Multiple sequence alignment - TraesCS2B01G364400

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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 TraesCS2B01G364400 chr2B 100.000 2780 0 0 1 2780 518739858 518742637 0.000000e+00 5134.0
1 TraesCS2B01G364400 chr2B 94.964 139 7 0 2393 2531 287571074 287571212 4.660000e-53 219.0
2 TraesCS2B01G364400 chr2D 95.663 2421 82 11 1 2402 440767135 440769551 0.000000e+00 3868.0
3 TraesCS2B01G364400 chr2D 97.007 735 22 0 1 735 185368037 185368771 0.000000e+00 1236.0
4 TraesCS2B01G364400 chr2D 85.962 577 78 1 5 578 440634022 440634598 5.090000e-172 614.0
5 TraesCS2B01G364400 chr2D 88.845 251 17 3 2529 2776 440769553 440769795 5.820000e-77 298.0
6 TraesCS2B01G364400 chr2A 95.528 2415 91 8 1 2402 584510872 584513282 0.000000e+00 3845.0
7 TraesCS2B01G364400 chr2A 86.159 578 76 2 5 578 584143481 584144058 3.040000e-174 621.0
8 TraesCS2B01G364400 chr2A 92.273 220 13 2 2562 2780 584513302 584513518 2.690000e-80 309.0
9 TraesCS2B01G364400 chr6D 97.007 735 21 1 1 735 100570339 100569606 0.000000e+00 1234.0
10 TraesCS2B01G364400 chr6D 96.871 735 23 0 1 735 216836565 216837299 0.000000e+00 1230.0
11 TraesCS2B01G364400 chr6D 98.450 129 2 0 2404 2532 81770257 81770385 7.750000e-56 228.0
12 TraesCS2B01G364400 chr3D 96.871 735 23 0 1 735 241044568 241043834 0.000000e+00 1230.0
13 TraesCS2B01G364400 chr3D 93.946 446 24 3 3 447 456355582 456355139 0.000000e+00 671.0
14 TraesCS2B01G364400 chr3D 97.744 133 3 0 2398 2530 443434233 443434365 2.150000e-56 230.0
15 TraesCS2B01G364400 chr3D 97.710 131 3 0 2401 2531 283321122 283321252 2.790000e-55 226.0
16 TraesCS2B01G364400 chr3D 93.151 146 10 0 2389 2534 371366874 371367019 6.030000e-52 215.0
17 TraesCS2B01G364400 chr7D 97.263 475 12 1 261 735 255422881 255423354 0.000000e+00 804.0
18 TraesCS2B01G364400 chr7D 93.750 144 9 0 2389 2532 234351209 234351352 1.680000e-52 217.0
19 TraesCS2B01G364400 chr7B 95.070 142 5 2 2390 2530 656518095 656518235 3.600000e-54 222.0
20 TraesCS2B01G364400 chr1B 95.000 140 5 2 2392 2530 683747948 683748086 4.660000e-53 219.0
21 TraesCS2B01G364400 chr1B 92.617 149 9 2 2387 2533 156406850 156406702 2.170000e-51 213.0
22 TraesCS2B01G364400 chr6A 96.875 32 0 1 2329 2359 33306915 33306884 5.000000e-03 52.8


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 TraesCS2B01G364400 chr2B 518739858 518742637 2779 False 5134 5134 100.0000 1 2780 1 chr2B.!!$F2 2779
1 TraesCS2B01G364400 chr2D 440767135 440769795 2660 False 2083 3868 92.2540 1 2776 2 chr2D.!!$F3 2775
2 TraesCS2B01G364400 chr2D 185368037 185368771 734 False 1236 1236 97.0070 1 735 1 chr2D.!!$F1 734
3 TraesCS2B01G364400 chr2D 440634022 440634598 576 False 614 614 85.9620 5 578 1 chr2D.!!$F2 573
4 TraesCS2B01G364400 chr2A 584510872 584513518 2646 False 2077 3845 93.9005 1 2780 2 chr2A.!!$F2 2779
5 TraesCS2B01G364400 chr2A 584143481 584144058 577 False 621 621 86.1590 5 578 1 chr2A.!!$F1 573
6 TraesCS2B01G364400 chr6D 100569606 100570339 733 True 1234 1234 97.0070 1 735 1 chr6D.!!$R1 734
7 TraesCS2B01G364400 chr6D 216836565 216837299 734 False 1230 1230 96.8710 1 735 1 chr6D.!!$F2 734
8 TraesCS2B01G364400 chr3D 241043834 241044568 734 True 1230 1230 96.8710 1 735 1 chr3D.!!$R1 734

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
741 746 2.26354 GAGGTTACTGCCGCCGAA 59.736 61.111 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2400 2424 0.042131 TTGGGACGGAGGGAGTACAT 59.958 55.0 0.0 0.0 0.0 2.29 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
20 21 4.373116 GCAGGAGGACGACGCCAA 62.373 66.667 10.28 0.00 42.23 4.52
741 746 2.263540 GAGGTTACTGCCGCCGAA 59.736 61.111 0.00 0.00 0.00 4.30
1149 1154 0.549950 CAGGGGAGACATTGCTGGAT 59.450 55.000 0.00 0.00 0.00 3.41
1248 1253 3.326006 AGATTCACCAGAACTTGAGCTCA 59.674 43.478 13.74 13.74 36.39 4.26
1362 1367 1.000866 AAGCCCCTTCCTCAATGGC 59.999 57.895 0.00 0.00 42.48 4.40
1428 1433 1.354368 CCAGTTGGTACCATGAAGGGT 59.646 52.381 17.17 0.00 43.89 4.34
1440 1445 4.352001 ACCATGAAGGGTGATACATATGCT 59.648 41.667 1.58 0.00 43.89 3.79
1768 1773 1.849097 GGCCTATAACAAGGACGACG 58.151 55.000 0.00 0.00 39.15 5.12
1784 1789 4.457496 CGCGGACACCTGATGGCT 62.457 66.667 0.00 0.00 36.10 4.75
1825 1835 1.940613 CCGCTTGGTCAGGCTTAATAC 59.059 52.381 3.70 0.00 0.00 1.89
1829 1839 2.309528 TGGTCAGGCTTAATACGCTG 57.690 50.000 0.00 0.00 0.00 5.18
1837 1847 3.118738 AGGCTTAATACGCTGCTACTTGT 60.119 43.478 0.00 0.00 0.00 3.16
1882 1892 2.903855 GGCATGCCCAGACATCCG 60.904 66.667 27.24 0.00 0.00 4.18
1883 1893 3.589881 GCATGCCCAGACATCCGC 61.590 66.667 6.36 0.00 0.00 5.54
1884 1894 2.191375 CATGCCCAGACATCCGCT 59.809 61.111 0.00 0.00 0.00 5.52
1912 1923 5.099042 ACCATTATACTGCCGGATAATCC 57.901 43.478 5.05 0.00 0.00 3.01
1913 1924 4.534500 ACCATTATACTGCCGGATAATCCA 59.466 41.667 5.05 0.00 35.91 3.41
1982 1993 8.749354 TGTAAGATTAGTCTGCATTGTCTCTTA 58.251 33.333 0.00 0.00 34.13 2.10
1984 1995 8.715191 AAGATTAGTCTGCATTGTCTCTTAAG 57.285 34.615 0.00 0.00 34.13 1.85
2005 2021 5.923733 AGTGCTAGTGCTTGTAGTATCTT 57.076 39.130 0.00 0.00 40.48 2.40
2073 2089 1.239968 GGAACAACTGGCCTGCTCTG 61.240 60.000 9.95 7.41 0.00 3.35
2090 2106 3.798202 CTCTGCAGTCCCCTATACAAAC 58.202 50.000 14.67 0.00 0.00 2.93
2181 2197 0.881118 CATGGCCGTTTTGTAGCACT 59.119 50.000 0.00 0.00 0.00 4.40
2226 2242 7.621428 ATGGTCATTATGTAGCATGCTAATC 57.379 36.000 28.44 17.52 32.84 1.75
2230 2246 7.551974 GGTCATTATGTAGCATGCTAATCATCT 59.448 37.037 28.44 15.48 31.79 2.90
2246 2262 2.965831 TCATCTCATTTACTCCCTCCGG 59.034 50.000 0.00 0.00 0.00 5.14
2248 2264 2.829023 TCTCATTTACTCCCTCCGGTT 58.171 47.619 0.00 0.00 0.00 4.44
2253 2269 4.344102 TCATTTACTCCCTCCGGTTCATAG 59.656 45.833 0.00 0.00 0.00 2.23
2263 2279 3.084039 TCCGGTTCATAGTAAGTGTCGT 58.916 45.455 0.00 0.00 0.00 4.34
2268 2284 4.624452 GGTTCATAGTAAGTGTCGTGGTTC 59.376 45.833 0.00 0.00 0.00 3.62
2281 2297 2.948979 TCGTGGTTCTGTGAATTTGCTT 59.051 40.909 0.00 0.00 0.00 3.91
2290 2306 7.646922 GGTTCTGTGAATTTGCTTGATGATATC 59.353 37.037 0.00 0.00 0.00 1.63
2314 2331 9.621239 ATCCCCTATCTCATTTGTCTCTTATTA 57.379 33.333 0.00 0.00 0.00 0.98
2371 2390 8.023706 GGAGTACCATTTTCTCTTGTGAATTTC 58.976 37.037 0.00 0.00 35.97 2.17
2374 2393 6.986250 ACCATTTTCTCTTGTGAATTTCCTC 58.014 36.000 0.00 0.00 0.00 3.71
2378 2397 6.727824 TTTCTCTTGTGAATTTCCTCGATC 57.272 37.500 0.00 0.00 0.00 3.69
2394 2418 5.044105 TCCTCGATCATATCCCCTATCTCAA 60.044 44.000 0.00 0.00 0.00 3.02
2396 2420 6.326064 CCTCGATCATATCCCCTATCTCAATT 59.674 42.308 0.00 0.00 0.00 2.32
2397 2421 7.353414 TCGATCATATCCCCTATCTCAATTC 57.647 40.000 0.00 0.00 0.00 2.17
2398 2422 7.128751 TCGATCATATCCCCTATCTCAATTCT 58.871 38.462 0.00 0.00 0.00 2.40
2399 2423 7.286546 TCGATCATATCCCCTATCTCAATTCTC 59.713 40.741 0.00 0.00 0.00 2.87
2400 2424 7.069208 CGATCATATCCCCTATCTCAATTCTCA 59.931 40.741 0.00 0.00 0.00 3.27
2401 2425 8.873156 ATCATATCCCCTATCTCAATTCTCAT 57.127 34.615 0.00 0.00 0.00 2.90
2402 2426 8.087303 TCATATCCCCTATCTCAATTCTCATG 57.913 38.462 0.00 0.00 0.00 3.07
2403 2427 7.681598 TCATATCCCCTATCTCAATTCTCATGT 59.318 37.037 0.00 0.00 0.00 3.21
2404 2428 8.985922 CATATCCCCTATCTCAATTCTCATGTA 58.014 37.037 0.00 0.00 0.00 2.29
2405 2429 6.672266 TCCCCTATCTCAATTCTCATGTAC 57.328 41.667 0.00 0.00 0.00 2.90
2406 2430 6.385443 TCCCCTATCTCAATTCTCATGTACT 58.615 40.000 0.00 0.00 0.00 2.73
2407 2431 6.495181 TCCCCTATCTCAATTCTCATGTACTC 59.505 42.308 0.00 0.00 0.00 2.59
2408 2432 6.295575 CCCCTATCTCAATTCTCATGTACTCC 60.296 46.154 0.00 0.00 0.00 3.85
2409 2433 6.295575 CCCTATCTCAATTCTCATGTACTCCC 60.296 46.154 0.00 0.00 0.00 4.30
2410 2434 6.496565 CCTATCTCAATTCTCATGTACTCCCT 59.503 42.308 0.00 0.00 0.00 4.20
2411 2435 5.860941 TCTCAATTCTCATGTACTCCCTC 57.139 43.478 0.00 0.00 0.00 4.30
2412 2436 4.651503 TCTCAATTCTCATGTACTCCCTCC 59.348 45.833 0.00 0.00 0.00 4.30
2413 2437 3.384789 TCAATTCTCATGTACTCCCTCCG 59.615 47.826 0.00 0.00 0.00 4.63
2414 2438 2.526888 TTCTCATGTACTCCCTCCGT 57.473 50.000 0.00 0.00 0.00 4.69
2415 2439 2.054232 TCTCATGTACTCCCTCCGTC 57.946 55.000 0.00 0.00 0.00 4.79
2416 2440 1.033574 CTCATGTACTCCCTCCGTCC 58.966 60.000 0.00 0.00 0.00 4.79
2417 2441 0.396695 TCATGTACTCCCTCCGTCCC 60.397 60.000 0.00 0.00 0.00 4.46
2418 2442 0.686441 CATGTACTCCCTCCGTCCCA 60.686 60.000 0.00 0.00 0.00 4.37
2419 2443 0.042131 ATGTACTCCCTCCGTCCCAA 59.958 55.000 0.00 0.00 0.00 4.12
2420 2444 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
2421 2445 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2422 2446 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2423 2447 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2424 2448 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2425 2449 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2426 2450 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2427 2451 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2428 2452 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2429 2453 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2430 2454 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2431 2455 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2432 2456 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2433 2457 4.758165 TCCGTCCCAAAATTCTTGTCTTAC 59.242 41.667 0.00 0.00 0.00 2.34
2434 2458 4.517453 CCGTCCCAAAATTCTTGTCTTACA 59.483 41.667 0.00 0.00 0.00 2.41
2435 2459 5.183140 CCGTCCCAAAATTCTTGTCTTACAT 59.817 40.000 0.00 0.00 0.00 2.29
2436 2460 6.294508 CCGTCCCAAAATTCTTGTCTTACATT 60.295 38.462 0.00 0.00 0.00 2.71
2437 2461 7.145323 CGTCCCAAAATTCTTGTCTTACATTT 58.855 34.615 0.00 0.00 0.00 2.32
2438 2462 7.114811 CGTCCCAAAATTCTTGTCTTACATTTG 59.885 37.037 0.00 0.00 0.00 2.32
2439 2463 7.926018 GTCCCAAAATTCTTGTCTTACATTTGT 59.074 33.333 0.00 0.00 27.14 2.83
2440 2464 8.141268 TCCCAAAATTCTTGTCTTACATTTGTC 58.859 33.333 0.00 0.00 27.14 3.18
2441 2465 8.143835 CCCAAAATTCTTGTCTTACATTTGTCT 58.856 33.333 0.00 0.00 27.14 3.41
2463 2487 9.764363 TGTCTAAATATGGATGTATCAAGTCAC 57.236 33.333 0.00 0.00 0.00 3.67
2464 2488 8.916654 GTCTAAATATGGATGTATCAAGTCACG 58.083 37.037 0.00 0.00 0.00 4.35
2465 2489 8.638873 TCTAAATATGGATGTATCAAGTCACGT 58.361 33.333 0.00 0.00 0.00 4.49
2466 2490 7.715265 AAATATGGATGTATCAAGTCACGTC 57.285 36.000 0.00 0.00 0.00 4.34
2467 2491 6.656632 ATATGGATGTATCAAGTCACGTCT 57.343 37.500 0.00 0.00 32.40 4.18
2468 2492 4.801330 TGGATGTATCAAGTCACGTCTT 57.199 40.909 0.00 0.00 32.40 3.01
2469 2493 5.907866 TGGATGTATCAAGTCACGTCTTA 57.092 39.130 0.00 0.00 32.40 2.10
2470 2494 5.891451 TGGATGTATCAAGTCACGTCTTAG 58.109 41.667 0.00 0.00 32.40 2.18
2471 2495 5.417894 TGGATGTATCAAGTCACGTCTTAGT 59.582 40.000 0.00 0.00 32.40 2.24
2472 2496 6.600427 TGGATGTATCAAGTCACGTCTTAGTA 59.400 38.462 0.00 0.00 32.40 1.82
2473 2497 7.284716 TGGATGTATCAAGTCACGTCTTAGTAT 59.715 37.037 0.00 0.00 32.40 2.12
2474 2498 8.136165 GGATGTATCAAGTCACGTCTTAGTATT 58.864 37.037 0.00 0.00 32.40 1.89
2477 2501 9.387257 TGTATCAAGTCACGTCTTAGTATTAGA 57.613 33.333 0.00 0.00 0.00 2.10
2481 2505 9.387257 TCAAGTCACGTCTTAGTATTAGATACA 57.613 33.333 0.00 0.00 38.21 2.29
2484 2508 9.001542 AGTCACGTCTTAGTATTAGATACATCC 57.998 37.037 0.00 0.00 38.21 3.51
2485 2509 7.956403 GTCACGTCTTAGTATTAGATACATCCG 59.044 40.741 0.00 0.00 38.21 4.18
2486 2510 7.658982 TCACGTCTTAGTATTAGATACATCCGT 59.341 37.037 0.00 0.00 38.21 4.69
2487 2511 8.929746 CACGTCTTAGTATTAGATACATCCGTA 58.070 37.037 0.00 0.00 38.21 4.02
2488 2512 9.664332 ACGTCTTAGTATTAGATACATCCGTAT 57.336 33.333 1.42 0.00 41.16 3.06
2504 2528 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
2505 2529 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
2506 2530 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
2507 2531 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
2508 2532 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
2509 2533 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
2517 2541 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
2518 2542 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
2519 2543 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
2520 2544 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
2521 2545 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
2522 2546 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2523 2547 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2524 2548 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2525 2549 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2526 2550 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2527 2551 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
2535 2559 0.249363 GGACGGAGGGAGTATTTCGC 60.249 60.000 0.00 0.00 38.95 4.70
2600 2624 6.986231 CCAATTTGGGTGCTAATAAAATCCTC 59.014 38.462 7.60 0.00 32.67 3.71
2631 2655 0.961019 TCCAAGCCATGTGTCTTTGC 59.039 50.000 0.00 0.00 0.00 3.68
2705 2735 5.937540 TCTGAAGACCGATTTTGAAGCATTA 59.062 36.000 0.00 0.00 0.00 1.90
2706 2736 6.599244 TCTGAAGACCGATTTTGAAGCATTAT 59.401 34.615 0.00 0.00 0.00 1.28
2707 2737 7.768582 TCTGAAGACCGATTTTGAAGCATTATA 59.231 33.333 0.00 0.00 0.00 0.98
2708 2738 8.275015 TGAAGACCGATTTTGAAGCATTATAA 57.725 30.769 0.00 0.00 0.00 0.98
2709 2739 8.902806 TGAAGACCGATTTTGAAGCATTATAAT 58.097 29.630 0.00 0.00 0.00 1.28
2728 2758 4.771590 AATGTGCAAAAGACATCGTCAT 57.228 36.364 0.00 0.00 34.60 3.06
2737 2767 3.791973 AGACATCGTCATCCTGACTTC 57.208 47.619 5.79 0.00 44.85 3.01
2744 2774 6.536582 ACATCGTCATCCTGACTTCTAAATTG 59.463 38.462 5.79 0.00 44.85 2.32
2753 2786 9.771534 ATCCTGACTTCTAAATTGTATTAGCTC 57.228 33.333 0.00 0.00 33.74 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
470 474 2.444895 GGATCTGGCCCTCGAGGT 60.445 66.667 29.25 10.39 38.26 3.85
711 716 1.318158 TAACCTCCGACTCGCTTCCC 61.318 60.000 0.00 0.00 0.00 3.97
1023 1028 3.061848 GGCACGATGTTGGGGTGG 61.062 66.667 0.00 0.00 32.42 4.61
1188 1193 4.560743 TGCAGCCACGCAAGACCA 62.561 61.111 0.00 0.00 39.45 4.02
1323 1328 1.486726 GTATCTCCACCTTCACCTGGG 59.513 57.143 0.00 0.00 0.00 4.45
1362 1367 1.375523 CCCAAACTCCCCGAAGTCG 60.376 63.158 0.00 0.00 39.44 4.18
1428 1433 5.122707 TGACCCCAAAAGCATATGTATCA 57.877 39.130 4.29 0.00 0.00 2.15
1440 1445 4.229582 AGCTCCAATAGTATGACCCCAAAA 59.770 41.667 0.00 0.00 0.00 2.44
1768 1773 2.821366 CAGCCATCAGGTGTCCGC 60.821 66.667 0.00 0.00 39.23 5.54
1784 1789 4.063967 ACAATCCGAGGCGTCGCA 62.064 61.111 22.70 9.42 45.41 5.10
1873 1883 0.109597 GGTTTTGCAGCGGATGTCTG 60.110 55.000 0.00 0.00 34.79 3.51
1882 1892 3.447742 GGCAGTATAATGGTTTTGCAGC 58.552 45.455 1.88 0.00 33.42 5.25
1883 1893 3.489059 CCGGCAGTATAATGGTTTTGCAG 60.489 47.826 1.88 0.00 33.42 4.41
1884 1894 2.425312 CCGGCAGTATAATGGTTTTGCA 59.575 45.455 1.88 0.00 33.42 4.08
1912 1923 1.864565 TACGGTGCCATGATCGAATG 58.135 50.000 0.00 0.00 0.00 2.67
1913 1924 2.037121 TGATACGGTGCCATGATCGAAT 59.963 45.455 0.00 0.00 0.00 3.34
1982 1993 5.923733 AGATACTACAAGCACTAGCACTT 57.076 39.130 0.00 0.00 45.49 3.16
1984 1995 5.869888 ACAAAGATACTACAAGCACTAGCAC 59.130 40.000 0.00 0.00 45.49 4.40
2005 2021 6.151985 ACACAACAAGAATTACAGTTCCACAA 59.848 34.615 0.00 0.00 0.00 3.33
2073 2089 2.429610 TCTCGTTTGTATAGGGGACTGC 59.570 50.000 0.00 0.00 43.88 4.40
2143 2159 7.360776 CGGCCATGCAAACAAAGTTAAATATTT 60.361 33.333 2.24 5.89 0.00 1.40
2181 2197 9.688091 GACCATATATGAGTAGGAGATAACAGA 57.312 37.037 14.54 0.00 0.00 3.41
2224 2240 4.881019 CGGAGGGAGTAAATGAGATGAT 57.119 45.455 0.00 0.00 0.00 2.45
2246 2262 5.345202 CAGAACCACGACACTTACTATGAAC 59.655 44.000 0.00 0.00 0.00 3.18
2248 2264 4.521639 ACAGAACCACGACACTTACTATGA 59.478 41.667 0.00 0.00 0.00 2.15
2253 2269 3.088194 TCACAGAACCACGACACTTAC 57.912 47.619 0.00 0.00 0.00 2.34
2263 2279 4.583907 TCATCAAGCAAATTCACAGAACCA 59.416 37.500 0.00 0.00 0.00 3.67
2268 2284 6.444633 GGGATATCATCAAGCAAATTCACAG 58.555 40.000 4.83 0.00 0.00 3.66
2281 2297 7.681598 AGACAAATGAGATAGGGGATATCATCA 59.318 37.037 4.83 0.00 44.10 3.07
2314 2331 6.878317 TCCGAAATAAGAGACAGATGACAAT 58.122 36.000 0.00 0.00 0.00 2.71
2316 2333 5.914898 TCCGAAATAAGAGACAGATGACA 57.085 39.130 0.00 0.00 0.00 3.58
2371 2390 4.797743 TGAGATAGGGGATATGATCGAGG 58.202 47.826 0.00 0.00 0.00 4.63
2374 2393 7.069208 TGAGAATTGAGATAGGGGATATGATCG 59.931 40.741 0.00 0.00 0.00 3.69
2378 2397 7.859540 ACATGAGAATTGAGATAGGGGATATG 58.140 38.462 0.00 0.00 0.00 1.78
2394 2418 2.959707 GACGGAGGGAGTACATGAGAAT 59.040 50.000 0.00 0.00 0.00 2.40
2396 2420 1.409802 GGACGGAGGGAGTACATGAGA 60.410 57.143 0.00 0.00 0.00 3.27
2397 2421 1.033574 GGACGGAGGGAGTACATGAG 58.966 60.000 0.00 0.00 0.00 2.90
2398 2422 0.396695 GGGACGGAGGGAGTACATGA 60.397 60.000 0.00 0.00 0.00 3.07
2399 2423 0.686441 TGGGACGGAGGGAGTACATG 60.686 60.000 0.00 0.00 0.00 3.21
2400 2424 0.042131 TTGGGACGGAGGGAGTACAT 59.958 55.000 0.00 0.00 0.00 2.29
2401 2425 0.178926 TTTGGGACGGAGGGAGTACA 60.179 55.000 0.00 0.00 0.00 2.90
2402 2426 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
2403 2427 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2404 2428 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
2405 2429 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
2406 2430 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2407 2431 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2408 2432 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2409 2433 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2410 2434 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2411 2435 4.517453 TGTAAGACAAGAATTTTGGGACGG 59.483 41.667 0.00 0.00 0.00 4.79
2412 2436 5.682943 TGTAAGACAAGAATTTTGGGACG 57.317 39.130 5.68 0.00 0.00 4.79
2413 2437 7.926018 ACAAATGTAAGACAAGAATTTTGGGAC 59.074 33.333 7.26 0.00 31.16 4.46
2414 2438 8.017418 ACAAATGTAAGACAAGAATTTTGGGA 57.983 30.769 7.26 0.00 31.16 4.37
2415 2439 8.143835 AGACAAATGTAAGACAAGAATTTTGGG 58.856 33.333 7.26 0.00 31.16 4.12
2437 2461 9.764363 GTGACTTGATACATCCATATTTAGACA 57.236 33.333 0.00 0.00 0.00 3.41
2438 2462 8.916654 CGTGACTTGATACATCCATATTTAGAC 58.083 37.037 0.00 0.00 0.00 2.59
2439 2463 8.638873 ACGTGACTTGATACATCCATATTTAGA 58.361 33.333 0.00 0.00 0.00 2.10
2440 2464 8.818141 ACGTGACTTGATACATCCATATTTAG 57.182 34.615 0.00 0.00 0.00 1.85
2441 2465 8.638873 AGACGTGACTTGATACATCCATATTTA 58.361 33.333 0.00 0.00 0.00 1.40
2442 2466 7.500992 AGACGTGACTTGATACATCCATATTT 58.499 34.615 0.00 0.00 0.00 1.40
2443 2467 7.055667 AGACGTGACTTGATACATCCATATT 57.944 36.000 0.00 0.00 0.00 1.28
2444 2468 6.656632 AGACGTGACTTGATACATCCATAT 57.343 37.500 0.00 0.00 0.00 1.78
2445 2469 6.465439 AAGACGTGACTTGATACATCCATA 57.535 37.500 0.00 0.00 0.00 2.74
2446 2470 5.344743 AAGACGTGACTTGATACATCCAT 57.655 39.130 0.00 0.00 0.00 3.41
2447 2471 4.801330 AAGACGTGACTTGATACATCCA 57.199 40.909 0.00 0.00 0.00 3.41
2448 2472 5.892568 ACTAAGACGTGACTTGATACATCC 58.107 41.667 0.00 0.00 0.00 3.51
2451 2475 9.387257 TCTAATACTAAGACGTGACTTGATACA 57.613 33.333 0.00 0.00 0.00 2.29
2455 2479 9.387257 TGTATCTAATACTAAGACGTGACTTGA 57.613 33.333 0.00 0.00 36.70 3.02
2458 2482 9.001542 GGATGTATCTAATACTAAGACGTGACT 57.998 37.037 0.00 0.00 36.70 3.41
2459 2483 7.956403 CGGATGTATCTAATACTAAGACGTGAC 59.044 40.741 0.00 0.00 36.70 3.67
2460 2484 7.658982 ACGGATGTATCTAATACTAAGACGTGA 59.341 37.037 0.00 0.00 36.70 4.35
2461 2485 7.804712 ACGGATGTATCTAATACTAAGACGTG 58.195 38.462 0.00 0.00 36.70 4.49
2462 2486 7.976135 ACGGATGTATCTAATACTAAGACGT 57.024 36.000 0.00 0.00 36.70 4.34
2478 2502 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
2479 2503 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
2480 2504 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
2481 2505 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
2482 2506 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
2483 2507 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
2491 2515 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
2492 2516 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
2493 2517 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
2494 2518 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
2495 2519 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
2496 2520 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
2497 2521 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
2498 2522 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
2499 2523 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
2500 2524 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2501 2525 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2502 2526 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2503 2527 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2504 2528 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2505 2529 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2506 2530 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2507 2531 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2508 2532 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2509 2533 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2510 2534 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2511 2535 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
2512 2536 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
2513 2537 1.835531 GAAATACTCCCTCCGTCCCAA 59.164 52.381 0.00 0.00 0.00 4.12
2514 2538 1.492764 GAAATACTCCCTCCGTCCCA 58.507 55.000 0.00 0.00 0.00 4.37
2515 2539 0.388294 CGAAATACTCCCTCCGTCCC 59.612 60.000 0.00 0.00 0.00 4.46
2516 2540 0.249363 GCGAAATACTCCCTCCGTCC 60.249 60.000 0.00 0.00 0.00 4.79
2517 2541 0.594284 CGCGAAATACTCCCTCCGTC 60.594 60.000 0.00 0.00 0.00 4.79
2518 2542 1.318158 ACGCGAAATACTCCCTCCGT 61.318 55.000 15.93 0.00 0.00 4.69
2519 2543 0.870307 CACGCGAAATACTCCCTCCG 60.870 60.000 15.93 0.00 0.00 4.63
2520 2544 1.152383 GCACGCGAAATACTCCCTCC 61.152 60.000 15.93 0.00 0.00 4.30
2521 2545 0.179108 AGCACGCGAAATACTCCCTC 60.179 55.000 15.93 0.00 0.00 4.30
2522 2546 0.179108 GAGCACGCGAAATACTCCCT 60.179 55.000 15.93 0.00 0.00 4.20
2523 2547 0.179108 AGAGCACGCGAAATACTCCC 60.179 55.000 15.93 0.00 0.00 4.30
2524 2548 0.924090 CAGAGCACGCGAAATACTCC 59.076 55.000 15.93 0.00 0.00 3.85
2525 2549 0.299003 GCAGAGCACGCGAAATACTC 59.701 55.000 15.93 11.59 0.00 2.59
2526 2550 2.373938 GCAGAGCACGCGAAATACT 58.626 52.632 15.93 1.34 0.00 2.12
2527 2551 4.955238 GCAGAGCACGCGAAATAC 57.045 55.556 15.93 0.00 0.00 1.89
2550 2574 2.437200 TGCCAACAATAGCAAAGTGC 57.563 45.000 0.00 0.00 45.46 4.40
2600 2624 4.081531 ACATGGCTTGGAAATGTATGTTGG 60.082 41.667 5.31 0.00 32.86 3.77
2631 2655 4.524053 GTCCAAGGTTGAAAGGTATAGGG 58.476 47.826 0.00 0.00 0.00 3.53
2705 2735 5.878332 TGACGATGTCTTTTGCACATTAT 57.122 34.783 0.00 0.00 34.49 1.28
2706 2736 5.163764 GGATGACGATGTCTTTTGCACATTA 60.164 40.000 0.00 0.00 34.49 1.90
2707 2737 4.379813 GGATGACGATGTCTTTTGCACATT 60.380 41.667 0.00 0.00 34.49 2.71
2708 2738 3.127548 GGATGACGATGTCTTTTGCACAT 59.872 43.478 0.00 0.00 37.18 3.21
2709 2739 2.483877 GGATGACGATGTCTTTTGCACA 59.516 45.455 0.00 0.00 33.15 4.57
2728 2758 8.982723 AGAGCTAATACAATTTAGAAGTCAGGA 58.017 33.333 0.00 0.00 32.02 3.86
2744 2774 5.311844 AGGGGGAAATGAAGAGCTAATAC 57.688 43.478 0.00 0.00 0.00 1.89
2753 2786 2.375146 CGGGTTTAGGGGGAAATGAAG 58.625 52.381 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.