Multiple sequence alignment - TraesCS3D01G533600

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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 TraesCS3D01G533600 chr3D 100.000 4268 0 0 1 4268 609085694 609081427 0.000000e+00 7882.0
1 TraesCS3D01G533600 chr3A 94.228 3985 191 19 45 4006 742440262 742436294 0.000000e+00 6048.0
2 TraesCS3D01G533600 chr3A 94.355 248 11 2 4021 4268 742434829 742434585 1.120000e-100 377.0
3 TraesCS3D01G533600 chr3A 90.335 269 15 5 4001 4268 742435880 742435622 4.090000e-90 342.0
4 TraesCS3D01G533600 chr3A 95.385 65 3 0 4044 4108 742435377 742435313 2.100000e-18 104.0
5 TraesCS3D01G533600 chr3A 100.000 43 0 0 4021 4063 742435294 742435252 3.540000e-11 80.5
6 TraesCS3D01G533600 chr3A 92.308 52 4 0 4057 4108 742434899 742434848 1.650000e-09 75.0
7 TraesCS3D01G533600 chr3B 93.387 3221 162 23 62 3271 819788677 819785497 0.000000e+00 4721.0
8 TraesCS3D01G533600 chr3B 94.091 440 16 3 3576 4006 819785465 819785027 0.000000e+00 660.0
9 TraesCS3D01G533600 chr3B 94.815 270 11 3 4001 4268 819784615 819784347 6.600000e-113 418.0
10 TraesCS3D01G533600 chr3B 97.674 43 1 0 1 43 819788766 819788724 1.650000e-09 75.0
11 TraesCS3D01G533600 chr3B 97.143 35 1 0 3292 3326 819785496 819785462 4.610000e-05 60.2
12 TraesCS3D01G533600 chr2D 87.891 256 16 9 979 1222 623474984 623474732 1.940000e-73 287.0
13 TraesCS3D01G533600 chr2D 75.771 227 44 7 1149 1373 598308983 598308766 2.100000e-18 104.0
14 TraesCS3D01G533600 chr2D 77.841 176 21 12 1016 1184 642203691 642203527 4.540000e-15 93.5
15 TraesCS3D01G533600 chr2B 87.963 216 17 6 284 498 765484586 765484379 3.300000e-61 246.0
16 TraesCS3D01G533600 chr2B 75.758 363 60 16 1016 1373 799614132 799614471 1.590000e-34 158.0
17 TraesCS3D01G533600 chr2A 83.550 231 27 3 902 1130 754707353 754707132 5.590000e-49 206.0
18 TraesCS3D01G533600 chr2A 75.540 278 49 14 1025 1297 766919414 766919151 7.500000e-23 119.0
19 TraesCS3D01G533600 chr2A 78.448 116 23 2 1103 1217 766973813 766973699 1.650000e-09 75.0


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 TraesCS3D01G533600 chr3D 609081427 609085694 4267 True 7882.000000 7882 100.000000 1 4268 1 chr3D.!!$R1 4267
1 TraesCS3D01G533600 chr3A 742434585 742440262 5677 True 1171.083333 6048 94.435167 45 4268 6 chr3A.!!$R1 4223
2 TraesCS3D01G533600 chr3B 819784347 819788766 4419 True 1186.840000 4721 95.422000 1 4268 5 chr3B.!!$R1 4267

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
957 1007 0.896940 AGCCCAACAACATCCAGCAG 60.897 55.0 0.0 0.0 0.00 4.24 F
2705 2761 0.457853 TTCATCGAAGAAGGACGGCG 60.458 55.0 4.8 4.8 43.58 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2820 2876 0.323908 AGTTCGGCTCTACTCCAGCT 60.324 55.000 0.0 0.0 37.05 4.24 R
3817 3885 4.817874 TTCAAGTTTCCCTTTTCCCCTA 57.182 40.909 0.0 0.0 0.00 3.53 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
43 44 6.681729 TCTCAAGGTAATTCAGTAACCACT 57.318 37.500 0.00 0.00 35.64 4.00
443 474 6.590234 ACTCACAGGTCATTTTATTTTCCC 57.410 37.500 0.00 0.00 0.00 3.97
495 529 1.542030 GTGCTCTCTTTCCTCTGTCGA 59.458 52.381 0.00 0.00 0.00 4.20
522 556 3.487120 AGAGAAACTAAACGCCTGGTT 57.513 42.857 0.00 0.00 41.76 3.67
641 675 8.969121 TTGCACATTTTCTCATTACTACATTG 57.031 30.769 0.00 0.00 0.00 2.82
667 702 5.824904 ATTATCACACTGTCTTCCATTGC 57.175 39.130 0.00 0.00 0.00 3.56
672 707 3.067180 CACACTGTCTTCCATTGCAGTTT 59.933 43.478 0.00 0.00 39.82 2.66
703 738 8.425577 TCTTGAGAGAAATCGGATTATTGTTC 57.574 34.615 3.22 0.00 0.00 3.18
708 744 9.709600 GAGAGAAATCGGATTATTGTTCTTTTC 57.290 33.333 3.22 2.50 0.00 2.29
711 747 7.396055 AGAAATCGGATTATTGTTCTTTTCCCA 59.604 33.333 3.22 0.00 0.00 4.37
719 755 9.927668 GATTATTGTTCTTTTCCCATCAGAAAA 57.072 29.630 0.00 0.00 42.07 2.29
862 912 4.736473 TGTGCTATACTGTCCCAGCTATA 58.264 43.478 8.90 0.00 34.37 1.31
893 943 3.447918 GCGAGGGCTACATTGTAGTTA 57.552 47.619 21.70 0.00 35.83 2.24
913 963 1.065126 AGTGAGGCCAGGCTGAATTAC 60.065 52.381 17.94 8.10 0.00 1.89
924 974 2.565841 GCTGAATTACCTAGCCCAGTG 58.434 52.381 0.00 0.00 0.00 3.66
928 978 4.562767 TGAATTACCTAGCCCAGTGGATA 58.437 43.478 11.95 2.12 0.00 2.59
957 1007 0.896940 AGCCCAACAACATCCAGCAG 60.897 55.000 0.00 0.00 0.00 4.24
977 1033 1.550130 TTTACCACTCCTCTGCCCCG 61.550 60.000 0.00 0.00 0.00 5.73
1194 1250 2.511600 CTGTTCGACCGGATGCCC 60.512 66.667 9.46 0.00 0.00 5.36
1395 1451 4.393155 TTCGGCGAGCAGGTGCAT 62.393 61.111 10.46 0.00 45.16 3.96
1404 1460 2.827190 CAGGTGCATGGCATCGCT 60.827 61.111 18.20 1.51 45.38 4.93
1546 1602 4.873129 CCTGGACCGCGGTGATCG 62.873 72.222 39.65 20.16 42.76 3.69
1753 1809 3.853330 CGGTGGTCAATGCGCTCG 61.853 66.667 9.73 0.00 0.00 5.03
1821 1877 3.081804 GTTTGATTCCATGGAGAACCGT 58.918 45.455 15.53 0.00 39.42 4.83
1938 1994 2.690778 GCAGCCGGATGTTTTCGCT 61.691 57.895 22.68 0.00 0.00 4.93
2070 2126 3.208594 TGCTCTGATTGACATGTATGCC 58.791 45.455 0.00 0.00 0.00 4.40
2076 2132 5.653330 TCTGATTGACATGTATGCCAAATGT 59.347 36.000 0.00 0.00 33.94 2.71
2085 2141 3.628942 TGTATGCCAAATGTGAGCATCTC 59.371 43.478 13.23 9.70 43.58 2.75
2202 2258 4.160439 ACAGGAGCAGTCGAAATATTCAGA 59.840 41.667 0.00 0.00 0.00 3.27
2373 2429 3.911365 GTGCTCTCATCGATGTCTATTCG 59.089 47.826 24.09 8.73 37.94 3.34
2534 2590 2.035632 CCTCTCTGGGCTAACACCTAG 58.964 57.143 0.00 0.00 39.57 3.02
2559 2615 2.025589 TCACGTTTGTTGCACTGGTA 57.974 45.000 0.00 0.00 0.00 3.25
2705 2761 0.457853 TTCATCGAAGAAGGACGGCG 60.458 55.000 4.80 4.80 43.58 6.46
2820 2876 2.381618 TGTTTTTGGGATGATGGGAGGA 59.618 45.455 0.00 0.00 0.00 3.71
3271 3327 2.289945 GCAGGATATAGCTGGTGAAGGG 60.290 54.545 0.00 0.00 0.00 3.95
3321 3379 0.107456 ACACACAGAGGCAGAAGTGG 59.893 55.000 0.00 0.00 36.35 4.00
3434 3492 6.367374 TGGTTGATGGTACTTACTGAATGA 57.633 37.500 0.00 0.00 0.00 2.57
3486 3545 7.939039 ACAGATGGTCTTGAATGAACTTTTCTA 59.061 33.333 0.00 0.00 0.00 2.10
3489 3548 5.473504 TGGTCTTGAATGAACTTTTCTAGCC 59.526 40.000 0.00 0.00 0.00 3.93
3491 3550 6.374578 GTCTTGAATGAACTTTTCTAGCCAC 58.625 40.000 0.00 0.00 0.00 5.01
3495 3554 3.746045 TGAACTTTTCTAGCCACGTCT 57.254 42.857 0.00 0.00 0.00 4.18
3503 3562 0.388649 CTAGCCACGTCTCCACACAC 60.389 60.000 0.00 0.00 0.00 3.82
3550 3609 6.422400 GCTTTGATATAGTAGTTCTGGCTGTC 59.578 42.308 0.00 0.00 0.00 3.51
3566 3625 7.450074 TCTGGCTGTCTTCTTTGATAACTTTA 58.550 34.615 0.00 0.00 0.00 1.85
3607 3670 4.290093 TGTCCAATGACTATCTGGCTAGT 58.710 43.478 0.00 0.00 42.28 2.57
3627 3690 8.905850 GGCTAGTTACTACTTACTGAAAGAGAT 58.094 37.037 0.00 0.00 38.67 2.75
3761 3829 3.673809 GGTTCAGTGTTGTTAGCTACTCG 59.326 47.826 0.00 0.00 0.00 4.18
3817 3885 9.468532 GCAGTAATTTGAATCTTCTTGTTTCTT 57.531 29.630 0.00 0.00 0.00 2.52
3822 3890 7.524717 TTTGAATCTTCTTGTTTCTTAGGGG 57.475 36.000 0.00 0.00 0.00 4.79
3856 3924 8.519799 AACTTGAATCTTCTGTACAGGAAAAA 57.480 30.769 22.48 8.63 0.00 1.94
3860 3928 8.553459 TGAATCTTCTGTACAGGAAAAAGATC 57.447 34.615 25.84 20.81 33.54 2.75
3921 3989 6.481976 CCAATTATACTGGAACATTAGCGTGA 59.518 38.462 0.00 0.00 38.20 4.35
4015 4504 0.898320 CGCTGGAAGGAGAGAGGAAA 59.102 55.000 0.00 0.00 0.00 3.13
4019 5074 3.618752 GCTGGAAGGAGAGAGGAAAAGAC 60.619 52.174 0.00 0.00 0.00 3.01
4108 5628 4.689612 TGTTGGTCTTGACTAGAAAGCT 57.310 40.909 0.00 0.00 33.81 3.74
4115 5635 4.513318 GTCTTGACTAGAAAGCTGCAGTTT 59.487 41.667 16.64 13.48 33.81 2.66
4210 5730 3.499338 TCATTTGAGGGCAGTGACAATT 58.501 40.909 0.00 0.00 0.00 2.32
4257 5779 6.206634 TGTTAGACTTTCACCTAAATTGCCAG 59.793 38.462 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.782049 ACTGAATTACCTTGAGATCGACATAA 58.218 34.615 0.00 0.00 0.00 1.90
236 265 3.775654 GACCAGTAGGCCTGCGCT 61.776 66.667 17.99 8.09 40.06 5.92
270 299 1.002379 AAGCCTTGCCTGAGAGCTG 60.002 57.895 0.00 0.00 33.18 4.24
271 300 1.299321 GAAGCCTTGCCTGAGAGCT 59.701 57.895 0.00 0.00 34.64 4.09
275 304 0.676151 GTCCTGAAGCCTTGCCTGAG 60.676 60.000 0.00 0.00 0.00 3.35
443 474 4.275443 AGCAGCAAACAGAGAAGAAGAAAG 59.725 41.667 0.00 0.00 0.00 2.62
495 529 7.827729 ACCAGGCGTTTAGTTTCTCTTATTAAT 59.172 33.333 0.00 0.00 0.00 1.40
522 556 0.108207 TTTACAAAGGGGCCGTCGAA 59.892 50.000 0.00 0.00 0.00 3.71
641 675 8.072567 GCAATGGAAGACAGTGTGATAATAATC 58.927 37.037 0.00 0.00 46.36 1.75
650 685 2.224606 ACTGCAATGGAAGACAGTGTG 58.775 47.619 0.00 0.00 46.36 3.82
703 738 9.895138 ATAATCCAATTTTTCTGATGGGAAAAG 57.105 29.630 0.00 0.00 43.22 2.27
735 771 2.821969 CCAAATCCAACCACTCAAGGAG 59.178 50.000 0.00 0.00 32.91 3.69
870 920 1.409064 CTACAATGTAGCCCTCGCTCA 59.591 52.381 7.55 0.00 43.95 4.26
883 933 3.535561 CCTGGCCTCACTAACTACAATG 58.464 50.000 3.32 0.00 0.00 2.82
887 937 1.134670 CAGCCTGGCCTCACTAACTAC 60.135 57.143 16.57 0.00 0.00 2.73
889 939 0.545309 TCAGCCTGGCCTCACTAACT 60.545 55.000 16.57 0.00 0.00 2.24
893 943 1.065126 GTAATTCAGCCTGGCCTCACT 60.065 52.381 16.57 0.00 0.00 3.41
913 963 0.398318 GCCTTATCCACTGGGCTAGG 59.602 60.000 2.02 1.07 41.20 3.02
957 1007 0.035343 GGGGCAGAGGAGTGGTAAAC 60.035 60.000 0.00 0.00 0.00 2.01
1174 1230 2.885644 CATCCGGTCGAACAGGCG 60.886 66.667 0.00 0.00 33.25 5.52
1175 1231 3.195698 GCATCCGGTCGAACAGGC 61.196 66.667 0.00 0.00 33.25 4.85
1188 1244 4.171103 AGGTTACGGCCGGGCATC 62.171 66.667 31.76 13.09 0.00 3.91
1194 1250 2.101770 GAGACGAGGTTACGGCCG 59.898 66.667 26.86 26.86 42.85 6.13
1200 1256 1.684734 GCCCCAGGAGACGAGGTTA 60.685 63.158 0.00 0.00 0.00 2.85
1546 1602 2.760385 AGCCTGAGAGTACCCCGC 60.760 66.667 0.00 0.00 0.00 6.13
1576 1632 0.971386 CCAAACAGCTCCAAGGCAAT 59.029 50.000 0.00 0.00 34.17 3.56
1753 1809 4.344448 GAGCACTTACAGTACAGATCGAC 58.656 47.826 0.00 0.00 0.00 4.20
1821 1877 3.253921 TCGTCGTCCAAGACACAAGATTA 59.746 43.478 0.00 0.00 40.98 1.75
2076 2132 2.301009 TCTTGCTTCTGTGAGATGCTCA 59.699 45.455 11.44 0.00 43.42 4.26
2085 2141 2.015736 ATACCGCTCTTGCTTCTGTG 57.984 50.000 0.00 0.00 36.97 3.66
2100 2156 2.446435 TCTGCCAAGGCTTCAAATACC 58.554 47.619 12.96 0.00 42.51 2.73
2202 2258 6.264067 GCTTTAGTGGGCAATATCTCATCTTT 59.736 38.462 0.00 0.00 0.00 2.52
2218 2274 2.027192 TCAGTAGGCTTGGCTTTAGTGG 60.027 50.000 1.22 0.00 0.00 4.00
2534 2590 2.159572 AGTGCAACAAACGTGAACTCAC 60.160 45.455 0.00 0.00 41.43 3.51
2559 2615 1.543429 GCCAGAGTACTTGCCACAGTT 60.543 52.381 0.00 0.00 0.00 3.16
2572 2628 0.689055 TGAGACATGCTTGCCAGAGT 59.311 50.000 0.00 0.00 0.00 3.24
2604 2660 3.937778 TCTTTGATGATCTGGGCATGA 57.062 42.857 0.00 0.00 0.00 3.07
2705 2761 2.031157 CCCGATGTTGACTCAAACAACC 60.031 50.000 0.00 0.00 42.98 3.77
2820 2876 0.323908 AGTTCGGCTCTACTCCAGCT 60.324 55.000 0.00 0.00 37.05 4.24
2883 2939 3.073062 ACTGTAGGCCTTCATTCACAAGT 59.927 43.478 12.58 0.83 0.00 3.16
2899 2955 9.214957 TGTGTTCATGGAGTTAAAATACTGTAG 57.785 33.333 0.00 0.00 0.00 2.74
3271 3327 3.938963 TCTTGCGAAGAATGTATGAACCC 59.061 43.478 0.00 0.00 33.83 4.11
3350 3408 8.678593 GGAGATACCCAGAATTTTTAAGTAGG 57.321 38.462 0.00 0.00 0.00 3.18
3473 3532 4.642429 AGACGTGGCTAGAAAAGTTCATT 58.358 39.130 0.00 0.00 0.00 2.57
3481 3540 1.000506 GTGTGGAGACGTGGCTAGAAA 59.999 52.381 0.00 0.00 0.00 2.52
3486 3545 1.966901 TTGTGTGTGGAGACGTGGCT 61.967 55.000 0.00 0.00 0.00 4.75
3489 3548 2.502213 TAGTTGTGTGTGGAGACGTG 57.498 50.000 0.00 0.00 0.00 4.49
3491 3550 4.621460 CAGTATTAGTTGTGTGTGGAGACG 59.379 45.833 0.00 0.00 0.00 4.18
3495 3554 3.904965 TCCCAGTATTAGTTGTGTGTGGA 59.095 43.478 0.00 0.00 0.00 4.02
3503 3562 4.999950 GCATCATCCTCCCAGTATTAGTTG 59.000 45.833 0.00 0.00 0.00 3.16
3607 3670 9.742144 ACTCTGATCTCTTTCAGTAAGTAGTAA 57.258 33.333 0.00 0.00 43.02 2.24
3627 3690 5.485620 CTGATCAAGTCATTCCAACTCTGA 58.514 41.667 0.00 0.00 35.97 3.27
3787 3855 6.865205 ACAAGAAGATTCAAATTACTGCAAGC 59.135 34.615 0.00 0.00 37.60 4.01
3817 3885 4.817874 TTCAAGTTTCCCTTTTCCCCTA 57.182 40.909 0.00 0.00 0.00 3.53
3820 3888 5.540337 AGAAGATTCAAGTTTCCCTTTTCCC 59.460 40.000 0.00 0.00 0.00 3.97
3822 3890 7.043961 ACAGAAGATTCAAGTTTCCCTTTTC 57.956 36.000 0.00 0.00 0.00 2.29
3901 3969 7.269316 TCAAATCACGCTAATGTTCCAGTATA 58.731 34.615 0.00 0.00 0.00 1.47
3921 3989 5.835280 AGGAACAAGTTCACCTGAATCAAAT 59.165 36.000 14.25 0.00 41.20 2.32
4015 4504 9.651913 TTCTTTGCTGAAAACTAATTTTGTCTT 57.348 25.926 0.00 0.00 38.17 3.01
4108 5628 7.953005 TCCAGATTCCAATTATAAAACTGCA 57.047 32.000 0.00 0.00 0.00 4.41
4115 5635 9.253832 TCTTGCTTTTCCAGATTCCAATTATAA 57.746 29.630 0.00 0.00 0.00 0.98
4223 5743 7.120923 AGGTGAAAGTCTAACACAAAGAGTA 57.879 36.000 10.20 0.00 36.42 2.59
4240 5762 7.014711 TGTTATGTTCTGGCAATTTAGGTGAAA 59.985 33.333 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.