Multiple sequence alignment - TraesCS5B01G202100

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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 TraesCS5B01G202100 chr5B 100.000 3744 0 0 530 4273 367908625 367912368 0.000000e+00 6914.0
1 TraesCS5B01G202100 chr5B 100.000 286 0 0 1 286 367908096 367908381 2.930000e-146 529.0
2 TraesCS5B01G202100 chr5B 92.366 131 7 2 2294 2423 566504189 566504317 2.620000e-42 183.0
3 TraesCS5B01G202100 chr5A 92.223 1813 97 21 2415 4196 412914699 412916498 0.000000e+00 2527.0
4 TraesCS5B01G202100 chr5A 91.364 1598 78 17 531 2093 412912969 412914541 0.000000e+00 2132.0
5 TraesCS5B01G202100 chr5D 92.252 1794 87 12 544 2306 318059386 318061158 0.000000e+00 2495.0
6 TraesCS5B01G202100 chr5D 91.040 1730 88 29 2410 4092 318061157 318062866 0.000000e+00 2274.0
7 TraesCS5B01G202100 chr5D 92.279 272 11 1 1 272 318058765 318059026 1.120000e-100 377.0
8 TraesCS5B01G202100 chr3A 95.968 124 4 1 2291 2414 707385980 707385858 2.610000e-47 200.0
9 TraesCS5B01G202100 chr7B 97.391 115 3 0 2305 2419 523682081 523681967 3.370000e-46 196.0
10 TraesCS5B01G202100 chr7B 95.082 122 5 1 2304 2424 22070299 22070420 1.570000e-44 191.0
11 TraesCS5B01G202100 chr3D 97.414 116 2 1 2300 2414 381640921 381640806 3.370000e-46 196.0
12 TraesCS5B01G202100 chr6B 97.368 114 3 0 2300 2413 623357767 623357880 1.210000e-45 195.0
13 TraesCS5B01G202100 chr6B 90.566 53 4 1 1673 1724 618944028 618944080 7.670000e-08 69.4
14 TraesCS5B01G202100 chr3B 98.198 111 2 0 2305 2415 70582106 70582216 1.210000e-45 195.0
15 TraesCS5B01G202100 chr3B 94.355 124 6 1 2288 2411 577429328 577429206 5.640000e-44 189.0
16 TraesCS5B01G202100 chr1B 95.041 121 6 0 2300 2420 495844167 495844047 1.570000e-44 191.0
17 TraesCS5B01G202100 chr4D 87.931 58 6 1 1668 1724 230473164 230473107 2.760000e-07 67.6
18 TraesCS5B01G202100 chr6D 84.746 59 7 1 1668 1724 384535005 384535063 1.660000e-04 58.4


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 TraesCS5B01G202100 chr5B 367908096 367912368 4272 False 3721.500000 6914 100.0000 1 4273 2 chr5B.!!$F2 4272
1 TraesCS5B01G202100 chr5A 412912969 412916498 3529 False 2329.500000 2527 91.7935 531 4196 2 chr5A.!!$F1 3665
2 TraesCS5B01G202100 chr5D 318058765 318062866 4101 False 1715.333333 2495 91.8570 1 4092 3 chr5D.!!$F1 4091

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
629 718 0.043310 GGACGTGCAATAACGATCGC 60.043 55.0 16.60 0.00 46.49 4.58 F
2321 2451 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.0 14.79 0.04 33.41 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2393 2523 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.0 14.79 0.04 33.41 4.30 R
4156 4333 0.247814 GCAACGAGAATGATGTGCCG 60.248 55.0 0.00 0.00 0.00 5.69 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
89 90 7.171678 AGACATGAAGACTCCTTAAAGAAAACG 59.828 37.037 0.00 0.00 31.62 3.60
122 123 2.048222 TGCTACTGCACGCCAGAC 60.048 61.111 10.29 1.31 45.31 3.51
123 124 3.914605 TGCTACTGCACGCCAGACG 62.915 63.158 10.29 2.70 45.31 4.18
148 149 2.884012 CTGATATCGAGCTCACCTCTGT 59.116 50.000 15.40 0.00 38.49 3.41
152 153 0.962855 TCGAGCTCACCTCTGTCCAG 60.963 60.000 15.40 0.00 38.49 3.86
169 170 2.746277 GGACCATGCACCGACACC 60.746 66.667 0.00 0.00 0.00 4.16
195 196 2.527624 TGGTGACTGAGCCAGGCT 60.528 61.111 16.12 16.12 40.76 4.58
201 202 4.383861 CTGAGCCAGGCTGCACGA 62.384 66.667 22.26 0.00 39.88 4.35
206 207 1.043116 AGCCAGGCTGCACGACTATA 61.043 55.000 15.24 0.00 37.57 1.31
272 273 2.432628 CGAAGACCGCACCTCACC 60.433 66.667 0.00 0.00 0.00 4.02
273 274 2.741092 GAAGACCGCACCTCACCA 59.259 61.111 0.00 0.00 0.00 4.17
274 275 1.296715 GAAGACCGCACCTCACCAT 59.703 57.895 0.00 0.00 0.00 3.55
275 276 0.321653 GAAGACCGCACCTCACCATT 60.322 55.000 0.00 0.00 0.00 3.16
276 277 0.321653 AAGACCGCACCTCACCATTC 60.322 55.000 0.00 0.00 0.00 2.67
277 278 1.003839 GACCGCACCTCACCATTCA 60.004 57.895 0.00 0.00 0.00 2.57
278 279 0.392998 GACCGCACCTCACCATTCAT 60.393 55.000 0.00 0.00 0.00 2.57
279 280 0.392998 ACCGCACCTCACCATTCATC 60.393 55.000 0.00 0.00 0.00 2.92
280 281 0.107508 CCGCACCTCACCATTCATCT 60.108 55.000 0.00 0.00 0.00 2.90
281 282 1.293924 CGCACCTCACCATTCATCTC 58.706 55.000 0.00 0.00 0.00 2.75
282 283 1.673168 GCACCTCACCATTCATCTCC 58.327 55.000 0.00 0.00 0.00 3.71
283 284 1.945387 CACCTCACCATTCATCTCCG 58.055 55.000 0.00 0.00 0.00 4.63
284 285 0.179000 ACCTCACCATTCATCTCCGC 59.821 55.000 0.00 0.00 0.00 5.54
285 286 0.533755 CCTCACCATTCATCTCCGCC 60.534 60.000 0.00 0.00 0.00 6.13
566 655 5.730550 CACTGGTTGTGCTAGTTCCTATTA 58.269 41.667 0.00 0.00 40.06 0.98
629 718 0.043310 GGACGTGCAATAACGATCGC 60.043 55.000 16.60 0.00 46.49 4.58
652 741 4.160329 TCTCTGCTCCCTTTGAGTTTCTA 58.840 43.478 0.00 0.00 43.48 2.10
718 807 7.801104 TGGTAGATTGGTCTCAGCAAATAATA 58.199 34.615 0.00 0.00 39.20 0.98
746 835 4.691685 TGAAGTACGGACGCATAAAAACAT 59.308 37.500 0.00 0.00 0.00 2.71
862 951 4.098894 CCGGCCTCTAACCCCTATAAATA 58.901 47.826 0.00 0.00 0.00 1.40
901 990 2.218603 CACTTCGCCTACACCAAAACT 58.781 47.619 0.00 0.00 0.00 2.66
902 991 2.616842 CACTTCGCCTACACCAAAACTT 59.383 45.455 0.00 0.00 0.00 2.66
933 1023 1.198867 CGCAGATCACGAGCTAGCTAT 59.801 52.381 19.38 7.41 0.00 2.97
955 1045 3.118775 TCTGAGCGCAGGAAATAGCTAAA 60.119 43.478 17.86 0.00 42.53 1.85
1110 1200 1.000827 GACATCATCATCGGCGTCTCT 60.001 52.381 6.85 0.00 0.00 3.10
1251 1341 2.481449 CGGAGGGTAAGGAAACAGATCG 60.481 54.545 0.00 0.00 0.00 3.69
1334 1428 3.445096 GGCTATTGCTTTCCTGAACATGT 59.555 43.478 0.00 0.00 39.59 3.21
1451 1570 5.509498 CAAGAATGGAAAGTAGGGGAATGA 58.491 41.667 0.00 0.00 0.00 2.57
1463 1582 7.613551 AGTAGGGGAATGATTAATAACGTCT 57.386 36.000 0.00 0.00 0.00 4.18
1507 1627 0.793861 GCCGCACAGACGAATGTTTA 59.206 50.000 0.00 0.00 34.06 2.01
1520 1640 5.416947 ACGAATGTTTACTGATGAGTACCC 58.583 41.667 0.00 0.00 34.23 3.69
1521 1641 4.809426 CGAATGTTTACTGATGAGTACCCC 59.191 45.833 0.00 0.00 34.23 4.95
1527 1647 2.032620 ACTGATGAGTACCCCGCTAAG 58.967 52.381 0.00 0.00 0.00 2.18
1738 1859 2.863401 AAAAGAAACTGTTCCACGCC 57.137 45.000 0.00 0.00 33.92 5.68
1740 1861 1.164041 AAGAAACTGTTCCACGCCCG 61.164 55.000 0.00 0.00 33.92 6.13
1813 1934 2.588877 AGCCATACGCATGTCCGC 60.589 61.111 0.00 0.00 41.38 5.54
1851 1972 8.604640 TTCATGTGTGAATTGTGCATTTATTT 57.395 26.923 0.00 0.00 39.36 1.40
1852 1973 8.604640 TCATGTGTGAATTGTGCATTTATTTT 57.395 26.923 0.00 0.00 0.00 1.82
1854 1975 8.496751 CATGTGTGAATTGTGCATTTATTTTGA 58.503 29.630 0.00 0.00 0.00 2.69
1908 2032 6.151663 GTTGGTGTAACAAACCCAAGTTAT 57.848 37.500 0.00 0.00 45.15 1.89
1920 2044 4.045022 ACCCAAGTTATAGGTACCATGCT 58.955 43.478 15.94 1.69 30.13 3.79
1938 2062 4.890158 TGCTTTGAATCTGAGTAGGTGA 57.110 40.909 0.00 0.00 0.00 4.02
1947 2071 2.041755 TCTGAGTAGGTGAGAAGGCAGA 59.958 50.000 0.00 0.00 0.00 4.26
1960 2084 0.786435 AGGCAGAAACCCCTTTCCAT 59.214 50.000 0.00 0.00 37.12 3.41
2003 2127 3.679025 TGCGAATCATGCAAATTTTGTCC 59.321 39.130 10.65 0.00 39.87 4.02
2083 2207 4.021192 CCCAAAATGCAATACTGTTCACCT 60.021 41.667 0.00 0.00 0.00 4.00
2093 2217 5.995565 ATACTGTTCACCTACACTAAGCA 57.004 39.130 0.00 0.00 0.00 3.91
2101 2225 1.001974 CCTACACTAAGCACACCTGCA 59.998 52.381 0.00 0.00 46.97 4.41
2102 2226 2.069273 CTACACTAAGCACACCTGCAC 58.931 52.381 0.00 0.00 46.97 4.57
2207 2337 9.891828 GCCAATTTTTCGTTGATGTATATATGA 57.108 29.630 0.00 0.00 0.00 2.15
2285 2415 7.332182 CACAGAGTTTATAGTTTCTCCCTGTTC 59.668 40.741 0.00 0.00 0.00 3.18
2290 2420 0.250338 AGTTTCTCCCTGTTCCGCAC 60.250 55.000 0.00 0.00 0.00 5.34
2297 2427 1.141254 TCCCTGTTCCGCACTTACAAA 59.859 47.619 0.00 0.00 0.00 2.83
2304 2434 3.738830 TCCGCACTTACAAACACTACT 57.261 42.857 0.00 0.00 0.00 2.57
2305 2435 4.852134 TCCGCACTTACAAACACTACTA 57.148 40.909 0.00 0.00 0.00 1.82
2306 2436 4.549458 TCCGCACTTACAAACACTACTAC 58.451 43.478 0.00 0.00 0.00 2.73
2307 2437 4.279169 TCCGCACTTACAAACACTACTACT 59.721 41.667 0.00 0.00 0.00 2.57
2308 2438 4.620184 CCGCACTTACAAACACTACTACTC 59.380 45.833 0.00 0.00 0.00 2.59
2309 2439 4.620184 CGCACTTACAAACACTACTACTCC 59.380 45.833 0.00 0.00 0.00 3.85
2310 2440 4.928020 GCACTTACAAACACTACTACTCCC 59.072 45.833 0.00 0.00 0.00 4.30
2311 2441 5.279356 GCACTTACAAACACTACTACTCCCT 60.279 44.000 0.00 0.00 0.00 4.20
2312 2442 6.388278 CACTTACAAACACTACTACTCCCTC 58.612 44.000 0.00 0.00 0.00 4.30
2313 2443 5.479724 ACTTACAAACACTACTACTCCCTCC 59.520 44.000 0.00 0.00 0.00 4.30
2314 2444 2.824341 ACAAACACTACTACTCCCTCCG 59.176 50.000 0.00 0.00 0.00 4.63
2315 2445 2.824341 CAAACACTACTACTCCCTCCGT 59.176 50.000 0.00 0.00 0.00 4.69
2316 2446 2.895242 ACACTACTACTCCCTCCGTT 57.105 50.000 0.00 0.00 0.00 4.44
2317 2447 2.720915 ACACTACTACTCCCTCCGTTC 58.279 52.381 0.00 0.00 0.00 3.95
2318 2448 1.669779 CACTACTACTCCCTCCGTTCG 59.330 57.143 0.00 0.00 0.00 3.95
2319 2449 1.307097 CTACTACTCCCTCCGTTCGG 58.693 60.000 4.74 4.74 0.00 4.30
2320 2450 0.911769 TACTACTCCCTCCGTTCGGA 59.088 55.000 13.34 13.34 0.00 4.55
2321 2451 0.038744 ACTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
2322 2452 1.341778 ACTACTCCCTCCGTTCGGAAT 60.342 52.381 14.79 2.09 33.41 3.01
2323 2453 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
2324 2454 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2325 2455 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2326 2456 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2327 2457 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2328 2458 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2329 2459 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2330 2460 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2331 2461 3.368116 CCTCCGTTCGGAATTACTTGTCT 60.368 47.826 14.79 0.00 33.41 3.41
2332 2462 3.841643 TCCGTTCGGAATTACTTGTCTC 58.158 45.455 11.66 0.00 0.00 3.36
2333 2463 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
2334 2464 3.495193 CGTTCGGAATTACTTGTCTCGA 58.505 45.455 0.00 0.00 0.00 4.04
2335 2465 3.916172 CGTTCGGAATTACTTGTCTCGAA 59.084 43.478 0.00 0.00 33.66 3.71
2336 2466 4.383649 CGTTCGGAATTACTTGTCTCGAAA 59.616 41.667 0.00 0.00 37.00 3.46
2337 2467 5.107760 CGTTCGGAATTACTTGTCTCGAAAA 60.108 40.000 0.00 0.00 37.00 2.29
2338 2468 6.400727 CGTTCGGAATTACTTGTCTCGAAAAT 60.401 38.462 0.00 0.00 37.00 1.82
2339 2469 6.403333 TCGGAATTACTTGTCTCGAAAATG 57.597 37.500 0.00 0.00 0.00 2.32
2340 2470 5.350365 TCGGAATTACTTGTCTCGAAAATGG 59.650 40.000 0.00 0.00 0.00 3.16
2341 2471 5.350365 CGGAATTACTTGTCTCGAAAATGGA 59.650 40.000 0.00 0.00 0.00 3.41
2342 2472 6.037172 CGGAATTACTTGTCTCGAAAATGGAT 59.963 38.462 0.00 0.00 0.00 3.41
2343 2473 7.189512 GGAATTACTTGTCTCGAAAATGGATG 58.810 38.462 0.00 0.00 0.00 3.51
2344 2474 7.148239 GGAATTACTTGTCTCGAAAATGGATGT 60.148 37.037 0.00 0.00 0.00 3.06
2345 2475 8.786826 AATTACTTGTCTCGAAAATGGATGTA 57.213 30.769 0.00 0.00 0.00 2.29
2346 2476 8.964476 ATTACTTGTCTCGAAAATGGATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
2347 2477 6.910536 ACTTGTCTCGAAAATGGATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
2348 2478 6.644347 ACTTGTCTCGAAAATGGATGTATCT 58.356 36.000 0.00 0.00 0.00 1.98
2349 2479 7.782049 ACTTGTCTCGAAAATGGATGTATCTA 58.218 34.615 0.00 0.00 0.00 1.98
2350 2480 7.923344 ACTTGTCTCGAAAATGGATGTATCTAG 59.077 37.037 0.00 0.00 0.00 2.43
2351 2481 7.582667 TGTCTCGAAAATGGATGTATCTAGA 57.417 36.000 0.00 0.00 0.00 2.43
2352 2482 8.007405 TGTCTCGAAAATGGATGTATCTAGAA 57.993 34.615 0.00 0.00 0.00 2.10
2353 2483 7.921214 TGTCTCGAAAATGGATGTATCTAGAAC 59.079 37.037 0.00 0.00 0.00 3.01
2354 2484 8.138712 GTCTCGAAAATGGATGTATCTAGAACT 58.861 37.037 0.00 0.00 0.00 3.01
2355 2485 9.350951 TCTCGAAAATGGATGTATCTAGAACTA 57.649 33.333 0.00 0.00 0.00 2.24
2356 2486 9.967346 CTCGAAAATGGATGTATCTAGAACTAA 57.033 33.333 0.00 0.00 0.00 2.24
2376 2506 9.793252 GAACTAAAATACGTCTAGATACAACCA 57.207 33.333 0.00 0.00 0.00 3.67
2381 2511 9.886132 AAAATACGTCTAGATACAACCATTTCT 57.114 29.630 0.00 0.00 0.00 2.52
2383 2513 9.962783 AATACGTCTAGATACAACCATTTCTAC 57.037 33.333 0.00 0.00 0.00 2.59
2384 2514 6.493116 ACGTCTAGATACAACCATTTCTACG 58.507 40.000 0.00 0.00 0.00 3.51
2385 2515 6.317140 ACGTCTAGATACAACCATTTCTACGA 59.683 38.462 0.00 0.00 29.41 3.43
2386 2516 6.632035 CGTCTAGATACAACCATTTCTACGAC 59.368 42.308 0.00 0.00 0.00 4.34
2387 2517 7.478322 GTCTAGATACAACCATTTCTACGACA 58.522 38.462 0.00 0.00 0.00 4.35
2388 2518 7.972277 GTCTAGATACAACCATTTCTACGACAA 59.028 37.037 0.00 0.00 0.00 3.18
2389 2519 8.188799 TCTAGATACAACCATTTCTACGACAAG 58.811 37.037 0.00 0.00 0.00 3.16
2390 2520 6.698380 AGATACAACCATTTCTACGACAAGT 58.302 36.000 0.00 0.00 0.00 3.16
2391 2521 7.833786 AGATACAACCATTTCTACGACAAGTA 58.166 34.615 0.00 0.00 0.00 2.24
2392 2522 8.308931 AGATACAACCATTTCTACGACAAGTAA 58.691 33.333 0.00 0.00 34.45 2.24
2393 2523 9.095065 GATACAACCATTTCTACGACAAGTAAT 57.905 33.333 0.00 0.00 34.45 1.89
2394 2524 7.739498 ACAACCATTTCTACGACAAGTAATT 57.261 32.000 0.00 0.00 34.45 1.40
2395 2525 7.803724 ACAACCATTTCTACGACAAGTAATTC 58.196 34.615 0.00 0.00 34.45 2.17
2396 2526 6.980051 ACCATTTCTACGACAAGTAATTCC 57.020 37.500 0.00 0.00 34.45 3.01
2397 2527 5.579511 ACCATTTCTACGACAAGTAATTCCG 59.420 40.000 0.00 0.00 34.45 4.30
2398 2528 5.808540 CCATTTCTACGACAAGTAATTCCGA 59.191 40.000 0.00 0.00 34.45 4.55
2399 2529 6.311935 CCATTTCTACGACAAGTAATTCCGAA 59.688 38.462 0.00 0.00 34.45 4.30
2400 2530 6.695292 TTTCTACGACAAGTAATTCCGAAC 57.305 37.500 0.00 0.00 34.45 3.95
2401 2531 4.406069 TCTACGACAAGTAATTCCGAACG 58.594 43.478 0.00 0.00 34.45 3.95
2402 2532 2.331194 ACGACAAGTAATTCCGAACGG 58.669 47.619 6.94 6.94 0.00 4.44
2403 2533 2.030007 ACGACAAGTAATTCCGAACGGA 60.030 45.455 12.04 12.04 43.52 4.69
2404 2534 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
2405 2535 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2406 2536 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2407 2537 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
2408 2538 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2411 2541 1.109609 ATTCCGAACGGAGGGAGTAC 58.890 55.000 15.34 0.00 46.06 2.73
2418 2548 4.559153 CGAACGGAGGGAGTACTTTTTAA 58.441 43.478 0.00 0.00 0.00 1.52
2444 2579 8.587952 AAAATCGCAAGCACTAATTACTTTTT 57.412 26.923 0.00 0.00 37.18 1.94
2482 2621 0.527817 CGGGCCGAAGTGATGTCTAC 60.528 60.000 24.41 0.00 0.00 2.59
2496 2635 2.980568 TGTCTACATTTAACCCAGCCG 58.019 47.619 0.00 0.00 0.00 5.52
2694 2849 4.016444 ACTCTCTCACATTCTCTCTCACC 58.984 47.826 0.00 0.00 0.00 4.02
2714 2870 4.024133 CACCTGACACTCTCTATCGATCTG 60.024 50.000 0.00 0.00 0.00 2.90
2767 2925 3.494336 CTTTGAGCAGAGGCCGCG 61.494 66.667 0.00 0.00 42.56 6.46
2883 3041 7.042187 GCTCGAGTTCATGATGAAGTAATCAAT 60.042 37.037 14.98 0.00 39.91 2.57
2884 3042 8.357796 TCGAGTTCATGATGAAGTAATCAATC 57.642 34.615 14.98 1.29 39.91 2.67
2885 3043 7.981225 TCGAGTTCATGATGAAGTAATCAATCA 59.019 33.333 14.98 0.00 39.91 2.57
2886 3044 8.274248 CGAGTTCATGATGAAGTAATCAATCAG 58.726 37.037 14.98 0.00 39.91 2.90
2887 3045 9.107177 GAGTTCATGATGAAGTAATCAATCAGT 57.893 33.333 14.98 0.00 39.91 3.41
2888 3046 9.107177 AGTTCATGATGAAGTAATCAATCAGTC 57.893 33.333 13.52 0.00 42.54 3.51
2889 3047 8.886719 GTTCATGATGAAGTAATCAATCAGTCA 58.113 33.333 8.33 0.00 42.54 3.41
2967 3127 1.659794 GGAACTTTGGTGCACGCAT 59.340 52.632 11.45 0.00 0.00 4.73
3084 3244 0.470341 GCTCTCCCCCTACATGTTCC 59.530 60.000 2.30 0.00 0.00 3.62
3206 3366 2.729479 CCTCAGCGCCATCCAGACT 61.729 63.158 2.29 0.00 0.00 3.24
3370 3535 5.353956 GTGTATGTATGATCAAGTGTTGCCA 59.646 40.000 0.00 0.00 0.00 4.92
3375 3540 5.585844 TGTATGATCAAGTGTTGCCATAGTG 59.414 40.000 0.00 0.00 31.54 2.74
3407 3572 0.725686 TACGTGCAGACTCTAGCGTC 59.274 55.000 4.64 4.64 34.38 5.19
3440 3605 0.889186 GTACTGGTGGCCCAAGTGTG 60.889 60.000 10.62 0.00 41.27 3.82
3473 3638 4.618067 ACCGTTCGTTTTGTTTTCTGTTTC 59.382 37.500 0.00 0.00 0.00 2.78
3474 3639 4.258704 CCGTTCGTTTTGTTTTCTGTTTCG 60.259 41.667 0.00 0.00 0.00 3.46
3475 3640 4.318854 CGTTCGTTTTGTTTTCTGTTTCGT 59.681 37.500 0.00 0.00 0.00 3.85
3477 3642 6.574245 GTTCGTTTTGTTTTCTGTTTCGTTT 58.426 32.000 0.00 0.00 0.00 3.60
3478 3643 6.750775 TCGTTTTGTTTTCTGTTTCGTTTT 57.249 29.167 0.00 0.00 0.00 2.43
3500 3666 2.976509 CGAGCTCGATGATGATGTACAC 59.023 50.000 32.06 0.00 43.02 2.90
3534 3700 7.639113 AGTGTATATGTTTGGGTGTATTTGG 57.361 36.000 0.00 0.00 0.00 3.28
3596 3768 4.004982 GGGAAGTTGCGTTATTTAGGTGA 58.995 43.478 0.00 0.00 0.00 4.02
3597 3769 4.638865 GGGAAGTTGCGTTATTTAGGTGAT 59.361 41.667 0.00 0.00 0.00 3.06
3620 3792 3.629398 GTGGTAATCTGATGGGCTTTGAG 59.371 47.826 0.00 0.00 0.00 3.02
3683 3855 5.067805 GGCCCATATAACTTTTCTGAAGTGG 59.932 44.000 0.00 0.00 0.00 4.00
3685 3857 5.067805 CCCATATAACTTTTCTGAAGTGGGC 59.932 44.000 0.00 0.00 0.00 5.36
3701 3873 2.552315 GTGGGCTTCGTTTCTGAATTCA 59.448 45.455 8.12 8.12 0.00 2.57
3711 3883 4.100529 GTTTCTGAATTCATCGCCACATG 58.899 43.478 8.96 0.00 0.00 3.21
3712 3884 2.989909 TCTGAATTCATCGCCACATGT 58.010 42.857 8.96 0.00 0.00 3.21
3713 3885 2.938451 TCTGAATTCATCGCCACATGTC 59.062 45.455 8.96 0.00 0.00 3.06
3714 3886 1.665169 TGAATTCATCGCCACATGTCG 59.335 47.619 3.38 0.00 0.00 4.35
3715 3887 1.933181 GAATTCATCGCCACATGTCGA 59.067 47.619 11.50 11.50 39.17 4.20
3716 3888 2.022764 ATTCATCGCCACATGTCGAA 57.977 45.000 12.90 0.00 38.28 3.71
3760 3935 4.497291 AAGAGATAGTGACGTCCTCTCT 57.503 45.455 21.61 21.61 43.36 3.10
3767 3942 4.608948 AGTGACGTCCTCTCTCAAAATT 57.391 40.909 14.12 0.00 0.00 1.82
3768 3943 4.962155 AGTGACGTCCTCTCTCAAAATTT 58.038 39.130 14.12 0.00 0.00 1.82
3773 3948 7.958025 GTGACGTCCTCTCTCAAAATTTAAATC 59.042 37.037 14.12 0.00 0.00 2.17
3774 3949 7.878127 TGACGTCCTCTCTCAAAATTTAAATCT 59.122 33.333 14.12 0.00 0.00 2.40
3850 4027 1.668751 AGCAACTCTGTTTCGCGAAAA 59.331 42.857 33.69 21.96 31.33 2.29
3861 4038 3.684103 TTCGCGAAAACAATCACAAGT 57.316 38.095 21.14 0.00 0.00 3.16
3868 4045 6.958752 CGCGAAAACAATCACAAGTAATATCA 59.041 34.615 0.00 0.00 0.00 2.15
3870 4047 7.962918 GCGAAAACAATCACAAGTAATATCACT 59.037 33.333 0.00 0.00 0.00 3.41
3948 4125 6.089417 GTCAATAGCAACATAAAAACAGTGCC 59.911 38.462 0.00 0.00 0.00 5.01
3954 4131 2.491693 ACATAAAAACAGTGCCCATCCG 59.508 45.455 0.00 0.00 0.00 4.18
3956 4133 1.112315 AAAAACAGTGCCCATCCGCA 61.112 50.000 0.00 0.00 36.08 5.69
3957 4134 1.112315 AAAACAGTGCCCATCCGCAA 61.112 50.000 0.00 0.00 41.30 4.85
3960 4137 1.213537 CAGTGCCCATCCGCAAAAG 59.786 57.895 0.00 0.00 41.30 2.27
3962 4139 0.962356 AGTGCCCATCCGCAAAAGAG 60.962 55.000 0.00 0.00 41.30 2.85
3966 4143 1.272212 GCCCATCCGCAAAAGAGAAAA 59.728 47.619 0.00 0.00 0.00 2.29
3988 4165 5.637006 AAACAGTGCACAGTGTAAAGAAA 57.363 34.783 21.04 0.00 43.66 2.52
3997 4174 9.463443 GTGCACAGTGTAAAGAAAAGAATTATT 57.537 29.630 13.17 0.00 0.00 1.40
4020 4197 5.496133 ACATTTCTGAGCAAGCATATCAC 57.504 39.130 0.00 0.00 0.00 3.06
4022 4199 2.229675 TCTGAGCAAGCATATCACCG 57.770 50.000 0.00 0.00 0.00 4.94
4046 4223 8.450964 CCGTAAACTTGTGAAAATATCTGACAT 58.549 33.333 0.00 0.00 0.00 3.06
4112 4289 5.316987 AGTTTGTTAACAAGATCCCTCTGG 58.683 41.667 19.72 0.00 37.15 3.86
4121 4298 6.200878 ACAAGATCCCTCTGGAAGTAAAAA 57.799 37.500 0.00 0.00 45.98 1.94
4124 4301 4.538089 AGATCCCTCTGGAAGTAAAAAGCT 59.462 41.667 0.00 0.00 45.98 3.74
4156 4333 1.555477 CGTCCCAAACAACACAAAGC 58.445 50.000 0.00 0.00 0.00 3.51
4171 4348 0.729116 AAAGCGGCACATCATTCTCG 59.271 50.000 1.45 0.00 0.00 4.04
4182 4359 4.556135 CACATCATTCTCGTTGCAAATGAC 59.444 41.667 11.86 0.00 40.95 3.06
4196 4373 5.728471 TGCAAATGACAGAAAGTTTCCAAA 58.272 33.333 12.05 0.00 0.00 3.28
4197 4374 6.347696 TGCAAATGACAGAAAGTTTCCAAAT 58.652 32.000 12.05 0.00 0.00 2.32
4198 4375 7.495901 TGCAAATGACAGAAAGTTTCCAAATA 58.504 30.769 12.05 0.00 0.00 1.40
4199 4376 7.437862 TGCAAATGACAGAAAGTTTCCAAATAC 59.562 33.333 12.05 0.09 0.00 1.89
4200 4377 7.653311 GCAAATGACAGAAAGTTTCCAAATACT 59.347 33.333 12.05 0.00 0.00 2.12
4201 4378 9.185192 CAAATGACAGAAAGTTTCCAAATACTC 57.815 33.333 12.05 0.00 0.00 2.59
4202 4379 6.877611 TGACAGAAAGTTTCCAAATACTCC 57.122 37.500 12.05 0.00 0.00 3.85
4203 4380 5.768164 TGACAGAAAGTTTCCAAATACTCCC 59.232 40.000 12.05 0.00 0.00 4.30
4204 4381 5.953571 ACAGAAAGTTTCCAAATACTCCCT 58.046 37.500 12.05 0.00 0.00 4.20
4205 4382 6.373759 ACAGAAAGTTTCCAAATACTCCCTT 58.626 36.000 12.05 0.00 0.00 3.95
4206 4383 6.490381 ACAGAAAGTTTCCAAATACTCCCTTC 59.510 38.462 12.05 0.00 0.00 3.46
4207 4384 6.717084 CAGAAAGTTTCCAAATACTCCCTTCT 59.283 38.462 12.05 0.00 0.00 2.85
4208 4385 7.231519 CAGAAAGTTTCCAAATACTCCCTTCTT 59.768 37.037 12.05 0.00 0.00 2.52
4209 4386 7.448777 AGAAAGTTTCCAAATACTCCCTTCTTC 59.551 37.037 12.05 0.00 0.00 2.87
4210 4387 5.571285 AGTTTCCAAATACTCCCTTCTTCC 58.429 41.667 0.00 0.00 0.00 3.46
4211 4388 5.074515 AGTTTCCAAATACTCCCTTCTTCCA 59.925 40.000 0.00 0.00 0.00 3.53
4212 4389 4.569719 TCCAAATACTCCCTTCTTCCAC 57.430 45.455 0.00 0.00 0.00 4.02
4213 4390 4.175962 TCCAAATACTCCCTTCTTCCACT 58.824 43.478 0.00 0.00 0.00 4.00
4214 4391 5.347124 TCCAAATACTCCCTTCTTCCACTA 58.653 41.667 0.00 0.00 0.00 2.74
4215 4392 5.425539 TCCAAATACTCCCTTCTTCCACTAG 59.574 44.000 0.00 0.00 0.00 2.57
4216 4393 5.189934 CCAAATACTCCCTTCTTCCACTAGT 59.810 44.000 0.00 0.00 0.00 2.57
4217 4394 6.296489 CCAAATACTCCCTTCTTCCACTAGTT 60.296 42.308 0.00 0.00 0.00 2.24
4218 4395 6.547930 AATACTCCCTTCTTCCACTAGTTC 57.452 41.667 0.00 0.00 0.00 3.01
4219 4396 3.858135 ACTCCCTTCTTCCACTAGTTCA 58.142 45.455 0.00 0.00 0.00 3.18
4220 4397 4.232091 ACTCCCTTCTTCCACTAGTTCAA 58.768 43.478 0.00 0.00 0.00 2.69
4221 4398 4.658901 ACTCCCTTCTTCCACTAGTTCAAA 59.341 41.667 0.00 0.00 0.00 2.69
4222 4399 5.310857 ACTCCCTTCTTCCACTAGTTCAAAT 59.689 40.000 0.00 0.00 0.00 2.32
4223 4400 5.560724 TCCCTTCTTCCACTAGTTCAAATG 58.439 41.667 0.00 0.00 0.00 2.32
4224 4401 5.309543 TCCCTTCTTCCACTAGTTCAAATGA 59.690 40.000 0.00 0.00 0.00 2.57
4225 4402 5.412904 CCCTTCTTCCACTAGTTCAAATGAC 59.587 44.000 0.00 0.00 0.00 3.06
4226 4403 5.120830 CCTTCTTCCACTAGTTCAAATGACG 59.879 44.000 0.00 0.00 0.00 4.35
4227 4404 4.566004 TCTTCCACTAGTTCAAATGACGG 58.434 43.478 0.00 0.00 0.00 4.79
4228 4405 4.282449 TCTTCCACTAGTTCAAATGACGGA 59.718 41.667 0.00 0.00 0.00 4.69
4229 4406 4.188247 TCCACTAGTTCAAATGACGGAG 57.812 45.455 0.00 0.00 0.00 4.63
4244 4421 2.643551 ACGGAGTATTGAATGGCAAGG 58.356 47.619 0.00 0.00 41.94 3.61
4245 4422 2.026262 ACGGAGTATTGAATGGCAAGGT 60.026 45.455 0.00 0.00 41.94 3.50
4246 4423 2.355756 CGGAGTATTGAATGGCAAGGTG 59.644 50.000 0.00 0.00 40.42 4.00
4247 4424 2.689983 GGAGTATTGAATGGCAAGGTGG 59.310 50.000 0.00 0.00 40.42 4.61
4248 4425 2.099756 GAGTATTGAATGGCAAGGTGGC 59.900 50.000 0.00 0.00 44.03 5.01
4249 4426 2.102578 GTATTGAATGGCAAGGTGGCT 58.897 47.619 0.00 0.00 44.10 4.75
4250 4427 2.530460 ATTGAATGGCAAGGTGGCTA 57.470 45.000 0.00 0.00 44.10 3.93
4251 4428 1.838112 TTGAATGGCAAGGTGGCTAG 58.162 50.000 0.00 0.00 44.10 3.42
4252 4429 0.991146 TGAATGGCAAGGTGGCTAGA 59.009 50.000 0.00 0.00 44.10 2.43
4253 4430 1.354031 TGAATGGCAAGGTGGCTAGAA 59.646 47.619 0.00 0.00 44.10 2.10
4254 4431 1.745653 GAATGGCAAGGTGGCTAGAAC 59.254 52.381 0.00 0.00 44.10 3.01
4255 4432 0.995024 ATGGCAAGGTGGCTAGAACT 59.005 50.000 0.00 0.00 44.10 3.01
4256 4433 0.771127 TGGCAAGGTGGCTAGAACTT 59.229 50.000 0.00 0.00 44.10 2.66
4257 4434 1.144913 TGGCAAGGTGGCTAGAACTTT 59.855 47.619 0.00 0.00 44.10 2.66
4258 4435 1.813178 GGCAAGGTGGCTAGAACTTTC 59.187 52.381 0.00 0.00 40.14 2.62
4259 4436 2.553247 GGCAAGGTGGCTAGAACTTTCT 60.553 50.000 0.00 0.00 40.14 2.52
4260 4437 3.149981 GCAAGGTGGCTAGAACTTTCTT 58.850 45.455 0.00 0.00 38.70 2.52
4261 4438 3.057946 GCAAGGTGGCTAGAACTTTCTTG 60.058 47.826 0.00 2.15 38.70 3.02
4269 4446 4.999751 CTAGAACTTTCTTGCAGTGGTC 57.000 45.455 0.00 0.00 38.70 4.02
4270 4447 3.567478 AGAACTTTCTTGCAGTGGTCT 57.433 42.857 0.00 0.00 32.55 3.85
4271 4448 3.471680 AGAACTTTCTTGCAGTGGTCTC 58.528 45.455 0.00 0.00 32.55 3.36
4272 4449 3.118261 AGAACTTTCTTGCAGTGGTCTCA 60.118 43.478 0.00 0.00 32.55 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 1.689258 GGTTTGGGGCATGCTATCCTT 60.689 52.381 18.92 0.00 0.00 3.36
119 120 2.550606 GAGCTCGATATCAGAACCGTCT 59.449 50.000 0.00 0.00 32.85 4.18
120 121 2.290916 TGAGCTCGATATCAGAACCGTC 59.709 50.000 9.64 0.00 0.00 4.79
121 122 2.033550 GTGAGCTCGATATCAGAACCGT 59.966 50.000 9.64 0.00 0.00 4.83
122 123 2.605823 GGTGAGCTCGATATCAGAACCG 60.606 54.545 9.64 0.00 0.00 4.44
123 124 2.625790 AGGTGAGCTCGATATCAGAACC 59.374 50.000 9.64 7.58 0.00 3.62
124 125 3.568007 AGAGGTGAGCTCGATATCAGAAC 59.432 47.826 9.64 0.00 0.00 3.01
125 126 3.567585 CAGAGGTGAGCTCGATATCAGAA 59.432 47.826 9.64 0.00 0.00 3.02
126 127 3.145286 CAGAGGTGAGCTCGATATCAGA 58.855 50.000 9.64 0.66 0.00 3.27
127 128 2.884012 ACAGAGGTGAGCTCGATATCAG 59.116 50.000 9.64 4.30 0.00 2.90
148 149 2.606213 TCGGTGCATGGTCCTGGA 60.606 61.111 0.00 0.00 0.00 3.86
152 153 2.746277 GGTGTCGGTGCATGGTCC 60.746 66.667 0.00 0.00 0.00 4.46
169 170 1.204467 GCTCAGTCACCAGAGAAGAGG 59.796 57.143 0.00 0.00 33.74 3.69
195 196 2.879026 AGCGATCTTCTATAGTCGTGCA 59.121 45.455 10.92 0.00 36.53 4.57
201 202 3.551046 CCAACGCAGCGATCTTCTATAGT 60.551 47.826 24.65 0.00 0.00 2.12
206 207 0.176680 ATCCAACGCAGCGATCTTCT 59.823 50.000 24.65 0.00 0.00 2.85
266 267 0.533755 GGCGGAGATGAATGGTGAGG 60.534 60.000 0.00 0.00 0.00 3.86
566 655 9.995003 TGATTTTAAGGATTTGTAAAATGCAGT 57.005 25.926 6.93 0.00 39.08 4.40
586 675 6.936335 CCAACTTTTAGGGCATCTTTGATTTT 59.064 34.615 0.00 0.00 0.00 1.82
652 741 3.894427 TCATGCCAAGTTGTATGGTTTGT 59.106 39.130 14.01 0.00 40.23 2.83
718 807 2.228138 TGCGTCCGTACTTCACTTTT 57.772 45.000 0.00 0.00 0.00 2.27
746 835 5.993748 TGTGTGGTGAGTATGTCTGATTA 57.006 39.130 0.00 0.00 0.00 1.75
862 951 3.933542 GACAGAGCTGGGAGGGGGT 62.934 68.421 0.00 0.00 34.19 4.95
901 990 1.554617 TGATCTGCGATGACAAGGGAA 59.445 47.619 0.00 0.00 0.00 3.97
902 991 1.134699 GTGATCTGCGATGACAAGGGA 60.135 52.381 0.00 0.00 0.00 4.20
933 1023 0.826715 AGCTATTTCCTGCGCTCAGA 59.173 50.000 9.73 0.00 42.95 3.27
955 1045 1.802337 TTACGAGCGAGCTGGTGTGT 61.802 55.000 20.29 6.03 35.80 3.72
1483 1602 0.665835 ATTCGTCTGTGCGGCAAAAA 59.334 45.000 3.23 0.00 0.00 1.94
1484 1603 0.040514 CATTCGTCTGTGCGGCAAAA 60.041 50.000 3.23 0.00 0.00 2.44
1489 1609 2.066262 AGTAAACATTCGTCTGTGCGG 58.934 47.619 0.00 0.00 0.00 5.69
1507 1627 2.032620 CTTAGCGGGGTACTCATCAGT 58.967 52.381 0.00 0.00 36.55 3.41
1520 1640 6.696148 CACTGTAGGAGTATAAAACTTAGCGG 59.304 42.308 0.00 0.00 39.07 5.52
1521 1641 7.256286 ACACTGTAGGAGTATAAAACTTAGCG 58.744 38.462 0.00 0.00 39.07 4.26
1527 1647 9.794685 GGTACTAACACTGTAGGAGTATAAAAC 57.205 37.037 0.00 0.00 31.73 2.43
1722 1843 1.597027 CGGGCGTGGAACAGTTTCT 60.597 57.895 0.00 0.00 41.80 2.52
1723 1844 2.613506 CCGGGCGTGGAACAGTTTC 61.614 63.158 0.00 0.00 41.80 2.78
1740 1861 1.737793 CAAAGATCGGGCACAAGTACC 59.262 52.381 0.00 0.00 0.00 3.34
1793 1914 2.311294 GGACATGCGTATGGCTGAC 58.689 57.895 19.26 0.00 42.28 3.51
1813 1934 7.395190 TTCACACATGAAGATTAAATCCAGG 57.605 36.000 0.00 0.00 40.01 4.45
1876 1997 5.288804 GTTTGTTACACCAACTACTACGGA 58.711 41.667 0.00 0.00 38.05 4.69
1879 2000 5.367302 TGGGTTTGTTACACCAACTACTAC 58.633 41.667 0.82 0.00 38.05 2.73
1908 2032 5.189736 ACTCAGATTCAAAGCATGGTACCTA 59.810 40.000 14.36 0.00 0.00 3.08
1920 2044 5.569630 GCCTTCTCACCTACTCAGATTCAAA 60.570 44.000 0.00 0.00 0.00 2.69
1938 2062 1.203063 GGAAAGGGGTTTCTGCCTTCT 60.203 52.381 0.00 0.00 0.00 2.85
1947 2071 4.675063 ACATAGTGATGGAAAGGGGTTT 57.325 40.909 0.00 0.00 37.39 3.27
1960 2084 4.234574 CAGACTAACGCACAACATAGTGA 58.765 43.478 0.00 0.00 42.05 3.41
2003 2127 2.353889 GGTTGAGTCATGCTATGCACAG 59.646 50.000 0.00 0.00 43.04 3.66
2044 2168 3.757947 TTGGGATCACTAGGAGTCTCA 57.242 47.619 1.47 0.00 0.00 3.27
2093 2217 2.106074 CGTGTGTGTGTGCAGGTGT 61.106 57.895 0.00 0.00 0.00 4.16
2116 2240 2.262637 TGTACTCCGGTCAAATTCCCT 58.737 47.619 0.00 0.00 0.00 4.20
2117 2241 2.773993 TGTACTCCGGTCAAATTCCC 57.226 50.000 0.00 0.00 0.00 3.97
2285 2415 4.553323 AGTAGTAGTGTTTGTAAGTGCGG 58.447 43.478 0.00 0.00 0.00 5.69
2290 2420 5.392811 CGGAGGGAGTAGTAGTGTTTGTAAG 60.393 48.000 0.00 0.00 0.00 2.34
2297 2427 2.720915 GAACGGAGGGAGTAGTAGTGT 58.279 52.381 0.00 0.00 0.00 3.55
2304 2434 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
2305 2435 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
2306 2436 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2307 2437 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
2308 2438 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2309 2439 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2310 2440 3.846360 AGACAAGTAATTCCGAACGGAG 58.154 45.455 15.34 5.60 46.06 4.63
2311 2441 3.671433 CGAGACAAGTAATTCCGAACGGA 60.671 47.826 12.04 12.04 43.52 4.69
2312 2442 2.597305 CGAGACAAGTAATTCCGAACGG 59.403 50.000 6.94 6.94 0.00 4.44
2313 2443 3.495193 TCGAGACAAGTAATTCCGAACG 58.505 45.455 0.00 0.00 0.00 3.95
2314 2444 5.834239 TTTCGAGACAAGTAATTCCGAAC 57.166 39.130 0.00 0.00 34.86 3.95
2315 2445 6.128391 CCATTTTCGAGACAAGTAATTCCGAA 60.128 38.462 0.00 0.00 33.57 4.30
2316 2446 5.350365 CCATTTTCGAGACAAGTAATTCCGA 59.650 40.000 0.00 0.00 0.00 4.55
2317 2447 5.350365 TCCATTTTCGAGACAAGTAATTCCG 59.650 40.000 0.00 0.00 0.00 4.30
2318 2448 6.737254 TCCATTTTCGAGACAAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
2319 2449 7.752695 ACATCCATTTTCGAGACAAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
2320 2450 7.687941 ACATCCATTTTCGAGACAAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
2321 2451 8.964476 ATACATCCATTTTCGAGACAAGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
2322 2452 8.258007 AGATACATCCATTTTCGAGACAAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
2323 2453 7.782049 AGATACATCCATTTTCGAGACAAGTA 58.218 34.615 0.00 0.00 0.00 2.24
2324 2454 6.644347 AGATACATCCATTTTCGAGACAAGT 58.356 36.000 0.00 0.00 0.00 3.16
2325 2455 8.138074 TCTAGATACATCCATTTTCGAGACAAG 58.862 37.037 0.00 0.00 0.00 3.16
2326 2456 8.007405 TCTAGATACATCCATTTTCGAGACAA 57.993 34.615 0.00 0.00 0.00 3.18
2327 2457 7.582667 TCTAGATACATCCATTTTCGAGACA 57.417 36.000 0.00 0.00 0.00 3.41
2328 2458 8.138712 AGTTCTAGATACATCCATTTTCGAGAC 58.861 37.037 0.00 0.00 0.00 3.36
2329 2459 8.239038 AGTTCTAGATACATCCATTTTCGAGA 57.761 34.615 0.00 0.00 0.00 4.04
2330 2460 9.967346 TTAGTTCTAGATACATCCATTTTCGAG 57.033 33.333 0.00 0.00 0.00 4.04
2350 2480 9.793252 TGGTTGTATCTAGACGTATTTTAGTTC 57.207 33.333 0.00 0.00 0.00 3.01
2355 2485 9.886132 AGAAATGGTTGTATCTAGACGTATTTT 57.114 29.630 0.00 0.00 0.00 1.82
2357 2487 9.962783 GTAGAAATGGTTGTATCTAGACGTATT 57.037 33.333 0.00 0.00 0.00 1.89
2358 2488 8.288208 CGTAGAAATGGTTGTATCTAGACGTAT 58.712 37.037 0.00 0.00 0.00 3.06
2359 2489 7.495606 TCGTAGAAATGGTTGTATCTAGACGTA 59.504 37.037 0.00 0.00 30.15 3.57
2360 2490 6.317140 TCGTAGAAATGGTTGTATCTAGACGT 59.683 38.462 0.00 0.00 30.15 4.34
2361 2491 6.632035 GTCGTAGAAATGGTTGTATCTAGACG 59.368 42.308 0.00 0.00 39.69 4.18
2362 2492 7.478322 TGTCGTAGAAATGGTTGTATCTAGAC 58.522 38.462 0.00 0.00 39.69 2.59
2363 2493 7.634671 TGTCGTAGAAATGGTTGTATCTAGA 57.365 36.000 0.00 0.00 39.69 2.43
2364 2494 7.974501 ACTTGTCGTAGAAATGGTTGTATCTAG 59.025 37.037 0.00 0.00 39.69 2.43
2365 2495 7.833786 ACTTGTCGTAGAAATGGTTGTATCTA 58.166 34.615 0.00 0.00 39.69 1.98
2366 2496 6.698380 ACTTGTCGTAGAAATGGTTGTATCT 58.302 36.000 0.00 0.00 39.69 1.98
2367 2497 6.963049 ACTTGTCGTAGAAATGGTTGTATC 57.037 37.500 0.00 0.00 39.69 2.24
2368 2498 9.444600 AATTACTTGTCGTAGAAATGGTTGTAT 57.555 29.630 0.00 0.00 39.69 2.29
2369 2499 8.836268 AATTACTTGTCGTAGAAATGGTTGTA 57.164 30.769 0.00 0.00 39.69 2.41
2370 2500 7.094933 GGAATTACTTGTCGTAGAAATGGTTGT 60.095 37.037 0.00 0.00 39.69 3.32
2371 2501 7.241376 GGAATTACTTGTCGTAGAAATGGTTG 58.759 38.462 0.00 0.00 39.69 3.77
2372 2502 6.091713 CGGAATTACTTGTCGTAGAAATGGTT 59.908 38.462 0.00 0.00 39.69 3.67
2373 2503 5.579511 CGGAATTACTTGTCGTAGAAATGGT 59.420 40.000 0.00 0.00 39.69 3.55
2374 2504 5.808540 TCGGAATTACTTGTCGTAGAAATGG 59.191 40.000 0.00 0.00 39.69 3.16
2375 2505 6.880822 TCGGAATTACTTGTCGTAGAAATG 57.119 37.500 0.00 0.00 39.69 2.32
2376 2506 6.034256 CGTTCGGAATTACTTGTCGTAGAAAT 59.966 38.462 0.00 0.00 39.69 2.17
2377 2507 5.343058 CGTTCGGAATTACTTGTCGTAGAAA 59.657 40.000 0.00 0.00 39.69 2.52
2378 2508 4.853196 CGTTCGGAATTACTTGTCGTAGAA 59.147 41.667 0.00 0.00 39.69 2.10
2379 2509 4.406069 CGTTCGGAATTACTTGTCGTAGA 58.594 43.478 0.00 0.00 0.00 2.59
2380 2510 3.545078 CCGTTCGGAATTACTTGTCGTAG 59.455 47.826 5.19 0.00 0.00 3.51
2381 2511 3.190327 TCCGTTCGGAATTACTTGTCGTA 59.810 43.478 11.66 0.00 0.00 3.43
2382 2512 2.030007 TCCGTTCGGAATTACTTGTCGT 60.030 45.455 11.66 0.00 0.00 4.34
2383 2513 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
2384 2514 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2385 2515 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2386 2516 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2387 2517 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2388 2518 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2389 2519 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2390 2520 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2391 2521 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
2392 2522 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
2393 2523 0.038744 AGTACTCCCTCCGTTCGGAA 59.961 55.000 14.79 0.04 33.41 4.30
2394 2524 0.038744 AAGTACTCCCTCCGTTCGGA 59.961 55.000 13.34 13.34 0.00 4.55
2395 2525 0.893447 AAAGTACTCCCTCCGTTCGG 59.107 55.000 4.74 4.74 0.00 4.30
2396 2526 2.738013 AAAAGTACTCCCTCCGTTCG 57.262 50.000 0.00 0.00 0.00 3.95
2397 2527 6.866010 TTTTAAAAAGTACTCCCTCCGTTC 57.134 37.500 0.00 0.00 0.00 3.95
2418 2548 8.587952 AAAAGTAATTAGTGCTTGCGATTTTT 57.412 26.923 0.00 0.00 31.76 1.94
2444 2579 6.091986 CGGCCCGTTTTAGTAATTAGTGTAAA 59.908 38.462 0.00 1.60 0.00 2.01
2445 2580 5.580297 CGGCCCGTTTTAGTAATTAGTGTAA 59.420 40.000 0.00 0.00 0.00 2.41
2446 2581 5.105554 TCGGCCCGTTTTAGTAATTAGTGTA 60.106 40.000 1.63 0.00 0.00 2.90
2482 2621 1.467374 CGCTTTCGGCTGGGTTAAATG 60.467 52.381 0.00 0.00 39.13 2.32
2496 2635 0.448197 GCAGAAGTTAGCCCGCTTTC 59.552 55.000 0.00 0.00 0.00 2.62
2506 2645 0.248289 GTACGGCCCAGCAGAAGTTA 59.752 55.000 0.00 0.00 0.00 2.24
2714 2870 6.743627 CAGCCGTTAGATACTTAGATTCGATC 59.256 42.308 0.00 0.00 0.00 3.69
2718 2874 7.204496 TCTCAGCCGTTAGATACTTAGATTC 57.796 40.000 0.00 0.00 0.00 2.52
2767 2925 1.198178 GAGAGTATGTCCGCGATCTCC 59.802 57.143 8.23 0.00 0.00 3.71
2883 3041 3.160585 CTGGGTGGGCTTGACTGA 58.839 61.111 0.00 0.00 0.00 3.41
2884 3042 2.674380 GCTGGGTGGGCTTGACTG 60.674 66.667 0.00 0.00 0.00 3.51
2885 3043 3.971702 GGCTGGGTGGGCTTGACT 61.972 66.667 0.00 0.00 0.00 3.41
2967 3127 4.020617 CCCCAGCTCGAACCTGCA 62.021 66.667 7.12 0.00 0.00 4.41
3370 3535 2.950309 CGTACAGCTACCACTCCACTAT 59.050 50.000 0.00 0.00 0.00 2.12
3375 3540 0.458025 GCACGTACAGCTACCACTCC 60.458 60.000 0.00 0.00 0.00 3.85
3407 3572 2.758979 ACCAGTACACTTACCAGATCGG 59.241 50.000 0.00 2.55 42.50 4.18
3440 3605 1.841663 AACGAACGGTGCACATCAGC 61.842 55.000 20.43 0.00 39.70 4.26
3481 3646 5.242615 ACATAGTGTACATCATCATCGAGCT 59.757 40.000 0.00 0.00 0.00 4.09
3482 3647 5.465051 ACATAGTGTACATCATCATCGAGC 58.535 41.667 0.00 0.00 0.00 5.03
3483 3648 8.293157 ACTAACATAGTGTACATCATCATCGAG 58.707 37.037 0.00 0.00 37.69 4.04
3484 3649 8.166422 ACTAACATAGTGTACATCATCATCGA 57.834 34.615 0.00 0.00 37.69 3.59
3516 3682 8.024145 AGAAAAACCAAATACACCCAAACATA 57.976 30.769 0.00 0.00 0.00 2.29
3517 3683 6.894682 AGAAAAACCAAATACACCCAAACAT 58.105 32.000 0.00 0.00 0.00 2.71
3518 3684 6.301169 AGAAAAACCAAATACACCCAAACA 57.699 33.333 0.00 0.00 0.00 2.83
3519 3685 7.011016 CAGAAGAAAAACCAAATACACCCAAAC 59.989 37.037 0.00 0.00 0.00 2.93
3530 3696 2.420722 ACGCGACAGAAGAAAAACCAAA 59.579 40.909 15.93 0.00 0.00 3.28
3534 3700 3.246936 ACCTAACGCGACAGAAGAAAAAC 59.753 43.478 15.93 0.00 0.00 2.43
3576 3747 6.021596 CACATCACCTAAATAACGCAACTTC 58.978 40.000 0.00 0.00 0.00 3.01
3596 3768 3.956199 CAAAGCCCATCAGATTACCACAT 59.044 43.478 0.00 0.00 0.00 3.21
3597 3769 3.010027 TCAAAGCCCATCAGATTACCACA 59.990 43.478 0.00 0.00 0.00 4.17
3620 3792 1.818642 AGACTCATTTGCCAGCTGAC 58.181 50.000 17.39 3.38 0.00 3.51
3683 3855 3.674423 CGATGAATTCAGAAACGAAGCC 58.326 45.455 14.54 0.00 0.00 4.35
3685 3857 3.125146 TGGCGATGAATTCAGAAACGAAG 59.875 43.478 21.85 7.61 0.00 3.79
3808 3985 3.554692 GCCTCGTCGTCATTGCCG 61.555 66.667 0.00 0.00 0.00 5.69
3850 4027 7.918033 CGAGAGAGTGATATTACTTGTGATTGT 59.082 37.037 1.15 0.00 0.00 2.71
3854 4031 7.625828 TTCGAGAGAGTGATATTACTTGTGA 57.374 36.000 1.15 0.00 43.69 3.58
3868 4045 7.123830 CGTTTTTATGTTGTTTTCGAGAGAGT 58.876 34.615 0.00 0.00 43.69 3.24
3870 4047 6.258287 TCCGTTTTTATGTTGTTTTCGAGAGA 59.742 34.615 0.00 0.00 39.20 3.10
3966 4143 5.637006 TTTCTTTACACTGTGCACTGTTT 57.363 34.783 24.86 21.14 0.00 2.83
3988 4165 8.742777 TGCTTGCTCAGAAATGTAATAATTCTT 58.257 29.630 0.00 0.00 31.26 2.52
3997 4174 5.528690 GGTGATATGCTTGCTCAGAAATGTA 59.471 40.000 0.00 0.00 0.00 2.29
4008 4185 4.142687 ACAAGTTTACGGTGATATGCTTGC 60.143 41.667 0.00 0.00 36.51 4.01
4020 4197 7.802738 TGTCAGATATTTTCACAAGTTTACGG 58.197 34.615 0.00 0.00 0.00 4.02
4112 4289 7.905493 CGGTTATGATCTGAAGCTTTTTACTTC 59.095 37.037 0.00 0.00 43.15 3.01
4121 4298 2.103263 GGGACGGTTATGATCTGAAGCT 59.897 50.000 0.00 0.00 0.00 3.74
4124 4301 4.258543 GTTTGGGACGGTTATGATCTGAA 58.741 43.478 0.00 0.00 0.00 3.02
4156 4333 0.247814 GCAACGAGAATGATGTGCCG 60.248 55.000 0.00 0.00 0.00 5.69
4171 4348 5.108517 TGGAAACTTTCTGTCATTTGCAAC 58.891 37.500 0.00 0.00 30.67 4.17
4182 4359 6.717084 AGAAGGGAGTATTTGGAAACTTTCTG 59.283 38.462 1.57 0.00 0.00 3.02
4196 4373 5.590818 TGAACTAGTGGAAGAAGGGAGTAT 58.409 41.667 0.00 0.00 0.00 2.12
4197 4374 5.006896 TGAACTAGTGGAAGAAGGGAGTA 57.993 43.478 0.00 0.00 0.00 2.59
4198 4375 3.858135 TGAACTAGTGGAAGAAGGGAGT 58.142 45.455 0.00 0.00 0.00 3.85
4199 4376 4.891992 TTGAACTAGTGGAAGAAGGGAG 57.108 45.455 0.00 0.00 0.00 4.30
4200 4377 5.309543 TCATTTGAACTAGTGGAAGAAGGGA 59.690 40.000 0.00 0.00 0.00 4.20
4201 4378 5.412904 GTCATTTGAACTAGTGGAAGAAGGG 59.587 44.000 0.00 0.00 0.00 3.95
4202 4379 5.120830 CGTCATTTGAACTAGTGGAAGAAGG 59.879 44.000 0.00 0.00 0.00 3.46
4203 4380 5.120830 CCGTCATTTGAACTAGTGGAAGAAG 59.879 44.000 0.00 0.00 0.00 2.85
4204 4381 4.994852 CCGTCATTTGAACTAGTGGAAGAA 59.005 41.667 0.00 0.00 0.00 2.52
4205 4382 4.282449 TCCGTCATTTGAACTAGTGGAAGA 59.718 41.667 0.00 0.00 0.00 2.87
4206 4383 4.566004 TCCGTCATTTGAACTAGTGGAAG 58.434 43.478 0.00 0.00 0.00 3.46
4207 4384 4.039973 ACTCCGTCATTTGAACTAGTGGAA 59.960 41.667 0.00 0.00 0.00 3.53
4208 4385 3.576982 ACTCCGTCATTTGAACTAGTGGA 59.423 43.478 0.00 0.00 0.00 4.02
4209 4386 3.926616 ACTCCGTCATTTGAACTAGTGG 58.073 45.455 0.00 0.00 0.00 4.00
4210 4387 6.811665 TCAATACTCCGTCATTTGAACTAGTG 59.188 38.462 0.00 0.00 0.00 2.74
4211 4388 6.931838 TCAATACTCCGTCATTTGAACTAGT 58.068 36.000 0.00 0.00 0.00 2.57
4212 4389 7.827819 TTCAATACTCCGTCATTTGAACTAG 57.172 36.000 0.00 0.00 32.88 2.57
4213 4390 7.279981 CCATTCAATACTCCGTCATTTGAACTA 59.720 37.037 0.00 0.00 38.64 2.24
4214 4391 6.094048 CCATTCAATACTCCGTCATTTGAACT 59.906 38.462 0.00 0.00 38.64 3.01
4215 4392 6.258160 CCATTCAATACTCCGTCATTTGAAC 58.742 40.000 0.00 0.00 38.64 3.18
4216 4393 5.163663 GCCATTCAATACTCCGTCATTTGAA 60.164 40.000 0.00 0.00 39.72 2.69
4217 4394 4.335315 GCCATTCAATACTCCGTCATTTGA 59.665 41.667 0.00 0.00 0.00 2.69
4218 4395 4.096231 TGCCATTCAATACTCCGTCATTTG 59.904 41.667 0.00 0.00 0.00 2.32
4219 4396 4.269183 TGCCATTCAATACTCCGTCATTT 58.731 39.130 0.00 0.00 0.00 2.32
4220 4397 3.884895 TGCCATTCAATACTCCGTCATT 58.115 40.909 0.00 0.00 0.00 2.57
4221 4398 3.558931 TGCCATTCAATACTCCGTCAT 57.441 42.857 0.00 0.00 0.00 3.06
4222 4399 3.270027 CTTGCCATTCAATACTCCGTCA 58.730 45.455 0.00 0.00 33.57 4.35
4223 4400 2.614057 CCTTGCCATTCAATACTCCGTC 59.386 50.000 0.00 0.00 33.57 4.79
4224 4401 2.026262 ACCTTGCCATTCAATACTCCGT 60.026 45.455 0.00 0.00 33.57 4.69
4225 4402 2.355756 CACCTTGCCATTCAATACTCCG 59.644 50.000 0.00 0.00 33.57 4.63
4226 4403 2.689983 CCACCTTGCCATTCAATACTCC 59.310 50.000 0.00 0.00 33.57 3.85
4227 4404 2.099756 GCCACCTTGCCATTCAATACTC 59.900 50.000 0.00 0.00 33.57 2.59
4228 4405 2.102578 GCCACCTTGCCATTCAATACT 58.897 47.619 0.00 0.00 33.57 2.12
4229 4406 2.102578 AGCCACCTTGCCATTCAATAC 58.897 47.619 0.00 0.00 33.57 1.89
4230 4407 2.530460 AGCCACCTTGCCATTCAATA 57.470 45.000 0.00 0.00 33.57 1.90
4231 4408 2.025037 TCTAGCCACCTTGCCATTCAAT 60.025 45.455 0.00 0.00 33.57 2.57
4232 4409 1.354031 TCTAGCCACCTTGCCATTCAA 59.646 47.619 0.00 0.00 0.00 2.69
4233 4410 0.991146 TCTAGCCACCTTGCCATTCA 59.009 50.000 0.00 0.00 0.00 2.57
4234 4411 1.745653 GTTCTAGCCACCTTGCCATTC 59.254 52.381 0.00 0.00 0.00 2.67
4235 4412 1.355720 AGTTCTAGCCACCTTGCCATT 59.644 47.619 0.00 0.00 0.00 3.16
4236 4413 0.995024 AGTTCTAGCCACCTTGCCAT 59.005 50.000 0.00 0.00 0.00 4.40
4237 4414 0.771127 AAGTTCTAGCCACCTTGCCA 59.229 50.000 0.00 0.00 0.00 4.92
4238 4415 1.813178 GAAAGTTCTAGCCACCTTGCC 59.187 52.381 0.00 0.00 0.00 4.52
4239 4416 2.784347 AGAAAGTTCTAGCCACCTTGC 58.216 47.619 0.00 0.00 35.34 4.01
4240 4417 3.057946 GCAAGAAAGTTCTAGCCACCTTG 60.058 47.826 0.00 0.00 36.28 3.61
4241 4418 3.149981 GCAAGAAAGTTCTAGCCACCTT 58.850 45.455 0.00 0.00 36.28 3.50
4242 4419 2.106511 TGCAAGAAAGTTCTAGCCACCT 59.893 45.455 0.00 0.00 36.28 4.00
4243 4420 2.485814 CTGCAAGAAAGTTCTAGCCACC 59.514 50.000 0.00 0.00 36.28 4.61
4244 4421 3.058639 CACTGCAAGAAAGTTCTAGCCAC 60.059 47.826 0.00 0.00 36.28 5.01
4245 4422 3.141398 CACTGCAAGAAAGTTCTAGCCA 58.859 45.455 0.00 0.00 36.28 4.75
4246 4423 2.485814 CCACTGCAAGAAAGTTCTAGCC 59.514 50.000 0.00 0.00 36.28 3.93
4247 4424 3.142174 ACCACTGCAAGAAAGTTCTAGC 58.858 45.455 0.00 0.00 36.28 3.42
4248 4425 4.636249 AGACCACTGCAAGAAAGTTCTAG 58.364 43.478 0.00 0.00 36.28 2.43
4249 4426 4.100963 TGAGACCACTGCAAGAAAGTTCTA 59.899 41.667 0.00 0.00 36.28 2.10
4250 4427 3.118261 TGAGACCACTGCAAGAAAGTTCT 60.118 43.478 0.00 0.00 39.74 3.01
4251 4428 3.206150 TGAGACCACTGCAAGAAAGTTC 58.794 45.455 0.00 0.00 37.43 3.01
4252 4429 3.281727 TGAGACCACTGCAAGAAAGTT 57.718 42.857 0.00 0.00 37.43 2.66


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

AutoCloner maintained by Alex Coulton.