Multiple sequence alignment - TraesCS5B01G532300

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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 TraesCS5B01G532300 chr5B 100.000 6309 0 0 1 6309 689900106 689906414 0.000000e+00 11651.0
1 TraesCS5B01G532300 chr5B 100.000 100 0 0 3028 3127 689903034 689903133 1.080000e-42 185.0
2 TraesCS5B01G532300 chr5B 100.000 100 0 0 2929 3028 689903133 689903232 1.080000e-42 185.0
3 TraesCS5B01G532300 chr5B 79.237 236 18 16 569 794 689878923 689879137 1.100000e-27 135.0
4 TraesCS5B01G532300 chr5D 94.782 3047 104 20 1 3028 546826235 546823225 0.000000e+00 4695.0
5 TraesCS5B01G532300 chr5D 96.291 1510 27 8 3028 4516 546823324 546821823 0.000000e+00 2451.0
6 TraesCS5B01G532300 chr5D 87.986 1673 130 34 4532 6181 546821838 546820214 0.000000e+00 1910.0
7 TraesCS5B01G532300 chr5D 77.951 449 31 25 987 1432 546682634 546683017 1.060000e-52 219.0
8 TraesCS5B01G532300 chr5D 100.000 28 0 0 4927 4954 164651441 164651468 1.100000e-02 52.8
9 TraesCS5B01G532300 chr4A 92.026 2621 152 29 1 2579 622174633 622177238 0.000000e+00 3629.0
10 TraesCS5B01G532300 chr4A 91.012 2659 120 35 3034 5628 622177632 622180235 0.000000e+00 3476.0
11 TraesCS5B01G532300 chr4A 89.414 444 30 7 2586 3028 622177298 622177725 1.550000e-150 544.0
12 TraesCS5B01G532300 chr4A 84.211 247 16 12 5959 6185 622180264 622180507 1.060000e-52 219.0
13 TraesCS5B01G532300 chr4A 84.579 214 18 3 1318 1531 622246097 622245899 1.390000e-46 198.0
14 TraesCS5B01G532300 chr4A 82.677 254 13 15 987 1237 622248235 622248010 4.990000e-46 196.0
15 TraesCS5B01G532300 chr3A 88.701 177 18 2 3308 3482 729155898 729155722 1.380000e-51 215.0
16 TraesCS5B01G532300 chr7A 82.653 196 33 1 3296 3490 11756326 11756521 8.410000e-39 172.0
17 TraesCS5B01G532300 chr7D 82.143 196 34 1 3296 3490 12307156 12307351 3.910000e-37 167.0
18 TraesCS5B01G532300 chr6D 93.023 43 3 0 4912 4954 142149660 142149702 5.280000e-06 63.9
19 TraesCS5B01G532300 chr5A 100.000 28 0 0 4927 4954 3362218 3362191 1.100000e-02 52.8
20 TraesCS5B01G532300 chr1B 100.000 28 0 0 4927 4954 296290747 296290774 1.100000e-02 52.8


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 TraesCS5B01G532300 chr5B 689900106 689906414 6308 False 4007.000000 11651 100.000000 1 6309 3 chr5B.!!$F2 6308
1 TraesCS5B01G532300 chr5D 546820214 546826235 6021 True 3018.666667 4695 93.019667 1 6181 3 chr5D.!!$R1 6180
2 TraesCS5B01G532300 chr4A 622174633 622180507 5874 False 1967.000000 3629 89.165750 1 6185 4 chr4A.!!$F1 6184

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
992 1008 0.106519 AGAGAGAGAGAGGGAGCAGC 60.107 60.000 0.0 0.0 0.00 5.25 F
1658 1681 2.076100 CTGACTAACAATGCGAGGCAA 58.924 47.619 0.0 0.0 43.62 4.52 F
1829 1852 0.978146 AATCTAGCGTGCCCCTCTGT 60.978 55.000 0.0 0.0 0.00 3.41 F
1855 1878 2.775384 TCCGGGTAAGTGGCTTCATATT 59.225 45.455 0.0 0.0 0.00 1.28 F
3975 4100 2.807967 TCAGTTCGATGTGAAGCCTTTG 59.192 45.455 0.0 0.0 37.23 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1829 1852 0.912487 AGCCACTTACCCGGAATGGA 60.912 55.000 0.73 0.00 42.00 3.41 R
3617 3737 0.677731 CAAAGCGGAATGAGGAGCCA 60.678 55.000 0.00 0.00 0.00 4.75 R
3975 4100 2.991866 GACTCGTTAGGTAAACACCTGC 59.008 50.000 6.59 0.00 40.93 4.85 R
4026 4151 7.477422 CACTTGTGTTCGAAATTAGGTAATTCG 59.523 37.037 0.00 1.03 35.00 3.34 R
5878 6070 0.036294 GAGTTTTGGGACGGAGGGAG 60.036 60.000 0.00 0.00 0.00 4.30 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
35 36 2.180769 CGTCCTCGCCATGTCGAA 59.819 61.111 0.00 0.00 38.08 3.71
48 49 1.710013 TGTCGAACTCGCCATTTCTC 58.290 50.000 0.00 0.00 39.60 2.87
198 199 4.373116 TGCTCGTTCGGCTCCACC 62.373 66.667 7.06 0.00 0.00 4.61
673 674 2.249413 CTTCATGAGCCCGTCCAGCT 62.249 60.000 0.00 0.00 45.23 4.24
674 675 2.513204 CATGAGCCCGTCCAGCTG 60.513 66.667 6.78 6.78 41.75 4.24
800 812 0.815734 CTCCCATGGCAAAGAGCTTG 59.184 55.000 6.09 0.00 44.79 4.01
808 820 1.968017 CAAAGAGCTTGGAGCCGCA 60.968 57.895 0.00 0.00 43.77 5.69
809 821 1.673665 AAAGAGCTTGGAGCCGCAG 60.674 57.895 0.00 0.00 43.77 5.18
817 829 1.892819 TTGGAGCCGCAGAGAGGAAG 61.893 60.000 0.00 0.00 0.00 3.46
851 867 0.107017 TGGATAAGCTTCAGCCCAGC 60.107 55.000 0.00 0.00 43.38 4.85
924 940 4.929211 GGCCCAACAAAAGAATACACATTC 59.071 41.667 0.00 0.00 40.85 2.67
982 998 3.631250 AGGGAAAGCTGTAGAGAGAGAG 58.369 50.000 0.00 0.00 0.00 3.20
983 999 3.268334 AGGGAAAGCTGTAGAGAGAGAGA 59.732 47.826 0.00 0.00 0.00 3.10
985 1001 3.632145 GGAAAGCTGTAGAGAGAGAGAGG 59.368 52.174 0.00 0.00 0.00 3.69
989 1005 2.851195 CTGTAGAGAGAGAGAGGGAGC 58.149 57.143 0.00 0.00 0.00 4.70
990 1006 2.172505 CTGTAGAGAGAGAGAGGGAGCA 59.827 54.545 0.00 0.00 0.00 4.26
991 1007 2.172505 TGTAGAGAGAGAGAGGGAGCAG 59.827 54.545 0.00 0.00 0.00 4.24
992 1008 0.106519 AGAGAGAGAGAGGGAGCAGC 60.107 60.000 0.00 0.00 0.00 5.25
1296 1316 3.379445 TTCTCCGACGTGCTCCCC 61.379 66.667 0.00 0.00 0.00 4.81
1535 1555 2.868583 CCTTGTTCTCGTATGCCATCAG 59.131 50.000 0.00 0.00 0.00 2.90
1618 1641 5.537188 CTGTTCTTACTGATCTCCTATGCC 58.463 45.833 0.00 0.00 0.00 4.40
1620 1643 5.069648 TGTTCTTACTGATCTCCTATGCCTG 59.930 44.000 0.00 0.00 0.00 4.85
1658 1681 2.076100 CTGACTAACAATGCGAGGCAA 58.924 47.619 0.00 0.00 43.62 4.52
1795 1818 2.369532 GTGGTGTTACCTACCCTGACAA 59.630 50.000 0.00 0.00 39.58 3.18
1796 1819 2.369532 TGGTGTTACCTACCCTGACAAC 59.630 50.000 0.00 0.00 39.58 3.32
1829 1852 0.978146 AATCTAGCGTGCCCCTCTGT 60.978 55.000 0.00 0.00 0.00 3.41
1855 1878 2.775384 TCCGGGTAAGTGGCTTCATATT 59.225 45.455 0.00 0.00 0.00 1.28
1860 1883 5.059833 GGGTAAGTGGCTTCATATTCTCAG 58.940 45.833 0.00 0.00 0.00 3.35
1862 1885 5.755861 GGTAAGTGGCTTCATATTCTCAGTC 59.244 44.000 0.00 0.00 0.00 3.51
1901 1924 5.877564 GGGCTCCTCTGAAATTATATAGTGC 59.122 44.000 0.00 0.00 0.00 4.40
1910 1933 8.978539 TCTGAAATTATATAGTGCGCAAGTTAG 58.021 33.333 14.00 0.00 41.68 2.34
2009 2032 4.701171 TGATGTGACATAGCTTGCATGAAA 59.299 37.500 0.00 0.00 0.00 2.69
2153 2197 9.605951 ATTTCCAGTCATATTTTGGCCTATAAT 57.394 29.630 3.32 3.52 31.94 1.28
2358 2404 6.238759 GGGTGAAGGTGTATTCAATTAGATGC 60.239 42.308 0.00 0.00 40.72 3.91
2492 2545 4.597404 TGTTTGCAAATTAGCATCACCA 57.403 36.364 16.21 1.33 45.19 4.17
2598 2707 4.129380 TCAACATTTCTATGCGGGATGAG 58.871 43.478 0.00 0.00 35.03 2.90
2696 2805 4.625607 ACATATTAGGAACAGCTAGGGC 57.374 45.455 0.00 0.00 39.06 5.19
3014 3123 9.485591 CCTACATTCGTTTTGTATGAATTGTAC 57.514 33.333 0.00 0.00 39.86 2.90
3015 3124 9.194716 CTACATTCGTTTTGTATGAATTGTACG 57.805 33.333 0.00 0.00 39.86 3.67
3016 3125 7.577979 ACATTCGTTTTGTATGAATTGTACGT 58.422 30.769 0.00 0.00 39.86 3.57
3017 3126 7.742963 ACATTCGTTTTGTATGAATTGTACGTC 59.257 33.333 0.00 0.00 39.86 4.34
3018 3127 6.766452 TCGTTTTGTATGAATTGTACGTCA 57.234 33.333 0.00 0.00 0.00 4.35
3019 3128 6.583160 TCGTTTTGTATGAATTGTACGTCAC 58.417 36.000 0.00 0.00 0.00 3.67
3020 3129 6.421501 TCGTTTTGTATGAATTGTACGTCACT 59.578 34.615 0.00 0.00 0.00 3.41
3021 3130 7.042590 TCGTTTTGTATGAATTGTACGTCACTT 60.043 33.333 0.00 0.00 0.00 3.16
3022 3131 8.215792 CGTTTTGTATGAATTGTACGTCACTTA 58.784 33.333 0.00 0.00 0.00 2.24
3025 3134 7.997107 TGTATGAATTGTACGTCACTTATCC 57.003 36.000 0.00 0.00 0.00 2.59
3026 3135 7.548967 TGTATGAATTGTACGTCACTTATCCA 58.451 34.615 0.00 0.00 0.00 3.41
3027 3136 8.201464 TGTATGAATTGTACGTCACTTATCCAT 58.799 33.333 0.00 0.00 0.00 3.41
3028 3137 9.042008 GTATGAATTGTACGTCACTTATCCATT 57.958 33.333 0.00 0.00 0.00 3.16
3029 3138 7.534085 TGAATTGTACGTCACTTATCCATTC 57.466 36.000 0.00 0.00 0.00 2.67
3030 3139 6.537301 TGAATTGTACGTCACTTATCCATTCC 59.463 38.462 0.00 0.00 0.00 3.01
3031 3140 5.408880 TTGTACGTCACTTATCCATTCCA 57.591 39.130 0.00 0.00 0.00 3.53
3032 3141 5.607939 TGTACGTCACTTATCCATTCCAT 57.392 39.130 0.00 0.00 0.00 3.41
3033 3142 5.356426 TGTACGTCACTTATCCATTCCATG 58.644 41.667 0.00 0.00 0.00 3.66
3051 3160 9.366216 CATTCCATGGATTGCATTAATTATGAG 57.634 33.333 20.62 0.00 36.26 2.90
3052 3161 7.470935 TCCATGGATTGCATTAATTATGAGG 57.529 36.000 11.44 0.00 36.26 3.86
3053 3162 6.071221 TCCATGGATTGCATTAATTATGAGGC 60.071 38.462 11.44 0.00 36.26 4.70
3054 3163 5.375417 TGGATTGCATTAATTATGAGGCG 57.625 39.130 0.00 0.00 36.26 5.52
3055 3164 4.826733 TGGATTGCATTAATTATGAGGCGT 59.173 37.500 0.00 0.00 36.26 5.68
3056 3165 5.301551 TGGATTGCATTAATTATGAGGCGTT 59.698 36.000 0.00 0.00 36.26 4.84
3057 3166 6.488344 TGGATTGCATTAATTATGAGGCGTTA 59.512 34.615 0.00 0.00 36.26 3.18
3058 3167 7.176515 TGGATTGCATTAATTATGAGGCGTTAT 59.823 33.333 0.00 0.00 36.26 1.89
3059 3168 8.028938 GGATTGCATTAATTATGAGGCGTTATT 58.971 33.333 0.00 0.00 36.26 1.40
3060 3169 9.410556 GATTGCATTAATTATGAGGCGTTATTT 57.589 29.630 0.00 0.00 36.26 1.40
3061 3170 8.572828 TTGCATTAATTATGAGGCGTTATTTG 57.427 30.769 0.00 0.00 36.26 2.32
3062 3171 7.711846 TGCATTAATTATGAGGCGTTATTTGT 58.288 30.769 0.00 0.00 36.26 2.83
3063 3172 8.194104 TGCATTAATTATGAGGCGTTATTTGTT 58.806 29.630 0.00 0.00 36.26 2.83
3064 3173 9.030301 GCATTAATTATGAGGCGTTATTTGTTT 57.970 29.630 0.00 0.00 36.26 2.83
3067 3176 9.724839 TTAATTATGAGGCGTTATTTGTTTAGC 57.275 29.630 0.00 0.00 0.00 3.09
3068 3177 6.745159 TTATGAGGCGTTATTTGTTTAGCA 57.255 33.333 0.00 0.00 0.00 3.49
3069 3178 4.413495 TGAGGCGTTATTTGTTTAGCAC 57.587 40.909 0.00 0.00 0.00 4.40
3070 3179 4.069304 TGAGGCGTTATTTGTTTAGCACT 58.931 39.130 0.00 0.00 0.00 4.40
3071 3180 5.239351 TGAGGCGTTATTTGTTTAGCACTA 58.761 37.500 0.00 0.00 0.00 2.74
3072 3181 5.350365 TGAGGCGTTATTTGTTTAGCACTAG 59.650 40.000 0.00 0.00 0.00 2.57
3073 3182 5.243207 AGGCGTTATTTGTTTAGCACTAGT 58.757 37.500 0.00 0.00 0.00 2.57
3074 3183 5.704053 AGGCGTTATTTGTTTAGCACTAGTT 59.296 36.000 0.00 0.00 0.00 2.24
3075 3184 6.206048 AGGCGTTATTTGTTTAGCACTAGTTT 59.794 34.615 0.00 0.00 0.00 2.66
3076 3185 6.859508 GGCGTTATTTGTTTAGCACTAGTTTT 59.140 34.615 0.00 0.00 0.00 2.43
3077 3186 8.016801 GGCGTTATTTGTTTAGCACTAGTTTTA 58.983 33.333 0.00 0.00 0.00 1.52
3078 3187 9.047871 GCGTTATTTGTTTAGCACTAGTTTTAG 57.952 33.333 0.00 0.00 0.00 1.85
3110 3219 9.787532 ATTCCTACATTCGTTTTGTATGAATTG 57.212 29.630 13.82 0.00 39.64 2.32
3111 3220 8.330466 TCCTACATTCGTTTTGTATGAATTGT 57.670 30.769 0.00 0.00 39.86 2.71
3112 3221 9.438228 TCCTACATTCGTTTTGTATGAATTGTA 57.562 29.630 0.00 0.00 39.86 2.41
3113 3222 9.485591 CCTACATTCGTTTTGTATGAATTGTAC 57.514 33.333 0.00 0.00 39.86 2.90
3162 3278 6.035975 GCTACATGGAAAATTATTGTTGTGCC 59.964 38.462 0.00 0.00 0.00 5.01
3163 3279 5.862845 ACATGGAAAATTATTGTTGTGCCA 58.137 33.333 0.00 0.00 0.00 4.92
3556 3676 7.201679 CCAGCAATACTAATTAGCTATGGCATC 60.202 40.741 22.73 0.00 41.70 3.91
3617 3737 6.942576 ACACTTCATTTGCTTCTTACAGGTAT 59.057 34.615 0.00 0.00 0.00 2.73
3975 4100 2.807967 TCAGTTCGATGTGAAGCCTTTG 59.192 45.455 0.00 0.00 37.23 2.77
4026 4151 8.045176 AGTTGCTGTTAATTGAATCCTTCTAC 57.955 34.615 0.00 0.00 0.00 2.59
4042 4167 8.813643 ATCCTTCTACGAATTACCTAATTTCG 57.186 34.615 3.04 3.04 36.13 3.46
4053 4178 4.483476 ACCTAATTTCGAACACAAGTGC 57.517 40.909 0.00 0.00 0.00 4.40
4087 4212 6.264292 GTCTAACATCTCCATCTCTGCTAAGA 59.736 42.308 0.00 0.00 0.00 2.10
4182 4325 8.906867 ACTTCTGCTGCATGTGTATATAATTTT 58.093 29.630 1.31 0.00 0.00 1.82
4612 4771 2.253603 GCTGTTCTTATTTTGCAGGCG 58.746 47.619 0.00 0.00 0.00 5.52
4759 4918 9.704098 GAAGTAGAACGAATAAAATTTAGCTGG 57.296 33.333 0.00 0.00 0.00 4.85
4786 4945 4.986659 TCGAAGTTGTAGTAGTTTTGCCTC 59.013 41.667 0.00 0.00 0.00 4.70
4954 5113 3.118149 GCCTAATAAACCGGAAAGGAGGA 60.118 47.826 9.46 0.00 45.00 3.71
4955 5114 4.704965 CCTAATAAACCGGAAAGGAGGAG 58.295 47.826 9.46 0.00 45.00 3.69
4957 5116 1.282382 TAAACCGGAAAGGAGGAGGG 58.718 55.000 9.46 0.00 45.00 4.30
4959 5118 0.910088 AACCGGAAAGGAGGAGGGAG 60.910 60.000 9.46 0.00 45.00 4.30
4960 5119 1.306226 CCGGAAAGGAGGAGGGAGT 60.306 63.158 0.00 0.00 45.00 3.85
4961 5120 1.617947 CCGGAAAGGAGGAGGGAGTG 61.618 65.000 0.00 0.00 45.00 3.51
5003 5162 9.512588 AAAGCCTAAAACTAGATATGATGGATG 57.487 33.333 0.00 0.00 0.00 3.51
5004 5163 8.441311 AGCCTAAAACTAGATATGATGGATGA 57.559 34.615 0.00 0.00 0.00 2.92
5005 5164 8.884323 AGCCTAAAACTAGATATGATGGATGAA 58.116 33.333 0.00 0.00 0.00 2.57
5006 5165 8.940952 GCCTAAAACTAGATATGATGGATGAAC 58.059 37.037 0.00 0.00 0.00 3.18
5007 5166 9.442047 CCTAAAACTAGATATGATGGATGAACC 57.558 37.037 0.00 0.00 39.54 3.62
5066 5225 0.675837 TCTCCACCGAATCGAGTCGT 60.676 55.000 30.24 17.42 39.43 4.34
5071 5230 1.582937 CCGAATCGAGTCGTCCGTG 60.583 63.158 30.24 13.47 39.43 4.94
5149 5308 4.256110 TCATTCTGCTGTTACAGGTGATG 58.744 43.478 14.63 7.61 38.26 3.07
5246 5405 2.495084 AGAGAGAAACTTTTGACGGCC 58.505 47.619 0.00 0.00 0.00 6.13
5277 5436 3.133362 TGGTTACTTCCAGAAGACAACGT 59.867 43.478 14.19 0.00 40.79 3.99
5329 5488 1.002087 CCCAGTTTCGTGAGGTTAGCT 59.998 52.381 0.00 0.00 0.00 3.32
5346 5505 0.239347 GCTTCTGTGTGATGTGTGCC 59.761 55.000 0.00 0.00 0.00 5.01
5360 5519 1.602377 GTGTGCCCTACTTGTGTGAAC 59.398 52.381 0.00 0.00 0.00 3.18
5391 5550 6.371809 TTGCAAAACCATTACTCGGATATC 57.628 37.500 0.00 0.00 0.00 1.63
5401 5560 6.210784 CCATTACTCGGATATCTGTTTCCCTA 59.789 42.308 11.35 0.00 0.00 3.53
5409 5568 5.823045 GGATATCTGTTTCCCTAACCACAAG 59.177 44.000 2.05 0.00 35.81 3.16
5420 5581 3.758554 CCTAACCACAAGCTAGCAATGTT 59.241 43.478 18.83 14.05 0.00 2.71
5426 5587 4.379186 CCACAAGCTAGCAATGTTTGAGAG 60.379 45.833 18.83 8.19 31.60 3.20
5460 5621 3.189618 TCATGACTGAGCCACATGATC 57.810 47.619 0.00 0.00 43.17 2.92
5482 5643 6.584185 TCCACGATCGATGAAGGATATTTA 57.416 37.500 24.34 0.00 0.00 1.40
5487 5649 9.066939 CACGATCGATGAAGGATATTTACTAAG 57.933 37.037 24.34 0.00 0.00 2.18
5504 5666 3.612860 ACTAAGAGAAATAAGCACACGCG 59.387 43.478 3.53 3.53 45.49 6.01
5505 5667 2.080286 AGAGAAATAAGCACACGCGT 57.920 45.000 5.58 5.58 45.49 6.01
5507 5669 3.782046 AGAGAAATAAGCACACGCGTAT 58.218 40.909 13.44 0.00 43.52 3.06
5534 5703 8.768955 TGTTTTAAAATGTGCCATTAACATGAC 58.231 29.630 3.52 0.00 38.27 3.06
5553 5722 6.374333 ACATGACAACCATACATTGACCTTAC 59.626 38.462 0.00 0.00 33.31 2.34
5558 5730 8.871629 ACAACCATACATTGACCTTACAAATA 57.128 30.769 0.00 0.00 33.44 1.40
5591 5763 4.604843 AAGTGTTGTGTGCATCGATATG 57.395 40.909 0.00 0.00 36.09 1.78
5689 5865 7.252678 AGGAAACTATAGATTATCAGAGGGCT 58.747 38.462 6.78 0.00 40.61 5.19
5690 5866 7.737149 AGGAAACTATAGATTATCAGAGGGCTT 59.263 37.037 6.78 0.00 40.61 4.35
5696 5872 4.036518 AGATTATCAGAGGGCTTGTCTGT 58.963 43.478 10.45 3.64 41.92 3.41
5700 5876 1.202687 TCAGAGGGCTTGTCTGTTGTG 60.203 52.381 10.45 0.00 41.92 3.33
5739 5915 1.291877 CCGTCTTCTTCCACCTTGCG 61.292 60.000 0.00 0.00 0.00 4.85
5760 5936 0.987294 TCTTCTCCAGCCCCTGAAAG 59.013 55.000 0.00 0.00 32.44 2.62
5761 5937 0.695347 CTTCTCCAGCCCCTGAAAGT 59.305 55.000 0.00 0.00 32.44 2.66
5763 5939 1.573108 TCTCCAGCCCCTGAAAGTAG 58.427 55.000 0.00 0.00 32.44 2.57
5768 5958 3.653836 TCCAGCCCCTGAAAGTAGTTAAA 59.346 43.478 0.00 0.00 32.44 1.52
5779 5969 5.242838 TGAAAGTAGTTAAATTGCCACCTGG 59.757 40.000 0.00 0.00 38.53 4.45
5785 5975 5.010282 AGTTAAATTGCCACCTGGAGTTAG 58.990 41.667 0.00 0.00 37.39 2.34
5786 5976 3.525800 AAATTGCCACCTGGAGTTAGT 57.474 42.857 0.00 0.00 37.39 2.24
5787 5977 3.525800 AATTGCCACCTGGAGTTAGTT 57.474 42.857 0.00 0.00 37.39 2.24
5788 5978 4.650972 AATTGCCACCTGGAGTTAGTTA 57.349 40.909 0.00 0.00 37.39 2.24
5789 5979 3.412237 TTGCCACCTGGAGTTAGTTAC 57.588 47.619 0.00 0.00 37.39 2.50
5790 5980 1.626825 TGCCACCTGGAGTTAGTTACC 59.373 52.381 0.00 0.00 37.39 2.85
5791 5981 1.907255 GCCACCTGGAGTTAGTTACCT 59.093 52.381 0.00 0.00 37.39 3.08
5792 5982 2.354805 GCCACCTGGAGTTAGTTACCTG 60.355 54.545 0.00 0.00 37.39 4.00
5793 5983 3.170717 CCACCTGGAGTTAGTTACCTGA 58.829 50.000 0.00 0.00 37.39 3.86
5794 5984 3.056035 CCACCTGGAGTTAGTTACCTGAC 60.056 52.174 0.00 0.00 37.39 3.51
5795 5985 3.576982 CACCTGGAGTTAGTTACCTGACA 59.423 47.826 0.00 0.00 29.85 3.58
5796 5986 4.039973 CACCTGGAGTTAGTTACCTGACAA 59.960 45.833 0.00 0.00 29.85 3.18
5797 5987 4.657039 ACCTGGAGTTAGTTACCTGACAAA 59.343 41.667 0.00 0.00 29.85 2.83
5798 5988 5.309806 ACCTGGAGTTAGTTACCTGACAAAT 59.690 40.000 0.00 0.00 29.85 2.32
5799 5989 5.875359 CCTGGAGTTAGTTACCTGACAAATC 59.125 44.000 0.00 0.00 29.85 2.17
5800 5990 6.295916 CCTGGAGTTAGTTACCTGACAAATCT 60.296 42.308 0.00 0.00 29.85 2.40
5801 5991 7.093465 CCTGGAGTTAGTTACCTGACAAATCTA 60.093 40.741 0.00 0.00 29.85 1.98
5819 6009 7.285401 ACAAATCTACTGGACATGTTTTGAACT 59.715 33.333 17.72 0.00 0.00 3.01
5825 6015 6.119536 ACTGGACATGTTTTGAACTAACTGA 58.880 36.000 0.00 0.00 0.00 3.41
5831 6021 8.050778 ACATGTTTTGAACTAACTGACTGAAA 57.949 30.769 0.00 0.00 0.00 2.69
5838 6028 8.958119 TTGAACTAACTGACTGAAACTAACAT 57.042 30.769 0.00 0.00 0.00 2.71
5847 6039 8.827677 ACTGACTGAAACTAACATACTGTTTTC 58.172 33.333 0.00 0.00 41.45 2.29
5865 6057 6.584488 TGTTTTCTACAGCCTGTAACTGTTA 58.416 36.000 5.98 0.00 46.01 2.41
5874 6066 5.742453 CAGCCTGTAACTGTTACTACGTATG 59.258 44.000 25.91 15.34 37.06 2.39
5878 6070 6.909357 CCTGTAACTGTTACTACGTATGCTAC 59.091 42.308 25.91 3.78 37.06 3.58
5879 6071 7.201679 CCTGTAACTGTTACTACGTATGCTACT 60.202 40.741 25.91 0.00 37.06 2.57
5880 6072 7.688372 TGTAACTGTTACTACGTATGCTACTC 58.312 38.462 25.91 0.70 37.06 2.59
5881 6073 5.747951 ACTGTTACTACGTATGCTACTCC 57.252 43.478 0.00 0.00 0.00 3.85
5882 6074 4.578105 ACTGTTACTACGTATGCTACTCCC 59.422 45.833 0.00 0.00 0.00 4.30
5883 6075 4.785301 TGTTACTACGTATGCTACTCCCT 58.215 43.478 0.00 0.00 0.00 4.20
5884 6076 4.818546 TGTTACTACGTATGCTACTCCCTC 59.181 45.833 0.00 0.00 0.00 4.30
5885 6077 2.861274 ACTACGTATGCTACTCCCTCC 58.139 52.381 0.00 0.00 0.00 4.30
5886 6078 1.805345 CTACGTATGCTACTCCCTCCG 59.195 57.143 0.00 0.00 0.00 4.63
5889 6081 0.960286 GTATGCTACTCCCTCCGTCC 59.040 60.000 0.00 0.00 0.00 4.79
5890 6082 0.178970 TATGCTACTCCCTCCGTCCC 60.179 60.000 0.00 0.00 0.00 4.46
5891 6083 2.043248 GCTACTCCCTCCGTCCCA 60.043 66.667 0.00 0.00 0.00 4.37
5892 6084 1.684734 GCTACTCCCTCCGTCCCAA 60.685 63.158 0.00 0.00 0.00 4.12
5893 6085 1.262640 GCTACTCCCTCCGTCCCAAA 61.263 60.000 0.00 0.00 0.00 3.28
5895 6087 0.978907 TACTCCCTCCGTCCCAAAAC 59.021 55.000 0.00 0.00 0.00 2.43
5896 6088 0.767060 ACTCCCTCCGTCCCAAAACT 60.767 55.000 0.00 0.00 0.00 2.66
5897 6089 0.036294 CTCCCTCCGTCCCAAAACTC 60.036 60.000 0.00 0.00 0.00 3.01
5901 6093 0.875059 CTCCGTCCCAAAACTCTTGC 59.125 55.000 0.00 0.00 0.00 4.01
5902 6094 0.536460 TCCGTCCCAAAACTCTTGCC 60.536 55.000 0.00 0.00 0.00 4.52
5904 6096 1.318576 CGTCCCAAAACTCTTGCCTT 58.681 50.000 0.00 0.00 0.00 4.35
5905 6097 2.500229 CGTCCCAAAACTCTTGCCTTA 58.500 47.619 0.00 0.00 0.00 2.69
5908 6100 4.336280 GTCCCAAAACTCTTGCCTTAGAT 58.664 43.478 0.00 0.00 0.00 1.98
5910 6102 5.243954 GTCCCAAAACTCTTGCCTTAGATTT 59.756 40.000 0.00 0.00 0.00 2.17
5912 6104 5.011023 CCCAAAACTCTTGCCTTAGATTTGT 59.989 40.000 0.00 0.00 28.79 2.83
5914 6106 6.015940 CCAAAACTCTTGCCTTAGATTTGTCT 60.016 38.462 0.00 0.00 28.79 3.41
5915 6107 7.174946 CCAAAACTCTTGCCTTAGATTTGTCTA 59.825 37.037 0.00 0.00 28.79 2.59
5936 6131 1.605058 ATACCTTGCGTGGCTCGACT 61.605 55.000 13.77 0.00 42.86 4.18
5939 6134 4.600576 TTGCGTGGCTCGACTGCA 62.601 61.111 13.77 0.00 42.86 4.41
5942 6137 2.661537 CGTGGCTCGACTGCAACA 60.662 61.111 2.21 0.00 42.86 3.33
5945 6140 1.737735 TGGCTCGACTGCAACATCG 60.738 57.895 8.07 8.07 39.72 3.84
5951 6146 1.139989 CGACTGCAACATCGTTGTCT 58.860 50.000 8.52 0.00 34.06 3.41
5957 6152 2.411748 TGCAACATCGTTGTCTTCGATC 59.588 45.455 8.52 0.00 44.49 3.69
5960 6155 2.516923 ACATCGTTGTCTTCGATCGAC 58.483 47.619 19.26 7.97 44.49 4.20
5962 6157 2.522372 TCGTTGTCTTCGATCGACTC 57.478 50.000 19.26 11.45 32.30 3.36
6020 6225 1.914051 CTGCATACGTGACAAGAGACG 59.086 52.381 0.00 0.00 41.41 4.18
6061 6266 5.536260 CATTTCTGTCTCTCTCAACACTGA 58.464 41.667 0.00 0.00 0.00 3.41
6062 6267 5.798125 TTTCTGTCTCTCTCAACACTGAT 57.202 39.130 0.00 0.00 0.00 2.90
6063 6268 4.780275 TCTGTCTCTCTCAACACTGATG 57.220 45.455 0.00 0.00 0.00 3.07
6064 6269 4.401925 TCTGTCTCTCTCAACACTGATGA 58.598 43.478 0.00 0.00 0.00 2.92
6065 6270 4.829492 TCTGTCTCTCTCAACACTGATGAA 59.171 41.667 0.00 0.00 0.00 2.57
6066 6271 5.479724 TCTGTCTCTCTCAACACTGATGAAT 59.520 40.000 0.00 0.00 0.00 2.57
6067 6272 6.014755 TCTGTCTCTCTCAACACTGATGAATT 60.015 38.462 0.00 0.00 0.00 2.17
6068 6273 7.177392 TCTGTCTCTCTCAACACTGATGAATTA 59.823 37.037 0.00 0.00 0.00 1.40
6070 6275 8.316946 TGTCTCTCTCAACACTGATGAATTATT 58.683 33.333 0.00 0.00 0.00 1.40
6072 6277 9.730705 TCTCTCTCAACACTGATGAATTATTTT 57.269 29.630 0.00 0.00 0.00 1.82
6151 6364 2.660064 CCCCGAGTCCTGGTCTTGG 61.660 68.421 17.52 17.52 36.50 3.61
6185 6398 6.327279 CATCCATGCATGATCATTAAGTGT 57.673 37.500 28.31 0.09 0.00 3.55
6186 6399 6.379386 CATCCATGCATGATCATTAAGTGTC 58.621 40.000 28.31 0.00 0.00 3.67
6187 6400 5.687780 TCCATGCATGATCATTAAGTGTCT 58.312 37.500 28.31 0.00 0.00 3.41
6188 6401 5.529800 TCCATGCATGATCATTAAGTGTCTG 59.470 40.000 28.31 5.24 0.00 3.51
6189 6402 5.529800 CCATGCATGATCATTAAGTGTCTGA 59.470 40.000 28.31 0.00 0.00 3.27
6190 6403 6.206829 CCATGCATGATCATTAAGTGTCTGAT 59.793 38.462 28.31 0.00 32.46 2.90
6191 6404 6.613755 TGCATGATCATTAAGTGTCTGATG 57.386 37.500 5.16 0.00 30.00 3.07
6192 6405 6.350906 TGCATGATCATTAAGTGTCTGATGA 58.649 36.000 5.16 0.00 33.50 2.92
6193 6406 6.996282 TGCATGATCATTAAGTGTCTGATGAT 59.004 34.615 5.16 0.00 40.79 2.45
6194 6407 7.501225 TGCATGATCATTAAGTGTCTGATGATT 59.499 33.333 5.16 0.00 38.85 2.57
6195 6408 8.996271 GCATGATCATTAAGTGTCTGATGATTA 58.004 33.333 5.16 0.00 38.85 1.75
6200 6413 9.703892 ATCATTAAGTGTCTGATGATTAGTAGC 57.296 33.333 0.00 0.00 36.17 3.58
6201 6414 8.695456 TCATTAAGTGTCTGATGATTAGTAGCA 58.305 33.333 0.00 0.00 0.00 3.49
6202 6415 8.759641 CATTAAGTGTCTGATGATTAGTAGCAC 58.240 37.037 0.00 0.00 0.00 4.40
6203 6416 6.537453 AAGTGTCTGATGATTAGTAGCACT 57.463 37.500 0.00 0.00 36.40 4.40
6204 6417 5.900425 AGTGTCTGATGATTAGTAGCACTG 58.100 41.667 9.45 0.00 34.02 3.66
6205 6418 5.046529 GTGTCTGATGATTAGTAGCACTGG 58.953 45.833 0.00 0.00 0.00 4.00
6206 6419 4.711846 TGTCTGATGATTAGTAGCACTGGT 59.288 41.667 0.00 0.00 0.00 4.00
6207 6420 5.891551 TGTCTGATGATTAGTAGCACTGGTA 59.108 40.000 0.00 0.00 0.00 3.25
6208 6421 6.551227 TGTCTGATGATTAGTAGCACTGGTAT 59.449 38.462 0.00 0.00 0.00 2.73
6209 6422 7.724061 TGTCTGATGATTAGTAGCACTGGTATA 59.276 37.037 0.00 0.00 0.00 1.47
6210 6423 8.744652 GTCTGATGATTAGTAGCACTGGTATAT 58.255 37.037 0.00 0.00 0.00 0.86
6211 6424 9.975218 TCTGATGATTAGTAGCACTGGTATATA 57.025 33.333 0.00 0.00 0.00 0.86
6283 6496 9.998752 ATATATGCTCTTAGTGGTAGGATTAGT 57.001 33.333 0.00 0.00 0.00 2.24
6284 6497 5.854010 TGCTCTTAGTGGTAGGATTAGTG 57.146 43.478 0.00 0.00 0.00 2.74
6285 6498 5.269991 TGCTCTTAGTGGTAGGATTAGTGT 58.730 41.667 0.00 0.00 0.00 3.55
6286 6499 6.429151 TGCTCTTAGTGGTAGGATTAGTGTA 58.571 40.000 0.00 0.00 0.00 2.90
6287 6500 7.067421 TGCTCTTAGTGGTAGGATTAGTGTAT 58.933 38.462 0.00 0.00 0.00 2.29
6288 6501 7.014326 TGCTCTTAGTGGTAGGATTAGTGTATG 59.986 40.741 0.00 0.00 0.00 2.39
6289 6502 7.230913 GCTCTTAGTGGTAGGATTAGTGTATGA 59.769 40.741 0.00 0.00 0.00 2.15
6290 6503 9.303116 CTCTTAGTGGTAGGATTAGTGTATGAT 57.697 37.037 0.00 0.00 0.00 2.45
6291 6504 9.656323 TCTTAGTGGTAGGATTAGTGTATGATT 57.344 33.333 0.00 0.00 0.00 2.57
6295 6508 8.648693 AGTGGTAGGATTAGTGTATGATTTACC 58.351 37.037 0.00 0.00 0.00 2.85
6296 6509 8.426489 GTGGTAGGATTAGTGTATGATTTACCA 58.574 37.037 0.00 0.00 35.68 3.25
6297 6510 8.647796 TGGTAGGATTAGTGTATGATTTACCAG 58.352 37.037 0.00 0.00 33.78 4.00
6298 6511 8.095169 GGTAGGATTAGTGTATGATTTACCAGG 58.905 40.741 0.00 0.00 0.00 4.45
6299 6512 7.691993 AGGATTAGTGTATGATTTACCAGGT 57.308 36.000 0.00 0.00 0.00 4.00
6300 6513 8.792830 AGGATTAGTGTATGATTTACCAGGTA 57.207 34.615 0.00 0.00 0.00 3.08
6301 6514 8.648693 AGGATTAGTGTATGATTTACCAGGTAC 58.351 37.037 0.00 0.00 0.00 3.34
6302 6515 8.426489 GGATTAGTGTATGATTTACCAGGTACA 58.574 37.037 0.00 0.00 0.00 2.90
6303 6516 9.998106 GATTAGTGTATGATTTACCAGGTACAT 57.002 33.333 0.00 0.00 0.00 2.29
6304 6517 9.778741 ATTAGTGTATGATTTACCAGGTACATG 57.221 33.333 2.73 0.00 0.00 3.21
6305 6518 7.432148 AGTGTATGATTTACCAGGTACATGA 57.568 36.000 9.54 0.00 0.00 3.07
6306 6519 7.500992 AGTGTATGATTTACCAGGTACATGAG 58.499 38.462 9.54 1.74 0.00 2.90
6307 6520 6.706270 GTGTATGATTTACCAGGTACATGAGG 59.294 42.308 9.54 0.00 0.00 3.86
6308 6521 4.771114 TGATTTACCAGGTACATGAGGG 57.229 45.455 9.54 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.202756 GACATGGCGAGGACGGTC 60.203 66.667 0.00 0.00 40.15 4.79
22 23 2.508891 GCGAGTTCGACATGGCGAG 61.509 63.158 24.88 13.76 41.79 5.03
48 49 1.711298 GCGCTGATCGATTTCTACTCG 59.289 52.381 0.00 0.00 41.67 4.18
159 160 2.512515 GTGACGAGCATCCTGGCC 60.513 66.667 0.00 0.00 0.00 5.36
198 199 4.802051 CAGATGGTGGTGCGGGGG 62.802 72.222 0.00 0.00 0.00 5.40
514 515 3.124921 GTTCGCGGACATGGTGGG 61.125 66.667 14.01 0.00 0.00 4.61
800 812 2.498726 CTTCCTCTCTGCGGCTCC 59.501 66.667 0.00 0.00 0.00 4.70
817 829 1.098050 ATCCATTTCCAGCTCGTTGC 58.902 50.000 0.00 0.00 43.29 4.17
897 913 2.101640 ATTCTTTTGTTGGGCCCACT 57.898 45.000 28.70 0.00 0.00 4.00
898 914 2.630580 TGTATTCTTTTGTTGGGCCCAC 59.369 45.455 28.70 20.43 0.00 4.61
900 916 2.630580 TGTGTATTCTTTTGTTGGGCCC 59.369 45.455 17.59 17.59 0.00 5.80
985 1001 3.574445 CATCGCTGCTGCTGCTCC 61.574 66.667 25.43 6.56 40.48 4.70
989 1005 1.227586 ATCTCCATCGCTGCTGCTG 60.228 57.895 14.03 5.96 36.97 4.41
990 1006 1.227586 CATCTCCATCGCTGCTGCT 60.228 57.895 14.03 0.00 36.97 4.24
991 1007 2.252346 CCATCTCCATCGCTGCTGC 61.252 63.158 5.34 5.34 0.00 5.25
992 1008 0.600518 CTCCATCTCCATCGCTGCTG 60.601 60.000 0.00 0.00 0.00 4.41
999 1019 2.356793 CGCGCCTCCATCTCCATC 60.357 66.667 0.00 0.00 0.00 3.51
1535 1555 0.532115 ATGCCCAAATGAGCCGAAAC 59.468 50.000 0.00 0.00 0.00 2.78
1618 1641 0.611618 TGCCCTGCCAAACCATACAG 60.612 55.000 0.00 0.00 0.00 2.74
1620 1643 0.611896 AGTGCCCTGCCAAACCATAC 60.612 55.000 0.00 0.00 0.00 2.39
1658 1681 0.183492 TCACTTTGTGCTCCTGGCTT 59.817 50.000 0.00 0.00 42.39 4.35
1715 1738 1.080569 CACAAAACCGGCAGGCATC 60.081 57.895 0.00 0.00 42.76 3.91
1717 1740 2.441164 ACACAAAACCGGCAGGCA 60.441 55.556 0.00 0.00 42.76 4.75
1795 1818 3.805108 GCTAGATTTCATCCAGGCATCGT 60.805 47.826 0.00 0.00 0.00 3.73
1796 1819 2.740981 GCTAGATTTCATCCAGGCATCG 59.259 50.000 0.00 0.00 0.00 3.84
1829 1852 0.912487 AGCCACTTACCCGGAATGGA 60.912 55.000 0.73 0.00 42.00 3.41
1855 1878 3.761218 CTGCAGAAGGACTAAGACTGAGA 59.239 47.826 8.42 0.00 0.00 3.27
1901 1924 1.265905 GGTGAACCCAACTAACTTGCG 59.734 52.381 0.00 0.00 0.00 4.85
1922 1945 6.925165 AGTTCAGCTTTGATTTAACCAACATG 59.075 34.615 0.00 0.00 0.00 3.21
1923 1946 7.054491 AGTTCAGCTTTGATTTAACCAACAT 57.946 32.000 0.00 0.00 0.00 2.71
1924 1947 6.463995 AGTTCAGCTTTGATTTAACCAACA 57.536 33.333 0.00 0.00 0.00 3.33
2250 2294 5.673337 TGAGCAAGTTGAACTTCATGTAC 57.327 39.130 7.75 0.00 36.03 2.90
2358 2404 7.033530 AGATCTCATTACAGGAAACTACTCG 57.966 40.000 0.00 0.00 40.21 4.18
3025 3134 9.366216 CTCATAATTAATGCAATCCATGGAATG 57.634 33.333 23.33 23.33 38.70 2.67
3026 3135 8.537016 CCTCATAATTAATGCAATCCATGGAAT 58.463 33.333 20.67 7.74 35.38 3.01
3027 3136 7.525859 GCCTCATAATTAATGCAATCCATGGAA 60.526 37.037 20.67 1.57 35.38 3.53
3028 3137 6.071221 GCCTCATAATTAATGCAATCCATGGA 60.071 38.462 18.88 18.88 35.38 3.41
3029 3138 6.103997 GCCTCATAATTAATGCAATCCATGG 58.896 40.000 4.97 4.97 35.38 3.66
3030 3139 5.803461 CGCCTCATAATTAATGCAATCCATG 59.197 40.000 0.00 0.00 35.38 3.66
3031 3140 5.477984 ACGCCTCATAATTAATGCAATCCAT 59.522 36.000 0.00 0.00 35.38 3.41
3032 3141 4.826733 ACGCCTCATAATTAATGCAATCCA 59.173 37.500 0.00 0.00 35.38 3.41
3033 3142 5.376854 ACGCCTCATAATTAATGCAATCC 57.623 39.130 0.00 0.00 35.38 3.01
3034 3143 8.970691 AATAACGCCTCATAATTAATGCAATC 57.029 30.769 0.00 0.00 35.38 2.67
3035 3144 9.195411 CAAATAACGCCTCATAATTAATGCAAT 57.805 29.630 0.00 0.00 35.38 3.56
3036 3145 8.194104 ACAAATAACGCCTCATAATTAATGCAA 58.806 29.630 0.00 0.00 35.38 4.08
3037 3146 7.711846 ACAAATAACGCCTCATAATTAATGCA 58.288 30.769 0.00 0.00 35.38 3.96
3038 3147 8.574196 AACAAATAACGCCTCATAATTAATGC 57.426 30.769 0.00 0.00 35.38 3.56
3041 3150 9.724839 GCTAAACAAATAACGCCTCATAATTAA 57.275 29.630 0.00 0.00 0.00 1.40
3042 3151 8.894731 TGCTAAACAAATAACGCCTCATAATTA 58.105 29.630 0.00 0.00 0.00 1.40
3043 3152 7.700656 GTGCTAAACAAATAACGCCTCATAATT 59.299 33.333 0.00 0.00 0.00 1.40
3044 3153 7.067008 AGTGCTAAACAAATAACGCCTCATAAT 59.933 33.333 0.00 0.00 0.00 1.28
3045 3154 6.373216 AGTGCTAAACAAATAACGCCTCATAA 59.627 34.615 0.00 0.00 0.00 1.90
3046 3155 5.878116 AGTGCTAAACAAATAACGCCTCATA 59.122 36.000 0.00 0.00 0.00 2.15
3047 3156 4.700213 AGTGCTAAACAAATAACGCCTCAT 59.300 37.500 0.00 0.00 0.00 2.90
3048 3157 4.069304 AGTGCTAAACAAATAACGCCTCA 58.931 39.130 0.00 0.00 0.00 3.86
3049 3158 4.680171 AGTGCTAAACAAATAACGCCTC 57.320 40.909 0.00 0.00 0.00 4.70
3050 3159 5.243207 ACTAGTGCTAAACAAATAACGCCT 58.757 37.500 0.00 0.00 0.00 5.52
3051 3160 5.541098 ACTAGTGCTAAACAAATAACGCC 57.459 39.130 0.00 0.00 0.00 5.68
3052 3161 7.847166 AAAACTAGTGCTAAACAAATAACGC 57.153 32.000 0.00 0.00 0.00 4.84
3086 3195 8.330466 ACAATTCATACAAAACGAATGTAGGA 57.670 30.769 9.16 9.16 40.92 2.94
3087 3196 9.485591 GTACAATTCATACAAAACGAATGTAGG 57.514 33.333 0.00 0.00 36.75 3.18
3088 3197 9.194716 CGTACAATTCATACAAAACGAATGTAG 57.805 33.333 0.00 0.00 36.75 2.74
3089 3198 8.710551 ACGTACAATTCATACAAAACGAATGTA 58.289 29.630 0.00 0.00 37.64 2.29
3090 3199 7.577979 ACGTACAATTCATACAAAACGAATGT 58.422 30.769 0.00 0.00 33.59 2.71
3091 3200 7.742525 TGACGTACAATTCATACAAAACGAATG 59.257 33.333 0.00 0.00 33.59 2.67
3092 3201 7.742963 GTGACGTACAATTCATACAAAACGAAT 59.257 33.333 0.00 0.00 33.59 3.34
3093 3202 7.042590 AGTGACGTACAATTCATACAAAACGAA 60.043 33.333 0.00 0.00 33.59 3.85
3094 3203 6.421501 AGTGACGTACAATTCATACAAAACGA 59.578 34.615 0.00 0.00 33.59 3.85
3095 3204 6.586751 AGTGACGTACAATTCATACAAAACG 58.413 36.000 0.00 0.00 35.38 3.60
3098 3207 8.875803 GGATAAGTGACGTACAATTCATACAAA 58.124 33.333 4.43 0.00 37.89 2.83
3099 3208 8.035984 TGGATAAGTGACGTACAATTCATACAA 58.964 33.333 4.43 0.00 37.89 2.41
3100 3209 7.548967 TGGATAAGTGACGTACAATTCATACA 58.451 34.615 4.43 3.05 37.89 2.29
3101 3210 7.997107 TGGATAAGTGACGTACAATTCATAC 57.003 36.000 4.43 1.18 37.89 2.39
3102 3211 8.417884 TGATGGATAAGTGACGTACAATTCATA 58.582 33.333 4.43 0.00 37.89 2.15
3103 3212 7.272244 TGATGGATAAGTGACGTACAATTCAT 58.728 34.615 4.43 4.81 37.89 2.57
3104 3213 6.635755 TGATGGATAAGTGACGTACAATTCA 58.364 36.000 4.43 0.00 37.89 2.57
3105 3214 7.653713 AGATGATGGATAAGTGACGTACAATTC 59.346 37.037 4.43 0.00 37.89 2.17
3106 3215 7.500992 AGATGATGGATAAGTGACGTACAATT 58.499 34.615 0.00 0.00 40.02 2.32
3107 3216 7.055667 AGATGATGGATAAGTGACGTACAAT 57.944 36.000 0.00 0.00 0.00 2.71
3108 3217 6.465439 AGATGATGGATAAGTGACGTACAA 57.535 37.500 0.00 0.00 0.00 2.41
3109 3218 6.321435 AGAAGATGATGGATAAGTGACGTACA 59.679 38.462 0.00 0.00 0.00 2.90
3110 3219 6.740110 AGAAGATGATGGATAAGTGACGTAC 58.260 40.000 0.00 0.00 0.00 3.67
3111 3220 6.961360 AGAAGATGATGGATAAGTGACGTA 57.039 37.500 0.00 0.00 0.00 3.57
3112 3221 5.860941 AGAAGATGATGGATAAGTGACGT 57.139 39.130 0.00 0.00 0.00 4.34
3113 3222 6.309980 GCATAGAAGATGATGGATAAGTGACG 59.690 42.308 0.00 0.00 0.00 4.35
3162 3278 6.274157 ACTGGTCTTAAGATAGTGACTGTG 57.726 41.667 18.88 2.53 0.00 3.66
3163 3279 6.919775 AACTGGTCTTAAGATAGTGACTGT 57.080 37.500 19.78 9.81 0.00 3.55
3532 3652 7.628234 AGATGCCATAGCTAATTAGTATTGCT 58.372 34.615 13.91 7.73 40.80 3.91
3617 3737 0.677731 CAAAGCGGAATGAGGAGCCA 60.678 55.000 0.00 0.00 0.00 4.75
3975 4100 2.991866 GACTCGTTAGGTAAACACCTGC 59.008 50.000 6.59 0.00 40.93 4.85
4026 4151 7.477422 CACTTGTGTTCGAAATTAGGTAATTCG 59.523 37.037 0.00 1.03 35.00 3.34
4042 4167 2.223479 ACGATGTTTGGCACTTGTGTTC 60.223 45.455 2.61 0.00 0.00 3.18
4053 4178 4.503910 TGGAGATGTTAGACGATGTTTGG 58.496 43.478 0.00 0.00 0.00 3.28
4087 4212 8.289939 ACATGCTATCAAGTCATTTTCTGAAT 57.710 30.769 0.00 0.00 35.07 2.57
4276 4429 4.825085 TCCTGGAACCATGTGTTAAAAGTC 59.175 41.667 0.00 0.00 37.29 3.01
4612 4771 9.481800 GTATAGTAATTAACAAAAAGTCGGTGC 57.518 33.333 0.00 0.00 0.00 5.01
4732 4891 9.704098 CAGCTAAATTTTATTCGTTCTACTTCC 57.296 33.333 0.00 0.00 0.00 3.46
4759 4918 5.905733 GCAAAACTACTACAACTTCGAAACC 59.094 40.000 0.00 0.00 0.00 3.27
4786 4945 4.872691 GTGGAACCATGAACATGACTAGAG 59.127 45.833 15.21 1.59 41.20 2.43
4883 5042 4.852134 TCATTGGTTGATTTCACACTGG 57.148 40.909 0.00 0.00 0.00 4.00
4914 5073 9.770097 TTATTAGGCTCATCTTAGAAATCACAG 57.230 33.333 0.00 0.00 0.00 3.66
4954 5113 3.073062 AGTGTGCAAATAAGTCACTCCCT 59.927 43.478 0.00 0.00 34.87 4.20
4955 5114 3.412386 AGTGTGCAAATAAGTCACTCCC 58.588 45.455 0.00 0.00 34.87 4.30
4957 5116 6.080406 GCTTTAGTGTGCAAATAAGTCACTC 58.920 40.000 7.10 0.00 39.54 3.51
4959 5118 5.048713 AGGCTTTAGTGTGCAAATAAGTCAC 60.049 40.000 0.00 0.00 0.00 3.67
4960 5119 5.070001 AGGCTTTAGTGTGCAAATAAGTCA 58.930 37.500 0.00 0.00 0.00 3.41
4961 5120 5.629079 AGGCTTTAGTGTGCAAATAAGTC 57.371 39.130 0.00 0.00 0.00 3.01
5005 5164 2.173569 GCCTCCATCTAGAACCATTGGT 59.826 50.000 1.37 1.37 37.65 3.67
5006 5165 2.173356 TGCCTCCATCTAGAACCATTGG 59.827 50.000 0.00 0.00 0.00 3.16
5007 5166 3.474600 CTGCCTCCATCTAGAACCATTG 58.525 50.000 0.00 0.00 0.00 2.82
5008 5167 2.441001 CCTGCCTCCATCTAGAACCATT 59.559 50.000 0.00 0.00 0.00 3.16
5009 5168 2.053244 CCTGCCTCCATCTAGAACCAT 58.947 52.381 0.00 0.00 0.00 3.55
5066 5225 1.264045 TGACAGCATGGGATCACGGA 61.264 55.000 0.00 0.00 43.62 4.69
5071 5230 2.502295 GGAATCTGACAGCATGGGATC 58.498 52.381 0.00 0.00 43.62 3.36
5139 5298 1.945580 TACCCACTGCATCACCTGTA 58.054 50.000 0.00 0.00 0.00 2.74
5149 5308 2.390427 GTGGCGTAATACCCACTGC 58.610 57.895 17.88 2.27 46.23 4.40
5246 5405 6.542370 TCTTCTGGAAGTAACCAAGTCAAAAG 59.458 38.462 9.73 0.00 39.59 2.27
5277 5436 6.568271 GCACATGTAATCCGCATCATTATTGA 60.568 38.462 0.00 0.00 36.00 2.57
5329 5488 0.473755 AGGGCACACATCACACAGAA 59.526 50.000 0.00 0.00 0.00 3.02
5346 5505 3.206150 AGTTGCTGTTCACACAAGTAGG 58.794 45.455 0.00 0.00 30.36 3.18
5376 5535 5.012148 AGGGAAACAGATATCCGAGTAATGG 59.988 44.000 0.00 0.00 36.54 3.16
5391 5550 2.863809 AGCTTGTGGTTAGGGAAACAG 58.136 47.619 0.00 0.00 40.08 3.16
5401 5560 3.636300 TCAAACATTGCTAGCTTGTGGTT 59.364 39.130 19.97 15.32 0.00 3.67
5409 5568 3.837213 TTGCTCTCAAACATTGCTAGC 57.163 42.857 8.10 8.10 38.10 3.42
5420 5581 9.577110 GTCATGAAATTTATGAATTGCTCTCAA 57.423 29.630 1.89 0.00 36.41 3.02
5426 5587 7.042925 GGCTCAGTCATGAAATTTATGAATTGC 60.043 37.037 1.89 7.85 36.41 3.56
5460 5621 6.390721 AGTAAATATCCTTCATCGATCGTGG 58.609 40.000 15.94 8.67 0.00 4.94
5482 5643 3.612860 CGCGTGTGCTTATTTCTCTTAGT 59.387 43.478 0.00 0.00 39.65 2.24
5487 5649 4.201685 ACAATACGCGTGTGCTTATTTCTC 60.202 41.667 24.59 0.00 41.25 2.87
5496 5658 4.932851 TTTTAAAACAATACGCGTGTGC 57.067 36.364 24.59 0.00 37.91 4.57
5502 5664 5.830900 TGGCACATTTTAAAACAATACGC 57.169 34.783 1.97 1.05 0.00 4.42
5509 5671 8.768955 TGTCATGTTAATGGCACATTTTAAAAC 58.231 29.630 1.97 5.47 43.45 2.43
5510 5672 8.893219 TGTCATGTTAATGGCACATTTTAAAA 57.107 26.923 2.51 2.51 43.45 1.52
5662 5838 7.821846 GCCCTCTGATAATCTATAGTTTCCTTG 59.178 40.741 0.00 0.00 0.00 3.61
5673 5849 5.211973 ACAGACAAGCCCTCTGATAATCTA 58.788 41.667 9.31 0.00 37.90 1.98
5689 5865 1.661617 CGAAACGTCCACAACAGACAA 59.338 47.619 0.00 0.00 33.70 3.18
5690 5866 1.282817 CGAAACGTCCACAACAGACA 58.717 50.000 0.00 0.00 33.70 3.41
5696 5872 1.595929 GGAGCCGAAACGTCCACAA 60.596 57.895 0.00 0.00 0.00 3.33
5700 5876 3.119096 GCTGGAGCCGAAACGTCC 61.119 66.667 0.00 0.00 34.31 4.79
5739 5915 1.207791 TTCAGGGGCTGGAGAAGATC 58.792 55.000 0.00 0.00 31.51 2.75
5760 5936 4.332828 ACTCCAGGTGGCAATTTAACTAC 58.667 43.478 0.00 0.00 34.44 2.73
5761 5937 4.650972 ACTCCAGGTGGCAATTTAACTA 57.349 40.909 0.00 0.00 34.44 2.24
5763 5939 4.765339 ACTAACTCCAGGTGGCAATTTAAC 59.235 41.667 0.00 0.00 34.44 2.01
5768 5958 3.308188 GGTAACTAACTCCAGGTGGCAAT 60.308 47.826 0.00 0.00 34.44 3.56
5785 5975 5.790593 TGTCCAGTAGATTTGTCAGGTAAC 58.209 41.667 0.00 0.00 0.00 2.50
5786 5976 6.013725 ACATGTCCAGTAGATTTGTCAGGTAA 60.014 38.462 0.00 0.00 0.00 2.85
5787 5977 5.483937 ACATGTCCAGTAGATTTGTCAGGTA 59.516 40.000 0.00 0.00 0.00 3.08
5788 5978 4.287067 ACATGTCCAGTAGATTTGTCAGGT 59.713 41.667 0.00 0.00 0.00 4.00
5789 5979 4.836825 ACATGTCCAGTAGATTTGTCAGG 58.163 43.478 0.00 0.00 0.00 3.86
5790 5980 6.808008 AAACATGTCCAGTAGATTTGTCAG 57.192 37.500 0.00 0.00 0.00 3.51
5791 5981 6.770303 TCAAAACATGTCCAGTAGATTTGTCA 59.230 34.615 0.00 0.00 0.00 3.58
5792 5982 7.202016 TCAAAACATGTCCAGTAGATTTGTC 57.798 36.000 0.00 0.00 0.00 3.18
5793 5983 7.285401 AGTTCAAAACATGTCCAGTAGATTTGT 59.715 33.333 0.00 0.00 0.00 2.83
5794 5984 7.651808 AGTTCAAAACATGTCCAGTAGATTTG 58.348 34.615 0.00 3.92 0.00 2.32
5795 5985 7.823745 AGTTCAAAACATGTCCAGTAGATTT 57.176 32.000 0.00 0.00 0.00 2.17
5796 5986 8.784043 GTTAGTTCAAAACATGTCCAGTAGATT 58.216 33.333 0.00 0.00 0.00 2.40
5797 5987 8.157476 AGTTAGTTCAAAACATGTCCAGTAGAT 58.843 33.333 0.00 0.00 0.00 1.98
5798 5988 7.441157 CAGTTAGTTCAAAACATGTCCAGTAGA 59.559 37.037 0.00 0.00 0.00 2.59
5799 5989 7.441157 TCAGTTAGTTCAAAACATGTCCAGTAG 59.559 37.037 0.00 0.00 0.00 2.57
5800 5990 7.225931 GTCAGTTAGTTCAAAACATGTCCAGTA 59.774 37.037 0.00 0.00 0.00 2.74
5801 5991 6.038271 GTCAGTTAGTTCAAAACATGTCCAGT 59.962 38.462 0.00 0.00 0.00 4.00
5847 6039 5.106396 ACGTAGTAACAGTTACAGGCTGTAG 60.106 44.000 25.00 17.12 45.36 2.74
5874 6066 1.262640 TTTGGGACGGAGGGAGTAGC 61.263 60.000 0.00 0.00 0.00 3.58
5878 6070 0.036294 GAGTTTTGGGACGGAGGGAG 60.036 60.000 0.00 0.00 0.00 4.30
5879 6071 0.473117 AGAGTTTTGGGACGGAGGGA 60.473 55.000 0.00 0.00 0.00 4.20
5880 6072 0.400594 AAGAGTTTTGGGACGGAGGG 59.599 55.000 0.00 0.00 0.00 4.30
5881 6073 1.523758 CAAGAGTTTTGGGACGGAGG 58.476 55.000 0.00 0.00 0.00 4.30
5882 6074 0.875059 GCAAGAGTTTTGGGACGGAG 59.125 55.000 0.00 0.00 0.00 4.63
5883 6075 0.536460 GGCAAGAGTTTTGGGACGGA 60.536 55.000 0.00 0.00 0.00 4.69
5884 6076 0.537371 AGGCAAGAGTTTTGGGACGG 60.537 55.000 0.00 0.00 0.00 4.79
5885 6077 1.318576 AAGGCAAGAGTTTTGGGACG 58.681 50.000 0.00 0.00 0.00 4.79
5886 6078 3.751518 TCTAAGGCAAGAGTTTTGGGAC 58.248 45.455 0.00 0.00 0.00 4.46
5889 6081 6.015940 AGACAAATCTAAGGCAAGAGTTTTGG 60.016 38.462 14.87 4.02 36.98 3.28
5890 6082 6.974965 AGACAAATCTAAGGCAAGAGTTTTG 58.025 36.000 11.38 11.38 37.93 2.44
5891 6083 8.691661 TTAGACAAATCTAAGGCAAGAGTTTT 57.308 30.769 0.60 0.00 41.58 2.43
5892 6084 8.691661 TTTAGACAAATCTAAGGCAAGAGTTT 57.308 30.769 0.60 0.00 45.93 2.66
5893 6085 8.870075 ATTTAGACAAATCTAAGGCAAGAGTT 57.130 30.769 0.00 0.00 45.93 3.01
5895 6087 8.831550 GGTATTTAGACAAATCTAAGGCAAGAG 58.168 37.037 0.00 0.00 45.93 2.85
5896 6088 8.548877 AGGTATTTAGACAAATCTAAGGCAAGA 58.451 33.333 0.00 0.00 45.93 3.02
5897 6089 8.738645 AGGTATTTAGACAAATCTAAGGCAAG 57.261 34.615 0.00 0.00 45.93 4.01
5901 6093 7.280205 ACGCAAGGTATTTAGACAAATCTAAGG 59.720 37.037 0.00 0.00 44.59 2.69
5902 6094 8.116753 CACGCAAGGTATTTAGACAAATCTAAG 58.883 37.037 0.00 0.00 44.59 2.18
5904 6096 6.537301 CCACGCAAGGTATTTAGACAAATCTA 59.463 38.462 0.00 0.00 46.39 1.98
5905 6097 5.354234 CCACGCAAGGTATTTAGACAAATCT 59.646 40.000 0.00 0.00 46.39 2.40
5908 6100 3.189702 GCCACGCAAGGTATTTAGACAAA 59.810 43.478 0.00 0.00 46.39 2.83
5910 6102 2.027561 AGCCACGCAAGGTATTTAGACA 60.028 45.455 0.00 0.00 46.39 3.41
5912 6104 2.737359 CGAGCCACGCAAGGTATTTAGA 60.737 50.000 0.00 0.00 46.39 2.10
5914 6106 1.205179 TCGAGCCACGCAAGGTATTTA 59.795 47.619 0.00 0.00 46.39 1.40
5915 6107 0.036765 TCGAGCCACGCAAGGTATTT 60.037 50.000 0.00 0.00 46.39 1.40
5936 6131 1.859383 TCGAAGACAACGATGTTGCA 58.141 45.000 9.45 0.00 40.74 4.08
5957 6152 1.586564 GGGCTTCGTCATCGAGTCG 60.587 63.158 6.09 6.09 46.81 4.18
5960 6155 1.227089 CCTGGGCTTCGTCATCGAG 60.227 63.158 0.00 0.00 46.81 4.04
5962 6157 2.202932 CCCTGGGCTTCGTCATCG 60.203 66.667 0.00 0.00 38.55 3.84
6070 6275 6.771573 TCCCTCCTAATTTTCACTTACGAAA 58.228 36.000 0.00 0.00 33.12 3.46
6072 6277 6.070424 ACATCCCTCCTAATTTTCACTTACGA 60.070 38.462 0.00 0.00 0.00 3.43
6078 6285 5.221126 GCATCACATCCCTCCTAATTTTCAC 60.221 44.000 0.00 0.00 0.00 3.18
6089 6302 2.362397 TCGAGTAAGCATCACATCCCTC 59.638 50.000 0.00 0.00 0.00 4.30
6118 6331 2.670592 GGGCCACCGTACAACACC 60.671 66.667 4.39 0.00 0.00 4.16
6181 6394 5.163468 CCAGTGCTACTAATCATCAGACACT 60.163 44.000 0.00 0.00 36.34 3.55
6182 6395 5.046529 CCAGTGCTACTAATCATCAGACAC 58.953 45.833 0.00 0.00 0.00 3.67
6183 6396 4.711846 ACCAGTGCTACTAATCATCAGACA 59.288 41.667 0.00 0.00 0.00 3.41
6184 6397 5.269505 ACCAGTGCTACTAATCATCAGAC 57.730 43.478 0.00 0.00 0.00 3.51
6185 6398 8.885693 ATATACCAGTGCTACTAATCATCAGA 57.114 34.615 0.00 0.00 0.00 3.27
6257 6470 9.998752 ACTAATCCTACCACTAAGAGCATATAT 57.001 33.333 0.00 0.00 0.00 0.86
6258 6471 9.244292 CACTAATCCTACCACTAAGAGCATATA 57.756 37.037 0.00 0.00 0.00 0.86
6259 6472 7.730784 ACACTAATCCTACCACTAAGAGCATAT 59.269 37.037 0.00 0.00 0.00 1.78
6260 6473 7.067421 ACACTAATCCTACCACTAAGAGCATA 58.933 38.462 0.00 0.00 0.00 3.14
6261 6474 5.900123 ACACTAATCCTACCACTAAGAGCAT 59.100 40.000 0.00 0.00 0.00 3.79
6262 6475 5.269991 ACACTAATCCTACCACTAAGAGCA 58.730 41.667 0.00 0.00 0.00 4.26
6263 6476 5.855740 ACACTAATCCTACCACTAAGAGC 57.144 43.478 0.00 0.00 0.00 4.09
6264 6477 8.693120 TCATACACTAATCCTACCACTAAGAG 57.307 38.462 0.00 0.00 0.00 2.85
6265 6478 9.656323 AATCATACACTAATCCTACCACTAAGA 57.344 33.333 0.00 0.00 0.00 2.10
6269 6482 8.648693 GGTAAATCATACACTAATCCTACCACT 58.351 37.037 0.00 0.00 0.00 4.00
6270 6483 8.426489 TGGTAAATCATACACTAATCCTACCAC 58.574 37.037 0.00 0.00 32.25 4.16
6271 6484 8.555896 TGGTAAATCATACACTAATCCTACCA 57.444 34.615 0.00 0.00 34.24 3.25
6272 6485 8.095169 CCTGGTAAATCATACACTAATCCTACC 58.905 40.741 0.00 0.00 0.00 3.18
6273 6486 8.648693 ACCTGGTAAATCATACACTAATCCTAC 58.351 37.037 0.00 0.00 0.00 3.18
6274 6487 8.792830 ACCTGGTAAATCATACACTAATCCTA 57.207 34.615 0.00 0.00 0.00 2.94
6275 6488 7.691993 ACCTGGTAAATCATACACTAATCCT 57.308 36.000 0.00 0.00 0.00 3.24
6276 6489 8.426489 TGTACCTGGTAAATCATACACTAATCC 58.574 37.037 8.40 0.00 0.00 3.01
6277 6490 9.998106 ATGTACCTGGTAAATCATACACTAATC 57.002 33.333 8.40 0.00 0.00 1.75
6278 6491 9.778741 CATGTACCTGGTAAATCATACACTAAT 57.221 33.333 8.40 0.00 0.00 1.73
6279 6492 8.983789 TCATGTACCTGGTAAATCATACACTAA 58.016 33.333 8.40 0.00 0.00 2.24
6280 6493 8.541899 TCATGTACCTGGTAAATCATACACTA 57.458 34.615 8.40 0.00 0.00 2.74
6281 6494 7.419057 CCTCATGTACCTGGTAAATCATACACT 60.419 40.741 8.40 0.00 0.00 3.55
6282 6495 6.706270 CCTCATGTACCTGGTAAATCATACAC 59.294 42.308 8.40 0.00 0.00 2.90
6283 6496 6.183361 CCCTCATGTACCTGGTAAATCATACA 60.183 42.308 8.40 3.34 0.00 2.29
6284 6497 6.231211 CCCTCATGTACCTGGTAAATCATAC 58.769 44.000 8.40 0.00 0.00 2.39
6285 6498 6.433847 CCCTCATGTACCTGGTAAATCATA 57.566 41.667 8.40 0.00 0.00 2.15
6286 6499 5.310409 CCCTCATGTACCTGGTAAATCAT 57.690 43.478 8.40 5.41 0.00 2.45
6287 6500 4.771114 CCCTCATGTACCTGGTAAATCA 57.229 45.455 8.40 3.03 0.00 2.57


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

AutoCloner maintained by Alex Coulton.