Multiple sequence alignment - TraesCS1B01G021100

Loading Multiple Alignment...

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 TraesCS1B01G021100 chr1B 100.000 2038 0 0 1 2038 9716727 9714690 0.000000e+00 3764
1 TraesCS1B01G021100 chr1B 91.587 832 61 7 1149 1972 9673023 9672193 0.000000e+00 1140
2 TraesCS1B01G021100 chr1B 100.000 516 0 0 2265 2780 9714463 9713948 0.000000e+00 953
3 TraesCS1B01G021100 chr1B 87.287 763 84 8 995 1747 9845459 9846218 0.000000e+00 859
4 TraesCS1B01G021100 chr1B 87.227 595 71 4 169 760 9673618 9673026 0.000000e+00 673
5 TraesCS1B01G021100 chr1D 94.956 2042 85 11 4 2038 7040597 7038567 0.000000e+00 3184
6 TraesCS1B01G021100 chr1D 90.881 1974 134 31 4 1962 7693118 7695060 0.000000e+00 2606
7 TraesCS1B01G021100 chr1D 85.798 1021 74 33 290 1261 7744311 7745309 0.000000e+00 1016
8 TraesCS1B01G021100 chr1D 84.248 984 129 16 991 1959 7707013 7707985 0.000000e+00 935
9 TraesCS1B01G021100 chr1D 93.571 420 24 3 2361 2780 7038385 7037969 8.460000e-175 623
10 TraesCS1B01G021100 chr1D 89.697 165 14 2 4 165 7411429 7411265 1.010000e-49 207
11 TraesCS1B01G021100 chr1A 91.998 1962 142 9 11 1962 9155368 9157324 0.000000e+00 2739
12 TraesCS1B01G021100 chr1A 92.367 1166 81 4 804 1962 9194294 9195458 0.000000e+00 1653
13 TraesCS1B01G021100 chrUn 90.950 1547 116 11 433 1962 276780873 276779334 0.000000e+00 2060
14 TraesCS1B01G021100 chrUn 92.135 1068 76 4 902 1962 278893720 278892654 0.000000e+00 1500
15 TraesCS1B01G021100 chrUn 91.579 285 18 3 518 796 76770494 76770778 3.360000e-104 388


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 TraesCS1B01G021100 chr1B 9713948 9716727 2779 True 2358.5 3764 100.0000 1 2780 2 chr1B.!!$R2 2779
1 TraesCS1B01G021100 chr1B 9672193 9673618 1425 True 906.5 1140 89.4070 169 1972 2 chr1B.!!$R1 1803
2 TraesCS1B01G021100 chr1B 9845459 9846218 759 False 859.0 859 87.2870 995 1747 1 chr1B.!!$F1 752
3 TraesCS1B01G021100 chr1D 7693118 7695060 1942 False 2606.0 2606 90.8810 4 1962 1 chr1D.!!$F1 1958
4 TraesCS1B01G021100 chr1D 7037969 7040597 2628 True 1903.5 3184 94.2635 4 2780 2 chr1D.!!$R2 2776
5 TraesCS1B01G021100 chr1D 7744311 7745309 998 False 1016.0 1016 85.7980 290 1261 1 chr1D.!!$F3 971
6 TraesCS1B01G021100 chr1D 7707013 7707985 972 False 935.0 935 84.2480 991 1959 1 chr1D.!!$F2 968
7 TraesCS1B01G021100 chr1A 9155368 9157324 1956 False 2739.0 2739 91.9980 11 1962 1 chr1A.!!$F1 1951
8 TraesCS1B01G021100 chr1A 9194294 9195458 1164 False 1653.0 1653 92.3670 804 1962 1 chr1A.!!$F2 1158
9 TraesCS1B01G021100 chrUn 276779334 276780873 1539 True 2060.0 2060 90.9500 433 1962 1 chrUn.!!$R1 1529
10 TraesCS1B01G021100 chrUn 278892654 278893720 1066 True 1500.0 1500 92.1350 902 1962 1 chrUn.!!$R2 1060

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
424 438 1.757118 TCTGGGAAGGATGCTCTAACG 59.243 52.381 0.00 0.0 0.0 3.18 F
1458 1535 0.677098 CCGACGGAGAGGAGAAGACA 60.677 60.000 8.64 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1560 1637 0.673333 CGCCTAGTGCAATGTCCACA 60.673 55.0 0.0 0.0 41.33 4.17 R
2276 2363 0.737367 ACATGAGACACGCCATCACG 60.737 55.0 0.0 0.0 39.50 4.35 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
44 45 1.977129 TGTGATGGAGTGATGGTGTCA 59.023 47.619 0.00 0.00 0.00 3.58
55 56 4.761739 AGTGATGGTGTCATTGTCGAAAAT 59.238 37.500 0.00 0.00 39.48 1.82
58 59 6.907212 GTGATGGTGTCATTGTCGAAAATATC 59.093 38.462 0.00 0.38 39.48 1.63
103 107 5.925509 TGTGGTTGATAGGGCTAACTAATC 58.074 41.667 0.00 0.00 0.00 1.75
114 118 7.932683 AGGGCTAACTAATCTAATTAGGTGT 57.067 36.000 12.54 0.00 42.46 4.16
124 128 9.627123 CTAATCTAATTAGGTGTTTGATTCCCA 57.373 33.333 12.54 0.00 38.81 4.37
127 131 7.410174 TCTAATTAGGTGTTTGATTCCCATGT 58.590 34.615 12.54 0.00 0.00 3.21
163 168 5.975988 TTTATCCTCTGCACTAATTCCCT 57.024 39.130 0.00 0.00 0.00 4.20
187 193 6.284475 TGCATAAATTGTTGCTTTGTGTTC 57.716 33.333 12.52 0.00 39.60 3.18
331 338 9.098355 CTCCCATCCACATTAACAATATATACG 57.902 37.037 0.00 0.00 0.00 3.06
358 366 6.548441 ACATGGCATGAAAAATTGTTTGAG 57.452 33.333 32.74 1.57 0.00 3.02
377 390 3.446873 TGAGGTTTGTCTTTGTGCATGTT 59.553 39.130 0.00 0.00 0.00 2.71
418 432 2.158696 GCAAGTATCTGGGAAGGATGCT 60.159 50.000 0.00 0.00 37.65 3.79
424 438 1.757118 TCTGGGAAGGATGCTCTAACG 59.243 52.381 0.00 0.00 0.00 3.18
506 522 4.705991 TCATGGATGCATGCTTGAAGTTAA 59.294 37.500 27.25 9.74 31.28 2.01
669 715 6.876257 ACTAATGTCTCCAGAAACTTGACATC 59.124 38.462 7.26 0.00 44.44 3.06
1261 1331 2.257461 ACTACAGGCCCCTCCCTCT 61.257 63.158 0.00 0.00 31.24 3.69
1458 1535 0.677098 CCGACGGAGAGGAGAAGACA 60.677 60.000 8.64 0.00 0.00 3.41
1560 1637 5.708736 TTGGTGGTGATAGTGTTGGATAT 57.291 39.130 0.00 0.00 0.00 1.63
1647 1724 1.238439 CCTTTGACATCGCCAACACT 58.762 50.000 0.00 0.00 0.00 3.55
1654 1732 1.238439 CATCGCCAACACTCCACTTT 58.762 50.000 0.00 0.00 0.00 2.66
1662 1740 1.846007 ACACTCCACTTTTGTTGGCA 58.154 45.000 0.00 0.00 0.00 4.92
1788 1866 8.349568 TGTCTATCAAGAAGTGAACTAAGCTA 57.650 34.615 0.00 0.00 40.50 3.32
2002 2089 3.181479 GGGTGAAAACCTTTGTCCACTTC 60.181 47.826 0.00 0.00 0.00 3.01
2290 2377 4.760047 GGGCGTGATGGCGTGTCT 62.760 66.667 0.00 0.00 46.04 3.41
2291 2378 3.188786 GGCGTGATGGCGTGTCTC 61.189 66.667 0.00 0.00 0.00 3.36
2292 2379 2.432456 GCGTGATGGCGTGTCTCA 60.432 61.111 0.00 0.00 0.00 3.27
2293 2380 1.811266 GCGTGATGGCGTGTCTCAT 60.811 57.895 0.00 0.00 0.00 2.90
2294 2381 2.001357 CGTGATGGCGTGTCTCATG 58.999 57.895 0.00 0.00 0.00 3.07
2295 2382 0.737367 CGTGATGGCGTGTCTCATGT 60.737 55.000 0.00 0.00 0.00 3.21
2296 2383 1.442769 GTGATGGCGTGTCTCATGTT 58.557 50.000 0.00 0.00 0.00 2.71
2297 2384 1.394917 GTGATGGCGTGTCTCATGTTC 59.605 52.381 0.00 0.00 0.00 3.18
2298 2385 1.276138 TGATGGCGTGTCTCATGTTCT 59.724 47.619 0.00 0.00 0.00 3.01
2299 2386 2.289631 TGATGGCGTGTCTCATGTTCTT 60.290 45.455 0.00 0.00 0.00 2.52
2300 2387 1.795768 TGGCGTGTCTCATGTTCTTC 58.204 50.000 0.00 0.00 0.00 2.87
2301 2388 1.344438 TGGCGTGTCTCATGTTCTTCT 59.656 47.619 0.00 0.00 0.00 2.85
2302 2389 2.224281 TGGCGTGTCTCATGTTCTTCTT 60.224 45.455 0.00 0.00 0.00 2.52
2303 2390 2.413453 GGCGTGTCTCATGTTCTTCTTC 59.587 50.000 0.00 0.00 0.00 2.87
2304 2391 3.321497 GCGTGTCTCATGTTCTTCTTCT 58.679 45.455 0.00 0.00 0.00 2.85
2305 2392 3.366422 GCGTGTCTCATGTTCTTCTTCTC 59.634 47.826 0.00 0.00 0.00 2.87
2306 2393 3.605916 CGTGTCTCATGTTCTTCTTCTCG 59.394 47.826 0.00 0.00 0.00 4.04
2307 2394 3.923461 GTGTCTCATGTTCTTCTTCTCGG 59.077 47.826 0.00 0.00 0.00 4.63
2308 2395 3.574396 TGTCTCATGTTCTTCTTCTCGGT 59.426 43.478 0.00 0.00 0.00 4.69
2309 2396 3.923461 GTCTCATGTTCTTCTTCTCGGTG 59.077 47.826 0.00 0.00 0.00 4.94
2310 2397 3.826729 TCTCATGTTCTTCTTCTCGGTGA 59.173 43.478 0.00 0.00 0.00 4.02
2311 2398 3.914312 TCATGTTCTTCTTCTCGGTGAC 58.086 45.455 0.00 0.00 0.00 3.67
2312 2399 3.320826 TCATGTTCTTCTTCTCGGTGACA 59.679 43.478 0.00 0.00 0.00 3.58
2313 2400 3.093717 TGTTCTTCTTCTCGGTGACAC 57.906 47.619 0.00 0.00 0.00 3.67
2314 2401 2.429250 TGTTCTTCTTCTCGGTGACACA 59.571 45.455 8.08 0.00 0.00 3.72
2315 2402 2.795175 TCTTCTTCTCGGTGACACAC 57.205 50.000 8.08 0.00 0.00 3.82
2316 2403 2.307768 TCTTCTTCTCGGTGACACACT 58.692 47.619 8.08 0.00 34.40 3.55
2317 2404 2.693591 TCTTCTTCTCGGTGACACACTT 59.306 45.455 8.08 0.00 34.40 3.16
2318 2405 2.509052 TCTTCTCGGTGACACACTTG 57.491 50.000 8.08 0.00 34.40 3.16
2319 2406 2.028876 TCTTCTCGGTGACACACTTGA 58.971 47.619 8.08 0.00 34.40 3.02
2320 2407 2.628178 TCTTCTCGGTGACACACTTGAT 59.372 45.455 8.08 0.00 34.40 2.57
2321 2408 2.438868 TCTCGGTGACACACTTGATG 57.561 50.000 8.08 0.00 34.40 3.07
2322 2409 0.792640 CTCGGTGACACACTTGATGC 59.207 55.000 8.08 0.00 34.40 3.91
2323 2410 0.943835 TCGGTGACACACTTGATGCG 60.944 55.000 8.08 0.00 34.40 4.73
2324 2411 1.221466 CGGTGACACACTTGATGCGT 61.221 55.000 8.08 0.00 34.40 5.24
2325 2412 0.944386 GGTGACACACTTGATGCGTT 59.056 50.000 8.08 0.00 34.40 4.84
2326 2413 1.333619 GGTGACACACTTGATGCGTTT 59.666 47.619 8.08 0.00 34.40 3.60
2327 2414 2.546368 GGTGACACACTTGATGCGTTTA 59.454 45.455 8.08 0.00 34.40 2.01
2328 2415 3.002862 GGTGACACACTTGATGCGTTTAA 59.997 43.478 8.08 0.00 34.40 1.52
2329 2416 4.320202 GGTGACACACTTGATGCGTTTAAT 60.320 41.667 8.08 0.00 34.40 1.40
2330 2417 5.212194 GTGACACACTTGATGCGTTTAATT 58.788 37.500 0.00 0.00 0.00 1.40
2331 2418 5.115472 GTGACACACTTGATGCGTTTAATTG 59.885 40.000 0.00 0.00 0.00 2.32
2332 2419 5.181690 ACACACTTGATGCGTTTAATTGT 57.818 34.783 0.00 0.00 0.00 2.71
2333 2420 4.975502 ACACACTTGATGCGTTTAATTGTG 59.024 37.500 17.78 17.78 39.43 3.33
2334 2421 4.975502 CACACTTGATGCGTTTAATTGTGT 59.024 37.500 14.07 0.00 36.70 3.72
2335 2422 6.139435 CACACTTGATGCGTTTAATTGTGTA 58.861 36.000 14.07 0.00 34.88 2.90
2336 2423 6.801377 CACACTTGATGCGTTTAATTGTGTAT 59.199 34.615 14.07 0.00 34.88 2.29
2337 2424 6.801377 ACACTTGATGCGTTTAATTGTGTATG 59.199 34.615 0.00 0.00 34.88 2.39
2338 2425 6.251163 CACTTGATGCGTTTAATTGTGTATGG 59.749 38.462 0.00 0.00 0.00 2.74
2339 2426 5.888691 TGATGCGTTTAATTGTGTATGGT 57.111 34.783 0.00 0.00 0.00 3.55
2340 2427 6.986904 TGATGCGTTTAATTGTGTATGGTA 57.013 33.333 0.00 0.00 0.00 3.25
2341 2428 7.561021 TGATGCGTTTAATTGTGTATGGTAT 57.439 32.000 0.00 0.00 0.00 2.73
2342 2429 7.990917 TGATGCGTTTAATTGTGTATGGTATT 58.009 30.769 0.00 0.00 0.00 1.89
2343 2430 7.912773 TGATGCGTTTAATTGTGTATGGTATTG 59.087 33.333 0.00 0.00 0.00 1.90
2344 2431 6.030849 TGCGTTTAATTGTGTATGGTATTGC 58.969 36.000 0.00 0.00 0.00 3.56
2345 2432 6.030849 GCGTTTAATTGTGTATGGTATTGCA 58.969 36.000 0.00 0.00 0.00 4.08
2346 2433 6.695278 GCGTTTAATTGTGTATGGTATTGCAT 59.305 34.615 0.00 0.00 0.00 3.96
2347 2434 7.221838 GCGTTTAATTGTGTATGGTATTGCATT 59.778 33.333 0.00 0.00 0.00 3.56
2348 2435 8.742188 CGTTTAATTGTGTATGGTATTGCATTC 58.258 33.333 0.00 0.00 0.00 2.67
2349 2436 9.801873 GTTTAATTGTGTATGGTATTGCATTCT 57.198 29.630 0.00 0.00 0.00 2.40
2351 2438 6.639632 ATTGTGTATGGTATTGCATTCTCC 57.360 37.500 0.00 0.00 0.00 3.71
2352 2439 5.109500 TGTGTATGGTATTGCATTCTCCA 57.891 39.130 7.54 7.54 0.00 3.86
2353 2440 4.881273 TGTGTATGGTATTGCATTCTCCAC 59.119 41.667 7.33 0.00 0.00 4.02
2354 2441 5.126067 GTGTATGGTATTGCATTCTCCACT 58.874 41.667 7.33 2.54 0.00 4.00
2355 2442 6.126911 TGTGTATGGTATTGCATTCTCCACTA 60.127 38.462 7.33 1.89 0.00 2.74
2356 2443 6.425114 GTGTATGGTATTGCATTCTCCACTAG 59.575 42.308 7.33 0.00 0.00 2.57
2357 2444 5.636903 ATGGTATTGCATTCTCCACTAGT 57.363 39.130 7.33 0.00 0.00 2.57
2358 2445 5.435686 TGGTATTGCATTCTCCACTAGTT 57.564 39.130 0.00 0.00 0.00 2.24
2359 2446 5.815581 TGGTATTGCATTCTCCACTAGTTT 58.184 37.500 0.00 0.00 0.00 2.66
2364 2451 4.713553 TGCATTCTCCACTAGTTTTGTCA 58.286 39.130 0.00 0.00 0.00 3.58
2465 2552 3.440522 GGGAGAAAGCATGTTACAAGGAC 59.559 47.826 0.00 0.00 0.00 3.85
2474 2561 3.495434 TGTTACAAGGACGGAATTGGT 57.505 42.857 0.00 0.00 0.00 3.67
2498 2585 2.241281 TCCTCCGTGATTCCAGGTAA 57.759 50.000 0.00 0.00 0.00 2.85
2513 2600 8.980143 ATTCCAGGTAATTTTGTAAAATGACG 57.020 30.769 10.11 0.00 39.60 4.35
2534 2621 6.712998 TGACGGAATTGGTCTCTAATTTTTCA 59.287 34.615 7.52 0.00 35.45 2.69
2615 2702 3.389656 CCCTGAAGATCCCTCCTTAGTTC 59.610 52.174 0.00 0.00 0.00 3.01
2616 2703 4.033709 CCTGAAGATCCCTCCTTAGTTCA 58.966 47.826 0.00 0.00 0.00 3.18
2626 2713 8.809468 ATCCCTCCTTAGTTCAATTTTTCTAC 57.191 34.615 0.00 0.00 0.00 2.59
2715 2802 6.329460 GGATAGAAATGGTTTAGGGGACTAGT 59.671 42.308 0.00 0.00 45.45 2.57
2731 2818 5.012251 GGGACTAGTGTTTTCTCTCTCCTTT 59.988 44.000 0.00 0.00 0.00 3.11
2744 2831 5.544176 TCTCTCTCCTTTCCACAATGTTAGT 59.456 40.000 0.00 0.00 0.00 2.24
2745 2832 5.551233 TCTCTCCTTTCCACAATGTTAGTG 58.449 41.667 0.00 0.00 36.76 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.380932 TCACAAGGGTACAGAGGAGGTA 59.619 50.000 0.00 0.00 0.00 3.08
1 2 1.149288 TCACAAGGGTACAGAGGAGGT 59.851 52.381 0.00 0.00 0.00 3.85
2 3 1.827969 CTCACAAGGGTACAGAGGAGG 59.172 57.143 0.00 0.00 0.00 4.30
7 8 3.035363 TCACAACTCACAAGGGTACAGA 58.965 45.455 0.00 0.00 0.00 3.41
76 77 0.537188 AGCCCTATCAACCACAGTCG 59.463 55.000 0.00 0.00 0.00 4.18
103 107 7.645058 ACATGGGAATCAAACACCTAATTAG 57.355 36.000 5.43 5.43 0.00 1.73
114 118 6.416631 TCAATCAACAACATGGGAATCAAA 57.583 33.333 0.00 0.00 0.00 2.69
127 131 9.187996 TGCAGAGGATAAATAATCAATCAACAA 57.812 29.630 0.00 0.00 36.20 2.83
163 168 6.538021 AGAACACAAAGCAACAATTTATGCAA 59.462 30.769 13.18 0.00 44.95 4.08
238 245 1.268845 ACAAACCGACGGATGCAAAAC 60.269 47.619 23.38 0.00 0.00 2.43
331 338 6.425577 AACAATTTTTCATGCCATGTATGC 57.574 33.333 4.31 0.00 0.00 3.14
358 366 4.045636 AGAACATGCACAAAGACAAACC 57.954 40.909 0.00 0.00 0.00 3.27
418 432 6.073314 ACCTAATACTTATGCTCCCGTTAGA 58.927 40.000 0.00 0.00 0.00 2.10
424 438 8.376270 AGTCAAATACCTAATACTTATGCTCCC 58.624 37.037 0.00 0.00 0.00 4.30
669 715 7.096640 CGTTTGCTTGTGGAATAGTTAACTTTG 60.097 37.037 14.49 0.00 0.00 2.77
681 727 1.403679 CAAGGTCGTTTGCTTGTGGAA 59.596 47.619 0.00 0.00 0.00 3.53
1047 1117 2.009681 GTTTCACCCTGGAAACCCAT 57.990 50.000 7.39 0.00 46.88 4.00
1261 1331 2.589157 CGTAGGGGTCAGTGGGCAA 61.589 63.158 0.00 0.00 0.00 4.52
1453 1527 5.370880 ACATATGCTTTATCCCCTCTGTCTT 59.629 40.000 1.58 0.00 0.00 3.01
1458 1535 4.751028 GCCAACATATGCTTTATCCCCTCT 60.751 45.833 1.58 0.00 0.00 3.69
1560 1637 0.673333 CGCCTAGTGCAATGTCCACA 60.673 55.000 0.00 0.00 41.33 4.17
1647 1724 1.047002 CCCATGCCAACAAAAGTGGA 58.953 50.000 0.00 0.00 38.54 4.02
1654 1732 1.907807 GCTCCACCCATGCCAACAA 60.908 57.895 0.00 0.00 0.00 2.83
1662 1740 1.153086 GATGAAGCGCTCCACCCAT 60.153 57.895 12.06 9.57 0.00 4.00
1948 2035 7.224949 GTCGGAGGATATTAACAAGAAAGAAGG 59.775 40.741 0.00 0.00 0.00 3.46
2002 2089 3.959975 CCACCGTGGTGTTTGCCG 61.960 66.667 17.31 0.00 44.02 5.69
2273 2360 4.760047 AGACACGCCATCACGCCC 62.760 66.667 0.00 0.00 36.19 6.13
2274 2361 3.188786 GAGACACGCCATCACGCC 61.189 66.667 0.00 0.00 36.19 5.68
2275 2362 1.811266 ATGAGACACGCCATCACGC 60.811 57.895 0.00 0.00 36.19 5.34
2276 2363 0.737367 ACATGAGACACGCCATCACG 60.737 55.000 0.00 0.00 39.50 4.35
2277 2364 1.394917 GAACATGAGACACGCCATCAC 59.605 52.381 0.00 0.00 0.00 3.06
2278 2365 1.276138 AGAACATGAGACACGCCATCA 59.724 47.619 0.00 0.00 0.00 3.07
2279 2366 2.015736 AGAACATGAGACACGCCATC 57.984 50.000 0.00 0.00 0.00 3.51
2280 2367 2.027745 AGAAGAACATGAGACACGCCAT 60.028 45.455 0.00 0.00 0.00 4.40
2281 2368 1.344438 AGAAGAACATGAGACACGCCA 59.656 47.619 0.00 0.00 0.00 5.69
2282 2369 2.086054 AGAAGAACATGAGACACGCC 57.914 50.000 0.00 0.00 0.00 5.68
2283 2370 3.321497 AGAAGAAGAACATGAGACACGC 58.679 45.455 0.00 0.00 0.00 5.34
2284 2371 3.605916 CGAGAAGAAGAACATGAGACACG 59.394 47.826 0.00 0.00 0.00 4.49
2285 2372 3.923461 CCGAGAAGAAGAACATGAGACAC 59.077 47.826 0.00 0.00 0.00 3.67
2286 2373 3.574396 ACCGAGAAGAAGAACATGAGACA 59.426 43.478 0.00 0.00 0.00 3.41
2287 2374 3.923461 CACCGAGAAGAAGAACATGAGAC 59.077 47.826 0.00 0.00 0.00 3.36
2288 2375 3.826729 TCACCGAGAAGAAGAACATGAGA 59.173 43.478 0.00 0.00 0.00 3.27
2289 2376 3.923461 GTCACCGAGAAGAAGAACATGAG 59.077 47.826 0.00 0.00 0.00 2.90
2290 2377 3.320826 TGTCACCGAGAAGAAGAACATGA 59.679 43.478 0.00 0.00 0.00 3.07
2291 2378 3.430218 GTGTCACCGAGAAGAAGAACATG 59.570 47.826 0.00 0.00 0.00 3.21
2292 2379 3.069586 TGTGTCACCGAGAAGAAGAACAT 59.930 43.478 0.00 0.00 0.00 2.71
2293 2380 2.429250 TGTGTCACCGAGAAGAAGAACA 59.571 45.455 0.00 0.00 0.00 3.18
2294 2381 2.795470 GTGTGTCACCGAGAAGAAGAAC 59.205 50.000 0.00 0.00 0.00 3.01
2295 2382 2.693591 AGTGTGTCACCGAGAAGAAGAA 59.306 45.455 0.00 0.00 34.49 2.52
2296 2383 2.307768 AGTGTGTCACCGAGAAGAAGA 58.692 47.619 0.00 0.00 34.49 2.87
2297 2384 2.797156 CAAGTGTGTCACCGAGAAGAAG 59.203 50.000 0.00 0.00 34.49 2.85
2298 2385 2.429250 TCAAGTGTGTCACCGAGAAGAA 59.571 45.455 0.00 0.00 34.49 2.52
2299 2386 2.028876 TCAAGTGTGTCACCGAGAAGA 58.971 47.619 0.00 0.00 34.49 2.87
2300 2387 2.509052 TCAAGTGTGTCACCGAGAAG 57.491 50.000 0.00 0.00 34.49 2.85
2301 2388 2.754472 CATCAAGTGTGTCACCGAGAA 58.246 47.619 0.00 0.00 34.49 2.87
2302 2389 1.605457 GCATCAAGTGTGTCACCGAGA 60.605 52.381 0.00 0.00 34.49 4.04
2303 2390 0.792640 GCATCAAGTGTGTCACCGAG 59.207 55.000 0.00 0.00 34.49 4.63
2304 2391 0.943835 CGCATCAAGTGTGTCACCGA 60.944 55.000 0.00 0.00 34.49 4.69
2305 2392 1.492873 CGCATCAAGTGTGTCACCG 59.507 57.895 0.00 0.00 34.49 4.94
2311 2398 5.484639 CACAATTAAACGCATCAAGTGTG 57.515 39.130 6.04 6.04 40.86 3.82
2312 2399 5.181690 ACACAATTAAACGCATCAAGTGT 57.818 34.783 0.00 0.00 44.39 3.55
2313 2400 6.251163 CCATACACAATTAAACGCATCAAGTG 59.749 38.462 0.00 0.00 0.00 3.16
2314 2401 6.072175 ACCATACACAATTAAACGCATCAAGT 60.072 34.615 0.00 0.00 0.00 3.16
2315 2402 6.321717 ACCATACACAATTAAACGCATCAAG 58.678 36.000 0.00 0.00 0.00 3.02
2316 2403 6.260870 ACCATACACAATTAAACGCATCAA 57.739 33.333 0.00 0.00 0.00 2.57
2317 2404 5.888691 ACCATACACAATTAAACGCATCA 57.111 34.783 0.00 0.00 0.00 3.07
2318 2405 7.096640 GCAATACCATACACAATTAAACGCATC 60.097 37.037 0.00 0.00 0.00 3.91
2319 2406 6.695278 GCAATACCATACACAATTAAACGCAT 59.305 34.615 0.00 0.00 0.00 4.73
2320 2407 6.030849 GCAATACCATACACAATTAAACGCA 58.969 36.000 0.00 0.00 0.00 5.24
2321 2408 6.030849 TGCAATACCATACACAATTAAACGC 58.969 36.000 0.00 0.00 0.00 4.84
2322 2409 8.627487 AATGCAATACCATACACAATTAAACG 57.373 30.769 0.00 0.00 0.00 3.60
2323 2410 9.801873 AGAATGCAATACCATACACAATTAAAC 57.198 29.630 0.00 0.00 0.00 2.01
2325 2412 8.629158 GGAGAATGCAATACCATACACAATTAA 58.371 33.333 0.00 0.00 0.00 1.40
2326 2413 7.777440 TGGAGAATGCAATACCATACACAATTA 59.223 33.333 0.00 0.00 28.48 1.40
2327 2414 6.606796 TGGAGAATGCAATACCATACACAATT 59.393 34.615 0.00 0.00 28.48 2.32
2328 2415 6.039717 GTGGAGAATGCAATACCATACACAAT 59.960 38.462 0.00 0.00 39.09 2.71
2329 2416 5.356751 GTGGAGAATGCAATACCATACACAA 59.643 40.000 0.00 0.00 39.09 3.33
2330 2417 4.881273 GTGGAGAATGCAATACCATACACA 59.119 41.667 0.00 0.00 39.09 3.72
2331 2418 5.126067 AGTGGAGAATGCAATACCATACAC 58.874 41.667 0.00 0.00 39.09 2.90
2332 2419 5.372343 AGTGGAGAATGCAATACCATACA 57.628 39.130 0.00 0.00 39.09 2.29
2333 2420 6.525629 ACTAGTGGAGAATGCAATACCATAC 58.474 40.000 0.00 0.00 39.09 2.39
2334 2421 6.747414 ACTAGTGGAGAATGCAATACCATA 57.253 37.500 0.00 0.00 39.09 2.74
2335 2422 5.636903 ACTAGTGGAGAATGCAATACCAT 57.363 39.130 0.00 0.00 39.09 3.55
2336 2423 5.435686 AACTAGTGGAGAATGCAATACCA 57.564 39.130 0.00 0.00 39.09 3.25
2337 2424 6.151144 ACAAAACTAGTGGAGAATGCAATACC 59.849 38.462 0.00 0.00 39.09 2.73
2338 2425 7.094805 TGACAAAACTAGTGGAGAATGCAATAC 60.095 37.037 0.00 0.00 39.09 1.89
2339 2426 6.939730 TGACAAAACTAGTGGAGAATGCAATA 59.060 34.615 0.00 0.00 39.09 1.90
2340 2427 5.769662 TGACAAAACTAGTGGAGAATGCAAT 59.230 36.000 0.00 0.00 39.09 3.56
2341 2428 5.129634 TGACAAAACTAGTGGAGAATGCAA 58.870 37.500 0.00 0.00 39.09 4.08
2342 2429 4.713553 TGACAAAACTAGTGGAGAATGCA 58.286 39.130 0.00 0.00 0.00 3.96
2343 2430 5.182001 ACATGACAAAACTAGTGGAGAATGC 59.818 40.000 0.00 0.00 0.00 3.56
2344 2431 6.652481 AGACATGACAAAACTAGTGGAGAATG 59.348 38.462 0.00 0.00 0.00 2.67
2345 2432 6.773638 AGACATGACAAAACTAGTGGAGAAT 58.226 36.000 0.00 0.00 0.00 2.40
2346 2433 6.174720 AGACATGACAAAACTAGTGGAGAA 57.825 37.500 0.00 0.00 0.00 2.87
2347 2434 5.808366 AGACATGACAAAACTAGTGGAGA 57.192 39.130 0.00 0.00 0.00 3.71
2348 2435 6.867662 AAAGACATGACAAAACTAGTGGAG 57.132 37.500 0.00 0.00 0.00 3.86
2349 2436 7.936847 ACATAAAGACATGACAAAACTAGTGGA 59.063 33.333 0.00 0.00 0.00 4.02
2350 2437 8.099364 ACATAAAGACATGACAAAACTAGTGG 57.901 34.615 0.00 0.00 0.00 4.00
2351 2438 9.950680 AAACATAAAGACATGACAAAACTAGTG 57.049 29.630 0.00 0.00 0.00 2.74
2352 2439 9.950680 CAAACATAAAGACATGACAAAACTAGT 57.049 29.630 0.00 0.00 0.00 2.57
2358 2445 9.624697 GCTAATCAAACATAAAGACATGACAAA 57.375 29.630 0.00 0.00 0.00 2.83
2359 2446 9.013229 AGCTAATCAAACATAAAGACATGACAA 57.987 29.630 0.00 0.00 0.00 3.18
2453 2540 4.007659 GACCAATTCCGTCCTTGTAACAT 58.992 43.478 0.00 0.00 0.00 2.71
2474 2561 2.103373 CTGGAATCACGGAGGAAGAGA 58.897 52.381 0.00 0.00 0.00 3.10
2498 2585 7.666623 AGACCAATTCCGTCATTTTACAAAAT 58.333 30.769 5.27 0.00 39.07 1.82
2534 2621 9.379791 CGTTTAAGATAAGGGTCACTAAAGAAT 57.620 33.333 0.00 0.00 0.00 2.40
2540 2627 9.193806 AGAATACGTTTAAGATAAGGGTCACTA 57.806 33.333 0.00 0.00 0.00 2.74
2559 2646 6.305877 GTCCATTAGATAAGCACGAGAATACG 59.694 42.308 0.00 0.00 39.31 3.06
2595 2682 5.683876 TTGAACTAAGGAGGGATCTTCAG 57.316 43.478 0.00 0.00 0.00 3.02
2596 2683 6.642733 AATTGAACTAAGGAGGGATCTTCA 57.357 37.500 0.00 0.00 0.00 3.02
2683 2770 9.434275 CCCCTAAACCATTTCTATCCTTAAAAT 57.566 33.333 0.00 0.00 0.00 1.82
2715 2802 4.771114 TGTGGAAAGGAGAGAGAAAACA 57.229 40.909 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.