Multiple sequence alignment - TraesCS1D01G149300

Loading Multiple Alignment...

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 TraesCS1D01G149300 chr1D 100.000 3060 0 0 1 3060 205479587 205482646 0 5651
1 TraesCS1D01G149300 chr1A 94.835 1665 64 10 1 1651 262013317 262014973 0 2579
2 TraesCS1D01G149300 chr1A 93.853 1399 64 9 1674 3060 262842219 262840831 0 2087
3 TraesCS1D01G149300 chr1B 91.958 1517 73 18 597 2083 301255721 301257218 0 2080
4 TraesCS1D01G149300 chr1B 94.515 948 47 4 2114 3060 301257213 301258156 0 1458
5 TraesCS1D01G149300 chr1B 95.567 609 20 3 1 605 301253530 301254135 0 968


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 TraesCS1D01G149300 chr1D 205479587 205482646 3059 False 5651 5651 100.000000 1 3060 1 chr1D.!!$F1 3059
1 TraesCS1D01G149300 chr1A 262013317 262014973 1656 False 2579 2579 94.835000 1 1651 1 chr1A.!!$F1 1650
2 TraesCS1D01G149300 chr1A 262840831 262842219 1388 True 2087 2087 93.853000 1674 3060 1 chr1A.!!$R1 1386
3 TraesCS1D01G149300 chr1B 301253530 301258156 4626 False 1502 2080 94.013333 1 3060 3 chr1B.!!$F1 3059


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
940 2541 0.247736 CCAGTCCAGTACAGCACTCC 59.752 60.0 0.0 0.0 34.26 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2738 4381 0.473326 GAGGAGATTGCAGAGGCCAT 59.527 55.0 5.01 0.0 40.13 4.4 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
352 356 1.469335 GGTGGTCGTCCTCCTTGTCA 61.469 60.000 11.86 0.00 42.33 3.58
363 367 0.615331 TCCTTGTCATCTCTGTGGCC 59.385 55.000 0.00 0.00 0.00 5.36
370 374 0.323178 CATCTCTGTGGCCCAGCTTT 60.323 55.000 14.49 1.58 41.25 3.51
437 441 1.202348 GGCCAACATGTTAACTCCAGC 59.798 52.381 11.53 5.77 0.00 4.85
474 479 4.724074 TTCCTGCCAAGAAATGCTAATG 57.276 40.909 0.00 0.00 0.00 1.90
553 558 4.643387 ACTCCGTTGGGGCTGCAC 62.643 66.667 0.50 0.00 34.94 4.57
570 575 1.395608 GCACCACGCTAATTCGCTTAA 59.604 47.619 0.08 0.00 37.77 1.85
571 576 2.031683 GCACCACGCTAATTCGCTTAAT 59.968 45.455 0.08 0.00 37.77 1.40
572 577 3.246699 GCACCACGCTAATTCGCTTAATA 59.753 43.478 0.08 0.00 37.77 0.98
577 582 5.339611 CCACGCTAATTCGCTTAATAATTGC 59.660 40.000 0.08 0.00 0.00 3.56
610 2211 4.085302 GCTGCTGCGTCTGTAGAG 57.915 61.111 0.00 0.00 0.00 2.43
619 2220 5.748630 TGCTGCGTCTGTAGAGTAAAATATG 59.251 40.000 0.00 0.00 0.00 1.78
641 2242 5.076182 TGAACACATTCCTGCCAAGAAATA 58.924 37.500 0.00 0.00 33.49 1.40
652 2253 8.548880 TCCTGCCAAGAAATACTAATAGTAGT 57.451 34.615 8.10 8.10 43.27 2.73
653 2254 9.650714 TCCTGCCAAGAAATACTAATAGTAGTA 57.349 33.333 12.13 12.13 44.93 1.82
668 2269 7.527568 AATAGTAGTACTATCTTGTGCCCTC 57.472 40.000 20.61 0.00 40.32 4.30
703 2304 8.838365 GCATCAGATTGATCTCTTAAGATTTGT 58.162 33.333 5.44 0.00 42.46 2.83
815 2416 2.500229 CCTTTGGCAAGAAGACGGTAA 58.500 47.619 0.00 0.00 30.57 2.85
816 2417 3.081804 CCTTTGGCAAGAAGACGGTAAT 58.918 45.455 0.00 0.00 30.57 1.89
913 2514 2.519771 TTTGGGCGGACTCTAGTCTA 57.480 50.000 9.84 0.00 44.20 2.59
926 2527 6.462067 GGACTCTAGTCTAGTCTAGTCCAGTC 60.462 50.000 26.78 22.83 44.20 3.51
927 2528 5.364735 ACTCTAGTCTAGTCTAGTCCAGTCC 59.635 48.000 19.35 0.00 38.66 3.85
928 2529 5.278873 TCTAGTCTAGTCTAGTCCAGTCCA 58.721 45.833 19.35 0.39 38.66 4.02
929 2530 4.497291 AGTCTAGTCTAGTCCAGTCCAG 57.503 50.000 6.77 0.00 0.00 3.86
930 2531 3.847780 AGTCTAGTCTAGTCCAGTCCAGT 59.152 47.826 6.77 0.00 0.00 4.00
940 2541 0.247736 CCAGTCCAGTACAGCACTCC 59.752 60.000 0.00 0.00 34.26 3.85
1005 2611 1.615124 TTGGGGAGGCGGAATGAGA 60.615 57.895 0.00 0.00 0.00 3.27
1638 3262 0.529378 GCCCTCCATTTGCAGAGTTG 59.471 55.000 0.61 0.00 0.00 3.16
1870 3509 1.260033 CTCTCGCCGAATTCATTCTGC 59.740 52.381 6.22 6.00 41.63 4.26
1871 3510 1.009078 CTCGCCGAATTCATTCTGCA 58.991 50.000 14.10 0.00 44.11 4.41
1874 3513 1.334419 CGCCGAATTCATTCTGCATCC 60.334 52.381 14.10 0.00 44.11 3.51
1883 3522 2.677836 TCATTCTGCATCCAGTAAACGC 59.322 45.455 0.00 0.00 40.09 4.84
1884 3523 2.177394 TTCTGCATCCAGTAAACGCA 57.823 45.000 0.00 0.00 40.09 5.24
1885 3524 1.438651 TCTGCATCCAGTAAACGCAC 58.561 50.000 0.00 0.00 40.09 5.34
1886 3525 0.095245 CTGCATCCAGTAAACGCACG 59.905 55.000 0.00 0.00 34.31 5.34
1887 3526 1.295357 TGCATCCAGTAAACGCACGG 61.295 55.000 0.00 0.00 0.00 4.94
1888 3527 1.423845 CATCCAGTAAACGCACGGC 59.576 57.895 0.00 0.00 0.00 5.68
1914 3553 0.663688 CCATGAGCTGAGCTGATTGC 59.336 55.000 13.71 0.00 39.88 3.56
1924 3566 1.969862 GCTGATTGCTGCCTTTGGT 59.030 52.632 0.00 0.00 38.95 3.67
2163 3805 6.339587 TGTAAAATTCCATGAAACCAGTCC 57.660 37.500 0.00 0.00 0.00 3.85
2179 3821 7.839680 AACCAGTCCAGTTTATTCAAATTCT 57.160 32.000 0.00 0.00 0.00 2.40
2187 3829 8.092068 TCCAGTTTATTCAAATTCTAGACGACA 58.908 33.333 0.00 0.00 0.00 4.35
2224 3866 9.941325 TTAAAATGTTCCTGCAATTCATTATGT 57.059 25.926 0.00 0.00 0.00 2.29
2313 3955 9.474920 TCATGTCAAAAATTTCCAAGTACATTC 57.525 29.630 0.00 0.00 0.00 2.67
2361 4003 2.124901 TTTACGGCGCCTCATGGG 60.125 61.111 26.68 10.34 38.36 4.00
2369 4011 0.663153 GCGCCTCATGGGAAACATAC 59.337 55.000 0.00 0.00 37.84 2.39
2414 4056 4.863491 ACTGTTACAATGCTTTCTTGCTG 58.137 39.130 0.00 0.00 0.00 4.41
2486 4128 6.529220 AGCTTTACTGATGTTGAAGAGTTCT 58.471 36.000 0.00 0.00 0.00 3.01
2516 4158 2.690881 TCAGTATGCCCCGGCCTT 60.691 61.111 0.00 0.00 41.09 4.35
2517 4159 2.275418 CAGTATGCCCCGGCCTTT 59.725 61.111 0.00 0.00 41.09 3.11
2518 4160 2.120909 CAGTATGCCCCGGCCTTTG 61.121 63.158 0.00 0.00 41.09 2.77
2616 4259 4.392940 GGCATTCAGACCAGCAAGTATAT 58.607 43.478 0.00 0.00 0.00 0.86
2695 4338 2.169789 CGCATCCTGGCTTGAGTCG 61.170 63.158 0.00 0.00 0.00 4.18
2738 4381 0.719015 AGACTCAGAGGATGGGGGAA 59.281 55.000 1.53 0.00 31.46 3.97
2803 4446 0.686789 TGAAGTGCCTAGCTTCAGCA 59.313 50.000 7.07 0.00 44.90 4.41
3015 4658 3.046870 GTGGCATTTCCGCACCAA 58.953 55.556 0.00 0.00 44.77 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 118 3.624410 CGATGGAGAAATGAGCATTGTCA 59.376 43.478 0.00 0.00 0.00 3.58
363 367 3.760151 TCCAGATGATGAACAAAAGCTGG 59.240 43.478 14.15 14.15 38.13 4.85
437 441 3.120060 GCAGGAATGTTACAAGTGCAGAG 60.120 47.826 0.00 0.00 0.00 3.35
474 479 3.669536 AGACACTAGAAAGGAGCAAAGC 58.330 45.455 0.00 0.00 0.00 3.51
553 558 5.339611 GCAATTATTAAGCGAATTAGCGTGG 59.660 40.000 9.09 0.00 43.00 4.94
577 582 1.009675 AGCGTTGCGTGCTTTCAAG 60.010 52.632 0.00 0.00 40.48 3.02
610 2211 6.862209 TGGCAGGAATGTGTTCATATTTTAC 58.138 36.000 0.00 0.00 36.01 2.01
619 2220 4.525912 ATTTCTTGGCAGGAATGTGTTC 57.474 40.909 13.13 0.00 25.39 3.18
641 2242 8.226112 AGGGCACAAGATAGTACTACTATTAGT 58.774 37.037 4.31 1.30 41.21 2.24
651 2252 1.854227 GCGAGGGCACAAGATAGTAC 58.146 55.000 0.00 0.00 39.62 2.73
652 2253 0.384309 CGCGAGGGCACAAGATAGTA 59.616 55.000 0.00 0.00 39.92 1.82
653 2254 1.141881 CGCGAGGGCACAAGATAGT 59.858 57.895 0.00 0.00 39.92 2.12
668 2269 1.135717 TCAATCTGATGCAAAACCGCG 60.136 47.619 0.00 0.00 33.35 6.46
779 2380 2.737252 CAAAGGCCTGTTCTTACGAGTC 59.263 50.000 5.69 0.00 0.00 3.36
913 2514 3.874584 GCTGTACTGGACTGGACTAGACT 60.875 52.174 0.00 0.00 0.00 3.24
926 2527 2.729194 AGAGTAGGAGTGCTGTACTGG 58.271 52.381 2.28 0.00 40.53 4.00
927 2528 3.310227 CGTAGAGTAGGAGTGCTGTACTG 59.690 52.174 2.28 0.00 40.53 2.74
928 2529 3.197333 TCGTAGAGTAGGAGTGCTGTACT 59.803 47.826 0.00 0.00 44.02 2.73
929 2530 3.529533 TCGTAGAGTAGGAGTGCTGTAC 58.470 50.000 0.00 0.00 33.40 2.90
930 2531 3.900966 TCGTAGAGTAGGAGTGCTGTA 57.099 47.619 0.00 0.00 0.00 2.74
1005 2611 5.176592 GGGTACGTCTTCTTATTCTGCTTT 58.823 41.667 0.00 0.00 0.00 3.51
1065 2671 1.429463 GCTTGACGAGGAACGATTGT 58.571 50.000 0.00 0.00 45.77 2.71
1186 2801 2.203153 CCGGCGGGTAGGGATTTG 60.203 66.667 20.56 0.00 0.00 2.32
1290 2911 3.094572 AGAACAAGGGCAGATTGATTGG 58.905 45.455 3.73 0.00 0.00 3.16
1296 2917 1.428912 TGGGAAGAACAAGGGCAGATT 59.571 47.619 0.00 0.00 0.00 2.40
1588 3212 4.083862 GGGCTCTTCCGCTTCCGT 62.084 66.667 0.00 0.00 34.94 4.69
1638 3262 6.254589 CACAAACTAGTAGTAGCATGAAGAGC 59.745 42.308 2.50 0.00 0.00 4.09
1870 3509 1.423845 GCCGTGCGTTTACTGGATG 59.576 57.895 0.00 0.00 0.00 3.51
1871 3510 3.884900 GCCGTGCGTTTACTGGAT 58.115 55.556 0.00 0.00 0.00 3.41
1914 3553 2.341176 GCAGGCAACCAAAGGCAG 59.659 61.111 0.00 0.00 37.17 4.85
1918 3560 1.662044 GTCTGGCAGGCAACCAAAG 59.338 57.895 15.50 0.00 36.56 2.77
2108 3750 1.109323 ACTTGCAAACTGGGGTCTGC 61.109 55.000 0.00 0.00 39.64 4.26
2179 3821 5.503662 TTAACGCAGGATAATGTCGTCTA 57.496 39.130 0.00 0.00 33.80 2.59
2187 3829 6.680378 GCAGGAACATTTTAACGCAGGATAAT 60.680 38.462 0.00 0.00 0.00 1.28
2224 3866 6.403049 TCAACTCTGCGTTCCATCTTATTTA 58.597 36.000 0.00 0.00 32.27 1.40
2233 3875 2.354510 CTGTTTTCAACTCTGCGTTCCA 59.645 45.455 0.00 0.00 32.27 3.53
2253 3895 2.787994 CCATTCTCCAAAGTGACTGCT 58.212 47.619 0.00 0.00 0.00 4.24
2256 3898 2.613977 CGAGCCATTCTCCAAAGTGACT 60.614 50.000 0.00 0.00 38.62 3.41
2259 3901 1.813513 ACGAGCCATTCTCCAAAGTG 58.186 50.000 0.00 0.00 38.62 3.16
2260 3902 3.260884 TCTTACGAGCCATTCTCCAAAGT 59.739 43.478 0.00 0.00 38.62 2.66
2312 3954 4.581077 CATCTGATTGATGGTCGAGAGA 57.419 45.455 0.00 0.00 46.55 3.10
2369 4011 9.741168 CAGTCAACAATTTATGTACTTTACGAG 57.259 33.333 0.00 0.00 42.99 4.18
2414 4056 5.255916 AGGGATAGGGGGTCTAGTAATCTAC 59.744 48.000 0.00 0.00 0.00 2.59
2486 4128 1.204704 CATACTGACTGCGTCCCTGAA 59.795 52.381 6.30 0.00 0.00 3.02
2502 4144 2.833121 CCAAAGGCCGGGGCATAC 60.833 66.667 23.67 0.00 44.11 2.39
2553 4195 0.698238 AGGATAACCAAGCACAGGCA 59.302 50.000 0.00 0.00 39.87 4.75
2599 4241 7.665559 AGAACAAAAATATACTTGCTGGTCTGA 59.334 33.333 0.00 0.00 0.00 3.27
2616 4259 9.650539 TTGATCATTTTCAGAACAGAACAAAAA 57.349 25.926 0.00 0.00 0.00 1.94
2695 4338 0.883833 CACCAAAGCCTGACCATGAC 59.116 55.000 0.00 0.00 0.00 3.06
2738 4381 0.473326 GAGGAGATTGCAGAGGCCAT 59.527 55.000 5.01 0.00 40.13 4.40
2803 4446 4.387026 TCCAGAGTGGGTTGATTTTGAT 57.613 40.909 0.00 0.00 38.32 2.57
3009 4652 2.098117 GCTATGGTGTGAATCTTGGTGC 59.902 50.000 0.00 0.00 0.00 5.01
3015 4658 4.785346 AGAATGGCTATGGTGTGAATCT 57.215 40.909 0.00 0.00 0.00 2.40



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

AutoCloner maintained by Alex Coulton.