Multiple sequence alignment - TraesCS7D01G230700

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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 TraesCS7D01G230700 chr7D 100.000 2933 0 0 1 2933 191797746 191794814 0.000000e+00 5417.0
1 TraesCS7D01G230700 chr7B 92.238 1649 56 26 508 2105 337025083 337023456 0.000000e+00 2270.0
2 TraesCS7D01G230700 chr7B 96.869 511 15 1 1 510 337025779 337025269 0.000000e+00 854.0
3 TraesCS7D01G230700 chr7B 88.718 195 13 3 2162 2347 337023325 337023131 2.270000e-56 230.0
4 TraesCS7D01G230700 chr7B 81.679 262 40 8 2346 2602 337023007 337022749 8.240000e-51 211.0
5 TraesCS7D01G230700 chr7B 82.036 167 18 10 2327 2490 260938398 260938241 6.600000e-27 132.0
6 TraesCS7D01G230700 chr7B 96.203 79 0 2 2789 2865 337022209 337022132 3.070000e-25 126.0
7 TraesCS7D01G230700 chr7B 82.812 128 11 5 2548 2675 337022681 337022565 1.440000e-18 104.0
8 TraesCS7D01G230700 chr7A 93.234 1271 37 15 865 2089 200510493 200509226 0.000000e+00 1825.0
9 TraesCS7D01G230700 chr7A 93.834 519 18 8 367 876 200511023 200510510 0.000000e+00 769.0
10 TraesCS7D01G230700 chr7A 94.135 341 6 1 1 341 200511348 200511022 9.380000e-140 507.0
11 TraesCS7D01G230700 chr7A 97.143 70 2 0 2864 2933 200508410 200508341 5.130000e-23 119.0
12 TraesCS7D01G230700 chr5B 84.146 164 18 4 2327 2490 712462366 712462211 5.060000e-33 152.0
13 TraesCS7D01G230700 chr5B 100.000 29 0 0 1492 1520 650338850 650338822 1.000000e-03 54.7
14 TraesCS7D01G230700 chrUn 82.927 164 20 5 2327 2490 127140184 127140029 1.100000e-29 141.0
15 TraesCS7D01G230700 chr3B 82.927 164 20 7 2327 2490 798557678 798557833 1.100000e-29 141.0
16 TraesCS7D01G230700 chr5A 82.635 167 20 6 2326 2490 369127668 369127509 3.940000e-29 139.0
17 TraesCS7D01G230700 chr5A 81.065 169 24 5 2323 2490 506546684 506546523 8.530000e-26 128.0
18 TraesCS7D01G230700 chr5A 97.059 34 1 0 1487 1520 645127447 645127414 1.140000e-04 58.4
19 TraesCS7D01G230700 chr2A 81.765 170 18 7 2325 2490 723065430 723065270 2.370000e-26 130.0
20 TraesCS7D01G230700 chr2A 89.583 48 4 1 2143 2190 41463236 41463282 3.160000e-05 60.2
21 TraesCS7D01G230700 chr2D 81.707 164 21 6 2327 2490 585383727 585383881 8.530000e-26 128.0
22 TraesCS7D01G230700 chr5D 95.238 42 2 0 2143 2184 461429769 461429728 1.890000e-07 67.6
23 TraesCS7D01G230700 chr1D 86.207 58 7 1 2142 2199 435509959 435510015 8.780000e-06 62.1
24 TraesCS7D01G230700 chr1D 86.207 58 7 1 2142 2199 435510845 435510901 8.780000e-06 62.1
25 TraesCS7D01G230700 chr1D 86.207 58 7 1 2142 2199 435513871 435513927 8.780000e-06 62.1
26 TraesCS7D01G230700 chr1D 86.207 58 7 1 2142 2199 435514872 435514928 8.780000e-06 62.1
27 TraesCS7D01G230700 chr1D 84.483 58 8 1 2142 2199 435518032 435518088 4.080000e-04 56.5
28 TraesCS7D01G230700 chr1D 83.607 61 8 2 2126 2184 462200194 462200254 4.080000e-04 56.5


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 TraesCS7D01G230700 chr7D 191794814 191797746 2932 True 5417.0 5417 100.000000 1 2933 1 chr7D.!!$R1 2932
1 TraesCS7D01G230700 chr7B 337022132 337025779 3647 True 632.5 2270 89.753167 1 2865 6 chr7B.!!$R2 2864
2 TraesCS7D01G230700 chr7A 200508341 200511348 3007 True 805.0 1825 94.586500 1 2933 4 chr7A.!!$R1 2932

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
434 435 0.659427 GGTTCCGCTAATTAACCGCC 59.341 55.0 0.00 0.0 33.85 6.13 F
777 972 1.226686 GCAGATATCGCAGCTGGTGG 61.227 60.0 17.12 0.0 41.17 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 1870 1.862827 ACGTACGACATCGATCGATCA 59.137 47.619 27.2 12.32 45.13 2.92 R
2617 3510 0.757935 GCCCCTGCATTCACCATGAT 60.758 55.000 0.0 0.00 34.31 2.45 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
22 23 0.675633 ATTTGGTGCAGGCAAGTCAC 59.324 50.000 0.00 0.00 0.00 3.67
138 139 4.746729 ACTGTATACGACGCACCAATAAA 58.253 39.130 0.00 0.00 0.00 1.40
434 435 0.659427 GGTTCCGCTAATTAACCGCC 59.341 55.000 0.00 0.00 33.85 6.13
435 436 1.371595 GTTCCGCTAATTAACCGCCA 58.628 50.000 0.90 0.00 0.00 5.69
608 798 1.401905 GAAGCAGCTAAAATCCACGGG 59.598 52.381 0.00 0.00 0.00 5.28
777 972 1.226686 GCAGATATCGCAGCTGGTGG 61.227 60.000 17.12 0.00 41.17 4.61
904 1143 3.625938 GCTTTGCTGCTTGATATACTGC 58.374 45.455 0.00 0.00 0.00 4.40
969 1209 4.056125 CACAGGCCGCGTCTGAGA 62.056 66.667 26.23 0.00 37.47 3.27
1590 1870 2.014128 GCCTTGTATACATGCCGTTGT 58.986 47.619 6.36 0.00 0.00 3.32
1601 1881 0.102300 TGCCGTTGTGATCGATCGAT 59.898 50.000 29.76 29.76 37.59 3.59
1860 2161 2.073101 GGTGGGATCCAGGGACTCC 61.073 68.421 15.23 2.15 34.60 3.85
2060 2378 3.365666 GGTCTGTTGATGCACTGACAATG 60.366 47.826 12.13 5.16 43.77 2.82
2105 2423 2.536066 TGCTTGCTTAGTACTCCCTCA 58.464 47.619 0.00 0.00 0.00 3.86
2106 2424 2.903784 TGCTTGCTTAGTACTCCCTCAA 59.096 45.455 0.00 0.00 0.00 3.02
2107 2425 3.055819 TGCTTGCTTAGTACTCCCTCAAG 60.056 47.826 16.37 16.37 34.32 3.02
2109 2427 4.499183 CTTGCTTAGTACTCCCTCAAGTG 58.501 47.826 0.00 0.00 0.00 3.16
2110 2428 3.507411 TGCTTAGTACTCCCTCAAGTGT 58.493 45.455 0.00 0.00 0.00 3.55
2111 2429 3.510360 TGCTTAGTACTCCCTCAAGTGTC 59.490 47.826 0.00 0.00 0.00 3.67
2115 2433 6.488769 TTAGTACTCCCTCAAGTGTCAAAA 57.511 37.500 0.00 0.00 0.00 2.44
2117 2435 5.123936 AGTACTCCCTCAAGTGTCAAAAAC 58.876 41.667 0.00 0.00 0.00 2.43
2118 2436 2.943033 ACTCCCTCAAGTGTCAAAAACG 59.057 45.455 0.00 0.00 0.00 3.60
2119 2437 1.673920 TCCCTCAAGTGTCAAAAACGC 59.326 47.619 0.00 0.00 38.74 4.84
2120 2438 1.403679 CCCTCAAGTGTCAAAAACGCA 59.596 47.619 0.00 0.00 41.03 5.24
2122 2440 3.490761 CCCTCAAGTGTCAAAAACGCATT 60.491 43.478 0.00 0.00 41.03 3.56
2124 2442 5.277825 CCTCAAGTGTCAAAAACGCATTTA 58.722 37.500 0.00 0.00 41.03 1.40
2126 2444 7.081349 CCTCAAGTGTCAAAAACGCATTTATA 58.919 34.615 0.00 0.00 41.03 0.98
2128 2446 9.128107 CTCAAGTGTCAAAAACGCATTTATATT 57.872 29.630 0.00 0.00 41.03 1.28
2140 2458 8.539770 AACGCATTTATATTATGAGACAGAGG 57.460 34.615 7.80 0.00 0.00 3.69
2141 2459 7.896811 ACGCATTTATATTATGAGACAGAGGA 58.103 34.615 7.80 0.00 0.00 3.71
2142 2460 8.535335 ACGCATTTATATTATGAGACAGAGGAT 58.465 33.333 7.80 0.00 0.00 3.24
2150 2468 7.904558 ATTATGAGACAGAGGATAGTGTCAA 57.095 36.000 5.35 0.00 44.70 3.18
2152 2470 6.611613 ATGAGACAGAGGATAGTGTCAAAA 57.388 37.500 5.35 0.00 44.70 2.44
2154 2472 6.223852 TGAGACAGAGGATAGTGTCAAAAAC 58.776 40.000 5.35 0.00 44.70 2.43
2155 2473 5.230942 AGACAGAGGATAGTGTCAAAAACG 58.769 41.667 5.35 0.00 44.70 3.60
2156 2474 3.746492 ACAGAGGATAGTGTCAAAAACGC 59.254 43.478 0.00 0.00 38.74 4.84
2160 2552 4.246458 AGGATAGTGTCAAAAACGCTCTC 58.754 43.478 0.00 0.00 45.69 3.20
2166 2558 8.942338 ATAGTGTCAAAAACGCTCTCATATTA 57.058 30.769 0.00 0.00 45.69 0.98
2167 2559 7.849804 AGTGTCAAAAACGCTCTCATATTAT 57.150 32.000 0.00 0.00 45.69 1.28
2170 2562 6.038161 TGTCAAAAACGCTCTCATATTATGGG 59.962 38.462 3.89 0.31 0.00 4.00
2178 2570 5.047731 CGCTCTCATATTATGGGACAGAAGA 60.048 44.000 1.94 0.00 45.00 2.87
2268 2661 7.462571 TCTAGACTTGTGTTCAGCTTGTATA 57.537 36.000 0.00 0.00 0.00 1.47
2269 2662 7.892609 TCTAGACTTGTGTTCAGCTTGTATAA 58.107 34.615 0.00 0.00 0.00 0.98
2302 2695 4.269123 ACGCATTTGAGCAATTGCAATATG 59.731 37.500 30.89 25.17 43.78 1.78
2303 2696 4.318475 CGCATTTGAGCAATTGCAATATGG 60.318 41.667 30.89 16.90 43.78 2.74
2304 2697 4.024387 GCATTTGAGCAATTGCAATATGGG 60.024 41.667 30.89 15.52 43.35 4.00
2306 2699 4.822685 TTGAGCAATTGCAATATGGGTT 57.177 36.364 30.89 7.98 45.16 4.11
2307 2700 5.929058 TTGAGCAATTGCAATATGGGTTA 57.071 34.783 30.89 5.41 45.16 2.85
2308 2701 5.518848 TGAGCAATTGCAATATGGGTTAG 57.481 39.130 30.89 0.00 45.16 2.34
2310 2703 4.289245 AGCAATTGCAATATGGGTTAGGT 58.711 39.130 30.89 3.18 45.16 3.08
2513 3093 5.869888 GTCCCTCTGTACAGAAATACTTGTG 59.130 44.000 25.14 10.86 36.94 3.33
2568 3148 8.401709 CAGCACTAGATATATCTATTTGAGCGA 58.598 37.037 23.58 6.02 38.60 4.93
2569 3149 9.130661 AGCACTAGATATATCTATTTGAGCGAT 57.869 33.333 23.58 8.32 38.60 4.58
2584 3283 5.592104 TGAGCGATAAGTATTTCCTGACA 57.408 39.130 0.00 0.00 0.00 3.58
2594 3293 9.875708 ATAAGTATTTCCTGACAGAGAGAGTAT 57.124 33.333 3.32 0.00 0.00 2.12
2690 3583 4.152402 GCTTCAAGATTTGTGAGCTCGTTA 59.848 41.667 9.64 0.00 37.67 3.18
2739 3632 6.017605 CACTAGGTCCATGCATGATAGTTTTC 60.018 42.308 28.31 8.15 0.00 2.29
2764 3659 3.451004 TTGCATGCATCACCCGCC 61.451 61.111 23.37 0.00 0.00 6.13
2785 3680 4.609301 CCCCATCTCCCATACTTTCAAAA 58.391 43.478 0.00 0.00 0.00 2.44
2786 3681 5.022787 CCCCATCTCCCATACTTTCAAAAA 58.977 41.667 0.00 0.00 0.00 1.94
2872 3857 5.439721 TGTTCAATCTACCCATCCATCTTG 58.560 41.667 0.00 0.00 0.00 3.02
2877 3862 3.736094 TCTACCCATCCATCTTGAGGTT 58.264 45.455 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.353376 CGGGCGTGTGCAACTTTG 60.353 61.111 0.00 0.00 45.35 2.77
138 139 5.065914 GTGTACCTGCATGTGGATCATTAT 58.934 41.667 12.69 0.00 34.09 1.28
434 435 1.018226 CAGAACGCTCCTCAGCCTTG 61.018 60.000 0.00 0.00 43.56 3.61
435 436 1.294780 CAGAACGCTCCTCAGCCTT 59.705 57.895 0.00 0.00 43.56 4.35
556 746 4.507916 TCGCGGGAGGAGGAGGAG 62.508 72.222 6.13 0.00 0.00 3.69
557 747 3.595428 TTTCGCGGGAGGAGGAGGA 62.595 63.158 6.13 0.00 0.00 3.71
889 1125 3.546815 GCAAACGGCAGTATATCAAGCAG 60.547 47.826 0.00 0.00 43.97 4.24
969 1209 0.472734 ACTTCACTCCTCAGCCCTGT 60.473 55.000 0.00 0.00 0.00 4.00
1227 1500 1.690985 CTCAGGGGTTCCTCCTCCC 60.691 68.421 0.00 0.00 42.67 4.30
1461 1734 2.755876 ATCTCCCTGACGAGCGCA 60.756 61.111 11.47 0.00 0.00 6.09
1590 1870 1.862827 ACGTACGACATCGATCGATCA 59.137 47.619 27.20 12.32 45.13 2.92
1601 1881 2.255316 CATGCATGTACACGTACGACA 58.745 47.619 24.41 16.44 38.85 4.35
1860 2161 4.025979 GGGTTTATCATGTAGAACGCTTCG 60.026 45.833 13.34 0.00 33.68 3.79
1987 2297 6.862209 ACATACACGGTTAACTTATTACCGA 58.138 36.000 18.49 0.00 45.77 4.69
2002 2312 5.371115 AACCAAGAATCAAACATACACGG 57.629 39.130 0.00 0.00 0.00 4.94
2060 2378 5.358298 AACCAAAATAAGCGAGTGAGAAC 57.642 39.130 0.00 0.00 0.00 3.01
2115 2433 8.367911 TCCTCTGTCTCATAATATAAATGCGTT 58.632 33.333 0.00 0.00 0.00 4.84
2117 2435 8.939201 ATCCTCTGTCTCATAATATAAATGCG 57.061 34.615 0.00 0.00 0.00 4.73
2124 2442 9.593565 TTGACACTATCCTCTGTCTCATAATAT 57.406 33.333 0.00 0.00 38.12 1.28
2126 2444 7.904558 TTGACACTATCCTCTGTCTCATAAT 57.095 36.000 0.00 0.00 38.12 1.28
2128 2446 7.718334 TTTTGACACTATCCTCTGTCTCATA 57.282 36.000 0.00 0.00 38.12 2.15
2129 2447 6.611613 TTTTGACACTATCCTCTGTCTCAT 57.388 37.500 0.00 0.00 38.12 2.90
2130 2448 6.223852 GTTTTTGACACTATCCTCTGTCTCA 58.776 40.000 0.00 0.00 38.12 3.27
2133 2451 4.143094 GCGTTTTTGACACTATCCTCTGTC 60.143 45.833 0.00 0.00 37.83 3.51
2134 2452 3.746492 GCGTTTTTGACACTATCCTCTGT 59.254 43.478 0.00 0.00 0.00 3.41
2135 2453 3.997021 AGCGTTTTTGACACTATCCTCTG 59.003 43.478 0.00 0.00 0.00 3.35
2136 2454 4.021016 AGAGCGTTTTTGACACTATCCTCT 60.021 41.667 0.00 0.00 0.00 3.69
2137 2455 4.246458 AGAGCGTTTTTGACACTATCCTC 58.754 43.478 0.00 0.00 0.00 3.71
2139 2457 3.994392 TGAGAGCGTTTTTGACACTATCC 59.006 43.478 0.00 0.00 29.67 2.59
2140 2458 5.786401 ATGAGAGCGTTTTTGACACTATC 57.214 39.130 0.00 0.00 31.06 2.08
2141 2459 7.849804 AATATGAGAGCGTTTTTGACACTAT 57.150 32.000 0.00 0.00 0.00 2.12
2142 2460 8.817100 CATAATATGAGAGCGTTTTTGACACTA 58.183 33.333 0.00 0.00 0.00 2.74
2143 2461 7.201644 CCATAATATGAGAGCGTTTTTGACACT 60.202 37.037 1.10 0.00 0.00 3.55
2144 2462 6.907212 CCATAATATGAGAGCGTTTTTGACAC 59.093 38.462 1.10 0.00 0.00 3.67
2146 2464 6.260050 TCCCATAATATGAGAGCGTTTTTGAC 59.740 38.462 1.10 0.00 0.00 3.18
2147 2465 6.260050 GTCCCATAATATGAGAGCGTTTTTGA 59.740 38.462 1.10 0.00 0.00 2.69
2150 2468 5.680619 TGTCCCATAATATGAGAGCGTTTT 58.319 37.500 1.10 0.00 0.00 2.43
2152 2470 4.588951 TCTGTCCCATAATATGAGAGCGTT 59.411 41.667 1.10 0.00 0.00 4.84
2154 2472 4.790765 TCTGTCCCATAATATGAGAGCG 57.209 45.455 1.10 0.00 0.00 5.03
2155 2473 6.352016 TCTTCTGTCCCATAATATGAGAGC 57.648 41.667 1.10 0.00 0.00 4.09
2156 2474 7.961351 ACTTCTTCTGTCCCATAATATGAGAG 58.039 38.462 1.10 0.00 0.00 3.20
2157 2475 7.921041 ACTTCTTCTGTCCCATAATATGAGA 57.079 36.000 1.10 0.00 0.00 3.27
2166 2558 6.821616 AAGATGATACTTCTTCTGTCCCAT 57.178 37.500 0.00 0.00 36.70 4.00
2167 2559 6.627087 AAAGATGATACTTCTTCTGTCCCA 57.373 37.500 0.00 0.00 36.70 4.37
2196 2588 3.016736 GCTTACCATACCAGTGCACAAT 58.983 45.455 21.04 6.17 0.00 2.71
2268 2661 3.987220 GCTCAAATGCGTTGGTGTTTATT 59.013 39.130 0.00 0.00 37.85 1.40
2269 2662 3.005261 TGCTCAAATGCGTTGGTGTTTAT 59.995 39.130 0.00 0.00 37.85 1.40
2381 2954 9.502091 TTCACTTATTTTGCTCTGTATGTAGTT 57.498 29.630 0.00 0.00 0.00 2.24
2434 3007 7.503521 TTTCAATGCAGACTACATACAAACA 57.496 32.000 0.00 0.00 0.00 2.83
2435 3008 8.454106 AGATTTCAATGCAGACTACATACAAAC 58.546 33.333 0.00 0.00 0.00 2.93
2438 3011 7.559486 AGAGATTTCAATGCAGACTACATACA 58.441 34.615 0.00 0.00 0.00 2.29
2439 3012 9.534565 TTAGAGATTTCAATGCAGACTACATAC 57.465 33.333 0.00 0.00 0.00 2.39
2466 3039 8.854117 GGACTCCGTTCCTAAATATAAGTCTTA 58.146 37.037 0.00 0.00 33.03 2.10
2491 3071 5.178797 CCACAAGTATTTCTGTACAGAGGG 58.821 45.833 23.97 12.61 38.88 4.30
2496 3076 8.630054 ATTTAAGCCACAAGTATTTCTGTACA 57.370 30.769 0.00 0.00 0.00 2.90
2542 3122 8.401709 TCGCTCAAATAGATATATCTAGTGCTG 58.598 37.037 23.38 17.62 42.20 4.41
2558 3138 8.201464 TGTCAGGAAATACTTATCGCTCAAATA 58.799 33.333 0.00 0.00 0.00 1.40
2568 3148 9.875708 ATACTCTCTCTGTCAGGAAATACTTAT 57.124 33.333 0.00 0.00 0.00 1.73
2610 3503 2.824936 TGCATTCACCATGATTTTCCGT 59.175 40.909 0.00 0.00 34.31 4.69
2617 3510 0.757935 GCCCCTGCATTCACCATGAT 60.758 55.000 0.00 0.00 34.31 2.45
2678 3571 7.014326 AGGACTATTCATATTAACGAGCTCACA 59.986 37.037 15.40 0.00 0.00 3.58
2791 3686 5.669477 ACACAAATATGCACACAACCTTTT 58.331 33.333 0.00 0.00 0.00 2.27
2792 3687 5.275067 ACACAAATATGCACACAACCTTT 57.725 34.783 0.00 0.00 0.00 3.11
2793 3688 4.935352 ACACAAATATGCACACAACCTT 57.065 36.364 0.00 0.00 0.00 3.50
2794 3689 4.340666 TGAACACAAATATGCACACAACCT 59.659 37.500 0.00 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.