Multiple sequence alignment - TraesCS3B01G063200

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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 TraesCS3B01G063200 chr3B 100.000 2348 0 0 1 2348 35460914 35463261 0.000000e+00 4337.0
1 TraesCS3B01G063200 chr3B 97.491 2352 49 8 1 2348 35639293 35641638 0.000000e+00 4008.0
2 TraesCS3B01G063200 chr3B 96.939 2352 47 9 1 2348 35573138 35575468 0.000000e+00 3921.0
3 TraesCS3B01G063200 chr3B 96.003 2352 63 5 1 2348 34523410 34521086 0.000000e+00 3794.0
4 TraesCS3B01G063200 chr3B 95.502 1334 31 3 1017 2348 34467267 34465961 0.000000e+00 2104.0
5 TraesCS3B01G063200 chr3B 97.371 989 24 2 2 988 34468251 34467263 0.000000e+00 1681.0
6 TraesCS3B01G063200 chr3B 96.939 882 27 0 1467 2348 35734310 35735191 0.000000e+00 1480.0
7 TraesCS3B01G063200 chr3B 96.825 882 28 0 1467 2348 35806344 35807225 0.000000e+00 1474.0
8 TraesCS3B01G063200 chr3B 96.712 882 29 0 1467 2348 35816595 35817476 0.000000e+00 1469.0
9 TraesCS3B01G063200 chr3B 96.599 882 30 0 1467 2348 35747416 35748297 0.000000e+00 1463.0
10 TraesCS3B01G063200 chr3B 96.259 882 33 0 1467 2348 35826685 35827566 0.000000e+00 1447.0
11 TraesCS3B01G063200 chr3B 94.099 949 29 10 876 1815 35697693 35698623 0.000000e+00 1417.0
12 TraesCS3B01G063200 chr3B 94.099 949 29 10 876 1815 35769630 35770560 0.000000e+00 1417.0
13 TraesCS3B01G063200 chr3B 94.167 840 38 6 1 838 35696867 35697697 0.000000e+00 1269.0
14 TraesCS3B01G063200 chr3B 94.048 840 39 6 1 838 35768804 35769634 0.000000e+00 1264.0
15 TraesCS3B01G063200 chr3B 98.214 56 1 0 1379 1434 35733170 35733225 5.340000e-17 99.0
16 TraesCS3B01G063200 chr3B 98.148 54 1 0 1379 1432 35805220 35805273 6.910000e-16 95.3
17 TraesCS3B01G063200 chrUn 96.825 882 28 0 1467 2348 338662708 338663589 0.000000e+00 1474.0
18 TraesCS3B01G063200 chrUn 94.615 947 26 11 876 1815 168645470 168644542 0.000000e+00 1443.0
19 TraesCS3B01G063200 chrUn 96.420 866 31 0 1467 2332 364390240 364389375 0.000000e+00 1428.0
20 TraesCS3B01G063200 chrUn 95.000 840 30 6 1 838 202840984 202840155 0.000000e+00 1308.0
21 TraesCS3B01G063200 chrUn 94.881 840 31 6 1 838 168646295 168645466 0.000000e+00 1303.0
22 TraesCS3B01G063200 chrUn 94.887 841 30 7 1 838 390422009 390421179 0.000000e+00 1303.0
23 TraesCS3B01G063200 chrUn 92.150 879 20 19 876 1747 352902277 352901441 0.000000e+00 1195.0
24 TraesCS3B01G063200 chrUn 97.421 504 9 3 876 1375 202840159 202839656 0.000000e+00 856.0


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 TraesCS3B01G063200 chr3B 35460914 35463261 2347 False 4337.00 4337 100.0000 1 2348 1 chr3B.!!$F1 2347
1 TraesCS3B01G063200 chr3B 35639293 35641638 2345 False 4008.00 4008 97.4910 1 2348 1 chr3B.!!$F3 2347
2 TraesCS3B01G063200 chr3B 35573138 35575468 2330 False 3921.00 3921 96.9390 1 2348 1 chr3B.!!$F2 2347
3 TraesCS3B01G063200 chr3B 34521086 34523410 2324 True 3794.00 3794 96.0030 1 2348 1 chr3B.!!$R1 2347
4 TraesCS3B01G063200 chr3B 34465961 34468251 2290 True 1892.50 2104 96.4365 2 2348 2 chr3B.!!$R2 2346
5 TraesCS3B01G063200 chr3B 35816595 35817476 881 False 1469.00 1469 96.7120 1467 2348 1 chr3B.!!$F5 881
6 TraesCS3B01G063200 chr3B 35747416 35748297 881 False 1463.00 1463 96.5990 1467 2348 1 chr3B.!!$F4 881
7 TraesCS3B01G063200 chr3B 35826685 35827566 881 False 1447.00 1447 96.2590 1467 2348 1 chr3B.!!$F6 881
8 TraesCS3B01G063200 chr3B 35696867 35698623 1756 False 1343.00 1417 94.1330 1 1815 2 chr3B.!!$F7 1814
9 TraesCS3B01G063200 chr3B 35768804 35770560 1756 False 1340.50 1417 94.0735 1 1815 2 chr3B.!!$F9 1814
10 TraesCS3B01G063200 chr3B 35733170 35735191 2021 False 789.50 1480 97.5765 1379 2348 2 chr3B.!!$F8 969
11 TraesCS3B01G063200 chr3B 35805220 35807225 2005 False 784.65 1474 97.4865 1379 2348 2 chr3B.!!$F10 969
12 TraesCS3B01G063200 chrUn 338662708 338663589 881 False 1474.00 1474 96.8250 1467 2348 1 chrUn.!!$F1 881
13 TraesCS3B01G063200 chrUn 364389375 364390240 865 True 1428.00 1428 96.4200 1467 2332 1 chrUn.!!$R2 865
14 TraesCS3B01G063200 chrUn 168644542 168646295 1753 True 1373.00 1443 94.7480 1 1815 2 chrUn.!!$R4 1814
15 TraesCS3B01G063200 chrUn 390421179 390422009 830 True 1303.00 1303 94.8870 1 838 1 chrUn.!!$R3 837
16 TraesCS3B01G063200 chrUn 352901441 352902277 836 True 1195.00 1195 92.1500 876 1747 1 chrUn.!!$R1 871
17 TraesCS3B01G063200 chrUn 202839656 202840984 1328 True 1082.00 1308 96.2105 1 1375 2 chrUn.!!$R5 1374

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
275 279 0.539438 TGGAAGCAAATCCGTGCCTT 60.539 50.0 0.0 0.0 46.14 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2145 3213 0.595095 GTCGTACCCTGTCAGAACGT 59.405 55.0 16.64 7.13 35.21 3.99 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
49 50 5.517054 GCGTCGAGATCTTCAAAACTAGATT 59.483 40.000 0.00 0.00 0.00 2.40
67 68 9.614792 AACTAGATTGTATGTTGATAGGTTTCC 57.385 33.333 0.00 0.00 0.00 3.13
131 134 1.954382 GAGAGCACGGTTTTCCCTTTT 59.046 47.619 0.00 0.00 36.42 2.27
134 137 2.296190 GAGCACGGTTTTCCCTTTTCAT 59.704 45.455 0.00 0.00 36.42 2.57
142 145 4.248058 GTTTTCCCTTTTCATGAGCATGG 58.752 43.478 10.31 0.00 39.24 3.66
200 203 5.185249 ACGAGAACTAAATTAGTGCCTCTCA 59.815 40.000 22.72 0.00 38.89 3.27
275 279 0.539438 TGGAAGCAAATCCGTGCCTT 60.539 50.000 0.00 0.00 46.14 4.35
299 303 4.567159 CACGAGAAGTAAATTAGTGCCTCC 59.433 45.833 0.00 0.00 0.00 4.30
338 342 4.763793 CCATGATTTTTCCCTCTCGCATAT 59.236 41.667 0.00 0.00 0.00 1.78
484 492 5.023533 AGCTGAGCTATTGAATTCGGTAA 57.976 39.130 4.49 0.00 36.99 2.85
527 535 8.971321 GGTAAAAATGATGACGTACGTATATGT 58.029 33.333 22.87 5.76 32.95 2.29
619 627 6.859017 TGCGTACATGTCTTAGTCTCATAAA 58.141 36.000 0.00 0.00 0.00 1.40
701 709 2.833913 GGTCCATCCATCGGCCCAT 61.834 63.158 0.00 0.00 35.97 4.00
853 861 8.967664 ACACCAAGAAAGTACACTGTTTATTA 57.032 30.769 0.00 0.00 0.00 0.98
1506 2570 3.192466 GTGAGAGAGAGAGGAGTACGTC 58.808 54.545 0.00 0.00 0.00 4.34
1520 2584 0.961857 TACGTCCGTCCAAGCAGCTA 60.962 55.000 0.00 0.00 0.00 3.32
1800 2868 4.873746 TTGGTTCCTCAACAAAACACAA 57.126 36.364 0.00 0.00 33.70 3.33
1988 3056 5.526479 CAGTGTACATGAAAGATCATCCAGG 59.474 44.000 0.00 0.00 44.53 4.45
2145 3213 6.053005 GGATCCAATCACAGTAATAAACCGA 58.947 40.000 6.95 0.00 0.00 4.69
2204 3272 4.766375 ACTACGGCACTAAATACTTGCAT 58.234 39.130 0.00 0.00 38.04 3.96
2209 3277 7.095695 ACGGCACTAAATACTTGCATAAATT 57.904 32.000 0.00 0.00 38.04 1.82
2335 3403 7.775397 AATTTGAGTCAGGTGTTTGAATTTG 57.225 32.000 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 5.408880 TCGTGGAAACCTATCAACATACA 57.591 39.130 0.00 0.00 0.00 2.29
131 134 0.323999 AAGCTTGGCCATGCTCATGA 60.324 50.000 37.76 7.97 40.38 3.07
134 137 0.679002 GAGAAGCTTGGCCATGCTCA 60.679 55.000 37.76 10.30 40.38 4.26
142 145 2.742372 TTCCGCGAGAAGCTTGGC 60.742 61.111 8.23 3.43 45.59 4.52
200 203 9.093458 AGACAAAATATGTTCTTTTCCTTCCAT 57.907 29.630 0.00 0.00 44.12 3.41
275 279 5.401531 AGGCACTAATTTACTTCTCGTGA 57.598 39.130 0.00 0.00 36.02 4.35
338 342 2.743664 CTCGTGGAGTCATGAATTTGCA 59.256 45.455 0.00 0.00 38.33 4.08
475 483 0.249398 ACGCTCTGGCTTACCGAATT 59.751 50.000 0.00 0.00 39.70 2.17
484 492 0.328258 ACCCAAAATACGCTCTGGCT 59.672 50.000 0.00 0.00 36.09 4.75
527 535 2.036604 TGAGCACGACCATTGAACTGTA 59.963 45.455 0.00 0.00 0.00 2.74
619 627 3.526931 AGCGTGTACACAGCAGATTAT 57.473 42.857 30.36 15.34 34.80 1.28
853 861 1.475034 CCATCACGGGATTCCATTCGT 60.475 52.381 0.00 2.29 36.19 3.85
1506 2570 3.414272 GCATAGCTGCTTGGACGG 58.586 61.111 7.79 0.00 45.32 4.79
1659 2723 6.039047 AGTCTTGCATATATCAAAAGTGCTGG 59.961 38.462 0.00 0.00 36.78 4.85
1765 2831 5.598005 TGAGGAACCAAAATGAGTGAAATGT 59.402 36.000 0.00 0.00 0.00 2.71
1800 2868 5.708230 TGTGTGTTCTCAAACAGTTTTAGGT 59.292 36.000 7.27 0.00 45.78 3.08
1954 3022 9.683069 ATCTTTCATGTACACTGTTTGAAATTC 57.317 29.630 17.50 0.00 36.17 2.17
1988 3056 7.770897 ACCAGTGTCTAATTAATTGACATCTCC 59.229 37.037 23.81 16.19 41.78 3.71
2145 3213 0.595095 GTCGTACCCTGTCAGAACGT 59.405 55.000 16.64 7.13 35.21 3.99


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

AutoCloner maintained by Alex Coulton.