Multiple sequence alignment - TraesCS3B01G013300

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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 TraesCS3B01G013300 chr3B 100.000 3844 0 0 1 3844 5956049 5952206 0.000000e+00 7099
1 TraesCS3B01G013300 chr3D 89.450 3327 220 66 7 3276 777323 774071 0.000000e+00 4078
2 TraesCS3B01G013300 chr3D 75.105 478 43 39 1 429 778006 777556 1.850000e-33 154
3 TraesCS3B01G013300 chr3A 87.063 3401 265 93 1 3313 8862550 8865863 0.000000e+00 3681
4 TraesCS3B01G013300 chr3A 91.139 316 23 4 3532 3844 8866151 8866464 1.280000e-114 424
5 TraesCS3B01G013300 chr3A 76.639 244 21 16 3315 3536 8865897 8866126 6.790000e-18 102


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 TraesCS3B01G013300 chr3B 5952206 5956049 3843 True 7099.000000 7099 100.0000 1 3844 1 chr3B.!!$R1 3843
1 TraesCS3B01G013300 chr3D 774071 778006 3935 True 2116.000000 4078 82.2775 1 3276 2 chr3D.!!$R1 3275
2 TraesCS3B01G013300 chr3A 8862550 8866464 3914 False 1402.333333 3681 84.9470 1 3844 3 chr3A.!!$F1 3843

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
472 1155 0.179048 TCATACATTGGCGAGCCCAG 60.179 55.0 12.05 3.96 46.39 4.45 F
2038 2797 0.179081 GCCCGGTCTTCAGATGTACC 60.179 60.0 0.00 0.00 0.00 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2399 3167 0.466372 GGTAGAAGCTTGGGATGGGC 60.466 60.0 2.1 0.0 0.00 5.36 R
3663 4527 0.237761 CTGCTTGCTTGTGCTGTCTC 59.762 55.0 0.0 0.0 40.48 3.36 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
66 745 4.717233 TTGGAATGTGGTGCATGATAAC 57.283 40.909 0.00 0.00 37.96 1.89
100 780 4.808364 TCAAAACTACCAACAGCAAATTGC 59.192 37.500 10.41 10.41 45.46 3.56
164 844 0.179240 CATGCTTGAACTCGACACGC 60.179 55.000 0.00 0.00 34.04 5.34
167 847 3.321723 CTTGAACTCGACACGCGCG 62.322 63.158 30.96 30.96 40.61 6.86
255 935 3.554934 TGCATGACCAAACTCTTTCAGT 58.445 40.909 0.00 0.00 36.64 3.41
256 936 4.713553 TGCATGACCAAACTCTTTCAGTA 58.286 39.130 0.00 0.00 32.30 2.74
257 937 4.515191 TGCATGACCAAACTCTTTCAGTAC 59.485 41.667 0.00 0.00 32.30 2.73
258 938 4.515191 GCATGACCAAACTCTTTCAGTACA 59.485 41.667 0.00 0.00 32.30 2.90
259 939 5.560953 GCATGACCAAACTCTTTCAGTACAC 60.561 44.000 0.00 0.00 32.30 2.90
276 956 6.202188 TCAGTACACTAAAGCAAGCTTTGTAC 59.798 38.462 25.86 25.86 44.84 2.90
353 1036 2.568062 TCACTAACGGGGTCATAGCAAA 59.432 45.455 0.00 0.00 0.00 3.68
354 1037 2.676342 CACTAACGGGGTCATAGCAAAC 59.324 50.000 0.00 0.00 0.00 2.93
355 1038 2.285977 CTAACGGGGTCATAGCAAACC 58.714 52.381 0.00 0.00 34.64 3.27
407 1090 1.251251 GGCATGCAGTTCCAAGAGTT 58.749 50.000 21.36 0.00 0.00 3.01
467 1150 9.254133 CTCCTAATATAATCATACATTGGCGAG 57.746 37.037 0.00 0.00 0.00 5.03
472 1155 0.179048 TCATACATTGGCGAGCCCAG 60.179 55.000 12.05 3.96 46.39 4.45
492 1175 7.504911 AGCCCAGCAAATATATATGATCCAATC 59.495 37.037 0.00 0.00 0.00 2.67
516 1199 5.082059 CGAGATTTGCATGTGTTGTCTTAC 58.918 41.667 0.00 0.00 0.00 2.34
517 1200 5.106948 CGAGATTTGCATGTGTTGTCTTACT 60.107 40.000 0.00 0.00 0.00 2.24
529 1212 5.692654 GTGTTGTCTTACTCTCTGGTTCTTC 59.307 44.000 0.00 0.00 0.00 2.87
531 1214 4.480115 TGTCTTACTCTCTGGTTCTTCCA 58.520 43.478 0.00 0.00 45.01 3.53
539 1222 7.693969 ACTCTCTGGTTCTTCCATTTATTTG 57.306 36.000 0.00 0.00 46.12 2.32
542 1225 6.434028 TCTCTGGTTCTTCCATTTATTTGGTG 59.566 38.462 0.00 0.00 46.12 4.17
543 1226 6.074648 TCTGGTTCTTCCATTTATTTGGTGT 58.925 36.000 0.00 0.00 46.12 4.16
545 1228 5.600484 TGGTTCTTCCATTTATTTGGTGTGT 59.400 36.000 0.00 0.00 41.93 3.72
547 1230 7.040062 TGGTTCTTCCATTTATTTGGTGTGTAG 60.040 37.037 0.00 0.00 41.93 2.74
551 1234 5.565509 TCCATTTATTTGGTGTGTAGCAGA 58.434 37.500 0.00 0.00 38.01 4.26
552 1235 6.186957 TCCATTTATTTGGTGTGTAGCAGAT 58.813 36.000 0.00 0.00 38.01 2.90
566 1252 1.009829 GCAGATCGCGAGGTCAATTT 58.990 50.000 16.66 0.00 45.97 1.82
662 1348 3.096461 CGATAATACCGACGGCGAATAG 58.904 50.000 15.16 0.00 40.82 1.73
667 1353 1.369689 CCGACGGCGAATAGGTACG 60.370 63.158 15.16 5.79 40.82 3.67
668 1354 1.643292 CGACGGCGAATAGGTACGA 59.357 57.895 16.62 0.00 40.82 3.43
702 1388 5.848369 TGGAGGATCTGGATTAGAATGACAT 59.152 40.000 0.00 0.00 39.30 3.06
764 1450 4.024133 TGTCAAACTCCACACATCAATTCG 60.024 41.667 0.00 0.00 0.00 3.34
841 1543 4.610945 ACAAGATTTTCTCTTTGTTGCGG 58.389 39.130 0.00 0.00 41.60 5.69
865 1568 4.274950 TGTCGGTTTCAATTCTTCCAAGAC 59.725 41.667 0.00 0.00 34.13 3.01
882 1585 4.144297 CAAGACTGGAAAATCCCAACTCA 58.856 43.478 0.00 0.00 35.03 3.41
1067 1774 4.570926 TCTTCCATTGTCCCTCCATCTAT 58.429 43.478 0.00 0.00 0.00 1.98
1117 1824 4.414999 GGTGACCATTTAACGGAACTTC 57.585 45.455 0.00 0.00 0.00 3.01
1119 1826 3.816523 GTGACCATTTAACGGAACTTCCA 59.183 43.478 8.59 0.00 35.91 3.53
1171 1878 2.429478 CACAGTCTGACAATGGCATCA 58.571 47.619 10.88 0.00 0.00 3.07
1190 1897 4.623932 TCACAGAACCATTAGAAGCTGT 57.376 40.909 0.00 0.00 37.09 4.40
1274 1981 3.500448 TGATGGTAAGCTTGTTGTGGA 57.500 42.857 9.86 0.00 0.00 4.02
1295 2002 7.721842 TGTGGATTATGGTTCAGTTTAACTTGA 59.278 33.333 0.00 0.00 0.00 3.02
1298 2005 8.956426 GGATTATGGTTCAGTTTAACTTGATGA 58.044 33.333 0.00 0.00 0.00 2.92
1302 2009 8.641498 ATGGTTCAGTTTAACTTGATGAATCT 57.359 30.769 0.00 0.00 33.23 2.40
1317 2029 9.270576 CTTGATGAATCTTTAACTGTTTGATCG 57.729 33.333 0.00 0.00 0.00 3.69
1343 2078 3.067320 GGATGGAGCAGCCTAATGAAAAC 59.933 47.826 0.00 0.00 36.92 2.43
1400 2135 2.781757 TGAAGCCTCTCCCATCATCATT 59.218 45.455 0.00 0.00 0.00 2.57
1414 2149 3.525537 TCATCATTGAGAAAGGAGACGC 58.474 45.455 0.00 0.00 0.00 5.19
1425 2160 2.740714 GGAGACGCGGTGCAACATC 61.741 63.158 12.47 0.00 39.98 3.06
1443 2178 3.058708 ACATCGTGTTGAAATCAGTGCAG 60.059 43.478 0.00 0.00 0.00 4.41
1684 2425 9.349713 GAAGAAGATGAAGGTAATCTCTCTCTA 57.650 37.037 0.00 0.00 33.17 2.43
1686 2427 9.300681 AGAAGATGAAGGTAATCTCTCTCTATG 57.699 37.037 0.00 0.00 33.17 2.23
1740 2483 9.881773 TTCCTTGCCCATTATCTTTATAAGATT 57.118 29.630 7.19 0.00 45.75 2.40
1766 2509 6.737254 TTCCTTTAGCATAACAGTTAGCAC 57.263 37.500 13.79 1.36 0.00 4.40
1771 2514 8.673711 CCTTTAGCATAACAGTTAGCACAATTA 58.326 33.333 13.79 0.20 0.00 1.40
1810 2568 0.179197 TCTTACAGAGAAGCGCGTCG 60.179 55.000 17.57 6.44 0.00 5.12
2014 2773 4.122337 TGGAAAGACTACTACTGTCCCA 57.878 45.455 0.00 0.00 40.12 4.37
2038 2797 0.179081 GCCCGGTCTTCAGATGTACC 60.179 60.000 0.00 0.00 0.00 3.34
2080 2839 6.480320 GCAGAGAGGTATATGTTACTTTGTGG 59.520 42.308 0.00 0.00 0.00 4.17
2097 2856 6.435277 ACTTTGTGGCATGAAAGATACAAGAT 59.565 34.615 21.87 2.01 34.02 2.40
2103 2862 5.474532 GGCATGAAAGATACAAGATATGGCA 59.525 40.000 0.00 0.00 38.99 4.92
2109 2868 5.234466 AGATACAAGATATGGCAAGGGAC 57.766 43.478 0.00 0.00 0.00 4.46
2132 2891 2.171659 GGGGAGAGGTTCTCATCCTTTC 59.828 54.545 8.23 0.00 45.12 2.62
2205 2968 2.907892 TGGAGGAACAGAGGATTCAGT 58.092 47.619 0.00 0.00 0.00 3.41
2210 2973 3.262915 AGGAACAGAGGATTCAGTTGGAG 59.737 47.826 0.00 0.00 33.74 3.86
2242 3006 7.447374 TGAAGGTAATTCGTCATTGTTTCAT 57.553 32.000 0.00 0.00 41.14 2.57
2251 3015 5.389778 TCGTCATTGTTTCATCATTTTCCG 58.610 37.500 0.00 0.00 0.00 4.30
2298 3066 7.384439 TGTGTACATGTTGAAGAGTTTTCAA 57.616 32.000 2.30 4.78 36.21 2.69
2308 3076 7.659390 TGTTGAAGAGTTTTCAAAACCAAACAT 59.341 29.630 9.49 0.00 39.76 2.71
2399 3167 0.109597 GCCTGACATTCAAAGCCACG 60.110 55.000 0.00 0.00 0.00 4.94
2462 3230 5.051153 GCTGAATACAAGAAGGTAGGTAGC 58.949 45.833 0.00 0.00 0.00 3.58
2463 3231 5.602628 CTGAATACAAGAAGGTAGGTAGCC 58.397 45.833 0.00 0.00 0.00 3.93
2496 3264 8.456214 AAATATCGATTTGCTAGCCCATTGGC 62.456 42.308 13.29 0.00 44.88 4.52
2528 3296 8.582437 TCTTCAGAAAATGCTTTGATCTTGAAT 58.418 29.630 0.00 0.00 0.00 2.57
2531 3299 8.464404 TCAGAAAATGCTTTGATCTTGAATAGG 58.536 33.333 0.00 0.00 0.00 2.57
2533 3301 8.465201 AGAAAATGCTTTGATCTTGAATAGGTC 58.535 33.333 0.00 0.00 34.35 3.85
2552 3320 4.641094 AGGTCTTAGTACTGATTCCTCACG 59.359 45.833 5.39 0.00 0.00 4.35
2554 3322 3.064958 TCTTAGTACTGATTCCTCACGCG 59.935 47.826 3.53 3.53 0.00 6.01
2563 3331 1.717194 TTCCTCACGCGTAATGAACC 58.283 50.000 13.44 0.00 0.00 3.62
2642 3410 2.359850 GCCGCCATGAACACCTCA 60.360 61.111 0.00 0.00 38.81 3.86
2709 3477 3.106407 GCGACAGACACGACAGCC 61.106 66.667 0.00 0.00 0.00 4.85
2719 3487 1.155889 CACGACAGCCACTGCAAATA 58.844 50.000 0.00 0.00 41.13 1.40
2786 3557 0.885879 CTGCAGCAAGCTCATCCAAA 59.114 50.000 0.00 0.00 45.94 3.28
2793 3564 2.929592 GCAAGCTCATCCAAAAAGCAGG 60.930 50.000 0.00 0.00 38.51 4.85
2794 3565 1.553706 AGCTCATCCAAAAAGCAGGG 58.446 50.000 0.00 0.00 38.51 4.45
2807 3581 4.100479 CAGGGCAAGAACCATGCA 57.900 55.556 0.00 0.00 45.60 3.96
2844 3618 2.100631 AACATCGCCGTGTGCTAGC 61.101 57.895 8.10 8.10 38.05 3.42
2870 3644 0.461961 ATCCGCTTCTTCTTCCTCCG 59.538 55.000 0.00 0.00 0.00 4.63
2871 3645 0.898789 TCCGCTTCTTCTTCCTCCGT 60.899 55.000 0.00 0.00 0.00 4.69
2881 3655 0.173708 CTTCCTCCGTCAGTACCTGC 59.826 60.000 0.00 0.00 0.00 4.85
2906 3680 3.107601 AGTGCTAGATCCTTGTGCCTTA 58.892 45.455 0.00 0.00 0.00 2.69
2910 3684 3.251972 GCTAGATCCTTGTGCCTTAATGC 59.748 47.826 0.00 0.00 0.00 3.56
2917 3691 2.875087 TGTGCCTTAATGCATCATGC 57.125 45.000 8.72 1.35 44.30 4.06
2925 3699 5.227908 CCTTAATGCATCATGCTGAAATCC 58.772 41.667 11.84 0.00 45.31 3.01
2938 3712 1.273041 TGAAATCCGAGTCCAGGAGGA 60.273 52.381 0.00 0.00 41.66 3.71
2939 3713 1.410882 GAAATCCGAGTCCAGGAGGAG 59.589 57.143 2.48 0.00 46.92 3.69
2940 3714 0.397816 AATCCGAGTCCAGGAGGAGG 60.398 60.000 2.48 0.56 46.92 4.30
2941 3715 1.289982 ATCCGAGTCCAGGAGGAGGA 61.290 60.000 8.69 8.69 46.92 3.71
2980 3754 6.954684 TCTCCCTAAGTTATGAGAGTGACTTT 59.045 38.462 7.75 0.00 34.46 2.66
2984 3758 5.470047 AAGTTATGAGAGTGACTTTCGGT 57.530 39.130 0.00 0.00 0.00 4.69
3028 3804 9.450807 GTGGCAATTAAGTTATGTCATGATAAC 57.549 33.333 10.10 10.10 38.56 1.89
3053 3829 4.322385 GCACACGGGGTTGCGAAC 62.322 66.667 0.00 0.00 0.00 3.95
3062 3838 4.659874 GTTGCGAACGTGCCGTGG 62.660 66.667 11.40 0.00 39.99 4.94
3087 3863 3.288092 AGGTCAGTCACAAGGGTTTTTC 58.712 45.455 0.00 0.00 0.00 2.29
3106 3882 9.803315 GGTTTTTCTGTCCTAATTATTTCATCC 57.197 33.333 0.00 0.00 0.00 3.51
3173 3950 8.310406 TGTCTCTGTACAGATAATGTTTGTTG 57.690 34.615 25.35 9.66 39.96 3.33
3174 3951 8.147704 TGTCTCTGTACAGATAATGTTTGTTGA 58.852 33.333 25.35 11.76 39.96 3.18
3345 4158 7.815840 TGGTTGTATAATGGGTGTGATATTG 57.184 36.000 0.00 0.00 0.00 1.90
3347 4160 7.284261 TGGTTGTATAATGGGTGTGATATTGTG 59.716 37.037 0.00 0.00 0.00 3.33
3361 4174 6.210385 TGTGATATTGTGGTTTTATGTGGCTT 59.790 34.615 0.00 0.00 0.00 4.35
3368 4181 4.518970 GTGGTTTTATGTGGCTTCTTCTGA 59.481 41.667 0.00 0.00 0.00 3.27
3369 4182 4.761739 TGGTTTTATGTGGCTTCTTCTGAG 59.238 41.667 0.00 0.00 0.00 3.35
3387 4211 6.468333 TCTGAGGAAGAGATTGAATCAGAG 57.532 41.667 8.03 0.00 37.40 3.35
3391 4215 6.386342 TGAGGAAGAGATTGAATCAGAGGAAT 59.614 38.462 8.03 0.00 0.00 3.01
3407 4231 7.950512 TCAGAGGAATCATTTTTACTTGCAAA 58.049 30.769 0.00 0.00 0.00 3.68
3443 4277 3.507162 TTGCCTTGAAACAGAGGATCA 57.493 42.857 0.00 0.00 37.82 2.92
3444 4278 3.726557 TGCCTTGAAACAGAGGATCAT 57.273 42.857 0.00 0.00 37.82 2.45
3446 4280 3.009363 TGCCTTGAAACAGAGGATCATCA 59.991 43.478 10.44 0.00 37.82 3.07
3447 4281 3.376546 GCCTTGAAACAGAGGATCATCAC 59.623 47.826 10.44 0.00 37.82 3.06
3448 4282 3.944015 CCTTGAAACAGAGGATCATCACC 59.056 47.826 10.44 0.00 37.82 4.02
3450 4284 3.942829 TGAAACAGAGGATCATCACCAC 58.057 45.455 10.44 0.00 37.82 4.16
3452 4286 2.260639 ACAGAGGATCATCACCACCT 57.739 50.000 10.44 0.00 37.82 4.00
3453 4287 3.404869 ACAGAGGATCATCACCACCTA 57.595 47.619 10.44 0.00 37.82 3.08
3454 4288 3.933886 ACAGAGGATCATCACCACCTAT 58.066 45.455 10.44 0.00 37.82 2.57
3456 4290 4.346418 ACAGAGGATCATCACCACCTATTC 59.654 45.833 10.44 0.00 37.82 1.75
3457 4291 4.592351 CAGAGGATCATCACCACCTATTCT 59.408 45.833 10.44 0.00 37.82 2.40
3460 4294 4.346418 AGGATCATCACCACCTATTCTGAC 59.654 45.833 0.00 0.00 0.00 3.51
3462 4296 4.743057 TCATCACCACCTATTCTGACTG 57.257 45.455 0.00 0.00 0.00 3.51
3463 4297 4.096681 TCATCACCACCTATTCTGACTGT 58.903 43.478 0.00 0.00 0.00 3.55
3464 4298 4.160439 TCATCACCACCTATTCTGACTGTC 59.840 45.833 0.00 0.00 0.00 3.51
3465 4299 3.506398 TCACCACCTATTCTGACTGTCA 58.494 45.455 10.50 10.50 0.00 3.58
3466 4300 3.511540 TCACCACCTATTCTGACTGTCAG 59.488 47.826 27.73 27.73 45.59 3.51
3467 4301 3.259374 CACCACCTATTCTGACTGTCAGT 59.741 47.826 30.74 18.81 44.58 3.41
3468 4302 3.904339 ACCACCTATTCTGACTGTCAGTT 59.096 43.478 30.74 22.83 44.58 3.16
3469 4303 4.348168 ACCACCTATTCTGACTGTCAGTTT 59.652 41.667 30.74 22.54 44.58 2.66
3470 4304 4.692625 CCACCTATTCTGACTGTCAGTTTG 59.307 45.833 30.74 20.92 44.58 2.93
3471 4305 4.153117 CACCTATTCTGACTGTCAGTTTGC 59.847 45.833 30.74 0.00 44.58 3.68
3472 4306 3.686726 CCTATTCTGACTGTCAGTTTGCC 59.313 47.826 30.74 0.00 44.58 4.52
3473 4307 1.967319 TTCTGACTGTCAGTTTGCCC 58.033 50.000 30.74 0.00 44.58 5.36
3474 4308 0.249868 TCTGACTGTCAGTTTGCCCG 60.250 55.000 30.74 9.85 44.58 6.13
3531 4366 4.562143 GCTCAAGGCAAACAAAATCCAGAT 60.562 41.667 0.00 0.00 41.35 2.90
3536 4371 5.969423 AGGCAAACAAAATCCAGATACATG 58.031 37.500 0.00 0.00 0.00 3.21
3557 4421 7.226441 ACATGGAGATAATTATTGCTGCTACA 58.774 34.615 0.00 0.00 0.00 2.74
3561 4425 6.094603 GGAGATAATTATTGCTGCTACATGGG 59.905 42.308 0.00 0.00 0.00 4.00
3583 4447 4.275936 GGGTATTTGGGACTGAATGATTCG 59.724 45.833 0.18 0.00 0.00 3.34
3585 4449 5.588648 GGTATTTGGGACTGAATGATTCGAA 59.411 40.000 0.00 0.00 0.00 3.71
3616 4480 7.090953 AGGAATTTCGTCAAAACTGTACAAA 57.909 32.000 0.00 0.00 0.00 2.83
3626 4490 9.113876 CGTCAAAACTGTACAAATAATTCCTTC 57.886 33.333 0.00 0.00 0.00 3.46
3667 4531 5.877012 TGAATCCTATGAAAACTGCAGAGAC 59.123 40.000 23.35 9.18 0.00 3.36
3669 4533 4.825422 TCCTATGAAAACTGCAGAGACAG 58.175 43.478 23.35 7.48 43.59 3.51
3684 4549 1.202687 AGACAGCACAAGCAAGCAGTA 60.203 47.619 0.00 0.00 45.49 2.74
3723 4589 4.154015 TCGAAATTCAGCACTTGTGGTATG 59.846 41.667 5.11 0.00 0.00 2.39
3738 4604 7.344612 ACTTGTGGTATGATAACTCCAGACATA 59.655 37.037 0.00 0.00 0.00 2.29
3743 4609 7.563556 TGGTATGATAACTCCAGACATAACAGA 59.436 37.037 0.00 0.00 36.60 3.41
3822 4688 8.877779 CAATCAATCTTAGTTCAGTCCTAGTTG 58.122 37.037 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
229 909 3.446442 AGAGTTTGGTCATGCATCCTT 57.554 42.857 0.00 0.00 0.00 3.36
231 911 3.507233 TGAAAGAGTTTGGTCATGCATCC 59.493 43.478 0.00 0.00 0.00 3.51
255 935 7.148474 GCATAGTACAAAGCTTGCTTTAGTGTA 60.148 37.037 18.52 14.80 0.00 2.90
256 936 6.348540 GCATAGTACAAAGCTTGCTTTAGTGT 60.349 38.462 18.52 15.68 0.00 3.55
257 937 6.024049 GCATAGTACAAAGCTTGCTTTAGTG 58.976 40.000 18.52 11.16 0.00 2.74
258 938 5.940470 AGCATAGTACAAAGCTTGCTTTAGT 59.060 36.000 18.52 18.77 37.12 2.24
259 939 6.428385 AGCATAGTACAAAGCTTGCTTTAG 57.572 37.500 18.52 14.97 37.12 1.85
276 956 8.637281 TTGCAATCATTTGTGATAAAGCATAG 57.363 30.769 0.00 0.00 33.78 2.23
321 1004 6.606796 TGACCCCGTTAGTGACATATAGTTAA 59.393 38.462 0.00 0.00 0.00 2.01
322 1005 6.128486 TGACCCCGTTAGTGACATATAGTTA 58.872 40.000 0.00 0.00 0.00 2.24
323 1006 4.957954 TGACCCCGTTAGTGACATATAGTT 59.042 41.667 0.00 0.00 0.00 2.24
324 1007 4.539726 TGACCCCGTTAGTGACATATAGT 58.460 43.478 0.00 0.00 0.00 2.12
325 1008 5.723672 ATGACCCCGTTAGTGACATATAG 57.276 43.478 0.00 0.00 0.00 1.31
326 1009 5.184479 GCTATGACCCCGTTAGTGACATATA 59.816 44.000 0.00 0.00 0.00 0.86
327 1010 4.021368 GCTATGACCCCGTTAGTGACATAT 60.021 45.833 0.00 0.00 0.00 1.78
340 1023 1.682087 GGACTGGTTTGCTATGACCCC 60.682 57.143 0.00 0.00 34.99 4.95
407 1090 2.364970 CAATTGGGCAGTGTCCTTTGAA 59.635 45.455 16.31 0.36 0.00 2.69
457 1140 3.866379 TTGCTGGGCTCGCCAATGT 62.866 57.895 10.51 0.00 37.98 2.71
459 1142 0.395586 TATTTGCTGGGCTCGCCAAT 60.396 50.000 10.51 3.25 37.98 3.16
461 1144 0.472044 TATATTTGCTGGGCTCGCCA 59.528 50.000 10.51 0.00 37.98 5.69
462 1145 1.826385 ATATATTTGCTGGGCTCGCC 58.174 50.000 0.00 0.00 0.00 5.54
467 1150 7.255730 GGATTGGATCATATATATTTGCTGGGC 60.256 40.741 0.00 0.00 0.00 5.36
472 1155 8.893219 TCTCGGATTGGATCATATATATTTGC 57.107 34.615 0.00 0.00 0.00 3.68
492 1175 2.485426 AGACAACACATGCAAATCTCGG 59.515 45.455 0.00 0.00 0.00 4.63
500 1183 4.309933 CAGAGAGTAAGACAACACATGCA 58.690 43.478 0.00 0.00 0.00 3.96
529 1212 5.895636 TCTGCTACACACCAAATAAATGG 57.104 39.130 0.00 0.00 46.38 3.16
531 1214 5.220854 GCGATCTGCTACACACCAAATAAAT 60.221 40.000 0.00 0.00 41.73 1.40
539 1222 0.867753 CTCGCGATCTGCTACACACC 60.868 60.000 10.36 0.00 43.27 4.16
542 1225 0.592754 GACCTCGCGATCTGCTACAC 60.593 60.000 10.36 0.00 43.27 2.90
543 1226 1.029947 TGACCTCGCGATCTGCTACA 61.030 55.000 10.36 0.65 43.27 2.74
545 1228 1.032794 ATTGACCTCGCGATCTGCTA 58.967 50.000 10.36 0.00 43.27 3.49
547 1230 1.009829 AAATTGACCTCGCGATCTGC 58.990 50.000 10.36 0.00 41.47 4.26
566 1252 3.547746 AGGAGACAAAGGTAACGCAAAA 58.452 40.909 0.00 0.00 46.39 2.44
641 1327 1.973138 ATTCGCCGTCGGTATTATCG 58.027 50.000 13.94 6.76 36.13 2.92
662 1348 3.698040 TCCTCCAATCAGTTACTCGTACC 59.302 47.826 0.00 0.00 0.00 3.34
667 1353 4.651503 TCCAGATCCTCCAATCAGTTACTC 59.348 45.833 0.00 0.00 0.00 2.59
668 1354 4.624913 TCCAGATCCTCCAATCAGTTACT 58.375 43.478 0.00 0.00 0.00 2.24
702 1388 2.696707 ACCGATAGCGACCAAATTAGGA 59.303 45.455 0.00 0.00 40.82 2.94
764 1450 4.652822 ACTACCTTCCAGGAAAATGACAC 58.347 43.478 2.72 0.00 37.67 3.67
792 1492 2.100916 CCCTTCACGTGGACACTATAGG 59.899 54.545 17.00 2.06 0.00 2.57
841 1543 4.274950 TCTTGGAAGAATTGAAACCGACAC 59.725 41.667 0.00 0.00 30.73 3.67
983 1686 2.679837 CCCATAGTACTGCTGCACAAAG 59.320 50.000 5.39 0.00 0.00 2.77
984 1687 2.039746 ACCCATAGTACTGCTGCACAAA 59.960 45.455 5.39 0.00 0.00 2.83
1067 1774 1.561717 CGGCGTTTCCATGTTGTCGA 61.562 55.000 0.00 0.00 34.01 4.20
1117 1824 0.607217 TCAGCATTGACAGTGCCTGG 60.607 55.000 18.29 9.40 43.50 4.45
1119 1826 1.884579 CTTTCAGCATTGACAGTGCCT 59.115 47.619 18.29 4.47 43.50 4.75
1171 1878 4.973168 TCAACAGCTTCTAATGGTTCTGT 58.027 39.130 0.00 0.00 36.46 3.41
1190 1897 6.888105 TGCTCAGTATCTCCATTTACATCAA 58.112 36.000 0.00 0.00 0.00 2.57
1295 2002 8.446273 CAGTCGATCAAACAGTTAAAGATTCAT 58.554 33.333 0.00 0.00 0.00 2.57
1298 2005 6.934645 TCCAGTCGATCAAACAGTTAAAGATT 59.065 34.615 0.00 0.00 0.00 2.40
1299 2006 6.464222 TCCAGTCGATCAAACAGTTAAAGAT 58.536 36.000 0.00 0.00 0.00 2.40
1300 2007 5.849510 TCCAGTCGATCAAACAGTTAAAGA 58.150 37.500 0.00 0.00 0.00 2.52
1301 2008 6.402550 CCATCCAGTCGATCAAACAGTTAAAG 60.403 42.308 0.00 0.00 0.00 1.85
1302 2009 5.411361 CCATCCAGTCGATCAAACAGTTAAA 59.589 40.000 0.00 0.00 0.00 1.52
1307 2019 3.193263 CTCCATCCAGTCGATCAAACAG 58.807 50.000 0.00 0.00 0.00 3.16
1317 2029 0.833287 TTAGGCTGCTCCATCCAGTC 59.167 55.000 0.00 0.00 37.29 3.51
1343 2078 6.644592 GCTCTGCAGTTATAGAGAACCATTAG 59.355 42.308 14.67 0.00 42.34 1.73
1400 2135 1.289066 CACCGCGTCTCCTTTCTCA 59.711 57.895 4.92 0.00 0.00 3.27
1425 2160 3.187022 TCATCTGCACTGATTTCAACACG 59.813 43.478 0.00 0.00 0.00 4.49
1436 2171 4.694037 TGATTCTCTTGTTCATCTGCACTG 59.306 41.667 0.00 0.00 0.00 3.66
1443 2178 6.892691 ACGTTTCTTGATTCTCTTGTTCATC 58.107 36.000 0.00 0.00 0.00 2.92
1586 2321 0.960364 TGGAATTCTTGTCGCTGGGC 60.960 55.000 5.23 0.00 0.00 5.36
1643 2384 1.767289 TCTTCGTCGAGCTTGTCAAC 58.233 50.000 0.00 0.00 0.00 3.18
1684 2425 4.099881 ACTCATGCAAAACAACAGGAACAT 59.900 37.500 0.00 0.00 0.00 2.71
1686 2427 4.044426 GACTCATGCAAAACAACAGGAAC 58.956 43.478 0.00 0.00 0.00 3.62
1739 2482 9.456147 TGCTAACTGTTATGCTAAAGGAATTAA 57.544 29.630 16.95 0.00 0.00 1.40
1740 2483 8.889717 GTGCTAACTGTTATGCTAAAGGAATTA 58.110 33.333 16.95 0.00 0.00 1.40
1741 2484 7.393234 TGTGCTAACTGTTATGCTAAAGGAATT 59.607 33.333 16.95 0.00 0.00 2.17
1742 2485 6.884295 TGTGCTAACTGTTATGCTAAAGGAAT 59.116 34.615 16.95 0.00 0.00 3.01
1743 2486 6.234920 TGTGCTAACTGTTATGCTAAAGGAA 58.765 36.000 16.95 0.71 0.00 3.36
1782 2525 6.795114 CGCGCTTCTCTGTAAGAAATTTTAAA 59.205 34.615 5.56 0.00 46.34 1.52
1785 2528 4.213482 ACGCGCTTCTCTGTAAGAAATTTT 59.787 37.500 5.73 0.00 46.34 1.82
1810 2568 1.019805 GTGGCTTCCTTGTAGTCGCC 61.020 60.000 0.00 0.00 38.01 5.54
1920 2678 7.618502 AGAGACAGGTGATATAAGCGTATAG 57.381 40.000 5.61 0.00 0.00 1.31
1987 2746 6.183360 GGACAGTAGTAGTCTTTCCATTCGAT 60.183 42.308 0.00 0.00 36.29 3.59
2014 2773 1.134280 CATCTGAAGACCGGGCTTGAT 60.134 52.381 31.83 22.22 0.00 2.57
2080 2839 6.564709 TGCCATATCTTGTATCTTTCATGC 57.435 37.500 0.00 0.00 0.00 4.06
2097 2856 0.988145 CTCCCCTGTCCCTTGCCATA 60.988 60.000 0.00 0.00 0.00 2.74
2103 2862 0.547954 GAACCTCTCCCCTGTCCCTT 60.548 60.000 0.00 0.00 0.00 3.95
2109 2868 1.127343 GGATGAGAACCTCTCCCCTG 58.873 60.000 1.34 0.00 42.73 4.45
2132 2891 5.186996 AGTACTGCAACAAACCATGAAAG 57.813 39.130 0.00 0.00 0.00 2.62
2205 2968 1.742308 ACCTTCAACCTAGCCTCCAA 58.258 50.000 0.00 0.00 0.00 3.53
2210 2973 3.869832 GACGAATTACCTTCAACCTAGCC 59.130 47.826 0.00 0.00 33.10 3.93
2251 3015 0.594110 GAGGACCCGTCGATCATCTC 59.406 60.000 0.00 0.00 0.00 2.75
2265 3029 6.260050 TCTTCAACATGTACACAAAAGAGGAC 59.740 38.462 0.00 0.00 0.00 3.85
2298 3066 9.295825 TGTAATAGATCAGTGAATGTTTGGTTT 57.704 29.630 0.00 0.00 0.00 3.27
2308 3076 9.889128 TCATTCACAATGTAATAGATCAGTGAA 57.111 29.630 15.37 15.37 45.28 3.18
2399 3167 0.466372 GGTAGAAGCTTGGGATGGGC 60.466 60.000 2.10 0.00 0.00 5.36
2488 3256 2.089980 CTGAAGACTGAAGCCAATGGG 58.910 52.381 0.00 0.00 37.18 4.00
2496 3264 6.732154 TCAAAGCATTTTCTGAAGACTGAAG 58.268 36.000 0.00 0.00 35.03 3.02
2497 3265 6.698008 TCAAAGCATTTTCTGAAGACTGAA 57.302 33.333 0.00 0.00 35.03 3.02
2498 3266 6.713903 AGATCAAAGCATTTTCTGAAGACTGA 59.286 34.615 0.00 0.00 35.03 3.41
2499 3267 6.910995 AGATCAAAGCATTTTCTGAAGACTG 58.089 36.000 0.00 0.00 35.03 3.51
2500 3268 7.230108 TCAAGATCAAAGCATTTTCTGAAGACT 59.770 33.333 0.00 0.00 35.03 3.24
2501 3269 7.365741 TCAAGATCAAAGCATTTTCTGAAGAC 58.634 34.615 0.00 0.00 35.03 3.01
2528 3296 5.821470 CGTGAGGAATCAGTACTAAGACCTA 59.179 44.000 0.00 0.00 0.00 3.08
2531 3299 4.352887 GCGTGAGGAATCAGTACTAAGAC 58.647 47.826 0.00 0.00 0.00 3.01
2533 3301 3.181499 ACGCGTGAGGAATCAGTACTAAG 60.181 47.826 12.93 0.00 0.00 2.18
2552 3320 2.729156 GCAAGCAAGAGGTTCATTACGC 60.729 50.000 0.00 0.00 32.07 4.42
2554 3322 3.084786 AGGCAAGCAAGAGGTTCATTAC 58.915 45.455 0.00 0.00 32.07 1.89
2563 3331 0.039437 CAACTGCAGGCAAGCAAGAG 60.039 55.000 19.93 0.00 45.13 2.85
2642 3410 1.380403 CGCTCTCCTCCGATGAGTGT 61.380 60.000 1.18 0.00 36.86 3.55
2709 3477 2.624316 CTGCTGTGGTATTTGCAGTG 57.376 50.000 0.00 0.00 45.31 3.66
2719 3487 3.292936 GCTTGCTGCTGCTGTGGT 61.293 61.111 17.00 0.00 40.48 4.16
2754 3525 0.388134 GCTGCAGGATGTTGTTGCTG 60.388 55.000 17.12 0.00 39.31 4.41
2755 3526 0.824595 TGCTGCAGGATGTTGTTGCT 60.825 50.000 17.12 0.00 39.31 3.91
2756 3527 0.032403 TTGCTGCAGGATGTTGTTGC 59.968 50.000 17.12 0.00 39.31 4.17
2757 3528 1.933500 GCTTGCTGCAGGATGTTGTTG 60.934 52.381 17.12 0.00 42.31 3.33
2758 3529 0.316204 GCTTGCTGCAGGATGTTGTT 59.684 50.000 17.12 0.00 42.31 2.83
2759 3530 0.538977 AGCTTGCTGCAGGATGTTGT 60.539 50.000 17.12 1.64 45.94 3.32
2760 3531 0.170561 GAGCTTGCTGCAGGATGTTG 59.829 55.000 17.12 4.86 45.94 3.33
2761 3532 0.251033 TGAGCTTGCTGCAGGATGTT 60.251 50.000 17.12 13.20 45.94 2.71
2786 3557 0.971386 CATGGTTCTTGCCCTGCTTT 59.029 50.000 0.00 0.00 0.00 3.51
2793 3564 0.388659 TTGTGTGCATGGTTCTTGCC 59.611 50.000 0.00 0.00 39.39 4.52
2794 3565 1.774639 CTTGTGTGCATGGTTCTTGC 58.225 50.000 0.00 0.00 40.55 4.01
2807 3581 1.519455 GAGCGCCGATAGCTTGTGT 60.519 57.895 2.29 0.00 46.13 3.72
2854 3628 0.243907 TGACGGAGGAAGAAGAAGCG 59.756 55.000 0.00 0.00 0.00 4.68
2881 3655 2.935201 GCACAAGGATCTAGCACTGAAG 59.065 50.000 0.00 0.00 0.00 3.02
2917 3691 1.137872 CCTCCTGGACTCGGATTTCAG 59.862 57.143 0.00 0.00 34.57 3.02
2925 3699 1.454847 CCTCCTCCTCCTGGACTCG 60.455 68.421 0.00 0.00 37.46 4.18
2938 3712 3.712016 GAGAAAAAGCCTTCTCCTCCT 57.288 47.619 8.84 0.00 43.73 3.69
2960 3734 6.622549 ACCGAAAGTCACTCTCATAACTTAG 58.377 40.000 0.00 0.00 31.94 2.18
2984 3758 2.026522 CCGCAAACCTCGGTTGAAA 58.973 52.632 1.44 0.00 41.85 2.69
3028 3804 1.068610 CAACCCCGTGTGCATAACTTG 60.069 52.381 0.00 0.00 0.00 3.16
3062 3838 1.374758 CCTTGTGACTGACCTCGCC 60.375 63.158 0.00 0.00 0.00 5.54
3087 3863 8.408601 CAAAGTGGGATGAAATAATTAGGACAG 58.591 37.037 0.00 0.00 0.00 3.51
3106 3882 8.192774 ACATCTGTGAATAAATATGCAAAGTGG 58.807 33.333 0.00 0.00 29.94 4.00
3160 3937 9.665719 AAACCCCATAAATCAACAAACATTATC 57.334 29.630 0.00 0.00 0.00 1.75
3187 3968 9.394767 TGAGTGCACAATATAACTTACATCAAT 57.605 29.630 21.04 0.00 0.00 2.57
3225 4006 2.037772 ACCACCAACAAGCAAACAAACA 59.962 40.909 0.00 0.00 0.00 2.83
3320 4133 8.004215 ACAATATCACACCCATTATACAACCAT 58.996 33.333 0.00 0.00 0.00 3.55
3334 4147 6.329496 CCACATAAAACCACAATATCACACC 58.671 40.000 0.00 0.00 0.00 4.16
3335 4148 5.804979 GCCACATAAAACCACAATATCACAC 59.195 40.000 0.00 0.00 0.00 3.82
3336 4149 5.714333 AGCCACATAAAACCACAATATCACA 59.286 36.000 0.00 0.00 0.00 3.58
3338 4151 6.663093 AGAAGCCACATAAAACCACAATATCA 59.337 34.615 0.00 0.00 0.00 2.15
3339 4152 7.100458 AGAAGCCACATAAAACCACAATATC 57.900 36.000 0.00 0.00 0.00 1.63
3345 4158 4.518970 TCAGAAGAAGCCACATAAAACCAC 59.481 41.667 0.00 0.00 0.00 4.16
3347 4160 4.156739 CCTCAGAAGAAGCCACATAAAACC 59.843 45.833 0.00 0.00 0.00 3.27
3368 4181 6.386342 TGATTCCTCTGATTCAATCTCTTCCT 59.614 38.462 0.00 0.00 30.16 3.36
3369 4182 6.590068 TGATTCCTCTGATTCAATCTCTTCC 58.410 40.000 0.00 0.00 30.16 3.46
3387 4211 8.872845 CATAGGTTTGCAAGTAAAAATGATTCC 58.127 33.333 0.00 0.00 0.00 3.01
3391 4215 6.644592 GCACATAGGTTTGCAAGTAAAAATGA 59.355 34.615 0.00 0.00 38.68 2.57
3407 4231 2.780010 AGGCAATTAGGAGCACATAGGT 59.220 45.455 0.00 0.00 0.00 3.08
3443 4277 4.096681 TGACAGTCAGAATAGGTGGTGAT 58.903 43.478 0.00 0.00 0.00 3.06
3444 4278 3.506398 TGACAGTCAGAATAGGTGGTGA 58.494 45.455 0.00 0.00 0.00 4.02
3457 4291 0.249868 CTCGGGCAAACTGACAGTCA 60.250 55.000 8.93 2.48 0.00 3.41
3460 4294 1.597854 TGCTCGGGCAAACTGACAG 60.598 57.895 8.00 0.00 46.36 3.51
3470 4304 0.532115 AAATTCCAACATGCTCGGGC 59.468 50.000 0.00 0.00 39.26 6.13
3471 4305 2.493278 AGAAAATTCCAACATGCTCGGG 59.507 45.455 0.00 0.00 0.00 5.14
3472 4306 3.855689 AGAAAATTCCAACATGCTCGG 57.144 42.857 0.00 0.00 0.00 4.63
3473 4307 4.736793 GCATAGAAAATTCCAACATGCTCG 59.263 41.667 0.00 0.00 35.56 5.03
3474 4308 5.045872 GGCATAGAAAATTCCAACATGCTC 58.954 41.667 14.10 6.25 37.89 4.26
3483 4317 3.195396 TGCAACTGGGCATAGAAAATTCC 59.805 43.478 0.00 0.00 39.25 3.01
3531 4366 8.374743 TGTAGCAGCAATAATTATCTCCATGTA 58.625 33.333 0.00 0.00 0.00 2.29
3536 4371 6.094603 CCCATGTAGCAGCAATAATTATCTCC 59.905 42.308 0.00 0.00 0.00 3.71
3539 4374 5.711976 ACCCCATGTAGCAGCAATAATTATC 59.288 40.000 0.00 0.00 0.00 1.75
3541 4376 5.060427 ACCCCATGTAGCAGCAATAATTA 57.940 39.130 0.00 0.00 0.00 1.40
3542 4377 3.914771 ACCCCATGTAGCAGCAATAATT 58.085 40.909 0.00 0.00 0.00 1.40
3557 4421 3.531397 TCATTCAGTCCCAAATACCCCAT 59.469 43.478 0.00 0.00 0.00 4.00
3561 4425 5.123227 TCGAATCATTCAGTCCCAAATACC 58.877 41.667 0.00 0.00 0.00 2.73
3583 4447 8.817100 AGTTTTGACGAAATTCCTTTGAAATTC 58.183 29.630 0.00 0.00 37.14 2.17
3585 4449 7.763985 ACAGTTTTGACGAAATTCCTTTGAAAT 59.236 29.630 0.00 0.00 33.32 2.17
3641 4505 7.712639 GTCTCTGCAGTTTTCATAGGATTCATA 59.287 37.037 14.67 0.00 0.00 2.15
3663 4527 0.237761 CTGCTTGCTTGTGCTGTCTC 59.762 55.000 0.00 0.00 40.48 3.36
3667 4531 0.946528 TGTACTGCTTGCTTGTGCTG 59.053 50.000 0.00 0.00 40.48 4.41
3669 4533 2.490328 TTTGTACTGCTTGCTTGTGC 57.510 45.000 0.00 0.00 40.20 4.57
3723 4589 7.324178 ACTGTTCTGTTATGTCTGGAGTTATC 58.676 38.462 0.00 0.00 0.00 1.75
3738 4604 2.987149 CGAGCACGATTACTGTTCTGTT 59.013 45.455 0.00 0.00 42.66 3.16
3743 4609 0.246635 AGGCGAGCACGATTACTGTT 59.753 50.000 8.01 0.00 42.66 3.16
3779 4645 9.981114 AGATTGATTGGTTAAAAATTTCGAAGT 57.019 25.926 0.00 0.00 0.00 3.01
3792 4658 7.918076 AGGACTGAACTAAGATTGATTGGTTA 58.082 34.615 0.00 0.00 34.45 2.85


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

AutoCloner maintained by Alex Coulton.