Multiple sequence alignment - TraesCS3D01G124500

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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 TraesCS3D01G124500 chr3D 100.000 3509 0 0 1 3509 82410917 82414425 0.000000e+00 6481.0
1 TraesCS3D01G124500 chr3B 94.315 2568 83 21 1 2562 128947376 128949886 0.000000e+00 3875.0
2 TraesCS3D01G124500 chr3B 94.579 535 13 4 2982 3509 128950281 128950806 0.000000e+00 813.0
3 TraesCS3D01G124500 chr3B 85.302 381 16 18 2569 2941 128949938 128950286 1.200000e-94 357.0
4 TraesCS3D01G124500 chr3B 83.333 126 12 6 284 401 63115175 63115299 1.330000e-19 108.0
5 TraesCS3D01G124500 chr3A 96.435 2132 51 17 435 2546 97972429 97974555 0.000000e+00 3493.0
6 TraesCS3D01G124500 chr3A 90.020 511 24 11 3004 3509 97974863 97975351 1.370000e-178 636.0
7 TraesCS3D01G124500 chr3A 88.863 422 36 7 1 413 97971922 97972341 3.120000e-140 508.0
8 TraesCS3D01G124500 chr3A 87.179 273 18 10 2678 2941 97974604 97974868 9.530000e-76 294.0
9 TraesCS3D01G124500 chr3A 87.963 108 12 1 271 377 51283410 51283303 3.680000e-25 126.0
10 TraesCS3D01G124500 chr2B 83.527 431 57 10 2032 2458 761328317 761327897 1.180000e-104 390.0
11 TraesCS3D01G124500 chr2B 81.643 414 68 6 2032 2438 761323208 761322796 1.560000e-88 337.0
12 TraesCS3D01G124500 chr2B 87.500 80 10 0 289 368 458083107 458083186 3.730000e-15 93.5
13 TraesCS3D01G124500 chr2A 81.818 429 68 8 2032 2458 752336944 752336524 5.570000e-93 351.0
14 TraesCS3D01G124500 chr2D 82.707 266 40 2 2196 2458 620684952 620684690 7.570000e-57 231.0
15 TraesCS3D01G124500 chr2D 80.982 163 25 5 244 401 386708323 386708484 1.320000e-24 124.0
16 TraesCS3D01G124500 chr5A 80.864 162 26 3 244 400 299766466 299766627 4.760000e-24 122.0
17 TraesCS3D01G124500 chrUn 79.141 163 27 5 244 400 137810866 137810705 4.790000e-19 106.0
18 TraesCS3D01G124500 chr7B 90.909 44 4 0 2948 2991 744092299 744092256 3.780000e-05 60.2


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 TraesCS3D01G124500 chr3D 82410917 82414425 3508 False 6481.000000 6481 100.000000 1 3509 1 chr3D.!!$F1 3508
1 TraesCS3D01G124500 chr3B 128947376 128950806 3430 False 1681.666667 3875 91.398667 1 3509 3 chr3B.!!$F2 3508
2 TraesCS3D01G124500 chr3A 97971922 97975351 3429 False 1232.750000 3493 90.624250 1 3509 4 chr3A.!!$F1 3508

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
694 818 0.738389 GAGCCTCCTCTCTCTTCACG 59.262 60.000 0.00 0.00 35.16 4.35 F
1567 1703 1.008652 CCGTCCGTACACACGTGAA 60.009 57.895 25.01 4.06 46.96 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2482 2626 0.179161 GAGATCAGGTCGTCCGTGTG 60.179 60.0 0.00 0.0 39.05 3.82 R
2593 2781 0.462759 CAGCTAAGCTACCAGCCCAC 60.463 60.0 10.38 0.0 43.77 4.61 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 49 8.055279 TCAATGAGATTTGGTTTTATGGAGTC 57.945 34.615 0.00 0.00 0.00 3.36
70 71 5.938125 GTCCGTGGCATAATAATAGGTGAAT 59.062 40.000 0.00 0.00 0.00 2.57
164 187 5.864418 ATGAATAGACTTTTGCCATGCAT 57.136 34.783 0.00 0.00 38.76 3.96
198 221 8.204836 AGTCGAGGTATGCTTTTTCTTATGTAT 58.795 33.333 0.00 0.00 0.00 2.29
199 222 9.472361 GTCGAGGTATGCTTTTTCTTATGTATA 57.528 33.333 0.00 0.00 0.00 1.47
200 223 9.692749 TCGAGGTATGCTTTTTCTTATGTATAG 57.307 33.333 0.00 0.00 0.00 1.31
201 224 9.477484 CGAGGTATGCTTTTTCTTATGTATAGT 57.523 33.333 0.00 0.00 0.00 2.12
204 227 9.665264 GGTATGCTTTTTCTTATGTATAGTTGC 57.335 33.333 0.00 0.00 0.00 4.17
207 230 9.740239 ATGCTTTTTCTTATGTATAGTTGCATG 57.260 29.630 0.00 0.00 34.31 4.06
208 231 8.739039 TGCTTTTTCTTATGTATAGTTGCATGT 58.261 29.630 0.00 0.00 30.26 3.21
209 232 9.573133 GCTTTTTCTTATGTATAGTTGCATGTT 57.427 29.630 0.00 0.00 30.26 2.71
213 236 9.665719 TTTCTTATGTATAGTTGCATGTTGAGA 57.334 29.630 0.00 0.00 30.26 3.27
214 237 8.877808 TCTTATGTATAGTTGCATGTTGAGAG 57.122 34.615 0.00 0.00 30.26 3.20
215 238 8.695456 TCTTATGTATAGTTGCATGTTGAGAGA 58.305 33.333 0.00 0.00 30.26 3.10
216 239 9.317936 CTTATGTATAGTTGCATGTTGAGAGAA 57.682 33.333 0.00 0.00 30.26 2.87
217 240 9.665719 TTATGTATAGTTGCATGTTGAGAGAAA 57.334 29.630 0.00 0.00 30.26 2.52
218 241 8.743085 ATGTATAGTTGCATGTTGAGAGAAAT 57.257 30.769 0.00 0.00 0.00 2.17
219 242 8.565896 TGTATAGTTGCATGTTGAGAGAAATT 57.434 30.769 0.00 0.00 0.00 1.82
220 243 9.013229 TGTATAGTTGCATGTTGAGAGAAATTT 57.987 29.630 0.00 0.00 0.00 1.82
224 275 8.345724 AGTTGCATGTTGAGAGAAATTTATCT 57.654 30.769 14.99 14.99 0.00 1.98
228 279 7.391275 TGCATGTTGAGAGAAATTTATCTGTGA 59.609 33.333 19.59 3.12 0.00 3.58
239 290 7.772757 AGAAATTTATCTGTGAAGATCACCTCC 59.227 37.037 7.94 0.00 46.40 4.30
278 329 9.643693 AACCTTACTTGCATTTTTCTATTCATG 57.356 29.630 0.00 0.00 0.00 3.07
338 389 5.236282 TGATGGGTGTAAAATTTACGTCGA 58.764 37.500 10.81 4.06 0.00 4.20
339 390 5.349270 TGATGGGTGTAAAATTTACGTCGAG 59.651 40.000 10.81 0.00 0.00 4.04
359 410 4.379708 CGAGCATGATTGATGTTGAACCAA 60.380 41.667 0.00 0.00 34.14 3.67
361 412 6.458615 CGAGCATGATTGATGTTGAACCAATA 60.459 38.462 0.00 0.00 34.14 1.90
378 429 9.005318 TGAACCAATAGAATATGTAACCCCTTA 57.995 33.333 0.00 0.00 0.00 2.69
415 472 2.946785 CTAGTACTCCCTTCGTCCCAT 58.053 52.381 0.00 0.00 0.00 4.00
420 477 2.262637 ACTCCCTTCGTCCCATAAACA 58.737 47.619 0.00 0.00 0.00 2.83
426 483 3.684788 CCTTCGTCCCATAAACACTCTTG 59.315 47.826 0.00 0.00 0.00 3.02
431 488 4.503007 CGTCCCATAAACACTCTTGTATCG 59.497 45.833 0.00 0.00 33.55 2.92
465 587 8.795842 AGGGAGTAGTAGATATAGAATGAACG 57.204 38.462 0.00 0.00 0.00 3.95
504 627 9.131791 GTGGACCATATCACTAATTAATTTGGT 57.868 33.333 15.18 15.18 37.41 3.67
582 706 8.270080 TCTGTGTTTGTTTCTATGTTTGTGTA 57.730 30.769 0.00 0.00 0.00 2.90
694 818 0.738389 GAGCCTCCTCTCTCTTCACG 59.262 60.000 0.00 0.00 35.16 4.35
725 850 2.673775 TCTTCATCCCAACAGGCAAA 57.326 45.000 0.00 0.00 34.51 3.68
1567 1703 1.008652 CCGTCCGTACACACGTGAA 60.009 57.895 25.01 4.06 46.96 3.18
1664 1800 3.909258 CTAGCCGCGTGTGTCCGTT 62.909 63.158 4.92 0.00 0.00 4.44
1675 1811 2.079158 TGTGTCCGTTCGTAGGAGTAG 58.921 52.381 0.00 0.00 38.65 2.57
2121 2265 1.670406 CTTCGTGCTGCAGAGCCTT 60.670 57.895 20.43 0.00 45.57 4.35
2430 2574 4.660938 AAGGCCTTCACCACCGGC 62.661 66.667 13.78 0.00 43.03 6.13
2463 2607 4.056805 ATGGTCGCCATCTCCACT 57.943 55.556 5.65 0.00 40.74 4.00
2472 2616 1.714794 CCATCTCCACTGACAACGAC 58.285 55.000 0.00 0.00 0.00 4.34
2550 2694 0.038159 CGGCCAAGGGATCGATCTAC 60.038 60.000 23.96 16.97 0.00 2.59
2554 2698 2.803492 GCCAAGGGATCGATCTACACAC 60.803 54.545 23.96 6.93 0.00 3.82
2562 2706 5.692204 GGGATCGATCTACACACACAATTAG 59.308 44.000 23.96 0.00 0.00 1.73
2590 2778 1.927487 AAAATGCCAGAGATGGTGCA 58.073 45.000 0.00 0.00 38.23 4.57
2591 2779 2.154567 AAATGCCAGAGATGGTGCAT 57.845 45.000 0.00 0.00 45.79 3.96
2592 2780 1.399714 AATGCCAGAGATGGTGCATG 58.600 50.000 0.00 0.00 43.23 4.06
2593 2781 0.467474 ATGCCAGAGATGGTGCATGG 60.467 55.000 0.00 0.00 42.48 3.66
2594 2782 1.077212 GCCAGAGATGGTGCATGGT 60.077 57.895 2.42 0.00 33.42 3.55
2601 2789 3.968837 ATGGTGCATGGTGGGCTGG 62.969 63.158 0.00 0.00 0.00 4.85
2605 2793 2.830370 GCATGGTGGGCTGGTAGC 60.830 66.667 0.00 0.00 41.46 3.58
2630 2818 3.586470 CTGAGGTAGCTAGGAGGAAGA 57.414 52.381 0.00 0.00 0.00 2.87
2660 2852 3.767230 CTGTCGTTCGTGCGGCTG 61.767 66.667 0.00 0.00 37.38 4.85
2661 2853 4.578898 TGTCGTTCGTGCGGCTGT 62.579 61.111 0.00 0.00 37.38 4.40
2662 2854 3.335534 GTCGTTCGTGCGGCTGTT 61.336 61.111 0.00 0.00 33.21 3.16
2663 2855 3.033764 TCGTTCGTGCGGCTGTTC 61.034 61.111 0.00 0.00 0.00 3.18
2664 2856 4.072088 CGTTCGTGCGGCTGTTCC 62.072 66.667 0.00 0.00 0.00 3.62
2665 2857 3.723348 GTTCGTGCGGCTGTTCCC 61.723 66.667 0.00 0.00 0.00 3.97
2672 2864 2.725008 CGGCTGTTCCCGCAAAAA 59.275 55.556 0.00 0.00 42.03 1.94
2872 3080 4.792068 TGGGAAAGAAGAAGACATGTTGT 58.208 39.130 0.00 0.00 0.00 3.32
2912 3121 0.613012 GGCTGCCTCCTGACCAAATT 60.613 55.000 12.43 0.00 0.00 1.82
2936 3145 8.675705 TTCTTGTTTTGTTATCACTGATCAGA 57.324 30.769 29.27 8.51 0.00 3.27
2941 3150 8.988934 TGTTTTGTTATCACTGATCAGAACTAC 58.011 33.333 29.27 18.55 0.00 2.73
2942 3151 9.209175 GTTTTGTTATCACTGATCAGAACTACT 57.791 33.333 29.27 2.25 0.00 2.57
2943 3152 8.988064 TTTGTTATCACTGATCAGAACTACTC 57.012 34.615 29.27 12.99 0.00 2.59
2945 3154 6.096987 TGTTATCACTGATCAGAACTACTCCC 59.903 42.308 29.27 8.48 0.00 4.30
2946 3155 4.047627 TCACTGATCAGAACTACTCCCA 57.952 45.455 29.27 0.00 0.00 4.37
2947 3156 4.416516 TCACTGATCAGAACTACTCCCAA 58.583 43.478 29.27 0.00 0.00 4.12
2948 3157 4.464244 TCACTGATCAGAACTACTCCCAAG 59.536 45.833 29.27 0.00 0.00 3.61
2950 3159 4.221703 ACTGATCAGAACTACTCCCAAGTG 59.778 45.833 29.27 0.00 36.92 3.16
2951 3160 4.160329 TGATCAGAACTACTCCCAAGTGT 58.840 43.478 0.00 0.00 36.92 3.55
2952 3161 4.220821 TGATCAGAACTACTCCCAAGTGTC 59.779 45.833 0.00 0.00 36.92 3.67
2955 3164 3.574396 CAGAACTACTCCCAAGTGTCAGA 59.426 47.826 0.00 0.00 36.92 3.27
2956 3165 4.039245 CAGAACTACTCCCAAGTGTCAGAA 59.961 45.833 0.00 0.00 36.92 3.02
2957 3166 4.654262 AGAACTACTCCCAAGTGTCAGAAA 59.346 41.667 0.00 0.00 36.92 2.52
2958 3167 5.130477 AGAACTACTCCCAAGTGTCAGAAAA 59.870 40.000 0.00 0.00 36.92 2.29
2959 3168 5.568620 ACTACTCCCAAGTGTCAGAAAAT 57.431 39.130 0.00 0.00 36.92 1.82
2960 3169 5.308825 ACTACTCCCAAGTGTCAGAAAATG 58.691 41.667 0.00 0.00 36.92 2.32
2961 3170 4.170468 ACTCCCAAGTGTCAGAAAATGT 57.830 40.909 0.00 0.00 33.32 2.71
2962 3171 4.536765 ACTCCCAAGTGTCAGAAAATGTT 58.463 39.130 0.00 0.00 33.32 2.71
2963 3172 4.956075 ACTCCCAAGTGTCAGAAAATGTTT 59.044 37.500 0.00 0.00 33.32 2.83
2964 3173 5.422012 ACTCCCAAGTGTCAGAAAATGTTTT 59.578 36.000 0.00 0.00 33.32 2.43
2965 3174 6.605594 ACTCCCAAGTGTCAGAAAATGTTTTA 59.394 34.615 0.00 0.00 33.32 1.52
2966 3175 6.801575 TCCCAAGTGTCAGAAAATGTTTTAC 58.198 36.000 0.00 0.00 0.00 2.01
2967 3176 6.378564 TCCCAAGTGTCAGAAAATGTTTTACA 59.621 34.615 0.00 0.00 0.00 2.41
2968 3177 7.069331 TCCCAAGTGTCAGAAAATGTTTTACAT 59.931 33.333 0.00 0.00 41.31 2.29
2981 3190 7.645058 AATGTTTTACATTATGGGACTGAGG 57.355 36.000 3.36 0.00 46.11 3.86
2982 3191 5.505780 TGTTTTACATTATGGGACTGAGGG 58.494 41.667 0.00 0.00 0.00 4.30
2983 3192 5.251932 TGTTTTACATTATGGGACTGAGGGA 59.748 40.000 0.00 0.00 0.00 4.20
2984 3193 5.630415 TTTACATTATGGGACTGAGGGAG 57.370 43.478 0.00 0.00 0.00 4.30
2985 3194 3.136641 ACATTATGGGACTGAGGGAGT 57.863 47.619 0.00 0.00 37.76 3.85
2986 3195 4.280789 ACATTATGGGACTGAGGGAGTA 57.719 45.455 0.00 0.00 33.83 2.59
2987 3196 4.227197 ACATTATGGGACTGAGGGAGTAG 58.773 47.826 0.00 0.00 33.83 2.57
2988 3197 4.078571 ACATTATGGGACTGAGGGAGTAGA 60.079 45.833 0.00 0.00 33.83 2.59
2989 3198 4.834406 TTATGGGACTGAGGGAGTAGAT 57.166 45.455 0.00 0.00 33.83 1.98
2990 3199 3.715648 ATGGGACTGAGGGAGTAGATT 57.284 47.619 0.00 0.00 33.83 2.40
2991 3200 4.834406 ATGGGACTGAGGGAGTAGATTA 57.166 45.455 0.00 0.00 33.83 1.75
2992 3201 4.834406 TGGGACTGAGGGAGTAGATTAT 57.166 45.455 0.00 0.00 33.83 1.28
2993 3202 5.157770 TGGGACTGAGGGAGTAGATTATT 57.842 43.478 0.00 0.00 33.83 1.40
2994 3203 5.148502 TGGGACTGAGGGAGTAGATTATTC 58.851 45.833 0.00 0.00 33.83 1.75
2995 3204 5.103043 TGGGACTGAGGGAGTAGATTATTCT 60.103 44.000 0.00 0.00 33.83 2.40
2996 3205 6.104243 TGGGACTGAGGGAGTAGATTATTCTA 59.896 42.308 0.00 0.00 33.83 2.10
2997 3206 7.011382 GGGACTGAGGGAGTAGATTATTCTAA 58.989 42.308 0.00 0.00 36.23 2.10
2998 3207 7.509659 GGGACTGAGGGAGTAGATTATTCTAAA 59.490 40.741 0.00 0.00 36.23 1.85
2999 3208 8.925338 GGACTGAGGGAGTAGATTATTCTAAAA 58.075 37.037 0.00 0.00 36.23 1.52
3108 3317 3.817647 GGCTGGTCAAATGATATGAGGAC 59.182 47.826 0.00 0.00 0.00 3.85
3248 3463 4.816385 CAGTGGACACGCATATTATTCCTT 59.184 41.667 0.00 0.00 36.20 3.36
3396 3617 2.686602 CAGACCATGCACAGGATCG 58.313 57.895 13.62 0.00 0.00 3.69
3433 3654 3.748568 TGCACACTTTTCATACATGCGTA 59.251 39.130 0.00 0.00 34.32 4.42
3434 3655 4.088648 GCACACTTTTCATACATGCGTAC 58.911 43.478 0.00 0.00 0.00 3.67
3435 3656 4.322934 CACACTTTTCATACATGCGTACG 58.677 43.478 11.84 11.84 0.00 3.67
3436 3657 3.991773 ACACTTTTCATACATGCGTACGT 59.008 39.130 17.90 0.00 0.00 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 6.429692 TCAATTCACCTATTATTATGCCACGG 59.570 38.462 0.00 0.00 0.00 4.94
164 187 2.496070 AGCATACCTCGACTTGCAACTA 59.504 45.455 0.00 0.00 37.56 2.24
175 198 9.477484 ACTATACATAAGAAAAAGCATACCTCG 57.523 33.333 0.00 0.00 0.00 4.63
198 221 9.453572 AGATAAATTTCTCTCAACATGCAACTA 57.546 29.630 0.00 0.00 0.00 2.24
199 222 8.242053 CAGATAAATTTCTCTCAACATGCAACT 58.758 33.333 3.24 0.00 0.00 3.16
200 223 8.025445 ACAGATAAATTTCTCTCAACATGCAAC 58.975 33.333 3.24 0.00 0.00 4.17
201 224 8.024865 CACAGATAAATTTCTCTCAACATGCAA 58.975 33.333 3.24 0.00 0.00 4.08
202 225 7.391275 TCACAGATAAATTTCTCTCAACATGCA 59.609 33.333 3.24 0.00 0.00 3.96
203 226 7.755591 TCACAGATAAATTTCTCTCAACATGC 58.244 34.615 3.24 0.00 0.00 4.06
204 227 9.770503 CTTCACAGATAAATTTCTCTCAACATG 57.229 33.333 3.24 0.00 0.00 3.21
205 228 9.730705 TCTTCACAGATAAATTTCTCTCAACAT 57.269 29.630 3.24 0.00 0.00 2.71
206 229 9.730705 ATCTTCACAGATAAATTTCTCTCAACA 57.269 29.630 3.24 0.00 38.06 3.33
208 231 9.948964 TGATCTTCACAGATAAATTTCTCTCAA 57.051 29.630 3.24 0.00 40.14 3.02
209 232 9.376075 GTGATCTTCACAGATAAATTTCTCTCA 57.624 33.333 3.24 0.00 46.22 3.27
228 279 4.111577 TGATTTAGGTGGGAGGTGATCTT 58.888 43.478 0.00 0.00 0.00 2.40
239 290 6.156519 GCAAGTAAGGTTTTGATTTAGGTGG 58.843 40.000 0.00 0.00 0.00 4.61
327 378 5.294306 ACATCAATCATGCTCGACGTAAATT 59.706 36.000 0.00 0.00 35.65 1.82
338 389 5.670792 ATTGGTTCAACATCAATCATGCT 57.329 34.783 0.00 0.00 35.65 3.79
339 390 6.798482 TCTATTGGTTCAACATCAATCATGC 58.202 36.000 0.00 0.00 35.65 4.06
359 410 7.351454 TGGGTTGTAAGGGGTTACATATTCTAT 59.649 37.037 0.00 0.00 37.27 1.98
361 412 5.493250 TGGGTTGTAAGGGGTTACATATTCT 59.507 40.000 0.00 0.00 37.27 2.40
371 422 0.927767 TTGTGTGGGTTGTAAGGGGT 59.072 50.000 0.00 0.00 0.00 4.95
378 429 4.367039 ACTAGCTAATTGTGTGGGTTGT 57.633 40.909 0.00 0.00 0.00 3.32
415 472 4.616604 CGTCCCACGATACAAGAGTGTTTA 60.617 45.833 0.00 0.00 46.05 2.01
420 477 0.815734 CCGTCCCACGATACAAGAGT 59.184 55.000 0.00 0.00 46.05 3.24
426 483 1.453762 CTCCCTCCGTCCCACGATAC 61.454 65.000 0.00 0.00 46.05 2.24
431 488 0.257039 TACTACTCCCTCCGTCCCAC 59.743 60.000 0.00 0.00 0.00 4.61
465 587 0.751452 GGTCCACGGGTAGAAGATCC 59.249 60.000 0.00 0.00 0.00 3.36
504 627 4.348461 TGTATGTGGTAGACAGAACCCAAA 59.652 41.667 0.00 0.00 38.23 3.28
582 706 1.613437 GCACTGGCGCCCAATTAATAT 59.387 47.619 26.77 0.00 30.80 1.28
694 818 6.151648 TGTTGGGATGAAGAAGATGATGAAAC 59.848 38.462 0.00 0.00 0.00 2.78
1653 1789 0.453950 CTCCTACGAACGGACACACG 60.454 60.000 0.00 0.00 40.31 4.49
1664 1800 6.467677 ACTGTGTAAGTAACTACTCCTACGA 58.532 40.000 0.00 0.00 37.36 3.43
1920 2064 8.218338 GCTGCTGCCATTTGTATTCTATATAT 57.782 34.615 3.85 0.00 0.00 0.86
1921 2065 7.615582 GCTGCTGCCATTTGTATTCTATATA 57.384 36.000 3.85 0.00 0.00 0.86
1922 2066 6.506500 GCTGCTGCCATTTGTATTCTATAT 57.493 37.500 3.85 0.00 0.00 0.86
1923 2067 5.947228 GCTGCTGCCATTTGTATTCTATA 57.053 39.130 3.85 0.00 0.00 1.31
2463 2607 4.893601 TTGGCGGCGTCGTTGTCA 62.894 61.111 12.58 1.77 38.89 3.58
2482 2626 0.179161 GAGATCAGGTCGTCCGTGTG 60.179 60.000 0.00 0.00 39.05 3.82
2589 2777 0.546122 TAAGCTACCAGCCCACCATG 59.454 55.000 0.00 0.00 43.77 3.66
2590 2778 0.839946 CTAAGCTACCAGCCCACCAT 59.160 55.000 0.00 0.00 43.77 3.55
2591 2779 1.910580 GCTAAGCTACCAGCCCACCA 61.911 60.000 4.01 0.00 43.77 4.17
2592 2780 1.153147 GCTAAGCTACCAGCCCACC 60.153 63.158 4.01 0.00 43.77 4.61
2593 2781 0.462759 CAGCTAAGCTACCAGCCCAC 60.463 60.000 10.38 0.00 43.77 4.61
2594 2782 0.617535 TCAGCTAAGCTACCAGCCCA 60.618 55.000 10.38 0.00 43.77 5.36
2655 2847 2.725008 TTTTTGCGGGAACAGCCG 59.275 55.556 0.00 0.00 37.63 5.52
2674 2866 7.780271 GGAGACATATATGGAGGAAACCTTTTT 59.220 37.037 16.96 0.00 31.76 1.94
2675 2867 7.091993 TGGAGACATATATGGAGGAAACCTTTT 60.092 37.037 16.96 0.00 30.18 2.27
2676 2868 6.389869 TGGAGACATATATGGAGGAAACCTTT 59.610 38.462 16.96 0.00 30.18 3.11
2718 2910 2.436646 GGACGCATCCACCACCAG 60.437 66.667 0.00 0.00 45.47 4.00
2872 3080 3.141398 CAGCAGCTAGAAGGAACAAACA 58.859 45.455 0.00 0.00 0.00 2.83
2900 3109 5.930837 ACAAAACAAGAATTTGGTCAGGA 57.069 34.783 4.29 0.00 41.08 3.86
2912 3121 8.559536 GTTCTGATCAGTGATAACAAAACAAGA 58.440 33.333 21.92 0.00 0.00 3.02
2936 3145 5.367945 TTTTCTGACACTTGGGAGTAGTT 57.632 39.130 0.00 0.00 33.90 2.24
2941 3150 5.520376 AAACATTTTCTGACACTTGGGAG 57.480 39.130 0.00 0.00 0.00 4.30
2942 3151 5.930837 AAAACATTTTCTGACACTTGGGA 57.069 34.783 0.00 0.00 0.00 4.37
2943 3152 6.568869 TGTAAAACATTTTCTGACACTTGGG 58.431 36.000 0.00 0.00 0.00 4.12
2947 3156 9.912634 CCATAATGTAAAACATTTTCTGACACT 57.087 29.630 10.29 0.00 45.80 3.55
2948 3157 9.139174 CCCATAATGTAAAACATTTTCTGACAC 57.861 33.333 10.29 0.00 45.80 3.67
2950 3159 9.353999 GTCCCATAATGTAAAACATTTTCTGAC 57.646 33.333 10.29 9.03 45.80 3.51
2951 3160 9.308000 AGTCCCATAATGTAAAACATTTTCTGA 57.692 29.630 10.29 1.93 45.80 3.27
2952 3161 9.357652 CAGTCCCATAATGTAAAACATTTTCTG 57.642 33.333 10.29 6.64 45.80 3.02
2955 3164 8.531146 CCTCAGTCCCATAATGTAAAACATTTT 58.469 33.333 10.29 0.81 45.80 1.82
2956 3165 7.124147 CCCTCAGTCCCATAATGTAAAACATTT 59.876 37.037 10.29 0.00 45.80 2.32
2958 3167 6.069088 TCCCTCAGTCCCATAATGTAAAACAT 60.069 38.462 0.00 0.00 41.31 2.71
2959 3168 5.251932 TCCCTCAGTCCCATAATGTAAAACA 59.748 40.000 0.00 0.00 0.00 2.83
2960 3169 5.751586 TCCCTCAGTCCCATAATGTAAAAC 58.248 41.667 0.00 0.00 0.00 2.43
2961 3170 5.491078 ACTCCCTCAGTCCCATAATGTAAAA 59.509 40.000 0.00 0.00 0.00 1.52
2962 3171 5.036916 ACTCCCTCAGTCCCATAATGTAAA 58.963 41.667 0.00 0.00 0.00 2.01
2963 3172 4.631234 ACTCCCTCAGTCCCATAATGTAA 58.369 43.478 0.00 0.00 0.00 2.41
2964 3173 4.280789 ACTCCCTCAGTCCCATAATGTA 57.719 45.455 0.00 0.00 0.00 2.29
2965 3174 3.136641 ACTCCCTCAGTCCCATAATGT 57.863 47.619 0.00 0.00 0.00 2.71
2966 3175 4.483950 TCTACTCCCTCAGTCCCATAATG 58.516 47.826 0.00 0.00 36.43 1.90
2967 3176 4.834406 TCTACTCCCTCAGTCCCATAAT 57.166 45.455 0.00 0.00 36.43 1.28
2968 3177 4.834406 ATCTACTCCCTCAGTCCCATAA 57.166 45.455 0.00 0.00 36.43 1.90
2969 3178 4.834406 AATCTACTCCCTCAGTCCCATA 57.166 45.455 0.00 0.00 36.43 2.74
2970 3179 3.715648 AATCTACTCCCTCAGTCCCAT 57.284 47.619 0.00 0.00 36.43 4.00
2971 3180 4.834406 ATAATCTACTCCCTCAGTCCCA 57.166 45.455 0.00 0.00 36.43 4.37
2972 3181 5.399113 AGAATAATCTACTCCCTCAGTCCC 58.601 45.833 0.00 0.00 36.43 4.46
2973 3182 8.480133 TTTAGAATAATCTACTCCCTCAGTCC 57.520 38.462 0.00 0.00 37.88 3.85
3248 3463 0.619255 TCCGTGGCCTATTCCTCCAA 60.619 55.000 3.32 0.00 0.00 3.53
3433 3654 3.571401 GTGCTACCCCACTATATACACGT 59.429 47.826 0.00 0.00 33.02 4.49
3434 3655 3.057033 GGTGCTACCCCACTATATACACG 60.057 52.174 0.00 0.00 36.03 4.49
3435 3656 3.899360 TGGTGCTACCCCACTATATACAC 59.101 47.826 3.33 0.00 37.50 2.90
3436 3657 4.201894 TGGTGCTACCCCACTATATACA 57.798 45.455 3.33 0.00 37.50 2.29


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

AutoCloner maintained by Alex Coulton.