Multiple sequence alignment - TraesCS5A01G067600

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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 TraesCS5A01G067600 chr5A 100.000 3258 0 0 1 3258 74947200 74950457 0.000000e+00 6017
1 TraesCS5A01G067600 chr5B 95.553 2968 98 10 1 2947 88357409 88360363 0.000000e+00 4719
2 TraesCS5A01G067600 chr5B 73.352 364 70 18 1638 1989 88745401 88745749 3.440000e-20 110
3 TraesCS5A01G067600 chr5D 94.854 3012 103 21 1 2999 78803261 78806233 0.000000e+00 4656
4 TraesCS5A01G067600 chr6A 91.511 966 74 7 360 1321 173604972 173605933 0.000000e+00 1323
5 TraesCS5A01G067600 chr4B 72.617 661 126 45 1623 2252 78604477 78603841 2.010000e-37 167
6 TraesCS5A01G067600 chr4D 72.247 663 125 48 1623 2252 53751926 53751290 2.020000e-32 150
7 TraesCS5A01G067600 chr4A 71.820 621 126 42 1638 2240 543375294 543375883 7.330000e-27 132


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 TraesCS5A01G067600 chr5A 74947200 74950457 3257 False 6017 6017 100.000 1 3258 1 chr5A.!!$F1 3257
1 TraesCS5A01G067600 chr5B 88357409 88360363 2954 False 4719 4719 95.553 1 2947 1 chr5B.!!$F1 2946
2 TraesCS5A01G067600 chr5D 78803261 78806233 2972 False 4656 4656 94.854 1 2999 1 chr5D.!!$F1 2998
3 TraesCS5A01G067600 chr6A 173604972 173605933 961 False 1323 1323 91.511 360 1321 1 chr6A.!!$F1 961

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
869 876 0.687354 TCCCTGCAACCTCTCAGAAC 59.313 55.0 0.0 0.0 32.26 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2794 2826 0.318445 ACGTCAACGGTCAGCTACAC 60.318 55.0 7.53 0.0 44.95 2.9 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
40 41 7.685594 GGATACGTTAGAATGAAGAAACCAAG 58.314 38.462 0.00 0.00 0.00 3.61
240 244 3.713826 TTCAGGATACCAACCTCCAAC 57.286 47.619 0.00 0.00 35.35 3.77
267 271 3.068448 TGCAAGTGTTGAACATCAATGCT 59.932 39.130 20.03 4.28 38.79 3.79
268 272 3.427528 GCAAGTGTTGAACATCAATGCTG 59.572 43.478 0.00 0.00 38.79 4.41
269 273 3.293311 AGTGTTGAACATCAATGCTGC 57.707 42.857 0.00 0.00 38.79 5.25
319 323 6.037500 TGAGAATTATTTGCAGATCAAGACCG 59.962 38.462 0.00 0.00 35.84 4.79
335 339 3.093057 AGACCGTGATATCCATAGAGGC 58.907 50.000 0.00 0.00 37.29 4.70
468 475 6.547880 ACCAACACCAGTACACATATTTTTGA 59.452 34.615 0.00 0.00 0.00 2.69
539 546 8.204836 TCTATTCCAAGGTAAACTCTTGCTATC 58.795 37.037 0.00 0.00 40.00 2.08
679 686 1.230324 GGACAAGTCACTGTCTTGCC 58.770 55.000 13.87 12.24 44.33 4.52
726 733 3.460857 AACTTGTCGTCTTCAGCTCTT 57.539 42.857 0.00 0.00 0.00 2.85
733 740 2.094494 TCGTCTTCAGCTCTTCACATCC 60.094 50.000 0.00 0.00 0.00 3.51
734 741 2.094286 CGTCTTCAGCTCTTCACATCCT 60.094 50.000 0.00 0.00 0.00 3.24
743 750 4.223700 AGCTCTTCACATCCTCACAACATA 59.776 41.667 0.00 0.00 0.00 2.29
744 751 4.331168 GCTCTTCACATCCTCACAACATAC 59.669 45.833 0.00 0.00 0.00 2.39
746 753 4.285775 TCTTCACATCCTCACAACATACCA 59.714 41.667 0.00 0.00 0.00 3.25
759 766 4.478699 CAACATACCAATGTCTGTTGCTG 58.521 43.478 9.88 0.00 46.09 4.41
869 876 0.687354 TCCCTGCAACCTCTCAGAAC 59.313 55.000 0.00 0.00 32.26 3.01
1080 1087 2.366533 GGCGAGGAGTCCGATATCATA 58.633 52.381 2.76 0.00 0.00 2.15
1163 1170 0.554792 CAGGCTTCCCATCCATCCTT 59.445 55.000 0.00 0.00 0.00 3.36
1200 1207 9.265901 GATCTTAATACAAGTGCATGTAGTGAT 57.734 33.333 9.96 5.82 39.04 3.06
1267 1275 6.126863 ACTATTTGGGTGATTCAAGTGAGA 57.873 37.500 0.00 0.00 0.00 3.27
1350 1358 8.194104 GGTGCTATCGAGTATCTGAATATGATT 58.806 37.037 0.00 0.00 0.00 2.57
1400 1408 2.259818 CGAGTCAAGCTGCGAGGT 59.740 61.111 0.00 0.00 0.00 3.85
1405 1413 0.319900 GTCAAGCTGCGAGGTTCTCA 60.320 55.000 0.00 0.00 32.99 3.27
1431 1439 3.190744 CGGTCAGTGCTACTAACAAGAGA 59.809 47.826 0.00 0.00 0.00 3.10
1458 1466 3.182967 CTCGGTGGAAGAAGAAATCGAG 58.817 50.000 0.00 0.00 37.21 4.04
1467 1475 0.038166 AAGAAATCGAGGGCCAAGCA 59.962 50.000 6.18 0.00 0.00 3.91
1528 1538 6.985059 ACCGGCTATGTCTTTTAGAAAGATAC 59.015 38.462 0.00 0.00 0.00 2.24
1547 1557 3.106242 ACGTTCATGCTGTTAGTGTGA 57.894 42.857 0.00 0.00 0.00 3.58
1557 1567 5.470368 TGCTGTTAGTGTGAATACTGACTC 58.530 41.667 4.27 0.00 37.86 3.36
1619 1629 0.798776 CACCGAAGCGAGCAAAGAAT 59.201 50.000 0.00 0.00 0.00 2.40
1685 1695 2.007360 ATGCTTCTCAAGAGTCTGCG 57.993 50.000 0.00 0.00 0.00 5.18
1948 1961 4.201891 GCTTCTGAACATTCATGCTACTGG 60.202 45.833 0.00 0.00 36.46 4.00
2147 2160 1.303970 TTCCATGGCGGACATTGCA 60.304 52.632 6.96 0.00 46.36 4.08
2277 2292 4.564782 AGAGATGATTTTGGCAGTCTCA 57.435 40.909 0.00 6.27 35.68 3.27
2286 2302 2.035442 GGCAGTCTCAAGCGGGAAC 61.035 63.158 0.00 0.00 0.00 3.62
2307 2323 5.493133 ACGCAGTTTGTGTTTGAGATAAA 57.507 34.783 0.00 0.00 37.78 1.40
2308 2324 5.270853 ACGCAGTTTGTGTTTGAGATAAAC 58.729 37.500 0.00 0.00 37.78 2.01
2309 2325 4.375698 CGCAGTTTGTGTTTGAGATAAACG 59.624 41.667 0.00 0.00 36.61 3.60
2310 2326 5.507077 GCAGTTTGTGTTTGAGATAAACGA 58.493 37.500 0.00 0.00 36.61 3.85
2311 2327 5.968848 GCAGTTTGTGTTTGAGATAAACGAA 59.031 36.000 0.00 0.00 36.61 3.85
2614 2630 1.891150 CAAAGTTGCAGCCTTGAGGAT 59.109 47.619 6.04 0.00 37.39 3.24
2688 2704 6.108015 TGGAATGAGCTTCATAATTTTTGGC 58.892 36.000 0.00 0.00 35.76 4.52
2794 2826 6.038161 TCCACTATGAAGAAAATAACCATGCG 59.962 38.462 0.00 0.00 0.00 4.73
2815 2847 0.318445 GTAGCTGACCGTTGACGTGT 60.318 55.000 0.00 0.50 37.74 4.49
2848 2880 8.442632 TTTGCATTGACATTTCCAACATAAAA 57.557 26.923 0.00 0.00 0.00 1.52
2949 2981 5.182001 GTGCACTCTCCATTCTAACATTTGT 59.818 40.000 10.32 0.00 0.00 2.83
2954 2986 7.493971 CACTCTCCATTCTAACATTTGTCCTAG 59.506 40.741 0.00 0.00 0.00 3.02
3000 3032 7.169158 TGAAAATAGGGTTTATTTCAGGCTG 57.831 36.000 8.58 8.58 36.99 4.85
3001 3033 6.951198 TGAAAATAGGGTTTATTTCAGGCTGA 59.049 34.615 14.43 14.43 36.99 4.26
3002 3034 6.775594 AAATAGGGTTTATTTCAGGCTGAC 57.224 37.500 18.55 4.84 0.00 3.51
3003 3035 3.087370 AGGGTTTATTTCAGGCTGACC 57.913 47.619 18.55 14.30 0.00 4.02
3004 3036 2.100197 GGGTTTATTTCAGGCTGACCC 58.900 52.381 18.55 19.56 38.55 4.46
3006 3038 3.053917 GGGTTTATTTCAGGCTGACCCTA 60.054 47.826 25.04 12.39 44.09 3.53
3007 3039 4.200092 GGTTTATTTCAGGCTGACCCTAG 58.800 47.826 18.55 0.00 44.09 3.02
3008 3040 4.080526 GGTTTATTTCAGGCTGACCCTAGA 60.081 45.833 18.55 0.00 44.09 2.43
3009 3041 5.398012 GGTTTATTTCAGGCTGACCCTAGAT 60.398 44.000 18.55 7.21 44.09 1.98
3010 3042 5.552870 TTATTTCAGGCTGACCCTAGATC 57.447 43.478 18.55 0.00 44.09 2.75
3011 3043 2.856760 TTCAGGCTGACCCTAGATCT 57.143 50.000 18.55 0.00 44.09 2.75
3012 3044 2.856760 TCAGGCTGACCCTAGATCTT 57.143 50.000 14.43 0.00 44.09 2.40
3013 3045 3.121929 TCAGGCTGACCCTAGATCTTT 57.878 47.619 14.43 0.00 44.09 2.52
3014 3046 2.768527 TCAGGCTGACCCTAGATCTTTG 59.231 50.000 14.43 0.00 44.09 2.77
3015 3047 1.488393 AGGCTGACCCTAGATCTTTGC 59.512 52.381 0.00 0.00 44.08 3.68
3016 3048 1.576356 GCTGACCCTAGATCTTTGCG 58.424 55.000 0.00 0.00 0.00 4.85
3017 3049 1.137086 GCTGACCCTAGATCTTTGCGA 59.863 52.381 0.00 0.00 0.00 5.10
3018 3050 2.815478 CTGACCCTAGATCTTTGCGAC 58.185 52.381 0.00 0.00 0.00 5.19
3019 3051 1.480954 TGACCCTAGATCTTTGCGACC 59.519 52.381 0.00 0.00 0.00 4.79
3020 3052 1.757699 GACCCTAGATCTTTGCGACCT 59.242 52.381 0.00 0.00 0.00 3.85
3021 3053 2.168728 GACCCTAGATCTTTGCGACCTT 59.831 50.000 0.00 0.00 0.00 3.50
3022 3054 3.371965 ACCCTAGATCTTTGCGACCTTA 58.628 45.455 0.00 0.00 0.00 2.69
3023 3055 3.132467 ACCCTAGATCTTTGCGACCTTAC 59.868 47.826 0.00 0.00 0.00 2.34
3024 3056 3.385111 CCCTAGATCTTTGCGACCTTACT 59.615 47.826 0.00 0.00 0.00 2.24
3025 3057 4.141914 CCCTAGATCTTTGCGACCTTACTT 60.142 45.833 0.00 0.00 0.00 2.24
3026 3058 5.420409 CCTAGATCTTTGCGACCTTACTTT 58.580 41.667 0.00 0.00 0.00 2.66
3027 3059 5.520649 CCTAGATCTTTGCGACCTTACTTTC 59.479 44.000 0.00 0.00 0.00 2.62
3028 3060 4.894784 AGATCTTTGCGACCTTACTTTCA 58.105 39.130 0.00 0.00 0.00 2.69
3029 3061 5.305585 AGATCTTTGCGACCTTACTTTCAA 58.694 37.500 0.00 0.00 0.00 2.69
3030 3062 5.940470 AGATCTTTGCGACCTTACTTTCAAT 59.060 36.000 0.00 0.00 0.00 2.57
3031 3063 6.431234 AGATCTTTGCGACCTTACTTTCAATT 59.569 34.615 0.00 0.00 0.00 2.32
3032 3064 6.385649 TCTTTGCGACCTTACTTTCAATTT 57.614 33.333 0.00 0.00 0.00 1.82
3033 3065 7.499321 TCTTTGCGACCTTACTTTCAATTTA 57.501 32.000 0.00 0.00 0.00 1.40
3034 3066 7.581476 TCTTTGCGACCTTACTTTCAATTTAG 58.419 34.615 0.00 0.00 0.00 1.85
3035 3067 5.873179 TGCGACCTTACTTTCAATTTAGG 57.127 39.130 0.00 0.00 0.00 2.69
3036 3068 5.310451 TGCGACCTTACTTTCAATTTAGGT 58.690 37.500 0.00 0.00 38.64 3.08
3037 3069 5.410439 TGCGACCTTACTTTCAATTTAGGTC 59.590 40.000 0.00 0.00 45.13 3.85
3041 3073 8.561738 GACCTTACTTTCAATTTAGGTCATGA 57.438 34.615 12.81 0.00 46.86 3.07
3042 3074 9.178758 GACCTTACTTTCAATTTAGGTCATGAT 57.821 33.333 12.81 0.00 46.86 2.45
3043 3075 8.960591 ACCTTACTTTCAATTTAGGTCATGATG 58.039 33.333 0.00 0.00 30.42 3.07
3044 3076 8.960591 CCTTACTTTCAATTTAGGTCATGATGT 58.039 33.333 0.00 0.00 0.00 3.06
3047 3079 8.181904 ACTTTCAATTTAGGTCATGATGTTGT 57.818 30.769 0.00 0.00 0.00 3.32
3048 3080 8.084073 ACTTTCAATTTAGGTCATGATGTTGTG 58.916 33.333 0.00 0.00 0.00 3.33
3049 3081 5.953183 TCAATTTAGGTCATGATGTTGTGC 58.047 37.500 0.00 0.00 0.00 4.57
3050 3082 4.621068 ATTTAGGTCATGATGTTGTGCG 57.379 40.909 0.00 0.00 0.00 5.34
3051 3083 2.022764 TAGGTCATGATGTTGTGCGG 57.977 50.000 0.00 0.00 0.00 5.69
3052 3084 0.677731 AGGTCATGATGTTGTGCGGG 60.678 55.000 0.00 0.00 0.00 6.13
3053 3085 0.960364 GGTCATGATGTTGTGCGGGT 60.960 55.000 0.00 0.00 0.00 5.28
3054 3086 0.881118 GTCATGATGTTGTGCGGGTT 59.119 50.000 0.00 0.00 0.00 4.11
3055 3087 1.135689 GTCATGATGTTGTGCGGGTTC 60.136 52.381 0.00 0.00 0.00 3.62
3056 3088 0.179192 CATGATGTTGTGCGGGTTCG 60.179 55.000 0.00 0.00 39.81 3.95
3057 3089 0.605319 ATGATGTTGTGCGGGTTCGT 60.605 50.000 0.00 0.00 38.89 3.85
3058 3090 0.816018 TGATGTTGTGCGGGTTCGTT 60.816 50.000 0.00 0.00 38.89 3.85
3059 3091 0.385473 GATGTTGTGCGGGTTCGTTG 60.385 55.000 0.00 0.00 38.89 4.10
3060 3092 1.098712 ATGTTGTGCGGGTTCGTTGT 61.099 50.000 0.00 0.00 38.89 3.32
3061 3093 1.298041 GTTGTGCGGGTTCGTTGTG 60.298 57.895 0.00 0.00 38.89 3.33
3062 3094 3.114647 TTGTGCGGGTTCGTTGTGC 62.115 57.895 0.00 0.00 38.89 4.57
3063 3095 3.276846 GTGCGGGTTCGTTGTGCT 61.277 61.111 0.00 0.00 38.89 4.40
3064 3096 2.970324 TGCGGGTTCGTTGTGCTC 60.970 61.111 0.00 0.00 38.89 4.26
3065 3097 4.072088 GCGGGTTCGTTGTGCTCG 62.072 66.667 0.00 0.00 38.89 5.03
3066 3098 3.411351 CGGGTTCGTTGTGCTCGG 61.411 66.667 0.00 0.00 0.00 4.63
3067 3099 3.723348 GGGTTCGTTGTGCTCGGC 61.723 66.667 0.00 0.00 0.00 5.54
3068 3100 2.970324 GGTTCGTTGTGCTCGGCA 60.970 61.111 0.00 0.00 35.60 5.69
3069 3101 2.551270 GTTCGTTGTGCTCGGCAG 59.449 61.111 0.00 0.00 40.08 4.85
3078 3110 2.437359 GCTCGGCAGCATGGTTCT 60.437 61.111 0.00 0.00 46.06 3.01
3079 3111 2.467826 GCTCGGCAGCATGGTTCTC 61.468 63.158 0.00 0.00 46.06 2.87
3080 3112 2.125552 TCGGCAGCATGGTTCTCG 60.126 61.111 0.00 0.00 35.86 4.04
3081 3113 2.125552 CGGCAGCATGGTTCTCGA 60.126 61.111 0.00 0.00 35.86 4.04
3082 3114 1.741401 CGGCAGCATGGTTCTCGAA 60.741 57.895 0.00 0.00 35.86 3.71
3083 3115 1.699656 CGGCAGCATGGTTCTCGAAG 61.700 60.000 0.00 0.00 35.86 3.79
3084 3116 1.372087 GGCAGCATGGTTCTCGAAGG 61.372 60.000 0.00 0.00 35.86 3.46
3085 3117 1.372087 GCAGCATGGTTCTCGAAGGG 61.372 60.000 0.00 0.00 35.86 3.95
3086 3118 1.078143 AGCATGGTTCTCGAAGGGC 60.078 57.895 0.00 0.00 0.00 5.19
3087 3119 2.115291 GCATGGTTCTCGAAGGGCC 61.115 63.158 0.00 0.00 0.00 5.80
3088 3120 1.815421 CATGGTTCTCGAAGGGCCG 60.815 63.158 0.00 0.00 0.00 6.13
3089 3121 1.987855 ATGGTTCTCGAAGGGCCGA 60.988 57.895 0.00 0.00 37.03 5.54
3090 3122 1.550130 ATGGTTCTCGAAGGGCCGAA 61.550 55.000 0.00 0.00 38.17 4.30
3091 3123 1.448013 GGTTCTCGAAGGGCCGAAG 60.448 63.158 0.00 0.00 38.17 3.79
3092 3124 2.101233 GTTCTCGAAGGGCCGAAGC 61.101 63.158 0.00 0.00 38.17 3.86
3093 3125 2.579657 TTCTCGAAGGGCCGAAGCA 61.580 57.895 0.00 0.00 42.56 3.91
3094 3126 2.507110 TTCTCGAAGGGCCGAAGCAG 62.507 60.000 0.00 0.00 42.56 4.24
3095 3127 2.994995 TCGAAGGGCCGAAGCAGA 60.995 61.111 0.00 0.00 42.56 4.26
3096 3128 2.187946 CGAAGGGCCGAAGCAGAT 59.812 61.111 0.00 0.00 42.56 2.90
3097 3129 1.884926 CGAAGGGCCGAAGCAGATC 60.885 63.158 0.00 0.00 42.56 2.75
3098 3130 1.524482 GAAGGGCCGAAGCAGATCT 59.476 57.895 0.00 0.00 42.56 2.75
3099 3131 0.107459 GAAGGGCCGAAGCAGATCTT 60.107 55.000 0.00 0.00 42.56 2.40
3100 3132 0.329596 AAGGGCCGAAGCAGATCTTT 59.670 50.000 0.00 0.00 42.56 2.52
3101 3133 1.204146 AGGGCCGAAGCAGATCTTTA 58.796 50.000 0.00 0.00 42.56 1.85
3102 3134 1.559682 AGGGCCGAAGCAGATCTTTAA 59.440 47.619 0.00 0.00 42.56 1.52
3103 3135 1.671328 GGGCCGAAGCAGATCTTTAAC 59.329 52.381 0.00 0.00 42.56 2.01
3104 3136 2.356135 GGCCGAAGCAGATCTTTAACA 58.644 47.619 0.00 0.00 42.56 2.41
3105 3137 2.945668 GGCCGAAGCAGATCTTTAACAT 59.054 45.455 0.00 0.00 42.56 2.71
3106 3138 3.378427 GGCCGAAGCAGATCTTTAACATT 59.622 43.478 0.00 0.00 42.56 2.71
3107 3139 4.346129 GCCGAAGCAGATCTTTAACATTG 58.654 43.478 0.00 0.00 39.53 2.82
3108 3140 4.731773 GCCGAAGCAGATCTTTAACATTGG 60.732 45.833 0.00 0.00 39.53 3.16
3109 3141 4.201950 CCGAAGCAGATCTTTAACATTGGG 60.202 45.833 0.00 0.00 34.56 4.12
3110 3142 4.635765 CGAAGCAGATCTTTAACATTGGGA 59.364 41.667 0.00 0.00 34.56 4.37
3111 3143 5.123820 CGAAGCAGATCTTTAACATTGGGAA 59.876 40.000 0.00 0.00 34.56 3.97
3112 3144 6.521151 AAGCAGATCTTTAACATTGGGAAG 57.479 37.500 0.00 0.00 0.00 3.46
3113 3145 5.819991 AGCAGATCTTTAACATTGGGAAGA 58.180 37.500 0.00 0.00 33.17 2.87
3114 3146 6.248433 AGCAGATCTTTAACATTGGGAAGAA 58.752 36.000 0.00 0.00 32.47 2.52
3115 3147 6.151817 AGCAGATCTTTAACATTGGGAAGAAC 59.848 38.462 0.00 2.27 32.47 3.01
3116 3148 6.071952 GCAGATCTTTAACATTGGGAAGAACA 60.072 38.462 0.00 0.00 32.47 3.18
3117 3149 7.363268 GCAGATCTTTAACATTGGGAAGAACAT 60.363 37.037 0.00 0.00 32.47 2.71
3118 3150 8.526147 CAGATCTTTAACATTGGGAAGAACATT 58.474 33.333 0.00 0.00 32.47 2.71
3119 3151 8.743714 AGATCTTTAACATTGGGAAGAACATTC 58.256 33.333 0.00 0.00 32.47 2.67
3120 3152 7.831691 TCTTTAACATTGGGAAGAACATTCA 57.168 32.000 0.00 0.00 0.00 2.57
3121 3153 8.421249 TCTTTAACATTGGGAAGAACATTCAT 57.579 30.769 0.00 0.00 0.00 2.57
3122 3154 9.527157 TCTTTAACATTGGGAAGAACATTCATA 57.473 29.630 0.00 0.00 0.00 2.15
3123 3155 9.793252 CTTTAACATTGGGAAGAACATTCATAG 57.207 33.333 0.00 0.00 0.00 2.23
3124 3156 9.527157 TTTAACATTGGGAAGAACATTCATAGA 57.473 29.630 0.00 0.00 0.00 1.98
3125 3157 7.636150 AACATTGGGAAGAACATTCATAGAG 57.364 36.000 0.00 0.00 0.00 2.43
3126 3158 6.725364 ACATTGGGAAGAACATTCATAGAGT 58.275 36.000 0.00 0.00 0.00 3.24
3127 3159 6.600822 ACATTGGGAAGAACATTCATAGAGTG 59.399 38.462 0.00 0.00 0.00 3.51
3128 3160 5.102953 TGGGAAGAACATTCATAGAGTGG 57.897 43.478 0.00 0.00 0.00 4.00
3129 3161 3.879892 GGGAAGAACATTCATAGAGTGGC 59.120 47.826 0.00 0.00 0.00 5.01
3130 3162 3.557595 GGAAGAACATTCATAGAGTGGCG 59.442 47.826 0.00 0.00 0.00 5.69
3131 3163 4.433615 GAAGAACATTCATAGAGTGGCGA 58.566 43.478 0.00 0.00 0.00 5.54
3132 3164 4.471904 AGAACATTCATAGAGTGGCGAA 57.528 40.909 0.00 0.00 0.00 4.70
3133 3165 4.437239 AGAACATTCATAGAGTGGCGAAG 58.563 43.478 0.00 0.00 0.00 3.79
3134 3166 3.185246 ACATTCATAGAGTGGCGAAGG 57.815 47.619 0.00 0.00 0.00 3.46
3147 3179 3.717294 GAAGGCCGCCAGGGAAGA 61.717 66.667 13.15 0.00 38.47 2.87
3148 3180 3.978571 GAAGGCCGCCAGGGAAGAC 62.979 68.421 13.15 0.00 38.47 3.01
3159 3191 2.909140 GGGAAGACCTCTCCTCCAG 58.091 63.158 0.00 0.00 35.85 3.86
3160 3192 1.334384 GGGAAGACCTCTCCTCCAGC 61.334 65.000 0.00 0.00 35.85 4.85
3161 3193 1.671901 GGAAGACCTCTCCTCCAGCG 61.672 65.000 0.00 0.00 0.00 5.18
3162 3194 2.291457 GAAGACCTCTCCTCCAGCGC 62.291 65.000 0.00 0.00 0.00 5.92
3163 3195 3.844090 GACCTCTCCTCCAGCGCC 61.844 72.222 2.29 0.00 0.00 6.53
3164 3196 4.390556 ACCTCTCCTCCAGCGCCT 62.391 66.667 2.29 0.00 0.00 5.52
3165 3197 3.080121 CCTCTCCTCCAGCGCCTT 61.080 66.667 2.29 0.00 0.00 4.35
3166 3198 1.758514 CCTCTCCTCCAGCGCCTTA 60.759 63.158 2.29 0.00 0.00 2.69
3167 3199 1.330655 CCTCTCCTCCAGCGCCTTAA 61.331 60.000 2.29 0.00 0.00 1.85
3168 3200 0.103937 CTCTCCTCCAGCGCCTTAAG 59.896 60.000 2.29 0.00 0.00 1.85
3169 3201 1.522580 CTCCTCCAGCGCCTTAAGC 60.523 63.158 2.29 0.00 38.52 3.09
3179 3211 2.993539 GCCTTAAGCGCTAGGGAAG 58.006 57.895 24.28 17.77 31.95 3.46
3180 3212 0.533085 GCCTTAAGCGCTAGGGAAGG 60.533 60.000 24.28 24.70 39.79 3.46
3181 3213 0.831307 CCTTAAGCGCTAGGGAAGGT 59.169 55.000 22.71 5.83 33.41 3.50
3182 3214 2.037144 CCTTAAGCGCTAGGGAAGGTA 58.963 52.381 22.71 4.96 33.41 3.08
3183 3215 2.433239 CCTTAAGCGCTAGGGAAGGTAA 59.567 50.000 22.71 11.30 33.41 2.85
3184 3216 3.455327 CTTAAGCGCTAGGGAAGGTAAC 58.545 50.000 12.05 0.00 0.00 2.50
3185 3217 0.175073 AAGCGCTAGGGAAGGTAACG 59.825 55.000 12.05 0.00 46.39 3.18
3186 3218 0.682209 AGCGCTAGGGAAGGTAACGA 60.682 55.000 8.99 0.00 46.39 3.85
3187 3219 0.248949 GCGCTAGGGAAGGTAACGAG 60.249 60.000 11.61 0.00 46.39 4.18
3188 3220 0.248949 CGCTAGGGAAGGTAACGAGC 60.249 60.000 0.00 0.00 46.39 5.03
3189 3221 0.248949 GCTAGGGAAGGTAACGAGCG 60.249 60.000 0.00 0.00 46.39 5.03
3190 3222 0.248949 CTAGGGAAGGTAACGAGCGC 60.249 60.000 0.00 0.00 46.39 5.92
3191 3223 1.669999 TAGGGAAGGTAACGAGCGCC 61.670 60.000 2.29 0.00 46.39 6.53
3192 3224 2.577593 GGAAGGTAACGAGCGCCT 59.422 61.111 2.29 0.00 46.39 5.52
3193 3225 1.669999 GGGAAGGTAACGAGCGCCTA 61.670 60.000 2.29 0.00 46.39 3.93
3194 3226 0.527169 GGAAGGTAACGAGCGCCTAC 60.527 60.000 2.29 0.47 46.39 3.18
3195 3227 0.171903 GAAGGTAACGAGCGCCTACA 59.828 55.000 2.29 0.00 46.39 2.74
3196 3228 0.172803 AAGGTAACGAGCGCCTACAG 59.827 55.000 2.29 0.00 46.39 2.74
3197 3229 1.226888 GGTAACGAGCGCCTACAGG 60.227 63.158 2.29 0.00 38.53 4.00
3207 3239 3.479203 CCTACAGGCGCCCCATCA 61.479 66.667 26.15 2.89 0.00 3.07
3208 3240 2.822637 CCTACAGGCGCCCCATCAT 61.823 63.158 26.15 0.00 0.00 2.45
3209 3241 1.598962 CTACAGGCGCCCCATCATG 60.599 63.158 26.15 16.71 0.00 3.07
3210 3242 3.118768 TACAGGCGCCCCATCATGG 62.119 63.158 26.15 0.00 37.25 3.66
3227 3259 4.338710 GGCCGGCCCACACAAGTA 62.339 66.667 36.64 0.00 0.00 2.24
3228 3260 3.053896 GCCGGCCCACACAAGTAC 61.054 66.667 18.11 0.00 0.00 2.73
3229 3261 2.740826 CCGGCCCACACAAGTACG 60.741 66.667 0.00 0.00 0.00 3.67
3230 3262 2.340809 CGGCCCACACAAGTACGA 59.659 61.111 0.00 0.00 0.00 3.43
3231 3263 1.301087 CGGCCCACACAAGTACGAA 60.301 57.895 0.00 0.00 0.00 3.85
3232 3264 0.881159 CGGCCCACACAAGTACGAAA 60.881 55.000 0.00 0.00 0.00 3.46
3233 3265 0.872388 GGCCCACACAAGTACGAAAG 59.128 55.000 0.00 0.00 0.00 2.62
3234 3266 0.237498 GCCCACACAAGTACGAAAGC 59.763 55.000 0.00 0.00 0.00 3.51
3235 3267 1.588674 CCCACACAAGTACGAAAGCA 58.411 50.000 0.00 0.00 0.00 3.91
3236 3268 2.151202 CCCACACAAGTACGAAAGCAT 58.849 47.619 0.00 0.00 0.00 3.79
3237 3269 2.552315 CCCACACAAGTACGAAAGCATT 59.448 45.455 0.00 0.00 0.00 3.56
3238 3270 3.004315 CCCACACAAGTACGAAAGCATTT 59.996 43.478 0.00 0.00 43.98 2.32
3248 3280 2.242769 GAAAGCATTTCGAACGGGAC 57.757 50.000 0.00 0.00 46.13 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 8.496751 CAGATCTGTATCATTCATTGTCATCAC 58.503 37.037 14.95 0.00 34.28 3.06
80 81 5.104374 GTGATAATGGACCAGCAAAATGTG 58.896 41.667 0.00 0.00 0.00 3.21
98 99 5.559770 TCAAACCAGAGAAATGCAGTGATA 58.440 37.500 0.00 0.00 0.00 2.15
240 244 4.862350 TGATGTTCAACACTTGCAAGATG 58.138 39.130 32.50 25.37 0.00 2.90
319 323 2.232452 AGCACGCCTCTATGGATATCAC 59.768 50.000 4.83 0.00 38.35 3.06
335 339 7.225538 ACTCAAAAGAGGATATATGAAAGCACG 59.774 37.037 0.00 0.00 0.00 5.34
468 475 4.924305 TGTGCTCATGCTTTCTTTCTTT 57.076 36.364 0.00 0.00 40.48 2.52
539 546 1.067821 GTCTATGAGCTCTGAACCGGG 59.932 57.143 16.19 0.00 0.00 5.73
703 710 3.123804 GAGCTGAAGACGACAAGTTTGA 58.876 45.455 0.00 0.00 0.00 2.69
704 711 3.126831 AGAGCTGAAGACGACAAGTTTG 58.873 45.455 0.00 0.00 0.00 2.93
726 733 4.632327 TTGGTATGTTGTGAGGATGTGA 57.368 40.909 0.00 0.00 0.00 3.58
743 750 2.079158 CGATCAGCAACAGACATTGGT 58.921 47.619 0.00 0.00 40.87 3.67
744 751 2.819422 CGATCAGCAACAGACATTGG 57.181 50.000 0.00 0.00 0.00 3.16
759 766 2.351726 GTGTGGTGATAGGTTTGCGATC 59.648 50.000 0.00 0.00 0.00 3.69
765 772 4.431416 TGAAGTGTGTGGTGATAGGTTT 57.569 40.909 0.00 0.00 0.00 3.27
767 774 3.869912 GCATGAAGTGTGTGGTGATAGGT 60.870 47.826 0.00 0.00 0.00 3.08
869 876 6.166279 TCAGGTGCTTTTATACTGTTCAGAG 58.834 40.000 6.83 0.00 0.00 3.35
1143 1150 1.152368 GGATGGATGGGAAGCCTGG 59.848 63.158 0.00 0.00 0.00 4.45
1267 1275 3.415087 GGAGCTGATGCCCAGGGT 61.415 66.667 7.55 0.00 43.13 4.34
1331 1339 7.015195 TGGTTGGAATCATATTCAGATACTCGA 59.985 37.037 2.36 0.00 0.00 4.04
1337 1345 7.234166 GGGAAATGGTTGGAATCATATTCAGAT 59.766 37.037 2.36 0.00 0.00 2.90
1350 1358 4.166539 ACAAATCATGGGAAATGGTTGGA 58.833 39.130 0.00 0.00 0.00 3.53
1400 1408 1.040646 AGCACTGACCGAGTTGAGAA 58.959 50.000 0.00 0.00 29.75 2.87
1405 1413 2.889045 TGTTAGTAGCACTGACCGAGTT 59.111 45.455 8.13 0.00 34.22 3.01
1431 1439 1.416401 TCTTCTTCCACCGAGTGCTTT 59.584 47.619 0.00 0.00 31.34 3.51
1458 1466 1.454201 GACTTACTCTTGCTTGGCCC 58.546 55.000 0.00 0.00 0.00 5.80
1467 1475 4.709397 CAGTCATCCTCAGGACTTACTCTT 59.291 45.833 0.00 0.00 40.90 2.85
1528 1538 4.668576 ATTCACACTAACAGCATGAACG 57.331 40.909 0.00 0.00 39.69 3.95
1557 1567 5.530915 TCCGACCCTGCAATTAATCAATTAG 59.469 40.000 0.00 0.00 32.96 1.73
1619 1629 2.727544 GCTTCGGTTTGCTTGGCA 59.272 55.556 0.00 0.00 36.47 4.92
1685 1695 2.489938 TTGGAGTAACACCAGCATCC 57.510 50.000 0.00 0.00 38.70 3.51
1948 1961 9.884465 CTTAGCATTTTTATTCATGTAGGCTAC 57.116 33.333 17.76 17.76 30.70 3.58
2286 2302 4.375698 CGTTTATCTCAAACACAAACTGCG 59.624 41.667 1.32 0.00 0.00 5.18
2305 2321 3.937079 AGTGGAGAACTCGTTTTTCGTTT 59.063 39.130 0.00 0.00 40.80 3.60
2306 2322 3.528532 AGTGGAGAACTCGTTTTTCGTT 58.471 40.909 0.00 0.00 40.80 3.85
2307 2323 3.175109 AGTGGAGAACTCGTTTTTCGT 57.825 42.857 0.00 0.00 40.80 3.85
2308 2324 4.084693 GGTTAGTGGAGAACTCGTTTTTCG 60.085 45.833 0.00 0.00 40.56 3.46
2309 2325 4.812626 TGGTTAGTGGAGAACTCGTTTTTC 59.187 41.667 0.00 0.00 40.56 2.29
2310 2326 4.773013 TGGTTAGTGGAGAACTCGTTTTT 58.227 39.130 0.00 0.00 40.56 1.94
2311 2327 4.411256 TGGTTAGTGGAGAACTCGTTTT 57.589 40.909 0.00 0.00 40.56 2.43
2611 2627 3.425162 AAGTGTCAGGGTTTGAGATCC 57.575 47.619 0.00 0.00 36.21 3.36
2614 2630 5.623956 TCTTAAAGTGTCAGGGTTTGAGA 57.376 39.130 0.00 0.00 36.21 3.27
2688 2704 0.388134 AGACCGAACGATTGTGTCCG 60.388 55.000 0.00 0.00 0.00 4.79
2739 2755 7.879677 GGTGGAGAAAATGGAATTGAGATTTTT 59.120 33.333 0.00 0.00 36.10 1.94
2741 2757 6.070596 GGGTGGAGAAAATGGAATTGAGATTT 60.071 38.462 0.00 0.00 36.10 2.17
2742 2758 5.423290 GGGTGGAGAAAATGGAATTGAGATT 59.577 40.000 0.00 0.00 36.10 2.40
2743 2759 4.958581 GGGTGGAGAAAATGGAATTGAGAT 59.041 41.667 0.00 0.00 36.10 2.75
2762 2778 6.840780 ATTTTCTTCATAGTGGAAAGGGTG 57.159 37.500 0.00 0.00 31.88 4.61
2794 2826 0.318445 ACGTCAACGGTCAGCTACAC 60.318 55.000 7.53 0.00 44.95 2.90
2925 2957 5.182001 ACAAATGTTAGAATGGAGAGTGCAC 59.818 40.000 9.40 9.40 0.00 4.57
2949 2981 7.554959 AGTTAGTTTGAGGATTTGTCTAGGA 57.445 36.000 0.00 0.00 0.00 2.94
2954 2986 7.730364 TCAGAAGTTAGTTTGAGGATTTGTC 57.270 36.000 0.00 0.00 0.00 3.18
2999 3031 1.480954 GGTCGCAAAGATCTAGGGTCA 59.519 52.381 0.00 0.00 0.00 4.02
3000 3032 1.757699 AGGTCGCAAAGATCTAGGGTC 59.242 52.381 0.00 0.00 38.87 4.46
3001 3033 1.867363 AGGTCGCAAAGATCTAGGGT 58.133 50.000 0.00 0.00 38.87 4.34
3002 3034 2.990066 AAGGTCGCAAAGATCTAGGG 57.010 50.000 0.00 0.39 39.99 3.53
3003 3035 4.657436 AGTAAGGTCGCAAAGATCTAGG 57.343 45.455 0.00 0.00 39.99 3.02
3004 3036 6.100004 TGAAAGTAAGGTCGCAAAGATCTAG 58.900 40.000 0.00 0.00 39.99 2.43
3005 3037 6.032956 TGAAAGTAAGGTCGCAAAGATCTA 57.967 37.500 0.00 0.00 39.99 1.98
3006 3038 4.894784 TGAAAGTAAGGTCGCAAAGATCT 58.105 39.130 0.00 0.00 43.50 2.75
3007 3039 5.607119 TTGAAAGTAAGGTCGCAAAGATC 57.393 39.130 0.00 0.00 0.00 2.75
3008 3040 6.575162 AATTGAAAGTAAGGTCGCAAAGAT 57.425 33.333 0.00 0.00 0.00 2.40
3009 3041 6.385649 AAATTGAAAGTAAGGTCGCAAAGA 57.614 33.333 0.00 0.00 0.00 2.52
3010 3042 6.801862 CCTAAATTGAAAGTAAGGTCGCAAAG 59.198 38.462 0.00 0.00 0.00 2.77
3011 3043 6.263617 ACCTAAATTGAAAGTAAGGTCGCAAA 59.736 34.615 0.00 0.00 31.78 3.68
3012 3044 5.766174 ACCTAAATTGAAAGTAAGGTCGCAA 59.234 36.000 0.00 0.00 31.78 4.85
3013 3045 5.310451 ACCTAAATTGAAAGTAAGGTCGCA 58.690 37.500 0.00 0.00 31.78 5.10
3014 3046 5.866075 GACCTAAATTGAAAGTAAGGTCGC 58.134 41.667 3.75 0.00 42.45 5.19
3017 3049 8.960591 CATCATGACCTAAATTGAAAGTAAGGT 58.039 33.333 0.00 0.00 39.99 3.50
3018 3050 8.960591 ACATCATGACCTAAATTGAAAGTAAGG 58.039 33.333 0.00 0.00 0.00 2.69
3021 3053 9.295825 ACAACATCATGACCTAAATTGAAAGTA 57.704 29.630 0.00 0.00 0.00 2.24
3022 3054 8.084073 CACAACATCATGACCTAAATTGAAAGT 58.916 33.333 0.00 0.00 0.00 2.66
3023 3055 7.062605 GCACAACATCATGACCTAAATTGAAAG 59.937 37.037 0.00 0.00 0.00 2.62
3024 3056 6.867816 GCACAACATCATGACCTAAATTGAAA 59.132 34.615 0.00 0.00 0.00 2.69
3025 3057 6.389091 GCACAACATCATGACCTAAATTGAA 58.611 36.000 0.00 0.00 0.00 2.69
3026 3058 5.391843 CGCACAACATCATGACCTAAATTGA 60.392 40.000 0.00 0.00 0.00 2.57
3027 3059 4.794762 CGCACAACATCATGACCTAAATTG 59.205 41.667 0.00 0.00 0.00 2.32
3028 3060 4.142403 CCGCACAACATCATGACCTAAATT 60.142 41.667 0.00 0.00 0.00 1.82
3029 3061 3.378112 CCGCACAACATCATGACCTAAAT 59.622 43.478 0.00 0.00 0.00 1.40
3030 3062 2.746904 CCGCACAACATCATGACCTAAA 59.253 45.455 0.00 0.00 0.00 1.85
3031 3063 2.355197 CCGCACAACATCATGACCTAA 58.645 47.619 0.00 0.00 0.00 2.69
3032 3064 1.406751 CCCGCACAACATCATGACCTA 60.407 52.381 0.00 0.00 0.00 3.08
3033 3065 0.677731 CCCGCACAACATCATGACCT 60.678 55.000 0.00 0.00 0.00 3.85
3034 3066 0.960364 ACCCGCACAACATCATGACC 60.960 55.000 0.00 0.00 0.00 4.02
3035 3067 0.881118 AACCCGCACAACATCATGAC 59.119 50.000 0.00 0.00 0.00 3.06
3036 3068 1.164411 GAACCCGCACAACATCATGA 58.836 50.000 0.00 0.00 0.00 3.07
3037 3069 0.179192 CGAACCCGCACAACATCATG 60.179 55.000 0.00 0.00 0.00 3.07
3038 3070 0.605319 ACGAACCCGCACAACATCAT 60.605 50.000 0.00 0.00 39.95 2.45
3039 3071 0.816018 AACGAACCCGCACAACATCA 60.816 50.000 0.00 0.00 39.95 3.07
3040 3072 0.385473 CAACGAACCCGCACAACATC 60.385 55.000 0.00 0.00 39.95 3.06
3041 3073 1.098712 ACAACGAACCCGCACAACAT 61.099 50.000 0.00 0.00 39.95 2.71
3042 3074 1.745864 ACAACGAACCCGCACAACA 60.746 52.632 0.00 0.00 39.95 3.33
3043 3075 1.298041 CACAACGAACCCGCACAAC 60.298 57.895 0.00 0.00 39.95 3.32
3044 3076 3.102985 CACAACGAACCCGCACAA 58.897 55.556 0.00 0.00 39.95 3.33
3045 3077 3.578272 GCACAACGAACCCGCACA 61.578 61.111 0.00 0.00 39.95 4.57
3046 3078 3.236618 GAGCACAACGAACCCGCAC 62.237 63.158 0.00 0.00 39.95 5.34
3047 3079 2.970324 GAGCACAACGAACCCGCA 60.970 61.111 0.00 0.00 39.95 5.69
3048 3080 4.072088 CGAGCACAACGAACCCGC 62.072 66.667 0.00 0.00 39.95 6.13
3049 3081 3.411351 CCGAGCACAACGAACCCG 61.411 66.667 0.00 0.00 42.50 5.28
3050 3082 3.723348 GCCGAGCACAACGAACCC 61.723 66.667 0.00 0.00 0.00 4.11
3051 3083 2.954753 CTGCCGAGCACAACGAACC 61.955 63.158 0.00 0.00 33.79 3.62
3052 3084 2.551270 CTGCCGAGCACAACGAAC 59.449 61.111 0.00 0.00 33.79 3.95
3053 3085 3.345808 GCTGCCGAGCACAACGAA 61.346 61.111 0.00 0.00 45.46 3.85
3061 3093 2.437359 AGAACCATGCTGCCGAGC 60.437 61.111 0.00 0.00 46.44 5.03
3062 3094 2.169789 CGAGAACCATGCTGCCGAG 61.170 63.158 0.00 0.00 0.00 4.63
3063 3095 2.125552 CGAGAACCATGCTGCCGA 60.126 61.111 0.00 0.00 0.00 5.54
3064 3096 1.699656 CTTCGAGAACCATGCTGCCG 61.700 60.000 0.00 0.00 0.00 5.69
3065 3097 1.372087 CCTTCGAGAACCATGCTGCC 61.372 60.000 0.00 0.00 0.00 4.85
3066 3098 1.372087 CCCTTCGAGAACCATGCTGC 61.372 60.000 0.00 0.00 0.00 5.25
3067 3099 1.372087 GCCCTTCGAGAACCATGCTG 61.372 60.000 0.00 0.00 0.00 4.41
3068 3100 1.078143 GCCCTTCGAGAACCATGCT 60.078 57.895 0.00 0.00 0.00 3.79
3069 3101 2.115291 GGCCCTTCGAGAACCATGC 61.115 63.158 0.00 0.00 0.00 4.06
3070 3102 1.815421 CGGCCCTTCGAGAACCATG 60.815 63.158 0.00 0.00 0.00 3.66
3071 3103 1.550130 TTCGGCCCTTCGAGAACCAT 61.550 55.000 0.00 0.00 40.42 3.55
3072 3104 2.167398 CTTCGGCCCTTCGAGAACCA 62.167 60.000 0.00 0.00 40.42 3.67
3073 3105 1.448013 CTTCGGCCCTTCGAGAACC 60.448 63.158 0.00 0.00 40.42 3.62
3074 3106 2.101233 GCTTCGGCCCTTCGAGAAC 61.101 63.158 0.00 0.00 40.42 3.01
3075 3107 2.264794 GCTTCGGCCCTTCGAGAA 59.735 61.111 0.00 0.00 40.42 2.87
3076 3108 2.994995 TGCTTCGGCCCTTCGAGA 60.995 61.111 0.00 0.00 40.42 4.04
3077 3109 2.303549 ATCTGCTTCGGCCCTTCGAG 62.304 60.000 0.00 0.00 40.42 4.04
3078 3110 2.298158 GATCTGCTTCGGCCCTTCGA 62.298 60.000 0.00 0.00 40.91 3.71
3079 3111 1.884926 GATCTGCTTCGGCCCTTCG 60.885 63.158 0.00 0.00 40.91 3.79
3080 3112 0.107459 AAGATCTGCTTCGGCCCTTC 60.107 55.000 0.00 0.00 40.91 3.46
3081 3113 0.329596 AAAGATCTGCTTCGGCCCTT 59.670 50.000 0.00 0.00 40.91 3.95
3082 3114 1.204146 TAAAGATCTGCTTCGGCCCT 58.796 50.000 0.00 0.00 40.91 5.19
3083 3115 1.671328 GTTAAAGATCTGCTTCGGCCC 59.329 52.381 0.00 0.00 40.91 5.80
3084 3116 2.356135 TGTTAAAGATCTGCTTCGGCC 58.644 47.619 0.00 0.00 40.91 6.13
3085 3117 4.346129 CAATGTTAAAGATCTGCTTCGGC 58.654 43.478 0.00 0.00 35.24 5.54
3086 3118 4.201950 CCCAATGTTAAAGATCTGCTTCGG 60.202 45.833 0.00 0.00 35.24 4.30
3087 3119 4.635765 TCCCAATGTTAAAGATCTGCTTCG 59.364 41.667 0.00 0.00 35.24 3.79
3088 3120 6.375455 TCTTCCCAATGTTAAAGATCTGCTTC 59.625 38.462 0.00 0.00 35.24 3.86
3089 3121 6.248433 TCTTCCCAATGTTAAAGATCTGCTT 58.752 36.000 0.00 0.00 38.88 3.91
3090 3122 5.819991 TCTTCCCAATGTTAAAGATCTGCT 58.180 37.500 0.00 0.00 0.00 4.24
3091 3123 6.071952 TGTTCTTCCCAATGTTAAAGATCTGC 60.072 38.462 0.00 0.00 0.00 4.26
3092 3124 7.452880 TGTTCTTCCCAATGTTAAAGATCTG 57.547 36.000 0.00 0.00 0.00 2.90
3093 3125 8.655935 AATGTTCTTCCCAATGTTAAAGATCT 57.344 30.769 0.00 0.00 0.00 2.75
3094 3126 8.522830 TGAATGTTCTTCCCAATGTTAAAGATC 58.477 33.333 0.00 0.00 0.00 2.75
3095 3127 8.421249 TGAATGTTCTTCCCAATGTTAAAGAT 57.579 30.769 0.00 0.00 0.00 2.40
3096 3128 7.831691 TGAATGTTCTTCCCAATGTTAAAGA 57.168 32.000 0.00 0.00 0.00 2.52
3097 3129 9.793252 CTATGAATGTTCTTCCCAATGTTAAAG 57.207 33.333 0.00 0.00 0.00 1.85
3098 3130 9.527157 TCTATGAATGTTCTTCCCAATGTTAAA 57.473 29.630 0.00 0.00 0.00 1.52
3099 3131 9.177608 CTCTATGAATGTTCTTCCCAATGTTAA 57.822 33.333 0.00 0.00 0.00 2.01
3100 3132 8.328758 ACTCTATGAATGTTCTTCCCAATGTTA 58.671 33.333 0.00 0.00 0.00 2.41
3101 3133 7.121759 CACTCTATGAATGTTCTTCCCAATGTT 59.878 37.037 0.00 0.00 0.00 2.71
3102 3134 6.600822 CACTCTATGAATGTTCTTCCCAATGT 59.399 38.462 0.00 0.00 0.00 2.71
3103 3135 6.039047 CCACTCTATGAATGTTCTTCCCAATG 59.961 42.308 0.00 0.00 0.00 2.82
3104 3136 6.125029 CCACTCTATGAATGTTCTTCCCAAT 58.875 40.000 0.00 0.00 0.00 3.16
3105 3137 5.500234 CCACTCTATGAATGTTCTTCCCAA 58.500 41.667 0.00 0.00 0.00 4.12
3106 3138 4.626287 GCCACTCTATGAATGTTCTTCCCA 60.626 45.833 0.00 0.00 0.00 4.37
3107 3139 3.879892 GCCACTCTATGAATGTTCTTCCC 59.120 47.826 0.00 0.00 0.00 3.97
3108 3140 3.557595 CGCCACTCTATGAATGTTCTTCC 59.442 47.826 0.00 0.00 0.00 3.46
3109 3141 4.433615 TCGCCACTCTATGAATGTTCTTC 58.566 43.478 0.00 0.00 0.00 2.87
3110 3142 4.471904 TCGCCACTCTATGAATGTTCTT 57.528 40.909 0.00 0.00 0.00 2.52
3111 3143 4.437239 CTTCGCCACTCTATGAATGTTCT 58.563 43.478 0.00 0.00 0.00 3.01
3112 3144 3.557595 CCTTCGCCACTCTATGAATGTTC 59.442 47.826 0.00 0.00 0.00 3.18
3113 3145 3.535561 CCTTCGCCACTCTATGAATGTT 58.464 45.455 0.00 0.00 0.00 2.71
3114 3146 2.743183 GCCTTCGCCACTCTATGAATGT 60.743 50.000 0.00 0.00 0.00 2.71
3115 3147 1.869767 GCCTTCGCCACTCTATGAATG 59.130 52.381 0.00 0.00 0.00 2.67
3116 3148 2.246719 GCCTTCGCCACTCTATGAAT 57.753 50.000 0.00 0.00 0.00 2.57
3117 3149 3.760693 GCCTTCGCCACTCTATGAA 57.239 52.632 0.00 0.00 0.00 2.57
3130 3162 3.717294 TCTTCCCTGGCGGCCTTC 61.717 66.667 21.46 0.00 0.00 3.46
3131 3163 4.035102 GTCTTCCCTGGCGGCCTT 62.035 66.667 21.46 0.00 0.00 4.35
3134 3166 4.475135 GAGGTCTTCCCTGGCGGC 62.475 72.222 0.00 0.00 46.51 6.53
3135 3167 2.685380 AGAGGTCTTCCCTGGCGG 60.685 66.667 0.00 0.00 46.51 6.13
3136 3168 2.726351 GGAGAGGTCTTCCCTGGCG 61.726 68.421 0.00 0.00 46.51 5.69
3137 3169 1.306568 AGGAGAGGTCTTCCCTGGC 60.307 63.158 0.00 0.00 46.51 4.85
3138 3170 0.689412 GGAGGAGAGGTCTTCCCTGG 60.689 65.000 0.00 0.00 46.51 4.45
3139 3171 0.041833 TGGAGGAGAGGTCTTCCCTG 59.958 60.000 1.46 0.00 46.41 4.45
3140 3172 0.338120 CTGGAGGAGAGGTCTTCCCT 59.662 60.000 1.46 0.00 46.41 4.20
3141 3173 1.334384 GCTGGAGGAGAGGTCTTCCC 61.334 65.000 1.46 0.00 46.41 3.97
3143 3175 1.813192 CGCTGGAGGAGAGGTCTTC 59.187 63.158 0.00 0.00 0.00 2.87
3144 3176 2.355193 GCGCTGGAGGAGAGGTCTT 61.355 63.158 0.00 0.00 0.00 3.01
3145 3177 2.757917 GCGCTGGAGGAGAGGTCT 60.758 66.667 0.00 0.00 0.00 3.85
3146 3178 3.844090 GGCGCTGGAGGAGAGGTC 61.844 72.222 7.64 0.00 0.00 3.85
3147 3179 2.516048 TAAGGCGCTGGAGGAGAGGT 62.516 60.000 7.64 0.00 0.00 3.85
3148 3180 1.330655 TTAAGGCGCTGGAGGAGAGG 61.331 60.000 7.64 0.00 0.00 3.69
3149 3181 0.103937 CTTAAGGCGCTGGAGGAGAG 59.896 60.000 7.64 0.00 0.00 3.20
3150 3182 1.961180 GCTTAAGGCGCTGGAGGAGA 61.961 60.000 7.64 0.00 0.00 3.71
3151 3183 1.522580 GCTTAAGGCGCTGGAGGAG 60.523 63.158 7.64 0.00 0.00 3.69
3152 3184 2.584608 GCTTAAGGCGCTGGAGGA 59.415 61.111 7.64 0.00 0.00 3.71
3161 3193 0.533085 CCTTCCCTAGCGCTTAAGGC 60.533 60.000 18.68 6.24 31.04 4.35
3162 3194 0.831307 ACCTTCCCTAGCGCTTAAGG 59.169 55.000 26.16 26.16 42.01 2.69
3163 3195 3.455327 GTTACCTTCCCTAGCGCTTAAG 58.545 50.000 18.68 14.27 0.00 1.85
3164 3196 2.159198 CGTTACCTTCCCTAGCGCTTAA 60.159 50.000 18.68 1.87 0.00 1.85
3165 3197 1.406539 CGTTACCTTCCCTAGCGCTTA 59.593 52.381 18.68 0.00 0.00 3.09
3166 3198 0.175073 CGTTACCTTCCCTAGCGCTT 59.825 55.000 18.68 0.00 0.00 4.68
3167 3199 0.682209 TCGTTACCTTCCCTAGCGCT 60.682 55.000 17.26 17.26 0.00 5.92
3168 3200 0.248949 CTCGTTACCTTCCCTAGCGC 60.249 60.000 0.00 0.00 0.00 5.92
3169 3201 0.248949 GCTCGTTACCTTCCCTAGCG 60.249 60.000 0.00 0.00 0.00 4.26
3170 3202 0.248949 CGCTCGTTACCTTCCCTAGC 60.249 60.000 0.00 0.00 0.00 3.42
3171 3203 0.248949 GCGCTCGTTACCTTCCCTAG 60.249 60.000 0.00 0.00 0.00 3.02
3172 3204 1.669999 GGCGCTCGTTACCTTCCCTA 61.670 60.000 7.64 0.00 0.00 3.53
3173 3205 2.577593 GCGCTCGTTACCTTCCCT 59.422 61.111 0.00 0.00 0.00 4.20
3174 3206 1.669999 TAGGCGCTCGTTACCTTCCC 61.670 60.000 7.64 0.00 34.92 3.97
3175 3207 0.527169 GTAGGCGCTCGTTACCTTCC 60.527 60.000 7.64 0.00 34.92 3.46
3176 3208 0.171903 TGTAGGCGCTCGTTACCTTC 59.828 55.000 7.64 0.00 34.92 3.46
3177 3209 0.172803 CTGTAGGCGCTCGTTACCTT 59.827 55.000 7.64 0.00 34.92 3.50
3178 3210 1.664321 CCTGTAGGCGCTCGTTACCT 61.664 60.000 7.64 0.00 37.61 3.08
3179 3211 1.226888 CCTGTAGGCGCTCGTTACC 60.227 63.158 7.64 0.00 0.00 2.85
3180 3212 4.396854 CCTGTAGGCGCTCGTTAC 57.603 61.111 7.64 6.18 0.00 2.50
3190 3222 2.822637 ATGATGGGGCGCCTGTAGG 61.823 63.158 28.56 0.00 38.53 3.18
3191 3223 1.598962 CATGATGGGGCGCCTGTAG 60.599 63.158 28.56 6.37 0.00 2.74
3192 3224 2.510411 CATGATGGGGCGCCTGTA 59.490 61.111 28.56 13.47 0.00 2.74
3193 3225 4.511246 CCATGATGGGGCGCCTGT 62.511 66.667 28.56 12.74 32.67 4.00
3210 3242 4.338710 TACTTGTGTGGGCCGGCC 62.339 66.667 38.57 38.57 0.00 6.13
3211 3243 3.053896 GTACTTGTGTGGGCCGGC 61.054 66.667 21.18 21.18 0.00 6.13
3212 3244 2.718747 TTCGTACTTGTGTGGGCCGG 62.719 60.000 0.00 0.00 0.00 6.13
3213 3245 0.881159 TTTCGTACTTGTGTGGGCCG 60.881 55.000 0.00 0.00 0.00 6.13
3214 3246 0.872388 CTTTCGTACTTGTGTGGGCC 59.128 55.000 0.00 0.00 0.00 5.80
3215 3247 0.237498 GCTTTCGTACTTGTGTGGGC 59.763 55.000 0.00 0.00 0.00 5.36
3216 3248 1.588674 TGCTTTCGTACTTGTGTGGG 58.411 50.000 0.00 0.00 0.00 4.61
3217 3249 3.896648 AATGCTTTCGTACTTGTGTGG 57.103 42.857 0.00 0.00 0.00 4.17
3229 3261 1.463528 CGTCCCGTTCGAAATGCTTTC 60.464 52.381 0.00 0.00 36.32 2.62
3230 3262 0.515564 CGTCCCGTTCGAAATGCTTT 59.484 50.000 0.00 0.00 0.00 3.51
3231 3263 1.908066 GCGTCCCGTTCGAAATGCTT 61.908 55.000 0.00 0.00 0.00 3.91
3232 3264 2.388232 GCGTCCCGTTCGAAATGCT 61.388 57.895 0.00 0.00 0.00 3.79
3233 3265 2.097728 GCGTCCCGTTCGAAATGC 59.902 61.111 0.00 0.00 0.00 3.56
3234 3266 1.693083 GGAGCGTCCCGTTCGAAATG 61.693 60.000 0.00 0.00 37.94 2.32
3235 3267 1.447314 GGAGCGTCCCGTTCGAAAT 60.447 57.895 0.00 0.00 37.94 2.17
3236 3268 2.048877 GGAGCGTCCCGTTCGAAA 60.049 61.111 0.00 0.00 37.94 3.46
3237 3269 4.409218 CGGAGCGTCCCGTTCGAA 62.409 66.667 9.04 0.00 44.23 3.71


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

AutoCloner maintained by Alex Coulton.