Multiple sequence alignment - TraesCS3B01G176800

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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 TraesCS3B01G176800 chr3B 100.000 4327 0 0 1 4327 179670491 179674817 0.000000e+00 7991
1 TraesCS3B01G176800 chr3D 93.847 3283 146 28 117 3384 125773335 125776576 0.000000e+00 4892
2 TraesCS3B01G176800 chr3D 93.939 660 24 6 3473 4121 125776953 125777607 0.000000e+00 983
3 TraesCS3B01G176800 chr3D 95.935 123 5 0 4118 4240 125777915 125778037 2.640000e-47 200
4 TraesCS3B01G176800 chr3D 91.367 139 9 2 1 137 125773181 125773318 2.050000e-43 187
5 TraesCS3B01G176800 chr3D 94.318 88 5 0 4238 4325 125779589 125779676 7.550000e-28 135
6 TraesCS3B01G176800 chr3D 93.182 88 6 0 4238 4325 125787096 125787183 3.510000e-26 130
7 TraesCS3B01G176800 chr3A 94.220 2422 89 27 1 2401 134599710 134602101 0.000000e+00 3650
8 TraesCS3B01G176800 chr3A 93.888 949 46 5 2443 3390 134602091 134603028 0.000000e+00 1421
9 TraesCS3B01G176800 chr3A 94.413 537 26 4 3472 4006 134603024 134603558 0.000000e+00 822
10 TraesCS3B01G176800 chr3A 93.810 210 11 2 4118 4327 134604019 134604226 9.030000e-82 315
11 TraesCS3B01G176800 chr3A 97.414 116 3 0 4006 4121 134603601 134603716 9.490000e-47 198


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 TraesCS3B01G176800 chr3B 179670491 179674817 4326 False 7991.0 7991 100.0000 1 4327 1 chr3B.!!$F1 4326
1 TraesCS3B01G176800 chr3D 125773181 125779676 6495 False 1279.4 4892 93.8812 1 4325 5 chr3D.!!$F2 4324
2 TraesCS3B01G176800 chr3A 134599710 134604226 4516 False 1281.2 3650 94.7490 1 4327 5 chr3A.!!$F1 4326

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
611 669 0.538746 TGGTGAGGTGACGACTGCTA 60.539 55.0 0.00 0.0 0.0 3.49 F
1011 1081 0.033504 ACGACGTCATGGACTGCTTT 59.966 50.0 17.16 0.0 0.0 3.51 F
2627 2704 0.398318 GTGGCTTCTCAGGTGGTTCT 59.602 55.0 0.00 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2304 2380 0.740737 GTGGAAATTGGCCGGAGATG 59.259 55.0 5.05 0.0 0.00 2.90 R
2634 2711 0.744771 GAGAAACCGATCCACAGCCC 60.745 60.0 0.00 0.0 0.00 5.19 R
3994 4455 0.685458 AGCAGATGGAATTGCCCACC 60.685 55.0 0.00 0.0 41.17 4.61 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
149 191 2.468670 TTGTTTGCACGCGAGCACT 61.469 52.632 30.47 0.00 45.61 4.40
168 210 3.381272 CACTCAAACACAGGTTCCATTGT 59.619 43.478 0.00 0.00 35.82 2.71
178 220 3.983988 CAGGTTCCATTGTAGATCGATCG 59.016 47.826 19.33 9.36 0.00 3.69
265 310 4.753662 TCCGACCGAGACCCCCAG 62.754 72.222 0.00 0.00 0.00 4.45
288 333 2.030490 AACCACTAACCGACCACGCA 62.030 55.000 0.00 0.00 38.29 5.24
333 383 8.295288 CGAATATAAACTATGACTACGGGTTCT 58.705 37.037 0.00 0.00 0.00 3.01
579 637 0.940126 CCAGGCGATGCATCTAACAC 59.060 55.000 23.73 9.47 0.00 3.32
580 638 1.655484 CAGGCGATGCATCTAACACA 58.345 50.000 23.73 0.00 0.00 3.72
581 639 1.596260 CAGGCGATGCATCTAACACAG 59.404 52.381 23.73 8.02 0.00 3.66
582 640 1.482182 AGGCGATGCATCTAACACAGA 59.518 47.619 23.73 0.00 37.79 3.41
583 641 1.594862 GGCGATGCATCTAACACAGAC 59.405 52.381 23.73 5.38 35.62 3.51
584 642 1.594862 GCGATGCATCTAACACAGACC 59.405 52.381 23.73 0.00 35.62 3.85
610 668 1.810606 CTGGTGAGGTGACGACTGCT 61.811 60.000 0.00 0.00 0.00 4.24
611 669 0.538746 TGGTGAGGTGACGACTGCTA 60.539 55.000 0.00 0.00 0.00 3.49
671 731 3.793819 ACCTACATGCATGCATATCCA 57.206 42.857 31.73 15.87 34.91 3.41
848 908 2.038813 TCCTCCACCGCTCCATCA 59.961 61.111 0.00 0.00 0.00 3.07
855 915 2.058001 ACCGCTCCATCACATCCGA 61.058 57.895 0.00 0.00 0.00 4.55
906 966 2.128035 GCTACGCCACAGATATGTGAC 58.872 52.381 21.78 9.50 42.02 3.67
907 967 2.223829 GCTACGCCACAGATATGTGACT 60.224 50.000 21.78 5.97 42.02 3.41
908 968 2.299993 ACGCCACAGATATGTGACTG 57.700 50.000 21.78 12.49 42.02 3.51
917 977 7.276658 GCCACAGATATGTGACTGCTTATATAC 59.723 40.741 21.78 0.00 42.02 1.47
920 985 8.744652 ACAGATATGTGACTGCTTATATACCTC 58.255 37.037 6.90 0.00 37.61 3.85
1011 1081 0.033504 ACGACGTCATGGACTGCTTT 59.966 50.000 17.16 0.00 0.00 3.51
1293 1363 1.825191 CCCACTCATGCCATTCCCG 60.825 63.158 0.00 0.00 0.00 5.14
1460 1530 1.628846 GGTCACCTCACTACCAATGGT 59.371 52.381 10.81 10.81 40.16 3.55
1569 1639 2.430610 GCCAGAGATCGAGGGCACT 61.431 63.158 16.48 0.00 45.70 4.40
1706 1776 0.664166 CTCGCCAACCACAATGCAAC 60.664 55.000 0.00 0.00 0.00 4.17
1887 1958 6.777101 TGCACATCACCGTGTATAATTAAAC 58.223 36.000 0.00 0.00 39.19 2.01
1888 1959 6.371825 TGCACATCACCGTGTATAATTAAACA 59.628 34.615 0.00 0.00 39.19 2.83
1937 2008 6.558771 TTACGCATTCCTTCCATTATGATG 57.441 37.500 0.00 0.00 0.00 3.07
1999 2070 9.673454 CTTTCCATACAAATCATCACATATGTG 57.327 33.333 26.83 26.83 46.91 3.21
2221 2293 3.184178 CCGCATGTTTCATTTCAAACACC 59.816 43.478 1.00 0.00 46.45 4.16
2227 2299 9.149225 GCATGTTTCATTTCAAACACCATTATA 57.851 29.630 1.00 0.00 46.45 0.98
2304 2380 3.248602 CACGAGGCAAAGGCATACTATTC 59.751 47.826 0.00 0.00 43.71 1.75
2316 2392 3.557054 GCATACTATTCATCTCCGGCCAA 60.557 47.826 2.24 0.00 0.00 4.52
2320 2396 4.137543 ACTATTCATCTCCGGCCAATTTC 58.862 43.478 2.24 0.00 0.00 2.17
2396 2472 3.782889 GCCCATGGCTAACTTTACTTG 57.217 47.619 6.09 0.00 46.69 3.16
2397 2473 3.089284 GCCCATGGCTAACTTTACTTGT 58.911 45.455 6.09 0.00 46.69 3.16
2398 2474 3.509967 GCCCATGGCTAACTTTACTTGTT 59.490 43.478 6.09 0.00 46.69 2.83
2399 2475 4.021456 GCCCATGGCTAACTTTACTTGTTT 60.021 41.667 6.09 0.00 46.69 2.83
2400 2476 5.510690 GCCCATGGCTAACTTTACTTGTTTT 60.511 40.000 6.09 0.00 46.69 2.43
2438 2514 7.762159 TCTTTACAAAACAAAAATGAGGGTCAC 59.238 33.333 0.00 0.00 0.00 3.67
2627 2704 0.398318 GTGGCTTCTCAGGTGGTTCT 59.602 55.000 0.00 0.00 0.00 3.01
2634 2711 2.160205 TCTCAGGTGGTTCTCTGTACG 58.840 52.381 0.00 0.00 33.13 3.67
2742 2819 3.013921 CAATGGAGCTTAAGGGCGTTTA 58.986 45.455 4.29 0.00 37.29 2.01
2801 2878 8.499403 AGCAAAGATTAAGTCTGGAAGTATTC 57.501 34.615 0.00 0.00 39.61 1.75
2898 2976 6.691508 AGTTTTTCTTGGATAATGCAGGTTC 58.308 36.000 0.00 0.00 0.00 3.62
2903 2981 2.917933 TGGATAATGCAGGTTCTTCCG 58.082 47.619 0.00 0.00 41.99 4.30
2912 2990 2.342648 GTTCTTCCGGGAGTGCGT 59.657 61.111 10.32 0.00 0.00 5.24
3137 3215 6.709018 TTTTTCTCGGAGAAAGATGGTTTT 57.291 33.333 26.74 0.00 44.14 2.43
3221 3299 5.121105 GGTGGACTTTTAGCGGTGTATAAT 58.879 41.667 0.00 0.00 0.00 1.28
3232 3310 3.303990 GCGGTGTATAATGATGCAACCAG 60.304 47.826 0.00 0.00 32.07 4.00
3312 3390 3.529533 ACTTCATCCAATCGAAGAGCAG 58.470 45.455 6.18 0.00 43.63 4.24
3314 3392 0.580578 CATCCAATCGAAGAGCAGCG 59.419 55.000 0.00 0.00 43.63 5.18
3370 3448 6.489603 AGTCAGTCTAGTATATAGGCATGCT 58.510 40.000 18.92 6.26 0.00 3.79
3390 3842 8.089597 GCATGCTAGATCAGTAGATGCATATAT 58.910 37.037 11.37 0.00 38.57 0.86
3864 4324 1.577616 GTAAATGAGCGCGCACACG 60.578 57.895 32.64 0.00 44.07 4.49
3977 4437 5.124936 GGACCATTTATGTTCAGGTAACCAC 59.875 44.000 0.00 0.00 37.27 4.16
4012 4516 0.685458 AGGTGGGCAATTCCATCTGC 60.685 55.000 0.00 0.00 45.86 4.26
4020 4524 4.812626 GGGCAATTCCATCTGCTAATTTTG 59.187 41.667 0.00 0.00 38.65 2.44
4148 4967 2.771943 TCATATCCACTTCACCCCTCAC 59.228 50.000 0.00 0.00 0.00 3.51
4203 5022 1.570803 ATCAGAGAGCACTGGAGCTT 58.429 50.000 0.00 0.00 46.75 3.74
4226 5045 1.203262 AGGGGTGTGTGAGTTAGGCTA 60.203 52.381 0.00 0.00 0.00 3.93
4271 6644 4.576463 AGTGTTCCATTCAACTGAAGTGAC 59.424 41.667 0.00 0.00 37.48 3.67
4288 6661 2.026822 GTGACCCACAGATGAATCCAGT 60.027 50.000 0.00 0.00 34.08 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 100 7.370383 ACGTACGAGAGATAAAAACACCTAAA 58.630 34.615 24.41 0.00 0.00 1.85
149 191 5.042463 TCTACAATGGAACCTGTGTTTGA 57.958 39.130 5.60 3.58 33.97 2.69
265 310 0.393820 TGGTCGGTTAGTGGTTGGTC 59.606 55.000 0.00 0.00 0.00 4.02
333 383 1.218047 CGGACAGGAGGCAATCGAA 59.782 57.895 0.00 0.00 0.00 3.71
433 487 1.202722 ACGAGACTAGGAGGAGCTAGC 60.203 57.143 6.62 6.62 0.00 3.42
434 488 2.489971 CACGAGACTAGGAGGAGCTAG 58.510 57.143 0.00 0.00 0.00 3.42
435 489 1.475392 GCACGAGACTAGGAGGAGCTA 60.475 57.143 0.00 0.00 0.00 3.32
436 490 0.750182 GCACGAGACTAGGAGGAGCT 60.750 60.000 0.00 0.00 0.00 4.09
563 621 1.594862 GTCTGTGTTAGATGCATCGCC 59.405 52.381 20.67 12.73 37.83 5.54
596 654 1.332375 CTAGCTAGCAGTCGTCACCTC 59.668 57.143 18.83 0.00 0.00 3.85
671 731 6.238842 CGATCTTGGATTGGAATATTGCTTGT 60.239 38.462 8.53 0.00 0.00 3.16
848 908 1.072331 GAAGCATGGGGTATCGGATGT 59.928 52.381 0.00 0.00 0.00 3.06
906 966 6.268847 AGGAAGAGGTTGAGGTATATAAGCAG 59.731 42.308 0.00 0.00 0.00 4.24
907 967 6.143915 AGGAAGAGGTTGAGGTATATAAGCA 58.856 40.000 0.00 0.00 0.00 3.91
908 968 6.570764 CGAGGAAGAGGTTGAGGTATATAAGC 60.571 46.154 0.00 0.00 0.00 3.09
917 977 1.066303 CGATCGAGGAAGAGGTTGAGG 59.934 57.143 10.26 0.00 0.00 3.86
920 985 1.202313 GGTCGATCGAGGAAGAGGTTG 60.202 57.143 20.09 0.00 0.00 3.77
979 1044 2.434185 GTCGTGGATGAAGCGGCA 60.434 61.111 1.45 0.00 0.00 5.69
982 1047 0.802222 ATGACGTCGTGGATGAAGCG 60.802 55.000 10.06 0.00 0.00 4.68
983 1048 0.647410 CATGACGTCGTGGATGAAGC 59.353 55.000 26.79 0.00 0.00 3.86
1011 1081 1.003355 CTTTCCTTCAGCCTCCGCA 60.003 57.895 0.00 0.00 37.52 5.69
1293 1363 1.162698 GGTACGTGGGGAAGCTTTTC 58.837 55.000 0.00 0.00 0.00 2.29
1569 1639 0.827507 GCTGCCCTTTGAACCTTCCA 60.828 55.000 0.00 0.00 0.00 3.53
1824 1895 7.724061 ACCTCATTAATTTCTAAAGTGGTGTGT 59.276 33.333 0.00 0.00 0.00 3.72
1953 2024 9.513906 TGGAAAGAAGTTACATGATGAATTACA 57.486 29.630 0.00 0.00 0.00 2.41
2096 2167 1.463674 ATGTGGTGATTTTCCTCGGC 58.536 50.000 0.00 0.00 0.00 5.54
2290 2366 4.804261 GCCGGAGATGAATAGTATGCCTTT 60.804 45.833 5.05 0.00 0.00 3.11
2291 2367 3.307059 GCCGGAGATGAATAGTATGCCTT 60.307 47.826 5.05 0.00 0.00 4.35
2292 2368 2.234908 GCCGGAGATGAATAGTATGCCT 59.765 50.000 5.05 0.00 0.00 4.75
2293 2369 2.622436 GCCGGAGATGAATAGTATGCC 58.378 52.381 5.05 0.00 0.00 4.40
2294 2370 2.028112 TGGCCGGAGATGAATAGTATGC 60.028 50.000 5.05 0.00 0.00 3.14
2295 2371 3.961480 TGGCCGGAGATGAATAGTATG 57.039 47.619 5.05 0.00 0.00 2.39
2304 2380 0.740737 GTGGAAATTGGCCGGAGATG 59.259 55.000 5.05 0.00 0.00 2.90
2400 2476 6.231211 TGTTTTGTAAAGAGGCAACCAAAAA 58.769 32.000 0.00 0.00 34.66 1.94
2405 2481 6.729391 TTTTTGTTTTGTAAAGAGGCAACC 57.271 33.333 0.00 0.00 37.17 3.77
2410 2486 7.272244 ACCCTCATTTTTGTTTTGTAAAGAGG 58.728 34.615 0.00 0.00 38.84 3.69
2627 2704 1.663379 CGATCCACAGCCCGTACAGA 61.663 60.000 0.00 0.00 0.00 3.41
2634 2711 0.744771 GAGAAACCGATCCACAGCCC 60.745 60.000 0.00 0.00 0.00 5.19
2742 2819 2.073816 CGAGAACTGGCGTTTTACCAT 58.926 47.619 0.00 0.00 36.36 3.55
2873 2950 6.670695 ACCTGCATTATCCAAGAAAAACTT 57.329 33.333 0.00 0.00 39.70 2.66
2898 2976 1.164041 AAACAACGCACTCCCGGAAG 61.164 55.000 0.73 0.00 0.00 3.46
2903 2981 1.606668 TCATGAAAACAACGCACTCCC 59.393 47.619 0.00 0.00 0.00 4.30
2912 2990 3.243805 CCACACCATGCTCATGAAAACAA 60.244 43.478 11.17 0.00 41.20 2.83
3083 3161 5.815581 TCCTGCACATAGAAGGTTTAACAT 58.184 37.500 0.00 0.00 32.59 2.71
3134 3212 6.435904 TCCACTCTTTTGACTTTCTTGGAAAA 59.564 34.615 0.00 0.00 0.00 2.29
3137 3215 5.110814 TCCACTCTTTTGACTTTCTTGGA 57.889 39.130 0.00 0.00 0.00 3.53
3221 3299 2.169978 CTCTGAGATCCTGGTTGCATCA 59.830 50.000 0.00 0.00 0.00 3.07
3232 3310 6.586344 TGTTGAACAATATCCTCTGAGATCC 58.414 40.000 6.17 0.00 0.00 3.36
3312 3390 8.856490 AAATAATTTGATCAAATAGGACACGC 57.144 30.769 29.16 0.00 39.88 5.34
3314 3392 8.958043 GCGAAATAATTTGATCAAATAGGACAC 58.042 33.333 29.16 18.51 39.88 3.67
3358 3436 7.255906 GCATCTACTGATCTAGCATGCCTATAT 60.256 40.741 15.66 2.88 30.98 0.86
3359 3437 6.040278 GCATCTACTGATCTAGCATGCCTATA 59.960 42.308 15.66 0.00 30.98 1.31
3360 3438 5.163426 GCATCTACTGATCTAGCATGCCTAT 60.163 44.000 15.66 5.31 30.98 2.57
3469 3921 8.898761 GCGTGCTAGCCTGATCTATATATATAT 58.101 37.037 13.29 10.10 0.00 0.86
3470 3922 8.103935 AGCGTGCTAGCCTGATCTATATATATA 58.896 37.037 13.29 2.49 38.01 0.86
3471 3923 6.945435 AGCGTGCTAGCCTGATCTATATATAT 59.055 38.462 13.29 0.00 38.01 0.86
3472 3924 6.299922 AGCGTGCTAGCCTGATCTATATATA 58.700 40.000 13.29 0.00 38.01 0.86
3473 3925 5.136828 AGCGTGCTAGCCTGATCTATATAT 58.863 41.667 13.29 0.00 38.01 0.86
3474 3926 4.527944 AGCGTGCTAGCCTGATCTATATA 58.472 43.478 13.29 0.00 38.01 0.86
3475 3927 3.360867 AGCGTGCTAGCCTGATCTATAT 58.639 45.455 13.29 0.00 38.01 0.86
3476 3928 2.796557 AGCGTGCTAGCCTGATCTATA 58.203 47.619 13.29 0.00 38.01 1.31
3477 3929 1.626686 AGCGTGCTAGCCTGATCTAT 58.373 50.000 13.29 0.00 38.01 1.98
3507 3959 0.949105 GTGTACAAGTGTGAGCGGGG 60.949 60.000 0.00 0.00 0.00 5.73
3908 4368 8.779303 ACTACTCGAACATTCTATACTGATCTG 58.221 37.037 0.00 0.00 0.00 2.90
3953 4413 5.124936 GTGGTTACCTGAACATAAATGGTCC 59.875 44.000 2.07 0.00 43.80 4.46
3994 4455 0.685458 AGCAGATGGAATTGCCCACC 60.685 55.000 0.00 0.00 41.17 4.61
4148 4967 3.057806 GGGAAAATGAAGGTGTTACCGTG 60.058 47.826 0.00 0.00 44.90 4.94
4203 5022 1.348064 CTAACTCACACACCCCTCCA 58.652 55.000 0.00 0.00 0.00 3.86
4226 5045 9.415008 ACACTCTACATCTTACAATAGATCACT 57.585 33.333 0.00 0.00 32.60 3.41
4271 6644 2.502947 TGAGACTGGATTCATCTGTGGG 59.497 50.000 0.00 0.00 0.00 4.61
4288 6661 5.146298 ACTATTCATGAGGAGCAGATGAGA 58.854 41.667 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.