Multiple sequence alignment - TraesCS7B01G491800

Loading Multiple Alignment...

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 TraesCS7B01G491800 chr7B 100.000 2801 0 0 1 2801 744268348 744271148 0.000000e+00 5173.0
1 TraesCS7B01G491800 chr7B 97.522 2139 43 2 663 2801 743709152 743711280 0.000000e+00 3648.0
2 TraesCS7B01G491800 chr7B 90.101 2182 146 28 632 2801 744331188 744329065 0.000000e+00 2769.0
3 TraesCS7B01G491800 chr7B 86.469 1552 170 20 632 2157 744239195 744240732 0.000000e+00 1666.0
4 TraesCS7B01G491800 chr7B 83.689 1171 161 21 982 2134 744339396 744338238 0.000000e+00 1077.0
5 TraesCS7B01G491800 chr7B 97.441 469 7 3 178 641 743708479 743708947 0.000000e+00 795.0
6 TraesCS7B01G491800 chr7B 91.346 312 25 2 663 974 743999571 743999262 2.580000e-115 425.0
7 TraesCS7B01G491800 chr7B 82.068 474 48 18 1 466 744000258 743999814 1.230000e-98 370.0
8 TraesCS7B01G491800 chr7B 97.315 149 3 1 663 811 743709003 743709150 4.630000e-63 252.0
9 TraesCS7B01G491800 chr7B 96.269 134 2 1 178 308 744238605 744238738 1.690000e-52 217.0
10 TraesCS7B01G491800 chr7B 91.892 111 5 2 1 107 743708337 743708447 4.830000e-33 152.0
11 TraesCS7B01G491800 chr7B 91.892 111 5 2 1 107 744238463 744238573 4.830000e-33 152.0
12 TraesCS7B01G491800 chr7A 87.976 1996 156 39 632 2589 736008710 736006761 0.000000e+00 2279.0
13 TraesCS7B01G491800 chr7A 80.993 1289 214 21 999 2281 671427319 671426056 0.000000e+00 994.0
14 TraesCS7B01G491800 chr7A 88.235 119 8 5 1 117 736008936 736008822 1.350000e-28 137.0
15 TraesCS7B01G491800 chrUn 86.929 1446 108 30 1372 2801 330873722 330875102 0.000000e+00 1548.0
16 TraesCS7B01G491800 chrUn 88.081 990 77 11 1375 2349 219093783 219092820 0.000000e+00 1136.0
17 TraesCS7B01G491800 chrUn 86.395 441 24 13 2362 2801 409760664 409761069 1.530000e-122 449.0
18 TraesCS7B01G491800 chr3B 88.284 1340 91 25 1463 2801 778534317 778535591 0.000000e+00 1544.0
19 TraesCS7B01G491800 chr7D 89.860 1075 89 11 999 2057 632033222 632034292 0.000000e+00 1363.0
20 TraesCS7B01G491800 chr7D 85.241 1267 166 6 795 2045 632079474 632080735 0.000000e+00 1284.0
21 TraesCS7B01G491800 chr7D 82.609 1173 176 12 906 2054 555047227 555048395 0.000000e+00 1011.0
22 TraesCS7B01G491800 chr7D 84.197 386 35 16 1 373 632078723 632079095 4.440000e-93 351.0
23 TraesCS7B01G491800 chr7D 97.143 35 1 0 632 666 632079415 632079449 3.010000e-05 60.2


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 TraesCS7B01G491800 chr7B 744268348 744271148 2800 False 5173.000000 5173 100.000000 1 2801 1 chr7B.!!$F1 2800
1 TraesCS7B01G491800 chr7B 744329065 744331188 2123 True 2769.000000 2769 90.101000 632 2801 1 chr7B.!!$R1 2169
2 TraesCS7B01G491800 chr7B 743708337 743711280 2943 False 1211.750000 3648 96.042500 1 2801 4 chr7B.!!$F2 2800
3 TraesCS7B01G491800 chr7B 744338238 744339396 1158 True 1077.000000 1077 83.689000 982 2134 1 chr7B.!!$R2 1152
4 TraesCS7B01G491800 chr7B 744238463 744240732 2269 False 678.333333 1666 91.543333 1 2157 3 chr7B.!!$F3 2156
5 TraesCS7B01G491800 chr7B 743999262 744000258 996 True 397.500000 425 86.707000 1 974 2 chr7B.!!$R3 973
6 TraesCS7B01G491800 chr7A 736006761 736008936 2175 True 1208.000000 2279 88.105500 1 2589 2 chr7A.!!$R2 2588
7 TraesCS7B01G491800 chr7A 671426056 671427319 1263 True 994.000000 994 80.993000 999 2281 1 chr7A.!!$R1 1282
8 TraesCS7B01G491800 chrUn 330873722 330875102 1380 False 1548.000000 1548 86.929000 1372 2801 1 chrUn.!!$F1 1429
9 TraesCS7B01G491800 chrUn 219092820 219093783 963 True 1136.000000 1136 88.081000 1375 2349 1 chrUn.!!$R1 974
10 TraesCS7B01G491800 chr3B 778534317 778535591 1274 False 1544.000000 1544 88.284000 1463 2801 1 chr3B.!!$F1 1338
11 TraesCS7B01G491800 chr7D 632033222 632034292 1070 False 1363.000000 1363 89.860000 999 2057 1 chr7D.!!$F2 1058
12 TraesCS7B01G491800 chr7D 555047227 555048395 1168 False 1011.000000 1011 82.609000 906 2054 1 chr7D.!!$F1 1148
13 TraesCS7B01G491800 chr7D 632078723 632080735 2012 False 565.066667 1284 88.860333 1 2045 3 chr7D.!!$F3 2044

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
627 769 0.322975 TGCCCTCTTCTGTTCAGCTC 59.677 55.0 0.0 0.0 0.0 4.09 F
1176 1567 0.458025 GGAGGAACATCACCGACGAC 60.458 60.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1503 1927 1.019278 CGATCTTGTCCCCAACCACG 61.019 60.000 0.0 0.0 0.0 4.94 R
2148 2572 7.598493 CGATTGAAACCACACCTGATTAATTTT 59.402 33.333 0.0 0.0 0.0 1.82 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
129 135 4.423732 GTTCACTTTTGACAATGTGCACT 58.576 39.130 19.41 0.00 37.76 4.40
138 144 1.151221 AATGTGCACTGCTGTCCCA 59.849 52.632 19.41 0.00 0.00 4.37
166 178 8.848474 TTTTTATTTTCACTTTCCAACACCAA 57.152 26.923 0.00 0.00 0.00 3.67
168 180 9.454859 TTTTATTTTCACTTTCCAACACCAAAT 57.545 25.926 0.00 0.00 0.00 2.32
169 181 8.655651 TTATTTTCACTTTCCAACACCAAATC 57.344 30.769 0.00 0.00 0.00 2.17
170 182 5.667539 TTTCACTTTCCAACACCAAATCA 57.332 34.783 0.00 0.00 0.00 2.57
171 183 4.647424 TCACTTTCCAACACCAAATCAC 57.353 40.909 0.00 0.00 0.00 3.06
172 184 4.277476 TCACTTTCCAACACCAAATCACT 58.723 39.130 0.00 0.00 0.00 3.41
173 185 4.709397 TCACTTTCCAACACCAAATCACTT 59.291 37.500 0.00 0.00 0.00 3.16
174 186 4.805192 CACTTTCCAACACCAAATCACTTG 59.195 41.667 0.00 0.00 34.52 3.16
175 187 4.466015 ACTTTCCAACACCAAATCACTTGT 59.534 37.500 0.00 0.00 32.65 3.16
176 188 4.383850 TTCCAACACCAAATCACTTGTG 57.616 40.909 0.00 0.00 32.65 3.33
226 241 1.273495 TGAAGGAGCAGGAGGACATCT 60.273 52.381 0.00 0.00 0.00 2.90
548 684 4.183686 GCGTGCGCATGAGGCAAT 62.184 61.111 32.94 0.00 45.17 3.56
627 769 0.322975 TGCCCTCTTCTGTTCAGCTC 59.677 55.000 0.00 0.00 0.00 4.09
629 771 1.675415 GCCCTCTTCTGTTCAGCTCAG 60.675 57.143 0.00 0.00 0.00 3.35
630 772 1.675415 CCCTCTTCTGTTCAGCTCAGC 60.675 57.143 0.00 0.00 33.48 4.26
741 979 1.888018 CTGTGGCATTGCTTCCCAG 59.112 57.895 8.82 5.92 0.00 4.45
1144 1535 4.404640 TCTCGACCTTAAGAACTTCCTCA 58.595 43.478 3.36 0.00 0.00 3.86
1176 1567 0.458025 GGAGGAACATCACCGACGAC 60.458 60.000 0.00 0.00 0.00 4.34
1298 1689 1.833630 CTCCTCAGATGCAGGGTGTTA 59.166 52.381 0.00 0.00 0.00 2.41
1503 1927 2.183046 GAGCTCGACAGGTCAGGC 59.817 66.667 0.00 3.29 45.20 4.85
1663 2087 1.737008 GTCTTCAACGACGAGGCCC 60.737 63.158 0.00 0.00 0.00 5.80
1798 2222 1.290009 GCAAAGGCCACGCTTCAAT 59.710 52.632 5.01 0.00 0.00 2.57
2148 2572 6.899089 TCATAGAAATGTTAGGATGCTTCCA 58.101 36.000 19.98 4.32 38.17 3.53
2363 2806 5.655488 AGATGGATATATAGCTTCACGTGC 58.345 41.667 11.67 0.00 0.00 5.34
2745 3195 5.767168 AGGAGCAAGATAGGTAAATGCATTC 59.233 40.000 13.38 0.46 39.42 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
62 64 9.736023 AAATCTGCTTAACAAGTTTTAACTCTG 57.264 29.630 0.00 0.63 38.57 3.35
63 65 9.736023 CAAATCTGCTTAACAAGTTTTAACTCT 57.264 29.630 0.00 0.00 38.57 3.24
65 67 8.352752 GCAAATCTGCTTAACAAGTTTTAACT 57.647 30.769 0.00 0.00 45.74 2.24
159 171 4.644234 TCATGTCACAAGTGATTTGGTGTT 59.356 37.500 6.15 0.00 42.18 3.32
160 172 4.206375 TCATGTCACAAGTGATTTGGTGT 58.794 39.130 6.15 0.00 42.18 4.16
161 173 4.834357 TCATGTCACAAGTGATTTGGTG 57.166 40.909 6.15 2.46 42.18 4.17
162 174 5.535783 TCAATCATGTCACAAGTGATTTGGT 59.464 36.000 6.15 1.27 39.76 3.67
163 175 6.016213 TCAATCATGTCACAAGTGATTTGG 57.984 37.500 6.15 0.00 39.76 3.28
166 178 6.487668 TCAACTCAATCATGTCACAAGTGATT 59.512 34.615 6.15 1.37 41.78 2.57
168 180 5.367302 TCAACTCAATCATGTCACAAGTGA 58.633 37.500 0.00 0.00 37.24 3.41
169 181 5.678132 TCAACTCAATCATGTCACAAGTG 57.322 39.130 0.00 0.00 0.00 3.16
170 182 6.263842 ACATTCAACTCAATCATGTCACAAGT 59.736 34.615 0.00 0.00 0.00 3.16
171 183 6.675026 ACATTCAACTCAATCATGTCACAAG 58.325 36.000 0.00 0.00 0.00 3.16
172 184 6.294120 GGACATTCAACTCAATCATGTCACAA 60.294 38.462 11.58 0.00 43.72 3.33
173 185 5.181811 GGACATTCAACTCAATCATGTCACA 59.818 40.000 11.58 0.00 43.72 3.58
174 186 5.413833 AGGACATTCAACTCAATCATGTCAC 59.586 40.000 11.58 3.13 43.72 3.67
175 187 5.563592 AGGACATTCAACTCAATCATGTCA 58.436 37.500 11.58 0.00 43.72 3.58
176 188 5.065731 GGAGGACATTCAACTCAATCATGTC 59.934 44.000 0.00 0.00 42.00 3.06
226 241 1.697432 ACCAACCTTTGAGATGGACGA 59.303 47.619 0.00 0.00 36.75 4.20
486 552 2.135933 CCGGTTGACACTTCAAGACTC 58.864 52.381 0.00 0.00 42.60 3.36
627 769 1.080705 GGAGCAAGCAAAGCAGCTG 60.081 57.895 10.11 10.11 45.89 4.24
629 771 0.458025 GATGGAGCAAGCAAAGCAGC 60.458 55.000 0.00 0.00 33.32 5.25
630 772 0.179171 CGATGGAGCAAGCAAAGCAG 60.179 55.000 0.00 0.00 0.00 4.24
659 851 1.012841 CGGAGAGAAGCAAAGCATCC 58.987 55.000 0.00 0.00 0.00 3.51
741 979 1.349357 GAGCCTGGAGGGATTGGTATC 59.651 57.143 0.00 0.00 37.23 2.24
1125 1516 4.022242 TCAGTGAGGAAGTTCTTAAGGTCG 60.022 45.833 1.85 0.00 0.00 4.79
1144 1535 3.378512 TGTTCCTCCTATCAGCATCAGT 58.621 45.455 0.00 0.00 0.00 3.41
1176 1567 1.597742 CCACCCAGACTTTGACAGTG 58.402 55.000 0.00 0.00 35.01 3.66
1298 1689 4.834496 TCATGCAGAAAAGAAAGGGATTGT 59.166 37.500 0.00 0.00 0.00 2.71
1370 1761 1.316651 GATGGAATCAAGCCTCTGGC 58.683 55.000 0.00 0.00 46.46 4.85
1503 1927 1.019278 CGATCTTGTCCCCAACCACG 61.019 60.000 0.00 0.00 0.00 4.94
1663 2087 2.260844 TTGCTGAAGTCACCTTGGAG 57.739 50.000 0.00 0.00 0.00 3.86
1798 2222 1.149101 AAGGCTTCCTTGAGGGTTCA 58.851 50.000 0.00 0.00 42.96 3.18
2148 2572 7.598493 CGATTGAAACCACACCTGATTAATTTT 59.402 33.333 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.