Multiple sequence alignment - TraesCS1D01G010900

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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 TraesCS1D01G010900 chr1D 100.000 4559 0 0 1 4559 5525147 5520589 0.000000e+00 8419.0
1 TraesCS1D01G010900 chr1D 79.475 2743 410 90 986 3648 407672555 407669886 0.000000e+00 1805.0
2 TraesCS1D01G010900 chr1D 79.845 2317 384 46 1241 3493 6721390 6719093 0.000000e+00 1615.0
3 TraesCS1D01G010900 chr1A 95.431 4027 158 9 538 4559 7191930 7187925 0.000000e+00 6394.0
4 TraesCS1D01G010900 chr1A 79.095 2454 413 59 1114 3511 7834789 7837198 0.000000e+00 1598.0
5 TraesCS1D01G010900 chr1A 78.977 2326 391 51 1238 3493 8159658 8157361 0.000000e+00 1496.0
6 TraesCS1D01G010900 chr1A 78.857 1750 313 36 1115 2837 9375542 9373823 0.000000e+00 1129.0
7 TraesCS1D01G010900 chr1A 92.464 491 29 4 43 528 7192843 7192356 0.000000e+00 695.0
8 TraesCS1D01G010900 chr1A 92.135 89 7 0 1238 1326 8088571 8088483 4.790000e-25 126.0
9 TraesCS1D01G010900 chr1B 95.093 4015 158 14 1 4004 8262562 8258576 0.000000e+00 6287.0
10 TraesCS1D01G010900 chr1B 79.221 2440 424 49 1115 3502 10007379 10004971 0.000000e+00 1620.0
11 TraesCS1D01G010900 chr1B 79.488 2345 392 51 1238 3516 8867032 8864711 0.000000e+00 1583.0
12 TraesCS1D01G010900 chr1B 78.789 2329 412 47 1238 3504 9161999 9164307 0.000000e+00 1489.0
13 TraesCS1D01G010900 chr1B 78.354 2102 340 60 1123 3183 9175492 9177519 0.000000e+00 1254.0
14 TraesCS1D01G010900 chr1B 92.494 453 34 0 4107 4559 8258577 8258125 0.000000e+00 649.0
15 TraesCS1D01G010900 chr5B 81.392 2816 448 48 896 3687 609094579 609097342 0.000000e+00 2228.0
16 TraesCS1D01G010900 chr5B 79.974 2337 374 45 1230 3513 549548192 549550487 0.000000e+00 1637.0
17 TraesCS1D01G010900 chr5B 81.443 97 15 3 4129 4224 313097573 313097667 4.890000e-10 76.8
18 TraesCS1D01G010900 chr5A 80.086 2566 414 52 1124 3636 12194100 12191579 0.000000e+00 1818.0
19 TraesCS1D01G010900 chr2D 79.680 2559 404 60 1125 3622 469984161 469986664 0.000000e+00 1738.0
20 TraesCS1D01G010900 chr2D 79.025 2441 422 54 1126 3506 469990710 469993120 0.000000e+00 1589.0
21 TraesCS1D01G010900 chr4B 80.306 2351 396 34 1240 3536 36635649 36633312 0.000000e+00 1714.0
22 TraesCS1D01G010900 chr2B 79.614 2433 413 46 1126 3506 548624113 548626514 0.000000e+00 1668.0
23 TraesCS1D01G010900 chr2B 76.763 2552 474 74 1114 3629 4754189 4751721 0.000000e+00 1317.0
24 TraesCS1D01G010900 chr2B 79.641 1783 263 55 1125 2859 548609634 548611364 0.000000e+00 1190.0
25 TraesCS1D01G010900 chr2B 80.219 915 148 23 2846 3739 548619285 548620187 0.000000e+00 656.0
26 TraesCS1D01G010900 chr2A 79.411 2443 408 58 1126 3506 611302951 611305360 0.000000e+00 1637.0
27 TraesCS1D01G010900 chr2A 81.811 1292 197 27 2473 3739 611297823 611299101 0.000000e+00 1050.0


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 TraesCS1D01G010900 chr1D 5520589 5525147 4558 True 8419.0 8419 100.0000 1 4559 1 chr1D.!!$R1 4558
1 TraesCS1D01G010900 chr1D 407669886 407672555 2669 True 1805.0 1805 79.4750 986 3648 1 chr1D.!!$R3 2662
2 TraesCS1D01G010900 chr1D 6719093 6721390 2297 True 1615.0 1615 79.8450 1241 3493 1 chr1D.!!$R2 2252
3 TraesCS1D01G010900 chr1A 7187925 7192843 4918 True 3544.5 6394 93.9475 43 4559 2 chr1A.!!$R4 4516
4 TraesCS1D01G010900 chr1A 7834789 7837198 2409 False 1598.0 1598 79.0950 1114 3511 1 chr1A.!!$F1 2397
5 TraesCS1D01G010900 chr1A 8157361 8159658 2297 True 1496.0 1496 78.9770 1238 3493 1 chr1A.!!$R2 2255
6 TraesCS1D01G010900 chr1A 9373823 9375542 1719 True 1129.0 1129 78.8570 1115 2837 1 chr1A.!!$R3 1722
7 TraesCS1D01G010900 chr1B 8258125 8262562 4437 True 3468.0 6287 93.7935 1 4559 2 chr1B.!!$R3 4558
8 TraesCS1D01G010900 chr1B 10004971 10007379 2408 True 1620.0 1620 79.2210 1115 3502 1 chr1B.!!$R2 2387
9 TraesCS1D01G010900 chr1B 8864711 8867032 2321 True 1583.0 1583 79.4880 1238 3516 1 chr1B.!!$R1 2278
10 TraesCS1D01G010900 chr1B 9161999 9164307 2308 False 1489.0 1489 78.7890 1238 3504 1 chr1B.!!$F1 2266
11 TraesCS1D01G010900 chr1B 9175492 9177519 2027 False 1254.0 1254 78.3540 1123 3183 1 chr1B.!!$F2 2060
12 TraesCS1D01G010900 chr5B 609094579 609097342 2763 False 2228.0 2228 81.3920 896 3687 1 chr5B.!!$F3 2791
13 TraesCS1D01G010900 chr5B 549548192 549550487 2295 False 1637.0 1637 79.9740 1230 3513 1 chr5B.!!$F2 2283
14 TraesCS1D01G010900 chr5A 12191579 12194100 2521 True 1818.0 1818 80.0860 1124 3636 1 chr5A.!!$R1 2512
15 TraesCS1D01G010900 chr2D 469984161 469986664 2503 False 1738.0 1738 79.6800 1125 3622 1 chr2D.!!$F1 2497
16 TraesCS1D01G010900 chr2D 469990710 469993120 2410 False 1589.0 1589 79.0250 1126 3506 1 chr2D.!!$F2 2380
17 TraesCS1D01G010900 chr4B 36633312 36635649 2337 True 1714.0 1714 80.3060 1240 3536 1 chr4B.!!$R1 2296
18 TraesCS1D01G010900 chr2B 4751721 4754189 2468 True 1317.0 1317 76.7630 1114 3629 1 chr2B.!!$R1 2515
19 TraesCS1D01G010900 chr2B 548609634 548611364 1730 False 1190.0 1190 79.6410 1125 2859 1 chr2B.!!$F1 1734
20 TraesCS1D01G010900 chr2B 548619285 548626514 7229 False 1162.0 1668 79.9165 1126 3739 2 chr2B.!!$F2 2613
21 TraesCS1D01G010900 chr2A 611297823 611305360 7537 False 1343.5 1637 80.6110 1126 3739 2 chr2A.!!$F1 2613

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
414 427 1.683790 GCCGTCGCTGTACACATGTC 61.684 60.0 0.0 0.0 0.0 3.06 F
1510 5663 0.682852 TGTCCTCCTACCCACAAACG 59.317 55.0 0.0 0.0 0.0 3.60 F
1913 6087 0.602905 CTGGACACCTCGGGTCAAAC 60.603 60.0 0.0 0.0 37.0 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1641 5803 0.911769 TGTATGAGCCAAGACCAGGG 59.088 55.000 0.0 0.0 0.00 4.45 R
3357 7617 1.851658 CAACCTTGCAAACCCTTTCG 58.148 50.000 0.0 0.0 0.00 3.46 R
3861 8141 1.000938 GCTCAAAAGCTCAACACCAGG 60.001 52.381 0.0 0.0 45.55 4.45 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
23 24 6.602564 GAAGCAAACACACTTAATCATTCG 57.397 37.500 0.00 0.00 0.00 3.34
24 25 4.475944 AGCAAACACACTTAATCATTCGC 58.524 39.130 0.00 0.00 0.00 4.70
71 72 7.049133 AGAGAGAATCATTCACCAAGATTGAG 58.951 38.462 0.00 0.00 39.29 3.02
72 73 6.955364 AGAGAATCATTCACCAAGATTGAGA 58.045 36.000 0.00 0.00 39.29 3.27
225 227 6.127758 ACGCACCTAAAGCAAATTATGAATCA 60.128 34.615 0.00 0.00 0.00 2.57
317 319 4.122776 CCTATGTATAGCCGCCATCAATC 58.877 47.826 0.00 0.00 0.00 2.67
390 400 4.787598 ACAAATTGCTCTAAACTTCTGCG 58.212 39.130 0.00 0.00 0.00 5.18
391 401 3.477899 AATTGCTCTAAACTTCTGCGC 57.522 42.857 0.00 0.00 0.00 6.09
414 427 1.683790 GCCGTCGCTGTACACATGTC 61.684 60.000 0.00 0.00 0.00 3.06
574 1002 9.859427 AATATTTGTGGTCACTCAATTATTGTG 57.141 29.630 4.77 5.21 36.41 3.33
611 1039 4.499357 CGGAGTTATAGCTGACCTTGGTAC 60.499 50.000 0.00 0.00 0.00 3.34
612 1040 4.650131 GGAGTTATAGCTGACCTTGGTACT 59.350 45.833 0.00 0.00 0.00 2.73
682 1110 6.824305 AATTTGTTGATGAAGTCTACTGGG 57.176 37.500 0.00 0.00 34.28 4.45
933 1363 5.184711 TCCTTCTCCGAAGAGTTAGTAGAC 58.815 45.833 5.24 0.00 41.26 2.59
1084 1526 2.505777 CTGCAGGCGACACTCTCG 60.506 66.667 5.57 0.00 45.97 4.04
1510 5663 0.682852 TGTCCTCCTACCCACAAACG 59.317 55.000 0.00 0.00 0.00 3.60
1641 5803 8.994429 TCATCTCAAAGAAGAGTCTCATTAAC 57.006 34.615 1.94 0.00 36.97 2.01
1905 6079 0.673985 TTGTCTCACTGGACACCTCG 59.326 55.000 0.00 0.00 44.55 4.63
1913 6087 0.602905 CTGGACACCTCGGGTCAAAC 60.603 60.000 0.00 0.00 37.00 2.93
1934 6108 7.279758 TCAAACAAAAATGATGTTTTGGTCTCC 59.720 33.333 13.29 0.00 45.43 3.71
2861 7084 2.644299 TGTCAAATGGGTCTCTGGATGT 59.356 45.455 0.00 0.00 0.00 3.06
3357 7617 6.231211 TGGTGACTTCAATTTAGAAGAGGTC 58.769 40.000 11.40 5.55 46.18 3.85
3754 8034 9.020731 GTTTTATCCCTTAAATCCTTGAGTTGA 57.979 33.333 0.00 0.00 30.03 3.18
3761 8041 8.150296 CCCTTAAATCCTTGAGTTGAAAATGTT 58.850 33.333 0.00 0.00 0.00 2.71
3786 8066 9.855021 TTGATGTATATATGAATGTCACTACCG 57.145 33.333 0.00 0.00 0.00 4.02
3791 8071 2.357327 TGAATGTCACTACCGGTTCG 57.643 50.000 15.04 7.30 0.00 3.95
3813 8093 7.258022 TCGTCATCAATAATGGTGTTTATGG 57.742 36.000 0.00 0.00 38.85 2.74
3817 8097 9.651913 GTCATCAATAATGGTGTTTATGGTTTT 57.348 29.630 0.00 0.00 38.85 2.43
3861 8141 1.478510 TCTCGGAGTTTGAGAGGATGC 59.521 52.381 4.69 0.00 37.55 3.91
3864 8144 1.741732 CGGAGTTTGAGAGGATGCCTG 60.742 57.143 0.00 0.00 31.76 4.85
3942 8222 4.141528 ACTGGAGGATCAAGATGATTGACC 60.142 45.833 0.00 0.00 38.98 4.02
3955 8235 0.909623 ATTGACCACGGGGAGTAAGG 59.090 55.000 12.96 0.00 38.05 2.69
3958 8238 0.248565 GACCACGGGGAGTAAGGAAC 59.751 60.000 12.96 0.00 38.05 3.62
3997 8277 2.063156 TTTGCACTTTAGGCATTGCG 57.937 45.000 1.91 0.00 41.58 4.85
4010 8290 8.453238 TTTAGGCATTGCGGATAAATAAGTTA 57.547 30.769 1.91 0.00 0.00 2.24
4071 8351 6.485984 CAGATATGAAGGTCAAGGGATCAAAG 59.514 42.308 0.00 0.00 0.00 2.77
4080 8360 6.434340 AGGTCAAGGGATCAAAGAAAATACAC 59.566 38.462 0.00 0.00 0.00 2.90
4086 8366 5.863935 GGGATCAAAGAAAATACACAAGTGC 59.136 40.000 0.00 0.00 0.00 4.40
4125 8405 0.390866 AACTGAGGCATGCAGAGACG 60.391 55.000 21.36 4.76 36.86 4.18
4179 8463 0.105453 ACTGTGAGAGAGGTGTGGGT 60.105 55.000 0.00 0.00 0.00 4.51
4180 8464 0.319728 CTGTGAGAGAGGTGTGGGTG 59.680 60.000 0.00 0.00 0.00 4.61
4199 8483 0.468400 GCCACCAGGGTTTACCAACA 60.468 55.000 0.69 0.00 43.89 3.33
4242 8526 2.373169 TCCTTGAGCCTCTCACACAAAT 59.627 45.455 0.00 0.00 40.46 2.32
4243 8527 3.582647 TCCTTGAGCCTCTCACACAAATA 59.417 43.478 0.00 0.00 40.46 1.40
4256 8540 5.559770 TCACACAAATAAGGAGCTCAATCA 58.440 37.500 17.19 0.00 0.00 2.57
4337 8621 2.759535 GCTTCCGGACCTTAGTAGACTT 59.240 50.000 1.83 0.00 0.00 3.01
4344 8628 3.442977 GGACCTTAGTAGACTTCGAAGCA 59.557 47.826 24.86 7.82 0.00 3.91
4376 8660 8.403606 ACGGATGTTACTTATTCTTAAGTTCG 57.596 34.615 1.63 0.00 44.48 3.95
4422 8706 3.290776 GCAAGGGTATGTAGCGAGG 57.709 57.895 0.00 0.00 0.00 4.63
4454 8738 5.226803 TCCCTCAATTGAGAATATCCCTCA 58.773 41.667 32.49 4.25 44.74 3.86
4528 8812 4.091509 AGCGCTACACTCAATTAAGAAACG 59.908 41.667 8.99 0.00 0.00 3.60
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 6.212187 TCTTGGTGAATGATTCTCTCTCTCAA 59.788 38.462 6.73 2.16 0.00 3.02
71 72 3.807622 TGACTCACTGGTTTTCGTTCATC 59.192 43.478 0.00 0.00 0.00 2.92
72 73 3.560068 GTGACTCACTGGTTTTCGTTCAT 59.440 43.478 1.58 0.00 0.00 2.57
225 227 9.182214 TGACTAGTGACTTCCTTACGTATTATT 57.818 33.333 0.00 0.00 0.00 1.40
317 319 9.906660 TTGATTTGTTTACAGTAGCCTAATTTG 57.093 29.630 0.00 0.00 0.00 2.32
390 400 3.564027 GTACAGCGACGGCATGGC 61.564 66.667 9.69 9.69 43.41 4.40
391 401 2.125713 TGTACAGCGACGGCATGG 60.126 61.111 0.00 0.00 43.41 3.66
404 417 8.126074 TGTGTTAATTTTGTGAGACATGTGTAC 58.874 33.333 1.15 0.00 0.00 2.90
682 1110 6.020678 GTGCAGGTCATAAACAAATATTTCGC 60.021 38.462 0.00 0.00 0.00 4.70
933 1363 3.057736 GGATCGATGGATGAATGCTTTGG 60.058 47.826 0.54 0.00 31.51 3.28
1084 1526 1.082104 CGAAAGTTTGACCTGCCGC 60.082 57.895 0.00 0.00 0.00 6.53
1641 5803 0.911769 TGTATGAGCCAAGACCAGGG 59.088 55.000 0.00 0.00 0.00 4.45
1905 6079 6.094742 ACCAAAACATCATTTTTGTTTGACCC 59.905 34.615 2.86 0.00 44.32 4.46
1913 6087 5.178067 GCTGGAGACCAAAACATCATTTTTG 59.822 40.000 2.04 2.04 43.34 2.44
2530 6744 3.365565 CCGTATAAAGGCAAACCACACAC 60.366 47.826 0.00 0.00 39.06 3.82
2531 6745 2.814919 CCGTATAAAGGCAAACCACACA 59.185 45.455 0.00 0.00 39.06 3.72
2559 6779 3.264450 CCATAATCCCTCCACCACTATCC 59.736 52.174 0.00 0.00 0.00 2.59
2861 7084 5.124457 GCATTGCTCTTCTTAAACAGATGGA 59.876 40.000 0.16 0.00 0.00 3.41
3357 7617 1.851658 CAACCTTGCAAACCCTTTCG 58.148 50.000 0.00 0.00 0.00 3.46
3761 8041 8.466798 CCGGTAGTGACATTCATATATACATCA 58.533 37.037 0.00 0.00 0.00 3.07
3774 8054 1.614903 TGACGAACCGGTAGTGACATT 59.385 47.619 18.76 0.00 0.00 2.71
3785 8065 3.621268 ACACCATTATTGATGACGAACCG 59.379 43.478 0.00 0.00 38.03 4.44
3786 8066 5.560966 AACACCATTATTGATGACGAACC 57.439 39.130 0.00 0.00 38.03 3.62
3791 8071 9.651913 AAAACCATAAACACCATTATTGATGAC 57.348 29.630 0.00 0.00 38.03 3.06
3817 8097 6.015918 AGACAATCAATTACCCACCATCAAA 58.984 36.000 0.00 0.00 0.00 2.69
3827 8107 5.012328 ACTCCGAGAGACAATCAATTACC 57.988 43.478 1.33 0.00 33.32 2.85
3861 8141 1.000938 GCTCAAAAGCTCAACACCAGG 60.001 52.381 0.00 0.00 45.55 4.45
3923 8203 3.806521 CGTGGTCAATCATCTTGATCCTC 59.193 47.826 0.00 0.00 35.76 3.71
3942 8222 0.974383 ACAGTTCCTTACTCCCCGTG 59.026 55.000 0.00 0.00 33.85 4.94
3958 8238 8.968242 GTGCAAAAGGAAGAAGTAAATTTACAG 58.032 33.333 26.06 6.05 36.12 2.74
4010 8290 3.451902 CCCACCATAGTTGCATTTTGGAT 59.548 43.478 12.88 0.00 0.00 3.41
4014 8294 4.411927 TGTACCCACCATAGTTGCATTTT 58.588 39.130 0.00 0.00 0.00 1.82
4015 8295 4.040936 TGTACCCACCATAGTTGCATTT 57.959 40.909 0.00 0.00 0.00 2.32
4017 8297 3.352648 GTTGTACCCACCATAGTTGCAT 58.647 45.455 0.00 0.00 0.00 3.96
4071 8351 4.944048 AGGTTTGGCACTTGTGTATTTTC 58.056 39.130 2.61 0.00 0.00 2.29
4179 8463 0.468400 GTTGGTAAACCCTGGTGGCA 60.468 55.000 0.00 0.00 37.83 4.92
4180 8464 0.468400 TGTTGGTAAACCCTGGTGGC 60.468 55.000 0.00 0.00 37.83 5.01
4199 8483 1.807814 AGAAGGTGAGTCTTGGTGGT 58.192 50.000 0.00 0.00 0.00 4.16
4242 8526 5.952347 TCTGAACTAGTGATTGAGCTCCTTA 59.048 40.000 12.15 0.00 0.00 2.69
4243 8527 4.774726 TCTGAACTAGTGATTGAGCTCCTT 59.225 41.667 12.15 0.00 0.00 3.36
4296 8580 0.392193 CACCTCTGGGTCATCTGCAC 60.392 60.000 0.00 0.00 45.41 4.57
4299 8583 1.222936 GCCACCTCTGGGTCATCTG 59.777 63.158 0.00 0.00 45.41 2.90
4337 8621 4.316205 ACATCCGTAACATATGCTTCGA 57.684 40.909 1.58 0.00 0.00 3.71
4376 8660 1.135112 GGGCCAACATGATTTCCGTTC 60.135 52.381 4.39 0.00 0.00 3.95
4403 8687 0.597637 CCTCGCTACATACCCTTGCG 60.598 60.000 0.00 0.00 46.71 4.85


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

AutoCloner maintained by Alex Coulton.