Multiple sequence alignment - TraesCS3D01G093100

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 TraesCS3D01G093100 chr3D 100.000 1558 0 0 962 2519 47094276 47092719 0.000000e+00 2878.0
1 TraesCS3D01G093100 chr3D 100.000 601 0 0 1 601 47095237 47094637 0.000000e+00 1110.0
2 TraesCS3D01G093100 chr3D 95.652 46 2 0 2327 2372 47085828 47085873 9.660000e-10 75.0
3 TraesCS3D01G093100 chr5A 94.592 980 51 2 962 1940 582094957 582093979 0.000000e+00 1515.0
4 TraesCS3D01G093100 chr5A 95.660 576 25 0 1 576 582095606 582095031 0.000000e+00 926.0
5 TraesCS3D01G093100 chr2D 96.954 591 18 0 1350 1940 467996079 467996669 0.000000e+00 992.0
6 TraesCS3D01G093100 chr2D 96.339 601 22 0 1 601 467989986 467990586 0.000000e+00 989.0
7 TraesCS3D01G093100 chr2D 96.961 362 11 0 993 1354 467990833 467991194 2.140000e-170 608.0
8 TraesCS3D01G093100 chr3B 83.187 571 56 24 1977 2519 73604714 73605272 1.050000e-133 486.0
9 TraesCS3D01G093100 chr3A 91.404 349 27 3 1977 2323 58844550 58844203 2.270000e-130 475.0
10 TraesCS3D01G093100 chr3A 86.713 143 11 4 2328 2470 58844163 58844029 4.340000e-33 152.0
11 TraesCS3D01G093100 chr3A 95.745 47 2 0 2326 2372 58834898 58834944 2.690000e-10 76.8
12 TraesCS3D01G093100 chr7A 72.967 984 234 24 975 1940 711304709 711305678 5.230000e-82 315.0


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 TraesCS3D01G093100 chr3D 47092719 47095237 2518 True 1994.0 2878 100.0000 1 2519 2 chr3D.!!$R1 2518
1 TraesCS3D01G093100 chr5A 582093979 582095606 1627 True 1220.5 1515 95.1260 1 1940 2 chr5A.!!$R1 1939
2 TraesCS3D01G093100 chr2D 467996079 467996669 590 False 992.0 992 96.9540 1350 1940 1 chr2D.!!$F1 590
3 TraesCS3D01G093100 chr2D 467989986 467991194 1208 False 798.5 989 96.6500 1 1354 2 chr2D.!!$F2 1353
4 TraesCS3D01G093100 chr3B 73604714 73605272 558 False 486.0 486 83.1870 1977 2519 1 chr3B.!!$F1 542
5 TraesCS3D01G093100 chr3A 58844029 58844550 521 True 313.5 475 89.0585 1977 2470 2 chr3A.!!$R1 493
6 TraesCS3D01G093100 chr7A 711304709 711305678 969 False 315.0 315 72.9670 975 1940 1 chr7A.!!$F1 965

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
544 545 1.079503 ATTTTCTCCGTCAGAAGCGC 58.92 50.0 0.0 0.0 42.37 5.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2489 2534 1.067582 GTCTGGGCGAAGATACGGG 59.932 63.158 0.0 0.0 0.0 5.28 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
98 99 3.265791 CTTCAATCAAGCCTTACTCGCT 58.734 45.455 0.00 0.00 38.53 4.93
121 122 3.553511 CGTCAAGCATGGAGATTACTCAC 59.446 47.826 0.00 0.00 44.22 3.51
122 123 4.507710 GTCAAGCATGGAGATTACTCACA 58.492 43.478 0.00 0.00 44.22 3.58
147 148 2.035193 CCAGACTCACTATGCGCTATGT 59.965 50.000 9.73 0.89 0.00 2.29
344 345 1.498865 CGCCATCGTACAAGCCCATC 61.499 60.000 0.00 0.00 0.00 3.51
347 348 1.406751 CCATCGTACAAGCCCATCACA 60.407 52.381 0.00 0.00 0.00 3.58
544 545 1.079503 ATTTTCTCCGTCAGAAGCGC 58.920 50.000 0.00 0.00 42.37 5.92
560 561 2.202703 GCGTACCGTCTCGCCATT 60.203 61.111 9.06 0.00 45.54 3.16
1210 1211 6.166984 TGTTACTTTTGAATGATTGCCCAA 57.833 33.333 0.00 0.00 0.00 4.12
1299 1300 1.606313 CAAACCGGCTCCCACCATT 60.606 57.895 0.00 0.00 0.00 3.16
1345 1346 1.135632 GCTATATCGACAGCCTCCGAC 60.136 57.143 4.54 0.00 37.64 4.79
1363 1364 2.362120 GCATTGAGCAGCACCCCT 60.362 61.111 0.00 0.00 44.79 4.79
1391 1392 1.134946 CATCACGAAGGGGAAAATGGC 59.865 52.381 0.00 0.00 0.00 4.40
1404 1405 1.497309 AAATGGCGGTCTCCCTGGAA 61.497 55.000 0.00 0.00 0.00 3.53
1517 1518 1.804151 GCTGAACGTTGATGGTGCTTA 59.196 47.619 5.00 0.00 0.00 3.09
1940 1945 2.747467 GCAATCTCTGCCAGCAGGATTA 60.747 50.000 23.77 9.83 46.13 1.75
1941 1946 3.548770 CAATCTCTGCCAGCAGGATTAA 58.451 45.455 23.77 6.84 43.75 1.40
1942 1947 4.142790 CAATCTCTGCCAGCAGGATTAAT 58.857 43.478 23.77 10.02 43.75 1.40
1943 1948 5.311265 CAATCTCTGCCAGCAGGATTAATA 58.689 41.667 23.77 5.71 43.75 0.98
1944 1949 4.342862 TCTCTGCCAGCAGGATTAATAC 57.657 45.455 19.04 0.00 43.75 1.89
1945 1950 3.711190 TCTCTGCCAGCAGGATTAATACA 59.289 43.478 19.04 0.00 43.75 2.29
1946 1951 4.164030 TCTCTGCCAGCAGGATTAATACAA 59.836 41.667 19.04 0.00 43.75 2.41
1947 1952 5.052693 TCTGCCAGCAGGATTAATACAAT 57.947 39.130 19.04 0.00 43.75 2.71
1948 1953 5.065914 TCTGCCAGCAGGATTAATACAATC 58.934 41.667 19.04 0.00 43.75 2.67
1949 1954 4.144297 TGCCAGCAGGATTAATACAATCC 58.856 43.478 0.00 7.77 45.08 3.01
1950 1955 4.144297 GCCAGCAGGATTAATACAATCCA 58.856 43.478 16.26 0.00 46.70 3.41
1951 1956 4.768968 GCCAGCAGGATTAATACAATCCAT 59.231 41.667 16.26 1.88 46.70 3.41
1952 1957 5.945784 GCCAGCAGGATTAATACAATCCATA 59.054 40.000 16.26 0.00 46.70 2.74
1953 1958 6.604795 GCCAGCAGGATTAATACAATCCATAT 59.395 38.462 16.26 1.28 46.70 1.78
1954 1959 7.201767 GCCAGCAGGATTAATACAATCCATATC 60.202 40.741 16.26 4.52 46.70 1.63
1955 1960 7.011763 CCAGCAGGATTAATACAATCCATATCG 59.988 40.741 16.26 3.29 46.70 2.92
1956 1961 7.550551 CAGCAGGATTAATACAATCCATATCGT 59.449 37.037 16.26 0.00 46.70 3.73
1957 1962 8.103305 AGCAGGATTAATACAATCCATATCGTT 58.897 33.333 16.26 0.00 46.70 3.85
1958 1963 8.730680 GCAGGATTAATACAATCCATATCGTTT 58.269 33.333 16.26 0.00 46.70 3.60
1960 1965 9.151471 AGGATTAATACAATCCATATCGTTTCG 57.849 33.333 16.26 0.00 46.70 3.46
1961 1966 7.903431 GGATTAATACAATCCATATCGTTTCGC 59.097 37.037 10.46 0.00 44.33 4.70
1962 1967 7.716768 TTAATACAATCCATATCGTTTCGCA 57.283 32.000 0.00 0.00 0.00 5.10
1963 1968 6.612247 AATACAATCCATATCGTTTCGCAA 57.388 33.333 0.00 0.00 0.00 4.85
1964 1969 4.273005 ACAATCCATATCGTTTCGCAAC 57.727 40.909 0.00 0.00 0.00 4.17
1965 1970 3.687212 ACAATCCATATCGTTTCGCAACA 59.313 39.130 0.00 0.00 32.54 3.33
1966 1971 4.155099 ACAATCCATATCGTTTCGCAACAA 59.845 37.500 0.00 0.00 32.54 2.83
1967 1972 4.955925 ATCCATATCGTTTCGCAACAAA 57.044 36.364 0.00 0.00 32.54 2.83
1968 1973 4.750952 TCCATATCGTTTCGCAACAAAA 57.249 36.364 0.00 0.00 32.54 2.44
1969 1974 5.109662 TCCATATCGTTTCGCAACAAAAA 57.890 34.783 0.00 0.00 32.54 1.94
1993 1999 8.831715 AAAAAGTCAACTTCTGTTCATTTTGT 57.168 26.923 0.00 0.00 34.61 2.83
2052 2058 3.119637 CCGTGTAACCATCCAACCATTTC 60.120 47.826 0.00 0.00 0.00 2.17
2101 2107 1.921982 ATGTGTTTGCACTATGGGCA 58.078 45.000 0.00 0.00 45.44 5.36
2109 2115 1.230635 GCACTATGGGCATGTAGGCG 61.231 60.000 0.00 0.00 45.36 5.52
2203 2209 7.698836 ATTTCTTGGTTTCGATTTGAAGTTG 57.301 32.000 0.00 0.00 37.99 3.16
2207 2213 3.629855 TGGTTTCGATTTGAAGTTGAGCA 59.370 39.130 0.00 0.00 37.99 4.26
2241 2250 5.410746 TCTTGAGATGAGTTCAGCAACATTC 59.589 40.000 0.00 0.00 34.60 2.67
2305 2314 9.693157 GATCTTTGATTTGAAAGTTTGTGTTTG 57.307 29.630 0.00 0.00 34.95 2.93
2308 2317 9.875675 CTTTGATTTGAAAGTTTGTGTTTGAAA 57.124 25.926 0.00 0.00 0.00 2.69
2323 2332 9.959749 TTGTGTTTGAAATTTAGTCCATTCTAC 57.040 29.630 0.00 0.00 0.00 2.59
2324 2333 9.349713 TGTGTTTGAAATTTAGTCCATTCTACT 57.650 29.630 0.00 0.00 0.00 2.57
2333 2377 4.457834 AGTCCATTCTACTCCGTTTCTG 57.542 45.455 0.00 0.00 0.00 3.02
2340 2384 3.340928 TCTACTCCGTTTCTGTCGATGA 58.659 45.455 0.00 0.00 0.00 2.92
2376 2420 3.208884 GACGTCACGTGGCTCTGGT 62.209 63.158 19.37 8.45 41.37 4.00
2395 2440 7.306866 GCTCTGGTCATCGACTTATAAATTCAC 60.307 40.741 0.00 0.00 32.47 3.18
2403 2448 7.655236 TCGACTTATAAATTCACGAAAACCA 57.345 32.000 0.00 0.00 0.00 3.67
2419 2464 7.852945 CACGAAAACCATTTATAATCTCTCTGC 59.147 37.037 0.00 0.00 0.00 4.26
2426 2471 2.540265 ATAATCTCTCTGCTTGGCGG 57.460 50.000 0.00 0.00 36.06 6.13
2427 2472 1.485124 TAATCTCTCTGCTTGGCGGA 58.515 50.000 1.03 1.03 42.08 5.54
2428 2473 0.107945 AATCTCTCTGCTTGGCGGAC 60.108 55.000 0.00 0.00 39.19 4.79
2429 2474 0.975040 ATCTCTCTGCTTGGCGGACT 60.975 55.000 0.00 0.00 39.19 3.85
2430 2475 1.153667 CTCTCTGCTTGGCGGACTC 60.154 63.158 0.00 0.00 39.19 3.36
2431 2476 1.603236 CTCTCTGCTTGGCGGACTCT 61.603 60.000 0.00 0.00 39.19 3.24
2432 2477 1.188219 TCTCTGCTTGGCGGACTCTT 61.188 55.000 0.00 0.00 39.19 2.85
2433 2478 0.532573 CTCTGCTTGGCGGACTCTTA 59.467 55.000 0.00 0.00 39.19 2.10
2434 2479 0.973632 TCTGCTTGGCGGACTCTTAA 59.026 50.000 0.00 0.00 39.19 1.85
2435 2480 1.346395 TCTGCTTGGCGGACTCTTAAA 59.654 47.619 0.00 0.00 39.19 1.52
2436 2481 2.151202 CTGCTTGGCGGACTCTTAAAA 58.849 47.619 0.00 0.00 37.02 1.52
2437 2482 2.151202 TGCTTGGCGGACTCTTAAAAG 58.849 47.619 0.00 0.00 0.00 2.27
2438 2483 2.224426 TGCTTGGCGGACTCTTAAAAGA 60.224 45.455 0.00 0.00 0.00 2.52
2439 2484 3.010420 GCTTGGCGGACTCTTAAAAGAT 58.990 45.455 0.00 0.00 33.93 2.40
2440 2485 3.440522 GCTTGGCGGACTCTTAAAAGATT 59.559 43.478 0.00 0.00 33.93 2.40
2464 2509 0.306533 GTGGTACGTGGTGCAACAAG 59.693 55.000 16.53 16.53 39.98 3.16
2478 2523 0.324943 AACAAGTCCGTCCATCCAGG 59.675 55.000 0.00 0.00 39.47 4.45
2489 2534 2.427095 GTCCATCCAGGGCACAAATAAC 59.573 50.000 0.00 0.00 43.39 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 3.447229 TGAGTAATCTCCATGCTTGACGA 59.553 43.478 0.22 0.00 39.75 4.20
121 122 2.159653 GCGCATAGTGAGTCTGGTTTTG 60.160 50.000 0.30 0.00 0.00 2.44
122 123 2.076863 GCGCATAGTGAGTCTGGTTTT 58.923 47.619 0.30 0.00 0.00 2.43
147 148 9.042008 GTTAGGATAATATCTCGCTTTCAACAA 57.958 33.333 0.00 0.00 0.00 2.83
389 390 2.423898 CCACCGCCCGTAGTCATCT 61.424 63.158 0.00 0.00 0.00 2.90
514 515 4.182339 GACGGAGAAAATACCTCTTGGAC 58.818 47.826 0.00 0.00 37.04 4.02
560 561 5.544650 CACATATGAGTGCTGGATATGTCA 58.455 41.667 10.38 0.00 39.97 3.58
972 973 4.152938 GCGAGGGAGTTTGTAATTAAACGT 59.847 41.667 0.00 0.00 43.51 3.99
1299 1300 1.896220 AAAACCTGCGAGATGCTTCA 58.104 45.000 2.07 0.00 46.63 3.02
1345 1346 2.874648 TAGGGGTGCTGCTCAATGCG 62.875 60.000 0.00 0.00 46.63 4.73
1363 1364 1.407618 CCCCTTCGTGATGTCGTCATA 59.592 52.381 0.00 0.00 39.48 2.15
1404 1405 4.065281 GTGTGGCTCCTACGCGGT 62.065 66.667 12.47 0.00 0.00 5.68
1932 1937 7.849804 ACGATATGGATTGTATTAATCCTGC 57.150 36.000 16.93 5.77 45.01 4.85
1940 1945 6.037720 TGTTGCGAAACGATATGGATTGTATT 59.962 34.615 0.88 0.00 0.00 1.89
1941 1946 5.525745 TGTTGCGAAACGATATGGATTGTAT 59.474 36.000 0.88 0.00 0.00 2.29
1942 1947 4.870991 TGTTGCGAAACGATATGGATTGTA 59.129 37.500 0.88 0.00 0.00 2.41
1943 1948 3.687212 TGTTGCGAAACGATATGGATTGT 59.313 39.130 0.88 0.00 0.00 2.71
1944 1949 4.271590 TGTTGCGAAACGATATGGATTG 57.728 40.909 0.88 0.00 0.00 2.67
1945 1950 4.955925 TTGTTGCGAAACGATATGGATT 57.044 36.364 0.88 0.00 0.00 3.01
1946 1951 4.955925 TTTGTTGCGAAACGATATGGAT 57.044 36.364 0.88 0.00 0.00 3.41
1947 1952 4.750952 TTTTGTTGCGAAACGATATGGA 57.249 36.364 0.88 0.00 0.00 3.41
1968 1973 8.831715 ACAAAATGAACAGAAGTTGACTTTTT 57.168 26.923 0.00 0.00 38.30 1.94
1969 1974 9.921637 TTACAAAATGAACAGAAGTTGACTTTT 57.078 25.926 0.00 0.00 38.30 2.27
1970 1975 9.353999 GTTACAAAATGAACAGAAGTTGACTTT 57.646 29.630 0.00 0.00 38.30 2.66
1971 1976 8.519526 TGTTACAAAATGAACAGAAGTTGACTT 58.480 29.630 0.00 0.00 38.30 3.01
1972 1977 8.050778 TGTTACAAAATGAACAGAAGTTGACT 57.949 30.769 0.00 0.00 38.30 3.41
1973 1978 8.682128 TTGTTACAAAATGAACAGAAGTTGAC 57.318 30.769 0.00 0.00 38.30 3.18
1974 1979 8.519526 ACTTGTTACAAAATGAACAGAAGTTGA 58.480 29.630 0.00 0.00 38.30 3.18
1975 1980 8.687824 ACTTGTTACAAAATGAACAGAAGTTG 57.312 30.769 0.00 0.00 38.30 3.16
1981 1986 7.424803 TGGATGACTTGTTACAAAATGAACAG 58.575 34.615 0.00 0.00 36.92 3.16
2067 2073 9.949174 GTGCAAACACATATATGTATTGAATGA 57.051 29.630 29.65 16.41 46.61 2.57
2109 2115 1.278238 CAAGTCGAGGCGGACAATAC 58.722 55.000 12.98 0.00 39.42 1.89
2137 2143 2.889512 TGGCTTCTAGTGAACCTCTGA 58.110 47.619 0.00 0.00 0.00 3.27
2228 2237 5.673337 TGTTGACTAGAATGTTGCTGAAC 57.327 39.130 0.00 0.00 0.00 3.18
2271 2280 5.371115 TTCAAATCAAAGATCCCAACGTC 57.629 39.130 0.00 0.00 0.00 4.34
2305 2314 7.845066 AACGGAGTAGAATGGACTAAATTTC 57.155 36.000 0.00 0.00 45.00 2.17
2308 2317 7.042335 CAGAAACGGAGTAGAATGGACTAAAT 58.958 38.462 0.00 0.00 45.00 1.40
2323 2332 2.672714 TGTTCATCGACAGAAACGGAG 58.327 47.619 3.92 0.00 0.00 4.63
2324 2333 2.804697 TGTTCATCGACAGAAACGGA 57.195 45.000 3.92 0.00 0.00 4.69
2333 2377 3.181540 CGTGTTGTGATCTGTTCATCGAC 60.182 47.826 0.00 0.00 36.54 4.20
2340 2384 2.755650 GTCTCCGTGTTGTGATCTGTT 58.244 47.619 0.00 0.00 0.00 3.16
2376 2420 8.385111 GGTTTTCGTGAATTTATAAGTCGATGA 58.615 33.333 0.00 0.00 0.00 2.92
2395 2440 8.147642 AGCAGAGAGATTATAAATGGTTTTCG 57.852 34.615 0.00 0.00 0.00 3.46
2403 2448 4.999950 CCGCCAAGCAGAGAGATTATAAAT 59.000 41.667 0.00 0.00 0.00 1.40
2419 2464 6.927294 ATAATCTTTTAAGAGTCCGCCAAG 57.073 37.500 0.00 0.00 38.66 3.61
2429 2474 9.590451 CCACGTACCACTAATAATCTTTTAAGA 57.410 33.333 0.00 0.00 39.78 2.10
2430 2475 9.374838 ACCACGTACCACTAATAATCTTTTAAG 57.625 33.333 0.00 0.00 0.00 1.85
2431 2476 9.153721 CACCACGTACCACTAATAATCTTTTAA 57.846 33.333 0.00 0.00 0.00 1.52
2432 2477 7.278424 GCACCACGTACCACTAATAATCTTTTA 59.722 37.037 0.00 0.00 0.00 1.52
2433 2478 6.093082 GCACCACGTACCACTAATAATCTTTT 59.907 38.462 0.00 0.00 0.00 2.27
2434 2479 5.583457 GCACCACGTACCACTAATAATCTTT 59.417 40.000 0.00 0.00 0.00 2.52
2435 2480 5.114081 GCACCACGTACCACTAATAATCTT 58.886 41.667 0.00 0.00 0.00 2.40
2436 2481 4.160814 TGCACCACGTACCACTAATAATCT 59.839 41.667 0.00 0.00 0.00 2.40
2437 2482 4.435425 TGCACCACGTACCACTAATAATC 58.565 43.478 0.00 0.00 0.00 1.75
2438 2483 4.475051 TGCACCACGTACCACTAATAAT 57.525 40.909 0.00 0.00 0.00 1.28
2439 2484 3.957591 TGCACCACGTACCACTAATAA 57.042 42.857 0.00 0.00 0.00 1.40
2440 2485 3.006644 TGTTGCACCACGTACCACTAATA 59.993 43.478 0.00 0.00 0.00 0.98
2464 2509 3.399181 TGCCCTGGATGGACGGAC 61.399 66.667 0.00 0.00 38.35 4.79
2478 2523 3.001939 CGAAGATACGGGTTATTTGTGCC 59.998 47.826 0.00 0.00 0.00 5.01
2489 2534 1.067582 GTCTGGGCGAAGATACGGG 59.932 63.158 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.