Multiple sequence alignment - TraesCS4D01G310400

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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 TraesCS4D01G310400 chr4D 100.000 2426 0 0 1 2426 477544516 477542091 0.000000e+00 4481.0
1 TraesCS4D01G310400 chr4D 92.764 843 46 9 667 1496 477558693 477559533 0.000000e+00 1205.0
2 TraesCS4D01G310400 chr4D 86.169 723 83 13 1716 2426 152896704 152895987 0.000000e+00 765.0
3 TraesCS4D01G310400 chr4D 86.536 661 70 7 1780 2426 506961154 506960499 0.000000e+00 710.0
4 TraesCS4D01G310400 chr4D 81.618 136 16 7 101 232 65102539 65102669 1.190000e-18 104.0
5 TraesCS4D01G310400 chr4D 100.000 31 0 0 1517 1547 477559534 477559564 9.370000e-05 58.4
6 TraesCS4D01G310400 chr4B 91.149 1062 60 16 670 1718 602893891 602892851 0.000000e+00 1410.0
7 TraesCS4D01G310400 chr4B 90.047 1065 71 18 670 1718 602873973 602872928 0.000000e+00 1347.0
8 TraesCS4D01G310400 chr4B 92.240 915 60 10 668 1575 603037716 603038626 0.000000e+00 1286.0
9 TraesCS4D01G310400 chr4B 89.300 1000 70 10 480 1471 603145475 603144505 0.000000e+00 1219.0
10 TraesCS4D01G310400 chr4B 87.788 1040 77 20 667 1686 603148128 603149137 0.000000e+00 1171.0
11 TraesCS4D01G310400 chr4B 94.127 613 34 2 861 1471 603026251 603025639 0.000000e+00 931.0
12 TraesCS4D01G310400 chr4B 92.530 415 28 3 1 415 603146697 603146286 2.080000e-165 592.0
13 TraesCS4D01G310400 chr4B 89.419 482 30 6 1 478 603029610 603029146 2.690000e-164 588.0
14 TraesCS4D01G310400 chr4B 92.288 389 25 2 478 865 603029091 603028707 4.560000e-152 547.0
15 TraesCS4D01G310400 chr4B 85.306 245 22 6 2 235 602890069 602890310 8.670000e-60 241.0
16 TraesCS4D01G310400 chr4B 87.248 149 19 0 244 392 602890561 602890709 1.150000e-38 171.0
17 TraesCS4D01G310400 chr4B 78.771 179 32 5 1510 1686 603160597 603160771 5.480000e-22 115.0
18 TraesCS4D01G310400 chr4B 91.071 56 3 2 1517 1571 603024377 603024323 9.300000e-10 75.0
19 TraesCS4D01G310400 chr4A 92.136 852 50 9 657 1496 684470852 684471698 0.000000e+00 1186.0
20 TraesCS4D01G310400 chr4A 84.914 464 38 16 1 460 684451223 684451658 7.960000e-120 440.0
21 TraesCS4D01G310400 chr4A 93.182 176 12 0 671 846 684449820 684449645 2.390000e-65 259.0
22 TraesCS4D01G310400 chr1A 83.173 933 105 31 667 1575 372316400 372315496 0.000000e+00 806.0
23 TraesCS4D01G310400 chr1B 82.110 967 126 31 667 1618 402039895 402038961 0.000000e+00 784.0
24 TraesCS4D01G310400 chr1B 89.385 179 13 3 478 656 610971289 610971461 1.130000e-53 220.0
25 TraesCS4D01G310400 chr1B 87.500 152 15 3 241 389 161207693 161207843 3.210000e-39 172.0
26 TraesCS4D01G310400 chr6D 88.431 631 67 3 1799 2426 411197214 411196587 0.000000e+00 756.0
27 TraesCS4D01G310400 chr6D 86.842 152 17 2 241 389 447441974 447441823 1.490000e-37 167.0
28 TraesCS4D01G310400 chr3B 85.475 716 93 5 1720 2426 790316873 790316160 0.000000e+00 736.0
29 TraesCS4D01G310400 chr3B 83.942 137 16 4 97 228 42470766 42470631 2.530000e-25 126.0
30 TraesCS4D01G310400 chr7B 84.078 716 102 8 1720 2425 637909882 637909169 0.000000e+00 680.0
31 TraesCS4D01G310400 chr7B 89.444 180 12 4 478 656 21199609 21199782 1.130000e-53 220.0
32 TraesCS4D01G310400 chr2B 84.006 719 103 8 1717 2425 296293070 296293786 0.000000e+00 680.0
33 TraesCS4D01G310400 chr2B 86.928 153 16 3 240 389 503985122 503985273 4.150000e-38 169.0
34 TraesCS4D01G310400 chr5A 83.498 709 106 8 1718 2423 522097968 522098668 0.000000e+00 651.0
35 TraesCS4D01G310400 chr5A 83.075 709 109 8 1718 2423 522093787 522094487 3.400000e-178 634.0
36 TraesCS4D01G310400 chr5A 82.934 709 110 8 1718 2423 522089461 522090161 1.580000e-176 628.0
37 TraesCS4D01G310400 chr7D 89.444 180 12 4 478 656 2260406 2260233 1.130000e-53 220.0
38 TraesCS4D01G310400 chr7D 89.444 180 12 4 478 656 162984858 162984685 1.130000e-53 220.0
39 TraesCS4D01G310400 chr5B 89.444 180 12 4 478 656 638783375 638783202 1.130000e-53 220.0
40 TraesCS4D01G310400 chr2A 89.444 180 12 4 478 656 138922555 138922382 1.130000e-53 220.0
41 TraesCS4D01G310400 chr2A 89.444 180 12 4 478 656 149237076 149237249 1.130000e-53 220.0
42 TraesCS4D01G310400 chr5D 86.275 153 17 3 240 389 550659484 550659333 1.930000e-36 163.0
43 TraesCS4D01G310400 chr5D 82.836 134 14 6 103 231 421498100 421497971 7.090000e-21 111.0
44 TraesCS4D01G310400 chr1D 86.275 153 17 3 240 389 452335331 452335180 1.930000e-36 163.0
45 TraesCS4D01G310400 chr1D 86.275 153 17 3 240 389 452352766 452352917 1.930000e-36 163.0
46 TraesCS4D01G310400 chr2D 84.783 138 17 3 101 235 503579334 503579470 4.210000e-28 135.0
47 TraesCS4D01G310400 chr2D 85.294 136 12 5 101 232 308906985 308906854 1.510000e-27 134.0


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 TraesCS4D01G310400 chr4D 477542091 477544516 2425 True 4481.000000 4481 100.00000 1 2426 1 chr4D.!!$R2 2425
1 TraesCS4D01G310400 chr4D 152895987 152896704 717 True 765.000000 765 86.16900 1716 2426 1 chr4D.!!$R1 710
2 TraesCS4D01G310400 chr4D 506960499 506961154 655 True 710.000000 710 86.53600 1780 2426 1 chr4D.!!$R3 646
3 TraesCS4D01G310400 chr4D 477558693 477559564 871 False 631.700000 1205 96.38200 667 1547 2 chr4D.!!$F2 880
4 TraesCS4D01G310400 chr4B 602892851 602893891 1040 True 1410.000000 1410 91.14900 670 1718 1 chr4B.!!$R2 1048
5 TraesCS4D01G310400 chr4B 602872928 602873973 1045 True 1347.000000 1347 90.04700 670 1718 1 chr4B.!!$R1 1048
6 TraesCS4D01G310400 chr4B 603037716 603038626 910 False 1286.000000 1286 92.24000 668 1575 1 chr4B.!!$F1 907
7 TraesCS4D01G310400 chr4B 603148128 603149137 1009 False 1171.000000 1171 87.78800 667 1686 1 chr4B.!!$F2 1019
8 TraesCS4D01G310400 chr4B 603144505 603146697 2192 True 905.500000 1219 90.91500 1 1471 2 chr4B.!!$R4 1470
9 TraesCS4D01G310400 chr4B 603024323 603029610 5287 True 535.250000 931 91.72625 1 1571 4 chr4B.!!$R3 1570
10 TraesCS4D01G310400 chr4B 602890069 602890709 640 False 206.000000 241 86.27700 2 392 2 chr4B.!!$F4 390
11 TraesCS4D01G310400 chr4A 684470852 684471698 846 False 1186.000000 1186 92.13600 657 1496 1 chr4A.!!$F2 839
12 TraesCS4D01G310400 chr1A 372315496 372316400 904 True 806.000000 806 83.17300 667 1575 1 chr1A.!!$R1 908
13 TraesCS4D01G310400 chr1B 402038961 402039895 934 True 784.000000 784 82.11000 667 1618 1 chr1B.!!$R1 951
14 TraesCS4D01G310400 chr6D 411196587 411197214 627 True 756.000000 756 88.43100 1799 2426 1 chr6D.!!$R1 627
15 TraesCS4D01G310400 chr3B 790316160 790316873 713 True 736.000000 736 85.47500 1720 2426 1 chr3B.!!$R2 706
16 TraesCS4D01G310400 chr7B 637909169 637909882 713 True 680.000000 680 84.07800 1720 2425 1 chr7B.!!$R1 705
17 TraesCS4D01G310400 chr2B 296293070 296293786 716 False 680.000000 680 84.00600 1717 2425 1 chr2B.!!$F1 708
18 TraesCS4D01G310400 chr5A 522089461 522098668 9207 False 637.666667 651 83.16900 1718 2423 3 chr5A.!!$F1 705

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
851 1867 2.158769 ACATGGCCACGTATGATCATGT 60.159 45.455 18.72 0.36 40.82 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1907 6680 1.213182 TGATCTCTGGCGAGGAGTAGT 59.787 52.381 0.0 0.0 37.86 2.73 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
44 45 2.685387 CTACCGATCTGCGCTGTCCC 62.685 65.000 9.73 1.25 39.11 4.46
95 96 5.954335 ACTCTGGTTTCTTGAAACAAACTG 58.046 37.500 22.51 12.26 33.76 3.16
339 590 8.971321 GCATGCTATATTTGGAGTTACAATTTG 58.029 33.333 11.37 0.00 0.00 2.32
386 637 9.693739 AAATCATTTGATATGTACTGTGGGTTA 57.306 29.630 0.00 0.00 33.73 2.85
712 1708 4.832823 AGGTTATTGCTTAACTTGTTGCCT 59.167 37.500 9.13 0.00 40.14 4.75
779 1786 4.270325 GCTAAAATCTCGCCGTATCAAACT 59.730 41.667 0.00 0.00 0.00 2.66
851 1867 2.158769 ACATGGCCACGTATGATCATGT 60.159 45.455 18.72 0.36 40.82 3.21
1143 4647 2.808206 GCCGTACCATGGAGGAGGG 61.808 68.421 21.47 17.82 41.22 4.30
1203 4715 2.360350 CTGAGGGTGTGCGCCAAT 60.360 61.111 4.18 0.00 0.00 3.16
1416 4928 2.027625 GTCCGAGTTCACTTGCCCG 61.028 63.158 0.00 0.00 0.00 6.13
1444 4966 2.567049 GGACGCGTACTGCTCACT 59.433 61.111 15.95 0.00 43.27 3.41
1478 6238 4.113354 AGATTTGCTTTCGATCCGTACTC 58.887 43.478 0.00 0.00 0.00 2.59
1575 6338 3.438087 TGTTTTTGGCAAACAACCATGTG 59.562 39.130 22.95 0.00 40.46 3.21
1576 6339 3.616956 TTTTGGCAAACAACCATGTGA 57.383 38.095 13.10 0.00 40.46 3.58
1577 6340 3.616956 TTTGGCAAACAACCATGTGAA 57.383 38.095 8.93 0.00 40.46 3.18
1578 6341 3.834489 TTGGCAAACAACCATGTGAAT 57.166 38.095 0.00 0.00 40.46 2.57
1580 6343 3.464907 TGGCAAACAACCATGTGAATTG 58.535 40.909 0.00 0.00 40.46 2.32
1581 6344 3.133542 TGGCAAACAACCATGTGAATTGA 59.866 39.130 0.00 0.00 40.46 2.57
1583 6346 5.011431 TGGCAAACAACCATGTGAATTGATA 59.989 36.000 0.00 0.00 40.46 2.15
1584 6347 6.108015 GGCAAACAACCATGTGAATTGATAT 58.892 36.000 0.00 0.00 40.46 1.63
1586 6349 7.413219 GGCAAACAACCATGTGAATTGATATTG 60.413 37.037 0.00 2.31 40.46 1.90
1587 6350 7.331440 GCAAACAACCATGTGAATTGATATTGA 59.669 33.333 0.00 0.00 40.46 2.57
1668 6431 4.944962 TTTCCGAAGCACAAGTATGATG 57.055 40.909 0.00 0.00 0.00 3.07
1692 6460 2.867472 GCGTGCACACACCCATAC 59.133 61.111 18.64 0.00 44.40 2.39
1693 6461 2.686816 GCGTGCACACACCCATACC 61.687 63.158 18.64 0.00 44.40 2.73
1724 6492 5.473504 TCTTCATTTTGGTGAACTAAGAGCC 59.526 40.000 0.00 0.00 34.58 4.70
1732 6500 3.764972 GGTGAACTAAGAGCCTCTACAGT 59.235 47.826 0.00 0.00 0.00 3.55
1734 6502 3.690139 TGAACTAAGAGCCTCTACAGTCG 59.310 47.826 8.82 0.00 0.00 4.18
1754 6522 2.819019 CGCATATGACAAATATGGCCCA 59.181 45.455 6.97 0.00 31.48 5.36
1760 6528 7.617225 CATATGACAAATATGGCCCATCAAAT 58.383 34.615 0.00 0.00 31.48 2.32
1763 6531 3.061322 CAAATATGGCCCATCAAATGCG 58.939 45.455 0.00 0.00 0.00 4.73
1918 6692 3.432933 CGTCTATCCTAACTACTCCTCGC 59.567 52.174 0.00 0.00 0.00 5.03
1920 6694 2.750141 ATCCTAACTACTCCTCGCCA 57.250 50.000 0.00 0.00 0.00 5.69
1935 6709 0.248661 CGCCAGAGATCACGACGATT 60.249 55.000 0.00 0.00 33.17 3.34
2015 8957 3.068691 TCCGGCCTCCTTCGTCTG 61.069 66.667 0.00 0.00 0.00 3.51
2017 8959 2.125912 CGGCCTCCTTCGTCTGTG 60.126 66.667 0.00 0.00 0.00 3.66
2043 8985 2.746671 TCGAGCTCGGCGAAGAGT 60.747 61.111 33.98 0.00 40.26 3.24
2147 11256 1.741770 GTTGCTCCGCCATCTCGTT 60.742 57.895 0.00 0.00 0.00 3.85
2160 11269 3.220999 CTCGTTGGACTGGGCGACA 62.221 63.158 0.00 0.00 0.00 4.35
2195 11304 0.610232 GCCTGCTCCATGTTGAAGGT 60.610 55.000 10.00 0.00 0.00 3.50
2220 11341 4.704103 TGCTGGTCCGGCTCCTCT 62.704 66.667 23.33 0.00 36.58 3.69
2256 13555 0.047176 TCTCCTCCTCCTCCTCCTCT 59.953 60.000 0.00 0.00 0.00 3.69
2259 13558 0.933700 CCTCCTCCTCCTCCTCTTCT 59.066 60.000 0.00 0.00 0.00 2.85
2281 13586 2.364842 GCTGCTCCTCCTCCTCCA 60.365 66.667 0.00 0.00 0.00 3.86
2292 13597 4.316823 TCCTCCACCGGCTCTGGT 62.317 66.667 0.00 0.00 45.21 4.00
2309 13614 2.604686 TGAGTTCGGAGGCAGCCT 60.605 61.111 16.12 16.12 36.03 4.58
2360 15657 2.363795 CACCCGGGTCTCCTGCTA 60.364 66.667 27.51 0.00 0.00 3.49
2374 15671 1.231221 CTGCTAGATCTCGTAGCGGT 58.769 55.000 14.34 0.00 45.05 5.68
2380 15677 1.725557 GATCTCGTAGCGGTGCTCCA 61.726 60.000 5.52 0.00 40.44 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 3.723764 CGTGGTTTGTGAAAGTTTGATCG 59.276 43.478 0.00 0.00 0.00 3.69
95 96 3.181526 CGCACACTCTTTTGCTAGATGAC 60.182 47.826 0.00 0.00 36.54 3.06
313 564 8.971321 CAAATTGTAACTCCAAATATAGCATGC 58.029 33.333 10.51 10.51 0.00 4.06
413 1353 0.406361 ACCAAAATACCGGGGCTTCA 59.594 50.000 6.32 0.00 0.00 3.02
417 1357 1.067974 GCAATACCAAAATACCGGGGC 59.932 52.381 6.32 0.00 0.00 5.80
518 1514 1.707239 CTAGAGCGAGTCGAAGGCGT 61.707 60.000 18.61 0.00 36.95 5.68
527 1523 2.748532 GACTACAACCACTAGAGCGAGT 59.251 50.000 0.00 0.00 0.00 4.18
557 1553 3.066208 ACCAGGTGATCTATGGACCAT 57.934 47.619 12.67 12.67 37.54 3.55
692 1688 8.348285 AGATAAGGCAACAAGTTAAGCAATAA 57.652 30.769 0.00 0.00 41.41 1.40
779 1786 3.750501 TGTCCTCTGGGTGTATCACTA 57.249 47.619 0.06 0.00 34.40 2.74
851 1867 2.223409 CGTAGTCGCTTAGGCATGTGTA 60.223 50.000 0.00 0.00 38.60 2.90
1323 4835 0.390735 GGTGGATGCCGAGTACGTTT 60.391 55.000 0.00 0.00 37.88 3.60
1329 4841 1.296715 GTTGAGGTGGATGCCGAGT 59.703 57.895 0.00 0.00 0.00 4.18
1416 4928 3.569690 CGCGTCCGTTAATGGGCC 61.570 66.667 12.74 0.00 0.00 5.80
1444 4966 0.380378 GCAAATCTTATTCGGCGCCA 59.620 50.000 28.98 8.41 0.00 5.69
1478 6238 5.170625 CACAACTCACGAAAAATAACAACGG 59.829 40.000 0.00 0.00 0.00 4.44
1513 6273 4.525912 ACAAGGATTCAAATGTGGAAGC 57.474 40.909 0.00 0.00 0.00 3.86
1583 6346 7.949434 TGCGCTCTGATGATATATATCTCAAT 58.051 34.615 20.74 8.59 33.88 2.57
1584 6347 7.338800 TGCGCTCTGATGATATATATCTCAA 57.661 36.000 20.74 4.33 33.88 3.02
1586 6349 8.081025 TGATTGCGCTCTGATGATATATATCTC 58.919 37.037 20.74 15.80 33.88 2.75
1587 6350 7.949434 TGATTGCGCTCTGATGATATATATCT 58.051 34.615 20.74 8.79 33.88 1.98
1603 6366 9.712305 ATTAACTAGAGTAATAATGATTGCGCT 57.288 29.630 9.73 2.83 40.10 5.92
1651 6414 4.318618 GCATCTCATCATACTTGTGCTTCG 60.319 45.833 0.00 0.00 0.00 3.79
1687 6455 6.150474 ACCAAAATGAAGAAACTACGGTATGG 59.850 38.462 0.00 0.00 0.00 2.74
1692 6460 5.682943 TCACCAAAATGAAGAAACTACGG 57.317 39.130 0.00 0.00 0.00 4.02
1693 6461 6.725246 AGTTCACCAAAATGAAGAAACTACG 58.275 36.000 0.00 0.00 39.25 3.51
1724 6492 7.062722 CCATATTTGTCATATGCGACTGTAGAG 59.937 40.741 0.00 0.00 36.82 2.43
1732 6500 3.081061 GGGCCATATTTGTCATATGCGA 58.919 45.455 4.39 0.00 32.22 5.10
1734 6502 4.463539 TGATGGGCCATATTTGTCATATGC 59.536 41.667 21.26 2.31 32.22 3.14
1754 6522 4.222589 CGTCCGCGCGCATTTGAT 62.223 61.111 32.61 0.00 0.00 2.57
1790 6559 4.783621 GCATCCCCGCTCACTGCA 62.784 66.667 0.00 0.00 43.06 4.41
1803 6572 4.151157 GCAACAAGTGAAATTTGAGGCATC 59.849 41.667 0.00 0.00 35.27 3.91
1805 6574 3.456280 GCAACAAGTGAAATTTGAGGCA 58.544 40.909 0.00 0.00 35.27 4.75
1857 6628 8.289618 TCTACTTCATTTTGCATGTCTTTGTAC 58.710 33.333 0.00 0.00 0.00 2.90
1900 6673 3.393609 TCTGGCGAGGAGTAGTTAGGATA 59.606 47.826 0.00 0.00 0.00 2.59
1907 6680 1.213182 TGATCTCTGGCGAGGAGTAGT 59.787 52.381 0.00 0.00 37.86 2.73
1918 6692 2.464865 GGAAATCGTCGTGATCTCTGG 58.535 52.381 0.00 0.00 35.84 3.86
1920 6694 2.476873 CGGAAATCGTCGTGATCTCT 57.523 50.000 0.00 0.00 35.84 3.10
2009 8951 2.962827 GACGCGGAGACACAGACGA 61.963 63.158 12.47 0.00 0.00 4.20
2015 8957 4.104417 AGCTCGACGCGGAGACAC 62.104 66.667 12.47 2.28 45.59 3.67
2017 8959 4.872485 CGAGCTCGACGCGGAGAC 62.872 72.222 32.06 5.00 45.59 3.36
2043 8985 3.680786 CAGGTGGAGTCCGACGCA 61.681 66.667 4.30 0.00 0.00 5.24
2160 11269 4.443266 GCGGAGGCAGAGTTCGCT 62.443 66.667 0.00 0.00 42.62 4.93
2220 11341 1.964223 GAGATGGCTTCGATGGAGGTA 59.036 52.381 0.00 0.00 0.00 3.08
2256 13555 3.077556 GAGGAGCAGCCGGGAGAA 61.078 66.667 2.18 0.00 43.43 2.87
2281 13586 2.932234 CGAACTCACCAGAGCCGGT 61.932 63.158 1.90 0.00 46.09 5.28
2292 13597 2.604686 AGGCTGCCTCCGAACTCA 60.605 61.111 17.22 0.00 0.00 3.41
2350 15647 2.482721 GCTACGAGATCTAGCAGGAGAC 59.517 54.545 10.50 0.00 37.22 3.36
2360 15657 1.448922 GGAGCACCGCTACGAGATCT 61.449 60.000 0.00 0.00 39.88 2.75
2380 15677 1.663379 TACTACGCCATGCTGACGCT 61.663 55.000 0.00 0.00 36.97 5.07


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

AutoCloner maintained by Alex Coulton.