Multiple sequence alignment - TraesCS1D01G188500

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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 TraesCS1D01G188500 chr1D 100.000 3224 0 0 1 3224 260980393 260977170 0.000000e+00 5954.0
1 TraesCS1D01G188500 chr1B 93.792 2803 89 28 237 3013 351438990 351441733 0.000000e+00 4133.0
2 TraesCS1D01G188500 chr1A 92.554 2713 81 42 329 3013 339482623 339485242 0.000000e+00 3779.0
3 TraesCS1D01G188500 chr1A 93.491 169 5 5 56 221 339482446 339482611 2.480000e-61 246.0
4 TraesCS1D01G188500 chr5D 95.337 193 3 1 3038 3224 63183516 63183324 5.230000e-78 302.0
5 TraesCS1D01G188500 chr5D 94.366 71 4 0 3149 3219 63183321 63183251 3.400000e-20 110.0
6 TraesCS1D01G188500 chr5D 91.837 49 4 0 3149 3197 63183243 63183195 5.770000e-08 69.4
7 TraesCS1D01G188500 chr6D 80.081 246 30 13 2508 2747 16011394 16011626 7.160000e-37 165.0
8 TraesCS1D01G188500 chr3B 96.970 33 1 0 1 33 59445214 59445246 4.490000e-04 56.5


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 TraesCS1D01G188500 chr1D 260977170 260980393 3223 True 5954.0 5954 100.0000 1 3224 1 chr1D.!!$R1 3223
1 TraesCS1D01G188500 chr1B 351438990 351441733 2743 False 4133.0 4133 93.7920 237 3013 1 chr1B.!!$F1 2776
2 TraesCS1D01G188500 chr1A 339482446 339485242 2796 False 2012.5 3779 93.0225 56 3013 2 chr1A.!!$F1 2957

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
34 35 0.258774 GTGCCATCCCTACCCACATT 59.741 55.000 0.0 0.0 0.00 2.71 F
1181 1213 0.739813 AAGGTACAGATCAACGGCGC 60.740 55.000 6.9 0.0 0.00 6.53 F
1204 1236 2.032071 AGAAAGGGGCCGTCAACG 59.968 61.111 0.0 0.0 39.44 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1187 1219 2.032071 CGTTGACGGCCCCTTTCT 59.968 61.111 0.00 0.0 35.37 2.52 R
2133 2186 0.034616 CGATCTCCTTGATGGCCTCC 59.965 60.000 3.32 0.0 35.14 4.30 R
3045 3121 0.393808 GCCTTGGAACCCTCGCATAA 60.394 55.000 0.00 0.0 0.00 1.90 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
25 26 4.431131 CTTGCGGGTGCCATCCCT 62.431 66.667 7.05 0.00 44.95 4.20
26 27 3.012119 TTGCGGGTGCCATCCCTA 61.012 61.111 7.05 0.00 44.95 3.53
27 28 3.338275 TTGCGGGTGCCATCCCTAC 62.338 63.158 7.05 1.06 44.95 3.18
28 29 4.564110 GCGGGTGCCATCCCTACC 62.564 72.222 7.05 0.00 44.95 3.18
31 32 2.595655 GGTGCCATCCCTACCCAC 59.404 66.667 0.00 0.00 0.00 4.61
32 33 2.305607 GGTGCCATCCCTACCCACA 61.306 63.158 0.00 0.00 0.00 4.17
33 34 1.645402 GGTGCCATCCCTACCCACAT 61.645 60.000 0.00 0.00 0.00 3.21
34 35 0.258774 GTGCCATCCCTACCCACATT 59.741 55.000 0.00 0.00 0.00 2.71
35 36 1.006813 TGCCATCCCTACCCACATTT 58.993 50.000 0.00 0.00 0.00 2.32
36 37 1.360852 TGCCATCCCTACCCACATTTT 59.639 47.619 0.00 0.00 0.00 1.82
37 38 2.225496 TGCCATCCCTACCCACATTTTT 60.225 45.455 0.00 0.00 0.00 1.94
76 77 0.745845 CACATTCTTGCGGAGGAGGG 60.746 60.000 0.00 0.00 0.00 4.30
93 94 4.288626 AGGAGGGTGTTAGCAATGAGTTTA 59.711 41.667 0.00 0.00 0.00 2.01
94 95 5.044846 AGGAGGGTGTTAGCAATGAGTTTAT 60.045 40.000 0.00 0.00 0.00 1.40
95 96 6.157994 AGGAGGGTGTTAGCAATGAGTTTATA 59.842 38.462 0.00 0.00 0.00 0.98
97 98 7.012421 GGAGGGTGTTAGCAATGAGTTTATAAG 59.988 40.741 0.00 0.00 0.00 1.73
98 99 7.630082 AGGGTGTTAGCAATGAGTTTATAAGA 58.370 34.615 0.00 0.00 0.00 2.10
128 130 3.003689 CCATGTTCCGCTGGATTGTATTC 59.996 47.826 0.00 0.00 34.24 1.75
140 142 4.158384 GGATTGTATTCTGCACGTTGTTG 58.842 43.478 0.00 0.00 0.00 3.33
141 143 4.320202 GGATTGTATTCTGCACGTTGTTGT 60.320 41.667 0.00 0.00 0.00 3.32
142 144 3.870723 TGTATTCTGCACGTTGTTGTC 57.129 42.857 0.00 0.00 0.00 3.18
270 275 3.498777 GCCTAATCAATAGAAACTCGCCC 59.501 47.826 0.00 0.00 33.04 6.13
272 277 3.536956 AATCAATAGAAACTCGCCCGA 57.463 42.857 0.00 0.00 0.00 5.14
273 278 2.579207 TCAATAGAAACTCGCCCGAG 57.421 50.000 15.46 15.46 46.91 4.63
357 365 6.318648 TCATCACTTTTGTATTATCTGGCACC 59.681 38.462 0.00 0.00 0.00 5.01
386 399 1.753141 GCATGGAGCCACAGGAATGAT 60.753 52.381 0.00 0.00 37.23 2.45
444 458 6.381498 TCCACCATCTCTTACCATTAACAA 57.619 37.500 0.00 0.00 0.00 2.83
457 471 3.440173 CCATTAACAACCACTACAGCCAG 59.560 47.826 0.00 0.00 0.00 4.85
847 878 1.177401 GGAGAAAAGGCGGCAGAAAT 58.823 50.000 13.08 0.00 0.00 2.17
958 989 1.135660 TCTCGACGCTTGTTAGCTCAG 60.136 52.381 0.00 0.00 45.51 3.35
1181 1213 0.739813 AAGGTACAGATCAACGGCGC 60.740 55.000 6.90 0.00 0.00 6.53
1182 1214 2.171725 GGTACAGATCAACGGCGCC 61.172 63.158 19.07 19.07 0.00 6.53
1183 1215 2.202690 TACAGATCAACGGCGCCG 60.203 61.111 44.88 44.88 46.03 6.46
1201 1233 4.388499 GCGAGAAAGGGGCCGTCA 62.388 66.667 0.00 0.00 0.00 4.35
1202 1234 2.345991 CGAGAAAGGGGCCGTCAA 59.654 61.111 0.00 0.00 0.00 3.18
1203 1235 2.033194 CGAGAAAGGGGCCGTCAAC 61.033 63.158 0.00 0.00 0.00 3.18
1204 1236 2.032071 AGAAAGGGGCCGTCAACG 59.968 61.111 0.00 0.00 39.44 4.10
1692 1745 3.063084 GAGCCGGTCGAGGACACT 61.063 66.667 1.90 0.00 33.68 3.55
2260 2313 4.523558 GTGATCCTCCCACCATAGTACTAC 59.476 50.000 4.31 0.00 0.00 2.73
2324 2382 5.682234 ATTTGGAATTGGACCTGGAAATC 57.318 39.130 0.00 0.00 0.00 2.17
2443 2507 5.049818 GCATAGGTGTAAGATTGCTGATGAC 60.050 44.000 0.00 0.00 0.00 3.06
2468 2532 8.042515 ACGCCTAGTAATTAAAGGATGTGTAAA 58.957 33.333 16.03 0.00 31.64 2.01
2519 2585 5.557891 ATTTTGTTGTGCTAGATCTGAGC 57.442 39.130 5.18 10.86 40.53 4.26
2535 2601 3.065510 TCTGAGCGTAGAGTATGTCTTGC 59.934 47.826 0.00 0.00 36.64 4.01
2537 2603 4.196971 TGAGCGTAGAGTATGTCTTGCTA 58.803 43.478 6.42 0.00 42.69 3.49
2538 2604 4.822350 TGAGCGTAGAGTATGTCTTGCTAT 59.178 41.667 6.42 0.00 42.69 2.97
2539 2605 5.049336 TGAGCGTAGAGTATGTCTTGCTATC 60.049 44.000 6.42 0.00 42.69 2.08
2627 2693 2.945008 TGAAGACTGTGGCTGTTCTTTG 59.055 45.455 0.00 0.00 0.00 2.77
2653 2719 9.658799 GCAATAGCAGAAGTAGGATTATTATGA 57.341 33.333 0.00 0.00 41.58 2.15
2659 2725 8.994170 GCAGAAGTAGGATTATTATGAAAGACC 58.006 37.037 0.00 0.00 0.00 3.85
2728 2799 2.279582 ATACGAGCTGAACCGTGAAG 57.720 50.000 8.31 0.00 39.54 3.02
2733 2804 1.940613 GAGCTGAACCGTGAAGTTTGT 59.059 47.619 0.00 0.00 0.00 2.83
2734 2805 3.128349 GAGCTGAACCGTGAAGTTTGTA 58.872 45.455 0.00 0.00 0.00 2.41
2782 2858 7.492524 TGTATGGTCTTCATTACTCTTGCTAG 58.507 38.462 0.00 0.00 37.30 3.42
2788 2864 6.754675 GTCTTCATTACTCTTGCTAGTCTTCC 59.245 42.308 0.00 0.00 0.00 3.46
2810 2886 1.669115 CTCAACGACACAGGCAGGG 60.669 63.158 0.00 0.00 0.00 4.45
2835 2911 8.445493 GGAGTGCCTTTTAATTTGAATCATTTG 58.555 33.333 0.00 0.00 0.00 2.32
2838 2914 8.229811 GTGCCTTTTAATTTGAATCATTTGGTC 58.770 33.333 0.00 0.00 0.00 4.02
2841 2917 9.154847 CCTTTTAATTTGAATCATTTGGTCCTC 57.845 33.333 0.00 0.00 0.00 3.71
2890 2966 4.249661 GTCCAAGACTCAAGAGAACCATC 58.750 47.826 3.73 0.00 0.00 3.51
3013 3089 3.304592 GGGTTGAATTGCCATTTTTGCAC 60.305 43.478 0.00 0.00 38.72 4.57
3014 3090 3.314635 GGTTGAATTGCCATTTTTGCACA 59.685 39.130 0.00 0.00 38.72 4.57
3015 3091 4.201990 GGTTGAATTGCCATTTTTGCACAA 60.202 37.500 0.00 0.00 38.72 3.33
3016 3092 4.548991 TGAATTGCCATTTTTGCACAAC 57.451 36.364 0.00 0.00 38.72 3.32
3017 3093 3.002042 TGAATTGCCATTTTTGCACAACG 59.998 39.130 0.00 0.00 38.72 4.10
3018 3094 2.015736 TTGCCATTTTTGCACAACGT 57.984 40.000 0.00 0.00 38.72 3.99
3019 3095 2.015736 TGCCATTTTTGCACAACGTT 57.984 40.000 0.00 0.00 32.85 3.99
3020 3096 1.929836 TGCCATTTTTGCACAACGTTC 59.070 42.857 0.00 0.00 32.85 3.95
3021 3097 1.260297 GCCATTTTTGCACAACGTTCC 59.740 47.619 0.00 0.00 0.00 3.62
3022 3098 2.544685 CCATTTTTGCACAACGTTCCA 58.455 42.857 0.00 0.00 0.00 3.53
3023 3099 2.932614 CCATTTTTGCACAACGTTCCAA 59.067 40.909 0.00 0.00 0.00 3.53
3024 3100 3.372206 CCATTTTTGCACAACGTTCCAAA 59.628 39.130 0.00 6.03 0.00 3.28
3025 3101 4.142816 CCATTTTTGCACAACGTTCCAAAA 60.143 37.500 19.10 19.10 35.93 2.44
3026 3102 4.653806 TTTTTGCACAACGTTCCAAAAG 57.346 36.364 20.68 5.62 38.11 2.27
3027 3103 1.634702 TTGCACAACGTTCCAAAAGC 58.365 45.000 0.00 0.00 0.00 3.51
3028 3104 0.528017 TGCACAACGTTCCAAAAGCA 59.472 45.000 0.00 0.00 0.00 3.91
3029 3105 1.135915 TGCACAACGTTCCAAAAGCAT 59.864 42.857 0.00 0.00 0.00 3.79
3030 3106 2.200899 GCACAACGTTCCAAAAGCATT 58.799 42.857 0.00 0.00 0.00 3.56
3031 3107 2.033832 GCACAACGTTCCAAAAGCATTG 60.034 45.455 0.00 0.00 0.00 2.82
3032 3108 2.033832 CACAACGTTCCAAAAGCATTGC 60.034 45.455 0.00 0.00 0.00 3.56
3033 3109 1.526464 CAACGTTCCAAAAGCATTGCC 59.474 47.619 4.70 0.00 0.00 4.52
3034 3110 0.749649 ACGTTCCAAAAGCATTGCCA 59.250 45.000 4.70 0.00 0.00 4.92
3035 3111 1.269726 ACGTTCCAAAAGCATTGCCAG 60.270 47.619 4.70 0.00 0.00 4.85
3036 3112 1.799544 GTTCCAAAAGCATTGCCAGG 58.200 50.000 4.70 2.60 0.00 4.45
3037 3113 0.686224 TTCCAAAAGCATTGCCAGGG 59.314 50.000 4.70 2.56 0.00 4.45
3038 3114 1.376295 CCAAAAGCATTGCCAGGGC 60.376 57.895 4.70 2.62 42.35 5.19
3039 3115 1.738830 CAAAAGCATTGCCAGGGCG 60.739 57.895 4.70 0.00 45.51 6.13
3040 3116 1.907807 AAAAGCATTGCCAGGGCGA 60.908 52.632 4.70 2.03 45.51 5.54
3041 3117 1.470996 AAAAGCATTGCCAGGGCGAA 61.471 50.000 3.97 1.17 45.51 4.70
3042 3118 1.880819 AAAGCATTGCCAGGGCGAAG 61.881 55.000 3.97 0.96 45.51 3.79
3059 3135 3.406559 GCGTTATGCGAGGGTTCC 58.593 61.111 0.00 0.00 44.77 3.62
3060 3136 1.448893 GCGTTATGCGAGGGTTCCA 60.449 57.895 0.00 0.00 44.77 3.53
3061 3137 1.022451 GCGTTATGCGAGGGTTCCAA 61.022 55.000 0.00 0.00 44.77 3.53
3062 3138 1.006832 CGTTATGCGAGGGTTCCAAG 58.993 55.000 0.00 0.00 44.77 3.61
3063 3139 1.379527 GTTATGCGAGGGTTCCAAGG 58.620 55.000 0.00 0.00 0.00 3.61
3064 3140 0.393808 TTATGCGAGGGTTCCAAGGC 60.394 55.000 0.00 0.00 0.00 4.35
3065 3141 1.271840 TATGCGAGGGTTCCAAGGCT 61.272 55.000 0.00 0.00 0.00 4.58
3066 3142 2.436824 GCGAGGGTTCCAAGGCTC 60.437 66.667 0.00 0.00 0.00 4.70
3067 3143 2.269241 CGAGGGTTCCAAGGCTCC 59.731 66.667 0.00 0.00 0.00 4.70
3068 3144 2.269241 GAGGGTTCCAAGGCTCCG 59.731 66.667 0.00 0.00 0.00 4.63
3069 3145 3.330720 AGGGTTCCAAGGCTCCGG 61.331 66.667 0.00 0.00 0.00 5.14
3072 3148 4.388499 GTTCCAAGGCTCCGGCGA 62.388 66.667 9.30 0.00 39.81 5.54
3073 3149 4.388499 TTCCAAGGCTCCGGCGAC 62.388 66.667 9.30 0.00 39.81 5.19
3075 3151 4.821589 CCAAGGCTCCGGCGACTC 62.822 72.222 9.30 0.00 39.81 3.36
3076 3152 3.764466 CAAGGCTCCGGCGACTCT 61.764 66.667 9.30 0.00 39.81 3.24
3077 3153 2.997897 AAGGCTCCGGCGACTCTT 60.998 61.111 9.30 3.62 39.81 2.85
3078 3154 3.302347 AAGGCTCCGGCGACTCTTG 62.302 63.158 9.30 0.00 39.81 3.02
3079 3155 4.821589 GGCTCCGGCGACTCTTGG 62.822 72.222 9.30 0.00 39.81 3.61
3080 3156 4.821589 GCTCCGGCGACTCTTGGG 62.822 72.222 9.30 0.00 0.00 4.12
3081 3157 4.821589 CTCCGGCGACTCTTGGGC 62.822 72.222 9.30 0.00 0.00 5.36
3171 3247 3.384532 CCCTGGTGGCCATGTTGC 61.385 66.667 9.72 0.00 30.82 4.17
3172 3248 3.751246 CCTGGTGGCCATGTTGCG 61.751 66.667 9.72 0.00 30.82 4.85
3173 3249 3.751246 CTGGTGGCCATGTTGCGG 61.751 66.667 9.72 0.00 30.82 5.69
3179 3255 3.058160 GCCATGTTGCGGCTGAGT 61.058 61.111 0.00 0.00 46.56 3.41
3180 3256 3.044059 GCCATGTTGCGGCTGAGTC 62.044 63.158 0.00 0.00 46.56 3.36
3181 3257 2.401766 CCATGTTGCGGCTGAGTCC 61.402 63.158 0.00 0.00 0.00 3.85
3191 3267 3.900892 CTGAGTCCGCCCGCGTAT 61.901 66.667 4.92 0.00 37.81 3.06
3192 3268 3.825833 CTGAGTCCGCCCGCGTATC 62.826 68.421 4.92 3.71 37.81 2.24
3193 3269 4.977126 GAGTCCGCCCGCGTATCG 62.977 72.222 4.92 5.06 37.81 2.92
3204 3280 4.647615 CGTATCGCTGCTCCCCCG 62.648 72.222 0.00 0.00 0.00 5.73
3205 3281 4.301027 GTATCGCTGCTCCCCCGG 62.301 72.222 0.00 0.00 0.00 5.73
3218 3294 4.301027 CCCGGGGTAGCAGCGATC 62.301 72.222 14.71 0.00 0.00 3.69
3219 3295 4.301027 CCGGGGTAGCAGCGATCC 62.301 72.222 0.00 0.00 0.00 3.36
3220 3296 4.301027 CGGGGTAGCAGCGATCCC 62.301 72.222 13.95 13.95 39.22 3.85
3221 3297 4.301027 GGGGTAGCAGCGATCCCG 62.301 72.222 8.30 0.00 40.72 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.645402 ATGTGGGTAGGGATGGCACC 61.645 60.000 0.00 0.00 0.00 5.01
15 16 0.258774 AATGTGGGTAGGGATGGCAC 59.741 55.000 0.00 0.00 0.00 5.01
16 17 1.006813 AAATGTGGGTAGGGATGGCA 58.993 50.000 0.00 0.00 0.00 4.92
17 18 2.159179 AAAATGTGGGTAGGGATGGC 57.841 50.000 0.00 0.00 0.00 4.40
36 37 4.345547 GTGGGTAGGGATTTGGTTCAAAAA 59.654 41.667 0.00 0.00 36.90 1.94
37 38 3.898741 GTGGGTAGGGATTTGGTTCAAAA 59.101 43.478 0.00 0.00 36.90 2.44
38 39 3.117093 TGTGGGTAGGGATTTGGTTCAAA 60.117 43.478 0.00 0.00 37.75 2.69
39 40 2.447429 TGTGGGTAGGGATTTGGTTCAA 59.553 45.455 0.00 0.00 0.00 2.69
40 41 2.066592 TGTGGGTAGGGATTTGGTTCA 58.933 47.619 0.00 0.00 0.00 3.18
41 42 2.891191 TGTGGGTAGGGATTTGGTTC 57.109 50.000 0.00 0.00 0.00 3.62
42 43 3.336694 AGAATGTGGGTAGGGATTTGGTT 59.663 43.478 0.00 0.00 0.00 3.67
43 44 2.926329 AGAATGTGGGTAGGGATTTGGT 59.074 45.455 0.00 0.00 0.00 3.67
44 45 3.669939 AGAATGTGGGTAGGGATTTGG 57.330 47.619 0.00 0.00 0.00 3.28
45 46 3.131046 GCAAGAATGTGGGTAGGGATTTG 59.869 47.826 0.00 0.00 0.00 2.32
46 47 3.365472 GCAAGAATGTGGGTAGGGATTT 58.635 45.455 0.00 0.00 0.00 2.17
47 48 2.683742 CGCAAGAATGTGGGTAGGGATT 60.684 50.000 0.00 0.00 43.02 3.01
48 49 1.134098 CGCAAGAATGTGGGTAGGGAT 60.134 52.381 0.00 0.00 43.02 3.85
49 50 0.251916 CGCAAGAATGTGGGTAGGGA 59.748 55.000 0.00 0.00 43.02 4.20
50 51 2.780595 CGCAAGAATGTGGGTAGGG 58.219 57.895 0.00 0.00 43.02 3.53
93 94 4.999950 GCGGAACATGGAATCATCTCTTAT 59.000 41.667 0.00 0.00 0.00 1.73
94 95 4.101585 AGCGGAACATGGAATCATCTCTTA 59.898 41.667 0.00 0.00 0.00 2.10
95 96 3.118112 AGCGGAACATGGAATCATCTCTT 60.118 43.478 0.00 0.00 0.00 2.85
97 98 2.547211 CAGCGGAACATGGAATCATCTC 59.453 50.000 0.00 0.00 0.00 2.75
98 99 2.569059 CAGCGGAACATGGAATCATCT 58.431 47.619 0.00 0.00 0.00 2.90
128 130 0.375454 TTTCCGACAACAACGTGCAG 59.625 50.000 0.00 0.00 0.00 4.41
140 142 8.716646 ATTCAAAATAATTGGGAATTTCCGAC 57.283 30.769 9.31 0.00 37.43 4.79
270 275 1.333308 TGGTTGCATGTGTGTTTCTCG 59.667 47.619 0.00 0.00 0.00 4.04
272 277 1.067516 GCTGGTTGCATGTGTGTTTCT 59.932 47.619 0.00 0.00 42.31 2.52
273 278 1.490621 GCTGGTTGCATGTGTGTTTC 58.509 50.000 0.00 0.00 42.31 2.78
305 310 2.032620 AGTATCCTGCTACTTGGACCG 58.967 52.381 0.00 0.00 34.90 4.79
357 365 1.869767 GTGGCTCCATGCGATAAGAAG 59.130 52.381 0.00 0.00 44.05 2.85
386 399 5.992829 TGTACAAGGTGATAAGCTCGAAAAA 59.007 36.000 0.00 0.00 0.00 1.94
444 458 0.178932 TGTCCTCTGGCTGTAGTGGT 60.179 55.000 0.00 0.00 33.96 4.16
457 471 4.754667 GGGGTCGCCGTTGTCCTC 62.755 72.222 0.00 0.00 0.00 3.71
531 550 4.173256 CTCGCTCTTTTCTCTTCTCTTCC 58.827 47.826 0.00 0.00 0.00 3.46
537 556 1.338200 TGGGCTCGCTCTTTTCTCTTC 60.338 52.381 0.00 0.00 0.00 2.87
538 557 0.687354 TGGGCTCGCTCTTTTCTCTT 59.313 50.000 0.00 0.00 0.00 2.85
539 558 0.036858 GTGGGCTCGCTCTTTTCTCT 60.037 55.000 0.00 0.00 0.00 3.10
540 559 0.320771 TGTGGGCTCGCTCTTTTCTC 60.321 55.000 0.00 0.00 0.00 2.87
541 560 0.321122 CTGTGGGCTCGCTCTTTTCT 60.321 55.000 0.00 0.00 0.00 2.52
847 878 6.128661 CGCTGCTTATATAATTCTACCGCAAA 60.129 38.462 0.00 0.00 0.00 3.68
893 924 2.237751 CGCGGAAATGCTACTCCCG 61.238 63.158 0.00 0.00 42.74 5.14
894 925 1.153429 ACGCGGAAATGCTACTCCC 60.153 57.895 12.47 0.00 0.00 4.30
896 927 1.917273 TACACGCGGAAATGCTACTC 58.083 50.000 12.47 0.00 0.00 2.59
901 932 4.408694 ACTTTTTATACACGCGGAAATGC 58.591 39.130 12.47 0.00 0.00 3.56
958 989 1.966451 CGGTGGTTGGAGTTGGAGC 60.966 63.158 0.00 0.00 0.00 4.70
1140 1172 2.282180 TTGGGCGCCTTCTTGGAC 60.282 61.111 28.56 7.32 38.35 4.02
1184 1216 3.894547 TTGACGGCCCCTTTCTCGC 62.895 63.158 0.00 0.00 0.00 5.03
1185 1217 2.033194 GTTGACGGCCCCTTTCTCG 61.033 63.158 0.00 0.00 0.00 4.04
1186 1218 2.033194 CGTTGACGGCCCCTTTCTC 61.033 63.158 0.00 0.00 35.37 2.87
1187 1219 2.032071 CGTTGACGGCCCCTTTCT 59.968 61.111 0.00 0.00 35.37 2.52
1198 1230 4.025401 CTTGCCGTGGCCGTTGAC 62.025 66.667 8.69 0.00 41.09 3.18
1199 1231 3.758973 TTCTTGCCGTGGCCGTTGA 62.759 57.895 8.69 0.00 41.09 3.18
1200 1232 3.254014 CTTCTTGCCGTGGCCGTTG 62.254 63.158 8.69 0.00 41.09 4.10
1201 1233 2.978010 CTTCTTGCCGTGGCCGTT 60.978 61.111 8.69 0.00 41.09 4.44
1674 1727 3.063084 GTGTCCTCGACCGGCTCT 61.063 66.667 0.00 0.00 0.00 4.09
2133 2186 0.034616 CGATCTCCTTGATGGCCTCC 59.965 60.000 3.32 0.00 35.14 4.30
2260 2313 5.052304 GCTAATTCGATCACTTCACGTGTAG 60.052 44.000 19.29 19.29 44.16 2.74
2324 2382 3.304391 GCTGCTCGAGTACTAGAATGGAG 60.304 52.174 15.13 7.99 0.00 3.86
2333 2391 1.662438 GAGGCAGCTGCTCGAGTACT 61.662 60.000 35.82 23.06 41.70 2.73
2443 2507 8.428186 TTTACACATCCTTTAATTACTAGGCG 57.572 34.615 7.63 4.98 0.00 5.52
2519 2585 6.307031 AGTGATAGCAAGACATACTCTACG 57.693 41.667 0.00 0.00 0.00 3.51
2535 2601 4.770795 CACAAGAAAGGGGGTAGTGATAG 58.229 47.826 0.00 0.00 0.00 2.08
2537 2603 2.290960 GCACAAGAAAGGGGGTAGTGAT 60.291 50.000 0.00 0.00 0.00 3.06
2538 2604 1.073284 GCACAAGAAAGGGGGTAGTGA 59.927 52.381 0.00 0.00 0.00 3.41
2539 2605 1.202879 TGCACAAGAAAGGGGGTAGTG 60.203 52.381 0.00 0.00 0.00 2.74
2627 2693 9.658799 TCATAATAATCCTACTTCTGCTATTGC 57.341 33.333 0.00 0.00 40.20 3.56
2760 2833 6.382570 AGACTAGCAAGAGTAATGAAGACCAT 59.617 38.462 0.00 0.00 36.99 3.55
2762 2835 6.215495 AGACTAGCAAGAGTAATGAAGACC 57.785 41.667 0.00 0.00 0.00 3.85
2765 2838 5.746245 CGGAAGACTAGCAAGAGTAATGAAG 59.254 44.000 0.00 0.00 0.00 3.02
2766 2839 5.185249 ACGGAAGACTAGCAAGAGTAATGAA 59.815 40.000 0.00 0.00 0.00 2.57
2768 2841 5.000012 ACGGAAGACTAGCAAGAGTAATG 58.000 43.478 0.00 0.00 0.00 1.90
2769 2842 5.887035 AGTACGGAAGACTAGCAAGAGTAAT 59.113 40.000 0.00 0.00 0.00 1.89
2770 2843 5.251764 AGTACGGAAGACTAGCAAGAGTAA 58.748 41.667 0.00 0.00 0.00 2.24
2806 2882 5.467035 TTCAAATTAAAAGGCACTCCCTG 57.533 39.130 0.00 0.00 45.62 4.45
2810 2886 8.445493 CCAAATGATTCAAATTAAAAGGCACTC 58.555 33.333 0.00 0.00 38.49 3.51
2835 2911 4.068599 CTCCAAGAGAAACAAAGAGGACC 58.931 47.826 0.00 0.00 0.00 4.46
2838 2914 3.480470 TGCTCCAAGAGAAACAAAGAGG 58.520 45.455 0.00 0.00 0.00 3.69
2841 2917 4.553323 CCAATGCTCCAAGAGAAACAAAG 58.447 43.478 0.00 0.00 0.00 2.77
2890 2966 5.989249 TCTTTGTTCTGTCGAATCACAATG 58.011 37.500 0.00 0.00 0.00 2.82
2989 3065 3.058085 GCAAAAATGGCAATTCAACCCTG 60.058 43.478 0.00 0.00 0.00 4.45
3013 3089 1.526464 GGCAATGCTTTTGGAACGTTG 59.474 47.619 5.00 0.00 34.22 4.10
3014 3090 1.137872 TGGCAATGCTTTTGGAACGTT 59.862 42.857 0.00 0.00 0.00 3.99
3015 3091 0.749649 TGGCAATGCTTTTGGAACGT 59.250 45.000 4.82 0.00 0.00 3.99
3016 3092 1.421382 CTGGCAATGCTTTTGGAACG 58.579 50.000 4.82 0.00 0.00 3.95
3017 3093 1.608801 CCCTGGCAATGCTTTTGGAAC 60.609 52.381 4.82 0.00 0.00 3.62
3018 3094 0.686224 CCCTGGCAATGCTTTTGGAA 59.314 50.000 4.82 0.00 0.00 3.53
3019 3095 1.829523 GCCCTGGCAATGCTTTTGGA 61.830 55.000 4.82 0.00 41.49 3.53
3020 3096 1.376295 GCCCTGGCAATGCTTTTGG 60.376 57.895 4.82 2.29 41.49 3.28
3021 3097 1.738830 CGCCCTGGCAATGCTTTTG 60.739 57.895 4.82 0.00 42.06 2.44
3022 3098 1.470996 TTCGCCCTGGCAATGCTTTT 61.471 50.000 4.82 0.00 42.06 2.27
3023 3099 1.880819 CTTCGCCCTGGCAATGCTTT 61.881 55.000 4.82 0.00 42.06 3.51
3024 3100 2.283101 TTCGCCCTGGCAATGCTT 60.283 55.556 4.82 0.00 42.06 3.91
3025 3101 2.753043 CTTCGCCCTGGCAATGCT 60.753 61.111 4.82 0.00 42.06 3.79
3026 3102 4.503314 GCTTCGCCCTGGCAATGC 62.503 66.667 9.17 0.00 42.06 3.56
3027 3103 4.183686 CGCTTCGCCCTGGCAATG 62.184 66.667 9.17 0.00 42.06 2.82
3028 3104 2.813226 TAACGCTTCGCCCTGGCAAT 62.813 55.000 9.17 0.00 42.06 3.56
3029 3105 2.813226 ATAACGCTTCGCCCTGGCAA 62.813 55.000 9.17 1.35 42.06 4.52
3030 3106 3.323758 ATAACGCTTCGCCCTGGCA 62.324 57.895 9.17 0.00 42.06 4.92
3031 3107 2.513897 ATAACGCTTCGCCCTGGC 60.514 61.111 0.00 0.00 37.85 4.85
3032 3108 2.823829 GCATAACGCTTCGCCCTGG 61.824 63.158 0.00 0.00 37.77 4.45
3033 3109 2.709475 GCATAACGCTTCGCCCTG 59.291 61.111 0.00 0.00 37.77 4.45
3034 3110 2.890474 CGCATAACGCTTCGCCCT 60.890 61.111 0.00 0.00 39.08 5.19
3035 3111 2.871427 CTCGCATAACGCTTCGCCC 61.871 63.158 0.00 0.00 43.23 6.13
3036 3112 2.621000 CTCGCATAACGCTTCGCC 59.379 61.111 0.00 0.00 43.23 5.54
3037 3113 2.621000 CCTCGCATAACGCTTCGC 59.379 61.111 0.00 0.00 43.23 4.70
3038 3114 1.082117 AACCCTCGCATAACGCTTCG 61.082 55.000 0.00 0.00 43.23 3.79
3039 3115 0.651031 GAACCCTCGCATAACGCTTC 59.349 55.000 0.00 0.00 43.23 3.86
3040 3116 0.743345 GGAACCCTCGCATAACGCTT 60.743 55.000 0.00 0.00 43.23 4.68
3041 3117 1.153429 GGAACCCTCGCATAACGCT 60.153 57.895 0.00 0.00 43.23 5.07
3042 3118 1.022451 TTGGAACCCTCGCATAACGC 61.022 55.000 0.00 0.00 43.23 4.84
3043 3119 1.006832 CTTGGAACCCTCGCATAACG 58.993 55.000 0.00 0.00 45.62 3.18
3044 3120 1.379527 CCTTGGAACCCTCGCATAAC 58.620 55.000 0.00 0.00 0.00 1.89
3045 3121 0.393808 GCCTTGGAACCCTCGCATAA 60.394 55.000 0.00 0.00 0.00 1.90
3046 3122 1.223487 GCCTTGGAACCCTCGCATA 59.777 57.895 0.00 0.00 0.00 3.14
3047 3123 2.044946 GCCTTGGAACCCTCGCAT 60.045 61.111 0.00 0.00 0.00 4.73
3048 3124 3.249189 AGCCTTGGAACCCTCGCA 61.249 61.111 0.00 0.00 0.00 5.10
3049 3125 2.436824 GAGCCTTGGAACCCTCGC 60.437 66.667 0.00 0.00 0.00 5.03
3050 3126 2.269241 GGAGCCTTGGAACCCTCG 59.731 66.667 0.00 0.00 0.00 4.63
3051 3127 2.269241 CGGAGCCTTGGAACCCTC 59.731 66.667 0.00 0.00 0.00 4.30
3052 3128 3.330720 CCGGAGCCTTGGAACCCT 61.331 66.667 0.00 0.00 0.00 4.34
3055 3131 4.388499 TCGCCGGAGCCTTGGAAC 62.388 66.667 5.05 0.00 34.57 3.62
3056 3132 4.388499 GTCGCCGGAGCCTTGGAA 62.388 66.667 5.05 0.00 34.57 3.53
3058 3134 4.821589 GAGTCGCCGGAGCCTTGG 62.822 72.222 5.05 0.00 34.57 3.61
3059 3135 3.302347 AAGAGTCGCCGGAGCCTTG 62.302 63.158 5.05 0.00 34.57 3.61
3060 3136 2.997897 AAGAGTCGCCGGAGCCTT 60.998 61.111 5.05 3.39 34.57 4.35
3061 3137 3.764466 CAAGAGTCGCCGGAGCCT 61.764 66.667 5.05 0.00 34.57 4.58
3062 3138 4.821589 CCAAGAGTCGCCGGAGCC 62.822 72.222 5.05 0.00 34.57 4.70
3063 3139 4.821589 CCCAAGAGTCGCCGGAGC 62.822 72.222 5.05 0.00 0.00 4.70
3064 3140 4.821589 GCCCAAGAGTCGCCGGAG 62.822 72.222 5.05 0.00 0.00 4.63
3154 3230 3.384532 GCAACATGGCCACCAGGG 61.385 66.667 8.16 0.00 39.88 4.45
3155 3231 3.751246 CGCAACATGGCCACCAGG 61.751 66.667 8.16 0.00 41.50 4.45
3156 3232 3.751246 CCGCAACATGGCCACCAG 61.751 66.667 8.16 3.32 36.75 4.00
3163 3239 2.401766 GGACTCAGCCGCAACATGG 61.402 63.158 0.00 0.00 0.00 3.66
3164 3240 2.743752 CGGACTCAGCCGCAACATG 61.744 63.158 0.00 0.00 45.38 3.21
3165 3241 2.434884 CGGACTCAGCCGCAACAT 60.435 61.111 0.00 0.00 45.38 2.71
3174 3250 3.825833 GATACGCGGGCGGACTCAG 62.826 68.421 18.03 0.00 44.69 3.35
3175 3251 3.896133 GATACGCGGGCGGACTCA 61.896 66.667 18.03 0.00 44.69 3.41
3176 3252 4.977126 CGATACGCGGGCGGACTC 62.977 72.222 18.03 9.41 44.69 3.36
3187 3263 4.647615 CGGGGGAGCAGCGATACG 62.648 72.222 0.00 0.00 0.00 3.06
3188 3264 4.301027 CCGGGGGAGCAGCGATAC 62.301 72.222 0.00 0.00 0.00 2.24
3201 3277 4.301027 GATCGCTGCTACCCCGGG 62.301 72.222 15.80 15.80 0.00 5.73
3202 3278 4.301027 GGATCGCTGCTACCCCGG 62.301 72.222 0.00 0.00 0.00 5.73
3203 3279 4.301027 GGGATCGCTGCTACCCCG 62.301 72.222 12.41 0.00 36.65 5.73
3204 3280 4.301027 CGGGATCGCTGCTACCCC 62.301 72.222 15.95 6.78 39.20 4.95


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

AutoCloner maintained by Alex Coulton.