Multiple sequence alignment - TraesCS5D01G086200

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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 TraesCS5D01G086200 chr5D 100.000 3248 0 0 1 3248 91612081 91615328 0.000000e+00 5999.0
1 TraesCS5D01G086200 chr5D 93.029 1162 45 15 1910 3052 91630399 91631543 0.000000e+00 1664.0
2 TraesCS5D01G086200 chr5D 93.009 1130 54 12 367 1489 91839145 91840256 0.000000e+00 1626.0
3 TraesCS5D01G086200 chr5D 96.032 882 33 2 1585 2466 91840256 91841135 0.000000e+00 1434.0
4 TraesCS5D01G086200 chr5D 87.608 581 44 13 2452 3022 91848759 91849321 0.000000e+00 649.0
5 TraesCS5D01G086200 chr5D 88.750 160 14 1 3019 3178 91849456 91849611 3.310000e-45 193.0
6 TraesCS5D01G086200 chr5D 99.000 100 1 0 1816 1915 91630145 91630244 2.570000e-41 180.0
7 TraesCS5D01G086200 chr5D 84.024 169 15 5 2988 3147 91631545 91631710 5.610000e-33 152.0
8 TraesCS5D01G086200 chr5B 94.919 2854 108 21 1 2836 96883211 96886045 0.000000e+00 4433.0
9 TraesCS5D01G086200 chr5B 91.414 198 9 3 2987 3182 96886157 96886348 6.910000e-67 265.0
10 TraesCS5D01G086200 chr5A 91.918 3217 151 53 1 3147 85261055 85264232 0.000000e+00 4399.0
11 TraesCS5D01G086200 chr5A 89.316 1301 84 28 1910 3182 85290595 85291868 0.000000e+00 1581.0
12 TraesCS5D01G086200 chr5A 96.296 108 4 0 1818 1925 85289136 85289243 9.260000e-41 178.0
13 TraesCS5D01G086200 chr7B 96.875 32 1 0 424 455 693507802 693507833 2.000000e-03 54.7
14 TraesCS5D01G086200 chr7B 96.875 32 1 0 424 455 699041248 699041279 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 TraesCS5D01G086200 chr5D 91612081 91615328 3247 False 5999.000000 5999 100.000000 1 3248 1 chr5D.!!$F1 3247
1 TraesCS5D01G086200 chr5D 91839145 91841135 1990 False 1530.000000 1626 94.520500 367 2466 2 chr5D.!!$F3 2099
2 TraesCS5D01G086200 chr5D 91630145 91631710 1565 False 665.333333 1664 92.017667 1816 3147 3 chr5D.!!$F2 1331
3 TraesCS5D01G086200 chr5D 91848759 91849611 852 False 421.000000 649 88.179000 2452 3178 2 chr5D.!!$F4 726
4 TraesCS5D01G086200 chr5B 96883211 96886348 3137 False 2349.000000 4433 93.166500 1 3182 2 chr5B.!!$F1 3181
5 TraesCS5D01G086200 chr5A 85261055 85264232 3177 False 4399.000000 4399 91.918000 1 3147 1 chr5A.!!$F1 3146
6 TraesCS5D01G086200 chr5A 85289136 85291868 2732 False 879.500000 1581 92.806000 1818 3182 2 chr5A.!!$F2 1364

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
231 238 0.530744 TCTGCTGCGTTCTAATCCGT 59.469 50.0 0.0 0.0 0.00 4.69 F
1319 1381 0.669625 AACGTCTTGAGTAAGCCCGC 60.670 55.0 0.0 0.0 33.87 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1434 1496 1.001268 GCTGCAGCATCCATCTCATTG 60.001 52.381 33.36 0.0 41.59 2.82 R
2977 4437 0.107993 AGACATGCATCCACGACCAG 60.108 55.000 0.00 0.0 0.00 4.00 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
36 37 2.733945 GGGAGCTCCTCGATCTGC 59.266 66.667 31.36 9.17 35.95 4.26
89 90 1.404315 CCTCGCTTACTGGTTCTGGAC 60.404 57.143 0.00 0.00 0.00 4.02
146 153 6.426980 TTCCTCACTGAATTTGATCGAATG 57.573 37.500 9.01 0.00 0.00 2.67
200 207 1.265365 GCTTGCTCCTGGATTAATCGC 59.735 52.381 9.32 7.26 0.00 4.58
201 208 2.843701 CTTGCTCCTGGATTAATCGCT 58.156 47.619 9.32 0.00 0.00 4.93
231 238 0.530744 TCTGCTGCGTTCTAATCCGT 59.469 50.000 0.00 0.00 0.00 4.69
264 271 1.168714 GTTTCAGCGATCAAGCCCTT 58.831 50.000 0.00 0.00 38.01 3.95
267 274 1.821332 CAGCGATCAAGCCCTTCCC 60.821 63.158 0.00 0.00 38.01 3.97
295 302 2.296692 CTGAGCAATCCGAAACCGCG 62.297 60.000 0.00 0.00 0.00 6.46
340 347 0.892063 GAGACAGGAACTCGAGCCTT 59.108 55.000 13.61 0.00 34.60 4.35
348 355 2.168728 GGAACTCGAGCCTTCAGGTAAT 59.831 50.000 13.61 0.00 37.57 1.89
363 371 7.177392 CCTTCAGGTAATAAATCCCATTCCATC 59.823 40.741 0.00 0.00 0.00 3.51
397 416 1.876664 GCCTTCTTCCGTTTCCTGC 59.123 57.895 0.00 0.00 0.00 4.85
402 421 2.270352 TCTTCCGTTTCCTGCAATGT 57.730 45.000 0.00 0.00 0.00 2.71
431 452 1.885850 GCCGTCTCCGTGTTTGTGT 60.886 57.895 0.00 0.00 0.00 3.72
554 607 3.696051 CCCCGTGATGATGTGAGAATTTT 59.304 43.478 0.00 0.00 0.00 1.82
640 694 0.740737 GCTGGTTGTTTCACAGTGCT 59.259 50.000 0.00 0.00 34.79 4.40
775 831 2.566913 TGTTGTTTACAGACATGCGGT 58.433 42.857 0.00 0.00 31.68 5.68
919 981 4.241590 TGTTCTAATGCACTTTGCCTTG 57.758 40.909 0.00 0.00 44.23 3.61
1206 1268 4.020662 AGTCCAAGTGATGAGGAGACTTTC 60.021 45.833 0.00 0.00 44.43 2.62
1214 1276 4.600207 GGAGACTTTCCTGCGGTC 57.400 61.111 0.00 0.00 43.16 4.79
1319 1381 0.669625 AACGTCTTGAGTAAGCCCGC 60.670 55.000 0.00 0.00 33.87 6.13
1352 1414 2.586792 GCTGATGGAAGCTCGGGT 59.413 61.111 0.00 0.00 40.20 5.28
1533 1595 8.100791 TGCTATACAGAAGTTATGGACAGTTTT 58.899 33.333 2.04 0.00 0.00 2.43
1534 1596 8.391106 GCTATACAGAAGTTATGGACAGTTTTG 58.609 37.037 2.04 0.00 0.00 2.44
1643 1705 7.829725 TGCAAGTGTTCAGCTTATGATATTTT 58.170 30.769 0.00 0.00 37.89 1.82
1779 1841 1.203441 AGGACAGCAGCTTGATCCCA 61.203 55.000 11.95 0.00 0.00 4.37
2108 3537 1.135575 CGAAAGCCCTGATTCTGTTGC 60.136 52.381 0.00 0.00 0.00 4.17
2162 3591 4.389374 GACACCAAGTTTCTTGATCTCCA 58.611 43.478 10.54 0.00 0.00 3.86
2321 3750 5.604565 TGTGTATAGTCAATCAGCCTGATG 58.395 41.667 8.21 3.08 37.15 3.07
2376 3805 1.884579 ACAAGCTTTGCACTGATCCTG 59.115 47.619 0.00 0.00 0.00 3.86
2539 3970 0.938008 GCCTAACTGCCGTATGCTTC 59.062 55.000 0.00 0.00 42.00 3.86
2614 4045 5.163774 GCAATAAAAGAGAAGCTGGTCAGAG 60.164 44.000 1.65 0.00 0.00 3.35
2679 4117 6.509418 TTGGATGTGGTAGCAAGAAATAAC 57.491 37.500 0.00 0.00 0.00 1.89
2753 4197 4.521146 TGGCATTGGTTTTTGTGTTCAAT 58.479 34.783 0.00 0.00 33.32 2.57
2831 4279 2.796032 GCAGTTGTCTGTGCCAAGTTTC 60.796 50.000 0.00 0.00 43.05 2.78
2833 4281 2.024414 GTTGTCTGTGCCAAGTTTCCT 58.976 47.619 0.00 0.00 0.00 3.36
2836 4284 3.892284 TGTCTGTGCCAAGTTTCCTTTA 58.108 40.909 0.00 0.00 0.00 1.85
2837 4285 4.469657 TGTCTGTGCCAAGTTTCCTTTAT 58.530 39.130 0.00 0.00 0.00 1.40
2838 4286 4.278170 TGTCTGTGCCAAGTTTCCTTTATG 59.722 41.667 0.00 0.00 0.00 1.90
2842 4290 4.404073 TGTGCCAAGTTTCCTTTATGTTGT 59.596 37.500 0.00 0.00 0.00 3.32
2843 4291 5.105146 TGTGCCAAGTTTCCTTTATGTTGTT 60.105 36.000 0.00 0.00 0.00 2.83
2844 4292 5.815222 GTGCCAAGTTTCCTTTATGTTGTTT 59.185 36.000 0.00 0.00 0.00 2.83
2845 4293 5.814705 TGCCAAGTTTCCTTTATGTTGTTTG 59.185 36.000 0.00 0.00 0.00 2.93
2846 4294 5.277297 GCCAAGTTTCCTTTATGTTGTTTGC 60.277 40.000 0.00 0.00 0.00 3.68
2847 4295 6.048509 CCAAGTTTCCTTTATGTTGTTTGCT 58.951 36.000 0.00 0.00 0.00 3.91
2848 4296 6.538381 CCAAGTTTCCTTTATGTTGTTTGCTT 59.462 34.615 0.00 0.00 0.00 3.91
2849 4297 7.401080 CAAGTTTCCTTTATGTTGTTTGCTTG 58.599 34.615 0.00 0.00 0.00 4.01
2850 4298 5.523552 AGTTTCCTTTATGTTGTTTGCTTGC 59.476 36.000 0.00 0.00 0.00 4.01
2851 4299 4.662468 TCCTTTATGTTGTTTGCTTGCA 57.338 36.364 0.00 0.00 0.00 4.08
2852 4300 5.212532 TCCTTTATGTTGTTTGCTTGCAT 57.787 34.783 0.00 0.00 0.00 3.96
2853 4301 5.609423 TCCTTTATGTTGTTTGCTTGCATT 58.391 33.333 0.00 0.00 0.00 3.56
2854 4302 6.054295 TCCTTTATGTTGTTTGCTTGCATTT 58.946 32.000 0.00 0.00 0.00 2.32
2855 4303 6.202570 TCCTTTATGTTGTTTGCTTGCATTTC 59.797 34.615 0.00 0.00 0.00 2.17
2856 4304 5.921004 TTATGTTGTTTGCTTGCATTTCC 57.079 34.783 0.00 0.00 0.00 3.13
2857 4305 3.540314 TGTTGTTTGCTTGCATTTCCT 57.460 38.095 0.00 0.00 0.00 3.36
2880 4328 1.032014 TGGTTTGCTGCAGTTTCTCC 58.968 50.000 16.64 12.01 0.00 3.71
2941 4392 2.301583 TGTGTGCAGCTGATGGTAAGTA 59.698 45.455 20.43 0.00 0.00 2.24
2964 4424 2.103263 AGTGATTCTGCCGTCCCTAATC 59.897 50.000 0.00 0.00 0.00 1.75
2971 4431 0.831307 GCCGTCCCTAATCTGGTTCT 59.169 55.000 0.00 0.00 0.00 3.01
2974 4434 1.139058 CGTCCCTAATCTGGTTCTGGG 59.861 57.143 5.56 5.56 35.93 4.45
2975 4435 2.197465 GTCCCTAATCTGGTTCTGGGT 58.803 52.381 10.28 0.00 36.01 4.51
2976 4436 2.576648 GTCCCTAATCTGGTTCTGGGTT 59.423 50.000 10.28 0.00 36.01 4.11
2977 4437 2.844348 TCCCTAATCTGGTTCTGGGTTC 59.156 50.000 10.28 0.00 36.01 3.62
2978 4438 2.846827 CCCTAATCTGGTTCTGGGTTCT 59.153 50.000 4.12 0.00 32.26 3.01
2980 4440 2.887151 AATCTGGTTCTGGGTTCTGG 57.113 50.000 0.00 0.00 0.00 3.86
2981 4441 1.747444 ATCTGGTTCTGGGTTCTGGT 58.253 50.000 0.00 0.00 0.00 4.00
2982 4442 1.056660 TCTGGTTCTGGGTTCTGGTC 58.943 55.000 0.00 0.00 0.00 4.02
2984 4444 1.052124 TGGTTCTGGGTTCTGGTCGT 61.052 55.000 0.00 0.00 0.00 4.34
2985 4445 0.602905 GGTTCTGGGTTCTGGTCGTG 60.603 60.000 0.00 0.00 0.00 4.35
3000 4545 2.224042 GGTCGTGGATGCATGTCTGATA 60.224 50.000 2.46 0.00 0.00 2.15
3115 4806 3.990546 CGCAAGAGTGTAGAGCGTA 57.009 52.632 0.00 0.00 43.08 4.42
3182 4874 5.825679 TGTTCCAGTGTGTTAAGCTTAATGT 59.174 36.000 21.28 3.08 0.00 2.71
3183 4875 6.993308 TGTTCCAGTGTGTTAAGCTTAATGTA 59.007 34.615 21.28 9.03 0.00 2.29
3184 4876 7.663905 TGTTCCAGTGTGTTAAGCTTAATGTAT 59.336 33.333 21.28 5.34 0.00 2.29
3185 4877 9.158233 GTTCCAGTGTGTTAAGCTTAATGTATA 57.842 33.333 21.28 7.60 0.00 1.47
3186 4878 9.727859 TTCCAGTGTGTTAAGCTTAATGTATAA 57.272 29.630 21.28 7.10 0.00 0.98
3187 4879 9.378551 TCCAGTGTGTTAAGCTTAATGTATAAG 57.621 33.333 21.28 9.56 0.00 1.73
3188 4880 9.162764 CCAGTGTGTTAAGCTTAATGTATAAGT 57.837 33.333 21.28 5.72 0.00 2.24
3190 4882 9.379791 AGTGTGTTAAGCTTAATGTATAAGTCC 57.620 33.333 21.28 5.80 0.00 3.85
3191 4883 8.325997 GTGTGTTAAGCTTAATGTATAAGTCCG 58.674 37.037 21.28 0.00 0.00 4.79
3192 4884 8.252417 TGTGTTAAGCTTAATGTATAAGTCCGA 58.748 33.333 21.28 0.00 0.00 4.55
3193 4885 9.090692 GTGTTAAGCTTAATGTATAAGTCCGAA 57.909 33.333 21.28 0.00 0.00 4.30
3194 4886 9.090692 TGTTAAGCTTAATGTATAAGTCCGAAC 57.909 33.333 21.28 6.44 0.00 3.95
3195 4887 9.310716 GTTAAGCTTAATGTATAAGTCCGAACT 57.689 33.333 21.28 0.00 37.32 3.01
3204 4896 8.888579 ATGTATAAGTCCGAACTAATTGAAGG 57.111 34.615 0.00 0.00 33.48 3.46
3205 4897 7.270047 TGTATAAGTCCGAACTAATTGAAGGG 58.730 38.462 0.00 0.00 33.48 3.95
3206 4898 2.987232 AGTCCGAACTAATTGAAGGGC 58.013 47.619 0.00 0.00 32.59 5.19
3207 4899 2.572104 AGTCCGAACTAATTGAAGGGCT 59.428 45.455 0.00 0.00 32.59 5.19
3208 4900 3.773119 AGTCCGAACTAATTGAAGGGCTA 59.227 43.478 0.00 0.00 31.19 3.93
3209 4901 4.120589 GTCCGAACTAATTGAAGGGCTAG 58.879 47.826 0.00 0.00 0.00 3.42
3210 4902 4.028131 TCCGAACTAATTGAAGGGCTAGA 58.972 43.478 0.00 0.00 0.00 2.43
3211 4903 4.120589 CCGAACTAATTGAAGGGCTAGAC 58.879 47.826 0.00 0.00 0.00 2.59
3212 4904 4.382685 CCGAACTAATTGAAGGGCTAGACA 60.383 45.833 0.00 0.00 0.00 3.41
3213 4905 5.175859 CGAACTAATTGAAGGGCTAGACAA 58.824 41.667 0.00 0.00 0.00 3.18
3214 4906 5.817816 CGAACTAATTGAAGGGCTAGACAAT 59.182 40.000 0.00 0.00 34.99 2.71
3215 4907 6.018669 CGAACTAATTGAAGGGCTAGACAATC 60.019 42.308 0.00 0.00 32.84 2.67
3216 4908 5.685728 ACTAATTGAAGGGCTAGACAATCC 58.314 41.667 0.00 0.00 32.84 3.01
3217 4909 4.591321 AATTGAAGGGCTAGACAATCCA 57.409 40.909 0.00 0.00 32.84 3.41
3218 4910 3.350219 TTGAAGGGCTAGACAATCCAC 57.650 47.619 0.00 0.00 0.00 4.02
3219 4911 2.265367 TGAAGGGCTAGACAATCCACA 58.735 47.619 0.00 0.00 0.00 4.17
3220 4912 2.846206 TGAAGGGCTAGACAATCCACAT 59.154 45.455 0.00 0.00 0.00 3.21
3221 4913 3.209410 GAAGGGCTAGACAATCCACATG 58.791 50.000 0.00 0.00 0.00 3.21
3222 4914 2.200081 AGGGCTAGACAATCCACATGT 58.800 47.619 0.00 0.00 0.00 3.21
3223 4915 3.384168 AGGGCTAGACAATCCACATGTA 58.616 45.455 0.00 0.00 0.00 2.29
3224 4916 3.976654 AGGGCTAGACAATCCACATGTAT 59.023 43.478 0.00 0.00 0.00 2.29
3225 4917 5.155161 AGGGCTAGACAATCCACATGTATA 58.845 41.667 0.00 0.00 0.00 1.47
3226 4918 5.012148 AGGGCTAGACAATCCACATGTATAC 59.988 44.000 0.00 0.00 0.00 1.47
3227 4919 5.012148 GGGCTAGACAATCCACATGTATACT 59.988 44.000 0.00 0.00 0.00 2.12
3228 4920 6.464465 GGGCTAGACAATCCACATGTATACTT 60.464 42.308 0.00 0.00 0.00 2.24
3229 4921 6.647067 GGCTAGACAATCCACATGTATACTTC 59.353 42.308 0.00 0.00 0.00 3.01
3230 4922 7.210174 GCTAGACAATCCACATGTATACTTCA 58.790 38.462 0.00 0.00 0.00 3.02
3231 4923 7.710907 GCTAGACAATCCACATGTATACTTCAA 59.289 37.037 0.00 0.00 0.00 2.69
3232 4924 7.849804 AGACAATCCACATGTATACTTCAAC 57.150 36.000 0.00 0.00 0.00 3.18
3233 4925 7.394016 AGACAATCCACATGTATACTTCAACA 58.606 34.615 0.00 0.00 0.00 3.33
3234 4926 7.334421 AGACAATCCACATGTATACTTCAACAC 59.666 37.037 0.00 0.00 0.00 3.32
3235 4927 6.374333 ACAATCCACATGTATACTTCAACACC 59.626 38.462 0.00 0.00 0.00 4.16
3236 4928 4.839121 TCCACATGTATACTTCAACACCC 58.161 43.478 0.00 0.00 0.00 4.61
3237 4929 3.945285 CCACATGTATACTTCAACACCCC 59.055 47.826 0.00 0.00 0.00 4.95
3238 4930 4.324254 CCACATGTATACTTCAACACCCCT 60.324 45.833 0.00 0.00 0.00 4.79
3239 4931 5.253330 CACATGTATACTTCAACACCCCTT 58.747 41.667 0.00 0.00 0.00 3.95
3240 4932 5.710099 CACATGTATACTTCAACACCCCTTT 59.290 40.000 0.00 0.00 0.00 3.11
3241 4933 5.944007 ACATGTATACTTCAACACCCCTTTC 59.056 40.000 0.00 0.00 0.00 2.62
3242 4934 5.570205 TGTATACTTCAACACCCCTTTCA 57.430 39.130 4.17 0.00 0.00 2.69
3243 4935 6.134535 TGTATACTTCAACACCCCTTTCAT 57.865 37.500 4.17 0.00 0.00 2.57
3244 4936 5.943416 TGTATACTTCAACACCCCTTTCATG 59.057 40.000 4.17 0.00 0.00 3.07
3245 4937 3.312736 ACTTCAACACCCCTTTCATGT 57.687 42.857 0.00 0.00 0.00 3.21
3246 4938 2.958355 ACTTCAACACCCCTTTCATGTG 59.042 45.455 0.00 0.00 36.11 3.21
3247 4939 2.746279 TCAACACCCCTTTCATGTGT 57.254 45.000 0.00 0.00 44.63 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.835895 GAGCTCCCCGGAGAGGAC 60.836 72.222 15.55 0.00 44.53 3.85
36 37 0.951040 GAACCCACCTCGAACAGCTG 60.951 60.000 13.48 13.48 0.00 4.24
146 153 0.391263 ATTCCGAAACCAGAGACGCC 60.391 55.000 0.00 0.00 0.00 5.68
200 207 1.484356 GCAGCAGAAGCAAACACAAG 58.516 50.000 0.00 0.00 45.49 3.16
201 208 0.248580 CGCAGCAGAAGCAAACACAA 60.249 50.000 0.00 0.00 45.49 3.33
231 238 2.226437 GCTGAAACGAGATTGCAGGAAA 59.774 45.455 0.00 0.00 0.00 3.13
264 271 1.499913 TTGCTCAGGGAATGCAGGGA 61.500 55.000 0.00 0.00 38.01 4.20
267 274 1.030457 GGATTGCTCAGGGAATGCAG 58.970 55.000 0.00 0.00 40.26 4.41
311 318 2.430382 TTCCTGTCTCGTGAACCCGC 62.430 60.000 0.00 0.00 0.00 6.13
340 347 6.468651 GGGATGGAATGGGATTTATTACCTGA 60.469 42.308 0.00 0.00 0.00 3.86
348 355 2.780592 TCGTGGGATGGAATGGGATTTA 59.219 45.455 0.00 0.00 0.00 1.40
363 371 0.673644 AGGCGTCAGAAATTCGTGGG 60.674 55.000 0.00 0.00 0.00 4.61
397 416 3.119743 AGACGGCATTTGATCACACATTG 60.120 43.478 0.00 0.00 0.00 2.82
402 421 1.737838 GGAGACGGCATTTGATCACA 58.262 50.000 0.00 0.00 0.00 3.58
431 452 5.068987 AGTTGTTGCTTCTTTGGAGCATTTA 59.931 36.000 1.02 0.00 38.43 1.40
554 607 3.192212 TGACAAGTTGCAACAACATGTGA 59.808 39.130 30.11 19.21 0.00 3.58
782 838 9.920946 AATAAATTTGCCTCTACTATTCAGGAA 57.079 29.630 0.00 0.00 0.00 3.36
783 839 9.342308 CAATAAATTTGCCTCTACTATTCAGGA 57.658 33.333 0.00 0.00 0.00 3.86
784 840 8.078596 GCAATAAATTTGCCTCTACTATTCAGG 58.921 37.037 0.00 0.00 39.38 3.86
1214 1276 1.171308 CTGGCATTGTGTTCCTGAGG 58.829 55.000 0.00 0.00 0.00 3.86
1319 1381 3.130160 GCCCAGCTGCTTCTTCGG 61.130 66.667 8.66 3.09 0.00 4.30
1352 1414 1.604308 CAGCCACCACCAGCAATGA 60.604 57.895 0.00 0.00 0.00 2.57
1418 1480 4.346709 TCTCATTGAACTTGAGTGGTGGTA 59.653 41.667 1.07 0.00 41.13 3.25
1434 1496 1.001268 GCTGCAGCATCCATCTCATTG 60.001 52.381 33.36 0.00 41.59 2.82
1533 1595 1.303236 CTTCGACACATTGGGGGCA 60.303 57.895 0.00 0.00 0.00 5.36
1534 1596 2.046285 CCTTCGACACATTGGGGGC 61.046 63.158 0.00 0.00 0.00 5.80
1643 1705 4.018870 TGTCCTTAACACATTGCCCATAGA 60.019 41.667 0.00 0.00 31.20 1.98
1779 1841 5.595952 ACTTCTTTCCTTCAGCTCAACATTT 59.404 36.000 0.00 0.00 0.00 2.32
2321 3750 3.802866 TGGACAAATTGGAAGTTTTGCC 58.197 40.909 0.00 0.00 36.51 4.52
2376 3805 2.914838 CGAAAATTTGCCGGTAAAGAGC 59.085 45.455 22.31 10.88 0.00 4.09
2679 4117 5.291371 CAGTGACAATCAGAGCAGTGATTAG 59.709 44.000 11.90 9.63 43.85 1.73
2753 4197 3.295093 TGCCTCATTCACAAGAAACCAA 58.705 40.909 0.00 0.00 37.29 3.67
2831 4279 5.927954 AATGCAAGCAAACAACATAAAGG 57.072 34.783 0.00 0.00 0.00 3.11
2833 4281 6.054295 AGGAAATGCAAGCAAACAACATAAA 58.946 32.000 0.00 0.00 0.00 1.40
2836 4284 4.075963 AGGAAATGCAAGCAAACAACAT 57.924 36.364 0.00 0.00 0.00 2.71
2837 4285 3.540314 AGGAAATGCAAGCAAACAACA 57.460 38.095 0.00 0.00 0.00 3.33
2838 4286 4.990426 ACATAGGAAATGCAAGCAAACAAC 59.010 37.500 0.00 0.00 0.00 3.32
2842 4290 3.577848 ACCACATAGGAAATGCAAGCAAA 59.422 39.130 0.00 0.00 41.22 3.68
2843 4291 3.164268 ACCACATAGGAAATGCAAGCAA 58.836 40.909 0.00 0.00 41.22 3.91
2844 4292 2.806434 ACCACATAGGAAATGCAAGCA 58.194 42.857 0.00 0.00 41.22 3.91
2845 4293 3.874392 AACCACATAGGAAATGCAAGC 57.126 42.857 0.00 0.00 41.22 4.01
2846 4294 3.928375 GCAAACCACATAGGAAATGCAAG 59.072 43.478 0.00 0.00 40.71 4.01
2847 4295 3.577848 AGCAAACCACATAGGAAATGCAA 59.422 39.130 0.00 0.00 42.22 4.08
2848 4296 3.056678 CAGCAAACCACATAGGAAATGCA 60.057 43.478 0.00 0.00 42.22 3.96
2849 4297 3.514645 CAGCAAACCACATAGGAAATGC 58.485 45.455 0.00 0.00 41.22 3.56
2850 4298 3.056678 TGCAGCAAACCACATAGGAAATG 60.057 43.478 0.00 0.00 41.22 2.32
2851 4299 3.164268 TGCAGCAAACCACATAGGAAAT 58.836 40.909 0.00 0.00 41.22 2.17
2852 4300 2.557924 CTGCAGCAAACCACATAGGAAA 59.442 45.455 0.00 0.00 41.22 3.13
2853 4301 2.161855 CTGCAGCAAACCACATAGGAA 58.838 47.619 0.00 0.00 41.22 3.36
2854 4302 1.073763 ACTGCAGCAAACCACATAGGA 59.926 47.619 15.27 0.00 41.22 2.94
2855 4303 1.538047 ACTGCAGCAAACCACATAGG 58.462 50.000 15.27 0.00 45.67 2.57
2856 4304 3.254166 AGAAACTGCAGCAAACCACATAG 59.746 43.478 15.27 0.00 0.00 2.23
2857 4305 3.221771 AGAAACTGCAGCAAACCACATA 58.778 40.909 15.27 0.00 0.00 2.29
2954 4405 1.139058 CCCAGAACCAGATTAGGGACG 59.861 57.143 0.00 0.00 37.75 4.79
2964 4424 0.320771 CGACCAGAACCCAGAACCAG 60.321 60.000 0.00 0.00 0.00 4.00
2971 4431 1.676968 CATCCACGACCAGAACCCA 59.323 57.895 0.00 0.00 0.00 4.51
2974 4434 0.729116 CATGCATCCACGACCAGAAC 59.271 55.000 0.00 0.00 0.00 3.01
2975 4435 0.324614 ACATGCATCCACGACCAGAA 59.675 50.000 0.00 0.00 0.00 3.02
2976 4436 0.108186 GACATGCATCCACGACCAGA 60.108 55.000 0.00 0.00 0.00 3.86
2977 4437 0.107993 AGACATGCATCCACGACCAG 60.108 55.000 0.00 0.00 0.00 4.00
2978 4438 0.391528 CAGACATGCATCCACGACCA 60.392 55.000 0.00 0.00 0.00 4.02
2980 4440 1.945387 ATCAGACATGCATCCACGAC 58.055 50.000 0.00 0.00 0.00 4.34
2981 4441 4.309933 GAATATCAGACATGCATCCACGA 58.690 43.478 0.00 0.00 0.00 4.35
2982 4442 3.434641 GGAATATCAGACATGCATCCACG 59.565 47.826 0.00 0.00 0.00 4.94
2984 4444 4.103627 ACTGGAATATCAGACATGCATCCA 59.896 41.667 0.00 0.00 38.11 3.41
2985 4445 4.649692 ACTGGAATATCAGACATGCATCC 58.350 43.478 0.00 0.00 38.11 3.51
3000 4545 5.600484 CAGTTAGTCTATCTGGGACTGGAAT 59.400 44.000 9.33 0.00 42.98 3.01
3046 4730 2.041976 TCCATCGCGGAAGATCTCC 58.958 57.895 6.13 0.00 42.52 3.71
3115 4806 0.241749 CAAATCACACATGCCGCAGT 59.758 50.000 0.00 0.00 0.00 4.40
3182 4874 6.099269 AGCCCTTCAATTAGTTCGGACTTATA 59.901 38.462 0.00 0.00 37.33 0.98
3183 4875 5.104485 AGCCCTTCAATTAGTTCGGACTTAT 60.104 40.000 0.00 0.00 37.33 1.73
3184 4876 4.224370 AGCCCTTCAATTAGTTCGGACTTA 59.776 41.667 0.00 0.00 37.33 2.24
3185 4877 3.009143 AGCCCTTCAATTAGTTCGGACTT 59.991 43.478 0.00 0.00 37.33 3.01
3186 4878 2.572104 AGCCCTTCAATTAGTTCGGACT 59.428 45.455 0.00 0.00 39.97 3.85
3187 4879 2.987232 AGCCCTTCAATTAGTTCGGAC 58.013 47.619 0.00 0.00 0.00 4.79
3188 4880 4.028131 TCTAGCCCTTCAATTAGTTCGGA 58.972 43.478 0.00 0.00 0.00 4.55
3189 4881 4.120589 GTCTAGCCCTTCAATTAGTTCGG 58.879 47.826 0.00 0.00 0.00 4.30
3190 4882 4.755411 TGTCTAGCCCTTCAATTAGTTCG 58.245 43.478 0.00 0.00 0.00 3.95
3191 4883 6.261158 GGATTGTCTAGCCCTTCAATTAGTTC 59.739 42.308 0.00 0.00 31.87 3.01
3192 4884 6.122964 GGATTGTCTAGCCCTTCAATTAGTT 58.877 40.000 0.00 0.00 31.87 2.24
3193 4885 5.191722 TGGATTGTCTAGCCCTTCAATTAGT 59.808 40.000 0.00 0.00 31.87 2.24
3194 4886 5.529060 GTGGATTGTCTAGCCCTTCAATTAG 59.471 44.000 0.00 0.00 31.87 1.73
3195 4887 5.045213 TGTGGATTGTCTAGCCCTTCAATTA 60.045 40.000 0.00 0.00 31.87 1.40
3196 4888 4.263905 TGTGGATTGTCTAGCCCTTCAATT 60.264 41.667 0.00 0.00 31.87 2.32
3197 4889 3.266772 TGTGGATTGTCTAGCCCTTCAAT 59.733 43.478 0.00 0.00 33.95 2.57
3198 4890 2.642311 TGTGGATTGTCTAGCCCTTCAA 59.358 45.455 0.00 0.00 0.00 2.69
3199 4891 2.265367 TGTGGATTGTCTAGCCCTTCA 58.735 47.619 0.00 0.00 0.00 3.02
3200 4892 3.209410 CATGTGGATTGTCTAGCCCTTC 58.791 50.000 0.00 0.00 0.00 3.46
3201 4893 2.578021 ACATGTGGATTGTCTAGCCCTT 59.422 45.455 0.00 0.00 0.00 3.95
3202 4894 2.200081 ACATGTGGATTGTCTAGCCCT 58.800 47.619 0.00 0.00 0.00 5.19
3203 4895 2.717639 ACATGTGGATTGTCTAGCCC 57.282 50.000 0.00 0.00 0.00 5.19
3204 4896 6.102897 AGTATACATGTGGATTGTCTAGCC 57.897 41.667 9.11 0.00 0.00 3.93
3205 4897 7.210174 TGAAGTATACATGTGGATTGTCTAGC 58.790 38.462 9.11 0.00 0.00 3.42
3206 4898 9.035607 GTTGAAGTATACATGTGGATTGTCTAG 57.964 37.037 9.11 0.00 0.00 2.43
3207 4899 8.536175 TGTTGAAGTATACATGTGGATTGTCTA 58.464 33.333 9.11 0.00 0.00 2.59
3208 4900 7.334421 GTGTTGAAGTATACATGTGGATTGTCT 59.666 37.037 9.11 0.00 0.00 3.41
3209 4901 7.414098 GGTGTTGAAGTATACATGTGGATTGTC 60.414 40.741 9.11 0.00 0.00 3.18
3210 4902 6.374333 GGTGTTGAAGTATACATGTGGATTGT 59.626 38.462 9.11 0.00 0.00 2.71
3211 4903 6.183360 GGGTGTTGAAGTATACATGTGGATTG 60.183 42.308 9.11 0.00 0.00 2.67
3212 4904 5.885912 GGGTGTTGAAGTATACATGTGGATT 59.114 40.000 9.11 0.00 0.00 3.01
3213 4905 5.437060 GGGTGTTGAAGTATACATGTGGAT 58.563 41.667 9.11 0.00 0.00 3.41
3214 4906 4.323945 GGGGTGTTGAAGTATACATGTGGA 60.324 45.833 9.11 0.00 0.00 4.02
3215 4907 3.945285 GGGGTGTTGAAGTATACATGTGG 59.055 47.826 9.11 0.00 0.00 4.17
3216 4908 4.843728 AGGGGTGTTGAAGTATACATGTG 58.156 43.478 9.11 0.00 0.00 3.21
3217 4909 5.514500 AAGGGGTGTTGAAGTATACATGT 57.486 39.130 2.69 2.69 0.00 3.21
3218 4910 5.943416 TGAAAGGGGTGTTGAAGTATACATG 59.057 40.000 5.50 0.00 0.00 3.21
3219 4911 6.134535 TGAAAGGGGTGTTGAAGTATACAT 57.865 37.500 5.50 0.00 0.00 2.29
3220 4912 5.570205 TGAAAGGGGTGTTGAAGTATACA 57.430 39.130 5.50 0.00 0.00 2.29
3221 4913 5.944007 ACATGAAAGGGGTGTTGAAGTATAC 59.056 40.000 0.00 0.00 0.00 1.47
3222 4914 5.943416 CACATGAAAGGGGTGTTGAAGTATA 59.057 40.000 0.00 0.00 0.00 1.47
3223 4915 4.766891 CACATGAAAGGGGTGTTGAAGTAT 59.233 41.667 0.00 0.00 0.00 2.12
3224 4916 4.141287 CACATGAAAGGGGTGTTGAAGTA 58.859 43.478 0.00 0.00 0.00 2.24
3225 4917 2.958355 CACATGAAAGGGGTGTTGAAGT 59.042 45.455 0.00 0.00 0.00 3.01
3226 4918 2.958355 ACACATGAAAGGGGTGTTGAAG 59.042 45.455 0.00 0.00 42.72 3.02
3227 4919 3.025322 ACACATGAAAGGGGTGTTGAA 57.975 42.857 0.00 0.00 42.72 2.69
3228 4920 2.746279 ACACATGAAAGGGGTGTTGA 57.254 45.000 0.00 0.00 42.72 3.18


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

AutoCloner maintained by Alex Coulton.