Multiple sequence alignment - TraesCS4B01G141000

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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 TraesCS4B01G141000 chr4B 100.000 2624 0 0 1 2624 185786300 185788923 0.000000e+00 4846
1 TraesCS4B01G141000 chr4A 93.871 1289 49 14 545 1803 448259691 448258403 0.000000e+00 1916
2 TraesCS4B01G141000 chr4A 93.978 465 28 0 1 465 448260981 448260517 0.000000e+00 704
3 TraesCS4B01G141000 chr4A 83.486 436 61 10 33 464 137489645 137489217 1.890000e-106 396
4 TraesCS4B01G141000 chr4D 95.724 912 32 2 736 1640 122246547 122247458 0.000000e+00 1461
5 TraesCS4B01G141000 chr4D 96.559 465 16 0 1 465 122215048 122215512 0.000000e+00 771
6 TraesCS4B01G141000 chr4D 86.628 172 6 7 1632 1803 122247612 122247766 9.650000e-40 174
7 TraesCS4B01G141000 chr6B 85.714 819 101 5 1809 2624 667163736 667162931 0.000000e+00 850
8 TraesCS4B01G141000 chr2D 85.053 475 58 9 1 464 444770406 444769934 3.060000e-129 472
9 TraesCS4B01G141000 chr2B 84.829 468 63 7 1 465 422517441 422517903 5.120000e-127 464
10 TraesCS4B01G141000 chr2B 77.912 249 44 11 2382 2624 114412214 114412457 7.570000e-31 145
11 TraesCS4B01G141000 chr6D 84.340 447 61 8 24 465 387891757 387891315 1.870000e-116 429
12 TraesCS4B01G141000 chr6D 75.547 274 62 5 2354 2624 105955744 105955473 2.120000e-26 130
13 TraesCS4B01G141000 chr6A 84.138 435 58 6 40 465 491909486 491909054 6.760000e-111 411
14 TraesCS4B01G141000 chr6A 83.111 450 64 10 24 465 309889015 309889460 1.460000e-107 399
15 TraesCS4B01G141000 chr7D 82.265 468 70 13 1 465 132821421 132820964 2.450000e-105 392
16 TraesCS4B01G141000 chr7D 75.824 273 63 3 2354 2624 161270053 161269782 4.560000e-28 135
17 TraesCS4B01G141000 chr7D 75.912 274 57 9 2354 2622 1246402 1246133 5.890000e-27 132
18 TraesCS4B01G141000 chr5B 77.510 249 45 11 2382 2624 89753400 89753643 3.520000e-29 139
19 TraesCS4B01G141000 chr5B 72.973 407 95 13 2226 2624 648161121 648160722 7.620000e-26 128
20 TraesCS4B01G141000 chr1B 73.286 423 96 15 2211 2624 476919204 476918790 3.520000e-29 139
21 TraesCS4B01G141000 chr7A 75.824 273 61 5 2355 2624 591628344 591628074 1.640000e-27 134


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 TraesCS4B01G141000 chr4B 185786300 185788923 2623 False 4846.0 4846 100.0000 1 2624 1 chr4B.!!$F1 2623
1 TraesCS4B01G141000 chr4A 448258403 448260981 2578 True 1310.0 1916 93.9245 1 1803 2 chr4A.!!$R2 1802
2 TraesCS4B01G141000 chr4D 122246547 122247766 1219 False 817.5 1461 91.1760 736 1803 2 chr4D.!!$F2 1067
3 TraesCS4B01G141000 chr6B 667162931 667163736 805 True 850.0 850 85.7140 1809 2624 1 chr6B.!!$R1 815

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
258 259 0.171455 AGCTACAAACTCGAGAGCCG 59.829 55.0 21.68 6.89 40.25 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2179 3125 0.036164 TGTTACCCAGCTGCAACGAT 59.964 50.0 8.66 0.0 0.0 3.73 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
26 27 8.664079 AGAACTAGCAATGGATAAGATAACCAT 58.336 33.333 0.00 0.00 44.87 3.55
78 79 3.846360 AGACCGGTAAAATCTCGAACAG 58.154 45.455 7.34 0.00 0.00 3.16
92 93 1.906966 CGAACAGCAAAAGCGCAATAG 59.093 47.619 11.47 0.00 0.00 1.73
104 105 3.332919 AGCGCAATAGAAGATGCATAGG 58.667 45.455 11.47 0.00 42.68 2.57
117 118 5.810525 AGATGCATAGGAAATCGTTTTTCG 58.189 37.500 0.00 0.00 41.41 3.46
245 246 3.165890 CGAACGATACGAACAAGCTACA 58.834 45.455 0.00 0.00 0.00 2.74
246 247 3.605056 CGAACGATACGAACAAGCTACAA 59.395 43.478 0.00 0.00 0.00 2.41
258 259 0.171455 AGCTACAAACTCGAGAGCCG 59.829 55.000 21.68 6.89 40.25 5.52
313 314 3.056393 CGGTCTACCAACTAACACCATGA 60.056 47.826 0.00 0.00 35.14 3.07
334 335 6.117975 TGAGACCGGTAAAATAGAAAACCT 57.882 37.500 7.34 0.00 0.00 3.50
339 340 8.323567 AGACCGGTAAAATAGAAAACCTATCAA 58.676 33.333 7.34 0.00 37.09 2.57
387 388 6.737720 ATCCACTTGAGCTAGATGATAACA 57.262 37.500 0.00 0.00 0.00 2.41
388 389 6.154203 TCCACTTGAGCTAGATGATAACAG 57.846 41.667 0.00 0.00 0.00 3.16
425 426 7.930217 TCAAGTTAGACAACCTTTCTTGATTG 58.070 34.615 0.00 0.00 37.87 2.67
448 449 3.423253 CGCCGACTCGATGTATACTAGTG 60.423 52.174 5.39 0.00 0.00 2.74
474 638 6.718593 TTGCTCCCCCATACATATAAGATT 57.281 37.500 0.00 0.00 0.00 2.40
523 698 3.322191 AACTAACCCCACCACACAAAT 57.678 42.857 0.00 0.00 0.00 2.32
534 709 3.633525 CACCACACAAATAGATCATGGGG 59.366 47.826 0.00 0.00 39.90 4.96
541 716 6.828785 ACACAAATAGATCATGGGGTAGTTTC 59.171 38.462 0.00 0.00 0.00 2.78
542 717 7.056635 CACAAATAGATCATGGGGTAGTTTCT 58.943 38.462 0.00 0.00 0.00 2.52
556 1303 0.712222 GTTTCTAGTACCGCGCACAC 59.288 55.000 8.75 0.87 0.00 3.82
585 1332 2.114625 CATCATCCGGGCCATGCT 59.885 61.111 4.39 0.00 0.00 3.79
636 1383 4.191544 GCAATCTCATAGTAGTTGCCACA 58.808 43.478 0.00 0.00 39.27 4.17
713 1460 4.642437 TGTTCCAAACAGCAGTGTTGATTA 59.358 37.500 14.47 0.00 46.68 1.75
766 1541 1.633945 GGGCCTAAGTTCCAAGGAAGA 59.366 52.381 0.84 0.00 34.58 2.87
790 1565 7.728083 AGAACTAGAGATGCTATGTGGTAATCT 59.272 37.037 0.00 0.00 0.00 2.40
797 1572 7.743749 AGATGCTATGTGGTAATCTCAAATCT 58.256 34.615 0.00 0.00 0.00 2.40
810 1585 5.296151 TCTCAAATCTCAAGTCACCAAGT 57.704 39.130 0.00 0.00 0.00 3.16
826 1601 3.261137 ACCAAGTTGCTCTTAGGTAGTCC 59.739 47.826 0.00 0.00 36.52 3.85
920 1702 3.738830 ATATTCCATTGCACACATGGC 57.261 42.857 10.55 0.00 35.51 4.40
954 1736 5.239525 GCTACCGAATTGGAGCAATAAATCT 59.760 40.000 0.00 0.00 42.00 2.40
967 1749 4.336433 GCAATAAATCTGAAGGCTGCACTA 59.664 41.667 0.50 0.00 0.00 2.74
1065 1848 4.463879 CAGGCTCCACTGCTCGGG 62.464 72.222 0.00 0.00 0.00 5.14
1363 2146 2.181777 GACTCATCGACAGCGCCA 59.818 61.111 2.29 0.00 37.46 5.69
1707 2652 5.511571 GCTTCAGTTGGTGTTAGTTTCTTC 58.488 41.667 0.00 0.00 0.00 2.87
1751 2696 6.091577 TGTGCTTTGACCTACAACATATTACG 59.908 38.462 0.00 0.00 38.29 3.18
1755 2700 6.534475 TTGACCTACAACATATTACGAGGT 57.466 37.500 0.00 0.00 38.53 3.85
1775 2720 3.868077 GGTAGTGAGAGCTATGCTTTGTG 59.132 47.826 0.00 0.00 39.88 3.33
1803 2748 6.069847 ACCTCTTCCGGTCTTAATTCCATTTA 60.070 38.462 0.00 0.00 29.14 1.40
1804 2749 6.998673 CCTCTTCCGGTCTTAATTCCATTTAT 59.001 38.462 0.00 0.00 0.00 1.40
1805 2750 7.502561 CCTCTTCCGGTCTTAATTCCATTTATT 59.497 37.037 0.00 0.00 0.00 1.40
1806 2751 8.817092 TCTTCCGGTCTTAATTCCATTTATTT 57.183 30.769 0.00 0.00 0.00 1.40
1807 2752 9.908747 TCTTCCGGTCTTAATTCCATTTATTTA 57.091 29.630 0.00 0.00 0.00 1.40
1875 2821 2.459060 TCGTCCGAAATAACCTGCAA 57.541 45.000 0.00 0.00 0.00 4.08
1895 2841 2.592102 AATGCAGTCAGGTGGTTCAT 57.408 45.000 0.00 0.00 0.00 2.57
1921 2867 9.448294 TTTAACCACACGTTACACAAATTATTC 57.552 29.630 0.00 0.00 36.65 1.75
1927 2873 6.018913 ACACGTTACACAAATTATTCGTGACA 60.019 34.615 18.37 0.00 46.26 3.58
1930 2876 4.398549 ACACAAATTATTCGTGACACCG 57.601 40.909 2.79 0.00 34.69 4.94
1932 2878 4.148166 CACAAATTATTCGTGACACCGTG 58.852 43.478 0.00 0.00 32.23 4.94
1948 2894 1.063806 CGTGCCTAGCTAATCGATGC 58.936 55.000 0.00 0.00 0.00 3.91
1971 2917 2.949678 CCCGTTCGCTGATCGTCG 60.950 66.667 0.59 0.59 39.67 5.12
1972 2918 3.607987 CCGTTCGCTGATCGTCGC 61.608 66.667 2.03 0.00 39.67 5.19
1973 2919 2.874315 CGTTCGCTGATCGTCGCA 60.874 61.111 2.03 0.00 39.67 5.10
1993 2939 0.036765 CCCACGAAATCTTCCACCGA 60.037 55.000 0.00 0.00 0.00 4.69
2026 2972 1.122227 GGAGCTGCTTGATCTCCTCT 58.878 55.000 2.53 0.00 42.31 3.69
2031 2977 5.187576 GGAGCTGCTTGATCTCCTCTATAAT 59.812 44.000 2.53 0.00 42.31 1.28
2035 2981 5.080337 TGCTTGATCTCCTCTATAATCGGT 58.920 41.667 0.00 0.00 0.00 4.69
2042 2988 2.492088 TCCTCTATAATCGGTCCATGCG 59.508 50.000 0.00 0.00 0.00 4.73
2043 2989 2.417379 CCTCTATAATCGGTCCATGCGG 60.417 54.545 0.00 0.00 0.00 5.69
2047 2993 2.693250 TAATCGGTCCATGCGGCGAG 62.693 60.000 12.98 0.00 31.49 5.03
2052 2998 1.663074 GTCCATGCGGCGAGAGATC 60.663 63.158 12.98 0.00 0.00 2.75
2054 3000 2.733301 CATGCGGCGAGAGATCCT 59.267 61.111 12.98 0.00 0.00 3.24
2056 3002 0.531532 CATGCGGCGAGAGATCCTTT 60.532 55.000 12.98 0.00 0.00 3.11
2059 3005 1.483424 GCGGCGAGAGATCCTTTTCG 61.483 60.000 12.98 0.00 36.23 3.46
2065 3011 2.675317 CGAGAGATCCTTTTCGTGGCTT 60.675 50.000 0.00 0.00 0.00 4.35
2074 3020 3.365364 CCTTTTCGTGGCTTCTTAGCTTG 60.365 47.826 0.00 0.00 46.90 4.01
2075 3021 2.543777 TTCGTGGCTTCTTAGCTTGT 57.456 45.000 0.00 0.00 46.90 3.16
2084 3030 3.753272 GCTTCTTAGCTTGTCCACAATCA 59.247 43.478 0.00 0.00 44.27 2.57
2087 3033 4.318332 TCTTAGCTTGTCCACAATCACAG 58.682 43.478 0.00 0.00 35.02 3.66
2122 3068 8.196802 TCTCAATATGGAGATTTTGTACGTTG 57.803 34.615 5.64 0.00 38.95 4.10
2123 3069 8.038351 TCTCAATATGGAGATTTTGTACGTTGA 58.962 33.333 5.64 0.00 38.95 3.18
2124 3070 8.196802 TCAATATGGAGATTTTGTACGTTGAG 57.803 34.615 0.00 0.00 0.00 3.02
2125 3071 7.822334 TCAATATGGAGATTTTGTACGTTGAGT 59.178 33.333 0.00 0.00 0.00 3.41
2126 3072 8.450964 CAATATGGAGATTTTGTACGTTGAGTT 58.549 33.333 0.00 0.00 0.00 3.01
2127 3073 5.666969 TGGAGATTTTGTACGTTGAGTTG 57.333 39.130 0.00 0.00 0.00 3.16
2128 3074 5.120399 TGGAGATTTTGTACGTTGAGTTGT 58.880 37.500 0.00 0.00 0.00 3.32
2129 3075 5.007234 TGGAGATTTTGTACGTTGAGTTGTG 59.993 40.000 0.00 0.00 0.00 3.33
2130 3076 4.844267 AGATTTTGTACGTTGAGTTGTGC 58.156 39.130 0.00 0.00 0.00 4.57
2131 3077 4.574828 AGATTTTGTACGTTGAGTTGTGCT 59.425 37.500 0.00 0.00 0.00 4.40
2132 3078 3.666883 TTTGTACGTTGAGTTGTGCTG 57.333 42.857 0.00 0.00 0.00 4.41
2158 3104 1.081041 TGCAGCTCTTTTGCATGCG 60.081 52.632 14.09 0.00 45.89 4.73
2159 3105 2.442188 GCAGCTCTTTTGCATGCGC 61.442 57.895 14.09 9.10 41.17 6.09
2160 3106 1.804326 CAGCTCTTTTGCATGCGCC 60.804 57.895 14.09 0.00 37.32 6.53
2173 3119 2.436646 GCGCCCAGCTCTGCTTTA 60.437 61.111 0.00 0.00 44.04 1.85
2179 3125 0.036388 CCAGCTCTGCTTTAACCGGA 60.036 55.000 9.46 0.00 36.40 5.14
2185 3131 2.343101 TCTGCTTTAACCGGATCGTTG 58.657 47.619 9.46 0.00 0.00 4.10
2188 3134 1.202031 GCTTTAACCGGATCGTTGCAG 60.202 52.381 9.46 0.00 0.00 4.41
2190 3136 0.036765 TTAACCGGATCGTTGCAGCT 60.037 50.000 9.46 0.00 0.00 4.24
2191 3137 0.739462 TAACCGGATCGTTGCAGCTG 60.739 55.000 9.46 10.11 0.00 4.24
2197 3143 0.727398 GATCGTTGCAGCTGGGTAAC 59.273 55.000 17.12 5.39 0.00 2.50
2198 3144 0.036164 ATCGTTGCAGCTGGGTAACA 59.964 50.000 17.12 0.71 33.64 2.41
2214 3160 2.045536 CACCTGGCAAGCTCCTCC 60.046 66.667 0.00 0.00 0.00 4.30
2224 3170 1.768684 AAGCTCCTCCCAAGAACGCA 61.769 55.000 0.00 0.00 0.00 5.24
2273 3219 1.409802 CGCCTCCCAACTCTCCTACTA 60.410 57.143 0.00 0.00 0.00 1.82
2293 3239 1.195442 TTGATGTAGCCCCGTCCACA 61.195 55.000 0.00 0.00 0.00 4.17
2297 3243 1.520787 GTAGCCCCGTCCACATTCG 60.521 63.158 0.00 0.00 0.00 3.34
2310 3256 2.086869 CACATTCGCCTTTGTCCATCT 58.913 47.619 0.00 0.00 0.00 2.90
2311 3257 2.086869 ACATTCGCCTTTGTCCATCTG 58.913 47.619 0.00 0.00 0.00 2.90
2320 3266 1.567357 TTGTCCATCTGTCATCCGGA 58.433 50.000 6.61 6.61 0.00 5.14
2336 3282 1.753368 CGGAGGCTTCCATCTCTCCC 61.753 65.000 16.07 0.00 44.26 4.30
2342 3288 0.462759 CTTCCATCTCTCCCGTTGGC 60.463 60.000 0.00 0.00 0.00 4.52
2359 3305 2.672996 CCCCCGTGAACCTGCTTG 60.673 66.667 0.00 0.00 0.00 4.01
2360 3306 3.365265 CCCCGTGAACCTGCTTGC 61.365 66.667 0.00 0.00 0.00 4.01
2367 3313 2.225467 GTGAACCTGCTTGCTCTTTCT 58.775 47.619 0.00 0.00 0.00 2.52
2377 3323 4.202441 GCTTGCTCTTTCTTCCATGGATA 58.798 43.478 17.06 4.00 0.00 2.59
2385 3331 3.407424 TCTTCCATGGATAGATTGCCG 57.593 47.619 17.06 0.00 0.00 5.69
2386 3332 1.808945 CTTCCATGGATAGATTGCCGC 59.191 52.381 17.06 0.00 0.00 6.53
2404 3350 2.932614 CCGCTCTTCCATTAAGTGACAG 59.067 50.000 0.00 0.00 36.51 3.51
2413 3359 4.223032 TCCATTAAGTGACAGACCCTTCTC 59.777 45.833 0.00 0.00 0.00 2.87
2416 3362 0.540830 AGTGACAGACCCTTCTCGCT 60.541 55.000 0.00 0.00 0.00 4.93
2421 3367 1.134670 ACAGACCCTTCTCGCTATTGC 60.135 52.381 0.00 0.00 0.00 3.56
2425 3371 1.134371 ACCCTTCTCGCTATTGCTTCC 60.134 52.381 0.00 0.00 36.97 3.46
2428 3374 0.810031 TTCTCGCTATTGCTTCCGCC 60.810 55.000 0.00 0.00 36.97 6.13
2439 3385 0.107459 GCTTCCGCCTCTTCAATCCT 60.107 55.000 0.00 0.00 0.00 3.24
2440 3386 1.680249 GCTTCCGCCTCTTCAATCCTT 60.680 52.381 0.00 0.00 0.00 3.36
2455 3401 3.795688 ATCCTTTGTCCTTCTCTTGCA 57.204 42.857 0.00 0.00 0.00 4.08
2461 3407 5.452356 CCTTTGTCCTTCTCTTGCATTGTTT 60.452 40.000 0.00 0.00 0.00 2.83
2464 3410 2.226437 TCCTTCTCTTGCATTGTTTCGC 59.774 45.455 0.00 0.00 0.00 4.70
2473 3419 1.007849 ATTGTTTCGCGCCAACCAC 60.008 52.632 15.69 0.00 0.00 4.16
2476 3422 1.007849 GTTTCGCGCCAACCACAAT 60.008 52.632 0.00 0.00 0.00 2.71
2482 3428 0.102844 GCGCCAACCACAATGCATAT 59.897 50.000 0.00 0.00 0.00 1.78
2509 3455 2.480419 CTGGACCTGTACAGCTTTTTCG 59.520 50.000 17.86 4.48 34.31 3.46
2518 3464 1.798813 ACAGCTTTTTCGTCATCGGAC 59.201 47.619 0.00 0.00 40.77 4.79
2539 3485 0.673644 CCTCCGCGAACCAAGACAAT 60.674 55.000 8.23 0.00 0.00 2.71
2546 3492 1.737793 CGAACCAAGACAATAGCCACC 59.262 52.381 0.00 0.00 0.00 4.61
2548 3494 2.789409 ACCAAGACAATAGCCACCTC 57.211 50.000 0.00 0.00 0.00 3.85
2560 3506 1.202580 AGCCACCTCGATAATGCAGTC 60.203 52.381 0.00 0.00 0.00 3.51
2570 3516 1.131638 TAATGCAGTCTGGGGGCTAG 58.868 55.000 1.14 0.00 0.00 3.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 7.228706 GTCTTATTTGAGGAAGTTTTCTCACCA 59.771 37.037 2.32 0.00 39.43 4.17
43 44 4.635699 ACCGGTCTTATTTGAGGAAGTT 57.364 40.909 0.00 0.00 0.00 2.66
44 45 5.750352 TTACCGGTCTTATTTGAGGAAGT 57.250 39.130 12.40 0.00 0.00 3.01
78 79 2.533129 GCATCTTCTATTGCGCTTTTGC 59.467 45.455 9.73 1.35 43.23 3.68
92 93 6.412072 CGAAAAACGATTTCCTATGCATCTTC 59.588 38.462 0.19 0.00 45.77 2.87
117 118 5.286558 GTGTCGTTACAAGCTCTAGTTCATC 59.713 44.000 0.00 0.00 37.36 2.92
245 246 2.584391 AAGGGCGGCTCTCGAGTTT 61.584 57.895 13.13 0.00 42.43 2.66
246 247 2.997897 AAGGGCGGCTCTCGAGTT 60.998 61.111 13.13 0.00 42.43 3.01
291 292 3.056393 TCATGGTGTTAGTTGGTAGACCG 60.056 47.826 0.00 0.00 39.43 4.79
313 314 7.854337 TGATAGGTTTTCTATTTTACCGGTCT 58.146 34.615 12.40 0.00 38.71 3.85
334 335 6.640499 CGCAAGAAAAATGTTTGTCCTTGATA 59.360 34.615 10.87 0.00 43.02 2.15
339 340 3.123050 GCGCAAGAAAAATGTTTGTCCT 58.877 40.909 0.30 0.00 43.02 3.85
341 342 4.713854 ATGCGCAAGAAAAATGTTTGTC 57.286 36.364 17.11 0.00 43.02 3.18
347 348 5.104374 AGTGGATTATGCGCAAGAAAAATG 58.896 37.500 17.11 0.00 43.02 2.32
353 354 2.938451 CTCAAGTGGATTATGCGCAAGA 59.062 45.455 17.11 6.31 43.02 3.02
354 355 2.540361 GCTCAAGTGGATTATGCGCAAG 60.540 50.000 17.11 3.11 43.44 4.01
404 405 5.147162 CGCAATCAAGAAAGGTTGTCTAAC 58.853 41.667 0.00 0.00 36.04 2.34
408 409 2.319472 GCGCAATCAAGAAAGGTTGTC 58.681 47.619 0.30 0.00 0.00 3.18
411 412 0.240945 CGGCGCAATCAAGAAAGGTT 59.759 50.000 10.83 0.00 0.00 3.50
425 426 0.237761 AGTATACATCGAGTCGGCGC 59.762 55.000 13.54 0.00 0.00 6.53
448 449 6.721318 TCTTATATGTATGGGGGAGCAATTC 58.279 40.000 0.00 0.00 0.00 2.17
474 638 4.018506 TCATGGGCTTGTATCAAGAGGAAA 60.019 41.667 12.77 0.00 0.00 3.13
503 667 2.830651 TTTGTGTGGTGGGGTTAGTT 57.169 45.000 0.00 0.00 0.00 2.24
505 669 4.295141 TCTATTTGTGTGGTGGGGTTAG 57.705 45.455 0.00 0.00 0.00 2.34
506 670 4.289934 TGATCTATTTGTGTGGTGGGGTTA 59.710 41.667 0.00 0.00 0.00 2.85
507 671 3.075283 TGATCTATTTGTGTGGTGGGGTT 59.925 43.478 0.00 0.00 0.00 4.11
509 673 3.364460 TGATCTATTTGTGTGGTGGGG 57.636 47.619 0.00 0.00 0.00 4.96
523 698 7.008941 GGTACTAGAAACTACCCCATGATCTA 58.991 42.308 0.00 0.00 0.00 1.98
534 709 2.180397 GTGCGCGGTACTAGAAACTAC 58.820 52.381 8.83 0.00 0.00 2.73
541 716 2.578713 CCGTGTGCGCGGTACTAG 60.579 66.667 15.19 0.00 46.11 2.57
573 1320 2.891941 CTTAAGCAGCATGGCCCGGA 62.892 60.000 0.73 0.00 35.86 5.14
636 1383 4.141756 TGTGGCTGTCAATTGGAATTTTGT 60.142 37.500 5.42 0.00 0.00 2.83
721 1469 5.965334 CGTTTGGAACATCGAATTCCTATTG 59.035 40.000 24.52 13.32 45.14 1.90
766 1541 7.507277 TGAGATTACCACATAGCATCTCTAGTT 59.493 37.037 8.52 0.00 40.34 2.24
790 1565 4.036734 GCAACTTGGTGACTTGAGATTTGA 59.963 41.667 0.00 0.00 0.00 2.69
797 1572 3.281727 AAGAGCAACTTGGTGACTTGA 57.718 42.857 0.00 0.00 37.45 3.02
810 1585 4.382685 CGATTTGGGACTACCTAAGAGCAA 60.383 45.833 0.00 0.00 37.39 3.91
826 1601 3.705604 ACTTTTGTGACTTGCGATTTGG 58.294 40.909 0.00 0.00 0.00 3.28
920 1702 3.181524 CCAATTCGGTAGCACTTTACGTG 60.182 47.826 0.00 0.00 46.58 4.49
954 1736 3.612517 CTGTGTAGTGCAGCCTTCA 57.387 52.632 0.00 0.00 0.00 3.02
967 1749 4.823989 GCAATGGGATTAATAGAGCTGTGT 59.176 41.667 0.00 0.00 0.00 3.72
976 1758 5.963092 TGGATTGGAGCAATGGGATTAATA 58.037 37.500 0.00 0.00 33.90 0.98
1065 1848 3.195698 GTCCGGCCGTCTGCATTC 61.196 66.667 26.12 0.99 43.89 2.67
1086 1869 0.598158 TGCCTACGACGGTTGTTGTC 60.598 55.000 6.30 0.00 41.91 3.18
1125 1908 2.992114 AGGTGCTTCGCGAGGTCT 60.992 61.111 19.98 11.79 0.00 3.85
1155 1938 1.657751 GGAATTCGAAGGCCAGCACC 61.658 60.000 5.01 0.00 0.00 5.01
1357 2140 4.728110 TGGCATCTGCTTGGCGCT 62.728 61.111 7.64 0.00 44.63 5.92
1751 2696 4.142049 ACAAAGCATAGCTCTCACTACCTC 60.142 45.833 0.00 0.00 38.25 3.85
1755 2700 4.808414 ACACAAAGCATAGCTCTCACTA 57.192 40.909 0.00 0.00 38.25 2.74
1775 2720 5.114780 GGAATTAAGACCGGAAGAGGTAAC 58.885 45.833 9.46 0.00 46.09 2.50
1875 2821 2.363306 TGAACCACCTGACTGCATTT 57.637 45.000 0.00 0.00 0.00 2.32
1895 2841 9.448294 GAATAATTTGTGTAACGTGTGGTTAAA 57.552 29.630 0.00 0.00 42.50 1.52
1921 2867 1.929806 TAGCTAGGCACGGTGTCACG 61.930 60.000 15.98 6.23 40.31 4.35
1924 2870 1.854227 GATTAGCTAGGCACGGTGTC 58.146 55.000 4.16 4.16 0.00 3.67
1927 2873 1.000163 CATCGATTAGCTAGGCACGGT 60.000 52.381 0.00 0.00 0.00 4.83
1930 2876 1.063806 CGCATCGATTAGCTAGGCAC 58.936 55.000 0.00 0.00 0.00 5.01
1932 2878 0.667487 TGCGCATCGATTAGCTAGGC 60.667 55.000 5.66 10.07 0.00 3.93
1954 2900 2.949678 CGACGATCAGCGAACGGG 60.950 66.667 11.39 1.98 44.57 5.28
1963 2909 2.423290 TTTCGTGGGTGCGACGATCA 62.423 55.000 0.00 0.00 43.21 2.92
1966 2912 1.735198 GATTTCGTGGGTGCGACGA 60.735 57.895 0.00 0.00 42.20 4.20
1971 2917 0.521735 GTGGAAGATTTCGTGGGTGC 59.478 55.000 0.00 0.00 0.00 5.01
1972 2918 1.165270 GGTGGAAGATTTCGTGGGTG 58.835 55.000 0.00 0.00 0.00 4.61
1973 2919 0.321298 CGGTGGAAGATTTCGTGGGT 60.321 55.000 0.00 0.00 0.00 4.51
2008 2954 5.720371 TTATAGAGGAGATCAAGCAGCTC 57.280 43.478 0.00 0.00 0.00 4.09
2011 2957 5.184864 ACCGATTATAGAGGAGATCAAGCAG 59.815 44.000 0.00 0.00 0.00 4.24
2026 2972 0.389296 CGCCGCATGGACCGATTATA 60.389 55.000 0.00 0.00 37.49 0.98
2035 2981 2.730733 GATCTCTCGCCGCATGGA 59.269 61.111 0.00 0.00 37.49 3.41
2042 2988 1.281899 CACGAAAAGGATCTCTCGCC 58.718 55.000 0.00 0.00 34.70 5.54
2043 2989 1.281899 CCACGAAAAGGATCTCTCGC 58.718 55.000 0.00 0.00 34.70 5.03
2047 2993 2.979240 AGAAGCCACGAAAAGGATCTC 58.021 47.619 0.00 0.00 0.00 2.75
2052 2998 2.902065 GCTAAGAAGCCACGAAAAGG 57.098 50.000 0.00 0.00 43.40 3.11
2065 3011 4.040339 TCTGTGATTGTGGACAAGCTAAGA 59.960 41.667 9.04 8.52 42.27 2.10
2074 3020 2.072298 GACTGCTCTGTGATTGTGGAC 58.928 52.381 0.00 0.00 0.00 4.02
2075 3021 1.002430 GGACTGCTCTGTGATTGTGGA 59.998 52.381 0.00 0.00 0.00 4.02
2084 3030 4.958509 CATATTGAGATGGACTGCTCTGT 58.041 43.478 0.00 0.00 32.44 3.41
2110 3056 4.597079 CAGCACAACTCAACGTACAAAAT 58.403 39.130 0.00 0.00 0.00 1.82
2121 3067 0.749091 ACAGCTTGCAGCACAACTCA 60.749 50.000 0.00 0.00 45.56 3.41
2122 3068 0.317603 CACAGCTTGCAGCACAACTC 60.318 55.000 0.00 0.00 45.56 3.01
2123 3069 1.731700 CACAGCTTGCAGCACAACT 59.268 52.632 0.00 0.00 45.56 3.16
2124 3070 4.314096 CACAGCTTGCAGCACAAC 57.686 55.556 0.00 0.00 45.56 3.32
2149 3095 3.751246 GAGCTGGGCGCATGCAAA 61.751 61.111 19.57 0.00 45.35 3.68
2158 3104 1.648467 CGGTTAAAGCAGAGCTGGGC 61.648 60.000 0.00 0.00 39.62 5.36
2159 3105 1.026718 CCGGTTAAAGCAGAGCTGGG 61.027 60.000 0.00 0.00 39.62 4.45
2160 3106 0.036388 TCCGGTTAAAGCAGAGCTGG 60.036 55.000 0.00 0.00 39.62 4.85
2173 3119 2.034879 CAGCTGCAACGATCCGGTT 61.035 57.895 0.00 0.00 0.00 4.44
2179 3125 0.036164 TGTTACCCAGCTGCAACGAT 59.964 50.000 8.66 0.00 0.00 3.73
2188 3134 1.228429 TTGCCAGGTGTTACCCAGC 60.228 57.895 0.00 0.00 39.75 4.85
2190 3136 1.228429 GCTTGCCAGGTGTTACCCA 60.228 57.895 0.00 0.00 39.75 4.51
2191 3137 0.960861 GAGCTTGCCAGGTGTTACCC 60.961 60.000 0.00 0.00 39.75 3.69
2197 3143 2.045536 GGAGGAGCTTGCCAGGTG 60.046 66.667 0.00 0.00 0.00 4.00
2198 3144 3.334054 GGGAGGAGCTTGCCAGGT 61.334 66.667 0.00 0.00 0.00 4.00
2214 3160 1.237285 CCAGGAAGGTGCGTTCTTGG 61.237 60.000 17.11 17.11 44.52 3.61
2263 3209 4.464597 GGGGCTACATCAATAGTAGGAGAG 59.535 50.000 0.00 0.00 39.42 3.20
2273 3219 0.180406 GTGGACGGGGCTACATCAAT 59.820 55.000 0.00 0.00 0.00 2.57
2293 3239 2.290260 TGACAGATGGACAAAGGCGAAT 60.290 45.455 0.00 0.00 0.00 3.34
2297 3243 2.019984 GGATGACAGATGGACAAAGGC 58.980 52.381 0.00 0.00 0.00 4.35
2310 3256 0.982852 ATGGAAGCCTCCGGATGACA 60.983 55.000 11.34 3.90 45.85 3.58
2311 3257 0.250081 GATGGAAGCCTCCGGATGAC 60.250 60.000 11.34 0.33 45.85 3.06
2320 3266 0.618968 AACGGGAGAGATGGAAGCCT 60.619 55.000 0.00 0.00 0.00 4.58
2325 3271 2.367202 GGCCAACGGGAGAGATGGA 61.367 63.158 0.00 0.00 34.96 3.41
2342 3288 2.672996 CAAGCAGGTTCACGGGGG 60.673 66.667 0.00 0.00 0.00 5.40
2346 3292 0.947244 AAAGAGCAAGCAGGTTCACG 59.053 50.000 0.00 0.00 0.00 4.35
2347 3293 2.225467 AGAAAGAGCAAGCAGGTTCAC 58.775 47.619 0.00 0.00 0.00 3.18
2348 3294 2.645838 AGAAAGAGCAAGCAGGTTCA 57.354 45.000 0.00 0.00 0.00 3.18
2349 3295 2.227626 GGAAGAAAGAGCAAGCAGGTTC 59.772 50.000 0.00 0.00 0.00 3.62
2350 3296 2.234143 GGAAGAAAGAGCAAGCAGGTT 58.766 47.619 0.00 0.00 0.00 3.50
2351 3297 1.143684 TGGAAGAAAGAGCAAGCAGGT 59.856 47.619 0.00 0.00 0.00 4.00
2359 3305 5.048852 GCAATCTATCCATGGAAGAAAGAGC 60.049 44.000 20.67 18.04 0.00 4.09
2360 3306 5.472820 GGCAATCTATCCATGGAAGAAAGAG 59.527 44.000 20.67 13.53 0.00 2.85
2367 3313 1.421268 AGCGGCAATCTATCCATGGAA 59.579 47.619 20.67 2.02 0.00 3.53
2377 3323 3.209410 CTTAATGGAAGAGCGGCAATCT 58.791 45.455 1.45 0.00 37.33 2.40
2385 3331 3.935828 GGTCTGTCACTTAATGGAAGAGC 59.064 47.826 0.00 0.00 38.65 4.09
2386 3332 4.223923 AGGGTCTGTCACTTAATGGAAGAG 59.776 45.833 0.00 0.00 38.65 2.85
2421 3367 2.409948 AAGGATTGAAGAGGCGGAAG 57.590 50.000 0.00 0.00 0.00 3.46
2425 3371 1.740025 GGACAAAGGATTGAAGAGGCG 59.260 52.381 0.00 0.00 38.94 5.52
2428 3374 5.803552 AGAGAAGGACAAAGGATTGAAGAG 58.196 41.667 0.00 0.00 38.94 2.85
2439 3385 5.591099 GAAACAATGCAAGAGAAGGACAAA 58.409 37.500 0.00 0.00 0.00 2.83
2440 3386 4.261155 CGAAACAATGCAAGAGAAGGACAA 60.261 41.667 0.00 0.00 0.00 3.18
2455 3401 1.007849 GTGGTTGGCGCGAAACAAT 60.008 52.632 24.80 0.00 0.00 2.71
2461 3407 4.036804 GCATTGTGGTTGGCGCGA 62.037 61.111 12.10 0.00 0.00 5.87
2464 3410 2.618241 AGTATATGCATTGTGGTTGGCG 59.382 45.455 3.54 0.00 0.00 5.69
2473 3419 3.328931 AGGTCCAGGGAGTATATGCATTG 59.671 47.826 3.54 0.00 0.00 2.82
2476 3422 2.329267 CAGGTCCAGGGAGTATATGCA 58.671 52.381 0.00 0.00 0.00 3.96
2482 3428 1.618888 GCTGTACAGGTCCAGGGAGTA 60.619 57.143 23.95 0.00 0.00 2.59
2539 3485 2.035961 GACTGCATTATCGAGGTGGCTA 59.964 50.000 0.00 0.00 0.00 3.93
2546 3492 1.270518 CCCCCAGACTGCATTATCGAG 60.271 57.143 0.00 0.00 0.00 4.04
2548 3494 0.886490 GCCCCCAGACTGCATTATCG 60.886 60.000 0.00 0.00 0.00 2.92
2560 3506 2.439104 GGAGTCAGCTAGCCCCCAG 61.439 68.421 12.13 0.00 0.00 4.45
2570 3516 4.593864 GATCCCGCCGGAGTCAGC 62.594 72.222 5.05 0.00 43.12 4.26


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

AutoCloner maintained by Alex Coulton.