Multiple sequence alignment - TraesCS5A01G174300

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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 TraesCS5A01G174300 chr5A 100.000 6719 0 0 1 6719 367599324 367592606 0.000000e+00 12408.0
1 TraesCS5A01G174300 chr5A 95.763 118 5 0 2271 2388 9610212 9610329 2.470000e-44 191.0
2 TraesCS5A01G174300 chr5A 96.552 116 3 1 2273 2388 69844783 69844897 2.470000e-44 191.0
3 TraesCS5A01G174300 chr5A 100.000 32 0 0 2013 2044 367597246 367597215 7.280000e-05 60.2
4 TraesCS5A01G174300 chr5A 100.000 32 0 0 2079 2110 367597312 367597281 7.280000e-05 60.2
5 TraesCS5A01G174300 chr5B 93.860 2329 75 30 1 2281 316369406 316367098 0.000000e+00 3446.0
6 TraesCS5A01G174300 chr5B 94.189 1652 48 17 2383 4004 316367101 316365468 0.000000e+00 2475.0
7 TraesCS5A01G174300 chr5B 92.206 911 45 11 5306 6207 316364376 316363483 0.000000e+00 1266.0
8 TraesCS5A01G174300 chr5B 88.842 708 70 5 4534 5238 292490456 292489755 0.000000e+00 861.0
9 TraesCS5A01G174300 chr5B 93.333 435 22 4 4111 4545 316364833 316364406 2.640000e-178 636.0
10 TraesCS5A01G174300 chr5B 95.087 346 14 1 6328 6670 316363054 316362709 5.930000e-150 542.0
11 TraesCS5A01G174300 chr5B 92.857 126 7 2 2266 2390 515669446 515669570 1.490000e-41 182.0
12 TraesCS5A01G174300 chr5B 98.571 70 1 0 5237 5306 316364416 316364347 2.540000e-24 124.0
13 TraesCS5A01G174300 chr5B 100.000 36 0 0 2077 2112 316367389 316367354 4.350000e-07 67.6
14 TraesCS5A01G174300 chr5D 92.724 2309 73 25 1 2281 278279744 278277503 0.000000e+00 3245.0
15 TraesCS5A01G174300 chr5D 96.552 1653 24 4 2383 4004 278277506 278275856 0.000000e+00 2706.0
16 TraesCS5A01G174300 chr5D 92.023 1028 50 18 5306 6318 278274648 278273638 0.000000e+00 1415.0
17 TraesCS5A01G174300 chr5D 95.046 545 21 6 4003 4545 278275218 278274678 0.000000e+00 852.0
18 TraesCS5A01G174300 chr5D 95.913 367 13 2 6317 6683 278273536 278273172 1.610000e-165 593.0
19 TraesCS5A01G174300 chr5D 94.286 70 4 0 5237 5306 278274688 278274619 2.560000e-19 108.0
20 TraesCS5A01G174300 chr5D 86.139 101 10 1 4117 4213 504100291 504100191 9.220000e-19 106.0
21 TraesCS5A01G174300 chr5D 90.476 42 2 1 2013 2052 278277665 278277624 3.000000e-03 54.7
22 TraesCS5A01G174300 chr2B 89.859 710 66 5 4534 5238 647094798 647094090 0.000000e+00 907.0
23 TraesCS5A01G174300 chr2B 92.308 104 8 0 5135 5238 53270954 53271057 1.510000e-31 148.0
24 TraesCS5A01G174300 chr6D 88.999 709 72 5 4534 5238 244542052 244541346 0.000000e+00 872.0
25 TraesCS5A01G174300 chr6D 96.552 116 4 0 2278 2393 435974348 435974463 6.880000e-45 193.0
26 TraesCS5A01G174300 chr1B 88.359 713 70 7 4533 5238 527289884 527289178 0.000000e+00 845.0
27 TraesCS5A01G174300 chr1A 87.571 708 79 5 4534 5238 393997294 393997995 0.000000e+00 811.0
28 TraesCS5A01G174300 chr1A 96.522 115 3 1 2274 2388 343396692 343396805 8.900000e-44 189.0
29 TraesCS5A01G174300 chr7D 87.324 710 78 7 4534 5238 496776625 496775923 0.000000e+00 802.0
30 TraesCS5A01G174300 chr7D 95.833 96 2 2 4025 4118 141292088 141292183 3.240000e-33 154.0
31 TraesCS5A01G174300 chr7D 94.681 94 4 1 4015 4107 529689595 529689688 1.950000e-30 145.0
32 TraesCS5A01G174300 chr7B 87.759 580 59 6 4542 5118 671278455 671279025 0.000000e+00 667.0
33 TraesCS5A01G174300 chr7A 87.209 602 58 12 4523 5111 126086324 126085729 0.000000e+00 667.0
34 TraesCS5A01G174300 chr7A 90.127 395 30 5 4786 5173 555638760 555638368 7.780000e-139 505.0
35 TraesCS5A01G174300 chr7A 95.652 92 3 1 4023 4113 136806104 136806195 5.430000e-31 147.0
36 TraesCS5A01G174300 chr4B 87.047 579 65 5 4534 5109 388972789 388972218 0.000000e+00 645.0
37 TraesCS5A01G174300 chr1D 97.391 115 3 0 2279 2393 247520958 247521072 5.320000e-46 196.0
38 TraesCS5A01G174300 chr1D 94.737 95 4 1 4024 4117 355171574 355171668 5.430000e-31 147.0
39 TraesCS5A01G174300 chr3D 97.345 113 3 0 2275 2387 98597603 98597491 6.880000e-45 193.0
40 TraesCS5A01G174300 chr2A 95.000 120 6 0 2273 2392 448553068 448553187 8.900000e-44 189.0
41 TraesCS5A01G174300 chr4D 89.928 139 13 1 2260 2398 466748358 466748221 1.930000e-40 178.0
42 TraesCS5A01G174300 chr4D 93.750 96 5 1 4020 4114 479997573 479997668 7.020000e-30 143.0
43 TraesCS5A01G174300 chr2D 97.701 87 1 1 4022 4107 436111426 436111340 1.510000e-31 148.0
44 TraesCS5A01G174300 chr2D 94.505 91 4 1 4018 4107 627260875 627260965 9.090000e-29 139.0
45 TraesCS5A01G174300 chr4A 89.720 107 9 2 4013 4117 714590094 714589988 1.180000e-27 135.0


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 TraesCS5A01G174300 chr5A 367592606 367599324 6718 True 4176.133333 12408 100.000000 1 6719 3 chr5A.!!$R1 6718
1 TraesCS5A01G174300 chr5B 316362709 316369406 6697 True 1222.371429 3446 95.320857 1 6670 7 chr5B.!!$R2 6669
2 TraesCS5A01G174300 chr5B 292489755 292490456 701 True 861.000000 861 88.842000 4534 5238 1 chr5B.!!$R1 704
3 TraesCS5A01G174300 chr5D 278273172 278279744 6572 True 1281.957143 3245 93.860000 1 6683 7 chr5D.!!$R2 6682
4 TraesCS5A01G174300 chr2B 647094090 647094798 708 True 907.000000 907 89.859000 4534 5238 1 chr2B.!!$R1 704
5 TraesCS5A01G174300 chr6D 244541346 244542052 706 True 872.000000 872 88.999000 4534 5238 1 chr6D.!!$R1 704
6 TraesCS5A01G174300 chr1B 527289178 527289884 706 True 845.000000 845 88.359000 4533 5238 1 chr1B.!!$R1 705
7 TraesCS5A01G174300 chr1A 393997294 393997995 701 False 811.000000 811 87.571000 4534 5238 1 chr1A.!!$F2 704
8 TraesCS5A01G174300 chr7D 496775923 496776625 702 True 802.000000 802 87.324000 4534 5238 1 chr7D.!!$R1 704
9 TraesCS5A01G174300 chr7B 671278455 671279025 570 False 667.000000 667 87.759000 4542 5118 1 chr7B.!!$F1 576
10 TraesCS5A01G174300 chr7A 126085729 126086324 595 True 667.000000 667 87.209000 4523 5111 1 chr7A.!!$R1 588
11 TraesCS5A01G174300 chr4B 388972218 388972789 571 True 645.000000 645 87.047000 4534 5109 1 chr4B.!!$R1 575

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
867 895 0.040692 GAAGCAAACCGAAACCGACC 60.041 55.000 0.00 0.0 0.00 4.79 F
1373 1401 0.958822 GGTGCAGTTGGGGTTTACAG 59.041 55.000 0.00 0.0 0.00 2.74 F
2318 2385 1.000506 ACTTGTCGCAAGTATGGACGT 59.999 47.619 19.21 0.0 39.48 4.34 F
2376 2443 1.060122 GCGACGAGTAATTTGGAACGG 59.940 52.381 0.00 0.0 0.00 4.44 F
4107 4863 1.418908 ATTATGGGGCGGAGGGAGTG 61.419 60.000 0.00 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2298 2365 1.000506 ACGTCCATACTTGCGACAAGT 59.999 47.619 22.53 22.53 0.00 3.16 R
2356 2423 1.060122 CCGTTCCAAATTACTCGTCGC 59.940 52.381 0.00 0.00 0.00 5.19 R
4124 4881 0.874390 GCGACACTTGCTTTGGATCA 59.126 50.000 0.00 0.00 0.00 2.92 R
4247 5004 1.001641 GTCAGCTGACCCAATGGCT 60.002 57.895 32.55 0.00 39.07 4.75 R
5759 6557 0.965866 CCACGTGCTGAGGGAGACTA 60.966 60.000 10.91 0.00 0.00 2.59 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
73 74 3.948719 AGCTTCCCGCCCGACAAA 61.949 61.111 0.00 0.00 40.39 2.83
136 137 1.948611 GCAATGACAAGGGGCGTCTTA 60.949 52.381 0.00 0.00 34.37 2.10
393 408 6.516860 CGAAATAAACCCTAGACGATCATCCT 60.517 42.308 0.00 0.00 0.00 3.24
538 553 2.898729 AATTCATCGACGGAGATGCT 57.101 45.000 14.91 5.05 45.57 3.79
683 702 2.366435 GTGGGGAATCGGGGAGGA 60.366 66.667 0.00 0.00 0.00 3.71
684 703 2.040884 TGGGGAATCGGGGAGGAG 60.041 66.667 0.00 0.00 0.00 3.69
695 714 2.784095 TCGGGGAGGAGAGAGAGAATAA 59.216 50.000 0.00 0.00 0.00 1.40
835 856 2.676471 CAGGCCGGGGTCCAAAAG 60.676 66.667 2.18 0.00 0.00 2.27
837 858 4.986708 GGCCGGGGTCCAAAAGCA 62.987 66.667 2.18 0.00 0.00 3.91
867 895 0.040692 GAAGCAAACCGAAACCGACC 60.041 55.000 0.00 0.00 0.00 4.79
1025 1053 1.134438 AGTTCCTTTTCCTCCCGCCT 61.134 55.000 0.00 0.00 0.00 5.52
1040 1068 1.223211 GCCTCCTTCCTTCAGCCTC 59.777 63.158 0.00 0.00 0.00 4.70
1171 1199 6.019748 TGAGGAGTCTTAGATTGGAGAAGTT 58.980 40.000 0.00 0.00 0.00 2.66
1373 1401 0.958822 GGTGCAGTTGGGGTTTACAG 59.041 55.000 0.00 0.00 0.00 2.74
1402 1433 2.514803 GGCTGTGTTGGGACTACATTT 58.485 47.619 0.00 0.00 0.00 2.32
1439 1475 3.190535 GGAATTGCGCTGACCTTTTCTTA 59.809 43.478 9.73 0.00 0.00 2.10
1507 1543 8.609176 TGATGTTTAGCTGATTATTTTCCGTAC 58.391 33.333 0.00 0.00 0.00 3.67
1748 1784 7.665559 TGTGGAAGTTTTAGCTTGAAGATGTAT 59.334 33.333 0.00 0.00 0.00 2.29
1749 1785 8.515414 GTGGAAGTTTTAGCTTGAAGATGTATT 58.485 33.333 0.00 0.00 0.00 1.89
1801 1837 4.320608 TTGGAAAGTTGGTGATTGAAGC 57.679 40.909 0.00 0.00 0.00 3.86
2044 2082 7.968405 GGTTAAAGTTGTAGGTTCAATATGCAG 59.032 37.037 0.00 0.00 0.00 4.41
2108 2171 8.051901 AGGTTAAAGTTGTAGGTTCAATATGC 57.948 34.615 0.00 0.00 0.00 3.14
2109 2172 7.668052 AGGTTAAAGTTGTAGGTTCAATATGCA 59.332 33.333 0.00 0.00 0.00 3.96
2110 2173 7.753580 GGTTAAAGTTGTAGGTTCAATATGCAC 59.246 37.037 0.00 0.00 0.00 4.57
2111 2174 6.892658 AAAGTTGTAGGTTCAATATGCACA 57.107 33.333 0.00 0.00 0.00 4.57
2112 2175 6.892658 AAGTTGTAGGTTCAATATGCACAA 57.107 33.333 0.00 0.00 0.00 3.33
2113 2176 7.466746 AAGTTGTAGGTTCAATATGCACAAT 57.533 32.000 0.00 0.00 0.00 2.71
2114 2177 7.466746 AGTTGTAGGTTCAATATGCACAATT 57.533 32.000 0.00 0.00 0.00 2.32
2115 2178 7.315142 AGTTGTAGGTTCAATATGCACAATTG 58.685 34.615 14.62 14.62 35.98 2.32
2132 2195 5.346551 CACAATTGCACATGTAGGTTCAATG 59.653 40.000 5.05 2.72 35.36 2.82
2284 2351 8.732746 ACAAACACTCATTAATATGTACTCCC 57.267 34.615 0.00 0.00 33.34 4.30
2285 2352 8.548877 ACAAACACTCATTAATATGTACTCCCT 58.451 33.333 0.00 0.00 33.34 4.20
2286 2353 9.046296 CAAACACTCATTAATATGTACTCCCTC 57.954 37.037 0.00 0.00 33.34 4.30
2287 2354 7.304497 ACACTCATTAATATGTACTCCCTCC 57.696 40.000 0.00 0.00 33.34 4.30
2288 2355 6.015350 ACACTCATTAATATGTACTCCCTCCG 60.015 42.308 0.00 0.00 33.34 4.63
2289 2356 6.015350 CACTCATTAATATGTACTCCCTCCGT 60.015 42.308 0.00 0.00 33.34 4.69
2290 2357 6.553852 ACTCATTAATATGTACTCCCTCCGTT 59.446 38.462 0.00 0.00 33.34 4.44
2291 2358 6.989659 TCATTAATATGTACTCCCTCCGTTC 58.010 40.000 0.00 0.00 33.34 3.95
2292 2359 5.796424 TTAATATGTACTCCCTCCGTTCC 57.204 43.478 0.00 0.00 0.00 3.62
2293 2360 3.614568 ATATGTACTCCCTCCGTTCCT 57.385 47.619 0.00 0.00 0.00 3.36
2294 2361 4.736611 ATATGTACTCCCTCCGTTCCTA 57.263 45.455 0.00 0.00 0.00 2.94
2295 2362 2.905415 TGTACTCCCTCCGTTCCTAA 57.095 50.000 0.00 0.00 0.00 2.69
2296 2363 3.393426 TGTACTCCCTCCGTTCCTAAT 57.607 47.619 0.00 0.00 0.00 1.73
2297 2364 3.716431 TGTACTCCCTCCGTTCCTAATT 58.284 45.455 0.00 0.00 0.00 1.40
2298 2365 4.870636 TGTACTCCCTCCGTTCCTAATTA 58.129 43.478 0.00 0.00 0.00 1.40
2299 2366 4.646492 TGTACTCCCTCCGTTCCTAATTAC 59.354 45.833 0.00 0.00 0.00 1.89
2300 2367 3.991683 ACTCCCTCCGTTCCTAATTACT 58.008 45.455 0.00 0.00 0.00 2.24
2301 2368 4.359996 ACTCCCTCCGTTCCTAATTACTT 58.640 43.478 0.00 0.00 0.00 2.24
2302 2369 4.161754 ACTCCCTCCGTTCCTAATTACTTG 59.838 45.833 0.00 0.00 0.00 3.16
2303 2370 4.098894 TCCCTCCGTTCCTAATTACTTGT 58.901 43.478 0.00 0.00 0.00 3.16
2304 2371 4.161001 TCCCTCCGTTCCTAATTACTTGTC 59.839 45.833 0.00 0.00 0.00 3.18
2305 2372 4.110482 CCTCCGTTCCTAATTACTTGTCG 58.890 47.826 0.00 0.00 0.00 4.35
2306 2373 3.514645 TCCGTTCCTAATTACTTGTCGC 58.485 45.455 0.00 0.00 0.00 5.19
2307 2374 3.056678 TCCGTTCCTAATTACTTGTCGCA 60.057 43.478 0.00 0.00 0.00 5.10
2308 2375 3.680937 CCGTTCCTAATTACTTGTCGCAA 59.319 43.478 0.00 0.00 0.00 4.85
2309 2376 4.201685 CCGTTCCTAATTACTTGTCGCAAG 60.202 45.833 15.16 15.16 0.00 4.01
2310 2377 4.387862 CGTTCCTAATTACTTGTCGCAAGT 59.612 41.667 22.53 22.53 39.48 3.16
2311 2378 5.574055 CGTTCCTAATTACTTGTCGCAAGTA 59.426 40.000 20.95 20.95 39.48 2.24
2312 2379 6.255020 CGTTCCTAATTACTTGTCGCAAGTAT 59.745 38.462 23.59 16.27 33.27 2.12
2313 2380 7.399523 GTTCCTAATTACTTGTCGCAAGTATG 58.600 38.462 23.59 16.54 33.27 2.39
2314 2381 6.046593 TCCTAATTACTTGTCGCAAGTATGG 58.953 40.000 23.59 21.37 33.27 2.74
2315 2382 6.046593 CCTAATTACTTGTCGCAAGTATGGA 58.953 40.000 23.59 14.66 33.27 3.41
2316 2383 5.796350 AATTACTTGTCGCAAGTATGGAC 57.204 39.130 23.59 0.00 33.27 4.02
2317 2384 1.710013 ACTTGTCGCAAGTATGGACG 58.290 50.000 19.21 0.00 39.48 4.79
2318 2385 1.000506 ACTTGTCGCAAGTATGGACGT 59.999 47.619 19.21 0.00 39.48 4.34
2319 2386 2.229543 ACTTGTCGCAAGTATGGACGTA 59.770 45.455 19.21 0.00 39.48 3.57
2320 2387 3.119245 ACTTGTCGCAAGTATGGACGTAT 60.119 43.478 19.21 0.00 39.48 3.06
2321 2388 3.074504 TGTCGCAAGTATGGACGTATC 57.925 47.619 0.00 0.00 39.48 2.24
2322 2389 2.686405 TGTCGCAAGTATGGACGTATCT 59.314 45.455 0.00 0.00 39.48 1.98
2323 2390 3.878699 TGTCGCAAGTATGGACGTATCTA 59.121 43.478 0.00 0.00 39.48 1.98
2324 2391 4.024302 TGTCGCAAGTATGGACGTATCTAG 60.024 45.833 0.00 0.00 39.48 2.43
2325 2392 4.212847 GTCGCAAGTATGGACGTATCTAGA 59.787 45.833 0.00 0.00 39.48 2.43
2326 2393 5.001874 TCGCAAGTATGGACGTATCTAGAT 58.998 41.667 10.73 10.73 39.48 1.98
2327 2394 5.089411 CGCAAGTATGGACGTATCTAGATG 58.911 45.833 15.79 1.92 0.00 2.90
2328 2395 5.334957 CGCAAGTATGGACGTATCTAGATGT 60.335 44.000 15.79 5.44 0.00 3.06
2329 2396 6.128363 CGCAAGTATGGACGTATCTAGATGTA 60.128 42.308 15.79 0.00 0.00 2.29
2330 2397 7.414208 CGCAAGTATGGACGTATCTAGATGTAT 60.414 40.741 15.79 0.00 0.00 2.29
2331 2398 8.244802 GCAAGTATGGACGTATCTAGATGTATT 58.755 37.037 15.79 0.00 0.00 1.89
2357 2424 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
2358 2425 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
2359 2426 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
2360 2427 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
2361 2428 3.384668 AGATACATCCATTTCTGCGACG 58.615 45.455 0.00 0.00 0.00 5.12
2362 2429 2.951457 TACATCCATTTCTGCGACGA 57.049 45.000 0.00 0.00 0.00 4.20
2363 2430 1.645034 ACATCCATTTCTGCGACGAG 58.355 50.000 0.00 0.00 0.00 4.18
2364 2431 1.066858 ACATCCATTTCTGCGACGAGT 60.067 47.619 0.00 0.00 0.00 4.18
2365 2432 2.165641 ACATCCATTTCTGCGACGAGTA 59.834 45.455 0.00 0.00 0.00 2.59
2366 2433 3.186909 CATCCATTTCTGCGACGAGTAA 58.813 45.455 0.00 0.00 0.00 2.24
2367 2434 3.520290 TCCATTTCTGCGACGAGTAAT 57.480 42.857 0.00 0.00 0.00 1.89
2368 2435 3.857052 TCCATTTCTGCGACGAGTAATT 58.143 40.909 0.00 0.00 0.00 1.40
2369 2436 4.250464 TCCATTTCTGCGACGAGTAATTT 58.750 39.130 0.00 0.00 0.00 1.82
2370 2437 4.092821 TCCATTTCTGCGACGAGTAATTTG 59.907 41.667 0.00 0.00 0.00 2.32
2371 2438 4.334443 CATTTCTGCGACGAGTAATTTGG 58.666 43.478 0.00 0.00 0.00 3.28
2372 2439 3.306917 TTCTGCGACGAGTAATTTGGA 57.693 42.857 0.00 0.00 0.00 3.53
2373 2440 3.306917 TCTGCGACGAGTAATTTGGAA 57.693 42.857 0.00 0.00 0.00 3.53
2374 2441 2.991190 TCTGCGACGAGTAATTTGGAAC 59.009 45.455 0.00 0.00 0.00 3.62
2375 2442 1.722464 TGCGACGAGTAATTTGGAACG 59.278 47.619 0.00 0.00 0.00 3.95
2376 2443 1.060122 GCGACGAGTAATTTGGAACGG 59.940 52.381 0.00 0.00 0.00 4.44
2377 2444 2.598589 CGACGAGTAATTTGGAACGGA 58.401 47.619 0.00 0.00 0.00 4.69
2378 2445 2.597305 CGACGAGTAATTTGGAACGGAG 59.403 50.000 0.00 0.00 0.00 4.63
2379 2446 2.928116 GACGAGTAATTTGGAACGGAGG 59.072 50.000 0.00 0.00 0.00 4.30
2380 2447 2.277084 CGAGTAATTTGGAACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
2381 2448 2.093869 CGAGTAATTTGGAACGGAGGGA 60.094 50.000 0.00 0.00 0.00 4.20
2382 2449 3.532542 GAGTAATTTGGAACGGAGGGAG 58.467 50.000 0.00 0.00 0.00 4.30
2383 2450 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
2384 2451 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
2385 2452 3.345508 AATTTGGAACGGAGGGAGTAC 57.654 47.619 0.00 0.00 0.00 2.73
2395 2462 6.183360 GGAACGGAGGGAGTACATAGTTATTT 60.183 42.308 0.00 0.00 0.00 1.40
2437 2504 9.469807 TGTTCAATATGTTTTGGTGTTTCATAC 57.530 29.630 0.00 0.00 0.00 2.39
2441 2508 9.086336 CAATATGTTTTGGTGTTTCATACATCC 57.914 33.333 0.00 0.00 37.04 3.51
2667 2734 8.243961 TGGGAAAAGAATAATTGTCTTCACAA 57.756 30.769 6.67 0.00 46.71 3.33
2803 2873 6.673154 TCTTCAAGATATTGTGCATGAGTG 57.327 37.500 0.00 0.00 0.00 3.51
2825 2895 7.165485 AGTGGAACATACTGTAACTTTGCATA 58.835 34.615 0.00 0.00 44.52 3.14
2974 3044 3.080300 TGTGCCGGAAATCAGGTATTT 57.920 42.857 5.05 0.00 40.59 1.40
3119 3189 5.875359 GTCCATCACCTGTAACTTCTTAAGG 59.125 44.000 1.85 0.00 0.00 2.69
3261 3359 2.246719 ACAACAAGCTGGAGTCTGAC 57.753 50.000 0.00 0.00 0.00 3.51
3623 3721 7.067981 CGATGAGTATGAGATCCATCATTCCTA 59.932 40.741 3.05 0.00 40.40 2.94
3632 3730 9.565090 TGAGATCCATCATTCCTAATTTTACTG 57.435 33.333 0.00 0.00 0.00 2.74
3684 3782 4.929211 TGTTTTGATACATCACTCTGACCG 59.071 41.667 0.00 0.00 36.36 4.79
3769 3867 2.408271 TGGTGATGATTGCAGAGGAC 57.592 50.000 0.00 0.00 0.00 3.85
3990 4088 4.890088 TGAACACATGTACAAGGAGGTAC 58.110 43.478 0.00 0.00 43.08 3.34
4033 4788 2.691011 GTCACTGTCATCTACTCCCTCC 59.309 54.545 0.00 0.00 0.00 4.30
4058 4813 7.069569 CGTCCCATAATATAAGAGCGTTTTTG 58.930 38.462 0.00 0.00 0.00 2.44
4066 4821 8.773404 AATATAAGAGCGTTTTTGACACTAGT 57.227 30.769 0.00 0.00 0.00 2.57
4067 4822 4.795970 AAGAGCGTTTTTGACACTAGTG 57.204 40.909 21.44 21.44 0.00 2.74
4096 4852 6.485313 TGTCAAAACGCTCTTATATTATGGGG 59.515 38.462 0.00 0.00 0.00 4.96
4107 4863 1.418908 ATTATGGGGCGGAGGGAGTG 61.419 60.000 0.00 0.00 0.00 3.51
4247 5004 9.023962 ACATATTTACAAAGGAATTTGCTCTCA 57.976 29.630 0.79 0.00 35.42 3.27
4342 5099 6.916360 ACCATGTCCATCTGTTATTTGTTT 57.084 33.333 0.00 0.00 0.00 2.83
4365 5122 8.893727 GTTTTTGCAGCTTATCTCTCCTATAAA 58.106 33.333 0.00 0.00 0.00 1.40
4447 5204 1.977854 TGGACTAGATGTGGCTTGTGT 59.022 47.619 0.00 0.00 0.00 3.72
4488 5245 4.229812 TGGAGTAGTGGATCTAAGTGAGGA 59.770 45.833 0.00 0.00 0.00 3.71
4512 5269 6.715347 ATTGTGTTTATATCCCTCAAAGCC 57.285 37.500 0.00 0.00 0.00 4.35
4635 5393 2.162681 GAGCTGTTTGGTTGCCACTAT 58.837 47.619 0.00 0.00 30.78 2.12
4642 5400 6.563222 TGTTTGGTTGCCACTATAAACTAC 57.437 37.500 13.00 0.00 30.78 2.73
4757 5522 2.649531 AAAAACGAGGGGACACATCA 57.350 45.000 0.00 0.00 0.00 3.07
4764 5529 3.322254 ACGAGGGGACACATCATTATCTC 59.678 47.826 0.00 0.00 0.00 2.75
4770 5535 4.505742 GGGACACATCATTATCTCTTCCCC 60.506 50.000 0.00 0.00 35.08 4.81
4777 5542 6.214412 ACATCATTATCTCTTCCCCCACTATC 59.786 42.308 0.00 0.00 0.00 2.08
4798 5564 0.603065 GCAACAATTCCCCTCGCTTT 59.397 50.000 0.00 0.00 0.00 3.51
4808 5574 3.126879 CTCGCTTTCATGCCGCCA 61.127 61.111 0.00 0.00 0.00 5.69
4984 5757 3.483808 TCTTATGCATGATACGGCCAA 57.516 42.857 10.16 0.00 0.00 4.52
5087 5871 2.084610 TGCAGTGCTAACAGCTAGTG 57.915 50.000 17.60 1.44 42.97 2.74
5283 6068 2.036604 TCACCGTATGTGTTCAGCTTGA 59.963 45.455 0.00 0.00 45.61 3.02
5284 6069 3.002791 CACCGTATGTGTTCAGCTTGAT 58.997 45.455 0.00 0.00 40.26 2.57
5285 6070 3.062639 CACCGTATGTGTTCAGCTTGATC 59.937 47.826 0.00 0.00 40.26 2.92
5286 6071 3.261580 CCGTATGTGTTCAGCTTGATCA 58.738 45.455 0.00 0.00 0.00 2.92
5287 6072 3.684305 CCGTATGTGTTCAGCTTGATCAA 59.316 43.478 8.12 8.12 29.01 2.57
5288 6073 4.333649 CCGTATGTGTTCAGCTTGATCAAT 59.666 41.667 8.96 0.00 29.01 2.57
5289 6074 5.163723 CCGTATGTGTTCAGCTTGATCAATT 60.164 40.000 8.96 0.00 29.01 2.32
5290 6075 6.317088 CGTATGTGTTCAGCTTGATCAATTT 58.683 36.000 8.96 0.00 29.01 1.82
5291 6076 7.413988 CCGTATGTGTTCAGCTTGATCAATTTA 60.414 37.037 8.96 0.00 29.01 1.40
5292 6077 7.962373 CGTATGTGTTCAGCTTGATCAATTTAA 59.038 33.333 8.96 0.00 29.01 1.52
5293 6078 9.282247 GTATGTGTTCAGCTTGATCAATTTAAG 57.718 33.333 8.96 0.00 29.01 1.85
5294 6079 7.275888 TGTGTTCAGCTTGATCAATTTAAGT 57.724 32.000 8.96 0.00 29.01 2.24
5295 6080 7.140705 TGTGTTCAGCTTGATCAATTTAAGTG 58.859 34.615 8.96 0.00 29.01 3.16
5296 6081 7.141363 GTGTTCAGCTTGATCAATTTAAGTGT 58.859 34.615 8.96 0.00 29.01 3.55
5297 6082 7.649306 GTGTTCAGCTTGATCAATTTAAGTGTT 59.351 33.333 8.96 0.00 29.01 3.32
5298 6083 7.862372 TGTTCAGCTTGATCAATTTAAGTGTTC 59.138 33.333 8.96 0.00 0.00 3.18
5299 6084 7.509141 TCAGCTTGATCAATTTAAGTGTTCA 57.491 32.000 8.96 2.59 0.00 3.18
5300 6085 7.939782 TCAGCTTGATCAATTTAAGTGTTCAA 58.060 30.769 8.96 15.06 34.88 2.69
5301 6086 8.077991 TCAGCTTGATCAATTTAAGTGTTCAAG 58.922 33.333 27.52 27.52 46.33 3.02
5302 6087 8.077991 CAGCTTGATCAATTTAAGTGTTCAAGA 58.922 33.333 32.09 11.69 46.42 3.02
5303 6088 8.632679 AGCTTGATCAATTTAAGTGTTCAAGAA 58.367 29.630 32.09 11.16 46.42 2.52
5304 6089 9.248291 GCTTGATCAATTTAAGTGTTCAAGAAA 57.752 29.630 32.09 10.90 46.42 2.52
5327 6112 6.170675 ACAGCTTGATCGATTTAAGTGTTC 57.829 37.500 18.63 7.46 0.00 3.18
5462 6247 7.424803 TGGAAACATGTGTGTAAAGAATTGAG 58.575 34.615 0.00 0.00 37.67 3.02
5560 6350 5.184671 AGTTTGAGATTTGGCTTCTTCATCC 59.815 40.000 0.00 0.00 0.00 3.51
5606 6404 3.144506 CACCCTCAGCAATCCATATCAC 58.855 50.000 0.00 0.00 0.00 3.06
5623 6421 2.179427 TCACCATGTCCTCGACAAGAT 58.821 47.619 0.00 0.00 45.96 2.40
5719 6517 7.093354 TGAAGACTTTGAGTATCTGCAGTAAG 58.907 38.462 14.67 9.21 34.92 2.34
5759 6557 2.564771 CCCTATTGCATCATCGTGTGT 58.435 47.619 0.00 0.00 0.00 3.72
5830 6629 0.396435 TGAGAATCACCTGTGCCGTT 59.604 50.000 0.00 0.00 42.56 4.44
5847 6646 3.609879 GCCGTTGGCTATTTAACGTTTGT 60.610 43.478 5.91 0.00 46.69 2.83
5902 6701 1.398390 GTAAAGGTCAGATGCCTTGCG 59.602 52.381 8.63 0.00 44.84 4.85
5964 6763 3.440173 CGGTGCTACAAGATGAATTTGGT 59.560 43.478 0.00 0.00 0.00 3.67
5973 6772 7.643569 ACAAGATGAATTTGGTACATGCATA 57.356 32.000 0.00 0.00 39.30 3.14
5998 6797 3.742433 AGATTAGCAATCTGACGAGGG 57.258 47.619 9.65 0.00 46.16 4.30
6005 6805 3.118956 AGCAATCTGACGAGGGAAAGTAG 60.119 47.826 0.00 0.00 0.00 2.57
6006 6806 3.119101 GCAATCTGACGAGGGAAAGTAGA 60.119 47.826 0.00 0.00 0.00 2.59
6007 6807 4.620803 GCAATCTGACGAGGGAAAGTAGAA 60.621 45.833 0.00 0.00 0.00 2.10
6062 6862 2.158928 ACGTAACTAACACCACCTTGCA 60.159 45.455 0.00 0.00 0.00 4.08
6066 6866 5.506649 CGTAACTAACACCACCTTGCAAAAT 60.507 40.000 0.00 0.00 0.00 1.82
6109 6915 8.707796 TCTCTTATTCTATATGGAGGACGTTT 57.292 34.615 0.00 0.00 0.00 3.60
6222 7032 6.624423 TGGTTACTAGTTTTCTAAGGCTACG 58.376 40.000 0.00 0.00 31.45 3.51
6241 7097 8.791675 AGGCTACGTTAGGAGTAGTATTTTATC 58.208 37.037 0.00 0.00 42.49 1.75
6262 7118 8.980143 TTATCTTTTTAGCACAAAATACTGCC 57.020 30.769 0.00 0.00 33.57 4.85
6263 7119 6.648879 TCTTTTTAGCACAAAATACTGCCT 57.351 33.333 0.00 0.00 33.57 4.75
6264 7120 6.446318 TCTTTTTAGCACAAAATACTGCCTG 58.554 36.000 0.00 0.00 33.57 4.85
6265 7121 3.848272 TTAGCACAAAATACTGCCTGC 57.152 42.857 0.00 0.00 33.57 4.85
6266 7122 1.915141 AGCACAAAATACTGCCTGCT 58.085 45.000 0.00 0.00 33.57 4.24
6267 7123 3.071874 AGCACAAAATACTGCCTGCTA 57.928 42.857 0.00 0.00 33.24 3.49
6268 7124 3.012518 AGCACAAAATACTGCCTGCTAG 58.987 45.455 0.00 0.00 33.24 3.42
6269 7125 3.009723 GCACAAAATACTGCCTGCTAGA 58.990 45.455 0.00 0.00 0.00 2.43
6318 7217 4.832248 CTGTGACCATTTGAGGCTTAGTA 58.168 43.478 0.00 0.00 0.00 1.82
6320 7219 6.553953 TGTGACCATTTGAGGCTTAGTATA 57.446 37.500 0.00 0.00 0.00 1.47
6321 7220 7.136822 TGTGACCATTTGAGGCTTAGTATAT 57.863 36.000 0.00 0.00 0.00 0.86
6322 7221 8.257602 TGTGACCATTTGAGGCTTAGTATATA 57.742 34.615 0.00 0.00 0.00 0.86
6442 7563 1.892209 AGTACCGGAGCTGTTTTTGG 58.108 50.000 9.46 0.00 0.00 3.28
6476 7597 3.884895 TGCCCACCATGAATTACTAGTG 58.115 45.455 5.39 0.00 0.00 2.74
6537 7661 1.210155 GCCAAAGACCGTGTCATGC 59.790 57.895 6.78 0.98 34.60 4.06
6650 7774 2.367512 ATCCTCTCCTGTGGGGGC 60.368 66.667 0.00 0.00 35.33 5.80
6660 7784 1.831652 CTGTGGGGGCGACTTTCTCT 61.832 60.000 0.00 0.00 0.00 3.10
6683 7807 5.551233 TCTGGTCTCCATCAAGTGTTAAAG 58.449 41.667 0.00 0.00 30.82 1.85
6684 7808 5.071788 TCTGGTCTCCATCAAGTGTTAAAGT 59.928 40.000 0.00 0.00 30.82 2.66
6685 7809 5.063204 TGGTCTCCATCAAGTGTTAAAGTG 58.937 41.667 0.00 0.00 0.00 3.16
6686 7810 4.083271 GGTCTCCATCAAGTGTTAAAGTGC 60.083 45.833 0.00 0.00 0.00 4.40
6687 7811 4.515191 GTCTCCATCAAGTGTTAAAGTGCA 59.485 41.667 0.00 0.00 0.00 4.57
6688 7812 5.008613 GTCTCCATCAAGTGTTAAAGTGCAA 59.991 40.000 0.00 0.00 0.00 4.08
6689 7813 5.239306 TCTCCATCAAGTGTTAAAGTGCAAG 59.761 40.000 0.00 0.00 0.00 4.01
6690 7814 4.887071 TCCATCAAGTGTTAAAGTGCAAGT 59.113 37.500 0.00 0.00 0.00 3.16
6691 7815 5.359576 TCCATCAAGTGTTAAAGTGCAAGTT 59.640 36.000 0.00 0.00 0.00 2.66
6692 7816 5.459762 CCATCAAGTGTTAAAGTGCAAGTTG 59.540 40.000 0.00 0.00 0.00 3.16
6693 7817 5.637006 TCAAGTGTTAAAGTGCAAGTTGT 57.363 34.783 4.48 0.00 0.00 3.32
6694 7818 5.636837 TCAAGTGTTAAAGTGCAAGTTGTC 58.363 37.500 4.48 0.00 0.00 3.18
6695 7819 4.273005 AGTGTTAAAGTGCAAGTTGTCG 57.727 40.909 4.48 0.00 0.00 4.35
6696 7820 2.781646 GTGTTAAAGTGCAAGTTGTCGC 59.218 45.455 4.48 3.94 0.00 5.19
6697 7821 2.420372 TGTTAAAGTGCAAGTTGTCGCA 59.580 40.909 4.48 0.00 35.30 5.10
6698 7822 3.066064 TGTTAAAGTGCAAGTTGTCGCAT 59.934 39.130 4.48 0.00 40.89 4.73
6699 7823 2.124011 AAAGTGCAAGTTGTCGCATG 57.876 45.000 4.48 0.00 40.89 4.06
6700 7824 1.308047 AAGTGCAAGTTGTCGCATGA 58.692 45.000 4.48 0.00 40.89 3.07
6701 7825 0.870393 AGTGCAAGTTGTCGCATGAG 59.130 50.000 4.48 0.00 40.89 2.90
6702 7826 0.110056 GTGCAAGTTGTCGCATGAGG 60.110 55.000 4.48 0.00 40.89 3.86
6703 7827 1.236616 TGCAAGTTGTCGCATGAGGG 61.237 55.000 4.48 0.00 31.95 4.30
6704 7828 1.926511 GCAAGTTGTCGCATGAGGGG 61.927 60.000 4.48 0.00 0.00 4.79
6705 7829 0.606401 CAAGTTGTCGCATGAGGGGT 60.606 55.000 0.00 0.00 0.00 4.95
6706 7830 0.110486 AAGTTGTCGCATGAGGGGTT 59.890 50.000 0.00 0.00 0.00 4.11
6707 7831 0.981183 AGTTGTCGCATGAGGGGTTA 59.019 50.000 0.00 0.00 0.00 2.85
6708 7832 1.349688 AGTTGTCGCATGAGGGGTTAA 59.650 47.619 0.00 0.00 0.00 2.01
6709 7833 1.467342 GTTGTCGCATGAGGGGTTAAC 59.533 52.381 0.00 0.00 0.00 2.01
6710 7834 0.687920 TGTCGCATGAGGGGTTAACA 59.312 50.000 8.10 0.00 0.00 2.41
6711 7835 1.084289 GTCGCATGAGGGGTTAACAC 58.916 55.000 8.10 2.97 0.00 3.32
6712 7836 0.390603 TCGCATGAGGGGTTAACACG 60.391 55.000 8.10 0.00 0.00 4.49
6713 7837 1.800681 GCATGAGGGGTTAACACGC 59.199 57.895 8.10 5.58 35.06 5.34
6714 7838 1.977594 GCATGAGGGGTTAACACGCG 61.978 60.000 3.53 3.53 36.70 6.01
6715 7839 0.390603 CATGAGGGGTTAACACGCGA 60.391 55.000 15.93 0.00 36.70 5.87
6716 7840 0.322322 ATGAGGGGTTAACACGCGAA 59.678 50.000 15.93 0.00 36.70 4.70
6717 7841 0.322322 TGAGGGGTTAACACGCGAAT 59.678 50.000 15.93 0.00 36.70 3.34
6718 7842 1.270947 TGAGGGGTTAACACGCGAATT 60.271 47.619 15.93 9.17 36.70 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 1.003233 GAAGAAGGCTGGCTCGGTT 60.003 57.895 3.48 0.00 0.00 4.44
136 137 2.116125 GCCAAGCCTGTCAACCCT 59.884 61.111 0.00 0.00 0.00 4.34
393 408 7.284820 CCCTCCTTCCGGAAGTAAATAAATAA 58.715 38.462 35.89 11.86 39.29 1.40
467 482 4.814294 ATCGGCCGGTCGTTGCTC 62.814 66.667 29.96 0.00 0.00 4.26
538 553 0.827925 ATCCAGCGATTCGAGGCCTA 60.828 55.000 4.42 0.00 0.00 3.93
635 650 1.283613 ACCCATCGCACCAAATTCCTA 59.716 47.619 0.00 0.00 0.00 2.94
666 681 2.366435 TCCTCCCCGATTCCCCAC 60.366 66.667 0.00 0.00 0.00 4.61
667 682 2.040884 CTCCTCCCCGATTCCCCA 60.041 66.667 0.00 0.00 0.00 4.96
668 683 1.839296 CTCTCCTCCCCGATTCCCC 60.839 68.421 0.00 0.00 0.00 4.81
669 684 0.830023 CTCTCTCCTCCCCGATTCCC 60.830 65.000 0.00 0.00 0.00 3.97
670 685 0.186386 TCTCTCTCCTCCCCGATTCC 59.814 60.000 0.00 0.00 0.00 3.01
671 686 1.144093 TCTCTCTCTCCTCCCCGATTC 59.856 57.143 0.00 0.00 0.00 2.52
683 702 6.775142 TCATTCCATCGTCTTATTCTCTCTCT 59.225 38.462 0.00 0.00 0.00 3.10
684 703 6.976088 TCATTCCATCGTCTTATTCTCTCTC 58.024 40.000 0.00 0.00 0.00 3.20
695 714 0.752658 TCGGCATCATTCCATCGTCT 59.247 50.000 0.00 0.00 0.00 4.18
732 751 4.087892 CTGCCTCTCCCACCCACG 62.088 72.222 0.00 0.00 0.00 4.94
733 752 2.607750 TCTGCCTCTCCCACCCAC 60.608 66.667 0.00 0.00 0.00 4.61
734 753 2.284921 CTCTGCCTCTCCCACCCA 60.285 66.667 0.00 0.00 0.00 4.51
735 754 2.039624 TCTCTGCCTCTCCCACCC 59.960 66.667 0.00 0.00 0.00 4.61
736 755 1.194781 TTGTCTCTGCCTCTCCCACC 61.195 60.000 0.00 0.00 0.00 4.61
828 849 1.275291 CTAGACGAGGGTGCTTTTGGA 59.725 52.381 0.00 0.00 0.00 3.53
829 850 1.275291 TCTAGACGAGGGTGCTTTTGG 59.725 52.381 0.00 0.00 0.00 3.28
831 852 2.613223 GCTTCTAGACGAGGGTGCTTTT 60.613 50.000 0.00 0.00 0.00 2.27
835 856 0.246635 TTGCTTCTAGACGAGGGTGC 59.753 55.000 0.00 0.00 0.00 5.01
837 858 1.275573 GGTTTGCTTCTAGACGAGGGT 59.724 52.381 0.00 0.00 0.00 4.34
959 987 2.683933 GCCGGTTGAGAGGGAGGA 60.684 66.667 1.90 0.00 0.00 3.71
995 1023 2.380064 AAAGGAACTCACCATGGCAA 57.620 45.000 13.04 0.00 38.49 4.52
1025 1053 2.982130 GCGAGGCTGAAGGAAGGA 59.018 61.111 0.00 0.00 0.00 3.36
1171 1199 3.755112 TTCACAGTCCGAAATGTACCA 57.245 42.857 0.00 0.00 0.00 3.25
1303 1331 1.344438 TGACAGTCTGAGATTTGCCGT 59.656 47.619 6.91 0.00 0.00 5.68
1402 1433 4.378978 CGCAATTCCAAATTTGTCGTAGGA 60.379 41.667 16.73 3.14 0.00 2.94
1507 1543 3.181485 CCCTCTTCTTAGACTAAGCACGG 60.181 52.174 16.17 12.71 35.76 4.94
1801 1837 3.436015 GCATCTGGCATATCACTAGCTTG 59.564 47.826 0.00 0.00 43.97 4.01
2086 2149 8.397575 TGTGCATATTGAACCTACAACTTTAA 57.602 30.769 0.00 0.00 32.50 1.52
2108 2171 4.502171 TGAACCTACATGTGCAATTGTG 57.498 40.909 9.11 0.00 0.00 3.33
2109 2172 5.010922 ACATTGAACCTACATGTGCAATTGT 59.989 36.000 9.11 7.80 40.84 2.71
2110 2173 5.472148 ACATTGAACCTACATGTGCAATTG 58.528 37.500 9.11 0.00 40.84 2.32
2111 2174 5.726980 ACATTGAACCTACATGTGCAATT 57.273 34.783 9.11 0.00 40.84 2.32
2112 2175 5.709631 TGTACATTGAACCTACATGTGCAAT 59.290 36.000 9.11 7.59 43.80 3.56
2113 2176 5.049060 GTGTACATTGAACCTACATGTGCAA 60.049 40.000 9.11 5.59 38.98 4.08
2114 2177 4.454161 GTGTACATTGAACCTACATGTGCA 59.546 41.667 9.11 0.00 35.96 4.57
2115 2178 4.695455 AGTGTACATTGAACCTACATGTGC 59.305 41.667 9.11 0.00 0.00 4.57
2116 2179 5.931724 TCAGTGTACATTGAACCTACATGTG 59.068 40.000 17.76 0.00 0.00 3.21
2281 2348 4.098894 ACAAGTAATTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
2282 2349 4.439968 GACAAGTAATTAGGAACGGAGGG 58.560 47.826 0.00 0.00 0.00 4.30
2283 2350 4.110482 CGACAAGTAATTAGGAACGGAGG 58.890 47.826 0.00 0.00 0.00 4.30
2284 2351 3.550678 GCGACAAGTAATTAGGAACGGAG 59.449 47.826 0.00 0.00 0.00 4.63
2285 2352 3.056678 TGCGACAAGTAATTAGGAACGGA 60.057 43.478 0.00 0.00 0.00 4.69
2286 2353 3.255725 TGCGACAAGTAATTAGGAACGG 58.744 45.455 0.00 0.00 0.00 4.44
2287 2354 4.387862 ACTTGCGACAAGTAATTAGGAACG 59.612 41.667 19.21 0.00 0.00 3.95
2288 2355 5.857822 ACTTGCGACAAGTAATTAGGAAC 57.142 39.130 19.21 0.00 0.00 3.62
2289 2356 6.537301 CCATACTTGCGACAAGTAATTAGGAA 59.463 38.462 25.44 11.09 36.45 3.36
2290 2357 6.046593 CCATACTTGCGACAAGTAATTAGGA 58.953 40.000 25.44 11.61 36.45 2.94
2291 2358 6.018994 GTCCATACTTGCGACAAGTAATTAGG 60.019 42.308 25.44 22.95 36.45 2.69
2292 2359 6.291637 CGTCCATACTTGCGACAAGTAATTAG 60.292 42.308 25.44 18.16 36.45 1.73
2293 2360 5.517411 CGTCCATACTTGCGACAAGTAATTA 59.483 40.000 25.44 15.71 36.45 1.40
2294 2361 4.328983 CGTCCATACTTGCGACAAGTAATT 59.671 41.667 25.44 14.21 36.45 1.40
2295 2362 3.863424 CGTCCATACTTGCGACAAGTAAT 59.137 43.478 25.44 16.10 36.45 1.89
2296 2363 3.247442 CGTCCATACTTGCGACAAGTAA 58.753 45.455 25.44 13.70 36.45 2.24
2297 2364 2.229543 ACGTCCATACTTGCGACAAGTA 59.770 45.455 24.52 24.52 37.18 2.24
2298 2365 1.000506 ACGTCCATACTTGCGACAAGT 59.999 47.619 22.53 22.53 0.00 3.16
2299 2366 1.710013 ACGTCCATACTTGCGACAAG 58.290 50.000 15.16 15.16 0.00 3.16
2300 2367 3.129813 AGATACGTCCATACTTGCGACAA 59.870 43.478 0.00 0.00 0.00 3.18
2301 2368 2.686405 AGATACGTCCATACTTGCGACA 59.314 45.455 0.00 0.00 0.00 4.35
2302 2369 3.351020 AGATACGTCCATACTTGCGAC 57.649 47.619 0.00 0.00 0.00 5.19
2303 2370 4.383173 TCTAGATACGTCCATACTTGCGA 58.617 43.478 0.00 0.00 0.00 5.10
2304 2371 4.744136 TCTAGATACGTCCATACTTGCG 57.256 45.455 0.00 0.00 0.00 4.85
2305 2372 6.015027 ACATCTAGATACGTCCATACTTGC 57.985 41.667 4.54 0.00 0.00 4.01
2331 2398 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
2332 2399 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
2333 2400 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
2334 2401 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
2335 2402 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
2336 2403 6.216569 GTCGCAGAAATGGATGTATCTAGAA 58.783 40.000 0.00 0.00 39.69 2.10
2337 2404 5.562890 CGTCGCAGAAATGGATGTATCTAGA 60.563 44.000 0.00 0.00 39.69 2.43
2338 2405 4.618912 CGTCGCAGAAATGGATGTATCTAG 59.381 45.833 0.00 0.00 39.69 2.43
2339 2406 4.277423 TCGTCGCAGAAATGGATGTATCTA 59.723 41.667 0.00 0.00 39.69 1.98
2340 2407 3.068165 TCGTCGCAGAAATGGATGTATCT 59.932 43.478 0.00 0.00 39.69 1.98
2341 2408 3.381045 TCGTCGCAGAAATGGATGTATC 58.619 45.455 0.00 0.00 39.69 2.24
2342 2409 3.181475 ACTCGTCGCAGAAATGGATGTAT 60.181 43.478 0.00 0.00 39.69 2.29
2343 2410 2.165641 ACTCGTCGCAGAAATGGATGTA 59.834 45.455 0.00 0.00 39.69 2.29
2344 2411 1.066858 ACTCGTCGCAGAAATGGATGT 60.067 47.619 0.00 0.00 39.69 3.06
2345 2412 1.645034 ACTCGTCGCAGAAATGGATG 58.355 50.000 0.00 0.00 39.69 3.51
2346 2413 3.520290 TTACTCGTCGCAGAAATGGAT 57.480 42.857 0.00 0.00 39.69 3.41
2347 2414 3.520290 ATTACTCGTCGCAGAAATGGA 57.480 42.857 0.00 0.00 39.69 3.41
2348 2415 4.334443 CAAATTACTCGTCGCAGAAATGG 58.666 43.478 0.00 0.00 39.69 3.16
2349 2416 4.092821 TCCAAATTACTCGTCGCAGAAATG 59.907 41.667 0.00 0.00 39.69 2.32
2350 2417 4.250464 TCCAAATTACTCGTCGCAGAAAT 58.750 39.130 0.00 0.00 39.69 2.17
2351 2418 3.655486 TCCAAATTACTCGTCGCAGAAA 58.345 40.909 0.00 0.00 39.69 2.52
2352 2419 3.306917 TCCAAATTACTCGTCGCAGAA 57.693 42.857 0.00 0.00 39.69 3.02
2353 2420 2.991190 GTTCCAAATTACTCGTCGCAGA 59.009 45.455 0.00 0.00 0.00 4.26
2354 2421 2.222508 CGTTCCAAATTACTCGTCGCAG 60.223 50.000 0.00 0.00 0.00 5.18
2355 2422 1.722464 CGTTCCAAATTACTCGTCGCA 59.278 47.619 0.00 0.00 0.00 5.10
2356 2423 1.060122 CCGTTCCAAATTACTCGTCGC 59.940 52.381 0.00 0.00 0.00 5.19
2357 2424 2.597305 CTCCGTTCCAAATTACTCGTCG 59.403 50.000 0.00 0.00 0.00 5.12
2358 2425 2.928116 CCTCCGTTCCAAATTACTCGTC 59.072 50.000 0.00 0.00 0.00 4.20
2359 2426 2.354403 CCCTCCGTTCCAAATTACTCGT 60.354 50.000 0.00 0.00 0.00 4.18
2360 2427 2.093869 TCCCTCCGTTCCAAATTACTCG 60.094 50.000 0.00 0.00 0.00 4.18
2361 2428 3.055312 ACTCCCTCCGTTCCAAATTACTC 60.055 47.826 0.00 0.00 0.00 2.59
2362 2429 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2363 2430 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2364 2431 3.839490 TGTACTCCCTCCGTTCCAAATTA 59.161 43.478 0.00 0.00 0.00 1.40
2365 2432 2.640826 TGTACTCCCTCCGTTCCAAATT 59.359 45.455 0.00 0.00 0.00 1.82
2366 2433 2.262637 TGTACTCCCTCCGTTCCAAAT 58.737 47.619 0.00 0.00 0.00 2.32
2367 2434 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
2368 2435 1.946984 ATGTACTCCCTCCGTTCCAA 58.053 50.000 0.00 0.00 0.00 3.53
2369 2436 2.024655 ACTATGTACTCCCTCCGTTCCA 60.025 50.000 0.00 0.00 0.00 3.53
2370 2437 2.664015 ACTATGTACTCCCTCCGTTCC 58.336 52.381 0.00 0.00 0.00 3.62
2371 2438 6.402456 AATAACTATGTACTCCCTCCGTTC 57.598 41.667 0.00 0.00 0.00 3.95
2372 2439 6.803366 AAATAACTATGTACTCCCTCCGTT 57.197 37.500 0.00 0.00 0.00 4.44
2373 2440 6.803366 AAAATAACTATGTACTCCCTCCGT 57.197 37.500 0.00 0.00 0.00 4.69
2395 2462 9.208022 CATATTGAACAGTCTACACAGAGAAAA 57.792 33.333 0.00 0.00 0.00 2.29
2437 2504 2.507471 AGGGCAAAGAGAGTTAGGGATG 59.493 50.000 0.00 0.00 0.00 3.51
2441 2508 4.006319 CTGAAAGGGCAAAGAGAGTTAGG 58.994 47.826 0.00 0.00 0.00 2.69
2667 2734 4.389374 CAAATAGCTACATGACCGGGAAT 58.611 43.478 6.32 0.00 0.00 3.01
2777 2844 7.644157 CACTCATGCACAATATCTTGAAGAATG 59.356 37.037 0.00 1.84 36.20 2.67
2778 2845 7.201794 CCACTCATGCACAATATCTTGAAGAAT 60.202 37.037 0.00 0.00 36.20 2.40
2974 3044 7.652524 AGAGCAGAGTTCACTTTATCATAGA 57.347 36.000 0.00 0.00 0.00 1.98
3119 3189 1.664151 GCACCACTGTTATAAGTCGCC 59.336 52.381 0.00 0.00 0.00 5.54
3623 3721 1.000394 GCCAACGCCCACAGTAAAATT 60.000 47.619 0.00 0.00 0.00 1.82
3632 3730 3.977244 CCAAGTGCCAACGCCCAC 61.977 66.667 0.00 0.00 0.00 4.61
3684 3782 2.036992 TGGGATGTTTGCATGGAAACAC 59.963 45.455 37.52 29.76 46.00 3.32
4033 4788 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
4065 4820 5.840940 ATAAGAGCGTTTTGACACTACAC 57.159 39.130 0.00 0.00 0.00 2.90
4066 4821 9.811995 ATAATATAAGAGCGTTTTGACACTACA 57.188 29.630 0.00 0.00 0.00 2.74
4079 4834 2.167693 TCCGCCCCATAATATAAGAGCG 59.832 50.000 0.00 0.00 41.84 5.03
4096 4852 2.841442 ATTAATAGCACTCCCTCCGC 57.159 50.000 0.00 0.00 0.00 5.54
4107 4863 6.859112 TGGATCAGAGGGAGTATTAATAGC 57.141 41.667 0.00 0.00 0.00 2.97
4124 4881 0.874390 GCGACACTTGCTTTGGATCA 59.126 50.000 0.00 0.00 0.00 2.92
4168 4925 9.778741 AGTAAGTGTCACATCTTTGAATTAAGA 57.221 29.630 5.62 0.00 38.43 2.10
4181 4938 4.893524 TCCGATCCATAGTAAGTGTCACAT 59.106 41.667 5.62 0.00 0.00 3.21
4247 5004 1.001641 GTCAGCTGACCCAATGGCT 60.002 57.895 32.55 0.00 39.07 4.75
4365 5122 8.574251 TGGCAGTCATAAGTTTGTTATGTTAT 57.426 30.769 5.01 0.00 34.78 1.89
4447 5204 9.159254 ACTACTCCATGGATAAAAGATACATGA 57.841 33.333 16.63 0.00 40.92 3.07
4481 5238 7.092444 TGAGGGATATAAACACAATTCCTCACT 60.092 37.037 7.37 0.00 42.00 3.41
4488 5245 6.183360 CGGCTTTGAGGGATATAAACACAATT 60.183 38.462 0.00 0.00 0.00 2.32
4512 5269 1.539388 TCACAATTAAGTGGGCAAGCG 59.461 47.619 7.93 0.00 39.93 4.68
4600 5358 5.413969 AACAGCTCGTTGTAACTAAAACC 57.586 39.130 1.44 0.00 36.12 3.27
4607 5365 3.359654 CAACCAAACAGCTCGTTGTAAC 58.640 45.455 5.42 0.00 38.07 2.50
4642 5400 8.721019 TCCTAAATACCACAGTATTAAAACCG 57.279 34.615 0.00 0.00 46.30 4.44
4752 5517 4.310740 AGTGGGGGAAGAGATAATGATGT 58.689 43.478 0.00 0.00 0.00 3.06
4757 5522 4.097418 CGGATAGTGGGGGAAGAGATAAT 58.903 47.826 0.00 0.00 0.00 1.28
4764 5529 0.463833 GTTGCGGATAGTGGGGGAAG 60.464 60.000 0.00 0.00 0.00 3.46
4770 5535 1.676006 GGGAATTGTTGCGGATAGTGG 59.324 52.381 0.00 0.00 0.00 4.00
4777 5542 3.051392 GCGAGGGGAATTGTTGCGG 62.051 63.158 0.00 0.00 0.00 5.69
4798 5564 3.451004 GTGGCAATGGCGGCATGA 61.451 61.111 26.50 7.17 44.06 3.07
4808 5574 3.055719 CGACAAGGCGGTGGCAAT 61.056 61.111 0.00 0.00 42.47 3.56
4880 5648 2.034799 GCATGGCCTCTAGGTACCAGA 61.035 57.143 15.94 13.45 37.57 3.86
4884 5652 1.271054 CCATGCATGGCCTCTAGGTAC 60.271 57.143 31.95 0.00 41.75 3.34
4984 5757 2.681778 AGCGCTGCTCTACCTGGT 60.682 61.111 10.39 4.05 30.62 4.00
5087 5871 5.865552 TGGTACAGTGACGTAAAATTAGCTC 59.134 40.000 0.00 0.00 0.00 4.09
5162 5947 5.541101 AGTCAGTAGGTACACAATACCACAA 59.459 40.000 5.93 0.00 39.99 3.33
5283 6068 8.416329 AGCTGTTTCTTGAACACTTAAATTGAT 58.584 29.630 0.00 0.00 43.13 2.57
5284 6069 7.771183 AGCTGTTTCTTGAACACTTAAATTGA 58.229 30.769 0.00 0.00 43.13 2.57
5285 6070 7.992180 AGCTGTTTCTTGAACACTTAAATTG 57.008 32.000 0.00 0.00 43.13 2.32
5286 6071 8.250332 TCAAGCTGTTTCTTGAACACTTAAATT 58.750 29.630 3.96 0.00 46.56 1.82
5287 6072 7.771183 TCAAGCTGTTTCTTGAACACTTAAAT 58.229 30.769 3.96 0.00 46.56 1.40
5288 6073 7.151999 TCAAGCTGTTTCTTGAACACTTAAA 57.848 32.000 3.96 0.00 46.56 1.52
5289 6074 6.751514 TCAAGCTGTTTCTTGAACACTTAA 57.248 33.333 3.96 0.00 46.56 1.85
5298 6083 7.269937 CACTTAAATCGATCAAGCTGTTTCTTG 59.730 37.037 15.90 0.00 43.53 3.02
5299 6084 7.041098 ACACTTAAATCGATCAAGCTGTTTCTT 60.041 33.333 15.90 0.00 0.00 2.52
5300 6085 6.428159 ACACTTAAATCGATCAAGCTGTTTCT 59.572 34.615 15.90 0.00 0.00 2.52
5301 6086 6.603095 ACACTTAAATCGATCAAGCTGTTTC 58.397 36.000 15.90 0.00 0.00 2.78
5302 6087 6.560253 ACACTTAAATCGATCAAGCTGTTT 57.440 33.333 15.90 1.58 0.00 2.83
5303 6088 6.204688 TGAACACTTAAATCGATCAAGCTGTT 59.795 34.615 22.67 22.67 31.93 3.16
5304 6089 5.700832 TGAACACTTAAATCGATCAAGCTGT 59.299 36.000 15.90 15.26 0.00 4.40
5305 6090 6.169419 TGAACACTTAAATCGATCAAGCTG 57.831 37.500 15.90 14.83 0.00 4.24
5306 6091 6.650807 TCTTGAACACTTAAATCGATCAAGCT 59.349 34.615 15.90 5.08 41.09 3.74
5307 6092 6.831769 TCTTGAACACTTAAATCGATCAAGC 58.168 36.000 15.90 4.70 41.09 4.01
5308 6093 9.107367 GTTTCTTGAACACTTAAATCGATCAAG 57.893 33.333 14.86 14.86 42.10 3.02
5309 6094 8.836413 AGTTTCTTGAACACTTAAATCGATCAA 58.164 29.630 0.00 0.00 40.84 2.57
5310 6095 8.378172 AGTTTCTTGAACACTTAAATCGATCA 57.622 30.769 0.00 0.00 40.84 2.92
5327 6112 9.941664 CATGCCATTTATACTCTTAGTTTCTTG 57.058 33.333 0.00 0.00 0.00 3.02
5364 6149 6.280643 TCTGGTGTCCTATTTGATTATGACG 58.719 40.000 0.00 0.00 0.00 4.35
5366 6151 9.342308 GAATTCTGGTGTCCTATTTGATTATGA 57.658 33.333 0.00 0.00 0.00 2.15
5450 6235 6.851330 CACCTTCGAAACACTCAATTCTTTAC 59.149 38.462 0.00 0.00 0.00 2.01
5462 6247 5.471257 ACTCTATCTTCACCTTCGAAACAC 58.529 41.667 0.00 0.00 0.00 3.32
5504 6294 4.149922 AGTTGTTACGTGTGACATCAATCG 59.850 41.667 0.00 0.00 0.00 3.34
5550 6340 2.421248 GCTTCTCCCCAGGATGAAGAAG 60.421 54.545 18.80 14.00 39.69 2.85
5560 6350 4.785453 GCCCACGCTTCTCCCCAG 62.785 72.222 0.00 0.00 0.00 4.45
5606 6404 2.967599 TCATCTTGTCGAGGACATGG 57.032 50.000 10.53 3.39 42.40 3.66
5623 6421 7.519032 AGAACCGGTTTCTGAAATAAAATCA 57.481 32.000 23.22 0.00 43.45 2.57
5759 6557 0.965866 CCACGTGCTGAGGGAGACTA 60.966 60.000 10.91 0.00 0.00 2.59
5830 6629 3.815962 TCTGCACAAACGTTAAATAGCCA 59.184 39.130 0.00 0.00 0.00 4.75
5902 6701 4.902443 TCTCTCCTGACGACAATGATAC 57.098 45.455 0.00 0.00 0.00 2.24
5973 6772 6.295011 CCCTCGTCAGATTGCTAATCTCTTAT 60.295 42.308 8.01 0.00 46.20 1.73
6005 6805 9.313118 GTCTCTTCTTATTTCAGATCCTTCTTC 57.687 37.037 0.00 0.00 0.00 2.87
6006 6806 9.045745 AGTCTCTTCTTATTTCAGATCCTTCTT 57.954 33.333 0.00 0.00 0.00 2.52
6007 6807 8.608185 AGTCTCTTCTTATTTCAGATCCTTCT 57.392 34.615 0.00 0.00 0.00 2.85
6062 6862 1.539827 GCCTGTGCCGTTCTACATTTT 59.460 47.619 0.00 0.00 0.00 1.82
6109 6915 5.148502 AGAGAAGGCCTATTTCTATTCGGA 58.851 41.667 5.16 0.00 35.14 4.55
6241 7097 5.119125 GCAGGCAGTATTTTGTGCTAAAAAG 59.881 40.000 4.08 0.00 39.76 2.27
6283 7171 1.064060 GGTCACAGCAATGGATAACGC 59.936 52.381 0.00 0.00 0.00 4.84
6396 7517 4.928601 TCGTATTACTGCGAATTACTGCT 58.071 39.130 0.00 0.00 36.53 4.24
6424 7545 0.240145 GCCAAAAACAGCTCCGGTAC 59.760 55.000 0.00 0.00 0.00 3.34
6442 7563 1.896660 TGGGCAACGAGGTCAAAGC 60.897 57.895 0.00 0.00 37.60 3.51
6476 7597 1.863454 CGTGCAGTATCTTCCTGATGC 59.137 52.381 0.00 0.00 37.94 3.91
6510 7634 0.107703 CGGTCTTTGGCCTATCTGCA 60.108 55.000 3.32 0.00 0.00 4.41
6650 7774 2.163509 TGGAGACCAGAGAGAAAGTCG 58.836 52.381 0.00 0.00 34.41 4.18
6660 7784 5.071788 ACTTTAACACTTGATGGAGACCAGA 59.928 40.000 0.00 0.00 36.75 3.86
6683 7807 0.110056 CCTCATGCGACAACTTGCAC 60.110 55.000 0.00 0.00 45.07 4.57
6684 7808 1.236616 CCCTCATGCGACAACTTGCA 61.237 55.000 0.00 0.00 46.51 4.08
6685 7809 1.503542 CCCTCATGCGACAACTTGC 59.496 57.895 0.00 0.00 0.00 4.01
6686 7810 0.606401 ACCCCTCATGCGACAACTTG 60.606 55.000 0.00 0.00 0.00 3.16
6687 7811 0.110486 AACCCCTCATGCGACAACTT 59.890 50.000 0.00 0.00 0.00 2.66
6688 7812 0.981183 TAACCCCTCATGCGACAACT 59.019 50.000 0.00 0.00 0.00 3.16
6689 7813 1.467342 GTTAACCCCTCATGCGACAAC 59.533 52.381 0.00 0.00 0.00 3.32
6690 7814 1.072489 TGTTAACCCCTCATGCGACAA 59.928 47.619 2.48 0.00 0.00 3.18
6691 7815 0.687920 TGTTAACCCCTCATGCGACA 59.312 50.000 2.48 0.00 0.00 4.35
6692 7816 1.084289 GTGTTAACCCCTCATGCGAC 58.916 55.000 2.48 0.00 0.00 5.19
6693 7817 0.390603 CGTGTTAACCCCTCATGCGA 60.391 55.000 2.48 0.00 0.00 5.10
6694 7818 1.977594 GCGTGTTAACCCCTCATGCG 61.978 60.000 2.48 0.00 35.07 4.73
6695 7819 1.800681 GCGTGTTAACCCCTCATGC 59.199 57.895 2.48 0.00 37.04 4.06
6696 7820 0.390603 TCGCGTGTTAACCCCTCATG 60.391 55.000 5.77 0.00 0.00 3.07
6697 7821 0.322322 TTCGCGTGTTAACCCCTCAT 59.678 50.000 5.77 0.00 0.00 2.90
6698 7822 0.322322 ATTCGCGTGTTAACCCCTCA 59.678 50.000 5.77 0.00 0.00 3.86
6699 7823 1.445871 AATTCGCGTGTTAACCCCTC 58.554 50.000 5.77 0.00 0.00 4.30
6700 7824 3.637184 AATTCGCGTGTTAACCCCT 57.363 47.368 5.77 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.