Multiple sequence alignment - TraesCS1D01G301200

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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 TraesCS1D01G301200 chr1D 100.000 2862 0 0 1 2862 398978814 398975953 0.000000e+00 5286.0
1 TraesCS1D01G301200 chr1B 95.810 2530 88 9 339 2862 534668168 534665651 0.000000e+00 4069.0
2 TraesCS1D01G301200 chr1B 94.258 209 6 3 1 208 534668511 534668308 5.950000e-82 315.0
3 TraesCS1D01G301200 chr1A 94.690 1695 72 6 1170 2862 495704325 495702647 0.000000e+00 2615.0
4 TraesCS1D01G301200 chr1A 91.995 762 37 12 339 1097 495705067 495704327 0.000000e+00 1048.0
5 TraesCS1D01G301200 chr1A 90.909 352 13 6 1 342 495705437 495705095 3.360000e-124 455.0
6 TraesCS1D01G301200 chr6A 86.885 61 5 3 732 789 89962030 89962090 6.620000e-07 65.8
7 TraesCS1D01G301200 chr6A 93.023 43 1 2 710 751 34560247 34560206 8.560000e-06 62.1
8 TraesCS1D01G301200 chr6A 100.000 31 0 0 757 787 61420448 61420478 1.110000e-04 58.4
9 TraesCS1D01G301200 chr4D 91.111 45 4 0 713 757 368007030 368007074 8.560000e-06 62.1
10 TraesCS1D01G301200 chr4B 95.000 40 1 1 749 787 3890849 3890810 8.560000e-06 62.1
11 TraesCS1D01G301200 chr7D 100.000 32 0 0 756 787 513211199 513211168 3.080000e-05 60.2
12 TraesCS1D01G301200 chr6B 92.857 42 2 1 747 787 485061234 485061275 3.080000e-05 60.2
13 TraesCS1D01G301200 chr2B 91.111 45 0 2 758 802 39782796 39782756 1.110000e-04 58.4
14 TraesCS1D01G301200 chrUn 97.059 34 0 1 710 743 470506527 470506495 3.980000e-04 56.5
15 TraesCS1D01G301200 chr5D 100.000 30 0 0 758 787 557554076 557554105 3.980000e-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 TraesCS1D01G301200 chr1D 398975953 398978814 2861 True 5286.000000 5286 100.000000 1 2862 1 chr1D.!!$R1 2861
1 TraesCS1D01G301200 chr1B 534665651 534668511 2860 True 2192.000000 4069 95.034000 1 2862 2 chr1B.!!$R1 2861
2 TraesCS1D01G301200 chr1A 495702647 495705437 2790 True 1372.666667 2615 92.531333 1 2862 3 chr1A.!!$R1 2861

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
176 177 0.179 ATAGGCTTCTTGGTCCTGCG 59.821 55.0 0.0 0.0 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 2053 0.244721 CTGCTGATCGAGTGTGGACA 59.755 55.0 0.0 0.0 0.0 4.02 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
123 124 1.950216 GCGGGGAAATCTGAATCTTCC 59.050 52.381 7.61 7.61 38.33 3.46
152 153 1.629353 CCCCATCATCATCAGGAGGAG 59.371 57.143 0.00 0.00 40.08 3.69
153 154 1.629353 CCCATCATCATCAGGAGGAGG 59.371 57.143 0.00 0.00 40.08 4.30
154 155 2.617658 CCATCATCATCAGGAGGAGGA 58.382 52.381 0.69 0.69 40.27 3.71
176 177 0.179000 ATAGGCTTCTTGGTCCTGCG 59.821 55.000 0.00 0.00 0.00 5.18
225 244 5.237815 TCGTTCTGCTCTCAACAATGTAAT 58.762 37.500 0.00 0.00 0.00 1.89
226 245 6.394809 TCGTTCTGCTCTCAACAATGTAATA 58.605 36.000 0.00 0.00 0.00 0.98
227 246 6.531594 TCGTTCTGCTCTCAACAATGTAATAG 59.468 38.462 0.00 0.00 0.00 1.73
228 247 6.531594 CGTTCTGCTCTCAACAATGTAATAGA 59.468 38.462 0.00 0.00 0.00 1.98
356 409 2.588027 TTTTCCTTGGCGTTCAAACC 57.412 45.000 0.00 0.00 34.56 3.27
409 462 5.857471 TTAATGAATGCATCTCCTTTGGG 57.143 39.130 0.00 0.00 32.35 4.12
450 503 1.126846 GGATCGTCTGAAACTGTTGCG 59.873 52.381 0.00 0.00 0.00 4.85
486 539 4.558538 AATATGTTGAGCAAGATTCGCC 57.441 40.909 0.00 0.00 0.00 5.54
506 559 2.549754 CCATCGTGCAGACAAACTTCTT 59.450 45.455 0.00 0.00 0.00 2.52
529 582 1.388547 TCTATTGGATTTGCCGTGGC 58.611 50.000 3.30 3.30 40.66 5.01
539 592 3.357079 GCCGTGGCTGTGACTTGG 61.357 66.667 2.98 0.00 38.26 3.61
558 613 5.012354 ACTTGGGCATCAAATCTGTTTCAAT 59.988 36.000 0.00 0.00 34.56 2.57
559 614 5.486735 TGGGCATCAAATCTGTTTCAATT 57.513 34.783 0.00 0.00 0.00 2.32
598 653 0.594796 GCACGTTTTTGGCTGGTCTG 60.595 55.000 0.00 0.00 0.00 3.51
1112 1171 6.980593 TCTTTATTGCATAGCTTGTGTTTGT 58.019 32.000 0.00 0.00 0.00 2.83
1164 1223 2.504175 GGTCAACTGATAGTAAGGCCCA 59.496 50.000 0.00 0.00 0.00 5.36
1165 1224 3.054655 GGTCAACTGATAGTAAGGCCCAA 60.055 47.826 0.00 0.00 0.00 4.12
1166 1225 4.385310 GGTCAACTGATAGTAAGGCCCAAT 60.385 45.833 0.00 0.00 0.00 3.16
1167 1226 5.193679 GTCAACTGATAGTAAGGCCCAATT 58.806 41.667 0.00 0.00 0.00 2.32
1193 1252 6.342338 AGGAAGCCGTTTATCGAGTTATAT 57.658 37.500 0.00 0.00 42.86 0.86
1194 1253 6.157211 AGGAAGCCGTTTATCGAGTTATATG 58.843 40.000 0.00 0.00 42.86 1.78
1305 1364 7.592164 GTGACTCTTATAACCGATCTAAAGAGC 59.408 40.741 9.23 4.40 42.24 4.09
1357 1416 5.243207 ACGCCAATAAAACAGTAAGTAGCT 58.757 37.500 0.00 0.00 0.00 3.32
1365 1424 6.872628 AAAACAGTAAGTAGCTTACAACCC 57.127 37.500 17.79 0.00 46.01 4.11
1391 1450 5.361285 ACTCATACTCTGGACACAAGGATAC 59.639 44.000 0.00 0.00 0.00 2.24
1429 1488 3.296322 TCCAATTTGGAATTCGTGCAC 57.704 42.857 15.83 6.82 45.00 4.57
1430 1489 2.890311 TCCAATTTGGAATTCGTGCACT 59.110 40.909 15.83 0.00 45.00 4.40
1608 1667 2.642154 ACCGGTACACAAATGTTCCA 57.358 45.000 4.49 0.00 44.48 3.53
1612 1671 1.538075 GGTACACAAATGTTCCACCGG 59.462 52.381 0.00 0.00 43.87 5.28
1613 1672 1.068816 GTACACAAATGTTCCACCGGC 60.069 52.381 0.00 0.00 40.48 6.13
1626 1685 4.067972 TCCACCGGCTCATTACTAATTC 57.932 45.455 0.00 0.00 0.00 2.17
1705 1764 1.993370 GAACTGGTCACGGAATTCGAG 59.007 52.381 0.00 0.00 42.43 4.04
1760 1819 6.361433 AGAGATAAGAAGGAGATCGACAAGA 58.639 40.000 0.00 0.00 0.00 3.02
1828 1887 3.530910 CCGGCCAGGTGACGAAGTT 62.531 63.158 2.24 0.00 36.29 2.66
1872 1931 1.273327 CAAAACCTGATGTTCCTGCCC 59.727 52.381 0.00 0.00 35.67 5.36
1893 1952 2.159184 CGCCAGTCAATAGAGCTTCAGA 60.159 50.000 0.00 0.00 0.00 3.27
1994 2053 5.485708 AGCAGAAGTAGGATTTCTTGGTAGT 59.514 40.000 0.00 0.00 32.75 2.73
2043 2102 3.118592 AGTTAGCCCAGCATCTGTAACTC 60.119 47.826 0.00 0.00 30.38 3.01
2077 2136 1.854743 CTGTCCATATGAACTCGCACG 59.145 52.381 3.65 0.00 0.00 5.34
2192 2253 1.135915 GCGTCTCACTCATGTCAGGAT 59.864 52.381 0.00 0.00 0.00 3.24
2198 2259 2.502947 TCACTCATGTCAGGATTCAGGG 59.497 50.000 0.00 0.00 0.00 4.45
2229 2290 8.642964 TTTATGGGATGGACATCTATATGGAT 57.357 34.615 11.67 0.00 37.43 3.41
2259 2320 1.073923 AGGGGTTTGATCGCTTGTTCT 59.926 47.619 0.00 0.00 0.00 3.01
2263 2324 3.689649 GGGTTTGATCGCTTGTTCTATGT 59.310 43.478 0.00 0.00 0.00 2.29
2280 2341 8.432013 TGTTCTATGTAGCCAGACATATCAATT 58.568 33.333 4.65 0.00 40.60 2.32
2281 2342 9.929180 GTTCTATGTAGCCAGACATATCAATTA 57.071 33.333 4.65 0.00 40.60 1.40
2282 2343 9.929180 TTCTATGTAGCCAGACATATCAATTAC 57.071 33.333 4.65 0.00 40.60 1.89
2588 2649 3.157252 ATGAGCACGATCCCGGCT 61.157 61.111 0.00 0.49 42.18 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 153 2.239907 AGGACCAAGAAGCCTATGTTCC 59.760 50.000 0.00 0.00 0.00 3.62
153 154 3.274288 CAGGACCAAGAAGCCTATGTTC 58.726 50.000 0.00 0.00 0.00 3.18
154 155 2.619074 GCAGGACCAAGAAGCCTATGTT 60.619 50.000 0.00 0.00 0.00 2.71
204 223 7.547370 ACTCTATTACATTGTTGAGAGCAGAAC 59.453 37.037 16.30 0.00 34.98 3.01
225 244 4.743651 GCATGCAGCCTGGTTATTACTCTA 60.744 45.833 14.21 0.00 37.23 2.43
226 245 3.813443 CATGCAGCCTGGTTATTACTCT 58.187 45.455 0.00 0.00 0.00 3.24
227 246 2.291741 GCATGCAGCCTGGTTATTACTC 59.708 50.000 14.21 0.00 37.23 2.59
228 247 2.301346 GCATGCAGCCTGGTTATTACT 58.699 47.619 14.21 0.00 37.23 2.24
356 409 4.253685 AGACCTCCAACAACAATATGACG 58.746 43.478 0.00 0.00 0.00 4.35
420 473 0.663688 CAGACGATCCTAGGGTGTCG 59.336 60.000 22.20 22.20 37.68 4.35
450 503 2.358898 ACATATTTGCCTGAATCCGCAC 59.641 45.455 0.00 0.00 33.97 5.34
486 539 3.548587 CAAGAAGTTTGTCTGCACGATG 58.451 45.455 0.00 0.00 0.00 3.84
506 559 2.752354 CACGGCAAATCCAATAGAACCA 59.248 45.455 0.00 0.00 34.01 3.67
529 582 3.087031 AGATTTGATGCCCAAGTCACAG 58.913 45.455 11.86 0.00 42.07 3.66
539 592 8.091385 AGAAAAATTGAAACAGATTTGATGCC 57.909 30.769 0.00 0.00 0.00 4.40
558 613 8.185505 ACGTGCTGTTTGTTTTAGATAGAAAAA 58.814 29.630 0.00 0.00 30.36 1.94
559 614 7.699566 ACGTGCTGTTTGTTTTAGATAGAAAA 58.300 30.769 0.00 0.00 0.00 2.29
598 653 7.118971 AGAGACTGCAGAAATATGAACAAGAAC 59.881 37.037 23.35 0.00 0.00 3.01
701 756 7.816995 TGTTTTGACAGTTTAAATTGAAGTGCT 59.183 29.630 16.68 0.00 32.03 4.40
779 834 9.460019 GTACTACTCCCTCTAACTCTAAAGAAA 57.540 37.037 0.00 0.00 0.00 2.52
781 836 8.155620 TGTACTACTCCCTCTAACTCTAAAGA 57.844 38.462 0.00 0.00 0.00 2.52
782 837 8.983702 ATGTACTACTCCCTCTAACTCTAAAG 57.016 38.462 0.00 0.00 0.00 1.85
861 917 7.465916 CGCTATGCCATAACATGATACCAATAC 60.466 40.741 0.00 0.00 0.00 1.89
900 957 5.413833 AGTGCTGATTTCACTATTTGACTGG 59.586 40.000 0.00 0.00 42.45 4.00
1112 1171 1.083489 GCACTACGTAGCATGGCAAA 58.917 50.000 22.40 0.00 0.00 3.68
1141 1200 3.054655 GGGCCTTACTATCAGTTGACCAA 60.055 47.826 0.84 0.00 0.00 3.67
1154 1213 4.023980 GCTTCCTTTAATTGGGCCTTACT 58.976 43.478 4.53 0.00 0.00 2.24
1164 1223 5.878669 ACTCGATAAACGGCTTCCTTTAATT 59.121 36.000 0.00 0.00 42.82 1.40
1165 1224 5.425630 ACTCGATAAACGGCTTCCTTTAAT 58.574 37.500 0.00 0.00 42.82 1.40
1166 1225 4.824289 ACTCGATAAACGGCTTCCTTTAA 58.176 39.130 0.00 0.00 42.82 1.52
1167 1226 4.460948 ACTCGATAAACGGCTTCCTTTA 57.539 40.909 0.00 0.00 42.82 1.85
1193 1252 5.790593 ACCAAAGAGCTCGATTTACTAACA 58.209 37.500 8.37 0.00 0.00 2.41
1194 1253 6.723131 AACCAAAGAGCTCGATTTACTAAC 57.277 37.500 8.37 0.00 0.00 2.34
1305 1364 4.260170 CATCTTCCACTTTCTTCTCCCAG 58.740 47.826 0.00 0.00 0.00 4.45
1357 1416 4.841813 TCCAGAGTATGAGTTGGGTTGTAA 59.158 41.667 0.00 0.00 0.00 2.41
1365 1424 4.021104 TCCTTGTGTCCAGAGTATGAGTTG 60.021 45.833 0.00 0.00 0.00 3.16
1391 1450 3.346315 TGGAAAGTCACATGCACCTATG 58.654 45.455 0.00 0.00 0.00 2.23
1424 1483 5.333263 GCATGGTTAATCAAAACAAGTGCAC 60.333 40.000 9.40 9.40 38.58 4.57
1429 1488 6.215121 TGTCAGCATGGTTAATCAAAACAAG 58.785 36.000 0.00 0.00 38.58 3.16
1430 1489 6.154203 TGTCAGCATGGTTAATCAAAACAA 57.846 33.333 0.00 0.00 38.58 2.83
1608 1667 3.134804 AGCTGAATTAGTAATGAGCCGGT 59.865 43.478 17.63 0.00 30.96 5.28
1612 1671 6.197981 GCTCAAAGCTGAATTAGTAATGAGC 58.802 40.000 15.05 15.05 43.22 4.26
1613 1672 6.256539 TCGCTCAAAGCTGAATTAGTAATGAG 59.743 38.462 0.00 0.00 39.60 2.90
1697 1756 0.997196 GTGGCACGTACCTCGAATTC 59.003 55.000 6.34 0.00 42.86 2.17
1828 1887 6.208007 TGTCCTCGAAAGACTGTTTACTCATA 59.792 38.462 14.41 0.00 35.21 2.15
1872 1931 2.159184 TCTGAAGCTCTATTGACTGGCG 60.159 50.000 0.00 0.00 0.00 5.69
1893 1952 3.254024 AATGGAGGCCGTGCTCGTT 62.254 57.895 7.47 0.00 35.01 3.85
1994 2053 0.244721 CTGCTGATCGAGTGTGGACA 59.755 55.000 0.00 0.00 0.00 4.02
2043 2102 2.885676 GACAGCGTGTGTGGTGCAG 61.886 63.158 0.00 0.00 40.56 4.41
2077 2136 7.538678 GGTGTCAATCAATCAGTACATTGTTTC 59.461 37.037 0.00 0.00 35.56 2.78
2192 2253 4.217510 CATCCCATAAATTCTGCCCTGAA 58.782 43.478 0.00 0.00 0.00 3.02
2198 2259 5.075493 AGATGTCCATCCCATAAATTCTGC 58.925 41.667 3.70 0.00 38.58 4.26
2226 2287 5.499004 TCAAACCCCTGCATATAGTATCC 57.501 43.478 0.00 0.00 0.00 2.59
2229 2290 4.562757 GCGATCAAACCCCTGCATATAGTA 60.563 45.833 0.00 0.00 0.00 1.82
2263 2324 9.725019 CCAAATAGTAATTGATATGTCTGGCTA 57.275 33.333 0.00 0.00 0.00 3.93
2280 2341 2.632377 GCTGCAGCTCACCAAATAGTA 58.368 47.619 31.33 0.00 38.21 1.82
2281 2342 1.457346 GCTGCAGCTCACCAAATAGT 58.543 50.000 31.33 0.00 38.21 2.12
2333 2394 0.033109 GGCACCCCTATTTCCTGCTT 60.033 55.000 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.