Multiple sequence alignment - TraesCS7A01G311500

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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 TraesCS7A01G311500 chr7A 100.000 2830 0 0 1 2830 441745150 441747979 0.000000e+00 5227.0
1 TraesCS7A01G311500 chr7A 95.853 1953 59 6 1 1931 217690247 217688295 0.000000e+00 3138.0
2 TraesCS7A01G311500 chr7A 100.000 38 0 0 2793 2830 610489312 610489275 1.410000e-08 71.3
3 TraesCS7A01G311500 chr2A 96.319 2825 68 11 1 2794 191974317 191977136 0.000000e+00 4608.0
4 TraesCS7A01G311500 chr2A 95.745 2820 90 15 1 2794 77762335 77759520 0.000000e+00 4516.0
5 TraesCS7A01G311500 chr2A 100.000 38 0 0 2793 2830 109110911 109110948 1.410000e-08 71.3
6 TraesCS7A01G311500 chr2A 100.000 38 0 0 2793 2830 666807377 666807414 1.410000e-08 71.3
7 TraesCS7A01G311500 chr3A 95.959 2821 84 9 1 2794 601662561 601659744 0.000000e+00 4551.0
8 TraesCS7A01G311500 chr3A 95.883 2769 91 9 47 2794 738756405 738753639 0.000000e+00 4460.0
9 TraesCS7A01G311500 chr3A 94.901 2824 105 11 1 2794 484552365 484549551 0.000000e+00 4381.0
10 TraesCS7A01G311500 chr3A 96.894 322 8 2 2474 2794 601650548 601650228 3.210000e-149 538.0
11 TraesCS7A01G311500 chr1A 95.925 2626 81 9 193 2794 13803376 13800753 0.000000e+00 4233.0
12 TraesCS7A01G311500 chr1A 95.487 2504 80 10 309 2794 406150855 406153343 0.000000e+00 3967.0
13 TraesCS7A01G311500 chr1A 96.061 330 7 3 1 324 406149086 406149415 1.490000e-147 532.0
14 TraesCS7A01G311500 chr1A 97.585 207 2 2 1 206 13803599 13803395 4.490000e-93 351.0
15 TraesCS7A01G311500 chr1D 93.562 2330 117 18 301 2606 492938032 492940352 0.000000e+00 3441.0
16 TraesCS7A01G311500 chr1D 95.238 105 4 1 199 302 492912186 492912290 6.270000e-37 165.0
17 TraesCS7A01G311500 chr1D 97.297 37 1 0 2794 2830 35436073 35436109 2.350000e-06 63.9
18 TraesCS7A01G311500 chr7B 92.056 2354 139 27 303 2615 554184533 554182187 0.000000e+00 3267.0
19 TraesCS7A01G311500 chr7B 88.037 326 15 5 1 302 554185127 554184802 5.760000e-97 364.0
20 TraesCS7A01G311500 chr1B 93.913 460 28 0 301 760 630554945 630554486 0.000000e+00 695.0
21 TraesCS7A01G311500 chr5B 95.528 246 9 2 2551 2795 636509186 636509430 2.640000e-105 392.0
22 TraesCS7A01G311500 chr4D 100.000 37 0 0 2794 2830 357316 357280 5.060000e-08 69.4
23 TraesCS7A01G311500 chr6A 97.368 38 1 0 2793 2830 325732261 325732298 6.540000e-07 65.8
24 TraesCS7A01G311500 chr6D 100.000 29 0 0 2793 2821 39219609 39219581 1.000000e-03 54.7
25 TraesCS7A01G311500 chr5D 100.000 29 0 0 2793 2821 149082182 149082154 1.000000e-03 54.7


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 TraesCS7A01G311500 chr7A 441745150 441747979 2829 False 5227.0 5227 100.0000 1 2830 1 chr7A.!!$F1 2829
1 TraesCS7A01G311500 chr7A 217688295 217690247 1952 True 3138.0 3138 95.8530 1 1931 1 chr7A.!!$R1 1930
2 TraesCS7A01G311500 chr2A 191974317 191977136 2819 False 4608.0 4608 96.3190 1 2794 1 chr2A.!!$F2 2793
3 TraesCS7A01G311500 chr2A 77759520 77762335 2815 True 4516.0 4516 95.7450 1 2794 1 chr2A.!!$R1 2793
4 TraesCS7A01G311500 chr3A 601659744 601662561 2817 True 4551.0 4551 95.9590 1 2794 1 chr3A.!!$R3 2793
5 TraesCS7A01G311500 chr3A 738753639 738756405 2766 True 4460.0 4460 95.8830 47 2794 1 chr3A.!!$R4 2747
6 TraesCS7A01G311500 chr3A 484549551 484552365 2814 True 4381.0 4381 94.9010 1 2794 1 chr3A.!!$R1 2793
7 TraesCS7A01G311500 chr1A 13800753 13803599 2846 True 2292.0 4233 96.7550 1 2794 2 chr1A.!!$R1 2793
8 TraesCS7A01G311500 chr1A 406149086 406153343 4257 False 2249.5 3967 95.7740 1 2794 2 chr1A.!!$F1 2793
9 TraesCS7A01G311500 chr1D 492938032 492940352 2320 False 3441.0 3441 93.5620 301 2606 1 chr1D.!!$F3 2305
10 TraesCS7A01G311500 chr7B 554182187 554185127 2940 True 1815.5 3267 90.0465 1 2615 2 chr7B.!!$R1 2614

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
271 326 0.322648 CCACACTCCTCACTGCATCA 59.677 55.0 0.00 0.00 0.00 3.07 F
1250 3063 0.373370 CCATGACCAACATACACGCG 59.627 55.0 3.53 3.53 37.46 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1427 3246 0.109412 GGTCGTCGTCTTCCATCGTT 60.109 55.0 0.0 0.0 0.0 3.85 R
2806 4639 0.037605 CCGACCAAACGCTACTCCTT 60.038 55.0 0.0 0.0 0.0 3.36 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
142 148 3.221771 TGTAAATTGGCAGTCACAGCTT 58.778 40.909 0.00 0.00 0.00 3.74
171 177 8.358895 TGACAAACAATGCATCTAAATTCTCAA 58.641 29.630 0.00 0.00 0.00 3.02
271 326 0.322648 CCACACTCCTCACTGCATCA 59.677 55.000 0.00 0.00 0.00 3.07
318 2096 4.063967 CGCCGTGGACCTGTGCTA 62.064 66.667 0.00 0.00 0.00 3.49
524 2302 1.043673 GTAGAGTGCGGGGAGGACAT 61.044 60.000 0.00 0.00 44.28 3.06
550 2328 3.263937 ACGTAAATACCTGGGGTTTAGCA 59.736 43.478 0.00 0.00 37.09 3.49
865 2660 1.538950 TGTGTATCAATTGCTTGCGCA 59.461 42.857 5.66 5.66 46.24 6.09
1018 2822 3.369471 CGGGATGTCTAAGCAAAGAAGGA 60.369 47.826 0.00 0.00 0.00 3.36
1023 2827 3.394606 TGTCTAAGCAAAGAAGGAAGGGT 59.605 43.478 0.00 0.00 0.00 4.34
1051 2855 2.018355 TGAGCCCAACTACTACCACA 57.982 50.000 0.00 0.00 0.00 4.17
1071 2875 3.434319 CGCAGCGGCAACAAGGAT 61.434 61.111 7.00 0.00 41.24 3.24
1214 3027 0.464036 CCATGTAGTTCGCAGCCCTA 59.536 55.000 0.00 0.00 0.00 3.53
1234 3047 1.731433 GGCAGCAACATCATCGCCAT 61.731 55.000 0.00 0.00 39.38 4.40
1237 3050 1.019673 AGCAACATCATCGCCATGAC 58.980 50.000 0.00 0.00 42.05 3.06
1250 3063 0.373370 CCATGACCAACATACACGCG 59.627 55.000 3.53 3.53 37.46 6.01
1328 3147 2.253452 GCACTGCTTTGTGGCTCG 59.747 61.111 0.00 0.00 38.31 5.03
1346 3165 0.969894 CGAACACCTTCCTGACCTCT 59.030 55.000 0.00 0.00 0.00 3.69
1483 3302 0.034186 TCCTGGAAAAGCATGCCGAT 60.034 50.000 15.66 0.00 0.00 4.18
1612 3434 1.673665 CCAGGAGCTGCAAGTGGAC 60.674 63.158 8.35 0.00 35.30 4.02
1772 3594 1.602237 GGAGTGGAAGATGGCCGAA 59.398 57.895 0.00 0.00 0.00 4.30
1860 3682 2.821366 GTACCGAGGAGTCGCCGA 60.821 66.667 0.00 0.00 45.41 5.54
2271 4096 1.291109 TCCGATGGGTTTATGTGGGT 58.709 50.000 0.00 0.00 33.83 4.51
2281 4106 0.322098 TTATGTGGGTGGTGAAGCGG 60.322 55.000 0.00 0.00 0.00 5.52
2659 4492 3.404773 CTGGAAGGTGGGAGGGAC 58.595 66.667 0.00 0.00 0.00 4.46
2741 4574 2.687566 GACCGGGTGAGGTGGGAT 60.688 66.667 3.30 0.00 46.09 3.85
2783 4616 4.441634 GCGACCTACCAACTGAGACATTAT 60.442 45.833 0.00 0.00 0.00 1.28
2794 4627 9.072375 CCAACTGAGACATTATGAGTAGAGATA 57.928 37.037 0.00 0.00 0.00 1.98
2801 4634 9.523168 AGACATTATGAGTAGAGATAACTACCC 57.477 37.037 0.00 0.00 42.34 3.69
2802 4635 9.298250 GACATTATGAGTAGAGATAACTACCCA 57.702 37.037 0.00 0.00 42.34 4.51
2803 4636 9.303116 ACATTATGAGTAGAGATAACTACCCAG 57.697 37.037 0.00 0.00 42.34 4.45
2804 4637 9.303116 CATTATGAGTAGAGATAACTACCCAGT 57.697 37.037 0.00 0.00 42.34 4.00
2805 4638 9.884814 ATTATGAGTAGAGATAACTACCCAGTT 57.115 33.333 0.00 0.00 46.77 3.16
2816 4649 3.022406 ACTACCCAGTTAAGGAGTAGCG 58.978 50.000 0.00 0.00 36.61 4.26
2817 4650 1.934410 ACCCAGTTAAGGAGTAGCGT 58.066 50.000 0.00 0.00 0.00 5.07
2818 4651 2.254508 ACCCAGTTAAGGAGTAGCGTT 58.745 47.619 0.00 0.00 0.00 4.84
2819 4652 2.636403 ACCCAGTTAAGGAGTAGCGTTT 59.364 45.455 0.00 0.00 0.00 3.60
2820 4653 3.000727 CCCAGTTAAGGAGTAGCGTTTG 58.999 50.000 0.00 0.00 0.00 2.93
2821 4654 3.000727 CCAGTTAAGGAGTAGCGTTTGG 58.999 50.000 0.00 0.00 0.00 3.28
2822 4655 3.556423 CCAGTTAAGGAGTAGCGTTTGGT 60.556 47.826 0.00 0.00 0.00 3.67
2823 4656 3.678548 CAGTTAAGGAGTAGCGTTTGGTC 59.321 47.826 0.00 0.00 0.00 4.02
2824 4657 2.642139 TAAGGAGTAGCGTTTGGTCG 57.358 50.000 0.00 0.00 0.00 4.79
2825 4658 0.037605 AAGGAGTAGCGTTTGGTCGG 60.038 55.000 0.00 0.00 0.00 4.79
2826 4659 2.098831 GGAGTAGCGTTTGGTCGGC 61.099 63.158 0.00 0.00 0.00 5.54
2827 4660 2.047560 AGTAGCGTTTGGTCGGCC 60.048 61.111 0.00 0.00 0.00 6.13
2828 4661 3.122971 GTAGCGTTTGGTCGGCCC 61.123 66.667 2.12 0.00 0.00 5.80
2829 4662 3.627952 TAGCGTTTGGTCGGCCCA 61.628 61.111 2.12 0.00 43.27 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 148 5.681337 TTTAGATGCATTGTTTGTCACGA 57.319 34.783 0.00 0.00 0.00 4.35
271 326 2.366153 GACACCACCCACCACCCATT 62.366 60.000 0.00 0.00 0.00 3.16
318 2096 1.078848 GCGGACATGGACTCAAGCT 60.079 57.895 0.00 0.00 0.00 3.74
524 2302 2.268107 ACCCCAGGTATTTACGTTCCA 58.732 47.619 0.00 0.00 32.11 3.53
550 2328 4.309950 GTCGTTCCCGCCACCAGT 62.310 66.667 0.00 0.00 0.00 4.00
865 2660 6.348622 CGATCTACTAGAAGCAACACGGATAT 60.349 42.308 0.00 0.00 0.00 1.63
1018 2822 0.985490 GGCTCATCCTCCTCACCCTT 60.985 60.000 0.00 0.00 0.00 3.95
1023 2827 0.252881 AGTTGGGCTCATCCTCCTCA 60.253 55.000 0.00 0.00 34.39 3.86
1071 2875 6.300703 GTCTAGAACCAGATAGAGGCTCTTA 58.699 44.000 24.13 9.15 33.78 2.10
1214 3027 2.117156 GGCGATGATGTTGCTGCCT 61.117 57.895 0.00 0.00 39.38 4.75
1234 3047 1.374885 CCCGCGTGTATGTTGGTCA 60.375 57.895 4.92 0.00 0.00 4.02
1237 3050 1.641123 GGTTCCCGCGTGTATGTTGG 61.641 60.000 4.92 0.00 0.00 3.77
1250 3063 1.204231 GTGTCGTAGAAGAGGGTTCCC 59.796 57.143 0.00 0.00 39.69 3.97
1328 3147 1.002544 CCAGAGGTCAGGAAGGTGTTC 59.997 57.143 0.00 0.00 0.00 3.18
1427 3246 0.109412 GGTCGTCGTCTTCCATCGTT 60.109 55.000 0.00 0.00 0.00 3.85
1568 3390 1.972223 AGAGTACGTGCCGCAGACT 60.972 57.895 0.00 0.00 0.00 3.24
1586 3408 3.051210 CAGCTCCTGGTGTCGACA 58.949 61.111 15.76 15.76 36.97 4.35
1911 3733 2.481854 CCGCCATCATCTTCTTCTCTG 58.518 52.381 0.00 0.00 0.00 3.35
2090 3912 4.036380 CCCTACAAATCCGAAAATGCCTAC 59.964 45.833 0.00 0.00 0.00 3.18
2271 4096 1.349688 ACATACCTTTCCGCTTCACCA 59.650 47.619 0.00 0.00 0.00 4.17
2281 4106 1.490910 CTCCCCTCCCACATACCTTTC 59.509 57.143 0.00 0.00 0.00 2.62
2329 4156 8.880878 ACCAAACATACAAGGAAACAATTAAC 57.119 30.769 0.00 0.00 0.00 2.01
2339 4166 9.703892 CAAATATCAAAACCAAACATACAAGGA 57.296 29.630 0.00 0.00 0.00 3.36
2659 4492 4.750172 CCGAGACGGTTTATTTTCGTAG 57.250 45.455 1.80 0.00 42.73 3.51
2686 4519 1.159905 TACTTGCTCCCACCTCCCA 59.840 57.895 0.00 0.00 0.00 4.37
2741 4574 2.350580 CGCGTTCCGGGTTTTATTTTCA 60.351 45.455 0.00 0.00 35.14 2.69
2783 4616 7.778853 CCTTAACTGGGTAGTTATCTCTACTCA 59.221 40.741 6.33 6.33 45.93 3.41
2796 4629 3.022406 ACGCTACTCCTTAACTGGGTAG 58.978 50.000 3.79 3.79 35.68 3.18
2798 4631 1.934410 ACGCTACTCCTTAACTGGGT 58.066 50.000 0.00 0.00 0.00 4.51
2799 4632 3.000727 CAAACGCTACTCCTTAACTGGG 58.999 50.000 0.00 0.00 0.00 4.45
2800 4633 3.000727 CCAAACGCTACTCCTTAACTGG 58.999 50.000 0.00 0.00 0.00 4.00
2801 4634 3.660865 ACCAAACGCTACTCCTTAACTG 58.339 45.455 0.00 0.00 0.00 3.16
2802 4635 3.613432 CGACCAAACGCTACTCCTTAACT 60.613 47.826 0.00 0.00 0.00 2.24
2803 4636 2.665052 CGACCAAACGCTACTCCTTAAC 59.335 50.000 0.00 0.00 0.00 2.01
2804 4637 2.353011 CCGACCAAACGCTACTCCTTAA 60.353 50.000 0.00 0.00 0.00 1.85
2805 4638 1.203052 CCGACCAAACGCTACTCCTTA 59.797 52.381 0.00 0.00 0.00 2.69
2806 4639 0.037605 CCGACCAAACGCTACTCCTT 60.038 55.000 0.00 0.00 0.00 3.36
2807 4640 1.590147 CCGACCAAACGCTACTCCT 59.410 57.895 0.00 0.00 0.00 3.69
2808 4641 2.098831 GCCGACCAAACGCTACTCC 61.099 63.158 0.00 0.00 0.00 3.85
2809 4642 2.098831 GGCCGACCAAACGCTACTC 61.099 63.158 0.00 0.00 35.26 2.59
2810 4643 2.047560 GGCCGACCAAACGCTACT 60.048 61.111 0.00 0.00 35.26 2.57
2811 4644 3.122971 GGGCCGACCAAACGCTAC 61.123 66.667 0.00 0.00 39.85 3.58


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

AutoCloner maintained by Alex Coulton.