Multiple sequence alignment - TraesCS1A01G095300

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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 TraesCS1A01G095300 chr1A 100.000 2800 0 0 1 2800 91060813 91058014 0.000000e+00 5171.0
1 TraesCS1A01G095300 chr1B 92.703 2138 97 21 671 2800 148434459 148436545 0.000000e+00 3029.0
2 TraesCS1A01G095300 chr1B 94.205 604 24 6 12 608 148433596 148434195 0.000000e+00 911.0
3 TraesCS1A01G095300 chr1B 95.455 44 1 1 591 634 148434209 148434251 5.000000e-08 69.4
4 TraesCS1A01G095300 chr1D 92.304 2144 94 20 671 2800 93112163 93114249 0.000000e+00 2979.0
5 TraesCS1A01G095300 chr1D 93.223 605 29 6 12 608 93111181 93111781 0.000000e+00 880.0
6 TraesCS1A01G095300 chr1D 91.250 80 3 3 591 669 93111797 93111873 3.810000e-19 106.0


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 TraesCS1A01G095300 chr1A 91058014 91060813 2799 True 5171.000000 5171 100.000 1 2800 1 chr1A.!!$R1 2799
1 TraesCS1A01G095300 chr1B 148433596 148436545 2949 False 1336.466667 3029 94.121 12 2800 3 chr1B.!!$F1 2788
2 TraesCS1A01G095300 chr1D 93111181 93114249 3068 False 1321.666667 2979 92.259 12 2800 3 chr1D.!!$F1 2788

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
705 1038 0.107945 CCAGCTAGGTCAACTCTGGC 60.108 60.0 0.00 0.00 38.00 4.85 F
1418 1758 0.179094 CAATTGGCCGCATGCAGATT 60.179 50.0 19.57 6.81 43.89 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1606 1946 0.106419 GATCCTCGACCACTCCTCCT 60.106 60.0 0.0 0.0 0.0 3.69 R
2256 2597 0.447801 GTTCTCGCCGTGATTTGCAT 59.552 50.0 0.0 0.0 0.0 3.96 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
136 142 7.275888 AGTTGACTGATTGATTGCTTTAACA 57.724 32.000 0.00 0.00 0.00 2.41
168 174 6.541641 AGCTTTCCTGAATTAGCTGTATCAAG 59.458 38.462 0.00 0.00 42.07 3.02
178 184 2.076863 GCTGTATCAAGCAGACCGTTT 58.923 47.619 0.00 0.00 43.01 3.60
184 190 0.593128 CAAGCAGACCGTTTCCCAAG 59.407 55.000 0.00 0.00 0.00 3.61
216 222 3.542969 TCCGATCCTGGGATATCTTCA 57.457 47.619 2.05 1.30 34.60 3.02
217 223 3.165875 TCCGATCCTGGGATATCTTCAC 58.834 50.000 2.05 0.00 34.60 3.18
218 224 2.094494 CCGATCCTGGGATATCTTCACG 60.094 54.545 2.05 0.60 34.60 4.35
280 286 2.308866 ACCCAAATGTCAACTCTAGGGG 59.691 50.000 0.00 0.00 39.38 4.79
323 329 7.495135 CCAAAAATTGGCAAAGAAATACACT 57.505 32.000 3.01 0.00 45.17 3.55
327 333 6.403866 AATTGGCAAAGAAATACACTCACA 57.596 33.333 3.01 0.00 0.00 3.58
405 411 4.326826 ACATATCCATGGCCAATCTAACG 58.673 43.478 10.96 0.00 36.39 3.18
483 493 2.629017 AATCTGATGGCCCAACCTTT 57.371 45.000 0.00 0.00 40.22 3.11
553 563 4.460034 CCATGTTGATCTGATGTTCCAACA 59.540 41.667 18.84 18.84 44.06 3.33
597 640 6.421801 CACACGAGTTGCATCTGATATATTGA 59.578 38.462 1.00 0.00 0.00 2.57
701 1034 1.205893 CTGGTCCAGCTAGGTCAACTC 59.794 57.143 5.79 0.00 39.02 3.01
705 1038 0.107945 CCAGCTAGGTCAACTCTGGC 60.108 60.000 0.00 0.00 38.00 4.85
713 1046 0.678048 GTCAACTCTGGCATCCCCAC 60.678 60.000 0.00 0.00 39.18 4.61
738 1071 1.149987 AACTCCGACGCGCAAAAATA 58.850 45.000 5.73 0.00 0.00 1.40
739 1072 1.149987 ACTCCGACGCGCAAAAATAA 58.850 45.000 5.73 0.00 0.00 1.40
740 1073 1.532007 ACTCCGACGCGCAAAAATAAA 59.468 42.857 5.73 0.00 0.00 1.40
741 1074 2.160813 ACTCCGACGCGCAAAAATAAAT 59.839 40.909 5.73 0.00 0.00 1.40
742 1075 3.371591 ACTCCGACGCGCAAAAATAAATA 59.628 39.130 5.73 0.00 0.00 1.40
743 1076 4.142859 ACTCCGACGCGCAAAAATAAATAA 60.143 37.500 5.73 0.00 0.00 1.40
744 1077 4.336101 TCCGACGCGCAAAAATAAATAAG 58.664 39.130 5.73 0.00 0.00 1.73
745 1078 4.092816 CCGACGCGCAAAAATAAATAAGT 58.907 39.130 5.73 0.00 0.00 2.24
746 1079 4.555747 CCGACGCGCAAAAATAAATAAGTT 59.444 37.500 5.73 0.00 0.00 2.66
747 1080 5.733572 CCGACGCGCAAAAATAAATAAGTTA 59.266 36.000 5.73 0.00 0.00 2.24
748 1081 6.412653 CCGACGCGCAAAAATAAATAAGTTAT 59.587 34.615 5.73 0.00 33.58 1.89
749 1082 7.044576 CCGACGCGCAAAAATAAATAAGTTATT 60.045 33.333 5.73 2.10 43.02 1.40
750 1083 8.935941 CGACGCGCAAAAATAAATAAGTTATTA 58.064 29.630 5.73 0.00 40.79 0.98
791 1124 9.288576 CCAAAGAATCAGCAGTATCCATTAATA 57.711 33.333 0.00 0.00 0.00 0.98
843 1177 7.701924 TGCAATCGGTGATCTCAAAAATAATTC 59.298 33.333 0.00 0.00 0.00 2.17
931 1265 1.067212 GACGCAACGGAGTCCAGATAT 59.933 52.381 10.49 0.00 45.00 1.63
932 1266 1.480954 ACGCAACGGAGTCCAGATATT 59.519 47.619 10.49 0.00 45.00 1.28
1212 1546 3.177249 GACAACTACGGCGTCGGC 61.177 66.667 19.21 9.07 41.39 5.54
1359 1699 6.033196 GCTACTGGTAATATACATTACACGCG 59.967 42.308 3.53 3.53 45.66 6.01
1370 1710 4.426416 ACATTACACGCGCTGATTAGTTA 58.574 39.130 5.73 0.00 0.00 2.24
1418 1758 0.179094 CAATTGGCCGCATGCAGATT 60.179 50.000 19.57 6.81 43.89 2.40
1494 1834 3.141522 AACTCGAACGACGGCCACA 62.142 57.895 2.24 0.00 42.82 4.17
1535 1875 2.276309 GAGCCATCAAGGACCTGGGG 62.276 65.000 0.00 0.00 41.22 4.96
1631 1971 2.036731 TGGTCGAGGATCCACCGT 59.963 61.111 15.82 0.00 44.74 4.83
1640 1980 4.148825 ATCCACCGTCGCAGCTCC 62.149 66.667 0.00 0.00 0.00 4.70
1926 2267 6.142498 TGTAAATCCCCATATTCTTTGGCAT 58.858 36.000 0.00 0.00 32.60 4.40
1936 2277 7.717875 CCCATATTCTTTGGCATTTCATTTCAT 59.282 33.333 0.00 0.00 32.60 2.57
2011 2352 3.802948 AATACTGAACGGGTCTGCTAG 57.197 47.619 0.00 0.00 0.00 3.42
2074 2415 6.886459 CCAATAGAGATACCAATAACATGGGG 59.114 42.308 0.00 0.00 45.18 4.96
2106 2447 3.014036 ACGCAAAGACGTGCACAG 58.986 55.556 18.64 12.16 46.28 3.66
2241 2582 1.472480 GGTTTGCGCCATTGTCAGTAT 59.528 47.619 4.18 0.00 0.00 2.12
2256 2597 4.183865 GTCAGTATGTAGCAGCATTGTCA 58.816 43.478 0.00 0.00 37.40 3.58
2285 2626 4.988065 GCGAGAACAGCCACTGTA 57.012 55.556 0.00 0.00 44.62 2.74
2288 2629 0.244994 CGAGAACAGCCACTGTAGCT 59.755 55.000 0.00 0.00 44.62 3.32
2378 2719 6.599638 GCAGTTGTCTAACATAGGGAGAAAAT 59.400 38.462 0.00 0.00 39.30 1.82
2384 2725 9.832445 TGTCTAACATAGGGAGAAAATTGTATC 57.168 33.333 0.00 0.00 0.00 2.24
2424 2770 3.955650 ATGGATAGTTAACCGATCCCG 57.044 47.619 24.40 0.00 38.75 5.14
2578 2924 6.484288 TGTTGAACTCCTGAATATCACCAAT 58.516 36.000 0.00 0.00 0.00 3.16
2661 3012 1.170442 CATGAGTGATGTGCCAAGCA 58.830 50.000 0.00 0.00 35.60 3.91
2693 3044 2.755103 CCTATTTGTTCACAGAAGGCCC 59.245 50.000 0.00 0.00 0.00 5.80
2696 3047 1.619654 TTGTTCACAGAAGGCCCATG 58.380 50.000 0.00 0.00 0.00 3.66
2702 3053 1.072266 ACAGAAGGCCCATGGTGTTA 58.928 50.000 11.73 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.848710 TTAAATTATATATGGACCGAACAACCA 57.151 29.630 0.00 0.00 38.09 3.67
41 42 1.482182 TGATAGCGACTGGTGCTGAAT 59.518 47.619 6.21 0.00 43.85 2.57
116 122 8.579682 AAGTTTGTTAAAGCAATCAATCAGTC 57.420 30.769 0.00 0.00 0.00 3.51
136 142 7.231519 ACAGCTAATTCAGGAAAGCTTAAGTTT 59.768 33.333 0.00 0.86 42.52 2.66
168 174 0.534203 TCACTTGGGAAACGGTCTGC 60.534 55.000 0.00 0.00 0.00 4.26
178 184 6.940298 GGATCGGAATAATAATTCACTTGGGA 59.060 38.462 0.99 0.00 42.88 4.37
184 190 6.472887 TCCCAGGATCGGAATAATAATTCAC 58.527 40.000 0.00 0.00 42.88 3.18
322 328 4.394712 GGGCGGTGGTCCTGTGAG 62.395 72.222 0.00 0.00 34.09 3.51
405 411 6.265196 TGAAATGGCCAGATACAAATGATACC 59.735 38.462 13.05 0.00 0.00 2.73
457 467 3.845781 TGGGCCATCAGATTTCTCTAC 57.154 47.619 0.00 0.00 0.00 2.59
553 563 2.095059 GTGATTGCGCAACTCCAATTCT 60.095 45.455 27.64 5.78 32.20 2.40
687 1020 0.610174 TGCCAGAGTTGACCTAGCTG 59.390 55.000 0.00 0.00 0.00 4.24
701 1034 3.099141 AGTTAATTTGTGGGGATGCCAG 58.901 45.455 5.30 0.00 0.00 4.85
705 1038 3.377172 GTCGGAGTTAATTTGTGGGGATG 59.623 47.826 0.00 0.00 0.00 3.51
713 1046 0.440758 TGCGCGTCGGAGTTAATTTG 59.559 50.000 8.43 0.00 0.00 2.32
739 1072 9.236006 GGACCATGCATGAGATAATAACTTATT 57.764 33.333 28.31 0.00 0.00 1.40
740 1073 7.831193 GGGACCATGCATGAGATAATAACTTAT 59.169 37.037 28.31 0.00 0.00 1.73
741 1074 7.168219 GGGACCATGCATGAGATAATAACTTA 58.832 38.462 28.31 0.00 0.00 2.24
742 1075 6.006449 GGGACCATGCATGAGATAATAACTT 58.994 40.000 28.31 0.00 0.00 2.66
743 1076 5.073554 TGGGACCATGCATGAGATAATAACT 59.926 40.000 28.31 0.00 0.00 2.24
744 1077 5.316167 TGGGACCATGCATGAGATAATAAC 58.684 41.667 28.31 8.32 0.00 1.89
745 1078 5.581350 TGGGACCATGCATGAGATAATAA 57.419 39.130 28.31 2.96 0.00 1.40
746 1079 5.581350 TTGGGACCATGCATGAGATAATA 57.419 39.130 28.31 5.21 0.00 0.98
747 1080 4.458256 TTGGGACCATGCATGAGATAAT 57.542 40.909 28.31 5.80 0.00 1.28
748 1081 3.949586 TTGGGACCATGCATGAGATAA 57.050 42.857 28.31 12.71 0.00 1.75
749 1082 3.459227 TCTTTGGGACCATGCATGAGATA 59.541 43.478 28.31 7.34 0.00 1.98
750 1083 2.242965 TCTTTGGGACCATGCATGAGAT 59.757 45.455 28.31 12.77 0.00 2.75
751 1084 1.634973 TCTTTGGGACCATGCATGAGA 59.365 47.619 28.31 16.93 0.00 3.27
752 1085 2.133281 TCTTTGGGACCATGCATGAG 57.867 50.000 28.31 19.16 0.00 2.90
753 1086 2.601240 TTCTTTGGGACCATGCATGA 57.399 45.000 28.31 4.41 0.00 3.07
754 1087 2.761767 TGATTCTTTGGGACCATGCATG 59.238 45.455 20.19 20.19 0.00 4.06
755 1088 3.028850 CTGATTCTTTGGGACCATGCAT 58.971 45.455 0.00 0.00 0.00 3.96
756 1089 2.449464 CTGATTCTTTGGGACCATGCA 58.551 47.619 0.00 0.00 0.00 3.96
757 1090 1.135721 GCTGATTCTTTGGGACCATGC 59.864 52.381 0.00 0.00 0.00 4.06
758 1091 2.426024 CTGCTGATTCTTTGGGACCATG 59.574 50.000 0.00 0.00 0.00 3.66
861 1195 9.432982 ACCCTGGATTGCTCAATTTTTATTATA 57.567 29.630 0.00 0.00 0.00 0.98
885 1219 1.069227 GGATGCGACACTGTTTTGACC 60.069 52.381 0.00 0.00 0.00 4.02
931 1265 4.396166 GTGCTGCTCTTCTTTATAAGCCAA 59.604 41.667 0.00 0.00 33.79 4.52
932 1266 3.941483 GTGCTGCTCTTCTTTATAAGCCA 59.059 43.478 0.00 0.00 33.79 4.75
1105 1439 4.927782 GCACCACACCGTCAGCCA 62.928 66.667 0.00 0.00 0.00 4.75
1334 1674 6.033196 CGCGTGTAATGTATATTACCAGTAGC 59.967 42.308 16.88 13.51 45.19 3.58
1335 1675 6.033196 GCGCGTGTAATGTATATTACCAGTAG 59.967 42.308 16.88 11.02 45.19 2.57
1336 1676 5.858049 GCGCGTGTAATGTATATTACCAGTA 59.142 40.000 16.88 0.00 45.19 2.74
1337 1677 4.682860 GCGCGTGTAATGTATATTACCAGT 59.317 41.667 16.88 0.00 45.19 4.00
1338 1678 4.921515 AGCGCGTGTAATGTATATTACCAG 59.078 41.667 16.88 12.44 45.19 4.00
1339 1679 4.682401 CAGCGCGTGTAATGTATATTACCA 59.318 41.667 16.88 5.51 45.19 3.25
1340 1680 4.919168 TCAGCGCGTGTAATGTATATTACC 59.081 41.667 16.88 9.28 45.19 2.85
1341 1681 6.627690 ATCAGCGCGTGTAATGTATATTAC 57.372 37.500 8.43 13.76 45.71 1.89
1344 1684 6.387465 ACTAATCAGCGCGTGTAATGTATAT 58.613 36.000 8.43 0.00 0.00 0.86
1359 1699 2.930040 TGCACGAAGCTAACTAATCAGC 59.070 45.455 6.22 0.00 45.94 4.26
1370 1710 1.466167 GTTCATGTCATGCACGAAGCT 59.534 47.619 8.03 0.00 45.94 3.74
1418 1758 0.972471 TCTCCGGCATCAAGCTCAGA 60.972 55.000 0.00 0.00 44.79 3.27
1494 1834 1.620739 ATCATGAGGTGCGGCTCACT 61.621 55.000 7.64 0.00 44.98 3.41
1606 1946 0.106419 GATCCTCGACCACTCCTCCT 60.106 60.000 0.00 0.00 0.00 3.69
1926 2267 7.162761 AGGATGAATGCAACAATGAAATGAAA 58.837 30.769 0.00 0.00 0.00 2.69
1936 2277 3.765381 TCTGGAAGGATGAATGCAACAA 58.235 40.909 0.00 0.00 0.00 2.83
1992 2333 2.688958 GACTAGCAGACCCGTTCAGTAT 59.311 50.000 0.00 0.00 0.00 2.12
2011 2352 4.513318 GCCTTAGATGAAATGGTAGCAGAC 59.487 45.833 0.00 0.00 0.00 3.51
2074 2415 1.234615 TGCGTTGCTTGCCTACCTTC 61.235 55.000 0.00 0.00 0.00 3.46
2106 2447 2.857748 GTTTGTTTGGCTAGTGTTGTGC 59.142 45.455 0.00 0.00 0.00 4.57
2256 2597 0.447801 GTTCTCGCCGTGATTTGCAT 59.552 50.000 0.00 0.00 0.00 3.96
2384 2725 4.336433 CCATAGACATTGCCCTTGTACTTG 59.664 45.833 0.00 0.00 0.00 3.16
2424 2770 5.940470 TCTTTGAGGTAAGCTCTTCCAATTC 59.060 40.000 0.00 0.00 0.00 2.17
2661 3012 3.245229 TGAACAAATAGGGACATGCCAGT 60.245 43.478 8.20 0.00 38.95 4.00
2668 3019 4.651778 CCTTCTGTGAACAAATAGGGACA 58.348 43.478 0.00 0.00 0.00 4.02
2693 3044 2.577606 TTGTCCCACCTAACACCATG 57.422 50.000 0.00 0.00 0.00 3.66
2696 3047 2.574824 AGGTATTGTCCCACCTAACACC 59.425 50.000 0.00 0.00 43.48 4.16


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

AutoCloner maintained by Alex Coulton.