Multiple sequence alignment - TraesCS7A01G459800

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 TraesCS7A01G459800 chr7A 100.000 2390 0 0 1 2390 655406992 655404603 0.000000e+00 4414
1 TraesCS7A01G459800 chr7A 96.995 832 24 1 1 831 694382164 694381333 0.000000e+00 1397
2 TraesCS7A01G459800 chr7A 96.882 834 20 3 1 834 698701984 698702811 0.000000e+00 1391
3 TraesCS7A01G459800 chr7A 95.819 861 34 1 832 1692 655419395 655418537 0.000000e+00 1389
4 TraesCS7A01G459800 chr7A 95.037 403 12 3 1696 2091 655412926 655412525 5.610000e-176 627
5 TraesCS7A01G459800 chr7D 94.242 1042 32 9 832 1854 568031922 568030890 0.000000e+00 1567
6 TraesCS7A01G459800 chr7D 95.736 258 10 1 1834 2091 568030879 568030623 4.750000e-112 414
7 TraesCS7A01G459800 chr7D 87.075 147 18 1 1088 1233 568235535 568235389 5.290000e-37 165
8 TraesCS7A01G459800 chr7D 96.875 64 2 0 2327 2390 568030342 568030279 9.030000e-20 108
9 TraesCS7A01G459800 chr7B 92.871 1066 52 13 832 1891 622687750 622686703 0.000000e+00 1526
10 TraesCS7A01G459800 chr7B 92.898 1056 51 13 842 1891 622674980 622673943 0.000000e+00 1513
11 TraesCS7A01G459800 chr7B 93.224 915 40 11 1189 2091 622765467 622764563 0.000000e+00 1327
12 TraesCS7A01G459800 chr7B 92.329 365 28 0 832 1196 622787985 622787621 9.790000e-144 520
13 TraesCS7A01G459800 chr7B 87.179 156 19 1 1079 1233 623270640 623270485 2.440000e-40 176
14 TraesCS7A01G459800 chr7B 87.755 147 17 1 1088 1233 623372736 623372590 1.140000e-38 171
15 TraesCS7A01G459800 chr7B 87.586 145 17 1 1088 1231 623537062 623536918 1.470000e-37 167
16 TraesCS7A01G459800 chr7B 82.162 185 18 9 2221 2390 622764186 622764002 6.890000e-31 145
17 TraesCS7A01G459800 chr5A 97.222 828 22 1 1 828 552656020 552656846 0.000000e+00 1400
18 TraesCS7A01G459800 chr5A 96.890 836 23 1 1 833 639225015 639225850 0.000000e+00 1397
19 TraesCS7A01G459800 chr5A 97.101 828 20 1 1 828 680124739 680125562 0.000000e+00 1393
20 TraesCS7A01G459800 chr3A 97.112 831 22 1 1 831 696336330 696335502 0.000000e+00 1400
21 TraesCS7A01G459800 chr2A 97.101 828 21 2 1 828 702435128 702435952 0.000000e+00 1393
22 TraesCS7A01G459800 chr1A 96.886 835 20 2 1 832 585702876 585703707 0.000000e+00 1393
23 TraesCS7A01G459800 chr6A 96.992 831 20 2 1 828 606660526 606661354 0.000000e+00 1391


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 TraesCS7A01G459800 chr7A 655404603 655406992 2389 True 4414.000000 4414 100.000000 1 2390 1 chr7A.!!$R1 2389
1 TraesCS7A01G459800 chr7A 694381333 694382164 831 True 1397.000000 1397 96.995000 1 831 1 chr7A.!!$R4 830
2 TraesCS7A01G459800 chr7A 698701984 698702811 827 False 1391.000000 1391 96.882000 1 834 1 chr7A.!!$F1 833
3 TraesCS7A01G459800 chr7A 655418537 655419395 858 True 1389.000000 1389 95.819000 832 1692 1 chr7A.!!$R3 860
4 TraesCS7A01G459800 chr7D 568030279 568031922 1643 True 696.333333 1567 95.617667 832 2390 3 chr7D.!!$R2 1558
5 TraesCS7A01G459800 chr7B 622686703 622687750 1047 True 1526.000000 1526 92.871000 832 1891 1 chr7B.!!$R2 1059
6 TraesCS7A01G459800 chr7B 622673943 622674980 1037 True 1513.000000 1513 92.898000 842 1891 1 chr7B.!!$R1 1049
7 TraesCS7A01G459800 chr7B 622764002 622765467 1465 True 736.000000 1327 87.693000 1189 2390 2 chr7B.!!$R7 1201
8 TraesCS7A01G459800 chr5A 552656020 552656846 826 False 1400.000000 1400 97.222000 1 828 1 chr5A.!!$F1 827
9 TraesCS7A01G459800 chr5A 639225015 639225850 835 False 1397.000000 1397 96.890000 1 833 1 chr5A.!!$F2 832
10 TraesCS7A01G459800 chr5A 680124739 680125562 823 False 1393.000000 1393 97.101000 1 828 1 chr5A.!!$F3 827
11 TraesCS7A01G459800 chr3A 696335502 696336330 828 True 1400.000000 1400 97.112000 1 831 1 chr3A.!!$R1 830
12 TraesCS7A01G459800 chr2A 702435128 702435952 824 False 1393.000000 1393 97.101000 1 828 1 chr2A.!!$F1 827
13 TraesCS7A01G459800 chr1A 585702876 585703707 831 False 1393.000000 1393 96.886000 1 832 1 chr1A.!!$F1 831
14 TraesCS7A01G459800 chr6A 606660526 606661354 828 False 1391.000000 1391 96.992000 1 828 1 chr6A.!!$F1 827

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
982 991 0.035317 ACAAGAAGATCACTGCGCCA 59.965 50.0 4.18 0.0 0.0 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2288 2616 0.77681 AATGGTGGACATGGGTCACA 59.223 50.0 14.27 1.94 46.17 3.58 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
25 26 4.174411 TCGAGACTAAAGGTGACATGTG 57.826 45.455 1.15 0.00 0.00 3.21
345 346 5.580691 TGGTGATGATTATGTTGAACTCGAC 59.419 40.000 0.00 0.00 0.00 4.20
481 482 6.207213 ACGACTACGATGATTTTTAGCTAGG 58.793 40.000 0.00 0.00 42.66 3.02
643 650 7.605410 AACATTTAGTATCGGTTGGTGTTAG 57.395 36.000 0.00 0.00 0.00 2.34
828 837 2.418368 ATTGCCCGATTCTGCACTAA 57.582 45.000 0.00 0.00 37.18 2.24
917 926 5.106157 CCAGTGTTAAGGCAATAGGAGTTTG 60.106 44.000 0.00 0.00 0.00 2.93
938 947 3.327757 TGATGCTTCCTAGTCTTTGTGGT 59.672 43.478 0.00 0.00 0.00 4.16
959 968 3.706594 GTCCTCTCTTCATATCCACACCA 59.293 47.826 0.00 0.00 0.00 4.17
968 977 3.054508 TCATATCCACACCATGCACAAGA 60.055 43.478 0.00 0.00 0.00 3.02
982 991 0.035317 ACAAGAAGATCACTGCGCCA 59.965 50.000 4.18 0.00 0.00 5.69
1035 1044 3.696548 GGAGGAACATTGGGAAGAATGTC 59.303 47.826 0.00 0.00 44.15 3.06
1065 1074 1.153823 CCTTCTACACGGGAGCGTG 60.154 63.158 0.00 0.00 44.56 5.34
1109 1118 1.545841 ACAGACATCCACTGCGTCTA 58.454 50.000 0.00 0.00 37.92 2.59
1255 1266 5.868454 TCTATGCATATACACATGTGCCTT 58.132 37.500 25.68 12.73 45.81 4.35
1366 1377 3.196039 TCCTGTTATAACGCTACCTGCAA 59.804 43.478 10.92 0.00 43.06 4.08
1490 1510 7.887996 TGTGTTCTTTATTTGGATGCAAATC 57.112 32.000 26.04 12.83 36.35 2.17
1560 1583 5.474532 TGCTTGTAAGATTCAAAGACATGCT 59.525 36.000 11.05 0.00 40.15 3.79
1693 1719 2.700371 GGAAATGGATTTCATGACCCCC 59.300 50.000 12.90 0.00 46.03 5.40
1850 1887 4.700213 CACGAGAAACAGGGTTGGAAATAT 59.300 41.667 0.00 0.00 0.00 1.28
1917 1985 0.810648 TGAGATTGCCAAATCGCACC 59.189 50.000 1.44 0.00 44.54 5.01
1995 2063 1.002087 GGAGATGTCAAAGGTCCGTGT 59.998 52.381 0.00 0.00 0.00 4.49
2011 2079 1.266718 CGTGTGCCAACTACTGCAATT 59.733 47.619 0.00 0.00 39.57 2.32
2139 2322 9.667107 AAAAGATTATCCTTTATCAACTCGACA 57.333 29.630 0.00 0.00 35.50 4.35
2140 2323 9.838339 AAAGATTATCCTTTATCAACTCGACAT 57.162 29.630 0.00 0.00 34.85 3.06
2185 2488 3.726291 CCCCCAATGCGGTAAAATAAG 57.274 47.619 0.00 0.00 0.00 1.73
2190 2493 4.340950 CCCAATGCGGTAAAATAAGGATGT 59.659 41.667 0.00 0.00 0.00 3.06
2200 2503 6.831868 GGTAAAATAAGGATGTTCTTAGGGCA 59.168 38.462 0.00 0.00 33.36 5.36
2216 2519 2.090267 AGGGCAATAGATGGAGAGGACT 60.090 50.000 0.00 0.00 0.00 3.85
2219 2522 4.020662 GGGCAATAGATGGAGAGGACTTAG 60.021 50.000 0.00 0.00 0.00 2.18
2223 2551 5.941146 ATAGATGGAGAGGACTTAGGACT 57.059 43.478 0.00 0.00 0.00 3.85
2241 2569 8.937207 TTAGGACTATATAAAGAGGAGGTGAC 57.063 38.462 0.00 0.00 0.00 3.67
2284 2612 1.134670 CCGATGTTGAAGGAGGAGGAC 60.135 57.143 0.00 0.00 0.00 3.85
2285 2613 1.134670 CGATGTTGAAGGAGGAGGACC 60.135 57.143 0.00 0.00 0.00 4.46
2286 2614 1.210722 GATGTTGAAGGAGGAGGACCC 59.789 57.143 0.00 0.00 36.73 4.46
2287 2615 0.104672 TGTTGAAGGAGGAGGACCCA 60.105 55.000 0.00 0.00 37.41 4.51
2288 2616 1.290134 GTTGAAGGAGGAGGACCCAT 58.710 55.000 0.00 0.00 37.41 4.00
2289 2617 1.065126 GTTGAAGGAGGAGGACCCATG 60.065 57.143 0.00 0.00 37.41 3.66
2290 2618 0.119155 TGAAGGAGGAGGACCCATGT 59.881 55.000 0.00 0.00 37.41 3.21
2291 2619 0.543749 GAAGGAGGAGGACCCATGTG 59.456 60.000 0.00 0.00 37.41 3.21
2292 2620 0.119155 AAGGAGGAGGACCCATGTGA 59.881 55.000 0.00 0.00 37.41 3.58
2293 2621 0.618968 AGGAGGAGGACCCATGTGAC 60.619 60.000 0.00 0.00 37.41 3.67
2323 2651 5.103129 TCCACCATTATGGATTCATTTCCCT 60.103 40.000 19.23 0.00 44.14 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 2.032680 TGGCCGTAAGCTAACCATTC 57.967 50.000 0.00 0.00 43.05 2.67
345 346 7.689812 CACTTTGTAACAGAAGCAAAGATATCG 59.310 37.037 19.01 3.18 46.98 2.92
643 650 0.035725 AGCCCTTTAGTACCGGTTGC 60.036 55.000 15.04 6.57 0.00 4.17
828 837 4.463539 TGCAATAATTCAGCACCACTTCAT 59.536 37.500 0.00 0.00 32.55 2.57
917 926 3.935828 GACCACAAAGACTAGGAAGCATC 59.064 47.826 0.00 0.00 0.00 3.91
938 947 3.994317 TGGTGTGGATATGAAGAGAGGA 58.006 45.455 0.00 0.00 0.00 3.71
959 968 1.736126 CGCAGTGATCTTCTTGTGCAT 59.264 47.619 0.00 0.00 0.00 3.96
968 977 2.244117 ATCCGTGGCGCAGTGATCTT 62.244 55.000 10.83 0.00 0.00 2.40
982 991 5.396436 CCCTCATCACCTTACTTTTATCCGT 60.396 44.000 0.00 0.00 0.00 4.69
1065 1074 1.463674 CCCTTATCACCTGGCAACAC 58.536 55.000 0.00 0.00 46.17 3.32
1109 1118 7.201794 CCAGTTCATGAGCTGTGAATTTATCAT 60.202 37.037 30.29 0.00 40.97 2.45
1490 1510 6.408869 AGTTCATGGCCATTTTCCTTTTATG 58.591 36.000 17.92 1.16 0.00 1.90
1560 1583 2.173758 TTGCGGTGGAATGCGGACTA 62.174 55.000 0.00 0.00 0.00 2.59
1639 1664 9.114952 TGATGTACTCAAACATAACTTGTCAAA 57.885 29.630 0.00 0.00 40.17 2.69
1850 1887 5.935945 TCAGGACCTTGTTATTGAAGAACA 58.064 37.500 0.63 0.63 35.03 3.18
1917 1985 3.798337 GGCTTTCCAAATCAATATGCACG 59.202 43.478 0.00 0.00 0.00 5.34
1995 2063 6.338214 TGAATTTAATTGCAGTAGTTGGCA 57.662 33.333 0.00 0.00 38.46 4.92
2075 2143 6.729690 TTTCATTCACAGGACCAAAAAGAT 57.270 33.333 0.00 0.00 0.00 2.40
2136 2319 4.511826 GGGGTTGAGTTCAATCGATATGTC 59.488 45.833 0.00 0.00 37.83 3.06
2138 2321 3.815401 GGGGGTTGAGTTCAATCGATATG 59.185 47.826 0.00 0.00 37.83 1.78
2139 2322 4.086706 GGGGGTTGAGTTCAATCGATAT 57.913 45.455 0.00 0.00 37.83 1.63
2140 2323 3.553828 GGGGGTTGAGTTCAATCGATA 57.446 47.619 0.00 0.00 37.83 2.92
2142 2325 3.948735 GGGGGTTGAGTTCAATCGA 57.051 52.632 0.00 0.00 37.83 3.59
2166 2469 3.292460 TCCTTATTTTACCGCATTGGGG 58.708 45.455 17.57 17.57 44.64 4.96
2167 2470 4.340950 ACATCCTTATTTTACCGCATTGGG 59.659 41.667 0.00 0.00 44.64 4.12
2168 2471 5.514274 ACATCCTTATTTTACCGCATTGG 57.486 39.130 0.00 0.00 46.41 3.16
2169 2472 6.795399 AGAACATCCTTATTTTACCGCATTG 58.205 36.000 0.00 0.00 0.00 2.82
2170 2473 7.404671 AAGAACATCCTTATTTTACCGCATT 57.595 32.000 0.00 0.00 0.00 3.56
2171 2474 7.228706 CCTAAGAACATCCTTATTTTACCGCAT 59.771 37.037 0.00 0.00 0.00 4.73
2172 2475 6.540914 CCTAAGAACATCCTTATTTTACCGCA 59.459 38.462 0.00 0.00 0.00 5.69
2185 2488 5.006386 CCATCTATTGCCCTAAGAACATCC 58.994 45.833 0.00 0.00 0.00 3.51
2190 2493 4.594920 CCTCTCCATCTATTGCCCTAAGAA 59.405 45.833 0.00 0.00 0.00 2.52
2200 2503 6.288096 AGTCCTAAGTCCTCTCCATCTATT 57.712 41.667 0.00 0.00 0.00 1.73
2216 2519 8.734763 AGTCACCTCCTCTTTATATAGTCCTAA 58.265 37.037 0.00 0.00 0.00 2.69
2219 2522 7.005296 TGAGTCACCTCCTCTTTATATAGTCC 58.995 42.308 0.00 0.00 36.86 3.85
2223 2551 8.783660 ACATTGAGTCACCTCCTCTTTATATA 57.216 34.615 0.00 0.00 36.86 0.86
2287 2615 1.002069 ATGGTGGACATGGGTCACAT 58.998 50.000 14.27 3.91 46.17 3.21
2288 2616 0.776810 AATGGTGGACATGGGTCACA 59.223 50.000 14.27 1.94 46.17 3.58
2289 2617 2.799126 TAATGGTGGACATGGGTCAC 57.201 50.000 0.00 2.25 46.17 3.67
2290 2618 2.091939 CCATAATGGTGGACATGGGTCA 60.092 50.000 0.00 0.00 42.02 4.02
2291 2619 2.174639 TCCATAATGGTGGACATGGGTC 59.825 50.000 0.00 0.00 43.20 4.46
2292 2620 2.213310 TCCATAATGGTGGACATGGGT 58.787 47.619 0.00 0.00 43.20 4.51
2302 2630 5.149976 CCAGGGAAATGAATCCATAATGGT 58.850 41.667 0.00 0.00 41.55 3.55
2323 2651 2.203480 GTGCAGGTTCCCAAGCCA 60.203 61.111 0.00 0.00 0.00 4.75
2362 2714 1.453155 CGCTGCAAACTAGGGAATGT 58.547 50.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.