Multiple sequence alignment - TraesCS4A01G308000

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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 TraesCS4A01G308000 chr4A 100.000 2600 0 0 1 2600 601692909 601690310 0.000000e+00 4802.0
1 TraesCS4A01G308000 chr4A 90.099 101 3 5 2301 2400 34610563 34610469 9.770000e-25 124.0
2 TraesCS4A01G308000 chr4A 90.099 101 2 7 2300 2399 329126763 329126670 9.770000e-25 124.0
3 TraesCS4A01G308000 chr7A 96.708 2339 38 4 2 2301 720224356 720222018 0.000000e+00 3856.0
4 TraesCS4A01G308000 chr3A 96.805 2316 35 6 2 2301 717429369 717431661 0.000000e+00 3831.0
5 TraesCS4A01G308000 chr3A 87.755 49 5 1 2537 2584 490683856 490683904 3.610000e-04 56.5
6 TraesCS4A01G308000 chr1A 96.376 2318 33 6 2 2301 14735481 14737765 0.000000e+00 3768.0
7 TraesCS4A01G308000 chr2B 95.097 2325 71 15 2 2305 83722170 83724472 0.000000e+00 3622.0
8 TraesCS4A01G308000 chr1D 93.170 2328 121 15 2 2304 419053266 419055580 0.000000e+00 3384.0
9 TraesCS4A01G308000 chr1D 92.374 2321 141 16 2 2301 34229436 34231741 0.000000e+00 3273.0
10 TraesCS4A01G308000 chr1D 89.423 104 2 8 2301 2403 283598480 283598575 3.510000e-24 122.0
11 TraesCS4A01G308000 chr5B 96.336 1965 53 5 14 1959 341514090 341512126 0.000000e+00 3212.0
12 TraesCS4A01G308000 chr5B 96.591 352 12 0 1951 2302 341512178 341511827 3.730000e-163 584.0
13 TraesCS4A01G308000 chr2D 96.109 1979 59 6 2 1964 302022217 302020241 0.000000e+00 3212.0
14 TraesCS4A01G308000 chr2D 96.296 351 13 0 1951 2301 302020298 302019948 6.240000e-161 577.0
15 TraesCS4A01G308000 chr4B 91.871 2325 139 21 2 2301 642268766 642271065 0.000000e+00 3201.0
16 TraesCS4A01G308000 chr5A 91.742 2325 134 22 2 2301 338458885 338456594 0.000000e+00 3177.0
17 TraesCS4A01G308000 chrUn 93.304 1150 38 13 1071 2205 435926144 435925019 0.000000e+00 1661.0
18 TraesCS4A01G308000 chr7B 89.899 99 8 2 2300 2398 630612977 630612881 2.720000e-25 126.0
19 TraesCS4A01G308000 chr7B 89.423 104 5 5 2300 2403 678347283 678347186 2.720000e-25 126.0
20 TraesCS4A01G308000 chr6D 90.000 100 6 4 2301 2400 218038202 218038297 2.720000e-25 126.0
21 TraesCS4A01G308000 chr6D 96.000 75 3 0 2301 2375 60269990 60270064 3.510000e-24 122.0
22 TraesCS4A01G308000 chr6A 90.625 96 7 2 2301 2395 569305871 569305965 2.720000e-25 126.0
23 TraesCS4A01G308000 chr6A 97.872 47 1 0 2554 2600 108556433 108556387 5.960000e-12 82.4
24 TraesCS4A01G308000 chr4D 88.679 106 5 6 2301 2403 331515022 331514921 3.510000e-24 122.0


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 TraesCS4A01G308000 chr4A 601690310 601692909 2599 True 4802.0 4802 100.0000 1 2600 1 chr4A.!!$R3 2599
1 TraesCS4A01G308000 chr7A 720222018 720224356 2338 True 3856.0 3856 96.7080 2 2301 1 chr7A.!!$R1 2299
2 TraesCS4A01G308000 chr3A 717429369 717431661 2292 False 3831.0 3831 96.8050 2 2301 1 chr3A.!!$F2 2299
3 TraesCS4A01G308000 chr1A 14735481 14737765 2284 False 3768.0 3768 96.3760 2 2301 1 chr1A.!!$F1 2299
4 TraesCS4A01G308000 chr2B 83722170 83724472 2302 False 3622.0 3622 95.0970 2 2305 1 chr2B.!!$F1 2303
5 TraesCS4A01G308000 chr1D 419053266 419055580 2314 False 3384.0 3384 93.1700 2 2304 1 chr1D.!!$F3 2302
6 TraesCS4A01G308000 chr1D 34229436 34231741 2305 False 3273.0 3273 92.3740 2 2301 1 chr1D.!!$F1 2299
7 TraesCS4A01G308000 chr5B 341511827 341514090 2263 True 1898.0 3212 96.4635 14 2302 2 chr5B.!!$R1 2288
8 TraesCS4A01G308000 chr2D 302019948 302022217 2269 True 1894.5 3212 96.2025 2 2301 2 chr2D.!!$R1 2299
9 TraesCS4A01G308000 chr4B 642268766 642271065 2299 False 3201.0 3201 91.8710 2 2301 1 chr4B.!!$F1 2299
10 TraesCS4A01G308000 chr5A 338456594 338458885 2291 True 3177.0 3177 91.7420 2 2301 1 chr5A.!!$R1 2299
11 TraesCS4A01G308000 chrUn 435925019 435926144 1125 True 1661.0 1661 93.3040 1071 2205 1 chrUn.!!$R1 1134

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
162 186 6.054860 ACTCTTGCATCCATGTAGTAACTT 57.945 37.5 0.0 0.0 0.0 2.66 F
952 990 6.405278 TGATGTTGTCTTCTCTACTTGTGA 57.595 37.5 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1051 1089 1.448540 CAGCTACAGCCTTGGTCGG 60.449 63.158 0.0 0.0 43.38 4.79 R
2352 2523 0.035534 CGGATGGTGATGACCCACAA 60.036 55.000 0.0 0.0 42.34 3.33 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
162 186 6.054860 ACTCTTGCATCCATGTAGTAACTT 57.945 37.500 0.00 0.00 0.00 2.66
952 990 6.405278 TGATGTTGTCTTCTCTACTTGTGA 57.595 37.500 0.00 0.00 0.00 3.58
1051 1089 6.878389 AGAAGATGGACAAGAATCAAACTCTC 59.122 38.462 0.00 0.00 0.00 3.20
1285 1323 3.023119 GAGCACAGGAAGAGAGATGAGA 58.977 50.000 0.00 0.00 0.00 3.27
1403 1441 1.085091 TCAGCCGTCGTCTCTACTTC 58.915 55.000 0.00 0.00 0.00 3.01
1967 2116 4.783621 TGGCGCCACATCAGCTCC 62.784 66.667 29.03 0.00 35.62 4.70
1968 2117 4.783621 GGCGCCACATCAGCTCCA 62.784 66.667 24.80 0.00 35.15 3.86
1969 2118 3.503363 GCGCCACATCAGCTCCAC 61.503 66.667 0.00 0.00 0.00 4.02
1970 2119 3.190849 CGCCACATCAGCTCCACG 61.191 66.667 0.00 0.00 0.00 4.94
1971 2120 3.503363 GCCACATCAGCTCCACGC 61.503 66.667 0.00 0.00 39.57 5.34
1988 2137 3.200593 CTGGCGCCACATCAGCTC 61.201 66.667 29.03 0.00 0.00 4.09
2240 2411 4.569180 CGCCCGGCCATCCTTGAT 62.569 66.667 2.24 0.00 0.00 2.57
2305 2476 3.463944 ACGACTTTCTTGTAGTGTTGGG 58.536 45.455 0.00 0.00 0.00 4.12
2306 2477 3.118519 ACGACTTTCTTGTAGTGTTGGGT 60.119 43.478 0.00 0.00 0.00 4.51
2307 2478 3.875134 CGACTTTCTTGTAGTGTTGGGTT 59.125 43.478 0.00 0.00 0.00 4.11
2308 2479 4.025145 CGACTTTCTTGTAGTGTTGGGTTC 60.025 45.833 0.00 0.00 0.00 3.62
2309 2480 3.875134 ACTTTCTTGTAGTGTTGGGTTCG 59.125 43.478 0.00 0.00 0.00 3.95
2310 2481 3.823281 TTCTTGTAGTGTTGGGTTCGA 57.177 42.857 0.00 0.00 0.00 3.71
2311 2482 3.102052 TCTTGTAGTGTTGGGTTCGAC 57.898 47.619 0.00 0.00 0.00 4.20
2312 2483 2.431419 TCTTGTAGTGTTGGGTTCGACA 59.569 45.455 0.00 0.00 35.05 4.35
2319 2490 3.102052 TGTTGGGTTCGACACTCTTAC 57.898 47.619 0.00 0.00 32.62 2.34
2320 2491 2.696707 TGTTGGGTTCGACACTCTTACT 59.303 45.455 0.00 0.00 32.62 2.24
2321 2492 3.133362 TGTTGGGTTCGACACTCTTACTT 59.867 43.478 0.00 0.00 32.62 2.24
2322 2493 4.341806 TGTTGGGTTCGACACTCTTACTTA 59.658 41.667 0.00 0.00 32.62 2.24
2323 2494 5.011329 TGTTGGGTTCGACACTCTTACTTAT 59.989 40.000 0.00 0.00 32.62 1.73
2324 2495 5.320549 TGGGTTCGACACTCTTACTTATC 57.679 43.478 0.00 0.00 0.00 1.75
2325 2496 4.142534 TGGGTTCGACACTCTTACTTATCG 60.143 45.833 0.00 0.00 0.00 2.92
2326 2497 4.095483 GGGTTCGACACTCTTACTTATCGA 59.905 45.833 0.00 0.00 36.85 3.59
2327 2498 5.392380 GGGTTCGACACTCTTACTTATCGAA 60.392 44.000 2.99 2.99 43.90 3.71
2328 2499 6.088824 GGTTCGACACTCTTACTTATCGAAA 58.911 40.000 8.30 0.00 46.48 3.46
2329 2500 6.250951 GGTTCGACACTCTTACTTATCGAAAG 59.749 42.308 8.30 0.00 46.48 2.62
2330 2501 5.877031 TCGACACTCTTACTTATCGAAAGG 58.123 41.667 10.65 0.00 35.80 3.11
2331 2502 5.645067 TCGACACTCTTACTTATCGAAAGGA 59.355 40.000 10.65 1.49 35.80 3.36
2332 2503 5.738225 CGACACTCTTACTTATCGAAAGGAC 59.262 44.000 10.65 0.00 0.00 3.85
2333 2504 6.403418 CGACACTCTTACTTATCGAAAGGACT 60.403 42.308 10.65 0.00 0.00 3.85
2334 2505 7.201591 CGACACTCTTACTTATCGAAAGGACTA 60.202 40.741 10.65 0.00 0.00 2.59
2335 2506 7.760437 ACACTCTTACTTATCGAAAGGACTAC 58.240 38.462 10.65 0.00 0.00 2.73
2336 2507 6.906143 CACTCTTACTTATCGAAAGGACTACG 59.094 42.308 10.65 0.00 0.00 3.51
2337 2508 6.820656 ACTCTTACTTATCGAAAGGACTACGA 59.179 38.462 10.65 0.00 40.18 3.43
2338 2509 7.498570 ACTCTTACTTATCGAAAGGACTACGAT 59.501 37.037 14.84 14.84 46.07 3.73
2339 2510 8.893219 TCTTACTTATCGAAAGGACTACGATA 57.107 34.615 13.42 13.42 44.33 2.92
2340 2511 8.986847 TCTTACTTATCGAAAGGACTACGATAG 58.013 37.037 15.42 13.25 45.19 2.08
2341 2512 8.893219 TTACTTATCGAAAGGACTACGATAGA 57.107 34.615 15.42 9.84 45.19 1.98
2342 2513 7.982761 ACTTATCGAAAGGACTACGATAGAT 57.017 36.000 15.42 9.33 45.19 1.98
2343 2514 8.031848 ACTTATCGAAAGGACTACGATAGATC 57.968 38.462 15.42 0.00 45.19 2.75
2344 2515 5.883503 ATCGAAAGGACTACGATAGATCC 57.116 43.478 10.82 0.00 43.32 3.36
2345 2516 4.070716 TCGAAAGGACTACGATAGATCCC 58.929 47.826 0.00 0.00 41.38 3.85
2346 2517 3.190953 CGAAAGGACTACGATAGATCCCC 59.809 52.174 0.00 0.00 41.38 4.81
2347 2518 4.409187 GAAAGGACTACGATAGATCCCCT 58.591 47.826 0.00 0.00 41.38 4.79
2348 2519 5.568392 GAAAGGACTACGATAGATCCCCTA 58.432 45.833 0.00 0.00 41.38 3.53
2349 2520 5.799978 AAGGACTACGATAGATCCCCTAT 57.200 43.478 0.00 0.00 40.66 2.57
2350 2521 6.905067 AAGGACTACGATAGATCCCCTATA 57.095 41.667 0.00 0.00 38.17 1.31
2351 2522 6.251255 AGGACTACGATAGATCCCCTATAC 57.749 45.833 0.00 0.00 38.17 1.47
2352 2523 5.971881 AGGACTACGATAGATCCCCTATACT 59.028 44.000 0.00 0.00 38.17 2.12
2353 2524 6.447735 AGGACTACGATAGATCCCCTATACTT 59.552 42.308 0.00 0.00 38.17 2.24
2354 2525 6.543100 GGACTACGATAGATCCCCTATACTTG 59.457 46.154 0.00 0.00 38.17 3.16
2355 2526 7.030234 ACTACGATAGATCCCCTATACTTGT 57.970 40.000 0.00 0.00 38.17 3.16
2356 2527 6.885376 ACTACGATAGATCCCCTATACTTGTG 59.115 42.308 0.00 0.00 38.17 3.33
2357 2528 5.017490 ACGATAGATCCCCTATACTTGTGG 58.983 45.833 0.00 0.00 38.17 4.17
2358 2529 4.402793 CGATAGATCCCCTATACTTGTGGG 59.597 50.000 0.00 0.00 38.17 4.61
2359 2530 3.726837 AGATCCCCTATACTTGTGGGT 57.273 47.619 0.00 0.00 39.31 4.51
2360 2531 3.588569 AGATCCCCTATACTTGTGGGTC 58.411 50.000 0.00 0.00 39.31 4.46
2361 2532 2.953093 TCCCCTATACTTGTGGGTCA 57.047 50.000 0.00 0.00 39.31 4.02
2362 2533 3.431411 TCCCCTATACTTGTGGGTCAT 57.569 47.619 0.00 0.00 39.31 3.06
2363 2534 3.314693 TCCCCTATACTTGTGGGTCATC 58.685 50.000 0.00 0.00 39.31 2.92
2364 2535 3.045634 CCCCTATACTTGTGGGTCATCA 58.954 50.000 0.00 0.00 39.31 3.07
2365 2536 3.181454 CCCCTATACTTGTGGGTCATCAC 60.181 52.174 0.00 0.00 39.31 3.06
2366 2537 3.181454 CCCTATACTTGTGGGTCATCACC 60.181 52.174 0.00 0.00 42.90 4.02
2367 2538 3.454447 CCTATACTTGTGGGTCATCACCA 59.546 47.826 0.00 0.00 45.94 4.17
2368 2539 4.103153 CCTATACTTGTGGGTCATCACCAT 59.897 45.833 0.00 0.00 45.94 3.55
2369 2540 2.496899 ACTTGTGGGTCATCACCATC 57.503 50.000 0.00 0.00 45.94 3.51
2370 2541 1.004745 ACTTGTGGGTCATCACCATCC 59.995 52.381 0.00 0.00 45.94 3.51
2371 2542 0.035534 TTGTGGGTCATCACCATCCG 60.036 55.000 0.00 0.00 45.94 4.18
2372 2543 1.153168 GTGGGTCATCACCATCCGG 60.153 63.158 0.00 0.00 45.94 5.14
2373 2544 2.203209 GGGTCATCACCATCCGGC 60.203 66.667 0.00 0.00 45.94 6.13
2374 2545 2.203209 GGTCATCACCATCCGGCC 60.203 66.667 0.00 0.00 43.17 6.13
2375 2546 2.588877 GTCATCACCATCCGGCCG 60.589 66.667 21.04 21.04 34.57 6.13
2376 2547 4.545706 TCATCACCATCCGGCCGC 62.546 66.667 22.85 0.00 34.57 6.53
2408 2579 4.179579 GCGCCGCCACCAATCTTC 62.180 66.667 0.00 0.00 0.00 2.87
2409 2580 3.508840 CGCCGCCACCAATCTTCC 61.509 66.667 0.00 0.00 0.00 3.46
2410 2581 3.140814 GCCGCCACCAATCTTCCC 61.141 66.667 0.00 0.00 0.00 3.97
2411 2582 2.440247 CCGCCACCAATCTTCCCC 60.440 66.667 0.00 0.00 0.00 4.81
2412 2583 2.824041 CGCCACCAATCTTCCCCG 60.824 66.667 0.00 0.00 0.00 5.73
2413 2584 3.140814 GCCACCAATCTTCCCCGC 61.141 66.667 0.00 0.00 0.00 6.13
2414 2585 2.824041 CCACCAATCTTCCCCGCG 60.824 66.667 0.00 0.00 0.00 6.46
2415 2586 3.508840 CACCAATCTTCCCCGCGC 61.509 66.667 0.00 0.00 0.00 6.86
2416 2587 4.796495 ACCAATCTTCCCCGCGCC 62.796 66.667 0.00 0.00 0.00 6.53
2466 2637 4.961511 GACGCCGCCACTGTGACA 62.962 66.667 9.86 0.00 0.00 3.58
2472 2643 3.649986 GCCACTGTGACACCGCAC 61.650 66.667 9.86 0.00 39.22 5.34
2473 2644 2.972505 CCACTGTGACACCGCACC 60.973 66.667 9.86 0.00 37.99 5.01
2474 2645 3.337889 CACTGTGACACCGCACCG 61.338 66.667 0.32 0.00 37.99 4.94
2502 2673 4.899239 CCTCGGCCGCCACATCTC 62.899 72.222 23.51 0.00 0.00 2.75
2534 2705 4.135153 CCCTCGCCTCCACTCGTG 62.135 72.222 0.00 0.00 0.00 4.35
2535 2706 3.374402 CCTCGCCTCCACTCGTGT 61.374 66.667 0.00 0.00 0.00 4.49
2536 2707 2.179517 CTCGCCTCCACTCGTGTC 59.820 66.667 0.00 0.00 0.00 3.67
2537 2708 3.669036 CTCGCCTCCACTCGTGTCG 62.669 68.421 0.00 0.00 0.00 4.35
2538 2709 4.778415 CGCCTCCACTCGTGTCGG 62.778 72.222 0.00 0.00 0.00 4.79
2539 2710 3.371063 GCCTCCACTCGTGTCGGA 61.371 66.667 8.02 8.02 0.00 4.55
2540 2711 2.711922 GCCTCCACTCGTGTCGGAT 61.712 63.158 8.54 0.00 0.00 4.18
2541 2712 1.433879 CCTCCACTCGTGTCGGATC 59.566 63.158 8.54 0.00 0.00 3.36
2542 2713 1.433879 CTCCACTCGTGTCGGATCC 59.566 63.158 0.00 0.00 0.00 3.36
2543 2714 2.102357 CCACTCGTGTCGGATCCG 59.898 66.667 28.62 28.62 41.35 4.18
2544 2715 2.102357 CACTCGTGTCGGATCCGG 59.898 66.667 32.79 18.28 40.25 5.14
2545 2716 3.823330 ACTCGTGTCGGATCCGGC 61.823 66.667 31.57 31.57 45.14 6.13
2551 2722 2.255856 GTCGGATCCGGCGAGATC 59.744 66.667 32.79 22.17 41.69 2.75
2555 2726 2.048690 GATCCGGCGAGATCCTGC 60.049 66.667 20.62 0.00 37.31 4.85
2598 2769 4.524318 GCGATCTTCCCCGGCGAA 62.524 66.667 9.30 0.79 0.00 4.70
2599 2770 2.585247 CGATCTTCCCCGGCGAAC 60.585 66.667 9.30 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.381387 GGTGAAACTTAACTTGATCTCGATTAC 58.619 37.037 0.00 0.00 36.74 1.89
9 10 6.379988 AGTGGTTTGGTGAAACTTAACTTGAT 59.620 34.615 0.00 0.00 41.21 2.57
162 186 1.565759 AGGCAAGGGAGCATCATACAA 59.434 47.619 0.00 0.00 36.25 2.41
952 990 7.338449 ACAAACATGGTTATAAGACGGCTTAAT 59.662 33.333 16.14 6.52 39.85 1.40
1051 1089 1.448540 CAGCTACAGCCTTGGTCGG 60.449 63.158 0.00 0.00 43.38 4.79
1285 1323 5.046014 TCTCAGCTTGCTTCTTCCTATTCTT 60.046 40.000 0.00 0.00 0.00 2.52
1403 1441 4.397103 ACATTCACACAGCTTCCATGTATG 59.603 41.667 0.00 0.00 0.00 2.39
1971 2120 3.200593 GAGCTGATGTGGCGCCAG 61.201 66.667 33.73 19.63 34.52 4.85
1972 2121 4.783621 GGAGCTGATGTGGCGCCA 62.784 66.667 29.03 29.03 46.34 5.69
1974 2123 3.503363 GTGGAGCTGATGTGGCGC 61.503 66.667 0.00 0.00 34.52 6.53
1975 2124 3.190849 CGTGGAGCTGATGTGGCG 61.191 66.667 0.00 0.00 34.52 5.69
1976 2125 3.503363 GCGTGGAGCTGATGTGGC 61.503 66.667 0.00 0.00 44.04 5.01
2240 2411 5.470437 TCCGTCACAAACATGCAAAATACTA 59.530 36.000 0.00 0.00 0.00 1.82
2305 2476 6.250951 CCTTTCGATAAGTAAGAGTGTCGAAC 59.749 42.308 7.42 0.00 44.53 3.95
2306 2477 6.149973 TCCTTTCGATAAGTAAGAGTGTCGAA 59.850 38.462 4.17 4.17 43.60 3.71
2307 2478 5.645067 TCCTTTCGATAAGTAAGAGTGTCGA 59.355 40.000 0.00 0.00 36.46 4.20
2308 2479 5.738225 GTCCTTTCGATAAGTAAGAGTGTCG 59.262 44.000 0.00 0.00 29.89 4.35
2309 2480 6.854778 AGTCCTTTCGATAAGTAAGAGTGTC 58.145 40.000 0.00 0.00 29.89 3.67
2310 2481 6.837471 AGTCCTTTCGATAAGTAAGAGTGT 57.163 37.500 0.00 0.00 29.89 3.55
2311 2482 6.906143 CGTAGTCCTTTCGATAAGTAAGAGTG 59.094 42.308 0.00 0.00 29.89 3.51
2312 2483 6.820656 TCGTAGTCCTTTCGATAAGTAAGAGT 59.179 38.462 0.00 0.00 29.89 3.24
2313 2484 7.244166 TCGTAGTCCTTTCGATAAGTAAGAG 57.756 40.000 0.00 0.00 29.89 2.85
2314 2485 7.798596 ATCGTAGTCCTTTCGATAAGTAAGA 57.201 36.000 0.00 0.00 41.46 2.10
2315 2486 8.986847 TCTATCGTAGTCCTTTCGATAAGTAAG 58.013 37.037 7.65 0.00 42.90 2.34
2316 2487 8.893219 TCTATCGTAGTCCTTTCGATAAGTAA 57.107 34.615 7.65 0.00 42.90 2.24
2317 2488 9.149225 GATCTATCGTAGTCCTTTCGATAAGTA 57.851 37.037 7.65 0.00 42.90 2.24
2318 2489 7.119553 GGATCTATCGTAGTCCTTTCGATAAGT 59.880 40.741 7.65 1.07 42.90 2.24
2319 2490 7.414319 GGGATCTATCGTAGTCCTTTCGATAAG 60.414 44.444 7.65 0.00 42.90 1.73
2320 2491 6.373774 GGGATCTATCGTAGTCCTTTCGATAA 59.626 42.308 7.65 1.63 42.90 1.75
2321 2492 5.879223 GGGATCTATCGTAGTCCTTTCGATA 59.121 44.000 0.00 0.00 42.78 2.92
2322 2493 4.701171 GGGATCTATCGTAGTCCTTTCGAT 59.299 45.833 0.00 0.00 44.53 3.59
2323 2494 4.070716 GGGATCTATCGTAGTCCTTTCGA 58.929 47.826 0.00 0.00 37.96 3.71
2324 2495 3.190953 GGGGATCTATCGTAGTCCTTTCG 59.809 52.174 0.00 0.00 0.00 3.46
2325 2496 4.409187 AGGGGATCTATCGTAGTCCTTTC 58.591 47.826 0.00 0.00 0.00 2.62
2326 2497 4.472690 AGGGGATCTATCGTAGTCCTTT 57.527 45.455 0.00 0.00 0.00 3.11
2327 2498 5.799978 ATAGGGGATCTATCGTAGTCCTT 57.200 43.478 0.00 0.00 33.60 3.36
2328 2499 5.971881 AGTATAGGGGATCTATCGTAGTCCT 59.028 44.000 0.00 0.00 39.30 3.85
2329 2500 6.251255 AGTATAGGGGATCTATCGTAGTCC 57.749 45.833 0.00 0.00 39.30 3.85
2330 2501 7.066043 CACAAGTATAGGGGATCTATCGTAGTC 59.934 44.444 0.00 0.00 39.30 2.59
2331 2502 6.885376 CACAAGTATAGGGGATCTATCGTAGT 59.115 42.308 0.00 0.00 39.30 2.73
2332 2503 6.319152 CCACAAGTATAGGGGATCTATCGTAG 59.681 46.154 0.00 0.00 39.30 3.51
2333 2504 6.185511 CCACAAGTATAGGGGATCTATCGTA 58.814 44.000 0.00 0.00 39.30 3.43
2334 2505 5.017490 CCACAAGTATAGGGGATCTATCGT 58.983 45.833 0.00 0.00 39.30 3.73
2335 2506 4.402793 CCCACAAGTATAGGGGATCTATCG 59.597 50.000 0.00 0.00 43.57 2.92
2336 2507 5.941555 CCCACAAGTATAGGGGATCTATC 57.058 47.826 0.00 0.00 43.57 2.08
2345 2516 3.454447 TGGTGATGACCCACAAGTATAGG 59.546 47.826 0.00 0.00 42.34 2.57
2346 2517 4.753516 TGGTGATGACCCACAAGTATAG 57.246 45.455 0.00 0.00 42.34 1.31
2347 2518 4.102524 GGATGGTGATGACCCACAAGTATA 59.897 45.833 0.00 0.00 42.34 1.47
2348 2519 3.117888 GGATGGTGATGACCCACAAGTAT 60.118 47.826 0.00 0.00 42.34 2.12
2349 2520 2.238646 GGATGGTGATGACCCACAAGTA 59.761 50.000 0.00 0.00 42.34 2.24
2350 2521 1.004745 GGATGGTGATGACCCACAAGT 59.995 52.381 0.00 0.00 42.34 3.16
2351 2522 1.755179 GGATGGTGATGACCCACAAG 58.245 55.000 0.00 0.00 42.34 3.16
2352 2523 0.035534 CGGATGGTGATGACCCACAA 60.036 55.000 0.00 0.00 42.34 3.33
2353 2524 1.601703 CGGATGGTGATGACCCACA 59.398 57.895 0.00 0.00 42.34 4.17
2354 2525 1.153168 CCGGATGGTGATGACCCAC 60.153 63.158 0.00 0.00 42.34 4.61
2355 2526 3.042733 GCCGGATGGTGATGACCCA 62.043 63.158 5.05 0.00 42.34 4.51
2356 2527 2.203209 GCCGGATGGTGATGACCC 60.203 66.667 5.05 0.00 42.34 4.46
2357 2528 2.203209 GGCCGGATGGTGATGACC 60.203 66.667 5.05 0.00 43.48 4.02
2358 2529 2.588877 CGGCCGGATGGTGATGAC 60.589 66.667 20.10 0.00 37.67 3.06
2359 2530 4.545706 GCGGCCGGATGGTGATGA 62.546 66.667 29.38 0.00 37.67 2.92
2391 2562 4.179579 GAAGATTGGTGGCGGCGC 62.180 66.667 26.17 26.17 0.00 6.53
2392 2563 3.508840 GGAAGATTGGTGGCGGCG 61.509 66.667 0.51 0.51 0.00 6.46
2393 2564 3.140814 GGGAAGATTGGTGGCGGC 61.141 66.667 0.00 0.00 0.00 6.53
2394 2565 2.440247 GGGGAAGATTGGTGGCGG 60.440 66.667 0.00 0.00 0.00 6.13
2395 2566 2.824041 CGGGGAAGATTGGTGGCG 60.824 66.667 0.00 0.00 0.00 5.69
2396 2567 3.140814 GCGGGGAAGATTGGTGGC 61.141 66.667 0.00 0.00 0.00 5.01
2397 2568 2.824041 CGCGGGGAAGATTGGTGG 60.824 66.667 0.00 0.00 0.00 4.61
2398 2569 3.508840 GCGCGGGGAAGATTGGTG 61.509 66.667 8.83 0.00 0.00 4.17
2399 2570 4.796495 GGCGCGGGGAAGATTGGT 62.796 66.667 8.83 0.00 0.00 3.67
2449 2620 4.961511 TGTCACAGTGGCGGCGTC 62.962 66.667 3.62 3.62 0.00 5.19
2455 2626 3.649986 GTGCGGTGTCACAGTGGC 61.650 66.667 5.12 0.00 36.97 5.01
2456 2627 2.972505 GGTGCGGTGTCACAGTGG 60.973 66.667 5.12 0.00 38.66 4.00
2457 2628 3.337889 CGGTGCGGTGTCACAGTG 61.338 66.667 5.12 0.00 38.66 3.66
2485 2656 4.899239 GAGATGTGGCGGCCGAGG 62.899 72.222 33.48 0.00 0.00 4.63
2517 2688 4.135153 CACGAGTGGAGGCGAGGG 62.135 72.222 0.00 0.00 0.00 4.30
2518 2689 3.343788 GACACGAGTGGAGGCGAGG 62.344 68.421 8.19 0.00 34.19 4.63
2519 2690 2.179517 GACACGAGTGGAGGCGAG 59.820 66.667 8.19 0.00 34.19 5.03
2520 2691 3.733960 CGACACGAGTGGAGGCGA 61.734 66.667 8.19 0.00 34.19 5.54
2521 2692 4.778415 CCGACACGAGTGGAGGCG 62.778 72.222 8.19 5.80 34.19 5.52
2522 2693 2.615262 GATCCGACACGAGTGGAGGC 62.615 65.000 8.19 2.69 34.75 4.70
2523 2694 1.433879 GATCCGACACGAGTGGAGG 59.566 63.158 8.19 9.96 34.75 4.30
2524 2695 1.433879 GGATCCGACACGAGTGGAG 59.566 63.158 8.19 1.21 34.75 3.86
2525 2696 2.404186 CGGATCCGACACGAGTGGA 61.404 63.158 30.62 6.62 42.83 4.02
2526 2697 2.102357 CGGATCCGACACGAGTGG 59.898 66.667 30.62 0.00 42.83 4.00
2527 2698 2.102357 CCGGATCCGACACGAGTG 59.898 66.667 35.42 12.07 42.83 3.51
2528 2699 3.823330 GCCGGATCCGACACGAGT 61.823 66.667 35.42 0.00 42.83 4.18
2529 2700 4.907034 CGCCGGATCCGACACGAG 62.907 72.222 35.42 18.02 42.83 4.18
2531 2702 4.907034 CTCGCCGGATCCGACACG 62.907 72.222 35.42 30.68 42.83 4.49
2532 2703 2.734756 GATCTCGCCGGATCCGACAC 62.735 65.000 35.42 21.62 42.83 3.67
2533 2704 2.518587 ATCTCGCCGGATCCGACA 60.519 61.111 35.42 16.67 42.83 4.35
2534 2705 2.255856 GATCTCGCCGGATCCGAC 59.744 66.667 35.42 23.92 42.83 4.79
2538 2709 2.048690 GCAGGATCTCGCCGGATC 60.049 66.667 5.05 0.00 40.78 3.36
2539 2710 3.620785 GGCAGGATCTCGCCGGAT 61.621 66.667 5.05 0.00 38.82 4.18
2581 2752 4.524318 TTCGCCGGGGAAGATCGC 62.524 66.667 28.37 0.00 0.00 4.58
2582 2753 2.585247 GTTCGCCGGGGAAGATCG 60.585 66.667 32.02 11.64 0.00 3.69


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

AutoCloner maintained by Alex Coulton.