Multiple sequence alignment - TraesCS5B01G235300

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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 TraesCS5B01G235300 chr5B 100.000 3572 0 0 1 3572 415647253 415650824 0.000000e+00 6597
1 TraesCS5B01G235300 chr5A 93.575 2179 97 12 843 3009 453343198 453345345 0.000000e+00 3208
2 TraesCS5B01G235300 chr5A 92.444 225 15 2 3349 3572 540726003 540725780 1.600000e-83 320
3 TraesCS5B01G235300 chr5D 91.314 2245 128 25 1042 3269 352693017 352695211 0.000000e+00 3003
4 TraesCS5B01G235300 chr5D 95.950 321 9 2 956 1276 352692898 352693214 5.290000e-143 518
5 TraesCS5B01G235300 chr5D 92.857 224 12 3 3351 3570 542698680 542698903 4.450000e-84 322
6 TraesCS5B01G235300 chr3A 91.677 781 60 5 1 779 709154523 709155300 0.000000e+00 1077
7 TraesCS5B01G235300 chr3A 88.689 778 76 6 4 779 170479153 170478386 0.000000e+00 939
8 TraesCS5B01G235300 chr3A 89.130 276 29 1 1 275 57174718 57174993 3.410000e-90 342
9 TraesCS5B01G235300 chr7A 91.060 783 57 8 6 786 78562392 78563163 0.000000e+00 1046
10 TraesCS5B01G235300 chr7A 86.667 780 84 16 7 781 42711393 42710629 0.000000e+00 846
11 TraesCS5B01G235300 chr4B 88.889 792 68 17 4 784 515049573 515048791 0.000000e+00 957
12 TraesCS5B01G235300 chr7D 87.852 782 78 13 1 780 12421513 12422279 0.000000e+00 902
13 TraesCS5B01G235300 chr7D 94.091 220 13 0 3353 3572 41057518 41057299 5.710000e-88 335
14 TraesCS5B01G235300 chr1A 86.979 791 85 9 1 783 504740113 504740893 0.000000e+00 874
15 TraesCS5B01G235300 chr1A 87.117 784 72 13 4 783 577834674 577833916 0.000000e+00 861
16 TraesCS5B01G235300 chr1A 86.507 793 87 9 1 783 504999441 505000223 0.000000e+00 854
17 TraesCS5B01G235300 chr4A 88.446 502 42 13 291 783 644776444 644775950 3.070000e-165 592
18 TraesCS5B01G235300 chr2D 94.545 220 12 0 3353 3572 37526614 37526833 1.230000e-89 340
19 TraesCS5B01G235300 chr2D 93.151 219 14 1 3355 3572 112871208 112870990 1.600000e-83 320
20 TraesCS5B01G235300 chr6B 92.952 227 14 2 3348 3572 4952976 4953202 2.660000e-86 329
21 TraesCS5B01G235300 chr6B 92.952 227 14 2 3348 3572 4975358 4975584 2.660000e-86 329
22 TraesCS5B01G235300 chr6B 92.511 227 15 2 3348 3572 5032753 5032979 1.240000e-84 324
23 TraesCS5B01G235300 chr6A 92.793 222 15 1 3352 3572 138271032 138271253 1.600000e-83 320


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 TraesCS5B01G235300 chr5B 415647253 415650824 3571 False 6597.0 6597 100.000 1 3572 1 chr5B.!!$F1 3571
1 TraesCS5B01G235300 chr5A 453343198 453345345 2147 False 3208.0 3208 93.575 843 3009 1 chr5A.!!$F1 2166
2 TraesCS5B01G235300 chr5D 352692898 352695211 2313 False 1760.5 3003 93.632 956 3269 2 chr5D.!!$F2 2313
3 TraesCS5B01G235300 chr3A 709154523 709155300 777 False 1077.0 1077 91.677 1 779 1 chr3A.!!$F2 778
4 TraesCS5B01G235300 chr3A 170478386 170479153 767 True 939.0 939 88.689 4 779 1 chr3A.!!$R1 775
5 TraesCS5B01G235300 chr7A 78562392 78563163 771 False 1046.0 1046 91.060 6 786 1 chr7A.!!$F1 780
6 TraesCS5B01G235300 chr7A 42710629 42711393 764 True 846.0 846 86.667 7 781 1 chr7A.!!$R1 774
7 TraesCS5B01G235300 chr4B 515048791 515049573 782 True 957.0 957 88.889 4 784 1 chr4B.!!$R1 780
8 TraesCS5B01G235300 chr7D 12421513 12422279 766 False 902.0 902 87.852 1 780 1 chr7D.!!$F1 779
9 TraesCS5B01G235300 chr1A 504740113 504740893 780 False 874.0 874 86.979 1 783 1 chr1A.!!$F1 782
10 TraesCS5B01G235300 chr1A 577833916 577834674 758 True 861.0 861 87.117 4 783 1 chr1A.!!$R1 779
11 TraesCS5B01G235300 chr1A 504999441 505000223 782 False 854.0 854 86.507 1 783 1 chr1A.!!$F2 782

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
989 1016 0.244178 GACCTAATCGGCGATCCTCC 59.756 60.0 24.2 8.05 35.61 4.30 F
1575 1644 0.175989 AGGAATCGCCGAAGAAGGAC 59.824 55.0 0.0 0.00 43.43 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2238 2307 0.452987 CAATGGCATCACCTTCACCG 59.547 55.0 0.00 0.0 40.22 4.94 R
3290 3368 0.036765 CCTGCAGCACATTGGCAAAT 60.037 50.0 8.66 0.0 37.06 2.32 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 3.385193 TCGCAACATCTCTTCTTCACA 57.615 42.857 0.00 0.00 0.00 3.58
110 111 6.884295 CAGATTTGTACCCTGATAACCTTTGA 59.116 38.462 0.00 0.00 0.00 2.69
178 179 1.212935 CTATACCTTTGGCCTGGCTGT 59.787 52.381 19.68 10.50 0.00 4.40
428 434 2.549611 GATGCAGCCGTCGACTCTGT 62.550 60.000 25.31 13.67 0.00 3.41
472 481 2.404559 CCCCCTATGGCTGTTAGTGTA 58.595 52.381 0.00 0.00 0.00 2.90
547 559 0.779997 AAATGTGAGCTGTTCCCCCT 59.220 50.000 0.00 0.00 0.00 4.79
548 560 0.779997 AATGTGAGCTGTTCCCCCTT 59.220 50.000 0.00 0.00 0.00 3.95
549 561 1.668826 ATGTGAGCTGTTCCCCCTTA 58.331 50.000 0.00 0.00 0.00 2.69
550 562 1.668826 TGTGAGCTGTTCCCCCTTAT 58.331 50.000 0.00 0.00 0.00 1.73
690 713 1.202533 CCAGTGGTGTCTTGAACTCGT 60.203 52.381 0.00 0.00 0.00 4.18
805 830 2.561478 AAAAAGCCCTTCGCACTAGA 57.439 45.000 0.00 0.00 41.38 2.43
806 831 2.561478 AAAAGCCCTTCGCACTAGAA 57.439 45.000 0.00 0.00 41.38 2.10
807 832 2.100605 AAAGCCCTTCGCACTAGAAG 57.899 50.000 0.00 0.14 45.26 2.85
812 837 3.532896 CTTCGCACTAGAAGGCCAA 57.467 52.632 5.01 0.00 42.78 4.52
813 838 1.808411 CTTCGCACTAGAAGGCCAAA 58.192 50.000 5.01 0.00 42.78 3.28
814 839 2.151202 CTTCGCACTAGAAGGCCAAAA 58.849 47.619 5.01 0.00 42.78 2.44
815 840 2.264005 TCGCACTAGAAGGCCAAAAA 57.736 45.000 5.01 0.00 0.00 1.94
816 841 2.151202 TCGCACTAGAAGGCCAAAAAG 58.849 47.619 5.01 0.00 0.00 2.27
817 842 1.401539 CGCACTAGAAGGCCAAAAAGC 60.402 52.381 5.01 0.00 0.00 3.51
826 851 2.839629 GCCAAAAAGCCCAAATCCG 58.160 52.632 0.00 0.00 0.00 4.18
827 852 1.298157 GCCAAAAAGCCCAAATCCGC 61.298 55.000 0.00 0.00 0.00 5.54
828 853 1.013524 CCAAAAAGCCCAAATCCGCG 61.014 55.000 0.00 0.00 0.00 6.46
829 854 1.374125 AAAAAGCCCAAATCCGCGC 60.374 52.632 0.00 0.00 0.00 6.86
830 855 2.093537 AAAAAGCCCAAATCCGCGCA 62.094 50.000 8.75 0.00 0.00 6.09
831 856 2.763627 AAAAGCCCAAATCCGCGCAC 62.764 55.000 8.75 0.00 0.00 5.34
834 859 3.202001 CCCAAATCCGCGCACGAT 61.202 61.111 8.75 4.42 43.93 3.73
835 860 2.023181 CCAAATCCGCGCACGATG 59.977 61.111 8.75 0.00 43.93 3.84
836 861 2.460275 CCAAATCCGCGCACGATGA 61.460 57.895 8.75 0.00 43.93 2.92
837 862 1.296867 CAAATCCGCGCACGATGAC 60.297 57.895 8.75 0.00 43.93 3.06
838 863 2.461110 AAATCCGCGCACGATGACC 61.461 57.895 8.75 0.00 43.93 4.02
848 873 0.389025 CACGATGACCGATCCATCCA 59.611 55.000 0.00 0.00 41.76 3.41
911 936 2.680352 TCCTCACCTCCGCTGGTC 60.680 66.667 0.00 0.00 38.45 4.02
918 943 4.742201 CTCCGCTGGTCCCACACG 62.742 72.222 0.00 0.00 0.00 4.49
934 959 1.202114 ACACGCATCCATCGCAAATTT 59.798 42.857 0.00 0.00 0.00 1.82
939 964 2.224113 GCATCCATCGCAAATTTCCCAT 60.224 45.455 0.00 0.00 0.00 4.00
944 969 3.382546 CCATCGCAAATTTCCCATCTCTT 59.617 43.478 0.00 0.00 0.00 2.85
966 993 1.573376 TCCCCAAATCGAATCCCCAAT 59.427 47.619 0.00 0.00 0.00 3.16
988 1015 3.796667 GACCTAATCGGCGATCCTC 57.203 57.895 24.20 11.04 35.61 3.71
989 1016 0.244178 GACCTAATCGGCGATCCTCC 59.756 60.000 24.20 8.05 35.61 4.30
1224 1251 1.392534 CCGATCCCCTAGCCCCTAT 59.607 63.158 0.00 0.00 0.00 2.57
1302 1365 0.537188 CTCCCTACCACAATGAGCGT 59.463 55.000 0.00 0.00 0.00 5.07
1422 1485 1.630878 CTCAAGGGCCTCACCTACTTT 59.369 52.381 6.46 0.00 40.87 2.66
1575 1644 0.175989 AGGAATCGCCGAAGAAGGAC 59.824 55.000 0.00 0.00 43.43 3.85
1581 1650 0.528684 CGCCGAAGAAGGACTCATCC 60.529 60.000 0.00 0.00 46.69 3.51
1595 1664 1.336440 CTCATCCGAGAAGAGCGATGT 59.664 52.381 0.00 0.00 42.34 3.06
1611 1680 2.675317 CGATGTGGAGGAGAACAAGGAC 60.675 54.545 0.00 0.00 0.00 3.85
1700 1769 4.094830 AGAAAAAGAAAGGGCGTAAGGA 57.905 40.909 0.00 0.00 38.28 3.36
1785 1854 4.093011 AGAGTGAGAGTGATAGCAAGGTT 58.907 43.478 0.00 0.00 0.00 3.50
1953 2022 0.907230 GCTCTGAGGAGGTGGAGGTT 60.907 60.000 6.83 0.00 39.80 3.50
1958 2027 2.237392 CTGAGGAGGTGGAGGTTTTAGG 59.763 54.545 0.00 0.00 0.00 2.69
1991 2060 2.612212 TCTCAACGGACAGCAAGAAAAC 59.388 45.455 0.00 0.00 0.00 2.43
1995 2064 1.164041 CGGACAGCAAGAAAACGGGT 61.164 55.000 0.00 0.00 0.00 5.28
2047 2116 6.320926 TCAGTCTGATTCTGAAGATTCGATCT 59.679 38.462 0.00 0.00 42.61 2.75
2097 2166 4.564782 AATTGAAGAGACAGATGAGCCA 57.435 40.909 0.00 0.00 0.00 4.75
2160 2229 0.615331 CCCAGAAGAAGGCTGCACTA 59.385 55.000 0.50 0.00 32.06 2.74
2184 2253 1.561769 ATGAGATGCCGGTTGGACCA 61.562 55.000 1.90 0.00 38.47 4.02
2238 2307 2.032681 GGTGGTGCACTGAGACCC 59.967 66.667 17.98 0.00 34.40 4.46
2436 2505 1.680735 AGTGCAGAGGATAAGAGAGCG 59.319 52.381 0.00 0.00 0.00 5.03
2481 2550 5.028549 AGAAGTCAAAGAGAGAGCACAAA 57.971 39.130 0.00 0.00 0.00 2.83
2610 2679 6.183360 GCTATTTTACAAAGAAATGGTTGCCG 60.183 38.462 0.00 0.00 30.45 5.69
2638 2707 8.761575 ATTAGTTATGCATGTTTTTCCTGTTG 57.238 30.769 10.16 0.00 0.00 3.33
2639 2708 6.160576 AGTTATGCATGTTTTTCCTGTTGT 57.839 33.333 10.16 0.00 0.00 3.32
2640 2709 6.581712 AGTTATGCATGTTTTTCCTGTTGTT 58.418 32.000 10.16 0.00 0.00 2.83
2641 2710 6.701400 AGTTATGCATGTTTTTCCTGTTGTTC 59.299 34.615 10.16 0.00 0.00 3.18
2642 2711 3.791245 TGCATGTTTTTCCTGTTGTTCC 58.209 40.909 0.00 0.00 0.00 3.62
2643 2712 3.450457 TGCATGTTTTTCCTGTTGTTCCT 59.550 39.130 0.00 0.00 0.00 3.36
2644 2713 3.803778 GCATGTTTTTCCTGTTGTTCCTG 59.196 43.478 0.00 0.00 0.00 3.86
2645 2714 4.680440 GCATGTTTTTCCTGTTGTTCCTGT 60.680 41.667 0.00 0.00 0.00 4.00
2651 2720 4.612264 TTCCTGTTGTTCCTGTAGTACC 57.388 45.455 0.00 0.00 0.00 3.34
2657 2726 4.202182 TGTTGTTCCTGTAGTACCAGTGAC 60.202 45.833 0.00 0.00 0.00 3.67
2697 2767 4.859629 AACTTCTGTTTTGTGTCGACTC 57.140 40.909 17.92 14.12 31.37 3.36
2777 2848 2.950975 TGATGTTTGTCAAGCTGCTTGA 59.049 40.909 34.40 34.40 46.50 3.02
2787 2858 4.081406 TCAAGCTGCTTGATTTACCACAT 58.919 39.130 34.40 0.00 44.27 3.21
2790 2861 5.567138 AGCTGCTTGATTTACCACATTAC 57.433 39.130 0.00 0.00 0.00 1.89
2876 2951 5.109903 GTGAGTGTGAAAGACAGTACAGTT 58.890 41.667 0.00 0.00 38.44 3.16
2877 2952 5.005779 GTGAGTGTGAAAGACAGTACAGTTG 59.994 44.000 0.00 0.00 38.44 3.16
2878 2953 3.871594 AGTGTGAAAGACAGTACAGTTGC 59.128 43.478 0.00 0.00 36.38 4.17
2879 2954 3.621268 GTGTGAAAGACAGTACAGTTGCA 59.379 43.478 0.00 0.00 34.28 4.08
2880 2955 4.273480 GTGTGAAAGACAGTACAGTTGCAT 59.727 41.667 0.00 0.00 34.28 3.96
2881 2956 5.465390 GTGTGAAAGACAGTACAGTTGCATA 59.535 40.000 0.00 0.00 34.28 3.14
2882 2957 6.018262 GTGTGAAAGACAGTACAGTTGCATAA 60.018 38.462 0.00 0.00 34.28 1.90
2883 2958 6.202762 TGTGAAAGACAGTACAGTTGCATAAG 59.797 38.462 0.00 0.00 0.00 1.73
2884 2959 5.179368 TGAAAGACAGTACAGTTGCATAAGC 59.821 40.000 0.00 0.00 42.57 3.09
2885 2960 4.543590 AGACAGTACAGTTGCATAAGCT 57.456 40.909 0.00 0.00 42.74 3.74
2886 2961 4.899502 AGACAGTACAGTTGCATAAGCTT 58.100 39.130 3.48 3.48 42.74 3.74
2887 2962 6.037786 AGACAGTACAGTTGCATAAGCTTA 57.962 37.500 8.99 8.99 42.74 3.09
2939 3014 1.065997 AAGGGGTGCTTGGGTACTGT 61.066 55.000 0.00 0.00 0.00 3.55
2960 3035 1.032014 GGTCTTCTTTGGCACTTGCA 58.968 50.000 3.15 0.00 44.36 4.08
2966 3041 4.099881 TCTTCTTTGGCACTTGCAGATTTT 59.900 37.500 3.15 0.00 44.36 1.82
2967 3042 3.719924 TCTTTGGCACTTGCAGATTTTG 58.280 40.909 3.15 0.00 44.36 2.44
2979 3054 8.581263 CACTTGCAGATTTTGAATAAATCTTCG 58.419 33.333 9.41 2.81 42.52 3.79
2985 3060 9.604626 CAGATTTTGAATAAATCTTCGCTATCC 57.395 33.333 9.41 0.00 42.52 2.59
3045 3121 4.873746 TTTCTCCTAAGATCATAGGCGG 57.126 45.455 17.55 12.81 41.93 6.13
3048 3124 5.452341 TCTCCTAAGATCATAGGCGGATA 57.548 43.478 17.55 1.36 41.93 2.59
3054 3130 6.536582 CCTAAGATCATAGGCGGATACATTTG 59.463 42.308 10.94 0.00 36.31 2.32
3055 3131 5.745312 AGATCATAGGCGGATACATTTGA 57.255 39.130 0.00 0.00 0.00 2.69
3058 3134 4.832248 TCATAGGCGGATACATTTGATCC 58.168 43.478 0.00 0.00 39.71 3.36
3063 3139 5.248640 AGGCGGATACATTTGATCCTTATG 58.751 41.667 0.52 0.00 40.77 1.90
3064 3140 5.003804 GGCGGATACATTTGATCCTTATGT 58.996 41.667 8.79 8.79 40.77 2.29
3066 3142 5.106555 GCGGATACATTTGATCCTTATGTGG 60.107 44.000 12.23 0.00 40.77 4.17
3067 3143 5.106555 CGGATACATTTGATCCTTATGTGGC 60.107 44.000 12.23 6.22 40.77 5.01
3083 3159 9.463443 CCTTATGTGGCAATTATTTAGTTTAGC 57.537 33.333 0.00 0.00 0.00 3.09
3123 3200 6.168389 GGATCCTTGTTTTGCTGAATTTCAT 58.832 36.000 3.84 0.00 0.00 2.57
3125 3202 5.299148 TCCTTGTTTTGCTGAATTTCATGG 58.701 37.500 0.00 0.00 0.00 3.66
3127 3204 3.401182 TGTTTTGCTGAATTTCATGGGC 58.599 40.909 0.00 1.05 0.00 5.36
3128 3205 3.071312 TGTTTTGCTGAATTTCATGGGCT 59.929 39.130 0.00 0.00 0.00 5.19
3129 3206 4.067192 GTTTTGCTGAATTTCATGGGCTT 58.933 39.130 0.00 0.00 0.00 4.35
3131 3208 5.480642 TTTGCTGAATTTCATGGGCTTTA 57.519 34.783 0.00 0.00 0.00 1.85
3132 3209 4.724074 TGCTGAATTTCATGGGCTTTAG 57.276 40.909 0.00 0.00 0.00 1.85
3168 3245 6.173427 TGATACACCTATGAGCAGCAATAA 57.827 37.500 0.00 0.00 0.00 1.40
3172 3249 6.780457 ACACCTATGAGCAGCAATAATTTT 57.220 33.333 0.00 0.00 0.00 1.82
3175 3252 8.917088 ACACCTATGAGCAGCAATAATTTTATT 58.083 29.630 0.00 0.00 33.82 1.40
3177 3254 8.362639 ACCTATGAGCAGCAATAATTTTATTGG 58.637 33.333 19.43 9.00 46.27 3.16
3205 3282 7.722949 ATTCAAATGGTTATTGTCATCACCT 57.277 32.000 0.00 0.00 28.96 4.00
3208 3285 6.150976 TCAAATGGTTATTGTCATCACCTGTC 59.849 38.462 0.00 0.00 28.96 3.51
3213 3290 5.705441 GGTTATTGTCATCACCTGTCAAGAA 59.295 40.000 0.00 0.00 36.55 2.52
3214 3291 6.206634 GGTTATTGTCATCACCTGTCAAGAAA 59.793 38.462 0.00 0.00 36.40 2.52
3215 3292 7.255451 GGTTATTGTCATCACCTGTCAAGAAAA 60.255 37.037 0.00 0.00 36.40 2.29
3216 3293 6.713762 ATTGTCATCACCTGTCAAGAAAAA 57.286 33.333 0.00 0.00 36.55 1.94
3217 3294 6.713762 TTGTCATCACCTGTCAAGAAAAAT 57.286 33.333 0.00 0.00 30.84 1.82
3218 3295 6.713762 TGTCATCACCTGTCAAGAAAAATT 57.286 33.333 0.00 0.00 0.00 1.82
3219 3296 7.815840 TGTCATCACCTGTCAAGAAAAATTA 57.184 32.000 0.00 0.00 0.00 1.40
3220 3297 8.231692 TGTCATCACCTGTCAAGAAAAATTAA 57.768 30.769 0.00 0.00 0.00 1.40
3221 3298 8.690884 TGTCATCACCTGTCAAGAAAAATTAAA 58.309 29.630 0.00 0.00 0.00 1.52
3228 3305 6.202762 CCTGTCAAGAAAAATTAAAACTGCCC 59.797 38.462 0.00 0.00 0.00 5.36
3239 3316 1.302907 AAACTGCCCTCCCATGATCT 58.697 50.000 0.00 0.00 0.00 2.75
3248 3326 3.212685 CCTCCCATGATCTTTCTCTTGC 58.787 50.000 0.00 0.00 0.00 4.01
3251 3329 2.611292 CCCATGATCTTTCTCTTGCGAC 59.389 50.000 0.00 0.00 0.00 5.19
3256 3334 5.644977 TGATCTTTCTCTTGCGACTAAGA 57.355 39.130 0.00 0.00 35.51 2.10
3258 3336 7.334844 TGATCTTTCTCTTGCGACTAAGATA 57.665 36.000 0.00 0.00 36.21 1.98
3269 3347 9.594478 TCTTGCGACTAAGATAAAATGAATGTA 57.406 29.630 0.00 0.00 32.02 2.29
3278 3356 8.918202 AAGATAAAATGAATGTATTAGGGCGA 57.082 30.769 0.00 0.00 0.00 5.54
3279 3357 9.520515 AAGATAAAATGAATGTATTAGGGCGAT 57.479 29.630 0.00 0.00 0.00 4.58
3280 3358 8.950210 AGATAAAATGAATGTATTAGGGCGATG 58.050 33.333 0.00 0.00 0.00 3.84
3281 3359 5.376854 AAATGAATGTATTAGGGCGATGC 57.623 39.130 0.00 0.00 0.00 3.91
3291 3369 3.924507 GGCGATGCCTGAAACCAT 58.075 55.556 0.00 0.00 46.69 3.55
3292 3370 2.192605 GGCGATGCCTGAAACCATT 58.807 52.632 0.00 0.00 46.69 3.16
3293 3371 0.532115 GGCGATGCCTGAAACCATTT 59.468 50.000 0.00 0.00 46.69 2.32
3294 3372 1.632422 GCGATGCCTGAAACCATTTG 58.368 50.000 0.00 0.00 0.00 2.32
3295 3373 1.632422 CGATGCCTGAAACCATTTGC 58.368 50.000 0.00 0.00 0.00 3.68
3296 3374 1.736696 CGATGCCTGAAACCATTTGCC 60.737 52.381 0.00 0.00 0.00 4.52
3297 3375 1.275856 GATGCCTGAAACCATTTGCCA 59.724 47.619 0.00 0.00 0.00 4.92
3298 3376 1.126488 TGCCTGAAACCATTTGCCAA 58.874 45.000 0.00 0.00 0.00 4.52
3299 3377 1.698532 TGCCTGAAACCATTTGCCAAT 59.301 42.857 0.00 0.00 0.00 3.16
3300 3378 2.078392 GCCTGAAACCATTTGCCAATG 58.922 47.619 3.53 3.53 39.79 2.82
3301 3379 2.550639 GCCTGAAACCATTTGCCAATGT 60.551 45.455 9.45 0.00 38.58 2.71
3302 3380 3.068560 CCTGAAACCATTTGCCAATGTG 58.931 45.455 9.45 4.13 38.58 3.21
3303 3381 2.481185 CTGAAACCATTTGCCAATGTGC 59.519 45.455 9.45 0.00 38.58 4.57
3304 3382 2.104451 TGAAACCATTTGCCAATGTGCT 59.896 40.909 9.45 0.00 38.58 4.40
3305 3383 2.172851 AACCATTTGCCAATGTGCTG 57.827 45.000 9.45 0.00 38.58 4.41
3306 3384 0.320946 ACCATTTGCCAATGTGCTGC 60.321 50.000 9.45 0.00 38.58 5.25
3307 3385 0.320858 CCATTTGCCAATGTGCTGCA 60.321 50.000 9.45 0.00 38.58 4.41
3308 3386 1.075542 CATTTGCCAATGTGCTGCAG 58.924 50.000 10.11 10.11 35.86 4.41
3309 3387 0.036765 ATTTGCCAATGTGCTGCAGG 60.037 50.000 17.12 1.22 36.21 4.85
3310 3388 2.718747 TTTGCCAATGTGCTGCAGGC 62.719 55.000 20.13 20.13 45.41 4.85
3333 3411 6.829229 CATATGTGCATTATCTGGGATGTT 57.171 37.500 0.00 0.00 0.00 2.71
3334 3412 7.926674 CATATGTGCATTATCTGGGATGTTA 57.073 36.000 0.00 0.00 0.00 2.41
3335 3413 7.982224 CATATGTGCATTATCTGGGATGTTAG 58.018 38.462 0.00 0.00 0.00 2.34
3336 3414 5.628797 TGTGCATTATCTGGGATGTTAGA 57.371 39.130 0.00 0.00 0.00 2.10
3337 3415 6.191657 TGTGCATTATCTGGGATGTTAGAT 57.808 37.500 0.00 0.00 37.42 1.98
3338 3416 5.999600 TGTGCATTATCTGGGATGTTAGATG 59.000 40.000 0.00 0.00 35.42 2.90
3339 3417 6.000219 GTGCATTATCTGGGATGTTAGATGT 59.000 40.000 0.00 0.00 35.42 3.06
3340 3418 6.148480 GTGCATTATCTGGGATGTTAGATGTC 59.852 42.308 0.00 0.00 35.42 3.06
3341 3419 6.183361 TGCATTATCTGGGATGTTAGATGTCA 60.183 38.462 0.00 0.00 35.42 3.58
3342 3420 6.883217 GCATTATCTGGGATGTTAGATGTCAT 59.117 38.462 0.00 0.00 35.42 3.06
3343 3421 7.392673 GCATTATCTGGGATGTTAGATGTCATT 59.607 37.037 0.00 0.00 35.42 2.57
3344 3422 9.948964 CATTATCTGGGATGTTAGATGTCATTA 57.051 33.333 0.00 0.00 35.42 1.90
3349 3427 9.778741 TCTGGGATGTTAGATGTCATTATAAAC 57.221 33.333 0.00 0.00 0.00 2.01
3350 3428 9.784531 CTGGGATGTTAGATGTCATTATAAACT 57.215 33.333 0.00 0.00 0.00 2.66
3363 3441 9.139734 TGTCATTATAAACTATACTCCTTCCGT 57.860 33.333 0.00 0.00 0.00 4.69
3364 3442 9.978044 GTCATTATAAACTATACTCCTTCCGTT 57.022 33.333 0.00 0.00 0.00 4.44
3370 3448 9.955102 ATAAACTATACTCCTTCCGTTTCTTTT 57.045 29.630 0.00 0.00 0.00 2.27
3371 3449 8.687292 AAACTATACTCCTTCCGTTTCTTTTT 57.313 30.769 0.00 0.00 0.00 1.94
3372 3450 9.783081 AAACTATACTCCTTCCGTTTCTTTTTA 57.217 29.630 0.00 0.00 0.00 1.52
3373 3451 8.999220 ACTATACTCCTTCCGTTTCTTTTTAG 57.001 34.615 0.00 0.00 0.00 1.85
3374 3452 8.591940 ACTATACTCCTTCCGTTTCTTTTTAGT 58.408 33.333 0.00 0.00 0.00 2.24
3375 3453 7.902387 ATACTCCTTCCGTTTCTTTTTAGTC 57.098 36.000 0.00 0.00 0.00 2.59
3376 3454 5.926663 ACTCCTTCCGTTTCTTTTTAGTCT 58.073 37.500 0.00 0.00 0.00 3.24
3377 3455 5.758784 ACTCCTTCCGTTTCTTTTTAGTCTG 59.241 40.000 0.00 0.00 0.00 3.51
3378 3456 4.514066 TCCTTCCGTTTCTTTTTAGTCTGC 59.486 41.667 0.00 0.00 0.00 4.26
3379 3457 4.274950 CCTTCCGTTTCTTTTTAGTCTGCA 59.725 41.667 0.00 0.00 0.00 4.41
3380 3458 5.048713 CCTTCCGTTTCTTTTTAGTCTGCAT 60.049 40.000 0.00 0.00 0.00 3.96
3381 3459 6.148811 CCTTCCGTTTCTTTTTAGTCTGCATA 59.851 38.462 0.00 0.00 0.00 3.14
3382 3460 7.148239 CCTTCCGTTTCTTTTTAGTCTGCATAT 60.148 37.037 0.00 0.00 0.00 1.78
3383 3461 8.780846 TTCCGTTTCTTTTTAGTCTGCATATA 57.219 30.769 0.00 0.00 0.00 0.86
3384 3462 8.780846 TCCGTTTCTTTTTAGTCTGCATATAA 57.219 30.769 0.00 0.00 0.00 0.98
3385 3463 8.879759 TCCGTTTCTTTTTAGTCTGCATATAAG 58.120 33.333 0.00 0.00 0.00 1.73
3386 3464 8.879759 CCGTTTCTTTTTAGTCTGCATATAAGA 58.120 33.333 0.00 0.00 0.00 2.10
3394 3472 9.679661 TTTTAGTCTGCATATAAGATTTGGTCA 57.320 29.630 0.00 0.00 0.00 4.02
3395 3473 9.679661 TTTAGTCTGCATATAAGATTTGGTCAA 57.320 29.630 0.00 0.00 0.00 3.18
3396 3474 9.679661 TTAGTCTGCATATAAGATTTGGTCAAA 57.320 29.630 0.00 0.00 34.46 2.69
3397 3475 8.218338 AGTCTGCATATAAGATTTGGTCAAAG 57.782 34.615 2.55 0.00 33.32 2.77
3398 3476 7.831193 AGTCTGCATATAAGATTTGGTCAAAGT 59.169 33.333 2.55 0.00 33.32 2.66
3399 3477 8.125448 GTCTGCATATAAGATTTGGTCAAAGTC 58.875 37.037 2.55 1.51 33.32 3.01
3400 3478 7.828717 TCTGCATATAAGATTTGGTCAAAGTCA 59.171 33.333 2.55 0.00 33.32 3.41
3401 3479 8.347004 TGCATATAAGATTTGGTCAAAGTCAA 57.653 30.769 2.55 0.00 33.32 3.18
3402 3480 8.801299 TGCATATAAGATTTGGTCAAAGTCAAA 58.199 29.630 2.55 0.00 37.29 2.69
3403 3481 9.076596 GCATATAAGATTTGGTCAAAGTCAAAC 57.923 33.333 2.55 0.00 35.97 2.93
3433 3511 5.476091 AGTTTGACCAACTTTGTTGGAAA 57.524 34.783 29.19 20.71 43.89 3.13
3434 3512 5.859495 AGTTTGACCAACTTTGTTGGAAAA 58.141 33.333 29.19 23.90 43.89 2.29
3435 3513 6.292150 AGTTTGACCAACTTTGTTGGAAAAA 58.708 32.000 29.19 23.64 43.89 1.94
3553 3631 7.562454 TTTTTCTATGAACTCGGTCAAAGTT 57.438 32.000 0.00 0.00 39.61 2.66
3554 3632 6.539649 TTTCTATGAACTCGGTCAAAGTTG 57.460 37.500 0.00 0.00 37.10 3.16
3555 3633 5.462530 TCTATGAACTCGGTCAAAGTTGA 57.537 39.130 0.00 0.00 37.10 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 5.297547 AGATGTTGCGAAGTTTCTCTGTTA 58.702 37.500 0.00 0.00 0.00 2.41
17 18 4.142730 GGACATGTGAAGAAGAGATGTTGC 60.143 45.833 1.15 0.00 0.00 4.17
35 36 0.540365 CCACCCTTGCAACTGGACAT 60.540 55.000 15.48 0.00 0.00 3.06
94 95 8.116026 AGAAATATTGTCAAAGGTTATCAGGGT 58.884 33.333 0.00 0.00 0.00 4.34
110 111 9.686683 AAAGTATAGCACCAAGAGAAATATTGT 57.313 29.630 0.00 0.00 0.00 2.71
178 179 1.259142 CCACATGGCCCAGCAAATCA 61.259 55.000 0.00 0.00 0.00 2.57
428 434 1.073923 GAGGGAAAAGGCAGGTGAAGA 59.926 52.381 0.00 0.00 0.00 2.87
456 465 8.982685 CAAGTATCATTACACTAACAGCCATAG 58.017 37.037 0.00 0.00 0.00 2.23
690 713 3.699025 AGGAAACTGGAAAGGGGAAAA 57.301 42.857 0.00 0.00 41.13 2.29
786 811 2.561478 TCTAGTGCGAAGGGCTTTTT 57.439 45.000 0.00 0.00 44.05 1.94
787 812 2.427506 CTTCTAGTGCGAAGGGCTTTT 58.572 47.619 0.00 0.00 44.05 2.27
788 813 2.100605 CTTCTAGTGCGAAGGGCTTT 57.899 50.000 0.00 0.00 44.05 3.51
789 814 3.842869 CTTCTAGTGCGAAGGGCTT 57.157 52.632 0.00 0.00 44.05 4.35
794 819 1.808411 TTTGGCCTTCTAGTGCGAAG 58.192 50.000 3.32 0.00 40.01 3.79
795 820 2.264005 TTTTGGCCTTCTAGTGCGAA 57.736 45.000 3.32 0.00 0.00 4.70
796 821 2.151202 CTTTTTGGCCTTCTAGTGCGA 58.849 47.619 3.32 0.00 0.00 5.10
797 822 1.401539 GCTTTTTGGCCTTCTAGTGCG 60.402 52.381 3.32 0.00 0.00 5.34
798 823 2.354109 GCTTTTTGGCCTTCTAGTGC 57.646 50.000 3.32 0.00 0.00 4.40
808 833 1.298157 GCGGATTTGGGCTTTTTGGC 61.298 55.000 0.00 0.00 40.96 4.52
809 834 1.013524 CGCGGATTTGGGCTTTTTGG 61.014 55.000 0.00 0.00 0.00 3.28
810 835 1.625759 GCGCGGATTTGGGCTTTTTG 61.626 55.000 8.83 0.00 43.75 2.44
811 836 1.374125 GCGCGGATTTGGGCTTTTT 60.374 52.632 8.83 0.00 43.75 1.94
812 837 2.261361 GCGCGGATTTGGGCTTTT 59.739 55.556 8.83 0.00 43.75 2.27
813 838 2.988684 TGCGCGGATTTGGGCTTT 60.989 55.556 8.83 0.00 46.86 3.51
814 839 3.747976 GTGCGCGGATTTGGGCTT 61.748 61.111 8.83 0.00 46.86 4.35
817 842 3.202001 ATCGTGCGCGGATTTGGG 61.202 61.111 21.04 0.00 38.89 4.12
818 843 2.023181 CATCGTGCGCGGATTTGG 59.977 61.111 21.04 0.00 38.89 3.28
819 844 1.296867 GTCATCGTGCGCGGATTTG 60.297 57.895 21.04 12.39 38.89 2.32
820 845 2.461110 GGTCATCGTGCGCGGATTT 61.461 57.895 21.04 0.00 38.89 2.17
821 846 2.890474 GGTCATCGTGCGCGGATT 60.890 61.111 21.04 2.11 38.89 3.01
825 850 3.682315 GATCGGTCATCGTGCGCG 61.682 66.667 14.79 14.79 40.32 6.86
826 851 3.330853 GGATCGGTCATCGTGCGC 61.331 66.667 0.00 0.00 40.32 6.09
827 852 1.278172 GATGGATCGGTCATCGTGCG 61.278 60.000 0.00 0.00 40.32 5.34
828 853 0.946221 GGATGGATCGGTCATCGTGC 60.946 60.000 0.00 0.00 41.24 5.34
829 854 0.389025 TGGATGGATCGGTCATCGTG 59.611 55.000 0.00 0.00 41.24 4.35
830 855 1.119684 TTGGATGGATCGGTCATCGT 58.880 50.000 0.00 0.00 41.24 3.73
831 856 1.867233 GTTTGGATGGATCGGTCATCG 59.133 52.381 0.00 0.00 41.24 3.84
832 857 2.222027 GGTTTGGATGGATCGGTCATC 58.778 52.381 0.00 1.66 40.02 2.92
833 858 1.475034 CGGTTTGGATGGATCGGTCAT 60.475 52.381 0.00 0.00 0.00 3.06
834 859 0.107897 CGGTTTGGATGGATCGGTCA 60.108 55.000 0.00 0.00 0.00 4.02
835 860 0.177141 TCGGTTTGGATGGATCGGTC 59.823 55.000 0.00 0.00 0.00 4.79
836 861 0.107848 GTCGGTTTGGATGGATCGGT 60.108 55.000 0.00 0.00 0.00 4.69
837 862 0.107897 TGTCGGTTTGGATGGATCGG 60.108 55.000 0.00 0.00 0.00 4.18
838 863 1.867233 GATGTCGGTTTGGATGGATCG 59.133 52.381 0.00 0.00 0.00 3.69
839 864 1.867233 CGATGTCGGTTTGGATGGATC 59.133 52.381 0.00 0.00 35.37 3.36
840 865 1.484653 TCGATGTCGGTTTGGATGGAT 59.515 47.619 2.25 0.00 40.29 3.41
841 866 0.899019 TCGATGTCGGTTTGGATGGA 59.101 50.000 2.25 0.00 40.29 3.41
848 873 0.608640 AGGCTTCTCGATGTCGGTTT 59.391 50.000 2.25 0.00 40.29 3.27
911 936 3.576356 GCGATGGATGCGTGTGGG 61.576 66.667 0.00 0.00 0.00 4.61
918 943 1.136695 TGGGAAATTTGCGATGGATGC 59.863 47.619 3.43 0.00 0.00 3.91
934 959 3.624707 CGATTTGGGGAAAAGAGATGGGA 60.625 47.826 0.00 0.00 0.00 4.37
939 964 4.270008 GGATTCGATTTGGGGAAAAGAGA 58.730 43.478 0.00 0.00 0.00 3.10
944 969 1.359474 TGGGGATTCGATTTGGGGAAA 59.641 47.619 0.00 0.00 0.00 3.13
987 1014 4.124351 GACATGGCGACCGACGGA 62.124 66.667 23.38 0.00 42.83 4.69
988 1015 4.129737 AGACATGGCGACCGACGG 62.130 66.667 13.61 13.61 42.83 4.79
989 1016 2.579787 GAGACATGGCGACCGACG 60.580 66.667 0.00 0.00 45.66 5.12
1284 1347 0.249120 CACGCTCATTGTGGTAGGGA 59.751 55.000 0.00 0.00 33.69 4.20
1422 1485 3.620300 CTTGACGCGGCGGTACTCA 62.620 63.158 27.37 17.64 0.00 3.41
1575 1644 1.336440 ACATCGCTCTTCTCGGATGAG 59.664 52.381 6.85 10.49 43.99 2.90
1581 1650 0.248825 CCTCCACATCGCTCTTCTCG 60.249 60.000 0.00 0.00 0.00 4.04
1595 1664 1.257743 CGAGTCCTTGTTCTCCTCCA 58.742 55.000 0.00 0.00 0.00 3.86
1611 1680 3.928343 GGACTCAGATTCCGACGAG 57.072 57.895 0.00 0.00 0.00 4.18
1700 1769 1.937108 GCTTGCTGCTAGAACGTCTGT 60.937 52.381 15.16 0.00 38.95 3.41
1728 1797 2.019951 GTGGCGACGATGTGAACGT 61.020 57.895 0.00 0.00 46.58 3.99
1732 1801 1.811645 TTCCTGTGGCGACGATGTGA 61.812 55.000 0.00 0.00 0.00 3.58
1734 1803 1.079819 CTTCCTGTGGCGACGATGT 60.080 57.895 0.00 0.00 0.00 3.06
1785 1854 2.774234 GGAACCCTCTGAATCCTCATCA 59.226 50.000 0.00 0.00 0.00 3.07
1958 2027 1.271102 CCGTTGAGATAGGGCTAGAGC 59.729 57.143 0.00 0.00 41.14 4.09
1991 2060 1.825474 TCTTCCTTGAGCTCTTACCCG 59.175 52.381 16.19 0.00 0.00 5.28
1995 2064 5.126384 GCTACTCTTCTTCCTTGAGCTCTTA 59.874 44.000 16.19 1.96 0.00 2.10
2047 2116 5.043737 TCATCAATGATGGCATCAGAAGA 57.956 39.130 31.39 26.60 43.53 2.87
2097 2166 1.661463 TTGCCTCTGGGTCAATCTCT 58.339 50.000 0.00 0.00 34.45 3.10
2160 2229 1.134280 CCAACCGGCATCTCATTCTCT 60.134 52.381 0.00 0.00 0.00 3.10
2238 2307 0.452987 CAATGGCATCACCTTCACCG 59.547 55.000 0.00 0.00 40.22 4.94
2262 2331 1.070758 CGCTTCCCCTGCTGTACATAT 59.929 52.381 0.00 0.00 0.00 1.78
2436 2505 2.351726 CTCGTAGTTAAACATGGCCAGC 59.648 50.000 13.05 0.00 0.00 4.85
2610 2679 8.190784 ACAGGAAAAACATGCATAACTAATAGC 58.809 33.333 0.00 0.00 33.22 2.97
2637 2706 2.555325 CGTCACTGGTACTACAGGAACA 59.445 50.000 4.45 0.00 42.75 3.18
2638 2707 2.555757 ACGTCACTGGTACTACAGGAAC 59.444 50.000 4.45 1.70 42.75 3.62
2639 2708 2.816087 GACGTCACTGGTACTACAGGAA 59.184 50.000 11.55 0.00 42.75 3.36
2640 2709 2.430465 GACGTCACTGGTACTACAGGA 58.570 52.381 11.55 0.00 42.75 3.86
2641 2710 1.129998 CGACGTCACTGGTACTACAGG 59.870 57.143 17.16 0.00 42.75 4.00
2642 2711 2.071540 TCGACGTCACTGGTACTACAG 58.928 52.381 17.16 0.00 44.03 2.74
2643 2712 2.071540 CTCGACGTCACTGGTACTACA 58.928 52.381 17.16 0.00 0.00 2.74
2644 2713 2.072298 ACTCGACGTCACTGGTACTAC 58.928 52.381 17.16 0.00 0.00 2.73
2645 2714 2.462456 ACTCGACGTCACTGGTACTA 57.538 50.000 17.16 0.00 0.00 1.82
2651 2720 1.139989 ATGCAAACTCGACGTCACTG 58.860 50.000 17.16 7.11 0.00 3.66
2657 2726 4.523813 AGTTACAAAATGCAAACTCGACG 58.476 39.130 0.00 0.00 0.00 5.12
2740 2811 7.211573 ACAAACATCACAACAATCATGAACAT 58.788 30.769 0.00 0.00 0.00 2.71
2757 2828 3.631145 TCAAGCAGCTTGACAAACATC 57.369 42.857 30.44 0.00 44.27 3.06
2810 2881 7.934855 ATGGTCATTCTATCTTATCATTGCC 57.065 36.000 0.00 0.00 0.00 4.52
2840 2914 3.068024 TCACACTCACAAATCCCAAAAGC 59.932 43.478 0.00 0.00 0.00 3.51
2846 2921 3.882888 TGTCTTTCACACTCACAAATCCC 59.117 43.478 0.00 0.00 0.00 3.85
2848 2923 5.741388 ACTGTCTTTCACACTCACAAATC 57.259 39.130 0.00 0.00 0.00 2.17
2853 2928 4.683832 ACTGTACTGTCTTTCACACTCAC 58.316 43.478 0.00 0.00 0.00 3.51
2857 2932 3.621268 TGCAACTGTACTGTCTTTCACAC 59.379 43.478 5.81 0.00 0.00 3.82
2876 2951 9.791801 TGATCCTAAACAATATAAGCTTATGCA 57.208 29.630 25.99 10.03 42.74 3.96
2881 2956 8.930846 ATGCTGATCCTAAACAATATAAGCTT 57.069 30.769 3.48 3.48 28.70 3.74
2882 2957 8.790718 CAATGCTGATCCTAAACAATATAAGCT 58.209 33.333 0.00 0.00 28.70 3.74
2883 2958 8.571336 ACAATGCTGATCCTAAACAATATAAGC 58.429 33.333 0.00 0.00 0.00 3.09
2904 2979 5.350633 CACCCCTTGCATGTTATAACAATG 58.649 41.667 21.57 18.78 43.03 2.82
2939 3014 1.691196 CAAGTGCCAAAGAAGACCCA 58.309 50.000 0.00 0.00 0.00 4.51
2960 3035 8.499162 CGGATAGCGAAGATTTATTCAAAATCT 58.501 33.333 7.08 7.08 45.87 2.40
2966 3041 6.277605 TGTTCGGATAGCGAAGATTTATTCA 58.722 36.000 0.00 0.00 0.00 2.57
2967 3042 6.641314 TCTGTTCGGATAGCGAAGATTTATTC 59.359 38.462 0.00 0.00 0.00 1.75
2979 3054 7.302524 TGTTAACAAAATTCTGTTCGGATAGC 58.697 34.615 5.64 0.00 40.08 2.97
3023 3099 5.087323 TCCGCCTATGATCTTAGGAGAAAT 58.913 41.667 29.86 0.81 40.47 2.17
3027 3103 4.950475 TGTATCCGCCTATGATCTTAGGAG 59.050 45.833 29.86 26.60 41.18 3.69
3042 3118 5.106555 CCACATAAGGATCAAATGTATCCGC 60.107 44.000 6.52 0.00 46.37 5.54
3043 3119 5.106555 GCCACATAAGGATCAAATGTATCCG 60.107 44.000 6.52 0.00 46.37 4.18
3045 3121 6.882610 TGCCACATAAGGATCAAATGTATC 57.117 37.500 6.52 3.67 32.70 2.24
3048 3124 6.549433 AATTGCCACATAAGGATCAAATGT 57.451 33.333 0.00 0.00 34.22 2.71
3063 3139 8.244113 AGTCAAGCTAAACTAAATAATTGCCAC 58.756 33.333 0.00 0.00 0.00 5.01
3064 3140 8.243426 CAGTCAAGCTAAACTAAATAATTGCCA 58.757 33.333 0.91 0.00 0.00 4.92
3066 3142 8.458843 TCCAGTCAAGCTAAACTAAATAATTGC 58.541 33.333 0.91 0.00 0.00 3.56
3082 3158 2.698855 TCCAAGCTATCCAGTCAAGC 57.301 50.000 0.00 0.00 36.48 4.01
3083 3159 3.390639 AGGATCCAAGCTATCCAGTCAAG 59.609 47.826 15.82 0.00 44.62 3.02
3175 3252 9.868277 GATGACAATAACCATTTGAATTAACCA 57.132 29.630 0.00 0.00 0.00 3.67
3176 3253 9.868277 TGATGACAATAACCATTTGAATTAACC 57.132 29.630 0.00 0.00 0.00 2.85
3185 3262 6.009589 TGACAGGTGATGACAATAACCATTT 58.990 36.000 7.17 0.00 39.63 2.32
3186 3263 5.569355 TGACAGGTGATGACAATAACCATT 58.431 37.500 7.17 0.00 39.63 3.16
3195 3272 6.713762 AATTTTTCTTGACAGGTGATGACA 57.286 33.333 0.00 0.00 0.00 3.58
3197 3274 9.528018 GTTTTAATTTTTCTTGACAGGTGATGA 57.472 29.630 0.00 0.00 0.00 2.92
3198 3275 9.533253 AGTTTTAATTTTTCTTGACAGGTGATG 57.467 29.630 0.00 0.00 0.00 3.07
3205 3282 6.883744 AGGGCAGTTTTAATTTTTCTTGACA 58.116 32.000 0.00 0.00 0.00 3.58
3208 3285 5.700832 GGGAGGGCAGTTTTAATTTTTCTTG 59.299 40.000 0.00 0.00 0.00 3.02
3213 3290 4.843516 TCATGGGAGGGCAGTTTTAATTTT 59.156 37.500 0.00 0.00 0.00 1.82
3214 3291 4.424842 TCATGGGAGGGCAGTTTTAATTT 58.575 39.130 0.00 0.00 0.00 1.82
3215 3292 4.059773 TCATGGGAGGGCAGTTTTAATT 57.940 40.909 0.00 0.00 0.00 1.40
3216 3293 3.756082 TCATGGGAGGGCAGTTTTAAT 57.244 42.857 0.00 0.00 0.00 1.40
3217 3294 3.269381 AGATCATGGGAGGGCAGTTTTAA 59.731 43.478 0.00 0.00 0.00 1.52
3218 3295 2.852449 AGATCATGGGAGGGCAGTTTTA 59.148 45.455 0.00 0.00 0.00 1.52
3219 3296 1.642762 AGATCATGGGAGGGCAGTTTT 59.357 47.619 0.00 0.00 0.00 2.43
3220 3297 1.302907 AGATCATGGGAGGGCAGTTT 58.697 50.000 0.00 0.00 0.00 2.66
3221 3298 1.302907 AAGATCATGGGAGGGCAGTT 58.697 50.000 0.00 0.00 0.00 3.16
3228 3305 2.871022 CGCAAGAGAAAGATCATGGGAG 59.129 50.000 0.00 0.00 43.02 4.30
3256 3334 7.362920 GGCATCGCCCTAATACATTCATTTTAT 60.363 37.037 0.00 0.00 44.06 1.40
3258 3336 5.278957 GGCATCGCCCTAATACATTCATTTT 60.279 40.000 0.00 0.00 44.06 1.82
3275 3353 1.632422 CAAATGGTTTCAGGCATCGC 58.368 50.000 0.00 0.00 0.00 4.58
3276 3354 1.632422 GCAAATGGTTTCAGGCATCG 58.368 50.000 0.00 0.00 0.00 3.84
3277 3355 1.275856 TGGCAAATGGTTTCAGGCATC 59.724 47.619 0.00 0.00 0.00 3.91
3278 3356 1.350071 TGGCAAATGGTTTCAGGCAT 58.650 45.000 0.00 0.00 0.00 4.40
3279 3357 1.126488 TTGGCAAATGGTTTCAGGCA 58.874 45.000 0.00 0.00 0.00 4.75
3280 3358 2.078392 CATTGGCAAATGGTTTCAGGC 58.922 47.619 3.01 0.00 39.69 4.85
3281 3359 3.068560 CACATTGGCAAATGGTTTCAGG 58.931 45.455 18.12 0.00 46.34 3.86
3282 3360 2.481185 GCACATTGGCAAATGGTTTCAG 59.519 45.455 18.12 2.28 46.34 3.02
3283 3361 2.104451 AGCACATTGGCAAATGGTTTCA 59.896 40.909 18.12 0.00 46.34 2.69
3284 3362 2.481185 CAGCACATTGGCAAATGGTTTC 59.519 45.455 18.12 4.15 46.34 2.78
3285 3363 2.496111 CAGCACATTGGCAAATGGTTT 58.504 42.857 18.12 0.00 46.34 3.27
3286 3364 1.878948 GCAGCACATTGGCAAATGGTT 60.879 47.619 18.12 2.69 46.34 3.67
3287 3365 0.320946 GCAGCACATTGGCAAATGGT 60.321 50.000 18.12 8.89 46.34 3.55
3288 3366 0.320858 TGCAGCACATTGGCAAATGG 60.321 50.000 18.12 8.14 46.34 3.16
3290 3368 0.036765 CCTGCAGCACATTGGCAAAT 60.037 50.000 8.66 0.00 37.06 2.32
3291 3369 1.368209 CCTGCAGCACATTGGCAAA 59.632 52.632 8.66 0.00 37.06 3.68
3292 3370 3.052954 CCTGCAGCACATTGGCAA 58.947 55.556 8.66 0.68 37.06 4.52
3293 3371 3.687102 GCCTGCAGCACATTGGCA 61.687 61.111 16.64 0.00 39.02 4.92
3310 3388 6.829229 AACATCCCAGATAATGCACATATG 57.171 37.500 0.00 0.00 0.00 1.78
3311 3389 7.921304 TCTAACATCCCAGATAATGCACATAT 58.079 34.615 0.00 0.00 0.00 1.78
3312 3390 7.315066 TCTAACATCCCAGATAATGCACATA 57.685 36.000 0.00 0.00 0.00 2.29
3313 3391 6.191657 TCTAACATCCCAGATAATGCACAT 57.808 37.500 0.00 0.00 0.00 3.21
3314 3392 5.628797 TCTAACATCCCAGATAATGCACA 57.371 39.130 0.00 0.00 0.00 4.57
3315 3393 6.000219 ACATCTAACATCCCAGATAATGCAC 59.000 40.000 0.00 0.00 30.32 4.57
3316 3394 6.183361 TGACATCTAACATCCCAGATAATGCA 60.183 38.462 0.00 0.00 30.32 3.96
3317 3395 6.233434 TGACATCTAACATCCCAGATAATGC 58.767 40.000 0.00 0.00 30.32 3.56
3318 3396 8.859236 AATGACATCTAACATCCCAGATAATG 57.141 34.615 0.00 0.00 30.32 1.90
3323 3401 9.778741 GTTTATAATGACATCTAACATCCCAGA 57.221 33.333 0.00 0.00 0.00 3.86
3324 3402 9.784531 AGTTTATAATGACATCTAACATCCCAG 57.215 33.333 0.00 0.00 0.00 4.45
3337 3415 9.139734 ACGGAAGGAGTATAGTTTATAATGACA 57.860 33.333 0.00 0.00 0.00 3.58
3338 3416 9.978044 AACGGAAGGAGTATAGTTTATAATGAC 57.022 33.333 0.00 0.00 0.00 3.06
3344 3422 9.955102 AAAAGAAACGGAAGGAGTATAGTTTAT 57.045 29.630 0.00 0.00 32.79 1.40
3345 3423 9.783081 AAAAAGAAACGGAAGGAGTATAGTTTA 57.217 29.630 0.00 0.00 32.79 2.01
3346 3424 8.687292 AAAAAGAAACGGAAGGAGTATAGTTT 57.313 30.769 0.00 0.00 34.95 2.66
3347 3425 9.433153 CTAAAAAGAAACGGAAGGAGTATAGTT 57.567 33.333 0.00 0.00 0.00 2.24
3348 3426 8.591940 ACTAAAAAGAAACGGAAGGAGTATAGT 58.408 33.333 0.00 0.00 0.00 2.12
3349 3427 8.999220 ACTAAAAAGAAACGGAAGGAGTATAG 57.001 34.615 0.00 0.00 0.00 1.31
3350 3428 8.810041 AGACTAAAAAGAAACGGAAGGAGTATA 58.190 33.333 0.00 0.00 0.00 1.47
3351 3429 7.603024 CAGACTAAAAAGAAACGGAAGGAGTAT 59.397 37.037 0.00 0.00 0.00 2.12
3352 3430 6.927381 CAGACTAAAAAGAAACGGAAGGAGTA 59.073 38.462 0.00 0.00 0.00 2.59
3353 3431 5.758784 CAGACTAAAAAGAAACGGAAGGAGT 59.241 40.000 0.00 0.00 0.00 3.85
3354 3432 5.334182 GCAGACTAAAAAGAAACGGAAGGAG 60.334 44.000 0.00 0.00 0.00 3.69
3355 3433 4.514066 GCAGACTAAAAAGAAACGGAAGGA 59.486 41.667 0.00 0.00 0.00 3.36
3356 3434 4.274950 TGCAGACTAAAAAGAAACGGAAGG 59.725 41.667 0.00 0.00 0.00 3.46
3357 3435 5.418310 TGCAGACTAAAAAGAAACGGAAG 57.582 39.130 0.00 0.00 0.00 3.46
3358 3436 7.681939 ATATGCAGACTAAAAAGAAACGGAA 57.318 32.000 0.00 0.00 0.00 4.30
3359 3437 8.780846 TTATATGCAGACTAAAAAGAAACGGA 57.219 30.769 0.00 0.00 0.00 4.69
3360 3438 8.879759 TCTTATATGCAGACTAAAAAGAAACGG 58.120 33.333 0.00 0.00 0.00 4.44
3368 3446 9.679661 TGACCAAATCTTATATGCAGACTAAAA 57.320 29.630 0.00 0.00 0.00 1.52
3369 3447 9.679661 TTGACCAAATCTTATATGCAGACTAAA 57.320 29.630 0.00 0.00 0.00 1.85
3370 3448 9.679661 TTTGACCAAATCTTATATGCAGACTAA 57.320 29.630 0.00 0.00 0.00 2.24
3371 3449 9.330063 CTTTGACCAAATCTTATATGCAGACTA 57.670 33.333 0.00 0.00 0.00 2.59
3372 3450 7.831193 ACTTTGACCAAATCTTATATGCAGACT 59.169 33.333 0.00 0.00 0.00 3.24
3373 3451 7.989826 ACTTTGACCAAATCTTATATGCAGAC 58.010 34.615 0.00 0.00 0.00 3.51
3374 3452 7.828717 TGACTTTGACCAAATCTTATATGCAGA 59.171 33.333 0.00 0.00 0.00 4.26
3375 3453 7.988737 TGACTTTGACCAAATCTTATATGCAG 58.011 34.615 0.00 0.00 0.00 4.41
3376 3454 7.936496 TGACTTTGACCAAATCTTATATGCA 57.064 32.000 0.00 0.00 0.00 3.96
3377 3455 9.076596 GTTTGACTTTGACCAAATCTTATATGC 57.923 33.333 0.00 0.00 35.14 3.14
3412 3490 6.546972 TTTTTCCAACAAAGTTGGTCAAAC 57.453 33.333 23.74 0.00 40.40 2.93
3529 3607 7.281324 TCAACTTTGACCGAGTTCATAGAAAAA 59.719 33.333 6.25 0.00 35.26 1.94
3530 3608 6.764085 TCAACTTTGACCGAGTTCATAGAAAA 59.236 34.615 6.25 0.00 35.26 2.29
3531 3609 6.285224 TCAACTTTGACCGAGTTCATAGAAA 58.715 36.000 6.25 0.00 35.26 2.52
3532 3610 5.849510 TCAACTTTGACCGAGTTCATAGAA 58.150 37.500 6.25 0.00 35.26 2.10
3533 3611 5.462530 TCAACTTTGACCGAGTTCATAGA 57.537 39.130 6.25 0.00 35.26 1.98
3543 3621 8.468381 AAAGTCAAACTTTGTCAACTTTGACCG 61.468 37.037 26.67 9.64 45.83 4.79
3544 3622 6.645003 AAAGTCAAACTTTGTCAACTTTGACC 59.355 34.615 26.67 17.24 45.83 4.02
3545 3623 7.637709 AAAGTCAAACTTTGTCAACTTTGAC 57.362 32.000 24.90 24.90 45.83 3.18


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

AutoCloner maintained by Alex Coulton.