Multiple sequence alignment - TraesCS2D01G089800

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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 TraesCS2D01G089800 chr2D 100.000 3956 0 0 1 3956 39607245 39611200 0 7306
1 TraesCS2D01G089800 chr2D 96.869 3961 111 8 1 3956 635037261 635041213 0 6615
2 TraesCS2D01G089800 chr3D 97.021 3961 106 7 1 3956 202611947 202615900 0 6650
3 TraesCS2D01G089800 chr7B 96.770 3963 112 9 1 3956 743066306 743070259 0 6595
4 TraesCS2D01G089800 chr7A 96.719 3962 116 8 1 3956 671960567 671956614 0 6584
5 TraesCS2D01G089800 chr7A 96.667 3960 118 9 1 3956 120828847 120824898 0 6569
6 TraesCS2D01G089800 chr4D 96.720 3964 113 9 1 3956 123367643 123371597 0 6584
7 TraesCS2D01G089800 chr5A 96.696 3965 115 8 1 3956 16623274 16619317 0 6582
8 TraesCS2D01G089800 chr2A 96.544 3964 120 8 1 3956 735172800 735176754 0 6545
9 TraesCS2D01G089800 chr3B 96.515 3960 125 8 1 3956 201635802 201631852 0 6536


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 TraesCS2D01G089800 chr2D 39607245 39611200 3955 False 7306 7306 100.000 1 3956 1 chr2D.!!$F1 3955
1 TraesCS2D01G089800 chr2D 635037261 635041213 3952 False 6615 6615 96.869 1 3956 1 chr2D.!!$F2 3955
2 TraesCS2D01G089800 chr3D 202611947 202615900 3953 False 6650 6650 97.021 1 3956 1 chr3D.!!$F1 3955
3 TraesCS2D01G089800 chr7B 743066306 743070259 3953 False 6595 6595 96.770 1 3956 1 chr7B.!!$F1 3955
4 TraesCS2D01G089800 chr7A 671956614 671960567 3953 True 6584 6584 96.719 1 3956 1 chr7A.!!$R2 3955
5 TraesCS2D01G089800 chr7A 120824898 120828847 3949 True 6569 6569 96.667 1 3956 1 chr7A.!!$R1 3955
6 TraesCS2D01G089800 chr4D 123367643 123371597 3954 False 6584 6584 96.720 1 3956 1 chr4D.!!$F1 3955
7 TraesCS2D01G089800 chr5A 16619317 16623274 3957 True 6582 6582 96.696 1 3956 1 chr5A.!!$R1 3955
8 TraesCS2D01G089800 chr2A 735172800 735176754 3954 False 6545 6545 96.544 1 3956 1 chr2A.!!$F1 3955
9 TraesCS2D01G089800 chr3B 201631852 201635802 3950 True 6536 6536 96.515 1 3956 1 chr3B.!!$R1 3955

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
319 321 1.160137 GGTGCTCAACTACAGGCTTG 58.840 55.0 0.00 0.00 0.0 4.01 F
1517 1527 0.256177 CTTTTCCTCTACAGGGGCCC 59.744 60.0 17.12 17.12 40.8 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2031 2046 0.764752 AATGGGTCGATCCTCCCCTC 60.765 60.0 17.4 0.0 42.80 4.30 R
3219 3236 0.105593 GCCTGTGCTGCTGCTATCTA 59.894 55.0 17.0 0.0 40.48 1.98 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
68 69 3.047857 TGGCTCACCATTATCTGATCCA 58.952 45.455 0.00 0.00 42.67 3.41
70 71 4.105217 TGGCTCACCATTATCTGATCCAAT 59.895 41.667 0.00 0.00 42.67 3.16
142 143 6.149129 CCCATATGGCTTTTCCTAAGAAAC 57.851 41.667 16.97 0.00 41.69 2.78
212 214 9.790389 GTTCATCGGATTCTTAGATATATTCGT 57.210 33.333 0.00 0.00 0.00 3.85
319 321 1.160137 GGTGCTCAACTACAGGCTTG 58.840 55.000 0.00 0.00 0.00 4.01
502 504 1.185315 CCCCAACGCCATTCATCTTT 58.815 50.000 0.00 0.00 0.00 2.52
525 527 1.737236 TCAAATCCGGTCTTTCATGCG 59.263 47.619 0.00 0.00 0.00 4.73
550 552 2.986479 GTTTCATTTTTGGCCGCTACTG 59.014 45.455 0.00 0.00 0.00 2.74
783 786 4.508124 AGTTAGAATCTAAATGAAGGCGCG 59.492 41.667 0.00 0.00 0.00 6.86
1083 1093 5.883115 GCTAGGAAGCATTACTCCTCTTTTT 59.117 40.000 0.00 0.00 28.40 1.94
1187 1197 6.127591 CCTCGGATACAATTCGATCCTTCTAT 60.128 42.308 11.62 0.00 39.69 1.98
1330 1340 2.107378 TGCATTTCAGTGGGTTGGTCTA 59.893 45.455 0.00 0.00 0.00 2.59
1465 1475 1.272369 TGCCAATCCCTATGTTGTGCA 60.272 47.619 0.00 0.00 32.80 4.57
1485 1495 4.343239 TGCAGAGCTGAGCATCTTCTATTA 59.657 41.667 7.39 0.00 35.51 0.98
1508 1518 3.370953 GCTGGGATCAAGCTTTTCCTCTA 60.371 47.826 19.72 9.62 0.00 2.43
1517 1527 0.256177 CTTTTCCTCTACAGGGGCCC 59.744 60.000 17.12 17.12 40.80 5.80
1629 1639 3.871006 CGTAAGCATAGCATTTCTGGTCA 59.129 43.478 0.00 0.00 34.31 4.02
1698 1708 3.890527 GGTACCTCGTAGGACCTCA 57.109 57.895 4.06 0.00 37.67 3.86
1900 1911 4.970662 TGGACGTAAACTCGTAAGCTAT 57.029 40.909 0.00 0.00 44.21 2.97
1984 1998 1.300697 GTTCCTCTGTCGTTGCCGT 60.301 57.895 0.00 0.00 35.01 5.68
2031 2046 6.009115 AGGATAAGTTGCTAAAACAAACGG 57.991 37.500 0.00 0.00 0.00 4.44
2085 2100 0.039708 GAAAGACTGTTGGCAGCAGC 60.040 55.000 28.20 20.65 46.30 5.25
2122 2137 1.836802 GCCCCCTTCCAAATAAATGCA 59.163 47.619 0.00 0.00 0.00 3.96
2164 2179 2.517127 AGGGTTCGAGAATAGGGTAGGA 59.483 50.000 0.00 0.00 0.00 2.94
2175 2191 7.204243 AGAATAGGGTAGGATTTTTACGGTT 57.796 36.000 0.00 0.00 0.00 4.44
2176 2192 7.636579 AGAATAGGGTAGGATTTTTACGGTTT 58.363 34.615 0.00 0.00 0.00 3.27
2287 2303 3.691342 CGCCACCACCCGAGAAGA 61.691 66.667 0.00 0.00 0.00 2.87
2347 2363 1.141053 GGTCTAATGACAAGGGCCGAT 59.859 52.381 0.00 0.00 44.61 4.18
2350 2366 2.705658 TCTAATGACAAGGGCCGATGAT 59.294 45.455 17.59 3.83 0.00 2.45
2395 2411 1.596603 TGTGGAAGTCTCACGTACGA 58.403 50.000 24.41 0.00 37.91 3.43
2400 2416 2.163010 GGAAGTCTCACGTACGATTCCA 59.837 50.000 24.41 0.00 35.79 3.53
2501 2517 5.049579 ACCATCATTATAGGGGTATGGGA 57.950 43.478 0.00 0.00 38.54 4.37
2535 2551 5.443283 AGAAAGATCAAGGCAGCATATCAA 58.557 37.500 0.00 0.00 0.00 2.57
2932 2949 6.334202 ACCACTTTAAGACAGATCGATCTTC 58.666 40.000 25.25 22.42 36.56 2.87
3021 3038 0.462789 CGGCCGTTAGGTCACCTATT 59.537 55.000 19.50 0.00 43.99 1.73
3022 3039 1.134610 CGGCCGTTAGGTCACCTATTT 60.135 52.381 19.50 0.00 43.99 1.40
3173 3190 1.076332 CCGCCGTCTGTTCCTAAAAG 58.924 55.000 0.00 0.00 0.00 2.27
3235 3252 0.817654 ACGTAGATAGCAGCAGCACA 59.182 50.000 3.17 0.00 45.49 4.57
3369 3386 1.237285 GGCTATTATGGCGTGGCTGG 61.237 60.000 0.00 0.00 0.00 4.85
3383 3400 3.490761 CGTGGCTGGAATGAACAAAAAGT 60.491 43.478 0.00 0.00 0.00 2.66
3743 3761 2.643232 GCCCGACCTGTAAGTCCGT 61.643 63.158 0.00 0.00 32.91 4.69
3769 3787 1.267121 AAAGCGAGGAGTTGAGCCTA 58.733 50.000 0.00 0.00 35.44 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 3.119459 CGACCTACTGTCTGTACTGCATT 60.119 47.826 0.00 0.00 42.13 3.56
70 71 1.810755 CGACCTACTGTCTGTACTGCA 59.189 52.381 0.00 0.00 42.13 4.41
212 214 0.245539 CGGCTCGAGAAAAGGTACCA 59.754 55.000 18.75 0.00 0.00 3.25
319 321 5.068723 TGTCTCGTCTCCCCATAAAATAGAC 59.931 44.000 0.00 0.00 34.55 2.59
418 420 8.746052 AGCCATACAATCTATCTAGTAGCTAG 57.254 38.462 0.00 2.17 35.57 3.42
419 421 7.776030 GGAGCCATACAATCTATCTAGTAGCTA 59.224 40.741 0.00 0.00 0.00 3.32
420 422 6.605594 GGAGCCATACAATCTATCTAGTAGCT 59.394 42.308 0.00 0.00 0.00 3.32
421 423 6.459024 CGGAGCCATACAATCTATCTAGTAGC 60.459 46.154 0.00 0.00 0.00 3.58
502 504 2.823924 TGAAAGACCGGATTTGACGA 57.176 45.000 9.46 0.00 0.00 4.20
525 527 2.029918 AGCGGCCAAAAATGAAACTCTC 60.030 45.455 2.24 0.00 0.00 3.20
550 552 4.703899 TCAAGAAGTTTTCTACGAACGC 57.296 40.909 0.00 0.00 39.61 4.84
558 560 3.565307 TGGTGCCATCAAGAAGTTTTCT 58.435 40.909 0.00 0.00 43.15 2.52
1017 1027 5.992217 ACCACTTAGATCGAAATAGCATTCC 59.008 40.000 0.00 0.00 0.00 3.01
1107 1117 3.309682 CGCACAGACCAATCAATCGTATT 59.690 43.478 0.00 0.00 0.00 1.89
1159 1169 4.528596 AGGATCGAATTGTATCCGAGGAAT 59.471 41.667 9.11 0.00 45.35 3.01
1249 1259 9.843334 GAATAATGAAAGACCGTCTATACCTAG 57.157 37.037 0.26 0.00 0.00 3.02
1251 1261 8.480133 AGAATAATGAAAGACCGTCTATACCT 57.520 34.615 0.26 0.00 0.00 3.08
1330 1340 6.842676 ACTCTTTCCCAAAACTTCTCATACT 58.157 36.000 0.00 0.00 0.00 2.12
1465 1475 4.834496 AGCTAATAGAAGATGCTCAGCTCT 59.166 41.667 0.00 0.00 32.93 4.09
1485 1495 1.357079 AGGAAAAGCTTGATCCCAGCT 59.643 47.619 21.92 10.12 41.08 4.24
1517 1527 3.515330 CGTAGGGGGTTTACTACACAG 57.485 52.381 0.00 0.00 39.55 3.66
1549 1559 5.163612 GGGACCTTTACTACTTTACGACGAT 60.164 44.000 0.00 0.00 0.00 3.73
1629 1639 1.133915 AGATGTGTGGTTCGGTGGTTT 60.134 47.619 0.00 0.00 0.00 3.27
1900 1911 2.553904 GGACGATTATCCCTACCCTCGA 60.554 54.545 0.00 0.00 31.94 4.04
1960 1974 3.128349 GCAACGACAGAGGAACTAACAA 58.872 45.455 0.00 0.00 41.55 2.83
1961 1975 2.547218 GGCAACGACAGAGGAACTAACA 60.547 50.000 0.00 0.00 41.55 2.41
1984 1998 2.492484 GGTCTCTTCGCCAAGAACTCTA 59.508 50.000 0.00 0.00 38.23 2.43
2031 2046 0.764752 AATGGGTCGATCCTCCCCTC 60.765 60.000 17.40 0.00 42.80 4.30
2085 2100 1.821136 GGGCCAAAGAAATGTCTCCAG 59.179 52.381 4.39 0.00 30.70 3.86
2122 2137 2.443016 CCGAGCTCTACCCTGCCT 60.443 66.667 12.85 0.00 0.00 4.75
2202 2218 2.175236 CTTCCTGCCCGAAAGAAGC 58.825 57.895 0.00 0.00 30.27 3.86
2250 2266 2.651703 CGAACAATGTTGCTTGCGTAAG 59.348 45.455 9.10 9.10 36.97 2.34
2251 2267 2.645163 CGAACAATGTTGCTTGCGTAA 58.355 42.857 2.20 0.00 0.00 3.18
2287 2303 3.433615 CGCCTTGACTCTCGAATCTTTTT 59.566 43.478 0.00 0.00 0.00 1.94
2347 2363 1.254975 TTCGTCCCGAGCTTCCATCA 61.255 55.000 0.00 0.00 37.14 3.07
2350 2366 2.970639 CTTCGTCCCGAGCTTCCA 59.029 61.111 0.00 0.00 37.14 3.53
2365 2381 2.501723 AGACTTCCACATCATACGGCTT 59.498 45.455 0.00 0.00 0.00 4.35
2378 2394 2.163010 GGAATCGTACGTGAGACTTCCA 59.837 50.000 16.05 0.00 32.73 3.53
2395 2411 1.213926 GCCACTCCCTTCTCATGGAAT 59.786 52.381 0.00 0.00 33.01 3.01
2400 2416 1.501582 GGTAGCCACTCCCTTCTCAT 58.498 55.000 0.00 0.00 0.00 2.90
2463 2479 1.306226 GGTAGAGTCAGGGGTGGCT 60.306 63.158 0.00 0.00 0.00 4.75
2501 2517 5.123027 GCCTTGATCTTTCTTTGTCTCGAAT 59.877 40.000 0.00 0.00 0.00 3.34
2806 2823 9.942850 CATGGGTATTGAAAATCTTAAAAACCT 57.057 29.630 0.00 0.00 0.00 3.50
2932 2949 4.100653 TCAGGAGTAGGCAATGATCTTCTG 59.899 45.833 0.00 0.00 34.23 3.02
3022 3039 5.126222 TGCTTGTGTGTCCATAACTCAAAAA 59.874 36.000 0.00 0.00 33.43 1.94
3173 3190 2.050350 GGGGCGCTAAGGGGTTTTC 61.050 63.158 7.64 0.00 0.00 2.29
3219 3236 0.105593 GCCTGTGCTGCTGCTATCTA 59.894 55.000 17.00 0.00 40.48 1.98
3235 3252 1.765230 ATTCGGACTTCGTAGAGCCT 58.235 50.000 0.00 0.00 38.43 4.58
3369 3386 9.467258 TTGAATCATCTCACTTTTTGTTCATTC 57.533 29.630 0.00 0.00 0.00 2.67
3415 3432 9.892130 AAACCTTTCGATCTATTAGAACAGATT 57.108 29.630 0.00 0.00 31.63 2.40
3743 3761 4.232221 CTCAACTCCTCGCTTTACGTTAA 58.768 43.478 0.00 0.00 44.19 2.01
3769 3787 0.179067 TGACTTCGGTTCGCCAGTTT 60.179 50.000 0.00 0.00 37.00 2.66
3932 3950 6.485830 CTGTCCCCAATAGAAGAATGACTA 57.514 41.667 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.