Multiple sequence alignment - TraesCS2A01G066600

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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 TraesCS2A01G066600 chr2A 100.000 2869 0 0 1 2869 29988541 29991409 0.000000e+00 5299.0
1 TraesCS2A01G066600 chr2A 94.253 87 5 0 2783 2869 173881590 173881676 1.790000e-27 134.0
2 TraesCS2A01G066600 chr2B 91.773 2674 129 34 174 2792 44157997 44160634 0.000000e+00 3635.0
3 TraesCS2A01G066600 chr2B 97.468 79 2 0 2791 2869 155967898 155967820 4.990000e-28 135.0
4 TraesCS2A01G066600 chr2D 93.867 2250 79 18 98 2321 27835907 27838123 0.000000e+00 3336.0
5 TraesCS2A01G066600 chr2D 94.235 451 21 1 2342 2792 27838183 27838628 0.000000e+00 684.0
6 TraesCS2A01G066600 chr2D 96.471 85 1 2 2787 2869 470666072 470665988 3.850000e-29 139.0
7 TraesCS2A01G066600 chr2D 87.500 80 4 4 1 74 27835781 27835860 1.420000e-13 87.9
8 TraesCS2A01G066600 chr4B 80.645 620 109 11 1234 1849 547093972 547094584 1.200000e-128 470.0
9 TraesCS2A01G066600 chr3D 77.922 539 106 12 1235 1768 157443377 157442847 9.910000e-85 324.0
10 TraesCS2A01G066600 chr3A 77.675 542 105 14 1235 1768 170811690 170812223 1.660000e-82 316.0
11 TraesCS2A01G066600 chr7D 84.691 307 44 2 1236 1539 501116276 501116582 1.290000e-78 303.0
12 TraesCS2A01G066600 chr7D 95.402 87 3 1 2784 2869 55286264 55286350 1.390000e-28 137.0
13 TraesCS2A01G066600 chr7D 95.294 85 4 0 2785 2869 256193860 256193944 4.990000e-28 135.0
14 TraesCS2A01G066600 chr7D 100.000 29 0 0 332 360 197341561 197341589 1.000000e-03 54.7
15 TraesCS2A01G066600 chr3B 76.923 546 111 14 1235 1774 228690784 228690248 2.160000e-76 296.0
16 TraesCS2A01G066600 chr3B 96.386 83 3 0 2787 2869 485231890 485231808 1.390000e-28 137.0
17 TraesCS2A01G066600 chr1D 76.575 508 96 15 1235 1732 191374481 191374975 1.020000e-64 257.0
18 TraesCS2A01G066600 chr5B 80.583 309 56 3 1233 1539 619927207 619926901 4.780000e-58 235.0
19 TraesCS2A01G066600 chr5B 76.627 338 59 19 1230 1555 662036914 662036585 4.920000e-38 169.0
20 TraesCS2A01G066600 chr5A 80.259 309 57 3 1233 1539 623504298 623503992 2.220000e-56 230.0
21 TraesCS2A01G066600 chr5A 95.349 86 3 1 2785 2869 484423624 484423709 4.990000e-28 135.0
22 TraesCS2A01G066600 chr5A 95.556 45 2 0 1114 1158 653717283 653717239 3.970000e-09 73.1
23 TraesCS2A01G066600 chr5D 77.151 337 59 15 1230 1555 526572117 526571788 2.270000e-41 180.0
24 TraesCS2A01G066600 chr5D 95.652 46 2 0 1115 1160 499246703 499246658 1.100000e-09 75.0
25 TraesCS2A01G066600 chr6D 98.734 79 1 0 2791 2869 141538180 141538258 1.070000e-29 141.0
26 TraesCS2A01G066600 chr4D 93.182 88 5 1 2783 2869 435929643 435929556 8.340000e-26 128.0


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 TraesCS2A01G066600 chr2A 29988541 29991409 2868 False 5299.0 5299 100.000000 1 2869 1 chr2A.!!$F1 2868
1 TraesCS2A01G066600 chr2B 44157997 44160634 2637 False 3635.0 3635 91.773000 174 2792 1 chr2B.!!$F1 2618
2 TraesCS2A01G066600 chr2D 27835781 27838628 2847 False 1369.3 3336 91.867333 1 2792 3 chr2D.!!$F1 2791
3 TraesCS2A01G066600 chr4B 547093972 547094584 612 False 470.0 470 80.645000 1234 1849 1 chr4B.!!$F1 615
4 TraesCS2A01G066600 chr3D 157442847 157443377 530 True 324.0 324 77.922000 1235 1768 1 chr3D.!!$R1 533
5 TraesCS2A01G066600 chr3A 170811690 170812223 533 False 316.0 316 77.675000 1235 1768 1 chr3A.!!$F1 533
6 TraesCS2A01G066600 chr3B 228690248 228690784 536 True 296.0 296 76.923000 1235 1774 1 chr3B.!!$R1 539

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
677 734 0.106918 TATTGACCCGGGAACATGGC 60.107 55.0 32.02 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2043 0.433492 CGATGACCGAACGTTCACAC 59.567 55.0 26.71 16.5 41.76 3.82 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
23 24 1.137825 CGTCGAGAGGAGCCACTTC 59.862 63.158 0.00 0.00 0.00 3.01
79 86 3.948719 ACTCCGCCGCCAAGGAAA 61.949 61.111 0.00 0.00 45.00 3.13
80 87 3.431725 CTCCGCCGCCAAGGAAAC 61.432 66.667 0.00 0.00 45.00 2.78
84 91 3.431725 GCCGCCAAGGAAACCGAG 61.432 66.667 0.00 0.00 45.00 4.63
85 92 2.746277 CCGCCAAGGAAACCGAGG 60.746 66.667 0.00 0.00 45.00 4.63
86 93 3.431725 CGCCAAGGAAACCGAGGC 61.432 66.667 13.56 13.56 42.16 4.70
185 215 1.609794 GAGAGAGGACCCCACCGTT 60.610 63.158 0.00 0.00 34.73 4.44
190 220 4.589675 GGACCCCACCGTTGCCAA 62.590 66.667 0.00 0.00 0.00 4.52
199 229 1.050204 ACCGTTGCCAACACCTACTA 58.950 50.000 8.51 0.00 0.00 1.82
240 275 0.561680 GGGAGGAGGAGGCCTAGTAA 59.438 60.000 4.42 0.00 38.73 2.24
284 319 1.995484 TCGATTGCTTTCAAGAGCGAG 59.005 47.619 0.00 0.00 45.64 5.03
297 332 1.596895 GAGCGAGACGAGGGAAAGGT 61.597 60.000 0.00 0.00 0.00 3.50
327 362 6.588719 TTTTCATCGGATGTTGGATCTTTT 57.411 33.333 17.01 0.00 0.00 2.27
364 399 6.349611 CCCTTCAATACAGACATCCAAACAAG 60.350 42.308 0.00 0.00 0.00 3.16
367 402 2.664402 ACAGACATCCAAACAAGGCT 57.336 45.000 0.00 0.00 0.00 4.58
419 456 5.535406 ACTCAGTGAACCCGGACTATATTAG 59.465 44.000 0.73 0.00 0.00 1.73
455 492 4.739195 TGTTTGTTTCTCACCCGAAAAAG 58.261 39.130 0.00 0.00 34.93 2.27
460 497 5.404096 TGTTTCTCACCCGAAAAAGAAAAC 58.596 37.500 0.00 0.00 38.91 2.43
487 524 5.394553 GCCCTATGAAAATCCAAGGAAACAG 60.395 44.000 0.00 0.00 0.00 3.16
592 642 2.583593 GAGTGGCGCCGACAGATC 60.584 66.667 23.90 10.84 0.00 2.75
615 672 1.024271 ATTAAACGCCGCATGCATCT 58.976 45.000 19.57 0.00 41.33 2.90
677 734 0.106918 TATTGACCCGGGAACATGGC 60.107 55.000 32.02 0.00 0.00 4.40
842 905 3.750155 CACGCCCACATGCATGCA 61.750 61.111 26.53 25.04 0.00 3.96
843 906 3.751246 ACGCCCACATGCATGCAC 61.751 61.111 25.37 8.20 0.00 4.57
844 907 4.840288 CGCCCACATGCATGCACG 62.840 66.667 25.37 19.13 0.00 5.34
845 908 4.501714 GCCCACATGCATGCACGG 62.502 66.667 25.37 22.45 0.00 4.94
846 909 3.829044 CCCACATGCATGCACGGG 61.829 66.667 28.11 28.11 0.00 5.28
847 910 4.501714 CCACATGCATGCACGGGC 62.502 66.667 25.37 0.34 41.68 6.13
904 968 2.204291 TTCCATCCCCCAGCAGGT 60.204 61.111 0.00 0.00 0.00 4.00
930 994 1.805254 CAGTGCAAGGCATGGCTAC 59.195 57.895 23.63 16.91 41.91 3.58
978 1042 1.299926 GGCCACTAGCGATACCACG 60.300 63.158 0.00 0.00 45.17 4.94
1039 1106 0.241481 GTCTCTTCGGCTCTTCGTGT 59.759 55.000 0.00 0.00 0.00 4.49
1165 1232 2.744318 CCATGGGTACGTGCGCAA 60.744 61.111 25.63 10.78 35.01 4.85
1167 1234 2.032634 CATGGGTACGTGCGCAAGT 61.033 57.895 30.63 30.63 41.68 3.16
1219 1287 3.439476 ACACAGAAAGAAGCTGATGATGC 59.561 43.478 0.00 0.00 36.86 3.91
1220 1288 2.676839 ACAGAAAGAAGCTGATGATGCG 59.323 45.455 0.00 0.00 36.86 4.73
1221 1289 2.934553 CAGAAAGAAGCTGATGATGCGA 59.065 45.455 0.00 0.00 35.39 5.10
1222 1290 3.560481 CAGAAAGAAGCTGATGATGCGAT 59.440 43.478 0.00 0.00 35.39 4.58
1223 1291 4.035324 CAGAAAGAAGCTGATGATGCGATT 59.965 41.667 0.00 0.00 35.39 3.34
1224 1292 3.965292 AAGAAGCTGATGATGCGATTG 57.035 42.857 0.00 0.00 35.28 2.67
1712 1783 0.186873 GGATGCCCATGTCCAGGAAT 59.813 55.000 0.00 0.00 34.57 3.01
1956 2037 2.654749 TGATCAGTGATCGGTGTGTC 57.345 50.000 24.52 4.13 41.51 3.67
1957 2038 1.135402 TGATCAGTGATCGGTGTGTCG 60.135 52.381 24.52 0.00 41.51 4.35
1958 2039 1.132453 GATCAGTGATCGGTGTGTCGA 59.868 52.381 17.11 0.00 43.61 4.20
1963 2044 3.599584 ATCGGTGTGTCGATCGGT 58.400 55.556 16.41 0.00 45.43 4.69
1964 2045 1.138883 ATCGGTGTGTCGATCGGTG 59.861 57.895 16.41 0.00 45.43 4.94
1965 2046 1.592400 ATCGGTGTGTCGATCGGTGT 61.592 55.000 16.41 0.00 45.43 4.16
1966 2047 2.086426 CGGTGTGTCGATCGGTGTG 61.086 63.158 16.41 0.00 0.00 3.82
1987 2068 1.372499 CGTTCGGTCATCGGTGTGT 60.372 57.895 0.00 0.00 39.77 3.72
1988 2069 1.342082 CGTTCGGTCATCGGTGTGTC 61.342 60.000 0.00 0.00 39.77 3.67
1989 2070 1.081041 TTCGGTCATCGGTGTGTCG 60.081 57.895 0.00 0.00 39.77 4.35
1990 2071 1.517210 TTCGGTCATCGGTGTGTCGA 61.517 55.000 0.00 1.05 43.61 4.20
2007 2088 1.136057 TCGATCGCGGTGATATCTTCG 60.136 52.381 11.09 8.80 37.47 3.79
2061 2142 0.107993 CTCTGCATCCGAGGCTTCAA 60.108 55.000 6.59 0.00 0.00 2.69
2079 2160 5.735354 GCTTCAAGATGACCAATATGCCAAG 60.735 44.000 0.00 0.00 0.00 3.61
2143 2231 8.785184 TCTTAAAATTTGGGAGGTTTTAGGAA 57.215 30.769 0.00 0.00 33.40 3.36
2151 2241 5.083821 TGGGAGGTTTTAGGAATTTTCTGG 58.916 41.667 0.00 0.00 0.00 3.86
2276 2385 4.318546 GTGTTTGACACTATGGAACACGAC 60.319 45.833 4.06 0.00 43.97 4.34
2294 2403 3.190535 ACGACGCTATCCTGCAAATTTTT 59.809 39.130 0.00 0.00 0.00 1.94
2296 2405 4.963953 CGACGCTATCCTGCAAATTTTTAG 59.036 41.667 0.00 0.00 0.00 1.85
2322 2431 7.670364 AGTTTAAAGGTTTGATGAGAAATGGG 58.330 34.615 0.00 0.00 0.00 4.00
2356 2504 6.310941 TCAAGGAGATCTTATCCTCTCGAAT 58.689 40.000 0.00 0.00 46.75 3.34
2384 2532 1.337118 TCCTTTTGAATGGTGTGCCC 58.663 50.000 0.00 0.00 0.00 5.36
2463 2611 5.927281 ATTTGTCTTGCCAGCAGATTTAT 57.073 34.783 0.00 0.00 0.00 1.40
2520 2668 3.365472 GAGCTGTATTTTCCAACCCCAT 58.635 45.455 0.00 0.00 0.00 4.00
2605 2753 0.035439 GATTCTCAACTTCCGGCCCA 60.035 55.000 0.00 0.00 0.00 5.36
2627 2775 9.051679 GCCCAGAAATAAATGTTACAAGTTTTT 57.948 29.630 0.00 0.00 0.00 1.94
2675 2823 6.039270 TGAAAGTGAATTTTCGTTCTCCATGT 59.961 34.615 0.00 0.00 39.39 3.21
2723 2871 3.579586 AGCTTCTCATTTGGCCAATTTGA 59.420 39.130 21.26 22.46 0.00 2.69
2792 2942 2.022330 AGGGTACACTATAGGCCCAAGT 60.022 50.000 19.32 0.00 41.67 3.16
2793 2943 2.104281 GGGTACACTATAGGCCCAAGTG 59.896 54.545 21.94 21.94 44.89 3.16
2807 2957 0.872388 CAAGTGTTGGGGAACGTAGC 59.128 55.000 0.00 0.00 0.00 3.58
2808 2958 0.470766 AAGTGTTGGGGAACGTAGCA 59.529 50.000 0.00 0.00 0.00 3.49
2809 2959 0.470766 AGTGTTGGGGAACGTAGCAA 59.529 50.000 0.00 0.00 0.00 3.91
2810 2960 1.073284 AGTGTTGGGGAACGTAGCAAT 59.927 47.619 0.00 0.00 0.00 3.56
2811 2961 2.303600 AGTGTTGGGGAACGTAGCAATA 59.696 45.455 0.00 0.00 0.00 1.90
2812 2962 3.075884 GTGTTGGGGAACGTAGCAATAA 58.924 45.455 0.00 0.00 0.00 1.40
2813 2963 3.692593 GTGTTGGGGAACGTAGCAATAAT 59.307 43.478 0.00 0.00 0.00 1.28
2814 2964 4.157105 GTGTTGGGGAACGTAGCAATAATT 59.843 41.667 0.00 0.00 0.00 1.40
2815 2965 4.767928 TGTTGGGGAACGTAGCAATAATTT 59.232 37.500 0.00 0.00 0.00 1.82
2816 2966 5.944599 TGTTGGGGAACGTAGCAATAATTTA 59.055 36.000 0.00 0.00 0.00 1.40
2817 2967 6.433404 TGTTGGGGAACGTAGCAATAATTTAA 59.567 34.615 0.00 0.00 0.00 1.52
2818 2968 7.039923 TGTTGGGGAACGTAGCAATAATTTAAA 60.040 33.333 0.00 0.00 0.00 1.52
2819 2969 7.463961 TGGGGAACGTAGCAATAATTTAAAA 57.536 32.000 0.00 0.00 0.00 1.52
2820 2970 8.068892 TGGGGAACGTAGCAATAATTTAAAAT 57.931 30.769 0.00 0.00 0.00 1.82
2821 2971 8.532819 TGGGGAACGTAGCAATAATTTAAAATT 58.467 29.630 0.00 0.00 0.00 1.82
2822 2972 9.373603 GGGGAACGTAGCAATAATTTAAAATTT 57.626 29.630 0.00 0.00 0.00 1.82
2836 2986 8.806177 AATTTAAAATTTTCCTACGTGTCACC 57.194 30.769 6.72 0.00 0.00 4.02
2837 2987 6.939132 TTAAAATTTTCCTACGTGTCACCA 57.061 33.333 6.72 0.00 0.00 4.17
2838 2988 5.838531 AAAATTTTCCTACGTGTCACCAA 57.161 34.783 0.00 0.00 0.00 3.67
2839 2989 5.432885 AAATTTTCCTACGTGTCACCAAG 57.567 39.130 0.00 0.00 0.00 3.61
2840 2990 3.823281 TTTTCCTACGTGTCACCAAGA 57.177 42.857 0.00 0.00 0.00 3.02
2841 2991 4.345859 TTTTCCTACGTGTCACCAAGAT 57.654 40.909 0.00 0.00 0.00 2.40
2842 2992 3.587797 TTCCTACGTGTCACCAAGATC 57.412 47.619 0.00 0.00 0.00 2.75
2843 2993 2.521126 TCCTACGTGTCACCAAGATCA 58.479 47.619 0.00 0.00 0.00 2.92
2844 2994 2.894765 TCCTACGTGTCACCAAGATCAA 59.105 45.455 0.00 0.00 0.00 2.57
2845 2995 3.513912 TCCTACGTGTCACCAAGATCAAT 59.486 43.478 0.00 0.00 0.00 2.57
2846 2996 3.865745 CCTACGTGTCACCAAGATCAATC 59.134 47.826 0.00 0.00 0.00 2.67
2847 2997 3.685139 ACGTGTCACCAAGATCAATCT 57.315 42.857 0.00 0.00 39.22 2.40
2848 2998 4.801330 ACGTGTCACCAAGATCAATCTA 57.199 40.909 0.00 0.00 35.76 1.98
2849 2999 4.748892 ACGTGTCACCAAGATCAATCTAG 58.251 43.478 0.00 0.00 35.76 2.43
2850 3000 4.115516 CGTGTCACCAAGATCAATCTAGG 58.884 47.826 0.00 0.00 35.76 3.02
2851 3001 4.142160 CGTGTCACCAAGATCAATCTAGGA 60.142 45.833 0.00 0.00 35.76 2.94
2852 3002 5.355596 GTGTCACCAAGATCAATCTAGGAG 58.644 45.833 0.00 0.00 35.76 3.69
2853 3003 5.127845 GTGTCACCAAGATCAATCTAGGAGA 59.872 44.000 0.00 0.00 35.76 3.71
2854 3004 5.901853 TGTCACCAAGATCAATCTAGGAGAT 59.098 40.000 0.00 0.00 36.28 2.75
2855 3005 7.014711 GTGTCACCAAGATCAATCTAGGAGATA 59.985 40.741 0.00 0.00 32.89 1.98
2856 3006 7.014711 TGTCACCAAGATCAATCTAGGAGATAC 59.985 40.741 0.00 0.00 32.89 2.24
2857 3007 7.232534 GTCACCAAGATCAATCTAGGAGATACT 59.767 40.741 0.00 0.00 32.89 2.12
2858 3008 8.448816 TCACCAAGATCAATCTAGGAGATACTA 58.551 37.037 0.00 0.00 32.89 1.82
2859 3009 8.739039 CACCAAGATCAATCTAGGAGATACTAG 58.261 40.741 0.00 0.00 41.41 2.57
2860 3010 7.396055 ACCAAGATCAATCTAGGAGATACTAGC 59.604 40.741 0.00 0.00 40.18 3.42
2861 3011 7.395772 CCAAGATCAATCTAGGAGATACTAGCA 59.604 40.741 0.00 0.00 40.18 3.49
2862 3012 8.801299 CAAGATCAATCTAGGAGATACTAGCAA 58.199 37.037 0.00 0.00 40.18 3.91
2863 3013 8.348285 AGATCAATCTAGGAGATACTAGCAAC 57.652 38.462 0.00 0.00 40.18 4.17
2864 3014 7.947332 AGATCAATCTAGGAGATACTAGCAACA 59.053 37.037 0.00 0.00 40.18 3.33
2865 3015 7.898014 TCAATCTAGGAGATACTAGCAACAA 57.102 36.000 0.00 0.00 40.18 2.83
2866 3016 7.946207 TCAATCTAGGAGATACTAGCAACAAG 58.054 38.462 0.00 0.00 40.18 3.16
2867 3017 7.780271 TCAATCTAGGAGATACTAGCAACAAGA 59.220 37.037 0.00 0.00 40.18 3.02
2868 3018 7.759489 ATCTAGGAGATACTAGCAACAAGAG 57.241 40.000 0.00 0.00 40.18 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 0.539669 TGTGAAGTGGCTCCTCTCGA 60.540 55.000 0.00 0.00 0.00 4.04
9 10 0.389166 CGTGTGAAGTGGCTCCTCTC 60.389 60.000 0.00 0.00 0.00 3.20
10 11 1.668294 CGTGTGAAGTGGCTCCTCT 59.332 57.895 0.00 0.00 0.00 3.69
23 24 2.568090 GGCTGCCAAATCCGTGTG 59.432 61.111 15.17 0.00 0.00 3.82
139 169 2.594592 GCGGTGGAGTTTGGTGCT 60.595 61.111 0.00 0.00 0.00 4.40
159 189 0.106217 GGGTCCTCTCTCTCTCCCTG 60.106 65.000 0.00 0.00 32.89 4.45
167 197 1.609794 AACGGTGGGGTCCTCTCTC 60.610 63.158 0.00 0.00 0.00 3.20
168 198 1.913762 CAACGGTGGGGTCCTCTCT 60.914 63.158 0.00 0.00 0.00 3.10
185 215 1.358152 AAGCCTAGTAGGTGTTGGCA 58.642 50.000 17.69 0.00 45.42 4.92
214 244 3.756783 CTCCTCCTCCCCTCCCGT 61.757 72.222 0.00 0.00 0.00 5.28
267 302 1.728971 CGTCTCGCTCTTGAAAGCAAT 59.271 47.619 0.00 0.00 42.62 3.56
269 304 0.313987 TCGTCTCGCTCTTGAAAGCA 59.686 50.000 0.00 0.00 42.62 3.91
284 319 2.434359 CGCCACCTTTCCCTCGTC 60.434 66.667 0.00 0.00 0.00 4.20
327 362 1.860641 TTGAAGGGCTCTGTATCGGA 58.139 50.000 0.00 0.00 0.00 4.55
364 399 5.359009 TCAAATCTGAAGAAATGATGGAGCC 59.641 40.000 0.00 0.00 0.00 4.70
367 402 8.683615 CAAGATCAAATCTGAAGAAATGATGGA 58.316 33.333 13.05 0.00 40.13 3.41
419 456 1.963515 ACAAACAAGATGCCCAGGAAC 59.036 47.619 0.00 0.00 0.00 3.62
455 492 3.181479 GGATTTTCATAGGGCCGGTTTTC 60.181 47.826 1.90 0.00 0.00 2.29
460 497 1.956477 CTTGGATTTTCATAGGGCCGG 59.044 52.381 0.00 0.00 0.00 6.13
487 524 1.541379 GTGGGTACACATGGGGAAAC 58.459 55.000 0.00 0.00 46.90 2.78
546 595 1.079127 ATCCGGGCTTCGTGTCTTG 60.079 57.895 0.00 0.00 37.11 3.02
592 642 0.565679 GCATGCGGCGTTTAATTTCG 59.434 50.000 9.37 0.00 0.00 3.46
615 672 1.826921 GTCGGGTCGAGGCTGGATA 60.827 63.158 1.57 0.00 36.23 2.59
677 734 1.988293 TTCTATCGGGAGAGCTCTGG 58.012 55.000 23.91 10.35 45.48 3.86
727 784 2.186826 GGCGAGCGGCATTATTGGT 61.187 57.895 11.71 0.00 46.16 3.67
762 819 3.680786 TGACGGGGACACGAGCTG 61.681 66.667 0.00 0.00 37.61 4.24
801 858 2.821366 CAGATGCGGGTGGAGTGC 60.821 66.667 0.00 0.00 0.00 4.40
904 968 2.113774 CCTTGCACTGCACTGGGA 59.886 61.111 2.26 0.00 38.71 4.37
930 994 5.127845 TGACAGGCAGATCTAGGAGTTTAAG 59.872 44.000 0.00 0.00 0.00 1.85
978 1042 6.018098 CCATGTTACAGAGATCAATGAAGCTC 60.018 42.308 7.99 7.99 0.00 4.09
1165 1232 6.527023 CACGATCGAATGAAGTTAACTACACT 59.473 38.462 24.34 0.00 0.00 3.55
1167 1234 6.614160 TCACGATCGAATGAAGTTAACTACA 58.386 36.000 24.34 0.00 0.00 2.74
1219 1287 2.350425 CTGCACGCATCGCAATCG 60.350 61.111 0.00 0.00 39.30 3.34
1220 1288 2.023741 CCTGCACGCATCGCAATC 59.976 61.111 0.00 0.00 39.30 2.67
1221 1289 4.183686 GCCTGCACGCATCGCAAT 62.184 61.111 2.56 0.00 39.30 3.56
1956 2037 1.670971 CCGAACGTTCACACCGATCG 61.671 60.000 26.71 8.51 45.99 3.69
1957 2038 0.665369 ACCGAACGTTCACACCGATC 60.665 55.000 26.71 0.00 0.00 3.69
1958 2039 0.665369 GACCGAACGTTCACACCGAT 60.665 55.000 26.71 0.36 0.00 4.18
1959 2040 1.299316 GACCGAACGTTCACACCGA 60.299 57.895 26.71 0.00 0.00 4.69
1960 2041 0.942410 ATGACCGAACGTTCACACCG 60.942 55.000 26.71 13.59 0.00 4.94
1961 2042 0.788391 GATGACCGAACGTTCACACC 59.212 55.000 26.71 11.62 0.00 4.16
1962 2043 0.433492 CGATGACCGAACGTTCACAC 59.567 55.000 26.71 16.50 41.76 3.82
1963 2044 0.665068 CCGATGACCGAACGTTCACA 60.665 55.000 26.71 21.50 41.76 3.58
1964 2045 0.665369 ACCGATGACCGAACGTTCAC 60.665 55.000 26.71 17.14 41.76 3.18
1965 2046 0.665068 CACCGATGACCGAACGTTCA 60.665 55.000 26.71 9.64 41.76 3.18
1966 2047 0.665369 ACACCGATGACCGAACGTTC 60.665 55.000 18.47 18.47 41.76 3.95
1987 2068 1.136057 CGAAGATATCACCGCGATCGA 60.136 52.381 21.57 0.02 38.10 3.59
1988 2069 1.251355 CGAAGATATCACCGCGATCG 58.749 55.000 11.69 11.69 35.39 3.69
1989 2070 0.985549 GCGAAGATATCACCGCGATC 59.014 55.000 20.43 1.29 38.27 3.69
1990 2071 3.108521 GCGAAGATATCACCGCGAT 57.891 52.632 20.43 0.00 38.27 4.58
2007 2088 1.641577 GACACAATACCTCGTCAGGC 58.358 55.000 0.00 0.00 45.05 4.85
2061 2142 4.785346 ACTCTTGGCATATTGGTCATCT 57.215 40.909 0.00 0.00 0.00 2.90
2079 2160 9.860898 ACCATAGCTTCAAATTTTATGAAACTC 57.139 29.630 0.00 0.00 35.48 3.01
2116 2204 9.214962 TCCTAAAACCTCCCAAATTTTAAGAAA 57.785 29.630 0.00 0.00 29.79 2.52
2276 2385 6.124088 ACTCTAAAAATTTGCAGGATAGCG 57.876 37.500 0.00 0.00 37.31 4.26
2296 2405 7.814587 CCCATTTCTCATCAAACCTTTAAACTC 59.185 37.037 0.00 0.00 0.00 3.01
2322 2431 3.124578 GATCTCCTTGATCCAAGCTCC 57.875 52.381 1.39 0.00 44.34 4.70
2356 2504 5.016173 CACCATTCAAAAGGATGGAAGGTA 58.984 41.667 9.71 0.00 37.60 3.08
2384 2532 5.468592 TGTTTGCATTGTACTGCTTAATGG 58.531 37.500 8.39 0.00 42.75 3.16
2463 2611 5.934043 ACATGTCATCGAGAACAGATTGAAA 59.066 36.000 8.42 0.00 0.00 2.69
2520 2668 3.525800 TGGATAGTCCGGATCATGAGA 57.474 47.619 7.81 0.00 40.17 3.27
2627 2775 5.508200 AACGAGTGGATTTAGCAACAAAA 57.492 34.783 0.00 0.00 0.00 2.44
2628 2776 5.066634 TCAAACGAGTGGATTTAGCAACAAA 59.933 36.000 0.00 0.00 0.00 2.83
2629 2777 4.576873 TCAAACGAGTGGATTTAGCAACAA 59.423 37.500 0.00 0.00 0.00 2.83
2630 2778 4.130857 TCAAACGAGTGGATTTAGCAACA 58.869 39.130 0.00 0.00 0.00 3.33
2631 2779 4.742438 TCAAACGAGTGGATTTAGCAAC 57.258 40.909 0.00 0.00 0.00 4.17
2700 2848 4.771577 TCAAATTGGCCAAATGAGAAGCTA 59.228 37.500 24.71 4.21 0.00 3.32
2792 2942 3.420300 TTATTGCTACGTTCCCCAACA 57.580 42.857 0.00 0.00 32.14 3.33
2793 2943 4.976224 AATTATTGCTACGTTCCCCAAC 57.024 40.909 0.00 0.00 0.00 3.77
2794 2944 7.463961 TTTAAATTATTGCTACGTTCCCCAA 57.536 32.000 0.00 0.00 0.00 4.12
2795 2945 7.463961 TTTTAAATTATTGCTACGTTCCCCA 57.536 32.000 0.00 0.00 0.00 4.96
2796 2946 8.936070 AATTTTAAATTATTGCTACGTTCCCC 57.064 30.769 0.54 0.00 0.00 4.81
2810 2960 9.896263 GGTGACACGTAGGAAAATTTTAAATTA 57.104 29.630 2.75 0.00 0.00 1.40
2811 2961 8.414778 TGGTGACACGTAGGAAAATTTTAAATT 58.585 29.630 2.75 0.00 33.40 1.82
2812 2962 7.942990 TGGTGACACGTAGGAAAATTTTAAAT 58.057 30.769 2.75 0.00 33.40 1.40
2813 2963 7.330900 TGGTGACACGTAGGAAAATTTTAAA 57.669 32.000 2.75 0.00 33.40 1.52
2814 2964 6.939132 TGGTGACACGTAGGAAAATTTTAA 57.061 33.333 2.75 0.00 33.40 1.52
2815 2965 6.766944 TCTTGGTGACACGTAGGAAAATTTTA 59.233 34.615 2.75 0.00 42.67 1.52
2816 2966 5.591067 TCTTGGTGACACGTAGGAAAATTTT 59.409 36.000 2.28 2.28 42.67 1.82
2817 2967 5.127491 TCTTGGTGACACGTAGGAAAATTT 58.873 37.500 0.00 0.00 42.67 1.82
2818 2968 4.710324 TCTTGGTGACACGTAGGAAAATT 58.290 39.130 0.00 0.00 42.67 1.82
2819 2969 4.345859 TCTTGGTGACACGTAGGAAAAT 57.654 40.909 0.00 0.00 42.67 1.82
2820 2970 3.823281 TCTTGGTGACACGTAGGAAAA 57.177 42.857 0.00 0.00 42.67 2.29
2821 2971 3.322541 TGATCTTGGTGACACGTAGGAAA 59.677 43.478 0.00 0.00 42.67 3.13
2822 2972 2.894765 TGATCTTGGTGACACGTAGGAA 59.105 45.455 0.00 0.00 42.67 3.36
2823 2973 2.521126 TGATCTTGGTGACACGTAGGA 58.479 47.619 0.00 0.00 42.67 2.94
2824 2974 3.313012 TTGATCTTGGTGACACGTAGG 57.687 47.619 0.00 0.00 42.67 3.18
2825 2975 4.748892 AGATTGATCTTGGTGACACGTAG 58.251 43.478 0.00 0.00 42.67 3.51
2826 2976 4.801330 AGATTGATCTTGGTGACACGTA 57.199 40.909 0.00 0.00 42.67 3.57
2827 2977 3.685139 AGATTGATCTTGGTGACACGT 57.315 42.857 0.00 0.00 42.67 4.49
2828 2978 4.115516 CCTAGATTGATCTTGGTGACACG 58.884 47.826 11.74 0.00 42.44 4.49
2829 2979 5.127845 TCTCCTAGATTGATCTTGGTGACAC 59.872 44.000 17.17 0.00 45.88 3.67
2830 2980 5.272402 TCTCCTAGATTGATCTTGGTGACA 58.728 41.667 17.17 2.34 45.88 3.58
2831 2981 5.860941 TCTCCTAGATTGATCTTGGTGAC 57.139 43.478 17.17 0.00 45.88 3.67
2833 2983 7.537596 AGTATCTCCTAGATTGATCTTGGTG 57.462 40.000 17.17 15.36 45.88 4.17
2834 2984 7.396055 GCTAGTATCTCCTAGATTGATCTTGGT 59.604 40.741 17.17 5.32 45.88 3.67
2835 2985 7.395772 TGCTAGTATCTCCTAGATTGATCTTGG 59.604 40.741 13.24 13.24 46.71 3.61
2836 2986 8.347004 TGCTAGTATCTCCTAGATTGATCTTG 57.653 38.462 0.00 0.00 37.24 3.02
2837 2987 8.802267 GTTGCTAGTATCTCCTAGATTGATCTT 58.198 37.037 0.00 0.00 37.24 2.40
2838 2988 7.947332 TGTTGCTAGTATCTCCTAGATTGATCT 59.053 37.037 0.00 0.00 37.24 2.75
2839 2989 8.116651 TGTTGCTAGTATCTCCTAGATTGATC 57.883 38.462 0.00 0.00 37.24 2.92
2840 2990 8.484214 TTGTTGCTAGTATCTCCTAGATTGAT 57.516 34.615 0.00 0.00 37.24 2.57
2841 2991 7.780271 TCTTGTTGCTAGTATCTCCTAGATTGA 59.220 37.037 0.00 0.00 37.24 2.57
2842 2992 7.946207 TCTTGTTGCTAGTATCTCCTAGATTG 58.054 38.462 0.00 0.00 37.24 2.67
2843 2993 8.177119 CTCTTGTTGCTAGTATCTCCTAGATT 57.823 38.462 0.00 0.00 37.24 2.40
2844 2994 7.759489 CTCTTGTTGCTAGTATCTCCTAGAT 57.241 40.000 0.00 0.00 37.24 1.98


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

AutoCloner maintained by Alex Coulton.