Multiple sequence alignment - TraesCS7B01G078100

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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 TraesCS7B01G078100 chr7B 100.000 3005 0 0 1 3005 88051115 88054119 0.000000e+00 5550.0
1 TraesCS7B01G078100 chr7B 93.478 46 2 1 1520 1565 88053143 88053099 1.930000e-07 67.6
2 TraesCS7B01G078100 chr7B 88.235 51 6 0 1008 1058 365368780 365368730 8.990000e-06 62.1
3 TraesCS7B01G078100 chr5A 96.422 2599 69 6 1 2594 513256579 513254000 0.000000e+00 4263.0
4 TraesCS7B01G078100 chr5A 95.904 415 14 3 2591 3005 513253965 513253554 0.000000e+00 669.0
5 TraesCS7B01G078100 chr5A 86.916 214 24 4 1873 2083 553341766 553341554 1.390000e-58 237.0
6 TraesCS7B01G078100 chr5A 84.524 84 13 0 2591 2674 372247056 372247139 1.920000e-12 84.2
7 TraesCS7B01G078100 chr5A 91.304 46 3 1 1520 1565 513254565 513254609 8.990000e-06 62.1
8 TraesCS7B01G078100 chr1A 96.308 2600 84 6 1 2594 46358958 46361551 0.000000e+00 4259.0
9 TraesCS7B01G078100 chr1A 95.663 415 14 3 2591 3005 46361586 46361996 0.000000e+00 664.0
10 TraesCS7B01G078100 chr1A 90.094 212 20 1 894 1104 561113158 561112947 1.060000e-69 274.0
11 TraesCS7B01G078100 chr1A 84.848 99 13 2 669 765 14481646 14481548 6.860000e-17 99.0
12 TraesCS7B01G078100 chr1A 85.714 98 9 1 2908 3005 532453554 532453462 6.860000e-17 99.0
13 TraesCS7B01G078100 chr1A 93.478 46 2 1 1520 1565 46360986 46360942 1.930000e-07 67.6
14 TraesCS7B01G078100 chr1A 95.000 40 2 0 757 796 561113231 561113192 2.500000e-06 63.9
15 TraesCS7B01G078100 chr2A 84.096 415 48 12 1669 2080 554017480 554017081 4.700000e-103 385.0
16 TraesCS7B01G078100 chr2A 85.000 100 15 0 2719 2818 690332423 690332522 5.300000e-18 102.0
17 TraesCS7B01G078100 chr2A 84.694 98 10 1 2908 3005 596413248 596413156 3.190000e-15 93.5
18 TraesCS7B01G078100 chr2A 82.653 98 12 1 2908 3005 431009279 431009371 6.900000e-12 82.4
19 TraesCS7B01G078100 chr2A 95.000 40 2 0 2678 2717 138829649 138829688 2.500000e-06 63.9
20 TraesCS7B01G078100 chr3A 88.618 246 27 1 111 356 279432924 279432680 6.300000e-77 298.0
21 TraesCS7B01G078100 chr3A 88.532 218 14 3 757 973 279432523 279432316 1.380000e-63 254.0
22 TraesCS7B01G078100 chr3A 89.503 181 17 2 579 759 279432662 279432484 8.380000e-56 228.0
23 TraesCS7B01G078100 chr3A 83.168 101 12 4 669 765 137909261 137909360 1.480000e-13 87.9
24 TraesCS7B01G078100 chr3A 84.524 84 13 0 2591 2674 509517896 509517979 1.920000e-12 84.2
25 TraesCS7B01G078100 chr6A 87.698 252 20 2 1637 1881 21403901 21404148 1.760000e-72 283.0
26 TraesCS7B01G078100 chr7A 89.954 219 18 1 1667 1881 188901669 188901451 2.280000e-71 279.0
27 TraesCS7B01G078100 chr7A 90.196 204 16 4 1877 2077 200007209 200007411 2.300000e-66 263.0
28 TraesCS7B01G078100 chr7A 88.263 213 21 1 1669 1881 200006962 200007170 4.970000e-63 252.0
29 TraesCS7B01G078100 chr1D 90.566 212 19 1 894 1104 468099924 468099713 2.280000e-71 279.0
30 TraesCS7B01G078100 chr1D 95.000 40 2 0 757 796 468099997 468099958 2.500000e-06 63.9
31 TraesCS7B01G078100 chr4A 89.767 215 18 1 1667 1881 37972785 37972575 3.820000e-69 272.0
32 TraesCS7B01G078100 chr4A 89.119 193 18 3 1883 2073 37972530 37972339 1.390000e-58 237.0
33 TraesCS7B01G078100 chr5D 91.237 194 13 4 1883 2073 34274295 34274103 8.260000e-66 261.0
34 TraesCS7B01G078100 chr5D 88.263 213 19 1 1669 1881 34274546 34274340 1.790000e-62 250.0
35 TraesCS7B01G078100 chr2D 88.263 213 19 1 1669 1881 433216057 433216263 1.790000e-62 250.0
36 TraesCS7B01G078100 chr2D 88.235 204 19 5 1877 2077 433216302 433216503 3.870000e-59 239.0
37 TraesCS7B01G078100 chr3D 89.637 193 18 2 1883 2073 556073467 556073275 8.320000e-61 244.0
38 TraesCS7B01G078100 chr3D 87.755 98 12 0 2908 3005 95583039 95582942 6.810000e-22 115.0
39 TraesCS7B01G078100 chr1B 85.965 228 22 6 1664 1888 661033380 661033600 5.010000e-58 235.0
40 TraesCS7B01G078100 chr5B 80.345 290 45 8 2232 2516 473506829 473506547 3.040000e-50 209.0
41 TraesCS7B01G078100 chr5B 85.455 110 16 0 2896 3005 469971432 469971541 6.810000e-22 115.0
42 TraesCS7B01G078100 chr5B 84.821 112 15 2 2894 3005 15139959 15139850 8.810000e-21 111.0
43 TraesCS7B01G078100 chr4B 80.620 258 35 8 383 627 21367278 21367533 5.120000e-43 185.0
44 TraesCS7B01G078100 chr4B 92.727 55 4 0 1031 1085 16551790 16551844 2.480000e-11 80.5
45 TraesCS7B01G078100 chr4B 90.909 55 5 0 1031 1085 550673850 550673904 1.160000e-09 75.0
46 TraesCS7B01G078100 chr7D 85.000 100 15 0 2719 2818 622371660 622371759 5.300000e-18 102.0
47 TraesCS7B01G078100 chr6B 83.636 110 13 1 2896 3005 559467753 559467857 6.860000e-17 99.0
48 TraesCS7B01G078100 chr3B 92.593 54 4 0 1031 1084 511031414 511031361 8.930000e-11 78.7
49 TraesCS7B01G078100 chr2B 97.368 38 0 1 2714 2751 658918855 658918819 2.500000e-06 63.9


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 TraesCS7B01G078100 chr7B 88051115 88054119 3004 False 5550.0 5550 100.000000 1 3005 1 chr7B.!!$F1 3004
1 TraesCS7B01G078100 chr5A 513253554 513256579 3025 True 2466.0 4263 96.163000 1 3005 2 chr5A.!!$R2 3004
2 TraesCS7B01G078100 chr1A 46358958 46361996 3038 False 2461.5 4259 95.985500 1 3005 2 chr1A.!!$F1 3004
3 TraesCS7B01G078100 chr3A 279432316 279432924 608 True 260.0 298 88.884333 111 973 3 chr3A.!!$R1 862

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
473 485 0.813184 ATCTGCACTTTCCCGCAATG 59.187 50.0 0.0 0.0 37.76 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2149 2170 0.543277 TCTTCGCCTCCATCATTGCT 59.457 50.0 0.0 0.0 0.0 3.91 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
230 231 3.298958 TGGCCGAGAGTGGTCATC 58.701 61.111 0.00 0.00 39.11 2.92
304 305 4.019321 GGGATAATAGCCATGGAACTAGCA 60.019 45.833 18.40 0.82 0.00 3.49
473 485 0.813184 ATCTGCACTTTCCCGCAATG 59.187 50.000 0.00 0.00 37.76 2.82
478 490 1.530419 ACTTTCCCGCAATGCCACA 60.530 52.632 0.00 0.00 0.00 4.17
654 667 4.393062 AGTTTAGACAATTGGCAGTCATCG 59.607 41.667 15.18 0.00 37.23 3.84
661 674 4.100529 CAATTGGCAGTCATCGACATTTC 58.899 43.478 0.00 0.00 34.60 2.17
1111 1126 3.066380 GCAAATCAAGCGGGTGAAAAAT 58.934 40.909 0.00 0.00 0.00 1.82
1159 1174 4.505922 GTCAAAATTGGTTTGCACGAATGA 59.494 37.500 0.00 0.00 45.38 2.57
1161 1176 2.723124 ATTGGTTTGCACGAATGACC 57.277 45.000 0.00 0.00 30.66 4.02
1186 1201 3.509967 TGAGAAGAGAGCGGAATACAACA 59.490 43.478 0.00 0.00 0.00 3.33
1232 1247 1.546961 AGACACCTTCTCCACTACGG 58.453 55.000 0.00 0.00 0.00 4.02
1326 1341 7.379529 CGATCACTAAAATTGCTTTTGTTCACT 59.620 33.333 0.00 0.00 36.09 3.41
1340 1355 9.601971 GCTTTTGTTCACTTTATTATACGACAA 57.398 29.630 0.00 0.00 0.00 3.18
1410 1425 3.059257 TGGTGTGTCGATGTCAAAATTCG 60.059 43.478 0.00 0.00 0.00 3.34
1415 1430 4.387862 GTGTCGATGTCAAAATTCGGTACT 59.612 41.667 0.00 0.00 33.82 2.73
1450 1465 6.095440 GTGACCTTATTTCCATATGCAGTTGT 59.905 38.462 0.00 0.00 0.00 3.32
1465 1482 4.511454 TGCAGTTGTAGATTTCAGTGTGAC 59.489 41.667 0.00 0.00 0.00 3.67
1466 1483 4.511454 GCAGTTGTAGATTTCAGTGTGACA 59.489 41.667 0.00 0.00 0.00 3.58
1487 1504 5.238583 ACATAGTTCCAGAGTGTACTTTGC 58.761 41.667 0.00 0.00 0.00 3.68
1556 1573 6.782988 AGGCTGCATATTCTACTAACTTCCTA 59.217 38.462 0.50 0.00 0.00 2.94
1717 1734 5.123979 CCATTTGCTAACTTAACCACCTCTC 59.876 44.000 0.00 0.00 0.00 3.20
1718 1735 5.562298 TTTGCTAACTTAACCACCTCTCT 57.438 39.130 0.00 0.00 0.00 3.10
1719 1736 4.803098 TGCTAACTTAACCACCTCTCTC 57.197 45.455 0.00 0.00 0.00 3.20
1720 1737 4.417437 TGCTAACTTAACCACCTCTCTCT 58.583 43.478 0.00 0.00 0.00 3.10
1779 1796 1.658994 TGTCGACAAGGGTGTTTGAC 58.341 50.000 17.62 6.35 40.83 3.18
1885 1906 6.822073 TGTTTCTGGATATGTTATTCGTCG 57.178 37.500 0.00 0.00 0.00 5.12
1899 1920 6.862608 TGTTATTCGTCGTGTAAGAAAGCTAA 59.137 34.615 0.00 0.00 0.00 3.09
2079 2100 6.985117 TCTTTCATTTTAATGCTTGAGTGCT 58.015 32.000 0.00 0.00 36.36 4.40
2089 2110 3.544684 TGCTTGAGTGCTTTTCTCTGAA 58.455 40.909 0.00 0.00 33.59 3.02
2149 2170 1.845627 CTTCTCCCTTGCCTGCTCCA 61.846 60.000 0.00 0.00 0.00 3.86
2173 2194 1.045350 TGATGGAGGCGAAGAGGAGG 61.045 60.000 0.00 0.00 0.00 4.30
2184 2205 1.139058 GAAGAGGAGGAGCGCCAATAA 59.861 52.381 9.88 0.00 36.29 1.40
2211 2232 3.264666 GCTATGAGCGTGTGAGGAG 57.735 57.895 0.00 0.00 0.00 3.69
2321 2342 1.763770 CCCCTTCTGCCACTCTTGT 59.236 57.895 0.00 0.00 0.00 3.16
2381 2402 7.735500 CGTTCTCGGATTTTGTTGTATTTCTA 58.264 34.615 0.00 0.00 0.00 2.10
2570 2591 0.875908 GGCGCATCGTCAGATAGCAA 60.876 55.000 10.83 0.00 39.71 3.91
2594 2615 5.479306 TGACTACAGGAAGAATACTGTTGC 58.521 41.667 0.00 0.00 45.03 4.17
2595 2616 5.246203 TGACTACAGGAAGAATACTGTTGCT 59.754 40.000 0.00 0.00 45.03 3.91
2596 2617 5.725362 ACTACAGGAAGAATACTGTTGCTC 58.275 41.667 0.00 0.00 45.03 4.26
2751 2810 2.557056 TCTCTTACGCAACTGCTACTGT 59.443 45.455 0.00 0.00 39.32 3.55
2758 2817 2.531912 CGCAACTGCTACTGTAATCGAG 59.468 50.000 0.00 0.00 39.32 4.04
2799 2858 7.178628 TGGTAAGATCTTTCTACACAGCTTAGT 59.821 37.037 14.36 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 63 9.814507 GACGTTATGATTATTTTTGTACACACA 57.185 29.630 0.00 0.00 0.00 3.72
304 305 9.125026 GTGGATCATGATAATTCACCTTTTACT 57.875 33.333 8.54 0.00 33.85 2.24
425 437 8.610896 CAGACAACATTTAAAAGGCAATTTCAA 58.389 29.630 0.00 0.00 0.00 2.69
473 485 1.845809 CTTGAGCAGTCCGTTGTGGC 61.846 60.000 0.00 0.00 37.80 5.01
478 490 1.598130 GCCACTTGAGCAGTCCGTT 60.598 57.895 0.00 0.00 30.92 4.44
631 644 4.393062 CGATGACTGCCAATTGTCTAAACT 59.607 41.667 4.43 0.00 34.57 2.66
640 653 3.129287 GGAAATGTCGATGACTGCCAATT 59.871 43.478 0.00 0.00 33.15 2.32
654 667 2.680339 GACCTTAGCTGCAGGAAATGTC 59.320 50.000 17.12 3.13 35.14 3.06
661 674 2.206576 AAAAGGACCTTAGCTGCAGG 57.793 50.000 17.12 11.42 37.45 4.85
1111 1126 5.049818 CACTTTTTGGTGTTTGTTCTTGCAA 60.050 36.000 0.00 0.00 33.04 4.08
1159 1174 0.394488 TCCGCTCTCTTCTCATCGGT 60.394 55.000 0.00 0.00 38.18 4.69
1161 1176 2.791383 ATTCCGCTCTCTTCTCATCG 57.209 50.000 0.00 0.00 0.00 3.84
1186 1201 1.134521 TCGGGCAATACATCGCTTCTT 60.135 47.619 0.00 0.00 0.00 2.52
1232 1247 0.248134 CGTAGGCGCTGTGAGTAGAC 60.248 60.000 7.64 0.00 0.00 2.59
1326 1341 9.497030 GTGAACATGCATTTGTCGTATAATAAA 57.503 29.630 0.00 0.00 0.00 1.40
1340 1355 5.182001 GGAGTACTTTCAGTGAACATGCATT 59.818 40.000 4.68 0.00 0.00 3.56
1415 1430 7.733773 TGGAAATAAGGTCACTCTAATCAGA 57.266 36.000 0.00 0.00 0.00 3.27
1450 1465 7.178451 TCTGGAACTATGTCACACTGAAATCTA 59.822 37.037 0.00 0.00 0.00 1.98
1465 1482 5.237815 TGCAAAGTACACTCTGGAACTATG 58.762 41.667 0.00 0.00 0.00 2.23
1466 1483 5.483685 TGCAAAGTACACTCTGGAACTAT 57.516 39.130 0.00 0.00 0.00 2.12
1487 1504 7.359262 ACATGCAGATTTTGAACAAATCATG 57.641 32.000 9.40 10.87 38.70 3.07
1556 1573 5.512749 CCTTCCTATGAGCATGCTTCTACAT 60.513 44.000 23.61 21.29 0.00 2.29
1717 1734 6.072008 TCAGAAACAACATGAGAGAGAGAGAG 60.072 42.308 0.00 0.00 0.00 3.20
1718 1735 5.772169 TCAGAAACAACATGAGAGAGAGAGA 59.228 40.000 0.00 0.00 0.00 3.10
1719 1736 6.023357 TCAGAAACAACATGAGAGAGAGAG 57.977 41.667 0.00 0.00 0.00 3.20
1720 1737 6.266330 TCTTCAGAAACAACATGAGAGAGAGA 59.734 38.462 0.00 0.00 0.00 3.10
1779 1796 1.811941 GCAGCCTTCCTAGATTTCCCG 60.812 57.143 0.00 0.00 0.00 5.14
1899 1920 5.659440 AATCACGTGGCCAAAATAAATCT 57.341 34.783 17.00 0.00 0.00 2.40
2089 2110 4.007659 CGCCACCATTAGGACTTAAAAGT 58.992 43.478 0.00 0.00 43.16 2.66
2149 2170 0.543277 TCTTCGCCTCCATCATTGCT 59.457 50.000 0.00 0.00 0.00 3.91
2173 2194 2.329379 CGACCTATCTTATTGGCGCTC 58.671 52.381 7.64 0.00 0.00 5.03
2321 2342 9.513906 TGAATACATAGAAATCACCAAAGAACA 57.486 29.630 0.00 0.00 0.00 3.18
2387 2408 9.236691 GCGCAAATCAATTATTTCTTCTCATAA 57.763 29.630 0.30 0.00 35.54 1.90
2570 2591 6.070538 AGCAACAGTATTCTTCCTGTAGTCAT 60.071 38.462 0.00 0.00 40.91 3.06
2606 2665 9.631452 CAAGAAAAAGGAAGTGATAAGAAATCC 57.369 33.333 0.00 0.00 0.00 3.01
2643 2702 7.414222 AGTTATCATCAAAGCATGGTTTCAT 57.586 32.000 19.59 10.53 0.00 2.57
2677 2736 0.613260 TGAAACCAGCGGCAGAGTAT 59.387 50.000 1.45 0.00 0.00 2.12
2751 2810 1.999735 CGCTTGCAAAGGACTCGATTA 59.000 47.619 0.00 0.00 46.35 1.75
2758 2817 1.234615 TACCAGCGCTTGCAAAGGAC 61.235 55.000 7.50 0.00 46.35 3.85
2960 3019 7.984422 TTCATGTGCATATCCAATAGTAAGG 57.016 36.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.