Multiple sequence alignment - TraesCS3B01G310600

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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 TraesCS3B01G310600 chr3B 100.000 3416 0 0 1 3416 499184072 499180657 0.000000e+00 6309
1 TraesCS3B01G310600 chr3B 96.844 2693 78 2 1 2686 259907430 259904738 0.000000e+00 4495
2 TraesCS3B01G310600 chr2B 97.130 3450 64 8 1 3416 166038482 166035034 0.000000e+00 5790
3 TraesCS3B01G310600 chr2B 97.621 2690 57 2 1 2683 9223420 9226109 0.000000e+00 4606
4 TraesCS3B01G310600 chr2B 98.053 719 13 1 2698 3416 9226221 9226938 0.000000e+00 1249
5 TraesCS3B01G310600 chr2B 97.914 719 14 1 2698 3416 481895439 481896156 0.000000e+00 1243
6 TraesCS3B01G310600 chr1B 97.919 2691 48 3 1 2683 551874325 551877015 0.000000e+00 4652
7 TraesCS3B01G310600 chr1B 97.586 2693 57 3 1 2686 670668824 670666133 0.000000e+00 4606
8 TraesCS3B01G310600 chr1B 97.775 719 15 1 2698 3416 551877127 551877844 0.000000e+00 1238
9 TraesCS3B01G310600 chr1B 97.493 718 17 1 2699 3416 670666023 670665307 0.000000e+00 1225
10 TraesCS3B01G310600 chr1B 98.319 119 2 0 3298 3416 659735246 659735128 3.450000e-50 209
11 TraesCS3B01G310600 chr7B 97.695 2690 55 2 1 2683 33887077 33889766 0.000000e+00 4617
12 TraesCS3B01G310600 chr7B 95.918 2695 101 3 1 2686 203602749 203600055 0.000000e+00 4359
13 TraesCS3B01G310600 chr6B 97.412 2628 56 2 1 2616 635286822 635284195 0.000000e+00 4466
14 TraesCS3B01G310600 chr3A 95.912 2691 102 4 1 2683 627952224 627954914 0.000000e+00 4353
15 TraesCS3B01G310600 chr5B 98.609 719 9 1 2698 3416 516275324 516276041 0.000000e+00 1271
16 TraesCS3B01G310600 chr5B 97.632 718 16 1 2699 3416 396075837 396076553 0.000000e+00 1230
17 TraesCS3B01G310600 chr4B 98.420 633 9 1 2698 3330 648181467 648182098 0.000000e+00 1112
18 TraesCS3B01G310600 chr4B 98.718 624 7 1 2707 3330 648202726 648203348 0.000000e+00 1107
19 TraesCS3B01G310600 chr4B 98.319 119 2 0 3298 3416 237020326 237020208 3.450000e-50 209


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 TraesCS3B01G310600 chr3B 499180657 499184072 3415 True 6309.0 6309 100.0000 1 3416 1 chr3B.!!$R2 3415
1 TraesCS3B01G310600 chr3B 259904738 259907430 2692 True 4495.0 4495 96.8440 1 2686 1 chr3B.!!$R1 2685
2 TraesCS3B01G310600 chr2B 166035034 166038482 3448 True 5790.0 5790 97.1300 1 3416 1 chr2B.!!$R1 3415
3 TraesCS3B01G310600 chr2B 9223420 9226938 3518 False 2927.5 4606 97.8370 1 3416 2 chr2B.!!$F2 3415
4 TraesCS3B01G310600 chr2B 481895439 481896156 717 False 1243.0 1243 97.9140 2698 3416 1 chr2B.!!$F1 718
5 TraesCS3B01G310600 chr1B 551874325 551877844 3519 False 2945.0 4652 97.8470 1 3416 2 chr1B.!!$F1 3415
6 TraesCS3B01G310600 chr1B 670665307 670668824 3517 True 2915.5 4606 97.5395 1 3416 2 chr1B.!!$R2 3415
7 TraesCS3B01G310600 chr7B 33887077 33889766 2689 False 4617.0 4617 97.6950 1 2683 1 chr7B.!!$F1 2682
8 TraesCS3B01G310600 chr7B 203600055 203602749 2694 True 4359.0 4359 95.9180 1 2686 1 chr7B.!!$R1 2685
9 TraesCS3B01G310600 chr6B 635284195 635286822 2627 True 4466.0 4466 97.4120 1 2616 1 chr6B.!!$R1 2615
10 TraesCS3B01G310600 chr3A 627952224 627954914 2690 False 4353.0 4353 95.9120 1 2683 1 chr3A.!!$F1 2682
11 TraesCS3B01G310600 chr5B 516275324 516276041 717 False 1271.0 1271 98.6090 2698 3416 1 chr5B.!!$F2 718
12 TraesCS3B01G310600 chr5B 396075837 396076553 716 False 1230.0 1230 97.6320 2699 3416 1 chr5B.!!$F1 717
13 TraesCS3B01G310600 chr4B 648181467 648182098 631 False 1112.0 1112 98.4200 2698 3330 1 chr4B.!!$F1 632
14 TraesCS3B01G310600 chr4B 648202726 648203348 622 False 1107.0 1107 98.7180 2707 3330 1 chr4B.!!$F2 623

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
754 757 1.078848 GAGCGTCTGCCTGTTGGAT 60.079 57.895 0.0 0.0 44.31 3.41 F
1366 1376 1.405797 CCGTATGTTACCCGCTTCCAA 60.406 52.381 0.0 0.0 0.00 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 1696 0.179137 CTTGATCTCGGTGCGCTACA 60.179 55.0 9.73 0.0 0.00 2.74 R
2683 2701 0.387929 CCATGGATGTGATGCAAGCC 59.612 55.0 5.56 0.0 33.18 4.35 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
164 165 1.229051 TGGGGAGATGACCGTGACA 60.229 57.895 0.00 0.00 0.00 3.58
567 568 1.549170 CTCTTGCCTACTTGTACCGGT 59.451 52.381 13.98 13.98 0.00 5.28
754 757 1.078848 GAGCGTCTGCCTGTTGGAT 60.079 57.895 0.00 0.00 44.31 3.41
1006 1015 3.956199 CTGTTTCATAGGTGGAATGGCAT 59.044 43.478 0.00 0.00 0.00 4.40
1229 1239 6.344500 CACTTCATAGGTAAGAGAGCATGTT 58.656 40.000 0.00 0.00 0.00 2.71
1327 1337 1.771255 AGGCAGCGGAAGATAAAGGAT 59.229 47.619 0.00 0.00 0.00 3.24
1366 1376 1.405797 CCGTATGTTACCCGCTTCCAA 60.406 52.381 0.00 0.00 0.00 3.53
1686 1696 7.066766 GGCTAACACATTCATTCTTTCTCATCT 59.933 37.037 0.00 0.00 0.00 2.90
1735 1745 4.075682 CCGATGAGAGCCAGTCTATTCTA 58.924 47.826 0.00 0.00 34.71 2.10
1821 1831 2.168313 TCGCATTCACTATGAGAGCCAA 59.832 45.455 0.00 0.00 38.02 4.52
1868 1878 7.045416 TCTTACACACTTGTTCATGTTACAGT 58.955 34.615 0.00 0.00 37.15 3.55
2073 2083 8.324191 TGAGTAATCCTTTAGATGTGATTCCT 57.676 34.615 0.00 0.00 34.56 3.36
2109 2119 3.283751 CCGGCCTTCACCATATTGTTTA 58.716 45.455 0.00 0.00 0.00 2.01
2201 2211 1.574526 TTCAAGCCTAGGCAGCCCAT 61.575 55.000 34.70 11.07 44.88 4.00
2400 2416 2.203139 CGTGGCACCAGGAACACA 60.203 61.111 12.86 0.00 34.13 3.72
2640 2657 3.526931 TCTAGTTATGTGAGTGCTGCC 57.473 47.619 0.00 0.00 0.00 4.85
2691 2876 3.592059 CAGTTTTGCTTATGGCTTGCAT 58.408 40.909 0.00 0.00 42.39 3.96
2692 2877 3.615496 CAGTTTTGCTTATGGCTTGCATC 59.385 43.478 0.00 0.00 42.39 3.91
2695 2880 1.836802 TGCTTATGGCTTGCATCACA 58.163 45.000 0.00 0.00 42.39 3.58
2696 2881 2.380941 TGCTTATGGCTTGCATCACAT 58.619 42.857 0.00 0.00 42.39 3.21
3148 3333 3.440173 ACAATCTGCGTATTGGTCCTTTG 59.560 43.478 13.52 0.00 40.48 2.77
3382 3567 8.774586 GCATAGTTCGGACATACAAAATATCTT 58.225 33.333 0.00 0.00 0.00 2.40
3391 3576 6.357367 ACATACAAAATATCTTCGCCCTTCT 58.643 36.000 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 1.329906 CAGTGGAGCATTCAGATTCGC 59.670 52.381 0.00 0.00 0.00 4.70
287 288 0.958091 CCTCCTCTACATCAGCCTCG 59.042 60.000 0.00 0.00 0.00 4.63
403 404 0.254178 AGCATGTGTCTGGATCACCC 59.746 55.000 0.00 0.00 35.25 4.61
404 405 1.661341 GAGCATGTGTCTGGATCACC 58.339 55.000 0.00 0.00 35.25 4.02
567 568 5.617528 TCACAAAACAGACCAACTACCTA 57.382 39.130 0.00 0.00 0.00 3.08
694 697 4.666512 AGAAGCAGATTACCACCAATGTT 58.333 39.130 0.00 0.00 0.00 2.71
695 698 4.307032 AGAAGCAGATTACCACCAATGT 57.693 40.909 0.00 0.00 0.00 2.71
754 757 4.069232 CCTGACGCTCTTCGGGCA 62.069 66.667 0.00 0.00 43.86 5.36
1006 1015 2.087462 CTCTCACCGCGCCATATGGA 62.087 60.000 26.47 1.11 37.39 3.41
1017 1027 1.218316 GTACCCCAAGCTCTCACCG 59.782 63.158 0.00 0.00 0.00 4.94
1047 1057 2.264480 CACATCGGGTTGAGGCGA 59.736 61.111 0.00 0.00 0.00 5.54
1229 1239 2.863740 CCGATGCTTAGACAATACGCAA 59.136 45.455 0.00 0.00 33.94 4.85
1327 1337 3.301070 GCATGATGCTTGCCCCAA 58.699 55.556 10.72 0.00 40.96 4.12
1366 1376 1.875576 CGAGCTTGCTCCACAGAAAGT 60.876 52.381 15.87 0.00 37.59 2.66
1686 1696 0.179137 CTTGATCTCGGTGCGCTACA 60.179 55.000 9.73 0.00 0.00 2.74
1735 1745 1.070289 GTTCCAACCGGTGTCTTCTCT 59.930 52.381 8.52 0.00 0.00 3.10
1821 1831 8.668510 AAGATATCAAACTTCGCAACATAGAT 57.331 30.769 5.32 0.00 0.00 1.98
1868 1878 2.814097 GCCTTAACTTCTTGGCCTGACA 60.814 50.000 3.32 0.00 39.49 3.58
1912 1922 5.070313 TGGTTCATCATATTCAGGATCACGA 59.930 40.000 0.00 0.00 0.00 4.35
2072 2082 2.190981 GCCGGTGTCGTAATCAAGTAG 58.809 52.381 1.90 0.00 33.95 2.57
2073 2083 1.135024 GGCCGGTGTCGTAATCAAGTA 60.135 52.381 1.90 0.00 33.95 2.24
2109 2119 1.915489 TCATGGCCCTATCACACAACT 59.085 47.619 0.00 0.00 0.00 3.16
2400 2416 2.106683 GCACTAATGCCTTCCGCGT 61.107 57.895 4.92 0.00 46.97 6.01
2640 2657 2.887360 CCATTTTGGCCTCCTGCG 59.113 61.111 3.32 0.00 42.61 5.18
2683 2701 0.387929 CCATGGATGTGATGCAAGCC 59.612 55.000 5.56 0.00 33.18 4.35
2686 2704 1.478916 CAAGCCATGGATGTGATGCAA 59.521 47.619 18.40 0.00 33.18 4.08
2691 2876 1.341187 TGATGCAAGCCATGGATGTGA 60.341 47.619 18.40 5.22 40.61 3.58
2692 2877 1.107945 TGATGCAAGCCATGGATGTG 58.892 50.000 18.40 11.66 40.61 3.21
2695 2880 1.961394 GATGTGATGCAAGCCATGGAT 59.039 47.619 18.40 6.18 43.60 3.41
2696 2881 1.395635 GATGTGATGCAAGCCATGGA 58.604 50.000 18.40 0.00 33.29 3.41
3148 3333 3.141398 TGAAGTGCCAGAAGATGTGAAC 58.859 45.455 0.00 0.00 0.00 3.18
3382 3567 1.841302 AAGCATGGACAGAAGGGCGA 61.841 55.000 0.00 0.00 0.00 5.54
3391 3576 2.151202 GACCGAAAGAAAGCATGGACA 58.849 47.619 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.