Multiple sequence alignment - TraesCS1D01G227700

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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 TraesCS1D01G227700 chr1D 100.000 6010 0 0 1 6010 315984122 315978113 0.000000e+00 11099
1 TraesCS1D01G227700 chr1B 97.385 2715 48 14 2842 5540 428071532 428068825 0.000000e+00 4599
2 TraesCS1D01G227700 chr1B 94.790 2284 75 22 1 2263 428074236 428071976 0.000000e+00 3518
3 TraesCS1D01G227700 chr1B 97.406 424 8 3 2425 2847 428071988 428071567 0.000000e+00 719
4 TraesCS1D01G227700 chr1B 92.114 317 12 2 5535 5851 428068737 428068434 9.250000e-118 435
5 TraesCS1D01G227700 chr1B 90.952 210 14 5 2262 2468 165334208 165334001 1.650000e-70 278
6 TraesCS1D01G227700 chr1B 83.117 154 12 10 4832 4980 630935613 630935469 1.760000e-25 128
7 TraesCS1D01G227700 chr1A 96.229 2042 68 8 3503 5540 396429740 396427704 0.000000e+00 3336
8 TraesCS1D01G227700 chr1A 91.823 2299 113 28 1 2263 396433094 396430835 0.000000e+00 3134
9 TraesCS1D01G227700 chr1A 94.542 1081 46 5 2425 3502 396430847 396429777 0.000000e+00 1657
10 TraesCS1D01G227700 chr1A 94.118 459 26 1 5535 5993 396427617 396427160 0.000000e+00 697
11 TraesCS1D01G227700 chr7A 97.714 175 1 3 2262 2433 254417802 254417628 1.270000e-76 298
12 TraesCS1D01G227700 chr7A 96.648 179 2 4 2262 2438 252185816 252185992 1.640000e-75 294
13 TraesCS1D01G227700 chr5A 97.714 175 1 3 2262 2433 366234991 366234817 1.270000e-76 298
14 TraesCS1D01G227700 chr3A 97.714 175 1 3 2262 2433 308688712 308688538 1.270000e-76 298
15 TraesCS1D01G227700 chrUn 96.629 178 4 2 2262 2437 95253659 95253482 1.640000e-75 294
16 TraesCS1D01G227700 chr4D 95.676 185 5 3 2262 2443 83146691 83146875 1.640000e-75 294
17 TraesCS1D01G227700 chr4D 96.133 181 3 4 2262 2440 306779220 306779042 5.890000e-75 292
18 TraesCS1D01G227700 chr2B 90.179 224 11 11 2262 2476 172488882 172489103 1.280000e-71 281
19 TraesCS1D01G227700 chr5B 90.714 140 12 1 4661 4800 702235123 702234985 1.030000e-42 185


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 TraesCS1D01G227700 chr1D 315978113 315984122 6009 True 11099.00 11099 100.00000 1 6010 1 chr1D.!!$R1 6009
1 TraesCS1D01G227700 chr1B 428068434 428074236 5802 True 2317.75 4599 95.42375 1 5851 4 chr1B.!!$R3 5850
2 TraesCS1D01G227700 chr1A 396427160 396433094 5934 True 2206.00 3336 94.17800 1 5993 4 chr1A.!!$R1 5992

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
451 465 0.739462 CGCAGCCATTTGAGTCCGTA 60.739 55.0 0.00 0.0 0.00 4.02 F
1840 1887 0.112218 AACCAGCTGTAATGTGGCCA 59.888 50.0 13.81 0.0 34.40 5.36 F
2344 2395 0.179037 TGCTATCCATGTGCCAGAGC 60.179 55.0 0.00 0.0 40.48 4.09 F
2351 2402 0.393944 CATGTGCCAGAGCCATGAGT 60.394 55.0 0.00 0.0 44.14 3.41 F
2352 2403 0.393944 ATGTGCCAGAGCCATGAGTG 60.394 55.0 0.00 0.0 38.69 3.51 F
4138 4270 0.458716 GGAGTAAGAGCTGGTGCGAC 60.459 60.0 0.00 0.0 45.42 5.19 F
4967 5100 1.414158 TCCTTCTCAATCTAGGCCCG 58.586 55.0 0.00 0.0 0.00 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2325 2376 0.179037 GCTCTGGCACATGGATAGCA 60.179 55.000 0.00 0.0 38.20 3.49 R
3032 3124 2.173356 CTCCTGGAGTATCATTGGGCAA 59.827 50.000 15.76 0.0 36.25 4.52 R
4138 4270 0.937304 CGTGCCTTTGTATGGGATCG 59.063 55.000 0.00 0.0 0.00 3.69 R
4506 4639 2.505628 AGATGCTGTCATACGCAGAG 57.494 50.000 0.00 0.0 39.82 3.35 R
4967 5100 0.668535 GGTGTTGTTCAGGTTCAGGC 59.331 55.000 0.00 0.0 0.00 4.85 R
4985 5118 1.103398 GCTTCAACGGATGGGGATGG 61.103 60.000 0.00 0.0 0.00 3.51 R
5972 6220 4.194640 CCAATTGGACCTCTACACATGAG 58.805 47.826 20.50 0.0 37.39 2.90 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
72 74 4.271816 CTCTCCGCGACCGATGGG 62.272 72.222 8.23 0.00 36.29 4.00
232 234 1.322538 GGCAGCGGATGGGTTTGAAT 61.323 55.000 0.00 0.00 0.00 2.57
424 438 0.960364 CCAATGACACTTGGGTCCCG 60.960 60.000 2.65 0.00 41.71 5.14
450 464 2.034879 CGCAGCCATTTGAGTCCGT 61.035 57.895 0.00 0.00 0.00 4.69
451 465 0.739462 CGCAGCCATTTGAGTCCGTA 60.739 55.000 0.00 0.00 0.00 4.02
574 591 3.748660 TACATGACATGCGGGCCCG 62.749 63.158 40.26 40.26 43.09 6.13
953 981 3.793144 CCGCGCTTCTGTTGCCTC 61.793 66.667 5.56 0.00 0.00 4.70
1353 1382 2.005451 CTGGAGGTGAGCATTTCTTCG 58.995 52.381 0.00 0.00 0.00 3.79
1422 1460 4.431416 ACACTACATGAACCCACTTTCA 57.569 40.909 0.00 0.00 39.79 2.69
1452 1490 0.533491 TTGATGCTGGGCTTGAATGC 59.467 50.000 0.00 0.00 0.00 3.56
1582 1621 7.776933 TTCAGCAATAGAATACACATCTGAC 57.223 36.000 0.00 0.00 0.00 3.51
1707 1753 4.940468 TGAATCATATGGGAGGCATCAT 57.060 40.909 0.00 0.00 0.00 2.45
1708 1754 4.851843 TGAATCATATGGGAGGCATCATC 58.148 43.478 0.00 0.00 0.00 2.92
1816 1862 0.593128 AAAGCATGGAGAACACGCAC 59.407 50.000 0.00 0.00 0.00 5.34
1840 1887 0.112218 AACCAGCTGTAATGTGGCCA 59.888 50.000 13.81 0.00 34.40 5.36
1841 1888 0.332632 ACCAGCTGTAATGTGGCCAT 59.667 50.000 9.72 0.00 34.40 4.40
1855 1902 3.647590 TGTGGCCATTATCTGCTGATAGA 59.352 43.478 9.72 5.89 36.62 1.98
1882 1929 5.801947 GCTTTAGTGCTGAATATGTTTGTGG 59.198 40.000 0.00 0.00 0.00 4.17
1884 1931 7.361713 GCTTTAGTGCTGAATATGTTTGTGGTA 60.362 37.037 0.00 0.00 0.00 3.25
2052 2099 2.113860 TCTACTGCCAATCTGGTTGC 57.886 50.000 0.00 0.00 40.46 4.17
2269 2320 6.819397 ATAAGTTGTTTGCTAAAGGAGACC 57.181 37.500 0.00 0.00 0.00 3.85
2270 2321 4.439253 AGTTGTTTGCTAAAGGAGACCT 57.561 40.909 0.00 0.00 33.87 3.85
2271 2322 4.137543 AGTTGTTTGCTAAAGGAGACCTG 58.862 43.478 0.00 0.00 32.13 4.00
2272 2323 4.134563 GTTGTTTGCTAAAGGAGACCTGA 58.865 43.478 0.00 0.00 32.13 3.86
2273 2324 4.431416 TGTTTGCTAAAGGAGACCTGAA 57.569 40.909 0.00 0.00 32.13 3.02
2274 2325 4.389374 TGTTTGCTAAAGGAGACCTGAAG 58.611 43.478 0.00 0.00 32.13 3.02
2275 2326 3.703001 TTGCTAAAGGAGACCTGAAGG 57.297 47.619 0.00 0.00 42.17 3.46
2276 2327 2.902608 TGCTAAAGGAGACCTGAAGGA 58.097 47.619 2.62 0.00 38.94 3.36
2277 2328 3.454858 TGCTAAAGGAGACCTGAAGGAT 58.545 45.455 2.62 0.00 38.94 3.24
2278 2329 3.846588 TGCTAAAGGAGACCTGAAGGATT 59.153 43.478 2.62 0.00 38.94 3.01
2279 2330 4.195416 GCTAAAGGAGACCTGAAGGATTG 58.805 47.826 2.62 0.00 38.94 2.67
2280 2331 3.728385 AAAGGAGACCTGAAGGATTGG 57.272 47.619 2.62 0.00 38.94 3.16
2281 2332 2.649742 AGGAGACCTGAAGGATTGGA 57.350 50.000 2.62 0.00 38.94 3.53
2282 2333 2.476199 AGGAGACCTGAAGGATTGGAG 58.524 52.381 2.62 0.00 38.94 3.86
2283 2334 2.192263 GGAGACCTGAAGGATTGGAGT 58.808 52.381 2.62 0.00 38.94 3.85
2284 2335 3.012959 AGGAGACCTGAAGGATTGGAGTA 59.987 47.826 2.62 0.00 38.94 2.59
2285 2336 3.970640 GGAGACCTGAAGGATTGGAGTAT 59.029 47.826 2.62 0.00 38.94 2.12
2286 2337 4.039852 GGAGACCTGAAGGATTGGAGTATC 59.960 50.000 2.62 0.00 38.94 2.24
2287 2338 4.624913 AGACCTGAAGGATTGGAGTATCA 58.375 43.478 2.62 0.00 38.94 2.15
2288 2339 4.407296 AGACCTGAAGGATTGGAGTATCAC 59.593 45.833 2.62 0.00 38.94 3.06
2289 2340 3.456277 ACCTGAAGGATTGGAGTATCACC 59.544 47.826 2.62 0.00 38.94 4.02
2290 2341 3.455910 CCTGAAGGATTGGAGTATCACCA 59.544 47.826 0.00 0.00 34.60 4.17
2291 2342 6.527086 ACCTGAAGGATTGGAGTATCACCAA 61.527 44.000 2.62 0.00 43.61 3.67
2292 2343 7.950045 ACCTGAAGGATTGGAGTATCACCAAA 61.950 42.308 2.62 0.00 43.17 3.28
2293 2344 9.647145 ACCTGAAGGATTGGAGTATCACCAAAG 62.647 44.444 2.62 0.00 43.17 2.77
2300 2351 5.086104 TGGAGTATCACCAAAGAACTAGC 57.914 43.478 0.00 0.00 36.25 3.42
2301 2352 4.777896 TGGAGTATCACCAAAGAACTAGCT 59.222 41.667 0.00 0.00 36.25 3.32
2302 2353 5.955959 TGGAGTATCACCAAAGAACTAGCTA 59.044 40.000 0.00 0.00 36.25 3.32
2303 2354 6.611642 TGGAGTATCACCAAAGAACTAGCTAT 59.388 38.462 0.00 0.00 36.25 2.97
2304 2355 6.926272 GGAGTATCACCAAAGAACTAGCTATG 59.074 42.308 0.00 0.00 36.25 2.23
2305 2356 6.821388 AGTATCACCAAAGAACTAGCTATGG 58.179 40.000 7.17 7.17 0.00 2.74
2306 2357 5.957771 ATCACCAAAGAACTAGCTATGGA 57.042 39.130 14.35 0.00 0.00 3.41
2307 2358 5.086104 TCACCAAAGAACTAGCTATGGAC 57.914 43.478 14.35 0.00 0.00 4.02
2308 2359 4.530553 TCACCAAAGAACTAGCTATGGACA 59.469 41.667 14.35 0.00 0.00 4.02
2309 2360 4.872691 CACCAAAGAACTAGCTATGGACAG 59.127 45.833 14.35 0.00 0.00 3.51
2310 2361 4.080863 ACCAAAGAACTAGCTATGGACAGG 60.081 45.833 14.35 5.47 0.00 4.00
2311 2362 4.446371 CAAAGAACTAGCTATGGACAGGG 58.554 47.826 0.00 0.00 0.00 4.45
2312 2363 2.683768 AGAACTAGCTATGGACAGGGG 58.316 52.381 0.00 0.00 0.00 4.79
2313 2364 2.022918 AGAACTAGCTATGGACAGGGGT 60.023 50.000 0.00 0.00 0.00 4.95
2314 2365 1.794714 ACTAGCTATGGACAGGGGTG 58.205 55.000 0.00 0.00 0.00 4.61
2315 2366 0.394565 CTAGCTATGGACAGGGGTGC 59.605 60.000 0.00 0.00 35.66 5.01
2316 2367 1.399744 TAGCTATGGACAGGGGTGCG 61.400 60.000 0.00 0.00 38.35 5.34
2317 2368 3.031417 GCTATGGACAGGGGTGCGT 62.031 63.158 0.00 0.00 38.35 5.24
2318 2369 1.153369 CTATGGACAGGGGTGCGTG 60.153 63.158 0.00 0.00 38.35 5.34
2319 2370 2.593468 CTATGGACAGGGGTGCGTGG 62.593 65.000 0.00 0.00 38.35 4.94
2321 2372 3.948719 GGACAGGGGTGCGTGGAA 61.949 66.667 0.00 0.00 0.00 3.53
2322 2373 2.358737 GACAGGGGTGCGTGGAAG 60.359 66.667 0.00 0.00 0.00 3.46
2323 2374 4.643387 ACAGGGGTGCGTGGAAGC 62.643 66.667 0.00 0.00 37.71 3.86
2324 2375 4.335647 CAGGGGTGCGTGGAAGCT 62.336 66.667 0.00 0.00 38.13 3.74
2325 2376 3.570212 AGGGGTGCGTGGAAGCTT 61.570 61.111 0.00 0.00 38.13 3.74
2326 2377 3.365265 GGGGTGCGTGGAAGCTTG 61.365 66.667 2.10 0.00 38.13 4.01
2327 2378 4.043200 GGGTGCGTGGAAGCTTGC 62.043 66.667 11.58 11.58 38.13 4.01
2328 2379 2.980233 GGTGCGTGGAAGCTTGCT 60.980 61.111 19.34 0.00 38.13 3.91
2329 2380 1.671054 GGTGCGTGGAAGCTTGCTA 60.671 57.895 19.34 2.82 38.13 3.49
2330 2381 1.026718 GGTGCGTGGAAGCTTGCTAT 61.027 55.000 19.34 0.00 38.13 2.97
2331 2382 0.375106 GTGCGTGGAAGCTTGCTATC 59.625 55.000 19.34 8.59 38.13 2.08
2332 2383 0.744414 TGCGTGGAAGCTTGCTATCC 60.744 55.000 19.34 6.99 38.13 2.59
2333 2384 0.744414 GCGTGGAAGCTTGCTATCCA 60.744 55.000 19.34 9.80 40.84 3.41
2334 2385 1.959042 CGTGGAAGCTTGCTATCCAT 58.041 50.000 19.34 0.00 44.55 3.41
2335 2386 1.600957 CGTGGAAGCTTGCTATCCATG 59.399 52.381 19.34 20.51 44.55 3.66
2336 2387 2.648059 GTGGAAGCTTGCTATCCATGT 58.352 47.619 19.34 0.00 44.55 3.21
2337 2388 2.357009 GTGGAAGCTTGCTATCCATGTG 59.643 50.000 19.34 0.00 44.55 3.21
2338 2389 1.336125 GGAAGCTTGCTATCCATGTGC 59.664 52.381 11.19 0.00 33.30 4.57
2339 2390 1.336125 GAAGCTTGCTATCCATGTGCC 59.664 52.381 2.10 0.00 0.00 5.01
2340 2391 0.256752 AGCTTGCTATCCATGTGCCA 59.743 50.000 0.00 0.00 0.00 4.92
2341 2392 0.666913 GCTTGCTATCCATGTGCCAG 59.333 55.000 0.00 0.00 0.00 4.85
2342 2393 1.748244 GCTTGCTATCCATGTGCCAGA 60.748 52.381 0.00 0.00 0.00 3.86
2343 2394 2.219458 CTTGCTATCCATGTGCCAGAG 58.781 52.381 0.00 0.00 0.00 3.35
2344 2395 0.179037 TGCTATCCATGTGCCAGAGC 60.179 55.000 0.00 0.00 40.48 4.09
2345 2396 0.888285 GCTATCCATGTGCCAGAGCC 60.888 60.000 0.00 0.00 38.69 4.70
2346 2397 0.471191 CTATCCATGTGCCAGAGCCA 59.529 55.000 0.00 0.00 38.69 4.75
2347 2398 1.073444 CTATCCATGTGCCAGAGCCAT 59.927 52.381 0.00 0.00 38.69 4.40
2348 2399 0.467474 ATCCATGTGCCAGAGCCATG 60.467 55.000 8.59 8.59 42.54 3.66
2349 2400 1.077285 CCATGTGCCAGAGCCATGA 60.077 57.895 14.22 0.00 44.14 3.07
2350 2401 1.101635 CCATGTGCCAGAGCCATGAG 61.102 60.000 14.22 5.17 44.14 2.90
2351 2402 0.393944 CATGTGCCAGAGCCATGAGT 60.394 55.000 0.00 0.00 44.14 3.41
2352 2403 0.393944 ATGTGCCAGAGCCATGAGTG 60.394 55.000 0.00 0.00 38.69 3.51
2363 2414 2.215907 CCATGAGTGGTCGTGAGATC 57.784 55.000 0.00 0.00 41.66 2.75
2364 2415 1.753649 CCATGAGTGGTCGTGAGATCT 59.246 52.381 0.00 0.00 43.23 2.75
2365 2416 2.167281 CCATGAGTGGTCGTGAGATCTT 59.833 50.000 0.00 0.00 43.23 2.40
2366 2417 3.381590 CCATGAGTGGTCGTGAGATCTTA 59.618 47.826 0.00 0.00 43.23 2.10
2367 2418 4.038522 CCATGAGTGGTCGTGAGATCTTAT 59.961 45.833 0.00 0.00 43.23 1.73
2368 2419 4.639135 TGAGTGGTCGTGAGATCTTATG 57.361 45.455 0.00 0.00 43.23 1.90
2369 2420 3.381590 TGAGTGGTCGTGAGATCTTATGG 59.618 47.826 6.85 0.00 43.23 2.74
2370 2421 2.695666 AGTGGTCGTGAGATCTTATGGG 59.304 50.000 6.85 0.00 43.23 4.00
2371 2422 2.431057 GTGGTCGTGAGATCTTATGGGT 59.569 50.000 6.85 0.00 43.23 4.51
2372 2423 3.104512 TGGTCGTGAGATCTTATGGGTT 58.895 45.455 6.85 0.00 43.23 4.11
2373 2424 3.517901 TGGTCGTGAGATCTTATGGGTTT 59.482 43.478 6.85 0.00 43.23 3.27
2374 2425 4.120589 GGTCGTGAGATCTTATGGGTTTC 58.879 47.826 6.85 0.00 45.19 2.78
2375 2426 4.382685 GGTCGTGAGATCTTATGGGTTTCA 60.383 45.833 6.85 0.00 45.19 2.69
2376 2427 4.567159 GTCGTGAGATCTTATGGGTTTCAC 59.433 45.833 6.85 2.02 45.19 3.18
2377 2428 3.871594 CGTGAGATCTTATGGGTTTCACC 59.128 47.826 0.00 0.00 37.60 4.02
2378 2429 4.383118 CGTGAGATCTTATGGGTTTCACCT 60.383 45.833 0.00 0.00 38.64 4.00
2379 2430 5.119694 GTGAGATCTTATGGGTTTCACCTC 58.880 45.833 0.00 0.00 38.64 3.85
2380 2431 5.032846 TGAGATCTTATGGGTTTCACCTCT 58.967 41.667 0.00 0.00 38.64 3.69
2381 2432 6.098409 GTGAGATCTTATGGGTTTCACCTCTA 59.902 42.308 0.00 0.00 38.64 2.43
2382 2433 6.325028 TGAGATCTTATGGGTTTCACCTCTAG 59.675 42.308 0.00 0.00 38.64 2.43
2383 2434 4.755266 TCTTATGGGTTTCACCTCTAGC 57.245 45.455 0.00 0.00 38.64 3.42
2384 2435 3.454812 TCTTATGGGTTTCACCTCTAGCC 59.545 47.826 0.00 0.00 38.64 3.93
2385 2436 1.972588 ATGGGTTTCACCTCTAGCCT 58.027 50.000 0.00 0.00 38.64 4.58
2386 2437 2.634639 TGGGTTTCACCTCTAGCCTA 57.365 50.000 0.00 0.00 38.64 3.93
2387 2438 2.185387 TGGGTTTCACCTCTAGCCTAC 58.815 52.381 0.00 0.00 38.64 3.18
2388 2439 1.485480 GGGTTTCACCTCTAGCCTACC 59.515 57.143 0.00 0.00 38.64 3.18
2389 2440 1.485480 GGTTTCACCTCTAGCCTACCC 59.515 57.143 0.00 0.00 34.73 3.69
2390 2441 1.485480 GTTTCACCTCTAGCCTACCCC 59.515 57.143 0.00 0.00 0.00 4.95
2391 2442 0.714180 TTCACCTCTAGCCTACCCCA 59.286 55.000 0.00 0.00 0.00 4.96
2392 2443 0.714180 TCACCTCTAGCCTACCCCAA 59.286 55.000 0.00 0.00 0.00 4.12
2393 2444 0.831307 CACCTCTAGCCTACCCCAAC 59.169 60.000 0.00 0.00 0.00 3.77
2394 2445 0.717196 ACCTCTAGCCTACCCCAACT 59.283 55.000 0.00 0.00 0.00 3.16
2395 2446 1.080666 ACCTCTAGCCTACCCCAACTT 59.919 52.381 0.00 0.00 0.00 2.66
2396 2447 1.486726 CCTCTAGCCTACCCCAACTTG 59.513 57.143 0.00 0.00 0.00 3.16
2397 2448 2.188817 CTCTAGCCTACCCCAACTTGT 58.811 52.381 0.00 0.00 0.00 3.16
2398 2449 2.572104 CTCTAGCCTACCCCAACTTGTT 59.428 50.000 0.00 0.00 0.00 2.83
2399 2450 2.983898 TCTAGCCTACCCCAACTTGTTT 59.016 45.455 0.00 0.00 0.00 2.83
2400 2451 1.995376 AGCCTACCCCAACTTGTTTG 58.005 50.000 0.00 0.00 34.63 2.93
2411 2462 3.977427 CAACTTGTTTGGGACTAAAGGC 58.023 45.455 0.00 0.00 0.00 4.35
2412 2463 3.595190 ACTTGTTTGGGACTAAAGGCT 57.405 42.857 0.00 0.00 0.00 4.58
2413 2464 3.910989 ACTTGTTTGGGACTAAAGGCTT 58.089 40.909 0.00 0.00 0.00 4.35
2414 2465 4.286707 ACTTGTTTGGGACTAAAGGCTTT 58.713 39.130 17.76 17.76 0.00 3.51
2415 2466 4.099419 ACTTGTTTGGGACTAAAGGCTTTG 59.901 41.667 22.32 13.97 0.00 2.77
2416 2467 3.637769 TGTTTGGGACTAAAGGCTTTGT 58.362 40.909 22.32 16.86 0.00 2.83
2417 2468 4.027437 TGTTTGGGACTAAAGGCTTTGTT 58.973 39.130 22.32 8.73 0.00 2.83
2418 2469 4.142049 TGTTTGGGACTAAAGGCTTTGTTG 60.142 41.667 22.32 13.85 0.00 3.33
2419 2470 3.306472 TGGGACTAAAGGCTTTGTTGT 57.694 42.857 22.32 16.69 0.00 3.32
2420 2471 3.637769 TGGGACTAAAGGCTTTGTTGTT 58.362 40.909 22.32 1.84 0.00 2.83
2421 2472 3.383185 TGGGACTAAAGGCTTTGTTGTTG 59.617 43.478 22.32 7.79 0.00 3.33
2422 2473 3.383505 GGGACTAAAGGCTTTGTTGTTGT 59.616 43.478 22.32 10.58 0.00 3.32
2423 2474 4.142026 GGGACTAAAGGCTTTGTTGTTGTT 60.142 41.667 22.32 0.00 0.00 2.83
2424 2475 4.803613 GGACTAAAGGCTTTGTTGTTGTTG 59.196 41.667 22.32 0.00 0.00 3.33
2425 2476 5.400066 ACTAAAGGCTTTGTTGTTGTTGT 57.600 34.783 22.32 0.00 0.00 3.32
2426 2477 5.789521 ACTAAAGGCTTTGTTGTTGTTGTT 58.210 33.333 22.32 0.00 0.00 2.83
2427 2478 5.637387 ACTAAAGGCTTTGTTGTTGTTGTTG 59.363 36.000 22.32 0.00 0.00 3.33
2428 2479 3.676291 AGGCTTTGTTGTTGTTGTTGT 57.324 38.095 0.00 0.00 0.00 3.32
2429 2480 4.001618 AGGCTTTGTTGTTGTTGTTGTT 57.998 36.364 0.00 0.00 0.00 2.83
2430 2481 4.384940 AGGCTTTGTTGTTGTTGTTGTTT 58.615 34.783 0.00 0.00 0.00 2.83
2431 2482 4.819088 AGGCTTTGTTGTTGTTGTTGTTTT 59.181 33.333 0.00 0.00 0.00 2.43
2432 2483 4.908730 GGCTTTGTTGTTGTTGTTGTTTTG 59.091 37.500 0.00 0.00 0.00 2.44
2433 2484 4.378323 GCTTTGTTGTTGTTGTTGTTTTGC 59.622 37.500 0.00 0.00 0.00 3.68
2434 2485 5.741388 TTTGTTGTTGTTGTTGTTTTGCT 57.259 30.435 0.00 0.00 0.00 3.91
2435 2486 6.564873 GCTTTGTTGTTGTTGTTGTTTTGCTA 60.565 34.615 0.00 0.00 0.00 3.49
2436 2487 6.844696 TTGTTGTTGTTGTTGTTTTGCTAA 57.155 29.167 0.00 0.00 0.00 3.09
2437 2488 6.844696 TGTTGTTGTTGTTGTTTTGCTAAA 57.155 29.167 0.00 0.00 0.00 1.85
2438 2489 7.246674 TGTTGTTGTTGTTGTTTTGCTAAAA 57.753 28.000 0.00 0.00 0.00 1.52
2439 2490 7.348201 TGTTGTTGTTGTTGTTTTGCTAAAAG 58.652 30.769 0.00 0.00 0.00 2.27
2440 2491 7.011482 TGTTGTTGTTGTTGTTTTGCTAAAAGT 59.989 29.630 0.00 0.00 0.00 2.66
2817 2869 8.686334 CAGCACCTTCTAAAAATATGTATTGGT 58.314 33.333 0.00 0.00 0.00 3.67
3128 3220 7.034685 TGATGTCCATTCTTAATGCTCATTG 57.965 36.000 5.43 0.00 37.57 2.82
3463 3557 3.142174 GCAGTGAGTATTTGCCCCTATC 58.858 50.000 0.00 0.00 31.79 2.08
3518 3648 3.515502 TCCATGCTGTTGTAGAGCTAACT 59.484 43.478 0.00 0.00 37.35 2.24
3899 4029 5.066375 TCCTGAAATACTTCATTCGCCAATG 59.934 40.000 0.00 0.00 40.78 2.82
3945 4075 6.964934 GTCTGGGCAATTTTGTACGTAATTAG 59.035 38.462 0.00 0.00 0.00 1.73
4138 4270 0.458716 GGAGTAAGAGCTGGTGCGAC 60.459 60.000 0.00 0.00 45.42 5.19
4967 5100 1.414158 TCCTTCTCAATCTAGGCCCG 58.586 55.000 0.00 0.00 0.00 6.13
4985 5118 0.307760 CGCCTGAACCTGAACAACAC 59.692 55.000 0.00 0.00 0.00 3.32
4998 5131 1.302949 CAACACCATCCCCATCCGT 59.697 57.895 0.00 0.00 0.00 4.69
5061 5194 4.962693 GTCATCTGACAAGTTGAAATCCG 58.037 43.478 10.54 0.00 44.18 4.18
5062 5195 3.436704 TCATCTGACAAGTTGAAATCCGC 59.563 43.478 10.54 0.00 30.76 5.54
5064 5197 3.476552 TCTGACAAGTTGAAATCCGCTT 58.523 40.909 10.54 0.00 0.00 4.68
5078 5211 3.853831 TCCGCTTACTATCAAACGACA 57.146 42.857 0.00 0.00 0.00 4.35
5409 5549 4.133820 TGGTTCTTGAAATTTCGAGCTCA 58.866 39.130 25.10 19.47 38.36 4.26
5482 5624 8.418662 AGTTAGTGTAAAATTTCCCTTTTCACC 58.581 33.333 0.00 0.00 32.58 4.02
5520 5662 8.017418 TCCAAATGACTAAACAGAAATTGGTT 57.983 30.769 0.00 0.00 40.59 3.67
5579 5815 2.089980 GCACCATCTCAGCAAGTGATT 58.910 47.619 0.00 0.00 33.51 2.57
5583 5819 3.008813 ACCATCTCAGCAAGTGATTGTCT 59.991 43.478 0.00 0.00 33.51 3.41
5584 5820 4.223700 ACCATCTCAGCAAGTGATTGTCTA 59.776 41.667 0.00 0.00 33.51 2.59
5604 5840 7.243487 TGTCTATTTTTGCGCTCTGAAAATAG 58.757 34.615 28.53 28.53 45.63 1.73
5611 5859 5.878332 TGCGCTCTGAAAATAGAATTGAA 57.122 34.783 9.73 0.00 0.00 2.69
5612 5860 6.252967 TGCGCTCTGAAAATAGAATTGAAA 57.747 33.333 9.73 0.00 0.00 2.69
5613 5861 6.855836 TGCGCTCTGAAAATAGAATTGAAAT 58.144 32.000 9.73 0.00 0.00 2.17
5614 5862 7.315142 TGCGCTCTGAAAATAGAATTGAAATT 58.685 30.769 9.73 0.00 0.00 1.82
5615 5863 7.814107 TGCGCTCTGAAAATAGAATTGAAATTT 59.186 29.630 9.73 0.00 0.00 1.82
5616 5864 9.289303 GCGCTCTGAAAATAGAATTGAAATTTA 57.711 29.630 0.00 0.00 0.00 1.40
5659 5907 0.250640 AGATCATCTTGCCCGCATCC 60.251 55.000 0.00 0.00 0.00 3.51
5702 5950 8.366671 TCTTTAGAAACTCTGAAGTTAAGTGC 57.633 34.615 7.74 0.00 45.07 4.40
5907 6155 9.149225 GTAGCACCATCTCTATGATCTAAAATG 57.851 37.037 0.00 0.00 34.84 2.32
5919 6167 6.302535 TGATCTAAAATGGTTTCTACGGGA 57.697 37.500 0.00 0.00 0.00 5.14
5926 6174 6.997239 AAATGGTTTCTACGGGAAATACTC 57.003 37.500 8.60 0.00 44.46 2.59
5972 6220 0.038159 CTATAGGGCCGTAGCTGTGC 60.038 60.000 11.42 0.00 39.73 4.57
5993 6241 3.624861 GCTCATGTGTAGAGGTCCAATTG 59.375 47.826 0.00 0.00 33.72 2.32
5994 6242 4.194640 CTCATGTGTAGAGGTCCAATTGG 58.805 47.826 19.08 19.08 0.00 3.16
5995 6243 3.587061 TCATGTGTAGAGGTCCAATTGGT 59.413 43.478 23.76 4.96 36.34 3.67
5996 6244 4.042809 TCATGTGTAGAGGTCCAATTGGTT 59.957 41.667 23.76 11.05 36.34 3.67
5997 6245 3.750371 TGTGTAGAGGTCCAATTGGTTG 58.250 45.455 23.76 0.00 36.34 3.77
5998 6246 3.137544 TGTGTAGAGGTCCAATTGGTTGT 59.862 43.478 23.76 11.77 36.34 3.32
5999 6247 4.348461 TGTGTAGAGGTCCAATTGGTTGTA 59.652 41.667 23.76 10.86 36.34 2.41
6000 6248 5.163184 TGTGTAGAGGTCCAATTGGTTGTAA 60.163 40.000 23.76 1.13 36.34 2.41
6001 6249 5.411669 GTGTAGAGGTCCAATTGGTTGTAAG 59.588 44.000 23.76 0.00 36.34 2.34
6002 6250 3.421844 AGAGGTCCAATTGGTTGTAAGC 58.578 45.455 23.76 13.56 36.34 3.09
6003 6251 3.153919 GAGGTCCAATTGGTTGTAAGCA 58.846 45.455 23.76 0.00 36.34 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 56 4.933064 CCATCGGTCGCGGAGAGC 62.933 72.222 6.13 0.56 43.53 4.09
66 68 4.918129 GCGCAATGCTGCCCATCG 62.918 66.667 0.30 0.00 46.56 3.84
141 143 1.226859 GACGCGCATGTGGTAGCTA 60.227 57.895 5.73 0.00 0.00 3.32
226 228 0.608035 GGCCACGTCTCCCATTCAAA 60.608 55.000 0.00 0.00 0.00 2.69
232 234 2.847234 ACAAGGCCACGTCTCCCA 60.847 61.111 5.01 0.00 0.00 4.37
424 438 3.211564 AAATGGCTGCGTGTGTGGC 62.212 57.895 0.00 0.00 0.00 5.01
496 510 0.737715 ACGTTGCTCTGGATTCTCGC 60.738 55.000 0.00 0.00 0.00 5.03
574 591 2.169978 AGTGGGCCTAGGTTATTCGTTC 59.830 50.000 11.31 0.00 0.00 3.95
576 593 1.761198 GAGTGGGCCTAGGTTATTCGT 59.239 52.381 11.31 0.00 0.00 3.85
606 623 2.050350 CCCGTAAGCGAGGTCCTCA 61.050 63.158 19.15 0.00 41.33 3.86
738 760 1.044611 GCTCTATTCCTTCCTCCGCT 58.955 55.000 0.00 0.00 0.00 5.52
806 832 3.643595 TTTGGGATCTGGGCAGCGG 62.644 63.158 0.00 0.00 0.00 5.52
807 833 2.045045 TTTGGGATCTGGGCAGCG 60.045 61.111 0.00 0.00 0.00 5.18
808 834 2.054453 GGTTTGGGATCTGGGCAGC 61.054 63.158 0.00 0.00 0.00 5.25
809 835 0.967380 GTGGTTTGGGATCTGGGCAG 60.967 60.000 0.00 0.00 0.00 4.85
810 836 1.076549 GTGGTTTGGGATCTGGGCA 59.923 57.895 0.00 0.00 0.00 5.36
893 921 1.225426 GCCTGGCCTGATCACATCA 59.775 57.895 11.88 0.00 37.76 3.07
1415 1453 6.974622 AGCATCAAAACTTTGTACTGAAAGTG 59.025 34.615 11.00 1.79 43.83 3.16
1422 1460 3.005791 GCCCAGCATCAAAACTTTGTACT 59.994 43.478 2.30 0.00 39.18 2.73
1452 1490 0.900421 TCTGCTCTCACCAGTGGATG 59.100 55.000 18.40 10.71 0.00 3.51
1707 1753 1.827344 ACGCAATCTCAGATCACCAGA 59.173 47.619 0.00 0.00 0.00 3.86
1708 1754 1.931841 CACGCAATCTCAGATCACCAG 59.068 52.381 0.00 0.00 0.00 4.00
1778 1824 5.006844 TGCTTTTCACATGCAAGAACAAATG 59.993 36.000 0.00 0.00 32.71 2.32
1816 1862 2.095768 CCACATTACAGCTGGTTGTTCG 60.096 50.000 19.93 7.35 32.56 3.95
1840 1887 9.217278 CACTAAAGCAATCTATCAGCAGATAAT 57.783 33.333 0.14 0.00 36.35 1.28
1841 1888 7.172190 GCACTAAAGCAATCTATCAGCAGATAA 59.828 37.037 0.14 0.00 36.35 1.75
1855 1902 7.543172 CACAAACATATTCAGCACTAAAGCAAT 59.457 33.333 0.00 0.00 36.85 3.56
1882 1929 4.770795 ACCTGGCAATCACTGAATACTAC 58.229 43.478 0.00 0.00 0.00 2.73
1884 1931 5.435686 TTACCTGGCAATCACTGAATACT 57.564 39.130 0.00 0.00 0.00 2.12
2052 2099 3.279434 AGACTTATTAAGGGGCAAAGCG 58.721 45.455 8.26 0.00 0.00 4.68
2215 2265 4.256920 GCAGATGGTGTCTAGAACATGTT 58.743 43.478 11.78 11.78 40.80 2.71
2263 2314 2.192263 ACTCCAATCCTTCAGGTCTCC 58.808 52.381 0.00 0.00 36.34 3.71
2265 2316 4.407296 GTGATACTCCAATCCTTCAGGTCT 59.593 45.833 0.00 0.00 36.34 3.85
2266 2317 4.443598 GGTGATACTCCAATCCTTCAGGTC 60.444 50.000 0.00 0.00 36.34 3.85
2267 2318 3.456277 GGTGATACTCCAATCCTTCAGGT 59.544 47.826 0.00 0.00 36.34 4.00
2268 2319 3.455910 TGGTGATACTCCAATCCTTCAGG 59.544 47.826 0.00 0.00 31.50 3.86
2269 2320 4.760530 TGGTGATACTCCAATCCTTCAG 57.239 45.455 0.00 0.00 31.50 3.02
2270 2321 5.250543 TCTTTGGTGATACTCCAATCCTTCA 59.749 40.000 6.20 0.00 43.25 3.02
2271 2322 5.745227 TCTTTGGTGATACTCCAATCCTTC 58.255 41.667 6.20 0.00 43.25 3.46
2272 2323 5.779241 TCTTTGGTGATACTCCAATCCTT 57.221 39.130 6.20 0.00 43.25 3.36
2273 2324 5.251700 AGTTCTTTGGTGATACTCCAATCCT 59.748 40.000 6.20 0.00 43.25 3.24
2274 2325 5.501156 AGTTCTTTGGTGATACTCCAATCC 58.499 41.667 6.20 0.00 43.25 3.01
2275 2326 6.258947 GCTAGTTCTTTGGTGATACTCCAATC 59.741 42.308 6.20 0.00 43.25 2.67
2276 2327 6.069963 AGCTAGTTCTTTGGTGATACTCCAAT 60.070 38.462 6.20 0.00 43.25 3.16
2277 2328 5.248477 AGCTAGTTCTTTGGTGATACTCCAA 59.752 40.000 0.00 0.00 42.29 3.53
2278 2329 4.777896 AGCTAGTTCTTTGGTGATACTCCA 59.222 41.667 0.00 0.00 0.00 3.86
2279 2330 5.346181 AGCTAGTTCTTTGGTGATACTCC 57.654 43.478 0.00 0.00 0.00 3.85
2280 2331 6.926272 CCATAGCTAGTTCTTTGGTGATACTC 59.074 42.308 0.00 0.00 32.65 2.59
2281 2332 6.611642 TCCATAGCTAGTTCTTTGGTGATACT 59.388 38.462 8.33 0.00 36.79 2.12
2282 2333 6.702282 GTCCATAGCTAGTTCTTTGGTGATAC 59.298 42.308 8.33 0.00 36.79 2.24
2283 2334 6.382859 TGTCCATAGCTAGTTCTTTGGTGATA 59.617 38.462 8.33 0.00 36.79 2.15
2284 2335 5.189736 TGTCCATAGCTAGTTCTTTGGTGAT 59.810 40.000 8.33 0.00 36.79 3.06
2285 2336 4.530553 TGTCCATAGCTAGTTCTTTGGTGA 59.469 41.667 8.33 0.00 36.79 4.02
2286 2337 4.832248 TGTCCATAGCTAGTTCTTTGGTG 58.168 43.478 8.33 0.00 36.79 4.17
2287 2338 4.080863 CCTGTCCATAGCTAGTTCTTTGGT 60.081 45.833 8.33 0.00 36.79 3.67
2288 2339 4.446371 CCTGTCCATAGCTAGTTCTTTGG 58.554 47.826 0.00 0.65 36.78 3.28
2289 2340 4.446371 CCCTGTCCATAGCTAGTTCTTTG 58.554 47.826 0.00 0.00 0.00 2.77
2290 2341 3.456277 CCCCTGTCCATAGCTAGTTCTTT 59.544 47.826 0.00 0.00 0.00 2.52
2291 2342 3.041946 CCCCTGTCCATAGCTAGTTCTT 58.958 50.000 0.00 0.00 0.00 2.52
2292 2343 2.022918 ACCCCTGTCCATAGCTAGTTCT 60.023 50.000 0.00 0.00 0.00 3.01
2293 2344 2.103263 CACCCCTGTCCATAGCTAGTTC 59.897 54.545 0.00 0.00 0.00 3.01
2294 2345 2.119495 CACCCCTGTCCATAGCTAGTT 58.881 52.381 0.00 0.00 0.00 2.24
2295 2346 1.794714 CACCCCTGTCCATAGCTAGT 58.205 55.000 0.00 0.00 0.00 2.57
2296 2347 0.394565 GCACCCCTGTCCATAGCTAG 59.605 60.000 0.00 0.00 0.00 3.42
2297 2348 1.399744 CGCACCCCTGTCCATAGCTA 61.400 60.000 0.00 0.00 0.00 3.32
2298 2349 2.735772 CGCACCCCTGTCCATAGCT 61.736 63.158 0.00 0.00 0.00 3.32
2299 2350 2.203070 CGCACCCCTGTCCATAGC 60.203 66.667 0.00 0.00 0.00 2.97
2300 2351 1.153369 CACGCACCCCTGTCCATAG 60.153 63.158 0.00 0.00 0.00 2.23
2301 2352 2.665089 CCACGCACCCCTGTCCATA 61.665 63.158 0.00 0.00 0.00 2.74
2302 2353 4.033776 CCACGCACCCCTGTCCAT 62.034 66.667 0.00 0.00 0.00 3.41
2304 2355 3.901797 CTTCCACGCACCCCTGTCC 62.902 68.421 0.00 0.00 0.00 4.02
2305 2356 2.358737 CTTCCACGCACCCCTGTC 60.359 66.667 0.00 0.00 0.00 3.51
2306 2357 4.643387 GCTTCCACGCACCCCTGT 62.643 66.667 0.00 0.00 0.00 4.00
2307 2358 3.850098 AAGCTTCCACGCACCCCTG 62.850 63.158 0.00 0.00 0.00 4.45
2308 2359 3.570212 AAGCTTCCACGCACCCCT 61.570 61.111 0.00 0.00 0.00 4.79
2309 2360 3.365265 CAAGCTTCCACGCACCCC 61.365 66.667 0.00 0.00 0.00 4.95
2310 2361 4.043200 GCAAGCTTCCACGCACCC 62.043 66.667 0.00 0.00 0.00 4.61
2311 2362 1.026718 ATAGCAAGCTTCCACGCACC 61.027 55.000 8.96 0.00 0.00 5.01
2312 2363 0.375106 GATAGCAAGCTTCCACGCAC 59.625 55.000 8.96 0.00 0.00 5.34
2313 2364 0.744414 GGATAGCAAGCTTCCACGCA 60.744 55.000 8.96 0.00 0.00 5.24
2314 2365 0.744414 TGGATAGCAAGCTTCCACGC 60.744 55.000 16.61 0.00 34.65 5.34
2315 2366 1.600957 CATGGATAGCAAGCTTCCACG 59.399 52.381 20.41 13.24 42.09 4.94
2316 2367 2.357009 CACATGGATAGCAAGCTTCCAC 59.643 50.000 20.41 0.00 42.09 4.02
2317 2368 2.646930 CACATGGATAGCAAGCTTCCA 58.353 47.619 20.33 20.33 43.37 3.53
2318 2369 1.336125 GCACATGGATAGCAAGCTTCC 59.664 52.381 0.00 7.95 0.00 3.46
2319 2370 1.336125 GGCACATGGATAGCAAGCTTC 59.664 52.381 0.00 0.00 0.00 3.86
2320 2371 1.341285 TGGCACATGGATAGCAAGCTT 60.341 47.619 0.00 0.00 0.00 3.74
2321 2372 0.256752 TGGCACATGGATAGCAAGCT 59.743 50.000 0.00 0.00 0.00 3.74
2322 2373 0.666913 CTGGCACATGGATAGCAAGC 59.333 55.000 0.00 0.00 38.20 4.01
2323 2374 2.219458 CTCTGGCACATGGATAGCAAG 58.781 52.381 0.00 0.00 38.20 4.01
2324 2375 1.748244 GCTCTGGCACATGGATAGCAA 60.748 52.381 0.00 0.00 38.20 3.91
2325 2376 0.179037 GCTCTGGCACATGGATAGCA 60.179 55.000 0.00 0.00 38.20 3.49
2326 2377 0.888285 GGCTCTGGCACATGGATAGC 60.888 60.000 0.00 0.00 38.20 2.97
2327 2378 0.471191 TGGCTCTGGCACATGGATAG 59.529 55.000 0.00 0.00 38.20 2.08
2328 2379 1.142936 ATGGCTCTGGCACATGGATA 58.857 50.000 0.00 0.00 41.84 2.59
2329 2380 0.467474 CATGGCTCTGGCACATGGAT 60.467 55.000 7.68 0.00 41.84 3.41
2330 2381 1.077285 CATGGCTCTGGCACATGGA 60.077 57.895 7.68 0.00 41.84 3.41
2331 2382 1.077285 TCATGGCTCTGGCACATGG 60.077 57.895 13.76 0.00 41.84 3.66
2332 2383 0.393944 ACTCATGGCTCTGGCACATG 60.394 55.000 8.97 8.97 41.84 3.21
2333 2384 0.393944 CACTCATGGCTCTGGCACAT 60.394 55.000 0.00 0.00 41.84 3.21
2334 2385 1.002990 CACTCATGGCTCTGGCACA 60.003 57.895 0.00 0.00 41.84 4.57
2335 2386 1.748122 CCACTCATGGCTCTGGCAC 60.748 63.158 0.00 0.00 41.84 5.01
2336 2387 2.672908 CCACTCATGGCTCTGGCA 59.327 61.111 0.00 0.00 39.82 4.92
2345 2396 3.516981 AAGATCTCACGACCACTCATG 57.483 47.619 0.00 0.00 0.00 3.07
2346 2397 4.038522 CCATAAGATCTCACGACCACTCAT 59.961 45.833 0.00 0.00 0.00 2.90
2347 2398 3.381590 CCATAAGATCTCACGACCACTCA 59.618 47.826 0.00 0.00 0.00 3.41
2348 2399 3.243569 CCCATAAGATCTCACGACCACTC 60.244 52.174 0.00 0.00 0.00 3.51
2349 2400 2.695666 CCCATAAGATCTCACGACCACT 59.304 50.000 0.00 0.00 0.00 4.00
2350 2401 2.431057 ACCCATAAGATCTCACGACCAC 59.569 50.000 0.00 0.00 0.00 4.16
2351 2402 2.747177 ACCCATAAGATCTCACGACCA 58.253 47.619 0.00 0.00 0.00 4.02
2352 2403 3.821421 AACCCATAAGATCTCACGACC 57.179 47.619 0.00 0.00 0.00 4.79
2353 2404 4.567159 GTGAAACCCATAAGATCTCACGAC 59.433 45.833 0.00 0.00 0.00 4.34
2354 2405 4.755411 GTGAAACCCATAAGATCTCACGA 58.245 43.478 0.00 0.00 0.00 4.35
2370 2421 1.485480 GGGGTAGGCTAGAGGTGAAAC 59.515 57.143 0.00 0.00 0.00 2.78
2371 2422 1.079825 TGGGGTAGGCTAGAGGTGAAA 59.920 52.381 0.00 0.00 0.00 2.69
2372 2423 0.714180 TGGGGTAGGCTAGAGGTGAA 59.286 55.000 0.00 0.00 0.00 3.18
2373 2424 0.714180 TTGGGGTAGGCTAGAGGTGA 59.286 55.000 0.00 0.00 0.00 4.02
2374 2425 0.831307 GTTGGGGTAGGCTAGAGGTG 59.169 60.000 0.00 0.00 0.00 4.00
2375 2426 0.717196 AGTTGGGGTAGGCTAGAGGT 59.283 55.000 0.00 0.00 0.00 3.85
2376 2427 1.486726 CAAGTTGGGGTAGGCTAGAGG 59.513 57.143 0.00 0.00 0.00 3.69
2377 2428 2.188817 ACAAGTTGGGGTAGGCTAGAG 58.811 52.381 7.96 0.00 0.00 2.43
2378 2429 2.337359 ACAAGTTGGGGTAGGCTAGA 57.663 50.000 7.96 0.00 0.00 2.43
2379 2430 3.081804 CAAACAAGTTGGGGTAGGCTAG 58.918 50.000 7.96 0.00 33.18 3.42
2380 2431 3.149005 CAAACAAGTTGGGGTAGGCTA 57.851 47.619 7.96 0.00 33.18 3.93
2381 2432 1.995376 CAAACAAGTTGGGGTAGGCT 58.005 50.000 7.96 0.00 33.18 4.58
2390 2441 3.636764 AGCCTTTAGTCCCAAACAAGTTG 59.363 43.478 0.00 0.00 36.94 3.16
2391 2442 3.910989 AGCCTTTAGTCCCAAACAAGTT 58.089 40.909 0.00 0.00 0.00 2.66
2392 2443 3.595190 AGCCTTTAGTCCCAAACAAGT 57.405 42.857 0.00 0.00 0.00 3.16
2393 2444 4.099419 ACAAAGCCTTTAGTCCCAAACAAG 59.901 41.667 0.00 0.00 0.00 3.16
2394 2445 4.027437 ACAAAGCCTTTAGTCCCAAACAA 58.973 39.130 0.00 0.00 0.00 2.83
2395 2446 3.637769 ACAAAGCCTTTAGTCCCAAACA 58.362 40.909 0.00 0.00 0.00 2.83
2396 2447 4.142026 ACAACAAAGCCTTTAGTCCCAAAC 60.142 41.667 0.00 0.00 0.00 2.93
2397 2448 4.027437 ACAACAAAGCCTTTAGTCCCAAA 58.973 39.130 0.00 0.00 0.00 3.28
2398 2449 3.637769 ACAACAAAGCCTTTAGTCCCAA 58.362 40.909 0.00 0.00 0.00 4.12
2399 2450 3.306472 ACAACAAAGCCTTTAGTCCCA 57.694 42.857 0.00 0.00 0.00 4.37
2400 2451 3.383505 ACAACAACAAAGCCTTTAGTCCC 59.616 43.478 0.00 0.00 0.00 4.46
2401 2452 4.649088 ACAACAACAAAGCCTTTAGTCC 57.351 40.909 0.00 0.00 0.00 3.85
2402 2453 5.407502 ACAACAACAACAAAGCCTTTAGTC 58.592 37.500 0.00 0.00 0.00 2.59
2403 2454 5.400066 ACAACAACAACAAAGCCTTTAGT 57.600 34.783 0.00 0.00 0.00 2.24
2404 2455 5.637387 ACAACAACAACAACAAAGCCTTTAG 59.363 36.000 0.00 0.00 0.00 1.85
2405 2456 5.542779 ACAACAACAACAACAAAGCCTTTA 58.457 33.333 0.00 0.00 0.00 1.85
2406 2457 4.384940 ACAACAACAACAACAAAGCCTTT 58.615 34.783 0.00 0.00 0.00 3.11
2407 2458 4.001618 ACAACAACAACAACAAAGCCTT 57.998 36.364 0.00 0.00 0.00 4.35
2408 2459 3.676291 ACAACAACAACAACAAAGCCT 57.324 38.095 0.00 0.00 0.00 4.58
2409 2460 4.740741 AAACAACAACAACAACAAAGCC 57.259 36.364 0.00 0.00 0.00 4.35
2410 2461 4.378323 GCAAAACAACAACAACAACAAAGC 59.622 37.500 0.00 0.00 0.00 3.51
2411 2462 5.746539 AGCAAAACAACAACAACAACAAAG 58.253 33.333 0.00 0.00 0.00 2.77
2412 2463 5.741388 AGCAAAACAACAACAACAACAAA 57.259 30.435 0.00 0.00 0.00 2.83
2413 2464 6.844696 TTAGCAAAACAACAACAACAACAA 57.155 29.167 0.00 0.00 0.00 2.83
2414 2465 6.844696 TTTAGCAAAACAACAACAACAACA 57.155 29.167 0.00 0.00 0.00 3.33
2415 2466 7.320087 CACTTTTAGCAAAACAACAACAACAAC 59.680 33.333 0.00 0.00 0.00 3.32
2416 2467 7.224753 TCACTTTTAGCAAAACAACAACAACAA 59.775 29.630 0.00 0.00 0.00 2.83
2417 2468 6.701841 TCACTTTTAGCAAAACAACAACAACA 59.298 30.769 0.00 0.00 0.00 3.33
2418 2469 7.111353 TCACTTTTAGCAAAACAACAACAAC 57.889 32.000 0.00 0.00 0.00 3.32
2419 2470 7.715265 TTCACTTTTAGCAAAACAACAACAA 57.285 28.000 0.00 0.00 0.00 2.83
2420 2471 7.715265 TTTCACTTTTAGCAAAACAACAACA 57.285 28.000 0.00 0.00 0.00 3.33
2423 2474 9.092876 CCTTATTTCACTTTTAGCAAAACAACA 57.907 29.630 0.00 0.00 0.00 3.33
2424 2475 9.308318 TCCTTATTTCACTTTTAGCAAAACAAC 57.692 29.630 0.00 0.00 0.00 3.32
2425 2476 9.877178 TTCCTTATTTCACTTTTAGCAAAACAA 57.123 25.926 0.00 0.00 0.00 2.83
2426 2477 9.877178 TTTCCTTATTTCACTTTTAGCAAAACA 57.123 25.926 0.00 0.00 0.00 2.83
2431 2482 9.912634 CATTCTTTCCTTATTTCACTTTTAGCA 57.087 29.630 0.00 0.00 0.00 3.49
2432 2483 9.914131 ACATTCTTTCCTTATTTCACTTTTAGC 57.086 29.630 0.00 0.00 0.00 3.09
3032 3124 2.173356 CTCCTGGAGTATCATTGGGCAA 59.827 50.000 15.76 0.00 36.25 4.52
3128 3220 8.068977 CAGATTTCTAGATGCAAAGTCAATAGC 58.931 37.037 0.00 0.00 0.00 2.97
3168 3260 6.349197 CCAGCACACATTTGTATACACATGAA 60.349 38.462 29.77 13.20 37.45 2.57
3176 3268 3.364460 AGCCCAGCACACATTTGTATA 57.636 42.857 0.00 0.00 33.30 1.47
3518 3648 3.003394 CTGCCCATTCATACAGGAACA 57.997 47.619 0.00 0.00 0.00 3.18
3899 4029 6.467047 CAGACATTTTGAACAATCGCATACTC 59.533 38.462 0.00 0.00 0.00 2.59
3945 4075 1.952296 CCCTTGCAAGCTGGATGTATC 59.048 52.381 21.43 0.00 0.00 2.24
4138 4270 0.937304 CGTGCCTTTGTATGGGATCG 59.063 55.000 0.00 0.00 0.00 3.69
4506 4639 2.505628 AGATGCTGTCATACGCAGAG 57.494 50.000 0.00 0.00 39.82 3.35
4967 5100 0.668535 GGTGTTGTTCAGGTTCAGGC 59.331 55.000 0.00 0.00 0.00 4.85
4985 5118 1.103398 GCTTCAACGGATGGGGATGG 61.103 60.000 0.00 0.00 0.00 3.51
5061 5194 5.796350 AATGGTGTCGTTTGATAGTAAGC 57.204 39.130 0.00 0.00 0.00 3.09
5062 5195 7.548075 AGGTAAATGGTGTCGTTTGATAGTAAG 59.452 37.037 0.00 0.00 34.32 2.34
5064 5197 6.938507 AGGTAAATGGTGTCGTTTGATAGTA 58.061 36.000 0.00 0.00 34.32 1.82
5078 5211 1.285078 GAGCCCCTCAAGGTAAATGGT 59.715 52.381 0.00 0.00 0.00 3.55
5409 5549 4.079385 ACCAGTTTAAACCTTCTCCTGGTT 60.079 41.667 16.35 5.56 46.72 3.67
5520 5662 5.973899 TTCAGCAAGCATAAAACATACCA 57.026 34.783 0.00 0.00 0.00 3.25
5579 5815 5.431420 TTTTCAGAGCGCAAAAATAGACA 57.569 34.783 11.47 0.00 0.00 3.41
5583 5819 9.075519 CAATTCTATTTTCAGAGCGCAAAAATA 57.924 29.630 11.47 17.22 35.07 1.40
5584 5820 7.814107 TCAATTCTATTTTCAGAGCGCAAAAAT 59.186 29.630 11.47 17.02 36.73 1.82
5611 5859 7.531716 TCTCCGCAAAAATGACGTTATAAATT 58.468 30.769 0.00 0.00 0.00 1.82
5612 5860 7.079182 TCTCCGCAAAAATGACGTTATAAAT 57.921 32.000 0.00 0.00 0.00 1.40
5613 5861 6.483385 TCTCCGCAAAAATGACGTTATAAA 57.517 33.333 0.00 0.00 0.00 1.40
5614 5862 6.671614 ATCTCCGCAAAAATGACGTTATAA 57.328 33.333 0.00 0.00 0.00 0.98
5615 5863 6.671614 AATCTCCGCAAAAATGACGTTATA 57.328 33.333 0.00 0.00 0.00 0.98
5616 5864 5.560966 AATCTCCGCAAAAATGACGTTAT 57.439 34.783 0.00 0.00 0.00 1.89
5617 5865 5.365403 AAATCTCCGCAAAAATGACGTTA 57.635 34.783 0.00 0.00 0.00 3.18
5618 5866 3.915437 AATCTCCGCAAAAATGACGTT 57.085 38.095 0.00 0.00 0.00 3.99
5619 5867 3.915437 AAATCTCCGCAAAAATGACGT 57.085 38.095 0.00 0.00 0.00 4.34
5620 5868 5.216566 TCTAAATCTCCGCAAAAATGACG 57.783 39.130 0.00 0.00 0.00 4.35
5621 5869 6.785191 TGATCTAAATCTCCGCAAAAATGAC 58.215 36.000 0.00 0.00 32.75 3.06
5622 5870 7.500227 AGATGATCTAAATCTCCGCAAAAATGA 59.500 33.333 0.00 0.00 32.75 2.57
5702 5950 8.019669 GCAGCTTATATGAAGATGTACCATTTG 58.980 37.037 8.63 0.00 36.17 2.32
5859 6107 9.569167 GCTACCAAATTCTTATAGGTTGTTTTC 57.431 33.333 0.00 0.00 33.91 2.29
5914 6162 6.732896 AAGATGATACAGAGTATTTCCCGT 57.267 37.500 0.00 0.00 0.00 5.28
5915 6163 8.438676 AAAAAGATGATACAGAGTATTTCCCG 57.561 34.615 0.00 0.00 0.00 5.14
5972 6220 4.194640 CCAATTGGACCTCTACACATGAG 58.805 47.826 20.50 0.00 37.39 2.90


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

AutoCloner maintained by Alex Coulton.