Multiple sequence alignment - TraesCS3A01G281100

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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 TraesCS3A01G281100 chr3A 100.000 3269 0 0 1 3269 509997799 509994531 0.000000e+00 6037
1 TraesCS3A01G281100 chr3D 89.437 2717 109 51 536 3147 389074796 389072153 0.000000e+00 3264
2 TraesCS3A01G281100 chr3D 91.493 529 26 7 1 524 389075688 389075174 0.000000e+00 710
3 TraesCS3A01G281100 chr3B 86.520 1951 82 64 533 2347 506621369 506619464 0.000000e+00 1978
4 TraesCS3A01G281100 chr3B 84.876 886 68 26 2408 3261 506619444 506618593 0.000000e+00 833
5 TraesCS3A01G281100 chr3B 87.452 526 30 16 1 524 506623923 506623432 1.020000e-159 573
6 TraesCS3A01G281100 chr2D 80.114 176 23 5 1458 1630 150087266 150087432 1.590000e-23 121


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 TraesCS3A01G281100 chr3A 509994531 509997799 3268 True 6037 6037 100.000000 1 3269 1 chr3A.!!$R1 3268
1 TraesCS3A01G281100 chr3D 389072153 389075688 3535 True 1987 3264 90.465000 1 3147 2 chr3D.!!$R1 3146
2 TraesCS3A01G281100 chr3B 506618593 506623923 5330 True 1128 1978 86.282667 1 3261 3 chr3B.!!$R1 3260

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
658 2737 0.178953 GCCTTCCCCATGCCATGTAT 60.179 55.0 3.63 0.00 0.0 2.29 F
1071 3218 0.179187 CTCTGTCTAGTGTCCACGCG 60.179 60.0 3.53 3.53 36.2 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2105 4340 0.108329 ACATGTCCAACCCGATCGTC 60.108 55.0 15.09 0.0 0.0 4.2 R
2804 5070 0.611714 GTTTACTTGCGAGGGAGGGA 59.388 55.0 5.79 0.0 0.0 4.2 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
24 25 0.887387 CGGGAATCCCACACGTTTGT 60.887 55.000 19.81 0.00 45.83 2.83
166 167 3.344515 GTCCATTCTACAGTTGGTTCCC 58.655 50.000 0.00 0.00 0.00 3.97
234 239 2.126307 CTGGACTCACTGGACGCG 60.126 66.667 3.53 3.53 0.00 6.01
252 257 0.811616 CGCAGCCCTGGTCAGATAAC 60.812 60.000 0.00 0.00 0.00 1.89
299 304 3.260884 TGCGATTATCTTATCCTGGGGTC 59.739 47.826 0.00 0.00 0.00 4.46
302 307 5.482908 CGATTATCTTATCCTGGGGTCTTG 58.517 45.833 0.00 0.00 0.00 3.02
303 308 5.246203 CGATTATCTTATCCTGGGGTCTTGA 59.754 44.000 0.00 0.00 0.00 3.02
304 309 6.070538 CGATTATCTTATCCTGGGGTCTTGAT 60.071 42.308 0.00 0.00 0.00 2.57
305 310 4.989875 ATCTTATCCTGGGGTCTTGATG 57.010 45.455 0.00 0.00 0.00 3.07
306 311 3.736094 TCTTATCCTGGGGTCTTGATGT 58.264 45.455 0.00 0.00 0.00 3.06
309 314 1.741028 TCCTGGGGTCTTGATGTTCA 58.259 50.000 0.00 0.00 0.00 3.18
310 315 2.278245 TCCTGGGGTCTTGATGTTCAT 58.722 47.619 0.00 0.00 0.00 2.57
311 316 2.025981 TCCTGGGGTCTTGATGTTCATG 60.026 50.000 0.00 0.00 0.00 3.07
366 371 7.412853 GCCTATCTGTCATGAGTTTTGTATTG 58.587 38.462 0.00 0.00 0.00 1.90
387 392 2.154462 GCAGTATCAGCACCTGTTTGT 58.846 47.619 0.00 0.00 32.61 2.83
388 393 2.554032 GCAGTATCAGCACCTGTTTGTT 59.446 45.455 0.00 0.00 32.61 2.83
389 394 3.004734 GCAGTATCAGCACCTGTTTGTTT 59.995 43.478 0.00 0.00 32.61 2.83
390 395 4.539870 CAGTATCAGCACCTGTTTGTTTG 58.460 43.478 0.00 0.00 32.61 2.93
459 464 8.327941 ACGCGAAAGGTATGTATAGATACTTA 57.672 34.615 15.93 0.00 34.41 2.24
460 465 8.233190 ACGCGAAAGGTATGTATAGATACTTAC 58.767 37.037 15.93 13.50 40.41 2.34
461 466 8.449397 CGCGAAAGGTATGTATAGATACTTACT 58.551 37.037 17.00 5.92 40.69 2.24
475 480 1.002087 ACTTACTTGCTTCCAGTCCCG 59.998 52.381 0.00 0.00 0.00 5.14
499 504 3.082701 AGCTCAGCTGGGCTCCTC 61.083 66.667 35.62 7.76 37.57 3.71
518 524 2.045536 CTTCCTCCCCACAGCTGC 60.046 66.667 15.27 0.00 0.00 5.25
568 2639 2.128853 AAATTGCACCGTGTCCAGCG 62.129 55.000 0.00 0.00 0.00 5.18
654 2733 4.528039 CCGCCTTCCCCATGCCAT 62.528 66.667 0.00 0.00 0.00 4.40
655 2734 3.221389 CGCCTTCCCCATGCCATG 61.221 66.667 0.00 0.00 0.00 3.66
656 2735 2.042639 GCCTTCCCCATGCCATGT 60.043 61.111 3.63 0.00 0.00 3.21
657 2736 1.229927 GCCTTCCCCATGCCATGTA 59.770 57.895 3.63 0.00 0.00 2.29
658 2737 0.178953 GCCTTCCCCATGCCATGTAT 60.179 55.000 3.63 0.00 0.00 2.29
659 2738 1.624336 CCTTCCCCATGCCATGTATG 58.376 55.000 3.63 0.00 0.00 2.39
660 2739 0.963962 CTTCCCCATGCCATGTATGC 59.036 55.000 3.63 0.00 0.00 3.14
664 2743 2.253154 CATGCCATGTATGCGCGG 59.747 61.111 8.83 0.00 0.00 6.46
742 2821 2.286935 AGCTAAATCCAGGAGGGGAA 57.713 50.000 0.00 0.00 41.12 3.97
743 2822 2.131023 AGCTAAATCCAGGAGGGGAAG 58.869 52.381 0.00 0.00 41.12 3.46
744 2823 1.143889 GCTAAATCCAGGAGGGGAAGG 59.856 57.143 0.00 0.00 41.12 3.46
745 2824 1.143889 CTAAATCCAGGAGGGGAAGGC 59.856 57.143 0.00 0.00 41.12 4.35
746 2825 1.584717 AAATCCAGGAGGGGAAGGCC 61.585 60.000 0.00 0.00 41.12 5.19
775 2857 1.630126 ATGGGATCCAAGACGCAGCT 61.630 55.000 15.23 0.00 36.95 4.24
776 2858 1.078143 GGGATCCAAGACGCAGCTT 60.078 57.895 15.23 0.00 0.00 3.74
938 3055 0.796312 GGTTTTGCTTCGAGATCGCA 59.204 50.000 0.00 0.00 39.60 5.10
939 3056 1.464189 GGTTTTGCTTCGAGATCGCAC 60.464 52.381 0.00 0.00 39.60 5.34
990 3119 0.248907 ACGAATGCGATAGTGGACCG 60.249 55.000 0.00 0.00 41.64 4.79
998 3127 1.738030 CGATAGTGGACCGAACCAACC 60.738 57.143 2.36 0.00 41.87 3.77
1007 3136 2.355115 GAACCAACCCCAGCCGAT 59.645 61.111 0.00 0.00 0.00 4.18
1008 3137 1.749258 GAACCAACCCCAGCCGATC 60.749 63.158 0.00 0.00 0.00 3.69
1009 3138 3.282374 AACCAACCCCAGCCGATCC 62.282 63.158 0.00 0.00 0.00 3.36
1010 3139 3.411517 CCAACCCCAGCCGATCCT 61.412 66.667 0.00 0.00 0.00 3.24
1011 3140 2.190578 CAACCCCAGCCGATCCTC 59.809 66.667 0.00 0.00 0.00 3.71
1071 3218 0.179187 CTCTGTCTAGTGTCCACGCG 60.179 60.000 3.53 3.53 36.20 6.01
1175 3336 2.035155 TCGGTCTTCTCCAGGCGA 59.965 61.111 0.00 0.00 0.00 5.54
1181 3342 3.798954 CTTCTCCAGGCGATCGGGC 62.799 68.421 18.30 10.00 42.69 6.13
1571 3768 4.057428 AGGCTGTCGACGCACTCC 62.057 66.667 25.67 15.56 0.00 3.85
1879 4076 1.226323 CGTACGAGGACTTCCGCAG 60.226 63.158 10.44 0.00 42.08 5.18
2042 4251 3.959991 GACGCTCTGCCCCTGAACC 62.960 68.421 0.00 0.00 0.00 3.62
2049 4284 4.547367 GCCCCTGAACCCGATCGG 62.547 72.222 27.65 27.65 37.81 4.18
2063 4298 3.257375 CCCGATCGGTGTTGATAGGATTA 59.743 47.826 31.22 0.00 41.97 1.75
2064 4299 4.081642 CCCGATCGGTGTTGATAGGATTAT 60.082 45.833 31.22 0.00 41.97 1.28
2065 4300 5.479306 CCGATCGGTGTTGATAGGATTATT 58.521 41.667 26.35 0.00 41.97 1.40
2073 4308 8.342634 CGGTGTTGATAGGATTATTAACCTTTG 58.657 37.037 0.00 0.00 35.82 2.77
2105 4340 0.591659 CGAGATGAATGGCATGGCAG 59.408 55.000 27.02 7.28 37.34 4.85
2113 4348 2.969238 GGCATGGCAGACGATCGG 60.969 66.667 20.98 2.45 0.00 4.18
2156 4391 0.666577 GCTTACGTGCGTTGTCTCCT 60.667 55.000 1.66 0.00 0.00 3.69
2192 4427 3.791245 CTGGATCTTGACCAGCTAACTC 58.209 50.000 0.00 0.00 46.30 3.01
2216 4451 0.604578 TTAGTTGGGAGTTCCGGACG 59.395 55.000 1.83 0.00 38.76 4.79
2230 4465 2.582978 GACGCCCCCTGTAGTTCC 59.417 66.667 0.00 0.00 0.00 3.62
2236 4471 1.218316 CCCCTGTAGTTCCGTCAGC 59.782 63.158 0.00 0.00 0.00 4.26
2278 4513 8.154649 AGTTTCTTGATGTTAACTTGTAGTGG 57.845 34.615 7.22 0.00 0.00 4.00
2279 4514 7.773690 AGTTTCTTGATGTTAACTTGTAGTGGT 59.226 33.333 7.22 0.00 0.00 4.16
2288 4523 1.900486 ACTTGTAGTGGTAGTCCAGCC 59.100 52.381 0.00 0.00 45.24 4.85
2292 4527 1.481363 GTAGTGGTAGTCCAGCCTTCC 59.519 57.143 0.00 0.00 45.24 3.46
2357 4592 9.333497 ACGCGATATATTTTGATTGATTGATTG 57.667 29.630 15.93 0.00 0.00 2.67
2371 4606 9.787532 GATTGATTGATTGAAGGTATTTTCGAA 57.212 29.630 0.00 0.00 0.00 3.71
2385 4620 3.984018 TTTCGAATTAGCTTTCGTCCG 57.016 42.857 17.57 4.03 46.50 4.79
2398 4633 2.304751 TCGTCCGGCTTTCTTATTCC 57.695 50.000 0.00 0.00 0.00 3.01
2399 4634 1.134610 TCGTCCGGCTTTCTTATTCCC 60.135 52.381 0.00 0.00 0.00 3.97
2400 4635 1.676746 GTCCGGCTTTCTTATTCCCC 58.323 55.000 0.00 0.00 0.00 4.81
2421 4656 4.148825 CCGTTCCTCCTCCCGCAG 62.149 72.222 0.00 0.00 0.00 5.18
2429 4664 0.462759 CTCCTCCCGCAGAATCAACC 60.463 60.000 0.00 0.00 0.00 3.77
2457 4692 3.837213 ATTGCAAATTCAGTCGACCTG 57.163 42.857 13.01 10.13 42.97 4.00
2476 4711 3.310774 CCTGCATATGGCTATTGCGATAC 59.689 47.826 4.56 0.00 41.41 2.24
2589 4855 1.004918 AACGAGCTCCCCACGAAAG 60.005 57.895 8.47 0.00 0.00 2.62
2590 4856 1.469335 AACGAGCTCCCCACGAAAGA 61.469 55.000 8.47 0.00 0.00 2.52
2612 4878 3.463048 AAACTCAATCCCCAAGAGCAT 57.537 42.857 0.00 0.00 32.71 3.79
2617 4883 3.958798 CTCAATCCCCAAGAGCATGAAAT 59.041 43.478 0.00 0.00 0.00 2.17
2649 4915 3.885724 TTTCTAGTCGCATGTGGATCA 57.114 42.857 6.39 0.00 0.00 2.92
2703 4969 1.355796 TATTCCGTGCTTCGTTGCGG 61.356 55.000 0.00 0.00 44.95 5.69
2710 4976 3.793144 CTTCGTTGCGGCTCTGCC 61.793 66.667 0.00 0.00 46.75 4.85
2759 5025 0.605589 AGGAGTAGCCGGCAAACAAC 60.606 55.000 31.54 20.65 43.43 3.32
2760 5026 1.495951 GAGTAGCCGGCAAACAACG 59.504 57.895 31.54 0.00 0.00 4.10
2802 5068 3.213402 CGTCCGGCCTCTCTCTCC 61.213 72.222 0.00 0.00 0.00 3.71
2803 5069 2.835895 GTCCGGCCTCTCTCTCCC 60.836 72.222 0.00 0.00 0.00 4.30
2804 5070 3.024356 TCCGGCCTCTCTCTCCCT 61.024 66.667 0.00 0.00 0.00 4.20
2805 5071 2.520741 CCGGCCTCTCTCTCCCTC 60.521 72.222 0.00 0.00 0.00 4.30
2806 5072 2.520741 CGGCCTCTCTCTCCCTCC 60.521 72.222 0.00 0.00 0.00 4.30
2807 5073 2.123033 GGCCTCTCTCTCCCTCCC 60.123 72.222 0.00 0.00 0.00 4.30
2808 5074 2.710826 GGCCTCTCTCTCCCTCCCT 61.711 68.421 0.00 0.00 0.00 4.20
2809 5075 1.152546 GCCTCTCTCTCCCTCCCTC 60.153 68.421 0.00 0.00 0.00 4.30
2814 5080 2.197324 CTCTCCCTCCCTCCCTCG 59.803 72.222 0.00 0.00 0.00 4.63
2832 5098 1.010574 GCAAGTAAACGCACACGCA 60.011 52.632 0.00 0.00 45.53 5.24
2852 5130 0.250338 GGCAGGGACATTACCGGATC 60.250 60.000 9.46 0.00 0.00 3.36
2853 5131 0.759346 GCAGGGACATTACCGGATCT 59.241 55.000 9.46 0.00 0.00 2.75
2854 5132 1.141053 GCAGGGACATTACCGGATCTT 59.859 52.381 9.46 0.00 0.00 2.40
2942 5221 4.360027 GGTATGCATGCGCTCGCG 62.360 66.667 14.09 6.98 45.51 5.87
2958 5237 2.123425 CGGGCTAGCTGGGTAGGA 60.123 66.667 15.72 0.00 0.00 2.94
2960 5239 1.839296 GGGCTAGCTGGGTAGGAGG 60.839 68.421 15.72 0.00 0.00 4.30
2961 5240 1.233369 GGCTAGCTGGGTAGGAGGA 59.767 63.158 15.72 0.00 0.00 3.71
2962 5241 0.830023 GGCTAGCTGGGTAGGAGGAG 60.830 65.000 15.72 0.00 0.00 3.69
2963 5242 0.830023 GCTAGCTGGGTAGGAGGAGG 60.830 65.000 7.70 0.00 0.00 4.30
2964 5243 0.854218 CTAGCTGGGTAGGAGGAGGA 59.146 60.000 0.00 0.00 0.00 3.71
2965 5244 0.854218 TAGCTGGGTAGGAGGAGGAG 59.146 60.000 0.00 0.00 0.00 3.69
2966 5245 1.458588 GCTGGGTAGGAGGAGGAGG 60.459 68.421 0.00 0.00 0.00 4.30
2967 5246 1.950748 GCTGGGTAGGAGGAGGAGGA 61.951 65.000 0.00 0.00 0.00 3.71
2968 5247 0.187361 CTGGGTAGGAGGAGGAGGAG 59.813 65.000 0.00 0.00 0.00 3.69
3037 5316 1.070289 GCTAGATTGGTAGGAACGGGG 59.930 57.143 0.00 0.00 0.00 5.73
3038 5317 1.692519 CTAGATTGGTAGGAACGGGGG 59.307 57.143 0.00 0.00 0.00 5.40
3079 5358 1.209127 GAATCGCACCAACCAACCG 59.791 57.895 0.00 0.00 0.00 4.44
3080 5359 2.195123 GAATCGCACCAACCAACCGG 62.195 60.000 0.00 0.00 38.77 5.28
3215 5521 3.716006 CAGTGTGCAGGGCGAACG 61.716 66.667 0.00 0.00 0.00 3.95
3216 5522 4.988598 AGTGTGCAGGGCGAACGG 62.989 66.667 0.00 0.00 0.00 4.44
3254 5560 2.173669 GCTGTGTGTCTGTGCACGT 61.174 57.895 13.13 0.00 41.94 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 4.679373 TGCAAGGGAGCAAATAACAAAA 57.321 36.364 0.00 0.00 42.46 2.44
54 55 1.607467 ACCTCCTGCCATTTGTGCC 60.607 57.895 0.00 0.00 0.00 5.01
55 56 1.588082 CACCTCCTGCCATTTGTGC 59.412 57.895 0.00 0.00 0.00 4.57
234 239 0.543749 AGTTATCTGACCAGGGCTGC 59.456 55.000 0.00 0.00 0.00 5.25
325 330 2.080654 AGGCCTAACAAACCAAGCAA 57.919 45.000 1.29 0.00 0.00 3.91
366 371 1.470098 CAAACAGGTGCTGATACTGCC 59.530 52.381 0.00 0.00 35.70 4.85
459 464 1.371558 GTCGGGACTGGAAGCAAGT 59.628 57.895 0.00 0.00 37.60 3.16
460 465 1.738099 CGTCGGGACTGGAAGCAAG 60.738 63.158 0.00 0.00 37.60 4.01
461 466 1.750341 TTCGTCGGGACTGGAAGCAA 61.750 55.000 0.00 0.00 37.60 3.91
462 467 2.204461 TTCGTCGGGACTGGAAGCA 61.204 57.895 0.00 0.00 37.60 3.91
499 504 2.612115 AGCTGTGGGGAGGAAGGG 60.612 66.667 0.00 0.00 0.00 3.95
518 524 0.401738 TCAGGAAAAGAGGTGCCCAG 59.598 55.000 0.00 0.00 0.00 4.45
524 530 3.412386 CGGTTTCATCAGGAAAAGAGGT 58.588 45.455 0.00 0.00 46.53 3.85
526 532 3.412386 ACCGGTTTCATCAGGAAAAGAG 58.588 45.455 0.00 0.00 46.53 2.85
528 534 3.146066 TGACCGGTTTCATCAGGAAAAG 58.854 45.455 9.42 0.00 46.53 2.27
530 536 2.940994 TGACCGGTTTCATCAGGAAA 57.059 45.000 9.42 0.00 43.07 3.13
645 2724 2.646719 GCGCATACATGGCATGGG 59.353 61.111 29.49 19.31 38.86 4.00
745 2824 2.124320 ATCCCATTTCACCCGCGG 60.124 61.111 21.04 21.04 0.00 6.46
746 2825 2.186826 GGATCCCATTTCACCCGCG 61.187 63.158 0.00 0.00 0.00 6.46
747 2826 0.682855 TTGGATCCCATTTCACCCGC 60.683 55.000 9.90 0.00 31.53 6.13
748 2827 1.064758 TCTTGGATCCCATTTCACCCG 60.065 52.381 9.90 0.00 31.53 5.28
749 2828 2.379005 GTCTTGGATCCCATTTCACCC 58.621 52.381 9.90 0.00 31.53 4.61
753 2832 1.672881 CTGCGTCTTGGATCCCATTTC 59.327 52.381 9.90 0.00 31.53 2.17
938 3055 1.605451 GCCTGGCCTTTTAACCGGT 60.605 57.895 7.66 0.00 0.00 5.28
939 3056 2.348104 GGCCTGGCCTTTTAACCGG 61.348 63.158 30.42 0.00 46.69 5.28
968 3097 0.174617 TCCACTATCGCATTCGTGCA 59.825 50.000 1.08 0.00 36.96 4.57
985 3114 2.033602 CTGGGGTTGGTTCGGTCC 59.966 66.667 0.00 0.00 0.00 4.46
990 3119 1.749258 GATCGGCTGGGGTTGGTTC 60.749 63.158 0.00 0.00 0.00 3.62
998 3127 3.237741 GGGAGAGGATCGGCTGGG 61.238 72.222 0.00 0.00 42.67 4.45
1007 3136 1.942271 GGGAGATGGAGGGAGAGGA 59.058 63.158 0.00 0.00 0.00 3.71
1008 3137 1.532794 CGGGAGATGGAGGGAGAGG 60.533 68.421 0.00 0.00 0.00 3.69
1009 3138 2.206536 GCGGGAGATGGAGGGAGAG 61.207 68.421 0.00 0.00 0.00 3.20
1010 3139 2.123251 GCGGGAGATGGAGGGAGA 60.123 66.667 0.00 0.00 0.00 3.71
1011 3140 3.237741 GGCGGGAGATGGAGGGAG 61.238 72.222 0.00 0.00 0.00 4.30
1056 3185 2.874780 CGCGCGTGGACACTAGAC 60.875 66.667 24.19 0.00 0.00 2.59
1220 3381 1.227674 GTAGGAGGGCAATGCGAGG 60.228 63.158 0.00 0.00 0.00 4.63
1879 4076 1.274728 CGATCATCTCCTCCATGGACC 59.725 57.143 11.44 0.00 40.56 4.46
1947 4156 1.251527 ACCAGGTACGTCTCCAGCAG 61.252 60.000 11.40 0.00 0.00 4.24
2042 4251 3.386768 AATCCTATCAACACCGATCGG 57.613 47.619 32.20 32.20 42.03 4.18
2049 4284 7.855904 CGCAAAGGTTAATAATCCTATCAACAC 59.144 37.037 0.00 0.00 33.27 3.32
2063 4298 4.499183 CTCTCACTCTCGCAAAGGTTAAT 58.501 43.478 0.00 0.00 0.00 1.40
2064 4299 3.861131 GCTCTCACTCTCGCAAAGGTTAA 60.861 47.826 0.00 0.00 0.00 2.01
2065 4300 2.352814 GCTCTCACTCTCGCAAAGGTTA 60.353 50.000 0.00 0.00 0.00 2.85
2073 4308 0.316937 CATCTCGCTCTCACTCTCGC 60.317 60.000 0.00 0.00 0.00 5.03
2105 4340 0.108329 ACATGTCCAACCCGATCGTC 60.108 55.000 15.09 0.00 0.00 4.20
2113 4348 0.881118 AACATCGCACATGTCCAACC 59.119 50.000 0.00 0.00 0.00 3.77
2156 4391 2.488204 TCCAGCCATGAATGAACGAA 57.512 45.000 0.00 0.00 0.00 3.85
2192 4427 1.439679 GGAACTCCCAACTAAGCACG 58.560 55.000 0.00 0.00 34.14 5.34
2216 4451 2.240162 CTGACGGAACTACAGGGGGC 62.240 65.000 0.00 0.00 0.00 5.80
2230 4465 1.823828 GTACAGTACCATCGCTGACG 58.176 55.000 0.00 0.00 42.01 4.35
2277 4512 2.187163 GCGGAAGGCTGGACTACC 59.813 66.667 0.00 0.00 39.11 3.18
2288 4523 1.391485 CGAGAACATTCACAGCGGAAG 59.609 52.381 0.00 0.00 0.00 3.46
2292 4527 1.388093 CTGACGAGAACATTCACAGCG 59.612 52.381 0.00 0.00 0.00 5.18
2296 4531 4.518217 CACAAACTGACGAGAACATTCAC 58.482 43.478 0.00 0.00 0.00 3.18
2354 4589 9.788960 GAAAGCTAATTCGAAAATACCTTCAAT 57.211 29.630 0.00 0.00 0.00 2.57
2371 4606 2.007608 GAAAGCCGGACGAAAGCTAAT 58.992 47.619 5.05 0.00 35.30 1.73
2381 4616 1.676746 GGGGAATAAGAAAGCCGGAC 58.323 55.000 5.05 0.00 0.00 4.79
2385 4620 1.107538 GCCGGGGGAATAAGAAAGCC 61.108 60.000 2.18 0.00 0.00 4.35
2421 4656 6.557291 TTTGCAATTTGAATGGGTTGATTC 57.443 33.333 0.00 0.00 33.59 2.52
2429 4664 5.634439 TCGACTGAATTTGCAATTTGAATGG 59.366 36.000 11.11 0.00 0.00 3.16
2457 4692 4.944962 TTGTATCGCAATAGCCATATGC 57.055 40.909 0.00 0.00 37.52 3.14
2476 4711 6.316640 AGAGTTGAATCAAGCAGAGATGATTG 59.683 38.462 5.79 0.00 44.15 2.67
2589 4855 3.573967 TGCTCTTGGGGATTGAGTTTTTC 59.426 43.478 0.00 0.00 0.00 2.29
2590 4856 3.575805 TGCTCTTGGGGATTGAGTTTTT 58.424 40.909 0.00 0.00 0.00 1.94
2617 4883 3.561503 CGACTAGAAATGTGTGTCGTCA 58.438 45.455 0.00 0.00 43.43 4.35
2624 4890 3.002791 CCACATGCGACTAGAAATGTGT 58.997 45.455 20.04 8.89 45.39 3.72
2631 4897 4.371786 GAAATGATCCACATGCGACTAGA 58.628 43.478 0.00 0.00 39.39 2.43
2649 4915 5.579511 CGTGTTAGAGTATTCGGTTGGAAAT 59.420 40.000 0.00 0.00 38.36 2.17
2703 4969 2.508526 CTTATTGTATGGGGGCAGAGC 58.491 52.381 0.00 0.00 0.00 4.09
2710 4976 6.538381 GGATTTTGTTTGCTTATTGTATGGGG 59.462 38.462 0.00 0.00 0.00 4.96
2759 5025 0.673644 ATTTGGCACTTCTCCGTCCG 60.674 55.000 0.00 0.00 0.00 4.79
2760 5026 1.200020 CAATTTGGCACTTCTCCGTCC 59.800 52.381 0.00 0.00 0.00 4.79
2761 5027 1.200020 CCAATTTGGCACTTCTCCGTC 59.800 52.381 1.71 0.00 0.00 4.79
2802 5068 0.976073 TTACTTGCGAGGGAGGGAGG 60.976 60.000 5.79 0.00 0.00 4.30
2803 5069 0.902531 TTTACTTGCGAGGGAGGGAG 59.097 55.000 5.79 0.00 0.00 4.30
2804 5070 0.611714 GTTTACTTGCGAGGGAGGGA 59.388 55.000 5.79 0.00 0.00 4.20
2805 5071 0.739813 CGTTTACTTGCGAGGGAGGG 60.740 60.000 5.79 0.00 0.00 4.30
2806 5072 1.359459 GCGTTTACTTGCGAGGGAGG 61.359 60.000 5.79 0.00 0.00 4.30
2807 5073 0.669318 TGCGTTTACTTGCGAGGGAG 60.669 55.000 5.79 0.00 0.00 4.30
2808 5074 0.947180 GTGCGTTTACTTGCGAGGGA 60.947 55.000 5.79 0.00 0.00 4.20
2809 5075 1.225376 TGTGCGTTTACTTGCGAGGG 61.225 55.000 5.79 0.00 0.00 4.30
2814 5080 3.809990 GCGTGTGCGTTTACTTGC 58.190 55.556 0.00 0.00 40.81 4.01
2832 5098 0.694444 ATCCGGTAATGTCCCTGCCT 60.694 55.000 0.00 0.00 0.00 4.75
2852 5130 7.502339 CGACTTCCGTTTGCATATTATAGAAG 58.498 38.462 0.00 0.00 35.48 2.85
2853 5131 7.402811 CGACTTCCGTTTGCATATTATAGAA 57.597 36.000 0.00 0.00 0.00 2.10
2877 5156 0.796312 ACACATTCATTCACGCCGAC 59.204 50.000 0.00 0.00 0.00 4.79
2942 5221 1.839296 CCTCCTACCCAGCTAGCCC 60.839 68.421 12.13 0.00 0.00 5.19
2951 5230 1.544703 CCTCCTCCTCCTCCTACCC 59.455 68.421 0.00 0.00 0.00 3.69
2963 5242 4.479993 ACATGCCTGCGCCTCCTC 62.480 66.667 4.18 0.00 0.00 3.71
2964 5243 4.790962 CACATGCCTGCGCCTCCT 62.791 66.667 4.18 0.00 0.00 3.69
2975 5254 4.101790 CCAACCCGACGCACATGC 62.102 66.667 0.00 0.00 37.78 4.06
3009 5288 3.451178 TCCTACCAATCTAGCAACCAGAC 59.549 47.826 0.00 0.00 0.00 3.51
3238 5544 0.868177 CGTACGTGCACAGACACACA 60.868 55.000 18.64 0.00 40.73 3.72
3240 5546 0.662085 TACGTACGTGCACAGACACA 59.338 50.000 30.25 3.44 40.73 3.72
3241 5547 1.047739 GTACGTACGTGCACAGACAC 58.952 55.000 30.25 14.07 37.19 3.67


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

AutoCloner maintained by Alex Coulton.