Multiple sequence alignment - TraesCS2A01G294600

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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 TraesCS2A01G294600 chr2A 100.000 2480 0 0 1 2480 507083071 507085550 0.000000e+00 4580
1 TraesCS2A01G294600 chr2D 93.115 2295 88 30 4 2275 374143938 374146185 0.000000e+00 3299
2 TraesCS2A01G294600 chr2D 92.347 196 12 1 2288 2480 374146446 374146641 2.430000e-70 276
3 TraesCS2A01G294600 chr2B 93.840 1802 58 22 438 2221 444844271 444846037 0.000000e+00 2663
4 TraesCS2A01G294600 chr2B 92.336 274 18 2 2210 2480 444847264 444847537 1.080000e-103 387
5 TraesCS2A01G294600 chr2B 91.667 144 9 1 293 433 444843202 444843345 1.950000e-46 196
6 TraesCS2A01G294600 chr2B 89.583 96 10 0 56 151 444842929 444843024 3.350000e-24 122


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 TraesCS2A01G294600 chr2A 507083071 507085550 2479 False 4580.0 4580 100.0000 1 2480 1 chr2A.!!$F1 2479
1 TraesCS2A01G294600 chr2D 374143938 374146641 2703 False 1787.5 3299 92.7310 4 2480 2 chr2D.!!$F1 2476
2 TraesCS2A01G294600 chr2B 444842929 444847537 4608 False 842.0 2663 91.8565 56 2480 4 chr2B.!!$F1 2424

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
969 1986 1.105759 GCTAGCTTCCATTGGCCTGG 61.106 60.0 7.7 4.05 37.66 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2166 3213 0.664761 CCTGCAAATCGGGCACATAG 59.335 55.0 0.0 0.0 36.11 2.23 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
29 30 5.529581 TTTTCCCTAAAAACCAGCTCAAG 57.470 39.130 0.00 0.00 31.88 3.02
30 31 3.876309 TCCCTAAAAACCAGCTCAAGT 57.124 42.857 0.00 0.00 0.00 3.16
31 32 4.986054 TCCCTAAAAACCAGCTCAAGTA 57.014 40.909 0.00 0.00 0.00 2.24
32 33 5.514500 TCCCTAAAAACCAGCTCAAGTAT 57.486 39.130 0.00 0.00 0.00 2.12
33 34 5.497474 TCCCTAAAAACCAGCTCAAGTATC 58.503 41.667 0.00 0.00 0.00 2.24
34 35 5.250774 TCCCTAAAAACCAGCTCAAGTATCT 59.749 40.000 0.00 0.00 0.00 1.98
188 280 4.717877 GAGACTTACCTAGTACTCCCTCC 58.282 52.174 0.00 0.00 37.17 4.30
192 284 6.392245 AGACTTACCTAGTACTCCCTCCAATA 59.608 42.308 0.00 0.00 37.17 1.90
194 286 4.472690 ACCTAGTACTCCCTCCAATAGG 57.527 50.000 0.00 0.00 46.09 2.57
241 333 3.355626 GGTTGAACCTCAGCTTTGAAC 57.644 47.619 7.20 0.00 34.73 3.18
244 336 4.023963 GGTTGAACCTCAGCTTTGAACTAC 60.024 45.833 7.20 0.00 34.73 2.73
278 370 7.556275 TCAAACCTTAGTTCAAAGTTGAGACAT 59.444 33.333 0.00 0.00 38.61 3.06
433 528 1.885163 TTCGTCCCTCCTTCCTTCGC 61.885 60.000 0.00 0.00 0.00 4.70
475 1491 2.168728 AGAGTCTCGAAGTTAATGGGGC 59.831 50.000 0.00 0.00 0.00 5.80
524 1540 3.694072 CCCCGCAAAAGATCAAATCTACA 59.306 43.478 0.00 0.00 39.08 2.74
797 1813 1.356494 CCCCTTCCATCTCCTTCCCC 61.356 65.000 0.00 0.00 0.00 4.81
909 1926 2.357881 TCAGCAAGGCAGCAGACG 60.358 61.111 4.78 0.00 36.85 4.18
918 1935 2.029073 CAGCAGACGACCGGTGTT 59.971 61.111 14.63 0.00 0.00 3.32
928 1945 2.203422 CCGGTGTTTGCCAAGGGA 60.203 61.111 0.00 0.00 0.00 4.20
969 1986 1.105759 GCTAGCTTCCATTGGCCTGG 61.106 60.000 7.70 4.05 37.66 4.45
1005 2027 1.663379 GCTTGATCTGCTGCATGGCA 61.663 55.000 1.31 0.27 40.15 4.92
1127 2149 1.647629 CTACGTCCTCCGATCACCG 59.352 63.158 0.00 0.00 40.70 4.94
1164 2186 3.873361 CGCAAGATCAAGCTGGAAGAATA 59.127 43.478 0.00 0.00 43.02 1.75
1167 2189 5.048852 GCAAGATCAAGCTGGAAGAATATCC 60.049 44.000 0.00 0.00 40.10 2.59
1542 2566 7.335422 CCTAGCTTCTTCTTGCTCAAATAAGAA 59.665 37.037 14.09 14.09 39.77 2.52
1543 2567 7.700022 AGCTTCTTCTTGCTCAAATAAGAAT 57.300 32.000 14.72 4.92 40.82 2.40
1544 2568 8.798859 AGCTTCTTCTTGCTCAAATAAGAATA 57.201 30.769 14.72 0.00 40.82 1.75
1545 2569 9.236006 AGCTTCTTCTTGCTCAAATAAGAATAA 57.764 29.630 14.72 0.00 40.82 1.40
1546 2570 9.500864 GCTTCTTCTTGCTCAAATAAGAATAAG 57.499 33.333 14.97 14.97 43.10 1.73
1605 2629 7.040062 TCGATCTTTTTGTGGTTTAATGGTGAT 60.040 33.333 0.00 0.00 0.00 3.06
1677 2716 5.007234 TGCCAATAATTCAGAAACGATACGG 59.993 40.000 0.00 0.00 0.00 4.02
1777 2816 5.430886 TGTGCTTGATGATGTTGCTAGTAT 58.569 37.500 0.00 0.00 0.00 2.12
1840 2883 7.308589 CCTTTGATTAGACAGTTCGGTGAAAAT 60.309 37.037 0.00 0.00 0.00 1.82
1841 2884 8.610248 TTTGATTAGACAGTTCGGTGAAAATA 57.390 30.769 0.00 0.00 0.00 1.40
1842 2885 8.610248 TTGATTAGACAGTTCGGTGAAAATAA 57.390 30.769 0.00 0.00 0.00 1.40
1843 2886 8.786826 TGATTAGACAGTTCGGTGAAAATAAT 57.213 30.769 0.00 0.00 0.00 1.28
1957 3001 2.685897 CGTCCAGGTGAACCTTTTCAAA 59.314 45.455 0.00 0.00 46.09 2.69
2080 3124 2.093869 GGCATTAACCACGTGACCTAGA 60.094 50.000 19.30 0.00 0.00 2.43
2085 3129 5.571784 TTAACCACGTGACCTAGATAGTG 57.428 43.478 19.30 0.00 0.00 2.74
2090 3134 3.024547 ACGTGACCTAGATAGTGCATGT 58.975 45.455 0.00 0.00 0.00 3.21
2092 3136 4.643334 ACGTGACCTAGATAGTGCATGTTA 59.357 41.667 0.00 0.00 0.00 2.41
2185 3232 0.664761 CTATGTGCCCGATTTGCAGG 59.335 55.000 0.00 0.00 39.87 4.85
2201 3248 0.742281 CAGGCGACACTTCATCCAGG 60.742 60.000 0.00 0.00 0.00 4.45
2205 3252 1.903877 CGACACTTCATCCAGGGGCT 61.904 60.000 0.00 0.00 0.00 5.19
2208 3255 1.273838 ACACTTCATCCAGGGGCTCTA 60.274 52.381 0.00 0.00 0.00 2.43
2215 4500 3.052109 TCATCCAGGGGCTCTAGTCTTAA 60.052 47.826 0.00 0.00 0.00 1.85
2277 4562 5.048504 CCAATTGCTGCTTCTAGAAGTTTCA 60.049 40.000 28.72 20.82 40.45 2.69
2288 4573 9.103861 GCTTCTAGAAGTTTCATATATATGGGC 57.896 37.037 28.72 9.45 40.45 5.36
2289 4574 9.307121 CTTCTAGAAGTTTCATATATATGGGCG 57.693 37.037 22.20 0.00 32.99 6.13
2330 4863 1.116536 TCGTGGAGTAAGGTGTGCCA 61.117 55.000 0.00 0.00 37.19 4.92
2361 4894 1.861982 GGCCTGTAGGACTCCTGTTA 58.138 55.000 7.98 0.00 41.12 2.41
2390 4923 1.581912 GCATCATGCGTGTGCTTCG 60.582 57.895 19.70 1.98 43.34 3.79
2394 4927 0.041400 TCATGCGTGTGCTTCGTTTG 60.041 50.000 5.68 0.00 43.34 2.93
2406 4942 4.148174 GTGCTTCGTTTGGAATTTAAGTGC 59.852 41.667 0.00 0.00 33.26 4.40
2407 4943 4.202060 TGCTTCGTTTGGAATTTAAGTGCA 60.202 37.500 0.00 0.00 33.26 4.57
2414 4950 6.863126 CGTTTGGAATTTAAGTGCAGAAATCT 59.137 34.615 0.00 0.00 0.00 2.40
2415 4951 8.020819 CGTTTGGAATTTAAGTGCAGAAATCTA 58.979 33.333 0.00 0.00 0.00 1.98
2438 4974 6.429521 ACACAGTAGTTACCAACCACTTAT 57.570 37.500 0.00 0.00 30.84 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.423931 ACTTGAGCTGGTTTTTAGGGAAAAA 59.576 36.000 0.00 0.00 41.24 1.94
7 8 4.959839 ACTTGAGCTGGTTTTTAGGGAAAA 59.040 37.500 0.00 0.00 34.93 2.29
8 9 4.542697 ACTTGAGCTGGTTTTTAGGGAAA 58.457 39.130 0.00 0.00 0.00 3.13
11 12 5.501156 AGATACTTGAGCTGGTTTTTAGGG 58.499 41.667 0.00 0.00 0.00 3.53
158 250 7.665145 GGAGTACTAGGTAAGTCTCGGATTTAT 59.335 40.741 0.00 0.00 39.80 1.40
165 257 4.379652 GAGGGAGTACTAGGTAAGTCTCG 58.620 52.174 0.00 0.00 39.80 4.04
172 264 5.237935 TCCTATTGGAGGGAGTACTAGGTA 58.762 45.833 0.00 0.00 46.70 3.08
175 267 7.433537 TTTTTCCTATTGGAGGGAGTACTAG 57.566 40.000 0.00 0.00 46.70 2.57
256 348 7.881775 AAATGTCTCAACTTTGAACTAAGGT 57.118 32.000 0.00 0.00 36.64 3.50
375 470 7.041848 CCCGAGCAATCAAATTTCTTTTCTTTT 60.042 33.333 0.00 0.00 0.00 2.27
433 528 0.837272 ACCCGACATTACTGATGGGG 59.163 55.000 15.19 10.90 41.62 4.96
475 1491 2.857618 GAGCAGTCAGTGTTCGTCTAG 58.142 52.381 0.00 0.00 0.00 2.43
505 1521 5.220739 CCTCCTGTAGATTTGATCTTTTGCG 60.221 44.000 0.00 0.00 40.76 4.85
524 1540 2.249139 GCCAATCGGTAGATACCTCCT 58.751 52.381 7.42 0.00 44.25 3.69
797 1813 1.218316 GACACGTTAGGGGGAGCAG 59.782 63.158 0.00 0.00 0.00 4.24
909 1926 2.561037 CCCTTGGCAAACACCGGTC 61.561 63.158 2.59 0.00 0.00 4.79
918 1935 3.454719 TGATTCTTGATCCCTTGGCAA 57.545 42.857 0.00 0.00 33.60 4.52
960 1977 3.011257 ACACACTAATTACCCAGGCCAAT 59.989 43.478 5.01 0.00 0.00 3.16
969 1986 5.682943 TCAAGCAACACACACTAATTACC 57.317 39.130 0.00 0.00 0.00 2.85
1005 2027 2.512286 TCGACGTCGCCGGAGTAT 60.512 61.111 32.19 0.00 39.60 2.12
1164 2186 0.250513 GCTTCTCCTTGGACGTGGAT 59.749 55.000 0.00 0.00 0.00 3.41
1167 2189 1.738099 CCGCTTCTCCTTGGACGTG 60.738 63.158 0.00 0.00 0.00 4.49
1542 2566 7.042335 CGGAAACAAGAAGGACAGTATCTTAT 58.958 38.462 0.00 0.00 32.38 1.73
1543 2567 6.209986 TCGGAAACAAGAAGGACAGTATCTTA 59.790 38.462 0.00 0.00 32.38 2.10
1544 2568 5.011738 TCGGAAACAAGAAGGACAGTATCTT 59.988 40.000 0.00 0.00 33.83 2.40
1545 2569 4.527038 TCGGAAACAAGAAGGACAGTATCT 59.473 41.667 0.00 0.00 0.00 1.98
1546 2570 4.817517 TCGGAAACAAGAAGGACAGTATC 58.182 43.478 0.00 0.00 0.00 2.24
1547 2571 4.283722 ACTCGGAAACAAGAAGGACAGTAT 59.716 41.667 0.00 0.00 0.00 2.12
1646 2670 9.990360 TCGTTTCTGAATTATTGGCAGTATATA 57.010 29.630 0.00 0.00 0.00 0.86
1647 2671 8.902540 TCGTTTCTGAATTATTGGCAGTATAT 57.097 30.769 0.00 0.00 0.00 0.86
1648 2672 8.902540 ATCGTTTCTGAATTATTGGCAGTATA 57.097 30.769 0.00 0.00 0.00 1.47
1649 2673 7.807977 ATCGTTTCTGAATTATTGGCAGTAT 57.192 32.000 0.00 0.00 0.00 2.12
1654 2678 5.007332 ACCGTATCGTTTCTGAATTATTGGC 59.993 40.000 0.00 0.00 0.00 4.52
1677 2716 8.589629 CATCACTAGCTAAAATTTTGCATCAAC 58.410 33.333 13.76 0.00 0.00 3.18
1798 2837 6.712179 ATCAAAGGTGGTAGCTAGTACTAC 57.288 41.667 0.00 9.13 41.33 2.73
1799 2838 8.277197 TCTAATCAAAGGTGGTAGCTAGTACTA 58.723 37.037 1.89 1.89 0.00 1.82
1800 2839 7.068470 GTCTAATCAAAGGTGGTAGCTAGTACT 59.932 40.741 0.00 0.00 0.00 2.73
1804 2847 6.127310 ACTGTCTAATCAAAGGTGGTAGCTAG 60.127 42.308 0.00 0.00 0.00 3.42
1957 3001 3.390135 CATGAAACCACGTCACTAGTGT 58.610 45.455 21.99 0.30 37.88 3.55
2080 3124 1.581934 ATGCGCGTAACATGCACTAT 58.418 45.000 8.43 0.00 42.11 2.12
2085 3129 1.157870 AGGGTATGCGCGTAACATGC 61.158 55.000 25.17 8.99 0.00 4.06
2090 3134 3.802507 GCAAGGGTATGCGCGTAA 58.197 55.556 11.68 0.00 36.45 3.18
2165 3212 1.382522 CTGCAAATCGGGCACATAGT 58.617 50.000 0.00 0.00 36.11 2.12
2166 3213 0.664761 CCTGCAAATCGGGCACATAG 59.335 55.000 0.00 0.00 36.11 2.23
2167 3214 2.792500 CCTGCAAATCGGGCACATA 58.208 52.632 0.00 0.00 36.11 2.29
2168 3215 3.607163 CCTGCAAATCGGGCACAT 58.393 55.556 0.00 0.00 36.11 3.21
2185 3232 1.450312 CCCCTGGATGAAGTGTCGC 60.450 63.158 0.00 0.00 0.00 5.19
2201 3248 4.538746 AGTGTGTTTAAGACTAGAGCCC 57.461 45.455 0.00 0.00 28.62 5.19
2205 3252 6.880484 TGAACCAAGTGTGTTTAAGACTAGA 58.120 36.000 0.00 0.00 30.71 2.43
2208 3255 6.617879 GTTTGAACCAAGTGTGTTTAAGACT 58.382 36.000 0.00 0.00 32.70 3.24
2233 4518 2.866762 GGCTAGCAAAGATTCCTGTACG 59.133 50.000 18.24 0.00 0.00 3.67
2277 4562 1.553248 ACCACGCACGCCCATATATAT 59.447 47.619 0.00 0.00 0.00 0.86
2286 4571 3.276846 AAACTGACCACGCACGCC 61.277 61.111 0.00 0.00 0.00 5.68
2287 4572 1.841663 ATCAAACTGACCACGCACGC 61.842 55.000 0.00 0.00 0.00 5.34
2288 4573 1.424403 TATCAAACTGACCACGCACG 58.576 50.000 0.00 0.00 0.00 5.34
2289 4574 3.000041 TCATATCAAACTGACCACGCAC 59.000 45.455 0.00 0.00 0.00 5.34
2330 4863 1.404391 CTACAGGCCGATTCAGTACGT 59.596 52.381 0.00 0.00 0.00 3.57
2390 4923 9.129209 GTAGATTTCTGCACTTAAATTCCAAAC 57.871 33.333 0.00 0.00 0.00 2.93
2406 4942 7.331193 GGTTGGTAACTACTGTGTAGATTTCTG 59.669 40.741 11.17 0.00 42.34 3.02
2407 4943 7.015877 TGGTTGGTAACTACTGTGTAGATTTCT 59.984 37.037 11.17 0.00 42.34 2.52


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

AutoCloner maintained by Alex Coulton.