Multiple sequence alignment - TraesCS1D01G123800

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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 TraesCS1D01G123800 chr1D 100.000 3734 0 0 1 3734 126471912 126475645 0.000000e+00 6896.0
1 TraesCS1D01G123800 chr1D 83.387 313 51 1 3333 3645 402008133 402008444 4.720000e-74 289.0
2 TraesCS1D01G123800 chr1B 96.236 3029 72 21 1 3007 190629370 190632378 0.000000e+00 4924.0
3 TraesCS1D01G123800 chr1B 94.240 434 23 2 3294 3725 190632656 190633089 0.000000e+00 662.0
4 TraesCS1D01G123800 chr1B 88.031 259 16 7 3039 3295 190632378 190632623 3.650000e-75 292.0
5 TraesCS1D01G123800 chr1B 80.636 346 58 7 3351 3696 83850487 83850823 3.700000e-65 259.0
6 TraesCS1D01G123800 chr1A 93.856 3076 91 19 1 3046 140959982 140962989 0.000000e+00 4543.0
7 TraesCS1D01G123800 chr1A 81.114 413 68 7 3302 3705 20906503 20906914 4.650000e-84 322.0
8 TraesCS1D01G123800 chr1A 85.106 188 26 2 3108 3295 140963086 140963271 1.370000e-44 191.0
9 TraesCS1D01G123800 chr3B 77.679 672 88 33 1942 2588 104971434 104972068 1.650000e-93 353.0
10 TraesCS1D01G123800 chr3B 86.905 168 19 3 1586 1752 104971043 104971208 6.370000e-43 185.0
11 TraesCS1D01G123800 chr3D 77.545 668 90 28 1942 2588 63779998 63780626 7.680000e-92 348.0
12 TraesCS1D01G123800 chr3D 76.695 472 78 25 1041 1484 63779054 63779521 2.240000e-57 233.0
13 TraesCS1D01G123800 chr5D 82.500 400 61 3 3306 3705 27436317 27435927 3.570000e-90 342.0
14 TraesCS1D01G123800 chr5D 81.377 247 42 3 3460 3705 487475769 487476012 8.180000e-47 198.0
15 TraesCS1D01G123800 chr7D 82.353 391 67 2 3337 3725 241738304 241738694 4.620000e-89 339.0
16 TraesCS1D01G123800 chr7D 97.753 178 3 1 1325 1502 634158526 634158350 4.690000e-79 305.0
17 TraesCS1D01G123800 chr7D 81.132 371 70 0 3335 3705 229231755 229231385 7.840000e-77 298.0
18 TraesCS1D01G123800 chr6D 82.337 368 52 6 3333 3700 2516523 2516877 1.300000e-79 307.0
19 TraesCS1D01G123800 chr4D 97.753 178 3 1 1325 1502 14673541 14673717 4.690000e-79 305.0
20 TraesCS1D01G123800 chr4D 78.986 138 25 4 1598 1733 446652937 446652802 1.430000e-14 91.6
21 TraesCS1D01G123800 chr3A 76.219 677 95 34 1942 2588 73513468 73514108 7.840000e-77 298.0
22 TraesCS1D01G123800 chr3A 77.113 485 77 23 1017 1472 73512500 73512979 2.230000e-62 250.0
23 TraesCS1D01G123800 chr3A 86.628 172 19 4 1586 1756 73513082 73513250 1.770000e-43 187.0
24 TraesCS1D01G123800 chr2A 83.446 296 42 5 3414 3705 566206331 566206623 6.150000e-68 268.0
25 TraesCS1D01G123800 chr4B 80.130 307 59 2 3337 3642 647630185 647629880 1.040000e-55 228.0
26 TraesCS1D01G123800 chr4B 78.986 138 25 4 1598 1733 558727281 558727146 1.430000e-14 91.6
27 TraesCS1D01G123800 chr6A 84.043 188 27 3 3108 3295 137390013 137389829 1.070000e-40 178.0
28 TraesCS1D01G123800 chr2D 88.079 151 17 1 3146 3295 524936418 524936268 1.070000e-40 178.0


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 TraesCS1D01G123800 chr1D 126471912 126475645 3733 False 6896.000000 6896 100.000000 1 3734 1 chr1D.!!$F1 3733
1 TraesCS1D01G123800 chr1B 190629370 190633089 3719 False 1959.333333 4924 92.835667 1 3725 3 chr1B.!!$F2 3724
2 TraesCS1D01G123800 chr1A 140959982 140963271 3289 False 2367.000000 4543 89.481000 1 3295 2 chr1A.!!$F2 3294
3 TraesCS1D01G123800 chr3B 104971043 104972068 1025 False 269.000000 353 82.292000 1586 2588 2 chr3B.!!$F1 1002
4 TraesCS1D01G123800 chr3D 63779054 63780626 1572 False 290.500000 348 77.120000 1041 2588 2 chr3D.!!$F1 1547
5 TraesCS1D01G123800 chr3A 73512500 73514108 1608 False 245.000000 298 79.986667 1017 2588 3 chr3A.!!$F1 1571

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
362 377 0.469070 GATCTGGGCATGCACTCTCT 59.531 55.0 22.81 2.82 0.0 3.10 F
832 874 0.551879 TAACGAGAGAGGGAGAGGGG 59.448 60.0 0.00 0.00 0.0 4.79 F
989 1036 1.517242 CACTGCTCTCTTGGTTCACC 58.483 55.0 0.00 0.00 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1892 2002 0.680618 ACCACAACCATTGCACATGG 59.319 50.000 19.95 19.95 44.54 3.66 R
2341 2524 1.203441 TGGGGCAGTTGAGCAGAGAT 61.203 55.000 0.00 0.00 35.83 2.75 R
2928 3141 1.915965 GCAAACAACAGAACGAGTCGC 60.916 52.381 13.59 0.00 0.00 5.19 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
78 79 2.367567 GGATATCTTGGTCCGTTGCCTA 59.632 50.000 2.05 0.00 0.00 3.93
80 81 2.622064 ATCTTGGTCCGTTGCCTATC 57.378 50.000 0.00 0.00 0.00 2.08
93 94 1.372997 CCTATCGGCGATTCGTGGG 60.373 63.158 28.93 12.17 0.00 4.61
94 95 2.022129 CTATCGGCGATTCGTGGGC 61.022 63.158 28.93 0.00 0.00 5.36
238 252 1.795286 GAGTCAAGCTTCTGTTCACCG 59.205 52.381 0.00 0.00 0.00 4.94
362 377 0.469070 GATCTGGGCATGCACTCTCT 59.531 55.000 22.81 2.82 0.00 3.10
367 382 2.373707 GGCATGCACTCTCTCCCCT 61.374 63.158 21.36 0.00 0.00 4.79
373 388 1.595882 CACTCTCTCCCCTGCACTG 59.404 63.158 0.00 0.00 0.00 3.66
374 389 2.289532 ACTCTCTCCCCTGCACTGC 61.290 63.158 0.00 0.00 0.00 4.40
375 390 2.203832 TCTCTCCCCTGCACTGCA 60.204 61.111 3.11 3.11 36.92 4.41
376 391 2.046507 CTCTCCCCTGCACTGCAC 60.047 66.667 0.00 0.00 33.79 4.57
377 392 2.527624 TCTCCCCTGCACTGCACT 60.528 61.111 0.00 0.00 33.79 4.40
589 612 6.142818 ACGAAACATCTTCCATTGTTTTCA 57.857 33.333 2.92 0.00 43.95 2.69
649 679 1.336795 GGTGCCAAAAATGAGTTCCCG 60.337 52.381 0.00 0.00 0.00 5.14
825 867 9.819267 ATTCTTTACTTAATTAACGAGAGAGGG 57.181 33.333 0.00 0.00 0.00 4.30
832 874 0.551879 TAACGAGAGAGGGAGAGGGG 59.448 60.000 0.00 0.00 0.00 4.79
833 875 2.197324 CGAGAGAGGGAGAGGGGG 59.803 72.222 0.00 0.00 0.00 5.40
855 897 2.111043 GCGCTAATGGCTGCCCTA 59.889 61.111 17.53 6.82 39.13 3.53
858 900 1.610624 GCGCTAATGGCTGCCCTAATA 60.611 52.381 17.53 0.00 39.13 0.98
989 1036 1.517242 CACTGCTCTCTTGGTTCACC 58.483 55.000 0.00 0.00 0.00 4.02
1000 1047 2.270986 GGTTCACCAGCAAGCCCTG 61.271 63.158 0.00 0.00 35.64 4.45
1046 1093 3.462678 GAGTCCTCAGGTCCGGCC 61.463 72.222 0.00 0.59 37.58 6.13
1511 1611 5.273674 TCTATCAGAATCAGCAAGACCAG 57.726 43.478 0.00 0.00 0.00 4.00
1892 2002 5.377358 CGACGATTCTAATGGAAATCATGC 58.623 41.667 0.00 0.00 37.49 4.06
1940 2117 4.088762 GGTACGCGGACGACACGA 62.089 66.667 16.72 0.00 43.93 4.35
2341 2524 3.138798 GGCGGCTACTCGTCCTCA 61.139 66.667 0.00 0.00 0.00 3.86
2619 2829 1.696832 GAGAATGACCGGCAAGCGTC 61.697 60.000 0.00 0.00 0.00 5.19
2782 2992 8.247562 TGCTTTCTTTTTGTTCTTGCTTTAGTA 58.752 29.630 0.00 0.00 0.00 1.82
2907 3120 6.381801 CGCACTTTGATGTAAATTCCTTCTT 58.618 36.000 0.00 0.00 0.00 2.52
2928 3141 7.395190 TCTTAATCCATGTGTTCTTCCATTG 57.605 36.000 0.00 0.00 0.00 2.82
3002 3215 1.792118 GCTTCAGCCGGGTTTCGTTT 61.792 55.000 1.64 0.00 37.11 3.60
3033 3246 1.594194 GCATCGTTGGAATGTGGGCA 61.594 55.000 0.00 0.00 0.00 5.36
3101 3314 1.401905 GCGGAAGACATCAAATCCACC 59.598 52.381 0.00 0.00 32.08 4.61
3102 3315 1.665679 CGGAAGACATCAAATCCACCG 59.334 52.381 0.00 0.00 32.08 4.94
3158 3406 6.845782 CGTCCACATTTGTGTATATCAAATCG 59.154 38.462 9.66 10.35 44.21 3.34
3175 3423 0.415830 TCGGGCCCCTCATATCCATA 59.584 55.000 18.66 0.00 0.00 2.74
3192 3440 9.528018 CATATCCATACAATACATGCACGTATA 57.472 33.333 5.76 0.00 31.76 1.47
3263 3511 9.845740 ATATCGGGCATAATTATAGCATAAACA 57.154 29.630 16.51 3.74 0.00 2.83
3281 3529 3.915437 ACAATCATCGGACAACCAAAC 57.085 42.857 0.00 0.00 35.59 2.93
3363 3645 4.717629 CGCCTCACGCTCCGACAA 62.718 66.667 0.00 0.00 34.21 3.18
3419 3701 1.066136 CCGCAGTCGATATGCATCTG 58.934 55.000 21.03 5.10 44.05 2.90
3426 3708 2.985809 GTCGATATGCATCTGTCTCTGC 59.014 50.000 0.19 0.00 38.87 4.26
3427 3709 2.029560 TCGATATGCATCTGTCTCTGCC 60.030 50.000 0.19 0.00 37.59 4.85
3473 3756 2.202610 CAATGAGCGCGTCCTCGA 60.203 61.111 8.43 0.00 39.71 4.04
3478 3761 1.093496 TGAGCGCGTCCTCGAGATTA 61.093 55.000 15.71 0.00 39.07 1.75
3593 3876 2.600122 CTTCGACTCGGGCTTCCTCG 62.600 65.000 0.00 0.00 0.00 4.63
3642 3925 2.978010 CCAACGGTGCCAGTGGAC 60.978 66.667 15.20 8.27 0.00 4.02
3700 3983 2.280552 GCGTACCTGGAGTGGGACA 61.281 63.158 0.00 0.00 40.96 4.02
3701 3984 1.890894 CGTACCTGGAGTGGGACAG 59.109 63.158 0.00 0.00 40.96 3.51
3721 4004 1.113517 AGCAGACTGTGTACCACCGT 61.114 55.000 3.99 0.00 34.71 4.83
3722 4005 0.944311 GCAGACTGTGTACCACCGTG 60.944 60.000 3.99 0.00 32.35 4.94
3723 4006 0.387929 CAGACTGTGTACCACCGTGT 59.612 55.000 0.00 0.00 32.35 4.49
3726 4009 1.595794 GACTGTGTACCACCGTGTTTG 59.404 52.381 0.00 0.00 32.35 2.93
3727 4010 1.207570 ACTGTGTACCACCGTGTTTGA 59.792 47.619 0.00 0.00 31.10 2.69
3728 4011 1.595794 CTGTGTACCACCGTGTTTGAC 59.404 52.381 0.00 0.00 32.73 3.18
3729 4012 1.066358 TGTGTACCACCGTGTTTGACA 60.066 47.619 0.00 0.00 32.73 3.58
3730 4013 1.328374 GTGTACCACCGTGTTTGACAC 59.672 52.381 1.21 1.21 45.26 3.67
3731 4014 5.733121 TGTGTACCACCGTGTTTGACACA 62.733 47.826 15.59 15.59 42.35 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 2.283676 ATCGTGGGGACGTCACCT 60.284 61.111 35.49 14.72 41.04 4.00
87 88 4.345962 CACACGTACCGCCCACGA 62.346 66.667 8.38 0.00 43.93 4.35
88 89 3.636313 ATCACACGTACCGCCCACG 62.636 63.158 0.00 0.00 44.80 4.94
89 90 1.808390 GATCACACGTACCGCCCAC 60.808 63.158 0.00 0.00 0.00 4.61
90 91 2.574929 GATCACACGTACCGCCCA 59.425 61.111 0.00 0.00 0.00 5.36
93 94 2.058798 CATATGGATCACACGTACCGC 58.941 52.381 0.00 0.00 0.00 5.68
94 95 2.672714 CCATATGGATCACACGTACCG 58.327 52.381 17.49 0.00 37.39 4.02
362 377 4.648626 GCAGTGCAGTGCAGGGGA 62.649 66.667 35.84 0.00 43.41 4.81
373 388 0.671781 CAGTAGGTCCAGTGCAGTGC 60.672 60.000 16.47 8.58 0.00 4.40
374 389 0.681733 ACAGTAGGTCCAGTGCAGTG 59.318 55.000 14.95 14.95 0.00 3.66
375 390 0.681733 CACAGTAGGTCCAGTGCAGT 59.318 55.000 0.00 0.00 0.00 4.40
376 391 0.681733 ACACAGTAGGTCCAGTGCAG 59.318 55.000 0.00 0.00 35.47 4.41
377 392 0.392706 CACACAGTAGGTCCAGTGCA 59.607 55.000 0.00 0.00 35.47 4.57
442 457 3.462678 GGCACGAGGGAGGGAGAC 61.463 72.222 0.00 0.00 0.00 3.36
464 479 2.917227 GCCCACACCCAAACCCAG 60.917 66.667 0.00 0.00 0.00 4.45
589 612 7.865889 GGAAAAATGTTTACGTGAGGAAAGAAT 59.134 33.333 0.00 0.00 46.34 2.40
628 658 1.336795 GGGAACTCATTTTTGGCACCG 60.337 52.381 0.00 0.00 0.00 4.94
649 679 2.507324 GGCCAGCTCGAGAACGAC 60.507 66.667 18.75 0.00 43.81 4.34
801 835 8.585471 TCCCTCTCTCGTTAATTAAGTAAAGA 57.415 34.615 10.17 10.17 0.00 2.52
807 841 5.010213 CCCTCTCCCTCTCTCGTTAATTAAG 59.990 48.000 0.00 0.00 0.00 1.85
1618 1718 3.123620 GCCTGCAGCTTCACGAGG 61.124 66.667 8.66 0.00 38.99 4.63
1892 2002 0.680618 ACCACAACCATTGCACATGG 59.319 50.000 19.95 19.95 44.54 3.66
2215 2398 2.874780 GCGCACCAGTCGTACTCG 60.875 66.667 0.30 0.00 38.55 4.18
2341 2524 1.203441 TGGGGCAGTTGAGCAGAGAT 61.203 55.000 0.00 0.00 35.83 2.75
2782 2992 7.088272 CACAAATCACATGATTGATCACAACT 58.912 34.615 7.86 0.00 43.41 3.16
2907 3120 4.096231 CGCAATGGAAGAACACATGGATTA 59.904 41.667 0.00 0.00 0.00 1.75
2928 3141 1.915965 GCAAACAACAGAACGAGTCGC 60.916 52.381 13.59 0.00 0.00 5.19
3002 3215 5.697473 TCCAACGATGCTTTTATCAACAA 57.303 34.783 0.00 0.00 0.00 2.83
3033 3246 1.764723 TGACGCATGAGAGGGATTGAT 59.235 47.619 2.50 0.00 0.00 2.57
3102 3315 3.591254 GAGTGTCCGGTCAGCCCAC 62.591 68.421 0.19 0.74 0.00 4.61
3158 3406 1.668826 TGTATGGATATGAGGGGCCC 58.331 55.000 17.12 17.12 0.00 5.80
3202 3450 5.327091 GTGCTAGTTCGTTGATCTACGTAA 58.673 41.667 25.03 16.44 42.01 3.18
3203 3451 4.201851 GGTGCTAGTTCGTTGATCTACGTA 60.202 45.833 25.03 15.78 42.01 3.57
3252 3500 6.017109 GGTTGTCCGATGATTGTTTATGCTAT 60.017 38.462 0.00 0.00 0.00 2.97
3261 3509 2.225491 CGTTTGGTTGTCCGATGATTGT 59.775 45.455 0.00 0.00 36.30 2.71
3263 3511 2.773487 TCGTTTGGTTGTCCGATGATT 58.227 42.857 0.00 0.00 36.30 2.57
3419 3701 0.037326 TCCATGACAACGGCAGAGAC 60.037 55.000 0.00 0.00 0.00 3.36
3426 3708 3.499737 GGCGCTCCATGACAACGG 61.500 66.667 7.64 0.00 0.00 4.44
3427 3709 3.853330 CGGCGCTCCATGACAACG 61.853 66.667 7.64 0.00 0.00 4.10
3473 3756 3.192922 GCGCGTGCCGGTTAATCT 61.193 61.111 10.56 0.00 37.44 2.40
3573 3856 2.184579 GGAAGCCCGAGTCGAAGG 59.815 66.667 15.64 8.90 0.00 3.46
3576 3859 2.888464 ATCGAGGAAGCCCGAGTCGA 62.888 60.000 15.64 0.00 39.78 4.20
3580 3863 2.333225 CGATCGAGGAAGCCCGAG 59.667 66.667 10.26 0.00 38.25 4.63
3583 3866 4.610714 GGCCGATCGAGGAAGCCC 62.611 72.222 18.66 1.66 37.66 5.19
3584 3867 4.610714 GGGCCGATCGAGGAAGCC 62.611 72.222 18.66 19.54 43.09 4.35


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

AutoCloner maintained by Alex Coulton.