Multiple sequence alignment - TraesCS3B01G108800

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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 TraesCS3B01G108800 chr3B 100.000 2946 0 0 1 2946 74816226 74819171 0.000000e+00 5441.0
1 TraesCS3B01G108800 chr3B 82.571 1400 143 54 788 2119 74761910 74763276 0.000000e+00 1140.0
2 TraesCS3B01G108800 chr3B 86.745 762 67 14 1371 2121 74805877 74806615 0.000000e+00 817.0
3 TraesCS3B01G108800 chr3B 78.871 549 67 21 788 1289 74805077 74805623 2.830000e-85 326.0
4 TraesCS3B01G108800 chr3D 92.559 2204 123 25 762 2946 47671277 47669096 0.000000e+00 3123.0
5 TraesCS3B01G108800 chr3D 81.765 1360 149 57 775 2086 47709017 47707709 0.000000e+00 1046.0
6 TraesCS3B01G108800 chr3D 93.531 572 28 4 20 584 47673733 47673164 0.000000e+00 843.0
7 TraesCS3B01G108800 chr3D 90.409 636 51 6 1372 2003 47704151 47703522 0.000000e+00 828.0
8 TraesCS3B01G108800 chr3D 87.883 718 68 16 1372 2086 47741143 47740442 0.000000e+00 826.0
9 TraesCS3B01G108800 chr3D 80.224 536 64 26 791 1291 47704732 47704204 6.000000e-97 364.0
10 TraesCS3B01G108800 chr3D 91.542 201 10 4 580 778 47671492 47671297 1.350000e-68 270.0
11 TraesCS3B01G108800 chr3D 84.112 107 17 0 2181 2287 463716865 463716971 1.440000e-18 104.0
12 TraesCS3B01G108800 chr3A 93.163 1682 72 17 518 2167 59824716 59823046 0.000000e+00 2429.0
13 TraesCS3B01G108800 chr3A 82.194 1404 155 45 775 2121 60006712 60005347 0.000000e+00 1120.0
14 TraesCS3B01G108800 chr3A 91.421 746 41 11 2208 2946 59823046 59822317 0.000000e+00 1002.0
15 TraesCS3B01G108800 chr3A 85.567 970 102 26 997 1958 59955733 59954794 0.000000e+00 981.0
16 TraesCS3B01G108800 chr3A 82.953 1138 133 37 1000 2118 60029763 60028668 0.000000e+00 970.0
17 TraesCS3B01G108800 chr3A 84.683 457 23 16 56 479 59825168 59824726 2.110000e-111 412.0
18 TraesCS3B01G108800 chr3A 90.099 202 9 4 56 248 59827895 59828094 4.870000e-63 252.0
19 TraesCS3B01G108800 chr3A 83.168 101 9 2 152 244 60068106 60068006 5.230000e-13 86.1
20 TraesCS3B01G108800 chr7B 83.333 96 14 2 2178 2272 6756338 6756432 1.450000e-13 87.9
21 TraesCS3B01G108800 chr2D 81.720 93 15 2 2196 2287 423464292 423464383 3.150000e-10 76.8
22 TraesCS3B01G108800 chr5B 90.909 44 4 0 2245 2288 650559876 650559919 3.170000e-05 60.2
23 TraesCS3B01G108800 chr5B 100.000 30 0 0 2855 2884 411623093 411623064 4.100000e-04 56.5
24 TraesCS3B01G108800 chr6D 77.895 95 17 4 2180 2272 57825578 57825670 4.100000e-04 56.5
25 TraesCS3B01G108800 chr6A 90.244 41 4 0 2242 2282 301093020 301093060 1.000000e-03 54.7


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 TraesCS3B01G108800 chr3B 74816226 74819171 2945 False 5441.0 5441 100.000000 1 2946 1 chr3B.!!$F2 2945
1 TraesCS3B01G108800 chr3B 74761910 74763276 1366 False 1140.0 1140 82.571000 788 2119 1 chr3B.!!$F1 1331
2 TraesCS3B01G108800 chr3B 74805077 74806615 1538 False 571.5 817 82.808000 788 2121 2 chr3B.!!$F3 1333
3 TraesCS3B01G108800 chr3D 47669096 47673733 4637 True 1412.0 3123 92.544000 20 2946 3 chr3D.!!$R2 2926
4 TraesCS3B01G108800 chr3D 47740442 47741143 701 True 826.0 826 87.883000 1372 2086 1 chr3D.!!$R1 714
5 TraesCS3B01G108800 chr3D 47703522 47709017 5495 True 746.0 1046 84.132667 775 2086 3 chr3D.!!$R3 1311
6 TraesCS3B01G108800 chr3A 59822317 59825168 2851 True 1281.0 2429 89.755667 56 2946 3 chr3A.!!$R5 2890
7 TraesCS3B01G108800 chr3A 60005347 60006712 1365 True 1120.0 1120 82.194000 775 2121 1 chr3A.!!$R2 1346
8 TraesCS3B01G108800 chr3A 59954794 59955733 939 True 981.0 981 85.567000 997 1958 1 chr3A.!!$R1 961
9 TraesCS3B01G108800 chr3A 60028668 60029763 1095 True 970.0 970 82.953000 1000 2118 1 chr3A.!!$R3 1118

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
432 464 0.107848 AGTATGCTTTCCCGGGTTCG 60.108 55.0 22.86 10.83 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2175 8470 1.632409 TGTGACGGAGGGAGTAGTACT 59.368 52.381 1.37 1.37 0.0 2.73 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
54 55 0.604073 TCATTGCACAAGTGGCATGG 59.396 50.000 2.00 0.00 41.58 3.66
137 139 5.861787 CCGACGAACATGCAACTATATATGA 59.138 40.000 0.00 0.00 0.00 2.15
166 168 1.678101 GGCCAAGATTAGCGAGCAATT 59.322 47.619 0.00 0.00 0.00 2.32
176 178 1.016627 GCGAGCAATTATCAGTGGCA 58.983 50.000 0.00 0.00 0.00 4.92
241 250 6.474140 TGCTTTGCTGATGGATTTAATCAT 57.526 33.333 7.29 0.00 33.69 2.45
278 287 2.017113 GCACCTAATTTCTGGGTCCCG 61.017 57.143 2.65 0.00 0.00 5.14
279 288 1.280998 CACCTAATTTCTGGGTCCCGT 59.719 52.381 2.65 0.00 0.00 5.28
301 310 6.103997 CGTAATAGTCCAAAGTGCTCCTTAA 58.896 40.000 0.00 0.00 31.48 1.85
304 313 7.396540 AATAGTCCAAAGTGCTCCTTAATTG 57.603 36.000 0.00 0.00 31.48 2.32
314 323 6.122964 AGTGCTCCTTAATTGAATTAGGACC 58.877 40.000 8.43 5.59 0.00 4.46
332 341 1.817099 CCCTCATCGAACTGCTGGC 60.817 63.158 0.00 0.00 0.00 4.85
369 401 6.530120 TGTATTGAGTTGAAACCTCTGCTAA 58.470 36.000 0.00 0.00 0.00 3.09
432 464 0.107848 AGTATGCTTTCCCGGGTTCG 60.108 55.000 22.86 10.83 0.00 3.95
511 550 9.974980 CCCTTTACAGCTTTCAAATTAAACTTA 57.025 29.630 0.00 0.00 0.00 2.24
653 2369 2.031157 CGTCCCCAACAAACAGTTCATC 60.031 50.000 0.00 0.00 38.74 2.92
654 2370 2.955660 GTCCCCAACAAACAGTTCATCA 59.044 45.455 0.00 0.00 38.74 3.07
655 2371 3.573967 GTCCCCAACAAACAGTTCATCAT 59.426 43.478 0.00 0.00 38.74 2.45
656 2372 3.573538 TCCCCAACAAACAGTTCATCATG 59.426 43.478 0.00 0.00 38.74 3.07
693 2409 4.153986 CACTTGAGCGACATGATTTTGAC 58.846 43.478 0.00 0.00 0.00 3.18
757 2473 4.580580 GCATATCTTTCCGGTTCCAATCTT 59.419 41.667 0.00 0.00 0.00 2.40
772 2488 2.798283 CAATCTTTGTGCAAACTGCTGG 59.202 45.455 0.00 0.00 45.31 4.85
913 2696 2.292267 CCAGCACCAGCAGTATAAAGG 58.708 52.381 0.00 0.00 45.49 3.11
1100 2906 0.745128 AAGTTCAACACGGACGGCAA 60.745 50.000 0.00 0.00 0.00 4.52
1164 2973 3.753434 AGCCTCGACCAGCACTCG 61.753 66.667 0.71 0.00 0.00 4.18
1230 3042 3.118000 TCAGCATCCAGATGAAGCTCATT 60.118 43.478 11.81 0.00 44.37 2.57
1232 3044 3.118000 AGCATCCAGATGAAGCTCATTCA 60.118 43.478 11.81 0.00 44.37 2.57
1293 3294 9.267096 GTAAGTTCATGAGCTTAATTTTTCGAG 57.733 33.333 27.32 0.00 36.20 4.04
1297 3298 7.672983 TCATGAGCTTAATTTTTCGAGAAGT 57.327 32.000 0.00 0.00 0.00 3.01
1298 3299 7.521529 TCATGAGCTTAATTTTTCGAGAAGTG 58.478 34.615 0.00 0.00 0.00 3.16
1396 3420 0.251916 TTTCTTCCGGTGATGGCGAT 59.748 50.000 0.00 0.00 0.00 4.58
1441 3465 3.650950 ATGGGCAACTCCAGCGGT 61.651 61.111 0.00 0.00 40.56 5.68
1732 7999 0.392863 CCATCGACTGGTCCAATGCA 60.393 55.000 0.00 0.00 40.49 3.96
1774 8041 1.214589 CTACTACGCCAACGCCTGT 59.785 57.895 0.00 0.00 45.53 4.00
1819 8086 1.153369 CAGCGACGGGTGGATGAAT 60.153 57.895 0.00 0.00 38.00 2.57
1831 8098 1.342496 TGGATGAATAGGCAGCTCGAG 59.658 52.381 8.45 8.45 0.00 4.04
2193 8488 6.271857 AGAATATAGTACTACTCCCTCCGTCA 59.728 42.308 4.31 0.00 0.00 4.35
2217 8512 8.447833 TCACATATTAGTTTTCGCTAAAGTTGG 58.552 33.333 0.00 0.00 34.98 3.77
2226 8521 6.956299 TTTCGCTAAAGTTGGTGTATCTAC 57.044 37.500 0.00 0.00 0.00 2.59
2260 8555 6.636705 AGTAGTAAATACATCCGTTTGAGCA 58.363 36.000 0.00 0.00 36.79 4.26
2398 8695 6.279882 TCTTGTGGTTGAATTCATTTTGACC 58.720 36.000 16.24 16.24 0.00 4.02
2431 8728 2.672714 TCGTTTGGTGAGAGATGTTCG 58.327 47.619 0.00 0.00 0.00 3.95
2438 8735 3.830178 TGGTGAGAGATGTTCGAAGGTAA 59.170 43.478 0.00 0.00 0.00 2.85
2458 8755 7.496747 AGGTAAAGTTTGCATGTGTACATTTT 58.503 30.769 0.00 0.00 33.61 1.82
2485 8796 8.293699 AGAAGTGAGTGTATGTGTGTATATGA 57.706 34.615 0.00 0.00 0.00 2.15
2486 8797 8.918116 AGAAGTGAGTGTATGTGTGTATATGAT 58.082 33.333 0.00 0.00 0.00 2.45
2487 8798 9.186323 GAAGTGAGTGTATGTGTGTATATGATC 57.814 37.037 0.00 0.00 0.00 2.92
2488 8799 8.237811 AGTGAGTGTATGTGTGTATATGATCA 57.762 34.615 0.00 0.00 0.00 2.92
2489 8800 8.864087 AGTGAGTGTATGTGTGTATATGATCAT 58.136 33.333 13.81 13.81 0.00 2.45
2490 8801 9.481340 GTGAGTGTATGTGTGTATATGATCATT 57.519 33.333 14.65 4.68 0.00 2.57
2578 8891 3.003897 CCGCACCAAAGTAAGCAGTAAAA 59.996 43.478 0.00 0.00 0.00 1.52
2591 8904 9.163899 AGTAAGCAGTAAAATAGGAAAACTAGC 57.836 33.333 0.00 0.00 34.56 3.42
2642 8955 0.528901 TGATCGCGTGATTTACCCGG 60.529 55.000 13.61 0.00 34.09 5.73
2665 8978 5.299279 GGGTGTCAATCTTTCTGAAGAAACA 59.701 40.000 1.31 0.00 44.61 2.83
2684 8997 1.742831 CAACGTCCATGGTGTTATGGG 59.257 52.381 19.83 8.35 46.16 4.00
2708 9021 6.479660 GGCAGAAAAGACAAAATCAATGTTGA 59.520 34.615 0.00 0.00 42.14 3.18
2851 9164 3.512724 CCCAAGCAGGATTGTGAAATCTT 59.487 43.478 0.00 0.00 41.22 2.40
2856 9169 4.872691 AGCAGGATTGTGAAATCTTAGTCG 59.127 41.667 0.00 0.00 0.00 4.18
2923 9236 7.822334 TCTTACATGAAGATCCGTGTACAAAAT 59.178 33.333 0.00 0.00 39.36 1.82
2924 9237 6.422776 ACATGAAGATCCGTGTACAAAATC 57.577 37.500 0.00 1.16 34.76 2.17
2925 9238 5.354234 ACATGAAGATCCGTGTACAAAATCC 59.646 40.000 0.00 0.00 34.76 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 9.730420 GTGCAATGAATATTAACCTATCGTTTT 57.270 29.630 0.00 0.00 35.79 2.43
18 19 8.898761 TGTGCAATGAATATTAACCTATCGTTT 58.101 29.630 0.00 0.00 35.79 3.60
24 25 7.416213 GCCACTTGTGCAATGAATATTAACCTA 60.416 37.037 0.00 0.00 0.00 3.08
54 55 6.622245 GCGGGTTAGAAATGGAGTAAAGTTTC 60.622 42.308 0.00 0.00 0.00 2.78
137 139 3.067180 CGCTAATCTTGGCCATTGATTGT 59.933 43.478 29.55 16.45 33.24 2.71
278 287 8.398665 CAATTAAGGAGCACTTTGGACTATTAC 58.601 37.037 0.00 0.00 40.64 1.89
279 288 8.325787 TCAATTAAGGAGCACTTTGGACTATTA 58.674 33.333 0.00 0.00 40.64 0.98
301 310 3.973973 TCGATGAGGGGTCCTAATTCAAT 59.026 43.478 0.00 0.00 31.76 2.57
304 313 3.388350 AGTTCGATGAGGGGTCCTAATTC 59.612 47.826 0.00 0.00 31.76 2.17
314 323 1.817099 GCCAGCAGTTCGATGAGGG 60.817 63.158 0.00 0.00 30.38 4.30
332 341 9.619316 TTCAACTCAATACAAAAATTCATACGG 57.381 29.630 0.00 0.00 0.00 4.02
361 393 8.265165 TCTGTATATACGGTGTATTAGCAGAG 57.735 38.462 19.03 2.05 34.25 3.35
414 446 0.108041 TCGAACCCGGGAAAGCATAC 60.108 55.000 32.02 7.64 36.24 2.39
432 464 1.206610 GGGGTTCCTAGGACGAAACTC 59.793 57.143 12.22 6.83 0.00 3.01
511 550 1.280421 CCAGAGGACTAGGCAAAAGCT 59.720 52.381 0.00 0.00 0.00 3.74
516 555 2.042569 TCTGTACCAGAGGACTAGGCAA 59.957 50.000 0.00 0.00 35.39 4.52
653 2369 0.033642 TGTGGTTGGTGCAATGCATG 59.966 50.000 12.38 0.00 41.91 4.06
654 2370 0.033781 GTGTGGTTGGTGCAATGCAT 59.966 50.000 12.38 0.00 41.91 3.96
655 2371 1.042003 AGTGTGGTTGGTGCAATGCA 61.042 50.000 2.72 2.72 35.60 3.96
656 2372 0.104671 AAGTGTGGTTGGTGCAATGC 59.895 50.000 0.00 0.00 0.00 3.56
693 2409 6.791887 ATTGTCGTTAGATGCCAATCATAG 57.208 37.500 0.00 0.00 35.05 2.23
742 2458 1.611491 GCACAAAGATTGGAACCGGAA 59.389 47.619 9.46 0.00 34.12 4.30
743 2459 1.243902 GCACAAAGATTGGAACCGGA 58.756 50.000 9.46 0.00 34.12 5.14
1021 2827 4.498520 CAGGACGACGGCGAGCAT 62.499 66.667 22.49 2.88 41.64 3.79
1230 3042 3.702048 CCGGCGGAGTTTCCCTGA 61.702 66.667 24.41 0.00 31.13 3.86
1293 3294 4.620982 AGCAATGTTAGTTTTGGCACTTC 58.379 39.130 0.00 0.00 0.00 3.01
1297 3298 2.961741 TGGAGCAATGTTAGTTTTGGCA 59.038 40.909 0.00 0.00 0.00 4.92
1298 3299 3.658757 TGGAGCAATGTTAGTTTTGGC 57.341 42.857 0.00 0.00 0.00 4.52
1492 3516 3.496160 GGTTGAACTGGTGCTCCTTCTTA 60.496 47.826 6.34 0.00 34.23 2.10
1732 7999 1.941975 CGGTACAAAACGTTGAAGGGT 59.058 47.619 0.00 0.00 38.20 4.34
1846 8113 3.530910 CTCCGCCCACTTCACGGTT 62.531 63.158 0.00 0.00 46.92 4.44
1968 8246 2.500910 TCAAACAATGGATGAATGCCCC 59.499 45.455 0.00 0.00 0.00 5.80
2167 8462 7.089106 ACGGAGGGAGTAGTACTATATTCTT 57.911 40.000 5.75 0.00 0.00 2.52
2168 8463 6.271857 TGACGGAGGGAGTAGTACTATATTCT 59.728 42.308 5.75 0.00 0.00 2.40
2170 8465 6.183361 TGTGACGGAGGGAGTAGTACTATATT 60.183 42.308 5.75 0.00 0.00 1.28
2174 8469 2.840038 TGTGACGGAGGGAGTAGTACTA 59.160 50.000 1.88 0.00 0.00 1.82
2175 8470 1.632409 TGTGACGGAGGGAGTAGTACT 59.368 52.381 1.37 1.37 0.00 2.73
2176 8471 2.119801 TGTGACGGAGGGAGTAGTAC 57.880 55.000 0.00 0.00 0.00 2.73
2193 8488 8.234546 CACCAACTTTAGCGAAAACTAATATGT 58.765 33.333 0.00 0.00 32.35 2.29
2239 8534 5.703592 TGTTGCTCAAACGGATGTATTTACT 59.296 36.000 0.00 0.00 42.10 2.24
2260 8555 8.075761 ACTTCCTCCGTCTTATATTAGTTGTT 57.924 34.615 0.00 0.00 0.00 2.83
2398 8695 1.665735 CCAAACGAACATTGCCGGAAG 60.666 52.381 5.05 0.00 0.00 3.46
2431 8728 6.067263 TGTACACATGCAAACTTTACCTTC 57.933 37.500 0.00 0.00 0.00 3.46
2438 8735 9.248291 CTTCTAAAAATGTACACATGCAAACTT 57.752 29.630 0.00 0.00 36.56 2.66
2642 8955 6.377327 TGTTTCTTCAGAAAGATTGACACC 57.623 37.500 2.07 0.00 43.82 4.16
2684 8997 7.467557 TCAACATTGATTTTGTCTTTTCTGC 57.532 32.000 0.00 0.00 31.01 4.26
2777 9090 7.199541 TGTGTAAAATTTCATGGCAAAATGG 57.800 32.000 0.00 0.00 0.00 3.16
2869 9182 6.942576 TCATGGATATATCGACTGAGACTTCA 59.057 38.462 6.64 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.