Multiple sequence alignment - TraesCS4B01G377000

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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 TraesCS4B01G377000 chr4B 100.000 2814 0 0 1 2814 660252768 660249955 0.000000e+00 5197
1 TraesCS4B01G377000 chr4B 91.161 2817 186 33 1 2802 660297843 660295075 0.000000e+00 3764
2 TraesCS4B01G377000 chr4B 91.245 2353 142 30 1 2332 660322363 660320054 0.000000e+00 3145
3 TraesCS4B01G377000 chr4B 88.263 213 23 2 532 743 660284049 660283838 1.290000e-63 254
4 TraesCS4B01G377000 chr4B 86.854 213 26 2 532 743 660330546 660330335 1.300000e-58 237
5 TraesCS4B01G377000 chr5A 91.041 2824 191 35 1 2814 699839852 699842623 0.000000e+00 3757
6 TraesCS4B01G377000 chr5A 91.006 2824 194 34 1 2814 699798505 699801278 0.000000e+00 3753
7 TraesCS4B01G377000 chr5A 92.639 1834 117 13 504 2332 699572802 699574622 0.000000e+00 2623
8 TraesCS4B01G377000 chr5A 93.935 1484 78 7 504 1984 700388379 700389853 0.000000e+00 2231
9 TraesCS4B01G377000 chr5A 85.261 1418 146 36 757 2147 699535626 699534245 0.000000e+00 1402
10 TraesCS4B01G377000 chr5A 86.035 1024 96 20 758 1761 699624485 699625481 0.000000e+00 1055
11 TraesCS4B01G377000 chrUn 90.883 2457 173 23 1 2448 231251609 231254023 0.000000e+00 3249
12 TraesCS4B01G377000 chrUn 91.356 2337 155 22 1 2332 156635273 156637567 0.000000e+00 3153
13 TraesCS4B01G377000 chrUn 91.358 2268 147 21 1 2260 190742423 190744649 0.000000e+00 3057
14 TraesCS4B01G377000 chrUn 91.822 2152 156 12 668 2814 156743161 156745297 0.000000e+00 2981
15 TraesCS4B01G377000 chrUn 92.756 1629 97 11 1189 2814 190750547 190752157 0.000000e+00 2335
16 TraesCS4B01G377000 chrUn 93.691 1490 82 7 504 1990 390208074 390206594 0.000000e+00 2220
17 TraesCS4B01G377000 chrUn 93.670 1485 81 8 504 1984 354303983 354305458 0.000000e+00 2209
18 TraesCS4B01G377000 chrUn 88.340 952 75 16 1 950 190749633 190750550 0.000000e+00 1110
19 TraesCS4B01G377000 chrUn 88.669 556 55 6 2260 2814 190746365 190746913 0.000000e+00 671
20 TraesCS4B01G377000 chrUn 92.537 469 34 1 1 468 354303527 354303995 0.000000e+00 671
21 TraesCS4B01G377000 chrUn 79.464 336 53 10 2338 2661 400724649 400724318 1.010000e-54 224
22 TraesCS4B01G377000 chrUn 79.167 336 54 10 2338 2661 278953434 278953103 4.720000e-53 219


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 TraesCS4B01G377000 chr4B 660249955 660252768 2813 True 5197.00 5197 100.00000 1 2814 1 chr4B.!!$R1 2813
1 TraesCS4B01G377000 chr4B 660295075 660297843 2768 True 3764.00 3764 91.16100 1 2802 1 chr4B.!!$R3 2801
2 TraesCS4B01G377000 chr4B 660320054 660322363 2309 True 3145.00 3145 91.24500 1 2332 1 chr4B.!!$R4 2331
3 TraesCS4B01G377000 chr5A 699839852 699842623 2771 False 3757.00 3757 91.04100 1 2814 1 chr5A.!!$F4 2813
4 TraesCS4B01G377000 chr5A 699798505 699801278 2773 False 3753.00 3753 91.00600 1 2814 1 chr5A.!!$F3 2813
5 TraesCS4B01G377000 chr5A 699572802 699574622 1820 False 2623.00 2623 92.63900 504 2332 1 chr5A.!!$F1 1828
6 TraesCS4B01G377000 chr5A 700388379 700389853 1474 False 2231.00 2231 93.93500 504 1984 1 chr5A.!!$F5 1480
7 TraesCS4B01G377000 chr5A 699534245 699535626 1381 True 1402.00 1402 85.26100 757 2147 1 chr5A.!!$R1 1390
8 TraesCS4B01G377000 chr5A 699624485 699625481 996 False 1055.00 1055 86.03500 758 1761 1 chr5A.!!$F2 1003
9 TraesCS4B01G377000 chrUn 231251609 231254023 2414 False 3249.00 3249 90.88300 1 2448 1 chrUn.!!$F3 2447
10 TraesCS4B01G377000 chrUn 156635273 156637567 2294 False 3153.00 3153 91.35600 1 2332 1 chrUn.!!$F1 2331
11 TraesCS4B01G377000 chrUn 156743161 156745297 2136 False 2981.00 2981 91.82200 668 2814 1 chrUn.!!$F2 2146
12 TraesCS4B01G377000 chrUn 390206594 390208074 1480 True 2220.00 2220 93.69100 504 1990 1 chrUn.!!$R2 1486
13 TraesCS4B01G377000 chrUn 190742423 190752157 9734 False 1793.25 3057 90.28075 1 2814 4 chrUn.!!$F4 2813
14 TraesCS4B01G377000 chrUn 354303527 354305458 1931 False 1440.00 2209 93.10350 1 1984 2 chrUn.!!$F5 1983

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
494 509 0.609131 CGGCCTGGAGGTGACAAAAT 60.609 55.0 0.0 0.0 37.57 1.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1920 1986 0.108992 CAGACACACAATGGCATGCC 60.109 55.0 30.54 30.54 39.81 4.4 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
44 45 1.474879 GTGAGAAGTTCCTCCTCTCCG 59.525 57.143 0.00 0.00 32.32 4.63
88 89 1.762370 CTCCTTTTGGTTGGGCACTTT 59.238 47.619 0.00 0.00 41.38 2.66
156 157 4.859798 CGAGAGACATCTGACCAAGTAAAC 59.140 45.833 0.00 0.00 35.30 2.01
177 180 4.686972 ACACCAGATTGACGTGATGATAG 58.313 43.478 0.00 0.00 0.00 2.08
184 187 3.982576 TGACGTGATGATAGCGTACAT 57.017 42.857 0.00 0.00 39.06 2.29
268 272 4.130857 TCTTCCTTGTTCGCACACAATAA 58.869 39.130 0.00 0.00 36.08 1.40
271 275 2.226437 CCTTGTTCGCACACAATAAGCT 59.774 45.455 0.00 0.00 36.08 3.74
280 284 2.416202 CACACAATAAGCTGCGTCATCA 59.584 45.455 0.00 0.00 0.00 3.07
488 503 3.846405 AAGGTCGGCCTGGAGGTGA 62.846 63.158 10.71 0.00 46.33 4.02
489 504 4.083862 GGTCGGCCTGGAGGTGAC 62.084 72.222 0.00 10.21 39.98 3.67
493 508 1.228124 CGGCCTGGAGGTGACAAAA 60.228 57.895 0.00 0.00 37.57 2.44
494 509 0.609131 CGGCCTGGAGGTGACAAAAT 60.609 55.000 0.00 0.00 37.57 1.82
495 510 1.632589 GGCCTGGAGGTGACAAAATT 58.367 50.000 0.00 0.00 37.57 1.82
496 511 1.970640 GGCCTGGAGGTGACAAAATTT 59.029 47.619 0.00 0.00 37.57 1.82
497 512 2.289010 GGCCTGGAGGTGACAAAATTTG 60.289 50.000 3.89 3.89 37.57 2.32
498 513 2.365293 GCCTGGAGGTGACAAAATTTGT 59.635 45.455 11.55 11.55 41.58 2.83
499 514 3.552890 GCCTGGAGGTGACAAAATTTGTC 60.553 47.826 26.73 26.73 46.62 3.18
582 599 3.364441 GCATGCGCACCAGACCAA 61.364 61.111 14.90 0.00 38.36 3.67
747 787 1.639298 GCATTGTGCCGACTCAGGAC 61.639 60.000 0.00 0.00 37.42 3.85
892 950 3.182967 GTCTATTGCTCACGAGTTCTGG 58.817 50.000 0.00 0.00 0.00 3.86
964 1022 3.119849 CGCCACAAACAGAAATAGGAAGG 60.120 47.826 0.00 0.00 0.00 3.46
999 1057 4.058817 AGAGCCAAAGACACTAAAACGAG 58.941 43.478 0.00 0.00 0.00 4.18
1059 1117 0.821301 TTGCGTTGGTCTCATGGCAA 60.821 50.000 0.00 0.00 38.34 4.52
1221 1284 8.807667 AATCAACTTTGTAAAATCTGAGCTTG 57.192 30.769 0.00 0.00 0.00 4.01
1330 1396 0.608640 CCAACCTCGACAAGCCTAGT 59.391 55.000 0.00 0.00 0.00 2.57
1552 1618 2.717390 GCCCCCAACAAAAACAAGTTT 58.283 42.857 0.00 0.00 0.00 2.66
1564 1630 6.995686 ACAAAAACAAGTTTTTCTCCAAGGTT 59.004 30.769 17.94 0.00 46.30 3.50
1633 1699 0.495923 AATTCAACCCCAACCCCCAT 59.504 50.000 0.00 0.00 0.00 4.00
1711 1777 0.318120 CCAATGCAGTGTTTGGGTCC 59.682 55.000 13.82 0.00 38.98 4.46
1729 1795 1.760613 TCCGACCCACCAATATCAGAC 59.239 52.381 0.00 0.00 0.00 3.51
1798 1864 3.985410 CCAGGCTCAATTCTGGGAA 57.015 52.632 3.47 0.00 44.99 3.97
1821 1887 6.481434 AAACAACCACTACTAAGTCAGACT 57.519 37.500 0.00 0.00 31.97 3.24
1837 1903 6.126409 AGTCAGACTTTTGTTGATTACCCAA 58.874 36.000 0.00 0.00 0.00 4.12
2016 2083 8.158169 TCACACTAATATGATCTCAATTTGCC 57.842 34.615 0.00 0.00 0.00 4.52
2038 2105 4.036262 CCTCTTTTGGAATTTGACGTGTCA 59.964 41.667 0.00 0.00 37.91 3.58
2088 2159 2.265589 TCTTTCCCCTTGTTCCGAAC 57.734 50.000 4.18 4.18 0.00 3.95
2149 2220 5.245531 TGCTAAAGTGAACACCTAGGATTG 58.754 41.667 17.98 6.83 0.00 2.67
2185 2272 3.701040 GTGAAGTATGCCATGGTTGGAAT 59.299 43.478 14.67 2.70 46.92 3.01
2198 2285 0.953471 TTGGAATCCGGTTGTGCTCG 60.953 55.000 0.00 0.00 0.00 5.03
2214 2301 3.057596 GTGCTCGGGATTGAAATGTGAAA 60.058 43.478 0.00 0.00 0.00 2.69
2222 2309 6.089820 CGGGATTGAAATGTGAAAGTTGAATG 59.910 38.462 0.00 0.00 0.00 2.67
2258 9310 0.393820 TGGGGTCGTTGTTGAGGTAC 59.606 55.000 0.00 0.00 0.00 3.34
2276 9328 0.613260 ACCTCGCTTTCTGGTGCATA 59.387 50.000 0.00 0.00 32.16 3.14
2281 9333 4.153117 CCTCGCTTTCTGGTGCATATAATC 59.847 45.833 0.00 0.00 0.00 1.75
2314 9366 3.330701 AGTCCCTTTGCTATGGAACTTGA 59.669 43.478 1.55 0.00 0.00 3.02
2318 9370 5.185635 TCCCTTTGCTATGGAACTTGATTTG 59.814 40.000 1.55 0.00 0.00 2.32
2333 9385 7.759489 ACTTGATTTGGTTATTGTTAGCTCA 57.241 32.000 0.00 0.00 0.00 4.26
2412 9465 9.487790 TTGATTGATGGTTTCTTTAATGGAAAC 57.512 29.630 18.39 18.39 46.67 2.78
2518 9572 4.694987 AATTGGGCACACCGGGGG 62.695 66.667 9.50 0.00 44.64 5.40
2547 9601 6.928492 GGTTTCAAAAATCAGCTCCAACATAA 59.072 34.615 0.00 0.00 0.00 1.90
2551 9605 7.894708 TCAAAAATCAGCTCCAACATAAATGA 58.105 30.769 0.00 0.00 0.00 2.57
2661 9715 7.775093 ACAAGCTGGTGATAGAAGCATTTTATA 59.225 33.333 0.00 0.00 39.47 0.98
2782 9836 2.541383 GCAAAAACAAGCCAAACATGCC 60.541 45.455 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 2.992089 CCACATAGGCCATGACGAC 58.008 57.895 18.41 0.00 38.10 4.34
66 67 1.063266 AGTGCCCAACCAAAAGGAGAA 60.063 47.619 0.00 0.00 0.00 2.87
88 89 2.967397 CGGCGACCTTAGTGGACA 59.033 61.111 0.00 0.00 39.71 4.02
156 157 3.492383 GCTATCATCACGTCAATCTGGTG 59.508 47.826 0.00 0.00 0.00 4.17
177 180 0.532862 ATGTAGCAGCCCATGTACGC 60.533 55.000 0.00 0.00 0.00 4.42
203 206 6.547141 CCACACATGAATCCACCTAATACATT 59.453 38.462 0.00 0.00 0.00 2.71
268 272 1.600957 GCAACATATGATGACGCAGCT 59.399 47.619 16.46 0.00 33.39 4.24
280 284 6.778834 TTGTCATGAAATCCAGCAACATAT 57.221 33.333 0.00 0.00 0.00 1.78
498 513 3.006752 GGCCATCAATTTTGTCACCTTGA 59.993 43.478 0.00 0.00 32.63 3.02
499 514 3.007182 AGGCCATCAATTTTGTCACCTTG 59.993 43.478 5.01 0.00 0.00 3.61
500 515 3.242011 AGGCCATCAATTTTGTCACCTT 58.758 40.909 5.01 0.00 0.00 3.50
501 516 2.893424 AGGCCATCAATTTTGTCACCT 58.107 42.857 5.01 0.00 0.00 4.00
502 517 3.683365 AAGGCCATCAATTTTGTCACC 57.317 42.857 5.01 0.00 0.00 4.02
503 518 5.132897 TGTAAGGCCATCAATTTTGTCAC 57.867 39.130 5.01 0.00 0.00 3.67
504 519 5.479724 TCATGTAAGGCCATCAATTTTGTCA 59.520 36.000 5.01 0.00 0.00 3.58
505 520 5.807011 GTCATGTAAGGCCATCAATTTTGTC 59.193 40.000 5.01 0.00 0.00 3.18
506 521 5.481473 AGTCATGTAAGGCCATCAATTTTGT 59.519 36.000 5.01 0.00 0.00 2.83
507 522 5.969423 AGTCATGTAAGGCCATCAATTTTG 58.031 37.500 5.01 0.00 0.00 2.44
508 523 6.400568 CAAGTCATGTAAGGCCATCAATTTT 58.599 36.000 5.01 0.00 0.00 1.82
509 524 5.105228 CCAAGTCATGTAAGGCCATCAATTT 60.105 40.000 5.01 0.00 0.00 1.82
747 787 5.824429 TCAAAGAAGCAATGTGAAACTCTG 58.176 37.500 0.00 0.00 38.04 3.35
892 950 4.399303 GGGATGCATGTGTTTATATAGGCC 59.601 45.833 2.46 0.00 0.00 5.19
964 1022 0.321653 TGGCTCTTCTTTTCTCCCGC 60.322 55.000 0.00 0.00 0.00 6.13
999 1057 1.433121 AGGAAGAGGAGGATGCCATC 58.567 55.000 0.00 0.00 0.00 3.51
1198 1260 6.183360 TGCAAGCTCAGATTTTACAAAGTTGA 60.183 34.615 0.00 0.00 0.00 3.18
1221 1284 1.672881 GGGCACAAGAGATGTACATGC 59.327 52.381 14.43 9.97 41.46 4.06
1330 1396 2.622977 GGATCCAACCTTGTTGGGCATA 60.623 50.000 22.16 6.83 39.96 3.14
1384 1450 2.584391 GCCGAGGGTGTTGAGTCCT 61.584 63.158 0.00 0.00 0.00 3.85
1552 1618 4.644685 CCTTTGTTGAGAACCTTGGAGAAA 59.355 41.667 0.00 0.00 0.00 2.52
1564 1630 4.704540 ACAAACACATCACCTTTGTTGAGA 59.295 37.500 0.00 0.00 35.10 3.27
1633 1699 1.902918 AATTGCAACAGCGGGCTGA 60.903 52.632 26.08 4.60 46.30 4.26
1711 1777 1.407618 TCGTCTGATATTGGTGGGTCG 59.592 52.381 0.00 0.00 0.00 4.79
1729 1795 0.813184 ATGCCTTGGCAAGAACATCG 59.187 50.000 28.18 11.36 0.00 3.84
1798 1864 6.481434 AGTCTGACTTAGTAGTGGTTGTTT 57.519 37.500 4.06 0.00 33.84 2.83
1821 1887 6.155393 ACTGGTCTTTTGGGTAATCAACAAAA 59.845 34.615 0.00 0.00 40.55 2.44
1837 1903 3.068590 CCTTCATTTGTGCACTGGTCTTT 59.931 43.478 19.41 0.00 0.00 2.52
1920 1986 0.108992 CAGACACACAATGGCATGCC 60.109 55.000 30.54 30.54 39.81 4.40
1921 1987 0.599558 ACAGACACACAATGGCATGC 59.400 50.000 9.90 9.90 39.81 4.06
2009 2076 5.466393 CGTCAAATTCCAAAAGAGGCAAATT 59.534 36.000 0.00 0.00 0.00 1.82
2016 2083 5.168526 TGACACGTCAAATTCCAAAAGAG 57.831 39.130 0.00 0.00 36.53 2.85
2130 2201 4.652822 GGACAATCCTAGGTGTTCACTTT 58.347 43.478 9.08 0.00 32.53 2.66
2131 2202 4.287766 GGACAATCCTAGGTGTTCACTT 57.712 45.455 9.08 0.00 32.53 3.16
2132 2203 3.983044 GGACAATCCTAGGTGTTCACT 57.017 47.619 9.08 0.00 32.53 3.41
2149 2220 3.045601 ACTTCACATGTAGTGCAGGAC 57.954 47.619 0.00 0.00 44.45 3.85
2157 2228 4.454678 ACCATGGCATACTTCACATGTAG 58.545 43.478 13.04 0.00 39.14 2.74
2198 2285 6.930722 ACATTCAACTTTCACATTTCAATCCC 59.069 34.615 0.00 0.00 0.00 3.85
2235 2322 0.324943 CTCAACAACGACCCCAGGAT 59.675 55.000 0.00 0.00 0.00 3.24
2242 2329 1.668047 CGAGGTACCTCAACAACGACC 60.668 57.143 35.32 10.77 42.86 4.79
2258 9310 1.959042 ATATGCACCAGAAAGCGAGG 58.041 50.000 0.00 0.00 0.00 4.63
2276 9328 8.903820 GCAAAGGGACTGTAAATTACTGATTAT 58.096 33.333 15.35 0.00 40.86 1.28
2281 9333 7.201732 CCATAGCAAAGGGACTGTAAATTACTG 60.202 40.741 8.23 8.23 40.86 2.74
2314 9366 9.435688 GGAAAATTGAGCTAACAATAACCAAAT 57.564 29.630 1.38 0.00 39.19 2.32
2318 9370 6.531594 GCTGGAAAATTGAGCTAACAATAACC 59.468 38.462 1.38 6.28 39.19 2.85
2333 9385 7.282901 AGCTAAAACAAAACATGCTGGAAAATT 59.717 29.630 0.00 0.00 0.00 1.82
2412 9465 5.793817 TGATACAATAATCCACCTCATCGG 58.206 41.667 0.00 0.00 39.35 4.18
2496 9550 1.552792 CCCGGTGTGCCCAATTTTTAT 59.447 47.619 0.00 0.00 0.00 1.40
2518 9572 3.320626 GAGCTGATTTTTGAAACCTGGC 58.679 45.455 0.00 0.00 0.00 4.85
2661 9715 4.379652 AGCAGGCAAAATTTTGTTTCGAT 58.620 34.783 27.13 12.81 40.24 3.59


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

AutoCloner maintained by Alex Coulton.