Multiple sequence alignment - TraesCS7D01G415900

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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 TraesCS7D01G415900 chr7D 100.000 3715 0 0 1 3715 534699018 534702732 0.000000e+00 6861.0
1 TraesCS7D01G415900 chr7D 85.567 485 60 6 298 782 236008912 236008438 1.990000e-137 499.0
2 TraesCS7D01G415900 chr2D 94.922 1477 50 8 2252 3715 623513069 623511605 0.000000e+00 2289.0
3 TraesCS7D01G415900 chr2D 94.267 1221 50 7 901 2113 623514423 623513215 0.000000e+00 1849.0
4 TraesCS7D01G415900 chr2D 87.557 659 55 12 2783 3423 623505905 623505256 0.000000e+00 737.0
5 TraesCS7D01G415900 chr2D 88.563 341 31 6 2459 2794 623506291 623505954 1.240000e-109 407.0
6 TraesCS7D01G415900 chr2D 91.892 185 11 3 3531 3712 623753659 623753842 4.760000e-64 255.0
7 TraesCS7D01G415900 chr2D 95.000 120 6 0 775 894 623514731 623514612 4.900000e-44 189.0
8 TraesCS7D01G415900 chr2D 76.261 337 53 11 1492 1825 623353520 623353832 1.790000e-33 154.0
9 TraesCS7D01G415900 chr2D 82.653 98 15 2 2171 2267 623513265 623513169 6.610000e-13 86.1
10 TraesCS7D01G415900 chr2B 95.393 1411 50 4 2206 3602 765548390 765546981 0.000000e+00 2231.0
11 TraesCS7D01G415900 chr2B 92.474 1249 56 8 873 2083 765549621 765548373 0.000000e+00 1751.0
12 TraesCS7D01G415900 chr2B 87.370 673 66 14 2513 3182 765542072 765541416 0.000000e+00 754.0
13 TraesCS7D01G415900 chr2B 86.331 417 43 8 3303 3715 765541420 765541014 3.410000e-120 442.0
14 TraesCS7D01G415900 chr2B 80.165 242 36 8 48 288 61101294 61101524 1.770000e-38 171.0
15 TraesCS7D01G415900 chr2B 73.611 432 85 17 988 1411 765543344 765542934 5.000000e-29 139.0
16 TraesCS7D01G415900 chr2B 96.667 60 2 0 3656 3715 765546982 765546923 2.360000e-17 100.0
17 TraesCS7D01G415900 chr2B 88.750 80 4 3 1487 1563 765542932 765542855 3.950000e-15 93.5
18 TraesCS7D01G415900 chr3A 94.865 779 27 5 1 769 251815939 251816714 0.000000e+00 1205.0
19 TraesCS7D01G415900 chr1A 91.913 779 45 11 2 765 559724994 559725769 0.000000e+00 1074.0
20 TraesCS7D01G415900 chr1A 89.791 813 48 17 1 793 483952566 483951769 0.000000e+00 1009.0
21 TraesCS7D01G415900 chr5A 92.021 752 38 7 35 769 540944132 540943386 0.000000e+00 1037.0
22 TraesCS7D01G415900 chr5A 75.263 190 35 9 2815 2996 595035798 595035983 3.080000e-11 80.5
23 TraesCS7D01G415900 chr1B 88.701 770 55 16 1 744 661129306 661128543 0.000000e+00 911.0
24 TraesCS7D01G415900 chr7B 89.979 469 43 4 299 767 352134530 352134066 1.480000e-168 603.0
25 TraesCS7D01G415900 chr7B 86.258 473 55 7 299 769 297213616 297214080 4.280000e-139 505.0
26 TraesCS7D01G415900 chr7B 86.726 339 30 6 1 330 352134889 352134557 2.730000e-96 363.0
27 TraesCS7D01G415900 chr5D 86.780 469 53 5 302 769 219539679 219540139 7.110000e-142 514.0
28 TraesCS7D01G415900 chr5D 76.064 188 37 6 2815 2996 475568504 475568689 1.420000e-14 91.6
29 TraesCS7D01G415900 chr2A 76.261 337 50 14 1492 1825 754454342 754454651 6.430000e-33 152.0
30 TraesCS7D01G415900 chr2A 91.071 112 10 0 1734 1845 754716563 754716452 6.430000e-33 152.0
31 TraesCS7D01G415900 chr2A 89.744 117 11 1 2773 2889 754715377 754715262 8.310000e-32 148.0
32 TraesCS7D01G415900 chr2A 80.000 120 21 1 988 1107 754716709 754716593 6.610000e-13 86.1
33 TraesCS7D01G415900 chr6B 78.926 242 30 15 48 288 488874044 488873823 1.080000e-30 145.0
34 TraesCS7D01G415900 chr7A 80.667 150 22 7 118 265 100077856 100077712 3.920000e-20 110.0
35 TraesCS7D01G415900 chr5B 76.064 188 37 6 2815 2996 582973647 582973832 1.420000e-14 91.6


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 TraesCS7D01G415900 chr7D 534699018 534702732 3714 False 6861.000000 6861 100.000000 1 3715 1 chr7D.!!$F1 3714
1 TraesCS7D01G415900 chr2D 623511605 623514731 3126 True 1103.275000 2289 91.710500 775 3715 4 chr2D.!!$R2 2940
2 TraesCS7D01G415900 chr2D 623505256 623506291 1035 True 572.000000 737 88.060000 2459 3423 2 chr2D.!!$R1 964
3 TraesCS7D01G415900 chr2B 765541014 765549621 8607 True 787.214286 2231 88.656571 873 3715 7 chr2B.!!$R1 2842
4 TraesCS7D01G415900 chr3A 251815939 251816714 775 False 1205.000000 1205 94.865000 1 769 1 chr3A.!!$F1 768
5 TraesCS7D01G415900 chr1A 559724994 559725769 775 False 1074.000000 1074 91.913000 2 765 1 chr1A.!!$F1 763
6 TraesCS7D01G415900 chr1A 483951769 483952566 797 True 1009.000000 1009 89.791000 1 793 1 chr1A.!!$R1 792
7 TraesCS7D01G415900 chr5A 540943386 540944132 746 True 1037.000000 1037 92.021000 35 769 1 chr5A.!!$R1 734
8 TraesCS7D01G415900 chr1B 661128543 661129306 763 True 911.000000 911 88.701000 1 744 1 chr1B.!!$R1 743
9 TraesCS7D01G415900 chr7B 352134066 352134889 823 True 483.000000 603 88.352500 1 767 2 chr7B.!!$R1 766

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
23 24 0.901580 GGGAGGGACGACACCAGTTA 60.902 60.000 0.00 0.00 0.00 2.24 F
990 1279 1.001764 TAGTCGTCTTCCTCCGGCA 60.002 57.895 0.00 0.00 0.00 5.69 F
1262 1553 0.035881 TCTCCGACGTGTGTACCTCT 59.964 55.000 0.00 0.00 0.00 3.69 F
1423 1734 0.109153 AACCTGCAGCAGATGTGTCA 59.891 50.000 24.90 0.00 32.44 3.58 F
2175 2504 0.021981 CGCGCGCGTATGTATGTATG 59.978 55.000 42.49 12.54 34.35 2.39 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1242 1533 0.447011 GAGGTACACACGTCGGAGAG 59.553 60.000 0.00 0.00 36.95 3.20 R
1832 2161 0.652592 GAGCGGTGAACATTCATCCG 59.347 55.000 21.28 21.28 45.70 4.18 R
2133 2462 0.652592 GCACACACACACAGAGACAC 59.347 55.000 0.00 0.00 0.00 3.67 R
2447 2893 1.490490 TGGACAGAAGGTTGCAGACTT 59.510 47.619 4.83 4.83 0.00 3.01 R
3529 4059 1.875813 CGTCATCTGAGTCGCTGCC 60.876 63.158 0.00 0.00 0.00 4.85 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
23 24 0.901580 GGGAGGGACGACACCAGTTA 60.902 60.000 0.00 0.00 0.00 2.24
29 30 3.700038 AGGGACGACACCAGTTATCTTAG 59.300 47.826 0.00 0.00 0.00 2.18
208 227 9.941991 GTTCATGAATTTTCAATACAATGTTCG 57.058 29.630 12.12 0.00 41.13 3.95
226 247 9.649024 CAATGTTCGCAAAAACAGAAAATAATT 57.351 25.926 3.19 0.00 42.09 1.40
608 695 1.144969 CGAAGCCGCAAACTGAACTA 58.855 50.000 0.00 0.00 0.00 2.24
771 863 2.228822 CACGGGCATTTTTGCTAGTCTT 59.771 45.455 0.00 0.00 34.73 3.01
773 865 2.749621 CGGGCATTTTTGCTAGTCTTCT 59.250 45.455 0.00 0.00 34.73 2.85
805 897 7.102346 ACAAAGATCGAGTGATGAGAAGAAAT 58.898 34.615 0.00 0.00 34.09 2.17
818 910 6.961359 TGAGAAGAAATAAAATCGAGCGAA 57.039 33.333 0.00 0.00 0.00 4.70
870 962 2.044551 GCCTCAAGAAGGGCCTGG 60.045 66.667 6.92 3.36 46.32 4.45
881 973 4.803426 GGCCTGGCTCGTGTCTCG 62.803 72.222 19.68 0.00 41.41 4.04
990 1279 1.001764 TAGTCGTCTTCCTCCGGCA 60.002 57.895 0.00 0.00 0.00 5.69
1120 1411 2.970640 GGGAACTATCACCCGAGGTATT 59.029 50.000 0.00 0.00 36.56 1.89
1132 1423 2.352388 CGAGGTATTTCTCCGCCAAAA 58.648 47.619 0.00 0.00 0.00 2.44
1209 1500 2.029666 AGCATCTACATCGCCCGC 59.970 61.111 0.00 0.00 0.00 6.13
1258 1549 1.505353 CCCTCTCCGACGTGTGTAC 59.495 63.158 0.00 0.00 0.00 2.90
1259 1550 1.505353 CCTCTCCGACGTGTGTACC 59.495 63.158 0.00 0.00 0.00 3.34
1260 1551 0.959372 CCTCTCCGACGTGTGTACCT 60.959 60.000 0.00 0.00 0.00 3.08
1261 1552 0.447011 CTCTCCGACGTGTGTACCTC 59.553 60.000 0.00 0.00 0.00 3.85
1262 1553 0.035881 TCTCCGACGTGTGTACCTCT 59.964 55.000 0.00 0.00 0.00 3.69
1263 1554 0.447011 CTCCGACGTGTGTACCTCTC 59.553 60.000 0.00 0.00 0.00 3.20
1423 1734 0.109153 AACCTGCAGCAGATGTGTCA 59.891 50.000 24.90 0.00 32.44 3.58
1561 1890 4.349365 AGGAGAAATCGTCTTCCTCTTCT 58.651 43.478 0.00 0.00 36.41 2.85
1562 1891 4.775253 AGGAGAAATCGTCTTCCTCTTCTT 59.225 41.667 0.00 0.00 36.41 2.52
1563 1892 5.105513 AGGAGAAATCGTCTTCCTCTTCTTC 60.106 44.000 0.00 0.00 36.41 2.87
1591 1920 3.023949 GCAGCCGGATCAGGACACT 62.024 63.158 16.86 0.09 0.00 3.55
1694 2023 4.324267 GGGTTTCGGATATTACATCAGGG 58.676 47.826 0.00 0.00 0.00 4.45
1729 2058 5.123227 GGATCTTTCCACACATATCCGAAA 58.877 41.667 0.00 0.00 42.12 3.46
1799 2128 4.438148 TCGCTATTTTCATGAACATCGGA 58.562 39.130 7.89 3.23 0.00 4.55
1832 2161 7.106239 TCTGTAAATCTCCTCAACTCAATTCC 58.894 38.462 0.00 0.00 0.00 3.01
1846 2175 4.396166 ACTCAATTCCGGATGAATGTTCAC 59.604 41.667 4.15 0.00 42.97 3.18
1856 2185 3.678056 TGAATGTTCACCGCTCTTACT 57.322 42.857 0.00 0.00 31.01 2.24
1932 2261 4.952071 TCAAGCTGGATTCCTCTGATAG 57.048 45.455 3.95 0.00 0.00 2.08
1936 2265 2.371510 GCTGGATTCCTCTGATAGCCTT 59.628 50.000 3.95 0.00 0.00 4.35
1946 2275 6.349300 TCCTCTGATAGCCTTACAATTTGAC 58.651 40.000 2.79 0.00 0.00 3.18
2018 2347 4.274602 TCGATGGCACCAAAAGTTAGTA 57.725 40.909 0.00 0.00 0.00 1.82
2101 2430 6.959671 TGTATGTGTGTATGTGTGTATGTG 57.040 37.500 0.00 0.00 0.00 3.21
2106 2435 6.459923 TGTGTGTATGTGTGTATGTGTGTAT 58.540 36.000 0.00 0.00 0.00 2.29
2107 2436 6.367422 TGTGTGTATGTGTGTATGTGTGTATG 59.633 38.462 0.00 0.00 0.00 2.39
2108 2437 6.367695 GTGTGTATGTGTGTATGTGTGTATGT 59.632 38.462 0.00 0.00 0.00 2.29
2109 2438 7.542824 GTGTGTATGTGTGTATGTGTGTATGTA 59.457 37.037 0.00 0.00 0.00 2.29
2110 2439 8.254508 TGTGTATGTGTGTATGTGTGTATGTAT 58.745 33.333 0.00 0.00 0.00 2.29
2111 2440 8.539674 GTGTATGTGTGTATGTGTGTATGTATG 58.460 37.037 0.00 0.00 0.00 2.39
2112 2441 8.254508 TGTATGTGTGTATGTGTGTATGTATGT 58.745 33.333 0.00 0.00 0.00 2.29
2113 2442 6.959671 TGTGTGTATGTGTGTATGTATGTG 57.040 37.500 0.00 0.00 0.00 3.21
2114 2443 6.459923 TGTGTGTATGTGTGTATGTATGTGT 58.540 36.000 0.00 0.00 0.00 3.72
2115 2444 6.367422 TGTGTGTATGTGTGTATGTATGTGTG 59.633 38.462 0.00 0.00 0.00 3.82
2116 2445 6.367695 GTGTGTATGTGTGTATGTATGTGTGT 59.632 38.462 0.00 0.00 0.00 3.72
2117 2446 7.542824 GTGTGTATGTGTGTATGTATGTGTGTA 59.457 37.037 0.00 0.00 0.00 2.90
2118 2447 8.254508 TGTGTATGTGTGTATGTATGTGTGTAT 58.745 33.333 0.00 0.00 0.00 2.29
2119 2448 8.539674 GTGTATGTGTGTATGTATGTGTGTATG 58.460 37.037 0.00 0.00 0.00 2.39
2120 2449 8.254508 TGTATGTGTGTATGTATGTGTGTATGT 58.745 33.333 0.00 0.00 0.00 2.29
2121 2450 9.738832 GTATGTGTGTATGTATGTGTGTATGTA 57.261 33.333 0.00 0.00 0.00 2.29
2123 2452 8.641499 TGTGTGTATGTATGTGTGTATGTATG 57.359 34.615 0.00 0.00 0.00 2.39
2124 2453 8.254508 TGTGTGTATGTATGTGTGTATGTATGT 58.745 33.333 0.00 0.00 0.00 2.29
2125 2454 8.539674 GTGTGTATGTATGTGTGTATGTATGTG 58.460 37.037 0.00 0.00 0.00 3.21
2126 2455 8.254508 TGTGTATGTATGTGTGTATGTATGTGT 58.745 33.333 0.00 0.00 0.00 3.72
2127 2456 8.539674 GTGTATGTATGTGTGTATGTATGTGTG 58.460 37.037 0.00 0.00 0.00 3.82
2128 2457 8.254508 TGTATGTATGTGTGTATGTATGTGTGT 58.745 33.333 0.00 0.00 0.00 3.72
2129 2458 6.959671 TGTATGTGTGTATGTATGTGTGTG 57.040 37.500 0.00 0.00 0.00 3.82
2130 2459 6.459923 TGTATGTGTGTATGTATGTGTGTGT 58.540 36.000 0.00 0.00 0.00 3.72
2131 2460 5.861222 ATGTGTGTATGTATGTGTGTGTG 57.139 39.130 0.00 0.00 0.00 3.82
2132 2461 4.698575 TGTGTGTATGTATGTGTGTGTGT 58.301 39.130 0.00 0.00 0.00 3.72
2133 2462 4.509600 TGTGTGTATGTATGTGTGTGTGTG 59.490 41.667 0.00 0.00 0.00 3.82
2134 2463 4.509970 GTGTGTATGTATGTGTGTGTGTGT 59.490 41.667 0.00 0.00 0.00 3.72
2135 2464 4.509600 TGTGTATGTATGTGTGTGTGTGTG 59.490 41.667 0.00 0.00 0.00 3.82
2136 2465 4.509970 GTGTATGTATGTGTGTGTGTGTGT 59.490 41.667 0.00 0.00 0.00 3.72
2137 2466 4.747605 TGTATGTATGTGTGTGTGTGTGTC 59.252 41.667 0.00 0.00 0.00 3.67
2138 2467 3.535280 TGTATGTGTGTGTGTGTGTCT 57.465 42.857 0.00 0.00 0.00 3.41
2139 2468 3.453424 TGTATGTGTGTGTGTGTGTCTC 58.547 45.455 0.00 0.00 0.00 3.36
2140 2469 2.988010 ATGTGTGTGTGTGTGTCTCT 57.012 45.000 0.00 0.00 0.00 3.10
2141 2470 2.008752 TGTGTGTGTGTGTGTCTCTG 57.991 50.000 0.00 0.00 0.00 3.35
2142 2471 1.275010 TGTGTGTGTGTGTGTCTCTGT 59.725 47.619 0.00 0.00 0.00 3.41
2143 2472 1.660607 GTGTGTGTGTGTGTCTCTGTG 59.339 52.381 0.00 0.00 0.00 3.66
2144 2473 1.275010 TGTGTGTGTGTGTCTCTGTGT 59.725 47.619 0.00 0.00 0.00 3.72
2145 2474 1.660607 GTGTGTGTGTGTCTCTGTGTG 59.339 52.381 0.00 0.00 0.00 3.82
2146 2475 1.275010 TGTGTGTGTGTCTCTGTGTGT 59.725 47.619 0.00 0.00 0.00 3.72
2147 2476 1.660607 GTGTGTGTGTCTCTGTGTGTG 59.339 52.381 0.00 0.00 0.00 3.82
2148 2477 1.275010 TGTGTGTGTCTCTGTGTGTGT 59.725 47.619 0.00 0.00 0.00 3.72
2149 2478 1.660607 GTGTGTGTCTCTGTGTGTGTG 59.339 52.381 0.00 0.00 0.00 3.82
2150 2479 1.275010 TGTGTGTCTCTGTGTGTGTGT 59.725 47.619 0.00 0.00 0.00 3.72
2151 2480 1.660607 GTGTGTCTCTGTGTGTGTGTG 59.339 52.381 0.00 0.00 0.00 3.82
2152 2481 0.652592 GTGTCTCTGTGTGTGTGTGC 59.347 55.000 0.00 0.00 0.00 4.57
2153 2482 0.805711 TGTCTCTGTGTGTGTGTGCG 60.806 55.000 0.00 0.00 0.00 5.34
2154 2483 1.882625 TCTCTGTGTGTGTGTGCGC 60.883 57.895 0.00 0.00 0.00 6.09
2155 2484 3.214306 CTCTGTGTGTGTGTGCGCG 62.214 63.158 0.00 0.00 0.00 6.86
2156 2485 4.943591 CTGTGTGTGTGTGCGCGC 62.944 66.667 27.26 27.26 36.27 6.86
2173 2502 3.818044 CGCGCGCGTATGTATGTA 58.182 55.556 42.49 0.00 34.35 2.29
2174 2503 2.345900 CGCGCGCGTATGTATGTAT 58.654 52.632 42.49 0.00 34.35 2.29
2175 2504 0.021981 CGCGCGCGTATGTATGTATG 59.978 55.000 42.49 12.54 34.35 2.39
2176 2505 1.057636 GCGCGCGTATGTATGTATGT 58.942 50.000 32.35 0.00 0.00 2.29
2177 2506 2.244251 GCGCGCGTATGTATGTATGTA 58.756 47.619 32.35 0.00 0.00 2.29
2178 2507 2.850060 GCGCGCGTATGTATGTATGTAT 59.150 45.455 32.35 0.00 0.00 2.29
2179 2508 3.300944 GCGCGCGTATGTATGTATGTATG 60.301 47.826 32.35 0.00 0.00 2.39
2180 2509 3.849708 CGCGCGTATGTATGTATGTATGT 59.150 43.478 24.19 0.00 0.00 2.29
2181 2510 5.023286 CGCGCGTATGTATGTATGTATGTA 58.977 41.667 24.19 0.00 0.00 2.29
2182 2511 5.053480 CGCGCGTATGTATGTATGTATGTAC 60.053 44.000 24.19 0.00 0.00 2.90
2183 2512 5.053480 GCGCGTATGTATGTATGTATGTACG 60.053 44.000 8.43 0.00 37.37 3.67
2186 2515 7.964545 CGTATGTATGTATGTATGTACGCAT 57.035 36.000 0.00 3.51 39.03 4.73
2187 2516 7.817831 CGTATGTATGTATGTATGTACGCATG 58.182 38.462 7.40 0.00 36.58 4.06
2188 2517 7.483691 CGTATGTATGTATGTATGTACGCATGT 59.516 37.037 0.00 0.00 36.58 3.21
2189 2518 9.777575 GTATGTATGTATGTATGTACGCATGTA 57.222 33.333 0.00 0.00 36.58 2.29
2196 2525 2.315356 GTACGCATGTACGCACGC 59.685 61.111 0.00 0.00 41.41 5.34
2197 2526 2.126424 TACGCATGTACGCACGCA 60.126 55.556 0.00 0.00 32.73 5.24
2198 2527 1.517475 TACGCATGTACGCACGCAT 60.517 52.632 0.00 0.00 32.73 4.73
2199 2528 1.747686 TACGCATGTACGCACGCATG 61.748 55.000 6.36 6.36 43.71 4.06
2293 2737 3.186409 CCGTCAATTAATGGTGATAGCCG 59.814 47.826 0.00 0.00 0.00 5.52
2346 2792 5.814705 CCAAACAGTTTGCAACCTTGAAATA 59.185 36.000 19.19 0.00 39.31 1.40
2447 2893 2.682856 GGTCTTGTTCTTGTTGCTCACA 59.317 45.455 0.00 0.00 0.00 3.58
2578 3030 4.825422 ACCATATACAATGCTCCGATCTG 58.175 43.478 0.00 0.00 0.00 2.90
2712 3164 3.610114 GCAATTCCATAATCGAATGCGCT 60.610 43.478 9.73 0.00 37.46 5.92
2780 3232 1.604915 GGGGGTTTGCTCTCTCTCC 59.395 63.158 0.00 0.00 0.00 3.71
2781 3233 0.912006 GGGGGTTTGCTCTCTCTCCT 60.912 60.000 0.00 0.00 0.00 3.69
3043 3555 0.828022 TGTCGGTCACCTGTTTCTGT 59.172 50.000 0.00 0.00 0.00 3.41
3058 3570 4.039973 TGTTTCTGTCCGGTTGAATCTACT 59.960 41.667 0.00 0.00 0.00 2.57
3172 3696 6.699575 ATAGCCATAAATGTGTTTCTGACC 57.300 37.500 0.00 0.00 0.00 4.02
3229 3753 0.107165 GCCCCTTGCTTAGATCCGTT 60.107 55.000 0.00 0.00 36.87 4.44
3529 4059 6.013379 TGGATACTATTCTTATGAAGGCTGGG 60.013 42.308 0.00 0.00 34.39 4.45
3543 4073 2.685017 TGGGGCAGCGACTCAGAT 60.685 61.111 0.00 0.00 0.00 2.90
3566 4096 9.261180 AGATGACGAAAATGTATGAACGATATT 57.739 29.630 0.00 0.00 0.00 1.28
3606 9990 4.469657 TGAGCCTTGTACCATTCTTGTTT 58.530 39.130 0.00 0.00 0.00 2.83
3621 10005 7.043192 CCATTCTTGTTTCTTTGCTGTTAACTG 60.043 37.037 7.22 7.67 0.00 3.16
3626 10010 7.328277 TGTTTCTTTGCTGTTAACTGTACAT 57.672 32.000 13.27 0.00 0.00 2.29
3658 10042 2.686915 CCCTTTTGCAGATGGAAGCTAG 59.313 50.000 10.47 0.00 0.00 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
195 214 6.746104 TCTGTTTTTGCGAACATTGTATTG 57.254 33.333 0.00 0.00 38.71 1.90
198 217 7.763172 ATTTTCTGTTTTTGCGAACATTGTA 57.237 28.000 0.00 0.00 38.71 2.41
450 532 6.772233 TGATCCACAACTGAATCAAAGAAAGA 59.228 34.615 0.00 0.00 0.00 2.52
608 695 5.070770 TGCCGTCTTTGCAAAATGATTAT 57.929 34.783 13.84 0.00 35.40 1.28
722 809 8.766151 GTTGCAACGGGAGAAAATTTAATTAAA 58.234 29.630 14.90 12.85 0.00 1.52
805 897 3.120616 CACTTCGTGTTCGCTCGATTTTA 59.879 43.478 0.00 0.00 41.74 1.52
818 910 2.365582 GGCCCAAATATCACTTCGTGT 58.634 47.619 0.00 0.00 34.79 4.49
854 946 2.044551 GCCAGGCCCTTCTTGAGG 60.045 66.667 0.00 0.00 45.86 3.86
857 949 2.437359 CGAGCCAGGCCCTTCTTG 60.437 66.667 8.22 0.00 0.00 3.02
870 962 1.499049 AAAAGAACCGAGACACGAGC 58.501 50.000 0.00 0.00 45.77 5.03
881 973 9.838339 TGAGATTGAGGAGAATATAAAAGAACC 57.162 33.333 0.00 0.00 0.00 3.62
1089 1380 1.330234 GATAGTTCCCCTCCTCGTCC 58.670 60.000 0.00 0.00 0.00 4.79
1132 1423 1.079127 CTCGGAACACTCGCCCAAT 60.079 57.895 0.00 0.00 0.00 3.16
1165 1456 1.661112 GAATGTACGGACTGCTTGCTC 59.339 52.381 0.00 0.00 0.00 4.26
1167 1458 1.726853 AGAATGTACGGACTGCTTGC 58.273 50.000 0.00 0.00 0.00 4.01
1242 1533 0.447011 GAGGTACACACGTCGGAGAG 59.553 60.000 0.00 0.00 36.95 3.20
1258 1549 1.150536 CGAGAGGGAGAGGGAGAGG 59.849 68.421 0.00 0.00 0.00 3.69
1259 1550 0.548989 TTCGAGAGGGAGAGGGAGAG 59.451 60.000 0.00 0.00 0.00 3.20
1260 1551 1.144093 GATTCGAGAGGGAGAGGGAGA 59.856 57.143 0.00 0.00 0.00 3.71
1261 1552 1.144913 AGATTCGAGAGGGAGAGGGAG 59.855 57.143 0.00 0.00 0.00 4.30
1262 1553 1.227249 AGATTCGAGAGGGAGAGGGA 58.773 55.000 0.00 0.00 0.00 4.20
1263 1554 2.080654 AAGATTCGAGAGGGAGAGGG 57.919 55.000 0.00 0.00 0.00 4.30
1694 2023 6.094186 GTGTGGAAAGATCCCTTAAGATCAAC 59.906 42.308 3.36 0.00 45.95 3.18
1745 2074 5.278266 CCTTATCGACTTCCTCTAAGCTCTG 60.278 48.000 0.00 0.00 38.93 3.35
1799 2128 8.112183 AGTTGAGGAGATTTACAGATTTGGATT 58.888 33.333 0.00 0.00 0.00 3.01
1832 2161 0.652592 GAGCGGTGAACATTCATCCG 59.347 55.000 21.28 21.28 45.70 4.18
1846 2175 6.261859 CAGATATGCACTATAGTAAGAGCGG 58.738 44.000 4.74 0.00 36.05 5.52
1856 2185 8.353423 TGAGTCAATAGCAGATATGCACTATA 57.647 34.615 15.82 0.00 37.25 1.31
1907 2236 4.927049 TCAGAGGAATCCAGCTTGAAAAT 58.073 39.130 0.61 0.00 0.00 1.82
1932 2261 6.016610 TGTTTCCTACAGTCAAATTGTAAGGC 60.017 38.462 0.00 0.00 31.17 4.35
1936 2265 7.554835 AGTTGTGTTTCCTACAGTCAAATTGTA 59.445 33.333 0.00 0.00 37.45 2.41
1946 2275 9.871238 ATTGTATACTAGTTGTGTTTCCTACAG 57.129 33.333 0.00 0.00 37.45 2.74
2085 2414 6.961359 ACATACACACATACACACATACAC 57.039 37.500 0.00 0.00 0.00 2.90
2093 2422 6.961359 ACACACATACATACACACATACAC 57.039 37.500 0.00 0.00 0.00 2.90
2101 2430 8.539674 CACACATACATACACACATACATACAC 58.460 37.037 0.00 0.00 0.00 2.90
2106 2435 6.367422 CACACACACATACATACACACATACA 59.633 38.462 0.00 0.00 0.00 2.29
2107 2436 6.367695 ACACACACACATACATACACACATAC 59.632 38.462 0.00 0.00 0.00 2.39
2108 2437 6.367422 CACACACACACATACATACACACATA 59.633 38.462 0.00 0.00 0.00 2.29
2109 2438 5.179182 CACACACACACATACATACACACAT 59.821 40.000 0.00 0.00 0.00 3.21
2110 2439 4.509600 CACACACACACATACATACACACA 59.490 41.667 0.00 0.00 0.00 3.72
2111 2440 4.509970 ACACACACACACATACATACACAC 59.490 41.667 0.00 0.00 0.00 3.82
2112 2441 4.509600 CACACACACACACATACATACACA 59.490 41.667 0.00 0.00 0.00 3.72
2113 2442 4.509970 ACACACACACACACATACATACAC 59.490 41.667 0.00 0.00 0.00 2.90
2114 2443 4.698575 ACACACACACACACATACATACA 58.301 39.130 0.00 0.00 0.00 2.29
2115 2444 4.988540 AGACACACACACACACATACATAC 59.011 41.667 0.00 0.00 0.00 2.39
2116 2445 5.010617 AGAGACACACACACACACATACATA 59.989 40.000 0.00 0.00 0.00 2.29
2117 2446 4.058124 GAGACACACACACACACATACAT 58.942 43.478 0.00 0.00 0.00 2.29
2118 2447 3.132111 AGAGACACACACACACACATACA 59.868 43.478 0.00 0.00 0.00 2.29
2119 2448 3.490896 CAGAGACACACACACACACATAC 59.509 47.826 0.00 0.00 0.00 2.39
2120 2449 3.132111 ACAGAGACACACACACACACATA 59.868 43.478 0.00 0.00 0.00 2.29
2121 2450 2.093500 ACAGAGACACACACACACACAT 60.093 45.455 0.00 0.00 0.00 3.21
2122 2451 1.275010 ACAGAGACACACACACACACA 59.725 47.619 0.00 0.00 0.00 3.72
2123 2452 1.660607 CACAGAGACACACACACACAC 59.339 52.381 0.00 0.00 0.00 3.82
2124 2453 1.275010 ACACAGAGACACACACACACA 59.725 47.619 0.00 0.00 0.00 3.72
2125 2454 1.660607 CACACAGAGACACACACACAC 59.339 52.381 0.00 0.00 0.00 3.82
2126 2455 1.275010 ACACACAGAGACACACACACA 59.725 47.619 0.00 0.00 0.00 3.72
2127 2456 1.660607 CACACACAGAGACACACACAC 59.339 52.381 0.00 0.00 0.00 3.82
2128 2457 1.275010 ACACACACAGAGACACACACA 59.725 47.619 0.00 0.00 0.00 3.72
2129 2458 1.660607 CACACACACAGAGACACACAC 59.339 52.381 0.00 0.00 0.00 3.82
2130 2459 1.275010 ACACACACACAGAGACACACA 59.725 47.619 0.00 0.00 0.00 3.72
2131 2460 1.660607 CACACACACACAGAGACACAC 59.339 52.381 0.00 0.00 0.00 3.82
2132 2461 2.006552 GCACACACACACAGAGACACA 61.007 52.381 0.00 0.00 0.00 3.72
2133 2462 0.652592 GCACACACACACAGAGACAC 59.347 55.000 0.00 0.00 0.00 3.67
2134 2463 0.805711 CGCACACACACACAGAGACA 60.806 55.000 0.00 0.00 0.00 3.41
2135 2464 1.927210 CGCACACACACACAGAGAC 59.073 57.895 0.00 0.00 0.00 3.36
2136 2465 1.882625 GCGCACACACACACAGAGA 60.883 57.895 0.30 0.00 0.00 3.10
2137 2466 2.628106 GCGCACACACACACAGAG 59.372 61.111 0.30 0.00 0.00 3.35
2138 2467 3.261216 CGCGCACACACACACAGA 61.261 61.111 8.75 0.00 0.00 3.41
2139 2468 4.943591 GCGCGCACACACACACAG 62.944 66.667 29.10 0.00 0.00 3.66
2157 2486 1.057636 ACATACATACATACGCGCGC 58.942 50.000 32.58 23.91 0.00 6.86
2158 2487 3.849708 ACATACATACATACATACGCGCG 59.150 43.478 30.96 30.96 0.00 6.86
2159 2488 5.053480 CGTACATACATACATACATACGCGC 60.053 44.000 5.73 0.00 0.00 6.86
2160 2489 5.053480 GCGTACATACATACATACATACGCG 60.053 44.000 3.53 3.53 46.64 6.01
2162 2491 7.483691 ACATGCGTACATACATACATACATACG 59.516 37.037 0.00 0.00 37.73 3.06
2163 2492 8.683550 ACATGCGTACATACATACATACATAC 57.316 34.615 0.00 0.00 33.67 2.39
2164 2493 9.777575 GTACATGCGTACATACATACATACATA 57.222 33.333 0.00 0.00 46.18 2.29
2165 2494 8.683550 GTACATGCGTACATACATACATACAT 57.316 34.615 0.00 0.00 46.18 2.29
2205 2534 7.875327 ATGATACATACATACATGCATGCAT 57.125 32.000 27.46 27.46 35.45 3.96
2206 2535 8.259411 TCTATGATACATACATACATGCATGCA 58.741 33.333 26.53 25.04 35.45 3.96
2207 2536 8.652810 TCTATGATACATACATACATGCATGC 57.347 34.615 26.53 11.82 35.45 4.06
2262 2706 7.335627 TCACCATTAATTGACGGAAATAGAGT 58.664 34.615 0.00 0.00 0.00 3.24
2272 2716 3.186409 CCGGCTATCACCATTAATTGACG 59.814 47.826 0.00 0.00 0.00 4.35
2293 2737 6.706716 AGTTAACTAACAGAGCTGAACTTTCC 59.293 38.462 6.26 0.00 38.62 3.13
2447 2893 1.490490 TGGACAGAAGGTTGCAGACTT 59.510 47.619 4.83 4.83 0.00 3.01
2578 3030 7.039714 CCCCACCTTTATTCATTAGCCTAATTC 60.040 40.741 0.00 0.00 0.00 2.17
2712 3164 4.724399 TCCACCAAAGCTTGAAGTAATCA 58.276 39.130 0.00 0.00 35.85 2.57
2780 3232 8.256605 TGGATAAAACAATGAGAGAGAGAGAAG 58.743 37.037 0.00 0.00 0.00 2.85
2781 3233 8.138928 TGGATAAAACAATGAGAGAGAGAGAA 57.861 34.615 0.00 0.00 0.00 2.87
3043 3555 4.202253 CCATCATCAGTAGATTCAACCGGA 60.202 45.833 9.46 0.00 30.20 5.14
3058 3570 6.575244 AAAGGGTAGAATGTACCATCATCA 57.425 37.500 8.90 0.00 39.31 3.07
3172 3696 5.050091 ACGAAACTAAAGATCAAGTGCTGTG 60.050 40.000 0.00 0.00 0.00 3.66
3529 4059 1.875813 CGTCATCTGAGTCGCTGCC 60.876 63.158 0.00 0.00 0.00 4.85
3606 9990 5.820423 ACACATGTACAGTTAACAGCAAAGA 59.180 36.000 8.61 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.