Multiple sequence alignment - TraesCS1B01G288400

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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 TraesCS1B01G288400 chr1B 100.000 2448 0 0 1 2448 502773649 502776096 0.000000e+00 4521.0
1 TraesCS1B01G288400 chr1B 95.230 587 27 1 2 587 502755467 502756053 0.000000e+00 928.0
2 TraesCS1B01G288400 chr2A 95.774 1609 65 3 588 2194 556948687 556950294 0.000000e+00 2591.0
3 TraesCS1B01G288400 chr2A 93.494 1614 90 8 588 2194 291665625 291667230 0.000000e+00 2385.0
4 TraesCS1B01G288400 chr2A 94.527 201 8 3 2250 2448 556954391 556954590 8.500000e-80 307.0
5 TraesCS1B01G288400 chr2A 95.312 64 3 0 2202 2265 291668018 291668081 4.310000e-18 102.0
6 TraesCS1B01G288400 chr2D 91.748 1236 89 8 588 1816 80029520 80030749 0.000000e+00 1705.0
7 TraesCS1B01G288400 chr2D 88.360 189 13 3 2261 2448 80031408 80031588 4.100000e-53 219.0
8 TraesCS1B01G288400 chr1D 91.041 1239 91 9 585 1816 198826973 198828198 0.000000e+00 1655.0
9 TraesCS1B01G288400 chr1D 90.955 199 15 3 2250 2446 247549131 247549328 5.190000e-67 265.0
10 TraesCS1B01G288400 chr1D 91.262 103 8 1 2347 2448 198875472 198875574 3.280000e-29 139.0
11 TraesCS1B01G288400 chr3A 82.047 1632 238 32 596 2201 667164728 667163126 0.000000e+00 1339.0
12 TraesCS1B01G288400 chr3D 82.980 1416 206 24 798 2201 418712592 418711200 0.000000e+00 1247.0
13 TraesCS1B01G288400 chr7D 82.839 1416 208 24 798 2201 136701352 136699960 0.000000e+00 1236.0
14 TraesCS1B01G288400 chr6A 83.694 1294 197 12 910 2192 563488504 563489794 0.000000e+00 1208.0
15 TraesCS1B01G288400 chr7A 82.494 1291 213 11 913 2192 106410384 106409096 0.000000e+00 1120.0
16 TraesCS1B01G288400 chr7A 84.706 170 23 3 2279 2446 642430060 642429892 1.510000e-37 167.0
17 TraesCS1B01G288400 chr7B 93.898 590 33 3 1 587 11243164 11243753 0.000000e+00 887.0
18 TraesCS1B01G288400 chr7B 93.526 587 35 3 2 586 549812262 549812847 0.000000e+00 870.0
19 TraesCS1B01G288400 chr3B 93.888 589 32 3 2 587 116818979 116818392 0.000000e+00 885.0
20 TraesCS1B01G288400 chr3B 93.548 589 34 3 2 587 116853662 116853075 0.000000e+00 874.0
21 TraesCS1B01G288400 chr3B 93.186 587 37 3 2 587 56674800 56675384 0.000000e+00 859.0
22 TraesCS1B01G288400 chr3B 93.015 587 37 4 2 587 56556908 56557491 0.000000e+00 854.0
23 TraesCS1B01G288400 chr6B 93.750 592 30 4 2 587 584073043 584073633 0.000000e+00 881.0
24 TraesCS1B01G288400 chr5B 93.379 589 35 3 2 587 596123197 596122610 0.000000e+00 869.0
25 TraesCS1B01G288400 chr5B 93.299 194 11 2 2256 2448 18596296 18596104 3.980000e-73 285.0
26 TraesCS1B01G288400 chr5A 89.727 623 53 5 595 1214 341536782 341536168 0.000000e+00 785.0
27 TraesCS1B01G288400 chr5A 94.330 194 9 2 2256 2448 341507120 341506928 1.840000e-76 296.0
28 TraesCS1B01G288400 chr5A 92.188 64 5 0 2202 2265 341510431 341510368 9.320000e-15 91.6


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 TraesCS1B01G288400 chr1B 502773649 502776096 2447 False 4521.0 4521 100.000 1 2448 1 chr1B.!!$F2 2447
1 TraesCS1B01G288400 chr1B 502755467 502756053 586 False 928.0 928 95.230 2 587 1 chr1B.!!$F1 585
2 TraesCS1B01G288400 chr2A 556948687 556950294 1607 False 2591.0 2591 95.774 588 2194 1 chr2A.!!$F1 1606
3 TraesCS1B01G288400 chr2A 291665625 291668081 2456 False 1243.5 2385 94.403 588 2265 2 chr2A.!!$F3 1677
4 TraesCS1B01G288400 chr2D 80029520 80031588 2068 False 962.0 1705 90.054 588 2448 2 chr2D.!!$F1 1860
5 TraesCS1B01G288400 chr1D 198826973 198828198 1225 False 1655.0 1655 91.041 585 1816 1 chr1D.!!$F1 1231
6 TraesCS1B01G288400 chr3A 667163126 667164728 1602 True 1339.0 1339 82.047 596 2201 1 chr3A.!!$R1 1605
7 TraesCS1B01G288400 chr3D 418711200 418712592 1392 True 1247.0 1247 82.980 798 2201 1 chr3D.!!$R1 1403
8 TraesCS1B01G288400 chr7D 136699960 136701352 1392 True 1236.0 1236 82.839 798 2201 1 chr7D.!!$R1 1403
9 TraesCS1B01G288400 chr6A 563488504 563489794 1290 False 1208.0 1208 83.694 910 2192 1 chr6A.!!$F1 1282
10 TraesCS1B01G288400 chr7A 106409096 106410384 1288 True 1120.0 1120 82.494 913 2192 1 chr7A.!!$R1 1279
11 TraesCS1B01G288400 chr7B 11243164 11243753 589 False 887.0 887 93.898 1 587 1 chr7B.!!$F1 586
12 TraesCS1B01G288400 chr7B 549812262 549812847 585 False 870.0 870 93.526 2 586 1 chr7B.!!$F2 584
13 TraesCS1B01G288400 chr3B 116818392 116818979 587 True 885.0 885 93.888 2 587 1 chr3B.!!$R1 585
14 TraesCS1B01G288400 chr3B 116853075 116853662 587 True 874.0 874 93.548 2 587 1 chr3B.!!$R2 585
15 TraesCS1B01G288400 chr3B 56674800 56675384 584 False 859.0 859 93.186 2 587 1 chr3B.!!$F2 585
16 TraesCS1B01G288400 chr3B 56556908 56557491 583 False 854.0 854 93.015 2 587 1 chr3B.!!$F1 585
17 TraesCS1B01G288400 chr6B 584073043 584073633 590 False 881.0 881 93.750 2 587 1 chr6B.!!$F1 585
18 TraesCS1B01G288400 chr5B 596122610 596123197 587 True 869.0 869 93.379 2 587 1 chr5B.!!$R2 585
19 TraesCS1B01G288400 chr5A 341536168 341536782 614 True 785.0 785 89.727 595 1214 1 chr5A.!!$R1 619

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
558 566 0.179 ATCACCCTCGACATTGGAGC 59.821 55.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2289 3469 1.079127 ATCAAACCTCGCTCGGTGG 60.079 57.895 0.0 0.0 37.36 4.61 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
282 284 5.514559 TGAACAACACACAATCGAACAAATG 59.485 36.000 0.00 0.00 0.00 2.32
378 385 4.699522 GGGCGGCGAACCTTGAGT 62.700 66.667 12.98 0.00 0.00 3.41
500 508 0.734942 CGGATTGTCTTGCGTACCGT 60.735 55.000 0.00 0.00 35.21 4.83
524 532 2.762234 CGGACGGGTCTCCTTCGAG 61.762 68.421 0.00 0.00 37.48 4.04
528 536 2.579738 GGGTCTCCTTCGAGGTGC 59.420 66.667 0.00 0.00 36.53 5.01
558 566 0.179000 ATCACCCTCGACATTGGAGC 59.821 55.000 0.00 0.00 0.00 4.70
591 599 3.712655 TCGTGTGCGAACAAGGTG 58.287 55.556 9.74 0.00 44.92 4.00
593 601 1.885388 CGTGTGCGAACAAGGTGGA 60.885 57.895 0.00 0.00 41.33 4.02
622 630 8.974060 TGTCTTTTTCTCTTAAACTGGTGTAT 57.026 30.769 0.00 0.00 0.00 2.29
647 657 4.292186 TCTTCCTGGTCTCCAATTGAAG 57.708 45.455 7.12 0.00 36.20 3.02
801 822 7.658575 GTGTAACATGGTCCTTGTAAGAAGTTA 59.341 37.037 10.65 0.00 36.32 2.24
852 874 8.359642 TGATGCAGCTTTACTTTACTGATTTTT 58.640 29.630 2.53 0.00 31.67 1.94
908 934 9.699703 GAGTAGGATTAATTGAGGTTCATCTAC 57.300 37.037 0.00 0.00 0.00 2.59
963 991 6.801539 TGACATGGTATTTCACTTGAACTC 57.198 37.500 0.00 0.00 33.13 3.01
997 1026 7.238486 TGTTTTATCTTGTAACGGGGTACTA 57.762 36.000 0.00 0.00 0.00 1.82
1263 1294 9.727627 TGGTTTTTATCAAATTGCAAAAATGAC 57.272 25.926 1.71 11.80 33.76 3.06
1753 1786 3.406512 AGAGTATAGTTGGGGAGCAGT 57.593 47.619 0.00 0.00 0.00 4.40
1792 1827 1.136329 AGACAGTTGAGCATGGGGGT 61.136 55.000 0.00 0.00 0.00 4.95
1831 1883 2.153547 ATTTCGGGGCCTTTGTTGCG 62.154 55.000 0.84 0.00 0.00 4.85
2066 2270 6.145371 CCATTGTTTGTGTTATGCCAACTAAC 59.855 38.462 0.65 0.00 32.51 2.34
2194 2594 2.447443 TGAGATGCCTGTCGAAGTACT 58.553 47.619 0.00 0.00 0.00 2.73
2195 2595 2.164422 TGAGATGCCTGTCGAAGTACTG 59.836 50.000 0.00 0.00 0.00 2.74
2210 3390 6.879993 TCGAAGTACTGGATGAGATATACTCC 59.120 42.308 0.00 0.00 44.34 3.85
2289 3469 5.619981 GCACCTGTGATACATTCTGGAAAAC 60.620 44.000 0.51 0.00 0.00 2.43
2292 3472 5.106157 CCTGTGATACATTCTGGAAAACCAC 60.106 44.000 0.00 0.00 0.00 4.16
2293 3473 4.764823 TGTGATACATTCTGGAAAACCACC 59.235 41.667 0.00 0.00 0.00 4.61
2294 3474 4.006989 TGATACATTCTGGAAAACCACCG 58.993 43.478 0.00 0.00 0.00 4.94
2295 3475 2.649531 ACATTCTGGAAAACCACCGA 57.350 45.000 0.00 0.00 0.00 4.69
2296 3476 2.504367 ACATTCTGGAAAACCACCGAG 58.496 47.619 0.00 0.00 0.00 4.63
2297 3477 1.200020 CATTCTGGAAAACCACCGAGC 59.800 52.381 0.00 0.00 0.00 5.03
2298 3478 0.882927 TTCTGGAAAACCACCGAGCG 60.883 55.000 0.00 0.00 0.00 5.03
2299 3479 1.301401 CTGGAAAACCACCGAGCGA 60.301 57.895 0.00 0.00 0.00 4.93
2308 3488 1.361668 CCACCGAGCGAGGTTTGATG 61.362 60.000 3.32 0.00 43.00 3.07
2312 3492 2.093658 ACCGAGCGAGGTTTGATGTAAT 60.094 45.455 0.07 0.00 43.00 1.89
2345 3525 4.678509 TGCACTTTCATATGTTCGTTCC 57.321 40.909 1.90 0.00 0.00 3.62
2360 3541 5.236478 TGTTCGTTCCTGATTTCAGTTCTTC 59.764 40.000 6.81 0.00 42.27 2.87
2364 3545 4.826274 TCCTGATTTCAGTTCTTCGGAT 57.174 40.909 6.81 0.00 42.27 4.18
2367 3548 4.331168 CCTGATTTCAGTTCTTCGGATGTC 59.669 45.833 6.81 0.00 42.27 3.06
2368 3549 4.253685 TGATTTCAGTTCTTCGGATGTCC 58.746 43.478 0.00 0.00 0.00 4.02
2376 3557 0.036010 CTTCGGATGTCCCTTGCAGT 60.036 55.000 0.00 0.00 0.00 4.40
2400 3581 3.476552 TGACTTGGTTCAACATGTCTCC 58.523 45.455 0.00 0.19 42.63 3.71
2410 3591 1.742761 ACATGTCTCCATTTGGCGAG 58.257 50.000 0.00 0.00 34.44 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
121 122 2.151202 GCAATTTCTCGGACCAACTCA 58.849 47.619 0.00 0.00 0.00 3.41
500 508 3.379445 GAGACCCGTCCGGAAGCA 61.379 66.667 5.23 0.00 37.50 3.91
591 599 7.410485 CAGTTTAAGAGAAAAAGACAGTGTCC 58.590 38.462 19.71 4.04 32.18 4.02
593 601 6.884836 ACCAGTTTAAGAGAAAAAGACAGTGT 59.115 34.615 0.00 0.00 0.00 3.55
622 630 4.289410 TCAATTGGAGACCAGGAAGAATCA 59.711 41.667 5.42 0.00 33.81 2.57
647 657 5.688176 GCTAGCATCTACTGTAGTAACAAGC 59.312 44.000 10.63 13.93 34.49 4.01
735 747 8.402472 GGAATACACATTATTTCGGTTTGATGA 58.598 33.333 0.00 0.00 0.00 2.92
852 874 6.989759 TCAGACTTGTGCTTATGAAACAACTA 59.010 34.615 0.00 0.00 30.93 2.24
908 934 9.859427 TTGCATTTATTCTTCAAAATACTCCAG 57.141 29.630 0.00 0.00 0.00 3.86
989 1018 7.201705 GCTGACTTGTATTCATTTTAGTACCCC 60.202 40.741 0.00 0.00 0.00 4.95
997 1026 6.734137 TGAAACGCTGACTTGTATTCATTTT 58.266 32.000 0.00 0.00 0.00 1.82
1090 1120 4.341806 TGCAACAGACAACATGGAAATTCT 59.658 37.500 0.00 0.00 0.00 2.40
1103 1133 1.832883 ACCACAAAGTGCAACAGACA 58.167 45.000 0.00 0.00 41.43 3.41
1178 1209 0.250684 ATGCCAACACGATGACACCA 60.251 50.000 0.00 0.00 0.00 4.17
1263 1294 9.060547 TCAAATATTTGTCGACATTGATTTTCG 57.939 29.630 20.80 12.76 39.18 3.46
1741 1774 1.338020 CAAGAACAACTGCTCCCCAAC 59.662 52.381 0.00 0.00 0.00 3.77
1792 1827 7.766278 CCGAAATTTCTAATCTCTCCTTCTCAA 59.234 37.037 15.92 0.00 0.00 3.02
1831 1883 3.532542 GACCAGGAACATAACTGTAGCC 58.467 50.000 0.00 0.00 33.36 3.93
2110 2444 9.964253 CTTCTCGAATCAAATATATCCGATTTG 57.036 33.333 13.48 13.48 42.94 2.32
2116 2450 6.650807 TGCACCTTCTCGAATCAAATATATCC 59.349 38.462 0.00 0.00 0.00 2.59
2120 2454 6.949352 ATTGCACCTTCTCGAATCAAATAT 57.051 33.333 0.00 0.00 0.00 1.28
2121 2455 6.374053 TCAATTGCACCTTCTCGAATCAAATA 59.626 34.615 0.00 0.00 0.00 1.40
2194 2594 3.591977 TCTCCCGGAGTATATCTCATCCA 59.408 47.826 14.36 0.00 44.40 3.41
2195 2595 4.204012 CTCTCCCGGAGTATATCTCATCC 58.796 52.174 14.36 0.00 44.40 3.51
2210 3390 2.185004 ATGTTGTGAAACCTCTCCCG 57.815 50.000 0.00 0.00 34.36 5.14
2253 3433 2.045524 CACAGGTGCTCCTCCATCTAT 58.954 52.381 3.81 0.00 43.07 1.98
2289 3469 1.079127 ATCAAACCTCGCTCGGTGG 60.079 57.895 0.00 0.00 37.36 4.61
2292 3472 2.004583 TTACATCAAACCTCGCTCGG 57.995 50.000 0.00 0.00 0.00 4.63
2293 3473 3.186909 TCATTACATCAAACCTCGCTCG 58.813 45.455 0.00 0.00 0.00 5.03
2294 3474 3.001736 GCTCATTACATCAAACCTCGCTC 59.998 47.826 0.00 0.00 0.00 5.03
2295 3475 2.939103 GCTCATTACATCAAACCTCGCT 59.061 45.455 0.00 0.00 0.00 4.93
2296 3476 2.677836 TGCTCATTACATCAAACCTCGC 59.322 45.455 0.00 0.00 0.00 5.03
2297 3477 4.944962 TTGCTCATTACATCAAACCTCG 57.055 40.909 0.00 0.00 0.00 4.63
2298 3478 5.039333 GCATTGCTCATTACATCAAACCTC 58.961 41.667 0.16 0.00 0.00 3.85
2299 3479 4.463539 TGCATTGCTCATTACATCAAACCT 59.536 37.500 10.49 0.00 0.00 3.50
2345 3525 6.649449 GGGACATCCGAAGAACTGAAATCAG 61.649 48.000 8.84 8.84 42.59 2.90
2360 3541 1.942657 CAATACTGCAAGGGACATCCG 59.057 52.381 0.00 0.00 39.30 4.18
2364 3545 3.411446 CAAGTCAATACTGCAAGGGACA 58.589 45.455 0.00 0.00 39.30 4.02
2367 3548 2.795329 ACCAAGTCAATACTGCAAGGG 58.205 47.619 0.00 0.00 39.30 3.95
2368 3549 3.820467 TGAACCAAGTCAATACTGCAAGG 59.180 43.478 0.00 0.00 39.30 3.61
2376 3557 5.705441 GGAGACATGTTGAACCAAGTCAATA 59.295 40.000 0.00 0.00 39.61 1.90
2400 3581 7.017645 GCTATATGTTAACATCTCGCCAAATG 58.982 38.462 24.00 6.59 37.76 2.32


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

AutoCloner maintained by Alex Coulton.