCCTGAACACGG 60.667 60.000 10.38 8.95 41.20 4.94
1350 1364 5.810095 AGAAAATTTAGCCACTGTCTAGCT 58.190 37.500 0.00 0.00 40.66 3.32
1379 1393 3.009473 AGTTCAGCTAGAGGGAATTGCAA 59.991 43.478 0.00 0.00 0.00 4.08
1441 1457 6.524192 GCTTCCCCACCTGAATATATTACCAT 60.524 42.308 0.00 0.00 0.00 3.55
1540 1556 8.504005 GCTGTAGTGTTTTGTCAGTATTTACAT 58.496 33.333 0.00 0.00 0.00 2.29
1592 1608 9.362151 ACAAATTCTTATACAAGGTTCCTTCAA 57.638 29.630 0.60 0.00 32.22 2.69
1593 1609 8.934023 ACAAATTCTTATACAAGGTTCCTTCA 57.066 30.769 0.60 0.00 32.22 3.02
1595 1611 9.239551 GGTACAAATTCTTATACAAGGTTCCTT 57.760 33.333 0.00 0.00 32.22 3.36
1596 1612 7.832685 GGGTACAAATTCTTATACAAGGTTCCT 59.167 37.037 0.00 0.00 32.22 3.36
1597 1613 7.832685 AGGGTACAAATTCTTATACAAGGTTCC 59.167 37.037 0.00 0.00 32.22 3.62
1598 1614 8.803397 AGGGTACAAATTCTTATACAAGGTTC 57.197 34.615 0.00 0.00 32.22 3.62
1599 1615 9.020731 CAAGGGTACAAATTCTTATACAAGGTT 57.979 33.333 0.00 0.00 32.22 3.50
1600 1616 8.168058 ACAAGGGTACAAATTCTTATACAAGGT 58.832 33.333 0.00 0.00 32.22 3.50
1631 1647 6.695292 ATCTGAAATTTGTGCAAACGAATC 57.305 33.333 0.00 0.00 32.51 2.52
1729 1745 4.024725 GGCACATCAACACGTTAGTTTGTA 60.025 41.667 0.00 0.00 0.00 2.41
1730 1746 3.242936 GGCACATCAACACGTTAGTTTGT 60.243 43.478 0.00 0.00 0.00 2.83
1731 1747 3.003275 AGGCACATCAACACGTTAGTTTG 59.997 43.478 0.00 0.00 0.00 2.93
1732 1748 3.211045 AGGCACATCAACACGTTAGTTT 58.789 40.909 0.00 0.00 0.00 2.66
1733 1749 2.846193 AGGCACATCAACACGTTAGTT 58.154 42.857 0.00 0.00 0.00 2.24
1734 1750 2.543777 AGGCACATCAACACGTTAGT 57.456 45.000 0.00 0.00 0.00 2.24
1735 1751 3.554524 CAAAGGCACATCAACACGTTAG 58.445 45.455 0.00 0.00 0.00 2.34
1746 1762 6.431722 ACATAAGTATAACCCAAAGGCACAT 58.568 36.000 0.00 0.00 36.11 3.21
1782 1798 7.587629 ACATCGATGGCATTGTATATTCAAAG 58.412 34.615 28.09 0.00 0.00 2.77
2004 2146 7.117956 GTGAAAGATTGTACTCCCTCTGTAAAC 59.882 40.741 0.00 0.00 0.00 2.01
2010 2173 6.497259 TGTTAGTGAAAGATTGTACTCCCTCT 59.503 38.462 0.00 0.00 0.00 3.69
2076 2247 4.666253 TCTGCCTGGTGCCCTTGC 62.666 66.667 0.00 0.00 40.16 4.01
2087 2258 2.903135 GCTACCATATTCTCCTCTGCCT 59.097 50.000 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.