Multiple sequence alignment - TraesCS1B01G145900

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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 TraesCS1B01G145900 chr1B 100.000 2450 0 0 1 2450 200995205 200997654 0 4525
1 TraesCS1B01G145900 chr1B 91.334 2458 185 20 1 2448 307385464 307383025 0 3334
2 TraesCS1B01G145900 chr1B 90.832 2465 197 16 1 2450 387430126 387427676 0 3273
3 TraesCS1B01G145900 chr1B 90.350 2456 198 26 1 2445 287516457 287518884 0 3186
4 TraesCS1B01G145900 chr3B 91.670 2461 174 19 1 2449 81050296 81052737 0 3380
5 TraesCS1B01G145900 chr3B 91.508 2461 177 14 1 2450 128995705 128993266 0 3358
6 TraesCS1B01G145900 chr3B 90.424 2454 202 21 1 2445 195665364 195667793 0 3199
7 TraesCS1B01G145900 chr3B 89.666 2458 233 16 1 2450 331024947 331027391 0 3112
8 TraesCS1B01G145900 chr2B 90.880 2478 191 21 1 2450 762706221 762708691 0 3291
9 TraesCS1B01G145900 chr2A 88.790 2462 244 24 1 2449 267980586 267983028 0 2988


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 TraesCS1B01G145900 chr1B 200995205 200997654 2449 False 4525 4525 100.000 1 2450 1 chr1B.!!$F1 2449
1 TraesCS1B01G145900 chr1B 307383025 307385464 2439 True 3334 3334 91.334 1 2448 1 chr1B.!!$R1 2447
2 TraesCS1B01G145900 chr1B 387427676 387430126 2450 True 3273 3273 90.832 1 2450 1 chr1B.!!$R2 2449
3 TraesCS1B01G145900 chr1B 287516457 287518884 2427 False 3186 3186 90.350 1 2445 1 chr1B.!!$F2 2444
4 TraesCS1B01G145900 chr3B 81050296 81052737 2441 False 3380 3380 91.670 1 2449 1 chr3B.!!$F1 2448
5 TraesCS1B01G145900 chr3B 128993266 128995705 2439 True 3358 3358 91.508 1 2450 1 chr3B.!!$R1 2449
6 TraesCS1B01G145900 chr3B 195665364 195667793 2429 False 3199 3199 90.424 1 2445 1 chr3B.!!$F2 2444
7 TraesCS1B01G145900 chr3B 331024947 331027391 2444 False 3112 3112 89.666 1 2450 1 chr3B.!!$F3 2449
8 TraesCS1B01G145900 chr2B 762706221 762708691 2470 False 3291 3291 90.880 1 2450 1 chr2B.!!$F1 2449
9 TraesCS1B01G145900 chr2A 267980586 267983028 2442 False 2988 2988 88.790 1 2449 1 chr2A.!!$F1 2448

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
296 297 0.107654 GGGTGGACTGAAATCCGGAG 60.108 60.000 11.34 0.0 42.24 4.63 F
742 749 1.133792 CCCTTGAGGTGTGTGAGGTTT 60.134 52.381 0.00 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1382 1392 0.956633 AACTCGGTCAACTCGCAGTA 59.043 50.000 0.00 0.00 0.00 2.74 R
1566 1581 1.001706 GAAACAGCTCACCGGGTTTTC 60.002 52.381 6.32 0.07 33.92 2.29 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
113 114 3.938289 GGATAGGCCTAGTTCTTACGG 57.062 52.381 19.33 0.00 0.00 4.02
283 284 4.927267 AAGAATTACTCACATGGGTGGA 57.073 40.909 1.53 0.00 45.32 4.02
293 294 1.340017 ACATGGGTGGACTGAAATCCG 60.340 52.381 0.00 0.00 42.24 4.18
296 297 0.107654 GGGTGGACTGAAATCCGGAG 60.108 60.000 11.34 0.00 42.24 4.63
319 320 7.124573 AGTATGTCATATAGGAGCAACAACA 57.875 36.000 0.00 0.00 0.00 3.33
332 333 5.411831 AGCAACAACACTGAGATCTCATA 57.588 39.130 25.30 4.16 39.13 2.15
338 339 6.169094 ACAACACTGAGATCTCATAGTTTGG 58.831 40.000 27.28 21.94 39.13 3.28
412 413 4.713553 TGCTCCACAACAGTCTTATTCAA 58.286 39.130 0.00 0.00 0.00 2.69
501 508 3.958018 ACCAACACCTTCAACACAAGTA 58.042 40.909 0.00 0.00 0.00 2.24
628 635 3.340814 TGAAGAAGATCAAGAGTGGGC 57.659 47.619 0.00 0.00 0.00 5.36
742 749 1.133792 CCCTTGAGGTGTGTGAGGTTT 60.134 52.381 0.00 0.00 0.00 3.27
750 757 2.088423 GTGTGTGAGGTTTCAACACCA 58.912 47.619 2.99 0.00 39.62 4.17
908 918 9.742144 ATCTACTACTGAAGAAGTACAAGAAGA 57.258 33.333 0.00 0.00 40.56 2.87
965 975 2.771372 TGCCTATTGTCATACCAGAGCA 59.229 45.455 0.00 0.00 0.00 4.26
1154 1164 6.519679 TCATAGTTACTTTCCTCGTGCTAA 57.480 37.500 0.00 0.00 0.00 3.09
1192 1202 6.326323 TGAAACATATCACTCCCATGCTAGTA 59.674 38.462 0.00 0.00 0.00 1.82
1318 1328 3.735237 TCGATGACTTAGAGGGCATTC 57.265 47.619 0.00 0.00 0.00 2.67
1321 1331 3.320541 CGATGACTTAGAGGGCATTCTCT 59.679 47.826 8.23 8.23 45.22 3.10
1324 1334 3.703556 TGACTTAGAGGGCATTCTCTCTG 59.296 47.826 4.86 0.00 42.57 3.35
1340 1350 4.284490 TCTCTCTGTCACTTGTATTGGCTT 59.716 41.667 0.00 0.00 0.00 4.35
1341 1351 4.318332 TCTCTGTCACTTGTATTGGCTTG 58.682 43.478 0.00 0.00 0.00 4.01
1342 1352 3.411446 TCTGTCACTTGTATTGGCTTGG 58.589 45.455 0.00 0.00 0.00 3.61
1344 1354 3.561143 TGTCACTTGTATTGGCTTGGTT 58.439 40.909 0.00 0.00 0.00 3.67
1366 1376 4.584874 TGTTGAGTGTTCTTTCAGGTTGA 58.415 39.130 0.00 0.00 0.00 3.18
1375 1385 3.554934 TCTTTCAGGTTGATGCTTGTGT 58.445 40.909 0.00 0.00 0.00 3.72
1378 1388 2.778299 TCAGGTTGATGCTTGTGTACC 58.222 47.619 0.00 0.00 0.00 3.34
1382 1392 4.022068 CAGGTTGATGCTTGTGTACCATTT 60.022 41.667 0.00 0.00 0.00 2.32
1386 1396 5.878332 TGATGCTTGTGTACCATTTACTG 57.122 39.130 0.00 0.00 0.00 2.74
1388 1398 2.482336 TGCTTGTGTACCATTTACTGCG 59.518 45.455 0.00 0.00 0.00 5.18
1389 1399 2.739913 GCTTGTGTACCATTTACTGCGA 59.260 45.455 0.00 0.00 0.00 5.10
1391 1401 3.671008 TGTGTACCATTTACTGCGAGT 57.329 42.857 0.00 0.00 0.00 4.18
1397 1407 1.393539 CCATTTACTGCGAGTTGACCG 59.606 52.381 0.00 0.00 0.00 4.79
1526 1541 3.515562 AGAGAAGCAAAAGGAGAGGAGA 58.484 45.455 0.00 0.00 0.00 3.71
1721 1742 6.763135 GGTGCTTGATGAGAATATGTGAACTA 59.237 38.462 0.00 0.00 0.00 2.24
1724 1745 7.011763 TGCTTGATGAGAATATGTGAACTAAGC 59.988 37.037 0.00 0.00 35.97 3.09
1786 1807 4.319839 GCTTTGCTGAAAGTAGTGGAAGTC 60.320 45.833 0.00 0.00 40.77 3.01
1956 1978 2.981784 AGCATGCTATGTTCCCTGGATA 59.018 45.455 21.21 0.00 0.00 2.59
1996 2018 5.447778 ACATGGAGAAGTGATGATTCCTT 57.552 39.130 0.00 0.00 0.00 3.36
2177 2202 2.061509 TACCATGTTCTCGGGATCGA 57.938 50.000 0.00 0.00 43.86 3.59
2428 2502 7.929941 AACTTGTTGATCCTCTTTTATCTCC 57.070 36.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 8.088981 TCTTACCTATCAGTTCTTGAACACTTC 58.911 37.037 14.80 0.00 39.77 3.01
113 114 2.224646 GGATGGCCTCTGGAATAAGGAC 60.225 54.545 3.32 0.00 41.48 3.85
264 265 3.941483 CAGTCCACCCATGTGAGTAATTC 59.059 47.826 0.00 0.00 45.76 2.17
283 284 6.672266 ATATGACATACTCCGGATTTCAGT 57.328 37.500 3.57 0.56 0.00 3.41
293 294 6.346477 TGTTGCTCCTATATGACATACTCC 57.654 41.667 0.00 0.00 0.00 3.85
296 297 6.986817 AGTGTTGTTGCTCCTATATGACATAC 59.013 38.462 0.00 0.00 0.00 2.39
319 320 6.865834 AGAACCAAACTATGAGATCTCAGT 57.134 37.500 28.26 19.43 43.61 3.41
332 333 7.716998 CCTGCATATGATTACTAGAACCAAACT 59.283 37.037 6.97 0.00 0.00 2.66
338 339 8.854614 AAATCCCTGCATATGATTACTAGAAC 57.145 34.615 6.97 0.00 0.00 3.01
412 413 5.482175 GGTGCTGAGGTATATGAATAGGAGT 59.518 44.000 0.00 0.00 0.00 3.85
490 497 6.266786 TCATCTTGAGTAGGTACTTGTGTTGA 59.733 38.462 0.00 0.00 41.75 3.18
628 635 5.127845 TCCTTACTTCTTCCACTAGCTCATG 59.872 44.000 0.00 0.00 0.00 3.07
729 736 1.404035 GGTGTTGAAACCTCACACACC 59.596 52.381 16.54 16.54 45.60 4.16
730 737 2.088423 TGGTGTTGAAACCTCACACAC 58.912 47.619 4.22 6.74 41.16 3.82
731 738 2.498644 TGGTGTTGAAACCTCACACA 57.501 45.000 4.22 0.00 41.16 3.72
732 739 2.948979 TGATGGTGTTGAAACCTCACAC 59.051 45.455 0.00 0.00 41.16 3.82
742 749 2.815503 CAGCTGAATGTGATGGTGTTGA 59.184 45.455 8.42 0.00 0.00 3.18
750 757 3.345508 TCTTGCTCAGCTGAATGTGAT 57.654 42.857 18.85 0.00 0.00 3.06
908 918 6.647229 TGTTCTTCATCTTCATCTACAGCAT 58.353 36.000 0.00 0.00 0.00 3.79
965 975 5.882557 GGATTGAGTAAACCTGACACATCAT 59.117 40.000 0.00 0.00 33.22 2.45
1179 1189 4.348863 AAGCTCAATACTAGCATGGGAG 57.651 45.455 0.00 0.00 42.62 4.30
1299 1309 3.320541 AGAGAATGCCCTCTAAGTCATCG 59.679 47.826 0.00 0.00 41.41 3.84
1318 1328 4.199432 AGCCAATACAAGTGACAGAGAG 57.801 45.455 0.00 0.00 0.00 3.20
1321 1331 3.181445 ACCAAGCCAATACAAGTGACAGA 60.181 43.478 0.00 0.00 0.00 3.41
1324 1334 3.317993 ACAACCAAGCCAATACAAGTGAC 59.682 43.478 0.00 0.00 0.00 3.67
1340 1350 3.694072 CCTGAAAGAACACTCAACAACCA 59.306 43.478 0.00 0.00 34.07 3.67
1341 1351 3.694566 ACCTGAAAGAACACTCAACAACC 59.305 43.478 0.00 0.00 34.07 3.77
1342 1352 4.965119 ACCTGAAAGAACACTCAACAAC 57.035 40.909 0.00 0.00 34.07 3.32
1344 1354 4.584874 TCAACCTGAAAGAACACTCAACA 58.415 39.130 0.00 0.00 34.07 3.33
1375 1385 3.592059 GGTCAACTCGCAGTAAATGGTA 58.408 45.455 0.00 0.00 0.00 3.25
1378 1388 2.333926 TCGGTCAACTCGCAGTAAATG 58.666 47.619 0.00 0.00 0.00 2.32
1382 1392 0.956633 AACTCGGTCAACTCGCAGTA 59.043 50.000 0.00 0.00 0.00 2.74
1386 1396 1.066114 CTCGAACTCGGTCAACTCGC 61.066 60.000 0.00 0.00 40.29 5.03
1388 1398 2.161808 TCATCTCGAACTCGGTCAACTC 59.838 50.000 0.00 0.00 40.29 3.01
1389 1399 2.095161 GTCATCTCGAACTCGGTCAACT 60.095 50.000 0.00 0.00 40.29 3.16
1391 1401 1.883926 TGTCATCTCGAACTCGGTCAA 59.116 47.619 0.00 0.00 40.29 3.18
1397 1407 3.452474 CAGGGAATGTCATCTCGAACTC 58.548 50.000 0.00 0.00 0.00 3.01
1526 1541 1.676916 CGATCACCTCACCAACTGCAT 60.677 52.381 0.00 0.00 0.00 3.96
1559 1574 2.617021 GCTCACCGGGTTTTCATAGGAA 60.617 50.000 6.32 0.00 0.00 3.36
1562 1577 2.009774 CAGCTCACCGGGTTTTCATAG 58.990 52.381 6.32 0.00 0.00 2.23
1563 1578 1.349688 ACAGCTCACCGGGTTTTCATA 59.650 47.619 6.32 0.00 0.00 2.15
1566 1581 1.001706 GAAACAGCTCACCGGGTTTTC 60.002 52.381 6.32 0.07 33.92 2.29
1721 1742 1.904287 TTACCAGGCATTCAACGCTT 58.096 45.000 0.00 0.00 0.00 4.68
1724 1745 4.000988 ACTAGTTTACCAGGCATTCAACG 58.999 43.478 0.00 0.00 0.00 4.10
1956 1978 3.222173 TGTTTGGTTCACATGCTACCT 57.778 42.857 11.42 0.00 33.05 3.08
2177 2202 3.053619 GTCTCCCCAAAGGAACATACCAT 60.054 47.826 0.00 0.00 46.94 3.55


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

AutoCloner maintained by Alex Coulton.