Multiple sequence alignment - TraesCS2D01G239700

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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 TraesCS2D01G239700 chr2D 100.000 5023 0 0 1 5023 255680859 255685881 0.000000e+00 9276.0
1 TraesCS2D01G239700 chr2D 91.729 931 49 4 4094 5023 131459110 131460013 0.000000e+00 1267.0
2 TraesCS2D01G239700 chr2D 90.610 607 21 11 4095 4700 495781926 495781355 0.000000e+00 773.0
3 TraesCS2D01G239700 chr2D 87.045 440 31 9 328 756 58971569 58971993 1.640000e-129 473.0
4 TraesCS2D01G239700 chr2D 96.324 136 3 2 4096 4230 273007710 273007576 6.550000e-54 222.0
5 TraesCS2D01G239700 chr2D 92.000 50 4 0 2159 2208 327614814 327614863 2.510000e-08 71.3
6 TraesCS2D01G239700 chr2D 93.617 47 2 1 1600 1645 326212635 326212681 9.020000e-08 69.4
7 TraesCS2D01G239700 chr2A 92.462 1393 52 19 3643 5023 236827711 236826360 0.000000e+00 1941.0
8 TraesCS2D01G239700 chr2A 98.316 772 10 1 1670 2441 236829132 236828364 0.000000e+00 1351.0
9 TraesCS2D01G239700 chr2A 88.985 926 73 17 4099 5022 57321272 57322170 0.000000e+00 1118.0
10 TraesCS2D01G239700 chr2A 98.689 610 7 1 2444 3052 236828316 236827707 0.000000e+00 1081.0
11 TraesCS2D01G239700 chr2A 86.037 931 97 15 4096 5023 404919650 404920550 0.000000e+00 968.0
12 TraesCS2D01G239700 chr2A 86.905 840 72 18 1 822 779466977 779467796 0.000000e+00 907.0
13 TraesCS2D01G239700 chr2A 86.801 841 72 18 1 822 779582086 779582906 0.000000e+00 902.0
14 TraesCS2D01G239700 chr2A 90.976 676 50 6 4 669 262290152 262290826 0.000000e+00 900.0
15 TraesCS2D01G239700 chr2A 89.568 671 60 4 1 661 127149843 127150513 0.000000e+00 843.0
16 TraesCS2D01G239700 chr2A 96.629 445 12 2 1234 1676 236833727 236833284 0.000000e+00 736.0
17 TraesCS2D01G239700 chr2A 98.016 252 5 0 978 1229 236834068 236833817 5.970000e-119 438.0
18 TraesCS2D01G239700 chr2A 96.026 151 4 2 4096 4245 319038263 319038412 1.400000e-60 244.0
19 TraesCS2D01G239700 chr2A 90.000 80 4 1 907 982 236834186 236834107 3.200000e-17 100.0
20 TraesCS2D01G239700 chr2A 89.474 57 4 2 2170 2226 125220085 125220139 2.510000e-08 71.3
21 TraesCS2D01G239700 chr2B 96.039 934 24 8 1243 2172 280476270 280475346 0.000000e+00 1507.0
22 TraesCS2D01G239700 chr2B 95.055 910 22 5 2443 3336 280475077 280474175 0.000000e+00 1410.0
23 TraesCS2D01G239700 chr2B 96.104 770 26 2 3334 4100 280474013 280473245 0.000000e+00 1253.0
24 TraesCS2D01G239700 chr2B 96.070 229 2 4 2214 2441 280475346 280475124 2.860000e-97 366.0
25 TraesCS2D01G239700 chr2B 93.254 252 4 4 978 1229 280482888 280482650 4.780000e-95 359.0
26 TraesCS2D01G239700 chr2B 94.444 72 1 2 4099 4170 388947139 388947207 1.910000e-19 108.0
27 TraesCS2D01G239700 chr2B 92.000 50 4 0 2159 2208 396927373 396927422 2.510000e-08 71.3
28 TraesCS2D01G239700 chr2B 92.308 52 1 3 2159 2208 693093554 693093504 2.510000e-08 71.3
29 TraesCS2D01G239700 chr2B 97.500 40 1 0 1606 1645 58979305 58979344 9.020000e-08 69.4
30 TraesCS2D01G239700 chr3D 91.192 931 53 6 4094 5023 67479955 67479053 0.000000e+00 1238.0
31 TraesCS2D01G239700 chr3D 91.183 930 50 16 4099 5023 237831444 237832346 0.000000e+00 1234.0
32 TraesCS2D01G239700 chr3D 91.145 926 55 10 4099 5023 443355382 443354483 0.000000e+00 1230.0
33 TraesCS2D01G239700 chr7A 89.892 930 67 3 4095 5023 213820348 213821251 0.000000e+00 1171.0
34 TraesCS2D01G239700 chr7A 95.098 204 8 2 4099 4301 409257548 409257346 2.260000e-83 320.0
35 TraesCS2D01G239700 chr3A 88.280 930 80 5 4095 5023 380875092 380874191 0.000000e+00 1086.0
36 TraesCS2D01G239700 chr7D 92.330 678 41 7 4 671 633012205 633011529 0.000000e+00 953.0
37 TraesCS2D01G239700 chr7D 84.222 938 98 30 4 914 546812887 546811973 0.000000e+00 867.0
38 TraesCS2D01G239700 chr7D 90.610 607 45 5 1 597 239675772 239676376 0.000000e+00 795.0
39 TraesCS2D01G239700 chr5D 91.324 680 48 5 1 670 459510941 459511619 0.000000e+00 918.0
40 TraesCS2D01G239700 chr5D 90.735 680 44 9 1 670 459565484 459566154 0.000000e+00 889.0
41 TraesCS2D01G239700 chr5D 96.753 308 10 0 4518 4825 7593129 7593436 9.640000e-142 514.0
42 TraesCS2D01G239700 chr5D 84.887 311 19 4 4088 4397 7592846 7593129 6.360000e-74 289.0
43 TraesCS2D01G239700 chr5D 90.299 134 5 5 748 874 483026704 483026836 8.650000e-38 169.0
44 TraesCS2D01G239700 chr5D 89.655 58 3 3 2153 2208 256744011 256743955 2.510000e-08 71.3
45 TraesCS2D01G239700 chr5D 93.478 46 2 1 1600 1644 543767892 543767847 3.250000e-07 67.6
46 TraesCS2D01G239700 chr5B 91.150 678 30 16 4099 4774 531823037 531822388 0.000000e+00 893.0
47 TraesCS2D01G239700 chr4D 80.430 930 151 15 4099 5023 235500093 235499190 0.000000e+00 680.0
48 TraesCS2D01G239700 chr1A 92.611 203 12 3 4096 4297 517097531 517097731 6.360000e-74 289.0
49 TraesCS2D01G239700 chr7B 90.361 166 12 3 4099 4261 472241637 472241473 1.100000e-51 215.0
50 TraesCS2D01G239700 chr7B 97.436 39 1 0 1607 1645 500726038 500726000 3.250000e-07 67.6
51 TraesCS2D01G239700 chr5A 92.308 52 1 3 2159 2208 622398155 622398205 2.510000e-08 71.3
52 TraesCS2D01G239700 chr5A 97.500 40 1 0 1606 1645 360086339 360086300 9.020000e-08 69.4
53 TraesCS2D01G239700 chr6A 92.157 51 1 2 2158 2208 93285693 93285740 9.020000e-08 69.4
54 TraesCS2D01G239700 chr6A 89.091 55 4 2 2170 2224 23967363 23967311 3.250000e-07 67.6
55 TraesCS2D01G239700 chr4B 93.617 47 1 2 1599 1645 54741097 54741053 9.020000e-08 69.4
56 TraesCS2D01G239700 chr1D 97.368 38 1 0 1608 1645 230670324 230670287 1.170000e-06 65.8


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 TraesCS2D01G239700 chr2D 255680859 255685881 5022 False 9276.000000 9276 100.000000 1 5023 1 chr2D.!!$F3 5022
1 TraesCS2D01G239700 chr2D 131459110 131460013 903 False 1267.000000 1267 91.729000 4094 5023 1 chr2D.!!$F2 929
2 TraesCS2D01G239700 chr2D 495781355 495781926 571 True 773.000000 773 90.610000 4095 4700 1 chr2D.!!$R2 605
3 TraesCS2D01G239700 chr2A 236826360 236829132 2772 True 1457.666667 1941 96.489000 1670 5023 3 chr2A.!!$R1 3353
4 TraesCS2D01G239700 chr2A 57321272 57322170 898 False 1118.000000 1118 88.985000 4099 5022 1 chr2A.!!$F1 923
5 TraesCS2D01G239700 chr2A 404919650 404920550 900 False 968.000000 968 86.037000 4096 5023 1 chr2A.!!$F6 927
6 TraesCS2D01G239700 chr2A 779466977 779467796 819 False 907.000000 907 86.905000 1 822 1 chr2A.!!$F7 821
7 TraesCS2D01G239700 chr2A 779582086 779582906 820 False 902.000000 902 86.801000 1 822 1 chr2A.!!$F8 821
8 TraesCS2D01G239700 chr2A 262290152 262290826 674 False 900.000000 900 90.976000 4 669 1 chr2A.!!$F4 665
9 TraesCS2D01G239700 chr2A 127149843 127150513 670 False 843.000000 843 89.568000 1 661 1 chr2A.!!$F3 660
10 TraesCS2D01G239700 chr2A 236833284 236834186 902 True 424.666667 736 94.881667 907 1676 3 chr2A.!!$R2 769
11 TraesCS2D01G239700 chr2B 280473245 280476270 3025 True 1134.000000 1507 95.817000 1243 4100 4 chr2B.!!$R3 2857
12 TraesCS2D01G239700 chr3D 67479053 67479955 902 True 1238.000000 1238 91.192000 4094 5023 1 chr3D.!!$R1 929
13 TraesCS2D01G239700 chr3D 237831444 237832346 902 False 1234.000000 1234 91.183000 4099 5023 1 chr3D.!!$F1 924
14 TraesCS2D01G239700 chr3D 443354483 443355382 899 True 1230.000000 1230 91.145000 4099 5023 1 chr3D.!!$R2 924
15 TraesCS2D01G239700 chr7A 213820348 213821251 903 False 1171.000000 1171 89.892000 4095 5023 1 chr7A.!!$F1 928
16 TraesCS2D01G239700 chr3A 380874191 380875092 901 True 1086.000000 1086 88.280000 4095 5023 1 chr3A.!!$R1 928
17 TraesCS2D01G239700 chr7D 633011529 633012205 676 True 953.000000 953 92.330000 4 671 1 chr7D.!!$R2 667
18 TraesCS2D01G239700 chr7D 546811973 546812887 914 True 867.000000 867 84.222000 4 914 1 chr7D.!!$R1 910
19 TraesCS2D01G239700 chr7D 239675772 239676376 604 False 795.000000 795 90.610000 1 597 1 chr7D.!!$F1 596
20 TraesCS2D01G239700 chr5D 459510941 459511619 678 False 918.000000 918 91.324000 1 670 1 chr5D.!!$F1 669
21 TraesCS2D01G239700 chr5D 459565484 459566154 670 False 889.000000 889 90.735000 1 670 1 chr5D.!!$F2 669
22 TraesCS2D01G239700 chr5D 7592846 7593436 590 False 401.500000 514 90.820000 4088 4825 2 chr5D.!!$F4 737
23 TraesCS2D01G239700 chr5B 531822388 531823037 649 True 893.000000 893 91.150000 4099 4774 1 chr5B.!!$R1 675
24 TraesCS2D01G239700 chr4D 235499190 235500093 903 True 680.000000 680 80.430000 4099 5023 1 chr4D.!!$R1 924

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
859 923 0.249155 ACGACGTGTGAAATGACCGT 60.249 50.000 0.00 0.00 0.00 4.83 F
863 927 0.320421 CGTGTGAAATGACCGTCCCT 60.320 55.000 0.00 0.00 0.00 4.20 F
885 950 0.733729 TACGTTTTGGGTGTGTGTGC 59.266 50.000 0.00 0.00 0.00 4.57 F
965 1034 1.135460 GTGCTTCTTCATTCAGCTGGC 60.135 52.381 15.13 6.36 34.42 4.85 F
1387 1587 1.203376 TGGGTGGAGACAGGAATGGTA 60.203 52.381 0.00 0.00 44.46 3.25 F
2213 2413 1.765230 AGAGCGTTTAGATCGGGAGT 58.235 50.000 0.00 0.00 40.85 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2744 3030 0.881118 CCGGTGTTCAACATTCCAGG 59.119 55.000 0.0 0.00 0.00 4.45 R
2765 3051 3.199727 TGACATGGCTAGGCATAGTTCAA 59.800 43.478 29.3 15.93 0.00 2.69 R
2863 3164 5.165676 TGTGGTGTTACAACGATATGTCTC 58.834 41.667 0.0 0.00 34.75 3.36 R
3077 3378 6.238320 GGTCAGTGATGATTTCTGATTAGTGC 60.238 42.308 0.0 0.00 39.77 4.40 R
3174 3475 0.698818 ACCCTTTGCCTCTACCCAAG 59.301 55.000 0.0 0.00 0.00 3.61 R
4321 4799 0.889186 GCAACCATCCGTTCACACCT 60.889 55.000 0.0 0.00 29.93 4.00 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
143 144 9.420551 CATATGAATCATCTACATCCATATCCG 57.579 37.037 0.00 0.00 0.00 4.18
161 162 0.949397 CGCATTGTCATCATCCCCTG 59.051 55.000 0.00 0.00 0.00 4.45
167 168 0.398318 GTCATCATCCCCTGCTACCC 59.602 60.000 0.00 0.00 0.00 3.69
252 253 3.754965 ACATGCAGACCACTTACATTGT 58.245 40.909 0.00 0.00 0.00 2.71
335 337 0.467474 ATGATCCGTCCTCGCTACCA 60.467 55.000 0.00 0.00 35.54 3.25
338 340 4.189188 CCGTCCTCGCTACCACCG 62.189 72.222 0.00 0.00 35.54 4.94
362 364 4.280929 TCATCACCGTCATATCCGATTTCT 59.719 41.667 0.00 0.00 0.00 2.52
413 416 5.902613 TCAAGATCCATTCAAACATCACC 57.097 39.130 0.00 0.00 0.00 4.02
425 428 4.020573 TCAAACATCACCTAACATCCTCGT 60.021 41.667 0.00 0.00 0.00 4.18
457 460 6.576662 TCCGTTTTTAAATCACTATGCCAA 57.423 33.333 0.00 0.00 0.00 4.52
459 462 6.207810 TCCGTTTTTAAATCACTATGCCAACT 59.792 34.615 0.00 0.00 0.00 3.16
515 530 0.972471 TGAGATTCGCTGGAGGCTCA 60.972 55.000 17.69 1.59 39.13 4.26
616 639 3.066342 GCGTCAGTATTACTAGGTGCTGA 59.934 47.826 8.14 8.14 0.00 4.26
633 656 2.415512 GCTGACGGCGTCTTTATTTTCT 59.584 45.455 36.17 0.00 33.15 2.52
715 738 1.536284 GCGACAGGAAGATAGGGTTCG 60.536 57.143 0.00 0.00 0.00 3.95
792 856 4.860261 GGGCGGGCGTACGTACAG 62.860 72.222 24.50 17.43 35.98 2.74
793 857 4.860261 GGCGGGCGTACGTACAGG 62.860 72.222 24.50 10.97 35.98 4.00
794 858 4.860261 GCGGGCGTACGTACAGGG 62.860 72.222 24.50 10.27 35.98 4.45
795 859 4.860261 CGGGCGTACGTACAGGGC 62.860 72.222 24.50 19.72 0.00 5.19
796 860 4.519437 GGGCGTACGTACAGGGCC 62.519 72.222 26.00 26.00 43.01 5.80
797 861 4.860261 GGCGTACGTACAGGGCCG 62.860 72.222 24.50 11.16 33.58 6.13
798 862 4.120331 GCGTACGTACAGGGCCGT 62.120 66.667 24.50 1.57 40.87 5.68
799 863 2.760159 GCGTACGTACAGGGCCGTA 61.760 63.158 24.50 0.45 38.43 4.02
835 899 3.469054 TACGGCGGGCGGGTATTT 61.469 61.111 27.66 8.29 0.00 1.40
843 907 2.753296 CGGGCGGGTATTTTAATACGA 58.247 47.619 6.55 0.00 41.66 3.43
858 922 1.688793 TACGACGTGTGAAATGACCG 58.311 50.000 11.56 0.00 0.00 4.79
859 923 0.249155 ACGACGTGTGAAATGACCGT 60.249 50.000 0.00 0.00 0.00 4.83
861 925 0.788391 GACGTGTGAAATGACCGTCC 59.212 55.000 0.00 0.00 41.37 4.79
862 926 0.601841 ACGTGTGAAATGACCGTCCC 60.602 55.000 0.00 0.00 0.00 4.46
863 927 0.320421 CGTGTGAAATGACCGTCCCT 60.320 55.000 0.00 0.00 0.00 4.20
864 928 1.876416 CGTGTGAAATGACCGTCCCTT 60.876 52.381 0.00 0.00 0.00 3.95
865 929 2.610976 CGTGTGAAATGACCGTCCCTTA 60.611 50.000 0.00 0.00 0.00 2.69
877 942 2.355007 CCGTCCCTTATACGTTTTGGGT 60.355 50.000 13.44 0.00 38.67 4.51
879 944 3.678289 GTCCCTTATACGTTTTGGGTGT 58.322 45.455 13.44 0.00 38.95 4.16
881 946 3.072768 TCCCTTATACGTTTTGGGTGTGT 59.927 43.478 13.44 0.00 38.95 3.72
882 947 3.189702 CCCTTATACGTTTTGGGTGTGTG 59.810 47.826 0.00 0.00 33.49 3.82
883 948 3.816523 CCTTATACGTTTTGGGTGTGTGT 59.183 43.478 0.00 0.00 0.00 3.72
884 949 4.319911 CCTTATACGTTTTGGGTGTGTGTG 60.320 45.833 0.00 0.00 0.00 3.82
885 950 0.733729 TACGTTTTGGGTGTGTGTGC 59.266 50.000 0.00 0.00 0.00 4.57
886 951 1.585002 CGTTTTGGGTGTGTGTGCG 60.585 57.895 0.00 0.00 0.00 5.34
887 952 1.876263 GTTTTGGGTGTGTGTGCGC 60.876 57.895 0.00 0.00 0.00 6.09
893 958 1.885388 GGTGTGTGTGCGCTGTACA 60.885 57.895 9.73 8.45 0.00 2.90
960 1029 4.082895 CCTTCCTTGTGCTTCTTCATTCAG 60.083 45.833 0.00 0.00 0.00 3.02
964 1033 2.156917 TGTGCTTCTTCATTCAGCTGG 58.843 47.619 15.13 0.00 34.42 4.85
965 1034 1.135460 GTGCTTCTTCATTCAGCTGGC 60.135 52.381 15.13 6.36 34.42 4.85
1387 1587 1.203376 TGGGTGGAGACAGGAATGGTA 60.203 52.381 0.00 0.00 44.46 3.25
2177 2377 6.853490 AGGTTATTCCCTGAATTATTCTCCC 58.147 40.000 6.50 0.00 33.95 4.30
2178 2378 6.625700 AGGTTATTCCCTGAATTATTCTCCCT 59.374 38.462 6.50 0.00 33.95 4.20
2179 2379 6.943146 GGTTATTCCCTGAATTATTCTCCCTC 59.057 42.308 6.50 0.00 33.95 4.30
2180 2380 5.590976 ATTCCCTGAATTATTCTCCCTCC 57.409 43.478 6.50 0.00 0.00 4.30
2181 2381 2.972713 TCCCTGAATTATTCTCCCTCCG 59.027 50.000 6.50 0.00 0.00 4.63
2182 2382 2.706190 CCCTGAATTATTCTCCCTCCGT 59.294 50.000 6.50 0.00 0.00 4.69
2183 2383 3.901844 CCCTGAATTATTCTCCCTCCGTA 59.098 47.826 6.50 0.00 0.00 4.02
2184 2384 4.347000 CCCTGAATTATTCTCCCTCCGTAA 59.653 45.833 6.50 0.00 0.00 3.18
2185 2385 5.163237 CCCTGAATTATTCTCCCTCCGTAAA 60.163 44.000 6.50 0.00 0.00 2.01
2186 2386 5.992217 CCTGAATTATTCTCCCTCCGTAAAG 59.008 44.000 6.50 0.00 0.00 1.85
2187 2387 6.183360 CCTGAATTATTCTCCCTCCGTAAAGA 60.183 42.308 6.50 0.00 0.00 2.52
2188 2388 7.190335 TGAATTATTCTCCCTCCGTAAAGAA 57.810 36.000 6.50 0.00 32.69 2.52
2189 2389 7.626390 TGAATTATTCTCCCTCCGTAAAGAAA 58.374 34.615 6.50 0.00 31.98 2.52
2190 2390 8.272173 TGAATTATTCTCCCTCCGTAAAGAAAT 58.728 33.333 6.50 0.00 31.98 2.17
2191 2391 9.774413 GAATTATTCTCCCTCCGTAAAGAAATA 57.226 33.333 0.00 0.00 31.98 1.40
2196 2396 8.543293 TTCTCCCTCCGTAAAGAAATATAAGA 57.457 34.615 0.00 0.00 0.00 2.10
2197 2397 8.179509 TCTCCCTCCGTAAAGAAATATAAGAG 57.820 38.462 0.00 0.00 0.00 2.85
2198 2398 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
2199 2399 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
2200 2400 6.214399 CCTCCGTAAAGAAATATAAGAGCGT 58.786 40.000 0.00 0.00 0.00 5.07
2201 2401 6.700520 CCTCCGTAAAGAAATATAAGAGCGTT 59.299 38.462 0.00 0.00 0.00 4.84
2202 2402 7.224167 CCTCCGTAAAGAAATATAAGAGCGTTT 59.776 37.037 0.00 0.00 0.00 3.60
2203 2403 9.241317 CTCCGTAAAGAAATATAAGAGCGTTTA 57.759 33.333 0.00 0.00 0.00 2.01
2204 2404 9.241317 TCCGTAAAGAAATATAAGAGCGTTTAG 57.759 33.333 0.00 0.00 0.00 1.85
2205 2405 9.241317 CCGTAAAGAAATATAAGAGCGTTTAGA 57.759 33.333 0.00 0.00 0.00 2.10
2209 2409 8.522178 AAGAAATATAAGAGCGTTTAGATCGG 57.478 34.615 0.00 0.00 40.85 4.18
2210 2410 7.091443 AGAAATATAAGAGCGTTTAGATCGGG 58.909 38.462 0.00 0.00 40.85 5.14
2211 2411 6.585695 AATATAAGAGCGTTTAGATCGGGA 57.414 37.500 0.00 0.00 40.85 5.14
2212 2412 2.873133 AAGAGCGTTTAGATCGGGAG 57.127 50.000 0.00 0.00 40.85 4.30
2213 2413 1.765230 AGAGCGTTTAGATCGGGAGT 58.235 50.000 0.00 0.00 40.85 3.85
2248 2490 6.459066 TGTCTGTCTGATCTCTTTTCGAAAT 58.541 36.000 12.12 0.00 0.00 2.17
2416 2659 4.243007 CCAGTTGGTTCTTCCATTGTTC 57.757 45.455 0.00 0.00 46.60 3.18
2744 3030 5.163258 ACATGATATGTCCTCCTTTGGTCTC 60.163 44.000 0.00 0.00 39.92 3.36
2765 3051 2.436417 CTGGAATGTTGAACACCGGAT 58.564 47.619 9.46 0.00 0.00 4.18
2781 3067 2.417719 CGGATTGAACTATGCCTAGCC 58.582 52.381 0.00 0.00 0.00 3.93
2863 3164 2.189342 GATGAACTTCTCGCCTTCTCG 58.811 52.381 0.00 0.00 0.00 4.04
3077 3378 5.922739 TGTTCTGTATGTACTTGCTGTTG 57.077 39.130 0.00 0.00 0.00 3.33
3106 3407 2.681848 CAGAAATCATCACTGACCCTGC 59.318 50.000 0.00 0.00 33.22 4.85
3112 3413 4.729918 CACTGACCCTGCCCTGCC 62.730 72.222 0.00 0.00 0.00 4.85
3129 3430 8.027524 TGCCCTGCCATATTCAATATTTAAAA 57.972 30.769 0.00 0.00 0.00 1.52
3173 3474 6.151144 GGTGGATAAACTTATGCTCACAACTT 59.849 38.462 3.13 0.00 33.27 2.66
3174 3475 7.244192 GTGGATAAACTTATGCTCACAACTTC 58.756 38.462 3.13 0.00 33.27 3.01
3175 3476 7.119846 GTGGATAAACTTATGCTCACAACTTCT 59.880 37.037 3.13 0.00 33.27 2.85
3208 3509 4.099419 GCAAAGGGTAAATTGGTAGGATGG 59.901 45.833 0.00 0.00 0.00 3.51
3272 3573 4.670221 GCGACCATTGTTTCACTGATCTTC 60.670 45.833 0.00 0.00 0.00 2.87
3306 3607 6.049955 TCTTTTCTTATGGGACCAGTAGTG 57.950 41.667 0.00 0.00 0.00 2.74
3307 3608 5.546499 TCTTTTCTTATGGGACCAGTAGTGT 59.454 40.000 0.00 0.00 0.00 3.55
3308 3609 6.727231 TCTTTTCTTATGGGACCAGTAGTGTA 59.273 38.462 0.00 0.00 0.00 2.90
3309 3610 5.927281 TTCTTATGGGACCAGTAGTGTAC 57.073 43.478 0.00 0.00 0.00 2.90
3317 3618 4.894114 GGGACCAGTAGTGTACAGTGATAT 59.106 45.833 13.66 0.00 0.00 1.63
3349 3814 9.538508 AGTACAAAACACTAGATAGAAACGTTT 57.461 29.630 14.57 14.57 0.00 3.60
3374 3839 5.010617 GGAAACAAAGTTAAATCAGCCCAGA 59.989 40.000 0.00 0.00 0.00 3.86
3517 3982 5.598005 TGGAGGCACCTTATTTGGAAATATG 59.402 40.000 1.84 0.00 39.86 1.78
3569 4034 6.156256 TCCATAAAGCCTGAAGAACTTAGCTA 59.844 38.462 0.00 0.00 0.00 3.32
3611 4076 8.637986 GGACAAACATTTTATGGAGGCAATATA 58.362 33.333 0.00 0.00 33.60 0.86
3636 4101 7.662604 AATGACAAATCAGAAGGAAAAATGC 57.337 32.000 0.00 0.00 38.57 3.56
3687 4152 3.998341 TGCTAATGGTAAACAAGACGACC 59.002 43.478 0.00 0.00 0.00 4.79
3706 4174 3.795877 ACCGTTTACGAAGAAACAAGGA 58.204 40.909 3.46 0.00 43.02 3.36
4161 4636 9.971922 CCATTGAAAAGAGAGAGTTTGTAATTT 57.028 29.630 0.00 0.00 0.00 1.82
4301 4779 5.665459 CTTTGATCCTACTCACTAAGGTGG 58.335 45.833 0.00 0.00 43.17 4.61
4308 4786 2.859165 CTCACTAAGGTGGGCTTTGA 57.141 50.000 0.00 0.00 43.17 2.69
4309 4787 3.356529 CTCACTAAGGTGGGCTTTGAT 57.643 47.619 0.00 0.00 43.17 2.57
4310 4788 3.274288 CTCACTAAGGTGGGCTTTGATC 58.726 50.000 0.00 0.00 43.17 2.92
4311 4789 2.026262 TCACTAAGGTGGGCTTTGATCC 60.026 50.000 0.00 0.00 43.17 3.36
4312 4790 2.025887 CACTAAGGTGGGCTTTGATCCT 60.026 50.000 0.00 0.00 39.59 3.24
4313 4791 3.199946 CACTAAGGTGGGCTTTGATCCTA 59.800 47.826 0.00 0.00 39.59 2.94
4314 4792 2.808906 AAGGTGGGCTTTGATCCTAC 57.191 50.000 0.00 0.00 34.72 3.18
4315 4793 1.972588 AGGTGGGCTTTGATCCTACT 58.027 50.000 0.00 0.00 35.66 2.57
4316 4794 1.840635 AGGTGGGCTTTGATCCTACTC 59.159 52.381 0.00 0.00 35.66 2.59
4317 4795 1.559682 GGTGGGCTTTGATCCTACTCA 59.440 52.381 0.00 0.00 35.66 3.41
4318 4796 2.633488 GTGGGCTTTGATCCTACTCAC 58.367 52.381 0.00 0.00 32.98 3.51
4319 4797 2.237392 GTGGGCTTTGATCCTACTCACT 59.763 50.000 0.00 0.00 32.98 3.41
4320 4798 3.451178 GTGGGCTTTGATCCTACTCACTA 59.549 47.826 0.00 0.00 32.98 2.74
4321 4799 4.081087 GTGGGCTTTGATCCTACTCACTAA 60.081 45.833 0.00 0.00 32.98 2.24
4322 4800 4.162320 TGGGCTTTGATCCTACTCACTAAG 59.838 45.833 0.00 0.00 0.00 2.18
4323 4801 4.443598 GGGCTTTGATCCTACTCACTAAGG 60.444 50.000 0.00 0.00 0.00 2.69
4324 4802 4.162509 GGCTTTGATCCTACTCACTAAGGT 59.837 45.833 0.00 0.00 34.30 3.50
4325 4803 5.112686 GCTTTGATCCTACTCACTAAGGTG 58.887 45.833 0.00 0.00 44.23 4.00
4942 5426 0.610687 GCTTATAGGCCCTCAGCGAT 59.389 55.000 0.00 0.00 45.17 4.58
4974 5458 0.678950 CCTTTGCCGTTTTGGGATGT 59.321 50.000 0.00 0.00 38.21 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
143 144 0.672342 GCAGGGGATGATGACAATGC 59.328 55.000 0.00 0.00 0.00 3.56
161 162 0.948678 TTTGACTTTGCACGGGTAGC 59.051 50.000 0.00 0.00 0.00 3.58
167 168 4.009798 TGTACTTGTTTGACTTTGCACG 57.990 40.909 0.00 0.00 0.00 5.34
252 253 5.304357 TGAGTTTGGATGAGTCTTACAGTGA 59.696 40.000 0.00 0.00 0.00 3.41
335 337 1.340248 GGATATGACGGTGATGACGGT 59.660 52.381 0.00 0.00 38.28 4.83
338 340 3.577649 ATCGGATATGACGGTGATGAC 57.422 47.619 0.00 0.00 0.00 3.06
362 364 5.801531 ATAAACGTGTATAGATGGAGGCA 57.198 39.130 0.00 0.00 0.00 4.75
413 416 6.976925 ACGGATTTTAGTTACGAGGATGTTAG 59.023 38.462 0.00 0.00 0.00 2.34
495 504 4.434685 GCCTCCAGCGAATCTCAG 57.565 61.111 0.00 0.00 0.00 3.35
506 515 2.927856 TTCGCCCTTGAGCCTCCA 60.928 61.111 0.00 0.00 0.00 3.86
599 622 2.361438 GCCGTCAGCACCTAGTAATACT 59.639 50.000 0.00 0.00 42.97 2.12
616 639 2.665052 GACGAGAAAATAAAGACGCCGT 59.335 45.455 0.00 0.00 0.00 5.68
633 656 3.755628 GCAGTACCTGGCCGACGA 61.756 66.667 0.00 0.00 31.21 4.20
691 714 1.300233 CTATCTTCCTGTCGCCGCC 60.300 63.158 0.00 0.00 0.00 6.13
693 716 1.364171 CCCTATCTTCCTGTCGCCG 59.636 63.158 0.00 0.00 0.00 6.46
817 881 3.738429 AAATACCCGCCCGCCGTAC 62.738 63.158 0.00 0.00 34.38 3.67
818 882 1.680522 TAAAATACCCGCCCGCCGTA 61.681 55.000 0.00 0.00 34.38 4.02
819 883 2.533974 TTAAAATACCCGCCCGCCGT 62.534 55.000 0.00 0.00 34.38 5.68
820 884 1.167781 ATTAAAATACCCGCCCGCCG 61.168 55.000 0.00 0.00 0.00 6.46
835 899 4.324135 CGGTCATTTCACACGTCGTATTAA 59.676 41.667 0.00 0.00 0.00 1.40
843 907 0.601841 GGGACGGTCATTTCACACGT 60.602 55.000 10.76 0.00 40.85 4.49
858 922 3.437741 CACACCCAAAACGTATAAGGGAC 59.562 47.826 18.66 0.00 42.25 4.46
859 923 3.072768 ACACACCCAAAACGTATAAGGGA 59.927 43.478 18.66 0.00 42.25 4.20
861 925 3.816523 ACACACACCCAAAACGTATAAGG 59.183 43.478 0.00 0.00 0.00 2.69
862 926 4.778904 CACACACACCCAAAACGTATAAG 58.221 43.478 0.00 0.00 0.00 1.73
863 927 3.003482 GCACACACACCCAAAACGTATAA 59.997 43.478 0.00 0.00 0.00 0.98
864 928 2.548904 GCACACACACCCAAAACGTATA 59.451 45.455 0.00 0.00 0.00 1.47
865 929 1.335496 GCACACACACCCAAAACGTAT 59.665 47.619 0.00 0.00 0.00 3.06
877 942 0.179097 TTCTGTACAGCGCACACACA 60.179 50.000 18.45 7.08 0.00 3.72
879 944 1.221466 GCTTCTGTACAGCGCACACA 61.221 55.000 23.55 9.44 0.00 3.72
881 946 3.951332 GCTTCTGTACAGCGCACA 58.049 55.556 23.55 4.18 0.00 4.57
886 951 1.355066 GAGGTGCGCTTCTGTACAGC 61.355 60.000 18.45 7.55 0.00 4.40
887 952 0.244994 AGAGGTGCGCTTCTGTACAG 59.755 55.000 17.17 17.17 29.30 2.74
960 1029 3.117171 CTCACTCGCAGTGCCAGC 61.117 66.667 9.89 0.00 45.54 4.85
978 1047 1.227380 CTTCTCCTCCAATCCCGCG 60.227 63.158 0.00 0.00 0.00 6.46
1067 1179 1.137872 GCTCGTTCATGGAGATGGAGT 59.862 52.381 2.03 0.00 33.27 3.85
1219 1331 7.024768 GCTAGCGACCAAAATATAACACAAAA 58.975 34.615 0.00 0.00 0.00 2.44
1225 1337 5.748592 CAAGGCTAGCGACCAAAATATAAC 58.251 41.667 9.00 0.00 0.00 1.89
1229 1341 2.014128 GCAAGGCTAGCGACCAAAATA 58.986 47.619 9.00 0.00 0.00 1.40
1230 1342 0.811281 GCAAGGCTAGCGACCAAAAT 59.189 50.000 9.00 0.00 0.00 1.82
1232 1344 1.674322 GGCAAGGCTAGCGACCAAA 60.674 57.895 9.00 0.00 0.00 3.28
1290 1487 4.331137 ACGATGAAATGTGCGTATTTTCG 58.669 39.130 13.48 13.48 36.81 3.46
1387 1587 0.460987 CGCTTCCCGATCTTGAGCTT 60.461 55.000 0.00 0.00 40.02 3.74
2172 2372 7.255871 GCTCTTATATTTCTTTACGGAGGGAGA 60.256 40.741 0.00 0.00 0.00 3.71
2173 2373 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
2174 2374 6.516194 CGCTCTTATATTTCTTTACGGAGGGA 60.516 42.308 0.00 0.00 34.63 4.20
2175 2375 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
2176 2376 6.214399 ACGCTCTTATATTTCTTTACGGAGG 58.786 40.000 0.00 0.00 0.00 4.30
2177 2377 7.695869 AACGCTCTTATATTTCTTTACGGAG 57.304 36.000 0.00 0.00 0.00 4.63
2178 2378 9.241317 CTAAACGCTCTTATATTTCTTTACGGA 57.759 33.333 0.00 0.00 0.00 4.69
2179 2379 9.241317 TCTAAACGCTCTTATATTTCTTTACGG 57.759 33.333 0.00 0.00 0.00 4.02
2183 2383 8.979574 CCGATCTAAACGCTCTTATATTTCTTT 58.020 33.333 0.00 0.00 0.00 2.52
2184 2384 7.599245 CCCGATCTAAACGCTCTTATATTTCTT 59.401 37.037 0.00 0.00 0.00 2.52
2185 2385 7.039923 TCCCGATCTAAACGCTCTTATATTTCT 60.040 37.037 0.00 0.00 0.00 2.52
2186 2386 7.088905 TCCCGATCTAAACGCTCTTATATTTC 58.911 38.462 0.00 0.00 0.00 2.17
2187 2387 6.989659 TCCCGATCTAAACGCTCTTATATTT 58.010 36.000 0.00 0.00 0.00 1.40
2188 2388 6.208994 ACTCCCGATCTAAACGCTCTTATATT 59.791 38.462 0.00 0.00 0.00 1.28
2189 2389 5.711036 ACTCCCGATCTAAACGCTCTTATAT 59.289 40.000 0.00 0.00 0.00 0.86
2190 2390 5.068636 ACTCCCGATCTAAACGCTCTTATA 58.931 41.667 0.00 0.00 0.00 0.98
2191 2391 3.890147 ACTCCCGATCTAAACGCTCTTAT 59.110 43.478 0.00 0.00 0.00 1.73
2192 2392 3.285484 ACTCCCGATCTAAACGCTCTTA 58.715 45.455 0.00 0.00 0.00 2.10
2193 2393 2.100989 ACTCCCGATCTAAACGCTCTT 58.899 47.619 0.00 0.00 0.00 2.85
2194 2394 1.765230 ACTCCCGATCTAAACGCTCT 58.235 50.000 0.00 0.00 0.00 4.09
2195 2395 3.705043 TTACTCCCGATCTAAACGCTC 57.295 47.619 0.00 0.00 0.00 5.03
2196 2396 5.979288 ATATTACTCCCGATCTAAACGCT 57.021 39.130 0.00 0.00 0.00 5.07
2197 2397 8.699283 AAATATATTACTCCCGATCTAAACGC 57.301 34.615 0.00 0.00 0.00 4.84
2206 2406 9.529823 AGACAGACATAAATATATTACTCCCGA 57.470 33.333 0.00 0.00 0.00 5.14
2207 2407 9.574458 CAGACAGACATAAATATATTACTCCCG 57.426 37.037 0.00 0.00 0.00 5.14
2433 2676 9.490379 TTTTGCTTTAGACTTCTACTCCTTTAG 57.510 33.333 0.00 0.00 0.00 1.85
2435 2678 8.926092 ATTTTGCTTTAGACTTCTACTCCTTT 57.074 30.769 0.00 0.00 0.00 3.11
2438 2681 9.438228 ACTTATTTTGCTTTAGACTTCTACTCC 57.562 33.333 0.00 0.00 0.00 3.85
2744 3030 0.881118 CCGGTGTTCAACATTCCAGG 59.119 55.000 0.00 0.00 0.00 4.45
2765 3051 3.199727 TGACATGGCTAGGCATAGTTCAA 59.800 43.478 29.30 15.93 0.00 2.69
2781 3067 8.299570 GCCCCAGTTTAGAATATTATTGACATG 58.700 37.037 0.00 0.00 0.00 3.21
2863 3164 5.165676 TGTGGTGTTACAACGATATGTCTC 58.834 41.667 0.00 0.00 34.75 3.36
3077 3378 6.238320 GGTCAGTGATGATTTCTGATTAGTGC 60.238 42.308 0.00 0.00 39.77 4.40
3129 3430 5.836898 TCCACCAGTTCTACGGTTATATGAT 59.163 40.000 0.00 0.00 31.41 2.45
3132 3433 7.844493 TTATCCACCAGTTCTACGGTTATAT 57.156 36.000 0.00 0.00 31.41 0.86
3173 3474 0.991920 CCCTTTGCCTCTACCCAAGA 59.008 55.000 0.00 0.00 0.00 3.02
3174 3475 0.698818 ACCCTTTGCCTCTACCCAAG 59.301 55.000 0.00 0.00 0.00 3.61
3175 3476 2.047769 TACCCTTTGCCTCTACCCAA 57.952 50.000 0.00 0.00 0.00 4.12
3272 3573 7.769507 GTCCCATAAGAAAAGAACCCTACTAAG 59.230 40.741 0.00 0.00 0.00 2.18
3308 3609 9.216117 GTGTTTTGTACTCCTAAATATCACTGT 57.784 33.333 0.00 0.00 0.00 3.55
3309 3610 9.436957 AGTGTTTTGTACTCCTAAATATCACTG 57.563 33.333 0.00 0.00 30.04 3.66
3332 3633 7.416154 TGTTTCCAAACGTTTCTATCTAGTG 57.584 36.000 11.37 0.00 41.74 2.74
3337 3802 7.980742 AACTTTGTTTCCAAACGTTTCTATC 57.019 32.000 11.37 2.06 41.74 2.08
3339 3804 9.857957 ATTTAACTTTGTTTCCAAACGTTTCTA 57.142 25.926 11.37 0.00 41.74 2.10
3349 3814 4.651503 TGGGCTGATTTAACTTTGTTTCCA 59.348 37.500 0.00 0.00 0.00 3.53
3374 3839 2.906389 TGTCTCCAGACTACTGCCATTT 59.094 45.455 8.19 0.00 44.99 2.32
3384 3849 7.732222 AATCTAATCTTCTTGTCTCCAGACT 57.268 36.000 8.19 0.00 44.99 3.24
3440 3905 5.052693 TGGATGGACAGGAATATTCTTGG 57.947 43.478 25.95 13.80 38.46 3.61
3494 3959 5.598417 ACATATTTCCAAATAAGGTGCCTCC 59.402 40.000 0.00 0.00 34.79 4.30
3517 3982 9.257651 ACTTAGTATTATATTCTCACCGCAAAC 57.742 33.333 0.00 0.00 0.00 2.93
3569 4034 3.777106 TGTCCAGATGTGAGCTTCTTT 57.223 42.857 0.00 0.00 0.00 2.52
3581 4046 5.127682 GCCTCCATAAAATGTTTGTCCAGAT 59.872 40.000 0.00 0.00 0.00 2.90
3611 4076 7.095523 CGCATTTTTCCTTCTGATTTGTCATTT 60.096 33.333 0.00 0.00 0.00 2.32
3618 4083 4.082026 CCCTCGCATTTTTCCTTCTGATTT 60.082 41.667 0.00 0.00 0.00 2.17
3636 4101 3.621715 GCACACTAATCTTAAACCCCTCG 59.378 47.826 0.00 0.00 0.00 4.63
4091 4560 5.209240 TGCGTTTTCTCGAAAAACAATAGG 58.791 37.500 23.27 14.11 41.37 2.57
4129 4598 7.684937 AACTCTCTCTTTTCAATGGAATGAG 57.315 36.000 10.07 10.07 36.32 2.90
4301 4779 4.162509 ACCTTAGTGAGTAGGATCAAAGCC 59.837 45.833 0.00 0.00 35.45 4.35
4302 4780 5.346181 ACCTTAGTGAGTAGGATCAAAGC 57.654 43.478 0.00 0.00 35.45 3.51
4315 4793 7.979069 CAACCATCCGTTCACACCTTAGTGA 62.979 48.000 0.00 0.00 46.12 3.41
4316 4794 5.856216 CAACCATCCGTTCACACCTTAGTG 61.856 50.000 0.00 0.00 40.57 2.74
4317 4795 1.975680 ACCATCCGTTCACACCTTAGT 59.024 47.619 0.00 0.00 0.00 2.24
4318 4796 2.742053 CAACCATCCGTTCACACCTTAG 59.258 50.000 0.00 0.00 29.93 2.18
4319 4797 2.773487 CAACCATCCGTTCACACCTTA 58.227 47.619 0.00 0.00 29.93 2.69
4320 4798 1.604604 CAACCATCCGTTCACACCTT 58.395 50.000 0.00 0.00 29.93 3.50
4321 4799 0.889186 GCAACCATCCGTTCACACCT 60.889 55.000 0.00 0.00 29.93 4.00
4322 4800 1.579429 GCAACCATCCGTTCACACC 59.421 57.895 0.00 0.00 29.93 4.16
4323 4801 1.206578 CGCAACCATCCGTTCACAC 59.793 57.895 0.00 0.00 29.93 3.82
4324 4802 2.612567 GCGCAACCATCCGTTCACA 61.613 57.895 0.30 0.00 29.93 3.58
4325 4803 2.175811 GCGCAACCATCCGTTCAC 59.824 61.111 0.30 0.00 29.93 3.18
4542 5026 3.871395 CCTGCTAGCCTGCCCCTC 61.871 72.222 13.29 0.00 0.00 4.30
4758 5242 1.134521 CACTGCTAAATCCGCCTACCA 60.135 52.381 0.00 0.00 0.00 3.25
4927 5411 1.528292 GACGATCGCTGAGGGCCTAT 61.528 60.000 16.60 0.00 37.74 2.57
4942 5426 1.542547 GGCAAAGGAAGAACAGGACGA 60.543 52.381 0.00 0.00 0.00 4.20
4974 5458 2.276409 CCCCTTGCTGCATGCCTA 59.724 61.111 16.68 0.00 42.00 3.93
5002 5486 0.248215 GATCAATGGGCGCTTCGTTG 60.248 55.000 21.53 21.53 33.69 4.10


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

AutoCloner maintained by Alex Coulton.