Multiple sequence alignment - TraesCS4A01G471900

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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 TraesCS4A01G471900 chr4A 100.000 2405 0 0 1 2405 732353894 732356298 0.000000e+00 4442.0
1 TraesCS4A01G471900 chr4A 90.586 2082 172 14 331 2405 731851993 731849929 0.000000e+00 2737.0
2 TraesCS4A01G471900 chr4A 86.848 1437 175 7 977 2405 731616801 731615371 0.000000e+00 1594.0
3 TraesCS4A01G471900 chr4A 83.291 1562 241 13 857 2405 731861877 731860323 0.000000e+00 1421.0
4 TraesCS4A01G471900 chr4A 83.226 1240 187 12 704 1935 732408716 732409942 0.000000e+00 1118.0
5 TraesCS4A01G471900 chr4A 84.503 755 78 12 3 750 731665151 731664429 0.000000e+00 710.0
6 TraesCS4A01G471900 chr4A 88.255 298 31 4 411 705 732395490 732395786 1.060000e-93 353.0
7 TraesCS4A01G471900 chr4A 77.722 395 68 13 130 514 731606540 731606156 8.650000e-55 224.0
8 TraesCS4A01G471900 chr4A 79.016 305 41 12 3 285 731852289 731851986 1.140000e-43 187.0
9 TraesCS4A01G471900 chr4A 81.773 203 22 8 516 708 732058217 732058414 3.200000e-34 156.0
10 TraesCS4A01G471900 chr4A 87.786 131 16 0 764 894 731664445 731664315 1.150000e-33 154.0
11 TraesCS4A01G471900 chr7A 93.885 2077 107 11 336 2405 56204321 56206384 0.000000e+00 3114.0
12 TraesCS4A01G471900 chr7A 82.935 1506 227 21 917 2404 80861975 80863468 0.000000e+00 1330.0
13 TraesCS4A01G471900 chr7A 79.605 304 37 13 3 285 56204023 56204322 6.780000e-46 195.0
14 TraesCS4A01G471900 chr7A 82.432 222 25 9 4 212 8587868 8588088 5.280000e-42 182.0
15 TraesCS4A01G471900 chr7D 82.931 1904 242 44 522 2405 8256417 8254577 0.000000e+00 1639.0
16 TraesCS4A01G471900 chr7D 82.147 1910 249 48 522 2405 7923965 7925808 0.000000e+00 1554.0
17 TraesCS4A01G471900 chr7D 84.570 1510 215 11 904 2405 8030614 8032113 0.000000e+00 1482.0
18 TraesCS4A01G471900 chr7D 83.422 1502 230 11 915 2405 8052779 8054272 0.000000e+00 1376.0
19 TraesCS4A01G471900 chr7D 82.768 1503 242 9 911 2405 7820321 7821814 0.000000e+00 1325.0
20 TraesCS4A01G471900 chr7D 82.594 1511 227 25 917 2404 76743550 76745047 0.000000e+00 1301.0
21 TraesCS4A01G471900 chr7D 83.974 755 81 13 3 750 8222507 8223228 0.000000e+00 688.0
22 TraesCS4A01G471900 chr7D 89.333 75 8 0 516 590 8233163 8233237 7.080000e-16 95.3
23 TraesCS4A01G471900 chr3B 86.209 1501 188 10 915 2405 741463153 741464644 0.000000e+00 1607.0
24 TraesCS4A01G471900 chr3B 91.304 69 6 0 177 245 741456834 741456902 7.080000e-16 95.3
25 TraesCS4A01G471900 chr7B 82.577 1498 239 16 917 2398 23596695 23598186 0.000000e+00 1301.0
26 TraesCS4A01G471900 chr7B 83.333 1296 200 11 1113 2398 23958186 23959475 0.000000e+00 1182.0
27 TraesCS4A01G471900 chr5B 80.697 373 49 19 71 428 37467602 37467966 3.940000e-68 268.0


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 TraesCS4A01G471900 chr4A 732353894 732356298 2404 False 4442.0 4442 100.0000 1 2405 1 chr4A.!!$F2 2404
1 TraesCS4A01G471900 chr4A 731615371 731616801 1430 True 1594.0 1594 86.8480 977 2405 1 chr4A.!!$R2 1428
2 TraesCS4A01G471900 chr4A 731849929 731852289 2360 True 1462.0 2737 84.8010 3 2405 2 chr4A.!!$R5 2402
3 TraesCS4A01G471900 chr4A 731860323 731861877 1554 True 1421.0 1421 83.2910 857 2405 1 chr4A.!!$R3 1548
4 TraesCS4A01G471900 chr4A 732408716 732409942 1226 False 1118.0 1118 83.2260 704 1935 1 chr4A.!!$F4 1231
5 TraesCS4A01G471900 chr4A 731664315 731665151 836 True 432.0 710 86.1445 3 894 2 chr4A.!!$R4 891
6 TraesCS4A01G471900 chr7A 56204023 56206384 2361 False 1654.5 3114 86.7450 3 2405 2 chr7A.!!$F3 2402
7 TraesCS4A01G471900 chr7A 80861975 80863468 1493 False 1330.0 1330 82.9350 917 2404 1 chr7A.!!$F2 1487
8 TraesCS4A01G471900 chr7D 8254577 8256417 1840 True 1639.0 1639 82.9310 522 2405 1 chr7D.!!$R1 1883
9 TraesCS4A01G471900 chr7D 7923965 7925808 1843 False 1554.0 1554 82.1470 522 2405 1 chr7D.!!$F2 1883
10 TraesCS4A01G471900 chr7D 8030614 8032113 1499 False 1482.0 1482 84.5700 904 2405 1 chr7D.!!$F3 1501
11 TraesCS4A01G471900 chr7D 8052779 8054272 1493 False 1376.0 1376 83.4220 915 2405 1 chr7D.!!$F4 1490
12 TraesCS4A01G471900 chr7D 7820321 7821814 1493 False 1325.0 1325 82.7680 911 2405 1 chr7D.!!$F1 1494
13 TraesCS4A01G471900 chr7D 76743550 76745047 1497 False 1301.0 1301 82.5940 917 2404 1 chr7D.!!$F7 1487
14 TraesCS4A01G471900 chr7D 8222507 8223228 721 False 688.0 688 83.9740 3 750 1 chr7D.!!$F5 747
15 TraesCS4A01G471900 chr3B 741463153 741464644 1491 False 1607.0 1607 86.2090 915 2405 1 chr3B.!!$F2 1490
16 TraesCS4A01G471900 chr7B 23596695 23598186 1491 False 1301.0 1301 82.5770 917 2398 1 chr7B.!!$F1 1481
17 TraesCS4A01G471900 chr7B 23958186 23959475 1289 False 1182.0 1182 83.3330 1113 2398 1 chr7B.!!$F2 1285

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
202 225 0.036483 TCGTCTTGCCTATTGCTGCA 60.036 50.0 0.00 0.0 42.0 4.41 F
1323 1398 0.179121 TACTTGGCTACATCACGCGG 60.179 55.0 12.47 0.0 0.0 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1390 1465 0.884704 TCTCCTCAACCAACTTGCGC 60.885 55.000 0.0 0.0 0.0 6.09 R
2235 2326 3.988379 TTTCAGATGACAGGTGTTTGC 57.012 42.857 0.0 0.0 0.0 3.68 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
46 47 8.470805 TCTGTTTATCTCATAACTCTGAGTTCC 58.529 37.037 25.12 4.24 42.68 3.62
47 48 7.258441 TGTTTATCTCATAACTCTGAGTTCCG 58.742 38.462 25.12 17.20 42.68 4.30
49 50 5.923733 ATCTCATAACTCTGAGTTCCGTT 57.076 39.130 25.12 5.28 42.68 4.44
53 54 4.461431 TCATAACTCTGAGTTCCGTTAGCA 59.539 41.667 25.12 7.05 39.51 3.49
54 55 3.963428 AACTCTGAGTTCCGTTAGCAT 57.037 42.857 17.00 0.00 31.77 3.79
61 62 5.127194 TCTGAGTTCCGTTAGCATATTCACT 59.873 40.000 0.00 0.00 0.00 3.41
62 63 5.109210 TGAGTTCCGTTAGCATATTCACTG 58.891 41.667 0.00 0.00 0.00 3.66
68 69 8.485591 GTTCCGTTAGCATATTCACTGTAATAC 58.514 37.037 0.00 0.00 0.00 1.89
69 70 7.718525 TCCGTTAGCATATTCACTGTAATACA 58.281 34.615 0.00 0.00 0.00 2.29
70 71 8.364894 TCCGTTAGCATATTCACTGTAATACAT 58.635 33.333 0.00 0.00 0.00 2.29
134 157 5.371115 AAAATCATTACCAGAACGTGTGG 57.629 39.130 14.31 14.31 41.30 4.17
183 206 3.541632 ACAAGTGACAGGTCGAAAACAT 58.458 40.909 0.00 0.00 0.00 2.71
184 207 3.560068 ACAAGTGACAGGTCGAAAACATC 59.440 43.478 0.00 0.00 0.00 3.06
197 220 4.334443 CGAAAACATCGTCTTGCCTATTG 58.666 43.478 0.00 0.00 46.52 1.90
202 225 0.036483 TCGTCTTGCCTATTGCTGCA 60.036 50.000 0.00 0.00 42.00 4.41
242 265 4.125703 AGTGAGAAAAGTCTTCACAGCAG 58.874 43.478 6.62 0.00 35.80 4.24
262 292 8.093307 ACAGCAGATATCACTTATTGTCCTATG 58.907 37.037 5.32 0.00 0.00 2.23
286 316 6.867816 TGTACAAGTTGGAAAATGATGCATTC 59.132 34.615 7.96 0.00 32.43 2.67
287 317 6.105397 ACAAGTTGGAAAATGATGCATTCT 57.895 33.333 7.96 0.00 32.43 2.40
288 318 7.230849 ACAAGTTGGAAAATGATGCATTCTA 57.769 32.000 7.96 0.00 32.43 2.10
289 319 7.092716 ACAAGTTGGAAAATGATGCATTCTAC 58.907 34.615 7.96 0.00 32.43 2.59
290 320 6.212888 AGTTGGAAAATGATGCATTCTACC 57.787 37.500 0.00 1.32 32.43 3.18
320 350 4.285775 AGGGGTTCAACATTATTTGGTTGG 59.714 41.667 0.00 0.00 43.44 3.77
321 351 4.284746 GGGGTTCAACATTATTTGGTTGGA 59.715 41.667 0.00 0.00 43.44 3.53
322 352 5.478407 GGGTTCAACATTATTTGGTTGGAG 58.522 41.667 0.00 0.00 43.44 3.86
323 353 4.929211 GGTTCAACATTATTTGGTTGGAGC 59.071 41.667 0.00 0.00 41.93 4.70
326 356 4.021544 TCAACATTATTTGGTTGGAGCCAC 60.022 41.667 0.00 0.00 43.44 5.01
421 452 6.530913 TCGACATCTAAATATTTGCTGAGC 57.469 37.500 11.05 0.00 0.00 4.26
430 461 4.889832 ATATTTGCTGAGCGAAAAGGAG 57.110 40.909 11.69 0.00 35.42 3.69
447 478 1.483415 GGAGGTGTTGTCGGCCTATAA 59.517 52.381 0.00 0.00 31.89 0.98
459 490 5.467399 TGTCGGCCTATAAAATATTTCCACG 59.533 40.000 0.00 1.02 0.00 4.94
472 503 6.721571 ATATTTCCACGCGAATATACCAAG 57.278 37.500 15.93 0.00 29.18 3.61
520 554 3.536956 TCCACTGCCCTTTTCTATACG 57.463 47.619 0.00 0.00 0.00 3.06
548 582 5.474578 TGGATTCCTTGATCTTATCTCCG 57.525 43.478 3.95 0.00 0.00 4.63
656 699 5.934625 AGTACTGTTGCTCTTTCACCTATTG 59.065 40.000 0.00 0.00 0.00 1.90
682 725 4.279671 ACAAGATCAAATTTGGGCGTTGTA 59.720 37.500 17.90 0.00 0.00 2.41
688 731 2.109425 ATTTGGGCGTTGTAGAGGTC 57.891 50.000 0.00 0.00 0.00 3.85
708 751 4.704057 GGTCAATTCTCTGCTCAATCCTTT 59.296 41.667 0.00 0.00 0.00 3.11
731 774 2.774439 TTGTTTTGCTCTTCTTCGGC 57.226 45.000 0.00 0.00 0.00 5.54
946 1005 3.877508 GTGTTCTGTCAGTGCTTAACCTT 59.122 43.478 0.00 0.00 0.00 3.50
990 1056 2.609747 ACAGTCCTTGTTCCTCTAGCA 58.390 47.619 0.00 0.00 36.31 3.49
1110 1179 4.513519 GGTGATGATCGCCGAACA 57.486 55.556 9.55 0.00 37.29 3.18
1323 1398 0.179121 TACTTGGCTACATCACGCGG 60.179 55.000 12.47 0.00 0.00 6.46
1390 1465 0.316607 CGTCCTCGAGAAGATCAGCG 60.317 60.000 15.71 0.00 39.71 5.18
1391 1466 0.593773 GTCCTCGAGAAGATCAGCGC 60.594 60.000 15.71 0.00 0.00 5.92
1392 1467 1.656875 CCTCGAGAAGATCAGCGCG 60.657 63.158 15.71 0.00 0.00 6.86
1484 1559 0.593128 GCGGCAGACACACTCAAAAT 59.407 50.000 0.00 0.00 0.00 1.82
1635 1710 4.067896 ACAACTCTTGCTAAGATGGTGTG 58.932 43.478 13.00 7.63 36.18 3.82
1703 1778 3.723260 TGCGTGTCAGACAACTTTGATA 58.277 40.909 4.32 0.00 0.00 2.15
1725 1800 3.383185 ACCGTTGCTCTTTTGAAATCCAA 59.617 39.130 0.00 0.00 0.00 3.53
1737 1812 7.992033 TCTTTTGAAATCCAACATTGAATTGGT 59.008 29.630 3.81 0.00 45.83 3.67
1939 2022 2.480037 CACATGTCGAAGCAAGCAAGTA 59.520 45.455 0.00 0.00 0.00 2.24
2138 2229 2.582052 TGGGTGGATTGTTGAGTTCAC 58.418 47.619 0.00 0.00 0.00 3.18
2200 2291 3.788142 ACATTGGGGATAATGACAGAGGT 59.212 43.478 5.58 0.00 39.79 3.85
2217 2308 5.367937 ACAGAGGTAAATATGAGGTCATGCT 59.632 40.000 2.56 0.00 37.15 3.79
2235 2326 8.072567 GGTCATGCTCATATTAAAGTTAAGCTG 58.927 37.037 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 5.086104 ACAGTGAATATGCTAACGGAACT 57.914 39.130 0.00 0.00 0.00 3.01
110 116 5.856455 CCACACGTTCTGGTAATGATTTTTC 59.144 40.000 1.34 0.00 0.00 2.29
116 130 1.803334 GCCACACGTTCTGGTAATGA 58.197 50.000 10.15 0.00 0.00 2.57
117 139 0.442310 CGCCACACGTTCTGGTAATG 59.558 55.000 10.15 0.00 36.87 1.90
159 182 2.234300 TTCGACCTGTCACTTGTTCC 57.766 50.000 0.00 0.00 0.00 3.62
192 215 3.062639 CACTAACGGTTCTGCAGCAATAG 59.937 47.826 9.47 7.86 0.00 1.73
197 220 0.790814 GTCACTAACGGTTCTGCAGC 59.209 55.000 9.47 0.00 0.00 5.25
202 225 3.131577 TCACTTGTGTCACTAACGGTTCT 59.868 43.478 4.27 0.00 0.00 3.01
262 292 7.092716 AGAATGCATCATTTTCCAACTTGTAC 58.907 34.615 0.00 0.00 33.90 2.90
320 350 2.119801 ACCATCATCACAAGTGGCTC 57.880 50.000 0.00 0.00 35.11 4.70
321 351 2.305635 TGTACCATCATCACAAGTGGCT 59.694 45.455 0.00 0.00 35.11 4.75
322 352 2.679837 CTGTACCATCATCACAAGTGGC 59.320 50.000 0.00 0.00 35.11 5.01
323 353 3.935203 GTCTGTACCATCATCACAAGTGG 59.065 47.826 0.00 0.00 37.74 4.00
326 356 5.121298 CAGTTGTCTGTACCATCATCACAAG 59.879 44.000 0.00 0.00 36.97 3.16
377 407 4.447054 CGATATTCAAGCTAAGCTCTGTGG 59.553 45.833 0.00 0.00 38.25 4.17
415 446 0.603975 ACACCTCCTTTTCGCTCAGC 60.604 55.000 0.00 0.00 0.00 4.26
416 447 1.532868 CAACACCTCCTTTTCGCTCAG 59.467 52.381 0.00 0.00 0.00 3.35
421 452 0.865769 CCGACAACACCTCCTTTTCG 59.134 55.000 0.00 0.00 0.00 3.46
430 461 6.628919 AATATTTTATAGGCCGACAACACC 57.371 37.500 0.00 0.00 0.00 4.16
447 478 7.499321 TTGGTATATTCGCGTGGAAATATTT 57.501 32.000 13.82 0.00 38.36 1.40
459 490 2.544267 GTGTGAGGCTTGGTATATTCGC 59.456 50.000 0.00 0.00 0.00 4.70
472 503 0.674895 AGATGGAAAGCGTGTGAGGC 60.675 55.000 0.00 0.00 0.00 4.70
520 554 3.010200 AGATCAAGGAATCCAACAGCC 57.990 47.619 0.61 0.00 0.00 4.85
548 582 2.840651 TGGAGAGAGGATGGAAGGAAAC 59.159 50.000 0.00 0.00 0.00 2.78
656 699 2.349590 GCCCAAATTTGATCTTGTGCC 58.650 47.619 19.86 0.00 0.00 5.01
682 725 4.383989 GGATTGAGCAGAGAATTGACCTCT 60.384 45.833 0.00 0.00 41.35 3.69
688 731 9.084164 CAAAATAAAGGATTGAGCAGAGAATTG 57.916 33.333 0.00 0.00 0.00 2.32
708 751 5.009610 AGCCGAAGAAGAGCAAAACAAAATA 59.990 36.000 0.00 0.00 0.00 1.40
777 820 3.847671 GCCTTTGCCCTACTAGAGAAT 57.152 47.619 0.00 0.00 0.00 2.40
838 881 6.349300 TGTATAGCTCTTGTTCATCCCTTTC 58.651 40.000 0.00 0.00 0.00 2.62
990 1056 2.098607 CGATTCTGCCATGTTCTTGCAT 59.901 45.455 0.00 0.00 33.97 3.96
1094 1163 1.003545 CCAATGTTCGGCGATCATCAC 60.004 52.381 27.79 16.25 0.00 3.06
1110 1179 2.937379 CTAGCAGCTGGCGCTCCAAT 62.937 60.000 17.12 0.00 45.15 3.16
1390 1465 0.884704 TCTCCTCAACCAACTTGCGC 60.885 55.000 0.00 0.00 0.00 6.09
1391 1466 1.466167 CATCTCCTCAACCAACTTGCG 59.534 52.381 0.00 0.00 0.00 4.85
1392 1467 2.783135 TCATCTCCTCAACCAACTTGC 58.217 47.619 0.00 0.00 0.00 4.01
1484 1559 6.373216 CCAAATATTTTGGTAGAGTCGTCCAA 59.627 38.462 14.86 14.86 39.12 3.53
1528 1603 1.228063 CAGCAGCTTGACCACCACT 60.228 57.895 0.00 0.00 0.00 4.00
1635 1710 5.763204 TGTTTCTGGACTTCTTGGTCATTAC 59.237 40.000 0.00 0.00 37.91 1.89
1703 1778 2.955660 TGGATTTCAAAAGAGCAACGGT 59.044 40.909 0.00 0.00 0.00 4.83
1737 1812 5.874810 GTGTCAGGCAGATCACTATTTACAA 59.125 40.000 0.00 0.00 0.00 2.41
1838 1920 7.075797 TCCTCCCACATTCTCTTATCTTCATA 58.924 38.462 0.00 0.00 0.00 2.15
1939 2022 1.136305 ACCGTGCACATTATAGACGCT 59.864 47.619 18.64 0.00 0.00 5.07
1942 2025 4.025145 GGCTTAACCGTGCACATTATAGAC 60.025 45.833 18.64 12.15 0.00 2.59
1994 2077 6.648192 TGTTTGAAAACAAGTCCCATGAATT 58.352 32.000 6.15 0.00 45.17 2.17
2138 2229 7.381766 TCTTCCATTCATGTACATGTTTCTG 57.618 36.000 30.03 21.88 39.72 3.02
2217 2308 8.026607 GGTGTTTGCAGCTTAACTTTAATATGA 58.973 33.333 10.89 0.00 39.79 2.15
2235 2326 3.988379 TTTCAGATGACAGGTGTTTGC 57.012 42.857 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.