Multiple sequence alignment - TraesCS3B01G444400

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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 TraesCS3B01G444400 chr3B 100.000 3134 0 0 1 3134 684514993 684511860 0.000000e+00 5788
1 TraesCS3B01G444400 chr3B 86.288 1568 118 37 1391 2922 684638623 684637117 0.000000e+00 1615
2 TraesCS3B01G444400 chr3B 85.554 1336 127 26 958 2255 685393499 685394806 0.000000e+00 1338
3 TraesCS3B01G444400 chr3B 84.506 981 88 27 2182 3134 685394806 685395750 0.000000e+00 911
4 TraesCS3B01G444400 chr3B 74.586 1208 225 49 989 2134 773747038 773748225 3.680000e-124 455
5 TraesCS3B01G444400 chr3B 73.469 1176 247 46 991 2135 685630646 685631787 1.760000e-102 383
6 TraesCS3B01G444400 chr3B 73.469 1176 247 46 991 2135 685659141 685660282 1.760000e-102 383
7 TraesCS3B01G444400 chr3A 91.820 2225 126 17 960 3134 655570668 655568450 0.000000e+00 3049
8 TraesCS3B01G444400 chr3D 92.299 1688 94 14 1109 2768 520097641 520095962 0.000000e+00 2364
9 TraesCS3B01G444400 chr3D 85.628 1329 132 24 958 2255 520426552 520427852 0.000000e+00 1341
10 TraesCS3B01G444400 chr3D 87.331 963 81 22 1 957 296430136 296431063 0.000000e+00 1064
11 TraesCS3B01G444400 chr3D 87.110 962 84 21 1 956 568577851 568576924 0.000000e+00 1053
12 TraesCS3B01G444400 chr3D 86.993 961 75 17 1 947 511068076 511069000 0.000000e+00 1037
13 TraesCS3B01G444400 chr3D 86.509 971 80 17 1 956 571451591 571450657 0.000000e+00 1020
14 TraesCS3B01G444400 chr3D 85.844 989 86 27 2182 3134 520427924 520428894 0.000000e+00 1002
15 TraesCS3B01G444400 chr3D 76.058 1725 276 86 1038 2672 579582755 579581078 0.000000e+00 771
16 TraesCS3B01G444400 chr3D 74.557 1128 237 37 1022 2135 520595042 520596133 6.170000e-122 448
17 TraesCS3B01G444400 chr3D 87.532 393 26 5 2763 3134 520082573 520082183 1.730000e-117 433
18 TraesCS3B01G444400 chr3D 77.219 755 148 18 1395 2134 58089426 58088681 1.340000e-113 420
19 TraesCS3B01G444400 chr3D 73.854 1178 216 60 991 2116 565641909 565643046 4.900000e-103 385
20 TraesCS3B01G444400 chr3D 81.773 406 66 8 1013 1416 520080501 520080102 1.800000e-87 333
21 TraesCS3B01G444400 chr3D 73.770 793 170 20 1351 2128 568017769 568018538 8.560000e-71 278
22 TraesCS3B01G444400 chr3D 73.494 747 167 21 1396 2128 566743056 566743785 1.440000e-63 254
23 TraesCS3B01G444400 chr3D 74.172 604 125 22 1547 2127 568111385 568111980 4.070000e-54 222
24 TraesCS3B01G444400 chr3D 76.562 320 64 8 1809 2121 569466472 569466157 6.950000e-37 165
25 TraesCS3B01G444400 chr1B 97.934 968 18 2 1 967 622622121 622621155 0.000000e+00 1676
26 TraesCS3B01G444400 chr2B 97.604 960 16 6 1 957 364960441 364961396 0.000000e+00 1639
27 TraesCS3B01G444400 chr7D 95.436 964 40 4 1 961 85599832 85598870 0.000000e+00 1533
28 TraesCS3B01G444400 chr4B 95.142 988 16 4 1 956 95668506 95669493 0.000000e+00 1530
29 TraesCS3B01G444400 chr4B 90.979 388 29 6 574 957 610788405 610788020 4.630000e-143 518
30 TraesCS3B01G444400 chr1A 94.573 866 33 10 94 956 13251695 13250841 0.000000e+00 1327
31 TraesCS3B01G444400 chr1A 94.651 860 29 10 94 950 9308650 9307805 0.000000e+00 1317
32 TraesCS3B01G444400 chr1D 87.111 931 80 21 1 925 321329266 321330162 0.000000e+00 1018
33 TraesCS3B01G444400 chr2A 75.773 776 160 15 1351 2106 45080376 45081143 1.780000e-97 366
34 TraesCS3B01G444400 chrUn 75.418 598 128 13 1544 2127 40962868 40963460 3.980000e-69 272
35 TraesCS3B01G444400 chrUn 75.418 598 128 13 1544 2127 326502005 326502597 3.980000e-69 272
36 TraesCS3B01G444400 chrUn 73.101 803 181 29 1351 2134 340248930 340248144 1.440000e-63 254
37 TraesCS3B01G444400 chr5A 90.361 83 8 0 2509 2591 16491618 16491700 3.300000e-20 110


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 TraesCS3B01G444400 chr3B 684511860 684514993 3133 True 5788.0 5788 100.0000 1 3134 1 chr3B.!!$R1 3133
1 TraesCS3B01G444400 chr3B 684637117 684638623 1506 True 1615.0 1615 86.2880 1391 2922 1 chr3B.!!$R2 1531
2 TraesCS3B01G444400 chr3B 685393499 685395750 2251 False 1124.5 1338 85.0300 958 3134 2 chr3B.!!$F4 2176
3 TraesCS3B01G444400 chr3B 773747038 773748225 1187 False 455.0 455 74.5860 989 2134 1 chr3B.!!$F3 1145
4 TraesCS3B01G444400 chr3B 685630646 685631787 1141 False 383.0 383 73.4690 991 2135 1 chr3B.!!$F1 1144
5 TraesCS3B01G444400 chr3B 685659141 685660282 1141 False 383.0 383 73.4690 991 2135 1 chr3B.!!$F2 1144
6 TraesCS3B01G444400 chr3A 655568450 655570668 2218 True 3049.0 3049 91.8200 960 3134 1 chr3A.!!$R1 2174
7 TraesCS3B01G444400 chr3D 520095962 520097641 1679 True 2364.0 2364 92.2990 1109 2768 1 chr3D.!!$R2 1659
8 TraesCS3B01G444400 chr3D 520426552 520428894 2342 False 1171.5 1341 85.7360 958 3134 2 chr3D.!!$F8 2176
9 TraesCS3B01G444400 chr3D 296430136 296431063 927 False 1064.0 1064 87.3310 1 957 1 chr3D.!!$F1 956
10 TraesCS3B01G444400 chr3D 568576924 568577851 927 True 1053.0 1053 87.1100 1 956 1 chr3D.!!$R3 955
11 TraesCS3B01G444400 chr3D 511068076 511069000 924 False 1037.0 1037 86.9930 1 947 1 chr3D.!!$F2 946
12 TraesCS3B01G444400 chr3D 571450657 571451591 934 True 1020.0 1020 86.5090 1 956 1 chr3D.!!$R5 955
13 TraesCS3B01G444400 chr3D 579581078 579582755 1677 True 771.0 771 76.0580 1038 2672 1 chr3D.!!$R6 1634
14 TraesCS3B01G444400 chr3D 520595042 520596133 1091 False 448.0 448 74.5570 1022 2135 1 chr3D.!!$F3 1113
15 TraesCS3B01G444400 chr3D 58088681 58089426 745 True 420.0 420 77.2190 1395 2134 1 chr3D.!!$R1 739
16 TraesCS3B01G444400 chr3D 565641909 565643046 1137 False 385.0 385 73.8540 991 2116 1 chr3D.!!$F4 1125
17 TraesCS3B01G444400 chr3D 520080102 520082573 2471 True 383.0 433 84.6525 1013 3134 2 chr3D.!!$R7 2121
18 TraesCS3B01G444400 chr3D 568017769 568018538 769 False 278.0 278 73.7700 1351 2128 1 chr3D.!!$F6 777
19 TraesCS3B01G444400 chr3D 566743056 566743785 729 False 254.0 254 73.4940 1396 2128 1 chr3D.!!$F5 732
20 TraesCS3B01G444400 chr3D 568111385 568111980 595 False 222.0 222 74.1720 1547 2127 1 chr3D.!!$F7 580
21 TraesCS3B01G444400 chr1B 622621155 622622121 966 True 1676.0 1676 97.9340 1 967 1 chr1B.!!$R1 966
22 TraesCS3B01G444400 chr2B 364960441 364961396 955 False 1639.0 1639 97.6040 1 957 1 chr2B.!!$F1 956
23 TraesCS3B01G444400 chr7D 85598870 85599832 962 True 1533.0 1533 95.4360 1 961 1 chr7D.!!$R1 960
24 TraesCS3B01G444400 chr4B 95668506 95669493 987 False 1530.0 1530 95.1420 1 956 1 chr4B.!!$F1 955
25 TraesCS3B01G444400 chr1A 13250841 13251695 854 True 1327.0 1327 94.5730 94 956 1 chr1A.!!$R2 862
26 TraesCS3B01G444400 chr1A 9307805 9308650 845 True 1317.0 1317 94.6510 94 950 1 chr1A.!!$R1 856
27 TraesCS3B01G444400 chr1D 321329266 321330162 896 False 1018.0 1018 87.1110 1 925 1 chr1D.!!$F1 924
28 TraesCS3B01G444400 chr2A 45080376 45081143 767 False 366.0 366 75.7730 1351 2106 1 chr2A.!!$F1 755
29 TraesCS3B01G444400 chrUn 40962868 40963460 592 False 272.0 272 75.4180 1544 2127 1 chrUn.!!$F1 583
30 TraesCS3B01G444400 chrUn 326502005 326502597 592 False 272.0 272 75.4180 1544 2127 1 chrUn.!!$F2 583
31 TraesCS3B01G444400 chrUn 340248144 340248930 786 True 254.0 254 73.1010 1351 2134 1 chrUn.!!$R1 783

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
399 408 1.437160 CACTGTGTGTGTTTGGGGC 59.563 57.895 0.0 0.0 41.53 5.80 F
1323 2408 0.675837 CACACGACTCCTCCCGTCTA 60.676 60.000 0.0 0.0 36.83 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1826 3045 0.030908 GACCTCGCCTTCATAGTCCG 59.969 60.0 0.00 0.0 0.00 4.79 R
2939 4381 0.103937 TCAAAAGCTGGCCAAAACGG 59.896 50.0 7.01 0.0 38.11 4.44 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
399 408 1.437160 CACTGTGTGTGTTTGGGGC 59.563 57.895 0.00 0.00 41.53 5.80
570 579 1.691219 GAGTTGATGGCTTGGGGGA 59.309 57.895 0.00 0.00 0.00 4.81
1291 2376 4.100084 CCGACCAGCTCCATGCCA 62.100 66.667 0.00 0.00 44.23 4.92
1299 2384 3.344215 CTCCATGCCATCGCTCGC 61.344 66.667 0.00 0.00 35.36 5.03
1323 2408 0.675837 CACACGACTCCTCCCGTCTA 60.676 60.000 0.00 0.00 36.83 2.59
1707 2902 0.678950 TTGACACCATCGCTGAGTCA 59.321 50.000 9.44 9.44 36.26 3.41
1826 3045 4.718961 AGTGTTGATATCTGGGTTATGCC 58.281 43.478 3.98 0.00 0.00 4.40
2123 3357 3.423123 GGTTATGTTGTGAACTCTTCGCG 60.423 47.826 0.00 0.00 42.95 5.87
2197 3456 1.207791 CCTTGGGTCCACTATGAGCT 58.792 55.000 0.00 0.00 33.34 4.09
2251 3583 5.246981 TGATCAAGAAGTCATGACCCTTT 57.753 39.130 22.21 10.31 0.00 3.11
2252 3584 5.248640 TGATCAAGAAGTCATGACCCTTTC 58.751 41.667 22.21 18.15 0.00 2.62
2253 3585 4.705110 TCAAGAAGTCATGACCCTTTCA 57.295 40.909 22.21 11.25 39.11 2.69
2320 3724 1.002888 CTGGAGTGGCTGTCATGACTT 59.997 52.381 25.55 5.50 0.00 3.01
2400 3804 5.954296 TCCTTTGATTCAGCTCTTCTTTG 57.046 39.130 0.00 0.00 0.00 2.77
2492 3903 4.471904 TTAGCTGACGATGAAATGAGGT 57.528 40.909 0.00 0.00 0.00 3.85
2632 4050 4.142773 CCTTTGCATTGCATCATTTGGAAC 60.143 41.667 12.95 0.00 38.59 3.62
2636 4054 5.353111 TGCATTGCATCATTTGGAACTATG 58.647 37.500 7.38 0.00 38.59 2.23
2688 4106 2.978156 AGGGCTGGAGAAATGAAACA 57.022 45.000 0.00 0.00 0.00 2.83
2844 4266 0.109735 GTGCCGGCTAGTTTCTTTGC 60.110 55.000 29.70 0.00 0.00 3.68
2862 4284 8.571461 TTCTTTGCTGATTATCATCAAGAAGT 57.429 30.769 10.67 0.00 39.04 3.01
2938 4380 7.346751 TGGGCTGATTCTAAAAATTATGGAC 57.653 36.000 0.00 0.00 0.00 4.02
2939 4381 6.323739 TGGGCTGATTCTAAAAATTATGGACC 59.676 38.462 0.00 0.00 0.00 4.46
3001 4444 2.158608 AGTGTCTCACCTTTCCCTTTGG 60.159 50.000 0.00 0.00 34.49 3.28
3003 4446 5.924740 AGTGTCTCACCTTTCCCTTTGGAA 61.925 45.833 0.00 0.00 41.08 3.53
3077 4524 7.016153 TCAACCAGTGGTTTCTTCATACTAT 57.984 36.000 25.30 0.00 44.33 2.12
3115 4562 5.438761 ACACTGGTTTGATGTTTCTAAGC 57.561 39.130 0.00 0.00 36.20 3.09
3117 4564 6.296026 ACACTGGTTTGATGTTTCTAAGCTA 58.704 36.000 0.00 0.00 36.48 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
865 913 5.271598 AGATCATTTGCCCCACTTTTCATA 58.728 37.500 0.00 0.00 0.00 2.15
1016 1064 3.894947 GGAGGAGAGGCGTCGCTC 61.895 72.222 18.11 12.76 38.80 5.03
1291 2376 3.121030 GTGTGCAAGGCGAGCGAT 61.121 61.111 0.00 0.00 33.85 4.58
1299 2384 1.374758 GGAGGAGTCGTGTGCAAGG 60.375 63.158 0.00 0.00 0.00 3.61
1323 2408 1.209019 ACGAGAATGAAGCAGGCATCT 59.791 47.619 0.00 0.00 0.00 2.90
1388 2488 3.149196 GGGTTGCAGATGAAGAACTTGA 58.851 45.455 0.00 0.00 0.00 3.02
1419 2521 2.991540 GGGAGGGGTGCAAACTGC 60.992 66.667 0.00 0.00 45.29 4.40
1821 3037 0.317160 CGCCTTCATAGTCCGGCATA 59.683 55.000 0.00 0.00 42.59 3.14
1826 3045 0.030908 GACCTCGCCTTCATAGTCCG 59.969 60.000 0.00 0.00 0.00 4.79
2011 3245 2.036217 CTCTGCAATGGAAACTGGCAAA 59.964 45.455 0.00 0.00 33.58 3.68
2123 3357 3.761311 ACCGACTCTATCAGACGAAAC 57.239 47.619 0.00 0.00 42.13 2.78
2320 3724 6.052360 TGTAAACTTAGCATCAACACTCACA 58.948 36.000 0.00 0.00 0.00 3.58
2388 3792 5.163874 GCACTGAGTAATCAAAGAAGAGCTG 60.164 44.000 0.00 0.00 0.00 4.24
2456 3867 6.260050 TCGTCAGCTAAAACAGAAAACAGAAT 59.740 34.615 0.00 0.00 0.00 2.40
2632 4050 9.469807 GGAGATACAGTGAAGTGATAAACATAG 57.530 37.037 0.00 0.00 0.00 2.23
2636 4054 6.640518 TGGGAGATACAGTGAAGTGATAAAC 58.359 40.000 0.00 0.00 0.00 2.01
2688 4106 8.814038 AACCTTTCTTCTGCTTATCAATACAT 57.186 30.769 0.00 0.00 0.00 2.29
2844 4266 8.819015 CAGTCAGAACTTCTTGATGATAATCAG 58.181 37.037 0.00 0.00 31.71 2.90
2862 4284 2.143122 GCGACCATGAAACAGTCAGAA 58.857 47.619 0.00 0.00 40.43 3.02
2938 4380 0.879839 CAAAAGCTGGCCAAAACGGG 60.880 55.000 7.01 0.00 34.06 5.28
2939 4381 0.103937 TCAAAAGCTGGCCAAAACGG 59.896 50.000 7.01 0.00 38.11 4.44
3034 4478 7.610865 TGGTTGAACTTCAAGAAACAAGAAAT 58.389 30.769 4.36 0.00 37.00 2.17
3041 4485 4.157840 ACCACTGGTTGAACTTCAAGAAAC 59.842 41.667 4.36 0.00 37.00 2.78
3048 4492 4.398044 TGAAGAAACCACTGGTTGAACTTC 59.602 41.667 27.45 27.45 46.20 3.01
3052 4496 5.690865 AGTATGAAGAAACCACTGGTTGAA 58.309 37.500 14.46 0.00 46.20 2.69
3087 4534 9.952030 TTAGAAACATCAAACCAGTGTATATCA 57.048 29.630 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.