Multiple sequence alignment - TraesCS2B01G003100

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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 TraesCS2B01G003100 chr2B 100.000 3286 0 0 1 3286 1763773 1767058 0.000000e+00 6069.0
1 TraesCS2B01G003100 chr2B 99.094 2429 20 2 859 3286 1749467 1751894 0.000000e+00 4362.0
2 TraesCS2B01G003100 chr2B 86.555 1071 125 11 1109 2171 1786811 1787870 0.000000e+00 1162.0
3 TraesCS2B01G003100 chr2B 98.487 595 9 0 1 595 490740065 490740659 0.000000e+00 1050.0
4 TraesCS2B01G003100 chr2B 86.054 294 30 5 2851 3133 43019156 43019449 4.120000e-79 305.0
5 TraesCS2B01G003100 chr2B 89.474 152 15 1 3135 3286 194382908 194382758 1.200000e-44 191.0
6 TraesCS2B01G003100 chr2B 100.000 31 0 0 1109 1139 1749690 1749720 1.270000e-04 58.4
7 TraesCS2B01G003100 chr2B 100.000 31 0 0 1082 1112 1749717 1749747 1.270000e-04 58.4
8 TraesCS2B01G003100 chr2B 100.000 31 0 0 1109 1139 1764854 1764884 1.270000e-04 58.4
9 TraesCS2B01G003100 chr2B 100.000 31 0 0 1082 1112 1764881 1764911 1.270000e-04 58.4
10 TraesCS2B01G003100 chr2D 86.490 1547 121 32 864 2381 7204068 7202581 0.000000e+00 1618.0
11 TraesCS2B01G003100 chr2D 84.058 345 41 9 2531 2862 7202590 7202247 1.470000e-83 320.0
12 TraesCS2B01G003100 chr2D 90.833 240 21 1 1542 1781 7206830 7206592 1.470000e-83 320.0
13 TraesCS2B01G003100 chr2D 75.123 611 126 19 1469 2060 37225014 37224411 2.510000e-66 263.0
14 TraesCS2B01G003100 chr2D 83.737 289 29 9 2851 3128 508094383 508094664 1.170000e-64 257.0
15 TraesCS2B01G003100 chr2D 85.020 247 26 4 2898 3133 95895531 95895777 1.180000e-59 241.0
16 TraesCS2B01G003100 chr2D 94.268 157 8 1 3130 3286 7202264 7202109 4.240000e-59 239.0
17 TraesCS2B01G003100 chr2D 73.191 843 143 53 1285 2060 3119290 3120116 9.170000e-56 228.0
18 TraesCS2B01G003100 chr2D 87.640 178 22 0 1357 1534 7213121 7212944 1.190000e-49 207.0
19 TraesCS2B01G003100 chr2D 79.600 250 25 4 1102 1349 7215365 7215140 4.390000e-34 156.0
20 TraesCS2B01G003100 chr3B 97.216 862 20 4 1 858 51118198 51119059 0.000000e+00 1456.0
21 TraesCS2B01G003100 chr3B 81.839 870 132 23 4 859 70109803 70108946 0.000000e+00 708.0
22 TraesCS2B01G003100 chr3B 96.310 271 7 3 593 862 94127239 94127507 3.010000e-120 442.0
23 TraesCS2B01G003100 chr3B 88.312 154 18 0 3133 3286 521607961 521608114 5.600000e-43 185.0
24 TraesCS2B01G003100 chr3B 87.662 154 19 0 3133 3286 521474720 521474873 2.610000e-41 180.0
25 TraesCS2B01G003100 chr1B 92.791 860 31 6 1 858 453750137 453749307 0.000000e+00 1216.0
26 TraesCS2B01G003100 chr1B 95.357 280 9 4 593 871 439795818 439796094 3.010000e-120 442.0
27 TraesCS2B01G003100 chr1B 84.431 167 26 0 1274 1440 606311105 606310939 7.290000e-37 165.0
28 TraesCS2B01G003100 chr1B 83.234 167 28 0 1274 1440 606306476 606306310 1.580000e-33 154.0
29 TraesCS2B01G003100 chr4B 91.309 863 67 4 1 858 584152404 584151545 0.000000e+00 1171.0
30 TraesCS2B01G003100 chr4B 88.095 294 23 8 2851 3133 273957596 273957888 4.060000e-89 339.0
31 TraesCS2B01G003100 chr4B 83.553 152 23 2 1290 1440 667604305 667604455 1.230000e-29 141.0
32 TraesCS2B01G003100 chr4B 78.082 146 30 2 1290 1434 605517524 605517668 1.260000e-14 91.6
33 TraesCS2B01G003100 chr1A 90.636 865 67 11 1 858 554310685 554309828 0.000000e+00 1136.0
34 TraesCS2B01G003100 chr1A 85.374 294 32 5 2851 3133 510397016 510396723 8.920000e-76 294.0
35 TraesCS2B01G003100 chr1A 82.036 167 30 0 1274 1440 540413911 540414077 3.420000e-30 143.0
36 TraesCS2B01G003100 chr1A 80.240 167 23 8 1274 1440 540401985 540401829 2.070000e-22 117.0
37 TraesCS2B01G003100 chrUn 98.319 595 10 0 1 595 84009061 84009655 0.000000e+00 1044.0
38 TraesCS2B01G003100 chr6A 95.216 648 27 4 1 644 1278427 1277780 0.000000e+00 1022.0
39 TraesCS2B01G003100 chr6A 85.091 275 30 5 2851 3114 454639830 454640104 1.500000e-68 270.0
40 TraesCS2B01G003100 chr2A 94.962 655 28 5 1 651 772795266 772794613 0.000000e+00 1022.0
41 TraesCS2B01G003100 chr2A 86.577 298 29 6 2851 3137 74783289 74782992 5.290000e-83 318.0
42 TraesCS2B01G003100 chr2A 83.402 241 28 4 2904 3133 448151692 448151931 2.570000e-51 213.0
43 TraesCS2B01G003100 chr4A 96.654 269 5 4 593 859 630472882 630473148 8.370000e-121 444.0
44 TraesCS2B01G003100 chr4A 96.324 272 6 4 593 863 718571289 718571557 8.370000e-121 444.0
45 TraesCS2B01G003100 chr4A 84.615 195 26 1 2851 3041 577086517 577086323 1.200000e-44 191.0
46 TraesCS2B01G003100 chr3A 96.310 271 6 4 593 861 28064525 28064793 3.010000e-120 442.0
47 TraesCS2B01G003100 chr3A 84.667 300 35 7 2845 3133 19356772 19357071 4.150000e-74 289.0
48 TraesCS2B01G003100 chr5B 95.652 276 7 5 593 866 500030251 500030523 3.890000e-119 438.0
49 TraesCS2B01G003100 chr5B 84.437 302 34 7 2851 3139 421543348 421543047 5.370000e-73 285.0
50 TraesCS2B01G003100 chr5B 71.335 764 169 39 1291 2026 537506318 537507059 5.680000e-33 152.0
51 TraesCS2B01G003100 chr1D 90.400 250 24 0 2845 3094 413588721 413588970 2.440000e-86 329.0
52 TraesCS2B01G003100 chr1D 83.333 168 28 0 1273 1440 445222323 445222490 4.390000e-34 156.0
53 TraesCS2B01G003100 chr1D 83.234 167 28 0 1274 1440 445189426 445189260 1.580000e-33 154.0
54 TraesCS2B01G003100 chr1D 88.696 115 11 2 2851 2965 377914164 377914052 4.420000e-29 139.0
55 TraesCS2B01G003100 chr1D 82.500 160 20 6 1274 1429 445188058 445187903 2.060000e-27 134.0
56 TraesCS2B01G003100 chr1D 77.215 158 28 6 1290 1443 12336993 12336840 5.840000e-13 86.1
57 TraesCS2B01G003100 chr1D 77.241 145 32 1 1290 1434 12067011 12067154 2.100000e-12 84.2
58 TraesCS2B01G003100 chr7B 86.897 290 38 0 2848 3137 703307201 703307490 3.160000e-85 326.0
59 TraesCS2B01G003100 chr7B 73.918 855 150 45 1285 2085 732200858 732200023 3.230000e-70 276.0
60 TraesCS2B01G003100 chr7B 73.684 855 152 45 1285 2085 732158987 732158152 6.990000e-67 265.0
61 TraesCS2B01G003100 chr7B 89.103 156 13 4 3133 3286 734907320 734907167 1.200000e-44 191.0
62 TraesCS2B01G003100 chr7D 86.170 282 39 0 2852 3133 571861606 571861325 4.120000e-79 305.0
63 TraesCS2B01G003100 chr7A 84.354 294 35 5 2844 3126 125276093 125275800 8.980000e-71 278.0
64 TraesCS2B01G003100 chr7A 88.535 157 14 4 3132 3286 558105332 558105486 1.560000e-43 187.0
65 TraesCS2B01G003100 chr5A 83.000 300 39 5 2851 3138 473399318 473399019 9.040000e-66 261.0
66 TraesCS2B01G003100 chr3D 84.328 268 25 8 2869 3136 396674480 396674230 2.530000e-61 246.0
67 TraesCS2B01G003100 chr3D 88.750 80 9 0 1289 1368 497015053 497014974 7.500000e-17 99.0
68 TraesCS2B01G003100 chr3D 87.654 81 8 2 1289 1368 497231572 497231493 3.490000e-15 93.5
69 TraesCS2B01G003100 chr5D 71.482 803 169 45 1291 2057 441327327 441328105 3.390000e-35 159.0
70 TraesCS2B01G003100 chr6D 82.278 79 14 0 1274 1352 14721842 14721764 5.880000e-08 69.4


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 TraesCS2B01G003100 chr2B 1763773 1767058 3285 False 2061.933333 6069 100.00000 1 3286 3 chr2B.!!$F5 3285
1 TraesCS2B01G003100 chr2B 1749467 1751894 2427 False 1492.933333 4362 99.69800 859 3286 3 chr2B.!!$F4 2427
2 TraesCS2B01G003100 chr2B 1786811 1787870 1059 False 1162.000000 1162 86.55500 1109 2171 1 chr2B.!!$F1 1062
3 TraesCS2B01G003100 chr2B 490740065 490740659 594 False 1050.000000 1050 98.48700 1 595 1 chr2B.!!$F3 594
4 TraesCS2B01G003100 chr2D 7202109 7206830 4721 True 624.250000 1618 88.91225 864 3286 4 chr2D.!!$R2 2422
5 TraesCS2B01G003100 chr2D 37224411 37225014 603 True 263.000000 263 75.12300 1469 2060 1 chr2D.!!$R1 591
6 TraesCS2B01G003100 chr2D 3119290 3120116 826 False 228.000000 228 73.19100 1285 2060 1 chr2D.!!$F1 775
7 TraesCS2B01G003100 chr3B 51118198 51119059 861 False 1456.000000 1456 97.21600 1 858 1 chr3B.!!$F1 857
8 TraesCS2B01G003100 chr3B 70108946 70109803 857 True 708.000000 708 81.83900 4 859 1 chr3B.!!$R1 855
9 TraesCS2B01G003100 chr1B 453749307 453750137 830 True 1216.000000 1216 92.79100 1 858 1 chr1B.!!$R1 857
10 TraesCS2B01G003100 chr4B 584151545 584152404 859 True 1171.000000 1171 91.30900 1 858 1 chr4B.!!$R1 857
11 TraesCS2B01G003100 chr1A 554309828 554310685 857 True 1136.000000 1136 90.63600 1 858 1 chr1A.!!$R3 857
12 TraesCS2B01G003100 chrUn 84009061 84009655 594 False 1044.000000 1044 98.31900 1 595 1 chrUn.!!$F1 594
13 TraesCS2B01G003100 chr6A 1277780 1278427 647 True 1022.000000 1022 95.21600 1 644 1 chr6A.!!$R1 643
14 TraesCS2B01G003100 chr2A 772794613 772795266 653 True 1022.000000 1022 94.96200 1 651 1 chr2A.!!$R2 650
15 TraesCS2B01G003100 chr7B 732200023 732200858 835 True 276.000000 276 73.91800 1285 2085 1 chr7B.!!$R2 800
16 TraesCS2B01G003100 chr7B 732158152 732158987 835 True 265.000000 265 73.68400 1285 2085 1 chr7B.!!$R1 800

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
492 502 1.204941 GTAGTGTGACTCGGGCATTCT 59.795 52.381 0.00 0.0 0.00 2.40 F
1163 3064 1.001641 GGGCTCAGGCTGACATGTT 60.002 57.895 14.43 0.0 38.73 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 3417 2.142292 GAGCAGGGGATGTGGGTTGT 62.142 60.000 0.0 0.0 0.0 3.32 R
2762 4761 6.479990 CGCAGATCAGAAATACAACATAGGAA 59.520 38.462 0.0 0.0 0.0 3.36 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
368 378 3.792053 GAGATCGGCGCGGGTGATT 62.792 63.158 15.48 0.00 0.00 2.57
444 454 2.596346 TGAGGAAAATGAAGCTTGGCA 58.404 42.857 2.10 0.00 0.00 4.92
492 502 1.204941 GTAGTGTGACTCGGGCATTCT 59.795 52.381 0.00 0.00 0.00 2.40
597 613 4.821589 CCTCTTGCGCGAGGGACC 62.822 72.222 26.78 0.00 45.53 4.46
601 617 2.203224 TTGCGCGAGGGACCAAAA 60.203 55.556 12.10 0.00 0.00 2.44
603 619 3.431725 GCGCGAGGGACCAAAAGG 61.432 66.667 12.10 0.00 0.00 3.11
1163 3064 1.001641 GGGCTCAGGCTGACATGTT 60.002 57.895 14.43 0.00 38.73 2.71
1287 3189 3.036429 ATCCTCGAGCCAAGGCCAC 62.036 63.158 6.99 1.65 43.17 5.01
1488 3417 3.393970 CTTCTCCCCGGCTGCTCA 61.394 66.667 0.00 0.00 0.00 4.26
1853 3817 3.212682 TGCCCGTTTTCTTGCGCA 61.213 55.556 5.66 5.66 0.00 6.09
2370 4357 0.549469 ACGACACCCCTCCAGTTTTT 59.451 50.000 0.00 0.00 0.00 1.94
2591 4578 6.893583 AGCTATGTCACATCTAAGTTTCCAT 58.106 36.000 0.00 0.00 0.00 3.41
2913 4912 5.680619 ACCACTTAGACTGTTTTGATGACA 58.319 37.500 0.00 0.00 0.00 3.58
3098 5097 1.993370 GCTGACGTGGACACTTGTATC 59.007 52.381 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
368 378 4.351938 CCGTCTTCACCGCCGTCA 62.352 66.667 0.00 0.00 0.00 4.35
461 471 4.615961 CGAGTCACACTACTTAAGGTTTCG 59.384 45.833 7.53 1.62 0.00 3.46
492 502 2.535012 TGCACACAAGGTGTTCGATA 57.465 45.000 0.00 0.00 45.08 2.92
601 617 1.203351 ACCGGGACTAAAGGTAACCCT 60.203 52.381 6.32 0.00 45.63 4.34
603 619 2.302733 TGAACCGGGACTAAAGGTAACC 59.697 50.000 6.32 0.00 37.26 2.85
605 621 4.323715 GGAATGAACCGGGACTAAAGGTAA 60.324 45.833 6.32 0.00 37.26 2.85
613 634 1.131303 TGGTGGAATGAACCGGGACT 61.131 55.000 6.32 0.00 40.86 3.85
1163 3064 0.382158 GAGCGACGACATGATCTCCA 59.618 55.000 0.00 0.00 0.00 3.86
1488 3417 2.142292 GAGCAGGGGATGTGGGTTGT 62.142 60.000 0.00 0.00 0.00 3.32
1853 3817 3.288381 ACCCCTGCCTCCTCCTCT 61.288 66.667 0.00 0.00 0.00 3.69
1889 3853 5.537300 TGAGTTTCTCAAAGCTACAGAGT 57.463 39.130 9.10 0.00 37.57 3.24
2142 4129 8.206126 ACCTTATTTTCTTTGGGATTGTCAAT 57.794 30.769 0.00 0.00 0.00 2.57
2762 4761 6.479990 CGCAGATCAGAAATACAACATAGGAA 59.520 38.462 0.00 0.00 0.00 3.36
2913 4912 8.489489 TCTCTCTCTTCTTTTATTATGTGCCAT 58.511 33.333 0.00 0.00 0.00 4.40
3098 5097 7.169476 TGCAACAGTTTGTATGTTCAATCATTG 59.831 33.333 0.00 0.00 38.80 2.82


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

AutoCloner maintained by Alex Coulton.