Multiple sequence alignment - TraesCS3B01G457900

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 TraesCS3B01G457900 chr3B 100.000 3922 0 0 1 3922 700357851 700361772 0.000000e+00 7243
1 TraesCS3B01G457900 chr3B 88.889 729 69 4 2 730 806110855 806111571 0.000000e+00 887
2 TraesCS3B01G457900 chr3D 92.768 2005 105 26 729 2721 529770181 529772157 0.000000e+00 2863
3 TraesCS3B01G457900 chr3D 91.233 730 62 2 2 730 64113234 64113962 0.000000e+00 992
4 TraesCS3B01G457900 chr3D 90.685 730 67 1 2 730 564488184 564487455 0.000000e+00 970
5 TraesCS3B01G457900 chr3D 91.721 616 37 10 742 1355 529756671 529757274 0.000000e+00 843
6 TraesCS3B01G457900 chr3D 83.603 866 69 27 3113 3921 529772541 529773390 0.000000e+00 745
7 TraesCS3B01G457900 chr3D 92.430 251 13 5 2719 2966 529772200 529772447 1.730000e-93 353
8 TraesCS3B01G457900 chr7B 96.443 731 24 2 2 730 78063948 78064678 0.000000e+00 1205
9 TraesCS3B01G457900 chr7B 95.115 737 33 3 2 735 196017782 196018518 0.000000e+00 1158
10 TraesCS3B01G457900 chr6B 95.342 730 33 1 2 730 712987871 712987142 0.000000e+00 1158
11 TraesCS3B01G457900 chr3A 91.354 694 46 7 1078 1766 663574394 663575078 0.000000e+00 937
12 TraesCS3B01G457900 chr3A 79.571 793 95 37 1963 2721 663575451 663576210 4.520000e-139 505
13 TraesCS3B01G457900 chr3A 92.334 287 11 6 729 1007 663573455 663573738 7.900000e-107 398
14 TraesCS3B01G457900 chr3A 79.832 238 25 13 2719 2940 663576253 663576483 6.790000e-33 152
15 TraesCS3B01G457900 chr3A 75.460 326 49 22 3396 3692 131461106 131460783 3.180000e-26 130
16 TraesCS3B01G457900 chr2D 90.714 700 64 1 2 700 595411655 595410956 0.000000e+00 931
17 TraesCS3B01G457900 chr7D 91.199 659 58 0 71 729 612408165 612408823 0.000000e+00 896
18 TraesCS3B01G457900 chr7D 80.925 173 32 1 3379 3551 245470667 245470838 6.840000e-28 135
19 TraesCS3B01G457900 chr1A 82.177 735 122 9 2 730 398128243 398127512 1.200000e-174 623
20 TraesCS3B01G457900 chr1A 82.184 174 27 4 3379 3551 477768030 477768200 3.160000e-31 147
21 TraesCS3B01G457900 chr5A 84.393 173 25 2 3379 3551 42115328 42115498 6.740000e-38 169
22 TraesCS3B01G457900 chr1D 82.143 196 24 9 3549 3735 33601543 33601350 1.460000e-34 158
23 TraesCS3B01G457900 chr1D 82.759 174 27 3 3379 3551 377201057 377201228 6.790000e-33 152
24 TraesCS3B01G457900 chr1D 74.384 406 64 24 3382 3752 377205074 377205474 1.900000e-28 137
25 TraesCS3B01G457900 chr1D 79.878 164 31 2 3379 3542 460184037 460184198 6.880000e-23 119
26 TraesCS3B01G457900 chr1D 79.532 171 28 7 3385 3551 33601735 33601568 8.910000e-22 115
27 TraesCS3B01G457900 chr7A 81.928 166 27 3 3387 3551 261825291 261825454 1.900000e-28 137
28 TraesCS3B01G457900 chr5B 83.673 147 19 4 3549 3692 666799330 666799186 2.460000e-27 134
29 TraesCS3B01G457900 chr5B 82.993 147 20 4 3549 3692 666824418 666824274 1.140000e-25 128


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 TraesCS3B01G457900 chr3B 700357851 700361772 3921 False 7243.000000 7243 100.000000 1 3922 1 chr3B.!!$F1 3921
1 TraesCS3B01G457900 chr3B 806110855 806111571 716 False 887.000000 887 88.889000 2 730 1 chr3B.!!$F2 728
2 TraesCS3B01G457900 chr3D 529770181 529773390 3209 False 1320.333333 2863 89.600333 729 3921 3 chr3D.!!$F3 3192
3 TraesCS3B01G457900 chr3D 64113234 64113962 728 False 992.000000 992 91.233000 2 730 1 chr3D.!!$F1 728
4 TraesCS3B01G457900 chr3D 564487455 564488184 729 True 970.000000 970 90.685000 2 730 1 chr3D.!!$R1 728
5 TraesCS3B01G457900 chr3D 529756671 529757274 603 False 843.000000 843 91.721000 742 1355 1 chr3D.!!$F2 613
6 TraesCS3B01G457900 chr7B 78063948 78064678 730 False 1205.000000 1205 96.443000 2 730 1 chr7B.!!$F1 728
7 TraesCS3B01G457900 chr7B 196017782 196018518 736 False 1158.000000 1158 95.115000 2 735 1 chr7B.!!$F2 733
8 TraesCS3B01G457900 chr6B 712987142 712987871 729 True 1158.000000 1158 95.342000 2 730 1 chr6B.!!$R1 728
9 TraesCS3B01G457900 chr3A 663573455 663576483 3028 False 498.000000 937 85.772750 729 2940 4 chr3A.!!$F1 2211
10 TraesCS3B01G457900 chr2D 595410956 595411655 699 True 931.000000 931 90.714000 2 700 1 chr2D.!!$R1 698
11 TraesCS3B01G457900 chr7D 612408165 612408823 658 False 896.000000 896 91.199000 71 729 1 chr7D.!!$F2 658
12 TraesCS3B01G457900 chr1A 398127512 398128243 731 True 623.000000 623 82.177000 2 730 1 chr1A.!!$R1 728

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
127 129 0.330604 AGTACGAGCCTGGTAGGTCA 59.669 55.0 0.0 0.0 37.8 4.02 F
1488 2093 0.250513 CCCTGTCCTCTGGTTGCTAC 59.749 60.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1802 2480 0.761187 GATCATCAGTAGCCCAGGCA 59.239 55.0 12.03 0.0 44.88 4.75 R
3009 3889 0.100503 GCGTGCCTTTGAACTGTGTT 59.899 50.0 0.00 0.0 0.00 3.32 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
54 55 1.224069 CGAGCCGCCACCATTATCTG 61.224 60.000 0.00 0.00 0.00 2.90
113 115 2.764572 ACCCATGAGGAGGTTAAGTACG 59.235 50.000 7.17 0.00 39.89 3.67
127 129 0.330604 AGTACGAGCCTGGTAGGTCA 59.669 55.000 0.00 0.00 37.80 4.02
248 250 2.514803 GCTGGGTAAAGGTGAACACAT 58.485 47.619 7.25 0.00 0.00 3.21
271 273 1.814394 GCTGCTGTTGATGTGAATGGA 59.186 47.619 0.00 0.00 0.00 3.41
527 532 8.618702 AATCAGCGAAATCAAATCATATCTCT 57.381 30.769 0.00 0.00 0.00 3.10
772 778 1.609208 TGTTTTCTTGGAGAGCAGGC 58.391 50.000 0.00 0.00 0.00 4.85
781 787 1.682257 GAGAGCAGGCCAAGGAGTT 59.318 57.895 5.01 0.00 0.00 3.01
978 993 1.287038 CCCCCTCCTCTTAAACCCCC 61.287 65.000 0.00 0.00 0.00 5.40
979 994 0.551624 CCCCTCCTCTTAAACCCCCA 60.552 60.000 0.00 0.00 0.00 4.96
980 995 1.378732 CCCTCCTCTTAAACCCCCAA 58.621 55.000 0.00 0.00 0.00 4.12
997 1019 1.151361 AACCCCCACTCCCCATTCT 60.151 57.895 0.00 0.00 0.00 2.40
1052 1074 3.936535 CCTCCAGAGGTACGTCCC 58.063 66.667 11.83 0.00 43.61 4.46
1112 1712 1.043116 ATCTGGCCTTGATCCGTCGA 61.043 55.000 3.32 0.00 0.00 4.20
1157 1757 7.925993 TGTTGGTTGTTGTTATTAGTCTGAAG 58.074 34.615 0.00 0.00 0.00 3.02
1179 1779 1.121407 TGGATCGATTGGCGGAGGAT 61.121 55.000 0.00 0.00 41.33 3.24
1194 1794 1.047034 AGGATCGGGTAGGGTTTCGG 61.047 60.000 0.00 0.00 0.00 4.30
1233 1837 3.602483 TCTAATTCGTGTGGGTTTAGGC 58.398 45.455 0.00 0.00 0.00 3.93
1241 1845 1.276989 TGTGGGTTTAGGCGTTAGAGG 59.723 52.381 0.00 0.00 0.00 3.69
1315 1919 1.195442 TCATGGGAGTACGGGTTGCA 61.195 55.000 0.00 0.00 0.00 4.08
1325 1929 1.164041 ACGGGTTGCAAGTTTCGGAG 61.164 55.000 0.00 0.00 0.00 4.63
1353 1957 1.338105 CGTGCTGTTCTTGGGATCTCA 60.338 52.381 0.00 0.00 0.00 3.27
1378 1982 0.474184 AATTAGGCGGGATGGTCTGG 59.526 55.000 0.00 0.00 0.00 3.86
1400 2004 7.770433 TCTGGTCTGTTGGATTAATCTGTTATG 59.230 37.037 14.95 2.82 0.00 1.90
1430 2034 7.927092 GGAGTATATTGTGTTTCTAGGGAGTTC 59.073 40.741 0.00 0.00 0.00 3.01
1447 2051 4.473199 GAGTTCGCACCAGTAAAAATTCC 58.527 43.478 0.00 0.00 0.00 3.01
1450 2054 5.068591 AGTTCGCACCAGTAAAAATTCCTTT 59.931 36.000 0.00 0.00 0.00 3.11
1473 2077 5.452078 TTTGTTTAGAAATCTGTGCCCTG 57.548 39.130 0.00 0.00 0.00 4.45
1485 2090 2.360475 GCCCTGTCCTCTGGTTGC 60.360 66.667 0.00 0.00 0.00 4.17
1486 2091 2.900106 GCCCTGTCCTCTGGTTGCT 61.900 63.158 0.00 0.00 0.00 3.91
1487 2092 1.553690 GCCCTGTCCTCTGGTTGCTA 61.554 60.000 0.00 0.00 0.00 3.49
1488 2093 0.250513 CCCTGTCCTCTGGTTGCTAC 59.749 60.000 0.00 0.00 0.00 3.58
1494 2099 2.047061 TCCTCTGGTTGCTACTGTGTT 58.953 47.619 0.00 0.00 0.00 3.32
1501 2106 2.224784 GGTTGCTACTGTGTTTAACCCG 59.775 50.000 0.00 0.00 33.27 5.28
1507 2112 2.725637 ACTGTGTTTAACCCGGTTTGT 58.274 42.857 8.44 0.00 0.00 2.83
1522 2127 1.262417 GTTTGTCCCTTCGGTTCGTTC 59.738 52.381 0.00 0.00 0.00 3.95
1523 2128 0.754472 TTGTCCCTTCGGTTCGTTCT 59.246 50.000 0.00 0.00 0.00 3.01
1524 2129 0.316204 TGTCCCTTCGGTTCGTTCTC 59.684 55.000 0.00 0.00 0.00 2.87
1525 2130 0.389556 GTCCCTTCGGTTCGTTCTCC 60.390 60.000 0.00 0.00 0.00 3.71
1543 2148 6.909357 CGTTCTCCTTTGCTGATGATTTATTC 59.091 38.462 0.00 0.00 0.00 1.75
1569 2174 3.487372 GGTGCAGGTTTTAGTCTTCCTT 58.513 45.455 0.00 0.00 0.00 3.36
1714 2319 1.541588 GATGGCTCCAAGCTTTTCGTT 59.458 47.619 0.00 0.00 41.99 3.85
1802 2480 8.606830 AGGTCTCAGTTTTATTTATCAGGTCTT 58.393 33.333 0.00 0.00 0.00 3.01
1923 2602 9.995003 TTGCCAAAAGTCATTTTATCTGTTATT 57.005 25.926 0.00 0.00 36.47 1.40
1951 2721 2.612212 CGGTGTTAGCTGTTTGTTCTGT 59.388 45.455 0.00 0.00 0.00 3.41
1952 2722 3.805422 CGGTGTTAGCTGTTTGTTCTGTA 59.195 43.478 0.00 0.00 0.00 2.74
1953 2723 4.451096 CGGTGTTAGCTGTTTGTTCTGTAT 59.549 41.667 0.00 0.00 0.00 2.29
1954 2724 5.614668 CGGTGTTAGCTGTTTGTTCTGTATG 60.615 44.000 0.00 0.00 0.00 2.39
1955 2725 5.238650 GGTGTTAGCTGTTTGTTCTGTATGT 59.761 40.000 0.00 0.00 0.00 2.29
1961 2733 5.696724 AGCTGTTTGTTCTGTATGTGTAGTC 59.303 40.000 0.00 0.00 0.00 2.59
2009 2796 5.979517 GCTATACATGGAAATTTGCTTGACC 59.020 40.000 25.57 8.20 0.00 4.02
2064 2852 9.546428 ACCTTGTACGGTGTATTAATTATTACC 57.454 33.333 12.66 6.51 35.52 2.85
2114 2902 1.726791 GCACGTGTTATCACTGACAGG 59.273 52.381 18.38 0.00 41.89 4.00
2207 2995 2.045926 ATGGACGGCAAGGTGAGC 60.046 61.111 0.00 0.00 0.00 4.26
2218 3006 2.242043 CAAGGTGAGCCAAAACCAGAT 58.758 47.619 0.00 0.00 39.05 2.90
2220 3008 2.962859 AGGTGAGCCAAAACCAGATTT 58.037 42.857 0.00 0.00 39.05 2.17
2222 3010 3.711190 AGGTGAGCCAAAACCAGATTTTT 59.289 39.130 0.00 0.00 38.50 1.94
2245 3033 3.809832 AGACATGTGTGCTGTTGTACTTC 59.190 43.478 1.15 0.00 0.00 3.01
2288 3076 5.073008 TGCCATTTAGATGCTTATCAGGGTA 59.927 40.000 0.00 0.00 31.67 3.69
2310 3098 9.131791 GGGTATGATAATTTTCACCATGTACTT 57.868 33.333 0.33 0.00 0.00 2.24
2353 3168 2.314323 AAGTTTTGTGCCTGCCTTTG 57.686 45.000 0.00 0.00 0.00 2.77
2376 3191 3.771216 CCAAATTGCCTAGGCCTGATAT 58.229 45.455 30.81 13.04 41.09 1.63
2403 3218 0.035056 ATGCTTCACTGGCCACTACC 60.035 55.000 0.00 0.00 0.00 3.18
2418 3233 6.159751 TGGCCACTACCTTTAAGGATCTAATT 59.840 38.462 18.97 0.00 37.67 1.40
2446 3261 0.898789 ATGCTTTGCAGGAGCTTGCT 60.899 50.000 20.45 0.00 43.65 3.91
2470 3285 1.134610 AGGAACGTCCGTGTGAACTTT 60.135 47.619 0.00 0.00 42.75 2.66
2720 3583 7.493320 TGATTATGTGGAACCTAATGTTACGTC 59.507 37.037 0.00 0.00 41.05 4.34
2731 3594 6.749118 ACCTAATGTTACGTCGTTCTATGTTC 59.251 38.462 1.78 0.00 0.00 3.18
2758 3621 8.848474 TTTTGGTTTTGGTTTGTTTCTTGATA 57.152 26.923 0.00 0.00 0.00 2.15
2795 3658 0.179100 TGTATGCTGCTTCGAGGCTC 60.179 55.000 20.92 12.49 0.00 4.70
2966 3846 4.708421 AGACTACCAGTGGCGTATTTTCTA 59.292 41.667 9.78 0.00 0.00 2.10
2969 3849 2.943033 ACCAGTGGCGTATTTTCTATGC 59.057 45.455 9.78 0.00 0.00 3.14
2972 3852 2.614057 AGTGGCGTATTTTCTATGCTGC 59.386 45.455 0.00 0.00 0.00 5.25
2973 3853 1.946768 TGGCGTATTTTCTATGCTGCC 59.053 47.619 0.00 0.00 41.56 4.85
2974 3854 1.069906 GGCGTATTTTCTATGCTGCCG 60.070 52.381 0.00 0.00 0.00 5.69
2975 3855 1.864711 GCGTATTTTCTATGCTGCCGA 59.135 47.619 0.00 0.00 0.00 5.54
2976 3856 2.286833 GCGTATTTTCTATGCTGCCGAA 59.713 45.455 0.00 0.00 0.00 4.30
2977 3857 3.242608 GCGTATTTTCTATGCTGCCGAAA 60.243 43.478 0.00 1.07 0.00 3.46
2979 3859 4.034048 CGTATTTTCTATGCTGCCGAAAGT 59.966 41.667 0.00 3.69 0.00 2.66
2980 3860 5.447279 CGTATTTTCTATGCTGCCGAAAGTT 60.447 40.000 0.00 0.00 0.00 2.66
2982 3862 5.545658 TTTTCTATGCTGCCGAAAGTTAG 57.454 39.130 0.00 0.00 0.00 2.34
2984 3864 4.465632 TCTATGCTGCCGAAAGTTAGAA 57.534 40.909 0.00 0.00 0.00 2.10
2987 3867 3.896648 TGCTGCCGAAAGTTAGAAAAG 57.103 42.857 0.00 0.00 0.00 2.27
2991 3871 4.261031 GCTGCCGAAAGTTAGAAAAGAACA 60.261 41.667 0.00 0.00 0.00 3.18
2993 3873 6.197364 TGCCGAAAGTTAGAAAAGAACAAA 57.803 33.333 0.00 0.00 0.00 2.83
2995 3875 6.750039 TGCCGAAAGTTAGAAAAGAACAAAAG 59.250 34.615 0.00 0.00 0.00 2.27
2996 3876 6.970613 GCCGAAAGTTAGAAAAGAACAAAAGA 59.029 34.615 0.00 0.00 0.00 2.52
3000 3880 9.841880 GAAAGTTAGAAAAGAACAAAAGACAGT 57.158 29.630 0.00 0.00 0.00 3.55
3005 3885 7.796958 AGAAAAGAACAAAAGACAGTTTTCG 57.203 32.000 0.00 0.00 37.45 3.46
3006 3886 6.806739 AGAAAAGAACAAAAGACAGTTTTCGG 59.193 34.615 0.00 0.00 37.45 4.30
3007 3887 5.890424 AAGAACAAAAGACAGTTTTCGGA 57.110 34.783 0.00 0.00 0.00 4.55
3008 3888 6.451064 AAGAACAAAAGACAGTTTTCGGAT 57.549 33.333 0.00 0.00 0.00 4.18
3009 3889 7.562454 AAGAACAAAAGACAGTTTTCGGATA 57.438 32.000 0.00 0.00 0.00 2.59
3010 3890 7.562454 AGAACAAAAGACAGTTTTCGGATAA 57.438 32.000 0.00 0.00 0.00 1.75
3011 3891 7.415229 AGAACAAAAGACAGTTTTCGGATAAC 58.585 34.615 3.49 3.49 0.00 1.89
3012 3892 6.687081 ACAAAAGACAGTTTTCGGATAACA 57.313 33.333 12.71 0.00 0.00 2.41
3013 3893 6.492254 ACAAAAGACAGTTTTCGGATAACAC 58.508 36.000 12.71 5.12 0.00 3.32
3014 3894 6.094325 ACAAAAGACAGTTTTCGGATAACACA 59.906 34.615 12.71 0.00 0.00 3.72
3015 3895 5.924475 AAGACAGTTTTCGGATAACACAG 57.076 39.130 12.71 5.78 0.00 3.66
3016 3896 4.957296 AGACAGTTTTCGGATAACACAGT 58.043 39.130 12.71 8.35 0.00 3.55
3017 3897 5.365619 AGACAGTTTTCGGATAACACAGTT 58.634 37.500 12.71 0.00 0.00 3.16
3018 3898 5.465724 AGACAGTTTTCGGATAACACAGTTC 59.534 40.000 12.71 3.15 0.00 3.01
3019 3899 5.120399 ACAGTTTTCGGATAACACAGTTCA 58.880 37.500 12.71 0.00 0.00 3.18
3020 3900 5.587043 ACAGTTTTCGGATAACACAGTTCAA 59.413 36.000 12.71 0.00 0.00 2.69
3021 3901 6.094325 ACAGTTTTCGGATAACACAGTTCAAA 59.906 34.615 12.71 0.00 0.00 2.69
3022 3902 6.632834 CAGTTTTCGGATAACACAGTTCAAAG 59.367 38.462 12.71 0.00 0.00 2.77
3023 3903 5.682943 TTTCGGATAACACAGTTCAAAGG 57.317 39.130 0.00 0.00 0.00 3.11
3024 3904 3.071479 TCGGATAACACAGTTCAAAGGC 58.929 45.455 0.00 0.00 0.00 4.35
3025 3905 2.811431 CGGATAACACAGTTCAAAGGCA 59.189 45.455 0.00 0.00 0.00 4.75
3026 3906 3.364964 CGGATAACACAGTTCAAAGGCAC 60.365 47.826 0.00 0.00 0.00 5.01
3027 3907 3.364964 GGATAACACAGTTCAAAGGCACG 60.365 47.826 0.00 0.00 0.00 5.34
3028 3908 0.100503 AACACAGTTCAAAGGCACGC 59.899 50.000 0.00 0.00 0.00 5.34
3029 3909 0.748005 ACACAGTTCAAAGGCACGCT 60.748 50.000 0.00 0.00 0.00 5.07
3030 3910 1.225855 CACAGTTCAAAGGCACGCTA 58.774 50.000 0.00 0.00 0.00 4.26
3031 3911 1.195448 CACAGTTCAAAGGCACGCTAG 59.805 52.381 0.00 0.00 0.00 3.42
3032 3912 1.202651 ACAGTTCAAAGGCACGCTAGT 60.203 47.619 0.00 0.00 0.00 2.57
3033 3913 2.036733 ACAGTTCAAAGGCACGCTAGTA 59.963 45.455 0.00 0.00 0.00 1.82
3034 3914 3.064207 CAGTTCAAAGGCACGCTAGTAA 58.936 45.455 0.00 0.00 0.00 2.24
3035 3915 3.496884 CAGTTCAAAGGCACGCTAGTAAA 59.503 43.478 0.00 0.00 0.00 2.01
3036 3916 4.024387 CAGTTCAAAGGCACGCTAGTAAAA 60.024 41.667 0.00 0.00 0.00 1.52
3037 3917 4.760204 AGTTCAAAGGCACGCTAGTAAAAT 59.240 37.500 0.00 0.00 0.00 1.82
3038 3918 5.240844 AGTTCAAAGGCACGCTAGTAAAATT 59.759 36.000 0.00 0.00 0.00 1.82
3039 3919 5.699097 TCAAAGGCACGCTAGTAAAATTT 57.301 34.783 0.00 0.00 0.00 1.82
3040 3920 5.457140 TCAAAGGCACGCTAGTAAAATTTG 58.543 37.500 0.00 0.00 0.00 2.32
3041 3921 5.009210 TCAAAGGCACGCTAGTAAAATTTGT 59.991 36.000 0.00 0.00 0.00 2.83
3042 3922 5.447624 AAGGCACGCTAGTAAAATTTGTT 57.552 34.783 0.00 0.00 0.00 2.83
3043 3923 4.794169 AGGCACGCTAGTAAAATTTGTTG 58.206 39.130 0.00 0.00 0.00 3.33
3044 3924 4.517453 AGGCACGCTAGTAAAATTTGTTGA 59.483 37.500 0.00 0.00 0.00 3.18
3045 3925 5.183140 AGGCACGCTAGTAAAATTTGTTGAT 59.817 36.000 0.00 0.00 0.00 2.57
3050 3930 9.864034 CACGCTAGTAAAATTTGTTGATATAGG 57.136 33.333 0.00 0.00 0.00 2.57
3052 3932 8.015658 CGCTAGTAAAATTTGTTGATATAGGCC 58.984 37.037 0.00 0.00 0.00 5.19
3053 3933 8.846211 GCTAGTAAAATTTGTTGATATAGGCCA 58.154 33.333 5.01 0.00 0.00 5.36
3062 3942 4.350816 TGTTGATATAGGCCAACCAGCTAT 59.649 41.667 5.01 0.00 41.26 2.97
3076 3956 6.206243 CCAACCAGCTATCAATGGAGAATTAG 59.794 42.308 0.00 0.00 39.02 1.73
3077 3957 6.753913 ACCAGCTATCAATGGAGAATTAGA 57.246 37.500 0.00 0.00 39.02 2.10
3078 3958 6.529220 ACCAGCTATCAATGGAGAATTAGAC 58.471 40.000 0.00 0.00 39.02 2.59
3079 3959 6.328672 ACCAGCTATCAATGGAGAATTAGACT 59.671 38.462 0.00 0.00 39.02 3.24
3083 3963 9.545928 AGCTATCAATGGAGAATTAGACTAGAT 57.454 33.333 0.00 0.00 0.00 1.98
3112 3992 9.495382 ACTTAGAAATTAGAATCTACTCCCAGT 57.505 33.333 0.00 0.00 0.00 4.00
3122 4002 8.783660 AGAATCTACTCCCAGTATATTTGTGA 57.216 34.615 0.00 0.00 30.63 3.58
3170 4050 6.601613 TGTCCATTTTTAAGTCTGTGACACTT 59.398 34.615 7.20 0.00 37.80 3.16
3173 4053 8.617809 TCCATTTTTAAGTCTGTGACACTTAAC 58.382 33.333 7.20 2.63 43.07 2.01
3175 4055 9.781834 CATTTTTAAGTCTGTGACACTTAACAA 57.218 29.630 7.20 8.18 43.07 2.83
3183 4070 8.952278 AGTCTGTGACACTTAACAATTAAAACA 58.048 29.630 7.20 0.00 34.60 2.83
3226 4113 9.791820 TCAAATGCAAATATTACAACAGAGATG 57.208 29.630 0.00 0.00 0.00 2.90
3246 4136 7.671398 AGAGATGTTCAATAGGTTTGTTTCCAT 59.329 33.333 0.00 0.00 0.00 3.41
3249 4139 8.877864 ATGTTCAATAGGTTTGTTTCCATAGA 57.122 30.769 0.00 0.00 0.00 1.98
3290 4208 5.432680 AGAATCACATCTCACTCCATTGT 57.567 39.130 0.00 0.00 0.00 2.71
3301 4219 0.329261 CTCCATTGTGCCCCTTGAGA 59.671 55.000 0.00 0.00 0.00 3.27
3307 4225 1.002069 TGTGCCCCTTGAGATCCATT 58.998 50.000 0.00 0.00 0.00 3.16
3311 4229 2.027385 GCCCCTTGAGATCCATTCAAC 58.973 52.381 0.00 0.00 31.66 3.18
3312 4230 2.621407 GCCCCTTGAGATCCATTCAACA 60.621 50.000 0.00 0.00 31.66 3.33
3313 4231 3.700538 CCCCTTGAGATCCATTCAACAA 58.299 45.455 0.00 0.00 31.66 2.83
3314 4232 3.698040 CCCCTTGAGATCCATTCAACAAG 59.302 47.826 0.00 0.00 39.01 3.16
3338 4256 4.931002 GGTACAAGCGTAAATCACAGGTTA 59.069 41.667 0.00 0.00 0.00 2.85
3340 4258 5.352643 ACAAGCGTAAATCACAGGTTAAC 57.647 39.130 0.00 0.00 0.00 2.01
3383 4301 8.981370 CAATTTGATGATTGTCAAGTTGTTTG 57.019 30.769 13.40 2.53 44.26 2.93
3384 4302 8.605746 CAATTTGATGATTGTCAAGTTGTTTGT 58.394 29.630 13.40 0.00 44.26 2.83
3385 4303 7.754069 TTTGATGATTGTCAAGTTGTTTGTC 57.246 32.000 2.11 0.00 39.13 3.18
3386 4304 6.448207 TGATGATTGTCAAGTTGTTTGTCA 57.552 33.333 2.11 4.77 38.01 3.58
3387 4305 6.861144 TGATGATTGTCAAGTTGTTTGTCAA 58.139 32.000 2.11 2.97 44.71 3.18
3388 4306 6.974048 TGATGATTGTCAAGTTGTTTGTCAAG 59.026 34.615 2.11 0.00 44.15 3.02
3389 4307 6.266168 TGATTGTCAAGTTGTTTGTCAAGT 57.734 33.333 2.11 0.00 44.15 3.16
3390 4308 6.686630 TGATTGTCAAGTTGTTTGTCAAGTT 58.313 32.000 2.11 0.00 46.71 2.66
3396 4314 4.250116 AGTTGTTTGTCAAGTTGCAACA 57.750 36.364 30.11 8.30 38.75 3.33
3397 4315 4.819769 AGTTGTTTGTCAAGTTGCAACAT 58.180 34.783 30.11 17.27 38.75 2.71
3398 4316 4.626604 AGTTGTTTGTCAAGTTGCAACATG 59.373 37.500 30.11 27.46 38.75 3.21
3410 4328 4.525487 AGTTGCAACATGGAGTGAATCAAT 59.475 37.500 30.11 1.64 0.00 2.57
3411 4329 5.711506 AGTTGCAACATGGAGTGAATCAATA 59.288 36.000 30.11 0.00 0.00 1.90
3417 4335 7.010738 GCAACATGGAGTGAATCAATAAATTGG 59.989 37.037 0.00 0.00 38.30 3.16
3421 4339 5.951148 TGGAGTGAATCAATAAATTGGCTGA 59.049 36.000 3.00 0.00 38.30 4.26
3437 4355 2.417933 GGCTGACATGTAGAGCAACAAG 59.582 50.000 23.87 4.05 34.20 3.16
3439 4357 3.124297 GCTGACATGTAGAGCAACAAGAC 59.876 47.826 19.74 0.00 32.02 3.01
3443 4361 2.232756 TGTAGAGCAACAAGACGCAA 57.767 45.000 0.00 0.00 0.00 4.85
3446 4364 3.563808 TGTAGAGCAACAAGACGCAAAAT 59.436 39.130 0.00 0.00 0.00 1.82
3453 4371 5.982516 AGCAACAAGACGCAAAATTTATGAA 59.017 32.000 0.00 0.00 0.00 2.57
3454 4372 6.646240 AGCAACAAGACGCAAAATTTATGAAT 59.354 30.769 0.00 0.00 0.00 2.57
3472 4390 1.463674 ATTTCATGGTTGACGAGCCC 58.536 50.000 0.00 0.00 0.00 5.19
3487 4405 4.016838 CCCGATGGCCACATTGTT 57.983 55.556 8.16 0.00 37.47 2.83
3499 4417 2.036217 CACATTGTTTTCACTCGTGCG 58.964 47.619 0.00 0.00 0.00 5.34
3502 4420 2.941891 TTGTTTTCACTCGTGCGATC 57.058 45.000 0.00 0.00 0.00 3.69
3528 4446 6.732154 CATCACAAAACTTCATGACTGAGTT 58.268 36.000 5.60 5.60 31.68 3.01
3529 4447 7.520453 GCATCACAAAACTTCATGACTGAGTTA 60.520 37.037 10.85 0.00 31.68 2.24
3535 4453 9.226345 CAAAACTTCATGACTGAGTTAAAAGAC 57.774 33.333 10.85 0.00 31.68 3.01
3557 4475 2.354303 GGTGTACCACCGATGAATGACA 60.354 50.000 0.00 0.00 44.95 3.58
3572 4490 1.533625 TGACATGCAAGTTGTAGGGC 58.466 50.000 10.34 7.54 0.00 5.19
3577 4495 0.036164 TGCAAGTTGTAGGGCGTGAT 59.964 50.000 4.48 0.00 0.00 3.06
3606 4524 2.046313 CTCGTGAAACAAAGCATGCAC 58.954 47.619 21.98 5.42 35.74 4.57
3623 4541 1.326245 GCACGTTTTGCCAAAAAGGTC 59.674 47.619 17.86 7.16 46.22 3.85
3624 4542 1.586123 CACGTTTTGCCAAAAAGGTCG 59.414 47.619 17.86 13.12 46.22 4.79
3640 4558 1.691801 GGTCGAGTCCCCTTCCCTTAT 60.692 57.143 0.00 0.00 0.00 1.73
3705 4623 0.603569 CATCCTTCCCGAGTATCCCG 59.396 60.000 0.00 0.00 0.00 5.14
3720 4638 1.729284 TCCCGGCGTCATTTTACTTC 58.271 50.000 6.01 0.00 0.00 3.01
3731 4649 6.470877 GCGTCATTTTACTTCTGAAACAACAA 59.529 34.615 0.00 0.00 0.00 2.83
3753 4683 6.040166 ACAAGAAAGCTCAATGACATTTGACT 59.960 34.615 0.00 0.00 32.39 3.41
3754 4684 6.010294 AGAAAGCTCAATGACATTTGACTG 57.990 37.500 0.00 0.00 32.39 3.51
3761 4698 1.234821 TGACATTTGACTGAACGGGC 58.765 50.000 0.00 0.00 0.00 6.13
3765 4702 0.250124 ATTTGACTGAACGGGCGTGA 60.250 50.000 0.00 0.00 0.00 4.35
3769 4706 1.352156 GACTGAACGGGCGTGATGTC 61.352 60.000 0.00 0.00 0.00 3.06
3771 4708 0.670546 CTGAACGGGCGTGATGTCTT 60.671 55.000 0.00 0.00 0.00 3.01
3782 4719 3.062639 GCGTGATGTCTTTCATGAACGAT 59.937 43.478 16.68 3.09 41.61 3.73
3796 4733 3.632333 TGAACGATGTCAGTAGAGGGAT 58.368 45.455 0.00 0.00 0.00 3.85
3804 4741 2.432510 GTCAGTAGAGGGATGAAGGGTG 59.567 54.545 0.00 0.00 0.00 4.61
3808 4745 1.225704 GAGGGATGAAGGGTGCCTG 59.774 63.158 0.00 0.00 37.56 4.85
3811 4748 1.566298 GGGATGAAGGGTGCCTGTCT 61.566 60.000 0.00 0.00 32.13 3.41
3834 4771 0.323629 GACGGATTCTGGGTGGACAA 59.676 55.000 0.00 0.00 0.00 3.18
3837 4774 0.036306 GGATTCTGGGTGGACAACGT 59.964 55.000 0.00 0.00 0.00 3.99
3855 4792 1.339097 GTCATAGTCCAGGCGGGTAT 58.661 55.000 2.94 0.00 38.11 2.73
3882 4819 3.884774 TGGGGGCTGCAAACGTCT 61.885 61.111 0.50 0.00 0.00 4.18
3886 4823 2.328099 GGGCTGCAAACGTCTGAGG 61.328 63.158 0.50 0.00 0.00 3.86
3887 4824 2.558313 GCTGCAAACGTCTGAGGC 59.442 61.111 0.00 0.00 0.00 4.70
3896 4833 2.753029 GTCTGAGGCTGCCTGGTT 59.247 61.111 28.82 0.57 31.76 3.67
3900 4837 0.835941 CTGAGGCTGCCTGGTTAGAT 59.164 55.000 28.82 0.00 31.76 1.98
3904 4841 2.182842 GCTGCCTGGTTAGATGCCG 61.183 63.158 0.00 0.00 0.00 5.69
3916 4853 1.122019 AGATGCCGGGGAGGTACATC 61.122 60.000 2.18 5.68 43.70 3.06
3921 4858 2.822399 GGGGAGGTACATCTGCGG 59.178 66.667 7.56 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.345715 CCCCGGGTCTAGCAAATCCT 61.346 60.000 21.85 0.00 0.00 3.24
54 55 4.718961 AGACCATATTGCCCACATAACTC 58.281 43.478 0.00 0.00 0.00 3.01
113 115 0.912486 ACCATTGACCTACCAGGCTC 59.088 55.000 0.00 0.00 39.63 4.70
222 224 2.271173 CCTTTACCCAGCCGGTCC 59.729 66.667 1.90 0.00 43.58 4.46
248 250 3.379057 CCATTCACATCAACAGCAGCATA 59.621 43.478 0.00 0.00 0.00 3.14
271 273 6.176183 CACAAGTCTAATGGATGAAGTTCCT 58.824 40.000 0.00 0.00 36.68 3.36
281 283 3.582647 TCTCTTGCCACAAGTCTAATGGA 59.417 43.478 7.18 0.00 35.33 3.41
287 289 2.027377 CCTGATCTCTTGCCACAAGTCT 60.027 50.000 7.18 0.00 0.00 3.24
527 532 4.060038 TGCGCAAACCCTGAAAATTTTA 57.940 36.364 8.16 0.00 0.00 1.52
745 751 4.764308 GCTCTCCAAGAAAACATTTCTCCT 59.236 41.667 5.86 0.00 0.00 3.69
772 778 5.405269 CCGATTTTGCTTTTAAACTCCTTGG 59.595 40.000 0.00 0.00 0.00 3.61
781 787 2.999355 GGCATGCCGATTTTGCTTTTAA 59.001 40.909 23.48 0.00 36.62 1.52
978 993 1.000359 GAATGGGGAGTGGGGGTTG 60.000 63.158 0.00 0.00 0.00 3.77
979 994 1.151361 AGAATGGGGAGTGGGGGTT 60.151 57.895 0.00 0.00 0.00 4.11
980 995 1.619669 GAGAATGGGGAGTGGGGGT 60.620 63.158 0.00 0.00 0.00 4.95
1067 1089 2.657944 GCCGCTGCGAGATCAGAG 60.658 66.667 25.45 4.87 36.19 3.35
1112 1712 0.983378 AGCAATCTAGCGGAAGGGGT 60.983 55.000 0.00 0.00 40.15 4.95
1157 1757 1.151668 CTCCGCCAATCGATCCATTC 58.848 55.000 0.00 0.00 41.67 2.67
1179 1779 1.672898 CAACCGAAACCCTACCCGA 59.327 57.895 0.00 0.00 0.00 5.14
1194 1794 3.051081 AGAGATCAGACAACAGGCAAC 57.949 47.619 0.00 0.00 0.00 4.17
1241 1845 0.765510 AATCCAACTCGATAGCCCCC 59.234 55.000 0.00 0.00 0.00 5.40
1315 1919 1.765727 GGTTCCCCCTCCGAAACTT 59.234 57.895 0.00 0.00 0.00 2.66
1325 1929 2.671963 GAACAGCACGGTTCCCCC 60.672 66.667 2.68 0.00 40.97 5.40
1337 1941 1.558756 AGGCTGAGATCCCAAGAACAG 59.441 52.381 0.00 0.00 0.00 3.16
1378 1982 6.318648 TGCCATAACAGATTAATCCAACAGAC 59.681 38.462 11.92 0.00 0.00 3.51
1400 2004 5.992217 CCTAGAAACACAATATACTCCTGCC 59.008 44.000 0.00 0.00 0.00 4.85
1413 2017 1.689813 TGCGAACTCCCTAGAAACACA 59.310 47.619 0.00 0.00 0.00 3.72
1450 2054 5.362430 ACAGGGCACAGATTTCTAAACAAAA 59.638 36.000 0.00 0.00 0.00 2.44
1459 2063 1.280421 AGAGGACAGGGCACAGATTTC 59.720 52.381 0.00 0.00 0.00 2.17
1464 2068 1.772819 AACCAGAGGACAGGGCACAG 61.773 60.000 0.00 0.00 0.00 3.66
1471 2075 1.620819 ACAGTAGCAACCAGAGGACAG 59.379 52.381 0.00 0.00 0.00 3.51
1473 2077 1.344763 ACACAGTAGCAACCAGAGGAC 59.655 52.381 0.00 0.00 0.00 3.85
1485 2090 3.878699 ACAAACCGGGTTAAACACAGTAG 59.121 43.478 13.79 0.00 0.00 2.57
1486 2091 3.876320 GACAAACCGGGTTAAACACAGTA 59.124 43.478 13.79 0.00 0.00 2.74
1487 2092 2.684374 GACAAACCGGGTTAAACACAGT 59.316 45.455 13.79 0.00 0.00 3.55
1488 2093 2.033675 GGACAAACCGGGTTAAACACAG 59.966 50.000 13.79 0.00 0.00 3.66
1494 2099 1.542987 CGAAGGGACAAACCGGGTTAA 60.543 52.381 13.79 0.00 40.11 2.01
1522 2127 7.330900 ACAGAATAAATCATCAGCAAAGGAG 57.669 36.000 0.00 0.00 0.00 3.69
1523 2128 6.037500 CGACAGAATAAATCATCAGCAAAGGA 59.962 38.462 0.00 0.00 0.00 3.36
1524 2129 6.197276 CGACAGAATAAATCATCAGCAAAGG 58.803 40.000 0.00 0.00 0.00 3.11
1525 2130 6.183360 ACCGACAGAATAAATCATCAGCAAAG 60.183 38.462 0.00 0.00 0.00 2.77
1543 2148 1.798813 GACTAAAACCTGCACCGACAG 59.201 52.381 0.00 0.00 37.42 3.51
1569 2174 2.613660 CTTGATGAGGGCCGCCATGA 62.614 60.000 17.10 0.00 0.00 3.07
1714 2319 1.452145 GGCAAGAAAACTCACCGCCA 61.452 55.000 0.00 0.00 37.98 5.69
1802 2480 0.761187 GATCATCAGTAGCCCAGGCA 59.239 55.000 12.03 0.00 44.88 4.75
1923 2602 5.299148 ACAAACAGCTAACACCGTGTATAA 58.701 37.500 4.17 0.00 0.00 0.98
1951 2721 9.154847 CAGATCTTGAAACAATGACTACACATA 57.845 33.333 0.00 0.00 0.00 2.29
1952 2722 7.879677 TCAGATCTTGAAACAATGACTACACAT 59.120 33.333 0.00 0.00 31.34 3.21
1953 2723 7.216494 TCAGATCTTGAAACAATGACTACACA 58.784 34.615 0.00 0.00 31.34 3.72
1954 2724 7.658179 TCAGATCTTGAAACAATGACTACAC 57.342 36.000 0.00 0.00 31.34 2.90
2009 2796 4.871993 AGAGCATCAGAATAAAAGCACG 57.128 40.909 0.00 0.00 37.82 5.34
2064 2852 4.973396 TGAAAGACAAGCATTATGAAGCG 58.027 39.130 0.00 0.00 35.48 4.68
2075 2863 4.222114 GTGCTGTAACATGAAAGACAAGC 58.778 43.478 0.00 0.00 0.00 4.01
2114 2902 2.661718 CCTCTAGACCTTCCAGTCTCC 58.338 57.143 0.00 0.00 43.76 3.71
2207 2995 7.169645 CACACATGTCTAAAAATCTGGTTTTGG 59.830 37.037 0.00 0.00 39.86 3.28
2214 3002 6.005583 ACAGCACACATGTCTAAAAATCTG 57.994 37.500 0.00 0.00 0.00 2.90
2218 3006 5.574891 ACAACAGCACACATGTCTAAAAA 57.425 34.783 0.00 0.00 0.00 1.94
2220 3008 5.364778 AGTACAACAGCACACATGTCTAAA 58.635 37.500 0.00 0.00 0.00 1.85
2222 3010 4.600692 AGTACAACAGCACACATGTCTA 57.399 40.909 0.00 0.00 0.00 2.59
2245 3033 6.757897 TGGCAGAAGTTTAACTCCATATTG 57.242 37.500 0.00 0.00 0.00 1.90
2288 3076 8.342634 GCGTAAGTACATGGTGAAAATTATCAT 58.657 33.333 0.00 0.00 41.68 2.45
2376 3191 1.179152 CCAGTGAAGCATGGCATCAA 58.821 50.000 0.00 0.00 37.99 2.57
2418 3233 1.551430 CCTGCAAAGCATTGGATGGAA 59.449 47.619 3.55 0.00 38.13 3.53
2446 3261 2.522436 ACACGGACGTTCCTCCCA 60.522 61.111 0.00 0.00 33.30 4.37
2470 3285 2.357034 GAAGGTCGCTCGTTGGCA 60.357 61.111 0.00 0.00 0.00 4.92
2503 3318 4.069232 CCGCCACGAGAGAAGCCA 62.069 66.667 0.00 0.00 0.00 4.75
2566 3384 3.776781 TATCCACCGCCACCACCG 61.777 66.667 0.00 0.00 0.00 4.94
2608 3426 1.562672 GGTCACCACCATAGCCACCT 61.563 60.000 0.00 0.00 43.17 4.00
2628 3446 5.359576 CAGTGCTCTTCTTAGTAGGACTCAT 59.640 44.000 0.00 0.00 39.55 2.90
2675 3493 9.003658 CATAATCAAGACACTGTCCTAAAAACT 57.996 33.333 5.51 0.00 32.18 2.66
2720 3583 6.754675 ACCAAAACCAAAAAGAACATAGAACG 59.245 34.615 0.00 0.00 0.00 3.95
2731 3594 7.643579 TCAAGAAACAAACCAAAACCAAAAAG 58.356 30.769 0.00 0.00 0.00 2.27
2758 3621 6.207417 AGCATACACAAATTAACTCTTGCACT 59.793 34.615 0.00 0.00 0.00 4.40
2795 3658 3.056536 TGAACTTCCTTGAGACTCATCCG 60.057 47.826 5.87 0.00 0.00 4.18
2908 3788 6.825721 ACCAAATTTCTAGCGAAGATCTCAAT 59.174 34.615 0.00 0.00 33.05 2.57
2909 3789 6.173339 ACCAAATTTCTAGCGAAGATCTCAA 58.827 36.000 0.00 0.00 33.05 3.02
2910 3790 5.734720 ACCAAATTTCTAGCGAAGATCTCA 58.265 37.500 0.00 0.00 33.05 3.27
2911 3791 7.772332 TTACCAAATTTCTAGCGAAGATCTC 57.228 36.000 0.00 0.00 33.05 2.75
2919 3799 6.056428 GGTACCATTACCAAATTTCTAGCG 57.944 41.667 7.15 0.00 46.59 4.26
2950 3830 3.546815 GCAGCATAGAAAATACGCCACTG 60.547 47.826 0.00 0.00 0.00 3.66
2966 3846 4.072131 TCTTTTCTAACTTTCGGCAGCAT 58.928 39.130 0.00 0.00 0.00 3.79
2969 3849 5.418310 TGTTCTTTTCTAACTTTCGGCAG 57.582 39.130 0.00 0.00 0.00 4.85
2972 3852 7.966204 TGTCTTTTGTTCTTTTCTAACTTTCGG 59.034 33.333 0.00 0.00 0.00 4.30
2973 3853 8.889849 TGTCTTTTGTTCTTTTCTAACTTTCG 57.110 30.769 0.00 0.00 0.00 3.46
2974 3854 9.841880 ACTGTCTTTTGTTCTTTTCTAACTTTC 57.158 29.630 0.00 0.00 0.00 2.62
2979 3859 9.337091 CGAAAACTGTCTTTTGTTCTTTTCTAA 57.663 29.630 0.00 0.00 0.00 2.10
2980 3860 7.966204 CCGAAAACTGTCTTTTGTTCTTTTCTA 59.034 33.333 0.00 0.00 0.00 2.10
2982 3862 6.804783 TCCGAAAACTGTCTTTTGTTCTTTTC 59.195 34.615 0.00 0.00 0.00 2.29
2984 3864 6.262193 TCCGAAAACTGTCTTTTGTTCTTT 57.738 33.333 0.00 0.00 0.00 2.52
2987 3867 7.165318 GTGTTATCCGAAAACTGTCTTTTGTTC 59.835 37.037 0.00 0.00 0.00 3.18
2991 3871 6.317893 ACTGTGTTATCCGAAAACTGTCTTTT 59.682 34.615 0.00 0.00 0.00 2.27
2993 3873 5.365619 ACTGTGTTATCCGAAAACTGTCTT 58.634 37.500 0.00 0.00 0.00 3.01
2995 3875 5.235616 TGAACTGTGTTATCCGAAAACTGTC 59.764 40.000 0.00 0.00 0.00 3.51
2996 3876 5.120399 TGAACTGTGTTATCCGAAAACTGT 58.880 37.500 0.00 0.00 0.00 3.55
3000 3880 5.506649 GCCTTTGAACTGTGTTATCCGAAAA 60.507 40.000 0.00 0.00 0.00 2.29
3001 3881 4.023536 GCCTTTGAACTGTGTTATCCGAAA 60.024 41.667 0.00 0.00 0.00 3.46
3002 3882 3.500680 GCCTTTGAACTGTGTTATCCGAA 59.499 43.478 0.00 0.00 0.00 4.30
3003 3883 3.071479 GCCTTTGAACTGTGTTATCCGA 58.929 45.455 0.00 0.00 0.00 4.55
3004 3884 2.811431 TGCCTTTGAACTGTGTTATCCG 59.189 45.455 0.00 0.00 0.00 4.18
3005 3885 3.364964 CGTGCCTTTGAACTGTGTTATCC 60.365 47.826 0.00 0.00 0.00 2.59
3006 3886 3.810373 CGTGCCTTTGAACTGTGTTATC 58.190 45.455 0.00 0.00 0.00 1.75
3007 3887 2.031157 GCGTGCCTTTGAACTGTGTTAT 60.031 45.455 0.00 0.00 0.00 1.89
3008 3888 1.332375 GCGTGCCTTTGAACTGTGTTA 59.668 47.619 0.00 0.00 0.00 2.41
3009 3889 0.100503 GCGTGCCTTTGAACTGTGTT 59.899 50.000 0.00 0.00 0.00 3.32
3010 3890 0.748005 AGCGTGCCTTTGAACTGTGT 60.748 50.000 0.00 0.00 0.00 3.72
3011 3891 1.195448 CTAGCGTGCCTTTGAACTGTG 59.805 52.381 0.00 0.00 0.00 3.66
3012 3892 1.202651 ACTAGCGTGCCTTTGAACTGT 60.203 47.619 0.00 0.00 0.00 3.55
3013 3893 1.512926 ACTAGCGTGCCTTTGAACTG 58.487 50.000 0.00 0.00 0.00 3.16
3014 3894 3.396260 TTACTAGCGTGCCTTTGAACT 57.604 42.857 0.00 0.00 0.00 3.01
3015 3895 4.477302 TTTTACTAGCGTGCCTTTGAAC 57.523 40.909 0.00 0.00 0.00 3.18
3016 3896 5.699097 AATTTTACTAGCGTGCCTTTGAA 57.301 34.783 0.00 0.00 0.00 2.69
3017 3897 5.009210 ACAAATTTTACTAGCGTGCCTTTGA 59.991 36.000 9.76 0.00 0.00 2.69
3018 3898 5.219633 ACAAATTTTACTAGCGTGCCTTTG 58.780 37.500 0.00 0.00 0.00 2.77
3019 3899 5.447624 ACAAATTTTACTAGCGTGCCTTT 57.552 34.783 0.00 0.00 0.00 3.11
3020 3900 5.009210 TCAACAAATTTTACTAGCGTGCCTT 59.991 36.000 0.00 0.00 0.00 4.35
3021 3901 4.517453 TCAACAAATTTTACTAGCGTGCCT 59.483 37.500 0.00 0.00 0.00 4.75
3022 3902 4.789784 TCAACAAATTTTACTAGCGTGCC 58.210 39.130 0.00 0.00 0.00 5.01
3023 3903 9.370126 CTATATCAACAAATTTTACTAGCGTGC 57.630 33.333 0.00 0.00 0.00 5.34
3024 3904 9.864034 CCTATATCAACAAATTTTACTAGCGTG 57.136 33.333 0.00 0.00 0.00 5.34
3025 3905 8.557029 GCCTATATCAACAAATTTTACTAGCGT 58.443 33.333 0.00 0.00 0.00 5.07
3026 3906 8.015658 GGCCTATATCAACAAATTTTACTAGCG 58.984 37.037 0.00 0.00 0.00 4.26
3027 3907 8.846211 TGGCCTATATCAACAAATTTTACTAGC 58.154 33.333 3.32 0.00 0.00 3.42
3030 3910 8.474831 GGTTGGCCTATATCAACAAATTTTACT 58.525 33.333 3.32 0.00 43.44 2.24
3031 3911 8.254508 TGGTTGGCCTATATCAACAAATTTTAC 58.745 33.333 3.32 0.00 43.44 2.01
3032 3912 8.367660 TGGTTGGCCTATATCAACAAATTTTA 57.632 30.769 3.32 0.00 43.44 1.52
3033 3913 7.251321 TGGTTGGCCTATATCAACAAATTTT 57.749 32.000 3.32 0.00 43.44 1.82
3034 3914 6.630188 GCTGGTTGGCCTATATCAACAAATTT 60.630 38.462 3.32 0.00 43.44 1.82
3035 3915 5.163416 GCTGGTTGGCCTATATCAACAAATT 60.163 40.000 3.32 0.00 43.44 1.82
3036 3916 4.342092 GCTGGTTGGCCTATATCAACAAAT 59.658 41.667 3.32 0.00 43.44 2.32
3037 3917 3.699038 GCTGGTTGGCCTATATCAACAAA 59.301 43.478 3.32 0.00 43.44 2.83
3038 3918 3.053693 AGCTGGTTGGCCTATATCAACAA 60.054 43.478 3.32 0.00 43.44 2.83
3039 3919 2.509548 AGCTGGTTGGCCTATATCAACA 59.490 45.455 3.32 0.00 43.44 3.33
3040 3920 3.214696 AGCTGGTTGGCCTATATCAAC 57.785 47.619 3.32 0.00 41.61 3.18
3041 3921 4.597075 TGATAGCTGGTTGGCCTATATCAA 59.403 41.667 3.32 0.00 34.44 2.57
3042 3922 4.167319 TGATAGCTGGTTGGCCTATATCA 58.833 43.478 3.32 3.81 34.70 2.15
3043 3923 4.826274 TGATAGCTGGTTGGCCTATATC 57.174 45.455 3.32 0.96 35.27 1.63
3044 3924 5.503927 CATTGATAGCTGGTTGGCCTATAT 58.496 41.667 3.32 0.00 35.27 0.86
3045 3925 4.263462 CCATTGATAGCTGGTTGGCCTATA 60.263 45.833 3.32 0.00 35.27 1.31
3050 3930 1.952296 CTCCATTGATAGCTGGTTGGC 59.048 52.381 0.00 0.00 34.03 4.52
3052 3932 6.994496 TCTAATTCTCCATTGATAGCTGGTTG 59.006 38.462 0.00 0.00 34.03 3.77
3053 3933 6.995091 GTCTAATTCTCCATTGATAGCTGGTT 59.005 38.462 0.00 0.00 34.03 3.67
3096 3976 9.877222 TCACAAATATACTGGGAGTAGATTCTA 57.123 33.333 4.54 0.00 40.52 2.10
3097 3977 8.643324 GTCACAAATATACTGGGAGTAGATTCT 58.357 37.037 4.54 0.00 40.52 2.40
3098 3978 7.873505 GGTCACAAATATACTGGGAGTAGATTC 59.126 40.741 4.54 0.00 40.52 2.52
3099 3979 7.347222 TGGTCACAAATATACTGGGAGTAGATT 59.653 37.037 0.00 0.00 42.47 2.40
3100 3980 6.844388 TGGTCACAAATATACTGGGAGTAGAT 59.156 38.462 0.00 0.00 34.39 1.98
3101 3981 6.199376 TGGTCACAAATATACTGGGAGTAGA 58.801 40.000 0.00 0.00 33.66 2.59
3102 3982 6.479972 TGGTCACAAATATACTGGGAGTAG 57.520 41.667 0.00 0.00 33.66 2.57
3104 3984 5.163195 GGATGGTCACAAATATACTGGGAGT 60.163 44.000 0.00 0.00 0.00 3.85
3105 3985 5.308825 GGATGGTCACAAATATACTGGGAG 58.691 45.833 0.00 0.00 0.00 4.30
3106 3986 4.104102 GGGATGGTCACAAATATACTGGGA 59.896 45.833 0.00 0.00 0.00 4.37
3107 3987 4.141274 TGGGATGGTCACAAATATACTGGG 60.141 45.833 0.00 0.00 0.00 4.45
3108 3988 4.821805 GTGGGATGGTCACAAATATACTGG 59.178 45.833 0.00 0.00 27.62 4.00
3109 3989 4.821805 GGTGGGATGGTCACAAATATACTG 59.178 45.833 0.00 0.00 36.90 2.74
3110 3990 4.726825 AGGTGGGATGGTCACAAATATACT 59.273 41.667 0.00 0.00 36.90 2.12
3111 3991 5.048846 AGGTGGGATGGTCACAAATATAC 57.951 43.478 0.00 0.00 36.90 1.47
3112 3992 5.044476 ACAAGGTGGGATGGTCACAAATATA 60.044 40.000 0.00 0.00 36.90 0.86
3114 3994 3.075283 ACAAGGTGGGATGGTCACAAATA 59.925 43.478 0.00 0.00 36.90 1.40
3115 3995 2.158325 ACAAGGTGGGATGGTCACAAAT 60.158 45.455 0.00 0.00 36.90 2.32
3116 3996 1.216678 ACAAGGTGGGATGGTCACAAA 59.783 47.619 0.00 0.00 36.90 2.83
3117 3997 0.850100 ACAAGGTGGGATGGTCACAA 59.150 50.000 0.00 0.00 36.90 3.33
3118 3998 0.400213 GACAAGGTGGGATGGTCACA 59.600 55.000 0.00 0.00 36.90 3.58
3119 3999 0.322546 GGACAAGGTGGGATGGTCAC 60.323 60.000 0.00 0.00 34.61 3.67
3120 4000 1.497309 GGGACAAGGTGGGATGGTCA 61.497 60.000 0.00 0.00 0.00 4.02
3121 4001 1.208165 AGGGACAAGGTGGGATGGTC 61.208 60.000 0.00 0.00 0.00 4.02
3122 4002 0.776080 AAGGGACAAGGTGGGATGGT 60.776 55.000 0.00 0.00 0.00 3.55
3290 4208 1.297968 TGAATGGATCTCAAGGGGCA 58.702 50.000 0.00 0.00 0.00 5.36
3301 4219 3.763897 GCTTGTACCCTTGTTGAATGGAT 59.236 43.478 0.00 0.00 0.00 3.41
3307 4225 3.472283 TTACGCTTGTACCCTTGTTGA 57.528 42.857 0.00 0.00 0.00 3.18
3311 4229 3.749088 TGTGATTTACGCTTGTACCCTTG 59.251 43.478 0.00 0.00 0.00 3.61
3312 4230 4.000988 CTGTGATTTACGCTTGTACCCTT 58.999 43.478 0.00 0.00 0.00 3.95
3313 4231 3.596214 CTGTGATTTACGCTTGTACCCT 58.404 45.455 0.00 0.00 0.00 4.34
3314 4232 2.676342 CCTGTGATTTACGCTTGTACCC 59.324 50.000 0.00 0.00 0.00 3.69
3340 4258 3.973516 TATAGGACGCGCTGCCGG 61.974 66.667 5.73 0.00 34.32 6.13
3381 4299 3.023119 ACTCCATGTTGCAACTTGACAA 58.977 40.909 34.69 22.42 36.49 3.18
3382 4300 2.358582 CACTCCATGTTGCAACTTGACA 59.641 45.455 34.69 23.40 36.49 3.58
3383 4301 2.618241 TCACTCCATGTTGCAACTTGAC 59.382 45.455 34.69 12.19 36.49 3.18
3384 4302 2.929641 TCACTCCATGTTGCAACTTGA 58.070 42.857 34.69 23.88 36.49 3.02
3385 4303 3.713858 TTCACTCCATGTTGCAACTTG 57.286 42.857 29.27 29.27 34.79 3.16
3386 4304 3.890756 TGATTCACTCCATGTTGCAACTT 59.109 39.130 28.61 20.54 0.00 2.66
3387 4305 3.489355 TGATTCACTCCATGTTGCAACT 58.511 40.909 28.61 12.75 0.00 3.16
3388 4306 3.921119 TGATTCACTCCATGTTGCAAC 57.079 42.857 22.83 22.83 0.00 4.17
3389 4307 6.587206 TTATTGATTCACTCCATGTTGCAA 57.413 33.333 0.00 0.00 0.00 4.08
3390 4308 6.587206 TTTATTGATTCACTCCATGTTGCA 57.413 33.333 0.00 0.00 0.00 4.08
3391 4309 7.010738 CCAATTTATTGATTCACTCCATGTTGC 59.989 37.037 4.07 0.00 40.14 4.17
3392 4310 7.010738 GCCAATTTATTGATTCACTCCATGTTG 59.989 37.037 4.07 0.00 40.14 3.33
3393 4311 7.043565 GCCAATTTATTGATTCACTCCATGTT 58.956 34.615 4.07 0.00 40.14 2.71
3394 4312 6.381994 AGCCAATTTATTGATTCACTCCATGT 59.618 34.615 4.07 0.00 40.14 3.21
3395 4313 6.700081 CAGCCAATTTATTGATTCACTCCATG 59.300 38.462 4.07 0.00 40.14 3.66
3396 4314 6.608405 TCAGCCAATTTATTGATTCACTCCAT 59.392 34.615 4.07 0.00 40.14 3.41
3397 4315 5.951148 TCAGCCAATTTATTGATTCACTCCA 59.049 36.000 4.07 0.00 40.14 3.86
3398 4316 6.127647 TGTCAGCCAATTTATTGATTCACTCC 60.128 38.462 4.07 0.00 40.14 3.85
3410 4328 4.842574 TGCTCTACATGTCAGCCAATTTA 58.157 39.130 21.34 4.73 31.68 1.40
3411 4329 3.689347 TGCTCTACATGTCAGCCAATTT 58.311 40.909 21.34 0.00 31.68 1.82
3417 4335 3.124297 GTCTTGTTGCTCTACATGTCAGC 59.876 47.826 18.68 18.68 0.00 4.26
3421 4339 2.069273 GCGTCTTGTTGCTCTACATGT 58.931 47.619 2.69 2.69 0.00 3.21
3437 4355 7.962917 ACCATGAAATTCATAAATTTTGCGTC 58.037 30.769 8.29 0.00 43.48 5.19
3439 4357 8.441608 TCAACCATGAAATTCATAAATTTTGCG 58.558 29.630 8.29 0.00 43.48 4.85
3443 4361 9.357652 CTCGTCAACCATGAAATTCATAAATTT 57.642 29.630 8.29 0.00 45.55 1.82
3446 4364 6.321717 GCTCGTCAACCATGAAATTCATAAA 58.678 36.000 8.29 0.00 34.28 1.40
3453 4371 1.463674 GGGCTCGTCAACCATGAAAT 58.536 50.000 0.00 0.00 37.30 2.17
3454 4372 0.953471 CGGGCTCGTCAACCATGAAA 60.953 55.000 0.00 0.00 37.30 2.69
3472 4390 2.030007 AGTGAAAACAATGTGGCCATCG 60.030 45.455 9.72 0.00 0.00 3.84
3478 4396 2.384382 GCACGAGTGAAAACAATGTGG 58.616 47.619 7.50 0.00 0.00 4.17
3479 4397 2.036217 CGCACGAGTGAAAACAATGTG 58.964 47.619 7.50 0.00 0.00 3.21
3487 4405 3.459027 GCGATCGCACGAGTGAAA 58.541 55.556 33.89 0.00 41.49 2.69
3499 4417 4.790140 GTCATGAAGTTTTGTGATGCGATC 59.210 41.667 0.00 0.00 0.00 3.69
3502 4420 3.910170 CAGTCATGAAGTTTTGTGATGCG 59.090 43.478 0.00 0.00 0.00 4.73
3552 4470 2.094675 GCCCTACAACTTGCATGTCAT 58.905 47.619 5.61 0.21 32.27 3.06
3554 4472 0.447801 CGCCCTACAACTTGCATGTC 59.552 55.000 5.61 0.00 32.27 3.06
3557 4475 0.036164 TCACGCCCTACAACTTGCAT 59.964 50.000 0.00 0.00 0.00 3.96
3585 4503 1.946081 TGCATGCTTTGTTTCACGAGA 59.054 42.857 20.33 0.00 0.00 4.04
3589 4507 1.838913 ACGTGCATGCTTTGTTTCAC 58.161 45.000 20.33 4.81 0.00 3.18
3606 4524 2.116366 CTCGACCTTTTTGGCAAAACG 58.884 47.619 24.04 22.09 40.22 3.60
3619 4537 2.039137 GGGAAGGGGACTCGACCT 59.961 66.667 0.00 0.00 42.68 3.85
3621 4539 1.413077 CATAAGGGAAGGGGACTCGAC 59.587 57.143 0.00 0.00 42.68 4.20
3622 4540 1.789523 CATAAGGGAAGGGGACTCGA 58.210 55.000 0.00 0.00 42.68 4.04
3623 4541 0.106894 GCATAAGGGAAGGGGACTCG 59.893 60.000 0.00 0.00 42.68 4.18
3624 4542 0.474614 GGCATAAGGGAAGGGGACTC 59.525 60.000 0.00 0.00 42.68 3.36
3664 4582 2.051345 GTTTGCGTGCGTGGAAGG 60.051 61.111 0.00 0.00 0.00 3.46
3665 4583 1.063327 TTGTTTGCGTGCGTGGAAG 59.937 52.632 0.00 0.00 0.00 3.46
3705 4623 5.103290 TGTTTCAGAAGTAAAATGACGCC 57.897 39.130 0.00 0.00 0.00 5.68
3720 4638 6.197842 GTCATTGAGCTTTCTTGTTGTTTCAG 59.802 38.462 0.00 0.00 0.00 3.02
3731 4649 5.766670 TCAGTCAAATGTCATTGAGCTTTCT 59.233 36.000 0.00 0.00 39.84 2.52
3753 4683 0.250124 AAAGACATCACGCCCGTTCA 60.250 50.000 0.00 0.00 0.00 3.18
3754 4684 0.442699 GAAAGACATCACGCCCGTTC 59.557 55.000 0.00 0.00 0.00 3.95
3761 4698 4.091945 ACATCGTTCATGAAAGACATCACG 59.908 41.667 23.57 14.74 40.86 4.35
3765 4702 5.240891 ACTGACATCGTTCATGAAAGACAT 58.759 37.500 23.57 15.51 40.17 3.06
3769 4706 5.518128 CCTCTACTGACATCGTTCATGAAAG 59.482 44.000 10.35 12.64 36.21 2.62
3771 4708 4.142160 CCCTCTACTGACATCGTTCATGAA 60.142 45.833 3.38 3.38 36.21 2.57
3782 4719 2.044492 ACCCTTCATCCCTCTACTGACA 59.956 50.000 0.00 0.00 0.00 3.58
3796 4733 2.431683 GCAGACAGGCACCCTTCA 59.568 61.111 0.00 0.00 0.00 3.02
3804 4741 3.665675 AATCCGTCCGCAGACAGGC 62.666 63.158 0.20 0.00 43.73 4.85
3808 4745 1.519455 CCAGAATCCGTCCGCAGAC 60.519 63.158 0.00 0.00 39.83 3.51
3811 4748 3.000819 ACCCAGAATCCGTCCGCA 61.001 61.111 0.00 0.00 0.00 5.69
3818 4755 0.036306 ACGTTGTCCACCCAGAATCC 59.964 55.000 0.00 0.00 0.00 3.01
3823 4760 1.275291 ACTATGACGTTGTCCACCCAG 59.725 52.381 0.00 0.00 0.00 4.45
3834 4771 2.423898 CCCGCCTGGACTATGACGT 61.424 63.158 0.00 0.00 37.49 4.34
3837 4774 1.338107 CATACCCGCCTGGACTATGA 58.662 55.000 0.00 0.00 37.49 2.15
3861 4798 2.524148 GTTTGCAGCCCCCACCTT 60.524 61.111 0.00 0.00 0.00 3.50
3882 4819 0.543277 CATCTAACCAGGCAGCCTCA 59.457 55.000 12.53 0.00 0.00 3.86
3886 4823 2.182842 CGGCATCTAACCAGGCAGC 61.183 63.158 0.00 0.00 0.00 5.25
3887 4824 1.524621 CCGGCATCTAACCAGGCAG 60.525 63.158 0.00 0.00 0.00 4.85
3896 4833 0.190069 ATGTACCTCCCCGGCATCTA 59.810 55.000 0.00 0.00 35.61 1.98
3900 4837 2.063979 CAGATGTACCTCCCCGGCA 61.064 63.158 0.00 0.00 35.61 5.69
3904 4841 2.822399 CCGCAGATGTACCTCCCC 59.178 66.667 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.