Multiple sequence alignment - TraesCS2B01G283000

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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 TraesCS2B01G283000 chr2B 100.000 3578 0 0 1 3578 391098662 391102239 0.000000e+00 6608.0
1 TraesCS2B01G283000 chr7B 98.613 2451 34 0 1 2451 742950730 742948280 0.000000e+00 4338.0
2 TraesCS2B01G283000 chr7B 98.124 2452 44 2 1 2451 716782615 716785065 0.000000e+00 4272.0
3 TraesCS2B01G283000 chr7B 94.211 760 38 2 2178 2937 325567218 325567971 0.000000e+00 1155.0
4 TraesCS2B01G283000 chr7B 91.718 483 19 7 3102 3578 325567964 325568431 0.000000e+00 651.0
5 TraesCS2B01G283000 chr7B 87.647 170 21 0 2707 2876 47160311 47160480 7.840000e-47 198.0
6 TraesCS2B01G283000 chr7B 97.059 68 2 0 3321 3388 106393267 106393334 8.120000e-22 115.0
7 TraesCS2B01G283000 chr2A 98.613 2452 33 1 1 2451 755478556 755481007 0.000000e+00 4338.0
8 TraesCS2B01G283000 chr2A 100.000 46 0 0 17 62 86679534 86679489 6.360000e-13 86.1
9 TraesCS2B01G283000 chr7A 98.572 2451 35 0 1 2451 60170759 60168309 0.000000e+00 4333.0
10 TraesCS2B01G283000 chr4D 93.338 2942 178 12 1 2932 241177507 241180440 0.000000e+00 4331.0
11 TraesCS2B01G283000 chr4D 98.205 2451 43 1 1 2451 123348130 123350579 0.000000e+00 4281.0
12 TraesCS2B01G283000 chr4D 90.351 114 9 1 3201 3314 241180493 241180604 8.000000e-32 148.0
13 TraesCS2B01G283000 chr5A 98.490 2451 36 1 1 2451 420183711 420186160 0.000000e+00 4320.0
14 TraesCS2B01G283000 chr5A 98.755 2409 30 0 43 2451 16542604 16545012 0.000000e+00 4283.0
15 TraesCS2B01G283000 chr1B 98.164 2451 44 1 1 2451 583563540 583561091 0.000000e+00 4276.0
16 TraesCS2B01G283000 chr6A 98.042 2451 48 0 1 2451 155855307 155857757 0.000000e+00 4261.0
17 TraesCS2B01G283000 chr3D 92.279 2176 145 17 769 2932 193436111 193433947 0.000000e+00 3066.0
18 TraesCS2B01G283000 chr3D 93.162 117 6 1 3201 3317 193433894 193433780 1.710000e-38 171.0
19 TraesCS2B01G283000 chr3B 98.387 186 3 0 2737 2922 377433053 377432868 9.580000e-86 327.0
20 TraesCS2B01G283000 chr3B 87.647 170 21 0 2707 2876 730349861 730350030 7.840000e-47 198.0
21 TraesCS2B01G283000 chr4B 86.869 198 24 2 2648 2844 587461408 587461604 1.670000e-53 220.0
22 TraesCS2B01G283000 chrUn 88.701 177 20 0 2707 2883 171063104 171063280 2.160000e-52 217.0
23 TraesCS2B01G283000 chr5B 87.500 176 22 0 2707 2882 34126907 34126732 1.680000e-48 204.0


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 TraesCS2B01G283000 chr2B 391098662 391102239 3577 False 6608.0 6608 100.0000 1 3578 1 chr2B.!!$F1 3577
1 TraesCS2B01G283000 chr7B 742948280 742950730 2450 True 4338.0 4338 98.6130 1 2451 1 chr7B.!!$R1 2450
2 TraesCS2B01G283000 chr7B 716782615 716785065 2450 False 4272.0 4272 98.1240 1 2451 1 chr7B.!!$F3 2450
3 TraesCS2B01G283000 chr7B 325567218 325568431 1213 False 903.0 1155 92.9645 2178 3578 2 chr7B.!!$F4 1400
4 TraesCS2B01G283000 chr2A 755478556 755481007 2451 False 4338.0 4338 98.6130 1 2451 1 chr2A.!!$F1 2450
5 TraesCS2B01G283000 chr7A 60168309 60170759 2450 True 4333.0 4333 98.5720 1 2451 1 chr7A.!!$R1 2450
6 TraesCS2B01G283000 chr4D 123348130 123350579 2449 False 4281.0 4281 98.2050 1 2451 1 chr4D.!!$F1 2450
7 TraesCS2B01G283000 chr4D 241177507 241180604 3097 False 2239.5 4331 91.8445 1 3314 2 chr4D.!!$F2 3313
8 TraesCS2B01G283000 chr5A 420183711 420186160 2449 False 4320.0 4320 98.4900 1 2451 1 chr5A.!!$F2 2450
9 TraesCS2B01G283000 chr5A 16542604 16545012 2408 False 4283.0 4283 98.7550 43 2451 1 chr5A.!!$F1 2408
10 TraesCS2B01G283000 chr1B 583561091 583563540 2449 True 4276.0 4276 98.1640 1 2451 1 chr1B.!!$R1 2450
11 TraesCS2B01G283000 chr6A 155855307 155857757 2450 False 4261.0 4261 98.0420 1 2451 1 chr6A.!!$F1 2450
12 TraesCS2B01G283000 chr3D 193433780 193436111 2331 True 1618.5 3066 92.7205 769 3317 2 chr3D.!!$R1 2548

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
534 535 3.017442 AGACTCGGAATCATTCTCACGA 58.983 45.455 0.00 0.0 0.0 4.35 F
1192 1195 1.522668 CAGCGGTGTGAAAGGAATCA 58.477 50.000 6.41 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1420 1423 2.147958 GGGTTCGTGCACAGATTTACA 58.852 47.619 18.64 0.0 0.0 2.41 R
3176 3190 0.320374 GATGGTCCGAACTCACACCA 59.680 55.000 0.00 0.0 43.1 4.17 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
403 404 7.287927 TCAATATGGGTAGGCTGCTATATCTAC 59.712 40.741 1.79 2.09 33.37 2.59
466 467 6.915349 ACTTATCTTATTACTCAGCTAGGCG 58.085 40.000 0.00 0.00 0.00 5.52
487 488 8.459911 AGGCGCTTACAAACCTATTTATTTAT 57.540 30.769 7.64 0.00 0.00 1.40
534 535 3.017442 AGACTCGGAATCATTCTCACGA 58.983 45.455 0.00 0.00 0.00 4.35
988 991 8.600668 TCTCCCTTCAAAATATCATCCATCTAG 58.399 37.037 0.00 0.00 0.00 2.43
1192 1195 1.522668 CAGCGGTGTGAAAGGAATCA 58.477 50.000 6.41 0.00 0.00 2.57
1273 1276 9.883142 CTATTAAAGAAGGAGATCTTGTCAAGT 57.117 33.333 12.30 0.29 39.54 3.16
1420 1423 3.999764 AAGCCCCAGGGATTATTGAAT 57.000 42.857 7.25 0.00 42.67 2.57
1918 1921 7.341769 CAGGGGATGTTTTCTATTTACATTCCA 59.658 37.037 12.48 0.00 45.81 3.53
2013 2016 1.893137 ACACAAGCTGGAGACGTATCA 59.107 47.619 12.92 0.00 0.00 2.15
2121 2124 4.271776 GCTATTAACGTTGGCTTATCCGTT 59.728 41.667 11.99 0.00 44.69 4.44
2246 2249 0.326264 GGGTCAGACCTTGATGCTGT 59.674 55.000 19.57 0.00 38.64 4.40
2452 2455 8.940397 TCCAGAATTACAAAAATCCTTCTTCT 57.060 30.769 0.00 0.00 0.00 2.85
2453 2456 9.367160 TCCAGAATTACAAAAATCCTTCTTCTT 57.633 29.630 0.00 0.00 0.00 2.52
2501 2504 1.768684 TTCTTCTGGCCTGGAAGCGT 61.769 55.000 24.43 0.00 39.75 5.07
2558 2566 1.734477 CTCAACGGTCGAGGCAGTG 60.734 63.158 0.00 0.00 0.00 3.66
2578 2586 0.183731 GGACCCCCTGATTGGATGAC 59.816 60.000 0.00 0.00 38.35 3.06
2592 2600 0.830648 GATGACGGGGAATCCTGACA 59.169 55.000 0.00 0.00 45.34 3.58
2654 2662 6.782494 AGGTAAAAGATGGAATTGACAACCTT 59.218 34.615 0.00 0.00 0.00 3.50
2727 2735 1.263217 CGACCCTTGAAGAACAAACGG 59.737 52.381 0.00 0.00 38.08 4.44
2938 2952 9.923143 ATTTAGTTAATTTTGTGTTAAGCTCCC 57.077 29.630 0.00 0.00 0.00 4.30
2939 2953 6.009115 AGTTAATTTTGTGTTAAGCTCCCG 57.991 37.500 0.00 0.00 0.00 5.14
2940 2954 5.533528 AGTTAATTTTGTGTTAAGCTCCCGT 59.466 36.000 0.00 0.00 0.00 5.28
2941 2955 4.499037 AATTTTGTGTTAAGCTCCCGTC 57.501 40.909 0.00 0.00 0.00 4.79
2942 2956 2.623878 TTTGTGTTAAGCTCCCGTCA 57.376 45.000 0.00 0.00 0.00 4.35
2943 2957 2.623878 TTGTGTTAAGCTCCCGTCAA 57.376 45.000 0.00 0.00 0.00 3.18
2944 2958 2.623878 TGTGTTAAGCTCCCGTCAAA 57.376 45.000 0.00 0.00 0.00 2.69
2945 2959 2.920524 TGTGTTAAGCTCCCGTCAAAA 58.079 42.857 0.00 0.00 0.00 2.44
2946 2960 3.482436 TGTGTTAAGCTCCCGTCAAAAT 58.518 40.909 0.00 0.00 0.00 1.82
2947 2961 4.643463 TGTGTTAAGCTCCCGTCAAAATA 58.357 39.130 0.00 0.00 0.00 1.40
2948 2962 5.064558 TGTGTTAAGCTCCCGTCAAAATAA 58.935 37.500 0.00 0.00 0.00 1.40
2949 2963 5.531659 TGTGTTAAGCTCCCGTCAAAATAAA 59.468 36.000 0.00 0.00 0.00 1.40
2950 2964 6.207810 TGTGTTAAGCTCCCGTCAAAATAAAT 59.792 34.615 0.00 0.00 0.00 1.40
2951 2965 7.390996 TGTGTTAAGCTCCCGTCAAAATAAATA 59.609 33.333 0.00 0.00 0.00 1.40
2952 2966 7.695201 GTGTTAAGCTCCCGTCAAAATAAATAC 59.305 37.037 0.00 0.00 0.00 1.89
2953 2967 5.479716 AAGCTCCCGTCAAAATAAATACG 57.520 39.130 0.00 0.00 35.20 3.06
2954 2968 4.761975 AGCTCCCGTCAAAATAAATACGA 58.238 39.130 0.00 0.00 37.53 3.43
2955 2969 4.809426 AGCTCCCGTCAAAATAAATACGAG 59.191 41.667 0.00 0.00 37.53 4.18
2956 2970 4.807304 GCTCCCGTCAAAATAAATACGAGA 59.193 41.667 0.00 0.00 37.53 4.04
2957 2971 5.292589 GCTCCCGTCAAAATAAATACGAGAA 59.707 40.000 0.00 0.00 37.53 2.87
2958 2972 6.651755 TCCCGTCAAAATAAATACGAGAAC 57.348 37.500 0.00 0.00 37.53 3.01
2959 2973 6.164876 TCCCGTCAAAATAAATACGAGAACA 58.835 36.000 0.00 0.00 37.53 3.18
2960 2974 6.649973 TCCCGTCAAAATAAATACGAGAACAA 59.350 34.615 0.00 0.00 37.53 2.83
2961 2975 7.172875 TCCCGTCAAAATAAATACGAGAACAAA 59.827 33.333 0.00 0.00 37.53 2.83
2962 2976 7.480542 CCCGTCAAAATAAATACGAGAACAAAG 59.519 37.037 0.00 0.00 37.53 2.77
2963 2977 7.480542 CCGTCAAAATAAATACGAGAACAAAGG 59.519 37.037 0.00 0.00 37.53 3.11
2964 2978 8.013378 CGTCAAAATAAATACGAGAACAAAGGT 58.987 33.333 0.00 0.00 37.53 3.50
2965 2979 9.113876 GTCAAAATAAATACGAGAACAAAGGTG 57.886 33.333 0.00 0.00 0.00 4.00
2966 2980 8.842280 TCAAAATAAATACGAGAACAAAGGTGT 58.158 29.630 0.00 0.00 40.75 4.16
2979 2993 4.405196 ACAAAGGTGTTACGTTTTTGACG 58.595 39.130 0.00 0.00 46.47 4.35
2980 2994 4.153835 ACAAAGGTGTTACGTTTTTGACGA 59.846 37.500 5.50 0.00 44.87 4.20
2981 2995 5.334724 ACAAAGGTGTTACGTTTTTGACGAA 60.335 36.000 5.50 0.00 44.87 3.85
2982 2996 6.786529 ACAAAGGTGTTACGTTTTTGACGAAA 60.787 34.615 5.50 0.00 44.87 3.46
2983 2997 8.205578 ACAAAGGTGTTACGTTTTTGACGAAAA 61.206 33.333 5.50 0.00 44.87 2.29
3012 3026 5.089970 TGTGAGAATCTCATGAAATCGGT 57.910 39.130 16.68 0.00 42.73 4.69
3013 3027 4.872124 TGTGAGAATCTCATGAAATCGGTG 59.128 41.667 16.68 0.00 42.73 4.94
3014 3028 4.872691 GTGAGAATCTCATGAAATCGGTGT 59.127 41.667 16.68 0.00 42.73 4.16
3015 3029 5.352569 GTGAGAATCTCATGAAATCGGTGTT 59.647 40.000 16.68 0.00 42.73 3.32
3016 3030 6.535150 GTGAGAATCTCATGAAATCGGTGTTA 59.465 38.462 16.68 0.00 42.73 2.41
3017 3031 6.535150 TGAGAATCTCATGAAATCGGTGTTAC 59.465 38.462 9.18 0.00 35.39 2.50
3018 3032 5.520288 AGAATCTCATGAAATCGGTGTTACG 59.480 40.000 0.00 0.00 0.00 3.18
3019 3033 4.182693 TCTCATGAAATCGGTGTTACGT 57.817 40.909 0.00 0.00 34.94 3.57
3020 3034 4.562082 TCTCATGAAATCGGTGTTACGTT 58.438 39.130 0.00 0.00 34.94 3.99
3021 3035 4.992319 TCTCATGAAATCGGTGTTACGTTT 59.008 37.500 0.00 0.00 34.94 3.60
3022 3036 5.467399 TCTCATGAAATCGGTGTTACGTTTT 59.533 36.000 0.00 0.00 38.16 2.43
3023 3037 6.017770 TCTCATGAAATCGGTGTTACGTTTTT 60.018 34.615 0.00 0.00 36.31 1.94
3024 3038 5.910166 TCATGAAATCGGTGTTACGTTTTTG 59.090 36.000 0.00 0.00 36.31 2.44
3025 3039 5.481200 TGAAATCGGTGTTACGTTTTTGA 57.519 34.783 0.00 0.00 36.31 2.69
3026 3040 5.264712 TGAAATCGGTGTTACGTTTTTGAC 58.735 37.500 0.00 0.00 36.31 3.18
3027 3041 4.879104 AATCGGTGTTACGTTTTTGACA 57.121 36.364 0.00 0.00 34.94 3.58
3028 3042 4.879104 ATCGGTGTTACGTTTTTGACAA 57.121 36.364 0.00 0.00 34.94 3.18
3029 3043 4.675190 TCGGTGTTACGTTTTTGACAAA 57.325 36.364 0.00 0.00 34.94 2.83
3030 3044 5.039480 TCGGTGTTACGTTTTTGACAAAA 57.961 34.783 9.30 9.30 34.94 2.44
3031 3045 5.455392 TCGGTGTTACGTTTTTGACAAAAA 58.545 33.333 19.67 19.67 37.99 1.94
3032 3046 5.568296 TCGGTGTTACGTTTTTGACAAAAAG 59.432 36.000 23.11 18.61 40.71 2.27
3033 3047 5.568296 CGGTGTTACGTTTTTGACAAAAAGA 59.432 36.000 23.11 11.16 40.71 2.52
3034 3048 6.087820 CGGTGTTACGTTTTTGACAAAAAGAA 59.912 34.615 23.11 15.47 40.71 2.52
3035 3049 7.358187 CGGTGTTACGTTTTTGACAAAAAGAAA 60.358 33.333 23.11 15.31 40.71 2.52
3036 3050 8.436970 GGTGTTACGTTTTTGACAAAAAGAAAT 58.563 29.630 23.11 12.82 40.71 2.17
3037 3051 9.245284 GTGTTACGTTTTTGACAAAAAGAAATG 57.755 29.630 23.11 12.08 40.71 2.32
3038 3052 7.952637 TGTTACGTTTTTGACAAAAAGAAATGC 59.047 29.630 23.11 11.45 40.71 3.56
3039 3053 5.546434 ACGTTTTTGACAAAAAGAAATGCG 58.454 33.333 23.11 21.81 40.71 4.73
3040 3054 5.346281 ACGTTTTTGACAAAAAGAAATGCGA 59.654 32.000 25.64 5.64 40.71 5.10
3041 3055 5.890497 CGTTTTTGACAAAAAGAAATGCGAG 59.110 36.000 23.11 6.07 40.71 5.03
3042 3056 6.237437 CGTTTTTGACAAAAAGAAATGCGAGA 60.237 34.615 23.11 0.00 40.71 4.04
3043 3057 7.452231 GTTTTTGACAAAAAGAAATGCGAGAA 58.548 30.769 23.11 0.00 40.71 2.87
3044 3058 7.769272 TTTTGACAAAAAGAAATGCGAGAAT 57.231 28.000 10.92 0.00 31.61 2.40
3045 3059 6.752335 TTGACAAAAAGAAATGCGAGAATG 57.248 33.333 0.00 0.00 0.00 2.67
3046 3060 5.830912 TGACAAAAAGAAATGCGAGAATGT 58.169 33.333 0.00 0.00 0.00 2.71
3047 3061 5.914635 TGACAAAAAGAAATGCGAGAATGTC 59.085 36.000 0.00 0.00 35.30 3.06
3059 3073 4.236755 CGAGAATGTCGTGAAATCAGTG 57.763 45.455 0.00 0.00 44.20 3.66
3060 3074 3.675225 CGAGAATGTCGTGAAATCAGTGT 59.325 43.478 0.00 0.00 44.20 3.55
3061 3075 4.150627 CGAGAATGTCGTGAAATCAGTGTT 59.849 41.667 0.00 0.00 44.20 3.32
3062 3076 5.344933 CGAGAATGTCGTGAAATCAGTGTTA 59.655 40.000 0.00 0.00 44.20 2.41
3063 3077 6.467723 AGAATGTCGTGAAATCAGTGTTAC 57.532 37.500 0.00 0.00 0.00 2.50
3064 3078 4.903638 ATGTCGTGAAATCAGTGTTACG 57.096 40.909 0.00 0.00 0.00 3.18
3065 3079 3.708890 TGTCGTGAAATCAGTGTTACGT 58.291 40.909 0.00 0.00 33.68 3.57
3066 3080 4.114073 TGTCGTGAAATCAGTGTTACGTT 58.886 39.130 0.00 0.00 33.68 3.99
3067 3081 4.567558 TGTCGTGAAATCAGTGTTACGTTT 59.432 37.500 0.00 0.00 33.68 3.60
3068 3082 5.063691 TGTCGTGAAATCAGTGTTACGTTTT 59.936 36.000 0.00 0.00 33.68 2.43
3069 3083 5.961263 GTCGTGAAATCAGTGTTACGTTTTT 59.039 36.000 0.00 0.00 33.68 1.94
3070 3084 5.960683 TCGTGAAATCAGTGTTACGTTTTTG 59.039 36.000 0.00 0.00 33.68 2.44
3071 3085 5.960683 CGTGAAATCAGTGTTACGTTTTTGA 59.039 36.000 0.00 0.00 0.00 2.69
3072 3086 6.076298 CGTGAAATCAGTGTTACGTTTTTGAC 60.076 38.462 0.00 0.00 0.00 3.18
3134 3148 9.736414 CTTGATAAGAAATATGATCATGAGGGT 57.264 33.333 18.72 2.11 0.00 4.34
3172 3186 8.550280 AGGTGTTAAGGGTTTTACCAATAAAA 57.450 30.769 0.00 0.00 41.02 1.52
3173 3187 9.161572 AGGTGTTAAGGGTTTTACCAATAAAAT 57.838 29.630 0.00 0.00 41.25 1.82
3181 3195 9.106977 AGGGTTTTACCAATAAAATAATGGTGT 57.893 29.630 6.92 0.00 46.56 4.16
3191 3205 5.622770 AAAATAATGGTGTGAGTTCGGAC 57.377 39.130 0.00 0.00 0.00 4.79
3288 3315 4.806342 AAACATCGCCCATTTATCGTAC 57.194 40.909 0.00 0.00 0.00 3.67
3314 3341 4.568956 TCTTGTGTACAGTCATCCACATG 58.431 43.478 0.00 0.00 37.63 3.21
3382 3409 1.305201 TTGAACAGAACGGCTTGGAC 58.695 50.000 0.00 0.00 0.00 4.02
3383 3410 0.534203 TGAACAGAACGGCTTGGACC 60.534 55.000 0.00 0.00 0.00 4.46
3405 3438 6.855836 ACCGTAGATTATTCGAGTGTAAACA 58.144 36.000 0.00 0.00 0.00 2.83
3408 3441 5.950965 AGATTATTCGAGTGTAAACAGCG 57.049 39.130 0.00 0.33 0.00 5.18
3426 3459 5.271625 ACAGCGTACGTGATCAAGTTATAG 58.728 41.667 19.43 9.64 0.00 1.31
3432 3465 4.549668 ACGTGATCAAGTTATAGGGGGTA 58.450 43.478 8.60 0.00 0.00 3.69
3439 3472 5.102967 TCAAGTTATAGGGGGTAAACCTGT 58.897 41.667 0.00 0.00 39.12 4.00
3461 3494 8.593842 CCTGTACGTGATCTAGTTATATACGAG 58.406 40.741 0.00 0.00 34.52 4.18
3477 3510 1.522569 GAGAATAGTGGTGGCGCCT 59.477 57.895 29.70 9.54 38.35 5.52
3485 3518 4.162690 GGTGGCGCCTGTAGAGGG 62.163 72.222 29.70 0.00 40.19 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
403 404 7.042797 TCCAAAACCTTTCATCTTCTCTTTG 57.957 36.000 0.00 0.00 0.00 2.77
487 488 2.304761 GACCAGACCCATGTGGAACTTA 59.695 50.000 7.06 0.00 42.06 2.24
553 554 0.824109 TGATCGATTGGCGGAGAAGT 59.176 50.000 0.00 0.00 41.33 3.01
988 991 8.027189 GGGTGAGAATTCCATACTTTAACAAAC 58.973 37.037 0.65 0.00 0.00 2.93
1273 1276 3.200605 ACATCCACAATAGATCCAGTGCA 59.799 43.478 0.00 0.00 0.00 4.57
1326 1329 1.303888 TACTCCCAAGGCGTCGACT 60.304 57.895 14.70 0.00 0.00 4.18
1420 1423 2.147958 GGGTTCGTGCACAGATTTACA 58.852 47.619 18.64 0.00 0.00 2.41
1891 1894 7.559897 GGAATGTAAATAGAAAACATCCCCTGA 59.440 37.037 0.00 0.00 32.80 3.86
2013 2016 2.376518 CACATTGGTGGGGATATAGGCT 59.623 50.000 0.00 0.00 41.45 4.58
2121 2124 3.807538 GCAGACCCGACGCGACTA 61.808 66.667 15.93 0.00 0.00 2.59
2246 2249 5.069648 CCTCTATTGAGTAATGCCTGAGTCA 59.930 44.000 3.47 0.00 38.61 3.41
2451 2454 4.307443 AGCTTTGAAAAGGAACCGAAAG 57.693 40.909 5.02 0.00 36.53 2.62
2452 2455 4.037089 GGTAGCTTTGAAAAGGAACCGAAA 59.963 41.667 0.00 0.00 36.53 3.46
2453 2456 3.566742 GGTAGCTTTGAAAAGGAACCGAA 59.433 43.478 0.00 0.00 36.53 4.30
2558 2566 0.993509 TCATCCAATCAGGGGGTCCC 60.994 60.000 0.00 0.00 45.90 4.46
2565 2573 0.546122 TTCCCCGTCATCCAATCAGG 59.454 55.000 0.00 0.00 39.47 3.86
2578 2586 1.452108 GCCTTGTCAGGATTCCCCG 60.452 63.158 0.00 0.00 44.19 5.73
2714 2722 4.927422 GGATGTTTTCCGTTTGTTCTTCA 58.073 39.130 0.00 0.00 33.93 3.02
2727 2735 7.308229 CCATTCCAAGATAGATCGGATGTTTTC 60.308 40.741 0.00 0.00 0.00 2.29
2922 2936 2.920524 TGACGGGAGCTTAACACAAAA 58.079 42.857 0.00 0.00 0.00 2.44
2925 2939 2.623878 TTTGACGGGAGCTTAACACA 57.376 45.000 0.00 0.00 0.00 3.72
2929 2943 6.817641 TCGTATTTATTTTGACGGGAGCTTAA 59.182 34.615 0.00 0.00 36.02 1.85
2930 2944 6.339730 TCGTATTTATTTTGACGGGAGCTTA 58.660 36.000 0.00 0.00 36.02 3.09
2931 2945 5.180271 TCGTATTTATTTTGACGGGAGCTT 58.820 37.500 0.00 0.00 36.02 3.74
2932 2946 4.761975 TCGTATTTATTTTGACGGGAGCT 58.238 39.130 0.00 0.00 36.02 4.09
2933 2947 4.807304 TCTCGTATTTATTTTGACGGGAGC 59.193 41.667 0.00 0.00 39.75 4.70
2934 2948 6.311935 TGTTCTCGTATTTATTTTGACGGGAG 59.688 38.462 0.00 0.00 44.86 4.30
2935 2949 6.164876 TGTTCTCGTATTTATTTTGACGGGA 58.835 36.000 0.00 0.00 42.73 5.14
2936 2950 6.411630 TGTTCTCGTATTTATTTTGACGGG 57.588 37.500 0.00 0.00 37.13 5.28
2937 2951 7.480542 CCTTTGTTCTCGTATTTATTTTGACGG 59.519 37.037 0.00 0.00 36.02 4.79
2938 2952 8.013378 ACCTTTGTTCTCGTATTTATTTTGACG 58.987 33.333 0.00 0.00 36.66 4.35
2939 2953 9.113876 CACCTTTGTTCTCGTATTTATTTTGAC 57.886 33.333 0.00 0.00 0.00 3.18
2940 2954 8.842280 ACACCTTTGTTCTCGTATTTATTTTGA 58.158 29.630 0.00 0.00 28.43 2.69
2941 2955 9.458374 AACACCTTTGTTCTCGTATTTATTTTG 57.542 29.630 0.00 0.00 42.67 2.44
2944 2958 8.437742 CGTAACACCTTTGTTCTCGTATTTATT 58.562 33.333 0.00 0.00 42.67 1.40
2945 2959 7.599998 ACGTAACACCTTTGTTCTCGTATTTAT 59.400 33.333 14.47 0.00 45.67 1.40
2946 2960 6.922957 ACGTAACACCTTTGTTCTCGTATTTA 59.077 34.615 14.47 0.00 45.67 1.40
2947 2961 5.754890 ACGTAACACCTTTGTTCTCGTATTT 59.245 36.000 14.47 0.00 45.67 1.40
2948 2962 5.291971 ACGTAACACCTTTGTTCTCGTATT 58.708 37.500 14.47 0.00 45.67 1.89
2949 2963 4.874970 ACGTAACACCTTTGTTCTCGTAT 58.125 39.130 14.47 0.00 45.67 3.06
2950 2964 4.305989 ACGTAACACCTTTGTTCTCGTA 57.694 40.909 14.47 0.00 45.67 3.43
2951 2965 3.169355 ACGTAACACCTTTGTTCTCGT 57.831 42.857 11.91 11.91 42.67 4.18
2952 2966 4.525411 AAACGTAACACCTTTGTTCTCG 57.475 40.909 0.00 11.01 42.67 4.04
2953 2967 6.249893 GTCAAAAACGTAACACCTTTGTTCTC 59.750 38.462 0.00 0.00 42.67 2.87
2954 2968 6.088173 GTCAAAAACGTAACACCTTTGTTCT 58.912 36.000 0.00 0.00 42.67 3.01
2955 2969 5.002747 CGTCAAAAACGTAACACCTTTGTTC 59.997 40.000 0.00 0.00 43.35 3.18
2956 2970 4.852650 CGTCAAAAACGTAACACCTTTGTT 59.147 37.500 0.00 0.00 46.42 2.83
2957 2971 4.405196 CGTCAAAAACGTAACACCTTTGT 58.595 39.130 0.00 0.00 46.42 2.83
2958 2972 4.984570 CGTCAAAAACGTAACACCTTTG 57.015 40.909 0.00 0.00 46.42 2.77
2984 2998 8.396390 CGATTTCATGAGATTCTCACATTTCTT 58.604 33.333 18.35 0.00 43.63 2.52
2985 2999 7.012138 CCGATTTCATGAGATTCTCACATTTCT 59.988 37.037 18.35 0.00 43.63 2.52
2986 3000 7.130917 CCGATTTCATGAGATTCTCACATTTC 58.869 38.462 18.35 10.75 43.63 2.17
2987 3001 6.600822 ACCGATTTCATGAGATTCTCACATTT 59.399 34.615 18.35 0.01 43.63 2.32
2988 3002 6.037940 CACCGATTTCATGAGATTCTCACATT 59.962 38.462 18.35 0.39 43.63 2.71
2989 3003 5.526479 CACCGATTTCATGAGATTCTCACAT 59.474 40.000 18.35 8.50 43.63 3.21
2990 3004 4.872124 CACCGATTTCATGAGATTCTCACA 59.128 41.667 18.35 5.84 43.63 3.58
2991 3005 4.872691 ACACCGATTTCATGAGATTCTCAC 59.127 41.667 18.35 4.31 43.63 3.51
2992 3006 5.089970 ACACCGATTTCATGAGATTCTCA 57.910 39.130 18.29 18.29 44.99 3.27
2993 3007 6.291849 CGTAACACCGATTTCATGAGATTCTC 60.292 42.308 6.73 6.73 0.00 2.87
2994 3008 5.520288 CGTAACACCGATTTCATGAGATTCT 59.480 40.000 0.00 0.00 0.00 2.40
2995 3009 5.291128 ACGTAACACCGATTTCATGAGATTC 59.709 40.000 0.00 0.00 0.00 2.52
2996 3010 5.175859 ACGTAACACCGATTTCATGAGATT 58.824 37.500 0.00 0.00 0.00 2.40
2997 3011 4.755411 ACGTAACACCGATTTCATGAGAT 58.245 39.130 0.00 0.00 0.00 2.75
2998 3012 4.182693 ACGTAACACCGATTTCATGAGA 57.817 40.909 0.00 0.00 0.00 3.27
2999 3013 4.921470 AACGTAACACCGATTTCATGAG 57.079 40.909 0.00 0.00 0.00 2.90
3000 3014 5.676532 AAAACGTAACACCGATTTCATGA 57.323 34.783 0.00 0.00 28.38 3.07
3001 3015 5.910166 TCAAAAACGTAACACCGATTTCATG 59.090 36.000 0.00 0.00 32.65 3.07
3002 3016 5.910723 GTCAAAAACGTAACACCGATTTCAT 59.089 36.000 0.00 0.00 32.65 2.57
3003 3017 5.163784 TGTCAAAAACGTAACACCGATTTCA 60.164 36.000 0.00 0.00 32.65 2.69
3004 3018 5.264712 TGTCAAAAACGTAACACCGATTTC 58.735 37.500 0.00 0.00 32.65 2.17
3005 3019 5.232610 TGTCAAAAACGTAACACCGATTT 57.767 34.783 0.00 0.00 34.83 2.17
3006 3020 4.879104 TGTCAAAAACGTAACACCGATT 57.121 36.364 0.00 0.00 0.00 3.34
3007 3021 4.879104 TTGTCAAAAACGTAACACCGAT 57.121 36.364 0.00 0.00 0.00 4.18
3008 3022 4.675190 TTTGTCAAAAACGTAACACCGA 57.325 36.364 0.00 0.00 0.00 4.69
3009 3023 5.568296 TCTTTTTGTCAAAAACGTAACACCG 59.432 36.000 17.56 6.89 35.57 4.94
3010 3024 6.931243 TCTTTTTGTCAAAAACGTAACACC 57.069 33.333 17.56 0.00 35.57 4.16
3011 3025 9.245284 CATTTCTTTTTGTCAAAAACGTAACAC 57.755 29.630 17.56 0.00 35.57 3.32
3012 3026 7.952637 GCATTTCTTTTTGTCAAAAACGTAACA 59.047 29.630 17.56 0.00 35.57 2.41
3013 3027 7.159659 CGCATTTCTTTTTGTCAAAAACGTAAC 59.840 33.333 17.56 7.00 35.57 2.50
3014 3028 7.061905 TCGCATTTCTTTTTGTCAAAAACGTAA 59.938 29.630 17.56 13.65 35.57 3.18
3015 3029 6.527023 TCGCATTTCTTTTTGTCAAAAACGTA 59.473 30.769 17.56 7.60 35.57 3.57
3016 3030 5.346281 TCGCATTTCTTTTTGTCAAAAACGT 59.654 32.000 17.56 3.80 35.57 3.99
3017 3031 5.780192 TCGCATTTCTTTTTGTCAAAAACG 58.220 33.333 17.56 17.13 35.57 3.60
3018 3032 6.988329 TCTCGCATTTCTTTTTGTCAAAAAC 58.012 32.000 17.56 7.76 35.57 2.43
3019 3033 7.588143 TTCTCGCATTTCTTTTTGTCAAAAA 57.412 28.000 19.69 19.69 37.99 1.94
3020 3034 7.277539 ACATTCTCGCATTTCTTTTTGTCAAAA 59.722 29.630 6.65 6.65 0.00 2.44
3021 3035 6.756074 ACATTCTCGCATTTCTTTTTGTCAAA 59.244 30.769 0.00 0.00 0.00 2.69
3022 3036 6.272318 ACATTCTCGCATTTCTTTTTGTCAA 58.728 32.000 0.00 0.00 0.00 3.18
3023 3037 5.830912 ACATTCTCGCATTTCTTTTTGTCA 58.169 33.333 0.00 0.00 0.00 3.58
3024 3038 5.058492 CGACATTCTCGCATTTCTTTTTGTC 59.942 40.000 0.00 0.00 35.06 3.18
3025 3039 4.911610 CGACATTCTCGCATTTCTTTTTGT 59.088 37.500 0.00 0.00 35.06 2.83
3026 3040 5.411779 CGACATTCTCGCATTTCTTTTTG 57.588 39.130 0.00 0.00 35.06 2.44
3039 3053 5.597813 AACACTGATTTCACGACATTCTC 57.402 39.130 0.00 0.00 0.00 2.87
3040 3054 5.118664 CGTAACACTGATTTCACGACATTCT 59.881 40.000 0.00 0.00 0.00 2.40
3041 3055 5.107607 ACGTAACACTGATTTCACGACATTC 60.108 40.000 0.00 0.00 33.81 2.67
3042 3056 4.748102 ACGTAACACTGATTTCACGACATT 59.252 37.500 0.00 0.00 33.81 2.71
3043 3057 4.304110 ACGTAACACTGATTTCACGACAT 58.696 39.130 0.00 0.00 33.81 3.06
3044 3058 3.708890 ACGTAACACTGATTTCACGACA 58.291 40.909 0.00 0.00 33.81 4.35
3045 3059 4.703899 AACGTAACACTGATTTCACGAC 57.296 40.909 0.00 0.00 33.81 4.34
3046 3060 5.721876 AAAACGTAACACTGATTTCACGA 57.278 34.783 0.00 0.00 33.81 4.35
3047 3061 5.960683 TCAAAAACGTAACACTGATTTCACG 59.039 36.000 0.00 0.00 35.62 4.35
3048 3062 6.076298 CGTCAAAAACGTAACACTGATTTCAC 60.076 38.462 0.00 0.00 46.42 3.18
3049 3063 5.960683 CGTCAAAAACGTAACACTGATTTCA 59.039 36.000 0.00 0.00 46.42 2.69
3050 3064 6.401477 CGTCAAAAACGTAACACTGATTTC 57.599 37.500 0.00 0.00 46.42 2.17
3064 3078 8.099746 TCTCGAATTTCTTTTTCGTCAAAAAC 57.900 30.769 5.82 0.00 44.69 2.43
3065 3079 8.676454 TTCTCGAATTTCTTTTTCGTCAAAAA 57.324 26.923 5.82 0.00 44.69 1.94
3066 3080 8.742188 CATTCTCGAATTTCTTTTTCGTCAAAA 58.258 29.630 5.82 0.00 44.69 2.44
3067 3081 7.913297 ACATTCTCGAATTTCTTTTTCGTCAAA 59.087 29.630 5.82 0.99 44.69 2.69
3068 3082 7.414436 ACATTCTCGAATTTCTTTTTCGTCAA 58.586 30.769 5.82 1.59 44.69 3.18
3069 3083 6.954944 ACATTCTCGAATTTCTTTTTCGTCA 58.045 32.000 5.82 0.00 44.69 4.35
3070 3084 6.244471 CGACATTCTCGAATTTCTTTTTCGTC 59.756 38.462 5.82 0.00 46.14 4.20
3071 3085 6.071463 CGACATTCTCGAATTTCTTTTTCGT 58.929 36.000 5.82 0.00 46.14 3.85
3072 3086 6.071463 ACGACATTCTCGAATTTCTTTTTCG 58.929 36.000 0.00 0.00 46.14 3.46
3073 3087 7.837898 AACGACATTCTCGAATTTCTTTTTC 57.162 32.000 0.00 0.00 46.14 2.29
3074 3088 9.724839 TTTAACGACATTCTCGAATTTCTTTTT 57.275 25.926 0.00 0.00 46.14 1.94
3075 3089 9.893305 ATTTAACGACATTCTCGAATTTCTTTT 57.107 25.926 0.00 1.29 46.14 2.27
3076 3090 9.893305 AATTTAACGACATTCTCGAATTTCTTT 57.107 25.926 0.00 0.00 46.14 2.52
3079 3093 9.422196 CCTAATTTAACGACATTCTCGAATTTC 57.578 33.333 0.00 0.00 46.14 2.17
3080 3094 7.908601 GCCTAATTTAACGACATTCTCGAATTT 59.091 33.333 0.00 0.00 46.14 1.82
3081 3095 7.280205 AGCCTAATTTAACGACATTCTCGAATT 59.720 33.333 0.00 0.00 46.14 2.17
3082 3096 6.761714 AGCCTAATTTAACGACATTCTCGAAT 59.238 34.615 0.00 0.00 46.14 3.34
3083 3097 6.103997 AGCCTAATTTAACGACATTCTCGAA 58.896 36.000 0.00 0.00 46.14 3.71
3084 3098 5.657474 AGCCTAATTTAACGACATTCTCGA 58.343 37.500 0.00 0.00 46.14 4.04
3086 3100 7.277981 TCAAGAGCCTAATTTAACGACATTCTC 59.722 37.037 0.00 0.00 0.00 2.87
3087 3101 7.103641 TCAAGAGCCTAATTTAACGACATTCT 58.896 34.615 0.00 0.00 0.00 2.40
3088 3102 7.303634 TCAAGAGCCTAATTTAACGACATTC 57.696 36.000 0.00 0.00 0.00 2.67
3089 3103 7.865706 ATCAAGAGCCTAATTTAACGACATT 57.134 32.000 0.00 0.00 0.00 2.71
3090 3104 8.958119 TTATCAAGAGCCTAATTTAACGACAT 57.042 30.769 0.00 0.00 0.00 3.06
3091 3105 8.255206 TCTTATCAAGAGCCTAATTTAACGACA 58.745 33.333 0.00 0.00 32.71 4.35
3092 3106 8.644318 TCTTATCAAGAGCCTAATTTAACGAC 57.356 34.615 0.00 0.00 32.71 4.34
3093 3107 9.661563 TTTCTTATCAAGAGCCTAATTTAACGA 57.338 29.630 0.00 0.00 39.03 3.85
3172 3186 2.569853 TGGTCCGAACTCACACCATTAT 59.430 45.455 0.00 0.00 33.83 1.28
3173 3187 1.972075 TGGTCCGAACTCACACCATTA 59.028 47.619 0.00 0.00 33.83 1.90
3174 3188 0.762418 TGGTCCGAACTCACACCATT 59.238 50.000 0.00 0.00 33.83 3.16
3175 3189 0.984230 ATGGTCCGAACTCACACCAT 59.016 50.000 0.00 0.00 43.53 3.55
3176 3190 0.320374 GATGGTCCGAACTCACACCA 59.680 55.000 0.00 0.00 43.10 4.17
3177 3191 0.608640 AGATGGTCCGAACTCACACC 59.391 55.000 0.00 0.00 0.00 4.16
3181 3195 1.899437 GCCCAGATGGTCCGAACTCA 61.899 60.000 0.00 0.00 36.04 3.41
3191 3205 3.331889 ACCAATATAGAAGGCCCAGATGG 59.668 47.826 0.00 0.00 37.09 3.51
3288 3315 3.007940 TGGATGACTGTACACAAGAAGGG 59.992 47.826 0.00 0.00 0.00 3.95
3356 3383 5.354234 CCAAGCCGTTCTGTTCAATATAAGT 59.646 40.000 0.00 0.00 0.00 2.24
3382 3409 6.074994 GCTGTTTACACTCGAATAATCTACGG 60.075 42.308 0.00 0.00 0.00 4.02
3383 3410 6.344002 CGCTGTTTACACTCGAATAATCTACG 60.344 42.308 0.00 0.00 0.00 3.51
3384 3411 6.471519 ACGCTGTTTACACTCGAATAATCTAC 59.528 38.462 6.74 0.00 0.00 2.59
3405 3438 4.261489 CCCTATAACTTGATCACGTACGCT 60.261 45.833 16.72 0.00 0.00 5.07
3408 3441 4.343239 ACCCCCTATAACTTGATCACGTAC 59.657 45.833 5.13 0.00 0.00 3.67
3426 3459 0.975887 TCACGTACAGGTTTACCCCC 59.024 55.000 0.00 0.00 36.42 5.40
3461 3494 0.177141 TACAGGCGCCACCACTATTC 59.823 55.000 31.54 0.00 43.14 1.75
3477 3510 5.254901 GAGTAACACTCTCTTCCCTCTACA 58.745 45.833 0.00 0.00 41.88 2.74


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

AutoCloner maintained by Alex Coulton.