Multiple sequence alignment - TraesCS7B01G091100

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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 TraesCS7B01G091100 chr7B 100.000 2255 0 0 1 2255 105229638 105231892 0 4165
1 TraesCS7B01G091100 chr7B 95.475 2254 101 1 1 2254 662724472 662722220 0 3596
2 TraesCS7B01G091100 chr6D 95.741 2254 95 1 1 2254 389255237 389252985 0 3629
3 TraesCS7B01G091100 chr6D 95.652 2254 97 1 1 2254 389250442 389248190 0 3618
4 TraesCS7B01G091100 chr5D 95.741 2254 94 2 1 2254 503239094 503236843 0 3629
5 TraesCS7B01G091100 chr5D 95.608 2254 94 3 1 2254 503243340 503241092 0 3609
6 TraesCS7B01G091100 chr5D 95.563 2254 96 2 1 2254 503229313 503227064 0 3605
7 TraesCS7B01G091100 chr5D 95.475 2254 95 2 1 2254 503267234 503269480 0 3591
8 TraesCS7B01G091100 chr3A 95.608 2254 97 2 1 2254 66007064 66009315 0 3613
9 TraesCS7B01G091100 chr3D 95.519 2254 99 2 1 2254 589265455 589267706 0 3602


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 TraesCS7B01G091100 chr7B 105229638 105231892 2254 False 4165.0 4165 100.0000 1 2255 1 chr7B.!!$F1 2254
1 TraesCS7B01G091100 chr7B 662722220 662724472 2252 True 3596.0 3596 95.4750 1 2254 1 chr7B.!!$R1 2253
2 TraesCS7B01G091100 chr6D 389248190 389255237 7047 True 3623.5 3629 95.6965 1 2254 2 chr6D.!!$R1 2253
3 TraesCS7B01G091100 chr5D 503236843 503243340 6497 True 3619.0 3629 95.6745 1 2254 2 chr5D.!!$R2 2253
4 TraesCS7B01G091100 chr5D 503227064 503229313 2249 True 3605.0 3605 95.5630 1 2254 1 chr5D.!!$R1 2253
5 TraesCS7B01G091100 chr5D 503267234 503269480 2246 False 3591.0 3591 95.4750 1 2254 1 chr5D.!!$F1 2253
6 TraesCS7B01G091100 chr3A 66007064 66009315 2251 False 3613.0 3613 95.6080 1 2254 1 chr3A.!!$F1 2253
7 TraesCS7B01G091100 chr3D 589265455 589267706 2251 False 3602.0 3602 95.5190 1 2254 1 chr3D.!!$F1 2253

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
166 167 0.548682 AGGAGTCTGGGCCATGTCTT 60.549 55.0 6.72 0.0 0.00 3.01 F
342 346 0.699577 TGTTGTTCCCCTCCCAAGGA 60.700 55.0 0.00 0.0 46.67 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1079 5332 0.035881 CTTGACCTGGCTCTGCTTCA 59.964 55.000 0.0 0.0 0.0 3.02 R
1532 10580 1.305887 GGACCGAGGAGAAAGGGGA 60.306 63.158 0.0 0.0 0.0 4.81 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
30 31 7.387265 TCCTATGCTTATTCCTCAAATACCA 57.613 36.000 0.00 0.00 29.39 3.25
63 64 3.991367 TCTCCGAGAAAAGAAGTTGACC 58.009 45.455 0.00 0.00 0.00 4.02
83 84 3.400188 CCGTAGGCCTTCCACCTT 58.600 61.111 12.58 0.00 46.14 3.50
166 167 0.548682 AGGAGTCTGGGCCATGTCTT 60.549 55.000 6.72 0.00 0.00 3.01
194 195 1.483827 GTGTGGCTGATCATCCTCTCA 59.516 52.381 16.28 10.00 0.00 3.27
212 213 4.285020 TCTCAGACCAGCTACTGATCATT 58.715 43.478 14.68 0.00 41.35 2.57
254 255 3.762288 TCACCAACTAGCTAATCAGACGT 59.238 43.478 0.00 0.00 0.00 4.34
283 284 1.383523 CTTGGGCGGATTTCTCCTTC 58.616 55.000 0.00 0.00 39.65 3.46
342 346 0.699577 TGTTGTTCCCCTCCCAAGGA 60.700 55.000 0.00 0.00 46.67 3.36
345 349 0.699577 TGTTCCCCTCCCAAGGACAA 60.700 55.000 0.00 0.00 46.67 3.18
353 357 3.267031 CCCTCCCAAGGACAAGTTCTTAT 59.733 47.826 0.00 0.00 46.67 1.73
397 401 1.670791 GAAACACCACTTCCCGTTCA 58.329 50.000 0.00 0.00 0.00 3.18
435 439 1.226974 GCTGCGAGCGTTCATCCTA 60.227 57.895 0.00 0.00 0.00 2.94
518 522 9.281371 TCATAGATAAAGCAGATTCAGAATTGG 57.719 33.333 0.00 0.00 0.00 3.16
575 579 6.560003 TTCAGATTATTAGCCTGGAGTTCA 57.440 37.500 0.00 0.00 0.00 3.18
596 600 1.065491 CCACCAGCAGTATAGCCAACA 60.065 52.381 0.00 0.00 34.23 3.33
639 643 2.852449 ACAAGCCTCTTATCCATTCCCA 59.148 45.455 0.00 0.00 0.00 4.37
665 669 3.072468 TGGCGGGGGAGTAAGTCG 61.072 66.667 0.00 0.00 0.00 4.18
727 731 4.759782 CTCGAACTGATTACTTCCACCAT 58.240 43.478 0.00 0.00 0.00 3.55
791 795 5.986135 CGTCCCATCGAGAAAGAGAATTAAT 59.014 40.000 0.00 0.00 0.00 1.40
794 798 6.986817 TCCCATCGAGAAAGAGAATTAATGAC 59.013 38.462 0.00 0.00 0.00 3.06
799 803 7.261325 TCGAGAAAGAGAATTAATGACTCCTG 58.739 38.462 15.02 4.58 0.00 3.86
818 822 3.771978 GGCAAAGGGGCGAGAAAA 58.228 55.556 0.00 0.00 33.57 2.29
913 917 3.543680 ATTGTGAACTGGTCCTATCGG 57.456 47.619 0.00 0.00 0.00 4.18
939 943 6.307776 AGTAGGATTGACTATGGATTCGAGA 58.692 40.000 0.00 0.00 0.00 4.04
967 5220 5.004061 CGCACATGCTTTCATAAAATCTGTG 59.996 40.000 1.82 0.00 39.32 3.66
969 5222 5.865013 CACATGCTTTCATAAAATCTGTGCA 59.135 36.000 0.00 0.00 0.00 4.57
1053 5306 4.079901 TCGATACTGGTAGGAGAAGAACCT 60.080 45.833 0.00 0.00 41.05 3.50
1092 5345 0.324285 AAGAGGTGAAGCAGAGCCAG 59.676 55.000 0.00 0.00 0.00 4.85
1145 10193 3.509575 TGCGCCAAAGATCTTACCATTTT 59.490 39.130 8.75 0.00 0.00 1.82
1158 10206 3.502123 ACCATTTTCGAAGGAACTGGA 57.498 42.857 10.65 0.00 40.86 3.86
1179 10227 7.869429 ACTGGAGCTACATTTCTTTTCAATTTG 59.131 33.333 0.00 0.00 0.00 2.32
1206 10254 8.954350 CATTCAAGAGTTTCTATCTGTTTCCAT 58.046 33.333 0.00 0.00 0.00 3.41
1222 10270 3.524095 TCCATGCCCTTTTCTTGAGAA 57.476 42.857 0.00 0.00 0.00 2.87
1226 10274 3.576078 TGCCCTTTTCTTGAGAACTCA 57.424 42.857 0.00 0.00 37.91 3.41
1255 10303 9.771534 ACATGAGGATAAATTACTTCTCTTAGC 57.228 33.333 0.00 0.00 0.00 3.09
1368 10416 8.365647 TCTTACCGAGACAGAATTTAGAACTTT 58.634 33.333 0.00 0.00 0.00 2.66
1425 10473 7.331934 CCTTTGTAGAAAGACTGATTCATTCGA 59.668 37.037 13.67 0.00 41.12 3.71
1458 10506 1.526575 CCCAACTCCGTTGCATTGCT 61.527 55.000 10.49 0.00 41.62 3.91
1480 10528 7.062322 TGCTAGAATCCATGTTCCATATTTGT 58.938 34.615 0.00 0.00 0.00 2.83
1494 10542 1.821216 ATTTGTAGCGGGTTGACCTG 58.179 50.000 4.58 4.58 45.30 4.00
1532 10580 2.264455 ACAATCCTCTTCCTGCTGAGT 58.736 47.619 0.00 0.00 0.00 3.41
1551 10599 2.722201 CCCCTTTCTCCTCGGTCCG 61.722 68.421 4.39 4.39 0.00 4.79
1552 10600 1.982938 CCCTTTCTCCTCGGTCCGT 60.983 63.158 11.88 0.00 0.00 4.69
1553 10601 1.215647 CCTTTCTCCTCGGTCCGTG 59.784 63.158 11.88 8.95 0.00 4.94
1558 10606 2.045242 TCCTCGGTCCGTGGAGAG 60.045 66.667 27.23 10.16 43.13 3.20
1563 10611 0.601558 TCGGTCCGTGGAGAGAAAAG 59.398 55.000 11.88 0.00 0.00 2.27
1580 10628 1.958288 AAGATGTAGGACTGGTGCCT 58.042 50.000 0.00 0.00 39.56 4.75
1607 10655 3.575630 TCATCACGGAAGAAAGAACTCG 58.424 45.455 0.00 0.00 0.00 4.18
1740 10789 9.232473 GAATTGTCTTTTCTGTATACTTTCCCT 57.768 33.333 4.17 0.00 0.00 4.20
1759 10808 2.029290 CCTATTCTATTGCTACCGCGGT 60.029 50.000 36.01 36.01 39.65 5.68
1793 10842 8.955388 CAATCGATCGGATCATATAGATATCCT 58.045 37.037 16.41 0.00 37.60 3.24
1852 10901 0.465460 TCACCAAAGCACGAAAGCCT 60.465 50.000 0.00 0.00 34.23 4.58
1916 10965 4.196971 GGATAAGCTCACATTAACCCGTT 58.803 43.478 0.00 0.00 0.00 4.44
1920 10969 7.658575 GGATAAGCTCACATTAACCCGTTAATA 59.341 37.037 11.48 0.00 42.11 0.98
1938 10987 6.205853 CGTTAATATTGGATCCAATTCGGGAA 59.794 38.462 38.12 23.08 43.32 3.97
2038 11087 4.262079 GCAAACGCTGTACCTAGAGGATAT 60.262 45.833 1.60 0.00 38.94 1.63
2061 11110 6.658555 TGGATAGAGGAAGAGGGAAAAATT 57.341 37.500 0.00 0.00 0.00 1.82
2127 11176 4.347583 AGATAGAAGAGCCCAGATTCCAAG 59.652 45.833 0.00 0.00 0.00 3.61
2164 11213 6.546428 ACTCGAAAAGGATCCTTCTGATTA 57.454 37.500 27.20 10.15 34.84 1.75
2183 11232 5.957168 TGATTATCAAAGAATGAGGGGCAAA 59.043 36.000 0.00 0.00 42.53 3.68
2254 11303 7.761409 TGATCTGCATATGTTTGGTAAAAGAC 58.239 34.615 4.29 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 7.387265 TGGTATTTGAGGAATAAGCATAGGA 57.613 36.000 0.00 0.00 32.20 2.94
9 10 9.812347 AATGATGGTATTTGAGGAATAAGCATA 57.188 29.630 0.00 0.00 32.20 3.14
24 25 6.414732 TCGGAGAAGAAACAATGATGGTATT 58.585 36.000 0.00 0.00 0.00 1.89
30 31 6.936900 TCTTTTCTCGGAGAAGAAACAATGAT 59.063 34.615 18.93 0.00 35.37 2.45
63 64 2.267961 GTGGAAGGCCTACGGGTG 59.732 66.667 5.16 0.00 34.31 4.61
160 161 1.279271 GCCACACTGGGACTAAGACAT 59.721 52.381 0.00 0.00 38.19 3.06
194 195 2.158842 GGCAATGATCAGTAGCTGGTCT 60.159 50.000 14.11 0.00 41.72 3.85
342 346 4.689345 GGTGAGTAACGCATAAGAACTTGT 59.311 41.667 0.00 0.00 0.00 3.16
345 349 3.675228 CGGGTGAGTAACGCATAAGAACT 60.675 47.826 0.00 0.00 41.73 3.01
353 357 1.372004 CGAACGGGTGAGTAACGCA 60.372 57.895 0.00 0.00 41.73 5.24
419 423 0.806102 GCTTAGGATGAACGCTCGCA 60.806 55.000 0.00 0.00 0.00 5.10
422 426 1.576356 CTGGCTTAGGATGAACGCTC 58.424 55.000 0.00 0.00 0.00 5.03
435 439 1.988107 TGGAGAGTTTGATCCTGGCTT 59.012 47.619 0.00 0.00 36.50 4.35
494 498 7.943447 AGCCAATTCTGAATCTGCTTTATCTAT 59.057 33.333 16.40 0.00 0.00 1.98
499 503 6.350445 GGAAAGCCAATTCTGAATCTGCTTTA 60.350 38.462 30.84 0.00 42.57 1.85
575 579 1.065418 GTTGGCTATACTGCTGGTGGT 60.065 52.381 0.00 0.00 0.00 4.16
596 600 2.963782 GGGATTGACGTGATAGGGTAGT 59.036 50.000 0.00 0.00 0.00 2.73
678 682 6.736581 TGATTATCCCTAAACCCAATGTGAA 58.263 36.000 0.00 0.00 0.00 3.18
791 795 1.492133 CCCCTTTGCCTCAGGAGTCA 61.492 60.000 0.00 0.00 32.41 3.41
794 798 2.044551 GCCCCTTTGCCTCAGGAG 60.045 66.667 0.00 0.00 32.41 3.69
799 803 0.893727 TTTTCTCGCCCCTTTGCCTC 60.894 55.000 0.00 0.00 0.00 4.70
818 822 0.915364 GGAGGAAGAGTGGCCTTGAT 59.085 55.000 3.32 0.00 33.84 2.57
913 917 6.982852 TCGAATCCATAGTCAATCCTACTTC 58.017 40.000 0.00 0.00 0.00 3.01
951 955 8.445493 GGGAAAATTGCACAGATTTTATGAAAG 58.555 33.333 7.41 0.00 36.96 2.62
1079 5332 0.035881 CTTGACCTGGCTCTGCTTCA 59.964 55.000 0.00 0.00 0.00 3.02
1088 5341 2.107204 ACCCATATCATCTTGACCTGGC 59.893 50.000 0.00 0.00 32.71 4.85
1092 5345 2.417719 GCGACCCATATCATCTTGACC 58.582 52.381 0.00 0.00 0.00 4.02
1145 10193 1.919240 TGTAGCTCCAGTTCCTTCGA 58.081 50.000 0.00 0.00 0.00 3.71
1158 10206 8.611654 AATGCAAATTGAAAAGAAATGTAGCT 57.388 26.923 0.00 0.00 0.00 3.32
1179 10227 7.094634 TGGAAACAGATAGAAACTCTTGAATGC 60.095 37.037 0.00 0.00 35.01 3.56
1206 10254 3.576078 TGAGTTCTCAAGAAAAGGGCA 57.424 42.857 0.00 0.00 35.58 5.36
1255 10303 7.537306 CCGTTATCCTTTTTCTTGTATGTGTTG 59.463 37.037 0.00 0.00 0.00 3.33
1344 10392 8.365647 AGAAAGTTCTAAATTCTGTCTCGGTAA 58.634 33.333 0.00 0.00 35.34 2.85
1402 10450 8.777865 ATTCGAATGAATCAGTCTTTCTACAA 57.222 30.769 10.50 0.00 40.90 2.41
1425 10473 3.325135 GGAGTTGGGTCCTCATATCGATT 59.675 47.826 1.71 0.00 33.30 3.34
1480 10528 1.369692 CACACAGGTCAACCCGCTA 59.630 57.895 0.00 0.00 38.74 4.26
1494 10542 3.319137 TGTACCATGAGAGAAGCACAC 57.681 47.619 0.00 0.00 0.00 3.82
1532 10580 1.305887 GGACCGAGGAGAAAGGGGA 60.306 63.158 0.00 0.00 0.00 4.81
1551 10599 5.415221 CAGTCCTACATCTTTTCTCTCCAC 58.585 45.833 0.00 0.00 0.00 4.02
1552 10600 4.467795 CCAGTCCTACATCTTTTCTCTCCA 59.532 45.833 0.00 0.00 0.00 3.86
1553 10601 4.468153 ACCAGTCCTACATCTTTTCTCTCC 59.532 45.833 0.00 0.00 0.00 3.71
1558 10606 3.010420 GGCACCAGTCCTACATCTTTTC 58.990 50.000 0.00 0.00 0.00 2.29
1580 10628 5.462530 TCTTTCTTCCGTGATGAACTGTA 57.537 39.130 2.98 0.00 0.00 2.74
1740 10789 3.319972 AGAACCGCGGTAGCAATAGAATA 59.680 43.478 34.44 0.00 45.49 1.75
1759 10808 4.881920 TGATCCGATCGATTGCATAAGAA 58.118 39.130 18.66 0.00 0.00 2.52
1793 10842 5.301555 TCGATGACCTATGTTGTGTTGAAA 58.698 37.500 0.00 0.00 0.00 2.69
1916 10965 8.719645 AAATTCCCGAATTGGATCCAATATTA 57.280 30.769 34.78 19.29 44.86 0.98
1938 10987 3.839778 TCCCGAAACTTCCCAAGAAAAT 58.160 40.909 0.00 0.00 0.00 1.82
1987 11036 9.488762 TCAATAGAGAACCTTTTCCTCTGTATA 57.511 33.333 0.00 0.00 28.56 1.47
2038 11087 6.217487 TCAATTTTTCCCTCTTCCTCTATCCA 59.783 38.462 0.00 0.00 0.00 3.41
2127 11176 5.915196 CCTTTTCGAGTTTCCATTTCTTCAC 59.085 40.000 0.00 0.00 0.00 3.18
2164 11213 3.102204 CCTTTGCCCCTCATTCTTTGAT 58.898 45.455 0.00 0.00 32.72 2.57
2183 11232 5.896073 AATCTTTCTCGGTATCAATCCCT 57.104 39.130 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.