Multiple sequence alignment - TraesCS3B01G212000

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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 TraesCS3B01G212000 chr3B 100.000 3907 0 0 1 3907 251266989 251270895 0.000000e+00 7215.0
1 TraesCS3B01G212000 chr3B 97.666 3814 73 3 95 3907 251181136 251184934 0.000000e+00 6536.0
2 TraesCS3B01G212000 chr3B 84.968 2774 321 48 595 3318 798551813 798549086 0.000000e+00 2724.0
3 TraesCS3B01G212000 chr3B 82.870 216 26 6 633 839 798557347 798557134 2.400000e-42 183.0
4 TraesCS3B01G212000 chr3B 79.394 165 25 7 3317 3474 828115215 828115053 1.480000e-19 108.0
5 TraesCS3B01G212000 chr3B 78.761 113 15 5 155 258 137779921 137779809 2.520000e-07 67.6
6 TraesCS3B01G212000 chr3A 84.864 2821 329 52 557 3323 726141963 726139187 0.000000e+00 2754.0
7 TraesCS3B01G212000 chr3D 84.959 2779 325 47 595 3323 595112250 595109515 0.000000e+00 2730.0
8 TraesCS3B01G212000 chr3D 81.437 167 25 6 3313 3474 610547639 610547474 8.810000e-27 132.0
9 TraesCS3B01G212000 chr7B 80.625 160 21 9 3346 3503 162624084 162623933 8.870000e-22 115.0
10 TraesCS3B01G212000 chr6A 79.355 155 19 8 3349 3503 454480628 454480487 3.210000e-16 97.1
11 TraesCS3B01G212000 chr1B 85.714 77 4 6 3374 3445 656201869 656201795 1.510000e-09 75.0
12 TraesCS3B01G212000 chr2B 93.182 44 2 1 94 137 239460266 239460308 3.260000e-06 63.9
13 TraesCS3B01G212000 chr2B 90.909 44 3 1 94 137 687242922 687242880 1.520000e-04 58.4


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 TraesCS3B01G212000 chr3B 251266989 251270895 3906 False 7215 7215 100.000 1 3907 1 chr3B.!!$F2 3906
1 TraesCS3B01G212000 chr3B 251181136 251184934 3798 False 6536 6536 97.666 95 3907 1 chr3B.!!$F1 3812
2 TraesCS3B01G212000 chr3B 798549086 798551813 2727 True 2724 2724 84.968 595 3318 1 chr3B.!!$R2 2723
3 TraesCS3B01G212000 chr3A 726139187 726141963 2776 True 2754 2754 84.864 557 3323 1 chr3A.!!$R1 2766
4 TraesCS3B01G212000 chr3D 595109515 595112250 2735 True 2730 2730 84.959 595 3323 1 chr3D.!!$R1 2728

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
730 735 0.391927 CAATAACGGGGCCGAGTTCA 60.392 55.0 17.4 7.06 42.83 3.18 F
1257 1268 0.188587 AGATGCAGGAGGGGTCGATA 59.811 55.0 0.0 0.00 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2717 2769 1.068885 CCGACTGTGTCTGAGAGTGAC 60.069 57.143 0.0 0.0 35.21 3.67 R
2939 2991 1.588674 TGTAATAAGCATTCCCCGCG 58.411 50.000 0.0 0.0 0.00 6.46 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
81 82 6.872628 AAAAACCCGGTTAAAAACAAAACA 57.127 29.167 2.39 0.00 0.00 2.83
82 83 6.483385 AAAACCCGGTTAAAAACAAAACAG 57.517 33.333 2.39 0.00 0.00 3.16
83 84 5.402997 AACCCGGTTAAAAACAAAACAGA 57.597 34.783 0.00 0.00 0.00 3.41
84 85 5.402997 ACCCGGTTAAAAACAAAACAGAA 57.597 34.783 0.00 0.00 0.00 3.02
85 86 5.791666 ACCCGGTTAAAAACAAAACAGAAA 58.208 33.333 0.00 0.00 0.00 2.52
86 87 6.228995 ACCCGGTTAAAAACAAAACAGAAAA 58.771 32.000 0.00 0.00 0.00 2.29
87 88 6.709397 ACCCGGTTAAAAACAAAACAGAAAAA 59.291 30.769 0.00 0.00 0.00 1.94
143 144 3.686760 GCCAGAAACCTCTTGGCC 58.313 61.111 0.00 0.00 38.72 5.36
144 145 1.979155 GCCAGAAACCTCTTGGCCC 60.979 63.158 0.00 0.00 38.72 5.80
187 188 0.537188 AGACCGAAGCCGAATGATGT 59.463 50.000 0.00 0.00 38.22 3.06
193 194 0.960364 AAGCCGAATGATGTGCCGTT 60.960 50.000 0.00 0.00 0.00 4.44
323 325 2.325393 GAATCGTCCCTGGCCGGATT 62.325 60.000 15.09 3.82 33.48 3.01
333 335 3.053291 GCCGGATTGAACCACGCA 61.053 61.111 5.05 0.00 0.00 5.24
423 425 3.917760 CCACGCCTCCGATCCTCC 61.918 72.222 0.00 0.00 38.29 4.30
424 426 2.835431 CACGCCTCCGATCCTCCT 60.835 66.667 0.00 0.00 38.29 3.69
432 434 3.893763 CGATCCTCCTGCGTCGCT 61.894 66.667 19.50 0.00 0.00 4.93
581 583 2.040278 AGCAACTGCAGATTGTTCCCTA 59.960 45.455 23.35 0.00 45.16 3.53
586 588 2.237143 CTGCAGATTGTTCCCTAGTCCA 59.763 50.000 8.42 0.00 0.00 4.02
730 735 0.391927 CAATAACGGGGCCGAGTTCA 60.392 55.000 17.40 7.06 42.83 3.18
790 795 1.151810 AGTTTCCTCCAGCCCTCCA 60.152 57.895 0.00 0.00 0.00 3.86
824 829 1.246056 TACTACCAGCACCGCGTCTT 61.246 55.000 4.92 0.00 0.00 3.01
860 865 2.900273 GCCCGTCACTGATGCCTA 59.100 61.111 0.00 0.00 0.00 3.93
866 871 2.184322 CACTGATGCCTACGCCGT 59.816 61.111 0.00 0.00 0.00 5.68
870 875 4.830765 GATGCCTACGCCGTGCCA 62.831 66.667 0.00 0.00 0.00 4.92
949 960 2.925170 ACCACTCTGCGCCCTTCT 60.925 61.111 4.18 0.00 0.00 2.85
1075 1086 2.738521 CACAGTTCGTGGCTCGGG 60.739 66.667 9.26 0.00 42.34 5.14
1137 1148 3.249080 GCACCAACTCGCAGTTTAACTTA 59.751 43.478 0.00 0.00 36.03 2.24
1240 1251 0.250467 GCCTGCACTGACAAAGGAGA 60.250 55.000 0.00 0.00 30.92 3.71
1256 1267 1.074926 AGATGCAGGAGGGGTCGAT 60.075 57.895 0.00 0.00 0.00 3.59
1257 1268 0.188587 AGATGCAGGAGGGGTCGATA 59.811 55.000 0.00 0.00 0.00 2.92
1312 1323 1.690219 GCTGGAGTGGGACCGATCAT 61.690 60.000 0.00 0.00 0.00 2.45
1440 1451 4.080695 GCAGATGATGAATATGAGGGGCTA 60.081 45.833 0.00 0.00 28.18 3.93
1475 1486 2.009774 GCTAGAAGAATTGAAGCGCCA 58.990 47.619 2.29 0.00 0.00 5.69
1546 1557 3.521126 ACCAGCTAAGGATGTTGAGATGT 59.479 43.478 0.00 0.00 0.00 3.06
1563 1574 5.222505 TGAGATGTAGATGGATGAGGAGGAT 60.223 44.000 0.00 0.00 0.00 3.24
1926 1940 3.737559 AGGCCAGACATATTTGGAACA 57.262 42.857 5.01 0.00 36.55 3.18
2298 2336 1.342874 CCCATGGGTCCTATGCCAAAA 60.343 52.381 23.93 0.00 0.00 2.44
2409 2450 1.643310 CAACCATGGTCAACCCCATT 58.357 50.000 20.07 0.00 42.70 3.16
2528 2569 2.475155 TGATGCTTCTCTGATCCCAGT 58.525 47.619 0.88 0.00 41.16 4.00
2578 2619 9.619316 CGGTAATGTTTCTTTTCATATGTTTCA 57.381 29.630 1.90 0.00 0.00 2.69
2624 2673 6.135290 TCCTGCAATGTCATGCTAATTTAC 57.865 37.500 0.67 0.00 46.54 2.01
2717 2769 4.550076 AGTTTTGGAGATCTCTGTCCAG 57.450 45.455 21.81 0.00 44.93 3.86
2939 2991 1.808343 CCAGTTTACTTACGGGGCAAC 59.192 52.381 0.00 0.00 30.77 4.17
2972 3024 6.620678 TGCTTATTACAACCAAGCTTCAATC 58.379 36.000 0.00 0.00 43.98 2.67
3018 3070 2.573462 AGTTGCTGCCTTCTGGATTCTA 59.427 45.455 0.00 0.00 34.57 2.10
3229 3282 3.309954 GCCGTATTAGCTTCTCCTGTTTG 59.690 47.826 0.00 0.00 0.00 2.93
3422 3475 5.105917 CCGTATCCAAAAACCTAACAATGCT 60.106 40.000 0.00 0.00 0.00 3.79
3456 3509 0.110486 AAACCGAGTGAGCACCCAAT 59.890 50.000 0.00 0.00 0.00 3.16
3554 3607 6.418057 AGACACTGTCTCTCTCTTTTCAAT 57.582 37.500 5.82 0.00 38.71 2.57
3600 3653 8.228464 GTGGAAAGCTTATGTTGTAGTTCTAAC 58.772 37.037 0.00 0.00 0.00 2.34
3879 3932 7.720957 TGTTTCATGGTGCTATTAATATCTGCT 59.279 33.333 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 6.709397 TCTGTTTTGTTTTTAACCGGGTTTTT 59.291 30.769 19.02 0.00 0.00 1.94
59 60 6.228995 TCTGTTTTGTTTTTAACCGGGTTTT 58.771 32.000 19.02 0.00 0.00 2.43
60 61 5.791666 TCTGTTTTGTTTTTAACCGGGTTT 58.208 33.333 19.02 2.39 0.00 3.27
61 62 5.402997 TCTGTTTTGTTTTTAACCGGGTT 57.597 34.783 17.83 17.83 0.00 4.11
62 63 5.402997 TTCTGTTTTGTTTTTAACCGGGT 57.597 34.783 6.32 0.00 0.00 5.28
63 64 6.723131 TTTTCTGTTTTGTTTTTAACCGGG 57.277 33.333 6.32 0.00 0.00 5.73
86 87 9.971922 CTTTTAGAAGATTCCTTGAATGTGTTT 57.028 29.630 0.00 0.00 34.71 2.83
87 88 8.579863 CCTTTTAGAAGATTCCTTGAATGTGTT 58.420 33.333 0.00 0.00 34.71 3.32
88 89 7.725844 ACCTTTTAGAAGATTCCTTGAATGTGT 59.274 33.333 0.00 0.00 34.71 3.72
89 90 8.115490 ACCTTTTAGAAGATTCCTTGAATGTG 57.885 34.615 0.00 0.00 34.71 3.21
90 91 8.712228 AACCTTTTAGAAGATTCCTTGAATGT 57.288 30.769 0.00 0.00 34.71 2.71
122 123 1.073199 CAAGAGGTTTCTGGCCGGT 59.927 57.895 12.43 0.00 32.79 5.28
143 144 1.283029 TCTTCCTTGCAGGATCCTTGG 59.717 52.381 13.00 12.12 45.34 3.61
144 145 2.795231 TCTTCCTTGCAGGATCCTTG 57.205 50.000 13.00 9.17 45.34 3.61
168 169 0.537188 ACATCATTCGGCTTCGGTCT 59.463 50.000 0.00 0.00 34.13 3.85
171 172 1.353103 GCACATCATTCGGCTTCGG 59.647 57.895 0.00 0.00 34.13 4.30
193 194 1.371183 CCTGTCGCTTCCACTTGGA 59.629 57.895 0.00 0.00 43.73 3.53
323 325 2.434185 GCCGATCTGCGTGGTTCA 60.434 61.111 0.00 0.00 38.67 3.18
417 419 3.842923 CCAGCGACGCAGGAGGAT 61.843 66.667 25.51 0.00 37.40 3.24
737 742 2.358247 GGTTGTGGGCGACGATGT 60.358 61.111 0.00 0.00 0.00 3.06
790 795 0.336048 TAGTAGGCGTGGTAGGGGTT 59.664 55.000 0.00 0.00 0.00 4.11
824 829 1.277326 CGAATGTTCGGCGATCTCAA 58.723 50.000 11.76 0.00 46.30 3.02
866 871 3.062466 CGTCCTCGGACTCTGGCA 61.062 66.667 13.74 0.00 42.54 4.92
949 960 4.927782 GGTCAGCGGTGCCACACA 62.928 66.667 18.91 0.00 35.86 3.72
1075 1086 2.233922 TCGTCAGGAAGTTCTTCCCATC 59.766 50.000 23.02 14.23 42.06 3.51
1137 1148 2.047274 CTGTGCGTGGGTCGGATT 60.047 61.111 0.00 0.00 42.55 3.01
1162 1173 2.034558 CGGCAAACATGGTGAAGAAAGT 59.965 45.455 0.00 0.00 0.00 2.66
1240 1251 0.188587 TCTATCGACCCCTCCTGCAT 59.811 55.000 0.00 0.00 0.00 3.96
1312 1323 1.079127 GTTGCTTCGCCTGCTCCTA 60.079 57.895 0.00 0.00 0.00 2.94
1440 1451 3.650298 TAGCGTAGGCGGGACAGGT 62.650 63.158 1.05 0.00 46.35 4.00
1446 1457 0.674534 ATTCTTCTAGCGTAGGCGGG 59.325 55.000 1.05 0.00 46.35 6.13
1475 1486 2.476199 CCAAGGTCTCCATCCTCTTCT 58.524 52.381 0.00 0.00 33.76 2.85
1546 1557 4.951603 TGCATATCCTCCTCATCCATCTA 58.048 43.478 0.00 0.00 0.00 1.98
1563 1574 4.365514 TCCTTCCTCAACAAGTTGCATA 57.634 40.909 8.04 0.00 40.24 3.14
1744 1758 2.030363 CGCTAATCGGAATGAGCTCTCT 60.030 50.000 16.19 1.00 37.24 3.10
1926 1940 5.249420 GCATTAGAAACCTCTTCCTCAGTT 58.751 41.667 0.00 0.00 32.70 3.16
2183 2197 4.279420 GGGTTTGGAGATGATAAGGCATTC 59.721 45.833 0.00 0.00 0.00 2.67
2409 2450 2.696125 GGAGCCTGGGGGATTCCA 60.696 66.667 4.80 0.00 37.64 3.53
2528 2569 3.016031 TGCTGAACAAGAAACTGCTCAA 58.984 40.909 0.00 0.00 0.00 3.02
2624 2673 2.576615 GCAGGGCCCTGTAGAAATAAG 58.423 52.381 44.45 22.00 45.24 1.73
2717 2769 1.068885 CCGACTGTGTCTGAGAGTGAC 60.069 57.143 0.00 0.00 35.21 3.67
2939 2991 1.588674 TGTAATAAGCATTCCCCGCG 58.411 50.000 0.00 0.00 0.00 6.46
2942 2994 4.441495 GCTTGGTTGTAATAAGCATTCCCC 60.441 45.833 0.00 0.00 44.59 4.81
2943 2995 4.402474 AGCTTGGTTGTAATAAGCATTCCC 59.598 41.667 10.36 0.00 46.90 3.97
2944 2996 5.582689 AGCTTGGTTGTAATAAGCATTCC 57.417 39.130 10.36 0.00 46.90 3.01
2945 2997 6.620678 TGAAGCTTGGTTGTAATAAGCATTC 58.379 36.000 2.10 10.47 46.90 2.67
2946 2998 6.588719 TGAAGCTTGGTTGTAATAAGCATT 57.411 33.333 2.10 2.81 46.90 3.56
2947 2999 6.588719 TTGAAGCTTGGTTGTAATAAGCAT 57.411 33.333 2.10 0.00 46.90 3.79
2948 3000 6.588719 ATTGAAGCTTGGTTGTAATAAGCA 57.411 33.333 2.10 0.00 46.90 3.91
2972 3024 4.202080 ACAAAAATGATCTCCATGATGGCG 60.202 41.667 6.59 0.00 37.47 5.69
3456 3509 7.931948 TGTCCTTTTTCCTTTTTGTGTTTGTTA 59.068 29.630 0.00 0.00 0.00 2.41
3554 3607 4.701651 CCACAGACCTTTCATGATAAGCAA 59.298 41.667 0.00 0.00 0.00 3.91
3600 3653 2.892852 ACATCACCCACAACTCCATTTG 59.107 45.455 0.00 0.00 0.00 2.32
3879 3932 8.875803 CGTGTAAAGACCTATGCTAAACATTAA 58.124 33.333 0.00 0.00 40.38 1.40


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

AutoCloner maintained by Alex Coulton.