Multiple sequence alignment - TraesCS1A01G395900

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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 TraesCS1A01G395900 chr1A 100.000 2453 0 0 1 2453 561597385 561594933 0.000000e+00 4530.0
1 TraesCS1A01G395900 chr1A 93.296 179 9 2 2276 2453 443079029 443079205 6.730000e-66 261.0
2 TraesCS1A01G395900 chr1D 93.974 1676 84 7 1 1666 468750203 468748535 0.000000e+00 2519.0
3 TraesCS1A01G395900 chr1D 87.500 56 7 0 201 256 101099565 101099620 5.660000e-07 65.8
4 TraesCS1A01G395900 chr1D 83.099 71 12 0 196 266 463291235 463291305 5.660000e-07 65.8
5 TraesCS1A01G395900 chr1B 92.917 1680 92 10 1 1665 648101437 648099770 0.000000e+00 2418.0
6 TraesCS1A01G395900 chr1B 93.819 453 24 2 1827 2276 648099511 648099060 0.000000e+00 678.0
7 TraesCS1A01G395900 chr1B 88.713 567 43 10 1109 1664 648063163 648062607 0.000000e+00 673.0
8 TraesCS1A01G395900 chr1B 93.785 177 10 1 1667 1843 648099708 648099533 5.200000e-67 265.0
9 TraesCS1A01G395900 chr1B 93.182 176 9 2 2279 2453 336935679 336935506 3.130000e-64 255.0
10 TraesCS1A01G395900 chr1B 93.182 176 9 2 2279 2453 336963483 336963310 3.130000e-64 255.0
11 TraesCS1A01G395900 chr7B 94.413 179 7 2 2276 2453 139049471 139049647 3.110000e-69 272.0
12 TraesCS1A01G395900 chr3A 94.857 175 6 2 2280 2453 220165013 220164841 1.120000e-68 270.0
13 TraesCS1A01G395900 chr3A 93.750 176 8 2 2279 2453 200941901 200941728 6.730000e-66 261.0
14 TraesCS1A01G395900 chr3A 78.182 110 23 1 184 292 651420594 651420703 4.380000e-08 69.4
15 TraesCS1A01G395900 chr3A 93.182 44 3 0 213 256 694532533 694532490 5.660000e-07 65.8
16 TraesCS1A01G395900 chr3A 85.000 60 6 2 198 255 668821218 668821160 9.470000e-05 58.4
17 TraesCS1A01G395900 chr2D 94.318 176 9 1 2279 2453 239094997 239094822 4.020000e-68 268.0
18 TraesCS1A01G395900 chr2D 96.154 52 2 0 127 178 115464335 115464386 4.350000e-13 86.1
19 TraesCS1A01G395900 chr2D 78.195 133 24 5 213 342 114529634 114529764 2.020000e-11 80.5
20 TraesCS1A01G395900 chr6A 90.816 196 14 3 2259 2453 346953939 346954131 2.420000e-65 259.0
21 TraesCS1A01G395900 chr7D 92.308 182 11 2 2273 2453 403144761 403144940 3.130000e-64 255.0
22 TraesCS1A01G395900 chr7D 88.083 193 19 3 1688 1878 131828213 131828023 2.450000e-55 226.0
23 TraesCS1A01G395900 chr5D 96.154 52 2 0 127 178 72495173 72495122 4.350000e-13 86.1
24 TraesCS1A01G395900 chr5B 96.154 52 2 0 127 178 567239853 567239904 4.350000e-13 86.1
25 TraesCS1A01G395900 chr5B 94.231 52 3 0 127 178 567296410 567296359 2.020000e-11 80.5
26 TraesCS1A01G395900 chr2A 86.792 53 6 1 215 266 596151616 596151668 9.470000e-05 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 TraesCS1A01G395900 chr1A 561594933 561597385 2452 True 4530.000000 4530 100.000 1 2453 1 chr1A.!!$R1 2452
1 TraesCS1A01G395900 chr1D 468748535 468750203 1668 True 2519.000000 2519 93.974 1 1666 1 chr1D.!!$R1 1665
2 TraesCS1A01G395900 chr1B 648099060 648101437 2377 True 1120.333333 2418 93.507 1 2276 3 chr1B.!!$R4 2275
3 TraesCS1A01G395900 chr1B 648062607 648063163 556 True 673.000000 673 88.713 1109 1664 1 chr1B.!!$R3 555

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
193 195 0.10576 TGTTTGGTGCCTCCATGGTT 60.106 50.0 12.58 0.0 46.6 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1760 1848 0.038618 AGAACACGCGTGACAGCATA 60.039 50.0 42.94 0.0 36.85 3.14 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
29 30 3.243267 ACGTAGATGCACATATACACGCA 60.243 43.478 13.97 0.00 35.78 5.24
52 53 8.385858 CGCACATATAATCACTTCTATGAATGG 58.614 37.037 0.00 0.00 30.15 3.16
73 75 3.877508 GGACACACCATACCTTTATGAGC 59.122 47.826 0.00 0.00 37.86 4.26
79 81 3.062763 CCATACCTTTATGAGCAGCTCG 58.937 50.000 17.81 4.62 37.86 5.03
112 114 1.134367 CGGCAGAACGTCCTGAGATTA 59.866 52.381 5.75 0.00 36.29 1.75
123 125 4.615223 CGTCCTGAGATTAACGAAGTCACA 60.615 45.833 0.00 0.00 45.00 3.58
125 127 5.869888 GTCCTGAGATTAACGAAGTCACATT 59.130 40.000 0.00 0.00 45.00 2.71
148 150 4.162651 AGGGCCTTTCATTTCAATGTTCT 58.837 39.130 0.00 0.00 37.65 3.01
162 164 1.996798 TGTTCTGTCTCGTCCCTCTT 58.003 50.000 0.00 0.00 0.00 2.85
178 180 6.570378 CGTCCCTCTTATTTTGCATCTTGTTT 60.570 38.462 0.00 0.00 0.00 2.83
188 190 1.619654 CATCTTGTTTGGTGCCTCCA 58.380 50.000 0.00 0.00 45.60 3.86
193 195 0.105760 TGTTTGGTGCCTCCATGGTT 60.106 50.000 12.58 0.00 46.60 3.67
197 199 1.294041 TGGTGCCTCCATGGTTGATA 58.706 50.000 12.58 0.00 41.93 2.15
275 278 6.425417 AGAAAAGAGCTAGCACTAGTGAAAAC 59.575 38.462 27.08 12.07 35.65 2.43
278 281 3.839293 AGCTAGCACTAGTGAAAACTCG 58.161 45.455 27.08 10.63 35.65 4.18
309 312 1.151699 TGGTGGGGAGGTTCCATCA 60.152 57.895 0.00 0.00 42.57 3.07
365 368 4.489683 CGCCGACGTTTTTCACAG 57.510 55.556 0.00 0.00 33.53 3.66
418 421 5.895636 TGCACCGAGAAATAAAATGACAT 57.104 34.783 0.00 0.00 0.00 3.06
518 530 6.866248 CACGCATATGAGTATGTATGGTAACA 59.134 38.462 11.99 0.00 45.01 2.41
549 561 2.622064 AGATTAACGGATCACCAGCC 57.378 50.000 0.00 0.00 35.59 4.85
604 616 3.691118 AGTCTTGCCGTGTACGTATTCTA 59.309 43.478 0.00 0.00 37.74 2.10
684 698 9.563898 CACGAAGATGTATGTACTACTACAAAA 57.436 33.333 0.00 0.00 36.43 2.44
939 956 2.495084 CCGTGAGATCGAGGTCATAGA 58.505 52.381 3.04 0.00 0.00 1.98
1035 1052 1.082366 GGCGCACGTGGTTACTTTG 60.082 57.895 18.88 0.00 0.00 2.77
1351 1368 2.806945 TTTCCCAGGTGAAGGCTATG 57.193 50.000 0.00 0.00 0.00 2.23
1357 1374 2.636830 CAGGTGAAGGCTATGACCAAG 58.363 52.381 11.00 1.55 0.00 3.61
1358 1375 2.237143 CAGGTGAAGGCTATGACCAAGA 59.763 50.000 11.00 0.00 0.00 3.02
1359 1376 2.237392 AGGTGAAGGCTATGACCAAGAC 59.763 50.000 11.00 0.00 0.00 3.01
1490 1508 0.172578 TGCTAGATGAACGTGTCCGG 59.827 55.000 0.00 0.00 38.78 5.14
1581 1605 7.013464 AGGATTAAGTCGGGATATTAGCTATCG 59.987 40.741 0.00 0.00 37.67 2.92
1589 1613 6.810182 TCGGGATATTAGCTATCGTAAAAAGC 59.190 38.462 0.00 0.00 37.67 3.51
1678 1766 5.509716 TTGTCCGCCCATATATAGTATCG 57.490 43.478 0.00 0.00 0.00 2.92
1716 1804 7.936301 AGAAGATGATTTCTGCCCTTTAGATAC 59.064 37.037 0.00 0.00 36.12 2.24
1732 1820 8.669243 CCTTTAGATACGAAAATCAAGCTTCTT 58.331 33.333 0.00 0.00 0.00 2.52
1748 1836 7.126421 TCAAGCTTCTTAGAGAAATATGTCCCT 59.874 37.037 0.00 0.00 33.19 4.20
1760 1848 9.190317 GAGAAATATGTCCCTTTTCTTACCAAT 57.810 33.333 0.00 0.00 39.22 3.16
1784 1872 2.596452 CTGTCACGCGTGTTCTTATCT 58.404 47.619 35.74 0.00 0.00 1.98
1789 1877 2.276540 CACGCGTGTTCTTATCTTCGAG 59.723 50.000 30.50 0.00 0.00 4.04
1833 1921 6.332630 CAATTCAAAGTAGGCTTAACCATGG 58.667 40.000 11.19 11.19 43.14 3.66
1839 1965 2.834638 AGGCTTAACCATGGATGCTT 57.165 45.000 21.47 10.03 43.14 3.91
1931 2060 8.527567 TCTTTCCATTTTATGTTTTTAAGGCG 57.472 30.769 0.00 0.00 0.00 5.52
1941 2070 8.764524 TTATGTTTTTAAGGCGCACAATAATT 57.235 26.923 10.83 0.00 0.00 1.40
1990 2119 0.040336 GCGAATCTCCGCGTAGATCA 60.040 55.000 14.98 0.00 45.86 2.92
2015 2144 1.821759 CACAAAGTGCGTGTCCCCA 60.822 57.895 0.00 0.00 0.00 4.96
2052 2181 1.407258 CCTCTTCCAGTCGCTTCCTAG 59.593 57.143 0.00 0.00 0.00 3.02
2101 2230 0.938713 CAGTAACAACGGTTCGCCAA 59.061 50.000 0.00 0.00 38.45 4.52
2109 2238 2.126346 GGTTCGCCAAGCATGCAC 60.126 61.111 21.98 7.01 37.19 4.57
2120 2249 2.156446 GCATGCACGACATTGCTGC 61.156 57.895 14.21 0.00 43.41 5.25
2161 2290 0.405198 TGTCACCCACCAGCAATCAT 59.595 50.000 0.00 0.00 0.00 2.45
2210 2339 5.399013 GTTTTATGCCCAACACACTGATAC 58.601 41.667 0.00 0.00 0.00 2.24
2211 2340 1.737838 ATGCCCAACACACTGATACG 58.262 50.000 0.00 0.00 0.00 3.06
2223 2352 5.168569 CACACTGATACGGAAGTTGTACAT 58.831 41.667 0.00 0.00 46.40 2.29
2259 2388 7.429374 AGACCATAGAGAATTCAGATTCACA 57.571 36.000 8.44 0.00 43.35 3.58
2270 2399 2.440627 TCAGATTCACATAGCCCAGCAT 59.559 45.455 0.00 0.00 0.00 3.79
2288 2417 5.683876 AGCATACTGAGACTGGTTGTAAT 57.316 39.130 0.00 0.00 0.00 1.89
2289 2418 5.423015 AGCATACTGAGACTGGTTGTAATG 58.577 41.667 0.00 0.00 0.00 1.90
2290 2419 4.572389 GCATACTGAGACTGGTTGTAATGG 59.428 45.833 0.00 0.00 0.00 3.16
2291 2420 3.703001 ACTGAGACTGGTTGTAATGGG 57.297 47.619 0.00 0.00 0.00 4.00
2292 2421 3.248024 ACTGAGACTGGTTGTAATGGGA 58.752 45.455 0.00 0.00 0.00 4.37
2293 2422 3.261897 ACTGAGACTGGTTGTAATGGGAG 59.738 47.826 0.00 0.00 0.00 4.30
2294 2423 3.248024 TGAGACTGGTTGTAATGGGAGT 58.752 45.455 0.00 0.00 0.00 3.85
2295 2424 4.422057 TGAGACTGGTTGTAATGGGAGTA 58.578 43.478 0.00 0.00 0.00 2.59
2296 2425 5.030147 TGAGACTGGTTGTAATGGGAGTAT 58.970 41.667 0.00 0.00 0.00 2.12
2297 2426 5.128827 TGAGACTGGTTGTAATGGGAGTATC 59.871 44.000 0.00 0.00 0.00 2.24
2298 2427 5.030147 AGACTGGTTGTAATGGGAGTATCA 58.970 41.667 0.00 0.00 36.25 2.15
2299 2428 5.667626 AGACTGGTTGTAATGGGAGTATCAT 59.332 40.000 0.00 0.00 36.25 2.45
2300 2429 6.844388 AGACTGGTTGTAATGGGAGTATCATA 59.156 38.462 0.00 0.00 36.25 2.15
2301 2430 7.514127 AGACTGGTTGTAATGGGAGTATCATAT 59.486 37.037 0.00 0.00 36.25 1.78
2302 2431 8.736097 ACTGGTTGTAATGGGAGTATCATATA 57.264 34.615 0.00 0.00 36.25 0.86
2303 2432 9.338968 ACTGGTTGTAATGGGAGTATCATATAT 57.661 33.333 0.00 0.00 36.25 0.86
2344 2473 9.445878 TGAAACTAGTATATGATACTACCTCCG 57.554 37.037 0.00 0.00 0.00 4.63
2345 2474 9.447157 GAAACTAGTATATGATACTACCTCCGT 57.553 37.037 0.00 0.00 0.00 4.69
2350 2479 8.223177 AGTATATGATACTACCTCCGTAATGC 57.777 38.462 0.00 0.00 0.00 3.56
2351 2480 7.832685 AGTATATGATACTACCTCCGTAATGCA 59.167 37.037 0.00 0.00 0.00 3.96
2352 2481 7.661536 ATATGATACTACCTCCGTAATGCAT 57.338 36.000 0.00 0.00 0.00 3.96
2353 2482 8.762481 ATATGATACTACCTCCGTAATGCATA 57.238 34.615 0.00 0.00 0.00 3.14
2354 2483 6.510879 TGATACTACCTCCGTAATGCATAG 57.489 41.667 0.00 0.00 0.00 2.23
2355 2484 6.008331 TGATACTACCTCCGTAATGCATAGT 58.992 40.000 0.00 0.00 0.00 2.12
2356 2485 7.170277 TGATACTACCTCCGTAATGCATAGTA 58.830 38.462 0.00 0.81 0.00 1.82
2357 2486 5.702349 ACTACCTCCGTAATGCATAGTAC 57.298 43.478 0.00 0.00 0.00 2.73
2358 2487 5.135383 ACTACCTCCGTAATGCATAGTACA 58.865 41.667 0.00 0.00 0.00 2.90
2359 2488 5.773680 ACTACCTCCGTAATGCATAGTACAT 59.226 40.000 0.00 0.00 0.00 2.29
2360 2489 5.135508 ACCTCCGTAATGCATAGTACATC 57.864 43.478 0.00 0.00 0.00 3.06
2361 2490 4.587262 ACCTCCGTAATGCATAGTACATCA 59.413 41.667 0.00 0.00 0.00 3.07
2362 2491 5.246203 ACCTCCGTAATGCATAGTACATCAT 59.754 40.000 0.00 0.00 0.00 2.45
2363 2492 6.436218 ACCTCCGTAATGCATAGTACATCATA 59.564 38.462 0.00 0.00 0.00 2.15
2364 2493 7.039293 ACCTCCGTAATGCATAGTACATCATAA 60.039 37.037 0.00 0.00 0.00 1.90
2365 2494 7.817478 CCTCCGTAATGCATAGTACATCATAAA 59.183 37.037 0.00 0.00 0.00 1.40
2366 2495 9.371136 CTCCGTAATGCATAGTACATCATAAAT 57.629 33.333 0.00 0.00 0.00 1.40
2367 2496 9.719355 TCCGTAATGCATAGTACATCATAAATT 57.281 29.630 0.00 0.00 0.00 1.82
2395 2524 9.626045 GTATCTTATGTTGCCTTATTAATTGCC 57.374 33.333 0.00 0.00 0.00 4.52
2396 2525 7.652524 TCTTATGTTGCCTTATTAATTGCCA 57.347 32.000 0.00 0.00 0.00 4.92
2397 2526 8.248904 TCTTATGTTGCCTTATTAATTGCCAT 57.751 30.769 0.00 0.00 0.00 4.40
2398 2527 8.143193 TCTTATGTTGCCTTATTAATTGCCATG 58.857 33.333 0.00 0.00 0.00 3.66
2399 2528 4.440880 TGTTGCCTTATTAATTGCCATGC 58.559 39.130 0.00 0.00 0.00 4.06
2400 2529 4.081254 TGTTGCCTTATTAATTGCCATGCA 60.081 37.500 0.00 0.00 36.47 3.96
2401 2530 4.959560 TGCCTTATTAATTGCCATGCAT 57.040 36.364 0.00 0.00 38.76 3.96
2402 2531 4.633175 TGCCTTATTAATTGCCATGCATG 58.367 39.130 20.19 20.19 38.76 4.06
2403 2532 4.344390 TGCCTTATTAATTGCCATGCATGA 59.656 37.500 28.31 8.76 38.76 3.07
2404 2533 4.687483 GCCTTATTAATTGCCATGCATGAC 59.313 41.667 28.31 17.77 38.76 3.06
2405 2534 5.739647 GCCTTATTAATTGCCATGCATGACA 60.740 40.000 28.31 20.53 38.76 3.58
2406 2535 5.693104 CCTTATTAATTGCCATGCATGACAC 59.307 40.000 28.31 16.49 38.76 3.67
2407 2536 4.739587 ATTAATTGCCATGCATGACACA 57.260 36.364 28.31 18.81 38.76 3.72
2408 2537 4.532314 TTAATTGCCATGCATGACACAA 57.468 36.364 28.31 25.14 38.76 3.33
2409 2538 3.404224 AATTGCCATGCATGACACAAA 57.596 38.095 28.31 8.33 38.76 2.83
2410 2539 2.442212 TTGCCATGCATGACACAAAG 57.558 45.000 28.31 10.23 38.76 2.77
2411 2540 1.330234 TGCCATGCATGACACAAAGT 58.670 45.000 28.31 0.00 31.71 2.66
2412 2541 2.512705 TGCCATGCATGACACAAAGTA 58.487 42.857 28.31 5.91 31.71 2.24
2413 2542 2.488937 TGCCATGCATGACACAAAGTAG 59.511 45.455 28.31 8.01 31.71 2.57
2414 2543 2.489329 GCCATGCATGACACAAAGTAGT 59.511 45.455 28.31 0.00 0.00 2.73
2415 2544 3.689161 GCCATGCATGACACAAAGTAGTA 59.311 43.478 28.31 0.00 0.00 1.82
2416 2545 4.336433 GCCATGCATGACACAAAGTAGTAT 59.664 41.667 28.31 0.00 0.00 2.12
2417 2546 5.527214 GCCATGCATGACACAAAGTAGTATA 59.473 40.000 28.31 0.00 0.00 1.47
2418 2547 6.038161 GCCATGCATGACACAAAGTAGTATAA 59.962 38.462 28.31 0.00 0.00 0.98
2419 2548 7.409697 CCATGCATGACACAAAGTAGTATAAC 58.590 38.462 28.31 0.00 0.00 1.89
2420 2549 7.065683 CCATGCATGACACAAAGTAGTATAACA 59.934 37.037 28.31 0.00 0.00 2.41
2421 2550 8.615211 CATGCATGACACAAAGTAGTATAACAT 58.385 33.333 22.59 0.00 0.00 2.71
2422 2551 8.560355 TGCATGACACAAAGTAGTATAACATT 57.440 30.769 0.00 0.00 0.00 2.71
2423 2552 9.008965 TGCATGACACAAAGTAGTATAACATTT 57.991 29.630 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.314740 TGTGCGTGTATATGTGCATCTA 57.685 40.909 0.00 0.00 39.85 1.98
52 53 4.513442 TGCTCATAAAGGTATGGTGTGTC 58.487 43.478 0.00 0.00 38.15 3.67
60 62 2.037772 CCCGAGCTGCTCATAAAGGTAT 59.962 50.000 27.46 0.00 0.00 2.73
73 75 2.242113 GCTCAATATGCCCGAGCTG 58.758 57.895 0.00 0.00 46.86 4.24
112 114 1.628846 AGGCCCTAATGTGACTTCGTT 59.371 47.619 0.00 0.00 0.00 3.85
123 125 6.441604 AGAACATTGAAATGAAAGGCCCTAAT 59.558 34.615 9.94 0.00 39.67 1.73
125 127 5.185635 CAGAACATTGAAATGAAAGGCCCTA 59.814 40.000 9.94 0.00 39.67 3.53
148 150 3.007506 TGCAAAATAAGAGGGACGAGACA 59.992 43.478 0.00 0.00 0.00 3.41
162 164 4.040217 AGGCACCAAACAAGATGCAAAATA 59.960 37.500 0.00 0.00 39.92 1.40
188 190 6.352516 GTCAGAAGACATTCCTATCAACCAT 58.647 40.000 0.00 0.00 44.34 3.55
216 218 1.865340 ACTTTTCGGCGAAGTCAGTTC 59.135 47.619 22.52 0.00 32.04 3.01
260 263 5.241064 AGTCTTCGAGTTTTCACTAGTGCTA 59.759 40.000 18.45 5.73 31.22 3.49
275 278 2.353803 CCACCAGGGTTAAGTCTTCGAG 60.354 54.545 0.00 0.00 0.00 4.04
297 300 5.117406 AGGTTTCTTATGATGGAACCTCC 57.883 43.478 7.19 0.00 36.96 4.30
298 301 7.110155 TGTTAGGTTTCTTATGATGGAACCTC 58.890 38.462 13.66 5.17 31.13 3.85
299 302 7.027874 TGTTAGGTTTCTTATGATGGAACCT 57.972 36.000 14.37 14.37 32.33 3.50
309 312 9.838339 CATACCTCAGATTGTTAGGTTTCTTAT 57.162 33.333 0.00 0.00 40.82 1.73
365 368 0.169009 GTGCCTTTTCGGAGACATGC 59.831 55.000 0.00 0.00 34.32 4.06
374 377 0.744281 ACAAACCAGGTGCCTTTTCG 59.256 50.000 0.00 0.00 0.00 3.46
435 447 3.916761 GTGTGTGTAATCACGTTCCCTA 58.083 45.455 0.00 0.00 46.49 3.53
518 530 7.650903 GTGATCCGTTAATCTACCGAGTTATTT 59.349 37.037 0.00 0.00 0.00 1.40
549 561 1.308998 GCGGATTTCATGTACCTGGG 58.691 55.000 0.00 0.00 0.00 4.45
684 698 6.655003 TCTGCCGATCTCAAAGTTATTTCTTT 59.345 34.615 0.00 0.00 38.04 2.52
687 701 6.293135 GGATCTGCCGATCTCAAAGTTATTTC 60.293 42.308 16.46 0.00 44.42 2.17
690 704 4.636249 GGATCTGCCGATCTCAAAGTTAT 58.364 43.478 16.46 0.00 44.42 1.89
778 792 8.671921 CATGTGCATTATGGGAAATATACTCTC 58.328 37.037 0.00 0.00 0.00 3.20
939 956 2.076863 GTTAGACGCAAGAGGCAATGT 58.923 47.619 0.00 0.00 45.17 2.71
992 1009 2.234143 CGCTCCCTCTCATGTCTGATA 58.766 52.381 0.00 0.00 0.00 2.15
1035 1052 1.026718 CAAGGGACCCGATGAGCAAC 61.027 60.000 12.66 0.00 0.00 4.17
1134 1151 1.540363 CCTCGTATAACCAGCCGCAAT 60.540 52.381 0.00 0.00 0.00 3.56
1351 1368 0.520404 CAGCATGTGCAGTCTTGGTC 59.480 55.000 7.83 0.00 45.16 4.02
1529 1547 2.433239 ACAACTTTACCGCGATCCCTAT 59.567 45.455 8.23 0.00 0.00 2.57
1538 1556 5.813080 AATCCTTGATACAACTTTACCGC 57.187 39.130 0.00 0.00 0.00 5.68
1636 1664 4.136051 CAAAAGGTGGAAATTGGCAATGT 58.864 39.130 14.47 8.32 0.00 2.71
1678 1766 4.954092 ATCATCTTCTTTCGCCAAAGAC 57.046 40.909 5.96 0.00 46.38 3.01
1694 1782 6.223852 TCGTATCTAAAGGGCAGAAATCATC 58.776 40.000 0.00 0.00 0.00 2.92
1700 1788 6.411376 TGATTTTCGTATCTAAAGGGCAGAA 58.589 36.000 0.00 0.00 0.00 3.02
1732 1820 9.053472 TGGTAAGAAAAGGGACATATTTCTCTA 57.947 33.333 0.00 0.00 41.28 2.43
1748 1836 5.391523 GCGTGACAGCATATTGGTAAGAAAA 60.392 40.000 0.00 0.00 37.05 2.29
1760 1848 0.038618 AGAACACGCGTGACAGCATA 60.039 50.000 42.94 0.00 36.85 3.14
1784 1872 2.708216 TGCATATTGAAGGCCTCGAA 57.292 45.000 5.23 1.44 0.00 3.71
1789 1877 1.683385 GGTCCTTGCATATTGAAGGCC 59.317 52.381 0.00 0.00 38.97 5.19
1833 1921 3.679389 TCTTCCTCTTCCACAAAGCATC 58.321 45.455 0.00 0.00 34.76 3.91
1839 1965 6.935240 TCTTCTTATCTTCCTCTTCCACAA 57.065 37.500 0.00 0.00 0.00 3.33
1905 2034 9.150348 CGCCTTAAAAACATAAAATGGAAAGAT 57.850 29.630 0.00 0.00 33.60 2.40
1918 2047 6.870965 TCAATTATTGTGCGCCTTAAAAACAT 59.129 30.769 4.18 0.00 0.00 2.71
1921 2050 6.216569 TGTCAATTATTGTGCGCCTTAAAAA 58.783 32.000 4.18 0.00 0.00 1.94
1931 2060 7.806690 ACCGATATACATGTCAATTATTGTGC 58.193 34.615 0.00 0.84 0.00 4.57
1990 2119 1.450669 ACGCACTTTGTGGACCGTT 60.451 52.632 0.00 0.00 33.64 4.44
2019 2148 0.749454 GAAGAGGATTGGGCACGCAT 60.749 55.000 0.00 0.00 0.00 4.73
2109 2238 1.069973 TCTTTGTTCGCAGCAATGTCG 60.070 47.619 0.00 0.00 0.00 4.35
2210 2339 6.176975 TCTATTTTGCATGTACAACTTCCG 57.823 37.500 0.00 0.00 0.00 4.30
2211 2340 9.109393 TCTATCTATTTTGCATGTACAACTTCC 57.891 33.333 0.00 0.00 0.00 3.46
2259 2388 2.632028 CAGTCTCAGTATGCTGGGCTAT 59.368 50.000 11.15 0.00 42.85 2.97
2270 2399 4.422057 TCCCATTACAACCAGTCTCAGTA 58.578 43.478 0.00 0.00 0.00 2.74
2276 2405 5.353394 TGATACTCCCATTACAACCAGTC 57.647 43.478 0.00 0.00 0.00 3.51
2277 2406 5.975988 ATGATACTCCCATTACAACCAGT 57.024 39.130 0.00 0.00 0.00 4.00
2318 2447 9.445878 CGGAGGTAGTATCATATACTAGTTTCA 57.554 37.037 0.00 0.00 31.41 2.69
2319 2448 9.447157 ACGGAGGTAGTATCATATACTAGTTTC 57.553 37.037 0.00 5.82 31.41 2.78
2324 2453 9.334947 GCATTACGGAGGTAGTATCATATACTA 57.665 37.037 3.25 3.25 0.00 1.82
2325 2454 7.832685 TGCATTACGGAGGTAGTATCATATACT 59.167 37.037 5.04 5.04 0.00 2.12
2326 2455 7.993101 TGCATTACGGAGGTAGTATCATATAC 58.007 38.462 0.00 0.00 0.00 1.47
2327 2456 8.762481 ATGCATTACGGAGGTAGTATCATATA 57.238 34.615 0.00 0.00 0.00 0.86
2328 2457 7.661536 ATGCATTACGGAGGTAGTATCATAT 57.338 36.000 0.00 0.00 0.00 1.78
2329 2458 7.832685 ACTATGCATTACGGAGGTAGTATCATA 59.167 37.037 3.54 0.00 0.00 2.15
2330 2459 6.663953 ACTATGCATTACGGAGGTAGTATCAT 59.336 38.462 3.54 0.00 0.00 2.45
2331 2460 6.008331 ACTATGCATTACGGAGGTAGTATCA 58.992 40.000 3.54 0.00 0.00 2.15
2332 2461 6.512342 ACTATGCATTACGGAGGTAGTATC 57.488 41.667 3.54 0.00 0.00 2.24
2333 2462 6.944290 TGTACTATGCATTACGGAGGTAGTAT 59.056 38.462 3.54 0.00 0.00 2.12
2334 2463 6.298361 TGTACTATGCATTACGGAGGTAGTA 58.702 40.000 3.54 0.00 0.00 1.82
2335 2464 5.135383 TGTACTATGCATTACGGAGGTAGT 58.865 41.667 3.54 0.88 0.00 2.73
2336 2465 5.700722 TGTACTATGCATTACGGAGGTAG 57.299 43.478 3.54 0.00 0.00 3.18
2337 2466 5.771165 TGATGTACTATGCATTACGGAGGTA 59.229 40.000 3.54 0.00 0.00 3.08
2338 2467 4.587262 TGATGTACTATGCATTACGGAGGT 59.413 41.667 3.54 0.00 0.00 3.85
2339 2468 5.134202 TGATGTACTATGCATTACGGAGG 57.866 43.478 3.54 0.00 0.00 4.30
2340 2469 8.757164 TTTATGATGTACTATGCATTACGGAG 57.243 34.615 3.54 0.00 0.00 4.63
2341 2470 9.719355 AATTTATGATGTACTATGCATTACGGA 57.281 29.630 3.54 0.00 0.00 4.69
2369 2498 9.626045 GGCAATTAATAAGGCAACATAAGATAC 57.374 33.333 8.84 0.00 41.41 2.24
2370 2499 9.360901 TGGCAATTAATAAGGCAACATAAGATA 57.639 29.630 12.71 0.00 41.41 1.98
2371 2500 8.248904 TGGCAATTAATAAGGCAACATAAGAT 57.751 30.769 12.71 0.00 41.41 2.40
2372 2501 7.652524 TGGCAATTAATAAGGCAACATAAGA 57.347 32.000 12.71 0.00 41.41 2.10
2373 2502 7.095523 GCATGGCAATTAATAAGGCAACATAAG 60.096 37.037 17.20 7.83 41.29 1.73
2374 2503 6.705381 GCATGGCAATTAATAAGGCAACATAA 59.295 34.615 17.20 0.00 41.29 1.90
2375 2504 6.183360 TGCATGGCAATTAATAAGGCAACATA 60.183 34.615 17.20 5.88 41.29 2.29
2376 2505 5.058490 GCATGGCAATTAATAAGGCAACAT 58.942 37.500 17.20 6.80 41.29 2.71
2377 2506 4.081254 TGCATGGCAATTAATAAGGCAACA 60.081 37.500 17.20 15.42 41.29 3.33
2378 2507 4.440880 TGCATGGCAATTAATAAGGCAAC 58.559 39.130 17.20 13.68 41.29 4.17
2379 2508 4.750021 TGCATGGCAATTAATAAGGCAA 57.250 36.364 17.20 4.23 41.29 4.52
2380 2509 4.344390 TCATGCATGGCAATTAATAAGGCA 59.656 37.500 25.97 16.08 43.62 4.75
2381 2510 4.687483 GTCATGCATGGCAATTAATAAGGC 59.313 41.667 26.04 7.25 43.62 4.35
2382 2511 5.693104 GTGTCATGCATGGCAATTAATAAGG 59.307 40.000 34.01 0.00 44.94 2.69
2383 2512 6.274579 TGTGTCATGCATGGCAATTAATAAG 58.725 36.000 34.01 0.13 44.94 1.73
2384 2513 6.218108 TGTGTCATGCATGGCAATTAATAA 57.782 33.333 34.01 7.61 44.94 1.40
2385 2514 5.848833 TGTGTCATGCATGGCAATTAATA 57.151 34.783 34.01 14.13 44.94 0.98
2386 2515 4.739587 TGTGTCATGCATGGCAATTAAT 57.260 36.364 34.01 0.00 44.94 1.40
2387 2516 4.532314 TTGTGTCATGCATGGCAATTAA 57.468 36.364 34.01 24.54 44.94 1.40
2388 2517 4.021280 ACTTTGTGTCATGCATGGCAATTA 60.021 37.500 34.01 20.55 44.94 1.40
2389 2518 3.244284 ACTTTGTGTCATGCATGGCAATT 60.244 39.130 34.01 11.75 44.94 2.32
2390 2519 2.300723 ACTTTGTGTCATGCATGGCAAT 59.699 40.909 34.01 15.19 44.94 3.56
2391 2520 1.687660 ACTTTGTGTCATGCATGGCAA 59.312 42.857 34.01 25.74 44.94 4.52
2392 2521 1.330234 ACTTTGTGTCATGCATGGCA 58.670 45.000 29.45 29.45 44.86 4.92
2393 2522 2.489329 ACTACTTTGTGTCATGCATGGC 59.511 45.455 24.40 24.40 0.00 4.40
2394 2523 7.065683 TGTTATACTACTTTGTGTCATGCATGG 59.934 37.037 25.97 10.76 0.00 3.66
2395 2524 7.973601 TGTTATACTACTTTGTGTCATGCATG 58.026 34.615 21.07 21.07 0.00 4.06
2396 2525 8.737168 ATGTTATACTACTTTGTGTCATGCAT 57.263 30.769 0.00 0.00 0.00 3.96
2397 2526 8.560355 AATGTTATACTACTTTGTGTCATGCA 57.440 30.769 0.00 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.