Multiple sequence alignment - TraesCS7A01G007400

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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 TraesCS7A01G007400 chr7A 100.000 5830 0 0 1 5830 3378609 3384438 0.000000e+00 10767.0
1 TraesCS7A01G007400 chr7A 90.614 2738 227 16 3044 5763 2552380 2549655 0.000000e+00 3605.0
2 TraesCS7A01G007400 chr7A 91.803 2574 194 10 3072 5633 3001941 2999373 0.000000e+00 3568.0
3 TraesCS7A01G007400 chr7A 91.041 2489 187 20 2592 5072 3582940 3585400 0.000000e+00 3328.0
4 TraesCS7A01G007400 chr7A 91.715 1038 82 2 989 2023 3004367 3003331 0.000000e+00 1437.0
5 TraesCS7A01G007400 chr7A 96.784 684 0 1 254 915 3378628 3379311 0.000000e+00 1122.0
6 TraesCS7A01G007400 chr7A 96.784 684 0 1 20 703 3378862 3379523 0.000000e+00 1122.0
7 TraesCS7A01G007400 chr7A 95.075 467 1 1 488 932 3378628 3379094 0.000000e+00 715.0
8 TraesCS7A01G007400 chr7A 95.075 467 1 1 20 486 3379096 3379540 0.000000e+00 715.0
9 TraesCS7A01G007400 chr7A 99.571 233 1 0 700 932 3378628 3378860 5.400000e-115 425.0
10 TraesCS7A01G007400 chr7A 99.571 233 1 0 20 252 3379308 3379540 5.400000e-115 425.0
11 TraesCS7A01G007400 chr7A 80.806 422 38 16 2598 3004 3002351 3001958 2.060000e-74 291.0
12 TraesCS7A01G007400 chr7A 98.684 76 1 0 1 76 679852833 679852908 1.020000e-27 135.0
13 TraesCS7A01G007400 chr7A 98.246 57 1 0 254 310 679852852 679852908 3.720000e-17 100.0
14 TraesCS7A01G007400 chr7A 98.246 57 1 0 488 544 679852852 679852908 3.720000e-17 100.0
15 TraesCS7A01G007400 chr7A 98.246 57 1 0 700 756 679852852 679852908 3.720000e-17 100.0
16 TraesCS7A01G007400 chr4A 90.212 3157 257 30 2620 5763 739808226 739811343 0.000000e+00 4071.0
17 TraesCS7A01G007400 chr4A 90.739 2991 232 27 2620 5599 740868112 740865156 0.000000e+00 3947.0
18 TraesCS7A01G007400 chr4A 89.294 3157 278 31 2622 5763 733927517 733924406 0.000000e+00 3903.0
19 TraesCS7A01G007400 chr4A 89.683 2869 250 22 2592 5445 739832908 739835745 0.000000e+00 3616.0
20 TraesCS7A01G007400 chr4A 89.145 2432 216 26 2598 5019 740061697 740059304 0.000000e+00 2985.0
21 TraesCS7A01G007400 chr4A 90.000 2300 189 25 2599 4888 742270089 742267821 0.000000e+00 2935.0
22 TraesCS7A01G007400 chr4A 88.059 1298 127 13 752 2038 741888088 741886808 0.000000e+00 1513.0
23 TraesCS7A01G007400 chr4A 91.162 1041 88 2 993 2029 739806199 739807239 0.000000e+00 1410.0
24 TraesCS7A01G007400 chr4A 91.005 1045 89 3 989 2029 740869558 740868515 0.000000e+00 1404.0
25 TraesCS7A01G007400 chr4A 89.658 1112 96 7 929 2028 740063338 740062234 0.000000e+00 1399.0
26 TraesCS7A01G007400 chr4A 89.128 1113 101 9 929 2028 742271735 742270630 0.000000e+00 1367.0
27 TraesCS7A01G007400 chr4A 91.869 578 32 4 4940 5504 742267812 742267237 0.000000e+00 793.0
28 TraesCS7A01G007400 chr4A 88.693 283 23 5 5482 5763 742078164 742078438 2.600000e-88 337.0
29 TraesCS7A01G007400 chr4A 88.028 284 24 5 5482 5763 739684182 739684457 1.570000e-85 327.0
30 TraesCS7A01G007400 chr4A 89.024 246 22 3 5474 5719 739835742 739835982 3.410000e-77 300.0
31 TraesCS7A01G007400 chr4A 80.563 355 40 8 2592 2943 740657851 740658179 4.510000e-61 246.0
32 TraesCS7A01G007400 chr4A 90.909 165 15 0 5568 5732 742267235 742267071 7.600000e-54 222.0
33 TraesCS7A01G007400 chr4A 86.188 181 22 3 306 486 741888088 741887911 5.960000e-45 193.0
34 TraesCS7A01G007400 chr4A 86.188 181 22 3 72 252 741888088 741887911 5.960000e-45 193.0
35 TraesCS7A01G007400 chr4A 87.730 163 17 3 540 702 741888088 741887929 2.770000e-43 187.0
36 TraesCS7A01G007400 chr7D 90.899 2659 201 17 3087 5732 2430080 2432710 0.000000e+00 3531.0
37 TraesCS7A01G007400 chr7D 89.174 2457 225 25 2620 5072 3699371 3701790 0.000000e+00 3025.0
38 TraesCS7A01G007400 chr7D 89.759 2324 206 18 2614 4934 3440481 3442775 0.000000e+00 2944.0
39 TraesCS7A01G007400 chr7D 89.055 1407 131 10 752 2147 2427001 2428395 0.000000e+00 1724.0
40 TraesCS7A01G007400 chr7D 91.022 1047 90 2 987 2029 3438496 3439542 0.000000e+00 1410.0
41 TraesCS7A01G007400 chr7D 87.738 1207 118 17 879 2072 3731373 3730184 0.000000e+00 1382.0
42 TraesCS7A01G007400 chr7D 85.870 1104 95 30 2592 3686 3583330 3584381 0.000000e+00 1118.0
43 TraesCS7A01G007400 chr7D 85.422 391 26 8 2620 3007 2429689 2430051 1.530000e-100 377.0
44 TraesCS7A01G007400 chr7D 89.960 249 14 5 5518 5763 3443415 3443655 1.580000e-80 311.0
45 TraesCS7A01G007400 chr7D 92.896 183 10 2 72 252 2427001 2427182 4.480000e-66 263.0
46 TraesCS7A01G007400 chr7D 92.896 183 10 2 306 486 2427001 2427182 4.480000e-66 263.0
47 TraesCS7A01G007400 chr7D 92.941 170 8 3 540 706 2427001 2427169 1.620000e-60 244.0
48 TraesCS7A01G007400 chr3A 100.000 74 0 0 3 76 6897341 6897414 2.830000e-28 137.0
49 TraesCS7A01G007400 chr3A 100.000 57 0 0 254 310 6897358 6897414 7.990000e-19 106.0
50 TraesCS7A01G007400 chr3A 100.000 57 0 0 488 544 6897358 6897414 7.990000e-19 106.0
51 TraesCS7A01G007400 chr3A 100.000 57 0 0 700 756 6897358 6897414 7.990000e-19 106.0
52 TraesCS7A01G007400 chrUn 97.368 76 2 0 1 76 103119606 103119681 4.740000e-26 130.0
53 TraesCS7A01G007400 chrUn 96.491 57 2 0 254 310 103119625 103119681 1.730000e-15 95.3
54 TraesCS7A01G007400 chrUn 96.491 57 2 0 488 544 103119625 103119681 1.730000e-15 95.3
55 TraesCS7A01G007400 chrUn 96.491 57 2 0 700 756 103119625 103119681 1.730000e-15 95.3
56 TraesCS7A01G007400 chr5B 85.345 116 15 2 2623 2736 695658468 695658583 1.030000e-22 119.0
57 TraesCS7A01G007400 chr3B 94.667 75 4 0 1 75 118604141 118604067 3.690000e-22 117.0
58 TraesCS7A01G007400 chr3B 96.491 57 2 0 699 755 118604123 118604067 1.730000e-15 95.3
59 TraesCS7A01G007400 chr3B 96.491 57 2 0 487 543 118604123 118604067 1.730000e-15 95.3
60 TraesCS7A01G007400 chr3B 96.491 57 2 0 253 309 118604123 118604067 1.730000e-15 95.3
61 TraesCS7A01G007400 chr3D 96.226 53 2 0 24 76 2472884 2472936 2.890000e-13 87.9
62 TraesCS7A01G007400 chr3D 96.226 53 2 0 258 310 2472884 2472936 2.890000e-13 87.9
63 TraesCS7A01G007400 chr3D 96.226 53 2 0 492 544 2472884 2472936 2.890000e-13 87.9
64 TraesCS7A01G007400 chr3D 96.226 53 2 0 704 756 2472884 2472936 2.890000e-13 87.9


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 TraesCS7A01G007400 chr7A 3378609 3384438 5829 False 10767.000000 10767 100.000000 1 5830 1 chr7A.!!$F1 5829
1 TraesCS7A01G007400 chr7A 2549655 2552380 2725 True 3605.000000 3605 90.614000 3044 5763 1 chr7A.!!$R1 2719
2 TraesCS7A01G007400 chr7A 3582940 3585400 2460 False 3328.000000 3328 91.041000 2592 5072 1 chr7A.!!$F2 2480
3 TraesCS7A01G007400 chr7A 2999373 3004367 4994 True 1765.333333 3568 88.108000 989 5633 3 chr7A.!!$R2 4644
4 TraesCS7A01G007400 chr7A 3378628 3379540 912 False 754.000000 1122 97.143333 20 932 6 chr7A.!!$F3 912
5 TraesCS7A01G007400 chr4A 733924406 733927517 3111 True 3903.000000 3903 89.294000 2622 5763 1 chr4A.!!$R1 3141
6 TraesCS7A01G007400 chr4A 739806199 739811343 5144 False 2740.500000 4071 90.687000 993 5763 2 chr4A.!!$F4 4770
7 TraesCS7A01G007400 chr4A 740865156 740869558 4402 True 2675.500000 3947 90.872000 989 5599 2 chr4A.!!$R3 4610
8 TraesCS7A01G007400 chr4A 740059304 740063338 4034 True 2192.000000 2985 89.401500 929 5019 2 chr4A.!!$R2 4090
9 TraesCS7A01G007400 chr4A 739832908 739835982 3074 False 1958.000000 3616 89.353500 2592 5719 2 chr4A.!!$F5 3127
10 TraesCS7A01G007400 chr4A 742267071 742271735 4664 True 1329.250000 2935 90.476500 929 5732 4 chr4A.!!$R5 4803
11 TraesCS7A01G007400 chr4A 741886808 741888088 1280 True 521.500000 1513 87.041250 72 2038 4 chr4A.!!$R4 1966
12 TraesCS7A01G007400 chr7D 3699371 3701790 2419 False 3025.000000 3025 89.174000 2620 5072 1 chr7D.!!$F2 2452
13 TraesCS7A01G007400 chr7D 3438496 3443655 5159 False 1555.000000 2944 90.247000 987 5763 3 chr7D.!!$F4 4776
14 TraesCS7A01G007400 chr7D 3730184 3731373 1189 True 1382.000000 1382 87.738000 879 2072 1 chr7D.!!$R1 1193
15 TraesCS7A01G007400 chr7D 3583330 3584381 1051 False 1118.000000 1118 85.870000 2592 3686 1 chr7D.!!$F1 1094
16 TraesCS7A01G007400 chr7D 2427001 2432710 5709 False 1067.000000 3531 90.684833 72 5732 6 chr7D.!!$F3 5660

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
979 991 5.652891 GGGACAGATTGTACTAGTGAAGAGA 59.347 44.000 5.39 0.00 30.12 3.10 F
1545 1560 1.208293 GAGGATCCTGTGGGAGTGAAC 59.792 57.143 22.02 0.00 45.86 3.18 F
2174 2235 0.249120 CATCCGCACACCTTAGGACA 59.751 55.000 4.77 0.00 35.36 4.02 F
2176 2237 0.320374 TCCGCACACCTTAGGACAAG 59.680 55.000 4.77 0.00 0.00 3.16 F
3982 5331 0.531532 CGTAGCATGCTTGGAGGGAG 60.532 60.000 28.02 4.89 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1891 1915 0.607762 TCATTGCTTTGCGGCCTGTA 60.608 50.000 0.00 0.0 0.00 2.74 R
2800 4098 0.694771 ACCTCTTTCTGAGCATGCCA 59.305 50.000 15.66 11.3 41.35 4.92 R
3917 5266 0.680618 TGGGCAGCACCTGAAAATTG 59.319 50.000 0.00 0.0 39.10 2.32 R
3990 5339 1.068333 CAACTTCAATGCCTTCCGTGG 60.068 52.381 0.00 0.0 0.00 4.94 R
4920 6275 1.016130 CACTCGAGAAGGCAACGCAT 61.016 55.000 21.68 0.0 46.39 4.73 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
979 991 5.652891 GGGACAGATTGTACTAGTGAAGAGA 59.347 44.000 5.39 0.00 30.12 3.10
980 992 6.153000 GGGACAGATTGTACTAGTGAAGAGAA 59.847 42.308 5.39 0.00 30.12 2.87
981 993 7.254852 GGACAGATTGTACTAGTGAAGAGAAG 58.745 42.308 5.39 0.00 0.00 2.85
982 994 7.121463 GGACAGATTGTACTAGTGAAGAGAAGA 59.879 40.741 5.39 0.00 0.00 2.87
983 995 8.050778 ACAGATTGTACTAGTGAAGAGAAGAG 57.949 38.462 5.39 0.00 0.00 2.85
1044 1056 2.968574 GGAAGCCACCATGAGATCTCTA 59.031 50.000 22.95 10.37 0.00 2.43
1185 1197 4.736896 GCCCTGGACGACCACGAC 62.737 72.222 1.37 0.00 41.77 4.34
1248 1260 2.479566 ACGACATGGAAGACTGCATT 57.520 45.000 0.00 0.00 29.85 3.56
1302 1314 2.101415 CCTCACCGATGTAAGATGCTCA 59.899 50.000 0.00 0.00 0.00 4.26
1430 1442 2.806019 GCAGCAGATATGGAGTGGACAG 60.806 54.545 0.00 0.00 0.00 3.51
1484 1499 2.013400 CCATGCTGTTACGTATGGCAA 58.987 47.619 17.11 5.95 39.67 4.52
1545 1560 1.208293 GAGGATCCTGTGGGAGTGAAC 59.792 57.143 22.02 0.00 45.86 3.18
1554 1569 1.274167 GTGGGAGTGAACGTGGACATA 59.726 52.381 0.00 0.00 0.00 2.29
1604 1625 4.343526 ACATGATAAAGGCTCTCATCGAGT 59.656 41.667 0.00 1.27 41.98 4.18
1609 1630 2.663826 AGGCTCTCATCGAGTTGTTC 57.336 50.000 0.00 0.00 41.98 3.18
1611 1632 2.564947 AGGCTCTCATCGAGTTGTTCTT 59.435 45.455 0.00 0.00 41.98 2.52
1669 1690 2.652313 GCCATGGCACTGTACCAAA 58.348 52.632 32.08 0.00 41.49 3.28
1731 1752 3.227948 GTCTCAGAACTTCGACGAAGAC 58.772 50.000 37.05 28.38 41.71 3.01
1802 1826 1.430369 AAGCCAAAGGAGGAGCAGGT 61.430 55.000 0.00 0.00 0.00 4.00
1891 1915 1.072159 GTGCCACTGCTCTCTGGTT 59.928 57.895 0.00 0.00 38.71 3.67
1968 2001 6.207417 ACCATGACCAACTTATTGAAGAACTG 59.793 38.462 0.00 0.00 38.15 3.16
2038 2091 8.032451 TGCTTTTCCTAAATTAGTAACCATTGC 58.968 33.333 0.00 0.00 0.00 3.56
2039 2092 7.220108 GCTTTTCCTAAATTAGTAACCATTGCG 59.780 37.037 0.00 0.00 0.00 4.85
2045 2098 2.018542 TAGTAACCATTGCGGACTGC 57.981 50.000 0.00 0.00 46.70 4.40
2079 2132 6.694447 CATCAAGTGTCTGAATTTTCCCAAT 58.306 36.000 0.00 0.00 0.00 3.16
2083 2136 7.710475 TCAAGTGTCTGAATTTTCCCAATTTTC 59.290 33.333 0.00 0.00 0.00 2.29
2085 2138 7.212274 AGTGTCTGAATTTTCCCAATTTTCAG 58.788 34.615 7.25 7.25 0.00 3.02
2100 2153 7.222611 CCCAATTTTCAGTGAACTTTACAACAG 59.777 37.037 4.68 0.00 0.00 3.16
2101 2154 7.759433 CCAATTTTCAGTGAACTTTACAACAGT 59.241 33.333 4.68 0.00 0.00 3.55
2110 2163 6.912591 GTGAACTTTACAACAGTTGGATGAAG 59.087 38.462 17.76 12.42 34.49 3.02
2111 2164 6.601613 TGAACTTTACAACAGTTGGATGAAGT 59.398 34.615 17.76 13.04 34.49 3.01
2117 2170 4.818546 ACAACAGTTGGATGAAGTTCAGAG 59.181 41.667 17.76 0.00 34.12 3.35
2123 2176 4.703645 TGGATGAAGTTCAGAGTACTCG 57.296 45.455 17.07 12.01 34.09 4.18
2131 2184 6.879993 TGAAGTTCAGAGTACTCGATCTTACT 59.120 38.462 24.64 18.25 30.38 2.24
2147 2208 9.004717 TCGATCTTACTATATTCTCACTTCCTG 57.995 37.037 0.00 0.00 0.00 3.86
2160 2221 5.018539 TCACTTCCTGTATAAACCATCCG 57.981 43.478 0.00 0.00 0.00 4.18
2166 2227 2.612212 CTGTATAAACCATCCGCACACC 59.388 50.000 0.00 0.00 0.00 4.16
2167 2228 2.237643 TGTATAAACCATCCGCACACCT 59.762 45.455 0.00 0.00 0.00 4.00
2168 2229 2.507407 ATAAACCATCCGCACACCTT 57.493 45.000 0.00 0.00 0.00 3.50
2170 2231 1.821216 AAACCATCCGCACACCTTAG 58.179 50.000 0.00 0.00 0.00 2.18
2172 2233 0.907704 ACCATCCGCACACCTTAGGA 60.908 55.000 4.77 0.00 37.17 2.94
2173 2234 0.462047 CCATCCGCACACCTTAGGAC 60.462 60.000 4.77 0.00 35.36 3.85
2174 2235 0.249120 CATCCGCACACCTTAGGACA 59.751 55.000 4.77 0.00 35.36 4.02
2175 2236 0.981183 ATCCGCACACCTTAGGACAA 59.019 50.000 4.77 0.00 35.36 3.18
2176 2237 0.320374 TCCGCACACCTTAGGACAAG 59.680 55.000 4.77 0.00 0.00 3.16
2177 2238 0.320374 CCGCACACCTTAGGACAAGA 59.680 55.000 4.77 0.00 0.00 3.02
2178 2239 1.270625 CCGCACACCTTAGGACAAGAA 60.271 52.381 4.77 0.00 0.00 2.52
2179 2240 2.489971 CGCACACCTTAGGACAAGAAA 58.510 47.619 4.77 0.00 0.00 2.52
2180 2241 2.875933 CGCACACCTTAGGACAAGAAAA 59.124 45.455 4.77 0.00 0.00 2.29
2182 2243 4.607955 GCACACCTTAGGACAAGAAAAAC 58.392 43.478 4.77 0.00 0.00 2.43
2183 2244 4.499188 GCACACCTTAGGACAAGAAAAACC 60.499 45.833 4.77 0.00 0.00 3.27
2184 2245 4.887655 CACACCTTAGGACAAGAAAAACCT 59.112 41.667 4.77 0.00 36.65 3.50
2185 2246 6.059484 CACACCTTAGGACAAGAAAAACCTA 58.941 40.000 4.77 0.00 34.42 3.08
2186 2247 6.715264 CACACCTTAGGACAAGAAAAACCTAT 59.285 38.462 4.77 0.00 35.37 2.57
2187 2248 7.881232 CACACCTTAGGACAAGAAAAACCTATA 59.119 37.037 4.77 0.00 35.37 1.31
2189 2250 8.727910 CACCTTAGGACAAGAAAAACCTATAAC 58.272 37.037 4.77 0.00 35.37 1.89
2190 2251 8.666821 ACCTTAGGACAAGAAAAACCTATAACT 58.333 33.333 4.77 0.00 35.37 2.24
2223 2583 7.035840 TGGAAATCTACGTAGGAATCTACAC 57.964 40.000 22.01 5.41 44.56 2.90
2225 2585 6.916932 GGAAATCTACGTAGGAATCTACACAC 59.083 42.308 22.01 1.82 44.56 3.82
2230 2590 7.660112 TCTACGTAGGAATCTACACACAAAAA 58.340 34.615 22.01 0.00 44.56 1.94
2269 2651 6.324561 TGCACTGTTAAGCACATCAATTTA 57.675 33.333 0.00 0.00 35.51 1.40
2311 2756 4.340950 TGGTGACTGAAAAATGGGAGTTTC 59.659 41.667 0.00 0.00 34.88 2.78
2312 2757 4.262036 GGTGACTGAAAAATGGGAGTTTCC 60.262 45.833 0.00 0.00 33.63 3.13
2314 2759 5.069119 GTGACTGAAAAATGGGAGTTTCCTT 59.931 40.000 0.00 0.00 36.57 3.36
2321 2766 8.421002 TGAAAAATGGGAGTTTCCTTAGAAAAG 58.579 33.333 0.00 0.00 43.48 2.27
2324 2769 8.727100 AAATGGGAGTTTCCTTAGAAAAGAAT 57.273 30.769 0.00 0.00 43.48 2.40
2328 2773 9.243105 TGGGAGTTTCCTTAGAAAAGAATAATG 57.757 33.333 0.00 0.00 43.48 1.90
2354 2857 7.413109 GCAAAGTTATGTAAGTAGTGGAGCTTC 60.413 40.741 0.00 0.00 0.00 3.86
2359 2863 5.916661 TGTAAGTAGTGGAGCTTCCTAAG 57.083 43.478 0.00 0.00 37.46 2.18
2407 2911 7.671495 AAAATTGCACAAGGAATATTTGTCC 57.329 32.000 0.00 0.00 36.67 4.02
2410 2914 5.132897 TGCACAAGGAATATTTGTCCAAC 57.867 39.130 0.00 0.00 36.67 3.77
2411 2915 4.021544 TGCACAAGGAATATTTGTCCAACC 60.022 41.667 0.00 0.00 36.67 3.77
2412 2916 4.220602 GCACAAGGAATATTTGTCCAACCT 59.779 41.667 0.00 0.00 36.67 3.50
2413 2917 5.279456 GCACAAGGAATATTTGTCCAACCTT 60.279 40.000 0.00 0.00 36.67 3.50
2414 2918 6.741240 GCACAAGGAATATTTGTCCAACCTTT 60.741 38.462 0.00 0.00 36.67 3.11
2415 2919 7.216494 CACAAGGAATATTTGTCCAACCTTTT 58.784 34.615 0.00 0.00 36.67 2.27
2418 2922 8.802267 CAAGGAATATTTGTCCAACCTTTTCTA 58.198 33.333 0.00 0.00 37.65 2.10
2419 2923 9.547279 AAGGAATATTTGTCCAACCTTTTCTAT 57.453 29.630 0.00 0.00 37.65 1.98
2420 2924 9.547279 AGGAATATTTGTCCAACCTTTTCTATT 57.453 29.630 0.00 0.00 37.65 1.73
2426 2930 8.710835 TTTGTCCAACCTTTTCTATTTGAAAC 57.289 30.769 0.00 0.00 43.55 2.78
2427 2931 7.654022 TGTCCAACCTTTTCTATTTGAAACT 57.346 32.000 0.00 0.00 43.55 2.66
2428 2932 7.488322 TGTCCAACCTTTTCTATTTGAAACTG 58.512 34.615 0.00 0.00 43.55 3.16
2434 2950 6.127196 ACCTTTTCTATTTGAAACTGGCAACA 60.127 34.615 9.84 0.00 44.34 3.33
2490 3095 8.107399 AGCAAATTTAGTACTTAACTTGGGTC 57.893 34.615 15.18 2.21 39.80 4.46
2517 3122 1.826720 ACAAGCCATGCCAAACCATAG 59.173 47.619 0.00 0.00 0.00 2.23
2518 3123 0.826062 AAGCCATGCCAAACCATAGC 59.174 50.000 0.00 0.00 31.28 2.97
2567 3173 8.561738 TTCTGTAACATTTAGAAAAGGCTAGG 57.438 34.615 0.00 0.00 0.00 3.02
2578 3184 9.886132 TTTAGAAAAGGCTAGGAAGTAACATAG 57.114 33.333 0.00 0.00 0.00 2.23
2579 3185 6.890293 AGAAAAGGCTAGGAAGTAACATAGG 58.110 40.000 0.00 0.00 0.00 2.57
2581 3187 6.487299 AAAGGCTAGGAAGTAACATAGGAG 57.513 41.667 0.00 0.00 0.00 3.69
2582 3188 5.145513 AGGCTAGGAAGTAACATAGGAGT 57.854 43.478 0.00 0.00 0.00 3.85
2584 3190 6.069994 AGGCTAGGAAGTAACATAGGAGTAC 58.930 44.000 0.00 0.00 0.00 2.73
2586 3192 7.073470 AGGCTAGGAAGTAACATAGGAGTACTA 59.927 40.741 0.00 0.00 35.80 1.82
2596 3888 9.322773 GTAACATAGGAGTACTAAAATTGGACC 57.677 37.037 0.00 0.00 34.79 4.46
2612 3904 7.573968 AATTGGACCTAAATAAGCTAGCAAG 57.426 36.000 18.83 4.08 0.00 4.01
2613 3905 5.693769 TGGACCTAAATAAGCTAGCAAGT 57.306 39.130 18.83 4.05 0.00 3.16
2617 3913 6.038382 GGACCTAAATAAGCTAGCAAGTTTCC 59.962 42.308 18.83 9.97 0.00 3.13
2618 3914 6.722328 ACCTAAATAAGCTAGCAAGTTTCCT 58.278 36.000 18.83 0.00 0.00 3.36
2682 3980 9.152595 CTCTTGATTGATGATATATGGTCTGTG 57.847 37.037 0.00 0.00 0.00 3.66
2696 3994 2.025887 GGTCTGTGGAAACATGGGAGAT 60.026 50.000 0.00 0.00 46.14 2.75
2719 4017 5.964758 TCATTAGAAATTGGTTGCCACATC 58.035 37.500 0.00 0.00 30.78 3.06
2726 4024 8.253867 AGAAATTGGTTGCCACATCATAATAT 57.746 30.769 0.00 0.00 30.78 1.28
2760 4058 9.705103 AGAAATTGGGAGATCATTAGAAATTGA 57.295 29.630 0.00 0.00 0.00 2.57
2763 4061 7.828508 TTGGGAGATCATTAGAAATTGATGG 57.171 36.000 0.00 0.00 32.84 3.51
2800 4098 3.701040 ACAAGATTTCAAGCTGTTGGTGT 59.299 39.130 0.00 0.00 34.09 4.16
2818 4116 1.093159 GTGGCATGCTCAGAAAGAGG 58.907 55.000 18.92 0.00 44.86 3.69
2857 4157 7.064609 TCTGCATACTGTTAATGTTCTAAGTGC 59.935 37.037 0.00 0.00 0.00 4.40
2862 4162 4.393834 TGTTAATGTTCTAAGTGCTGCCA 58.606 39.130 0.00 0.00 0.00 4.92
2864 4164 5.476599 TGTTAATGTTCTAAGTGCTGCCAAT 59.523 36.000 0.00 0.00 0.00 3.16
2893 4193 6.575162 AAGTCTATTTCTTCATGGCGTTTT 57.425 33.333 0.00 0.00 0.00 2.43
2894 4194 6.183309 AGTCTATTTCTTCATGGCGTTTTC 57.817 37.500 0.00 0.00 0.00 2.29
2896 4196 2.697431 TTTCTTCATGGCGTTTTCGG 57.303 45.000 0.00 0.00 44.29 4.30
2906 4206 0.675522 GCGTTTTCGGATCCCCAAGA 60.676 55.000 6.06 0.00 44.29 3.02
2918 4218 2.597455 TCCCCAAGAAGCAAAGAAAGG 58.403 47.619 0.00 0.00 0.00 3.11
2985 4321 4.701765 CGAAGGAGATGGAACTGATCATT 58.298 43.478 0.00 0.00 0.00 2.57
3070 4406 1.597854 CACGAGGCAGCAAAGGTCA 60.598 57.895 0.00 0.00 0.00 4.02
3088 4424 3.169908 GTCAGGAGAAAGAAGAGGTCCT 58.830 50.000 0.00 0.00 38.21 3.85
3098 4437 4.073425 AGAAGAGGTCCTTGAGGAGATT 57.927 45.455 0.00 0.00 46.49 2.40
3239 4579 1.005450 GTGGCTCCCCTTACATTGGAA 59.995 52.381 0.00 0.00 0.00 3.53
3284 4624 3.902261 TGCTATAATGATTTGCCAGCG 57.098 42.857 0.00 0.00 0.00 5.18
3332 4672 0.540597 GCATATTCCCCAAGGGCTCC 60.541 60.000 0.00 0.00 43.94 4.70
3335 4675 1.619298 TATTCCCCAAGGGCTCCAAT 58.381 50.000 0.00 0.00 43.94 3.16
3428 4768 4.437239 CAGAGGAAGTCGCAGAAACATAT 58.563 43.478 0.00 0.00 39.69 1.78
3633 4981 2.483877 CGACTTTCCATGCAAAGCAGTA 59.516 45.455 9.10 0.00 43.65 2.74
3644 4992 2.034558 GCAAAGCAGTAGTTCCAAGCAA 59.965 45.455 0.00 0.00 0.00 3.91
3698 5046 2.308039 GCGGTCACTGACGGTGTTC 61.308 63.158 14.06 8.64 45.50 3.18
3709 5057 2.027625 CGGTGTTCGGAAGCCAGAC 61.028 63.158 10.61 0.00 34.75 3.51
3728 5076 1.080025 CCGACGACTCCCTTTCCAC 60.080 63.158 0.00 0.00 0.00 4.02
3734 5082 1.270147 CGACTCCCTTTCCACTCGTTT 60.270 52.381 0.00 0.00 0.00 3.60
3779 5127 1.916181 GATCTTGAGGGTTGGAAGGGA 59.084 52.381 0.00 0.00 0.00 4.20
3802 5150 9.533253 GGGATTGACAAATAAACATCTAAATGG 57.467 33.333 0.00 0.00 37.19 3.16
3816 5164 6.932400 ACATCTAAATGGCATATGCAAAATGG 59.068 34.615 28.07 12.75 44.36 3.16
3893 5241 6.998968 AAGATTGAGAAGCTCCAGTATTTG 57.001 37.500 0.00 0.00 0.00 2.32
3947 5296 1.962822 GCTGCCCAAAGCTTTTGGC 60.963 57.895 35.79 35.79 46.12 4.52
3950 5299 1.597854 GCCCAAAGCTTTTGGCCAC 60.598 57.895 33.75 14.40 41.66 5.01
3982 5331 0.531532 CGTAGCATGCTTGGAGGGAG 60.532 60.000 28.02 4.89 0.00 4.30
3983 5332 0.543749 GTAGCATGCTTGGAGGGAGT 59.456 55.000 28.02 0.00 0.00 3.85
3990 5339 2.871453 TGCTTGGAGGGAGTAAAAACC 58.129 47.619 0.00 0.00 0.00 3.27
4022 5371 2.559698 TGAAGTTGCCCGATGAGAAA 57.440 45.000 0.00 0.00 0.00 2.52
4079 5428 3.514706 CAGGGATTGAGATCGATGAGGAT 59.485 47.826 0.54 0.00 32.84 3.24
4151 5500 5.182190 TGCCATTTACAAGCTCAATAAACGA 59.818 36.000 0.00 0.00 0.00 3.85
4175 5524 0.946221 GCGGTCAGACCTTCACACAG 60.946 60.000 17.95 0.31 35.66 3.66
4184 5533 1.060713 CCTTCACACAGTTACGCTCG 58.939 55.000 0.00 0.00 0.00 5.03
4259 5608 6.357367 TGAGGGCTCTGATTTTATTAACTCC 58.643 40.000 0.00 0.00 0.00 3.85
4280 5629 1.078143 GGACACCATGTCTGCTCCC 60.078 63.158 8.75 0.00 46.19 4.30
4349 5701 4.646492 CCCCCAAAGTGGATTAAAGATCTG 59.354 45.833 0.00 0.00 40.96 2.90
4436 5788 3.964031 AGGACCTGCCAAAATTGTTTACA 59.036 39.130 0.00 0.00 40.02 2.41
4532 5884 3.579709 CGATAGGGAGATCATTGTTCCG 58.420 50.000 0.00 0.00 31.59 4.30
4625 5977 2.711542 ACAGGAAAAGAGGTAATGCCG 58.288 47.619 0.00 0.00 43.70 5.69
4657 6009 4.526970 AGGATTGATATGCGGTTTGAAGT 58.473 39.130 0.00 0.00 0.00 3.01
4920 6275 3.139397 AGTGGGGGTTGTTTCATCAAGTA 59.861 43.478 0.00 0.00 0.00 2.24
4938 6295 0.530744 TATGCGTTGCCTTCTCGAGT 59.469 50.000 13.13 0.00 0.00 4.18
5136 6495 4.457603 TGTTTGATTGGGATTTCTGTACCG 59.542 41.667 0.00 0.00 0.00 4.02
5263 6646 5.049680 AGGCAATGTAGAGTTTGTGTTAACG 60.050 40.000 0.26 0.00 33.26 3.18
5286 6670 0.611714 TTTACCAGGAACTCCCGCTC 59.388 55.000 0.00 0.00 40.87 5.03
5331 6840 1.332195 AGCAAAGAAGAAACCCCTGC 58.668 50.000 0.00 0.00 0.00 4.85
5400 6909 6.936374 GTAGCAAACTACGTCAAGTTTTGTA 58.064 36.000 12.65 6.02 45.20 2.41
5463 6979 7.815383 ACAAAGTCATATCATAGGAATTCCCA 58.185 34.615 21.22 8.16 37.41 4.37
5633 7155 0.029267 AGGAGCATGGGGGAGAGAAT 60.029 55.000 0.00 0.00 0.00 2.40
5636 7158 1.003003 GAGCATGGGGGAGAGAATAGC 59.997 57.143 0.00 0.00 0.00 2.97
5663 7187 1.298859 ATCTCGGCCGACAAAGCAAC 61.299 55.000 27.28 0.00 0.00 4.17
5707 7231 3.329386 TGATCTTCTGCGAAGAAACAGG 58.671 45.455 19.73 0.00 34.57 4.00
5732 7256 5.296151 AGTTACTACCACTGCATGCATAT 57.704 39.130 22.97 10.03 0.00 1.78
5763 7287 5.584649 GTGTGTCGATATGATTTCCTGGAAA 59.415 40.000 23.08 23.08 35.94 3.13
5764 7288 6.093495 GTGTGTCGATATGATTTCCTGGAAAA 59.907 38.462 24.44 10.72 35.11 2.29
5765 7289 6.657117 TGTGTCGATATGATTTCCTGGAAAAA 59.343 34.615 24.44 16.34 35.11 1.94
5786 7310 6.421377 AAAACATTCAAGCTTGTTTGTTCC 57.579 33.333 31.04 0.00 43.33 3.62
5787 7311 4.058721 ACATTCAAGCTTGTTTGTTCCC 57.941 40.909 25.19 0.00 0.00 3.97
5788 7312 3.450457 ACATTCAAGCTTGTTTGTTCCCA 59.550 39.130 25.19 0.22 0.00 4.37
5789 7313 4.081198 ACATTCAAGCTTGTTTGTTCCCAA 60.081 37.500 25.19 9.83 0.00 4.12
5790 7314 4.543590 TTCAAGCTTGTTTGTTCCCAAA 57.456 36.364 25.19 6.10 38.22 3.28
5791 7315 4.122143 TCAAGCTTGTTTGTTCCCAAAG 57.878 40.909 25.19 0.00 41.09 2.77
5792 7316 3.766591 TCAAGCTTGTTTGTTCCCAAAGA 59.233 39.130 25.19 0.00 41.09 2.52
5793 7317 4.221703 TCAAGCTTGTTTGTTCCCAAAGAA 59.778 37.500 25.19 0.00 41.09 2.52
5794 7318 4.817318 AGCTTGTTTGTTCCCAAAGAAA 57.183 36.364 0.00 0.00 41.56 2.52
5795 7319 5.159273 AGCTTGTTTGTTCCCAAAGAAAA 57.841 34.783 0.00 0.00 41.56 2.29
5796 7320 5.178061 AGCTTGTTTGTTCCCAAAGAAAAG 58.822 37.500 0.00 0.00 41.56 2.27
5797 7321 4.332543 GCTTGTTTGTTCCCAAAGAAAAGG 59.667 41.667 0.00 0.00 41.56 3.11
5798 7322 5.729510 CTTGTTTGTTCCCAAAGAAAAGGA 58.270 37.500 0.00 0.00 41.56 3.36
5799 7323 5.746990 TGTTTGTTCCCAAAGAAAAGGAA 57.253 34.783 0.00 0.00 41.09 3.36
5813 7337 5.447624 GAAAAGGAACATTTTCTTCGGGA 57.552 39.130 14.53 0.00 43.01 5.14
5814 7338 5.838529 GAAAAGGAACATTTTCTTCGGGAA 58.161 37.500 14.53 0.00 43.01 3.97
5815 7339 4.848562 AAGGAACATTTTCTTCGGGAAC 57.151 40.909 0.00 0.00 33.13 3.62
5816 7340 3.827722 AGGAACATTTTCTTCGGGAACA 58.172 40.909 0.00 0.00 33.13 3.18
5817 7341 4.211920 AGGAACATTTTCTTCGGGAACAA 58.788 39.130 0.00 0.00 33.13 2.83
5818 7342 4.647399 AGGAACATTTTCTTCGGGAACAAA 59.353 37.500 0.00 0.00 33.13 2.83
5819 7343 4.743151 GGAACATTTTCTTCGGGAACAAAC 59.257 41.667 0.00 0.00 33.13 2.93
5820 7344 4.316205 ACATTTTCTTCGGGAACAAACC 57.684 40.909 0.00 0.00 33.13 3.27
5821 7345 3.069016 ACATTTTCTTCGGGAACAAACCC 59.931 43.478 0.00 0.00 45.92 4.11
5822 7346 1.694844 TTTCTTCGGGAACAAACCCC 58.305 50.000 0.00 0.00 46.62 4.95
5823 7347 0.551879 TTCTTCGGGAACAAACCCCA 59.448 50.000 0.00 0.00 46.62 4.96
5824 7348 0.551879 TCTTCGGGAACAAACCCCAA 59.448 50.000 0.00 0.00 46.62 4.12
5825 7349 1.063867 TCTTCGGGAACAAACCCCAAA 60.064 47.619 0.00 0.00 46.62 3.28
5826 7350 1.967779 CTTCGGGAACAAACCCCAAAT 59.032 47.619 0.00 0.00 46.62 2.32
5827 7351 2.973983 TCGGGAACAAACCCCAAATA 57.026 45.000 0.00 0.00 46.62 1.40
5828 7352 3.459710 TCGGGAACAAACCCCAAATAT 57.540 42.857 0.00 0.00 46.62 1.28
5829 7353 4.587976 TCGGGAACAAACCCCAAATATA 57.412 40.909 0.00 0.00 46.62 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 7.122650 TCCAAAAATAATCTTCTGCCTGTTAGG 59.877 37.037 0.00 0.00 38.80 2.69
12 13 8.055279 TCCAAAAATAATCTTCTGCCTGTTAG 57.945 34.615 0.00 0.00 0.00 2.34
13 14 8.593945 ATCCAAAAATAATCTTCTGCCTGTTA 57.406 30.769 0.00 0.00 0.00 2.41
14 15 6.916360 TCCAAAAATAATCTTCTGCCTGTT 57.084 33.333 0.00 0.00 0.00 3.16
15 16 7.486407 AATCCAAAAATAATCTTCTGCCTGT 57.514 32.000 0.00 0.00 0.00 4.00
16 17 8.782339 AAAATCCAAAAATAATCTTCTGCCTG 57.218 30.769 0.00 0.00 0.00 4.85
17 18 7.761249 CGAAAATCCAAAAATAATCTTCTGCCT 59.239 33.333 0.00 0.00 0.00 4.75
18 19 7.759433 TCGAAAATCCAAAAATAATCTTCTGCC 59.241 33.333 0.00 0.00 0.00 4.85
979 991 2.103771 TCTTCTGCTTCTGTGTGCTCTT 59.896 45.455 0.00 0.00 0.00 2.85
980 992 1.690893 TCTTCTGCTTCTGTGTGCTCT 59.309 47.619 0.00 0.00 0.00 4.09
981 993 2.160822 TCTTCTGCTTCTGTGTGCTC 57.839 50.000 0.00 0.00 0.00 4.26
982 994 2.424557 CATCTTCTGCTTCTGTGTGCT 58.575 47.619 0.00 0.00 0.00 4.40
983 995 1.467734 CCATCTTCTGCTTCTGTGTGC 59.532 52.381 0.00 0.00 0.00 4.57
1044 1056 4.101448 CCGCCCAGCTTGCCTAGT 62.101 66.667 0.00 0.00 0.00 2.57
1185 1197 2.037136 CCAACTCTTGAGCTGGCGG 61.037 63.158 7.08 0.00 0.00 6.13
1190 1202 2.039480 TGCTTCATCCAACTCTTGAGCT 59.961 45.455 0.00 0.00 0.00 4.09
1302 1314 3.309682 CGTAGATTGCCGTCACAATGAAT 59.690 43.478 0.85 0.00 40.31 2.57
1430 1442 1.039785 GGAGCTTCTTGGGATTGGGC 61.040 60.000 0.00 0.00 0.00 5.36
1519 1534 2.659063 CCACAGGATCCTCCGTGCA 61.659 63.158 21.55 0.00 42.75 4.57
1533 1548 1.331399 TGTCCACGTTCACTCCCACA 61.331 55.000 0.00 0.00 0.00 4.17
1545 1560 1.268794 CCGAGCTTCTCTATGTCCACG 60.269 57.143 0.00 0.00 0.00 4.94
1554 1569 2.294078 CCAACCCCCGAGCTTCTCT 61.294 63.158 0.00 0.00 0.00 3.10
1604 1625 5.048083 CCGAATCCAATCAAGGAAAGAACAA 60.048 40.000 0.00 0.00 41.92 2.83
1609 1630 3.129287 CCACCGAATCCAATCAAGGAAAG 59.871 47.826 0.00 0.00 41.92 2.62
1611 1632 2.041081 ACCACCGAATCCAATCAAGGAA 59.959 45.455 0.00 0.00 41.92 3.36
1669 1690 6.168389 GGCAGTCAAATTCATTCCTGAAATT 58.832 36.000 0.00 0.00 44.29 1.82
1802 1826 2.981914 CTTCCCTGTGTTGCTGCCCA 62.982 60.000 0.00 0.00 0.00 5.36
1845 1869 4.670221 CGCTTCACTGAGCTTTTAATGTCC 60.670 45.833 0.00 0.00 40.52 4.02
1891 1915 0.607762 TCATTGCTTTGCGGCCTGTA 60.608 50.000 0.00 0.00 0.00 2.74
2038 2091 1.721389 GATGCATACATACGCAGTCCG 59.279 52.381 0.00 0.00 43.93 4.79
2039 2092 2.754472 TGATGCATACATACGCAGTCC 58.246 47.619 0.00 0.00 43.93 3.85
2045 2098 5.043248 TCAGACACTTGATGCATACATACG 58.957 41.667 0.00 0.00 36.35 3.06
2047 2100 8.510243 AAATTCAGACACTTGATGCATACATA 57.490 30.769 0.00 0.00 36.35 2.29
2050 2103 6.749118 GGAAAATTCAGACACTTGATGCATAC 59.251 38.462 0.00 0.00 0.00 2.39
2079 2132 7.040340 TCCAACTGTTGTAAAGTTCACTGAAAA 60.040 33.333 18.38 0.00 35.70 2.29
2083 2136 5.811399 TCCAACTGTTGTAAAGTTCACTG 57.189 39.130 18.38 0.02 35.70 3.66
2085 2138 6.371809 TCATCCAACTGTTGTAAAGTTCAC 57.628 37.500 18.38 0.00 35.70 3.18
2100 2153 4.859798 CGAGTACTCTGAACTTCATCCAAC 59.140 45.833 20.34 0.00 0.00 3.77
2101 2154 4.765339 TCGAGTACTCTGAACTTCATCCAA 59.235 41.667 20.34 0.00 0.00 3.53
2147 2208 2.914059 AGGTGTGCGGATGGTTTATAC 58.086 47.619 0.00 0.00 0.00 1.47
2153 2214 0.907704 TCCTAAGGTGTGCGGATGGT 60.908 55.000 0.00 0.00 0.00 3.55
2160 2221 4.499188 GGTTTTTCTTGTCCTAAGGTGTGC 60.499 45.833 0.00 0.00 0.00 4.57
2201 2561 7.478322 TGTGTGTAGATTCCTACGTAGATTTC 58.522 38.462 24.15 15.41 46.37 2.17
2324 2769 9.378551 CTCCACTACTTACATAACTTTGCATTA 57.621 33.333 0.00 0.00 0.00 1.90
2328 2773 5.875359 AGCTCCACTACTTACATAACTTTGC 59.125 40.000 0.00 0.00 0.00 3.68
2413 2917 9.995003 ATAAATGTTGCCAGTTTCAAATAGAAA 57.005 25.926 0.00 0.00 43.71 2.52
2418 2922 9.206870 CAGTTATAAATGTTGCCAGTTTCAAAT 57.793 29.630 4.75 0.00 30.40 2.32
2419 2923 8.417106 TCAGTTATAAATGTTGCCAGTTTCAAA 58.583 29.630 12.28 0.00 30.40 2.69
2420 2924 7.946207 TCAGTTATAAATGTTGCCAGTTTCAA 58.054 30.769 12.28 0.00 30.40 2.69
2421 2925 7.517614 TCAGTTATAAATGTTGCCAGTTTCA 57.482 32.000 12.28 0.00 30.40 2.69
2422 2926 8.082242 AGTTCAGTTATAAATGTTGCCAGTTTC 58.918 33.333 12.28 0.00 30.40 2.78
2425 2929 7.524717 AAGTTCAGTTATAAATGTTGCCAGT 57.475 32.000 12.28 0.00 0.00 4.00
2426 2930 9.906660 TTAAAGTTCAGTTATAAATGTTGCCAG 57.093 29.630 12.28 0.00 0.00 4.85
2554 3160 7.842743 TCCTATGTTACTTCCTAGCCTTTTCTA 59.157 37.037 0.00 0.00 0.00 2.10
2561 3167 6.069994 AGTACTCCTATGTTACTTCCTAGCC 58.930 44.000 0.00 0.00 0.00 3.93
2584 3190 9.120538 TGCTAGCTTATTTAGGTCCAATTTTAG 57.879 33.333 17.23 0.00 35.80 1.85
2586 3192 7.954666 TGCTAGCTTATTTAGGTCCAATTTT 57.045 32.000 17.23 0.00 35.80 1.82
2589 3195 6.663734 ACTTGCTAGCTTATTTAGGTCCAAT 58.336 36.000 17.23 0.00 35.80 3.16
2590 3196 6.062258 ACTTGCTAGCTTATTTAGGTCCAA 57.938 37.500 17.23 0.00 35.80 3.53
2593 3885 6.824196 AGGAAACTTGCTAGCTTATTTAGGTC 59.176 38.462 17.23 2.03 37.44 3.85
2596 3888 8.950208 AGTAGGAAACTTGCTAGCTTATTTAG 57.050 34.615 17.23 6.20 43.67 1.85
2629 3925 4.341366 ACCTGCCAAGAAAAAGGAAATG 57.659 40.909 0.00 0.00 33.78 2.32
2682 3980 7.830099 ATTTCTAATGATCTCCCATGTTTCC 57.170 36.000 0.00 0.00 0.00 3.13
2696 3994 5.479724 TGATGTGGCAACCAATTTCTAATGA 59.520 36.000 0.00 0.00 34.18 2.57
2738 4036 7.453752 CCCATCAATTTCTAATGATCTCCCAAT 59.546 37.037 0.00 0.00 34.12 3.16
2739 4037 6.779049 CCCATCAATTTCTAATGATCTCCCAA 59.221 38.462 0.00 0.00 34.12 4.12
2740 4038 6.103057 TCCCATCAATTTCTAATGATCTCCCA 59.897 38.462 0.00 0.00 34.12 4.37
2741 4039 6.546484 TCCCATCAATTTCTAATGATCTCCC 58.454 40.000 0.00 0.00 34.12 4.30
2742 4040 7.230027 ACTCCCATCAATTTCTAATGATCTCC 58.770 38.462 0.00 0.00 34.12 3.71
2743 4041 9.784531 TTACTCCCATCAATTTCTAATGATCTC 57.215 33.333 0.00 0.00 34.12 2.75
2757 4055 9.483489 TCTTGTAGTTACTATTACTCCCATCAA 57.517 33.333 0.00 0.00 0.00 2.57
2758 4056 9.656323 ATCTTGTAGTTACTATTACTCCCATCA 57.344 33.333 0.00 0.00 0.00 3.07
2800 4098 0.694771 ACCTCTTTCTGAGCATGCCA 59.305 50.000 15.66 11.30 41.35 4.92
2818 4116 6.051717 ACAGTATGCAGATAATCAGTTCCAC 58.948 40.000 0.00 0.00 42.53 4.02
2857 4157 6.928520 AGAAATAGACTTTTGGAATTGGCAG 58.071 36.000 0.00 0.00 0.00 4.85
2862 4162 8.037166 GCCATGAAGAAATAGACTTTTGGAATT 58.963 33.333 0.00 0.00 35.19 2.17
2864 4164 6.349280 CGCCATGAAGAAATAGACTTTTGGAA 60.349 38.462 0.00 0.00 35.19 3.53
2893 4193 0.695924 TTTGCTTCTTGGGGATCCGA 59.304 50.000 5.45 0.00 35.24 4.55
2894 4194 1.098050 CTTTGCTTCTTGGGGATCCG 58.902 55.000 5.45 0.00 35.24 4.18
2896 4196 3.194329 CCTTTCTTTGCTTCTTGGGGATC 59.806 47.826 0.00 0.00 0.00 3.36
2906 4206 3.643320 CCCTTCTTTCCCTTTCTTTGCTT 59.357 43.478 0.00 0.00 0.00 3.91
2918 4218 6.240549 TGAGATCTTGTATCCCTTCTTTCC 57.759 41.667 0.00 0.00 0.00 3.13
2985 4321 2.799017 AGGAACATCAGCTGAATGCAA 58.201 42.857 22.50 0.00 45.94 4.08
3029 4365 5.111989 GGATCAGAAACACGATCATTGAGA 58.888 41.667 0.00 0.00 39.88 3.27
3070 4406 3.837731 CTCAAGGACCTCTTCTTTCTCCT 59.162 47.826 0.00 0.00 32.41 3.69
3088 4424 6.380846 CCCACAATATTTCCAAATCTCCTCAA 59.619 38.462 0.00 0.00 0.00 3.02
3098 4437 1.364328 AGGCCCCCACAATATTTCCAA 59.636 47.619 0.00 0.00 0.00 3.53
3191 4531 6.024552 TCTGGAAATAATGACTTGCAAACC 57.975 37.500 0.00 0.00 0.00 3.27
3239 4579 2.915869 TCAAGTATCCTTGTGACCCCT 58.084 47.619 0.00 0.00 46.70 4.79
3284 4624 3.204526 CAATGAGCAGGTCTTGAGATCC 58.795 50.000 0.38 0.00 0.00 3.36
3332 4672 6.421202 GGGTCAGACGCTTCTTACTAATATTG 59.579 42.308 10.36 0.00 0.00 1.90
3335 4675 4.036027 CGGGTCAGACGCTTCTTACTAATA 59.964 45.833 15.18 0.00 0.00 0.98
3617 4965 2.819608 GGAACTACTGCTTTGCATGGAA 59.180 45.455 0.00 0.00 38.13 3.53
3633 4981 4.889409 TGTTGAATTCTCTTGCTTGGAACT 59.111 37.500 7.05 0.00 0.00 3.01
3644 4992 6.041296 AGTTCATGCCTTTTGTTGAATTCTCT 59.959 34.615 7.05 0.00 31.39 3.10
3692 5040 1.671379 GGTCTGGCTTCCGAACACC 60.671 63.158 0.00 0.00 0.00 4.16
3698 5046 4.796231 CGTCGGGTCTGGCTTCCG 62.796 72.222 0.00 0.00 44.59 4.30
3709 5057 2.280552 TGGAAAGGGAGTCGTCGGG 61.281 63.158 0.00 0.00 0.00 5.14
3802 5150 3.062909 CAGCACAACCATTTTGCATATGC 59.937 43.478 21.09 21.09 38.81 3.14
3816 5164 3.503748 AGGCTCAAATACTTCAGCACAAC 59.496 43.478 0.00 0.00 33.22 3.32
3893 5241 5.179533 GTCTCCCTTATGTCAAGAGTTTCC 58.820 45.833 0.00 0.00 0.00 3.13
3917 5266 0.680618 TGGGCAGCACCTGAAAATTG 59.319 50.000 0.00 0.00 39.10 2.32
3921 5270 1.747325 GCTTTGGGCAGCACCTGAAA 61.747 55.000 0.00 0.00 39.83 2.69
3924 5273 1.751349 AAAGCTTTGGGCAGCACCTG 61.751 55.000 11.80 0.00 42.84 4.00
3947 5296 2.742372 CGGAGCCGTTTGAGGTGG 60.742 66.667 0.00 0.00 34.35 4.61
3982 5331 1.320507 TGCCTTCCGTGGGTTTTTAC 58.679 50.000 0.00 0.00 0.00 2.01
3983 5332 2.296073 ATGCCTTCCGTGGGTTTTTA 57.704 45.000 0.00 0.00 0.00 1.52
3990 5339 1.068333 CAACTTCAATGCCTTCCGTGG 60.068 52.381 0.00 0.00 0.00 4.94
3993 5342 3.406682 GCAACTTCAATGCCTTCCG 57.593 52.632 0.00 0.00 37.85 4.30
4013 5362 4.119862 TCGGCTCCTTATTTTTCTCATCG 58.880 43.478 0.00 0.00 0.00 3.84
4014 5363 5.760253 TCATCGGCTCCTTATTTTTCTCATC 59.240 40.000 0.00 0.00 0.00 2.92
4022 5371 3.378427 GTGCTTTCATCGGCTCCTTATTT 59.622 43.478 0.00 0.00 0.00 1.40
4079 5428 1.280133 AGGCTTGCTACAGCTGATGAA 59.720 47.619 23.35 3.78 42.66 2.57
4151 5500 1.985116 GAAGGTCTGACCGCCCTCT 60.985 63.158 20.49 0.00 44.90 3.69
4175 5524 2.103538 TCGATGGCCGAGCGTAAC 59.896 61.111 11.55 0.00 43.23 2.50
4184 5533 2.094649 GCTACATAGGTACTCGATGGCC 60.095 54.545 0.00 0.00 41.75 5.36
4199 5548 2.154462 GTTTGCAGACCACAGCTACAT 58.846 47.619 0.00 0.00 0.00 2.29
4280 5629 2.889045 CAGGCCAATGATGTATCTTGGG 59.111 50.000 5.01 9.61 36.48 4.12
4349 5701 8.966069 AAAGGGTTAGCTTGTAGAGATTATTC 57.034 34.615 0.00 0.00 0.00 1.75
4436 5788 1.687123 ACGCTGAGTGTAAAGGTGAGT 59.313 47.619 0.00 0.00 0.00 3.41
4532 5884 1.836802 AGACTCTTGAATCCTCCAGGC 59.163 52.381 0.00 0.00 34.44 4.85
4625 5977 3.672808 CATATCAATCCTCTCCAGTGCC 58.327 50.000 0.00 0.00 0.00 5.01
4657 6009 3.426787 TGCCGTAAATCCCTTCAAAGA 57.573 42.857 0.00 0.00 0.00 2.52
4920 6275 1.016130 CACTCGAGAAGGCAACGCAT 61.016 55.000 21.68 0.00 46.39 4.73
4938 6295 5.252547 TGGATGCAGTCTGTTTATTTAGCA 58.747 37.500 0.93 0.00 35.03 3.49
5263 6646 2.941064 GCGGGAGTTCCTGGTAAAATAC 59.059 50.000 8.99 0.00 42.72 1.89
5286 6670 5.176774 TGCTAAGACAATCAAACACGTACAG 59.823 40.000 0.00 0.00 0.00 2.74
5364 6873 2.028476 AGTTTGCTACAGTATGGTCGCA 60.028 45.455 0.00 0.00 43.62 5.10
5487 7003 9.092876 CAGCCAAAATTTCAAAAACTGTTACTA 57.907 29.630 0.00 0.00 0.00 1.82
5633 7155 3.120105 CCGAGATGAGGTGCGCTA 58.880 61.111 9.73 0.00 0.00 4.26
5663 7187 2.998670 ACTGACACTTCGCATCATTCTG 59.001 45.455 0.00 0.00 0.00 3.02
5732 7256 6.202762 GGAAATCATATCGACACACTATGCAA 59.797 38.462 0.00 0.00 0.00 4.08
5740 7264 5.351948 TTCCAGGAAATCATATCGACACA 57.648 39.130 0.00 0.00 0.00 3.72
5763 7287 5.353956 GGGAACAAACAAGCTTGAATGTTTT 59.646 36.000 33.62 22.65 44.91 2.43
5765 7289 4.081198 TGGGAACAAACAAGCTTGAATGTT 60.081 37.500 33.69 33.69 41.31 2.71
5766 7290 3.450457 TGGGAACAAACAAGCTTGAATGT 59.550 39.130 32.50 28.34 37.44 2.71
5767 7291 4.057406 TGGGAACAAACAAGCTTGAATG 57.943 40.909 32.50 27.74 37.44 2.67
5791 7315 5.447624 TCCCGAAGAAAATGTTCCTTTTC 57.552 39.130 0.00 1.95 42.72 2.29
5792 7316 5.128008 TGTTCCCGAAGAAAATGTTCCTTTT 59.872 36.000 0.00 0.00 35.85 2.27
5793 7317 4.647399 TGTTCCCGAAGAAAATGTTCCTTT 59.353 37.500 0.00 0.00 35.85 3.11
5794 7318 4.211920 TGTTCCCGAAGAAAATGTTCCTT 58.788 39.130 0.00 0.00 35.85 3.36
5795 7319 3.827722 TGTTCCCGAAGAAAATGTTCCT 58.172 40.909 0.00 0.00 35.85 3.36
5796 7320 4.577834 TTGTTCCCGAAGAAAATGTTCC 57.422 40.909 0.00 0.00 35.85 3.62
5797 7321 4.743151 GGTTTGTTCCCGAAGAAAATGTTC 59.257 41.667 1.73 0.00 35.72 3.18
5798 7322 4.442332 GGGTTTGTTCCCGAAGAAAATGTT 60.442 41.667 1.73 0.00 35.72 2.71
5799 7323 3.069016 GGGTTTGTTCCCGAAGAAAATGT 59.931 43.478 1.73 0.00 35.72 2.71
5800 7324 3.649073 GGGTTTGTTCCCGAAGAAAATG 58.351 45.455 1.73 0.00 35.72 2.32


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

AutoCloner maintained by Alex Coulton.