Multiple sequence alignment - TraesCS6A01G102000

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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 TraesCS6A01G102000 chr6A 100.000 3322 0 0 1 3322 70936769 70933448 0.000000e+00 6135
1 TraesCS6A01G102000 chr6A 90.137 1095 97 8 70 1156 60157146 60156055 0.000000e+00 1413
2 TraesCS6A01G102000 chr6A 87.016 1032 116 8 1322 2335 68502113 68503144 0.000000e+00 1147
3 TraesCS6A01G102000 chr6D 95.962 2749 99 4 1 2738 56297246 56294499 0.000000e+00 4451
4 TraesCS6A01G102000 chr6D 87.278 1014 129 0 1322 2335 47267110 47266097 0.000000e+00 1158
5 TraesCS6A01G102000 chr6D 95.178 477 20 3 2842 3317 56294500 56294026 0.000000e+00 750
6 TraesCS6A01G102000 chr6B 95.131 2485 102 6 257 2738 126729866 126727398 0.000000e+00 3901
7 TraesCS6A01G102000 chr6B 87.172 1029 117 5 1322 2335 124466101 124467129 0.000000e+00 1155
8 TraesCS6A01G102000 chr6B 96.935 261 6 1 1 259 126743129 126742869 1.420000e-118 436
9 TraesCS6A01G102000 chr6B 93.863 277 17 0 2842 3118 126727399 126727123 5.130000e-113 418
10 TraesCS6A01G102000 chr6B 91.866 209 16 1 3110 3317 126725984 126725776 1.170000e-74 291
11 TraesCS6A01G102000 chr6B 98.261 115 2 0 2734 2848 460495299 460495413 5.620000e-48 202
12 TraesCS6A01G102000 chr3A 89.858 1124 101 11 38 1156 715137193 715138308 0.000000e+00 1432
13 TraesCS6A01G102000 chr2A 89.327 1115 101 9 38 1146 758294869 758293767 0.000000e+00 1384
14 TraesCS6A01G102000 chr7A 88.978 1125 109 12 38 1156 672452117 672453232 0.000000e+00 1376
15 TraesCS6A01G102000 chr7A 85.000 200 30 0 1855 2054 729889836 729890035 1.560000e-48 204
16 TraesCS6A01G102000 chr7D 87.721 1132 99 20 38 1156 325937639 325936535 0.000000e+00 1284
17 TraesCS6A01G102000 chr7D 97.414 116 3 0 2736 2851 556642494 556642379 7.270000e-47 198
18 TraesCS6A01G102000 chr4A 90.795 880 76 4 281 1156 614522783 614521905 0.000000e+00 1171
19 TraesCS6A01G102000 chr7B 91.357 833 66 5 328 1156 164154010 164154840 0.000000e+00 1134
20 TraesCS6A01G102000 chr7B 100.000 109 0 0 2737 2845 297402292 297402184 5.620000e-48 202
21 TraesCS6A01G102000 chr7B 100.000 109 0 0 2735 2843 730205222 730205114 5.620000e-48 202
22 TraesCS6A01G102000 chr5D 100.000 110 0 0 2737 2846 408792000 408791891 1.560000e-48 204
23 TraesCS6A01G102000 chr1D 99.099 111 1 0 2734 2844 19774679 19774789 2.020000e-47 200
24 TraesCS6A01G102000 chr1D 99.099 111 1 0 2733 2843 414643238 414643348 2.020000e-47 200
25 TraesCS6A01G102000 chr5B 84.772 197 30 0 1861 2057 591662262 591662066 7.270000e-47 198
26 TraesCS6A01G102000 chr4D 96.639 119 3 1 2729 2847 479457598 479457481 2.610000e-46 196
27 TraesCS6A01G102000 chr2D 84.080 201 30 2 1855 2054 645837135 645837334 3.380000e-45 193
28 TraesCS6A01G102000 chr2D 94.355 124 6 1 2720 2843 427121179 427121301 4.380000e-44 189
29 TraesCS6A01G102000 chr5A 90.083 121 9 2 16 134 692233157 692233038 1.600000e-33 154


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 TraesCS6A01G102000 chr6A 70933448 70936769 3321 True 6135.000000 6135 100.000 1 3322 1 chr6A.!!$R2 3321
1 TraesCS6A01G102000 chr6A 60156055 60157146 1091 True 1413.000000 1413 90.137 70 1156 1 chr6A.!!$R1 1086
2 TraesCS6A01G102000 chr6A 68502113 68503144 1031 False 1147.000000 1147 87.016 1322 2335 1 chr6A.!!$F1 1013
3 TraesCS6A01G102000 chr6D 56294026 56297246 3220 True 2600.500000 4451 95.570 1 3317 2 chr6D.!!$R2 3316
4 TraesCS6A01G102000 chr6D 47266097 47267110 1013 True 1158.000000 1158 87.278 1322 2335 1 chr6D.!!$R1 1013
5 TraesCS6A01G102000 chr6B 126725776 126729866 4090 True 1536.666667 3901 93.620 257 3317 3 chr6B.!!$R2 3060
6 TraesCS6A01G102000 chr6B 124466101 124467129 1028 False 1155.000000 1155 87.172 1322 2335 1 chr6B.!!$F1 1013
7 TraesCS6A01G102000 chr3A 715137193 715138308 1115 False 1432.000000 1432 89.858 38 1156 1 chr3A.!!$F1 1118
8 TraesCS6A01G102000 chr2A 758293767 758294869 1102 True 1384.000000 1384 89.327 38 1146 1 chr2A.!!$R1 1108
9 TraesCS6A01G102000 chr7A 672452117 672453232 1115 False 1376.000000 1376 88.978 38 1156 1 chr7A.!!$F1 1118
10 TraesCS6A01G102000 chr7D 325936535 325937639 1104 True 1284.000000 1284 87.721 38 1156 1 chr7D.!!$R1 1118
11 TraesCS6A01G102000 chr4A 614521905 614522783 878 True 1171.000000 1171 90.795 281 1156 1 chr4A.!!$R1 875
12 TraesCS6A01G102000 chr7B 164154010 164154840 830 False 1134.000000 1134 91.357 328 1156 1 chr7B.!!$F1 828

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
64 67 1.002792 TCGTAATCGGCTCGACATGAG 60.003 52.381 0.00 0.0 39.18 2.90 F
1589 1641 1.750399 CCCCATGCTTACGCTTGCT 60.750 57.895 1.92 0.0 39.30 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2024 2076 0.670706 CGATCTCTTCATCGGCTCCA 59.329 55.000 0.0 0.0 41.71 3.86 R
2484 2536 1.077716 ACTGGGTATTGAAGCGGCC 60.078 57.895 0.0 0.0 0.00 6.13 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
28 31 9.703892 TGACTTTTGTATCCATTTACATTTTGG 57.296 29.630 0.00 0.00 32.39 3.28
62 65 2.051879 ATCGTAATCGGCTCGACATG 57.948 50.000 0.00 0.00 39.18 3.21
63 66 1.018910 TCGTAATCGGCTCGACATGA 58.981 50.000 0.00 0.54 39.18 3.07
64 67 1.002792 TCGTAATCGGCTCGACATGAG 60.003 52.381 0.00 0.00 39.18 2.90
65 68 1.772182 GTAATCGGCTCGACATGAGG 58.228 55.000 0.00 0.00 45.38 3.86
161 180 5.193728 TCCTTCCTCTGCCCATAGTTAATTT 59.806 40.000 0.00 0.00 0.00 1.82
252 271 4.898861 AGAACAAAGGGCACAAAATCCTTA 59.101 37.500 0.00 0.00 39.72 2.69
331 350 3.125146 TCGCTTCAGTTTCACATGCATAC 59.875 43.478 0.00 0.00 0.00 2.39
646 667 4.021104 CCTATTCGTATCAGCATTCCCTCA 60.021 45.833 0.00 0.00 0.00 3.86
712 735 6.932356 ATAGTGCATTTACACAGGAATCAG 57.068 37.500 0.00 0.00 43.23 2.90
716 739 4.696877 TGCATTTACACAGGAATCAGACAG 59.303 41.667 0.00 0.00 0.00 3.51
792 815 5.911280 CCTAGCATCGCATGACTTATTTTTG 59.089 40.000 0.00 0.00 0.00 2.44
991 1014 4.842531 TCATCTTATGCCTTTCCACTCA 57.157 40.909 0.00 0.00 0.00 3.41
1074 1105 4.343239 AGAGTCCTTTTCATTGCAAAAGCT 59.657 37.500 1.71 0.00 40.62 3.74
1087 1121 5.429681 TGCAAAAGCTAGTACTCCCATTA 57.570 39.130 0.00 0.00 0.00 1.90
1320 1354 4.184649 ACCAGTTCCTCCAAATTCAGTT 57.815 40.909 0.00 0.00 0.00 3.16
1586 1638 2.824041 CGCCCCATGCTTACGCTT 60.824 61.111 0.00 0.00 38.05 4.68
1589 1641 1.750399 CCCCATGCTTACGCTTGCT 60.750 57.895 1.92 0.00 39.30 3.91
1738 1790 2.203098 CCCCACAAACCACGTCGT 60.203 61.111 0.00 0.00 0.00 4.34
1839 1891 4.802051 ATGGCATGCCGGCGAACT 62.802 61.111 30.87 2.98 45.16 3.01
1925 1977 2.045926 GTGGACCTTGCCAGCGAT 60.046 61.111 0.00 0.00 38.95 4.58
2202 2254 2.690510 TGATGGGCATGGACGGGA 60.691 61.111 0.00 0.00 0.00 5.14
2204 2256 3.774599 GATGGGCATGGACGGGACC 62.775 68.421 0.00 0.00 0.00 4.46
2306 2358 2.099062 CTCGCGCACTTCATTGCC 59.901 61.111 8.75 0.00 39.53 4.52
2392 2444 4.065088 TCTCACCAGATTTTTCTGTTCGG 58.935 43.478 2.61 0.00 36.06 4.30
2473 2525 2.103373 TGAGGAGGTCAGTGATAGTGC 58.897 52.381 0.00 0.00 0.00 4.40
2474 2526 2.103373 GAGGAGGTCAGTGATAGTGCA 58.897 52.381 0.00 0.00 0.00 4.57
2477 2529 3.024547 GGAGGTCAGTGATAGTGCAGTA 58.975 50.000 3.17 3.17 0.00 2.74
2484 2536 2.362397 AGTGATAGTGCAGTACGATGGG 59.638 50.000 2.64 0.00 0.00 4.00
2494 2546 2.661066 TACGATGGGGCCGCTTCAA 61.661 57.895 28.08 16.62 0.00 2.69
2509 2561 0.323302 TTCAATACCCAGTCAGCGCA 59.677 50.000 11.47 0.00 0.00 6.09
2554 2606 0.764752 AGCTCCCGGCCTATAGCTTT 60.765 55.000 14.75 0.00 42.52 3.51
2559 2611 0.468226 CCGGCCTATAGCTTTGACCA 59.532 55.000 0.00 0.00 43.05 4.02
2582 2634 3.368843 GCAGATCTATATGTGCGGGATGT 60.369 47.826 0.00 0.00 41.88 3.06
2611 2663 1.077858 GCTGAAAGGGAGGGCTCAG 60.078 63.158 0.00 0.00 38.66 3.35
2612 2664 1.846712 GCTGAAAGGGAGGGCTCAGT 61.847 60.000 0.00 0.00 38.05 3.41
2729 2782 2.886523 TGGCACAAACCTGAAGAAGATG 59.113 45.455 0.00 0.00 31.92 2.90
2730 2783 3.149196 GGCACAAACCTGAAGAAGATGA 58.851 45.455 0.00 0.00 0.00 2.92
2736 2789 6.261826 CACAAACCTGAAGAAGATGAGTTTCT 59.738 38.462 0.00 0.00 36.49 2.52
2737 2790 7.442364 CACAAACCTGAAGAAGATGAGTTTCTA 59.558 37.037 0.00 0.00 33.92 2.10
2738 2791 7.442666 ACAAACCTGAAGAAGATGAGTTTCTAC 59.557 37.037 0.00 0.00 33.92 2.59
2739 2792 6.926630 ACCTGAAGAAGATGAGTTTCTACT 57.073 37.500 0.00 0.00 33.92 2.57
2749 2802 3.507103 GAGTTTCTACTCCCTCCGTTC 57.493 52.381 0.00 0.00 44.15 3.95
2750 2803 1.817447 AGTTTCTACTCCCTCCGTTCG 59.183 52.381 0.00 0.00 0.00 3.95
2751 2804 1.135170 GTTTCTACTCCCTCCGTTCGG 60.135 57.143 4.74 4.74 0.00 4.30
2752 2805 0.329261 TTCTACTCCCTCCGTTCGGA 59.671 55.000 13.34 13.34 0.00 4.55
2753 2806 0.329261 TCTACTCCCTCCGTTCGGAA 59.671 55.000 14.79 0.04 33.41 4.30
2754 2807 1.064166 TCTACTCCCTCCGTTCGGAAT 60.064 52.381 14.79 2.09 33.41 3.01
2755 2808 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
2756 2809 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2757 2810 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2758 2811 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2759 2812 1.753073 TCCCTCCGTTCGGAATTACTC 59.247 52.381 14.79 0.00 33.41 2.59
2760 2813 1.535437 CCCTCCGTTCGGAATTACTCG 60.535 57.143 14.79 1.97 33.41 4.18
2761 2814 1.133790 CCTCCGTTCGGAATTACTCGT 59.866 52.381 14.79 0.00 33.41 4.18
2762 2815 2.448219 CTCCGTTCGGAATTACTCGTC 58.552 52.381 14.79 0.00 33.41 4.20
2763 2816 1.133025 TCCGTTCGGAATTACTCGTCC 59.867 52.381 11.66 0.00 0.00 4.79
2764 2817 1.135315 CCGTTCGGAATTACTCGTCCA 60.135 52.381 5.19 0.00 33.10 4.02
2765 2818 2.598589 CGTTCGGAATTACTCGTCCAA 58.401 47.619 0.00 0.00 33.10 3.53
2766 2819 2.597305 CGTTCGGAATTACTCGTCCAAG 59.403 50.000 0.00 0.00 33.10 3.61
2767 2820 3.671433 CGTTCGGAATTACTCGTCCAAGA 60.671 47.826 0.00 0.00 33.10 3.02
2768 2821 4.240096 GTTCGGAATTACTCGTCCAAGAA 58.760 43.478 0.00 0.00 33.10 2.52
2769 2822 4.524316 TCGGAATTACTCGTCCAAGAAA 57.476 40.909 0.00 0.00 33.10 2.52
2770 2823 5.080969 TCGGAATTACTCGTCCAAGAAAT 57.919 39.130 0.00 0.00 33.10 2.17
2771 2824 4.868171 TCGGAATTACTCGTCCAAGAAATG 59.132 41.667 0.00 0.00 33.10 2.32
2772 2825 4.868171 CGGAATTACTCGTCCAAGAAATGA 59.132 41.667 0.00 0.00 33.10 2.57
2773 2826 5.350365 CGGAATTACTCGTCCAAGAAATGAA 59.650 40.000 0.00 0.00 33.10 2.57
2774 2827 6.037172 CGGAATTACTCGTCCAAGAAATGAAT 59.963 38.462 0.00 0.00 33.10 2.57
2775 2828 7.189512 GGAATTACTCGTCCAAGAAATGAATG 58.810 38.462 0.00 0.00 33.79 2.67
2776 2829 7.148239 GGAATTACTCGTCCAAGAAATGAATGT 60.148 37.037 0.00 0.00 33.79 2.71
2777 2830 8.786826 AATTACTCGTCCAAGAAATGAATGTA 57.213 30.769 0.00 0.00 0.00 2.29
2778 2831 8.964476 ATTACTCGTCCAAGAAATGAATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
2779 2832 6.910536 ACTCGTCCAAGAAATGAATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
2780 2833 6.644347 ACTCGTCCAAGAAATGAATGTATCT 58.356 36.000 0.00 0.00 0.00 1.98
2781 2834 7.782049 ACTCGTCCAAGAAATGAATGTATCTA 58.218 34.615 0.00 0.00 0.00 1.98
2782 2835 7.923344 ACTCGTCCAAGAAATGAATGTATCTAG 59.077 37.037 0.00 0.00 0.00 2.43
2783 2836 8.007405 TCGTCCAAGAAATGAATGTATCTAGA 57.993 34.615 0.00 0.00 0.00 2.43
2784 2837 8.642432 TCGTCCAAGAAATGAATGTATCTAGAT 58.358 33.333 10.73 10.73 0.00 1.98
2785 2838 8.706936 CGTCCAAGAAATGAATGTATCTAGATG 58.293 37.037 15.79 0.00 0.00 2.90
2786 2839 9.553064 GTCCAAGAAATGAATGTATCTAGATGT 57.447 33.333 15.79 0.00 0.00 3.06
2817 2870 8.862325 AGTTGTAGATACATCCATTTTTGTGA 57.138 30.769 0.00 0.00 35.89 3.58
2818 2871 8.730680 AGTTGTAGATACATCCATTTTTGTGAC 58.269 33.333 0.00 0.00 35.89 3.67
2819 2872 8.511321 GTTGTAGATACATCCATTTTTGTGACA 58.489 33.333 0.00 0.00 35.89 3.58
2820 2873 8.628630 TGTAGATACATCCATTTTTGTGACAA 57.371 30.769 0.00 0.00 0.00 3.18
2821 2874 8.729756 TGTAGATACATCCATTTTTGTGACAAG 58.270 33.333 0.00 0.00 0.00 3.16
2822 2875 7.765695 AGATACATCCATTTTTGTGACAAGT 57.234 32.000 0.00 0.00 0.00 3.16
2823 2876 8.862325 AGATACATCCATTTTTGTGACAAGTA 57.138 30.769 0.00 0.00 0.00 2.24
2824 2877 9.295825 AGATACATCCATTTTTGTGACAAGTAA 57.704 29.630 0.00 0.00 0.00 2.24
2827 2880 8.816640 ACATCCATTTTTGTGACAAGTAATTC 57.183 30.769 0.00 0.00 0.00 2.17
2828 2881 7.872483 ACATCCATTTTTGTGACAAGTAATTCC 59.128 33.333 0.00 0.00 0.00 3.01
2829 2882 6.442952 TCCATTTTTGTGACAAGTAATTCCG 58.557 36.000 0.00 0.00 0.00 4.30
2830 2883 6.263392 TCCATTTTTGTGACAAGTAATTCCGA 59.737 34.615 0.00 0.00 0.00 4.55
2831 2884 6.920758 CCATTTTTGTGACAAGTAATTCCGAA 59.079 34.615 0.00 0.00 0.00 4.30
2832 2885 7.096230 CCATTTTTGTGACAAGTAATTCCGAAC 60.096 37.037 0.00 0.00 0.00 3.95
2833 2886 4.718858 TTGTGACAAGTAATTCCGAACG 57.281 40.909 0.00 0.00 0.00 3.95
2834 2887 3.061322 TGTGACAAGTAATTCCGAACGG 58.939 45.455 6.94 6.94 0.00 4.44
2835 2888 3.243805 TGTGACAAGTAATTCCGAACGGA 60.244 43.478 12.04 12.04 43.52 4.69
2836 2889 3.367025 GTGACAAGTAATTCCGAACGGAG 59.633 47.826 15.34 5.60 46.06 4.63
2837 2890 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2838 2891 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2839 2892 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
2840 2893 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2844 2897 2.734755 TTCCGAACGGAGGGAGTATA 57.265 50.000 15.34 0.00 46.06 1.47
3119 4319 5.174037 TGGGAAGTTTTCAGTATGTAGGG 57.826 43.478 0.00 0.00 37.40 3.53
3124 4324 7.040494 GGAAGTTTTCAGTATGTAGGGTCTAC 58.960 42.308 0.00 0.00 37.40 2.59
3133 4333 1.757118 TGTAGGGTCTACATGCTCAGC 59.243 52.381 3.89 0.00 0.00 4.26
3136 4336 2.752030 AGGGTCTACATGCTCAGCTTA 58.248 47.619 0.00 0.00 0.00 3.09
3148 4348 2.673368 GCTCAGCTTAAGTTGTACGCAT 59.327 45.455 17.56 0.00 0.00 4.73
3154 4354 6.695713 TCAGCTTAAGTTGTACGCATGTATAG 59.304 38.462 17.56 0.00 32.11 1.31
3179 4379 6.932356 TTGAAAATGCAGTATGATCTCTCC 57.068 37.500 0.00 0.00 39.69 3.71
3236 4437 5.876357 AGCATAGTCTTTGGTTTGGAGTTA 58.124 37.500 0.00 0.00 0.00 2.24
3270 4471 5.521010 CCTTAGTTACCGATATTTGACGCAA 59.479 40.000 0.00 0.00 0.00 4.85
3280 4481 1.308047 TTTGACGCAAGACACATGCT 58.692 45.000 0.00 0.00 42.75 3.79
3312 4513 4.671377 TGTAAAGCAGAAAACAAGTGCAG 58.329 39.130 0.00 0.00 39.80 4.41
3317 4518 3.252701 AGCAGAAAACAAGTGCAGATGAG 59.747 43.478 5.71 0.00 39.80 2.90
3318 4519 3.004106 GCAGAAAACAAGTGCAGATGAGT 59.996 43.478 5.71 0.00 37.16 3.41
3319 4520 4.781071 CAGAAAACAAGTGCAGATGAGTC 58.219 43.478 5.71 0.84 0.00 3.36
3320 4521 4.514441 CAGAAAACAAGTGCAGATGAGTCT 59.486 41.667 5.71 2.79 34.14 3.24
3321 4522 5.008415 CAGAAAACAAGTGCAGATGAGTCTT 59.992 40.000 5.71 0.00 30.42 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 31 6.144080 CCGATTACGATTCTCCATCTGTAAAC 59.856 42.308 0.00 0.00 42.66 2.01
65 68 4.030452 GTTGTGGCTGCCTCACGC 62.030 66.667 21.93 14.21 37.91 5.34
66 69 1.518056 ATTGTTGTGGCTGCCTCACG 61.518 55.000 21.93 0.00 37.91 4.35
67 70 0.675633 AATTGTTGTGGCTGCCTCAC 59.324 50.000 21.93 16.66 35.82 3.51
68 71 1.412079 AAATTGTTGTGGCTGCCTCA 58.588 45.000 21.03 19.82 0.00 3.86
161 180 8.146053 TCCTGAAATCCAACTAGAACTGAATA 57.854 34.615 0.00 0.00 0.00 1.75
174 193 8.748412 CCATACAAATACTTTCCTGAAATCCAA 58.252 33.333 0.00 0.00 0.00 3.53
178 197 9.753674 TTCTCCATACAAATACTTTCCTGAAAT 57.246 29.630 0.00 0.00 0.00 2.17
252 271 2.507471 GGAGGGTTTCACTGATCTGGAT 59.493 50.000 4.49 0.00 0.00 3.41
488 508 3.202151 ACTGAAGGAGGGTTTTCTTCACA 59.798 43.478 0.00 0.00 41.04 3.58
1042 1073 7.125811 TGCAATGAAAAGGACTCTAGGTAGTAT 59.874 37.037 0.00 0.00 0.00 2.12
1320 1354 2.269023 TGGAGGAAGATGGAGCTTGAA 58.731 47.619 0.00 0.00 0.00 2.69
1586 1638 4.056125 ACTAGCTCGCACGCAGCA 62.056 61.111 13.96 3.47 46.13 4.41
1589 1641 4.435436 CCCACTAGCTCGCACGCA 62.435 66.667 0.00 0.00 0.00 5.24
1639 1691 1.402896 ATGGACCATCTCGACGGCAT 61.403 55.000 0.00 0.00 0.00 4.40
1640 1692 0.753848 TATGGACCATCTCGACGGCA 60.754 55.000 11.17 0.00 0.00 5.69
1738 1790 3.874873 CGATGCTGACGCCAAAGA 58.125 55.556 0.00 0.00 34.43 2.52
1925 1977 2.910479 AGGTCGACGTCTGTGCCA 60.910 61.111 14.70 0.00 0.00 4.92
1929 1981 3.681835 GGCCAGGTCGACGTCTGT 61.682 66.667 14.70 0.00 0.00 3.41
2024 2076 0.670706 CGATCTCTTCATCGGCTCCA 59.329 55.000 0.00 0.00 41.71 3.86
2069 2121 1.522092 CTGGAATAGCAGGCCGACA 59.478 57.895 0.00 0.00 0.00 4.35
2306 2358 0.108186 TCAATCAGTGCTGCCGGTAG 60.108 55.000 16.18 16.18 0.00 3.18
2392 2444 6.694447 CATATCAATCCCATGGAATCCAAAC 58.306 40.000 15.22 0.00 36.95 2.93
2473 2525 3.385749 AAGCGGCCCCATCGTACTG 62.386 63.158 0.00 0.00 0.00 2.74
2474 2526 3.081409 AAGCGGCCCCATCGTACT 61.081 61.111 0.00 0.00 0.00 2.73
2477 2529 1.978455 TATTGAAGCGGCCCCATCGT 61.978 55.000 0.00 0.00 0.00 3.73
2484 2536 1.077716 ACTGGGTATTGAAGCGGCC 60.078 57.895 0.00 0.00 0.00 6.13
2494 2546 2.584608 GGTGCGCTGACTGGGTAT 59.415 61.111 9.73 0.00 0.00 2.73
2513 2565 3.818787 CTGCTGCATCCCCGCAAC 61.819 66.667 1.31 0.00 42.45 4.17
2532 2584 1.472662 GCTATAGGCCGGGAGCTGAA 61.473 60.000 15.96 0.00 43.05 3.02
2554 2606 3.305608 CGCACATATAGATCTGCTGGTCA 60.306 47.826 5.18 0.00 0.00 4.02
2559 2611 2.529632 TCCCGCACATATAGATCTGCT 58.470 47.619 5.18 0.00 0.00 4.24
2582 2634 4.577677 TTTCAGCTGCCACCGCCA 62.578 61.111 9.47 0.00 0.00 5.69
2611 2663 2.067013 GGACTGTTCGGAAGCTTGTAC 58.933 52.381 2.10 0.00 0.00 2.90
2612 2664 1.689813 TGGACTGTTCGGAAGCTTGTA 59.310 47.619 2.10 0.00 0.00 2.41
2729 2782 5.278309 CCGAACGGAGGGAGTAGAAACTC 62.278 56.522 7.53 0.00 43.81 3.01
2730 2783 1.817447 CGAACGGAGGGAGTAGAAACT 59.183 52.381 0.00 0.00 39.21 2.66
2736 2789 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
2737 2790 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
2738 2791 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2739 2792 1.753073 GAGTAATTCCGAACGGAGGGA 59.247 52.381 15.34 2.49 46.06 4.20
2740 2793 1.535437 CGAGTAATTCCGAACGGAGGG 60.535 57.143 15.34 0.00 46.06 4.30
2741 2794 1.133790 ACGAGTAATTCCGAACGGAGG 59.866 52.381 15.34 4.28 46.06 4.30
2742 2795 2.448219 GACGAGTAATTCCGAACGGAG 58.552 52.381 15.34 5.60 46.06 4.63
2743 2796 1.133025 GGACGAGTAATTCCGAACGGA 59.867 52.381 12.04 12.04 43.52 4.69
2744 2797 1.135315 TGGACGAGTAATTCCGAACGG 60.135 52.381 6.94 6.94 0.00 4.44
2745 2798 2.267188 TGGACGAGTAATTCCGAACG 57.733 50.000 0.00 0.00 0.00 3.95
2746 2799 3.841643 TCTTGGACGAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
2747 2800 4.524316 TTCTTGGACGAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
2748 2801 4.524316 TTTCTTGGACGAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
2749 2802 4.868171 TCATTTCTTGGACGAGTAATTCCG 59.132 41.667 0.00 0.00 0.00 4.30
2750 2803 6.737254 TTCATTTCTTGGACGAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
2751 2804 7.752695 ACATTCATTTCTTGGACGAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
2752 2805 7.687941 ACATTCATTTCTTGGACGAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
2753 2806 8.964476 ATACATTCATTTCTTGGACGAGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
2754 2807 8.258007 AGATACATTCATTTCTTGGACGAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
2755 2808 7.782049 AGATACATTCATTTCTTGGACGAGTA 58.218 34.615 0.00 0.00 0.00 2.59
2756 2809 6.644347 AGATACATTCATTTCTTGGACGAGT 58.356 36.000 0.00 0.00 0.00 4.18
2757 2810 8.138074 TCTAGATACATTCATTTCTTGGACGAG 58.862 37.037 0.00 0.00 0.00 4.18
2758 2811 8.007405 TCTAGATACATTCATTTCTTGGACGA 57.993 34.615 0.00 0.00 0.00 4.20
2759 2812 8.706936 CATCTAGATACATTCATTTCTTGGACG 58.293 37.037 4.54 0.00 0.00 4.79
2760 2813 9.553064 ACATCTAGATACATTCATTTCTTGGAC 57.447 33.333 4.54 0.00 0.00 4.02
2791 2844 9.952030 TCACAAAAATGGATGTATCTACAACTA 57.048 29.630 0.00 0.00 39.99 2.24
2792 2845 8.730680 GTCACAAAAATGGATGTATCTACAACT 58.269 33.333 0.00 0.00 39.99 3.16
2793 2846 8.511321 TGTCACAAAAATGGATGTATCTACAAC 58.489 33.333 0.00 0.00 39.99 3.32
2794 2847 8.628630 TGTCACAAAAATGGATGTATCTACAA 57.371 30.769 0.00 0.00 39.99 2.41
2795 2848 8.628630 TTGTCACAAAAATGGATGTATCTACA 57.371 30.769 0.00 0.00 40.98 2.74
2796 2849 8.730680 ACTTGTCACAAAAATGGATGTATCTAC 58.269 33.333 0.00 0.00 0.00 2.59
2797 2850 8.862325 ACTTGTCACAAAAATGGATGTATCTA 57.138 30.769 0.00 0.00 0.00 1.98
2798 2851 7.765695 ACTTGTCACAAAAATGGATGTATCT 57.234 32.000 0.00 0.00 0.00 1.98
2801 2854 9.906660 GAATTACTTGTCACAAAAATGGATGTA 57.093 29.630 0.00 0.00 0.00 2.29
2802 2855 7.872483 GGAATTACTTGTCACAAAAATGGATGT 59.128 33.333 0.00 0.00 0.00 3.06
2803 2856 7.062138 CGGAATTACTTGTCACAAAAATGGATG 59.938 37.037 0.00 0.00 0.00 3.51
2804 2857 7.040062 TCGGAATTACTTGTCACAAAAATGGAT 60.040 33.333 0.00 0.00 0.00 3.41
2805 2858 6.263392 TCGGAATTACTTGTCACAAAAATGGA 59.737 34.615 0.00 0.00 0.00 3.41
2806 2859 6.442952 TCGGAATTACTTGTCACAAAAATGG 58.557 36.000 0.00 0.00 0.00 3.16
2807 2860 7.357206 CGTTCGGAATTACTTGTCACAAAAATG 60.357 37.037 0.00 0.00 0.00 2.32
2808 2861 6.635239 CGTTCGGAATTACTTGTCACAAAAAT 59.365 34.615 0.00 0.00 0.00 1.82
2809 2862 5.966503 CGTTCGGAATTACTTGTCACAAAAA 59.033 36.000 0.00 0.00 0.00 1.94
2810 2863 5.503498 CGTTCGGAATTACTTGTCACAAAA 58.497 37.500 0.00 0.00 0.00 2.44
2811 2864 4.024725 CCGTTCGGAATTACTTGTCACAAA 60.025 41.667 5.19 0.00 0.00 2.83
2812 2865 3.495377 CCGTTCGGAATTACTTGTCACAA 59.505 43.478 5.19 0.00 0.00 3.33
2813 2866 3.061322 CCGTTCGGAATTACTTGTCACA 58.939 45.455 5.19 0.00 0.00 3.58
2814 2867 3.319755 TCCGTTCGGAATTACTTGTCAC 58.680 45.455 11.66 0.00 0.00 3.67
2815 2868 3.581755 CTCCGTTCGGAATTACTTGTCA 58.418 45.455 14.79 0.00 33.41 3.58
2816 2869 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2817 2870 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2818 2871 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2819 2872 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2820 2873 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2821 2874 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2822 2875 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2823 2876 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
2824 2877 2.083628 ATACTCCCTCCGTTCGGAAT 57.916 50.000 14.79 2.14 33.41 3.01
2825 2878 2.734755 TATACTCCCTCCGTTCGGAA 57.265 50.000 14.79 0.00 33.41 4.30
2826 2879 2.158564 ACATATACTCCCTCCGTTCGGA 60.159 50.000 13.34 13.34 0.00 4.55
2827 2880 2.030185 CACATATACTCCCTCCGTTCGG 60.030 54.545 4.74 4.74 0.00 4.30
2828 2881 2.621998 ACACATATACTCCCTCCGTTCG 59.378 50.000 0.00 0.00 0.00 3.95
2829 2882 4.826183 AGTACACATATACTCCCTCCGTTC 59.174 45.833 0.00 0.00 28.86 3.95
2830 2883 4.801164 AGTACACATATACTCCCTCCGTT 58.199 43.478 0.00 0.00 28.86 4.44
2831 2884 4.450305 AGTACACATATACTCCCTCCGT 57.550 45.455 0.00 0.00 28.86 4.69
2832 2885 4.825634 TCAAGTACACATATACTCCCTCCG 59.174 45.833 0.00 0.00 34.18 4.63
2833 2886 6.722129 AGATCAAGTACACATATACTCCCTCC 59.278 42.308 0.00 0.00 34.18 4.30
2834 2887 7.768807 AGATCAAGTACACATATACTCCCTC 57.231 40.000 0.00 0.00 34.18 4.30
2835 2888 7.785028 TGAAGATCAAGTACACATATACTCCCT 59.215 37.037 0.00 0.00 34.18 4.20
2836 2889 7.952671 TGAAGATCAAGTACACATATACTCCC 58.047 38.462 0.00 0.00 34.18 4.30
2837 2890 7.596995 GCTGAAGATCAAGTACACATATACTCC 59.403 40.741 0.00 0.00 34.18 3.85
2838 2891 7.596995 GGCTGAAGATCAAGTACACATATACTC 59.403 40.741 0.00 0.00 34.18 2.59
2839 2892 7.069950 TGGCTGAAGATCAAGTACACATATACT 59.930 37.037 0.00 0.00 36.96 2.12
2840 2893 7.210174 TGGCTGAAGATCAAGTACACATATAC 58.790 38.462 0.00 0.00 0.00 1.47
2844 2897 4.558226 TGGCTGAAGATCAAGTACACAT 57.442 40.909 0.00 0.00 0.00 3.21
3071 3124 6.313519 TCTATGGGCTGTAAATTCTCAAGT 57.686 37.500 0.00 0.00 0.00 3.16
3100 3153 7.609056 TGTAGACCCTACATACTGAAAACTTC 58.391 38.462 2.95 0.00 0.00 3.01
3119 4319 4.932200 ACAACTTAAGCTGAGCATGTAGAC 59.068 41.667 12.74 0.00 0.00 2.59
3124 4324 3.484229 GCGTACAACTTAAGCTGAGCATG 60.484 47.826 12.74 4.39 0.00 4.06
3133 4333 9.244799 TCAATCTATACATGCGTACAACTTAAG 57.755 33.333 0.00 0.00 0.00 1.85
3136 4336 8.487313 TTTCAATCTATACATGCGTACAACTT 57.513 30.769 0.00 0.00 0.00 2.66
3154 4354 7.308469 GGGAGAGATCATACTGCATTTTCAATC 60.308 40.741 0.00 0.00 0.00 2.67
3179 4379 2.972021 ACCTTGATTTTGTTTCTGGGGG 59.028 45.455 0.00 0.00 0.00 5.40
3236 4437 2.812011 CGGTAACTAAGGCAGCTTTTGT 59.188 45.455 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.