Multiple sequence alignment - TraesCS5B01G488200

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 TraesCS5B01G488200 chr5B 100.000 3194 0 0 1 3194 658762050 658758857 0.000000e+00 5899
1 TraesCS5B01G488200 chr5D 90.547 2137 111 25 582 2689 522489879 522487805 0.000000e+00 2743
2 TraesCS5B01G488200 chr5D 91.054 313 26 2 2883 3194 41127426 41127737 3.810000e-114 422
3 TraesCS5B01G488200 chr5D 90.196 204 19 1 2692 2894 522487702 522487499 6.790000e-67 265
4 TraesCS5B01G488200 chr5A 86.963 2071 150 59 582 2601 650519372 650517371 0.000000e+00 2218
5 TraesCS5B01G488200 chrUn 89.482 599 44 11 1 580 77392964 77392366 0.000000e+00 739
6 TraesCS5B01G488200 chr7A 90.345 435 41 1 146 579 116550405 116549971 1.290000e-158 569
7 TraesCS5B01G488200 chr7A 86.364 110 13 2 2059 2167 33147912 33148020 5.600000e-23 119
8 TraesCS5B01G488200 chr7A 86.364 110 13 2 2059 2167 33149336 33149228 5.600000e-23 119
9 TraesCS5B01G488200 chr3A 91.785 353 28 1 229 580 143492989 143493341 1.030000e-134 490
10 TraesCS5B01G488200 chr3A 90.476 147 14 0 3 149 143491900 143492046 9.040000e-46 195
11 TraesCS5B01G488200 chr3A 96.591 88 3 0 146 233 143492086 143492173 2.570000e-31 147
12 TraesCS5B01G488200 chr4B 92.880 309 22 0 2886 3194 625511855 625512163 1.750000e-122 449
13 TraesCS5B01G488200 chr3D 92.880 309 22 0 2886 3194 520452714 520452406 1.750000e-122 449
14 TraesCS5B01G488200 chr3D 84.800 125 18 1 456 580 303356265 303356142 1.200000e-24 124
15 TraesCS5B01G488200 chr3D 86.364 110 13 2 2059 2167 310697041 310697149 5.600000e-23 119
16 TraesCS5B01G488200 chr6D 92.182 307 24 0 2888 3194 464700437 464700131 4.890000e-118 435
17 TraesCS5B01G488200 chr1D 91.693 313 26 0 2882 3194 396286005 396286317 4.890000e-118 435
18 TraesCS5B01G488200 chr1D 87.681 138 15 2 451 587 66998065 66998201 3.300000e-35 159
19 TraesCS5B01G488200 chr4D 91.883 308 24 1 2886 3193 434958347 434958041 2.280000e-116 429
20 TraesCS5B01G488200 chr4D 91.205 307 27 0 2888 3194 4589045 4589351 4.930000e-113 418
21 TraesCS5B01G488200 chr1B 91.531 307 26 0 2888 3194 491359022 491358716 1.060000e-114 424
22 TraesCS5B01G488200 chr1B 91.339 127 11 0 1849 1975 655099668 655099542 1.180000e-39 174
23 TraesCS5B01G488200 chr1B 88.571 140 13 3 441 580 67665285 67665421 1.970000e-37 167
24 TraesCS5B01G488200 chr4A 91.447 304 26 0 2888 3191 737142809 737143112 4.930000e-113 418
25 TraesCS5B01G488200 chr4A 84.677 124 17 1 457 578 630755928 630756051 4.330000e-24 122
26 TraesCS5B01G488200 chr2B 82.494 417 53 8 183 580 510908761 510909176 6.560000e-92 348
27 TraesCS5B01G488200 chr6B 88.889 126 14 0 455 580 670587302 670587177 4.270000e-34 156
28 TraesCS5B01G488200 chr6B 87.273 110 12 2 2059 2167 563806144 563806036 1.200000e-24 124
29 TraesCS5B01G488200 chr7D 86.275 102 14 0 1400 1501 55128514 55128615 9.370000e-21 111
30 TraesCS5B01G488200 chr3B 81.818 121 19 3 457 576 810931850 810931968 7.290000e-17 99
31 TraesCS5B01G488200 chr1A 84.158 101 16 0 1400 1500 53898946 53898846 7.290000e-17 99


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 TraesCS5B01G488200 chr5B 658758857 658762050 3193 True 5899.000000 5899 100.000000 1 3194 1 chr5B.!!$R1 3193
1 TraesCS5B01G488200 chr5D 522487499 522489879 2380 True 1504.000000 2743 90.371500 582 2894 2 chr5D.!!$R1 2312
2 TraesCS5B01G488200 chr5A 650517371 650519372 2001 True 2218.000000 2218 86.963000 582 2601 1 chr5A.!!$R1 2019
3 TraesCS5B01G488200 chrUn 77392366 77392964 598 True 739.000000 739 89.482000 1 580 1 chrUn.!!$R1 579
4 TraesCS5B01G488200 chr3A 143491900 143493341 1441 False 277.333333 490 92.950667 3 580 3 chr3A.!!$F1 577

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
519 1384 0.110678 TGTGCCAACAACCGGGATTA 59.889 50.0 6.32 0.0 31.82 1.75 F
1794 2703 0.610174 TCCAGAGTTGCATCTTCGCT 59.390 50.0 0.00 0.0 0.00 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1870 2779 0.167470 CTGCAACGATGACCAGCAAG 59.833 55.0 0.00 0.0 34.45 4.01 R
2967 4030 0.029567 TTTTCGACCGCGCATGTTTT 59.970 45.0 8.75 0.0 37.46 2.43 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
112 113 0.392336 GAGTAGCAGGCTAGCAGCAT 59.608 55.000 26.63 15.51 44.75 3.79
138 163 2.505557 GCAACATTGCGAGCAGGC 60.506 61.111 0.00 0.00 45.11 4.85
139 164 2.956194 CAACATTGCGAGCAGGCA 59.044 55.556 0.00 0.00 42.12 4.75
142 167 3.057548 CATTGCGAGCAGGCACCA 61.058 61.111 0.76 0.00 43.82 4.17
177 221 1.514678 TTGTGTTGTGCGGATGCTCC 61.515 55.000 0.00 0.00 43.34 4.70
269 1133 2.203280 CGGGGGAAGCACACAACA 60.203 61.111 0.00 0.00 0.00 3.33
277 1141 2.051804 AAGCACACAACAGCAGCGAC 62.052 55.000 0.00 0.00 0.00 5.19
381 1245 6.317391 GGACAGAAATTGAGGTGGAAGATAAG 59.683 42.308 0.00 0.00 0.00 1.73
394 1258 5.128827 GTGGAAGATAAGTATGACAGGTGGA 59.871 44.000 0.00 0.00 0.00 4.02
497 1362 6.404293 CGATTTGGACCGGAATTGATAAGTTT 60.404 38.462 9.46 0.00 0.00 2.66
519 1384 0.110678 TGTGCCAACAACCGGGATTA 59.889 50.000 6.32 0.00 31.82 1.75
596 1461 5.295787 ACTTTTTCACTGCTCGTTACATCAA 59.704 36.000 0.00 0.00 0.00 2.57
597 1462 5.743026 TTTTCACTGCTCGTTACATCAAA 57.257 34.783 0.00 0.00 0.00 2.69
601 1466 3.740832 CACTGCTCGTTACATCAAACTCA 59.259 43.478 0.00 0.00 0.00 3.41
722 1608 3.780925 GCTTGTGAGCCATCAACAC 57.219 52.632 0.00 0.00 43.29 3.32
749 1635 3.371097 TAGCCGAAAGCCTGAGCCG 62.371 63.158 0.00 0.00 45.47 5.52
771 1657 1.006102 CCACGACTTTCTCACCGCT 60.006 57.895 0.00 0.00 0.00 5.52
782 1668 1.134521 TCTCACCGCTCTCTCTCTCTC 60.135 57.143 0.00 0.00 0.00 3.20
821 1709 2.203126 CTCCGGAGCAGCCAATCC 60.203 66.667 20.67 0.00 35.94 3.01
832 1720 0.682209 AGCCAATCCACCATGTGAGC 60.682 55.000 0.00 0.00 35.23 4.26
963 1856 1.285023 GCTGCTTGCCACTGAACTG 59.715 57.895 0.00 0.00 35.15 3.16
981 1874 2.520536 GGGCTGGACTGGTGACACT 61.521 63.158 5.39 0.00 35.60 3.55
983 1876 1.963338 GCTGGACTGGTGACACTGC 60.963 63.158 5.39 0.00 35.60 4.40
992 1885 2.968697 TGACACTGCTGCACGCTG 60.969 61.111 0.00 11.50 42.62 5.18
1198 2091 3.415983 AGCACCACCACCACCACA 61.416 61.111 0.00 0.00 0.00 4.17
1293 2186 0.748367 TCGACGAGATCCAGGAGGTG 60.748 60.000 0.00 0.00 35.89 4.00
1441 2334 5.240891 TCTCCAGTTCTGTTGTGAATCATC 58.759 41.667 0.00 0.00 0.00 2.92
1460 2353 2.206750 TCGCTGATTATTTGCCGTACC 58.793 47.619 0.00 0.00 0.00 3.34
1466 2362 3.127895 TGATTATTTGCCGTACCACTTGC 59.872 43.478 0.00 0.00 0.00 4.01
1504 2404 3.632333 TCCACTCGTCTTGATACCTCAT 58.368 45.455 0.00 0.00 0.00 2.90
1574 2474 7.242079 GTGCAATCATCAGTAATCATATCAGC 58.758 38.462 0.00 0.00 0.00 4.26
1584 2484 3.577649 ATCATATCAGCGTTAGACCCG 57.422 47.619 0.00 0.00 0.00 5.28
1590 2490 1.753463 AGCGTTAGACCCGGAGAGG 60.753 63.158 0.73 0.00 40.63 3.69
1591 2491 1.751927 GCGTTAGACCCGGAGAGGA 60.752 63.158 0.73 0.00 45.00 3.71
1607 2507 7.441458 CCCGGAGAGGAGTACTTAATTTTATTG 59.559 40.741 0.73 0.00 45.00 1.90
1610 2510 8.272889 GGAGAGGAGTACTTAATTTTATTGGGT 58.727 37.037 0.00 0.00 0.00 4.51
1641 2541 6.677781 TTTGGATATCTGAACTTTAAGCCG 57.322 37.500 2.05 0.00 0.00 5.52
1714 2614 8.254178 TGTGTGGAAATGATTGATTAATTTGC 57.746 30.769 0.00 0.00 33.67 3.68
1739 2639 5.180492 TGGACACGTATTCCAAAACAGATTC 59.820 40.000 14.28 0.00 40.35 2.52
1741 2641 5.997385 ACACGTATTCCAAAACAGATTCAC 58.003 37.500 0.00 0.00 0.00 3.18
1769 2678 5.651530 TGTGTATACACTGCTTCTTCTAGC 58.348 41.667 30.69 5.64 46.55 3.42
1794 2703 0.610174 TCCAGAGTTGCATCTTCGCT 59.390 50.000 0.00 0.00 0.00 4.93
1814 2723 4.031652 CGCTTCTTTTGGTTCAAAGTGTTG 59.968 41.667 0.00 0.00 34.72 3.33
1870 2779 7.224949 AGCGATTAAGCTCTGTCCTTAATTAAC 59.775 37.037 12.77 0.00 45.67 2.01
1973 2882 1.457346 CCAAGATGGAAGGTGAGCAC 58.543 55.000 0.00 0.00 40.96 4.40
1984 2909 2.963498 GGTGAGCACCGTAAACTTTC 57.037 50.000 3.57 0.00 42.29 2.62
2014 2939 7.611467 TCAGGTTCAGTAAAATTGCAGATACAT 59.389 33.333 0.00 0.00 0.00 2.29
2206 3132 3.905678 CCTAGCCTGCCGACGAGG 61.906 72.222 0.00 0.00 44.97 4.63
2215 3141 4.367023 CCGACGAGGCCGACCAAA 62.367 66.667 0.00 0.00 39.06 3.28
2216 3142 3.110178 CGACGAGGCCGACCAAAC 61.110 66.667 0.00 0.00 39.06 2.93
2247 3176 1.559065 GGATTCCAACGGGTCCTGGA 61.559 60.000 1.89 0.00 40.03 3.86
2262 3191 2.522705 TCCTGGATCATGGTAGGTAGGT 59.477 50.000 0.00 0.00 0.00 3.08
2300 3229 2.724708 GAACGTGAGCAGCTCAGCG 61.725 63.158 29.84 29.84 41.46 5.18
2359 3288 4.790962 CAGGCAGCCGCTGACCAT 62.791 66.667 23.11 1.81 41.11 3.55
2471 3416 4.264638 GCGGCGCTTGGTTGTGTT 62.265 61.111 26.86 0.00 0.00 3.32
2472 3417 2.411290 CGGCGCTTGGTTGTGTTT 59.589 55.556 7.64 0.00 0.00 2.83
2537 3499 2.051345 GGCGCGTGGTGTTTCTTG 60.051 61.111 8.43 0.00 0.00 3.02
2574 3540 4.170723 GCGTGTGGCTCTGTACTC 57.829 61.111 0.00 0.00 39.11 2.59
2575 3541 1.587054 GCGTGTGGCTCTGTACTCT 59.413 57.895 0.00 0.00 39.11 3.24
2591 3557 9.493206 CTCTGTACTCTTCGTTTATCTTCTTAC 57.507 37.037 0.00 0.00 0.00 2.34
2593 3559 9.279904 CTGTACTCTTCGTTTATCTTCTTACTG 57.720 37.037 0.00 0.00 0.00 2.74
2639 3605 1.290203 ATCGATTACCTGCACTTGCG 58.710 50.000 0.00 0.00 45.83 4.85
2640 3606 0.037697 TCGATTACCTGCACTTGCGT 60.038 50.000 0.00 0.00 45.83 5.24
2641 3607 0.796312 CGATTACCTGCACTTGCGTT 59.204 50.000 0.00 0.00 45.83 4.84
2649 3615 0.027455 TGCACTTGCGTTTTCTCGTG 59.973 50.000 0.00 0.00 45.83 4.35
2656 3622 1.131504 TGCGTTTTCTCGTGCTTTTGT 59.868 42.857 0.00 0.00 0.00 2.83
2657 3623 2.352034 TGCGTTTTCTCGTGCTTTTGTA 59.648 40.909 0.00 0.00 0.00 2.41
2675 3641 0.459899 TAGAAGTGATGCGGCGATGT 59.540 50.000 12.98 0.00 0.00 3.06
2676 3642 0.391661 AGAAGTGATGCGGCGATGTT 60.392 50.000 12.98 0.00 0.00 2.71
2677 3643 0.447801 GAAGTGATGCGGCGATGTTT 59.552 50.000 12.98 0.00 0.00 2.83
2678 3644 0.168788 AAGTGATGCGGCGATGTTTG 59.831 50.000 12.98 0.00 0.00 2.93
2680 3646 0.521242 GTGATGCGGCGATGTTTGAC 60.521 55.000 12.98 0.00 0.00 3.18
2682 3648 1.643868 GATGCGGCGATGTTTGACCA 61.644 55.000 12.98 0.00 0.00 4.02
2683 3649 1.240641 ATGCGGCGATGTTTGACCAA 61.241 50.000 12.98 0.00 0.00 3.67
2684 3650 1.442017 GCGGCGATGTTTGACCAAC 60.442 57.895 12.98 0.00 35.71 3.77
2685 3651 1.154488 CGGCGATGTTTGACCAACG 60.154 57.895 0.00 0.00 38.36 4.10
2686 3652 4.130857 GCGATGTTTGACCAACGC 57.869 55.556 0.00 0.00 46.59 4.84
2688 3654 3.835686 CGATGTTTGACCAACGCAA 57.164 47.368 0.00 0.00 38.36 4.85
2689 3655 2.112475 CGATGTTTGACCAACGCAAA 57.888 45.000 0.00 0.00 38.36 3.68
2701 3764 2.539476 CAACGCAAACCTTGAAGCTTT 58.461 42.857 0.00 0.00 0.00 3.51
2740 3803 2.260434 GGCGACTCACCTTGCGTA 59.740 61.111 0.00 0.00 0.00 4.42
2751 3814 2.942376 CACCTTGCGTATGCCTGAAATA 59.058 45.455 4.05 0.00 41.78 1.40
2766 3829 4.250464 CTGAAATAACACCGGAGCTACAA 58.750 43.478 9.46 0.00 0.00 2.41
2772 3835 1.270678 ACACCGGAGCTACAAACCTTC 60.271 52.381 9.46 0.00 0.00 3.46
2780 3843 1.608283 GCTACAAACCTTCGACTGGCT 60.608 52.381 3.75 0.00 0.00 4.75
2792 3855 7.403671 ACCTTCGACTGGCTTATATCTATCTA 58.596 38.462 3.75 0.00 0.00 1.98
2804 3867 9.815306 GCTTATATCTATCTATCCCCTATGTGA 57.185 37.037 0.00 0.00 0.00 3.58
2824 3887 3.006430 TGATGTGGAGTAGCTTCGAAACA 59.994 43.478 0.00 0.00 0.00 2.83
2826 3889 2.626266 TGTGGAGTAGCTTCGAAACAGA 59.374 45.455 0.00 0.00 0.00 3.41
2829 3892 3.258372 TGGAGTAGCTTCGAAACAGACAT 59.742 43.478 0.00 0.00 0.00 3.06
2845 3908 0.744414 ACATGGGCCGACTCAAATCG 60.744 55.000 0.00 0.00 41.89 3.34
2846 3909 0.461870 CATGGGCCGACTCAAATCGA 60.462 55.000 0.00 0.00 45.13 3.59
2851 3914 2.163613 GGGCCGACTCAAATCGAAAAAT 59.836 45.455 0.00 0.00 45.13 1.82
2882 3945 2.287915 CGGCATAATGTTCTTCTTCCCG 59.712 50.000 0.00 0.00 0.00 5.14
2889 3952 7.656137 GCATAATGTTCTTCTTCCCGTATTAGA 59.344 37.037 0.00 0.00 0.00 2.10
2890 3953 9.197694 CATAATGTTCTTCTTCCCGTATTAGAG 57.802 37.037 0.00 0.00 0.00 2.43
2891 3954 5.007385 TGTTCTTCTTCCCGTATTAGAGC 57.993 43.478 0.00 0.00 0.00 4.09
2892 3955 4.464951 TGTTCTTCTTCCCGTATTAGAGCA 59.535 41.667 0.00 0.00 0.00 4.26
2894 3957 5.871396 TCTTCTTCCCGTATTAGAGCAAT 57.129 39.130 0.00 0.00 0.00 3.56
2895 3958 6.235231 TCTTCTTCCCGTATTAGAGCAATT 57.765 37.500 0.00 0.00 0.00 2.32
2896 3959 6.281405 TCTTCTTCCCGTATTAGAGCAATTC 58.719 40.000 0.00 0.00 0.00 2.17
2897 3960 5.871396 TCTTCCCGTATTAGAGCAATTCT 57.129 39.130 0.00 0.00 40.06 2.40
2898 3961 6.971726 TCTTCCCGTATTAGAGCAATTCTA 57.028 37.500 0.00 0.00 37.36 2.10
2899 3962 6.982852 TCTTCCCGTATTAGAGCAATTCTAG 58.017 40.000 0.00 0.00 39.50 2.43
2900 3963 5.135508 TCCCGTATTAGAGCAATTCTAGC 57.864 43.478 0.00 0.00 39.50 3.42
2901 3964 4.587262 TCCCGTATTAGAGCAATTCTAGCA 59.413 41.667 0.00 0.00 39.50 3.49
2902 3965 4.926238 CCCGTATTAGAGCAATTCTAGCAG 59.074 45.833 0.00 0.00 39.50 4.24
2903 3966 5.279006 CCCGTATTAGAGCAATTCTAGCAGA 60.279 44.000 0.00 0.00 39.50 4.26
2904 3967 5.631512 CCGTATTAGAGCAATTCTAGCAGAC 59.368 44.000 0.00 0.00 39.50 3.51
2905 3968 5.631512 CGTATTAGAGCAATTCTAGCAGACC 59.368 44.000 0.00 0.00 39.50 3.85
2906 3969 2.998316 AGAGCAATTCTAGCAGACCC 57.002 50.000 0.00 0.00 33.23 4.46
2907 3970 1.488393 AGAGCAATTCTAGCAGACCCC 59.512 52.381 0.00 0.00 33.23 4.95
2908 3971 0.179000 AGCAATTCTAGCAGACCCCG 59.821 55.000 0.00 0.00 0.00 5.73
2909 3972 1.440145 GCAATTCTAGCAGACCCCGC 61.440 60.000 0.00 0.00 0.00 6.13
2910 3973 0.107703 CAATTCTAGCAGACCCCGCA 60.108 55.000 0.00 0.00 0.00 5.69
2911 3974 0.618458 AATTCTAGCAGACCCCGCAA 59.382 50.000 0.00 0.00 0.00 4.85
2912 3975 0.618458 ATTCTAGCAGACCCCGCAAA 59.382 50.000 0.00 0.00 0.00 3.68
2913 3976 0.398696 TTCTAGCAGACCCCGCAAAA 59.601 50.000 0.00 0.00 0.00 2.44
2914 3977 0.398696 TCTAGCAGACCCCGCAAAAA 59.601 50.000 0.00 0.00 0.00 1.94
2915 3978 1.004277 TCTAGCAGACCCCGCAAAAAT 59.996 47.619 0.00 0.00 0.00 1.82
2916 3979 1.818674 CTAGCAGACCCCGCAAAAATT 59.181 47.619 0.00 0.00 0.00 1.82
2917 3980 0.603065 AGCAGACCCCGCAAAAATTC 59.397 50.000 0.00 0.00 0.00 2.17
2918 3981 0.732538 GCAGACCCCGCAAAAATTCG 60.733 55.000 0.00 0.00 0.00 3.34
2919 3982 0.878416 CAGACCCCGCAAAAATTCGA 59.122 50.000 0.00 0.00 0.00 3.71
2920 3983 0.879090 AGACCCCGCAAAAATTCGAC 59.121 50.000 0.00 0.00 0.00 4.20
2921 3984 0.109458 GACCCCGCAAAAATTCGACC 60.109 55.000 0.00 0.00 0.00 4.79
2922 3985 1.214325 CCCCGCAAAAATTCGACCC 59.786 57.895 0.00 0.00 0.00 4.46
2923 3986 1.154112 CCCGCAAAAATTCGACCCG 60.154 57.895 0.00 0.00 0.00 5.28
2924 3987 1.799916 CCGCAAAAATTCGACCCGC 60.800 57.895 0.00 0.00 0.00 6.13
2925 3988 1.081774 CGCAAAAATTCGACCCGCA 60.082 52.632 0.00 0.00 0.00 5.69
2926 3989 0.661780 CGCAAAAATTCGACCCGCAA 60.662 50.000 0.00 0.00 0.00 4.85
2927 3990 1.492720 GCAAAAATTCGACCCGCAAA 58.507 45.000 0.00 0.00 0.00 3.68
2928 3991 1.861575 GCAAAAATTCGACCCGCAAAA 59.138 42.857 0.00 0.00 0.00 2.44
2929 3992 2.348125 GCAAAAATTCGACCCGCAAAAC 60.348 45.455 0.00 0.00 0.00 2.43
2930 3993 2.860735 CAAAAATTCGACCCGCAAAACA 59.139 40.909 0.00 0.00 0.00 2.83
2931 3994 2.128367 AAATTCGACCCGCAAAACAC 57.872 45.000 0.00 0.00 0.00 3.32
2932 3995 0.040781 AATTCGACCCGCAAAACACG 60.041 50.000 0.00 0.00 0.00 4.49
2933 3996 1.161563 ATTCGACCCGCAAAACACGT 61.162 50.000 0.00 0.00 0.00 4.49
2934 3997 1.367599 TTCGACCCGCAAAACACGTT 61.368 50.000 0.00 0.00 0.00 3.99
2935 3998 1.062845 CGACCCGCAAAACACGTTT 59.937 52.632 0.00 0.00 0.00 3.60
2943 4006 2.687233 CAAAACACGTTTGCGGTTTC 57.313 45.000 1.93 0.00 40.25 2.78
2944 4007 1.986378 CAAAACACGTTTGCGGTTTCA 59.014 42.857 1.93 0.00 40.25 2.69
2945 4008 2.349297 AAACACGTTTGCGGTTTCAA 57.651 40.000 0.00 0.00 43.45 2.69
2946 4009 2.349297 AACACGTTTGCGGTTTCAAA 57.651 40.000 0.00 0.00 43.45 2.69
2947 4010 2.349297 ACACGTTTGCGGTTTCAAAA 57.651 40.000 0.00 0.00 43.45 2.44
2948 4011 2.673833 ACACGTTTGCGGTTTCAAAAA 58.326 38.095 0.00 0.00 43.45 1.94
2949 4012 2.664085 ACACGTTTGCGGTTTCAAAAAG 59.336 40.909 0.00 0.00 43.45 2.27
2950 4013 2.917971 CACGTTTGCGGTTTCAAAAAGA 59.082 40.909 0.00 0.00 43.45 2.52
2951 4014 3.549873 CACGTTTGCGGTTTCAAAAAGAT 59.450 39.130 0.00 0.00 43.45 2.40
2952 4015 3.794564 ACGTTTGCGGTTTCAAAAAGATC 59.205 39.130 0.00 0.00 43.45 2.75
2953 4016 3.794028 CGTTTGCGGTTTCAAAAAGATCA 59.206 39.130 0.00 0.00 37.65 2.92
2954 4017 4.444056 CGTTTGCGGTTTCAAAAAGATCAT 59.556 37.500 0.00 0.00 37.65 2.45
2955 4018 5.610124 CGTTTGCGGTTTCAAAAAGATCATG 60.610 40.000 0.00 0.00 37.65 3.07
2956 4019 4.582701 TGCGGTTTCAAAAAGATCATGT 57.417 36.364 0.00 0.00 0.00 3.21
2957 4020 4.942852 TGCGGTTTCAAAAAGATCATGTT 58.057 34.783 0.00 0.00 0.00 2.71
2958 4021 5.355596 TGCGGTTTCAAAAAGATCATGTTT 58.644 33.333 0.00 0.00 0.00 2.83
2959 4022 5.233902 TGCGGTTTCAAAAAGATCATGTTTG 59.766 36.000 0.00 2.61 34.29 2.93
2960 4023 5.669122 CGGTTTCAAAAAGATCATGTTTGC 58.331 37.500 9.65 0.00 33.26 3.68
2961 4024 5.610124 CGGTTTCAAAAAGATCATGTTTGCG 60.610 40.000 9.65 5.56 33.26 4.85
2962 4025 5.333263 GGTTTCAAAAAGATCATGTTTGCGG 60.333 40.000 9.65 0.00 33.26 5.69
2963 4026 3.911868 TCAAAAAGATCATGTTTGCGGG 58.088 40.909 9.65 0.00 33.26 6.13
2964 4027 3.320541 TCAAAAAGATCATGTTTGCGGGT 59.679 39.130 9.65 0.00 33.26 5.28
2965 4028 3.575965 AAAAGATCATGTTTGCGGGTC 57.424 42.857 0.00 0.00 0.00 4.46
2966 4029 1.086696 AAGATCATGTTTGCGGGTCG 58.913 50.000 0.00 0.00 0.00 4.79
2967 4030 0.249120 AGATCATGTTTGCGGGTCGA 59.751 50.000 0.00 0.00 0.00 4.20
2968 4031 1.083489 GATCATGTTTGCGGGTCGAA 58.917 50.000 0.00 0.00 0.00 3.71
2969 4032 1.466950 GATCATGTTTGCGGGTCGAAA 59.533 47.619 0.00 0.00 0.00 3.46
2970 4033 1.309950 TCATGTTTGCGGGTCGAAAA 58.690 45.000 0.00 0.00 31.42 2.29
2974 4037 3.855630 TTTGCGGGTCGAAAACATG 57.144 47.368 0.00 0.00 28.61 3.21
2975 4038 0.318275 TTTGCGGGTCGAAAACATGC 60.318 50.000 0.00 0.00 28.61 4.06
2976 4039 2.202298 GCGGGTCGAAAACATGCG 60.202 61.111 0.00 0.00 0.00 4.73
2977 4040 2.202298 CGGGTCGAAAACATGCGC 60.202 61.111 0.00 0.00 0.00 6.09
2978 4041 2.202298 GGGTCGAAAACATGCGCG 60.202 61.111 0.00 0.00 0.00 6.86
2979 4042 2.202298 GGTCGAAAACATGCGCGG 60.202 61.111 8.83 0.00 0.00 6.46
2980 4043 2.554272 GTCGAAAACATGCGCGGT 59.446 55.556 8.83 0.00 0.00 5.68
2981 4044 1.509162 GTCGAAAACATGCGCGGTC 60.509 57.895 8.83 0.00 0.00 4.79
2982 4045 2.570581 CGAAAACATGCGCGGTCG 60.571 61.111 8.83 1.18 39.07 4.79
2983 4046 2.857448 GAAAACATGCGCGGTCGA 59.143 55.556 8.83 0.00 38.10 4.20
2984 4047 1.205568 GAAAACATGCGCGGTCGAA 59.794 52.632 8.83 0.00 38.10 3.71
2985 4048 0.384974 GAAAACATGCGCGGTCGAAA 60.385 50.000 8.83 0.00 38.10 3.46
2986 4049 0.029567 AAAACATGCGCGGTCGAAAA 59.970 45.000 8.83 0.00 38.10 2.29
2987 4050 0.385473 AAACATGCGCGGTCGAAAAG 60.385 50.000 8.83 0.00 38.10 2.27
2988 4051 1.225376 AACATGCGCGGTCGAAAAGA 61.225 50.000 8.83 0.00 38.10 2.52
2989 4052 1.225376 ACATGCGCGGTCGAAAAGAA 61.225 50.000 8.83 0.00 38.10 2.52
2990 4053 0.789383 CATGCGCGGTCGAAAAGAAC 60.789 55.000 8.83 0.00 38.10 3.01
2991 4054 1.908066 ATGCGCGGTCGAAAAGAACC 61.908 55.000 8.83 0.00 38.10 3.62
2992 4055 2.858158 CGCGGTCGAAAAGAACCC 59.142 61.111 0.00 0.00 38.10 4.11
2993 4056 2.858158 GCGGTCGAAAAGAACCCG 59.142 61.111 4.17 4.17 40.32 5.28
2994 4057 1.957695 GCGGTCGAAAAGAACCCGT 60.958 57.895 9.69 0.00 39.74 5.28
2995 4058 0.667184 GCGGTCGAAAAGAACCCGTA 60.667 55.000 9.69 0.00 39.74 4.02
2996 4059 2.000429 CGGTCGAAAAGAACCCGTAT 58.000 50.000 0.57 0.00 34.81 3.06
2997 4060 1.922545 CGGTCGAAAAGAACCCGTATC 59.077 52.381 0.57 0.00 34.81 2.24
2998 4061 2.671914 CGGTCGAAAAGAACCCGTATCA 60.672 50.000 0.57 0.00 34.81 2.15
2999 4062 3.328505 GGTCGAAAAGAACCCGTATCAA 58.671 45.455 0.00 0.00 0.00 2.57
3000 4063 3.747529 GGTCGAAAAGAACCCGTATCAAA 59.252 43.478 0.00 0.00 0.00 2.69
3001 4064 4.213906 GGTCGAAAAGAACCCGTATCAAAA 59.786 41.667 0.00 0.00 0.00 2.44
3002 4065 5.142265 GTCGAAAAGAACCCGTATCAAAAC 58.858 41.667 0.00 0.00 0.00 2.43
3003 4066 4.213906 TCGAAAAGAACCCGTATCAAAACC 59.786 41.667 0.00 0.00 0.00 3.27
3004 4067 4.214758 CGAAAAGAACCCGTATCAAAACCT 59.785 41.667 0.00 0.00 0.00 3.50
3005 4068 5.447624 AAAAGAACCCGTATCAAAACCTG 57.552 39.130 0.00 0.00 0.00 4.00
3006 4069 2.433436 AGAACCCGTATCAAAACCTGC 58.567 47.619 0.00 0.00 0.00 4.85
3007 4070 2.156098 GAACCCGTATCAAAACCTGCA 58.844 47.619 0.00 0.00 0.00 4.41
3008 4071 2.507407 ACCCGTATCAAAACCTGCAT 57.493 45.000 0.00 0.00 0.00 3.96
3009 4072 3.637911 ACCCGTATCAAAACCTGCATA 57.362 42.857 0.00 0.00 0.00 3.14
3010 4073 3.958018 ACCCGTATCAAAACCTGCATAA 58.042 40.909 0.00 0.00 0.00 1.90
3011 4074 4.532834 ACCCGTATCAAAACCTGCATAAT 58.467 39.130 0.00 0.00 0.00 1.28
3012 4075 4.953579 ACCCGTATCAAAACCTGCATAATT 59.046 37.500 0.00 0.00 0.00 1.40
3013 4076 5.420739 ACCCGTATCAAAACCTGCATAATTT 59.579 36.000 0.00 0.00 0.00 1.82
3014 4077 5.748152 CCCGTATCAAAACCTGCATAATTTG 59.252 40.000 10.37 10.37 34.81 2.32
3015 4078 6.405286 CCCGTATCAAAACCTGCATAATTTGA 60.405 38.462 17.71 17.71 43.53 2.69
3016 4079 7.032580 CCGTATCAAAACCTGCATAATTTGAA 58.967 34.615 18.71 9.91 42.89 2.69
3017 4080 7.543868 CCGTATCAAAACCTGCATAATTTGAAA 59.456 33.333 18.71 4.48 42.89 2.69
3018 4081 8.920665 CGTATCAAAACCTGCATAATTTGAAAA 58.079 29.630 18.71 11.11 42.89 2.29
3060 4123 9.539825 AAAATTGCACAAACATAGTTTATCACA 57.460 25.926 0.00 0.00 0.00 3.58
3061 4124 9.709495 AAATTGCACAAACATAGTTTATCACAT 57.291 25.926 0.00 0.00 0.00 3.21
3063 4126 9.787532 ATTGCACAAACATAGTTTATCACATAC 57.212 29.630 0.00 0.00 0.00 2.39
3064 4127 8.560355 TGCACAAACATAGTTTATCACATACT 57.440 30.769 0.00 0.00 0.00 2.12
3065 4128 9.660180 TGCACAAACATAGTTTATCACATACTA 57.340 29.630 0.00 0.00 0.00 1.82
3066 4129 9.916397 GCACAAACATAGTTTATCACATACTAC 57.084 33.333 0.00 0.00 0.00 2.73
3099 4162 9.838975 CATTACATGATAAACAAACTACAAGCA 57.161 29.630 0.00 0.00 0.00 3.91
3103 4166 9.231297 ACATGATAAACAAACTACAAGCATAGT 57.769 29.630 0.00 0.00 36.96 2.12
3140 4203 9.909365 ACCATATTAAACTAGTAATAGAGGGGT 57.091 33.333 3.83 12.02 33.50 4.95
3143 4206 6.966534 TTAAACTAGTAATAGAGGGGTCGG 57.033 41.667 3.83 0.00 0.00 4.79
3144 4207 4.803329 AACTAGTAATAGAGGGGTCGGA 57.197 45.455 3.83 0.00 0.00 4.55
3145 4208 5.336491 AACTAGTAATAGAGGGGTCGGAT 57.664 43.478 3.83 0.00 0.00 4.18
3146 4209 4.920999 ACTAGTAATAGAGGGGTCGGATC 58.079 47.826 3.83 0.00 0.00 3.36
3147 4210 4.602732 ACTAGTAATAGAGGGGTCGGATCT 59.397 45.833 3.83 0.00 0.00 2.75
3148 4211 3.768878 AGTAATAGAGGGGTCGGATCTG 58.231 50.000 0.00 0.00 0.00 2.90
3149 4212 3.398292 AGTAATAGAGGGGTCGGATCTGA 59.602 47.826 0.00 0.00 0.00 3.27
3150 4213 2.296073 ATAGAGGGGTCGGATCTGAC 57.704 55.000 24.13 24.13 38.17 3.51
3151 4214 0.179026 TAGAGGGGTCGGATCTGACG 60.179 60.000 24.89 6.08 39.83 4.35
3152 4215 2.442272 AGGGGTCGGATCTGACGG 60.442 66.667 24.89 0.00 39.83 4.79
3153 4216 4.222847 GGGGTCGGATCTGACGGC 62.223 72.222 24.89 14.01 39.83 5.68
3154 4217 4.570663 GGGTCGGATCTGACGGCG 62.571 72.222 24.89 4.80 39.83 6.46
3155 4218 4.570663 GGTCGGATCTGACGGCGG 62.571 72.222 24.89 0.00 39.83 6.13
3159 4222 4.933064 GGATCTGACGGCGGCGAG 62.933 72.222 38.93 25.22 0.00 5.03
3160 4223 4.933064 GATCTGACGGCGGCGAGG 62.933 72.222 38.93 24.39 0.00 4.63
3173 4236 3.864686 CGAGGTCGCGGCAAATGG 61.865 66.667 14.93 0.00 0.00 3.16
3174 4237 2.435938 GAGGTCGCGGCAAATGGA 60.436 61.111 14.93 0.00 0.00 3.41
3175 4238 2.746277 AGGTCGCGGCAAATGGAC 60.746 61.111 14.93 0.00 0.00 4.02
3182 4245 4.160635 GGCAAATGGACGACGCCG 62.161 66.667 0.00 0.00 42.50 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.724623 GCGTTGACTATCAAAGACGCA 59.275 47.619 17.18 0.00 46.93 5.24
81 82 0.175760 TGCTACTCGCCATTGGAGTC 59.824 55.000 6.95 0.00 43.39 3.36
82 83 0.176680 CTGCTACTCGCCATTGGAGT 59.823 55.000 6.95 4.53 46.05 3.85
112 113 4.999212 CAATGTTGCCATGCTGCA 57.001 50.000 4.13 4.13 40.07 4.41
124 149 3.058160 GGTGCCTGCTCGCAATGT 61.058 61.111 0.00 0.00 41.30 2.71
127 152 3.057548 CATGGTGCCTGCTCGCAA 61.058 61.111 0.00 0.00 41.30 4.85
131 156 3.446570 GTGCCATGGTGCCTGCTC 61.447 66.667 14.67 0.00 0.00 4.26
133 158 2.103339 AAAAGTGCCATGGTGCCTGC 62.103 55.000 14.67 0.00 0.00 4.85
134 159 0.037975 GAAAAGTGCCATGGTGCCTG 60.038 55.000 14.67 0.00 0.00 4.85
135 160 0.178953 AGAAAAGTGCCATGGTGCCT 60.179 50.000 14.67 3.81 0.00 4.75
136 161 1.544724 TAGAAAAGTGCCATGGTGCC 58.455 50.000 14.67 1.25 0.00 5.01
137 162 3.874392 AATAGAAAAGTGCCATGGTGC 57.126 42.857 14.67 6.59 0.00 5.01
138 163 5.406175 CACAAAATAGAAAAGTGCCATGGTG 59.594 40.000 14.67 0.40 0.00 4.17
139 164 5.070313 ACACAAAATAGAAAAGTGCCATGGT 59.930 36.000 14.67 0.00 33.69 3.55
142 167 6.479660 CACAACACAAAATAGAAAAGTGCCAT 59.520 34.615 0.00 0.00 33.69 4.40
277 1141 1.443407 CTGCTCAGTATGGGGGACG 59.557 63.158 0.00 0.00 36.76 4.79
310 1174 1.248785 ACATGCTTGCAGCCTCCTTG 61.249 55.000 0.87 0.00 41.51 3.61
311 1175 1.076192 ACATGCTTGCAGCCTCCTT 59.924 52.632 0.87 0.00 41.51 3.36
319 1183 4.083324 GCTACTAAAACTCACATGCTTGCA 60.083 41.667 0.00 0.00 0.00 4.08
381 1245 2.301870 TGACTTGGTCCACCTGTCATAC 59.698 50.000 16.08 0.00 41.42 2.39
394 1258 2.363680 CACTCTCACTGACTGACTTGGT 59.636 50.000 0.00 0.00 0.00 3.67
448 1312 1.459592 CCTGGAGCTGTTTTTACGTCG 59.540 52.381 0.00 0.00 0.00 5.12
497 1362 1.228003 CCCGGTTGTTGGCACACTA 60.228 57.895 0.00 0.00 39.29 2.74
519 1384 5.552178 AGCTAAATCGAACCTTGAACTCTT 58.448 37.500 0.00 0.00 0.00 2.85
573 1438 5.342806 TGATGTAACGAGCAGTGAAAAAG 57.657 39.130 0.00 0.00 0.00 2.27
580 1445 3.990092 TGAGTTTGATGTAACGAGCAGT 58.010 40.909 0.00 0.00 33.26 4.40
596 1461 1.871080 CGGTTGAGAGTGCTTGAGTT 58.129 50.000 0.00 0.00 0.00 3.01
597 1462 0.601311 GCGGTTGAGAGTGCTTGAGT 60.601 55.000 0.00 0.00 0.00 3.41
601 1466 0.613260 TATGGCGGTTGAGAGTGCTT 59.387 50.000 0.00 0.00 0.00 3.91
749 1635 2.357034 TGAGAAAGTCGTGGGCGC 60.357 61.111 0.00 0.00 38.14 6.53
771 1657 3.620488 GGCAGAAAGAGAGAGAGAGAGA 58.380 50.000 0.00 0.00 0.00 3.10
782 1668 0.726827 TTATTGCGCGGCAGAAAGAG 59.273 50.000 8.83 0.00 40.61 2.85
821 1709 1.025113 CCTGAGCTGCTCACATGGTG 61.025 60.000 27.35 16.36 35.39 4.17
921 1809 5.002516 GCTGAGCTGAGCTATTTTGGATAT 58.997 41.667 18.71 0.00 39.88 1.63
963 1856 2.032681 GTGTCACCAGTCCAGCCC 59.967 66.667 0.00 0.00 0.00 5.19
1242 2135 0.886490 CGCTGAGCAGGAACCTTGTT 60.886 55.000 4.88 0.00 0.00 2.83
1330 2223 1.611673 CCTTCTGACATCACCACCACC 60.612 57.143 0.00 0.00 0.00 4.61
1331 2224 1.611673 CCCTTCTGACATCACCACCAC 60.612 57.143 0.00 0.00 0.00 4.16
1332 2225 0.692476 CCCTTCTGACATCACCACCA 59.308 55.000 0.00 0.00 0.00 4.17
1368 2261 2.407090 CTCGTGTTCTTCACATCAGCA 58.593 47.619 0.00 0.00 46.44 4.41
1369 2262 1.127582 GCTCGTGTTCTTCACATCAGC 59.872 52.381 0.00 0.00 46.44 4.26
1370 2263 2.156504 GTGCTCGTGTTCTTCACATCAG 59.843 50.000 0.00 0.00 46.44 2.90
1388 2281 4.030452 GCTCCTGCGTGTTGGTGC 62.030 66.667 0.00 0.00 36.02 5.01
1421 2314 3.425359 GCGATGATTCACAACAGAACTGG 60.425 47.826 6.76 0.00 34.19 4.00
1441 2334 1.937223 TGGTACGGCAAATAATCAGCG 59.063 47.619 0.00 0.00 0.00 5.18
1466 2362 5.445142 CGAGTGGAATCAAATCTTCAGAACG 60.445 44.000 0.00 0.00 0.00 3.95
1574 2474 0.394080 ACTCCTCTCCGGGTCTAACG 60.394 60.000 0.00 0.00 0.00 3.18
1584 2484 8.272889 ACCCAATAAAATTAAGTACTCCTCTCC 58.727 37.037 0.00 0.00 0.00 3.71
1607 2507 7.286316 AGTTCAGATATCCAAATGAAATCACCC 59.714 37.037 6.68 0.00 33.74 4.61
1641 2541 6.138761 GTCATCATTGTATTTCCGCATCTTC 58.861 40.000 0.00 0.00 0.00 2.87
1683 2583 7.951530 AATCAATCATTTCCACACAAAAGAC 57.048 32.000 0.00 0.00 0.00 3.01
1714 2614 4.062293 TCTGTTTTGGAATACGTGTCCAG 58.938 43.478 18.76 10.11 45.79 3.86
1769 2678 2.434428 AGATGCAACTCTGGAAGCAAG 58.566 47.619 0.00 0.00 40.76 4.01
1814 2723 0.179156 CACATGATGTGCCGGCTTTC 60.179 55.000 29.70 20.75 41.89 2.62
1858 2767 6.456988 CGATGACCAGCAAGTTAATTAAGGAC 60.457 42.308 0.00 0.00 0.00 3.85
1870 2779 0.167470 CTGCAACGATGACCAGCAAG 59.833 55.000 0.00 0.00 34.45 4.01
1930 2839 0.884704 GTGCTTCTTCACCTTGCCGA 60.885 55.000 0.00 0.00 0.00 5.54
1952 2861 0.322816 GCTCACCTTCCATCTTGGCA 60.323 55.000 0.00 0.00 37.47 4.92
1973 2882 5.054477 TGAACCTGAAGAGAAAGTTTACGG 58.946 41.667 0.00 0.00 0.00 4.02
1984 2909 6.205464 TCTGCAATTTTACTGAACCTGAAGAG 59.795 38.462 0.00 0.00 0.00 2.85
2014 2939 3.328382 AACAGACGCAGCTTGGTTATA 57.672 42.857 0.00 0.00 0.00 0.98
2206 3132 1.206831 GCTTCTTCGTTTGGTCGGC 59.793 57.895 0.00 0.00 0.00 5.54
2209 3135 2.028385 TCCTAGGCTTCTTCGTTTGGTC 60.028 50.000 2.96 0.00 0.00 4.02
2211 3137 2.762535 TCCTAGGCTTCTTCGTTTGG 57.237 50.000 2.96 0.00 0.00 3.28
2212 3138 3.623510 GGAATCCTAGGCTTCTTCGTTTG 59.376 47.826 21.60 0.00 0.00 2.93
2213 3139 3.263425 TGGAATCCTAGGCTTCTTCGTTT 59.737 43.478 21.60 0.00 0.00 3.60
2214 3140 2.838202 TGGAATCCTAGGCTTCTTCGTT 59.162 45.455 21.60 0.11 0.00 3.85
2215 3141 2.467880 TGGAATCCTAGGCTTCTTCGT 58.532 47.619 21.60 0.00 0.00 3.85
2216 3142 3.198872 GTTGGAATCCTAGGCTTCTTCG 58.801 50.000 21.60 0.00 0.00 3.79
2247 3176 3.898123 CACAGCTACCTACCTACCATGAT 59.102 47.826 0.00 0.00 0.00 2.45
2262 3191 3.140623 TCACGTAGTACACACACAGCTA 58.859 45.455 0.38 0.00 41.61 3.32
2471 3416 1.202758 ACGAGATCCACAGCACCAAAA 60.203 47.619 0.00 0.00 0.00 2.44
2472 3417 0.396435 ACGAGATCCACAGCACCAAA 59.604 50.000 0.00 0.00 0.00 3.28
2537 3499 1.470890 CTCCGAGTCTGAGGACAAGAC 59.529 57.143 3.74 0.00 44.36 3.01
2591 3557 6.962116 CGAACGCTCATAGGAGTATATTACAG 59.038 42.308 6.23 0.00 43.37 2.74
2593 3559 6.840075 ACGAACGCTCATAGGAGTATATTAC 58.160 40.000 6.23 0.00 43.37 1.89
2595 3561 5.961396 ACGAACGCTCATAGGAGTATATT 57.039 39.130 6.23 0.00 43.37 1.28
2597 3563 7.168804 CGATATACGAACGCTCATAGGAGTATA 59.831 40.741 6.23 0.96 45.77 1.47
2598 3564 6.018913 CGATATACGAACGCTCATAGGAGTAT 60.019 42.308 6.23 0.00 45.77 2.12
2599 3565 5.290400 CGATATACGAACGCTCATAGGAGTA 59.710 44.000 6.23 0.00 45.77 2.59
2600 3566 4.093115 CGATATACGAACGCTCATAGGAGT 59.907 45.833 6.23 0.00 45.77 3.85
2601 3567 4.579564 CGATATACGAACGCTCATAGGAG 58.420 47.826 0.00 0.00 45.77 3.69
2602 3568 4.595198 CGATATACGAACGCTCATAGGA 57.405 45.455 0.00 0.00 45.77 2.94
2639 3605 5.677178 CACTTCTACAAAAGCACGAGAAAAC 59.323 40.000 0.00 0.00 0.00 2.43
2640 3606 5.583061 TCACTTCTACAAAAGCACGAGAAAA 59.417 36.000 0.00 0.00 0.00 2.29
2641 3607 5.113383 TCACTTCTACAAAAGCACGAGAAA 58.887 37.500 0.00 0.00 0.00 2.52
2649 3615 2.729156 GCCGCATCACTTCTACAAAAGC 60.729 50.000 0.00 0.00 0.00 3.51
2656 3622 0.459899 ACATCGCCGCATCACTTCTA 59.540 50.000 0.00 0.00 0.00 2.10
2657 3623 0.391661 AACATCGCCGCATCACTTCT 60.392 50.000 0.00 0.00 0.00 2.85
2675 3641 1.819288 TCAAGGTTTGCGTTGGTCAAA 59.181 42.857 0.00 0.00 39.96 2.69
2676 3642 1.464734 TCAAGGTTTGCGTTGGTCAA 58.535 45.000 0.00 0.00 39.96 3.18
2677 3643 1.403679 CTTCAAGGTTTGCGTTGGTCA 59.596 47.619 0.00 0.00 39.96 4.02
2678 3644 1.864029 GCTTCAAGGTTTGCGTTGGTC 60.864 52.381 0.00 0.00 39.96 4.02
2680 3646 0.385390 AGCTTCAAGGTTTGCGTTGG 59.615 50.000 0.00 0.00 39.96 3.77
2682 3648 2.959507 AAAGCTTCAAGGTTTGCGTT 57.040 40.000 13.80 0.00 43.44 4.84
2683 3649 2.959507 AAAAGCTTCAAGGTTTGCGT 57.040 40.000 15.20 0.00 44.21 5.24
2701 3764 5.768317 CCTCGCTTTTTCTCCAATGTAAAA 58.232 37.500 0.00 0.00 0.00 1.52
2706 3769 1.466360 CGCCTCGCTTTTTCTCCAATG 60.466 52.381 0.00 0.00 0.00 2.82
2707 3770 0.804989 CGCCTCGCTTTTTCTCCAAT 59.195 50.000 0.00 0.00 0.00 3.16
2710 3773 0.670854 AGTCGCCTCGCTTTTTCTCC 60.671 55.000 0.00 0.00 0.00 3.71
2731 3794 2.128771 ATTTCAGGCATACGCAAGGT 57.871 45.000 0.00 0.00 46.39 3.50
2740 3803 2.643551 CTCCGGTGTTATTTCAGGCAT 58.356 47.619 0.00 0.00 0.00 4.40
2751 3814 0.763035 AGGTTTGTAGCTCCGGTGTT 59.237 50.000 0.00 0.00 0.00 3.32
2766 3829 6.722129 AGATAGATATAAGCCAGTCGAAGGTT 59.278 38.462 6.98 4.41 0.00 3.50
2772 3835 6.207810 GGGGATAGATAGATATAAGCCAGTCG 59.792 46.154 0.00 0.00 0.00 4.18
2792 3855 3.066208 ACTCCACATCACATAGGGGAT 57.934 47.619 0.00 0.00 0.00 3.85
2804 3867 3.258372 TCTGTTTCGAAGCTACTCCACAT 59.742 43.478 13.36 0.00 0.00 3.21
2824 3887 0.620556 ATTTGAGTCGGCCCATGTCT 59.379 50.000 0.00 0.00 0.00 3.41
2826 3889 0.744414 CGATTTGAGTCGGCCCATGT 60.744 55.000 0.00 0.00 37.94 3.21
2829 3892 0.035598 TTTCGATTTGAGTCGGCCCA 59.964 50.000 0.00 0.00 41.74 5.36
2845 3908 1.890174 CCGGTGCCTCCCATTTTTC 59.110 57.895 0.00 0.00 0.00 2.29
2846 3909 2.282783 GCCGGTGCCTCCCATTTTT 61.283 57.895 1.90 0.00 0.00 1.94
2851 3914 2.382770 ATTATGCCGGTGCCTCCCA 61.383 57.895 1.90 0.00 36.33 4.37
2882 3945 5.929415 GGGTCTGCTAGAATTGCTCTAATAC 59.071 44.000 0.00 0.00 36.17 1.89
2889 3952 0.179000 CGGGGTCTGCTAGAATTGCT 59.821 55.000 0.00 0.00 0.00 3.91
2890 3953 1.440145 GCGGGGTCTGCTAGAATTGC 61.440 60.000 0.00 0.00 0.00 3.56
2891 3954 0.107703 TGCGGGGTCTGCTAGAATTG 60.108 55.000 0.00 0.00 0.00 2.32
2892 3955 0.618458 TTGCGGGGTCTGCTAGAATT 59.382 50.000 0.00 0.00 0.00 2.17
2894 3957 0.398696 TTTTGCGGGGTCTGCTAGAA 59.601 50.000 0.00 0.00 0.00 2.10
2895 3958 0.398696 TTTTTGCGGGGTCTGCTAGA 59.601 50.000 0.00 0.00 0.00 2.43
2896 3959 1.463674 ATTTTTGCGGGGTCTGCTAG 58.536 50.000 0.30 0.00 0.00 3.42
2897 3960 1.816224 GAATTTTTGCGGGGTCTGCTA 59.184 47.619 0.30 0.00 0.00 3.49
2898 3961 0.603065 GAATTTTTGCGGGGTCTGCT 59.397 50.000 0.30 0.00 0.00 4.24
2899 3962 0.732538 CGAATTTTTGCGGGGTCTGC 60.733 55.000 0.00 0.00 0.00 4.26
2900 3963 0.878416 TCGAATTTTTGCGGGGTCTG 59.122 50.000 0.00 0.00 0.00 3.51
2901 3964 0.879090 GTCGAATTTTTGCGGGGTCT 59.121 50.000 0.00 0.00 0.00 3.85
2902 3965 0.109458 GGTCGAATTTTTGCGGGGTC 60.109 55.000 0.00 0.00 0.00 4.46
2903 3966 1.529152 GGGTCGAATTTTTGCGGGGT 61.529 55.000 0.00 0.00 0.00 4.95
2904 3967 1.214325 GGGTCGAATTTTTGCGGGG 59.786 57.895 0.00 0.00 0.00 5.73
2905 3968 1.154112 CGGGTCGAATTTTTGCGGG 60.154 57.895 0.00 0.00 0.00 6.13
2906 3969 1.799916 GCGGGTCGAATTTTTGCGG 60.800 57.895 0.00 0.00 0.00 5.69
2907 3970 0.661780 TTGCGGGTCGAATTTTTGCG 60.662 50.000 0.00 0.00 0.00 4.85
2908 3971 1.492720 TTTGCGGGTCGAATTTTTGC 58.507 45.000 0.00 0.00 0.00 3.68
2909 3972 2.860735 TGTTTTGCGGGTCGAATTTTTG 59.139 40.909 0.00 0.00 0.00 2.44
2910 3973 2.861335 GTGTTTTGCGGGTCGAATTTTT 59.139 40.909 0.00 0.00 0.00 1.94
2911 3974 2.465855 GTGTTTTGCGGGTCGAATTTT 58.534 42.857 0.00 0.00 0.00 1.82
2912 3975 1.598430 CGTGTTTTGCGGGTCGAATTT 60.598 47.619 0.00 0.00 0.00 1.82
2913 3976 0.040781 CGTGTTTTGCGGGTCGAATT 60.041 50.000 0.00 0.00 0.00 2.17
2914 3977 1.161563 ACGTGTTTTGCGGGTCGAAT 61.162 50.000 0.00 0.00 0.00 3.34
2915 3978 1.367599 AACGTGTTTTGCGGGTCGAA 61.368 50.000 0.00 0.00 0.00 3.71
2916 3979 1.367599 AAACGTGTTTTGCGGGTCGA 61.368 50.000 0.00 0.00 0.00 4.20
2917 3980 1.062845 AAACGTGTTTTGCGGGTCG 59.937 52.632 0.00 0.00 0.00 4.79
2918 3981 2.572664 CAAACGTGTTTTGCGGGTC 58.427 52.632 0.00 0.00 38.37 4.46
2919 3982 4.796225 CAAACGTGTTTTGCGGGT 57.204 50.000 0.00 0.00 38.37 5.28
2924 3987 1.986378 TGAAACCGCAAACGTGTTTTG 59.014 42.857 2.90 0.00 46.57 2.44
2925 3988 2.349297 TGAAACCGCAAACGTGTTTT 57.651 40.000 2.90 0.00 40.40 2.43
2926 3989 2.349297 TTGAAACCGCAAACGTGTTT 57.651 40.000 1.02 1.02 41.87 2.83
2927 3990 2.349297 TTTGAAACCGCAAACGTGTT 57.651 40.000 0.00 0.00 37.70 3.32
2928 3991 2.349297 TTTTGAAACCGCAAACGTGT 57.651 40.000 0.00 0.00 37.48 4.49
2929 3992 2.917971 TCTTTTTGAAACCGCAAACGTG 59.082 40.909 0.00 0.00 37.48 4.49
2930 3993 3.219052 TCTTTTTGAAACCGCAAACGT 57.781 38.095 0.00 0.00 37.48 3.99
2931 3994 3.794028 TGATCTTTTTGAAACCGCAAACG 59.206 39.130 0.00 0.00 37.48 3.60
2932 3995 5.234116 ACATGATCTTTTTGAAACCGCAAAC 59.766 36.000 0.00 0.00 37.48 2.93
2933 3996 5.355596 ACATGATCTTTTTGAAACCGCAAA 58.644 33.333 0.00 0.00 36.08 3.68
2934 3997 4.942852 ACATGATCTTTTTGAAACCGCAA 58.057 34.783 0.00 0.00 0.00 4.85
2935 3998 4.582701 ACATGATCTTTTTGAAACCGCA 57.417 36.364 0.00 0.00 0.00 5.69
2936 3999 5.669122 CAAACATGATCTTTTTGAAACCGC 58.331 37.500 0.00 0.00 32.91 5.68
2937 4000 5.610124 CGCAAACATGATCTTTTTGAAACCG 60.610 40.000 14.61 7.51 32.91 4.44
2938 4001 5.333263 CCGCAAACATGATCTTTTTGAAACC 60.333 40.000 14.61 1.52 32.91 3.27
2939 4002 5.333263 CCCGCAAACATGATCTTTTTGAAAC 60.333 40.000 14.61 1.77 32.91 2.78
2940 4003 4.749099 CCCGCAAACATGATCTTTTTGAAA 59.251 37.500 14.61 0.00 32.91 2.69
2941 4004 4.202202 ACCCGCAAACATGATCTTTTTGAA 60.202 37.500 14.61 0.00 32.91 2.69
2942 4005 3.320541 ACCCGCAAACATGATCTTTTTGA 59.679 39.130 14.61 0.00 32.91 2.69
2943 4006 3.652274 ACCCGCAAACATGATCTTTTTG 58.348 40.909 0.00 0.04 34.05 2.44
2944 4007 3.611530 CGACCCGCAAACATGATCTTTTT 60.612 43.478 0.00 0.00 0.00 1.94
2945 4008 2.095263 CGACCCGCAAACATGATCTTTT 60.095 45.455 0.00 0.00 0.00 2.27
2946 4009 1.468520 CGACCCGCAAACATGATCTTT 59.531 47.619 0.00 0.00 0.00 2.52
2947 4010 1.086696 CGACCCGCAAACATGATCTT 58.913 50.000 0.00 0.00 0.00 2.40
2948 4011 0.249120 TCGACCCGCAAACATGATCT 59.751 50.000 0.00 0.00 0.00 2.75
2949 4012 1.083489 TTCGACCCGCAAACATGATC 58.917 50.000 0.00 0.00 0.00 2.92
2950 4013 1.529226 TTTCGACCCGCAAACATGAT 58.471 45.000 0.00 0.00 0.00 2.45
2951 4014 1.002251 GTTTTCGACCCGCAAACATGA 60.002 47.619 0.00 0.00 41.11 3.07
2952 4015 1.268794 TGTTTTCGACCCGCAAACATG 60.269 47.619 11.81 0.00 44.57 3.21
2953 4016 1.025812 TGTTTTCGACCCGCAAACAT 58.974 45.000 11.81 0.00 44.57 2.71
2954 4017 2.478989 TGTTTTCGACCCGCAAACA 58.521 47.368 11.81 11.81 46.35 2.83
2955 4018 1.404477 CATGTTTTCGACCCGCAAAC 58.596 50.000 7.45 7.45 41.61 2.93
2956 4019 0.318275 GCATGTTTTCGACCCGCAAA 60.318 50.000 0.00 0.00 0.00 3.68
2957 4020 1.284408 GCATGTTTTCGACCCGCAA 59.716 52.632 0.00 0.00 0.00 4.85
2958 4021 2.950673 GCATGTTTTCGACCCGCA 59.049 55.556 0.00 0.00 0.00 5.69
2959 4022 2.202298 CGCATGTTTTCGACCCGC 60.202 61.111 0.00 0.00 0.00 6.13
2960 4023 2.202298 GCGCATGTTTTCGACCCG 60.202 61.111 0.30 0.00 0.00 5.28
2961 4024 2.202298 CGCGCATGTTTTCGACCC 60.202 61.111 8.75 0.00 0.00 4.46
2962 4025 2.202298 CCGCGCATGTTTTCGACC 60.202 61.111 8.75 0.00 0.00 4.79
2963 4026 1.509162 GACCGCGCATGTTTTCGAC 60.509 57.895 8.75 0.00 0.00 4.20
2964 4027 2.857448 GACCGCGCATGTTTTCGA 59.143 55.556 8.75 0.00 0.00 3.71
2965 4028 2.487443 TTCGACCGCGCATGTTTTCG 62.487 55.000 8.75 5.59 37.46 3.46
2966 4029 0.384974 TTTCGACCGCGCATGTTTTC 60.385 50.000 8.75 0.00 37.46 2.29
2967 4030 0.029567 TTTTCGACCGCGCATGTTTT 59.970 45.000 8.75 0.00 37.46 2.43
2968 4031 0.385473 CTTTTCGACCGCGCATGTTT 60.385 50.000 8.75 0.00 37.46 2.83
2969 4032 1.206578 CTTTTCGACCGCGCATGTT 59.793 52.632 8.75 0.00 37.46 2.71
2970 4033 1.225376 TTCTTTTCGACCGCGCATGT 61.225 50.000 8.75 3.08 37.46 3.21
2971 4034 0.789383 GTTCTTTTCGACCGCGCATG 60.789 55.000 8.75 0.00 37.46 4.06
2972 4035 1.495951 GTTCTTTTCGACCGCGCAT 59.504 52.632 8.75 0.00 37.46 4.73
2973 4036 2.600475 GGTTCTTTTCGACCGCGCA 61.600 57.895 8.75 0.00 37.46 6.09
2974 4037 2.172659 GGTTCTTTTCGACCGCGC 59.827 61.111 0.00 0.00 37.46 6.86
2975 4038 2.858158 GGGTTCTTTTCGACCGCG 59.142 61.111 0.00 0.00 36.78 6.46
2976 4039 2.858158 CGGGTTCTTTTCGACCGC 59.142 61.111 0.00 0.00 37.93 5.68
2978 4041 2.963432 TGATACGGGTTCTTTTCGACC 58.037 47.619 0.00 0.00 35.14 4.79
2979 4042 4.996062 TTTGATACGGGTTCTTTTCGAC 57.004 40.909 0.00 0.00 0.00 4.20
2980 4043 4.213906 GGTTTTGATACGGGTTCTTTTCGA 59.786 41.667 0.00 0.00 0.00 3.71
2981 4044 4.214758 AGGTTTTGATACGGGTTCTTTTCG 59.785 41.667 0.00 0.00 0.00 3.46
2982 4045 5.458015 CAGGTTTTGATACGGGTTCTTTTC 58.542 41.667 0.00 0.00 0.00 2.29
2983 4046 4.261867 GCAGGTTTTGATACGGGTTCTTTT 60.262 41.667 0.00 0.00 0.00 2.27
2984 4047 3.254903 GCAGGTTTTGATACGGGTTCTTT 59.745 43.478 0.00 0.00 0.00 2.52
2985 4048 2.817844 GCAGGTTTTGATACGGGTTCTT 59.182 45.455 0.00 0.00 0.00 2.52
2986 4049 2.224670 TGCAGGTTTTGATACGGGTTCT 60.225 45.455 0.00 0.00 0.00 3.01
2987 4050 2.156098 TGCAGGTTTTGATACGGGTTC 58.844 47.619 0.00 0.00 0.00 3.62
2988 4051 2.279935 TGCAGGTTTTGATACGGGTT 57.720 45.000 0.00 0.00 0.00 4.11
2989 4052 2.507407 ATGCAGGTTTTGATACGGGT 57.493 45.000 0.00 0.00 0.00 5.28
2990 4053 5.514274 AATTATGCAGGTTTTGATACGGG 57.486 39.130 0.00 0.00 0.00 5.28
2991 4054 6.559810 TCAAATTATGCAGGTTTTGATACGG 58.440 36.000 13.60 0.00 34.20 4.02
2992 4055 8.459521 TTTCAAATTATGCAGGTTTTGATACG 57.540 30.769 16.65 0.00 37.76 3.06
3034 4097 9.539825 TGTGATAAACTATGTTTGTGCAATTTT 57.460 25.926 6.01 0.00 0.00 1.82
3035 4098 9.709495 ATGTGATAAACTATGTTTGTGCAATTT 57.291 25.926 6.01 0.00 0.00 1.82
3037 4100 9.787532 GTATGTGATAAACTATGTTTGTGCAAT 57.212 29.630 6.01 0.00 0.00 3.56
3038 4101 9.008965 AGTATGTGATAAACTATGTTTGTGCAA 57.991 29.630 6.01 0.00 0.00 4.08
3039 4102 8.560355 AGTATGTGATAAACTATGTTTGTGCA 57.440 30.769 6.01 0.00 0.00 4.57
3040 4103 9.916397 GTAGTATGTGATAAACTATGTTTGTGC 57.084 33.333 6.01 0.00 0.00 4.57
3077 4140 9.231297 ACTATGCTTGTAGTTTGTTTATCATGT 57.769 29.630 0.00 0.00 30.95 3.21
3114 4177 9.909365 ACCCCTCTATTACTAGTTTAATATGGT 57.091 33.333 0.00 2.77 0.00 3.55
3117 4180 9.252635 CCGACCCCTCTATTACTAGTTTAATAT 57.747 37.037 0.00 0.00 0.00 1.28
3118 4181 8.448008 TCCGACCCCTCTATTACTAGTTTAATA 58.552 37.037 0.00 0.00 0.00 0.98
3119 4182 7.300658 TCCGACCCCTCTATTACTAGTTTAAT 58.699 38.462 0.00 0.00 0.00 1.40
3120 4183 6.672593 TCCGACCCCTCTATTACTAGTTTAA 58.327 40.000 0.00 0.00 0.00 1.52
3121 4184 6.266131 TCCGACCCCTCTATTACTAGTTTA 57.734 41.667 0.00 0.00 0.00 2.01
3122 4185 5.134725 TCCGACCCCTCTATTACTAGTTT 57.865 43.478 0.00 0.00 0.00 2.66
3123 4186 4.803329 TCCGACCCCTCTATTACTAGTT 57.197 45.455 0.00 0.00 0.00 2.24
3124 4187 4.602732 AGATCCGACCCCTCTATTACTAGT 59.397 45.833 0.00 0.00 0.00 2.57
3125 4188 4.944930 CAGATCCGACCCCTCTATTACTAG 59.055 50.000 0.00 0.00 0.00 2.57
3126 4189 4.600547 TCAGATCCGACCCCTCTATTACTA 59.399 45.833 0.00 0.00 0.00 1.82
3127 4190 3.398292 TCAGATCCGACCCCTCTATTACT 59.602 47.826 0.00 0.00 0.00 2.24
3128 4191 3.506844 GTCAGATCCGACCCCTCTATTAC 59.493 52.174 0.00 0.00 0.00 1.89
3129 4192 3.764218 GTCAGATCCGACCCCTCTATTA 58.236 50.000 0.00 0.00 0.00 0.98
3130 4193 2.599677 GTCAGATCCGACCCCTCTATT 58.400 52.381 0.00 0.00 0.00 1.73
3131 4194 1.545875 CGTCAGATCCGACCCCTCTAT 60.546 57.143 3.47 0.00 31.91 1.98
3132 4195 0.179026 CGTCAGATCCGACCCCTCTA 60.179 60.000 3.47 0.00 31.91 2.43
3133 4196 1.454111 CGTCAGATCCGACCCCTCT 60.454 63.158 3.47 0.00 31.91 3.69
3134 4197 2.491022 CCGTCAGATCCGACCCCTC 61.491 68.421 3.47 0.00 31.91 4.30
3135 4198 2.442272 CCGTCAGATCCGACCCCT 60.442 66.667 3.47 0.00 31.91 4.79
3136 4199 4.222847 GCCGTCAGATCCGACCCC 62.223 72.222 3.47 0.00 31.91 4.95
3137 4200 4.570663 CGCCGTCAGATCCGACCC 62.571 72.222 3.47 0.00 31.91 4.46
3138 4201 4.570663 CCGCCGTCAGATCCGACC 62.571 72.222 3.47 0.00 31.91 4.79
3142 4205 4.933064 CTCGCCGCCGTCAGATCC 62.933 72.222 0.00 0.00 35.54 3.36
3143 4206 4.933064 CCTCGCCGCCGTCAGATC 62.933 72.222 0.00 0.00 35.54 2.75
3156 4219 3.864686 CCATTTGCCGCGACCTCG 61.865 66.667 8.23 0.00 43.27 4.63
3157 4220 2.435938 TCCATTTGCCGCGACCTC 60.436 61.111 8.23 0.00 0.00 3.85
3158 4221 2.746277 GTCCATTTGCCGCGACCT 60.746 61.111 8.23 0.00 0.00 3.85
3159 4222 4.160635 CGTCCATTTGCCGCGACC 62.161 66.667 8.23 0.00 0.00 4.79
3160 4223 3.115892 TCGTCCATTTGCCGCGAC 61.116 61.111 8.23 0.00 0.00 5.19
3161 4224 3.115892 GTCGTCCATTTGCCGCGA 61.116 61.111 8.23 0.00 0.00 5.87
3162 4225 4.499023 CGTCGTCCATTTGCCGCG 62.499 66.667 0.00 0.00 0.00 6.46
3163 4226 4.811761 GCGTCGTCCATTTGCCGC 62.812 66.667 0.00 0.00 0.00 6.53
3164 4227 4.160635 GGCGTCGTCCATTTGCCG 62.161 66.667 0.00 0.00 35.77 5.69
3165 4228 4.160635 CGGCGTCGTCCATTTGCC 62.161 66.667 0.00 0.00 42.29 4.52


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

AutoCloner maintained by Alex Coulton.