Multiple sequence alignment - TraesCS7B01G385100

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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 TraesCS7B01G385100 chr7B 100.000 2399 0 0 1 2399 650456623 650454225 0.000000e+00 4431.0
1 TraesCS7B01G385100 chr7B 95.045 2442 54 14 1 2399 650295722 650293305 0.000000e+00 3777.0
2 TraesCS7B01G385100 chr7B 94.713 2440 64 18 1 2399 650362917 650360502 0.000000e+00 3731.0
3 TraesCS7B01G385100 chr7B 94.584 2437 71 14 1 2399 650318647 650316234 0.000000e+00 3712.0
4 TraesCS7B01G385100 chr7B 94.551 2441 67 21 1 2399 650409902 650407486 0.000000e+00 3711.0
5 TraesCS7B01G385100 chr7B 95.522 1608 35 5 1 1575 650301860 650300257 0.000000e+00 2536.0
6 TraesCS7B01G385100 chr7B 95.536 448 16 3 1955 2399 613664987 613664541 0.000000e+00 713.0
7 TraesCS7B01G385100 chr7B 91.784 426 24 5 1985 2399 702269724 702269299 1.240000e-162 582.0
8 TraesCS7B01G385100 chr7B 86.577 149 15 3 244 387 625612104 625612252 2.470000e-35 159.0
9 TraesCS7B01G385100 chr7B 81.905 105 14 5 276 377 724225303 724225201 1.530000e-12 84.2
10 TraesCS7B01G385100 chr7D 92.003 1488 93 15 435 1914 582651347 582649878 0.000000e+00 2065.0
11 TraesCS7B01G385100 chr7D 91.196 1488 88 21 435 1914 582545874 582544422 0.000000e+00 1982.0
12 TraesCS7B01G385100 chr7D 89.822 1179 90 18 478 1637 582748408 582747241 0.000000e+00 1485.0
13 TraesCS7B01G385100 chr7D 87.551 1221 99 23 435 1637 582662724 582661539 0.000000e+00 1363.0
14 TraesCS7B01G385100 chr7D 87.833 1200 94 22 456 1637 582557529 582556364 0.000000e+00 1360.0
15 TraesCS7B01G385100 chr7D 91.453 117 9 1 445 561 582745186 582745071 2.470000e-35 159.0
16 TraesCS7B01G385100 chr7D 88.889 117 10 2 445 561 583035775 583035662 8.940000e-30 141.0
17 TraesCS7B01G385100 chr7D 79.412 170 27 4 435 598 582562047 582561880 1.950000e-21 113.0
18 TraesCS7B01G385100 chr7D 79.412 170 27 4 435 598 582667373 582667206 1.950000e-21 113.0
19 TraesCS7B01G385100 chr7A 87.266 1390 132 32 445 1802 674506716 674505340 0.000000e+00 1544.0
20 TraesCS7B01G385100 chr7A 89.609 1203 99 20 446 1636 674738309 674737121 0.000000e+00 1506.0
21 TraesCS7B01G385100 chr7A 89.609 1203 99 20 446 1636 674753043 674751855 0.000000e+00 1506.0
22 TraesCS7B01G385100 chr7A 88.101 395 32 9 435 817 674522976 674522585 2.810000e-124 455.0
23 TraesCS7B01G385100 chr7A 87.657 397 33 10 435 819 674527245 674526853 4.700000e-122 448.0
24 TraesCS7B01G385100 chr7A 85.714 119 14 2 267 384 290969875 290969991 3.240000e-24 122.0
25 TraesCS7B01G385100 chr7A 86.275 51 7 0 267 317 22258034 22257984 3.330000e-04 56.5
26 TraesCS7B01G385100 chrUn 93.757 961 29 10 1446 2399 388900209 388901145 0.000000e+00 1413.0
27 TraesCS7B01G385100 chrUn 93.757 961 29 13 1446 2399 388901873 388902809 0.000000e+00 1413.0
28 TraesCS7B01G385100 chrUn 95.312 448 17 3 1951 2395 289013317 289013763 0.000000e+00 708.0
29 TraesCS7B01G385100 chr3B 95.740 446 17 2 1951 2395 756177710 756177266 0.000000e+00 717.0
30 TraesCS7B01G385100 chr3B 95.333 450 18 3 1951 2399 576307619 576308066 0.000000e+00 712.0
31 TraesCS7B01G385100 chr3B 85.574 305 36 6 116 415 446983220 446983521 1.790000e-81 313.0
32 TraesCS7B01G385100 chr5B 95.133 452 18 4 1951 2399 526265375 526264925 0.000000e+00 710.0
33 TraesCS7B01G385100 chr1B 95.111 450 20 2 1951 2399 55392327 55391879 0.000000e+00 708.0
34 TraesCS7B01G385100 chr1B 94.923 453 18 4 1951 2399 652029189 652028738 0.000000e+00 704.0
35 TraesCS7B01G385100 chr1B 94.889 450 20 3 1951 2399 55420018 55419571 0.000000e+00 701.0
36 TraesCS7B01G385100 chr1B 91.502 506 27 6 1910 2399 659399627 659400132 0.000000e+00 682.0
37 TraesCS7B01G385100 chr2B 83.848 421 45 13 1985 2399 46355966 46356369 1.740000e-101 379.0
38 TraesCS7B01G385100 chr2A 83.333 126 15 4 286 408 736743370 736743248 7.010000e-21 111.0
39 TraesCS7B01G385100 chr4A 80.714 140 18 6 266 401 716104169 716104035 1.520000e-17 100.0
40 TraesCS7B01G385100 chr4A 80.714 140 18 6 266 401 716119153 716119019 1.520000e-17 100.0
41 TraesCS7B01G385100 chr1A 82.524 103 13 4 279 380 465974992 465974894 4.250000e-13 86.1


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 TraesCS7B01G385100 chr7B 650454225 650456623 2398 True 4431.0 4431 100.0000 1 2399 1 chr7B.!!$R7 2398
1 TraesCS7B01G385100 chr7B 650293305 650295722 2417 True 3777.0 3777 95.0450 1 2399 1 chr7B.!!$R2 2398
2 TraesCS7B01G385100 chr7B 650360502 650362917 2415 True 3731.0 3731 94.7130 1 2399 1 chr7B.!!$R5 2398
3 TraesCS7B01G385100 chr7B 650316234 650318647 2413 True 3712.0 3712 94.5840 1 2399 1 chr7B.!!$R4 2398
4 TraesCS7B01G385100 chr7B 650407486 650409902 2416 True 3711.0 3711 94.5510 1 2399 1 chr7B.!!$R6 2398
5 TraesCS7B01G385100 chr7B 650300257 650301860 1603 True 2536.0 2536 95.5220 1 1575 1 chr7B.!!$R3 1574
6 TraesCS7B01G385100 chr7D 582649878 582651347 1469 True 2065.0 2065 92.0030 435 1914 1 chr7D.!!$R4 1479
7 TraesCS7B01G385100 chr7D 582544422 582545874 1452 True 1982.0 1982 91.1960 435 1914 1 chr7D.!!$R1 1479
8 TraesCS7B01G385100 chr7D 582661539 582662724 1185 True 1363.0 1363 87.5510 435 1637 1 chr7D.!!$R5 1202
9 TraesCS7B01G385100 chr7D 582556364 582557529 1165 True 1360.0 1360 87.8330 456 1637 1 chr7D.!!$R2 1181
10 TraesCS7B01G385100 chr7D 582745071 582748408 3337 True 822.0 1485 90.6375 445 1637 2 chr7D.!!$R8 1192
11 TraesCS7B01G385100 chr7A 674505340 674506716 1376 True 1544.0 1544 87.2660 445 1802 1 chr7A.!!$R2 1357
12 TraesCS7B01G385100 chr7A 674737121 674738309 1188 True 1506.0 1506 89.6090 446 1636 1 chr7A.!!$R3 1190
13 TraesCS7B01G385100 chr7A 674751855 674753043 1188 True 1506.0 1506 89.6090 446 1636 1 chr7A.!!$R4 1190
14 TraesCS7B01G385100 chr7A 674522585 674527245 4660 True 451.5 455 87.8790 435 819 2 chr7A.!!$R5 384
15 TraesCS7B01G385100 chrUn 388900209 388902809 2600 False 1413.0 1413 93.7570 1446 2399 2 chrUn.!!$F2 953
16 TraesCS7B01G385100 chr1B 659399627 659400132 505 False 682.0 682 91.5020 1910 2399 1 chr1B.!!$F1 489

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
466 488 1.667236 ACGTATCGTGTCCATCCGTA 58.333 50.0 0.0 0.0 39.18 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 8013 0.179092 CGGGAGTAAAGGCCCTTACG 60.179 60.0 16.79 3.44 42.4 3.18 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
30 31 2.904835 TCGGGAGAGGGCGAAATAA 58.095 52.632 0.00 0.00 0.00 1.40
105 106 6.093909 CAGGAATTGGAAATTGTATTTTGCCC 59.906 38.462 0.00 0.00 0.00 5.36
169 170 4.584638 TTGGACTTGTTGCCCATATAGT 57.415 40.909 0.00 0.00 0.00 2.12
306 310 5.762279 AGACCGTAATAATTTGGACCCATT 58.238 37.500 0.00 0.00 0.00 3.16
307 311 6.192044 AGACCGTAATAATTTGGACCCATTT 58.808 36.000 0.00 0.00 0.00 2.32
466 488 1.667236 ACGTATCGTGTCCATCCGTA 58.333 50.000 0.00 0.00 39.18 4.02
496 518 4.081420 AGCCAGTATGACAAACCAGAGTAG 60.081 45.833 0.00 0.00 39.69 2.57
615 4924 5.013391 TGTCATGGTCTGATGCCATATATGT 59.987 40.000 11.73 0.00 44.25 2.29
1928 7949 8.516811 AGTTACATTGACACTAGTAGAAAACG 57.483 34.615 3.59 0.00 0.00 3.60
1953 7997 1.047002 TTTGTCCCGGTTCGTAAGGA 58.953 50.000 0.00 0.00 38.47 3.36
1971 8015 2.375173 GACATTTAGTCCCGGTTCGT 57.625 50.000 0.00 0.00 41.56 3.85
1972 8016 3.508744 GACATTTAGTCCCGGTTCGTA 57.491 47.619 0.00 0.00 41.56 3.43
1973 8017 3.848726 GACATTTAGTCCCGGTTCGTAA 58.151 45.455 0.00 0.00 41.56 3.18
1974 8018 3.853475 ACATTTAGTCCCGGTTCGTAAG 58.147 45.455 0.00 0.00 0.00 2.34
1975 8019 3.192466 CATTTAGTCCCGGTTCGTAAGG 58.808 50.000 0.00 0.00 38.47 2.69
1976 8020 1.185315 TTAGTCCCGGTTCGTAAGGG 58.815 55.000 0.00 0.00 46.40 3.95
1977 8021 1.322538 TAGTCCCGGTTCGTAAGGGC 61.323 60.000 0.00 0.00 44.70 5.19
1978 8022 3.393106 TCCCGGTTCGTAAGGGCC 61.393 66.667 0.00 0.00 44.70 5.80
1979 8023 3.396570 CCCGGTTCGTAAGGGCCT 61.397 66.667 0.00 0.00 38.51 5.19
1980 8024 2.666812 CCGGTTCGTAAGGGCCTT 59.333 61.111 24.44 24.44 38.47 4.35
1981 8025 1.002990 CCGGTTCGTAAGGGCCTTT 60.003 57.895 26.29 5.08 38.47 3.11
1982 8026 0.249955 CCGGTTCGTAAGGGCCTTTA 59.750 55.000 26.29 2.60 38.47 1.85
1983 8027 1.362768 CGGTTCGTAAGGGCCTTTAC 58.637 55.000 26.29 24.18 38.47 2.01
1984 8028 1.066645 CGGTTCGTAAGGGCCTTTACT 60.067 52.381 28.91 1.50 32.58 2.24
1985 8029 2.625737 GGTTCGTAAGGGCCTTTACTC 58.374 52.381 28.91 19.99 32.58 2.59
1986 8030 2.625737 GTTCGTAAGGGCCTTTACTCC 58.374 52.381 28.91 16.00 32.58 3.85
2018 8062 3.217626 ACCGGGACTAATAGGTCGTTAG 58.782 50.000 6.32 0.00 37.12 2.34
2044 8093 1.614226 TCCCCCTTTAGTCCCGGTG 60.614 63.158 0.00 0.00 0.00 4.94
2051 8100 2.093128 CCTTTAGTCCCGGTGCTTACAT 60.093 50.000 0.00 0.00 0.00 2.29
2067 8116 1.275666 ACATGAACCGGGACAGATGA 58.724 50.000 6.32 0.00 0.00 2.92
2076 8125 0.543277 GGGACAGATGAGCATCCACA 59.457 55.000 6.84 0.00 38.58 4.17
2140 8189 0.037139 TGGTGACATAAACCGGGACG 60.037 55.000 6.32 0.00 45.91 4.79
2174 8278 1.302351 GTCAGAAGCTGGCTGCAGT 60.302 57.895 16.64 5.71 45.94 4.40
2395 10204 9.223099 CCTACTAATCATGCATCATCATACAAA 57.777 33.333 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 4.439057 CCTTGCCGTAACTAGCTTGATTA 58.561 43.478 1.04 0.00 0.00 1.75
105 106 1.204704 TCCATTCTGGTCACGTAGCTG 59.795 52.381 0.00 0.00 39.03 4.24
438 460 3.243468 TGGACACGATACGTTCAACTTGA 60.243 43.478 0.00 0.00 38.32 3.02
443 465 2.732912 CGGATGGACACGATACGTTCAA 60.733 50.000 0.00 0.00 38.32 2.69
466 488 0.973632 TGTCATACTGGCTCGTTGGT 59.026 50.000 0.00 0.00 0.00 3.67
615 4924 5.968676 AGTGTAGCCATAATAACCTGGAA 57.031 39.130 0.00 0.00 34.24 3.53
1628 7629 7.864108 TCCTCATACACATACAATCCTTTTG 57.136 36.000 0.00 0.00 0.00 2.44
1928 7949 2.283604 AACCGGGACAAATGCCCC 60.284 61.111 6.32 0.00 42.92 5.80
1953 7997 3.368739 CCTTACGAACCGGGACTAAATGT 60.369 47.826 6.32 0.00 0.00 2.71
1955 7999 2.169144 CCCTTACGAACCGGGACTAAAT 59.831 50.000 6.32 0.00 40.55 1.40
1964 8008 1.066645 AGTAAAGGCCCTTACGAACCG 60.067 52.381 16.79 0.00 36.96 4.44
1965 8009 2.625737 GAGTAAAGGCCCTTACGAACC 58.374 52.381 16.79 6.07 36.96 3.62
1966 8010 2.625737 GGAGTAAAGGCCCTTACGAAC 58.374 52.381 16.79 12.49 36.96 3.95
1967 8011 1.556451 GGGAGTAAAGGCCCTTACGAA 59.444 52.381 16.79 0.00 41.31 3.85
1968 8012 1.197812 GGGAGTAAAGGCCCTTACGA 58.802 55.000 16.79 0.00 41.31 3.43
1969 8013 0.179092 CGGGAGTAAAGGCCCTTACG 60.179 60.000 16.79 3.44 42.40 3.18
1970 8014 0.179702 CCGGGAGTAAAGGCCCTTAC 59.820 60.000 15.36 15.36 42.40 2.34
1971 8015 0.252835 ACCGGGAGTAAAGGCCCTTA 60.253 55.000 6.32 0.00 42.40 2.69
1972 8016 1.138228 AACCGGGAGTAAAGGCCCTT 61.138 55.000 6.32 0.00 42.40 3.95
1973 8017 1.540617 AACCGGGAGTAAAGGCCCT 60.541 57.895 6.32 0.00 42.40 5.19
1974 8018 1.077930 GAACCGGGAGTAAAGGCCC 60.078 63.158 6.32 0.00 41.11 5.80
1975 8019 0.327259 AAGAACCGGGAGTAAAGGCC 59.673 55.000 6.32 0.00 0.00 5.19
1976 8020 1.002773 TCAAGAACCGGGAGTAAAGGC 59.997 52.381 6.32 0.00 0.00 4.35
1977 8021 3.072211 GTTCAAGAACCGGGAGTAAAGG 58.928 50.000 6.32 0.00 35.36 3.11
2018 8062 2.158652 GGACTAAAGGGGGAGGCATTAC 60.159 54.545 0.00 0.00 0.00 1.89
2044 8093 1.066430 TCTGTCCCGGTTCATGTAAGC 60.066 52.381 0.00 0.00 0.00 3.09
2051 8100 1.191489 TGCTCATCTGTCCCGGTTCA 61.191 55.000 0.00 0.00 0.00 3.18
2067 8116 4.119363 AGCGGCCATGTGGATGCT 62.119 61.111 2.24 11.27 40.72 3.79
2140 8189 1.134694 GACGCGTGGATGCCTTTTC 59.865 57.895 20.70 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.