Multiple sequence alignment - TraesCS4D01G041600

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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 TraesCS4D01G041600 chr4D 100.000 2219 0 0 913 3131 19461923 19459705 0.000000e+00 4098.0
1 TraesCS4D01G041600 chr4D 100.000 168 0 0 1 168 19462835 19462668 8.430000e-81 311.0
2 TraesCS4D01G041600 chr4D 98.333 60 1 0 1581 1640 19461225 19461166 4.270000e-19 106.0
3 TraesCS4D01G041600 chr4D 98.333 60 1 0 1611 1670 19461255 19461196 4.270000e-19 106.0
4 TraesCS4D01G041600 chr4A 95.316 982 37 1 1611 2583 581456054 581457035 0.000000e+00 1550.0
5 TraesCS4D01G041600 chr4A 94.239 677 15 3 963 1639 581455460 581456112 0.000000e+00 1013.0
6 TraesCS4D01G041600 chr4A 95.297 489 19 2 2644 3131 581457405 581457890 0.000000e+00 773.0
7 TraesCS4D01G041600 chr4A 86.466 133 6 6 1 127 581454884 581455010 5.450000e-28 135.0
8 TraesCS4D01G041600 chr4A 93.617 47 3 0 2572 2618 581457359 581457405 1.560000e-08 71.3
9 TraesCS4D01G041600 chr4A 100.000 36 0 0 913 948 581455434 581455469 2.020000e-07 67.6
10 TraesCS4D01G041600 chr4B 92.176 933 55 6 1641 2558 31972346 31971417 0.000000e+00 1303.0
11 TraesCS4D01G041600 chr4B 95.757 707 21 4 913 1610 31973023 31972317 0.000000e+00 1131.0
12 TraesCS4D01G041600 chr4B 92.280 557 17 8 2581 3131 31970552 31970016 0.000000e+00 767.0
13 TraesCS4D01G041600 chr4B 91.235 251 13 1 2342 2583 31971139 31970889 1.800000e-87 333.0
14 TraesCS4D01G041600 chr4B 92.126 127 7 3 1 125 31973425 31973300 3.210000e-40 176.0
15 TraesCS4D01G041600 chr4B 100.000 30 0 0 1611 1640 31972346 31972317 4.360000e-04 56.5


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 TraesCS4D01G041600 chr4D 19459705 19462835 3130 True 1155.25 4098 99.166500 1 3131 4 chr4D.!!$R1 3130
1 TraesCS4D01G041600 chr4A 581454884 581457890 3006 False 601.65 1550 94.155833 1 3131 6 chr4A.!!$F1 3130
2 TraesCS4D01G041600 chr4B 31970016 31973425 3409 True 627.75 1303 93.929000 1 3131 6 chr4B.!!$R1 3130

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
56 69 1.344291 CCCCCAACCCAATCAATCCAT 60.344 52.381 0.0 0.0 0.0 3.41 F
1439 1464 0.250901 ATTTTGACGAGGGTGCTGCT 60.251 50.000 0.0 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1781 1806 1.064060 GCATTGCCACCGTTGACTATC 59.936 52.381 0.0 0.0 0.00 2.08 R
2290 2323 2.285827 TTGCCCCGCAAAATAAATCG 57.714 45.000 0.0 0.0 45.96 3.34 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
56 69 1.344291 CCCCCAACCCAATCAATCCAT 60.344 52.381 0.00 0.00 0.00 3.41
161 174 2.443016 CCCAGAGAGAGGTCGGGG 60.443 72.222 0.00 0.00 44.35 5.73
162 175 3.151022 CCAGAGAGAGGTCGGGGC 61.151 72.222 0.00 0.00 0.00 5.80
163 176 2.043450 CAGAGAGAGGTCGGGGCT 60.043 66.667 0.00 0.00 0.00 5.19
164 177 2.124693 CAGAGAGAGGTCGGGGCTC 61.125 68.421 0.00 0.00 0.00 4.70
166 179 3.700831 GAGAGAGGTCGGGGCTCGA 62.701 68.421 4.77 4.77 46.77 4.04
1439 1464 0.250901 ATTTTGACGAGGGTGCTGCT 60.251 50.000 0.00 0.00 0.00 4.24
1466 1491 2.877691 GACGGCAACCTTGATGGC 59.122 61.111 0.00 0.00 40.22 4.40
1489 1514 3.508840 CTTGGACGGGATTGCGCC 61.509 66.667 4.18 0.00 0.00 6.53
1559 1584 0.466372 TTGTTGCCGGTGACAATGGA 60.466 50.000 17.25 0.34 31.30 3.41
1623 1648 2.695147 GGAGGTAATCCCCAAAATGCTG 59.305 50.000 0.00 0.00 43.01 4.41
1639 1664 3.500448 TGCTGTGAACAATGGAGGTAA 57.500 42.857 0.00 0.00 0.00 2.85
1640 1665 4.032960 TGCTGTGAACAATGGAGGTAAT 57.967 40.909 0.00 0.00 0.00 1.89
1641 1666 4.009675 TGCTGTGAACAATGGAGGTAATC 58.990 43.478 0.00 0.00 0.00 1.75
1655 1680 4.737054 GAGGTAATCCACAAAATGCTGTG 58.263 43.478 0.00 0.00 45.24 3.66
1664 1689 4.669206 ACAAAATGCTGTGAACAATGGA 57.331 36.364 0.00 0.00 0.00 3.41
1665 1690 4.624015 ACAAAATGCTGTGAACAATGGAG 58.376 39.130 0.00 0.00 0.00 3.86
1666 1691 3.947910 AAATGCTGTGAACAATGGAGG 57.052 42.857 0.00 0.00 0.00 4.30
1667 1692 2.592102 ATGCTGTGAACAATGGAGGT 57.408 45.000 0.00 0.00 0.00 3.85
1730 1755 3.506108 GAGCATCGCATGGCAAGT 58.494 55.556 0.00 0.00 0.00 3.16
1942 1967 0.465705 ATCCGATGACGTGCTTCCAT 59.534 50.000 0.00 0.00 37.88 3.41
2004 2029 4.014847 TGCTATGTTTTTGTAGCGCATC 57.985 40.909 11.47 1.90 44.81 3.91
2227 2252 3.115390 AGCTTCAGCCCTCCACTATTAA 58.885 45.455 0.00 0.00 43.38 1.40
2243 2268 9.787435 TCCACTATTAAATGTTGTTCTAACTGT 57.213 29.630 0.00 0.00 0.00 3.55
2262 2295 2.307392 TGTGCAAATAGCCTAGGGTTCA 59.693 45.455 20.59 1.57 44.83 3.18
2290 2323 6.259608 CACTGTGGGTCAGATTAAATCTCATC 59.740 42.308 0.00 0.00 46.27 2.92
2294 2327 6.708054 GTGGGTCAGATTAAATCTCATCGATT 59.292 38.462 0.00 0.00 44.10 3.34
2410 2944 9.520515 ACCTACAAACTGTGAAAGATGAATATT 57.479 29.630 0.00 0.00 0.00 1.28
2422 2956 7.840716 TGAAAGATGAATATTCTGTTTCCCCAT 59.159 33.333 21.85 7.39 0.00 4.00
2521 3055 3.083848 TTGTCACGAGGTGCCACGT 62.084 57.895 7.83 7.83 43.34 4.49
2618 3526 4.808558 TGTTTGCTTATGTTGCCATCTTC 58.191 39.130 0.00 0.00 32.29 2.87
2619 3527 4.523943 TGTTTGCTTATGTTGCCATCTTCT 59.476 37.500 0.00 0.00 32.29 2.85
2620 3528 4.970662 TTGCTTATGTTGCCATCTTCTC 57.029 40.909 0.00 0.00 32.29 2.87
2621 3529 3.954200 TGCTTATGTTGCCATCTTCTCA 58.046 40.909 0.00 0.00 32.29 3.27
2622 3530 4.529897 TGCTTATGTTGCCATCTTCTCAT 58.470 39.130 0.00 0.00 32.29 2.90
2623 3531 5.683681 TGCTTATGTTGCCATCTTCTCATA 58.316 37.500 0.00 0.00 32.29 2.15
2624 3532 6.121590 TGCTTATGTTGCCATCTTCTCATAA 58.878 36.000 0.00 0.00 32.29 1.90
2625 3533 6.038603 TGCTTATGTTGCCATCTTCTCATAAC 59.961 38.462 0.00 0.00 32.29 1.89
2626 3534 6.603237 TTATGTTGCCATCTTCTCATAACG 57.397 37.500 0.00 0.00 32.29 3.18
2627 3535 4.200838 TGTTGCCATCTTCTCATAACGA 57.799 40.909 0.00 0.00 0.00 3.85
2628 3536 4.183865 TGTTGCCATCTTCTCATAACGAG 58.816 43.478 0.00 0.00 43.80 4.18
2629 3537 2.826428 TGCCATCTTCTCATAACGAGC 58.174 47.619 0.00 0.00 41.98 5.03
2630 3538 2.432146 TGCCATCTTCTCATAACGAGCT 59.568 45.455 0.00 0.00 41.98 4.09
2631 3539 3.118629 TGCCATCTTCTCATAACGAGCTT 60.119 43.478 0.00 0.00 41.98 3.74
2632 3540 4.099419 TGCCATCTTCTCATAACGAGCTTA 59.901 41.667 0.00 0.00 41.98 3.09
2633 3541 5.221521 TGCCATCTTCTCATAACGAGCTTAT 60.222 40.000 0.00 0.00 41.98 1.73
2634 3542 5.698545 GCCATCTTCTCATAACGAGCTTATT 59.301 40.000 0.00 0.00 41.98 1.40
2635 3543 6.203723 GCCATCTTCTCATAACGAGCTTATTT 59.796 38.462 0.00 0.00 41.98 1.40
2636 3544 7.385205 GCCATCTTCTCATAACGAGCTTATTTA 59.615 37.037 0.00 0.00 41.98 1.40
2637 3545 9.429359 CCATCTTCTCATAACGAGCTTATTTAT 57.571 33.333 0.00 0.00 41.98 1.40
2692 3600 0.543277 TCTCTATGCCCTGGTGCTTG 59.457 55.000 8.32 0.63 0.00 4.01
2700 3608 1.142870 GCCCTGGTGCTTGGTGATATA 59.857 52.381 0.00 0.00 0.00 0.86
2745 3653 6.096282 GCATACCTGATAGGGTTCTAGATCTC 59.904 46.154 0.00 0.00 40.58 2.75
2801 3709 6.647334 TTGCTCAACAAAATATCTGGTCAA 57.353 33.333 0.00 0.00 34.56 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
136 149 1.827789 CTCTCTCTGGGAGGCGAGG 60.828 68.421 4.41 0.00 42.10 4.63
1466 1491 1.676006 GCAATCCCGTCCAAGGTAATG 59.324 52.381 0.00 0.00 0.00 1.90
1489 1514 2.362369 ATGGTCTCAGCCTGGTCCG 61.362 63.158 0.00 0.00 0.00 4.79
1639 1664 4.669206 TTGTTCACAGCATTTTGTGGAT 57.331 36.364 6.33 0.00 46.55 3.41
1640 1665 4.370049 CATTGTTCACAGCATTTTGTGGA 58.630 39.130 6.33 0.00 46.55 4.02
1641 1666 3.495377 CCATTGTTCACAGCATTTTGTGG 59.505 43.478 6.33 0.00 46.55 4.17
1643 1668 4.501915 CCTCCATTGTTCACAGCATTTTGT 60.502 41.667 0.00 0.00 0.00 2.83
1644 1669 3.991773 CCTCCATTGTTCACAGCATTTTG 59.008 43.478 0.00 0.00 0.00 2.44
1645 1670 3.642848 ACCTCCATTGTTCACAGCATTTT 59.357 39.130 0.00 0.00 0.00 1.82
1646 1671 3.233507 ACCTCCATTGTTCACAGCATTT 58.766 40.909 0.00 0.00 0.00 2.32
1647 1672 2.880443 ACCTCCATTGTTCACAGCATT 58.120 42.857 0.00 0.00 0.00 3.56
1648 1673 2.592102 ACCTCCATTGTTCACAGCAT 57.408 45.000 0.00 0.00 0.00 3.79
1649 1674 3.146066 GTTACCTCCATTGTTCACAGCA 58.854 45.455 0.00 0.00 0.00 4.41
1650 1675 3.146066 TGTTACCTCCATTGTTCACAGC 58.854 45.455 0.00 0.00 0.00 4.40
1651 1676 4.389374 ACTGTTACCTCCATTGTTCACAG 58.611 43.478 0.00 0.00 34.43 3.66
1652 1677 4.141597 TGACTGTTACCTCCATTGTTCACA 60.142 41.667 0.00 0.00 0.00 3.58
1653 1678 4.385825 TGACTGTTACCTCCATTGTTCAC 58.614 43.478 0.00 0.00 0.00 3.18
1654 1679 4.346709 TCTGACTGTTACCTCCATTGTTCA 59.653 41.667 0.00 0.00 0.00 3.18
1655 1680 4.894784 TCTGACTGTTACCTCCATTGTTC 58.105 43.478 0.00 0.00 0.00 3.18
1656 1681 4.974645 TCTGACTGTTACCTCCATTGTT 57.025 40.909 0.00 0.00 0.00 2.83
1657 1682 4.642429 GTTCTGACTGTTACCTCCATTGT 58.358 43.478 0.00 0.00 0.00 2.71
1658 1683 3.679980 CGTTCTGACTGTTACCTCCATTG 59.320 47.826 0.00 0.00 0.00 2.82
1659 1684 3.306780 CCGTTCTGACTGTTACCTCCATT 60.307 47.826 0.00 0.00 0.00 3.16
1660 1685 2.233922 CCGTTCTGACTGTTACCTCCAT 59.766 50.000 0.00 0.00 0.00 3.41
1661 1686 1.616865 CCGTTCTGACTGTTACCTCCA 59.383 52.381 0.00 0.00 0.00 3.86
1662 1687 1.617357 ACCGTTCTGACTGTTACCTCC 59.383 52.381 0.00 0.00 0.00 4.30
1663 1688 4.022503 AGTTACCGTTCTGACTGTTACCTC 60.023 45.833 0.00 0.00 0.00 3.85
1664 1689 3.893813 AGTTACCGTTCTGACTGTTACCT 59.106 43.478 0.00 0.00 0.00 3.08
1665 1690 3.985925 CAGTTACCGTTCTGACTGTTACC 59.014 47.826 0.00 0.00 35.84 2.85
1666 1691 3.427863 GCAGTTACCGTTCTGACTGTTAC 59.572 47.826 4.52 0.00 41.11 2.50
1667 1692 3.068448 TGCAGTTACCGTTCTGACTGTTA 59.932 43.478 4.52 0.00 41.11 2.41
1730 1755 1.093972 CAAATACATCCAGCACGGCA 58.906 50.000 0.00 0.00 33.14 5.69
1781 1806 1.064060 GCATTGCCACCGTTGACTATC 59.936 52.381 0.00 0.00 0.00 2.08
1942 1967 1.765904 TCTATACATGGCGGCAAAGGA 59.234 47.619 18.31 9.24 0.00 3.36
2146 2171 0.460987 ATAGTGGCAGAAGCACGCTC 60.461 55.000 0.00 0.00 44.61 5.03
2227 2252 6.863126 GCTATTTGCACAGTTAGAACAACATT 59.137 34.615 0.00 0.00 42.31 2.71
2243 2268 3.352648 GTTGAACCCTAGGCTATTTGCA 58.647 45.455 2.05 0.00 45.15 4.08
2262 2295 4.447138 TTTAATCTGACCCACAGTGGTT 57.553 40.909 18.82 3.52 45.86 3.67
2290 2323 2.285827 TTGCCCCGCAAAATAAATCG 57.714 45.000 0.00 0.00 45.96 3.34
2422 2956 4.837860 AGCAACCAGAATAAAATTGGTCCA 59.162 37.500 0.00 0.00 44.15 4.02
2640 3548 9.899226 GCTCTCACTGAAAAATACAATTTACTT 57.101 29.630 0.00 0.00 0.00 2.24
2641 3549 9.066892 TGCTCTCACTGAAAAATACAATTTACT 57.933 29.630 0.00 0.00 0.00 2.24
2642 3550 9.846248 ATGCTCTCACTGAAAAATACAATTTAC 57.154 29.630 0.00 0.00 0.00 2.01
2692 3600 4.085357 TCACCACCAGCATTATATCACC 57.915 45.455 0.00 0.00 0.00 4.02
2700 3608 2.719739 CAGAGAATCACCACCAGCATT 58.280 47.619 0.00 0.00 37.82 3.56
2745 3653 3.615496 GCAGCAATGCAACTAATTCAAGG 59.385 43.478 8.35 0.00 34.41 3.61
2824 3732 7.135591 TGGGATTCACAGACATCAATATACA 57.864 36.000 0.00 0.00 0.00 2.29
2825 3733 8.627208 AATGGGATTCACAGACATCAATATAC 57.373 34.615 0.00 0.00 0.00 1.47
2827 3735 9.293404 CTTAATGGGATTCACAGACATCAATAT 57.707 33.333 0.00 0.00 0.00 1.28
2828 3736 8.493607 TCTTAATGGGATTCACAGACATCAATA 58.506 33.333 0.00 0.00 0.00 1.90
3041 3955 6.499106 TCCTCTATATGCAAATGAGGACAA 57.501 37.500 20.06 5.91 45.61 3.18


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

AutoCloner maintained by Alex Coulton.