Multiple sequence alignment - TraesCS1D01G184100

Loading Multiple Alignment...

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 TraesCS1D01G184100 chr1D 100.000 3955 0 0 4077 8031 254607712 254611666 0.000000e+00 7304.0
1 TraesCS1D01G184100 chr1D 100.000 3002 0 0 793 3794 254604428 254607429 0.000000e+00 5544.0
2 TraesCS1D01G184100 chr1D 100.000 457 0 0 1 457 254603636 254604092 0.000000e+00 845.0
3 TraesCS1D01G184100 chr1B 94.096 3269 140 32 4384 7617 358024945 358021695 0.000000e+00 4918.0
4 TraesCS1D01G184100 chr1B 93.587 2869 136 26 4920 7756 358024380 358021528 0.000000e+00 4235.0
5 TraesCS1D01G184100 chr1B 97.767 1388 31 0 796 2183 358028253 358026866 0.000000e+00 2392.0
6 TraesCS1D01G184100 chr1B 94.236 694 29 4 3093 3785 358026356 358025673 0.000000e+00 1050.0
7 TraesCS1D01G184100 chr1B 90.956 387 29 3 2209 2595 358026869 358026489 4.300000e-142 516.0
8 TraesCS1D01G184100 chr1B 91.209 364 28 2 2 362 358028920 358028558 7.240000e-135 492.0
9 TraesCS1D01G184100 chr1B 93.377 302 14 3 4090 4388 358025364 358025066 7.400000e-120 442.0
10 TraesCS1D01G184100 chr1B 92.500 240 10 3 7793 8031 358021451 358021219 3.590000e-88 337.0
11 TraesCS1D01G184100 chr1A 97.494 2753 55 7 4914 7654 326211663 326214413 0.000000e+00 4689.0
12 TraesCS1D01G184100 chr1A 97.439 2148 48 4 796 2943 326207918 326210058 0.000000e+00 3655.0
13 TraesCS1D01G184100 chr1A 96.292 836 14 7 4089 4923 326210826 326211645 0.000000e+00 1356.0
14 TraesCS1D01G184100 chr1A 98.299 529 9 0 3089 3617 326210063 326210591 0.000000e+00 928.0
15 TraesCS1D01G184100 chr1A 93.066 274 18 1 185 457 326201696 326201969 4.520000e-107 399.0
16 TraesCS1D01G184100 chr1A 93.724 239 14 1 7786 8023 326215049 326215287 2.760000e-94 357.0
17 TraesCS1D01G184100 chr1A 97.203 143 1 1 2 141 326201553 326201695 1.040000e-58 239.0
18 TraesCS1D01G184100 chr6B 80.663 362 66 2 4 362 699883057 699883417 2.210000e-70 278.0
19 TraesCS1D01G184100 chr6B 87.654 81 7 2 364 441 699803956 699804036 3.090000e-14 91.6
20 TraesCS1D01G184100 chr6B 87.654 81 7 2 364 441 699843858 699843938 3.090000e-14 91.6
21 TraesCS1D01G184100 chr6B 87.654 81 7 2 364 441 699934345 699934425 3.090000e-14 91.6
22 TraesCS1D01G184100 chr6B 90.000 70 4 2 364 430 699883469 699883538 3.990000e-13 87.9
23 TraesCS1D01G184100 chr5A 80.435 368 63 9 2 361 9514871 9514505 1.030000e-68 272.0
24 TraesCS1D01G184100 chr7D 93.506 154 9 1 2936 3088 610227298 610227145 2.250000e-55 228.0
25 TraesCS1D01G184100 chrUn 97.826 46 0 1 2990 3034 11560378 11560333 2.400000e-10 78.7
26 TraesCS1D01G184100 chr7B 97.561 41 1 0 3048 3088 743136885 743136925 4.020000e-08 71.3


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 TraesCS1D01G184100 chr1D 254603636 254611666 8030 False 4564.333333 7304 100.0000 1 8031 3 chr1D.!!$F1 8030
1 TraesCS1D01G184100 chr1B 358021219 358028920 7701 True 1797.750000 4918 93.4660 2 8031 8 chr1B.!!$R1 8029
2 TraesCS1D01G184100 chr1A 326207918 326215287 7369 False 2197.000000 4689 96.6496 796 8023 5 chr1A.!!$F2 7227

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
366 370 0.250467 CCACACCAGGTCCAGTGAAG 60.250 60.000 16.66 9.53 37.43 3.02 F
368 372 1.056700 ACACCAGGTCCAGTGAAGCT 61.057 55.000 16.66 0.00 37.43 3.74 F
371 375 1.079543 CAGGTCCAGTGAAGCTCCG 60.080 63.158 0.00 0.00 0.00 4.63 F
374 427 1.446966 GTCCAGTGAAGCTCCGCTC 60.447 63.158 0.00 0.00 38.25 5.03 F
1551 1607 1.669999 GCTGGGCTTCGGCATTTCAT 61.670 55.000 6.55 0.00 46.73 2.57 F
2753 2815 0.320421 ACATTCGGACCACGGTTCTG 60.320 55.000 0.00 0.00 44.45 3.02 F
2754 2816 1.375523 ATTCGGACCACGGTTCTGC 60.376 57.895 0.00 0.00 44.45 4.26 F
3791 3854 0.662619 GGATGGTGTGTGTGTGTGTG 59.337 55.000 0.00 0.00 0.00 3.82 F
3793 3856 1.063912 GATGGTGTGTGTGTGTGTGTG 59.936 52.381 0.00 0.00 0.00 3.82 F
4500 4694 1.905215 ACTCATCCTCTCCCTGTTGTG 59.095 52.381 0.00 0.00 0.00 3.33 F
6049 6282 2.076863 AGAGCAGAATGTTTACCACGC 58.923 47.619 0.00 0.00 39.31 5.34 F
6792 7025 2.158325 TGGGATTTGGCTCCTCTTTGTT 60.158 45.455 0.00 0.00 35.50 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2017 2073 1.206578 CGACCACCGTTGAACATGC 59.793 57.895 0.00 0.00 0.00 4.06 R
2255 2311 5.589855 TGATCCTAACAACATTGCATTCGAT 59.410 36.000 0.00 0.00 0.00 3.59 R
2680 2742 5.946942 AAATCAGGCTAGTGATTGAGAGA 57.053 39.130 8.82 0.00 44.72 3.10 R
2681 2743 6.481644 GGTAAAATCAGGCTAGTGATTGAGAG 59.518 42.308 8.82 0.00 44.72 3.20 R
2763 2825 0.832626 AGCCGACATGACATGGATCA 59.167 50.000 19.39 0.00 33.60 2.92 R
3713 3776 2.889512 ACTATGTGACACTGTCCTGGA 58.110 47.619 7.20 0.00 0.00 3.86 R
4279 4345 4.764679 TTGTTGTGGCATAGCAAAGTAG 57.235 40.909 10.85 0.00 0.00 2.57 R
5811 6044 1.003349 AGAGCTCAAGAACTGCAGCAT 59.997 47.619 17.77 2.22 33.27 3.79 R
5937 6170 1.132453 CAGCACCATCAACATCTGCTG 59.868 52.381 3.72 3.72 46.41 4.41 R
6329 6562 1.771854 TGTTGTGGTGCCCTTAGAAGA 59.228 47.619 0.00 0.00 0.00 2.87 R
7003 7236 0.249573 CAGTGTTTTTGGCTGGCCTG 60.250 55.000 13.05 4.26 36.94 4.85 R
7947 8713 1.185618 TAGCAACCTCCAGCTCGTGT 61.186 55.000 0.00 0.00 42.05 4.49 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
18 19 3.715871 TCAAAGACCACCGATGCAA 57.284 47.368 0.00 0.00 0.00 4.08
47 48 1.198713 GGAGACAGGGAAGCAGATCA 58.801 55.000 0.00 0.00 0.00 2.92
66 70 4.742201 CGGAGACCACCAGCACCG 62.742 72.222 0.00 0.00 34.77 4.94
70 74 1.816863 GAGACCACCAGCACCGAGAA 61.817 60.000 0.00 0.00 0.00 2.87
93 97 2.604046 AGCCACTTATCATCACCGTC 57.396 50.000 0.00 0.00 0.00 4.79
100 104 4.733887 CACTTATCATCACCGTCGAAGTAC 59.266 45.833 0.00 0.00 0.00 2.73
151 155 3.305516 GGGTGGCTGCCAAACCAG 61.306 66.667 28.83 0.00 36.38 4.00
160 164 2.284112 CCAAACCAGGCCAGCCAT 60.284 61.111 12.03 0.00 38.92 4.40
245 249 4.758251 CGTCGACCATGGCTGCCA 62.758 66.667 25.65 25.65 38.19 4.92
246 250 2.359850 GTCGACCATGGCTGCCAA 60.360 61.111 27.24 9.47 36.95 4.52
311 315 4.003788 AAGTAGCCGCAGCCACGT 62.004 61.111 0.00 0.00 41.25 4.49
333 337 3.161450 ACAGGGTCACACCACGCT 61.161 61.111 0.00 0.00 41.02 5.07
362 366 3.941188 CGCCACACCAGGTCCAGT 61.941 66.667 0.00 0.00 0.00 4.00
364 368 2.818169 GCCACACCAGGTCCAGTGA 61.818 63.158 16.66 0.00 37.43 3.41
365 369 1.836391 CCACACCAGGTCCAGTGAA 59.164 57.895 16.66 0.00 37.43 3.18
366 370 0.250467 CCACACCAGGTCCAGTGAAG 60.250 60.000 16.66 9.53 37.43 3.02
368 372 1.056700 ACACCAGGTCCAGTGAAGCT 61.057 55.000 16.66 0.00 37.43 3.74
371 375 1.079543 CAGGTCCAGTGAAGCTCCG 60.080 63.158 0.00 0.00 0.00 4.63
374 427 1.446966 GTCCAGTGAAGCTCCGCTC 60.447 63.158 0.00 0.00 38.25 5.03
384 437 4.200283 CTCCGCTCCGTCAGCCTC 62.200 72.222 0.00 0.00 46.74 4.70
456 512 3.373565 GGAACTGCCCGGGCTTTG 61.374 66.667 43.34 32.91 42.51 2.77
1146 1202 9.774742 GTATTTCCAGAAACAAGCAATACTAAG 57.225 33.333 0.00 0.00 32.51 2.18
1240 1296 6.492007 TTGAAGATGAGAAGTCTGATTTGC 57.508 37.500 0.00 0.00 0.00 3.68
1272 1328 3.139077 AGTTTGTTCTGGGAAGCTTACG 58.861 45.455 1.68 0.00 0.00 3.18
1551 1607 1.669999 GCTGGGCTTCGGCATTTCAT 61.670 55.000 6.55 0.00 46.73 2.57
1927 1983 7.148641 AGTAGAAGCATGTTAATACCGAGATG 58.851 38.462 0.00 0.00 0.00 2.90
2236 2292 1.816835 GGAGTACCTCACATCGACACA 59.183 52.381 0.00 0.00 31.08 3.72
2255 2311 6.061022 ACACAGTCATACCATTGATTACCA 57.939 37.500 0.00 0.00 0.00 3.25
2499 2561 5.300752 TCAGTTGAACTCATTTCTGGTCTC 58.699 41.667 0.00 0.00 34.97 3.36
2717 2779 5.420104 AGCCTGATTTTACCTTTGATTCCAG 59.580 40.000 0.00 0.00 0.00 3.86
2753 2815 0.320421 ACATTCGGACCACGGTTCTG 60.320 55.000 0.00 0.00 44.45 3.02
2754 2816 1.375523 ATTCGGACCACGGTTCTGC 60.376 57.895 0.00 0.00 44.45 4.26
2763 2825 2.167487 ACCACGGTTCTGCAAACATTTT 59.833 40.909 11.93 0.00 0.00 1.82
2833 2895 9.298250 ACTTCTTATGTCAGTTACTCAGTTCTA 57.702 33.333 0.00 0.00 0.00 2.10
2847 2909 5.879223 ACTCAGTTCTAGGATGCTGAATTTG 59.121 40.000 0.00 3.13 37.50 2.32
2851 2913 7.334421 TCAGTTCTAGGATGCTGAATTTGTTAC 59.666 37.037 0.00 0.00 35.36 2.50
2869 2931 4.998033 TGTTACGAATGCCATTTCTGTACA 59.002 37.500 0.00 0.00 0.00 2.90
2962 3024 1.794512 AATGTTCAAACCGCATTGGC 58.205 45.000 0.00 0.00 43.94 4.52
2964 3026 1.610363 TGTTCAAACCGCATTGGCTA 58.390 45.000 0.00 0.00 43.94 3.93
2966 3028 2.362397 TGTTCAAACCGCATTGGCTAAA 59.638 40.909 0.00 0.00 43.94 1.85
2968 3030 4.218635 TGTTCAAACCGCATTGGCTAAATA 59.781 37.500 0.00 0.00 43.94 1.40
2970 3032 5.590530 TCAAACCGCATTGGCTAAATATT 57.409 34.783 0.00 0.00 43.94 1.28
2971 3033 5.971763 TCAAACCGCATTGGCTAAATATTT 58.028 33.333 5.89 5.89 43.94 1.40
2974 3036 8.200792 TCAAACCGCATTGGCTAAATATTTATT 58.799 29.630 8.34 0.00 43.94 1.40
2975 3037 9.469807 CAAACCGCATTGGCTAAATATTTATTA 57.530 29.630 8.34 0.00 43.94 0.98
2997 3059 8.635765 ATTAAAAAGAAAGTAGTCATCAGGCA 57.364 30.769 0.00 0.00 0.00 4.75
2998 3060 8.635765 TTAAAAAGAAAGTAGTCATCAGGCAT 57.364 30.769 0.00 0.00 0.00 4.40
3000 3062 4.414337 AGAAAGTAGTCATCAGGCATCC 57.586 45.455 0.00 0.00 0.00 3.51
3003 3065 4.574674 AAGTAGTCATCAGGCATCCAAA 57.425 40.909 0.00 0.00 0.00 3.28
3004 3066 4.148128 AGTAGTCATCAGGCATCCAAAG 57.852 45.455 0.00 0.00 0.00 2.77
3005 3067 3.521126 AGTAGTCATCAGGCATCCAAAGT 59.479 43.478 0.00 0.00 0.00 2.66
3006 3068 3.446442 AGTCATCAGGCATCCAAAGTT 57.554 42.857 0.00 0.00 0.00 2.66
3007 3069 3.771216 AGTCATCAGGCATCCAAAGTTT 58.229 40.909 0.00 0.00 0.00 2.66
3008 3070 4.922206 AGTCATCAGGCATCCAAAGTTTA 58.078 39.130 0.00 0.00 0.00 2.01
3009 3071 5.324409 AGTCATCAGGCATCCAAAGTTTAA 58.676 37.500 0.00 0.00 0.00 1.52
3010 3072 5.183904 AGTCATCAGGCATCCAAAGTTTAAC 59.816 40.000 0.00 0.00 0.00 2.01
3011 3073 4.462483 TCATCAGGCATCCAAAGTTTAACC 59.538 41.667 0.00 0.00 0.00 2.85
3012 3074 3.838565 TCAGGCATCCAAAGTTTAACCA 58.161 40.909 0.00 0.00 0.00 3.67
3013 3075 4.415596 TCAGGCATCCAAAGTTTAACCAT 58.584 39.130 0.00 0.00 0.00 3.55
3014 3076 5.575157 TCAGGCATCCAAAGTTTAACCATA 58.425 37.500 0.00 0.00 0.00 2.74
3015 3077 6.194235 TCAGGCATCCAAAGTTTAACCATAT 58.806 36.000 0.00 0.00 0.00 1.78
3016 3078 6.321181 TCAGGCATCCAAAGTTTAACCATATC 59.679 38.462 0.00 0.00 0.00 1.63
3017 3079 6.096705 CAGGCATCCAAAGTTTAACCATATCA 59.903 38.462 0.00 0.00 0.00 2.15
3018 3080 6.667414 AGGCATCCAAAGTTTAACCATATCAA 59.333 34.615 0.00 0.00 0.00 2.57
3019 3081 6.980397 GGCATCCAAAGTTTAACCATATCAAG 59.020 38.462 0.00 0.00 0.00 3.02
3020 3082 6.476706 GCATCCAAAGTTTAACCATATCAAGC 59.523 38.462 0.00 0.00 0.00 4.01
3021 3083 7.546358 CATCCAAAGTTTAACCATATCAAGCA 58.454 34.615 0.00 0.00 0.00 3.91
3022 3084 6.919721 TCCAAAGTTTAACCATATCAAGCAC 58.080 36.000 0.00 0.00 0.00 4.40
3023 3085 6.491745 TCCAAAGTTTAACCATATCAAGCACA 59.508 34.615 0.00 0.00 0.00 4.57
3024 3086 6.808212 CCAAAGTTTAACCATATCAAGCACAG 59.192 38.462 0.00 0.00 0.00 3.66
3025 3087 7.370383 CAAAGTTTAACCATATCAAGCACAGT 58.630 34.615 0.00 0.00 0.00 3.55
3026 3088 8.511321 CAAAGTTTAACCATATCAAGCACAGTA 58.489 33.333 0.00 0.00 0.00 2.74
3027 3089 7.849804 AGTTTAACCATATCAAGCACAGTAG 57.150 36.000 0.00 0.00 0.00 2.57
3028 3090 7.394816 AGTTTAACCATATCAAGCACAGTAGT 58.605 34.615 0.00 0.00 0.00 2.73
3030 3092 4.142609 ACCATATCAAGCACAGTAGTGG 57.857 45.455 1.92 0.00 45.98 4.00
3031 3093 3.774766 ACCATATCAAGCACAGTAGTGGA 59.225 43.478 1.92 0.00 45.98 4.02
3032 3094 4.410228 ACCATATCAAGCACAGTAGTGGAT 59.590 41.667 1.92 0.00 45.98 3.41
3033 3095 4.993584 CCATATCAAGCACAGTAGTGGATC 59.006 45.833 1.92 0.00 45.98 3.36
3034 3096 3.550437 ATCAAGCACAGTAGTGGATCC 57.450 47.619 4.20 4.20 45.98 3.36
3035 3097 2.256306 TCAAGCACAGTAGTGGATCCA 58.744 47.619 11.44 11.44 45.98 3.41
3036 3098 2.637382 TCAAGCACAGTAGTGGATCCAA 59.363 45.455 18.20 0.00 45.98 3.53
3037 3099 3.072330 TCAAGCACAGTAGTGGATCCAAA 59.928 43.478 18.20 4.78 45.98 3.28
3038 3100 3.788227 AGCACAGTAGTGGATCCAAAA 57.212 42.857 18.20 4.35 45.98 2.44
3039 3101 4.307032 AGCACAGTAGTGGATCCAAAAT 57.693 40.909 18.20 8.34 45.98 1.82
3040 3102 4.666512 AGCACAGTAGTGGATCCAAAATT 58.333 39.130 18.20 5.29 45.98 1.82
3041 3103 4.702131 AGCACAGTAGTGGATCCAAAATTC 59.298 41.667 18.20 3.21 45.98 2.17
3042 3104 4.458989 GCACAGTAGTGGATCCAAAATTCA 59.541 41.667 18.20 0.00 45.98 2.57
3043 3105 5.392380 GCACAGTAGTGGATCCAAAATTCAG 60.392 44.000 18.20 6.29 45.98 3.02
3044 3106 5.124457 CACAGTAGTGGATCCAAAATTCAGG 59.876 44.000 18.20 4.27 42.13 3.86
3045 3107 4.096984 CAGTAGTGGATCCAAAATTCAGGC 59.903 45.833 18.20 0.00 0.00 4.85
3046 3108 3.173953 AGTGGATCCAAAATTCAGGCA 57.826 42.857 18.20 0.00 0.00 4.75
3047 3109 2.827921 AGTGGATCCAAAATTCAGGCAC 59.172 45.455 18.20 0.00 0.00 5.01
3048 3110 2.827921 GTGGATCCAAAATTCAGGCACT 59.172 45.455 18.20 0.00 43.88 4.40
3049 3111 4.016444 GTGGATCCAAAATTCAGGCACTA 58.984 43.478 18.20 0.00 36.02 2.74
3050 3112 4.096984 GTGGATCCAAAATTCAGGCACTAG 59.903 45.833 18.20 0.00 36.02 2.57
3051 3113 4.263905 TGGATCCAAAATTCAGGCACTAGT 60.264 41.667 13.46 0.00 36.02 2.57
3052 3114 4.706962 GGATCCAAAATTCAGGCACTAGTT 59.293 41.667 6.95 0.00 36.02 2.24
3053 3115 5.393461 GGATCCAAAATTCAGGCACTAGTTG 60.393 44.000 6.95 0.00 36.02 3.16
3054 3116 4.724399 TCCAAAATTCAGGCACTAGTTGA 58.276 39.130 0.00 0.00 36.02 3.18
3055 3117 5.136828 TCCAAAATTCAGGCACTAGTTGAA 58.863 37.500 10.18 10.18 36.02 2.69
3056 3118 5.241506 TCCAAAATTCAGGCACTAGTTGAAG 59.758 40.000 12.66 1.75 36.02 3.02
3057 3119 4.773323 AAATTCAGGCACTAGTTGAAGC 57.227 40.909 12.66 4.79 36.02 3.86
3058 3120 2.928801 TTCAGGCACTAGTTGAAGCA 57.071 45.000 4.67 0.00 36.02 3.91
3059 3121 3.423539 TTCAGGCACTAGTTGAAGCAT 57.576 42.857 4.67 0.00 36.02 3.79
3060 3122 2.977914 TCAGGCACTAGTTGAAGCATC 58.022 47.619 5.41 0.00 36.02 3.91
3061 3123 2.302733 TCAGGCACTAGTTGAAGCATCA 59.697 45.455 5.41 0.00 36.02 3.07
3062 3124 3.054875 TCAGGCACTAGTTGAAGCATCAT 60.055 43.478 5.41 0.00 36.02 2.45
3063 3125 3.693085 CAGGCACTAGTTGAAGCATCATT 59.307 43.478 5.41 0.00 36.02 2.57
3064 3126 4.877823 CAGGCACTAGTTGAAGCATCATTA 59.122 41.667 5.41 0.00 36.02 1.90
3065 3127 4.878397 AGGCACTAGTTGAAGCATCATTAC 59.122 41.667 5.41 0.00 36.02 1.89
3066 3128 4.035675 GGCACTAGTTGAAGCATCATTACC 59.964 45.833 5.41 0.00 34.96 2.85
3067 3129 4.878397 GCACTAGTTGAAGCATCATTACCT 59.122 41.667 0.00 0.00 34.96 3.08
3068 3130 5.007136 GCACTAGTTGAAGCATCATTACCTC 59.993 44.000 0.00 0.00 34.96 3.85
3069 3131 6.108687 CACTAGTTGAAGCATCATTACCTCA 58.891 40.000 0.00 0.00 34.96 3.86
3070 3132 6.036517 CACTAGTTGAAGCATCATTACCTCAC 59.963 42.308 0.00 0.00 34.96 3.51
3071 3133 4.910195 AGTTGAAGCATCATTACCTCACA 58.090 39.130 0.00 0.00 34.96 3.58
3072 3134 4.940046 AGTTGAAGCATCATTACCTCACAG 59.060 41.667 0.00 0.00 34.96 3.66
3073 3135 4.824479 TGAAGCATCATTACCTCACAGA 57.176 40.909 0.00 0.00 0.00 3.41
3074 3136 5.363562 TGAAGCATCATTACCTCACAGAT 57.636 39.130 0.00 0.00 0.00 2.90
3075 3137 5.748402 TGAAGCATCATTACCTCACAGATT 58.252 37.500 0.00 0.00 0.00 2.40
3076 3138 5.819379 TGAAGCATCATTACCTCACAGATTC 59.181 40.000 0.00 0.00 0.00 2.52
3077 3139 5.363562 AGCATCATTACCTCACAGATTCA 57.636 39.130 0.00 0.00 0.00 2.57
3078 3140 5.748402 AGCATCATTACCTCACAGATTCAA 58.252 37.500 0.00 0.00 0.00 2.69
3079 3141 6.182627 AGCATCATTACCTCACAGATTCAAA 58.817 36.000 0.00 0.00 0.00 2.69
3080 3142 6.832384 AGCATCATTACCTCACAGATTCAAAT 59.168 34.615 0.00 0.00 0.00 2.32
3081 3143 7.994911 AGCATCATTACCTCACAGATTCAAATA 59.005 33.333 0.00 0.00 0.00 1.40
3082 3144 8.288208 GCATCATTACCTCACAGATTCAAATAG 58.712 37.037 0.00 0.00 0.00 1.73
3083 3145 9.551734 CATCATTACCTCACAGATTCAAATAGA 57.448 33.333 0.00 0.00 0.00 1.98
3085 3147 9.605275 TCATTACCTCACAGATTCAAATAGAAG 57.395 33.333 0.00 0.00 40.15 2.85
3086 3148 9.605275 CATTACCTCACAGATTCAAATAGAAGA 57.395 33.333 0.00 0.00 40.15 2.87
3087 3149 9.829507 ATTACCTCACAGATTCAAATAGAAGAG 57.170 33.333 0.00 0.00 40.15 2.85
3340 3402 2.357637 CGGTGGCGATGGAATTGTTAAT 59.642 45.455 0.00 0.00 0.00 1.40
3428 3490 5.841209 TGGGGTCTAGTGTGGTATAGTAAA 58.159 41.667 0.00 0.00 0.00 2.01
3498 3561 9.129209 CTGGATTTTCTAAATTTTCCGAACTTC 57.871 33.333 0.00 0.00 0.00 3.01
3581 3644 1.599071 CAACCGCCATAGCACATACTG 59.401 52.381 0.00 0.00 39.83 2.74
3597 3660 6.642131 GCACATACTGATTTCACACATTTGTT 59.358 34.615 0.00 0.00 31.66 2.83
3713 3776 7.509546 TCATCAGGAAGAGTACAGTTCTTTTT 58.490 34.615 0.00 0.00 35.14 1.94
3727 3790 3.924114 TCTTTTTCCAGGACAGTGTCA 57.076 42.857 24.20 1.00 33.68 3.58
3785 3848 3.256936 CAGCGGATGGTGTGTGTG 58.743 61.111 0.00 0.00 38.78 3.82
3786 3849 1.597854 CAGCGGATGGTGTGTGTGT 60.598 57.895 0.00 0.00 38.78 3.72
3787 3850 1.597854 AGCGGATGGTGTGTGTGTG 60.598 57.895 0.00 0.00 0.00 3.82
3788 3851 1.891919 GCGGATGGTGTGTGTGTGT 60.892 57.895 0.00 0.00 0.00 3.72
3789 3852 1.941072 CGGATGGTGTGTGTGTGTG 59.059 57.895 0.00 0.00 0.00 3.82
3790 3853 0.813610 CGGATGGTGTGTGTGTGTGT 60.814 55.000 0.00 0.00 0.00 3.72
3791 3854 0.662619 GGATGGTGTGTGTGTGTGTG 59.337 55.000 0.00 0.00 0.00 3.82
3792 3855 1.378531 GATGGTGTGTGTGTGTGTGT 58.621 50.000 0.00 0.00 0.00 3.72
3793 3856 1.063912 GATGGTGTGTGTGTGTGTGTG 59.936 52.381 0.00 0.00 0.00 3.82
4279 4345 8.986477 AAAAAGTTTGCATACACCATATTCTC 57.014 30.769 10.02 0.00 0.00 2.87
4280 4346 7.944729 AAAGTTTGCATACACCATATTCTCT 57.055 32.000 10.02 0.00 0.00 3.10
4363 4432 7.203218 ACTCAGAAGGTTTAAATTGTTTCAGC 58.797 34.615 0.00 0.00 0.00 4.26
4432 4626 9.918630 TGTATGTTTACTACTGTCTAACCTTTC 57.081 33.333 0.00 0.00 0.00 2.62
4500 4694 1.905215 ACTCATCCTCTCCCTGTTGTG 59.095 52.381 0.00 0.00 0.00 3.33
4805 5002 9.926158 AACTTTGCATATAATTTGTTGACATCA 57.074 25.926 0.00 0.00 0.00 3.07
4897 5094 5.297569 AGATACACCTTTAGGGATTCAGC 57.702 43.478 0.10 0.00 40.27 4.26
4953 5177 4.568152 AATGGTGCTTGTACACTGAAAC 57.432 40.909 0.00 0.00 40.52 2.78
5098 5324 5.705441 CCTAATGTTAGCTGTTCTGTTGGAA 59.295 40.000 0.00 0.00 0.00 3.53
5099 5325 5.695851 AATGTTAGCTGTTCTGTTGGAAG 57.304 39.130 0.00 0.00 34.23 3.46
5111 5337 3.094572 CTGTTGGAAGCTTCATCCCAAT 58.905 45.455 27.02 0.00 40.35 3.16
5144 5370 4.737855 ATAGCGTGTCCTATTGTTGAGT 57.262 40.909 0.00 0.00 0.00 3.41
5304 5530 4.321899 CCATGGACCCACACAAAAATACAG 60.322 45.833 5.56 0.00 0.00 2.74
5324 5550 4.163078 ACAGCACAGCTCCACTCTTAATAT 59.837 41.667 0.00 0.00 36.40 1.28
5827 6060 6.261603 TCCATTTATATGCTGCAGTTCTTGAG 59.738 38.462 16.64 0.00 0.00 3.02
6049 6282 2.076863 AGAGCAGAATGTTTACCACGC 58.923 47.619 0.00 0.00 39.31 5.34
6214 6447 6.503560 TTAGGGAGGACAAGTACTTTCAAA 57.496 37.500 5.07 0.00 0.00 2.69
6329 6562 7.744087 TTGACTGCTACAAATGACACTAAAT 57.256 32.000 0.00 0.00 0.00 1.40
6792 7025 2.158325 TGGGATTTGGCTCCTCTTTGTT 60.158 45.455 0.00 0.00 35.50 2.83
6815 7048 5.748402 TGAGCATCCAGTTTTACTCATCAT 58.252 37.500 0.00 0.00 0.00 2.45
6819 7052 5.503031 GCATCCAGTTTTACTCATCATGACG 60.503 44.000 0.00 0.00 0.00 4.35
6943 7176 2.438021 GTGTGGTATTGATGGGGAGCTA 59.562 50.000 0.00 0.00 0.00 3.32
7003 7236 0.517316 AGCAAAGTCGTTTGATCGGC 59.483 50.000 2.90 0.00 45.22 5.54
7019 7252 2.820973 GCAGGCCAGCCAAAAACA 59.179 55.556 9.39 0.00 38.92 2.83
7101 7334 2.614983 TGTACAACCGGCAACTTTCTTC 59.385 45.455 0.00 0.00 0.00 2.87
7212 7445 2.236146 TGCCAGACGGTGACATTTATCT 59.764 45.455 0.00 0.00 33.28 1.98
7216 7449 5.050490 CCAGACGGTGACATTTATCTAAGG 58.950 45.833 0.00 0.00 0.00 2.69
7269 7502 0.440371 GCTTCTCTTCGTTTCGCCTG 59.560 55.000 0.00 0.00 0.00 4.85
7327 7560 1.847328 TCTGATCAGCGTACTTGGGA 58.153 50.000 18.36 0.00 0.00 4.37
7330 7563 0.105039 GATCAGCGTACTTGGGAGGG 59.895 60.000 0.00 0.00 0.00 4.30
7331 7564 0.325296 ATCAGCGTACTTGGGAGGGA 60.325 55.000 0.00 0.00 0.00 4.20
7332 7565 0.325296 TCAGCGTACTTGGGAGGGAT 60.325 55.000 0.00 0.00 0.00 3.85
7476 7709 0.325933 TGTCCCTGATCAGCTTGTGG 59.674 55.000 17.76 12.46 0.00 4.17
7477 7710 0.326264 GTCCCTGATCAGCTTGTGGT 59.674 55.000 17.76 0.00 0.00 4.16
7492 7725 2.634600 TGTGGTGTTTACAGAAAGCGT 58.365 42.857 0.00 0.00 0.00 5.07
7622 7861 1.067743 TGTGTTTGTGTTTGTGCGCG 61.068 50.000 0.00 0.00 0.00 6.86
7748 8038 4.323417 TGTTGGTCGCATAGAACTGAATT 58.677 39.130 0.00 0.00 37.49 2.17
7791 8557 7.040823 GGAGGGCTGAAACTTATTAATCATCAG 60.041 40.741 0.00 1.93 36.71 2.90
7851 8617 3.726517 CCACGCTTCTGGCAACCG 61.727 66.667 0.00 0.00 41.91 4.44
7864 8630 1.548269 GGCAACCGGGATCATTGAAAA 59.452 47.619 6.32 0.00 0.00 2.29
8004 8770 3.204827 GCACCTGGCGATTGCGAT 61.205 61.111 0.00 0.00 44.10 4.58
8005 8771 3.017323 CACCTGGCGATTGCGATC 58.983 61.111 3.59 3.59 44.10 3.69
8006 8772 1.522355 CACCTGGCGATTGCGATCT 60.522 57.895 12.19 0.00 44.10 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.522668 CTTGCATCGGTGGTCTTTGA 58.477 50.000 0.00 0.00 0.00 2.69
18 19 1.611851 CCTGTCTCCTGTCTGCCCT 60.612 63.158 0.00 0.00 0.00 5.19
47 48 3.626924 GTGCTGGTGGTCTCCGGT 61.627 66.667 0.00 0.00 36.33 5.28
66 70 4.813697 GTGATGATAAGTGGCTTCCTTCTC 59.186 45.833 0.00 0.00 0.00 2.87
70 74 2.158900 CGGTGATGATAAGTGGCTTCCT 60.159 50.000 0.00 0.00 0.00 3.36
183 187 2.187946 GTGATGGCGCCACTAGCT 59.812 61.111 35.50 16.95 40.39 3.32
193 197 1.527844 GGCAGATCCCTGTGATGGC 60.528 63.158 0.00 0.00 42.35 4.40
351 355 1.484444 GGAGCTTCACTGGACCTGGT 61.484 60.000 0.00 0.00 0.00 4.00
804 860 9.158233 TGTGCCTTAGTATGTTGTATAAGAAAC 57.842 33.333 0.00 0.00 0.00 2.78
940 996 5.300286 GCATTGGAGCTACATGTTAGGAAAT 59.700 40.000 2.30 0.00 0.00 2.17
1161 1217 6.579666 TCTTTGCTTGCATCTTCTACATTT 57.420 33.333 0.00 0.00 0.00 2.32
1172 1228 4.322499 CCTTTTCTGGATCTTTGCTTGCAT 60.322 41.667 0.00 0.00 0.00 3.96
1240 1296 5.105473 TCCCAGAACAAACTTCGTATCCTAG 60.105 44.000 0.00 0.00 0.00 3.02
1272 1328 4.392138 ACGCTTCTGCCTTTGTTATCTAAC 59.608 41.667 0.00 0.00 34.74 2.34
1454 1510 5.906113 TGCTTGTGGTAAAACTCAGAAAA 57.094 34.783 0.00 0.00 0.00 2.29
1532 1588 1.669999 ATGAAATGCCGAAGCCCAGC 61.670 55.000 0.00 0.00 38.69 4.85
1927 1983 2.084546 GCAACCACCCAAGTAGATGTC 58.915 52.381 0.00 0.00 0.00 3.06
2017 2073 1.206578 CGACCACCGTTGAACATGC 59.793 57.895 0.00 0.00 0.00 4.06
2173 2229 8.589701 TTTCTTTATGGAGGGAGTAATTTTCC 57.410 34.615 1.08 1.08 0.00 3.13
2236 2292 6.419484 TCGATGGTAATCAATGGTATGACT 57.581 37.500 0.00 0.00 32.61 3.41
2255 2311 5.589855 TGATCCTAACAACATTGCATTCGAT 59.410 36.000 0.00 0.00 0.00 3.59
2680 2742 5.946942 AAATCAGGCTAGTGATTGAGAGA 57.053 39.130 8.82 0.00 44.72 3.10
2681 2743 6.481644 GGTAAAATCAGGCTAGTGATTGAGAG 59.518 42.308 8.82 0.00 44.72 3.20
2717 2779 0.837272 TGTAGGGCCAGGCTAATGAC 59.163 55.000 12.43 3.61 0.00 3.06
2753 2815 5.640357 ACATGACATGGATCAAAATGTTTGC 59.360 36.000 19.39 0.00 37.15 3.68
2754 2816 6.034150 CGACATGACATGGATCAAAATGTTTG 59.966 38.462 19.39 10.99 37.15 2.93
2763 2825 0.832626 AGCCGACATGACATGGATCA 59.167 50.000 19.39 0.00 33.60 2.92
2833 2895 5.677091 GCATTCGTAACAAATTCAGCATCCT 60.677 40.000 0.00 0.00 0.00 3.24
2847 2909 5.539582 TGTACAGAAATGGCATTCGTAAC 57.460 39.130 14.04 9.04 34.46 2.50
2851 2913 5.490139 AAGATGTACAGAAATGGCATTCG 57.510 39.130 14.04 7.85 34.46 3.34
2869 2931 6.105397 ACTGAATGGCAAAATGTCAAAGAT 57.895 33.333 0.00 0.00 34.67 2.40
2943 3005 1.344114 AGCCAATGCGGTTTGAACATT 59.656 42.857 0.00 0.00 44.33 2.71
2944 3006 0.968405 AGCCAATGCGGTTTGAACAT 59.032 45.000 0.00 0.00 44.33 2.71
2946 3008 2.715737 TTAGCCAATGCGGTTTGAAC 57.284 45.000 0.00 0.00 44.33 3.18
2947 3009 3.951775 ATTTAGCCAATGCGGTTTGAA 57.048 38.095 0.00 0.00 44.33 2.69
2948 3010 5.590530 AATATTTAGCCAATGCGGTTTGA 57.409 34.783 0.00 0.00 44.33 2.69
2949 3011 7.945033 ATAAATATTTAGCCAATGCGGTTTG 57.055 32.000 13.15 0.00 44.33 2.93
2971 3033 9.733556 TGCCTGATGACTACTTTCTTTTTAATA 57.266 29.630 0.00 0.00 0.00 0.98
2974 3036 7.336931 GGATGCCTGATGACTACTTTCTTTTTA 59.663 37.037 0.00 0.00 0.00 1.52
2975 3037 6.151817 GGATGCCTGATGACTACTTTCTTTTT 59.848 38.462 0.00 0.00 0.00 1.94
2982 3044 4.018960 ACTTTGGATGCCTGATGACTACTT 60.019 41.667 0.00 0.00 0.00 2.24
2984 3046 3.878778 ACTTTGGATGCCTGATGACTAC 58.121 45.455 0.00 0.00 0.00 2.73
2985 3047 4.574674 AACTTTGGATGCCTGATGACTA 57.425 40.909 0.00 0.00 0.00 2.59
2987 3049 5.402398 GTTAAACTTTGGATGCCTGATGAC 58.598 41.667 0.00 0.00 0.00 3.06
2995 3057 6.476706 GCTTGATATGGTTAAACTTTGGATGC 59.523 38.462 0.00 0.00 0.00 3.91
2996 3058 7.489113 GTGCTTGATATGGTTAAACTTTGGATG 59.511 37.037 0.00 0.00 0.00 3.51
2997 3059 7.178274 TGTGCTTGATATGGTTAAACTTTGGAT 59.822 33.333 0.00 0.00 0.00 3.41
2998 3060 6.491745 TGTGCTTGATATGGTTAAACTTTGGA 59.508 34.615 0.00 0.00 0.00 3.53
3000 3062 7.370383 ACTGTGCTTGATATGGTTAAACTTTG 58.630 34.615 0.00 0.00 0.00 2.77
3003 3065 7.334421 CACTACTGTGCTTGATATGGTTAAACT 59.666 37.037 0.00 0.00 37.38 2.66
3004 3066 7.414098 CCACTACTGTGCTTGATATGGTTAAAC 60.414 40.741 0.00 0.00 42.54 2.01
3005 3067 6.597672 CCACTACTGTGCTTGATATGGTTAAA 59.402 38.462 0.00 0.00 42.54 1.52
3006 3068 6.070481 TCCACTACTGTGCTTGATATGGTTAA 60.070 38.462 0.00 0.00 42.54 2.01
3007 3069 5.423931 TCCACTACTGTGCTTGATATGGTTA 59.576 40.000 0.00 0.00 42.54 2.85
3008 3070 4.225042 TCCACTACTGTGCTTGATATGGTT 59.775 41.667 0.00 0.00 42.54 3.67
3009 3071 3.774766 TCCACTACTGTGCTTGATATGGT 59.225 43.478 0.00 0.00 42.54 3.55
3010 3072 4.406648 TCCACTACTGTGCTTGATATGG 57.593 45.455 0.00 0.00 42.54 2.74
3011 3073 4.993584 GGATCCACTACTGTGCTTGATATG 59.006 45.833 6.95 0.00 42.54 1.78
3012 3074 4.655649 TGGATCCACTACTGTGCTTGATAT 59.344 41.667 11.44 0.00 42.54 1.63
3013 3075 4.030216 TGGATCCACTACTGTGCTTGATA 58.970 43.478 11.44 0.00 42.54 2.15
3014 3076 2.840038 TGGATCCACTACTGTGCTTGAT 59.160 45.455 11.44 0.00 42.54 2.57
3015 3077 2.256306 TGGATCCACTACTGTGCTTGA 58.744 47.619 11.44 0.00 42.54 3.02
3016 3078 2.768253 TGGATCCACTACTGTGCTTG 57.232 50.000 11.44 0.00 42.54 4.01
3017 3079 3.788227 TTTGGATCCACTACTGTGCTT 57.212 42.857 15.91 0.00 42.54 3.91
3018 3080 3.788227 TTTTGGATCCACTACTGTGCT 57.212 42.857 15.91 0.00 42.54 4.40
3019 3081 4.458989 TGAATTTTGGATCCACTACTGTGC 59.541 41.667 15.91 0.07 42.54 4.57
3020 3082 5.124457 CCTGAATTTTGGATCCACTACTGTG 59.876 44.000 15.91 3.25 43.45 3.66
3021 3083 5.256474 CCTGAATTTTGGATCCACTACTGT 58.744 41.667 15.91 0.00 0.00 3.55
3022 3084 4.096984 GCCTGAATTTTGGATCCACTACTG 59.903 45.833 15.91 8.40 0.00 2.74
3023 3085 4.263905 TGCCTGAATTTTGGATCCACTACT 60.264 41.667 15.91 0.00 0.00 2.57
3024 3086 4.016444 TGCCTGAATTTTGGATCCACTAC 58.984 43.478 15.91 5.36 0.00 2.73
3025 3087 4.016444 GTGCCTGAATTTTGGATCCACTA 58.984 43.478 15.91 5.60 0.00 2.74
3026 3088 2.827921 GTGCCTGAATTTTGGATCCACT 59.172 45.455 15.91 0.00 0.00 4.00
3027 3089 2.827921 AGTGCCTGAATTTTGGATCCAC 59.172 45.455 15.91 2.71 0.00 4.02
3028 3090 3.173953 AGTGCCTGAATTTTGGATCCA 57.826 42.857 11.44 11.44 0.00 3.41
3029 3091 4.273318 ACTAGTGCCTGAATTTTGGATCC 58.727 43.478 4.20 4.20 0.00 3.36
3030 3092 5.415701 TCAACTAGTGCCTGAATTTTGGATC 59.584 40.000 0.00 0.00 0.00 3.36
3031 3093 5.324409 TCAACTAGTGCCTGAATTTTGGAT 58.676 37.500 0.00 0.00 0.00 3.41
3032 3094 4.724399 TCAACTAGTGCCTGAATTTTGGA 58.276 39.130 0.00 0.00 0.00 3.53
3033 3095 5.452078 TTCAACTAGTGCCTGAATTTTGG 57.548 39.130 0.00 0.00 0.00 3.28
3034 3096 4.919754 GCTTCAACTAGTGCCTGAATTTTG 59.080 41.667 8.54 0.41 0.00 2.44
3035 3097 4.584325 TGCTTCAACTAGTGCCTGAATTTT 59.416 37.500 8.54 0.00 0.00 1.82
3036 3098 4.144297 TGCTTCAACTAGTGCCTGAATTT 58.856 39.130 8.54 0.00 0.00 1.82
3037 3099 3.754965 TGCTTCAACTAGTGCCTGAATT 58.245 40.909 8.54 0.00 0.00 2.17
3038 3100 3.423539 TGCTTCAACTAGTGCCTGAAT 57.576 42.857 8.54 0.00 0.00 2.57
3039 3101 2.928801 TGCTTCAACTAGTGCCTGAA 57.071 45.000 7.96 7.96 0.00 3.02
3040 3102 2.302733 TGATGCTTCAACTAGTGCCTGA 59.697 45.455 0.00 0.00 0.00 3.86
3041 3103 2.703416 TGATGCTTCAACTAGTGCCTG 58.297 47.619 0.00 0.00 0.00 4.85
3042 3104 3.641434 ATGATGCTTCAACTAGTGCCT 57.359 42.857 6.36 0.00 34.96 4.75
3043 3105 4.035675 GGTAATGATGCTTCAACTAGTGCC 59.964 45.833 6.36 0.38 34.96 5.01
3044 3106 4.878397 AGGTAATGATGCTTCAACTAGTGC 59.122 41.667 6.36 0.00 34.96 4.40
3045 3107 6.036517 GTGAGGTAATGATGCTTCAACTAGTG 59.963 42.308 6.36 0.00 34.96 2.74
3046 3108 6.109359 GTGAGGTAATGATGCTTCAACTAGT 58.891 40.000 6.36 0.00 34.96 2.57
3047 3109 6.108687 TGTGAGGTAATGATGCTTCAACTAG 58.891 40.000 6.36 0.00 34.96 2.57
3048 3110 6.048732 TGTGAGGTAATGATGCTTCAACTA 57.951 37.500 6.36 0.00 34.96 2.24
3049 3111 4.910195 TGTGAGGTAATGATGCTTCAACT 58.090 39.130 6.36 3.23 34.96 3.16
3050 3112 4.937620 TCTGTGAGGTAATGATGCTTCAAC 59.062 41.667 6.36 1.35 34.96 3.18
3051 3113 5.164620 TCTGTGAGGTAATGATGCTTCAA 57.835 39.130 6.36 0.00 34.96 2.69
3052 3114 4.824479 TCTGTGAGGTAATGATGCTTCA 57.176 40.909 4.57 4.57 36.00 3.02
3053 3115 5.819379 TGAATCTGTGAGGTAATGATGCTTC 59.181 40.000 0.00 0.00 0.00 3.86
3054 3116 5.748402 TGAATCTGTGAGGTAATGATGCTT 58.252 37.500 0.00 0.00 0.00 3.91
3055 3117 5.363562 TGAATCTGTGAGGTAATGATGCT 57.636 39.130 0.00 0.00 0.00 3.79
3056 3118 6.441093 TTTGAATCTGTGAGGTAATGATGC 57.559 37.500 0.00 0.00 0.00 3.91
3057 3119 9.551734 TCTATTTGAATCTGTGAGGTAATGATG 57.448 33.333 0.00 0.00 0.00 3.07
3059 3121 9.605275 CTTCTATTTGAATCTGTGAGGTAATGA 57.395 33.333 0.00 0.00 33.71 2.57
3060 3122 9.605275 TCTTCTATTTGAATCTGTGAGGTAATG 57.395 33.333 0.00 0.00 33.71 1.90
3061 3123 9.829507 CTCTTCTATTTGAATCTGTGAGGTAAT 57.170 33.333 0.00 0.00 33.71 1.89
3062 3124 7.766278 GCTCTTCTATTTGAATCTGTGAGGTAA 59.234 37.037 0.00 0.00 33.71 2.85
3063 3125 7.268586 GCTCTTCTATTTGAATCTGTGAGGTA 58.731 38.462 0.00 0.00 33.71 3.08
3064 3126 6.112058 GCTCTTCTATTTGAATCTGTGAGGT 58.888 40.000 0.00 0.00 33.71 3.85
3065 3127 5.526846 GGCTCTTCTATTTGAATCTGTGAGG 59.473 44.000 0.00 0.00 33.71 3.86
3066 3128 6.347696 AGGCTCTTCTATTTGAATCTGTGAG 58.652 40.000 0.00 0.00 33.71 3.51
3067 3129 6.070596 TGAGGCTCTTCTATTTGAATCTGTGA 60.071 38.462 16.72 0.00 33.71 3.58
3068 3130 6.111382 TGAGGCTCTTCTATTTGAATCTGTG 58.889 40.000 16.72 0.00 33.71 3.66
3069 3131 6.305272 TGAGGCTCTTCTATTTGAATCTGT 57.695 37.500 16.72 0.00 33.71 3.41
3070 3132 6.822676 ACTTGAGGCTCTTCTATTTGAATCTG 59.177 38.462 16.72 0.00 33.71 2.90
3071 3133 6.956497 ACTTGAGGCTCTTCTATTTGAATCT 58.044 36.000 16.72 0.00 33.71 2.40
3072 3134 7.984617 AGTACTTGAGGCTCTTCTATTTGAATC 59.015 37.037 16.72 0.00 33.71 2.52
3073 3135 7.856415 AGTACTTGAGGCTCTTCTATTTGAAT 58.144 34.615 16.72 0.00 33.71 2.57
3074 3136 7.246171 AGTACTTGAGGCTCTTCTATTTGAA 57.754 36.000 16.72 0.00 0.00 2.69
3075 3137 6.859112 AGTACTTGAGGCTCTTCTATTTGA 57.141 37.500 16.72 0.00 0.00 2.69
3076 3138 7.913674 AAAGTACTTGAGGCTCTTCTATTTG 57.086 36.000 16.72 0.00 0.00 2.32
3077 3139 7.939588 ACAAAAGTACTTGAGGCTCTTCTATTT 59.060 33.333 16.72 7.13 0.00 1.40
3078 3140 7.454225 ACAAAAGTACTTGAGGCTCTTCTATT 58.546 34.615 16.72 1.13 0.00 1.73
3079 3141 7.010339 ACAAAAGTACTTGAGGCTCTTCTAT 57.990 36.000 16.72 0.00 0.00 1.98
3080 3142 6.267928 AGACAAAAGTACTTGAGGCTCTTCTA 59.732 38.462 16.72 0.00 0.00 2.10
3081 3143 5.071115 AGACAAAAGTACTTGAGGCTCTTCT 59.929 40.000 16.72 4.15 0.00 2.85
3082 3144 5.178438 CAGACAAAAGTACTTGAGGCTCTTC 59.822 44.000 16.72 1.91 0.00 2.87
3083 3145 5.059833 CAGACAAAAGTACTTGAGGCTCTT 58.940 41.667 16.72 2.61 0.00 2.85
3084 3146 4.503991 CCAGACAAAAGTACTTGAGGCTCT 60.504 45.833 16.72 2.70 0.00 4.09
3085 3147 3.748568 CCAGACAAAAGTACTTGAGGCTC 59.251 47.826 9.34 7.79 0.00 4.70
3086 3148 3.136626 ACCAGACAAAAGTACTTGAGGCT 59.863 43.478 9.34 9.45 0.00 4.58
3087 3149 3.477530 ACCAGACAAAAGTACTTGAGGC 58.522 45.455 9.34 7.09 0.00 4.70
3340 3402 7.390440 GCATGGCATTAATATACACTAACCTCA 59.610 37.037 0.00 0.00 0.00 3.86
3360 3422 4.937015 ACCAACAAAAAGAATATGCATGGC 59.063 37.500 10.16 0.00 31.21 4.40
3428 3490 8.602472 ACTGACACTAGGATTATCTTTTCTCT 57.398 34.615 0.00 0.00 0.00 3.10
3558 3621 3.876198 GTGCTATGGCGGTTGGCG 61.876 66.667 0.00 0.00 44.92 5.69
3597 3660 7.876936 ATTAAGTAGTAGTCGAATCCAGACA 57.123 36.000 0.00 0.00 40.84 3.41
3631 3694 3.965379 TGCATGTCAGGCATTCAAAAT 57.035 38.095 8.34 0.00 36.11 1.82
3694 3757 5.470437 CCTGGAAAAAGAACTGTACTCTTCC 59.530 44.000 0.00 0.00 31.85 3.46
3695 3758 6.203145 GTCCTGGAAAAAGAACTGTACTCTTC 59.797 42.308 0.00 0.00 31.85 2.87
3713 3776 2.889512 ACTATGTGACACTGTCCTGGA 58.110 47.619 7.20 0.00 0.00 3.86
4077 4140 9.391006 GGATTTTGTACATTCTGTGGACTATAA 57.609 33.333 0.00 0.00 42.56 0.98
4078 4141 8.544622 TGGATTTTGTACATTCTGTGGACTATA 58.455 33.333 0.00 0.00 42.56 1.31
4079 4142 7.336931 GTGGATTTTGTACATTCTGTGGACTAT 59.663 37.037 0.00 0.00 42.56 2.12
4080 4143 6.653320 GTGGATTTTGTACATTCTGTGGACTA 59.347 38.462 0.00 0.00 42.56 2.59
4081 4144 5.473504 GTGGATTTTGTACATTCTGTGGACT 59.526 40.000 0.00 0.00 42.56 3.85
4082 4145 5.240623 TGTGGATTTTGTACATTCTGTGGAC 59.759 40.000 0.00 0.00 42.41 4.02
4083 4146 5.240623 GTGTGGATTTTGTACATTCTGTGGA 59.759 40.000 0.00 0.00 0.00 4.02
4084 4147 5.241506 AGTGTGGATTTTGTACATTCTGTGG 59.758 40.000 0.00 0.00 0.00 4.17
4085 4148 6.205464 AGAGTGTGGATTTTGTACATTCTGTG 59.795 38.462 0.00 0.00 39.12 3.66
4086 4149 6.299141 AGAGTGTGGATTTTGTACATTCTGT 58.701 36.000 0.00 0.00 39.12 3.41
4087 4150 6.808008 AGAGTGTGGATTTTGTACATTCTG 57.192 37.500 0.00 0.00 39.12 3.02
4140 4206 6.071952 GCAGAATTTCTTTCAGGGTATTGTGA 60.072 38.462 0.00 0.00 36.75 3.58
4279 4345 4.764679 TTGTTGTGGCATAGCAAAGTAG 57.235 40.909 10.85 0.00 0.00 2.57
4280 4346 5.720371 AATTGTTGTGGCATAGCAAAGTA 57.280 34.783 16.50 0.00 0.00 2.24
4403 4597 9.251440 AGGTTAGACAGTAGTAAACATACATGA 57.749 33.333 0.00 0.00 0.00 3.07
4500 4694 9.226345 GCACTTAGCACACAAATATCTATTTTC 57.774 33.333 0.00 0.00 44.79 2.29
4746 4943 9.349713 AGGAGTGAAAACATACATAGAAAACAA 57.650 29.630 0.00 0.00 0.00 2.83
4747 4944 8.918202 AGGAGTGAAAACATACATAGAAAACA 57.082 30.769 0.00 0.00 0.00 2.83
4762 4959 5.410067 CAAAGTTGCAAAGAGGAGTGAAAA 58.590 37.500 0.00 0.00 0.00 2.29
4953 5177 5.760253 ACAGAAAGATATTTGGATACTGGCG 59.240 40.000 0.00 0.00 37.61 5.69
5098 5324 2.489329 CACGTGAAATTGGGATGAAGCT 59.511 45.455 10.90 0.00 0.00 3.74
5099 5325 2.487762 TCACGTGAAATTGGGATGAAGC 59.512 45.455 17.62 0.00 0.00 3.86
5304 5530 4.509600 GTCATATTAAGAGTGGAGCTGTGC 59.490 45.833 0.00 0.00 0.00 4.57
5811 6044 1.003349 AGAGCTCAAGAACTGCAGCAT 59.997 47.619 17.77 2.22 33.27 3.79
5827 6060 4.119136 GCTTCTGGTATTTCTCTGAGAGC 58.881 47.826 4.17 0.30 0.00 4.09
5937 6170 1.132453 CAGCACCATCAACATCTGCTG 59.868 52.381 3.72 3.72 46.41 4.41
6049 6282 1.795768 TGCTAGACAAACTTGAGGCG 58.204 50.000 0.00 0.00 0.00 5.52
6214 6447 1.902508 TGGAGCGATTCTTCTGGTTCT 59.097 47.619 0.00 0.00 0.00 3.01
6329 6562 1.771854 TGTTGTGGTGCCCTTAGAAGA 59.228 47.619 0.00 0.00 0.00 2.87
6792 7025 5.164620 TGATGAGTAAAACTGGATGCTCA 57.835 39.130 0.00 0.00 41.46 4.26
6815 7048 7.827236 ACTAGAATTGGATAATTGTTTCCGTCA 59.173 33.333 0.00 0.00 36.66 4.35
6943 7176 1.687612 CTGCCCCTTGACATGGAGT 59.312 57.895 8.93 0.00 0.00 3.85
7003 7236 0.249573 CAGTGTTTTTGGCTGGCCTG 60.250 55.000 13.05 4.26 36.94 4.85
7019 7252 9.635520 GTGATGTATTTACAGTTACTGTACAGT 57.364 33.333 30.13 30.13 45.13 3.55
7101 7334 5.188434 TCTGGATGCAGAGGTAAAAAGATG 58.812 41.667 13.58 0.00 0.00 2.90
7212 7445 6.615726 AGACCAGATAGGCTTTACATTCCTTA 59.384 38.462 0.00 0.00 43.14 2.69
7216 7449 4.513318 GCAGACCAGATAGGCTTTACATTC 59.487 45.833 0.00 0.00 43.14 2.67
7269 7502 2.396590 TCCGATACCAGCCAAAGAAC 57.603 50.000 0.00 0.00 0.00 3.01
7303 7536 4.038042 CCCAAGTACGCTGATCAGATAGAA 59.962 45.833 27.04 3.37 0.00 2.10
7440 7673 3.278574 GGACATAGCATTGGCAGTGTTA 58.721 45.455 11.82 10.29 44.61 2.41
7476 7709 4.033587 TCTGTTCACGCTTTCTGTAAACAC 59.966 41.667 0.00 0.00 0.00 3.32
7477 7710 4.185394 TCTGTTCACGCTTTCTGTAAACA 58.815 39.130 0.00 0.00 0.00 2.83
7492 7725 6.398095 ACACGACATGATAGAAATCTGTTCA 58.602 36.000 0.00 0.00 32.93 3.18
7748 8038 2.515398 CAGGGGTTGTCAGGCACA 59.485 61.111 0.00 0.00 0.00 4.57
7791 8557 3.363673 CCGAACGCTTTACAGACCTTTTC 60.364 47.826 0.00 0.00 0.00 2.29
7864 8630 7.335171 GTGATGGTTTCCGTACCTAAATAAAGT 59.665 37.037 0.00 0.00 39.04 2.66
7906 8672 7.119553 GTCCTACAATTATCAAACCAACGGTTA 59.880 37.037 0.00 0.00 46.20 2.85
7947 8713 1.185618 TAGCAACCTCCAGCTCGTGT 61.186 55.000 0.00 0.00 42.05 4.49


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

AutoCloner maintained by Alex Coulton.