Multiple sequence alignment - TraesCS3B01G314100

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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 TraesCS3B01G314100 chr3B 100.000 2549 0 0 1 2549 505017690 505015142 0.000000e+00 4708
1 TraesCS3B01G314100 chr3D 94.997 1519 54 8 538 2051 388381600 388380099 0.000000e+00 2364
2 TraesCS3B01G314100 chr3D 96.130 491 18 1 8 497 388382084 388381594 0.000000e+00 800
3 TraesCS3B01G314100 chr3D 90.270 370 20 7 2183 2549 388379881 388379525 1.070000e-128 470
4 TraesCS3B01G314100 chr3D 85.380 171 20 1 228 398 149764619 149764784 3.370000e-39 172
5 TraesCS3B01G314100 chr3D 84.746 177 20 3 224 398 100389546 100389375 1.210000e-38 171
6 TraesCS3B01G314100 chr3D 84.571 175 22 1 224 398 87925992 87926161 4.360000e-38 169
7 TraesCS3B01G314100 chr3D 88.806 134 13 2 2050 2183 388380061 388379930 2.030000e-36 163
8 TraesCS3B01G314100 chr3A 91.364 1158 48 24 926 2051 509444677 509443540 0.000000e+00 1537
9 TraesCS3B01G314100 chr3A 89.858 424 22 9 398 800 509445194 509444771 2.250000e-145 525
10 TraesCS3B01G314100 chr3A 88.983 354 25 7 2183 2531 509443322 509442978 2.340000e-115 425
11 TraesCS3B01G314100 chr3A 82.114 246 21 9 9 232 509445445 509445201 3.350000e-44 189
12 TraesCS3B01G314100 chr3A 90.299 134 11 2 2050 2183 509443502 509443371 9.370000e-40 174
13 TraesCS3B01G314100 chr1B 83.168 202 31 3 992 1192 591359703 591359504 5.600000e-42 182
14 TraesCS3B01G314100 chr2A 86.310 168 18 1 231 398 135473390 135473228 7.250000e-41 178
15 TraesCS3B01G314100 chr7D 85.799 169 18 4 231 398 619121489 619121652 9.370000e-40 174
16 TraesCS3B01G314100 chr6A 85.380 171 20 4 232 401 595172448 595172282 3.370000e-39 172
17 TraesCS3B01G314100 chr4B 85.380 171 19 3 231 400 178081101 178081266 3.370000e-39 172
18 TraesCS3B01G314100 chr4A 85.714 168 19 1 232 399 150653313 150653475 3.370000e-39 172


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 TraesCS3B01G314100 chr3B 505015142 505017690 2548 True 4708.00 4708 100.00000 1 2549 1 chr3B.!!$R1 2548
1 TraesCS3B01G314100 chr3D 388379525 388382084 2559 True 949.25 2364 92.55075 8 2549 4 chr3D.!!$R2 2541
2 TraesCS3B01G314100 chr3A 509442978 509445445 2467 True 570.00 1537 88.52360 9 2531 5 chr3A.!!$R1 2522

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
574 596 0.249398 AGTGGTGGATAACGGAGCAC 59.751 55.0 0.0 0.0 38.18 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1670 1715 0.469917 ATACCACAGGGAATGGCGAG 59.53 55.0 0.0 0.0 41.31 5.03 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
62 63 1.687123 CTGGTAGAACCCATCCCGTAG 59.313 57.143 0.00 0.00 37.50 3.51
240 262 7.554959 TCTTGAGTTGTTTTATACTCCCTCT 57.445 36.000 0.00 0.00 40.00 3.69
243 265 6.464222 TGAGTTGTTTTATACTCCCTCTGTG 58.536 40.000 0.00 0.00 40.00 3.66
256 278 7.056844 ACTCCCTCTGTGTCTAAATATAAGC 57.943 40.000 0.00 0.00 0.00 3.09
258 280 5.307196 TCCCTCTGTGTCTAAATATAAGCCC 59.693 44.000 0.00 0.00 0.00 5.19
470 492 0.654683 GAGCGACATTCAGTCCATGC 59.345 55.000 0.00 0.00 44.66 4.06
536 558 0.529555 CAACCAAACAAGCCCCAACG 60.530 55.000 0.00 0.00 0.00 4.10
567 589 2.304761 TCCCTTGACAGTGGTGGATAAC 59.695 50.000 0.00 0.00 0.00 1.89
574 596 0.249398 AGTGGTGGATAACGGAGCAC 59.751 55.000 0.00 0.00 38.18 4.40
588 610 0.737715 GAGCACGGCGAGAACATTCT 60.738 55.000 16.62 0.00 41.00 2.40
744 787 2.343101 TCTGAATTTTCGGTGGCTACG 58.657 47.619 0.00 0.00 35.11 3.51
800 843 6.437928 TGAATTTGCGCTATCATATGTTTCC 58.562 36.000 9.73 0.00 0.00 3.13
906 949 8.419922 AACCTTGCTTCTAGTTAAGTACTACT 57.580 34.615 0.00 0.00 38.33 2.57
1050 1093 2.286935 AGGGATTTAGAGGAAGGGCA 57.713 50.000 0.00 0.00 0.00 5.36
1340 1383 5.619981 GCCTTGCATTCTGTGGTTTAAGTAG 60.620 44.000 0.00 0.00 0.00 2.57
1434 1477 1.345741 CTGAACAGGAAGGTGCTCTCA 59.654 52.381 0.00 0.00 0.00 3.27
1449 1492 2.001159 CTCTCAGAGCTGTCAATGCAC 58.999 52.381 0.00 0.00 0.00 4.57
1672 1717 6.463995 AGGTGACTCATGTAATCTCTTCTC 57.536 41.667 0.00 0.00 32.90 2.87
1742 1787 0.686224 TTGCTCATTTGGCCCCTTTG 59.314 50.000 0.00 0.00 0.00 2.77
1759 1804 5.186198 CCCTTTGTGTTGGTCTTATAGAGG 58.814 45.833 0.00 0.00 0.00 3.69
1764 1809 5.091552 TGTGTTGGTCTTATAGAGGGAGTT 58.908 41.667 0.00 0.00 0.00 3.01
1785 1857 7.349412 AGTTCTCTCTGTGTTACAAGTTACT 57.651 36.000 0.00 0.00 0.00 2.24
1858 1931 7.376435 TGTGTTGTGTCATCTATAATTGTGG 57.624 36.000 0.00 0.00 0.00 4.17
1863 1936 4.023707 GTGTCATCTATAATTGTGGCCAGC 60.024 45.833 5.11 1.20 0.00 4.85
1871 1944 2.236489 ATTGTGGCCAGCAAATACCT 57.764 45.000 19.94 5.44 0.00 3.08
1874 1947 1.098050 GTGGCCAGCAAATACCTCTG 58.902 55.000 5.11 0.00 0.00 3.35
1926 2001 2.930826 AGAGAGCGAAACAAAGGGAA 57.069 45.000 0.00 0.00 0.00 3.97
1952 2028 4.064388 TGCACGTCTCTTCATTTTCATCA 58.936 39.130 0.00 0.00 0.00 3.07
2044 2120 2.119457 GCCTTGTTTGTTTCAGCTTCG 58.881 47.619 0.00 0.00 0.00 3.79
2090 2205 4.079665 GGGACGTGCTTCAAGAAAATAC 57.920 45.455 7.11 0.00 0.00 1.89
2091 2206 3.500680 GGGACGTGCTTCAAGAAAATACA 59.499 43.478 7.11 0.00 0.00 2.29
2093 2208 4.213482 GGACGTGCTTCAAGAAAATACACT 59.787 41.667 0.00 0.00 0.00 3.55
2094 2209 5.095691 ACGTGCTTCAAGAAAATACACTG 57.904 39.130 0.00 0.00 0.00 3.66
2095 2210 4.814234 ACGTGCTTCAAGAAAATACACTGA 59.186 37.500 0.00 0.00 0.00 3.41
2096 2211 5.295787 ACGTGCTTCAAGAAAATACACTGAA 59.704 36.000 0.00 0.00 0.00 3.02
2150 2265 2.583143 ACAAACAAGGCCTAAGTCCAC 58.417 47.619 5.16 0.00 0.00 4.02
2192 2356 3.704566 CAGTAACAGACCTACCAGCCATA 59.295 47.826 0.00 0.00 0.00 2.74
2217 2381 8.596781 ACATTGGTGTATAGAAGAGAACTAGT 57.403 34.615 0.00 0.00 36.63 2.57
2220 2384 8.749026 TTGGTGTATAGAAGAGAACTAGTAGG 57.251 38.462 0.00 0.00 0.00 3.18
2222 2386 8.212312 TGGTGTATAGAAGAGAACTAGTAGGAG 58.788 40.741 0.00 0.00 0.00 3.69
2223 2387 8.212995 GGTGTATAGAAGAGAACTAGTAGGAGT 58.787 40.741 0.00 0.00 0.00 3.85
2229 2393 8.378115 AGAAGAGAACTAGTAGGAGTAGTACA 57.622 38.462 2.52 0.00 33.44 2.90
2230 2394 8.995577 AGAAGAGAACTAGTAGGAGTAGTACAT 58.004 37.037 2.52 0.00 33.44 2.29
2231 2395 9.617523 GAAGAGAACTAGTAGGAGTAGTACATT 57.382 37.037 2.52 0.00 33.44 2.71
2232 2396 9.978336 AAGAGAACTAGTAGGAGTAGTACATTT 57.022 33.333 2.52 0.00 33.44 2.32
2233 2397 9.978336 AGAGAACTAGTAGGAGTAGTACATTTT 57.022 33.333 2.52 0.00 33.44 1.82
2248 2412 7.437713 AGTACATTTTACTGATCAGATGGGA 57.562 36.000 29.27 11.26 0.00 4.37
2255 2419 2.775960 ACTGATCAGATGGGATGCTCAA 59.224 45.455 29.27 0.00 0.00 3.02
2275 2439 2.110901 AATCTCAGCTCACTTGGCAG 57.889 50.000 0.00 0.00 0.00 4.85
2281 2445 2.435586 CTCACTTGGCAGGGAGCG 60.436 66.667 0.44 0.00 43.88 5.03
2282 2446 3.245668 CTCACTTGGCAGGGAGCGT 62.246 63.158 0.44 0.00 43.88 5.07
2301 2465 3.059597 GCGTCGCATATGCTAAAACAGAT 60.060 43.478 24.56 0.00 39.32 2.90
2314 2478 7.050377 TGCTAAAACAGATATTCTTCTCCTGG 58.950 38.462 0.00 0.00 0.00 4.45
2364 2528 6.192044 TCCTTTGTCCCTTTCTTTACTTTGT 58.808 36.000 0.00 0.00 0.00 2.83
2365 2529 6.320418 TCCTTTGTCCCTTTCTTTACTTTGTC 59.680 38.462 0.00 0.00 0.00 3.18
2379 2543 6.633500 TTACTTTGTCAATGTTCCCAAGAG 57.367 37.500 9.18 0.00 0.00 2.85
2388 2552 1.280133 TGTTCCCAAGAGCCATCTGAG 59.720 52.381 0.00 0.00 35.37 3.35
2393 2557 2.172082 CCCAAGAGCCATCTGAGAATGA 59.828 50.000 0.00 0.00 35.37 2.57
2396 2560 4.202377 CCAAGAGCCATCTGAGAATGATCT 60.202 45.833 0.00 0.00 35.37 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.227263 CCTTGCGACCTACGGGATG 60.227 63.158 0.00 0.00 42.83 3.51
1 2 3.090219 GCCTTGCGACCTACGGGAT 62.090 63.158 0.00 0.00 42.83 3.85
2 3 3.766691 GCCTTGCGACCTACGGGA 61.767 66.667 0.00 0.00 42.83 5.14
3 4 4.832608 GGCCTTGCGACCTACGGG 62.833 72.222 0.00 0.00 42.83 5.28
5 6 3.927163 AACGGCCTTGCGACCTACG 62.927 63.158 0.00 0.00 45.66 3.51
6 7 2.047560 AACGGCCTTGCGACCTAC 60.048 61.111 0.00 0.00 0.00 3.18
62 63 2.510918 GGGGTAGTTTCGCTCGGC 60.511 66.667 0.00 0.00 0.00 5.54
233 255 6.459923 GGCTTATATTTAGACACAGAGGGAG 58.540 44.000 0.00 0.00 0.00 4.30
281 303 2.224305 ACTTTGCTCCGCCCTATATGTC 60.224 50.000 0.00 0.00 0.00 3.06
387 409 6.849697 ACAGGGATTTTCATATACTACCTCCA 59.150 38.462 0.00 0.00 0.00 3.86
470 492 0.255890 ATCCTTCCACACAATCCCCG 59.744 55.000 0.00 0.00 0.00 5.73
567 589 3.989698 ATGTTCTCGCCGTGCTCCG 62.990 63.158 0.00 0.00 0.00 4.63
588 610 0.544357 ATCCCGGTGAGGAGTTGACA 60.544 55.000 0.00 0.00 45.00 3.58
800 843 7.329717 CCTGCACTACACTAAAAACTCTTAGAG 59.670 40.741 7.82 7.82 33.78 2.43
1071 1114 0.391793 CTTTCTCAACCCTCTCCCGC 60.392 60.000 0.00 0.00 0.00 6.13
1340 1383 3.670091 GCAGTCAGATGCAAGAAAAGAGC 60.670 47.826 0.00 0.00 45.77 4.09
1434 1477 1.018226 GCTCGTGCATTGACAGCTCT 61.018 55.000 4.26 0.00 39.41 4.09
1449 1492 1.293924 CCTTGAAGCTGTATGGCTCG 58.706 55.000 0.00 0.00 42.24 5.03
1486 1529 2.361610 CCCCGGAAATGCAGTGCT 60.362 61.111 17.60 0.00 0.00 4.40
1629 1674 3.600388 CTCCCGGATACAAGATATTGGC 58.400 50.000 0.73 0.00 0.00 4.52
1670 1715 0.469917 ATACCACAGGGAATGGCGAG 59.530 55.000 0.00 0.00 41.31 5.03
1672 1717 1.134098 AGAATACCACAGGGAATGGCG 60.134 52.381 0.00 0.00 41.31 5.69
1742 1787 5.422650 AGAACTCCCTCTATAAGACCAACAC 59.577 44.000 0.00 0.00 0.00 3.32
1759 1804 5.203060 ACTTGTAACACAGAGAGAACTCC 57.797 43.478 0.00 0.00 43.53 3.85
1764 1809 8.857098 ACATTAGTAACTTGTAACACAGAGAGA 58.143 33.333 0.00 0.00 0.00 3.10
1863 1936 6.441093 TGCATTTAGAAGCAGAGGTATTTG 57.559 37.500 0.00 0.00 35.51 2.32
1871 1944 8.560355 TTTACAAGTATGCATTTAGAAGCAGA 57.440 30.769 3.54 0.00 44.94 4.26
1874 1947 8.237267 ACACTTTACAAGTATGCATTTAGAAGC 58.763 33.333 3.54 0.00 40.46 3.86
1905 1980 4.345859 TTCCCTTTGTTTCGCTCTCTAA 57.654 40.909 0.00 0.00 0.00 2.10
1926 2001 4.275689 TGAAAATGAAGAGACGTGCAACAT 59.724 37.500 0.00 0.00 35.74 2.71
1952 2028 5.555017 ACATCATGCACTCTTAACTCTTGT 58.445 37.500 0.00 0.00 0.00 3.16
2006 2082 0.815615 GCCTTACTGGGATTGAGCCG 60.816 60.000 0.00 0.00 36.00 5.52
2012 2088 3.165071 CAAACAAGGCCTTACTGGGATT 58.835 45.455 20.00 3.42 36.00 3.01
2044 2120 4.024809 GTGTACTTCAGTGGCAAAGAAGTC 60.025 45.833 28.34 21.70 46.47 3.01
2090 2205 3.529533 CTGAATCTAGGCCACTTCAGTG 58.470 50.000 20.06 0.00 45.23 3.66
2091 2206 2.093235 GCTGAATCTAGGCCACTTCAGT 60.093 50.000 24.90 1.91 44.06 3.41
2093 2208 2.191400 AGCTGAATCTAGGCCACTTCA 58.809 47.619 5.01 7.30 0.00 3.02
2094 2209 2.998316 AGCTGAATCTAGGCCACTTC 57.002 50.000 5.01 2.44 0.00 3.01
2095 2210 3.350833 CAAAGCTGAATCTAGGCCACTT 58.649 45.455 5.01 0.00 0.00 3.16
2096 2211 2.943199 GCAAAGCTGAATCTAGGCCACT 60.943 50.000 5.01 0.00 0.00 4.00
2099 2214 1.028130 GGCAAAGCTGAATCTAGGCC 58.972 55.000 0.00 0.00 0.00 5.19
2100 2215 1.028130 GGGCAAAGCTGAATCTAGGC 58.972 55.000 0.00 0.00 0.00 3.93
2102 2217 3.272574 TCAGGGCAAAGCTGAATCTAG 57.727 47.619 0.00 0.00 0.00 2.43
2103 2218 3.614092 CTTCAGGGCAAAGCTGAATCTA 58.386 45.455 0.00 0.00 36.65 1.98
2150 2265 4.202264 ACTGACCAAGAGTAACAAGGACAG 60.202 45.833 0.00 0.00 44.11 3.51
2192 2356 8.596781 ACTAGTTCTCTTCTATACACCAATGT 57.403 34.615 0.00 0.00 43.30 2.71
2217 2381 9.916360 TCTGATCAGTAAAATGTACTACTCCTA 57.084 33.333 21.92 0.00 0.00 2.94
2220 2384 9.469807 CCATCTGATCAGTAAAATGTACTACTC 57.530 37.037 21.92 0.00 0.00 2.59
2222 2386 8.421784 TCCCATCTGATCAGTAAAATGTACTAC 58.578 37.037 21.92 0.00 0.00 2.73
2223 2387 8.547481 TCCCATCTGATCAGTAAAATGTACTA 57.453 34.615 21.92 0.00 0.00 1.82
2224 2388 7.437713 TCCCATCTGATCAGTAAAATGTACT 57.562 36.000 21.92 0.00 0.00 2.73
2227 2391 5.533903 GCATCCCATCTGATCAGTAAAATGT 59.466 40.000 21.92 1.02 0.00 2.71
2228 2392 5.768662 AGCATCCCATCTGATCAGTAAAATG 59.231 40.000 21.92 16.81 0.00 2.32
2229 2393 5.950023 AGCATCCCATCTGATCAGTAAAAT 58.050 37.500 21.92 5.73 0.00 1.82
2230 2394 5.104402 TGAGCATCCCATCTGATCAGTAAAA 60.104 40.000 21.92 3.34 34.36 1.52
2231 2395 4.409901 TGAGCATCCCATCTGATCAGTAAA 59.590 41.667 21.92 3.73 34.36 2.01
2232 2396 3.969312 TGAGCATCCCATCTGATCAGTAA 59.031 43.478 21.92 4.51 34.36 2.24
2233 2397 3.580039 TGAGCATCCCATCTGATCAGTA 58.420 45.455 21.92 9.67 34.36 2.74
2234 2398 2.405559 TGAGCATCCCATCTGATCAGT 58.594 47.619 21.92 7.26 34.36 3.41
2235 2399 3.487120 TTGAGCATCCCATCTGATCAG 57.513 47.619 17.07 17.07 39.87 2.90
2248 2412 3.952931 AGTGAGCTGAGATTTTGAGCAT 58.047 40.909 0.00 0.00 35.03 3.79
2255 2419 2.434428 CTGCCAAGTGAGCTGAGATTT 58.566 47.619 0.00 0.00 0.00 2.17
2301 2465 6.891306 TCCTTCATTTCCAGGAGAAGAATA 57.109 37.500 15.58 0.00 39.78 1.75
2314 2478 5.461737 TGCACGAAATTTGTTCCTTCATTTC 59.538 36.000 0.00 0.00 0.00 2.17
2364 2528 2.309755 AGATGGCTCTTGGGAACATTGA 59.690 45.455 0.00 0.00 42.32 2.57
2365 2529 2.426024 CAGATGGCTCTTGGGAACATTG 59.574 50.000 0.00 0.00 42.32 2.82
2388 2552 5.015067 CATGTGCATGTACGAGATCATTC 57.985 43.478 9.48 0.00 34.23 2.67
2465 2631 8.531982 TGCGGCTCTATTTCTATATGAGTATTT 58.468 33.333 0.00 0.00 0.00 1.40
2515 2683 7.719193 AGCAATGGTAAGCACATATAACATGTA 59.281 33.333 0.00 0.00 30.12 2.29


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

AutoCloner maintained by Alex Coulton.