Multiple sequence alignment - TraesCS1D01G264400

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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 TraesCS1D01G264400 chr1D 100.000 4170 0 0 1 4170 360366311 360370480 0.000000e+00 7701
1 TraesCS1D01G264400 chr1D 95.424 743 32 2 3421 4163 11339580 11340320 0.000000e+00 1182
2 TraesCS1D01G264400 chr1D 94.793 749 38 1 3417 4165 464785509 464786256 0.000000e+00 1166
3 TraesCS1D01G264400 chr1D 94.765 745 38 1 3421 4165 29803713 29802970 0.000000e+00 1158
4 TraesCS1D01G264400 chr1B 92.607 2881 132 27 3 2835 482189373 482192220 0.000000e+00 4065
5 TraesCS1D01G264400 chr1B 94.899 745 37 1 3421 4165 401344657 401345400 0.000000e+00 1164
6 TraesCS1D01G264400 chr1B 91.748 412 33 1 2991 3401 482192233 482192644 4.680000e-159 571
7 TraesCS1D01G264400 chr1A 90.321 2118 136 19 3 2080 459524393 459526481 0.000000e+00 2712
8 TraesCS1D01G264400 chr1A 87.537 682 58 12 2157 2813 459526565 459527244 0.000000e+00 763
9 TraesCS1D01G264400 chr1A 90.233 430 37 3 2993 3421 459527407 459527832 1.310000e-154 556
10 TraesCS1D01G264400 chr3D 96.667 720 23 1 3446 4165 113579780 113580498 0.000000e+00 1195
11 TraesCS1D01G264400 chr3D 94.779 747 35 4 3420 4165 132507838 132508581 0.000000e+00 1160
12 TraesCS1D01G264400 chr2A 95.308 746 31 4 3421 4165 763006846 763006104 0.000000e+00 1181
13 TraesCS1D01G264400 chr3B 94.927 749 35 3 3418 4165 709769278 709770024 0.000000e+00 1170
14 TraesCS1D01G264400 chr5D 94.906 746 34 3 3421 4165 518965417 518966159 0.000000e+00 1164


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 TraesCS1D01G264400 chr1D 360366311 360370480 4169 False 7701.000000 7701 100.000000 1 4170 1 chr1D.!!$F2 4169
1 TraesCS1D01G264400 chr1D 11339580 11340320 740 False 1182.000000 1182 95.424000 3421 4163 1 chr1D.!!$F1 742
2 TraesCS1D01G264400 chr1D 464785509 464786256 747 False 1166.000000 1166 94.793000 3417 4165 1 chr1D.!!$F3 748
3 TraesCS1D01G264400 chr1D 29802970 29803713 743 True 1158.000000 1158 94.765000 3421 4165 1 chr1D.!!$R1 744
4 TraesCS1D01G264400 chr1B 482189373 482192644 3271 False 2318.000000 4065 92.177500 3 3401 2 chr1B.!!$F2 3398
5 TraesCS1D01G264400 chr1B 401344657 401345400 743 False 1164.000000 1164 94.899000 3421 4165 1 chr1B.!!$F1 744
6 TraesCS1D01G264400 chr1A 459524393 459527832 3439 False 1343.666667 2712 89.363667 3 3421 3 chr1A.!!$F1 3418
7 TraesCS1D01G264400 chr3D 113579780 113580498 718 False 1195.000000 1195 96.667000 3446 4165 1 chr3D.!!$F1 719
8 TraesCS1D01G264400 chr3D 132507838 132508581 743 False 1160.000000 1160 94.779000 3420 4165 1 chr3D.!!$F2 745
9 TraesCS1D01G264400 chr2A 763006104 763006846 742 True 1181.000000 1181 95.308000 3421 4165 1 chr2A.!!$R1 744
10 TraesCS1D01G264400 chr3B 709769278 709770024 746 False 1170.000000 1170 94.927000 3418 4165 1 chr3B.!!$F1 747
11 TraesCS1D01G264400 chr5D 518965417 518966159 742 False 1164.000000 1164 94.906000 3421 4165 1 chr5D.!!$F1 744

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
321 325 0.035820 TTCGTTCCCCAAATCCTCCG 60.036 55.0 0.00 0.0 0.00 4.63 F
1069 1094 0.232303 GTTCGCCAGTTTGACTCACG 59.768 55.0 0.00 0.0 0.00 4.35 F
1720 1784 0.401356 TGTGGCAGGCATCTGAAGAA 59.599 50.0 0.00 0.0 43.49 2.52 F
2873 3126 0.600557 TATTGCGTGCACAAAAGGGG 59.399 50.0 18.64 0.0 32.27 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1295 1359 0.179129 CGCATTTCCATTGACAGCCC 60.179 55.0 0.00 0.0 0.00 5.19 R
2958 3211 0.101759 CGCTGCTTAGCATGGCAATT 59.898 50.0 16.59 0.0 38.13 2.32 R
2963 3216 0.247814 CGAAACGCTGCTTAGCATGG 60.248 55.0 7.58 5.2 38.13 3.66 R
4089 4346 0.108089 TACATACGCGGCACCATGTT 60.108 50.0 12.47 0.0 33.78 2.71 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
137 141 4.451652 GCTGTCCGCTTTCGCTGC 62.452 66.667 0.00 0.00 35.14 5.25
142 146 3.494336 CCGCTTTCGCTGCTCCTG 61.494 66.667 0.00 0.00 0.00 3.86
193 197 0.325602 AATCTACAACGGCGGGGAAA 59.674 50.000 13.24 0.00 0.00 3.13
321 325 0.035820 TTCGTTCCCCAAATCCTCCG 60.036 55.000 0.00 0.00 0.00 4.63
359 363 4.162690 GACTGGGATTCGGCCGCT 62.163 66.667 23.51 10.55 0.00 5.52
509 517 1.018148 CCGTTTGTTGCTGTGTGGTA 58.982 50.000 0.00 0.00 0.00 3.25
537 546 1.376683 CAATCTCCGCGGGTTTCCA 60.377 57.895 27.83 2.94 0.00 3.53
552 561 4.010349 GGTTTCCACTCGGATCTTTCATT 58.990 43.478 0.00 0.00 42.41 2.57
586 607 3.980646 AGTCGCATGCAGTTTTGTTTA 57.019 38.095 19.57 0.00 0.00 2.01
676 697 1.804151 TGCTCGATACCAAGTGTTTGC 59.196 47.619 0.00 0.00 32.79 3.68
688 709 4.931002 CCAAGTGTTTGCCCATTCTAAATG 59.069 41.667 0.00 0.00 32.79 2.32
725 746 5.759059 AGCCCATTTTCTATCTTGTCATGA 58.241 37.500 0.00 0.00 0.00 3.07
750 771 3.494048 GGAACAGGAGCAGTATCCATGAG 60.494 52.174 0.00 0.00 42.26 2.90
789 810 0.833287 ACGAGGATTCCCAGTGATGG 59.167 55.000 0.00 0.00 33.88 3.51
818 839 5.221244 GGGTTCACTAAATTTGTTCAGTGCT 60.221 40.000 12.17 0.00 38.60 4.40
819 840 5.687285 GGTTCACTAAATTTGTTCAGTGCTG 59.313 40.000 12.17 0.00 38.60 4.41
820 841 4.858935 TCACTAAATTTGTTCAGTGCTGC 58.141 39.130 12.17 0.00 38.60 5.25
832 853 2.294233 TCAGTGCTGCCATTGTTTTCTC 59.706 45.455 0.00 0.00 31.31 2.87
911 933 4.005650 TGAATCACCTGTTCATTGCTCTC 58.994 43.478 0.00 0.00 31.07 3.20
914 936 2.634453 TCACCTGTTCATTGCTCTCTGA 59.366 45.455 0.00 0.00 0.00 3.27
961 986 8.666821 AGGATGGCTGTTGATGCATATATATAT 58.333 33.333 0.00 0.00 0.00 0.86
962 987 9.948964 GGATGGCTGTTGATGCATATATATATA 57.051 33.333 0.00 4.92 0.00 0.86
1067 1092 1.295792 GTGTTCGCCAGTTTGACTCA 58.704 50.000 0.00 0.00 0.00 3.41
1069 1094 0.232303 GTTCGCCAGTTTGACTCACG 59.768 55.000 0.00 0.00 0.00 4.35
1076 1101 2.158449 CCAGTTTGACTCACGAAGATGC 59.842 50.000 0.00 0.00 0.00 3.91
1202 1227 3.326006 TCCATCAGGTATGAAGAGGATGC 59.674 47.826 0.00 0.00 39.39 3.91
1294 1358 3.785486 CGACTAGATCAAACATCAGGCA 58.215 45.455 0.00 0.00 0.00 4.75
1295 1359 3.801050 CGACTAGATCAAACATCAGGCAG 59.199 47.826 0.00 0.00 0.00 4.85
1296 1360 4.125703 GACTAGATCAAACATCAGGCAGG 58.874 47.826 0.00 0.00 0.00 4.85
1307 1371 2.050350 CAGGCAGGGCTGTCAATGG 61.050 63.158 14.11 0.00 37.73 3.16
1353 1417 4.023707 CCAAGGACATTGTCTGTGAAGAAC 60.024 45.833 16.02 0.00 38.54 3.01
1368 1432 7.644503 TGTGAAGAACAACACCTCAGAGGTC 62.645 48.000 20.30 7.38 40.81 3.85
1458 1522 4.813750 ACCAGGTGTTACTGTGGTATAC 57.186 45.455 0.00 0.00 41.65 1.47
1471 1535 2.950309 GTGGTATACGAGCAAGAGGAGA 59.050 50.000 0.00 0.00 37.28 3.71
1545 1609 3.706373 GACGGGCCTGCTCCAGAA 61.706 66.667 12.89 0.00 32.44 3.02
1720 1784 0.401356 TGTGGCAGGCATCTGAAGAA 59.599 50.000 0.00 0.00 43.49 2.52
1820 1884 6.832900 TCAGCCATATGACCAAAATGAATACA 59.167 34.615 3.65 0.00 0.00 2.29
1996 2060 1.589803 CCGATGGGGTTATTCCGTTC 58.410 55.000 0.00 0.00 37.00 3.95
2025 2089 6.148150 CGCCTTTATTGTGGTTGTAGTCTAAA 59.852 38.462 0.00 0.00 0.00 1.85
2044 2108 9.131791 AGTCTAAAAGCTTCATTTTGAACCTTA 57.868 29.630 0.00 0.00 32.74 2.69
2150 2253 3.788227 ATAGCTTGACCAAACCAGTGA 57.212 42.857 0.00 0.00 0.00 3.41
2166 2269 6.455360 ACCAGTGATTTAATAGCCATGTTG 57.545 37.500 0.00 0.00 0.00 3.33
2194 2297 3.485463 TTCTTCCAAACGGATCACTGT 57.515 42.857 0.00 0.00 37.19 3.55
2211 2314 9.906660 GGATCACTGTATTCTATTAGAAGTCAG 57.093 37.037 23.81 23.81 40.86 3.51
2237 2340 7.703058 AATTTAATCTGTTCATCTCCGGTTT 57.297 32.000 0.00 0.00 0.00 3.27
2251 2354 9.104965 TCATCTCCGGTTTGTATGTAAATAAAG 57.895 33.333 0.00 0.00 0.00 1.85
2462 2579 4.224991 TGTGATCAAGATTCTCATGGCA 57.775 40.909 0.00 0.00 0.00 4.92
2515 2632 8.426881 TCGTGCTGCAACATAAATTAGTATTA 57.573 30.769 2.77 0.00 0.00 0.98
2517 2634 9.106286 CGTGCTGCAACATAAATTAGTATTATG 57.894 33.333 2.77 5.07 43.29 1.90
2542 2660 9.639563 TGAATTACTTGGCATTAGATGGATTTA 57.360 29.630 0.00 0.00 0.00 1.40
2680 2798 3.118261 GGCTGGAGGTGATCTATGTTCAA 60.118 47.826 0.00 0.00 0.00 2.69
2707 2828 6.049149 TCCTAGTTGTTCTTTTCTGTCAGTG 58.951 40.000 0.00 0.00 0.00 3.66
2719 2840 7.706607 TCTTTTCTGTCAGTGGTAATGATATCG 59.293 37.037 0.00 0.00 0.00 2.92
2720 2841 6.465439 TTCTGTCAGTGGTAATGATATCGT 57.535 37.500 0.00 0.00 0.00 3.73
2746 2867 7.923414 ATAGTGGAAGTTAAAACCAGTGATC 57.077 36.000 0.00 0.00 37.80 2.92
2757 2878 6.727824 AAAACCAGTGATCTCTAAATCGTG 57.272 37.500 0.00 0.00 0.00 4.35
2777 2898 8.731275 ATCGTGTGAAGTTAATGATTTATCCA 57.269 30.769 0.00 0.00 0.00 3.41
2778 2899 7.970384 TCGTGTGAAGTTAATGATTTATCCAC 58.030 34.615 0.00 0.00 0.00 4.02
2779 2900 7.065324 TCGTGTGAAGTTAATGATTTATCCACC 59.935 37.037 0.00 0.00 0.00 4.61
2780 2901 7.065803 CGTGTGAAGTTAATGATTTATCCACCT 59.934 37.037 0.00 0.00 0.00 4.00
2781 2902 9.391006 GTGTGAAGTTAATGATTTATCCACCTA 57.609 33.333 0.00 0.00 0.00 3.08
2790 2917 8.940397 AATGATTTATCCACCTAGGGTTTATG 57.060 34.615 14.81 1.09 38.24 1.90
2798 2925 3.265995 CACCTAGGGTTTATGGTGGAAGT 59.734 47.826 14.81 0.00 44.33 3.01
2823 3076 7.947782 TCCTTAAGTAGGGATACATTGGAAT 57.052 36.000 0.97 0.00 44.86 3.01
2840 3093 8.514594 ACATTGGAATAATACAATTATGCTCCG 58.485 33.333 0.00 0.00 35.26 4.63
2841 3094 8.514594 CATTGGAATAATACAATTATGCTCCGT 58.485 33.333 0.00 0.00 35.26 4.69
2842 3095 9.733556 ATTGGAATAATACAATTATGCTCCGTA 57.266 29.630 6.15 0.00 33.80 4.02
2843 3096 9.733556 TTGGAATAATACAATTATGCTCCGTAT 57.266 29.630 6.15 0.00 0.00 3.06
2844 3097 9.161629 TGGAATAATACAATTATGCTCCGTATG 57.838 33.333 6.15 0.00 0.00 2.39
2845 3098 9.162764 GGAATAATACAATTATGCTCCGTATGT 57.837 33.333 0.00 0.00 0.00 2.29
2846 3099 9.973246 GAATAATACAATTATGCTCCGTATGTG 57.027 33.333 0.00 0.00 0.00 3.21
2847 3100 9.719355 AATAATACAATTATGCTCCGTATGTGA 57.281 29.630 0.00 0.00 0.00 3.58
2848 3101 7.421530 AATACAATTATGCTCCGTATGTGAC 57.578 36.000 0.00 0.00 0.00 3.67
2849 3102 4.765273 ACAATTATGCTCCGTATGTGACA 58.235 39.130 0.00 0.00 0.00 3.58
2850 3103 4.570772 ACAATTATGCTCCGTATGTGACAC 59.429 41.667 0.00 0.00 0.00 3.67
2851 3104 4.672587 ATTATGCTCCGTATGTGACACT 57.327 40.909 7.20 0.00 0.00 3.55
2852 3105 5.784578 ATTATGCTCCGTATGTGACACTA 57.215 39.130 7.20 0.00 0.00 2.74
2853 3106 5.784578 TTATGCTCCGTATGTGACACTAT 57.215 39.130 7.20 1.82 0.00 2.12
2854 3107 4.672587 ATGCTCCGTATGTGACACTATT 57.327 40.909 7.20 0.00 0.00 1.73
2855 3108 5.784578 ATGCTCCGTATGTGACACTATTA 57.215 39.130 7.20 0.00 0.00 0.98
2856 3109 5.784578 TGCTCCGTATGTGACACTATTAT 57.215 39.130 7.20 0.00 0.00 1.28
2857 3110 6.156748 TGCTCCGTATGTGACACTATTATT 57.843 37.500 7.20 0.00 0.00 1.40
2858 3111 5.983118 TGCTCCGTATGTGACACTATTATTG 59.017 40.000 7.20 0.00 0.00 1.90
2859 3112 5.107453 GCTCCGTATGTGACACTATTATTGC 60.107 44.000 7.20 1.08 0.00 3.56
2860 3113 4.979815 TCCGTATGTGACACTATTATTGCG 59.020 41.667 7.20 1.35 0.00 4.85
2861 3114 4.743151 CCGTATGTGACACTATTATTGCGT 59.257 41.667 7.20 0.00 0.00 5.24
2862 3115 5.332280 CCGTATGTGACACTATTATTGCGTG 60.332 44.000 7.20 0.00 34.92 5.34
2863 3116 4.536364 ATGTGACACTATTATTGCGTGC 57.464 40.909 7.20 0.00 32.07 5.34
2864 3117 3.330267 TGTGACACTATTATTGCGTGCA 58.670 40.909 7.20 0.00 32.07 4.57
2865 3118 3.124466 TGTGACACTATTATTGCGTGCAC 59.876 43.478 6.82 6.82 36.81 4.57
2866 3119 3.124466 GTGACACTATTATTGCGTGCACA 59.876 43.478 18.64 0.00 36.56 4.57
2867 3120 3.748568 TGACACTATTATTGCGTGCACAA 59.251 39.130 18.64 4.77 32.07 3.33
2868 3121 4.214332 TGACACTATTATTGCGTGCACAAA 59.786 37.500 18.64 11.05 32.27 2.83
2869 3122 5.114785 ACACTATTATTGCGTGCACAAAA 57.885 34.783 18.64 10.66 32.27 2.44
2870 3123 5.153513 ACACTATTATTGCGTGCACAAAAG 58.846 37.500 18.64 7.30 32.27 2.27
2871 3124 4.558470 CACTATTATTGCGTGCACAAAAGG 59.442 41.667 18.64 0.39 32.27 3.11
2872 3125 2.430546 TTATTGCGTGCACAAAAGGG 57.569 45.000 18.64 0.00 32.27 3.95
2873 3126 0.600557 TATTGCGTGCACAAAAGGGG 59.399 50.000 18.64 0.00 32.27 4.79
2874 3127 1.112315 ATTGCGTGCACAAAAGGGGA 61.112 50.000 18.64 0.00 32.27 4.81
2875 3128 1.733402 TTGCGTGCACAAAAGGGGAG 61.733 55.000 18.64 0.00 0.00 4.30
2876 3129 2.644992 CGTGCACAAAAGGGGAGC 59.355 61.111 18.64 0.00 0.00 4.70
2877 3130 1.898574 CGTGCACAAAAGGGGAGCT 60.899 57.895 18.64 0.00 0.00 4.09
2878 3131 0.605319 CGTGCACAAAAGGGGAGCTA 60.605 55.000 18.64 0.00 0.00 3.32
2879 3132 1.168714 GTGCACAAAAGGGGAGCTAG 58.831 55.000 13.17 0.00 0.00 3.42
2880 3133 0.771127 TGCACAAAAGGGGAGCTAGT 59.229 50.000 0.00 0.00 0.00 2.57
2881 3134 1.144913 TGCACAAAAGGGGAGCTAGTT 59.855 47.619 0.00 0.00 0.00 2.24
2882 3135 2.239400 GCACAAAAGGGGAGCTAGTTT 58.761 47.619 0.00 0.00 0.00 2.66
2883 3136 3.181438 TGCACAAAAGGGGAGCTAGTTTA 60.181 43.478 0.00 0.00 0.00 2.01
2884 3137 3.824443 GCACAAAAGGGGAGCTAGTTTAA 59.176 43.478 0.00 0.00 0.00 1.52
2885 3138 4.462834 GCACAAAAGGGGAGCTAGTTTAAT 59.537 41.667 0.00 0.00 0.00 1.40
2886 3139 5.047306 GCACAAAAGGGGAGCTAGTTTAATT 60.047 40.000 0.00 0.00 0.00 1.40
2887 3140 6.518369 GCACAAAAGGGGAGCTAGTTTAATTT 60.518 38.462 0.00 0.00 0.00 1.82
2888 3141 7.441836 CACAAAAGGGGAGCTAGTTTAATTTT 58.558 34.615 0.00 0.00 0.00 1.82
2889 3142 7.598869 CACAAAAGGGGAGCTAGTTTAATTTTC 59.401 37.037 0.00 0.00 0.00 2.29
2890 3143 7.509318 ACAAAAGGGGAGCTAGTTTAATTTTCT 59.491 33.333 0.00 0.00 0.00 2.52
2891 3144 8.367911 CAAAAGGGGAGCTAGTTTAATTTTCTT 58.632 33.333 0.00 0.00 0.00 2.52
2892 3145 8.492415 AAAGGGGAGCTAGTTTAATTTTCTTT 57.508 30.769 0.00 0.00 0.00 2.52
2893 3146 7.704578 AGGGGAGCTAGTTTAATTTTCTTTC 57.295 36.000 0.00 0.00 0.00 2.62
2894 3147 7.471041 AGGGGAGCTAGTTTAATTTTCTTTCT 58.529 34.615 0.00 0.00 0.00 2.52
2895 3148 7.394641 AGGGGAGCTAGTTTAATTTTCTTTCTG 59.605 37.037 0.00 0.00 0.00 3.02
2896 3149 7.176865 GGGGAGCTAGTTTAATTTTCTTTCTGT 59.823 37.037 0.00 0.00 0.00 3.41
2897 3150 8.023706 GGGAGCTAGTTTAATTTTCTTTCTGTG 58.976 37.037 0.00 0.00 0.00 3.66
2898 3151 7.539022 GGAGCTAGTTTAATTTTCTTTCTGTGC 59.461 37.037 0.00 0.00 0.00 4.57
2899 3152 7.940850 AGCTAGTTTAATTTTCTTTCTGTGCA 58.059 30.769 0.00 0.00 0.00 4.57
2900 3153 8.579863 AGCTAGTTTAATTTTCTTTCTGTGCAT 58.420 29.630 0.00 0.00 0.00 3.96
2901 3154 9.196552 GCTAGTTTAATTTTCTTTCTGTGCATT 57.803 29.630 0.00 0.00 0.00 3.56
2905 3158 8.946935 GTTTAATTTTCTTTCTGTGCATTTTGC 58.053 29.630 0.00 0.00 45.29 3.68
2917 3170 2.199236 GCATTTTGCATTAGCCAGAGC 58.801 47.619 0.00 0.00 44.26 4.09
2918 3171 2.417651 GCATTTTGCATTAGCCAGAGCA 60.418 45.455 0.00 0.00 44.26 4.26
2919 3172 3.740141 GCATTTTGCATTAGCCAGAGCAT 60.740 43.478 0.00 0.00 44.26 3.79
2920 3173 4.500205 GCATTTTGCATTAGCCAGAGCATA 60.500 41.667 0.00 0.00 44.26 3.14
2921 3174 5.593968 CATTTTGCATTAGCCAGAGCATAA 58.406 37.500 0.00 0.00 43.56 1.90
2922 3175 4.906065 TTTGCATTAGCCAGAGCATAAG 57.094 40.909 0.00 0.00 43.56 1.73
2923 3176 3.843893 TGCATTAGCCAGAGCATAAGA 57.156 42.857 0.00 0.00 43.56 2.10
2924 3177 4.362470 TGCATTAGCCAGAGCATAAGAT 57.638 40.909 0.00 0.00 43.56 2.40
2925 3178 4.722220 TGCATTAGCCAGAGCATAAGATT 58.278 39.130 0.00 0.00 43.56 2.40
2926 3179 4.758674 TGCATTAGCCAGAGCATAAGATTC 59.241 41.667 0.00 0.00 43.56 2.52
2927 3180 5.002516 GCATTAGCCAGAGCATAAGATTCT 58.997 41.667 0.00 0.00 43.56 2.40
2928 3181 5.472820 GCATTAGCCAGAGCATAAGATTCTT 59.527 40.000 4.03 4.03 43.56 2.52
2929 3182 6.016443 GCATTAGCCAGAGCATAAGATTCTTT 60.016 38.462 3.86 0.00 43.56 2.52
2930 3183 7.583230 CATTAGCCAGAGCATAAGATTCTTTC 58.417 38.462 3.86 0.00 43.56 2.62
2931 3184 5.370875 AGCCAGAGCATAAGATTCTTTCT 57.629 39.130 3.86 0.00 43.56 2.52
2932 3185 5.753716 AGCCAGAGCATAAGATTCTTTCTT 58.246 37.500 3.86 0.00 44.07 2.52
2933 3186 6.186234 AGCCAGAGCATAAGATTCTTTCTTT 58.814 36.000 3.86 0.00 41.03 2.52
2934 3187 6.318396 AGCCAGAGCATAAGATTCTTTCTTTC 59.682 38.462 3.86 0.00 41.03 2.62
2935 3188 6.713520 CCAGAGCATAAGATTCTTTCTTTCG 58.286 40.000 3.86 0.00 42.15 3.46
2936 3189 6.536582 CCAGAGCATAAGATTCTTTCTTTCGA 59.463 38.462 3.86 0.00 42.15 3.71
2937 3190 7.397970 CAGAGCATAAGATTCTTTCTTTCGAC 58.602 38.462 3.86 0.00 42.15 4.20
2938 3191 7.277539 CAGAGCATAAGATTCTTTCTTTCGACT 59.722 37.037 3.86 0.00 42.15 4.18
2939 3192 7.821846 AGAGCATAAGATTCTTTCTTTCGACTT 59.178 33.333 3.86 0.00 42.15 3.01
2940 3193 8.329203 AGCATAAGATTCTTTCTTTCGACTTT 57.671 30.769 3.86 0.00 42.15 2.66
2941 3194 8.447053 AGCATAAGATTCTTTCTTTCGACTTTC 58.553 33.333 3.86 0.00 42.15 2.62
2942 3195 8.447053 GCATAAGATTCTTTCTTTCGACTTTCT 58.553 33.333 3.86 0.00 42.15 2.52
2943 3196 9.752274 CATAAGATTCTTTCTTTCGACTTTCTG 57.248 33.333 3.86 0.00 42.15 3.02
2944 3197 6.793492 AGATTCTTTCTTTCGACTTTCTGG 57.207 37.500 0.00 0.00 0.00 3.86
2945 3198 6.292150 AGATTCTTTCTTTCGACTTTCTGGT 58.708 36.000 0.00 0.00 0.00 4.00
2946 3199 7.442656 AGATTCTTTCTTTCGACTTTCTGGTA 58.557 34.615 0.00 0.00 0.00 3.25
2947 3200 7.931948 AGATTCTTTCTTTCGACTTTCTGGTAA 59.068 33.333 0.00 0.00 0.00 2.85
2948 3201 6.839820 TCTTTCTTTCGACTTTCTGGTAAC 57.160 37.500 0.00 0.00 0.00 2.50
2949 3202 6.579865 TCTTTCTTTCGACTTTCTGGTAACT 58.420 36.000 0.00 0.00 37.61 2.24
2950 3203 7.719483 TCTTTCTTTCGACTTTCTGGTAACTA 58.281 34.615 0.00 0.00 37.61 2.24
2951 3204 7.866393 TCTTTCTTTCGACTTTCTGGTAACTAG 59.134 37.037 0.00 0.00 37.61 2.57
2952 3205 6.889301 TCTTTCGACTTTCTGGTAACTAGA 57.111 37.500 0.00 0.00 37.61 2.43
2953 3206 6.675987 TCTTTCGACTTTCTGGTAACTAGAC 58.324 40.000 0.00 0.00 37.61 2.59
2954 3207 4.675190 TCGACTTTCTGGTAACTAGACG 57.325 45.455 0.00 0.00 37.61 4.18
2955 3208 4.318332 TCGACTTTCTGGTAACTAGACGA 58.682 43.478 0.00 0.00 37.61 4.20
2956 3209 4.940046 TCGACTTTCTGGTAACTAGACGAT 59.060 41.667 0.00 0.00 37.61 3.73
2957 3210 5.029014 CGACTTTCTGGTAACTAGACGATG 58.971 45.833 0.00 0.00 37.61 3.84
2958 3211 5.163784 CGACTTTCTGGTAACTAGACGATGA 60.164 44.000 0.00 0.00 37.61 2.92
2959 3212 6.585695 ACTTTCTGGTAACTAGACGATGAA 57.414 37.500 0.00 0.00 37.61 2.57
2960 3213 7.171630 ACTTTCTGGTAACTAGACGATGAAT 57.828 36.000 0.00 0.00 37.61 2.57
2961 3214 7.612677 ACTTTCTGGTAACTAGACGATGAATT 58.387 34.615 0.00 0.00 37.61 2.17
2962 3215 7.545965 ACTTTCTGGTAACTAGACGATGAATTG 59.454 37.037 0.00 0.00 37.61 2.32
2963 3216 5.348986 TCTGGTAACTAGACGATGAATTGC 58.651 41.667 0.00 0.00 37.61 3.56
2964 3217 4.439057 TGGTAACTAGACGATGAATTGCC 58.561 43.478 0.00 0.00 37.61 4.52
2965 3218 4.081365 TGGTAACTAGACGATGAATTGCCA 60.081 41.667 0.00 0.00 37.61 4.92
2966 3219 5.057149 GGTAACTAGACGATGAATTGCCAT 58.943 41.667 0.00 0.00 0.00 4.40
2967 3220 5.050091 GGTAACTAGACGATGAATTGCCATG 60.050 44.000 0.00 0.00 0.00 3.66
2968 3221 2.874701 ACTAGACGATGAATTGCCATGC 59.125 45.455 0.00 0.00 0.00 4.06
2969 3222 2.048444 AGACGATGAATTGCCATGCT 57.952 45.000 0.00 0.00 0.00 3.79
2970 3223 3.198409 AGACGATGAATTGCCATGCTA 57.802 42.857 0.00 0.00 0.00 3.49
2971 3224 3.544684 AGACGATGAATTGCCATGCTAA 58.455 40.909 0.00 0.00 0.00 3.09
2972 3225 3.562973 AGACGATGAATTGCCATGCTAAG 59.437 43.478 0.00 0.00 0.00 2.18
2973 3226 2.033801 ACGATGAATTGCCATGCTAAGC 59.966 45.455 0.00 0.00 0.00 3.09
2974 3227 2.033675 CGATGAATTGCCATGCTAAGCA 59.966 45.455 0.00 0.00 44.86 3.91
2975 3228 3.639538 GATGAATTGCCATGCTAAGCAG 58.360 45.455 0.00 0.00 43.65 4.24
2986 3239 2.867456 GCTAAGCAGCGTTTCGTAAA 57.133 45.000 0.00 0.00 38.22 2.01
2988 3241 2.900655 GCTAAGCAGCGTTTCGTAAAAC 59.099 45.455 0.00 0.00 41.16 2.43
2989 3242 2.394545 AAGCAGCGTTTCGTAAAACC 57.605 45.000 0.00 0.00 41.46 3.27
2995 3248 4.451557 CAGCGTTTCGTAAAACCTTAGTG 58.548 43.478 0.00 0.00 41.46 2.74
3020 3274 6.142958 GGAGAAAAACAAAATTGCTCTTCTCG 59.857 38.462 16.87 0.00 38.61 4.04
3040 3294 2.352617 CGTGTGTTTGGCCATGCTAAAT 60.353 45.455 6.09 0.00 40.72 1.40
3042 3296 4.423732 GTGTGTTTGGCCATGCTAAATAG 58.576 43.478 6.09 0.00 40.72 1.73
3043 3297 4.082245 GTGTGTTTGGCCATGCTAAATAGT 60.082 41.667 6.09 0.00 40.72 2.12
3046 3300 4.398988 TGTTTGGCCATGCTAAATAGTCTG 59.601 41.667 6.09 0.00 40.72 3.51
3054 3308 6.567321 GCCATGCTAAATAGTCTGCATAGTTG 60.567 42.308 0.00 0.00 43.24 3.16
3083 3337 2.352503 AAGCCATGTTTGTTCGCATC 57.647 45.000 0.00 0.00 0.00 3.91
3128 3382 1.357690 GCACACATGCCATGGATCG 59.642 57.895 18.40 4.38 46.97 3.69
3213 3467 1.227380 GTCCAAGATGCCGCGAGAT 60.227 57.895 8.23 0.00 0.00 2.75
3218 3472 1.600957 CAAGATGCCGCGAGATTGAAT 59.399 47.619 8.23 0.00 0.00 2.57
3232 3486 5.563475 CGAGATTGAATGAAAAACAGGCAGT 60.563 40.000 0.00 0.00 0.00 4.40
3248 3502 1.374631 AGTGTGCACATCGACGCAT 60.375 52.632 24.69 0.00 40.89 4.73
3249 3503 0.950555 AGTGTGCACATCGACGCATT 60.951 50.000 24.69 0.00 40.89 3.56
3356 3610 2.524306 TGGGTTTGTGATTTAGCCAGG 58.476 47.619 0.00 0.00 34.73 4.45
3360 3614 3.440522 GGTTTGTGATTTAGCCAGGTCTC 59.559 47.826 0.00 0.00 0.00 3.36
3410 3664 8.052748 TGGTGCTATGGATATTTGTTTCTTAGT 58.947 33.333 0.00 0.00 0.00 2.24
3483 3738 5.427378 TGCTGGTGCACGCATATATAATAT 58.573 37.500 14.43 0.00 45.31 1.28
3795 4052 2.513204 CGGAGAGGTAGACCGCGA 60.513 66.667 8.23 0.00 40.98 5.87
3856 4113 1.321474 CAAAGCAACTCCTGGAGCAA 58.679 50.000 23.43 0.00 32.04 3.91
3956 4213 2.125552 TGCCGCTTCGATGACCAG 60.126 61.111 1.89 0.00 0.00 4.00
4014 4271 3.113979 TAGAGCGTCGCGTGTCGA 61.114 61.111 19.29 0.00 46.29 4.20
4165 4422 2.203139 CGGGGCGTGCATATGGAA 60.203 61.111 4.56 0.00 0.00 3.53
4166 4423 1.821759 CGGGGCGTGCATATGGAAA 60.822 57.895 4.56 0.00 0.00 3.13
4167 4424 1.733526 GGGGCGTGCATATGGAAAC 59.266 57.895 4.56 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
229 233 1.239347 GCTTCCTTCCGATAATGGCC 58.761 55.000 0.00 0.00 0.00 5.36
321 325 2.735134 CGAACACTGTAGGTTTAGGTGC 59.265 50.000 0.00 0.00 0.00 5.01
359 363 3.928779 GCGCAGGGGATCCGATCA 61.929 66.667 0.30 0.00 38.33 2.92
456 464 1.055849 GGGCAACAAAACCCCATTCT 58.944 50.000 0.00 0.00 40.56 2.40
481 489 1.001745 GCAACAAACGGAATGCGGAC 61.002 55.000 0.00 0.00 0.00 4.79
509 517 1.452651 CGGAGATTGCTGGGCACAT 60.453 57.895 0.00 0.00 38.71 3.21
537 546 3.070302 GCCCTAGAATGAAAGATCCGAGT 59.930 47.826 0.00 0.00 0.00 4.18
586 607 2.968574 ACCAGAATCATATCTCCGCACT 59.031 45.455 0.00 0.00 0.00 4.40
705 726 9.565090 TTCCTATCATGACAAGATAGAAAATGG 57.435 33.333 23.15 10.69 44.91 3.16
709 730 8.206867 CCTGTTCCTATCATGACAAGATAGAAA 58.793 37.037 23.15 11.23 44.91 2.52
725 746 3.928754 TGGATACTGCTCCTGTTCCTAT 58.071 45.455 0.00 0.00 36.20 2.57
750 771 4.223258 GTGAACTACACCGCACAACGAC 62.223 54.545 0.00 0.00 43.05 4.34
789 810 4.948341 ACAAATTTAGTGAACCCCAACC 57.052 40.909 0.00 0.00 0.00 3.77
818 839 7.551585 TCTAACAAAAAGAGAAAACAATGGCA 58.448 30.769 0.00 0.00 0.00 4.92
819 840 8.419076 TTCTAACAAAAAGAGAAAACAATGGC 57.581 30.769 0.00 0.00 0.00 4.40
832 853 3.989817 GCACCCTGCATTCTAACAAAAAG 59.010 43.478 0.00 0.00 44.26 2.27
1067 1092 5.931146 GGATCAATATCTGAAGCATCTTCGT 59.069 40.000 0.00 0.00 37.67 3.85
1069 1094 5.931146 ACGGATCAATATCTGAAGCATCTTC 59.069 40.000 0.00 0.00 40.45 2.87
1076 1101 8.138074 TCTTGTAAGACGGATCAATATCTGAAG 58.862 37.037 0.00 0.00 40.45 3.02
1119 1144 5.523552 CACATACGCACTTCCATCTTCAATA 59.476 40.000 0.00 0.00 0.00 1.90
1202 1227 5.766670 ACATTTGTGCCTCCATATGACATAG 59.233 40.000 3.65 0.00 31.00 2.23
1294 1358 1.188863 GCATTTCCATTGACAGCCCT 58.811 50.000 0.00 0.00 0.00 5.19
1295 1359 0.179129 CGCATTTCCATTGACAGCCC 60.179 55.000 0.00 0.00 0.00 5.19
1296 1360 0.179129 CCGCATTTCCATTGACAGCC 60.179 55.000 0.00 0.00 0.00 4.85
1307 1371 0.536724 AAAGGAATGGCCCGCATTTC 59.463 50.000 0.00 0.00 37.37 2.17
1368 1432 7.858583 TCAGAAATTCTGCATAAGATTCATCG 58.141 34.615 17.58 0.00 43.95 3.84
1458 1522 1.403514 GGTGTCTTCTCCTCTTGCTCG 60.404 57.143 0.00 0.00 0.00 5.03
1471 1535 2.587060 TCATATCCAGGGGGTGTCTT 57.413 50.000 0.00 0.00 34.93 3.01
1545 1609 7.767198 CAGATTAAATCCTGACCATGCAAATTT 59.233 33.333 0.00 0.00 32.37 1.82
1697 1761 1.702182 TCAGATGCCTGCCACAAAAA 58.298 45.000 0.00 0.00 40.20 1.94
1698 1762 1.614903 CTTCAGATGCCTGCCACAAAA 59.385 47.619 0.00 0.00 40.20 2.44
1699 1763 1.202915 TCTTCAGATGCCTGCCACAAA 60.203 47.619 0.00 0.00 40.20 2.83
1820 1884 5.182760 CAGTGGCTTTTCTCATAAGCTCTTT 59.817 40.000 7.43 0.00 45.62 2.52
1978 2042 2.612212 CAAGAACGGAATAACCCCATCG 59.388 50.000 0.00 0.00 34.64 3.84
1996 2060 2.288152 ACAACCACAATAAAGGCGCAAG 60.288 45.455 10.83 0.00 43.44 4.01
2044 2108 4.142600 GCTTATCAACACCTCGCTGAAATT 60.143 41.667 0.00 0.00 0.00 1.82
2211 2314 7.787725 ACCGGAGATGAACAGATTAAATTAC 57.212 36.000 9.46 0.00 0.00 1.89
2262 2365 9.904198 TCAAGATTTGTTGTTCTATGATCCATA 57.096 29.630 0.00 0.00 0.00 2.74
2279 2387 8.469200 TCCAAGCCACTTAAATATCAAGATTTG 58.531 33.333 4.48 3.88 31.51 2.32
2462 2579 2.907042 AGCCTTAGAAACTGCTACAGGT 59.093 45.455 0.00 0.00 35.51 4.00
2515 2632 8.716674 AATCCATCTAATGCCAAGTAATTCAT 57.283 30.769 0.00 0.00 0.00 2.57
2519 2636 9.812347 TGATAAATCCATCTAATGCCAAGTAAT 57.188 29.630 0.00 0.00 0.00 1.89
2520 2637 9.639563 TTGATAAATCCATCTAATGCCAAGTAA 57.360 29.630 0.00 0.00 0.00 2.24
2557 2675 3.983344 CAGTTTTGGTAGCAAAGCATGAC 59.017 43.478 28.28 19.34 35.03 3.06
2560 2678 4.813027 CATCAGTTTTGGTAGCAAAGCAT 58.187 39.130 28.28 15.79 35.03 3.79
2680 2798 6.591935 TGACAGAAAAGAACAACTAGGATGT 58.408 36.000 0.00 0.00 0.00 3.06
2707 2828 9.924650 AACTTCCACTATAACGATATCATTACC 57.075 33.333 3.12 0.00 0.00 2.85
2719 2840 8.611654 TCACTGGTTTTAACTTCCACTATAAC 57.388 34.615 0.00 0.00 0.00 1.89
2720 2841 9.444600 GATCACTGGTTTTAACTTCCACTATAA 57.555 33.333 0.00 0.00 0.00 0.98
2735 2856 5.639506 CACACGATTTAGAGATCACTGGTTT 59.360 40.000 2.56 0.00 0.00 3.27
2738 2859 4.998788 TCACACGATTTAGAGATCACTGG 58.001 43.478 2.56 0.00 0.00 4.00
2754 2875 7.065803 AGGTGGATAAATCATTAACTTCACACG 59.934 37.037 0.00 0.00 0.00 4.49
2757 2878 9.057089 CCTAGGTGGATAAATCATTAACTTCAC 57.943 37.037 0.00 0.00 38.35 3.18
2777 2898 3.538387 ACTTCCACCATAAACCCTAGGT 58.462 45.455 8.29 0.00 37.65 3.08
2778 2899 4.524053 GAACTTCCACCATAAACCCTAGG 58.476 47.826 0.06 0.06 0.00 3.02
2779 2900 4.227527 AGGAACTTCCACCATAAACCCTAG 59.772 45.833 10.57 0.00 39.61 3.02
2780 2901 4.180723 AGGAACTTCCACCATAAACCCTA 58.819 43.478 10.57 0.00 39.61 3.53
2781 2902 2.993863 AGGAACTTCCACCATAAACCCT 59.006 45.455 10.57 0.00 39.61 4.34
2823 3076 8.145122 TGTCACATACGGAGCATAATTGTATTA 58.855 33.333 0.00 0.00 0.00 0.98
2835 3088 5.107453 GCAATAATAGTGTCACATACGGAGC 60.107 44.000 5.62 0.00 0.00 4.70
2836 3089 5.117135 CGCAATAATAGTGTCACATACGGAG 59.883 44.000 5.62 0.00 0.00 4.63
2837 3090 4.979815 CGCAATAATAGTGTCACATACGGA 59.020 41.667 5.62 0.00 0.00 4.69
2838 3091 4.743151 ACGCAATAATAGTGTCACATACGG 59.257 41.667 5.62 0.00 0.00 4.02
2839 3092 5.656537 CACGCAATAATAGTGTCACATACG 58.343 41.667 5.62 1.16 0.00 3.06
2840 3093 5.006261 TGCACGCAATAATAGTGTCACATAC 59.994 40.000 5.62 0.00 38.10 2.39
2841 3094 5.006261 GTGCACGCAATAATAGTGTCACATA 59.994 40.000 0.00 0.00 39.85 2.29
2842 3095 3.938334 TGCACGCAATAATAGTGTCACAT 59.062 39.130 5.62 0.00 38.10 3.21
2843 3096 3.124466 GTGCACGCAATAATAGTGTCACA 59.876 43.478 0.00 0.00 39.85 3.58
2844 3097 3.124466 TGTGCACGCAATAATAGTGTCAC 59.876 43.478 13.13 0.00 40.15 3.67
2845 3098 3.330267 TGTGCACGCAATAATAGTGTCA 58.670 40.909 13.13 0.00 38.10 3.58
2846 3099 4.335082 TTGTGCACGCAATAATAGTGTC 57.665 40.909 13.13 0.00 38.10 3.67
2847 3100 4.757799 TTTGTGCACGCAATAATAGTGT 57.242 36.364 13.13 0.00 38.10 3.55
2848 3101 4.558470 CCTTTTGTGCACGCAATAATAGTG 59.442 41.667 13.13 0.00 38.77 2.74
2849 3102 4.380444 CCCTTTTGTGCACGCAATAATAGT 60.380 41.667 13.13 0.00 0.00 2.12
2850 3103 4.104776 CCCTTTTGTGCACGCAATAATAG 58.895 43.478 13.13 5.00 0.00 1.73
2851 3104 3.119316 CCCCTTTTGTGCACGCAATAATA 60.119 43.478 13.13 0.00 0.00 0.98
2852 3105 2.353605 CCCCTTTTGTGCACGCAATAAT 60.354 45.455 13.13 0.00 0.00 1.28
2853 3106 1.000283 CCCCTTTTGTGCACGCAATAA 60.000 47.619 13.13 0.00 0.00 1.40
2854 3107 0.600557 CCCCTTTTGTGCACGCAATA 59.399 50.000 13.13 0.00 0.00 1.90
2855 3108 1.112315 TCCCCTTTTGTGCACGCAAT 61.112 50.000 13.13 0.00 0.00 3.56
2856 3109 1.733402 CTCCCCTTTTGTGCACGCAA 61.733 55.000 13.13 4.65 0.00 4.85
2857 3110 2.124109 TCCCCTTTTGTGCACGCA 60.124 55.556 13.13 0.00 0.00 5.24
2858 3111 2.644992 CTCCCCTTTTGTGCACGC 59.355 61.111 13.13 0.00 0.00 5.34
2859 3112 0.605319 TAGCTCCCCTTTTGTGCACG 60.605 55.000 13.13 0.00 0.00 5.34
2860 3113 1.168714 CTAGCTCCCCTTTTGTGCAC 58.831 55.000 10.75 10.75 0.00 4.57
2861 3114 0.771127 ACTAGCTCCCCTTTTGTGCA 59.229 50.000 0.00 0.00 0.00 4.57
2862 3115 1.911057 AACTAGCTCCCCTTTTGTGC 58.089 50.000 0.00 0.00 0.00 4.57
2863 3116 6.590234 AATTAAACTAGCTCCCCTTTTGTG 57.410 37.500 0.00 0.00 0.00 3.33
2864 3117 7.509318 AGAAAATTAAACTAGCTCCCCTTTTGT 59.491 33.333 0.00 0.00 0.00 2.83
2865 3118 7.896811 AGAAAATTAAACTAGCTCCCCTTTTG 58.103 34.615 0.00 0.00 0.00 2.44
2866 3119 8.492415 AAGAAAATTAAACTAGCTCCCCTTTT 57.508 30.769 0.00 0.00 0.00 2.27
2867 3120 8.492415 AAAGAAAATTAAACTAGCTCCCCTTT 57.508 30.769 0.00 0.00 0.00 3.11
2868 3121 7.950684 AGAAAGAAAATTAAACTAGCTCCCCTT 59.049 33.333 0.00 0.00 0.00 3.95
2869 3122 7.394641 CAGAAAGAAAATTAAACTAGCTCCCCT 59.605 37.037 0.00 0.00 0.00 4.79
2870 3123 7.176865 ACAGAAAGAAAATTAAACTAGCTCCCC 59.823 37.037 0.00 0.00 0.00 4.81
2871 3124 8.023706 CACAGAAAGAAAATTAAACTAGCTCCC 58.976 37.037 0.00 0.00 0.00 4.30
2872 3125 7.539022 GCACAGAAAGAAAATTAAACTAGCTCC 59.461 37.037 0.00 0.00 0.00 4.70
2873 3126 8.076178 TGCACAGAAAGAAAATTAAACTAGCTC 58.924 33.333 0.00 0.00 0.00 4.09
2874 3127 7.940850 TGCACAGAAAGAAAATTAAACTAGCT 58.059 30.769 0.00 0.00 0.00 3.32
2875 3128 8.748380 ATGCACAGAAAGAAAATTAAACTAGC 57.252 30.769 0.00 0.00 0.00 3.42
2879 3132 8.946935 GCAAAATGCACAGAAAGAAAATTAAAC 58.053 29.630 0.00 0.00 44.26 2.01
2894 3147 6.928486 GCTCTGGCTAATGCAAAATGCACA 62.928 45.833 7.25 0.09 45.37 4.57
2895 3148 4.524855 GCTCTGGCTAATGCAAAATGCAC 61.525 47.826 7.25 0.00 45.37 4.57
2896 3149 2.417651 GCTCTGGCTAATGCAAAATGCA 60.418 45.455 7.57 7.57 46.07 3.96
2897 3150 2.199236 GCTCTGGCTAATGCAAAATGC 58.801 47.619 0.00 0.00 41.91 3.56
2898 3151 3.513680 TGCTCTGGCTAATGCAAAATG 57.486 42.857 0.00 0.00 41.91 2.32
2899 3152 5.595542 TCTTATGCTCTGGCTAATGCAAAAT 59.404 36.000 0.00 0.00 41.91 1.82
2900 3153 4.949238 TCTTATGCTCTGGCTAATGCAAAA 59.051 37.500 0.00 0.00 41.91 2.44
2901 3154 4.525996 TCTTATGCTCTGGCTAATGCAAA 58.474 39.130 0.00 0.00 41.91 3.68
2902 3155 4.155063 TCTTATGCTCTGGCTAATGCAA 57.845 40.909 0.00 0.00 41.91 4.08
2903 3156 3.843893 TCTTATGCTCTGGCTAATGCA 57.156 42.857 0.00 0.00 41.91 3.96
2904 3157 5.002516 AGAATCTTATGCTCTGGCTAATGC 58.997 41.667 0.00 0.00 39.59 3.56
2905 3158 7.444792 AGAAAGAATCTTATGCTCTGGCTAATG 59.555 37.037 0.00 0.00 33.39 1.90
2906 3159 7.516452 AGAAAGAATCTTATGCTCTGGCTAAT 58.484 34.615 0.00 0.00 33.39 1.73
2907 3160 6.893583 AGAAAGAATCTTATGCTCTGGCTAA 58.106 36.000 0.00 0.00 33.39 3.09
2908 3161 6.491714 AGAAAGAATCTTATGCTCTGGCTA 57.508 37.500 0.00 0.00 33.39 3.93
2909 3162 5.370875 AGAAAGAATCTTATGCTCTGGCT 57.629 39.130 0.00 0.00 33.39 4.75
2921 3174 6.292150 ACCAGAAAGTCGAAAGAAAGAATCT 58.708 36.000 0.00 0.00 45.01 2.40
2922 3175 6.546972 ACCAGAAAGTCGAAAGAAAGAATC 57.453 37.500 0.00 0.00 45.01 2.52
2923 3176 7.715686 AGTTACCAGAAAGTCGAAAGAAAGAAT 59.284 33.333 0.00 0.00 45.01 2.40
2924 3177 7.046033 AGTTACCAGAAAGTCGAAAGAAAGAA 58.954 34.615 0.00 0.00 45.01 2.52
2925 3178 6.579865 AGTTACCAGAAAGTCGAAAGAAAGA 58.420 36.000 0.00 0.00 45.01 2.52
2926 3179 6.846325 AGTTACCAGAAAGTCGAAAGAAAG 57.154 37.500 0.00 0.00 45.01 2.62
2927 3180 7.650903 GTCTAGTTACCAGAAAGTCGAAAGAAA 59.349 37.037 0.00 0.00 45.01 2.52
2928 3181 7.144000 GTCTAGTTACCAGAAAGTCGAAAGAA 58.856 38.462 0.00 0.00 45.01 2.52
2929 3182 6.567321 CGTCTAGTTACCAGAAAGTCGAAAGA 60.567 42.308 0.00 0.00 38.16 2.52
2930 3183 5.568296 CGTCTAGTTACCAGAAAGTCGAAAG 59.432 44.000 0.00 0.00 0.00 2.62
2931 3184 5.239306 TCGTCTAGTTACCAGAAAGTCGAAA 59.761 40.000 0.00 0.00 0.00 3.46
2932 3185 4.756642 TCGTCTAGTTACCAGAAAGTCGAA 59.243 41.667 0.00 0.00 0.00 3.71
2933 3186 4.318332 TCGTCTAGTTACCAGAAAGTCGA 58.682 43.478 0.00 0.00 0.00 4.20
2934 3187 4.675190 TCGTCTAGTTACCAGAAAGTCG 57.325 45.455 0.00 0.00 0.00 4.18
2935 3188 6.192234 TCATCGTCTAGTTACCAGAAAGTC 57.808 41.667 0.00 0.00 0.00 3.01
2936 3189 6.585695 TTCATCGTCTAGTTACCAGAAAGT 57.414 37.500 0.00 0.00 0.00 2.66
2937 3190 7.464710 GCAATTCATCGTCTAGTTACCAGAAAG 60.465 40.741 0.00 0.00 0.00 2.62
2938 3191 6.312918 GCAATTCATCGTCTAGTTACCAGAAA 59.687 38.462 0.00 0.00 0.00 2.52
2939 3192 5.810587 GCAATTCATCGTCTAGTTACCAGAA 59.189 40.000 0.00 0.00 0.00 3.02
2940 3193 5.348986 GCAATTCATCGTCTAGTTACCAGA 58.651 41.667 0.00 0.00 0.00 3.86
2941 3194 4.508124 GGCAATTCATCGTCTAGTTACCAG 59.492 45.833 0.00 0.00 0.00 4.00
2942 3195 4.081365 TGGCAATTCATCGTCTAGTTACCA 60.081 41.667 0.00 0.00 0.00 3.25
2943 3196 4.439057 TGGCAATTCATCGTCTAGTTACC 58.561 43.478 0.00 0.00 0.00 2.85
2944 3197 5.559035 GCATGGCAATTCATCGTCTAGTTAC 60.559 44.000 0.00 0.00 0.00 2.50
2945 3198 4.511454 GCATGGCAATTCATCGTCTAGTTA 59.489 41.667 0.00 0.00 0.00 2.24
2946 3199 3.313526 GCATGGCAATTCATCGTCTAGTT 59.686 43.478 0.00 0.00 0.00 2.24
2947 3200 2.874701 GCATGGCAATTCATCGTCTAGT 59.125 45.455 0.00 0.00 0.00 2.57
2948 3201 3.136763 AGCATGGCAATTCATCGTCTAG 58.863 45.455 0.00 0.00 0.00 2.43
2949 3202 3.198409 AGCATGGCAATTCATCGTCTA 57.802 42.857 0.00 0.00 0.00 2.59
2950 3203 2.048444 AGCATGGCAATTCATCGTCT 57.952 45.000 0.00 0.00 0.00 4.18
2951 3204 3.851105 GCTTAGCATGGCAATTCATCGTC 60.851 47.826 0.00 0.00 0.00 4.20
2952 3205 2.033801 GCTTAGCATGGCAATTCATCGT 59.966 45.455 0.00 0.00 0.00 3.73
2953 3206 2.033675 TGCTTAGCATGGCAATTCATCG 59.966 45.455 1.39 0.00 35.40 3.84
2954 3207 3.639538 CTGCTTAGCATGGCAATTCATC 58.360 45.455 7.58 0.00 38.13 2.92
2955 3208 2.223971 GCTGCTTAGCATGGCAATTCAT 60.224 45.455 7.58 0.00 38.13 2.57
2956 3209 1.135527 GCTGCTTAGCATGGCAATTCA 59.864 47.619 7.58 0.00 38.13 2.57
2957 3210 1.849097 GCTGCTTAGCATGGCAATTC 58.151 50.000 7.58 0.00 38.13 2.17
2958 3211 0.101759 CGCTGCTTAGCATGGCAATT 59.898 50.000 16.59 0.00 38.13 2.32
2959 3212 1.033746 ACGCTGCTTAGCATGGCAAT 61.034 50.000 16.59 3.47 38.13 3.56
2960 3213 1.243342 AACGCTGCTTAGCATGGCAA 61.243 50.000 16.59 0.00 38.13 4.52
2961 3214 1.243342 AAACGCTGCTTAGCATGGCA 61.243 50.000 16.59 0.00 38.13 4.92
2962 3215 0.524180 GAAACGCTGCTTAGCATGGC 60.524 55.000 7.58 7.93 38.13 4.40
2963 3216 0.247814 CGAAACGCTGCTTAGCATGG 60.248 55.000 7.58 5.20 38.13 3.66
2964 3217 0.443869 ACGAAACGCTGCTTAGCATG 59.556 50.000 7.58 6.20 38.13 4.06
2965 3218 2.004583 TACGAAACGCTGCTTAGCAT 57.995 45.000 7.58 0.00 38.13 3.79
2966 3219 1.785768 TTACGAAACGCTGCTTAGCA 58.214 45.000 6.76 6.76 36.92 3.49
2967 3220 2.867456 TTTACGAAACGCTGCTTAGC 57.133 45.000 0.00 0.00 0.00 3.09
2968 3221 3.185797 AGGTTTTACGAAACGCTGCTTAG 59.814 43.478 0.00 0.00 44.83 2.18
2969 3222 3.132925 AGGTTTTACGAAACGCTGCTTA 58.867 40.909 0.00 0.00 44.83 3.09
2970 3223 1.944709 AGGTTTTACGAAACGCTGCTT 59.055 42.857 0.00 0.00 44.83 3.91
2971 3224 1.589803 AGGTTTTACGAAACGCTGCT 58.410 45.000 0.00 0.00 44.83 4.24
2972 3225 2.394545 AAGGTTTTACGAAACGCTGC 57.605 45.000 0.00 0.00 44.83 5.25
2973 3226 4.451557 CACTAAGGTTTTACGAAACGCTG 58.548 43.478 0.00 0.00 44.83 5.18
2974 3227 3.495753 CCACTAAGGTTTTACGAAACGCT 59.504 43.478 0.00 0.00 44.83 5.07
2975 3228 3.494251 TCCACTAAGGTTTTACGAAACGC 59.506 43.478 0.00 0.00 44.83 4.84
2976 3229 4.984161 TCTCCACTAAGGTTTTACGAAACG 59.016 41.667 0.00 0.00 44.83 3.60
2977 3230 6.849588 TTCTCCACTAAGGTTTTACGAAAC 57.150 37.500 0.00 0.00 43.50 2.78
2980 3233 6.822676 TGTTTTTCTCCACTAAGGTTTTACGA 59.177 34.615 0.00 0.00 39.02 3.43
2981 3234 7.018635 TGTTTTTCTCCACTAAGGTTTTACG 57.981 36.000 0.00 0.00 39.02 3.18
2986 3239 7.279981 GCAATTTTGTTTTTCTCCACTAAGGTT 59.720 33.333 0.00 0.00 39.02 3.50
2988 3241 6.986231 AGCAATTTTGTTTTTCTCCACTAAGG 59.014 34.615 0.00 0.00 39.47 2.69
2989 3242 7.922811 AGAGCAATTTTGTTTTTCTCCACTAAG 59.077 33.333 0.00 0.00 0.00 2.18
2995 3248 6.142958 CGAGAAGAGCAATTTTGTTTTTCTCC 59.857 38.462 22.75 12.65 46.82 3.71
3020 3274 2.810439 TTTAGCATGGCCAAACACAC 57.190 45.000 10.96 0.00 0.00 3.82
3054 3308 1.173913 AACATGGCTTTAGTTCGGGC 58.826 50.000 0.00 0.00 0.00 6.13
3083 3337 1.725641 TGGCATAAGTTCTGCAGACG 58.274 50.000 18.03 2.06 41.47 4.18
3213 3467 4.431809 CACACTGCCTGTTTTTCATTCAA 58.568 39.130 0.00 0.00 0.00 2.69
3218 3472 1.135141 GTGCACACTGCCTGTTTTTCA 60.135 47.619 13.17 0.00 44.23 2.69
3232 3486 1.127766 GTTAATGCGTCGATGTGCACA 59.872 47.619 24.08 24.08 45.07 4.57
3244 3498 1.269102 ACCGATCGAGGAGTTAATGCG 60.269 52.381 18.66 0.00 34.73 4.73
3248 3502 2.928334 AGCTACCGATCGAGGAGTTAA 58.072 47.619 18.66 0.00 34.73 2.01
3249 3503 2.634815 AGCTACCGATCGAGGAGTTA 57.365 50.000 18.66 0.00 34.73 2.24
3356 3610 2.029828 ACACCGAAGATCACACAGAGAC 60.030 50.000 0.00 0.00 0.00 3.36
3360 3614 2.989840 GAGAACACCGAAGATCACACAG 59.010 50.000 0.00 0.00 0.00 3.66
3412 3666 8.629158 TGCAAATTATTTGTCTACAGAAACTGT 58.371 29.630 17.51 9.32 43.70 3.55
3413 3667 9.462174 TTGCAAATTATTTGTCTACAGAAACTG 57.538 29.630 17.51 0.00 42.56 3.16
3483 3738 3.967987 GTTGAGATAGAGGCCTTCCCTTA 59.032 47.826 6.77 0.00 46.60 2.69
3721 3978 3.128764 TGAGCTCGATATTCACTTCGTGT 59.871 43.478 9.64 0.00 36.74 4.49
3795 4052 4.095932 TCTTGTCTACTGCGATAACGTCAT 59.904 41.667 0.00 0.00 41.98 3.06
3856 4113 4.375272 CGAATGCTCTTGGATATGTCAGT 58.625 43.478 0.00 0.00 0.00 3.41
3956 4213 1.910580 TTGGGCCCTCGTTGATCTCC 61.911 60.000 25.70 0.00 0.00 3.71
4014 4271 4.790962 CGACTGGGCTGGCTGCAT 62.791 66.667 18.32 0.16 45.15 3.96
4089 4346 0.108089 TACATACGCGGCACCATGTT 60.108 50.000 12.47 0.00 33.78 2.71


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

AutoCloner maintained by Alex Coulton.