Multiple sequence alignment - TraesCS1D01G032900

Loading Multiple Alignment...

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 TraesCS1D01G032900 chr1D 100.000 1735 0 0 824 2558 13228888 13227154 0.000000e+00 3205
1 TraesCS1D01G032900 chr1D 88.421 950 58 6 893 1805 422066404 422065470 0.000000e+00 1098
2 TraesCS1D01G032900 chr1D 100.000 372 0 0 1 372 13229711 13229340 0.000000e+00 688
3 TraesCS1D01G032900 chr1D 83.333 750 102 19 1815 2554 194912286 194911550 0.000000e+00 671
4 TraesCS1D01G032900 chr1D 87.268 377 44 4 2186 2558 222147194 222147570 6.540000e-116 427
5 TraesCS1D01G032900 chr5B 89.930 1003 61 10 836 1803 639140049 639141046 0.000000e+00 1256
6 TraesCS1D01G032900 chr5B 92.808 292 19 2 10 300 639139236 639139526 3.040000e-114 422
7 TraesCS1D01G032900 chr5B 86.685 368 35 11 8 372 275005961 275006317 1.840000e-106 396
8 TraesCS1D01G032900 chr3B 89.751 1005 52 9 851 1813 503033480 503034475 0.000000e+00 1238
9 TraesCS1D01G032900 chr3B 85.826 1023 68 18 836 1803 107955417 107956417 0.000000e+00 1014
10 TraesCS1D01G032900 chr3B 86.742 528 57 11 1803 2328 650552711 650552195 2.210000e-160 575
11 TraesCS1D01G032900 chr5D 89.126 984 51 16 873 1803 434724330 434725310 0.000000e+00 1173
12 TraesCS1D01G032900 chr5D 86.807 523 54 12 1815 2331 337089176 337088663 1.030000e-158 569
13 TraesCS1D01G032900 chr5D 92.628 312 14 2 10 321 444747592 444747290 8.400000e-120 440
14 TraesCS1D01G032900 chr7B 87.427 1034 68 7 824 1803 518467278 518466253 0.000000e+00 1133
15 TraesCS1D01G032900 chr7B 85.714 931 60 7 932 1808 123403187 123402276 0.000000e+00 915
16 TraesCS1D01G032900 chr7B 90.630 651 47 5 929 1565 713627374 713628024 0.000000e+00 852
17 TraesCS1D01G032900 chr7B 90.000 330 27 6 10 335 518467895 518467568 3.040000e-114 422
18 TraesCS1D01G032900 chr7B 88.301 359 31 8 12 368 42761531 42761182 1.090000e-113 420
19 TraesCS1D01G032900 chr2B 86.940 1026 72 15 825 1805 74213819 74214827 0.000000e+00 1096
20 TraesCS1D01G032900 chr6D 89.402 887 57 6 939 1798 308325140 308324264 0.000000e+00 1083
21 TraesCS1D01G032900 chr6D 88.004 917 58 16 922 1804 42043495 42042597 0.000000e+00 1037
22 TraesCS1D01G032900 chr6D 83.360 625 80 20 1842 2449 107244446 107243829 8.000000e-155 556
23 TraesCS1D01G032900 chr6D 87.027 370 39 9 2186 2548 307085912 307086279 2.370000e-110 409
24 TraesCS1D01G032900 chr6D 86.957 368 41 7 2193 2554 323996020 323995654 8.520000e-110 407
25 TraesCS1D01G032900 chr6D 87.744 359 28 10 14 372 18144372 18144030 3.060000e-109 405
26 TraesCS1D01G032900 chr6B 86.187 1028 74 24 843 1807 114517060 114516038 0.000000e+00 1050
27 TraesCS1D01G032900 chr3D 88.953 869 40 11 987 1803 426936966 426936102 0.000000e+00 1022
28 TraesCS1D01G032900 chr3D 86.114 965 56 25 899 1805 545070921 545069977 0.000000e+00 968
29 TraesCS1D01G032900 chr3D 87.123 365 42 5 2198 2558 489812662 489813025 2.370000e-110 409
30 TraesCS1D01G032900 chr6A 85.812 1022 68 23 847 1805 579130546 579131553 0.000000e+00 1013
31 TraesCS1D01G032900 chr3A 86.688 954 71 8 908 1808 744560836 744559886 0.000000e+00 1007
32 TraesCS1D01G032900 chr5A 86.896 931 70 14 892 1770 131800368 131799438 0.000000e+00 996
33 TraesCS1D01G032900 chr2D 87.598 895 60 18 948 1803 264816778 264817660 0.000000e+00 990
34 TraesCS1D01G032900 chr2D 88.269 520 51 9 1815 2331 155795453 155794941 4.680000e-172 614
35 TraesCS1D01G032900 chr2D 88.235 357 42 0 2198 2554 285736167 285735811 6.540000e-116 427
36 TraesCS1D01G032900 chr4D 88.055 879 48 11 983 1805 92671301 92670424 0.000000e+00 989
37 TraesCS1D01G032900 chr4D 85.388 657 36 15 1207 1807 314522111 314521459 6.010000e-176 627
38 TraesCS1D01G032900 chr4D 87.476 519 49 13 1815 2328 245490427 245490934 3.670000e-163 584
39 TraesCS1D01G032900 chr4D 91.223 319 22 5 3 321 490104292 490103980 1.820000e-116 429
40 TraesCS1D01G032900 chr4D 92.617 298 16 5 8 304 92671988 92671696 8.460000e-115 424
41 TraesCS1D01G032900 chr2A 82.497 977 93 36 871 1787 750151215 750150257 0.000000e+00 785
42 TraesCS1D01G032900 chr7D 87.572 523 46 15 1814 2331 339588522 339588014 2.840000e-164 588
43 TraesCS1D01G032900 chr7D 86.807 523 50 15 1814 2331 339501808 339501300 1.330000e-157 566
44 TraesCS1D01G032900 chr7D 87.395 357 45 0 2198 2554 232641403 232641759 6.590000e-111 411
45 TraesCS1D01G032900 chr4B 87.006 531 58 9 1803 2331 190832585 190833106 2.840000e-164 588
46 TraesCS1D01G032900 chr4B 89.736 341 34 1 2215 2554 190833169 190833509 3.910000e-118 435
47 TraesCS1D01G032900 chr4B 88.949 371 14 3 1458 1805 102470097 102469731 1.410000e-117 433
48 TraesCS1D01G032900 chr1B 93.252 326 16 4 8 333 540346991 540347310 2.300000e-130 475


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 TraesCS1D01G032900 chr1D 13227154 13229711 2557 True 1946.5 3205 100.0000 1 2558 2 chr1D.!!$R3 2557
1 TraesCS1D01G032900 chr1D 422065470 422066404 934 True 1098.0 1098 88.4210 893 1805 1 chr1D.!!$R2 912
2 TraesCS1D01G032900 chr1D 194911550 194912286 736 True 671.0 671 83.3330 1815 2554 1 chr1D.!!$R1 739
3 TraesCS1D01G032900 chr5B 639139236 639141046 1810 False 839.0 1256 91.3690 10 1803 2 chr5B.!!$F2 1793
4 TraesCS1D01G032900 chr3B 503033480 503034475 995 False 1238.0 1238 89.7510 851 1813 1 chr3B.!!$F2 962
5 TraesCS1D01G032900 chr3B 107955417 107956417 1000 False 1014.0 1014 85.8260 836 1803 1 chr3B.!!$F1 967
6 TraesCS1D01G032900 chr3B 650552195 650552711 516 True 575.0 575 86.7420 1803 2328 1 chr3B.!!$R1 525
7 TraesCS1D01G032900 chr5D 434724330 434725310 980 False 1173.0 1173 89.1260 873 1803 1 chr5D.!!$F1 930
8 TraesCS1D01G032900 chr5D 337088663 337089176 513 True 569.0 569 86.8070 1815 2331 1 chr5D.!!$R1 516
9 TraesCS1D01G032900 chr7B 123402276 123403187 911 True 915.0 915 85.7140 932 1808 1 chr7B.!!$R2 876
10 TraesCS1D01G032900 chr7B 713627374 713628024 650 False 852.0 852 90.6300 929 1565 1 chr7B.!!$F1 636
11 TraesCS1D01G032900 chr7B 518466253 518467895 1642 True 777.5 1133 88.7135 10 1803 2 chr7B.!!$R3 1793
12 TraesCS1D01G032900 chr2B 74213819 74214827 1008 False 1096.0 1096 86.9400 825 1805 1 chr2B.!!$F1 980
13 TraesCS1D01G032900 chr6D 308324264 308325140 876 True 1083.0 1083 89.4020 939 1798 1 chr6D.!!$R4 859
14 TraesCS1D01G032900 chr6D 42042597 42043495 898 True 1037.0 1037 88.0040 922 1804 1 chr6D.!!$R2 882
15 TraesCS1D01G032900 chr6D 107243829 107244446 617 True 556.0 556 83.3600 1842 2449 1 chr6D.!!$R3 607
16 TraesCS1D01G032900 chr6B 114516038 114517060 1022 True 1050.0 1050 86.1870 843 1807 1 chr6B.!!$R1 964
17 TraesCS1D01G032900 chr3D 426936102 426936966 864 True 1022.0 1022 88.9530 987 1803 1 chr3D.!!$R1 816
18 TraesCS1D01G032900 chr3D 545069977 545070921 944 True 968.0 968 86.1140 899 1805 1 chr3D.!!$R2 906
19 TraesCS1D01G032900 chr6A 579130546 579131553 1007 False 1013.0 1013 85.8120 847 1805 1 chr6A.!!$F1 958
20 TraesCS1D01G032900 chr3A 744559886 744560836 950 True 1007.0 1007 86.6880 908 1808 1 chr3A.!!$R1 900
21 TraesCS1D01G032900 chr5A 131799438 131800368 930 True 996.0 996 86.8960 892 1770 1 chr5A.!!$R1 878
22 TraesCS1D01G032900 chr2D 264816778 264817660 882 False 990.0 990 87.5980 948 1803 1 chr2D.!!$F1 855
23 TraesCS1D01G032900 chr2D 155794941 155795453 512 True 614.0 614 88.2690 1815 2331 1 chr2D.!!$R1 516
24 TraesCS1D01G032900 chr4D 92670424 92671988 1564 True 706.5 989 90.3360 8 1805 2 chr4D.!!$R3 1797
25 TraesCS1D01G032900 chr4D 314521459 314522111 652 True 627.0 627 85.3880 1207 1807 1 chr4D.!!$R1 600
26 TraesCS1D01G032900 chr4D 245490427 245490934 507 False 584.0 584 87.4760 1815 2328 1 chr4D.!!$F1 513
27 TraesCS1D01G032900 chr2A 750150257 750151215 958 True 785.0 785 82.4970 871 1787 1 chr2A.!!$R1 916
28 TraesCS1D01G032900 chr7D 339588014 339588522 508 True 588.0 588 87.5720 1814 2331 1 chr7D.!!$R2 517
29 TraesCS1D01G032900 chr7D 339501300 339501808 508 True 566.0 566 86.8070 1814 2331 1 chr7D.!!$R1 517
30 TraesCS1D01G032900 chr4B 190832585 190833509 924 False 511.5 588 88.3710 1803 2554 2 chr4B.!!$F1 751

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
77 78 1.574428 CGTCTGAGGCCAAAAACGG 59.426 57.895 5.01 0.0 0.00 4.44 F
1044 1138 1.004918 CAAGTCGGGCTTCTTCGGT 60.005 57.895 0.00 0.0 34.69 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1335 1480 1.102222 GGACGTACTCCGGATGCTCT 61.102 60.0 3.57 0.0 42.24 4.09 R
2357 2840 0.811616 CCCGGCTCAAGAGGAATTCG 60.812 60.0 0.00 0.0 0.00 3.34 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
77 78 1.574428 CGTCTGAGGCCAAAAACGG 59.426 57.895 5.01 0.00 0.00 4.44
174 176 3.727673 CGGTGCAAATTTACATCACGAGG 60.728 47.826 2.67 0.00 0.00 4.63
226 228 2.983592 CGCCCAACCACCACTTCC 60.984 66.667 0.00 0.00 0.00 3.46
311 321 2.592861 GCCGCCCACATCAGATCC 60.593 66.667 0.00 0.00 0.00 3.36
317 327 2.446848 CCACATCAGATCCGGCCCT 61.447 63.158 0.00 0.00 0.00 5.19
353 363 4.099170 GCTGCTGCTTCCACGCTG 62.099 66.667 8.53 0.00 36.03 5.18
1004 1098 2.044352 TCACCGCTCTCCGATGGA 60.044 61.111 0.00 0.00 40.02 3.41
1044 1138 1.004918 CAAGTCGGGCTTCTTCGGT 60.005 57.895 0.00 0.00 34.69 4.69
1265 1362 4.506979 GGCCATCAAGATGAAGGAGATCAT 60.507 45.833 11.48 0.00 37.42 2.45
1268 1365 6.477253 CCATCAAGATGAAGGAGATCATGAT 58.523 40.000 8.25 8.25 37.42 2.45
1277 1422 5.130643 TGAAGGAGATCATGATGAAGAAGCT 59.869 40.000 14.30 1.32 0.00 3.74
1295 1440 1.333619 GCTGTTGGTTGTCGTCAATGT 59.666 47.619 0.00 0.00 35.92 2.71
1373 1518 1.755008 AGGCCGAGCTGGAGTACTC 60.755 63.158 14.87 14.87 42.00 2.59
1374 1519 1.755008 GGCCGAGCTGGAGTACTCT 60.755 63.158 21.88 2.22 42.00 3.24
1414 1589 1.229209 AAGAAGGAGGACGAGGCCA 60.229 57.895 5.01 0.00 0.00 5.36
1517 1730 2.362632 CGACCCGGAGAAGGAGGT 60.363 66.667 0.73 0.00 34.57 3.85
1877 2158 9.914131 GGCCTGATTTCTTTTAACCATATATTC 57.086 33.333 0.00 0.00 0.00 1.75
1970 2257 1.094073 CCGCCAAGCCTCAATCTCAG 61.094 60.000 0.00 0.00 0.00 3.35
1985 2273 1.425066 TCTCAGGTGCTTTTCATGGGT 59.575 47.619 0.00 0.00 0.00 4.51
2169 2463 3.217626 CAGGCAGGATAACCCAGATTTC 58.782 50.000 0.00 0.00 37.41 2.17
2174 2469 2.844348 AGGATAACCCAGATTTCGGTGT 59.156 45.455 0.00 0.00 37.41 4.16
2213 2511 5.422012 ACCAGCCAATCAAAAGGGTAAATAG 59.578 40.000 0.00 0.00 33.59 1.73
2242 2542 3.502123 TTATTGAATAGGAAGCCCCCG 57.498 47.619 0.00 0.00 34.66 5.73
2257 2557 2.550208 GCCCCCGAGTGACCATAATAAG 60.550 54.545 0.00 0.00 0.00 1.73
2357 2840 3.385577 AGAACTCAAACTTGCGAGAGAC 58.614 45.455 8.31 0.00 33.33 3.36
2474 2957 5.385509 TCCTTCTTTTTAAGCCGGAAATG 57.614 39.130 5.05 0.00 0.00 2.32
2481 2964 5.975693 TTTTAAGCCGGAAATGTTCTGAT 57.024 34.783 5.05 0.00 38.34 2.90
2495 2978 7.910441 AATGTTCTGATGGCCTTTAAATTTG 57.090 32.000 3.32 0.00 0.00 2.32
2540 3023 0.253894 ACCGGGTTATTTTCCCTCCG 59.746 55.000 6.32 0.00 42.56 4.63
2548 3031 1.295020 ATTTTCCCTCCGATGACCCA 58.705 50.000 0.00 0.00 0.00 4.51
2554 3037 0.689745 CCTCCGATGACCCAGGGTTA 60.690 60.000 14.23 9.66 35.25 2.85
2555 3038 1.424638 CTCCGATGACCCAGGGTTAT 58.575 55.000 15.99 15.99 35.25 1.89
2556 3039 1.070758 CTCCGATGACCCAGGGTTATG 59.929 57.143 20.79 12.12 35.25 1.90
2557 3040 1.128200 CCGATGACCCAGGGTTATGA 58.872 55.000 20.79 1.84 35.25 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 1.079750 GGACCGTCTGTTGGAGCTC 60.080 63.158 4.71 4.71 0.00 4.09
162 164 2.418609 CCAGATGCACCTCGTGATGTAA 60.419 50.000 0.00 0.00 35.23 2.41
218 220 1.202891 CGGGAAAGGAAAGGAAGTGGT 60.203 52.381 0.00 0.00 0.00 4.16
226 228 3.440415 GCGGGCGGGAAAGGAAAG 61.440 66.667 0.00 0.00 0.00 2.62
301 311 3.112205 GCAGGGCCGGATCTGATGT 62.112 63.158 23.12 0.00 33.11 3.06
337 347 4.099170 GCAGCGTGGAAGCAGCAG 62.099 66.667 0.00 0.00 46.77 4.24
977 1071 3.781770 GAGCGGTGAGAGCGATGGG 62.782 68.421 0.00 0.00 38.05 4.00
1104 1201 2.803817 GGGGTACGTGCCGATCCAT 61.804 63.158 16.91 0.00 0.00 3.41
1244 1341 5.866207 TCATGATCTCCTTCATCTTGATGG 58.134 41.667 10.29 3.64 41.54 3.51
1265 1362 3.554934 ACAACCAACAGCTTCTTCATCA 58.445 40.909 0.00 0.00 0.00 3.07
1268 1365 1.939934 CGACAACCAACAGCTTCTTCA 59.060 47.619 0.00 0.00 0.00 3.02
1277 1422 1.595328 CGACATTGACGACAACCAACA 59.405 47.619 1.63 0.00 38.90 3.33
1332 1477 1.655329 GTACTCCGGATGCTCTCGG 59.345 63.158 3.57 5.97 46.89 4.63
1335 1480 1.102222 GGACGTACTCCGGATGCTCT 61.102 60.000 3.57 0.00 42.24 4.09
1373 1518 3.121030 CCGCCTCACGCTTCCAAG 61.121 66.667 0.00 0.00 41.76 3.61
1374 1519 3.589654 CTCCGCCTCACGCTTCCAA 62.590 63.158 0.00 0.00 41.76 3.53
1414 1589 1.753463 GGATCACCGTCGAGGGACT 60.753 63.158 29.83 13.48 46.96 3.85
1517 1730 2.281484 GGAACTGCGCCCAGAACA 60.281 61.111 4.18 0.00 41.77 3.18
1826 2103 5.828747 TGTAGCCTTGATTATACGACTCAC 58.171 41.667 0.00 0.00 0.00 3.51
1970 2257 1.212751 GCGACCCATGAAAAGCACC 59.787 57.895 0.00 0.00 0.00 5.01
1985 2273 3.998341 GGATTAACTTAGTGGTTGTGCGA 59.002 43.478 0.00 0.00 0.00 5.10
2055 2343 6.544928 AAGACCCTGAACTTGTCAAAATTT 57.455 33.333 0.00 0.00 35.22 1.82
2174 2469 3.264706 TGGCTGGTATGCTAGGTGTAAAA 59.735 43.478 0.00 0.00 0.00 1.52
2184 2480 2.762327 CCTTTTGATTGGCTGGTATGCT 59.238 45.455 0.00 0.00 0.00 3.79
2191 2487 6.681368 GCTCTATTTACCCTTTTGATTGGCTG 60.681 42.308 0.00 0.00 0.00 4.85
2213 2511 7.094592 GGGCTTCCTATTCAATAAACATAGCTC 60.095 40.741 0.00 0.00 0.00 4.09
2230 2530 1.684734 GTCACTCGGGGGCTTCCTA 60.685 63.158 0.00 0.00 35.33 2.94
2242 2542 6.769512 TGGGCTTATCTTATTATGGTCACTC 58.230 40.000 0.00 0.00 0.00 3.51
2357 2840 0.811616 CCCGGCTCAAGAGGAATTCG 60.812 60.000 0.00 0.00 0.00 3.34
2474 2957 5.120674 GTGCAAATTTAAAGGCCATCAGAAC 59.879 40.000 5.01 0.00 0.00 3.01
2481 2964 3.845781 TTGGTGCAAATTTAAAGGCCA 57.154 38.095 5.01 0.00 0.00 5.36
2495 2978 1.508088 GCTACTGCCACATTGGTGC 59.492 57.895 0.00 0.00 43.88 5.01
2516 2999 1.207811 GGGAAAATAACCCGGTCTCGA 59.792 52.381 0.00 0.00 37.85 4.04
2517 3000 1.660167 GGGAAAATAACCCGGTCTCG 58.340 55.000 0.00 0.00 37.85 4.04


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

AutoCloner maintained by Alex Coulton.