Multiple sequence alignment - TraesCS1B01G071300

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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 TraesCS1B01G071300 chr1B 100.000 1934 0 0 860 2793 56140945 56139012 0.000000e+00 3572
1 TraesCS1B01G071300 chr1B 91.929 1685 127 7 860 2540 55998316 55999995 0.000000e+00 2350
2 TraesCS1B01G071300 chr1B 91.731 1693 123 8 860 2540 55977049 55978736 0.000000e+00 2335
3 TraesCS1B01G071300 chr1B 92.180 1202 93 1 860 2060 56016968 56018169 0.000000e+00 1698
4 TraesCS1B01G071300 chr1B 100.000 545 0 0 1 545 56141804 56141260 0.000000e+00 1007
5 TraesCS1B01G071300 chr1B 76.655 1178 228 38 867 2022 39672090 39673242 2.380000e-170 608
6 TraesCS1B01G071300 chr1B 85.890 489 55 8 59 544 56016177 56016654 2.480000e-140 508
7 TraesCS1B01G071300 chr1B 84.146 492 59 11 59 545 55976421 55976898 2.540000e-125 459
8 TraesCS1B01G071300 chr1B 86.017 236 19 3 1 228 55944609 55944838 1.000000e-59 241
9 TraesCS1B01G071300 chr1B 86.017 236 19 3 1 228 55955862 55956091 1.000000e-59 241
10 TraesCS1B01G071300 chr1B 80.308 325 39 10 2108 2432 56018275 56018574 3.620000e-54 222
11 TraesCS1B01G071300 chr1B 84.343 198 18 8 267 460 55944843 55945031 6.150000e-42 182
12 TraesCS1B01G071300 chr1A 89.607 1578 136 15 995 2546 35525788 35527363 0.000000e+00 1980
13 TraesCS1B01G071300 chr1A 94.236 1197 68 1 867 2062 35536206 35537402 0.000000e+00 1827
14 TraesCS1B01G071300 chr1A 93.688 1204 75 1 860 2062 35578639 35577436 0.000000e+00 1801
15 TraesCS1B01G071300 chr1A 91.286 1205 91 7 860 2062 35486008 35487200 0.000000e+00 1631
16 TraesCS1B01G071300 chr1A 93.605 735 44 2 2059 2792 35577409 35576677 0.000000e+00 1094
17 TraesCS1B01G071300 chr1A 93.431 548 32 3 1 545 35579310 35578764 0.000000e+00 809
18 TraesCS1B01G071300 chr1A 91.598 488 39 2 2059 2546 35487228 35487713 0.000000e+00 673
19 TraesCS1B01G071300 chr1A 85.424 542 58 9 1 529 35514505 35515038 6.800000e-151 544
20 TraesCS1B01G071300 chr1A 86.492 496 48 8 1 484 35535411 35535899 6.850000e-146 527
21 TraesCS1B01G071300 chr1A 84.263 502 47 16 1 483 35484980 35485468 7.050000e-126 460
22 TraesCS1B01G071300 chr1A 77.706 619 77 25 2059 2660 35537430 35538004 3.470000e-84 322
23 TraesCS1B01G071300 chr1D 94.113 1206 66 4 861 2062 36315617 36316821 0.000000e+00 1829
24 TraesCS1B01G071300 chr1D 93.782 788 48 1 860 1646 36363143 36362356 0.000000e+00 1182
25 TraesCS1B01G071300 chr1D 92.867 715 46 3 2059 2770 36361949 36361237 0.000000e+00 1033
26 TraesCS1B01G071300 chr1D 93.033 488 31 3 2059 2546 36316849 36317333 0.000000e+00 710
27 TraesCS1B01G071300 chr1D 90.018 551 41 7 1 545 36363815 36363273 0.000000e+00 701
28 TraesCS1B01G071300 chr1D 88.356 292 27 4 154 441 36314955 36315243 7.410000e-91 344
29 TraesCS1B01G071300 chr5D 92.308 130 8 2 2656 2783 412100093 412100222 1.710000e-42 183
30 TraesCS1B01G071300 chr5D 89.855 138 13 1 2656 2792 53583241 53583104 2.860000e-40 176
31 TraesCS1B01G071300 chr6D 90.299 134 11 2 2659 2791 431160668 431160800 1.030000e-39 174
32 TraesCS1B01G071300 chr4D 89.781 137 12 2 2658 2792 238640022 238640158 1.030000e-39 174
33 TraesCS1B01G071300 chr7A 89.706 136 13 1 2658 2792 691723809 691723674 3.700000e-39 172
34 TraesCS1B01G071300 chr3D 89.706 136 13 1 2658 2792 87925999 87926134 3.700000e-39 172
35 TraesCS1B01G071300 chr3D 88.652 141 14 2 2653 2792 200383812 200383951 1.330000e-38 171


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 TraesCS1B01G071300 chr1B 56139012 56141804 2792 True 2289.500000 3572 100.000000 1 2793 2 chr1B.!!$R1 2792
1 TraesCS1B01G071300 chr1B 55998316 55999995 1679 False 2350.000000 2350 91.929000 860 2540 1 chr1B.!!$F3 1680
2 TraesCS1B01G071300 chr1B 55976421 55978736 2315 False 1397.000000 2335 87.938500 59 2540 2 chr1B.!!$F5 2481
3 TraesCS1B01G071300 chr1B 56016177 56018574 2397 False 809.333333 1698 86.126000 59 2432 3 chr1B.!!$F6 2373
4 TraesCS1B01G071300 chr1B 39672090 39673242 1152 False 608.000000 608 76.655000 867 2022 1 chr1B.!!$F1 1155
5 TraesCS1B01G071300 chr1A 35525788 35527363 1575 False 1980.000000 1980 89.607000 995 2546 1 chr1A.!!$F2 1551
6 TraesCS1B01G071300 chr1A 35576677 35579310 2633 True 1234.666667 1801 93.574667 1 2792 3 chr1A.!!$R1 2791
7 TraesCS1B01G071300 chr1A 35484980 35487713 2733 False 921.333333 1631 89.049000 1 2546 3 chr1A.!!$F3 2545
8 TraesCS1B01G071300 chr1A 35535411 35538004 2593 False 892.000000 1827 86.144667 1 2660 3 chr1A.!!$F4 2659
9 TraesCS1B01G071300 chr1A 35514505 35515038 533 False 544.000000 544 85.424000 1 529 1 chr1A.!!$F1 528
10 TraesCS1B01G071300 chr1D 36361237 36363815 2578 True 972.000000 1182 92.222333 1 2770 3 chr1D.!!$R1 2769
11 TraesCS1B01G071300 chr1D 36314955 36317333 2378 False 961.000000 1829 91.834000 154 2546 3 chr1D.!!$F1 2392

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
148 163 1.152922 TCCAAAAGCCCGAAACGGT 60.153 52.632 9.28 0.0 46.8 4.83 F
1336 1578 0.806868 CGCAGTCGACAAGTACCCTA 59.193 55.000 19.50 0.0 38.1 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1783 2038 1.079503 GTTGACAGGGTCAGCGATTC 58.920 55.0 0.0 0.0 43.69 2.52 R
2331 2660 0.243907 AGTGACGAACTACGCAGCAT 59.756 50.0 0.0 0.0 46.94 3.79 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
145 160 1.289066 GCCTCCAAAAGCCCGAAAC 59.711 57.895 0.00 0.00 0.00 2.78
148 163 1.152922 TCCAAAAGCCCGAAACGGT 60.153 52.632 9.28 0.00 46.80 4.83
178 194 3.575687 CCCTTTTGTTGGAGATGCTCTTT 59.424 43.478 0.00 0.00 0.00 2.52
265 283 5.049680 ACCAAAACATGTCTTACACGTCATC 60.050 40.000 0.00 0.00 0.00 2.92
311 334 8.399425 TGTTGTCGAATGAAGCTTTAAAGTAAA 58.601 29.630 16.38 1.41 0.00 2.01
460 487 5.892348 ACAATGGTCTACAGGGAGAAATTT 58.108 37.500 0.00 0.00 0.00 1.82
461 488 5.711976 ACAATGGTCTACAGGGAGAAATTTG 59.288 40.000 0.00 0.00 0.00 2.32
534 613 7.610580 TCACCATTTCATAAATAAATCCCCC 57.389 36.000 0.00 0.00 0.00 5.40
879 1108 1.832167 GCAAGCAAACCCACCCTCA 60.832 57.895 0.00 0.00 0.00 3.86
888 1117 1.381872 CCCACCCTCATCCTCGTCT 60.382 63.158 0.00 0.00 0.00 4.18
905 1134 4.951254 TCGTCTTATCTCAGATCTCGTCT 58.049 43.478 0.00 0.00 37.80 4.18
907 1136 5.818336 TCGTCTTATCTCAGATCTCGTCTTT 59.182 40.000 0.00 0.00 34.00 2.52
908 1137 6.985059 TCGTCTTATCTCAGATCTCGTCTTTA 59.015 38.462 0.00 0.00 34.00 1.85
909 1138 7.042590 TCGTCTTATCTCAGATCTCGTCTTTAC 60.043 40.741 0.00 0.00 34.00 2.01
910 1139 7.357303 GTCTTATCTCAGATCTCGTCTTTACC 58.643 42.308 0.00 0.00 34.00 2.85
911 1140 7.012515 GTCTTATCTCAGATCTCGTCTTTACCA 59.987 40.741 0.00 0.00 34.00 3.25
912 1141 4.966965 TCTCAGATCTCGTCTTTACCAC 57.033 45.455 0.00 0.00 34.00 4.16
913 1142 4.332828 TCTCAGATCTCGTCTTTACCACA 58.667 43.478 0.00 0.00 34.00 4.17
914 1143 4.950475 TCTCAGATCTCGTCTTTACCACAT 59.050 41.667 0.00 0.00 34.00 3.21
915 1144 5.066634 TCTCAGATCTCGTCTTTACCACATC 59.933 44.000 0.00 0.00 34.00 3.06
916 1145 4.705023 TCAGATCTCGTCTTTACCACATCA 59.295 41.667 0.00 0.00 34.00 3.07
922 1151 3.007506 TCGTCTTTACCACATCACACCAT 59.992 43.478 0.00 0.00 0.00 3.55
1015 1256 2.264480 CCATGGTGAACTCGGCGA 59.736 61.111 10.14 10.14 0.00 5.54
1199 1441 2.589442 GTGCGTTCCCGTCAACCA 60.589 61.111 0.00 0.00 36.15 3.67
1336 1578 0.806868 CGCAGTCGACAAGTACCCTA 59.193 55.000 19.50 0.00 38.10 3.53
1706 1958 4.422057 AGGGACCCGTTTTTAATTCCATT 58.578 39.130 4.40 0.00 0.00 3.16
1817 2072 0.179059 TCAACTCAACAAGCGCCTCA 60.179 50.000 2.29 0.00 0.00 3.86
1866 2121 3.402110 TCGCAGATCACAGTTCACATTT 58.598 40.909 0.00 0.00 0.00 2.32
2095 2382 1.598132 CATTGCTCTTGATGCTCGAGG 59.402 52.381 15.58 0.00 0.00 4.63
2188 2515 3.743521 TCAGTGCATACAGTTTCTTGCT 58.256 40.909 0.00 0.00 36.10 3.91
2189 2516 4.893608 TCAGTGCATACAGTTTCTTGCTA 58.106 39.130 0.00 0.00 36.10 3.49
2255 2584 0.182537 TGCCAGTACTGCTTGGTTGT 59.817 50.000 17.86 0.00 0.00 3.32
2269 2598 3.562343 TGGTTGTGTTGTAGCTGGTTA 57.438 42.857 0.00 0.00 0.00 2.85
2271 2600 3.880490 TGGTTGTGTTGTAGCTGGTTAAG 59.120 43.478 0.00 0.00 0.00 1.85
2278 2607 4.041075 TGTTGTAGCTGGTTAAGATGTGGA 59.959 41.667 0.00 0.00 0.00 4.02
2315 2644 2.597510 GAAAACCCTGGCACCGCT 60.598 61.111 0.00 0.00 0.00 5.52
2375 2704 0.328258 CCTGATTCCTCGTGGGGTTT 59.672 55.000 3.23 0.00 35.33 3.27
2434 2763 6.073447 ACATACATGTATCCAAACCCTTGA 57.927 37.500 15.60 0.00 39.68 3.02
2497 2826 0.802994 CCGCACGGTTCATACGCTTA 60.803 55.000 0.00 0.00 34.00 3.09
2498 2827 0.993532 CGCACGGTTCATACGCTTAA 59.006 50.000 0.00 0.00 34.00 1.85
2614 2943 9.329913 CGCTTATTTGTCAGCATATATTAAACC 57.670 33.333 0.00 0.00 35.60 3.27
2636 2965 5.613329 CCAATTTGGTTCATATCAATGGGG 58.387 41.667 7.31 0.00 31.16 4.96
2670 3002 4.189639 ACTGTGAAATACTCCTTCCGTC 57.810 45.455 0.00 0.00 0.00 4.79
2688 3020 8.989980 CCTTCCGTCCTTAAATATAAGTCATTC 58.010 37.037 0.00 0.00 37.42 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
141 156 1.388837 AAGGGCAACACCACCGTTTC 61.389 55.000 0.00 0.00 42.05 2.78
145 160 1.067250 CAAAAGGGCAACACCACCG 59.933 57.895 0.00 0.00 42.05 4.94
148 163 0.539051 CCAACAAAAGGGCAACACCA 59.461 50.000 0.00 0.00 42.05 4.17
209 225 3.153919 ACGACCTAAAACAATGCATGGT 58.846 40.909 0.00 0.00 0.00 3.55
210 226 3.190327 TGACGACCTAAAACAATGCATGG 59.810 43.478 0.00 0.00 0.00 3.66
448 475 5.994250 TCCATCTCTACAAATTTCTCCCTG 58.006 41.667 0.00 0.00 0.00 4.45
460 487 4.403734 TGTGTGTACACTCCATCTCTACA 58.596 43.478 25.60 15.21 46.55 2.74
484 513 5.622346 TTTCCTGTTTTATGTGGGCTTTT 57.378 34.783 0.00 0.00 0.00 2.27
510 569 7.135522 TGGGGGATTTATTTATGAAATGGTGA 58.864 34.615 0.00 0.00 32.38 4.02
879 1108 4.935205 CGAGATCTGAGATAAGACGAGGAT 59.065 45.833 0.00 0.00 0.00 3.24
888 1117 6.602009 TGTGGTAAAGACGAGATCTGAGATAA 59.398 38.462 0.00 0.00 37.88 1.75
905 1134 3.308545 GGGGTATGGTGTGATGTGGTAAA 60.309 47.826 0.00 0.00 0.00 2.01
907 1136 1.841277 GGGGTATGGTGTGATGTGGTA 59.159 52.381 0.00 0.00 0.00 3.25
908 1137 0.623723 GGGGTATGGTGTGATGTGGT 59.376 55.000 0.00 0.00 0.00 4.16
909 1138 0.918983 AGGGGTATGGTGTGATGTGG 59.081 55.000 0.00 0.00 0.00 4.17
910 1139 1.839994 AGAGGGGTATGGTGTGATGTG 59.160 52.381 0.00 0.00 0.00 3.21
911 1140 2.119495 GAGAGGGGTATGGTGTGATGT 58.881 52.381 0.00 0.00 0.00 3.06
912 1141 2.118679 TGAGAGGGGTATGGTGTGATG 58.881 52.381 0.00 0.00 0.00 3.07
913 1142 2.568546 TGAGAGGGGTATGGTGTGAT 57.431 50.000 0.00 0.00 0.00 3.06
914 1143 2.505407 CAATGAGAGGGGTATGGTGTGA 59.495 50.000 0.00 0.00 0.00 3.58
915 1144 2.923121 CAATGAGAGGGGTATGGTGTG 58.077 52.381 0.00 0.00 0.00 3.82
916 1145 1.212935 GCAATGAGAGGGGTATGGTGT 59.787 52.381 0.00 0.00 0.00 4.16
922 1151 2.742116 GGCGGCAATGAGAGGGGTA 61.742 63.158 3.07 0.00 0.00 3.69
1480 1722 2.472909 GCGGCCTCTTTAGCGCATT 61.473 57.895 11.47 0.00 32.54 3.56
1783 2038 1.079503 GTTGACAGGGTCAGCGATTC 58.920 55.000 0.00 0.00 43.69 2.52
1817 2072 2.065899 TGCTTGCTTACTGTTGGGTT 57.934 45.000 0.00 0.00 0.00 4.11
1866 2121 1.832883 ACAATGGCAGCACCGAATTA 58.167 45.000 0.00 0.00 43.94 1.40
1920 2175 6.493802 GGATCCATACATACCAACTCTGACTA 59.506 42.308 6.95 0.00 0.00 2.59
2095 2382 7.165483 GTGTACTAGCATCAACGAACATACTAC 59.835 40.741 0.00 0.00 0.00 2.73
2255 2584 4.041075 TCCACATCTTAACCAGCTACAACA 59.959 41.667 0.00 0.00 0.00 3.33
2269 2598 2.298661 GGTCCCGGGTCCACATCTT 61.299 63.158 29.47 0.00 0.00 2.40
2271 2600 2.132089 TTTGGTCCCGGGTCCACATC 62.132 60.000 35.49 10.90 33.38 3.06
2331 2660 0.243907 AGTGACGAACTACGCAGCAT 59.756 50.000 0.00 0.00 46.94 3.79
2395 2724 8.985315 ACATGTATGTCATTCAATTACCTCAT 57.015 30.769 0.00 0.00 35.87 2.90
2434 2763 2.251818 CAGGACGATGATAGGGACCAT 58.748 52.381 0.00 0.00 0.00 3.55
2471 2800 3.419759 GAACCGTGCGGCGTCATT 61.420 61.111 9.37 0.00 39.32 2.57
2497 2826 2.162906 AGCCCCACTCACACCCATT 61.163 57.895 0.00 0.00 0.00 3.16
2498 2827 2.532715 AGCCCCACTCACACCCAT 60.533 61.111 0.00 0.00 0.00 4.00
2614 2943 6.482898 TCCCCATTGATATGAACCAAATTG 57.517 37.500 0.00 0.00 33.37 2.32


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

AutoCloner maintained by Alex Coulton.