Multiple sequence alignment - TraesCS4B01G266800

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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 TraesCS4B01G266800 chr4B 100.000 2249 0 0 1 2249 539044541 539046789 0.000000e+00 4154.0
1 TraesCS4B01G266800 chr4B 95.572 1671 50 7 569 2216 539064123 539065792 0.000000e+00 2654.0
2 TraesCS4B01G266800 chr4B 96.764 618 18 2 1 617 539063515 539064131 0.000000e+00 1029.0
3 TraesCS4B01G266800 chr4B 94.969 159 8 0 1179 1337 430673627 430673785 1.330000e-62 250.0
4 TraesCS4B01G266800 chr4B 81.385 231 27 10 1911 2128 191008574 191008347 8.260000e-40 174.0
5 TraesCS4B01G266800 chr4B 100.000 44 0 0 2206 2249 539066051 539066094 5.150000e-12 82.4
6 TraesCS4B01G266800 chr4B 80.180 111 18 4 509 619 252552210 252552316 1.850000e-11 80.5
7 TraesCS4B01G266800 chr3D 94.912 511 26 0 1 511 588741918 588741408 0.000000e+00 800.0
8 TraesCS4B01G266800 chr3D 94.318 88 4 1 2116 2203 170325213 170325127 1.400000e-27 134.0
9 TraesCS4B01G266800 chr2D 94.912 511 26 0 1 511 615899588 615900098 0.000000e+00 800.0
10 TraesCS4B01G266800 chr2D 94.716 511 27 0 1 511 166834347 166834857 0.000000e+00 795.0
11 TraesCS4B01G266800 chr2D 91.816 501 18 2 1725 2203 646456795 646456296 0.000000e+00 676.0
12 TraesCS4B01G266800 chr2D 93.333 45 3 0 772 816 635128996 635129040 1.440000e-07 67.6
13 TraesCS4B01G266800 chr7D 94.912 511 25 1 1 511 593329086 593329595 0.000000e+00 798.0
14 TraesCS4B01G266800 chr7D 94.716 511 27 0 1 511 167308746 167309256 0.000000e+00 795.0
15 TraesCS4B01G266800 chr7D 90.909 528 24 3 1685 2188 188030085 188030612 0.000000e+00 688.0
16 TraesCS4B01G266800 chr7D 85.876 531 41 16 583 1093 188029304 188029820 3.290000e-148 534.0
17 TraesCS4B01G266800 chr7D 92.035 226 18 0 1085 1310 188029861 188030086 3.600000e-83 318.0
18 TraesCS4B01G266800 chr7D 86.975 238 22 4 583 819 477159966 477160195 2.220000e-65 259.0
19 TraesCS4B01G266800 chr7D 97.436 39 1 0 1397 1435 633595020 633594982 1.440000e-07 67.6
20 TraesCS4B01G266800 chr5B 94.727 512 26 1 1 511 63833055 63832544 0.000000e+00 795.0
21 TraesCS4B01G266800 chr5B 82.301 226 24 10 1911 2123 685117711 685117933 4.930000e-42 182.0
22 TraesCS4B01G266800 chr5B 81.818 110 19 1 508 617 702400633 702400741 8.550000e-15 91.6
23 TraesCS4B01G266800 chr5B 100.000 44 0 0 2206 2249 22573922 22573965 5.150000e-12 82.4
24 TraesCS4B01G266800 chr4D 94.716 511 27 0 1 511 8305602 8306112 0.000000e+00 795.0
25 TraesCS4B01G266800 chr1D 94.716 511 27 0 1 511 457569643 457570153 0.000000e+00 795.0
26 TraesCS4B01G266800 chr1D 79.439 107 21 1 511 617 139662725 139662830 8.610000e-10 75.0
27 TraesCS4B01G266800 chr6B 93.714 350 15 4 1334 1681 43083403 43083059 3.310000e-143 518.0
28 TraesCS4B01G266800 chr6B 82.301 226 24 9 1911 2123 704616217 704615995 4.930000e-42 182.0
29 TraesCS4B01G266800 chr6B 80.357 112 20 2 511 621 122762646 122762536 1.430000e-12 84.2
30 TraesCS4B01G266800 chr2A 84.746 295 24 15 1911 2188 12325818 12326108 2.200000e-70 276.0
31 TraesCS4B01G266800 chr2A 82.018 228 25 10 1911 2125 64500950 64501174 1.770000e-41 180.0
32 TraesCS4B01G266800 chrUn 96.226 159 6 0 1179 1337 101499903 101500061 6.160000e-66 261.0
33 TraesCS4B01G266800 chrUn 94.615 130 7 0 1679 1808 101500062 101500191 3.790000e-48 202.0
34 TraesCS4B01G266800 chrUn 94.444 108 6 0 1205 1312 230762021 230762128 1.380000e-37 167.0
35 TraesCS4B01G266800 chrUn 94.444 108 6 0 1205 1312 296769321 296769214 1.380000e-37 167.0
36 TraesCS4B01G266800 chrUn 94.444 108 6 0 1205 1312 341500457 341500564 1.380000e-37 167.0
37 TraesCS4B01G266800 chrUn 95.000 60 3 0 1679 1738 230762147 230762206 6.610000e-16 95.3
38 TraesCS4B01G266800 chrUn 100.000 44 0 0 2206 2249 101501474 101501517 5.150000e-12 82.4
39 TraesCS4B01G266800 chrUn 100.000 44 0 0 2206 2249 230765259 230765302 5.150000e-12 82.4
40 TraesCS4B01G266800 chrUn 100.000 44 0 0 2206 2249 294273614 294273657 5.150000e-12 82.4
41 TraesCS4B01G266800 chrUn 100.000 44 0 0 2206 2249 365316294 365316337 5.150000e-12 82.4
42 TraesCS4B01G266800 chrUn 100.000 44 0 0 2206 2249 365358252 365358295 5.150000e-12 82.4
43 TraesCS4B01G266800 chrUn 97.143 35 1 0 1179 1213 230761065 230761099 2.410000e-05 60.2
44 TraesCS4B01G266800 chrUn 97.143 35 1 0 1179 1213 341499500 341499534 2.410000e-05 60.2
45 TraesCS4B01G266800 chr4A 86.134 238 24 4 583 819 196522082 196521853 4.800000e-62 248.0
46 TraesCS4B01G266800 chr4A 94.444 108 6 0 1205 1312 714669698 714669805 1.380000e-37 167.0
47 TraesCS4B01G266800 chr4A 97.143 35 1 0 1179 1213 714668742 714668776 2.410000e-05 60.2
48 TraesCS4B01G266800 chr2B 84.810 237 21 6 583 819 64822211 64821990 8.080000e-55 224.0
49 TraesCS4B01G266800 chr1B 81.579 228 26 10 1911 2125 34338233 34338457 8.260000e-40 174.0
50 TraesCS4B01G266800 chr1B 89.535 86 9 0 649 734 384238316 384238231 2.360000e-20 110.0
51 TraesCS4B01G266800 chr1B 90.541 74 7 0 879 952 39263026 39263099 5.110000e-17 99.0
52 TraesCS4B01G266800 chr1B 80.583 103 19 1 511 613 18400397 18400498 6.660000e-11 78.7
53 TraesCS4B01G266800 chr7B 79.358 218 21 12 879 1073 685613988 685614204 5.040000e-27 132.0
54 TraesCS4B01G266800 chr7B 100.000 44 0 0 2206 2249 62679135 62679178 5.150000e-12 82.4
55 TraesCS4B01G266800 chr3A 100.000 71 0 0 2116 2186 275851227 275851297 5.040000e-27 132.0
56 TraesCS4B01G266800 chr5A 87.387 111 12 2 512 621 179928772 179928663 2.340000e-25 126.0
57 TraesCS4B01G266800 chr6A 75.954 262 48 10 366 621 478056090 478056342 1.090000e-23 121.0
58 TraesCS4B01G266800 chr6A 81.132 106 19 1 511 616 199834433 199834329 1.430000e-12 84.2
59 TraesCS4B01G266800 chr3B 89.286 84 6 1 885 965 87711530 87711447 3.950000e-18 102.0
60 TraesCS4B01G266800 chr3B 96.078 51 1 1 2200 2249 228267860 228267810 5.150000e-12 82.4


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 TraesCS4B01G266800 chr4B 539044541 539046789 2248 False 4154.000000 4154 100.000000 1 2249 1 chr4B.!!$F3 2248
1 TraesCS4B01G266800 chr4B 539063515 539066094 2579 False 1255.133333 2654 97.445333 1 2249 3 chr4B.!!$F4 2248
2 TraesCS4B01G266800 chr3D 588741408 588741918 510 True 800.000000 800 94.912000 1 511 1 chr3D.!!$R2 510
3 TraesCS4B01G266800 chr2D 615899588 615900098 510 False 800.000000 800 94.912000 1 511 1 chr2D.!!$F2 510
4 TraesCS4B01G266800 chr2D 166834347 166834857 510 False 795.000000 795 94.716000 1 511 1 chr2D.!!$F1 510
5 TraesCS4B01G266800 chr7D 593329086 593329595 509 False 798.000000 798 94.912000 1 511 1 chr7D.!!$F3 510
6 TraesCS4B01G266800 chr7D 167308746 167309256 510 False 795.000000 795 94.716000 1 511 1 chr7D.!!$F1 510
7 TraesCS4B01G266800 chr7D 188029304 188030612 1308 False 513.333333 688 89.606667 583 2188 3 chr7D.!!$F4 1605
8 TraesCS4B01G266800 chr5B 63832544 63833055 511 True 795.000000 795 94.727000 1 511 1 chr5B.!!$R1 510
9 TraesCS4B01G266800 chr4D 8305602 8306112 510 False 795.000000 795 94.716000 1 511 1 chr4D.!!$F1 510
10 TraesCS4B01G266800 chr1D 457569643 457570153 510 False 795.000000 795 94.716000 1 511 1 chr1D.!!$F2 510

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
646 691 0.472543 TCCATCATGCCTCCTCGGAT 60.473 55.0 0.0 0.0 33.16 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 2102 0.383231 AAGCTAGAATGCGGCATTGC 59.617 50.0 31.03 25.86 33.9 3.56 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
29 31 7.519809 GCATACAATAAAGCGACAACCATATGA 60.520 37.037 3.65 0.00 0.00 2.15
321 324 2.919228 GTTGGAGAAACTGACACCTGT 58.081 47.619 0.00 0.00 35.75 4.00
391 394 2.491152 GCGTAATGTCGGTCCGGA 59.509 61.111 12.29 0.00 0.00 5.14
500 503 7.739498 TCTACTCGTGCATATAACATCTACA 57.261 36.000 0.00 0.00 0.00 2.74
525 528 4.717279 AAACCTGCACTACTAGGGAAAA 57.283 40.909 0.00 0.00 38.42 2.29
576 579 2.608090 GGGTTAGTTTCATGCGCTACTC 59.392 50.000 9.73 0.00 0.00 2.59
646 691 0.472543 TCCATCATGCCTCCTCGGAT 60.473 55.000 0.00 0.00 33.16 4.18
664 709 3.731264 CGGATAGGCAGTAATAGTAGCGC 60.731 52.174 0.00 0.00 0.00 5.92
672 717 2.114825 GTAATAGTAGCGCGTGGTGTC 58.885 52.381 11.60 4.06 0.00 3.67
681 726 2.612567 GCGTGGTGTCAAATCCGCA 61.613 57.895 0.00 0.00 40.72 5.69
687 732 1.463444 GGTGTCAAATCCGCACTACAC 59.537 52.381 0.00 0.00 37.17 2.90
868 913 7.875971 ACAAAACAAAACAAAAACCAGCAATA 58.124 26.923 0.00 0.00 0.00 1.90
869 914 8.518702 ACAAAACAAAACAAAAACCAGCAATAT 58.481 25.926 0.00 0.00 0.00 1.28
999 1084 2.598394 GGAAAGCAGTGGCCAGCA 60.598 61.111 18.35 0.00 42.56 4.41
1003 1088 1.117142 AAAGCAGTGGCCAGCAATGT 61.117 50.000 18.35 0.00 42.56 2.71
1281 1412 2.538449 CCGTGGCAATTCGTAGATGTAC 59.462 50.000 0.00 0.00 35.04 2.90
1285 1416 5.050490 GTGGCAATTCGTAGATGTACAGAT 58.950 41.667 0.33 0.00 35.04 2.90
1337 1468 2.584391 GGCTCCTGTGACGAACCCT 61.584 63.158 0.00 0.00 0.00 4.34
1379 1510 1.448985 GCCTGTTATCACTTTGCCGA 58.551 50.000 0.00 0.00 0.00 5.54
1437 1568 0.962356 GCAATCCCCCACACAGACAG 60.962 60.000 0.00 0.00 0.00 3.51
1721 1852 0.248336 CTAGCGTATCGGCGTGAACA 60.248 55.000 6.85 0.00 38.18 3.18
1738 1869 6.764877 GTGAACAACGTCTCTTTCAGAATA 57.235 37.500 0.00 0.00 30.72 1.75
1742 1873 7.441157 TGAACAACGTCTCTTTCAGAATACATT 59.559 33.333 0.00 0.00 30.72 2.71
1829 1960 4.156922 TGGCGTTTTTGGTTCGATATCAAT 59.843 37.500 3.12 0.00 0.00 2.57
1949 2102 1.153745 GAGCTGGCCGTACAGACAG 60.154 63.158 7.65 7.65 40.97 3.51
1955 2108 1.425428 GCCGTACAGACAGCAATGC 59.575 57.895 0.00 0.00 0.00 3.56
2047 2200 5.069251 AGTGGTATATACCTGCAGAACTGTC 59.931 44.000 28.12 0.00 46.58 3.51
2056 2209 3.379240 CTGCAGAACTGTCTCCATATCG 58.621 50.000 8.42 0.00 28.78 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
321 324 1.153066 TTCGCACAAAGGTGGCTGA 60.153 52.632 0.00 0.00 45.38 4.26
391 394 2.290641 TGGTATTGTTGGATGAAGCGGT 60.291 45.455 0.00 0.00 0.00 5.68
500 503 4.359105 TCCCTAGTAGTGCAGGTTTATGT 58.641 43.478 0.00 0.00 0.00 2.29
525 528 9.962809 CTACTAGTAAGCTCCTATGTATAAGGT 57.037 37.037 3.76 0.00 35.48 3.50
535 538 3.474600 CCACGCTACTAGTAAGCTCCTA 58.525 50.000 16.91 0.00 0.00 2.94
646 691 2.031420 CACGCGCTACTATTACTGCCTA 60.031 50.000 5.73 0.00 0.00 3.93
664 709 1.206578 GTGCGGATTTGACACCACG 59.793 57.895 0.00 0.00 0.00 4.94
672 717 3.370978 CACTTAGGTGTAGTGCGGATTTG 59.629 47.826 0.00 0.00 36.88 2.32
681 726 6.183360 GCTACTGCTATTCACTTAGGTGTAGT 60.183 42.308 4.75 4.55 39.12 2.73
687 732 3.553096 CGGGCTACTGCTATTCACTTAGG 60.553 52.174 0.00 0.00 39.59 2.69
868 913 1.075525 TGGAAGGGGGTCGATCGAT 60.076 57.895 22.50 3.29 0.00 3.59
869 914 2.056223 GTGGAAGGGGGTCGATCGA 61.056 63.158 15.15 15.15 0.00 3.59
966 1011 4.051167 CCCTCCACATGCAGGCCA 62.051 66.667 5.01 0.00 0.00 5.36
999 1084 3.208747 ACAAAGGAGACGAACCACATT 57.791 42.857 0.00 0.00 0.00 2.71
1003 1088 1.476110 CCCAACAAAGGAGACGAACCA 60.476 52.381 0.00 0.00 0.00 3.67
1281 1412 2.821366 GTGCTCCCCGTGCATCTG 60.821 66.667 0.00 0.00 42.69 2.90
1285 1416 3.610619 CTCATGTGCTCCCCGTGCA 62.611 63.158 0.00 0.00 38.19 4.57
1337 1468 5.637810 GCGGATACTACAAAATGCATAGCTA 59.362 40.000 0.00 0.00 0.00 3.32
1379 1510 2.239681 ATCGTCTGGGAGAGTTTCCT 57.760 50.000 0.00 0.00 45.98 3.36
1437 1568 1.198637 GCACTCCTGATGTGAAGTTGC 59.801 52.381 0.00 0.00 37.60 4.17
1671 1802 2.477104 TCTGGACTGGATGCCTATCA 57.523 50.000 0.00 0.00 34.90 2.15
1829 1960 4.069304 AGCATTCAAACGTAACTTAGCCA 58.931 39.130 0.00 0.00 0.00 4.75
1949 2102 0.383231 AAGCTAGAATGCGGCATTGC 59.617 50.000 31.03 25.86 33.90 3.56
1955 2108 1.959042 ATGGTGAAGCTAGAATGCGG 58.041 50.000 0.00 0.00 38.13 5.69
2047 2200 0.979665 ACATGGCCCTCGATATGGAG 59.020 55.000 7.72 7.72 0.00 3.86
2056 2209 4.799564 TTCAAACAATAACATGGCCCTC 57.200 40.909 0.00 0.00 0.00 4.30
2105 2259 5.810074 GCATAAGAACCAACACAACACTTTT 59.190 36.000 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.