Multiple sequence alignment - TraesCS3A01G227300

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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 TraesCS3A01G227300 chr3A 100.000 3089 0 0 1 3089 425149519 425146431 0.000000e+00 5705
1 TraesCS3A01G227300 chr3A 100.000 93 0 0 3419 3511 425146101 425146009 4.660000e-39 172
2 TraesCS3A01G227300 chr3D 93.616 2945 121 38 1 2928 306264473 306261579 0.000000e+00 4335
3 TraesCS3A01G227300 chr3B 91.199 1977 102 30 1 1928 414826737 414828690 0.000000e+00 2621
4 TraesCS3A01G227300 chr3B 91.214 1013 55 20 1973 2962 414828692 414829693 0.000000e+00 1347
5 TraesCS3A01G227300 chr1A 95.699 93 4 0 3419 3511 356441073 356440981 2.180000e-32 150


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 TraesCS3A01G227300 chr3A 425146009 425149519 3510 True 2938.5 5705 100.0000 1 3511 2 chr3A.!!$R1 3510
1 TraesCS3A01G227300 chr3D 306261579 306264473 2894 True 4335.0 4335 93.6160 1 2928 1 chr3D.!!$R1 2927
2 TraesCS3A01G227300 chr3B 414826737 414829693 2956 False 1984.0 2621 91.2065 1 2962 2 chr3B.!!$F1 2961

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
946 952 0.037882 CATCCATCCATCGACCCTCG 60.038 60.0 0.0 0.0 42.10 4.63 F
1402 1437 0.037697 CCGTCTCGGTGATGAAACCA 60.038 55.0 0.0 0.0 42.73 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 2090 0.508641 CGCGTGAGAAGGAAACACAG 59.491 55.0 0.0 0.0 34.69 3.66 R
2720 2806 0.975040 CCCCACTAGAGCAGAGCAGT 60.975 60.0 0.0 0.0 0.00 4.40 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
79 80 5.416271 TGTCTACCGCCTTAATCTTTTCT 57.584 39.130 0.00 0.00 0.00 2.52
119 120 2.290960 GGAGTGGATTGGCTAACAACCT 60.291 50.000 0.00 0.00 42.94 3.50
242 243 0.182775 AAACGAAAGGTCAGGCTGGT 59.817 50.000 15.73 0.00 0.00 4.00
266 267 3.959535 TTGGAAATCAAAGGATGGTGC 57.040 42.857 0.00 0.00 32.92 5.01
278 279 1.542547 GGATGGTGCCCTACGTTATGG 60.543 57.143 0.00 0.00 0.00 2.74
284 285 3.433173 GGTGCCCTACGTTATGGATTTCT 60.433 47.826 0.00 0.00 0.00 2.52
288 289 4.511826 GCCCTACGTTATGGATTTCTCTTG 59.488 45.833 0.00 0.00 0.00 3.02
300 301 8.992835 ATGGATTTCTCTTGCTTTTTAATGTC 57.007 30.769 0.00 0.00 0.00 3.06
355 356 2.480416 CCTCTAGACAAAGCCGCTACTG 60.480 54.545 0.00 0.00 0.00 2.74
356 357 2.164624 CTCTAGACAAAGCCGCTACTGT 59.835 50.000 7.58 7.58 0.00 3.55
400 403 6.560253 ACTACAAAGATTAGTGCAACCAAG 57.440 37.500 0.00 0.00 37.80 3.61
406 409 3.994392 AGATTAGTGCAACCAAGTACGTG 59.006 43.478 0.00 1.33 37.80 4.49
416 419 2.025699 ACCAAGTACGTGGGCCAATTAT 60.026 45.455 28.15 5.26 43.56 1.28
525 531 0.320160 AACCTCGTACGAAACCCAGC 60.320 55.000 20.00 0.00 0.00 4.85
597 603 2.762360 GGAATGCGTCCGACATGAA 58.238 52.632 0.00 0.00 36.40 2.57
798 804 4.527944 CAAGTTTCCTCTTATTCCCTCCC 58.472 47.826 0.00 0.00 0.00 4.30
799 805 4.095616 AGTTTCCTCTTATTCCCTCCCT 57.904 45.455 0.00 0.00 0.00 4.20
800 806 4.041464 AGTTTCCTCTTATTCCCTCCCTC 58.959 47.826 0.00 0.00 0.00 4.30
801 807 2.797285 TCCTCTTATTCCCTCCCTCC 57.203 55.000 0.00 0.00 0.00 4.30
849 855 3.541632 GGAAGAAACCTATGATTCCGCA 58.458 45.455 0.00 0.00 30.90 5.69
944 950 1.130054 CCCATCCATCCATCGACCCT 61.130 60.000 0.00 0.00 0.00 4.34
945 951 0.322975 CCATCCATCCATCGACCCTC 59.677 60.000 0.00 0.00 0.00 4.30
946 952 0.037882 CATCCATCCATCGACCCTCG 60.038 60.000 0.00 0.00 42.10 4.63
998 1011 1.270907 TCTTGAGGGAGGAAGACAGC 58.729 55.000 0.00 0.00 0.00 4.40
1023 1036 1.356938 CTCGTTTTCTTAGGCCGTCC 58.643 55.000 0.00 0.00 0.00 4.79
1025 1038 1.070445 TCGTTTTCTTAGGCCGTCCAA 59.930 47.619 0.00 0.00 33.74 3.53
1045 1058 1.065126 ACTGCATTGCCTACCTTCTCC 60.065 52.381 6.12 0.00 0.00 3.71
1048 1061 1.475930 GCATTGCCTACCTTCTCCTCC 60.476 57.143 0.00 0.00 0.00 4.30
1059 1072 1.209261 CTTCTCCTCCTCCTTGCCTTC 59.791 57.143 0.00 0.00 0.00 3.46
1060 1073 0.415429 TCTCCTCCTCCTTGCCTTCT 59.585 55.000 0.00 0.00 0.00 2.85
1061 1074 0.540923 CTCCTCCTCCTTGCCTTCTG 59.459 60.000 0.00 0.00 0.00 3.02
1062 1075 1.077858 CCTCCTCCTTGCCTTCTGC 60.078 63.158 0.00 0.00 41.77 4.26
1081 1094 1.563435 CTGCTGCGGTGAGTTGTCTG 61.563 60.000 0.00 0.00 0.00 3.51
1082 1095 1.595382 GCTGCGGTGAGTTGTCTGT 60.595 57.895 0.00 0.00 0.00 3.41
1089 1102 2.540101 CGGTGAGTTGTCTGTTCTTGTC 59.460 50.000 0.00 0.00 0.00 3.18
1091 1104 2.540101 GTGAGTTGTCTGTTCTTGTCCG 59.460 50.000 0.00 0.00 0.00 4.79
1093 1106 3.195661 GAGTTGTCTGTTCTTGTCCGTT 58.804 45.455 0.00 0.00 0.00 4.44
1094 1107 3.195661 AGTTGTCTGTTCTTGTCCGTTC 58.804 45.455 0.00 0.00 0.00 3.95
1095 1108 3.118738 AGTTGTCTGTTCTTGTCCGTTCT 60.119 43.478 0.00 0.00 0.00 3.01
1096 1109 3.093717 TGTCTGTTCTTGTCCGTTCTC 57.906 47.619 0.00 0.00 0.00 2.87
1097 1110 2.223971 TGTCTGTTCTTGTCCGTTCTCC 60.224 50.000 0.00 0.00 0.00 3.71
1098 1111 1.000607 TCTGTTCTTGTCCGTTCTCCG 60.001 52.381 0.00 0.00 0.00 4.63
1099 1112 0.599204 TGTTCTTGTCCGTTCTCCGC 60.599 55.000 0.00 0.00 34.38 5.54
1100 1113 0.319641 GTTCTTGTCCGTTCTCCGCT 60.320 55.000 0.00 0.00 34.38 5.52
1103 1116 0.790814 CTTGTCCGTTCTCCGCTTTC 59.209 55.000 0.00 0.00 34.38 2.62
1104 1117 0.391597 TTGTCCGTTCTCCGCTTTCT 59.608 50.000 0.00 0.00 34.38 2.52
1105 1118 1.250328 TGTCCGTTCTCCGCTTTCTA 58.750 50.000 0.00 0.00 34.38 2.10
1106 1119 1.822990 TGTCCGTTCTCCGCTTTCTAT 59.177 47.619 0.00 0.00 34.38 1.98
1107 1120 2.232941 TGTCCGTTCTCCGCTTTCTATT 59.767 45.455 0.00 0.00 34.38 1.73
1108 1121 3.259902 GTCCGTTCTCCGCTTTCTATTT 58.740 45.455 0.00 0.00 34.38 1.40
1109 1122 3.306434 GTCCGTTCTCCGCTTTCTATTTC 59.694 47.826 0.00 0.00 34.38 2.17
1110 1123 2.608090 CCGTTCTCCGCTTTCTATTTCC 59.392 50.000 0.00 0.00 34.38 3.13
1111 1124 3.522553 CGTTCTCCGCTTTCTATTTCCT 58.477 45.455 0.00 0.00 0.00 3.36
1112 1125 3.552294 CGTTCTCCGCTTTCTATTTCCTC 59.448 47.826 0.00 0.00 0.00 3.71
1113 1126 4.504858 GTTCTCCGCTTTCTATTTCCTCA 58.495 43.478 0.00 0.00 0.00 3.86
1114 1127 4.819105 TCTCCGCTTTCTATTTCCTCAA 57.181 40.909 0.00 0.00 0.00 3.02
1115 1128 5.160607 TCTCCGCTTTCTATTTCCTCAAA 57.839 39.130 0.00 0.00 0.00 2.69
1116 1129 5.178797 TCTCCGCTTTCTATTTCCTCAAAG 58.821 41.667 0.00 0.00 0.00 2.77
1117 1130 5.046591 TCTCCGCTTTCTATTTCCTCAAAGA 60.047 40.000 0.00 0.00 0.00 2.52
1118 1131 5.745227 TCCGCTTTCTATTTCCTCAAAGAT 58.255 37.500 0.00 0.00 0.00 2.40
1119 1132 5.817816 TCCGCTTTCTATTTCCTCAAAGATC 59.182 40.000 0.00 0.00 0.00 2.75
1120 1133 5.819901 CCGCTTTCTATTTCCTCAAAGATCT 59.180 40.000 0.00 0.00 0.00 2.75
1121 1134 6.238320 CCGCTTTCTATTTCCTCAAAGATCTG 60.238 42.308 0.00 0.00 0.00 2.90
1122 1135 6.314896 CGCTTTCTATTTCCTCAAAGATCTGT 59.685 38.462 0.00 0.00 0.00 3.41
1123 1136 7.148340 CGCTTTCTATTTCCTCAAAGATCTGTT 60.148 37.037 0.00 0.00 0.00 3.16
1130 1143 3.565482 TCCTCAAAGATCTGTTTGTGTGC 59.435 43.478 0.00 0.00 38.38 4.57
1144 1157 2.276201 TGTGTGCGCATTAGGTATGAC 58.724 47.619 15.91 0.00 36.26 3.06
1181 1216 4.410743 GCGAAAGGCTGTGCTGGC 62.411 66.667 0.00 0.00 39.11 4.85
1214 1249 1.754803 CCAAATCTGGATGCTGCATGT 59.245 47.619 21.53 0.00 46.92 3.21
1245 1280 1.880027 GTGCATCCACGGAAAGAAAGT 59.120 47.619 0.00 0.00 31.34 2.66
1289 1324 5.222631 ACATTTCGCAAATCTTTTCACCTC 58.777 37.500 0.00 0.00 0.00 3.85
1309 1344 5.064834 ACCTCACACGTTTCTTCTTCTTTTC 59.935 40.000 0.00 0.00 0.00 2.29
1339 1374 1.423395 GAACAGAACAGCGGAGAGTG 58.577 55.000 0.00 0.00 0.00 3.51
1402 1437 0.037697 CCGTCTCGGTGATGAAACCA 60.038 55.000 0.00 0.00 42.73 3.67
1444 1479 1.141881 CACTTCCGCATCCTACGCT 59.858 57.895 0.00 0.00 0.00 5.07
1562 1627 3.069946 CCGGCGGTGGTGGTACTA 61.070 66.667 19.97 0.00 0.00 1.82
1768 1833 4.874977 GGCGTAGACTGCTCGGCC 62.875 72.222 0.00 0.00 42.65 6.13
1780 1845 2.284625 TCGGCCATCCAGACAGGT 60.285 61.111 2.24 0.00 39.02 4.00
1930 1995 2.989840 CAGTAAGCTCAACGTCTCCAAG 59.010 50.000 0.00 0.00 0.00 3.61
1937 2002 1.660575 AACGTCTCCAAGACACGCG 60.661 57.895 3.53 3.53 45.30 6.01
1938 2003 2.050351 CGTCTCCAAGACACGCGT 60.050 61.111 5.58 5.58 45.30 6.01
1939 2004 1.208358 CGTCTCCAAGACACGCGTA 59.792 57.895 13.44 0.00 45.30 4.42
1940 2005 1.063951 CGTCTCCAAGACACGCGTAC 61.064 60.000 13.44 9.70 45.30 3.67
1941 2006 0.039798 GTCTCCAAGACACGCGTACA 60.040 55.000 13.44 0.00 44.45 2.90
1942 2007 0.885879 TCTCCAAGACACGCGTACAT 59.114 50.000 13.44 0.00 0.00 2.29
1943 2008 0.992072 CTCCAAGACACGCGTACATG 59.008 55.000 13.44 12.37 0.00 3.21
1944 2009 0.599060 TCCAAGACACGCGTACATGA 59.401 50.000 13.44 0.87 0.00 3.07
1945 2010 1.203758 TCCAAGACACGCGTACATGAT 59.796 47.619 13.44 0.00 0.00 2.45
1946 2011 1.324435 CCAAGACACGCGTACATGATG 59.676 52.381 13.44 6.69 0.00 3.07
1965 2030 7.396907 ACATGATGATACATTTCTTCCCAAACA 59.603 33.333 0.00 0.00 0.00 2.83
1974 2039 5.982890 TTTCTTCCCAAACATTCTCATCC 57.017 39.130 0.00 0.00 0.00 3.51
1982 2047 5.945784 CCCAAACATTCTCATCCTTGAACTA 59.054 40.000 0.00 0.00 0.00 2.24
2015 2080 4.410099 TGGCAGAATCTTTCCAACTGAAT 58.590 39.130 0.00 0.00 31.67 2.57
2034 2101 1.408969 TTTTCAGCCCCTGTGTTTCC 58.591 50.000 0.00 0.00 32.61 3.13
2047 2114 1.070776 GTGTTTCCTTCTCACGCGAAC 60.071 52.381 15.93 3.51 0.00 3.95
2102 2169 4.250464 CAGTATCCAGCGTCAAGGTAAAA 58.750 43.478 0.00 0.00 0.00 1.52
2103 2170 4.693566 CAGTATCCAGCGTCAAGGTAAAAA 59.306 41.667 0.00 0.00 0.00 1.94
2354 2440 0.604073 TGTACGGATCAAACTCGCCA 59.396 50.000 0.00 0.00 0.00 5.69
2636 2722 3.659092 CTGCCGCGAAACCTTGCA 61.659 61.111 8.23 5.60 0.00 4.08
2637 2723 3.879351 CTGCCGCGAAACCTTGCAC 62.879 63.158 8.23 0.00 0.00 4.57
2638 2724 3.959975 GCCGCGAAACCTTGCACA 61.960 61.111 8.23 0.00 0.00 4.57
2720 2806 2.181777 CTGCTTCTAGCGTCGCCA 59.818 61.111 14.86 0.00 46.26 5.69
2758 2844 4.301072 GGGGGCAGCAGATGTTTATATA 57.699 45.455 0.00 0.00 0.00 0.86
2824 2913 8.773645 TCATTTCCTTATTTACGCTGTGATATG 58.226 33.333 0.00 0.00 0.00 1.78
2879 2968 6.202226 GTGTTTCACTTTGAGGAATCTTGAC 58.798 40.000 0.00 0.00 0.00 3.18
2917 3006 4.522722 AAAGTGAACCAAACGTCCAAAA 57.477 36.364 0.00 0.00 0.00 2.44
2924 3013 1.399089 CCAAACGTCCAAAACACGACT 59.601 47.619 0.00 0.00 39.75 4.18
2935 3024 7.517101 CGTCCAAAACACGACTCAAAATAACTA 60.517 37.037 0.00 0.00 39.75 2.24
2936 3025 8.287503 GTCCAAAACACGACTCAAAATAACTAT 58.712 33.333 0.00 0.00 0.00 2.12
2943 3032 6.019801 CACGACTCAAAATAACTATTCCCTCG 60.020 42.308 0.00 0.00 0.00 4.63
2950 3039 6.704056 AAATAACTATTCCCTCGATCCCAT 57.296 37.500 0.00 0.00 0.00 4.00
2958 3047 9.148879 ACTATTCCCTCGATCCCATAATATAAG 57.851 37.037 0.00 0.00 0.00 1.73
2962 3051 7.132805 TCCCTCGATCCCATAATATAAGACAT 58.867 38.462 0.00 0.00 0.00 3.06
2963 3052 7.623677 TCCCTCGATCCCATAATATAAGACATT 59.376 37.037 0.00 0.00 0.00 2.71
2964 3053 8.924303 CCCTCGATCCCATAATATAAGACATTA 58.076 37.037 0.00 0.00 0.00 1.90
3024 3113 5.712152 AAAGAGTTGCTCAGTTAATTGGG 57.288 39.130 0.00 0.00 32.06 4.12
3025 3114 4.640771 AGAGTTGCTCAGTTAATTGGGA 57.359 40.909 1.33 0.00 32.06 4.37
3026 3115 4.985538 AGAGTTGCTCAGTTAATTGGGAA 58.014 39.130 1.33 0.00 32.06 3.97
3027 3116 5.385198 AGAGTTGCTCAGTTAATTGGGAAA 58.615 37.500 1.33 0.00 32.06 3.13
3028 3117 5.833131 AGAGTTGCTCAGTTAATTGGGAAAA 59.167 36.000 1.33 0.00 32.06 2.29
3029 3118 6.323739 AGAGTTGCTCAGTTAATTGGGAAAAA 59.676 34.615 1.33 0.00 32.06 1.94
3030 3119 6.280643 AGTTGCTCAGTTAATTGGGAAAAAC 58.719 36.000 1.33 3.24 0.00 2.43
3031 3120 5.208463 TGCTCAGTTAATTGGGAAAAACC 57.792 39.130 1.33 0.00 38.08 3.27
3032 3121 4.234574 GCTCAGTTAATTGGGAAAAACCG 58.765 43.478 1.33 0.00 40.11 4.44
3033 3122 4.022676 GCTCAGTTAATTGGGAAAAACCGA 60.023 41.667 1.33 0.00 40.11 4.69
3034 3123 5.441709 TCAGTTAATTGGGAAAAACCGAC 57.558 39.130 0.00 0.00 40.11 4.79
3035 3124 4.278919 TCAGTTAATTGGGAAAAACCGACC 59.721 41.667 0.00 0.00 40.11 4.79
3036 3125 3.253921 AGTTAATTGGGAAAAACCGACCG 59.746 43.478 0.00 0.00 40.11 4.79
3037 3126 1.984066 AATTGGGAAAAACCGACCGA 58.016 45.000 0.00 0.00 40.11 4.69
3038 3127 1.984066 ATTGGGAAAAACCGACCGAA 58.016 45.000 0.00 0.00 40.11 4.30
3039 3128 1.760192 TTGGGAAAAACCGACCGAAA 58.240 45.000 0.00 0.00 40.11 3.46
3040 3129 1.760192 TGGGAAAAACCGACCGAAAA 58.240 45.000 0.00 0.00 40.11 2.29
3041 3130 1.404748 TGGGAAAAACCGACCGAAAAC 59.595 47.619 0.00 0.00 40.11 2.43
3042 3131 1.269206 GGGAAAAACCGACCGAAAACC 60.269 52.381 0.00 0.00 40.11 3.27
3043 3132 1.404748 GGAAAAACCGACCGAAAACCA 59.595 47.619 0.00 0.00 0.00 3.67
3044 3133 2.542205 GGAAAAACCGACCGAAAACCAG 60.542 50.000 0.00 0.00 0.00 4.00
3045 3134 2.041251 AAAACCGACCGAAAACCAGA 57.959 45.000 0.00 0.00 0.00 3.86
3046 3135 2.265589 AAACCGACCGAAAACCAGAT 57.734 45.000 0.00 0.00 0.00 2.90
3047 3136 2.265589 AACCGACCGAAAACCAGATT 57.734 45.000 0.00 0.00 0.00 2.40
3048 3137 3.405823 AACCGACCGAAAACCAGATTA 57.594 42.857 0.00 0.00 0.00 1.75
3049 3138 2.691927 ACCGACCGAAAACCAGATTAC 58.308 47.619 0.00 0.00 0.00 1.89
3050 3139 2.004733 CCGACCGAAAACCAGATTACC 58.995 52.381 0.00 0.00 0.00 2.85
3051 3140 2.354403 CCGACCGAAAACCAGATTACCT 60.354 50.000 0.00 0.00 0.00 3.08
3052 3141 3.119029 CCGACCGAAAACCAGATTACCTA 60.119 47.826 0.00 0.00 0.00 3.08
3053 3142 4.110482 CGACCGAAAACCAGATTACCTAG 58.890 47.826 0.00 0.00 0.00 3.02
3054 3143 4.381292 CGACCGAAAACCAGATTACCTAGT 60.381 45.833 0.00 0.00 0.00 2.57
3055 3144 5.485620 GACCGAAAACCAGATTACCTAGTT 58.514 41.667 0.00 0.00 0.00 2.24
3056 3145 6.610075 ACCGAAAACCAGATTACCTAGTTA 57.390 37.500 0.00 0.00 0.00 2.24
3057 3146 7.008021 ACCGAAAACCAGATTACCTAGTTAA 57.992 36.000 0.00 0.00 0.00 2.01
3058 3147 7.627311 ACCGAAAACCAGATTACCTAGTTAAT 58.373 34.615 0.00 0.00 0.00 1.40
3059 3148 8.105197 ACCGAAAACCAGATTACCTAGTTAATT 58.895 33.333 0.00 0.00 0.00 1.40
3060 3149 9.603921 CCGAAAACCAGATTACCTAGTTAATTA 57.396 33.333 0.00 0.00 0.00 1.40
3073 3162 7.054751 ACCTAGTTAATTATGAAGGACCAAGC 58.945 38.462 12.18 0.00 0.00 4.01
3074 3163 6.202954 CCTAGTTAATTATGAAGGACCAAGCG 59.797 42.308 0.00 0.00 0.00 4.68
3075 3164 5.741011 AGTTAATTATGAAGGACCAAGCGA 58.259 37.500 0.00 0.00 0.00 4.93
3076 3165 6.177610 AGTTAATTATGAAGGACCAAGCGAA 58.822 36.000 0.00 0.00 0.00 4.70
3077 3166 6.657541 AGTTAATTATGAAGGACCAAGCGAAA 59.342 34.615 0.00 0.00 0.00 3.46
3078 3167 5.975693 AATTATGAAGGACCAAGCGAAAA 57.024 34.783 0.00 0.00 0.00 2.29
3079 3168 4.759516 TTATGAAGGACCAAGCGAAAAC 57.240 40.909 0.00 0.00 0.00 2.43
3080 3169 2.341846 TGAAGGACCAAGCGAAAACT 57.658 45.000 0.00 0.00 0.00 2.66
3081 3170 3.478857 TGAAGGACCAAGCGAAAACTA 57.521 42.857 0.00 0.00 0.00 2.24
3082 3171 4.015872 TGAAGGACCAAGCGAAAACTAT 57.984 40.909 0.00 0.00 0.00 2.12
3083 3172 4.000988 TGAAGGACCAAGCGAAAACTATC 58.999 43.478 0.00 0.00 0.00 2.08
3084 3173 3.695830 AGGACCAAGCGAAAACTATCA 57.304 42.857 0.00 0.00 0.00 2.15
3085 3174 3.335579 AGGACCAAGCGAAAACTATCAC 58.664 45.455 0.00 0.00 0.00 3.06
3086 3175 3.071479 GGACCAAGCGAAAACTATCACA 58.929 45.455 0.00 0.00 0.00 3.58
3087 3176 3.125316 GGACCAAGCGAAAACTATCACAG 59.875 47.826 0.00 0.00 0.00 3.66
3088 3177 2.484264 ACCAAGCGAAAACTATCACAGC 59.516 45.455 0.00 0.00 0.00 4.40
3436 3525 3.863942 CGTCGAGACAACATGCATG 57.136 52.632 25.09 25.09 0.00 4.06
3437 3526 1.070821 CGTCGAGACAACATGCATGT 58.929 50.000 26.61 26.61 44.20 3.21
3438 3527 1.201845 CGTCGAGACAACATGCATGTG 60.202 52.381 31.98 25.28 41.61 3.21
3439 3528 1.800586 GTCGAGACAACATGCATGTGT 59.199 47.619 31.98 27.94 41.61 3.72
3440 3529 2.068519 TCGAGACAACATGCATGTGTC 58.931 47.619 32.60 32.60 41.61 3.67
3441 3530 1.799994 CGAGACAACATGCATGTGTCA 59.200 47.619 36.27 3.18 40.13 3.58
3442 3531 2.417586 CGAGACAACATGCATGTGTCAT 59.582 45.455 36.27 28.27 40.13 3.06
3443 3532 3.484721 CGAGACAACATGCATGTGTCATC 60.485 47.826 36.27 30.67 40.13 2.92
3444 3533 2.417586 AGACAACATGCATGTGTCATCG 59.582 45.455 36.27 24.04 41.61 3.84
3445 3534 1.135603 ACAACATGCATGTGTCATCGC 60.136 47.619 31.98 0.00 41.61 4.58
3446 3535 0.452987 AACATGCATGTGTCATCGCC 59.547 50.000 31.98 0.00 41.61 5.54
3447 3536 0.677414 ACATGCATGTGTCATCGCCA 60.677 50.000 30.92 0.00 40.03 5.69
3448 3537 0.666374 CATGCATGTGTCATCGCCAT 59.334 50.000 18.91 0.00 0.00 4.40
3449 3538 0.949397 ATGCATGTGTCATCGCCATC 59.051 50.000 0.00 0.00 0.00 3.51
3450 3539 0.392729 TGCATGTGTCATCGCCATCA 60.393 50.000 0.00 0.00 0.00 3.07
3451 3540 0.028505 GCATGTGTCATCGCCATCAC 59.971 55.000 0.00 0.00 0.00 3.06
3452 3541 1.660167 CATGTGTCATCGCCATCACT 58.340 50.000 0.00 0.00 0.00 3.41
3453 3542 1.596260 CATGTGTCATCGCCATCACTC 59.404 52.381 0.00 0.00 0.00 3.51
3454 3543 0.108186 TGTGTCATCGCCATCACTCC 60.108 55.000 0.00 0.00 0.00 3.85
3455 3544 0.176680 GTGTCATCGCCATCACTCCT 59.823 55.000 0.00 0.00 0.00 3.69
3456 3545 0.461548 TGTCATCGCCATCACTCCTC 59.538 55.000 0.00 0.00 0.00 3.71
3457 3546 0.249657 GTCATCGCCATCACTCCTCC 60.250 60.000 0.00 0.00 0.00 4.30
3458 3547 1.070445 CATCGCCATCACTCCTCCC 59.930 63.158 0.00 0.00 0.00 4.30
3459 3548 2.143419 ATCGCCATCACTCCTCCCC 61.143 63.158 0.00 0.00 0.00 4.81
3460 3549 2.611964 ATCGCCATCACTCCTCCCCT 62.612 60.000 0.00 0.00 0.00 4.79
3461 3550 1.457643 CGCCATCACTCCTCCCCTA 60.458 63.158 0.00 0.00 0.00 3.53
3462 3551 1.048724 CGCCATCACTCCTCCCCTAA 61.049 60.000 0.00 0.00 0.00 2.69
3463 3552 1.213296 GCCATCACTCCTCCCCTAAA 58.787 55.000 0.00 0.00 0.00 1.85
3464 3553 1.564348 GCCATCACTCCTCCCCTAAAA 59.436 52.381 0.00 0.00 0.00 1.52
3465 3554 2.422093 GCCATCACTCCTCCCCTAAAAG 60.422 54.545 0.00 0.00 0.00 2.27
3466 3555 2.422093 CCATCACTCCTCCCCTAAAAGC 60.422 54.545 0.00 0.00 0.00 3.51
3467 3556 0.902531 TCACTCCTCCCCTAAAAGCG 59.097 55.000 0.00 0.00 0.00 4.68
3468 3557 0.613777 CACTCCTCCCCTAAAAGCGT 59.386 55.000 0.00 0.00 0.00 5.07
3469 3558 0.903236 ACTCCTCCCCTAAAAGCGTC 59.097 55.000 0.00 0.00 0.00 5.19
3470 3559 0.902531 CTCCTCCCCTAAAAGCGTCA 59.097 55.000 0.00 0.00 0.00 4.35
3471 3560 1.486726 CTCCTCCCCTAAAAGCGTCAT 59.513 52.381 0.00 0.00 0.00 3.06
3472 3561 1.485066 TCCTCCCCTAAAAGCGTCATC 59.515 52.381 0.00 0.00 0.00 2.92
3473 3562 1.571919 CTCCCCTAAAAGCGTCATCG 58.428 55.000 0.00 0.00 40.37 3.84
3486 3575 1.257936 CGTCATCGCCATCCTTAAACG 59.742 52.381 0.00 0.00 0.00 3.60
3487 3576 2.277084 GTCATCGCCATCCTTAAACGT 58.723 47.619 0.00 0.00 0.00 3.99
3488 3577 2.676342 GTCATCGCCATCCTTAAACGTT 59.324 45.455 0.00 0.00 0.00 3.99
3489 3578 2.675844 TCATCGCCATCCTTAAACGTTG 59.324 45.455 0.00 0.00 0.00 4.10
3490 3579 2.459060 TCGCCATCCTTAAACGTTGA 57.541 45.000 0.00 0.00 0.00 3.18
3491 3580 2.343101 TCGCCATCCTTAAACGTTGAG 58.657 47.619 0.00 3.05 0.00 3.02
3492 3581 2.028839 TCGCCATCCTTAAACGTTGAGA 60.029 45.455 0.00 0.00 0.00 3.27
3493 3582 2.739913 CGCCATCCTTAAACGTTGAGAA 59.260 45.455 0.00 0.00 0.00 2.87
3494 3583 3.424433 CGCCATCCTTAAACGTTGAGAAC 60.424 47.826 0.00 0.00 0.00 3.01
3495 3584 3.500680 GCCATCCTTAAACGTTGAGAACA 59.499 43.478 0.00 0.00 0.00 3.18
3496 3585 4.612939 GCCATCCTTAAACGTTGAGAACAC 60.613 45.833 0.00 0.00 0.00 3.32
3497 3586 4.377022 CCATCCTTAAACGTTGAGAACACG 60.377 45.833 0.00 0.00 0.00 4.49
3498 3587 4.044336 TCCTTAAACGTTGAGAACACGA 57.956 40.909 0.00 0.00 0.00 4.35
3499 3588 3.798337 TCCTTAAACGTTGAGAACACGAC 59.202 43.478 0.00 0.00 0.00 4.34
3500 3589 3.800506 CCTTAAACGTTGAGAACACGACT 59.199 43.478 0.00 0.00 0.00 4.18
3501 3590 4.085210 CCTTAAACGTTGAGAACACGACTC 60.085 45.833 0.00 0.00 35.26 3.36
3502 3591 1.849097 AACGTTGAGAACACGACTCC 58.151 50.000 0.00 0.00 33.95 3.85
3503 3592 0.317603 ACGTTGAGAACACGACTCCG 60.318 55.000 0.00 0.00 42.50 4.63
3504 3593 0.040692 CGTTGAGAACACGACTCCGA 60.041 55.000 0.00 0.00 39.50 4.55
3505 3594 1.406447 GTTGAGAACACGACTCCGAC 58.594 55.000 0.00 0.00 39.50 4.79
3506 3595 1.001597 GTTGAGAACACGACTCCGACT 60.002 52.381 0.00 0.00 39.50 4.18
3507 3596 1.315690 TGAGAACACGACTCCGACTT 58.684 50.000 0.00 0.00 39.50 3.01
3508 3597 1.266175 TGAGAACACGACTCCGACTTC 59.734 52.381 0.00 0.00 39.50 3.01
3509 3598 0.237761 AGAACACGACTCCGACTTCG 59.762 55.000 0.00 0.00 41.14 3.79
3510 3599 1.335697 GAACACGACTCCGACTTCGC 61.336 60.000 0.00 0.00 38.88 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 80 6.001460 CACTCCTTCACACCATAAAAAGGTA 58.999 40.000 0.00 0.00 37.23 3.08
119 120 7.280356 AGTTGTGCTCTAACTTCTTTCCTTTA 58.720 34.615 0.00 0.00 34.91 1.85
227 228 3.193479 CCAATAAACCAGCCTGACCTTTC 59.807 47.826 0.00 0.00 0.00 2.62
242 243 6.405538 GCACCATCCTTTGATTTCCAATAAA 58.594 36.000 0.00 0.00 34.23 1.40
266 267 4.511826 GCAAGAGAAATCCATAACGTAGGG 59.488 45.833 0.00 0.00 0.00 3.53
278 279 8.084684 AGTGGACATTAAAAAGCAAGAGAAATC 58.915 33.333 0.00 0.00 0.00 2.17
288 289 8.682710 TGGTGATTATAGTGGACATTAAAAAGC 58.317 33.333 0.00 0.00 0.00 3.51
298 299 8.450578 TGATCAAAATGGTGATTATAGTGGAC 57.549 34.615 0.00 0.00 38.38 4.02
388 391 1.270412 CCCACGTACTTGGTTGCACTA 60.270 52.381 16.54 0.00 34.44 2.74
390 393 1.946267 CCCACGTACTTGGTTGCAC 59.054 57.895 16.54 0.00 34.44 4.57
400 403 2.335316 TGGATAATTGGCCCACGTAC 57.665 50.000 0.00 0.00 0.00 3.67
406 409 3.575805 TGGATCTTTGGATAATTGGCCC 58.424 45.455 0.00 0.00 31.46 5.80
459 465 2.852449 AGGATTGGTAGGAAATGGCTGA 59.148 45.455 0.00 0.00 0.00 4.26
484 490 6.429078 GGTTCCAGTATATTAACCGGATTTCC 59.571 42.308 9.46 0.00 32.69 3.13
525 531 3.684103 TGGCTTTGCGGTTTTATATCG 57.316 42.857 0.00 0.00 0.00 2.92
597 603 6.842676 AGTACTTTGGAGGTGAAAGAATTCT 58.157 36.000 0.88 0.88 36.48 2.40
849 855 5.179368 GTGCATATATACCTGACGCAATGTT 59.821 40.000 0.00 0.00 0.00 2.71
944 950 4.388499 GCTCCCGAACAAGCCCGA 62.388 66.667 0.00 0.00 32.22 5.14
945 951 4.697756 TGCTCCCGAACAAGCCCG 62.698 66.667 0.00 0.00 37.73 6.13
946 952 2.747855 CTGCTCCCGAACAAGCCC 60.748 66.667 0.00 0.00 37.73 5.19
998 1011 1.401905 GCCTAAGAAAACGAGCCATGG 59.598 52.381 7.63 7.63 0.00 3.66
1023 1036 2.421424 GAGAAGGTAGGCAATGCAGTTG 59.579 50.000 7.79 0.00 40.90 3.16
1025 1038 1.065126 GGAGAAGGTAGGCAATGCAGT 60.065 52.381 7.79 0.00 0.00 4.40
1045 1058 4.633769 GCAGAAGGCAAGGAGGAG 57.366 61.111 0.00 0.00 43.97 3.69
1059 1072 2.667536 AACTCACCGCAGCAGCAG 60.668 61.111 0.82 0.00 42.27 4.24
1060 1073 2.974148 CAACTCACCGCAGCAGCA 60.974 61.111 0.82 0.00 42.27 4.41
1061 1074 2.959357 GACAACTCACCGCAGCAGC 61.959 63.158 0.00 0.00 37.42 5.25
1062 1075 1.301244 AGACAACTCACCGCAGCAG 60.301 57.895 0.00 0.00 0.00 4.24
1081 1094 0.319641 AGCGGAGAACGGACAAGAAC 60.320 55.000 0.00 0.00 44.51 3.01
1082 1095 0.391597 AAGCGGAGAACGGACAAGAA 59.608 50.000 0.00 0.00 44.51 2.52
1089 1102 2.608090 GGAAATAGAAAGCGGAGAACGG 59.392 50.000 0.00 0.00 44.51 4.44
1091 1104 4.504858 TGAGGAAATAGAAAGCGGAGAAC 58.495 43.478 0.00 0.00 0.00 3.01
1093 1106 4.819105 TTGAGGAAATAGAAAGCGGAGA 57.181 40.909 0.00 0.00 0.00 3.71
1094 1107 5.178797 TCTTTGAGGAAATAGAAAGCGGAG 58.821 41.667 0.00 0.00 0.00 4.63
1095 1108 5.160607 TCTTTGAGGAAATAGAAAGCGGA 57.839 39.130 0.00 0.00 0.00 5.54
1096 1109 5.819901 AGATCTTTGAGGAAATAGAAAGCGG 59.180 40.000 0.00 0.00 0.00 5.52
1097 1110 6.314896 ACAGATCTTTGAGGAAATAGAAAGCG 59.685 38.462 0.00 0.00 0.00 4.68
1098 1111 7.622893 ACAGATCTTTGAGGAAATAGAAAGC 57.377 36.000 0.00 0.00 0.00 3.51
1099 1112 9.837525 CAAACAGATCTTTGAGGAAATAGAAAG 57.162 33.333 1.49 0.00 33.61 2.62
1100 1113 9.354673 ACAAACAGATCTTTGAGGAAATAGAAA 57.645 29.630 12.99 0.00 35.46 2.52
1103 1116 8.019669 CACACAAACAGATCTTTGAGGAAATAG 58.980 37.037 12.99 0.00 35.46 1.73
1104 1117 7.522073 GCACACAAACAGATCTTTGAGGAAATA 60.522 37.037 12.99 0.00 35.46 1.40
1105 1118 6.736794 GCACACAAACAGATCTTTGAGGAAAT 60.737 38.462 12.99 0.00 35.46 2.17
1106 1119 5.450412 GCACACAAACAGATCTTTGAGGAAA 60.450 40.000 12.99 0.00 35.46 3.13
1107 1120 4.036734 GCACACAAACAGATCTTTGAGGAA 59.963 41.667 12.99 0.00 35.46 3.36
1108 1121 3.565482 GCACACAAACAGATCTTTGAGGA 59.435 43.478 12.99 0.00 35.46 3.71
1109 1122 3.607775 CGCACACAAACAGATCTTTGAGG 60.608 47.826 12.99 7.70 35.46 3.86
1110 1123 3.548587 CGCACACAAACAGATCTTTGAG 58.451 45.455 12.99 8.22 35.46 3.02
1111 1124 2.286950 GCGCACACAAACAGATCTTTGA 60.287 45.455 12.99 0.00 35.46 2.69
1112 1125 2.046313 GCGCACACAAACAGATCTTTG 58.954 47.619 0.30 5.73 37.20 2.77
1113 1126 1.675483 TGCGCACACAAACAGATCTTT 59.325 42.857 5.66 0.00 0.00 2.52
1114 1127 1.308047 TGCGCACACAAACAGATCTT 58.692 45.000 5.66 0.00 0.00 2.40
1115 1128 1.527034 ATGCGCACACAAACAGATCT 58.473 45.000 14.90 0.00 0.00 2.75
1116 1129 2.336554 AATGCGCACACAAACAGATC 57.663 45.000 14.90 0.00 0.00 2.75
1117 1130 2.162208 CCTAATGCGCACACAAACAGAT 59.838 45.455 14.90 0.00 0.00 2.90
1118 1131 1.535028 CCTAATGCGCACACAAACAGA 59.465 47.619 14.90 0.00 0.00 3.41
1119 1132 1.266718 ACCTAATGCGCACACAAACAG 59.733 47.619 14.90 1.82 0.00 3.16
1120 1133 1.313772 ACCTAATGCGCACACAAACA 58.686 45.000 14.90 0.00 0.00 2.83
1121 1134 3.126171 TCATACCTAATGCGCACACAAAC 59.874 43.478 14.90 0.00 35.38 2.93
1122 1135 3.126171 GTCATACCTAATGCGCACACAAA 59.874 43.478 14.90 0.00 35.38 2.83
1123 1136 2.675844 GTCATACCTAATGCGCACACAA 59.324 45.455 14.90 0.00 35.38 3.33
1130 1143 4.620982 TCTGTCATGTCATACCTAATGCG 58.379 43.478 0.00 0.00 35.38 4.73
1144 1157 3.668757 CGCACCAAAACATCTCTGTCATG 60.669 47.826 0.00 0.00 33.36 3.07
1181 1216 4.022416 TCCAGATTTGGGTTCGTTCAAATG 60.022 41.667 1.81 0.00 45.10 2.32
1214 1249 2.419990 CGTGGATGCACTCCCAATTCTA 60.420 50.000 15.82 0.00 44.23 2.10
1289 1324 5.909610 GGATGAAAAGAAGAAGAAACGTGTG 59.090 40.000 0.00 0.00 0.00 3.82
1309 1344 1.271543 TGTTCTGTTCCTGCAGGGATG 60.272 52.381 32.23 20.13 44.66 3.51
1325 1360 1.016653 GCTTCCACTCTCCGCTGTTC 61.017 60.000 0.00 0.00 0.00 3.18
1339 1374 0.036388 TGAGTCGGTTGGATGCTTCC 60.036 55.000 11.69 11.69 42.94 3.46
1444 1479 3.536917 CTGGAGGACGCCGGCATA 61.537 66.667 28.98 0.00 0.00 3.14
1768 1833 1.222936 GCTCCCACCTGTCTGGATG 59.777 63.158 2.23 0.00 39.71 3.51
1780 1845 2.436109 GGGTTGAAGCAGCTCCCA 59.564 61.111 11.39 2.99 38.15 4.37
1930 1995 3.368495 TGTATCATCATGTACGCGTGTC 58.632 45.455 24.59 15.41 33.51 3.67
1937 2002 8.450578 TTGGGAAGAAATGTATCATCATGTAC 57.549 34.615 0.00 0.00 0.00 2.90
1938 2003 8.902806 GTTTGGGAAGAAATGTATCATCATGTA 58.097 33.333 0.00 0.00 0.00 2.29
1939 2004 7.396907 TGTTTGGGAAGAAATGTATCATCATGT 59.603 33.333 0.00 0.00 0.00 3.21
1940 2005 7.774134 TGTTTGGGAAGAAATGTATCATCATG 58.226 34.615 0.00 0.00 0.00 3.07
1941 2006 7.959658 TGTTTGGGAAGAAATGTATCATCAT 57.040 32.000 0.00 0.00 0.00 2.45
1942 2007 7.959658 ATGTTTGGGAAGAAATGTATCATCA 57.040 32.000 0.00 0.00 0.00 3.07
1943 2008 8.689972 AGAATGTTTGGGAAGAAATGTATCATC 58.310 33.333 0.00 0.00 0.00 2.92
1944 2009 8.599624 AGAATGTTTGGGAAGAAATGTATCAT 57.400 30.769 0.00 0.00 0.00 2.45
1945 2010 7.669304 TGAGAATGTTTGGGAAGAAATGTATCA 59.331 33.333 0.00 0.00 0.00 2.15
1946 2011 8.055279 TGAGAATGTTTGGGAAGAAATGTATC 57.945 34.615 0.00 0.00 0.00 2.24
1965 2030 4.681781 CGGCTGTAGTTCAAGGATGAGAAT 60.682 45.833 0.00 0.00 36.78 2.40
1974 2039 2.031157 CCAAAACCGGCTGTAGTTCAAG 60.031 50.000 0.00 0.00 0.00 3.02
2015 2080 1.063266 AGGAAACACAGGGGCTGAAAA 60.063 47.619 0.00 0.00 35.18 2.29
2025 2090 0.508641 CGCGTGAGAAGGAAACACAG 59.491 55.000 0.00 0.00 34.69 3.66
2029 2096 1.499049 AGTTCGCGTGAGAAGGAAAC 58.501 50.000 5.77 0.00 0.00 2.78
2047 2114 4.215399 TGAACCTGCAAAGGTCGAAATAAG 59.785 41.667 0.00 0.00 42.20 1.73
2102 2169 9.449719 CAGTTGGTTATTCATTAGTAGGAACTT 57.550 33.333 0.00 0.00 41.75 2.66
2103 2170 8.822805 TCAGTTGGTTATTCATTAGTAGGAACT 58.177 33.333 0.00 0.00 46.37 3.01
2523 2609 3.583806 CATAGGATTGCCATCTCGAGAC 58.416 50.000 19.30 5.87 36.29 3.36
2528 2614 1.811359 GCTGCATAGGATTGCCATCTC 59.189 52.381 0.00 0.00 42.06 2.75
2720 2806 0.975040 CCCCACTAGAGCAGAGCAGT 60.975 60.000 0.00 0.00 0.00 4.40
2824 2913 3.704231 ATCATGGTCAGCGGGCCAC 62.704 63.158 13.86 0.00 37.62 5.01
2898 2987 2.820787 TGTTTTGGACGTTTGGTTCACT 59.179 40.909 0.00 0.00 32.45 3.41
2917 3006 6.708285 AGGGAATAGTTATTTTGAGTCGTGT 58.292 36.000 0.00 0.00 0.00 4.49
2924 3013 6.100569 TGGGATCGAGGGAATAGTTATTTTGA 59.899 38.462 0.00 0.00 0.00 2.69
2935 3024 7.623677 TGTCTTATATTATGGGATCGAGGGAAT 59.376 37.037 0.00 0.00 0.00 3.01
2936 3025 6.957606 TGTCTTATATTATGGGATCGAGGGAA 59.042 38.462 0.00 0.00 0.00 3.97
3000 3089 6.323739 TCCCAATTAACTGAGCAACTCTTTTT 59.676 34.615 0.00 0.00 0.00 1.94
3001 3090 5.833131 TCCCAATTAACTGAGCAACTCTTTT 59.167 36.000 0.00 0.00 0.00 2.27
3002 3091 5.385198 TCCCAATTAACTGAGCAACTCTTT 58.615 37.500 0.00 0.00 0.00 2.52
3003 3092 4.985538 TCCCAATTAACTGAGCAACTCTT 58.014 39.130 0.00 0.00 0.00 2.85
3004 3093 4.640771 TCCCAATTAACTGAGCAACTCT 57.359 40.909 0.00 0.00 0.00 3.24
3005 3094 5.705609 TTTCCCAATTAACTGAGCAACTC 57.294 39.130 0.00 0.00 0.00 3.01
3006 3095 6.280643 GTTTTTCCCAATTAACTGAGCAACT 58.719 36.000 0.00 0.00 0.00 3.16
3007 3096 5.465390 GGTTTTTCCCAATTAACTGAGCAAC 59.535 40.000 0.00 0.00 0.00 4.17
3008 3097 5.606505 GGTTTTTCCCAATTAACTGAGCAA 58.393 37.500 0.00 0.00 0.00 3.91
3009 3098 4.261825 CGGTTTTTCCCAATTAACTGAGCA 60.262 41.667 0.00 0.00 0.00 4.26
3010 3099 4.022676 TCGGTTTTTCCCAATTAACTGAGC 60.023 41.667 0.00 0.00 32.53 4.26
3011 3100 5.458015 GTCGGTTTTTCCCAATTAACTGAG 58.542 41.667 0.00 0.00 36.77 3.35
3012 3101 4.278919 GGTCGGTTTTTCCCAATTAACTGA 59.721 41.667 0.00 0.00 34.46 3.41
3013 3102 4.552355 GGTCGGTTTTTCCCAATTAACTG 58.448 43.478 0.00 0.00 0.00 3.16
3014 3103 3.253921 CGGTCGGTTTTTCCCAATTAACT 59.746 43.478 0.00 0.00 0.00 2.24
3015 3104 3.252944 TCGGTCGGTTTTTCCCAATTAAC 59.747 43.478 0.00 0.00 0.00 2.01
3016 3105 3.484407 TCGGTCGGTTTTTCCCAATTAA 58.516 40.909 0.00 0.00 0.00 1.40
3017 3106 3.137446 TCGGTCGGTTTTTCCCAATTA 57.863 42.857 0.00 0.00 0.00 1.40
3018 3107 1.984066 TCGGTCGGTTTTTCCCAATT 58.016 45.000 0.00 0.00 0.00 2.32
3019 3108 1.984066 TTCGGTCGGTTTTTCCCAAT 58.016 45.000 0.00 0.00 0.00 3.16
3020 3109 1.760192 TTTCGGTCGGTTTTTCCCAA 58.240 45.000 0.00 0.00 0.00 4.12
3021 3110 1.404748 GTTTTCGGTCGGTTTTTCCCA 59.595 47.619 0.00 0.00 0.00 4.37
3022 3111 1.269206 GGTTTTCGGTCGGTTTTTCCC 60.269 52.381 0.00 0.00 0.00 3.97
3023 3112 1.404748 TGGTTTTCGGTCGGTTTTTCC 59.595 47.619 0.00 0.00 0.00 3.13
3024 3113 2.355444 TCTGGTTTTCGGTCGGTTTTTC 59.645 45.455 0.00 0.00 0.00 2.29
3025 3114 2.367486 TCTGGTTTTCGGTCGGTTTTT 58.633 42.857 0.00 0.00 0.00 1.94
3026 3115 2.041251 TCTGGTTTTCGGTCGGTTTT 57.959 45.000 0.00 0.00 0.00 2.43
3027 3116 2.265589 ATCTGGTTTTCGGTCGGTTT 57.734 45.000 0.00 0.00 0.00 3.27
3028 3117 2.265589 AATCTGGTTTTCGGTCGGTT 57.734 45.000 0.00 0.00 0.00 4.44
3029 3118 2.613725 GGTAATCTGGTTTTCGGTCGGT 60.614 50.000 0.00 0.00 0.00 4.69
3030 3119 2.004733 GGTAATCTGGTTTTCGGTCGG 58.995 52.381 0.00 0.00 0.00 4.79
3031 3120 2.968675 AGGTAATCTGGTTTTCGGTCG 58.031 47.619 0.00 0.00 0.00 4.79
3032 3121 5.082251 ACTAGGTAATCTGGTTTTCGGTC 57.918 43.478 0.00 0.00 33.05 4.79
3033 3122 5.494390 AACTAGGTAATCTGGTTTTCGGT 57.506 39.130 0.00 0.00 43.35 4.69
3034 3123 8.502105 AATTAACTAGGTAATCTGGTTTTCGG 57.498 34.615 13.42 0.00 43.35 4.30
3047 3136 8.208903 GCTTGGTCCTTCATAATTAACTAGGTA 58.791 37.037 0.00 0.00 0.00 3.08
3048 3137 7.054751 GCTTGGTCCTTCATAATTAACTAGGT 58.945 38.462 0.00 0.00 0.00 3.08
3049 3138 6.202954 CGCTTGGTCCTTCATAATTAACTAGG 59.797 42.308 0.00 0.00 0.00 3.02
3050 3139 6.984474 TCGCTTGGTCCTTCATAATTAACTAG 59.016 38.462 0.00 0.00 0.00 2.57
3051 3140 6.880484 TCGCTTGGTCCTTCATAATTAACTA 58.120 36.000 0.00 0.00 0.00 2.24
3052 3141 5.741011 TCGCTTGGTCCTTCATAATTAACT 58.259 37.500 0.00 0.00 0.00 2.24
3053 3142 6.431198 TTCGCTTGGTCCTTCATAATTAAC 57.569 37.500 0.00 0.00 0.00 2.01
3054 3143 7.175990 AGTTTTCGCTTGGTCCTTCATAATTAA 59.824 33.333 0.00 0.00 0.00 1.40
3055 3144 6.657541 AGTTTTCGCTTGGTCCTTCATAATTA 59.342 34.615 0.00 0.00 0.00 1.40
3056 3145 5.476945 AGTTTTCGCTTGGTCCTTCATAATT 59.523 36.000 0.00 0.00 0.00 1.40
3057 3146 5.010282 AGTTTTCGCTTGGTCCTTCATAAT 58.990 37.500 0.00 0.00 0.00 1.28
3058 3147 4.394729 AGTTTTCGCTTGGTCCTTCATAA 58.605 39.130 0.00 0.00 0.00 1.90
3059 3148 4.015872 AGTTTTCGCTTGGTCCTTCATA 57.984 40.909 0.00 0.00 0.00 2.15
3060 3149 2.863809 AGTTTTCGCTTGGTCCTTCAT 58.136 42.857 0.00 0.00 0.00 2.57
3061 3150 2.341846 AGTTTTCGCTTGGTCCTTCA 57.658 45.000 0.00 0.00 0.00 3.02
3062 3151 4.000988 TGATAGTTTTCGCTTGGTCCTTC 58.999 43.478 0.00 0.00 0.00 3.46
3063 3152 3.751698 GTGATAGTTTTCGCTTGGTCCTT 59.248 43.478 0.00 0.00 0.00 3.36
3064 3153 3.244422 TGTGATAGTTTTCGCTTGGTCCT 60.244 43.478 0.00 0.00 0.00 3.85
3065 3154 3.071479 TGTGATAGTTTTCGCTTGGTCC 58.929 45.455 0.00 0.00 0.00 4.46
3066 3155 3.424962 GCTGTGATAGTTTTCGCTTGGTC 60.425 47.826 0.00 0.00 0.00 4.02
3067 3156 2.484264 GCTGTGATAGTTTTCGCTTGGT 59.516 45.455 0.00 0.00 0.00 3.67
3068 3157 3.122937 GCTGTGATAGTTTTCGCTTGG 57.877 47.619 0.00 0.00 0.00 3.61
3418 3507 1.070821 ACATGCATGTTGTCTCGACG 58.929 50.000 26.61 0.00 37.90 5.12
3419 3508 1.800586 ACACATGCATGTTGTCTCGAC 59.199 47.619 29.48 0.00 39.39 4.20
3420 3509 2.068519 GACACATGCATGTTGTCTCGA 58.931 47.619 32.47 0.00 39.39 4.04
3421 3510 1.799994 TGACACATGCATGTTGTCTCG 59.200 47.619 35.37 25.71 39.39 4.04
3422 3511 3.484721 CGATGACACATGCATGTTGTCTC 60.485 47.826 35.37 30.28 39.39 3.36
3423 3512 2.417586 CGATGACACATGCATGTTGTCT 59.582 45.455 35.37 27.86 39.39 3.41
3424 3513 2.777494 CGATGACACATGCATGTTGTC 58.223 47.619 32.78 32.78 39.39 3.18
3425 3514 1.135603 GCGATGACACATGCATGTTGT 60.136 47.619 29.48 26.88 39.39 3.32
3426 3515 1.541475 GCGATGACACATGCATGTTG 58.459 50.000 29.48 24.18 39.39 3.33
3427 3516 0.452987 GGCGATGACACATGCATGTT 59.547 50.000 29.48 19.82 39.39 2.71
3428 3517 0.677414 TGGCGATGACACATGCATGT 60.677 50.000 26.61 26.61 42.84 3.21
3429 3518 0.666374 ATGGCGATGACACATGCATG 59.334 50.000 25.09 25.09 0.00 4.06
3430 3519 0.949397 GATGGCGATGACACATGCAT 59.051 50.000 0.00 0.00 0.00 3.96
3431 3520 0.392729 TGATGGCGATGACACATGCA 60.393 50.000 0.00 0.00 0.00 3.96
3432 3521 0.028505 GTGATGGCGATGACACATGC 59.971 55.000 0.00 0.00 34.05 4.06
3433 3522 1.596260 GAGTGATGGCGATGACACATG 59.404 52.381 0.67 0.00 35.97 3.21
3434 3523 1.473965 GGAGTGATGGCGATGACACAT 60.474 52.381 0.67 0.00 35.97 3.21
3435 3524 0.108186 GGAGTGATGGCGATGACACA 60.108 55.000 0.67 0.00 35.97 3.72
3436 3525 0.176680 AGGAGTGATGGCGATGACAC 59.823 55.000 0.67 0.00 0.00 3.67
3437 3526 0.461548 GAGGAGTGATGGCGATGACA 59.538 55.000 0.67 0.00 0.00 3.58
3438 3527 0.249657 GGAGGAGTGATGGCGATGAC 60.250 60.000 0.00 0.00 0.00 3.06
3439 3528 1.402896 GGGAGGAGTGATGGCGATGA 61.403 60.000 0.00 0.00 0.00 2.92
3440 3529 1.070445 GGGAGGAGTGATGGCGATG 59.930 63.158 0.00 0.00 0.00 3.84
3441 3530 2.143419 GGGGAGGAGTGATGGCGAT 61.143 63.158 0.00 0.00 0.00 4.58
3442 3531 1.944896 TAGGGGAGGAGTGATGGCGA 61.945 60.000 0.00 0.00 0.00 5.54
3443 3532 1.048724 TTAGGGGAGGAGTGATGGCG 61.049 60.000 0.00 0.00 0.00 5.69
3444 3533 1.213296 TTTAGGGGAGGAGTGATGGC 58.787 55.000 0.00 0.00 0.00 4.40
3445 3534 2.422093 GCTTTTAGGGGAGGAGTGATGG 60.422 54.545 0.00 0.00 0.00 3.51
3446 3535 2.743183 CGCTTTTAGGGGAGGAGTGATG 60.743 54.545 0.00 0.00 0.00 3.07
3447 3536 1.486726 CGCTTTTAGGGGAGGAGTGAT 59.513 52.381 0.00 0.00 0.00 3.06
3448 3537 0.902531 CGCTTTTAGGGGAGGAGTGA 59.097 55.000 0.00 0.00 0.00 3.41
3449 3538 0.613777 ACGCTTTTAGGGGAGGAGTG 59.386 55.000 0.00 0.00 31.71 3.51
3450 3539 0.903236 GACGCTTTTAGGGGAGGAGT 59.097 55.000 0.00 0.00 31.71 3.85
3451 3540 0.902531 TGACGCTTTTAGGGGAGGAG 59.097 55.000 0.00 0.00 31.71 3.69
3452 3541 1.485066 GATGACGCTTTTAGGGGAGGA 59.515 52.381 0.00 0.00 31.71 3.71
3453 3542 1.806623 CGATGACGCTTTTAGGGGAGG 60.807 57.143 0.00 0.00 31.71 4.30
3454 3543 1.571919 CGATGACGCTTTTAGGGGAG 58.428 55.000 0.00 0.00 31.71 4.30
3455 3544 3.752796 CGATGACGCTTTTAGGGGA 57.247 52.632 0.00 0.00 31.71 4.81
3466 3555 1.257936 CGTTTAAGGATGGCGATGACG 59.742 52.381 0.00 0.00 42.93 4.35
3467 3556 2.277084 ACGTTTAAGGATGGCGATGAC 58.723 47.619 0.00 0.00 0.00 3.06
3468 3557 2.675844 CAACGTTTAAGGATGGCGATGA 59.324 45.455 0.00 0.00 0.00 2.92
3469 3558 2.675844 TCAACGTTTAAGGATGGCGATG 59.324 45.455 0.00 0.00 0.00 3.84
3470 3559 2.936498 CTCAACGTTTAAGGATGGCGAT 59.064 45.455 0.00 0.00 0.00 4.58
3471 3560 2.028839 TCTCAACGTTTAAGGATGGCGA 60.029 45.455 0.00 0.00 0.00 5.54
3472 3561 2.343101 TCTCAACGTTTAAGGATGGCG 58.657 47.619 0.00 0.00 0.00 5.69
3473 3562 3.500680 TGTTCTCAACGTTTAAGGATGGC 59.499 43.478 0.00 0.00 0.00 4.40
3474 3563 4.377022 CGTGTTCTCAACGTTTAAGGATGG 60.377 45.833 0.00 0.00 0.00 3.51
3475 3564 4.446385 TCGTGTTCTCAACGTTTAAGGATG 59.554 41.667 0.00 0.00 0.00 3.51
3476 3565 4.446719 GTCGTGTTCTCAACGTTTAAGGAT 59.553 41.667 0.00 0.00 0.00 3.24
3477 3566 3.798337 GTCGTGTTCTCAACGTTTAAGGA 59.202 43.478 0.00 0.00 0.00 3.36
3478 3567 3.800506 AGTCGTGTTCTCAACGTTTAAGG 59.199 43.478 0.00 0.00 0.00 2.69
3479 3568 4.085210 GGAGTCGTGTTCTCAACGTTTAAG 60.085 45.833 0.00 0.00 34.04 1.85
3480 3569 3.798337 GGAGTCGTGTTCTCAACGTTTAA 59.202 43.478 0.00 0.00 34.04 1.52
3481 3570 3.374745 GGAGTCGTGTTCTCAACGTTTA 58.625 45.455 0.00 0.00 34.04 2.01
3482 3571 2.199236 GGAGTCGTGTTCTCAACGTTT 58.801 47.619 0.00 0.00 34.04 3.60
3483 3572 1.849097 GGAGTCGTGTTCTCAACGTT 58.151 50.000 0.00 0.00 34.04 3.99
3484 3573 0.317603 CGGAGTCGTGTTCTCAACGT 60.318 55.000 0.00 0.00 34.04 3.99
3485 3574 0.040692 TCGGAGTCGTGTTCTCAACG 60.041 55.000 0.00 0.00 37.69 4.10
3486 3575 1.001597 AGTCGGAGTCGTGTTCTCAAC 60.002 52.381 0.00 0.00 37.69 3.18
3487 3576 1.315690 AGTCGGAGTCGTGTTCTCAA 58.684 50.000 0.00 0.00 37.69 3.02
3488 3577 1.266175 GAAGTCGGAGTCGTGTTCTCA 59.734 52.381 0.00 0.00 37.69 3.27
3489 3578 1.725292 CGAAGTCGGAGTCGTGTTCTC 60.725 57.143 3.48 0.00 37.69 2.87
3490 3579 0.237761 CGAAGTCGGAGTCGTGTTCT 59.762 55.000 3.48 0.00 37.69 3.01
3491 3580 1.335697 GCGAAGTCGGAGTCGTGTTC 61.336 60.000 11.36 0.00 39.46 3.18
3492 3581 1.371389 GCGAAGTCGGAGTCGTGTT 60.371 57.895 11.36 0.00 39.46 3.32
3493 3582 2.254651 GCGAAGTCGGAGTCGTGT 59.745 61.111 11.36 0.00 39.46 4.49


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

AutoCloner maintained by Alex Coulton.