Multiple sequence alignment - TraesCS3D01G241100

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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 TraesCS3D01G241100 chr3D 100.000 3006 0 0 1 3006 334153378 334156383 0.000000e+00 5552.0
1 TraesCS3D01G241100 chr3D 93.333 45 2 1 2301 2345 7263930 7263887 6.960000e-07 65.8
2 TraesCS3D01G241100 chr3B 90.680 2382 63 62 1 2298 433531205 433533511 0.000000e+00 3022.0
3 TraesCS3D01G241100 chr3B 93.169 688 19 8 2346 3006 433533449 433534135 0.000000e+00 985.0
4 TraesCS3D01G241100 chr3A 90.932 2338 48 44 34 2298 452931810 452934056 0.000000e+00 2992.0
5 TraesCS3D01G241100 chr3A 95.253 316 6 2 2357 2672 452934005 452934311 2.690000e-135 492.0
6 TraesCS3D01G241100 chr3A 92.735 234 14 1 2776 3006 452940860 452941093 4.800000e-88 335.0
7 TraesCS3D01G241100 chr3A 95.833 48 2 0 1 48 452931749 452931796 8.930000e-11 78.7
8 TraesCS3D01G241100 chr5D 91.176 68 3 3 2830 2895 456709386 456709452 4.130000e-14 89.8
9 TraesCS3D01G241100 chr7B 100.000 29 0 0 2323 2351 545104493 545104521 2.000000e-03 54.7


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 TraesCS3D01G241100 chr3D 334153378 334156383 3005 False 5552.000000 5552 100.0000 1 3006 1 chr3D.!!$F1 3005
1 TraesCS3D01G241100 chr3B 433531205 433534135 2930 False 2003.500000 3022 91.9245 1 3006 2 chr3B.!!$F1 3005
2 TraesCS3D01G241100 chr3A 452931749 452934311 2562 False 1187.566667 2992 94.0060 1 2672 3 chr3A.!!$F2 2671

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
192 247 0.105760 TGCAAAATGACACCCCACCT 60.106 50.0 0.0 0.0 0.0 4.00 F
851 945 0.110104 ATCCCGTACCCTACCTCTCG 59.890 60.0 0.0 0.0 0.0 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1051 1167 0.107993 TCGAGCAGAGAAGGCAATGG 60.108 55.0 0.0 0.0 0.0 3.16 R
2319 2477 0.328258 CTCCCTCCGTCCCAAAACAT 59.672 55.0 0.0 0.0 0.0 2.71 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
48 87 6.365247 AGTTTTGTCTAGCTGTACGTATTGTG 59.635 38.462 0.00 0.00 0.00 3.33
49 88 4.365899 TGTCTAGCTGTACGTATTGTGG 57.634 45.455 0.00 0.00 0.00 4.17
50 89 4.011698 TGTCTAGCTGTACGTATTGTGGA 58.988 43.478 0.00 0.00 0.00 4.02
51 90 4.643334 TGTCTAGCTGTACGTATTGTGGAT 59.357 41.667 0.00 0.00 0.00 3.41
52 91 4.976731 GTCTAGCTGTACGTATTGTGGATG 59.023 45.833 0.00 0.00 0.00 3.51
53 92 3.887621 AGCTGTACGTATTGTGGATGT 57.112 42.857 0.00 0.00 0.00 3.06
73 112 7.651704 TGGATGTAGATGTAACGTAACATGATG 59.348 37.037 0.00 0.00 40.17 3.07
192 247 0.105760 TGCAAAATGACACCCCACCT 60.106 50.000 0.00 0.00 0.00 4.00
556 622 0.393077 CCTCCACGTCCCCATATGTC 59.607 60.000 1.24 0.00 0.00 3.06
575 651 0.818852 CTGTGTGTGTGTGCATGGGA 60.819 55.000 0.00 0.00 0.00 4.37
636 712 1.815003 GCCACATCCTTCTTTGACCAG 59.185 52.381 0.00 0.00 0.00 4.00
825 919 2.373269 CCACGTCGTCGCTATAAGAAG 58.627 52.381 0.99 0.00 41.18 2.85
849 943 0.482006 GGATCCCGTACCCTACCTCT 59.518 60.000 0.00 0.00 0.00 3.69
851 945 0.110104 ATCCCGTACCCTACCTCTCG 59.890 60.000 0.00 0.00 0.00 4.04
918 1012 6.839820 AGCTAGTGTGTGTTAACTGTTAAC 57.160 37.500 28.02 28.02 44.43 2.01
967 1061 1.722636 GACACCCCCTAGCTACGTCG 61.723 65.000 0.00 0.00 0.00 5.12
1073 1189 1.189752 TTGCCTTCTCTGCTCGATCT 58.810 50.000 0.00 0.00 0.00 2.75
1074 1190 2.058593 TGCCTTCTCTGCTCGATCTA 57.941 50.000 0.00 0.00 0.00 1.98
1535 1666 1.215912 CGTACATGGCCACGTACCA 59.784 57.895 30.61 11.55 42.61 3.25
1540 1671 2.949909 ATGGCCACGTACCAAGCGA 61.950 57.895 8.16 0.00 41.49 4.93
1541 1672 2.125269 GGCCACGTACCAAGCGAT 60.125 61.111 0.00 0.00 0.00 4.58
1542 1673 2.461110 GGCCACGTACCAAGCGATG 61.461 63.158 0.00 0.00 0.00 3.84
1550 1681 4.260355 CCAAGCGATGGCATGCGG 62.260 66.667 12.44 7.10 43.80 5.69
1551 1682 4.918129 CAAGCGATGGCATGCGGC 62.918 66.667 12.44 12.21 43.41 6.53
1570 1701 2.482316 GGCCATACACGCATACACACTA 60.482 50.000 0.00 0.00 0.00 2.74
1571 1702 3.390135 GCCATACACGCATACACACTAT 58.610 45.455 0.00 0.00 0.00 2.12
1581 1712 4.144221 CGCATACACACTATCTTACGAACG 59.856 45.833 0.00 0.00 0.00 3.95
1582 1713 4.440103 GCATACACACTATCTTACGAACGG 59.560 45.833 0.00 0.00 0.00 4.44
1588 1719 3.486108 CACTATCTTACGAACGGACATGC 59.514 47.826 0.00 0.00 0.00 4.06
1597 1728 3.006430 ACGAACGGACATGCATATCCATA 59.994 43.478 23.43 0.00 34.35 2.74
1606 1737 6.591834 GGACATGCATATCCATACTAACTGAC 59.408 42.308 19.36 0.00 34.87 3.51
1612 1743 6.372659 GCATATCCATACTAACTGACCATTGG 59.627 42.308 0.00 0.00 0.00 3.16
2027 2179 4.085357 ACAAAGAAGATGCTGTGGTACA 57.915 40.909 0.00 0.00 0.00 2.90
2102 2254 3.243168 TGCATGACAGTTGAAGCTGAAAC 60.243 43.478 0.00 4.04 39.62 2.78
2214 2372 2.198406 GAGCCGACGTTTGCATATACA 58.802 47.619 12.03 0.00 0.00 2.29
2215 2373 2.201732 AGCCGACGTTTGCATATACAG 58.798 47.619 12.03 0.00 0.00 2.74
2216 2374 1.931172 GCCGACGTTTGCATATACAGT 59.069 47.619 5.48 0.00 0.00 3.55
2217 2375 3.117794 GCCGACGTTTGCATATACAGTA 58.882 45.455 5.48 0.00 0.00 2.74
2218 2376 3.060740 GCCGACGTTTGCATATACAGTAC 60.061 47.826 5.48 0.00 0.00 2.73
2219 2377 4.357142 CCGACGTTTGCATATACAGTACT 58.643 43.478 0.00 0.00 0.00 2.73
2220 2378 4.440103 CCGACGTTTGCATATACAGTACTC 59.560 45.833 0.00 0.00 0.00 2.59
2221 2379 4.440103 CGACGTTTGCATATACAGTACTCC 59.560 45.833 0.00 0.00 0.00 3.85
2223 2381 5.726397 ACGTTTGCATATACAGTACTCCAA 58.274 37.500 0.00 0.00 0.00 3.53
2226 2384 6.701841 CGTTTGCATATACAGTACTCCAAGAT 59.298 38.462 0.00 0.00 0.00 2.40
2227 2385 7.865889 CGTTTGCATATACAGTACTCCAAGATA 59.134 37.037 0.00 0.00 0.00 1.98
2228 2386 8.979574 GTTTGCATATACAGTACTCCAAGATAC 58.020 37.037 0.00 0.00 0.00 2.24
2230 2388 9.582648 TTGCATATACAGTACTCCAAGATACTA 57.417 33.333 0.00 0.00 30.36 1.82
2231 2389 9.755122 TGCATATACAGTACTCCAAGATACTAT 57.245 33.333 0.00 0.00 30.36 2.12
2253 2411 8.951541 ACTATCTACTAGTAGACCATCTTTCCT 58.048 37.037 30.33 15.39 44.11 3.36
2294 2452 3.818387 GCATGATGATTACAGCGAATGG 58.182 45.455 0.00 0.00 34.93 3.16
2295 2453 3.251729 GCATGATGATTACAGCGAATGGT 59.748 43.478 0.00 0.00 34.93 3.55
2296 2454 4.452114 GCATGATGATTACAGCGAATGGTA 59.548 41.667 0.00 0.00 34.93 3.25
2297 2455 5.615544 GCATGATGATTACAGCGAATGGTAC 60.616 44.000 0.00 0.00 34.93 3.34
2298 2456 4.048504 TGATGATTACAGCGAATGGTACG 58.951 43.478 0.00 0.00 34.93 3.67
2310 2468 5.766702 CGAATGGTACGCTAGTGTAAAAA 57.233 39.130 17.47 7.02 0.00 1.94
2329 2487 5.523438 AAAAACGCTCTTATGTTTTGGGA 57.477 34.783 4.09 0.00 44.92 4.37
2330 2488 4.499037 AAACGCTCTTATGTTTTGGGAC 57.501 40.909 0.00 0.00 34.82 4.46
2331 2489 2.073816 ACGCTCTTATGTTTTGGGACG 58.926 47.619 0.00 0.00 0.00 4.79
2332 2490 1.396996 CGCTCTTATGTTTTGGGACGG 59.603 52.381 0.00 0.00 0.00 4.79
2333 2491 2.706890 GCTCTTATGTTTTGGGACGGA 58.293 47.619 0.00 0.00 0.00 4.69
2334 2492 2.678336 GCTCTTATGTTTTGGGACGGAG 59.322 50.000 0.00 0.00 0.00 4.63
2335 2493 3.270877 CTCTTATGTTTTGGGACGGAGG 58.729 50.000 0.00 0.00 0.00 4.30
2336 2494 2.026636 TCTTATGTTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
2337 2495 1.659022 TATGTTTTGGGACGGAGGGA 58.341 50.000 0.00 0.00 0.00 4.20
2338 2496 0.328258 ATGTTTTGGGACGGAGGGAG 59.672 55.000 0.00 0.00 0.00 4.30
2339 2497 1.057851 TGTTTTGGGACGGAGGGAGT 61.058 55.000 0.00 0.00 0.00 3.85
2340 2498 0.978907 GTTTTGGGACGGAGGGAGTA 59.021 55.000 0.00 0.00 0.00 2.59
2341 2499 1.558294 GTTTTGGGACGGAGGGAGTAT 59.442 52.381 0.00 0.00 0.00 2.12
2342 2500 1.492764 TTTGGGACGGAGGGAGTATC 58.507 55.000 0.00 0.00 0.00 2.24
2343 2501 0.635009 TTGGGACGGAGGGAGTATCT 59.365 55.000 0.00 0.00 33.73 1.98
2344 2502 1.526315 TGGGACGGAGGGAGTATCTA 58.474 55.000 0.00 0.00 33.73 1.98
2345 2503 1.144503 TGGGACGGAGGGAGTATCTAC 59.855 57.143 0.00 0.00 33.73 2.59
2346 2504 1.424684 GGGACGGAGGGAGTATCTACT 59.575 57.143 0.00 0.00 39.71 2.57
2347 2505 2.641815 GGGACGGAGGGAGTATCTACTA 59.358 54.545 0.00 0.00 36.50 1.82
2348 2506 3.307621 GGGACGGAGGGAGTATCTACTAG 60.308 56.522 0.00 0.00 36.50 2.57
2349 2507 3.327464 GGACGGAGGGAGTATCTACTAGT 59.673 52.174 0.00 0.00 36.50 2.57
2350 2508 4.530161 GGACGGAGGGAGTATCTACTAGTA 59.470 50.000 1.89 1.89 36.50 1.82
2351 2509 5.337491 GGACGGAGGGAGTATCTACTAGTAG 60.337 52.000 21.87 21.87 36.50 2.57
2352 2510 5.401750 ACGGAGGGAGTATCTACTAGTAGA 58.598 45.833 29.96 29.96 45.24 2.59
2353 2511 5.245977 ACGGAGGGAGTATCTACTAGTAGAC 59.754 48.000 30.33 20.61 44.11 2.59
2354 2512 5.337491 CGGAGGGAGTATCTACTAGTAGACC 60.337 52.000 30.33 25.23 44.11 3.85
2355 2513 5.786975 GGAGGGAGTATCTACTAGTAGACCT 59.213 48.000 30.33 28.53 44.11 3.85
2356 2514 6.273026 GGAGGGAGTATCTACTAGTAGACCTT 59.727 46.154 30.33 23.02 44.11 3.50
2357 2515 7.320384 AGGGAGTATCTACTAGTAGACCTTC 57.680 44.000 30.33 25.18 44.11 3.46
2358 2516 7.084285 AGGGAGTATCTACTAGTAGACCTTCT 58.916 42.308 30.33 23.63 44.11 2.85
2359 2517 7.573616 AGGGAGTATCTACTAGTAGACCTTCTT 59.426 40.741 30.33 21.16 44.11 2.52
2360 2518 8.219868 GGGAGTATCTACTAGTAGACCTTCTTT 58.780 40.741 30.33 17.29 44.11 2.52
2361 2519 9.276590 GGAGTATCTACTAGTAGACCTTCTTTC 57.723 40.741 30.33 19.90 44.11 2.62
2362 2520 9.276590 GAGTATCTACTAGTAGACCTTCTTTCC 57.723 40.741 30.33 14.16 44.11 3.13
2363 2521 8.780003 AGTATCTACTAGTAGACCTTCTTTCCA 58.220 37.037 30.33 8.15 44.11 3.53
2364 2522 9.577222 GTATCTACTAGTAGACCTTCTTTCCAT 57.423 37.037 30.33 14.95 44.11 3.41
2365 2523 7.883391 TCTACTAGTAGACCTTCTTTCCATG 57.117 40.000 25.58 0.00 37.28 3.66
2366 2524 7.640313 TCTACTAGTAGACCTTCTTTCCATGA 58.360 38.462 25.58 1.41 37.28 3.07
2367 2525 8.282982 TCTACTAGTAGACCTTCTTTCCATGAT 58.717 37.037 25.58 0.00 37.28 2.45
2368 2526 7.118496 ACTAGTAGACCTTCTTTCCATGATG 57.882 40.000 3.59 0.00 0.00 3.07
2369 2527 5.365021 AGTAGACCTTCTTTCCATGATGG 57.635 43.478 4.74 4.74 39.43 3.51
2370 2528 3.659183 AGACCTTCTTTCCATGATGGG 57.341 47.619 12.26 0.00 38.32 4.00
2371 2529 2.922283 AGACCTTCTTTCCATGATGGGT 59.078 45.455 12.26 0.00 38.32 4.51
2372 2530 3.019564 GACCTTCTTTCCATGATGGGTG 58.980 50.000 12.26 2.45 38.32 4.61
2373 2531 2.291800 ACCTTCTTTCCATGATGGGTGG 60.292 50.000 12.26 7.53 38.32 4.61
2374 2532 2.025037 CCTTCTTTCCATGATGGGTGGA 60.025 50.000 12.26 4.50 43.77 4.02
2375 2533 3.373438 CCTTCTTTCCATGATGGGTGGAT 60.373 47.826 12.26 0.00 44.75 3.41
2376 2534 3.301794 TCTTTCCATGATGGGTGGATG 57.698 47.619 12.26 0.00 44.75 3.51
2377 2535 1.684983 CTTTCCATGATGGGTGGATGC 59.315 52.381 12.26 0.00 44.75 3.91
2378 2536 0.630134 TTCCATGATGGGTGGATGCA 59.370 50.000 12.26 0.00 44.75 3.96
2379 2537 0.854908 TCCATGATGGGTGGATGCAT 59.145 50.000 12.26 0.00 40.72 3.96
2380 2538 0.966179 CCATGATGGGTGGATGCATG 59.034 55.000 2.46 0.00 39.12 4.06
2381 2539 1.699730 CATGATGGGTGGATGCATGT 58.300 50.000 2.46 0.00 33.50 3.21
2382 2540 1.611977 CATGATGGGTGGATGCATGTC 59.388 52.381 2.46 0.00 33.50 3.06
2383 2541 0.464193 TGATGGGTGGATGCATGTCG 60.464 55.000 2.46 0.00 0.00 4.35
2384 2542 1.789078 GATGGGTGGATGCATGTCGC 61.789 60.000 2.46 2.51 42.89 5.19
2403 2561 2.896289 GCATGACGATTACAGCGAATG 58.104 47.619 0.00 0.00 33.13 2.67
2515 2673 1.520192 CCCCAACGGTCGATCATCA 59.480 57.895 0.00 0.00 0.00 3.07
2589 2752 1.548357 GGGCTTCTGAGAGTGAGGCA 61.548 60.000 8.22 0.00 38.12 4.75
2596 2759 1.248785 TGAGAGTGAGGCACCGTACC 61.249 60.000 0.00 0.00 34.49 3.34
2712 2889 6.576662 TGGACCGTGCTTCATAAATTTTTA 57.423 33.333 0.00 0.00 0.00 1.52
2801 2978 2.279517 GGTCAGCGTCTATGCCCG 60.280 66.667 0.00 0.00 34.65 6.13
2878 3062 4.481930 TTCACATTCCGTTCAACATCAC 57.518 40.909 0.00 0.00 0.00 3.06
2907 3091 8.533657 AGACATTGCAATTTTCATATCTGGAAA 58.466 29.630 9.83 0.00 34.35 3.13
2918 3102 6.122850 TCATATCTGGAAATTGCTTTCACG 57.877 37.500 1.41 0.00 42.17 4.35
2935 3119 8.604035 TGCTTTCACGATAAGATAACTGAAATC 58.396 33.333 0.00 0.00 0.00 2.17
2936 3120 7.789759 GCTTTCACGATAAGATAACTGAAATCG 59.210 37.037 9.60 9.60 38.66 3.34
2951 3135 7.365840 ACTGAAATCGAAAATGACCTAGAAC 57.634 36.000 0.00 0.00 0.00 3.01
2952 3136 6.934645 ACTGAAATCGAAAATGACCTAGAACA 59.065 34.615 0.00 0.00 0.00 3.18
2953 3137 7.444183 ACTGAAATCGAAAATGACCTAGAACAA 59.556 33.333 0.00 0.00 0.00 2.83
2954 3138 7.806690 TGAAATCGAAAATGACCTAGAACAAG 58.193 34.615 0.00 0.00 0.00 3.16
2955 3139 7.659799 TGAAATCGAAAATGACCTAGAACAAGA 59.340 33.333 0.00 0.00 0.00 3.02
2958 3142 7.979444 TCGAAAATGACCTAGAACAAGAAAT 57.021 32.000 0.00 0.00 0.00 2.17
2960 3144 9.496873 TCGAAAATGACCTAGAACAAGAAATTA 57.503 29.630 0.00 0.00 0.00 1.40
2964 3148 9.914131 AAATGACCTAGAACAAGAAATTAAAGC 57.086 29.630 0.00 0.00 0.00 3.51
2965 3149 8.635765 ATGACCTAGAACAAGAAATTAAAGCA 57.364 30.769 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 87 7.116376 CCATCATGTTACGTTACATCTACATCC 59.884 40.741 16.75 0.00 36.64 3.51
49 88 7.865889 TCCATCATGTTACGTTACATCTACATC 59.134 37.037 16.75 0.00 36.64 3.06
50 89 7.722363 TCCATCATGTTACGTTACATCTACAT 58.278 34.615 16.75 5.01 36.64 2.29
51 90 7.102847 TCCATCATGTTACGTTACATCTACA 57.897 36.000 16.75 2.97 36.64 2.74
52 91 7.359264 GCATCCATCATGTTACGTTACATCTAC 60.359 40.741 16.75 0.00 36.64 2.59
53 92 6.645003 GCATCCATCATGTTACGTTACATCTA 59.355 38.462 16.75 9.08 36.64 1.98
192 247 4.941263 CAGTCTTTAATTTCCATCCACGGA 59.059 41.667 0.00 0.00 0.00 4.69
242 297 2.897350 GGTGCGCTGTATCAGGCC 60.897 66.667 9.73 0.00 30.52 5.19
243 298 3.264897 CGGTGCGCTGTATCAGGC 61.265 66.667 9.73 2.06 31.21 4.85
556 622 0.818852 TCCCATGCACACACACACAG 60.819 55.000 0.00 0.00 0.00 3.66
575 651 0.249741 CGTGAAACCGGGAACAGTCT 60.250 55.000 6.32 0.00 0.00 3.24
650 726 3.200593 CTCTCATGCGCCTGTGGC 61.201 66.667 12.54 0.00 46.75 5.01
825 919 2.668106 TAGGGTACGGGATCCTGGGC 62.668 65.000 24.68 15.55 39.89 5.36
849 943 1.096967 GCACATGTGGATGGATGCGA 61.097 55.000 26.55 0.00 33.39 5.10
851 945 1.038681 TGGCACATGTGGATGGATGC 61.039 55.000 26.55 9.89 33.03 3.91
967 1061 2.031944 GCTTCGAGACCAAACCAAAGAC 60.032 50.000 0.00 0.00 0.00 3.01
1051 1167 0.107993 TCGAGCAGAGAAGGCAATGG 60.108 55.000 0.00 0.00 0.00 3.16
1073 1189 6.209589 CAGTAGGAGCTACTTGCAGGAATATA 59.790 42.308 2.22 0.00 43.82 0.86
1074 1190 5.011533 CAGTAGGAGCTACTTGCAGGAATAT 59.988 44.000 2.22 0.00 43.82 1.28
1473 1598 2.904866 GCACGCACCTTTGGTCCA 60.905 61.111 0.00 0.00 31.02 4.02
1548 1679 0.808060 TGTGTATGCGTGTATGGCCG 60.808 55.000 0.00 0.00 0.00 6.13
1549 1680 0.655733 GTGTGTATGCGTGTATGGCC 59.344 55.000 0.00 0.00 0.00 5.36
1550 1681 1.651987 AGTGTGTATGCGTGTATGGC 58.348 50.000 0.00 0.00 0.00 4.40
1551 1682 4.871513 AGATAGTGTGTATGCGTGTATGG 58.128 43.478 0.00 0.00 0.00 2.74
1552 1683 6.086371 CGTAAGATAGTGTGTATGCGTGTATG 59.914 42.308 0.00 0.00 43.02 2.39
1553 1684 6.017687 TCGTAAGATAGTGTGTATGCGTGTAT 60.018 38.462 0.00 0.00 45.01 2.29
1554 1685 5.294060 TCGTAAGATAGTGTGTATGCGTGTA 59.706 40.000 0.00 0.00 45.01 2.90
1555 1686 4.095334 TCGTAAGATAGTGTGTATGCGTGT 59.905 41.667 0.00 0.00 45.01 4.49
1556 1687 4.594136 TCGTAAGATAGTGTGTATGCGTG 58.406 43.478 0.00 0.00 45.01 5.34
1557 1688 4.888038 TCGTAAGATAGTGTGTATGCGT 57.112 40.909 0.00 0.00 45.01 5.24
1570 1701 8.407065 TGGATATGCATGTCCGTTCGTAAGAT 62.407 42.308 30.32 3.47 43.05 2.40
1571 1702 7.180165 TGGATATGCATGTCCGTTCGTAAGA 62.180 44.000 30.32 12.36 42.34 2.10
1581 1712 6.591834 GTCAGTTAGTATGGATATGCATGTCC 59.408 42.308 30.02 30.02 38.43 4.02
1582 1713 6.591834 GGTCAGTTAGTATGGATATGCATGTC 59.408 42.308 19.03 14.60 0.00 3.06
1588 1719 7.388776 CACCAATGGTCAGTTAGTATGGATATG 59.611 40.741 0.00 0.00 31.02 1.78
1597 1728 2.949177 TGCACCAATGGTCAGTTAGT 57.051 45.000 0.00 0.00 31.02 2.24
2027 2179 1.270550 CTTGCGTGCCCTCAAAAAGAT 59.729 47.619 0.00 0.00 0.00 2.40
2087 2239 3.976942 CCATTTCGTTTCAGCTTCAACTG 59.023 43.478 3.80 0.00 39.12 3.16
2102 2254 3.403936 GGGGGAGTGATCCATTTCG 57.596 57.895 0.00 0.00 0.00 3.46
2136 2289 0.974383 GAGGAAACAAGACGGGAGGA 59.026 55.000 0.00 0.00 0.00 3.71
2192 2350 1.732941 ATATGCAAACGTCGGCTCAA 58.267 45.000 11.93 0.00 0.00 3.02
2218 2376 9.880157 GGTCTACTAGTAGATAGTATCTTGGAG 57.120 40.741 30.33 13.58 44.24 3.86
2219 2377 9.389949 TGGTCTACTAGTAGATAGTATCTTGGA 57.610 37.037 30.33 4.60 44.24 3.53
2227 2385 8.951541 AGGAAAGATGGTCTACTAGTAGATAGT 58.048 37.037 30.33 20.11 46.70 2.12
2228 2386 9.802039 AAGGAAAGATGGTCTACTAGTAGATAG 57.198 37.037 30.33 9.75 43.32 2.08
2230 2388 8.282982 TCAAGGAAAGATGGTCTACTAGTAGAT 58.717 37.037 30.33 17.93 43.32 1.98
2231 2389 7.640313 TCAAGGAAAGATGGTCTACTAGTAGA 58.360 38.462 25.58 25.58 39.67 2.59
2232 2390 7.883391 TCAAGGAAAGATGGTCTACTAGTAG 57.117 40.000 21.87 21.87 34.56 2.57
2233 2391 8.239038 CATCAAGGAAAGATGGTCTACTAGTA 57.761 38.462 1.89 1.89 39.30 1.82
2234 2392 7.118496 CATCAAGGAAAGATGGTCTACTAGT 57.882 40.000 0.00 0.00 39.30 2.57
2253 2411 1.766494 GACATGCATCCACCCATCAA 58.234 50.000 0.00 0.00 0.00 2.57
2307 2465 5.286438 GTCCCAAAACATAAGAGCGTTTTT 58.714 37.500 0.00 0.00 42.00 1.94
2308 2466 4.555906 CGTCCCAAAACATAAGAGCGTTTT 60.556 41.667 0.00 0.00 44.08 2.43
2309 2467 3.058501 CGTCCCAAAACATAAGAGCGTTT 60.059 43.478 0.00 0.00 36.92 3.60
2310 2468 2.482721 CGTCCCAAAACATAAGAGCGTT 59.517 45.455 0.00 0.00 0.00 4.84
2311 2469 2.073816 CGTCCCAAAACATAAGAGCGT 58.926 47.619 0.00 0.00 0.00 5.07
2312 2470 1.396996 CCGTCCCAAAACATAAGAGCG 59.603 52.381 0.00 0.00 0.00 5.03
2313 2471 2.678336 CTCCGTCCCAAAACATAAGAGC 59.322 50.000 0.00 0.00 0.00 4.09
2314 2472 3.270877 CCTCCGTCCCAAAACATAAGAG 58.729 50.000 0.00 0.00 0.00 2.85
2315 2473 2.026636 CCCTCCGTCCCAAAACATAAGA 60.027 50.000 0.00 0.00 0.00 2.10
2316 2474 2.026636 TCCCTCCGTCCCAAAACATAAG 60.027 50.000 0.00 0.00 0.00 1.73
2317 2475 1.986631 TCCCTCCGTCCCAAAACATAA 59.013 47.619 0.00 0.00 0.00 1.90
2318 2476 1.557832 CTCCCTCCGTCCCAAAACATA 59.442 52.381 0.00 0.00 0.00 2.29
2319 2477 0.328258 CTCCCTCCGTCCCAAAACAT 59.672 55.000 0.00 0.00 0.00 2.71
2320 2478 1.057851 ACTCCCTCCGTCCCAAAACA 61.058 55.000 0.00 0.00 0.00 2.83
2321 2479 0.978907 TACTCCCTCCGTCCCAAAAC 59.021 55.000 0.00 0.00 0.00 2.43
2322 2480 1.835531 GATACTCCCTCCGTCCCAAAA 59.164 52.381 0.00 0.00 0.00 2.44
2323 2481 1.007963 AGATACTCCCTCCGTCCCAAA 59.992 52.381 0.00 0.00 0.00 3.28
2324 2482 0.635009 AGATACTCCCTCCGTCCCAA 59.365 55.000 0.00 0.00 0.00 4.12
2325 2483 1.144503 GTAGATACTCCCTCCGTCCCA 59.855 57.143 0.00 0.00 0.00 4.37
2326 2484 1.424684 AGTAGATACTCCCTCCGTCCC 59.575 57.143 0.00 0.00 0.00 4.46
2327 2485 2.955342 AGTAGATACTCCCTCCGTCC 57.045 55.000 0.00 0.00 0.00 4.79
2328 2486 4.622260 ACTAGTAGATACTCCCTCCGTC 57.378 50.000 3.59 0.00 37.73 4.79
2329 2487 5.245977 GTCTACTAGTAGATACTCCCTCCGT 59.754 48.000 30.33 0.00 43.32 4.69
2330 2488 5.337491 GGTCTACTAGTAGATACTCCCTCCG 60.337 52.000 30.33 3.60 43.32 4.63
2331 2489 5.786975 AGGTCTACTAGTAGATACTCCCTCC 59.213 48.000 30.33 23.45 43.32 4.30
2332 2490 6.940430 AGGTCTACTAGTAGATACTCCCTC 57.060 45.833 30.33 17.03 43.32 4.30
2333 2491 7.084285 AGAAGGTCTACTAGTAGATACTCCCT 58.916 42.308 30.33 26.68 43.32 4.20
2334 2492 7.320384 AGAAGGTCTACTAGTAGATACTCCC 57.680 44.000 30.33 25.22 43.32 4.30
2335 2493 9.276590 GAAAGAAGGTCTACTAGTAGATACTCC 57.723 40.741 30.33 25.53 43.32 3.85
2336 2494 9.276590 GGAAAGAAGGTCTACTAGTAGATACTC 57.723 40.741 30.33 24.37 43.32 2.59
2337 2495 8.780003 TGGAAAGAAGGTCTACTAGTAGATACT 58.220 37.037 30.33 26.59 43.32 2.12
2338 2496 8.977267 TGGAAAGAAGGTCTACTAGTAGATAC 57.023 38.462 30.33 25.17 43.32 2.24
2339 2497 9.575868 CATGGAAAGAAGGTCTACTAGTAGATA 57.424 37.037 30.33 11.06 43.32 1.98
2340 2498 8.282982 TCATGGAAAGAAGGTCTACTAGTAGAT 58.717 37.037 30.33 17.93 43.32 1.98
2341 2499 7.640313 TCATGGAAAGAAGGTCTACTAGTAGA 58.360 38.462 25.58 25.58 39.67 2.59
2342 2500 7.883391 TCATGGAAAGAAGGTCTACTAGTAG 57.117 40.000 21.87 21.87 34.56 2.57
2343 2501 7.287927 CCATCATGGAAAGAAGGTCTACTAGTA 59.712 40.741 0.00 1.89 40.96 1.82
2344 2502 6.098982 CCATCATGGAAAGAAGGTCTACTAGT 59.901 42.308 0.00 0.00 40.96 2.57
2345 2503 6.463614 CCCATCATGGAAAGAAGGTCTACTAG 60.464 46.154 4.75 0.00 40.96 2.57
2346 2504 5.366768 CCCATCATGGAAAGAAGGTCTACTA 59.633 44.000 4.75 0.00 40.96 1.82
2347 2505 4.164988 CCCATCATGGAAAGAAGGTCTACT 59.835 45.833 4.75 0.00 40.96 2.57
2348 2506 4.080299 ACCCATCATGGAAAGAAGGTCTAC 60.080 45.833 4.75 0.00 40.96 2.59
2349 2507 4.080356 CACCCATCATGGAAAGAAGGTCTA 60.080 45.833 4.75 0.00 40.96 2.59
2350 2508 2.922283 ACCCATCATGGAAAGAAGGTCT 59.078 45.455 4.75 0.00 40.96 3.85
2351 2509 3.019564 CACCCATCATGGAAAGAAGGTC 58.980 50.000 4.75 0.00 40.96 3.85
2352 2510 2.291800 CCACCCATCATGGAAAGAAGGT 60.292 50.000 4.75 0.00 40.96 3.50
2353 2511 2.025037 TCCACCCATCATGGAAAGAAGG 60.025 50.000 4.75 0.00 43.43 3.46
2354 2512 3.370840 TCCACCCATCATGGAAAGAAG 57.629 47.619 4.75 0.00 43.43 2.85
2361 2519 0.966179 CATGCATCCACCCATCATGG 59.034 55.000 0.00 0.00 38.71 3.66
2362 2520 1.611977 GACATGCATCCACCCATCATG 59.388 52.381 0.00 0.00 40.07 3.07
2363 2521 1.816572 CGACATGCATCCACCCATCAT 60.817 52.381 0.00 0.00 0.00 2.45
2364 2522 0.464193 CGACATGCATCCACCCATCA 60.464 55.000 0.00 0.00 0.00 3.07
2365 2523 1.789078 GCGACATGCATCCACCCATC 61.789 60.000 0.00 0.00 45.45 3.51
2366 2524 1.825191 GCGACATGCATCCACCCAT 60.825 57.895 0.00 0.00 45.45 4.00
2367 2525 2.438254 GCGACATGCATCCACCCA 60.438 61.111 0.00 0.00 45.45 4.51
2382 2540 0.920664 TTCGCTGTAATCGTCATGCG 59.079 50.000 0.00 0.00 43.95 4.73
2383 2541 2.348872 CCATTCGCTGTAATCGTCATGC 60.349 50.000 0.00 0.00 0.00 4.06
2384 2542 2.866156 ACCATTCGCTGTAATCGTCATG 59.134 45.455 0.00 0.00 0.00 3.07
2385 2543 3.179443 ACCATTCGCTGTAATCGTCAT 57.821 42.857 0.00 0.00 0.00 3.06
2386 2544 2.665649 ACCATTCGCTGTAATCGTCA 57.334 45.000 0.00 0.00 0.00 4.35
2387 2545 3.441163 TGTACCATTCGCTGTAATCGTC 58.559 45.455 0.00 0.00 0.00 4.20
2388 2546 3.513680 TGTACCATTCGCTGTAATCGT 57.486 42.857 0.00 0.00 0.00 3.73
2389 2547 3.802139 ACATGTACCATTCGCTGTAATCG 59.198 43.478 0.00 0.00 0.00 3.34
2390 2548 4.211374 GGACATGTACCATTCGCTGTAATC 59.789 45.833 0.00 0.00 0.00 1.75
2391 2549 4.127171 GGACATGTACCATTCGCTGTAAT 58.873 43.478 0.00 0.00 0.00 1.89
2392 2550 3.196901 AGGACATGTACCATTCGCTGTAA 59.803 43.478 3.84 0.00 0.00 2.41
2393 2551 2.764010 AGGACATGTACCATTCGCTGTA 59.236 45.455 3.84 0.00 0.00 2.74
2394 2552 1.555075 AGGACATGTACCATTCGCTGT 59.445 47.619 3.84 0.00 0.00 4.40
2395 2553 1.935873 CAGGACATGTACCATTCGCTG 59.064 52.381 3.84 0.00 0.00 5.18
2396 2554 1.743772 GCAGGACATGTACCATTCGCT 60.744 52.381 3.84 0.00 0.00 4.93
2397 2555 0.657840 GCAGGACATGTACCATTCGC 59.342 55.000 3.84 0.00 0.00 4.70
2398 2556 2.315925 AGCAGGACATGTACCATTCG 57.684 50.000 3.84 0.00 0.00 3.34
2399 2557 3.428045 GCAAAGCAGGACATGTACCATTC 60.428 47.826 3.84 0.00 0.00 2.67
2400 2558 2.493278 GCAAAGCAGGACATGTACCATT 59.507 45.455 3.84 0.00 0.00 3.16
2401 2559 2.094675 GCAAAGCAGGACATGTACCAT 58.905 47.619 3.84 0.00 0.00 3.55
2402 2560 1.073763 AGCAAAGCAGGACATGTACCA 59.926 47.619 3.84 0.00 0.00 3.25
2403 2561 1.826385 AGCAAAGCAGGACATGTACC 58.174 50.000 3.84 5.34 0.00 3.34
2508 2666 6.924612 CCTGATATATGCAGCTACTGATGATC 59.075 42.308 0.00 0.00 32.44 2.92
2515 2673 2.503356 GCCCCTGATATATGCAGCTACT 59.497 50.000 0.00 0.00 32.06 2.57
2589 2752 2.100916 CGAGATTGGAAGATGGTACGGT 59.899 50.000 0.00 0.00 0.00 4.83
2712 2889 4.334481 CGTACAACCTCCTTTGTCAAAGTT 59.666 41.667 21.12 9.15 40.29 2.66
2801 2978 9.659830 AAAATGTAATGTCTTTACGTGAAGAAC 57.340 29.630 22.65 17.25 42.68 3.01
2878 3062 9.406828 CCAGATATGAAAATTGCAATGTCTATG 57.593 33.333 13.82 5.89 0.00 2.23
2907 3091 8.492673 TTCAGTTATCTTATCGTGAAAGCAAT 57.507 30.769 0.00 0.00 0.00 3.56
2942 3126 8.730680 TCATGCTTTAATTTCTTGTTCTAGGTC 58.269 33.333 0.00 0.00 0.00 3.85
2953 3137 9.846248 GGCGAATAATATCATGCTTTAATTTCT 57.154 29.630 0.00 0.00 0.00 2.52
2954 3138 8.788813 CGGCGAATAATATCATGCTTTAATTTC 58.211 33.333 0.00 0.00 0.00 2.17
2955 3139 7.754924 CCGGCGAATAATATCATGCTTTAATTT 59.245 33.333 9.30 0.00 0.00 1.82
2958 3142 5.391523 GCCGGCGAATAATATCATGCTTTAA 60.392 40.000 12.58 0.00 0.00 1.52
2960 3144 3.119849 GCCGGCGAATAATATCATGCTTT 60.120 43.478 12.58 0.00 0.00 3.51
2964 3148 5.741425 CATAAGCCGGCGAATAATATCATG 58.259 41.667 23.20 9.17 0.00 3.07
2965 3149 4.273480 GCATAAGCCGGCGAATAATATCAT 59.727 41.667 23.20 0.00 33.58 2.45


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

AutoCloner maintained by Alex Coulton.